# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanocaldococcus_jannaschii_DSM_2661_uid57713/NC_000909.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanocaldococcus_jannaschii_DSM_2661_uid57713/NC_000909.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanocaldococcus_jannaschii_DSM_2661_uid57713/NC_000909.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|15668173|ref|NP_246964.1|  [L=375]
Description: aspartate aminotransferase AspB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-69  234.3   0.0    2.5e-69  234.2   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.6e-11   43.8   0.0      2e-11   43.5   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    1.4e-09   37.0   0.1    2.1e-09   36.4   0.1    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      2e-09   37.2   0.0    2.8e-09   36.8   0.0    1.1  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.5e-05   23.7   0.0    5.3e-05   22.6   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
       0.02   14.8   0.5       0.11   12.4   0.1    2.4  3  DUF1246          Protein of unknown function (DUF1246)
      0.027   13.3   0.0       0.08   11.7   0.0    1.7  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
      0.058   11.9   0.1      0.088   11.3   0.1    1.2  1  Met_gamma_lyase  Methionine gamma-lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.2   0.0   1.1e-72   2.5e-69       2     361 ..      24     368 ..      23     370 .. 0.94

  Alignments for each domain:
  == domain 1  score: 234.2 bits;  conditional E-value: 1.1e-72
                                   EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHH CS
                 Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalie 82 
                                   d+inLg++e+++d    t++++++a+k+ al+ g+++ y+p+ g pel+e++   l+++++l+++++ +++v+ Ga++++ 
  gi|15668173|ref|NP_246964.1|  24 DCINLGIGEPDFD----TPKHIIEAAKR-ALDEGKTH-YSPNNGIPELREEISNKLKDDYNLDVDKD-NIIVTCGASEALM 97 
                                   79***********....***********.77777765.888888***********************.************* PP

                                   HHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                 Aminotran_1_2  83 alifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                   + i+ l +++gde+l+p+p++ sy    + + g++  + l+  e+f++dle+++e +++      ktk+i+++sp+NPtG+
  gi|15668173|ref|NP_246964.1|  98 LSIMTL-IDRGDEVLIPNPSFVSYFSLTEFAEGKIKNIDLD--ENFNIDLEKVKESITK------KTKLIIFNSPSNPTGK 169
                                   ******.9*******************************99..****************......**************** PP

                                   B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEH......H CS
                 Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgna......a 238
                                   v+++e+++ l+++a+ ynl++++De+Y +  ++++     ++ ++  + +++ +++sK ++++G+R+Gy+++++      +
  gi|15668173|ref|NP_246964.1| 170 VYDKETIKGLAEIAEDYNLIIVSDEVYDKIIYDKKH----YSPMQFTDRCILINGFSKTYAMTGWRIGYLAVSDelnkelD 246
                                   ********************************9553....3444444459**********************887***999 PP

                                   HHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH.C CS
                 Aminotran_1_2 239 vvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae.t 316
                                   +++ + k+++      ++ +q+ ++aal+ +++    +e+m+++++ rr+ ++++L ++ +kv +++++++ + d+s++ +
  gi|15668173|ref|NP_246964.1| 247 LINNMIKIHQYSFAcaTTFAQYGALAALRGSQK---CVEDMVREFKMRRDLIYNGL-KDIFKVNKPDGAFYIFPDVSEYgD 323
                                   9999999997655567****************8...9*******************.779*******************99 PP

                                   HHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHH CS
                 Aminotran_1_2 317 akelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelve 361
                                     e++kkL+e+ +v+++pg  f+    + +R+++ +++ e++e+++ 
  gi|15668173|ref|NP_246964.1| 324 GVEVAKKLIEN-KVLCVPGVAFGEngANYIRFSY-ATKYEDIEKALG 368
                                   9**********.************9999******.999999998875 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   9.1e-15     2e-11      47     177 ..      68     195 ..      38     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 9.1e-15
                                   HHHHHHHHHHT-S.TGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSC CS
                   Aminotran_5  47 earekvaelinae.seeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeege 126
                                   e+ +k+++ +n + ++++ii+t G++ea+ l +++l   +++gde+++ +    + +     l ++   k+k i lde+ +
  gi|15668173|ref|NP_246964.1|  68 EISNKLKDDYNLDvDKDNIIVTCGASEALMLSIMTL---IDRGDEVLIPNPSFVSYF----SLTEFAEGKIKNIDLDENFN 141
                                   555555555554423599******************...9**********9999999....77778889************ PP

                                   BEGGGHHHH--TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE-T CS
                   Aminotran_5 127 ldldelekllnektklvaithvsnvtGtiqp...veeigklakkkgalvlvDaa 177
                                   +dl+++++ +++ktkl++++  sn tG + +   ++ ++++a +++ +++ D +
  gi|15668173|ref|NP_246964.1| 142 IDLEKVKESITKKTKLIIFNSPSNPTGKVYDketIKGLAEIAEDYNLIIVSDEV 195
                                   ****************************87633366778888999999999987 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1   9.4e-13   2.1e-09      69     174 ..      84     194 ..      74     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 9.4e-13
                                   EEEEESSHHH.HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTEEEEEEESS- CS
               Cys_Met_Meta_PP  69 aalavssGma.AiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdtsdleelekaikentklvylEtpt 147
                                     ++v++G + A++++i++l+  Gde+++ +  + + ++l +    k  +i+ +     dle++++ i+++tkl+ + +p+
  gi|15668173|ref|NP_246964.1|  84 DNIIVTCGASeALMLSIMTLIDRGDEVLIPNPSFVSYFSLTEFAEGKiKNIDLDENFNIDLEKVKESITKKTKLIIFNSPS 164
                                   56788899876999*********************9999999988885678888888899********************* PP

                                   TTTT----...HHHHHHHHHHTT-EEEEEG CS
               Cys_Met_Meta_PP 148 npllkvvD...iekiaklakkagvlvvvDn 174
                                   np+ kv D   i+ +a++a + ++++v D 
  gi|15668173|ref|NP_246964.1| 165 NPTGKVYDketIKGLAEIAEDYNLIIVSDE 194
                                   ********4444455777777778888776 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   1.2e-12   2.8e-09      38     144 ..      83     193 ..      39     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.2e-12
                                   -SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE.. CS
               DegT_DnrJ_EryC1  38 vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIl.. 116
                                   +++ i ++ +++Al+l+++ l +++gdeV++p  +Fv+  +    +  k   +D d + +nid +++++ it++tk I+  
  gi|15668173|ref|NP_246964.1|  83 KDNIIVTCGASEALMLSIMTL-IDRGDEVLIPNPSFVSYFSLTEFAEGKIKNIDLD-ENFNIDLEKVKESITKKTKLIIfn 161
                                   5678999999********987.8889******************************.89*******************966 PP

                                   .EB-GGGB---...HHHHHHHHHHCT-EEEEE CS
               DegT_DnrJ_EryC1 117 .pVhlyGqvad...mdalkaiaakhglkvieD 144
                                    p +  G+v d   ++ l +ia++++l++++D
  gi|15668173|ref|NP_246964.1| 162 sPSNPTGKVYDketIKGLAEIAEDYNLIIVSD 193
                                   678999***9833355667999*******999 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.4e-08   5.3e-05      39     167 ..      75     193 ..      37     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.4e-08
                                   HHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS- CS
               Beta_elim_lyase  39 davaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaik 119
                                   d  +  ++k+ ++ +     A  +++++l+ rg+ev++ +p+ +       + e+a+ k ++++ +e+ ++dlek+++ i+
  gi|15668173|ref|NP_246964.1|  75 DDYNLDVDKDNIIVTCGASEALMLSIMTLIDRGDEVLIPNPSFVSYF---SLTEFAEGKIKNIDLDENFNIDLEKVKESIT 152
                                   333334555555555555566666779999********999977655...5677888899*******9************* PP

                                   -S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
               Beta_elim_lyase 120 evgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                   +      k+kli+     n   G+v+  e ++ +a+ia++y++ ++ D
  gi|15668173|ref|NP_246964.1| 153 K------KTKLIIFNSPSNP-TGKVYDKETIKGLAEIAEDYNLIIVSD 193
                                   9......5899999999995.9********************998887 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.1e-05      0.11      42      90 ..      84     132 ..      67     155 .. 0.86
   2 ?   -2.6   0.1       2.3   5.1e+03      32      52 ..     203     223 ..     195     227 .. 0.82
   3 ?   -1.1   0.0      0.77   1.7e+03      57      75 ..     326     344 ..     265     352 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-05
                                   SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHHHC-HHHHHC-SS- CS
                       DUF1246  42 devivldkfkdilkeevqeklreenailvPhgsfveYvgiekieelkvp 90 
                                   d++iv    ++ l  ++++ + + + +l+P+ sfv+Y ++ ++ e k++
  gi|15668173|ref|NP_246964.1|  84 DNIIVTCGASEALMLSIMTLIDRGDEVLIPNPSFVSYFSLTEFAEGKIK 132
                                   88999999999999999999999****************9998876665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                                   HHHHHTTTT-SEEEE.S.S.. CS
                       DUF1246  32 eklYekfkvidevivldkfkd 52 
                                   +k Y+  ++ d++i+++ f+ 
  gi|15668173|ref|NP_246964.1| 203 KKHYSPMQFTDRCILINGFSK 223
                                   677888899999999998875 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.77
                                   --HHHHHHTTCEE--BTTH CS
                       DUF1246  57 evqeklreenailvPhgsf 75 
                                   ev++kl+e++++ vP  +f
  gi|15668173|ref|NP_246964.1| 326 EVAKKLIENKVLCVPGVAF 344
                                   5778999999999997776 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.6e-05      0.08     126     216 ..     109     196 ..      51     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                                   EEEEEES--HHHHHHHHHHT-EEEEEEEETT.EE-HHHHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT---SS CS
                Aminotran_MocR 126 kllvtvpGydrhfllleelGielltvdlqdd.GpdvdaveklvaedasvkGilavpkysnptGetiseevarrlaalkaaa 205
                                    +l++ p +  +f l+e    ++  +dl+++   d+++v++ +++ + +  i+     snptG+++ +e ++ la +    
  gi|15668173|ref|NP_246964.1| 109 EVLIPNPSFVSYFSLTEFAEGKIKNIDLDENfNIDLEKVKESITKKTKL--II-FNSPSNPTGKVYDKETIKGLAEIAE-D 185
                                   5799**************999*******987357*******99998754..33.34559***********999987632.2 PP

                                   TT-EEEEE-TT CS
                Aminotran_MocR 206 pdfrifadday 216
                                    ++ i  d+ y
  gi|15668173|ref|NP_246964.1| 186 YNLIIVSDEVY 196
                                   33445556665 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   3.9e-05     0.088     124     200 ..     122     196 ..     113     211 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.9e-05
               Met_gamma_lyase 124 slkdfg.ikykevdlleegkvdieavkeaikektkliliqrskGyserkslsieeieeiiklvkeinedvivfvdncy 200
                                   sl +f   k k++dl e+ ++d+e+vke+i++ktkli    s    + k +  e i+ + ++  +   ++i+  d+ y
  gi|15668173|ref|NP_246964.1| 122 SLTEFAeGKIKNIDLDENFNIDLEKVKESITKKTKLIIFN-SPSNPTGKVYDKETIKGLAEIAED--YNLIIVSDEVY 196
                                   566664146799************************9765.444444444444444444333322..23455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.56
# Mc/sec: 2004.34
//
Query:       gi|15668174|ref|NP_246965.1|  [L=243]
Description: hypothetical protein MJ_0002 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-22   78.9   0.0    5.5e-22   78.6   0.0    1.0  1  RlaP      RNA repair pathway DNA polymerase beta family


Domain annotation for each model (and alignments):
>> RlaP  RNA repair pathway DNA polymerase beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   3.1e-26   5.5e-22      21     239 ..       9     227 ..       6     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 3.1e-26
                          RlaP  21 lyacesGSrawGfpspdsDyDvrfiyiepaewylgl....ertrdvielpiddelDlvgwelrKalrLllksNptvlewls 97 
                                   ++++ sGS ++G+p p sD+D r+ +i  +e  ++     +++++vi  +  ++ D v +el K+lr llk N++++e   
  gi|15668174|ref|NP_246965.1|   9 IFVVISGSDLYGIPNP-SDVDIRGAHILDRELFIKNclykSKEEEVIN-KMFGKCDFVSFELGKFLRELLKPNANFIEIAL 87 
                                   799***********98.8***************997778666688888.999***************************** PP

                          RlaP  98 spivyledtseleellrlaekvflsrrvahhYlgmakkqlrrylkgeevrlKkylyvlRpllagrwllekgetpPmefesl 178
                                   s+ v l  ++ +e ++  a +++  ++++hh+ g+ak   +  +k+ +++ K +ly+lR+  +g   le+ge     f+s 
  gi|15668174|ref|NP_246965.1|  88 SDKV-LYSSKYHEDVKGIAYNCI-CKKLYHHWKGFAKPLQKLCEKESYNNPKTLLYILRAYYQGILCLESGE-----FKSD 161
                                   ****.99999999*********9.9***********************************************.....8888 PP

                          RlaP 179 laalv..dasleaeieeLlaikkggeekeagkrvpeldafiere...Lesaeeesklped.pdlael 239
                                     +    d + e+ +  L + k ++++ +++   +++++++ +    L++++++s+l+++  ++a++
  gi|15668174|ref|NP_246965.1| 162 FSSFRclDCYDEDIVSYLFECKVNKKPVDES-YKKKIKSYFYELgvlLDESYKNSNLIDEpSETAKI 227
                                   888887788999999*************996.45556666655556699999999999997666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1584.51
//
Query:       gi|15668175|ref|NP_246966.1|  [L=156]
Description: hypothetical protein MJ_0003 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.5   0.2      0.057   13.7   0.2    1.4  1  Tctex-1   Tctex-1 family
       0.06   12.3   0.0      0.091   11.8   0.0    1.3  1  PhnJ      Phosphonate metabolism protein PhnJ
       0.13   12.2   0.9       0.61   10.0   0.2    2.2  2  DUF5049   Domain of unknown function (DUF5049)


Domain annotation for each model (and alignments):
>> Tctex-1  Tctex-1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   9.5e-06     0.057      16      56 ..      63      99 ..      56     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.5e-06
                                  TSSS--CCCHHHHHHHHHHHHHHHHHHHTS.SS..SCEEEE CS
                       Tctex-1 16 saesYdhekveqwnstiinsilkalksestelelpryKfiv 56
                                  ++e+Yd ++ +++++++ + i k l+    e ++++yKfi 
  gi|15668175|ref|NP_246966.1| 63 TKEEYDTKEYRELCKKLLEPIIKYLQ----EYKKDNYKFIL 99
                                  5678**********************....45568****95 PP

>> PhnJ  Phosphonate metabolism protein PhnJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.5e-05     0.091     116     170 ..      42      96 ..      31     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
                          PhnJ 116 ilvlqvPipeplrvvepseaetkklhaeedysklwvklyedivrfgeiatsadyP 170
                                     ++q+P+pe +     +e +tk+ + +++y +l  kl e i+++ +  +  +y 
  gi|15668175|ref|NP_246966.1|  42 YGIIQLPCPELIYLGIDREGKTKEEYDTKEYRELCKKLLEPIIKYLQEYKKDNYK 96 
                                   4578**********99*****************************9888877775 PP

>> DUF5049  Domain of unknown function (DUF5049)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2    0.0001      0.61      37      56 ..      82     101 ..      64     102 .. 0.86
   2 ?   -0.0   0.0      0.14   8.4e+02      44      55 ..     139     150 ..     128     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0001
                       DUF5049  37 eLvvyleehkkeYarFILTG 56 
                                    ++ yl+e+kk+  +FIL G
  gi|15668175|ref|NP_246966.1|  82 PIIKYLQEYKKDNYKFILIG 101
                                   5789**************88 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.14
                       DUF5049  44 ehkkeYarFILT 55 
                                   +++k+Y +F+ T
  gi|15668175|ref|NP_246966.1| 139 KNEKDYNKFVKT 150
                                   678999999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1143  (0.0637515); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1065.89
//
Query:       gi|15668176|ref|NP_246967.1|  [L=243]
Description: (R)-2-hydroxyglutaryl-CoA dehydratase activator [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-46  157.0   0.8    1.2e-45  156.1   0.8    1.4  1  BcrAD_BadFG    BadF/BadG/BcrA/BcrD ATPase family
     0.0016   17.1   0.4       0.28    9.7   0.1    2.8  3  MutL           MutL protein
      0.002   18.5   2.6       0.21   12.0   0.1    2.5  2  FtsA           Cell division protein FtsA
     0.0027   17.3   2.9       0.11   12.0   0.1    3.0  3  ROK            ROK family
     0.0041   16.9   0.0     0.0092   15.7   0.0    1.6  2  FGGY_C         FGGY family of carbohydrate kinases, C-termina
     0.0044   16.6   1.0        2.4    7.7   0.1    2.3  2  FGGY_N         FGGY family of carbohydrate kinases, N-termina
  ------ inclusion threshold ------
       0.01   15.6   0.1      0.022   14.5   0.0    1.6  2  Peptidase_M22  Glycoprotease family
      0.021   15.0   0.6      0.073   13.3   0.1    2.1  2  Phage_CII      Bacteriophage CII protein
      0.026   13.5   0.6       0.05   12.6   0.6    1.4  1  DDR            Diol dehydratase reactivase ATPase-like domain
      0.058   12.4   1.1          3    6.8   0.2    2.6  3  PilM_2         Type IV pilus assembly protein PilM;
      0.068   12.3   6.0       0.76    8.9   0.3    2.1  2  DUF1464        Protein of unknown function (DUF1464)
       0.16   12.3   0.5        4.4    7.7   0.2    2.7  2  BDM            Putative biofilm-dependent modulation protein
       0.61    9.8   3.4        1.3    8.7   0.1    2.6  2  Hydant_A_N     Hydantoinase/oxoprolinase N-terminal region


Domain annotation for each model (and alignments):
>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.1   0.8   8.5e-49   1.2e-45       1     265 [.       3     242 ..       3     243 .] 0.94

  Alignments for each domain:
  == domain 1  score: 156.1 bits;  conditional E-value: 8.5e-49
                                   EEEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCTCTTB CS
                   BcrAD_BadFG   1 vGiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratlpekf 81 
                                   +GiD+GsTttk vlm++++ +  +    +  +e           e++l +++++ +++   i+++  v+tgyGr+++   f
  gi|15668176|ref|NP_246967.1|   3 LGIDVGSTTTKMVLMEDSKIIWYKIEDIGVVIE-----------EDILLKMVKEIEQK-YPIDKI--VATGYGRHKVS--F 67 
                                   8*****************999999999988888...........48999999999887.789999..***********..* PP

                                   SEEE-..HHHHHHHHHHHH-TT--EEEEEETTEEEEEEEE.TTEEEEEEEESS--TTSHHHHHHHHHHHT--TTTHHHHHT CS
                   BcrAD_BadFG  82 ekeiirseilvhgdGavalypgtrtvldigGqdskgiqid.kgkvenfqmndrcaageGrylgiiadelnmglreldglae 161
                                   +++i+  e+ + g+Ga +++ ++ +v+digGqd+k+++id +gkv++f   d+caag+G++l+ + d l++  +e+     
  gi|15668176|ref|NP_246967.1|  68 ADKIVP-EVIALGKGANYFFNEADGVIDIGGQDTKVLKIDkNGKVVDFILSDKCAAGTGKFLEKALDILKIDKNEINKY-- 145
                                   *99998.999*****************************************************************9975.. PP

                                   T--S-------SHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG-HHHHHHH.....H CS
                   BcrAD_BadFG 162 katkkarinstcavfaeaelrdalsggekaedIlaglhraialrvialisrsggvtdevtltGGvakneaavkelrklvke 242
                                   k+++ a+i+s+cavfae+e+++ ls+   +e Il g+ ++i+ rvi + +r++  +  +++ GGvakn+ +v+++     e
  gi|15668176|ref|NP_246967.1| 146 KSDNIAKISSMCAVFAESEIISLLSKKVPKEGILMGVYESIINRVIPMTNRLKIQN--IVFSGGVAKNKVLVEMF-----E 219
                                   6777788***********************************************94..**************999.....7 PP

                                   HHH-S-EE--GGGGGHHHHHHHH CS
                   BcrAD_BadFG 243 nygevkininpdsiytgalGAal 265
                                   +++++k  i++++++   +GA+l
  gi|15668176|ref|NP_246967.1| 220 KKLNKKLLIPKEPQIVCCVGAIL 242
                                   7777788899**********997 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00021      0.28       1      29 [.       2      27 ..       2      50 .. 0.73
   2 !    4.6   0.0    0.0073        10     198     266 ..      45     106 ..      32     124 .. 0.78
   3 ?   -0.3   0.0      0.22     3e+02     381     423 ..     197     235 ..     154     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00021
                          MutL  1 ilviDiGSttTkvtlvdlekvderllgqa 29
                                  il iD+GSttTk++l++++k    ++++ 
  gi|15668176|ref|NP_246967.1|  2 ILGIDVGSTTTKMVLMEDSK---IIWYKI 27
                                  6889************9965...444544 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0073
                          MutL 198 aIrevF.lehivkakglskleelvsaeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvae 266
                                   +I++ + +++iv a g+ + +   +++i+p   A +k+++ + +e +       v+D+GG  T v  + +
  gi|15668176|ref|NP_246967.1|  45 EIEQKYpIDKIV-ATGYGRHKVSFADKIVPEVIALGKGANYFFNEADG------VIDIGGQDTKVLKI-D 106
                                   555555245555.999999999999***************99995454......89********9988.3 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.22
                          MutL 381 tavkliigtGGvLthaprpeqilkalldakeeevllPeeaell 423
                                    +++ i+ +GGv +++      +++  ++ +++ l P+e++++
  gi|15668176|ref|NP_246967.1| 197 LKIQNIVFSGGVAKNKVL----VEMFEKKLNKKLLIPKEPQIV 235
                                   578889999998655443....233333555578889888876 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00015      0.21       2      28 ..       4      30 ..       3      50 .. 0.84
   2 !    6.3   0.4    0.0093        13       2      99 ..      92     235 ..      91     239 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                                  EEEE-SSSEEEEEEETTEEEEEEEES- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          FtsA  2 lvDiGagktdvavaedgalvhlrvigv 28
                                  ++D+G+++t+++++ed++++++++  +
  gi|15668176|ref|NP_246967.1|  4 GIDVGSTTTKMVLMEDSKIIWYKIEDI 30
                                  79****************999665444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0093
                                   EEEE-SSSEEEEEEETTE.EEE..................EEEES--HHHHHHHHHHHHT--HHHHHHHHHHH--S--... CS
                                   xxxxxxxxxxxxxxxxxx.xxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                          FtsA   2 lvDiGagktdvavaedga.lvh..................lrvigvggngitkdiakalrtaveeAerikikyGsala... 60 
                                   ++DiG++ t+v+ +++++ +v+                  l                +l++  +e  + k +     +   
  gi|15668176|ref|NP_246967.1|  92 VIDIGGQDTKVLKIDKNGkVVDfilsdkcaagtgkflekaL---------------DILKIDKNEINKYKSD-----Niak 152
                                   79999999999988874422224443333333333333333...............4555555555555511.....0111 PP

                                   .................EEEEEHHHHH................................GGGGSTTHHHHHHHHHT-..HH CS
                                   .................xxxxxxxxxx................................xxxxxxxxxxxxxxxxxxxxxx RF
                          FtsA  61 .................ekeigrkels................................ggsalpnleelaeralspklee 92 
                                                    +k++                                      g+++ + l+e++e+ l+ kl  
  gi|15668176|ref|NP_246967.1| 153 issmcavfaeseiisllSKKV-----PkegilmgvyesiinrvipmtnrlkiqnivfsgGVAKNKVLVEMFEKKLNKKLLI 228
                                   122322333333333333333.....0333335666666666666666667777778888888888888888887443222 PP

                                   HT-GGGH CS
                                   xxxxxxx RF
                          FtsA  93 vsdpeya 99 
                                    ++p+++
  gi|15668176|ref|NP_246967.1| 229 PKEPQIV 235
                                   3555555 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.084   1.2e+02       2      27 ..       3      28 ..       2      61 .. 0.70
   2 ?    2.5   0.0     0.062        85       4      42 ..      93     131 ..      91     154 .. 0.78
   3 !   12.0   0.1   7.9e-05      0.11     223     267 ..     187     231 ..     158     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.084
                                  EEEEE-SSEEEEEEEETTS-EEEEEE CS
                           ROK  2 igidiGgtkialalvdeegeilarek 27
                                  +gid+G t +++ l++++  i ++ +
  gi|15668176|ref|NP_246967.1|  3 LGIDVGSTTTKMVLMEDSKIIWYKIE 28
                                  79************998877776654 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.062
                                   EEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHH CS
                           ROK   4 idiGgtkialalvdeegeilarekvetptetteetlvda 42 
                                   idiGg+++++  +d++g++++    ++ +  t + l++a
  gi|15668176|ref|NP_246967.1|  93 IDIGGQDTKVLKIDKNGKVVDFILSDKCAAGTGKFLEKA 131
                                   9*****************998666555555555555555 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 7.9e-05
                                   HHHHHHHHHHH--SEEEEEHCCCTSTTHHHHHHHHHHHCCTTTTC CS
                           ROK 223 akaiadlinlfdpqaivlgGgvseadklleairklvkkylnkkle 267
                                    + ++ ++n +++q iv+ Ggv + + l+e+ +k+++k l+  +e
  gi|15668176|ref|NP_246967.1| 187 INRVIPMTNRLKIQNIVFSGGVAKNKVLVEMFEKKLNKKLLIPKE 231
                                   5566778999*******************9999999988765544 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.8   6.6e+03     138     157 ..      38      59 ..      36      59 .. 0.74
   2 !   15.7   0.0   6.7e-06    0.0092     137     192 ..     188     242 ..     160     243 .] 0.80

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.8
                        FGGY_C 138 ilealekd..sgkpldrlavdG 157
                                   il ++ k+  ++ p+d+++++G
  gi|15668176|ref|NP_246967.1|  38 ILLKMVKEieQKYPIDKIVATG 59 
                                   6667777665678899999998 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 6.7e-06
                        FGGY_C 137 ailealekdsgkpldrlavdGGgskndllmqllAdilgvpVerpkt.aeatalGaAi 192
                                   +++  +++  + ++++++ +GG +kn++l++++   l++++ +pk+ +  +++Ga++
  gi|15668176|ref|NP_246967.1| 188 NRVIPMTN--RLKIQNIVFSGGVAKNKVLVEMFEKKLNKKLLIPKEpQIVCCVGAIL 242
                                   44444433..479*********************************88889999987 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0018       2.4       1      21 [.       1      21 [.       1      36 [. 0.87
   2 !    7.7   0.1    0.0017       2.4       4      25 ..      92     113 ..      91     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0018
                                  EEEEEEEESSEEEEEEEETTS CS
                        FGGY_N  1 lilglDcGttstkaivldekg 21
                                  +ilg+D+G t tk+++++  +
  gi|15668176|ref|NP_246967.1|  1 MILGIDVGSTTTKMVLMEDSK 21
                                  79**************98654 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0017
                                   EEEEESSEEEEEEEETTS-EEE CS
                        FGGY_N   4 glDcGttstkaivldekgkvva 25 
                                   ++D+G++ tk++ +d++gkvv 
  gi|15668176|ref|NP_246967.1|  92 VIDIGGQDTKVLKIDKNGKVVD 113
                                   69******************95 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         2   2.8e+03     195     230 ..      21      58 ..       7      72 .. 0.55
   2 ?   14.5   0.0   1.6e-05     0.022     185     258 ..     162     230 ..     100     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2
                                   T.....HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEE CS
                 Peptidase_M22 195 e.....vedlaasfqeavvdhlvekteralklpkakelvil 230
                                   +     +ed+   ++e+    l ++++++ +++ ++++v  
  gi|15668176|ref|NP_246967.1|  21 KiiwykIEDIGVVIEED---ILLKMVKEIEQKYPIDKIVAT 58 
                                   24444566777777764...333444444344555555444 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHHSTT..HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCHCCHHHHTTSEEEXXX CS
                 Peptidase_M22 185 ktavlkeleke..vedlaasfqeavvdhlvekteralklpkakelvilGGvaankrLrealeeeaeelglkliiPp 258
                                   +++++++l+k+  +e + + + e++++ ++ +t r     k++++v +GGva+nk L e+ e+   +l+ kl+iP+
  gi|15668176|ref|NP_246967.1| 162 ESEIISLLSKKvpKEGILMGVYESIINRVIPMTNRL----KIQNIVFSGGVAKNKVLVEMFEK---KLNKKLLIPK 230
                                   455555553323466666666776666666666655....*******************9984...3455688886 PP

>> Phage_CII  Bacteriophage CII protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.7   7.8e+03      29      44 ..      11      26 ..       7      32 .. 0.78
   2 ?   13.3   0.1   5.3e-05     0.073      27      74 ..     129     173 ..     121     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.7
                                  HHHHHTSSTTTHHHHH CS
                     Phage_CII 29 vaeaiGvdeskisrwk 44
                                  + +++ +++ski  +k
  gi|15668176|ref|NP_246967.1| 11 TTKMVLMEDSKIIWYK 26
                                  6789999999997666 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.3e-05
                                   HHHHHHHTSSTTTHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHHHHH CS
                     Phage_CII  27 rkvaeaiGvdeskisrwktDwipkasvLlavlefGvaddelarlakkv 74 
                                   +k  +++ +d+ +i ++k+D i k+s ++av+    +++ ++ l kkv
  gi|15668176|ref|NP_246967.1| 129 EKALDILKIDKNEINKYKSDNIAKISSMCAVF---AESEIISLLSKKV 173
                                   56778999**********************75...3566666666665 PP

>> DDR  Diol dehydratase reactivase ATPase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   3.6e-05      0.05     137     263 ..      92     222 ..      86     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.6e-05
                           DDR 137 ilDlGaGstDaalieeegevkavhl.....AGAGemvtlliaseLgledrelaEdiKkyplakveslfhireEdgtvqFfd 212
                                   ++D+G+  t    i+++g+v    l     AG G+ +  +++  L + d +  ++ K   +ak+ s+  +  E   ++ + 
  gi|15668176|ref|NP_246967.1|  92 VIDIGGQDTKVLKIDKNGKVVDFILsdkcaAGTGKFLEKALD-ILKI-DKNEINKYKSDNIAKISSMCAVFAESEIISLLS 170
                                   899999999999999999987654433333899999998886.5888.55556789999********************** PP

                           DDR 213 kpldpevfarvvllke.delvpleedlslekirsvRreaKekvfvtnalRal 263
                                   k+++ e +   v  +  ++++p++++l++++i      aK+kv+v+   + l
  gi|15668176|ref|NP_246967.1| 171 KKVPKEGILMGVYESIiNRVIPMTNRLKIQNIVFSGGVAKNKVLVEMFEKKL 222
                                   ***99988777776656999*************9999******998766655 PP

>> PilM_2  Type IV pilus assembly protein PilM;
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0022         3       1      37 [.       4      40 ..       4      70 .. 0.78
   2 ?   -1.4   0.0      0.67   9.3e+02       2      19 ..      93     110 ..      86     149 .. 0.77
   3 ?    3.5   0.0     0.022        30     270     301 ..     194     225 ..     183     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0022
                        PilM_2  1 GiDissssvklvelskkk.gslrvealaieplekdavv 37
                                  GiD++s+  k+v+++++k   +++e++ + ++e+d++ 
  gi|15668176|ref|NP_246967.1|  4 GIDVGSTTTKMVLMEDSKiIWYKIEDIGV-VIEEDILL 40
                                  99************996648899999876.56776654 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.67
                        PilM_2   2 iDissssvklvelskkkg 19 
                                   iDi+ +  k+++++k+++
  gi|15668176|ref|NP_246967.1|  93 IDIGGQDTKVLKIDKNGK 110
                                   577777777777666554 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.022
                        PilM_2 270 sqqnkvdkilLaGGtaslpgleelleeelgis 301
                                   +++ k+++i+++GG a+ + l e+ e++l+ +
  gi|15668176|ref|NP_246967.1| 194 TNRLKIQNIVFSGGVAKNKVLVEMFEKKLNKK 225
                                   566799*****************999998765 PP

>> DUF1464  Protein of unknown function (DUF1464)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3   0.00055      0.76       1      58 [.       4      62 ..       4      78 .. 0.71
   2 ?    6.6   1.2    0.0027       3.8     127     276 ..      68     224 ..      64     235 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00055
                       DUF1464  1 GiDPGtksydvvvvddlgkvvlekeiptdevekdps.vlvkaieearadivalpSGyGl 58
                                  GiD G+ + ++v ++d++ +  + e    ++e+d+   +vk ie++ +   ++  GyG 
  gi|15668176|ref|NP_246967.1|  4 GIDVGSTTTKMVLMEDSKIIWYKIEDIGVVIEEDILlKMVKEIEQKYPIDKIVATGYGR 62
                                  9***************5555555555556666665414678888776655566789985 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0027
                       DUF1464 127 ADKlasavlavadeaeeeeyrelsFilvEvG.sgfnaviaVknGkivDGlGgti.lpGflsaGalDgEvAyllgkvakiek 205
                                   ADK++  v+a+ + a++  ++e++ ++ ++G +  + + + knGk+vD + +     G  +  +l+  +  l   +++i+k
  gi|15668176|ref|NP_246967.1|  68 ADKIVPEVIALGKGANYF-FNEADGVI-DIGgQDTKVLKIDKNGKVVDFILSDKcAAG--TGKFLEKALDILKIDKNEINK 144
                                   788888888777777765.44555554.454044555556789999999988876777..777888887777776666666 PP

                       DUF1464 206 slifs.gGvasiagea...elekklsee.....aferlke.vvksvaellsskykleeiivSGrlkrikelgkklesrlee 276
                                    +  + + ++s++++    e+   ls++      +  ++e ++  v  +     k+++i+ SG  ++ k l + +e++l++
  gi|15668176|ref|NP_246967.1| 145 YKSDNiAKISSMCAVFaesEIISLLSKKvpkegILMGVYEsIINRVIPMTNRL-KIQNIVFSGGVAKNKVLVEMFEKKLNK 224
                                   43322122345554445556666666666666766777788999999999988.9***********999999999999865 PP

>> BDM  Putative biofilm-dependent modulation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0032       4.4      27      45 ..      29      47 ..      25      55 .. 0.90
   2 ?    1.4   0.0       0.3   4.1e+02      30      64 ..     159     191 ..     152     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0032
                           BDM 27 elGvvteddilmeltkwve 45
                                  + Gvv e+dil+++ k +e
  gi|15668176|ref|NP_246967.1| 29 DIGVVIEEDILLKMVKEIE 47
                                  57*************9888 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.3
                           BDM  30 vvteddilmeltkwveasdndilsdiyqqtinyvv 64 
                                   v +e +i+  l+k v    + il  +y+  in v+
  gi|15668176|ref|NP_246967.1| 159 VFAESEIISLLSKKVP--KEGILMGVYESIINRVI 191
                                   7778888888888875..5789**********987 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00094       1.3       2      28 ..       3      27 ..       2      60 .. 0.79
   2 ?    1.2   0.4      0.19   2.6e+02       4      24 ..      93     112 ..      92     229 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00094
                    Hydant_A_N  2 igIDvGGTfTDavaldekeeevavlKl 28
                                  +gIDvG+T T +v++++   +++++K+
  gi|15668176|ref|NP_246967.1|  3 LGIDVGSTTTKMVLMEDS--KIIWYKI 27
                                  69**************65..5666665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                    Hydant_A_N   4 IDvGGTfTDavaldekeeeva 24 
                                   ID+GG  T ++ +d++ + v+
  gi|15668176|ref|NP_246967.1|  93 IDIGGQDTKVLKIDKNGK-VV 112
                                   666666666666665532.22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1791.12
//
Query:       gi|15668177|ref|NP_246968.1|  [L=379]
Description: formate dehydrogenase subunit beta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.4e-38  129.6   0.3    8.4e-38  129.6   0.3    2.2  2  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    2.5e-19   69.2   0.0    3.9e-19   68.6   0.0    1.3  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    2.5e-06   27.9  18.0    2.3e-05   24.8  14.4    3.0  3  Fer4_17      4Fe-4S dicluster domain
    1.4e-05   24.7  16.9    6.9e-05   22.5   2.6    3.1  3  Fer4         4Fe-4S binding domain
    0.00034   20.9   4.5    0.00034   20.9   4.5    3.6  3  Fer4_4       4Fe-4S binding domain
    0.00044   21.1  13.1      0.091   13.7   0.7    3.6  3  Fer4_16      4Fe-4S double cluster binding domain
    0.00056   20.0  30.3     0.0018   18.4   2.6    3.1  3  Fer4_10      4Fe-4S dicluster domain
     0.0012   18.8   3.2     0.0012   18.8   3.2    3.0  1  Fer4_6       4Fe-4S binding domain
     0.0017   18.5  21.2     0.0061   16.7  16.9    3.3  3  Fer4_9       4Fe-4S dicluster domain
      0.003   17.6   1.9      0.003   17.6   1.9    3.6  4  Fer4_2       4Fe-4S binding domain
     0.0043   17.2   7.1       0.35   11.1   0.3    3.5  3  Fer4_18      4Fe-4S dicluster domain
     0.0078   15.8   2.9       0.54    9.9   0.1    3.1  3  CAP_C        Adenylate cyclase associated (CAP) C terminal
  ------ inclusion threshold ------
       0.01   16.2  17.7       0.01   16.2  17.7    2.6  4  Fer4_8       4Fe-4S dicluster domain
      0.037   15.0   3.6      0.037   15.0   3.6    3.8  3  Fer4_3       4Fe-4S binding domain
      0.048   13.8  12.4       0.12   12.6   1.0    3.2  3  Fer4_21      4Fe-4S dicluster domain
      0.052   14.1  21.7      0.051   14.2  17.9    2.8  3  Fer4_7       4Fe-4S dicluster domain
       0.07   14.0  18.5       0.72   10.7   1.0    2.9  2  Fer4_22      4Fe-4S dicluster domain
        2.1    8.9  17.4        3.4    8.3   4.0    2.9  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.6   0.3   8.4e-41   8.4e-38       1     154 [.      86     238 ..      86     239 .. 0.97
   2 ?   -0.8   3.2       1.2   1.2e+03      56     100 ..     244     290 ..     237     296 .. 0.45

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 8.4e-41
                   FrhB_FdhB_C   1 lkkvavvGtPCqiaalrklqk.kklkekilltiglfCggnfspealrk.lleelgvdpedvkklefrgkgkfrvelkd..e 77 
                                   +kk+av  +PC+++a+r+l+k ++ + + +++igl+Cgg+ sp  ++k ++  ++v+p dv+k e+ +kgkf++elk+  +
  gi|15668177|ref|NP_246968.1|  86 DKKIAVPAKPCDAMAIRELAKlNQINLDNVYMIGLNCGGTISPITAMKmIELFYEVNPLDVVKEEI-DKGKFIIELKNgeH 165
                                   589*******************7888888*******************9999**************.9************9 PP

                   FrhB_FdhB_C  78 keislkelee...firpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveageleleelde 154
                                   k ++++elee    +r++C++C+ +++++AD+++G++      g  ++g+++v +++e+g++l+e+a+++g++++++++e
  gi|15668177|ref|NP_246968.1| 166 KAVKIEELEEkgfGRRKNCQRCEIMIPRMADLACGNW------G-AEKGWTFVEICSERGRKLVEDAEKDGYIKIKQPSE 238
                                   99**********99***********************......8.9******************************9987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                   FrhB_FdhB_C  56 pedvkklefrgk.gkfrvelkd..ekeislkelee..firpsCkvCkdkt 100
                                    e+++++ ++   +kf+ +  +  e+ +sl++ ++   +  +C+ C+d+ 
  gi|15668177|ref|NP_246968.1| 244 REKIESIMIK-LaKKFQKK--HleEEYPSLEKWKKywNRCIKCYGCRDNC 290
                                   4566666664.22333332..12233344443333655555666666553 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0     4e-22   3.9e-19       5      76 ..       7      79 ..       3      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 4e-22
                   FrhB_FdhB_N  5 rstdkeirkkaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYt.lspnlkl 76
                                   +td+ i+++a++GG+vtal+kylL+++++dgv++ ++++d ++ +p+++t++ el+++aGs ++ +++  kl
  gi|15668177|ref|NP_246968.1|  7 QATDNGILRRAECGGAVTALFKYLLDKKLVDGVLALKRGEDVYDGIPTFITNSNELVETAGSLHCaPTNFGKL 79
                                  69***************************************************************66666555 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       6.6   6.6e+03      49      53 ..     184     188 ..     169     192 .. 0.73
   2 !   15.0   3.2   2.8e-05     0.028      26      57 ..     255     291 ..     234     294 .. 0.68
   3 !   24.8  14.4   2.3e-08   2.3e-05       1      61 []     279     345 ..     279     345 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.6
                       Fer4_17  49 CgeCe 53 
                                   C++Ce
  gi|15668177|ref|NP_246968.1| 184 CQRCE 188
                                   44443 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.8e-05
                       Fer4_17  26 lraaklgllee.....aekeekaslCieCgeCerkCP 57 
                                   +++++ + lee     ++ ++++++Ci+C +C+  CP
  gi|15668177|ref|NP_246968.1| 255 AKKFQKKHLEEeypslEKWKKYWNRCIKCYGCRDNCP 291
                                   444444444442333233458***************9 PP

  == domain 3  score: 24.8 bits;  conditional E-value: 2.3e-08
                       Fer4_17   1 rCiqCgyClpeCpsyea..ydnepkkllraakl....glleeaekeekaslCieCgeCerkCPqgld 61 
                                   rCi+C  C+++Cp + +   + e++ + ++ k+     +++++  ++  ++Ci+Cg+Ce +CP++++
  gi|15668177|ref|NP_246968.1| 279 RCIKCYGCRDNCPLCFCveCSLEKDYIEEKGKIppnpLIFQGIRLSHISQSCINCGQCEDACPMDIP 345
                                   7************8777334445555555555555545788888899*****************985 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       6.2   6.1e+03      11      15 ..     184     188 ..     182     189 .. 0.58
   2 !   11.3   1.6   0.00024      0.24       5      19 ..     277     291 ..     273     292 .. 0.90
   3 !   22.5   2.6   6.9e-08   6.9e-05       7      21 ..     329     343 ..     325     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.2
                                   -THHH CS
                          Fer4  11 CGaCv 15 
                                   C +C+
  gi|15668177|ref|NP_246968.1| 184 CQRCE 188
                                   66664 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00024
                                   TTTSSS-THHHHHST CS
                          Fer4   5 eekCigCGaCvevCP 19 
                                   +++Ci+C  C + CP
  gi|15668177|ref|NP_246968.1| 277 WNRCIKCYGCRDNCP 291
                                   78************* PP

  == domain 3  score: 22.5 bits;  conditional E-value: 6.9e-08
                                   TSSS-THHHHHSTTT CS
                          Fer4   7 kCigCGaCvevCPvg 21 
                                    Ci+CG+C+++CP +
  gi|15668177|ref|NP_246968.1| 329 SCINCGQCEDACPMD 343
                                   6************98 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.6       1.9   1.9e+03       3       7 ..     183     187 ..     181     189 .. 0.59
   2 ?    6.6   7.0     0.013        13       2      15 ..     278     291 ..     277     294 .. 0.93
   3 !   20.9   4.5   3.4e-07   0.00034       1      16 [.     327     342 ..     327     343 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.9
                        Fer4_4   3 rCigC 7  
                                   +C++C
  gi|15668177|ref|NP_246968.1| 183 NCQRC 187
                                   56655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.013
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   +rCi C  C++ CP
  gi|15668177|ref|NP_246968.1| 278 NRCIKCYGCRDNCP 291
                                   8************9 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 3.4e-07
                        Fer4_4   1 qerCigCgsCvaaCPq 16 
                                   +++Ci+Cg+C++aCP+
  gi|15668177|ref|NP_246968.1| 327 SQSCINCGQCEDACPM 342
                                   589************7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.18   1.8e+02      24      61 ..     150     188 ..     141     192 .. 0.73
   2 !    9.2   3.0    0.0024       2.4      17      65 ..     233     291 ..     231     293 .. 0.59
   3 !   13.7   0.7   9.2e-05     0.091       2      15 ..     330     343 ..     328     358 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.18
                       Fer4_16  24 eiearecisy.ntaekkdlaedeekckkqeaitgCdiCq 61 
                                   ei++ + i + ++ e+k ++++e ++k  ++ + C++C+
  gi|15668177|ref|NP_246968.1| 150 EIDKGKFIIElKNGEHKAVKIEELEEKGFGRRKNCQRCE 188
                                   45555544443566778899999999988999******7 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0024
                       Fer4_16  17 ikekkekeiearecisy......ntaekkdlaede...ekckkq.eaitgCdiCqdvCP 65 
                                   ik+++ek i+ re+i++      ++ +kk l+e++   ek kk+ ++++ C  C d CP
  gi|15668177|ref|NP_246968.1| 233 IKQPSEKAIQVREKIESimiklaKKFQKKHLEEEYpslEKWKKYwNRCIKCYGCRDNCP 291
                                   56666666666666666666666444444444444221444433377899********9 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 9.2e-05
                       Fer4_16   2 CgtCgkCaevCPtn 15 
                                   C++Cg+C ++CP +
  gi|15668177|ref|NP_246968.1| 330 CINCGQCEDACPMD 343
                                   99*********975 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.91   9.1e+02      34      48 ..     173     187 ..     160     201 .. 0.63
   2 !   15.0  19.9   1.9e-05     0.019       7      56 .]     278     341 ..     272     341 .. 0.90
   3 !   18.4   2.6   1.8e-06    0.0018       6      23 ..     327     344 ..     322     365 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.91
                       Fer4_10  34 eeeavrkkvekCtgc 48 
                                    ee+  +  ++C++c
  gi|15668177|ref|NP_246968.1| 173 LEEKGFGRRKNCQRC 187
                                   444455555566666 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.9e-05
                       Fer4_10   7 dtCirCgkCvkaCPadl..............tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   ++Ci+C  C++ CP ++               +   ++ + ++ + ++ +++C++cg+C +aCP
  gi|15668177|ref|NP_246968.1| 278 NRCIKCYGCRDNCPLCFcvecslekdyieekGKIPPNPLIFQGIRLSHISQSCINCGQCEDACP 341
                                   79*************99**********98655555678999**********************9 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.8e-06
                       Fer4_10   6 ddtCirCgkCvkaCPadl 23 
                                   +++Ci+Cg+C +aCP+d+
  gi|15668177|ref|NP_246968.1| 327 SQSCINCGQCEDACPMDI 344
                                   689************966 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   3.2   1.2e-06    0.0012       6      22 ..     327     343 ..     324     345 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                        Fer4_6   6 pdkCigCgdCvrvCPeg 22 
                                    ++Ci Cg C+++CP++
  gi|15668177|ref|NP_246968.1| 327 SQSCINCGQCEDACPMD 343
                                   689************87 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.3   1.3e+03       4       9 ..     183     188 ..     159     200 .. 0.74
   2 !    7.3   6.7    0.0054       5.4      33      47 ..     266     291 ..     231     295 .. 0.74
   3 !   16.7  16.9   6.1e-06    0.0061       1      49 [.     279     343 ..     279     345 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.3
                        Fer4_9   4 gCgaCv 9  
                                   +C++C+
  gi|15668177|ref|NP_246968.1| 183 NCQRCE 188
                                   344443 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0054
                        Fer4_9  33 e...........eaCigCgaCveaCp 47 
                                   e           ++Ci+C  C + Cp
  gi|15668177|ref|NP_246968.1| 266 EypslekwkkywNRCIKCYGCRDNCP 291
                                   13334444557789***********9 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 6.1e-06
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.................eaCigCgaCveaCpkg 49 
                                   +C++C  C + Cp + +ve + e+    ++ ++                 ++Ci Cg+C++aCp +
  gi|15668177|ref|NP_246968.1| 279 RCIKCYGCRDNCPLCFCVECSLEKDYIEEK-GKippnplifqgirlshisQSCINCGQCEDACPMD 343
                                   5************99999888887766544.446999*************99************98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.4       6.2   6.1e+03      12      16 ..     183     187 ..     182     189 .. 0.56
   2 !   11.3   1.1    0.0003       0.3       8      21 ..     278     291 ..     273     292 .. 0.92
   3 ?   -1.9   0.1       4.5   4.5e+03      10      14 ..     295     299 ..     294     300 .. 0.83
   4 !   17.6   1.9     3e-06     0.003       7      21 ..     327     341 ..     323     342 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.2
                        Fer4_2  12 gCgaC 16 
                                   +C  C
  gi|15668177|ref|NP_246968.1| 183 NCQRC 187
                                   45555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0003
                        Fer4_2   8 drCigCgaCvsaCP 21 
                                   +rCi C  C+++CP
  gi|15668177|ref|NP_246968.1| 278 NRCIKCYGCRDNCP 291
                                   69****99*****9 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.5
                        Fer4_2  10 CigCg 14 
                                   C++C+
  gi|15668177|ref|NP_246968.1| 295 CVECS 299
                                   9***6 PP

  == domain 4  score: 17.6 bits;  conditional E-value: 3e-06
                        Fer4_2   7 tdrCigCgaCvsaCP 21 
                                   +++Ci+Cg C +aCP
  gi|15668177|ref|NP_246968.1| 327 SQSCINCGQCEDACP 341
                                   578************ PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0       0.1        99      20      77 ..     139     197 ..     126     203 .. 0.75
   2 ?    4.3   1.0     0.043        43      54      74 ..     273     293 ..     246     306 .. 0.71
   3 !   11.1   0.3   0.00035      0.35      83      96 ..     328     341 ..     317     356 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.1
                       Fer4_18  20 ydeetllvv.ydakrGekiagrkkekkalkekeerkekgagdcidcescvkvcPtgidi 77 
                                   y+ + l vv  +  +G+ i++ k+ +++  + ee +ekg g   +c+ c  + P   d+
  gi|15668177|ref|NP_246968.1| 139 YEVNPLDVVkEEIDKGKFIIELKNGEHKAVKIEELEEKGFGRRKNCQRCEIMIPRMADL 197
                                   55555554414567888888888888888888888999999999999999999988776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.043
                       Fer4_18  54 kekgagdcidcescvkvcPtg 74 
                                    +k  + ci+c  c + cP  
  gi|15668177|ref|NP_246968.1| 273 WKKYWNRCIKCYGCRDNCPLC 293
                                   456677888888888888865 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00035
                       Fer4_18  83 leciscllcidacd 96 
                                    +ci+c++c dac 
  gi|15668177|ref|NP_246968.1| 328 QSCINCGQCEDACP 341
                                   35666666666663 PP

>> CAP_C  Adenylate cyclase associated (CAP) C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.11   1.1e+02      36      75 ..      93     132 ..      80     141 .. 0.83
   2 ?    2.2   0.1      0.13   1.3e+02       4      46 ..     148     191 ..     146     195 .. 0.85
   3 !    9.9   0.1   0.00054      0.54      22      61 ..     220     258 ..     204     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.11
                         CAP_C  36 ifkCknstiqikgKvnaitldnckkvsvvvdsvvSsvevi 75 
                                      C+ + i+   K+n+i ldn + + + +  ++S +  +
  gi|15668177|ref|NP_246968.1|  93 AKPCDAMAIRELAKLNQINLDNVYMIGLNCGGTISPITAM 132
                                   5669999999999***********9999999999987665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                         CAP_C   4 klelegnkwlvenqennk.eieieetelkqsvyifkCknstiqi 46 
                                   k e+++ k+++e  ++++  ++iee e k      +C+ + i i
  gi|15668177|ref|NP_246968.1| 148 KEEIDKGKFIIELKNGEHkAVKIEELEEKGFGRRKNCQRCEIMI 191
                                   56788999****998666599***99999999999999999988 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00054
                         CAP_C  22 eieieetelkqsvyifkCknstiqikgKvnaitldnckkv 61 
                                   +  +e++e++  + i + ++  iq+++K+ +i+++  kk+
  gi|15668177|ref|NP_246968.1| 220 K-LVEDAEKDGYIKIKQPSEKAIQVREKIESIMIKLAKKF 258
                                   3.45679***************************999886 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       3.3   3.3e+03      52      57 ..     182     187 ..     153     205 .. 0.72
   2 ?    9.2   5.5    0.0017       1.7      45      62 ..     274     291 ..     226     293 .. 0.68
   3 ?   16.2  17.7     1e-05      0.01       3      65 .]     278     344 ..     275     344 .. 0.68
   4 ?   13.3   3.2   8.6e-05     0.086       4      17 ..     329     342 ..     326     359 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.3
                        Fer4_8  52 ttcgaC 57 
                                    +c++C
  gi|15668177|ref|NP_246968.1| 182 KNCQRC 187
                                   445555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0017
                        Fer4_8  45 eealwsCttcgaCtevCp 62 
                                   ++++++C  c  C+++Cp
  gi|15668177|ref|NP_246968.1| 274 KKYWNRCIKCYGCRDNCP 291
                                   556666666666666666 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1e-05
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaae.........dvqeeqvlee...eealwsCttcgaCtevCpvgi 65 
                                   ++Ci+C  C+++Cp++ +      +d  +e ++         +        +    ++ +sC +cg+C+++Cp++i
  gi|15668177|ref|NP_246968.1| 278 NRCIKCYGCRDNCPLCFCVEcSLEKDYIEE-KGkippnplifQ--------GirlSHISQSCINCGQCEDACPMDI 344
                                   69************8888663333333333.222445554432........13335789**************987 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 8.6e-05
                        Fer4_8   4 kCieCgaCqsaCpv 17 
                                   +Ci+Cg C++aCp+
  gi|15668177|ref|NP_246968.1| 329 SCINCGQCEDACPM 342
                                   68888888888873 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.6       8.8   8.7e+03       4       8 ..     184     188 ..     183     200 .. 0.68
   2 ?    1.5   5.4      0.75   7.5e+02       1      12 [.     280     291 ..     280     300 .. 0.94
   3 ?   15.0   3.6   3.7e-05     0.037       1      13 [.     330     342 ..     330     344 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 8.8
                        Fer4_3   4 CgaCv 8  
                                   C++C+
  gi|15668177|ref|NP_246968.1| 184 CQRCE 188
                                   66663 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.75
                        Fer4_3   1 CtgCgaCvevCP 12 
                                   C+ C+ C + CP
  gi|15668177|ref|NP_246968.1| 280 CIKCYGCRDNCP 291
                                   9***99****99 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 3.7e-05
                        Fer4_3   1 CtgCgaCvevCPv 13 
                                   C++Cg+C+++CP 
  gi|15668177|ref|NP_246968.1| 330 CINCGQCEDACPM 342
                                   ************6 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.3   2.3e+03      40      45 ..     183     188 ..     154     195 .. 0.62
   2 ?    5.4   3.1     0.021        21      39      57 ..     278     296 ..     260     306 .. 0.80
   3 ?   12.6   1.0   0.00012      0.12       6      19 ..     328     341 ..     317     347 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.3
                       Fer4_21  40 eCvGCn 45 
                                   +C  C+
  gi|15668177|ref|NP_246968.1| 183 NCQRCE 188
                                   444443 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.021
                       Fer4_21  39 deCvGCnlCssvCPvedci 57 
                                   ++C+ C  C + CP+  c+
  gi|15668177|ref|NP_246968.1| 278 NRCIKCYGCRDNCPLCFCV 296
                                   6788888888888876665 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00012
                       Fer4_21   6 dkCigCgkCliaCe 19 
                                   ++Ci+Cg+C  aC+
  gi|15668177|ref|NP_246968.1| 328 QSCINCGQCEDACP 341
                                   45666666666665 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.8   2.8e+03      37      41 ..     183     187 ..     156     200 .. 0.72
   2 ?    6.0   5.5     0.018        18      29      49 ..     271     291 ..     211     294 .. 0.75
   3 ?   14.2  17.9   5.2e-05     0.051       1      51 [.     279     343 ..     279     344 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.8
                        Fer4_7  37 kClgC 41 
                                   +C+ C
  gi|15668177|ref|NP_246968.1| 183 NCQRC 187
                                   44444 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.018
                        Fer4_7  29 ekveidpekClgCgaCvavCP 49 
                                   ek++   ++C+ C+ C + CP
  gi|15668177|ref|NP_246968.1| 271 EKWKKYWNRCIKCYGCRDNCP 291
                                   556666677777777777777 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 5.2e-05
                        Fer4_7   1 rCigCgaCvaaCp....vkaieldeeenekgt..........ekveidpekClgCgaCvavCPtg 51 
                                   rCi+C  C ++Cp    v++   +++ +ekg+           ++ + +++C++Cg+C+++CP +
  gi|15668177|ref|NP_246968.1| 279 RCIKCYGCRDNCPlcfcVECSLEKDYIEEKGKippnplifqgIRLSHISQSCINCGQCEDACPMD 343
                                   8************9555444444455555544444444443344477789*************87 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   7.0   0.00093      0.93       1      24 [.     279     302 ..     279     311 .. 0.82
   2 ?   10.7   1.0   0.00072      0.72      79      96 .]     327     344 ..     318     344 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00093
                       Fer4_22   1 rClsCgaCtlvCptCsCfdvedet 24 
                                   rC++C  C   Cp C+C++++ e+
  gi|15668177|ref|NP_246968.1| 279 RCIKCYGCRDNCPLCFCVECSLEK 302
                                   7****************9987655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00072
                       Fer4_22  79 esgCvGCgRCieacpvki 96 
                                   +++C+ Cg C++acp++i
  gi|15668177|ref|NP_246968.1| 327 SQSCINCGQCEDACPMDI 344
                                   678999999999999876 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   5.5     0.029        29       5      26 ..     279     300 ..     278     313 .. 0.81
   2 ?    8.3   4.0    0.0034       3.4       4      17 ..     328     341 ..     326     343 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.029
                       Fer4_13   5 tCiacgaCvelaPdvFeeddeg 26 
                                   +Ci c  C++ +P +F  +   
  gi|15668177|ref|NP_246968.1| 279 RCIKCYGCRDNCPLCFCVECSL 300
                                   8**************9876555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0034
                       Fer4_13   4 dtCiacgaCvelaP 17 
                                   ++Ci+cg+C +++P
  gi|15668177|ref|NP_246968.1| 328 QSCINCGQCEDACP 341
                                   68************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2450.01
//
Query:       gi|15668178|ref|NP_246969.1|  [L=378]
Description: formate dehydrogenase subunit alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-44  150.0   0.9    7.8e-24   84.4   0.1    2.1  2  Molybdopterin   Molybdopterin oxidoreductase
    5.3e-18   64.8   2.1      1e-17   63.9   2.1    1.5  1  Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
  ------ inclusion threshold ------
      0.048   13.6   0.0      0.098   12.6   0.0    1.5  1  DUF2195         Uncharacterized protein conserved in bacteria


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   1.6e-21   9.5e-18       1     159 [.      58     192 ..      58     214 .. 0.83
   2 !   84.4   0.1   1.3e-27   7.8e-24     333     432 .]     264     355 ..     240     355 .. 0.88

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 1.6e-21
                                   B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECCG CS
                 Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfydwya 81 
                                   Rlk+P+++   + +Gk+v+++WdeAl +ia++lk+    y+ d +  f++++ + +e  ++lkkl+  l  k+++++ +  
  gi|15668178|ref|NP_246969.1|  58 RLKKPLIK---K-NGKLVEATWDEALSFIAEKLKN----YNADDIT-FIASGKCTNEDNYALKKLVDSLKAKIGHCICNSP 129
                                   9*******...6.8*********************....9999999.77777777****************9998887776 PP

                                   GGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-H.CGGGCS CS
                 Molybdopterin  82 dlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryae.llkfad 159
                                   ++         ++      e s+++ d+en++ ii++G +v  e+ +   +++ka  k + kv ++ ++ +e l   ad
  gi|15668178|ref|NP_246969.1| 130 KV---------NYA-----EVSTTIDDIENAKNIIIIG-DVFSEHALIGRKVIKAKEK-GSKVTIFNTEEKEiLKLNAD 192
                                   66.........333.....45889**************.7999999996666665555.69999999998885333444 PP

  == domain 2  score: 84.4 bits;  conditional E-value: 1.3e-27
                                   HHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESS CS
                 Molybdopterin 333 llkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstalyaDiiLPaatwyEkedlytndegrfqhlkqav 413
                                   llk  + k+ly++g+np   ++d       l++ +++vv d+++t+ta++aD++LP+++w Ek+++++n++ r+q++++av
  gi|15668178|ref|NP_246969.1| 264 LLK--NSKFLYIMGENPALVDKD--V----LKNVEFLVVQDIIMTETAEMADVVLPSTCWAEKDGTFINTDKRIQKINKAV 336
                                   555..5789*****555443332..2....3589*********************************************** PP

                                   S-STT-BEHHHHHHHHHHH CS
                 Molybdopterin 414 sppgeaksdwkIlkaLakk 432
                                   +ppg+a +dw I+k La+k
  gi|15668178|ref|NP_246969.1| 337 NPPGDAMDDWLIIKSLAEK 355
                                   *****************96 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   2.1   1.7e-21     1e-17       1      55 []       1      55 [.       1      55 [. 0.98

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.7e-21
                                  SEEEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCCCB CS
                Molybdop_Fe4S4  1 ekvvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllervyn 55
                                  +kvv+t+Cp C+vgCg+++ vkd+k+v + ++++hp+neg++C  G++ ++++y+
  gi|15668178|ref|NP_246969.1|  1 MKVVHTICPGCSVGCGIDLIVKDDKVVGTYPYKRHPINEGKNCSNGKNSYKIIYH 55
                                  89**************************************************996 PP

>> DUF2195  Uncharacterized protein conserved in bacteria (DUF2195)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.6e-05     0.098      37      71 ..     104     139 ..      83     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                       DUF2195  37 vaenlialkttvklrksiGeCgCmSalinYts.svk 71 
                                    ++n  + k+  +l+  iG+C C S  +nY+  s++
  gi|15668178|ref|NP_246969.1| 104 NEDNYALKKLVDSLKAKIGHCICNSPKVNYAEvSTT 139
                                   4455555556668999**************873333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2267.39
//
Query:       gi|15668179|ref|NP_246970.1|  [L=373]
Description: 2-hydroxyglutaryl-CoA dehydratase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-90  302.9   0.4    4.5e-90  302.7   0.4    1.0  1  HGD-D       2-hydroxyglutaryl-CoA dehydratase, D-component
  ------ inclusion threshold ------
       0.26   11.3   1.7        1.3    9.0   0.1    2.3  2  RTX_C       RTX C-terminal domain
       0.43   11.2   3.2       0.47   11.1   0.6    2.4  2  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold


Domain annotation for each model (and alignments):
>> HGD-D  2-hydroxyglutaryl-CoA dehydratase, D-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.7   0.4   7.5e-94   4.5e-90       1     323 []      36     373 .]      36     373 .] 0.96

  Alignments for each domain:
  == domain 1  score: 302.7 bits;  conditional E-value: 7.5e-94
                                   STTS-HHHHHHTT-EEEE-.----GGGHHHHTTTS-SSS-HHHHHHHHHHHT......HH-SEEEEES-SHHHHHHHHHHT CS
                         HGD-D   1 qwyypeellaAaglvpiflargpsrepldlaekylpsfgCglardalgaale......kpddlvvanttCdqvkkilenla 75 
                                   + y+p e++ Aa+++p++l +g++++ +  ae++lp+++C+l+++++g++ +      +++d+v+++ttC ++kk++e ++
  gi|15668179|ref|NP_246970.1|  36 CAYVPIEIILAANAIPVGL-CGGKNDTIPIAEEDLPRNLCPLIKSSYGFKKAktcpyfEASDIVIGETTCEGKKKMFELME 115
                                   88***************99.************99**************88889**************************** PP

                                   TTS-EEEE---....HHHHHHHHHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHTTSSS-SS-HHHHHH CS
                         HGD-D  76 kiipytvldiP....eeavkyledelenliaaleeitgkrideesleaaikeanetrellkelytllpqspapihgfdlll 152
                                   +++p++++++P    e+++k + +e+e+l++++e+ tg++i+ee+l++ +++ n+ rel+ +ly+l++++papi g d+l 
  gi|15668179|ref|NP_246970.1| 116 RLVPMHIMHLPhmkdEDSLKIWIKEVEKLKELVEKETGNKITEEKLKETVDKVNKVRELFYKLYELRKNKPAPIKGLDVLK 196
                                   ********************************************************************************* PP

                                   HHHHTT.S-HHHHHHHHHHHHHHHHHH.T..S..TS-EEEEEES---TT--HHHHHHHHT.T-EEEEEESTTTHHHHS-.S CS
                         HGD-D 153 lakvvf.lgkeeatealeelleeleer.sk.s..eriRllltGipvellaaklmkaleaglgavvvnndacypsrlvry.v 227
                                   l++ ++ l+ ++ + +le l+eeleer +k +  e  R+l+tG+p+  +++k+ +++e+  g+vvv ++ c+++r++++ v
  gi|15668179|ref|NP_246970.1| 197 LFQFAYlLDIDDTIGILEDLIEELEERvKKgEgyEGKRILITGCPMVAGNNKIVEIIEEV-GGVVVGEESCTGTRFFENfV 276
                                   **999988******************65544468************************99.66**************7776 PP

                                   SHHH.HHHHHHHHHT..--TTS.S-HHHHHHHHHHHHHTT-SEEEEEEETT-HHHHHHHHHHHHHHHHTT--EEEEEE-S- CS
                         HGD-D 228 gdvgqplealasgyy..kcpvs.pkerrlewirdlideykvdgvifqtgggCrpasgyiglirralekegiPvlsletDqs 305
                                     +g ++e +a++y+  +c+++ ++++r+e+i++l++e  vdgv+++t++ C++++++ + +++al++egiP++ +etD+s
  gi|15668179|ref|NP_246970.1| 277 --EGYSVEDIAKRYFkiPCACRfKNDERVENIKRLVKELDVDGVVYYTLQYCHTFNIEGAKVEEALKEEGIPIIRIETDYS 355
                                   ..6779*****9999999999559********************************************************* PP

                                   STTHHHHHHHHHHHHHH- CS
                         HGD-D 306 diregqlktRVeaflEiL 323
                                   +++ +qlktR+eaf+E++
  gi|15668179|ref|NP_246970.1| 356 ESDREQLKTRLEAFIEMI 373
                                   ****************95 PP

>> RTX_C  RTX C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00022       1.3      76     110 ..     142     177 ..     130     193 .. 0.81
   2 ?    0.8   0.1     0.074   4.4e+02      58      74 ..     245     261 ..     241     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00022
                         RTX_C  76 qqvdeLiak.gngkisaeelskvinnknkleeklss 110
                                   +++ eL++k +++ki++e+l + +++ nk+ e+++ 
  gi|15668179|ref|NP_246970.1| 142 EKLKELVEKeTGNKITEEKLKETVDKVNKVRELFYK 177
                                   46778887626788****************999885 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.074
                         RTX_C  58 lnnkiEeiigkdGerit 74 
                                    nnki eii+  G  ++
  gi|15668179|ref|NP_246970.1| 245 GNNKIVEIIEEVGGVVV 261
                                   59********9998776 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.95   5.7e+03      41      65 ..       7      26 ..       2      34 .. 0.50
   2 ?   11.1   0.6   7.9e-05      0.47      34      85 ..     137     190 ..     131     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.95
                    5_3_exonuc 41 leeilenldelkekklkekLeenke 65
                                  +e+++++ +     ++ke+L ++ke
  gi|15668179|ref|NP_246970.1|  7 IEKLMQKFA-----SRKEQLYKQKE 26
                                  333333222.....24455555554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 7.9e-05
                    5_3_exonuc  34 Llkeygsleeilenld..elkekklkekLeenkeearlskkLatiktdvplele 85 
                                   ++ke+++l+e++e+    +++e+klke++ + ++  +l++kL +++++ p +++
  gi|15668179|ref|NP_246970.1| 137 WIKEVEKLKELVEKETgnKITEEKLKETVDKVNKVRELFYKLYELRKNKPAPIK 190
                                   89***********8766688889999999999999999********99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1286  (0.0717274); expected 358.6 (0.02)
Passed bias filter:                      755  (0.0421105); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2432.41
//
Query:       gi|15668180|ref|NP_246971.1|  [L=220]
Description: hypothetical protein MJ_0008 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-08   34.6   0.0    1.7e-08   34.2   0.0    1.2  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   9.3e-13   1.7e-08      68     205 ..      55     174 ..      30     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 9.3e-13
                                   HHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHHHH CS
                  AP_endonuc_2  68 svdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgdeelarll 148
                                   s+  lk+ ie  +  +  +++lh G       +  + + e+l+e+l  + ++aek+g+kl++E+l + ++++    + ++ 
  gi|15668180|ref|NP_246971.1|  55 SIIILKNIIENIKGRDYLTIHLHNG-------KYGKINKETLIENLSIVNEFAEKNGIKLCIENLRKGFSSNP-NNIIEIA 127
                                   5555666666555444344444433.......33334567******************************999.******* PP

                                   HHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEEST CS
                  AP_endonuc_2 149 davdspnvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpi 205
                                   d+++   + +++D+gH+ ++  +  ++l+   dr+   H+  +++     ++ h+p+
  gi|15668180|ref|NP_246971.1| 128 DEIN---CYITFDVGHIPYN--RRLEFLEICSDRVYNSHVYEIEV-----DGKHLPP 174
                                   ***9...**********998..88999999999999888855555.....6666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1440.46
//
Query:       gi|15668181|ref|NP_246972.1|  [L=276]
Description: hypothetical protein MJ_0009 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1679.36
//
Query:       gi|15668182|ref|NP_246973.1|  [L=428]
Description: BcpC phosphonopyruvate decarboxylase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-42  143.3   0.0    8.9e-42  143.2   0.0    1.0  1  Metalloenzyme    Metalloenzyme superfamily
    1.1e-36  126.3   0.0    1.6e-36  125.7   0.0    1.3  1  PhosphMutase     2,3-bisphosphoglycerate-independent phosphog
      0.002   17.8   0.0       0.18   11.3   0.0    2.2  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
  ------ inclusion threshold ------
       0.06   12.3   0.0      0.092   11.7   0.0    1.2  1  Alk_phosphatase  Alkaline phosphatase
       0.13   11.7   0.0       0.96    8.8   0.0    2.0  2  Sulfatase        Sulfatase


Domain annotation for each model (and alignments):
>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.2   0.0   2.5e-45   8.9e-42       1     246 [.       1     396 [.       1     398 [. 0.98

  Alignments for each domain:
  == domain 1  score: 143.2 bits;  conditional E-value: 2.5e-45
                                   -EEEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH........... CS
                                   xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                 Metalloenzyme   1 kkvvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel........... 67 
                                   ++++l++lDGlG+++++ ln    +++AktP+ld+L+++       +++g++++++e++  ++ev+H+ l           
  gi|15668182|ref|NP_246973.1|   1 MRAILILLDGLGDRASEILNNktpLQFAKTPNLDRLAEN-------GMCGLMTTYKEGIPLGTEVAHFLLwgysleefpgr 74 
                                   5789*****************9*****************.......89********************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Metalloenzyme  68 ................................................................................. 67 
                                                                                                                    
  gi|15668182|ref|NP_246973.1|  75 gviealgedieieknaiylraslgfvkkdekgflvidrrtkdisreeieklvdslptcvdgykfelfysfdvhfilkiker 155
                                   ********************************************************************************* PP

                                   ................................................................HHHHTT-----EEEEEE CS
                                   ................................................................xxxxxxxxxxxxxxxxx RF
                 Metalloenzyme  68 ................................................................lrisetvkfahvtffwn 84 
                                                                                                   +r++ ++++a+++++ +
  gi|15668182|ref|NP_246973.1| 156 ngwisdkisdsdpfyknryvmkvkairelckseveyskakdtaralnkyllnvykilqnhkinrKRRKLEKMPANFLLTKW 236
                                   ****************************************************************999************** PP

                                   EE-S---SSHHHHHT--EEEE--SHH........STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme  85 ggrsgyfnpleereeipsdtvitfdl........qpemkavevaekaldailsgkfdlvvvniknaDmvGHtgdleatiaa 157
                                   ++r++++++++e++++++ ++++ +l          +  + e +e+ +d i + ++d++++++k++D+++Ht+++ +++++
  gi|15668182|ref|NP_246973.1| 237 ASRYKRVESFKEKWGMNAVILAESSLfkglakflGMDFIKIESFEEGIDLIPELDYDFIHLHTKETDEAAHTKNPLNKVKV 317
                                   ********************************99999999999**********9*************************** PP

                                   HHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS........-----EEEEEESTT----S--S.SHHHHTT-TTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                 Metalloenzyme 158 ieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglapdkvke.gakfrekggLanva 237
                                   ie++D+ ++++   ++++d +l++tADH++++  +         H+ e+VPil++gk+++ d+vke ++ ++++g+L +++
  gi|15668182|ref|NP_246973.1| 318 IEKIDKLIGNLK--LREDD-LLIITADHSTPSVGNL-------IHSGESVPILFYGKNVRVDNVKEfNEISCSNGHL-RIR 387
                                   *********996..77888.************9999.......9*********************************.899 PP

                                   GGGHHHHHH CS
                                   xxxxxxxxx RF
                 Metalloenzyme 238 atllnllgl 246
                                   ++ l++l l
  gi|15668182|ref|NP_246973.1| 388 GEELMHLIL 396
                                   888888766 PP

>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.7   0.0   4.5e-40   1.6e-36       1     170 []      37     218 ..      37     218 .. 0.96

  Alignments for each domain:
  == domain 1  score: 125.7 bits;  conditional E-value: 4.5e-40
                                   HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC....TTCEEETTGGG CS
                  PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdee..dgiiidrragr 79 
                                   A++G++Gl++t++egi+ g++vA++ ++Gy+  + ++GRG++EAlg ++e++++ +++R+ l  v+++  + ++idrr+++
  gi|15668182|ref|NP_246973.1|  37 AENGMCGLMTTYKEGIPLGTEVAHFLLWGYS-LEEFPGRGVIEALGEDIEIEKNAIYLRASLGFVKKDekGFLVIDRRTKD 116
                                   89****************************7.888**************************999987766788******** PP

                                   -.-TTHHHHHHHT-EEE.TTEEEEEEE-STTEEEEEE......--S-B--S--..SSTTS------BS.........SGGG CS
                  PhosphMutase  80 isteeakeLikalneeleegvevkfypgveyrhllvl......lsdkitdtdpphdkegkeikellpl.k.......seea 146
                                   is+ee ++L+++l + + +g+++++ ++ +++++l +       sdki+d+dp   ++++ +++++++ +       +++a
  gi|15668182|ref|NP_246973.1| 117 ISREEIEKLVDSLPTCV-DGYKFELFYSFDVHFILKIkerngwISDKISDSDP--FYKNRYVMKVKAIrElckseveYSKA 194
                                   *****************.59*********************************..9****99999998559999999889* PP

                                   HHHHHHHHHHHHHHHHHHHHSHHH CS
                  PhosphMutase 147 ketaellnelieksqeiLedhpvN 170
                                   k+ta++ln++++++++iL++h++N
  gi|15668182|ref|NP_246973.1| 195 KDTARALNKYLLNVYKILQNHKIN 218
                                   ***********************9 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0065        23       2      39 ..       4      47 ..       3      49 .. 0.73
   2 !   11.3   0.0   5.1e-05      0.18     155     243 ..     268     351 ..     164     359 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0065
                                  EEEEETT-B...TTHHHHHG.S...TSHHHHHHHHHSEEESEEE- CS
                  Phosphodiest  2 lvislDGlr...adlldrla.e...llpnlaaLakegvsapnlrp 39
                                  ++i+lDGl     ++l++       ++pnl++La++g  +  +++
  gi|15668182|ref|NP_246973.1|  4 ILILLDGLGdraSEILNNKTpLqfaKTPNLDRLAENGMCGL-MTT 47
                                  8999999998884444442221355************9987.765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.1e-05
                                   HHHHCHTHSHHHHHCT........SSESEEEEEECCCHHHHHHH-T.TSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEE CS
                  Phosphodiest 155 twldaafakvvlekel........ekpdlllvyleetDtvgHkfGp.dspevedalrrvDkaigdLlealderglsaetni 226
                                   ++l ++f k  +e  +         ++d+++++  etD + H   p ++    + ++++Dk ig+L   l+e+       +
  gi|15668182|ref|NP_246973.1| 268 KFLGMDFIK--IESFEegidlipeLDYDFIHLHTKETDEAAHTKNPlNK---VKVIEKIDKLIGNLK--LRED-----DLL 336
                                   347777766..4433356777776778***************8865444...5689999*****994..4444.....34* PP

                                   EEEES---EEEHTTSEE CS
                  Phosphodiest 227 ilvSDHGmadvsddkvi 243
                                   i+++DH   +v   ++i
  gi|15668182|ref|NP_246973.1| 337 IITADHSTPSV--GNLI 351
                                   ******99988..5555 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.6e-05     0.092     262     326 ..     302     361 ..     294     407 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.6e-05
                                   HHHHHHTTTHHHHHHHHHHHHHHHHHHHHHCHHCTTEEEEEEESSEESEEEESTTSTT..TTSEE CS
               Alk_phosphatase 262 IDhaaHendavgalsEvvefdeAvkaalefakkeketlvvvTaDHshvfsfggyttrgesvlgle 326
                                    D+aaH  ++ ++++ + ++d+ + +     k  ++ l++ TaDHs+  s+g +  +gesv  l 
  gi|15668182|ref|NP_246973.1| 302 TDEAAHTKNPLNKVKVIEKIDKLIGN----LKLREDDLLIITADHST-PSVGNLIHSGESVPILF 361
                                   69999****99999999999987765....3335689**********.99999999999876553 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00027      0.96       4      37 ..       4      41 ..       2      43 .. 0.91
   2 ?    0.2   0.0      0.11   3.8e+02     227     253 ..     320     346 ..     308     389 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00027
                                  EEEEESSE-TTGSGGGTTTSCS....SHHHHHHHHTSE CS
                     Sulfatase  4 vliladdlgagdlglyggktat....tpnldrlaeegl 37
                                  +lil+d lg+   ++ ++kt+     tpnldrlae+g+
  gi|15668182|ref|NP_246973.1|  4 ILILLDGLGDRASEILNNKTPLqfakTPNLDRLAENGM 41
                                  89******************777777**********97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.11
                                   HHHHHHHHTTTGGGEEEEEEESSSSCC CS
                     Sulfatase 227 rvlaaLeenglldntlvvftSDhgasl 253
                                   ++ + +  ++l+++ l+++t+Dh    
  gi|15668182|ref|NP_246973.1| 320 KIDKLIGNLKLREDDLLIITADHSTPS 346
                                   444444455899999********8655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2966.34
//
Query:       gi|15668183|ref|NP_246974.1|  [L=197]
Description: hypothetical protein MJ_0011 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-15   54.2   0.1    1.4e-14   53.3   0.0    1.6  2  DUF3343   Protein of unknown function (DUF3343)


Domain annotation for each model (and alignments):
>> DUF3343  Protein of unknown function (DUF3343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   7.8e-19   1.4e-14       1      67 [.      27      92 ..      27      94 .. 0.96
   2 ?   -3.1   0.0      0.31   5.6e+03      41      55 ..     146     160 ..     146     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 7.8e-19
                       DUF3343  1 yyvitFssthhAiaaekalkeggiearliplPreisagCGlalrvneedieeasrllseaeipyegi 67
                                  +++i+F++t +A++ae++lk + ++++++  P+ei+ gC la++++  d+  ++r l+ + i++ ++
  gi|15668183|ref|NP_246974.1| 27 KGLIIFENTKDAMRAESILKDK-YKIKVVAPPPEIREGCDLAIEYELIDEFGIKRELESNDIKPLKF 92
                                  689*****************87.***************************************99876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.31
                       DUF3343  41 lalrvneedieeasr 55 
                                   lal+++ ++i+ +++
  gi|15668183|ref|NP_246974.1| 146 LALKLKGRNIKDIKE 160
                                   688998888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1180.21
//
Query:       gi|15668184|ref|NP_246976.1|  [L=162]
Description: hypothetical protein MJ_0013 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1010.52
//
Query:       gi|15668185|ref|NP_246977.1|  [L=213]
Description: hypothetical protein MJ_0014 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-22   79.9   0.0    2.8e-22   79.4   0.0    1.2  1  Resolvase      Resolvase, N terminal domain
      2e-11   43.9   0.3    4.4e-11   42.8   0.3    1.6  1  HTH_17         Helix-turn-helix domain
    6.4e-09   35.4   0.0    1.2e-08   34.6   0.0    1.5  1  MerR           MerR family regulatory protein
    1.8e-08   34.4   0.1    4.3e-08   33.1   0.1    1.7  1  MerR_1         MerR HTH family regulatory protein
     0.0063   16.3   0.3      0.026   14.3   0.0    2.2  3  HTH_23         Homeodomain-like domain
  ------ inclusion threshold ------
       0.02   15.0   0.2       0.11   12.7   0.1    2.1  2  DUF3853        Protein of unknown function (DUF3853)
      0.021   15.0   0.0       0.05   13.7   0.0    1.7  1  HTH_28         Helix-turn-helix domain
      0.024   14.4   0.1       0.21   11.4   0.0    2.4  2  HTH_8          Bacterial regulatory protein, Fis family
      0.075   13.6   0.1       0.21   12.2   0.0    1.8  2  LZ_Tnp_IS481   leucine-zipper of insertion element IS481
       0.11   12.5   0.1       0.32   11.1   0.1    1.8  2  Peptidase_C92  Permuted papain-like amidase enzyme, YaeF/YiiX
       0.18   11.2   0.0       0.42   10.1   0.0    1.6  1  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.0   1.7e-25   2.8e-22       1     138 [.      64     195 ..      64     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 1.7e-25
                                   EEEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCCC-S... CS
                     Resolvase   1 aigYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekldRLaRsvr 81 
                                   +igYaRvS + q+d+lerQ++ ++ ya+eng++i ++ +D   SG +++R+ +k+ll+ + ++k++ +++   dRL+R  +
  gi|15668185|ref|NP_246977.1|  64 IIGYARVSFNAQKDDLERQIQLIKSYAEENGWDI-QILKDI-GSGLNEKRKNYKKLLKMVMNRKVEKVIIAYPDRLTRFGF 142
                                   69*******************************9.779999.************************************876 PP

                                   S-HHHHHHHHHTT-EEEESS..SS----HHHHHHHHHHHHHHHHHHHHHCT-TTHHH CS
                     Resolvase  82 dlltlleelrekgvslvsldegidtstpmgrlllqilaalaeferelirertkegla 138
                                   +   l e +++ g ++v++++  + +tp+ +l+ +++ ++++f  +l  +++++ ++
  gi|15668185|ref|NP_246977.1| 143 ET--LKEFFKSYGTEIVIINK--KHKTPQEELVEDLITIVSHFAGKLYGMHSHKYKK 195
                                   65..57899***********5..7889***************999999888877655 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.3   2.7e-14   4.4e-11       2      47 ..       8      54 ..       8      55 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 2.7e-14
                        HTH_17  2 ltveEaAelLgvsrstvyrlirrgelpaak.iGrrwriprsdleewl 47
                                  +t +Ea+++Lgvs +t++r+ ++g++++ + +G+++r+p+s++ + l
  gi|15668185|ref|NP_246977.1|  8 YTLKEASKILGVSIKTLQRWDKAGKIKCIRtLGGKRRVPESEIKRIL 54
                                  8****************************99************9876 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   7.1e-12   1.2e-08       2      37 ..      10      44 ..       9      45 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 7.1e-12
                                  HHHHHHHHTTTHHHHHHHHHTTSSTSEEETTTSSEE CS
                          MerR  2 IgevAeltGvsprtLRyYEreGLipppeRtegGyRl 37
                                   +e+++++Gvs++tL ++++ G+i + +Rt gG R+
  gi|15668185|ref|NP_246977.1| 10 LKEASKILGVSIKTLQRWDKAGKI-KCIRTLGGKRR 44
                                  58**********************.**********8 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   2.6e-11   4.3e-08       1      50 [.       8      57 ..       8      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.6e-11
                                  EEHHHHHHHHTS-HHHHHHHHHHTT-S-EE-TTS-EEEEHHHHHHHHHHH CS
                        MerR_1  1 ysigevakilgvtthtlrywekegllkpkrteggrryYtdedierLklik 50
                                  y+++e++kilgv+ +tl+ w+k g++k+ rt gg r+  +++i+r+  ik
  gi|15668185|ref|NP_246977.1|  8 YTLKEASKILGVSIKTLQRWDKAGKIKCIRTLGGKRRVPESEIKRILGIK 57
                                  99****************************999999999*9999999988 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.6e-05     0.026      17      37 ..       7      27 ..       2      36 .. 0.91
   2 ?   -2.7   0.0       3.6   5.9e+03      19      29 ..      46      56 ..      42      57 .. 0.74
   3 ?   -3.2   0.0       4.9     8e+03       9      17 ..      84      94 ..      79      96 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                        HTH_23 17 GlsvreIAreLgvsrrTvyrw 37
                                   ++ +e++++Lgvs  T++rw
  gi|15668185|ref|NP_246977.1|  7 HYTLKEASKILGVSIKTLQRW 27
                                  5899***************** PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.6
                        HTH_23 19 svreIAreLgv 29
                                  + +eI r+Lg+
  gi|15668185|ref|NP_246977.1| 46 PESEIKRILGI 56
                                  56788888887 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.9
                        HTH_23  9 rillllae..G 17
                                  + ++ +ae  G
  gi|15668185|ref|NP_246977.1| 84 QLIKSYAEenG 94
                                  44444444344 PP

>> DUF3853  Protein of unknown function (DUF3853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   6.7e-05      0.11      46      80 ..       8      42 ..       3      58 .. 0.83
   2 ?   -0.6   0.0      0.95   1.6e+03      11      31 ..     149     169 ..     144     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.7e-05
                       DUF3853 46 yGikglarllGislptanrikksGkiDkaitqiGr 80
                                  y +k+ +++lG+s+ t +r  k Gki    t  G+
  gi|15668185|ref|NP_246977.1|  8 YTLKEASKILGVSIKTLQRWDKAGKIKCIRTLGGK 42
                                  7899**********************765555555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.95
                       DUF3853  11 lkmtGeellfLlkkaetkeea 31 
                                   +k  G e+++++kk +t +e 
  gi|15668185|ref|NP_246977.1| 149 FKSYGTEIVIINKKHKTPQEE 169
                                   566799999999988776654 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.1e-05      0.05      11      34 ..       6      29 ..       1      39 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.1e-05
                        HTH_28 11 aGhsvreaArelgisrrtvyrWik 34
                                  ++ + +ea+++lg+s  t++rW k
  gi|15668185|ref|NP_246977.1|  6 RHYTLKEASKILGVSIKTLQRWDK 29
                                  445*******************98 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.21      14      37 ..       4      26 ..       1      26 [. 0.84
   2 ?   -0.5   0.0      0.68   1.1e+03       8      22 ..      84      98 ..      78      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                  HHHTTT-HHHHHHHHTS-HHHHHH CS
                         HTH_8 14 LertgGnkskAArlLGisRrtLyr 37
                                  +er+   +++A+++LG+s +tL r
  gi|15668185|ref|NP_246977.1|  4 MERHY-TLKEASKILGVSIKTLQR 26
                                  55655.89**************87 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.68
                                  HHHHHHHHHTTT-HH CS
                         HTH_8  8 elIeaALertgGnks 22
                                  +lI+   e++g+ ++
  gi|15668185|ref|NP_246977.1| 84 QLIKSYAEENGWDIQ 98
                                  6899999*****875 PP

>> LZ_Tnp_IS481  leucine-zipper of insertion element IS481
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.21      21      60 ..       3      42 ..       1      63 [. 0.80
   2 ?   -2.4   0.0       4.3   7.1e+03       1      12 [.     188     199 ..     188     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                  LZ_Tnp_IS481 21 vvedrrtvaqvarelGvslrtaykwlarfraeGldGlldr 60
                                  ++e ++t++++++ lGvs +t  +w    +   ++ l  +
  gi|15668185|ref|NP_246977.1|  3 IMERHYTLKEASKILGVSIKTLQRWDKAGKIKCIRTLGGK 42
                                  7999*********************776666666666555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.3
                  LZ_Tnp_IS481   1 mnshknarltvl 12 
                                   m shk  +lt+ 
  gi|15668185|ref|NP_246977.1| 188 MHSHKYKKLTKT 199
                                   889999999975 PP

>> Peptidase_C92  Permuted papain-like amidase enzyme, YaeF/YiiX, C92 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.8     3e+03      46      68 ..      12      33 ..       5      51 .. 0.73
   2 ?   11.1   0.1   0.00019      0.32      53     100 ..     140     189 ..     110     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.8
                 Peptidase_C92 46 eaaakegvrvtpLseflarrssi 68
                                  ea++  gv +++L+++ ++ ++i
  gi|15668185|ref|NP_246977.1| 12 EASKILGVSIKTLQRWDKA-GKI 33
                                  6766679999999999774.444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                 Peptidase_C92  53 vrvtpLseflar.rssiavyrlkea.ltaeqrqkaaeaalrrlgkpYdfg 100
                                   +   +L+ef ++  ++i++   k + +++e  ++++ ++ ++ gk Y++ 
  gi|15668185|ref|NP_246977.1| 140 FGFETLKEFFKSyGTEIVIINKKHKtPQEELVEDLITIVSHFAGKLYGMH 189
                                   55689*******866666666666679********************987 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00026      0.42      29      49 ..       9      29 ..       2      31 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00026
                  HTH_Tnp_ISL3 29 svkavArqlgvSwtTVwrild 49
                                  + k+++++lgvS +T++r+ +
  gi|15668185|ref|NP_246977.1|  9 TLKEASKILGVSIKTLQRWDK 29
                                  889***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1315.16
//
Query:       gi|15668186|ref|NP_246978.1|  [L=98]
Description: hypothetical protein MJ_0015 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0017   18.4   0.0     0.0018   18.4   0.0    1.1  1  HAD_2        Haloacid dehalogenase-like hydrolase
     0.0028   17.7   0.0     0.0043   17.1   0.0    1.3  1  Hydrolase_6  Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.043   13.4   0.0      0.051   13.2   0.0    1.1  1  CobU         Cobinamide kinase / cobinamide phosphate guanylt
      0.071   12.8   0.0      0.098   12.4   0.0    1.2  1  PNK3P        Polynucleotide kinase 3 phosphatase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.9e-07    0.0018      61     108 ..      45      90 ..      11      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.9e-07
                         HAD_2  61 kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksrea 108
                                   + ++l+ +y+++ ++  ++++++v+e+L e k++gy l +vT+++ ++
  gi|15668186|ref|NP_246978.1|  45 INKRLIGDYVKKIEE--FELLPNVREALIEFKKMGYLLIVVTNQQGSK 90 
                                   567788888888888..**************************98766 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   9.6e-07    0.0043       1      42 [.      37      89 ..      37      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.6e-07
                                  EEEESTTTSE...........ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS CS
                   Hydrolase_6  1 flfDidGvLw...........rgdkaipgaaealnalraagkpvvllTNnssk 42
                                  +++D dGv+            ++ +++p++ eal  ++++g+ ++++TN+ ++
  gi|15668186|ref|NP_246978.1| 37 IFLDRDGVINkrligdyvkkiEEFELLPNVREALIEFKKMGYLLIVVTNQQGS 89
                                  57999***99777777777777999************************9775 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.1e-05     0.051      65     127 ..      13      88 ..       3      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                          CobU  65 ealkeeekkevvLvDcltlwltnllleeeaek..............veekleeeveellealkelkatvvlVsnEvg 127
                                    +l++   ++ v +Dcl ++l+++++ +++                 e +l  +v+e l  +k++   +++V+n  g
  gi|15668186|ref|NP_246978.1|  13 LLLERLGLQQLVWMDCLVMMLNKAIFLDRD-GvinkrligdyvkkiEEFELLPNVREALIEFKKMGYLLIVVTNQQG 88 
                                   344444447899************998664.35999******99855559999*********************876 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.2e-05     0.098      19      58 ..      52      90 ..      35      94 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                         PNK3P 19 efakdaddwkllsesvlekLkklkeegykivifsNqggvv 58
                                     k+ ++++ll  +v e L + k+ gy +++++Nq+g +
  gi|15668186|ref|NP_246978.1| 52 DYVKKIEEFELLP-NVREALIEFKKMGYLLIVVTNQQGSK 90
                                  3445578888875.7*********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 630.26
//
Query:       gi|15668187|ref|NP_246979.1|  [L=58]
Description: hypothetical protein MJ_0016 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 394.30
//
Query:       gi|15668188|ref|NP_246980.1|  [L=214]
Description: transposase, IS240 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-14   54.5   0.0    2.7e-14   53.6   0.0    1.4  1  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.32   11.2   0.0    1.7  2  rve            Integrase core domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0     3e-18   2.7e-14       5     137 ..      82     211 ..      79     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 3e-18
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkelkregelf 84 
                                   ++DE  +k+  k  Y + a+D e++  l++++sk R+   +++f + +lk    +  +i++D+ + y+ al++l+ e+e+ 
  gi|15668188|ref|NP_246980.1|  82 AIDEIKLKVGDKYIYAWSAIDVETKeCLGVYISKTRNYLDTILFVKSILKFC-SNKPKILVDGGKWYPWALRKLGLEFEKV 161
                                   79********************9999*************************9.566689*****************86633 PP

                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrl.rptrgf...kslksaaktlagfeavknlrk 137
                                   +         l+n +Es ++ lK+r+    + f    +++++ ++++ f +++n  k
  gi|15668188|ref|NP_246980.1| 162 KF-------GLRNCVESFFSVLKRRTkAFFNRFpnnSKFDTVISWIKSFMMFYNWVK 211
                                   22.......77**************95345666222457788888888888888766 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.6e-05      0.32       8      76 ..      81     145 ..      74     154 .. 0.83
   2 ?   -1.5   0.0      0.31   2.8e+03     108     118 ..     169     179 ..     165     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.6e-05
                           rve   8 wqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngs 76 
                                   + +D  +++   g++ +y   ++d+ ++++l++++s+  +  +++ +++  +++  ++ p ++l D g+
  gi|15668188|ref|NP_246980.1|  81 IAIDEIKLK--VGDKYIYAWSAIDVETKECLGVYISKTRNYLDTILFVKSILKFCSNK-P-KILVDGGK 145
                                   556666666..66777*********************************999999996.4.66777766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.31
                           rve 108 vErfhrtlkde 118
                                   vE+f+  lk++
  gi|15668188|ref|NP_246980.1| 169 VESFFSVLKRR 179
                                   78888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1360.66
//
Query:       gi|15668189|ref|NP_246981.1|  [L=524]
Description: hypothetical protein MJ_0018 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-07   29.3   2.1    9.8e-07   28.6   2.1    1.4  1  Class_IIIsignal  Class III signal peptide


Domain annotation for each model (and alignments):
>> Class_IIIsignal  Class III signal peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   2.1   5.5e-11   9.8e-07       1      25 [.       6      30 ..       6      32 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.5e-11
               Class_IIIsignal  1 kKGQiSlEyiLLilavlviaiiaiy 25
                                  +KGQ++lE+iLLil+++v++i++++
  gi|15668189|ref|NP_246981.1|  6 RKGQLTLEFILLILGMTVVGIVITM 30
                                  7*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 3160.34
//
Query:       gi|15668190|ref|NP_246982.1|  [L=630]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-73  246.8   0.0    1.4e-72  244.4   0.0    2.1  2  GatB_N      GatB/GatE catalytic domain
    4.5e-31  107.7   2.8    4.5e-31  107.7   2.8    2.8  3  GatB_Yqey   GatB domain
    1.2e-25   89.6   1.0    1.2e-25   89.6   1.0    2.6  3  GAD         GAD domain
    1.4e-06   28.5   0.4    4.7e-06   26.7   0.4    2.0  1  YqeY        Yqey-like protein
    0.00016   21.7   0.0    0.00036   20.5   0.0    1.5  1  TraB        TraB family
  ------ inclusion threshold ------
       0.98    9.8   5.0       0.48   10.8   1.3    2.4  2  TSNAXIP1_N  Translin-associated factor X-interacting N-termin
        6.6    7.2  10.2        3.6    8.0   0.6    3.3  3  FAM25       FAM25 family


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.4   0.0   5.3e-76   1.4e-72       2     273 .]      11     446 ..      10     446 .. 0.96
   2 ?   -1.4   0.0      0.48   1.2e+03     200     231 ..     560     593 ..     525     617 .. 0.72

  Alignments for each domain:
  == domain 1  score: 244.4 bits;  conditional E-value: 5.3e-76
                                   EEEEEEEEEB--SB-SSSSSBSSSSCE..........S.TTSS--TTTTTS...........................TT. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx..........x.xxxxxxxxxxxx...........................xxx RF
                        GatB_N   2 viGlEiHaqlktksKlFssasteeege..........e.pnsevsevdlal...........................PGt 44 
                                   ++GlEiH+ql+tk+KlF++++t   ++          + + se++evd a+                           P  
  gi|15668190|ref|NP_246982.1|  11 KVGLEIHQQLNTKRKLFCHCPTILRDDepdgeivrvlRpSLSEMGEVDRAAliearkgkkfiyqfyndttclveldeeP-- 89 
                                   89*******************873333355668888843778999999988************************9998.. PP

                                   .--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEEEEEE---EEE CS
                                   xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                        GatB_N  45 lPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrierihlEeDaaksv 123
                                    P+ +++ea+++a+++al +n+++ +  +++RK+++++++++g+Q+t     la++G++e+ e kv+i++++lEeDaa+++
  gi|15668190|ref|NP_246982.1|  90 -PHpPSEEALRIALEVALLMNMNVVDVAYTMRKIVIDGSNTSGFQRTI---FLARDGYIETsEGKVGITSLCLEEDAARKI 166
                                   .9999******************************************9...789******9889***************** PP

                                   EEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 124 heekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvE 204
                                   +++ + ++++l+R+G+pL+Ei+t+pd+++p+ a++++++++e+lra+g++++++  G++R+D+N+S+++       g+r+E
  gi|15668190|ref|NP_246982.1| 167 EDRGDAVVYNLDRLGIPLVEISTAPDIKTPKMAKEAARRIGEILRATGKVKRGL--GTIRQDINISIKD-------GARIE 238
                                   ******************************************************..************4.......49*** PP

                                   EEEE-SHHHHHHHHHHHHHHHHHHH........................................................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx........................................................ RF
                        GatB_N 205 iKnlnslksiekaieyeierqiell........................................................ 229
                                   +K++++l+ iek++e+e+ rq++ll                                                        
  gi|15668190|ref|NP_246982.1| 239 VKGVQDLDLIEKVVENEVIRQLNLLkirdelrernaevvekifdvteifkdckskiiqnalkkkngkvkavllkgfaglvg 319
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                        GatB_N 230 ................................................................................. 229
                                                                                                                    
  gi|15668190|ref|NP_246982.1| 320 keiqpgrrlgtefsdrakviagvgglfhtdelpkygiteeevkklkefvnaeendaviivadeeskvdraleavierakea 400
                                   ********************************************************************************* PP

                                   .....-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHHHH CS
                                   .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 230 .....qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseelie 273
                                        +eTr++ ed g+t +lR+ + a   r++pe+d+pp+ i++e+ie
  gi|15668190|ref|NP_246982.1| 401 ligvpEETRRALED-GNTAYLRPLPGA--ARMYPETDIPPIIIKKEFIE 446
                                   **************.**********77..5****************996 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.48
                                   .--EEEEEE-SH..HHHHHHHHHHHHHHHHHH-E CS
                                   xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 200 gtrvEiKnlnsl..ksiekaieyeierqiellqe 231
                                    +  EiK+l+ l  +++ek+ie  i+ ++++++e
  gi|15668190|ref|NP_246982.1| 560 DEILEIKGLKGLskEEVEKIIEGIIKEHLNVVKE 593
                                   6678999999662257999999999998888754 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.2      0.21   5.3e+02      77     120 ..     254     295 ..     237     314 .. 0.68
   2 ?   -2.6   0.4       1.7   4.4e+03      89     108 ..     381     400 ..     355     412 .. 0.60
   3 !  107.7   2.8   1.8e-34   4.5e-31       1     148 []     484     627 ..     484     627 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.21
                                   HHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTST CS
                     GatB_Yqey  77 eeiieekgLkqisdeeeleklveeviaenpkavedyksgkekal 120
                                   +e+i++ +L +i+d  el++  +ev+++  ++ e +k+ k k +
  gi|15668190|ref|NP_246982.1| 254 NEVIRQLNLLKIRD--ELRERNAEVVEKIFDVTEIFKDCKSKII 295
                                   56778888888877..7777777777777777776666665543 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                                   XXSSXHHHHHHHHHHTXHHH CS
                     GatB_Yqey  89 sdeeeleklveeviaenpka 108
                                    +e+++ +++e vi++ ++a
  gi|15668190|ref|NP_246982.1| 381 DEESKVDRALEAVIERAKEA 400
                                   34566666666666666655 PP

  == domain 3  score: 107.7 bits;  conditional E-value: 1.8e-34
                                   HHHHHHHHHSS..HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHHHH CS
                     GatB_Yqey   1 dffeevvkegad.aklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspeei 79 
                                   d+fe ++k+ ++ ++ +++ +l+ +l+e+++eg +i++  l++++l+e +k ++egkI+k+ + evl+ ++e  +ks++ei
  gi|15668190|ref|NP_246982.1| 484 DLFEDLCKKFKNvKPVLIATTLEGTLKEIKREGYDIDK--LEDRHLEETFKALSEGKIAKEGIVEVLKGFCEFpDKSIDEI 562
                                   79********9989999*********************..9**************************************** PP

                                   HHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                     GatB_Yqey  80 ieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                   +e kgLk +s  ee+ek++e +i+e+   ++ +k++ eka +fl+G++M k++Gkad+klvn++l++kL
  gi|15668190|ref|NP_246982.1| 563 LEIKGLKGLSK-EEVEKIIEGIIKEH---LNVVKEKGEKAYGFLMGRCMAKLRGKADGKLVNDILRKKL 627
                                   **********8.**************...99************************************98 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   1.0   4.5e-29   1.2e-25       1      95 []     295     390 ..     295     390 .. 0.98
   2 ?   -2.4   0.0       2.3   5.9e+03      45      69 ..     536     562 ..     509     576 .. 0.56
   3 ?   -1.3   0.1         1   2.7e+03      20      42 ..     576     598 ..     556     603 .. 0.54

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 4.5e-29
                                   HHHHHHS.TEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TTE CS
                           GAD   1 fsealks.ggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeegD 79 
                                   +++alk+ +g+vka+ ++g +a+l++kei++++++++e+++++++ ++v+g ++t++++k+ +teeevkkl+e v+aee+D
  gi|15668190|ref|NP_246982.1| 295 IQNALKKkNGKVKAVLLKG-FAGLVGKEIQPGRRLGTEFSDRAKVIAGVGGLFHTDELPKYgITEEEVKKLKEFVNAEEND 374
                                   68999999***********.8************************************************************ PP

                                   EEEEEEEEHHHHHHHH CS
                           GAD  80 illfvAdkkktvnkal 95 
                                   ++++vAd++++v++al
  gi|15668190|ref|NP_246982.1| 375 AVIIVADEESKVDRAL 390
                                   *************997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
                                   EEEESSGGEETTTCCC..S-HHHHHHH CS
                           GAD  45 wikvegegltgpiakf..lteeevkkl 69 
                                     k+ +eg+ + +  f  +  + + ++
  gi|15668190|ref|NP_246982.1| 536 EGKIAKEGIVEVLKGFceFPDKSIDEI 562
                                   444444444444444433333333333 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1
                                   -TTTSHHHHHHHHHHHHHTTHSH CS
                           GAD  20 aaklsrkeideleefakelgakg 42 
                                    +k++   i+e  +++ke+g k+
  gi|15668190|ref|NP_246982.1| 576 VEKIIEGIIKEHLNVVKEKGEKA 598
                                   33444444444446666666665 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.4   1.8e-09   4.7e-06      90     143 .]     570     627 ..     561     627 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.8e-09
                                   ---HHHHHHHHHHHHHHT....T--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH- CS
                          YqeY  90 qlseeeiealvkeaiaev....gaesmkdmGkvmkalkpkvkGkaDgkkvsalvkekL 143
                                    ls+ee+e++++ +i+e     ++++ k+ G +m+  ++k++GkaDgk v+ ++++kL
  gi|15668190|ref|NP_246982.1| 570 GLSKEEVEKIIEGIIKEHlnvvKEKGEKAYGFLMGRCMAKLRGKADGKLVNDILRKKL 627
                                   5899****99999999855544899*****************************9987 PP

>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.4e-07   0.00036      77     186 ..     456     581 ..     440     610 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.4e-07
                          TraB  77 seelyarlqkalak.rglplaaldkm...................kPwllalllslaelakkkagldpel.vDrylaktak 136
                                   +ee ++r++k  +   +l  +    m                   kP l+a +l+ + ++ k++g+d+++  Dr+l++t+k
  gi|15668190|ref|NP_246982.1| 456 PEEKFERFKKEYKLnDELAKK----MvlsyyvdlfedlckkfknvKPVLIATTLEGTLKEIKREGYDIDKlEDRHLEETFK 532
                                   555555555554442123332....12222333333334444444**********************99999********* PP

                          TraB 137 ragkpvgglEtveeqlsllsslpdeeqleale.etldeleeakdlleelve 186
                                   +      + E + e+l+ + ++pd+  +e le + l+ l   k+++e+++e
  gi|15668190|ref|NP_246982.1| 533 ALSEGKIAKEGIVEVLKGFCEFPDKSIDEILEiKGLKGLS--KEEVEKIIE 581
                                   *******************55**********977777777..888888887 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       2.1   5.4e+03       4      35 ..     265     296 ..     261     301 .. 0.58
   2 ?   10.8   1.3   0.00019      0.48       1      45 [.     457     501 ..     457     526 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.1
                    TSNAXIP1_N   4 lekelqklkctedgpqekrlqvyrevFedlie 35 
                                   +++el++ + +   + ++ +++++++ +++i+
  gi|15668190|ref|NP_246982.1| 265 IRDELRERNAEVVEKIFDVTEIFKDCKSKIIQ 296
                                   55555555444445555666666666666665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00019
                    TSNAXIP1_N   1 EkklekelqklkctedgpqekrlqvyrevFedlieefkaYkdlLs 45 
                                   E+k e+ ++++k +++  +++ l  y + Fedl+++fk  k++L 
  gi|15668190|ref|NP_246982.1| 457 EEKFERFKKEYKLNDELAKKMVLSYYVDLFEDLCKKFKNVKPVLI 501
                                   6788999999999999**************************994 PP

>> FAM25  FAM25 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.8     0.025        65       4      31 ..     276     302 ..     273     311 .. 0.81
   2 ?   -2.6   0.1       2.9   7.5e+03       7      19 ..     388     400 ..     383     401 .. 0.71
   3 ?    8.0   0.6    0.0014       3.6       3      23 ..     578     598 ..     576     602 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.025
                         FAM25   4 aveevvkevveHaKeaGEKAiadalKkA 31 
                                   +ve  + +v e  K+   K i +alKk 
  gi|15668190|ref|NP_246982.1| 276 VVEK-IFDVTEIFKDCKSKIIQNALKKK 302
                                   4444.45999****************95 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.9
                         FAM25   7 evvkevveHaKea 19 
                                        v+e aKea
  gi|15668190|ref|NP_246982.1| 388 RALEAVIERAKEA 400
                                   5566788888886 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0014
                         FAM25   3 haveevvkevveHaKeaGEKA 23 
                                   +++e+++ke ++ +Ke GEKA
  gi|15668190|ref|NP_246982.1| 578 KIIEGIIKEHLNVVKEKGEKA 598
                                   689*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (630 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 3685.55
//
Query:       gi|15668191|ref|NP_246983.1|  [L=417]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-63  213.1   0.2    9.4e-63  211.2   0.0    1.8  2  Asparaginase    Asparaginase, N-terminal
      4e-37  126.9   0.1    1.2e-35  122.2   0.0    2.2  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    5.3e-18   64.1   9.3      1e-17   63.2   6.8    2.4  2  GatD_N          GatD N-terminal domain
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.19   11.4   0.0    1.3  1  RNA_pol_Rpc82   RNA polymerase III subunit RPC82


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.2   0.0   2.1e-66   9.4e-63       2     179 ..      76     258 ..      75     271 .. 0.96
   2 ?   -0.9   0.0      0.23     1e+03     138     154 ..     336     352 ..     326     363 .. 0.77

  Alignments for each domain:
  == domain 1  score: 211.2 bits;  conditional E-value: 2.1e-66
                                   EEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.-SEEEE CS
                  Asparaginase   2 vlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.ydgfVv 81 
                                   + +l+tGGT+as++d+++ga++p+++a++l++a+pel +ia+++ + ++ni S+nm+p+ w+k+ae+i++++ee +dg+V+
  gi|15668191|ref|NP_246983.1|  76 ISILSTGGTVASKVDYKTGAVHPSFTADDLIRAVPELLDIANIKGRAVMNILSENMKPEYWRKIAEEIKKEIEEgADGIVI 156
                                   89**********************************************************************666****** PP

                                   E--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.......EEETTT CS
                  Asparaginase  82 lhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.......llranr 155
                                   +hGTDT++ytAsaLs+m+k  d+p++l+G+qr++++++sD++ Nl++A+l+a ++  i+gv+vv++g+       l+++ +
  gi|15668191|ref|NP_246983.1| 157 AHGTDTMSYTASALSFMVKA-DVPIILVGAQRSSDRPSSDAALNLISAVLAAREP--IKGVYVVMHGEsgdtfcyLHKGVK 234
                                   ******************99.*******************************998..************************ PP

                                   EEE-BSSSSS-EEETTT--SEEEE CS
                  Asparaginase 156 vtKvhtssldaFespnlgplaeve 179
                                   v+K h+s++daF+s+n  p+a+++
  gi|15668191|ref|NP_246983.1| 235 VRKCHSSRRDAFKSINSIPVAKIN 258
                                   *********************993 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.23
                                   TTSECEEEETTEEEETT CS
                  Asparaginase 138 riagvlvvfngkllran 154
                                     +gv+vv+  + ++++
  gi|15668191|ref|NP_246983.1| 336 TDKGVVVVMTTQTINGR 352
                                   46799999999999887 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.033   1.5e+02      16      57 ..     143     182 ..      95     203 .. 0.76
   2 !  122.2   0.0   2.7e-39   1.2e-35       1     113 [.     288     399 ..     288     400 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.033
                                   HHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEE CS
                Asparaginase_C  16 lkallkkgakGvvlegtGvGnlpsallealkeakargivvva 57 
                                   +k+ +++ga+G+v++ +  +   s +  al+ ++++++++++
  gi|15668191|ref|NP_246983.1| 143 IKKEIEEGADGIVIAHGTDT--MSYTASALSFMVKADVPIIL 182
                                   4444599*******987443..45666666666666776665 PP

  == domain 2  score: 122.2 bits;  conditional E-value: 2.7e-39
                                   -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHHHT CS
                Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkelerlg 81 
                                   +V+++k++pgmd+++++ +++k++kG+vlegtG G++p+ + e +k a+++g+vvv+t+q+++g+v++++y++g+el++lg
  gi|15668191|ref|NP_246983.1| 288 KVALIKVYPGMDGEIIRFYVDKEYKGIVLEGTGLGHAPEYIFEHIKYATDKGVVVVMTTQTINGRVNMNVYSNGRELQKLG 368
                                   7******************************************************************************** PP

                                   EEE-TT--HHHHHHHHHHHCTT---HHHHHHH CS
                Asparaginase_C  82 visaddmtpeaarikLmlllgkgldpaevrkl 113
                                   vi ++dm pe a +kLm+llg+  +p+ev+kl
  gi|15668191|ref|NP_246983.1| 369 VIGCEDMPPEVALVKLMYLLGNY-EPEEVKKL 399
                                   *********************86.89999987 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   6.8   2.3e-21     1e-17       1      55 []       1      52 [.       1      52 [. 0.98
   2 ?    0.4   0.0     0.088   3.9e+02      13      22 ..     308     317 ..     299     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 2.3e-21
                                  --TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
                        GatD_N  1 ievGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                                  ++vGD+i+ve+++  +eGil+P+    +++ii++K++nGYN+Gi +e++++ie++
  gi|15668191|ref|NP_246983.1|  1 MNVGDVIRVETDKGIFEGILLPST---NENIITIKMKNGYNVGILKENVKNIEII 52
                                  689*********************...**************************98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.088
                                   S-EEEEEE-- CS
                        GatD_N  13 greyeGilmP 22 
                                   ++ey+Gi+++
  gi|15668191|ref|NP_246983.1| 308 DKEYKGIVLE 317
                                   689****997 PP

>> RNA_pol_Rpc82  RNA polymerase III subunit RPC82
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.3e-05      0.19     164     236 ..      98     181 ..      79     185 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.3e-05
                                   TCSCSSTHHHH-STT-----------...--------------..-------.----........---HHHHHHHHHHHHH CS
                 RNA_pol_Rpc82 164 itftandiaralpksldlsksigKrk...ssnssaaekkklkt..eeseees.eeng........qarlslieqhLklLas 230
                                    +fta+d+ ra+p+ ld+++   K++   ++ s++ +++  ++  e + +++ ee+          +++s+ +++L+ ++ 
  gi|15668191|ref|NP_246983.1|  98 PSFTADDLIRAVPELLDIANI--KGRavmNILSENMKPEYWRKiaE-EIKKEiEEGAdgiviahgTDTMSYTASALSFMVK 175
                                   68*******************..66666644444444455555642.333332333346677777999********99999 PP

                                   SSSSSS CS
                 RNA_pol_Rpc82 231 dslefl 236
                                    +++++
  gi|15668191|ref|NP_246983.1| 176 ADVPII 181
                                   988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      703  (0.0392102); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2431.54
//
Query:       gi|15668192|ref|NP_246984.1|  [L=375]
Description: hypothetical protein MJ_0021 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-13   51.5   3.9    2.2e-12   47.7   0.5    3.0  3  Radical_SAM  Radical SAM superfamily
    1.4e-08   34.9   0.2    3.5e-08   33.6   0.2    1.7  1  Fer4_14      4Fe-4S single cluster domain
    4.8e-07   30.1   1.5      1e-06   29.1   0.5    2.0  2  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.097   12.9   0.0       0.27   11.4   0.0    1.8  1  Sigma_reg_C  Sigma factor regulator C-terminal


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.5     5e-16   2.2e-12       3     115 ..      34     147 ..      32     189 .. 0.85
   2 ?    0.6   0.0      0.14   6.4e+02      53     101 ..     171     218 ..     165     248 .. 0.77
   3 ?    2.7   0.1     0.033   1.5e+02      50     101 ..     290     338 ..     250     350 .. 0.75

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 5e-16
                                   EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                   xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                   +t  Cn++C +C+ +e+     v       + +vee +ee+k  +     k+v ++gg+pll  + +++ +++ k++ +++
  gi|15668192|ref|NP_246984.1|  34 ITGICNNNCYYCPLSEKrknkdVIYANERLITTVEEAIEEAKLCS----SKGVGITGGNPLLKINRTVKFLKALKKEFDEF 110
                                   6789************99988888888888888999999999998....************************9999**** PP

                                   EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaadde 115
                                   + ++ t + +++ee l++l+e+ +d + l+   + +e
  gi|15668192|ref|NP_246984.1| 111 HAHLYTTPETVNEENLKLLKEADLDEIRLHPTKIFNE 147
                                   *************************999988777777 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.14
                                   ESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  53 gggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelg 101
                                   +g e  + p+++ ++++la+   +gi  ++ +n++  +ee   +l ++g
  gi|15668192|ref|NP_246984.1| 171 VGVEIPAIPNMENEILKLAEA-IDGIAKFMNINELEFSEENYHELEKRG 218
                                   566777777777777777777.499999999999999999999999988 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.033
                                   EEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  50 vilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelg 101
                                   ++++  e +l ++++e+le+   +  + i   +  n++ + e+++e++++ +
  gi|15668192|ref|NP_246984.1| 290 IMIFDNEDDL-KEMAEILEENEIE-FEIIDKNICLNPFIL-EDIIEEMKRQR 338
                                   4455555555.5555555555555.59999**********.*******9977 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.2   7.9e-12   3.5e-08       1      90 [.      32     119 ..      32     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 7.9e-12
                       Fer4_14   1 lfvrlsgCnlsCkgCdnketwkselgkpqteelleqilk..dlkkseikiqglvltGGePLhyenkkellklvkrlkeeyp 79 
                                   lf+ ++ Cn +C  C  +e ++++   ++++e l + ++    +++ ++ +g+ +tGG+PL   + +  +k++k lk+e+ 
  gi|15668192|ref|NP_246984.1|  32 LFI-TGICNNNCYYCPLSE-KRKNKDVIYANERLITTVEeaIEEAKLCSSKGVGITGGNPL--LKINRTVKFLKALKKEFD 108
                                   578.999********9777.555666666666666666644467888999***********..6788899*********** PP

                       Fer4_14  80 ekkiwletngt 90 
                                   e++ +l+t   
  gi|15668192|ref|NP_246984.1| 109 EFHAHLYTTPE 119
                                   ******99754 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.5   2.2e-10     1e-06       5     111 ..      27     132 ..      24     137 .. 0.69
   2 ?   -1.7   0.0      0.74   3.3e+03      86     102 ..     317     333 ..     291     348 .. 0.59

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.2e-10
                       Fer4_12   5 Gvrlslfvsg.CnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi...egltllGGEPllpenaeallelvkevke 81 
                                   G+ l+lf++g Cn +C +C   e ++ k     ++ l+  + e +++ +    +g+ ++GG Pll  + +  ++++k +k+
  gi|15668192|ref|NP_246984.1|  27 GGKLVLFITGiCNNNCYYCPLSEKRKNKDVIYANERLITTVEEAIEEAKLcssKGVGITGGNPLL--KINRTVKFLKALKK 105
                                   77889996655********9777666665555556666555555555433444************..888999******** PP

                       Fer4_12  82 ekpekdiwlytgytleelskkekeellkei 111
                                   e+ e    lyt     e  ++e  +llke 
  gi|15668192|ref|NP_246984.1| 106 EFDEFHAHLYTTP---ETVNEENLKLLKEA 132
                                   *996544444432...22223345666665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.74
                       Fer4_12  86 kdiwlytgytleelskk 102
                                    + ++ + ++le++ ++
  gi|15668192|ref|NP_246984.1| 317 DKNICLNPFILEDIIEE 333
                                   34667777777777655 PP

>> Sigma_reg_C  Sigma factor regulator C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     6e-05      0.27      56     146 ..     212     304 ..     186     313 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6e-05
                   Sigma_reg_C  56 seteaiGfkvnpsssekddkkkypkelekaeehfislL..kyl.sdqeeivktleeslekek.lkerydyvkkngvkiyGv 132
                                   +e e  Gf++++  s++++ ++++ ++  + ++f + L  +y  s  ++ +++ ++  +++k +++ y+ ++++g+   G+
  gi|15668192|ref|NP_246984.1| 212 HELEKRGFMPKDDVSNAIAGSEETALK--VIKEFKGDLfiNYCpSVLKDAIQMRNRLINRAKnVAKPYEVITEDGLLLRGI 290
                                   567777888888877777777555555..666666665223332234677888888899999******************* PP

                   Sigma_reg_C 133 vvtGpkkeLlkLek 146
                                   ++  + ++L+++++
  gi|15668192|ref|NP_246984.1| 291 MIFDNEDDLKEMAE 304
                                   **********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2379.50
//
Query:       gi|15668193|ref|NP_246985.1|  [L=362]
Description: cobalt-precorrin-6A synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-99  329.9   3.4    1.3e-98  329.4   3.4    1.2  1  CbiD      CbiD


Domain annotation for each model (and alignments):
>> CbiD  CbiD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.4   3.4    7e-103   1.3e-98       2     252 .]      10     266 ..       9     266 .. 0.99

  Alignments for each domain:
  == domain 1  score: 329.4 bits;  conditional E-value: 7e-103
                          CbiD   2 rsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleee..aavikdaGddpDvTngaeivaeve.. 78 
                                   + GyTtGscAaA+a +Al++l  g+kl+ veie+ +g+kl ipiek+++  ++  a+vikdaG d+D+Tng+ei++eve  
  gi|15668193|ref|NP_246985.1|  10 KFGYTTGSCAAAGAYSALYYLKFGKKLSYVEIENLNGDKLIIPIEKIEKCGNKakAVVIKDAGGDIDITNGIEIITEVElk 90 
                                   78*******************98**************************999899************************** PP

                          CbiD  79 ...eeieiegGeGvGrvtkpgLevevgeaAInpvprkmieenveevleeakegvevtisvpeGeelAkkTlNprlGivgGi 156
                                      + ++i+gGeGvG+vtk+gL+v+ ge+AInp pr+mi++n+ ++l++ +e vevtis+p+G+elAkkTlNp+lGivgG+
  gi|15668193|ref|NP_246985.1|  91 kgkKDVIIKGGEGVGIVTKNGLQVKKGEPAINPKPREMIRNNLLKLLND-DEVVEVTISIPKGKELAKKTLNPKLGIVGGL 170
                                   ***88******************************************98.88***************************** PP

                          CbiD 157 SiLGTtGivepmSeeallesireelkvaaaeglkelvlvtGnkgeklakkklglpeealvkvsnfvgealeeaaekgvkkv 237
                                   SiLGTtGiv+pmS+ea+++s++ +++va+a+g+k+l++v+Gn+g+k+ak+ l+ +++++++vsnf+g++l++a+ekgv+++
  gi|15668193|ref|NP_246985.1| 171 SILGTTGIVRPMSNEAYMNSLAPQIDVALANGYKRLIFVPGNIGTKYAKQLLNANDDEIIEVSNFWGFMLDKAKEKGVEEI 251
                                   ********************************************************************************* PP

                          CbiD 238 llvghiGKlvKlagG 252
                                   l++gh GK++KlagG
  gi|15668193|ref|NP_246985.1| 252 LIFGHAGKIIKLAGG 266
                                   *************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 2179.83
//
Query:       gi|15668194|ref|NP_246986.1|  [L=118]
Description: hypothetical protein MJ_0023 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.031   13.4   0.4      0.035   13.2   0.4    1.2  1  CyRPA     Cysteine-Rich Protective Antigen 6 bladed domain


Domain annotation for each model (and alignments):
>> CyRPA  Cysteine-Rich Protective Antigen 6 bladed domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4     2e-06     0.035       5      57 ..      14      67 ..      11     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-06
                         CyRPA  5 kspiqCirdiyf.lfkkelykvClqkvkkgrteiyvlvqkkvkeeWetkskllk 57
                                  +++  C  ++++ +f +ely+  ++ +k+++t i + v +++ +e  tk+++l 
  gi|15668194|ref|NP_246986.1| 14 RDNASCFDETFLkSFAEELYNAIIEIIKENKTIIKNEVRDELRNELATKEDILL 67
                                  67899******956*******************************999999873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1380  (0.0769703); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 741.55
//
Query:       gi|15668195|ref|NP_246987.1|  [L=139]
Description: hypothetical protein MJ_0024 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-49  166.1   2.0    5.4e-49  166.0   2.0    1.0  1  Archease  Archease protein family (MTH1598/TM1083)


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.0   2.0     3e-53   5.4e-49       1     137 [.       2     138 ..       2     139 .] 0.98

  Alignments for each domain:
  == domain 1  score: 166.0 bits;  conditional E-value: 3e-53
                                   EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S----E CS
                      Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvfkevk 81 
                                   ++y++ tAD+++ea+Gksleeaf++ a++l+++m+d++kv++ke+ e+e+++edle+lL++fL+ell++ d+e++vf++++
  gi|15668195|ref|NP_246987.1|   2 FNYFETTADLGVEAKGKSLEEAFKEGAKGLYNIMVDIDKVDKKEKIEFEITGEDLEELLYNFLNELLFYTDVENLVFNDFD 82 
                                   89******************************************************************************9 PP

                                   EEE.E-SSSEEEEEEEE----.-TT--------B--S---EEEEETTEEEEEEEEE CS
                      Archease  82 vdeeeeeeeleleaeargekfdkekhevqtevKAvTyhelrieeeddgweayvvvD 137
                                   v+ e+++++++l+++a+gek++kekh++++evKAvTyh+++i++e+dgw+++ +vD
  gi|15668195|ref|NP_246987.1|  83 VKIEKNDNGYRLKCTAYGEKINKEKHNIKEEVKAVTYHKMEIKQEEDGWKIRYIVD 138
                                   98889999***********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 914.38
//
Query:       gi|15668196|ref|NP_246988.1|  [L=338]
Description: RNA 3'-terminal-phosphate cyclase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.3e-81  270.4   0.0    9.5e-81  270.2   0.0    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
    1.2e-11   45.0   0.0    2.8e-11   43.9   0.0    1.6  1  RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert d


Domain annotation for each model (and alignments):
>> RTC  RNA 3'-terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.2   0.0   1.1e-84   9.5e-81       1     222 []      10     322 ..      10     322 .. 0.99

  Alignments for each domain:
  == domain 1  score: 270.2 bits;  conditional E-value: 1.1e-84
                                   STTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RTC   1 lgegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikageyevd 81 
                                   ++egGgqi+Rta++Lsalt+kpv+I nIR++Rk+ GL++qh++av++++k++naev g ++gs+el+F P++++++++++d
  gi|15668196|ref|NP_246988.1|  10 YLEGGGQIIRTAVSLSALTQKPVKIINIRKKRKNKGLAPQHVSAVKAVKKLCNAEVFGLNVGSEELTFIPSKLSPKDFTID 90 
                                   68******************************************************************************* PP

                                   EESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB-EEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RTC  82 igtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkGgGevelev 162
                                   igtAGsi+l++qtllpl l  +k++++++kGgT+v+ ap++dy+k+v+l++l++fg + +el++ krGfyp+GgGev +ev
  gi|15668196|ref|NP_246988.1|  91 IGTAGSISLVIQTLLPLSLGINKKFTVKIKGGTDVKRAPPIDYVKNVTLKILRNFG-VLTELKVLKRGFYPEGGGEVIFEV 170
                                   ********************************************************.699********************* PP

                                   E-.-S---EB....................................................................... CS
                                   xxxxxxxxxx....................................................................... RF
                           RTC 163 epskklkpie....................................................................... 172
                                   +ps k+k+++                                                                       
  gi|15668196|ref|NP_246988.1| 171 KPS-KIKKFDliehsksnlvegisyvqnldesiarrmrkkavdllnkekllpnikiecskgistgagivlwndtlggsclg 250
                                   *96.799999999******************************************************************** PP

                                   ........................BSS-HHHHHHHHHHHHHHT.-EEEEESS--HHHHHHHHHHHHHSS-EEEE CS
                                   ........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RTC 173 ........................acvDehlqdqlilfmaLakgksrirvaeltlhtetairvieqflgvkfkv 222
                                                           +++D+++ dq+i+f+a+ kg   + v+e+t+ht+t+++v+++fl+v f++
  gi|15668196|ref|NP_246988.1| 251 ekglraeivaeravnellkeresgMALDKYMGDQIIPFLAFGKG--IVGVSEITNHTKTNMWVVKHFLDVDFEI 322
                                   ******************************************99..7999**********************97 PP

>> RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   3.1e-15   2.8e-11       9     101 ..     189     270 ..     182     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 3.1e-15
                                   EEEEEEEESS-THHHHHHHHHHHHHHTTT..SSEEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEEEEEEE-TT--H CS
                    RTC_insert   9 irGvafaarvspsvanrmveaargvLnkl..lpdvyiytdvvkegkesgkspGfgisLvaetttegvllgaealgekgvpp 87 
                                   ++G++++ ++  s+a+rm ++a  +Lnk   lp+++i+         +g s G+gi+L+  t      lg+++lgekg ++
  gi|15668196|ref|NP_246988.1| 189 VEGISYVQNLDESIARRMRKKAVDLLNKEklLPNIKIECS-------KGISTGAGIVLWNDT------LGGSCLGEKGLRA 256
                                   79*************************8644888885555.......8999*********99......689********** PP

                                   HHHHHHHHHHHHHH CS
                    RTC_insert  88 edvGeeaaeeLlee 101
                                   e v+e+a++eLl+e
  gi|15668196|ref|NP_246988.1| 257 EIVAERAVNELLKE 270
                                   ************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2058.01
//
Query:       gi|15668197|ref|NP_246989.1|  [L=274]
Description: proliferating cell nuclear antigen [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-78  260.4   0.1    1.2e-77  260.1   0.1    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    1.2e-05   25.5   0.0    1.6e-05   25.1   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
    7.5e-05   23.2   0.1    0.00022   21.7   0.0    1.8  2  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
      9e-05   22.1   0.1    0.00014   21.5   0.1    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    9.6e-05   23.0   0.0    0.00019   22.0   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    0.00012   21.9   0.5    0.00017   21.4   0.5    1.2  1  Methyltransf_31  Methyltransferase domain
     0.0006   19.6   0.6      0.013   15.2   0.1    2.2  2  Met_10           Met-10+ like-protein
     0.0013   18.5   0.0     0.0022   17.8   0.0    1.5  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0037   16.7   0.2      0.016   14.7   0.1    2.0  2  Methyltransf_4   Putative methyltransferase
     0.0056   15.8   0.0      0.011   14.9   0.0    1.5  1  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
      0.011   14.8   0.0      0.019   14.0   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.019   14.3   0.0      0.038   13.3   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.021   15.1   0.1       0.03   14.6   0.1    1.3  1  DUF2431          Domain of unknown function (DUF2431)


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.1   0.1   8.5e-81   1.2e-77       2     200 .]      77     272 ..      76     272 .. 0.98

  Alignments for each domain:
  == domain 1  score: 260.1 bits;  conditional E-value: 8.5e-81
                                   HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC....E CS
               Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg..elf 80 
                                   ++L+p+e+++ilD+caaPGgKTth+a+lmknkgt+vAv+++k+R+k++++n++r+gv nti+++aD+rk++++l +  ++f
  gi|15668197|ref|NP_246989.1|  77 IVLNPREDDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKSNINRMGVLNTIIINADMRKYKDYLLKneIFF 157
                                   79***********************************************************************9988799* PP

                                   EEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTEE CS
               Methyltr_RsmB-F  81 DriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredve 161
                                   D+iLlDaPCsg+++++++++v    +e+di++++ +qkel+++ idllkk+G lvYsTCs++veEneevi+++L+kr+dve
  gi|15668197|ref|NP_246989.1| 158 DKILLDAPCSGNIIKDKNRNV----SEEDIKYCSLRQKELIDIGIDLLKKDGELVYSTCSMEVEENEEVIKYILQKRNDVE 234
                                   *********************....9******************************************************* PP

                                   EESSBSTTSTTSSECEEC..TSEEE-TTTTSS-SEEEEEEE CS
               Methyltr_RsmB-F 162 lvetelsepkglklgeea..gtlrllPhtenkdgffiaklk 200
                                   l+ ++++e+kg++++e++  gtlr++P +   ++ffiakl+
  gi|15668197|ref|NP_246989.1| 235 LIIIKANEFKGINIKEGYikGTLRVFPPN---EPFFIAKLR 272
                                   ****************99889*******9...9******96 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.2e-08   1.6e-05      24     147 ..      86     225 ..      21     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.2e-08
                                   EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS......HHHTTEEEE.....CS-CCCSSHHHHHCHCHHHSSEEEEEE CS
                          FtsJ  24 tvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm......aplpgvtti.....qgditdpetiekikealserkvdlvvs 93 
                                    ++D +aaPGg +  l+q +++kg +vav + +       ++++++ ++     ++d ++ +   + +e      +d ++ 
  gi|15668197|ref|NP_246989.1|  86 FILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTrtkalkSNINRMGVLntiiiNADMRKYKDYLLKNEI----FFDKILL 162
                                   489*****************999********999787655233322222222225555554444433343....5999999 PP

                                   --S-SS-CHHHHHHHHH.........CCCCHHHHCCHCCCCECCCEEEECCCH..CCCHHHHHHH CS
                          FtsJ  94 Dgapdvsgvhdldeylq.........sqLllaalelalkllkpggtfvlkifr..geeteallkq 147
                                   D    +sg+  +d+ ++         s   +  + ++++llk++g +v  ++    ee e+++k 
  gi|15668197|ref|NP_246989.1| 163 DAP--CSGNIIKDKNRNvseedikycSLRQKELIDIGIDLLKKDGELVYSTCSmeVEENEEVIKY 225
                                   986..777766666666668888874344566678999999999999988877544445566665 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.6e-07   0.00022      24      90 .]       5      73 ..       1      73 [. 0.84
   2 ?   -2.2   0.0       4.4     6e+03      11      38 ..     103     130 ..      97     137 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.6e-07
                                  HH-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES---....TTSHHHHTTS-EE--TTTH CS
               Methyltr_RsmF_N 24 leeprkkglRvNtlKisveeleklse..efelepvpwceeGfyleeee.rpgkhplheaGlyYiQEpSam 90
                                  ++ ++ + +RvNtlKi++e l+k  e  ++ le+  + + +f +++++ + g +p++  G+y  Q  S+m
  gi|15668197|ref|NP_246989.1|  5 YKGEKMQFIRVNTLKINPEVLKKRLEnkGVVLEK-TFLDYAFEVKKSPfSIGSTPEYLFGYYMPQSISSM 73
                                  67788899**************988864455555.7999999999986366******************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.4
                                   HHHGGGHHHHHHHHH-----EEE--TTS CS
               Methyltr_RsmF_N  11 ellgeeaeaflaaleeprkkglRvNtlK 38 
                                   +l++++ + +   ++++r+k+l+ N ++
  gi|15668197|ref|NP_246989.1| 103 QLMKNKGTIVAVEISKTRTKALKSNINR 130
                                   5566655556666778888888888766 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   9.9e-08   0.00014       3      91 ..      86     176 ..      84     243 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.9e-08
               Methyltransf_15   3 vilDlfsGaGGnviqfalv...fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpP 80 
                                    ilD+++  GG++ ++a+      +++a+ei++ + +  + N +  gv + i ++ +d+ +    l  ++i +d ++l  P
  gi|15668197|ref|NP_246989.1|  86 FILDMCAAPGGKTTHLAQLmknKGTIVAVEISKTRTKALKSNINRMGVLNTI-IINADMRKYKDYLLKNEIFFDKILLDAP 165
                                   69*************99984433479***********************999.5899************************ PP

               Methyltransf_15  81 wGGpsYkkqek 91 
                                   + G   k+++ 
  gi|15668197|ref|NP_246989.1| 166 CSGNIIKDKNR 176
                                   99988777775 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.4e-07   0.00019       1      69 [.      87     161 ..      87     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.4e-07
                                   EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS....SSTTTEEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp....fedgsfDlvv 69 
                                   +Ld+++ +G  t +la+ + +k+++++v+is++  +a ++++++ g+ n  ++++d+++++     ++  fD ++
  gi|15668197|ref|NP_246989.1|  87 ILDMCAAPGGKTTHLAQLMkNKGTIVAVEISKTRTKALKSNINRMGVlNTIIINADMRKYKdyllKNEIFFDKIL 161
                                   8*****************9669*********************99999*********997633323444666665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.5   1.3e-07   0.00017       7     127 ..      87     221 ..      81     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.3e-07
               Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.lekl.ledekfDlilsnevl. 84 
                                   +lD  ++ G +t  la+++  k+++v ++is++  +  ++n  + g+ n     +d+ + ++ l  ++  fD il ++++ 
  gi|15668197|ref|NP_246989.1|  87 ILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKSNINRMGVLNTIIINADMRKyKDYLlKNEIFFDKILLDAPCs 167
                                   89***************9999**************************************777665555779******7778 PP

               Methyltransf_31  85 .................naladpdkileeiervlkpggilliedprllaelpakveeesk 127
                                                    ++   +++ +   +++lk++g+l+ ++++       +vee+++
  gi|15668197|ref|NP_246989.1| 168 gniikdknrnvseedikYCSLRQKELIDIGIDLLKKDGELVYSTCS------MEVEENEE 221
                                   8444444444444444455555555555889***************......33333333 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   9.6e-06     0.013      99     177 ..      82     165 ..      76     183 .. 0.82
   2 ?    2.6   0.1      0.07        97      17      47 ..     215     245 ..     202     263 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.6e-06
                                   -TT-EEEETT-TTTCCHHHCCHHTTSS.EEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.....TT-EEEEE CS
                        Met_10  99 eegevVvdvfAGiGpfaipiakyskak.rvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.....eqladrvv 173
                                   +e++ ++d+ A  G  +  +a++ k+k +++a+++  +  k lk+ni++  v +++  i++D r++       e ++d+++
  gi|15668197|ref|NP_246989.1|  82 REDDFILDMCAAPGGKTTHLAQLMKNKgTIVAVEISKTRTKALKSNINRMGVLNTI-IINADMRKYKDyllknEIFFDKIL 161
                                   5778999**99999999999988766538**************************9.9******98764444455666666 PP

                                   E--T CS
                        Met_10 174 mnlp 177
                                   +++p
  gi|15668197|ref|NP_246989.1| 162 LDAP 165
                                   6665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.07
                                   TSSHHHHHHHHHHHHHSS-SCEEEE-S-SBT CS
                        Met_10  17 elkeykkvigevildktkvktvlrkvseveg 47 
                                   e++e ++vi+ ++ ++++v+ ++ k +e +g
  gi|15668197|ref|NP_246989.1| 215 EVEENEEVIKYILQKRNDVELIIIKANEFKG 245
                                   5555555554444444455555555444433 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.6e-06    0.0022      74     135 ..      84     145 ..      23     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                                   T-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGG CS
                          PCMT  74 garvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrk 135
                                    + +L++ +  G +t  la+l+++kg++v++e +k  +++ k n+++ ++ n i++ +D rk
  gi|15668197|ref|NP_246989.1|  84 DDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKSNINRMGVLNTIIINADMRK 145
                                   45699***************************************************999765 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.2e-05     0.016       4      72 ..      86     154 ..      83     163 .. 0.85
   2 ?   -0.8   0.0      0.66   9.2e+02      96     124 ..     190     218 ..     188     246 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                   EEEEET-TTSHHHHHHHH.HSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTS CS
                Methyltransf_4   4 vvleiGcGkGeflvalAk.knPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgs 72 
                                    +l+++ + G+ + +lA+ ++ + +++++Ei++++++++ ++i++ ++ N  i++ d  +  +++l +++
  gi|15668197|ref|NP_246989.1|  86 FILDMCAAPGGKTTHLAQlMKNKGTIVAVEISKTRTKALKSNINRMGVLNTIIINADM-RKYKDYLLKNE 154
                                   5799*************9446677899******************************5.66666665554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.66
                                   SHHHHHHHHHHEEEEEEEEEEESHHHHHH CS
                Methyltransf_4  96 qpellkelarvLkkgGvlelaTDveeyae 124
                                   q+el++   + Lkk G+l+  T   e+ e
  gi|15668197|ref|NP_246989.1| 190 QKELIDIGIDLLKKDGELVYSTCSMEVEE 218
                                   56667777778888888888776555443 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.8e-06     0.011      70     134 ..      83     149 ..      69     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.8e-06
                                   TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTST..TEEEEES-TTSGGGG CS
                   Fibrillarin  70 kgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRk..nivPileDArkPekY 134
                                   +++ +L + aa G    H++ +++++g++ ave s++ ++ l +  ++    n + i +D rk ++Y
  gi|15668197|ref|NP_246989.1|  83 EDDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKSNINRMGvlNTIIINADMRKYKDY 149
                                   67779999********************************998766655411444455555555555 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.4e-05     0.019      26      91 ..      79     149 ..      74     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                                   H-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHH CS
                        RrnaAD  26 lnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdeklkvvhqDflkfetp 91 
                                   ln++e++ +l++ + +G  T++La+ +      v++E+ +   k l+ +++     +  ++++D+ k++ +
  gi|15668197|ref|NP_246989.1|  79 LNPREDDFILDMCAAPGGKTTHLAQLMknkGTIVAVEISKTRTKALKSNINrmGVLNTIIINADMRKYKDY 149
                                   799************************5433589*************999965455666688888887655 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.8e-05     0.038      44     105 ..      80     141 ..      76     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.8e-05
                                   -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE- CS
               Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqa 105
                                   ++++   +lD+++  g  + +l++ +++kg++v ++i+++  k  +  +++ g+ n   ++a
  gi|15668197|ref|NP_246989.1|  80 NPREDDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKSNINRMGVLNTIIINA 141
                                   56777889************************************999999999987665555 PP

>> DUF2431  Domain of unknown function (DUF2431)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.2e-05      0.03      47     133 ..     123     216 ..      96     252 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                       DUF2431  47 eLeee......gvkvlfgVDatkleksklqeklkkek.fdriifnFPhvggkstdvnr.....qvranqeLlvsffksake 115
                                   +L+++        +++ + D +k+++      lk+e  fd+i+   P+ g  ++d+nr     ++++     ++++    +
  gi|15668197|ref|NP_246989.1| 123 ALKSNinrmgvLNTIIINADMRKYKD----YLLKNEIfFDKILLDAPCSGNIIKDKNRnvseeDIKYCSLRQKELIDIGID 199
                                   33333443333356778888888884....456777789*******************44444444443333344444455 PP

                       DUF2431 116 llsekpgeilvtlfegep 133
                                   ll+++ ge++ + ++ e 
  gi|15668197|ref|NP_246989.1| 200 LLKKD-GELVYSTCSMEV 216
                                   56666.777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 2087.32
//
Query:       gi|15668198|ref|NP_246990.1|  [L=184]
Description: hypothetical protein MJ_0027 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-17   63.6  10.8    2.3e-17   63.4  10.8    1.0  1  Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
  ------ inclusion threshold ------
        1.3    8.4  12.8        1.7    8.0  12.8    1.2  1  DUF2417          Region of unknown function (DUF2417)


Domain annotation for each model (and alignments):
>> Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4  10.8   2.6e-21   2.3e-17     103     253 ..      29     169 ..      21     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 2.6e-21
               Exosortase_EpsH 103 llfpllllllalPlpavlvaqlslpLqllvaavagfllsllgipvereGnviqlptgqveVaeaCsGlrsllallalglll 183
                                   +l ++ +++l++    ++++     L+ +v+ ++  + +++  ++ + +n+i+lp+ +veV+e+C+G     ++l++gll+
  gi|15668198|ref|NP_246990.1|  29 FLIKFYIIFLVVF---FILSYFGKYLIGIVTYLSYIFTKIIISDARLADNFIYLPNNTVEVVEECTG-----SFLIAGLLA 101
                                   3334444433333...3344444469***************9*************************.....999999999 PP

               Exosortase_EpsH 184 allfrrrlwkrklllllaavpiaflaNlvRilllvllayhygpeaaegllHeiaGw.llfgvalllllgll 253
                                   +++++ +  k  +++ ++ v++af++N++Ri+l+++l++  +pe+   l HeiaG+ +++ ++ +l++g l
  gi|15668198|ref|NP_246990.1| 102 LIIVYSKNIKE-FIIGIFFVLLAFFVNIFRIVLICYLVNM-HPESS-YLYHEIAGYgVILTLVPVLVIGYL 169
                                   99999999977.*************************997.56665.79*******777777767777665 PP

>> DUF2417  Region of unknown function (DUF2417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  12.8   0.00019       1.7      49     162 ..      29     140 ..      16     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00019
                       DUF2417  49 illlinliwlvllLisdFvslpglnnrgsgFndlalillslianllnllffglpSkldrvlnivlavLllvnllllllvky 129
                                   +l+ + +i+lv+++i +++    +     ++ + +++ + +    l+  f++lp++   v++  +  +l+  ll l++v  
  gi|15668198|ref|NP_246990.1|  29 FLIKFYIIFLVVFFILSYFG--KYLIGIVTYLSYIFTKIIISDARLADNFIYLPNNTVEVVEECTGSFLIAGLLALIIVYS 107
                                   45556678888888888884..344467889999999999999999999******************************** PP

                       DUF2417 130 tReregfvgiasvlWaaltfllgilldryvekg 162
                                    + +e ++gi++vl a+++ ++ i+l  y+ ++
  gi|15668198|ref|NP_246990.1| 108 KNIKEFIIGIFFVLLAFFVNIFRIVLICYLVNM 140
                                   ************************998888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1149  (0.0640861); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1134.60
//
Query:       gi|15668199|ref|NP_246991.1|  [L=319]
Description: thiamine monphosphate kinase ThiL [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-21   74.2   0.0    1.7e-20   73.4   0.0    1.4  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.0   9.6e-25   1.7e-20       1      93 [.      27     138 ..      27     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 9.6e-25
                                   SSSE.........EEEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.......HHHH CS
                          AIRS   1 dDaa.........vvvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp.......wlee 57 
                                   dD+a         +v+ttd     ++v++ h         iG + +++n+sD+a+mGA+Pla+l+s++l+        ++e
  gi|15668199|ref|NP_246991.1|  27 DDCAiikidenfyLVATTD-----MMVKKAHIpsilspyeIGGRILTANVSDIASMGAKPLAFLVSISLSkeeanekFIKE 102
                                   8***655555555599999.....99988888899999999**************************************** PP

                                   HHHHHHHHHHHTT-EEEEEEEEEESSEEEEEEEEEE CS
                          AIRS  58 vvrglaeaaeelgvplvgGdtsfsneptisvtavGl 93 
                                   +++gl +  + +++p+vgGdt++++e+++s ta+G+
  gi|15668199|ref|NP_246991.1| 103 LYSGLDDFSKLYDCPVVGGDTNRGDELILSGTAFGI 138
                                   ***********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1844.92
//
Query:       gi|15668200|ref|NP_246993.1|  [L=183]
Description: coenzyme F420-reducing hydrogenase subunit delta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-39  134.5   1.6    2.3e-39  134.2   1.6    1.1  1  HycI            Hydrogenase maturation protease
  ------ inclusion threshold ------
      0.046   13.6   0.0      0.074   12.9   0.0    1.3  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer


Domain annotation for each model (and alignments):
>> HycI  Hydrogenase maturation protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.2   1.6   2.5e-43   2.3e-39       1     130 []      45     179 ..      45     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 2.5e-43
                                   HHHHHHHHHHEC--T..TEEEEEECT-SGGGHHHHCC....-SEEEEEEE--SSS-TT-EEEEECCHHHHHHTTC.CGCCC CS
                          HycI   1 vrvvekLkrryefke..nvtviDgGtqglelvgtlee....adkliivDavdfglepGevkiikddevpkklkakkmsaHq 75 
                                   v+v+ekL++ +++ke  +++++D+G++++++v tl +    ++k+i+vD++d+g +pGe+kii++de+p+  k+++++ H+
  gi|15668200|ref|NP_246993.1|  45 VHVIEKLNKILTDKEkqKIALVDAGAGAPQQVLTLIDenskTKKIIVVDVIDWGIKPGEIKIIEKDELPN-PKYHRLDSHD 124
                                   89**********999999**************99998899*****************************7.********** PP

                                   HCHHHHHHHHHHCCS--SEEEEEEE--S-BST.CCS--HHHHCCHHHHHHHCCCH CS
                          HycI  76 lplaevlklleekgeipkevillgvqpesledvgielseevkkavekavelilee 130
                                   +pla++l++++ek++i+++v++++++++s +dv+i+lseev+kav+kave+il+e
  gi|15668200|ref|NP_246993.1| 125 WPLAPLLREVAEKYNIEVKVVGCQAKYISEPDVYIGLSEEVEKAVDKAVEIILRE 179
                                   ****************************************************985 PP

>> Topo-VIb_trans  Topoisomerase VI B subunit, transducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.3e-06     0.074      95     144 ..     132     181 ..     118     183 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.3e-06
                Topo-VIb_trans  95 eqpedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLk 144
                                   ++ ++++ + v+v++ +  + se   +i+  ee+ek +++a++ + r+L+
  gi|15668200|ref|NP_246993.1| 132 REVAEKYNIEVKVVGCQAKYISEPDVYIGLSEEVEKAVDKAVEIILRELR 181
                                   456779999***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1111.07
//
Query:       gi|15668201|ref|NP_246994.1|  [L=230]
Description: coenzyme F420-reducing hydrogenase subunit gamma [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-32  111.6   3.4    2.3e-32  111.6   3.4    2.2  3  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
    1.4e-10   40.5  13.1    1.5e-08   34.1   2.6    3.5  3  Fer4         4Fe-4S binding domain
    3.4e-09   36.4  11.4    1.1e-05   25.3   2.2    2.9  2  Fer4_6       4Fe-4S binding domain
    1.7e-07   31.2  10.5    1.7e-07   31.2  10.5    2.4  2  Fer4_10      4Fe-4S dicluster domain
    2.2e-06   27.7  26.2    1.2e-05   25.4  12.5    2.7  2  Fer4_9       4Fe-4S dicluster domain
    2.7e-06   27.4  24.5    2.7e-05   24.2  11.9    3.0  3  Fer4_21      4Fe-4S dicluster domain
      1e-05   26.0  13.5      1e-05   26.0  13.5    3.0  3  Fer4_7       4Fe-4S dicluster domain
    2.9e-05   24.9  10.1     0.0013   19.7   1.3    3.0  2  Fer4_16      4Fe-4S double cluster binding domain
    0.00021   21.2   2.9    0.00021   21.2   2.9    3.5  2  Fer4_2       4Fe-4S binding domain
     0.0083   16.6  14.3      0.079   13.5   2.2    3.6  4  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
       0.01   16.3   3.3       0.01   16.3   3.3    3.6  2  Fer4_4       4Fe-4S binding domain
      0.019   15.7   0.6      0.019   15.7   0.6    3.3  3  Fer4_15      4Fe-4S single cluster domain
        2.5    8.7  26.3       0.56   10.8   3.6    3.4  3  Fer4_17      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6   3.4   1.7e-35   2.3e-32       1     130 [.      15     141 ..      15     142 .. 0.92
   2 ?   -2.0   2.3       2.2     3e+03      75      85 ..     177     187 ..     163     204 .. 0.75
   3 ?   -3.1   0.2       4.6   6.4e+03      76      85 ..     207     216 ..     203     218 .. 0.75

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 1.7e-35
                                   -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESH CS
                   Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGt 81 
                                   C Gc +sl++++e+lld+l+ iel+y +++lad++    e++  e+d+++veG+v+ ++++ le+++e+++kak+v+a+G+
  gi|15668201|ref|NP_246994.1|  15 CCGCLVSLADTYEKLLDVLNSIELVY-CQTLADAR----EIP--ECDIALVEGSVCLDDHHSLEVAQEVRKKAKIVVALGA 88 
                                   99************************.88889999....778..8************************************ PP

                                   HHHH-TGGGSTT-T..EE-..HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHH CS
                   Oxidored_q6  82 CAafGGipaaannp..svg..eevgellevvpvdinipGCPphpeailetlla 130
                                   CAa+GG+++  +    s+   +++++l ev++vd+ ipGCPp+peai+++++a
  gi|15668201|ref|NP_246994.1|  89 CAATGGVTRYCKGNqlSKPvhSSFSPLTEVIKVDLAIPGCPPSPEAIVGVITA 141
                                   ********88776534332468899*************************987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                                   EEEEESHHHHH CS
                   Oxidored_q6  75 aviavGtCAaf 85 
                                   +++ +GtCAa 
  gi|15668201|ref|NP_246994.1| 177 LCMGCGTCAAA 187
                                   56788999986 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4.6
                                   EEEESHHHHH CS
                   Oxidored_q6  76 viavGtCAaf 85 
                                   +i +G+C+++
  gi|15668201|ref|NP_246994.1| 207 CIKCGACSVQ 216
                                   6788888875 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3       7.3     1e+04      17      23 ..     163     169 ..     162     170 .. 0.58
   2 !   34.1   2.6   1.1e-11   1.5e-08       2      24 .]     172     194 ..     171     194 .. 0.95
   3 !   19.0   3.0   6.4e-07   0.00088       3      19 ..     202     218 ..     200     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7.3
                                   HSTTTEE CS
                          Fer4  17 vCPvgAI 23 
                                   +C  ++I
  gi|15668201|ref|NP_246994.1| 163 ACGCDVI 169
                                   6666665 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 1.1e-11
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   v+++++C+gCG+C+ +CP+ AI+
  gi|15668201|ref|NP_246994.1| 172 VVNKSLCMGCGTCAAACPTRAIE 194
                                   79*******************96 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 6.4e-07
                                   EETTTSSS-THHHHHST CS
                          Fer4   3 ideekCigCGaCvevCP 19 
                                   + +e+Ci+CGaC   CP
  gi|15668201|ref|NP_246994.1| 202 VLKELCIKCGACSVQCP 218
                                   5679************* PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   2.2   7.7e-09   1.1e-05       3      24 .]     172     193 ..     171     193 .. 0.95
   2 !   15.1   1.9   1.3e-05     0.018       6      20 ..     204     218 ..     200     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 7.7e-09
                        Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                   ++++++C gCg C+++CP+ ai
  gi|15668201|ref|NP_246994.1| 172 VVNKSLCMGCGTCAAACPTRAI 193
                                   699****************998 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.3e-05
                        Fer4_6   6 pdkCigCgdCvrvCP 20 
                                   +++Ci Cg+C + CP
  gi|15668201|ref|NP_246994.1| 204 KELCIKCGACSVQCP 218
                                   689***********9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       2.4   3.4e+03      31      49 ..      75      93 ..      60     100 .. 0.65
   2 !   31.2  10.5   1.2e-10   1.7e-07       3      56 .]     172     218 ..     170     218 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.4
                       Fer4_10 31 easeeeavrkkvekCtgcg 49
                                  e  +++++ +++++C + g
  gi|15668201|ref|NP_246994.1| 75 EVRKKAKIVVALGACAATG 93
                                  4455666667777777665 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 1.2e-10
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   v++++ C++Cg+C +aCP+       +++++ +++ ++  e C++cgaC  +CP
  gi|15668201|ref|NP_246994.1| 172 VVNKSLCMGCGTCAAACPT-------RAIEMLDGRPNVLKELCIKCGACSVQCP 218
                                   678999*************.......9**************************9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   5.8   1.2e-05     0.016      33      51 .]     175     193 ..     148     193 .. 0.78
   2 !   25.4  12.5   8.6e-09   1.2e-05       2      48 ..     178     219 ..     177     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                        Fer4_9  33 eeaCigCgaCveaCpkgai 51 
                                   ++ C+gCg+C++aCp+ ai
  gi|15668201|ref|NP_246994.1| 175 KSLCMGCGTCAAACPTRAI 193
                                   368************9987 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 8.6e-09
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                                   C+gCg+C +aCp+ ++++ +++  +  +      Ci+CgaC   Cp+
  gi|15668201|ref|NP_246994.1| 178 CMGCGTCAAACPTRAIEMLDGRPNVLKE-----LCIKCGACSVQCPR 219
                                   ****************888887777753.....6************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.7       1.3   1.7e+03      37      44 ..      11      18 ..       2      32 .. 0.67
   2 !   16.1   4.7   6.5e-06     0.009      35      59 .]     172     195 ..     153     195 .. 0.81
   3 !   24.2  11.9   1.9e-08   2.7e-05       2      52 ..     172     218 ..     171     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.3
                       Fer4_21 37 vedeCvGC 44
                                  +  +C GC
  gi|15668201|ref|NP_246994.1| 11 QLCSCCGC 18
                                  44456666 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 6.5e-06
                       Fer4_21  35 kvvedeCvGCnlCssvCPvedciem 59 
                                    v ++ C+GC  C++ CP+  +iem
  gi|15668201|ref|NP_246994.1| 172 VVNKSLCMGCGTCAAACPT-RAIEM 195
                                   4568899999999999996.89988 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 1.9e-08
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                   +++++ C+gCg C+ aC++    aie+ + +  +v+++ C+ C  Cs  CP
  gi|15668201|ref|NP_246994.1| 172 VVNKSLCMGCGTCAAACPT---RAIEMLDGR-PNVLKELCIKCGACSVQCP 218
                                   58999*************6...677665444.4899*************** PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       2.4   3.3e+03      23      39 ..      74      90 ..      35     102 .. 0.62
   2 !   26.0  13.5   7.5e-09     1e-05       2      49 ..     178     218 ..     177     220 .. 0.93
   3 !   10.7   4.0   0.00046      0.64       2      14 ..     207     219 ..     206     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.4
                        Fer4_7 23 enekgtekveidpekCl 39
                                  ++ ++++k+++    C 
  gi|15668201|ref|NP_246994.1| 74 QEVRKKAKIVVALGACA 90
                                  33334445555555554 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 7.5e-09
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                   C+gCg C+aaCp++aie+ +        ++++  e C+ CgaC   CP
  gi|15668201|ref|NP_246994.1| 178 CMGCGTCAAACPTRAIEMLDG-------RPNVLKELCIKCGACSVQCP 218
                                   ******************774.......68999*************** PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00046
                        Fer4_7   2 CigCgaCvaaCpv 14 
                                   Ci+CgaC + Cp 
  gi|15668201|ref|NP_246994.1| 207 CIKCGACSVQCPR 219
                                   9**********94 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.3   9.1e-07    0.0013       2      19 ..     178     195 ..     177     203 .. 0.91
   2 !    8.8   2.0    0.0023       3.2       2      14 ..     207     219 ..     206     227 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.1e-07
                       Fer4_16   2 CgtCgkCaevCPtnaike 19 
                                   C +Cg Ca +CPt+ai++
  gi|15668201|ref|NP_246994.1| 178 CMGCGTCAAACPTRAIEM 195
                                   ****************85 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0023
                       Fer4_16   2 CgtCgkCaevCPt 14 
                                   C++Cg+C   CP 
  gi|15668201|ref|NP_246994.1| 207 CIKCGACSVQCPR 219
                                   ************6 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   2.9   1.5e-07   0.00021       4      22 .]     172     190 ..     170     190 .. 0.92
   2 !   12.1   2.9   0.00012      0.17       7      21 ..     204     218 ..     200     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.5e-07
                        Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                   vv+   C+gCg+C  aCP+
  gi|15668201|ref|NP_246994.1| 172 VVNKSLCMGCGTCAAACPT 190
                                   689999************7 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00012
                        Fer4_2   7 tdrCigCgaCvsaCP 21 
                                    + Ci CgaC   CP
  gi|15668201|ref|NP_246994.1| 204 KELCIKCGACSVQCP 218
                                   578*******555*9 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.5   4.8e+03      40      52 ..     117     129 ..     107     131 .. 0.81
   2 ?   -2.3   0.0       4.8   6.6e+03      42      56 ..     155     169 ..     148     170 .. 0.80
   3 !   13.5   2.2   5.7e-05     0.079       1      18 [.     173     190 ..     173     191 .. 0.94
   4 !    8.9   1.6    0.0016       2.2       3      19 ..     204     220 ..     202     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.5
                       Fer4_13  40 ekadaeeAadaCP 52 
                                   e  ++  A+ +CP
  gi|15668201|ref|NP_246994.1| 117 EVIKVDLAIPGCP 129
                                   56678899999*9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.8
                       Fer4_13  42 adaeeAadaCPvesI 56 
                                   ++ae+  +aC  + I
  gi|15668201|ref|NP_246994.1| 155 ELAEKGSEACGCDVI 169
                                   678888899998877 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 5.7e-05
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   V+++ C++cg+C++++P 
  gi|15668201|ref|NP_246994.1| 173 VNKSLCMGCGTCAAACPT 190
                                   8999*************5 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0016
                       Fer4_13   3 rdtCiacgaCvelaPdv 19 
                                   ++ Ci cgaC   +P +
  gi|15668201|ref|NP_246994.1| 204 KELCIKCGACSVQCPRI 220
                                   578************75 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   3.3   7.3e-06      0.01       2      17 .]     176     191 ..     175     191 .. 0.88
   2 ?    9.3   3.7    0.0013       1.8       1      15 [.     204     218 ..     204     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.3e-06
                        Fer4_4   2 erCigCgsCvaaCPqg 17 
                                   + C gCg C aaCP++
  gi|15668201|ref|NP_246994.1| 176 SLCMGCGTCAAACPTR 191
                                   56************85 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0013
                        Fer4_4   1 qerCigCgsCvaaCP 15 
                                   +e Ci Cg+C   CP
  gi|15668201|ref|NP_246994.1| 204 KELCIKCGACSVQCP 218
                                   588***********9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   2.1       9.3   1.3e+04       8      33 ..      13      37 ..      11      81 .. 0.60
   2 ?   15.7   0.6   1.4e-05     0.019       2      31 ..     172     201 ..     172     205 .. 0.79
   3 ?    5.7   1.9     0.019        26       5      20 ..     204     219 ..     201     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.3
                       Fer4_15  8 CigcglCvaeapevfeldedglasvl 33
                                  C  cg  v +a+++ +l  d l+s+ 
  gi|15668201|ref|NP_246994.1| 13 CSCCGCLVSLADTYEKLL-DVLNSIE 37
                                  666665555555555554.5555555 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.4e-05
                       Fer4_15   2 vvDrdaCigcglCvaeapevfeldedglas 31 
                                   vv++++C+gcg C+a++p++  +  dg + 
  gi|15668201|ref|NP_246994.1| 172 VVNKSLCMGCGTCAAACPTRAIEMLDGRPN 201
                                   5899*************9876555566665 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.019
                       Fer4_15   5 rdaCigcglCvaeape 20 
                                   +++Ci cg+C   +p+
  gi|15668201|ref|NP_246994.1| 204 KELCIKCGACSVQCPR 219
                                   589***********85 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.7         3   4.1e+03      44      50 ..      11      17 ..       4      20 .. 0.73
   2 ?    9.9   5.4   0.00079       1.1      44      58 ..     176     190 ..     158     193 .. 0.86
   3 ?   10.8   3.6    0.0004      0.56      44      57 ..     205     218 ..     191     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3
                       Fer4_17 44 slCieCg 50
                                  +lC++Cg
  gi|15668201|ref|NP_246994.1| 11 QLCSCCG 17
                                  6777776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00079
                       Fer4_17  44 slCieCgeCerkCPq 58 
                                   slC++Cg C+++CP 
  gi|15668201|ref|NP_246994.1| 176 SLCMGCGTCAAACPT 190
                                   789999999999996 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0004
                       Fer4_17  44 slCieCgeCerkCP 57 
                                   +lCi+Cg C+ +CP
  gi|15668201|ref|NP_246994.1| 205 ELCIKCGACSVQCP 218
                                   78999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1491.36
//
Query:       gi|15668202|ref|NP_246995.1|  [L=287]
Description: coenzyme F420-reducing hydrogenase subunit beta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-48  164.0   0.1    3.3e-48  163.4   0.1    1.3  1  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    9.6e-26   89.7   0.1    1.5e-25   89.1   0.1    1.3  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   0.1   3.7e-52   3.3e-48       2     154 ..     100     252 ..      99     253 .. 0.98

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 3.7e-52
                   FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqk.....kklkekilltiglfCggnfspealrk.lleelgvdpedvkklefrgkgkfrvelkd 76 
                                   +k++vvGtPCq++a+rkl+k     +++ +ki+l+ig+fC++nf + +l+  ++e++gv++edv+k+++ gkgkf+v+++ 
  gi|15668202|ref|NP_246995.1| 100 EKIGVVGTPCQVRAVRKLMKypvgfRHVPDKIALIIGIFCMENFPYYGLKLiVEEHCGVKMEDVVKMDI-GKGKFWVYTRW 179
                                   79***********************99************************999***************.*******9999 PP

                   FrhB_FdhB_C  77 ..ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveageleleelde 154
                                     +k i+lke++ +++ +C+vC+d+taelADis+G+v      g +++g+stv++rt+kgee+++k+ve+g+le+++++e
  gi|15668202|ref|NP_246995.1| 180 geTKAIKLKETHPYEQIACHVCTDYTAELADISTGSV------G-SPDGWSTVFIRTAKGEEIFNKMVEDGYLEVKPIEE 252
                                   9999*********************************......9.********************************986 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.1   1.7e-29   1.5e-25       1      78 []      15      91 ..      15      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 1.7e-29
                   FrhB_FdhB_N  1 vvaArstdkeirkkaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYtlspnlklLk 78
                                  vv+Arst ke++kkaq+GGiv++ ++y Le+++ dgviv+++   +++++p +att+ee+l+aaG+kYt++pn+++Lk
  gi|15668202|ref|NP_246995.1| 15 VVSARSTLKEVLKKAQDGGIVSTAFIYGLENNLLDGVIVADNA-GEFKAVPKVATTPEEVLEAAGTKYTVCPNISVLK 91
                                  689**************************************99.479*****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 2157.89
//
Query:       gi|15668203|ref|NP_246996.1|  [L=539]
Description: succinate dehydrogenase flavoprotein subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     5e-102  342.1   0.1   6.4e-102  341.7   0.1    1.1  1  FAD_binding_2   FAD binding domain
    1.9e-24   86.1   0.1    4.2e-24   84.9   0.1    1.5  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    8.8e-06   25.1   2.6    0.00012   21.5   2.6    2.5  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.7   0.1  1.1e-105  6.4e-102       1     417 []       4     374 ..       4     374 .. 0.98

  Alignments for each domain:
  == domain 1  score: 341.7 bits;  conditional E-value: 1.1e-105
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-HHH CS
                 FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldeladqpl 81 
                                   D+++iG+G+A  +AA+e+++++  ++ v+  + ++g t++++Gg +av +        kds ++h++dt+k+++  ++++l
  gi|15668203|ref|NP_246996.1|   4 DILIIGGGGAAARAAIECRDKNV-IIAVKGLFGKSGCTVMAEGGYNAVFN-------PKDSFKKHFYDTVKGGGFINNPKL 76 
                                   99****************99888.8899999******************3.......359********************* PP

                                   HHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCT.EEEEES CS
                 FAD_binding_2  82 veafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarkag.vdfqer 161
                                   ve++v++ap+++  Le++g+ f+rtedg +++r++Gg+s + rt++ ++d+      tgh+++  l+e++ k + ++++e+
  gi|15668203|ref|NP_246996.1|  77 VEILVKNAPKELLNLERFGALFDRTEDGFIAQRPFGGQSFN-RTCY-CGDR------TGHEIMRGLMEYISKFErIKILEE 149
                                   *****************************************.****.****......****************9******* PP

                                   EEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S-HHHHHHHCTTSSEES CS
                 FAD_binding_2 162 teadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtGdglalalragaalnd 242
                                     a +Liv+d+r++Ga++ ++++g+++ i aka++latgG+g+           +  t+n+ + tGdg a+a+  ga+l d
  gi|15668203|ref|NP_246996.1| 150 VMAIKLIVKDNRCYGAIFLDLKTGNIFPIFAKATILATGGAGQ----------LYPITSNPIQKTGDGFAIAYNEGAELID 220
                                   *******************************************..........**************************** PP

                                   ..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH.......GGGS-HHHHHHHHH.HHHHTTTS.CCBEEE CS
                 FAD_binding_2 243 drmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm.......nelasrdvvsrailekeiaeggs.eanvyl 315
                                     me+vqfhPt++v    g+giL+tea+rgeGgil++k  +rFm       +el +rdvv+rai  kei+eg++ +  vyl
  gi|15668203|ref|NP_246996.1| 221 --MEMVQFHPTGMV----GTGILVTEAVRGEGGILYNKYKERFMvrydkerMELSTRDVVARAIY-KEIQEGRGvNGGVYL 294
                                   ..************....***********************************************.99*999999889*** PP

                                   E-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEEEES-EEEBETTSBESTTEEESSBTEE CS
                 FAD_binding_2 316 dashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqhytmgGvetdengrvldadgqpipGLY 396
                                   d+sh l+ e +e++le++ +++ + ++      id++++p+        v+p++h +mgG++++e++++      +i GL+
  gi|15668203|ref|NP_246996.1| 295 DVSH-LPNEVIEKKLETMLKQFLR-VG------IDIRKEPMI-------VSPTAHHFMGGLKINERCET------NIIGLF 354
                                   ****.************8888888.88......*********.......********************......****** PP

                                   E-STCEESSSSTTS--TTHHH CS
                 FAD_binding_2 397 AaGevaaggvhganrlgGnsl 417
                                   A+Gev+ ggvhganrlgGn l
  gi|15668203|ref|NP_246996.1| 355 ACGEVT-GGVHGANRLGGNAL 374
                                   ******.************87 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.1   7.1e-28   4.2e-24       3     100 ..     428     519 ..     427     535 .. 0.88

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 7.1e-28
                                   HHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-BTTBEB CS
                Succ_DH_flav_C   3 eLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESrGaHar 83 
                                   +L+k+m+++v++ R+e+gLk+al++++e++++++nvkv++       +l ++ el+n++ +A++++ksAl RkESrGaH+r
  gi|15668203|ref|NP_246996.1| 428 DLRKVMWDYVSIIRNEDGLKKALEKIDEIERNIDNVKVNGII-----DLQNYFELKNMVVVAKLVTKSALYRKESRGAHYR 503
                                   799***********************************8765.....79999***************************** PP

                                   TTS-SEETTT-SEEEEE CS
                Succ_DH_flav_C  84 edfperdDenwlkhtla 100
                                   edfpe + e+w+   ++
  gi|15668203|ref|NP_246996.1| 504 EDFPETK-EEWRGNIII 519
                                   ****655.588877766 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   2.6     2e-08   0.00012       2     280 ..       4     362 ..       3     375 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2e-08
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH.HC.HHHHHHHHHHHHH....................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxx....................... RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll.sk.allgvaedaeias....................... 57 
                                   d+++iGgG A+ +aa++ + +++ +++ +    +   gc + ++  + +v  +++ ++                       
  gi|15668203|ref|NP_246996.1|   4 DILIIGGGGAAARAAIECRDKNVIIAVKG---LFGKSGCTVmAEgGYNAVFNPKDSFKkhfydtvkgggfinnpklveilv 81 
                                   89******************988888875...3333333332221222222222222244456777777777888888888 PP

                                   ......................................................HHHHCHHHHCCCCHCCTCEEEEESCEE CS
                                   ......................................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 ......................................................evvkklnqgielllgeevvkidpgkkk 84 
                                                                                         e ++k++  i+ l ++ ++k++     
  gi|15668203|ref|NP_246996.1|  82 knapkellnlerfgalfdrtedgfiaqrpfggqsfnrtcycgdrtgheimrglmEYISKFER-IKILEEVMAIKLI----- 156
                                   88888899999********************************9988877777755555553.4444443333333..... PP

                                   EEETEEEC..........TCEEEEEESEEEE---EEE-BCTCTTC....TTBEECCSECHHHHHHCCSS-T.SEEEEES-S CS
                                   xxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                   Pyr_redox_2  85 vklekkke..........gdeekiaydklvlAtGssprdlgipGv...aenvgklvrtldsaealklkllp.krivvvGgG 151
                                     ++++++          g+ + i +++ +lAtG+   + +i      +++ g+ + + + ae +  ++++   +  vG G
  gi|15668203|ref|NP_246996.1| 157 --VKDNRCygaifldlktGNIFPIFAKATILATGGAGQLYPITSNpiqKTGDGFAIAYNEGAELIDMEMVQfHPTGMVGTG 235
                                   ..2222224444444444****************988888888777777888888899999999999999999999***99 PP

                                   HHHHHHHHH.....HHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEE CS
                                   xxxxxxxxx.....xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 152 yiGvElAaa.....laklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeei 226
                                      +E         ++k++++  + ++ +r+  ++ d  ++a+++e  e +Gv+  +     ++   ++  ev++++ e++
  gi|15668203|ref|NP_246996.1| 236 ILVTEAVRGeggilYNKYKERFMVRYDKERMElSTRDVVARAIYKEIQEGRGVNGGVY---LDVSHLPN--EVIEKKLETM 311
                                   888877555666668999888888888888889999999**************97744...45555555..5777777776 PP

                                   EESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 227 dadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvagg 280
                                     + + v++ +r ++ ++           gg++++e+++tn+ g++a+G v+gg
  gi|15668203|ref|NP_246996.1| 312 LKQFLRVGIDIRKEPMIV-SPTAH--HFMGGLKINERCETNIIGLFACGEVTGG 362
                                   666665555555555554.33333..347**********************933 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 3196.53
//
Query:       gi|15668204|ref|NP_246997.1|  [L=316]
Description: hypothetical protein MJ_0034 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-35  122.5   0.9      3e-35  121.9   0.9    1.3  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.9   0.9   1.7e-39     3e-35       5     218 .]      91     312 ..      87     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 1.7e-39
                       UPF0051   5 rtlivveegaevtiieeyagc...........gvveifvgenAklkyvkvqnw..sedavnlstkra..eegr..daklel 68 
                                    + i++ee+++++++   ++c           ++  i +g+nAk++y + +++  ++d+++ +t+++  +eg+   ++++l
  gi|15668204|ref|NP_246997.1|  91 DVEIILEEDSSISLM---SHCsfpkgkgikhiMNGIIKIGKNAKFSYNEFHYHgmDGDILVKPTVKVeiDEGGiyISNFTL 168
                                   6789***********...7777777777787799999****************7777999999999944444477778888 PP

                       UPF0051  69 ttvslggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaq 149
                                   t++++g   + +     ++ ++a +++++ ++a +++ ++++  v++ng+n+++ i+s+g++ d+++++ + ki  + +a 
  gi|15668204|ref|NP_246997.1| 169 TKGRIGTLDIEQ---EIIAKKDAIIDITTRTYAIKEDVVKVNEVVKLNGENAKCIIKSRGAAMDNSKISLKLKI--EGNAP 244
                                   888888876666...345669*********************************************99998888..***** PP

                       UPF0051 150 ktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                    +++h+++  ++ ++ a++++iP++ ++ d+++++H+A++G++d++ql  Lm++Gl+e+eA+++iv+g+
  gi|15668204|ref|NP_246997.1| 245 YSKGHIDCAEIVKGN-AEVESIPIVVVRDDKARITHEAAIGSVDKKQLETLMAKGLDEDEATEIIVKGM 312
                                   **************8.***************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1979.40
//
Query:       gi|15668205|ref|NP_246998.1|  [L=250]
Description: ABC transporter [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-26   94.1   0.0    1.3e-26   93.7   0.0    1.1  1  ABC_tran     ABC transporter
    2.7e-12   46.6   0.0    3.5e-12   46.2   0.0    1.1  1  SMC_N        RecF/RecN/SMC N terminal domain
      6e-08   32.8   0.2     0.0018   18.2   0.2    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00016   22.2   0.2    0.00023   21.7   0.2    1.3  1  AAA_23       AAA domain
    0.00058   19.5   0.0     0.0011   18.6   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0048   16.5   0.0     0.0083   15.7   0.0    1.3  1  AAA_27       AAA domain
  ------ inclusion threshold ------
      0.019   14.7   0.3      0.041   13.6   0.3    1.4  1  AAA_15       AAA ATPase domain
      0.024   14.9   0.1       0.96    9.7   0.0    2.2  2  AAA_22       AAA domain
      0.056   13.2   0.1       0.18   11.5   0.0    1.8  2  IstB_IS21    IstB-like ATP binding protein
      0.073   13.0   0.0       0.15   12.0   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
      0.082   12.5   0.0       0.16   11.5   0.0    1.7  1  AAA_25       AAA domain
      0.085   12.6   0.2       0.23   11.2   0.1    1.7  2  AAA_24       AAA domain
      0.094   12.9   0.0       0.32   11.1   0.0    2.0  1  AAA_33       AAA domain
        0.1   13.1   1.5        2.5    8.7   1.5    2.6  1  AAA_18       AAA domain
       0.15   11.5   0.0       0.24   10.8   0.0    1.3  1  PhoH         PhoH-like protein
        0.3   11.5   1.0        1.1    9.7   1.0    2.1  1  AAA          ATPase family associated with various cellular a
       0.36   11.1   0.1       0.36   11.1   0.1    2.1  1  zf-HC2       Putative zinc-finger


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.0   1.3e-29   1.3e-26       1     136 [.      22     173 ..      22     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 1.3e-29
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTS..S--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagl..lkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvre 78 
                                   lk v+l+++e+e++ai+G+nGaGKStL+ +++g   +kpt+G+i ++g d+ + + +e++r  +    qep  f++++v++
  gi|15668205|ref|NP_246998.1|  22 LKGVNLTVEENEIHAIIGPNGAGKSTLAYTIMGIsgYKPTKGRIIFKGVDIIDkNITERARMGMTLAWQEPARFEGIKVKN 102
                                   799****************************99744799********999988678899999***************9988 PP

                                   H..............HHHTCHHHHHHHSTTGGTT.CBGESTTS.GGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   x..............xxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  79 n..............esdeeiekalsklglkelk.dtvvkssp.ssLSgGqkqrvalarallkkpkllllDEpt 136
                                                   +    ek+++ l+l++l+ d+ +++   ++LSgG+++r++la +++ +p+l +lDEp 
  gi|15668205|ref|NP_246998.1| 103 YlmlgmnekykkdkeIA---EEKIREALKLVNLDpDKYLDRYVdETLSGGERKRIELASIICMEPDLAILDEPD 173
                                   8*****99985433333...445555555555330555655557****************************95 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   3.3e-15   3.5e-12      23     211 ..      31     217 ..       4     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 3.3e-15
                                   TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrv 103
                                   ++++ ai+GpNG+GKs l   i   +G + +k  + + + + +    +k+ +++a++ +t+  ++ +   + e ++++  +
  gi|15668205|ref|NP_246998.1|  31 ENEIHAIIGPNGAGKSTLAYTI---MGISGYKPTKGRIIFKGVDI-IDKNITERARMGMTLAWQEPA---RFEGIKVKNYL 104
                                   45799*****************...88777766665554444443.666888889988887655554...66889999999 PP

                                   ETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 104 krkgeseykingkevtkkevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                   + + + +yk + ke+ +++++e l+ ++++++         +LSgGe++ + la ++ ++      l +lDe d+ +D   
  gi|15668205|ref|NP_246998.1| 105 MLGMNEKYKKD-KEIAEEKIREALKLVNLDPDkyldryvdeTLSGGERKRIELASIICME----PDLAILDEPDSGIDIVS 180
                                   99999888865.5677789********************************999886543....4599**********876 PP

                                   H...HHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                   x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 176 v...kkvaellkeksknaQfivislreemlekadklvgv 211
                                       k+v ++lk k   + ++vi++ree+ e+ad++  +
  gi|15668205|ref|NP_246998.1| 181 FdeiKRVFDYLKDKG--CSLLVITHREELAEHADRVSLI 217
                                   500055555555555..9****************98765 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   1.7e-06    0.0018       1      25 [.      34      58 ..      34      84 .. 0.72
   2 !   13.0   0.0   6.3e-05     0.067     237     298 ..     144     204 ..      86     209 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                  + ++iGpNg+GKS+L +++ +++++
  gi|15668205|ref|NP_246998.1| 34 IHAIIGPNGAGKSTLAYTIMGISGY 58
                                  579************9999777654 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.3e-05
                        AAA_21 237 l..SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                   +  S G ++ + l++++   +   +l ++DEp++g++     ++ +++++l+++g  +++ TH 
  gi|15668205|ref|NP_246998.1| 144 EtlSGGERKRIELASIICMEP---DLAILDEPDSGIDIVSFDEIKRVFDYLKDKGCSLLVITHR 204
                                   335999999988888888888...99************999**********************5 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   2.2e-07   0.00023      17     125 ..      27     146 ..       7     194 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.2e-07
                        AAA_23  17 F...skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkay.velt......fenkdgryt 87 
                                   +   ++ + +I+GpNGaGK+T+   i  + + + p+ +r   +g    d +i+ +   ++  ++l       fe ++ ++ 
  gi|15668205|ref|NP_246998.1|  27 LtveENEIHAIIGPNGAGKSTLAYTIMGISGYK-PTKGRIIFKGVDIIDKNITER---ARMgMTLAwqeparFEGIKVKN- 102
                                   3445678999************99998777664.445555544444444444333...2223444455555566655553. PP

                        AAA_23  88 rsiererelskkkgkttkkaklellei......deleqfisell 125
                                   + +  + e++kk+++   ++++e l+       + l+++++e l
  gi|15668205|ref|NP_246998.1| 103 YLMLGMNEKYKKDKEIAEEKIREALKLvnldpdKYLDRYVDETL 146
                                   44444555555554444444444444444355555566666644 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06    0.0011      13      38 ..      23      48 ..      14      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTl 38
                                  +g  +++++++++ ++Gp+G+GKSTl
  gi|15668205|ref|NP_246998.1| 23 KGVNLTVEENEIHAIIGPNGAGKSTL 48
                                  56778889888**************9 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   7.9e-06    0.0083      19      45 ..      25      51 ..      19      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.9e-06
                        AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrA 45
                                  +++  ee+++h i+GpN AGKst+   
  gi|15668205|ref|NP_246998.1| 25 VNLTVEENEIHAIIGPNGAGKSTLAYT 51
                                  5677789****************8755 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   3.9e-05     0.041      23      48 ..      31      57 ..      22     144 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
                        AAA_15 23 ee.ltvliGkNnsGKSsilealdlFln 48
                                  e+ +  +iG+N++GKS++++ +  +  
  gi|15668205|ref|NP_246998.1| 31 ENeIHAIIGPNGAGKSTLAYTIMGISG 57
                                  44499**************99954444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00091      0.96       6      23 ..      33      50 ..      29      56 .. 0.84
   2 ?    3.2   0.0     0.097     1e+02      91     132 ..     163     206 ..     111     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00091
                        AAA_22  6 gilvvtGesGtGKTtllr 23
                                   i +++G+ G+GK+tl+ 
  gi|15668205|ref|NP_246998.1| 33 EIHAIIGPNGAGKSTLAY 50
                                  5779***********985 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.097
                        AAA_22  91 vielliiDEaqh.lrseealeeLrsllnl.srkgvqliLvGtp.e 132
                                    + l i+DE +  +     + e+++ ++  ++kg++l+++ ++ e
  gi|15668205|ref|NP_246998.1| 163 EPDLAILDEPDSgI-DIVSFDEIKRVFDYlKDKGCSLLVITHReE 206
                                   37899*******99.899999999999999999999988877655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.18      44      72 ..      29      58 ..      18      89 .. 0.77
   2 ?   -1.5   0.0       1.6   1.7e+03     107     137 ..     162     194 ..     147     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                     IstB_IS21 44 iekkenivllGpsGvGKshlaia.lgveav 72
                                  +e++e  +++Gp G+GKs la + +g ++ 
  gi|15668205|ref|NP_246998.1| 29 VEENEIHAIIGPNGAGKSTLAYTiMGISGY 58
                                  67888899*************872465555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                     IstB_IS21 107 lkvdllilD..dlgllpldqaeaellfeviekr 137
                                   +++dl ilD  d g+  ++ +e + +f+ ++++
  gi|15668205|ref|NP_246998.1| 162 MEPDLAILDepDSGIDIVSFDEIKRVFDYLKDK 194
                                   567899999444788888888888888777664 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.15      96     121 ..      28      54 ..       7      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                   HCTT.SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallp 121
                                    +++ ++ +++G+ G+GKStL  ++++
  gi|15668205|ref|NP_246998.1|  28 TVEEnEIHAIIGPNGAGKSTLAYTIMG 54 
                                   55555999*************988765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.16      30      53 ..      29      52 ..      17     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                        AAA_25 30 lpagelallaGapgtGKttlaldl 53
                                  + ++e+++++G+ g+GK+tla+ +
  gi|15668205|ref|NP_246998.1| 29 VEENEIHAIIGPNGAGKSTLAYTI 52
                                  678999**************9865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00022      0.23       6      23 ..      36      57 ..      32      90 .. 0.86
   2 ?   -1.7   0.0       1.9     2e+03      43      71 ..     175     201 ..     152     215 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                        AAA_24  6 liyGpsgiGKTtlakel....g 23
                                  +i+Gp+g+GK+tla+++    g
  gi|15668205|ref|NP_246998.1| 36 AIIGPNGAGKSTLAYTImgisG 57
                                  79*************9865553 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
                        AAA_24  43 fpdieswedfldevvelaaeladyktlvi 71 
                                   + di s+++++  +++l  ++++++ lvi
  gi|15668205|ref|NP_246998.1| 175 GIDIVSFDEIKRVFDYL--KDKGCSLLVI 201
                                   44455666666666665..3444555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00031      0.32       4      20 ..      37      53 ..      34     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                        AAA_33  4 lvGlpGsGKstlaerll 20
                                  ++G++G+GKstla  ++
  gi|15668205|ref|NP_246998.1| 37 IIGPNGAGKSTLAYTIM 53
                                  79**********98776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.5    0.0023       2.5       3      67 ..      37     133 ..      36     225 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0023
                        AAA_18   3 ltGtpGvGKttlakeLskrlgf...............gvnlrdvakenglllevdpe.................aldeskr 51 
                                   + G+ G+GK+tla  +    g+                 n+++ a+ +++l +++p+                 ++++ k+
  gi|15668205|ref|NP_246998.1|  37 IIGPNGAGKSTLAYTIMGISGYkptkgriifkgvdiiDKNITERARMGMTLAWQEPArfegikvknylmlgmneKYKKDKE 117
                                   89***********99955445577777777777666655555555555555555555555555555555544444566666 PP

                        AAA_18  52 ldedkldklldaleen 67 
                                   + e+k  ++l++++  
  gi|15668205|ref|NP_246998.1| 118 IAEEKIREALKLVNLD 133
                                   6666655555555554 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00023      0.24      16      44 ..      29      58 ..      18      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                                  HHH-SEEEEE--TTSSTTHHHHH.HHHHHH CS
                          PhoH 16 lkkndivfaiGpaGtGKtylava.laveal 44
                                  +++n+i  +iGp G+GK+ la + ++++ +
  gi|15668205|ref|NP_246998.1| 29 VEENEIHAIIGPNGAGKSTLAYTiMGISGY 58
                                  56999****************752566655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.0     0.001       1.1       3      37 ..      37      75 ..      36     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.001
                                  EESSTTSSHHHHHHHHHHHHTHE....EEEEETTTCSSS CS
                           AAA  3 lyGppGtGKTllakavakelgve....fleisgsellsk 37
                                  ++Gp G GK++la  ++  +g +     + ++g ++++k
  gi|15668205|ref|NP_246998.1| 37 IIGPNGAGKSTLAYTIMGISGYKptkgRIIFKGVDIIDK 75
                                  68**************99986443333455555555555 PP

>> zf-HC2  Putative zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00035      0.36       7      25 ..     137     155 ..     135     157 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00035
                                   HHHHHHCCT-SCCCHCCCH CS
                        zf-HC2   7 lLsaYlDGeLspeerarve 25 
                                   +L+ Y+D +Ls+ er r+e
  gi|15668205|ref|NP_246998.1| 137 YLDRYVDETLSGGERKRIE 155
                                   89***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1579.32
//
Query:       gi|15668206|ref|NP_246999.1|  [L=153]
Description: 30S ribosomal protein S15 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-30  103.8   0.2      1e-29  102.4   0.1    1.7  2  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    3.9e-20   71.8   0.6    5.8e-20   71.3   0.6    1.3  1  Ribosomal_S15    Ribosomal protein S15
  ------ inclusion threshold ------
      0.052   13.7   2.3       0.14   12.3   0.0    2.8  3  HTH_21           HTH-like domain


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4   0.1   1.7e-33     1e-29       1      60 []       1      60 [.       1      60 [. 1.00
   2 ?   -1.7   0.0      0.52   3.1e+03      29      48 ..     118     137 ..     109     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 1.7e-33
                                  X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
               Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                  Marmh+r++G+SgS+rP+r+e+p+W+++++e+ve+l+v+lakkG++++qIG+iLRD yG+
  gi|15668206|ref|NP_246999.1|  1 MARMHARKRGRSGSKRPVRKEVPEWVQYTPEQVEQLVVELAKKGYQSAQIGLILRDTYGI 60
                                  ***********************************************************9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.52
                                   -HHHHHHHHHHHHHTT--HH CS
               Ribosomal_S13_N  29 skeeveelivklakkGltpS 48 
                                    ++++  l+  ++ kG+ p+
  gi|15668206|ref|NP_246999.1| 118 IESKIRRLVKYYKSKGVLPA 137
                                   55667777777777887765 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.6   9.7e-24   5.8e-20       3      80 ..      73     148 ..      70     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 9.7e-24
                                   HHHHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHCTS CS
                 Ribosomal_S15   3 elikefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkklieklgl 80 
                                   +++ke++  +    ++++++ +l++r++nl++hl++++kD hs+rgL++++sk+r+l+kY+k+k v  ++++++ e++ l
  gi|15668206|ref|NP_246999.1|  73 KIMKEHGLYP----KVPEDLLNLMRRAVNLRKHLEQHPKDLHSKRGLQLIESKIRRLVKYYKSKGVlpADWRYTPETARL 148
                                   6799999999....9*************************************************************9976 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.35   2.1e+03      12      25 ..       3      16 ..       1      17 [. 0.82
   2 ?   12.3   0.0   2.3e-05      0.14      38      56 ..      66      84 ..      42      87 .. 0.78
   3 ?   -1.8   0.0      0.61   3.6e+03       9      17 ..     121     129 ..     109     134 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.35
                        HTH_21 12 eifeeskgrYGyrr 25
                                  + +++++gr G++r
  gi|15668206|ref|NP_246999.1|  3 RMHARKRGRSGSKR 16
                                  56889999999988 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.3e-05
                        HTH_21 38 vnhkrVrRlMrelGLrgvq 56
                                  +  k++ ++M+e+GL +++
  gi|15668206|ref|NP_246999.1| 66 ITGKKISKIMKEHGLYPKV 84
                                  5669***********9986 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.61
                        HTH_21   9 lireifees 17 
                                   +ir++++ +
  gi|15668206|ref|NP_246999.1| 121 KIRRLVKYY 129
                                   366666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1015.49
//
Query:       gi|15668207|ref|NP_247000.1|  [L=238]
Description: hypothetical protein MJ_0037 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-06   28.9   6.7    3.6e-06   27.6   6.7    1.7  1  Metallophos    Calcineurin-like phosphoesterase
    4.6e-06   26.9   0.0    7.3e-06   26.3   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   6.7   4.1e-10   3.6e-06       4      86 ..      24     127 ..      22     208 .. 0.65

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.1e-10
                                   EEEESBTB......TTCCTHHHHHH..HHHHHH...HHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH...TSEEEEE CS
                   Metallophos   4 lvigDlHl......algggqlddll..kllddl...lreekpdlvllaGDlvdrgdlekellellaalvky...pipvyll 70 
                                   ++i+D+H+       +gg++++ l+  ++++++   +++ k++ ++++GD+ +   +  + +++l++++++    i+v+l+
  gi|15668207|ref|NP_247000.1|  24 AIIADTHIgfdvffGEGGANFPLLQkdEVIKRTlniIDKYKINNLIINGDIKHNFKPYPKEIKFLKEFIEFlreYINVILI 104
                                   79***********9777777777775533333333345568888999***9999955555777777777777778****** PP

                                   C-TTS......CHHH.HHHHHHH CS
                   Metallophos  71 lGNHe......gfee.ellnkyg 86 
                                   +GNH+      g+e+ +++++  
  gi|15668207|ref|NP_247000.1| 105 KGNHDtfissaGYEIfDYFELGN 127
                                   *****555555433333333322 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   8.1e-10   7.3e-06       3     128 ..      23     155 ..      22     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 8.1e-10
                 Metallophos_2   3 laiiSDlH.................snldaleavlealkevgvdaiihaGDl......eeeepevleellela....pvla 56 
                                   +aii+D+H                 ++ + +++ l+++++ +++ +i  GD+      + +e ++l+e++e +     v+ 
  gi|15668207|ref|NP_247000.1|  23 YAIIADTHigfdvffgegganfpllQKDEVIKRTLNIIDKYKINNLIINGDIkhnfkpYPKEIKFLKEFIEFLreyiNVIL 103
                                   79*****************999999889999999*****************76443455555579999999889999**** PP

                 Metallophos_2  57 VrGNnDeevveedvlreaaelgtdlpeeaele.lagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtH 128
                                   ++GN+D             ++  +   ++ ++ ++  + l++Hgd    + +++++l +    +++ ++GH H
  gi|15668207|ref|NP_247000.1| 104 IKGNHD-------------TFISSA-GYEIFDyFELGNYLIFHGD---KEIKIDRDLLK----EKFWILGHEH 155
                                   ******.............333333.2333332455568888887...56666666666....5678888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1651.77
//
Query:       gi|15668208|ref|NP_247001.1|  [L=217]
Description: hypothetical protein MJ_0038 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-76  255.4   1.5    3.5e-76  255.2   1.5    1.0  1  DUF655    Protein of unknown function (DUF655)
     0.0056   16.9   0.0       0.01   16.1   0.0    1.4  1  HHH_6     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.2   1.5     4e-80   3.5e-76       1     181 []      25     199 ..      25     199 .. 0.99

  Alignments for each domain:
  == domain 1  score: 255.2 bits;  conditional E-value: 4e-80
                                   X--EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GGGS-HH CS
                        DUF655   1 leeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisyedLtdv 81 
                                   +e++a+vLDylp+Gypd++     d+p+vq+lge++++L+e++p+++vdi+  ++v+igkgk+dki++++r+i+ye+Lt++
  gi|15668208|ref|NP_247001.1|  25 FENYAWVLDYLPYGYPDKP-----DEPIVQGLGEYQFLLMEMIPKPNVDIELGERVYIGKGKRDKIDHVRRMIKYEQLTPT 100
                                   599****************.....8******************************************************** PP

                                   HHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT---HHHHHH CS
                        DUF655  82 araeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglkdpaeilv 162
                                   a++eL +vv++ vk +Edrfv+ffne+ pit+RlH+LelLp+++kk+++ki+eeRe+++FesF+d+++r+   k+p++i++
  gi|15668208|ref|NP_247001.1| 101 AKSELLYVVMEAVKIQEDRFVRFFNECPPITTRLHTLELLPEIKKKYMWKIIEEREAKKFESFKDFEERIG--KNPVRIIA 179
                                   **********************************************************************9..******** PP

                                   HHHHHHHH-T.TSS--SS-- CS
                        DUF655 163 erileEiedk.tekYylFve 181
                                   +ri +E++d+ ++kYylFv+
  gi|15668208|ref|NP_247001.1| 180 KRIEKELSDDkKDKYYLFVK 199
                                   *******99989******96 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.1e-06      0.01      32      65 ..     140     172 ..     134     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-06
                         HHH_6  32 ikglgeaaaerivaeRekegpfksledlarrvds 65 
                                   + +++++ + +i++eRe +++f+s++d+ +r+++
  gi|15668208|ref|NP_247001.1| 140 LPEIKKKYMWKIIEERE-AKKFESFKDFEERIGK 172
                                   5678999999******9.8************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1458.94
//
Query:       gi|15668209|ref|NP_247002.1|  [L=115]
Description: hypothetical protein MJ_0039 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-09   37.6   0.7    2.8e-09   37.3   0.7    1.2  1  RNA_pol_Rpb4  RNA polymerase Rpb4
  ------ inclusion threshold ------
      0.092   12.6   2.2       0.11   12.4   0.9    1.9  2  IF2_N         Translation initiation factor IF-2, N-terminal 


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.7   3.1e-13   2.8e-09      34     122 ..      31     114 ..       3     115 .] 0.84

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 3.1e-13
                                   SHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTSTSTHHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHH CS
                  RNA_pol_Rpb4  34 keevkgnlnkilkktleyltnkfsrlkneekfnelvellksfeLtkaEklqlvnlkPesavelktlieeleerfedeqlee 114
                                   ++   g+l++++  +l+yl++ f++l+ +e++++lve+l s +++++ ++++ +++Pe++++l+++  +   r   e+ ee
  gi|15668209|ref|NP_247002.1|  31 NRAQIGELSYEQGCALDYLQK-FAKLD-KEEAKKLVEELISLGIDEKTAVKIADILPEDLDDLRAIYYK---RELPENAEE 106
                                   445567788888889*****9.*****.9999**********************************865...558999*** PP

                                   HHHHHHHH CS
                  RNA_pol_Rpb4 115 iLdelkev 122
                                   iL++++++
  gi|15668209|ref|NP_247002.1| 107 ILEIVRKY 114
                                   *****998 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   1.2e-05      0.11       7      35 ..      50      77 ..      49      82 .. 0.90
   2 ?   -3.1   0.0      0.81   7.3e+03      44      49 ..     104     109 ..     101     114 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                         IF2_N  7 yeLAkeLgvkskevikkLfkelGievksh 35
                                  + +Ak  + ++k+++++L + lGi+ k++
  gi|15668209|ref|NP_247002.1| 50 QKFAKLDKEEAKKLVEELIS-LGIDEKTA 77
                                  6799999***********76.****9997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.81
                         IF2_N  44 aeliae 49 
                                   ae+i+e
  gi|15668209|ref|NP_247002.1| 104 AEEILE 109
                                   444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 744.55
//
Query:       gi|15668210|ref|NP_247003.1|  [L=98]
Description: 50S ribosomal protein L21e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-39  131.9   1.7    6.8e-39  131.8   1.7    1.0  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.8   1.7   3.8e-43   6.8e-39       2      99 ..       3      96 ..       2      98 .] 0.98

  Alignments for each domain:
  == domain 1  score: 131.8 bits;  conditional E-value: 3.8e-43
                                  --S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEEETTE. CS
                Ribosomal_L21e  2 knskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkkvggki 84
                                  ++s+g+rr+trk++sk++r++g+ p++++lre+k+G++V+i+idpsv+kgmph+r+hG+tg v  v+k+++++iv++++ggk 
  gi|15668210|ref|NP_247003.1|  3 QMSEGFRRKTRKKLSKHPRERGLYPITRALREFKEGEYVHIVIDPSVHKGMPHPRFHGRTGIV--VGKQGRAFIVKVRDGGK- 82
                                  789************************************************************..*****************. PP

                                  .EEEEEE-GGGEEE- CS
                Ribosomal_L21e 85 leKriivriehlkks 99
                                    K+ii+ ++hl++ 
  gi|15668210|ref|NP_247003.1| 83 -YKQIIAYPQHLRPA 96
                                  .***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 618.06
//
Query:       gi|15668211|ref|NP_247004.1|  [L=454]
Description: putative pseudouridylate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-09   37.8   1.8    1.9e-09   37.8   1.8    2.1  2  THUMP        THUMP domain
     0.0031   17.4   2.3       0.17   11.8   0.1    2.9  3  DUF2202      Uncharacterized protein domain (DUF2202)


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   1.8   2.1e-13   1.9e-09      33     144 .]      95     206 ..      51     206 .. 0.77
   2 ?   -3.5   0.1       1.1     1e+04      66      88 ..     300     323 ..     290     328 .. 0.63

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.1e-13
                                   EEETHHHHHHHHHTSTTECEEEEE........EEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS........ CS
                         THUMP  33 peedeellkealekargiqrvipv........cevceadledileaakeivkkkfeeeketFaVrvkrrgkhf........ 97 
                                     ed e+                +         +    ++e++l++a e+ k++ ++   tF +++  + +          
  gi|15668211|ref|NP_247004.1|  95 RLEDIEI----------------EkencpwcrGIFNKQKMEKLLNKAIELLKEYDFD---TFLIGTHIPEEIKdlekeiet 156
                                   2333333................2333335336677789******************...***********99******** PP

                                   ...SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEEC CS
                         THUMP  98 ...eftsreinrevGkaivektglkVdlenPdivvrveiikdkayisidr 144
                                      e +++e+ re Gk++  ++ +  d e Pdivv++ +  +++y++i++
  gi|15668211|ref|NP_247004.1| 157 efmESIKQEFGREFGKMLAVRLDKAPDKEYPDIVVHINPYTEEIYLQINP 206
                                   ************************************************96 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHHCT-.EEEE CS
                         THUMP  66 dileaakeivkkkfeeeke.tFaV 88 
                                   d+++ a+ei+k+   e  +  F V
  gi|15668211|ref|NP_247004.1| 300 DLNKIAEEINKDGRVEVLNlEFGV 323
                                   455666666666555555555555 PP

>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.25   2.2e+03      70      97 ..      34      61 ..      30      78 .. 0.79
   2 !   11.8   0.1   1.8e-05      0.17      62     117 ..     109     163 ..      89     167 .. 0.86
   3 !    4.0   0.1    0.0045        41      58     122 ..     323     390 ..     311     405 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.25
                       DUF2202 70 elqelYnkLvekgsksledaLkvgatie 97
                                   +  lY kL+++++++   aLk    +e
  gi|15668211|ref|NP_247004.1| 34 CFGRLYAKLLHTTNTERGRALKLYKALE 61
                                  5778999999999999999998766655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.8e-05
                       DUF2202  62 erGkfedeelqelYnkLvekgsksledaLkvgatiedldiaDlekalketdnkdik 117
                                    rG+f+++++++l nk +e  ++   d   +g+ i + +i+Dlek ++++  + ik
  gi|15668211|ref|NP_247004.1| 109 CRGIFNKQKMEKLLNKAIELLKEYDFDTFLIGTHIPE-EIKDLEKEIETEFMESIK 163
                                   69******************99999**********98.8******99887776665 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0045
                       DUF2202  58 vkederGkfedeelqelYnkLvekgsksledaLkv.gatiedldiaDl..eka.lketdnkdikevYen 122
                                   v++d + +f+++  ++ Y +Lve ++k   + Lk     +e+  i+    +++  +  d + i +vY+ 
  gi|15668211|ref|NP_247004.1| 323 VRKD-KVIFKNTPHRKTYRALVECSDKITDEELKLlEKELENRTIYQKtpKRVlHRRADLERIRKVYKV 390
                                   5666.479*******************999999862567888888876444441456677778888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       957  (0.0533772); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2959.13
//
Query:       gi|15668212|ref|NP_247005.1|  [L=215]
Description: hypothetical protein MJ_0042 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-06   26.0   0.4    1.6e-05   24.7   0.4    1.8  1  zinc_ribbon_4    zinc-ribbon domain
      3e-05   24.0   3.1        0.1   12.7   0.5    2.6  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
     0.0002   20.7   1.3      0.035   13.6   0.1    2.4  2  Mu-like_Com      Mu-like prophage protein Com
    0.00034   19.9   4.2       0.35   10.4   0.2    3.0  3  zf-ribbon_3      zinc-ribbon domain
    0.00053   19.6   2.0     0.0022   17.6   1.8    2.3  2  Ribosomal_S27e   Ribosomal protein S27
     0.0031   17.2   1.6        1.7    8.5   0.2    2.5  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
     0.0083   16.0   0.2        3.3    7.7   0.0    2.4  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0093   16.1   2.8        1.6    8.9   0.2    2.6  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
  ------ inclusion threshold ------
      0.011   15.5   0.6      0.051   13.4   0.6    2.2  1  zinc_ribbon_5    zinc-ribbon domain
      0.011   15.9   0.8      0.024   14.9   0.8    1.5  1  IBR              IBR domain, a half RING-finger domain
      0.019   14.9   0.5        2.3    8.3   0.0    2.4  2  Ogr_Delta        Ogr/Delta-like zinc finger
      0.023   14.8   1.6       0.31   11.1   0.1    2.5  2  CpXC             CpXC protein
      0.025   14.3   0.1       0.12   12.0   0.1    1.9  1  Crr6             Chlororespiratory reduction 6
      0.028   14.4   2.0        4.6    7.3   0.1    2.5  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.037   14.3   0.8        1.4    9.3   0.0    2.6  3  GFA              Glutathione-dependent formaldehyde-activatin
       0.04   13.5   1.1          6    6.6   0.1    2.4  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.05   13.6   0.9      0.085   12.9   0.3    1.6  1  DZR              Double zinc ribbon
      0.052   13.8   1.8         24    5.3   0.1    3.1  3  zf-LITAF-like    LITAF-like zinc ribbon domain
      0.052   14.0   0.2        7.7    7.0   0.0    2.6  2  zf-IS66          zinc-finger binding domain of transposase IS
        0.1   12.7   2.6         11    6.3   0.2    2.4  2  UPF0547          Uncharacterised protein family UPF0547
       0.11   12.5   0.2       0.53   10.3   0.2    2.0  1  zf-C3HC          C3HC zinc finger-like
       0.12   12.1   0.5         17    5.2   0.1    2.6  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.14   12.3   1.6        3.8    7.8   0.1    2.9  2  zf-RING_7        C4-type zinc ribbon domain
       0.16   12.0   0.5       0.44   10.6   0.3    1.8  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.17   12.3   1.5       0.54   10.7   1.0    2.0  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.27   10.9   6.8        3.8    7.2   1.4    2.4  2  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
       0.39   10.8   3.7       0.15   12.2   0.6    1.8  2  HTH_56           Cch helix turn helix domain
        0.4   10.2   7.1        3.3    7.3   4.8    2.9  3  TF_Zn_Ribbon     TFIIB zinc-binding
       0.56   10.0  10.0       0.67    9.8   0.3    2.9  3  zinc_ribbon_2    zinc-ribbon domain
        1.3    9.0   3.5        1.5    8.8   0.4    2.6  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
        1.4    8.9   5.3         23    5.0   5.3    2.3  1  Prok-RING_1      Prokaryotic RING finger family 1
          2    8.6   8.3       0.35   11.0   3.4    2.3  1  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.4   2.9e-08   1.6e-05       1      35 [.       1      35 [.       1      36 [. 0.88

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.9e-08
                 zinc_ribbon_4  1 MkitCpsCkakyeiddeklpakgvkvrCskCghvF 35
                                  M++ Cp+C+a   + +e   +++++v+C+kCg+++
  gi|15668212|ref|NP_247005.1|  1 MNVKCPECGAWIYVVEEDSGGDAMEVKCPKCGTSI 35
                                  9*********7666666799999*********985 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00054       0.3       2      12 ..       3      13 ..       3      16 .. 0.91
   2 !   12.7   0.5   0.00018       0.1       2      12 ..      26      36 ..      26      37 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00054
                        zf-ACC  2 tKCpsCgemly 12
                                  +KCp+Cg+ +y
  gi|15668212|ref|NP_247005.1|  3 VKCPECGAWIY 13
                                  7*******999 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00018
                        zf-ACC  2 tKCpsCgemly 12
                                  +KCp+Cg+++y
  gi|15668212|ref|NP_247005.1| 26 VKCPKCGTSIY 36
                                  7*********9 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.014       7.6      24      32 ..       2      10 ..       1      21 [. 0.83
   2 !   13.6   0.1   6.2e-05     0.035      21      40 ..      22      42 ..      16      52 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.014
                   Mu-like_Com 24 tiKCPRCGt 32
                                  ++KCP CG 
  gi|15668212|ref|NP_247005.1|  2 NVKCPECGA 10
                                  69******7 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.2e-05
                   Mu-like_Com 21 DeltiKCPRCGtLnH.lkaes 40
                                  D +++KCP+CGt    +k + 
  gi|15668212|ref|NP_247005.1| 22 DAMEVKCPKCGTSIYvVKPMG 42
                                  6678*******9543155555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1   0.00085      0.48       2      11 ..       2      12 ..       1      19 [. 0.80
   2 !   10.4   0.2   0.00062      0.35       2      10 ..      25      33 ..      24      36 .. 0.77
   3 ?   -1.4   0.0       3.1   1.7e+03      21      24 ..     119     122 ..     119     125 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00085
                   zf-ribbon_3  2 tvrCPnCGa.p 11
                                   v+CP+CGa +
  gi|15668212|ref|NP_247005.1|  2 NVKCPECGAwI 12
                                  589*****966 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00062
                   zf-ribbon_3  2 tvrCPnCGa 10
                                  +v+CP+CG+
  gi|15668212|ref|NP_247005.1| 25 EVKCPKCGT 33
                                  789999997 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.1
                   zf-ribbon_3  21 yCGt 24 
                                   yCG+
  gi|15668212|ref|NP_247005.1| 119 YCGS 122
                                   5554 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.8     4e-06    0.0022       6      47 ..       1      48 [.       1      55 [. 0.76
   2 ?   -2.2   0.0       6.3   3.5e+03       4      12 ..      52      60 ..      49      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4e-06
                                  EEEE-TTTS-EEEEESS-....SS-EEESSSTCE..EEEECSSSEEES CS
                Ribosomal_S27e  6 ldvkCpdCenetvvFsha....atvvkCisCgkv..LvePtGGkaklk 47
                                  ++vkCp+C++   v +      a  vkC +Cg+   +v+P G k k k
  gi|15668212|ref|NP_247005.1|  1 MNVKCPECGAWIYVVEEDsggdAMEVKCPKCGTSiyVVKPMGEKMKNK 48
                                  79*******9877776531233679*******963379****999866 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.3
                                  -EEEEE-TT CS
                Ribosomal_S27e  4 kFldvkCpd 12
                                   Fldvk  +
  gi|15668212|ref|NP_247005.1| 52 DFLDVKILE 60
                                  69***9766 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0054         3       2      11 ..       3      12 ..       2      20 .. 0.82
   2 !    8.5   0.2     0.003       1.7       2      11 ..      26      35 ..      25      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0054
                                  EE-SSS--EE CS
                zf-C4_Topoisom  2 ekCPkCggdL 11
                                  +kCP+Cg+ +
  gi|15668212|ref|NP_247005.1|  3 VKCPECGAWI 12
                                  79*****865 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.003
                                  EE-SSS--EE CS
                zf-C4_Topoisom  2 ekCPkCggdL 11
                                  +kCPkCg  +
  gi|15668212|ref|NP_247005.1| 26 VKCPKCGTSI 35
                                  79*****655 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0     0.006       3.3      13      22 ..       4      13 ..       3      25 .. 0.86
   2 ?    6.1   0.1     0.018        10      13      22 ..      27      36 ..      26      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.006
                       DUF35_N 13 rCpdCGtvqf 22
                                  +Cp CG++++
  gi|15668212|ref|NP_247005.1|  4 KCPECGAWIY 13
                                  7*******98 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.018
                       DUF35_N 13 rCpdCGtvqf 22
                                  +Cp+CGt ++
  gi|15668212|ref|NP_247005.1| 27 KCPKCGTSIY 36
                                  7999999876 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2     0.012       6.7      16      31 ..       2      17 ..       1      23 [. 0.85
   2 !    8.9   0.2    0.0028       1.6      15      30 ..      24      39 ..      19      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                      zf-Mss51 16 dfeCpdCGiptycsee 31
                                  +++Cp+CG  +y+ ee
  gi|15668212|ref|NP_247005.1|  2 NVKCPECGAWIYVVEE 17
                                  689******9999887 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0028
                      zf-Mss51 15 vdfeCpdCGiptycse 30
                                  ++++Cp+CG ++y+ +
  gi|15668212|ref|NP_247005.1| 24 MEVKCPKCGTSIYVVK 39
                                  6789********9865 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6     9e-05     0.051       1      32 [.       1      32 [.       1      38 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9e-05
                 zinc_ribbon_5  1 LiirCpdCdtkFklvdsklKksgkkVrCakCa 32
                                  + ++Cp+C+    +v++        V+C kC+
  gi|15668212|ref|NP_247005.1|  1 MNVKCPECGAWIYVVEEDSGGDAMEVKCPKCG 32
                                  6789*********999995566679******8 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.8   4.3e-05     0.024      19      47 ..       3      34 ..       1      35 [. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.3e-05
                           IBR 19 kwCprpdCeaii....ekseg..cksvtCskCgfe 47
                                  ++Cp  +C+a+i    e+s g    +v+C+kCg++
  gi|15668212|ref|NP_247005.1|  3 VKCP--ECGAWIyvveEDS-GgdAMEVKCPKCGTS 34
                                  68**..***9996553333.3456669*****986 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0041       2.3       1      11 [.       4      14 ..       4      17 .. 0.87
   2 ?    4.6   0.1     0.056        31       1      10 [.      27      36 ..      27      39 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0041
                     Ogr_Delta  1 rCPhCgapaaa 11
                                  +CP+Cga++++
  gi|15668212|ref|NP_247005.1|  4 KCPECGAWIYV 14
                                  6******9875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.056
                     Ogr_Delta  1 rCPhCgapaa 10
                                  +CP+Cg+ ++
  gi|15668212|ref|NP_247005.1| 27 KCPKCGTSIY 36
                                  6*****9876 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2      0.24   1.3e+02      38      46 ..       3      11 ..       1      18 [. 0.72
   2 ?   11.1   0.1   0.00056      0.31      33      56 ..      21      44 ..      14     103 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.24
                          CpXC 38 atCpkCgat 46
                                  ++Cp+Cga 
  gi|15668212|ref|NP_247005.1|  3 VKCPECGAW 11
                                  678888875 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00056
                          CpXC 33 gslfeatCpkCgatakleapllyh 56
                                  g+  e++CpkCg+++++  p+  +
  gi|15668212|ref|NP_247005.1| 21 GDAMEVKCPKCGTSIYVVKPMGEK 44
                                  778899**********99998633 PP

>> Crr6  Chlororespiratory reduction 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00022      0.12      91     145 ..     118     173 ..      85     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                          Crr6  91 HqfsrkeGiqfnp.ealeifvmkkvfvladwlkkqgiesksrlkslaqllGyeldd 145
                                   H   + +  +f+  e+ +i+v +k  +++   k++    k+r++++a+ lG+el++
  gi|15668212|ref|NP_247005.1| 118 HYCGSVKTKNFQVdEDNDIYVKQKFGIIEGVNKSKIKLPKERMEEIAEKLGFELKE 173
                                   444444444555426789******777777666665556**************986 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0083       4.6       1      10 [.       4      13 ..       4      23 .. 0.76
   2 ?    6.2   0.2     0.019        11       1       9 [.      27      35 ..      27      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0083
                DNA_ligase_ZBD  1 hCPvCGsavv 10
                                  +CP+CG+ + 
  gi|15668212|ref|NP_247005.1|  4 KCPECGAWIY 13
                                  6*****8765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.019
                DNA_ligase_ZBD  1 hCPvCGsav 9 
                                  +CP CG+ +
  gi|15668212|ref|NP_247005.1| 27 KCPKCGTSI 35
                                  6*****975 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.059        33      51      66 ..       4      19 ..       1      24 [. 0.77
   2 ?    9.3   0.0    0.0026       1.4      40      64 ..      16      40 ..      13      48 .. 0.78
   3 ?   -2.2   0.0       9.9   5.6e+03      52      70 ..     120     138 ..     111     155 .. 0.48

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.059
                           GFA 51 fCpeCgsplyseesaa 66
                                   CpeCg+ +y+ e+  
  gi|15668212|ref|NP_247005.1|  4 KCPECGAWIYVVEEDS 19
                                  6*********876554 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0026
                           GFA 40 tadsgnkvtrsfCpeCgsplysees 64
                                  ++dsg ++ +  Cp+Cg+ +y+ + 
  gi|15668212|ref|NP_247005.1| 16 EEDSGGDAMEVKCPKCGTSIYVVKP 40
                                  578999999************8543 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 9.9
                           GFA  52 CpeCgsplyseesaapevv 70 
                                   C +  ++ +   + ++ +v
  gi|15668212|ref|NP_247005.1| 120 CGSVKTKNFQVDEDNDIYV 138
                                   3333333333233333333 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.025        14       3      16 ..       3      16 ..       2      19 .. 0.76
   2 ?    6.6   0.1     0.011         6       3      13 ..      26      36 ..      25      40 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.025
                        zf_UBZ  3 ylCerCgkeipese 16
                                  + C++Cg+ i + e
  gi|15668212|ref|NP_247005.1|  3 VKCPECGAWIYVVE 16
                                  68*****9877665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                        zf_UBZ  3 ylCerCgkeip 13
                                  + C++Cg++i 
  gi|15668212|ref|NP_247005.1| 26 VKCPKCGTSIY 36
                                  58******996 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   0.00015     0.085      15      37 ..       5      34 ..       2      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                           DZR 15 CseCgtklkavaa.......edrCpsCgek 37
                                  C+eCg+ +  v++       e +Cp+Cg++
  gi|15668212|ref|NP_247005.1|  5 CPECGAWIYVVEEdsggdamEVKCPKCGTS 34
                                  *******987777999************97 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.058        32      57      68 ..       3      14 ..       1      16 [. 0.75
   2 ?    5.3   0.1     0.042        24      56      67 ..      25      36 ..      21      39 .. 0.64
   3 ?    1.4   0.0      0.68   3.8e+02      52      61 ..     113     122 ..     109     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.058
                 zf-LITAF-like 57 hyCpnCgallgt 68
                                   +Cp+Cga++ +
  gi|15668212|ref|NP_247005.1|  3 VKCPECGAWIYV 14
                                  689999998865 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.042
                 zf-LITAF-like 56 ehyCpnCgallg 67
                                  e +Cp+Cg+ + 
  gi|15668212|ref|NP_247005.1| 25 EVKCPKCGTSIY 36
                                  556777766654 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.68
                 zf-LITAF-like  52 lkdvehyCpn 61 
                                    k v hyC++
  gi|15668212|ref|NP_247005.1| 113 VKSVSHYCGS 122
                                   699*****85 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.085        48       3      15 ..       4      16 ..       3      19 .. 0.69
   2 ?    7.0   0.0     0.014       7.7       3      17 ..      27      44 ..      25      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.085
                       zf-IS66  3 tCpcCGgllkpig 15
                                  +Cp+CG+    ++
  gi|15668212|ref|NP_247005.1|  4 KCPECGAWIYVVE 16
                                  59***98655555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.014
                       zf-IS66  3 tCpcCGgl...lkpiged 17
                                  +Cp+CG+    +kp+ge+
  gi|15668212|ref|NP_247005.1| 27 KCPKCGTSiyvVKPMGEK 44
                                  6*****977999999987 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2     0.019        11       2       7 ..       4       9 ..       3      12 .. 0.66
   2 ?    6.2   0.2      0.02        11      16      23 ..      27      34 ..      26      35 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.019
                       UPF0547 2 vCPeCe 7
                                 +CPeC 
  gi|15668212|ref|NP_247005.1| 4 KCPECG 9
                                 577775 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.02
                       UPF0547 16 fCphCGyv 23
                                  +Cp CG++
  gi|15668212|ref|NP_247005.1| 27 KCPKCGTS 34
                                  68888875 PP

>> zf-C3HC  C3HC zinc finger-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00095      0.53      41     108 ..      23      89 ..       2     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00095
                       zf-C3HC  41 kdrlkCevCgaslvlklksseeesdeqlnkklaekylkqlveaHeenClWrnkecpesleslplakp.e 108
                                   +  +kC  Cg s++++ k+  e+ +++  k+  +    +++e+ +++ ++++++ +++l++l+++++ +
  gi|15668212|ref|NP_247005.1|  23 AMEVKCPKCGTSIYVV-KPMGEKMKNKRDKDFLDVKILEIEET-KKTSPYKDTKSEDVLKALRVKANiN 89 
                                   5579************.88888888888888888777777665.6677999999999999999877655 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1      0.03        17      18      25 ..       3      10 ..       2      13 .. 0.84
   2 ?    4.3   0.1     0.056        32      18      25 ..      26      33 ..      19      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.03
                                  ---SSS-- CS
                DNA_RNApol_7kD 18 iRCkeCGh 25
                                  ++C eCG 
  gi|15668212|ref|NP_247005.1|  3 VKCPECGA 10
                                  89*****7 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.056
                                  ---SSS-- CS
                DNA_RNApol_7kD 18 iRCkeCGh 25
                                  ++C +CG 
  gi|15668212|ref|NP_247005.1| 26 VKCPKCGT 33
                                  89*****7 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0067       3.8      24      32 ..       3      11 ..       2      12 .. 0.87
   2 ?    2.5   0.1      0.29   1.6e+02      24      30 ..      26      32 ..      18      33 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0067
                                  EE-TTT--E CS
                     zf-RING_7 24 vtCpeCGRI 32
                                  v+CpeCG++
  gi|15668212|ref|NP_247005.1|  3 VKCPECGAW 11
                                  79*****97 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.29
                                  EE-TTT- CS
                     zf-RING_7 24 vtCpeCG 30
                                  v+Cp CG
  gi|15668212|ref|NP_247005.1| 26 VKCPKCG 32
                                  89****9 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00078      0.44      70      95 ..       2      34 ..       1      48 [. 0.66
   2 ?   -1.8   0.0       5.7   3.2e+03      87     108 ..     118     139 ..      98     141 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00078
                                  EEEETTTS-EEECHH.....H..HHS-TTTSSS CS
                          HypA 70 kvrCreCgkefelee.....k..alrCpkCgsa 95
                                  +v+C eCg+ + + e     +  +++CpkCg++
  gi|15668212|ref|NP_247005.1|  2 NVKCPECGAWIYVVEedsggDamEVKCPKCGTS 34
                                  689*****88774432334323445*****985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.7
                                   HS-TTTSSS-EEEEESSSEEEE CS
                          HypA  87 lrCpkCgsadveivsGeellvk 108
                                     C++ +++++++ + ++++vk
  gi|15668212|ref|NP_247005.1| 118 HYCGSVKTKNFQVDEDNDIYVK 139
                                   3466666677777777777776 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.0   0.00097      0.54       5      37 ..       4      38 ..       2      52 .. 0.70
   2 ?   -1.3   0.0       5.3     3e+03      33      42 ..     119     129 ..      89     138 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00097
               Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga....s 37
                                   CP Cg    ++++ ++     + v C +Cg     +
  gi|15668212|ref|NP_247005.1|  4 KCPECGAWIYVVEEDSGGDA--MEVKCPKCGTsiyvV 38
                                  6******9777777666653..49*******944442 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.3
               Lar_restr_allev  33 dCga.stpwfk 42 
                                    Cg   t+ f+
  gi|15668212|ref|NP_247005.1| 119 YCGSvKTKNFQ 129
                                   36664333333 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3     0.014       7.7      12      18 ..       4      10 ..       3      11 .. 0.91
   2 ?    7.2   1.4    0.0068       3.8      12      18 ..      27      33 ..      26      34 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                       zf-tcix 12 kCpkCGt 18
                                  kCp+CG+
  gi|15668212|ref|NP_247005.1|  4 KCPECGA 10
                                  9*****8 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0068
                       zf-tcix 12 kCpkCGt 18
                                  kCpkCGt
  gi|15668212|ref|NP_247005.1| 27 KCPKCGT 33
                                  9*****9 PP

>> HTH_56  Cch helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.2   4.6e+03      77      92 ..      57      72 ..      46      91 .. 0.61
   2 ?   12.2   0.6   0.00026      0.15      19      64 ..     126     170 ..     122     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.2
                        HTH_56 77 Gllesekdrntkkrtv 92
                                  ++le e+ ++t+ ++ 
  gi|15668212|ref|NP_247005.1| 57 KILEIEETKKTSPYKD 72
                                  4566666555555544 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00026
                        HTH_56  19 skFkeegkeasnpneiwGkiekkkektevyIlknvfdkileeagFe 64 
                                   ++F+++ +++ + ++ +G+ie  + k ++   k+ +++i e++gFe
  gi|15668212|ref|NP_247005.1| 126 KNFQVDEDNDIYVKQKFGIIEGVN-KSKIKLPKERMEEIAEKLGFE 170
                                   89******988999********99.689*****************5 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.8    0.0058       3.3       2      27 ..       4      33 ..       3      35 .. 0.73
   2 ?    6.2   0.6     0.013       7.2       2      11 ..      27      36 ..      26      44 .. 0.73
   3 ?   -2.0   0.0       4.7   2.7e+03       6      28 ..     120     123 ..     119     136 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0058
                                  EETTTTC.EE.CHEE..TSTTCEEESSSSB CS
                  TF_Zn_Ribbon  2 kCPnCgs.tn.lveD..pergelvCtdCGl 27
                                  kCP+Cg   + ++eD   +  e+ C++CG+
  gi|15668212|ref|NP_247005.1|  4 KCPECGAwIYvVEEDsgGDAMEVKCPKCGT 33
                                  9*****977745555554555889****96 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.013
                                  EETTTTCEEC CS
                  TF_Zn_Ribbon  2 kCPnCgstnl 11
                                  kCP+Cg++ +
  gi|15668212|ref|NP_247005.1| 27 KCPKCGTSIY 36
                                  8*****8644 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.7
                                   TTCEECHEETSTTCEEESSSSBE CS
                  TF_Zn_Ribbon   6 CgstnlveDpergelvCtdCGlV 28 
                                   Cgs                   V
  gi|15668212|ref|NP_247005.1| 120 CGS-------------------V 123
                                   443...................3 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.5     0.018       9.8       1       7 [.       4      10 ..       3      10 .. 0.75
   2 ?    9.8   0.3    0.0012      0.67       1       9 [.      27      35 ..      25      36 .. 0.68
   3 ?   -2.3   0.2       7.3   4.1e+03      18      20 ..     119     121 ..     118     122 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.018
                 zinc_ribbon_2  1 fCpnCGa 7 
                                  +Cp+CGa
  gi|15668212|ref|NP_247005.1|  4 KCPECGA 10
                                  6888885 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                 zinc_ribbon_2  1 fCpnCGael 9 
                                  +Cp+CG+ +
  gi|15668212|ref|NP_247005.1| 27 KCPKCGTSI 35
                                  577777654 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 7.3
                 zinc_ribbon_2  18 yCG 20 
                                   yCG
  gi|15668212|ref|NP_247005.1| 119 YCG 121
                                   788 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.4    0.0026       1.5      30      55 ..       4      34 ..       2      36 .. 0.79
   2 ?   -2.2   0.0       7.5   4.2e+03      31      40 ..     117     126 ..     115     133 .. 0.74
   3 ?   -1.2   0.0       3.7     2e+03       6      24 ..     158     176 ..     157     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
                OrfB_Zn_ribbon 30 tCseCgsknke.....alsgrtfkCpnCgfe 55
                                  +C+eCg+  +        +  ++kCp+Cg++
  gi|15668212|ref|NP_247005.1|  4 KCPECGAWIYVveedsGGDAMEVKCPKCGTS 34
                                  7*****8666665577777889******986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.5
                OrfB_Zn_ribbon  31 CseCgsknke 40 
                                   ++ Cgs++++
  gi|15668212|ref|NP_247005.1| 117 SHYCGSVKTK 126
                                   5789999887 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.7
                OrfB_Zn_ribbon   6 eqleykakeyGikveevnp 24 
                                   e++e+ a++ G +++e ++
  gi|15668212|ref|NP_247005.1| 158 ERMEEIAEKLGFELKEGDE 176
                                   78999******99998875 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   5.3     0.042        23       5      29 ..       3      34 ..       2      36 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.042
                   Prok-RING_1  5 kkCpvCgkel...kee..dDi..VvCpeCgtp 29
                                   kCp Cg  +   +e+   D+  V Cp+Cgt+
  gi|15668212|ref|NP_247005.1|  3 VKCPECGAWIyvvEEDsgGDAmeVKCPKCGTS 34
                                  6899998876332222446765699*****97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.4   0.00063      0.35       7      34 ..       4      33 ..       2      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00063
                   Zn-ribbon_8  7 rCeeCghefevlqsis.daplta.CPeCgs 34
                                  +C eCg    v+ + s  +++++ CP+Cg 
  gi|15668212|ref|NP_247005.1|  4 KCPECGAWIYVVEEDSgGDAMEVkCPKCGT 33
                                  8*****999988888886666666****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1370.36
//
Query:       gi|15668213|ref|NP_247006.1|  [L=785]
Description: hypothetical protein MJ_0043 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-08   33.2   1.6     0.0002   21.3   0.0    3.0  3  Intein_splicing  Intein splicing domain
    0.00096   19.4   0.3       0.03   14.6   0.1    3.0  3  LAGLIDADG_3      LAGLIDADG-like domain
      0.003   17.3   0.0     0.0064   16.2   0.0    1.6  1  PHP_C            PHP-associated
     0.0039   17.5   0.0     0.0077   16.5   0.0    1.5  1  Hint_2           Hint domain
      0.004   17.5   0.0     0.0092   16.3   0.0    1.7  1  PHP              PHP domain
     0.0045   17.2   0.8       0.12   12.7   0.1    2.8  2  PT-HINT          Pretoxin HINT domain
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.027   14.5   0.1    1.6  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.02   15.3   0.7      0.075   13.4   0.7    2.0  1  DUF4379          Probable Zinc-ribbon domain
      0.037   13.8   2.5      0.085   12.6   2.5    1.6  1  zinc_ribbon_5    zinc-ribbon domain
      0.045   14.1   0.0       0.14   12.5   0.0    1.9  1  EntA_Immun       Enterocin A Immunity
      0.088   12.9   0.7       0.21   11.7   0.7    1.7  1  Zn-ribbon_8      Zinc ribbon domain
      0.093   12.5   1.7       0.23   11.2   1.0    2.0  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.14   12.4   3.8        1.6    9.0   0.1    3.5  4  DUF272           Protein of unknown function (DUF272)
       0.15   12.0   7.4      0.038   13.9   2.1    2.6  2  zinc_ribbon_4    zinc-ribbon domain
       0.17   11.4   0.0       0.45   10.0   0.0    1.6  1  Hint             Hint module


Domain annotation for each model (and alignments):
>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0006      0.72      19      73 ..     150     201 ..     130     207 .. 0.72
   2 !   21.3   0.0   1.7e-07    0.0002      75     134 .]     235     520 ..     229     520 .. 0.97
   3 ?   -2.6   0.1         4   4.8e+03      26      60 ..     708     742 ..     700     751 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0006
                                   CTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS.-EEEEETT-EEEECCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxxxxxxx RF
               Intein_splicing  19 egeevlslnledlklevksvkkliklklk.elyeiklesg.rkikaTpeHkllvvrd 73 
                                    g++vl     + +   k+v+k+ k ++   +++ik++ + ++i++TpeH++ +++ 
  gi|15668213|ref|NP_247006.1| 150 VGDKVL-----THENRFKKVEKVYKRRYIgDIIKIKVRYFpEEIILTPEHPVYAIKT 201
                                   444444.....3444556799999999988******9987579*********99953 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.7e-07
                                   EEEEEECCC--TT-EEEEE.............................................................. CS
                                   xxxxxxxxxxxxxxxxxxx.............................................................. RF
               Intein_splicing  75 givEkradeLkegdliavp.............................................................. 93 
                                   ++    a++Lk+gd+i+ p                                                              
  gi|15668213|ref|NP_247006.1| 235 EW--IIAKDLKVGDVIVYPipnrvrdikylsldkylsnikrefcrsripekievseefcrlvgyflsegycfrdgigfalg 313
                                   67..689************************************************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15668213|ref|NP_247006.1| 314 enekkiiddieylmkkifnlkpkirddgrsegielkyysrvlrdffgdmfycgdekrawnkalpneflylpknkqlqifig 394
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15668213|ref|NP_247006.1| 395 wwrgdkgvttseilmnqlrlislrlgfiitfskhvpknpkigdrevikyharwqgrvsildekivdelknediklpkkdvr 475
                                   ********************************************************************************* PP

                                   ....HSCEEEEEEEEEEEEECEEEEEEEEETTT-EEEECTTEEE- CS
                                   ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  94 ....dadvvwdkvksievedeeeyVYdltvednhNFvangiivHN 134
                                       +++ ++  + +i +e +++ VY l+ved + +v     +HN
  gi|15668213|ref|NP_247006.1| 476 ygwiKGNYLYAPIIRIGREYYDGFVYNLEVEDDSSYVTVSGTLHN 520
                                   ************************************995555666 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4
                                   EETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  26 lnledlklevksvkkliklklkelyeiklesgrki 60 
                                   l +e  k + ++++ li+ ++ el +i+ +  ++i
  gi|15668213|ref|NP_247006.1| 708 LWEEFIKKYGNEIEVLINADIDELSKIHPKVAETI 742
                                   44555566666677777777777777765555554 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   2.5e-05      0.03       7      78 ..     293     358 ..     287     362 .. 0.82
   2 ?    1.0   0.0      0.45   5.4e+02      31      63 ..     403     435 ..     401     458 .. 0.81
   3 ?   -2.7   0.0       6.4   7.6e+03      27      49 ..     692     713 ..     680     720 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                                   HHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHH.HCT.HSCEEEE.EEE-SCCCCECCCHCHCTTCGG CS
                   LAGLIDADG_3   7 LrGlfdaDGsvskskkkgvsisltssskelledvqrlLl.rlGIestiyek.kkakgrgvyrlliisgenlkrF 78 
                                   L G+f ++G+   ++ +     l+ ++k++++d+ +l++  ++++ +i+ + +    +    +l + ++ l++F
  gi|15668213|ref|NP_247006.1| 293 LVGYFLSEGYCFRDGIG---FALGENEKKIIDDIEYLMKkIFNLKPKIRDDgR----SEGI-ELKYYSRVLRDF 358
                                   78*************88...99*****************99**********33....3333.566666666666 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.45
                                   ES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCC CS
                   LAGLIDADG_3  31 ssskelledvqrlLlrlGIestiyekkkakgrg 63 
                                   ++s+ l+++++ + lrlG + t  ++ +++ + 
  gi|15668213|ref|NP_247006.1| 403 TTSEILMNQLRLISLRLGFIITFSKHVPKNPKI 435
                                   79999*************999999985555444 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.4
                                   EEEEES-HHHHHHHHHHHHHCT. CS
                   LAGLIDADG_3  27 isltssskelledvqrlLlrlGI 49 
                                   islt  +  + + vq l++++ I
  gi|15668213|ref|NP_247006.1| 692 ISLTIGKGIFTKAVQSLWEEF-I 713
                                   777888888889999999999.5 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.3e-06    0.0064       6      54 ..     556     611 ..     552     613 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.3e-06
                         PHP_C   6 rArrfAeklglpgtgGSDAH..rleeVGrayTefeepia.....tpdelleaireg 54 
                                   +A+ + e ++lp++ +SDAH  ++  +Gr ++++e +       +++++ +ai+  
  gi|15668213|ref|NP_247006.1| 556 MADMIPELRDLPFLSNSDAHsyHPHRLGREFNQIEVDYIggiedNFEQIKKAIKHN 611
                                   677777889***********88899*********6666666665669999999976 PP

>> Hint_2  Hint domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.4e-06    0.0077       2      45 ..     129     172 ..     128     207 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.4e-06
                        Hint_2   2 CflagtliatpeGevaveeLrvGdlVvtadgglqpvrwigsrtl 45 
                                   C  ++tl+  ++G  ++ +++vGd+V+t+++  ++v ++ +r++
  gi|15668213|ref|NP_247006.1| 129 CVPPDTLLILENGFKRIVDIKVGDKVLTHENRFKKVEKVYKRRY 172
                                   77899*************************************98 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.7e-06    0.0092       1     102 [.       6      99 ..       6     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.7e-06
                                   EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE............... CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           PHP   1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddsekerpshl 80 
                                   dlH+H+ +s +++  +++e+++k  k +gl  i+  D     +y+e++k+ k+++     +i+ +e      ++k+r +hl
  gi|15668213|ref|NP_247006.1|   6 DLHIHSRFSgGTSKDMNVENILKYGKLKGLNIIGTGDCT-HPDYLEEIKQYKDRE-----LILTTE-----IEDKNRVHHL 75 
                                   89********78799999************999977765.589*****9996555.....899999.....3345799999 PP

                                   .....E....EHHHHHHHHHHHHH CS
                                   xxx..xxxxxxxxxxxxxxxxxxx RF
                           PHP  81 tll..aknqeGyknllkllskayl 102
                                   +ll  +   e+++++lk+ sk+  
  gi|15668213|ref|NP_247006.1|  76 ILLpsISKVEELREILKKYSKDID 99 
                                   998444445557777777777654 PP

>> PT-HINT  Pretoxin HINT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   9.7e-05      0.12       6      71 ..     140     198 ..     135     204 .. 0.77
   2 ?    1.8   0.0      0.22   2.7e+02      72      87 ..     233     248 ..     218     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.7e-05
                       PT-HINT   6 dGykaiarikaGdrvlakdeasgkvaekpvlarygneyqelvylkisdgignsevlisnkihPfys 71 
                                   +G+k i  ik Gd+vl+++ + +k  ek    ry     +++ +k+       e +i + +hP y+
  gi|15668213|ref|NP_247006.1| 140 NGFKRIVDIKVGDKVLTHE-NRFKKVEKVYKRRYIG---DIIKIKVRY---FPEEIILTPEHPVYA 198
                                   79**************765.5677777777777754...678888887...667788888999986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.22
                       PT-HINT  72 kgkfieakelkvGdkl 87 
                                   k ++i ak+lkvGd +
  gi|15668213|ref|NP_247006.1| 233 KREWIIAKDLKVGDVI 248
                                   468**********976 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.3e-05     0.027      71      95 ..     629     656 ..     593     669 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                                   EEETTTS-EEECHH.H..HHS-TTTSSS CS
                          HypA  71 vrCreCgkefelee.k..alrCpkCgsa 95 
                                   + C++C+++f+le+ k  + +CpkCg++
  gi|15668213|ref|NP_247006.1| 629 TACSKCHTRFKLEDaKkyNWKCPKCGGS 656
                                   57*********887433567*****985 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7   6.3e-05     0.075      22      48 ..     640     666 ..     627     670 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-05
                       DUF4379  22 pgskkkvwWkCakCgheWeasvsnrtk 48 
                                       kk+ WkC+kCg + ++ v +r++
  gi|15668213|ref|NP_247006.1| 640 LEDAKKYNWKCPKCGGSIKKGVLSRVE 666
                                   56789************9999999984 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.5   7.1e-05     0.085       3      32 ..     629     654 ..     628     657 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-05
                 zinc_ribbon_5   3 irCpdCdtkFklvdsklKksgkkVrCakCa 32 
                                   + C +C t Fkl d k K +    +C kC+
  gi|15668213|ref|NP_247006.1| 629 TACSKCHTRFKLEDAK-KYNW---KCPKCG 654
                                   78**************.5553...677776 PP

>> EntA_Immun  Enterocin A Immunity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.14       5      40 ..      69     104 ..      65     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                    EntA_Immun   5 lnelynlildpeikeneelrevLltaknklekgknv 40 
                                    n++  lil p+i++ eelre+L +++++++k+  +
  gi|15668213|ref|NP_247006.1|  69 KNRVHHLILLPSISKVEELREILKKYSKDIDKEGRP 104
                                   688999*************************98766 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   0.00018      0.21       8      38 ..     631     659 ..     625     661 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                   Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgsevrr 38 
                                   C +C+++f    + +   + +CP+Cg+  ++
  gi|15668213|ref|NP_247006.1| 631 CSKCHTRFKLEDAKK--YNWKCPKCGGSIKK 659
                                   *********666433..3455*****98876 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.7   4.5e+03       2      20 ..     142     160 ..     142     163 .. 0.71
   2 ?   11.2   1.0   0.00019      0.23      25      51 ..     631     654 ..     620     657 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.7
                zinc_ribbon_10   2 fDrvldvLvGddetsaknr 20 
                                   f r++d+ vGd     +nr
  gi|15668213|ref|NP_247006.1| 142 FKRIVDIKVGDKVLTHENR 160
                                   679****9**988444444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00019
                zinc_ribbon_10  25 CskChshnGlapkeeleevkyrCpkCg 51 
                                   CskCh+ + l    ++++ +++CpkCg
  gi|15668213|ref|NP_247006.1| 631 CSKCHTRFKLE---DAKKYNWKCPKCG 654
                                   *******9887...999*********8 PP

>> DUF272  Protein of unknown function (DUF272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.8   5.7e+03      73      93 ..     159     180 ..     145     187 .. 0.62
   2 ?    9.0   0.1    0.0014       1.6      66     106 ..     574     614 ..     570     627 .. 0.90
   3 ?   -1.9   0.0         3   3.6e+03      20      49 ..     628     667 ..     619     677 .. 0.56
   4 ?    2.2   0.0      0.17     2e+02      27      60 ..     698     734 ..     689     748 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.8
                        DUF272  73 seerkypea.sakyfGkildkk 93 
                                   +  +k+ ++ + +y+G+i+  k
  gi|15668213|ref|NP_247006.1| 159 NRFKKVEKVyKRRYIGDIIKIK 180
                                   4444444441457999998655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                        DUF272  66 veqyqeaseerkypeasakyfGkildkknkLkkdcngkkik 106
                                   +++y++++  r++++++ +y+G i d+ +++kk  +++ki 
  gi|15668213|ref|NP_247006.1| 574 AHSYHPHRLGREFNQIEVDYIGGIEDNFEQIKKAIKHNKII 614
                                   678999**************************999988775 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3
                        DUF272  20 LelghfFegtFeekeng..kweckk........Yvkeiek 49 
                                   L+  +  +  F+ +  +  +w+c k         + ++e+
  gi|15668213|ref|NP_247006.1| 628 LTACSKCHTRFKLEDAKkyNWKCPKcggsikkgVLSRVEE 667
                                   5555555566665554434688888444444444444444 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.17
                        DUF272  27 egtFeekengkwe..ckkYvkeiekllegsv.knnki 60 
                                   +g+F++  ++ we   kkY +eie l++  + +  ki
  gi|15668213|ref|NP_247006.1| 698 KGIFTKAVQSLWEefIKKYGNEIEVLINADIdELSKI 734
                                   799****99988744699**********999655666 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2       1.1   1.4e+03       6      13 ..     223     230 ..     223     230 .. 0.92
   2 ?   13.9   2.1   3.2e-05     0.038       3      34 ..     629     656 ..     628     658 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                 zinc_ribbon_4   6 psCkakye 13 
                                   psCk++y+
  gi|15668213|ref|NP_247006.1| 223 PSCKKRYR 230
                                   89*****7 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.2e-05
                 zinc_ribbon_4   3 itCpsCkakyeiddeklpakgvkvrCskCghv 34 
                                   + C +C+++++++d    ak+ + +C+kCg +
  gi|15668213|ref|NP_247006.1| 629 TACSKCHTRFKLED----AKKYNWKCPKCGGS 656
                                   57************....68999******965 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00037      0.45      11     112 ..     128     248 ..     125     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX CS
                          Hint  11 gCFpgestvtvedgeqkslseLepGdkVlavdesgevvfsevllfldrdseqraefveieteng.ekltlTpaHLvfvsen 90 
                                    C p + +  +e+g  k++ ++++GdkVl+ ++     f++v     r  +   + ++i+ +   e++ lTp+H v++ ++
  gi|15668213|ref|NP_247006.1| 128 HCVPPDTLLILENG-FKRIVDIKVGDKVLTHENR----FKKVEKVYKR--RYIGDIIKIKVRYFpEEIILTPEHPVYAIKT 201
                                   69999999999999.78999*********99865....4555544444..4566788888887669999999999999888 PP

                                   XXXXXXXX.........................XXXXXXXXXXXXXX CS
                          Hint  91 ekssseee.........................eavfaskvregdyv 112
                                   ek+ + ++                         e + a++ + gd++
  gi|15668213|ref|NP_247006.1| 202 EKRCDGSHgickfncltqytnpsckkryrkykrEWIIAKDLKVGDVI 248
                                   77665544556666666666666666666665555566666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (785 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 5413.41
//
Query:       gi|15668214|ref|NP_247007.1|  [L=260]
Description: hypothetical protein MJ_0044 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-43  147.8   0.0    4.2e-43  147.7   0.0    1.0  1  AA_kinase     Amino acid kinase family
  ------ inclusion threshold ------
       0.17   11.7   0.0       0.27   11.0   0.0    1.4  1  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.7   0.0   4.7e-47   4.2e-43       1     226 [.       1     225 [.       1     236 [. 0.89

  Alignments for each domain:
  == domain 1  score: 147.7 bits;  conditional E-value: 4.7e-47
                                   TEEEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHT.......TEEEEEE--HHHHHHHHHHTCCCCCHHHC....E CS
                     AA_kinase   1 krvVvKlGGssltdkee......aslrrlaeqiaalkesg.......nklvvVhGggsftdgllalksglssgelaaglrs 68 
                                   +++++KlGGs+l+dk+       ++l+r+a +i+++           +kl++VhGgg+f++  ++++ ++++g+++     
  gi|15668214|ref|NP_247007.1|   1 MLTILKLGGSILSDKNVpysikwDNLERIAMEIKNALD-YyknqnkeIKLILVHGGGAFGHPVAKKYLKIEDGKKI----F 76 
                                   689*********************************44.45899999****************************9....9 PP

                                   ..HHHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEE CS
                     AA_kinase  69 tleeagevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigl 149
                                    + e+g+++ ++a+  ++ ++ + l+++ +pav+++++++ ++ ++            d++ai+e+l+++ vpv++g+i++
  gi|15668214|ref|NP_247007.1|  77 INMEKGFWEIQRAMRRFNNIIIDTLQSYDIPAVSIQPSSFVVFGDKL---------IFDTSAIKEMLKRNLVPVIHGDIVI 148
                                   *****************************************887666.........************************* PP

                                   ETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.......CSSS.TTTHHHHCH CS
                     AA_kinase 150 deegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.......saselatgGmkvkh 223
                                   d++++  ++s+D i  +lA++l+Ad ++++tdVdGV+ ++       +++++i+ + + +       s+s ++tgGmk k+
  gi|15668214|ref|NP_247007.1| 149 DDKNGYRIISGDDIVPYLANELKADLILYATDVDGVLIDN-------KPIKRIDKNNIYKilnylsgSNSIDVTGGMKYKI 222
                                   *****99*****************************7554.......4444444444444444787888**********98 PP

                                   HHH CS
                     AA_kinase 224 paa 226
                                   +  
  gi|15668214|ref|NP_247007.1| 223 DMI 225
                                   754 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     3e-05      0.27     181     232 ..      42     114 ..      26     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3e-05
                                   T....SEEEESGGGTT......................TTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHHCHHH CS
                  Amidohydro_2 181 n....lkivlaHgGgp......................serlraalellarrpnvyvklsglytellyfdspladppa 232
                                   n     k++l HgGg+                       ++++++ ++++r++n+ +++       +y +++++++p+
  gi|15668214|ref|NP_247007.1|  42 NqnkeIKLILVHGGGAfghpvakkylkiedgkkifinmEKGFWEIQRAMRRFNNIIIDTLQ-----SYDIPAVSIQPS 114
                                   555559****************************************************977.....777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1527.26
//
Query:       gi|15668215|ref|NP_247008.1|  [L=221]
Description: hypothetical protein MJ_0045 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.033   13.7   6.2      0.016   14.8   4.1    1.5  2  Terminase_3  Phage terminase large subunit


Domain annotation for each model (and alignments):
>> Terminase_3  Phage terminase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   4.1   8.7e-07     0.016      80     174 ..      42     140 ..      14     144 .. 0.79
   2 ?   -2.4   0.0      0.16   2.9e+03     109     157 ..     159     203 ..     157     212 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.7e-07
                   Terminase_3  80 skflFkglddpaklkSiknlsdlwlEEasevseedidelvetlr...apeqekqiilsfNPv.sesnwvykrffkddekek 156
                                   s f+ +g ++  +++S  ++  l  EE++e  ++d+d +++ lr   +++++ + + +   + ++++ +yk+f++d++ + 
  gi|15668215|ref|NP_247008.1|  42 SSFCAEGNKKGYNITSSDKIYNLKPEEIEEKCKKDLDFMEKHLRgmfKNNFNWNEFKTVDEWkKTRERTYKTFIEDYKTNR 122
                                   55899999999*********************************988777777777787755156899******8888666 PP

                   Terminase_3 157 dekddvlihkstyrdnef 174
                                   +    + + k+ ++d+ef
  gi|15668215|ref|NP_247008.1| 123 KRYIYTTYPKTNFKDDEF 140
                                   656788899999***999 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.16
                   Terminase_3 109 evseedidelvetlrapeqekqiilsfNPvsesnwvykrffkddekekd 157
                                   ++++e+idel+       +e +i+   N ++e+     + +k+++++++
  gi|15668215|ref|NP_247008.1| 159 QFHKETIDELLR----ISEEIRIFPILNLRGEKSIFLDKILKEYKARIE 203
                                   555555655542....235666666666666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1356.07
//
Query:       gi|15668216|ref|NP_247009.1|  [L=261]
Description: hypothetical protein MJ_0046 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-14   52.5   0.1    8.8e-14   51.5   0.1    1.6  1  Methyltransf_10  RNA methyltransferase
    3.6e-11   42.9   0.0    1.6e-10   40.8   0.0    1.8  2  MTS              Methyltransferase small domain
    1.1e-08   35.6   0.0    2.2e-08   34.7   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    3.2e-08   33.5   0.2    6.2e-08   32.6   0.2    1.5  1  Methyltransf_31  Methyltransferase domain
    1.3e-07   31.3   0.0      2e-07   30.7   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.1e-06   28.6   1.0      2e-06   27.8   0.0    1.8  2  Methyltransf_18  Methyltransferase domain
    5.1e-06   27.0   0.0      1e-05   26.1   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    5.8e-06   27.0   0.1    1.6e-05   25.6   0.0    1.7  2  Methyltransf_12  Methyltransferase domain
    6.7e-05   22.7   0.0    0.00011   22.0   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase
    0.00067   18.8   0.0     0.0012   17.9   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0015   17.9   0.7      0.012   15.0   0.7    2.1  1  Spermine_synth   Spermine/spermidine synthase domain
     0.0036   16.5   1.7     0.0052   16.0   0.1    1.8  2  Methyltransf_3   O-methyltransferase
     0.0079   15.8   0.0      0.014   15.1   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0099   15.6   0.0      0.016   14.9   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.012   15.5   0.1       0.03   14.2   0.1    1.7  1  YppF             YppF-like protein
      0.015   14.8   0.2       0.03   13.9   0.1    1.5  2  TrmK             tRNA (adenine(22)-N(1))-methyltransferase
      0.028   14.8   1.3      0.028   14.8   1.3    2.1  3  DUF4467          Domain of unknown function with cystatin-lik
      0.039   13.7   0.2      0.064   13.0   0.0    1.6  2  Met_10           Met-10+ like-protein
      0.062   13.1   0.0       0.12   12.2   0.0    1.6  2  N6-adenineMlase  Probable N6-adenine methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_10  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.1   9.3e-17   8.8e-14      23     195 ..      10     173 ..       5     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 9.3e-17
                                   HHHXHHHHTTXEEXTTSXEES-TTSHHHHHHHHHHHHHHHH----.---TTS----HHHHHHHHHHHHHHHTGGGSGTTS- CS
               Methyltransf_10  23 ikvvPelkqfvilnpkGrvsidfadPlavkalnkallrefygvsewdiPdgfliPpvPgradyihyvadllgkadsdisaq 103
                                   ik + +lk++v ++   +  i+f+d +a+  +nk++l+  +++ + +  ++ liP+   r  +i    + l +   +++  
  gi|15668216|ref|NP_247009.1|  10 IKYNEKLKKYVYKKG-DKLRINFKDKEALIEYNKTVLKVLFDLDI-EFHKNGLIPTPINRYLFIKSTFETLKELGIEKP-- 86 
                                   566778999998754.5889************************9.9*********999*9999999999988777765.. PP

                                   -EEEEES-TTTTHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHHT.T-TTTEEEEE--TT-SCCHHSSTTSS.-EEEEEE CS
               Methyltransf_10 104 vraldiGvGanCiyPllGvteyGWrfvgsevddvslasakaivesnsklsdaiklrkqkekkaifdglieene.rydvtlC 183
                                     +l+iG+G + i  ll ++ y  +  ++evd+  ++ ak+++e+n kl+  ik+   + k + ++g+ e ++ ++d+ + 
  gi|15668216|ref|NP_247009.1|  87 -TVLEIGTGHSAIISLLIKKFYNAEVYATEVDEEFIDFAKRNIEKN-KLD--IKI--INSKGRAIEGIEELKDkKFDLIIS 161
                                   .689******************************************.554..555..45667789***997666******* PP

                                   -S---SS----- CS
               Methyltransf_10 184 nPPfhaslaeak 195
                                    PPf++    a 
  gi|15668216|ref|NP_247009.1| 162 YPPFYSKNSVAS 173
                                   *****8776554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   1.7e-13   1.6e-10      29     112 ..      80     170 ..      73     178 .. 0.83
   2 ?   -0.7   0.0      0.96   9.1e+02     119     143 ..     199     223 ..     190     242 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.7e-13
                                   CC..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-.....STTTTSTTS-EEEEE CS
                           MTS  29 ke..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvas.....dvleeveekkfdliv 102
                                   +   ++ +vl +G+G  ++   l k+  +aev +++vd + +++ak+n+e+nkl++++++s     +++ee+++kkfdli+
  gi|15668216|ref|NP_247009.1|  80 ELgiEKPTVLEIGTGHSAIISLLIKKFYNAEVYATEVDEEFIDFAKRNIEKNKLDIKIINSkgraiEGIEELKDKKFDLII 160
                                   44445667********99999999999999*************************8887662222267899********** PP

                                   E---STTTCH CS
                           MTS 103 sNPPfhagka 112
                                   s PPf +++ 
  gi|15668216|ref|NP_247009.1| 161 SYPPFYSKNS 170
                                   *****98775 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.96
                                   HHHHHHHHHHEEEEEEEEEEEETTS CS
                           MTS 119 eeliaeAkeaLkegGeLliVanrkl 143
                                    ++i+e  ++L+++G + + + +k 
  gi|15668216|ref|NP_247009.1| 199 FKIIEEGINFLNKKGVISLMMPKKP 223
                                   5788999999999998887766554 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   2.3e-11   2.2e-08       1      71 [.      88     162 ..      88     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.3e-11
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS....SSTTTEEEEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp....fedgsfDlvvss 71 
                                   vL++G+G+  ++  l k++ +a+v++++++ee+++ a++++e+++l++++++ + ++++    ++d++fDl++s 
  gi|15668216|ref|NP_247009.1|  88 VLEIGTGHSAIISLLIKKFYNAEVYATEVDEEFIDFAKRNIEKNKLDIKIINSKGRAIEgieeLKDKKFDLIISY 162
                                   9*****************977*******************************9999986555579********94 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.2   6.5e-11   6.2e-08       6      85 ..      87     169 ..      84     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 6.5e-11
               Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlilsnevl 84 
                                   +vl++G+G ++++  l  + + +aev+  + +ee i +A+ n +k++ld  +  ++g + e +e+ l+d+kfDli+s  ++
  gi|15668216|ref|NP_247009.1|  87 TVLEIGTGHSAIISLLI-KKFYNAEVYATEVDEEFIDFAKRNIEKNKLDiKIINSKGRAIEgIEE-LKDKKFDLIISYPPF 165
                                   79***************.66679*************************96555555777777888.799*******97444 PP

               Methyltransf_31  85 ...n 85 
                                      n
  gi|15668216|ref|NP_247009.1| 166 yskN 169
                                   3333 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   2.1e-10     2e-07     153     232 ..      76     161 ..      70     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.1e-10
                          PrmA 153 ealeklvkegeevlDvGtG.SGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk......eek 226
                                   e+l +l  e+ +vl +GtG S+i+++  +k+  ++v+a+ +De  ++ ak+N+e+Nk++ k+ ++ ++++++      ++k
  gi|15668216|ref|NP_247009.1|  76 ETLKELGIEKPTVLEIGTGhSAIISLLIKKFYNAEVYATEVDEEFIDFAKRNIEKNKLDIKI-INSKGRAIEgieelkDKK 155
                                   566666677889*******99*************************************9988.555555552233344799 PP

                          PrmA 227 adviva 232
                                   +d+i++
  gi|15668216|ref|NP_247009.1| 156 FDLIIS 161
                                   999985 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   2.1e-09     2e-06      15      87 ..      85     160 ..      73     161 .. 0.84
   2 ?   -2.6   0.0       4.9   4.6e+03      96     123 ..     198     225 ..     193     245 .. 0.52

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.1e-09
               Methyltransf_18  15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkiev...rlsdGleklkeeevdtvv 87 
                                   + +v+ iGt H  +   l+k+    +v+a+++ e+ ++ ak+niek++l+ ki     r  +G+e+lk++++d ++
  gi|15668216|ref|NP_247009.1|  85 KPTVLEIGTGHSAIISLLIKKFYNAEVYATEVDEEFIDFAKRNIEKNKLDIKIINskgRAIEGIEELKDKKFDLII 160
                                   568999*******************************************998866111555677777777788775 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.9
               Methyltransf_18  96 ileILeeakeklkkikklilqpnseaee 123
                                     +I+ee+ + l+k   + l   ++ e+
  gi|15668216|ref|NP_247009.1| 198 SFKIIEEGINFLNKKGVISLMMPKKPEK 225
                                   5566666655555443333333333333 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.1e-08     1e-05       1      68 [.      89     162 ..      89     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.1e-08
                                   EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC...T.SS-TT-EEEEEEE CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaek...l.pfednsfDlvvss 68 
                                   L++G+G  ++   l k++  a+v+++++++e+++ ak+++++++l ++++ +  +    +  ++d++fDl++s+
  gi|15668216|ref|NP_247009.1|  89 LEIGTGHSAIISLLIKKFynAEVYATEVDEEFIDFAKRNIEKNKLDIKIINSKGRAiegIeELKDKKFDLIISY 162
                                   89****9999999996666*************************977776665554223556*********985 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       8.9   8.4e+03      32      56 ..       9      32 ..       7      41 .. 0.74
   2 !   25.6   0.0   1.7e-08   1.6e-05       1      72 [.      89     161 ..      89     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.9
               Methyltransf_12 32 aiedakeklakrennnnnnveleal 56
                                  ai +  ekl+k+  ++ ++++++ +
  gi|15668216|ref|NP_247009.1|  9 AI-KYNEKLKKYVYKKGDKLRINFK 32
                                  67.7889999998888888777655 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 1.7e-08
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg...ssfDlvva 72 
                                   LeiG+G +++++ l +k+ ++e++++++++++i+ ak+ + k++ ++ + ++ + + ++   ++   ++fDl+++
  gi|15668216|ref|NP_247009.1|  89 LEIGTGHSAIISLLIKKFYNAEVYATEVDEEFIDFAKRNIEKNK-LDIKIINSKGRAIEGI-EElkdKKFDLIIS 161
                                   8********************************77777777766.5666555554443322.224669*****96 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.2e-07   0.00011      36     135 ..      74     170 ..      64     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.2e-07
               Methyltransf_16  36 lakelganelsklsvlELGsG.tGlvGlavaellpeakviltDlee.llellkknielnknalkskvkvevLdWgeeleed 114
                                   ++++l++   +k +vlE+G G + ++ l +++   +a+v+ t ++e  +++ k+nie nk  l+ k+  ++    e + e+
  gi|15668216|ref|NP_247009.1|  74 TFETLKELGIEKPTVLEIGTGhSAIISLLIKKF-YNAEVYATEVDEeFIDFAKRNIEKNK--LDIKIINSKGRAIEGI-EE 150
                                   3445777789999********446888888888.89*******98779**********88..9999988888888888.55 PP

               Methyltransf_16 115 llekeevDlilaaDcvYleds 135
                                   l + +++Dli+     Y ++s
  gi|15668216|ref|NP_247009.1| 151 L-KDKKFDLIISYPPFYSKNS 170
                                   5.6677999998766666655 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.3e-06    0.0012      29     144 ..      81     226 ..      67     229 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                                   G..TTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-CCGHHHHHHHCT........ CS
                        RrnaAD  29 e..ekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls.kdeklkvvhqDflkfetpeevte........ 96 
                                      ek tvleig+G  +    L k +   +v + E de+++ + + +++ ++  +k+++  +   e  ee+ +        
  gi|15668216|ref|NP_247009.1|  81 LgiEKPTVLEIGTGHSAIISLLIKKFynAEVYATEVDEEFIDFAKRNIEkNKLDIKIINSKGRAIEGIEELKDkkfdliis 161
                                   246899**********99999999998999****************9996667899*****99999999998888888888 PP

                                   ..................TTCCCCEEEEEEE--TTTHHHHHHHHHH.GGGGCEEEEEEEEEHHHHHH CS
                        RrnaAD  97 ..................kdsihqeflvvanlPyeistqlvkqlle.esrfglvkmllwlqkefarr 144
                                                      + ++ e++  +    e s +++   ++ +++  +  + l+++k++ +r
  gi|15668216|ref|NP_247009.1| 162 yppfysknsvasgrkfggALAKNVELIGGGKFGEEFSFKIIEEGINfLNK--KGVISLMMPKKPEKR 226
                                   88888877666666665555555555555555555555555555542222..346777777777766 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.7   1.3e-05     0.012      22     148 ..      88     235 ..      76     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                   EEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTT...............CGGCTTEEEEESTCHHHHC CS
                Spermine_synth  22 vLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslais...............afndarvklvlgdgfkflk 87 
                                   vL iG g   ++  ++k     ++   ++D++ idf k+++ + + +                ++d++++l++     + k
  gi|15668216|ref|NP_247009.1|  88 VLEIGTGHSAIISLLIKKFYNAEVYATEVDEEFIDFAKRNIEKNKLDikiinskgraiegieELKDKKFDLIISYPPFYSK 168
                                   677777777777777664444899999***************99988889***********99********9998776766 PP

                                   TCSS...-E..EEEEEECCSTTCSSCGCSSHHHHHHHHHTEEEEEEEEEEE.EETTTCHHHHHHHHH CS
                Spermine_synth  88 ayek...kf..dvvivdsldpvgpaenlFskeffdllkkvlkedGviilqa.ekpelekelvinvdk 148
                                   +  +   kf  +  ++++l   g+  ++Fs+++++  ++ l++ Gvi+l   +kpe  +el+i+  k
  gi|15668216|ref|NP_247009.1| 169 NSVAsgrKFggALAKNVELIGGGKFGEEFSFKIIEEGINFLNKKGVISLMMpKKPEKRRELIIKKMK 235
                                   666689977446777777778888899*********************9999*****9999987655 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       0.8   7.6e+02      86     113 ..      14      41 ..       4      55 .. 0.67
   2 !   16.0   0.1   5.5e-06    0.0052      50     128 ..      87     160 ..      76     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.8
                                   HHHHHHHHHTT-GGGEEEEES-HHHHHH CS
                Methyltransf_3  86 eialkfiqkagvaekieliegdalkvLe 113
                                   e  +k++ k g + +i+++  +al   +
  gi|15668216|ref|NP_247009.1|  14 EKLKKYVYKKGDKLRINFKDKEALIEYN 41 
                                   4456777777777888888777765444 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 5.5e-06
                                   EEEEE--TTSHHHHHHHT.TS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSSS---EEEEE CS
                Methyltransf_3  50 rvleiGvftGyslLatal.alPeDGkilaididreayeialkfiqkagvaekieliegdalkvLeelvkdkklpefDfif 128
                                    vleiG  tG+s++   l +   + ++ a ++d+e  + a++ i+k  ++ ki   +g a + +eel+++k    fD+i 
  gi|15668216|ref|NP_247009.1|  87 TVLEIG--TGHSAIISLLiKKFYNAEVYATEVDEEFIDFAKRNIEKNKLDIKIINSKGRAIEGIEELKDKK----FDLII 160
                                   589999..699987654415567899****************************************98777....99985 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.5e-05     0.014      32     128 ..      74     170 ..      70     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                   HHHHHCCC.HCC-EEEETT-TTSHHHHHHHHT.T-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--S CS
                 Cons_hypoth95  32 lFnilaae.iegarvLDlfaGsGalglEAlSR.gakkavlvekdkeavkilkenleelkleeetaelkedaleallklakk 110
                                    F++l++  ie+ +vL++  G  a+    +   + +++++ e d+e +   k+n+e+ kl+ ++ + k  a e +++l  k
  gi|15668216|ref|NP_247009.1|  74 TFETLKELgIEKPTVLEIGTGHSAIISLLIKKfYNAEVYATEVDEEFIDFAKRNIEKNKLDIKIINSKGRAIEGIEEL--K 152
                                   5666666666777777776665554333333314578999*******************9998999999999999999..8 PP

                                   S-EEEEEEE--SSSTTCH CS
                 Cons_hypoth95 111 keefdivflDPPyakell 128
                                   +++fd++   PP+ +++ 
  gi|15668216|ref|NP_247009.1| 153 DKKFDLIISYPPFYSKNS 170
                                   899*********988764 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.7e-05     0.016      75     131 ..     107     165 ..      90     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                                   HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--.GGG--.STTS---EEEE---- CS
                       UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqad.aakLr.lkegevdvivtnpPY 131
                                   +++++y+ + d++ ++ a++N ek +++ +i  s+   +  ++ lk++++d+i++ pP+
  gi|15668216|ref|NP_247009.1| 107 YNAEVYATEVDEEFIDFAKRNIEKNKLDIKIINSKGRaIEGIEeLKDKKFDLIISYPPF 165
                                   56789**********************977766665515678876777**********8 PP

>> YppF  YppF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   3.1e-05      0.03       4      40 ..     100     136 ..      98     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                          YppF   4 neLkkkFiavkkYepesaneLLDFarklYlqgeisia 40 
                                   + L kkF +   Y++e  +e +DFa++   +++++i+
  gi|15668216|ref|NP_247009.1| 100 SLLIKKFYNAEVYATEVDEEFIDFAKRNIEKNKLDIK 136
                                   56889***********************999999985 PP

>> TrmK  tRNA (adenine(22)-N(1))-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   3.2e-05      0.03       2      64 ..      89     151 ..      88     160 .. 0.87
   2 ?   -3.5   0.0       6.7   6.3e+03      82      94 ..     200     212 ..     193     234 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
                          TrmK   2 aDiGsDHAyLpiylvknnkvsvaiagevnegplesAkknvkkskleekievrlgdGlavleke 64 
                                   + iG+ H+ +   l+k+     + a ev e   + Ak+n++k+kl  ki + +g  ++ +e+ 
  gi|15668216|ref|NP_247009.1|  89 LEIGTGHSAIISLLIKKFYNAEVYATEVDEEFIDFAKRNIEKNKLDIKIINSKGRAIEGIEEL 151
                                   68***********************************************99888777776653 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.7
                          TrmK  82 eILeegkekLkkv 94 
                                   +I+eeg ++L+k+
  gi|15668216|ref|NP_247009.1| 200 KIIEEGINFLNKK 212
                                   4555555555443 PP

>> DUF4467  Domain of unknown function with cystatin-like fold (DUF4467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.3     3e-05     0.028       4      38 ..       5      39 ..       4      54 .. 0.90
   2 ?   -2.8   0.1       8.6   8.2e+03      36      36 ..     134     134 ..     112     157 .. 0.57
   3 ?   -2.2   0.2       5.7   5.3e+03      16      41 ..     231     257 ..     221     260 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-05
                       DUF4467  4 eidkvvkiqekkqqklakkgndvevdikkedanvy 38
                                  +i++++k  ek ++++ kkg++ ++++k ++a + 
  gi|15668216|ref|NP_247009.1|  5 KIEDAIKYNEKLKKYVYKKGDKLRINFKDKEALIE 39
                                  69***************************999875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.6
                       DUF4467  36 n 36 
                                    
  gi|15668216|ref|NP_247009.1| 134 D 134
                                   2 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.7
                       DUF4467  16 qqklakkgndvevd.ikkedanvyVye 41 
                                    +k++ +g dvevd ik  +  +y+ +
  gi|15668216|ref|NP_247009.1| 231 IKKMKEVGLDVEVDeIKTGNRLRYIIK 257
                                   466777777888887887777777655 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       7.3   6.9e+03      15      31 ..      34      50 ..      17      54 .. 0.65
   2 ?   13.0   0.0   6.8e-05     0.064     115     170 ..     100     153 ..      84     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 7.3
                                  -TTSSHHHHHHHHHHHH CS
                        Met_10 15 reelkeykkvigevild 31
                                  +e l ey+k++ +v++d
  gi|15668216|ref|NP_247009.1| 34 KEALIEYNKTVLKVLFD 50
                                  44566777777777766 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.8e-05
                                   HHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.TT-EE CS
                        Met_10 115 aipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.eqlad 170
                                   ++ i+k+ +a+ v+a +++ e + + k+ni+ Nk++ ++  i++ gr +   e+l d
  gi|15668216|ref|NP_247009.1| 100 SLLIKKFYNAE-VYATEVDEEFIDFAKRNIEKNKLDIKI--INSKGRAIEGiEELKD 153
                                   44577766665.***********************9777..8888888776544444 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       8.1   7.7e+03      50      62 ..      44      56 ..      34      58 .. 0.69
   2 ?   12.2   0.0   0.00013      0.12       8     116 ..      68     183 ..      64     234 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.1
               N6-adenineMlase 50 ekvlLleiDkrFe 62
                                     +L+++D  F+
  gi|15668216|ref|NP_247009.1| 44 VLKVLFDLDIEFH 56
                                  4567999998885 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
               N6-adenineMlase   8 fwysdetaealakelleeeeskkiaclsaP..svyealkkek.kkekvlLleiDkrFealygeekfvfYdlnnpe.elp.. 82 
                                   +++ ++t e+l++    + e+ +++ +++    + + l k k  + +v+  e+D+ F  ++++      ++++++ +++  
  gi|15668216|ref|NP_247009.1|  68 YLFIKSTFETLKEL---GIEKPTVLEIGTGhsAIISLLIK-KfYNAEVYATEVDEEFIDFAKR------NIEKNKlDIKii 138
                                   78888888888888...43344566676653123333333.2467899999999999666444......444444334444 PP

               N6-adenineMlase  83 ..........eel.kgkfdviviDPPFlseeclkklaktaklllk 116
                                             eel ++kfd+i+  PPF s++ + + +k    l+k
  gi|15668216|ref|NP_247009.1| 139 nskgraiegiEELkDKKFDLIISYPPFYSKNSVASGRKFGGALAK 183
                                   5666777777777799***********999887776655555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       967  (0.053935); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1610.65
//
Query:       gi|15668217|ref|NP_247010.1|  [L=428]
Description: putative mRNA 3'-end processing factor 1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-18   65.2   0.0    1.2e-17   64.2   0.0    1.5  1  Beta-Casp        Beta-Casp domain
    2.9e-12   46.4   0.2    5.6e-12   45.5   0.2    1.4  1  Lactamase_B_6    Metallo-beta-lactamase superfamily domain
    1.4e-11   44.8   0.1    1.2e-10   41.7   0.1    2.1  1  Lactamase_B      Metallo-beta-lactamase superfamily
    6.6e-08   32.3   0.1    1.6e-07   31.0   0.0    1.7  2  Lactamase_B_2    Beta-lactamase superfamily domain
      1e-07   31.7   0.0    2.4e-07   30.6   0.0    1.7  1  RMMBL            Zn-dependent metallo-hydrolase RNA specifici
    0.00016   21.0   0.7    0.00016   21.0   0.7    2.2  2  Beta_lactamase3  Putative beta-lactamase-like family
    0.00084   19.3   0.2     0.0043   17.0   0.1    2.2  3  Lactamase_B_3    Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   4.7e-21   1.2e-17       1     110 []     234     348 ..     234     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 4.7e-21
                                   HHHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG...........E-SHH.....HHH.H...HHHS-SSEE CS
                     Beta-Casp   1 aqellylLeelwkekkledlklpiyldsplaskatevYkeyae...........veaks.lewmesk.ke.elnsskgpkv 67 
                                   aqe+l++L+++  +       +piyld+ +a ++t++  +y++            ++ + +e  e++ k  e n sk+  +
  gi|15668217|ref|NP_247010.1| 234 AQEILLILNDYNID-------APIYLDG-MAVEVTKLMLNYKHmlnessqlekaLKNVKiIEKSEDRiKAiE-NLSKNGGI 305
                                   6**********955.......59*****.********99999999999999988555555666677765544.577899** PP

                                   EEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                     Beta-Casp  68 ilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                   ++++ gml+gG++ ++lk ++++p+n+++l+gyq++++ gr+l
  gi|15668217|ref|NP_247010.1| 306 VVTTAGMLDGGPILYYLKLFMHNPKNALLLTGYQVRDSNGRHL 348
                                   *****************************************97 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.2   2.2e-15   5.6e-12       3     176 ..      20     180 ..      18     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 2.2e-15
                 Lactamase_B_6   3 eldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvsl 83 
                                   + d+ kiLlD+G++  k ++      l++ i +vd + +sha l+h Ga+++l+++      +++pv +t   +kL +v+l
  gi|15668217|ref|NP_247010.1|  20 KTDKSKILLDCGVKLGK-EI--EYPILDNSIRDVDKVFISHAHLDHSGALPVLFHR-----KMDVPVITTELSKKLIKVLL 92 
                                   7899*********9652.23..467899*********************9988754.....469***************** PP

                 Lactamase_B_6  84 ldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWki.skesekivYavdwn 163
                                    d ++ ++++   ++   + +d++ea  + ++l Y+ k+  k    + +   ++aGh +G +   +  ++ ++i+Y  d+ 
  gi|15668217|ref|NP_247010.1|  93 KDMVKIAETE--NKKIPYNNHDVKEAIRHTIPLNYNDKKYYK----DFSYELFSAGHIPGSASILLnYQNNKTILYTGDVK 167
                                   **98876554..445567889****************96555....5677779*******9988883467889***99998 PP

                 Lactamase_B_6 164 hakeshLngaall 176
                                    +  ++ +ga+l+
  gi|15668217|ref|NP_247010.1| 168 LRDTRLTKGADLS 180
                                   7777776777765 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.1   4.7e-14   1.2e-10       5     152 ..      13     167 ..      10     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 4.7e-14
                                   SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCH CS
                   Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfme 85 
                                   + +++ i +d++ iL D+G+   ++ +      l+  ++dvd v+++H+HlDH G+l+ l ++   ++++  e  ++l++ 
  gi|15668217|ref|NP_247010.1|  13 GRSCIEIKTDKSKILLDCGVKLGKEIEY---PILDNSIRDVDKVFISHAHLDHSGALPVLFHRKMDVPVITTELSKKLIKV 90 
                                   56788899*******************7...5**********************************999999999998888 PP

                                   HHHHHHHHCCHH.........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE.TTCCEEEECTTT CS
                   Lactamase_B  86 eaddaasrkgll.........lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey.gggkvlftGDal 152
                                    ++d     + +         +  + +++ ++    +  +  +     +  g+ +g+ ++ + y  ++++l+tGD+ 
  gi|15668217|ref|NP_247010.1|  91 LLKDMVKIAETEnkkipynnhDVKEAIRHTIPLNYNDKKYYKDFSYELFSAGHIPGSASILLNYqNNKTILYTGDVK 167
                                   88665555554476667776655555555555555555555555556666666666666666664555666666665 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   6.3e-11   1.6e-07       2     149 ..      25     178 ..      24     214 .. 0.74
   2 ?   -3.1   0.0       1.8   4.5e+03     178     200 ..     375     397 ..     371     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 6.3e-11
                                   EEEES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEE...HHHHHHCCTTCGHHH CS
                 Lactamase_B_2   2 riLiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyap...kgvlavleanfvyla 78 
                                    iL+D+g  l +  + + l      ++++++d V+++haH DH   l+ l + r+ ++p++ +   k++++vl + +v +a
  gi|15668217|ref|NP_247010.1|  25 KILLDCGVKLGKEiEYPIL-----DNSIRDVDKVFISHAHLDHSGALPVLFH-RKMDVPVITTelsKKLIKVLLKDMVKIA 99 
                                   59*******9888666666.....8899****************99999999.4557998866566888888888888888 PP

                                   CHTTTTEEEEEE-TTSEEEE............CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE.CTTEEEEEESS-S-- CS
                 Lactamase_B_2  79 leeepavnvheldwgesfel............gdggleitatparhksgrrldrnagdtlGlrie.gggkrvyyigDtgyi 146
                                     e+++++ +  d +e ++             +  +++ +++ a h  g          ++ ++  +++k+++y+gD++  
  gi|15668217|ref|NP_247010.1| 100 ETENKKIPYNNHDVKEAIRHtiplnyndkkyyK--DFSYELFSAGHIPGS---------ASILLNyQNNKTILYTGDVKLR 169
                                   887767777777766666665577887777654..566888877777777.........8888888999999999999966 PP

                                   -......HH CS
                 Lactamase_B_2 147 p......ee 149
                                   +      ++
  gi|15668217|ref|NP_247010.1| 170 DtrltkgAD 178
                                   632323333 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.8
                                   ---STSHHHHCTTSSSSEEEEES CS
                 Lactamase_B_2 178 HltpeeaveaaadlgakrlvliH 200
                                   H+ ++e  e++++++++ l+  H
  gi|15668217|ref|NP_247010.1| 375 HAGMDELHEIIKKVNPELLIIQH 397
                                   999999999*****999999887 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   9.3e-11   2.4e-07       5      62 .]     364     420 ..     360     420 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 9.3e-11
                         RMMBL   5 karieeidfSgHadknellelirklkprnvilvHGeeeatsalarllkeeegidvfiP 62 
                                   ++++  ++fS Ha+ +el e+i+k++p+ +i+ HGee ++  l++++  e g d+++P
  gi|15668217|ref|NP_247010.1| 364 NLEVCMYNFSCHAGMDELHEIIKKVNPELLIIQHGEEVQATILRNWA-LEHGFDAITP 420
                                   66777899***************************************.9999999998 PP

>> Beta_lactamase3  Putative beta-lactamase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.7   6.1e-08   0.00016      47     180 ..      36     169 ..       9     198 .. 0.80
   2 ?    0.4   0.1      0.13   3.3e+02      80     123 ..     247     290 ..     233     306 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.1e-08
               Beta_lactamase3  47 kklkleiikvkaenidkifvts.....snslgifFl.kkdvpiYiTkpvYeqlllrlkellslqvvyeeeeekqdlkivee 121
                                   k+++  i      ++dk+f+++     s +l ++F  k dvp+  T+   + +++ lk+++++   +e++++     + ++
  gi|15668217|ref|NP_247010.1|  36 KEIEYPILDNSIRDVDKVFISHahldhSGALPVLFHrKMDVPVITTELSKKLIKVLLKDMVKIAE-TENKKI-----PYNN 110
                                   56777777778889999999963333378******83569**98888888888889999888764.344444.....5788 PP

               Beta_lactamase3 122 idierlkrnvkfiryneliyfddltieakaagtflGWvnyllevekkkilayisslslk 180
                                    d++++ r+ +  +yn+  y +d++ e  +ag   G    ll+ +++k++ y+  + l+
  gi|15668217|ref|NP_247010.1| 111 HDVKEAIRHTIPLNYNDKKYYKDFSYELFSAGHIPGSASILLNYQNNKTILYTGDVKLR 169
                                   999999**********************************************9888765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.13
               Beta_lactamase3  80 dvpiYiTkpvYeqlllrlkellslqvvyeeeeekqdlkiveeid 123
                                   d piY+     e  +l l++ + l+  ++ e+  +++ki+e+++
  gi|15668217|ref|NP_247010.1| 247 DAPIYLDGMAVEVTKLMLNYKHMLNESSQLEKALKNVKIIEKSE 290
                                   44566655555555555555555666666666667888887654 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.7e-06    0.0043       6     115 ..      13     167 ..      12     208 .. 0.60
   2 ?   -0.3   0.0      0.34   8.6e+02       9      52 ..     149     201 ..     142     225 .. 0.56
   3 ?   -2.8   0.0         2     5e+03     143     160 ..     377     394 ..     374     397 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.7e-06
                 Lactamase_B_3   6 ghnsflletagarilvDPfka.nlgyeppa.....eeaDlvlisqaledHahletl.kqlaenvkvlee...........g 68 
                                   g +++ ++t+  +il+D + + +++ e+p      +++D v is+a+ dH  + ++    + +v+v+++           +
  gi|15668217|ref|NP_247010.1|  13 GRSCIEIKTDKSKILLDCGVKlGKEIEYPIldnsiRDVDKVFISHAHLDHSGALPVlFHRKMDVPVITTelskklikvllK 93 
                                   89***************986443333333377999***************8654431333667777777444444444443 PP

                 Lactamase_B_3  69 eslevggleiravatsh...........................davggsergenngflleqdgltiyhlGhla 115
                                   + ++++++e ++++ ++                             + g+ +g  ++ l  q++ ti++ G++ 
  gi|15668217|ref|NP_247010.1|  94 DMVKIAETENKKIPYNNhdvkeairhtiplnyndkkyykdfsyeLFSAGHIPGSASILLNYQNNKTILYTGDVK 167
                                   33555555555555555233223333333333333333222222223334446666666666666666666655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.34
                 Lactamase_B_3   9 sflleta.garilvDPf..........kanlgyeppaeeaDlvlisqaledHahl 52 
                                   s+ll+ + +++il   +          ++++++ + ++++D+++i +   +  h+
  gi|15668217|ref|NP_247010.1| 149 SILLNYQnNKTILY--TgdvklrdtrlTKGADLSYTKDDIDILIIESTYGNSIHP 201
                                   44444321233332..123444444432245555556777777776666555555 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2
                 Lactamase_B_3 143 gqeealelakrLkpklvl 160
                                   g +e +e++k+++p+l +
  gi|15668217|ref|NP_247010.1| 377 GMDELHEIIKKVNPELLI 394
                                   6789999*******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2729.80
//
Query:       gi|15668218|ref|NP_247011.1|  [L=105]
Description: hypothetical protein MJ_0047.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 703.43
//
Query:       gi|15668219|ref|NP_247012.1|  [L=228]
Description: translation initiation factor IF-6 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-63  214.2   2.2    1.3e-63  214.0   2.2    1.0  1  eIF-6     eIF-6 family


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.0   2.2   7.2e-68   1.3e-63       3     197 .]       8     207 ..       6     207 .. 0.98

  Alignments for each domain:
  == domain 1  score: 214.0 bits;  conditional E-value: 7.2e-68
                                   -BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHHHHH CS
                         eIF-6   3 siegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeeleklkesl 83 
                                    ++g ++iGv a +t++++l+p  ++++ v++++e+L++++++t+i+gs+lvGsl v+N+ gll+p++v+deel+++k+ l
  gi|15668219|ref|NP_247012.1|   8 YFSGIPTIGVLALTTEEITLLPIFLDKDDVNEVSEVLETKCLQTNIGGSSLVGSLSVANKYGLLLPKIVEDEELDRIKNFL 88 
                                   58899**************************************************************************99 PP

                                   H.....---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE-TT-- CS
                         eIF-6  84 k.....leverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvhpkat 159
                                   k     l+ve++++k tAlGN+il+NDk+Al++p+l++  ++ i+d L+vev+ gtia+++tvGs avvtnkg+l+hp ++
  gi|15668219|ref|NP_247012.1|  89 KennldLNVEIIKSKNTALGNLILTNDKGALISPELKD-FKKDIEDSLNVEVEIGTIAELPTVGSNAVVTNKGCLTHPLVE 168
                                   998888999***************************98.99**************************************** PP

                                   HHHHHHHHHHHT-S.EEE--BTTTBS-GGGTEEE-SS-E CS
                         eIF-6 160 eeeleeleellkve.veagTvNrGsklvgsglvaNdkga 197
                                   ++ele+l++l+kve + +gT N+G++ vg++++aN+kga
  gi|15668219|ref|NP_247012.1| 169 DDELEFLKSLFKVEyIGKGTANKGTTSVGACIIANSKGA 207
                                   **************9**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1796.79
//
Query:       gi|15668220|ref|NP_247013.1|  [L=87]
Description: 50S ribosomal protein L31e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-18   66.3   2.8    2.5e-18   66.1   2.8    1.0  1  Ribosomal_L31e  Ribosomal protein L31e


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   2.8   1.4e-22   2.5e-18       5      70 ..       9      74 ..       6      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 1.4e-22
                Ribosomal_L31e  5 reytInihkrihgvgfkkraprAlkeikkfamkemgtpdvridtrLnkavwakgirnvpyrirvrl 70
                                  r ytI +   i +  ++kraprA+k+ik+f +++m+ + v+id++Ln+ +w++gi+++p+r+rv+ 
  gi|15668220|ref|NP_247013.1|  9 RIYTIPLRDVINKSVRTKRAPRAIKKIKQFLKRHMKAEIVKIDNELNEKIWERGIQKPPARVRVKA 74
                                  569*************************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 550.31
//
Query:       gi|15668221|ref|NP_247014.1|  [L=396]
Description: L-tyrosine decarboxylase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-28   98.7   0.0    4.2e-28   98.1   0.0    1.1  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    4.6e-10   39.2   0.1    0.00044   19.5   0.0    2.1  2  Aminotran_1_2    Aminotransferase class I and II
    3.7e-09   36.0   0.0    6.8e-08   31.9   0.0    2.1  2  Aminotran_5      Aminotransferase class-V
     0.0001   21.7   0.0    0.00015   21.2   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0026   16.5   0.1      0.019   13.6   0.0    2.0  2  Aminotran_3      Aminotransferase class-III
  ------ inclusion threshold ------
      0.022   14.7   0.1      0.085   12.8   0.0    2.0  3  Phage_Gp15       Bacteriophage Gp15 protein
      0.033   13.5   0.0      0.097   12.0   0.0    1.7  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.034   14.5   1.1        2.1    8.7   0.1    3.3  2  Radical_SAM      Radical SAM superfamily
      0.051   13.9   0.2       0.68   10.3   0.1    2.5  2  YqaH             Uncharacterized YqaH-like


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.0   2.1e-31   4.2e-28      93     369 ..      82     339 ..      66     343 .. 0.87

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 2.1e-31
                                   T--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHHHCCEEEEEETTS-HHHHHHHHHHT-EEEEE- CS
                 Pyridoxal_deC  93 glpeeflekegggvlqvgssestllallAartkvikemkekgkelkeaeildklvlytsdqahssvekaalvlgvklrvip 173
                                   +      +k++ g + +g++e++l+al  +++ ++++ ++   +      ++ + +     ah s ek  ++++++ ++ p
  gi|15668221|ref|NP_247014.1|  82 N------NKDAYGHIVSGGTEANLMALRCIKNIWREKRRKGLSK------NEHPKIIVPITAHFSFEKGREMMDLEYIYAP 150
                                   3......33688999****************9998765544433......78999999999******************** PP

                                   -BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEEE-TTGGGGGGSGGGGG..GGT CS
                 Pyridoxal_deC 174 ldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHvDAAyaGsaficpeirh..llk 252
                                   ++e++++  +  + a+e+ +  G i      ++Gtt lg  d+++el +i ++ ++ +HvDAA++G  ++ p+     + k
  gi|15668221|ref|NP_247014.1| 151 IKEDYTIDEKFVKDAVEDYDVDGIIG-----IAGTTELGTIDNIEELSKIAKENNIYIHVDAAFGG--LVIPFLDDkyKKK 224
                                   *****999999***********8877.....9**********************************..9999999888788 PP

                                   TGGG.......ESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TTTTTSEECCCGSSSSSG.HHTHHHHHH CS
                 Pyridoxal_deC 253 gier.......adSitvnphKlllvlldcsalivkdkealqqalqleaeYLehedsdvaadlgtkaiplsr.rvrilklwf 325
                                   g+++       +dSit+ phK++  ++  + +++kd +  ++ l ++a YL         ++++ +i   r  +  +  + 
  gi|15668221|ref|NP_247014.1| 225 GVNYkfdfslgVDSITIDPHKMGHCPIPSGGILFKDIGY-KRYLDVDAPYLT--------ETRQATILGTRvGFGGACTYA 296
                                   888666666679************************885.88999******9........7889999999999******** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEECSTTBSSE CS
                 Pyridoxal_deC 326 vlralGveglqnqirksvelakyleklirkderfeivaevelgl 369
                                   vlr lG+eg ++ +++++e+  yl+k+++++ +f+ v e+ l  
  gi|15668221|ref|NP_247014.1| 297 VLRYLGREGQRKIVNECMENTLYLYKKLKEN-NFKPVIEPILNI 339
                                   ***************************9875.566666665555 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.2e-07   0.00044      45     195 ..      65     214 ..      56     228 .. 0.82
   2 !   17.7   0.0   8.2e-07    0.0016     278     362 ..     310     389 ..     291     390 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.2e-07
                                   HHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH............HTTT-EEEEEESS-THHHHHHHHT CS
                 Aminotran_1_2  45 glpeleealakflgrseklklkreaavvvgsGagaliealifllk............lnpgdeilvpdptyasyknilrls 113
                                   g + lee+   +lg    l+ +++a     sG ++++ ++ +++k            +n + +i+vp   + s++++ +++
  gi|15668221|ref|NP_247014.1|  65 GTKLLEEKAVALLG--SLLN-NKDAYGHIVSGGTEANLMALRCIKniwrekrrkglsKNEHPKIIVPITAHFSFEKGREMM 142
                                   66777788888888..3333.33334555666666777777888889999999999999********************** PP

                                   TSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCB CS
                 Aminotran_1_2 114 ggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfv 194
                                   ++e ++ p++  ed+++d + +++a+++         +i +++     Gt+ + eel k+   ak++n+++ vD a++g+v
  gi|15668221|ref|NP_247014.1| 143 DLEYIYAPIK--EDYTIDEKFVKDAVEDYD--VD--GIIGIAG-TTELGTIDNIEELSKI---AKENNIYIHVDAAFGGLV 213
                                   ********99..***************954..33..3355555.4579************...****************99 PP

                                   S CS
                 Aminotran_1_2 195 f 195
                                    
  gi|15668221|ref|NP_247014.1| 214 I 214
                                   7 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 8.2e-07
                                   HHHHHHHHHHHHHHHHHSTEEEECCS.CSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEEC.TTS-HHHH CS
                 Aminotran_1_2 278 rqrlqkrrkelrdeLaelglkvlasq.sgmflltdlsaetakelskkLleevgvyvtpgtsftvpgrlRitv.Aglteeel 356
                                   + +  +++ +l+++L+e ++k ++++  +++ + d +    ke++kkL+++ g+yv+    + + + lRi v ++ ++e +
  gi|15668221|ref|NP_247014.1| 310 VNECMENTLYLYKKLKENNFKPVIEPiLNIVAIEDED---YKEVCKKLRDR-GIYVSV---CNCVKALRIVVmPHIKREHI 383
                                   5566788889*****9999999998645555555555...56*********.******...555559************** PP

                                   HHHHHH CS
                 Aminotran_1_2 357 eelvea 362
                                   ++++e 
  gi|15668221|ref|NP_247014.1| 384 DNFIEI 389
                                   **9985 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   3.4e-11   6.8e-08      66     177 ..      90     208 ..      65     217 .. 0.83
   2 ?    2.0   0.0      0.04        80     252     336 ..     285     362 ..     250     386 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3.4e-11
                                   EESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHH....HHHHTEEEEEE..EBETTSCBEGGGHHHH--.TT CS
                   Aminotran_5  66 ftsGtteainlvalslarslkpgdeivvteaehhanlvpwqel....akrtgakvkvi..pldeegeldldeleklln.ek 139
                                    +sG+tea+ ++++++++ ++++++  ++++eh   +vp+ +     + r+ +++++i  p++e+ ++d + ++++++  +
  gi|15668221|ref|NP_247014.1|  90 IVSGGTEANLMALRCIKNIWREKRRKGLSKNEHPKIIVPITAHfsfeKGREMMDLEYIyaPIKEDYTIDEKFVKDAVEdYD 170
                                   38**************988********************98652221234446677765599*******9999**997479 PP

                                   EEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                   Aminotran_5 140 tklvaithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                   ++ ++  +  +++Gti+ +ee+ k+ak+++++++vDaa
  gi|15668221|ref|NP_247014.1| 171 VDGIIGIAGTTELGTIDNIEELSKIAKENNIYIHVDAA 208
                                   999999*******************************9 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.04
                                   S--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEE.EEETTCSHHHHHHHHHHT CS
                   Aminotran_5 252 Tpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivs.fnfkgvhaedvatlLdee 331
                                   T   +g     a+l+yl + g ++i ++  e + yl+++lk+ +   +++p        i++ +++++ + ++v + L+++
  gi|15668221|ref|NP_247014.1| 285 TRVGFGGACTYAVLRYLGREGQRKIVNECMENTLYLYKKLKENNFKPVIEP--------ILNiVAIEDEDYKEVCKKLRDR 357
                                   5555566666799****************************9998777554........3330334566666777777777 PP

                                   TEEEE CS
                   Aminotran_5 332 gIavr 336
                                   gI v+
  gi|15668221|ref|NP_247014.1| 358 GIYVS 362
                                   77776 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   7.5e-08   0.00015      53     219 ..      91     267 ..      40     372 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.5e-08
                                   ES-HHHHHHHHH............HHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS-- CS
               Beta_elim_lyase  53 vpqGtaAnsill............kill.qrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaike 120
                                   v  Gt An ++l            k l  + ++++iv ++ah+ f   + +  l+ +    +++ke+ ++d + +++a+++
  gi|15668221|ref|NP_247014.1|  91 VSGGTEANLMALrcikniwrekrrKGLSkNEHPKIIVPITAHFSFEKGREMMDLEYI---YAPIKEDYTIDEKFVKDAVED 168
                                   556788888888777666666665333335667788888899999999888777666...666667669999999999999 PP

                                   S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHH.........HHHTS-CHHHHTT.SSE CS
               Beta_elim_lyase 121 vgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaa.........kslgeivkemfsy.vDs 191
                                       ++  ++i ++ T++   G   ++++++e+++iak+++i +h+D+A  +            k+ g+  k  fs  vDs
  gi|15668221|ref|NP_247014.1| 169 ----YDVDGIIGIAGTTEL--G---TIDNIEELSKIAKENNIYIHVDAA--FGGLvipflddkyKKKGVNYKFDFSLgVDS 238
                                   ....366899********8..6...57*********************9..333447888987888888888777655999 PP

                                   EEEESSSTT--SS-.EEEEE-HH....HH CS
               Beta_elim_lyase 192 vtmslkKdllanvG.gvlafrddeledyl 219
                                   +t+   K +++++  g ++f+d +++ yl
  gi|15668221|ref|NP_247014.1| 239 ITIDPHKMGHCPIPsGGILFKDIGYKRYL 267
                                   99999999999996666667777774444 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       0.1   2.1e+02      92     116 ..      90     114 ..      67     141 .. 0.74
   2 !   13.6   0.0   9.5e-06     0.019     348     404 ..     340     392 ..     292     393 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.1
                                   EESSHHHHHHHHHHHHHHHHHHTSH CS
                   Aminotran_3  92 lansGseAvetAlKlarkyarekka 116
                                   ++  G+eA+  Al+ +++  rek++
  gi|15668221|ref|NP_247014.1|  90 IVSGGTEANLMALRCIKNIWREKRR 114
                                   56789***********997776652 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.5e-06
                                   EEEEEBCCCETTCHHHHHHHHHCTEE-EEETT.TEEEE---TT--HHHHHHHHHHHHH CS
                   Aminotran_3 348 iaielkeeaevkekeilkkakekGvlilsaGd.nvirllppliitdeeidelleilkk 404
                                   +aie   +++   ke++kk+++ G+++  +   +++r++ +  i+ e+id+++eil+ 
  gi|15668221|ref|NP_247014.1| 340 VAIE---DEDY--KEVCKKLRDRGIYVSVCNCvKALRIVVMPHIKREHIDNFIEILNS 392
                                   4442...2332..48*************99989*********************9976 PP

>> Phage_Gp15  Bacteriophage Gp15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.7   7.5e+03      90     104 ..      19      35 ..       3      39 .. 0.46
   2 ?   12.8   0.0   4.3e-05     0.085      41     113 ..      71     158 ..      52     164 .. 0.78
   3 ?   -3.2   0.0       3.6   7.1e+03      61      75 ..     313     327 ..     301     353 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.7
                    Phage_Gp15  90 k..qiysfsqDaeyIya 104
                                   k  + +++++ +  I++
  gi|15668221|ref|NP_247014.1|  19 KkyRSLDLKYEDGNIFG 35 
                                   12244555555555555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.3e-05
                    Phage_Gp15  41 eKinlalellld...eepedleeaiekllwfyscgkeeeqkkskkdkkgnklk.......qiysfsq.....DaeyIyaaF 106
                                   eK+  +l  ll+      +++    e+ l+ ++c k+   +k +k  ++n+ +       + +sf++     D eyIya +
  gi|15668221|ref|NP_247014.1|  71 EKAVALLGSLLNnkdAYGHIVSGGTEANLMALRCIKNIWREKRRKGLSKNEHPkiivpitAHFSFEKgremmDLEYIYAPI 151
                                   566666666666233333455677888889999999999999999999998867999999779**965555699******* PP

                    Phage_Gp15 107 lqqYgiD 113
                                   +++Y iD
  gi|15668221|ref|NP_247014.1| 152 KEDYTID 158
                                   ******9 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.6
                    Phage_Gp15  61 aiekllwfyscgkee 75 
                                    +e+ l++y++ ke+
  gi|15668221|ref|NP_247014.1| 313 CMENTLYLYKKLKEN 327
                                   444444444433332 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.9e-05     0.097      44     146 ..      91     208 ..      75     211 .. 0.81
   2 ?   -2.0   0.0      0.84   1.7e+03     183     203 ..     340     360 ..     339     375 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.9e-05
                                   ESSHHHHHHHHHHH..........TTTT....TT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--T CS
               DegT_DnrJ_EryC1  44 vssGtaAlhlaLra..........lgvg....pgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaite 110
                                   vs Gt+A+++aLr              g    +  ++Ivp +  ++  +    + ++ +++ ++ ++y+id + ++ a++ 
  gi|15668221|ref|NP_247014.1|  91 VSGGTEANLMALRCikniwrekrrK--GlsknEHPKIIVPITAHFSFEKGREMMDLEYIYAPIK-EDYTIDEKFVKDAVED 168
                                   7888888888888865554444442..0444467789999999999999999999999999998.89************** PP

                                   TE....EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-T CS
               DegT_DnrJ_EryC1 111 rt....kaIlpVhlyGqvadmdalkaiaakhglkvieDaA 146
                                          +I     +G + ++++l +ia++ ++++  DaA
  gi|15668221|ref|NP_247014.1| 169 YDvdgiIGIAGTTELGTIDNIEELSKIAKENNIYIHVDAA 208
                                   999666667777889************************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.84
                                   EEESTHHHHHHHHHHHBTTCE CS
               DegT_DnrJ_EryC1 183 vvtndeelaekarvlrnhGlk 203
                                   v  +de+++e +++lr  G+ 
  gi|15668221|ref|NP_247014.1| 340 VAIEDEDYKEVCKKLRDRGIY 360
                                   566788888888888877764 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.061   1.2e+02      74     106 ..     158     204 ..       6     223 .. 0.57
   2 ?    8.7   0.1    0.0011       2.1     126     165 ..     343     388 ..     302     390 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.061
                                   C.............CCTEEEEEEECSSCHG.HHHHHHHHHTT-SEEE CS
                                   x.............xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                   Radical_SAM  74 a.............vpgiritvetngtlpd.eeklerllelgvdrvs 106
                                   +             +  i i+ +t  +++d  e l ++++ +  +++
  gi|15668221|ref|NP_247014.1| 158 DekfvkdavedydvDGIIGIAGTTELGTIDnIEELSKIAKENNIYIH 204
                                   02222233333444455555555555555555555555553333333 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHHHHHTTSET......EEEEEEEBTTTSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 126 tfeevlealeklreagikr......vvdrivglpGendeeleelle 165
                                   + e+++e+++klr++gi +         riv++p   +e++++++e
  gi|15668221|ref|NP_247014.1| 343 EDEDYKEVCKKLRDRGIYVsvcncvKALRIVVMPHIKREHIDNFIE 388
                                   4599************999999999899*************99886 PP

>> YqaH  Uncharacterized YqaH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00034      0.68      28      63 ..     161     200 ..     152     209 .. 0.77
   2 ?    0.4   0.0       0.4     8e+02      68      83 ..     348     363 ..     320     368 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00034
                          YqaH  28 lLaealkegDfegaielagsi....vvlskDlkrlehkek 63 
                                   ++ +a+++ D +g i +ag+     +++ ++l++++++++
  gi|15668221|ref|NP_247014.1| 161 FVKDAVEDYDVDGIIGIAGTTelgtIDNIEELSKIAKENN 200
                                   5689***************962222567778888887664 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.4
                          YqaH  68 yeiaskfakrGlnvsv 83 
                                    e+  k+ +rG+ vsv
  gi|15668221|ref|NP_247014.1| 348 KEVCKKLRDRGIYVSV 363
                                   4667777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2568.61
//
Query:       gi|15668222|ref|NP_247015.1|  [L=115]
Description: peptidyl-tRNA hydrolase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-44  150.4   0.0    2.7e-44  150.2   0.0    1.0  1  PTH2      Peptidyl-tRNA hydrolase PTH2


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.2   0.0   1.5e-48   2.7e-44       1     117 []       1     115 []       1     115 [] 0.99

  Alignments for each domain:
  == domain 1  score: 150.2 bits;  conditional E-value: 1.5e-48
                                   EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SEEEE CS
                          PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglpaali 81 
                                   +kmv+v+r+DL+m+kGk++aq +hA ++++ +++++ n+ ++++eW +egqkk+v+kv+se+eL ++++ka+++glp+++i
  gi|15668222|ref|NP_247015.1|   1 MKMVVVIRNDLGMGKGKMVAQGGHAIIEAFLDAKRK-NP-RAVDEWLREGQKKVVVKVNSEKELIDIYNKARSEGLPCSII 79 
                                   69*********************************9.99.8**************************************** PP

                                   EETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                          PTH2  82 rDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                   rDag+tq+epgt T++aigP +++++dk+tg+Lkll
  gi|15668222|ref|NP_247015.1|  80 RDAGHTQLEPGTLTAVAIGPEKDEKIDKITGHLKLL 115
                                   **********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 730.16
//
Query:       gi|15668223|ref|NP_247016.1|  [L=222]
Description: hypothetical protein MJ_0052 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-16   60.4   0.0    3.9e-16   59.5   0.0    1.5  1  Rhodanese       Rhodanese-like domain
  ------ inclusion threshold ------
      0.083   12.9   0.0       0.11   12.4   0.0    1.2  1  Y_phosphatase3  Tyrosine phosphatase family


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.0   4.3e-20   3.9e-16       2     106 ..      96     218 ..      95     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 4.3e-20
                     Rhodanese   2 akelkellekgkvallDvRppeeYekghIpgAvnv....................skdtlsrakkseapllelpeellelg 62 
                                   ++el el++k++v+++D+R+p e+++  +pgA+n+                    +k +   ++ +e++l+ ++ e+++l 
  gi|15668223|ref|NP_247016.1|  96 VSELLELIKKEDVIIVDTRSPREFKEETLPGAINIplflddehaligktykqesrEKAIEIATDIVEKSLKRILNEAKKL- 175
                                   7899*************************************998887777777776677777777777777777777777. PP

                     Rhodanese  63 idnkktvvvycdgggr.aaaaaallkklGyknvsvldGGfkawke 106
                                    d++k +vv+c+ gg  ++  a +l+ lG  +v+ l GGfka+k 
  gi|15668223|ref|NP_247016.1| 176 -DRDKLIVVFCARGGMrSQTMALILQLLG-FKVKRLIGGFKAFKH 218
                                   .**********9999945555889999**.7************96 PP

>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05      0.11      53     150 ..     110     207 ..      94     220 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                Y_phosphatase3  53 viDLRspeErea.eaplegaryvhlpv....eeaaeeekeeeeaeetlaelYrellesakkayrkvfealadeepvlfHCt 128
                                   ++D Rsp+E ++ + p      +++p+    e+a   ++ ++e++e+  e+  +++e++ k++ +  ++l +++ +++ C+
  gi|15668223|ref|NP_247016.1| 110 IVDTRSPREFKEeTLP----GAINIPLflddEHALIGKTYKQESREKAIEIATDIVEKSLKRILNEAKKLDRDKLIVVFCA 186
                                   89*******6553455....67888887654234667778888899999999999997666666666666665599***** PP

                Y_phosphatase3 129 aGKDRTGvlaalllsllGvdee 150
                                    G  R   ++al+l+llG + +
  gi|15668223|ref|NP_247016.1| 187 RGGMRS-QTMALILQLLGFKVK 207
                                   **9999.88999*****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1354.91
//
Query:       gi|15668224|ref|NP_247017.1|  [L=227]
Description: hypothetical protein MJ_0053 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00042   20.9   1.0     0.0011   19.4   0.2    2.1  2  AAA_18       AAA domain
  ------ inclusion threshold ------
      0.017   15.2   0.4       0.03   14.4   0.4    1.4  1  FlbT         Flagellar protein FlbT
      0.018   15.3   0.1      0.031   14.5   0.1    1.7  1  AAA_22       AAA domain
      0.027   14.2   0.0        0.8    9.3   0.0    2.3  2  CoaE         Dephospho-CoA kinase
      0.038   13.4   0.3       0.74    9.2   0.0    2.2  2  TniB         Bacterial TniB protein
      0.044   14.3   0.7       0.12   12.8   0.0    1.9  2  ABC_tran     ABC transporter
      0.069   13.1   0.3       0.14   12.0   0.1    1.6  2  YfdX         YfdX protein
       0.15   12.3   0.0       0.27   11.5   0.0    1.5  1  AAA_28       AAA domain
       0.19   11.6   4.4        1.1    9.1   0.0    2.6  3  RsgA_GTPase  RsgA GTPase
       0.23   11.9   3.6        1.1    9.7   0.3    2.8  2  AAA_17       AAA domain
        1.4    9.0   4.8          2    8.5   0.9    2.6  3  DUF269       Protein of unknown function, DUF269


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   7.1e-07    0.0011       3     114 ..      15     129 ..      14     144 .. 0.62
   2 ?   -1.6   0.0       2.2   3.7e+03      25      56 ..     189     217 ..     173     226 .. 0.46

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.1e-07
                        AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss........aleegk 75 
                                   l G+ G+GKt++ +eL+k++  ++ + ++a+ +g+ l++  +   +s+++ +   +k +++ ++           + + +k
  gi|15668224|ref|NP_247017.1|  15 LFGKTGCGKTEILNELKKHH-PVIDIEEIARTRGSILGDLYHLSMRSQEEFDYLINKEIEKAKKFGYavveyegrKIGGEK 94 
                                   78**************9995.466666666666666666666333333333333333333333333355555555566677 PP

                        AAA_18  76 nlvidghlaeleseaakdikkvvLtaspeelleRlekRg 114
                                    l i  +la+   + +k    + +++++e  + Rl    
  gi|15668224|ref|NP_247017.1|  95 KLKIPELLADIKNYTYK----ILIDCPYECQINRLVSIY 129
                                   77777777777777666....888888888888887754 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                        AAA_18  25 gvnlrdvakenglllevdpealdeskrldedk 56 
                                    +n++++ ++   + e+ ++   + k++de  
  gi|15668224|ref|NP_247017.1| 189 MRNVKKIKPDLIVYNEDVKK---SAKIIDEFI 217
                                   55555555554444444444...444444443 PP

>> FlbT  Flagellar protein FlbT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.4   1.9e-05      0.03      65     121 ..     130     186 ..     120     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                          FlbT  65 pedaeeareellelleelleveaapealaaleaieeaveagryYkaLkalrkLleyE 121
                                   + ++e+ +e l +    l e +++pe+++a+++i e +++++yY+a k + + l +E
  gi|15668224|ref|NP_247017.1| 130 KPKNEKEKEILINKFLILKESFKKPEMIEAVDNIIELIKQDKYYEAAKLIEEKLYRE 186
                                   4556666777777777788999************************99987655555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.9e-05     0.031      10      70 ..      15      78 ..      10     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-05
                        AAA_22 10 vtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsst..sskdllrellralglelka 70
                                  ++G +G+GKT  l++l++ ++ ++++ee  + ++ ++ +l +++  s++++   + ++++  +k 
  gi|15668224|ref|NP_247017.1| 15 LFGKTGCGKTEILNELKKHHP-VIDIEEiaRTRGSILGDLYHLSmrSQEEFDYLINKEIEKAKKF 78
                                  79****************975.7888888877888877777777778888888888888766655 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00049       0.8       2      36 ..      12      45 ..      11      55 .. 0.91
   2 ?    2.5   0.0     0.061     1e+02     125     152 ..     111     138 ..      96     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00049
                                  EEEEEESTTSSHHHHHHHHHHTT-EEEEHHHHHHH CS
                          CoaE  2 ivgltGgiasGKstvanlfadlgvpivDaDlvArq 36
                                  i gl G  ++GK+ + n ++++  p++D   +Ar 
  gi|15668224|ref|NP_247017.1| 12 IFGLFGKTGCGKTEILNELKKH-HPVIDIEEIART 45
                                  78*****************997.69********96 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.061
                                   EEEEE--HHHHHHHHHHCCTSTHHHHHH CS
                          CoaE 125 vlvvdvelelqveRlvardgvseeevka 152
                                    +++d++ e q++Rlv+  + ++e+ k+
  gi|15668224|ref|NP_247017.1| 111 KILIDCPYECQINRLVSIYKPKNEKEKE 138
                                   4789**********99866555554444 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00046      0.74      39      63 ..      14      38 ..       6      67 .. 0.84
   2 ?    2.1   0.2     0.069   1.1e+02       5      62 ..     167     223 ..     163     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00046
                          TniB 39 llvGdsnnGKtmivekFarlhppek 63
                                   l+G++ +GKt i+++ +++hp  +
  gi|15668224|ref|NP_247017.1| 14 GLFGKTGCGKTEILNELKKHHPVID 38
                                  589******************9875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.069
                          TniB   5 iradrwigyprakeilerLeeLleypkrkrmpnlllvGdsnnGKt.mivekFarlhppe 62 
                                   i++d++  y++ak i e+L + + + + k+++  l+v + ++ K+ +i+++F +++ +e
  gi|15668224|ref|NP_247017.1| 167 IKQDKY--YEAAKLIEEKLYREHYMRNVKKIKPDLIVYNEDVKKSaKIIDEFIKKKLKE 223
                                   556654..889999*****8888888888887777777777777636999999988665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.6e-05      0.12       7      36 ..       6      35 ..       1     103 [. 0.77
   2 ?    0.1   0.1      0.67   1.1e+03      51      80 ..     148     204 ..     122     226 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.6e-05
                                  EEETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  7 klkegekvaivGenGaGKStLlkllagllk 36
                                  + ++  + +++G++G+GK+ +l+ l +++ 
  gi|15668224|ref|NP_247017.1|  6 NGENMIIFGLFGKTGCGKTEILNELKKHHP 35
                                  555556789*************99987765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.67
                                   G......B-HHHCCHCEEEE-SS--S-TTSBHHHH.....................H CS
                                   x......xxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................x RF
                      ABC_tran  51 e......qeleslrkeigvlpqepqlfpeltvren.....................e 80 
                                   +      + +e +++ i+ ++q++     + ++e+                     e
  gi|15668224|ref|NP_247017.1| 148 KesfkkpEMIEAVDNIIELIKQDKYYEAAKLIEEKlyrehymrnvkkikpdlivynE 204
                                   333333667777777788888885555544455555555465555555555555442 PP

>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   8.8e-05      0.14     113     137 ..     156     180 ..     154     184 .. 0.89
   2 ?   -3.8   0.0       6.8   1.1e+04     113     126 ..     202     215 ..     198     219 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
                                   HHHHHHHHHHHHHTT-HHHHHHHHH CS
                          YfdX 113 ypaavkkAaelleegkyyeAkeaLk 137
                                   + +av+ ++el+++ kyyeA ++++
  gi|15668224|ref|NP_247017.1| 156 MIEAVDNIIELIKQDKYYEAAKLIE 180
                                   5789****************99876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.8
                                   HHHHHHHHHHHHHT CS
                          YfdX 113 ypaavkkAaellee 126
                                   y ++vkk a+ ++e
  gi|15668224|ref|NP_247017.1| 202 YNEDVKKSAKIIDE 215
                                   66677777777765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016      0.27       4      33 ..      15      45 ..      13      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                        AAA_28  4 itGgestGKTtlleaLaar.gypvvpEaare 33
                                  ++G  ++GKT +l++L+++  +  ++E+ar+
  gi|15668224|ref|NP_247017.1| 15 LFGKTGCGKTEILNELKKHhPVIDIEEIART 45
                                  57889************99345567999996 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00069       1.1     104     131 ..      15      43 ..       5      48 .. 0.78
   2 ?   -1.7   0.0       1.4   2.3e+03      65      88 ..      68      91 ..      57     113 .. 0.67
   3 ?    1.1   2.7      0.19   3.2e+02      16      99 ..     122     219 ..     111     223 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00069
                                   EECSTTSSHHHHHHHHCTT-.----S--- CS
                   RsgA_GTPase 104 lvGqSGvGKStLinallpel.elktgevs 131
                                   l G++G GK+ ++n+l+ ++  + ++e+ 
  gi|15668224|ref|NP_247017.1|  15 LFGKTGCGKTEILNELKKHHpVIDIEEIA 43 
                                   79**************9954266666665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                                  HHHHHHHHHHTTSEEEE--TTTHT CS
                   RsgA_GTPase 65 leelkeelealgyevllvsaktke 88
                                  +++  e+ +++gy+v+  + ++  
  gi|15668224|ref|NP_247017.1| 68 INKEIEKAKKFGYAVVEYEGRKIG 91
                                  566677888888888877665443 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.19
                                   --EEEEEEESTTTT--HHHHHHHHHHHHHTT.......-EEEEEEE-GGG--HHH.......HHHHHHHHHHHTTSEEEE- CS
                   RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlaeekg.......iepvivlnKiDlleeee.......eleelkeelealgyevllv 82 
                                   +++l+ +   k+++ ++ l+++fL+l e+ +       ++ +i l K D + e+          e+++ +++++  ++++ 
  gi|15668224|ref|NP_247017.1| 122 INRLVSIYKPKNEKEKEILINKFLILKESFKkpemieaVDNIIELIKQDKYYEAAklieeklYREHYMRNVKKIKPDLIVY 202
                                   555666666677777788899999998876511111113445556666655555566665555666666777777777777 PP

                                   -TTTHTTHHHHHHHCTT CS
                   RsgA_GTPase  83 saktkegleelkellkd 99 
                                   +++ k++++ + e +k+
  gi|15668224|ref|NP_247017.1| 203 NEDVKKSAKIIDEFIKK 219
                                   77766666666666665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00069       1.1       2     114 ..      17     120 ..      16     138 .. 0.68
   2 ?    2.2   0.4      0.13   2.2e+02      51     110 ..     178     205 ..     133     225 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00069
                                   E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEE CS
                        AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghpri 82 
                                   G  G+GK++++++l+++  +  ++      e a+ +g+    +++  l+++ ++e++ ++ ++i++++k + ++v+   r 
  gi|15668224|ref|NP_247017.1|  17 GKTGCGKTEILNELKKHHPVIDIE------EIARTRGS--ILGDLYHLSMRSQEEFDYLINKEIEKAKKFGYAVVEYEGRK 89 
                                   788************998776666......66666666..67888999999999999999999998876666666544443 PP

                                   EETTEEEESSHHHHHHHH...SEEEEEE--HHH CS
                        AAA_17  83 keqagfldglpkevleel.kpdaiilleadpee 114
                                      ++   ++p+  l+++ +++  il++++ e 
  gi|15668224|ref|NP_247017.1|  90 IGGEK-KLKIPE-LLADIkNYTYKILIDCPYEC 120
                                   33222.334443.33333144666677776664 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE- CS
                        AAA_17  51 leekkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpkevleelkpdaiillea 110
                                   l e                               ++ +++++ ++v +++kpd+i++ e+
  gi|15668224|ref|NP_247017.1| 178 LIE-------------------------------EKLYREHYMRNV-KKIKPDLIVYNED 205
                                   333...............................333444444443.4556666666443 PP

>> DUF269  Protein of unknown function, DUF269
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.29   4.8e+02      79      96 ..      67      84 ..      66      98 .. 0.85
   2 ?    8.5   0.9    0.0012         2       3      51 ..     134     182 ..     132     194 .. 0.84
   3 ?   -1.7   0.1       1.8     3e+03       4      20 ..     207     223 ..     205     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.29
                                  EEEEEE-SGGG--BSSHH CS
                        DUF269 79 vvsktlrdvhrFgFesle 96
                                  +++k ++++++Fg++ +e
  gi|15668224|ref|NP_247017.1| 67 LINKEIEKAKKFGYAVVE 84
                                  68999*********8665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0012
                                   TS-HHHHHGGGB--HHHHCCS-SSSS--HHH.HHHHHHHHHHHHHHHHHH CS
                        DUF269   3 kksdeellkpfivtkekkreipiigdvdpet.llrielfynavalaiEke 51 
                                   +k++e l+++f++ ke+ ++ ++i+ vd+ + l + + +y+a a  iE++
  gi|15668224|ref|NP_247017.1| 134 EKEKEILINKFLILKESFKKPEMIEAVDNIIeLIKQDKYYEA-AKLIEEK 182
                                   45667778*********************997889999**99.5566654 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.8
                                   S-HHHHHGGGB--HHHH CS
                        DUF269   4 ksdeellkpfivtkekk 20 
                                   k+ ++++++fi +k k+
  gi|15668224|ref|NP_247017.1| 207 KKSAKIIDEFIKKKLKE 223
                                   57789999999888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1141  (0.0636399); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1409.10
//
Query:       gi|15668225|ref|NP_247018.1|  [L=281]
Description: hypothetical protein MJ_0054 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.5e-111  370.5   6.6     4e-111  370.3   6.6    1.0  1  DUF2099   Uncharacterized protein conserved in archaea (DUF20
  ------ inclusion threshold ------
      0.022   14.8   0.0      0.032   14.2   0.0    1.3  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> DUF2099  Uncharacterized protein conserved in archaea (DUF2099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.3   6.6  4.4e-115    4e-111       1     257 []       4     257 ..       4     257 .. 0.99

  Alignments for each domain:
  == domain 1  score: 370.3 bits;  conditional E-value: 4.4e-115
                       DUF2099   1 HiiealgkarvvvkdgkvvevgepkikyCPlfkklrgikeitkeaikkniefrikefGlftkkRkleskedfvsfGasEil 81 
                                   H++ealgkarvvv++g+vvev+epkikyCPlf+k+rgikeitke+ik+niefrik+fGlftk+R++e+++++v fGasEil
  gi|15668225|ref|NP_247018.1|   4 HVMEALGKARVVVENGRVVEVTEPKIKYCPLFAKHRGIKEITKESIKENIEFRIKDFGLFTKNRVVEESRYIVPFGASEIL 84 
                                   9******************************************************************************** PP

                       DUF2099  82 stalkeglidaavivcdgaGtvivtnpelvqglggrisGlveTePieevierieeeggivldketaeidqveGvkkAiekg 162
                                   ++alk+++id aviv+d+aGt+i++np+lvqgl+grisG++eT+Pi evie+ie++gg+vl+k+taei+q+eGvkkAie  
  gi|15668225|ref|NP_247018.1|  85 MSALKRKAIDVAVIVADCAGTIITSNPNLVQGLCGRISGIIETSPILEVIEKIEKAGGVVLNKKTAEINQFEGVKKAIELD 165
                                   ********************************************************************************* PP

                       DUF2099 163 ykkiavtvaeaedakklrelekeegvkilifavhttgiskeeaeelveaaDlvtacAskeireivkkkallqvgksvpvfa 243
                                   ykkiavtv++ edak++++le+ +++kil+f+vh+tgi  e  ee+++++DlvtacAsk +re +k k ++q+gk++p+fa
  gi|15668225|ref|NP_247018.1| 166 YKKIAVTVTNLEDAKRCKSLEN-DEIKILTFGVHLTGI--EGSEEIAKYFDLVTACASKVLREKLKGKIKAQIGKTIPIFA 243
                                   *********************9.9**************..78899************************************ PP

                       DUF2099 244 ltekGkelilerlk 257
                                   l++ Gke++ler+k
  gi|15668225|ref|NP_247018.1| 244 LSDFGKEILLERAK 257
                                   ***********986 PP

>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.6e-06     0.032     122     190 ..      59     126 ..       5     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-06
                                   EEEEESSHHHHHHHHCT-CEEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC..--HHHHHHHHHHHHHHHT CS
                          PAC2 122 vtgaatdeelleeleeseyggivgitglLlsaakergipavgllaevphyl..pdPkaaaalleflskllg 190
                                    +g +t +  +   ees+y +++g++ +L+sa+k++ i++++++a + + +   +P+  + l  ++s +++
  gi|15668225|ref|NP_247018.1|  59 DFGLFTKNRVV---EESRYIVPFGASEILMSALKRKAIDVAVIVADCAGTIitSNPNLVQGLCGRISGIIE 126
                                   34555444444...4669******************************99877789988888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1774.16
//
Query:       gi|15668226|ref|NP_247019.1|  [L=227]
Description: 3,4-dihydroxy-2-butanone 4-phosphate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-66  223.5   0.0    1.8e-66  223.3   0.0    1.0  1  DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
  ------ inclusion threshold ------
      0.099   12.3   0.1       0.25   11.1   0.1    1.7  1  TFA2_Winged_2  TFA2 Winged helix domain 2


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.3   0.0     2e-70   1.8e-66       1     192 []       5     219 ..       5     219 .. 0.94

  Alignments for each domain:
  == domain 1  score: 223.3 bits;  conditional E-value: 2e-70
                                   HHHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-S......... CS
                 DHBP_synthase   1 eeaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveene......... 72 
                                   e+aiealk+G++++v+D+++re+e+d+++a++++tpe++++m+++a+Glic+al+++ +++L++p+mv+  e         
  gi|15668226|ref|NP_247019.1|   5 EKAIEALKKGEIILVYDSDEREGETDMVVASQFITPEHIRIMRKDAGGLICTALHPDICNKLGIPFMVDILEfasqkfkvl 85 
                                   68******************************************************************6333777889999 PP

                                   .........STT---BB--EEESST-SSS-SHHHHHHHHHHHH-..T....T--GGGEEEEEEEEEEEE-TTGGGTS-SHH CS
                 DHBP_synthase  73 .........dkhktaftvsvdaaegttTGIsaaDRalTirklad..p....kakpedfrrPGhvfplrareggvleRrghT 138
                                              +k++f+++++++ +t+TGI+++DRa Ti+kla+  +    +   ++fr+PGhv +lra+eg v++R+ghT
  gi|15668226|ref|NP_247019.1|  86 relypndipYDEKSSFSITINHR-KTFTGITDNDRAFTIKKLAElvKegrfNDFGKEFRSPGHVTLLRAAEGLVKNRQGHT 165
                                   ******9995568**********.9*******************6535666445599************************ PP

                                   HHHHHHHHHTTS-SBEEEEEBB-TTSCB-BHHHHHHHHHHHT-EEEEHHHHHHH CS
                 DHBP_synthase 139 EaavdLarlaglkpaavicellnddgtmarrdeleefakkhglkiitiedliey 192
                                   E++v+La+la+l p+ +ice++ ddg++++++e +++a+kh+l ++++e++i+y
  gi|15668226|ref|NP_247019.1| 166 EMTVALAELANLVPITTICEMMGDDGNAMSKNETKRYAEKHNLIYLSGEEIINY 219
                                   ****************************************************98 PP

>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   2.8e-05      0.25      28      55 ..       1      29 [.       1      34 [. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.8e-05
                 TFA2_Winged_2 28 wpdveealeeLeaegeilvl..rtkkdgqp 55
                                  + +ve+a+e+L++ gei+++  + +++g  
  gi|15668226|ref|NP_247019.1|  1 MNNVEKAIEALKK-GEIILVydSDEREGET 29
                                  579**********.9987662222366644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1432.72
//
Query:       gi|15668227|ref|NP_247020.1|  [L=136]
Description: riboflavin kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-38  130.1   0.1    4.9e-38  129.9   0.1    1.0  1  CTP-dep_RFKase  Domain of unknown function DUF120
  ------ inclusion threshold ------
      0.022   14.7   0.5      0.083   12.8   0.2    2.0  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> CTP-dep_RFKase  Domain of unknown function DUF120
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   0.1   5.4e-42   4.9e-38       1     120 [.      11     129 ..      11     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 5.4e-42
                                   EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEE.... CS
                CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypaki.... 77 
                                   VvsGlgeG+y++sl+ yke f++ lgfepy+GTLN+kld+e       ++k+k ie e+fe ++++f +vkv+p+ki    
  gi|15668227|ref|NP_247020.1|  11 VVSGLGEGRYFLSLPPYKEIFKKILGFEPYEGTLNLKLDRE-----FDINKFKYIETEDFEFNGKRFFGVKVLPIKIlign 86 
                                   89************************************998.....67899**************************9996 PP

                                   CCEEEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEE CS
                CTP-dep_RFKase  78 ekikaavvvperthyeedvlEiiapekLReklelkdgdeveve 120
                                   +ki++a+vvp++t ++++++Eiiap+kLRe+++lkdgd +++ 
  gi|15668227|ref|NP_247020.1|  87 KKIDGAIVVPKKTYHSSEIIEIIAPMKLREQFNLKDGDVIKIL 129
                                   699**************************************96 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.22   1.9e+03       7      13 ..      91      97 ..      90      98 .. 0.83
   2 ?   12.8   0.2   9.3e-06     0.083      12      35 ..     111     134 ..     111     136 .] 0.94

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.22
                                  EEEEE-C CS
                MazE_antitoxin  7 gavriPk 13
                                  ga++ Pk
  gi|15668227|ref|NP_247020.1| 91 GAIVVPK 97
                                  7999999 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.3e-06
                                   -CCCHHHCCEECTCEEEEEECTTC CS
                MazE_antitoxin  12 PkevrfelgireGdevelevdgdk 35 
                                   P+ +r++ +++ Gd + + ++gdk
  gi|15668227|ref|NP_247020.1| 111 PMKLREQFNLKDGDVIKILIKGDK 134
                                   99********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 905.99
//
Query:       gi|15668228|ref|NP_247021.1|  [L=426]
Description: Na+/H+ antiporter [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-55  188.8  34.4    1.7e-55  188.4  34.4    1.1  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.4  34.4   9.6e-60   1.7e-55       3     375 ..      13     387 ..       8     403 .. 0.91

  Alignments for each domain:
  == domain 1  score: 188.4 bits;  conditional E-value: 9.6e-60
                                   HHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHH CS
                Na_H_Exchanger   3 llillallvgllarrlklpeivgliiaGlllGpsglglieps..eedlevlselglilllFlaGleldlrelrknlksill 81 
                                   +l+l +l++++ a++lk+p+i++l+++Gl++Gp+++  i ++  +e++e+   +gli++l+  ++ + ++ l++++k+++ 
  gi|15668228|ref|NP_247021.1|  13 ALVLGSLVAKI-AEKLKIPDIPLLLLLGLIIGPFLQI-IPSDsaMEIFEYAGPIGLIFILLGGAFTMRISLLKRVIKTVVR 91 
                                   45555677777.**********************998.555569************************************* PP

                                   HHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHH CS
                Na_H_Exchanger  82 lallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavl 162
                                   l ++ +lit++++G++++++l l+++   + lfgai +atdp+++++++  + r++ +++++l++es++nD +++v ++v+
  gi|15668228|ref|NP_247021.1|  92 LDTITFLITLLISGFIFNMVLNLPYTSPVGYLFGAITAATDPATLIPVF-SRVRTNPEVAITLEAESIFNDPLGIVSTSVI 171
                                   ******************87889**************************.******************************* PP

                                   HHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS...CTHHHHHHHHHHHHHHHH..HHHHHTS.XXXH CS
                Na_H_Exchanger 163 lalakeeaggetslllllliflvvavgglllglvigwllrlitrft...dddrelevllvlllalla..allaell.gvsg 237
                                   l+l      g +s++++l+ ++++a+g++++gl++  ++++i+ ++   ++ + l + +++ll+++    l + +  g+sg
  gi|15668228|ref|NP_247021.1| 172 LGLF-----GLFSSSNPLIDLITLAGGAIVVGLLLAKIYEKIIIHCdfhEYVAPLVLGGAMLLLYVGddLLPSICGyGFSG 247
                                   ***9.....*************************************9999999999999999999999667777779**** PP

                                   HHHHHHHHHHHHHHHHHTT.HHHH.HHHHHH...HHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHH CS
                Na_H_Exchanger 238 ilgaflaGlvlseyefsnk.lsek.lesfre...glfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavfl 313
                                    +++ ++Gl+l++  f+ + +  k + sf++    l+ +++Fv++G+ + l++l+   + ++ +l++l +i+l+r+l+vfl
  gi|15668228|ref|NP_247021.1| 248 YMAVAIMGLYLGDALFRADdIDYKyIVSFCDdlsLLARVFIFVFLGACIKLSMLE--NYFIPGLLVALGSIFLARPLGVFL 326
                                   ************9999999877778********99*******************7..99********************** PP

                                   HTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTT.SSTTTCSTSXHHHHHHHHH CS
                Na_H_Exchanger 314 llrllglslrealiigfgglqrgavalalaalgpalgllarel.yallivvvlftvlvqGlsl 375
                                    l  +++s++e+l++++ g  rg v +ala+ +  + +l+++  +++ i+  ++ + ++G+++
  gi|15668228|ref|NP_247021.1| 327 GLIGSKHSFKEKLYFALEGP-RGVVPAALAVTVGIE-ILKNADkIPASITKYITPTDIAGTII 387
                                   ********************.**************9.77775556666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2719.20
//
Query:       gi|15668229|ref|NP_247022.1|  [L=391]
Description: ammonium transporter AmtB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.3e-106  354.7  31.4   6.1e-106  354.5  31.4    1.0  1  Ammonium_transp  Ammonium Transporter Family
  ------ inclusion threshold ------
        1.9    8.3   5.9         28    4.6   0.2    3.6  3  DDDD             Putative mitochondrial precursor protein


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.5  31.4  6.8e-110  6.1e-106       2     399 .]      14     388 ..      12     388 .. 0.95

  Alignments for each domain:
  == domain 1  score: 354.5 bits;  conditional E-value: 6.8e-110
                                   HHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-TTTTSCCGCCTTC CS
               Ammonium_transp   2 flllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfignlglsaagvqdetl 82 
                                   f++ +a l++fm+agf+ le g++r+knv  ++v +lldla+v+++y+++Gy++++g    +++++  +        +   
  gi|15668229|ref|NP_247022.1|  14 FFMWAASLIFFMKAGFIALEIGQFRAKNVSYHCVLKLLDLAAVFIAYLFIGYGISYG----FENIMPLITG------TFDA 84 
                                   677788899999*******************************************99....5566666332......2223 PP

                                   CHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--.-SSSTTTTHHHHHHH CS
               Ammonium_transp  83 ldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvliDfAgstvVHlvggva 163
                                     g++++ +++faa+a+ti++g+vaerik+ +y++ ++++g++ yp+v h+vwg gg+++   +++D+Ags++VHl+gg++
  gi|15668229|ref|NP_247022.1|  85 DLGAWWMKMVMFAAAAVTIITGGVAERIKILPYFIGALIVGGILYPIVEHLVWG-GGFANLGINFHDYAGSGAVHLFGGLV 164
                                   34789*************************************************.************************** PP

                                   HHHHHHHHS-STTTTG.TTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH..HHHHHHHHHHHHHHHHHHHH CS
               Ammonium_transp 164 gLaaalvlgkregrfe.gkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrara.raavtTllAaaagaltallis 242
                                   gL+aa+vlg+r++++  gk++ai+ghn+p+avlG+++L+fgW+gFN Gsa ++ +  +  ++a++T++A+a+g+++  l s
  gi|15668229|ref|NP_247022.1| 165 GLMAAYVLGPRIDKYInGKPQAIPGHNIPIAVLGAFILAFGWYGFNIGSASGIANGVELaSVAMATTMALAGGIIGGALSS 245
                                   ***************99***********************************999998889******************** PP

                                   HHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTC-CTTHHHHHHHHHHHHHHHHHH CS
               Ammonium_transp 243 rlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklkidDsldvvavHgvgGiwGllavg 323
                                   r++      l++anG++AGlVA++++ ++++p+gA+i+Gl+Ag+++ +++k+++eklkidD++ + +vH+++G++G+++ g
  gi|15668229|ref|NP_247022.1| 246 RND-----PLYTANGMCAGLVAVCSGVDLFTPIGAFIVGLLAGIQQPFTYKFIEEKLKIDDVCAIGPVHAMSGLIGVICAG 321
                                   **9.....************************************************************************* PP

                                   HHTSHHHCSSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB--HHHHHHSHHHHHHSSSSB CS
               Ammonium_transp 324 ifaaekvvaskisggllsgegkqlvvqligilvilayafvvtlilllllklllgLrvseeeeevglDvaehgetay 399
                                   i +  k       ++ +s+ +  ++ q+ig++vi+++a+v +li+++ l+l++gLrvsee+e+vglD+a  ++tay
  gi|15668229|ref|NP_247022.1| 322 IPFLLK-------ADAVSKVS--ITGQIIGAIVIALIAIVGGLIIYKGLDLTIGLRVSEEAEKVGLDTAILQTTAY 388
                                   ****98.......45677766..999*******************************************9999998 PP

>> DDDD  Putative mitochondrial precursor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.013   1.2e+02      35      60 ..      49      74 ..      31      77 .. 0.86
   2 ?    1.7   0.1     0.024   2.2e+02      32      55 ..     256     279 ..     249     286 .. 0.85
   3 ?    4.6   0.2    0.0031        28      30      55 ..     308     333 ..     304     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.013
                          DDDD 35 gLlrvilvVipgllvGtliSknvAnl 60
                                   Ll + +v i +l++G  iS  + n+
  gi|15668229|ref|NP_247022.1| 49 KLLDLAAVFIAYLFIGYGISYGFENI 74
                                  5899999*************887765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.024
                          DDDD  32 tpFgLlrvilvVipgllvGtliSk 55 
                                   +  gL++v+  V ++  +G+ i  
  gi|15668229|ref|NP_247022.1| 256 MCAGLVAVCSGVDLFTPIGAFIVG 279
                                   6779****************9965 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0031
                          DDDD  30 kktpFgLlrvilvVipgllvGtliSk 55 
                                    +   gL++vi++ ip+ll    +Sk
  gi|15668229|ref|NP_247022.1| 308 VHAMSGLIGVICAGIPFLLKADAVSK 333
                                   556679************98888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2520.44
//
Query:       gi|15668230|ref|NP_247023.1|  [L=112]
Description: nitrogen regulatory protein P-II GlnB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-40  136.6   3.3    4.2e-40  136.5   3.3    1.0  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.5   3.3   2.3e-44   4.2e-40       1     102 []       4     105 ..       4     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 136.5 bits;  conditional E-value: 2.3e-44
                                   EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHHH-SS CS
                          P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiikaaktg 81 
                                   +eaiirpekle vk+aL++ag+ g+tv+evkGrG q g +e yrg+ey v+l+pkvk+e+vv++edv++v+++i+++a+tg
  gi|15668230|ref|NP_247023.1|   4 VEAIIRPEKLEIVKKALSDAGYVGMTVSEVKGRGVQGGIVERYRGREYIVDLIPKVKIELVVKEEDVDNVIDIICENARTG 84 
                                   79******************************************************************************* PP

                                   STTSEEEEEEEESEEEETTTT CS
                          P-II  82 eiGDGkiFvlpveevirirtg 102
                                   ++GDGkiFv+pve+v+r+rt+
  gi|15668230|ref|NP_247023.1|  85 NPGDGKIFVIPVERVVRVRTK 105
                                   *******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 718.79
//
Query:       gi|15668231|ref|NP_247024.1|  [L=252]
Description: methylthioadenosine phosphorylase MtaP [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-44  151.4   0.0    2.6e-44  151.2   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.2   0.0   1.5e-48   2.6e-44       2     233 ..       2     231 ..       1     232 [. 0.92

  Alignments for each domain:
  == domain 1  score: 151.2 bits;  conditional E-value: 1.5e-48
                                   EEEEESSH.HHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--....SSHHHHHHHHHHHHHHHC--SEEEEEE CS
                     PNP_UDP_1   2 iaiivgsp.gevellaespleetpfgregrgfkfvtGtlkgkpvvivstG....iGkpnaavvaeirllkefgvkaiiriG 77 
                                   i+ii+g++  e+    +++  +t++g+       v+   ++++v+++++G    i ++ ++++a+i +lk +gv++i++i+
  gi|15668231|ref|NP_247024.1|   2 IGIIGGTGiAEILKGDKEEIINTKYGKA-----RVIIDKENEVVLLFRHGvrhnIPPHKINYRANIYALKKLGVERILAIN 77 
                                   6788888853333333334555555555.....666666799*************************************** PP

                                   EEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS-CH CS
                     PNP_UDP_1  78 taGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfyaet 158
                                   ++G+l++dlk+G + +p+d+i f+  +  ++++e+ + ++d++d+ ++pelr++lk  + +++  + +Gv+++++g+++et
  gi|15668231|ref|NP_247024.1|  78 SVGSLKEDLKPGMFFVPNDFIEFTKKREETFYDEGKVVHIDMTDP-YCPELRNILKSILDKNNFSYGEGVYVCTEGPRFET 157
                                   *********************************************.*********************************** PP

                                   HHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHHHHHH CS
                     PNP_UDP_1 159 eaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaaknaaalllall 233
                                   + e+++++++g d+v+M+++++++lArel++++++++ ++++a g+  +  t++ev e  +e ++++ ++++ ++
  gi|15668231|ref|NP_247024.1| 158 KKEIAIYKNWG-DVVGMTGYPEVVLARELEMCYVSLCNITNYACGISKNILTVDEVLEKIKEMENKILKVVEDFI 231
                                   ***********.*****************************999999999999*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1578.45
//
Query:       gi|15668232|ref|NP_247025.1|  [L=80]
Description: ferredoxin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-11   43.8  12.5    2.4e-06   27.3   2.2    2.1  2  Fer4_6    4Fe-4S binding domain
    1.7e-11   43.4  12.6    2.8e-06   26.9   3.3    2.2  2  Fer4      4Fe-4S binding domain
    1.9e-08   34.7  22.2    9.4e-06   26.1  13.3    2.0  2  Fer4_7    4Fe-4S dicluster domain
    5.8e-08   32.8  12.4    8.8e-08   32.2  12.4    1.3  1  Fer4_9    4Fe-4S dicluster domain
    3.7e-07   29.9  12.0    0.00079   19.4   1.6    2.2  2  Fer4_2    4Fe-4S binding domain
    2.8e-06   27.3  11.2    3.8e-06   26.9  11.2    1.2  1  Fer4_21   4Fe-4S dicluster domain
    9.9e-06   25.6  15.1    1.9e-05   24.7  14.9    1.6  1  Fer4_10   4Fe-4S dicluster domain
      3e-05   24.5   6.8       0.02   15.4   0.9    2.1  2  Fer4_17   4Fe-4S dicluster domain
    0.00025   21.9  12.1      0.016   16.1   2.0    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00034   21.0   8.9      0.074   13.5   0.5    2.1  2  Fer4_8    4Fe-4S dicluster domain
     0.0033   17.8  14.0       0.18   12.4   2.6    2.2  2  Fer4_4    4Fe-4S binding domain
     0.0044   17.9   3.7     0.0044   17.9   3.7    2.2  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.057   13.6  12.0       0.15   12.3   2.8    2.0  2  Fer4_18   4Fe-4S dicluster domain
       0.21   12.2  12.0       0.28   11.8   1.7    2.2  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.23   12.2   9.3       0.27   12.0   0.6    2.2  2  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   2.8   8.7e-08    0.0001       1      22 [.      22      43 ..      22      47 .. 0.89
   2 !   27.3   2.2     2e-09   2.4e-06       1      24 []      52      75 ..      52      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.7e-08
                        Fer4_6  1 vveidpdkCigCgdCvrvCPeg 22
                                  ++eid++kC  C  C+rvC  +
  gi|15668232|ref|NP_247025.1| 22 IIEIDYNKCKNCLSCYRVCKNN 43
                                  69*****************755 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2e-09
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  vv+ ++++C+ Cg+C +vC +gai
  gi|15668232|ref|NP_247025.1| 52 VVVKNENNCTKCGECLKVCRYGAI 75
                                  68889*****************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   2.0   6.8e-08   8.1e-05       1      22 [.      23      44 ..      23      46 .. 0.92
   2 !   26.9   3.3   2.4e-09   2.8e-06       1      23 [.      53      75 ..      53      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 6.8e-08
                                  EEEETTTSSS-THHHHHSTTTE CS
                          Fer4  1 vvideekCigCGaCvevCPvgA 22
                                  ++id++kC +C  C+ vC +++
  gi|15668232|ref|NP_247025.1| 23 IEIDYNKCKNCLSCYRVCKNNV 44
                                  68****************9986 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 2.4e-09
                                  EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                  vv +e+ C++CG+C +vC +gAI
  gi|15668232|ref|NP_247025.1| 53 VVKNENNCTKCGECLKVCRYGAI 75
                                  689*******************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   1.5   9.1e-07    0.0011      18      51 ..      10      43 ..       6      44 .. 0.86
   2 !   26.1  13.3   7.9e-09   9.4e-06       1      52 []      29      74 ..      29      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.1e-07
                        Fer4_7 18 eldeeenekgtekveidpekClgCgaCvavCPtg 51
                                  + +e+ +ek ++ +eid++kC +C +C +vC  +
  gi|15668232|ref|NP_247025.1| 10 KGKEKIEEKSNKIIEIDYNKCKNCLSCYRVCKNN 43
                                  567778888999*******************877 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 7.9e-09
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  +C +C  C ++C+++++ +++       + v+ ++++C+ Cg+C +vC +ga
  gi|15668232|ref|NP_247025.1| 29 KCKNCLSCYRVCKNNVFAIKNN------RVVVKNENNCTKCGECLKVCRYGA 74
                                  7******************774......5688899*************9997 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2  12.4   7.4e-11   8.8e-08       1      51 []      29      75 ..      29      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 7.4e-11
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  kC +C +C ++C+++v+  ++++  +++++    +C++Cg+C+++C  gai
  gi|15668232|ref|NP_247025.1| 29 KCKNCLSCYRVCKNNVFAIKNNRVVVKNEN----NCTKCGECLKVCRYGAI 75
                                  7********************999999865....7************9987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.6   6.6e-07   0.00079       3      21 ..      23      41 ..      21      42 .. 0.91
   2 !   15.9   3.2   8.2e-06    0.0099       2      20 ..      52      70 ..      51      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.6e-07
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  +++d ++C +C +C+ +C 
  gi|15668232|ref|NP_247025.1| 23 IEIDYNKCKNCLSCYRVCK 41
                                  789***************5 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 8.2e-06
                        Fer4_2  2 pvvvdtdrCigCgaCvsaC 20
                                  +vv ++++C+ Cg C+++C
  gi|15668232|ref|NP_247025.1| 52 VVVKNENNCTKCGECLKVC 70
                                  57889************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9  11.2   3.2e-09   3.8e-06       2      52 ..      24      71 ..      23      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.2e-09
                       Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52
                                   id +kC +C +C+ +C++   +   i++++v+   e++C+ C  C++vC 
  gi|15668232|ref|NP_247025.1| 24 EIDYNKCKNCLSCYRVCKN---NVFAIKNNRVVVKNENNCTKCGECLKVCR 71
                                  599***************5...55556678998899**************6 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7  14.9   1.6e-08   1.9e-05       2      55 ..      23      70 ..      22      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.6e-08
                       Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55
                                  ++id ++C +C  C ++C      +++  +++++ +v k+  +Ct+cg+C ++C
  gi|15668232|ref|NP_247025.1| 23 IEIDYNKCKNCLSCYRVC------KNNVFAIKNNRVVVKNENNCTKCGECLKVC 70
                                  789***************......577778888888888*************** PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.6   0.00011      0.13      36      60 ..      20      44 ..       4      45 .. 0.73
   2 !   15.4   0.9   1.7e-05      0.02      44      59 ..      58      73 ..      46      77 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                       Fer4_17 36 eaekeekaslCieCgeCerkCPqgl 60
                                  + + e   ++C +C  C r+C +++
  gi|15668232|ref|NP_247025.1| 20 NKIIEIDYNKCKNCLSCYRVCKNNV 44
                                  333346889************9986 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.7e-05
                       Fer4_17 44 slCieCgeCerkCPqg 59
                                  ++C++CgeC ++C +g
  gi|15668232|ref|NP_247025.1| 58 NNCTKCGECLKVCRYG 73
                                  6788888888888664 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   1.9   0.00029      0.35       1      29 [.      29      57 ..      29      59 .. 0.84
   2 !   16.1   2.0   1.3e-05     0.016       1      18 [.      59      76 ..      59      80 .] 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00029
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkekeieare 29
                                  +C++C  C  vC  n++  k+++++ ++e
  gi|15668232|ref|NP_247025.1| 29 KCKNCLSCYRVCKNNVFAIKNNRVVVKNE 57
                                  6**************99988778777665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.3e-05
                       Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                  +C++Cg+C++vC  +ai 
  gi|15668232|ref|NP_247025.1| 59 NCTKCGECLKVCRYGAII 76
                                  6**************996 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.5   6.2e-05     0.074      45      65 .]      24      44 ..       4      44 .. 0.72
   2 !   11.8   2.3   0.00021      0.25      49      62 ..      58      71 ..      48      74 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.2e-05
                        Fer4_8 45 eealwsCttcgaCtevCpvgi 65
                                  e   ++C +c +C +vC++++
  gi|15668232|ref|NP_247025.1| 24 EIDYNKCKNCLSCYRVCKNNV 44
                                  66789************9986 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00021
                        Fer4_8 49 wsCttcgaCtevCp 62
                                  ++Ct cg+C +vC 
  gi|15668232|ref|NP_247025.1| 58 NNCTKCGECLKVCR 71
                                  56888888877776 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   2.6   0.00015      0.18       1      15 [.      27      41 ..      27      46 .. 0.90
   2 !   11.0   3.7   0.00041      0.48       2      16 ..      58      72 ..      57      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                        Fer4_4  1 qerCigCgsCvaaCP 15
                                  +++C +C sC+++C+
  gi|15668232|ref|NP_247025.1| 27 YNKCKNCLSCYRVCK 41
                                  589***********8 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00041
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  ++C+ Cg C  +C +
  gi|15668232|ref|NP_247025.1| 58 NNCTKCGECLKVCRY 72
                                  79***********76 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   3.8     0.031        37       1      14 [.      30      43 ..      30      44 .. 0.87
   2 !   17.9   3.7   3.7e-06    0.0044       1      15 []      60      74 ..      60      74 .. 0.98

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.031
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C +C  C +vC ++
  gi|15668232|ref|NP_247025.1| 30 CKNCLSCYRVCKNN 43
                                  99**88*****765 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.7e-06
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  Ct Cg C++vC++gA
  gi|15668232|ref|NP_247025.1| 60 CTKCGECLKVCRYGA 74
                                  **************9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.3    0.0037       4.5      45      75 ..      14      44 ..       6      52 .. 0.73
   2 ?   12.3   2.8   0.00012      0.15      49      74 ..      48      73 ..      41      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0037
                       Fer4_18 45 kalkekeerkekgagdcidcescvkvcPtgi 75
                                  k  +++++  e + ++c +c sc +vc  ++
  gi|15668232|ref|NP_247025.1| 14 KIEEKSNKIIEIDYNKCKNCLSCYRVCKNNV 44
                                  3444555556678899***********8765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00012
                       Fer4_18 49 ekeerkekgagdcidcescvkvcPtg 74
                                  ++++   k++++c++c+ c+kvc  g
  gi|15668232|ref|NP_247025.1| 48 KNNRVVVKNENNCTKCGECLKVCRYG 73
                                  4455567899*************866 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.7   0.00023      0.28       1      32 [.      25      55 ..      25      58 .. 0.79
   2 ?    6.6   3.1    0.0097        12       2      16 ..      56      70 ..      53      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                       Fer4_13  1 VDrdtCiacgaCvelaP.dvFeeddeggasvva 32
                                  +D ++C +c +C+ ++  +vF+++++  ++vv+
  gi|15668232|ref|NP_247025.1| 25 IDYNKCKNCLSCYRVCKnNVFAIKNN--RVVVK 55
                                  7999************7369999876..55555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0097
                       Fer4_13  2 DrdtCiacgaCvela 16
                                  ++++C+ cg C +++
  gi|15668232|ref|NP_247025.1| 56 NENNCTKCGECLKVC 70
                                  5799********999 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   0.00023      0.27       1      25 [.      23      48 ..      23      58 .. 0.80
   2 ?    5.3   2.3     0.027        33       4      18 ..      56      70 ..      52      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                       Fer4_15  1 VvvDrdaCigcglCvaea.pevfeld 25
                                  +++D ++C  c  C++++  +vf ++
  gi|15668232|ref|NP_247025.1| 23 IEIDYNKCKNCLSCYRVCkNNVFAIK 48
                                  79****************54566655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.027
                       Fer4_15  4 DrdaCigcglCvaea 18
                                  ++++C+ cg C++++
  gi|15668232|ref|NP_247025.1| 56 NENNCTKCGECLKVC 70
                                  5789********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1490  (0.0831056); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 510.03
//
Query:       gi|15668233|ref|NP_247026.1|  [L=207]
Description: hypothetical protein MJ_0062 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-48  163.6   0.2    3.7e-48  163.4   0.2    1.1  1  Sua5_yciO_yrdC  Telomere recombination


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   0.2   2.1e-52   3.7e-48       3     179 .]      29     197 ..      27     197 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 2.1e-52
                                   HHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEEEE CS
                Sua5_yciO_yrdC   3 lrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitlllk 83 
                                   + +G+iv+  t+t Yg+ ++a ne+av+++++iK+r+ +kpl+++v++ ++++k+a   v++ a k++++f+PGp+t++lk
  gi|15668233|ref|NP_247026.1|  29 ILNGKIVICGTDTLYGISANALNEKAVRKVYNIKRREFNKPLSICVRDKNEIEKYAY--VNDLAKKIIDKFLPGPLTIILK 107
                                   679*****************************************************9..********************** PP

                                   ..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---SSS---E CS
                Sua5_yciO_yrdC  84 rskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeiavgvdst 164
                                   ++   +p+ va  ++ +G+r+Pd+p++r+L      pl++TSan+sg++s+t+ +e+++e+ ++vd+++d g+++ + +st
  gi|15668233|ref|NP_247026.1| 108 KKPG-IPDIVA--KDYIGIRIPDEPIIRELSIV---PLTTTSANISGKESPTTVDEIDKEVLKKVDYVIDIGKCKYSKPST 182
                                   6444.****97..59****************99...********************************************* PP

                                   EEETTSSTSSECEXX CS
                Sua5_yciO_yrdC 165 VvdltegkpkilRrG 179
                                   ++++ ++k+  +R+G
  gi|15668233|ref|NP_247026.1| 183 IIKIEDDKIISIREG 197
                                   *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1416.20
//
Query:       gi|15668234|ref|NP_247027.1|  [L=181]
Description: hypothetical protein MJ_0063 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0088   16.0   2.4     0.0088   16.0   2.4    2.1  2  PhaP_Bmeg        Polyhydroxyalkanoic acid inclusion protein (
  ------ inclusion threshold ------
      0.014   15.2  10.3       0.33   10.8   1.1    2.2  2  DUF724           Protein of unknown function (DUF724)
      0.018   15.3   7.2      0.024   14.9   1.0    2.7  2  DUF948           Bacterial protein of unknown function (DUF94
      0.019   15.1   6.1       0.14   12.4   2.8    2.8  2  CHDCT2           CHDCT2 (NUC038) domain
      0.028   14.9  10.0       0.11   13.1   1.3    2.7  2  Syntaxin-6_N     Syntaxin 6, N-terminal
      0.031   14.0  14.9      0.093   12.4   7.3    2.5  2  GrpE             GrpE
      0.037   14.2   6.3       0.25   11.5   0.6    2.6  2  SesA             N-terminal domain on NACHT_NTPase and P-loop
      0.042   13.1  12.1      0.053   12.8  12.1    1.1  1  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
      0.045   13.5   2.3       0.17   11.5   0.9    2.1  2  DUF4239          Protein of unknown function (DUF4239)
      0.077   12.2  17.6       0.12   11.5   0.5    3.0  3  Taxilin          Myosin-like coiled-coil protein
       0.11   12.1  13.5       0.14   11.7   0.4    2.9  3  Fzo_mitofusin    fzo-like conserved region
       0.14   12.5  17.9        1.8    8.9   1.7    3.2  3  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.17   11.5  16.9       0.11   12.0   1.9    1.9  2  CENP-K           Centromere-associated protein K
       0.17   11.5   5.3       0.37   10.4   0.6    2.4  2  IL11             Interleukin 11
       0.17   12.1   0.6         12    6.2   0.0    3.1  3  WXG100           Proteins of 100 residues with WXG
       0.22   11.4  14.4       0.49   10.3   6.9    2.7  2  Sec34            Sec34-like family
       0.27   11.3  16.9      0.045   13.8   8.6    2.5  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.28    8.9  12.1       0.34    8.6  12.1    1.1  1  Nup88            Nuclear pore component
       0.34   11.0  10.7        1.9    8.5   2.7    2.8  3  DUF1664          Protein of unknown function (DUF1664)
       0.34   10.3   1.0          3    7.2   0.2    2.0  2  Mce4_CUP1        Cholesterol uptake porter CUP1 of Mce4, puta
       0.35   10.7   4.7        1.1    9.1   1.8    2.5  2  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.42   10.9   5.5        1.2    9.5   0.1    2.9  2  Rx_N             Rx N-terminal domain
       0.47   11.4   9.8       0.12   13.3   3.1    2.2  2  PRKG1_interact   cGMP-dependent protein kinase interacting do
       0.56   10.5  12.1        1.4    9.2   1.3    3.2  3  KxDL             Uncharacterized conserved protein
       0.73    9.1   8.0        2.9    7.1   0.6    2.6  2  DUF3450          Protein of unknown function (DUF3450)
       0.77    9.6  10.8       0.49   10.2   3.8    2.2  2  PCRF             PCRF domain
        0.8    8.8  12.4        1.4    8.0  12.4    1.5  1  APG17            Autophagy protein Apg17
       0.98    8.6  15.7      0.031   13.6   2.5    2.7  3  FmiP_Thoc5       Fms-interacting protein/Thoc5
       0.98    7.3  12.2       0.27    9.1   4.8    2.0  2  V_ATPase_I       V-type ATPase 116kDa subunit family
        1.2    8.9   6.7       0.53   10.0   0.4    2.3  2  Fibin            Fin bud initiation factor homologue
        1.2    9.3  13.9       0.27   11.4   7.2    2.3  2  Fib_alpha        Fibrinogen alpha/beta chain family
        1.2    9.3   5.4       0.52   10.4   2.2    2.1  1  ArnB_C           Archaellum regulatory network B, C-terminal 
        1.7    9.1  13.4        4.2    7.9   0.2    3.4  4  NPV_P10          Nucleopolyhedrovirus P10 protein
        2.2    9.1   7.7        5.9    7.7   2.2    2.6  3  Occludin_ELL     Occludin homology domain
          4    7.5  14.3        3.1    7.9   0.8    3.1  3  DivIVA           DivIVA protein
          4    7.6  10.8       0.78    9.9   4.1    2.3  2  CREPT            Cell-cycle alteration and expression-elevate
        6.2    7.0  16.3        4.4    7.5   0.5    3.9  4  bZIP_1           bZIP transcription factor
        6.2    6.0   8.9        3.1    7.0   1.2    2.1  2  TMPIT            TMPIT-like protein
        7.5    6.4  14.3        2.4    8.0   2.2    3.4  3  DASH_Duo1        DASH complex subunit Duo1
        7.7    7.0  14.6         41    4.7   5.5    3.2  2  Snapin_Pallidin  Snapin/Pallidin


Domain annotation for each model (and alignments):
>> PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3      0.63   2.8e+02      19      59 ..      20      60 ..       4      70 .. 0.56
   2 !   16.0   2.4     2e-05    0.0088      43     132 ..      76     159 ..      73     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.63
                     PhaP_Bmeg 19 eslerfaslskqvEqltLkalkqqqdlvkeltkalseleke 59
                                  +sl r+a   k+  +   ++l q  +++ ++ k l+ +ek+
  gi|15668234|ref|NP_247027.1| 20 KSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKN 60
                                  44444433333333333356666666666666666666665 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2e-05
                     PhaP_Bmeg  43 qdlvkeltkalselekeskqltaeledqlqktvenlrskaGnkvednieEwtdkleevsakleklalspsKssldllkkae 123
                                   +++++++ k l++l k   ++++   ++l++ +en +s         ++E tdkl+ + + +   a+   K  +d+l+  +
  gi|15668234|ref|NP_247027.1|  76 NEIIQKFVKPLENLIKVIENIESTS-NNLKNEIENCASSIP-----TLKEITDKLKIINMESATQAIEEFKIAYDMLEDNR 150
                                   688999999*****99999999998.888999999966654.....569******************************** PP

                     PhaP_Bmeg 124 eqleetvks 132
                                   ++l+e +++
  gi|15668234|ref|NP_247027.1| 151 KNLDELIEK 159
                                   **9997764 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.1   0.00074      0.33     126     185 ..       6      65 ..       2      68 .. 0.92
   2 ?    9.3   2.5    0.0021      0.93     105     184 ..      80     160 ..      73     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00074
                        DUF724 126 rkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFeava 185
                                   ++ +e + +l++ i+ l r +  +k+++e+ ++ + +l    ++++++le +e++F+ ++
  gi|15668234|ref|NP_247027.1|   6 NRNDELFIKLDSSIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKNFQIIL 65 
                                   56789999************************************************9876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0021
                        DUF724 105 tklleerkklekkieeeesekrkleeeidelekkilelerqlallk.ekkeaadkeiarlkseaekleeeledveqeFeav 184
                                   +k  + +++l k ie+ es +++l++ei++  + i +l++  + lk  ++e+a + i + k   ++le++ ++  +  e++
  gi|15668234|ref|NP_247027.1|  80 QKFVKPLENLIKVIENIESTSNNLKNEIENCASSIPTLKEITDKLKiINMESATQAIEEFKIAYDMLEDNRKNLDELIEKT 160
                                   66677788899999999*************************999998999999999999999999999888877666655 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.0   5.4e-05     0.024      19      86 ..      38     105 ..      12     108 .. 0.96
   2 ?    3.3   0.6      0.23     1e+02      53      86 ..     136     169 ..     109     180 .. 0.46

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.4e-05
                        DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                    vll+l+++ld++ +t+e +ek+ + ilk+ e      ne+ +   + le++ +++e+++ +++++++
  gi|15668234|ref|NP_247027.1|  38 NVLLQLAEMLDNIDKTLEIIEKNFQIILKNRESGKFSNNEIIQKFVKPLENLIKVIENIESTSNNLKN 105
                                   589************************************************************99875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.23
                        DUF948  53 lakvnelledvneklekvdplteavadlgesvse 86 
                                   +++ +   + +++  +++d+l+e+ + l +++++
  gi|15668234|ref|NP_247027.1| 136 IEEFKIAYDMLEDNRKNLDELIEKTKILKDKLKN 169
                                   3333333333333333333333333333333332 PP

>> CHDCT2  CHDCT2 (NUC038) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.8    0.0003      0.14      97     163 ..      51     127 ..       1     134 [. 0.71
   2 ?    0.1   0.1       1.8     8e+02      96     136 ..     138     178 ..     125     180 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0003
                        CHDCT2  97 faelellaeshqkllkesaagnknanavle..........kvLnqleelLsdmkadvsrlpatlsrlrpvaeRLqms 163
                                    ++le++ +  q +lk+ ++g+ + n++++          kv++++e   +++k++++   ++++ l+ ++++L++ 
  gi|15668234|ref|NP_247027.1|  51 DKTLEIIEKNFQIILKNRESGKFSNNEIIQkfvkplenliKVIENIESTSNNLKNEIENCASSIPTLKEITDKLKII 127
                                   2334555555566666666677777777777777888888**********************************975 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.8
                        CHDCT2  96 rfaelellaeshqkllkesaagnknanavlekvLnqleelL 136
                                   +f+ +  + e ++k l e  +  k  ++ l+++L q+++ L
  gi|15668234|ref|NP_247027.1| 138 EFKIAYDMLEDNRKNLDELIEKTKILKDKLKNLLLQIDNFL 178
                                   34444444444455555555556666666777777777666 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.3   0.00023      0.11      25      83 ..      20      80 ..       6      94 .. 0.72
   2 ?    6.1   2.9     0.037        16      36      91 ..      93     156 ..      73     179 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00023
                  Syntaxin-6_N 25 erlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsr 83
                                  ++ll+++++  +++e++++   +L + l++i+++le +e+  +i+ kn++  k +++e+ +
  gi|15668234|ref|NP_247027.1| 20 KSLLRSAREfkKENESISNVLLQLAEMLDNIDKTLEIIEKNFQIILKNRESGKFSNNEIIQ 80
                                  3334444444346888888888999999999999999999999999999999999999864 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.037
                  Syntaxin-6_N  36 seeldetrteLrkalrsiewdledLeetv...riv.....eknpskfkidekelsrrrafveev 91 
                                    e++++t+++L++++++    +  L+e     +i+      +  ++fki  + l+  r+ ++e+
  gi|15668234|ref|NP_247027.1|  93 IENIESTSNNLKNEIENCASSIPTLKEITdklKIInmesaTQAIEEFKIAYDMLEDNRKNLDEL 156
                                   3444444444444444444443333333322222222111222344555555555555554444 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   7.3   0.00021     0.093       9     117 ..      14     132 ..       5     139 .. 0.80
   2 ?    5.7   1.1     0.024        11      11      46 ..     143     178 ..     133     181 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00021
                                   TTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHH...HHHHH......HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          GrpE   9 eeedeeeeleeeleelekevkelkekllrllaefenlrkrt...ekeke......eakkfaiekfakdLLpvlDnleralk 80 
                                   +++  +++l +   e++ke +++++ ll+l++ ++n+ k +   ek+++      e  kf++ +++++++++l+nl ++++
  gi|15668234|ref|NP_247027.1|  14 KLDSSIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLeiiEKNFQiilknrESGKFSNNEIIQKFVKPLENLIKVIE 94 
                                   5677788899999999999999999999999999999988744433332111112667999******************** PP

                                   C...HHH-HHHHHHHHHHHHHHHHHHHHHTT-EE---T CS
                          GrpE  81 sak.eneeekslleGvemtlkqllkiLekhgvekiepk 117
                                   +++ +++++k+ +e        l++i +k ++  +e+ 
  gi|15668234|ref|NP_247027.1|  95 NIEsTSNNLKNEIENCASSIPTLKEITDKLKIINMESA 132
                                   **999999999999999999999999999999888765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.024
                                   HHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHH CS
                          GrpE  11 edeeeeleeeleelekevkelkekllrllaefenlr 46 
                                    d +e+++++l+el ++ k lk+kl++ll +++n+ 
  gi|15668234|ref|NP_247027.1| 143 YDMLEDNRKNLDELIEKTKILKDKLKNLLLQIDNFL 178
                                   5678889999***********************996 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6   0.00056      0.25      20      79 ..      38      96 ..      16     100 .. 0.83
   2 ?    7.7   1.5    0.0086       3.9       5      63 ..      83     140 ..      78     165 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00056
                          SesA 20 d.ikglpeaFrevgkrLplvqetLedaksqlesskldedtesaikpvlesckekatkleei 79
                                  + + +l e ++++ k L+++++ ++ + ++ es+k+++++   i++ ++  ++ ++ +e+i
  gi|15668234|ref|NP_247027.1| 38 NvLLQLAEMLDNIDKTLEIIEKNFQIILKNRESGKFSNNE--IIQKFVKPLENLIKVIENI 96
                                  45668999999**************************984..5**********99999988 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0086
                          SesA   5 iaiveaaiklydaikd.ikglpeaFrevgkrLplvqetLedaksqlesskldedtesa..ik 63 
                                   +  +e +ik++++i++  ++l++++++ ++++p++    ++++++l+  + +++t++   +k
  gi|15668234|ref|NP_247027.1|  83 VKPLENLIKVIENIEStSNNLKNEIENCASSIPTL----KEITDKLKIINMESATQAIeeFK 140
                                   44555566666666554555666666666666643....33333333333333333322233 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  12.1   0.00012     0.053     142     291 ..      19     180 ..       5     181 .] 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                ALIX_LYPXL_bnd 142 lrsllekldelkaereqllkdlkekaen.dDitpkl..........ltekkrdiaanefealfeeelekydplqeqleqsl 211
                                   ++sll    e k+e e++ + l + ae  d+i ++l          l++ ++ ++ ++ +++ ++ ++ ++ l++ +e+  
  gi|15668234|ref|NP_247027.1|  19 IKSLLRSAREFKKENESISNVLLQLAEMlDNIDKTLeiieknfqiiLKNRES-GKFSN-NEIIQKFVKPLENLIKVIENIE 97 
                                   5666666666666666666655443332133433332222222221444444.66666.7799999999999999998888 PP

                ALIX_LYPXL_bnd 212 akqeellkeiqeaneefeqskksdseq...sqrqreevlqkleaaydkykelksnleeglkFYndltelleklqkkvkdfv 289
                                   +  ++l +ei++  +++   k+  ++    + ++  +++++++ ayd  ++ ++nl+e ++  + l+++l++l+ +++ f+
  gi|15668234|ref|NP_247027.1|  98 STSNNLKNEIENCASSIPTLKEITDKLkiiNMESATQAIEEFKIAYDMLEDNRKNLDELIEKTKILKDKLKNLLLQIDNFL 178
                                   88999999**99999999999888765555588899********************************************9 PP

                ALIX_LYPXL_bnd 290 fa 291
                                   ++
  gi|15668234|ref|NP_247027.1| 179 NE 180
                                   85 PP

>> DUF4239  Protein of unknown function (DUF4239)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.058        26      79     118 ..       6      45 ..       2      53 .. 0.80
   2 ?   11.5   0.9   0.00039      0.17      33     126 ..      31     120 ..      27     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.058
                       DUF4239  79 asrgelslkasseltkLldllaevkgdassesaaveells 118
                                   ++ +el +k +s ++ Ll  + e+k+++ s s+   +l +
  gi|15668234|ref|NP_247027.1|   6 NRNDELFIKLDSSIKSLLRSAREFKKENESISNVLLQLAE 45 
                                   4566999**********************99887666655 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00039
                       DUF4239  33 kEAslLrlvtrnlislftselerkeakaliadyvktivseerslvrasrgelslkasseltkLldllaevkgdassesaav 113
                                   kE   +++v   l++++ +++  ++  ++i +  ++i ++  s+   s +e+  k  ++l++L + +++++    + ++  
  gi|15668234|ref|NP_247027.1|  31 KENESISNVLLQLAEML-DNI--DKTLEIIEKNFQIILKNRESGK-FSNNEIIQKFVKPLENLIKVIENIESTSNNLKNEI 107
                                   56667777777888888.455..7889999999999998888887.788878888************************** PP

                       DUF4239 114 eellseiaqltel 126
                                   e+  s i+ l+e+
  gi|15668234|ref|NP_247027.1| 108 ENCASSIPTLKEI 120
                                   **********997 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   3.7     0.017       7.8      97     162 ..       4      69 ..       1      72 [. 0.94
   2 ?   11.5   0.5   0.00027      0.12     236     279 ..      76     119 ..      74     140 .. 0.84
   3 ?    4.3   1.8     0.044        20      46      75 ..     141     170 ..     114     181 .] 0.55

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.017
                       Taxilin  97 eeekrkelaekfqakLkdiqaqieekserneklreenaelteKlkslieqyelreehfekllktke 162
                                    e++++el  k+ +++k++  +  e +++ne+  +   +l+e l+++ +  e+ e++f+ +lk +e
  gi|15668234|ref|NP_247027.1|   4 MENRNDELFIKLDSSIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKNFQIILKNRE 69 
                                   5788999999****************************************************9998 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00027
                       Taxilin 236 nelFatFkkEmekmtkktkklEketnlwkskfektnkallemae 279
                                   ne++++F k +e++ k ++++E  +n++k+  e++   +  + e
  gi|15668234|ref|NP_247027.1|  76 NEIIQKFVKPLENLIKVIENIESTSNNLKNEIENCASSIPTLKE 119
                                   9**********************************999866555 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.044
                       Taxilin  46 kkleqlqkekeqlqaelskaalaksKLekL 75 
                                     ++ l  ++++l +  +k++ +k+KL +L
  gi|15668234|ref|NP_247027.1| 141 IAYDMLEDNRKNLDELIEKTKILKDKLKNL 170
                                   444444444444444445555555555444 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.7       0.7   3.1e+02      98     145 ..      14      61 ..       2      76 .. 0.61
   2 ?   11.7   0.4   0.00031      0.14     106     144 ..      92     130 ..      70     143 .. 0.78
   3 ?    7.9   1.7    0.0046       2.1     115     157 ..     137     179 ..     129     181 .] 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.7
                 Fzo_mitofusin  98 elsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnka 145
                                   +l+s ++ l ++ +e +ke e+  + l +  e+l+++ k+++++ +  
  gi|15668234|ref|NP_247027.1|  14 KLDSSIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKNF 61 
                                   555666666666666666655555555555566666666666665544 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00031
                 Fzo_mitofusin 106 lcqqvdetekeleeeikelekeiekleevqkkakllrnk 144
                                   + ++++ t+++l++ei++  ++i +l+e++ k+k++  +
  gi|15668234|ref|NP_247027.1|  92 VIENIESTSNNLKNEIENCASSIPTLKEITDKLKIINME 130
                                   45678999**************************99754 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0046
                 Fzo_mitofusin 115 keleeeikelekeiekleevqkkakllrnkaslleseLekfee 157
                                   +e++   + le + ++l+e+++k k+l++k ++l  ++++f +
  gi|15668234|ref|NP_247027.1| 137 EEFKIAYDMLEDNRKNLDELIEKTKILKDKLKNLLLQIDNFLN 179
                                   566667788999999************************9976 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.7     0.004       1.8      27      80 ..       3      56 ..       1      62 [. 0.83
   2 ?    6.4   2.8     0.025        11      28      86 ..      74     138 ..      50     142 .. 0.61
   3 ?    7.0   1.4     0.016       7.3      36      70 ..     143     177 ..     137     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.004
                       BLOC1_2 27 klNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeea 80
                                  ++ ++  e + kl+++++sl +++ + ++++e++++ l q+ ++ +++++  e+
  gi|15668234|ref|NP_247027.1|  3 QMENRNDELFIKLDSSIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEI 56
                                  67778888899***********************99999988888888765444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.025
                       BLOC1_2  28 lNeaaseky....kklkdvaaslekkleklnekyeelqpylqqidqiekq..vteLeeavseLDe 86 
                                    N++ ++k+    ++l +v++++e+++++l+++ e+ ++ +  +++i ++  +  +e+a ++++e
  gi|15668234|ref|NP_247027.1|  74 SNNEIIQKFvkplENLIKVIENIESTSNNLKNEIENCASSIPTLKEITDKlkIINMESATQAIEE 138
                                   55555555522113455667788888888888888888888888888775224567777777776 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.016
                       BLOC1_2  36 ykklkdvaaslekkleklnekyeelqpylqqidqi 70 
                                   y+ l+d+ ++l + +ek++ ++++l+++l qid++
  gi|15668234|ref|NP_247027.1| 143 YDMLEDNRKNLDELIEKTKILKDKLKNLLLQIDNF 177
                                   8899999*************************986 PP

>> CENP-K  Centromere-associated protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   7.9     0.048        22     108     214 ..      18     124 ..      10     129 .. 0.90
   2 ?   12.0   1.9   0.00025      0.11     127     179 ..     129     181 .]     125     181 .] 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.048
                        CENP-K 108 klkedLkrEqewleeqqeilesLkektkelkkqvvafsektrksaelkekirkikeykeeLltaLgefLdehfplpeeeea 188
                                    +k  L+  +e+ +e+++i + L +  + l +  +++   ++ ++++ +     k  ++e++++  + L++     e+ e+
  gi|15668234|ref|NP_247027.1|  18 SIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKNFQIILKNRESGKFSNNEIIQKFVKPLENLIKVIENIES 98 
                                   5778888999999999******999999999999999999899999999999999999*******************9999 PP

                        CENP-K 189 svkkkkkqkqeptlnlitlkeilEiL 214
                                   +++  k+++++ +  + tlkei ++L
  gi|15668234|ref|NP_247027.1|  99 TSNNLKNEIENCASSIPTLKEITDKL 124
                                   999999999999999******98877 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00025
                        CENP-K 127 lesLkektkelkkqvvafsektrksaelkekirkikeykeeLltaLgefLdeh 179
                                   +es ++ ++e k     + ++++ + el ek + +k   ++Ll  +++fL+eh
  gi|15668234|ref|NP_247027.1| 129 MESATQAIEEFKIAYDMLEDNRKNLDELIEKTKILKDKLKNLLLQIDNFLNEH 181
                                   677888888999888888888888****************************9 PP

>> IL11  Interleukin 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00083      0.37      50     126 ..      29     107 ..       4     144 .. 0.76
   2 ?    4.0   0.9     0.076        34      37     117 ..     104     179 ..      94     181 .] 0.54

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00083
                          IL11  50 lsnsasdlss..levkstLsqLhtdlksyekHfdWLkkvskkskhslepklgelisklkrLlkslqllmskleaprvpv 126
                                    +++ +++s+  l++ ++L  +++ l++ ek f+ + k+ +  k s ++ +++ ++ l++L+k +++  s  +  ++++
  gi|15668234|ref|NP_247027.1|  29 FKKENESISNvlLQLAEMLDNIDKTLEIIEKNFQIILKNRESGKFSNNEIIQKFVKPLENLIKVIENIESTSNNLKNEI 107
                                   555556666544799***************************9999999999999999999999987665555555444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.076
                          IL11  37 psdvehrlksLPalsnsasdlsslevkstLsqLhtdlksyekHfdWLkkvskkskhslepklgelisklkrLlkslqllms 117
                                   ++++e   +s+P+l++   +l+ ++++s+     + ++ ++   d L+ + k+ ++ + +k++ l+ klk+Ll ++++ ++
  gi|15668234|ref|NP_247027.1| 104 KNEIENCASSIPTLKEITDKLKIINMESAT----QAIEEFKIAYDMLEDNRKNLDELI-EKTKILKDKLKNLLLQIDNFLN 179
                                   555565566666666666666666655553....334445555555666555444444.5556666666666666655555 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.027        12      10      37 ..      23      50 ..      14      62 .. 0.74
   2 ?    1.9   0.0      0.58   2.6e+02      21      37 ..      94     110 ..      80     125 .. 0.63
   3 ?    0.6   0.1       1.5   6.8e+02      10      34 ..     133     157 ..     126     176 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.027
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                        WXG100 10 rqaaarfqkqaeeledelqrlkaevdal 37
                                    +a++f+k++e+++++l +l+ ++d++
  gi|15668234|ref|NP_247027.1| 23 LRSAREFKKENESISNVLLQLAEMLDNI 50
                                  5567778888888888887777777776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.58
                                   HHHHHHHHHHHHHHHHC CS
                        WXG100  21 eeledelqrlkaevdal 37 
                                   e++e+  ++lk+e++++
  gi|15668234|ref|NP_247027.1|  94 ENIESTSNNLKNEIENC 110
                                   34444444444444444 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100  10 rqaaarfqkqaeeledelqrlkaev 34 
                                   +qa+ +f+ + + led  ++l+  +
  gi|15668234|ref|NP_247027.1| 133 TQAIEEFKIAYDMLEDNRKNLDELI 157
                                   4444444444444444444444433 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.9     0.045        20      35     107 ..      21      56 ..       3      74 .. 0.54
   2 ?   10.3   6.9    0.0011      0.49       7     105 ..      81     178 ..      65     181 .] 0.92

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.045
                         Sec34  35 svsektsslheaceqlleeqkrleelaeeieekLkyFeeldpitrkLnspgsslvksesFlemLkklDeclef 107
                                   s   + ++++++ e++ +   +l e+ ++i++ L                                     e 
  gi|15668234|ref|NP_247027.1|  21 SLLRSAREFKKENESISNVLLQLAEMLDNIDKTL-------------------------------------EI 56 
                                   4444444444444444444444444444444444.....................................33 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0011
                         Sec34   7 skeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpitrkLnspgss 87 
                                   +  + +++l++ +++++++ ++l+++ ++ +++  +l+e +++l  +  ++e+ +++iee    ++ l+   ++L++  ++
  gi|15668234|ref|NP_247027.1|  81 KFVKPLENLIKVIENIESTSNNLKNEIENCASSIPTLKEITDKL--KIINMESATQAIEEFKIAYDMLEDNRKNLDELIEK 159
                                   55677899***********************************9..57889999***********************9999 PP

                         Sec34  88 .lvksesFlemLkklDecl 105
                                     + +++ +++L ++D+ l
  gi|15668234|ref|NP_247027.1| 160 tKILKDKLKNLLLQIDNFL 178
                                   99**************854 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   8.6    0.0001     0.045      30     111 ..      37     117 ..      33     140 .. 0.69
   2 ?    2.3   2.0      0.34   1.5e+02      56      95 ..     134     179 ..     115     180 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.0001
                  Baculo_PEP_C  30 vqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLnn 110
                                   +++l qla++ld+i+++L+ ++++++  l++ ++   ++ + +++ ++ l+ +l + ++n++s  +nL +++ N  s++  
  gi|15668234|ref|NP_247027.1|  37 SNVLLQLAEMLDNIDKTLEIIEKNFQIILKNRESGKFSNNEIIQKFVKPLE-NLIKVIENIESTSNNLKNEIENCASSIPT 116
                                   67889**********************999988843334444555555554.56666777777777777777776665443 PP

                  Baculo_PEP_C 111 l 111
                                   l
  gi|15668234|ref|NP_247027.1| 117 L 117
                                   3 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.34
                  Baculo_PEP_C  56 sllaeldt......rldtlltnLtdalnalq...dtlrneLtnlnsilt 95 
                                   ++++   +      +l+++ +nL++ + + +   d+l+n L  +++ l+
  gi|15668234|ref|NP_247027.1| 134 QAIE---EfkiaydMLEDNRKNLDELIEKTKilkDKLKNLLLQIDNFLN 179
                                   2233...233355577888888888877765445777776666666555 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  12.1   0.00077      0.34     570     707 ..      22     165 ..      12     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00077
                         Nup88 570 qleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelekikeklkslknalkq 650
                                    l+  ++ ++e +s+s+   +lAe +++i +  e + +  + +lk+ +s  ++  e+ +++ k le++ + +++++ + ++
  gi|15668234|ref|NP_247027.1|  22 LLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKNFQIILKNRESGKFSNNEIIQKFVKPLENLIKVIENIESTSNN 102
                                   5666778899**************************************************************999999999 PP

                         Nup88 651 vkkkldkqrkqiakskeeekksslelsekqk......ktikeiLkeegeeieelikqvkdikk 707
                                   +k+ ++  ++ i   ke+++k ++   e+        k+  ++L+++ ++++eli++ k +k 
  gi|15668234|ref|NP_247027.1| 103 LKNEIENCASSIPTLKEITDKLKIINMESATqaieefKIAYDMLEDNRKNLDELIEKTKILKD 165
                                   99999999998887777766655544444440111115556799999********99998886 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.6      0.02       8.7      49      95 ..      14      60 ..       3      71 .. 0.50
   2 ?    8.5   2.7    0.0043       1.9      49     118 ..      88     158 ..      73     166 .. 0.77
   3 ?    1.9   0.5      0.49   2.2e+02      57      82 ..     146     171 ..     125     181 .] 0.44

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.02
                       DUF1664 49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevred 95
                                  +l++  +sl +  r+++++ +++ + l + +e+  +i++ ++ ++++
  gi|15668234|ref|NP_247027.1| 14 KLDSSIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKN 60
                                  44444444444444444444444444444444444444444444444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0043
                       DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeike.evtevredlseigedvesvkeavegleskle 118
                                   +l +v e++++t ++L+++i++  +++   kei+ ++k  +++++ + ++e++   + +++  ++l++ +e
  gi|15668234|ref|NP_247027.1|  88 NLIKVIENIESTSNNLKNEIENCASSIPTLKEITDKLKIiNMESATQAIEEFKIAYDMLEDNRKNLDELIE 158
                                   56678899999999********9999999999999887436777777777777777777777777776655 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.49
                       DUF1664  57 laatkrhLssridrvdkkldeqkeis 82 
                                   l++ +++L + i++     d+ k++ 
  gi|15668234|ref|NP_247027.1| 146 LEDNRKNLDELIEKTKILKDKLKNLL 171
                                   33333333333333333333333332 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0067         3      40     136 ..       8     104 ..       3     125 .. 0.80
   2 ?    4.1   0.1     0.062        28      39     106 ..      95     163 ..      81     178 .. 0.46

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0067
                     Mce4_CUP1  40 lnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsntgadllerngdn 120
                                    +e++ +l++++ +l +  re+++ ++  +++  +l ++Ldn+ +t + i+++ + + +   +     n+  + + +  +n
  gi|15668234|ref|NP_247027.1|   8 NDELFIKLDSSIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKNFQIILKNRESGKFSNNEIIQKFVKPLEN 88 
                                   567788999999999999999999999999999999999999999999998887777777666666667778888888888 PP

                     Mce4_CUP1 121 LirlaadlrptlelLa 136
                                   Li+++++ + t++ L+
  gi|15668234|ref|NP_247027.1|  89 LIKVIENIESTSNNLK 104
                                   8888888888877665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.062
                     Mce4_CUP1  39 dlnevLdelNprlpqlredireladladvYadaa.pdlldaLdnavttsrTiveqqaeLdalllaavgl 106
                                   ++++  ++l +++++  + i +l++++d  + +  +   +a++++    + +++++++Ld+l+ ++  l
  gi|15668234|ref|NP_247027.1|  95 NIESTSNNLKNEIENCASSIPTLKEITDKLKIINmESATQAIEEFKIAYDMLEDNRKNLDELIEKTKIL 163
                                   333333333333333333333333333333332212234455555555555555555555555555544 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.8    0.0024       1.1      95     171 ..      43     120 ..      17     121 .. 0.69
   2 ?    1.7   0.1      0.44     2e+02     106     147 ..     129     170 ..     118     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0024
                                   H..............HHHHHHHHHHHHHHH.HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  95 iieiqkeindsvesleetrqrveegselve.etgealkeiveavaevadlvqeiaaaseeqsasieevnqaveevakv 171
                                   ++e+  +i++++e++e+  q + +  e  + + +e +++ v+  +++ +++++i ++s+++ + ie+ ++++  ++++
  gi|15668234|ref|NP_247027.1|  43 LAEMLDNIDKTLEIIEKNFQIILKNRESGKfSNNEIIQKFVKPLENLIKVIENIESTSNNLKNEIENCASSIPTLKEI 120
                                   23455566666666666666665555444424567789999999***********************99999887766 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.44
                                   ....HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal 106 vesleetrqrveegselveetgealkeiveavaevadlvqei 147
                                   +es +++ ++ + + ++ e+ +++l e+ e+++ ++d ++++
  gi|15668234|ref|NP_247027.1| 129 MESATQAIEEFKIAYDMLEDNRKNLDELIEKTKILKDKLKNL 170
                                   455566667777889999999999999999999998888886 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0027       1.2      36      73 ..      18      55 ..      10      74 .. 0.92
   2 ?    2.1   1.6      0.52   2.3e+02      21      42 ..     158     179 ..      76     181 .] 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0027
                          Rx_N 36 siqavLedaeerqikdeavkeWlkelrdlaydaeDvlD 73
                                  si+++L+ a e + ++e++ + l +l ++  +++  l+
  gi|15668234|ref|NP_247027.1| 18 SIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLE 55
                                  89*******************************99887 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.52
                          Rx_N  21 kgvkeeleklkdeLesiqavLe 42 
                                   ++ k   +klk+ L +i+ +L+
  gi|15668234|ref|NP_247027.1| 158 EKTKILKDKLKNLLLQIDNFLN 179
                                   2333333445555555555554 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   3.0      0.14        61       9      89 ..      29     106 ..       3     106 .. 0.68
   2 ?   13.3   3.1   0.00026      0.12      14      89 ..      87     166 ..      79     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.14
                PRKG1_interact   9 ekeenerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkiseleeelkeleeLraenqrLkdE 89 
                                    k+ene + + L +l + l+++ ++le ++++ q  + k+ ++ +++  +++ +++ ++ le+ +k++e++ + ++ Lk+E
  gi|15668234|ref|NP_247027.1|  29 FKKENESISNVLLQLAEMLDNIDKTLEIIEKNFQI-ILKNRESGKFS--NNEIIQKFVKPLENLIKVIENIESTSNNLKNE 106
                                   46777777777777777777777777777644222.22222222222..22334444556799999999999999999998 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00026
                PRKG1_interact  14 erLkreLeelekelselkseleklkqq..rqesvskrssllelekrerrslerkis.el.eeelkeleeLraenqrLkdE 89 
                                   e+L + +e++e   ++lk+e+e+ +++    ++++++ +++++e+  +   e ki+ ++ e++ k+l+eL ++ + Lkd 
  gi|15668234|ref|NP_247027.1|  87 ENLIKVIENIESTSNNLKNEIENCASSipTLKEITDKLKIINMESATQAIEEFKIAyDMlEDNRKNLDELIEKTKILKDK 166
                                   677888999999999*******999887777899********************9985559***********99999986 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.7      0.21        93      31      70 ..      21      60 ..       3      69 .. 0.50
   2 ?    3.3   0.0      0.22     1e+02      37      76 ..      80     119 ..      76     127 .. 0.71
   3 ?    9.2   1.3    0.0031       1.4      43      79 ..     132     168 ..     123     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.21
                          KxDL 31 eLlelnalsqerlaklrarfkqgtkllkevkkdLesifkk 70
                                   Ll+   + +++ +++++ + q +++l ++ k Le i k+
  gi|15668234|ref|NP_247027.1| 21 SLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKN 60
                                  3333444444444444444444444444444444444444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.22
                          KxDL  37 alsqerlaklrarfkqgtkllkevkkdLesifkkirslka 76 
                                   ++  + l++l + +++   +++++k+++e++ + i +lk+
  gi|15668234|ref|NP_247027.1|  80 QKFVKPLENLIKVIENIESTSNNLKNEIENCASSIPTLKE 119
                                   5555667777777777778888888888888888877776 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0031
                          KxDL  43 laklrarfkqgtkllkevkkdLesifkkirslkakla 79 
                                    +++ ++fk    +l + +k+L+ + +k++ lk+kl+
  gi|15668234|ref|NP_247027.1| 132 ATQAIEEFKIAYDMLEDNRKNLDELIEKTKILKDKLK 168
                                   5678899****************************97 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.6    0.0066       2.9      41      89 ..      14      62 ..       2      72 .. 0.84
   2 ?    5.0   0.5     0.029        13      57     112 ..      83     139 ..      74     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0066
                       DUF3450 41 klddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqie 89
                                  kld   ++ll+  r+ k+e+es++    ql++++++ +++++ +e++ +
  gi|15668234|ref|NP_247027.1| 14 KLDSSIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKNFQ 62
                                  78888899999999**********************9999999998765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.029
                       DUF3450  57 keeleslevyneqlerlvasqeqeiasleeqieeieeierelvpl.lekmidrLeqf 112
                                    + le+l +  e+ e+  +++++ei++   +i  ++ei ++l+ + +e+  +++e+f
  gi|15668234|ref|NP_247027.1|  83 VKPLENLIKVIENIESTSNNLKNEIENCASSIPTLKEITDKLKIInMESATQAIEEF 139
                                   566788888888899999999999999999999999999988865477777766666 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.9      0.12        53      33      94 ..      18      69 ..       4      94 .. 0.61
   2 ?   10.2   3.8    0.0011      0.49      18      94 ..     101     175 ..      79     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.12
                                  HTHHHHHHHHHHHHHTTTHHH...HT....-S-..-GGGTHHHHHHHHHH..HHHHHT-..S CS
                          PCRF 33 eleeivealeeleealedleeakelleedeelaelaeeeleelekeleeleeelkklLlpkd 94
                                  ++++++++++e+++++e++++   ll    +la    e l++++k+le +e++++++L +++
  gi|15668234|ref|NP_247027.1| 18 SIKSLLRSAREFKKENESISN--VLL----QLA----EMLDNIDKTLEIIEKNFQIILKNRE 69
                                  444455555555555555555..222....333....3366666666666666666666443 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                                   TTTGGGSSSTTHHHHHTHHHHHHHH..HHHHHTTTHHH...HT....-S-..-GGGTHHHHHHHHHH..HHHHHT-..S CS
                          PCRF  18 wedqekakklskelaeleeiveale..eleealedleeakelleedeelaelaeeeleelekeleeleeelkklLlpkd 94 
                                    + +++++++++++  l+ei+++l+  ++e+a++ +ee k ++    ++ e  +++l+el ++ + l+++lk+lLl  d
  gi|15668234|ref|NP_247027.1| 101 NNLKNEIENCASSIPTLKEITDKLKiiNMESATQAIEEFKIAY----DMLEDNRKNLDELIEKTKILKDKLKNLLLQID 175
                                   3345678888888888888888766336677888888877777....899999999*******************9554 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  12.4    0.0031       1.4      26     147 ..      28     172 ..      15     181 .] 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0031
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIIIIIIIIIIIIIIIIIHHHHHHHHHHHHHHHHHHHHHTSS-TTS.... CS
                         APG17  26 sarqeleeavkllakteflrdglkqQlkllekirkslerklekgkeefkdlikeldaanerLektlekLrktkvepsfrpe 106
                                   + ++e e++ ++l +++ + d++++ l+++ek  + + +++e+gk   +++i+++ +  e+L k +e  ++t + +    e
  gi|15668234|ref|NP_247027.1|  28 EFKKENESISNVLLQLAEMLDNIDKTLEIIEKNFQIILKNRESGKFSNNEIIQKFVKPLENLIKVIENIESTSNNLKNEIE 108
                                   556677788899999999********************************************************9993333 PP

                                   ........STGGGCS--TTTTHHHHHHHHH....................HHHHHHHHHHHHTTHH CS
                         APG17 107 gee.....ktLlDFvdedsveelkealkes....................idelqaaqkkldssll 147
                                     +      tL++  d+ ++ ++++a +++                    i++++ +++kl++ ll
  gi|15668234|ref|NP_247027.1| 109 --NcassiPTLKEITDKLKIINMESATQAIeefkiaydmlednrknldelIEKTKILKDKLKNLLL 172
                                   ..36799*9999999999997777765554333333333333333322224444444444444444 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.5   6.8e-05     0.031     106     161 ..      14      69 ..       2      86 .. 0.86
   2 ?    0.7   0.4      0.56   2.5e+02     109     144 ..      91     119 ..      72     145 .. 0.49
   3 ?    2.9   1.0      0.12        56     103     133 ..     149     179 ..     144     181 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.8e-05
                    FmiP_Thoc5 106 elaeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealglpltker 161
                                   +l++ +k+l ++ ++ ++e+e+  + L +L+++L+++ k+++ +++++++ l++++
  gi|15668234|ref|NP_247027.1|  14 KLDSSIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKNFQIILKNRE 69 
                                   79999*******************************************98666443 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.56
                    FmiP_Thoc5 109 eqlkeleekkkkleqeieekkkfLssLppkLkslkk 144
                                   + ++++e+  ++l++ei       ++ ++ + +lk+
  gi|15668234|ref|NP_247027.1|  91 KVIENIESTSNNLKNEI-------ENCASSIPTLKE 119
                                   23333333333333333.......333333333333 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.12
                    FmiP_Thoc5 103 qRkelaeqlkeleekkkkleqeieekkkfLs 133
                                    Rk+l+e +++++  k kl++   +  +fL+
  gi|15668234|ref|NP_247027.1| 149 NRKNLDELIEKTKILKDKLKNLLLQIDNFLN 179
                                   7999999999999999999999999999987 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.6     0.048        22      64     124 ..       5      66 ..       2      81 .. 0.78
   2 ?    9.1   4.8   0.00059      0.27      15     117 ..      76     179 ..      72     181 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.048
                    V_ATPase_I  64 eapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleee.eeeee 124
                                   e+++++ + +l++++++l ++ +e+++++e++++ l +l e+   + k+ e++e++ +   +
  gi|15668234|ref|NP_247027.1|   5 ENRNDELFIKLDSSIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKNfQIILK 66 
                                   567777889999999999999*************9999999999999999999887443333 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00059
                    V_ATPase_I  15 nedvnafqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenlekl 95 
                                   ne +++f +   + ++ ++++e + + l++eie+ ++ + + +e++++l+  ++++  +  ee++ +++ l++ ++nl++l
  gi|15668234|ref|NP_247027.1|  76 NEIIQKFVKPLENLIKVIENIESTSNNLKNEIENCASSIPTLKEITDKLKIINMESATQAIEEFKIAYDMLEDNRKNLDEL 156
                                   55577888888999********************99999999999999999999999999999999999999999999999 PP

                    V_ATPase_I  96 kkelnelv.elkavlekakefle 117
                                    ++++ l+ +lk++l ++++fl+
  gi|15668234|ref|NP_247027.1| 157 IEKTKILKdKLKNLLLQIDNFLN 179
                                   99988887246788888888886 PP

>> Fibin  Fin bud initiation factor homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4    0.0012      0.53     104     168 ..      41     108 ..      30     116 .. 0.87
   2 ?    2.3   0.7      0.27   1.2e+02     116     174 ..     116     174 ..     108     177 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                         Fibin 104 sqiseafsnsdksllelevkfk...qsqeqekreekrlnddflkkvaevrellketldisaglrdkhe 168
                                    q++e   n dk+l  +e+ f+   + +e+ k  ++++ ++f+k +++  +++++  + s  l+++ e
  gi|15668234|ref|NP_247027.1|  41 LQLAEMLDNIDKTLEIIEKNFQiilKNRESGKFSNNEIIQKFVKPLENLIKVIENIESTSNNLKNEIE 108
                                   599999***************8544678888888999**************************99877 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.27
                         Fibin 116 sllelevkfkqsqeqekreekrlnddflkkvaevrellketldisaglrdkhellsliv 174
                                   +l+e+  k+k  + +   +  +  +   +++++ r+ l e  + +  l+dk + l l +
  gi|15668234|ref|NP_247027.1| 116 TLKEITDKLKIINMESATQAIEEFKIAYDMLEDNRKNLDELIEKTKILKDKLKNLLLQI 174
                                   67777777776665555555555555668899999999999999999999987776655 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   7.2    0.0006      0.27      26     127 ..      29     123 ..      19     128 .. 0.70
   2 ?    4.9   6.0     0.061        27      38     120 ..      84     169 ..      73     180 .. 0.36

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0006
                                   CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                     Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirv 106
                                   ++k ++++++ l +l + l++i ++    e + k+ + +l+++++ k  n+++i+k+ k le +   l + i + es+ ++
  gi|15668234|ref|NP_247027.1|  29 FKKENESISNVLLQLAEMLDNIDKT---LEIIEKNFQIILKNRESGKFSNNEIIQKFVKPLE-N---LIKVIENIESTSNN 102
                                   3444555555555555555555443...3444466778899999999999************.4...44455555688888 PP

                                   HHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 107 LqnvlesneqkiqkLeqdidq 127
                                   L+n +e+  ++i  L++  d+
  gi|15668234|ref|NP_247027.1| 103 LKNEIENCASSIPTLKEITDK 123
                                   999999999999999987766 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.061
                                   CCCCCCCCCCCCHHHHHHHHHHHHHHHHHH..HHHHHHHH..HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHH CS
                     Fib_alpha  38 ekleneleeisnstkeaeelvkeikdslre..kqkskkdn..dnvikksskeleeeilrlketidaqesnirvLqnvlesn 114
                                   + len ++ i+n ++++++l +ei++   +  + k+ +d+     +++ ++ +e e     + + ++ +n+ +L +  + +
  gi|15668234|ref|NP_247027.1|  84 KPLENLIKVIENIESTSNNLKNEIENCASSipTLKEITDKlkIINMESATQAIE-EFKIAYDMLEDNRKNLDELIEKTKIL 163
                                   444444444444444444444444433322002222222211111122222222.22222223333334444444444444 PP

                                   HHHHHH CS
                     Fib_alpha 115 eqkiqk 120
                                   + k+++
  gi|15668234|ref|NP_247027.1| 164 KDKLKN 169
                                   444444 PP

>> ArnB_C  Archaellum regulatory network B, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.2    0.0012      0.52      11      60 ..     115     169 ..     101     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
                                   HHHHHHHHHHHTT-HHHHHHHHHHHH...HHHHHHT-H..HHHHHHTT--S-HHH CS
                        ArnB_C  11 ellkkysealeagnlkeATrilqele...eiAeqTrri..eliEaTrrLsrdles 60 
                                    +lk+++++l+  n+++AT+ ++e +   ++ e  r+   eliE+T+ L+++l++
  gi|15668234|ref|NP_247027.1| 115 PTLKEITDKLKIINMESATQAIEEFKiayDMLEDNRKNldELIEKTKILKDKLKN 169
                                   5799******************9976333667889995559**********9987 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.8      0.11        51      39      66 ..      28      55 ..       9      67 .. 0.60
   2 ?    2.6   2.7      0.41   1.8e+02       3      63 ..      37      98 ..      34     104 .. 0.66
   3 ?    7.9   0.2    0.0094       4.2      13      47 ..      93     127 ..      86     139 .. 0.82
   4 ?    4.1   1.4      0.14        64      26      59 ..     142     175 ..     126     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.11
                       NPV_P10 39 elnekLdaqsaqLaeletkvenIqdiLn 66
                                  e +++ +++s+ L +l + ++nI+++L 
  gi|15668234|ref|NP_247027.1| 28 EFKKENESISNVLLQLAEMLDNIDKTLE 55
                                  4445555566666666666666665554 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.41
                       NPV_P10  3 qniLlvIradikavddkVdalqqqvddvqenlpdvtel.nekLdaqsaqLaeletkvenIqd 63
                                   n+Ll+  +   ++d+ ++ ++++ + + +n +  +   ne +++  + L++l + +enI++
  gi|15668234|ref|NP_247027.1| 37 SNVLLQLAEMLDNIDKTLEIIEKNFQIILKNRESGKFSnNEIIQKFVKPLENLIKVIENIES 98
                                  58888888888888888888888887777776653322144466666666666667777766 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0094
                       NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaq 47 
                                   i+++++  + l++++++ ++ +p+++e+++kL  +
  gi|15668234|ref|NP_247027.1|  93 IENIESTSNNLKNEIENCASSIPTLKEITDKLKII 127
                                   667777778899*******************9765 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.14
                       NPV_P10  26 qvddvqenlpdvtelnekLdaqsaqLaeletkve 59 
                                   + d +++n ++++el ek   + ++L++l  +++
  gi|15668234|ref|NP_247027.1| 142 AYDMLEDNRKNLDELIEKTKILKDKLKNLLLQID 175
                                   4577889999999998888888888887755444 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2      0.23   1.1e+02      38      70 ..      12      44 ..       3      67 .. 0.62
   2 ?    2.5   0.2      0.52   2.3e+02      27      58 ..      29      60 ..      23      98 .. 0.52
   3 ?    7.7   2.2     0.013       5.9      26      99 ..     102     177 ..      88     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.23
                  Occludin_ELL 38 fseLerelkelkegskeykkieeeilqeykklk 70
                                  f +L++ +k+l ++ +e+kk +e+i + + +l 
  gi|15668234|ref|NP_247027.1| 12 FIKLDSSIKSLLRSAREFKKENESISNVLLQLA 44
                                  666666666666666666666666655554443 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.52
                  Occludin_ELL 27 lhaeleevskkfseLerelkelkegskeykki 58
                                   ++e e++s+ + +L ++l++ +++ + ++k 
  gi|15668234|ref|NP_247027.1| 29 FKKENESISNVLLQLAEMLDNIDKTLEIIEKN 60
                                  44444555555555555555554443322222 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.013
                  Occludin_ELL  26 elhaeleevskkfseLerelkelkegsk.eykkieeeilqeykklkk.dpeyqekkkrceyLkekLshiKklikey 99 
                                   +l++e+e++++ +  L++ +++lk  +    ++++ee    y  l+   ++  e  ++++ Lk+kL+ +  +i ++
  gi|15668234|ref|NP_247027.1| 102 NLKNEIENCASSIPTLKEITDKLKIINMeSATQAIEEFKIAYDMLEDnRKNLDELIEKTKILKDKLKNLLLQIDNF 177
                                   6888999999999999999998887666577777888899999998856667777899999999999998888776 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.8       0.1        47      34      68 ..      19      53 ..       9      77 .. 0.56
   2 ?    7.9   0.8    0.0068       3.1      27      66 ..      86     125 ..      74     141 .. 0.80
   3 ?    3.9   1.9      0.12        55      32      72 ..     134     174 ..     128     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.1
                                  HHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXX CS
                        DivIVA 34 yeallkeneelkekvkeleeklkeykeleetLkkt 68
                                  +++ll+  +e k++ +   + l + +e+ +++ kt
  gi|15668234|ref|NP_247027.1| 19 IKSLLRSAREFKKENESISNVLLQLAEMLDNIDKT 53
                                  33444444444444444444444444444444444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0068
                                   HHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXX CS
                        DivIVA  27 LdqvakdyeallkeneelkekvkeleeklkeykeleetLk 66 
                                   L++++k +e++ + +++lk+++++  +++   ke+ ++Lk
  gi|15668234|ref|NP_247027.1|  86 LENLIKVIENIESTSNNLKNEIENCASSIPTLKEITDKLK 125
                                   7889999999999999999999999999999999999987 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXX CS
                        DivIVA  32 kdyeallkeneelkekvkeleeklkeykeleetLkktlvva 72 
                                   + +e++    + l+++ k+l+e +++ k l+++Lk+ l+  
  gi|15668234|ref|NP_247027.1| 134 QAIEEFKIAYDMLEDNRKNLDELIEKTKILKDKLKNLLLQI 174
                                   66777777788899999999999999999999999988865 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.8      0.96   4.3e+02      47     102 ..       9      64 ..       3      91 .. 0.59
   2 ?    9.9   4.1    0.0017      0.78       2      89 ..      88     175 ..      87     181 .] 0.72

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.96
                         CREPT  47 ekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleel 102
                                   ++l+ + +++++ l       ++e e  +++  +l+++l ++ ++l+  e++ + +
  gi|15668234|ref|NP_247027.1|   9 DELFIKLDSSIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKNFQII 64 
                                   45555555555555555566666666666666666666666666666666665555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0017
                         CREPT   2 elikaLkeLensassdaavReriaklP...pevsdvsllekikdkeeaekllkqveealellaeYnkrLeaeleeRkklak 79 
                                   +lik+++++e++     +++++i +     p+++++    ki + e+a++ +++ + a+ +l++  k L++ +e+ k l+ 
  gi|15668234|ref|NP_247027.1|  88 NLIKVIENIEST---SNNLKNEIENCAssiPTLKEITDKLKIINMESATQAIEEFKIAYDMLEDNRKNLDELIEKTKILKD 165
                                   567777776655...334444443333000345555555578899************************************ PP

                         CREPT  80 mledfleaqk 89 
                                   +l+++l ++ 
  gi|15668234|ref|NP_247027.1| 166 KLKNLLLQID 175
                                   **99886655 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.4     0.023        10      27      59 ..      18      50 ..      14      55 .. 0.88
   2 ?   -2.1   0.0       9.3   4.2e+03      11      17 ..      65      71 ..      62      74 .. 0.82
   3 ?    7.5   0.5    0.0098       4.4      28      63 ..      93     128 ..      79     129 .. 0.80
   4 ?    2.0   0.9       0.5   2.2e+02      28      45 ..     153     170 ..     133     180 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.023
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1 27 eieeLerrvkaLekeNksLkseleelkkevekL 59
                                  +i+ L r + +++keN+s ++ l +l+++ ++ 
  gi|15668234|ref|NP_247027.1| 18 SIKSLLRSAREFKKENESISNVLLQLAEMLDNI 50
                                  68999999******************9998876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.3
                                  --HHHHH CS
                        bZIP_1 11 qkNReaA 17
                                  +kNRe+ 
  gi|15668234|ref|NP_247027.1| 65 LKNRESG 71
                                  59**995 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0098
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                   ie+ e+ +  L++e ++ +s + +lk+  +kLk  +
  gi|15668234|ref|NP_247027.1|  93 IENIESTSNNLKNEIENCASSIPTLKEITDKLKIIN 128
                                   677788888888888888888888888888888665 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.5
                                   HHHHHHHHHHHHHHHHHH CS
                        bZIP_1  28 ieeLerrvkaLekeNksL 45 
                                    +eL ++ k L+ + k+L
  gi|15668234|ref|NP_247027.1| 153 LDELIEKTKILKDKLKNL 170
                                   334444444444444443 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.2    0.0069       3.1       7      87 ..      15      98 ..       9     100 .. 0.70
   2 ?    5.6   3.2     0.018         8      21      79 ..      82     140 ..      74     180 .. 0.45

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0069
                         TMPIT  7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk...eeeeeeveelkeelkerkkvlkeve 86
                                  l +++k+l  +a+e+k++ e++s+   ++++ +++  k l+ ++++++ + k+ +    +++e++++  + l++  kv++++e
  gi|15668234|ref|NP_247027.1| 15 LDSSIKSLLRSAREFKKENESISNVLLQLAEMLDNIDKTLEIIEKNFQIILKNREsgkFSNNEIIQKFVKPLENLIKVIENIE 97
                                  66677777777777777777777777777777777777777777777766555333336677888888888888888887777 PP

                         TMPIT 87 s 87
                                  s
  gi|15668234|ref|NP_247027.1| 98 S 98
                                  6 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.018
                         TMPIT  21 ykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79 
                                   + + le+l k ++++ ++ ++ k++++++ ss+ +lk+ +++ +  ++e+ ++ ++e k
  gi|15668234|ref|NP_247027.1|  82 FVKPLENLIKVIENIESTSNNLKNEIENCASSIPTLKEITDKLKIINMESATQAIEEFK 140
                                   44555555555555555555555555555555555554443222222222222222221 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.9     0.096        43      12      38 ..      32      58 ..      21      70 .. 0.52
   2 ?    8.0   2.2    0.0053       2.4       3      45 ..      80     122 ..      75     136 .. 0.74
   3 ?    0.5   1.6       1.2   5.3e+02      15      22 ..     135     142 ..     103     179 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.096
                     DASH_Duo1 12 inevienviesLkkaksniervketve 38
                                   ne i+nv  +L ++ +ni++  e +e
  gi|15668234|ref|NP_247027.1| 32 ENESISNVLLQLAEMLDNIDKTLEIIE 58
                                  455555555555555555554444443 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0053
                     DASH_Duo1   3 ekEleqLrkinevienviesLkkaksniervketvestntLLd 45 
                                   +k ++ L+++++vien++++ ++ k++ie+ ++++ + +++ d
  gi|15668234|ref|NP_247027.1|  80 QKFVKPLENLIKVIENIESTSNNLKNEIENCASSIPTLKEITD 122
                                   5666777888888888888888888888877777777666666 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.2
                     DASH_Duo1  15 vienvies 22 
                                   +ie ++ +
  gi|15668234|ref|NP_247027.1| 135 AIEEFKIA 142
                                   33333333 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.4      0.21        96      31      81 ..      14      63 ..      10      69 .. 0.71
   2 ?    4.7   5.5     0.091        41      35      89 ..     116     170 ..      74     171 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.21
               Snapin_Pallidin 31 eLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqk 81
                                  +L +++++l ++ +e+++++e ++ + l + a+ L ni k ++ +++  q 
  gi|15668234|ref|NP_247027.1| 14 KLDSSIKSLLRSAREFKKENE-SISNVLLQLAEMLDNIDKTLEIIEKNFQI 63
                                  577777777777777777777.55556666678888888888888777665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.091
               Snapin_Pallidin  35 qldrlnekLkeleeaqe.aevlpdlkeyakKLvnikkrmsslnerlqklkkRaekL 89 
                                   +l++ ++kLk ++ +++ +++++++k   + L   +k++ +l e+++ lk+++++L
  gi|15668234|ref|NP_247027.1| 116 TLKEITDKLKIIN-MESaTQAIEEFKIAYDMLEDNRKNLDELIEKTKILKDKLKNL 170
                                   2334444554333.333356677777777777777777777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2111  (0.117742); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.85u 0.26s 00:00:01.10 Elapsed: 00:00:00.49
# Mc/sec: 1102.76
//
Query:       gi|15668235|ref|NP_247028.1|  [L=189]
Description: hypothetical protein MJ_0064 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-05   24.5   5.8     0.0009   19.1   1.4    2.1  2  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
    0.00051   19.0  13.3    0.00064   18.7  13.3    1.0  1  Spc7             Spc7 kinetochore protein
    0.00054   20.3  11.2       0.13   12.7   2.4    3.1  3  Snapin_Pallidin  Snapin/Pallidin
    0.00079   19.5  12.6      0.014   15.5   2.0    3.1  3  DUF1664          Protein of unknown function (DUF1664)
    0.00089   18.3  15.0    0.00091   18.3   8.8    2.0  2  IFT57            Intra-flagellar transport protein 57
     0.0014   16.9  12.2     0.0014   16.9  12.2    1.7  1  EzrA             Septation ring formation regulator, EzrA
     0.0019   18.5   6.0       0.63   10.4   0.1    3.1  3  DUF4164          Domain of unknown function (DUF4164)
     0.0052   16.1  11.7     0.0057   16.0   8.1    1.9  2  TMPIT            TMPIT-like protein
      0.006   16.0   8.7       0.01   15.2   8.7    1.4  1  Tropomyosin      Tropomyosin
     0.0075   16.3  13.6      0.039   14.0   5.7    2.1  2  Laminin_II       Laminin Domain II
     0.0077   15.9  12.1     0.0077   15.9  12.1    2.1  2  YkyA             Putative cell-wall binding lipoprotein
  ------ inclusion threshold ------
      0.014   15.2   1.8      0.041   13.6   1.6    1.9  1  DUF745           Protein of unknown function (DUF745)
      0.022   14.3   4.5      0.027   14.0   4.5    1.2  1  Exonuc_VII_L     Exonuclease VII, large subunit
      0.028   14.8   1.8      0.061   13.7   0.8    1.8  2  DUF5063          Domain of unknown function (DUF5063)
      0.035   14.3   0.1      0.057   13.6   0.1    1.4  1  Lsr2             Lsr2
      0.042   14.0  11.5        1.4    9.1   0.6    3.0  3  IFT20            Intraflagellar transport complex B, subunit 
      0.048   13.1  10.5      0.088   12.3   6.3    1.8  2  Golgin_A5        Golgin subfamily A member 5
      0.053   13.4  10.8       0.14   12.0  10.8    1.7  1  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
      0.054   13.6   0.9       0.17   12.0   0.9    1.8  1  DUF840           Lagovirus protein of unknown function (DUF84
      0.096   13.4   5.3        1.5    9.5   2.5    2.4  2  DUF2203          Uncharacterized conserved protein (DUF2203)
      0.098   12.9   8.3         24    5.3   0.2    2.9  2  DUF948           Bacterial protein of unknown function (DUF94
       0.12   12.6  16.0      0.076   13.2   9.1    2.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
       0.12   11.1  13.8       0.32    9.7   6.7    2.1  2  Tektin           Tektin family
       0.12   11.2   2.2        0.4    9.5   0.7    1.9  2  DUF1729          Domain of unknown function (DUF1729)
       0.13   11.5   8.6       0.09   12.1   4.2    2.2  2  DUF3450          Protein of unknown function (DUF3450)
       0.14   12.3   4.2        5.4    7.1   0.2    2.6  2  Nup54            Nucleoporin complex subunit 54
        0.2   11.9   2.4        1.4    9.2   0.6    2.7  2  FliJ             Flagellar FliJ protein
       0.23   12.0  10.7       0.44   11.1   7.1    2.3  1  APG6_N           Apg6 coiled-coil region
       0.35   11.0   6.0        8.7    6.5   6.0    2.3  1  ETRAMP           Malarial early transcribed membrane protein 
       0.37   10.4  14.4        0.5    9.9   3.7    2.2  2  DUF4795          Domain of unknown function (DUF4795)
       0.47   11.0  10.1        1.6    9.3   3.9    2.6  2  DUF16            Protein of unknown function DUF16
       0.48   10.8   7.2       0.63   10.5   6.5    1.5  1  Fez1             Fez1
       0.53   10.0  15.9       0.98    9.1  12.1    2.0  2  LXG              LXG domain of WXG superfamily
       0.53   10.6  19.4         49    4.2  17.8    2.8  1  DUF5082          Domain of unknown function (DUF5082)
       0.56    9.3  14.1        1.8    7.6  14.1    1.8  1  APG17            Autophagy protein Apg17
       0.61   10.3   6.0        0.6   10.3   4.6    1.7  1  PHM7_cyt         Cytosolic domain of 10TM putative phosphate 
       0.62   10.5  17.7        0.1   13.1  10.4    2.0  2  PIN_12           PIN domain
       0.64   10.4  17.9        6.7    7.1   0.8    2.5  2  Syntaxin_2       Syntaxin-like protein
       0.74   10.1  10.1        0.9    9.9   0.6    3.2  4  KxDL             Uncharacterized conserved protein
       0.76    9.8   8.3          1    9.4   1.2    3.1  3  SOAR             STIM1 Orai1-activating region
       0.77   10.5   2.2        3.8    8.3   0.3    2.3  2  Sulfatase_C      C-terminal region of aryl-sulfatase
       0.77    9.7  13.8       0.95    9.4   0.6    2.7  3  Alpha-2-MRAP_C   Alpha-2-macroglobulin RAP, C-terminal domain
          1    9.1  12.7       0.26   11.0   3.7    2.9  3  DUF1366          Protein of unknown function (DUF1366)
          1   10.1   8.3        2.8    8.6   7.6    1.9  1  AATF-Che1        Apoptosis antagonizing transcription factor
        1.1    9.1  18.7        1.4    8.7   1.0    3.8  4  DASH_Duo1        DASH complex subunit Duo1
        1.1    7.8   6.9        5.4    5.6   6.9    1.9  1  Tweety           Tweety
        1.4    9.5   7.1          2    9.0   1.0    2.5  2  Spectrin         Spectrin repeat
        1.6    8.8  10.5        1.1    9.3   6.6    2.2  2  DHR10            Designed helical repeat protein 10 domain
        1.6    8.6  12.9        1.4    8.9   3.0    3.1  3  MIP-T3_C         Microtubule-binding protein MIP-T3 C-termina
        1.8    8.4   9.1        6.7    6.6   7.4    2.4  2  STAT_alpha       STAT protein, all-alpha domain
        2.1    8.4  16.1         17    5.5   9.9    3.8  2  Prefoldin_2      Prefoldin subunit
        2.1    7.6  13.8        3.9    6.7  13.8    1.5  1  CorA             CorA-like Mg2+ transporter protein
          3    8.5  11.0         56    4.4   9.7    2.4  1  Syntaxin-6_N     Syntaxin 6, N-terminal
        3.8    7.2  10.5        6.7    6.4  10.5    1.4  1  Cactin_mid       Conserved mid region of cactin
        4.5    7.5  17.2        4.9    7.4   6.9    2.9  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        5.2    7.3  17.2       0.95    9.7  12.0    1.9  2  zf-C4H2          Zinc finger-containing protein
        6.8    6.7   6.8         21    5.2   0.4    2.8  4  Noelin-1         Neurogenesis glycoprotein


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.2    0.0081       2.5     103     169 ..       6      73 ..       1      76 [. 0.68
   2 !   19.1   1.4   2.9e-06    0.0009      79     161 ..      84     163 ..      79     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0081
                                   .......HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal 103 ndsvesleetrqrveegselveetgealkeiveavaevadlvqe.iaaaseeqsasieevnqaveeva 169
                                   ++ ++ l++  ++ +++s+ v et+ +l ei ++ +++ +++++ i+     +  + e +n +v+e++
  gi|15668235|ref|NP_247028.1|   6 DKQADWLNKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINNyITEIHYGLRITNERINLSVSELD 73 
                                   45567788889999999999999999999998887665555554233344445556666777777666 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.9e-06
                                   HHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  79 kLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasie 159
                                   + Ae+ +++ ++++++ii++++e+ d  +slee+  ++++  +l+e+t   lk+ ++++++++++++ ++++ e + +si+
  gi|15668235|ref|NP_247028.1|  84 DFAENMKKSVENTHNAIIAVKNEMRDIKHSLEESSLKISNRYNLMEDT---LKHHSKKIESLSNSIKSLSKTQESIINSIN 161
                                   78999999********************************99999987...66778899*************999999988 PP

                                   HH CS
                     MCPsignal 160 ev 161
                                   ++
  gi|15668235|ref|NP_247028.1| 162 ST 163
                                   76 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7  13.3     2e-06   0.00064     135     303 ..      10     174 ..       8     180 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2e-06
                          Spc7 135 qllegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaei 215
                                    +l++L e+l++  +++ e + +L++   +l++l  e++++ +e++  l+  +e+ +    +   eL el ++l+e     
  gi|15668235|ref|NP_247028.1|  10 DWLNKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINNYITEIHYGLRITNERIN----LSVSELDELEKKLKEYLDFA 86 
                                   5999******************************************99999999764....68899999999********* PP

                          Spc7 216 eekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivslsgstlel 296
                                   e+ kk +++  + + ++++++ ++k + +e   +i++  +++e + ++ ++ +++l ++ k+l ++ +  i s++++ + l
  gi|15668235|ref|NP_247028.1|  87 ENMKKSVENTHNAIIAVKNEMRDIKHSLEESSLKISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQESIINSINSTKMLL 167
                                   ***********************************************************************9999886655 PP

                          Spc7 297 tyrsele 303
                                    +  +l+
  gi|15668235|ref|NP_247028.1| 168 YITIALT 174
                                   5555554 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2      0.33     1e+02      12      48 ..      13      49 ..       4      66 .. 0.69
   2 !   12.7   2.4    0.0004      0.13      34      83 ..      70     118 ..      58     123 .. 0.90
   3 !    9.3   0.1    0.0048       1.5       5      40 ..     129     164 ..     125     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.33
               Snapin_Pallidin 12 epkldeldeklkelrqsQeeLleqldrlnekLkelee 48
                                     ++eld++ +++ ++   L e +++ln+ + e+++
  gi|15668235|ref|NP_247028.1| 13 NKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINN 49
                                  4556677777777777777777777777776666665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0004
               Snapin_Pallidin  34 eqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklk 83 
                                   ++ld+l +kLke+ + +e ++ + +++ ++ ++++k++m  ++++l++  
  gi|15668235|ref|NP_247028.1|  70 SELDELEKKLKEYLDFAE-NMKKSVENTHNAIIAVKNEMRDIKHSLEESS 118
                                   579**************9.9999********************9998765 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0048
               Snapin_Pallidin   5 egllellepkldeldeklkelrqsQeeLleqldrln 40 
                                   e  l++ + k++ l +++k+l ++Qe   +++++ +
  gi|15668235|ref|NP_247028.1| 129 EDTLKHHSKKIESLSNSIKSLSKTQESIINSINSTK 164
                                   5567888999*******************9999876 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3     0.035        11      64     108 ..      12      56 ..       3      68 .. 0.54
   2 !   15.5   2.0   4.4e-05     0.014      39     117 ..      40     121 ..      39     125 .. 0.81
   3 ?    7.7   1.2     0.011       3.4      49      92 ..     120     163 ..     111     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.035
                       DUF1664  64 Lssridrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                   L++ i+++dk+  ++ e+   ++e +t++++ +sei++ +++++ 
  gi|15668235|ref|NP_247028.1|  12 LNKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINNYITEIHY 56 
                                   444555555555555555555555555555555555555555544 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.4e-05
                       DUF1664  39 lsdavesvskqleqvseslaatkrhLs...sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                   l++ ++++ + ++++   l+ t ++++   s++d+++kkl+e  + ++++k+ v++ ++ + +++++++ +k+  e+   k
  gi|15668235|ref|NP_247028.1|  40 LNNLISEINNYITEIHYGLRITNERINlsvSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSLEESSLK 120
                                   5667777778888877666655555432247899999***********************************999887777 PP

                       DUF1664 117 l 117
                                   +
  gi|15668235|ref|NP_247028.1| 121 I 121
                                   6 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.011
                       DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtev 92 
                                   ++ + ++ +++t +h s++i+++ +++++ ++++++i + +++ 
  gi|15668235|ref|NP_247028.1| 120 KISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQESIINSINST 163
                                   55566667777777788888888888888888877777777654 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   8.8   2.9e-06   0.00091     215     335 ..       4     128 ..       1     129 [. 0.87
   2 ?    6.3   0.8     0.013       4.1     277     318 ..     123     164 ..     119     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.9e-06
                         IFT57 215 ikadakdWrah.leqmkkhkksiees...lpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevke 291
                                   ++ ++ dW ++ +e++ k ++s+ e+   l e+ ++l++l ++i++++++i    ++ n++++ +++e+ e++++l+e  +
  gi|15668235|ref|NP_247028.1|   4 MNDKQADWLNKlIEELDKSSSSVLETeivLDEIITKLNNLISEINNYITEIHYGLRITNERINLSVSELDELEKKLKEYLD 84 
                                   44555699877357888888866553333899999********************************************** PP

                         IFT57 292 kykqlsegvseltrelaeiseelekvkqemeergssmtDgsplv 335
                                     ++++++v++  +    +++e++++k  +ee + ++++  +l+
  gi|15668235|ref|NP_247028.1|  85 FAENMKKSVENTHNAIIAVKNEMRDIKHSLEESSLKISNRYNLM 128
                                   *********************************99999987765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                         IFT57 277 qeyreaqeelsevkekykqlsegvseltrelaeiseelekvk 318
                                   + y+ ++++l++ ++k++ ls+++++l++++++i + ++++k
  gi|15668235|ref|NP_247028.1| 123 NRYNLMEDTLKHHSKKIESLSNSIKSLSKTQESIINSINSTK 164
                                   6799999************************99999998887 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9  12.2   4.5e-06    0.0014      74     182 ..      34     144 ..      28     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.5e-06
                                   HHHTHHHHHT-GGGT--S-SHHH..HHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT- CS
                          EzrA  74 tkklpeieellfeaeelldkykf..kkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkl 152
                                   ++ + ++++l+ e++++++++++  + ++++++   +elde+e+k+k+ l+  +++++s e+ +++i ++k++ r+++++l
  gi|15668235|ref|NP_247028.1|  34 DEIITKLNNLISEINNYITEIHYglRITNERINLSVSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSL 114
                                   5678999***********9877633779999************************************************** PP

                                   -TTTTHHHHHHHHHHHHHHHH--------- CS
                          EzrA 153 lanrfsygealeelekqleniekefsefee 182
                                   ++ + + ++ ++ +e+ l++  k+++++++
  gi|15668235|ref|NP_247028.1| 115 EESSLKISNRYNLMEDTLKHHSKKIESLSN 144
                                   ****************99999999988776 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1     0.002      0.63      49      85 ..      13      49 ..       9      53 .. 0.93
   2 !    8.5   0.5    0.0074       2.3      39      72 ..      67     100 ..      58     123 .. 0.83
   3 ?    1.5   0.1       1.2   3.8e+02      65      85 ..     128     148 ..     104     163 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.002
                       DUF4164 49 sRLaeeLdqaearaarleevnrEvsrrLkaaietira 85
                                  ++L eeLd+++    + e+v +E+  +L+ +i +i++
  gi|15668235|ref|NP_247028.1| 13 NKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINN 49
                                  6899*******************************96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0074
                       DUF4164  39 aeiealgedrsRLaeeLdqaearaarleevnrEv 72 
                                     +++l+e +++L e Ld ae+  +++e++ + +
  gi|15668235|ref|NP_247028.1|  67 LSVSELDELEKKLKEYLDFAENMKKSVENTHNAI 100
                                   57899***********************997655 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 1.2
                       DUF4164  65 leevnrEvsrrLkaaietira 85 
                                   +e++ +  s++++++ ++i++
  gi|15668235|ref|NP_247028.1| 128 MEDTLKHHSKKIESLSNSIKS 148
                                   333333333333333333333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.36   1.1e+02      41      87 ..       7      56 ..       1      65 [. 0.53
   2 !   16.0   8.1   1.8e-05    0.0057       9     109 ..      70     181 ..      62     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.36
                         TMPIT 41 kqkkrlkelksslkklkksvk...eeeeeeveelkeelkerkkvlkeves 87
                                  kq   l++l ++l+k ++sv       +e++++l++ ++e+++++ e++ 
  gi|15668235|ref|NP_247028.1|  7 KQADWLNKLIEELDKSSSSVLeteIVLDEIITKLNNLISEINNYITEIHY 56
                                  44444445555555544443222234456666666666666666666654 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.8e-05
                         TMPIT   9 kefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..........eeeeeeveelkeelkerk 79 
                                   +e++ele++ key    e+++k+ +++ ++i   k++++++k+sl++ + +++          +++++++e+l++++k+ +
  gi|15668235|ref|NP_247028.1|  70 SELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSLEESSLKISnrynlmedtlKHHSKKIESLSNSIKSLS 150
                                   678899999999999999999999999999999999999999999998888767788888999999999999999999999 PP

                         TMPIT  80 kvlkevesllpkk.nglylklvlGnvnvsll 109
                                   k+ +++ +++ ++   ly+ + l+ vn+ + 
  gi|15668235|ref|NP_247028.1| 151 KTQESIINSINSTkMLLYITIALTVVNLIIS 181
                                   9999888888877688899999999998765 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   8.7   3.3e-05      0.01      28     159 ..      34     162 ..       3     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.3e-05
                   Tropomyosin  28 ekkaekaeaEvaalnrriqlleeelerteerleealekLeeaekaadeserarKvlEnrelkdeekleeleaqlkeakeia 108
                                   ++ ++k ++  + +n+ i+ +   l+ t+er++ + ++L+e+ek+ +e    +   En + + e+  +   a  +e++ i+
  gi|15668235|ref|NP_247028.1|  34 DEIITKLNNLISEINNYITEIHYGLRITNERINLSVSELDELEKKLKEY---LDFAENMKKSVENTHNAIIAVKNEMRDIK 111
                                   34556667777889999***************************99997...33445555666666667777788888888 PP

                   Tropomyosin 109 eeadrkyeEvarklvvvesdLeraeeraeaaeskiveLeeeLkvvgnnlks 159
                                   ++ ++    ++ +  ++e+ L++  +++e+  + i++L  + + + n++ s
  gi|15668235|ref|NP_247028.1| 112 HSLEESSLKISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQESIINSINS 162
                                   888888888999**************************9999888888765 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   5.7   0.00012     0.039       2      97 ..      13     112 ..      12     117 .. 0.94
   2 !    8.6   5.6    0.0055       1.7       3      81 ..      91     166 ..      84     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00012
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                    Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                   ++l++e +++ ++vle    l++ + ++++ +sein+ + e++  ++  n+ i++  ++  +Lek++ + ld  +++k+  
  gi|15668235|ref|NP_247028.1|  13 NKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINNYITEIHYGLRITNERINLSVSELDELEKKLKEYLDFAENMKKSV 93 
                                   57899**************************************************************************99 PP

                                   HH.......HHHHHHHHHH CS
                    Laminin_II  83 easss....lsdniseike 97 
                                   e+ ++    +++++  ik 
  gi|15668235|ref|NP_247028.1|  94 ENTHNaiiaVKNEMRDIKH 112
                                   9988889999999999986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0055
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                    Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                   + +++  + + +v++ + +++  le+ + k   i +  + +++ +k  +k i++ ++s+k L k+ + +++ +++ k+l
  gi|15668235|ref|NP_247028.1|  91 KSVENTHNAIIAVKNEMRDIKHSLEESSLK---ISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQESIINSINSTKML 166
                                   333333334444444444444444444444...4455567899999************************999988876 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.7      0.58   1.8e+02     146     182 ..      10      46 ..       1      54 [. 0.44
   2 !   15.9  12.1   2.5e-05    0.0077      37     134 ..      60     156 ..      56     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.58
                          YkyA 146 eeleeqiekiNesyeevkeaneqFneatkkyneekke 182
                                   + l++ ie++ +s++ v e+   ++e ++k n++ +e
  gi|15668235|ref|NP_247028.1|  10 DWLNKLIEELDKSSSSVLETEIVLDEIITKLNNLISE 46 
                                   3344444444444444444444444444444443333 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.5e-05
                          YkyA  37 lyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieeiedeelkkeaeelieameeryeay 117
                                   + +e i+l+ +e+d+++k+ +e l+ +e+ ++ +e+  ++i + k+e+ +ik ++ee   + + +  + ++++++   +++
  gi|15668235|ref|NP_247028.1|  60 ITNERINLSVSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSLEESSLK-ISNRYNLMEDTLKHHSKKI 139
                                   678999****************************************************766.9****************** PP

                          YkyA 118 dklykaYkealeldkeL 134
                                   ++l ++ k++ ++++++
  gi|15668235|ref|NP_247028.1| 140 ESLSNSIKSLSKTQESI 156
                                   ***99999988888876 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.6   0.00013     0.041      63     146 ..      36     119 ..      20     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00013
                        DUF745  63 lveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqllea 143
                                   ++ +l++ ++e ++ + e++  l+ +++ +++  +  ++ +++l+   ++ +++k+++en++++   +++e+++ ++ le+
  gi|15668235|ref|NP_247028.1|  36 IITKLNNLISEINNYITEIHYGLRITNERINLSVSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSLEE 116
                                   788999999**************************************************************9997766666 PP

                        DUF745 144 Akk 146
                                   +  
  gi|15668235|ref|NP_247028.1| 117 SSL 119
                                   544 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   4.5   8.6e-05     0.027     160     261 ..      40     151 ..       4     171 .. 0.40

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.6e-05
                  Exonuc_VII_L 160 ikrlleekkqrleklasrlkspeellerkrqrldeleerler......alkkqlkkkrerleelkerlk...ekleekker 231
                                   +++l++e ++ +++++  l+  +e+++ + ++ldele++l++      ++kk++++ ++++  +k++++   ++lee + +
  gi|15668235|ref|NP_247028.1|  40 LNNLISEINNYITEIHYGLRITNERINLSVSELDELEKKLKEyldfaeNMKKSVENTHNAIIAVKNEMRdikHSLEESSLK 120
                                   223333333333333333333334444444444444444444111111122222222222222222221111111111111 PP

                  Exonuc_VII_L 232 lkklkerle........lleekkerleeleeklealsp 261
                                   +       +        +l+++++++e+l++++++ls 
  gi|15668235|ref|NP_247028.1| 121 I-------SnrynlmedTLKHHSKKIESLSNSIKSLSK 151
                                   1.......111112223344444444444444444443 PP

>> DUF5063  Domain of unknown function (DUF5063)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.8   0.00019     0.061      61     144 ..      22     107 ..       4     109 .. 0.82
   2 ?    5.7   0.3     0.057        18      11      82 ..      76     143 ..      71     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00019
                       DUF5063  61 eleerve.EedyealrealarlLgekddYlevfdpdmkysdtpiaasisedLadIyqdlknglavyr..egneeemeeAlw 138
                                   +  +++e E  ++++  +l++l+ e + Y+ ++++ ++ +++ i+ s+se L ++ ++lk++l+  +  +++ e++++A+ 
  gi|15668235|ref|NP_247028.1|  22 SSSSVLEtEIVLDEIITKLNNLISEINNYITEIHYGLRITNERINLSVSE-LDELEKKLKEYLDFAEnmKKSVENTHNAII 101
                                   3334444577799************************************8.99***********99966677788889999 PP

                       DUF5063 139 awqesF 144
                                   a+++++
  gi|15668235|ref|NP_247028.1| 102 AVKNEM 107
                                   888765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.057
                       DUF5063  11 vavareycaliesvaeserkefvdeiaklLplLylkasllpea.erleedveleerve..EedyealrealarlL 82 
                                    +  +ey+++ e++++s     v+++++++    +++ +++++ e++  + ++ +r++  E++++   +++++l 
  gi|15668235|ref|NP_247028.1|  76 EKKLKEYLDFAENMKKS-----VENTHNAIIAVKNEMRDIKHSlEES--SLKISNRYNlmEDTLKHHSKKIESLS 143
                                   567899******99988.....9*****************9995444..56666666666777777777777764 PP

>> Lsr2  Lsr2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   0.00018     0.057      21      98 ..      53     126 ..      35     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00018
                          Lsr2  21 tvefgldgveYeiDLseenaeklrdaLapyieaarrvggrkkkrrarrkaaaaasreqaaaiReWakengievserGr 98 
                                   ++++gl  ++  i+Ls ++ ++l+++L++y++ a  ++++     +++++a  a +++ ++i++  +e  +++s+r  
  gi|15668235|ref|NP_247028.1|  53 EIHYGLRITNERINLSVSELDELEKKLKEYLDFAENMKKS----VENTHNAIIAVKNEMRDIKHSLEESSLKISNRYN 126
                                   688888889999***********************99854....4555555556666777777777777777777755 PP

>> IFT20  Intraflagellar transport complex B, subunit 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       2.2   7.1e+02      23      56 ..      14      47 ..       2      55 .. 0.48
   2 ?    8.8   3.2    0.0054       1.7      32      79 ..      69     116 ..      30     124 .. 0.86
   3 ?    9.1   0.6    0.0046       1.4      18      61 ..     122     165 ..     118     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.2
                         IFT20 23 elkeeckeFvkkinefqklvkelievleelakkv 56
                                  +l ee ++ ++++ e + + +e+i  l++l +++
  gi|15668235|ref|NP_247028.1| 14 KLIEELDKSSSSVLETEIVLDEIITKLNNLISEI 47
                                  4444444444444444444444444444444444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0054
                         IFT20  32 vkkinefqklvkelievleelakkvekeKlkAigarnllkseakqrea 79 
                                   v++++e++k  ke++++ e++ k+ve+     i+++n +++++ + e+
  gi|15668235|ref|NP_247028.1|  69 VSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSLEE 116
                                   47899*********************************9999887555 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0046
                         IFT20  18 aeeteelkeeckeFvkkinefqklvkelievleelakkvekeKl 61 
                                   +++ + ++++ k+ +kki+++++ +k+l+++ e++ +++++ K+
  gi|15668235|ref|NP_247028.1| 122 SNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQESIINSINSTKM 165
                                   55666789999********************************9 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.7      0.17        53      49     118 ..      12      81 ..       3      88 .. 0.63
   2 ?   12.3   6.3   0.00028     0.088      49     135 ..      79     165 ..      73     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.17
                     Golgin_A5  49 ldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaeler 118
                                   l++l +e d   +++ ++++ ++++ t+l++l ++ ++ + +++  l+  +e+++ + ++  e+e++l++
  gi|15668235|ref|NP_247028.1|  12 LNKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINNYITEIHYGLRITNERINLSVSELDELEKKLKE 81 
                                   5555566666666666666666666666666666666666666666666666666666666666666554 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00028
                     Golgin_A5  49 ldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleee 129
                                   l e  +  + +++++++++++i  +++e++d++++ ++ + ++ ++ + +e++l++ +k+ e++++ +++l++ ++++ + 
  gi|15668235|ref|NP_247028.1|  79 LKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSLEESSLKISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQESIINS 159
                                   55555556778999*********************************************************9999888777 PP

                     Golgin_A5 130 lvrska 135
                                      +k+
  gi|15668235|ref|NP_247028.1| 160 INSTKM 165
                                   666665 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0  10.8   0.00044      0.14      63     174 ..      33     153 ..       2     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00044
                  Bacillus_HBL  63 lnevkPqliktiqdiigYstkFqsyyktlveav.........dkkdkaellellekLqeeiqqnqkevkqlikeLkklklk 134
                                   l+e+  +l ++i++i++Y t+        +e +          +k+ +e l+  e++++++ +  +++ ++ +e+++ k +
  gi|15668235|ref|NP_247028.1|  33 LDEIITKLNNLISEINNYITEIHYGLRITNERInlsvseldeLEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHS 113
                                   567777888888889999887654444444555666688864345557889999*************************** PP

                  Bacillus_HBL 135 lakdsknFktdvdeltsilagdsgvisqlqneiedlqgki 174
                                   l++ s + ++  + ++ +l+  s++i+ l n i++l +++
  gi|15668235|ref|NP_247028.1| 114 LEESSLKISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQ 153
                                   ***********************************99876 PP

>> DUF840  Lagovirus protein of unknown function (DUF840)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.9   0.00055      0.17      66     111 ..     110     155 ..      87     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00055
                        DUF840  66 vrlsnmhndasvvnaynvynpasngirkkikslnnsvkiynttges 111
                                   ++ s       + n yn+ + + +   kki sl ns+k    t es
  gi|15668235|ref|NP_247028.1| 110 IKHSLEESSLKISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQES 155
                                   555555556678899*************************999998 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3     0.092        29       9      86 ..      13      85 ..       3      93 .. 0.66
   2 ?    9.5   2.5    0.0048       1.5       8      72 ..      86     149 ..      71     162 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.092
                       DUF2203  9 nalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleaglvDF 86
                                  n+l+ +l++  + + +++  l e+ ++l++  +e ++   +e +  l+  +++i+  v+e++el  ++k+     +DF
  gi|15668235|ref|NP_247028.1| 13 NKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINN-YITEIHYGLRITNERINLSVSELDELEKKLKEY----LDF 85
                                  5666666666666666666666666666666666543.366666677777777777777777777777766....555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0048
                       DUF2203   8 AnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieel 72 
                                   A+++   ++++ ++++a+++e+++++++lee++ + ++  ++ +e +l++ +++ie+l + i++l
  gi|15668235|ref|NP_247028.1|  86 AENMKKSVENTHNAIIAVKNEMRDIKHSLEESSLKISN-RYNLMEDTLKHHSKKIESLSNSIKSL 149
                                   44455566666677777777777777777777666543.36677777777777777766666654 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   6.6      0.15        46      23      82 ..      88     151 ..       9     158 .. 0.57
   2 ?    5.3   0.2     0.077        24      25      58 ..     129     162 ..     118     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.15
                        DUF948  23 klkktldeaaatieelekqvdpilkevedllakvne....lledvneklekvdplteavadlge 82 
                                   ++kk ++++ ++i  ++++++ i + +e+   k+ +    + + ++++++k+++l ++++ l++
  gi|15668235|ref|NP_247028.1|  88 NMKKSVENTHNAIIAVKNEMRDIKHSLEESSLKISNrynlMEDTLKHHSKKIESLSNSIKSLSK 151
                                   3345555555555555555554444444432222222332444455566666666666666665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.077
                        DUF948  25 kktldeaaatieelekqvdpilkevedllakvne 58 
                                   ++tl++ ++ ie+l + +++++k  e +++ +n 
  gi|15668235|ref|NP_247028.1| 129 EDTLKHHSKKIESLSNSIKSLSKTQESIINSINS 162
                                   5677777777777777777777777777777765 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   7.9     0.014       4.5      26     119 ..      19     115 ..      12     122 .. 0.76
   2 ?   13.2   9.1   0.00024     0.076      36     117 ..      71     152 ..      66     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.014
                                   CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHCCCHHHHHHHCCHH CS
                     Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn....dnvikksskeleeeilrlketidaqes 102
                                   l+k  ++v ++   l + +++++n  +e++++++ei+  lr +++  + +    d++ kk+++ l+   +++k+++ ++ +
  gi|15668235|ref|NP_247028.1|  19 LDKSSSSVLETEIVLDEIITKLNNLISEINNYITEIHYGLRITNERINLSvselDELEKKLKEYLD-FAENMKKSVENTHN 98 
                                   556666666666668888999999999999999999988877766665543345888888888888.88999999999999 PP

                                   HHHHHHHHHHHHHHHHH CS
                     Fib_alpha 103 nirvLqnvlesneqkiq 119
                                    i + +n +++ +++++
  gi|15668235|ref|NP_247028.1|  99 AIIAVKNEMRDIKHSLE 115
                                   99999999998887665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00024
                                   HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHH CS
                     Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneq 116
                                   +l++le++l+e+ +  +++++ v+++++ + + +++ +d ++ +++ss ++ ++++ +++t++++ ++i+ L n ++s+++
  gi|15668235|ref|NP_247028.1|  71 ELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSLEESSLKISNRYNLMEDTLKHHSKKIESLSNSIKSLSK 151
                                   799**************************99999999999************************************99887 PP

                                   H CS
                     Fib_alpha 117 k 117
                                    
  gi|15668235|ref|NP_247028.1| 152 T 152
                                   5 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   6.7     0.001      0.32      54     158 ..      11     116 ..       3     119 .. 0.88
   2 ?    7.6   1.2    0.0044       1.4      38      97 ..     111     170 ..     110     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.001
                        Tektin  54 diefwkeeLekeleelkeeieaLeeekrrlekalealeeplhiaqeclelRekRqgidlvh.DevekeLlkEveliegvqe 133
                                    ++++ eeL+k+ + + e+   L e+ ++l++ ++++++ +  ++  l + ++R++  + + De ek+L++ ++  e++++
  gi|15668235|ref|NP_247028.1|  11 WLNKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINNYITEIHYGLRITNERINLSVSElDELEKKLKEYLDFAENMKK 91 
                                   466777888888888888888999999999999999999999999999999999999988789******9999******** PP

                        Tektin 134 llkrtleqaeeqlrllraakhkLek 158
                                    +++t + ++   +++r++kh Le+
  gi|15668235|ref|NP_247028.1|  92 SVENTHNAIIAVKNEMRDIKHSLEE 116
                                   ******9999999999999999996 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0044
                        Tektin  38 kktqadsnkrLeeRiediefwkeeLekeleelkeeieaLeeekrrlekalealeeplhia 97 
                                   k++ ++s+ ++++R + +e   +  +k++e l + i++L+++++ + ++++++++ l i+
  gi|15668235|ref|NP_247028.1| 111 KHSLEESSLKISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQESIINSINSTKMLLYIT 170
                                   56678899999999999999999999999************9999999999999998876 PP

>> DUF1729  Domain of unknown function (DUF1729)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.22        69     137     213 ..      14      91 ..       6     102 .. 0.76
   2 ?    9.5   0.7    0.0013       0.4     106     181 ..      89     171 ..      85     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.22
                       DUF1729 137 klwkeldetifsleavekrkaalekkrdeiierlnkdyakpwfavdeegelveleemtYsevvrRlve.Laflksrke 213
                                   kl++eld+   s+ ++e    ++ +k +++i+++n+  +  ++++  + e ++l   +  e+ ++l e L f ++ k+
  gi|15668235|ref|NP_247028.1|  14 KLIEELDKSSSSVLETEIVLDEIITKLNNLISEINNYITEIHYGLRITNERINLSVSELDELEKKLKEyLDFAENMKK 91 
                                   778899999999888888888889999999999999999999999988888888887777777777663445555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                       DUF1729 106 WeatykkpaGgvvsvrSelgepihkia.......nraaklwkeldetifsleavekrkaalekkrdeiierlnkdyakpwf 179
                                    +++++++   +++v+ e+++  h ++       nr   +  +l ++  ++e+  +  + l+k +++ii+ +n++ +  ++
  gi|15668235|ref|NP_247028.1|  89 MKKSVENTHNAIIAVKNEMRDIKHSLEesslkisNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQESIINSINSTKMLLYI 169
                                   567888888889999999998778666000000055555555566666677777888899**************9777676 PP

                       DUF1729 180 av 181
                                   ++
  gi|15668235|ref|NP_247028.1| 170 TI 171
                                   55 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.74   2.3e+02      73     114 ..       4      45 ..       1      53 [. 0.65
   2 ?   12.1   4.2   0.00029      0.09      16     101 ..      70     159 ..      64     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.74
                       DUF3450  73 lvasqeqeiasleeqieeieeierelvpllekmidrLeqfve 114
                                   + ++q   +++l e++++ +    e + +l+++i++L++++ 
  gi|15668235|ref|NP_247028.1|   4 MNDKQADWLNKLIEELDKSSSSVLETEIVLDEIITKLNNLIS 45 
                                   455666666666666666666666667777777777776664 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00029
                       DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeele..slevyneq..lerlvasqeqeiasleeqieeie 92 
                                   ++ld+++k+ ++  + a+ + k +++  +    +++e+r++k  le  sl++ n++  +e+ +++  ++i+sl ++i++++
  gi|15668235|ref|NP_247028.1|  70 SELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSLEesSLKISNRYnlMEDTLKHHSKKIESLSNSIKSLS 150
                                   578888999999999999999999999999999999999998766522566666544478888899999999999999999 PP

                       DUF3450  93 eierelvpl 101
                                   ++++++   
  gi|15668235|ref|NP_247028.1| 151 KTQESIINS 159
                                   999887655 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.4     0.033        10      30      86 ..      57     112 ..      31     121 .. 0.83
   2 ?    7.1   0.2     0.017       5.4      34      76 ..     121     162 ..     116     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.033
                                   CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Nup54  30 GFedLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelsh 86 
                                   G    ++R ++   e+++++++lke  d +e+++ k   +t++++  +k++   ++h
  gi|15668235|ref|NP_247028.1|  57 GLRITNERINLSVSELDELEKKLKEYLDFAENMK-KSVENTHNAIIAVKNEMRDIKH 112
                                   5555678999999999999999999999999999.8888899999999988887777 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.017
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Nup54  34 LakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlek 76 
                                   +++R ++ ++ ++ h ++++++s+++++l+ k q ++ + ++ 
  gi|15668235|ref|NP_247028.1| 121 ISNRYNLMEDTLKHHSKKIESLSNSIKSLS-KTQESIINSINS 162
                                   678999999*********************.888877777765 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.6    0.0043       1.4      12      75 ..      63     121 ..      20     129 .. 0.87
   2 ?    1.5   0.0         1   3.3e+02      10      37 ..     128     155 ..     120     171 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0043
                          FliJ  12 relqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqv 75 
                                    +++   ++l+ele+ ++ey   +++           n+++ i a+++++  +k++l+ +  ++
  gi|15668235|ref|NP_247028.1|  63 ERINLSVSELDELEKKLKEYLDFAENMK-----KSVENTHNAIIAVKNEMRDIKHSLEESSLKI 121
                                   5566677899999999999988888877.....9999999999999999999999999877665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1
                          FliJ  10 aqrelqqaeekleeleqyrqeyqkqlsg 37 
                                   ++  l+ + +k+e+l + +++++k +++
  gi|15668235|ref|NP_247028.1| 128 MEDTLKHHSKKIESLSNSIKSLSKTQES 155
                                   4555555555666666555555554444 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   7.1    0.0014      0.44      16     106 ..      70     161 ..      61     167 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0014
                        APG6_N  16 kqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeell....eeLkelekereeleaelaaleeele 92 
                                   ++l+++ek+ ++Y++f +++kk+ +++    + + + ++e+++++   ee      +  + +e++ +   +++++l++  +
  gi|15668235|ref|NP_247028.1|  70 SELDELEKKLKEYLDFAENMKKSVENTH---NAIIAVKNEMRDIKHSLEESSlkisNRYNLMEDTLKHHSKKIESLSNSIK 147
                                   699******************9966654...45555555544433333222200002223345555555555555555555 PP

                        APG6_N  93 aleeeeerfwreyn 106
                                    l + +e  +++ n
  gi|15668235|ref|NP_247028.1| 148 SLSKTQESIINSIN 161
                                   55555555554444 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   6.0     0.028       8.7      32      68 ..     105     178 ..       5     188 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.028
                        ETRAMP  32 k.....................................ekakkaikkiddkiekkkkkkKliiistiatalall 68 
                                   +                                      ++ k++ k +++i +  +++K +++ tia +++ l
  gi|15668235|ref|NP_247028.1| 105 NemrdikhsleesslkisnrynlmedtlkhhskkieslSNSIKSLSKTQESIINSINSTKMLLYITIALTVVNL 178
                                   05555555555555556666666666663333333344455555555555666666666666666666555555 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   6.3      0.02       6.2      66     153 ..      16     107 ..       2     116 .. 0.63
   2 ?    9.9   3.7    0.0016       0.5       3      58 ..      94     153 ..      92     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.02
                       DUF4795  66 eelaekadkeaLatkvsrdqfDeakkeLekmleellekleeqeealkkaldtLq......eelkekld..rlelepLkeql 138
                                    e+  k+  + L+t +    +De +++L++ ++e+ + ++e    l+   + ++      +el++kl    +  e++k+ +
  gi|15668235|ref|NP_247028.1|  16 IEELDKSSSSVLETEI---VLDEIITKLNNLISEINNYITEIHYGLRITNERINlsvselDELEKKLKeyLDFAENMKKSV 93 
                                   4555666666666666...57888888888887777777766666666666666666666688888877434457888999 PP

                       DUF4795 139 eerlkelqkelqeam 153
                                   e++ +++  ++++ m
  gi|15668235|ref|NP_247028.1|  94 ENTHNAII-AVKNEM 107
                                   88887776.334333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0016
                       DUF4795   3 vnsaellkklqeaieklqeelek....leekvkelekrledkekklealkkqieelekvk 58 
                                    n+ +++  +++++++++ +le+    ++++ + +e++l+  +kk+e+l ++i+ l k+ 
  gi|15668235|ref|NP_247028.1|  94 ENTHNAIIAVKNEMRDIKHSLEEsslkISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQ 153
                                   5677778889999999999998766669999999*********************99876 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   6.7      0.37   1.2e+02      34     101 ..      70     141 ..       2     143 .. 0.74
   2 ?    9.3   3.9    0.0051       1.6      22      82 ..     104     164 ..      77     178 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.37
                                   HHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...........HHHHHHHHHHHHHHHHHH CS
                         DUF16  34 qrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln....kvdetleliletLqkinkRlDs 101
                                    +L ++e+k++      +++++ ve+  + i   k+e+   +++l+    k+ +  +l+ +tL++ +k++ s
  gi|15668235|ref|NP_247028.1|  70 SELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSLEesslKISNRYNLMEDTLKHHSKKIES 141
                                   567777777777777777777777777777777777776666666677777888888888888888887766 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0051
                                   HHHHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                         DUF16  22 rkqlnefkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82 
                                   + ++ + k+s ++   ki ++ +  +  +++  +k+e + + ik l+++q+   +++n+ +
  gi|15668235|ref|NP_247028.1| 104 KNEMRDIKHSLEESSLKISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQESIINSINSTK 164
                                   3455556666666666677777777778888888888888888777777766666665443 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   6.5     0.002      0.63      36     155 ..      40     157 ..      28     166 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.002
                          Fez1  36 lkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaale 116
                                   l + + e+++ ++e    ++ ++e+++    el+++e++l++  + ae++++ ve++++ +  +++e+++ +++ ee++l+
  gi|15668235|ref|NP_247028.1|  40 LNNLISEINNYITEIHYGLRITNERINLSVSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSLEESSLK 120
                                   555556666666666666666777777777788888888888877777777777777777777777777766665555544 PP

                          Fez1 117 sdeakaqrqeaeeleelkreverlraeLkeerqkkeeqa 155
                                    ++ +  +  +++l++ ++++e l +++k   +++e+  
  gi|15668235|ref|NP_247028.1| 121 ISN-RY-NLMEDTLKHHSKKIESLSNSIKSLSKTQESII 157
                                   444.22.22345666666777777777666666666544 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.6     0.051        16      76     123 ..      11      55 ..       1      85 [. 0.50
   2 ?    9.1  12.1    0.0031      0.98      62     184 ..      36     162 ..      35     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.051
                           LXG  76 fLkkikealesvepssngfidedfLeqelenglkkakevteelkdein 123
                                    L+k +e+l     ss+ +++ +++ +e+  +l+++ ++++++  ei 
  gi|15668235|ref|NP_247028.1|  11 WLNKLIEELDK---SSSSVLETEIVLDEIITKLNNLISEINNYITEIH 55 
                                   44555555555...5566666666666664444444444444444443 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0031
                           LXG  62 lltslqdlieqyeefLkkikealesvepssngfidedfLeqelenglkkakevteelkdeinkil.......asvsdivsl 135
                                   ++t l++li+++++   +i   l    +++   ++ + L+ ele++lk+     e++k++++++        ++ +di + 
  gi|15668235|ref|NP_247028.1|  36 IITKLNNLISEINNYITEIHYGLRI--TNERINLSVSELD-ELEKKLKEYLDFAENMKKSVENTHnaiiavkNEMRDIKHS 113
                                   6777777888877777777777777..6677777788888.9999998887777777777777554444444777777777 PP

                           LXG 136 pelddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkalkt 184
                                    e ++ ++ + ++ +++++++  +k+e + ++ ks+ +++es ++++++
  gi|15668235|ref|NP_247028.1| 114 LEESSLKISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQESIINSINS 162
                                   7777777777777777777777777777777777777777777776665 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  17.8      0.16        49      29     122 ..      58     150 ..       2     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.16
                       DUF5082  29 LkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessyqtyvdkldelidaieeEIerLenqiseaqg 109
                                   L+ + +++    ++l++ +kkl+++l   e+ k++ en+++ i   ++ +++ +++ l+e   +i++  + +e +++++++
  gi|15668235|ref|NP_247028.1|  58 LRITNERINLSVSELDELEKKLKEYLDFAENMKKSVENTHNAI-IAVKNEMRDIKHSLEESSLKISNRYNLMEDTLKHHSK 137
                                   7788888999999**************************9876.579********************************** PP

                       DUF5082 110 vldtlqsqlnslk 122
                                   ++++l+++++sl+
  gi|15668235|ref|NP_247028.1| 138 KIESLSNSIKSLS 150
                                   **********997 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  14.1    0.0057       1.8      50     184 ..       7     157 ..       1     163 [. 0.55

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0057
                                   HHHHHHHHIIIIIIIII...IIIIIIIIHHHHHHHHHHHHHHHHHHHHHTSS-TTS...................STGGGC CS
                         APG17  50 qQlkllekirkslerkl...ekgkeefkdlikeldaanerLektlekLrktkvepsfrpegee............ktLlDF 115
                                   +Q + l+k+ ++l +      +++ +++++i++l++  +++++ +++ +       +r ++e+            k+L+++
  gi|15668235|ref|NP_247028.1|   7 KQADWLNKLIEELDKSSssvLETEIVLDEIITKLNNLISEINNYITEIH-----YGLRITNERinlsvseldeleKKLKEY 82 
                                   5666666666665555533233333444555555555444444444433.....222222211233334466677777777 PP

                                   S-.....-TTTTHHHHHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHH.-------STCCHHHHHHHHHHHHH CS
                         APG17 116 vd.....edsveelkealkesidelqaaqkkldssllefdtdlrelkkel.sksksksessslipellkelesle 184
                                    d     ++sve+ ++a+ ++++e+ +++++l++s l+++++ + ++++l ++sk+ ++ s++i++l k++es+ 
  gi|15668235|ref|NP_247028.1|  83 LDfaenmKKSVENTHNAIIAVKNEMRDIKHSLEESSLKISNRYNLMEDTLkHHSKKIESLSNSIKSLSKTQESII 157
                                   776666667777777777777777777777777777777777777777774333333466666777777666655 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   4.6    0.0019       0.6      17     117 ..      45     153 ..      28     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0019
                      PHM7_cyt  17 eklkeffeelypgkvvesvqivrdvkkldklveerekavrkleaalskykkngkklpkkr............pthklgflg 85 
                                    +++++++e++ g  +++  i+  v++ld+l ++ ++++   e +++  + + +  ++ +             + k++   
  gi|15668235|ref|NP_247028.1|  45 SEINNYITEIHYGLRITNERINLSVSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKnemrdikhsleeSSLKISN-- 123
                                   6799******************************999988888887666666665555556777877666443333332.. PP

                      PHM7_cyt  86 lkligkkvdaidyyrekleeldeeieeerekv 117
                                         + d++++ ++k+e+l+  i+ + ++ 
  gi|15668235|ref|NP_247028.1| 124 --RYNLMEDTLKHHSKKIESLSNSIKSLSKTQ 153
                                   ..234468999999999999999999887643 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  10.4   0.00032       0.1      14     124 ..       5     122 ..       2     127 .. 0.54
   2 ?    1.4   3.0       1.3   4.1e+02      27     108 ..     113     161 ..     102     179 .. 0.41

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00032
                        PIN_12  14 rlseeealkklleliesgkiklivpdivldEflknrekkieeskklekalks.....lsklksakkklnekkkllslkeik 89 
                                   ++++++ l+kl e +++   +++ ++ivldE++ ++++ i+e+++ + ++        ++++    +l+e++k   + +  
  gi|15668235|ref|NP_247028.1|   5 NDKQADWLNKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINNYITEIHYglritNERINLSVSELDELEK---KLKEY 82 
                                   566777899**9999999*************************555544443343243333333333333222...22222 PP

                        PIN_12  90 kkieekvees.....lkkllekleaikvipetndevkkil 124
                                    +++e+ ++s     ++ +  k+e+ +++ + +++  ki 
  gi|15668235|ref|NP_247028.1|  83 LDFAENMKKSventhNAIIAVKNEMRDIKHSLEESSLKIS 122
                                   2222222222111112222333333555555555555555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.3
                        PIN_12  27 liesgkiklivpdivldEflknrekkiees....kklekalkslsklksakkklnekkkllslkeikkkieekveeslkkl 103
                                    +e+  +k+      ++ +lk+ +kkie+     k+l+k+                                     ++++
  gi|15668235|ref|NP_247028.1| 113 SLEESSLKISNRYNLMEDTLKHHSKKIESLsnsiKSLSKT-------------------------------------QESI 156
                                   3333333333333333334444444444332222222222.....................................2333 PP

                        PIN_12 104 lekle 108
                                   ++ ++
  gi|15668235|ref|NP_247028.1| 157 INSIN 161
                                   33332 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.8     0.021       6.7       9      49 ..      13      54 ..       7      62 .. 0.64
   2 ?    5.5  15.4     0.069        22       4      98 ..      36     161 ..      33     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.021
                    Syntaxin_2  9 nsnvstleklvkq.Lgtkkdteelreklhelieeinelikkt 49
                                  n+++ +l+k  ++ L+t    +e+  kl++li+ein+ i+++
  gi|15668235|ref|NP_247028.1| 13 NKLIEELDKSSSSvLETEIVLDEIITKLNNLISEINNYITEI 54
                                  556666666666656666666666666666666666666655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.069
                    Syntaxin_2   4 nlqkinsnvstleklvkqLgtkkdteelr......................eklhelieeinelikktnellkklsqldns 62 
                                    ++k+n+++s+++++++ ++     ++ r                      e++++++e++ + i ++++ ++++++  + 
  gi|15668235|ref|NP_247028.1|  36 IITKLNNLISEINNYITEIHYGLRITNERinlsvseldelekklkeyldfaENMKKSVENTHNAIIAVKNEMRDIKHSLEE 116
                                   588888889999998888777733222223355666666667777777777999999999999999999999999999988 PP

                    Syntaxin_2  63 ssds.........qqkl.qkekLkkdfkealqeFqkiqrqyaekek 98 
                                   ss +            l  ++k  ++++++++++ k+q+++ +  +
  gi|15668235|ref|NP_247028.1| 117 SSLKisnrynlmeD-TLkHHSKKIESLSNSIKSLSKTQESIINSIN 161
                                   88889998888743.3347888889999999999999999987765 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0         6   1.9e+03      43      74 ..      12      43 ..       2      53 .. 0.50
   2 ?    9.9   0.6    0.0029       0.9      36      78 ..      65     107 ..      59     111 .. 0.90
   3 ?    3.7   1.8      0.23        74      25      68 ..     114     157 ..     108     167 .. 0.55
   4 ?    1.2   0.1       1.4   4.4e+02       9      33 ..     144     168 ..     141     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 6
                          KxDL 43 laklrarfkqgtkllkevkkdLesifkkirsl 74
                                  l+kl +++ +    + e+   L+ i  k+++l
  gi|15668235|ref|NP_247028.1| 12 LNKLIEELDKSSSSVLETEIVLDEIITKLNNL 43
                                  44444444444444444444444444444444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0029
                          KxDL  36 nalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakl 78 
                                   ++ls ++l +l++++k++   + ++kk  e+++  i + k ++
  gi|15668235|ref|NP_247028.1|  65 INLSVSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEM 107
                                   6789999***************************999988876 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.23
                          KxDL  25 lnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesif 68 
                                   l++++ ++++  +l++  l+++++++++  + +k++ k  esi 
  gi|15668235|ref|NP_247028.1| 114 LEESSLKISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQESII 157
                                   55555555555555555555555555555555555555544444 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 1.4
                          KxDL   9 edldeilalQaqtsgrlnkknreLl 33 
                                   + +++  ++Q+ + + +n+++  L 
  gi|15668235|ref|NP_247028.1| 144 NSIKSLSKTQESIINSINSTKMLLY 168
                                   5678888999999999999987765 PP

>> SOAR  STIM1 Orai1-activating region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.7   5.4e+02      40      80 ..      16      55 ..       3      67 .. 0.57
   2 ?    9.4   1.2    0.0033         1      58      88 ..      89     119 ..      61     132 .. 0.75
   3 ?    2.8   0.3      0.35   1.1e+02      57      84 ..     134     161 ..     121     166 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.7
                          SOAR 40 veklkkkrssllgslrlahssslddvdkkileakqaleevt 80
                                  +e l+k  ss+l    ++ ++ + ++++ i e+ + ++e++
  gi|15668235|ref|NP_247028.1| 16 IEELDKSSSSVLE-TEIVLDEIITKLNNLISEINNYITEIH 55
                                  5566666555553.344555555555555555555555555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0033
                          SOAR  58 hssslddvdkkileakqaleevtkelkerqe 88 
                                     +s++++ ++i+++k+++++++++l+e++ 
  gi|15668235|ref|NP_247028.1|  89 MKKSVENTHNAIIAVKNEMRDIKHSLEESSL 119
                                   568999**********************875 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.35
                          SOAR  57 ahssslddvdkkileakqaleevtkelk 84 
                                    hs++++++ ++i ++ ++ e++ ++++
  gi|15668235|ref|NP_247028.1| 134 HHSKKIESLSNSIKSLSKTQESIINSIN 161
                                   5888888888888888888888877665 PP

>> Sulfatase_C  C-terminal region of aryl-sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3     0.012       3.8      63     107 ..      69     113 ..      64     126 .. 0.85
   2 ?    2.2   0.1       0.9   2.8e+02      77     110 ..     122     155 ..     111     167 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.012
                                   TT--S-TTSTTCCHHHHHHHHHHHHHHHCCC------TCCHHCHS CS
                   Sulfatase_C  63 psEkyplsaespeykevlkeikkaveehkktlkpvpnqlakgell 107
                                   +sE  +l+++ +ey +  +++kk ve+ ++ + +v+n++   +++
  gi|15668235|ref|NP_247028.1|  69 VSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHS 113
                                   68999999999****************************998554 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.9
                                   HHHHHHHHHHHHHHCCC------TCCHHCHS.-G CS
                   Sulfatase_C  77 kevlkeikkaveehkktlkpvpnqlakgellpkp 110
                                   ++  + +++ +++h k+++  +n +++++++++ 
  gi|15668235|ref|NP_247028.1| 122 SNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQES 155
                                   4445556666777777777777777766555443 PP

>> Alpha-2-MRAP_C  Alpha-2-macroglobulin RAP, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       3.3     1e+03      24      57 ..      12      42 ..       4      66 .. 0.63
   2 ?    6.2   4.2     0.029         9      21      75 ..      62     115 ..      56     131 .. 0.70
   3 ?    9.4   0.6     0.003      0.95      29      64 ..     130     165 ..     125     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.3
                Alpha-2-MRAP_C 24 LekLkeEfkhhqeKideYnsLleelekeeekheN 57
                                  L+kL eE+++    + e + +l+e+ ++ +   N
  gi|15668235|ref|NP_247028.1| 12 LNKLIEELDKSSSSVLETEIVLDEIITKLN---N 42
                                  666777777766666666666666554444...2 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.029
                Alpha-2-MRAP_C  21 eeeLekLkeEfkhhqeKideYnsLleelekeeekheNaiseeeldkvneieeeee 75 
                                   +e ++   +E++  ++K++eY +  e+++k+ e+++Nai   + +++++i+++ e
  gi|15668235|ref|NP_247028.1|  62 NERINLSVSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVK-NEMRDIKHSLE 115
                                   55566667899999*******************9999977433.44444444333 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.003
                Alpha-2-MRAP_C  29 eEfkhhqeKideYnsLleelekeeekheNaiseeel 64 
                                   + +khh +Ki+ + + +++l+k++e+  N+i++ ++
  gi|15668235|ref|NP_247028.1| 130 DTLKHHSKKIESLSNSIKSLSKTQESIINSINSTKM 165
                                   5689***************************98765 PP

>> DUF1366  Protein of unknown function (DUF1366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3      0.28        88      71     106 ..      12      47 ..       3      55 .. 0.75
   2 ?   11.0   3.7   0.00083      0.26      47     108 ..      45     106 ..      31     114 .. 0.74
   3 ?    1.7   0.4      0.65     2e+02      70     108 ..     124     162 ..     118     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.28
                       DUF1366  71 FneldeliekakatiektEemlkaatetLneiidkl 106
                                    n+l e  +k+  ++  tE +l ++ + Ln++i ++
  gi|15668235|ref|NP_247028.1|  12 LNKLIEELDKSSSSVLETEIVLDEIITKLNNLISEI 47 
                                   456667777888888888888888888888888775 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00083
                       DUF1366  47 tellkeaekviYqelfPqrAenEkFneldeliekakatiektEemlkaatetLneiidklke 108
                                   +e+ +   ++ Y     +   n    eldel +k k+ ++  E+m k +++t n ii+   e
  gi|15668235|ref|NP_247028.1|  45 SEINNYITEIHYGLRITNERINLSVSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNE 106
                                   44444455555555555555555667*******************************97444 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.65
                       DUF1366  70 kFneldeliekakatiektEemlkaatetLneiidklke 108
                                   ++n +++  ++  ++ie   + +k  ++t  +ii+ +  
  gi|15668235|ref|NP_247028.1| 124 RYNLMEDTLKHHSKKIESLSNSIKSLSKTQESIINSINS 162
                                   566677778888888999999999999999999998765 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   7.6     0.009       2.8      18     124 ..      26     152 ..      21     165 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.009
                     AATF-Che1  18 lLelRIklQkaltaanqLp................qpetlkefles.......................seefeealeeae 59 
                                   +Le+ I l  ++t+ n L                 +         +                       +e++++ +e+++
  gi|15668235|ref|NP_247028.1|  26 VLETEIVLDEIITKLNNLIseinnyiteihyglriT---------NerinlsvseldelekklkeyldfAENMKKSVENTH 97 
                                   566667777777777766644333333333333331.........022222222233333333334444677777777777 PP

                     AATF-Che1  60 kalkklleslleLreelleqne..ikklaeskeeeekkkskrkrkkkkkeetsleelwkelekleka 124
                                   +a+ ++ +++ +++++l e+++  i+           ++ +  +++ k++++++e+l++ +++l k+
  gi|15668235|ref|NP_247028.1|  98 NAIIAVKNEMRDIKHSL-EESSlkIS-----------NRYNLMEDTLKHHSKKIESLSNSIKSLSKT 152
                                   77777777777777777.33332221...........111222222222223333333333333332 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.2       2.5   7.7e+02      15      27 ..      15      23 ..       6      46 .. 0.44
   2 ?    2.6   0.6      0.37   1.1e+02      13      30 ..      37      54 ..      27      78 .. 0.53
   3 ?    8.7   1.0    0.0045       1.4       2      41 ..      79     118 ..      78     130 .. 0.83
   4 ?    7.7   2.4    0.0097       3.1       9      44 ..     132     167 ..     128     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 2.5
                     DASH_Duo1 15 vienviesLkkak 27
                                   ie ++    k++
  gi|15668235|ref|NP_247028.1| 15 LIEELD----KSS 23
                                  222222....222 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.37
                     DASH_Duo1 13 nevienviesLkkaksni 30
                                  ++ ++n+i+++++  ++i
  gi|15668235|ref|NP_247028.1| 37 ITKLNNLISEINNYITEI 54
                                  333333333333322222 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0045
                     DASH_Duo1   2 LekEleqLrkinevienviesLkkaksniervketvestn 41 
                                   L++ l+  +++ + +en ++++ ++k+++  +k+++e+++
  gi|15668235|ref|NP_247028.1|  79 LKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSLEESS 118
                                   556666678999***********************99875 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0097
                     DASH_Duo1   9 LrkinevienviesLkkaksniervketvestntLL 44 
                                   L+   + ie++ +s+k+ ++  e++ ++++st++LL
  gi|15668235|ref|NP_247028.1| 132 LKHHSKKIESLSNSIKSLSKTQESIINSINSTKMLL 167
                                   55666789**************************99 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.9     0.017       5.4      99     173 ..      38     116 ..      32     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.017
                        Tweety  99 rkanhtlagikklvseteesl...eekleeeLtkleeifakrtdlletlrlvqeqveevvqqlselp.flkkkdvslte 173
                                   +k n++++ i++ ++e++  l   +e+++ ++ +l+e+ +k +++l   +++++ ve+  +++ +++  +++ + sl+e
  gi|15668235|ref|NP_247028.1|  38 TKLNNLISEINNYITEIHYGLritNERINLSVSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKnEMRDIKHSLEE 116
                                   5678888888888888777663334667777888888888888888888888888887777776666555555555443 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.0    0.0063         2       5      71 ..      39     111 ..      35     133 .. 0.73
   2 ?    5.3   1.0     0.089        28      23      70 ..     106     152 ..      88     168 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0063
                                   HHHHHHHHHHHHHHHHHHHH..CCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHTT CS
                      Spectrin   5 qfaqdadeleeWieekeell..ssedlgkdleevqallkkhkaleaelaaqqervkaln....elaeklldeg 71 
                                   ++++ ++e+++ i+e++  l  ++e++  +++e+ +l+kk+k++ +  +++++ v++      ++++++ d +
  gi|15668235|ref|NP_247028.1|  39 KLNNLISEINNYITEIHYGLriTNERINLSVSELDELEKKLKEYLDFAENMKKSVENTHnaiiAVKNEMRDIK 111
                                   6788899999999999887776888889999999999999999998888888888887733334444443333 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.089
                                   HHCCSSCSSSHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      Spectrin  23 llssedlgkdleevqallk.khkaleaelaaqqervkalnelaekllde 70 
                                   ++  +d+ ++lee   ++  ++  +e++l+ + +++++l    ++l + 
  gi|15668235|ref|NP_247028.1| 106 EM--RDIKHSLEESSLKISnRYNLMEDTLKHHSKKIESLSNSIKSLSKT 152
                                   44..566777777777766677777777777777777776544444332 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   5.1      0.27        84      53     102 ..      59     108 ..       7     117 .. 0.53
   2 ?    9.3   6.6    0.0036       1.1       8      82 ..      80     155 ..      62     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.27
                         DHR10  53 eeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqae 102
                                   + ++++++    +l+e+e++l+e+    e +++ +en +  +  ++++++
  gi|15668235|ref|NP_247028.1|  59 RITNERINLSVSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMR 108
                                   55555555555555555555555555555555555555544444443333 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0036
                         DHR10   8 keelaelErkarelqakidalqvvekdlrscikllee.ieaelakleeakkklkelrdaleekeielrelerkeer 82 
                                   ke l+ +E+  + ++++++a+  v++++r +   lee   +  ++++  +++lk++++++e++++  + l++++e 
  gi|15668235|ref|NP_247028.1|  80 KEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSLEEsSLKISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQES 155
                                   7888899999999******************999999555677999999******************999999986 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.8      0.23        72      90     134 ..      11      55 ..       3      66 .. 0.75
   2 ?    8.9   3.0    0.0044       1.4      86     135 ..      74     123 ..      69     146 .. 0.85
   3 ?    2.4   0.2      0.45   1.4e+02      52      82 ..     132     162 ..     123     167 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.23
                      MIP-T3_C  90 WrseyrqqaeelaeerrateealeplkaqlaeleeaIkdqkekis 134
                                   W ++  ++  + +    +te  l+++  +l++l ++I+++  +i+
  gi|15668235|ref|NP_247028.1|  11 WLNKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINNYITEIH 55 
                                   555555555666666678888999999999999999999988886 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0044
                      MIP-T3_C  86 ELemWrseyrqqaeelaeerrateealeplkaqlaeleeaIkdqkekisn 135
                                   ELe+  +ey   ae++++  + t++a+  +k+++ ++++++++   kisn
  gi|15668235|ref|NP_247028.1|  74 ELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHSLEESSLKISN 123
                                   888889999999************************************98 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.45
                      MIP-T3_C  52 iekLresiQkltksvnPLgklldfiqdDids 82 
                                   +++  ++i +l+ s++ L k  + i + i+s
  gi|15668235|ref|NP_247028.1| 132 LKHHSKKIESLSNSIKSLSKTQESIINSINS 162
                                   4555566667777777777776666666655 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1       1.4   4.4e+02      73      73 ..      34      34 ..       2      73 .. 0.54
   2 ?    6.6   7.4     0.021       6.7       3      86 ..      88     167 ..      32     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.4
                    STAT_alpha 73 k 73
                                   
  gi|15668235|ref|NP_247028.1| 34 D 34
                                  1 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.021
                    STAT_alpha   3 eieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkleqeraesekkelkkqkellqqmlnaLdqkRkelvdklkell 83 
                                   ++++++e+ ++ +  +++++r++++  ee ++++++  +l    +e + k+ +k+ e+l +++++L+++++++++ ++ + 
  gi|15668235|ref|NP_247028.1|  88 NMKKSVENTHNAIIAVKNEMRDIKHSLEESSLKISNRYNL----MEDTLKHHSKKIESLSNSIKSLSKTQESIINSINSTK 164
                                   5778889999999999999999999999999999888888....4455555778888888888889999999999999887 PP

                    STAT_alpha  84 nll 86 
                                   +ll
  gi|15668235|ref|NP_247028.1| 165 MLL 167
                                   766 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4      0.89   2.8e+02      64     101 ..      12      49 ..       3      54 .. 0.60
   2 ?    5.5   9.9     0.053        17      12     103 ..      63     150 ..      58     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.89
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                   Prefoldin_2  64 keeLeerketlekeiktlekqleklekeleelkeelqk 101
                                   +++L e++++ +  + + e  l+++ ++l++l +e+++
  gi|15668235|ref|NP_247028.1|  12 LNKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINN 49 
                                   45555555555555555566666667777777666665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.053
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  12 qqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktlekqleklekel 92 
                                   +++   ++++++le++lke  +  e++++  e+t        + vk++  ++k  Lee+  +++ +++ +e+ l+++ k++
  gi|15668235|ref|NP_247028.1|  63 ERINLSVSELDELEKKLKEYLDFAENMKKSVENTHNA----IIAVKNEMRDIKHSLEESSLKISNRYNLMEDTLKHHSKKI 139
                                   5566666666666666666666666666666662222....2347888889999999999999999999999999999999 PP

                                   HHHHHHHHCCT CS
                   Prefoldin_2  93 eelkeelqkkl 103
                                   e l ++++++ 
  gi|15668235|ref|NP_247028.1| 140 ESLSNSIKSLS 150
                                   99988888765 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  13.8     0.012       3.9      98     227 ..      19     158 ..       2     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                          CorA  98 lkdeggkpkspgellyrlldeivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlk. 175
                                   l+    k +s+   ++ +ldei+ +l++l+++++  + e+   l   +++ +  ++el +l+++l ++ + + ++++ ++ 
  gi|15668235|ref|NP_247028.1|  19 LD----KSSSSVLETEIVLDEIITKLNNLISEINNYITEIHYGLriTNERINLSVSELDELEKKLKEYLDFAENMKKSVEn 95 
                                   44....4455555566799***********************999999999999**************7777777777764 PP

                          CorA 176 .....rlla........kaddkllddedkeylrdlldelerllemlealrerleslqdtysslls 227
                                           a        k+  ++ + + +++++ ++d l++ ++++e+l++ + sl+ t  s+++
  gi|15668235|ref|NP_247028.1|  96 thnaiI--AvknemrdiKHSLEESSLKISNRYNLMEDTLKHHSKKIESLSNSIKSLSKTQESIIN 158
                                   444220..242344445556666666666777777777777888888888888887777777776 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   9.7      0.18        56      29      97 ..      62     148 ..       2     150 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.18
                  Syntaxin-6_N  29 edtsss...tseeldetrteLrkalrsiewdledLeetvriv...ek...............npskfkidekelsrrrafv 88 
                                   ++   +   + +elde++++L++ l+ +e+  +  e+t +++   ++                 +++++ e++l+ + + +
  gi|15668235|ref|NP_247028.1|  62 NE---RinlSVSELDELEKKLKEYLDFAENMKKSVENTHNAIiavKNemrdikhsleesslkISNRYNLMEDTLKHHSKKI 139
                                   33...13335666666666666666554444444444443331112244445555555555333569************** PP

                  Syntaxin-6_N  89 eevreevke 97 
                                   e++ + +k+
  gi|15668235|ref|NP_247028.1| 140 ESLSNSIKS 148
                                   999999986 PP

>> Cactin_mid  Conserved mid region of cactin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  10.5     0.021       6.7      75     170 ..      66     163 ..       3     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.021
                    Cactin_mid  75 glsleeleeleediksylel.ekseknaefWkallvvckdeleklkkkeee.....keaaeeaeesgihasveadikkilk 149
                                   +ls++el+ele+++k+yl+  e+ +k +e  ++  + +k+e++ +k++ ee     +  ++ + +++  ++ +++i+++  
  gi|15668235|ref|NP_247028.1|  66 NLSVSELDELEKKLKEYLDFaENMKKSVENTHNAIIAVKNEMRDIKHSLEEsslkiS--NRYNLMEDTLKHHSKKIESL-- 142
                                   389*****************5555888898888888899999998887776444221..13334445566667778877.. PP

                    Cactin_mid 150 gksleeLeelekqikekLesg 170
                                     s++ L++ +++i ++++s 
  gi|15668235|ref|NP_247028.1| 143 SNSIKSLSKTQESIINSINST 163
                                   899999******999999976 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.3     0.048        15      63     107 ..       6      50 ..       1      51 [. 0.85
   2 ?    7.4   6.9     0.016       4.9      24     104 ..      65     146 ..      58     149 .. 0.82
   3 ?    2.4   0.2      0.58   1.8e+02      74      93 ..     137     156 ..     126     167 .. 0.44

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.048
                                   CCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS--- CS
                  Seryl_tRNA_N  63 kkkkedaeeliaevkelkeelkaleaelkeleaeleklllaiPNi 107
                                    k+ +  ++li+e ++ +  + ++e  l+e+ ++l++l+++i N 
  gi|15668235|ref|NP_247028.1|   6 DKQADWLNKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINNY 50 
                                   444466789*********************************996 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.016
                                   CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCC.CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                  Seryl_tRNA_N  24 dkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaee.liaevkelkeelkaleaelkeleaelekllla 103
                                    ++ v el el++k +e    +e++++   +  ++I   k++  d+++ l +++ +++++ + +e++lk  ++++e+l  +
  gi|15668235|ref|NP_247028.1|  65 INLSVSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRDIKHsLEESSLKISNRYNLMEDTLKHHSKKIESLSNS 145
                                   567899999999999999999999999999999999999988866655155556799999999999999999999988766 PP

                                   S CS
                  Seryl_tRNA_N 104 i 104
                                   i
  gi|15668235|ref|NP_247028.1| 146 I 146
                                   6 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.58
                                   CCCHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  74 aevkelkeelkaleaelkel 93 
                                   +++++l++ +k l+++++ +
  gi|15668235|ref|NP_247028.1| 137 KKIESLSNSIKSLSKTQESI 156
                                   23333333333333333333 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2         2   6.4e+02       8      52 ..       8      52 ..       1      57 [. 0.64
   2 ?    9.7  12.0     0.003      0.95       5     101 ..      65     165 ..      59     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2
                       zf-C4H2  8 ktleleklknklakevealekeekcleeykkelelLeqEkmaHve 52
                                  + + l+kl ++l k  +++ ++e +l e+  +l++L +E ++ + 
  gi|15668235|ref|NP_247028.1|  8 QADWLNKLIEELDKSSSSVLETEIVLDEIITKLNNLISEINNYIT 52
                                  445566777777777777777777777777777777777665555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.003
                       zf-C4H2   5 irektleleklknklakevealekeekcleeykkelelLeqEkm..aHv..eeLrlIhaDinalEsvikeaeeekekslek 81 
                                   i+  ++el++l++kl++ +++ e+ +k +e++++ +  +++E +  +H+  e   +I +  n +E+++k+  ++ e   ++
  gi|15668235|ref|NP_247028.1|  65 INLSVSELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRdiKHSleESSLKISNRYNLMEDTLKHHSKKIESLSNS 145
                                   5567899***************************9999999965224533256678************************* PP

                       zf-C4H2  82 akklyeeykklkeevnelrs 101
                                   +k+l++  + + +++n+++ 
  gi|15668235|ref|NP_247028.1| 146 IKSLSKTQESIINSINSTKM 165
                                   ****************9876 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       2.2     7e+02      68      83 ..      36      51 ..       4      68 .. 0.52
   2 ?    3.2   0.3      0.28        87      39      91 ..      38      91 ..      28     100 .. 0.54
   3 ?    3.4   0.3      0.23        73      53      92 ..      70     109 ..      53     126 .. 0.64
   4 ?    5.2   0.4     0.067        21      39      76 ..     130     167 ..     123     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2.2
                      Noelin-1 68 yvrktetllktleskl 83
                                   ++k ++l++++++ +
  gi|15668235|ref|NP_247028.1| 36 IITKLNNLISEINNYI 51
                                  2344444444444444 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.28
                      Noelin-1 39 rqlrqllekvqnlsqsievldlRtsrdlq.yvrktetllktlesklkvveedrk 91
                                  ++l +l  +++n  ++i+   + t++ ++  v++ ++l k+l++ l+ +e+ +k
  gi|15668235|ref|NP_247028.1| 38 TKLNNLISEINNYITEIHYGLRITNERINlSVSELDELEKKLKEYLDFAENMKK 91
                                  566777777777777776655555554441233344444444444444444333 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.23
                      Noelin-1  53 qsievldlRtsrdlqyvrktetllktlesklkvveedrke 92 
                                    +++ l+++ ++ l++ +++++ +++ ++ +  v+++ + 
  gi|15668235|ref|NP_247028.1|  70 SELDELEKKLKEYLDFAENMKKSVENTHNAIIAVKNEMRD 109
                                   3456666666666666666666666666666555555444 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.067
                      Noelin-1  39 rqlrqllekvqnlsqsievldlRtsrdlqyvrktetll 76 
                                     l++ ++k++ ls+si+ l++  ++ ++ +++t+ ll
  gi|15668235|ref|NP_247028.1| 130 DTLKHHSKKIESLSNSIKSLSKTQESIINSINSTKMLL 167
                                   57999999*************99999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2742  (0.152937); expected 358.6 (0.02)
Passed bias filter:                      876  (0.0488594); expected 358.6 (0.02)
Passed Vit filter:                       150  (0.00836633); expected 17.9 (0.001)
Passed Fwd filter:                        67  (0.00373696); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              57  [number of targets reported over threshold]
# CPU time: 0.99u 0.38s 00:00:01.37 Elapsed: 00:00:00.68
# Mc/sec: 834.61
//
Query:       gi|15668236|ref|NP_247029.1|  [L=363]
Description: hypothetical protein MJ_0065 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-74  248.5  13.2    6.9e-74  247.9  13.2    1.3  1  DUF2117   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2117  Uncharacterized protein conserved in archaea (DUF2117)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.9  13.2   3.8e-78   6.9e-74       1     212 []      72     281 ..      72     281 .. 0.91

  Alignments for each domain:
  == domain 1  score: 247.9 bits;  conditional E-value: 3.8e-78
                       DUF2117   1 DivfLlnygksketGhvFgkiVverskekkpliqierpgekdgeiilwn...ekaek.lakklseelglkivkpeevekei 77 
                                   Di++L+nygksk+tGh+FgkiVver++ +kp+iqierpge+dg+ii+wn   +k++k +a++ls+el+lki k  +   e+
  gi|15668236|ref|NP_247029.1|  72 DILILMNYGKSKITGHTFGKIVVERANLNKPIIQIERPGEEDGTIIIWNddnSKIVKeIANYLSKELNLKIEKCISNGLEV 152
                                   9************************************************66633444489999********6666666666 PP

                       DUF2117  78 veskgkrvvrkiagvspgenilvnGiviGkaeseevtivaedgkivdikggeiKehGvekLgkvdlekaivktgllRrskv 158
                                    e++g rv rk++gv+ ge+ilvnGiv+Gka+s+ev+++ae+gk+vdi+gge+Ke G+ekL++vdl+ka++ktg lRr+ +
  gi|15668236|ref|NP_247029.1| 153 WEKEG-RVFRKVHGVDVGEAILVNGIVVGKAKSNEVILIAENGKLVDIIGGELKEGGIEKLKNVDLKKAVIKTGILRRHPT 232
                                   67766.569*********************************************************************765 PP

                       DUF2117 159 kekllkkkklkkkkekkvgkvvlidHaaedvlelakk..adlvvtvGDDTTavagd 212
                                   ++k++       +ke ++g +++i+Ha+edv+e++k+  + +v+t+GDDTT+++gd
  gi|15668236|ref|NP_247029.1| 233 NPKIE-------SKEIDEGYTIIINHAGEDVIEMIKNkgVVAVITIGDDTTTICGD 281
                                   55555.......4567899****************99999***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2226.66
//
Query:       gi|15668237|ref|NP_247030.1|  [L=480]
Description: hypothetical protein MJ_0066 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-52  177.6   0.1    1.5e-51  174.9   0.0    2.0  2  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
    1.9e-17   63.0   2.6    4.8e-17   61.7   2.6    1.8  1  PUA          PUA domain
    0.00055   20.1   0.8    0.00055   20.1   0.8    2.4  3  UPF0113      UPF0113 PUA domain
     0.0024   17.6   0.0      0.004   16.9   0.0    1.4  1  ATP_bind_3   PP-loop family
  ------ inclusion threshold ------
      0.054   13.0   0.0       0.12   11.9   0.0    1.5  1  QueC         Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.19   6.8e+02      40      90 ..      90     138 ..      69     175 .. 0.69
   2 !  174.9   0.0   4.1e-55   1.5e-51       2     173 ..     258     430 ..     257     431 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.19
                                   HHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-.THHHC.HHHHHHTHHH CS
                   PAPS_reduct  40 tiefvdeleeryglrlkvyepeeevaekinaekhgs.slyee.aaeriaKvep 90 
                                    +e + + e +y   l+++++++e ++k++ +  g  +l e+ a+++i+K+++
  gi|15668237|ref|NP_247030.1|  90 AYEIIVDGEVKY---LIYFDEDKE-KWKVKLKLNGAkDLMEKgAYKKIIKIKN 138
                                   555555555555...444444444.5555555445405555599999999874 PP

  == domain 2  score: 174.9 bits;  conditional E-value: 4.1e-55
                                   EEEE--SSCTCHHHHHHHHHHCTT.HEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHCH CS
                   PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkp.vpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyeea 81 
                                   ++v++sgGkdslV+l+L+lka+ + + vvf+dtg ef+et++ v+++e++yg++ ++  + e+++ek+++++++ ++y++ 
  gi|15668237|ref|NP_247030.1| 258 VMVAFSGGKDSLVTLILTLKALGKdIDVVFIDTGLEFEETLKNVEDVERHYGIK-IIRLRGENFWEKVKEYGIPARDYRW- 336
                                   689******************999679**************************9.7889999******************. PP

                                   HHHHHTHHHHHHHHHCT..TECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT--B-CCCC CS
                   PAPS_reduct  82 aeriaKveplkkaLekl..dedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilrenipynpLyd 160
                                   +++i+K+eplkk +e++  d+++ ++G+R++es++ra+++ +++++ ++k+++ +P+++W++ +vw y+lre+ pyn+Ly+
  gi|15668237|ref|NP_247030.1| 337 CSEICKLEPLKKFIEENyeDDVLSFVGIRKYESFNRATKKRIHRNTYIKKQINALPIFHWSSLHVWIYLLREKAPYNKLYE 417
                                   ***************997888999********************************************************* PP

                                   TT-SS--BCTTB- CS
                   PAPS_reduct 161 qgfrsiGcvpctg 173
                                   +gf++iGc++c++
  gi|15668237|ref|NP_247030.1| 418 KGFDRIGCFMCPA 430
                                   ***********86 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   2.6   1.3e-20   4.8e-17       3      73 ..     134     205 ..     132     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.3e-20
                                   EEE-HHHHHHHHT.T-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                           PUA   3 vvvddgAvkalls.gasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                   + +++ +v++l++ + s+l pG+ve+ +d+ee+d V ivde++++v+vGla +sse+++ +++gk+v+++ +
  gi|15668237|ref|NP_247030.1| 134 IKIKNDVVEFLKNrKGSVLRPGIVEFTDDIEEKDDVIIVDENDRVVGVGLAVVSSEDIKNMEKGKVVKVRFF 205
                                   67999********777*****************************************************975 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.2   4.2e+03       6      24 ..      67      85 ..      62     100 .. 0.73
   2 !   20.1   0.8   1.5e-07   0.00055      17      64 ..     150     200 ..     132     204 .. 0.85
   3 ?   -3.3   0.0       3.3   1.2e+04      37      48 ..     235     246 ..     229     258 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                       UPF0113  6 ekaeklFLYGrdvlkesil 24
                                  e ++k++L G+ +l ++i 
  gi|15668237|ref|NP_247030.1| 67 EFGAKNVLNGKIILLNKIP 85
                                  6689999999999888775 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.5e-07
                       UPF0113  17 dvlkesilkitesvkenqvvvVlnengeplGiGkirkdt...kaspgkivv 64 
                                    vl+ +i+++t++++e++ v++++en++++G+G +  ++   k  ++++vv
  gi|15668237|ref|NP_247030.1| 150 SVLRPGIVEFTDDIEEKDDVIIVDENDRVVGVGLAVVSSediKNMEKGKVV 200
                                   589999*****************************9998875444444444 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.3
                       UPF0113  37 vVlnengeplGi 48 
                                   v++n +++++G+
  gi|15668237|ref|NP_247030.1| 235 VIDNYERNAIGF 246
                                   678888888887 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-06     0.004       2     113 ..     258     362 ..     257     413 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS.TCHHHHHHHHHHHHHHTT-EEEEEE--HHHCTTSTCCCHHH CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr.eeskeeaelvkelckklnikleiekvdvakkkgknleeaAR 81 
                                   v+vA+SgG DS++ l l+ k    lg ++ ++ +d gl  e   e  + v+++ ++++ik++  + +   +k k+    AR
  gi|15668237|ref|NP_247030.1| 258 VMVAFSGGKDSLVTLILTLKA---LGKDIDVVFIDTGLEfE---ETLKNVEDVERHYGIKIIRLRGENFWEKVKEYGIPAR 332
                                   68*********9988888877...4559*********9844...4455667777777777766666653334455555688 PP

                                   HHHHHHHHHCHHCCT.CEEE---BHHHHHHHH CS
                    ATP_bind_3  82 elRYevlkealkkegievlllAhhadDqaEtf 113
                                   + R  + +e++k e ++ ++    +dD +  +
  gi|15668237|ref|NP_247030.1| 333 DYR--WCSEICKLEPLKKFIEENYEDDVLSFV 362
                                   855..567777777777666666666666555 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.2e-05      0.12       3      57 ..     259     311 ..     257     328 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                                   EEE--SSHHHHHHHHHH.HHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EE CS
                          QueC   3 vvllSGGlDSttvlala.kkegkevealtfdYgqrhkkeleaakkiakelgveehk 57 
                                   +v +SGG DS + l+l  k+ gk + ++ +d g   +++l+ ++++ +++g+   k
  gi|15668237|ref|NP_247030.1| 259 MVAFSGGKDSLVTLILTlKALGKDIDVVFIDTGLEFEETLKNVEDVERHYGI---K 311
                                   689*******9887765156689**************************999...3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3051.51
//
Query:       gi|15668238|ref|NP_247031.1|  [L=103]
Description: hypothetical protein MJ_0067 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-11   44.6  11.5    2.6e-11   43.8  11.5    1.4  1  FUN14     FUN14 family


Domain annotation for each model (and alignments):
>> FUN14  FUN14 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8  11.5   1.4e-15   2.6e-11       1      91 []      13     100 ..      13     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.4e-15
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                         FUN14   1 igiGaviGlvtGfalkkvgKlaaiavGggllllqilasqgyikvnwdkiekdveelldrnkdgklgtede.klltenlpfs 80 
                                   ig G++iG+v+G+a+kk+ K++a+++G+ +l l +la+ g+i++n ++ ++ +     + ++++l   d+   l ++++f+
  gi|15668238|ref|NP_247031.1|  13 IGSGFIIGFVIGWAAKKAIKVVAFLIGIYILSLLYLAKIGVISINKEAFSALLG----NLENSLLVFGDKiIGLIHSFSFG 89 
                                   689***********************************************5444....34444444443444445679999 PP

                                   xxxxxxxxxxx RF
                         FUN14  81 agFlaGfllGl 91 
                                   ++Fl+Gf lG+
  gi|15668238|ref|NP_247031.1|  90 TSFLIGFGLGF 100
                                   ********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 737.32
//
Query:       gi|15668239|ref|NP_247032.1|  [L=115]
Description: hypothetical protein MJ_0068 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-43  145.3   0.5      7e-43  145.1   0.5    1.0  1  DUF555    Protein of unknown function (DUF555)


Domain annotation for each model (and alignments):
>> DUF555  Protein of unknown function (DUF555)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.1   0.5   3.9e-47     7e-43       1     101 []       3     104 ..       3     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 145.1 bits;  conditional E-value: 3.9e-47
                        DUF555   1 dyevvleaawivrdvksvddAigiAiseagkrlnpe.ldfveievgetecPkcgeelesalvvadtalvglllemkvfnae 80 
                                   +y+v+l+aa+ivr+v++v+dAi++ is++gk+ln+e l++v+i++g t cPkcge ++++lvva+talvg+ll+mkvfnae
  gi|15668239|ref|NP_247032.1|   3 NYHVTLQAAYIVRNVDDVEDAISVTISQIGKMLNKEgLNYVDIDIGLTICPKCGELVDCVLVVARTALVGVLLSMKVFNAE 83 
                                   8******************************************************************************** PP

                        DUF555  81 seEhaeriakseigkaledvP 101
                                   s Eha riak++igk l+++P
  gi|15668239|ref|NP_247032.1|  84 SPEHAIRIAKATIGKVLKNIP 104
                                   ********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 778.60
//
Query:       gi|15668240|ref|NP_247033.1|  [L=300]
Description: acetylglutamate kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-48  165.2   3.7    2.2e-48  165.0   3.7    1.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.0   3.7   1.2e-52   2.2e-48       1     241 []      28     276 ..      28     276 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.0 bits;  conditional E-value: 1.2e-52
                                   TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHHHHH CS
                     AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevatrda 81 
                                   k++V+K GG+++ d+++   +  a+++  lk  g+++vvVhGgg+ +++ +++ +g ++++ + glr+t+ee+++++++++
  gi|15668240|ref|NP_247033.1|  28 KIFVIKYGGHAMIDEKA--KNWTAQDVVLLKYVGINPVVVHGGGPEINKAMEK-MGKKPEFVH-GLRVTDEETLDIVEMVL 104
                                   689*******8887777..7999******************************.*********.***************** PP

                                   HHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE.................HHHTTTCEEECCHHHHHHHTT-EEEEESEE CS
                     AA_kinase  82 laslgerlvaallaaglpavglsaaaldateagr...............degsdgnvesvdaeaieelleagvvpvltgfi 147
                                   +++++ ++v++l + g +avgls+++  ++ a++               d g++g+  +v++e +e l+++g++pv++++ 
  gi|15668240|ref|NP_247033.1| 105 AGKINGDIVSKLSKFGGKAVGLSGKSGRIILAKKklkkiktekgeeievDLGRVGETVEVNTELLEILINNGYIPVVSPI- 184
                                   *******************************************************************************6. PP

                                   EEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.CSSS.TTTHHHHCHHHHH CS
                     AA_kinase 148 gldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.saselatgGmkvkhpaal 227
                                   glde+ge +++++Dt+a  +A al+A+kli++tdVdG++d+ ++ +   +l ++++++e++e ++++ ++gGm++k ++al
  gi|15668240|ref|NP_247033.1| 185 GLDEKGEAYNLNADTVAGDIAGALKAEKLILITDVDGIMDDINNPE---TLHRKLTASELKEmIEDGRIKGGMIPKAESAL 262
                                   6******************************************999...9999*********999**************** PP

                                   HHHHCTT-EEEEEE CS
                     AA_kinase 228 aaarrggipvvItn 241
                                    a+++g+  v+I+n
  gi|15668240|ref|NP_247033.1| 263 YALEHGVKSVHIIN 276
                                   ************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2063.65
//
Query:       gi|15668241|ref|NP_247034.1|  [L=82]
Description: hypothetical protein MJ_0070 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.046   14.1   4.4      0.046   14.1   4.4    2.1  2  FlaC_arch       Flagella accessory protein C (FlaC)
      0.049   13.7   0.1      0.063   13.3   0.1    1.2  1  NDK             Nucleoside diphosphate kinase
      0.073   12.9   1.7       0.14   12.0   1.7    1.5  1  Matrilin_ccoil  Trimeric coiled-coil oligomerisation domain o
      0.087   12.0   3.2      0.091   12.0   3.2    1.0  1  TMPIT           TMPIT-like protein
       0.16   12.5  11.3       0.51   10.9   8.4    2.0  2  HSCB_C          HSCB C-terminal oligomerisation domain
       0.16   12.0   2.6       0.26   11.4   2.6    1.5  1  DUF1664         Protein of unknown function (DUF1664)
       0.35   11.0   4.8       0.67   10.1   4.8    1.5  1  Fib_alpha       Fibrinogen alpha/beta chain family
       0.45    9.1   7.7       0.45    9.1   7.7    1.0  1  FapA            Flagellar Assembly Protein A
       0.58   10.0   8.0      0.078   12.8   3.9    1.7  2  DivIC           Septum formation initiator
        0.6   10.8   4.8       0.75   10.5   4.8    1.2  1  YabA            Initiation control protein YabA
        0.9    9.0   8.7       0.11   12.0   4.7    1.5  2  FIN1            Filaments in between nuclei protein-1
        3.3    7.6   6.5         11    5.9   6.5    1.8  1  ACCA            Acetyl co-enzyme A carboxylase carboxyltransf


Domain annotation for each model (and alignments):
>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   4.4   3.1e-05     0.046       4      38 ..       3      37 ..       1      42 [. 0.87
   2 ?    1.6   0.4      0.25   3.7e+02      25      41 ..      48      64 ..      38      74 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                     FlaC_arch  4 elEnklsklsteletvkkeneelsksveelkenVk 38
                                  ++ +++ +++tel+ +kk  +e+s+ +e+l+ +  
  gi|15668241|ref|NP_247034.1|  3 NINKEIAQIETELNELKKLRDEISERIEKLEIKLL 37
                                  6889*************************996655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.25
                     FlaC_arch 25 elsksveelkenVkdll 41
                                  e +++ ee+ e+Vk+ l
  gi|15668241|ref|NP_247034.1| 48 EFEEDYEEIIEDVKKSL 64
                                  55566666666666544 PP

>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.2e-05     0.063      15      51 ..      20      56 ..      16      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.2e-05
                                  T-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGG CS
                           NDK 15 gligeiisrleekglkivalkmlrlteeqaeehYaeh 51
                                  +l +ei +r+e+ + k+++lk l + ee++ee Y+e 
  gi|15668241|ref|NP_247034.1| 20 KLRDEISERIEKLEIKLLKLKALAIPEEEFEEDYEEI 56
                                  6889******************************986 PP

>> Matrilin_ccoil  Trimeric coiled-coil oligomerisation domain of matrilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.7   9.5e-05      0.14      19      45 .]      10      36 ..       9      36 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.5e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                Matrilin_ccoil 19 kVeseiqaLtqkLeavtkRlealEnkl 45
                                  + e+e++ L +  +++++R+e+lE kl
  gi|15668241|ref|NP_247034.1| 10 QIETELNELKKLRDEISERIEKLEIKL 36
                                  578999******************886 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.2   6.1e-05     0.091      14      81 ..       4      70 ..       1      79 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.1e-05
                         TMPIT 14 leetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkv 81
                                  ++++  +++++l+el+kl +++s++i+k + +l +lk+ l   +++ +e++ee++e++k++l+++++v
  gi|15668241|ref|NP_247034.1|  4 INKEIAQIETELNELKKLRDEISERIEKLEIKLLKLKA-LAIPEEEFEEDYEEIIEDVKKSLDKKETV 70
                                  6777789999********************99999976.5566777889*************999876 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   8.4   0.00034      0.51       9      63 ..       1      61 [.       1      63 [. 0.79
   2 ?    4.5   1.6     0.034        51      31      64 ..      45      78 ..      33      80 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                                  HHHHHHHHHCGGGSSSHHHHHHHHHHHHHHHHHHHHHHHHHH.....HTT...-HHHHHHHHH CS
                        HSCB_C  9 vMelrEeleeaeeaadkeeleelkaeveerieeleaeleeaf.....ekk...dleaaadllr 63
                                  ++ ++ e++++ e ++ +el++l++e++erie+le +l ++      e++   d+e++ + + 
  gi|15668241|ref|NP_247034.1|  1 MLNINKEIAQI-E-TELNELKKLRDEISERIEKLEIKLLKLKalaipEEEfeeDYEEIIEDVK 61
                                  799********.4.489*****************99998776666763334558888877765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.034
                                  HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                        HSCB_C 31 lkaeveerieeleaeleeafekkdleaaadllrr 64
                                   ++e ee  ee+++ +++ ++kk+   a ++l +
  gi|15668241|ref|NP_247034.1| 45 PEEEFEEDYEEIIEDVKKSLDKKETVPAEEALKE 78
                                  5678888888888888888877766666666655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.6   0.00017      0.26      48      97 ..       9      61 ..       1      79 [. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                       DUF1664 48 kqleqvseslaatkrhLssridrvdkkldeqkeis...keikeevtevredls 97
                                   q+e+  ++l++ ++++s+ri++++ kl + k+++   +e +e+ +e+ ed++
  gi|15668241|ref|NP_247034.1|  9 AQIETELNELKKLRDEISERIEKLEIKLLKLKALAipeEEFEEDYEEIIEDVK 61
                                  34444456666667777777777777777666653222455555555555555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.8   0.00045      0.67      33      87 ..       4      58 ..       1      79 [. 0.51

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00045
                                  CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 33 vkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskele 87
                                  ++k+++++e el+e+++   e++e +++++ +l + ++ + ++++  +++++ +e
  gi|15668241|ref|NP_247034.1|  4 INKEIAQIETELNELKKLRDEISERIEKLEIKLLKLKALAIPEEEFEEDYEEIIE 58
                                  5566666666666666666666666666665555544444443333333333333 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.7    0.0003      0.45     334     394 ..      10      67 ..       1      79 [. 0.66

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0003
                          FapA 334 elkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeel 394
                                   ++  +l+el+++  e+ e++ekl+ k+ kl++l++    e+e++e++++++e+ +k  ++ 
  gi|15668241|ref|NP_247034.1|  10 QIETELNELKKLRDEISERIEKLEIKLLKLKALAI---PEEEFEEDYEEIIEDVKKSLDKK 67 
                                   34455567777777777778888877777777666...44688888888888887766554 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.9   5.2e-05     0.078      21      50 ..       3      32 ..       1      41 [. 0.94
   2 ?   -1.3   0.1       1.3   1.9e+03      31      32 ..      62      63 ..      47      81 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.2e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                         DivIC 21 qlkqeiaalqaelaklkaeneeLeaevkdL 50
                                   +++eia+++ el++lk+ ++e  +++++L
  gi|15668241|ref|NP_247034.1|  3 NINKEIAQIETELNELKKLRDEISERIEKL 32
                                  689*************************99 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                                  HH CS
                         DivIC 31 ae 32
                                  + 
  gi|15668241|ref|NP_247034.1| 62 KS 63
                                  22 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.8    0.0005      0.75      12      73 ..       3      64 ..       1      79 [. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...XXXXXXXXXXXXXXXXXXXXX CS
                          YabA 12 eleeqleelleeleelkeelaelleenaeLeleneklrerl...eeeekkekekkkelsegkenL 73
                                  +++++++++ +el+elk+   e+ e+ ++Le+   kl+ +    e   + e++ ++ +++ k++L
  gi|15668241|ref|NP_247034.1|  3 NINKEIAQIETELNELKKLRDEISERIEKLEIKLLKLKALAipeE---EFEEDYEEIIEDVKKSL 64
                                  68999********************************99985541...33333333333333333 PP

>> FIN1  Filaments in between nuclei protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.7   7.4e-05      0.11     206     241 ..       5      40 ..       1      42 [. 0.88
   2 ?   -1.8   0.1       1.2   1.8e+03      72      76 ..      60      64 ..      44      78 .. 0.45

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.4e-05
                          FIN1 206 ddeeeeikkelkdikklleellerqdelesrlskle 241
                                   ++e  +i++el+++kkl  e+ er+++le +l kl+
  gi|15668241|ref|NP_247034.1|   5 NKEIAQIETELNELKKLRDEISERIEKLEIKLLKLK 40 
                                   4555899*************************9987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                          FIN1 72 vtqsl 76
                                  v +sl
  gi|15668241|ref|NP_247034.1| 60 VKKSL 64
                                  11222 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   6.5    0.0071        11       2      45 ..       2      41 ..       1      79 [. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0071
                          ACCA  2 ldfekpiaeleekieelkklaeesevdlseeieklekkleklkk 45
                                  l+++k+ia++e++++elkkl +e    +se+iekle kl klk+
  gi|15668241|ref|NP_247034.1|  2 LNINKEIAQIETELNELKKLRDE----ISERIEKLEIKLLKLKA 41
                                  78999************999665....66777777776666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2497  (0.139272); expected 358.6 (0.02)
Passed bias filter:                     1249  (0.0696637); expected 358.6 (0.02)
Passed Vit filter:                       182  (0.0101512); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 550.46
//
Query:       gi|15668242|ref|NP_247035.1|  [L=90]
Description: hypothetical protein MJ_0071 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-09   37.4   1.4    3.4e-09   37.2   1.4    1.1  1  ParE_toxin  ParE toxin of type II toxin-antitoxin system, par
     0.0013   18.8   0.1     0.0016   18.5   0.1    1.1  1  Gp49        Phage derived protein Gp49-like (DUF891)
  ------ inclusion threshold ------
      0.025   14.7   0.3      0.039   14.1   0.3    1.3  1  PYRIN       PAAD/DAPIN/Pyrin domain
       0.15   12.5   0.0        0.2   12.0   0.0    1.4  1  SPOR        Sporulation related domain


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   1.4   7.7e-13   3.4e-09       1      87 [.       5      84 ..       5      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 7.7e-13
                                  EEEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEE...CTSTC...CTTEEEEEECTEEEEEEEETSTTE CS
                    ParE_toxin  1 vrltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrp...rrelg...lkglrririgdyriiYriddeelv 77
                                  v++++r+lkdlk++            + l++++e +e+l +np + ++       +    ++++r+rig++r+ Y + +++++
  gi|15668242|ref|NP_247035.1|  5 VEIHKRVLKDLKDLP----------PSNLKKFKELIETLKTNPIPKEKfdiK---RlkgSDEVYRVRIGKFRVQYVVLWDDRI 74
                                  789***********5..........5899999*************9995533...2457889***************9999** PP

                                  EEEEEEEEHH CS
                    ParE_toxin 78 vvilrvlhrs 87
                                  ++i ++ +r+
  gi|15668242|ref|NP_247035.1| 75 IIIRKISRRE 84
                                  *677676665 PP

>> Gp49  Phage derived protein Gp49-like (DUF891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   3.6e-07    0.0016       1      67 [.      13      77 ..      13      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.6e-07
                          Gp49  1 eeldalpkkarakilaaldlleeggpdlgkplvkkle..dglwElrpksaggiiRvlyafdpgrkvilL 67
                                  ++l++lp++  +k+ ++++ l+ +  + +k  +k l+  d+++ +r+    g +Rv y++  ++++i++
  gi|15668242|ref|NP_247035.1| 13 KDLKDLPPSNLKKFKELIETLKTNPIPKEKFDIKRLKgsDEVYRVRI----GKFRVQYVVLWDDRIIII 77
                                  689*********************976777777777789********....9*********99999975 PP

>> PYRIN  PAAD/DAPIN/Pyrin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   8.6e-06     0.039       2      35 ..      11      42 ..      10      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.6e-06
                                  HCCCCCCC-HHHHHHHHHHHHH.--SSSHTTHCC CS
                         PYRIN  2 LllyLeeLseeelkkFKslLkeeeeglksiprge 35
                                  +l+ L++L   +lkkFK+l ++   + ++ip+ +
  gi|15668242|ref|NP_247035.1| 11 VLKDLKDLPPSNLKKFKELIET--LKTNPIPKEK 42
                                  6777****************65..4556888655 PP

>> SPOR  Sporulation related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.6e-05       0.2      17      52 ..      25      63 ..      10      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.6e-05
                                  HHHHHHHHCCHHT--......EEECCSSSCEEEEESSBC CS
                          SPOR 17 nAerlaakLrakgfaaav...avvsgggglyrVrvGpfa 52
                                    ++l++ L+++ ++      ++ +g + +yrVr+G f 
  gi|15668242|ref|NP_247035.1| 25 KFKELIETLKTNPIPKEKfdiKRLKGSDEVYRVRIGKFR 63
                                  55666666666655544467799*************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 591.67
//
Query:       gi|15668243|ref|NP_247036.1|  [L=44]
Description: hypothetical protein MJ_0072 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.021   15.0   0.0      0.022   14.8   0.0    1.0  1  Hydrolase_6  Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.2e-06     0.022       1      37 [.       3      38 ..       3      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-06
                                  EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE CS
                   Hydrolase_6  1 flfDidGvLwrgdkaipgaaealnalraagkpvvllT 37
                                  +l+D+ G++  ++k+ +g++e l++l+++  ++++l+
  gi|15668243|ref|NP_247036.1|  3 ILLDLNGTIATDGKIKEGVKERLTILKER-AEIYILS 38
                                  699***********************998.4555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 309.65
//
Query:       gi|15668244|ref|NP_247037.1|  [L=93]
Description: hypothetical protein MJ_0073, partial [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00081   19.2   0.3    0.00097   18.9   0.2    1.3  1  Hydrolase_3  haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.025   14.3   0.8      0.057   13.2   0.1    1.9  2  STN          Secretin and TonB N terminus short domain
      0.085   13.1   0.1       0.11   12.7   0.1    1.2  1  Hydrolase    haloacid dehalogenase-like hydrolase
       0.14   10.9   0.0       0.16   10.7   0.0    1.1  1  RHSP         Retrotransposon hot spot protein


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   2.2e-07   0.00097     187     228 ..      14      53 ..       7      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.2e-07
                                   SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEE CS
                   Hydrolase_3 187 sKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAm 228
                                    K + l++l      +++++ia+G+g+ND  +L+ a+lg+++
  gi|15668244|ref|NP_247037.1|  14 AKLKILEELK--KENPNKKIIAIGNGNNDELLLKNADLGICV 53 
                                   4444444444..3457899*********************97 PP

>> STN  Secretin and TonB N terminus short domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.36   1.6e+03      31      39 ..      42      50 ..      41      51 .. 0.81
   2 ?   13.2   0.1   1.3e-05     0.057       8      41 ..      57      90 ..      53      93 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.36
                           STN 31 eLLkgtgLq 39
                                  +LLk+ +L 
  gi|15668244|ref|NP_247037.1| 42 LLLKNADLG 50
                                  79***9986 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.3e-05
                           STN  8 elvrgnqtvslnignvtideaLdeLLkgtgLqyk 41
                                  e +  ++ +s +i  + i +aLd+LL ++ L ++
  gi|15668244|ref|NP_247037.1| 57 EGAWSKTILSSDIVVKDINDALDLLLNENRLKAT 90
                                  5666677788899999*************99987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.5e-05      0.11     173     210 .]       9      48 ..       2      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                                   TTSHHHHHHHHHHHT..STGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 173 kpspegkvaaireLq..gkpeevamVGDgvnDaaalaaAg 210
                                   + ++ +k+++++eL+   + ++++++G g nD   l++A+
  gi|15668244|ref|NP_247037.1|   9 GSEKIAKLKILEELKkeNPNKKIIAIGNGNNDELLLKNAD 48 
                                   56677899******96555889***************998 PP

>> RHSP  Retrotransposon hot spot protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.7e-05      0.16      52      93 ..      43      84 ..      27      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.7e-05
                          RHSP 52 lPrrgnleiavltsqkgWPytrflrdvvdedaeekkdyvfdd 93
                                  l ++ +l i v+  + +W  t + +d+v +d+++  d ++++
  gi|15668244|ref|NP_247037.1| 43 LLKNADLGICVIGDEGAWSKTILSSDIVVKDINDALDLLLNE 84
                                  5567899***************************98988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 783.78
//
Query:       gi|15668245|ref|NP_247038.1|  [L=358]
Description: hypothetical protein MJ_0074 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-97  325.6   7.7    3.4e-97  324.9   7.7    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
    2.4e-08   34.5   0.0    9.3e-08   32.6   0.0    1.9  2  AAA_16           AAA ATPase domain
    4.3e-08   33.3   8.8    0.00025   21.1   0.1    3.3  3  AAA_14           AAA domain
    1.3e-07   32.0   0.0    2.9e-07   30.8   0.0    1.6  1  AAA_22           AAA domain
    1.4e-05   24.0   0.1      0.008   15.0   0.1    2.1  2  RNA12            RNA12 protein
    3.9e-05   24.1   0.2     0.0012   19.3   0.0    2.8  2  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.034   13.7   0.0      0.091   12.3   0.0    1.8  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.038   13.2   0.0       0.58    9.3   0.0    2.2  2  NB-ARC           NB-ARC domain
      0.043   13.9   0.7      0.097   12.8   0.1    2.1  2  MMR_HSR1         50S ribosome-binding GTPase
      0.059   14.3   0.9       0.51   11.3   0.1    2.7  2  DUF2624          Protein of unknown function (DUF2624)
      0.067   13.6   0.1       0.82   10.1   0.0    2.6  3  RNA_helicase     RNA helicase
      0.088   12.2   0.0        3.8    6.9   0.0    2.5  2  TniB             Bacterial TniB protein
      0.095   13.2   1.0        5.5    7.6   0.1    3.1  3  RPAP3_C          Potential Monad-binding region of RPAP3
      0.098   12.2   0.0       0.24   10.9   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
       0.12   12.2   0.0       0.22   11.4   0.0    1.6  1  NACHT            NACHT domain
       0.15   11.8   0.3        1.7    8.3   0.0    2.5  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.9   7.7  3.1e-100   3.4e-97       1     233 []       3     250 ..       3     250 .. 0.97

  Alignments for each domain:
  == domain 1  score: 324.9 bits;  conditional E-value: 3.1e-100
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...eeeekkkl 78 
                                   FfdReke+ e+++il+rep+++yfiYGp++sGKtaL++eii+n++dkdkyv++y++lre++isk+d+fie   ee+e +k 
  gi|15668245|ref|NP_247038.1|   3 FFDREKEIAEILHILNREPDDVYFIYGPINSGKTALINEIINNRLDKDKYVVFYFDLREIFISKYDDFIEvlfEEYEGNKK 83 
                                   9************************************************************************77776644 PP

                      ATPase_2  79 ekal............giavpkaeleeilk.eksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLl 146
                                      +            gi+ pk++leeilk +++k+vf++i+++l++ikk+gk++i+iiDelqk++d+++n  ++l++eL+
  gi|15668245|ref|NP_247038.1|  84 PVEIikslikdvpslcGIPAPKNTLEEILKkKTTKNVFRYITKVLMDIKKEGKQPILIIDELQKIGDMKIN--GFLIYELF 162
                                   444468999*********************9****************************************..******** PP

                      ATPase_2 147 nliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkel.eelskedfeeiyryvGGk 226
                                   n+++sltk+khlc+v+clsS++lfiervyne++l gr+ky+lvdd+dketal+f+++++ke+ ++l++ed+e+iy+yvGGk
  gi|15668245|ref|NP_247038.1| 163 NYFVSLTKHKHLCHVFCLSSDSLFIERVYNEAMLDGRAKYLLVDDFDKETALKFMDFLAKENnISLTNEDKELIYNYVGGK 243
                                   **************************************************************999**************** PP

                      ATPase_2 227 Pkalvel 233
                                   Pk+++++
  gi|15668245|ref|NP_247038.1| 244 PKDIKYV 250
                                   ****986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   8.3e-11   9.3e-08       1     150 [.       2     151 ..       2     175 .. 0.72
   2 ?   -1.3   0.0       2.2   2.5e+03     134     160 ..     198     222 ..     184     230 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 8.3e-11
                        AAA_16   1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellr.alekdggiflrgkcdqlesaipysalaqalaree 80 
                                   +++ Re+e++++l++l+r  +    + +++G+  +GK++l++e+ + +l kd+ ++++ + ++         +++     +
  gi|15668245|ref|NP_247038.1|   2 KFFDREKEIAEILHILNREPD---DVYFIYGPINSGKTALINEIINnRLDKDKYVVFYFDLREI--------FISKY-D-D 69 
                                   5899************95544...699**************99986488888777788888888........55555.2.4 PP

                        AAA_16  81 llrqllde..aesaeleawrekleeala......avpelagaea....srllellkrllallsrderplvlvlDdlqwade 149
                                   +++ l +e   +++ +e  +  ++++ +      + + l+  ++    + +++ +++ l+ +++++++ +l++D+lq++ +
  gi|15668245|ref|NP_247038.1|  70 FIEVLFEEyeGNKKPVEIIKSLIKDVPSlcgipaPKNTLEEILKkkttKNVFRYITKVLMDIKKEGKQPILIIDELQKIGD 150
                                   4554444432112222222332222222444422333344333377889999999****999999999*********9877 PP

                        AAA_16 150 a 150
                                   +
  gi|15668245|ref|NP_247038.1| 151 M 151
                                   5 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                        AAA_16 134 erplvlvlDdlqwadeaslqllaaLlr 160
                                   +r  +l++Dd++  +e+ l+++++L++
  gi|15668245|ref|NP_247038.1| 198 GRAKYLLVDDFD--KETALKFMDFLAK 222
                                   55568999***9..5555666666665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   2.2e-07   0.00025       4      66 ..      24      84 ..      22      94 .. 0.78
   2 !   13.6   0.2   4.6e-05     0.052      49     119 ..     117     202 ..     103     214 .. 0.71
   3 ?    2.4   0.6      0.14   1.5e+02      32      84 ..     225     282 ..     212     295 .. 0.58

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.2e-07
                        AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekkt 66
                                  +++i G+  +GKT l++++i+++l +k++++ + +d  +   ++++++++e+++e+++++kk 
  gi|15668245|ref|NP_247038.1| 24 VYFIYGPINSGKTALINEIINNRL-DKDKYVVFYFDLREIF-ISKYDDFIEVLFEEYEGNKKP 84
                                  789*********************.8888888877776665.344566788888887665554 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.6e-05
                        AAA_14  49 pekllelileklke....ekktylflDEiqev..........pewekalkslvdegknldvivtGSnskllskeiats.la 114
                                   ++++ ++i + l++     k+ +l++DE q++           e++++  sl ++++ ++v++  S s+++ +  ++  l 
  gi|15668245|ref|NP_247038.1| 117 TKNVFRYITKVLMDikkeGKQPILIIDELQKIgdmkingfliYELFNYFVSLTKHKHLCHVFCLSSDSLFIERVYNEAmLD 197
                                   22344444443222223468899*********999999999988889999999999899*********9999866654156 PP

                        AAA_14 115 grvae 119
                                   gr+++
  gi|15668245|ref|NP_247038.1| 198 GRAKY 202
                                   66655 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.14
                        AAA_14  32 silyinldderdkkla..dpekllelilek.lke..ekktylflDEiqevpewekalk 84 
                                   +i   n d+e  +++   +p+++  ++ e+ +k+  e   yl+ DEi++++ + ++l 
  gi|15668245|ref|NP_247038.1| 225 NISLTNEDKELIYNYVggKPKDIKYVVEESnFKDlkEVLDYLLNDEISKLDMFLEILD 282
                                   4444444444444433334444443333334333444556788888888888887776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.6e-10   2.9e-07       6     128 ..      23     179 ..      18     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.6e-10
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsst..sskdllrellralglelka............ 70 
                                    + +++G+  +GKT l++++ ++          ++++v  +++l +    + +d+ + l+++++ ++k             
  gi|15668245|ref|NP_247038.1|  23 DVYFIYGPINSGKTALINEIINNRLD-------KDKYVvfYFDLREIFisKYDDFIEVLFEEYEGNKKPveiikslikdvp 96 
                                   6789****************999853.......4444446999999999999999*********98888************ PP

                        AAA_22  71 ................erlsseellealeqalrarav...ielliiDEaqhlr..s......eealeeLrsllnlsrkgvq 124
                                                   + ++++ +++++++ l + ++   +++liiDE q++   +       e++++++sl +  +k++ 
  gi|15668245|ref|NP_247038.1|  97 slcgipapkntleeilKKKTTKNVFRYITKVLMDIKKegkQPILIIDELQKIGdmKingfliYELFNYFVSLTK--HKHLC 175
                                   ****************999999999999999999999999************6552667777888888888888..88888 PP

                        AAA_22 125 liLv 128
                                   ++++
  gi|15668245|ref|NP_247038.1| 176 HVFC 179
                                   8876 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0018         2       1      59 [.       6      68 ..       6      76 .. 0.83
   2 !   15.0   0.1   7.1e-06     0.008     144     317 ..     132     302 ..     105     318 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0018
                         RNA12  1 RkekiedlkewleEnvntFivvkGPrGSGkkeLvldrvlkdrkk.....vlvidCdelvkarnd 59
                                  R+++i ++ + l+ +++    + GP  SGk+ L+ ++++++r +     v+++d +e++ ++ d
  gi|15668245|ref|NP_247038.1|  6 REKEIAEILHILNREPDDVYFIYGPINSGKTALI-NEIINNRLDkdkyvVFYFDLREIFISKYD 68
                                  778889999999999999999************9.77777765556668899999999988877 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 7.1e-06
                         RNA12 144 ahpeakPvvvidnflakaek..ngvvykklaeWaasLvqsn.iahViflted.vsaskaLskaLpnqvfktislgDasees 220
                                   +++ ++P+++id+ ++  +   ng++  +l ++  sL++++ + hV  l++d   ++++ ++a+ +   k + + D ++e+
  gi|15668245|ref|NP_247038.1| 132 KKEGKQPILIIDELQKIGDMkiNGFLIYELFNYFVSLTKHKhLCHVFCLSSDsLFIERVYNEAMLDGRAKYLLVDDFDKET 212
                                   456678*********98876679**************986439********956678999********************* PP

                         RNA12 221 arkyVlsklkeeaekeekktassesaakdeeeseeqkkkdkaasakleekdlkeldealek.lGGRltDLealvrrvksge 300
                                   a k+  + l++e + + +++++    ++  ++ ++        +  +ee++ k+l+e+l+  l   +  L+++ + +  ++
  gi|15668245|ref|NP_247038.1| 213 ALKFM-DFLAKENNISLTNEDKELIYNYVGGKPKDI-------KYVVEESNFKDLKEVLDYlLNDEISKLDMFLEILDYSK 285
                                   ****5.777666555544444433333322222221.......11234444444444444312344555555555554444 PP

                         RNA12 301 tpkeAveeiieqsaeei 317
                                      e  +e+ie + e+i
  gi|15668245|ref|NP_247038.1| 286 PRVEVGNEVIEINKEDI 302
                                   44444445555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.1e-06    0.0012       3      74 ..      27     152 ..      25     204 .. 0.78
   2 ?   -0.9   0.0       1.8     2e+03      32      67 ..     233     271 ..     213     275 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                                   EESSTTSSHHHHHHHHHHHH....THEEEEEETTTCS.SS......................................... CS
                           AAA   3 lyGppGtGKTllakavakel....gvefleisgsell.sk......................................... 37 
                                   +yGp   GKT+l++ ++++     +  ++ +++ e++ sk                                         
  gi|15668245|ref|NP_247038.1|  27 IYGPINSGKTALINEIINNRldkdKYVVFYFDLREIFiSKyddfievlfeeyegnkkpveiikslikdvpslcgipapknt 107
                                   8*****************944544455666666666666677777777777777789999999999999999999999999 PP

                                   ........STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                           AAA  38 ........yvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                           + ++  + i +++ ++k++ k+ il+iDE+ +++  +
  gi|15668245|ref|NP_247038.1| 108 leeilkkkTTKNVFRYITKVLMDIKKEGKQPILIIDELQKIGDMK 152
                                   999988888888899999999999999877*********998766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.8
                                   TTCSSSSTTHHHHHHHHHHHHHHHTS..TS.EEEEEETG CS
                           AAA  32 sellskyvgesekkirelfkeakeka..kp.silfiDEi 67 
                                   +el+ +yvg ++k+i+ +++e   k   +    l+ DEi
  gi|15668245|ref|NP_247038.1| 233 KELIYNYVGGKPKDIKYVVEESNFKDlkEVlDYLLNDEI 271
                                   345556999999999999988655444422355666666 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.1e-05     0.091       2      31 ..      24      53 ..      23      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.1e-05
                                  EEEEEESTTCCHHHHHHHHHCT--SS-EEE CS
                          cobW  2 vtvltGflGsGKTtLlnhllenraglklav 31
                                  v+ + G++ sGKT+L+n++++nr +++  v
  gi|15668245|ref|NP_247038.1| 24 VYFIYGPINSGKTALINEIINNRLDKDKYV 53
                                  67899***************9887776554 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00051      0.58       2      45 ..       7      46 ..       6      74 .. 0.75
   2 ?    1.2   0.0      0.15   1.7e+02     181     226 ..      86     130 ..      69     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00051
                                  HHHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHC CS
                        NB-ARC  2 eksvekviekLlekdelqslvvalvGmgGvGKttlakqilnksd 45
                                  ek++ ++ + L    e++ +v +++G   +GKt l+++i+n+  
  gi|15668245|ref|NP_247038.1|  7 EKEIAEILHILN--REPD-DVYFIYGPINSGKTALINEIINN-R 46
                                  566667777676..6777.799*****************998.3 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
                                   ..CHHHHHHHHHHCTT-HHHHHHHHHHHC-TCSCCHHHHHHHHHHC CS
                        NB-ARC 181 esleevakeivekckGlPlalkvlggllstkktveewkkvlekles 226
                                   e ++ + k + + c G P+  ++l ++l++k+t + ++++ ++l +
  gi|15668245|ref|NP_247038.1|  86 EIIKSLIKDVPSLC-GIPAPKNTLEEILKKKTTKNVFRYITKVLMD 130
                                   34888888888888.99************99999999999998865 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   8.7e-05     0.097       4      25 ..      27      48 ..      24     152 .. 0.89
   2 ?   -2.9   0.0       6.2   6.9e+03      75      86 ..     273     284 ..     245     312 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.7e-05
                                  EEESTTSSHHHHHHHHHTSTEE CS
                      MMR_HSR1  4 ivGrpNvGKStLinaltgekai 25
                                  i+G  N+GK+ Lin +++++  
  gi|15668245|ref|NP_247038.1| 27 IYGPINSGKTALINEIINNRLD 48
                                  89***************98654 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.2
                                   CTSEEEEEEETT CS
                      MMR_HSR1  75 eadlillvvdas 86 
                                   + d++l ++d s
  gi|15668245|ref|NP_247038.1| 273 KLDMFLEILDYS 284
                                   345555555544 PP

>> DUF2624  Protein of unknown function (DUF2624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.4   1.6e+03      33      72 ..     114     154 ..     105     166 .. 0.59
   2 ?   11.3   0.1   0.00045      0.51      23      71 ..     220     267 ..     211     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.4
                       DUF2624  33 ksqAekivkilrekkidifnkeerk.kllkelakitspqta 72 
                                   k+ +++++ ++ +  +di ++ ++   ++ el+ki + ++ 
  gi|15668245|ref|NP_247038.1| 114 KKTTKNVFRYITKVLMDIKKEGKQPiLIIDELQKIGDMKIN 154
                                   55667777777777777755544331345677777766664 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00045
                       DUF2624  23 yakqygveltksqAekivkilrekkidifnkeerkkllkelakitspqt 71 
                                   +ak+++++lt+++ e i +++ +k  di +    ++ +k+l+++ +  +
  gi|15668245|ref|NP_247038.1| 220 LAKENNISLTNEDKELIYNYVGGKPKDI-KYVVEESNFKDLKEVLDYLL 267
                                   79***********************999.44444455666666666555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00073      0.82       2      63 ..      26      83 ..      25     110 .. 0.75
   2 ?   -0.2   0.0       1.2   1.3e+03      49      78 ..     136     167 ..     104     176 .. 0.70
   3 ?   -1.7   0.0       3.3   3.7e+03      51      62 ..     201     212 ..     166     238 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00073
                  RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkd 63
                                  ++yGp + GK+ l++e++++ l    +k k  v++   ++ f ++Y++   v++++   +k+
  gi|15668245|ref|NP_247038.1| 26 FIYGPINSGKTALINEIINNRL----DKDKYVVFYFDLREIFISKYDDFIEVLFEEYEGNKK 83
                                  79**************887777....344455555688888888888777777777766664 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                  RNA_helicase  49 gqevvvidDfgqvkdee.nps.dlaelirlvs 78 
                                   +q++++id++ ++ d + n   +++ ++  vs
  gi|15668245|ref|NP_247038.1| 136 KQPILIIDELQKIGDMKiNGFlIYELFNYFVS 167
                                   79999999999998887666655555555555 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.3
                  RNA_helicase  51 evvvidDfgqvk 62 
                                   +++++dDf + +
  gi|15668245|ref|NP_247038.1| 201 KYLLVDDFDKET 212
                                   555566665443 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0034       3.8      24      61 ..      11      48 ..       3      58 .. 0.72
   2 ?    2.5   0.0     0.077        86     108     131 ..     125     148 ..     103     156 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0034
                          TniB 24 eeLleypkrkrmpnlllvGdsnnGKtmivekFarlhpp 61
                                  +e+l+  +r+    + ++G+ n GKt+++++  +++ +
  gi|15668245|ref|NP_247038.1| 11 AEILHILNREPDDVYFIYGPINSGKTALINEIINNRLD 48
                                  4444444444446689*************998877655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.077
                          TniB 108 eqqvlrllrelkvrvLiiDEihnl 131
                                   ++  + + +e k  +LiiDE++++
  gi|15668245|ref|NP_247038.1| 125 TKVLMDIKKEGKQPILIIDELQKI 148
                                   44445555666778*******987 PP

>> RPAP3_C  Potential Monad-binding region of RPAP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0049       5.5      30      83 ..     104     152 ..      86     158 .. 0.85
   2 ?   -1.8   0.0       4.2   4.7e+03      63      83 ..     207     227 ..     187     231 .. 0.68
   3 ?    2.3   0.1      0.22   2.5e+02      21      61 ..     246     291 ..     223     310 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0049
                       RPAP3_C  30 npkqlpkiFknsledeilsdildalnerlqeekaedsslvleiLdrLskvkRFd 83 
                                   ++++l++i+k++ + +++  i ++l + ++e k++     + i d+L+k+  ++
  gi|15668245|ref|NP_247038.1| 104 PKNTLEEILKKKTTKNVFRYITKVLMDIKKEGKQP-----ILIIDELQKIGDMK 152
                                   5689***************************9876.....88888888887665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.2
                       RPAP3_C  63 aedsslvleiLdrLskvkRFd 83 
                                   + d++++l+++d L+k +  +
  gi|15668245|ref|NP_247038.1| 207 DFDKETALKFMDFLAKENNIS 227
                                   345678889999888866655 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.22
                       RPAP3_C  21 dlkavllqinpkqlpkiFknslede.....ilsdildalnerlqee 61 
                                   d k+v+ + n k+l+++++ +l+de     ++ +ild+ + r+++ 
  gi|15668245|ref|NP_247038.1| 246 DIKYVVEESNFKDLKEVLDYLLNDEiskldMFLEILDYSKPRVEVG 291
                                   4444444455577777777777665222226777777777776665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00021      0.24      37      69 ..      26      59 ..      10      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                         AAA_7 37 llvGptGtGKtviikd.llkkldkekylsltinf 69
                                  +++Gp  +GKt++i++ + ++ldk+ky++  + +
  gi|15668245|ref|NP_247038.1| 26 FIYGPINSGKTALINEiINNRLDKDKYVVFYFDL 59
                                  578*************99999******9988766 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.22       2      72 ..      24     100 ..      23     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C........... CS
                         NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse........... 71 
                                   + ++ G+  sGKT+L+ +++      +l++++  +vF++ lre+  s+    ++++lf+++   ++pv+            
  gi|15668245|ref|NP_247038.1|  24 VYFIYGPINSGKTALINEIINN----RLDKDK-YVVFYFDLREIFISKYD-DFIEVLFEEYEGNKKPVEIikslikdvpsl 98 
                                   5678888889******999975....555654.89*********998766.999*****9999999997644444444444 PP

                                   .C CS
                         NACHT  72 .v 72 
                                    +
  gi|15668245|ref|NP_247038.1|  99 cG 100
                                   40 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.45     5e+02       9      22 ..      33      46 ..      33      61 .. 0.83
   2 ?    8.3   0.0    0.0015       1.7      34      73 ..     108     147 ..      86     152 .. 0.69
   3 ?   -3.6   0.1       6.6   7.3e+03     219     233 ..     164     178 ..     163     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.45
               Viral_helicase1  9 cGKStlirkllrts 22
                                  +GK+ li ++++++
  gi|15668245|ref|NP_247038.1| 33 SGKTALINEIINNR 46
                                  8**********994 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0015
               Viral_helicase1  34 lltegkpklpnlsvrtvdsflmalvkstkgkililDEyll 73 
                                   l    k+k++++  r++ ++lm  +k+ k  ili+DE ++
  gi|15668245|ref|NP_247038.1| 108 LEEILKKKTTKNVFRYITKVLMDIKKEGKQPILIIDELQK 147
                                   222233678888899************99********987 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 6.6
               Viral_helicase1 219 llvAlTRhrkslvil 233
                                    +v lT h+  ++++
  gi|15668245|ref|NP_247038.1| 164 YFVSLTKHKHLCHVF 178
                                   589999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2234.28
//
Query:       gi|15668246|ref|NP_247039.1|  [L=365]
Description: hypothetical protein MJ_0075 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-84  281.9   5.8    4.8e-84  281.9   5.8    1.9  2  ATPase_2      ATPase domain predominantly from Archaea
    4.7e-08   33.4   0.0      2e-07   31.3   0.0    2.1  2  AAA_22        AAA domain
    9.2e-08   32.6   0.0    5.3e-07   30.2   0.0    2.1  2  AAA_16        AAA ATPase domain
    3.5e-07   30.3   7.1     0.0002   21.4   0.1    3.0  3  AAA_14        AAA domain
    4.1e-05   22.5   0.1       0.24   10.1   0.2    3.0  3  RNA12         RNA12 protein
    7.4e-05   23.2   0.2     0.0059   17.0   0.0    2.8  2  AAA           ATPase family associated with various cellular 
     0.0012   18.7   0.1     0.0039   17.1   0.0    1.9  2  TK            Thymidine kinase
     0.0019   18.1   1.3     0.0019   18.1   1.3    3.0  3  Bac_DnaA      Bacterial dnaA  protein
      0.005   16.0   0.3      0.025   13.7   0.0    2.1  2  NB-ARC        NB-ARC domain
  ------ inclusion threshold ------
       0.01   15.8   1.6      0.045   13.8   0.1    2.6  2  ResIII        Type III restriction enzyme, res subunit
       0.02   15.3   0.0      0.079   13.4   0.0    2.1  1  RNA_helicase  RNA helicase
      0.034   14.0   0.3       0.31   10.9   0.0    2.6  3  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.041   13.5   0.1       0.24   11.0   0.1    2.2  1  Zot           Zonular occludens toxin (Zot)
      0.064   13.8   0.2       0.72   10.4   0.0    2.4  2  AAA_18        AAA domain
       0.13   11.9   0.0       0.62    9.6   0.0    2.1  3  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.14   12.1   1.6       0.95    9.5   0.0    3.1  5  TFX_C         DNA_binding protein, TFX, C-term
       0.22   11.7   1.5       0.27   11.4   0.2    1.7  2  CHDCT2        CHDCT2 (NUC038) domain


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.9   5.8   4.5e-87   4.8e-84       1     233 []       5     263 ..       5     263 .. 0.98
   2 ?    0.0   0.6      0.62   6.5e+02      45      74 ..     283     318 ..     271     363 .. 0.52

  Alignments for each domain:
  == domain 1  score: 281.9 bits;  conditional E-value: 4.5e-87
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...eeeekkkl 78 
                                   FfdRe+e++e++ il+++p++iyfiYGp++sGKt+L++eii++l+d +ky+i+y++lr+++is++++f++   e +e++k+
  gi|15668246|ref|NP_247039.1|   5 FFDREREINEILGILDETPDNIYFIYGPINSGKTTLMMEIINRLKDDKKYRIFYYNLRGVRISSYSDFFDimfEIREDNKF 85 
                                   9******************************************************************************** PP

                      ATPase_2  79 ekal......................giavpkaeleeilk.eksklvfkaielllekikkkgkkiiiiiDelqklidlgln 136
                                   ++++                      +i +p++ ++ il+ +k  +vf+++e+++++++kkg k++iiiDelq+l+  gl+
  gi|15668246|ref|NP_247039.1|  86 KQMVkdadvlvegikfiektaklfneSIILPSDLAKVILSkQKGFDVFRYLERVFREMNKKGLKPVIIIDELQRLK--GLK 164
                                   **************************9************99***********************************..888 PP

                      ATPase_2 137 gaellvkeLlnliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkel..eelsked 215
                                   ++++l+++L+n++++ltke h+++++clsS++lfie+vy+++el+gr++yilvdd+dketal+f++++++++  ++ls+++
  gi|15668246|ref|NP_247039.1| 165 SNGELIDDLFNFFVRLTKELHITHCFCLSSDSLFIEYVYDRAELRGRADYILVDDFDKETALKFMDFLSEDIlgRKLSEDE 245
                                   88**********************************************************************98888**** PP

                      ATPase_2 216 feeiyryvGGkPkalvel 233
                                   +e+iy+yvGGkPk+++++
  gi|15668246|ref|NP_247039.1| 246 KELIYSYVGGKPKDVYDV 263
                                   **************9876 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.62
                      ATPase_2  45 edkdkyviyyialreesiskldefie......eeee 74 
                                   e+ +k + ++ +++e++++ +++ ++      e++e
  gi|15668246|ref|NP_247039.1| 283 EEIQKLKYFLEDVKEDDEELYNKIVDalkifkENYE 318
                                   344445555555555555555555444444432222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   1.9e-10     2e-07       5     117 ..      24     182 ..      20     198 .. 0.79
   2 ?   -1.5   0.0       2.6   2.8e+03      76     102 ..     195     222 ..     180     254 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.9e-10
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka.............. 70 
                                   ++i +++G+  +GKTtl+ ++ ++l+ +     ++ ++++++l +   ss + + ++  ++ +++k               
  gi|15668246|ref|NP_247039.1|  24 DNIYFIYGPINSGKTTLMMEIINRLKDD-----KKYRIFYYNLRGVRiSSYSDFFDIMFEIREDNKFkqmvkdadvlvegi 99 
                                   67999********************643.....688889*********66666666666666666666************* PP

                        AAA_22  71 .........................erlsseellealeqalrarav...ielliiDEaqhlr...s.....eealeeLrsl 115
                                                            + ++  +++++le+ +r+  +   ++++iiDE q+l    s     +++++++++l
  gi|15668246|ref|NP_247039.1| 100 kfiektaklfnesiilpsdlakvilSKQKGFDVFRYLERVFREMNKkglKPVIIIDELQRLKglkSngeliDDLFNFFVRL 180
                                   ************************9666666666666666666666666************66542555666666666665 PP

                        AAA_22 116 ln 117
                                    +
  gi|15668246|ref|NP_247039.1| 181 TK 182
                                   54 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.6
                        AAA_22  76 eell.ealeqalraravielliiDEaqh 102
                                   + l+ e++++ ++ r++   +++D++++
  gi|15668246|ref|NP_247039.1| 195 DSLFiEYVYDRAELRGRADYILVDDFDK 222
                                   5555566777666666667888998887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0     5e-10   5.3e-07       1     148 [.       4     161 ..       4     187 .. 0.70
   2 ?   -0.6   0.0       1.5   1.5e+03     124     146 ..     199     222 ..     192     253 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 5e-10
                        AAA_16   1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd...ggif...lrgkcdqlesaipysalaqa 75 
                                   +++ Re+e++++l +l+ + +   ++ +++G+  +GK++l+ e+ ++l++d   + if   lrg   ++     ys + ++
  gi|15668246|ref|NP_247039.1|   4 KFFDREREINEILGILDETPD---NIYFIYGPINSGKTTLMMEIINRLKDDkkyR-IFyynLRGVRISS-----YSDFFDI 75 
                                   5899************96644...8**************************8743.3332333333333.....6555555 PP

                        AAA_16  76 lar...eellrqlldeaesaeleawrekleeala............avpelagaea.......srllellkrllallsrde 134
                                    ++   +  ++q+  +  ++ l +  +++e++++            a                 ++++ l r ++ + +++
  gi|15668246|ref|NP_247039.1|  76 MFEireDNKFKQMVKD--ADVLVEGIKFIEKTAKlfnesiilpsdlAK-------VilskqkgFDVFRYLERVFREMNKKG 147
                                   5220002333333333..445555556666666699977766554333.......13344456999999999998888878 PP

                        AAA_16 135 rplvlvlDdlqwad 148
                                    + v+++D+lq+++
  gi|15668246|ref|NP_247039.1| 148 LKPVIIIDELQRLK 161
                                   88*********876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                        AAA_16 124 krll.allsrderplvlvlDdlqw 146
                                    + + ++++ ++r  ++++Dd+++
  gi|15668246|ref|NP_247039.1| 199 IEYVyDRAELRGRADYILVDDFDK 222
                                   556667777777888999999993 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   1.9e-07    0.0002       3      58 ..      25      81 ..      23      95 .. 0.83
   2 !   12.3   0.1   0.00012      0.13      30     121 ..     116     216 ..      90     226 .. 0.64
   3 ?   -1.5   0.3       2.3   2.5e+03      40      40 ..     297     297 ..     262     340 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.9e-07
                        AAA_14  3 kilvitGaRrvGKTtllkqlikell.vkkesilyinldderdkkladpekllelile 58
                                  +i++i G+  +GKTtl+ ++i++l   kk +i+y+nl   r ++++d+ +++ +i+e
  gi|15668246|ref|NP_247039.1| 25 NIYFIYGPINSGKTTLMMEIINRLKdDKKYRIFYYNLRGVRISSYSDFFDIMFEIRE 81
                                  6899*****************999999999*********999999987555544444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00012
                        AAA_14  30 kesilyinldderdkkladpekllelileklkeekktylflDEiqev..........pewekalkslvdegknldvivtGS 100
                                   +++   + l +++  +   ++ l+++++e+ k+  k ++++DE q++          ++++++  +l +e +  ++++  S
  gi|15668246|ref|NP_247039.1| 116 PSDLAKVILSKQKGFDV--FRYLERVFREMNKKGLKPVIIIDELQRLkglksngeliDDLFNFFVRLTKELHITHCFCLSS 194
                                   44444444444333332..3347778888754557899*********7777777666666666666666666677888888 PP

                        AAA_14 101 nskllsk.eiatslagrvaeie 121
                                    s+++     + +l+gr+++i 
  gi|15668246|ref|NP_247039.1| 195 DSLFIEYvYDRAELRGRADYIL 216
                                   8887766233467777777665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.3
                        AAA_14  40 d 40 
                                   +
  gi|15668246|ref|NP_247039.1| 297 E 297
                                   1 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0     0.002       2.1       1      43 [.       8      52 ..       8      61 .. 0.83
   2 ?    2.1   0.0     0.062        65     143     193 ..     143     196 ..      80     235 .. 0.72
   3 !   10.1   0.2   0.00023      0.24     271     362 ..     241     333 ..     218     344 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.002
                         RNA12  1 RkekiedlkewleEnvntFivvkGPrGSGkkeLvldrv..lkdrk 43
                                  R+ +i+++   l+E+++    + GP  SGk+ L+++ +  lkd+k
  gi|15668246|ref|NP_247039.1|  8 REREINEILGILDETPDNIYFIYGPINSGKTTLMMEIInrLKDDK 52
                                  77889999999***********************98432255555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.062
                         RNA12 143 eahpeakPvvvidnflaka..ekngvvykklaeWaasLvqs.niahVifltedv 193
                                    +++  kPv++id+ ++ +  ++ng + + l ++  +L+++  i+h   l++d 
  gi|15668246|ref|NP_247039.1| 143 MNKKGLKPVIIIDELQRLKglKSNGELIDDLFNFFVRLTKElHITHCFCLSSDS 196
                                   4677789******99874412448889999988888888754788888888775 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00023
                         RNA12 271 dlkeldeal.eklGGRltDLealvrrvksgetpkeAveeiieqsaeeilkmflldseeakkakw.tkeqaWklikklskkg 349
                                   ++++ +e + + +GG+  D   ++ ++k g++ k+ +e ++++  +++ k fl d +e++++ + +  +a k+ k+  + +
  gi|15668246|ref|NP_247039.1| 241 LSEDEKELIySYVGGKPKDVYDVIIKLKLGKELKDILEFMLKEEIQKL-KYFLEDVKEDDEELYnKIVDALKIFKENYEIE 320
                                   4444444443789***************************99988775.78999655555554404456777776666666 PP

                         RNA12 350 sieynellleelf 362
                                    i+  + + e l 
  gi|15668246|ref|NP_247039.1| 321 DIKIPKNIREFLV 333
                                   6666555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.6e-06    0.0059       3      99 ..      29     183 ..      27     218 .. 0.69
   2 ?   -2.5   0.0       6.2   6.5e+03      37      57 ..     251     271 ..     233     317 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.6e-06
                                   EESSTTSSHHHHHHHHHHHHT....HEEEEEETTTCS.SS......................................... CS
                           AAA   3 lyGppGtGKTllakavakelg....vefleisgsell.sk......................................... 37 
                                   +yGp   GKT+l+  +++ l+     +++  ++  ++ s+                                         
  gi|15668246|ref|NP_247039.1|  29 IYGPINSGKTTLMMEIINRLKddkkYRIFYYNLRGVRiSSysdffdimfeirednkfkqmvkdadvlvegikfiektaklf 109
                                   8******************96444444333333333322346666777777777777778888888888888888888888 PP

                                   ..................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
                           AAA  38 ..................yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                                                        +  + ++ +f+e+ +k  + +++iDE+ +l + +      ++ ++++ L++++ +++k+
  gi|15668246|ref|NP_247039.1| 110 nesiilpsdlakvilskqKGFDVFRYLERVFREMNKKGLKPVIIIDELQRLKGLK------SNGELIDDLFNFFVRLTKE 183
                                   88999999999887555533334456666776666665349999***99998877......5666677777666666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.2
                                   SSTTHHHHHHHHHHHHHHHTS CS
                           AAA  37 kyvgesekkirelfkeakeka 57 
                                   +yvg ++k++ +++ ++k  +
  gi|15668246|ref|NP_247039.1| 251 SYVGGKPKDVYDVIIKLKLGK 271
                                   566666666666555543333 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.7e-06    0.0039       2      35 ..      25      58 ..      24     110 .. 0.86
   2 ?   -1.9   0.0       2.5   2.7e+03      78      90 ..     149     161 ..     126     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.7e-06
                            TK  2 sielilgpmfaGKsteLlrrvkryqlaekkvvvi 35
                                  +i++i+gp+++GK+t +++ ++r++  +k  +++
  gi|15668246|ref|NP_247039.1| 25 NIYFIYGPINSGKTTLMMEIINRLKDDKKYRIFY 58
                                  699********************99877655555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                            TK  78 vdvvlvDEaqFfe 90 
                                     v+++DE q ++
  gi|15668246|ref|NP_247039.1| 149 KPVIIIDELQRLK 161
                                   3589999999776 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.3   1.8e-06    0.0019      35     115 ..      25     108 ..      18     149 .. 0.79
   2 ?    0.8   0.2      0.36   3.8e+02     100     134 ..     151     185 ..     137     189 .. 0.80
   3 ?    0.7   0.1      0.38     4e+02     172     203 ..     310     341 ..     281     353 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-06
                                   --EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEE..EEHHHH..HHHHHHHHHT.T-HHHHHHHHTT-SEEEEE-GGGGT CS
                      Bac_DnaA  35 nPlfiygevGlGktHLlkaignevlenapelrvvY..ltaeeF..lnelvkalrd.kkaeefkeklrkvDvLliDDiqfla 110
                                   n  fiyg++  Gkt L+  i n+++++ ++ r+ Y  l + +    +++ +++ + ++ ++fk+ ++++DvL ++ i+f++
  gi|15668246|ref|NP_247039.1|  25 NIYFIYGPINSGKTTLMMEIINRLKDD-KKYRIFYynLRGVRIssYSDFFDIMFEiREDNKFKQMVKDADVL-VEGIKFIE 103
                                   668******************998765.56788883433333322578999887769999**********97.799***99 PP

                                   T-HHH CS
                      Bac_DnaA 111 gkekt 115
                                   +  k 
  gi|15668246|ref|NP_247039.1| 104 KTAKL 108
                                   87654 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.36
                                   EEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEE CS
                      Bac_DnaA 100 vLliDDiqflagkektqeelfhtfnalleegkqvv 134
                                   v++iD++q l+g ++  e +  +fn ++   k + 
  gi|15668246|ref|NP_247039.1| 151 VIIIDELQRLKGLKSNGELIDDLFNFFVRLTKELH 185
                                   89**********99888888889998887777665 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.38
                                   HHHHHHHHHHTT----TTHHHHHHHH--S-HH CS
                      Bac_DnaA 172 lailkkkieaeklevpeevlefiaervtdnvR 203
                                   l+i k + e e++++p+++ ef+ ++    + 
  gi|15668246|ref|NP_247039.1| 310 LKIFKENYEIEDIKIPKNIREFLVKKNILFLN 341
                                   56777888888889999999998876555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   2.4e-05     0.025       2      50 ..       9      53 ..       8     101 .. 0.75
   2 ?   -0.3   0.3      0.48     5e+02      66     107 ..     300     339 ..     259     340 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-05
                                  HHHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCC CS
                        NB-ARC  2 eksvekviekLlekdelqslvvalvGmgGvGKttlakqilnksdevegr 50
                                  e +++++ + L+e   ++  + +++G   +GKttl+ +i+n ++  +++
  gi|15668246|ref|NP_247039.1|  9 EREINEILGILDE--TPD-NIYFIYGPINSGKTTLMMEIINRLKD-DKK 53
                                  7789999999994..444.589******************98443.333 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.48
                                   HHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCCCTTEEE CS
                        NB-ARC  66 eeiletilkeLslseddleekeeveslkrklvrlLltkrfll 107
                                   ee+ ++i+  L+  +++ e+ e+ + + ++++++L +k+ l+
  gi|15668246|ref|NP_247039.1| 300 EELYNKIVDALKIFKENYEI-EDIK-IPKNIREFLVKKNILF 339
                                   44555555555444333332.3333.6788888888888877 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.2e-05     0.045      19     158 ..      19     175 ..       7     182 .. 0.60
   2 ?   -1.4   0.1         2   2.1e+03      63      90 ..     299     323 ..     279     342 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                                   ....TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH...........HHGGGGTGG........ CS
                        ResIII  19 lkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl...........eefkkflseayke.... 84 
                                   l+++ d+ ++i  +  +GKT +++++i rl+  +k++ f     +  + +              ++fk++ ++a+      
  gi|15668246|ref|NP_247039.1|  19 LDETPDNIYFIYGPINSGKTTLMMEIINRLKDDKKYRIFYYNLRGVRISSYSDffdimfeiredNKFKQMVKDADVLvegi 99 
                                   55455556667777789***************9887633333333333222222233333334455566665554335533 PP

                                   .GEEEESSS-B--..........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHH.HHHT-- CS
                        ResIII  85 .igkkvsgdkkka...kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswre.ilekfk 158
                                        +++  k +       s+ +k+++++ + +d  +  e+  +e ++++ ++viiiDE  rl++ ks  e i + f+
  gi|15668246|ref|NP_247039.1| 100 kF---IEKTAKLFnesIILPSDLAKVILSKQKGFDVFRYLERVFREMNKKGLKPVIIIDELQRLKGLKSNGElIDDLFN 175
                                   21...3332222222223357778888888888888887779999999999999******9999987655442555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                                   SHHHHHHHHHHGGGGTGG....GEEEES CS
                        ResIII  63 rkslleqtleefkkflseaykeigkkvs 90 
                                    ++l+++  +++k f++++     ++++
  gi|15668246|ref|NP_247039.1| 299 DEELYNKIVDALKIFKENYE---IEDIK 323
                                   56788888888888888874...33333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.5e-05     0.079       2      41 ..      28      63 ..      27     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.5e-05
                  RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnped 41
                                  ++yGp + GK+tl+ e++++l     ++kk ++++ n + 
  gi|15668246|ref|NP_247039.1| 28 FIYGPINSGKTTLMMEIINRLK----DDKKYRIFYYNLRG 63
                                  79**************888888....55555665555544 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00029      0.31       3      26 ..      28      51 ..      26      58 .. 0.81
   2 ?   -1.3   0.0       1.8   1.9e+03      85     100 ..      85     100 ..      68     108 .. 0.69
   3 ?   -1.6   0.0       2.2   2.3e+03      89     106 ..     210     227 ..     199     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                          MobB  3 givgksgsGKTtLleklipelkar 26
                                   i g  +sGKTtL+ ++i+ lk+ 
  gi|15668246|ref|NP_247039.1| 28 FIYGPINSGKTTLMMEIINRLKDD 51
                                  577889***************974 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.8
                          MobB  85 larl.sevDlvlvEGfk 100
                                   ++++ +++D vlvEG k
  gi|15668246|ref|NP_247039.1|  85 FKQMvKDAD-VLVEGIK 100
                                   333326667.8999987 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.2
                          MobB  89 sevDlvlvEGfkkealpk 106
                                    ++D +lv  f ke+  k
  gi|15668246|ref|NP_247039.1| 210 GRADYILVDDFDKETALK 227
                                   5689*****999988766 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00023      0.24       2      53 ..      26      78 ..      25     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                           Zot  2 islvtGapGsgKtsgavkkdllpalke...gRkiitnidGlrlerieqvlgekvs 53
                                  i++ +G+  sgKt     +++ + lk+    R+++ n++G r+      +   ++
  gi|15668246|ref|NP_247039.1| 26 IYFIYGPINSGKTTLM--MEIINRLKDdkkYRIFYYNLRGVRISSYSDFFDIMFE 78
                                  89***********865..55667666423489*********99887776666655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00068      0.72       2      67 ..      28     102 ..      28     159 .. 0.77
   2 ?    0.7   0.2       0.7   7.4e+02      14      69 ..     269     318 ..     265     339 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00068
                        AAA_18   2 lltGtpGvGKttlakeLskrlgf............gvnlrdvakenglllevdpealdeskrldedkldklldaleen 67 
                                   ++ G++ +GKttl  e+ +rl+             gv+++++    ++ +e  ++  +++k++++d  d+l+++++ +
  gi|15668246|ref|NP_247039.1|  28 FIYGPINSGKTTLMMEIINRLKDdkkyrifyynlrGVRISSYSDFFDIMFEIRED--NKFKQMVKDA-DVLVEGIKFI 102
                                   689*************955542234456778888888888888888888888888..7777777777.6666666555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.7
                        AAA_18  14 lakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss 69 
                                   l+keL++       l +++ke+   l ++ e+++e +++  +k   +l++++en++
  gi|15668246|ref|NP_247039.1| 269 LGKELKDI------LEFMLKEEIQKLKYFLEDVKEDDEELYNKIVDALKIFKENYE 318
                                   45555444......455555555555555555666888888888888888888865 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00059      0.62       3      28 ..      27      53 ..      25      61 .. 0.79
   2 ?   -3.2   0.0         5   5.3e+03     131     146 ..      81      96 ..      78      97 .. 0.82
   3 ?   -2.0   0.0       2.1   2.2e+03      58      88 ..     187     217 ..     136     219 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00059
                                  EEEEESTTCCHHHHHHHHH.CT--SS- CS
                          cobW  3 tvltGflGsGKTtLlnhll.enraglk 28
                                  + + G++ sGKTtL+ +++ + ++++k
  gi|15668246|ref|NP_247039.1| 27 YFIYGPINSGKTTLMMEIInRLKDDKK 53
                                  67899**************65555555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5
                                   HHHHHHHHHHTSSEEE CS
                          cobW 131 ieekaedqlaaadllv 146
                                   + +k++++++ ad+lv
  gi|15668246|ref|NP_247039.1|  81 EDNKFKQMVKDADVLV 96 
                                   5678999999999987 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.1
                                   TTTECCHCTT-HHHHHHHHHHHHTT-SEEEE CS
                          cobW  58 nGciCctlredllkelealeereerldvili 88 
                                   + c C +  + +++ + + +e+++r d+il+
  gi|15668246|ref|NP_247039.1| 187 THCFCLSSDSLFIEYVYDRAELRGRADYILV 217
                                   3466666666666777777777777777776 PP

>> TFX_C  DNA_binding protein, TFX, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.2   2.4e+03      47      62 ..      41      56 ..      39      66 .. 0.84
   2 ?   -2.8   0.0         6   6.3e+03      45      59 ..      70      84 ..      55      96 .. 0.71
   3 ?    9.5   0.0    0.0009      0.95      13      42 ..     120     149 ..     115     178 .. 0.91
   4 ?   -3.0   0.0         7   7.4e+03      15      34 ..     263     282 ..     262     287 .. 0.78
   5 ?   -1.7   0.1       2.8   2.9e+03      25      45 ..     306     326 ..     294     333 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.2
                                  HHHHHHHHHHH-SSS- CS
                         TFX_C 47 tieLikllreeapeai 62
                                  ++e+i++l++ ++ +i
  gi|15668246|ref|NP_247039.1| 41 MMEIINRLKDDKKYRI 56
                                  589******9987665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6
                                  --HHHHHHHHHHH-S CS
                         TFX_C 45 ydtieLikllreeap 59
                                   d+ +++  +re ++
  gi|15668246|ref|NP_247039.1| 70 SDFFDIMFEIREDNK 84
                                  467788888888775 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0009
                                   --EEEEE--GGGHHHHHHHHHHHHHHHS-S CS
                         TFX_C  13 apvlvtieeGtdlfdipkiiyaeadkagik 42 
                                   a+v+++ ++G d+f+  +++++e++k+g+k
  gi|15668246|ref|NP_247039.1| 120 AKVILSKQKGFDVFRYLERVFREMNKKGLK 149
                                   78999999********************98 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 7
                                   EEEEE--GGGHHHHHHHHHH CS
                         TFX_C  15 vlvtieeGtdlfdipkiiya 34 
                                   v+++++ G++l di +  ++
  gi|15668246|ref|NP_247039.1| 263 VIIKLKLGKELKDILEFMLK 282
                                   78889999999998776665 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 2.8
                                   HHHHHHHHHHHHHHHS-S--- CS
                         TFX_C  25 lfdipkiiyaeadkagikvky 45 
                                   ++d+ ki+ ++ + ++ik++ 
  gi|15668246|ref|NP_247039.1| 306 IVDALKIFKENYEIEDIKIPK 326
                                   344444444455555666655 PP

>> CHDCT2  CHDCT2 (NUC038) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00025      0.27      11     102 ..      58     145 ..      47     162 .. 0.86
   2 ?   -2.3   0.1       4.3   4.5e+03     124     147 ..     280     303 ..     269     309 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                        CHDCT2  11 yWllagvvlhGyaRwqDiqndprfaiinepFkseaekgnfleiknkflarrfklleqalvieeqlrraallnlqeekekvg 91 
                                   y+ l gv +  y+ + Di+ + r    ++ Fk+++++++ l    kf+++  kl+++++++  +l ++  l++q+  +   
  gi|15668246|ref|NP_247039.1|  58 YYNLRGVRISSYSDFFDIMFEIRE---DNKFKQMVKDADVLVEGIKFIEKTAKLFNESIILPSDLAKV-ILSKQKGFDVFR 134
                                   777888999999999999866664...578*********99999*********************999.666788888888 PP

                        CHDCT2  92 slaqrfaelel 102
                                    l++ f+e++ 
  gi|15668246|ref|NP_247039.1| 135 YLERVFREMNK 145
                                   88888888865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.3
                        CHDCT2 124 vlekvLnqleelLsdmkadvsrlp 147
                                   +l++ +++l+  L+d+k+d + l 
  gi|15668246|ref|NP_247039.1| 280 MLKEEIQKLKYFLEDVKEDDEELY 303
                                   455566777778888888766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 2114.10
//
Query:       gi|15668247|ref|NP_247040.1|  [L=382]
Description: hypothetical protein MJ_0077 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-05   23.3   0.0    0.00088   19.9   0.0    2.5  2  VWA_2     von Willebrand factor type A domain
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.017   14.5   0.0    1.4  1  VWA_CoxE  VWA domain containing CoxE-like protein
      0.057   13.7   0.1       0.37   11.0   0.1    2.3  1  VWA       von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.18   1.1e+03      63      91 ..      80     108 ..      59     145 .. 0.81
   2 !   19.9   0.0   1.5e-07   0.00088       2     107 .]     227     321 ..     226     321 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.18
                         VWA_2  63 lnalrnleakgggtnlaaaLqlarkalkk 91 
                                    ++l++l++kg + ++ + L+ +++ +++
  gi|15668247|ref|NP_247040.1|  80 CEKLKELKEKGREEDISELLDELESYMEN 108
                                   57889999989999999988888877765 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.5e-07
                         VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallk.slp.gdrvglvtfsdgpevlipltkdkakilnalrnleak.gggtnla 79 
                                   v++lD SgSmr++     +   ak+++  l++ sl+ + r+  + f+dg++ +    + k +++++l+      gggtn++
  gi|15668247|ref|NP_247040.1| 227 VVCLDLSGSMRGN-----KEIWAKAIALCLMDiSLKrNKRYISILFDDGVRDIKIY-EKKVSFDEILEFASVFyGGGTNFE 301
                                   99**********9.....4555666666666666653889999******9743322.334555555555555559****** PP

                         VWA_2  80 aaLqlarkalkkrrkgekrvivlitDge 107
                                   + L+ a k            iv+itDge
  gi|15668247|ref|NP_247040.1| 302 KPLREALKFNG--------DIVFITDGE 321
                                   *****999855........699999986 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.9e-06     0.017      58     140 ..     224     308 ..     203     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-06
                      VWA_CoxE  58 relvllvDvSgSmaaysaiflallhAllqqlp.....rtevfaFdtrlvdlTralrerDpaeaLarvsaavedlgGgTrig 133
                                    + v+++D SgSm    +i+++ ++ +l  ++     r+  ++Fd+ + d+    ++ + +e L+ +s      gGgT+  
  gi|15668247|ref|NP_247040.1| 224 GDFVVCLDLSGSMRGNKEIWAKAIALCLMDISlkrnkRYISILFDDGVRDIKIYEKKVSFDEILEFAS---VFYGGGTNFE 301
                                   479**********9988888877776666555555569999999999999866555555555555555...3388899888 PP

                      VWA_CoxE 134 aalaefl 140
                                   + l+e+l
  gi|15668247|ref|NP_247040.1| 302 KPLREAL 308
                                   8888766 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   6.1e-05      0.37       3     167 ..     227     373 ..     225     380 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.1e-05
                                   EEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGSSC-HHH CS
                           VWA   3 vfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkysgggttntgk 83 
                                   v+ lD Sgsm ++n e   ++i   + +++  +++ r+  + f + v+ +  + ++ s +e+l+  +     +gg tn +k
  gi|15668247|ref|NP_247040.1| 227 VVCLDLSGSM-RGNKEIWAKAIALCLMDIS-LKRNKRYISILFDDGVRDIKIYEKKVSFDEILEFASV---FYGGGTNFEK 302
                                   6667777777.4444444444444444444.3555666666677666666444444444555554444...3333343777 PP

                                   HHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.HTHHHHHHHHGC.TEEEEEEEESSSHHHHHHHHHSSSSCHHCEEE CS
                           VWA  84 alkyaleklfkssagaRenakkviilltdGksndg.dpkeaaneakeq.gikvfavGvgnadekelLnkiasepgeghvft 162
                                    l +al+      +g        i+++tdG+ + + + +e+++e k++ +ik++++ ++   + + L++i+  +   ++++
  gi|15668247|ref|NP_247040.1| 303 PLREALK-----FNG-------DIVFITDGECEVSlEFLEKIKEEKQRrKIKIYSICINTKPTVS-LRQISDVSV--TIYE 368
                                   7777766.....333.......499*******9977999***9999999*********8887777.999977776..6676 PP

                                   ESSHH CS
                           VWA 163 vtdfe 167
                                   +t+ +
  gi|15668247|ref|NP_247040.1| 369 LTSKT 373
                                   66655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1234  (0.068827); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2549.74
//
Query:       gi|15668248|ref|NP_247041.1|  [L=113]
Description: hypothetical protein MJ_0076 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 711.77
//
Query:       gi|15668249|ref|NP_247042.1|  [L=207]
Description: hypothetical protein MJ_0078 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0024   18.2   0.0      0.022   15.1   0.0    2.2  2  HEAT_2          HEAT repeats
     0.0066   16.1   0.7      0.079   12.6   0.1    2.4  2  ToxS            Trans-membrane regulatory protein ToxS
  ------ inclusion threshold ------
       0.06   13.6   0.0       0.19   12.1   0.0    1.8  1  HEAT            HEAT repeat
       0.14   11.5   0.0        0.2   11.0   0.0    1.2  1  Cellulase-like  Sugar-binding cellulase-like
       0.15   12.1   0.0       0.63   10.2   0.0    2.0  2  Arm             Armadillo/beta-catenin-like repeat
       0.76    9.7   5.6        1.1    9.2   0.7    2.3  2  DUF758          Domain of unknown function (DUF758)


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.26   7.6e+02      59      80 ..      15      36 ..      11      50 .. 0.85
   2 !   15.1   0.0   7.5e-06     0.022      33      78 ..      95     143 ..      64     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.26
                        HEAT_2 59 gdpealpaLkellddddddvvR 80
                                  g+ e l++Lkel++ + d++++
  gi|15668249|ref|NP_247042.1| 15 GNREKLKVLKELYQMEVDEITK 36
                                  7788999999999999988766 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7.5e-06
                        HEAT_2  33 lpaLvellededpavRraaaeaLgaigdpe...alpaLkellddddddv 78 
                                   +p+L++ll++e + +R a aeaL+ i ++    a+p L + ld++  + 
  gi|15668249|ref|NP_247042.1|  95 IPYLIKLLDSEFECIRFASAEALANIPSKLtiyAYPKLIKKLDNEVYAK 143
                                   89************************98765558899999999987765 PP

>> ToxS  Trans-membrane regulatory protein ToxS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   2.6e-05     0.079     106     141 ..      16      51 ..      10      55 .. 0.91
   2 ?    0.7   0.0      0.13   3.8e+02     103     122 ..     164     183 ..     148     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                          ToxS 106 seeqlklikklfkldaeqsrridivnektlLltsLn 141
                                   ++e+lk++k+l++++ ++  +++i+++   Llts +
  gi|15668249|ref|NP_247042.1|  16 NREKLKVLKELYQMEVDEITKLNILDDVFELLTSTK 51 
                                   5789*****************************976 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.13
                          ToxS 103 kdfseeqlklikklfkldae 122
                                   ++f+e  l +ik+l+k d e
  gi|15668249|ref|NP_247042.1| 164 ENFNEYSLYVIKELYKYDKE 183
                                   789999*********99876 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.2e-05      0.19       2      27 ..      95     120 ..      95     120 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.2e-05
                                   HHHHHHHHT-SSHHHHHHHHHHHHHH CS
                          HEAT   2 lPlllkllsDpspeVReaAakaLgal 27 
                                   +P l+kll ++   +R a+a+aL+++
  gi|15668249|ref|NP_247042.1|  95 IPYLIKLLDSEFECIRFASAEALANI 120
                                   79*********************987 PP

>> Cellulase-like  Sugar-binding cellulase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.7e-05       0.2      66     107 ..      31      72 ..      12      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.7e-05
                                   -SS-EEEE-TTHHHHHHHHHHHTT-EEEEE-----BTT-GGG CS
                Cellulase-like  66 spakaevkirealrellkaarerglkvalsswfreDsderrl 107
                                     + ++++i +++ ell++++erg +  +s+++ +Ds+++ +
  gi|15668249|ref|NP_247042.1|  31 VDEITKLNILDDVFELLTSTKERGFEDIISTHYTSDSKNKAI 72 
                                   55678999*****************************99865 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00021      0.63      14      39 ..      95     120 ..      90     120 .. 0.96
   2 ?   -1.8   0.0       1.3   3.7e+03      16      25 ..     144     154 ..     143     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00021
                                   HHHHHHHTTTSSHHHHHHHHHHHHHH CS
                           Arm  14 vppLvrLLssedeevqeeAawALsNL 39 
                                   +p L++LL+se e +++++a AL+N+
  gi|15668249|ref|NP_247042.1|  95 IPYLIKLLDSEFECIRFASAEALANI 120
                                   799**********************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                                   HHHHHTT.TSS CS
                           Arm  16 pLvrLLs.sed 25 
                                   +Lv+L+  s++
  gi|15668249|ref|NP_247042.1| 144 VLVKLIMkSDN 154
                                   69999986665 PP

>> DUF758  Domain of unknown function (DUF758)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.7   0.00037       1.1      18      72 ..      29      88 ..      18      91 .. 0.69
   2 ?    2.8   0.4     0.035   1.1e+02      41      87 ..     131     177 ..     121     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00037
                        DUF758 18 masksvaklfiddtssellde.....lykllkeytgnkkeaekvvKniiKvvvKvgvllr 72
                                  m  ++++kl i d   ell +     +++++  + ++ ++ + ++  +iK++ Kvg+ + 
  gi|15668249|ref|NP_247042.1| 29 MEVDEITKLNILDDVFELLTStkergFEDIISTHYTSDSKNKAIIYYCIKIIEKVGIKYP 88
                                  55556666555555555555511111345699999999******************9875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.035
                        DUF758  41 kllkeytgnkkeaekvvKniiKvvvKvgvllrn.kqlsaeelallekf 87 
                                   kl+k+   n+  a+ +vK i+K   K ++ll+  +++++  l+ ++++
  gi|15668249|ref|NP_247042.1| 131 KLIKK-LDNEVYAKVLVKLIMKSDNKEAILLKLfENFNEYSLYVIKEL 177
                                   67886.77899999999****999999999987677877777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1353.49
//
Query:       gi|15668250|ref|NP_247043.1|  [L=380]
Description: regulatory protein MoxR [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-27   93.7   0.0    1.9e-26   92.7   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
    2.5e-19   68.9   1.2    2.5e-19   68.9   1.2    3.7  3  AAA_lid_8        AAA lid domain
    0.00025   21.5   0.0     0.0012   19.3   0.0    2.2  1  AAA              ATPase family associated with various cellul
    0.00036   19.7   0.2     0.0053   15.9   0.0    2.5  3  MCM              MCM P-loop domain
     0.0011   18.9   0.0     0.0019   18.0   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
     0.0028   17.6   1.4      0.005   16.8   0.0    2.2  3  RsgA_GTPase      RsgA GTPase
     0.0083   15.9   0.0      0.015   15.1   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0094   15.7   0.0      0.016   14.9   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.019   15.4   0.0      0.091   13.1   0.0    1.9  2  AAA_16           AAA ATPase domain
        0.1   12.1   0.0       0.22   11.0   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
       0.11   12.3   0.5        1.1    9.0   0.0    2.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.55   10.6   2.7        2.8    8.3   0.4    2.5  2  ARS2             Arsenite-resistance protein 2


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   0.0   1.3e-29   1.9e-26       2     138 .]      39     166 ..      38     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 1.3e-29
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------....G-SEEEEESGGG CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraar....egeilvlDEver 76 
                                    + +G+pG++Ks+l++ +a+ +n++++++++tr+tte++l+g+++ik  +++ ++v      +      ++ei++lDEv++
  gi|15668250|ref|NP_247043.1|  39 TVFLGNPGVAKSQLIRAIASHINANYFEKLITRFTTEDELFGPLSIKelKDNDRFVR-----KTSgylpTAEIAFLDEVFK 114
                                   6789******************************************66633333333.....3334445************ PP

                                   --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                         AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                   a+s++ln+Lls+++er ++  +g++ +k++       +++++++n+l+ ++ne   a+++Rf
  gi|15668250|ref|NP_247043.1| 115 ANSSILNALLSIINERIYH--NGDKIEKVPL------ISLFGASNELP-EENE-LLAFYDRF 166
                                   *******************..*********9......***********.9999.899****9 PP

>> AAA_lid_8  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.2   1.9e+03       1      15 [.       3      17 ..       3      29 .. 0.72
   2 !   68.9   1.2   1.7e-22   2.5e-19       2      72 .]     217     285 ..     216     285 .. 0.97
   3 ?   -1.6   3.2       1.8   2.7e+03       2      26 ..     331     355 ..     299     366 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                     AAA_lid_8  1 evlelileiknklee 15
                                  e++  + +i+++l++
  gi|15668250|ref|NP_247043.1|  3 EIMHKLEKIREELNS 17
                                  588889999999965 PP

  == domain 2  score: 68.9 bits;  conditional E-value: 1.7e-22
                     AAA_lid_8   2 vlelileiknkleeeeeaiyvSDRRwkkivkllkasAylngrdevnlsDllllkhclWnepeqkekvkkiv 72 
                                   ++ ++ +ik+kl   ++ iy+SDRR+kk+vk +k  Aylngr+e +++Dl +l+h++W++ +++ +v k++
  gi|15668250|ref|NP_247043.1| 217 IIGYLVDIKKKL--SQNHIYISDRRFKKSVKAIKCFAYLNGRREAEIEDLEILRHIFWDDIDDILIVSKVI 285
                                   78899*******..99***************************************************9987 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.8
                     AAA_lid_8   2 vlelileiknkleeeeeaiyvSDRR 26 
                                   +l  +  i+ +l++++++ ++  R+
  gi|15668250|ref|NP_247043.1| 331 ILCKMAYIRLELKKIRNEAIINKRK 355
                                   3333445556666666666666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   8.1e-07    0.0012       2     124 ..      40     166 ..      39     173 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.1e-07
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.......STTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHH CS
                           AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk.......yvgesekkirelfkeakeka....kpsilfiDEidala 71 
                                   ++ G+pG+ K+ l++a+a++++++++e   ++++ +        +    k++++  + +++ +    +  i f+DE+ + +
  gi|15668250|ref|NP_247043.1|  40 VFLGNPGVAKSQLIRAIASHINANYFEKLITRFTTEdelfgplSI----KELKDNDRFVRKTSgylpTAEIAFLDEVFKAN 116
                                   589*******************************55587665422....222222222333334555669******99987 PP

                                   HHHTTCCCHHHHHHHHHHHHHHHHTTTS.......SSTEEEEEEESSGGGSTHHHHS.TTS CS
                           AAA  72 ksrsgseseeeervvnqLlteldgvkkk.......eskvivigatnrpdkldpallr.gRf 124
                                   +s            +n+Ll+ +++   +          + + ga+n+  + ++ l   +Rf
  gi|15668250|ref|NP_247043.1| 117 SSI-----------LNALLSIINERIYHngdkiekVPLISLFGASNELPEENELLAFyDRF 166
                                   777...........89999888877666666655433355566777655555555555555 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.6e-06    0.0053      52     140 ..      31     122 ..       5     130 .. 0.67
   2 ?    2.7   0.0     0.039        58       9      47 ..     114     153 ..     105     161 .. 0.79
   3 ?   -4.0   0.1       4.3   6.4e+03       5      32 ..     315     342 ..     314     344 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.6e-06
                                   SBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEE..SSSSSSSHS.SSEEEEESSSSS.EEEE.ETHHHHTTTSEEEE CS
                           MCM  52 tklrgdinvllvgdpgtaKsqlLkyveklapravyts..gkgssaagL.taavvrdeetge.fvle.aGalvladkGvcci 127
                                   t++ ++ + +++g+pg+aKsql++++++ ++ + + +   + +++ +L  +   ++ + ++ fv + +G l   +  ++ +
  gi|15668250|ref|NP_247043.1|  31 TSILANEHTVFLGNPGVAKSQLIRAIASHINANYFEKliTRFTTEDELfGPLSIKELKDNDrFVRKtSGYLP--TAEIAFL 109
                                   567788899******************999988876422566777777534444444444413333133333..3346677 PP

                                   ESGGGSTCHHHHH CS
                           MCM 128 Defdkmkeedrsa 140
                                   De+ k +++  +a
  gi|15668250|ref|NP_247043.1| 110 DEVFKANSSILNA 122
                                   7776666655555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.039
                                   HTSSTHHHHHHHHSSTTSSS-HH.HHHHHHHHHH---EBB CS
                           MCM   9 akekdiieklvksiapsiyghed.vkkaillqlfggvkkk 47 
                                   +++++i++ l+++i ++iy + d + k  l++lfg++++ 
  gi|15668250|ref|NP_247043.1| 114 KANSSILNALLSIINERIYHNGDkIEKVPLISLFGASNEL 153
                                   567789999999******9976559999999999998854 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 4.3
                                   HHHHHTSSTHHHHHHHHSSTTSSS-HHH CS
                           MCM   5 ikelakekdiieklvksiapsiyghedv 32 
                                   ik++ + k+ ++kl++++++  y + + 
  gi|15668250|ref|NP_247043.1| 315 IKKIGECKKDYNKLIEILCKMAYIRLEL 342
                                   6677777777888888888777665555 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.3e-06    0.0019       1      97 [.      38     138 ..      38     159 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.3e-06
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfe...ekekefefkkGpv.fanllladeinrappk 77 
                                   h ++ g PG+ak +l++a+a+++++++    +t      ++ G   ++   ++++ ++ ++G +  a++ + de+ +a++ 
  gi|15668250|ref|NP_247043.1|  38 HTVFLGNPGVAKSQLIRAIASHINANYFEKLITRFTTEDELFGPLSIKelkDNDRFVRKTSGYLpTAEIAFLDEVFKANSS 118
                                   778889*******************987766666666677777543330103445556667777357999*********** PP

                         AAA_3  78 tqsalleameerqvtveget 97 
                                   +  all +++er    +++ 
  gi|15668250|ref|NP_247043.1| 119 ILNALLSIINERIYHNGDKI 138
                                   **********9976655555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.4e-06     0.005      81     124 ..      19      61 ..       1      76 [. 0.75
   2 ?   -2.6   0.1       2.9   4.4e+03      49      81 ..     180     211 ..     159     235 .. 0.49
   3 ?   -2.2   0.2       2.3   3.4e+03      34      55 ..     296     317 ..     272     358 .. 0.50

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.4e-06
                                   E--TTTHTTHH.HHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-- CS
                   RsgA_GTPase  81 lvsaktkegle.elkellkdktsvlvGqSGvGKStLinallpele 124
                                   ++  +++e+++ +l++ l+++ +v++G+ Gv KS Li a++++ +
  gi|15668250|ref|NP_247043.1|  19 FL--ERREEIDiALTSILANEHTVFLGNPGVAKSQLIRAIASHIN 61 
                                   33..34455554899*************************99865 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.9
                                   EEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE CS
                   RsgA_GTPase  49 pvivlnKiDlleeeeeleelkeelealgyevll 81 
                                    ++ l K+D   + + ++   +el++++ +   
  gi|15668250|ref|NP_247043.1| 180 NLVKLIKLDEEYKPK-TTISIKELRKMQEKANE 211
                                   445555555544444.33333333433333333 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.3
                                   HHHHHHHHHHHTT-EEEEEEE- CS
                   RsgA_GTPase  34 lldrfLvlaeekgiepvivlnK 55 
                                    ld++ ++ + k+    i + K
  gi|15668250|ref|NP_247043.1| 296 VLDKAEIIKNLKNELKYIDIKK 317
                                   3333222222222223333333 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.7e-06     0.015       2      87 ..      40     128 ..      39     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.7e-06
               Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegk...........pklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                   v  G pG  KS+lir ++++      n + +e l  ++            k+ +++ r v++ ++  +++  ++i +lDE 
  gi|15668250|ref|NP_247043.1|  40 VFLGNPGVAKSQLIRAIASHI-----NANYFEKLITRFttedelfgplsIKELKDNDRFVRK-TSGYLPT--AEIAFLDEV 112
                                   67799*************994.....333333333333344556666856666666666665.5666665..9******** PP

               Viral_helicase1  72 lllhaGyilllaalsk 87 
                                   +++++ ++++l+ + +
  gi|15668250|ref|NP_247043.1| 113 FKANSSILNALLSIIN 128
                                   *******999887766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.1e-05     0.016      42     138 ..      31     131 ..      11     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                     IstB_IS21  42 sfiekkenivllGpsGvGKshlaialgveavr...aglsvlfvrvedLveelkra..rrdgklaralkrllkv.dllilDd 116
                                     i ++e  v+lG +Gv Ks l  a++ +  +   + l ++f++ ++L+  l+++  ++++++ r+ + +l + ++  lD+
  gi|15668250|ref|NP_247043.1|  31 TSILANEHTVFLGNPGVAKSQLIRAIASHINAnyfEKLITRFTTEDELFGPLSIKelKDNDRFVRKTSGYLPTaEIAFLDE 111
                                   456678999*****************987555233566789********98876622567888888877665438999999 PP

                     IstB_IS21 117 lgllpldqaeaellfeviekry 138
                                   +   + ++   + l+ +i++r 
  gi|15668250|ref|NP_247043.1| 112 VF--KANSSILNALLSIINERI 131
                                   74..556666777888887775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.1e-05     0.091       3      55 ..      20      65 ..      18      84 .. 0.78
   2 ?   -1.2   0.0       1.6   2.4e+03      38      69 ..     117     143 ..     114     227 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.1e-05
                        AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                    R+ee+     al ++ ++  e +++ G++Gv Ks l+r+++ +++++  +f
  gi|15668250|ref|NP_247043.1| 20 LERREEI---DIALTSILAN--EHTVFLGNPGVAKSQLIRAIASHINAN--YF 65
                                  5666676...6677777777..6899********************998..33 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                        AAA_16  38 sslvrellralekdggiflrgkcdqlesaipy 69 
                                   ss++++ll  ++++    ++ + d+  +++p+
  gi|15668250|ref|NP_247043.1| 117 SSILNALLSIINER----IYHNGDKI-EKVPL 143
                                   77888888888887....77777776.33332 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00015      0.22      30      70 ..      33      73 ..      25      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                         AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldkekylsltinfs 70
                                  + ++ ++++ G+ G++K+ +i+ + ++++ + +  l+  f+
  gi|15668250|ref|NP_247043.1| 33 ILANEHTVFLGNPGVAKSQLIRAIASHINANYFEKLITRFT 73
                                  456788999********************888888887776 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00072       1.1      32      61 ..      35      64 ..       9     131 .. 0.86
   2 ?   -1.4   0.1       1.1   1.7e+03      78     115 ..     187     224 ..     177     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00072
                        RuvB_N 32 aldhvllyGpPGlGkttlakiiakelgvkl 61
                                  a +h+++ G PG+ k+ l + ia+ ++++ 
  gi|15668250|ref|NP_247043.1| 35 ANEHTVFLGNPGVAKSQLIRAIASHINANY 64
                                  678*********************999875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                        RuvB_N  78 lltnleekdvlfideihrlsraveevlysamedfrldi 115
                                   l  + ++k  + i e+ +++++++ev    +  + +di
  gi|15668250|ref|NP_247043.1| 187 LDEEYKPKTTISIKELRKMQEKANEVDIENIIGYLVDI 224
                                   55567778888999999999999999888888887777 PP

>> ARS2  Arsenite-resistance protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4    0.0019       2.8      24      62 ..     186     227 ..     180     241 .. 0.85
   2 ?    1.6   0.1      0.21   3.2e+02      88     109 ..     352     373 ..     345     376 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0019
                          ARS2  24 kleellseketlseeeilklgkkdpekevEk...fvqantqE 62 
                                   kl+e +++k+t+s  e+ k+++k +e ++E+   ++  +++ 
  gi|15668250|ref|NP_247043.1| 186 KLDEEYKPKTTISIKELRKMQEKANEVDIENiigYLVDIKKK 227
                                   788999************************955555555555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.21
                          ARS2  88 lnKHaekveevrkevefFnnyl 109
                                    ++  + + ev ke + Fnny+
  gi|15668250|ref|NP_247043.1| 352 NKRKTDFIDEVIKETDEFNNYI 373
                                   3446799**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1199  (0.0668749); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2455.47
//
Query:       gi|15668251|ref|NP_247044.1|  [L=127]
Description: hypothetical protein MJ_0080 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-11   42.6   1.3    7.2e-11   41.6   1.3    1.5  1  RHH_1            Ribbon-helix-helix protein, copG family
    1.5e-10   41.1   0.2    2.1e-10   40.6   0.2    1.2  1  NikR_C           NikR C terminal nickel binding domain
    0.00017   21.5   3.1     0.0004   20.3   3.1    1.6  1  RHH_3            Ribbon-helix-helix domain
     0.0007   19.7   0.7     0.0018   18.3   0.2    1.8  2  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
     0.0091   15.7   1.3        0.5   10.1   0.1    2.2  2  DUF956           Domain of unknown function (DUF956)
  ------ inclusion threshold ------
      0.028   14.7   0.1      0.038   14.2   0.1    1.2  1  DUF5300          Domain of unknown function (DUF5300)
       0.12   12.9   0.4       0.25   11.9   0.1    1.7  2  CopG_antitoxin   CopG antitoxin of type II toxin-antitoxin sy


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   1.3   2.8e-14   7.2e-11       1      39 []       3      41 ..       3      41 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.8e-14
                                  EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHH CS
                         RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyler 39
                                  r+s++++++ll+++de++ +++ SrSe+IR+Al+ y+++
  gi|15668251|ref|NP_247044.1|  3 RISLTIEKNLLKEVDEIINKERISRSEFIRRALEYYVKK 41
                                  8***********************************975 PP

>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.2   8.4e-14   2.1e-10       1      77 []      52     124 ..      52     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 8.4e-14
                                   EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEEE CS
                        NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltli 77 
                                   +G it++y+    +  e++ +++ +y+d++i sl +  + + ++ +i++kG+ ++i e+++kl++++ V+ ++lt+i
  gi|15668251|ref|NP_247044.1|  52 IGEITVIYNS---KAVEDIVKLESQYKDIVIISLEIPFEGK-IIRMIAIKGQRDRIIEFTNKLKGISSVELAQLTTI 124
                                   689******9...99**********************9998.********************************986 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   3.1   1.5e-07    0.0004       3      43 ..       2      42 ..       2      43 .. 0.97

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.5e-07
                         RHH_3  3 trttvsidpelaekLkaLSekTrIprSklldeAiellLekY 43
                                  +r++ +i+++l+++ +++ +k rI rS+ ++ A+e + +kY
  gi|15668251|ref|NP_247044.1|  2 ERISLTIEKNLLKEVDEIINKERISRSEFIRRALEYYVKKY 42
                                  68999************************************ PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   7.2e-07    0.0018      90     122 ..       2      34 ..       1      35 [. 0.94
   2 ?   -0.6   0.0      0.54   1.4e+03      53      81 ..      56      85 ..      46     100 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.2e-07
               HicB_lk_antitox  90 eriNitlpervlkriDaavkaagesRSgflaka 122
                                   eri +t+ +++lk++D+++++++ sRS f+ +a
  gi|15668251|ref|NP_247044.1|   2 ERISLTIEKNLLKEVDEIINKERISRSEFIRRA 34 
                                   89***************************9875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.54
               HicB_lk_antitox 53 eeipepssieella.npeyaggiwalvdvd 81
                                  + i +++ +e++++ +++y++++++  ++ 
  gi|15668251|ref|NP_247044.1| 56 TVIYNSKAVEDIVKlESQYKDIVIISLEIP 85
                                  555566677766532677888887777775 PP

>> DUF956  Domain of unknown function (DUF956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.1    0.0084        22      87     109 ..       9      31 ..       3      41 .. 0.85
   2 !   10.1   0.1    0.0002       0.5      37      85 ..      59     109 ..      51     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0084
                        DUF956  87 skkvLkavrkyvgkekvvrslsl 109
                                   +k++Lk v + ++ke++ rs+ +
  gi|15668251|ref|NP_247044.1|   9 EKNLLKEVDEIINKERISRSEFI 31 
                                   6899**************99755 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0002
                        DUF956  37 yndknvedyiqi..pWeevdsvvasvlfkgklirrfaivtkkngkfsFssk 85 
                                   yn+k ved +++   ++++  +  ++ f+gk+ir  ai+ +++  ++F+ k
  gi|15668251|ref|NP_247044.1|  59 YNSKAVEDIVKLesQYKDIVIISLEIPFEGKIIRMIAIKGQRDRIIEFTNK 109
                                   9********998335889999999999***************999999887 PP

>> DUF5300  Domain of unknown function (DUF5300)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.5e-05     0.038      18      75 ..      53     114 ..      47     127 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                   S-EEEESSSS-EEEE--B..-TT-EE....EEEESSS----EEEEEEBTTS-EEEEEE---- CS
                       DUF5300  18 knvkvkfngekevtvgalekgsketi....elsedaksitkvevsGttesgkkFtghFsGlv 75 
                                     + v +n +   ++ +le++ k+ +    e++ + k i  + ++G+     +Ft+  +G+ 
  gi|15668251|ref|NP_247044.1|  53 GEITVIYNSKAVEDIVKLESQYKDIViislEIPFEGKIIRMIAIKGQRDRIIEFTNKLKGIS 114
                                   5799*****************999653444889999************************85 PP

>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   9.8e-05      0.25      43      77 ..       2      36 ..       1      38 [. 0.94
   2 ?   -2.7   0.0       3.5   8.9e+03      44      49 ..      79      84 ..      60      87 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.8e-05
                CopG_antitoxin 43 ksislrlpedlLealkekAnkrdvpyqslikelle 77
                                  ++isl ++++lL+++ e  nk  ++ +++i+ +le
  gi|15668251|ref|NP_247044.1|  2 ERISLTIEKNLLKEVDEIINKERISRSEFIRRALE 36
                                  68*****************************9997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.5
                CopG_antitoxin 44 sislrl 49
                                   isl++
  gi|15668251|ref|NP_247044.1| 79 IISLEI 84
                                  345555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 847.37
//
Query:       gi|15668252|ref|NP_247045.1|  [L=447]
Description: methyl coenzyme M reductase II subunit MrtB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   3.8e-137  455.8   4.4   4.9e-137  455.4   4.4    1.1  1  MCR_beta    Methyl-coenzyme M reductase beta subunit, C-termi
    1.3e-85  285.6   0.2    2.5e-85  284.7   0.2    1.5  1  MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-termi
     0.0052   16.4   0.4      0.017   14.7   0.1    1.9  2  DUF4147     Domain of unknown function (DUF4147)


Domain annotation for each model (and alignments):
>> MCR_beta  Methyl-coenzyme M reductase beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.4   4.4  8.2e-141  4.9e-137       1     249 []     189     437 ..     189     437 .. 1.00

  Alignments for each domain:
  == domain 1  score: 455.4 bits;  conditional E-value: 8.2e-141
                      MCR_beta   1 GyalrnikanhvvaitkknalnaaalssileqtavfemGdavGaferahllglayqGlnannlvydlvkengkegtvGtvv 81 
                                   Gy+lrni+anh+va+t+k++lna+al+sileqta+fe Gda+Gafer hllgla+qGlnannl+y+lvkengk+gtvGtvv
  gi|15668252|ref|NP_247045.1| 189 GYGLRNIMANHIVAVTRKKTLNAVALASILEQTAMFETGDALGAFERLHLLGLAFQGLNANNLTYELVKENGKDGTVGTVV 269
                                   9******************************************************************************** PP

                      MCR_beta  82 eslveraiedkvikvekklpsgyklyetkdvalwnayaaaGllaavivnvgaaraaqavsstllyyndlleketglpGvdf 162
                                   +s+vera+ed+vi+  k++psg+++ye+ d+alwnayaa+Gl+aavivnvgaaraaq+v+st+lyynd+le+etglp vdf
  gi|15668252|ref|NP_247045.1| 270 ASVVERALEDGVIRPLKTMPSGFTVYEPVDWALWNAYAASGLVAAVIVNVGAARAAQGVASTVLYYNDILEYETGLPSVDF 350
                                   ********************************************************************************* PP

                      MCR_beta 163 GrveGtavGfsffshsiyGGGGpGifnGnhvvtrhskGfaipcvaaavaldaGtqlfspeatsglvgevfgeidefreplk 243
                                   Gr+eGtavGfsffshsiyGGGGpG f+GnhvvtrhskGfaipc+aaa++ldaGtq+fs+e+ts+lvg+v+++id++replk
  gi|15668252|ref|NP_247045.1| 351 GRAEGTAVGFSFFSHSIYGGGGPGTFHGNHVVTRHSKGFAIPCAAAAMCLDAGTQMFSVERTSALVGTVYSAIDHLREPLK 431
                                   ********************************************************************************* PP

                      MCR_beta 244 avaeaa 249
                                   +vae+a
  gi|15668252|ref|NP_247045.1| 432 YVAEGA 437
                                   ***986 PP

>> MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.7   0.2   4.3e-89   2.5e-85       1     182 []       6     187 ..       6     187 .. 1.00

  Alignments for each domain:
  == domain 1  score: 284.7 bits;  conditional E-value: 4.3e-89
                    MCR_beta_N   1 DkidlyddkGkllesdvpleaisPlknpaikkivkdvkrtvavnlagiekalktgkvggkaskilGreldldivenadaia 81 
                                   D+idlyd++Gklle++vpleaisPlknp+i+kiv+d+kr+va+nlagie+alktg+vggka++++Greldl+ivena+ ia
  gi|15668252|ref|NP_247045.1|   6 DRIDLYDERGKLLEENVPLEAISPLKNPTIEKIVNDIKRSVAINLAGIENALKTGAVGGKACFCPGRELDLPIVENAEIIA 86 
                                   89******************************************************************************* PP

                    MCR_beta_N  82 ekikelvqveedddtkvkllngGkqllvqvPskRleaaaeysvallataaavveaiidefdvdmfdasvvkaavlGryPqt 162
                                   ekik++vq+eedddt vkl+ngGkqll+q+PskRl++aa+y+v++l+ + a+v+ai+d fdvdmfda+vvk+av+GryPqt
  gi|15668252|ref|NP_247045.1|  87 EKIKRMVQIEEDDDTVVKLINGGKQLLLQLPSKRLRVAADYTVSALIGGGATVQAIVDAFDVDMFDAPVVKTAVMGRYPQT 167
                                   ********************************************************************************* PP

                    MCR_beta_N 163 vdlaggnvasilsipqkneG 182
                                   vd++g+n+a++l+ p  +eG
  gi|15668252|ref|NP_247045.1| 168 VDFHGANIATLLGPPVLLEG 187
                                   ****************9998 PP

>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   2.9e-06     0.017      93     152 ..      84     142 ..      75     143 .. 0.87
   2 ?   -1.4   0.0      0.23   1.4e+03     174     205 ..     270     301 ..     261     323 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-06
                                   HHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHHHHHHHCT--HHHH CS
                       DUF4147  93 eaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqaltkaLlasGasIqel 152
                                     a+ki ++++  ++dd+v+ li GG   ll++P++ + ++    +++aL+  Ga++q +
  gi|15668252|ref|NP_247045.1|  84 IIAEKIKRMVQIEEDDDTVVKLINGGKQLLLQLPSKRLRVAAD-YTVSALIGGGATVQAI 142
                                   56999******989999*********************99875.5678999999999976 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.23
                                   SEEEEEEE--STT--TTTGGG-TTS-----HH CS
                       DUF4147 174 arvvsLilSDVvgddldvIASGPtvpdsstfa 205
                                   a+vv  +l D v  +l+++ SG tv+++ ++a
  gi|15668252|ref|NP_247045.1| 270 ASVVERALEDGVIRPLKTMPSGFTVYEPVDWA 301
                                   567788889999999*********99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 2688.44
//
Query:       gi|15668253|ref|NP_247046.1|  [L=266]
Description: methyl coenzyme M reductase II subunit MtrG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.1e-132  440.8   0.2   1.3e-132  440.6   0.2    1.0  1  MCR_gamma  Methyl-coenzyme M reductase gamma subunit


Domain annotation for each model (and alignments):
>> MCR_gamma  Methyl-coenzyme M reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.6   0.2  7.1e-137  1.3e-132       1     245 [.       5     250 ..       5     251 .. 0.99

  Alignments for each domain:
  == domain 1  score: 440.6 bits;  conditional E-value: 7.1e-137
                     MCR_gamma   1 aqyyPGeskvaenrrkfmdpeaeleklreisdedvvkilghraPGeeyksvhPPleemdepedpirelvePieGakaGdrv 81 
                                   +q+yPG++ +aenrrk+m+pe+el+klr+i+d+++vkilghr+PGe+yk+vhPPleemd++edpi+++vePi+Gak+G rv
  gi|15668253|ref|NP_247046.1|   5 PQFYPGNTLIAENRRKHMNPEVELKKLRDIPDDEIVKILGHRNPGESYKTVHPPLEEMDFEEDPIKDIVEPIQGAKEGVRV 85 
                                   7******************************************************************************** PP

                     MCR_gamma  82 ryiqfadsmyfaPaqPyqrarlellryrgvdtGtlsGrqiievrerdlekiske.lletelfdpartgirGatvhGhslrl 161
                                   ryiqfadsmy+aPaqPy+rar++++r+rg+dtGtlsGrq+ie+re dlekisk+ l++te+fdpa++girGatvhGhslrl
  gi|15668253|ref|NP_247046.1|  86 RYIQFADSMYNAPAQPYDRARTYMWRFRGIDTGTLSGRQVIEMRELDLEKISKNfLIDTEFFDPATCGIRGATVHGHSLRL 166
                                   *****************************************************8468************************ PP

                     MCR_gamma 162 denGlmfdalqrlvldeedgevkyvkdqvgvpldkkvdvGkpldedelkkkttiyrldgvalrddkevvevvkrihelrtk 242
                                   denGlmfd lqr+++de++g+v yvkdqvg+pld++vdvG+pl +d l k+ttiyr+d++ +r+dke++evv+ ihe+rtk
  gi|15668253|ref|NP_247046.1| 167 DENGLMFDGLQRYIYDEKTGHVLYVKDQVGRPLDEPVDVGEPLPHDYLAKITTIYRKDNIGMREDKEALEVVQIIHEARTK 247
                                   ********************************************************************************* PP

                     MCR_gamma 243 lgf 245
                                   +gf
  gi|15668253|ref|NP_247046.1| 248 GGF 250
                                   **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1686.73
//
Query:       gi|15668254|ref|NP_247047.1|  [L=552]
Description: methyl coenzyme M reductase II subunit MtrA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   9.3e-151  500.7   0.0   1.2e-150  500.3   0.0    1.1  1  MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-ter
    2.4e-69  231.6   2.5    8.8e-69  229.8   2.7    1.8  2  MCR_alpha    Methyl-coenzyme M reductase alpha subunit, C-ter
  ------ inclusion threshold ------
      0.054   13.1   0.0      0.097   12.3   0.0    1.4  1  MCR_beta_N   Methyl-coenzyme M reductase beta subunit, N-term


Domain annotation for each model (and alignments):
>> MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  500.3   0.0    2e-154  1.2e-150       1     270 []       5     271 ..       5     271 .. 0.99

  Alignments for each domain:
  == domain 1  score: 500.3 bits;  conditional E-value: 2e-154
                                   XX--HHHHHHH-S.S-TT--B---S-S-GGGG-HHHHHHHHHHHHHHHHH.-S----TTS...S--S-SS---EEEBTTS- CS
                   MCR_alpha_N   1 eklflkalkkkfkkedpeekktkfykfeGlkqserkrefveaakkiakkr.gislynpdilhlGvplGqrklmpykvsgtd 80 
                                   +klflkalk+kf+ edp+ek+tkfy f+G++qs+rkrefve a+k+ +kr gi++ynpdi   GvplGqrklm+yk+sgtd
  gi|15668254|ref|NP_247047.1|   5 KKLFLKALKEKFE-EDPKEKYTKFYIFGGWRQSARKREFVEFAQKLIEKRgGIPFYNPDI---GVPLGQRKLMTYKISGTD 81 
                                   689**********.9********************************99977******99...****************** PP

                                   -EEEGGGSSGGG-HHHHHHHHHHHTEEEEE-HHHHHHHHHTT-----HHHHHHHHHHHHHHTTT--SS-TT-----TTT-T CS
                   MCR_alpha_N  81 vlvegddlhfvnnaalqqlwddirrtvivgldtahevlekrlGkevtPetineylevlnhalPGgavvqehmvethPalve 161
                                   ++vegddlhf+nnaa+qql+ddi+rtvivg+dtah+vlekrlG+evtPetiney+e++nhalPGgavvqehmve+hP+lv+
  gi|15668254|ref|NP_247047.1|  82 AFVEGDDLHFCNNAAIQQLVDDIKRTVIVGMDTAHAVLEKRLGVEVTPETINEYMETINHALPGGAVVQEHMVEVHPGLVW 162
                                   ********************************************************************************* PP

                                   T-EEEEEES-HHHHTTS-GGGB--HHHHS-HHHHHHHHHHH-S-EEEEEE--HHHHHHS-HHHHHHHHHHHHHHHHHHHHT CS
                   MCR_alpha_N 162 dcyvkvftGddeladeidkqflidinkefpeeqaeqlkkaiGkklyqvvriPtivsrtcdGgttsrwsamqigmsfisayk 242
                                   dcy+k+ftG+deladeidk+flidinkefpeeqaeq+kk iG+++yqv+r+Ptiv+r+cdGgt+srwsamqigmsfi+ayk
  gi|15668254|ref|NP_247047.1| 163 DCYAKIFTGNDELADEIDKRFLIDINKEFPEEQAEQIKKYIGNRTYQVSRVPTIVVRCCDGGTVSRWSAMQIGMSFITAYK 243
                                   ********************************************************************************* PP

                                   --SS-TTHHHHHHHHHTTSEEES---B- CS
                   MCR_alpha_N 243 lcaGeaavadlayaakhaeviemgellP 270
                                   lcaGeaa+ad++yaakha+vi+mg +lP
  gi|15668254|ref|NP_247047.1| 244 LCAGEAAIADFSYAAKHADVIQMGMILP 271
                                   *************************998 PP

>> MCR_alpha  Methyl-coenzyme M reductase alpha subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.6   9.8e+03      11      37 ..     282     308 ..     279     311 .. 0.82
   2 !  229.8   2.7   1.5e-72   8.8e-69       1     127 []     318     443 ..     318     443 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.6
                     MCR_alpha  11 GGvGftqyataaytdnilddfvyygvd 37 
                                   GGv f  +a    t  + dd +  +++
  gi|15668254|ref|NP_247047.1| 282 GGVPFGIFADIIQTSRVSDDPAQVTLE 308
                                   999999999999999999997766555 PP

  == domain 2  score: 229.8 bits;  conditional E-value: 1.5e-72
                     MCR_alpha   1 dqiwlGsymsGGvGftqyataaytdnilddfvyygvdyvkdkygglakvkatlevvkdiatevtlyaleqyekyptlledh 81 
                                   dq+wlGsymsGGvGftqya+a+ytd+ilddfvyyg+dyv++ky gl+ vk+++evvkdiatevtly+leqy++yp+lledh
  gi|15668254|ref|NP_247047.1| 318 DQVWLGSYMSGGVGFTQYASATYTDDILDDFVYYGMDYVEKKY-GLCGVKPSMEVVKDIATEVTLYGLEQYDEYPALLEDH 397
                                   9******************************************.799********************************** PP

                     MCR_alpha  82 fGGsqraavlaaaagistalatgnsnaGlngwylsmllhkeahsrl 127
                                   fGGsqra+v+aaaag+s+a+atgnsnaG+ngwyls++lhke hsrl
  gi|15668254|ref|NP_247047.1| 398 FGGSQRAGVTAAAAGCSVAFATGNSNAGINGWYLSQILHKEYHSRL 443
                                   *********************************************8 PP

>> MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.6e-05     0.097      25      53 ..      92     120 ..      81     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                    MCR_beta_N  25 lknpaikkivkdvkrtvavnlagiekalk 53 
                                    +n+ai+++v+d+krtv v ++   + l+
  gi|15668254|ref|NP_247047.1|  92 CNNAAIQQLVDDIKRTVIVGMDTAHAVLE 120
                                   68*****************9998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3430.58
//
Query:       gi|15668255|ref|NP_247048.1|  [L=249]
Description: CODH nickel-insertion accessory protein CooC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-14   52.6   0.2    7.3e-14   51.9   0.2    1.3  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    9.3e-08   31.8   0.4    2.9e-07   30.2   0.4    1.9  1  ParA          NUBPL iron-transfer P-loop NTPase
      8e-07   28.8   0.0    0.00032   20.3   0.0    2.1  2  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
    2.8e-06   27.3   1.0    9.4e-06   25.7   0.1    2.0  2  AAA_31        AAA domain
    1.1e-05   24.8   0.5    0.00024   20.4   0.0    2.5  2  ArsA_ATPase   Anion-transporting ATPase
    2.2e-05   24.0   2.0    0.00029   20.4   0.1    2.2  2  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    0.00012   22.0   0.0    0.00026   20.9   0.0    1.5  1  APS_kinase    Adenylylsulphate kinase
    0.00072   19.4   0.0     0.0024   17.6   0.0    1.7  1  AAA_15        AAA ATPase domain
    0.00092   18.5   0.1     0.0032   16.8   0.1    1.8  2  Zeta_toxin    Zeta toxin
     0.0016   18.7   1.1       0.29   11.4   0.0    3.3  2  TrkA_N        TrkA-N domain
     0.0039   17.7   0.5      0.011   16.2   0.5    1.9  1  AAA_18        AAA domain
     0.0046   16.7   0.1      0.026   14.3   0.1    2.1  2  AAA_24        AAA domain
     0.0059   15.9   0.0      0.015   14.6   0.0    1.7  2  MipZ          ATPase MipZ
     0.0062   16.3   0.0      0.041   13.7   0.0    2.1  2  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
     0.0069   16.2   0.0      0.012   15.4   0.0    1.4  1  PRK           Phosphoribulokinase / Uridine kinase family
     0.0081   16.6   0.0      0.023   15.1   0.0    1.8  2  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
       0.01   15.7   0.1       0.02   14.8   0.1    1.5  1  Rad17         Rad17 P-loop domain
      0.013   15.9   0.0      0.045   14.1   0.1    1.9  2  RNA_helicase  RNA helicase
      0.014   14.9   0.1      0.061   12.8   0.0    2.0  2  KTI12         Chromatin associated protein KTI12
      0.014   15.9   0.7      0.025   15.1   0.2    1.9  2  ABC_tran      ABC transporter
      0.015   15.4   1.1        3.6    7.7   0.0    2.5  2  MMR_HSR1      50S ribosome-binding GTPase
      0.015   15.4   0.2      0.015   15.4   0.2    2.5  3  DUF87         Helicase HerA, central domain
       0.02   14.7   0.2      0.045   13.6   0.0    1.7  2  Cofilin_ADF   Cofilin/tropomyosin-type actin-binding protein
      0.038   13.0   0.0      0.066   12.2   0.0    1.4  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.038   13.6   0.6       0.67    9.6   0.1    2.4  2  SRP54         SRP54-type protein, GTPase domain
      0.073   12.1   0.0        3.3    6.7   0.1    2.1  2  LpxK          Tetraacyldisaccharide-1-P 4'-kinase
       0.13   12.4   0.2        1.4    9.1   0.1    2.2  2  Roc           Ras of Complex, Roc, domain of DAPkinase
       0.17   11.6   0.1       0.33   10.7   0.1    1.5  1  IstB_IS21     IstB-like ATP binding protein
       0.26   10.8   1.1       0.75    9.3   1.1    2.0  1  GTP_EFTU      Elongation factor Tu GTP binding domain
       0.55    9.8   4.9        1.1    8.9   1.3    2.7  2  cobW          CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.2   1.2e-16   7.3e-14       6     125 ..       7     230 ..       3     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.2e-16
                                   SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH................................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                          CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep................................ 54 
                                   +kGG GK+++++ La+ +a++g++Vl++D D    +l+  + l +d+ +                                
  gi|15668255|ref|NP_247048.1|   7 GKGGCGKSSITTLLAKEFAKKGHNVLVIDGDESNLSLH--KLLGMDLPKdfieylggrkefmkklrekmdgkevelfegei 85 
                                   8****************************998855544..333333333668889999999******************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|15668255|ref|NP_247048.1|  86 sidslpkeylvekdnikllaigkihdfgegcacpmgallreflkslklkdkevvivdteagiehfgrgveggcdviiaiid 166
                                   ********************************************************************************* PP

                                   ...CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHT CS
                                   ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ...dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparg 125
                                        +rl++ +e++g+k+    k + +++n+vd e ++      le+++   +++v++vip +++++++   g
  gi|15668255|ref|NP_247048.1| 167 ptyESIRLSKKIEEIGEKL---GKKVYFIVNKVDDE-TKD---LILENVN---KDKVIAVIPNNKEIMKCGLMG 230
                                   ***6667777777777664...467*********98.233...3455566...899***********9987665 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.4   4.9e-10   2.9e-07      10      55 ..       6      51 ..       2     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4.9e-10
                          ParA 10 SgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee 55
                                   gKGG GKS++++ lA ++akkg++v ++D D    s+ +llg++ 
  gi|15668255|ref|NP_247048.1|  6 CGKGGCGKSSITTLLAKEFAKKGHNVLVIDGDESNLSLHKLLGMDL 51
                                  7*****************************************9875 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   5.4e-07   0.00032      10      43 ..       8      41 ..       2      60 .. 0.88
   2 !    6.6   0.0     0.008       4.8     103     158 ..     122     177 ..      94     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.4e-07
                      CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDlspdnl 43
                                  +GG+G++s+++ La+ + + g++vlviD   +nl
  gi|15668255|ref|NP_247048.1|  8 KGGCGKSSITTLLAKEFAKKGHNVLVIDGDESNL 41
                                  6***************************988886 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.008
                      CBP_BcsQ 103 eallaalkelk.eqyrwillDlpagasaltrellaladlvllvvepdanchvrLhqq 158
                                     l ++lk+lk ++ + +++D  ag ++  r +   +d+ ++++ p   + +rL ++
  gi|15668255|ref|NP_247048.1| 122 ALLREFLKSLKlKDKEVVIVDTEAGIEHFGRGVEGGCDVIIAIIDPTYES-IRLSKK 177
                                   5577889999989999******************************9876.777664 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   1.6e-08   9.4e-06       9     101 ..       7      98 ..       2     189 .. 0.66
   2 ?    0.8   0.5      0.67     4e+02      53      93 ..     183     226 ..     129     248 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.6e-08
                        AAA_31   9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevli.eeknikeaiiktkvenldlipssi 88 
                                    KGG GK+  ++ la+ +ak+g+ vL++D D  +n++ + ++   ++ k+++e l  +++ +k++  k + ++++l  ++i
  gi|15668255|ref|NP_247048.1|   7 GKGGCGKSSITTLLAKEFAKKGHNVLVIDGDE-SNLSLH-KLLGMDLPKDFIEYLGgRKEFMKKLREKMDGKEVELFEGEI 85 
                                   5******************************6.677773.33455666677777653455555555555566666666666 PP

                        AAA_31  89 dLaeaeielvele 101
                                   ++ ++ +e +  +
  gi|15668255|ref|NP_247048.1|  86 SIDSLPKEYLVEK 98 
                                   6666665543333 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.67
                        AAA_31  53 neiektlyevli.eeknikeaiiktkvenl..dlipssidLaea 93 
                                   +++ k++y +++  + ++k++i ++ +++    +ip + +++++
  gi|15668255|ref|NP_247048.1| 183 EKLGKKVYFIVNkVDDETKDLILENVNKDKviAVIPNNKEIMKC 226
                                   33556666666645667778887666444446788887777665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     4e-07   0.00024       4      38 ..       3      37 ..       1      79 [. 0.93
   2 ?    2.6   0.1      0.11        65     125     169 ..     158     203 ..     122     248 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4e-07
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                   ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                  i + GKGG GK+++ + +a + ++kg++vl+i  D
  gi|15668255|ref|NP_247048.1|  3 ISICGKGGCGKSSITTLLAKEFAKKGHNVLVIDGD 37
                                  6789****************************887 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                                   SSEEEEESBSCCHTCGGGGHHHHHHHHH.HHHHHHHHHHHHHHHHH CS
                   ArsA_ATPase 125 ydvvvlDtaPTGhtlrllslpevlekll.eklvklkeklsplakql 169
                                    dv++    PT +++rl +  e +++ l +k++ + +k+ + +k l
  gi|15668255|ref|NP_247048.1| 158 CDVIIAIIDPTYESIRLSKKIEEIGEKLgKKVYFIVNKVDDETKDL 203
                                   5888888889999999887666555555145555555554433333 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   4.9e-07   0.00029       1      59 [.       1      59 [.       1      88 [. 0.84
   2 ?    3.4   0.2     0.074        44     158     220 ..     171     229 ..     156     245 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.9e-07
                     Fer4_NifH  1 rkiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtl 59
                                  +ki+i GkGG Gks  ++ l++ +a++g+ vl++  D  + s + llg  + +  ++ l
  gi|15668255|ref|NP_247048.1|  1 MKISICGKGGCGKSSITTLLAKEFAKKGHNVLVIDGDESNLSLHKLLGMDLPKDFIEYL 59
                                  689*******************************9999888888888877777777666 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.074
                     Fer4_NifH 158 anniakgiekyaksggvrlgGliinsrkvdde.reliekfaeelgtkvlevvPrdeivrkaelr 220
                                   + +++k ie+  ++ g ++   i+n  kvdde ++li + +++   kv++v+P ++++ k  l 
  gi|15668255|ref|NP_247048.1| 171 SIRLSKKIEEIGEKLGKKVY-FIVN--KVDDEtKDLILENVNK--DKVIAVIPNNKEIMKCGLM 229
                                   55666777777666666654.4567..3555415676665554..6899999999999887665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   4.4e-07   0.00026       5      52 ..       3      50 ..       1      58 [. 0.92

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.4e-07
                                  EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SS CS
                    APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfs 52
                                  + + G  g GKs+i++ l+k+  +kg++v ++dGd+    L k Lg++
  gi|15668255|ref|NP_247048.1|  3 ISICGKGGCGKSSITTLLAKEFAKKGHNVLVIDGDESNLSLHKLLGMD 50
                                  668999*******************************99999999975 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     4e-06    0.0024      27      84 ..       4     199 ..       2     247 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4e-06
                        AAA_15  27 vliGkNnsGKSsilealdlFlnnkekkn................................kkvikiekedleifenisesk 75 
                                    ++Gk ++GKSsi+ +l + + +k  +n                                k+++k+  e+++ +e + ++ 
  gi|15668255|ref|NP_247048.1|   4 SICGKGGCGKSSITTLLAKEFAKK-GHNvlvidgdesnlslhkllgmdlpkdfieylggrKEFMKKLREKMDGKEVELFEG 83 
                                   59***************8877755.45588999999999999*****************9999999999999999999999 PP

                        AAA_15  76 dikIdvef......................................................................... 83 
                                   +i Id                                                                            
  gi|15668255|ref|NP_247048.1|  84 EISIDSLPkeylvekdnikllaigkihdfgegcacpmgallreflkslklkdkevvivdteagiehfgrgveggcdviiai 164
                                   999996554458888888888888888888888888888888888888887777777777777777777777777777776 PP

                        AAA_15  84 ..................................a 84 
                                                                     +
  gi|15668255|ref|NP_247048.1| 165 idptyesirlskkieeigeklgkkvyfivnkvddE 199
                                   66655554444444443333333333333333320 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   5.4e-06    0.0032      21      53 ..       5      38 ..       2      41 .. 0.92
   2 ?   -1.8   0.0       2.6   1.5e+03      48      66 ..     207     225 ..     165     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.4e-06
                    Zeta_toxin 21 lgGqpGAGKselaellkdele.rqgnvvrldpDd 53
                                  + G  G+GKs++ +ll++e++ ++ nv+++d+D+
  gi|15668255|ref|NP_247048.1|  5 ICGKGGCGKSSITTLLAKEFAkKGHNVLVIDGDE 38
                                  789*****************98999********7 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                    Zeta_toxin  48 rldpDdlRelhPeyeeilk 66 
                                    +++D++ + +P+ +ei+k
  gi|15668255|ref|NP_247048.1| 207 NVNKDKVIAVIPNNKEIMK 225
                                   4677777778888777776 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00049      0.29       4      36 ..      11      43 ..       3      53 .. 0.77
   2 ?    2.4   0.5      0.31   1.8e+02      63      90 ..     158     187 ..     122     216 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00049
                                  ES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHH CS
                        TrkA_N  4 iGlGrvGrslaeeLse.ggkdvvvidkdeervee 36
                                  +G + +++ la+e+ + g ++v+vid de+++  
  gi|15668255|ref|NP_247048.1| 11 CGKSSITTLLAKEFAKkG-HNVLVIDGDESNLSL 43
                                  666777788888888844.57********98765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.31
                                   ESEEEE-SSSHHHHHHHHHHHHHHTSS..S CS
                        TrkA_N  63 adaviaatgddeanilavllakelnpk..k 90 
                                   +d++ia ++   ++i +++ + e+ +k  k
  gi|15668255|ref|NP_247048.1| 158 CDVIIAIIDPTYESIRLSKKIEEIGEKlgK 187
                                   455555555556666666666666665553 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.5   1.9e-05     0.011       1      89 [.       3      97 ..       3     143 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.9e-05
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgf..........gvnlrdvakenglllevdpealdeskrldedkldklldaleenssalee 73
                                  I ++G+ G+GK++++  L+k+             g    ++++ + ll ++ p+++ e++  ++++++kl +++++    +  
  gi|15668255|ref|NP_247048.1|  3 ISICGKGGCGKSSITTLLAKEF-AkkghnvlvidG--DESNLSLHKLLGMDLPKDFIEYLGGRKEFMKKLREKMDGKEV-ELF 81
                                  779***************8884.135666788552..444555555555555555555555555555555555555543.222 PP

                        AAA_18 74 gknlvidghlaelese 89
                                  ++ + id+++ e++ e
  gi|15668255|ref|NP_247048.1| 82 EGEISIDSLPKEYLVE 97
                                  3334666666666554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   4.3e-05     0.026       4      60 ..       2      95 ..       1     143 [. 0.70
   2 ?    0.3   0.0       0.8   4.8e+02      22      36 ..     131     148 ..     123     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-05
                        AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie........swedfldevvel............ 59
                                  ki i G+ g GK+++ + l       g ++l+id +++  sl    + d++        + ++f++++ e             
  gi|15668255|ref|NP_247048.1|  2 KISICGKGGCGKSSITTLLakefakkGHNVLVIDGDESNLSLHKLLGMDLPkdfieylgGRKEFMKKLREKmdgkevelfege 84
                                  899*********99877777778**************9999888887777766666666555555555554555555555555 PP

                        AAA_24 60 ..........a 60
                                             
  gi|15668255|ref|NP_247048.1| 85 isidslpkeyL 95
                                  55555555553 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.8
                        AAA_24  22 l...gpkplfidtekGlk 36 
                                   l    ++++++dte+G  
  gi|15668255|ref|NP_247048.1| 131 LklkDKEVVIVDTEAGIE 148
                                   344568899999999986 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.5e-05     0.015       9      48 ..       8      47 ..       3      81 .. 0.94
   2 ?   -1.9   0.0       2.7   1.6e+03     103     130 ..     139     166 ..     124     205 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                                  STTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHH CS
                          MipZ  9 kGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryl 48
                                  kGG Gks ++  +a  ++kkG++v +id d    +l++ l
  gi|15668255|ref|NP_247048.1|  8 KGGCGKSSITTLLAKEFAKKGHNVLVIDGDESNLSLHKLL 47
                                  9*****************************9999999876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.7
                                   EEEE--SS--HHHHHHHHT-SEEEEEEE CS
                          MipZ 103 ividtPGsdsalsrlahsladtlvtPln 130
                                   +++dt    ++  r +    d +++ ++
  gi|15668255|ref|NP_247048.1| 139 VIVDTEAGIEHFGRGVEGGCDVIIAIID 166
                                   5555544444444444444444444333 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   6.8e-05     0.041       1      31 [.       7      37 ..       7      96 .. 0.85
   2 ?    0.5   0.0      0.75   4.5e+02      99     119 ..     132     152 ..     120     195 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.8e-05
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlD 31
                                  G+  +GKS++++lL+ + ++kg++++++D D
  gi|15668255|ref|NP_247048.1|  7 GKGGCGKSSITTLLAKEFAKKGHNVLVIDGD 37
                                  66689************************99 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.75
                        CLP1_P  99 kkakasgliIntpGwvkglga 119
                                   k   ++++i++t   ++ +g+
  gi|15668255|ref|NP_247048.1| 132 KLKDKEVVIVDTEAGIEHFGR 152
                                   334567777777777776654 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     2e-05     0.012       2      36 ..       3      37 ..       2      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
                           PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegd 36
                                  I+++g+ G+Gk++++  l k f++++ +  +i+gd
  gi|15668255|ref|NP_247048.1|  3 ISICGKGGCGKSSITTLLAKEFAKKGHNVLVIDGD 37
                                  9**********************988887777665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.9e-05     0.023      29      86 ..       5      60 ..       3     143 .. 0.58
   2 ?   -2.2   0.0       7.6   4.6e+03      43      76 ..     180     208 ..     175     243 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.9e-05
                        AAA_16 29 lsGesGvGKsslvrellralekdg..giflrgkcdqlesaipysalaqalareellrqll 86
                                  + G  G+GKss+ + l++++ k+g  ++++ g+   l    ++  l+ +   +++++ l+
  gi|15668255|ref|NP_247048.1|  5 ICGKGGCGKSSITTLLAKEFAKKGhnVLVIDGDESNL----SLHKLLGMDLPKDFIEYLG 60
                                  7799*******************52255555555555....3333222222223333333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.6
                        AAA_16  43 ellralekdggiflrgkcdqlesaipysalaqal 76 
                                   e+ + l k+ ++f+  k d+ ++++    +++  
  gi|15668255|ref|NP_247048.1| 180 EIGEKLGKK-VYFIVNKVDDETKDL----ILENV 208
                                   555566666.777777777764442....33333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   3.4e-05      0.02      50     152 ..       5     101 ..       2     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-05
                         Rad17  50 isGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqksdfkgltekesrflsqiesfkeleLkdakylklqklGddlr 130
                                   i+G  GCgks +   L+ke++ k ++ l  +   e++     ++g+   ++ f+  +   ke+ +k+ +  k++  G++++
  gi|15668255|ref|NP_247048.1|   5 ICGKGGCGKSSITTLLAKEFAKKGHNVL-VIDGDESNLSLHKLLGMDLPKD-FIEYLGGRKEF-MKKLRE-KMD--GKEVE 79 
                                   9*******************98876554.4443556668888899888888.99999999999.666666.555..99999 PP

                         Rad17 131 tdkklilvedlPnkfyrdsdal 152
                                        i ++ lP ++  + d++
  gi|15668255|ref|NP_247048.1|  80 LFEGEISIDSLPKEYLVEKDNI 101
                                   9888999999998887777665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   7.6e-05     0.045       1      26 [.       3      28 ..       3      45 .. 0.86
   2 ?   -2.3   0.0       9.7   5.8e+03      15      36 ..     120     141 ..     113     153 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.6e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                  i ++G+ g+GKS++++ Lak+++kk 
  gi|15668255|ref|NP_247048.1|  3 ISICGKGGCGKSSITTLLAKEFAKKG 28
                                  5699******************9765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.7
                  RNA_helicase  15 akeLakallkklklkkkdsvys 36 
                                   +  L +++lk+lklk k+ v++
  gi|15668255|ref|NP_247048.1| 120 MGALLREFLKSLKLKDKEVVIV 141
                                   5567788888887777666655 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0    0.0001     0.061       4      41 ..       3      40 ..       1      50 [. 0.88
   2 ?   -1.3   0.0         2   1.2e+03      67      79 ..     132     144 ..     124     151 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                                  EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                         KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41
                                  + ++G    GKs+++  Lak++++++ +v vid +  +
  gi|15668255|ref|NP_247048.1|  3 ISICGKGGCGKSSITTLLAKEFAKKGHNVLVIDGDESN 40
                                  569******************************66555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                                   HHTT.SEEEE-S- CS
                         KTI12  67 dLskekvVIvDsl 79 
                                   +L+ ++vVIvD  
  gi|15668255|ref|NP_247048.1| 132 KLKDKEVVIVDTE 144
                                   5777788888865 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.2   4.2e-05     0.025      13      43 ..       2      32 ..       1     145 [. 0.85
   2 ?   -1.2   0.0       4.4   2.6e+03      30      79 ..     160     207 ..     158     242 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.2e-05
                                  EEEEEESTTSSHHHHHHHHTTSS--SEEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeil 43
                                  k+ i G+ G+GKS++  lla++  ++  ++l
  gi|15668255|ref|NP_247048.1|  2 KISICGKGGCGKSSITTLLAKEFAKKGHNVL 32
                                  578******************9987666553 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4.4
                                   HHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                      ABC_tran  30 llagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren 79 
                                   +++   +pt ++i+l  k+++e   e+l k++ ++  + +   ++l + en
  gi|15668255|ref|NP_247048.1| 160 VIIAIIDPTYESIRLS-KKIEE-IGEKLGKKVYFIVNKvDDETKDL-ILEN 207
                                   5666667777777554.44444.45566666666666523333333.5555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2     0.022        13       1      26 [.       2      27 ..       2      34 .. 0.85
   2 ?    7.7   0.0     0.006       3.6      42     114 .]     132     195 ..     124     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.022
                                  EEEEEESTTSSHHHHHHHHHTSTEEE CS
                      MMR_HSR1  1 evaivGrpNvGKStLinaltgekaiv 26
                                  ++ i G+   GKS++   l +e a+ 
  gi|15668255|ref|NP_247048.1|  2 KISICGKGGCGKSSITTLLAKEFAKK 27
                                  5899************9999987665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.006
                                   EETTEEEEEEEC.GGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  42 klkgkeielvDt.pGliegaseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                   klk+ke+++vDt +G ie       +g+ ++    +d+i+ ++d + e   +l +++ee+ e+ +k++ +++nk
  gi|15668255|ref|NP_247048.1| 132 KLKDKEVVIVDTeAG-IE------HFGRGVEG--GCDVIIAIIDPTYE-SIRLSKKIEEIGEKLGKKVYFIVNK 195
                                   556778888888566.77......56666664..59********6644.4456688899988889999999998 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.2   2.5e-05     0.015      26      59 ..       3      35 ..       1      38 [. 0.94
   2 ?   -2.0   0.0       5.4   3.2e+03      41      59 ..     121     142 ..     115     149 .. 0.74
   3 ?    0.5   0.1      0.88   5.3e+02     187     221 ..     172     206 ..     159     220 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                         DUF87 26 lAilgsTGsGKSntvavLleellekkgatililD 59
                                  + i g+ G GKS  + +L +e + kkg ++l++D
  gi|15668255|ref|NP_247048.1|  3 ISICGKGGCGKSSITTLLAKEFA-KKGHNVLVID 35
                                  6899*******************.*********9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.4
                         DUF87  41 avLleelle...kkgatililD 59 
                                   + Ll+e l+    k+ +++i+D
  gi|15668255|ref|NP_247048.1| 121 GALLREFLKslkLKDKEVVIVD 142
                                   6677777776656666888888 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.88
                         DUF87 187 tdliallleklekegkitiidlsgvdelaqqlvvs 221
                                    +l ++++e+ ek gk + + +++vd+++++l+  
  gi|15668255|ref|NP_247048.1| 172 IRLSKKIEEIGEKLGKKVYFIVNKVDDETKDLILE 206
                                   45556666666666666666666666666666543 PP

>> Cofilin_ADF  Cofilin/tropomyosin-type actin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       7.4   4.4e+03      21      44 ..      34      59 ..      22      79 .. 0.51
   2 ?   13.6   0.0   7.5e-05     0.045      13     102 ..     157     241 ..     132     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.4
                                  EECTTTEEEEEE..SS-HHHHHHHHH CS
                   Cofilin_ADF 21 idddkeeivvee..egetyeelreel 44
                                  id+d+ ++ + +    +  ++++e l
  gi|15668255|ref|NP_247048.1| 34 IDGDESNLSLHKllGMDLPKDFIEYL 59
                                  44444455555533222333444433 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.5e-05
                                   .SSEEEEEEECTTTEEEEEESS-HHHHHHHHHHTTT-EEEEEEEEEECCS..ECCEEEEEEEEE--TTS-HHHHHHHHHHH CS
                   Cofilin_ADF  13 ktkyilfkidddkeeivveeegetyeelreelpeseprYavydveyehdd..eskrsklvfIswvPdsapikqkmlyassk 91 
                                    ++ i+  id+  e+i++++   ++ee+ e+l + ++ ++v +v+ e++d   ++ +k   I+ +P++   k+ m++  + 
  gi|15668255|ref|NP_247048.1| 157 GCDVIIAIIDPTYESIRLSK---KIEEIGEKLGK-KVYFIVNKVDDETKDliLENVNKDKVIAVIPNN---KEIMKCGLMG 230
                                   57889999**********99...6899999**88.9**************99778899999******9...5666666666 PP

                                   HHHHHHCTTSE CS
                   Cofilin_ADF  92 dalkkelkgis 102
                                   ++l  el++i+
  gi|15668255|ref|NP_247048.1| 231 EELNAELSEIK 241
                                   66666665555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011     0.066      31      67 ..       2      38 ..       1      48 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                  EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                          MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDP 67
                                  ++ + G  G Gks ++  l+ e++++G+ v v+  D 
  gi|15668255|ref|NP_247048.1|  2 KISICGKGGCGKSSITTLLAKEFAKKGHNVLVIDGDE 38
                                  57899*************************9997665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0011      0.67       4      38 ..       3      37 ..       1      41 [. 0.92
   2 ?    2.1   0.0      0.21   1.2e+02      72      93 ..     124     146 ..     109     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  i ++G  G GK + ++ La+ + k+g++vl++  D
  gi|15668255|ref|NP_247048.1|  3 ISICGKGGCGKSSITTLLAKEFAKKGHNVLVIDGD 37
                                  6689***************************9888 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.21
                                   HHHHHHHHHHTTSSEEEEEE.-- CS
                         SRP54  72 akeavekakeekidvvlvDT.aG 93 
                                   ++e +++ k ++ +vv+vDT aG
  gi|15668255|ref|NP_247048.1| 124 LREFLKSLKLKDKEVVIVDTeAG 146
                                   5667889999999******9455 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0055       3.3      46      71 ..       9      34 ..       6      35 .. 0.95
   2 ?    3.5   0.0     0.054        32     150     185 ..     104     142 ..      94     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0055
                                  S-HSHHHHHHHHHHHTTTS..-EEEE CS
                          LpxK 46 GGtGKTPlvialvkllqarglkvgvl 71
                                  GG GK +++  l+k ++++g +v v+
  gi|15668255|ref|NP_247048.1|  9 GGCGKSSITTLLAKEFAKKGHNVLVI 34
                                  9**********************998 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.054
                                   EEE..EHHHHC--BTTTSS.BSS-GG..GGGG-SEEEE. CS
                          LpxK 150 vvvdaergfgngrllPaGp.LREpls..rlkradlviln 185
                                   + + + + fg+g+  P G  LRE l+  +lk+ ++vi+ 
  gi|15668255|ref|NP_247048.1| 104 LAIGKIHDFGEGCACPMGAlLREFLKslKLKDKEVVIVD 142
                                   555566789*********746***994455566667764 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0024       1.4       1      35 [.       2      35 ..       2      50 .. 0.76
   2 ?    0.8   0.0       0.9   5.4e+02      81     119 ..     159     197 ..     135     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0024
                                  EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEE CS
                           Roc  1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvd 35
                                  K+ ++G++g GK+s+ + +  ++f +k ++ + +d
  gi|15668255|ref|NP_247048.1|  2 KISICGKGGCGKSSITTLLA-KEFAKKGHNVLVID 35
                                  899***********987666.66766666555555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.9
                                   CEEEEEEEGH.HHHCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                           Roc  81 alailvydsr.ssenlkeWlkelkkvagkspvilvgnkiD 119
                                   +++i+++d + +s +l++ ++e+ ++ gk++ ++ +nk+D
  gi|15668255|ref|NP_247048.1| 159 DVIIAIIDPTyESIRLSKKIEEIGEKLGKKVYFI-VNKVD 197
                                   6788888855245678888999988888776655.58887 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00055      0.33      50      80 ..       3      33 ..       1      44 [. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00055
                     IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvlf 80
                                  i ++G  G GKs +++ l++e +++g++vl 
  gi|15668255|ref|NP_247048.1|  3 ISICGKGGCGKSSITTLLAKEFAKKGHNVLV 33
                                  679*************************985 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.1    0.0013      0.75      66     139 ..     132     203 ..       1     240 [. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0013
                                   TCSSEEEEEEEE.SSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHH CS
                      GTP_EFTU  66 etkkylinliDt.PGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkael 139
                                   + k++++ ++Dt  G + F + v+ g   +D+ + ++d +      ++++ ++  k+g ++ +++NK+D   ++l
  gi|15668255|ref|NP_247048.1| 132 KLKDKEVVIVDTeAGIEHFGRGVEGG---CDVIIAIIDPTYESIRLSKKIEEIGEKLGKKVYFIVNKVDDETKDL 203
                                   68899999999977999999999988...89**************************************985544 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.41   2.4e+02       4      38 ..       4      40 ..       1      47 [. 0.66
   2 ?    8.9   1.3    0.0018       1.1      16     163 ..      65     209 ..      57     225 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.41
                                  EEEESTTCCH...HHHHHHHHCT--SS-EEEEESS-SS CS
                          cobW  4 vltGflGsGK...TtLlnhllenraglklavivNefge 38
                                   ++G  G GK   TtLl +  + ++g ++ vi ++ ++
  gi|15668255|ref|NP_247048.1|  4 SICGKGGCGKssiTTLLAKEFA-KKGHNVLVIDGDESN 40
                                  68899999**444455554443.477788888877665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0018
                                   HHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCCCT........EEEETTTTECCHCTT-HHHHHHHHHHHHTT-SEEEEE CS
                          cobW  16 LlnhllenraglklavivNefgevsiDaellretgve.......ivelenGciCctlredllkelealeereerldviliE 89 
                                   ++++l e+ +g+++ + ++e++  s+ +e l e+++        i ++ +Gc C      ll+e+ + ++++ + +v+++ 
  gi|15668255|ref|NP_247048.1|  65 FMKKLREKMDGKEVELFEGEISIDSLPKEYLVEKDNIkllaigkIHDFGEGCACPM--GALLREFLKSLKLK-DKEVVIVD 142
                                   56666677777777888888776666666665553334677778888889999888..77777777777777.67778777 PP

                                   E.CTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHH CS
                          cobW  90 t.tGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekle 163
                                   t  G+ +             +   d+++a++D +  + + +k+ e+++++l +   +++nK+D  +++  le+++
  gi|15668255|ref|NP_247048.1| 143 TeAGIEHFGRG--------VEGGCDVIIAIIDPTYESIRLSKKIEEIGEKLGKKVYFIVNKVDDETKDLILENVN 209
                                   62456554443........3778999******9766778889999999999999*********887774445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      703  (0.0392102); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 1513.98
//
Query:       gi|15668256|ref|NP_247049.1|  [L=373]
Description: iron transport periplasmic binding protein CeuE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-25   90.5   0.0    1.7e-25   89.9   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.0   9.7e-30   1.7e-25       1     234 [.      59     305 ..      59     308 .. 0.87

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 9.7e-30
                                   EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT.........TS-BSBESS...SB-HHHHHHH--SEEEE-GGG.. CS
                  Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee.......aivevgadg...eidvEklaalkPDlvilskglgl 71 
                                   i++ +p+  ++ + l atdkvvgv+ t + +++  +          + +++g++g    ++ E+++++kPD++++ ++   
  gi|15668256|ref|NP_247049.1|  59 IVCCGPGCLRLIVYLNATDKVVGVEDTEKKWTPWTRPYRiahpelaNLPTIGQGGpcpKPNPEAIIQVKPDVIFVTYMP-K 138
                                   89999999999999**********99999988887544355565664444444442225555*****************.9 PP

                                   .GGGHHHHHHHS-EEE----TTS....HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT....-EEEEEEEE CS
                  Peripla_BP_2  72 tdedeellksgiptvivessntg....eslkeqiralgellgledeaeklvaeidsklaaaksaidse...kpkpvlvfgg 145
                                    + d  ++k gip+v+  +++ +    e+l ++++  g++lg+e++a++++++i++   +++++++ +   k++ v v g 
  gi|15668256|ref|NP_247049.1| 139 DEVDALQQKTGIPVVVLSYGQLAtfnnEDLFKSLELAGKILGKEERAKEVIEFIKNCQNDLNERTKDIpddKKPSVYVGGI 219
                                   9999999************998799***************************************99999767777777777 PP

                                   TTE..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-S.HHHHTSHH CS
                  Peripla_BP_2 146 adeggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflken.pllaelpA 225
                                   +++g + + ++ +   +++  ++++n+a+e +k++   +  Eqil+++pd+if++       k ++e+ k+n + +++l+A
  gi|15668256|ref|NP_247049.1| 220 GYKGLHGIDSTECKYPPFVA-VNAKNVADELGKEGHVFVTKEQILKWNPDIIFIDEG---GLKLVVEDYKRNkEFYNSLKA 296
                                   88899999999999999999.**********9***********************99...************5556777** PP

                                   HHTT-EEEE CS
                  Peripla_BP_2 226 vkngrVyal 234
                                   +kng+Vy+l
  gi|15668256|ref|NP_247049.1| 297 FKNGDVYGL 305
                                   *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2351.54
//
Query:       gi|15668257|ref|NP_247050.1|  [L=372]
Description: methyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-12   44.8   0.0    1.5e-11   44.0   0.0    1.4  1  Methyltransf_2   O-methyltransferase domain
      3e-07   30.3   0.1    5.9e-07   29.4   0.1    1.5  1  Dimerisation2    Dimerisation domain
     0.0019   18.0   0.0     0.0032   17.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.015   15.2   0.5      0.046   13.7   0.5    1.8  1  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
       0.04   14.6   0.0        0.1   13.3   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
      0.075   13.8   0.0       0.31   11.8   0.0    2.2  1  Methyltransf_12  Methyltransferase domain
      0.094   12.6   0.0        3.7    7.5   0.0    2.5  2  PASTA            PASTA domain
       0.27   11.3   1.2       0.48   10.5   0.1    2.0  2  Dimerisation     Dimerisation domain


Domain annotation for each model (and alignments):
>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   6.7e-15   1.5e-11      51     161 ..     156     267 ..     131     292 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 6.7e-15
                                   HHHHHH...SS-.GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS-----TTEEEEES-TTTS---- CS
                Methyltransf_2  51 akkvle...afd.leglkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehlsageeervefvgGdffkdslPe 127
                                    +kvl+   +++ +++ k+l+D+ GG G  a   + +  ++k+ vfDlp+V+e+ k++++  ++++v  + Gdf+kd + +
  gi|15668257|ref|NP_247050.1| 156 LQKVLNymaKYEeFKNAKKLLDLAGGHGLYAIGFSMLNRNLKCYVFDLPNVIEETKKFIKKYNAKNVFTITGDFYKDDIGK 236
                                   45555411155579999**************************************************************98 PP

                                   -SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-E CS
                Methyltransf_2 128 aDaillkrvlhDwsdekcvklLkrvkkalpagGk 161
                                   +  i++ +       +k  k+ ++v++al++gG 
  gi|15668257|ref|NP_247050.1| 237 GYDIIFCS---YNPGGKNPKIAEKVYNALNEGGL 267
                                   75555433...23456677777788888877775 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   2.6e-10   5.9e-07      15      89 ..      30     101 ..      21     102 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.6e-10
                 Dimerisation2  15 LftAceLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntelastyLvsssp 89 
                                   L tA +L++F+ L +   ++a+e+ae l+a++  +e +l+ +  L+L e++  +e +  Y+n+e+++ yL ++s+
  gi|15668257|ref|NP_247050.1|  30 LRTAIDLNLFEYLSS--FKTAKELAEILDADLILMEYMLKILNELDLIESKVVSE-RIYYKNAEITNIYLKKDSN 101
                                   779**********98..999*****************************886666.59**************996 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.4e-06    0.0032      63     170 ..     161     269 ..     155     273 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                                   HHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SE CS
                          PCMT  63 alalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPY 143
                                    ++ ++ e+k+ ++ L++ +G G  +  +++l ++      +   ++++ee+k+ +kk +++nv +++gD +k       Y
  gi|15668257|ref|NP_247050.1| 161 NYMAKYEEFKNAKKLLDLAGGHGLYAIGFSMLNRNLK--CYVFDLPNVIEETKKFIKKYNAKNVFTITGDFYKDDI-GKGY 238
                                   56788889***************99998887765543..567789*************************998644.457* PP

                                   EEEEES....SBBSS--HHHHHTEEEEEEEE CS
                          PCMT 144 daihvg....aaapeiPealidQLkeGGrlv 170
                                   d i+ +       p+i e+  + L+eGG ++
  gi|15668257|ref|NP_247050.1| 239 DIIFCSynpgGKNPKIAEKVYNALNEGGLFI 269
                                   ***996221145799************9765 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   2.1e-05     0.046      54      96 ..      46      89 ..      38     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
               Phage_rep_org_N 54 ytaemlalifnreletvrlaLkvlkdleliei.sedkvikiknw 96
                                   ta++la i++ +l  ++ +Lk+l++l lie  + ++ i+ kn 
  gi|15668257|ref|NP_247050.1| 46 KTAKELAEILDADLILMEYMLKILNELDLIESkVVSERIYYKNA 89
                                  589****************************8656777777775 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-05       0.1       2      97 .]     176     266 ..     175     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                                   EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
               Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                   Ldl+ G+G +++ ++    + k + +D+ ++ +e++++ +++ ++ nv  ++gd+ + +  +  +D++++s++    +  +
  gi|15668257|ref|NP_247050.1| 176 LDLAGGHGLYAIGFSMLNRNLKCYVFDL-PNVIEETKKFIKKYNAkNVFTITGDFYKDDIGK-GYDIIFCSYN----PGGK 250
                                   9**********999987558*******9.8999*******998888999******9988665.9******855....6667 PP

                                   HHHHHHHHHHHEEEEE CS
               Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                    +k+ ++++++L++gG
  gi|15668257|ref|NP_247050.1| 251 NPKIAEKVYNALNEGG 266
                                   7899999999999998 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.31       1      97 [.     176     266 ..     176     268 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                   L++ +G G ++  +   +++++ ++ D+ p++ie +k+ ++k++++n+  ++ +      +d g+ +D++++s       +
  gi|15668257|ref|NP_247050.1| 176 LDLAGGHGLYAIGFSMLNRNLKCYVFDL-PNVIEETKKFIKKYNAKNVFTITGDFYK---DDIGKGYDIIFCSYNPGG--K 250
                                   899************************9.8999777777777777666666666655...455679*****9964443..3 PP

               Methyltransf_12  82 irevldnirklLkpgG 97 
                                     ++ ++++++L+ gG
  gi|15668257|ref|NP_247050.1| 251 NPKIAEKVYNALNEGG 266
                                   4455666666666666 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0016       3.7       3      52 ..     203     252 ..     201     259 .. 0.82
   2 ?    2.4   0.0     0.063   1.4e+02       9      25 ..     311     327 ..     307     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0016
                                   --TTTTSBHHHHHHHHHHTT--CCCEEEECTCCGTTB.EEEECS-TTSEEC CS
                         PASTA   3 vPdvtGmsvdeAkatLkalGlkiktveetsddvpeGt.VisQsPeaGtevs 52 
                                    P+v+  +++  k+   ++ ++i+++  + dd+++G+ +i  s ++G + +
  gi|15668257|ref|NP_247050.1| 203 LPNVIEETKKFIKKYNAKNVFTITGDF-YKDDIGKGYdIIFCSYNPGGKNP 252
                                   688888888888888888888777777.99*****************8865 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.063
                                   SBHHHHHHHHHHTT--C CS
                         PASTA   9 msvdeAkatLkalGlki 25 
                                   +++ ++ + L++lG+ki
  gi|15668257|ref|NP_247050.1| 311 LNLNDYLKYLEDLGFKI 327
                                   57789**********76 PP

>> Dimerisation  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00021      0.48       2      33 ..      29      56 ..      28      61 .. 0.87
   2 ?   -3.0   0.1       3.6     8e+03       2      13 ..      65      76 ..      64      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00021
                  Dimerisation  2 vLKaAiELglldiiakaggkplspsEiaskLp 33
                                   L++Ai+L+l++ + +      +++E+a++L 
  gi|15668257|ref|NP_247050.1| 29 LLRTAIDLNLFEYLSSFK----TAKELAEILD 56
                                  69************9876....9999998885 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.6
                  Dimerisation  2 vLKaAiELglld 13
                                  +LK   EL+l++
  gi|15668257|ref|NP_247050.1| 65 MLKILNELDLIE 76
                                  588888999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2276.85
//
Query:       gi|15668258|ref|NP_247051.1|  [L=349]
Description: hemin permease HemU [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-99  330.4  34.3      1e-98  330.2  34.3    1.0  1  FecCD            FecCD transport family
    3.3e-06   26.8  20.6    3.3e-06   26.8  20.6    1.6  2  ABC-3            ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.2  34.3  1.2e-102     1e-98       2     312 .]      25     344 ..      20     344 .. 0.98

  Alignments for each domain:
  == domain 1  score: 330.2 bits;  conditional E-value: 1.2e-102
                         FecCD   2 lllllllslllgavkispsevfeallgkadsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilGissg 82 
                                   l+l+ +++l++g++k+++ +v++al+g +++  + +++++rlpr++aa+++G++LavaGa++Q ++rNpLa+P ++Gis+g
  gi|15668258|ref|NP_247051.1|  25 LFLSSIYALCVGDYKLTVNQVVNALMGYGKDDINLVIWNIRLPRIFAAIISGMSLAVAGAVMQCILRNPLASPFTMGISHG 105
                                   455677789************************************************************************ PP

                         FecCD  83 aalgavlallll..........lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllll 153
                                   a++ga++a++++          ++  + + ++++aflgal++++++llla k +g +p+ +iLaG+a+s+l++a t+l+++
  gi|15668258|ref|NP_247051.1| 106 AMFGACFAIIMFgfggaestgrIFINNPYMITIFAFLGALIGVVVILLLA-KLRGLTPEAMILAGVAMSSLFTAGTMLIQY 185
                                   *********************99999************************.****************************** PP

                         FecCD 154 llneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltav 234
                                   ++++ +l+++++w++G+l++a w+++++++++++ +l+++++ + ++++l+ g+etAkslGvn+er+rl+ +l+++llt+v
  gi|15668258|ref|NP_247051.1| 186 FADDLQLAAMVYWTFGDLGRAIWTEIYIMAAVMIPSLIYFMYKRWDYNALEAGEETAKSLGVNTERTRLIGMLVASLLTSV 266
                                   ********************************************************************************* PP

                         FecCD 235 avalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiylllr 312
                                    va+ G+igFvGLi Phi+r+++g d+r l+p+sal+Ga+lll+ad++ar++++p+ lpvgi+t+++Gap+f+ylll+
  gi|15668258|ref|NP_247051.1| 267 NVAFLGIIGFVGLICPHIVRICIGGDYRFLIPISALFGAVLLLIADTFARTIIAPIVLPVGILTSFLGAPMFLYLLLK 344
                                   ***************************************************************************986 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.49   4.4e+03     117     195 ..      18      25 ..      12      41 .. 0.55
   2 !   26.8  20.6   3.7e-10   3.3e-06       5     226 ..      69     309 ..      65     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.49
                         ABC-3 117 GniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviLvial 195
                                   G i                                                                       L+i+l
  gi|15668258|ref|NP_247051.1|  18 GII-----------------------------------------------------------------------LLITL 25 
                                   322.......................................................................22222 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 3.7e-10
                         ABC-3   5 lqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvn................lllgailvgliaav 69 
                                   ++ a++ ++ +++a a++ + +    +s +  ++sH a+ G ++a+++                   +++ a+l +li+ v
  gi|15668258|ref|NP_247051.1|  69 IFAAIISGMSLAVAGAVMQCILRNPLASPFTMGISHGAMFGACFAIIMFGFggaestgrifinnpymITIFAFLGALIGVV 149
                                   7889999************9999999*******************876544478999*******987788888999***** PP

                         ABC-3  70 alellkrktklkedtai..givlsvflalglvlvslikk..skvdldsyLfGniltisqedliliaiieavvllllllfwk 146
                                   ++ ll++   l  +++i  g+ +s+ +  g +l+++  +    + +  + fG++     ++++++a++ +  l+++++++ 
  gi|15668258|ref|NP_247051.1| 150 VILLLAKLRGLTPEAMIlaGVAMSSLFTAGTMLIQYFADdlQLAAMVYWTFGDLGRAIWTEIYIMAAVMIPSLIYFMYKRW 230
                                   *******999999986555*****************99885445555668******************************* PP

                         ABC-3 147 elllitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvv 226
                                   +  ++   ee+Ak+ g+++++ +l+ +++ +l  +v + + G+i  +  li P ++ + ++ + + l+ +++l+g+v ++
  gi|15668258|ref|NP_247051.1| 231 DYNALEAGEETAKSLGVNTERTRLIGMLVASLLTSVNVAFLGIIGFVG-LICPHIVRICIGGDYRFLIPISALFGAVLLL 309
                                   ******************************************998887.589****999999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2073.72
//
Query:       gi|15668259|ref|NP_247052.1|  [L=180]
Description: hypothetical protein MJ_0088 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1073.60
//
Query:       gi|15668260|ref|NP_247053.1|  [L=254]
Description: ferric enterobactin transport ATP-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-34  119.7   0.0    1.6e-34  119.3   0.0    1.1  1  ABC_tran     ABC transporter
    1.6e-07   31.5   3.5     0.0074   16.1   0.1    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    6.9e-05   22.4   3.3    0.00037   20.0   3.3    1.9  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00011   21.9   0.0    0.00022   20.9   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00065   20.1   0.0    0.00084   19.8   0.0    1.4  1  AAA_16       AAA ATPase domain
    0.00074   20.1   0.6     0.0011   19.5   0.5    1.5  1  AAA_23       AAA domain
     0.0012   18.9   0.8      0.029   14.4   0.0    2.2  2  AAA_14       AAA domain
     0.0015   18.3   7.6     0.0024   17.7   1.8    2.1  2  AAA_15       AAA ATPase domain
     0.0015   17.6   0.0     0.0024   16.9   0.0    1.2  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0063   16.4   0.1      0.014   15.3   0.1    1.5  1  RsgA_GTPase  RsgA GTPase
     0.0067   16.7   3.3       0.16   12.2   3.3    2.2  1  AAA_22       AAA domain
     0.0092   14.8   1.4       0.61    8.8   0.0    2.8  2  ABC_ATPase   Predicted ATPase of the ABC class
  ------ inclusion threshold ------
      0.042   13.4   0.0      0.068   12.8   0.0    1.2  1  AAA_27       AAA domain
      0.043   13.1   0.0       0.07   12.4   0.0    1.3  1  Zeta_toxin   Zeta toxin
       0.05   12.8   1.9       0.16   11.1   1.9    1.9  1  NB-ARC       NB-ARC domain
      0.073   12.8   0.0       0.13   11.9   0.0    1.4  2  AAA_30       AAA domain
      0.087   12.9   0.8       0.17   11.9   0.3    1.5  1  DUF87        Helicase HerA, central domain
        0.1   13.1   0.3        1.3    9.5   0.0    2.2  2  AAA_18       AAA domain
       0.13   12.5   0.0        1.4    9.2   0.0    2.1  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.19   11.7   0.1       0.48   10.3   0.0    1.7  2  NACHT        NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.3   0.0   1.8e-37   1.6e-34       1     137 []      21     167 ..      21     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 1.8e-37
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+n+++++k+ge+v i+G nGaGKStLlk++ + lkp+ G+il+d+ d+k+ +  +l k++g++pq ++ ++ + v +   
  gi|15668260|ref|NP_247053.1|  21 LNNIKFEVKRGEVVSILGVNGAGKSTLLKCINKILKPKRGTILIDNFDIKNLDNLELAKKVGYVPQRAEGNYMT-VFDAvl 100
                                   79*************************************************9999************8777777.999999 PP

                                   ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                              sd++ie  ++ l+l +l+d  + + +++LSgG+ q+v +aral+++p++lllDEpt+
  gi|15668260|ref|NP_247053.1| 101 lgrkphikweVSDRDIEITHKVLKLLNLEDYAL-RYTNELSGGELQKVIIARALVQEPQILLLDEPTN 167
                                   9999**999767777777777777777666665.667******************************8 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.7   8.6e-06    0.0077       4      60 ..      36      75 ..      33     122 .. 0.63
   2 !   16.1   0.1   8.3e-06    0.0074     227     290 ..     129     187 ..     108     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.6e-06
                        AAA_21  4 liGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfef 60
                                  + G Ng+GKS+LL+++  +             l    +++  + l+d+ d++  +++
  gi|15668260|ref|NP_247053.1| 36 ILGVNGAGKSTLLKCINKI-------------L----KPKRGTILIDNFDIKNLDNL 75
                                  89**************433.............3....44444444444444444443 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 8.3e-06
                        AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrnga 290
                                   +d+  +  +elS G ++   ++ al + +    +ll+DEp n+L+ k + ++++++ + s+  +
  gi|15668260|ref|NP_247053.1| 129 EDYALRYTNELSGGELQKVIIARALVQEP---QILLLDEPTNNLDLKNQLEVMKIIMDISK--S 187
                                   45555556678999999955555555555...9*************999999999955554..3 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   3.3   4.2e-07   0.00037      25     200 ..      32     200 ..      14     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.2e-07
                                   SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEE.EEEEEEETTEESSSSSSCEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkae.veitfdnedkklkiekeevsisrr 102
                                   ++ +i+G NG+GKs ll  i        +k l+ ++ + li +   k+ ++++ a+ v  + +  +     +   v   + 
  gi|15668260|ref|NP_247053.1|  32 EVVSILGVNGAGKSTLLKCI--------NKILKPKRGTILIDNfdIKNLDNLELAKkVGYVPQRAEG----NYMTVFDAVL 100
                                   5789****************........5689999******99554555555555413332233333....3333333444 PP

                                   EETTSEEEEEETTEEE-H.HHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 103 vkrkgeseykingkevtk.kevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                   + rk + ++++ +++++  ++v +ll+ ++    + ++LSgGe +     +++A   v+   + llDe   +LD kn  +v
  gi|15668260|ref|NP_247053.1| 101 LGRKPHIKWEVSDRDIEItHKVLKLLNLEDYalrYTNELSGGELQK----VIIARALVQEPQILLLDEPTNNLDLKNQLEV 177
                                   45555577778888887767888888766541125689****9653....34455556777899***************** PP

                                   HHHHH..HHCTTSEEEEE-SSHH CS
                                   xxxxx..xxxxxxxxxxxxxxxx RF
                         SMC_N 180 aellk..eksknaQfivislree 200
                                    +++   +ks+n   iv+ ++ +
  gi|15668260|ref|NP_247053.1| 178 MKIIMdiSKSQNIASIVVMHDLN 200
                                   ****9455556666777777655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.4e-07   0.00022      16      50 ..      25      59 ..      19      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.4e-07
                        AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                  ++e+++ +++ + G +G+GKSTll  i+ +L p++
  gi|15668260|ref|NP_247053.1| 25 KFEVKRGEVVSILGVNGAGKSTLLKCINKILKPKR 59
                                  567776669**********************9986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   9.3e-07   0.00084      11      61 ..      19      68 ..      12     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.3e-07
                        AAA_16 11 qLlsale.rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcd 61
                                  q+l+ ++  v++g  e+v + G  G GKs+l++++ + l+ ++g  l  ++d
  gi|15668260|ref|NP_247053.1| 19 QILNNIKfEVKRG--EVVSILGVNGAGKSTLLKCINKILKPKRGTILIDNFD 68
                                  4566666577777..89*******************9999997666555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.5   1.2e-06    0.0011      15      43 ..      24      55 ..      15     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-06
                        AAA_23 15 idF...skgltlItGpNGaGKTTildAiklaL 43
                                  i F      ++ I G NGaGK+T+l +i  +L
  gi|15668260|ref|NP_247053.1| 24 IKFevkRGEVVSILGVNGAGKSTLLKCINKIL 55
                                  445444446899****************8655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.2e-05     0.029       3      71 ..      32      97 ..      30     101 .. 0.64
   2 ?    3.0   0.2      0.11        97      35      82 ..     125     174 ..     110     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyi.nldderdkkladpekllelileklkeekktylflD 71
                                  +++ i G+  +GK+tllk + ++ l +k+ ++ i n+d +++++l+   k   ++ +++  e++++ ++D
  gi|15668260|ref|NP_247053.1| 32 EVVSILGVNGAGKSTLLKCI-NKILKPKRGTILIdNFDIKNLDNLELA-KKVGYVPQRA--EGNYMTVFD 97
                                  7899************8655.555535555555526776666665544.3444555543..367778887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                        AAA_14  35 yinldderdkkladpe..kllelilek.lkeekktylflDEiqevpeweka 82 
                                    +nl+d  ++  ++ +  +l ++i ++ l + + ++l+lDE  +  ++++ 
  gi|15668260|ref|NP_247053.1| 125 LLNLEDYALRYTNELSggELQKVIIARaLVQ-EPQILLLDEPTNNLDLKNQ 174
                                   5788888887666555667888888874444.8999*****8876444443 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.8   2.6e-06    0.0024      24      75 ..      31      79 ..      18      82 .. 0.82
   2 ?    4.0   0.4     0.038        34     322     356 ..     155     189 ..     145     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.6e-06
                        AAA_15 24 e.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenisesk 75
                                    +  + G N++GKS++l+ ++++l+ k      +i i++ d+++ +n +  k
  gi|15668260|ref|NP_247053.1| 31 GeVVSILGVNGAGKSTLLKCINKILKPK----RGTILIDNFDIKNLDNLELAK 79
                                  2488999********************9....899999999999999887666 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.038
                        AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnk 356
                                   +++ ill++EP ++L  ++q +++k + +++++ +
  gi|15668260|ref|NP_247053.1| 155 QEPQILLLDEPTNNLDLKNQLEVMKIIMDISKSQN 189
                                   4679***************************9876 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.6e-06    0.0024      14      54 ..      16      56 ..       5      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-06
                                  HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHH CS
                          MeaB 14 eakellerllakaGraqvvGltGvPGaGkstlvealglelr 54
                                  +++++l+++  +  r +vv + Gv GaGkstl++ +   l+
  gi|15668260|ref|NP_247053.1| 16 KSRQILNNIKFEVKRGEVVSILGVNGAGKSTLLKCINKILK 56
                                  799*****************************998877665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.5e-05     0.014      84     122 ..      15      54 ..       4      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                                   TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  84 aktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                    k+++ l+++k ++k  +++ ++G  G+GKStL++ ++  
  gi|15668260|ref|NP_247053.1|  15 YKSRQILNNIKFEVKRgEVVSILGVNGAGKSTLLKCINKI 54 
                                   56678899999999988****************9988764 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   3.3   0.00018      0.16       6     130 ..      32     197 ..      27     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee....................................erpevv......f 44 
                                    ++ + G  G+GK+tll+ + + l+      +                                     ++  v      +
  gi|15668260|ref|NP_247053.1|  32 EVVSILGVNGAGKSTLLKCINKILKPK----RgtilidnfdiknldnlelakkvgyvpqraegnymtvFDA--VllgrkpH 106
                                   56789999*************999543....2335699999999999999988888888888877755222..13355556 PP

                        AAA_22  45 vtlpsstsskdllrellralglelkaerlsseellealeqalrarav...ielliiDEaqh.lrs.eealeeLrsllnl.s 119
                                   ++  +s    ++ +++l+ l+le  a r ++e     l++ + ara    +++l++DE  + l   +++le  ++++++ +
  gi|15668260|ref|NP_247053.1| 107 IKWEVSDRDIEITHKVLKLLNLEDYALRYTNELSGGELQKVIIARALvqePQILLLDEPTNnL-DlKNQLEVMKIIMDIsK 186
                                   6666666668889999999999999855555555588888888888889999******99999.55777777777777776 PP

                        AAA_22 120 rkgvqliLvGt 130
                                   +++++ i+v +
  gi|15668260|ref|NP_247053.1| 187 SQNIASIVVMH 197
                                   88888887765 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00068      0.61     242     266 ..      28      53 ..      19      57 .. 0.92
   2 ?    3.6   0.3     0.026        23     324     412 ..     140     213 ..     117     220 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00068
                                   E-SS.EEEEEE-TTSSHHHHHHHHHH CS
                    ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAlek 266
                                   +++G v+ I G +  GKsTLL+ ++k
  gi|15668260|ref|NP_247053.1|  28 VKRGeVVSILGVNGAGKSTLLKCINK 53 
                                   78999*****************9975 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.026
                                   -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTTT CS
                    ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgdyldv 404
                                   SG   q + i++al  + ++lL+DE t    l  + e               +++ ++++ k+ ++ +i+v+  ++  l+ 
  gi|15668260|ref|NP_247053.1| 140 SGGELQKVIIARALVQEPQILLLDEPTNNLDLKNQLE---------------VMKIIMDISKSQNIASIVVMHDLNLALRY 205
                                   6666666666666666666666666543222222111...............24556666666667777777777777777 PP

                                   -SEEEEEE CS
                    ABC_ATPase 405 Adtvilme 412
                                   +d+ i+++
  gi|15668260|ref|NP_247053.1| 206 SDKFIMLK 213
                                   77666665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.6e-05     0.068      18      50 ..      23      55 ..      21      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.6e-05
                        AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                  +++f+ ++ ++  i+G N AGKst+l+ i+++l
  gi|15668260|ref|NP_247053.1| 23 NIKFEVKRGEVVSILGVNGAGKSTLLKCINKIL 55
                                  5789999999999**************999876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.8e-05      0.07      12      56 ..      27      71 ..      17      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.8e-05
                    Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56
                                  + +r  ++ + G  GAGKs+l++ +++ l+++++ + +d  d+++
  gi|15668260|ref|NP_247053.1| 27 EVKRGEVVSILGVNGAGKSTLLKCINKILKPKRGTILIDNFDIKN 71
                                  5567778888899*************************9988876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.9   0.00018      0.16      21      79 ..      32     129 ..      15     196 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                                   EEEEEEESTTSSHHHHHHHHCCSHCCCCC.....CBTEEEEE.....................................EE CS
                        NB-ARC  21 lvvalvGmgGvGKttlakqilnksdeveg.....rFdsvawv.....................................vv 59 
                                    vv++ G  G GK+tl+k i++ ++  +g     +Fd+   +                                      v
  gi|15668260|ref|NP_247053.1|  32 EVVSILGVNGAGKSTLLKCINKILKPKRGtilidNFDIKN-LdnlelakkvgyvpqraegnymtvfdavllgrkphikwEV 111
                                   59****************9998765444311111444322.1344555555555555555555555555555555555555 PP

                                   ESXXHHHHHHHXXHHHHHCC CS
                        NB-ARC  60 sktdkseeiletilkeLsls 79 
                                   s+ d   ei++++lk L+l+
  gi|15668260|ref|NP_247053.1| 112 SDRD--IEITHKVLKLLNLE 129
                                   5443..34555555555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00015      0.13      18      49 ..      31      62 ..      19      92 .. 0.87
   2 ?   -3.1   0.0       5.9   5.3e+03      81      97 ..     142     165 ..     113     185 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                        AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrv 49
                                    v+ + G+ G+GK+t+lk ++++++ + g++
  gi|15668260|ref|NP_247053.1| 31 GEVVSILGVNGAGKSTLLKCINKILKPKRGTI 62
                                  4588999***************9998875555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.9
                        AAA_30  81 k.......grarlepgtllivDEa 97 
                                   +       +ra +++ ++l+ DE 
  gi|15668260|ref|NP_247053.1| 142 GelqkviiARALVQEPQILLLDEP 165
                                   044445544445556677777774 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00019      0.17      26      57 ..      34      64 ..      32      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                         DUF87 26 lAilgsTGsGKSntvavLleellekkgatili 57
                                  + ilg  G+GKS++ + + + l   k++tili
  gi|15668260|ref|NP_247053.1| 34 VSILGVNGAGKSTLLKCINKILK-PKRGTILI 64
                                  579*************9866555.77777776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0015       1.3       3      33 ..      36      68 ..      34     100 .. 0.80
   2 ?    1.7   0.1      0.41   3.6e+02      25      83 ..     147     200 ..     120     220 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0015
                        AAA_18  3 ltGtpGvGKttlakeLskrlgf..gvnlrdvak 33
                                  + G+ G+GK+tl k ++k l+   g++l+d++ 
  gi|15668260|ref|NP_247053.1| 36 ILGVNGAGKSTLLKCINKILKPkrGTILIDNFD 68
                                  89************9988874456777777765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.41
                        AAA_18  25 gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghl 83 
                                   +++ r +++e ++ll ++p      + ld +++ +++++++ +s+++  ++ +v+ ++ 
  gi|15668260|ref|NP_247053.1| 147 VIIARALVQEPQILLLDEPT-----NNLDLKNQLEVMKIIMDISKSQNIASIVVMHDLN 200
                                   45566666666666666666.....8899999999999999998865666666665554 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0016       1.4      31      88 ..     137     181 ..     127     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0016
                       SbcCD_C  31 gtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                   ++lSGGe q+   +++a al   +       + +++++LDE  ++lD +++ ++++++
  gi|15668260|ref|NP_247053.1| 137 NELSGGELQK---VIIARAL---V-------QEPQILLLDEPTNNLDLKNQLEVMKII 181
                                   5666666643...4444332...2.......34899**************99999875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00053      0.48       2      24 ..      33      55 ..      32      67 .. 0.86
   2 ?   -1.9   0.0       3.1   2.8e+03     112     140 ..     148     176 ..     137     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                                  CEEEEC-TTTCHHHHHHHHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                  +v + G +G GK+tLl+ +   +
  gi|15668260|ref|NP_247053.1| 33 VVSILGVNGAGKSTLLKCINKIL 55
                                  7889************9887666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.1
                                   HHCTTTTT--EEEEEEECCCHHHHCTTSS CS
                         NACHT 112 lirkkllpeasllltvrpralrdleeqle 140
                                   +i ++l++e  +ll   p++  dl+ qle
  gi|15668260|ref|NP_247053.1| 148 IIARALVQEPQILLLDEPTNNLDLKNQLE 176
                                   46666777777777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 1481.21
//
Query:       gi|15668261|ref|NP_247054.1|  [L=407]
Description: collagenase PrtC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-83  278.2   0.2    5.4e-83  277.7   0.2    1.2  1  Peptidase_U32    Peptidase family U32
     0.0027   18.0   1.6     0.0087   16.4   1.5    2.0  2  GTP_EFTU_D2      Elongation factor Tu domain 2
  ------ inclusion threshold ------
      0.072   13.2   0.3       0.18   11.9   0.3    1.7  1  Cys_box          Anosmin cysteine rich domain
       0.11   12.8   0.2       0.34   11.2   0.2    1.8  1  Peptidase_U32_C  Peptidase family U32 C-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_U32  Peptidase family U32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.7   0.2   1.2e-86   5.4e-83       1     230 [.      76     303 ..      76     306 .. 0.98

  Alignments for each domain:
  == domain 1  score: 277.7 bits;  conditional E-value: 1.2e-86
                 Peptidase_U32   1 leklrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikaikek 81 
                                   l+k++++l+++++++vdaviv+D+g ++la+e    l++h+S+q+n+tns +++f++++ a+rv+l+REl+l++ik+i+e+
  gi|15668261|ref|NP_247054.1|  76 LKKVEEILDFANSAEVDAVIVSDLGTMQLANEL--GLRVHASVQCNVTNSLTAKFYSKF-AKRVILSRELTLNQIKEIREN 153
                                   689******************************..************************.********************* PP

                 Peptidase_U32  82 vp....dvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrldyrlieekekgeeepieedekgtyllspkdlcl 158
                                   ++    d+elE fvhGalcva+sGrc+lssyl gr an+g+c qpcr++++li+e+ +g++e++   ++g+yllspkdlc+
  gi|15668261|ref|NP_247054.1| 154 LKkdkvDLELEGFVHGALCVAISGRCFLSSYLFGRHANCGDCLQPCRRKWKLINEHHDGTYEIV---CEGKYLLSPKDLCM 231
                                   *999999***************************************************999965...78************ PP

                 Peptidase_U32 159 ieelpelleaGvdslKIeGRmkspeyvatvvrvYreaidallagr.eevkeelkeeleklanrgltsgfllgr 230
                                   ie++pel+e   ds+KIeGR k+++yv +++++Yreaid++l+g  ++++e +k+el+k++nr +++gf++++
  gi|15668261|ref|NP_247054.1| 232 IEHIPELMEV-FDSFKIEGRAKNADYVMRTTKIYREAIDSVLDGSyYDKLEYFKKELQKVYNRSYDTGFYFRD 303
                                   *********8.***********************************************************986 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.5     2e-06    0.0087      13      59 ..     347     391 ..     346     399 .. 0.91
   2 ?   -2.2   0.0       1.3   5.6e+03      13      22 ..     394     403 ..     393     406 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2e-06
                                   EETTEEEEEECTCTTSEE.EEEEEEEEEEETEEESEEETTSEEEEEEE CS
                   GTP_EFTU_D2  13 lkkGdevrilgndtskke.ivtrissletfhededeavaganaGviva 59 
                                   lk Gd++ i+g++t   +   + ++s++ +h+d+++a +g+++Gv+++
  gi|15668261|ref|NP_247054.1| 347 LKIGDTILIIGKTT---GcVEEVVKSMQINHKDVEIAKKGERVGVKLN 391
                                   899******99766...3489************************985 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                                   EETTEEEEEE CS
                   GTP_EFTU_D2  13 lkkGdevril 22 
                                   +++Gd+v++l
  gi|15668261|ref|NP_247054.1| 394 VREGDRVYLL 403
                                   899****994 PP

>> Cys_box  Anosmin cysteine rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   4.1e-05      0.18      37      57 ..     189     209 ..     185     232 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.1e-05
                       Cys_box  37 hkqCskclepCkeswelkkkl 57 
                                   h +C  cl+pC+ +w+l +++
  gi|15668261|ref|NP_247054.1| 189 HANCGDCLQPCRRKWKLINEH 209
                                   889************984433 PP

>> Peptidase_U32_C  Peptidase family U32 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   7.7e-05      0.34       7      79 ..     327     398 ..     324     399 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.7e-05
               Peptidase_U32_C   7 Gevl.sydeeglaeveqRNkfsvGdelEvltPkgenveftveelydedgeeievaphpgqkvkiklpvelepgd 79 
                                   G v   y++ + ae+e    ++ Gd++ +++ +  +ve +v+++   + + +e a ++g++v +kl++ + +gd
  gi|15668261|ref|NP_247054.1| 327 GRVVnFYKKVSVAEIELWHDLKIGDTILIIGKTTGCVEEVVKSM-QINHKDVEIA-KKGERVGVKLNHLVREGD 398
                                   5555456665599*******************888***9*****.89999*****.669999999877777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1092  (0.0609069); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2659.29
//
Query:       gi|15668262|ref|NP_247055.1|  [L=302]
Description: Na+/Ca+ exchanger protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-52  177.6  38.6    2.3e-26   92.5  15.5    2.0  2  Na_Ca_ex  Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5  15.5   1.3e-30   2.3e-26       3     148 ..       6     141 ..       4     144 .. 0.91
   2 !   91.3  15.1   3.2e-30   5.7e-26       2     146 ..     164     296 ..     163     299 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.3e-30
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHH CS
                      Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllvi 83 
                                   +++f+l+l+l++ ++d++v   e ia+++++s  v+G t++A+g+slpE+++s +a   + + ++ign++Gs+i n++lv+
  gi|15668262|ref|NP_247055.1|   6 VGYFLLGLILLYYGSDWFVLGSERIARHFNVSNFVIGATVMAIGTSLPEILTSAYASYMHAPGISIGNAIGSCICNIGLVL 86 
                                   679****************************************************************************** PP

                                   HHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHH CS
                      Na_Ca_ex  84 GlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvl 148
                                   Gl+a+i+++ vd++   l+ ++l++++++++++v+  +         ++ +g+vll+l+++yl +
  gi|15668262|ref|NP_247055.1|  87 GLSAIISPIIVDKN---LQKNILVYLLFVIFAAVIG-I------DGFSWIDGVVLLILFIIYLRW 141
                                   ********999974...5666667777777776776.4......69****************965 PP

  == domain 2  score: 91.3 bits;  conditional E-value: 3.2e-30
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTH CS
                      Na_Ca_ex   2 lfvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllv 82 
                                   ++vl+i++l+++ v+a+++v+ a +ia  l+is++v+G tl+A+g+slpEl++s++aa+++ + +++gnv+Gsni+++++ 
  gi|15668262|ref|NP_247055.1| 164 SLVLLIIGLIGVLVGAELFVDGAKKIALALDISDKVIGFTLVAFGTSLPELMVSLAAAKRNLGGMVLGNVIGSNIADIGGA 244
                                   789****************************************************************************** PP

                                   HHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHH CS
                      Na_Ca_ex  83 iGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalyl 146
                                   +++  l++ l+ ++ +      + +lv++ lll++++ +       ++ +++g+++l+lY++ +
  gi|15668262|ref|NP_247055.1| 245 LAVGSLFMHLPAENVQ------MAVLVIMSLLLYLFAKY------SKIGRWQGILFLALYIIAI 296
                                   *******885555544......23355666666889999......****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2093.00
//
Query:       gi|15668263|ref|NP_247056.1|  [L=489]
Description: succinate dehydrogenase/fumarate reductase iron-sulfur subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-41  140.0   1.3    1.3e-20   73.3   0.5    2.7  2  CCG       Cysteine-rich domain
    8.5e-28   96.5   0.2    3.2e-27   94.7   0.0    2.1  2  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
    4.4e-10   39.9   3.9    4.4e-10   39.9   3.9    2.6  2  Fer4_8    4Fe-4S dicluster domain
    1.3e-08   34.9   5.4    1.3e-08   34.9   5.4    3.3  3  Fer4_9    4Fe-4S dicluster domain
      6e-08   33.1   4.9      6e-08   33.1   4.9    3.3  4  Fer4_17   4Fe-4S dicluster domain
    7.1e-07   29.2   6.6    7.1e-07   29.2   6.6    3.2  4  Fer4_10   4Fe-4S dicluster domain
    9.3e-07   29.3   7.0    9.3e-07   29.3   7.0    3.2  3  Fer4_7    4Fe-4S dicluster domain
    9.5e-07   29.0   6.3    0.00075   19.7   0.2    3.1  3  Fer4_18   4Fe-4S dicluster domain
    1.2e-06   28.4   0.2    1.2e-06   28.4   0.2    2.8  3  Fer2      2Fe-2S iron-sulfur cluster binding domain
      2e-06   27.8   0.0    9.6e-06   25.6   0.0    2.2  1  Fer2_4    2Fe-2S iron-sulfur cluster binding domain
    2.9e-06   28.1   5.6    2.9e-06   28.1   5.6    2.7  2  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.015   15.4   1.0      0.015   15.4   1.0    4.8  5  Fer4_2    4Fe-4S binding domain
      0.039   14.1   0.6      0.039   14.1   0.6    3.9  4  Fer4_21   4Fe-4S dicluster domain
       0.14   12.7  11.8          3    8.5   1.6    3.2  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.5     1e-23   1.3e-20       1      85 []     262     345 ..     262     345 .. 0.98
   2 !   64.7   0.0   5.3e-21   6.8e-18       1      85 []     377     460 ..     377     460 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 1e-23
                           CCG   1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgCl 81 
                                   va+f+gC l++ + ++v+k   k+l+a+gv +++++++ CCG++ +r+g+ ++ae l ++n+e ++++++d++vt+c+gC 
  gi|15668263|ref|NP_247056.1| 262 VAFFTGC-LVDFRLQNVGKDAIKVLNAHGVSVVIPKNQVCCGSPFFRTGQRDVAEMLKRKNLEIFNKLDVDCVVTICAGCG 341
                                   89*****.************************************************************************* PP

                           CCG  82 lqlk 85 
                                    +lk
  gi|15668263|ref|NP_247056.1| 342 STLK 345
                                   9985 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 5.3e-21
                           CCG   1 vayfdgChllraa..ypevrkalkkllealgveleelekesCCGagggrsgkee.laealakrnvetaeetgadaivtacp 78 
                                   ++y+d+Chl r++  y+++r++lk ++e +++++e    + CCGaggg+++ ++ +a+ ++k +++++ ++++da++t cp
  gi|15668263|ref|NP_247056.1| 377 ITYHDPCHLRRGQkiYKQPREILKSIPELEFIDIE----ARCCGAGGGVRSGKPdIANLIGKSRARMIYDANVDAVITVCP 453
                                   69*********************************....77*****999888888************************** PP

                           CCG  79 gCllqlk 85 
                                   +C ++++
  gi|15668263|ref|NP_247056.1| 454 FCEYHIR 460
                                   ***9985 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   0.0   2.5e-30   3.2e-27       2     108 ..       4      98 ..       3      99 .. 0.94
   2 ?   -2.3   0.0       3.4   4.4e+03      49      63 ..     329     343 ..     310     359 .. 0.77

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 2.5e-30
                        Fer2_3   2 lkvkRfdprrdrgkqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlakq 82 
                                   + vkRf+     +k+++++yev+ +   tvl+aL++i+++++ ++ frasCr++ CGscav+inG+p+laC+++++d    
  gi|15668263|ref|NP_247056.1|   4 ITVKRFNG----EKEYLESYEVPENI--TVLEALEYINKHYEANILFRASCRNAQCGSCAVTINGEPRLACETKVEDG--- 75 
                                   7899***9....689********765..9***********************************************95... PP

                        Fer2_3  83 kseieleplpkfpvirDLvvDideml 108
                                      + +epl++f+virDL+vD+++++
  gi|15668263|ref|NP_247056.1|  76 ---MIIEPLRGFKVIRDLIVDREPYY 98 
                                   ...57*****************9875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                        Fer2_3  49 rasCregiCGscava 63 
                                   + +C  +iC  c+ +
  gi|15668263|ref|NP_247056.1| 329 DVDCVVTICAGCGST 343
                                   568999999888765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   1.3       6.3   8.1e+03      53      58 ..      52      57 ..      46      70 .. 0.72
   2 !   39.9   3.9   3.4e-13   4.4e-10       2      65 .]     131     200 ..     130     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.3
                        Fer4_8 53 tcgaCt 58
                                  +cg+C+
  gi|15668263|ref|NP_247056.1| 52 QCGSCA 57
                                  455554 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 3.4e-13
                        Fer4_8   2 lekCieCgaCqsaCp...........vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                   l+ Ci C  C s Cp           ++r+ +++ +d+r+e    + +       e++++Cttc +C+evCp++i
  gi|15668263|ref|NP_247056.1| 131 LRGCIDCLSCLSVCParevsdypgptFMRQLARFAFDKRDEDGR-EITAYF----ENIYNCTTCAKCVEVCPKEI 200
                                   788***********988888888888888888*********988.888888....88***************987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.45   5.8e+02      33      43 ..      42      57 ..      22      61 .. 0.59
   2 !   34.9   5.4   9.9e-12   1.3e-08       2      49 ..     134     199 ..     133     200 .. 0.95
   3 ?   -1.3   0.1         2   2.6e+03      35      40 ..     336     341 ..     304     344 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.45
                        Fer4_9 33 e...eaC..igCgaCv 43
                                       +C   +Cg+C+
  gi|15668263|ref|NP_247056.1| 42 IlfrASCrnAQCGSCA 57
                                  2444456555688885 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 9.9e-12
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase..................eaCigCgaCveaCpkg 49 
                                   C++C +C ++Cpa  v++  +++++r+ a+ +                   +C++C +Cve+Cpk+
  gi|15668263|ref|NP_247056.1| 134 CIDCLSCLSVCPAREVSDYPGPTFMRQLARFAfdkrdedgreitayfeniYNCTTCAKCVEVCPKE 199
                                   **************************9777669*****************99************97 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2
                        Fer4_9  35 aCigCg 40 
                                    C gCg
  gi|15668263|ref|NP_247056.1| 336 ICAGCG 341
                                   455555 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.4       3.7   4.7e+03       4       8 ..      52      56 ..      33      70 .. 0.77
   2 !   12.1   0.8   0.00017      0.22      33      58 ..     121     146 ..     104     149 .. 0.78
   3 !   33.1   4.9   4.7e-11     6e-08       2      61 .]     134     201 ..     133     201 .. 0.77
   4 ?    0.3   0.2      0.82   1.1e+03      15      50 ..     306     341 ..     298     344 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.7
                       Fer4_17  4 qCgyC 8 
                                  qCg C
  gi|15668263|ref|NP_247056.1| 52 QCGSC 56
                                  34444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00017
                       Fer4_17  33 lleeaekeekaslCieCgeCerkCPq 58 
                                   + +++e++++   Ci C  C ++CP+
  gi|15668263|ref|NP_247056.1| 121 IPKYVEENKELRGCIDCLSCLSVCPA 146
                                   5567888999***************6 PP

  == domain 3  score: 33.1 bits;  conditional E-value: 4.7e-11
                       Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraakl.......glleeaeke.....ekaslCieCgeCerkCPqgld 61 
                                   Ci C  Cl +Cp  e  d    +++r+++        ++ +    e     e++ +C++C +C+++CP+++d
  gi|15668263|ref|NP_247056.1| 134 CIDCLSCLSVCPAREVSDYPGPTFMRQLARfafdkrdEDGR----EitayfENIYNCTTCAKCVEVCPKEID 201
                                   *************9998887677777765545554333333....2445688*****************997 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.82
                       Fer4_17  15 yeaydnepkkllraaklglleeaekeekaslCieCg 50 
                                   ++  + + +++l++ +l+++++   ++++  C++Cg
  gi|15668263|ref|NP_247056.1| 306 FRTGQRDVAEMLKRKNLEIFNKLDVDCVVTICAGCG 341
                                   555555555666666778888888889999999998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.5       4.2   5.4e+03      11      15 ..      52      56 ..      42      59 .. 0.58
   2 !   29.2   6.6   5.5e-10   7.1e-07       6      56 .]     131     197 ..     127     197 .. 0.82
   3 ?   -2.7   0.2       5.4   6.9e+03       8      13 ..     336     341 ..     319     343 .. 0.65
   4 ?   -1.3   0.0       1.9   2.5e+03      17      24 ..     450     459 ..     442     478 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.2
                       Fer4_10 11 rCgkC 15
                                  +Cg C
  gi|15668263|ref|NP_247056.1| 52 QCGSC 56
                                  44444 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 5.5e-10
                       Fer4_10   6 ddtCirCgkCvkaCPadl...............tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                      Ci C  C ++CPa                  + ++++e+ +e +    ++++Ct+c +Cve+CP
  gi|15668263|ref|NP_247056.1| 131 LRGCIDCLSCLSVCPAREvsdypgptfmrqlarFAFDKRDEDGREITAYFeNIYNCTTCAKCVEVCP 197
                                   567*************88*************99455555555555555445***************9 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5.4
                       Fer4_10   8 tCirCg 13 
                                    C +Cg
  gi|15668263|ref|NP_247056.1| 336 ICAGCG 341
                                   355554 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.9
                       Fer4_10  17 kaCPadl..t 24 
                                   ++CP++    
  gi|15668263|ref|NP_247056.1| 450 TVCPFCEyhI 459
                                   5788865543 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3       2.1   2.7e+03       4       9 ..      52      57 ..      31      71 .. 0.77
   2 !   29.3   7.0   7.3e-10   9.3e-07       2      51 ..     134     199 ..     133     200 .. 0.66
   3 ?   -2.0   0.1       4.4   5.7e+03      33      42 ..     332     341 ..     301     343 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.1
                        Fer4_7  4 gCgaCv 9 
                                  +Cg C+
  gi|15668263|ref|NP_247056.1| 52 QCGSCA 57
                                  455554 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 7.3e-10
                        Fer4_7   2 CigCgaCvaaCpvkaie...............ldeeenekgtekvei..dpekClgCgaCvavCPtg 51 
                                   Ci C  C ++Cp++ ++               +d+  +e+g+e +++  +  +C++C +Cv+vCP++
  gi|15668263|ref|NP_247056.1| 134 CIDCLSCLSVCPAREVSdypgptfmrqlarfaFDK-RDEDGREITAYfeNIYNCTTCAKCVEVCPKE 199
                                   ***********866666555555544444433333.34555443333226889************87 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.4
                        Fer4_7  33 idpekClgCg 42 
                                    + + C gCg
  gi|15668263|ref|NP_247056.1| 332 CVVTICAGCG 341
                                   4455677776 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.2   0.00024      0.31      54      73 ..     127     146 ..     110     150 .. 0.83
   2 !   19.7   0.2   5.9e-07   0.00075      57      78 ..     182     203 ..     164     213 .. 0.85
   3 ?   -2.8   0.1       5.4     7e+03      66      79 ..     447     461 ..     442     465 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                       Fer4_18  54 kekgagdcidcescvkvcPt 73 
                                   ++k+   cidc sc++vcP 
  gi|15668263|ref|NP_247056.1| 127 ENKELRGCIDCLSCLSVCPA 146
                                   5677889************6 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 5.9e-07
                       Fer4_18  57 gagdcidcescvkvcPtgidir 78 
                                   +  +c++c +cv+vcP +idi 
  gi|15668263|ref|NP_247056.1| 182 NIYNCTTCAKCVEVCPKEIDIV 203
                                   5569****************95 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.4
                       Fer4_18  66 scvkvcPt.gidirk 79 
                                   + ++vcP  +  ir+
  gi|15668263|ref|NP_247056.1| 447 AVITVCPFcEYHIRD 461
                                   556777742455555 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.2   9.3e-10   1.2e-06       9      77 ..      18      72 ..      12      73 .. 0.87
   2 ?   -2.5   0.8       4.1   5.2e+03      40      48 ..     186     193 ..     182     211 .. 0.65
   3 ?   -3.5   0.0       8.4   1.1e+04      26      38 ..     405     417 ..     394     419 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 9.3e-10
                                  EEEEETTTHBHHHHHH......HTTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSEE CS
                          Fer2  9 evevadgettlldaae......enggidipysCggggCgtClvevlegevqsdetelegeeldegklrlaCqtiv 77
                                  ++ev+++ t +l+a+e      e+ +i +++sC++++Cg+C+v+++            ge+      rlaC t+v
  gi|15668263|ref|NP_247056.1| 18 SYEVPENIT-VLEALEyinkhyEA-NILFRASCRNAQCGSCAVTIN------------GEP------RLACETKV 72
                                  567777778.99999999997666.9******************99............898......7****998 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.1
                                   SSTTEEEEE CS
                          Fer2  40 CgtClvevl 48 
                                   C tC+ +++
  gi|15668263|ref|NP_247056.1| 186 CTTCA-KCV 193
                                   66666.444 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 8.4
                                   TTTTTSTTSSSSS CS
                          Fer2  26 nggidipysCggg 38 
                                    + idi++ C g+
  gi|15668263|ref|NP_247056.1| 405 LEFIDIEARCCGA 417
                                   4578898888774 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   7.5e-09   9.6e-06      12      78 ..      18      79 ..       8      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 7.5e-09
                        Fer2_4 12 evtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnvracstpvedGlkve 78
                                  +++vpe+ tv++Al   + +  +           c  ++C  C V+++gep   ac t+vedG+ +e
  gi|15668263|ref|NP_247056.1| 18 SYEVPENITVLEALEYINKHYEANILF----RASCRNAQCGSCAVTINGEP-RLACETKVEDGMIIE 79
                                  799999999999999999888754444....358999**************.679*********987 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       4.3   5.5e+03       4       9 ..      52      57 ..      27      59 .. 0.76
   2 !   28.1   5.6   2.3e-09   2.9e-06       2      66 ..     134     198 ..     133     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.3
                       Fer4_16  4 tCgkCa 9 
                                  +Cg Ca
  gi|15668263|ref|NP_247056.1| 52 QCGSCA 57
                                  455554 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.3e-09
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                   C++C  C++vCP++ ++    +++  +    + ++ ++d +e ++  ++ +++t C++C++vCP 
  gi|15668263|ref|NP_247056.1| 134 CIDCLSCLSVCPAREVSDYPGPTFMRQLARFAFDKRDEDGREITAYFENIYNCTTCAKCVEVCPK 198
                                   *****************99666765444444445555555555555566789************5 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.8      0.23     3e+02       9      17 ..      47      57 ..      42      59 .. 0.75
   2 ?   15.4   1.0   1.1e-05     0.015      10      22 .]     134     146 ..     123     146 .. 0.90
   3 ?   11.5   2.6   0.00019      0.25       9      21 ..     185     197 ..     178     198 .. 0.88
   4 ?   -0.3   0.8       1.1   1.4e+03       9      14 ..     336     341 ..     328     342 .. 0.82
   5 ?   -2.4   0.1       5.4   6.9e+03      18      21 ..     450     453 ..     449     454 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.23
                        Fer4_2  9 rCig..CgaCv 17
                                  +C +  Cg+C 
  gi|15668263|ref|NP_247056.1| 47 SCRNaqCGSCA 57
                                  686666****5 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.1e-05
                        Fer4_2  10 CigCgaCvsaCPa 22 
                                   Ci C +C+s+CPa
  gi|15668263|ref|NP_247056.1| 134 CIDCLSCLSVCPA 146
                                   ************8 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00019
                        Fer4_2   9 rCigCgaCvsaCP 21 
                                   +C+ C +Cv +CP
  gi|15668263|ref|NP_247056.1| 185 NCTTCAKCVEVCP 197
                                   7***********9 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.1
                        Fer4_2   9 rCigCg 14 
                                   +C gCg
  gi|15668263|ref|NP_247056.1| 336 ICAGCG 341
                                   7****9 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 5.4
                        Fer4_2  18 saCP 21 
                                   ++CP
  gi|15668263|ref|NP_247056.1| 450 TVCP 453
                                   89** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.2   1.5e+03      10      17 ..      52      59 ..      43      90 .. 0.68
   2 ?    9.4   1.0   0.00088       1.1      40      53 ..     133     146 ..     121     151 .. 0.76
   3 ?   14.1   0.6   3.1e-05     0.039      40      53 ..     185     198 ..     168     204 .. 0.82
   4 ?   -3.4   0.4         9   1.2e+04      40      44 ..     336     340 ..     323     343 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                       Fer4_21 10 gCgkClia 17
                                  +Cg+C+++
  gi|15668263|ref|NP_247056.1| 52 QCGSCAVT 59
                                  57777654 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00088
                       Fer4_21  40 eCvGCnlCssvCPv 53 
                                    C+ C  C+svCP 
  gi|15668263|ref|NP_247056.1| 133 GCIDCLSCLSVCPA 146
                                   58888888888885 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 3.1e-05
                       Fer4_21  40 eCvGCnlCssvCPv 53 
                                   +C+ C+ C++vCP 
  gi|15668263|ref|NP_247056.1| 185 NCTTCAKCVEVCPK 198
                                   7************4 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 9
                       Fer4_21  40 eCvGC 44 
                                    C GC
  gi|15668263|ref|NP_247056.1| 336 ICAGC 340
                                   46666 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.6    0.0023         3       5      18 ..     133     146 ..     130     147 .. 0.90
   2 ?    7.6   3.0    0.0044       5.6       5      18 ..     185     198 ..     183     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0023
                       Fer4_13   5 tCiacgaCvelaPd 18 
                                    Ci+c +C +++P 
  gi|15668263|ref|NP_247056.1| 133 GCIDCLSCLSVCPA 146
                                   7************5 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0044
                       Fer4_13   5 tCiacgaCvelaPd 18 
                                   +C+ c++Cve++P+
  gi|15668263|ref|NP_247056.1| 185 NCTTCAKCVEVCPK 198
                                   6************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3115.43
//
Query:       gi|15668264|ref|NP_247057.1|  [L=142]
Description: hypothetical protein MJ_0093 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.014   15.4   3.4       0.82    9.7   0.5    2.6  2  DUF4974      Domain of unknown function (DUF4974)
      0.015   15.6   0.2      0.026   14.8   0.2    1.4  1  LAGLIDADG_3  LAGLIDADG-like domain
       0.11   12.0   0.1       0.17   11.4   0.0    1.4  1  DUF4992      Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF4974  Domain of unknown function (DUF4974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.5   0.00014      0.82      11      62 ..      25      76 ..      24      82 .. 0.87
   2 ?    5.7   0.1    0.0025        15      36      56 ..      89     110 ..      84     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00014
                                  HHHHHHHHHHT--EEE-TTS----EEEEEES-.-.HHHHHHHHHHHH--EEE CS
                       DUF4974 11 eilkkLerwYnveivieneelknyrftgtfsrnesleevLelLektggikyk 62
                                  +i+ +L    nv+++i+ +e+ n ++ + + ++e+l e+ ++Le+++  k +
  gi|15668264|ref|NP_247057.1| 25 SIIARLIEICNVKFDIREDEIYNVKYPVLIGKEEDLKEAKKYLELITEAKLT 76
                                  5777777777**********************************99887755 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0025
                                   EEEEE.S-.-.HHHHHHHHHHH CS
                       DUF4974  36 ftgtf.srnesleevLelLekt 56 
                                   + +++ +++e+l ++L++L++ 
  gi|15668264|ref|NP_247057.1|  89 VKAKIyTDDEDLRYILDVLSND 110
                                   5677778999*********976 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   4.3e-06     0.026      26      73 ..      66     110 ..      55     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.3e-06
                                   SEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHC CS
                   LAGLIDADG_3  26 sisltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisge 73 
                                   +++l +  k  l+d++rl  r+ ++++iy++   + +  y l + s++
  gi|15668264|ref|NP_247057.1|  66 YLELITEAKLTLRDIARLARRFKVKAKIYTD---DEDLRYILDVLSND 110
                                   38888999999********************...66666655555544 PP

>> DUF4992  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.8e-05      0.17      79     138 ..       4      68 ..       2     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.8e-05
                       DUF4992  79 YevslynvddpenPvav.....vedsliDgcsvavakieDtnYklsiktlgNeklnNkdaesate 138
                                   +++++y++d+ e P+       +   li+ c+v++++ eD+ Y++   +l  ++ + k+a++  e
  gi|15668264|ref|NP_247057.1|   4 FNFKCYDIDEKEIPIPPglpqsIIARLIEICNVKFDIREDEIYNVKYPVLIGKEEDLKEAKKYLE 68 
                                   678889999999988755344456678899****************9999999988888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 886.23
//
Query:       gi|15668265|ref|NP_247058.1|  [L=310]
Description: methyl coenzyme M reductase II protein MtrC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-122  408.2   2.3   1.4e-122  408.0   2.3    1.1  1  MCR_C     Methyl-coenzyme M reductase operon protein C


Domain annotation for each model (and alignments):
>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.0   2.3    8e-127  1.4e-122       1     271 []       6     269 ..       6     269 .. 0.99

  Alignments for each domain:
  == domain 1  score: 408.0 bits;  conditional E-value: 8e-127
                         MCR_C   1 lepltyeGGvykhdellelieDlGGyilqknvialevvltllvPkedvelieelakellgklteaPlagteiavvsptLar 81 
                                   +e++ yeGGvyk+++++e+ieD+GG+++q++v++l+v++tl++P++++e+i+e+ak+++gk+ e+Plagteiavv+p+L+r
  gi|15668265|ref|NP_247058.1|   6 YEIVRYEGGVYKNNIFKEWIEDIGGFVIQEHVMQLDVYMTLAIPQNELENIKEEAKKYKGKIIETPLAGTEIAVVAPSLSR 86 
                                   799****************************************************************************** PP

                         MCR_C  82 hhlPhsaCDvaeylrraGaktnmiGlarGvgkriaqikeeekrlinehDlavfvlGnfkdCikkkkeklfedievPvvvtg 162
                                   hhlPh+aCD++eylrr+Gak nmiGlarGvg++iaq++e+e+rli+ehDlav+v+Gnf+dCik+ k++lf d+++Pvvvtg
  gi|15668265|ref|NP_247058.1|  87 HHLPHTACDISEYLRRFGAKPNMIGLARGVGRDIAQLREKERRLIEEHDLAVYVMGNFEDCIKN-KTHLF-DVDIPVVVTG 165
                                   ****************************************************************.9****.9********* PP

                         MCR_C 163 gPeelkleevpgaeayvgglGriahrlrkeeeiealdelveeveevldkkreelakDpllvsparvkkeieeqveeieevl 243
                                   gPe++++        yvg+lGr +hrlr++eei+al+++ve ++e+++++r+el+ Dp++v+p++vk+eie+qvee+ ++l
  gi|15668265|ref|NP_247058.1| 166 GPEKIDIPY-----PYVGNLGRRSHRLRHGEEIRALRKMVEVITELINERRRELSYDPPIVPPVVVKDEIEKQVEEVYSIL 241
                                   **8888777.....7****************************************************************** PP

                         MCR_C 244 sPapitlqldglrvklpydeyaekieev 271
                                   sP+pi++qldglrvkl+yd+ya+ki+ev
  gi|15668265|ref|NP_247058.1| 242 SPMPIVTQLDGLRVKLDYDKYADKIREV 269
                                   *************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2315.52
//
Query:       gi|15668266|ref|NP_247059.1|  [L=126]
Description: hypothetical protein MJ_0095 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-42  143.6   2.9    3.7e-42  143.5   2.9    1.0  1  DUF2209   Uncharacterized protein conserved in archaea (DUF22
  ------ inclusion threshold ------
      0.052   14.2   1.0      0.084   13.5   0.9    1.4  1  DUF5499   Family of unknown function (DUF5499)


Domain annotation for each model (and alignments):
>> DUF2209  Uncharacterized protein conserved in archaea (DUF2209)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.5   2.9   4.2e-46   3.7e-42       1     120 [.       1     119 [.       1     120 [. 0.98

  Alignments for each domain:
  == domain 1  score: 143.5 bits;  conditional E-value: 4.2e-46
                       DUF2209   1 vavDiSGRHkekdgeylmvcaaVslevsadriekveqvkilvvaseeepkledvvklieeaveel.keegtivaEkGelyn 80 
                                   +a+DiSGRH+e+ + +++v+a+V +e++adri +ve+++ ++v++ee++kl+d+vk+++e ++++ +e ++i++E+Ge++n
  gi|15668266|ref|NP_247059.1|   1 MAIDISGRHHEN-DIFFRVYAGVLVEIKADRIVHVEKID-VMVKEEETQKLRDIVKEVKELIDKVgDEFDYILCERGEFFN 79 
                                   79*******999.77************************.999**********************9999************ PP

                       DUF2209  81 epewlveailkkefkyqeslgEreaielAHhvslsarkll 120
                                    ++++++ailkke+++++++gE+eai++AHhvs+s+rkll
  gi|15668266|ref|NP_247059.1|  80 ISKDIISAILKKEVIFPKTRGELEAINIAHHVSYSVRKLL 119
                                   ***************************************9 PP

>> DUF5499  Family of unknown function (DUF5499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.9   9.4e-06     0.084      37      84 ..      26      74 ..      18      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.4e-06
                       DUF5499 37 frsdkwrrmkgidsevkdelnrqlrgevrklkksv.yidddfdyntsqr 84
                                  +++d+  +++ id  vk+e  ++lr  v+++k+ +  + d+fdy  ++r
  gi|15668266|ref|NP_247059.1| 26 IKADRIVHVEKIDVMVKEEETQKLRDIVKEVKELIdKVGDEFDYILCER 74
                                  4789999999**********************9884689*****87666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1582  (0.0882369); expected 358.6 (0.02)
Passed bias filter:                      846  (0.0471861); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 835.80
//
Query:       gi|15668267|ref|NP_247060.1|  [L=262]
Description: hypothetical protein MJ_0096 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00031   20.8  18.2     0.0025   17.9  16.4    2.7  1  SpoIIM         Stage II sporulation protein M
  ------ inclusion threshold ------
      0.069   13.5   3.2        1.6    9.1   0.2    2.5  2  Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  16.4   2.8e-07    0.0025      17     151 ..      48     223 ..      32     225 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-07
                        SpoIIM  17 a.....................snfaeqis.....seskensalslflaifanNlrv.alllfllGllll........... 59 
                                                         +     +s        ++n  l+ +l++++ N++   +++f+lG l+            
  gi|15668267|ref|NP_247060.1|  48 IlksnfisepaklaqsvgtakfN----AVSsavsnTVGVKNAYLTYALSYIVSNFMGcLIIMFALGALAYlykkdlekakt 124
                                   25555555555555544433221....111333354456667778888888888877366788***644477777777777 PP

                        SpoIIM  60 .............giptilvl.linGfvlGavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal....rsr 122
                                                 ++++++  +in +  G++++ ++        l+++lPhg++e + +  a+++g++l+ ++    +  
  gi|15668267|ref|NP_247060.1| 125 leekeelfkcyqkYLLILFIFtVINPL-TGLIGVNLQYSD-----LIAVLPHGFFEFFGFATAVVVGVELSNKIlpivK-- 197
                                   777777777766634444433366654.555544444434.....99***************************76431.. PP

                        SpoIIM 123 rkalkeakrellklllllvpllliAaliE 151
                                      ++   ++++ l+  + ++++iA+++E
  gi|15668267|ref|NP_247060.1| 198 ---REITSKKIVILIACSFIFIFIAGMLE 223
                                   ...4446666666666666699***9998 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00017       1.6      24      78 ..      91     145 ..      41     176 .. 0.83
   2 ?    5.0   0.2    0.0034        30      54      92 ..     191     229 ..     171     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00017
                                   HHCSSSHHHHHHHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHH CS
                 Cytochrom_B_C  24 LraipakllGvvamgaaivilfllpwldrskvksiryrkplakvllallvvsfvv 78 
                                   L +i ++++G +++++a+  l+ l   d +k k  + ++ l+k+    l++ f++
  gi|15668267|ref|NP_247060.1|  91 LSYIVSNFMGCLIIMFALGALAYLYKKDLEKAKTLEEKEELFKCYQKYLLILFIF 145
                                   5567799*******************************99999865555554443 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0034
                                   SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHTS-SSCCHH CS
                 Cytochrom_B_C  54 kvksiryrkplakvllallvvsfvvLgylGvqppeevav 92 
                                   k+  i +r+ ++k +++l+++sf+++ ++G+ +p + ++
  gi|15668267|ref|NP_247060.1| 191 KILPIVKREITSKKIVILIACSFIFIFIAGMLEPIDWFI 229
                                   55567788899999*****************98877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1149  (0.0640861); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1682.42
//
Query:       gi|15668268|ref|NP_247061.1|  [L=143]
Description: translation initiation factor IF-2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-33  114.7   0.0    2.5e-33  114.4   0.0    1.1  1  eIF-5_eIF-2B  Domain found in IF2B/IF5
  ------ inclusion threshold ------
      0.054   13.1   0.8       0.16   11.6   0.1    2.1  2  zf_C2H2_13    Zinc finger domain


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4   0.0   2.8e-37   2.5e-33       7     116 ..      29     136 ..      24     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 2.8e-37
                                   SSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHHHHHH CS
                  eIF-5_eIF-2B   7 kkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldkyieey 87 
                                   +k+r+++p++++ +eg+ +t+i+Nf+e+aka+nrd+e ++kyllke g++g++ e+grlil+ +++ + l++ ++++++ey
  gi|15668268|ref|NP_247061.1|  29 QKDRFELPEIEILIEGN-RTIIRNFRELAKAVNRDEEFFAKYLLKETGSAGNL-EGGRLILQRRISPELLKSRINDFLREY 107
                                   678**************.***********************************.9************************** PP

                                   TSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                  eIF-5_eIF-2B  88 VlCkeCkspetelekeerllvlkCkaCga 116
                                   V+C+eC++p+t+++ke+r+++lkC aCga
  gi|15668268|ref|NP_247061.1| 108 VICRECGKPDTKIIKEGRVHLLKCMACGA 136
                                   ****************************7 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.7e-05      0.16      15      26 ..     105     116 ..      94     121 .. 0.87
   2 ?   -1.1   0.1      0.16   1.4e+03      20      27 ..     131     140 ..     129     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.7e-05
                    zf_C2H2_13  15 lnYRvCnkCGkP 26 
                                    +Y +C +CGkP
  gi|15668268|ref|NP_247061.1| 105 REYVICRECGKP 116
                                   5899*******9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.16
                    zf_C2H2_13  20 CnkCG..kPi 27 
                                   C +CG  +Pi
  gi|15668268|ref|NP_247061.1| 131 CMACGaiRPI 140
                                   999*944465 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 966.95
//
Query:       gi|15668269|ref|NP_247062.1|  [L=61]
Description: 50S ribosomal protein L37e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-27   94.4  12.8    3.9e-27   94.2  12.8    1.1  1  Ribosomal_L37e  Ribosomal protein L37e
  ------ inclusion threshold ------
      0.033   14.2   0.9      0.039   14.0   0.9    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.078   13.5  10.1      0.079   13.4  10.1    1.1  1  Protamine_P2    Sperm histone P2
       0.13   12.3   1.2        4.5    7.3   0.1    2.2  2  YhfH            YhfH-like protein
       0.14   12.0   2.6        0.8    9.6   0.1    2.2  2  HalOD2          Halobacterial output domain 2
       0.27   10.9   1.3       0.41   10.3   1.3    1.3  1  MraY_sig1       Phospho-N-acetylmuramoyl-pentapeptide-transfe
       0.28   11.3   4.6        2.7    8.2   4.7    2.0  2  Zn-ribbon_8     Zinc ribbon domain
       0.79    9.5  12.0        3.8    7.4   1.7    2.1  2  Ribosomal_S14   Ribosomal protein S14p/S29e


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.2  12.8   1.8e-30   3.9e-27       1      53 [.       2      54 ..       2      55 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 1.8e-30
                Ribosomal_L37e  1 tkGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGypsaklrkynWsaKa 53
                                  +kGt+s+Gkr+k   Hi+CrrCg+r+yhv+kk+Ca+cG+p++++rky+W++K+
  gi|15668269|ref|NP_247062.1|  2 SKGTPSMGKRNKGSYHIRCRRCGRRAYHVRKKRCAACGFPNKRMRKYSWQNKK 54
                                  69*************************************************97 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.9   1.7e-05     0.039      69      97 ..      16      43 ..       8      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                                  -EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                          HypA 69 vkvrCreCgkefeleekalrCpkCgsadv 97
                                   ++rCr+Cg++  + + + rC +Cg  + 
  gi|15668269|ref|NP_247062.1| 16 YHIRCRRCGRRAYHVR-KKRCAACGFPNK 43
                                  679******9988554.469****97765 PP

>> Protamine_P2  Sperm histone P2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4  10.1   3.5e-05     0.079      37      77 ..       5      47 ..       1      61 [] 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-05
                  Protamine_P2 37 vevyGrthrGryhyrhrrcsrrrrkrikrrrrrscr...rrrrr 77
                                   +  G+  +G yh r rrc rr  +  +++r  +c    +r r+
  gi|15668269|ref|NP_247062.1|  5 TPSMGKRNKGSYHIRCRRCGRRAYHV-RKKRCAACGfpnKRMRK 47
                                  6889***************9976665.89999999622133333 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.023        51      29      37 .]      15      23 ..      11      25 .. 0.83
   2 ?    7.3   0.1     0.002       4.5      13      20 ..      32      39 ..      28      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.023
                          YhfH 29 cYgneCekC 37
                                  +Y+  C +C
  gi|15668269|ref|NP_247062.1| 15 SYHIRCRRC 23
                                  888999988 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.002
                          YhfH 13 kKkCteCG 20
                                  kK C+ CG
  gi|15668269|ref|NP_247062.1| 32 KKRCAACG 39
                                  8******9 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00036       0.8      23      39 ..       9      25 ..       2      30 .. 0.86
   2 ?    2.8   0.3     0.051   1.1e+02       3      10 ..      33      40 ..      31      46 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00036
                        HalOD2 23 GyrqLGayvWkCtrCGe 39
                                  G r+ G+y  +C rCG 
  gi|15668269|ref|NP_247062.1|  9 GKRNKGSYHIRCRRCGR 25
                                  78899***********6 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.051
                        HalOD2  3 ekCseCsl 10
                                  ++C++C++
  gi|15668269|ref|NP_247062.1| 33 KRCAACGF 40
                                  57888876 PP

>> MraY_sig1  Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.3   0.00018      0.41       2       8 ..       3       9 ..       3       9 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                     MraY_sig1 2 kGTPTMG 8
                                 kGTP+MG
  gi|15668269|ref|NP_247062.1| 3 KGTPSMG 9
                                 8*****9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.7    0.0012       2.7       4      38 ..      16      44 ..      15      45 .. 0.80
   2 ?    6.6   0.2    0.0038       8.6       7      22 ..      34      49 ..      27      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                   Zn-ribbon_8  4 YeYrCeeCghefevlqsisdapltaCPeCgsevrr 38
                                  Y  rC++Cg++  +++      ++ C +Cg + +r
  gi|15668269|ref|NP_247062.1| 16 YHIRCRRCGRRAYHVR------KKRCAACGFPNKR 44
                                  8889*****9999998......566*9**965555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0038
                   Zn-ribbon_8  7 rCeeCghefevlqsis 22
                                  rC +Cg    ++++ s
  gi|15668269|ref|NP_247062.1| 34 RCAACGFPNKRMRKYS 49
                                  6999999888888877 PP

>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.8    0.0018         4       7      30 ..      11      32 ..       7      33 .. 0.83
   2 ?    7.4   1.7    0.0017       3.8      15      31 ..      32      48 ..      26      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0018
                                  -SS..CTTT---SSS--SSSEE-G CS
                 Ribosomal_S14  7 rnssptrirnrCrvtGrprGvirk 30
                                  rn+  +  + rCr +Gr+   +rk
  gi|15668269|ref|NP_247062.1| 11 RNK--GSYHIRCRRCGRRAYHVRK 32
                                  666..89999*******9877776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0017
                                  T---SSS--SSSEE-GG CS
                 Ribosomal_S14 15 rnrCrvtGrprGvirkf 31
                                  ++rC+ +G p   +rk+
  gi|15668269|ref|NP_247062.1| 32 KKRCAACGFPNKRMRKY 48
                                  78*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 408.25
//
Query:       gi|15668270|ref|NP_247063.1|  [L=131]
Description: ferredoxin II [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-12   47.1  17.4    4.6e-07   29.4   3.2    2.2  2  Fer4      4Fe-4S binding domain
    4.9e-12   46.3  39.7    2.3e-07   31.3  16.4    2.0  3  Fer4_7    4Fe-4S dicluster domain
    7.1e-09   35.7  14.5      1e-08   35.1  14.5    1.3  1  Fer4_21   4Fe-4S dicluster domain
    3.4e-08   33.1  15.1    0.00015   21.7   1.8    2.4  2  Fer4_2    4Fe-4S binding domain
    4.2e-08   32.9  17.3    5.8e-06   26.1   2.7    2.2  2  Fer4_6    4Fe-4S binding domain
    1.4e-07   31.8   7.4    6.7e-05   23.2   0.2    2.2  2  Fer4_8    4Fe-4S dicluster domain
    1.7e-07   31.2  28.3    5.2e-05   23.3  17.7    2.2  2  Fer4_10   4Fe-4S dicluster domain
    7.9e-07   29.1  14.7    2.5e-06   27.6  15.1    1.6  2  Fer4_9    4Fe-4S dicluster domain
    8.8e-07   28.7   0.0    1.5e-06   27.9   0.0    1.4  1  NIL       NIL domain
    3.6e-06   27.8  13.7     0.0058   17.5   2.7    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
    1.1e-05   25.5  14.9     0.0036   17.7   3.5    2.2  2  Fer4_4    4Fe-4S binding domain
    0.00033   21.1  16.1      0.031   14.8   4.7    2.3  3  Fer4_17   4Fe-4S dicluster domain
     0.0058   17.4  12.9       0.13   13.1   1.4    2.2  2  Fer4_22   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.025   15.5  23.1      0.066   14.2   5.0    2.2  2  Fer4_3    4Fe-4S binding domain
      0.055   13.7   0.1      0.096   12.9   0.1    1.3  1  ALS_ss_C  Small subunit of acetolactate synthase
      0.058   13.6  14.0       0.27   11.4   1.8    2.1  2  Fer4_18   4Fe-4S dicluster domain
        1.5    9.4  15.6    1.1e+02    3.4  15.6    2.4  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   6.4   2.8e-08     3e-05       2      24 .]      76      98 ..      75      98 .. 0.92
   2 !   29.4   3.2   4.4e-10   4.6e-07       1      24 []     105     128 ..     105     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.8e-08
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  + d ekC++CG C+  CP ++I+
  gi|15668270|ref|NP_247063.1| 76 KRDLEKCVHCGCCITQCPINVIY 98
                                  6799*****************96 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 4.4e-10
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                   vv+ ee+C+gC++C ++CP+ AI+
  gi|15668270|ref|NP_247063.1| 105 VVFKEEDCVGCKNCLKACPFKAIE 128
                                   57889******************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   4.8   1.4e-06    0.0015      29      51 ..      73      95 ..      39      96 .. 0.79
   2 !   31.3  16.4   2.2e-10   2.3e-07       1      52 []      81     126 ..      81     126 .. 0.94
   3 !   20.0   2.7   7.2e-07   0.00076       2      20 ..     112     130 ..     111     131 .] 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-06
                        Fer4_7 29 ekveidpekClgCgaCvavCPtg 51
                                  + ++ d ekC++Cg C++ CP +
  gi|15668270|ref|NP_247063.1| 73 KVIKRDLEKCVHCGCCITQCPIN 95
                                  5668899**************87 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 2.2e-10
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C++Cg C   Cp ++i++de+        v++++e+C+gC++C ++CP++a
  gi|15668270|ref|NP_247063.1|  81 KCVHCGCCITQCPINVIYMDED------YNVVFKEEDCVGCKNCLKACPFKA 126
                                   7******************998......4589*****************987 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 7.2e-07
                        Fer4_7   2 CigCgaCvaaCpvkaield 20 
                                   C+gC++C +aCp kaie+ 
  gi|15668270|ref|NP_247063.1| 112 CVGCKNCLKACPFKAIEIF 130
                                   ***************9975 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1  14.5   9.9e-12     1e-08       5      58 ..      79     128 ..      74     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 9.9e-12
                       Fer4_21   5 edkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                    +kC++Cg C++ C+   ++ i +d++  +   e++CvGC+ C++ CP  ++ie
  gi|15668270|ref|NP_247063.1|  79 LEKCVHCGCCITQCP---INVIYMDEDYNVVFKEEDCVGCKNCLKACPF-KAIE 128
                                   589************...8******99999999***************7.7776 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   5.7   6.1e-06    0.0064       3      21 ..      75      93 ..      73      93 .. 0.91
   2 !   21.7   1.8   1.4e-07   0.00015       3      21 ..     105     123 ..     103     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.1e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  ++ d ++C++Cg C++ CP
  gi|15668270|ref|NP_247063.1| 75 IKRDLEKCVHCGCCITQCP 93
                                  67899*************9 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.4e-07
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   vv+ ++ C+gC+ C++aCP
  gi|15668270|ref|NP_247063.1| 105 VVFKEEDCVGCKNCLKACP 123
                                   6889999************ PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   6.8   0.00011      0.11       2      24 .]      75      97 ..      74      97 .. 0.89
   2 !   26.1   2.7   5.5e-09   5.8e-06       2      24 .]     105     127 ..     104     127 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                        Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                  +  d +kC++Cg C++ CP ++i
  gi|15668270|ref|NP_247063.1| 75 IKRDLEKCVHCGCCITQCPINVI 97
                                  77899**************8886 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 5.5e-09
                        Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                   v+++++ C+gC +C ++CP++ai
  gi|15668270|ref|NP_247063.1| 105 VVFKEEDCVGCKNCLKACPFKAI 127
                                   89******************998 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.2   6.4e-08   6.7e-05      44      65 .]      68      96 ..      26      96 .. 0.74
   2 !   11.5   2.3   0.00029      0.31       4      17 ..     111     124 ..     108     127 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.4e-08
                        Fer4_8 44 e.......eealwsCttcgaCtevCpvgi 65
                                          ++ l++C++cg+C ++Cp+++
  gi|15668270|ref|NP_247063.1| 68 VeeiskviKRDLEKCVHCGCCITQCPINV 96
                                  03444555788999***********9986 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00029
                        Fer4_8   4 kCieCgaCqsaCpv 17 
                                   +C++C  C +aCp+
  gi|15668270|ref|NP_247063.1| 111 DCVGCKNCLKACPF 124
                                   57777777777774 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3  17.7   4.9e-08   5.2e-05       3      56 .]      76     123 ..      74     123 .. 0.83
   2 !   19.9   2.8   5.4e-07   0.00057       2      21 ..     105     124 ..     104     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.9e-08
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   ++d ++C++Cg C + CP       +  + +e+  v  k e+C gc +C +aCP
  gi|15668270|ref|NP_247063.1|  76 KRDLEKCVHCGCCITQCPI------NVIYMDEDYNVVFKEEDCVGCKNCLKACP 123
                                   6899***************......444445555555689*************9 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 5.4e-07
                       Fer4_10   2 vvidddtCirCgkCvkaCPa 21 
                                   vv+ ++ C++C++C kaCP+
  gi|15668270|ref|NP_247063.1| 105 VVFKEEDCVGCKNCLKACPF 124
                                   688999*************9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   6.2   0.00012      0.13      28      50 ..      74      96 ..      57      97 .. 0.71
   2 !   27.6  15.1   2.4e-09   2.5e-06       1      51 []      81     127 ..      81     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                        Fer4_9 28 lraaseeaCigCgaCveaCpkga 50
                                  + +++ e+C++Cg C+  Cp ++
  gi|15668270|ref|NP_247063.1| 74 VIKRDLEKCVHCGCCITQCPINV 96
                                  33334489***********9775 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 2.4e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   kC+ Cg C+++Cp +v+ +d+  + +  ++    +C+gC+ C++aCp +ai
  gi|15668270|ref|NP_247063.1|  81 KCVHCGCCITQCPINVIYMDEDYNVVFKEE----DCVGCKNCLKACPFKAI 127
                                   7******************99999988754....6************9987 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.4e-09   1.5e-06      10      67 ..      12      65 ..       9      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.4e-09
                                  -S-SS-HHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHHT CS
                           NIL 10 ksavePllshlvrqlglevnIlqGsveriqgtpfGqlvielsgsqesiaaalqylrkr 67
                                  ++ ++P++s+ +   g+++nIl+++ve     +   l++el gs+e i++al+yl+k 
  gi|15668270|ref|NP_247063.1| 12 EHINKPVISDTILNTGVKINILKAKVE----PQEAFLILELFGSKETIEKALNYLSKF 65
                                  56789*********************9....55678*******************985 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   3.3   1.9e-05      0.02       1      26 [.      81     106 ..      81     111 .. 0.85
   2 !   17.5   2.7   5.5e-06    0.0058       2      18 ..     112     128 ..     111     131 .] 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeie 26 
                                   +C+ Cg C+  CP n+i +++++++ 
  gi|15668270|ref|NP_247063.1|  81 KCVHCGCCITQCPINVIYMDEDYNVV 106
                                   5*****************99877765 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.5e-06
                       Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                   C++C++C+++CP +ai+
  gi|15668270|ref|NP_247063.1| 112 CVGCKNCLKACPFKAIE 128
                                   ***************97 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   3.5   3.4e-06    0.0036       2      15 ..      80      93 ..      79     105 .. 0.88
   2 !   13.6   3.6     7e-05     0.073       2      16 ..     110     124 ..     108     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.4e-06
                        Fer4_4  2 erCigCgsCvaaCP 15
                                  e+C++Cg+C+  CP
  gi|15668270|ref|NP_247063.1| 80 EKCVHCGCCITQCP 93
                                  89***********9 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7e-05
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   e C+gC+ C  aCP+
  gi|15668270|ref|NP_247063.1| 110 EDCVGCKNCLKACPF 124
                                   56************8 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   4.6   6.9e-05     0.073      32      59 ..      66      95 ..      50      97 .. 0.63
   2 !   14.8   4.7     3e-05     0.031       1      24 [.      81     104 ..      81     110 .. 0.84
   3 !   12.7   3.0   0.00014      0.14      44      58 ..     110     124 ..      96     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.9e-05
                       Fer4_17 32 glleeaeke..ekaslCieCgeCerkCPqg 59
                                  g++ee++k   +  ++C++Cg C ++CP +
  gi|15668270|ref|NP_247063.1| 66 GEVEEISKVikRDLEKCVHCGCCITQCPIN 95
                                  555555443436778888888888888855 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3e-05
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkk 24 
                                   +C +Cg+C+ +Cp + +y +e  +
  gi|15668270|ref|NP_247063.1|  81 KCVHCGCCITQCPINVIYMDEDYN 104
                                   6*************9998877655 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00014
                       Fer4_17  44 slCieCgeCerkCPq 58 
                                   ++C++C++C ++CP 
  gi|15668270|ref|NP_247063.1| 110 EDCVGCKNCLKACPF 124
                                   79***********95 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   4.2    0.0013       1.4      77      95 ..      77      95 ..      50      96 .. 0.74
   2 !   13.1   1.4   0.00012      0.13      72      94 ..     102     124 ..      95     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                       Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                   + ++Cv Cg Ci++cp +
  gi|15668270|ref|NP_247063.1| 77 RDLEKCVHCGCCITQCPIN 95
                                  37789***********976 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00012
                       Fer4_22  72 efkekfgesgCvGCgRCieacpv 94 
                                   +++  f+e+ CvGC  C +acp 
  gi|15668270|ref|NP_247063.1| 102 DYNVVFKEEDCVGCKNCLKACPF 124
                                   556678999************96 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  10.2    0.0093       9.8       1      14 [.      82      95 ..      82      96 .. 0.93
   2 ?   14.2   5.0   6.3e-05     0.066       1      15 []     112     126 ..     112     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0093
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C++Cg C   CP +
  gi|15668270|ref|NP_247063.1| 82 CVHCGCCITQCPIN 95
                                  ************76 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6.3e-05
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+gC  C+++CP +A
  gi|15668270|ref|NP_247063.1| 112 CVGCKNCLKACPFKA 126
                                   ****99******998 PP

>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.1e-05     0.096      32      63 ..      39      71 ..      29      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-05
                                  EETTEEEEEEEE-HHHHHHHHHHS-GGG.EEEE CS
                      ALS_ss_C 32 vspdsliieltgteekidaliellkpfg.ilev 63
                                   ++ +li+el g++e i++ ++ l++fg + e+
  gi|15668270|ref|NP_247063.1| 39 PQEAFLILELFGSKETIEKALNYLSKFGeVEEI 71
                                  56789***********************66665 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  14.7    0.0072       7.6      53      95 ..      74     122 ..      51     122 .. 0.72
   2 ?   11.4   1.8   0.00026      0.27      56      74 ..     107     125 ..      96     131 .] 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0072
                       Fer4_18  53 rkekgagdcidcescvkvcPtgidirk.Glql.....eciscllcidac 95 
                                     +++  +c++c+ c++ cP+++   +    +     +c+ c +c+ ac
  gi|15668270|ref|NP_247063.1|  74 VIKRDLEKCVHCGCCITQCPINVIYMDeDYNVvfkeeDCVGCKNCLKAC 122
                                   44567789************997433313222222238**********9 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00026
                       Fer4_18  56 kgagdcidcescvkvcPtg 74 
                                    ++ dc+ c+ c+k cP +
  gi|15668270|ref|NP_247063.1| 107 FKEEDCVGCKNCLKACPFK 125
                                   5678*************74 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4  15.6      0.11   1.1e+02       2      57 ..      78     128 ..      75     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.11
                       Fer4_13   2 DrdtCiacgaCvelaP.dvFeeddeggasvvaeqptseeekadaeeAadaCPvesIg 57 
                                   D ++C+ cg C   +P +v  +d++++  vv++    ee+   +++ ++aCP ++I+
  gi|15668270|ref|NP_247063.1|  78 DLEKCVHCGCCITQCPiNVIYMDEDYN--VVFK----EEDCVGCKNCLKACPFKAIE 128
                                   779*************66666776644..4444....44556799999*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1151  (0.0641977); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 929.97
//
Query:       gi|15668271|ref|NP_247064.1|  [L=509]
Description: hypothetical protein MJ_0100 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   3.1e-144  480.1   0.2   4.1e-144  479.7   0.2    1.2  1  HcyBio          Homocysteine biosynthesis enzyme, sulfur-inco
    9.3e-32  109.3   6.2    4.5e-16   59.0   0.0    3.1  3  CBS             CBS domain
  ------ inclusion threshold ------
       0.07   13.4   0.1       0.34   11.2   0.1    2.0  2  SepF            Cell division protein SepF
       0.26   11.8   5.0        0.9   10.0   0.1    3.0  3  Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain


Domain annotation for each model (and alignments):
>> HcyBio  Homocysteine biosynthesis enzyme, sulfur-incorporation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.7   0.2  9.2e-148  4.1e-144       1     347 []      18     368 ..      18     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: 479.7 bits;  conditional E-value: 9.2e-148
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio   1 avVltaeelkklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaepkikiekvwLngvpayaglaavdlylgataes 81 
                                   avV+taee++k+v+e+g+k+aa+ vDVVttgTfg+m+ssg+++n+g+++p+ik+ +++Ln+v+ay glaavd+y+ga++++
  gi|15668271|ref|NP_247064.1|  18 AVVVTAEEMIKIVEEEGAKRAADYVDVVTTGTFGAMCSSGVFINFGHSDPPIKMLRIYLNNVEAYGGLAAVDAYIGAAQPN 98 
                                   8******************************************************************************** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio  82 eddkeeeeyGGghviedLvagkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnYnaavNsseetiytymg 162
                                   ed + + +yGG+hviedLv+gkevel ae+++tdcyprke++  itldd+n+ai+vnpRn+yq Y+aa+Ns ee+iytymg
  gi|15668271|ref|NP_247064.1|  99 EDPDVDIDYGGAHVIEDLVRGKEVELYAEGYTTDCYPRKEVNVRITLDDVNQAIMVNPRNCYQTYAAATNSREEKIYTYMG 179
                                   *555555************************************************************************** PP

                                   xxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio 163 elkpnlgnatysgaGelsPllnD.....pelktigiGtrilLgGaeGyvigeGTqsspekkrengvplgpagtLavigdlk 238
                                    l p+++n++ysgaG+l+Pl+nD     ++++tigiGtri+LgG++GyvigeGTq++p           p+gtL+v+gdlk
  gi|15668271|ref|NP_247064.1| 180 ILLPEYNNVHYSGAGQLNPLQNDynpetKSFNTIGIGTRIFLGGGIGYVIGEGTQHNP-----------PFGTLMVKGDLK 249
                                   ***********************99888899**************************5...........699********* PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx. RF
                        HcyBio 239 eMspeylrgafltsyGpelivgvgipiPvldeevleelavkdedielpvvDvserrrerktlgevsYael..Gkieiegk. 316
                                   +M+p+++r+a++ +yG++l+vg+gipiPvl+e+++e++a++dedie+p++D++ +rr+r+ +++++Y+ l  Gki+++ + 
  gi|15668271|ref|NP_247064.1| 250 QMNPKFIRAATMPRYGSTLYVGIGIPIPVLNEKIAERCAIRDEDIEVPIYDYGFPRRDRPLIAKTNYKVLrsGKITLNVNi 330
                                   ********************************************************************99**888665555 PP

                                   .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio 317 .......evktarlsslkrareiaeeLkewiekgeflL 347
                                          +vkt ++ss+k+are+ae+Lk+wi++g+flL
  gi|15668271|ref|NP_247064.1| 331 dgkdvekTVKTGSVSSYKMAREVAETLKQWILDGKFLL 368
                                   555777778999************************97 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       0.8   3.6e+03      17      39 ..       5      23 ..       4      34 .. 0.67
   2 !   59.0   0.0     1e-19   4.5e-16       1      56 [.     390     445 ..     390     446 .. 0.98
   3 !   51.9   0.8   1.7e-17   7.5e-14       2      53 ..     452     503 ..     451     507 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.8
                                  BHHHHHHHHHHHTSSEEEEEETT CS
                           CBS 17 tleealelmrekgvsrlPVVded 39
                                  t++e+ e++ +kg  ++ VV   
  gi|15668271|ref|NP_247064.1|  5 TIKEINEKI-KKGE-AV-VVT-A 23
                                  789999999.7774.77.662.2 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 1e-19
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   V+di +++++t++ + ++ ea+++++++++++lP+Vde gklvGi+t  D+++al+
  gi|15668271|ref|NP_247064.1| 390 VKDILSKPPITAHSNISIMEAAKILIKHNINHLPIVDEHGKLVGIITSWDIAKALA 445
                                   89**********************99***************************996 PP

  == domain 3  score: 51.9 bits;  conditional E-value: 1.7e-17
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                   ++imtr+v+t+++d+++  ++ +m ++++s++PVVd++ ++vGivt +D+ r
  gi|15668271|ref|NP_247064.1| 452 EEIMTRNVITAHEDEPVDHVAIKMSKYNISGVPVVDDYRRVVGIVTSEDISR 503
                                   79***********************************************976 PP

>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   7.6e-05      0.34      12      53 ..       6      51 ..       3      60 .. 0.87
   2 ?   -1.4   0.0      0.65   2.9e+03       4      21 ..     342     359 ..     339     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.6e-05
                                  HHHHHHHHHTT-EEEEE-CCCTC....HHHHHHHHHHHHHHHHCT- CS
                          SepF 12 aqeiadalkegkiVilnledldk....eeakrivdflsgvvyaldG 53
                                  ++ei + +k+g++V++  e++ k    e akr+ d++  v+ +  G
  gi|15668271|ref|NP_247064.1|  6 IKEINEKIKKGEAVVVTAEEMIKiveeEGAKRAADYVDVVTTGTFG 51
                                  689******************999999********99888776655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.65
                                   EE-SSGGGHHHHHHHHHT CS
                          SepF   4 veprsfedaqeiadalke 21 
                                     ++s++ a+e+a++lk+
  gi|15668271|ref|NP_247064.1| 342 GSVSSYKMAREVAETLKQ 359
                                   5689999*******9986 PP

>> Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2       3.8   1.7e+04       4      13 ..       7      17 ..       5      28 .. 0.50
   2 ?    3.1   0.1     0.031   1.4e+02      15      66 ..     327     378 ..     315     385 .. 0.81
   3 ?   10.0   0.1    0.0002       0.9      22      50 ..     425     452 ..     406     474 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.8
                                  HHHHHHHSS.. CS
                Ribosomal_L9_C  4 ealaekLea.k 13
                                  +++ ek+++ +
  gi|15668271|ref|NP_247064.1|  7 KEINEKIKKgE 17
                                  34445554422 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.031
                                   -EEEE--B-TT-BBSS---HHHHHHHHHHHT-----GGGEE-TTT-SBSSEE CS
                Ribosomal_L9_C  15 kvtikakagedgklFGsVtakdIaealkkklgieidkkkieleepiktlGey 66 
                                   +v+i  k  e+    GsV++ + a ++++ l+  i   k+ l+e++ tlG  
  gi|15668271|ref|NP_247064.1| 327 NVNIDGKDVEKTVKTGSVSSYKMAREVAETLKQWILDGKFLLTERVDTLGRA 378
                                   4566666666666669**************9999999999999999999976 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0002
                                   B-TT-BBSS---HHHHHHHHHHHT----- CS
                Ribosomal_L9_C  22 agedgklFGsVtakdIaealkkklgieid 50 
                                   + e+gkl G +t+ dIa+al+++   +i+
  gi|15668271|ref|NP_247064.1| 425 VDEHGKLVGIITSWDIAKALAQNK-KTIE 452
                                   6789****************9984.3332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3245.87
//
Query:       gi|15668272|ref|NP_247065.1|  [L=451]
Description: signal recognition particle protein Srp54 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-78  261.3   1.1    4.7e-78  261.3   1.1    1.9  2  SRP54            SRP54-type protein, GTPase domain
    5.9e-31  107.0   6.6    2.5e-30  105.0   1.5    3.3  3  SRP_SPB          Signal peptide binding domain
    1.1e-17   64.0   9.7    4.3e-17   62.1   6.8    3.5  2  SRP54_N          SRP54-type protein, helical bundle domain
    4.4e-07   30.0   0.0    1.5e-06   28.3   0.0    2.0  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    6.4e-06   26.6   0.4    6.4e-06   26.6   0.4    3.7  3  AAA_17           AAA domain
    9.2e-06   26.0   0.1    3.3e-05   24.2   0.1    2.0  1  AAA_22           AAA domain
    9.8e-06   25.0   0.1    2.5e-05   23.7   0.1    1.7  1  Zeta_toxin       Zeta toxin
    1.5e-05   24.6   3.4    4.9e-05   23.0   1.6    2.5  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
    3.4e-05   23.7   1.0    0.00013   21.8   0.2    2.2  2  AAA_30           AAA domain
    0.00032   20.1   0.2    0.00082   18.7   0.0    1.8  1  6PF2K            6-phosphofructo-2-kinase
    0.00039   20.8   0.0      0.001   19.5   0.0    1.8  1  AAA_16           AAA ATPase domain
    0.00044   20.1   0.0       0.38   10.5   0.0    2.9  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
    0.00066   19.9   0.0     0.0013   18.9   0.0    1.5  1  AAA_33           AAA domain
    0.00084   18.8   0.9       0.83    9.1   0.1    2.9  2  SRPRB            Signal recognition particle receptor beta su
     0.0013   18.5   0.2     0.0042   16.8   0.1    2.0  2  AAA_24           AAA domain
     0.0015   17.9   0.2     0.0015   17.9   0.2    1.6  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0015   18.4   0.1     0.0043   16.9   0.0    1.8  1  APS_kinase       Adenylylsulphate kinase
     0.0017   18.7   0.1     0.0042   17.4   0.1    1.7  1  AAA_19           AAA domain
     0.0017   18.3   1.1     0.0017   18.3   1.1    2.2  1  ResIII           Type III restriction enzyme, res subunit
     0.0022   17.2   0.0     0.0046   16.2   0.0    1.6  1  G-alpha          G-protein alpha subunit
     0.0025   17.9   3.1     0.0028   17.7   0.5    2.4  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0026   18.3   0.0     0.0097   16.5   0.0    2.1  1  AAA_18           AAA domain
     0.0033   17.7   1.1      0.039   14.2   0.0    2.9  2  MT0933_antitox   MT0933-like antitoxin protein
     0.0045   16.7   1.4     0.0097   15.6   0.1    2.0  2  SWI2_SNF2        SWI2/SNF2 ATPase
      0.005   16.7   0.0      0.013   15.4   0.0    1.7  1  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0089   15.0   0.0      0.021   13.8   0.0    1.6  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
  ------ inclusion threshold ------
      0.011   14.7   2.5       0.02   13.9   0.0    2.4  3  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.011   15.6   0.4      0.053   13.4   0.0    2.3  2  AAA_31           AAA domain
      0.014   15.4   1.0       0.33   10.9   0.0    2.7  2  NTPase_1         NTPase
      0.014   14.5   0.0      0.036   13.2   0.0    1.6  2  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
      0.016   14.7   0.0      0.035   13.5   0.0    1.6  1  KTI12            Chromatin associated protein KTI12
      0.017   15.0   0.7      0.059   13.3   0.2    2.1  2  NACHT            NACHT domain
      0.019   14.4   0.0      0.046   13.2   0.0    1.7  1  ParA             NUBPL iron-transfer P-loop NTPase
      0.019   14.9   0.0       0.05   13.6   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
      0.025   13.9   0.0      0.071   12.4   0.0    1.7  1  DUF1611          Domain of unknown function (DUF1611_C) P-loo
      0.026   13.9   0.0      0.051   12.9   0.0    1.4  1  KduI             KduI/IolB family
      0.029   14.8   0.1       0.29   11.5   0.1    2.3  1  RNA_helicase     RNA helicase
      0.032   13.5   0.1      0.093   12.0   0.0    1.8  1  AAA_8            P-loop containing dynein motor region D4
      0.033   14.4   0.0      0.079   13.2   0.0    1.7  1  AAA_28           AAA domain
      0.035   13.9   0.7       0.16   11.7   0.0    2.5  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.037   14.0   0.2       0.11   12.5   0.1    1.9  1  AAA_14           AAA domain
      0.038   13.7   0.0      0.038   13.7   0.0    2.5  2  Thymidylate_kin  Thymidylate kinase
      0.046   13.2   0.0      0.092   12.3   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
      0.048   13.7   0.0        0.1   12.6   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.06   13.5   0.6        1.3    9.2   0.0    2.4  2  DUF2856          Protein of unknown function (DUF2856)
      0.066   12.8   0.6        0.7    9.4   0.2    2.3  2  AAA_25           AAA domain
        0.1   12.5   0.8         19    5.2   0.0    2.7  2  Thiamine_BP      Thiamine-binding protein
       0.15   10.9   0.1       0.22   10.3   0.1    1.2  1  PPV_E1_C         Papillomavirus helicase
       0.23   11.2   1.2        8.8    6.0   0.0    3.0  2  IstB_IS21        IstB-like ATP binding protein
       0.66   10.4   8.3      0.076   13.4   0.7    3.3  3  AAA              ATPase family associated with various cellul
        2.3    9.0   7.4        2.1    9.1   0.1    3.4  3  KIAA1430         KIAA1430 homologue


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.3   1.1   1.3e-80   4.7e-78       2     196 .]     101     295 ..     100     295 .. 0.97
   2 ?   -1.3   0.1       4.1   1.4e+03      98     121 ..     328     351 ..     302     385 .. 0.64

  Alignments for each domain:
  == domain 1  score: 261.3 bits;  conditional E-value: 1.3e-80
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE.SSTTSCHHHHHHHHHHHHHH CS
                         SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvik.kkeeadpaavakeavekake 81 
                                   nvillvG+qG+GKTtt+aKLa++++k+g k++l+aaDt+R+aA+eQLk+laek++vp+++ ++++++p++++ke++ek+k+
  gi|15668272|ref|NP_247065.1| 101 NVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGdETRTKSPVDIVKEGMEKFKK 181
                                   89*********************************************************95566669************99 PP

                                   TTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHS.SCSEEEEESTTSSSSTTHHHH CS
                         SRP54  82 ekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeav.gitgviltklDgdakgGaals 161
                                     +dv+++DTaGr++++k l+ee+k+ik++++pde++lv+d+t+gq+a  qakaFkeav +i+++i+tklDg+akgG+als
  gi|15668272|ref|NP_247065.1| 182 --ADVLIIDTAGRHKEEKGLLEEMKQIKEITNPDEIILVIDGTIGQQAGIQAKAFKEAVgEIGSIIVTKLDGSAKGGGALS 260
                                   ..9*******************************************************967******************** PP

                                   HHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                         SRP54 162 iaaelklPikfigvGekiedleefdperlvsrllg 196
                                   ++ae+k Pikfig+Ge i+dle+fdp++++srllg
  gi|15668272|ref|NP_247065.1| 261 AVAETKAPIKFIGIGEGIDDLEPFDPKKFISRLLG 295
                                   *********************************95 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.1
                                   HHHHHHHHHHHHHHHSSSEEEEEE CS
                         SRP54  98 dkelmeelkkikkvvkpdevllvl 121
                                    +elm++l++i+++ + +++l  +
  gi|15668272|ref|NP_247065.1| 328 LNELMTQLEAIENMGSMKKILSMI 351
                                   357888888888888766666554 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1       1.4   4.9e+02       7      34 ..     199     229 ..     196     247 .. 0.71
   2 ?    0.8   0.0       2.2   7.6e+02       9      35 ..     288     314 ..     284     323 .. 0.71
   3 !  105.0   1.5     7e-33   2.5e-30       1      97 [.     325     422 ..     325     424 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1.4
                                   HHHHHHHHHCCCCCCHHHHCCC........H CS
                       SRP_SPB   7 lleqlqqikkmGplskllsmiPgmsae...a 34 
                                   lle+++qik++ + ++++  i g+  +    
  gi|15668272|ref|NP_247065.1| 199 LLEEMKQIKEITNPDEIILVIDGTIGQqagI 229
                                   6899***************999977654321 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 2.2
                                   HHHHHHHCCCCCCHHHHCCC.....H. CS
                       SRP_SPB   9 eqlqqikkmGplskllsmiPgmsaeak 35 
                                   + ++++  mG+l++ll++   m +e++
  gi|15668272|ref|NP_247065.1| 288 KFISRLLGMGDLESLLEKAEDMVDEKT 314
                                   56778889*******999888776543 PP

  == domain 3  score: 105.0 bits;  conditional E-value: 7e-33
                                   SSCTHHHHHHHHHHHCCCCCCHHHHCCC.......H.....CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHHHHH CS
                       SRP_SPB   1 eftlrdlleqlqqikkmGplskllsmiPgmsae..akae..eeaekklkrieaiidSMTkeErdspekllkesRkrRiArG 77 
                                   +ftl++l++ql+ i++mG+++k+lsmiPg++    +  e  + +e k+k++++ii+SMTkeEr++p+ ++k+sR+rRiArG
  gi|15668272|ref|NP_247065.1| 325 KFTLNELMTQLEAIENMGSMKKILSMIPGFGGAmpK--ElsHLTEAKIKKYKVIISSMTKEERENPK-IIKASRIRRIARG 402
                                   6****************************9988553..44477899*********************.9999********* PP

                                   TTS-HHHHHHHHHHHHHHHH CS
                       SRP_SPB  78 sGtsvqevnellkqfeqmkk 97 
                                   sGt+ ++v+e+l+ +e++k+
  gi|15668272|ref|NP_247065.1| 403 SGTTENDVREVLRYYETTKN 422
                                   ****************9987 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   6.8   1.2e-19   4.3e-17       1      75 []       5      82 ..       5      82 .. 0.96
   2 ?   -0.1   0.0       3.2   1.1e+03      41      53 ..     417     429 ..     393     449 .. 0.68

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 1.2e-19
                                  HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                       SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                                  Lg++ln+al+kl+ +  +d+++++e++k++++aL++aDV+vk+v k+ ++++++a++ek    l++k++++kiv++eL
  gi|15668272|ref|NP_247065.1|  5 LGENLNKALNKLKAAAFVDKKLIKEVIKDIQRALIQADVNVKLVLKMSKEIERRALEEKTpkgLSKKEHIIKIVYEEL 82
                                  899************************************************998888555*****************8 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.2
                                   HHHHHHHHHHHHH CS
                       SRP54_N  41 vkvvkklienvkk 53 
                                   ++++k+ i++++k
  gi|15668272|ref|NP_247065.1| 417 YETTKNAIDKLRK 429
                                   4555555666655 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   4.3e-09   1.5e-06       9      55 ..     110     277 ..     103     392 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 4.3e-09
                                   TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH.................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.................................. RF
                          CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep.................................. 54 
                                   G+GKTt+aa+Lar++++rgl+ +l+ aD+ ++++   l++l +   +                                  
  gi|15668272|ref|NP_247065.1| 110 GSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEqLKQLAE---Kihvpiygdetrtkspvdivkegmekfkkadvlii 187
                                   99*******************************8734444444...24559999999999999999999999999999999 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|15668272|ref|NP_247065.1| 188 dtagrhkeekglleemkqikeitnpdeiilvidgtigqqagiqakafkeavgeigsiivtkldgsakgggalsavaetkap 268
                                   999999999999999999999999999999999988888877666666666666666666666555555555555555555 PP

                                   ........C CS
                                   ........x RF
                          CbiA  55 ........d 55 
                                           +
  gi|15668272|ref|NP_247065.1| 269 ikfigigeG 277
                                   555555550 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.7         3   1.1e+03      32      73 ..      61     101 ..      32     105 .. 0.60
   2 !   26.6   0.4   1.8e-08   6.4e-06       1     108 [.     106     218 ..     106     222 .. 0.80
   3 ?   -0.6   0.1       4.7   1.6e+03      55      92 ..     300     338 ..     287     350 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 3
                                   HHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSE CS
                        AAA_17  32 eeakrgglakardemrklpleekkelqkeaaekiaeeakkkg 73 
                                   ee +++gl+k+++ ++ +++e  k l +ea++ ++ + kk++
  gi|15668272|ref|NP_247065.1|  61 EEKTPKGLSKKEHIIKIVYEELVKLLGEEAKK-LELNPKKQN 101
                                   33344566555555556666666666666654.333334444 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 1.8e-08
                                   EE-TTSSHHHHHHHHH...HHHTEE.EEEHHHHHHHHHHTTTSHSSHHHHC...TSHHHHHHHHHHHHHHHHHHHHHSSEE CS
                        AAA_17   1 lGgPGsGKgtqceklv...ekygft.hlsaGdllreeakrgglakardemr...klpleekkelqkeaaekiaeeakkkgv 74 
                                   +G+ GsGK+t ++kl+   +k g++  l a d  r  a  ++l++  ++++    +++ ++k   ++++e +++ +k + +
  gi|15668272|ref|NP_247065.1| 106 VGIQGSGKTTTAAKLAryiQKRGLKpALIAADTYRPAAY-EQLKQLAEKIHvpiYGDETRTKSPVDIVKEGMEKFKKADVL 185
                                   79*************9333455775489999*9997664.4444555555544478888888888888888888888999* PP

                                   EEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                        AAA_17  75 lvdghprikeqagfldglpkevleelkpdaiill 108
                                   ++d+  r ke++g+l+++++ ++e  +pd iil+
  gi|15668272|ref|NP_247065.1| 186 IIDTAGRHKEEKGLLEEMKQ-IKEITNPDEIILV 218
                                   *****************995.99999****9996 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 4.7
                                   HHHHHHHHHHHHHHH.HSSEEEEEE-SEEEETTEEEESS CS
                        AAA_17  55 kelqkeaaekiaeea.kkkgvlvdghprikeqagfldgl 92 
                                   + l+++a++ + e+  ++ ++++ g+++++e + +l+ +
  gi|15668272|ref|NP_247065.1| 300 ESLLEKAEDMVDEKTeESIDAIMRGKFTLNELMTQLEAI 338
                                   678888888888887344458888888887766666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   9.3e-08   3.3e-05       3     126 ..      98     218 ..      76     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 9.3e-08
                        AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleale 83 
                                   k++++++++G  G+GKTt++++l++  +++      +p ++  +   +    + l++l+++++++  + + +++  ++ + 
  gi|15668272|ref|NP_247065.1|  98 KKQNVILLVGIQGSGKTTTAAKLARYIQKRG----LKPALIAADTYRPA-AYEQLKQLAEKIHVPIYGDETRTKSPVDIVK 173
                                   5899*********************986443....47777766666666.4444588899999998888888899999999 PP

                        AAA_22  84 qalraravielliiDEaqhlr.s...eealeeLrsllnlsrkgvqli 126
                                   + +++ ++  +liiD a +   +    e +++++++ n   + + l+
  gi|15668272|ref|NP_247065.1| 174 EGMEKFKKADVLIIDTAGRHKeEkglLEEMKQIKEITN--PDEIILV 218
                                   99988888899******998553355555555566666..5555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1     7e-08   2.5e-05      10      64 ..      94     147 ..      86     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 7e-08
                    Zeta_toxin  10 ypsqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelhPeyeei 64 
                                     + ++  +ill+G +G+GK+++a++l+++++ r+ +   + +D++R+    ye++
  gi|15668272|ref|NP_247065.1|  94 ELNPKKQNVILLVGIQGSGKTTTAAKLARYIQkRGLKPALIAADTYRPAA--YEQL 147
                                   45668889************************88899**********976..5555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   1.6   1.4e-07   4.9e-05       2     156 ..     102     255 ..     101     270 .. 0.79
   2 ?   -1.7   0.0       5.5   1.9e+03      68      99 ..     330     362 ..     303     426 .. 0.56

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.4e-07
                                   EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHHH CS
                          cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelealeere 80 
                                   v++l+G  GsGKTt   +l    +++glk a+i  + +      e l++ +++i     G    t +   +  +++ +e+ 
  gi|15668272|ref|NP_247065.1| 102 VILLVGIQGSGKTTTAAKLAryIQKRGLKPALIAADTY-RPAAYEQLKQLAEKIHVPIYGDETRT-K-SPVDIVKEGMEKF 179
                                   789************99999887789************.55566666777677777778888777.4.4444555555555 PP

                                   TT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC CS
                          cobW  81 erldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldee 156
                                   ++ dv++i t G   e + ++ + +++k+ ++ d ++ v+D+  + ++   +++ +++ +     ++++K D   + 
  gi|15668272|ref|NP_247065.1| 180 KKADVLIIDTAGrHKEEKGLLEEMKQIKEITNPDEIILVIDG-TIGQQAGIQAKAFKEAVGEIGSIIVTKLDGSAKG 255
                                   59**********666667776779******************.55577888889999**************976665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.5
                                   -HHHHHHHHHHHHTT-SEEE..EEECTTTTHHHH CS
                          cobW  68 dllkelealeereerldvil..iEttGlaePapv 99 
                                   +l+ +lea+e++  ++  il  i   G a P+++
  gi|15668272|ref|NP_247065.1| 330 ELMTQLEAIENMG-SMKKILsmIPGFGGAMPKEL 362
                                   5555555555555.33333211333444444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.2   3.6e-07   0.00013      17     101 ..      99     194 ..      93     248 .. 0.67
   2 ?   -1.0   0.0       3.4   1.2e+03     138     174 ..     397     432 ..     384     436 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.6e-07
                        AAA_30  17 gdrvavltGpAGtGKttalkalreaweaag.grviglAptgkaAkv..Laeelgieastiakllkrlk............g 82 
                                   ++ v +l+G  G+GKtt+ ++l++ ++++g ++ +++A t + A+   L+      a+ i+  ++  +            g
  gi|15668272|ref|NP_247065.1|  99 KQNVILLVGIQGSGKTTTAAKLARYIQKRGlKPALIAADTYRPAAYeqLK----QLAEKIHVPIYGDEtrtkspvdivkeG 175
                                   567999***********************856777888887766421244....333333333333333333444566678 PP

                        AAA_30  83 rarlepgtllivDEagmvd 101
                                   +++++++++li+D ag   
  gi|15668272|ref|NP_247065.1| 176 MEKFKKADVLIIDTAGRHK 194
                                   889999*******999873 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.4
                        AAA_30 138 rdlveaagigtaeLtevvRqkeseeraaalalregda 174
                                   r +++ +g++   ++ev R+  ++ ++a ++lr+g++
  gi|15668272|ref|NP_247065.1| 397 RRIARGSGTTENDVREVLRY-YETTKNAIDKLRKGKM 432
                                   34445566777777788888.4567777788887775 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.3e-06   0.00082      11      89 ..      98     176 ..      89     220 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.3e-06
                                   .S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS---GGGGSTT-HHHHHHHHHHHHHHHHHHH CS
                         6PF2K  11 nsklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaskalsdaeffrpdneealklreklalaalkdll 89 
                                   +++ vi+lvG+   gKt+++ kl ry++  g++     +  yr  a ++l++     +    + + r k   + +k+ +
  gi|15668272|ref|NP_247065.1|  98 KKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGM 176
                                   56779****************************9999999999988888666555555555555555555555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.9e-06     0.001      24      88 ..     100     162 ..      71     232 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.9e-06
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                    +++ll+G +G+GK++ + +l+r+++k+g   +   +d + + ++y +l q++++   +   +de
  gi|15668272|ref|NP_247065.1| 100 QNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTY-RPAAYEQLKQLAEK-IHVPIYGDE 162
                                   389*************************533355555555.33555555555422.333333333 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.023         8       2      32 ..     108     138 ..     107     143 .. 0.90
   2 !   10.5   0.0    0.0011      0.38      67     137 ..     158     218 ..     140     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.023
                        CLP1_P   2 pkdsGKSTlarlLlNyalrkgrkpvyvDlDv 32 
                                    + sGK+T a+ L+ y+ ++g kp+++ +D 
  gi|15668272|ref|NP_247065.1| 108 IQGSGKTTTAAKLARYIQKRGLKPALIAADT 138
                                   578**********************999886 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0011
                        CLP1_P  67 ffGdtspsdnpslylalvkelareveekleenkkakasgliIntpGwvkgl.g.aellleliealepdvvvvl 137
                                    +Gd++ +++p   +++vke +++++         ka++liI+t G  k++ g +e ++++ e+ +pd ++++
  gi|15668272|ref|NP_247065.1| 158 IYGDETRTKSP---VDIVKEGMEKFK---------KADVLIIDTAGRHKEEkGlLEEMKQIKEITNPDEIILV 218
                                   56666666666...677777777777.........89***********9875755999*********998876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.7e-06    0.0013       1      42 [.     102     148 ..     102     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.7e-06
                        AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlrrrlfgtdq 42 
                                   ++llvG +GsGK+t a +l   ++k+g    l++ dt+r + +++ +
  gi|15668272|ref|NP_247065.1| 102 VILLVGIQGSGKTTTAAKLaryIQKRGlkPALIAADTYRPAAYEQLK 148
                                   89***************99555566669999******9988876444 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0024      0.83       2      25 ..      99     122 ..      98     149 .. 0.87
   2 !    7.3   0.1     0.008       2.8      44      90 ..     177     226 ..     158     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0024
                                   ---EEEEE-STTSSHHHHHHHHHH CS
                         SRPRB   2 skpavllvGlsdsGKTslftrLtt 25 
                                   +++ +llvG++ sGKT+   +L  
  gi|15668272|ref|NP_247065.1|  99 KQNVILLVGIQGSGKTTTAAKLAR 122
                                   7999*************9888875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.008
                                   ...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEE...EEEEEEETTS-HH CS
                         SRPRB  44 ksekgskltliDfPGheklrqklleklkaksslk...glvfvvDStidpk 90 
                                   ++ k+  + +iD  G +k  + lle++k+ +++     ++ v+D ti ++
  gi|15668272|ref|NP_247065.1| 177 EKFKKADVLIIDTAGRHKEEKGLLEEMKQIKEITnpdEIILVIDGTIGQQ 226
                                   445899999****************9999888752337********9886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.2e-05    0.0042       3      77 ..     101     193 ..      99     221 .. 0.73
   2 ?   -2.0   0.0       7.2   2.5e+03     109     135 ..     359     385 ..     313     412 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-05
                        AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel.....................aae 62 
                                   + il++G +g+GKTt+a++l   + +i+  +   +l a++  ++ ++e++++ ++++                      ++
  gi|15668272|ref|NP_247065.1| 101 NVILLVGIQGSGKTTTAAKL---ARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIhvpiygdetrtkspvdivkegMEK 178
                                   689*****************...5555554433355555555566777777777777888888888888888888888999 PP

                        AAA_24  63 ladyktlviDtidel 77 
                                    ++ ++l+iDt++  
  gi|15668272|ref|NP_247065.1| 179 FKKADVLIIDTAGRH 193
                                   99999******9854 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.2
                        AAA_24 109 eefrrllkklqelrknvifiahektrk 135
                                   ++  + l+  +  ++ vi+ + +k+++
  gi|15668272|ref|NP_247065.1| 359 PKELSHLTEAKIKKYKVIISSMTKEER 385
                                   333333333333333555555555554 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       7.3   2.6e+03      39      74 ..      43      78 ..      25      94 .. 0.68
   2 !   17.9   0.2   4.2e-06    0.0015       2     132 ..     101     221 ..     100     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.3
                       DUF2075 39 vNhplvlvlrealakkeekkkkkeafeklssfinnl 74
                                  vN +lvl++ +++++++ ++k  + ++k + +i+ +
  gi|15668272|ref|NP_247065.1| 43 VNVKLVLKMSKEIERRALEEKTPKGLSKKEHIIKIV 78
                                  677777777777777776666666666666655544 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 4.2e-06
                       DUF2075   2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkk..kkeafeklssfinnlsefkka 80 
                                   +v+l  G  G+GKt  + +l+  +   +++  +  l+     + + +e+l++ +ek +  +  + ++ +s +  ++     
  gi|15668272|ref|NP_247065.1| 101 NVILLVGIQGSGKTTTAAKLARYI---QKRGLKPALIAADTYRPAAYEQLKQLAEKIHvpIYGDETRTKSPVDIVK----- 173
                                   588999******************...6677777788888999999999988883333113455666666666666..... PP

                       DUF2075  81 eekkeepkedvvivDEAhrlltksdqaekqseenqlkelmkrakvvvalvDe 132
                                   e +++ +k+dv+i+D A r  +++      +e +q+ke+ +  + +++++D+
  gi|15668272|ref|NP_247065.1| 174 EGMEKFKKADVLIIDTAGRHKEEKGL---LEEMKQIKEITN-PDEIILVIDG 221
                                   778999***************96666...66789****999.5567778876 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.2e-05    0.0043       3      50 ..     101     148 ..      99     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-05
                                   EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT-- CS
                    APS_kinase   3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLg 50 
                                    v++l G+ gsGK+t a +l+++++++g +  l+  d+ R   +++L 
  gi|15668272|ref|NP_247065.1| 101 NVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLK 148
                                   689***************************999999999987777665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.2e-05    0.0042       9      94 ..      99     203 ..      91     234 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-05
                        AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae..........atTiHrlal.. 77 
                                   k++v+l+++  G+GKT++  +  ++++  +g+kp+ i++ ++   A ++l++  +++ ++                  +  
  gi|15668272|ref|NP_247065.1|  99 KQNVILLVGIQGSGKTTTAAKLARYIQ-KRGLKPALIAADTYRPAAYEQLKQLAEKIHVPiygdetrtksP-------Vdi 171
                                   678999**********99776665555.5558888888888888888888887777666655444332220.......122 PP

                        AAA_19  78 ...............ldfddlltealelleea 94 
                                                  +d+ ++ +e+ +llee 
  gi|15668272|ref|NP_247065.1| 172 vkegmekfkkadvliIDTAGRHKEEKGLLEEM 203
                                   33333444444444444444444444444433 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.1     5e-06    0.0017      21      82 ..      84     159 ..      48     223 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5e-06
                                   ...............TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH..HHHHHHHHHGGGGTGG.. CS
                        ResIII  21 s.............krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprk..slleqtleefkkflseay 82 
                                   +             k+++ +l++   G+GKT +aakl+++++k ++ + +l+ +++   + +eq+++  +k+  + y
  gi|15668272|ref|NP_247065.1|  84 KllgeeakklelnpKKQNVILLVGIQGSGKTTTAAKLARYIQK-RGLKPALIAADTYrpAAYEQLKQLAEKIHVPIY 159
                                   244445555777768888999****************987776.677899999997544778888765544444333 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.3e-05    0.0046      20     120 ..      96     207 ..      81     330 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                                   E...EEEEEEEESTTSSHHHHHHHHH.HHCS----HHHH.HC.CHHHHHHHHHHHHHHHHHHHHHTT.......HHHC-SS CS
                       G-alpha  20 k.krevkllllGqseSGKsTilkqlk.llykkgfseeel.at.wraviqlnivrsiktilealesleselsesfelqelke 96 
                                   + k++  +ll+G ++SGK+T+  +l   + k g +   + a  +r+  ++++ + +++i   +   e +   ++  + +ke
  gi|15668272|ref|NP_247065.1|  96 NpKKQNVILLVGIQGSGKTTTAAKLArYIQKRGLKPALIaADtYRPAAYEQLKQLAEKIHVPIYGDETRT--KSPVDIVKE 174
                                   1334457**************8888724556667777554445777666666666666655555533333..445677788 PP

                                   -SCCCS-HCHHHH...................H CS
                       G-alpha  97 rldplkkveasliaklssateee.........q 120
                                    ++++kk++  +i++    +ee+         +
  gi|15668272|ref|NP_247065.1| 175 GMEKFKKADVLIIDTAGRHKEEKglleemkqiK 207
                                   888888888877776666665556665555431 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.5   7.9e-06    0.0028       2      87 ..     103     226 ..     102     248 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.9e-06
                                   EEEEESTTSSHHHHHHHHHT.............................STEEESSSTTSSSSEEEEEEEETTEE...... CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg.............................ekaivsdkpgtTrdinegrvklkgke...... 47 
                                   +++vG   +GK+t   +l +                             e                        +      
  gi|15668272|ref|NP_247065.1| 103 ILLVGIQGSGKTTTAAKLARyiqkrglkpaliaadtyrpaayeqlkqlaE------------------------Kihvpiy 159
                                   67889999999999999986444333333333332232222222222211........................0222222 PP

                                   ........................EEEEECGGCSSHHHHHHHHHHHHHHHHC...TSEEEEEEETT...T CS
                      MMR_HSR1  48 ........................ielvDtpGliegaseekglgkaflalee...adlillvvdas...e 87 
                                                           + ++Dt+G    ++eekgl +++++++e    d i+lv+d +   +
  gi|15668272|ref|NP_247065.1| 160 gdetrtkspvdivkegmekfkkadVLIIDTAG-R--HKEEKGLLEEMKQIKEitnPDEIILVIDGTigqQ 226
                                   222333333333333333344444********.4..46777777777777765325********545432 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.8e-05    0.0097       1      82 [.     103     190 ..     103     226 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.8e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf................gvnlrdvakenglllevdpealdeskrldedkldklldal 64 
                                   Ill G++G+GKtt a  L++   +                  ++l+++a + +  ++ d+   + +  +d+ k  + ++++
  gi|15668272|ref|NP_247065.1| 103 ILLVGIQGSGKTTTAAKLARYIqKRglkpaliaadtyrpaaYEQLKQLAEKIHVPIYGDET--RTKSPVDIVK--EGMEKF 179
                                   99************99996653222447777887888888888888888888887777777..4444444333..444444 PP

                        AAA_18  65 eenssaleegknlvidgh 82 
                                   ++       +++l+id  
  gi|15668272|ref|NP_247065.1| 180 KK-------ADVLIIDTA 190
                                   44.......355666654 PP

>> MT0933_antitox  MT0933-like antitoxin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2       2.1   7.5e+02      21      29 ..      17      25 ..       1      36 [. 0.74
   2 !   14.2   0.0   0.00011     0.039      16      33 ..     300     317 ..     297     330 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2.1
                MT0933_antitox 21 KAgdavddk 29
                                  KA+ +vd+k
  gi|15668272|ref|NP_247065.1| 17 KAAAFVDKK 25
                                  689999988 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00011
                MT0933_antitox  16 dqgiDKAgdavddktGgK 33 
                                   +  ++KA+d+vd+kt + 
  gi|15668272|ref|NP_247065.1| 300 ESLLEKAEDMVDEKTEES 317
                                   5689***********984 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.4       2.1   7.4e+02      67     126 ..      11      78 ..       3     106 .. 0.54
   2 !   15.6   0.1   2.8e-05    0.0097      26     145 ..     108     238 ..      76     247 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.1
                     SWI2_SNF2  67 ktfakageekpkqaesrkeLkelleke..sekiifttiqKfeee.ek.....eklevlsereniivlv 126
                                   k ++k++ ++ + ++  ke+ + ++++  ++++ + ++ K+++e e+     ++ + ls++e+ii +v
  gi|15668272|ref|NP_247065.1|  11 KALNKLKAAAFVDKKLIKEVIKDIQRAliQADVNVKLVLKMSKEiERraleeKTPKGLSKKEHIIKIV 78 
                                   44455444444455555555555544445677777777777643222233322334555555555554 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.8e-05
                     SWI2_SNF2  26 tqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfaka.....geekpkqaesrkeLkelle..kesekiif 99 
                                    qGSGK+ t ++la+ ++++ lk + +   t R    +Ql++ ++k+     g+e+ ++++  + +ke +e  k+++ +i+
  gi|15668272|ref|NP_247065.1| 108 IQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIhvpiyGDET-RTKSPVDIVKEGMEkfKKADVLII 187
                                   6******************8899999999999*********999998555432332.333444444444531244666677 PP

                     SWI2_SNF2 100 ttiqKfeeeek.....eklevlsereniivlvDEaHRsqygelakklrkal 145
                                    t  + +ee+      ++++++++ ++ii+++D     q g  ak  ++a+
  gi|15668272|ref|NP_247065.1| 188 DTAGRHKEEKGlleemKQIKEITNPDEIILVIDGTIGQQAGIQAKAFKEAV 238
                                   777777644335544577899999999******998888888888777776 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.8e-05     0.013       1      33 [.     102     134 ..     102     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-05
                          MobB   1 vlgivgksgsGKTtLleklipelkarglrvgti 33 
                                   v+ +vg +gsGKTt   kl + +++rgl+ ++i
  gi|15668272|ref|NP_247065.1| 102 VILLVGIQGSGKTTTAAKLARYIQKRGLKPALI 134
                                   6889*************************9988 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0     6e-05     0.021      15      48 ..     100     135 ..      93     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6e-05
                 TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairarg..draiv 48 
                                   ++ il+vG +GsGKt+++ kl r i++rg     i 
  gi|15668272|ref|NP_247065.1| 100 QNVILLVGIQGSGKTTTAAKLARYIQKRGlkPALIA 135
                                   56799***********************95344444 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.7e-05      0.02      29      67 ..     100     138 ..      86     144 .. 0.89
   2 ?   -0.4   0.3       1.3   4.5e+02     152     176 ..     225     248 ..     177     270 .. 0.66
   3 ?   -3.1   0.1       8.9   3.1e+03     196     214 ..     380     397 ..     364     432 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-05
                                   SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                          MeaB  29 aqvvGltGvPGaGkstlvealglelrrrGkrvavlavDP 67 
                                    +v+ l G+ G+Gk t+  +l+  +++rG + a++a D 
  gi|15668272|ref|NP_247065.1| 100 QNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADT 138
                                   5788999*****************************995 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
                                   SSTTTTTTT--CCCHHH-SEEEEE- CS
                          MeaB 152 peaGDelqgikkGileiaDiivvnk 176
                                   ++aG + +++k+ + ei+ iiv  k
  gi|15668272|ref|NP_247065.1| 225 QQAGIQAKAFKEAVGEIGSIIVT-K 248
                                   45677778899999999998875.4 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 8.9
                                   CSTTBTTB--EEEEEBCCC CS
                          MeaB 196 eeekekeWrpkvlktsave 214
                                    + ke+  +pk++k+s  +
  gi|15668272|ref|NP_247065.1| 380 MT-KEERENPKIIKASRIR 397
                                   33.3444577777777654 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00015     0.053      12      47 ..     110     145 ..     102     209 .. 0.74
   2 ?   -1.9   0.1       7.7   2.7e+03     112     112 ..     349     349 ..     303     395 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00015
                        AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanattg 47 
                                   G GKTTt+ +la  + k+g k  l+ +D+   a+ +
  gi|15668272|ref|NP_247065.1| 110 GSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYE 145
                                   89**************************98777663 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.7
                        AAA_31 112 e 112
                                   +
  gi|15668272|ref|NP_247065.1| 349 S 349
                                   1 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00093      0.33       2      29 ..     103     130 ..     102     143 .. 0.89
   2 ?    2.1   0.3      0.46   1.6e+02      91     129 ..     177     217 ..     162     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00093
                                   EEEE--TTSSHHHHHHHHHHHH...GGG CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvk 29 
                                   +++ G +G+GKtT   k+++ ++++g+k
  gi|15668272|ref|NP_247065.1| 103 ILLVGIQGSGKTTTAAKLARYIQKRGLK 130
                                   7889*********************987 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.46
                                   HHHHHH-EEEE---STT..GGG-HHHHHHHHHHHTTTSEEE CS
                      NTPase_1  91 kalseadviviDEiGkm..ElkskkfkeaveevLksekpvl 129
                                   +++++adv++iD  G+   E    +  ++++e+ ++++++l
  gi|15668272|ref|NP_247065.1| 177 EKFKKADVLIIDTAGRHkeEKGLLEEMKQIKEITNPDEIIL 217
                                   34699*******99976213333344456666666666555 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0    0.0001     0.036      45      98 ..     108     162 ..      74     166 .. 0.80
   2 ?   -2.2   0.0       4.9   1.7e+03     170     194 ..     173     197 ..     167     234 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                                   SS-HSHHHHHHHHHHHTTTS..-EEEEE.--TSSSS-S.EEEEEETT-HHHH-HH CS
                          LpxK  45 vGGtGKTPlvialvkllqarglkvgvlS.RGYggkskgapvlvsaessaaevGDE 98 
                                   + G+GKT +++ l++++q+rglk++ ++   Y+ ++ ++   + ++ ++   GDE
  gi|15668272|ref|NP_247065.1| 108 IQGSGKTTTAAKLARYIQKRGLKPALIAaDTYRPAAYEQLKQLAEKIHVPIYGDE 162
                                   569*********************9986146777666666666666677777777 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.9
                                   SS-GGGGGG-SEEEE.......... CS
                          LpxK 170 REplsrlkradlvilngakaeeeea 194
                                    E +++ k+ad++i+  a +++ee+
  gi|15668272|ref|NP_247065.1| 173 KEGMEKFKKADVLIIDTAGRHKEEK 197
                                   5788889999999984443333332 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0    0.0001     0.035       4      41 ..     103     140 ..     101     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0001
                                   EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                         KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                                   ++l G+  sGK+t a++La+++++++ +  +i  ++++
  gi|15668272|ref|NP_247065.1| 103 ILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYR 140
                                   899*********************99999999999887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   0.00017     0.059       2      30 ..     102     130 ..     101     190 .. 0.92
   2 ?   -1.6   0.0       6.4   2.2e+03      77      89 ..     209     221 ..     192     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00017
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                         NACHT   2 lvilqGeaGsGKTtLlqklalawaegklp 30 
                                   +++l G +GsGKTt ++kla+ ++++ l+
  gi|15668272|ref|NP_247065.1| 102 VILLVGIQGSGKTTTAAKLARYIQKRGLK 130
                                   799******************99998875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.4
                                   CCSCCCEEEEEE- CS
                         NACHT  77 lelperlLlilDg 89 
                                   +++p+ + l++Dg
  gi|15668272|ref|NP_247065.1| 209 ITNPDEIILVIDG 221
                                   6789999*****9 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00013     0.046       6      53 ..     102     149 ..      98     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                          ParA   6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgv 53 
                                   ++ l g  G GK+t+a++lA  ++k+glk +l+ aD y p   + l+ 
  gi|15668272|ref|NP_247065.1| 102 VILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQ 149
                                   4555677799**************************999877666554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00014      0.05       2      46 ..     103     152 ..     102     197 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00014
                                   EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT-....-HHHHH--B- CS
                         AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdt....teedlkgrre 46 
                                   +lLvG +G+gK++ a +la+ + +r +   ++ +dt     +e+lk+  e
  gi|15668272|ref|NP_247065.1| 103 ILLVGIQGSGKTTTAAKLARYIqKRGLKPALIAADTyrpaAYEQLKQLAE 152
                                   69********************8777777777776622224556655554 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0002     0.071      11      50 ..      99     137 ..      89     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                       DUF1611  11 kakrvlvvGTdcavGKrttaleleealeerGlkaafvaTg 50 
                                   k +++l vG  +  GK tta +l++ +++rGlk a++a +
  gi|15668272|ref|NP_247065.1|  99 KQNVILLVGI-QGSGKTTTAAKLARYIQKRGLKPALIAAD 137
                                   5678888887.568*********************99976 PP

>> KduI  KduI/IolB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00014     0.051      43     151 ..     311     427 ..     294     437 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                                   HGCSEEEEEEEECCEEEECC...TT.EEEEE-TTSSGGG.S..EEEEE-TT--EEEEE.SSTEEEEEEEEE-SS----EEE CS
                          KduI  43 etedrEvcvvllaGkvtvev...ageefeelgeRksvFe.gkpdavYvpkgakvtita.etdaevavasapaeeelptrli 118
                                   +++++E +  ++ Gk+t +    + e  e++g+ k++ +  +     +pk+ +  ++a  ++ +v++ s + ee+ +++ i
  gi|15668272|ref|NP_247065.1| 311 DEKTEESIDAIMRGKFTLNElmtQLEAIENMGSMKKILSmIPGFGGAMPKELSHLTEAkIKKYKVIISSMTKEERENPKII 391
                                   556666666666777766655433356666666666666444444556777677777777889****************** PP

                                   -CCCSEEEEESSCCCT...EEEEEEESTTT---SS- CS
                          KduI 119 apeeveveerGkgans...RqvhnilpeseaeadsL 151
                                   +++ +++  rG+g+++   R+v  + +++++  d+L
  gi|15668272|ref|NP_247065.1| 392 KASRIRRIARGSGTTEndvREVLRYYETTKNAIDKL 427
                                   ****************88888888888777777766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00082      0.29       1      73 [.     103     206 ..     103     222 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00082
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl.................................klkkkdsvys.rnpeddfwdgY 47 
                                   i+l+G +g GK+t+a +La+ ++k+                                  +     ++ s     ++ ++++
  gi|15668272|ref|NP_247065.1| 103 ILLVGIQGSGKTTTAAKLARYIQKRGlkpaliaadtyrpaayeqlkqlaekihvpiygdE----TRTKSpVDIVKEGMEKF 179
                                   6899*******************8886777777777777777777777666666543221....22222234455566666 PP

                  RNA_helicase  48 tgqevvvidDfgqvkdee.npsdlael 73 
                                   ++ +v++id  g++k+e+   ++++++
  gi|15668272|ref|NP_247065.1| 180 KKADVLIIDTAGRHKEEKgLLEEMKQI 206
                                   666777777777777664444444444 PP

>> AAA_8  P-loop containing dynein motor region D4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00026     0.093      27      76 ..     103     153 ..      95     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                         AAA_8  27 aLlvGvgGsGrqs.ltkLAafiaelelfqievtkkykekefredlkkllkk 76 
                                   +LlvG++GsG+ +  +kLA +i++  l    +  +  +    e+lk+l +k
  gi|15668272|ref|NP_247065.1| 103 ILLVGIQGSGKTTtAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEK 153
                                   79*********862689******9998865555444444444667777665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00022     0.079       2      48 ..     103     156 ..     102     192 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00022
                        AAA_28   2 ivitGgestGKTtlleaLaar....gyp..vv.pEaareileeklakgedalpw 48 
                                   i ++G +++GKTt++++La+     g +   + ++++r    e+l++  ++++ 
  gi|15668272|ref|NP_247065.1| 103 ILLVGIQGSGKTTTAAKLARYiqkrGLKpaLIaADTYRPAAYEQLKQLAEKIHV 156
                                   7899***************65555554433445888888888877666665554 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00045      0.16       2      34 ..     106     138 ..     105     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00045
                    ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLDP 34 
                                   vG  GsGKtt   +l+ ++++rg ++a++  D+
  gi|15668272|ref|NP_247065.1| 106 VGIQGSGKTTTAAKLARYIQKRGLKPALIAADT 138
                                   899*********************999987774 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00032      0.11       2      50 ..     100     148 ..      99     216 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00032
                        AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe 50 
                                   +++++++G+  +GKTt + +l++    +  +   i+ d+ r +++++ +
  gi|15668272|ref|NP_247065.1| 100 QNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLK 148
                                   6799*****************9776633334444444444443333332 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.5       4.4   1.5e+03     108     169 ..      32      90 ..      17     102 .. 0.63
   2 ?   13.7   0.0   0.00011     0.038       3      27 ..     107     132 ..     105     150 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.4
                                   HHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHHTTSTE CS
               Thymidylate_kin 108 lslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelakederi 169
                                   + +++ ++ + d+ + l ++ +++++R a +++  +   +++++ + v e + +l+   e+ 
  gi|15668272|ref|NP_247065.1|  32 KDIQRALI-QADVNVKLVLKMSKEIERRALEEKTPKGLSKKEHIIKIVYEELVKLLG--EEA 90 
                                   33444433.777777778888888888888888777778888877777777776663..333 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00011
                                   ESTTSSHHHHHHHHHHHHHHTTE..E CS
               Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik.v 27 
                                   G+ G+GKtt a++l+++++++g+k +
  gi|15668272|ref|NP_247065.1| 107 GIQGSGKTTTAAKLARYIQKRGLKpA 132
                                   9********************98855 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00026     0.092      31      69 ..      98     136 ..      91     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00026
                         AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkekylsltinf 69 
                                   k+++ +llvG +G+GKt+++ +l + ++k+ ++++ i  
  gi|15668272|ref|NP_247065.1|  98 KKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAA 136
                                   778899******************999999888887765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00029       0.1      16      98 ..      92     188 ..      78     214 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00029
                                   HCH......TEEEEEEESTTSSHHHHHHHHHHHTT--.....----TTTTSEEEEEE..SS...EEEEE-T....T-SSTH CS
                          TsaE  16 kal......gdvilLeGdLGaGKTtlvrglakalgve.....evkSPTFtlveeYelekeg...lyHfDlY....Rledee 78 
                                   k l      ++vilL G  G+GKTt + +la+ ++ +      +   T+  +  Ye+ k +    +H+ +Y    R +++ 
  gi|15668272|ref|NP_247065.1|  92 K-LelnpkkQNVILLVGIQGSGKTTTAAKLARYIQKRglkpaLIAADTYRPAA-YEQLK-QlaeKIHVPIYgdetRTKSPV 169
                                   3.2345555778******************99885433324446666665443.33222.124566666663333455555 PP

                                   HHHHCTTCCCCSTSCEEEEE CS
                          TsaE  79 eleelgleeyleeeavvlvE 98 
                                   ++ + g+e++  ++ v+++ 
  gi|15668272|ref|NP_247065.1| 170 DIVKEGMEKFK-KADVLIID 188
                                   66666665554.33366665 PP

>> DUF2856  Protein of unknown function (DUF2856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0037       1.3       3      46 ..     156     199 ..     154     213 .. 0.90
   2 ?    2.0   0.2      0.66   2.3e+02      43      94 ..     370     424 ..     357     427 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0037
                       DUF2856   3 aplygaddprrcsgnsvsevldkfrknydlimslpqetkeekef 46 
                                    p+yg +   +   + v e ++kf+k   li+      keek +
  gi|15668272|ref|NP_247065.1| 156 VPIYGDETRTKSPVDIVKEGMEKFKKADVLIIDTAGRHKEEKGL 199
                                   699**98888899999*************************965 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.66
                       DUF2856  43 ekefrhciwlaekeerer...iyqtairpfrkatytkfieidprlrdyrsrygai 94 
                                    k+++  i    keere    i  + ir + + + t   ++   lr y +   ai
  gi|15668272|ref|NP_247065.1| 370 IKKYKVIISSMTKEERENpkiIKASRIRRIARGSGTTENDVREVLRYYETTKNAI 424
                                   3567777777778888743324455677777776676666667777777766665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2     0.002       0.7      33      56 ..     100     123 ..      97     138 .. 0.87
   2 ?    1.0   0.0      0.79   2.8e+02     101     153 ..     143     192 ..     125     197 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.002
                        AAA_25  33 gelallaGapgtGKttlaldlala 56 
                                   + ++ll+G +g+GKtt a  la  
  gi|15668272|ref|NP_247065.1| 100 QNVILLVGIQGSGKTTTAAKLARY 123
                                   6799****************9975 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.79
                        AAA_25 101 arllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsr 153
                                   a +++ +la++  +++   ++ +t++++ vd + + +e+ +++++++iD+  r
  gi|15668272|ref|NP_247065.1| 143 AYEQLKQLAEK--IHVPIYGD-ETRTKSPVDIVKEGMEKFKKADVLIIDTAGR 192
                                   45555555544..33332222.22234445558899999999*******9765 PP

>> Thiamine_BP  Thiamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.4     0.082        29      49      88 ..      27      64 ..      20      67 .. 0.86
   2 ?    5.2   0.0     0.054        19      16      63 ..     114     161 ..     103     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.082
                                  HHHHHHHHHHHHHCTTSSEEEEEEEEEEESSS---HHHHH CS
                   Thiamine_BP 49 vmevvkkahealfeaGakRvstvikiddrrdkeqtleeKv 88
                                  + ev+k++++al++a    v +v+k+ +  ++ + leeK+
  gi|15668272|ref|NP_247065.1| 27 IKEVIKDIQRALIQA-DVNVKLVLKMSKEIER-RALEEKT 64
                                  568************.5679******999999.8888886 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.054
                                   HHHHHHHHHHHHTTSSEEEEETTEEEEEEEHHHHHHHHHHHHHHHHCT CS
                   Thiamine_BP  16 skyVakvvevlkesglkyeltpmgTtiegeldevmevvkkahealfea 63 
                                    +  ak  +++++ glk  l +  T   + ++++ ++ +k+h  ++ +
  gi|15668272|ref|NP_247065.1| 114 TTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGD 161
                                   55678999*********************************9776655 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00063      0.22     180     287 ..      17     125 ..       9     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00063
                      PPV_E1_C 180 narafLksnnqakivkdcatmvrhykraemkkmsmsewikkrlkevedegdWkeivkflryqgvelisfltalkefLkgvP 260
                                    a+af+ ++    ++kd+           +  + ms+ i++r  e +     ++  + ++    el+++l +  + L+  P
  gi|15668272|ref|NP_247065.1|  17 KAAAFVDKKLIKEVIKDIQRALIQADVNVKLVLKMSKEIERRALEEKTPKGLSKKEHIIKIVYEELVKLLGEEAKKLELNP 97 
                                   688899988888899999887777777777889*********999998888999999999999********99999**999 PP

                      PPV_E1_C 261 kk.nclvllGppntGkslfamslikfLk 287
                                   kk n+++l+G   +Gk++ a  l ++++
  gi|15668272|ref|NP_247065.1|  98 KKqNVILLVGIQGSGKTTTAAKLARYIQ 125
                                   87588999************99999887 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.025       8.8      46      76 ..      98     129 ..      80     140 .. 0.81
   2 ?    2.4   0.0      0.32   1.1e+02     100     123 ..     173     196 ..     159     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.025
                     IstB_IS21  46 kken.ivllGpsGvGKshlaialgveavragl 76 
                                   kk+n i+l+G  G GK+  a+ l++   ++gl
  gi|15668272|ref|NP_247065.1|  98 KKQNvILLVGIQGSGKTTTAAKLARYIQKRGL 129
                                   556615679***********999987766665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.32
                     IstB_IS21 100 aralkrllkvdllilDdlgllpld 123
                                   ++ ++++ k+d+li+D  g ++ +
  gi|15668272|ref|NP_247065.1| 173 KEGMEKFKKADVLIIDTAGRHKEE 196
                                   5678999**********9988755 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7   0.00022     0.076       1      26 [.     103     142 ..     103     289 .. 0.63
   2 ?   -0.7   0.1       5.2   1.8e+03      84     100 ..     326     370 ..     308     403 .. 0.54
   3 ?   -1.6   0.0       9.3   3.3e+03      29      33 ..     391     395 ..     341     424 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00022
                                   EEEESSTTSSHHHHHHHHHHHHTHE..............E CS
                           AAA   1 vllyGppGtGKTllakavakelgve..............f 26 
                                   +ll+G  G GKT++a  +a+ ++ +               
  gi|15668272|ref|NP_247065.1| 103 ILLVGIQGSGKTTTAAKLARYIQKRglkpaliaadtyrpA 142
                                   69******************98533222233323332331 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 5.2
                                   HHHHHHHHHHHHTTTS............................S CS
                           AAA  84 rvvnqLlteldgvkkk............................e 100
                                    ++n+L+t+l+  ++                              
  gi|15668272|ref|NP_247065.1| 326 FTLNELMTQLEAIENMgsmkkilsmipgfggampkelshlteakI 370
                                   566777777777666544444444444444444444444444441 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 9.3
                                   EETTT CS
                           AAA  29 isgse 33 
                                   i++s+
  gi|15668272|ref|NP_247065.1| 391 IKASR 395
                                   22222 PP

>> KIAA1430  KIAA1430 homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.4       2.7   9.4e+02      20      58 ..      19      58 ..       8     119 .. 0.68
   2 ?    0.2   0.0       3.7   1.3e+03      41      56 ..     193     208 ..     162     225 .. 0.81
   3 ?    9.1   0.1    0.0061       2.1      10      90 ..     352     435 ..     344     437 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 2.7
                      KIAA1430 20 pshlskkkkklqlee.erlkeiereNqiLleklseimrrk 58
                                  +++  kk+ k+ ++  +r+      N +L+ k+s+  +r+
  gi|15668272|ref|NP_247065.1| 19 AAFVDKKLIKEVIKDiQRALIQADVNVKLVLKMSKEIERR 58
                                  4455666666666664555555557999999998755555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 3.7
                      KIAA1430  41 ereNqiLleklseimr 56 
                                   ++e + Lle++++i++
  gi|15668272|ref|NP_247065.1| 193 HKEEKGLLEEMKQIKE 208
                                   5688899999999987 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0061
                      KIAA1430  10 ssidnkapkkpsh.lskkkkklqleeerlkeiereNqiLl..eklseimrrkgkkksassqsqksktaskslnaenrkkel 87 
                                   + +    pk+ sh ++ k kk+++  + +++ ereN +++  +++ +i r +g++++  ++  +   ++k+   + rk ++
  gi|15668272|ref|NP_247065.1| 352 PGFGGAMPKELSHlTEAKIKKYKVIISSMTKEERENPKIIkaSRIRRIARGSGTTENDVREVLRYYETTKNAIDKLRKGKM 432
                                   5555567999999888899********************73359********99666666666666666666666677777 PP

                      KIAA1430  88 qkI 90 
                                    +I
  gi|15668272|ref|NP_247065.1| 433 LRI 435
                                   776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1166  (0.0650343); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                       141  (0.00786435); expected 17.9 (0.001)
Passed Fwd filter:                        52  (0.00290033); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              51  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.49
# Mc/sec: 2773.52
//
Query:       gi|15668273|ref|NP_247066.1|  [L=184]
Description: phenylacrylic acid decarboxylase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-30  104.7   0.1      5e-30  104.3   0.1    1.1  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.1   2.8e-34     5e-30       1     125 [.       1     162 [.       1     175 [. 0.88

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 2.8e-34
                                   EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHG.GS........TCSSHHHHHHCT............. CS
                  Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiske.klklaa....redpilhielrr............. 63 
                                   +ki+++iTG++++i+a++lle Lk+  +ev+++++++Akk+i++e ++++++                             
  gi|15668273|ref|NP_247066.1|   1 MKIIVCITGASGVIYAKRLLEVLKD-RAEVNLIISNSAKKIIKEElDIDWKEikklA----------Tdyyenddffspla 70 
                                   79**********************7.*****************99766665533331..........13344456666777 PP

                                   ....TESEEEEEEEEHHHHHHHHTT--SSHH..............................HHHHHTHCCTTEEEEE.--H CS
                  Flavoprotein  64 ....wadllviaPasantlakianGiadnll..............................tlilratakkpiliaPamnp 110
                                       ++d++v++P+s++tl++ianG++ nl+                              +l+l   ++ +++++P + p
  gi|15668273|ref|NP_247066.1|  71 sgsnKFDAVVVVPCSMKTLSAIANGYSANLIvrvcdialkerrkliimprempfnsihlenMLKL---SNLGAIVMP-PIP 147
                                   7777******************************************************9999999...99*******.*** PP

                                   HCCTCSTCHHHHHHH CS
                  Flavoprotein 111 amyenpqtlknlekl 125
                                   a+y++p++++++ ++
  gi|15668273|ref|NP_247066.1| 148 AFYNKPKNVNDIINF 162
                                   ************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1238.86
//
Query:       gi|15668274|ref|NP_247067.1|  [L=433]
Description: hypothetical protein MJ_0103 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-25   88.4   0.1    1.3e-24   87.5   0.1    1.4  1  Radical_SAM  Radical SAM superfamily
    0.00036   20.7   0.1     0.0012   19.0   0.1    1.9  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.056   13.7   0.1       0.12   12.7   0.1    1.6  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.1   2.1e-28   1.3e-24       6     166 ..     117     283 ..     115     284 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 2.1e-28
                                   EESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHH..HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC.CCTEEE CS
                                   xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                   Radical_SAM   6 gCnlrCsfCarpet..vrregrgrslsveeileevkelk..aekg.vkevilgggepllypdfvellerlakla.vpgiri 80 
                                   gCnl+C+fC++ e   +++++  +++++e+++e  k++   +e+  ++  + g gep+ly+++v+l+ +la++  + +  +
  gi|15668274|ref|NP_247067.1| 117 GCNLNCIFCSVDEGefSKTRKNDYYVDLEYLIENYKKIVdfKENKfIEAHLDGQGEPSLYYPLVDLVQELAEINkKGNGIV 197
                                   9*********************************999988544447***************************9999999* PP

                                   EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn..rghtfeevlealeklreagikrvvdrivglpGendee 159
                                   ++ tngt+++ + +++l e+g+ r++l+++a+d++   k++   r ++++++l+  e+++++ i+   +  ++lp+ ndee
  gi|15668274|ref|NP_247067.1| 198 SMQTNGTVLNYKLIDELEEAGLHRINLSINALDEK-MAKMLSgrRDYNIKKILDIAEYIKNSKIH-LLIAPLLLPNINDEE 276
                                   ***********************************.55555559*********************.*************** PP

                                   HHHHHHH CS
                                   xxxxxxx RF
                   Radical_SAM 160 leellel 166
                                   ++ ++e+
  gi|15668274|ref|NP_247067.1| 277 FKRVIEY 283
                                   **99886 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1     2e-07    0.0012       7     101 ..     117     214 ..     113     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2e-07
                       Fer4_14   7 gCnlsCkgCd......nketwkselgkpqte.elleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeeyp 79 
                                   gCnl+C +C        k+ +++ +   +   e  ++i+ d+k++++   +  l G GeP +y+   +l++ + ++ +++ 
  gi|15668274|ref|NP_247067.1| 117 GCNLNCIFCSvdegefSKTRKNDYYVDLEYLiENYKKIV-DFKENKF--IEAHLDGqGEPSLYYPLVDLVQELAEINKKG- 193
                                   9********986666544444444444333314444555.6666666..3357*******99*99999999999999999. PP

                       Fer4_14  80 ekkiwletngtleielektpdl 101
                                   +  + ++tngt+  + + +++l
  gi|15668274|ref|NP_247067.1| 194 NGIVSMQTNGTVL-NYKLIDEL 214
                                   7889******986.55544444 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.9e-05      0.12      14      98 ..     117     208 ..     106     261 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                       Fer4_12  14 gCnlsCkgCfnketwsfk.sgkef..t....kelleeiiedlkkesiegltllG.GEPllpenaeallelvkevkeekpek 86 
                                   gCnl+C +C   e    k +++++  +     e  ++i+ d+k+++ ++  l G GEP+l++   +l++ + e+ +++   
  gi|15668274|ref|NP_247067.1| 117 GCNLNCIFCSVDEGEFSKtRKNDYyvDleylIENYKKIV-DFKENKFIEAHLDGqGEPSLYYPLVDLVQELAEINKKGNGI 196
                                   9********988887655223333233312233333444.445566688899999*****888877777777777777778 PP

                       Fer4_12  87 diwlytgytlee 98 
                                   + + ++g+ l+ 
  gi|15668274|ref|NP_247067.1| 197 VSMQTNGTVLNY 208
                                   899999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3052.39
//
Query:       gi|15668275|ref|NP_247068.1|  [L=663]
Description: DNA-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-59  199.6   0.3    1.5e-58  198.6   0.3    1.6  1  AAA_11           AAA domain
      3e-58  196.7   2.6      9e-58  195.2   2.6    1.9  1  AAA_12           AAA domain
    7.1e-11   42.2   0.0    6.9e-08   32.4   0.0    2.6  3  AAA_30           AAA domain
    2.9e-08   34.2   0.0    1.7e-07   31.7   0.0    2.2  1  AAA_19           AAA domain
    8.1e-08   32.3   0.0      0.032   14.0   0.0    3.2  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    5.4e-05   22.9   0.0    0.00058   19.6   0.0    2.5  3  UvrD_C_2         UvrD-like helicase C-terminal domain
    9.8e-05   21.7   0.3      0.023   13.9   0.0    2.6  2  PIF1             PIF1-like helicase
    0.00073   19.4   0.3     0.0056   16.5   0.0    2.6  3  Helicase_RecD    Helicase
     0.0011   19.2   0.0      0.018   15.3   0.0    2.7  2  AAA_22           AAA domain
     0.0019   18.6   0.1      0.014   15.8   0.0    2.6  3  AAA              ATPase family associated with various cellul
     0.0023   18.0   3.1     0.0038   17.3   0.2    2.7  2  ResIII           Type III restriction enzyme, res subunit
     0.0025   17.4   6.9     0.0049   16.4   2.1    2.7  3  UvrD-helicase    UvrD/REP helicase N-terminal domain
     0.0026   16.9   0.1     0.0067   15.5   0.0    1.7  2  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.045   13.5   0.0    1.8  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.015   15.6   0.0      0.033   14.6   0.0    1.6  1  AAA_16           AAA ATPase domain
      0.017   14.9   1.3       0.12   12.2   0.1    2.6  3  DEAD             DEAD/DEAH box helicase
      0.032   13.7   0.1       0.18   11.2   0.0    2.1  2  PhoH             PhoH-like protein
      0.045   14.4   0.3        9.5    7.1   0.0    3.0  2  TPR_6            Tetratricopeptide repeat
      0.096   12.2   0.0       0.18   11.3   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
       0.16   10.9   0.5       0.24   10.3   0.5    1.1  1  DUF2722          Protein of unknown function (DUF2722)


Domain annotation for each model (and alignments):
>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.6   0.3   1.7e-61   1.5e-58       1     261 []     184     437 ..     184     437 .. 0.89

  Alignments for each domain:
  == domain 1  score: 198.6 bits;  conditional E-value: 1.7e-61
                        AAA_11   1 klndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrgllds 81 
                                   +ln+sq+ a+k+a+ ++++ li+GPPGtgKT+ti+e++ q          k +k+++L++a SN A D++le l++     
  gi|15668275|ref|NP_247068.1| 184 NLNESQKLAVKKAVLSRDLYLIHGPPGTGKTRTITEVIVQE--------VKFNKHKVLATADSNIAADNILEYLIK----- 251
                                   59**************************************9........689************************..... PP

                        AAA_11  82 egekykpkivRvgneeeriseavksvsleekvekrlekeekaqlakeiskeleklakelrafeeeeek............. 149
                                     +  ++k+vRvg++  ris+++ ++sl + +e++ + +e  +l ++i++ +e+ +k l+ +     +             
  gi|15668275|ref|NP_247068.1| 252 --KYPDLKVVRVGHPT-RISKDLIQHSLPYLIENHEKYQEILALREKIKEIKEQRDKFLKPSP----Rwrrgmsdeqilkv 325
                                   ..999***********.9*****************9887666666666666666666665554....34445999999999 PP

                        AAA_11 150 ...eklkkskekskskleqerrklkkerkelskeleeaeesleeevldeaeivltTlsgagsklleklakkfdvviIDEAa 227
                                      +k+ +   k+k    +e    +k++k++ ++l+e++e++++e+l ea+++++T+s ags+ l+    +fdv++IDE +
  gi|15668275|ref|NP_247068.1| 326 akrKKSYRGIPKEKIVSMAEWIIRNKKIKRIINNLDEITEKIMNEILAEADVIVATNSMAGSEILKGW--EFDVIVIDEGS 404
                                   55544445555566666667777899999999************************************..9********** PP

                        AAA_11 228 qavEpstliPlrlgakkvvLvGDpkQLpatvisk 261
                                   qa+Eps+liP+ +g +k++++GD+kQLp+tv+s+
  gi|15668275|ref|NP_247068.1| 405 QAMEPSCLIPIVKG-RKLIMAGDHKQLPPTVLSE 437
                                   **************.*****************96 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.2   2.6     1e-60     9e-58       2     198 ..     442     633 ..     441     634 .. 0.94

  Alignments for each domain:
  == domain 1  score: 195.2 bits;  conditional E-value: 1e-60
                        AAA_12   2 erSlferllkkekekvvlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkrele.........aqealeepleplvfidve 73 
                                   +++lferl+kk++e +++L++qYRm+++I++fp+k+fY++kLk++esvk+ +l          + ++      p+ fi+ve
  gi|15668275|ref|NP_247068.1| 442 KKTLFERLIKKYPEFSSILEIQYRMNEKIMEFPNKMFYNNKLKADESVKNITLLdlvkeeeidEVDRDIINEIPVQFINVE 522
                                   79********************************************9999988889999988777788888899******* PP

                        AAA_12  74 kseeekekkeksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeksekeievntvdgfQGr 154
                                   + e +++++  sy+N eEae v+++v+kl+k    +      vitpY aqv++l++ ++e++ +     ievntvdgfQGr
  gi|15668275|ref|NP_247068.1| 523 GIERKDKES-PSYYNIEEAEKVLEIVKKLVKYKIPT-----NVITPYDAQVRYLRRLFEEHNID-----IEVNTVDGFQGR 592
                                   999999876.*********************99999.....8*****************65444.....************ PP

                        AAA_12 155 ekdviilslVRsnekkeigflkderrlNValTRAkskliivGnk 198
                                   e+++i++s+VR+   k++gflkd rrlNVa+TRAk+kli++Gn+
  gi|15668275|ref|NP_247068.1| 593 ENEAIVISFVRT---KNFGFLKDLRRLNVAITRAKRKLILIGNE 633
                                   ***********9...79*************************97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   7.8e-11   6.9e-08       2      63 ..     185     246 ..     184     279 .. 0.90
   2 !    6.9   0.0    0.0053       4.7      88     130 ..     394     432 ..     344     437 .. 0.76
   3 ?   -3.2   0.0       6.7     6e+03     103     125 ..     611     633 ..     610     635 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 7.8e-11
                        AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkal.reaweaaggrviglAptgkaAkvLa 63 
                                   ln++Q+ av++++ s+d + +++Gp+GtGKt +++++ ++ ++ ++++v++ A ++ aA+++ 
  gi|15668275|ref|NP_247068.1| 185 LNESQKLAVKKAVLSRD-LYLIHGPPGTGKTRTITEViVQEVKFNKHKVLATADSNIAADNIL 246
                                   89**************9.*************999988799999999*************9965 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0053
                        AAA_30  88 pgtllivDEagmvdtkqlaallkaaekagakvilvGDerQlas 130
                                   + +++++DE + +   +   l+ ++  +g k+i++GD++Ql++
  gi|15668275|ref|NP_247068.1| 394 EFDVIVIDEGSQAMEPS--CLIPIV--KGRKLIMAGDHKQLPP 432
                                   44899999999876665..467777..379***********97 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6.7
                        AAA_30 103 kqlaallkaaekagakvilvGDe 125
                                   k+l++l  a+++a+ k+il+G e
  gi|15668275|ref|NP_247068.1| 611 KDLRRLNVAITRAKRKLILIGNE 633
                                   678899999999999*****976 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   1.9e-10   1.7e-07       1     143 [.     189     432 ..     189     434 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.9e-10
                        AAA_19   1 qreave..alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.......atTi 72 
                                   q+ av+   l++++ l+ ++pGtGKTr++++++   v+ +    +++l+ a  + Aa+++ e l   + +           
  gi|15668275|ref|NP_247068.1| 189 QKLAVKkaVLSRDLYLIHGPPGTGKTRTITEVIVQEVKFN---KHKVLATADSNIAADNILEYL-IKKYPdlkvvrvG--- 262
                                   566773345788999**************99887666666...379****************99.3333355554440... PP

                        AAA_19  73 Hrlal............................................................................ 77 
                                                                                                                    
  gi|15668275|ref|NP_247068.1| 263 ----Hptriskdliqhslpylienhekyqeilalrekikeikeqrdkflkpsprwrrgmsdeqilkvakrkksyrgipkek 339
                                   ....244444555666667788888889999999999999999999999******************************** PP

                        AAA_19  78 ................................ldfddlltealelle.........eaeeekklqeee...llivDEfqdv 114
                                                                   l                       + + ++ l +++   ++++DE ++ 
  gi|15668275|ref|NP_247068.1| 340 ivsmaewiirnkkikriinnldeitekimneiL-------------AeadvivatnSMAGSEIL-KGWefdVIVIDEGSQA 406
                                   ********9999999998776555555444432.............244555555433344444.4433469*****9987 PP

                        AAA_19 115 delqyrLlkallgekkklllvGDpdQliy 143
                                    e    L+  ++  + kl++ GD++Ql++
  gi|15668275|ref|NP_247068.1| 407 MEP-SCLIPIVK--GRKLIMAGDHKQLPP 432
                                   633.34666555..5559*********97 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00082      0.73       2      32 ..     204     231 ..     203     263 .. 0.69
   2 ?    5.2   0.0     0.017        15      61     125 ..     393     452 ..     353     508 .. 0.76
   3 !   14.0   0.0   3.6e-05     0.032     173     233 ..     570     630 ..     515     631 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00082
               Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrpta 32 
                                   ++hG pG GK++ i +++ ++++   n+   
  gi|15668275|ref|NP_247068.1| 204 LIHGPPGTGKTRTITEVIVQEVK--FNKH-K 231
                                   79***************999533..3333.3 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.017
               Viral_helicase1  61 tkgkililDEylllhaGyilllaalskaklvilfGDplQipfhsrnasfllahlpsslshrvgrr 125
                                    +++++++DE  ++   +   l+ + k + +i+ GD++Q p       +++  l+++l +r  ++
  gi|15668275|ref|NP_247068.1| 393 WEFDVIVIDEGSQAM--EPSCLIPIVKGRKLIMAGDHKQLPPTV-L--SENEELKKTLFERLIKK 452
                                   45899******8876..56668889**************99764.2..46777777776666555 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3.6e-05
               Viral_helicase1 173 tqalkealgvr.evttvhevqGltfdkVtlvllketdlelisesrenllvAlTRhrkslvil 233
                                    ++l+e+++ + ev+tv + qG + +  ++   ++++   + ++   l vA+TR++++l+++
  gi|15668275|ref|NP_247068.1| 570 LRRLFEEHNIDiEVNTVDGFQGRENEAIVISFVRTKNFG-FLKDLRRLNVAITRAKRKLILI 630
                                   5567778888899**********9998776666444444.4467999***********9876 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       6.3   5.6e+03      30      41 ..      98     109 ..      87     109 .. 0.64
   2 ?   -0.3   0.0       1.1   9.5e+02      11      24 ..     391     404 ..     390     410 .. 0.79
   3 !   19.6   0.0   6.5e-07   0.00058       5      52 .]     584     630 ..     580     630 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.3
                      UvrD_C_2  30 mgelrrrlLYta 41 
                                   +++l+++ +Y++
  gi|15668275|ref|NP_247068.1|  98 QSDLYANVIYVG 109
                                   356799****97 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                      UvrD_C_2  11 QGsefpaVivfdpd 24 
                                   +G ef+++++++ +
  gi|15668275|ref|NP_247068.1| 391 KGWEFDVIVIDEGS 404
                                   899******97765 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 6.5e-07
                      UvrD_C_2   5 ltihkaQGsefpaVivfdpdlaaarmgelrrrlLYtavTRAreklilv 52 
                                    t+  +QG e +a+++  + + ++ ++    r L +a+TRA++klil+
  gi|15668275|ref|NP_247068.1| 584 NTVDGFQGRENEAIVISFVRTKNF-GFLKDLRRLNVAITRAKRKLILI 630
                                   5999************77777775.58789****************96 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.5e-05     0.023       2      66 ..     185     245 ..     184     248 .. 0.79
   2 ?    5.0   0.1     0.013        12     141     186 ..     418     466 ..     369     537 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                                   --HHHHHHHHHH......HCTS-EEEEESTTSSCHH.HHHHHHHHCHCTCCCEEEEESSHHHHHCC CS
                          PIF1   2 LneeQkkvfdaiieavlnekgklfFvtGsgGtgKtf.lwkallkklrsegkivlavAssGvAalll 66 
                                   Lne+Qk +++++   v   +  l  ++G  GtgKt  + + +++ ++ ++++vla+A s +Aa ++
  gi|15668275|ref|NP_247068.1| 185 LNESQKLAVKKA---V--LSRDLYLIHGPPGTGKTRtITEVIVQEVKFNKHKVLATADSNIAADNI 245
                                   777788777776...2..334566689********6256678999*****************9776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.013
                                   C-EEEEE--TTS-----SSSS...S---BGC...CSCHHHH--EEEE-S CS
                          PIF1 141 GktvvlgGDfrQilPviekgs...raeivaasikeSklWkevkvlkLtk 186
                                   G  ++++GD +Q++P +   +   +++ ++  ik+ +  +++  ++   
  gi|15668275|ref|NP_247068.1| 418 GRKLIMAGDHKQLPPTVLSENeelKKTLFERLIKKYPEFSSILEIQYRM 466
                                   899************8854431124455556666655555544444444 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.3e-06    0.0056       2      58 ..     205     275 ..     204     322 .. 0.75
   2 ?   -1.2   0.0       1.8   1.6e+03      90     111 ..     394     416 ..     347     426 .. 0.69
   3 ?   -1.7   0.1       2.5   2.2e+03      57     111 ..     485     551 ..     434     561 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.3e-06
                 Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke..............e 58 
                                   + + +G+GK+ ++  ++ + ++ +k ++l ta s+ ++++++e l+k+  +l++ +              +
  gi|15668275|ref|NP_247068.1| 205 IHGPPGTGKTRTITEVIVQEVKFNKHKVLATADSNIAADNILEYLIKKYPDLKVVRvghptriskdliqhS 275
                                   78899*******************************************99999877544444333333330 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                 Helicase_RecD  90 qadllvvDEAA.aiplpllkkll 111
                                   + d++v+DE + a++ ++l  ++
  gi|15668275|ref|NP_247068.1| 394 EFDVIVIDEGSqAMEPSCLIPIV 416
                                   56999999987345555555555 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.5
                 Helicase_RecD  57 e............eekkkkaekaelrvrkqrieyiapdellklkeqa.dllvvDEAAaiplpllkkll 111
                                                 ++++  e  +  +++  +++i+ + + ++++++     ++EA  + l+++kkl+
  gi|15668275|ref|NP_247068.1| 485 AdesvknitlldlVKEEEIDEVDRDIINEIPVQFINVEGIERKDKESpSYYNIEEAEKV-LEIVKKLV 551
                                   33233333333332222222222233347777777777776655443366667776554.56666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     2e-05     0.018       5      32 ..     200     227 ..     197     305 .. 0.75
   2 ?    0.2   0.0      0.91   8.2e+02     108     135 ..     606     637 ..     562     647 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldee 32 
                                   + + +++G++GtGKT+++ ++  q ++ 
  gi|15668275|ref|NP_247068.1| 200 RDLYLIHGPPGTGKTRTITEVIVQEVKF 227
                                   56789**************999887643 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.91
                        AAA_22 108 aleeLrsllnl....srkgvqliLvGtpelrk 135
                                   ++ +L++l  l     r + +liL+G ++l k
  gi|15668275|ref|NP_247068.1| 606 NFGFLKDLRRLnvaiTRAKRKLILIGNENLLK 637
                                   44444444333335788888888888887765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-05     0.014       2      25 ..     204     228 ..     203     304 .. 0.70
   2 ?   -1.8   0.0       4.4     4e+03      99     110 ..     370     382 ..     317     402 .. 0.59
   3 ?   -2.1   0.0       5.3   4.8e+03      17      53 ..     509     550 ..     507     560 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                                   EEESSTTSSHHHHHH.HHHHHHTHE CS
                           AAA   2 llyGppGtGKTllak.avakelgve 25 
                                   l++GppGtGKT ++   +++e++++
  gi|15668275|ref|NP_247068.1| 204 LIHGPPGTGKTRTITeVIVQEVKFN 228
                                   89*********76650556666543 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.4
                                   S.SSTEEEEEEES CS
                           AAA  99 k.eskvivigatn 110
                                   +  ++  vi+atn
  gi|15668275|ref|NP_247068.1| 370 EiLAEADVIVATN 382
                                   1322223444444 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.3
                                   HHHHHHTHEEEEEETTTCSSS.....STTHHHHHHHHHHHHH CS
                           AAA  17 avakelgvefleisgsellsk.....yvgesekkirelfkea 53 
                                    +++e+ v+f++++g e  +k     y  e ++k+ e++k++
  gi|15668275|ref|NP_247068.1| 509 DIINEIPVQFINVEGIERKDKespsyYNIEEAEKVLEIVKKL 550
                                   578899999999999998877888888888888888887775 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   4.2e-06    0.0038       2      95 ..     183     305 ..     182     408 .. 0.54
   2 ?   -1.8   0.3         3   2.7e+03      96     121 ..     490     531 ..     442     548 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.2e-06
                                   -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH....HHHHHHHHHG.... CS
                        ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprk....slleqtleef.... 74 
                                   ++l+e Q+ a+++ + ++       +li+ + GtGKT++++++i +  k +k  k+l  ++++    ++le +++++    
  gi|15668275|ref|NP_247068.1| 183 KNLNESQKLAVKKAVLSR-----DLYLIHGPPGTGKTRTITEVIVQEVKFNK-HKVLATADSNiaadNILEYLIKKYpdlk 257
                                   578888888888888555.....599****************9999998644.6999999999444444444445557777 PP

                                   .......................................GGGTGG....GEEEESSS-B- CS
                        ResIII  75 .......................................kkflseaykeigkkvsgdkkk 95 
                                                                          k            +++++++k
  gi|15668275|ref|NP_247068.1| 258 vvrvghptriskdliqhslpylienhekyqeilalrekiK------------EIKEQRDK 305
                                   7777777666666666665554444433333333333330............23333333 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                                   -.......................-SEEEEEHHHHHHTH... CS
                        ResIII  96 a................kekdstnkkilvttiqsldadseee 121
                                   +                 +  ++++ + +++++ + ++ +e 
  gi|15668275|ref|NP_247068.1| 490 KnitlldlvkeeeidevDRDIINEIPVQFINVEGIERKDKES 531
                                   112222233333333345555788888888888888777443 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.1   5.5e-06    0.0049       2     171 ..     186     357 ..     185     376 .. 0.59
   2 ?    4.0   0.2     0.033        30     174     294 ..     314     429 ..     267     431 .. 0.67
   3 ?   -1.9   0.5         2   1.8e+03     198     198 ..     523     523 ..     433     658 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.5e-06
                                   SHHHHHHHHS...-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT- CS
                 UvrD-helicase   2 npeqreaias...lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdd 79 
                                   n++q+ a+++   ++   l+   +G+GKT++++e+i++ +k +    +++l+    n Aa+ + e + ++    ++ + ++
  gi|15668275|ref|NP_247068.1| 186 NESQKLAVKKavlSRDLYLIHGPPGTGKTRTITEVIVQEVKFN---KHKVLATADSNIAADNILEYLIKKYPDLKVVRVGH 263
                                   66666666665545667799999***************99877...89999999999999999888888666555555555 PP

                                   H.HHHHHHHHCTTSEEEEHHHHHHHHH..HHHHGGTT......SHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTTTHHH CS
                 UvrD-helicase  80 e.rlrlalqnlseanisTlHsfcqkil..kkeanrig......ldpnfrildeedeedlkqqellkelleksaddslnldk 151
                                     r+ + l ++s       H+  q+il  ++++++i+      l+p  r+ +  +      +++lk      ++++  ++k
  gi|15668275|ref|NP_247068.1| 264 PtRISKDLIQHSLPYLIENHEKYQEILalREKIKEIKeqrdkfLKPSPRWRRGMS-----DEQILKVAK--RKKSYRGIPK 337
                                   4577777777777766666766666651134444444433333222222222222.....223332222..3444555666 PP

                                   HHHHHHHHHHHCCCCCHHHH CS
                 UvrD-helicase 152 kkleklikelsksrnikkee 171
                                   +k+ ++++ ++++++ik + 
  gi|15668275|ref|NP_247068.1| 338 EKIVSMAEWIIRNKKIKRII 357
                                   66666655555555555444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.033
                                   CHHHHHCHHHHHHHHHHHTTCCTTHHCHSS...TSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHH CS
                 UvrD-helicase 174 lskskaeelrelvskakekqlspkelkkaf...ekasdlqkkiaeflkeyqeqkkeenalDfsdllhallelleeneelae 251
                                       + e++ ++ ++ k+   +pke+   +    + +++ k i++ l e+ e+  +e +++ + ++  + +   +++e+++
  gi|15668275|ref|NP_247068.1| 314 RRGMSDEQILKVAKRKKSYRGIPKEKIVSMaewIIRNKKIKRIINNLDEITEKIMNEILAEADVIVA-TNS--MAGSEILK 391
                                   4445566777777777777777777666557766777788888888899888888888887765543.333..35789999 PP

                                   HHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG CS
                 UvrD-helicase 252 alrerykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQ 294
                                    ++  +++i iDE    + +  + l  +++g+ +l+m GD kQ
  gi|15668275|ref|NP_247068.1| 392 GWE--FDVIVIDEG--SQAMEPSCLIPIVKGR-KLIMAGDHKQ 429
                                   985..899999994..5556667777778886.7999999999 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2
                                   H CS
                 UvrD-helicase 198 e 198
                                    
  gi|15668275|ref|NP_247068.1| 523 G 523
                                   1 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.5e-06    0.0067     111     165 ..     182     237 ..     128     249 .. 0.85
   2 ?   -3.0   0.0       3.3     3e+03      37      89 ..     530     590 ..     496     615 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.5e-06
                         T2SSE 111 eealkekiaevlrkavrerglilvsGgTgsGKt.tllyallkeinksderivtvED 165
                                   +++l+e ++ +++kav +r l l+ G+ g+GKt t++ ++++e++ ++++++   D
  gi|15668275|ref|NP_247068.1| 182 DKNLNESQKLAVKKAVLSRDLYLIHGPPGTGKTrTITEVIVQEVKFNKHKVLATAD 237
                                   45666889999**********************5566999***9999888776655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.3
                         T2SSE  37 reveelekaalerlisriaalakldiseer.plqdarlp.......ekgvrlrvvllPvva 89 
                                   +  +  + +++e +++ ++ l+k +i ++   + da++        e++++++v+++  ++
  gi|15668275|ref|NP_247068.1| 530 ESPSYYNIEEAEKVLEIVKKLVKYKIPTNViTPYDAQVRylrrlfeEHNIDIEVNTVDGFQ 590
                                   3333345667777888888888888766541467777776667766666777776665555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     5e-05     0.045      29      63 ..     196     231 ..     177     270 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                        RuvB_N  29 reealdhvllyGpPGlGkt.tlakiiakelgvklki 63 
                                      + d  l++GpPG Gkt t++++i +e++ + + 
  gi|15668275|ref|NP_247068.1| 196 AVLSRDLYLIHGPPGTGKTrTITEVIVQEVKFNKHK 231
                                   44567899**********9889*******9987554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.7e-05     0.033      25      45 ..     201     221 ..     189     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-05
                        AAA_16  25 elvllsGesGvGKsslvrell 45 
                                    l l++G++G+GK++ ++e+ 
  gi|15668275|ref|NP_247068.1| 201 DLYLIHGPPGTGKTRTITEVI 221
                                   4789*************9875 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00013      0.12       4     116 ..     189     295 ..     186     306 .. 0.80
   2 ?    0.2   0.0      0.62   5.6e+02      85     129 ..     351     402 ..     320     409 .. 0.45
   3 ?   -2.3   0.0       3.7   3.3e+03      60     105 ..     540     586 ..     538     603 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                   HHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   4 Qaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig 83 
                                   Q+ a++ ++ + +  l++++ G+GKT      ++q+v    + ++ k+l  + +   a ++l+ l   kky dl+v+ +  
  gi|15668275|ref|NP_247068.1| 189 QKLAVKKAVlSRDLYLIHGPPGTGKTRTITEVIVQEV----KFNKHKVLATADSNIAADNILEYLI--KKYPDLKVVRV-- 261
                                   56566555525555689********************....79999*****************995..56667888744.. PP

                                   TSSHHHHHHHHHTTCSEEEEEHHHHHHHH.HCTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                          DEAD  84 gvaardqlskldngvdivvgtpgrlddll.stgk 116
                                   g+++r  ++ +++++ +++ ++++ +++l  ++k
  gi|15668275|ref|NP_247068.1| 262 GHPTRISKDLIQHSLPYLIENHEKYQEILaLREK 295
                                   8999999999988899999999999997753444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.62
                                   SSHHHHHHHH...........HTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEET CS
                                   xxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  85 vaardqlskl...........dngvdivvgtpgrlddllstgklnlsqvrflVlDE 129
                                   ++ ++ +++l            +++d++v+t ++  + +     +  ++ ++V+DE
  gi|15668275|ref|NP_247068.1| 351 KKIKRIINNLdeitekimneiLAEADVIVATNSMAGSEIL----KGWEFDVIVIDE 402
                                   3333333333211111111102335555555555544321....122445566666 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.7
                                   HHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHH..HTTCSEEEEEH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                          DEAD  60 aeqtlnnlkkfkkyidlrvlliiggvaardqlskl..dngvdivvgtp 105
                                   ae++l+ +kk+ ky ++ +++i+  +a+ + l++l  ++++di v t 
  gi|15668275|ref|NP_247068.1| 540 AEKVLEIVKKLVKY-KIPTNVITPYDAQVRYLRRLfeEHNIDIEVNTV 586
                                   68889999999997.455555666666655566654335588877775 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0002      0.18       5      64 ..     185     245 ..     183     255 .. 0.77
   2 ?   -0.9   0.0         1   9.4e+02     121     158 ..     396     430 ..     343     453 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                   -SHHHHHHHHHHH.H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT-- CS
                          PhoH   5 ktkeQkeylealk.kndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveagee 64 
                                    +++Qk +++    + d+  + Gp GtGKt   + + v+ +k +k k +  +  ++ a++ 
  gi|15668275|ref|NP_247068.1| 185 LNESQKLAVKKAVlSRDLYLIHGPPGTGKTRTITEVIVQEVKFNKHKVLATADSNIAADNI 245
                                   57888888765444****************9999999999888887776666666666555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                                   EEEEE-S.GGG--HHHHHHHHTTB-TT-EEEEEE----- CS
                          PhoH 121 afvilDE.AQnttkeqmkmfltRlGenskvvvtGdvtqi 158
                                    ++++DE +Q ++++    +l+ + ++ k++++Gd +q 
  gi|15668275|ref|NP_247068.1| 396 DVIVIDEgSQAMEPS----CLIPIVKGRKLIMAGDHKQL 430
                                   367777733444443....56666788899999998886 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0       0.1        94      18      32 ..     241     255 ..     234     256 .. 0.88
   2 ?    7.1   0.0     0.011       9.5      20      32 ..     443     455 ..     437     455 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.1
                                   HHHHHHHHHHHH-TT CS
                         TPR_6  18 kAlealerlikeYPd 32 
                                   +A  +le lik+YPd
  gi|15668275|ref|NP_247068.1| 241 AADNILEYLIKKYPD 255
                                   57889*********8 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.011
                                   HHHHHHHHHH-TT CS
                         TPR_6  20 lealerlikeYPd 32 
                                   ++++erlik+YP+
  gi|15668275|ref|NP_247068.1| 443 KTLFERLIKKYPE 455
                                   789*********5 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.18      25      66 ..     192     234 ..     185     263 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                         AAA_7  25 llelllknkkpvllvGptGtGKtviikd.llkkldkekylslt 66 
                                    +++ + ++   l+ Gp GtGKt +i++ ++++++ +k+++l 
  gi|15668275|ref|NP_247068.1| 192 AVKKAVLSRDLYLIHGPPGTGKTRTITEvIVQEVKFNKHKVLA 234
                                   567777788889****************777777755555544 PP

>> DUF2722  Protein of unknown function (DUF2722)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.5   0.00026      0.24     101     128 ..     533     560 ..     526     563 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00026
                       DUF2722 101 eYYklEianknLeilktAlqAqiPvnlI 128
                                   +YY +E a+k Lei+k  ++ +iP+n I
  gi|15668275|ref|NP_247068.1| 533 SYYNIEEAEKVLEIVKKLVKYKIPTNVI 560
                                   7*************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (663 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1411  (0.0786993); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.52
# Mc/sec: 3855.97
//
Query:       gi|15668276|ref|NP_247069.1|  [L=152]
Description: hypothetical protein MJ_0105 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-29  102.6   1.3    1.4e-29  102.3   1.3    1.1  1  DUF473    Protein of unknown function (DUF473)
  ------ inclusion threshold ------
      0.042   14.4   0.2      0.061   13.9   0.2    1.3  1  YuiB      Putative membrane protein


Domain annotation for each model (and alignments):
>> DUF473  Protein of unknown function (DUF473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   1.3   1.6e-33   1.4e-29       1     109 [.      39     142 ..      39     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 1.6e-33
                        DUF473   1 MkvvaLtGiseevieeLkknklrtielrsahNvitllklevgdlvFlTsvsleDltkGteGiiaevlsveistkrvvesse 81 
                                   Mkv+ L Gi+e++i+++++n+++t+++ +a N+ t+++l++gdlvF+Ts+ +eDl++GteGi+ +v++v+++ +++     
  gi|15668276|ref|NP_247069.1|  39 MKVYGLFGINENAINDFIENHIKTFTIINALNLETVKNLKEGDLVFITSTLREDLRNGTEGILGRVINVSLVPQMI----- 114
                                   9*************************************************************************99..... PP

                        DUF473  82 sfieErEttvarvqlkllglgrvrevke 109
                                   + +eE+E+++ rvql++lg+++++++++
  gi|15668276|ref|NP_247069.1| 115 NGFEEKEIIAGRVQLEMLGFAKCVKYES 142
                                   579*********************9876 PP

>> YuiB  Putative membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   6.8e-06     0.061      16      80 ..      21      89 ..      15     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-06
                          YuiB 16 igfilnmllrttWilaviypivvllivdkvklleyltepkeafasl....leklvelalvDililvsgl 80
                                  i + lnml  + W +  i+ +  l+ ++++ + +++++  ++f+ +    le++ +l+  D++ ++s+l
  gi|15668276|ref|NP_247069.1| 21 ILYCLNMLKLSNWYFGGIMKVYGLFGINENAINDFIENHIKTFTIInalnLETVKNLKEGDLVFITSTL 89
                                  7789**********************************9999987622234788999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1021.90
//
Query:       gi|15668277|ref|NP_247070.1|  [L=238]
Description: hypothetical protein MJ_0106 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-35  123.1   0.0    1.8e-35  122.9   0.0    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.9   0.0     1e-39   1.8e-35       2     213 .]      21     220 ..      20     220 .. 0.94

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 1e-39
                                   EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEE...E-HSC CS
                          PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqg...repil 79 
                                   i++fpg+G+Vg++a   +i  l+++++g+++ d+ +      p +++e+g +++p+r ya++    d+++l +   ++p  
  gi|15668277|ref|NP_247070.1|  21 IEAFPGTGLVGSIAGFQIIKDLNLKYFGYFEVDG-IL-----PLTTIEKGIPYPPVRAYANK----DFIILFSdiiISPFK 91 
                                   99********************************.66.....689**************995....699999999888888 PP

                                   HHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT....-CEEEEHHHHHHHHHHHH CS
                          PAC2  80 qyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees....eyggivgitglLlsaake 156
                                    +  +a+ +++ ++  + k  v Lgg+ ag++        ekv+g+a+ eel+e+l++     + g+++g+ g Ll  ++ 
  gi|15668277|ref|NP_247070.1|  92 ING-LAEFIVKTFSNKNPKLFVSLGGIMAGKS--------EKVFGIANKEELIEDLKNYveifDFGVVGGMGGNLLIKCHD 163
                                   888.************************8876........49**************855667899**************** PP

                                   TT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHHH CS
                          PAC2 157 rgipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleela 213
                                   +g++a+gllae+ +  pdP+  a lle+l+k+++l+v+ e+L+++ae++e++l+ela
  gi|15668277|ref|NP_247070.1| 164 NGFDAIGLLAETVGIRPDPRGGANLLEVLNKMFNLNVNIENLIKEAEAIENKLKELA 220
                                   ******************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      797  (0.0444531); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1718.61
//
Query:       gi|15668278|ref|NP_247071.1|  [L=525]
Description: dihydropteroate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-14   52.8   0.1    6.9e-14   52.1   0.1    1.3  1  Pterin_bind  Pterin binding enzyme
    1.9e-10   40.8   0.2    6.8e-09   35.8   0.2    2.7  3  DUF4346      Domain of unknown function (DUF4346)
  ------ inclusion threshold ------
      0.039   13.1   0.1       0.33   10.1   0.0    2.2  2  DUF561       Protein of unknown function (DUF561)
      0.077   13.5   0.4       0.24   11.9   0.1    2.1  2  DUF4830      Domain of unknown function (DUF4830)
      0.085   13.1   0.0        0.2   11.9   0.0    1.6  1  TetR_C_10    Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.1   1.9e-17   6.9e-14      30     238 ..     184     367 ..     173     372 .. 0.82

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.9e-17
                                   HHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHH CS
                   Pterin_bind  30 mveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDttkaevaeaAlkagadivNdvsgeerdpkml 110
                                    +e+GAd++D+g+ s          e+  +++  +l+  rd +d pis+Dt +++ + +A++ gad++ +v +++   +++
  gi|15668278|ref|NP_247071.1| 184 YLESGADMIDLGMVSN---------ENNADKIKDMLKIARDLTDNPISVDTLNTKELIEAINLGADMILSVDAGN-LDELI 254
                                   5799********8777.........8888999999996666669*******************************.899** PP

                                   HHHHHHT-EEEEESECSSTTTHCCCC.CCCSSHHHHHHHHHHHHHHHHHHTT--GGGEEEETTTTS.STTHHHHHHHHHTH CS
                   Pterin_bind 111 elvaeagaavvvmhmrgtpktmqeee.gqyedvveeveaflearveaaeeaGvaperillDpgigf.gkteehnlellrrl 189
                                   + ++++++avvv+ ++       +++    e+++ ++++  e  ++++  aG+++  i+ Dp + + + +  + +e + + 
  gi|15668278|ref|NP_247071.1| 255 PYLKDSETAVVVLPTN-------YKTnYVPETIEGKIKSLEE-NIKKLIDAGIEK--IVADPILEPiNNAGCSFIESVIAC 325
                                   *************999.......2222467999999998776.6677777***66..*******99888888888999999 PP

                                   HHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHHHHHHTT- CS
                   Pterin_bind 190 delrealevpvllGvSrksflgrllelgkaeeRdagtaaflalaaaaGa 238
                                    e++++ ++p++ Gv ++  l++        + + ++a ++a++a+ Ga
  gi|15668278|ref|NP_247071.1| 326 REFKKRNKLPLFFGVGNVTELFDA-------DSNGVNALLAAIGAEIGA 367
                                   99999999*********9999874.......444555555555555555 PP

>> DUF4346  Domain of unknown function (DUF4346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.8   6.6e+03      24      68 ..     296     337 ..     294     340 .. 0.68
   2 !    4.9   0.1    0.0071        25      15      37 ..     443     465 ..     432     468 .. 0.84
   3 !   35.8   0.2   1.9e-12   6.8e-09      47     118 .]     452     520 ..     450     520 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.8
                       DUF4346  24 dreaklivakhysnainekGlavdpetgevisckgkkkreaekvy 68 
                                   d+  ++iva+     in+ G +       vi+c++ kkr++  ++
  gi|15668278|ref|NP_247071.1| 296 DAGIEKIVADPILEPINNAGCSFIE---SVIACREFKKRNKLPLF 337
                                   5556677777777778887776543...48899988888776555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0071
                       DUF4346  15 paGYflikvdreaklivakhysn 37 
                                    +G f i++dr++k+iva ++++
  gi|15668278|ref|NP_247071.1| 443 DEGSFKIEIDRKNKEIVAIYFNK 465
                                   4799**************99975 PP

  == domain 3  score: 35.8 bits;  conditional E-value: 1.9e-12
                       DUF4346  47 dpetgevisckgkkkreaekvyrgrtakelcvkileeeeelpvtkldhaaYlGRelqraeaaLlsgkeYiqD 118
                                   d +  e +++  +k+re+  + rg+  ke+    +   +   + kldha Y+GRel +ae+aL  gk+Y qD
  gi|15668278|ref|NP_247071.1| 452 DRKNKEIVAIYFNKRREPVLIIRGKKPKEIYETAI---RLNLIKKLDHASYFGRELAKAEIALRIGKKYNQD 520
                                   67777788888899999999999999999754443...345699***************************9 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.095   3.4e+02      53      87 ..      91     125 ..      84     131 .. 0.88
   2 ?   10.1   0.0   9.3e-05      0.33      51      93 ..     208     253 ..     185     280 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.095
                        DUF561  53 vkkvksvsniPiCvsaveakllleavkaGadlvei 87 
                                    k+ +++s+iPi +  ++  +l     a  +l+ei
  gi|15668278|ref|NP_247071.1|  91 FKSTREASDIPILIENLDKIKLSTKEYADLQLLEI 125
                                   5778999**************99999999999998 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 9.3e-05
                        DUF561  51 klvkkvksvsniPiCvsaveakllleavkaGadlv...eiGnfdsl 93 
                                   +++k  ++ ++ Pi v ++++k+l+ea+  Gad++   + Gn d l
  gi|15668278|ref|NP_247071.1| 208 DMLKIARDLTDNPISVDTLNTKELIEAINLGADMIlsvDAGNLDEL 253
                                   677788899999*********************9633377888866 PP

>> DUF4830  Domain of unknown function (DUF4830)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.2   1.1e+04      11      27 ..     266     282 ..     256     292 .. 0.63
   2 ?   11.9   0.1   6.7e-05      0.24      17      59 ..     384     430 ..     376     463 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.2
                       DUF4830  11 ekpietkevkiPkefee 27 
                                     p+++k+  +P+++e 
  gi|15668278|ref|NP_247071.1| 266 VLPTNYKTNYVPETIEG 282
                                   44566777777777765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.7e-05
                       DUF4830  17 kevkiPkefeevyaeynelqkdiGldLekykgk....evtrytYelk 59 
                                   ke+ki +++    ++ n l kdiG++L +yk+k    e+t  +Y++ 
  gi|15668278|ref|NP_247071.1| 384 KELKIASKMMFLAKKRNSLPKDIGYNLINYKDKrfeeEITFNSYNIP 430
                                   5677777777778999****************933333444455555 PP

>> TetR_C_10  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.6e-05       0.2      32      81 ..     252     301 ..     249     310 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.6e-05
                     TetR_C_10  32 rlvefakeneqaflflethkdakyLdeeskelfeelmdfltdliekGkek 81 
                                    l+ + k++e+a+++l t+ +++y+ e+ +  ++ l + +++li++G+ek
  gi|15668278|ref|NP_247071.1| 252 ELIPYLKDSETAVVVLPTNYKTNYVPETIEGKIKSLEENIKKLIDAGIEK 301
                                   5889*******************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 3524.12
//
Query:       gi|15668279|ref|NP_247072.1|  [L=447]
Description: pyruvate kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-82  277.8  12.3      2e-82  276.9  12.3    1.4  1  PK         Pyruvate kinase, barrel domain
    1.2e-18   67.5   3.2      4e-18   65.7   0.0    3.0  3  PK_C       Pyruvate kinase, alpha/beta domain
    3.6e-06   26.3   0.1    9.2e-06   24.9   0.1    1.6  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.9  12.3   3.4e-86     2e-82       1     342 [.       5     320 ..       5     325 .. 0.91

  Alignments for each domain:
  == domain 1  score: 276.9 bits;  conditional E-value: 3.4e-86
                                   ---SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BTTCS CS
                            PK   1 lrrtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllkdgk 81 
                                   +r+tki+ tlGP+ e+  kl+k i+  ++ vr+n sh + ++ ++ ++ + +      +++a ++D+kG +ir++ +k   
  gi|15668279|ref|NP_247072.1|   5 MRKTKILVTLGPSLEN--KLDKAINL-IDGVRFNMSHATTDYCEKFLNILEK------NNIAKVMDLKGIKIRIKEVKL-- 74 
                                   69**********9654..45554443.4558***********9988876643......568999***********9999.. PP

                                   SSEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EEE-SS-BE CS
                            PK  82 kdielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgvlgskkgv 162
                                   k+  lk g+k+ +  d           i+l+y+  ++ +e G+ il++DG+++l+v e++++      ve++g++++  gv
  gi|15668279|ref|NP_247072.1|  75 KNKILKMGEKVVIGED-----------IKLNYN--IDTIEEGHFILINDGKIKLRVVEKTDKI--IAVVEVGGEIKEGMGV 140
                                   4677999999996554...........556665..799******************9998766..667899********** PP

                                   E-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHHTHHHHHHHSSEE CS
                            PK 163 nlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegvenldeileasDgi 243
                                   nlp+t+++lp + e D ++++f+v+++ + ia+sfvr+ +Dvke+++++ e + + ++i+kie +eg++n+ ei ++sDg+
  gi|15668279|ref|NP_247072.1| 141 NLPDTRIELPIIDETDLKNIKFAVEKDFEYIALSFVRNKEDVKELKDIISEYKGDCEVISKIETKEGLKNIKEIARESDGV 221
                                   ********************************************************************************* PP

                                   EEEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT-SEEEESHHHHTSS-H CS
                            PK 244 mvarGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDGtDavmLsgetakGkyP 324
                                   mvarGDlG+e+p e++++ qk +++ +n+ g   itatq+l+smi+nP ptraev+D+ana+ DGtD++mLs et  GkyP
  gi|15668279|ref|NP_247072.1| 222 MVARGDLGVEVPIENIPIEQKNILRIANRYGILSITATQILDSMINNPFPTRAEVTDIANAIYDGTDCLMLSNETTIGKYP 302
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHTS CS
                            PK 325 veavkamaevaleaekal 342
                                   +ea+k++++va+ a++  
  gi|15668279|ref|NP_247072.1| 303 IEAIKVLNKVAKVADEHY 320
                                   ************999875 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.072   4.3e+02      81     104 ..      69      92 ..       4     101 .. 0.53
   2 ?   -3.0   0.2       1.4   8.4e+03      89     103 ..     116     130 ..     110     137 .. 0.75
   3 !   65.7   0.0   6.7e-22     4e-18       3     116 ..     338     444 ..     336     445 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.072
                                   HHHHHHHTTSS-STSEEEEEE-SS CS
                          PK_C  81 avkvakeaglvkkgdevvvtaGtp 104
                                   + +v ++++++k g++vv+   ++
  gi|15668279|ref|NP_247072.1|  69 IKEVKLKNKILKMGEKVVIGEDIK 92 
                                   133444488888899888866655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                                   TSS-STSEEEEEE-S CS
                          PK_C  89 glvkkgdevvvtaGt 103
                                   ++v+k d+++++  +
  gi|15668279|ref|NP_247072.1| 116 RVVEKTDKIIAVVEV 130
                                   678999999998654 PP

  == domain 3  score: 65.7 bits;  conditional E-value: 6.7e-22
                                   HHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTSHHHHHHH CS
                          PK_C   3 iakaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestdellreavk 83 
                                   +++a+ e+ ++l+ k+++++t sG+tA+lisk+r + +iia tpn +t ++l l++Gv + l+e+    +++++++++  +
  gi|15668279|ref|NP_247072.1| 338 LVYAVYELYKKLNTKLVITPTYSGRTAKLISKLRINSKIIAPTPNIRTLKRLRLVWGVESCLMEE---FDDMEKIINTCRE 415
                                   568999*******************************************************9875...5555555554444 PP

                                   HHHHTTSS-STSEEEEEE-SSSS..SS--EEEE CS
                          PK_C  84 vakeaglvkkgdevvvtaGtpkgesgttNtlrV 116
                                   +ak+   + kg    +t G p+g +++tNt++V
  gi|15668279|ref|NP_247072.1| 416 MAKK--EIGKG-IYLITLGHPIG-QKKTNTIKV 444
                                   4444..46666.556677889**.9*******9 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   1.5e-09   9.2e-06      76     147 ..     158     224 ..     145     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.5e-09
                                   HHGG.HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH.TSTTEEEE CS
                     HpcH_HpaI  76 qdle.vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIa.avegldgv 147
                                   ++++ ++++ ++ + + +v ++e+++e++ ++ e +       +   ++  iE++eg+kn++eIa +++g++++
  gi|15668279|ref|NP_247072.1| 158 KNIKfAVEKDFEYIALSFVRNKEDVKELKDIISEYK-------GDCEVISKIETKEGLKNIKEIArESDGVMVA 224
                                   457789****************************99.......8899******************999999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3016.60
//
Query:       gi|15668280|ref|NP_247073.1|  [L=252]
Description: bifunctional inositol-1 monophosphatase/fructose-1,6-bisphosphatase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-33  115.9   0.0    2.8e-33  115.6   0.0    1.1  1  Inositol_P  Inositol monophosphatase family
     0.0027   17.2   0.0     0.0048   16.4   0.0    1.4  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.6   0.0   3.1e-37   2.8e-33      10     260 ..       8     245 ..       2     252 .] 0.84

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 3.1e-37
                                   HHHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEE CS
                    Inositol_P  10 velaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwiv 90 
                                    ++a+++ + +  +f+ ++++ + ++ + + d  +  d+ +e++ l+ l+       i++ee + + +     ++++t+++
  gi|15668280|ref|NP_247073.1|   8 KNIAKEIEKEILPYFGRKDKSYVVGT-SPSGDETEIFDKISEDIALKYLKSLN--VNIVSEELGVIDN-----SSEWTVVI 80 
                                   57788999999999998888888888.78999999999999999999987776..8899988888888.....555***** PP

                                   EEEETHHHHHHT-SG-EEEEEEEETTEEEEEEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTEEEEEESSSSSSH CS
                    Inositol_P  91 DPiDGTknFvrgipqvaVsigllvegkpvlGviaqPllgqlysaakgkGaflngeklplsrappiseallvtlfavssrkd 171
                                   DPiDG  nF++gip +a + g++++ +p  G+ ++ l++++y a+kgkGa+lng+k+++++ +  +++++++    s+++d
  gi|15668280|ref|NP_247073.1|  81 DPIDGSFNFINGIPFFAFCFGVFKNNEPYYGLTYEFLTKSFYEAYKGKGAYLNGRKIKVKDFN--PNNIVIS-YYPSKKID 158
                                   ************************************************************999..7787766.33444444 PP

                                   HHHCHHHHHHHCCCCCHEEEBESSHHHHHHHHHHTSTSEEEEEC..EBHHHHHHHHHHHHHTTEEEEESSSC..SSSTTSS CS
                    Inositol_P 172 tseasllekvesavsaegvrsvgssalklaavaeGkadaylefg.rekkWDhAAGeaileeaGGvvtdakge..grlllar 249
                                    +      k+   v++  vr +g+ +l++++va G +da+ + + ++   D+A   +i++eaG+ +td +g+  +++l+a+
  gi|15668280|ref|NP_247073.1| 159 LE------KLRNKVKR--VRIFGAFGLEMCYVAKGTLDAVFDVRpKVRAVDIASSYIICKEAGALITDENGDelKFDLNAT 231
                                   44......44333333..5888*********************999**************************997888654 PP

                                   ...EEEEESCHHHH CS
                    Inositol_P 250 ...giiaanqkela 260
                                      +ii+an+ke+ 
  gi|15668280|ref|NP_247073.1| 232 drlNIIVANSKEML 245
                                   44588888866654 PP

>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.4e-07    0.0048      57     118 ..      36      90 ..       8     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.4e-07
                        FBPase  57 tGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSnid 118
                                    Gde +  D ++++i  + lk+  +   +vSEE   l v+   ++++++v++DP+DGS n  
  gi|15668280|ref|NP_247073.1|  36 SGDETEIFDKISEDIALKYLKSL-N-VNIVSEE---LGVI--DNSSEWTVVIDPIDGSFNFI 90 
                                   69999999*******99999987.3.4688987...6777..67799***********9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1685.75
//
Query:       gi|15668281|ref|NP_247074.1|  [L=93]
Description: hypothetical protein MJ_0110 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-10   41.2   1.0    1.1e-10   41.2   1.0    1.7  1  PQ-loop          PQ loop repeat
    1.3e-07   31.5   2.5    1.6e-07   31.3   2.5    1.2  1  MtN3_slv         Sugar efflux transporter for intercellular e
    2.1e-06   27.7   0.8    2.9e-06   27.3   0.8    1.2  1  LAB_N            Lipid A Biosynthesis N-terminal domain
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.016   15.0   0.1    1.3  1  Asp-Al_Ex        Predicted Permease Membrane Region
      0.027   15.3   0.8       0.04   14.8   0.1    1.6  2  ER_lumen_recept  ER lumen protein retaining receptor


Domain annotation for each model (and alignments):
>> PQ-loop  PQ loop repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   1.0     3e-14   1.1e-10       3      58 ..      10      65 ..       9      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 3e-14
                       PQ-loop  3 eilgyislvlwlvsyiPQiikNykrkSteGlSilflllwllGdilsllylilngfp 58
                                  +++gyi+ +l+ ++ +PQ+ik  k k ++++S+ f++  ++G +l+l+y il+++ 
  gi|15668281|ref|NP_247074.1| 10 TVIGYIAGTLTTFASLPQLIKSLKEKDMSNISLAFVITFTTGLTLWLIYGILRNDY 65
                                  689************************************************99875 PP

>> MtN3_slv  Sugar efflux transporter for intercellular exchange
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   2.5   4.4e-11   1.6e-07      13      71 ..      19      77 ..       7      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 4.4e-11
                      MtN3_slv 13 avFlsPlsilrkiikkksveelsfllflagllsallWllYGllkkdaliiivNlvgvll 71
                                  +  ++ l++l k +k k+++++s++ +++ + + +lWl+YG+l +d+ ii+ N++ +++
  gi|15668281|ref|NP_247074.1| 19 LTTFASLPQLIKSLKEKDMSNISLAFVITFTTGLTLWLIYGILRNDYPIIVFNILSLMF 77
                                  344567***********************************************997765 PP

>> LAB_N  Lipid A Biosynthesis N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.8     8e-10   2.9e-06       1      65 [.      12      77 ..      12      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 8e-10
                         LAB_N  1 lGflgqllFtlRfvvQwiasekkkk.svlpvlFWvlSllGslllliYailrkDpvlilgqslglvi 65
                                  +G+++ +l t+  + Q i s k+k  s ++++F +   +G +l liY+ilr+D+ +i+ ++l+l+ 
  gi|15668281|ref|NP_247074.1| 12 IGYIAGTLTTFASLPQLIKSLKEKDmSNISLAFVITFTTGLTLWLIYGILRNDYPIIVFNILSLMF 77
                                  899*****************98875389********************************999875 PP

>> Asp-Al_Ex  Predicted Permease Membrane Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   4.4e-06     0.016     109     162 ..       3      59 ..       1      69 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.4e-06
                     Asp-Al_Ex 109 lkldla.llaGllaGalTstpalgaandalaeldlpa..vgyavtYplgvvllilva 162
                                   +++d+  +++G +aG+lT+ ++l   +  l+e d+++  +++ +t+ +g++l ++++
  gi|15668281|ref|NP_247074.1|   3 INMDFDiTVIGYIAGTLTTFASLPQLIKSLKEKDMSNisLAFVITFTTGLTLWLIYG 59 
                                   5566651568***************99999**9999955666677788888777766 PP

>> ER_lumen_recept  ER lumen protein retaining receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.1e-05      0.04     100     143 ..      15      58 ..       4      62 .. 0.84
   2 ?   -1.1   0.1      0.86   3.1e+03      41      47 ..      72      78 ..      53      92 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
               ER_lumen_recept 100 fsiiLesvAilPQlillqktgevesltshyvfalglyRalylln 143
                                   ++  L ++A lPQli   k+++++++   +v++++    l l++
  gi|15668281|ref|NP_247074.1|  15 IAGTLTTFASLPQLIKSLKEKDMSNISLAFVITFTTGLTLWLIY 58 
                                   556799***************************99877777766 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.86
               ER_lumen_recept 41 ialills 47
                                  i+ + + 
  gi|15668281|ref|NP_247074.1| 72 ILSLMFW 78
                                  2222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 640.85
//
Query:       gi|15668282|ref|NP_247075.1|  [L=396]
Description: preprotein translocase subunit SecD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-20   73.4   7.6    3.9e-20   72.0   7.6    1.6  1  SecD_SecF  Protein export membrane protein
    4.2e-08   32.4   0.2    1.1e-07   31.1   0.3    1.7  2  Sec_GG     SecD/SecF GG Motif
     0.0003   18.6   8.1    0.00034   18.4   6.4    1.7  2  ACR_tran   AcrB/AcrD/AcrF family
     0.0008   18.4   6.7     0.0013   17.7   6.7    1.4  1  MMPL       MMPL family
  ------ inclusion threshold ------
      0.043   11.9  10.5      0.062   11.4  10.5    1.1  1  Patched    Patched family
      0.087   13.4   0.1        2.9    8.5   0.0    2.4  2  POTRA      Surface antigen variable number repeat


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   7.6   1.3e-23   3.9e-20      14     173 ..     227     379 ..     216     391 .. 0.86

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 1.3e-23
                                   EEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-H.HHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHH CS
                     SecD_SecF  14 ekisvetvgpsvskelaekavlallialvliliyvalrFew.rvalaaiialvhDviitvgvlsllgievdlatvaalLti 93 
                                    +  ++t++p+++ke+ +  ++all+a++++ i v++r+++ ++a+ ++i+ ++ vii++g+ sl+  ++dl ++a+++  
  gi|15668282|ref|NP_247075.1| 227 DIEYISTISPEFGKEFLKGTAIALLLAFIAVGIIVSIRYKQpKIAIPILITCISEVIIILGFASLIDWKLDLPSIAGIIAA 307
                                   5667899********************************86379************************************* PP

                                   TTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTT CS
                     SecD_SecF  94 iGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgty 173
                                   +G  v++++v++d   ++            i  s++  +    +  +t + +++ l++lg ++lk+fa++ + G+++g++
  gi|15668282|ref|NP_247075.1| 308 VGTGVDNQIVITDEALKRG----AG----KIRASIKRAFFIIFASAATSIAAMLPLFVLGVGMLKGFAITTIAGVLIGIF 379
                                   *************877772....33....35556666666444444555667889***********************86 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.3   3.7e-11   1.1e-07       1      27 [.      24      50 ..      24      51 .. 0.95
   2 ?   -2.8   0.0       1.7     5e+03      17      27 ..     258     268 ..     258     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 3.7e-11
                                  .HHHHC--EE-TTTS-EEEEEEEE-TT CS
                        Sec_GG  1 islftkGlNLGlDFtGGthielqfdqp 27
                                  +++++kGl +G+D+ GGt+i+l++++p
  gi|15668282|ref|NP_247075.1| 24 FLIVFKGLDFGIDLSGGTIIVLKAEKP 50
                                  6899*********************98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                                   EEEEEEEE-TT CS
                        Sec_GG  17 Gthielqfdqp 27 
                                   G ++ ++++qp
  gi|15668282|ref|NP_247075.1| 258 GIIVSIRYKQP 268
                                   778999***98 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0     0.087   2.6e+02     523     588 ..       6      68 ..       3      85 .. 0.71
   2 !   18.4   6.4   1.1e-07   0.00034     812    1008 ..     193     380 ..     188     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.087
                                   HHHSHHHHHHHHHHHHHHHHHHHHCS-BESS----TSEEEEEEE-STTB-HHHHHHHHHHHHHHHH CS
                      ACR_tran 523 vlrhravvllvalvllvlsvllfvripkeflPeedegvlvtsvqlppgvsleqtqkvlkqvekilk 588
                                   +l+ r+++  ++++++ lsv+l+v+ +  f  ++  g ++ ++++ + +s ++ ++ +k++++ l+
  gi|15668282|ref|NP_247075.1|   6 LLKDRKIL--ILIIFVTLSVFLIVFKGLDFGIDLSGGTII-VLKAEKPMSDKEIEATIKIITERLN 68 
                                   55555554..455666778999999999998888877765.4677777888888888888887776 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.1e-07
                                    EEEEEEEEESTTS-HHHHHHHHHHHCTT..SSTTEEEEEEHHHHHH..HHHHCHHHHHHHHHHHHHHHHHHHHHTSSST CS
                      ACR_tran  812 rsvvisgnvaegdslseaeeavekiakkvklpegvtiewtgqaeqe..qeasnsllilvalalllvflvLaalyeslse 888 
                                    +++++ + +++++   ea+++ +++++   lp  ++ie+  +   e  +e  + + i + la+++v ++  + y+  ++
  gi|15668282|ref|NP_247075.1|  193 QVITVGAYPPTKEEIDEAMAIYSALKSG-ALPVKLDIEYISTISPEfgKEFLKGTAIALLLAFIAVGIIVSIRYKQPKI 270 
                                    67888899999999999********999.*********9877655423677889999999******************* PP

                                    CHHHHTTHHHHHHHHHHHHHHTT--BSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHHHCHHHH. CS
                      ACR_tran  889 pllilltvPlalvGallalllrglelsviaqvGlilliGlavkNaillvefakelrekegksleeaileaakeRLrPi. 966 
                                    ++ il+t    ++  l  ++l + +l++ ++ G+i+ +G  v N i++ + a +  +  gk      ++a+ +R   i 
  gi|15668282|ref|NP_247075.1|  271 AIPILITCISEVIIILGFASLIDWKLDLPSIAGIIAAVGTGVDNQIVITDEALKRGA--GK------IRASIKRAFFIi 341 
                                    *******9999998888899*****************************99988777..55......355555544440 PP

                                    HHHHHHHHHHHHHHHCT-STTHHHHHHHHHHHHHHHHHHHHH CS
                      ACR_tran  967 LMTalaailGvlPLalstgaGselqqplgivvlgGlvtstvL 1008
                                       a ++i  +lPL +    G ++ +  +i+ + G+++  ++
  gi|15668282|ref|NP_247075.1|  342 FASAATSIAAMLPLFV---LGVGMLKGFAITTIAGVLIGIFI 380 
                                    4455556677899976...57778888888888888776665 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   6.7   4.5e-07    0.0013     137     292 ..     238     382 ..     154     389 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.5e-07
                          MMPL 137 lrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvl.liavGt 216
                                   + + + + ++++ +++++ + +i  i y+ + +a+ +l+t + ++++ lg+      ++ ++ +   ++++ ++ ++++G+
  gi|15668282|ref|NP_247075.1| 238 FGKEFLKGTAIALLLAFIAVGIIVSIRYKQPKIAIPILITCISEVIIILGF------ASLIDWKLDLPSIAGIIaAVGTGV 312
                                   555566778888999999999999999999999999999999999998888......56667777777786655269**** PP

                          MMPL 217 DYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivl 292
                                   D  + ++    e+l++g  +   +   ++++   ++a+++t ++aml L v+ +++l++++++   Gvl+ ++i++
  gi|15668282|ref|NP_247075.1| 313 DNQIVIT---DEALKRGAGK---IRASIKRAFFIIFASAATSIAAMLPLFVLGVGMLKGFAITTIAGVLIGIFITR 382
                                   *999986...5999999999...8888899999****************************************987 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  10.5   2.1e-05     0.062     663     796 ..     250     379 ..     239     381 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.1e-05
                       Patched 663 ivlallcmfvvallfipelitvlvitlsivsidigviGflslWgvdLDpismitiimsiGfsvdlsaHiayafvrsekdda 743
                                   ++la++ + ++  +   ++ +++ i ++++s  i ++Gf sl   +LD  s++ ii ++G  vd    i+ +  +      
  gi|15668282|ref|NP_247075.1| 250 LLLAFIAVGIIVSIRYKQPKIAIPILITCISEVIIILGFASLIDWKLDLPSIAGIIAAVGTGVDNQIVITDEALKR----G 326
                                   456777777777788899**********************************************987777655554....4 PP

                       Patched 744 keRvvealealgwPvvqgalSTilgvlvLlfvdsymvqvFfktvvLvvvigll 796
                                   + +++++++   + ++ +a   i+++l L++    m + F+ t +  v+ig++
  gi|15668282|ref|NP_247075.1| 327 AGKIRASIKRAFFIIFASAATSIAAMLPLFVLGVGMLKGFAITTIAGVLIGIF 379
                                   58999999999999999999999***************************986 PP

>> POTRA  Surface antigen variable number repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00097       2.9      25      69 ..      45      83 ..      37      90 .. 0.77
   2 ?    2.1   0.0       0.1     3e+02      40      68 ..      95     125 ..      93     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00097
                                  SSTTSBHCHHHHHHHHHHHHHHHHCTT-EE.EEEEEEHSSTTSEE CS
                         POTRA 25 lkegdvynpekleadkealksryanlGyfdasVqvelpeddedkn 69
                                  lk  ++ + +++ea+++ +++r++ +G  d  V +     +  ++
  gi|15668282|ref|NP_247075.1| 45 LKAEKPMSDKEIEATIKIITERLNYNGLND-VVIY-----PRGND 83
                                  7888999*********************98.4433.....33333 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.1
                                   HHHHHHHHHCTT-EE.EE.EEEE.HSSTTSE CS
                         POTRA  40 kealksryanlGyfdasV.qvel.peddedk 68 
                                    +++ + + ++G+f a++ ++++ +++d ++
  gi|15668282|ref|NP_247075.1|  95 TDRIIKILKQQGVFVAKIdNITAyTGSDVQN 125
                                   57788899**********9888875555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2669.98
//
Query:       gi|15668283|ref|NP_247076.1|  [L=488]
Description: acetyl-CoA decarbonylase/synthase complex subunit gamma [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   3.4e-163  542.9   1.4   4.1e-163  542.6   1.4    1.1  1  CdhD         CO dehydrogenase/acetyl-CoA synthase delta subun
    7.2e-17   60.7   2.0    7.2e-17   60.7   2.0    2.2  2  FeS          Putative Fe-S cluster
    0.00029   20.6   0.5    0.00049   19.9   0.5    1.3  1  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.6   1.4  6.9e-167  4.1e-163       1     385 [.      69     469 ..      69     470 .. 0.97

  Alignments for each domain:
  == domain 1  score: 542.6 bits;  conditional E-value: 6.9e-167
                                   EEEESSGCG-EEEE----SSTTTS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE....ETTEEEE--EEEEE--SSS CS
                          CdhD   1 evvlGaeekavkiGgeevLyrfeltffnptaiaidvsDelseellkalaerieevvddwakkrvgekltldaiairlistd 81 
                                   ev++G+eek++++Gg+ev+yr++l+ffnpt i +d+sDelsee++k++a++ie++v++    r+gekl+ld+i+ir++s+d
  gi|15668283|ref|NP_247076.1|  69 EVWFGNEEKKAVMGGDEVMYRYQLSFFNPTPIGVDISDELSEEEIKNRAKEIENFVFE----RTGEKLKLDFIVIRNASGD 145
                                   8********************************************************9....******************* PP

                                   T.HHHHHHHHHHHCC--SEEEEE-SSHHHHHHHHTTTCCC--EEEEE-TTTHHHHHHHHHHTT--EEE.E-.SSHHHHHHH CS
                          CdhD  82 PakkfakavekvakavkvplvlggsdpevlkaalevvederpllyaAtkddykeiaelaleykvpvvl.lsindleelkel 161
                                    ++kf+ka+e v+k++k+p+++++++pev+k+al+vv+ ++p++yaAtk+++++++++++e+k++vvl ls+n++++lk++
  gi|15668283|ref|NP_247076.1| 146 -VEKFKKAIEIVEKETKMPICIASLNPEVIKEALKVVK-SKPMVYAATKETLNDFIKVIKEVKKDVVLvLSSNNVKDLKNM 224
                                   .7************************************.**************************998799********** PP

                                   HHHHHCTT---EEEE---SH.....HHHHHHHHHHHHHHHHS.-TTS-S-BEEE---SSHHHHHHHHH............. CS
                          CdhD 162 arkllkagvkdivldPttaalGegleetidnvvriRraaikg.dkdlafPilslttnawlaresdeve............. 228
                                   a+k+l++g++d+vl+P+t++  e+++et+d +v+iRr+ai++ dk+l+fPil+l++na+++++++e               
  gi|15668283|ref|NP_247076.1| 225 AAKCLANGIEDLVLEPHTYP--ENIAETLDLNVMIRRSAIEKeDKYLGFPILNLPINAYYYALKNECPisgffedkevvak 303
                                   ********************..***************************************99555445566666666699 PP

                                   .........HHHTT-SEEEES---HHHHHHHHHHHHHHTS-SSS--B--SSEEEESS--TTS-EEEEESBHHHHHHHHHHH CS
                          CdhD 229 .........lvvrYadililrslekeellPvltlrqniYtDPrkPvavdpglyeigdrdensPvflttnfsLtyYtvegdl 300
                                            l++rYad+li+++++++el+Pvltlrq+iYtDPrkP+av+pgly+ig++densPv+lttnfsLt+Ytv+gd+
  gi|15668283|ref|NP_247076.1| 304 mfeatiantLMNRYADALIMHGMDIWELMPVLTLRQCIYTDPRKPQAVEPGLYPIGNPDENSPVILTTNFSLTFYTVTGDF 384
                                   999****************************************************************************** PP

                                   HHTTS-EEEEEE-SSS--HHHHHHTTSSSHHHHHHHHHHTTHHHHSSS-EEEE-GGGGGGHHHHHHHHTSEEEE--SSGGG CS
                          CdhD 301 esdkitayLLvldteGlgvevslaggqleaekvkdlieetgieekvkhrflilPglvavlkgkiedltgwkvlvgprdsse 381
                                   e+d++t++LLv+dt+G++v+vs+aggq+++e++k+lieetgi++kv+hr++ilP+l+a+++g+ied+tgw+++vg+rdss+
  gi|15668283|ref|NP_247076.1| 385 EKDNVTCWLLVMDTGGKAVDVSVAGGQYNGENAKKLIEETGIADKVSHRIIILPALAASTRGDIEDKTGWTCVVGTRDSSQ 465
                                   ********************************************************************************* PP

                                   HHHH CS
                          CdhD 382 ivav 385
                                   ++++
  gi|15668283|ref|NP_247076.1| 466 VGDF 469
                                   9987 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   2.0   1.2e-20   7.2e-17       1      32 [.      14      45 ..      14      46 .. 0.98
   2 ?   -1.7   0.1       0.4   2.4e+03      18      31 ..     152     165 ..     151     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1.2e-20
                           FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCp 32
                                  LP+tNC++CGyp+CmafA++l+e+ea++++Cp
  gi|15668283|ref|NP_247076.1| 14 LPKTNCKKCGYPSCMAFATKLLEKEATIDQCP 45
                                  9******************************9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.4
                           FeS  18 AealvegeaqledC 31 
                                   A  +ve+e++   C
  gi|15668283|ref|NP_247076.1| 152 AIEIVEKETKMPIC 165
                                   6789*****98777 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.5   8.2e-08   0.00049      54     134 ..     142     223 ..     138     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.2e-08
                                   HHHHHHHHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHT..TSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTH CS
                   Pterin_bind  54 eeeelervvpvlealrdeadvpisiDttkaevaeaAlka..gadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktm 132
                                   +  ++e++ + +e +++e+++pi+i + ++ev+++Alk+   + +v   + e+  ++++++++e +  vv+  + ++ k+ 
  gi|15668283|ref|NP_247076.1| 142 ASGDVEKFKKAIEIVEKETKMPICIASLNPEVIKEALKVvkSKPMVYAATKET-LNDFIKVIKEVKKDVVLVLSSNNVKDL 221
                                   566889999****999***********************87779**9999999.999************999888666655 PP

                                   CC CS
                   Pterin_bind 133 qe 134
                                   ++
  gi|15668283|ref|NP_247076.1| 222 KN 223
                                   54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2977.55
//
Query:       gi|15668284|ref|NP_247077.1|  [L=405]
Description: acetyl-CoA decarbonylase/synthase complex subunit delta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-95  319.3   1.1    1.7e-89  300.3   0.0    3.0  3  CdhD         CO dehydrogenase/acetyl-CoA synthase delta subun
  ------ inclusion threshold ------
      0.028   14.1   0.0        1.7    8.3   0.0    2.2  1  Pterin_bind  Pterin binding enzyme
      0.052   11.7   0.0      0.079   11.1   0.0    1.1  1  HSP70        Hsp70 protein


Domain annotation for each model (and alignments):
>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.3   0.0   2.8e-93   1.7e-89       1     226 [.      89     336 ..      89     338 .. 0.99
   2 !    5.8   0.1   0.00078       4.6     267     292 ..     337     358 ..     336     366 .. 0.84
   3 !   11.9   0.1   1.1e-05     0.065     349     384 ..     366     402 ..     356     404 .. 0.88

  Alignments for each domain:
  == domain 1  score: 300.3 bits;  conditional E-value: 2.8e-93
                                   EEEESS......GCG-EEEE----SSTTTS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE.......ETTEEEE--E CS
                          CdhD   1 evvlGa......eekavkiGgeevLyrfeltffnptaiaidvsDelseellkalaerieevvdd...wakkrvgekltlda 72 
                                   ev++G+      ++k vkiGg+++Lyrfe++++np+++++d++D+++++l+k++++ +++v++d   wakk+v+e +++d+
  gi|15668284|ref|NP_247077.1|  89 EVQFGKpkseggRGKVVKIGGQRALYRFEEPQPNPPVVTFDIFDIPMPGLPKPIRQFFQDVMEDpceWAKKCVKE-FGADM 168
                                   7999999999999**************************************************************.***** PP

                                   EEEE--SSST.......HHHHHHHHHHHCC--SEEEEE-S.....SHHHHHHHHTTTCCC--EEEEE-TT.THHHHHHHHH CS
                          CdhD  73 iairlistdP......akkfakavekvakavkvplvlggs.....dpevlkaalevvederpllyaAtkd.dykeiaelal 141
                                   i+i++istdP      +k++ak +e++++av+vp+v+ggs     dp vl+a++ev+e++r+ll++A+++ dyk+i+++a+
  gi|15668284|ref|NP_247077.1| 169 ITIHHISTDPkikdksPKEAAKLMEDLLQAVDVPFVIGGSgnpqkDPLVLEACAEVAEGDRCLLASANLElDYKKIVDAAM 249
                                   ********************************************************************************* PP

                                   HTT--EEEE-.SSHHHHHHHHHHHHCTT-..--EEEE---SH.....HHHHHHHHHHHHHHHHS-TTS-S-BEEE---SSH CS
                          CdhD 142 eykvpvvllsindleelkelarkllkagv..kdivldPttaalGegleetidnvvriRraaikgdkdlafPilslttnawl 220
                                   +y+++v+++si+d +++++l+rkl++ag+  ++iv+dPtt+alG+g+e++i+++vr+R++++kgd+ +++P++s+ttna++
  gi|15668284|ref|NP_247077.1| 250 KYDHNVLAWSIMDPNMARDLNRKLVEAGLdpNRIVMDPTTCALGYGIEFSINAMVRLRLNGLKGDELVNMPMSSGTTNAIG 330
                                   *****************************999************************************************* PP

                                   HHHHHH CS
                          CdhD 221 aresde 226
                                   are+++
  gi|15668284|ref|NP_247077.1| 331 AREAWM 336
                                   *****8 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.00078
                                   --SSEEEESS--TTS-EEEEESBHHH CS
                          CdhD 267 vdpglyeigdrdensPvflttnfsLt 292
                                   ++p++   g+r+++ P++++t+  +t
  gi|15668284|ref|NP_247077.1| 337 NNPEW---GPREYRLPLWEITT-GIT 358
                                   57899...*************9.666 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 1.1e-05
                                   -EEEE.-GGGGGGHHHHHHHHTSEEEE--SSGGGHHH CS
                          CdhD 349 rflil.Pglvavlkgkiedltgwkvlvgprdsseiva 384
                                    f++l P++v++lk++ ++lt++  +v+ +++++ + 
  gi|15668284|ref|NP_247077.1| 366 LFMMLnPISVKTLKEIGKTLTTKPGEVKLNTNNYEWI 402
                                   499**************************99998765 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00029       1.7     146     173 ..     265     289 ..     144     327 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00029
                                   HHHHHHHHHHHHHHTT--GGGEEEETTT CS
                   Pterin_bind 146 veaflearveaaeeaGvaperillDpgi 173
                                   +++     +++++eaG++p+ri++Dp +
  gi|15668284|ref|NP_247077.1| 265 MARD---LNRKLVEAGLDPNRIVMDPTT 289
                                   3333...346677888888888888876 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.3e-05     0.079     159     180 ..     276     297 ..     270     305 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.3e-05
                                   TTXEEEEEEEHHHHHHHHHHTC CS
                         HSP70 159 AGLnvlRivNepTAaalaYGld 180
                                   AGL+  Riv +pT  al YG++
  gi|15668284|ref|NP_247077.1| 276 AGLDPNRIVMDPTTCALGYGIE 297
                                   9*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2730.51
//
Query:       gi|15668285|ref|NP_247078.1|  [L=303]
Description: hypothetical protein MJ_0114 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0052   16.6   0.2      0.012   15.4   0.2    1.6  1  Gar1            Gar1/Naf1 RNA binding region
  ------ inclusion threshold ------
       0.17   11.5   0.0        0.3   10.7   0.0    1.3  1  Lipoprotein_15  Secreted repeat of unknown function


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   1.4e-06     0.012       4      58 ..      74     128 ..      71     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-06
                                   -S----TT----TTS-EEEEEEEEEEETTEEEEEE---S--B-.-BTT-EEEETT- CS
                          Gar1   4 lppvekedieigppeevleiGtvssivenevviksttsgekkv.ldfnsilflenk 58 
                                   +++v+   i+++p+e+++ei+++s ++enev+ +s ++  +k   ++n ++f+ ++
  gi|15668285|ref|NP_247078.1|  74 EKEVKSALINFKPEESIVEISKLSLVFENEVILNSYNDV-YKYlTYINKVIFMPKR 128
                                   5667777899**************************665.5552699*****9775 PP

>> Lipoprotein_15  Secreted repeat of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.4e-05       0.3      11      29 ..     244     261 ..     240     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.4e-05
                Lipoprotein_15  11 qvaykGmPLYtFakDkkpg 29 
                                    va++G+P+Y F +D  +g
  gi|15668285|ref|NP_247078.1| 244 IVAKDGKPVYAFLNDY-DG 261
                                   699***********97.45 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1880.27
//
Query:       gi|15668286|ref|NP_247079.1|  [L=155]
Description: hypothetical protein MJ_0115 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.014   15.0   0.2        3.5    7.3   0.0    2.3  2  STAT1_TAZ2bind  STAT1 TAZ2 binding domain
      0.089   12.7   0.1       0.24   11.3   0.0    1.7  2  GIT_CC          GIT coiled-coil Rho guanine nucleotide exchan
        0.1   12.1   0.1       0.29   10.6   0.0    1.6  2  PRORP           Protein-only RNase P


Domain annotation for each model (and alignments):
>> STAT1_TAZ2bind  STAT1 TAZ2 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0022        13      12      17 ..      40      45 ..      38      46 .. 0.94
   2 ?    7.3   0.0   0.00059       3.5      13      21 ..      92     100 ..      91     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0022
                STAT1_TAZ2bind 12 MSPedY 17
                                  MSPe++
  gi|15668286|ref|NP_247079.1| 40 MSPEEF 45
                                  *****9 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00059
                STAT1_TAZ2bind  13 SPedYgELe 21 
                                   SP++Y EL 
  gi|15668286|ref|NP_247079.1|  92 SPDEYMELK 100
                                   *******96 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.76   4.5e+03      16      24 ..      43      51 ..      40      54 .. 0.83
   2 ?   11.3   0.0     4e-05      0.24       7      27 ..      85     105 ..      83     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.76
                        GIT_CC 16 eeylelKka 24
                                  ee++ +K++
  gi|15668286|ref|NP_247079.1| 43 EEFIRIKEE 51
                                  89**9*997 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4e-05
                        GIT_CC   7 dLsdgpVtleeylelKkalaa 27 
                                   +L +  ++ +ey+elKk+la 
  gi|15668286|ref|NP_247079.1|  85 ELAKNNISPDEYMELKKQLAE 105
                                   578889999**********95 PP

>> PRORP  Protein-only RNase P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.24   1.5e+03      11      33 ..      32      54 ..      28      58 .. 0.79
   2 ?   10.6   0.0   4.9e-05      0.29      10      45 ..      82     117 ..      76     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.24
                         PRORP 11 kekLesidlseeefeelresllk 33
                                  ++ L  +++s+eef +++e++ k
  gi|15668286|ref|NP_247079.1| 32 HKALAVLKMSPEEFIRIKEEFGK 54
                                  56788889999999999988755 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 4.9e-05
                         PRORP  10 CkekLesidlseeefeelresllkkvleredkfkkt 45 
                                    + +L + ++s++e+ el+++l+++++++++ fk +
  gi|15668286|ref|NP_247079.1|  82 RDYELAKNNISPDEYMELKKQLAEEIIRNSQFFKEA 117
                                   56689999*********************9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 994.34
//
Query:       gi|15668287|ref|NP_247080.1|  [L=225]
Description: hypothetical protein MJ_0116 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-14   52.1   0.0    1.1e-13   51.2   0.0    1.4  1  Creatininase  Creatinine amidohydrolase


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   6.2e-18   1.1e-13      15     239 ..      16     218 ..       9     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 6.2e-18
                  Creatininase  15 ddvailPvGs.tEqHGphlplgtDtliaealaervaeklgak..alvlPtlpyGvseehlgfpGTislspetliavlrdil 92 
                                    +v i+++Gs +E+HG  lp+ tD  ia+++a ++   +gak   +v P   y +          i+ +pe +++++r ++
  gi|15668287|ref|NP_247080.1|  16 HKVGIIALGSfLENHGAVLPIDTDIKIASYIALKASILTGAKflGVVIPSTEYEY------VKHGIHNKPEEVYSYMRFLI 90 
                                   578999***966**********************966666664444555555555......55569*************** PP

                  Creatininase  93 eslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaaeaaeeseeeegggHAgelEtSl 173
                                   ++  + G++++++vn Hggn+ +++ ++++l  e+ ++ v      + ++                      HA+  E+S+
  gi|15668287|ref|NP_247080.1|  91 NEGKKIGVEKFLIVNCHGGNI-LVESFLKDLEYEF-DIKV------EMINI------------------TFTHASTEEVSV 145
                                   *********************.*************.5533......23444..................789999999999 PP

                  Creatininase 174 mlalrpelVrmdraedpeeaklakeg............vstaedaeelspsGvlGdpskataekGealleaaveelae 239
                                      +     +++++++++  ++ +e                +++a+ ++         k +++ Ge++l+ a+e+++e
  gi|15668287|ref|NP_247080.1| 146 GYIIGIAKADEETLKEHNNFEKYPEVgmvglkearennKAIDKEAKVVK-----RFGVKLDKKLGEKILNNAIEKVVE 218
                                   9998888888888777665444444366666443222222222222222.....233477888888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1428.64
//
Query:       gi|15668288|ref|NP_247081.1|  [L=60]
Description: hypothetical protein MJ_0116.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-23   82.0   1.0    2.6e-23   81.8   1.0    1.1  1  Nop10p           Nucleolar RNA-binding protein, Nop10p family
     0.0001   20.4   0.2     0.0001   20.4   0.2    1.0  1  PolC_DP2         DNA polymerase II large subunit DP2
     0.0011   18.4   0.5     0.0016   17.9   0.5    1.3  1  RecR             RecR protein
     0.0013   18.3   0.4       0.67    9.7   0.0    2.2  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
     0.0017   18.4   2.5       0.12   12.6   0.1    2.1  2  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
     0.0038   17.0   4.1       0.42   10.4   0.5    2.4  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
     0.0042   16.4   7.8       0.15   11.5   8.0    2.2  1  zf-ribbon_3      zinc-ribbon domain
      0.005   16.5   5.2       0.75    9.6   0.8    2.4  2  zinc_ribbon_2    zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.4   0.2      0.011   15.4   0.2    2.6  3  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
       0.02   14.9   2.2      0.035   14.1   2.2    1.5  1  DZR              Double zinc ribbon
      0.033   13.0   0.3      0.033   13.0   0.3    1.1  1  NRDD             Anaerobic ribonucleoside-triphosphate reduct
       0.04   13.8   1.4       0.11   12.3   1.4    1.7  1  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.051   13.7   5.4        1.5    9.0   0.2    2.2  2  Zn-ribbon_8      Zinc ribbon domain
        0.1   12.3   3.5        4.1    7.2   0.2    2.2  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.14   11.8   7.0       0.79    9.3   0.7    2.4  2  zf_C2H2_10       C2H2 type zinc-finger
        0.2   11.7   3.7        3.1    7.9   0.4    2.2  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
       0.23   11.3   3.8        4.2    7.3   0.2    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.28   11.3   2.4        4.5    7.3   0.1    2.1  2  CpXC             CpXC protein
       0.78   10.5   6.0          2    9.1   0.6    2.2  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        1.1    8.7   6.0        4.4    6.7   0.4    2.2  2  zf-TFIIB         Transcription factor zinc-finger
        1.1    9.3   6.9          3    7.9   0.5    2.4  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        1.1    9.6   7.1        2.8    8.4   0.4    2.2  2  Lar_restr_allev  Restriction alleviation protein Lar
        1.1    9.2   9.5        4.6    7.2   0.9    2.6  3  zf-C2HC_2        zinc-finger of a C2HC-type
        1.2    9.2   7.2        4.1    7.4   0.9    2.2  2  DUF1936          Domain of unknown function (DUF1936)
        1.2    9.3   5.5        2.7    8.1   0.5    2.2  2  zf-C3H2C3        Zinc-finger
        1.4    9.0  11.4        1.1    9.3   1.8    2.2  2  DUF1610          Domain of unknown function (DUF1610)
        1.6    8.3   7.5        2.5    7.7   0.6    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
        2.2    8.3   4.9        5.3    7.1   0.2    2.2  2  Ogr_Delta        Ogr/Delta-like zinc finger
        3.1    7.8  10.4        3.6    7.7   2.7    2.3  2  YhfH             YhfH-like protein
        3.9    7.1   5.8         11    5.8   0.6    2.2  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
        8.5    6.6  10.4         12    6.1   2.1    2.5  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   1.0   4.5e-26   2.6e-23       2      50 ..       3      51 ..       2      53 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 4.5e-26
                                  ----EE-TTT--EESSSB-TTT-SB-B-SS--S--TT-TTCHHHHHCHH CS
                        Nop10p  2 ksylrkcgkcrvYTLkkvcpecggptksahPaRFSPdDkyskyRralKk 50
                                  +++++kc+kc+ YTLk++cp+cg++t+ ++P++FS +D+++kyRr+lK+
  gi|15668288|ref|NP_247081.1|  3 EMRMKKCPKCGLYTLKEICPKCGEKTVIPKPPKFSLEDRWGKYRRMLKR 51
                                  689*********************************************8 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.2   1.8e-07    0.0001     614     642 ..       2      30 ..       1      59 [. 0.80

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.8e-07
                      PolC_DP2 614 veiarrkCkkCgketlearCeeCgektee 642
                                   ve+  +kC+kCg  tl+  C++Cgekt  
  gi|15668288|ref|NP_247081.1|   2 VEMRMKKCPKCGLYTLKEICPKCGEKTVI 30 
                                   8999*********************9976 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.5   2.8e-06    0.0016      15      35 ..       5      25 ..       2      28 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                                  H-EE-TTT--EESSSS-CCCC CS
                          RecR 15 kvrhCsrCgnlteedlCaICs 35
                                  +++ C++Cg +t +++C+ C 
  gi|15668288|ref|NP_247081.1|  5 RMKKCPKCGLYTLKEICPKCG 25
                                  689***************995 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0084       4.9      20      29 ..       5      14 ..       5      16 .. 0.78
   2 !    9.7   0.0    0.0012      0.67       6      14 ..      21      29 ..      19      30 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0084
                 zf-NADH-PPase 20 warvCpaCgl 29
                                  +++ Cp Cgl
  gi|15668288|ref|NP_247081.1|  5 RMKKCPKCGL 14
                                  5788999997 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                 zf-NADH-PPase  6 CgrCGapte 14
                                  C++CG +t+
  gi|15668288|ref|NP_247081.1| 21 CPKCGEKTV 29
                                  *******97 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.3    0.0049       2.8      21      35 ..       4      18 ..       1      20 [. 0.79
   2 !   12.6   0.1    0.0002      0.12      23      60 ..      18      58 ..      16      60 .] 0.70

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0049
                  NOB1_Zn_bind 21 mtkkFCpkCGnktLk 35
                                  m+ k CpkCG  tLk
  gi|15668288|ref|NP_247081.1|  4 MRMKKCPKCGLYTLK 18
                                  55666********98 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0002
                  NOB1_Zn_bind 23 kkFCpkCGnktLkr..vavsvden.gelklhlkknfqlnlr 60
                                  k+ CpkCG+kt+     + s++++ g+++ +lk+  + +++
  gi|15668288|ref|NP_247081.1| 18 KEICPKCGEKTVIPkpPKFSLEDRwGKYRRMLKRALKNKNK 58
                                  788*******9853114566777688888888887776655 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.2    0.0045       2.6       2       8 ..       7      13 ..       6      17 .. 0.85
   2 !   10.4   0.5   0.00073      0.42       2      12 ..      19      29 ..      18      36 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0045
                                  EE-SSS- CS
                zf-C4_Topoisom  2 ekCPkCg 8 
                                  +kCPkCg
  gi|15668288|ref|NP_247081.1|  7 KKCPKCG 13
                                  59****9 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00073
                                  EE-SSS--EEE CS
                zf-C4_Topoisom  2 ekCPkCggdLv 12
                                  e CPkCg++ v
  gi|15668288|ref|NP_247081.1| 19 EICPKCGEKTV 29
                                  79*****7644 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   8.0   0.00027      0.15       2      25 ..       6      27 ..       5      28 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                   zf-ribbon_3  2 tvrCPnCGaplssddnvCpyCGtk 25
                                  +++CP+CG    +   +Cp+CG+k
  gi|15668288|ref|NP_247081.1|  6 MKKCPKCGLY--TLKEICPKCGEK 27
                                  89******74..7889******87 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.2    0.0024       1.4       1       6 [.       8      13 ..       4      14 .. 0.73
   2 !    9.6   0.8    0.0013      0.75       2       8 ..      21      27 ..      20      28 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0024
                 zinc_ribbon_2  1 fCpnCG 6 
                                  +Cp+CG
  gi|15668288|ref|NP_247081.1|  8 KCPKCG 13
                                  566666 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                 zinc_ribbon_2  2 CpnCGae 8 
                                  Cp+CG++
  gi|15668288|ref|NP_247081.1| 21 CPKCGEK 27
                                  6777665 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.2   1.8e-05     0.011       9      19 ..       5      15 ..       2      16 .. 0.88
   2 ?    5.5   0.4     0.023        13      13      17 ..      21      25 ..      17      28 .. 0.88
   3 ?   -1.9   0.3       4.7   2.7e+03      23      30 ..      51      58 ..      50      59 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                       zf-tcix  9 GvrkCpkCGty 19
                                  + +kCpkCG y
  gi|15668288|ref|NP_247081.1|  5 RMKKCPKCGLY 15
                                  79*******88 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.023
                       zf-tcix 13 CpkCG 17
                                  CpkCG
  gi|15668288|ref|NP_247081.1| 21 CPKCG 25
                                  ***** PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.7
                       zf-tcix 23 RglsCkNk 30
                                  R+l  kNk
  gi|15668288|ref|NP_247081.1| 51 RALKNKNK 58
                                  66666776 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.2   6.1e-05     0.035      12      39 ..       6      30 ..       2      36 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-05
                           DZR 12 arfCseCgtk.lkavaaedrCpsCgek.vd 39
                                   + C++Cg   lk     + Cp+Cgek v 
  gi|15668288|ref|NP_247081.1|  6 MKKCPKCGLYtLK-----EICPKCGEKtVI 30
                                  678*****98465.....9******99655 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   5.7e-05     0.033     506     528 ..       5      27 ..       2      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-05
                                   -EEEETT.--EESSSB-TTT--B CS
                          NRDD 506 kidvCnecgykgeiekCpkCgse 528
                                   +++ C++cg   ++e CpkCg++
  gi|15668288|ref|NP_247081.1|   5 RMKKCPKCGLYTLKEICPKCGEK 27 
                                   6789******999999*****54 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.4    0.0002      0.11      12      35 ..       7      28 ..       5      29 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                       DUF35_N 12 qrCpdCGtvqfPPravCphCgsdd 35
                                   +Cp+CG +      +Cp+Cg ++
  gi|15668288|ref|NP_247081.1|  7 KKCPKCGLYTL--KEICPKCGEKT 28
                                  69*******96..9******9765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2    0.0026       1.5      26      37 ..       6      18 ..       1      20 [. 0.71
   2 ?    4.8   5.8     0.054        31      26      35 ..      17      27 ..       8      30 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0026
                   Zn-ribbon_8 26 ltaCPeCgs.evr 37
                                  +++CP+Cg  +++
  gi|15668288|ref|NP_247081.1|  6 MKKCPKCGLyTLK 18
                                  678*****86665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.054
                   Zn-ribbon_8 26 lta.CPeCgse 35
                                  l++ CP+Cg++
  gi|15668288|ref|NP_247081.1| 17 LKEiCPKCGEK 27
                                  45559999984 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2    0.0089       5.1       2      13 ..       4      15 ..       3      17 .. 0.83
   2 ?    7.2   0.2    0.0071       4.1       4      14 ..      18      28 ..      15      31 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0089
                       zf-RRN7  2 ekgppCgvCgcr 13
                                  ++++ C+ Cg +
  gi|15668288|ref|NP_247081.1|  4 MRMKKCPKCGLY 15
                                  6899******75 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0071
                       zf-RRN7  4 gppCgvCgcrs 14
                                  +++C+ Cg ++
  gi|15668288|ref|NP_247081.1| 18 KEICPKCGEKT 28
                                  799*****976 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.8     0.016       9.4       5       9 ..       9      13 ..       7      17 .. 0.86
   2 ?    9.3   0.7    0.0014      0.79       5      11 ..      21      27 ..      18      31 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.016
                    zf_C2H2_10  5 CPKCq 9 
                                  CPKC+
  gi|15668288|ref|NP_247081.1|  9 CPKCG 13
                                  ****7 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
                    zf_C2H2_10  5 CPKCqek 11
                                  CPKC+ek
  gi|15668288|ref|NP_247081.1| 21 CPKCGEK 27
                                  *****97 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.042        24       1       6 [.       8      13 ..       8      16 .. 0.92
   2 ?    7.9   0.4    0.0054       3.1       2      10 ..      21      29 ..      21      39 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.042
                DNA_ligase_ZBD  1 hCPvCG 6 
                                  +CP CG
  gi|15668288|ref|NP_247081.1|  8 KCPKCG 13
                                  6****9 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0054
                DNA_ligase_ZBD  2 CPvCGsavv 10
                                  CP CG ++v
  gi|15668288|ref|NP_247081.1| 21 CPKCGEKTV 29
                                  *****9987 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.5     0.033        19       2       7 ..       8      13 ..       7      16 .. 0.86
   2 ?    7.3   0.2    0.0073       4.2       3      11 ..      21      29 ..      19      31 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.033
                       TFIIS_C  2 kCpkCg 7 
                                  kCpkCg
  gi|15668288|ref|NP_247081.1|  8 KCPKCG 13
                                  8****8 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0073
                       TFIIS_C  3 CpkCgsrea 11
                                  CpkCg++ +
  gi|15668288|ref|NP_247081.1| 21 CPKCGEKTV 29
                                  *****9976 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.065        38      36      45 ..       5      14 ..       2      20 .. 0.74
   2 ?    7.3   0.1    0.0078       4.5      40      51 ..      21      32 ..      17      51 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.065
                          CpXC 36 featCpkCga 45
                                  ++ +CpkCg 
  gi|15668288|ref|NP_247081.1|  5 RMKKCPKCGL 14
                                  6678999985 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0078
                          CpXC 40 CpkCgataklea 51
                                  CpkCg+++ ++ 
  gi|15668288|ref|NP_247081.1| 21 CPKCGEKTVIPK 32
                                  777777665554 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.5      0.09        52       4      12 ..       8      16 ..       6      19 .. 0.80
   2 ?    9.1   0.6    0.0035         2       4      14 ..      20      30 ..      18      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.09
                       zf-ISL3  4 rCPnCgskt 12
                                  +CP+Cg  t
  gi|15668288|ref|NP_247081.1|  8 KCPKCGLYT 16
                                  6****9765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0035
                       zf-ISL3  4 rCPnCgsktvv 14
                                   CP+Cg+ktv 
  gi|15668288|ref|NP_247081.1| 20 ICPKCGEKTVI 30
                                  6*******974 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.4    0.0076       4.4       1      11 [.       8      19 ..       8      20 .. 0.73
   2 ?    5.0   0.8     0.026        15       2       7 ..      21      26 ..      20      32 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0076
                      zf-TFIIB  1 kCPkCqd.elee 11
                                  kCPkC+  +l+e
  gi|15668288|ref|NP_247081.1|  8 KCPKCGLyTLKE 19
                                  7****8557765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.026
                      zf-TFIIB  2 CPkCqd 7 
                                  CPkC+ 
  gi|15668288|ref|NP_247081.1| 21 CPKCGE 26
                                  999986 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.5     0.021        12      20      30 ..       8      15 ..       4      20 .. 0.75
   2 ?    7.9   0.5    0.0051         3      20      28 ..      20      28 ..      14      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.021
                 Zn_Tnp_IS1595 20 vCPhCgsrkay 30
                                   CP+Cg   +y
  gi|15668288|ref|NP_247081.1|  8 KCPKCG---LY 15
                                  5****9...44 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0051
                 Zn_Tnp_IS1595 20 vCPhCgsrk 28
                                  +CP+Cg ++
  gi|15668288|ref|NP_247081.1| 20 ICPKCGEKT 28
                                  7*****875 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.4     0.056        32       3      10 ..       6      13 ..       4      19 .. 0.86
   2 ?    8.4   0.4    0.0049       2.8       6      17 ..      21      32 ..      16      40 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.056
               Lar_restr_allev  3 LkpCPfCg 10
                                   k CP Cg
  gi|15668288|ref|NP_247081.1|  6 MKKCPKCG 13
                                  799****9 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0049
               Lar_restr_allev  6 CPfCggravler 17
                                  CP Cg++ v+ +
  gi|15668288|ref|NP_247081.1| 21 CPKCGEKTVIPK 32
                                  *******99876 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.9     0.008       4.6       2       9 ..       6      13 ..       5      13 .. 0.89
   2 ?    7.0   0.9    0.0094       5.5       3      11 ..      19      27 ..      18      27 .. 0.83
   3 ?   -1.6   0.0       4.8   2.8e+03      12      19 ..      36      44 ..      35      44 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.008
                     zf-C2HC_2  2 lvpCpkCg 9 
                                  + +CpkCg
  gi|15668288|ref|NP_247081.1|  6 MKKCPKCG 13
                                  789****9 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0094
                     zf-C2HC_2  3 vpCpkCgRs 11
                                  + CpkCg +
  gi|15668288|ref|NP_247081.1| 19 EICPKCGEK 27
                                  57*****75 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.8
                     zf-C2HC_2 12 F.npdrlek 19
                                  F  +dr+ k
  gi|15668288|ref|NP_247081.1| 36 FsLEDRWGK 44
                                  667899976 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.7     0.027        16       2       7 ..       9      14 ..       8      18 .. 0.83
   2 ?    7.4   0.9    0.0071       4.1       1       6 [.      20      25 ..      20      31 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.027
                                  -TTTSS CS
                       DUF1936  2 CPKCnv 7 
                                  CPKC+ 
  gi|15668288|ref|NP_247081.1|  9 CPKCGL 14
                                  ****95 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0071
                                  B-TTTS CS
                       DUF1936  1 lCPKCn 6 
                                  +CPKC+
  gi|15668288|ref|NP_247081.1| 20 ICPKCG 25
                                  8****9 PP

>> zf-C3H2C3  Zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.5      0.11        65      30      35 .]       8      13 ..       5      13 .. 0.83
   2 ?    8.1   0.5    0.0046       2.7      28      35 .]      18      25 ..      16      25 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.11
                     zf-C3H2C3 30 vCPkCk 35
                                   CPkC+
  gi|15668288|ref|NP_247081.1|  8 KCPKCG 13
                                  6****7 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0046
                     zf-C3H2C3 28 eevCPkCk 35
                                  +e+CPkC+
  gi|15668288|ref|NP_247081.1| 18 KEICPKCG 25
                                  69*****7 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   2.4     0.048        28      19      23 ..       9      13 ..       8      13 .. 0.94
   2 ?    9.3   1.8    0.0019       1.1      18      24 .]      20      26 ..      20      26 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.048
                       DUF1610 19 CPNCG 23
                                  CP+CG
  gi|15668288|ref|NP_247081.1|  9 CPKCG 13
                                  ****9 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0019
                       DUF1610 18 pCPNCGE 24
                                  +CP+CGE
  gi|15668288|ref|NP_247081.1| 20 ICPKCGE 26
                                  6*****9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   7.4      0.27   1.5e+02       2      27 ..       8      26 ..       8      28 .. 0.63
   2 ?    7.7   0.6    0.0043       2.5       2      10 ..      20      28 ..      19      41 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.27
                                  EETTTTCEECHEETSTTCEEESSSSB CS
                  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                  kCP+Cg ++ + +      +C++CG+
  gi|15668288|ref|NP_247081.1|  8 KCPKCGLYT-LKE------ICPKCGE 26
                                  688888542.343......7888886 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0043
                                  EETTTTCEE CS
                  TF_Zn_Ribbon  2 kCPnCgstn 10
                                  +CP+Cg ++
  gi|15668288|ref|NP_247081.1| 20 ICPKCGEKT 28
                                  588888876 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.8      0.15        88       1       6 [.       8      13 ..       8      14 .. 0.90
   2 ?    7.1   0.2    0.0091       5.3       2      11 ..      21      30 ..      20      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.15
                     Ogr_Delta  1 rCPhCg 6 
                                  +CP+Cg
  gi|15668288|ref|NP_247081.1|  8 KCPKCG 13
                                  6****9 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0091
                     Ogr_Delta  2 CPhCgapaaa 11
                                  CP+Cg++ ++
  gi|15668288|ref|NP_247081.1| 21 CPKCGEKTVI 30
                                  *****99776 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.7    0.0062       3.6      13      21 ..       6      14 ..       3      20 .. 0.81
   2 ?    5.4   0.8     0.031        18      16      22 ..      21      27 ..      15      30 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0062
                          YhfH 13 kKkCteCGk 21
                                  +KkC++CG 
  gi|15668288|ref|NP_247081.1|  6 MKKCPKCGL 14
                                  8*******5 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.031
                          YhfH 16 CteCGke 22
                                  C++CG++
  gi|15668288|ref|NP_247081.1| 21 CPKCGEK 27
                                  *****97 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.5     0.047        27       3       9 ..       7      13 ..       5      19 .. 0.83
   2 ?    5.8   0.6     0.018        11       4      11 ..      20      27 ..      18      32 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.047
                        zf_UBZ  3 ylCerCg 9 
                                    C++Cg
  gi|15668288|ref|NP_247081.1|  7 KKCPKCG 13
                                  58****9 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.018
                        zf_UBZ  4 lCerCgke 11
                                  +C++Cg++
  gi|15668288|ref|NP_247081.1| 20 ICPKCGEK 27
                                  7*****86 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.1     0.021        12       3       8 ..       8      13 ..       7      19 .. 0.84
   2 ?    4.4   1.2     0.068        39      21      26 .]      19      24 ..      17      24 .. 0.86
   3 ?    4.6   1.4     0.059        34       4       9 ..      21      26 ..      20      27 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.021
                        zf-ACC  3 KCpsCg 8 
                                  KCp+Cg
  gi|15668288|ref|NP_247081.1|  8 KCPKCG 13
                                  9****9 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.068
                        zf-ACC 21 yVCPkC 26
                                  ++CPkC
  gi|15668288|ref|NP_247081.1| 19 EICPKC 24
                                  68***9 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.059
                        zf-ACC  4 CpsCge 9 
                                  Cp+Cge
  gi|15668288|ref|NP_247081.1| 21 CPKCGE 26
                                  777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 366.65
//
Query:       gi|15668289|ref|NP_247082.1|  [L=266]
Description: translation initiation factor IF-2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-29  101.6   0.6    2.7e-29  101.6   0.6    1.6  2  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
      5e-18   65.2   1.4      5e-18   65.2   1.4    2.1  2  S1           S1 RNA binding domain
    0.00057   20.5   0.5     0.0055   17.3   0.1    2.5  2  EXOSC1       Exosome component EXOSC1/CSL4
     0.0063   17.4   0.1      0.018   15.9   0.1    1.7  1  CwfJ_C_2     Protein similar to CwfJ C-terminus 2
  ------ inclusion threshold ------
       0.23   12.0   1.3        0.9   10.1   0.2    2.1  2  Carbpep_Y_N  Carboxypeptidase Y pro-peptide


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.5   5.5e+03      68      86 ..      47      65 ..      38      87 .. 0.60
   2 !  101.6   0.6   7.5e-33   2.7e-29       2     116 .]     122     233 ..     121     233 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                                  STTHHHHHHHHHHHHST.S CS
                   EIF_2_alpha 68 tkdGveaIkeaLkageeas 86
                                  t+  v++I++  k g+++ 
  gi|15668289|ref|NP_247082.1| 47 TSGWVKNIRDHVKVGQRVV 65
                                  4455777777777666644 PP

  == domain 2  score: 101.6 bits;  conditional E-value: 7.5e-33
                                   HHCTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHHHH CS
                   EIF_2_alpha   2 yeevgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaLka 81 
                                   +eevg+ l++++g++y+aF  ++i+++evld+lei+ee++++L e +k+ ++ ++v++++ ie++++++dG+++Ik+aL++
  gi|15668289|ref|NP_247082.1| 122 WEEVGYLLEDEFGELYNAFeTMVIEGKEVLDDLEISEEWKNVLYEVAKESIELTNVEVEGVIEMKSYAPDGIKQIKKALTT 202
                                   789****************9999*********************************************************6 PP

                                   HST.S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                   EIF_2_alpha  82 geeasneeeveeeeevkikliapPeYvltvetldk 116
                                   + +a    +  e++evki++i++P+Y++ v ++d+
  gi|15668289|ref|NP_247082.1| 203 ALKA----NPYEDVEVKITYIGAPKYRVVVIAPDY 233
                                   6663....34579*****************99996 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   1.4   1.4e-21     5e-18       2      75 .]       9      83 ..       9      83 .. 0.98
   2 ?   -0.3   0.2      0.39   1.4e+03      41      60 ..     224     243 ..     173     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 1.4e-21
                                  STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                            S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                  pe+g++v G+V++v ++GafVel+   g eg++++se+ +   v+++ +++kvG++v +kvl+vd+ ++ i+ls+k
  gi|15668289|ref|NP_247082.1|  9 PEEGDIVIGTVKDVKPYGAFVELLeyPGKEGMIHISEVTSG-WVKNIRDHVKVGQRVVAKVLRVDERKGHIDLSLK 83
                                  799**********************99*************9.********************************86 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.39
                                   CEESCHHHCEETTEEEEEEE CS
                            S1  41 arvedpdevlkvGdevkvkv 60 
                                   +rv ++   +k G+ev +kv
  gi|15668289|ref|NP_247082.1| 224 YRVVVIAPDYKSGEEVFKKV 243
                                   56666666777777777777 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   1.5e-06    0.0055       2      58 ..       9      63 ..       8      92 .. 0.76
   2 ?   -1.4   0.0         1   3.7e+03      15      15 ..     170     170 ..     139     232 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-06
                                  S-TT-EEEEEEEEEESSEEEEEEEEECTBSBCCCEEECCCTTSS--STS.TTSSCCHC CS
                        EXOSC1  2 PkegdvVLarvtrlrkkqalveilsvegennvlsdsgvgangegavkei.eaggglds 58
                                  P+egd+V++ v +++   a+ve+l   g++   +  +++++ +g vk+i + +  ++ 
  gi|15668289|ref|NP_247082.1|  9 PEEGDIVIGTVKDVKPYGAFVELLEYPGKE---GMIHISEVTSGWVKNIrDHVKVGQR 63
                                  9*************************9994...5567777788888877655555544 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1
                                   E CS
                        EXOSC1  15 l 15 
                                    
  gi|15668289|ref|NP_247082.1| 170 E 170
                                   1 PP

>> CwfJ_C_2  Protein similar to CwfJ C-terminus 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   4.9e-06     0.018      29      91 ..      28      99 ..      17     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.9e-06
                                  EEEE.TTT-..-EEE----HHHH-TT......HHHHHHHHHTT--TTT.SS--..----S--H.HHHHHHHH CS
                      CwfJ_C_2 29 yvqf.dykgekgyghviedeerfdlq......FareviaglLdlekrrkwrkp..krqskeeeekrveaFkk 91
                                  +v++ +y g+ g++h+ e  + + ++       +++v+a++L++++r+   +   kr ++++++++v+++k+
  gi|15668289|ref|NP_247082.1| 28 FVELlEYPGKEGMIHISEVTSGWVKNirdhvkVGQRVVAKVLRVDERKGHIDLslKRVTEQQKRAKVQEWKR 99
                                  455558999**************9999999*****************5433322355566666666665553 PP

>> Carbpep_Y_N  Carboxypeptidase Y pro-peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00025       0.9      54      99 ..      93     140 ..      64     152 .. 0.78
   2 ?    0.9   0.1      0.18   6.4e+02      60     102 ..     158     203 ..     136     213 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                   Carbpep_Y_N  54 kknnv..fekiskvlneplkeltseakkiWsemelkfPdavsklkfkt 99 
                                   k+++   f+++sk+l+ + ++l +++ ++W+e+  +  d++++l + +
  gi|15668289|ref|NP_247082.1|  93 KVQEWkrFQRASKMLERAAEKLGKSLEEAWEEVGYLLEDEFGELYNAF 140
                                   333333499************************999999999987665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
                   Carbpep_Y_N  60 ekiskvlneplk...eltseakkiWsemelkfPdavsklkfktkpk 102
                                   e++++vl e  k   elt+   +   em+ ++Pd ++++k+ +  +
  gi|15668289|ref|NP_247082.1| 158 EEWKNVLYEVAKesiELTNVEVEGVIEMKSYAPDGIKQIKKALTTA 203
                                   4444444444332223333333333688888888888888776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1484  (0.0827709); expected 358.6 (0.02)
Passed bias filter:                      843  (0.0470188); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1705.28
//
Query:       gi|15668290|ref|NP_247083.1|  [L=167]
Description: methyl coenzyme M reductase II protein MtrD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-59  198.7   0.3    4.3e-59  198.5   0.3    1.0  1  MCR_D     Methyl-coenzyme M reductase operon protein D


Domain annotation for each model (and alignments):
>> MCR_D  Methyl-coenzyme M reductase operon protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.5   0.3   2.4e-63   4.3e-59       1     142 [.      16     161 ..      16     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 2.4e-63
                         MCR_D   1 dveifpeRlLkpetteklLnelvelegikrvvihGprLPkkvpygpakGkevehkerkvievkgeeveLkvkvGrillele 81 
                                   dv+ifp+R+Lk+ettek+Lne+++l+gi+rv++hG+ LPk+vp+gpa+G +v+h++rkvi+vkgee+eL+vkvG+i++++e
  gi|15668290|ref|NP_247083.1|  16 DVKIFPHRYLKAETTEKVLNEIYDLDGIVRVIVHGQPLPKTVPFGPARGLPVNHQDRKVIKVKGEEMELRVKVGEIIITVE 96 
                                   79******************************************************************************* PP

                         MCR_D  82 ...deeviekieeiceevlpfsyeikegkfirkkktvsDyakyGee.eadkrllGlvDpksklee 142
                                       e++++ ieeic++++pf+y+i +g f++ k+tv+Dy+kyG+  ++d+rl+G+vD++++l++
  gi|15668290|ref|NP_247083.1|  97 gekLEKIMDGIEEICKRNFPFGYDIYVGAFTKIKPTVTDYMKYGDIsSIDPRLIGMVDASARLKD 161
                                   887889***************************************989*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1134.76
//
Query:       gi|15668291|ref|NP_247084.1|  [L=224]
Description: carbon monoxide dehydrogenase subunit gamma CdhE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.6e-14   51.3   2.0    1.4e-13   50.2   2.0    1.6  1  FeS          Putative Fe-S cluster
  ------ inclusion threshold ------
       0.15   12.1   0.7       0.36   10.9   0.7    1.6  1  TFIID-18kDa  Transcription initiation factor IID, 18kD subuni


Domain annotation for each model (and alignments):
>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   2.0   1.6e-17   1.4e-13       1      33 []      21      53 ..      21      53 .. 0.98

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.6e-17
                           FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                  LPg NCgaCGy+ C+ fAeal++++++ledCp+
  gi|15668291|ref|NP_247084.1| 21 LPGFNCGACGYKRCDLFAEALLNKDVKLEDCPF 53
                                  9*******************************6 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7     4e-05      0.36      53      90 ..      44      82 ..      36      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4e-05
                                  .XXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX CS
                   TFIID-18kDa 53 rkitlEDllfliR.kDkkKlnRlkellslkellkkakKq 90
                                  + ++lED  fl+R + k+  ++lke+l +k  +kk++K 
  gi|15668291|ref|NP_247084.1| 44 KDVKLEDCPFLLReRFKENYEKLKEILKIKGKIKKEEKY 82
                                  689**********4458899*************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1422.95
//
Query:       gi|15668292|ref|NP_247085.1|  [L=233]
Description: urease accessory protein UreG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-14   53.7   0.0    3.1e-14   53.0   0.0    1.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00021   21.0   0.0     0.0028   17.3   0.0    2.5  2  SRP54            SRP54-type protein, GTPase domain
     0.0003   19.9   0.2      0.054   12.5   0.1    2.3  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0027   18.1   0.1     0.0047   17.3   0.1    1.4  1  AAA_19           AAA domain
      0.004   17.2   0.1     0.0094   16.0   0.0    1.4  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
  ------ inclusion threshold ------
      0.015   14.6   0.0       0.02   14.1   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.018   15.0   0.1      0.039   13.8   0.0    1.6  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.018   14.4   0.0      0.031   13.6   0.0    1.3  1  Zeta_toxin       Zeta toxin
      0.032   14.1   0.0      0.061   13.2   0.0    1.5  1  TK               Thymidine kinase
      0.076   12.7   0.2       0.12   12.1   0.2    1.2  1  AAA_30           AAA domain
       0.09   12.5   0.3        1.1    9.0   0.0    2.2  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.11   12.3   0.0       0.17   11.6   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.11   12.0   0.3        0.2   11.1   0.3    1.4  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
       0.18   12.2   0.0        0.3   11.4   0.0    1.4  1  AAA_16           AAA ATPase domain
       0.21   12.1   0.7       0.45   11.1   0.3    1.9  2  AAA_18           AAA domain
       0.23   11.5   0.1        0.6   10.1   0.0    1.6  2  ResIII           Type III restriction enzyme, res subunit
       0.24   10.4   0.2       0.66    9.0   0.3    1.6  2  LpxK             Tetraacyldisaccharide-1-P 4'-kinase


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   2.9e-17   3.1e-14       2     175 ..       3     162 ..       2     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 2.9e-17
                                   EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT..EEEETTTTECCHCTT-HHHHHHHHHHH CS
                          cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgve.ivelenGciCctlredllkelealeer 79 
                                   v +++G +G+GKT++l h++    ++g+k  v+  +      D  + ++ g + +v l++  ++   +    +e+ + +++
  gi|15668292|ref|NP_247085.1|   3 VAIVAGTPGAGKTSVLIHTIrtLINEGYKPVVVKIDCL-YTDDDVRYKKLGIPvLVGLSKDMCPDHFAIYNFEEMVDWAKD 82 
                                   789*****************887799***********9.55566666666676699****999988555555555555555 PP

                                   HTT-SEEEEEECTTTT.HHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..H CS
                          cobW  80 eerldviliEttGlae.PapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeall 159
                                   +   d++liEt Gl +  ap           ++ +  ++v+Da    +++ ++++k++  l+ ad++v++K D +++++  
  gi|15668292|ref|NP_247085.1|  83 K--GDILLIETAGLCHrCAPY----------TKNSLGICVIDA----TSGPNTPRKVGPFLTSADIVVITKGDIISQAER- 146
                                   5..9*********66515555..........899999******....99*****************************88. PP

                                   HHHHHHHHHHHTTS-E CS
                          cobW 160 ekleerlrqlnpeakv 175
                                   e+++er+ ++np+ ++
  gi|15668292|ref|NP_247085.1| 147 EVFRERVLEMNPNCRI 162
                                   ***********99876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.6e-06    0.0028       2     140 ..       2     130 ..       1     146 [. 0.71
   2 ?   -3.0   0.0       4.4   4.7e+03     113     140 ..     157     184 ..     150     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.6e-06
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHT CS
                         SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakee 82 
                                   +v +++G+ GaGKT+ l    + l +eg+k+++v  D+         k l+  + v + k    ++ a + +e++    ++
  gi|15668292|ref|NP_247085.1|   2 KVAIVAGTPGAGKTSVLIHTIRTLINEGYKPVVVKIDCLYTDDDVRYKKLGIPVLVGLSKDMCPDHFAIYNFEEMVDWAKD 82 
                                   68899*********************************9887766666666666666555444445555667777777777 PP

                                   TSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHS CS
                         SRP54  83 kidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeav 140
                                   k d++l+ TaG  +           ++  +k+   + v+dat+g ++ +++  F  ++
  gi|15668292|ref|NP_247085.1|  83 KGDILLIETAGLCHR----------CAPYTKNSLGICVIDATSGPNTPRKVGPFLTSA 130
                                   88*********9875..........344445555555555555555555555555555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.4
                                   SSSEEEEEEETTBHTHHHHHHHHHHHHS CS
                         SRP54 113 kpdevllvldattgqeavkqakaFkeav 140
                                   +p+  ++ ++++tgq  v+ ak+  e+ 
  gi|15668292|ref|NP_247085.1| 157 NPNCRIYEVNGLTGQGCVEIAKEIIESK 184
                                   5666667778888888888888766655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   5.1e-05     0.054      34      66 ..       6      38 ..       1      42 [. 0.91
   2 !    5.5   0.0    0.0071       7.5     165     231 ..     126     186 ..      77     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-05
                                  EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                          MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                  + G+PGaGk  ++ + + +l+++G++  v+ +D
  gi|15668292|ref|NP_247085.1|  6 VAGTPGAGKTSVLIHTIRTLINEGYKPVVVKID 38
                                  78**********99****************999 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0071
                                   CHHH-SEEEEE---.HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHH CS
                          MeaB 165 ileiaDiivvnkaD.kkeaekaarelraaleleeekekeWrpkvlktsavegeGidelvdaieehrev 231
                                    l  aDi+v+ k D  ++ae+     + +l      e + + ++ ++ +++g+G  e++++i e +++
  gi|15668292|ref|NP_247085.1| 126 FLTSADIVVITKGDiISQAEREV-FRERVL------EMNPNCRIYEVNGLTGQGCVEIAKEIIESKDI 186
                                   566799******99545555432.223333......34457889999999999999999999887765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   4.4e-06    0.0047      11      40 ..       2      31 ..       1      43 [. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.4e-06
                        AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggv 40
                                  kv +v + pG GKT vl h ++ l+++g  
  gi|15668292|ref|NP_247085.1|  2 KVAIVAGTPGAGKTSVLIHTIRTLINEGYK 31
                                  6889********************999854 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.9e-06    0.0094       1      36 [.       3      38 ..       3      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.9e-06
                                  EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  1 iaiastkGGvGKTtlaanLaralarrglrVllvDaD 36
                                  +ai++++ G+GKT+++++ +r l ++g++ ++v+ D
  gi|15668292|ref|NP_247085.1|  3 VAIVAGTPGAGKTSVLIHTIRTLINEGYKPVVVKID 38
                                  699*******************************99 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05      0.02       2      29 ..       2      27 ..       1      44 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                       DUF2075  2 avvlVtGvaGtGKtvvllnllaeledde 29
                                  +v +V G +G+GKt vl++ + +l   +
  gi|15668292|ref|NP_247085.1|  2 KVAIVAGTPGAGKTSVLIHTIRTL--IN 27
                                  689****************99988..33 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.7e-05     0.039       4      36 ..       6      38 ..       3      49 .. 0.87
   2 ?   -3.6   0.0       8.9   9.4e+03      80      97 ..      72      90 ..      69      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.7e-05
                          MobB  4 ivgksgsGKTtLleklipelkarglrvgtiKha 36
                                  ++g+ g+GKT+ l + i++l ++g++  ++K +
  gi|15668292|ref|NP_247085.1|  6 VAGTPGAGKTSVLIHTIRTLINEGYKPVVVKID 38
                                  6799*************************9966 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.9
                          MobB 80 sleellarl.sevDlvlvE 97
                                  ++ee++++  ++ D++l+E
  gi|15668292|ref|NP_247085.1| 72 NFEEMVDWAkDKGDILLIE 90
                                  5677888884558999998 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.9e-05     0.031      18      52 ..       3      38 ..       2      44 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-05
                    Zeta_toxin 18 lillgGqpGAGKselaellkdele.rqgnvvrldpD 52
                                  + +++G pGAGK++++  + + l  ++ + v+++ D
  gi|15668292|ref|NP_247085.1|  3 VAIVAGTPGAGKTSVLIHTIRTLInEGYKPVVVKID 38
                                  679**********99877777766466667777666 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.8e-05     0.061       2      74 ..       2      81 ..       1      96 [. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.8e-05
                            TK  2 sielilgpmfaGKsteLlrrvkryqlaekkvvvik.....aakdnRysegkvvthdgisleak..ksktssleeikeele 74
                                  ++ ++ g+  aGK++ L+++++ +    +k vv+k     +  d Ry++  +    g+s +    + ++ ++ee+++ ++
  gi|15668292|ref|NP_247085.1|  2 KVAIVAGTPGAGKTSVLIHTIRTLINEGYKPVVVKidclyTDDDVRYKKLGIPVLVGLSKDMCpdHFAIYNFEEMVDWAK 81
                                  6788999999***********************99333322346677776555554444443333555666666555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00011      0.12      19      48 ..       2      31 ..       1      36 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaaggr 48
                                  +va++ G +G+GKt +l +  +++ ++g++
  gi|15668292|ref|NP_247085.1|  2 KVAIVAGTPGAGKTSVLIHTIRTLINEGYK 31
                                  5899************99887776667654 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.25   2.6e+02       1      17 [.       1      17 [.       1      28 [. 0.84
   2 ?    9.0   0.0    0.0011       1.1      81     140 ..     120     179 ..     102     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.25
                     PduV-EutP  1 mkkilliGkvgsGKttL 17
                                  mk  ++ G+ g+GKt++
  gi|15668292|ref|NP_247085.1|  1 MKVAIVAGTPGAGKTSV 17
                                  7888999********95 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0011
                     PduV-EutP  81 ppgfasvfnkeviGiitkidlaedeenieaveelLksaGaekifevsavekegieellky 140
                                   p ++  +++   i +itk d+ ++ e+    e+ L++    +i+ev+ ++ +g  e+ k 
  gi|15668292|ref|NP_247085.1| 120 PRKVGPFLTSADIVVITKGDIISQAEREVFRERVLEMNPNCRIYEVNGLTGQGCVEIAKE 179
                                   66777778888899********8887777888999******************9998775 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016      0.17       2      27 ..       5      29 ..       4      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
               Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltv 27
                                  +v+G pG+GK++++ + +rt li   
  gi|15668292|ref|NP_247085.1|  5 IVAGTPGAGKTSVLIHTIRT-LINEG 29
                                  79***************999.44333 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00019       0.2      17      44 ..       5      31 ..       1      36 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                                  EEEE-TTSSHHHHHHHHHHHHHHTSSST CS
                 UvrD-helicase 17 lveAsAGsGKTfvlaerilrlikeeeie 44
                                  +v+  +G+GKT vl++ i  li+e+ ++
  gi|15668292|ref|NP_247085.1|  5 IVAGTPGAGKTSVLIHTIRTLINEG-YK 31
                                  577779****************998.65 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029       0.3      27      69 ..       4      48 ..       2      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                        AAA_16 27 vllsGesGvGKsslv.rellralekdg.giflrgkcdqlesaipy 69
                                   ++ G +G GK+s++  ++++ +++ +  ++++ +c   + +++y
  gi|15668292|ref|NP_247085.1|  4 AIVAGTPGAGKTSVLiHTIRTLINEGYkPVVVKIDCLYTDDDVRY 48
                                  5899**********9788887777776688888888777666666 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00043      0.45       2      15 ..       5      18 ..       5     111 .. 0.67
   2 ?   -2.8   0.0       8.1   8.6e+03       4      21 ..     166     183 ..     164     215 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00043
                        AAA_18  2 lltGtpGvGKttla 15
                                  +++GtpG+GKt++ 
  gi|15668292|ref|NP_247085.1|  5 IVAGTPGAGKTSVL 18
                                  79*********985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.1
                        AAA_18   4 tGtpGvGKttlakeLskr 21 
                                   +G  G G  ++ake+ ++
  gi|15668292|ref|NP_247085.1| 166 NGLTGQGCVEIAKEIIES 183
                                   566666666666666333 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00056       0.6      28      56 ..       5      32 ..       2      41 .. 0.82
   2 ?   -2.3   0.0       3.6   3.8e+03      61      75 ..     135     154 ..     129     204 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00056
                                  EEEESTTSTHHHHHHHHHHHH-S.....- CS
                        ResIII 28 likmaTGtGKTlvaaklierllkkgkeek 56
                                  +++ + G+GKT v++++i+ l ++g++  
  gi|15668292|ref|NP_247085.1|  5 IVAGTPGAGKTSVLIHTIRTLINEGYK-P 32
                                  566788*****************9885.3 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                                   ESSHHHHHHHHHHG.....G CS
                        ResIII  61 vprkslleqtleef.....k 75 
                                   + + ++++q+++e+      
  gi|15668292|ref|NP_247085.1| 135 ITKGDIISQAEREVfrervL 154
                                   44555555655433222221 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3   0.00063      0.66      47      71 ..      11      35 ..       5      36 .. 0.93
   2 ?   -2.2   0.0       1.6   1.7e+03     176     205 ..     127     156 ..     124     203 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00063
                                  -HSHHHHHHHHHHHTTTS..-EEEE CS
                          LpxK 47 GtGKTPlvialvkllqarglkvgvl 71
                                  G+GKT++ i+ +++l ++g+k++v+
  gi|15668292|ref|NP_247085.1| 11 GAGKTSVLIHTIRTLINEGYKPVVV 35
                                  9**********************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                                   GGG-SEEEE..........-TTTSSSS-EE CS
                          LpxK 176 lkradlvilngakaeeeeaekaeeksipvl 205
                                   l +ad+v+++++++ +++++++ ++++ ++
  gi|15668292|ref|NP_247085.1| 127 LTSADIVVITKGDIISQAEREVFRERVLEM 156
                                   567888888877777666666555333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1505.97
//
Query:       gi|15668293|ref|NP_247086.1|  [L=261]
Description: SN-glycerol-3-phosphate transport ATP-binding protein UgpC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-14   52.6   0.1    1.2e-13   51.8   0.1    1.3  1  ABC_tran  ABC transporter
    1.1e-10   41.8   0.3    5.4e-06   26.4   0.0    2.6  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00011   21.8   1.2    0.00045   19.7   0.8    2.0  1  SMC_N     RecF/RecN/SMC N terminal domain
     0.0037   17.5   0.1      0.023   15.0   0.1    2.0  1  AAA_22    AAA domain
      0.008   16.6   0.0      0.016   15.6   0.0    1.6  1  AAA_16    AAA ATPase domain
  ------ inclusion threshold ------
       0.01   15.6   0.1      0.045   13.5   0.1    2.0  1  AAA_30    AAA domain
      0.025   14.3   0.0      0.054   13.2   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
      0.095   12.3   0.0       0.22   11.1   0.0    1.6  1  AAA_25    AAA domain
       0.16   11.5   0.0       0.27   10.7   0.0    1.4  1  AAA_7     P-loop containing dynein motor region
       0.17   11.8   2.6       0.41   10.5   0.7    2.3  2  ATPase_2  ATPase domain predominantly from Archaea
       0.19   11.1   1.9        2.4    7.6   0.1    2.8  3  PhoH      PhoH-like protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.1   7.3e-17   1.2e-13       6     135 ..      24     168 ..      22     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 7.3e-17
                                   EEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren... 79 
                                   +++k+ge+v++vG++G+GKS L++ + +l +     + +il++g+      ++   +++i+ l+q+ ++  ++tv+e    
  gi|15668293|ref|NP_247086.1|  24 VTIKRGEIVGVVGPTGSGKSNLISDIEQLAQGdtiSKRRILVNGEVPPIeMRRDPKKRRIAQLSQNMNFLADMTVEEFilm 104
                                   79***********************9999987655666677775433333577778889********************** PP

                                   .......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHH.HHHHTSSEEEEEST CS
                                   .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                      ABC_tran  80 .......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalar.allkkpkllllDEp 135
                                          ++++ ++++++  +    +  + +++ + LSgGq + +++a  a++++++++l+DE 
  gi|15668293|ref|NP_247086.1| 105 haksrgvYRENIVDEVIELANRLTGEPIKKDYNLTILSGGQSRSLMVADvAVISDSPIVLIDEI 168
                                   88877774444455555555444422333334459*************6368899*******95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   3.3e-09   5.4e-06       2     111 ..      32     134 ..      31     138 .. 0.83
   2 !   14.7   0.1   1.2e-05      0.02     178     301 ..     117     198 ..      82     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.3e-09
                        AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersq 82 
                                    +++Gp gsGKSnL+  ++ la      +g+t++++++  ++++p    ++dp+++   +++    q++++   +++e+++
  gi|15668293|ref|NP_247086.1|  32 VGVVGPTGSGKSNLISDIEQLA------QGDTISKRRILVNGEVPPIEMRRDPKKRRIAQLS----QNMNFLADMTVEEFI 102
                                   689***************9997......6***************************999999....999999999999999 PP

                        AAA_21  83 v...eeklssvetllesgllldkrsleeedvf 111
                                   +   + +   +e+     + l +r + e+ ++
  gi|15668293|ref|NP_247086.1| 103 LmhaKSRGVYRENIVDEVIELANRLTGEPIKK 134
                                   98777777666666666666666666666555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.2e-05
                        AAA_21 178 fakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkg 258
                                    +++++l+ rl++++ + + +l+ l                                   S G+ r   +++ ++   ++ 
  gi|15668293|ref|NP_247086.1| 117 VDEVIELANRLTGEPIKKDYNLTIL-----------------------------------SGGQSRS-LMVADVAVISDS- 160
                                   4566677777777777777777777...................................*******.***********9. PP

                        AAA_21 259 sllliDEpEng.LHPkllrrllell.kelsrngaQviltTHSpll 301
                                   +++liDE+En  +     ++ lell  + +     v++ TH+p+l
  gi|15668293|ref|NP_247086.1| 161 PIVLIDEIENAgIKK---HEALELLaGYGKI----VLVITHDPVL 198
                                   **********76777...6666666233323....4777777776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.8   2.7e-07   0.00045      26     170 ..      31     171 ..      22     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.7e-07
                                   EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--....BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk....skekasvkkaeveitfdnedkklkiekeevsisrr 102
                                   +  +vGp GSGKsnl+  i  +   ++  + r+     l++      + ++  kk +++ + +n +  + ++ ee+ ++  
  gi|15668293|ref|NP_247086.1|  31 IVGVVGPTGSGKSNLISDIEQLAQGDTI-SKRRI----LVNGevppIEMRRDPKKRRIAQLSQNMNFLADMTVEEFILMHA 106
                                   6789***************644333333.33333....3333333368889999999999888888888888899988888 PP

                                   EETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 103 vkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                   ++r+   e  +++     + ++    +++ + + LSgG+   +++a    +  ++ +p++l+Dei+ a
  gi|15668293|ref|NP_247086.1| 107 KSRGVYRENIVDEVIELANRLTGEPIKKDYNLTILSGGQSRSLMVAD---VAVISDSPIVLIDEIENA 171
                                   888887777777776666788888788888888******98666665...5678899********976 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.4e-05     0.023       5     112 ..      29     182 ..      24     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee................................erpevvfvtlpsstss 53 
                                     i+ v+G++G+GK+ l+  + + ++ +   ++                                ++ +v ++ l + +s+
  gi|15668293|ref|NP_247086.1|  29 GEIVGVVGPTGSGKSNLISDIEQLAQGDTISKRrilvngevppiemrrdpkkrriaqlsqnmnflADMTVEEFILMHAKSR 109
                                   567779*****************9977666666999999999999999998888888887777764444434444444444 PP

                        AAA_22  54 kdllrellralglelka...............erlsseellealeqalraravielliiDEaqhlr..seealeeL 112
                                      +++++ ++ + +++               ++++s+ l+  +++ +   +  ++++iDE+++    ++eale L
  gi|15668293|ref|NP_247086.1| 110 GVYRENIVDEVIELANRltgepikkdynltilSGGQSRSLM--VADVAVISDS-PIVLIDEIENAGikKHEALELL 182
                                   44455555555555555665666667777655555555544..3333333333.7889*****9855559999988 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.7e-06     0.016      19      63 ..      24      72 ..      20     192 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.7e-06
                        AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekd....ggiflrgkcdql 63
                                  v   r+e+v ++G+ G+GKs l+  + + +++d    + i+++g+    
  gi|15668293|ref|NP_247086.1| 24 VTIKRGEIVGVVGPTGSGKSNLISDIEQLAQGDtiskRRILVNGEVPPI 72
                                  6667889****************99998777775554344444444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.7e-05     0.045      10     108 ..      21     179 ..      18     196 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                        AAA_30  10 vealltsgdrvavltGpAGtGKttalkalreaweaag..............grvi.glAptgkaAkvLaeelgi.eastia 74 
                                   v++++ ++  ++ ++Gp G+GK+ +++ ++++++ +                       p+++  ++L++++++ + +t++
  gi|15668293|ref|NP_247086.1|  21 VREVTIKRGEIVGVVGPTGSGKSNLISDIEQLAQGDTiskrrilvngevppI--EmRRDPKKRRIAQLSQNMNFlADMTVE 99 
                                   67788888899*******************9999775677666666555321..212234555555555555543445555 PP

                        AAA_30  75 kllkrlk..............................................grarlepgtllivDEagmvdtkqlaal 108
                                   +++  ++                                              + a ++++ ++++DE+  +++k+ +al
  gi|15668293|ref|NP_247086.1| 100 EFILMHAksrgvyrenivdevielanrltgepikkdynltilsggqsrslmvaDVAVISDSPIVLIDEIENAGIKKHEAL 179
                                   55555555566666666666666666666777777777777777777777776445555667777777777766666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.3e-05     0.054      16      42 ..      23      49 ..      19      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
                        AAA_29 16 tieidlkgatlltGpsGsGKSTllDAi 42
                                  +++i++ +++ ++Gp+GsGKS l+  i
  gi|15668293|ref|NP_247086.1| 23 EVTIKRGEIVGVVGPTGSGKSNLISDI 49
                                  56777666999***********99655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.22      29     138 ..      25     125 ..       8     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                        AAA_25  29 llpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldla 109
                                    + +ge++ ++G++g+GK+ l +d+   +a+G+   ++     ++  +   E+++d  +rR++++ +++++   l+ ++  
  gi|15668293|ref|NP_247086.1|  25 TIKRGEIVGVVGPTGSGKSNLISDI-EQLAQGDTISKR--RILVNGEVPPIEMRRDPKKRRIAQLSQNMNF---LADMT-- 97 
                                   57899*****************998.589999977662..2344444455566666666777777777743...33333.. PP

                        AAA_25 110 gveslpLfakdrggtlltadvdaleaaie 138
                                    ve+  L++++++g  ++  vd++++ ++
  gi|15668293|ref|NP_247086.1|  98 -VEEFILMHAKSRGVYRENIVDEVIELAN 125
                                   .3556888888888888877777777665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00017      0.27      28      60 ..      24      56 ..      19      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                         AAA_7 28 lllknkkpvllvGptGtGKtviikdllkkldke 60
                                    +k++  v +vGptG+GK+ +i+d+ +  + +
  gi|15668293|ref|NP_247086.1| 24 VTIKRGEIVGVVGPTGSGKSNLISDIEQLAQGD 56
                                  5678888899*************9976655544 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.7   0.00025      0.41      20     134 ..      29     174 ..      22     189 .. 0.64
   2 ?   -2.9   0.0       3.3   5.3e+03      67      82 ..     215     230 ..     207     245 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                      ATPase_2  20 neiyfiYGpegsGKtaLlkeiienl..edkdkyviyyi....alreesiskldefieeeeekkklekal............ 82 
                                    ei+ + Gp gsGK+ L+  i +    +  +k++i ++    +++ ++  k+++  + +++ ++l++++            
  gi|15668293|ref|NP_247086.1|  29 GEIVGVVGPTGSGKSNLISDIEQLAqgDTISKRRILVNgevpPIEMRRDPKKRRIAQLSQNMNFLADMTveefilmhaksr 109
                                   5788899***********998776633445556666543333455555555555544444444444444666667777888 PP

                      ATPase_2  83 ...................giavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlg 134
                                                      g++++k+   +il+       ++ +l+ +++      +i++iDe+ +++ ++
  gi|15668293|ref|NP_247086.1| 110 gvyrenivdevielanrltGEPIKKDYNLTILS-----GGQSRSLMVADVAVISDSPIVLIDEIENAG-IK 174
                                   888888888877776666666666666655544.....233445566666666667888888888887.44 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.3
                      ATPase_2  67 efieeeeekkklekal 82 
                                   + ie++ee+k++++++
  gi|15668293|ref|NP_247086.1| 215 KIIETTEEEKEISRKI 230
                                   3444555555555554 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0015       2.4      16      35 ..      26      45 ..      21      65 .. 0.85
   2 ?    0.2   0.0      0.26   4.2e+02     148     203 ..      62     123 ..      55     125 .. 0.62
   3 ?    1.0   0.0      0.15   2.4e+02     122     182 ..     162     227 ..     155     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0015
                                  HHH-SEEEEE--TTSSTTHH CS
                          PhoH 16 lkkndivfaiGpaGtGKtyl 35
                                  +k+ +iv ++Gp+G+GK+ l
  gi|15668293|ref|NP_247086.1| 26 IKRGEIVGVVGPTGSGKSNL 45
                                  67889************976 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.26
                                   EEEEEE----------....----THHHHHHTTT..-TTEEEEE--GGG----HHHHHHHHH CS
                          PhoH 148 kvvvtGdvtqidlpkg....kksGlaealevlkn..vegieivelkkkdvvRhplvkkivka 203
                                   ++ v+G+v  i+++++    +   l++ ++ l +  ve++ +++ k++ v R+++v +++++
  gi|15668293|ref|NP_247086.1|  62 RILVNGEVPPIEMRRDpkkrRIAQLSQNMNFLADmtVEEFILMHAKSRGVYRENIVDEVIEL 123
                                   56666766655554332001455666667777773344555556677789999999998875 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.15
                                   EEEE-SGGG--HHHHHHHHTTB-TT.-EEEEEE---...-----.------THHHHHHTTT-TTEE CS
                          PhoH 122 fvilDEAQnttkeqmkmfltRlGen.skvvvtGdvt...qidlp.kgkksGlaealevlknvegie 182
                                   +v++DE  n+  ++ + +    G +   +v+t+d+     +d + + ++ G+++++e+ +++++i+
  gi|15668293|ref|NP_247086.1| 162 IVLIDEIENAGIKKHEALELLAGYGkIVLVITHDPVlalMTDRRiVMRNGGMQKIIETTEEEKEIS 227
                                   688899999876666655555554413578999987222356664446888999998888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      696  (0.0388198); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 1618.98
//
Query:       gi|15668294|ref|NP_247087.1|  [L=308]
Description: translation initiation factor IF-2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-96  321.8   0.8    3.8e-96  321.6   0.8    1.0  1  IF-2B         Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.029   14.8   0.0        3.1    8.3   0.0    2.7  2  FumaraseC_C   Fumarase C C-terminus
      0.039   13.3   0.0      0.084   12.2   0.0    1.5  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 
      0.072   13.4   0.3       0.15   12.4   0.3    1.6  1  TraC          TraC-like protein


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.6   0.8  8.5e-100   3.8e-96       1     282 []      22     292 ..      22     292 .. 0.99

  Alignments for each domain:
  == domain 1  score: 321.6 bits;  conditional E-value: 8.5e-100
                                   SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHH CS
                         IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakkslie 81 
                                   ++rG+ +i++aa+++l+e++ ++++ + +e+k+++r+a++ L++arPtavsl n+++++lk         ++++ k+++ie
  gi|15668294|ref|NP_247087.1|  22 EIRGAGRIGRAAAKALKEYALKISHLNEEEFKNKMREAGNILISARPTAVSLPNVVKYVLK-------GLNEENPKERVIE 95 
                                   589**********************************************************.......789********** PP

                                   HHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHHHTTXEEE CS
                         IF-2B  82 kikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLvqagipvt 162
                                   +++e+i++ ++a e+ig+++a++ikdgdtilT+cns+++++v+++a +e+k++kV+++E+rPr+qG ltak+L + gi+vt
  gi|15668294|ref|NP_247087.1|  96 RADEFINSSLKAIENIGKFGANRIKDGDTILTHCNSEAAISVIKTAYDEGKDIKVFCTETRPRNQGYLTAKTLYDYGIDVT 176
                                   ********************************************************************************* PP

                                   EEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSXXBEXTHHHH CS
                         IF-2B 163 litdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedifieerdpeell 243
                                   li+dsav+y+++e +d v+vGAd+i++nG+++nkiGTs++A++A+e+++p+l++ae++kf++++ ++e i ieer pee++
  gi|15668294|ref|NP_247087.1| 177 LIVDSAVRYFIKE-IDIVVVGADAITANGCLVNKIGTSQIALIANESRVPFLTAAETYKFHPKTIVGELIEIEERSPEEVA 256
                                   *************.******************************************************************* PP

                                   EETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                         IF-2B 244 nitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                   +++++ +    +k++npafDvtP+++I++iITevG++pp
  gi|15668294|ref|NP_247087.1| 257 VFEDKYK---GIKIRNPAFDVTPAKYIDAIITEVGLIPP 292
                                   ****998...***************************98 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.023     1e+02      26      45 ..      35      54 ..      28      57 .. 0.87
   2 ?    8.3   0.0   0.00069       3.1      12      43 ..     132     168 ..     132     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.023
                                  --HHHHHHHTT-.-HHHHHH CS
                   FumaraseC_C 26 ktlreavlelgllteeelde 45
                                  k l+e +l+  +l eee++ 
  gi|15668294|ref|NP_247087.1| 35 KALKEYALKISHLNEEEFKN 54
                                  789**************975 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00069
                                   HHHHHHHHHHHHHT--HHHHHHH.....TT-.-HHHH CS
                   FumaraseC_C  12 ekAakIAkeAlkegktlreavle.....lgllteeel 43 
                                   e+A ++ k+A+ egk ++  + e     +g+lt+++l
  gi|15668294|ref|NP_247087.1| 132 EAAISVIKTAYDEGKDIKVFCTEtrprnQGYLTAKTL 168
                                   67889*****************999999999999876 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.9e-05     0.084      37      73 ..      19      55 ..       6      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                                  SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                  2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                                  k + i G+GrIG+a+ak lk+  +k+   +  + k++
  gi|15668294|ref|NP_247087.1| 19 KNMEIRGAGRIGRAAAKALKEYALKISHLNEEEFKNK 55
                                  567799*******************999988766554 PP

>> TraC  TraC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   3.4e-05      0.15      11      36 ..      11      36 ..       4      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                          TraC 11 iakLqerlkqaevreAeRigRiAlka 36
                                  i+   e+ k++e+r A RigR+A ka
  gi|15668294|ref|NP_247087.1| 11 IKETYEKIKNMEIRGAGRIGRAAAKA 36
                                  55667999****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1987.98
//
Query:       gi|15668295|ref|NP_247088.1|  [L=110]
Description: hypothetical protein MJ_0123 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.1e-10   38.9   0.5      1e-09   38.8   0.5    1.0  1  DUF45          Protein of unknown function DUF45
     0.0001   21.6   3.5    0.00012   21.3   3.5    1.1  1  Peptidase_M56  BlaR1 peptidase M56
    0.00071   19.4   0.3    0.00082   19.2   0.3    1.3  1  SprT-like      SprT-like family
  ------ inclusion threshold ------
      0.053   13.6   0.1       0.17   12.0   0.0    1.8  2  FANCI_S1-cap   FANCI solenoid 1 cap


Domain annotation for each model (and alignments):
>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.5   2.3e-13     1e-09     113     196 ..       7      95 ..       2     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.3e-13
                         DUF45 113 keeleerlaklaaklgv.kprsvsikdmktrWGsc.sskgkirlnwrLvk.appevidYVvvHElaHllek..nHskrFwa 188
                                   k+++++ ++++   l++ +  +++ik mk++ +s   +++++rln  +v+ + +e+++Y+++HEl+H++ k  nH+ +F +
  gi|15668295|ref|NP_247088.1|   7 KKDIKDIVNEILISLNInESINIEIKPMKQKIASFsFKTKTLRLNKYVVEnFDEELLHYIILHELIHFKIKsiNHGIKFEN 87 
                                   6778888888888888844568*************99********9999659***************8765559******* PP

                         DUF45 189 lvekllPd 196
                                   ++ +++ +
  gi|15668295|ref|NP_247088.1|  88 ELRNYFSK 95 
                                   **999865 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   3.5   2.8e-08   0.00012     141     210 ..       8      77 ..       2      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.8e-08
                 Peptidase_M56 141 eelkeaLkeakeemqlkrnikirlsssidsPavlgllkprIvlPadflkklsdeeleyillHElaHlkrk 210
                                   + +k++++e+    ++   i+i +++  ++ a++      + l +++++++++e l+yi+lHEl+H+k k
  gi|15668295|ref|NP_247088.1|   8 KDIKDIVNEILISLNINESINIEIKPMKQKIASFSFKTKTLRLNKYVVENFDEELLHYIILHELIHFKIK 77 
                                   567899999999999****************************************************976 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   1.8e-07   0.00082      27      79 ..      32      78 ..       8     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.8e-07
                     SprT-like 27 krlnttaGranlkratvrhhasIeLseklldsrsedrllntLaHElcHlalfv 79
                                  k +++++   ++k+      ++++L++ ++++ +e+ l+ +++HEl+H  +  
  gi|15668295|ref|NP_247088.1| 32 KPMKQKIASFSFKT------KTLRLNKYVVENFDEELLHYIILHELIHFKIKS 78
                                  46777777777777......9***************************86633 PP

>> FANCI_S1-cap  FANCI solenoid 1 cap
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.7e-05      0.17       1      33 [.      34      66 ..      34      71 .. 0.91
   2 ?   -1.3   0.0      0.52   2.3e+03      15      29 ..      87     101 ..      83     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                  FANCI_S1-cap  1 mdqkIlsLaaedsteeLqkfLqtLkedeLteli 33
                                  m+qkI s++ + +t +L k+  +  ++eL + i
  gi|15668295|ref|NP_247088.1| 34 MKQKIASFSFKTKTLRLNKYVVENFDEELLHYI 66
                                  99******************9999999998876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.52
                  FANCI_S1-cap  15 eeLqkfLqtLkedeL 29 
                                   +eL+++ ++ + de 
  gi|15668295|ref|NP_247088.1|  87 NELRNYFSKNECDEI 101
                                   689998888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 693.42
//
Query:       gi|298575366|ref|NP_247089.4|  [L=1075]
Description: Type I restriction-modification enzyme helicase subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.3e-45  153.8   9.2      1e-43  149.6   7.0    3.1  2  SWI2_SNF2   SWI2/SNF2 ATPase
    6.4e-27   94.8   0.2    6.4e-27   94.8   0.2    5.3  5  HSDR_N      Type I restriction enzyme R protein N terminus (H
    1.3e-16   61.1   9.8    1.4e-12   47.9   4.5    4.9  5  ResIII      Type III restriction enzyme, res subunit
     0.0054   16.6   0.1     0.0054   16.6   0.1    4.1  5  DUF4411     Domain of unknown function (DUF4411)
  ------ inclusion threshold ------
      0.039   14.3   0.1       0.35   11.2   0.0    2.7  1  Helicase_C  Helicase conserved C-terminal domain
       0.65   10.1   4.1         19    5.3   0.0    4.4  2  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
        2.6    8.2   9.7         28    4.9   3.0    3.8  2  ColG_sub    Collagenase G catalytic helper subdomain


Domain annotation for each model (and alignments):
>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.6   7.0     4e-47     1e-43       2     204 ..     182     496 ..     181     517 .. 0.82
   2 ?   -2.3   0.0       1.1   2.8e+03      42      57 ..     639     656 ..     585     656 .. 0.68

  Alignments for each domain:
  == domain 1  score: 149.6 bits;  conditional E-value: 4e-47
                      SWI2_SNF2   2 Qyravekavervke....gdrkgGviWHtqGSGKsltmvflakkllee.elknpkvvvvtDRkdLdkQlsktfakageek 76 
                                    Qy+a++ka++r+ e    +++++G+iWH qGSGK++tm+f+a+  l++   +np +++v+DR dL++Q ++ +++++e+k
  gi|298575366|ref|NP_247089.4| 182 QYFATKKAMKRIDEylsgDSKNKGLIWHWQGSGKTYTMFFIANYFLDKyFSENPVIFFVVDRVDLERQSKEFYEAIQEKK 261
                                    *************999987799************************96467******************99999987555 PP

                      SWI2_SNF2  77 p....kqaesrkeLkelle....k....e..sekiifttiqKfe....eeek............................ 110
                                         k+++s ++L e ++    +    +   ++i++ttiqKf+    +  k                            
  gi|298575366|ref|NP_247089.4| 262 FktilKRIDSINKLYEVIKsikmSelsnKviVRGIYTTTIQKFQyersK--Kekdnnkekdkddedldlskpieeiikki 339
                                    4112256777776666663222212221224678899******976541..1457888999******************* PP

                      SWI2_SNF2 111 ...........................................................eklevlsereniivlvDEaHR 131
                                                                                                +l  +++ ++i++l+DEaHR
  gi|298575366|ref|NP_247089.4| 340 edklkkeekegkikglkdlliilafiylkhlkeknpeeykkhienlkklkdkdkkeeylINLGNIKR-KHILILIDEAHR 418
                                    **************************************************99987654433455555.55********** PP

                      SWI2_SNF2 132 sqygelakklrkalpnaafigFTGTPilkkdkktkevFg......eyidkYtikeaveDgavvpilYesrlaklelkee 204
                                    +qyg l    + ++pna  +gFTGTP++k++k+t ++F        y+d Y i ++++D+ ++p++Y+  +++ ++k+e
  gi|298575366|ref|NP_247089.4| 419 TQYGILGGMRKITFPNAITFGFTGTPVFKNEKNTFTEFSypekgeFYLDVYFIGDSIKDKFTLPLTYQI-VKEGDIKSE 496
                                    ******9999999*************************75555545*********************84.344444444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                      SWI2_SNF2  42 llee..elknpkvvvvtD 57 
                                    ++ee  + +npk+++vtD
  gi|298575366|ref|NP_247089.4| 639 IREEflNSENPKILIVTD 656
                                    333212346777777776 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.2   2.5e-30   6.4e-27      78     192 ..       2     116 ..       1     118 [. 0.93
   2 ?    3.6   0.3     0.021        55      32     126 ..     313     468 ..     239     484 .. 0.72
   3 ?   -2.5   0.2       1.6     4e+03      66     113 ..     602     637 ..     572     651 .. 0.51
   4 ?   -1.1   0.7      0.61   1.6e+03      48     107 ..     722     779 ..     695     804 .. 0.59
   5 ?   -4.2   4.5       5.3   1.4e+04      26      60 ..     963    1020 ..     884    1058 .. 0.64

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 2.5e-30
                                    HHHHTS.-EEEETS-EEEEESS-SSSGGGS-EEEEE----S.SSS---EEEEEEETTEEEEEEEE--T...T-HHHHHHH CS
                         HSDR_N  78 ellkeg.kvkfkegrkknikLiDkknlenNrfqvvnQvtvt.gnqkrrpDivlfvnglplvviElKrp...gtieeAinQ 152
                                    ++lk+g  v +k+++k++ kLiD+kn+ +N+f+++ +++++ ++++ rpDi+lf+ng+p+v+iE+K+     +  e+i+Q
  gi|298575366|ref|NP_247089.4|   2 DYLKYGiEVVVKKSEKRKFKLIDYKNIDKNTFFYLCEAEFKgNPKNSRPDITLFINGIPVVIIEAKATlkiDSHLEGISQ 81 
                                    5899998888889999*************************9999***********************965499****** PP

                                    HTSS---.---SSSGGGGG--EEEEE-SS-EEEEE--SSS CS
                         HSDR_N 153 ikryrkeksdvsipqlfrYlqfgvisngketrfyaktkrr 192
                                    i+ry+k       p+lfr++qf +++  ++++++++++ +
  gi|298575366|ref|NP_247089.4|  82 IRRYEKF-----SPDLFRFVQFAISYGEEQLYTPTMPNWY 116
                                    *****99.....6*********************999865 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.021
                                    .......----SHHHHHHHHHHHHHHHH...........-HHHHHHHH.........TT--HHHHHHHHHTS-EEEETS- CS
                         HSDR_N  32 egrrpevrkskaevaleknlreqlgaln...........ikkltkrla.........lsdgnkefyellkegkvkfkegr 91 
                                    + +++e+ k+ ++ +l k ++e +++++           ik l+ +l          l ++n e y++  e+  k+k++ 
  gi|298575366|ref|NP_247089.4| 313 KDNNKEKDKDDEDLDLSKPIEEIIKKIEdklkkeekegkIKGLKDLLIilafiylkhLKEKNPEEYKKHIENLKKLKDKD 392
                                    22222244444555555556666666656655555777755555555566677777777777777777666644545555 PP

                                    EEEEESS-SSSGGG.........................................S-EEEEE----SSSS---EEE CS
                         HSDR_N  92 kknikLiDkknlen.........................................NrfqvvnQvtvtgnqkrrpDi 126
                                    kk+  Li+ +n+++                                         N+ +   ++++ ++++ ++D+
  gi|298575366|ref|NP_247089.4| 393 KKEEYLINLGNIKRkhililideahrtqygilggmrkitfpnaitfgftgtpvfkNEKNTFTEFSYPEKGEFYLDV 468
                                    5555588888888777777777777777888888888888888888888888888777777888888888888887 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.6
                                    HHH.TT--HHHHHHHHHTS.-EEEETS-EEEEESS-SSSGGGS-EEEEE- CS
                         HSDR_N  66 rla.lsdgnkefyellkeg.kvkfkegrkknikLiDkknlenNrfqvvnQ 113
                                    + + ++  n+e  e +++  k k              k+ + N+f+ +nQ
  gi|298575366|ref|NP_247089.4| 602 EVVmTYHHNEEEKEIIEYMkKLK--------------KERNSNDFNEINQ 637
                                    33343333333333333333333..............1223334433333 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.61
                                    HHHHHHHHHHHH.....-HHHHHHHH.TT--HHHHHHHHHTS-EEEETS-EEEEESS-SSSGGGS- CS
                         HSDR_N  48 eknlreqlgaln.....ikkltkrla.lsdgnkefyellkegkvkfkegrkknikLiDkknlenNr 107
                                    e+++re ++  n     i++++++++  ++  ke ++ lk       ++++  i++ + k+l++N+
  gi|298575366|ref|NP_247089.4| 722 EEEIREDFK--NnlissIDEIFQEFKlKLEMVKESLKNLKI------NDEDLSIDVNTLKTLTKNK 779
                                    334444444..234556777777777544444444443333......3445555555555555554 PP

  == domain 5  score: -4.2 bits;  conditional E-value: 5.3
                                     ...............----SHHHHHHHHHHHHHHHH.....................- CS
                         HSDR_N   26 kkdveiegrrpe..vrkskaevaleknlreqlgaln.....................i 60  
                                     + d++i+g+      ++s++ ++ e+ l++q  +ln                      
  gi|298575366|ref|NP_247089.4|  963 NYDKKIKGKSSIerIKESISTYIGENILKDQDIKLNlenteklitkmqnlnklsklqR 1020
                                     4444444444444555555555555555555555554444343222222223333333 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   4.5   5.6e-16   1.4e-12       7     130 ..     181     321 ..     175     332 .. 0.73
   2 !   25.5   0.2   4.4e-09   1.1e-05      85     169 ..     348     444 ..     325     446 .. 0.69
   3 ?   -1.3   0.5      0.74   1.9e+03      79     122 ..     590     633 ..     550     656 .. 0.49
   4 ?   -1.0   0.4       0.6   1.5e+03      72     119 ..     727     780 ..     681     797 .. 0.45
   5 ?    0.8   1.1      0.17   4.4e+02      70     121 ..     953    1019 ..     892    1048 .. 0.63

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 5.6e-16
                                    HHHHHHHHHT..........TTSEEEEEESTTSTHHHHHHHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTGG CS
                         ResIII   7 yQeeaienlleklks....krdkrglikmaTGtGKTlvaaklierllkkgkee..kflflvprkslleqtleefkkflse 80 
                                     Q  a ++ ++ +++    + +++gli++  G+GKT++++ ++ ++l k+  e   ++f+v+r +l  q +e ++ ++++
  gi|298575366|ref|NP_247089.4| 181 NQYFATKKAMKRIDEylsgDSKNKGLIWHWQGSGKTYTMFFIANYFLDKYFSEnpVIFFVVDRVDLERQSKEFYEAIQEK 260
                                    55555555555554455449999*************************9988877799********************** PP

                                    ...........GEEEESSS-B--..........-SEEEEEHHHHHHTH.........HHHT CS
                         ResIII  81 ayke.......igkkvsgdkkka...kekdstnkkilvttiqsldadseee.eeeseellr 130
                                    ++k        i+k ++  k ++    +++   + i+ ttiq+++ +++++ + +++e+++
  gi|298575366|ref|NP_247089.4| 261 KFKTilkridsINKLYEVIKSIKmseLSNKVIVRGIYTTTIQKFQYERSKKeKDNNKEKDK 321
                                    *999887777755555555555543344444556788999***999996664223333333 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 4.4e-09
                                    GEEEESSS-B--..................-SEEEEEHHHHHHTH.........HHHTTT-SEEEEETGGGTTS...TTT CS
                         ResIII  85 igkkvsgdkkka...........kekdstnkkilvttiqsldadseee.eeeseellrdrfdviiiDEaHrlgak..ksw 150
                                    +++k++g k+             kek+ ++ k ++++ ++l+ + ++e    +  + + ++ +i+iDEaHr+++     +
  gi|298575366|ref|NP_247089.4| 348 KEGKIKGLKDLLiilafiylkhlKEKNPEEYKKHIENLKKLKDKDKKEeYLINLGNIKRKHILILIDEAHRTQYGilGGM 427
                                    33444444444466777777777777888899999999999888855534445555666666************85559* PP

                                    HHHHHT---SEEEEEESS- CS
                         ResIII 151 reilekfkeavllglTATp 169
                                    r+i   f++a+ +g+T+Tp
  gi|298575366|ref|NP_247089.4| 428 RKI--TFPNAITFGFTGTP 444
                                    *98..7899*********9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.74
                                    GG....GEEEESSS-B--.......-SEEEEEHHHHHHTH...... CS
                         ResIII  79 seaykeigkkvsgdkkkakekdstnkkilvttiqsldadseee..e 122
                                    +e++ ++ +k+ +   +   +++++ k +++  ++l+++++++  +
  gi|298575366|ref|NP_247089.4| 590 KEKFGDEAEKWAEVVMTY--HHNEEEKEIIEYMKKLKKERNSNdfN 633
                                    333333333333333333..44444444444444444444333330 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.6
                                    HHGGGGTGG..........GEEEESSS-B--.................-SEEEEEHHHHHHTH. CS
                         ResIII  72 eefkkflseayke......igkkvsgdkkka..........kekdstnkkilvttiqsldadse 119
                                    e+fk+ l +  +e                 +           ++++++ +i v t ++l+++++
  gi|298575366|ref|NP_247089.4| 727 EDFKNNLISSIDEifqefkL----------KlemvkeslknLKINDEDLSIDVNTLKTLTKNKD 780
                                    22222222222222222221..........0233333333345667777888888888887773 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.17
                                     HHHHGGGGTGG.....................GEEEESSS-B--.......-SEEEEEHHHHHHTH... CS
                         ResIII   70 tleefkkflseayke.................igkkvsgdkkkakekdstnkkilvttiqsldadseee 121 
                                     +++++++++++++k+                 ig+++ +d++++   + +n++ l+t+ q l++ s+ +
  gi|298575366|ref|NP_247089.4|  953 AIKNLMELKNNYDKKikgkssierikesistyIGENILKDQDIK--LNLENTEKLITKMQNLNKLSKLQ 1019
                                     44455555555554422222222222222222333344444433..44445555555555555555333 PP

>> DUF4411  Domain of unknown function (DUF4411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       1.8   4.7e+03      49      84 ..     248     280 ..     227     328 .. 0.58
   2 ?   -2.2   0.2       1.3   3.3e+03      59      98 ..     313     349 ..     266     365 .. 0.59
   3 ?    0.7   0.3      0.17   4.4e+02      44     103 ..     586     645 ..     565     655 .. 0.69
   4 ?   -0.4   0.4      0.37   9.5e+02      27      79 ..     724     775 ..     722     795 .. 0.74
   5 !   16.6   0.1   2.1e-06    0.0054      18      64 ..     853     899 ..     842     929 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.8
                        DUF4411  49 rgedelskWakenesieklesaedlavveevgkvak 84 
                                    r+++e+++ ++e++ +++l   +  + ++++++v+k
  gi|298575366|ref|NP_247089.4| 248 RQSKEFYEAIQEKKFKTIL---KRIDSINKLYEVIK 280
                                    5555555555554442111...12222333333332 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                        DUF4411  59 kenesieklesaedlavveevgkvakwvivesekyskaak 98 
                                    k+n++ ek +++edl++ + + +++k +  e++ ++++++
  gi|298575366|ref|NP_247089.4| 313 KDNNK-EKDKDDEDLDLSKPIEEIIKKI--EDKLKKEEKE 349
                                    33333.3445555566666666666663..4444444444 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.17
                        DUF4411  44 krElerg.edelskWakenesieklesaedlavveevgkvakwv.ivesekyskaakkefls 103
                                     + l+++ +de++kWa+   +     ++e+++++e ++k++k   +++ ++ +++  +efl+
  gi|298575366|ref|NP_247089.4| 586 DKYLKEKfGDEAEKWAEVVMT--YHHNEEEKEIIEYMKKLKKERnSNDFNEINQIIREEFLN 645
                                    445555579999****99999..577778888999999998887444444444444677764 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.37
                        DUF4411  27 wleeeveegkllsikeVkrElergedelskWakenesieklesaedlavveev 79 
                                     ++e ++++ + si+e+ +E + + + +++ +k+ +  + ++ + d ++++++
  gi|298575366|ref|NP_247089.4| 724 EIREDFKNNLISSIDEIFQEFKLKLEMVKESLKNLKI-NDEDLSIDVNTLKTL 775
                                    5788999*************99987777777776666.455666665555555 PP

  == domain 5  score: 16.6 bits;  conditional E-value: 2.1e-06
                        DUF4411  18 fdifpsfWewleeeveegkllsikeVkrElergedelskWakenesi 64 
                                    ++  ++fWe l   +++++l+    V++E++ + d+l k++ken  +
  gi|298575366|ref|NP_247089.4| 853 KKSNRKFWEELISFIHNKMLVDDLTVIEEINLNPDDLDKILKENIGK 899
                                    566789*************************************9884 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.35      47     109 ..     633     690 ..     567     692 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                    STTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                     Helicase_C  47 hgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                    +  ++q  ree l++    + ++Li td++ +G d p++++ + +d p   +++ q+i Rt R
  gi|298575366|ref|NP_247089.4| 633 NE-INQIIREEFLNSE---NPKILIVTDMLLTGFDAPRLKV-MYLDKPLYGHRLLQAIARTNR 690
                                    22.3333333333333...356***************9985.568889888999999999998 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0076        19      74     122 ..     234     282 ..     212     289 .. 0.80
   2 ?    1.5   1.7      0.11   2.8e+02      74     102 ..     598     625 ..     315    1059 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0076
                                    ..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  74 lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeap 122
                                      ++++v+ rvd e+++++ +ea++e k+++ ++ +++i +  +v++++
  gi|298575366|ref|NP_247089.4| 234 NPVIFFVVDRVDLERQSKEFYEAIQEKKFKTILKRIDSINKLYEVIKSI 282
                                    5799**********************99888666666666666666655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
                                    ..EEEEEEEEESS...-TTCHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  74 lkiagvvlnrvdgeneetllkealeelkq 102
                                     k+a vv + + +e ee++++e +++lk+
  gi|298575366|ref|NP_247089.4| 598 EKWAEVVMTYHHNE-EEKEIIEYMKKLKK 625
                                    44555555444443.34444444444443 PP

>> ColG_sub  Collagenase G catalytic helper subdomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.0     0.011        28       4      62 ..     250     308 ..     247     327 .. 0.86
   2 ?    4.6   0.6     0.013        34       7      36 ..     366     395 ..     362     398 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.011
                                    -GGGTS------HHHHHHHHHHHHT--S-EEEEEE-SSEEEEEEEEEEEESS---HHHH CS
                       ColG_sub   4 sddYlkkheeksleeikseiedvaklkdvkikkeksqffktftlrgtytggkskGesed 62 
                                    s ++ +  +ek+ + i + i+++ kl +v  + + s+  +   +rg+yt + +k ++e 
  gi|298575366|ref|NP_247089.4| 250 SKEFYEAIQEKKFKTILKRIDSINKLYEVIKSIKMSELSNKVIVRGIYTTTIQKFQYER 308
                                    67888999*****************************************9998876654 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.013
                                    GTS------HHHHHHHHHHHHT--S-EEEE CS
                       ColG_sub   7 Ylkkheeksleeikseiedvaklkdvkikk 36 
                                    Ylk+ +ek+ ee k++ie+  klkd + k+
  gi|298575366|ref|NP_247089.4| 366 YLKHLKEKNPEEYKKHIENLKKLKDKDKKE 395
                                    9************************88766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1075 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2823  (0.157454); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 1.07u 0.36s 00:00:01.43 Elapsed: 00:00:00.51
# Mc/sec: 6359.30
//
Query:       gi|15668296|ref|NP_247090.1|  [L=116]
Description: hypothetical protein MJ_0125 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-25   89.7   0.7    1.5e-25   89.4   0.7    1.1  1  DUF86     Protein of unknown function DUF86
  ------ inclusion threshold ------
       0.02   14.5   1.5      0.035   13.7   1.4    1.3  2  AIPR      AIPR protein


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.7   1.6e-29   1.5e-25       2     118 ..      14     108 ..      13     109 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1.6e-29
                                   HHHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHTTSS-HHHHHHHHHH CS
                         DUF86   2 kealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdyifeilaekgviaeepeepwrkm 82 
                                   + +++++  ft+++d+eef++++  ++av+r+l+vigEa+++i+k+                      +++++p++p++++
  gi|15668296|ref|NP_247090.1|  14 LSYMDDIINFTKDMDYEEFINNKAIKYAVIRCLEVIGEAVKKIPKD----------------------IREKYPHIPFKEL 72 
                                   6789999***************************************......................************* PP

                                   HCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHHHH CS
                         DUF86  83 iglRNrLvHgYlgidpeivwsiikenlpdleefles 118
                                   +g+R++L+H+Y+g+d+ +vw+++k ++p++++  e+
  gi|15668296|ref|NP_247090.1|  73 AGMRDKLIHQYFGVDYLTVWETAKYEIPEIKKEFEK 108
                                   ******************************998776 PP

>> AIPR  AIPR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2    0.0016        14     243     290 ..       7      56 ..       3      66 .. 0.85
   2 ?   13.7   1.4   3.9e-06     0.035     202     288 ..      25     114 ..      16     116 .] 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0016
                          AIPR 243 anivyyilaalrkllkkk..ldllkiweeqkisqelekllekiaeeveds 290
                                   + ++y+il+++  +++    +d+++ ++++ i+ ++ ++le i e+v+++
  gi|15668296|ref|NP_247090.1|   7 KAFLYDILSYMDDIINFTkdMDYEEFINNKAIKYAVIRCLEVIGEAVKKI 56 
                                   56899999999999887777999**********99999999999888875 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.9e-06
                          AIPR 202 kgskyekifkekltykkliasvilfkklekkikkelkegykanivyyilaalrkllkkk...ldllkiweeqkis.qelek 278
                                   k+  ye+ +++k+  + +i  + ++ ++ kki k  +e+y  +i ++ la +r  l  +   +d+l++we++k++  e++k
  gi|15668296|ref|NP_247090.1|  25 KDMDYEEFINNKAIKYAVIRCLEVIGEAVKKIPKDIREKY-PHIPFKELAGMRDKLIHQyfgVDYLTVWETAKYEiPEIKK 104
                                   56778888888888889999999999999999999999**.7888888887777766667**************9999999 PP

                          AIPR 279 llekiaeeve 288
                                    +eki + +e
  gi|15668296|ref|NP_247090.1| 105 EFEKIIKDLE 114
                                   9999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 778.26
//
Query:       gi|15668297|ref|NP_247091.1|  [L=98]
Description: hypothetical protein MJ_0126 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-21   77.0   1.8    1.2e-21   76.8   1.8    1.1  1  NTP_transf_2    Nucleotidyltransferase domain
    9.4e-14   51.3   3.1    1.2e-13   50.9   3.1    1.2  1  Polbeta         Polymerase beta, Nucleotidyltransferase
    0.00046   20.4   0.1    0.00051   20.2   0.1    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm
     0.0033   17.4   0.0     0.0035   17.3   0.0    1.1  1  Adenyl_cycl_N   Adenylate cyclase NT domain
  ------ inclusion threshold ------
      0.063   13.1   0.0      0.071   12.9   0.0    1.2  1  DUF294          Putative nucleotidyltransferase DUF294
      0.079   13.1   0.3       0.09   12.9   0.3    1.4  1  SMODS           Second Messenger Oligonucleotide or Dinucleot
        0.3   10.8   0.0       0.34   10.7   0.0    1.2  1  MdcG            Phosphoribosyl-dephospho-CoA transferase MdcG


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   1.8   4.6e-25   1.2e-21       1      94 [.      11      97 ..      11      98 .] 0.97

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 4.6e-25
                                  HHHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCT CS
                  NTP_transf_2  1 lkklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpl 83
                                  l+k+++elke+++v+++++fGSyar++ +++SDiD+l+ + e+        +l+kl+e +  l+ ll ++vdl+t++++++p+
  gi|15668297|ref|NP_247091.1| 11 LRKHKKELKEKYKVKSIAIFGSYARNEQTETSDIDILIDYYEP-------ISLLKLIELENYLSDLLEIKVDLITKNSIHNPY 86
                                  689****************************************.......779****************************** PP

                                  EEEEEECEEEH CS
                  NTP_transf_2 84 lvksileerpl 94
                                  ++ksi+e+ ++
  gi|15668297|ref|NP_247091.1| 87 VKKSIEEDLIY 97
                                  *******9987 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   3.1   4.8e-17   1.2e-13       4      82 ..       8      93 ..       5      98 .] 0.84

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 4.8e-17
                                  TTTHHHHH.......HHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETT.TS-HHHHH CS
                       Polbeta  4 keilekek.......eielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdln.eappllly 78
                                  keil+k+k       +++ + +FGS+a+++++e SDiD+ + + e  +l + +el++ l+d+ l+ kvDl++ n   +p++++
  gi|15668297|ref|NP_247091.1|  8 KEILRKHKkelkekyKVKSIAIFGSYARNEQTETSDIDILIDYYEPISLLKLIELENYLSDL-LEIKVDLITKNsIHNPYVKK 89
                                  555555533333444***********************************************.99*******99778899988 PP

                                  HHHH CS
                       Polbeta 79 eilk 82
                                  +i +
  gi|15668297|ref|NP_247091.1| 90 SIEE 93
                                  8865 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1     2e-07   0.00051       8      52 ..       5      53 ..       2      94 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2e-07
                                  HHHHHHHHHHHHHH-TT-E...EEE-HHHHTT-.SEESSEEEEEEBTTB CS
                DNA_pol_B_palm  8 ealealvkkaakeldpeve...vivcGSYRRga.essGDvDvlitkkda 52
                                  ++++++++k+ kel+++++   + + GSY R++ +++ D+D+li   + 
  gi|15668297|ref|NP_247091.1|  5 SEIKEILRKHKKELKEKYKvksIAIFGSYARNEqTETSDIDILIDYYEP 53
                                  46677777777777777651116799***886516799******86655 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.4e-06    0.0035      75     133 ..       8      65 ..       1      83 [. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.4e-06
                 Adenyl_cycl_N  75 arsaeekekkekakeaaieglylmGStgsiaqsekSDlDiWvchrselsaeelelLekK 133
                                   ++  ++++k+  +++++++++   GS +   q+e+SD+Di + + + +s  +l +Le+ 
  gi|15668297|ref|NP_247091.1|   8 KEILRKHKKE-LKEKYKVKSIAIFGSYARNEQTETSDIDILIDYYEPISLLKLIELENY 65 
                                   3333333333.34689************************9998888877777777664 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.8e-05     0.071      40      73 ..      15      48 ..       4      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                        DUF294 40 eeelgkppvpfallvmGSeGReEqtlktDqDnal 73
                                  ++el+++    +  ++GS +R+Eqt  +D D  +
  gi|15668297|ref|NP_247091.1| 15 KKELKEKYKVKSIAIFGSYARNEQTETSDIDILI 48
                                  555555555556789**************99765 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   3.5e-05      0.09      28      60 ..       4      38 ..       1      94 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.5e-05
                         SMODS 28 vkaitkrLnkdfrelks..kiaesllvGSyardTa 60
                                   ++i++ L+k+++elk+  k+++   +GSyar+  
  gi|15668297|ref|NP_247091.1|  4 LSEIKEILRKHKKELKEkyKVKSIAIFGSYARNEQ 38
                                  5799**********999556778899******854 PP

>> MdcG  Phosphoribosyl-dephospho-CoA transferase MdcG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00013      0.34     127     163 ..      39      76 ..      10      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                          MdcG 127 hesSDLDLlirvasalqlarlldllaaleaaa.vrlDg 163
                                   +e+SD+D+li++ ++ +l +l +l + l+++  +++D+
  gi|15668297|ref|NP_247091.1|  39 TETSDIDILIDYYEPISLLKLIELENYLSDLLeIKVDL 76 
                                   689*******************9999999985488885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1320  (0.0736237); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 743.95
//
Query:       gi|15668298|ref|NP_247092.1|  [L=121]
Description: hypothetical protein MJ_0127 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-27   95.7   1.0      2e-27   95.4   1.0    1.1  1  DUF86     Protein of unknown function DUF86


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   1.0   1.1e-31     2e-27       1     115 [.      13     109 ..      13     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 1.1e-31
                                   HHHHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHTTSS-HHHHHHHHH CS
                         DUF86   1 ikealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdyifeilaekgviaeepeepwrk 81 
                                   i+e+++++ +ft++++++efl+d++++ av+r l+vigEa+++++++                      +i+++p++pw+ 
  gi|15668298|ref|NP_247092.1|  13 ILENMKDIIDFTNDMTFDEFLKDKKTQKAVIRSLEVIGEAVKNLPED----------------------FINKYPQVPWKG 71 
                                   689********************************************......................************ PP

                                   HHCCHHHHHT-CCCTTHHHHHHHHHHTC....HHHHHH CS
                         DUF86  82 miglRNrLvHgYlgidpeivwsiikenl....pdleef 115
                                   m++lR++L+H+Y+gi++ei+w+i+ +++    +++ee+
  gi|15668298|ref|NP_247092.1|  72 MARLRDKLIHHYFGINYEIIWDIVINKVpndiKEIEEI 109
                                   *************************9995444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 767.94
//
Query:       gi|15668299|ref|NP_247093.1|  [L=98]
Description: hypothetical protein MJ_0128 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.8e-20   70.7   2.3    1.1e-19   70.5   2.3    1.1  1  NTP_transf_2    Nucleotidyltransferase domain
      2e-15   56.6   2.8    2.6e-15   56.3   2.8    1.2  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0051   17.0   0.0     0.0054   16.9   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
      0.028   14.3   0.0      0.029   14.3   0.0    1.1  1  Adenyl_cycl_N   Adenylate cyclase NT domain
      0.061   13.5   0.2        0.1   12.7   0.2    1.5  1  SMODS           Second Messenger Oligonucleotide or Dinucleot
      0.083   12.7   0.0      0.089   12.6   0.0    1.2  1  DUF294          Putative nucleotidyltransferase DUF294


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   2.3   3.8e-23   1.1e-19       1      94 [.      11      97 ..      11      98 .] 0.96

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 3.8e-23
                                  HHHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCT CS
                  NTP_transf_2  1 lkklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpl 83
                                  l+k++++lke+++v+++++fGSyar++ ++ SDiD+lv + e           +k  e ++ l+ llg++vdlv++  +++p+
  gi|15668299|ref|NP_247093.1| 11 LRKHKKILKEKYKVKSIAIFGSYARNEQTEKSDIDILVEFYET-------PDYLKFFELEDYLSDLLGIKVDLVIKGAIKNPY 86
                                  689****************************************.......4469***************************** PP

                                  EEEEEECEEEH CS
                  NTP_transf_2 84 lvksileerpl 94
                                  ++ksi+e+ ++
  gi|15668299|ref|NP_247093.1| 87 IKKSIEEDLIY 97
                                  *******9987 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   2.8   8.7e-19   2.6e-15       4      82 ..      15      93 ..       5      98 .] 0.90

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 8.7e-19
                                  TTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETT.TS-HHHHHHHHH CS
                       Polbeta  4 keilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdln.eapplllyeilk 82
                                  k+il+++ +++ + +FGS+a+++++e+SDiD+ v + e+ d+ + +el++ l+d+ lg kvDlv+    ++p+++++i +
  gi|15668299|ref|NP_247093.1| 15 KKILKEKYKVKSIAIFGSYARNEQTEKSDIDILVEFYETPDYLKFFELEDYLSDL-LGIKVDLVIKGaIKNPYIKKSIEE 93
                                  78888888***********************************************.9********776888999988865 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.8e-06    0.0054       8      52 ..       5      53 ..       2      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-06
                                  HHHHHHHHHHHHHH-TT-E...EEE-HHHHTT-.SEESSEEEEEEBTTB CS
                DNA_pol_B_palm  8 ealealvkkaakeldpeve...vivcGSYRRga.essGDvDvlitkkda 52
                                  ++++++++k+ k l+++++   + + GSY R++ ++  D+D+l+   ++
  gi|15668299|ref|NP_247093.1|  5 SEIKDILRKHKKILKEKYKvksIAIFGSYARNEqTEKSDIDILVEFYET 53
                                  56677777777777777551116799***887615689*****986655 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   9.7e-06     0.029      80     117 ..      13      49 ..       1      69 [. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.7e-06
                 Adenyl_cycl_N  80 ekekkekakeaaieglylmGStgsiaqsekSDlDiWvc 117
                                   + +kk  +++++++++   GS +   q+ekSD+Di v 
  gi|15668299|ref|NP_247093.1|  13 K-HKKILKEKYKVKSIAIFGSYARNEQTEKSDIDILVE 49 
                                   2.2222336899**********************9875 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   3.5e-05       0.1      27      83 ..       3      52 ..       1      70 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                         SMODS 27 rvkaitkrLnkdfrelks..kiaesllvGSyardTaikpvsdkdmlfeldvdllvvvne 83
                                   +++i++ L+k+++ lk+  k+++   +GSyar+   +         ++d+d+lv++ e
  gi|15668299|ref|NP_247093.1|  3 TISEIKDILRKHKKILKEkyKVKSIAIFGSYARNEQTE---------KSDIDILVEFYE 52
                                  578999999999988887456788899******84333.........567777776655 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     3e-05     0.089      51      71 ..      26      46 ..       2      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                        DUF294 51 allvmGSeGReEqtlktDqDn 71
                                  +  ++GS +R+Eqt k+D D 
  gi|15668299|ref|NP_247093.1| 26 SIAIFGSYARNEQTEKSDIDI 46
                                  46789*************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 753.78
//
Query:       gi|15668300|ref|NP_247094.1|  [L=170]
Description: hypothetical protein MJ_0129 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-68  230.1  25.5    1.6e-68  229.5  25.5    1.2  1  DUF5418          Family of unknown function (DUF5418)
     0.0013   18.4   0.8     0.0047   16.6   0.8    2.0  1  PhoLip_ATPase_N  Phospholipid-translocating ATPase N-terminal


Domain annotation for each model (and alignments):
>> DUF5418  Family of unknown function (DUF5418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.5  25.5   1.8e-72   1.6e-68       1     151 []      16     168 ..      16     168 .. 0.99

  Alignments for each domain:
  == domain 1  score: 229.5 bits;  conditional E-value: 1.8e-72
                       DUF5418   1 mvnehkahasfilkvilalvsysialilaiiiysiffkieenlfllc..illalpiiyflilillGlthreleylsiydky 79 
                                   mvnehkah+s+i+k+ila+v++si++il+ii+++if++++++lfl++  il++++++y+l+l+l+G+threl+yls+ydky
  gi|15668300|ref|NP_247094.1|  16 MVNEHKAHLSVIQKMILAVVNGSITIILSIIVFYIFYPQNISLFLITagILTVFVFLYGLLLFLFGFTHRELSYLSKYDKY 96 
                                   9**********************************************9********************************* PP

                       DUF5418  80 kllckfvreltlsllasalatiatlvlyqiqhPlktiefvllvglvlivglvvikllikkyliiikklkkle 151
                                   k+lckf++e+++sl+++a++ti+++vlyqiqhP++ti+f++++g+++i+++vv++l++k+y+iiik+lkkle
  gi|15668300|ref|NP_247094.1|  97 KFLCKFTIEMFSSLTNHAFLTISAIVLYQIQHPKPTIDFIVMIGMITISVIVVMLLFLKTYSIIIKQLKKLE 168
                                   **********************************************************************96 PP

>> PhoLip_ATPase_N  Phospholipid-translocating ATPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.8   5.2e-07    0.0047      22      55 ..      91     124 ..      90     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.2e-07
               PhoLip_ATPase_N  22 sKYtlltFlpknLfeqFrrvaNlYFLviailqli 55 
                                   sKY  ++Fl k+ +e F+ + N  FL i+ + l 
  gi|15668300|ref|NP_247094.1|  91 SKYDKYKFLCKFTIEMFSSLTNHAFLTISAIVLY 124
                                   7**************************9876553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1426  (0.0795359); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1160.08
//
Query:       gi|298575369|ref|NP_247095.2|  [L=343]
Description: Type I restriction-modification enzyme subunit S [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-69  232.5  20.3      3e-46  157.7  13.8    2.1  2  Methylase_S  Type I restriction modification DNA specificity 
  ------ inclusion threshold ------
      0.024   14.9   2.7          4    7.8   0.0    3.7  4  DUF5603      Domain of unknown function (DUF5603)


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.7  13.8   3.4e-50     3e-46       1     168 []      17     197 ..      17     197 .. 0.99
   2 !   79.2   0.4   4.7e-26   4.2e-22       1      97 [.     225     333 ..     225     343 .] 0.92

  Alignments for each domain:
  == domain 1  score: 157.7 bits;  conditional E-value: 3.4e-50
                                    ETT-EEEEHHHHEEE.EE-----TT..GGTTT--EEEE-HH.HCCT.........EE-HHHHCCTT---B-TT-EEEE-S CS
                    Methylase_S   1 pedwevvkLgdvfei.kkgktpkkk..elkengkypyirag.ilnn.........kvvkdglgykkkyilpkgdilissr 67 
                                    pedwe+v+L+dv++  k g tpk++  e+++ng++p+++++ i+n+         k++++gl++++++i+pk+++l+++ 
  gi|298575369|ref|NP_247095.2|  17 PEDWEIVELKDVCKKiKAGGTPKTSveEYYKNGTIPFVKIEdITNSnkyltntkiKITEEGLNNSNAWIVPKNSVLFAMY 96 
                                    89************99*************************98888********************************** PP

                                    SSTT-EEEESS-BEE-TTEEEEEESTTT--HHHHHHHHHHCHHHHHHHCCSSTTT---HHHHCC-EEEE--HHHHHHHHH CS
                    Methylase_S  68 atiGkvayrdkkyylnqsvivlipknkkkineflylylllklkklkslsvgstqpkltkenlkkikIplPpleeQkkIak 147
                                    ++iG++a+++ ++ +nq +  +ipk++++++efly++l++++++ ++l +++tq++l+ + +k++kIplPpleeQk+Iak
  gi|298575369|ref|NP_247095.2|  97 GSIGETAINKIEVATNQAILGIIPKDNILESEFLYYILAKNKNYYSKLGMQTTQKNLNAQIVKSFKIPLPPLEEQKQIAK 176
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHH CS
                    Methylase_S 148 iLsqldntielekkikneier 168
                                    iL+++d+ ie+++k +n++er
  gi|298575369|ref|NP_247095.2| 177 ILTKIDEGIEIIEKSINKLER 197
                                    *******************96 PP

  == domain 2  score: 79.2 bits;  conditional E-value: 4.7e-26
                                    ETT-EEEEHHHHEEEEE-----TT..GGTTT--EEEE-HHHCCT............EE-HHHHCCTT---B-TT-EEEE- CS
                    Methylase_S   1 pedwevvkLgdvfeikkgktpkkk..elkengkypyiragilnn............kvvkdglgykkkyilpkgdiliss 66 
                                    pedwev++++d+fe+k+g+tp++k  e++eng++ +i++ +l+             kv+k +l++++ +++pkg+i+is+
  gi|298575369|ref|NP_247095.2| 225 PEDWEVFEIKDIFEVKTGTTPSTKksEYWENGEINWITPLDLSRlnekiyigsserKVTKIALEKCNLNLIPKGSIIIST 304
                                    89********************9999**************8888899********************************* PP

                                    SSSTT-EEEESS-BEE-TTEEEEEESTTT-- CS
                    Methylase_S  67 ratiGkvayrdkkyylnqsvivlipknkkki 97 
                                    ra++G+va  +++ ++nq+++ l +k    i
  gi|298575369|ref|NP_247095.2| 305 RAPVGYVAVLTVESTFNQGCKGLFQKI--TI 333
                                    ***********************9965..33 PP

>> DUF5603  Domain of unknown function (DUF5603)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0054        48      31      65 ..      68     104 ..      39     117 .. 0.72
   2 ?   -1.7   0.0       0.4   3.6e+03      40      65 ..     127     152 ..     103     158 .. 0.78
   3 ?    7.8   0.0   0.00045         4      52      74 ..     159     182 ..     151     190 .. 0.82
   4 ?   -1.0   0.1      0.24   2.1e+03       7      42 ..     189     224 ..     185     232 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0054
                                    HHH...HHCT..SSSEEEES..SSEEEE--SHHHHHH CS
                        DUF5603  31 eeklkdeelg..kiafvlvgkneksykiygsleeqkk 65 
                                    + k+k  e g  +    +v kn   +++ygs+ e  +
  gi|298575369|ref|NP_247095.2|  68 NTKIKITEEGlnNSNAWIVPKNSVLFAMYGSIGETAI 104
                                    45555555442155667999************99754 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.4
                                    TSSSEEEES..SSEEEE--SHHHHHH CS
                        DUF5603  40 gkiafvlvgkneksykiygsleeqkk 65 
                                     ++ + ++ kn++ y   g    qk 
  gi|298575369|ref|NP_247095.2| 127 SEFLYYILAKNKNYYSKLGMQTTQKN 152
                                    46677888899998888888877776 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00045
                                    SEEEE-.-SHHHHHHHHHHHHHHH CS
                        DUF5603  52 ksykiy.gsleeqkkvskvldkls 74 
                                    ks+ki+   leeqk+++k+l k++
  gi|298575369|ref|NP_247095.2| 159 KSFKIPlPPLEEQKQIAKILTKID 182
                                    799998457***********9986 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.24
                                    ES-HHHHHHHHHHTT---EE-TTH.HHH...HHCTSS CS
                        DUF5603   7 kgdlnklleelkkeglrveedkek.eeklkdeelgki 42 
                                      ++nk le++kk  ++   +k+  + ++k +e g+i
  gi|298575369|ref|NP_247095.2| 189 EKSINK-LERIKKGLMHKLLTKGIgHSRFKKSEIGEI 224
                                    557777.599999777655555541445667777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2659.81
//
Query:       gi|15668301|ref|NP_247096.1|  [L=103]
Description: hypothetical protein MJ_0131 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 720.67
//
Query:       gi|15668302|ref|NP_247097.1|  [L=220]
Description: type I restriction-modification enzyme 2 subunit M [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-54  185.4   0.1    1.8e-54  185.1   0.1    1.1  1  N6_Mtase  N-6 DNA Methylase
  ------ inclusion threshold ------
       0.22   11.0   0.0       0.22   11.0   0.0    1.4  2  Utp21     Utp21 specific WD40 associated putative domain


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.1   0.1   2.1e-58   1.8e-54     151     312 .]      22     184 ..       2     184 .. 0.92

  Alignments for each domain:
  == domain 1  score: 185.1 bits;  conditional E-value: 2.1e-58
                      N6_Mtase 151 frea.vapksnadlafllhiieslkpkGraavvlangvLfrggkegkIrkalvekdlveavialpeklFyntsiptcilvl 230
                                   f  +  +pk++ad+a+++++++ +++  ++++vl++g+Lfrggke+kIrk++vekdl+ea+i lpeklFyn+++p+++++l
  gi|15668302|ref|NP_247097.1|  22 FVRGgYPPKQSADWAWVQLMLYFARK--KVGIVLDSGALFRGGKEKKIRKEIVEKDLIEAIILLPEKLFYNVTAPGIVMIL 100
                                   222259*******************9..9**************************************************** PP

                      N6_Mtase 231 kkekae.rkgkvlfidaseefkkkd..rkknklteediekildtykekskevdkfskvveleeiaendynlnvgryvetee 308
                                   +k+k+e rkgk+lfi+as ef+k++  r+ n+l ee+i+ki+d+y+++ +++++fs+vv+leei++ndynlnv+ yv + e
  gi|15668302|ref|NP_247097.1| 101 NKNKPEeRKGKILFINASLEFEKHPevRRLNRLGEENIDKIVDVYENW-EDIEGFSRVVDLEEIRKNDYNLNVSLYVFPVE 180
                                   ****999*****************99999*******************.******************************99 PP

                      N6_Mtase 309 eeed 312
                                   e+ed
  gi|15668302|ref|NP_247097.1| 181 EKED 184
                                   9985 PP

>> Utp21  Utp21 specific WD40 associated putative domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.3      0.98   8.7e+03      48      57 ..      99     108 ..      98     111 .. 0.78
   2 ?   11.0   0.0   2.4e-05      0.22     193     230 ..     180     217 ..     165     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 0.98
                                   XXXXXXXXXX CS
                         Utp21  48 IKeRnkPkea 57 
                                   I ++nkP+e 
  gi|15668302|ref|NP_247097.1|  99 ILNKNKPEER 108
                                   67899*9986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.4e-05
                                   TT-SH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Utp21 193 aeeeeeelkealeelkeeqeeewerldelvkyclgvvg 230
                                    e+e+ +l+++lee+ke  ++e+e lde+++y  g+++
  gi|15668302|ref|NP_247097.1| 180 EEKEDIDLRKELEEFKEIEKKEKEVLDEVIGYVEGILR 217
                                   3444449***************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1720.34
//
Query:       gi|15668303|ref|NP_247099.1|  [L=273]
Description: hypothetical protein MJ_0133 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-21   76.3   0.0    2.7e-21   76.0   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
    1.1e-05   24.8   0.1    1.7e-05   24.2   0.1    1.3  1  UvdE          UV-endonuclease UvdE
  ------ inclusion threshold ------
      0.021   14.5   0.1      0.033   13.8   0.1    1.3  1  Cut8          Cut8, nuclear proteasome tether protein
      0.066   13.9   0.4       0.15   12.8   0.1    1.8  2  PBECR1        phage-Barnase-EndoU-ColicinE5/D-RelE like nucle


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.0   5.9e-25   2.7e-21       2     208 ..      26     232 ..      25     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 5.9e-25
                                   HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHH CS
                  AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaL 82 
                                   + ++++   ++El +  +v ++       ++++k l+e+g  i      +++ +++ +e e++     + ++r i++a+ L
  gi|15668303|ref|NP_247099.1|  26 DVLRKLNLGAMELEFVKGVYMK-------EDYAKKLKEYGEDIIFSAHAPHYINLNANEEEKV----ENSIRRIIKTAKVL 95 
                                   67899999*************8.......8************************999988888....88999999999999 PP

                                   T..BSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHT..SEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEE CS
                  AP_endonuc_2  83 G..apllvlhpGtagagpkgseeeawerlaeslneladyaekeg..vklalEtlagsgvelgdeelarlldavdspnvgvc 159
                                   +  +++lv+hpG   ++ k+s+e++++r+ +++++++d++e+ +  v+l  Et+ +++++   +e+++l+ +++   +  c
  gi|15668303|ref|NP_247099.1|  96 NncGKNLVFHPG---YYLKRSKEVTYNRIKSNIQRILDKLEALNlnVMLRPETTGKTTQFGDIDETLKLCFELN---ILPC 170
                                   877899******...**************************77766************97777**********9...**** PP

                                   EEHHHHHHH.......TTTHHHHHHHHHGG.......EEEEEE.EESSTTTTSSTTEESTTSS CS
                  AP_endonuc_2 160 lDtgHllia.......eedvddalraladr.......ikhvHikDakgdlgagrdrhvpigeG 208
                                   +D++H++++        + ++++l+++++          h+H++ ++  +++g+ rh+p++e 
  gi|15668303|ref|NP_247099.1| 171 IDFSHIYARsrgvindYNSFYKILEKVENVlgkeaikDMHIHLSGIEY-GKGGERRHLPLNES 232
                                   *************55555555555555555888884434555566666.9999999*999986 PP

>> UvdE  UV-endonuclease UvdE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   3.8e-09   1.7e-05     103     249 ..      63     214 ..      43     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.8e-09
                          UvdE 103 ltfHPeqftllnSdrkevtesairdlayHdklldalklaeqqdavliiHvGGkf.gdkeaalerfkenikrlpdsvke... 179
                                    + H  +++ ln++ +e +e++ir +   +k+l+  +      + l+ H G    + ke + +r+k ni+r+ d++ +   
  gi|15668303|ref|NP_247099.1|  63 FSAHAPHYINLNANEEEKVENSIRRIIKTAKVLNNCG------KNLVFHPGYYLkRSKEVTYNRIKSNIQRILDKLEAlnl 137
                                   46799*******************9999999998776......4699****6542579999***********998653222 PP

                          UvdE 180 rlvLENDdksyt.....vadlLpvceelniPlVlDyHHhnvld.lreesldeslplveriveTWerkgikq.kvHlS 249
                                    ++L  +  + t     ++++L++c elni   +D+ H ++      ++ +   +++e++ +   +++ik   +HlS
  gi|15668303|ref|NP_247099.1| 138 NVMLRPETTGKTtqfgdIDETLKLCFELNILPCIDFSHIYARSrGVINDYNSFYKILEKVENVLGKEAIKDmHIHLS 214
                                   67776666555522333579**********999*****999864444555666667777777777776654256666 PP

>> Cut8  Cut8, nuclear proteasome tether protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   7.5e-06     0.033      92     144 ..      88     140 ..      71     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.5e-06
                          Cut8  92 iesllelLkekkenilkslPykgdkeddyaYlRvkphLleFlncLsDfilnfl 144
                                   i ++ ++L++  +n+  +  y  +++ + +Y+R+k++++  l+ L+   ln +
  gi|15668303|ref|NP_247099.1|  88 IIKTAKVLNNCGKNLVFHPGYYLKRSKEVTYNRIKSNIQRILDKLEALNLNVM 140
                                   45678899999999999999999**********************98888764 PP

>> PBECR1  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.3e-05      0.15       6      71 ..      32     103 ..      27     134 .. 0.81
   2 ?   -2.5   0.0       1.8   7.9e+03      48      61 ..     192     205 ..     174     234 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                        PBECR1   6 dlGdIDlvwGe.....vtdakkkkgfGLahilekhledfkefk.ekaeklinkleeiiekgkvkeeeevnti 71 
                                   +lG ++l + +      + akk k++G   i+++h  ++ + + +++ek+ n+++ ii+  kv ++ ++n +
  gi|15668303|ref|NP_247099.1|  32 NLGAMELEFVKgvymkEDYAKKLKEYGEDIIFSAHAPHYINLNaNEEEKVENSIRRIIKTAKVLNNCGKNLV 103
                                   67776666655545534567889*************99999886777***************9888777655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                        PBECR1  48 klinkleeiiekgk 61 
                                   k+ +k+e+++ k  
  gi|15668303|ref|NP_247099.1| 192 KILEKVENVLGKEA 205
                                   23333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1692.35
//
Query:       gi|15668304|ref|NP_247100.1|  [L=282]
Description: L-isoaspartyl protein carboxyl methyltransferase PimT [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-31  108.4   0.2    2.5e-28   99.4   0.1    3.1  2  GCD14            tRNA methyltransferase complex GCD14 subunit
      5e-07   29.6   0.1    5.2e-06   26.3   0.1    2.2  1  Methyltransf_31  Methyltransferase domain
    1.4e-06   27.8   0.1    3.3e-06   26.6   0.1    1.6  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    9.4e-06   25.5   0.0    1.5e-05   24.9   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    4.8e-05   24.0   0.0    0.00015   22.4   0.0    2.0  2  Methyltransf_25  Methyltransferase domain
    5.5e-05   22.4   0.0    0.00011   21.3   0.0    1.4  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0038   17.9   0.1       0.01   16.5   0.1    1.9  1  Methyltransf_12  Methyltransferase domain
     0.0042   17.0   0.0      0.008   16.0   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
     0.0052   17.8   0.0      0.012   16.6   0.0    1.7  1  Methyltransf_24  Methyltransferase domain
      0.009   15.4   0.2      0.062   12.7   0.0    2.0  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
       0.01   16.5   0.1      0.028   15.0   0.1    2.0  1  Methyltransf_11  Methyltransferase domain
      0.012   15.7   0.0      0.019   15.1   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
       0.02   14.9   0.0      0.028   14.4   0.0    1.4  1  Methyltransf_32  Methyltransferase domain
      0.068   12.8   0.1       0.27   10.9   0.1    1.9  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.14   12.2   0.2        1.4    9.0   0.0    2.6  3  PTR              Phage tail repeat like


Domain annotation for each model (and alignments):
>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4   0.1   2.1e-31   2.5e-28      23     180 ..      70     248 ..      48     252 .. 0.84
   2 ?    4.5   0.0      0.02        24     228     246 ..     251     269 ..     246     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 2.1e-31
                         GCD14  23 ilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehel............. 90 
                                    l  +Di +ii +  +++G  vve+GtGsg+l+ +++ +v+ tG++ t++   + a+ ar+++ + +              
  gi|15668304|ref|NP_247100.1|  70 TLLPKDIGFIIARAGIREGETVVEAGTGSGALTMYLSNAVGKTGKVITYDIRPEFAKVARKNLLRVGAikkgqkiigldee 150
                                   56779********************************************************98665544666556787777 PP

                         GCD14  91 ...sqlvtvthrD.....vckeGf.deevsg.kvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLre 161
                                      ++ + ++  D     ++k G  +e++++ +vD + LDlP Pw+ +++a+kal+k+ gr+ ++ P ieqv++t+e+L+e
  gi|15668304|ref|NP_247100.1| 151 fddEDEIEIE--DglfnvIQKIGDvREKIDEkDVDVIVLDLPDPWNVVENAKKALNKKRGRIVTYLPYIEQVKKTVEKLKE 229
                                   7433345554..3333336788877899975269*********************************************** PP

                         GCD14 162 lgfteietlevllrtyevr 180
                                    gf +i+t e+  r+ e+ 
  gi|15668304|ref|NP_247100.1| 230 EGFWDIHTYEIIEREIEIS 248
                                   *************998875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.02
                         GCD14 228 llkPvselkghtgyLtfat 246
                                    ++P + + ghtgy+t a+
  gi|15668304|ref|NP_247100.1| 251 GVRPSTRMIGHTGYITVAR 269
                                   57999***********997 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   4.3e-09   5.2e-06       2     128 ..      86     230 ..      85     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.3e-09
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld....nveFeq....gdieelekl.lede 73 
                                   ++g +v+++G+G+G+lt  l   +g+ ++v+  Di +e  ++Ar+n+ + g           +    +++ + ++  +ed 
  gi|15668304|ref|NP_247100.1|  86 REGETVVEAGTGSGALTMYLSNAVGKTGKVITYDIRPEFAKVARKNLLRVGAIkkgqK----IigldEEFDDEDEIeIEDG 162
                                   57889****************************************6655555432212....1223355555666668899 PP

               Methyltransf_31  74 kfDlilsn............evl.naladpdkileeiervlkpggilliedprllaelpakveeeska 128
                                    f++i               +v+  +l+dp ++ e+++++l+++   ++++    +++++ ve+  ++
  gi|15668304|ref|NP_247100.1| 163 LFNVIQKIgdvrekidekdvDVIvLDLPDPWNVVENAKKALNKKRGRIVTYLPYIEQVKKTVEKLKEE 230
                                   99997666666666666666444789**************9988777777777688888777777664 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   2.8e-09   3.3e-06      38     105 ..      78     146 ..      58     180 .. 0.81
   2 ?   -1.5   0.0       1.1   1.3e+03      99     121 ..     216     237 ..     165     268 .. 0.52

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.8e-09
                                   HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE- CS
               Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqa 105
                                   f++ + + ++g++v++  +G+g l++ ls++vg++gkv+  Di ++  kv++k l + g i + + + +
  gi|15668304|ref|NP_247100.1|  78 FIIARAGIREGETVVEAGTGSGALTMYLSNAVGKTGKVITYDIRPEFAKVARKNLLRVGAIkKGQKIIG 146
                                   8899999***********************************************999887733333443 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                                   TEEEEE--TTT-TTS-T-EEEEE CS
               Ubie_methyltran  99 nieflqanaeeLpfeddsfDvvt 121
                                    ie ++   e+L++ ++  D+ t
  gi|15668304|ref|NP_247100.1| 216 YIEQVKKTVEKLKE-EGFWDIHT 237
                                   44444444444432.24444444 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.2e-08   1.5e-05      51     122 ..      65     136 ..      36     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.2e-08
                                   ETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCT CS
                          PCMT  51 gynatiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkld 122
                                      +t   p+ +++++    +++g+ v+e G+GsG lt  l++ vg++g+v++ +  +e+++ a++nl + +
  gi|15668304|ref|NP_247100.1|  65 KRTVTTLLPKDIGFIIARAGIREGETVVEAGTGSGALTMYLSNAVGKTGKVITYDIRPEFAKVARKNLLRVG 136
                                   5555556666667777777899*********************************************97765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.3e-07   0.00015       1      43 [.      91     134 ..      91     205 .. 0.84
   2 ?   -1.6   0.0       3.7   4.4e+03      33      43 ..     195     205 ..     170     236 .. 0.55

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.3e-07
                                   EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraee 43 
                                   v+++G+G+G lt++l++++g  +kv+  Di +e+ + ar+++ +
  gi|15668304|ref|NP_247100.1|  91 VVEAGTGSGALTMYLSNAVGkTGKVITYDIRPEFAKVARKNLLR 134
                                   899****************669******************9955 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.7
                                   HHHHHHHHHHH CS
               Methyltransf_25  33 mleaareraee 43 
                                    +e+a++ +++
  gi|15668304|ref|NP_247100.1| 195 VVENAKKALNK 205
                                   34444444433 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   9.5e-08   0.00011      22      73 ..      79     133 ..      73     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9.5e-08
                                   HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT CS
                        RrnaAD  22 IldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls 73 
                                   I+  + ++e  tv+e g+G G+lT  L + +    +v  + +++++ak+ +k+l 
  gi|15668304|ref|NP_247100.1|  79 IIARAGIREGETVVEAGTGSGALTMYLSNAVgktGKVITYDIRPEFAKVARKNLL 133
                                   9999***********************999998789***************9876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   8.6e-06      0.01       1      71 [.      92     186 ..      92     210 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.6e-06
               Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnn.nnvelealdlldldgg............... 64 
                                   +e G+G+G+l+++l ++  ++ +++ +Di p++ + a++ l + ++ +  +++   +++ +d+d +               
  gi|15668304|ref|NP_247100.1|  92 VEAGTGSGALTMYLSNAVgKTGKVITYDIRPEFAKVARKNLLRVGAIKKgQKIIGLDEEFDDED-Eieiedglfnviqkig 171
                                   589***************9***************888887776654332033333333333333.2466666666666666 PP

               Methyltransf_12  65 ........ssfDlvv 71 
                                           + +D++v
  gi|15668304|ref|NP_247100.1| 172 dvrekideKDVDVIV 186
                                   666666666666665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.7e-06     0.008      19      86 ..      82     167 ..      58     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.7e-06
               Methyltransf_23  19 k..lraggrvLdiGcGtGillevl.rengf..svtgvDlspeaveiae.............kakkaqkdqfdeqeaaepqg 81 
                                   +   r+g  v++ G+G+G l+ +l  + g+  +v+ +D++pe  + a+             k++    +  de+e++ ++g
  gi|15668304|ref|NP_247100.1|  82 RagIREGETVVEAGTGSGALTMYLsNAVGKtgKVITYDIRPEFAKVARknllrvgaikkgqKIIGLDEEFDDEDEIEIEDG 162
                                   23367888****************555588899********9888888999999999988877777666666777777777 PP

               Methyltransf_23  82 kfdlI 86 
                                    f++I
  gi|15668304|ref|NP_247100.1| 163 LFNVI 167
                                   77777 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     1e-05     0.012       1      79 [.      92     191 ..      92     211 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-05
               Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare..................aglddrvrlikads..... 58 
                                   vE G+ sG  t++l  a+ ++g+  +++ d  p   e+a++ar+                  ++           +     
  gi|15668304|ref|NP_247100.1|  92 VEAGTGSGALTMYLSNAVGKTGK--VITYDIRP---EFAKVARKnllrvgaikkgqkiigldEE-----------Fddede 156
                                   89******************995..********...9999999644443333333333333322...........022222 PP

               Methyltransf_24  59 ..............eealaslaagsiDllfiDggh 79 
                                                  +++++ +++++D++++D + 
  gi|15668304|ref|NP_247100.1| 157 ieiedglfnviqkiGDVREKIDEKDVDVIVLDLPD 191
                                   22222222333222677777778999999999874 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   5.2e-05     0.062     159     206 ..      85     134 ..      78     167 .. 0.80
   2 ?    0.8   0.0      0.22   2.7e+02      37      79 ..     190     231 ..     156     249 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-05
                          PrmA 159 vkegeevlDvGtGSGiLaiaaa.kLg.akkvvavDiDevAvkvakeNael 206
                                   ++ege+v+  GtGSG L++  +  +g + kv+ +Di +   kva++N+ +
  gi|15668304|ref|NP_247100.1|  85 IREGETVVEAGTGSGALTMYLSnAVGkTGKVITYDIRPEFAKVARKNLLR 134
                                   6899*************9864414442569*****************754 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.22
                          PrmA  37 leeedifepaleeeelkeevkvkalfkeeteakeliaqlkese 79 
                                    + ++++e+a+++ + k++ ++ ++++  +++k+++++lke+ 
  gi|15668304|ref|NP_247100.1| 190 PDPWNVVENAKKALN-KKRGRIVTYLPYIEQVKKTVEKLKEEG 231
                                   346667754444443.788999999999999999999998865 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   2.4e-05     0.028       2      42 ..      93     136 ..      92     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                                   EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT CS
               Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeg 42 
                                   ++G+G+G+l+ +l +++   ++v++ D+ +e+ k+a+++  + g
  gi|15668304|ref|NP_247100.1|  93 EAGTGSGALTMYLSNAVgktGKVITYDIRPEFAKVARKNLLRVG 136
                                   78************6666889****************9987665 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.6e-05     0.019      17      97 ..      84     191 ..      58     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                                   T-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.HHHTTEEEE.CS-CCCSSHHHHHCHCHHH.......... CS
                          FtsJ  17 klfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.aplpgvtti.qgditdpetiekikealse.......... 85 
                                   + +++g+tvv+ g + G+ + +l++ +g++gkv+ +D++p  a++ + +++  g i++ ++i  + e +++          
  gi|15668304|ref|NP_247100.1|  84 G-IREGETVVEAGTGSGALTMYLSNAVGKTGKVITYDIRPEfAKVARKNLLrVGAIKKGQKIIGLDEEFDDedeieiedgl 163
                                   5.67899*********************99********9997455555555444455555555555444445555555555 PP

                                   ................SSEEEEEE--S- CS
                          FtsJ  86 ................rkvdlvvsDgap 97 
                                                   + vd++v D+  
  gi|15668304|ref|NP_247100.1| 164 fnviqkigdvrekideKDVDVIVLDLPD 191
                                   5566666666666666999999999754 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.4e-05     0.028      25      80 ..      87     140 ..      68     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
               Methyltransf_32  25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnk 80 
                                   + +tvv++G G g L+  l+  ++ +  kv+  d++ e ++ a+k   ++g +++k
  gi|15668304|ref|NP_247100.1|  87 EGETVVEAGTGSGALTMYLSN-AVGKTGKVITYDIRPEFAKVARKNLLRVG-AIKK 140
                                   5689****************9.7789******************9998888.4433 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00022      0.27       7      59 ..      86     138 ..      83     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                                   -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT-- CS
               Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt 59 
                                   +e+et++++ ++ G+ T ++++ + ++g+v+  d+  e +k   +nl r+g  
  gi|15668304|ref|NP_247100.1|  86 REGETVVEAGTGSGALTMYLSNAVGKTGKVITYDIRPEFAKVARKNLLRVGAI 138
                                   689**********************************************9975 PP

>> PTR  Phage tail repeat like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0012       1.4      11      37 ..      30      56 ..      28      69 .. 0.81
   2 ?   -1.2   0.0       1.9   2.2e+03      11      24 ..     167     180 ..     165     183 .. 0.81
   3 ?   -1.8   0.0       2.9   3.5e+03      32      42 ..     216     226 ..     195     242 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                           PTR 11 IanitnLqetLnrKadkgHTHtIanIt 37
                                  I ++++++e  + K+ kgHT ++ + t
  gi|15668304|ref|NP_247100.1| 30 IVDMKDIEEGVELKSHKGHTFYLVEPT 56
                                  77899999************9887655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                           PTR  11 IanitnLqetLnrK 24 
                                   I++i + +e++++K
  gi|15668304|ref|NP_247100.1| 167 IQKIGDVREKIDEK 180
                                   78899999999888 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.9
                           PTR  32 tIanItnLqet 42 
                                   +I +++   e+
  gi|15668304|ref|NP_247100.1| 216 YIEQVKKTVEK 226
                                   33333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 1687.98
//
Query:       gi|15668305|ref|NP_247101.1|  [L=230]
Description: ribonuclease HII [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-71  240.1   1.7      2e-71  240.0   1.7    1.0  1  RNase_HII  Ribonuclease HII
     0.0093   15.2   2.5      0.014   14.6   2.5    1.3  1  YjeJ       YjeJ-like
  ------ inclusion threshold ------
      0.025   14.8   0.6      0.047   13.9   0.6    1.4  1  DUF4332    Domain of unknown function (DUF4332)
      0.036   12.9   0.3      0.041   12.7   0.3    1.2  1  NRDD       Anaerobic ribonucleoside-triphosphate reductase
      0.039   14.3   1.8       0.06   13.6   1.2    1.5  2  TerB_C     TerB-C domain
      0.073   13.5   0.9      0.073   13.5   0.9    2.4  2  HTH_40     Helix-turn-helix domain
       0.39   10.3   8.1       0.13   11.8   4.2    1.9  2  LepB_N     LepB N-terminal domain


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.0   1.7   7.7e-75     2e-71       1     198 []       4     215 ..       4     215 .. 0.98

  Alignments for each domain:
  == domain 1  score: 240.0 bits;  conditional E-value: 7.7e-75
                                   EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHH..SEEEEEEE-HHHHH.HHTTTS-HHH CS
                     RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklik..kkiekrklvaeeikyaseneinlne 79 
                                   iGiDEaGrGpvlGp+vv+a+a+ekereeelkklgvkDSK+L+k+kr++L+kl++   ++ekr l+aeei+ + +n+inln+
  gi|15668305|ref|NP_247101.1|   4 IGIDEAGRGPVLGPMVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLEnlGYVEKRILEAEEIN-QLMNSINLND 83 
                                   8*****************************************************999*************.99******** PP

                                   HHHHHHHHHHH.HHHHTCEECC..ECCCE--SS.....HHHHHHHHHHHHC.....CEEEEETTGGGT-HHHHHHHHHHHH CS
                     RNase_HII  80 ikaaltlavik.lleklgvkvd..eilvdgvtt.....peslkkkleqiik.....ikvtvekkadekyllvaaASiiAkv 147
                                   i+++++++v+k l+ekl+++ d  ei++d+++t     ++s+k+k+e+iik     ik+++e+kad+ky++v+aASiiAk+
  gi|15668305|ref|NP_247101.1|  84 IEINAFSKVAKnLIEKLNIRDDeiEIYIDACSTntkkfEDSFKDKIEDIIKernlnIKIIAEHKADAKYPVVSAASIIAKA 164
                                   ***********899999*****8889******99999999**************999************************ PP

                                   HHHHHHHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHHH CS
                     RNase_HII 148 erdeelellkrkpgtldkgsGyasdektrallkkgats..klpdivrlsfktv 198
                                   erde+++++k+ +g  d+gsGy+sd+kt ++l++++++  klpdi+r+++kt+
  gi|15668305|ref|NP_247101.1| 165 ERDEIIDYYKKIYG--DIGSGYPSDPKTIKFLEDYFKKhkKLPDIARTHWKTC 215
                                   ************98..**********************99***********98 PP

>> YjeJ  YjeJ-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   2.5   5.6e-06     0.014      59     143 ..      35     116 ..      22     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.6e-06
                          YjeJ  59 klsenekekyekardkvvkklveniPaieeeelknadinrrvesltlkdneeesltlvlvlhdgskselvvdelqievlvi 139
                                   kl  ++ ++  k++  + kkl+en+  +e+  l+  +in+ ++s++l+d e ++  +  ++  + + +l + +  ie+ + 
  gi|15668305|ref|NP_247101.1|  35 KLGVKDSKELTKNKRAYLKKLLENLGYVEKRILEAEEINQLMNSINLNDIEINA--F-SKVAKNLIEKLNIRDDEIEIYID 112
                                   55566778889999**********************************999887..4.45666778889999999999888 PP

                          YjeJ 140 aiir 143
                                   a   
  gi|15668305|ref|NP_247101.1| 113 ACST 116
                                   7665 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   1.8e-05     0.047       3      57 ..      25      77 ..      24      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                       DUF4332  3 igkeeaekLkkaGikttedLlelgktekgrkalaeklgisernvlklanlAdLar 57
                                  i ke +e+Lkk G+k++++L++ ++   ++  l+e+lg  e+++l+  ++ +L++
  gi|15668305|ref|NP_247101.1| 25 IEKEREEELKKLGVKDSKELTKNKRAYLKK--LLENLGYVEKRILEAEEINQLMN 77
                                  678899*****************9999999..**************999999985 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   1.6e-05     0.041     272     356 ..      71     181 ..      23     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                   EEEEEEEEEEHHHHHH.........HH-......................HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          NRDD 272 rgslgvvtiNlprlal.......eakgd......................eekffelLdellelakealeerrkileklla 323
                                     ++ + +iNl+++ +       +   +                      ++kf +++++++e + +  + + ki+++ +a
  gi|15668305|ref|NP_247101.1|  71 EINQLMNSINLNDIEInafskvaK---NlieklnirddeieiyidacstnTKKFEDSFKDKIEDIIKERNLNIKIIAEHKA 148
                                   56888899********66555550...15555555555666666666666******************************* PP

                                   TT.-HHH.HTTSS-GE.............EEEEE CS
                          NRDD 324 kg.lpflmgkgylksrkkkdeveevlkngtltiG 356
                                   +  +p++  + ++  + ++de+ +++k+ +  iG
  gi|15668305|ref|NP_247101.1| 149 DAkYPVVSAASIIA-KAERDEIIDYYKKIYGDIG 181
                                   999***98888885.5557888888888877776 PP

>> TerB_C  TerB-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.2   2.4e-05      0.06      67     145 ..      29     112 ..      22     116 .. 0.81
   2 ?   -2.1   0.0       1.6   4.2e+03      57      57 ..     153     153 ..     122     211 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                        TerB_C  67 aetalad.kvaesegLdeaeaalLraLlareswpreeveslarekglmpdvliesINekafdefddtvie....dddppei 142
                                   +e++l++  v++s +L+++++a+L++Ll++    ++++ ++ + ++lm ++ + +I   af  +   +ie    +dd++ei
  gi|15668305|ref|NP_247101.1|  29 REEELKKlGVKDSKELTKNKRAYLKKLLENLGYVEKRILEAEEINQLMNSINLNDIEINAFSKVAKNLIEklniRDDEIEI 109
                                   33333220334458******************************************999*******999977677999999 PP

                        TerB_C 143 ned 145
                                   + d
  gi|15668305|ref|NP_247101.1| 110 YID 112
                                   766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                        TerB_C  57 e 57 
                                   +
  gi|15668305|ref|NP_247101.1| 153 P 153
                                   2 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.4       0.8   2.1e+03      46      46 ..      64      64 ..      22     103 .. 0.58
   2 ?   13.5   0.9   2.9e-05     0.073      14      64 ..     128     176 ..     120     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.8
                        HTH_40 46 e 46
                                  +
  gi|15668305|ref|NP_247101.1| 64 K 64
                                  2 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.9e-05
                        HTH_40  14 sieeIAkerglkesTIegHLaelieegeeidlerlvseeeekeIeeaiekv 64 
                                   +ie+I ker+l+ + I++H a++      +++  ++ + e++eI+++++k+
  gi|15668305|ref|NP_247101.1| 128 KIEDIIKERNLNIKIIAEHKADAKYP--VVSAASIIAKAERDEIIDYYKKI 176
                                   69*****************9996655..59999***************994 PP

>> LepB_N  LepB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   4.2   5.2e-05      0.13      78     179 ..      37     141 ..      23     145 .. 0.73
   2 ?   -0.1   0.1      0.23     6e+02      84     116 ..     192     224 ..     171     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.2e-05
                        LepB_N  78 Glfnlkkftkg...Yilnykkikglfpaiaekakklkekldekllkdivskalkkipadlldketk..kelakylgidsfk 153
                                   G+   k++tk+   Y+ +  +  g++++   +a+++++ ++   l+di  +a++k+ ++l++k ++  +e+  y+   s +
  gi|15668305|ref|NP_247101.1|  37 GVKDSKELTKNkraYLKKLLENLGYVEKRILEAEEINQLMNSINLNDIEINAFSKVAKNLIEKLNIrdDEIEIYIDACSTN 117
                                   6666677777622266666667899************************************87665115666666666677 PP

                        LepB_N 154 evsfgeegnyqefakdlakilkkrlk 179
                                   +++f  e+++++ ++d++k  +  +k
  gi|15668305|ref|NP_247101.1| 118 TKKF--EDSFKDKIEDIIKERNLNIK 141
                                   7777..56666666667776666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.23
                        LepB_N  84 kftkgYilnykkikglfpaiaekakklkeklde 116
                                   kf  +Y+ + kk++ +  +  +  k + +k ++
  gi|15668305|ref|NP_247101.1| 192 KFLEDYFKKHKKLPDIARTHWKTCKRILDKSKQ 224
                                   678899999999988888877777777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1576  (0.0879023); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1391.07
//
Query:       gi|15668306|ref|NP_247102.1|  [L=361]
Description: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-87  290.6   0.0    5.4e-87  290.2   0.0    1.2  1  DUF1297   Domain of unknown function (DUF1297)
    2.6e-48  163.0   0.0      4e-48  162.4   0.0    1.3  1  DUF1246   Protein of unknown function (DUF1246)


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.2   0.0   6.1e-91   5.4e-87       1     187 [.     174     360 ..     174     361 .] 0.99

  Alignments for each domain:
  == domain 1  score: 290.2 bits;  conditional E-value: 6.1e-91
                                   HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT----EE CS
                       DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelevepeyv 81 
                                   ef++k+e+l+++g++++ed+++a+ieeyvvG+nf+++yfysplk+evellg+d+Ryesn+dglvr+pak+qle++++p+yv
  gi|15668306|ref|NP_247102.1| 174 EFYKKAEDLKKRGILTDEDIANAHIEEYVVGTNFCIHYFYSPLKDEVELLGMDKRYESNIDGLVRIPAKDQLEMNINPSYV 254
                                   79******************************************************************************* PP

                                   EEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--CCHHHTTSS CS
                       DUF1297  82 vvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegspyskllfge 162
                                   ++Gnipvv+REsll++vfe+g+k+v +ak+lvppG+iGpFcLqs+++++lelvvf++saR++ggtn +m+g+pys l+ ge
  gi|15668306|ref|NP_247102.1| 255 ITGNIPVVIRESLLPQVFEMGDKLVAKAKELVPPGMIGPFCLQSLCNENLELVVFEMSARVDGGTNSFMNGGPYSFLYNGE 335
                                   ********************************************************************************* PP

                                   ---HHHHHHHHHHHHHHCT-GGGCE CS
                       DUF1297 163 plsmGrrialEikeaiekdrleeiv 187
                                   plsmG+ria+Eik+a++ d++++i+
  gi|15668306|ref|NP_247102.1| 336 PLSMGQRIAREIKMALQLDMIDKII 360
                                   ************************9 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.4   0.0   4.5e-52     4e-48       1     122 []      21     143 ..      21     143 .. 0.99

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 4.5e-52
                                   EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTTTT-SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHHHC-H CS
                       DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekfkvidevivldkfkdilkeevqeklreenailvPhgsfveYvgi 81 
                                   iatl+SH++l+ilkgAk egf+t++++ kgr+ +Y++fkv+d++i +d+f+di +ee+qeklre n+i+vPhgsf++Y+g+
  gi|15668306|ref|NP_247102.1|  21 IATLGSHTSLHILKGAKLEGFSTVCITMKGRDVPYKRFKVADKFIYVDNFSDIKNEEIQEKLRELNSIVVPHGSFIAYCGL 101
                                   89******************************************************************************* PP

                                   HHHH.C-SS-EES-TTHHHHHCSHHHHHHHHHHTT-BB--BE CS
                       DUF1246  82 ekie.elkvpifGnrkllrwEerrekkrkyLekAgiriPkki 122
                                   +++e ++ vp+fGnr++lrwE++r+ + k+L++Ag+r+Pkk+
  gi|15668306|ref|NP_247102.1| 102 DNVEnSFLVPMFGNRRILRWESERSLEGKLLREAGLRVPKKY 143
                                   ****************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2213.77
//
Query:       gi|15668307|ref|NP_247103.1|  [L=286]
Description: hypothetical protein MJ_0137 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.1e-163  543.0   1.1   1.3e-163  542.8   1.1    1.0  1  SDH_sah        Serine dehydrogenase proteinase
    5.5e-09   36.2   0.5    3.7e-07   30.2   0.1    2.2  2  CLP_protease   Clp protease
    3.7e-05   23.1   0.0    0.00026   20.4   0.0    2.1  2  ECH_1          Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.041   13.8   0.0    1.4  1  Peptidase_S49  Peptidase family S49


Domain annotation for each model (and alignments):
>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.8   1.1  2.9e-167  1.3e-163       2     284 ..       4     284 ..       3     286 .] 0.98

  Alignments for each domain:
  == domain 1  score: 542.8 bits;  conditional E-value: 2.9e-167
                       SDH_sah   2 eksdplss.lssllwfllflylllapqlkrkqlllarlkvlrkleekrksrvitmihrqesigflGipiykfitiedseev 81 
                                   ek+dpls+ +ssl+w+llf+yl++apq+++kql+larlk+lr+l++kr+s+vitmihrqesig++Gip+ykfitiedsee+
  gi|15668307|ref|NP_247103.1|   4 EKMDPLSGfISSLIWWLLFFYLIMAPQIQYKQLQLARLKILRELSNKRNSTVITMIHRQESIGLFGIPVYKFITIEDSEEI 84 
                                   689****9899********************************************************************** PP

                       SDH_sah  82 lrairltpkdkpidliihtpGGlvlaatqiakalkehkaktrvivphyamsGGtlialaadeiildenavlGpvdpqlgqy 162
                                   lrair++pkdkpidliihtpGGlvlaatqiakalk+h+a+trvivphyamsGGtlialaad+ii+denavlGpvdpqlgqy
  gi|15668307|ref|NP_247103.1|  85 LRAIRAAPKDKPIDLIIHTPGGLVLAATQIAKALKAHPAETRVIVPHYAMSGGTLIALAADKIIMDENAVLGPVDPQLGQY 165
                                   ********************************************************************************* PP

                       SDH_sah 163 paasilkvvekkeakdiddktliladiakkaikqveefvyellkdkydeekakeiakklteGrwthdypltveelkelGle 243
                                   pa+si+k+ve+k+a+++dd+tliladiakkai+qv++fvy+llkdky+eekake++k+lteGrwthdyp+tvee+kelGl+
  gi|15668307|ref|NP_247103.1| 166 PAPSIVKAVEQKGADKADDQTLILADIAKKAINQVQNFVYNLLKDKYGEEKAKELSKILTEGRWTHDYPITVEEAKELGLD 246
                                   ********************************************************************************* PP

                       SDH_sah 244 vntnvpeevyellelyeqplgqrpsveyipvpvkkkeqekn 284
                                   v+tnvpeevy+l+ely+qp++qr++ve++p+pvk   qe++
  gi|15668307|ref|NP_247103.1| 247 VDTNVPEEVYTLMELYKQPVRQRGTVEFMPYPVK---QENG 284
                                   **********************************...4444 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   8.3e-11   3.7e-07      36      98 ..      84     146 ..      48     155 .. 0.81
   2 !    4.3   0.1    0.0076        34     128     174 ..     193     245 ..     184     251 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 8.3e-11
                                   HHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEETHHHHHHHTS-T CS
                  CLP_protease  36 qLllLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticlGlaaSmgslllaagek 98 
                                    L ++ a  +dk+i l+i++pGG v a++ I+ +++ + ++  +i+   a+S g+l+++a++k
  gi|15668307|ref|NP_247103.1|  84 ILRAIRAAPKDKPIDLIIHTPGGLVLAATQIAKALKAHPAETRVIVPHYAMSGGTLIALAADK 146
                                   3456667799***************************************************98 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0076
                                   HHHHHHHHHHHHHHHHHHHHTS-H.HHHHH.....HHCSTEEEEHHHHHHHTS CS
                  CLP_protease 128 eaeellkikerlneilakhtgqsl.ekiek.....dldrdtflsaeeAveyGL 174
                                     + ++++++ + ++l+++ g++  ++++k       + d+ +++eeA+e GL
  gi|15668307|ref|NP_247103.1| 193 AKKAINQVQNFVYNLLKDKYGEEKaKELSKiltegRWTHDYPITVEEAKELGL 245
                                   556777777777777776666543134444444668899999**********9 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.9e-08   0.00026      98     147 ..     132     180 ..     117     200 .. 0.84
   2 ?    0.4   0.0     0.076   3.4e+02     157     178 ..     233     255 ..     203     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.9e-08
                                   EEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHH CS
                         ECH_1  98 aaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGks 147
                                   +a+ GG ++ala+D +i+++na+ g    +lG +p+  +++ +++k G  
  gi|15668307|ref|NP_247103.1| 132 YAMSGGTLIALAADKIIMDENAVLGPVDPQLGQYPAPSIVKAVEQK-GAD 180
                                   89*********************************87777766654.444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.076
                                   -EEEHHHHHHCTS.SSEEESGGG CS
                         ECH_1 157 kkisaqealkvGl.vdkvvpeeq 178
                                    +i+++ea++ Gl vd+ vpee 
  gi|15668307|ref|NP_247103.1| 233 YPITVEEAKELGLdVDTNVPEEV 255
                                   47899*******99999999875 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.1e-06     0.041      11      40 ..     127     156 ..     121     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.1e-06
                                   EEEEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                 Peptidase_S49  11 asaenvaaSggYylasaadkivanpstivg 40 
                                   +++  +a Sgg ++a aadki+++ +++ g
  gi|15668307|ref|NP_247103.1| 127 VIVPHYAMSGGTLIALAADKIIMDENAVLG 156
                                   567789********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1835.75
//
Query:       gi|15668308|ref|NP_247104.1|  [L=482]
Description: cobyrinic acid a,c-diamide synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-13   50.6   1.5    4.5e-10   39.7   0.0    2.7  3  AAA_26      AAA domain
    1.2e-12   47.9   0.0    1.9e-12   47.2   0.0    1.3  1  GATase_3    CobB/CobQ-like glutamine amidotransferase domain
    1.4e-08   34.9   0.1    2.8e-08   33.9   0.1    1.6  1  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
    2.1e-05   24.4   0.3    5.7e-05   23.0   0.2    1.8  1  SNO         SNO glutamine amidotransferase family
    0.00044   19.6   0.0    0.00066   19.0   0.0    1.2  1  Zeta_toxin  Zeta toxin
     0.0014   18.4   0.0     0.0081   16.0   0.0    2.2  3  DJ-1_PfpI   DJ-1/PfpI family
     0.0034   17.2   0.0     0.0076   16.0   0.0    1.7  1  GATase      Glutamine amidotransferase class-I
  ------ inclusion threshold ------
      0.052   12.6   0.0       0.17   11.0   0.0    1.8  2  GATase_5    CobB/CobQ-like glutamine amidotransferase domain
      0.068   13.7   0.2       0.34   11.5   0.0    2.2  2  AAA_18      AAA domain


Domain annotation for each model (and alignments):
>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.1   4.3e+03      91     124 ..      25      62 ..      21      66 .. 0.77
   2 !    9.0   0.2   0.00055       1.1       1      28 [.     244     271 ..     244     277 .. 0.86
   3 !   39.7   0.0   2.3e-13   4.5e-10      86     187 ..     309     418 ..     289     425 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.1
                        AAA_26  91 iv....kelekdadivvVEGagglgvpiteellnadia 124
                                   i+    ++  kd d +++ G + + + +++++l  +i+
  gi|15668308|ref|NP_247104.1|  25 IItennYKEIKDLDALIIPGGSLIESKSLNDDLKKEII 62 
                                   44555456678999999999999999999999988887 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00055
                        AAA_26   1 rtifvtgtdtgvGKTvvslgLvralkrk 28 
                                   r+i++ +t+ ++GKT+++++L ++l+ +
  gi|15668308|ref|NP_247104.1| 244 RGIILLATSSNSGKTFLTTALSSKLNGR 271
                                   68999*****************999655 PP

  == domain 3  score: 39.7 bits;  conditional E-value: 2.3e-13
                        AAA_26  86 idlekivkelek.dadivvVEGagglgvpiteellnadiaknlgapvilVarg....glgtinqllltiealrqknvrvlG 161
                                   +d++k+ + ++k d+d ++VEG+ g  +  +++ + ++iak+lg pv +V +      +g++  +++ +++l++ +++v G
  gi|15668308|ref|NP_247104.1| 309 VDVSKFLDYIKKsDYDYIIVEGVMGAFTAALKNISSYQIAKKLGFPVYIVSACnisgIEGAFVEAMAYYSLLKDIGIKVEG 389
                                   677888866555599***********************************987444356789999**************** PP

                        AAA_26 162 vilNkvrnp...envetlekksgipvlGv 187
                                   vilNkv +    +++++l +k++i+++Gv
  gi|15668308|ref|NP_247104.1| 390 VILNKVYDWnsfNKLKSLAEKHNIKLYGV 418
                                   *****74445557***********99985 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   9.7e-16   1.9e-12      33     194 ..      30     187 ..      14     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 9.7e-16
                      GATase_3  33 kdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageveglglLdi 113
                                   + +++ +d+d++i+pGg+  ++ + l +  +l+++i ++   +g ++giC G+q+L ++i    ++ + +   eglglLd+
  gi|15668308|ref|NP_247104.1|  30 NYKEI-KDLDALIIPGGSLIES-KSLND--DLKKEIINF---NGYIIGICSGFQILAKKIDI-GRKSSVPIIKEGLGLLDV 102
                                   44566.67*********75544.44444..479999886...68***************854.4555788899******** PP

                      GATase_3 114 etefekekltgqvegevel.aaegeevkGyEiH.sGrtilkekakpllkvkv.ggnng....ekdGavkksedgnvlGtYl 187
                                   e       +t +ve ev+     + + +G+  H +G+    +k++++l+v++ ++ n     ek  ++++  +g+v+Gt +
  gi|15668308|ref|NP_247104.1| 103 EFSPLV--CTDRVEFEVKKsIFGEGKGEGFHCHtYGNIEVVDKETKILTVSKvKKLNYklgaEK-EIISGAFKGKVFGTMV 180
                                   998776..66666666666433347889999996799999999999999988633332466433.344455566******* PP

                      GATase_3 188 Hglfdnr 194
                                   H ++dn+
  gi|15668308|ref|NP_247104.1| 181 HNFLDNE 187
                                   *999985 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.1   1.4e-11   2.8e-08       1     125 [.     246     442 ..     246     446 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.4e-11
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   i++ +t++++GKT+l+++L   l+    rV++ + + +             i p                           
  gi|15668308|ref|NP_247104.1| 246 IILLATSSNSGKTFLTTALSSKLNG---RVFVAKIGGDVRD----------IVPalyllrekmtkynsikigergwvdvsk 313
                                   67889*******************9...9999998888333..........33333333334444778999********** PP

                                   ................................................CCHCCCHHHHHHCHCHHHH......EEEEEEEE CS
                                   ................................................xxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                          CbiA  55 ................................................dlkrllellealgkkkall....lkiagvvlnr 83 
                                                                                   +++ +++ + +    ++ll    +k+ gv+ln+
  gi|15668308|ref|NP_247104.1| 314 fldyikksdydyiivegvmgaftaalknissyqiakklgfpvyivsacNISGIEGAFVEAMAYYSLLkdigIKVEGVILNK 394
                                   ************************************************99999999988888888889999********** PP

                                   ESS...-TTCHHHHHHHHHHC......TS-EEEEEE--CCHCCCCHHT CS
                                   xxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  84 vdgeneetllkealeelkqry......gvpvlgviprdeavaeaparg 125
                                   v  +n++++lk+  e+++ ++      +++  g+ip++e  +e+ +r+
  gi|15668308|ref|NP_247104.1| 395 VYDWNSFNKLKSLAEKHNIKLygvgkiANESRGLIPEVEIDYESFCRN 442
                                   *****************9888888888888888999999888887776 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.2   2.9e-08   5.7e-05      28      98 ..      31     102 ..      20     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.9e-08
                                   GGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB.......SS-SS--CCE CS
                           SNO  28 kedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelene.......lvktlellkv 98 
                                    ++++++daliiPGG       lie   l +dl++ + n +  ++G C+G+ +l+k++++          + l+ll+v
  gi|15668308|ref|NP_247104.1|  31 YKEIKDLDALIIPGG------SLIESKSLNDDLKKEIINFNGYIIGICSGFQILAKKIDIGrkssvpiIKEGLGLLDV 102
                                   5678999*******9......48999999****************************998643433322234666666 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.3e-07   0.00066      11     126 ..     238     357 ..     228     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.3e-07
                    Zeta_toxin  11 psq.erPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdaselvekllqe 90 
                                   ++  ++  +ill+ ++ +GK+ l ++l  +l+ ++ +v   + d+R   P    ++++  k +s+ + +  ++ v k l++
  gi|15668308|ref|NP_247104.1| 238 KDVnKKRGIILLATSSNSGKTFLTTALSSKLN-GRVFVAKIGGDVRDIVPALYLLREKMTKYNSIKIGERGWVDVSKFLDY 317
                                   333488889**********************5.77778888889************************************* PP

                    Zeta_toxin  91 aiengyn.iivegtlrspdvvkk...laealkkaGYevev 126
                                   + +  y+ iiveg +     + k     + +kk G+ v +
  gi|15668308|ref|NP_247104.1| 318 IKKSDYDyIIVEGVMGAFTAALKnisSYQIAKKLGFPVYI 357
                                   ******97899***99888777732223445577776655 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.1e-06    0.0081      54     113 ..      31      84 ..      19      99 .. 0.77
   2 ?   -1.6   0.0         1   2.1e+03      50      69 ..     311     330 ..     286     340 .. 0.80
   3 ?   -3.6   0.0       4.2   8.4e+03      14      36 ..     371     393 ..     370     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.1e-06
                                   GGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTT CS
                     DJ-1_PfpI  54 lddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaagvl 113
                                   +++   ++ Dal++pGG    e+ +      +l ke  + ++ +  IC g q+La++  +
  gi|15668308|ref|NP_247104.1|  31 YKE--IKDLDALIIPGGSL-IESKSL---NDDLKKEIINFNGYIIGICSGFQILAKKIDI 84 
                                   554..4578********98.444443...4688999******************997554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                                   -SEEGGGCTCCG-SEEEE-- CS
                     DJ-1_PfpI  50 vdaslddvkaaeyDalvlpG 69 
                                   v + ld +k+++yD +++ G
  gi|15668308|ref|NP_247104.1| 311 VSKFLDYIKKSDYDYIIVEG 330
                                   34457889999999999977 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.2
                                   HHHHHHHHHHHHTTEEEEEEESS CS
                     DJ-1_PfpI  14 vElivpvdvlkragikvdvvsvd 36 
                                   vE+++ ++ lk  gikv+ v ++
  gi|15668308|ref|NP_247104.1| 371 VEAMAYYSLLKDIGIKVEGVILN 393
                                   68888899999999999988776 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.8e-06    0.0076      35      91 ..      29     101 ..      20     214 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.8e-06
                                   HHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTT................E CS
                        GATase  35 eilellknpdgilvsgGpgspgvegkieaikearenkiPiLGICLGmQllaiefgr................k 91 
                                   +++++ k+ d+++++gG    +     ++ ke+++ +  i+GIC G+Q+la+++                  +
  gi|15668308|ref|NP_247104.1|  29 NNYKEIKDLDALIIPGGSLIESKSLNDDLKKEIINFNGYIIGICSGFQILAKKIDIgrkssvpiikeglgllD 101
                                   33335789**************999999*******8888***********98653222655555555555550 PP

>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.5e-05      0.17      75     106 ..      50      81 ..      32      91 .. 0.80
   2 ?   -2.3   0.0      0.92   1.8e+03     216     240 ..     172     196 ..     170     211 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.5e-05
                      GATase_5  75 neklrealekflnredtlaLGiCnGfqlLvkl 106
                                   +++l+++l+k + + ++ ++GiC Gfq+L+k 
  gi|15668308|ref|NP_247104.1|  50 SKSLNDDLKKEIINFNGYIIGICSGFQILAKK 81 
                                   456666776666666889***********985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.92
                      GATase_5 216 dGRvlalmpHpervveavqksiipe 240
                                   +G+v+++m H    +e v  +++++
  gi|15668308|ref|NP_247104.1| 172 KGKVFGTMVHNFLDNEFVRDNFLKH 196
                                   699*****99876666666665554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1         2     4e+03      28      55 ..     189     217 ..     177     242 .. 0.55
   2 ?   11.5   0.0   0.00017      0.34       1      84 [.     247     333 ..     247     345 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2
                        AAA_18  28 lrdvakenglllevdpe.aldeskrlded 55 
                                   +rd++ ++  ++e+++e  ++++k+++++
  gi|15668308|ref|NP_247104.1| 189 VRDNFLKHLGVTEDEKEeIFEKNKIIKDE 217
                                   55555555555555555333333333322 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00017
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf......gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleeg 74 
                                   Ill+  + +GKt l+ +Ls++l g       g  +rd+++  +ll e   +   +s ++ e     +++ l+ + +   + 
  gi|15668308|ref|NP_247104.1| 247 ILLATSSNSGKTFLTTALSSKLnGRvfvakiGGDVRDIVPALYLLREKMTK--YNSIKIGERGWVDVSKFLDYIKK--SDY 323
                                   66666789*************95559******************9999999..88888888888888888888865..889 PP

                        AAA_18  75 knlvidghla 84 
                                   + ++++g+++
  gi|15668308|ref|NP_247104.1| 324 DYIIVEGVMG 333
                                   9999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 3533.70
//
Query:       gi|15668309|ref|NP_247105.1|  [L=209]
Description: potassium channel protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-17   62.5  26.6    5.8e-17   61.7  26.6    1.3  1  Ion_trans    Ion transport protein
    3.3e-16   59.0   6.3    3.3e-16   59.0   6.3    2.7  2  Ion_trans_2  Ion channel
  ------ inclusion threshold ------
        2.5    7.7  13.1        3.4    7.3   3.9    2.3  2  HlyIII       Haemolysin-III related


Domain annotation for each model (and alignments):
>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7  26.6   9.7e-21   5.8e-17       2     224 ..      10     199 ..       9     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 9.7e-21
                                   HHHHHHHHHHHHHHHHHHHCCCSSSSHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHCHSHHHHHHHHHHHHHH CS
                     Ion_trans   2 svfelfilllillncvflaletyfpedelektileilelvftaiftlemllkilalgllikkrYlrdpwnilDflvvlpsl 82 
                                   +++e+++l++++  ++ + l+ty+p+  +  ++l  l+++ +++ft+e++ +++      k ++++d+ ni+D +vv+ +l
  gi|15668309|ref|NP_247105.1|  10 KIMEVLSLIFTFEIVASFILSTYNPP--YQ-DLLIKLDYISIMFFTFEFIYNFYYVED--KAKFFKDIYNIVDAIVVIAFL 85 
                                   6789999*******************..55.89*********************9999..9******************** PP

                                   HHH..HHHH..HHHHHHHHHHHHGGGGGGHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCCC CS
                     Ion_trans  83 lsl..vlse..esllllsvlrlfrvlrllklisrleglrtlvtalirsvkdllnvlllllvvlfifaligvqlfkgklrek 159
                                   l    v     +++l+l+v+ l+r+l ll++i    +lr l        ++l+n+l ll +++++  li +          
  gi|15668309|ref|NP_247105.1|  86 LYSlqV--FysKAFLGLRVINLLRILVLLRII----KLRKLEE-----NQALINFLTLLTICFIASCLIWIVES------- 148
                                   944342..133689999999999999999999....5555333.....68999999999999998888874444....... PP

                                   CCSCCSTSSSTTTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHH CS
                     Ion_trans 160 necaktwenpnngntnFdnfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsfl 224
                                         + np       +nff+a+++++ ++tt+g+gdi+++t  +k    +i+f +++++++++
  gi|15668309|ref|NP_247105.1| 149 ------GVNP-----AINNFFDAFYFTTISITTVGYGDITPKTDAGK---LIIIFSVLFFISGLI 199
                                   ......5555.....5559****************************...999999999999886 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   4.6       1.9   1.1e+04      28      33 ..      48      53 ..      14      95 .. 0.61
   2 !   59.0   6.3   5.5e-20   3.3e-16       8      70 ..     134     202 ..     127     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.9
                                  HHHHHH CS
                   Ion_trans_2 28 alYfsf 33
                                   ++f+f
  gi|15668309|ref|NP_247105.1| 48 IMFFTF 53
                                  333333 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 5.5e-20
                                   HHHHHHHHT..........T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHH CS
                   Ion_trans_2   8 ifgaviysl......eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalfl 70 
                                   +++++  +l      + + + ++f+da+Yf+++++tT+GYGdi+p+tdag+l++i+ +l+ ++ +++ l
  gi|15668309|ref|NP_247105.1| 134 TICFIASCLiwivesGVNPAINNFFDAFYFTTISITTVGYGDITPKTDAGKLIIIFSVLFFISGLITSL 202
                                   2222222223345665556799**********************************9999887666655 PP

>> HlyIII  Haemolysin-III related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.9   0.00058       3.4      71     151 ..      35     114 ..      11     121 .. 0.63
   2 ?    6.8   2.7   0.00082       4.9      24      90 ..     106     172 ..      96     207 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00058
                        HlyIII  71 klrkffaklDysgIslliagsylplilyalakapkagllylslilalgvlgiisklvplfsrpearplrav.lfillgllg 150
                                    ++ ++ klDy++I+++ +  + +++++   ka  ++ +   ++ a++v+++++  + +f ++++  lr++ l  +l ll 
  gi|15668309|ref|NP_247105.1|  35 PYQDLLIKLDYISIMFFTFEFIYNFYYVED-KAKFFKDI-YNIVDAIVVIAFLLYSLQVFYSKAFLGLRVInLLRILVLLR 113
                                   5788999****9998877655554444443.54555555.56666666777776666666665654444431444444444 PP

                        HlyIII 151 v 151
                                   +
  gi|15668309|ref|NP_247105.1| 114 I 114
                                   4 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00082
                        HlyIII  24 ailllslaevkensklakvvvlvfllgallcllcSalyHtlsihseeklrkffaklDysgIslliag 90 
                                   + +l+ l  +k  +  ++ +++ fl  + +c+++S l+ ++++  +  +++ff  + ++ Is+  +g
  gi|15668309|ref|NP_247105.1| 106 LRILVLLRIIKLRKLEENQALINFLTLLTICFIASCLIWIVESGVNPAINNFFDAFYFTTISITTVG 172
                                   434444443443345677888889999999*************9999********999999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1105  (0.061632); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1662.13
//
Query:       gi|15668310|ref|NP_247106.1|  [L=333]
Description: potassium channel protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-34  116.7   0.4    1.2e-33  115.8   0.1    1.6  2  TrkA_N           TrkA-N domain
    4.4e-17   61.8  14.0    7.5e-17   61.1  14.0    1.4  1  Ion_trans_2      Ion channel
    1.6e-13   50.3   0.0    2.9e-13   49.4   0.0    1.4  1  TrkA_C           TrkA-C domain
    0.00066   19.0   8.4     0.0015   17.8   8.4    1.6  1  Ion_trans        Ion transport protein
  ------ inclusion threshold ------
      0.018   15.3   0.1       0.13   12.5   0.0    2.2  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.05   13.5   0.0      0.096   12.6   0.0    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.13   13.0   0.0        0.4   11.4   0.0    1.7  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   0.1   4.8e-37   1.2e-33       1     116 []     110     227 ..     110     227 .. 0.96
   2 ?   -3.0   0.0       3.2   8.3e+03      44      60 ..     264     280 ..     244     296 .. 0.56

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 4.8e-37
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSE..EEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreegle..vvvgdatdeevLeeagiekadaviaatgddeanila 79 
                                   +ii+G+Gr+G+ +aee+++ ++++v+id+de+ +ee+ e+  +  ++vgdat++++L++a+ieka+++i ++++d++n+++
  gi|15668310|ref|NP_247106.1| 110 YIICGYGRLGKVIAEEFKKCNIPFVIIDSDEKLLEEALEKDPNliCIVGDATSDDILKKAKIEKAKGLISVVSSDAENVFI 190
                                   79*****************6668*****************97766999********************************* PP

                                   HHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                        TrkA_N  80 vllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                   +l+ak+lnp+++i+a+a++p++ ++l k+gad+++ p
  gi|15668310|ref|NP_247106.1| 191 TLSAKKLNPNIYIVAKAEKPSTLDKLIKAGADRAVCP 227
                                   **********************************987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.2
                                   EEES-TTSHHHHHHTTG CS
                        TrkA_N  44 vvvgdatdeevLeeagi 60 
                                   +v+    d ++L++ gi
  gi|15668310|ref|NP_247106.1| 264 IVKNKELDNKLLKDSGI 280
                                   34444445555555555 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1  14.0   2.9e-20   7.5e-17       2      78 ..      13      86 ..      12      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 2.9e-20
                                  HHHHTCHHHHHHHHT....T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Ion_trans_2  2 vlllvlifgaviysleegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkvlt 78
                                  v++l++++ +vi +    +e+w+f++a+Y ++vt++T+GYGd++p+t +g+l +i+yi+ G++ +a+++ +++++++
  gi|15668310|ref|NP_247106.1| 13 VIILLILIESVILMT---VEGWDFFTAFYTAVVTISTVGYGDYTPQTFLGKLSVIIYIFAGVGAVAYTMGNIASFFI 86
                                  677777788888888...7999***************************************************9986 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.0   1.1e-16   2.9e-13       4      68 ..     262     328 ..     260     330 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.1e-16
                                   EEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                        TrkA_C   4 vtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                     + ++  l++k lk++++r++ g++++a+++g + +++p++dtv++ GD+++ +g++++l++l+++
  gi|15668310|ref|NP_247106.1| 262 RYIVKNKELDNKLLKDSGIREKtGATILAVKKGdKTITSPPPDTVINIGDIIYAFGTKEQLEKLKRY 328
                                   45667999**********************9999******************************986 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   8.4     6e-07    0.0015     178     239 ..      32      87 ..      11      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6e-07
                                   SHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Ion_trans 178 nfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsflllNlliaviadnfqe 239
                                   +ffta+++++++++t+g+gd +++t  +k      + vi++i++++  +++  ++ia+ f e
  gi|15668310|ref|NP_247106.1|  32 DFFTAFYTAVVTISTVGYGDYTPQTFLGK------LSVIIYIFAGVGAVAYTMGNIASFFIE 87 
                                   59***************************......**********************98866 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     5e-05      0.13       2      77 ..     111     181 ..     110     196 .. 0.85
   2 ?    4.0   0.2     0.022        56       9      71 ..     157     222 ..     156     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-05
                                   EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE-S CS
               Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnls 77 
                                   +i G+G+ G+++ae+ ++ + +   ++++d +++ le++++  + +++++i  da  ++  L+++ +++++ +++++
  gi|15668310|ref|NP_247106.1| 111 IICGYGRLGKVIAEEFKKCN-I--PFVIIDSDEKLLEEALE--KDPNLICIVGDATSDDI-LKKAkIEKAKGLISVV 181
                                   688*************9985.7..7**********999998..78999999999988886.7777688888777775 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.022
                                   HHHHHHHHHHCTCCT-G...EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS.S CS
               Sacchrp_dh_NADP   9 vGqavaellarhfdvda...eitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg.d 71 
                                   vG a+ ++++++ ++++    i v++ + e++  ++ +a++ + +++ + +++++++L++l+k g d
  gi|15668310|ref|NP_247106.1| 157 VGDATSDDILKKAKIEKakgLISVVSSDAENVFITL-SAKKLNPNIYIVAKAEKPSTLDKLIKAGaD 222
                                   788888888888888887777888888888865554.55999999999***************9864 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.7e-05     0.096       4      69 ..     112     180 ..     110     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.7e-05
                                   EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH...HHHCCTTTTSS-HHHHCCCHHCEEE CS
                       3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdiseealekalekiek...sleklvekgklkeeeveaalarisf 69 
                                   ++G G +G+ ia+ f + +++ v++d +e+ le+alek  +    +  + ++  lk++++e+a   is+
  gi|15668310|ref|NP_247106.1| 112 ICGYGRLGKVIAEEFKKCNIPFVIIDSDEKLLEEALEKDPNlicIVGDATSDDILKKAKIEKAKGLISV 180
                                   79*********************************9986665545566666666666666666666664 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016       0.4       6      57 ..     113     162 ..     110     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                   -TTSHHHHHHHCTS.T.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG CS
               Methyltransf_25   6 cGtGrltlalakrl.g.kakvtgvDiseemleaareraeeeglnvefvqgdaed 57 
                                   cG Grl + +a+++ + +  ++ +D +e++le+a e+     +n+ +++gda++
  gi|15668310|ref|NP_247106.1| 113 CGYGRLGKVIAEEFkKcNIPFVIIDSDEKLLEEALEKD----PNLICIVGDATS 162
                                   **************5368889*************9998....899999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2124.79
//
Query:       gi|15668311|ref|NP_247107.1|  [L=100]
Description: hypothetical protein MJ_0139.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 622.51
//
Query:       gi|15668312|ref|NP_247108.1|  [L=206]
Description: hypothetical protein MJ_0140 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-20   71.2   0.2    2.3e-19   69.8   0.1    1.7  2  NAD_binding_7    Putative NAD(P)-binding
    3.2e-05   24.2   0.3    8.8e-05   22.8   0.1    1.8  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00027   21.2   0.3    0.00048   20.4   0.3    1.5  1  TrkA_N           TrkA-N domain
    0.00052   20.0   0.1    0.00073   19.6   0.1    1.5  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
     0.0006   19.4   0.8     0.0019   17.8   0.8    1.8  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
     0.0025   17.2   0.0     0.0046   16.3   0.0    1.4  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0084   16.3   0.0       0.22   11.7   0.0    2.3  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
  ------ inclusion threshold ------
      0.014   15.3   0.0       0.02   14.8   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
       0.03   13.7   0.2      0.067   12.6   0.2    1.7  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.043   13.5   0.4      0.043   13.5   0.4    1.8  2  2-Hacid_dh       D-isomer specific 2-hydroxyacid dehydrogenas
      0.091   12.5   3.8       0.52   10.0   3.8    2.0  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
        0.1   12.6   9.0       0.91    9.6   0.6    3.4  4  Med26            TFIIS helical bundle-like domain
       0.12   12.3   0.7       0.33   10.8   0.1    2.1  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.12   11.9   0.4        0.6    9.7   0.0    2.4  2  LEM              LEM domain
       0.24   12.1   1.4       0.75   10.5   0.8    2.2  3  PTS_IIB          PTS system, Lactose/Cellobiose specific IIB 
       0.87    9.5   8.5        6.1    6.8   0.8    2.9  2  Tom37_C          Tom37 C-terminal domain
       0.99    9.5   5.2        1.4    9.0   0.8    2.2  2  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
        1.9    9.1   7.4        2.7    8.6   0.5    3.1  3  DUF4473          Domain of unknown function (DUF4473)


Domain annotation for each model (and alignments):
>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.1   2.3e-22   2.3e-19       2     104 .]       5     120 ..       4     120 .. 0.88
   2 ?   -1.3   0.0       2.9   2.9e+03      55      94 ..     148     187 ..     129     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 2.3e-22
                 NAD_binding_7   2 fldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele..............elvklaeeelekdlegadlviaa 68 
                                   +l ++gkkv v+G G+v+ r+++k+l++g  v ++++e+ ee++              ++ +l++eel++ + ++d++++a
  gi|15668312|ref|NP_247108.1|   5 LLSFEGKKVAVFGCGSVGKRRAKKILKSGGIVDIYSKEFDEEIKklkesnknlnlieiDINQLSDEELKNIIMKYDFIVTA 85 
                                   6889**********************************977777777778777554444444678888999********** PP

                 NAD_binding_7  69 tddrelneriaeaakarrilvnvadkpelcdfifpa 104
                                   + ++e+n+ri+++ak+ +++vn ++k e  +fi+pa
  gi|15668312|ref|NP_247108.1|  86 I-NDEINKRIVKLAKELNKFVNSSTKTEGVNFIIPA 120
                                   *.789******************************7 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.9
                 NAD_binding_7  55 lekdlegadlviaatddrelneriaeaakarrilvnvadk 94 
                                   +e+ l+ +d+ ++a  ++ l+e i ++  +++il  +  +
  gi|15668312|ref|NP_247108.1| 148 VENYLKSTDINMIAYIREFLKETIPKQKDREKILKKIFEN 187
                                   4667777777777777777777777777666666665555 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   8.9e-08   8.8e-05       1      91 [.      13     100 ..      13     121 .. 0.86
   2 ?   -1.0   0.0       1.9   1.9e+03      39      69 ..     170     200 ..     145     204 .. 0.58

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8.9e-08
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESS.HHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrs.keklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppi 80 
                                   v ++G+GsvG+  a+++++++ +   + + +++ +e+ ++l+++ ++ +++ i ++   +e+ L+ ++ ++d++v ++ + 
  gi|15668312|ref|NP_247108.1|  13 VAVFGCGSVGKRRAKKILKSGGI---VDIYSKEfDEEIKKLKESNKNLNLIEIDINQLSDEE-LKNIIMKYDFIVTAINDE 89 
                                   679******************99...555555424445778887799999999999999999.****************** PP

                                   GHHHHHHHHHH CS
               Sacchrp_dh_NADP  81 ssldvlkaCie 91 
                                    +  ++k++ e
  gi|15668312|ref|NP_247108.1|  90 INKRIVKLAKE 100
                                   *****999977 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.9
                                   HHHCHHTTTCEEEEE--TTTHHHHHHHHHTT CS
               Sacchrp_dh_NADP  39 alaakalgvrfeaialdaenyeavLaallke 69 
                                    + +++ ++++ ++ +  e+ ++ L++l+++
  gi|15668312|ref|NP_247108.1| 170 TIPKQKDREKILKKIFENEKFREELKKLIEK 200
                                   4555556666666666666666666666654 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   4.8e-07   0.00048       1      88 [.      13     103 ..      13     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.8e-07
                                   EEEES-SHHHHHHHHHHHH.TT.EEEEEEESSHHHHHHHHHTT..SEEEES-TT..SHHHHHHTTGGGESEEEE-SSSHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.gg.kdvvvidkdeerveelreeg..levvvgdat..deevLeeagiekadaviaatgddea 75 
                                   +++ G+G vG++ a+++ + gg  d++  + d e +++l+e +  l+ +  d    ++e L+++ i+k+d +++a+ +de 
  gi|15668312|ref|NP_247108.1|  13 VAVFGCGSVGKRRAKKILKsGGiVDIYSKEFD-EEIKKLKESNknLNLIEIDINqlSDEELKNI-IMKYDFIVTAI-NDEI 90 
                                   689****************5555234444444.5566665555458888876651156666666.899**999999.99** PP

                                   HHHHHHHHHHHTS CS
                        TrkA_N  76 nilavllakelnp 88 
                                   n  +v+lakeln+
  gi|15668312|ref|NP_247108.1|  91 NKRIVKLAKELNK 103
                                   **********997 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   7.3e-07   0.00073       1      93 [.      12     102 ..      12     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.3e-07
                                   -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHH CS
                NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsqa 81 
                                   k+av+G Gs G   Ak + + g  v ++++e    eei++ +e +k L+ i+++ n    ++l++ + + d+iv ++  ++
  gi|15668312|ref|NP_247108.1|  12 KVAVFGCGSVGKRRAKKILKSGGIVDIYSKE--FDEEIKKLKESNKNLNLIEIDINQLSDEELKNIIMKYDFIVTAINDEI 90 
                                   79********************999998766..557778888888888899999999*********************998 PP

                                   HHHHHHHHCCC- CS
                NAD_Gly3P_dh_N  82 lrevlkklkgll 93 
                                    ++++k +k+l 
  gi|15668312|ref|NP_247108.1|  91 NKRIVKLAKELN 102
                                   888877666543 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.8   1.9e-06    0.0019       3      78 ..       9      96 ..       7     116 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.9e-06
                                  HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHT............T-EEEEHHHHHHT-SEEEE-S-HHHH CS
                          IlvN  3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkee............gfevltvaeavkkadvvmiliPDelq 73
                                  +gkk+av G+Gs G+ +a+++  sg  v +  +e ++ +kk ke+             ++  ++++++ k d++++ i De++
  gi|15668312|ref|NP_247108.1|  9 EGKKVAVFGCGSVGKRRAKKILKSGGIVDIYSKEFDEEIKKLKESnknlnlieidinQLSDEELKNIIMKYDFIVTAINDEIN 91
                                  79*****************9999987777766666655544443300011110101033344556777888888888888888 PP

                                  HHHHH CS
                          IlvN 74 kevye 78
                                  k++++
  gi|15668312|ref|NP_247108.1| 92 KRIVK 96
                                  88873 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.6e-06    0.0046      30      99 ..      12      86 ..       7     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.6e-06
                                  EEEEESTSHHHHHHHHHHHHTT-EEEE....EESSHHHHHHHHH.TTTCECEEHCHHHHHHHHHHHH-SEEEE-- CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtv....lDvrparleqles.lgakfvevlksqeellaeavkeadvvigtv 99
                                  kv v+G G +G   ++   + g +V +    +D ++++l++ ++ l+   +++ + + e+l++ + + d +++++
  gi|15668312|ref|NP_247108.1| 12 KVAVFGCGSVGKRRAKKILKSGGIVDIyskeFDEEIKKLKESNKnLNLIEIDINQLSDEELKNIIMKYDFIVTAI 86
                                  8************************9932224555666666655777777888********************98 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00022      0.22       1      75 [.      12     130 ..      12     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SS.HHHHHHHHHTT...................................... CS
                 NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrt.kekveelvaeg...................................... 42 
                                   k+++ G G  G+  a+++lk+g  v +y  +  e++++l +++                                      
  gi|15668312|ref|NP_247108.1|  12 KVAVFGCGSVGKRRAKKILKSGGIVDIYSKEfDEEIKKLKESNknlnlieidinqlsdeelkniimkydfivtaindeink 92 
                                   68999*****************99999997735778888888788999998877666666666666666665555555555 PP

                                   ..EEE-SSHHHHHHHC...SEEEE-SSSHHHHHHHHHS CS
                 NAD_binding_2  43 ..akaaesieelvasl...dvvitmvkagkavdevieg 75 
                                     +k+a++++++v+s    + v ++++a ++vdevi++
  gi|15668312|ref|NP_247108.1|  93 riVKLAKELNKFVNSStktEGVNFIIPAYTEVDEVIFS 130
                                   55666666666666655556666666666666666665 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     2e-05      0.02       4      85 ..      19      98 ..      17     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                                  SHHHHHHHHHHHHC-T-EEEEEETT.HHHCHHHH.CTTTCEEEE--TT-..CCHHHHHHTT-SEEEES---TCCHHHHHHHHH CS
                NAD_binding_10  4 GkvGrllvkellargghevtalvRn.peklaele.aeeglevvegdvtd..vedlaealkgadaVvsalggggkdeegakniv 82
                                  G+vG++ +k++l++g   v ++  +  e++++l+ ++++l+++e+d+++   e+l++ +  +d +v+a++ + +     k+iv
  gi|15668312|ref|NP_247108.1| 19 GSVGKRRAKKILKSG-GIVDIYSKEfDEEIKKLKeSNKNLNLIEIDINQlsDEELKNIIMKYDFIVTAINDEIN-----KRIV 95
                                  99************7.5789999887788999874669********98533799***************87665.....2222 PP

                                  HHH CS
                NAD_binding_10 83 daa 85
                                  + a
  gi|15668312|ref|NP_247108.1| 96 KLA 98
                                  222 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   6.7e-05     0.067      33      72 ..       7      46 ..       3     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.7e-05
                                  -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHH CS
                  2-Hacid_dh_C 33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkke 72
                                  + +gk+v+++G+G++G++ ak++ + g  v +y++  ++e
  gi|15668312|ref|NP_247108.1|  7 SFEGKKVAVFGCGSVGKRRAKKILKSGGIVDIYSKEFDEE 46
                                  5689*************99988776666665555543322 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   4.4e-05     0.043       9      66 ..      44     105 ..      35     117 .. 0.74
   2 ?   -1.5   0.1       1.8   1.8e+03      17      38 ..     169     199 ..     155     202 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.4e-05
                                   HHHHHHHHH..TTEEEEEES....CSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEE CS
                                   xxxxxxxxx..xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh   9 eeelellke..egvevevkd....ellteellekakdadalivrsntkvtaevlealpkLkvia 66 
                                   +ee++ lke  +  ++++ +    +l++eel+  + ++d+++++ n+++++++ + +++L   +
  gi|15668312|ref|NP_247108.1|  44 DEEIKKLKEsnK--NLNLIEidinQLSDEELKNIIMKYDFIVTAINDEINKRIVKLAKELNKFV 105
                                   455666666542..3333333356799999*************************999986555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.8
                                   H........TTE.EEEEESCSSHHHCHHHHT CS
                                   x........xxx.xxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh  17 e........egv.evevkdellteellekak 38 
                                   e        e++ +  +++e+ +eel++ ++
  gi|15668312|ref|NP_247108.1| 169 EtipkqkdrEKIlKKIFENEKFREELKKLIE 199
                                   3333333343443445555777777777665 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.8   0.00052      0.52      29     137 ..       7     100 ..       3     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00052
                                   -STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHHSTSTSEEESHHSHH CS
                 ELFV_dehydrog  29 slegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldieellelkeerksvkeykkssekkaeyieneeel 109
                                   s+egk+va+ G G vg+  a+++ + g    +++D        + +d ee+++lke++k+++ ++     +++ +++e el
  gi|15668312|ref|NP_247108.1|   7 SFEGKKVAVFGCGSVGKRRAKKILKSG----GIVDIYS-----KEFD-EEIKKLKESNKNLNLIE---I-DINQLSDE-EL 72 
                                   699********************7755....5666332.....3344.68999999999988888...3.57888886.88 PP

                                   HHS..S-SEEEE-SSTTSB-HHHHTHTHHT CS
                 ELFV_dehydrog 110 lel..kvdilvPcAtqneideenakalikn 137
                                    ++  k+d++v  A+++ei+++ +k l k+
  gi|15668312|ref|NP_247108.1|  73 KNIimKYDFIV-TAINDEINKRIVK-LAKE 100
                                   77656888766.6899999998888.6654 PP

>> Med26  TFIIS helical bundle-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       7.3   7.3e+03      39      47 ..      23      31 ..      23      36 .. 0.76
   2 ?   -2.0   0.1         4   3.9e+03      31      41 ..      40      50 ..      26      53 .. 0.68
   3 ?    7.0   0.2    0.0057       5.7       6      45 ..      57     101 ..      55     103 .. 0.76
   4 ?    9.6   0.6   0.00091      0.91      23      50 ..     179     202 ..     165     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.3
                                  HHHHHHHHH CS
                         Med26 39 ktlAksLve 47
                                  k++Ak++++
  gi|15668312|ref|NP_247108.1| 23 KRRAKKILK 31
                                  578888876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4
                                  -TTS-HHHHHH CS
                         Med26 31 hkhetaevktl 41
                                  +k+ ++e+k+l
  gi|15668312|ref|NP_247108.1| 40 SKEFDEEIKKL 50
                                  45667777776 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0057
                                   S---....HHHHHHSHHHHHHHHH.....H-TTS-HHHHHHHHHH CS
                         Med26   6 LeklpittetLkstgIGkvVnalr.....khkhetaevktlAksL 45 
                                   L+ + i++++L    +  +++++       +++ ++++ +lAk+L
  gi|15668312|ref|NP_247108.1|  57 LNLIEIDINQLSDEELKNIIMKYDfivtaINDEINKRIVKLAKEL 101
                                   5556678888888888888888876665526788*********98 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00091
                                   HHHHHHHH-TTS-HHHHHHHHHHHHHHH CS
                         Med26  23 kvVnalrkhkhetaevktlAksLvekWk 50 
                                   k+ +++     e+++ ++  k+L+ekW 
  gi|15668312|ref|NP_247108.1| 179 KILKKIF----ENEKFREELKKLIEKWE 202
                                   5555664....4***************6 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00033      0.33       1      46 [.      12      57 ..      12     109 .. 0.68
   2 ?   -1.3   0.1       1.8   1.8e+03      46      72 ..     167     193 ..     147     201 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                                  EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHH CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksl 46
                                  kvav G+G +G+  a+ ++++g  V ++  + +   k l++ +k+l
  gi|15668312|ref|NP_247108.1| 12 KVAVFGCGSVGKRRAKKILKSGGIVDIYSKEFDEEIKKLKESNKNL 57
                                  79********************988888774433333333333333 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.8
                                   HHCCTTTTSS-HHHHCCCHHCEEEES- CS
                       3HCDH_N  46 leklvekgklkeeeveaalarisfttd 72 
                                   l++ + k+k  e+  ++++++ +f ++
  gi|15668312|ref|NP_247108.1| 167 LKETIPKQKDREKILKKIFENEKFREE 193
                                   333333333333333333333333333 PP

>> LEM  LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0006       0.6       1      22 [.      63      84 ..      63      89 .. 0.86
   2 ?   -1.6   0.2       2.1   2.1e+03       8      17 ..     188     197 ..     187     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0006
                           LEM  1 dvasLsDeeLreeLkkyGvspG 22
                                  d+ +LsDeeL++   ky + + 
  gi|15668312|ref|NP_247108.1| 63 DINQLSDEELKNIIMKYDFIVT 84
                                  789*********9999998775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.1
                           LEM   8 eeLreeLkky 17 
                                   e  reeLkk+
  gi|15668312|ref|NP_247108.1| 188 EKFREELKKL 197
                                   6779999985 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         6     6e+03      65      89 ..       8      31 ..       5      38 .. 0.77
   2 ?   10.5   0.8   0.00076      0.75      18      67 ..      48      99 ..      46     128 .. 0.78
   3 ?    0.0   0.1       1.4   1.4e+03      20      50 ..      94     126 ..      90     183 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6
                                  HTTSEEEEECTTHHHCCHCHHHHHH CS
                       PTS_IIB 65 fagkpvavinikdalgimdgekvlk 89
                                  f+gk+vav      +g+  ++k+lk
  gi|15668312|ref|NP_247108.1|  8 FEGKKVAVFGCGS-VGKRRAKKILK 31
                                  6777788888887.78888888876 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00076
                                  HHHHHHHHHCT.EEEEETTEEGGGHHHHHHT-SEEEEEESSGG.CTHHHHTT CS
                       PTS_IIB 18 eklekaakelg.ieaegeagveleaeeiaddaDlvllapqvrv.kdlarfag 67
                                  +kl++  k+l+ ie+ +++ +  e ++i  ++D++++a + ++ k + + a+
  gi|15668312|ref|NP_247108.1| 48 KKLKESNKNLNlIEIDINQLSDEELKNIIMKYDFIVTAINDEInKRIVKLAK 99
                                  68888889999**********9999999999********9987543333333 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.4
                                   HHHHHHHCT......EEEEETTEEGGGHHHHHHT-SE CS
                       PTS_IIB  20 lekaakelg......ieaegeagveleaeeiaddaDl 50 
                                   + k akel+       ++eg++ +     ++++ +D 
  gi|15668312|ref|NP_247108.1|  94 IVKLAKELNkfvnssTKTEGVNFI---IPAYTE-VDE 126
                                   556666666554444333333333...233333.333 PP

>> Tom37_C  Tom37 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.5      0.02        20      93     143 ..      84     134 ..      23     137 .. 0.80
   2 ?    6.8   0.8    0.0061       6.1      27      57 ..     172     202 ..     164     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.02
                       Tom37_C  93 ehLekklsseeldklskkleels.slesnskveiRdptfkEqgnvimslynl 143
                                   + ++++++ + + kl k+l+++  s++++++v++  p ++E  +vi s+y +
  gi|15668312|ref|NP_247108.1|  84 TAINDEIN-KRIVKLAKELNKFVnSSTKTEGVNFIIPAYTEVDEVIFSIYTK 134
                                   55533333.44667788887764266777899999**************987 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0061
                       Tom37_C  27 ekkkknkeeLqnlknnlqylkrlkevlkewi 57 
                                    k+k +++ L+++ +n ++ ++lk+++++w+
  gi|15668312|ref|NP_247108.1| 172 PKQKDREKILKKIFENEKFREELKKLIEKWE 202
                                   567788899*********************7 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.8    0.0014       1.4      21      51 ..       8      38 ..       4      51 .. 0.89
   2 ?    2.5   0.3      0.14   1.4e+02     114     151 ..      60      99 ..      43     112 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                                  -TTSEEEEE--SHHHHHHHHHHHHCT-EEEE CS
                 AdoHcyase_NAD 21 laGkvavvaGyGdvGkGcaaslkglGarviv 51
                                  + Gk++ v G G vGk  a+ + + G +v +
  gi|15668312|ref|NP_247108.1|  8 FEGKKVAVFGCGSVGKRRAKKILKSGGIVDI 38
                                  57*******************9999999876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                                   TTBTHHHHHTTT-EEEEEETTEEEEE-TT..S-EEEEEGG CS
                 AdoHcyase_NAD 114 seidvaaleanalkkeevkpqvdrvtlkd..gkkiillae 151
                                    eid+++l+ ++lk++ +k +     ++d  +k+i+ la+
  gi|15668312|ref|NP_247108.1|  60 IEIDINQLSDEELKNIIMKYDFIVTAINDeiNKRIVKLAK 99 
                                   6899999999988888888776666666645677777776 PP

>> DUF4473  Domain of unknown function (DUF4473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.51   5.1e+02      23      44 ..      34      56 ..      33      75 .. 0.79
   2 ?    1.8   0.1      0.35   3.5e+02      40      65 ..      86     110 ..      70     113 .. 0.76
   3 ?    8.6   0.5    0.0027       2.7      19      62 ..     155     200 ..     150     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.51
                       DUF4473 23 glvkiaek.fksefakakgdkea 44
                                  g+v+i  k f +e++k k ++++
  gi|15668312|ref|NP_247108.1| 34 GIVDIYSKeFDEEIKKLKESNKN 56
                                  78899877688888888666655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.35
                       DUF4473  40 gdkeaakkafeklkaevdafiktqse 65 
                                    + e +k ++ kl +e+++f+++ ++
  gi|15668312|ref|NP_247108.1|  86 INDEINKRIV-KLAKELNKFVNSSTK 110
                                   5666666666.999******999776 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0027
                       DUF4473  19 kaadglvkiaekfksefakakgdkeaakkafe..klkaevdafikt 62 
                                   + ++ ++ i e  k+ ++k+k+ ++  kk+fe  k+ +e+++ i++
  gi|15668312|ref|NP_247108.1| 155 TDINMIAYIREFLKETIPKQKDREKILKKIFEneKFREELKKLIEK 200
                                   5688899999999******************999******999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2383  (0.132913); expected 358.6 (0.02)
Passed bias filter:                      820  (0.045736); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 1243.04
//
Query:       gi|15668313|ref|NP_247109.1|  [L=99]
Description: hypothetical protein MJ_0141 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-14   53.1   2.4    3.3e-14   52.9   2.4    1.1  1  NTP_transf_2    Nucleotidyltransferase domain
    1.9e-10   40.7   2.0    2.4e-10   40.4   2.0    1.2  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0018   18.5   0.1     0.0019   18.4   0.1    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   2.4   5.5e-18   3.3e-14       2      88 ..       8      92 ..       6      99 .] 0.78

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 5.5e-18
                                  HHHHHHHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCC. CS
                  NTP_transf_2  2 kklleelkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekled. 81
                                  k++++++++  +    +v+lfGSyarG++ ++SD+D+l++++e+        +l+++ +iik  ++   l++d+++  ++++ 
  gi|15668313|ref|NP_247109.1|  8 KEFKKDISTILKdkLDRVILFGSYARGDYDEESDVDVLILVKEM-------PTLKEKQKIIKIASR-YSLKYDILISPIIYKk 82
                                  6666666666666679****************************.......78999********99.999****966666652 PP

                                  ...CTEEEEE CS
                  NTP_transf_2 82 ...pllvksi 88
                                     ++ ++++
  gi|15668313|ref|NP_247109.1| 83 tikTSFIDEV 92
                                  2225555444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   2.0   3.9e-14   2.4e-10       2      65 ..      13      72 ..       4      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 3.9e-14
                                  STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEE CS
                       Polbeta  2 kikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvD 65
                                   i+ il+++  ++ ++lFGS+a+g++ eeSD+D+ +l+ke  +l+e+ ++ +  ++ +l  k D
  gi|15668313|ref|NP_247109.1| 13 DISTILKDK--LDRVILFGSYARGDYDEESDVDVLILVKEMPTLKEKQKIIKIASRYSL--KYD 72
                                  466666666..******************************888887777766666633..333 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   3.2e-07    0.0019       9      66 ..       5      64 ..       1      92 [. 0.67

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.2e-07
                                  HHHHHHHHHHHHH-TT..-EEEE-HHHHTT-.SEESSEEEEEEBTTBSTTSS--HHHHHHH CS
                DNA_pol_B_palm  9 alealvkkaakeldpe..vevivcGSYRRga.essGDvDvlitkkdakseskklkkllekl 66
                                  ++ +  kk ++++ ++   +vi  GSY Rg  ++  DvDvli  k++ + + +++k+++  
  gi|15668313|ref|NP_247109.1|  5 EIIKEFKKDISTILKDklDRVILFGSYARGDyDEESDVDVLILVKEMPTLK-EKQKIIKIA 64
                                  555555666666655543468899*****9735678*******99999855.455555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 623.54
//
Query:       gi|15668314|ref|NP_247110.1|  [L=147]
Description: hypothetical protein MJ_0142 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-26   91.6   7.1    4.6e-26   91.3   7.1    1.1  1  HEPN      HEPN domain
     0.0037   17.2   1.0     0.0037   17.2   1.0    1.6  2  DUF1803   Domain of unknown function (DUF1803)


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   7.1   5.2e-30   4.6e-26       2     117 ..      15     130 ..      14     131 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 5.2e-30
                                   HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHC..CHHHT...-HHHHHHHHHH CS
                          HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLle..elkkelkeseelreeleeL 80 
                                   e+++++Ae+ lea+e+l+++++yd+a++++++++++++KAlll+k+++p+k++++++++   ++k+++    el e+++e+
  gi|15668314|ref|NP_247110.1|  15 EKLIEKAEKSLEASENLYNSEFYDFAVSRIYYSMFYCVKALLLTKEINPKKHSGVLKMFAkeFIKTNEL-DVELFEYINEA 94 
                                   89**********************************************************999999999.*********** PP

                                   HCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHHH CS
                          HEPN  81 ekayiesrYpdakeeyteedaeealkdaeevlelvee 117
                                    +++++++Y+++ e  ++e+ae +l++ + +l++ ++
  gi|15668314|ref|NP_247110.1|  95 YNYRQTADYDATIEI-KKEEAEYLLHKGHIFLNKTKK 130
                                   **************7.***********9999998765 PP

>> DUF1803  Domain of unknown function (DUF1803)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.44     4e+03      75      75 ..      21      21 ..       7      45 .. 0.52
   2 !   17.2   1.0   4.2e-07    0.0037      28      90 ..      69     130 ..      58     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.44
                       DUF1803 75 a 75
                                  a
  gi|15668314|ref|NP_247110.1| 21 A 21
                                  1 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 4.2e-07
                       DUF1803  28 iLRelkkeFadqkkldrlldelidaglikRenkrYklnlpifeieeaaelileeevfveeese 90 
                                   +L+   keF ++++ld  l e+i++ +  R+   Y  +++i + eea+ l  + ++f++++++
  gi|15668314|ref|NP_247110.1|  69 VLKMFAKEFIKTNELDVELFEYINEAYNYRQTADYDATIEI-KKEEAEYLLHKGHIFLNKTKK 130
                                   688899***********************************.778888888888999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1076  (0.0600145); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 926.85
//
Query:       gi|15668315|ref|NP_247111.1|  [L=392]
Description: glutamyl-tRNA reductase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-42  145.4   0.4    1.1e-42  145.4   0.4    1.9  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    1.8e-33  115.4   0.4    4.2e-33  114.2   0.1    1.8  2  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
    2.3e-09   37.6   2.6    2.3e-09   37.6   2.6    2.4  2  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
    3.8e-09   37.0   0.7    1.2e-08   35.4   0.7    1.9  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    1.7e-08   33.8   0.1    2.9e-08   33.0   0.1    1.4  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    1.8e-06   27.4   0.3    3.6e-06   26.5   0.3    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    4.9e-06   26.9   0.1    1.7e-05   25.2   0.1    1.9  1  NAD_binding_7    Putative NAD(P)-binding
    9.8e-05   21.7   0.2      0.015   14.6   0.0    2.6  3  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
    0.00018   21.1   0.0    0.00036   20.1   0.0    1.5  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
    0.00024   21.4   0.2      0.001   19.3   0.1    2.2  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0012   19.1   0.4     0.0038   17.4   0.0    2.0  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0031   17.8   0.8      0.024   14.9   0.4    2.4  2  Hydrolase        haloacid dehalogenase-like hydrolase
     0.0081   16.2   0.3       0.03   14.4   0.1    2.0  2  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
  ------ inclusion threshold ------
      0.012   15.7   1.1      0.027   14.6   0.0    2.2  2  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.019   15.2   0.3       0.07   13.4   0.3    2.1  1  TrkA_N           TrkA-N domain
      0.028   14.5   0.4       0.13   12.4   0.1    2.3  2  Hydrolase_6      Haloacid dehalogenase-like hydrolase
      0.032   15.1   0.1      0.085   13.7   0.1    1.7  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.032   14.4   0.3      0.032   14.4   0.3    2.5  2  Ribosomal_L22    Ribosomal protein L22p/L17e
      0.033   13.7   0.1      0.058   13.0   0.1    1.3  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.045   13.5   0.4       0.12   12.1   0.4    1.7  1  COQ7             Ubiquinone biosynthesis protein COQ7
      0.046   13.9   1.3       0.09   12.9   0.1    2.1  2  Mannitol_dh      Mannitol dehydrogenase Rossmann domain
      0.051   13.5   0.0       0.09   12.7   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
      0.097   12.7   0.6       0.22   11.6   0.1    1.9  2  OTCace           Aspartate/ornithine carbamoyltransferase, As
       0.21   11.0   0.1       0.33   10.3   0.1    1.2  1  DUF3530          Protein of unknown function (DUF3530)
       0.23   11.4   3.1        1.3    9.0   0.1    2.6  2  LpxI_N           LpxI N-terminal domain
       0.71    9.2  11.7      0.062   12.7   1.5    3.2  4  RNase_E_G        Ribonuclease E/G family
        1.3    8.9   5.7        1.8    8.4   4.5    1.8  2  CemA             CemA family


Domain annotation for each model (and alignments):
>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.4   0.4   1.6e-45   1.1e-42       1     137 [.     148     275 ..     148     276 .. 0.97
   2 ?   -2.6   0.1       7.8   5.2e+03      46      74 ..     299     323 ..     285     341 .. 0.56

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 1.6e-45
                                   HHHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE CS
                  Shikimate_DH   1 elakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvis 81 
                                   ela+k+++ l++k+vlliGaGema+lv+k+L +k++k+++vaNRt+e+a++la+el+g    a+k+++l+e+l+ ad+vis
  gi|15668315|ref|NP_247111.1| 148 ELAEKIFG-LEGKNVLLIGAGEMANLVIKALKEKNIKAIIVANRTYEKAEKLAKELGGM---AIKFDKLEEALRYADIVIS 224
                                   79*****8.**************************************************...******************* PP

                                   -SSSSS-SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHH CS
                  Shikimate_DH  82 ataseepilekeeveealkkrkkplllvDiavPRdvepevaeledvrlytvDdLke 137
                                   at++++pil+ke++++a k      +++Dia+PRd +++++el d++l+t+DdL+ 
  gi|15668315|ref|NP_247111.1| 225 ATGAPHPILNKERLKNAGKT-----IIIDIANPRDTTDDIRELPDIFLFTIDDLRL 275
                                   ***************99855.....*****************************85 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.8
                                   HHHHHHHHHHHT.ET-EEEEGCGHHHHHH CS
                  Shikimate_DH  46 lerakelaeelkgeeiealkleelkella 74 
                                   ler ke+ ++++ e    ++++el ++++
  gi|15668315|ref|NP_247111.1| 299 LERLKEFLDKMRFE----TAIKELGQYIE 323
                                   45555555555333....33333333333 PP

>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2   0.1   6.4e-36   4.2e-33       3     146 .]       6     133 ..       4     133 .. 0.85
   2 ?   -2.3   0.0         5   3.3e+03     122     140 ..     316     334 ..     281     353 .. 0.61

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 6.4e-36
                       GlutR_N   3 inhktapvelreklafseeelkellkeleekvkeaviLsTCNRtEiylsaeeeeeaseellellaevs.leelk.eklyvl 81 
                                   +++k+ +v+ +ekl ++ee++ e+++       +a++L+TCNR+Ei + a++     e       e++  e+++ ek+ +l
  gi|15668315|ref|NP_247111.1|   6 ADYKKYNVSELEKLRMDEEKFYETFD-------NAILLQTCNRVEIIFDADSL----E-------EIKgIENIDlEKFDIL 68 
                                   5899************9888666555.......57************644332....2.......2222344445789*** PP

                       GlutR_N  82 egeeavrHlfrVasGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                                    g++a++HlfrVa+GL+S+++GEdqIlgQ+k+ay +ake+g ++k Le+++ kai++++r+r et
  gi|15668315|ref|NP_247111.1|  69 FGDKAIEHLFRVACGLESMIVGEDQILGQLKNAYLKAKEKGRISKKLEKIILKAIHTGQRARVET 133
                                   **************************************************************997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5
                       GlutR_N 122 gtlgkvLerlfqkaikvak 140
                                   + lg+++e + +k ++ ak
  gi|15668315|ref|NP_247111.1| 316 KELGQYIENVRKKEVEKAK 334
                                   3333444444444444444 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       5.1   3.4e+03      50      72 ..     103     125 ..      92     156 .. 0.51
   2 !   37.6   2.6   3.4e-12   2.3e-09       1      80 [.     290     370 ..     290     384 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.1
                                   .--------TTHHHHHHHHHHHH CS
                   GlutR_dimer  50 ldgedreelekltrslvnkllhe 72 
                                   l+ +++  + k +++++ k +h+
  gi|15668315|ref|NP_247111.1| 103 LKAKEKGRISKKLEKIILKAIHT 125
                                   45555555555555555555554 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 3.4e-12
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S..-------.-TTHHHHHHHHHHHHHHHHHHSS CS
                   GlutR_dimer   1 kAeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkklaldgedree.lekltrslvnkllheptarLkea 80 
                                   k+e iI ee+e++++ l++++++ +Ik+l +++e++r++e+e+a+k l+ +++  ee le+++++l ++++ + ++   + 
  gi|15668315|ref|NP_247111.1| 290 KVEMIICEELERLKEFLDKMRFETAIKELGQYIENVRKKEVEKAKKILKNKNKPVEEvLEDFSKALCKRIIYDIIKIFENV 370
                                   699**********************************************555556666**************999877776 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.7   1.8e-11   1.2e-08       4      97 .]     163     252 ..     160     252 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.8e-11
                                   EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGH CS
                 F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.vkvtavdneeaaeeadvvvlavkpedveevlselak 83 
                                   +iGaG+m+  +++ l +++    + +++++r+ ekae+la+elg   ++  + eea++ ad+v+ a    +     + l  
  gi|15668315|ref|NP_247111.1| 163 LIGAGEMANLVIKALKEKN---IKAIIVANRTYEKAEKLAKELGgMAIKFDKLEEALRYADIVISATGAPHPILNKERL-- 238
                                   79****************9...5555566***************54444456799*********999888755444444.. PP

                                   HHHTTSEEEEESSS CS
                 F420_oxidored  84 dalkgklvisvlag 97 
                                   ++  ++++i+++++
  gi|15668315|ref|NP_247111.1| 239 KNAGKTIIIDIANP 252
                                   77888999999996 PP

>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.1   4.3e-11   2.9e-08     132     219 ..     161     245 ..     144     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.3e-11
                                   EEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGG CS
               OCD_Mu_crystall 132 laiiGaGvqaetqlealkavldikevriydrdeeaaekfaenlqefefevsackseeeavegadivvtvTaakapilkaew 212
                                   + +iGaG +a++ ++alk+  +ik + + +r+ e+aek+a++l +  ++++  ++ eea   adiv+ +T a +pil +e 
  gi|15668315|ref|NP_247111.1| 161 VLLIGAGEMANLVIKALKE-KNIKAIIVANRTYEKAEKLAKELGG--MAIK-FDKLEEALRYADIVISATGAPHPILNKER 237
                                   458**************87.58*********************95..7776.58899***********************9 PP

                                   S-.TT-EE CS
               OCD_Mu_crystall 213 vk.pGahi 219
                                   +k +G  i
  gi|15668315|ref|NP_247111.1| 238 LKnAGKTI 245
                                   97356555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.3   5.4e-09   3.6e-06      28     122 ..     150     246 ..     121     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 5.4e-09
                                   CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-E.EEEESSSHHHHH....CHHHHTCEECSHHHHHHH-SEEEE-S--ST CS
                  2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmk.viaydrskkkee....eeeelgvelvsleellaesDivslhlpltp 103
                                   a ++  l+gk v +iG+G++++ v+k lk+ ++k +i+ +r+ +k e    e   + +++++lee+l+ +Div+    +t 
  gi|15668315|ref|NP_247111.1| 150 AEKIFGLEGKNVLLIGAGEMANLVIKALKEKNIKaIIVANRTYEKAEklakELGGMAIKFDKLEEALRYADIVIS---ATG 227
                                   5567789**********************99995255556655555545434444556999**********9975...677 PP

                                   TTTTSBSHHHHHCSTTTEE CS
                  2-Hacid_dh_C 104 etrhlinaeelakmkkgai 122
                                   + + ++n+e+l+   k+ i
  gi|15668315|ref|NP_247111.1| 228 APHPILNKERLKNAGKTII 246
                                   8999999999999887654 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   2.6e-08   1.7e-05       5      91 ..     156     249 ..     153     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.6e-08
                 NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk......laeeelekdlegadlviaatddre..lner 77 
                                   l+gk+vl++G+Ge+A   ++ l e++ k ++va+++ e++e+l k      ++ ++le+ l  ad+vi at  ++  ln++
  gi|15668315|ref|NP_247111.1| 156 LEGKNVLLIGAGEMANLVIKALKEKNIKAIIVANRTYEKAEKLAKelggmaIKFDKLEEALRYADIVISATGAPHpiLNKE 236
                                   89*********************************8888887666655544567889999***********8643227777 PP

                 NAD_binding_7  78 iaeaakarrilvnv 91 
                                     ++a  + i + +
  gi|15668315|ref|NP_247111.1| 237 RLKNAG-KTIIIDI 249
                                   666664.4555555 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.9   2.6e+03      36      58 ..      83     105 ..      76     110 .. 0.78
   2 ?    4.1   0.0     0.038        25      30      76 ..     152     197 ..     141     203 .. 0.73
   3 !   14.6   0.0   2.3e-05     0.015      71     109 ..     210     251 ..     204     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.9
                                   T-EEEEE---TTTHHHHHHHHHC CS
                 THF_DHG_CYH_C  36 gkkvvvvGrsnivgkplallLle 58 
                                   g + ++vG+ +i+g+  ++ L++
  gi|15668315|ref|NP_247111.1|  83 GLESMIVGEDQILGQLKNAYLKA 105
                                   67789999999999876666665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.038
                                   CT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHH CS
                 THF_DHG_CYH_C  30 tgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaei 76 
                                   +   legk+v+ +G++++    +++ L+ekn    ++ ++t + ae+
  gi|15668315|ref|NP_247111.1| 152 KIFGLEGKNVLLIGAGEMANLVIKA-LKEKNIKAIIVANRTYEKAEK 197
                                   45679***********998877765.677788777777777555544 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 2.3e-05
                                   CCHHHHHCCSSEEEE-SS-TT.-B-GGGS-T..T-EEEE--- CS
                 THF_DHG_CYH_C  71 kdlaeitreadivvvavGkpe.likaemvke..gavviDvGi 109
                                   ++l+e +r adiv++a+G p+ ++++e +k+  ++++iD+  
  gi|15668315|ref|NP_247111.1| 210 DKLEEALRYADIVISATGAPHpILNKERLKNagKTIIIDIAN 251
                                   6899****************9445888998643578999865 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.4e-07   0.00036      11     139 ..     141     256 ..     138     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.4e-07
                   Glu_dehyd_C  11 siveKaielaeasrsafewepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpv 91 
                                   si   a+elae   + f  e + +l++GaG +  L + +l+   ++++ + v +r  + +++ +l +elG+  ++      
  gi|15668315|ref|NP_247111.1| 141 SIGSAAVELAE---KIFGLEGKNVLLIGAGEMANLVIKALKE--KNIKAIIVANR-TY-EKAEKLAKELGGMAIK-----F 209
                                   55556666655...4689999*******************85..78886655554.44.566779******9995.....7 PP

                   Glu_dehyd_C  92 deipeaseemdlvvEaTGsakhafeaiealapnGvaaLlGvpedseve 139
                                   d++ ea +  d+v+ aTG+++ +++  e l+ +G ++++ + ++++  
  gi|15668315|ref|NP_247111.1| 210 DKLEEALRYADIVISATGAPHPILNK-ERLKNAGKTIIIDIANPRDTT 256
                                   8888899***********99888875.677888877777777766555 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.5e-06     0.001       1      76 [.     161     225 ..     161     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-06
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE- CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnl 76 
                                   vl+iGaG ++  v++ l++++     i+va r+ ek+e+la+++ g  +++ +         L+++l+ +d+v+++
  gi|15668315|ref|NP_247111.1| 161 VLLIGAGEMANLVIKALKEKNIK--AIIVANRTYEKAEKLAKELGGMAIKFDK---------LEEALRYADIVISA 225
                                   79**************9998754..9**************9887777555544.........44455555555555 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.8e-06    0.0038       3      68 ..     162     231 ..     160     259 .. 0.83
   2 ?   -1.3   0.0       3.3   2.2e+03      31      60 ..     329     361 ..     314     385 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.8e-06
                                   EEE--SHHHHHHHHHHHHTT-E.EEEE-SSHHHHHHHHHTT...EEE-SSHHHHHHHCSEEEE-SSSHHH CS
                 NAD_binding_2   3 gfiGlGvMGsnmalnllkagyk.vavynrtkekveelvaeg...akaaesieelvasldvvitmvkagka 68 
                                    +iG G+M +  ++ l+++++k ++v nrt ek+e+l++e    a  ++++ee+++ +d+vi    a ++
  gi|15668315|ref|NP_247111.1| 162 LLIGAGEMANLVIKALKEKNIKaIIVANRTYEKAEKLAKELggmAIKFDKLEEALRYADIVISATGAPHP 231
                                   58******9999999987776538999************95578999**************987776655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.3
                                   SHHHHHHHHHTTEEE-SSHH.HHHHHC..SEEE CS
                 NAD_binding_2  31 tkekveelvaegakaaesie.elvasl..dvvi 60 
                                   + ek++++++++ k++e++  ++ ++l  +++ 
  gi|15668315|ref|NP_247111.1| 329 EVEKAKKILKNKNKPVEEVLeDFSKALckRIIY 361
                                   445666666666555555431343333654444 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.4   3.6e-05     0.024     123     160 ..     170     209 ..      90     231 .. 0.83
   2 ?    0.8   0.0      0.76   5.1e+02     129     187 ..     215     274 ..     208     294 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-05
                                   HHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..GGGE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                     Hydrolase 123 aaeavasLkaagievvlltgdnpetaeraanqlG..ddyf 160
                                   a  ++++Lk+++i+ +++ +   e ae++a++lG  + +f
  gi|15668315|ref|NP_247111.1| 170 ANLVIKALKEKNIKAIIVANRTYEKAEKLAKELGgmAIKF 209
                                   4599******************************773333 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.76
                                   HHHHTTEEEEEEESSEHHHHH.HHHHHTTGGGE.SEEEEHHCESSTTTSHHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 129 sLkaagievvlltgdnpetae.raanqlGddyf.daviasdietvakpspegkvaaireLq 187
                                   +L+ a i v+ +tg  +   + + ++++G+ ++ d+   +d++     +p++++ +i+ L+
  gi|15668315|ref|NP_247111.1| 215 ALRYADI-VISATGAPHPILNkERLKNAGKTIIiDIANPRDTTDDIRELPDIFLFTIDDLR 274
                                   5666677.88888888888888888888822222333333333333337888888887776 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   4.5e-05      0.03      21     107 ..     156     247 ..     146     264 .. 0.76
   2 ?   -2.0   0.0       4.9   3.3e+03      75     103 ..     259     287 ..     253     338 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.5e-05
                                   -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-...S-HHHHHHHHCTT-EE-..-HHHCTTT-SEEEE-SSSSS.SB-HH CS
                 AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivte...vdPicalqaameGfevv..tleevvkkadivvtttGnkd.iitle 95 
                                   l Gk+++++G G++     ++lk++  + i+      +    l   + G+ ++  +lee+++ adiv+++tG+   i+++e
  gi|15668315|ref|NP_247111.1| 156 LEGKNVLLIGAGEMANLVIKALKEKNIKAIIVAnrtYEKAEKLAKELGGMAIKfdKLEEALRYADIVISATGAPHpILNKE 236
                                   679*******************9998776654311145666788888998775449****************965266777 PP

                                   HHCCS-TTEEEE CS
                 AdoHcyase_NAD  96 hlkkmkddaivc 107
                                   +lk+  ++ i  
  gi|15668315|ref|NP_247111.1| 237 RLKNAGKTII-I 247
                                   7766555444.4 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.9
                                   CTTT-SEEEE-SSSSSSB-HHHHCCS-TT CS
                 AdoHcyase_NAD  75 vvkkadivvtttGnkdiitlehlkkmkdd 103
                                   + +  di++ t     ++  e+lkk k++
  gi|15668315|ref|NP_247111.1| 259 IRELPDIFLFTIDDLRLVAEENLKKRKEE 287
                                   55555666666666666666666665554 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.1e-05     0.027       2      93 ..     160     244 ..     159     256 .. 0.70
   2 ?   -1.9   0.0       5.2   3.5e+03      42      75 ..     316     352 ..     291     359 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.1e-05
                                   EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEB.SSHHHHHHH-SEEEE-S-HHHHH CS
                        DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavt.ddleevlekadvliDFTtpeavl 81 
                                   +v+++Ga G m + v+ka++e ++++   + +r+  e       e l ++  g+a++ d+lee+l+ ad++i  T      
  gi|15668315|ref|NP_247111.1| 160 NVLLIGA-GEMANLVIKALKE-KNIKAIIVANRTY-EK-----AEKLAKELGGMAIKfDKLEEALRYADIVISATGAPHPI 232
                                   6899**9.************9.5555555555554.12.....222333334666666***************99555444 PP

                                   HHHHHHHHTT-E CS
                        DapB_N  82 enlklalekgvk 93 
                                    n + + ++g+ 
  gi|15668315|ref|NP_247111.1| 233 LNKERLKNAGKT 244
                                   444555555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.2
                                   TBHHHHSSSS.--S-BEBSSHHHHHHH..-SEEEE-S CS
                        DapB_N  42 kdagellglg.klgvavtddleevlek..advliDFT 75 
                                   k++g+ ++   k +v+  +++ + ++k   +vl DF+
  gi|15668315|ref|NP_247111.1| 316 KELGQYIENVrKKEVEKAKKILKNKNKpvEEVLEDFS 352
                                   4445444433355555555555555555556666666 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   0.00011      0.07       1      53 [.     161     214 ..     161     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                                   EEEES-SHHHHHHHHHHHHTT.EEEEEEESSHHHHHHHHHTT.SEEEES-TTSHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLsegg.kdvvvidkdeerveelreeg.levvvgdatdee 53 
                                   +++iG+G+++  +++ L+e++ k ++v  +  e++e+l++e   ++++ d  + e
  gi|15668315|ref|NP_247111.1| 161 VLLIGAGEMANLVIKALKEKNiKAIIVANRTYEKAEKLAKELgGMAIKFDKLE-E 214
                                   689****************7745566666666999999887757788877763.3 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00019      0.13      19      60 ..     170     211 ..     161     247 .. 0.78
   2 ?   -2.1   0.0       6.6   4.4e+03      20      20 ..     331     331 ..     294     354 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                                   HHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----G CS
                   Hydrolase_6  19 aaealnalraagkpvvllTNnsskseeeyakkleklgvdite 60 
                                   a  +++al++++++ +++ N++ ++ e++ak+l  + +++++
  gi|15668315|ref|NP_247111.1| 170 ANLVIKALKEKNIKAIIVANRTYEKAEKLAKELGGMAIKFDK 211
                                   6779*****************************888777543 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.6
                                   H CS
                   Hydrolase_6  20 a 20 
                                   +
  gi|15668315|ref|NP_247111.1| 331 E 331
                                   2 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   0.00013     0.085       2      68 ..     160     224 ..     159     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00013
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE..EESSHHHHHTCTTESEEEE CS
                  GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve..aysdleelladpeidaviv 68 
                                   +v++iGaG ++   +++l+e+  + + + + ++  e+ae++a+++g     +++lee l+   +d+vi 
  gi|15668315|ref|NP_247111.1| 160 NVLLIGAGEMANLVIKALKEK--NIKAIIVANRTYEKAEKLAKELGGMaiKFDKLEEALR--YADIVIS 224
                                   89*************999998..8888999***************988789999999999..5566554 PP

>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.4       1.9   1.2e+03      31      53 ..     102     125 ..      92     192 .. 0.64
   2 ?   14.4   0.3   4.9e-05     0.032       6      39 ..     311     356 ..     307     384 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.9
                                   HHHT.-SSTTHHHHHHHHHHHHHH CS
                 Ribosomal_L22  31 yLkf.skkkaakfvlklLknaean 53 
                                   yLk  +k + +k ++k++ +a+  
  gi|15668315|ref|NP_247111.1| 102 YLKAkEKGRISKKLEKIILKAIHT 125
                                   455444444555555554444433 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.9e-05
                                   ESS-HHHHHHHHHHHTTSBHHHHHHHHHT-SST............T CS
                 Ribosomal_L22   6 lrvsfkklrevarlIrgmkveeAlkyLkfskkk............a 39 
                                   +++ +k+l + ++ +r+++ve+A+k+Lk+++k              
  gi|15668315|ref|NP_247111.1| 311 FETAIKELGQYIENVRKKEVEKAKKILKNKNKPveevledfskalC 356
                                   6788999**********************99885555555555442 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   8.7e-05     0.058       2      66 ..     156     224 ..     155     234 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.7e-05
                                   HHTS-EEEES-SHHHHHHHHHHHHTT-.-EEEEE-TT-HHHHHHHHTT...-EEEEHHHHHHT-SEEEE CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgl.dvvvglregsksvkkAkeeg...fevltvaeavkkadvvmi 66 
                                   l+gk++ +iG G  ++   + l++  +  ++v++r+ +k  k Ake g   ++  +++ea + ad+v+ 
  gi|15668315|ref|NP_247111.1| 156 LEGKNVLLIGAGEMANLVIKALKEKNIkAIIVANRTYEKAEKLAKELGgmaIKFDKLEEALRYADIVIS 224
                                   789***********************94477888989999999999763335667899********986 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   0.00018      0.12      96     166 ..     291     360 ..     286     364 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                          COQ7  96 vEtvigeHYneqlreleelee.eedkelleiikqfrddEleHldtAvendaekapaykllsaviklgcrvai 166
                                   vE  i e +++  + l +++  ++ kel ++i+++r+ E+e+++  ++n  ++ p++++l+ + k+ c+  i
  gi|15668315|ref|NP_247111.1| 291 VEMIICEELERLKEFLDKMRFeTAIKELGQYIENVRKKEVEKAKKILKN--KNKPVEEVLEDFSKALCKRII 360
                                   777777776655555555443689*********************9999..6779*************9765 PP

>> Mannitol_dh  Mannitol dehydrogenase Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00014      0.09      14     150 ..     145     298 ..     137     299 .. 0.84
   2 ?   -1.6   0.1       3.9   2.6e+03      62      88 ..     324     351 ..     306     375 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                                   HTHHHHHHHHTT--TT-EEEEEE-STTHHHHHHHTTTT-EEEEE-SSS---EEEE--EEEEEEGGG-HHHHHHHHTSTT-- CS
                   Mannitol_dh  14 ahqayiddLlaeegldwgivevnlrevdareaLkaqdelyvviekgeeskearlvgsvnavlsveedlealieamaePeir 94 
                                   a ++  ++++  eg+++ +++++++    ++aLk+++   +++++ + +k ++l +++  +  +    ++l ea+    ++
  gi|15668315|ref|NP_247111.1| 145 AAVELAEKIFGLEGKNVLLIGAGEMANLVIKALKEKNIKAIIVANRTYEKAEKLAKELGGMAIK---FDKLEEALRY--AD 220
                                   555577899999999********999999*******9999999995555555555555554444...5689999999..** PP

                                   EEEE---TTT.BETTTEB-TTSHHHHHHHH-TT.....................HHHHHHHHHHHTT----EEEE-SS CS
                   Mannitol_dh  95 ivsltvtekG.idatgeletdlpaiaadlakpe.....................llvealkrrraaglkpltiisCdn 150
                                   iv +++++   i ++++l++  + i  d+a+p+                     l++e   ++r++  ++ + i C++
  gi|15668315|ref|NP_247111.1| 221 IVISATGAPHpILNKERLKNAGKTIIIDIANPRdttddirelpdiflftiddlrLVAEENLKKRKEEIPKVEMIICEE 298
                                   *****99977788****************************************9888888888888899999999*97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.9
                                   ---EEEE--EEEEEEGGG-.HHHHHHHH CS
                   Mannitol_dh  62 skearlvgsvnavlsveed.lealieam 88 
                                   + ++++v++ +++l+ +++ +e+++e +
  gi|15668315|ref|NP_247111.1| 324 NVRKKEVEKAKKILKNKNKpVEEVLEDF 351
                                   4455566666666665555556666554 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00014      0.09       3      74 ..     166     234 ..     165     252 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                   TSHHHHHHHHHHHHC-T-EEEEEE.TTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC..H CS
                NAD_binding_10   3 tGkvGrllvkellargghevtalv.RnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk..d 74 
                                    G  + l++k l +++ ++  +++ R+ ek+++l++e     + g + + ++l+eal+ ad+V+sa+g+ +   +
  gi|15668315|ref|NP_247111.1| 166 AGEMANLVIKALKEKN-IKAIIVAnRTYEKAEKLAKE-----LGGMAIKFDKLEEALRYADIVISATGAPHPilN 234
                                   6999999**9999995.66555542778999988643.....44444556899**************99876552 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00032      0.22       2      79 ..     158     226 ..     157     250 .. 0.83
   2 ?   -2.3   0.1       6.3   4.2e+03      63      63 ..     324     324 ..     281     355 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                                   C.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE-- CS
                        OTCace   2 glkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdv 79 
                                   g+++ ++G   + +an +ik+l   +++  +va  ++e+       a+k ak+ gg     ++leea+  aD+v++ +
  gi|15668315|ref|NP_247111.1| 158 GKNVLLIGA--GEMANLVIKALKEKNIKAIIVANRTYEK-------AEKLAKELGGMAIKFDKLEEALRYADIVISAT 226
                                   788888883..5899999999999999988888888877.......7788888899999999************9865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.3
                                   S CS
                        OTCace  63 e 63 
                                   +
  gi|15668315|ref|NP_247111.1| 324 N 324
                                   1 PP

>> DUF3530  Protein of unknown function (DUF3530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00049      0.33     186     249 ..     145     205 ..     127     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00049
                       DUF3530 186 aaiaflnqrgae...nivllghgtgAywaarylaekksakvdaLvlvdarepaeaaekqLaeqlakl 249
                                   aa++++++       n++l+g g+ A ++++ l+ek++++    ++v+ r+ ++a  ++La+ l ++
  gi|15668315|ref|NP_247111.1| 145 AAVELAEKIFGLegkNVLLIGAGEMANLVIKALKEKNIKA----IIVANRTYEKA--EKLAKELGGM 205
                                   677777775333455********************77666....44555555555..5666666655 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0019       1.3       4      59 ..     162     217 ..     160     220 .. 0.78
   2 ?    1.8   0.6      0.31   2.1e+02      46     116 ..     310     387 ..     274     390 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0019
                        LpxI_N   4 liAGsGrlPllvaeaakaagrevvvvaleg.eadeelekivdevaevsvgqlgklik 59 
                                   l+ G+G+++ lv++a+k+++++ ++va +  e  e+l+k+    + +++ +l+++++
  gi|15668315|ref|NP_247111.1| 162 LLIGAGEMANLVIKALKEKNIKAIIVANRTyEKAEKLAKELG-GMAIKFDKLEEALR 217
                                   566******************999999887577777777544.56677777766665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.31
                        LpxI_N  46 vaevsvgqlgklikaLkregvtevvmaGkvekpklldlrpDlralkllak.......lkdrgddalLravveelekeG 116
                                     e  +++lg+ i+  ++++v+++  + k + + + +++ D++ +   +        +++ +d+++++ +++e++k G
  gi|15668315|ref|NP_247111.1| 310 RFETAIKELGQYIENVRKKEVEKAKKILKNKNKPVEEVLEDFSKALCKRIiydiikiFENVEDKEVFECLAKEFKKLG 387
                                   457778888889999888888887666666555555555555432222113335555556667777777777776665 PP

>> RNase_E_G  Ribonuclease E/G family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       4.1   2.7e+03     100     123 ..      11      34 ..       4      61 .. 0.65
   2 ?    2.3   0.5      0.14        94      84     126 ..     161     202 ..     104     251 .. 0.72
   3 ?   -1.1   0.0       1.5     1e+03     207     229 ..     231     253 ..     224     262 .. 0.79
   4 ?   12.7   1.5   9.3e-05     0.062      58     121 ..     310     372 ..     278     390 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.1
                     RNase_E_G 100 llnedieeivvddkelyeeikeyl 123
                                   +  +++e++ +d+++ ye+  + +
  gi|15668315|ref|NP_247111.1|  11 YNVSELEKLRMDEEKFYETFDNAI 34 
                                   555778888999999998887766 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                     RNase_E_G  84 sllyeeedlllrvlrdllnedieeivvddkelyeeikeyleev 126
                                    ll  + ++++ v++ l +++i+ i+v + ++ye++++ ++e+
  gi|15668315|ref|NP_247111.1| 161 VLLIGAGEMANLVIKALKEKNIKAIIVAN-RTYEKAEKLAKEL 202
                                   56666666666677777777777777764.3455555554443 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.5
                     RNase_E_G 207 eiarqlrLRnlgGiIviDFIdmk 229
                                    i ++ rL+n g  I+iD  + +
  gi|15668315|ref|NP_247111.1| 231 PILNKERLKNAGKTIIIDIANPR 253
                                   5777779***********87655 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 9.3e-05
                     RNase_E_G  58 elekdleelkkkweeilekakkrkapsllyeeedlllrvlrdllnedieeivvddkelyeeike 121
                                    +e+ ++el + +e++++k   +ka ++l ++++ +++vl+d++++ +++i++d  +++e++++
  gi|15668315|ref|NP_247111.1| 310 RFETAIKELGQYIENVRKKEV-EKAKKILKNKNKPVEEVLEDFSKALCKRIIYDIIKIFENVED 372
                                   566677888888888888886.899***********************************9976 PP

>> CemA  CemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.5   3.7e+03      27      63 ..      91     126 ..      80     151 .. 0.70
   2 ?    8.4   4.5    0.0028       1.8      37     130 ..     279     371 ..     269     391 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.5
                          CemA  27 knlvveplvdrflekeqaelflnkeleeealeelkef 63 
                                   ++ ++++l + +l k++++  ++k+le+ +l+ +++ 
  gi|15668315|ref|NP_247111.1|  91 EDQILGQLKNAYL-KAKEKGRISKKLEKIILKAIHTG 126
                                   5566667777777.56666777777777777776653 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0028
                          CemA  37 rflekeqaelflnkeleeealeelkefeekleleeligeapelseeeieeelkekaeelakeyreesseaiknifadlvsl 117
                                   + l+k+++e+   + +  e le+lkef +k+++e++i+e  +  e+  +++  eka+++ k+ ++  +e ++++   l+  
  gi|15668315|ref|NP_247111.1| 279 ENLKKRKEEIPKVEMIICEELERLKEFLDKMRFETAIKELGQYIENV-RKKEVEKAKKILKNKNKPVEEVLEDFSKALCKR 358
                                   45567777887888888899******************999875554.455557899999999999999999988888888 PP

                          CemA 118 iafvvllllskee 130
                                   i++ ++ ++++ e
  gi|15668315|ref|NP_247111.1| 359 IIYDIIKIFENVE 371
                                   8887777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1852  (0.103296); expected 358.6 (0.02)
Passed bias filter:                      790  (0.0440627); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 2446.34
//
Query:       gi|15668316|ref|NP_247112.1|  [L=258]
Description: hypothetical protein MJ_0144 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-09   36.2   0.0    7.4e-06   25.3   0.0    3.0  3  Dus       Dihydrouridine synthase (Dus)
     0.0073   15.6   0.2      0.013   14.7   0.2    1.4  1  DHO_dh    Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.016   15.2   0.2      0.029   14.3   0.1    1.5  1  DUF655    Protein of unknown function (DUF655)
      0.064   13.5   0.7        0.7   10.2   0.0    2.4  3  Fer4_12   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.027   1.2e+02       1      13 [.      16      28 ..      16      39 .. 0.78
   2 !   25.3   0.0   1.7e-09   7.4e-06      63     133 ..      97     165 ..      70     183 .. 0.78
   3 !    5.7   0.0    0.0015       6.9     169     216 ..     196     242 ..     187     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.027
                                  EE---TTTS-HHH CS
                           Dus  1 llaPmagvtdlpf 13
                                  +laPmag+td  f
  gi|15668316|ref|NP_247112.1| 16 VLAPMAGITDGDF 28
                                  59********866 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1.7e-09
                                   S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESES CS
                           Dus  63 sdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigi 133
                                    d +++++     a+  ad+I+lN+ C ++++t+ g+G  L+++++l+++ +++++  ++ P+ +kir+  
  gi|15668316|ref|NP_247112.1|  97 VDIDEAYDKLLTIAK-HADIIELNCHCRQPEITSLGIGQELMKNKNLLKEFLTKMK-ELNKPIFLKIRLNC 165
                                   555555555444444.8*************************************96.5899*******975 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0015
                                   G--CHHHHHHHHH-S.S-EEEESS--SHHHHHHHHHHH--SEEEESCHH CS
                           Dus 169 tadweaIkevkqavs.ipviaNGdIkdaedaqaileetGadgvmigrga 216
                                    ad ++ k + ++++   +i+N  I ++e+a+++l++   d v ++r  
  gi|15668316|ref|NP_247112.1| 196 YADMDSLKILAEEFNdKIIIGNNSIDSIEKAKEMLKY--SDFVSVARTI 242
                                   5889999999999999889******************..7777777765 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2     3e-06     0.013      82     170 ..      74     162 ..      63     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-06
                                   HHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGGESEEEEES-S..CTCC..T.SCCCGCHHHHHHHHHHHH CS
                        DHO_dh  82 ekllkrrkeqeekkelginlskakktenavddyvevvrkigpfadilelNvSs..Pntp..g.lrdlqekeelkaillkvv 157
                                   ++++++ k+  e  ++ +++++   +   +d+    + +i++ adi+elN  +  P++   g +++l ++++l +++l ++
  gi|15668316|ref|NP_247112.1|  74 SYIIEQIKKARE-SNALVSVNVRFVD---IDEAYDKLLTIAKHADIIELNCHCrqPEITslGiGQELMKNKNLLKEFLTKM 150
                                   455555555443.5567777777777...889999999**************98888774533689999999999999999 PP

                                   HHHHSSEEEEEE- CS
                        DHO_dh 158 kevskvpvlvKla 170
                                   ke + +p++ K+ 
  gi|15668316|ref|NP_247112.1| 151 KELN-KPIFLKIR 162
                                   9999.89999995 PP

>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   6.5e-06     0.029      51      93 ..     208     250 ..     107     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.5e-06
                                   -TT-EEE-SSS--SSEEEEEEE--GGGS-HHHHHHHHHHHHHH CS
                        DUF655  51 lkldevaigkgksdkivkikreisyedLtdvaraeLpdvveki 93 
                                   + +d++ ig+++ d i+k k +++y d  +var+ L+  ve i
  gi|15668316|ref|NP_247112.1| 208 EFNDKIIIGNNSIDSIEKAKEMLKYSDFVSVARTILKGNVEWI 250
                                   3789******************************999888754 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00016       0.7      53     119 ..      35      96 ..      24     116 .. 0.79
   2 ?    1.4   0.1     0.078   3.5e+02      47      83 ..     118     154 ..      99     172 .. 0.66
   3 ?   -2.8   0.0       1.6   7.2e+03      97     113 ..     221     235 ..     202     248 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00016
                       Fer4_12  53 iegltllGGEPllpenaeallelvkevkeekpekdiwlytgytleelskkekeellkeidvlvdGkf 119
                                    + ++ +GG  l  + ++a  ++ k+ ++e++  +  +++ y++e+++k++ ++ l    v v ++f
  gi|15668316|ref|NP_247112.1|  35 LFAIVTIGGYNLDSATYKASRDIEKRGRKEFS-INLEEFNSYIIEQIKKARESNAL----VSVNVRF 96 
                                   4789999******99****************9.89************987444444....3444444 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.078
                       Fer4_12  47 dlkkesiegltllG.GEPllpenaeallelvkevkeek 83 
                                      + +++++t lG G  l+ +n++ l e++ ++ke +
  gi|15668316|ref|NP_247112.1| 118 LNCHCRQPEITSLGiGQELM-KNKNLLKEFLTKMKELN 154
                                   43344555666665555555.56666777777666654 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.6
                       Fer4_12  97 eelskkekeellkeidv 113
                                   + ++  + +e+lk+ d+
  gi|15668316|ref|NP_247112.1| 221 DSIE--KAKEMLKYSDF 235
                                   3333..34666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1674.13
//
Query:       gi|15668317|ref|NP_247113.1|  [L=268]
Description: GTP cyclohydrolase III [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.2e-129  428.3   0.3   8.2e-129  428.1   0.3    1.0  1  GCH_III   GTP cyclohydrolase III
     0.0086   15.8   0.0      0.014   15.2   0.0    1.3  1  RQC       RQC domain
     0.0097   16.2   0.0        5.5    7.3   0.0    2.2  2  GGDEF_2   GGDEF-like domain
  ------ inclusion threshold ------
      0.054   13.5   0.2       0.09   12.8   0.2    1.3  1  Nyv1_N    Vacuolar R-SNARE Nyv1 N terminal


Domain annotation for each model (and alignments):
>> GCH_III  GTP cyclohydrolase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.1   0.3  1.8e-132  8.2e-129       2     246 .]       5     250 ..       1     250 [. 0.99

  Alignments for each domain:
  == domain 1  score: 428.1 bits;  conditional E-value: 1.8e-132
                                   EEEEETTHHHHCCSSS---HHHHHHHHHHHHHHHHHHHHTTT-EEE-TTSSEEEEE-TT--HHHHHHHHHHHHHHSSS-EE CS
                       GCH_III   2 tviqidnYgpWtvepaprreadlqalqarlyadlqkelaardGlvfatRfDnllaitngidleehkRiqesirnrypvtvs 82 
                                   tviqidnYgpWtv+p+prre+dlqalq+rlyadl+ +++a++Glvf+tRfDnl+aitngidl++hkRiqesirnryp+tvs
  gi|15668317|ref|NP_247113.1|   5 TVIQIDNYGPWTVTPNPRRESDLQALQSRLYADLNLMFGAHKGLVFYTRFDNLIAITNGIDLITHKRIQESIRNRYPFTVS 85 
                                   9******************************************************************************** PP

                                   EEEEEESSHHHHHHHHHHHHHHH--TT-TT----EEE.S---SS--EEEEEEEETTHHHHTTTTS-HHHHHHHHHHHHHHH CS
                       GCH_III  83 mgigaaetPldaleaaseaLreagsaqdeeRkevlsv.delvtegyvqiahiDinnitgtltdivsavrtylevnkvkakl 162
                                   m+i++aetP++a++ a+e+L+e+gsaqde+Rkevl+v +elv++gyvqiahiDinnitgtltdivsa++tyl+vnkvk++l
  gi|15668317|ref|NP_247113.1|  86 MVIASAETPYEAQKLATETLQEYGSAQDENRKEVLDVaNELVVDGYVQIAHIDINNITGTLTDIVSAYDTYLNVNKVKLAL 166
                                   ********************************************************************************* PP

                                   HHHHHTTT---EEEETTEEEEE-TT--HHHHHHHHHHHHHHHS--EEEEEEEESSHHHHHHHHHHHHHHHHTTSSSSSEEE CS
                       GCH_III 163 akklekegallqfiGGDnilavcneleeedvldiinevkekvdvdlkaGiGiadtaedaaaladeaLeeiRgklvegplvv 243
                                   +++l k++all+fiGGDn++a++n+++eed+ldi+n++++k++++lkaGiGi++taeda++lad++Le+iRgklv++++++
  gi|15668317|ref|NP_247113.1| 167 MEELLKYNALLFFIGGDNFMAPSNGMSEEDFLDIFNRINKKYKIELKAGIGIGRTAEDASNLADIGLEKIRGKLVDKNVCT 247
                                   ********************************************************************************* PP

                                   EET CS
                       GCH_III 244 akq 246
                                   +kq
  gi|15668317|ref|NP_247113.1| 248 LKQ 250
                                   997 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.1e-06     0.014      43      83 ..      98     142 ..      77     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-06
                                   CCTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEE......S CS
                           RQC  43 rqlghdklstfGigkdlskkewrrlirqLiaegyLeedve....e 83 
                                   ++l  ++l+ +G+ +d ++ke+ +++++L+ +gy++  +      
  gi|15668317|ref|NP_247113.1|  98 QKLATETLQEYGSAQDENRKEVLDVANELVVDGYVQIAHIdinnI 142
                                   5567789****************************5544333353 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0012       5.5      35      95 ..      24      90 ..       2     104 .. 0.67
   2 !    6.9   0.0    0.0016       7.2      51     104 ..     175     229 ..     130     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0012
                       GGDEF_2 35 erllraleeal.ralg......pdalvavrgdrlvlllpaedeedaeallerlarrlgglsvriGiGs 95
                                  e+ l+al++ l ++l+      ++ ++ +r d+l+++  + d  + ++++e +++r++  +v++ i s
  gi|15668317|ref|NP_247113.1| 24 ESDLQALQSRLyADLNlmfgahKGLVFYTRFDNLIAITNGIDLITHKRIQESIRNRYPF-TVSMVIAS 90
                                  3333333333322222222332666667899***************************9.99999876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0016
                       GGDEF_2  51 dalvavrgdrlvlllpaedeedaeallerlarrlgg.lsvriGiGspveglaglr 104
                                     l+++ gd++ +   + +eed  ++ +r+ ++++  l++ iGiG+++e++++l+
  gi|15668317|ref|NP_247113.1| 175 ALLFFIGGDNFMAPSNGMSEEDFLDIFNRINKKYKIeLKAGIGIGRTAEDASNLA 229
                                   567778888888888888888888************99999********999886 PP

>> Nyv1_N  Vacuolar R-SNARE Nyv1 N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2     2e-05      0.09      20      81 ..     101     161 ..      85     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                        Nyv1_N  20 keekessYgsiseedkaatkkvfhkLikdlvlpkvvkveGnkvtkvslklidGydcyYttsd 81 
                                   ++e+ ++Ygs ++e++++  +v ++L+ d  + ++ +++ n +t + ++++  yd+y   ++
  gi|15668317|ref|NP_247113.1| 101 ATETLQEYGSAQDENRKEVLDVANELVVDGYV-QIAHIDINNITGTLTDIVSAYDTYLNVNK 161
                                   4556699******9999999999999999877.699*********************88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1823.32
//
Query:       gi|15668318|ref|NP_247114.1|  [L=69]
Description: 2-ketoglutarate ferredoxin oxidoreductase subunit delta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-13   47.9  15.2    2.9e-07   30.0   2.5    2.1  2  Fer4      4Fe-4S binding domain
    1.7e-10   40.5  15.2    3.5e-05   23.7   4.0    2.1  2  Fer4_6    4Fe-4S binding domain
    5.2e-10   39.8   8.3    6.2e-10   39.5   8.3    1.1  1  Fer4_7    4Fe-4S dicluster domain
    2.8e-08   33.8   7.3    4.8e-08   33.0   7.3    1.4  1  Fer4_9    4Fe-4S dicluster domain
    7.1e-08   33.3   9.5     0.0013   19.6   0.8    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    8.7e-08   31.8  13.7    0.00013   21.9   1.9    2.1  2  Fer4_2    4Fe-4S binding domain
    9.5e-08   32.0  23.8    2.5e-06   27.5  12.2    1.7  2  Fer4_10   4Fe-4S dicluster domain
    1.1e-07   31.8  14.2     0.0039   17.3   3.3    2.0  1  Fer4_21   4Fe-4S dicluster domain
    0.00032   21.2   8.7       0.11   13.0   0.4    2.1  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0016   19.0  11.4      0.055   14.0  11.4    2.0  1  Fer4_17   4Fe-4S dicluster domain
     0.0017   18.7  13.3       0.12   13.0   3.7    2.2  2  Fer4_4    4Fe-4S binding domain
     0.0094   16.1   7.4      0.048   13.8   7.4    1.8  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
     0.0095   16.8  16.2       0.44   11.6   3.7    2.2  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.011   16.5   8.7       0.23   12.2   0.5    2.4  2  Fer4_15   4Fe-4S single cluster domain
      0.031   15.1   6.4        1.3    9.9   1.7    2.1  2  Fer4_22   4Fe-4S dicluster domain
      0.071   13.6  13.2       0.55   10.7   3.6    2.1  2  Fer4_8    4Fe-4S dicluster domain
       0.45   10.7  12.6        1.2    9.3   2.9    2.1  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   5.0   2.2e-08   2.3e-05       1      23 [.       3      25 ..       3      26 .. 0.92
   2 !   30.0   2.5   2.8e-10   2.9e-07       1      24 []      40      63 ..      40      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.2e-08
                                  EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                  ++i+e+ C gC +C+ vCP g+ 
  gi|15668318|ref|NP_247114.1|  3 IEINENFCKGCDICIVVCPRGVF 25
                                  689****************9985 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 2.8e-10
                                  EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                  + +++ekC++C++C+  CP  AI+
  gi|15668318|ref|NP_247114.1| 40 IPVNPEKCTKCNLCILQCPDQAIS 63
                                  579*******************96 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   4.0   3.3e-08   3.5e-05       1      23 [.       2      24 ..       2      25 .. 0.93
   2 !   22.8   3.4   6.3e-08   6.7e-05       4      24 .]      42      62 ..      41      62 .. 0.97

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.3e-08
                        Fer4_6  1 vveidpdkCigCgdCvrvCPega 23
                                  ++ei+++ C gC+ C++vCP g+
  gi|15668318|ref|NP_247114.1|  2 KIEINENFCKGCDICIVVCPRGV 24
                                  69******************886 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 6.3e-08
                        Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                  ++p+kC+ C+ C+  CP +ai
  gi|15668318|ref|NP_247114.1| 42 VNPEKCTKCNLCILQCPDQAI 62
                                  79******************8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   8.3   5.9e-13   6.2e-10       2      52 .]      10      61 ..       9      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 5.9e-13
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgt.ekveidpekClgCgaCvavCPtga 52
                                  C gC  C ++Cp +++e  ++ n+kg+ + + ++pekC+ C+ C+  CP +a
  gi|15668318|ref|NP_247114.1| 10 CKGCDICIVVCPRGVFEKSKKLNKKGIyPPIPVNPEKCTKCNLCILQCPDQA 61
                                  *************************99788899****************876 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   7.3   4.6e-11   4.8e-08       2      51 .]      10      62 ..       9      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.6e-11
                        Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase...eaCigCgaCveaCpkgai 51
                                  C gC+ C+ +Cp gv++++++ +k  +        e+C++C+ C+  Cp +ai
  gi|15668318|ref|NP_247114.1| 10 CKGCDICIVVCPRGVFEKSKKLNKKGIYPPIPvnpEKCTKCNLCILQCPDQAI 62
                                  ****************88777666665444337889**************997 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.8   1.3e-06    0.0013       1      25 [.       9      31 ..       9      38 .. 0.84
   2 !   18.5   2.3   2.8e-06    0.0029       1      19 [.      46      64 ..      46      69 .] 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-06
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkekei 25
                                  +C++C  C+ vCP +++++   k++
  gi|15668318|ref|NP_247114.1|  9 FCKGCDICIVVCPRGVFEKS--KKL 31
                                  6***************9998..444 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.8e-06
                       Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                  +C++C+ C+  CP +ai+ 
  gi|15668318|ref|NP_247114.1| 46 KCTKCNLCILQCPDQAISI 64
                                  6****************85 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.9   1.2e-07   0.00013       2      21 ..       2      21 ..       1      22 [. 0.93
   2 !   15.7   4.4   1.1e-05     0.011       1      21 [.      38      58 ..      38      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-07
                        Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                  +++++++ C gC +C+ +CP
  gi|15668318|ref|NP_247114.1|  2 KIEINENFCKGCDICIVVCP 21
                                  5899**************** PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.1e-05
                        Fer4_2  1 apvvvdtdrCigCgaCvsaCP 21
                                  +p+ v++++C+ C+ C+  CP
  gi|15668318|ref|NP_247114.1| 38 PPIPVNPEKCTKCNLCILQCP 58
                                  57889***************9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5  12.2   2.4e-09   2.5e-06       1      56 []       2      58 ..       2      58 .. 0.90
   2 !   15.7   3.7   1.1e-05     0.012       4      21 ..      42      59 ..      39      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.4e-09
                       Fer4_10  1 kvvidddtCirCgkCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  k++i+++ C +C  C  +CP  + +++++ +++ +  ++ +++ekCt+c  C+ +CP
  gi|15668318|ref|NP_247114.1|  2 KIEINENFCKGCDICIVVCPRGVfEKSKKLNKKGIYPPIPVNPEKCTKCNLCILQCP 58
                                  5899*****************88877777777777888899***************9 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.1e-05
                       Fer4_10  4 idddtCirCgkCvkaCPa 21
                                  +++++C++C+ C   CP 
  gi|15668318|ref|NP_247114.1| 42 VNPEKCTKCNLCILQCPD 59
                                  578999999999999997 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   3.3   3.7e-06    0.0039      35      52 ..       4      21 ..       1      27 [. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.7e-06
                       Fer4_21 35 kvvedeCvGCnlCssvCP 52
                                  ++ e+ C GC++C+ vCP
  gi|15668318|ref|NP_247114.1|  4 EINENFCKGCDICIVVCP 21
                                  677899************ PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.4   0.00011      0.11       1      25 [.       5      30 ..       5      38 .. 0.82
   2 !   12.1   2.6    0.0002      0.21       1      18 [.      42      59 ..      42      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                       Fer4_13  1 VDrdtCiacgaCvelaPd.vFeedde 25
                                  ++++ C +c++C  ++P  vFe  ++
  gi|15668318|ref|NP_247114.1|  5 INENFCKGCDICIVVCPRgVFEKSKK 30
                                  67889************768888776 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0002
                       Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                  V+ ++C+ c++C   +Pd
  gi|15668318|ref|NP_247114.1| 42 VNPEKCTKCNLCILQCPD 59
                                  899**************8 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0  11.4   5.2e-05     0.055       1      58 [.       9      59 ..       9      62 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.2e-05
                       Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58
                                  +C +C  C+ +Cp++   ++  kkl ++   g+        + ++C++C++C  +CP 
  gi|15668318|ref|NP_247114.1|  9 FCKGCDICIVVCPRGVFEKS--KKLNKK---GIYPP--IPVNPEKCTKCNLCILQCPD 59
                                  6*************998666..444444...22222..2457899************7 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   2.1   0.00036      0.38       4      16 ..      10      22 ..       6      29 .. 0.91
   2 !   13.0   3.7   0.00011      0.12       1      17 []      44      60 ..      44      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                        Fer4_4  4 CigCgsCvaaCPq 16
                                  C gC+ C+ +CP 
  gi|15668318|ref|NP_247114.1| 10 CKGCDICIVVCPR 22
                                  9***********6 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00011
                        Fer4_4  1 qerCigCgsCvaaCPqg 17
                                  +e+C+ C  C+  CP++
  gi|15668318|ref|NP_247114.1| 44 PEKCTKCNLCILQCPDQ 60
                                  69*************86 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   7.4   4.6e-05     0.048      36      92 ..       6      64 ..       1      68 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                                  HTHHHHHS-THHHH-TTS-EEEEETT..TTSSEEEEE-CCC--S--HHHHH-TT--EEE CS
                        ETF_QO 36 kvnlekyagpeqryCPagvyeivede..eakekklqinaqnCvhCktCdikdpsqniew 92
                                  ++n+ k  +++  +CP gv+e  ++   +   + + +n + C  C+ C ++ p+q i+ 
  gi|15668318|ref|NP_247114.1|  6 NENFCKGCDICIVVCPRGVFEKSKKLnkKGIYPPIPVNPEKCTKCNLCILQCPDQAISI 64
                                  55555555677789*******999761144567899*******************9986 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   4.7   0.00056      0.59       1      14 [.      10      23 ..      10      24 .. 0.94
   2 !   11.6   3.7   0.00041      0.44       1      12 [.      47      58 ..      47      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00056
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C gC  C +vCP g
  gi|15668318|ref|NP_247114.1| 10 CKGCDICIVVCPRG 23
                                  99**********98 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00041
                        Fer4_3  1 CtgCgaCvevCP 12
                                  Ct C++C   CP
  gi|15668318|ref|NP_247114.1| 47 CTKCNLCILQCP 58
                                  ***********9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   0.00022      0.23       1      25 [.       3      28 ..       3      35 .. 0.80
   2 ?    8.1   2.1    0.0042       4.4       3      20 ..      42      59 ..      40      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                       Fer4_15  1 VvvDrdaCigcglCvaeape.vfeld 25
                                  ++++++ C gc  C+ ++p+ vfe+ 
  gi|15668318|ref|NP_247114.1|  3 IEINENFCKGCDICIVVCPRgVFEKS 28
                                  7899999***********75266655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0042
                       Fer4_15  3 vDrdaCigcglCvaeape 20
                                  v+ ++C+ c+lC+  +p+
  gi|15668318|ref|NP_247114.1| 42 VNPEKCTKCNLCILQCPD 59
                                  7789************97 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.7    0.0012       1.3      76      95 ..       4      23 ..       1      24 [. 0.84
   2 ?    8.3   0.2    0.0039       4.1      80      94 ..      45      59 ..      26      62 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                       Fer4_22 76 kfgesgCvGCgRCieacpvk 95
                                  +++e+ C GC  Ci +cp +
  gi|15668318|ref|NP_247114.1|  4 EINENFCKGCDICIVVCPRG 23
                                  568899***********976 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0039
                       Fer4_22 80 sgCvGCgRCieacpv 94
                                  ++C+ C+ Ci +cp 
  gi|15668318|ref|NP_247114.1| 45 EKCTKCNLCILQCPD 59
                                  566666666666664 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.1    0.0026       2.7      51      65 .]      10      24 ..       5      24 .. 0.86
   2 ?   10.7   3.6   0.00052      0.55      49      62 ..      45      58 ..      25      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0026
                        Fer4_8 51 CttcgaCtevCpvgi 65
                                  C +c  C +vCp g+
  gi|15668318|ref|NP_247114.1| 10 CKGCDICIVVCPRGV 24
                                  999999999999876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00052
                        Fer4_8 49 wsCttcgaCtevCp 62
                                  ++Ct c+ C  +Cp
  gi|15668318|ref|NP_247114.1| 45 EKCTKCNLCILQCP 58
                                  56777777777777 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.9    0.0012       1.2      58      75 ..       7      24 ..       2      36 .. 0.85
   2 ?    8.1   1.9    0.0028       2.9      59      73 ..      45      59 ..      25      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                       Fer4_18 58 agdcidcescvkvcPtgi 75
                                  ++ c  c+ c+ vcP g+
  gi|15668318|ref|NP_247114.1|  7 ENFCKGCDICIVVCPRGV 24
                                  56699**********997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0028
                       Fer4_18 59 gdcidcescvkvcPt 73
                                   +c++c+ c+  cP 
  gi|15668318|ref|NP_247114.1| 45 EKCTKCNLCILQCPD 59
                                  68***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 477.60
//
Query:       gi|15668319|ref|NP_247115.1|  [L=371]
Description: hypothetical protein MJ_0147 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.8e-89  298.6   9.3    3.8e-89  298.6   9.3    1.8  2  ATPase_2    ATPase domain predominantly from Archaea
    1.2e-11   45.3   0.0    3.1e-11   43.9   0.0    1.7  2  AAA_16      AAA ATPase domain
    1.8e-09   37.7  14.7    5.8e-05   23.1   0.2    3.5  4  AAA_14      AAA domain
    2.8e-05   24.4   0.1    0.00015   22.1   0.0    2.2  2  AAA_22      AAA domain
    0.00017   22.0   1.4      0.016   15.7   0.0    3.0  2  AAA         ATPase family associated with various cellular ac
    0.00037   19.4   2.5      0.011   14.6   0.6    2.8  2  AAA_35      AAA-like domain
     0.0073   15.8   0.0      0.017   14.6   0.0    1.6  1  AAA_7       P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.011   15.2   0.2      0.098   12.1   0.2    2.0  1  Elong_Iki1  Elongator subunit Iki1
      0.023   14.3   0.0      0.043   13.4   0.0    1.5  1  cobW        CobW/HypB/UreG, nucleotide-binding domain
      0.024   14.5   0.2       0.12   12.3   0.1    2.2  2  TK          Thymidine kinase
      0.041   14.2   3.6       0.14   12.5   1.7    2.6  2  DUF5497     Family of unknown function (DUF5497)
      0.096   13.0   0.8       0.53   10.6   0.2    2.4  2  AAA_19      AAA domain
       0.11   12.5   0.0       0.25   11.4   0.0    1.6  1  TsaE        Threonylcarbamoyl adenosine biosynthesis protein 
       0.15   12.4   0.8       0.56   10.6   0.5    2.2  2  zf-CCCH_7   Chromatin remodeling factor Mit1 C-terminal Zn fi
       0.17   10.6   2.4       0.29    9.8   2.4    1.5  1  MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family
        3.3    8.2  12.3    1.2e+02    3.1  12.2    2.8  1  AAA_23      AAA domain


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.6   9.3   3.4e-92   3.8e-89       1     233 []       7     260 ..       7     260 .. 0.98
   2 ?   -0.9   0.2       1.1   1.2e+03     197     220 ..     312     335 ..     267     341 .. 0.65

  Alignments for each domain:
  == domain 1  score: 298.6 bits;  conditional E-value: 3.4e-92
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...eeeekkkl 78 
                                   Ff+Reke+ e+++ile epn iyfiYGp +sGKtaL+k+iien+++ d+y+++yi++r++ is+++efie   ++++++++
  gi|15668319|ref|NP_247115.1|   7 FFNREKEIHEILSILEGEPNIIYFIYGPLNSGKTALIKHIIENKLS-DDYKVFYINFRTYLISEKREFIEaifTTKKDDFF 86 
                                   9*******************************************77.668***********************99999999 PP

                      ATPase_2  79 ekal.................giavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellv 142
                                   ek +                 gi++p++e++++++ek++++f++++++l ++kk+gk++++i+Delq+++d+ ln +++l+
  gi|15668319|ref|NP_247115.1|  87 EKIKdksevlnlitkgakiltGIPIPEVEFDKLFEEKINDAFQYLNSILLEVKKSGKQPVLILDELQMIKDVVLNWQKYLL 167
                                   9999***************************************************************************** PP

                      ATPase_2 143 keLlnliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkel..eelskedfeeiyr 221
                                   keL+++++sltke+hlc+v+clsS++lfie+vy+ +elegr+ky+lvdd+dketal+f+++++ke+  ++ls+ed+e+iy+
  gi|15668319|ref|NP_247115.1| 168 KELFQFLVSLTKEQHLCHVFCLSSDSLFIEYVYSAGELEGRAKYLLVDDFDKETALKFMDFLAKEIlnKKLSDEDKELIYN 248
                                   ******************************************************************87777********** PP

                      ATPase_2 222 yvGGkPkalvel 233
                                   yvGGkP +++ +
  gi|15668319|ref|NP_247115.1| 249 YVGGKPVYIYSV 260
                                   ********9875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                      ATPase_2 197 alnflkegfkeleelskedf.eeiy 220
                                   + n lk +fke++e s++d+ e +y
  gi|15668319|ref|NP_247115.1| 312 IINALK-LFKENYEVSDDDIpEPVY 335
                                   344333.467777777777655555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   2.8e-14   3.1e-11       1     163 [.       6     179 ..       6     187 .. 0.79
   2 ?   -2.0   0.0       3.6     4e+03     138     159 ..     211     230 ..     195     247 .. 0.71

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 2.8e-14
                        AAA_16   1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellr.alekdg.giflrgkcdqlesaipysalaqalar 78 
                                   +++ Re+e++++ls+le    g+p  + +++G+  +GK++l++++ +  l++d+ +++++ ++   +++++++  + + ++
  gi|15668319|ref|NP_247115.1|   6 KFFNREKEIHEILSILE----GEPnIIYFIYGPLNSGKTALIKHIIEnKLSDDYkVFYINFRTYLISEKREFIEAIFTTKK 82 
                                   6899**********999....88866789*************999974777775355577777777999999997777779 PP

                        AAA_16  79 eellrqlldeaesaeleawrekleealaavpelagaea.....srllellkrllallsrderplvlvlDdlq........w 146
                                   ++++++++d++e  +l    +k+++ +  +pe++ ++      ++ ++ l+++l   ++ +++ vl+lD+lq        w
  gi|15668319|ref|NP_247115.1|  83 DDFFEKIKDKSEVLNLITKGAKILTGIP-IPEVEFDKLfeekiNDAFQYLNSILLEVKKSGKQPVLILDELQmikdvvlnW 162
                                   9*********999999999999998888.7888888878877799999999999666676888*********666666666 PP

                        AAA_16 147 adeaslqllaaLlrlle 163
                                    +    +l+++L++l++
  gi|15668319|ref|NP_247115.1| 163 QKYLLKELFQFLVSLTK 179
                                   66666666666666555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.6
                        AAA_16 138 vlvlDdlqwadeaslqllaaLl 159
                                   +l++Dd++  +e+ l+++++L+
  gi|15668319|ref|NP_247115.1| 211 YLLVDDFD--KETALKFMDFLA 230
                                   78899999..444455555554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   5.1e-08   5.8e-05       4      58 ..      28      80 ..      25      99 .. 0.78
   2 !   20.7   0.5   2.9e-07   0.00032      33     120 ..     111     212 ..      92     223 .. 0.80
   3 ?    2.4   0.9      0.13   1.5e+02      37      96 ..     227     287 ..     209     290 .. 0.54
   4 ?    0.9   2.7      0.37   4.2e+02      31      77 ..     262     308 ..     228     330 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.1e-08
                        AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelile 58
                                  i++i G+  +GKT l+k++i+++l ++ +++yin+ +   ++++++  ++ ++  
  gi|15668319|ref|NP_247115.1| 28 IYFIYGPLNSGKTALIKHIIENKLSDDYKVFYINFRTYLISEKREF--IEAIFTT 80
                                  899*********************9************999888866..3333333 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.9e-07
                        AAA_14  33 ilyinldderdkklad.pekllelileklkeekktylflDEiqev............pewekalkslvdegknldvivtGS 100
                                   i ++++d+  ++k++d ++ l++++le  k+ k+ +l+lDE q++            +e++++l sl +e++ ++v++  S
  gi|15668319|ref|NP_247115.1| 111 IPEVEFDKLFEEKINDaFQYLNSILLEVKKSGKQPVLILDELQMIkdvvlnwqkyllKELFQFLVSLTKEQHLCHVFCLSS 191
                                   567888887777766525456666666533468999***********************************99******** PP

                        AAA_14 101 nskllsk.eiatslagrvaei 120
                                    s+++     a +l gr++++
  gi|15668319|ref|NP_247115.1| 192 DSLFIEYvYSAGELEGRAKYL 212
                                   **9998745667888888766 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.13
                        AAA_14  37 nldderdkkladpekllelileklke.ekktylflDEiqevpewekalkslvdeg.knldvi 96 
                                   ++  ++  +++ +++  eli + + + +   y ++DE+ +++++e++l+ +++e+ ++l+++
  gi|15668319|ref|NP_247115.1| 227 DFLAKEILNKKLSDEDKELIYNYVGGkPVYIYSVIDEM-RYRKLEDILNLMLKEEtQKLKYF 287
                                   33333333333222334444444322234456899998.56889999998888765666665 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.37
                        AAA_14  31 esilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                   +++ y +l+d  + +l+++++ l+++l++l   k ++ + DEi e++
  gi|15668319|ref|NP_247115.1| 262 DEMRYRKLEDILNLMLKEETQKLKYFLKELDYIKPKVELKDEIIEIK 308
                                   34446666666666655555556666666322355666667776664 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.3e-07   0.00015       7     127 ..      28     187 ..      24     196 .. 0.66
   2 ?   -2.1   0.0       3.9   4.3e+03      90     117 ..     207     235 ..     187     246 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-07
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsstsskdllrellralglelka... 70 
                                   i +++G+  +GKT l++ + e++  +    +              e++e  f+++   t+ +d+++++  + ++ +     
  gi|15668319|ref|NP_247115.1|  28 IYFIYGPLNSGKTALIKHIIENKLSD----DykvfyinfrtylisEKRE--FIEAIFTTKKDDFFEKIKDKSEVLNLItkg 102
                                   6789*****************98654....2344476544444333333..555555556677777777777654444888 PP

                        AAA_22  71 ....................erlsseellealeqalraravielliiDEaqhlrs...........eealeeLrsllnlsr 120
                                                       + ++  ++l+ +   +++ +++++li+DE q + +           +e++++L+sl +  +
  gi|15668319|ref|NP_247115.1| 103 akiltgipipevefdklfeeKINDAFQYLNSILLEVKKSGKQPVLILDELQMI-KdvvlnwqkyllKELFQFLVSLTK--E 180
                                   999******888888886555555555555555555555559***********.623333445666666666666666..6 PP

                        AAA_22 121 kgvqliL 127
                                   +++ +++
  gi|15668319|ref|NP_247115.1| 181 QHLCHVF 187
                                   5555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.9
                        AAA_22  90 avielliiDEaqh.lrseealeeL.rslln 117
                                   ++ + l++D++++     + + +L +++ln
  gi|15668319|ref|NP_247115.1| 207 GRAKYLLVDDFDKeT-ALKFMDFLaKEILN 235
                                   334578888888733.45555555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.4e-05     0.016       3      70 ..      31     155 ..      29     197 .. 0.56
   2 ?   -0.8   0.3       1.7   1.9e+03      34      50 ..     272     288 ..     206     331 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                                   EESSTTSSHHHHHHHHHHH.....HTHEEEEEETTTCS.SS........................................ CS
                           AAA   3 lyGppGtGKTllakavake.....lgvefleisgsell.sk........................................ 37 
                                   +yGp   GKT+l+k ++++        +++ i+  + l s+                                        
  gi|15668319|ref|NP_247115.1|  31 IYGPLNSGKTALIKHIIENklsddY--KVFYINFRTYLiSEkrefieaifttkkddffekikdksevlnlitkgakiltgi 109
                                   8****************99543331..334444333332222333444444444444444777777777777777777777 PP

                                   .............STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGH CS
                           AAA  38 .............yvgesekkirelfkeakekakpsilfiDEidal 70 
                                                 + ++ + ++ ++ e+k++ k+ +l++DE+  +
  gi|15668319|ref|NP_247115.1| 110 pipevefdklfeeKINDAFQYLNSILLEVKKSGKQPVLILDELQMI 155
                                   7777773332222444444444444444444446699999998777 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                                   CSSSSTTHHHHHHHHHH CS
                           AAA  34 llskyvgesekkirelf 50 
                                   +l+ +++e  +k++ ++
  gi|15668319|ref|NP_247115.1| 272 ILNLMLKEETQKLKYFL 288
                                   22223333333333333 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.6   9.5e-06     0.011      35     139 ..      30     155 ..       6     182 .. 0.65
   2 ?    3.1   0.1     0.032        36     216     282 ..     237     305 ..     215     322 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.5e-06
                        AAA_35  35 rikapkkmGKtSLlarilakakqqgyktvsldlql........adkeils.dldkflrwfcanvsrqLklenkl....... 99 
                                    i +p + GKt L+++i++++ + +yk++++++++        + ++i++ + d f++++  + s+ L+l +k        
  gi|15668319|ref|NP_247115.1|  30 FIYGPLNSGKTALIKHIIENKLSDDYKVFYINFRTylisekreFIEAIFTtKKDDFFEKIKDK-SEVLNLITKGakiltgi 109
                                   5889*****************************862221111123334331334455555332.33344432112335666 PP

                        AAA_35 100 ...deyWdeelgskvs.ctayleeylLkeid..kplvLaldevdrl 139
                                      + ++d+ ++ k++ + +yl+++lL+  +  k  vL+lde++ +
  gi|15668319|ref|NP_247115.1| 110 pipEVEFDKLFEEKINdAFQYLNSILLEVKKsgKQPVLILDELQMI 155
                                   6666777887777765255788888876543225567778887765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.032
                        AAA_35 216 elsekqleqLmslvgGhPylvrlalyhlaqeelt..leelleeaateegiYsdhLrrllvkLqekpeLa 282
                                   +ls+++ e +++ vgG+P  +   ++++  ++l+  l+ +l+e +++ + + + L     k++ k e++
  gi|15668319|ref|NP_247115.1| 237 KLSDEDKELIYNYVGGKPVYIYSVIDEMRYRKLEdiLNLMLKEETQKLKYFLKELDYIKPKVELKDEII 305
                                   566666788899**************9998876443555556555555555555555444444444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.5e-05     0.017      37      94 ..      30      86 ..      19      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                         AAA_7 37 llvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvy 94
                                  +++Gp  +GKt++ik+++++  +++y++  inf  +  +++ +++ie+ +  ++ + +
  gi|15668319|ref|NP_247115.1| 30 FIYGPLNSGKTALIKHIIENKLSDDYKVFYINFRTYLISEK-REFIEAIFTTKKDDFF 86
                                  578*************7766666***********9988876.5677777666666655 PP

>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   8.7e-05     0.098      27     154 ..      40     235 ..      26     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.7e-05
                    Elong_Iki1  27 kplleelirrakssktkvifvsfetlkk.............................................pkgvdvfi 62 
                                   + l++++i++  s++ kv +++f+t                                                  + d++ 
  gi|15668319|ref|NP_247115.1|  40 TALIKHIIENKLSDDYKVFYINFRTYLIsekrefieaifttkkddffekikdksevlnlitkgakiltgipipEVEFDKLF 120
                                   679999**99999**********9654434466666677666677777777777777777666666555543222333333 PP

                    Elong_Iki1  63 eaterskklkelakeiksalspkssekk......kkalviiDslnplas......likeeslaaflssllsspsvslvavY 131
                                   e      k+++  + ++s l              k+ ++i+D l+++            ++l +fl sl+++++   v ++
  gi|15668319|ref|NP_247115.1| 121 EE-----KINDAFQYLNSIL-------LevkksgKQPVLILDELQMIKDvvlnwqKYLLKELFQFLVSLTKEQHLCHVFCL 189
                                   33.....3333333333333.......033333488999******87779998773356899********99999999999 PP

                    Elong_Iki1 132 Htdv.......................eyapspltlLkylAttilt 154
                                    +d                          + ++l+++++lA+ il+
  gi|15668319|ref|NP_247115.1| 190 SSDSlfieyvysagelegrakyllvddFDKETALKFMDFLAKEILN 235
                                   9999999999999999999999999988888999999999999886 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.9e-05     0.043       3      31 ..      29      57 ..      27      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.9e-05
                                  EEEEESTTCCHHHHHHHHHCT--SS-EEE CS
                          cobW  3 tvltGflGsGKTtLlnhllenraglklav 31
                                  + + G+l sGKT+L++h++en+ + ++ v
  gi|15668319|ref|NP_247115.1| 29 YFIYGPLNSGKTALIKHIIENKLSDDYKV 57
                                  6799***************8876666555 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1    0.0001      0.12       3      37 ..      28      62 ..      26     132 .. 0.63
   2 ?   -1.0   0.0       1.2   1.4e+03      64      94 ..     129     159 ..     114     175 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                            TK  3 ielilgpmfaGKsteLlrrvkryqlaekkvvvika 37
                                  i++i+gp+++GK++ + + +++    ++kv  i  
  gi|15668319|ref|NP_247115.1| 28 IYFIYGPLNSGKTALIKHIIENKLSDDYKVFYINF 62
                                  89**********98777777777777888877653 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                            TK  64 ssleeikeeleee.dvdvvlvDEaqFfeqdiv 94 
                                   + l++i  e++++ +  v+++DE q ++ d+v
  gi|15668319|ref|NP_247115.1| 129 QYLNSILLEVKKSgKQPVLILDELQMIK-DVV 159
                                   444444444444313467788**99999.654 PP

>> DUF5497  Family of unknown function (DUF5497)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.79   8.9e+02      33      60 ..     197     224 ..     175     245 .. 0.80
   2 ?   12.5   1.7   0.00013      0.14      18      87 ..     275     346 ..     263     348 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.79
                       DUF5497  33 eyanlemqieeeikyievddgeeintik 60 
                                   ey     ++e   ky+ vdd ++  ++k
  gi|15668319|ref|NP_247115.1| 197 EYVYSAGELEGRAKYLLVDDFDKETALK 224
                                   5666666788889999999987666555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00013
                       DUF5497  18 fkigevaqrlnyylqeyanlemqieeeikyievddgeeintiktfllnsmstseq..rdlyalalklnslli 87 
                                   + + e +q+l+y+l+e   ++ ++e +   ie+   + in++k f  n   + ++    +y   +k n l++
  gi|15668319|ref|NP_247115.1| 275 LMLKEETQKLKYFLKELDYIKPKVELKDEIIEIKKDDIINALKLFKENYEVSDDDipEPVYIYLVKKNILFL 346
                                   4567889*********999999999888899999999********988644333212346666666666655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00047      0.53      14     120 ..      30     161 ..      19     186 .. 0.55
   2 ?   -3.3   0.0       9.3     1e+04     104     115 ..     209     221 ..     191     245 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                        AAA_19  14 lvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae......................atTi 72 
                                   ++ ++  +GKT ++khi++  ++    k+  i   ++     +e  e++ +                          a   
  gi|15668319|ref|NP_247115.1|  30 FIYGPLNSGKTALIKHIIENKLSDD-YKVFYINFRTYLISEKREFIEAIFT---TkkddffekikdksevlnlitkgA--- 103
                                   5566667899999999998877666.3343333333333333333333322...222344444444444444434441... PP

                        AAA_19  73 Hrlal.............ldfddlltealelle......eaeeekklqeeellivDEfqdvdelqyr 120
                                                       f++++++a+++l+      +     k  ++ +li DE q+++++  +
  gi|15668319|ref|NP_247115.1| 104 ----KiltgipipevefdKLFEEKINDAFQYLNsillevK-----KSGKQPVLILDELQMIKDVVLN 161
                                   ....033345556655542355566677777777654322.....2324458********9965443 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.3
                        AAA_19 104 e.llivDEfqdvd 115
                                   + +l+vD f   +
  gi|15668319|ref|NP_247115.1| 209 AkYLLVDDFDKET 221
                                   3477777765433 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022      0.25       8      43 ..      15      50 ..       8      76 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                                  HHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHT CS
                          TsaE  8 ealgkklakalgdvilLeGdLGaGKTtlvrglakal 43
                                  +++ + l  + + + +++G+L +GKT+l+++++++ 
  gi|15668319|ref|NP_247115.1| 15 HEILSILEGEPNIIYFIYGPLNSGKTALIKHIIENK 50
                                  44444444433556889***************9864 PP

>> zf-CCCH_7  Chromatin remodeling factor Mit1 C-terminal Zn finger 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.7   6.4e+03      29      52 ..     249     272 ..     229     283 .. 0.65
   2 ?   10.6   0.5    0.0005      0.56      15      57 ..     293     335 ..     278     344 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.7
                                   ---B-----S--S-----EESS-- CS
                     zf-CCCH_7  29 lekDdpvfsykviekehrLvansv 52 
                                   +    pv+ y vi++     ++++
  gi|15668319|ref|NP_247115.1| 249 YVGGKPVYIYSVIDEMRYRKLEDI 272
                                   444678888888877655555555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0005
                                   HHHHHT-----------B-----S--S-----EESS---HHHH CS
                     zf-CCCH_7  15 evkrkvekseyvrelekDdpvfsykviekehrLvansvsklvl 57 
                                    +k+kve+ ++++e++kDd + + k+++++  +   ++++ v+
  gi|15668319|ref|NP_247115.1| 293 YIKPKVELKDEIIEIKKDDIINALKLFKENYEVSDDDIPEPVY 335
                                   4799***************************999999999775 PP

>> MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.4   0.00026      0.29      44     151 ..     130     233 ..      67     324 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00026
                                   HHHHHST-----....-SS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS---SS--TSS--HHHHH CS
                    MAP65_ASE1  44 glksiLheepvdvpqsekkelsLlqkkkkldtaleelrkekaerlaeflelleqlqklceelgeeplsllidslpkleele 124
                                    l siL e    v +s k+++ +l +++ +++ +   +k + + l +fl +l + q+lc   +   +sl+i+++ +  ele
  gi|15668319|ref|NP_247115.1| 130 YLNSILLE----VKKSGKQPVLILDELQMIKDVVLNWQKYLLKELFQFLVSLTKEQHLCHVFCLSSDSLFIEYVYSAGELE 206
                                   23355555....6679*************************************************************9988 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    MAP65_ASE1 125 slrkhleelkeekerRleeikelkkqI 151
                                      k l      ke  l+ ++ l+k+I
  gi|15668319|ref|NP_247115.1| 207 GRAKYLLVDDFDKETALKFMDFLAKEI 233
                                   888877666665655555555555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1  12.2       0.1   1.2e+02      21     197 ..      28     309 ..      18     311 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.1
                        AAA_23  21 ltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenkdgry............... 86 
                                   ++ I+Gp  +GKT+++  i     ++ ++  +      +   ++     ++++++e  f++k+++                
  gi|15668319|ref|NP_247115.1|  28 IYFIYGPLNSGKTALIKHII---ENKLSDDYK-----VFYINFRTYLISEKREFIEAIFTTKKDDFfekikdksevlnlit 100
                                   67899999999999987764...333333333.....33333333334577889999988888866333333333333333 PP

                        AAA_23  87 ............trsiererelskkkgkttkkaklelleideleqfisellgskki.......ilnlilflgqer...... 142
                                                +                 ++kl++ +i++  q+++++l   k+       il+ +      +      
  gi|15668319|ref|NP_247115.1| 101 kgakiltgipipEV----------------EFDKLFEEKINDAFQYLNSILLEVKKsgkqpvlILDEL------Qmikdvv 159
                                   33333333333311................33344444444444444442222222122223322222......1232333 PP

                        AAA_23 143 ........feefelkdkke.............................................................. 153
                                           +      + ++                                                              
  gi|15668319|ref|NP_247115.1| 160 lnwqkyllK------ELFQflvsltkeqhlchvfclssdslfieyvysagelegrakyllvddfdketalkfmdflakeil 234
                                   443333221......222233333333455555555555555555555555555555555555555555666666666666 PP

                        AAA_23 154 ..............................rleelekelee.ledekkllekleqekekekeleeleeeleeilk 197
                                                                 r ++le+ l+  l++e ++l+  ++e+++ k   el++e+ ei+k
  gi|15668319|ref|NP_247115.1| 235 nkklsdedkeliynyvggkpvyiysvidemRYRKLEDILNLmLKEETQKLKYFLKELDYIKPKVELKDEIIEIKK 309
                                   66666799999*******************99999999999667799999999********99999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2688.62
//
Query:       gi|15668320|ref|NP_247116.1|  [L=336]
Description: H/ACA RNA-protein complex component Cbf5p [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-26   93.2   0.0    4.5e-23   82.3   0.0    3.2  1  TruB_N    TruB family pseudouridylate synthase (N terminal do
    9.9e-26   89.7   0.0    1.9e-25   88.8   0.0    1.5  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    4.6e-21   74.6   0.4    4.3e-20   71.5   0.1    2.4  3  DKCLD     DKCLD (NUC011) domain
    2.2e-18   66.0   5.7    4.9e-18   64.9   5.7    1.6  1  PUA       PUA domain
    4.5e-05   23.6   2.1    4.5e-05   23.6   0.2    2.1  3  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.0   1.3e-26   4.5e-23       1     149 []      66     179 ..      66     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 1.3e-26
                                   HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHH CS
                        TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleevl 81 
                                   k++l+ +k+Gh+GtLDp++tGvL+va+++aTk++ + +  +KeY++ ++l+ + ++eD                  + +v+
  gi|15668320|ref|NP_247116.1|  66 KKILNLDKAGHGGTLDPKVTGVLPVALERATKTIPMWHIPPKEYVCLMHLHRDASEED------------------ILRVF 128
                                   899************************************************9988888..................7789* PP

                                   HHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
                        TruB_N  82 kkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtYi 149
                                   k+ftG+i+q+pp  +Avk                 r+ r  +i+elell+ + ++v ++v+c++GtYi
  gi|15668320|ref|NP_247116.1| 129 KEFTGRIYQRPPLKAAVK-----------------RRLRIRKIHELELLDKDGKDVLFRVKCQSGTYI 179
                                   ******************.................899*****************************9 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.0   5.2e-29   1.9e-25       1      63 [.     180     245 ..     180     246 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 5.2e-29
                                   HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
                      TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke..dee.LdrlllPlesal 63 
                                   R+Lc+DiGeaLg+ Ah++eLRRt++g f+e+d+v l+dL da+ ++ke  dee L+r+++P+e  l
  gi|15668320|ref|NP_247116.1| 180 RKLCEDIGEALGTSAHMQELRRTKSGCFEEKDAVYLQDLLDAYVFWKEdgDEEeLRRVIKPMEYGL 245
                                   9***********************************************996667*********865 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.1   1.2e-23   4.3e-20       8      57 ..      12      61 ..       6      62 .. 0.95
   2 ?   -4.0   0.1       4.7   1.7e+04      44      48 ..      69      73 ..      68      74 .. 0.80
   3 ?    0.0   0.0      0.25     9e+02       6      37 ..     243     274 ..     239     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1.2e-23
                                  ..XXX-EEESS-----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHHH CS
                         DKCLD  8 LknydkllvrtehytplpaGssPlkRpieeyikyGvinLDKPsnPsSHEV 57
                                  ++++++l+v++e +t++++G++P++R+ie++ikyGv+ +DKP++P+SHEV
  gi|15668320|ref|NP_247116.1| 12 INDKEELIVKEEVETNWDYGCNPYERKIEDLIKYGVVVVDKPRGPTSHEV 61
                                  57899********************************************9 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 4.7
                                  EEEEE CS
                         DKCLD 44 inLDK 48
                                   nLDK
  gi|15668320|ref|NP_247116.1| 69 LNLDK 73
                                  79**9 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.25
                                   ....XXX-EEESS-----TTSS--GGG--HHH CS
                         DKCLD   6 llLknydkllvrtehytplpaGssPlkRpiee 37 
                                     L++ +k++v+ ++   + +G + + R i +
  gi|15668320|ref|NP_247116.1| 243 YGLRHLKKVVVKDSAVDAICHGADVYVRGIAK 274
                                   56889999********9999999988888865 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   5.7   1.4e-21   4.9e-18       1      74 []     249     322 ..     249     322 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 1.4e-21
                                   CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
                           PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveiervl 74 
                                   ++vvv+d+Av+a+++ga++++ G+ +  + + +g++V + + +ge+vavG+a+++++e+  +++g++v++erv+
  gi|15668320|ref|NP_247116.1| 249 KKVVVKDSAVDAICHGADVYVRGIAKLSKGIGKGETVLVETLKGEAVAVGKALMNTKEILNADKGVAVDVERVY 322
                                   58*********************************************************************985 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.9   1.4e+04      26      40 ..      39      51 ..      36      54 .. 0.56
   2 ?   -2.9   0.0       2.4   8.8e+03      60      76 .]     165     181 ..     159     181 .. 0.70
   3 !   23.6   0.2   1.3e-08   4.5e-05       1      75 [.     250     330 ..     250     331 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.9
                       UPF0113 26 itesvkenqvvvVln 40
                                  i++ +k  ++vvV++
  gi|15668320|ref|NP_247116.1| 39 IEDLIK--YGVVVVD 51
                                  555555..5566655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.4
                       UPF0113  60 gkivvknlaDiGeYlRr 76 
                                   ++++++  +  G+Y+R+
  gi|15668320|ref|NP_247116.1| 165 KDVLFRVKCQSGTYIRK 181
                                   55666666778999996 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 1.3e-08
                       UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt....kaspgkivv...knlaDiGeYl 74 
                                   kvvvk +a   +  G dv+  +i k+++++ +++ v+V   +ge++++Gk+  +t    +  ++++ v   +  +D+G+Y 
  gi|15668320|ref|NP_247116.1| 250 KVVVKDSAVDAICHGADVYVRGIAKLSKGIGKGETVLVETLKGEAVAVGKALMNTkeilN-ADKGVAVdveRVYMDRGTYP 329
                                   79***************************************************9997432.33333331113457888886 PP

                       UPF0113  75 R 75 
                                   R
  gi|15668320|ref|NP_247116.1| 330 R 330
                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2462.99
//
Query:       gi|15668321|ref|NP_247117.1|  [L=58]
Description: hypothetical protein MJ_0149 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-06   28.2   6.3    1.6e-06   28.2   6.3    1.0  1  ATPase_gene1     Putative F0F1-ATPase subunit Ca2+/Mg2+ trans
     0.0042   16.7   0.9     0.0049   16.5   0.9    1.0  1  PMT              Dolichyl-phosphate-mannose-protein mannosylt
  ------ inclusion threshold ------
      0.016   15.4   1.0      0.018   15.2   1.0    1.0  1  FUSC_2           Fusaric acid resistance protein-like
      0.069   13.5   1.4      0.095   13.0   1.4    1.2  1  Phage_holin_5_2  Phage holin family Hol44, in holin superfami
      0.084   12.8   1.5      0.089   12.7   1.5    1.1  1  DUF1275          Protein of unknown function (DUF1275)
       0.21   11.5   0.6        0.2   11.6   0.6    1.0  1  RseC_MucC        Positive regulator of sigma(E), RseC/MucC
       0.22   11.8   5.1       0.26   11.6   5.1    1.1  1  DUF4064          Protein of unknown function (DUF4064)
        1.7    8.8   3.9         19    5.4   0.3    2.1  2  UPF0154          Uncharacterised protein family (UPF0154)


Domain annotation for each model (and alignments):
>> ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   6.3   7.2e-10   1.6e-06       7      54 .]       5      51 ..       1      51 [. 0.92

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 7.2e-10
                  ATPase_gene1  7 iGielvapillggllGywLDkkfgtspwfliiglllGlaaGfynvyrl 54
                                  i++e+ + i+lg+++Gy + ++  +  ++ +++lllG++ +f  ++++
  gi|15668321|ref|NP_247117.1|  5 IAFEFFIMIALGIFIGYIIAEYTDN-NLWIVVFLLLGIFCAFGRLFKM 51
                                  89*******************9985.7***************988876 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.9   2.2e-06    0.0049     134     184 ..       1      52 [.       1      53 [. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.2e-06
                           PMT 134 illdspLlfftllsmyclvkfe.rkapfsrswwlwllltgvalglavsvKwv 184
                                   +l d+++ ff++ ++  ++ +   + +  + w+  +ll+g+ ++++ + K++
  gi|15668321|ref|NP_247117.1|   1 MLRDIAFEFFIMIALGIFIGYIiAEYTDNNLWIVVFLLLGIFCAFGRLFKMI 52 
                                   6889***************999877789999*****************9986 PP

>> FUSC_2  Fusaric acid resistance protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.0     8e-06     0.018      36      75 ..       6      45 ..       4      57 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8e-06
                        FUSC_2 36 avqRilGtvlGavlallllyllpgnlalallvfllvflia 75
                                  a++ ++  +lG+++++++  ++++nl ++++++l +f+++
  gi|15668321|ref|NP_247117.1|  6 AFEFFIMIALGIFIGYIIAEYTDNNLWIVVFLLLGIFCAF 45
                                  567788899****************555555555555542 PP

>> Phage_holin_5_2  Phage holin family Hol44, in holin superfamily V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.4   4.2e-05     0.095      25      62 ..      10      44 ..       8      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.2e-05
               Phage_holin_5_2 25 lilgiiGiilgvvivftadfqaedilifgaiiqGilsg 62
                                  +i++++Gi++g   +++a++ +++ +i   ++ Gi+++
  gi|15668321|ref|NP_247117.1| 10 FIMIALGIFIG---YIIAEYTDNNLWIVVFLLLGIFCA 44
                                  689999*****...555799*******99******998 PP

>> DUF1275  Protein of unknown function (DUF1275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.5     4e-05     0.089     156     191 ..       7      43 ..       1      44 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4e-05
                       DUF1275 156 laiilafllGavvGallvks.aaalwlaaallllval 191
                                   + ++++++lG ++G +++ +  + lw+++ lll +++
  gi|15668321|ref|NP_247117.1|   7 FEFFIMIALGIFIGYIIAEYtDNNLWIVVFLLLGIFC 43 
                                   56899****************************9986 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   8.8e-05       0.2      70     116 ..       9      53 ..       1      58 [] 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.8e-05
                     RseC_MucC  70 vYllPllllilgallgsallgssellaalgallglvlgflivrllsk 116
                                   ++++  l++++g++++++   +++l+ +++ llg++ +f  + ++ k
  gi|15668321|ref|NP_247117.1|   9 FFIMIALGIFIGYIIAEYT--DNNLWIVVFLLLGIFCAFGRLFKMIK 53 
                                   5555566777777777777..89999999999999999887666555 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   5.1   0.00012      0.26      68     102 ..       9      45 ..       5      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                       DUF4064  68 aliaivlgivgalllk..knkkvsGilfiiaailslf 102
                                   ++i+i+lgi+  +++   ++++++ ++f++ +i+++f
  gi|15668321|ref|NP_247117.1|   9 FFIMIALGIFIGYIIAeyTDNNLWIVVFLLLGIFCAF 45 
                                   6899999998888887677888*************99 PP

>> UPF0154  Uncharacterised protein family (UPF0154)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3    0.0084        19       2      18 ..      10      26 ..       9      30 .. 0.85
   2 ?    5.1   0.3      0.01        23       1      23 [.      33      55 ..      33      58 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0084
                       UPF0154  2 vialivGlvlGffiark 18
                                  +i++ +G+++G++ia +
  gi|15668321|ref|NP_247117.1| 10 FIMIALGIFIGYIIAEY 26
                                  578899********975 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.01
                       UPF0154  1 ivialivGlvlGffiarkymkkq 23
                                  iv++l++G++  f    k++k++
  gi|15668321|ref|NP_247117.1| 33 IVVFLLLGIFCAFGRLFKMIKDY 55
                                  699**********9999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 442.30
//
Query:       gi|15668322|ref|NP_247118.1|  [L=173]
Description: hypothetical protein MJ_0150 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-16   60.1   1.1    2.3e-16   59.5   1.1    1.3  1  V4R            V4R domain
    1.6e-07   31.3   0.0    2.3e-07   30.8   0.0    1.2  1  DUF2507        Protein of unknown function (DUF2507)
     0.0026   18.5   0.2     0.0047   17.7   0.2    1.4  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   1.1   3.9e-20   2.3e-16       5      61 ..     110     166 ..     106     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 3.9e-20
                                   EEEES-S-TT---SS---HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEEEE CS
                           V4R   5 ieespelaglpgkeePvCyleaGllagalsellgkrveveEveCaaeGhdhCeFeve 61 
                                    ++++ +   p+ +  +C++eaGl+ag+l+++l ++v+  E++C+++G+++CeF v+
  gi|15668322|ref|NP_247118.1| 110 LKDCISCHNVPNVGTTLCHFEAGLIAGTLEKKLRRKVNAVETKCCGKGDEYCEFLVK 166
                                   689***************************************************997 PP

>> DUF2507  Protein of unknown function (DUF2507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   3.8e-11   2.3e-07      21     112 ..      56     153 ..      43     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3.8e-11
                       DUF2507  21 eeilYwaGkelArkfples......ledlieffekagwGtLellkekkkelefeLsgeiveerlkekeekefqLEaGflAe 95 
                                   e+i+Y +Gk++ r++  +       le+ +e  +ka+ G Le++k +++e++  L+  i  +++ +  ++  ++EaG++A 
  gi|15668322|ref|NP_247118.1|  56 EAIIYNIGKDIGREVISRYvdrdnlLESFAEILKKAKIGILEVKKVEENEMILILKDCISCHNVPNVGTTLCHFEAGLIAG 136
                                   68***********9865441111113556677789***********************9999999999************* PP

                       DUF2507  96 qieqqkevvaeakeekk 112
                                   ++e++ ++ ++a+e+k 
  gi|15668322|ref|NP_247118.1| 137 TLEKKLRRKVNAVETKC 153
                                   ********999998864 PP

>> ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   7.8e-07    0.0047      27     143 ..      57     163 ..      37     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.8e-07
                 ATC_hydrolase  27 eiirkalerlgkergkklaekakakkdkadvekflalyseifekenalkf.evleedkdeleidvtrCpyceawkkeGlpe 106
                                   +ii+++ +++g+e   ++  +         +e+f     ei +k  ++++ ev++ +++e+ +  + C  c     +++p+
  gi|15668322|ref|NP_247118.1|  57 AIIYNIGKDIGREVISRYVDRDN------LLESF----AEILKK-AKIGIlEVKKVEENEMILILKDCISC-----HNVPN 121
                                   44444444444444444444433......23333....334444.44555588888999999999999998.....79*** PP

                 ATC_hydrolase 107 lgkllCeiDkavaeginpkvkler......tktlaeGgdcCdf 143
                                   +g +lC ++  ++ g  +k kl+r      tk  ++G+++C+f
  gi|15668322|ref|NP_247118.1| 122 VGTTLCHFEAGLIAGTLEK-KLRRkvnaveTKCCGKGDEYCEF 163
                                   ************9999999.5666666666************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1036.16
//
Query:       gi|15668323|ref|NP_247119.1|  [L=148]
Description: transcriptional regulator [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-17   60.3   2.6    2.2e-16   59.1   1.8    1.9  2  HTH_24          Winged helix-turn-helix DNA-binding
    2.4e-16   59.3   0.3    3.9e-16   58.6   0.3    1.3  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    5.5e-14   51.9   0.0    7.4e-14   51.5   0.0    1.2  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    9.1e-07   28.7   0.2    8.2e-06   25.7   0.1    2.2  2  HTH_11          HTH domain
    1.7e-06   28.0   0.0    1.1e-05   25.4   0.0    2.0  2  HTH_20          Helix-turn-helix domain
    7.7e-06   25.6   0.1    1.5e-05   24.6   0.1    1.4  1  HTH_23          Homeodomain-like domain
    1.3e-05   24.6   0.3    2.9e-05   23.5   0.3    1.6  1  Sigma70_r4      Sigma-70, region 4
    1.7e-05   24.6   0.0    7.1e-05   22.6   0.0    1.8  2  MarR_2          MarR family
    3.5e-05   23.4   0.2    0.00011   21.8   0.0    1.9  2  Sigma70_r4_2    Sigma-70, region 4
    3.8e-05   23.4   0.0    0.00059   19.6   0.0    2.1  2  HTH_5           Bacterial regulatory protein, arsR family
    0.00017   21.6   0.1    0.00037   20.6   0.1    1.5  1  HTH_28          Helix-turn-helix domain
    0.00028   20.8   0.0    0.00074   19.4   0.0    1.6  1  MarR            MarR family
     0.0003   20.5   0.6    0.00051   19.7   0.6    1.4  1  HTH_38          Helix-turn-helix domain
    0.00053   19.7   0.0      0.001   18.8   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
    0.00054   20.1   0.0        0.4   10.9   0.0    2.3  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00056   19.5   0.0     0.0012   18.4   0.0    1.6  1  HTH_50          Helix-turn-helix domain
    0.00063   19.6   0.0      0.021   14.7   0.0    2.4  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00096   18.7   0.0     0.0019   17.7   0.0    1.4  1  GerE            Bacterial regulatory proteins, luxR family
     0.0015   18.3   0.1     0.0047   16.7   0.0    1.8  2  LexA_DNA_bind   LexA DNA binding domain
     0.0018   17.7   0.0     0.0028   17.0   0.0    1.3  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
     0.0021   17.8   0.4     0.0063   16.2   0.1    1.9  2  HTH_DeoR        DeoR-like helix-turn-helix domain
     0.0043   17.5   0.1      0.012   16.1   0.0    1.7  2  HTH_27          Winged helix DNA-binding domain
     0.0047   17.5   0.0      0.011   16.4   0.0    1.6  1  Mga             Mga helix-turn-helix domain
     0.0063   16.7   0.3      0.016   15.4   0.1    1.7  2  PaaX            PaaX-like protein
  ------ inclusion threshold ------
      0.018   15.1   0.0      0.036   14.1   0.0    1.5  1  HTH_29          Winged helix-turn helix
      0.021   15.0   0.0      0.036   14.2   0.0    1.4  1  HTH_34          Winged helix DNA-binding domain
      0.021   14.7   0.7       0.97    9.3   0.1    2.3  2  MtrG            Tetrahydromethanopterin S-methyltransferase, 
      0.026   14.2   0.1      0.069   12.8   0.0    1.8  1  GntR            Bacterial regulatory proteins, gntR family
      0.052   13.2   0.2       0.15   11.7   0.1    1.8  2  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
      0.056   13.4   0.3       0.11   12.5   0.0    1.6  1  HTH_36          Helix-turn-helix domain
      0.057   13.1   0.1        1.2    8.8   0.0    2.1  2  DUF4423         Domain of unknown function (DUF4423)
      0.082   12.8   0.1       0.17   11.8   0.1    1.7  1  HxlR            HxlR-like helix-turn-helix
      0.096   13.0   0.0       0.13   12.5   0.0    1.3  1  Syntaxin-18_N   SNARE-complex protein Syntaxin-18 N-terminus
      0.096   12.5   0.0       0.29   11.0   0.0    1.7  2  HTH_10          HTH DNA binding domain
       0.11   12.5   0.1       0.16   12.0   0.1    1.5  1  DUF2089         Protein of unknown function (DUF2089)
       0.14   12.0   0.0       0.28   11.0   0.0    1.5  1  HTH_30          PucR C-terminal helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   1.8   4.5e-19   2.2e-16       1      48 []       2      49 ..       2      49 .. 0.98
   2 ?   -0.8   0.0       2.3   1.2e+03      27      43 ..      70      86 ..      69      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 4.5e-19
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  ld++d+kIL++L  n+r s re+ ++lg+S +tv+ r+krL+e+G+I+
  gi|15668323|ref|NP_247119.1|  2 LDRIDLKILRILNGNARKSFREIGRELGISEGTVRNRVKRLTEKGIIT 49
                                  79*********************************************6 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.3
                        HTH_24 27 lglSpstvnrrlkrLee 43
                                  l + ps v + l++L+e
  gi|15668323|ref|NP_247119.1| 70 LYIKPSKVEETLNKLKE 86
                                  568899999999*9987 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.3   7.8e-19   3.9e-16       1      41 [.       2      42 ..       2      43 .. 0.99

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 7.8e-19
                 HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                  LD+iD+kIL++L  +aR s++e+++++G+Se tv++Rv+rL
  gi|15668323|ref|NP_247119.1|  2 LDRIDLKILRILNGNARKSFREIGRELGISEGTVRNRVKRL 42
                                  8***************************************9 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   1.5e-16   7.4e-14       5      75 .]      72     139 ..      68     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.5e-16
                                   E-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                AsnC_trans_reg   5 lepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                   ++p++   +ee   +l+el+e+ve+y++tG+yd ++++  +d+e+l +fl ek++ l +v   + ++vl+t
  gi|15668323|ref|NP_247119.1|  72 IKPSK---VEETLNKLKELDEIVELYQTTGEYDAVCIAILKDIESLGKFLAEKIYPLVNVNGCKVTLVLRT 139
                                   56667...99***********************************************************86 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   1.6e-08   8.2e-06       3      44 ..       7      47 ..       6      53 .. 0.87
   2 ?    0.3   0.0       1.4   6.7e+02      32      43 ..     107     118 ..     106     130 .. 0.64

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.6e-08
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                  l+il++L + +   s  e+ +eL++S+ tvr+++k+L+e+g+
  gi|15668323|ref|NP_247119.1|  7 LKILRIL-NGNARKSFREIGRELGISEGTVRNRVKRLTEKGI 47
                                  5899999.555558**************************94 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.4
                        HTH_11  32 vrrdIkaLeelg 43 
                                   + +dI++L + +
  gi|15668323|ref|NP_247119.1| 107 ILKDIESLGKFL 118
                                   778888886655 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   2.1e-08   1.1e-05       9      55 ..       3      49 ..       1      50 [. 0.93
   2 ?    0.1   0.0       1.8   8.9e+02      36      55 ..      72      92 ..      63      95 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.1e-08
                                  -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                  ++  ++ilr L++++  ++ e+ ++l++s  t++++++ L e g+++
  gi|15668323|ref|NP_247119.1|  3 DRIDLKILRILNGNARKSFREIGRELGISEGTVRNRVKRLTEKGIIT 49
                                  566689***************************************98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.8
                                  S-HHHHHHHHHHHHH.CTTEE CS
                        HTH_20 36 lskntlsyHLrvLee.agLve 55
                                  ++++ +   L++L e  ++ve
  gi|15668323|ref|NP_247119.1| 72 IKPSKVEETLNKLKElDEIVE 92
                                  677888889999999777776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1     3e-08   1.5e-05      17      46 ..      18      47 ..       7      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3e-08
                        HTH_23 17 GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                  ++s reI reLg+s+ Tv++ +kr  e+G+
  gi|15668323|ref|NP_247119.1| 18 RKSFREIGRELGISEGTVRNRVKRLTEKGI 47
                                  8999*********************99996 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.3   5.9e-08   2.9e-05      21      44 ..      19      42 ..       9      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5.9e-08
                                  --HHHHHHHHTS-HHHHHHHHHHH CS
                    Sigma70_r4 21 lTleEIgerlgiSrerVrqiekrA 44
                                   ++ EIg++lgiS+++Vr + kr 
  gi|15668323|ref|NP_247119.1| 19 KSFREIGRELGISEGTVRNRVKRL 42
                                  6899*****************996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.4e-07   7.1e-05      10      52 ..       9      49 ..       2      53 .. 0.85
   2 ?   -0.9   0.0       3.2   1.6e+03      31      48 ..      70      87 ..      68      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.4e-07
                                  HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                        MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                  +L  L  + + + + +e+ r+lg+s ++v +++krL ++G ++
  gi|15668323|ref|NP_247119.1|  9 ILRILNGNAR-K-SFREIGRELGISEGTVRNRVKRLTEKGIIT 49
                                  5666666665.3.99*************************996 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.2
                                  HTSSHHHHHHHHHHHHHT CS
                        MarR_2 31 lglsksavsrilkrLvaa 48
                                  l +++s v  +l++L + 
  gi|15668323|ref|NP_247119.1| 70 LYIKPSKVEETLNKLKEL 87
                                  678999999999999886 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.2e-07   0.00011      27      49 ..      19      41 ..      17      45 .. 0.93
   2 ?   -1.5   0.0       4.2   2.1e+03       4      15 ..      77      88 ..      76      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.2e-07
                                  --HHHHHHHHT--HHHHHHHHHH CS
                  Sigma70_r4_2 27 lsykEIAellgisegtVksrlsR 49
                                  +s +EI ++lgisegtV++r++R
  gi|15668323|ref|NP_247119.1| 19 KSFREIGRELGISEGTVRNRVKR 41
                                  589*****************998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.2
                                  HHHHHTTS-HHH CS
                  Sigma70_r4_2  4 lrealaeLperq 15
                                  ++e l++L e +
  gi|15668323|ref|NP_247119.1| 77 VEETLNKLKELD 88
                                  678899998876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.2e-06   0.00059       5      45 ..       7      48 ..       5      49 .. 0.94
   2 ?    1.3   0.0      0.66   3.3e+02      27      42 ..      72      87 ..      67      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-06
                                  HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                  lkIL++L+    +++ e+ +elg+s++tv+   k+L e G++
  gi|15668323|ref|NP_247119.1|  7 LKILRILNGnARKSFREIGRELGISEGTVRNRVKRLTEKGII 48
                                  89*******666****************************98 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.66
                                  S-HHHHHHHHHHHHHT CS
                         HTH_5 27 lsqstvShHLkkLrea 42
                                  + +s+v + L+kL+e+
  gi|15668323|ref|NP_247119.1| 72 IKPSKVEETLNKLKEL 87
                                  6799999******997 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   7.4e-07   0.00037       6      41 ..       9      47 ..       9      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.4e-07
                        HTH_28  6 ikllaaGh...svreaArelgisrrtvyrWikryeegGi 41
                                  i+++++G+   s re+ relgis+ tv+  +kr+ e Gi
  gi|15668323|ref|NP_247119.1|  9 ILRILNGNarkSFREIGRELGISEGTVRNRVKRLTEKGI 47
                                  567788855579999******************999986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.5e-06   0.00074       6      48 ..       7      49 ..       4      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.5e-06
                                  HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                  ++iLril  +   s  e+++ lg+s +tv + ++rL +kG i+
  gi|15668323|ref|NP_247119.1|  7 LKILRILNGNARKSFREIGRELGISEGTVRNRVKRLTEKGIIT 49
                                  689*************************************996 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.6     1e-06   0.00051      18      43 ..      16      41 ..       7      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1e-06
                        HTH_38 18 aeGlslreIArrLgrspsTIsRElkR 43
                                  ++ +s+reI+r+Lg s +T+ + +kR
  gi|15668323|ref|NP_247119.1| 16 NARKSFREIGRELGISEGTVRNRVKR 41
                                  4669********************99 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.1e-06     0.001       6      48 ..       7      48 ..       5      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.1e-06
                                  HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                      HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                  l iL++l+  ++  +++e+ r++g++  tv++ ++ L+e G++
  gi|15668323|ref|NP_247119.1|  7 LKILRILNGNARK-SFREIGRELGISEGTVRNRVKRLTEKGII 48
                                  78**********9.9*************************987 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0    0.0008       0.4      23      51 ..      19      47 ..       8      50 .. 0.82
   2 ?    6.9   0.0     0.014       7.2      32      48 ..      70      86 ..      68      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0008
                                  B-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGy 51
                                   +  ++ ++L++s  +V   +k+L ++G 
  gi|15668323|ref|NP_247119.1| 19 KSFREIGRELGISEGTVRNRVKRLTEKGI 47
                                  5667999*******************995 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.014
                                  HTS-HHHHHHHHHHHHH CS
                Fe_dep_repress 32 LnvspssVsemlkkLek 48
                                  L ++ps V e+l+kL++
  gi|15668323|ref|NP_247119.1| 70 LYIKPSKVEETLNKLKE 86
                                  679************87 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.4e-06    0.0012      24      46 ..      19      41 ..       2      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.4e-06
                        HTH_50 24 pStRklAkrLGvShtaianklrk 46
                                  +S+R +++ LG+S  ++ n++++
  gi|15668323|ref|NP_247119.1| 19 KSFREIGRELGISEGTVRNRVKR 41
                                  8********************98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.3e-05     0.021      12      53 ..       8      49 ..       2      59 .. 0.84
   2 ?    2.4   0.0      0.29   1.4e+02      36      63 ..      74     101 ..      69     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.3e-05
                                  CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                          TrmB 12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                  k+   L  + +++ +ei +elg+++ +v + +++L +kG+++
  gi|15668323|ref|NP_247119.1|  8 KILRILNGNARKSFREIGRELGISEGTVRNRVKRLTEKGIIT 49
                                  55555556788899*************************986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.29
                                   CHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                          TrmB  36 rskvYevLrsLedkGlVerekgrpklYr 63 
                                    skv e+L++L++ + +    +++  Y 
  gi|15668323|ref|NP_247119.1|  74 PSKVEETLNKLKELDEIVELYQTTGEYD 101
                                   699********99876666555555555 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.7e-06    0.0019      18      44 ..      19      45 ..       8      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.7e-06
                                  S-HHHHHHHHTS-HHHHHHHHHHHHHH CS
                          GerE 18 ksnkeIAeelniSekTVkvhksnimkK 44
                                  ks  eI++el+iSe TV++ ++++ +K
  gi|15668323|ref|NP_247119.1| 19 KSFREIGRELGISEGTVRNRVKRLTEK 45
                                  5778*******************9887 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   9.4e-06    0.0047      27      56 ..      20      48 ..      11      52 .. 0.94
   2 ?   -2.0   0.0       6.1   3.1e+03      40      51 ..      74      85 ..      68      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.4e-06
                                  -HHHHHHHHTS-.HHHHHHHHHHHHHTTSE CS
                 LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyi 56
                                  s rei+r+lg++   +v ++ k+L  KG+i
  gi|15668323|ref|NP_247119.1| 20 SFREIGRELGIS-EGTVRNRVKRLTEKGII 48
                                  88*********7.99*************99 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.1
                                  HHHHHHHHHHHH CS
                 LexA_DNA_bind 40 psaveehLkaLe 51
                                  ps vee L++L+
  gi|15668323|ref|NP_247119.1| 74 PSKVEETLNKLK 85
                                  899999999986 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.6e-06    0.0028      28      51 ..      19      42 ..      15      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.6e-06
                  HTH_Tnp_ISL3 28 rsvkavArqlgvSwtTVwrildry 51
                                  +s++++ r+lg+S+ TV+++++r+
  gi|15668323|ref|NP_247119.1| 19 KSFREIGRELGISEGTVRNRVKRL 42
                                  69********************97 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.3e-05    0.0063       4      48 ..       8      52 ..       4      56 .. 0.89
   2 ?   -1.5   0.0       4.3   2.1e+03      17      27 ..      87      97 ..      81      99 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                      HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRth 48
                                  +il  l+     s  e+  +lg+Se T+R+  + L+e+g++t  h
  gi|15668323|ref|NP_247119.1|  8 KILRILNGNARKSFREIGRELGISEGTVRNRVKRLTEKGIITGFH 52
                                  688888888888999999**********************99666 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.3
                      HTH_DeoR 17 veelvellgvS 27
                                  ++e+vel++++
  gi|15668323|ref|NP_247119.1| 87 LDEIVELYQTT 97
                                  56777777765 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.3e-05     0.012       5      48 ..       6      48 ..       2      58 .. 0.89
   2 ?   -1.8   0.0       9.1   4.5e+03      34      46 ..      76      88 ..      70      98 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.3e-05
                        HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                  +  +L+ ++  ++rk+ +++ + l ++  ++ + +k+LtekG +
  gi|15668323|ref|NP_247119.1|  6 DLKILRILN-GNARKSFREIGRELGISEGTVRNRVKRLTEKGII 48
                                  566999999.99******************************87 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 9.1
                        HTH_27 34 hisyslkkLtekG 46
                                   + + l+kL e +
  gi|15668323|ref|NP_247119.1| 76 KVEETLNKLKELD 88
                                  5667788887764 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.1e-05     0.011      16      65 ..       4      55 ..       1      64 [. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.1e-05
                                  SHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH..HCHCCT-EE CS
                           Mga 16 slkyqllkflfeeeevsieelaqelyiSestlkrkikelnk..lLkefdlel 65
                                  ++++++l+ l  ++++s+ e+ +el iSe t+ + +k+l +   +  f+ ++
  gi|15668323|ref|NP_247119.1|  4 RIDLKILRILNGNARKSFREIGRELGISEGTVRNRVKRLTEkgIITGFHASI 55
                                  7899**********************************97622455666666 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   3.3e-05     0.016      29      55 ..      24      50 ..      16      54 .. 0.89
   2 ?   -2.1   0.0       9.3   4.6e+03       7      25 ..      65      83 ..      64      94 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.3e-05
                          PaaX 29 llaelGiseslvRaalsRlakaGwlvr 55
                                  +  elGise++vR  + Rl+++G +++
  gi|15668323|ref|NP_247119.1| 24 IGRELGISEGTVRNRVKRLTEKGIITG 50
                                  6679*******************9985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.3
                          PaaX  7 vtlygdyveprggaiwlgs 25
                                  v ++g y++p+  +  l++
  gi|15668323|ref|NP_247119.1| 65 VAILGLYIKPSKVEETLNK 83
                                  6788888888766555544 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.3e-05     0.036      16      46 ..      22      52 ..       9      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.3e-05
                        HTH_29 16 sqiAkllglsrrtvyrwlkrfeegGlaalld 46
                                  ++i + lg+s+ tv++ +kr  e+G+    +
  gi|15668323|ref|NP_247119.1| 22 REIGRELGISEGTVRNRVKRLTEKGIITGFH 52
                                  78889********************966555 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.3e-05     0.036       2      45 ..       6      49 ..       5      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.3e-05
                        HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                   l++l +L+ + + +f+e+  +l++++g     +k L ++g i+
  gi|15668323|ref|NP_247119.1|  6 DLKILRILNGNARKSFREIGRELGISEGTVRNRVKRLTEKGIIT 49
                                  699************************************99886 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1     0.002      0.97      19      52 ..       2      35 ..       1      37 [. 0.90
   2 ?    3.6   0.0      0.12        61       7      30 ..      72      95 ..      67     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.002
                          MtrG 19 LdeieekvefvnsEiaqriGkkvGRdiGilYGlv 52
                                  Ld+i+ k+  +    a++  +++GR++Gi  G v
  gi|15668323|ref|NP_247119.1|  2 LDRIDLKILRILNGNARKSFREIGRELGISEGTV 35
                                  89999999999999999999*********98876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                          MtrG  7 vdpddfnevkkrLdeieekvefvn 30
                                  + p   +e  ++L e++e ve ++
  gi|15668323|ref|NP_247119.1| 72 IKPSKVEETLNKLKELDEIVELYQ 95
                                  56677889999********99764 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014     0.069      28      55 ..      22      49 ..      11      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                                  HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          GntR 28 reLaaefgVsrttvReALrrLeaeglve 55
                                  re+  e+g+s  tvR   +rL+++g+++
  gi|15668323|ref|NP_247119.1| 22 REIGRELGISEGTVRNRVKRLTEKGIIT 49
                                  99************************97 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0003      0.15      27      55 ..      22      50 ..       7      54 .. 0.87
   2 ?   -1.8   0.0         5   2.5e+03      10      18 ..      87      95 ..      70     101 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                  HrcA_DNA-bdg 27 eeiAevlkrneGtvRNqlqsLkalgLveg 55
                                  +ei   l+  eGtvRN ++ L   g++ g
  gi|15668323|ref|NP_247119.1| 22 REIGRELGISEGTVRNRVKRLTEKGIITG 50
                                  799****************9998888776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5
                  HrcA_DNA-bdg 10 lqaLielyr 18
                                  l +++ely+
  gi|15668323|ref|NP_247119.1| 87 LDEIVELYQ 95
                                  445566665 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00022      0.11      24      55 .]      17      48 ..       9      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
                        HTH_36 24 cfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                  +  s++ + + lg+s+ Tv++ +k L ++G+i
  gi|15668323|ref|NP_247119.1| 17 ARKSFREIGRELGISEGTVRNRVKRLTEKGII 48
                                  4468999999********************98 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0024       1.2      35      69 ..      17      49 ..       8      59 .. 0.89
   2 ?    2.4   0.1      0.22   1.1e+02      48      70 ..      70      92 ..      53     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0024
                       DUF4423 35 fkadpeelakrlrpkisaeevekalefLlklgllk 69
                                  ++++ +e+ + l+  is+  v++ +++L++ g+++
  gi|15668323|ref|NP_247119.1| 17 ARKSFREIGRELG--ISEGTVRNRVKRLTEKGIIT 49
                                  468899*******..*****************996 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.22
                       DUF4423 48 pkisaeevekalefLlklgllkk 70
                                    i+ ++ve++l+ L++l+ + +
  gi|15668323|ref|NP_247119.1| 70 LYIKPSKVEETLNKLKELDEIVE 92
                                  559999***********998876 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00034      0.17      10      60 ..       9      59 ..       3      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                                  HHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-E CS
                          HxlR 10 ilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpk 60
                                  il+ l    +k f e+ r+l +is+ +  +r ++L ++g+i     +  P+ 
  gi|15668323|ref|NP_247119.1|  9 ILRILNGnARKSFREIGREL-GISEGTVRNRVKRLTEKGIITGFHASINPKN 59
                                  5554433255669*******.9*******************87777766665 PP

>> Syntaxin-18_N  SNARE-complex protein Syntaxin-18 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00027      0.13      30      64 ..      86     120 ..      49     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00027
                 Syntaxin-18_N  30 rkkkrlkkskekdeFikeAkeilkhItkLrkfLle 64 
                                   + +++ + ++++ e+   ++ ilk I +L kfL+e
  gi|15668323|ref|NP_247119.1|  86 ELDEIVELYQTTGEYDAVCIAILKDIESLGKFLAE 120
                                   3344556678888********************98 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00058      0.29      23      50 ..      18      45 ..      14      48 .. 0.89
   2 ?   -2.3   0.0       7.9   3.9e+03      35      46 ..      72      83 ..      68      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00058
                        HTH_10 23 rvtlkeLAkelGIskstlsehLrkaesk 50
                                  r + +e+  elGIs+ t+ +++++ ++k
  gi|15668323|ref|NP_247119.1| 18 RKSFREIGRELGISEGTVRNRVKRLTEK 45
                                  77899*****************998776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.9
                        HTH_10 35 IskstlsehLrk 46
                                  I++s ++e L+k
  gi|15668323|ref|NP_247119.1| 72 IKPSKVEETLNK 83
                                  788999999987 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00031      0.16      49      76 ..      18      45 ..       2      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00031
                       DUF2089 49 rGnlkevekelgisYpTvrnrldeilea 76
                                  r +++e+ +elgis  Tvrnr+++++e+
  gi|15668323|ref|NP_247119.1| 18 RKSFREIGRELGISEGTVRNRVKRLTEK 45
                                  56799*****************999875 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00057      0.28      14      38 ..      20      44 ..       9      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00057
                                  -HHHHHHHHTS-HHHHHHHHHHHHH CS
                        HTH_30 14 nisatAkaLhvHrnTlryRLrriee 38
                                  + ++  ++L+++  T+r+R++r+ e
  gi|15668323|ref|NP_247119.1| 20 SFREIGRELGISEGTVRNRVKRLTE 44
                                  6678899***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 908.63
//
Query:       gi|15668324|ref|NP_247120.1|  [L=748]
Description: bifunctional acetyl-CoA decarbonylase/synthase complex subunit alpha/beta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-63  213.8   0.9    2.7e-63  212.5   0.9    1.8  1  CdhC      CO dehydrogenase/acetyl-CoA synthase complex beta s
      6e-21   74.3   2.2    6.5e-21   74.2   0.3    2.1  2  CODH_A_N  Carbon monoxide dehydrogenase subunit alpha N-termi
  ------ inclusion threshold ------
       0.11   12.2   2.3        0.2   11.3   2.3    1.6  1  RasGAP    GTPase-activator protein for Ras-like GTPase
        9.5    6.9  10.8        6.6    7.4   1.3    4.3  4  ThiS      ThiS family


Domain annotation for each model (and alignments):
>> CdhC  CO dehydrogenase/acetyl-CoA synthase complex beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.5   0.9     6e-67   2.7e-63       1     155 []     298     448 ..     298     448 .. 0.97

  Alignments for each domain:
  == domain 1  score: 212.5 bits;  conditional E-value: 6e-67
                          CdhC   1 ipvevspafeGeriRkedlyvelggkktkafElvkvkeadevedgkieviGpdideveegsrlplailvevaGkkleedlE 81 
                                   ipv+v+p+ eGer+R  d+yvel+g k+ +fElvkv +  + ed k+e+iG+dide+eegsr p+ai+vev+G++leedlE
  gi|15668324|ref|NP_247120.1| 298 IPVSVGPMNEGERVRGPDMYVELAGPKSYGFELVKVVN--KAED-KVEIIGKDIDEMEEGSRNPFAIIVEVSGSNLEEDLE 375
                                   8************************99*********55..5566.9*********************************** PP

                          CdhC  82 pvlERriHeflnyieGvmHlgqRdiiwvRiskeavekGlrlkhigevlyaklkeefeaivdkvevtlitdeekv 155
                                   +vlERriHeflnyieGvmHl+qRd++w+Ri+k++++kGlrlkhigev+ +++ke f +iv+k++v +itd++kv
  gi|15668324|ref|NP_247120.1| 376 GVLERRIHEFLNYIEGVMHLNQRDQVWIRINKNSFNKGLRLKHIGEVVKQLFKEHF-PIVEKCNVIIITDPDKV 448
                                   ********************************************************.**************997 PP

>> CODH_A_N  Carbon monoxide dehydrogenase subunit alpha N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.3   1.4e-24   6.5e-21       4      82 ..      26     102 ..      24     103 .. 0.95
   2 ?   -3.3   0.1       2.2   9.8e+03      34      54 ..     667     687 ..     665     701 .. 0.72

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 1.4e-24
                      CODH_A_N   4 lekaikkygkdkkvefPdTAYylPviyaltGekvktlgdleevLerarsllkeeetLedaldaGlatllaaEiieAlkY 82 
                                    +++++k +++ kv++P T Y lP+iy+l+G+k++t++dl+e++++++  +k+eetLe+aldaG+ tl++aE ieAlkY
  gi|15668324|ref|NP_247120.1|  26 TKEILEKEDENLKVSYPGTNYNLPIIYGLLGKKIETVKDLKELINSLE--IKDEETLENALDAGVVTLICAEAIEALKY 102
                                   5788999**************************************985..99*************************** PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.2
                      CODH_A_N  34 GekvktlgdleevLerarsll 54 
                                    e+vkt ++l + L++  + +
  gi|15668324|ref|NP_247120.1| 667 EEDVKTTDELIKFLKEKGHPI 687
                                   578999999999988766544 PP

>> RasGAP  GTPase-activator protein for Ras-like GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.3   4.5e-05       0.2      14      85 ..     390     470 ..     377     725 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.5e-05
                        RasGAP  14 enpndllrsnsvvsklleeytkrpegqeyLkkilkpllqki..l.ekedlnlelDPrkiyeelkkkkesktgkk......s 85 
                                   e + +l + ++v++++ ++ ++++   +++ +++k+l+++   + ek +  + +DP k++eel+k+ke  ++++       
  gi|15668324|ref|NP_247120.1| 390 EGVMHLNQRDQVWIRINKNSFNKGLRLKHIGEVVKQLFKEHfpIvEKCNVIIITDPDKVKEELEKAKEIYKKRDektksiR 470
                                   5566777999*****877655555999999999999999863323788888999************998655443333330 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.16   7.1e+02      20      40 ..      61      84 ..      54     103 .. 0.75
   2 ?   -1.4   0.1      0.83   3.7e+03      28      71 ..     392     442 ..     366     464 .. 0.67
   3 ?    2.2   0.5     0.063   2.8e+02      14      63 ..     663     707 ..     654     709 .. 0.75
   4 ?    7.4   1.3    0.0015       6.6      12      49 ..     704     743 ..     694     747 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.16
                                  STSBHHHHHHHHHHHTCHHG...T CS
                          ThiS 20 egstvaelleaLgerypela...l 40
                                  + + ++el+++L+ +++e     l
  gi|15668324|ref|NP_247120.1| 61 TVKDLKELINSLEIKDEETLenaL 84
                                  567899999999999976655554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.83
                                   HHHHHHHTCHHG......TTTTEEEEETTEEEGC.CTTTSB--TTCEEEEE CS
                          ThiS  28 leaLgerypela......lerrvavavNgeivpr.lwldtelkdgDevail 71 
                                   +++L++r++ +        ++++++   ge+v++   +++++ +   v i+
  gi|15668324|ref|NP_247120.1| 392 VMHLNQRDQVWIrinknsFNKGLRLKHIGEVVKQlFKEHFPIVEKCNVIII 442
                                   556666665555555555445555555566666644666666666666665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.063
                                   EEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGC.CTTTSB-- CS
                          ThiS  14 eelelaegstvaelleaLgerypelalerrvavavNgeivpr.lwldtelk 63 
                                   +   +++ +t +el++ L+e++        ++    +e+v++ +++++e+k
  gi|15668324|ref|NP_247120.1| 663 KIATEEDVKTTDELIKFLKEKG------HPIVKKTEEEVVEEvEEEKEEVK 707
                                   56678899***********999......77777777777777666666666 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0015
                                   T..CEEEEESSTSBHHHHHHHHHHHTCHHG.TTTTEEEEET CS
                          ThiS  12 g..eeelelaegstvaelleaLgerypela.lerrvavavN 49 
                                   +  + ++e++eg  v+el+ +L+++++ ++   ++v + +N
  gi|15668324|ref|NP_247120.1| 704 EevKATEEEKEGIEVGELITKLAKEGG-IQiIMKNVKIVIN 743
                                   3367899***************99985.4456667777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (748 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1461  (0.0814881); expected 358.6 (0.02)
Passed bias filter:                      769  (0.0428914); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.84u 0.30s 00:00:01.13 Elapsed: 00:00:00.50
# Mc/sec: 4519.53
//
Query:       gi|15668325|ref|NP_247121.1|  [L=774]
Description: acetyl-CoA decarbonylase/synthase complex subunit alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-98  329.2  15.3    8.1e-86  288.7   0.1    2.0  2  Prismane  Prismane/CO dehydrogenase family
    4.3e-07   30.4  14.3    3.8e-06   27.4   8.6    3.3  3  Fer4_7    4Fe-4S dicluster domain
    8.9e-07   29.4  11.7     0.0041   17.6   0.2    4.3  4  Fer4_17   4Fe-4S dicluster domain
    2.3e-05   24.5   9.9    2.3e-05   24.5   9.9    3.8  3  Fer4_9    4Fe-4S dicluster domain
    9.2e-05   22.5  19.1    0.00011   22.2  10.4    3.6  3  Fer4_10   4Fe-4S dicluster domain
    0.00039   21.3  15.0       0.08   13.9   0.4    4.5  4  Fer4_16   4Fe-4S double cluster binding domain
    0.00099   19.5  12.4    0.00099   19.5  12.4    4.0  4  Fer4_8    4Fe-4S dicluster domain
     0.0015   18.5   0.1      0.016   15.2   0.0    2.5  2  CODH_A_N  Carbon monoxide dehydrogenase subunit alpha N-termi
     0.0017   18.5   5.0     0.0017   18.5   5.0    3.9  3  Fer4_21   4Fe-4S dicluster domain
     0.0022   18.4  15.2     0.0034   17.8   1.7    4.1  3  Fer4_4    4Fe-4S binding domain
     0.0063   16.3   2.7     0.0063   16.3   2.7    4.8  4  Fer4      4Fe-4S binding domain
  ------ inclusion threshold ------
       0.42   11.2  14.1       0.16   12.5   0.5    3.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        1.4    9.9  18.7       0.38   11.6   3.1    3.8  4  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6  10.2   1.2e-14   1.6e-11       2      58 ..      75     131 ..      74     140 .. 0.95
   2 !  288.7   0.1   5.9e-89   8.1e-86     114     511 .]     151     681 ..     137     681 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.2e-14
                                   EE-SSTCT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane   2 fCrqCengpCritknkrGvCGkdadtavardlliavlkgaaahaahareladtliak 58 
                                   +C++C++g+C++++ k+G+CG + ++++ar +lia++ gaa+ha h r+l+++li++
  gi|15668325|ref|NP_247121.1|  75 LCCLCTFGKCDLSRGKKGACGLNIKAQQARIVLIACCIGAACHAGHSRHLVHHLIET 131
                                   7****************************************************9986 PP

  == domain 2  score: 288.7 bits;  conditional E-value: 5.9e-89
                                   HHHHHCCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHCCCCTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---.... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                      Prismane 114 irslkellpkglkglyaehaivlgyadeevveflaktlaglesdpldllskalrlGlldlkgmelldeantslfGtP.... 190
                                    r++++++pk+l +l    +++l y +e+++++l+++++g+e+d+ld++skal++G++d  + e+ d a++++++ P    
  gi|15668325|ref|NP_247121.1| 151 ARTVTGIKPKTLGDL----EKILDYCEEQITHLLSAAHTGQEGDYLDFESKALHAGMIDDLAREAGDLAQIVAYNMPkgde 227
                                   58999999****999....**********************************************************9999 PP

                                   --EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCCCCCCGCCCCCCHHHHHH.HHHCCEEEEECSSGGGHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                      Prismane 191 eppltevnlgvldkdkvnIlvsGHdladleelleqtegkglnvythgemLpghcctalk.lkyrhlvgnvGnawqqekaef 270
                                    +pl+e+++g++dk+k++Il +GH+++  +++le++e++ ++++++   + g+ccta + ++++   ++vG + +q ++++
  gi|15668325|ref|NP_247121.1| 228 DAPLIELGFGCIDKSKPVILCIGHNVVPGSYILEYLEENSMEDEVE---VCGICCTAIDiTRVSDKPKVVGPLSRQLMFVR 305
                                   788*******************************************...******************************** PP

                                   CCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-TTSEEE-.-CTTCH.............HHHHHHHHHHHCCHCCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.............xxxxxxxxxxxxxxxxx RF
                      Prismane 271 tgavdaivvdtnCivpplasvaekyktrlittsevakpgakhie.eeekad.............kdaseiiekAielakar 337
                                   +g++d+++vd++Ci++++ ++  k+++ li+t+e+++ g+++++  +e+ +              d +++ ++A+e+ak+ 
  gi|15668325|ref|NP_247121.1| 306 SGVADVVIVDEQCIRTDILEEVLKTGAVLIATNEKMCLGLEDVShMDED-EiigyllrnraallLDEKKVGKVAVEVAKIV 385
                                   ********************999**************666666621133.1334445555666655555555555555555 PP

                                   TCGG.-................................................HHH........................ CS
                                   xxxxxx................................................xxx........................ RF
                      Prismane 338 eekkve................................................ida........................ 346
                                   ++++ +                                                i                          
  gi|15668325|ref|NP_247121.1| 386 AKERKDrktlpdlnevvelakqctecgwcnrncpnafkvkeamalakqgnfkgfI-Dlykrcygcgrceaicprnlpivsm 465
                                   4433334456999999888888877777777777777776666666666666662.0466666666666677777777777 PP

                                   ..................................HHTTSS-EEEEE-B---TTCGCCHHHHHHHHCHHTTEEEEEECHHHH CS
                                   ..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane 347 ..................................iksGtIkgvvlvvGCdnakkgrdyytelakelikrdvlvltaGCaky 393
                                                                     i+ G+I+gvv++vGC+n ++g++ ++ +ake+++r+++v+++GCa++
  gi|15668325|ref|NP_247121.1| 466 ttkvgeayykdlkfkmragrgpikdveirsvgapIVFGDIPGVVALVGCSNHPNGEEEVAMIAKEFLERKYIVVATGCAAM 546
                                   7777778888888888888888888899999999*********************************************** PP

                                   HC...CCTTTTEC...GHHHHSTHCEESEEEEESCCCHHHHHHHHHHHHHHT.......TS.SGGGSSE...EEEECC-.. CS
                                   xx...xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xx.xxxxxxx...xxxxxxx.. RF
                      Prismane 394 al...nklglgti...eaaelagegiPrvLdvGsCvdnyrivvialklaeal.......gv.dindLpl...aalalew.. 455
                                   a+   ++++++t+   ++ e+ ++g   ++++GsC++n +i+++a+k+a+++       ++ +++d++l   +a+ ++w  
  gi|15668325|ref|NP_247121.1| 547 AIgmwKDKDGKTLyekYPGEFRAGG---LVNCGSCLSNCHITGAAIKIANIFakvplrgNYaEVADYILnkvGAVGVAWga 624
                                   *****9999999999999*****99...******************************8788*********99******** PP

                                   -SHHHHHHHHHHHHTT-CEEECSS-TTTT-HHHHHHHHCHHH.HHHCEEEECHCHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                      Prismane 456 yeqKAvailltllalGinihlgptlpafgspnvlkvlvedfe.driggivtveedpe 511
                                   ++qKA+ai+++++++Gi+++lgp++ ++++  + +    +++ +++g+i+++e++pe
  gi|15668325|ref|NP_247121.1| 625 MSQKAAAIATGVNRWGIPVILGPHGAKYRRLYLSNGEKFKVKdKKTGEILEIEPAPE 681
                                   ******************************999987777754147888999999885 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       4.5   6.2e+03      26      39 ..     300     319 ..     273     323 .. 0.48
   2 !   27.4   8.6   2.8e-09   3.8e-06       1      51 [.     407     459 ..     407     460 .. 0.81
   3 ?    4.8   0.0     0.032        44       3      13 ..     573     583 ..     572     671 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.5
                        Fer4_7  26 k......gtekveidpekCl 39 
                                   +      g+++v+i+ e+C+
  gi|15668325|ref|NP_247121.1| 300 QlmfvrsGVADVVIVDEQCI 319
                                   03333336677777788886 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.8e-09
                        Fer4_7   1 rCigCgaCvaaCpvkaieldee..enekgtekveid.pekClgCgaCvavCPtg 51 
                                   +C++Cg C ++Cp +a++++e+    ++g+ k  id + +C+gCg+C+a CP +
  gi|15668325|ref|NP_247121.1| 407 QCTECGWCNRNCP-NAFKVKEAmaLAKQGNFKGFIDlYKRCYGCGRCEAICPRN 459
                                   6************.56666653225567889999996789************76 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.032
                        Fer4_7   3 igCgaCvaaCp 13 
                                   ++Cg C ++C 
  gi|15668325|ref|NP_247121.1| 573 VNCGSCLSNCH 583
                                   58999999995 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2       2.2   3.1e+03      43      56 ..      70      84 ..      36      87 .. 0.65
   2 !   17.6   0.2     3e-06    0.0041      40      60 ..     399     422 ..     364     423 .. 0.75
   3 !   15.0   0.3     2e-05     0.027      42      61 .]     442     461 ..     424     461 .. 0.82
   4 ?    1.6   0.0       0.3   4.2e+02       4      13 ..     574     583 ..     570     610 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.2
                       Fer4_17 43 aslCieCgeCe.rkC 56
                                  +  C  C +C+  kC
  gi|15668325|ref|NP_247121.1| 70 MPICDLCCLCTfGKC 84
                                  445555555554444 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3e-06
                       Fer4_17  40 e...ekaslCieCgeCerkCPqgl 60 
                                   +   e a++C+eCg C+r CP+ +
  gi|15668325|ref|NP_247121.1| 399 NevvELAKQCTECGWCNRNCPNAF 422
                                   1445789**************965 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2e-05
                       Fer4_17  42 kaslCieCgeCerkCPqgld 61 
                                     ++C +Cg+Ce+ CP +l+
  gi|15668325|ref|NP_247121.1| 442 LYKRCYGCGRCEAICPRNLP 461
                                   5789************9985 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.3
                       Fer4_17   4 qCgyClpeCp 13 
                                   +Cg Cl +C 
  gi|15668325|ref|NP_247121.1| 574 NCGSCLSNCH 583
                                   5777777775 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   3.4   0.00055      0.76      33      49 ..     398     421 ..     382     422 .. 0.67
   2 !   24.5   9.9   1.7e-08   2.3e-05       1      49 [.     407     459 ..     407     461 .. 0.82
   3 ?    3.5   0.1     0.059        81       4      13 ..     574     583 ..     543     602 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00055
                        Fer4_9  33 e.......eaCigCgaCveaCpkg 49 
                                           ++C++Cg C   Cp+ 
  gi|15668325|ref|NP_247121.1| 398 LnevvelaKQCTECGWCNRNCPNA 421
                                   1334445568***********985 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.7e-08
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkg 49 
                                   +Ct+Cg C + Cp+   v++a +   + + ++     ++C+gCg+C+++Cp++
  gi|15668325|ref|NP_247121.1| 407 QCTECGWCNRNCPNAFKVKEAMALAKQGNFKGFidlyKRCYGCGRCEAICPRN 459
                                   6***********988777777666666655555889999************97 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.059
                        Fer4_9   4 gCgaCveaCp 13 
                                   +Cg+C + C 
  gi|15668325|ref|NP_247121.1| 574 NCGSCLSNCH 583
                                   4555555553 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2  10.4   8.1e-08   0.00011       5      56 .]     404     457 ..     400     457 .. 0.79
   2 !   14.3   1.4   2.4e-05     0.034       7      24 ..     444     467 ..     439     483 .. 0.72
   3 ?    1.2   0.0      0.29     4e+02      11      23 ..     574     584 ..     570     619 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.1e-08
                       Fer4_10   5 dddtCirCgkCvkaCPadl.tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                    +++C++Cg C++ CP  +  +     ++ ++ +  +  +++C gcg C ++CP
  gi|15668325|ref|NP_247121.1| 404 LAKQCTECGWCNRNCPNAFkVKEAMALAKQGNFKGFIdLYKRCYGCGRCEAICP 457
                                   5789*************887555555556666666666899************9 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.4e-05
                       Fer4_10   7 dtCirCgkCvkaCPadl......t 24 
                                   ++C +Cg+C + CP +l      t
  gi|15668325|ref|NP_247121.1| 444 KRCYGCGRCEAICPRNLpivsmtT 467
                                   689999999999999777666543 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.29
                       Fer4_10  11 rCgkCvkaCPadl 23 
                                   +Cg C + C  ++
  gi|15668325|ref|NP_247121.1| 574 NCGSCLSNC--HI 584
                                   688888888..55 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3         2   2.7e+03      46      61 ..     264     279 ..     247     281 .. 0.75
   2 !   11.6   0.6    0.0003      0.41      26      66 ..     380     420 ..     366     421 .. 0.79
   3 !   13.9   0.4   5.8e-05      0.08      51      67 .]     443     459 ..     423     460 .. 0.81
   4 ?    3.0   0.1      0.14     2e+02      34      64 ..     552     582 ..     528     585 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2
                       Fer4_16  46 ekckkqeaitgCdiCq 61 
                                   e++ ++ ++  C+iC 
  gi|15668325|ref|NP_247121.1| 264 EENSMEDEVEVCGICC 279
                                   44556778899**995 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0003
                       Fer4_16  26 earecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                   e  + ++++ +++k+l++ +e  + ++++t C+ C++ CP+
  gi|15668325|ref|NP_247121.1| 380 EVAKIVAKERKDRKTLPDLNEVVELAKQCTECGWCNRNCPN 420
                                   5556666677888888888888889999***********96 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 5.8e-05
                       Fer4_16  51 qeaitgCdiCqdvCPan 67 
                                   +++++gC++C+++CP n
  gi|15668325|ref|NP_247121.1| 443 YKRCYGCGRCEAICPRN 459
                                   57788999999999876 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.14
                       Fer4_16  34 ntaekkdlaedeekckkqeaitgCdiCqdvC 64 
                                   ++++ k+l+e++  + +++ +  C+ C   C
  gi|15668325|ref|NP_247121.1| 552 KDKDGKTLYEKYPGEFRAGGLVNCGSCLSNC 582
                                   6667777777777777777788888888887 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   3.4   0.00011      0.15      45      63 ..     402     420 ..     370     422 .. 0.68
   2 !   19.5  12.4   7.2e-07   0.00099       3      64 ..     406     459 ..     403     460 .. 0.82
   3 !   13.7   1.1   4.7e-05     0.065       3      17 ..     444     472 ..     441     498 .. 0.66
   4 !    6.3   0.0    0.0094        13       6      18 ..     573     585 ..     573     632 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                        Fer4_8  45 eealwsCttcgaCtevCpv 63 
                                    e +++Ct+cg C+++Cp+
  gi|15668325|ref|NP_247121.1| 402 VELAKQCTECGWCNRNCPN 420
                                   5778999999999999996 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 7.2e-07
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   ++C+eCg C+ +Cp + + k+    a++++ +     +        ++C +cg+C+  Cp +
  gi|15668325|ref|NP_247121.1| 406 KQCTECGWCNRNCPNAFKVKEAMALAKQGNFK-G-FIDL------YKRCYGCGRCEAICPRN 459
                                   79************999999777777777666.3.3344......59*************87 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 4.7e-05
                        Fer4_8   3 ekCieCgaCqsaCp..............v 17 
                                   ++C +Cg+C++ Cp              +
  gi|15668325|ref|NP_247121.1| 444 KRCYGCGRCEAICPrnlpivsmttkvgeA 472
                                   68999999999998776655444444442 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0094
                        Fer4_8   6 ieCgaCqsaCpvl 18 
                                   ++Cg C s+C++ 
  gi|15668325|ref|NP_247121.1| 573 VNCGSCLSNCHIT 585
                                   58********954 PP

>> CODH_A_N  Carbon monoxide dehydrogenase subunit alpha N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.1e-05     0.016       7      60 ..     128     189 ..     122     211 .. 0.71
   2 ?   -0.1   0.0       0.7   9.6e+02      26      52 ..     381     407 ..     375     411 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                      CODH_A_N   7 aikkygkdkkvefPdT.AYylPviyaltGekvktlgdleevLerarsllkeeet.......L 60 
                                    i++ g+d ++   +      P+   +tG k ktlgdle++L+ +++++++  +        
  gi|15668325|ref|NP_247121.1| 128 LIETLGRDYPIDLGNEiEVEAPIARTVTGIKPKTLGDLEKILDYCEEQITHLLSaahtgqeG 189
                                   566666666666665314567999*************************9987744444440 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.7
                      CODH_A_N  26 lPviyaltGekvktlgdleevLerars 52 
                                   ++ i+a   ++ ktl dl+ev+e a++
  gi|15668325|ref|NP_247121.1| 381 VAKIVAKERKDRKTLPDLNEVVELAKQ 407
                                   566788888999**********99987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   1.4       8.1   1.1e+04      35      48 ..     266     279 ..     237     284 .. 0.52
   2 !   18.5   5.0   1.2e-06    0.0017       6      52 ..     406     457 ..     400     463 .. 0.77
   3 ?    4.0   0.3     0.038        53       9      28 ..     573     591 ..     570     599 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.1
                       Fer4_21  35 kvvedeCvGCnlCs 48 
                                   + +ede   C +C 
  gi|15668325|ref|NP_247121.1| 266 NSMEDEVEVCGICC 279
                                   34566666666665 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.2e-06
                       Fer4_21   6 dkCigCgkCliaCedt..shqaieidaktvlkvv...edeCvGCnlCssvCP 52 
                                   ++C +Cg C   C+++    +a+ ++++  +k      ++C GC  C ++CP
  gi|15668325|ref|NP_247121.1| 406 KQCTECGWCNRNCPNAfkVKEAMALAKQGNFKGFidlYKRCYGCGRCEAICP 457
                                   68************8522467887776665544222379************* PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.038
                       Fer4_21   9 igCgkCliaCedtshqaiei 28 
                                   ++Cg+Cl  C+ t+  ai+i
  gi|15668325|ref|NP_247121.1| 573 VNCGSCLSNCHITG-AAIKI 591
                                   79********9654.46655 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.7     0.059        82       4      15 ..     408     419 ..     399     430 .. 0.90
   2 !   17.8   1.7   2.4e-06    0.0034       2      16 ..     444     458 ..     443     468 .. 0.91
   3 ?    3.4   0.5     0.097   1.3e+02       5      14 ..     573     582 ..     573     589 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.059
                        Fer4_4   4 CigCgsCvaaCP 15 
                                   C++Cg C + CP
  gi|15668325|ref|NP_247121.1| 408 CTECGWCNRNCP 419
                                   *********999 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.4e-06
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   +rC gCg+C+a+CP 
  gi|15668325|ref|NP_247121.1| 444 KRCYGCGRCEAICPR 458
                                   89************5 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.097
                        Fer4_4   5 igCgsCvaaC 14 
                                   ++CgsC + C
  gi|15668325|ref|NP_247121.1| 573 VNCGSCLSNC 582
                                   58*****999 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   1.0       9.3   1.3e+04      11      14 ..     275     278 ..     274     278 .. 0.93
   2 !    9.8   1.8   0.00052      0.72       7      20 ..     407     420 ..     404     422 .. 0.91
   3 !   16.3   2.7   4.5e-06    0.0063       6      21 ..     444     459 ..     442     461 .. 0.91
   4 ?    0.3   1.7      0.51     7e+02       9      18 ..     573     582 ..     573     582 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 9.3
                                   -THH CS
                          Fer4  11 CGaC 14 
                                   CG+C
  gi|15668325|ref|NP_247121.1| 275 CGIC 278
                                   **** PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00052
                                   TSSS-THHHHHSTT CS
                          Fer4   7 kCigCGaCvevCPv 20 
                                    C+ CG C   CP+
  gi|15668325|ref|NP_247121.1| 407 QCTECGWCNRNCPN 420
                                   5************7 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 4.5e-06
                                   TTSSS-THHHHHSTTT CS
                          Fer4   6 ekCigCGaCvevCPvg 21 
                                    +C gCG+C+ +CP +
  gi|15668325|ref|NP_247121.1| 444 KRCYGCGRCEAICPRN 459
                                   58************87 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.51
                                   SS-THHHHHS CS
                          Fer4   9 igCGaCvevC 18 
                                   ++CG C + C
  gi|15668325|ref|NP_247121.1| 573 VNCGSCLSNC 582
                                   68****9988 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   0.00012      0.16       4      25 ..     406     427 ..     402     435 .. 0.86
   2 ?    7.7   0.7    0.0036         5       4      18 ..     444     458 ..     440     464 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                       Fer4_13   4 dtCiacgaCvelaPdvFeedde 25 
                                   ++C++cg C   +P+ F+ ++ 
  gi|15668325|ref|NP_247121.1| 406 KQCTECGWCNRNCPNAFKVKEA 427
                                   69***************99875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0036
                       Fer4_13   4 dtCiacgaCvelaPd 18 
                                   ++C +cg C +++P 
  gi|15668325|ref|NP_247121.1| 444 KRCYGCGRCEAICPR 458
                                   68************7 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   2.7     0.043        60      80      94 ..     406     420 ..     376     422 .. 0.74
   2 ?    3.9   2.8     0.071        98       1      16 [.     407     422 ..     407     436 .. 0.73
   3 ?   11.6   3.1   0.00028      0.38      79      95 ..     443     459 ..     422     460 .. 0.80
   4 ?    0.9   0.2      0.59   8.2e+02      74      93 ..     564     583 ..     554     586 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.043
                       Fer4_22  80 sgCvGCgRCieacpv 94 
                                   ++C+ Cg C+++cp+
  gi|15668325|ref|NP_247121.1| 406 KQCTECGWCNRNCPN 420
                                   568888888888875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.071
                       Fer4_22   1 rClsCgaCtlvCptCs 16 
                                   +C +Cg C+  Cp  +
  gi|15668325|ref|NP_247121.1| 407 QCTECGWCNRNCPNAF 422
                                   5888888888888654 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00028
                       Fer4_22  79 esgCvGCgRCieacpvk 95 
                                    + C GCgRC++ cp +
  gi|15668325|ref|NP_247121.1| 443 YKRCYGCGRCEAICPRN 459
                                   468***********986 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.59
                       Fer4_22  74 kekfgesgCvGCgRCieacp 93 
                                     +f + g v Cg C ++c+
  gi|15668325|ref|NP_247121.1| 564 PGEFRAGGLVNCGSCLSNCH 583
                                   55666677788999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (774 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 4891.83
//
Query:       gi|15668326|ref|NP_247122.1|  [L=146]
Description: acetyl-CoA decarbonylase/synthase complex subunit epsilon [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      9e-44  149.2   1.9    1.1e-43  148.9   1.9    1.1  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha
    0.00042   21.1   0.2    0.00075   20.3   0.1    1.5  2  RTTN_N        Rotatin, an armadillo repeat protein, centriole
    0.00066   19.4   0.0     0.0027   17.5   0.0    1.9  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.9   1.9   1.9e-47   1.1e-43       3     168 .]       6     144 ..       4     144 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 1.9e-47
                                   XXXXXXXXXXXXXXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEETHHHTT-G..GGSE CS
                         CO_dh   3 lekiPfdeaaianskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvatalkeaglkdyekkn 83 
                                   +++iP   +a +n+++a+++++ ++v++mi++ak+P+li+G++++++e +e ++k i++++lk+++t+         e++n
  gi|15668326|ref|NP_247122.1|   6 IAYIP---TAGSNVAHAEITSP-TLVKMMIRRAKKPILILGENLEENE-KELISKLIEKFNLKTIKTP---------EEMN 72 
                                   67889...9*************.*************************.9******************.........9*** PP

                                   -HHHHHHHHHSTT--TTTSS---SEEEEES--HHHHHHHHHHHHHH-TT-EEEE-SSS--TTSSEEE---GGGHHHHHHHH CS
                         CO_dh  84 klveltkllkdpepkgfdgegeydlvlfiGviyYyasqalsslkkftdkittiaidkyyhpdAdvslanlskeeeeyleml 164
                                    ++++++l+++          +ydl+lf+G++yYy++qa+++lk+f+ +++ti+idkyy+p++ +s++nlskee  yl++l
  gi|15668326|ref|NP_247122.1|  73 LMAIMKYLASS----------DYDLALFTGITYYYLAQAATHLKQFS-NVVTISIDKYYQPNTLYSFPNLSKEE--YLDYL 140
                                   ***********..........**************************.**************************..***** PP

                                   HHHH CS
                         CO_dh 165 eell 168
                                   ++ll
  gi|15668326|ref|NP_247122.1| 141 RKLL 144
                                   *985 PP

>> RTTN_N  Rotatin, an armadillo repeat protein, centriole functioning
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.3e-07   0.00075      18      74 ..      39      98 ..      29     120 .. 0.81
   2 ?   -2.7   0.0       1.8   1.1e+04      45      57 ..     132     144 ..     124     145 .. 0.55

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                        RTTN_N 18 llseedl.vkekellkkLlewFnfepvp..eeeevLaLllkllkspsaaellkkigavef 74
                                  l++ e+l  +ekel+ kL+e Fn++++   ee + +a+++ l+ s++  +l+  i++  +
  gi|15668326|ref|NP_247122.1| 39 LILGENLeENEKELISKLIEKFNLKTIKtpEEMNLMAIMKYLASSDYDLALFTGITYYYL 98
                                  7788899899**************987633778899************999999987655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.8
                        RTTN_N  45 eeeevLaLllkll 57 
                                    +ee L+ l+kll
  gi|15668326|ref|NP_247122.1| 132 SKEEYLDYLRKLL 144
                                   3455566666654 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.5e-07    0.0027       7      49 ..      30      71 ..      26     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.5e-07
                                  HHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGT CS
                  TPP_enzyme_M  7 llkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgk 49
                                  ++++ak+p++++G     ++ +e + +l+ek+++  + t+   
  gi|15668326|ref|NP_247122.1| 30 MIRRAKKPILILGENLE-ENEKELISKLIEKFNLKTIKTPEEM 71
                                  89**************9.88999999***********999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1112.88
//
Query:       gi|15668327|ref|NP_247123.1|  [L=151]
Description: formate dehydrogenase, iron-sulfur subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-12   46.6  41.8    3.3e-08   33.0   6.5    5.9  6  Fer4      4Fe-4S binding domain
    4.2e-11   42.8  13.2    4.2e-11   42.8  13.2    2.1  2  Fer4_11   4Fe-4S dicluster domain
    5.8e-10   39.6  28.2    0.00072   20.1  14.2    4.2  5  Fer4_7    4Fe-4S dicluster domain
    9.6e-10   38.5  23.9    2.6e-05   24.3  10.6    3.3  3  Fer4_9    4Fe-4S dicluster domain
    7.1e-09   35.6  32.3    2.3e-05   24.4  10.5    2.8  3  Fer4_10   4Fe-4S dicluster domain
    9.8e-09   34.9  41.4    2.2e-05   24.3   6.3    4.8  4  Fer4_6    4Fe-4S binding domain
    8.8e-07   28.7  32.8    0.00023   21.1   3.1    4.3  4  Fer4_2    4Fe-4S binding domain
    0.00016   21.9  31.5     0.0013   19.0   1.3    5.1  4  Fer4_4    4Fe-4S binding domain
    0.00029   21.7  31.8       0.29   12.1   1.2    4.7  5  Fer4_16   4Fe-4S double cluster binding domain
    0.00076   19.6  34.9      0.033   14.3   8.9    3.9  3  Fer4_21   4Fe-4S dicluster domain
     0.0026   18.2   2.1     0.0026   18.2   2.1    4.2  5  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.041   14.8  37.5        2.7    9.1   1.5    4.4  4  Fer4_3    4Fe-4S binding domain
        3.9    8.0  32.6         12    6.5  10.3    4.3  3  Fer4_8    4Fe-4S dicluster domain
        5.6    7.8  25.6          6    7.7   0.7    4.5  3  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   4.5   1.1e-05     0.014       1      18 [.       6      23 ..       6      25 .. 0.93
   2 ?    3.1   0.2     0.074        94       9      17 ..      40      48 ..      40      48 .. 0.86
   3 !   11.0   1.0   0.00023      0.29      14      24 .]      50      60 ..      50      60 .. 0.95
   4 !   33.0   6.5   2.5e-11   3.3e-08       1      23 [.      66      88 ..      66      89 .. 0.95
   5 ?    0.2   0.1       0.6   7.7e+02       7      11 ..      97     101 ..      94     103 .. 0.84
   6 ?    5.3   0.2     0.015        19      13      22 ..     110     119 ..     110     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                                  EEEETTTSSS-THHHHHS CS
                          Fer4  1 vvideekCigCGaCvevC 18
                                  +v ++ekC++C  C+++C
  gi|15668327|ref|NP_247123.1|  6 IVLNPEKCTKCYDCINIC 23
                                  588*************** PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.074
                                  SS-THHHHH CS
                          Fer4  9 igCGaCvev 17
                                  i+C++C+++
  gi|15668327|ref|NP_247123.1| 40 IFCMQCENA 48
                                  79****986 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00023
                                  HHHHSTTTEEE CS
                          Fer4 14 CvevCPvgAIt 24
                                  C e+CPv+AI+
  gi|15668327|ref|NP_247123.1| 50 CKEICPVDAIY 60
                                  99********6 PP

  == domain 4  score: 33.0 bits;  conditional E-value: 2.5e-11
                                  EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                  +++d+e+Ci+CG C+ +CP gAI
  gi|15668327|ref|NP_247123.1| 66 PIVDKERCIACGMCAIACPIGAI 88
                                  689*******************9 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.6
                                   TSSS- CS
                          Fer4   7 kCigC 11 
                                   kC+ C
  gi|15668327|ref|NP_247123.1|  97 KCTLC 101
                                   89999 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.015
                                   HHHHHSTTTE CS
                          Fer4  13 aCvevCPvgA 22 
                                   aCve+C   A
  gi|15668327|ref|NP_247123.1| 110 ACVEACKDKA 119
                                   7*****8777 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.7      0.12   1.5e+02       5      24 ..       8      25 ..       5      41 .. 0.65
   2 !   42.8  13.2   3.3e-14   4.2e-11       6      96 ..      38     121 ..      33     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.12
                       Fer4_11  5 flpeqCrhCleppCvasaps 24
                                  + pe+C +C +  C++++++
  gi|15668327|ref|NP_247123.1|  8 LNPEKCTKCYD--CINICKE 25
                                  56888888875..6666654 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 3.3e-14
                       Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGllpac 86 
                                   +p  C++C+++pC++++p++ai+ ++  G+ ++d++++   + +++ acP  +++ ++   +++kC++cld  +   +pac
  gi|15668327|ref|NP_247123.1|  38 IPIFCMQCENAPCKEICPVDAIYLKD--GIPIVDKERCI-ACGMCAIACPIGAIFIKN--RVAHKCTLCLDVDR--ITPAC 111
                                   6889*******************976..**********7.*************99965..4569******9988..89*** PP

                       Fer4_11  87 vescptgaln 96 
                                   ve+c  +al 
  gi|15668327|ref|NP_247123.1| 112 VEACKDKALL 121
                                   ****988775 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   2.6   6.9e-05     0.088      31      49 ..       6      24 ..       2      26 .. 0.87
   2 !   12.9   2.0    0.0001      0.13      25      52 .]      29      58 ..      24      58 .. 0.86
   3 !   20.1  14.2   5.6e-07   0.00072       2      52 .]      42      87 ..      41      87 .. 0.89
   4 !   15.4  12.4   1.6e-05     0.021       1      49 [.      72     116 ..      72     119 .. 0.72
   5 !    8.7   0.4    0.0021       2.6       1      22 [.      97     125 ..      97     147 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.9e-05
                        Fer4_7 31 veidpekClgCgaCvavCP 49
                                  ++++pekC+ C+ C++ C 
  gi|15668327|ref|NP_247123.1|  6 IVLNPEKCTKCYDCINICK 24
                                  6789**************5 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.0001
                        Fer4_7 25 ekgtekveidpekClgCga..CvavCPtga 52
                                  e++++kv++ p  C++C++  C + CP++a
  gi|15668327|ref|NP_247123.1| 29 ESRVRKVDGIPIFCMQCENapCKEICPVDA 58
                                  4567889999999*****99********97 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 5.6e-07
                        Fer4_7  2 CigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  C++C+   C + Cpv+ai+l++         + +d e+C+ Cg+C+ +CP ga
  gi|15668327|ref|NP_247123.1| 42 CMQCEnaPCKEICPVDAIYLKDG-------IPIVDKERCIACGMCAIACPIGA 87
                                  ****7669************774.......567899**************997 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 1.6e-05
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgC....gaCvavCP 49 
                                   rCi Cg C+ aCp +ai ++++        v+++ + Cl+      aCv++C 
  gi|15668327|ref|NP_247123.1|  72 RCIACGMCAIACPIGAIFIKNR--------VAHKCTLCLDVdritPACVEACK 116
                                   8******************887........44444555553222246999997 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0021
                        Fer4_7   1 rCigCg.......aCvaaCpvkaieldee 22 
                                   +C+ C        aCv+aC+ ka+ l  e
  gi|15668327|ref|NP_247123.1|  97 KCTLCLdvdritpACVEACKDKALLLVSE 125
                                   68888444445559*****9999887654 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.7   4.1e-05     0.052      34      47 ..      11      24 ..       2      33 .. 0.79
   2 !   24.3  10.6     2e-08   2.6e-05       2      51 .]      42      88 ..      41      88 .. 0.92
   3 !    9.2   0.3     0.001       1.3      35      50 ..      97     119 ..      89     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                        Fer4_9 34 eaCigCgaCveaCp 47
                                  e+C++C +C+++C+
  gi|15668327|ref|NP_247123.1| 11 EKCTKCYDCINICK 24
                                  57999999999997 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2e-08
                        Fer4_9  2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  C++C +  C e Cp +++  +++  ++  +     +Ci Cg C+ aCp gai
  gi|15668327|ref|NP_247123.1| 42 CMQCENapCKEICPVDAIYLKDGIPIVDKE-----RCIACGMCAIACPIGAI 88
                                  ****9888***************9999974.....6************9987 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.001
                        Fer4_9  35 aCigCga.......CveaCpkga 50 
                                   +C+ C +       CveaC+ +a
  gi|15668327|ref|NP_247123.1|  97 KCTLCLDvdritpaCVEACKDKA 119
                                   68888777778888888887765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5  14.5   1.1e-05     0.014       2      56 .]       6      55 ..       5      55 .. 0.92
   2 !    8.0   3.3    0.0023         3       8      22 ..      41      57 ..      34      64 .. 0.82
   3 !   24.4  10.5   1.8e-08   2.3e-05       3      55 ..      67     115 ..      65     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                       Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg..aCveaCP 56
                                  +v+++++C++C +C + C       + +  +s+  +v++ +  C++c+   C e+CP
  gi|15668327|ref|NP_247123.1|  6 IVLNPEKCTKCYDCINIC-------KEIHGESRVRKVDGIPIFCMQCEnaPCKEICP 55
                                  789***************.......789999999999999*******7669*****9 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0023
                       Fer4_10  8 tCirCg..kCvkaCPad 22
                                   C++C+   C++ CP+d
  gi|15668327|ref|NP_247123.1| 41 FCMQCEnaPCKEICPVD 57
                                  6****9889******93 PP

  == domain 3  score: 24.4 bits;  conditional E-value: 1.8e-08
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg....aCveaC 55 
                                   ++d+++Ci Cg C  aCP         g++ ++++v +k+  C ++     aCveaC
  gi|15668327|ref|NP_247123.1|  67 IVDKERCIACGMCAIACPI--------GAIFIKNRVAHKCTLCLDVDritpACVEAC 115
                                   789****************........**********99999999756668****** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   2.7   3.5e-07   0.00045       4      21 ..       8      25 ..       5      28 .. 0.87
   2 !    6.1   4.6    0.0096        12       9      24 .]      42      59 ..      41      59 .. 0.88
   3 !   24.3   6.3   1.7e-08   2.2e-05       1      24 []      65      88 ..      65      88 .. 0.94
   4 ?    1.9   4.3      0.21   2.7e+02       8      24 .]      97     120 ..      94     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.5e-07
                        Fer4_6  4 idpdkCigCgdCvrvCPe 21
                                   +p+kC+ C+dC+++C e
  gi|15668327|ref|NP_247123.1|  8 LNPEKCTKCYDCINICKE 25
                                  59**************86 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0096
                        Fer4_6  9 CigCgd..CvrvCPegai 24
                                  C +C++  C  +CP +ai
  gi|15668327|ref|NP_247123.1| 42 CMQCENapCKEICPVDAI 59
                                  88997779*******998 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 1.7e-08
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  ++ +d+++Ci Cg C+++CP gai
  gi|15668327|ref|NP_247123.1| 65 IPIVDKERCIACGMCAIACPIGAI 88
                                  5789****************9998 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.21
                        Fer4_6   8 kCigCgd.......CvrvCPegai 24 
                                   kC+ C d       Cv +C  +a+
  gi|15668327|ref|NP_247123.1|  97 KCTLCLDvdritpaCVEACKDKAL 120
                                   67777666777777*****98875 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.9   1.4e-05     0.018       3      21 ..       6      24 ..       3      25 .. 0.89
   2 ?    5.7   3.1     0.013        17      10      21 ..      42      55 ..      38      56 .. 0.90
   3 !   21.1   3.1   1.8e-07   0.00023       3      21 ..      66      84 ..      64      84 .. 0.93
   4 ?    4.3   1.9     0.039        49       9      20 ..      97     115 ..      92     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  +v ++++C+ C  C++ C 
  gi|15668327|ref|NP_247123.1|  6 IVLNPEKCTKCYDCINICK 24
                                  899***************5 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                        Fer4_2 10 CigCg..aCvsaCP 21
                                  C++C+  +C   CP
  gi|15668327|ref|NP_247123.1| 42 CMQCEnaPCKEICP 55
                                  ****889**999** PP

  == domain 3  score: 21.1 bits;  conditional E-value: 1.8e-07
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  + vd +rCi+Cg C  aCP
  gi|15668327|ref|NP_247123.1| 66 PIVDKERCIACGMCAIACP 84
                                  789***************9 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.039
                        Fer4_2   9 rCigCg.......aCvsaC 20 
                                   +C+ C        aCv aC
  gi|15668327|ref|NP_247123.1|  97 KCTLCLdvdritpACVEAC 115
                                   7999966777889****** PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   2.5   0.00029      0.37       1      15 [.      10      24 ..      10      33 .. 0.92
   2 ?    6.1   1.5     0.015        19       7      15 ..      42      55 ..      42      57 .. 0.47
   3 !   19.0   1.3     1e-06    0.0013       1      15 [.      70      84 ..      70      94 .. 0.93
   4 ?    0.5   4.0      0.88   1.1e+03       8      16 ..     109     117 ..      95     119 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                        Fer4_4  1 qerCigCgsCvaaCP 15
                                  +e+C+ C  C+++C+
  gi|15668327|ref|NP_247123.1| 10 PEKCTKCYDCINICK 24
                                  69************7 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.015
                        Fer4_4  7 CgsCvaa.....CP 15
                                  C++C++a     CP
  gi|15668327|ref|NP_247123.1| 42 CMQCENApckeiCP 55
                                  66655554222277 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 1e-06
                        Fer4_4  1 qerCigCgsCvaaCP 15
                                  +erCi Cg C +aCP
  gi|15668327|ref|NP_247123.1| 70 KERCIACGMCAIACP 84
                                  69************9 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.88
                        Fer4_4   8 gsCvaaCPq 16 
                                   ++Cv aC++
  gi|15668327|ref|NP_247123.1| 109 PACVEACKD 117
                                   47*****86 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.4     0.026        34       1      12 [.      12      23 ..      12      34 .. 0.89
   2 !   12.1   1.2   0.00022      0.29       1      20 [.      41      62 ..      41      71 .. 0.88
   3 !    8.3   9.5    0.0035       4.5       1      20 [.      72      91 ..      72     101 .. 0.82
   4 ?   -0.2   0.2       1.5     2e+03       3      11 ..      96     104 ..      94     104 .. 0.74
   5 !    7.9   0.1    0.0046       5.8       7      34 ..     110     137 ..     109     151 .] 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                       Fer4_16  1 rCgtCgkCaevC 12
                                  +C++C  C+++C
  gi|15668327|ref|NP_247123.1| 12 KCTKCYDCINIC 23
                                  5**********9 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00022
                       Fer4_16  1 rCgtCgk..CaevCPtnaikek 20
                                  +C +C++  C e+CP++ai  k
  gi|15668327|ref|NP_247123.1| 41 FCMQCENapCKEICPVDAIYLK 62
                                  6****9999**********876 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0035
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  rC+ Cg Ca +CP +ai  k
  gi|15668327|ref|NP_247123.1| 72 RCIACGMCAIACPIGAIFIK 91
                                  6***************9766 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.5
                       Fer4_16   3 gtCgkCaev 11 
                                   ++C+ C++v
  gi|15668327|ref|NP_247123.1|  96 HKCTLCLDV 104
                                   578888875 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0046
                       Fer4_16   7 kCaevCPtnaikekkekeiearecisyn 34 
                                   +C+e+C  +a+   +e++++  ++++ +
  gi|15668327|ref|NP_247123.1| 110 ACVEACKDKALLLVSEETLDMMKEEKRK 137
                                   6*************99999988887763 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1  13.8    0.0011       1.4       3      57 ..       8      59 ..       6      61 .. 0.75
   2 !   14.3   8.9   2.6e-05     0.033       2      29 ..      67      91 ..      66     109 .. 0.72
   3 ?    2.1   1.7      0.17   2.2e+02      13      26 ..     110     123 ..      95     141 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                       Fer4_21  3 idedkCigCgkCliaCedtshqaieidak.tvlkvvedeCvGCnl..CssvCPvedci 57
                                  ++++kC +C  C+  C++     i+++++ +++  +   C+ C+   C ++CPv d+i
  gi|15668327|ref|NP_247123.1|  8 LNPEKCTKCYDCINICKE-----IHGESRvRKVDGIPIFCMQCENapCKEICPV-DAI 59
                                  6899*************7.....665433134444577899997555******9.887 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.6e-05
                       Fer4_21  2 ridedkCigCgkCliaCedtshqaieid 29
                                  ++d+++Ci Cg C+iaC+   + ai i+
  gi|15668327|ref|NP_247123.1| 67 IVDKERCIACGMCAIACP---IGAIFIK 91
                                  578899999999999998...5566554 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.17
                       Fer4_21  13 kCliaCedtshqai 26 
                                    C+ aC+d++   +
  gi|15668327|ref|NP_247123.1| 110 ACVEACKDKALLLV 123
                                   48888888665444 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.8   0.00065      0.83       2      20 ..       9      27 ..       8      34 .. 0.87
   2 ?   -1.3   2.0       2.5   3.2e+03       6      17 ..      42      55 ..      40      56 .. 0.67
   3 ?    1.5   1.4      0.36   4.6e+02      49      56 ..      52      59 ..      44      61 .. 0.84
   4 !   18.2   2.1   2.1e-06    0.0026       1      17 [.      68      84 ..      68      92 .. 0.96
   5 ?   -2.3   0.3       5.2   6.6e+03      11      18 ..     110     117 ..     108     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00065
                       Fer4_13  2 DrdtCiacgaCvelaPdvF 20
                                  + ++C+ c  C +++ ++ 
  gi|15668327|ref|NP_247123.1|  9 NPEKCTKCYDCINICKEIH 27
                                  579************9986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.5
                       Fer4_13  6 Ciacga..CvelaP 17
                                  C+ c++  C e++P
  gi|15668327|ref|NP_247123.1| 42 CMQCENapCKEICP 55
                                  66665444888888 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.36
                       Fer4_13 49 daCPvesI 56
                                  + CPv++I
  gi|15668327|ref|NP_247123.1| 52 EICPVDAI 59
                                  679**999 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 2.1e-06
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  VD+++Ciacg C+ ++P
  gi|15668327|ref|NP_247123.1| 68 VDKERCIACGMCAIACP 84
                                  9***************9 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 5.2
                       Fer4_13  11 aCvelaPd 18 
                                   aCve++ d
  gi|15668327|ref|NP_247123.1| 110 ACVEACKD 117
                                   69999976 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   2.2      0.01        13       1      11 [.      13      23 ..      13      27 .. 0.93
   2 ?    8.6   4.7    0.0031         4       1      15 []      42      58 ..      42      58 .. 0.91
   3 ?    7.8   6.2    0.0058       7.4       1      15 []      73      87 ..      73      87 .. 0.97
   4 ?    9.1   1.5    0.0021       2.7       1      12 [.      98     116 ..      97     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.01
                        Fer4_3  1 CtgCgaCvevC 11
                                  Ct C+ C + C
  gi|15668327|ref|NP_247123.1| 13 CTKCYDCINIC 23
                                  *********** PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0031
                        Fer4_3  1 CtgCg..aCvevCPvgA 15
                                  C++C+  +C e CPv+A
  gi|15668327|ref|NP_247123.1| 42 CMQCEnaPCKEICPVDA 58
                                  99**8778*******98 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0058
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ Cg C  +CP gA
  gi|15668327|ref|NP_247123.1| 73 CIACGMCAIACPIGA 87
                                  9************98 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0021
                        Fer4_3   1 CtgCg.......aCvevCP 12 
                                   Ct C        aCve+C 
  gi|15668327|ref|NP_247123.1|  98 CTLCLdvdritpACVEACK 116
                                   9999557889999*****5 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   3.1     0.011        14       4      16 ..      12      24 ..       9      40 .. 0.69
   2 ?    4.3   2.8     0.043        55      51      64 ..      42      57 ..      27      58 .. 0.85
   3 ?    6.5  10.3    0.0091        12       3      17 ..      71      89 ..      69     150 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.011
                        Fer4_8  4 kCieCgaCqsaCp 16
                                  kC++C  C + C 
  gi|15668327|ref|NP_247123.1| 12 KCTKCYDCINICK 24
                                  5666666666664 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.043
                        Fer4_8 51 Cttcga..CtevCpvg 64
                                  C++c++  C+e Cpv+
  gi|15668327|ref|NP_247123.1| 42 CMQCENapCKEICPVD 57
                                  9999989999999985 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0091
                        Fer4_8  3 ekCieCgaCqsaCp....v 17
                                  e+Ci Cg+C  aCp    +
  gi|15668327|ref|NP_247123.1| 71 ERCIACGMCAIACPigaiF 89
                                  6899999999999844431 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.7    0.0047         6       1      23 [.       6      28 ..       6      38 .. 0.85
   2 ?    3.2   0.3      0.12   1.5e+02      58      65 ..      53      60 ..      50      61 .. 0.84
   3 ?    3.2  12.3      0.12   1.5e+02       3      19 ..      68      84 ..      67     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0047
                       Fer4_15  1 VvvDrdaCigcglCvaeapevfe 23
                                  +v++ ++C+ c  C+  ++e+  
  gi|15668327|ref|NP_247123.1|  6 IVLNPEKCTKCYDCINICKEIHG 28
                                  688999************98755 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.12
                       Fer4_15 58 aCPvdAIr 65
                                   CPvdAI 
  gi|15668327|ref|NP_247123.1| 53 ICPVDAIY 60
                                  6******6 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.12
                       Fer4_15  3 vDrdaCigcglCvaeap 19
                                  vD+++Ci cg+C+ ++p
  gi|15668327|ref|NP_247123.1| 68 VDKERCIACGMCAIACP 84
                                  9**************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1084  (0.0604607); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 952.47
//
Query:       gi|15668328|ref|NP_247124.1|  [L=469]
Description: acetyl-CoA decarbonylase/synthase complex subunit beta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-65  217.7   0.5    6.7e-65  217.7   0.5    1.7  2  CdhC      CO dehydrogenase/acetyl-CoA synthase complex beta s
  ------ inclusion threshold ------
       0.02   14.3   0.7        1.4    8.3   0.0    2.3  2  PcrB      PcrB family


Domain annotation for each model (and alignments):
>> CdhC  CO dehydrogenase/acetyl-CoA synthase complex beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.7   0.5   7.5e-69   6.7e-65       1     155 []       5     155 ..       5     155 .. 0.97
   2 ?   -2.4   0.1      0.43   3.9e+03      37      57 ..     407     427 ..     388     436 .. 0.69

  Alignments for each domain:
  == domain 1  score: 217.7 bits;  conditional E-value: 7.5e-69
                          CdhC   1 ipvevspafeGeriRkedlyvelggkktkafElvkvkeadevedgkieviGpdideveegsrlplailvevaGkkleedlE 81 
                                   ipv+v+p+ eGer+R  d+yvel+g k+ +fElvkv +  + ed k+e+iG+dide+eegsr p+ai+vev+G++leedlE
  gi|15668328|ref|NP_247124.1|   5 IPVSVGPMNEGERVRGPDMYVELAGPKSYGFELVKVVN--KAED-KVEIIGKDIDEMEEGSRNPFAIIVEVSGSNLEEDLE 82 
                                   8************************99*********55..5566.9*********************************** PP

                          CdhC  82 pvlERriHeflnyieGvmHlgqRdiiwvRiskeavekGlrlkhigevlyaklkeefeaivdkvevtlitdeekv 155
                                   +vlERriHeflnyieGvmHl+qRd++w+Ri+k++++kGlrlkhig+v+++++k+ef ++++k++vt+itd+ekv
  gi|15668328|ref|NP_247124.1|  83 GVLERRIHEFLNYIEGVMHLNQRDQVWIRINKDSFNKGLRLKHIGKVVQRLFKAEF-PFIEKCDVTIITDPEKV 155
                                   ********************************************************.***************97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.43
                          CdhC  37 keadevedgkieviGpdidev 57 
                                    e++eve++  ev G ++ ++
  gi|15668328|ref|NP_247124.1| 407 IEEEEVEEEMEEVEGIEVPTM 427
                                   355667777667777666655 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1    0.0033        30     157     218 ..      23      88 ..      18      95 .. 0.78
   2 ?    8.3   0.0   0.00015       1.4      17      86 ..     378     451 ..     365     468 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0033
                                   EEEE-TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCCSSEEEE-CHHHHHH....HCH CS
                          PcrB 157 iYlEasGaledveevialkkklekarlivGGGirsaEkAkevveaADvivvGnvveekd....erk 218
                                   +Y+E +G +    e++++++k e++  i+G  i++ E+  +   a  v v G  +ee+     er+
  gi|15668328|ref|NP_247124.1|  23 MYVELAGPKSYGFELVKVVNKAEDKVEIIGKDIDEMEEGSRNPFAIIVEVSGSNLEEDLegvlERR 88 
                                   79999998777755666777777777889***********99999999999999999984444444 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00015
                                   S-CHHHHHHHHCTT-S.EEEEECST...CHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSEEEEEEETTB CS
                          PcrB  17 enpdEiveiviesgtD.avmigGsq...svtldntvrllkkvsriklPivlepsnvegvvryaDalFvmsllns 86 
                                   +++dE ++ + e+g   a  ig       ++++++ + +++v+ i++P +  p+   g+ +++ ++ + +++ +
  gi|15668328|ref|NP_247124.1| 378 KTTDELIKFLKEKGHPcAERIGAEVeeeAIEEEEVEEEMEEVEGIEVPTMTLPGTFAGLPPGIKIVLYNAVIKA 451
                                   56777777776655441344544434568899***********************************9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2869.16
//
Query:       gi|15668329|ref|NP_247125.1|  [L=96]
Description: hypothetical protein MJ_0157 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-22   77.8   0.2    6.6e-22   77.7   0.2    1.0  1  DUF2098         Uncharacterized protein conserved in archaea 
  ------ inclusion threshold ------
       0.02   15.0   4.9      0.056   13.6   5.0    1.7  1  HAS-barrel      HAS barrel domain
      0.029   14.5   0.5      0.043   13.9   0.5    1.3  1  SH3_12          Xrn1 SH3-like domain
       0.13   12.6   0.1       0.26   11.6   0.1    1.6  1  Reg_prop        Two component regulator propeller
        0.2   12.4   2.6       0.52   11.0   2.6    1.7  1  CarD_CdnL_TRCF  CarD-like/TRCF domain


Domain annotation for each model (and alignments):
>> DUF2098  Uncharacterized protein conserved in archaea (DUF2098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.2   1.8e-25   6.6e-22       1      93 [.       8      95 ..       8      96 .] 0.90

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 1.8e-25
                       DUF2098  1 eievGsvVrYinTgTvGkVvdikkeedgevwvkLdstdLyYrvdtLevidekekkkekeekekedleelekkekeleeevdee 83
                                  +i+vG++V YinTgT G+Vvdi+k+e+g++wv L +++L+Yr + L+vid++ k +e++e+ +e +++lek+e e+ + +d +
  gi|15668329|ref|NP_247125.1|  8 NIKVGDYVVYINTGTKGRVVDIRKDENGDIWVVL-DNNLMYRPHLLRVIDKS-KITERKEDIDEVVKKLEKEELEEGKLIDLD 88
                                  59********************************.579************65.99******************9999888877 PP

                       DUF2098 84 ketdesceGG 93
                                       +++G+
  gi|15668329|ref|NP_247125.1| 89 L---GDACGA 95
                                  7...445555 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   5.0   1.6e-05     0.056      21      73 ..       7      68 ..       3      86 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                    HAS-barrel 21 kdvkvGeyVeielpdgeivlGmvtdirrgn.....................selsndlalvlsleeleeangdd 73
                                  +++kvG+yV+++   ++ + G+v+dir+                       +++s+++++ +++         d
  gi|15668329|ref|NP_247125.1|  7 VNIKVGDYVVYI---NTGTKGRVVDIRKDEngdiwvvldnnlmyrphllrvIDKSKITERKEDI---------D 68
                                  489*********...559*********9557777777777764444444443333333333333.........3 PP

>> SH3_12  Xrn1 SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   1.2e-05     0.043       2      44 ..       8      46 ..       7      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                        SH3_12  2 qfrLgdrVvyvrdngksVPlGlrGtVVg...rsdtlleVlfDeefl 44
                                  ++++gd Vvy+++       G++G VV     ++  + V++D+  +
  gi|15668329|ref|NP_247125.1|  8 NIKVGDYVVYINT-------GTKGRVVDirkDENGDIWVVLDNNLM 46
                                  6899********9.......7*******9653345566****9876 PP

>> Reg_prop  Two component regulator propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   7.2e-05      0.26       5      20 ..      24      39 ..      20      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.2e-05
                                  SCEEEEEE-TTSCEEE CS
                      Reg_prop  5 nnvtaileDsdGrlWv 20
                                  ++v +i +D +G++Wv
  gi|15668329|ref|NP_247125.1| 24 GRVVDIRKDENGDIWV 39
                                  5899***********9 PP

>> CarD_CdnL_TRCF  CarD-like/TRCF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.6   0.00015      0.52       2      25 ..      10      34 ..       9      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                CarD_CdnL_TRCF  2 kvGDyVvhedhGi.Griegiekrev 25
                                  kvGDyVv+ + G  Gr+++i+k e 
  gi|15668329|ref|NP_247125.1| 10 KVGDYVVYINTGTkGRVVDIRKDEN 34
                                  89**********77******77744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1358  (0.0757432); expected 358.6 (0.02)
Passed bias filter:                      880  (0.0490825); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 621.28
//
Query:       gi|15668330|ref|NP_247126.1|  [L=374]
Description: selenocystein synthase SelA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-06   27.3   0.1    2.5e-06   26.7   0.1    1.3  1  SelA             L-seryl-tRNA selenium transferase
    3.1e-06   26.0   0.1    1.6e-05   23.7   0.0    1.9  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00012   21.2   0.1     0.0002   20.4   0.1    1.5  1  Aminotran_5      Aminotransferase class-V
    0.00079   18.7   0.0     0.0011   18.2   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    0.00093   17.9   0.0     0.0013   17.4   0.0    1.2  1  SHMT             Serine hydroxymethyltransferase
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.021   14.1   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
       0.15   12.2   0.0       0.68   10.1   0.0    2.0  2  PGM_PMM_III      Phosphoglucomutase/phosphomannomutase, alpha


Domain annotation for each model (and alignments):
>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.1   9.9e-10   2.5e-06     164     260 ..     166     255 ..     136     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 9.9e-10
                                   HHHHHHT--EEEEEES-B-S-GGGGT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHHHHSTHHHHTB- CS
                          SelA 164 elgkekglpvleDlGsGllvdlseyglskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkkelieklkknplkraLrv 244
                                   + +k+k+  v+ D  sG+ v l    +++ P    al+ G+dlv  s Dkl+ gp+ G++ Gkkel++k+  +  k  L  
  gi|15668330|ref|NP_247126.1| 166 NTAKNKEAIVFVDDASGARVRL---LFNQPP----ALKLGADLVVTSTDKLMEGPRGGLLAGKKELVDKIYIEGTKFGLEA 239
                                   5566666666666677766654...233333....5789*******************************99888888888 PP

                                   -HHHHHHHHHHHHHHH CS
                          SelA 245 Dkltlaaleatlrlyl 260
                                       la++  +l+ + 
  gi|15668330|ref|NP_247126.1| 240 QPPLLAGIYRALKNFN 255
                                   8888888888777764 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   6.1e-09   1.6e-05     117     251 ..     121     256 ..     111     269 .. 0.77
   2 ?    0.6   0.0      0.06   1.5e+02     118     152 ..     265     302 ..     245     318 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.1e-09
                                   CEEEEESTTSHHHHHHHCCTTEEEEEEESS-TT.TT----HHHHHHHHHHTT-EEEEEGTTTHT...TTS-G..GGGT-SE CS
               Cys_Met_Meta_PP 117 ievkfvdtsdleelekaikentklvylEtptnp.llkvvDiekiaklakkagvlvvvDntfasp...llqrp..lklgaDi 191
                                   +++k+++ +++ e+ ++i++ t ++ + +  +  ++++  ++k++++ak+++++v+vD +  +    l+ +p  lklgaD+
  gi|15668330|ref|NP_247126.1| 121 VNAKYFESDKVGEILNKIDKDTLVIITGSTMDLkVIELENFKKVINTAKNKEAIVFVDDASGARvrlLFNQPpaLKLGADL 201
                                   67899999999*********999999887766515788999******************999985533444445******* PP

                                   EEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHHHHHT-B--HHHHHHHHHHHTTHHH CS
               Cys_Met_Meta_PP 192 vvhSaTKylgGhsdvvaGvivvkgkeelkkelkflqnalGavlspfdawlllrGlkTLsl 251
                                   vv S+ K ++G     +G+++  gk+el ++++    ++G   +p     + r lk  +l
  gi|15668330|ref|NP_247126.1| 202 VVTSTDKLMEGPR---GGLLA--GKKELVDKIYIEGTKFGLEAQPPLLAGIYRALKNFNL 256
                                   ***********76...67777..4457777777777777777777666666666666655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.06
                                   EEEEESTTSHHHHHH...HCCTTEEEEEEESS-TTTT- CS
               Cys_Met_Meta_PP 118 evkfvdtsdleelek...aikentklvylEtptnpllk 152
                                   ++k +d s++e+l+k   ai++n ++vy  tpt  ++k
  gi|15668330|ref|NP_247126.1| 265 RAKNFDLSKIEKLNKelkAIDDNINIVYERTPTGFVIK 302
                                   5566777777777752226788*********9977665 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   7.9e-08    0.0002     155     221 ..     158     228 ..     119     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.9e-08
                                   B--HHHHHHHHHHTT-EEEEE-TTTTTTS....---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS CS
                   Aminotran_5 155 iqpveeigklakkkgalvlvDaaqavghi....pidvkklgvDflafsghK.llgPtGiGvlyvrkellekl 221
                                   ++ ++++++ ak+k+a+v+vD a+++  +    +    klg+D+++ s+ K + gP G G+l ++kel  k+
  gi|15668330|ref|NP_247126.1| 158 LENFKKVINTAKNKEAIVFVDDASGARVRllfnQPPALKLGADLVVTSTDKlMEGPRG-GLLAGKKELVDKI 228
                                   56789999**************99876552222667889************999****.*********9987 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.4e-07    0.0011      80     355 ..      88     354 ..      59     359 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.4e-07
                                   HHHHHHHHHHHTTT-EEEE.EE.SS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS- CS
                 Aminotran_1_2  80 liealifllklnpgdeilv.pd.ptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesph 158
                                   +i a i +lk  p+++i   p+ p ++s+++ +++  ++ ++            + ++++++++       t ++++++ +
  gi|15668330|ref|NP_247126.1|  88 AILATILALK--PKKVIHYlPElPGHPSIERSCKIVNAKYFESD---------KVGEILNKIDK------DT-LVIITG-S 149
                                   4444444444..77666431324888888888888888877777.........88999999997......22.444444.6 PP

                                   TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHH CS
                 Aminotran_1_2 159 NPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaav 239
                                    ++ +v+ le  +k++++ak +++++fvD+a ++ v     +++  + ++ + + l+v+s  K +   G R G ++g++++
  gi|15668330|ref|NP_247126.1| 150 TMDLKVIELENFKKVINTAKNKEAIVFVDDASGARVRL--LFNQ-PPALKLGAD-LVVTSTDKLM--EGPRGGLLAGKKEL 224
                                   89****************************98887776..3333.555555555.8888777765..66667********* PP

                                   HHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHS....TEEEECCSCSSEEEEEE CS
                 Aminotran_1_2 240 vsqlrklsrpfls..ssllqaavaaalsdallkqs..eleemrqrlqkrrkelrdeLael....glkvlasqsgmflltdl 312
                                   v+ + +  + f    + +l a +  al++++l++    +e ++    ++ ++l +eL+++    ++ +   ++g++  +++
  gi|15668330|ref|NP_247126.1| 225 VDKIYIEGTKFGLeaQPPLLAGIYRALKNFNLERIrkAFERAKNFDLSKIEKLNKELKAIddniNIVYERTPTGFVIKRVY 305
                                   ***999999988867445555555555555554334644444444455555566666555655577777777888777777 PP

                                   THH..CHHHHHHH...HHHTCTEE.EEEGGGGTSTTEEEEECTTS-HHH CS
                 Aminotran_1_2 313 sae..takelskk...Lleevgvy.vtpgtsftvpgrlRitvAglteee 355
                                   +    + k+l +    Ll+++g++ +t    ++++++lRi + + ++e 
  gi|15668330|ref|NP_247126.1| 306 KDDtiNIKKLIEIgfnLLKNYGIItITVAGMPGASKSLRIDLTSRDAER 354
                                   7775555555555999777766651566667788999**9986655555 PP

>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.2e-07    0.0013     171     248 ..     143     224 ..     119     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.2e-07
                                   SEEEEE-SST-S---HHHHHHH...HHHTT-EEEEE-GGGHHHHHTTSS--GCC.TSSEEEEESSSTT-S-S-EEEEEC-S CS
                          SHMT 171 klivaGtsaysrlidyarlrei...adevgayllvdmahiaGlvaagvipsPfe.yadvvtttthktlrGprgglillrkg 247
                                    +i++G++   ++i+ ++++++   a++ +a+++vd a  a +      p  ++  ad+v t t k + Gprggl+  +k 
  gi|15668330|ref|NP_247126.1| 143 LVIITGSTMDLKVIELENFKKVintAKNKEAIVFVDDASGARVRLLFNQPPALKlGADLVVTSTDKLMEGPRGGLLAGKKE 223
                                   478999999999999888888733256678999**9997665544444444454269******************988865 PP

                                   E CS
                          SHMT 248 v 248
                                   +
  gi|15668330|ref|NP_247126.1| 224 L 224
                                   3 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.2e-06     0.021     102     216 ..     119     252 ..     110     359 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.2e-06
                                   -EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-C CS
               Beta_elim_lyase 102 knkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeiv 182
                                   k+ +a +++ +k+ +++++ +   +++ +i++  T+     +v++le+ ++v ++ak+++  +++D A  a     l  ++
  gi|15668330|ref|NP_247126.1| 119 KIVNAKYFESDKVGEILNKID---KDTLVIITGSTMDL---KVIELENFKKVINTAKNKEAIVFVDDASGARV-RLLFNQP 192
                                   555556788899999999944...5899999999***9...*************************7755543.4555666 PP

                                   HHHHTTSSEEEEESSSTT--SS-EEEEE-HH............................. CS
               Beta_elim_lyase 183 kemfsyvDsvtmslkKdllanvGgvlafrddel..........................e 216
                                     +  ++D v+ s  K +  + Gg+la++++                            +
  gi|15668330|ref|NP_247126.1| 193 PALKLGADLVVTSTDKLMEGPRGGLLAGKKELVdkiyiegtkfgleaqppllagiyralK 252
                                   667789***********************9965666666666666666666666666663 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00027      0.68      39      93 ..      43      96 ..      40     100 .. 0.81
   2 ?   -1.8   0.0       1.4   3.5e+03      36      52 ..     283     299 ..     276     307 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                                  HHTT-EEEEESSSCHHHHHHHHHTTE.CEEEETT.CEEEETTTBSS--HHHHHHHHH CS
                   PGM_PMM_III 39 kklgiklvetkvGdkyvleemkeega.vlGgEeS.ghiifldeattkDGilaallvl 93
                                  ++++  l++t +G++y++e+++e g+ +lGg e+   + f++      +ila +l+l
  gi|15668330|ref|NP_247126.1| 43 DEKDKALLNTYIGSSYFAEKVNEYGLkHLGGDENdKCVGFNRT---SSAILATILAL 96
                                  567778999****************659******666666655...88888888876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                                   HHHHHTT-EEEEESSSC CS
                   PGM_PMM_III  36 rvakklgiklvetkvGd 52 
                                    + ++ +i + +t++G+
  gi|15668330|ref|NP_247126.1| 283 AIDDNINIVYERTPTGF 299
                                   55566788999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 2665.79
//
Query:       gi|15668331|ref|NP_247127.1|  [L=542]
Description: hypothetical protein MJ_0159 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.7e-131  435.0   4.3    4.4e-68  229.1   0.3    2.2  2  NRD1_2    NrpR regulatory domains NRD1 and 2
    3.1e-31  107.1   1.9    7.1e-31  106.0   1.9    1.7  1  HTH_12    Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
       0.14   12.3   0.4       0.87    9.8   0.1    2.4  2  HTH_21    HTH-like domain


Domain annotation for each model (and alignments):
>> NRD1_2  NrpR regulatory domains NRD1 and 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.4   0.5   3.1e-65   1.9e-61       2     237 ..      87     304 ..      86     305 .. 0.97
   2 !  229.1   0.3   7.3e-72   4.4e-68       1     237 [.     322     537 ..     322     538 .. 0.97

  Alignments for each domain:
  == domain 1  score: 207.4 bits;  conditional E-value: 3.1e-65
                                   --HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE........EEEEEE- CS
                        NRD1_2   2 gfviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegekelevpegkvgiatvC 82 
                                   g+++s+i e+++  ++    + G V++N + +   d++++l+i+k v++sgl+v+drv i+++++         v+i+t+C
  gi|15668331|ref|NP_247127.1|  87 GSIYSNILEKTISANY----RFGYVVINRCQVY-ADFNDVLKIIKSVYESGLAVGDRVGIIDREKF--------VEINTLC 154
                                   7889999999999999....99**********5.******************************99........******* PP

                                   CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEEEEEEEEETTTH CS
                        NRD1_2  83 SitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkilAnlReipvsar 163
                                   S+++d++Ll+nGI   + ++G++++ed++pv+F+e+I+Y++tsidPl++fi+kk T+v+ +ie+geg+++An+R + v+  
  gi|15668331|ref|NP_247127.1| 155 SLNFDNILLQNGIFPLHVCAGVVKYEDGKPVEFKEIIDYKSTSIDPLRAFIEKKETDVMGIIENGEGYLPANFRYFGVEFL 235
                                   ********************************************************************************* PP

                                   HHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEEEEEGGGSE CS
                        NRD1_2 164 ekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsglidiselk 237
                                   e++e+i   l+ ++++ ++++g+  e+vlg++v ++kvg++++gGl+pia+++e+++ vei ++s+++++++l+
  gi|15668331|ref|NP_247127.1| 236 ERFETI---LEIDELKCIISYGT--ENVLGLDVGDDKVGVALIGGLTPIAPFVENNYCVEICPMSSIVRLESLH 304
                                   ******...8899**********..*********************************************9997 PP

  == domain 2  score: 229.1 bits;  conditional E-value: 7.3e-72
                                   ---HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE........EEEEEE CS
                        NRD1_2   1 vgfviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegekelevpegkvgiatv 81 
                                   ++  +sk+ + + kvt+d+++ +G+VivN+++idk++l+ea++ilke++k+gl +sdr+ i+ee+++        ++i+t+
  gi|15668331|ref|NP_247127.1| 322 IKTALSKMFNAMAKVTYDIDEADGDVIVNTAFIDKKYLDEAFDILKEAYKKGLGISDRFGIVEENDR--------IKIQTI 394
                                   57789**************************************************************........****** PP

                                   -CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEEEEEEEEETTT CS
                        NRD1_2  82 CSitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkilAnlReipvsa 162
                                   C +t+dg++l+n +p+ pkyGG+lei +  + rF+++I Y+g+s+dP+evf++           + e++ lA +Re++ +a
  gi|15668331|ref|NP_247127.1| 395 CAVTLDGIFLRNSVPLIPKYGGILEITED-KERFIDIIGYDGSSLDPHEVFFNF---------VDCEKTFLAGFREVHRVA 465
                                   ***************************99.67********************98.........68999************* PP

                                   HHHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEEEEEGGGSE CS
                        NRD1_2 163 rekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsglidiselk 237
                                   rek+ee+l+kl   +++g+ +igepn+e++g+ v+++++g+v++gG+np++ lke++i++e+ka+++++++s+lk
  gi|15668331|ref|NP_247127.1| 466 REKLEEVLKKL---NWNGIKAIGEPNNELYGIGVNKDMCGVVTMGGINPLVLLKENEIPIELKAMHEVVRFSDLK 537
                                   *******7777...899999*****************************************************98 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   1.9   1.2e-34   7.1e-31       1      66 []      12      77 ..      12      77 .. 0.99

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 1.2e-34
                        HTH_12  1 veILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGleeL 66
                                  +eIL+il++s++p+gak+ia+eL+krgy+igeravRy+L+ l+ ++lt++vgyagr +tE+GleeL
  gi|15668331|ref|NP_247127.1| 12 IEILDILSKSKEPVGAKIIAKELNKRGYKIGERAVRYHLKLLDGMKLTKKVGYAGRVITERGLEEL 77
                                  79**************************************************************98 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00015      0.87       7      44 ..      11      47 ..       5      54 .. 0.83
   2 ?   -0.9   0.0       0.3   1.8e+03      34      44 ..     105     115 ..      96     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00015
                        HTH_21  7 lalireifeeskgrYGyrriwaeLrreggvrvnhkrVr 44
                                  l +i +i  +sk   G++ i++eL+++g+ +++++ Vr
  gi|15668331|ref|NP_247127.1| 11 LIEILDILSKSKEPVGAKIIAKELNKRGY-KIGERAVR 47
                                  344999*********************77.6***9998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.3
                        HTH_21  34 ggvrvnhkrVr 44 
                                   g+v++n++ V+
  gi|15668331|ref|NP_247127.1| 105 GYVVINRCQVY 115
                                   7899****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3690.99
//
Query:       gi|15668332|ref|NP_247128.1|  [L=472]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit B [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.7e-92  307.7   0.0    9.4e-92  307.3   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
    9.5e-49  165.1   5.1    9.5e-49  165.1   5.1    1.9  2  GatB_Yqey  GatB domain
  ------ inclusion threshold ------
      0.092   13.2   1.8          1    9.8   0.2    2.7  2  SAPIS-gp6  Pathogenicity island protein gp6 in Staphylococcus


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.3   0.0   1.6e-95   9.4e-92       2     273 .]      11     278 ..      10     278 .. 0.95

  Alignments for each domain:
  == domain 1  score: 307.3 bits;  conditional E-value: 1.6e-95
                                   EEEEEEEEEB--SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--.EEHHHHHHHHHHHHHTTEEE..-SEE-EEEEE-T CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                        GatB_N   2 viGlEiHaqlktksKlFssasteeegeepnsevsevdlalPGtlPv.lnkeavelaikaalalncei..aeeskfdRKnyf 79 
                                   ++GlEiH+q++tksKlF+++st+  ++epn++v++v+l+lPG+ P  +nk+ave+ai++a++l+c+i   e ++f+RK+y 
  gi|15668332|ref|NP_247128.1|  11 KCGLEIHVQIDTKSKLFCNCSTNYLDAEPNTNVCPVCLGLPGAKPLpPNKKAVEVAIMVAKMLGCKIvvDEDIYFQRKHYD 91 
                                   89*******************9888899******************9******************98335789******** PP

                                   CTTCTTSEEEEESSS.SEEEEEEEETEEEEEEEEEEEE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N  80 ypdlpkgyQitqkeeplakeGslelekkvrierihlEeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavv 160
                                   ypdlp+gyQ+t+  +p+  +G+      ++i+++hlEeD ++   +     +vd+nR+G+pLiEivt+pd++speear+++
  gi|15668332|ref|NP_247128.1|  92 YPDLPSGYQRTS--TPIGVDGEFM---GIGIHEVHLEEDPGQYNPS---FGIVDYNRSGTPLIEIVTKPDIKSPEEAREFL 164
                                   ************..9*******99...9*************99875...56****************************** PP

                                   HHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH.......-EEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxx RF
                        GatB_N 161 eklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaieyeierqiell.......qeTrk 234
                                   ++l +l+r+lg  +g   eG++R+DvN+S++       +g+rvE+Kn+ns+k + k+++ye  rq +++       +eTr+
  gi|15668332|ref|NP_247128.1| 165 KQLMTLFRYLGCLRG---EGTMRADVNISIEYM---GVQGNRVEVKNVNSIKGVYKVLKYELIRQKNIIkrggevkRETRA 239
                                   **********99887...59***********55...4569***************************************** PP

                                   EETTTTEEEEECC----...-EEE-TTS--EE--HHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 235 fdedkgetvslRskeeaedYryfpepdlppleiseelie 273
                                   f e++  t+++Rske+aedYry+p+pd++p++ise++++
  gi|15668332|ref|NP_247128.1| 240 FLESQMITKAMRSKETAEDYRYIPDPDIQPIVISEKWVK 278
                                   ************************************985 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.22   1.3e+03      56      85 ..     271     301 ..     267     311 .. 0.84
   2 !  165.1   5.1   1.6e-52   9.5e-49       2     148 .]     318     470 ..     317     470 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.22
                                   SSGHHHHHHHHHHHHHH.TXXHHHHHHHCTX CS
                     GatB_Yqey  56 kIskkiakevleellee.gkspeeiieekgL 85 
                                    Is+k +ke+ e++ e+   + +  +ee+g+
  gi|15668332|ref|NP_247128.1| 271 VISEKWVKEIEEKMPETpLAKKKRFVEEYGI 301
                                   5999999999999999989999999999986 PP

  == domain 2  score: 165.1 bits;  conditional E-value: 1.6e-52
                                   HHHHHHHHS....S.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHH.HH.TXXH CS
                     GatB_Yqey   2 ffeevvkeg....adaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleell.ee.gksp 76 
                                   +feevvk+     ++  la++w+ nel ++l+++++++ e+ +++e+++el+kli+eg Is+kiake+++ l+ +  +k p
  gi|15668332|ref|NP_247128.1| 318 MFEEVVKSLgvnkENVDLAVTWIRNELRRSLQYHKVDLYESGVKAEHIVELIKLIKEGVISQKIAKEIVDLLViNRgKKMP 398
                                   688888877543245899****************************************************9997557999* PP

                                   HHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                     GatB_Yqey  77 eeiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                   +e++ee gL+ i+de++l k+vee+i++npkavedy +gk++al+fl+GqvM+ t+G+adpk+v ellke+L
  gi|15668332|ref|NP_247128.1| 399 KELVEELGLTVIRDEDALVKAVEEAIKNNPKAVEDYLNGKKEALNFLMGQVMRLTRGRADPKRVIELLKERL 470
                                   **********************************************************************98 PP

>> SAPIS-gp6  Pathogenicity island protein gp6 in Staphylococcus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.056   3.3e+02      14      50 ..     296     330 ..     288     349 .. 0.80
   2 ?    9.8   0.2   0.00017         1      22      43 ..     411     432 ..     391     443 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.056
                     SAPIS-gp6  14 AkalkLneeDknlLieAvdlDiKnnmqeiskElrene 50 
                                    + ++++eeD ++L+   dlD+ +  +e+ k l  n+
  gi|15668332|ref|NP_247128.1| 296 VEEYGIDEEDAKVLVS--DLDMAEMFEEVVKSLGVNK 330
                                   5668999999999996..8888888888887766555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00017
                     SAPIS-gp6  22 eDknlLieAvdlDiKnnmqeis 43 
                                    D ++L++Av++ iKnn + + 
  gi|15668332|ref|NP_247128.1| 411 RDEDALVKAVEEAIKNNPKAVE 432
                                   699**************88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3233.66
//
Query:       gi|15668333|ref|NP_247129.1|  [L=172]
Description: acetolactate synthase 3 regulatory subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-29   99.4   0.5    6.4e-28   96.8   0.0    2.1  2  ALS_ss_C         Small subunit of acetolactate synthase
    2.4e-19   68.9   0.3    4.8e-19   68.0   0.3    1.5  1  ACT_5            ACT domain
      2e-16   59.4   0.4    3.7e-16   58.6   0.4    1.4  1  ACT              ACT domain
    9.3e-05   23.0   1.5    0.00015   22.3   1.5    1.3  1  ACT_4            ACT domain
    0.00074   19.9   0.4       0.11   12.9   0.3    2.2  2  Acylphosphatase  Acylphosphatase
     0.0074   16.7   0.1      0.011   16.1   0.1    1.4  1  Saccharop_dh_N   LOR/SDH bifunctional enzyme conserved region
  ------ inclusion threshold ------
       0.13   13.3   0.0       0.19   12.7   0.0    1.4  1  LytR_C           LytR cell envelope-related transcriptional a


Domain annotation for each model (and alignments):
>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.22   5.7e+02      37      58 ..      52      73 ..      38      84 .. 0.66
   2 !   96.8   0.0   2.5e-31   6.4e-28       1      74 []      90     164 ..      90     164 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.22
                                  EEEEEEE-HHHHHHHHHHS-GG CS
                      ALS_ss_C 37 liieltgteekidaliellkpf 58
                                  ++i + g+ + ++++i+ l+++
  gi|15668333|ref|NP_247129.1| 52 VTIVVNGDDKILEQVIKQLNKL 73
                                  5666666666666666666543 PP

  == domain 2  score: 96.8 bits;  conditional E-value: 2.5e-31
                                   EEEEEEEEE.-SC.HHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHHHHHHHHHS-GGGEEEEEEEEEEEEEST CS
                      ALS_ss_C   1 RElaLiKVkaeke.erseileiaeifrakivdvspdsliieltgteekidaliellkpfgilevvRtGrvAleRG 74 
                                   REl+LiK+ a++e  +s++++ ++ifr+++vd+sp+sli+e+tg+e+ki+a+i+l+kp+gi+e++RtG++Al+RG
  gi|15668333|ref|NP_247129.1|  90 RELCLIKIYAPTEsAKSQVIQYTSIFRGNVVDLSPESLIVEITGSEDKINAFIDLVKPLGIKEMARTGITALARG 164
                                   9***********88************************************************************8 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.3   1.9e-22   4.8e-19       2      62 .]      18      79 ..      17      79 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.9e-22
                         ACT_5  2 apgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvelLsnQleKLidVlkV 62
                                  +pgvL+R+ ++++rrgF+++s+++  te+ + +r++++V++ ++ +e++++Ql+KLidV+kV
  gi|15668333|ref|NP_247129.1| 18 KPGVLQRISGLFTRRGFNISSITVGITENPQISRVTIVVNGdDKILEQVIKQLNKLIDVIKV 79
                                  7***********************************************************98 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.4   1.4e-19   3.7e-16       1      66 [.       9      74 ..       9      75 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 1.4e-19
                                  EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                           ACT  1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66
                                  +v++ +v ++PG+L r++g++++rg+Ni si+++ +e  + ++v++v+ +d++ le+v+++l+kl+
  gi|15668333|ref|NP_247129.1|  9 HVISALVLNKPGVLQRISGLFTRRGFNISSITVGITENPQISRVTIVVNGDDKILEQVIKQLNKLI 74
                                  689999**********************************************************97 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   1.5   5.9e-08   0.00015       9      79 ..      11      80 ..       5      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.9e-08
                         ACT_4  9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVk.dvehLsrviakLraipgVisVe 79
                                  ++  + +++g+L++i+ +++  + ni+s+++  ++  +    ++t+ V+ d + L++vi++L+++ +Vi+V+
  gi|15668333|ref|NP_247129.1| 11 ISALVLNKPGVLQRISGLFTRRGFNISSITVGITE--NPQISRVTIVVNgDDKILEQVIKQLNKLIDVIKVS 80
                                  778899***************************65..45666666666536788****************95 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.3   4.5e-05      0.11      29      74 ..      42      87 ..      37      92 .. 0.89
   2 ?    5.0   0.0     0.013        33      28      58 ..     116     146 ..     109     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.5e-05
               Acylphosphatase 29 GyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveel 74
                                  G ++N +  +V iv+ g+++ +e+++++l++    ++v+e+e +++
  gi|15668333|ref|NP_247129.1| 42 GITENPQISRVTIVVNGDDKILEQVIKQLNKLIDVIKVSELEEKKS 87
                                  889999999**********************999999999998765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.013
               Acylphosphatase  28 kGyvrNlsdgsVeivaegeeekvekfleelk 58 
                                   +G v  ls +s+ ++++g+e+k+++f++ +k
  gi|15668333|ref|NP_247129.1| 116 RGNVVDLSPESLIVEITGSEDKINAFIDLVK 146
                                   6888889999999**************9877 PP

>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   4.4e-06     0.011       9      83 ..       9      86 ..       3     109 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.4e-06
                                  XXTTSSHHHH..HHHHHHHT..TXEEEEEEEEXXSSTT.SXEEEEEEEEESSHHHHHHHHHHHHHHHHHSCCCCEEEECE CS
                Saccharop_dh_N  9 hliDsgilnk..vldlilea..ggsfevlefevGkkkk.dtSyaelevsaedeevLeeileeltelgaelveeedvklek 83
                                  h+i +++lnk  vl +i  +     f++ +++vG +++ + S +++ v+++d + Le+++++l++l + ++ +++++ +k
  gi|15668333|ref|NP_247129.1|  9 HVISALVLNKpgVLQRISGLftRRGFNISSITVGITENpQISRVTIVVNGDD-KILEQVIKQLNKLIDVIK-VSELEEKK 86
                                  55555555554456666543113459********876627799999999988.89*********9965544.23343333 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.6e-05      0.19      12      71 ..      18      86 ..      15     114 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.6e-05
                        LytR_C 12 vsGlAarvadaLeerGftvgevg.n.agnadee..ttivyreaaa......aaakalaaalglgelqeds 71
                                  ++G+ +r++ ++++rGf++++++   ++n + +  t +v++++ +      ++ ++l + ++++el+e++
  gi|15668333|ref|NP_247129.1| 18 KPGVLQRISGLFTRRGFNISSITvGiTENPQISrvTIVVNGDD-KileqviKQLNKLIDVIKVSELEEKK 86
                                  68999***************99944566665448555554333.23553333444555555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1196.73
//
Query:       gi|15668334|ref|NP_247130.1|  [L=421]
Description: putative mRNA 3'-end processing factor 3 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-24   83.9   0.0      3e-23   82.2   0.0    1.9  2  Beta-Casp        Beta-Casp domain
    1.1e-14   54.9   0.1    4.7e-14   52.9   0.1    1.9  1  Lactamase_B      Metallo-beta-lactamase superfamily
    2.9e-13   49.5   0.0      8e-13   48.1   0.0    1.8  1  RMMBL            Zn-dependent metallo-hydrolase RNA specifici
    3.6e-12   46.1   0.1    1.3e-11   44.3   0.0    1.9  2  Lactamase_B_6    Metallo-beta-lactamase superfamily domain
      1e-09   38.2   0.0    1.5e-09   37.6   0.0    1.2  1  Lactamase_B_2    Beta-lactamase superfamily domain
    1.1e-06   28.7   0.0    3.3e-06   27.1   0.0    1.7  1  Lactamase_B_3    Beta-lactamase superfamily domain
     0.0067   15.7   0.1      0.013   14.7   0.1    1.5  1  Beta_lactamase3  Putative beta-lactamase-like family


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.3   3.3e+03      52      52 ..     114     114 ..      67     179 .. 0.54
   2 !   82.2   0.0   1.2e-26     3e-23       1     110 []     222     338 ..     222     338 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                                   . CS
                     Beta-Casp  52 m 52 
                                    
  gi|15668334|ref|NP_247130.1| 114 Y 114
                                   2 PP

  == domain 2  score: 82.2 bits;  conditional E-value: 1.2e-26
                                   HHHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGGE-SHH....HHH.H....HH................HS CS
                     Beta-Casp   1 aqellylLeelwkekkledlklpiyldsplaskatevYkeyaeveakslewmesk.ke..eln................ss 62 
                                   aqe+l++++++++++kl   ++piy d++l ++at+vY +y       ++w++ k k+  e n                 +
  gi|15668334|ref|NP_247130.1| 222 AQEILLIINNYIRSGKL--RDVPIYTDGSL-IHATAVYMSY-------INWLNPKiKNmvE-NrinpfgeikkadeslvFN 291
                                   7*************875..346******55.8999**9***.......9999999854443.3588999999*******77 PP

                                   -SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                     Beta-Casp  63 kgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                   k+p++i+++sgm++gG++ ++lk ll+dp+n +il+gyqaegTlgr+l
  gi|15668334|ref|NP_247130.1| 292 KEPCIIVSTSGMVQGGPVLKYLK-LLKDPKNKLILTGYQAEGTLGREL 338
                                   8********************97.78********************86 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.1   1.8e-17   4.7e-14       7     162 ..      16     165 ..      13     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.8e-17
                                   EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHH CS
                   Lactamase_B   7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeea 87 
                                   +++ +e+ +g +L D+G+s++++ +       ++++k vdavi++H+HlDH+G+ +  + +  ++++  a+  +  +++ +
  gi|15668334|ref|NP_247130.1|  16 SCVEVETQKGRVLLDCGMSPDTGEIP------KVDDKAVDAVIVSHAHLDHCGAIPFYKFKKIYCTHPTADLMFITWRDTL 90 
                                   578899*******************7......9************************************************ PP

                                   HHHHHHCCHHTTCHCGCCEEEEETTTEE..CCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
                   Lactamase_B  88 ddaasrkglllagvsadkpdvdeeeldg..naggrralyvtggpghghghgvveygggkvlftGDallagetgridl 162
                                   +    +k+    + +a+ +++ ++ +++  ++  +++     g+  g+ ++ +e +g+k+l+tGD     ++ +++ 
  gi|15668334|ref|NP_247130.1|  91 NLTKAYKEE--DIQHAMENIECLNYYEErqITENIKFKFYNAGHILGSASIYLEVDGKKILYTGDINEGVSRTLLPA 165
                                   999999996..77777788888887776224556667777778888888999999**********977666666666 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   3.1e-16     8e-13       2      62 .]     352     413 ..     351     413 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 3.1e-16
                         RMMBL   2 ipvkarieeidfSgHadknellelirklkprn.vilvHGeeeatsalarllkeeegidvfiP 62 
                                   ip++ ++ +i+fS+H d+n+l ++i+k+ ++   i+ HGe+ + +++a ++++  +i +f+P
  gi|15668334|ref|NP_247130.1| 352 IPIRGKVVKIEFSAHGDYNSLVRYIKKIPKPEkAIVMHGERYQSLSFAMTIWKTLKIPTFVP 413
                                   89**************************55556*********************9****998 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0     5e-15   1.3e-11       5     169 ..      23     161 ..      18     175 .. 0.82
   2 ?   -1.8   0.0      0.68   1.7e+03     116     143 ..     310     335 ..     308     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 5e-15
                 Lactamase_B_6   5 dnvkiLlDvGwdeskvslesalkelekv.iptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvsll 84 
                                    + ++LlD+G++  +        e+ kv  + vd++++sha l+h Ga +  ++kfk       ++y+t+p++ L  ++  
  gi|15668334|ref|NP_247130.1|  23 QKGRVLLDCGMSPDTG-------EIPKVdDKAVDAVIVSHAHLDHCGAIP--FYKFK-------KIYCTHPTADLMFITWR 87 
                                   45699******98633.......3444414789**************964..44554.......79*********988888 PP

                 Lactamase_B_6  85 dlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYavdwnha 165
                                   d+ + +++         + edi++a+++i+ l Y  + ++++   ++ +  ynaGh lG +   ++   +ki+Y  d+n+ 
  gi|15668334|ref|NP_247130.1|  88 DTLNLTKA--------YKEEDIQHAMENIECLNYYEERQITE---NIKFKFYNAGHILGSASIYLEVDGKKILYTGDINEG 157
                                   88654433........4568*****************99985...8***************999***************86 PP

                 Lactamase_B_6 166 kesh 169
                                     + 
  gi|15668334|ref|NP_247130.1| 158 VSRT 161
                                   5555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.68
                 Lactamase_B_6 116 lkYsQklelkskldgltitaynaGhtlG 143
                                   lkY     lk++ ++l++t y+a  tlG
  gi|15668334|ref|NP_247130.1| 310 LKYLKL--LKDPKNKLILTGYQAEGTLG 335
                                   566655..78889*********988887 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0     6e-13   1.5e-09       2     169 ..      26     184 ..      25     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 6e-13
                                   EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH..........HCCT CS
                 Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla..........vlea 72 
                                   r+L+D+g +   + +    P  ++d+ +++daV+++haH DH+ g+  + ++++    +y++  +++          +l++
  gi|15668334|ref|NP_247130.1|  26 RVLLDCGMS---PDTGEI-P--KVDD-KAVDAVIVSHAHLDHC-GAIPFYKFKK----IYCTHPTADlmfitwrdtlNLTK 94 
                                   899999999...434444.3..3456.7***************.7777777644....99999999988887777666666 PP

                                   TCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HH.... CS
                 Lactamase_B_2  73 nfvylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipee.... 149
                                     + +  +++  +n++ l+  e+ +++ +++++++  a h  g          ++  +e +gk+++y+gD ++   +    
  gi|15668334|ref|NP_247130.1|  95 AYKEEDIQHA-MENIECLNYYEERQIT-ENIKFKFYNAGHILGS---------ASIYLEVDGKKILYTGDINEGVSRtllp 164
                                   6555555555.99*************8.689*******999999.........9999999************766442333 PP

                                   HHHHHCT-SEEEEE-S-SST CS
                 Lactamase_B_2 150 igerlggadllllditayed 169
                                   +++ ++ +d+l+++ t+ ++
  gi|15668334|ref|NP_247130.1| 165 ADTDIDEIDVLIIESTYGSP 184
                                   45889999999999987655 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.3e-09   3.3e-06       5     134 ..      13     177 ..      11     199 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.3e-09
                 Lactamase_B_3   5 lghnsflletagarilvDPfka.nlgyeppa...eeaDlvlisqaledHahletlkql....................... 58 
                                   +g +++ +et+  r+l+D +    +g e+p+   + +D+v++s+a+ dH+ + +  +                        
  gi|15668334|ref|NP_247130.1|  13 IGMSCVEVETQKGRVLLDCGMSpDTG-EIPKvddKAVDAVIVSHAHLDHCGAIPFYKFkkiycthptadlmfitwrdtlnl 92 
                                   699***************99753333.333367799****************99999555555555555555555555555 PP

                 Lactamase_B_3  59 ...aenvkvleegeslev.ggleiravatsh...davggsergenngflleqdgltiyhlGhlahelsseel...kelgrv 129
                                      +++ ++ +  e++e+ +  e r++++++       g+  g  +++l e+dg +i++ G++    s + l     + ++
  gi|15668334|ref|NP_247130.1|  93 tkaYKEEDIQHAMENIEClNYYEERQITENIkfkFYNAGHILGSASIYL-EVDGKKILYTGDINEGVSRTLLpadTDIDEI 172
                                   5542222222223444432334444444444222444688889999996.799**********998888777333455566 PP

                 Lactamase_B_3 130 Dvvlt 134
                                   Dv+++
  gi|15668334|ref|NP_247130.1| 173 DVLII 177
                                   66665 PP

>> Beta_lactamase3  Putative beta-lactamase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   5.2e-06     0.013      52     138 ..      39     130 ..      36     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.2e-06
               Beta_lactamase3  52 eiikvkaenidkifvtss..nsl.gifFlkkdvpiYiTkpvYeqlllrlkellslqvvyeeeeekq...dlkiveeidier 126
                                   ei+kv  + +d ++v++   +   +i F k +  iY T+p    + + +++ l+l   y+ee++++   + ++++  +  +
  gi|15668334|ref|NP_247130.1|  39 EIPKVDDKAVDAVIVSHAhlDHCgAIPFYKFKK-IYCTHPTADLMFITWRDTLNLTKAYKEEDIQHameNIECLNYYEERQ 118
                                   689999999999999987223332577888876.****************************9988666777777888899 PP

               Beta_lactamase3 127 lkrnvkfiryne 138
                                   +  n+kf  yn 
  gi|15668334|ref|NP_247130.1| 119 ITENIKFKFYNA 130
                                   9******99995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2911.90
//
Query:       gi|15668335|ref|NP_247131.1|  [L=187]
Description: hypothetical protein MJ_0163 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-10   40.1   0.0    3.2e-10   39.7   0.0    1.2  1  Robl_LC7  Roadblock/LC7 domain
  ------ inclusion threshold ------
      0.016   15.2   0.2      0.028   14.4   0.2    1.4  1  FixQ      Cbb3-type cytochrome oxidase component FixQ
       0.15   12.1   0.1       0.28   11.2   0.1    1.5  1  DUF1043   Protein of unknown function (DUF1043)
       0.26   11.3   5.0       0.34   10.9   0.3    2.7  3  DUF1310   Protein of unknown function (DUF1310)


Domain annotation for each model (and alignments):
>> Robl_LC7  Roadblock/LC7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   7.1e-14   3.2e-10       3      78 ..      62     136 ..      60     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 7.1e-14
                                   HHHHHHCCHHCTECEEEEEETTS-EEEECCSSSS-HHHHHHHHHHHHHHHHHHHHHCT..SSSECEEEEEETTEEEEE CS
                      Robl_LC7   3 eelleelqsvpgvrgalvvskdGlviatstldnddadqlAalasgllsaakaaarelg..egelkelliegkkgelyl 78 
                                   e +l e++  +++++++vv+ +Glviat   + +dad+++a+as++++++k+++ +++      ++++++++  +ly 
  gi|15668335|ref|NP_247131.1|  62 EFDLVEIALSYDIEDIIVVNDEGLVIAT---TLKDADEVGATASSIFEYIKKLCGNIKkvVIFKEDSYLYIYPLKLYG 136
                                   67788999999*****************...**************************977777777777777777665 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   6.3e-06     0.028      12      37 ..       6      31 ..       2      34 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.3e-06
                          FixQ 12 swgllflvllfygvviyafrpgnrkd 37
                                  ++++lf v++++gv +y ++ + rk+
  gi|15668335|ref|NP_247131.1|  6 IFLILFIVGVLIGVGVYYYKEKERKK 31
                                  799*****************999643 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   6.3e-05      0.28       2      29 ..       8      35 ..       7      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.3e-05
                       DUF1043  2 liglvvGiiiGalilrltnsklkkqkkl 29
                                  li ++vG+ iG+ ++++ +++ kk  k+
  gi|15668335|ref|NP_247131.1|  8 LILFIVGVLIGVGVYYYKEKERKKTYKI 35
                                  799***************9998887764 PP

>> DUF1310  Protein of unknown function (DUF1310)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   7.5e-05      0.34       2      42 ..       4      44 ..       3      55 .. 0.75
   2 ?   -0.5   0.0      0.25   1.1e+03      33      52 ..      77      96 ..      57     107 .. 0.60
   3 ?    1.2   0.1     0.075   3.3e+02       7      46 ..     115     155 ..     109     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.5e-05
                       DUF1310  2 iivlvilvivilavGvkfyldeeklneEmvnvvkSdeakev 42
                                  ii++ il iv++ +Gv +y  +ek ++   ++++ + ++++
  gi|15668335|ref|NP_247131.1|  4 IIIFLILFIVGVLIGVGVYYYKEKERKKTYKIIEMEIIENL 44
                                  57777888888888888888888888888888877666555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.25
                       DUF1310 33 vvkSdeakeviekelkelDa 52
                                  ++  ++   vi ++lk++D+
  gi|15668335|ref|NP_247131.1| 77 IIVVNDEGLVIATTLKDADE 96
                                  34444444444444444444 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.075
                       DUF1310   7 ilvivilavGvkfyldeekl.neEmvnvvkSdeakevieke 46 
                                   i  +vi+    ++y+   kl  e +  +++S+ a  vie++
  gi|15668335|ref|NP_247131.1| 115 IKKVVIFKEDSYLYIYPLKLyGENLYVIIESKIALDVIEEK 155
                                   55677888888899999999777889999999999999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1280  (0.0713927); expected 358.6 (0.02)
Passed bias filter:                      793  (0.04423); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1255.66
//
Query:       gi|15668336|ref|NP_247132.1|  [L=395]
Description: hypothetical protein MJ_0164 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     1e-138  461.7  46.0    1.2e-78  264.5  17.7    3.0  3  DUF2226   Uncharacterized protein conserved in archaea (DUF22
  ------ inclusion threshold ------
        4.5    7.4   5.7        0.5   10.5   0.8    1.9  2  OGG_N     8-oxoguanine DNA glycosylase, N-terminal domain


Domain annotation for each model (and alignments):
>> DUF2226  Uncharacterized protein conserved in archaea (DUF2226)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.5  17.7   1.3e-82   1.2e-78       1     178 [.       1     218 [.       1     218 [. 1.00
   2 !   13.3   1.7   4.4e-06      0.04      82     105 ..     215     244 ..     215     263 .. 0.73
   3 !  198.8  13.0   1.4e-62   1.3e-58     167     297 .]     263     388 ..     252     388 .. 0.96

  Alignments for each domain:
  == domain 1  score: 264.5 bits;  conditional E-value: 1.3e-82
                       DUF2226   1 mmepkikvveseyvk....gnleeiieeissadlGyvritvkegeklldafilvedGkiVgayledvrsteelsgeeavee 77 
                                   m+e++ikvv++eyvk    gnleeii+ei++   Gy++i+vkeg+kl++++i+vedGkiVg+y++d++ste+++++e+v+e
  gi|15668336|ref|NP_247132.1|   1 MRENMIKVVDGEYVKtlyeGNLEEIINEIDT---GYILILVKEGNKLHEGYIFVEDGKIVGCYYTDSESTEVFGNKEKVIE 78 
                                   99*****************************...*********************************************** PP

                       DUF2226  78 llglesavvDvyeleedkielikelnd............eknedisekrdiveklleikleieldnliean.......... 136
                                   ll++e++v+D+y++++dki+l+k+l++            ekned+sekrdivek+l+ikl+i+ldnliean          
  gi|15668336|ref|NP_247132.1|  79 LLNYENKVIDIYKYNKDKINLMKWLYPeifackdtnkvsEKNEDMSEKRDIVEKYLNIKLDIPLDNLIEANtkdfekyled 159
                                   ********************************************************************************* PP

                       DUF2226 137 .................kgyiiykgqipiaaayEcdleellgkdayekleevlkepetv 178
                                                    +gyiiykgq+piaaayEcdl++llgkdayeklee+lk+++tv
  gi|15668336|ref|NP_247132.1| 160 nkyiiinayrkkdgkfeNGYIIYKGQTPIAAAYECDLGVLLGKDAYEKLEEMLKDENTV 218
                                   *********************************************************86 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.4e-06
                       DUF2226  82 esavvDvyeleedkielikelnd......e 105
                                   e+ v+Dvye++e k  +i+el++      e
  gi|15668336|ref|NP_247132.1| 215 ENTVIDVYEYNEKKTHVILELYPqmkildE 244
                                   799********************5555541 PP

  == domain 3  score: 198.8 bits;  conditional E-value: 1.4e-62
                       DUF2226 167 kleevlkepetvsReelLkKlGikepdeesietiledvfepsdeelaeddleelkekilseivlkvkrmegvvdvlvnlki 247
                                    ++e+++e+ tvsReelLkKlGikepde++ietiledvf+psdeel     eelkeki+seiv+kvkrmegv+dvlvnlki
  gi|15668336|ref|NP_247132.1| 263 TTAEEIEEESTVSREELLKKLGIKEPDENWIETILEDVFRPSDEEL-----EELKEKIESEIVNKVKRMEGVSDVLVNLKI 338
                                   57888999999***********************************.....****************************** PP

                       DUF2226 248 kveegryyifgdvnvvrkrileiikkdidpsivkfeidntikelvskttr 297
                                   k+e+gryyifgdvnv+rkril+iikkdidpsivkfeidntik++vsk+t+
  gi|15668336|ref|NP_247132.1| 339 KWENGRYYIFGDVNVKRKRILGIIKKDIDPSIVKFEIDNTIKKYVSKYTS 388
                                   ***********************************************986 PP

>> OGG_N  8-oxoguanine DNA glycosylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.8   5.5e-05       0.5      32      92 ..      67     148 ..      57     179 .. 0.73
   2 ?   -2.1   0.4      0.43   3.9e+03      57      57 ..     257     257 ..     211     317 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.5e-05
                                   EEEETT..EEEEEE.EETTEEEEET--.............................HHHHHHTHHHHTTTTS-..HHHHHH CS
                         OGG_N  32 vgvlgd..rvveLk.qeeddllyrtlesess................tkasseeakeeeteeilrdYfnLdvd..leelyk 91 
                                   + v+g+  +v+eL  +e++ + ++ +++++                 +k s+++++++e+++i+++Y+n+++d  l++l++
  gi|15668336|ref|NP_247132.1|  67 TEVFGNkeKVIELLnYENKVIDIYKYNKDKInlmkwlypeifackdtNKVSEKNEDMSEKRDIVEKYLNIKLDipLDNLIE 147
                                   444443337777663566666666666666589999999999999989999999**************9655422777764 PP

                                   H CS
                         OGG_N  92 e 92 
                                    
  gi|15668336|ref|NP_247132.1| 148 A 148
                                   4 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.43
                                   . CS
                         OGG_N  57 e 57 
                                   e
  gi|15668336|ref|NP_247132.1| 257 E 257
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1576  (0.0879023); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2926.86
//
Query:       gi|15668337|ref|NP_247133.1|  [L=256]
Description: hypothetical protein MJ_0165 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-19   70.0   3.9    2.2e-19   69.5   3.1    1.6  2  AIRC          AIR carboxylase
     0.0018   18.3   0.1          3    7.9   0.0    2.5  2  Hpr_kinase_N  HPr Serine kinase N terminus


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.24   2.2e+03       4      43 ..      53      93 ..      52     104 .. 0.68
   2 !   69.5   3.1   2.4e-23   2.2e-19       1     128 [.     126     252 ..     126     256 .] 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.24
                                  EEESSGGGHH.HHHHHHHHHHHTT-EEEEEE--TTTSHHHH CS
                          AIRC  4 iimGSdsDle.vmkkaaeilkelgveyevrvvSahrtpeel 43
                                  ++ G   D++ ++k++ +++++ g+++ +++    +  +e+
  gi|15668337|ref|NP_247133.1| 53 VVYGKGKDIDeIIKATLKLVEKNGIALATKIEDIEKLSDEI 93
                                  56677777752556777888888888888876666655555 PP

  == domain 2  score: 69.5 bits;  conditional E-value: 2.4e-23
                                   EEEEEESSGGGHHHHHHHHHHHHHTT-....EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSS CS
                          AIRC   1 kVgiimGSdsDlevmkkaaeilkelgv....eyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvasltt 77 
                                   kVgi+++ +sD++v+++a+++l+ +gv    +y+v ++  hr    l++++e    +++ +iI++AG++ +Lp+v+as+++
  gi|15668337|ref|NP_247133.1| 126 KVGILTAGTSDIPVAEEAKDTLEIMGVeaitAYDVGIAGIHRLFPALKRMIE----EDVCCIIVVAGMEGALPSVIASMVD 202
                                   69*************************888889*********9888888877....5689********************* PP

                                   S-EEEEEE--STTCCHHHHHHHHT--T.TS--EE-SSTHHHHHHHHHHHHHT CS
                          AIRC  78 lPVigvPvkskalkgldsllSivqmPs.gvpvatvaigkaknAallAaqila 128
                                   +PVigvP++++    +  ll +++ +s g++v  v+i+++  A+++A  i  
  gi|15668337|ref|NP_247133.1| 203 IPVIGVPTSTSYGIKITPLLTMLHSCSpGIAV--VNIDNGFGAGVFAGLIAK 252
                                   **********9999999*******99856655..566699999999977765 PP

>> Hpr_kinase_N  HPr Serine kinase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00036       3.2      59     124 ..      29      96 ..      25      96 .. 0.79
   2 !    7.9   0.0   0.00033         3      72     115 ..     171     213 ..     166     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00036
                                   HHHHT-HHHHH..HHHHHHTT--S-EEEETTT---HHH...HHHHHHH---EEEESS-HHHHHTTHHHH CS
                  Hpr_kinase_N  59 sYleklseeerkerleklfskkipciiltrgleppeel...lelaeeygvpllrtklstsefiaeliry 124
                                   +Y+e+++e   k  +++ f++++p +++ +g +++e +   l+l e++g++l +  +   ++++e++++
  gi|15668337|ref|NP_247133.1|  29 NYYEEIEERL-KLDINRQFRTGVPEVVYGKGKDIDEIIkatLKLVEKNGIALATKIEDIEKLSDEIRKW 96 
                                   6777776554.566777889***********99765442227899********9999999999999887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00033
                                   HHHHHHTT--S-EEEETTT---HHHHHHHHHH---EEEESS-HH CS
                  Hpr_kinase_N  72 rleklfskkipciiltrgleppeellelaeeygvpllrtklsts 115
                                   +l+++++++++cii+  g+e       +a   ++p++  + sts
  gi|15668337|ref|NP_247133.1| 171 ALKRMIEEDVCCIIVVAGME-GALPSVIASMVDIPVIGVPTSTS 213
                                   6899***************9.44455566777888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1097  (0.0611858); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1607.18
//
Query:       gi|15668338|ref|NP_247134.1|  [L=255]
Description: hypothetical protein MJ_0166 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-66  222.1   0.0    6.9e-66  221.7   0.0    1.1  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.7   0.0   3.8e-70   6.9e-66       4     204 ..      44     252 ..      42     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 221.7 bits;  conditional E-value: 3.8e-70
                                   --SEEEEEEEEE-TT---EEEEE--B-SS-.-TTSS-TT-B--B-HHHHHHHHHHHHGGG......GGSTT-EEEE--S-S CS
                tRNA_deacylase   4 dvdliiflSrHssesgkplLTvHvtGnlge.aelGGkpeelapaaPrllkallralkkia......ekleefevtlEatHH 77 
                                    +d++iflS+H+s ++kp+LTvH+ Gnl+e +++GG+p+e++p+ + l++ ll+++ k        +k  ef+v++E++HH
  gi|15668338|ref|NP_247134.1|  44 YADYYIFLSKHKSIANKPSLTVHTPGNLTEdNTFGGNPKEVCPCDAVLNTLLLKNIYKNYktyyedGKIGEFDVSFEVVHH 124
                                   579****************************************************999888888888888*********** PP

                                   S-----S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH--....----EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-G CS
                tRNA_deacylase  78 GPtelkvPslFvEiGSteeeWkdedaaeavaeavlellese....eekekvlvgiGGgHYaprftklvletevavGhilsk 154
                                   +Pt lk+P++FvEiGS+e+eW  ++a+e++a++vle+++       +k+  ++g+GGgHYap+ftkl+le+++++G++++k
  gi|15668338|ref|NP_247134.1| 125 SPTGLKAPTVFVEIGSSEKEWILKEAGEIIAKSVLETIDAMksknYDKKVRAIGFGGGHYAPKFTKLALEDKYYFGYLVPK 205
                                   **************************************9999988888999****************************** PP

                                   GGGGG--HHHHHHHHHHH.T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                tRNA_deacylase 155 yaleelkeevikqaleksegadvalidkkslkseqkeaieelleelgiev 204
                                   y  ++++e+v++q+++k+ ++d alid+k++++++k++++e++e++gie+
  gi|15668338|ref|NP_247134.1| 206 Y--ASVSEDVLNQLISKM-EVDKALIDWKGCRGDDKRRYIEFFENNGIEW 252
                                   *..99*************.*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1660.75
//
Query:       gi|15668339|ref|NP_247135.1|  [L=163]
Description: molybdenum cofactor biosynthesis protein MoaB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-31  107.4   0.1    5.8e-31  107.1   0.1    1.0  1  MoCF_biosynth   Probable molybdopterin binding domain
  ------ inclusion threshold ------
      0.028   13.1   0.1      0.032   12.9   0.1    1.2  1  Acetate_kinase  Acetokinase family


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   0.1   6.5e-35   5.8e-31       1     138 [.      11     150 ..      11     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 6.5e-35
                                   EEEEE-HHHHTTSS.....GBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHH..HHHHHTSSEEEEESS-SSSTT--H CS
                 MoCF_biosynth   1 avitvGdellsgki.....eDtngpllaellkelgvevskytvvpDdeeeikeal..laaleeadviittGGtGptpdDvt 74 
                                   av+tv+d++++  i     +D++g+ll+++l+     ++ yt++pD+++ ik  +  + ++ ++d+i++tGGtG++++Dvt
  gi|15668339|ref|NP_247135.1|  11 AVVTVSDSRYNDLIkgkevDDKSGKLLKKELN-----AKVYTIIPDNKNMIKGIVehIVEFFDVDCIVFTGGTGIAERDVT 86 
                                   79********555555555*************.....8889**************887777777***************** PP

                                   HHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE.....TTEEEEE-SSHHHHHHHHHHHH CS
                 MoCF_biosynth  75 pealaklfekelegfeeafrrvslkpgkpvgvapgailsrav.....gktiigLPGspkavkealeeil 138
                                   +eal++++ekel+gf+++f+++s+++     v+  a+lsra+     gk i++LPGs +a+++al++i+
  gi|15668339|ref|NP_247135.1|  87 VEALKEIIEKELDGFKIIFQKLSYEE-----VGFSAMLSRAMagiykGKIIYALPGSVNACRTALKIIK 150
                                   *************************9.....999999*********555588**************998 PP

>> Acetate_kinase  Acetokinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.6e-06     0.032     308     370 ..      56     121 ..      27     132 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.6e-06
                Acetate_kinase 308 akyigeyaavlegkvDaivFTgGigenaalvrelvlk...alevlglevdkeknk.nrsGedelist 370
                                    k i e+++ +   vD ivFTgG g    +v   +lk   + e+ g+++  +k   ++ G ++++s 
  gi|15668339|ref|NP_247135.1|  56 IKGIVEHIVEF-FDVDCIVFTGGTGIAERDVTVEALKeiiEKELDGFKIIFQKLSyEEVGFSAMLSR 121
                                   56788888888.59********866665555555554111446778887767665577777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1201.30
//
Query:       gi|15668340|ref|NP_247136.1|  [L=67]
Description: histone A1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.5e-21   74.2   3.2    8.2e-21   74.1   3.2    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    6.8e-13   49.1   1.2    7.4e-13   49.0   1.2    1.1  1  Histone        Core histone H2A/H2B/H3/H4
      1e-07   32.0   0.9    1.1e-07   31.9   0.9    1.1  1  TAF            TATA box binding protein associated factor (TA
    9.1e-07   29.2   0.2      1e-06   29.0   0.2    1.1  1  CENP-S         CENP-S protein
    1.3e-05   25.6   0.3    1.5e-05   25.4   0.3    1.2  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 
    2.2e-05   24.5   0.1    2.4e-05   24.4   0.1    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
    2.9e-05   24.0   0.0    3.5e-05   23.7   0.0    1.0  1  Bromo_TP       Bromodomain associated
      3e-05   24.1   0.2    3.2e-05   24.0   0.2    1.0  1  CENP-T_C       Centromere kinetochore component CENP-T histon
    0.00039   20.4   0.1    0.00043   20.3   0.1    1.1  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu
     0.0022   18.1   1.1     0.0024   18.0   1.1    1.0  1  DUF1931        Domain of unknown function (DUF1931)


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   3.2   4.6e-24   8.2e-21       1      65 []       2      65 ..       2      65 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 4.6e-24
                                  XXXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                 CBFD_NFYB_HMF  1 aeLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                  aeLP+a+ ++I+k++ +a++++++A e++ae+vee + e+a+eA+e++k++krKt+k e+iklA+
  gi|15668340|ref|NP_247136.1|  2 AELPVAPFERILKKA-GAERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLAL 65
                                  69*************.***********************************************97 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   1.2   4.2e-16   7.4e-13      63     129 ..       5      66 ..       1      67 [] 0.93

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 4.2e-16
                                   XHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                       Histone  63 qklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                   + +pf+R++++         r+s+ a ++l+ea+E +  e+++eA  lakhaKR+T+  +Di+lA++
  gi|15668340|ref|NP_247136.1|   5 PVAPFERILKKAGA-----ERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALK 66 
                                   5689***9998876.....9*********************************************97 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.9   6.1e-11   1.1e-07      16      66 .]      16      66 ..       2      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 6.1e-11
                                  TT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH- CS
                           TAF 16 lGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsALr 66
                                   G + +s  aa+ Lae ve+   ei++ea+   +h+kR++  v+D+  AL+
  gi|15668340|ref|NP_247136.1| 16 AGAERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALK 66
                                  688889999****************************************98 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.2   5.7e-10     1e-06      24      72 ..      19      67 .]       9      67 .] 0.88

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 5.7e-10
                        CENP-S 24 veatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLlaRr 72
                                   ++++ + + l+e v + + ++ak     akHAkR+t++++D++L +++
  gi|15668340|ref|NP_247136.1| 19 ERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALKK 67
                                  468888899999***99999*************************9886 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.3   8.5e-09   1.5e-05      21      64 ..      24      67 .]      11      67 .] 0.89

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.5e-09
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH CS
                   TFIID_20kDa 21 dvedlLleiaddFvesvtkfacklakhRksdklevrDiqlhler 64
                                     + L+e +++   ++ k a++lakh k +++ v Di+l l++
  gi|15668340|ref|NP_247136.1| 24 AAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALKK 67
                                  567889999999999***************************96 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   1.3e-08   2.4e-05      12      68 ..      10      66 ..       5      67 .] 0.95

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.3e-08
                   TFIID-31kDa 12 hliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiq 68
                                  + iL++ g + ++    + L + +     ++ ++A  la+hak+k+v+++d++lA++
  gi|15668340|ref|NP_247136.1| 10 ERILKKAGAERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALK 66
                                  679****************************************************86 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.9e-08   3.5e-05      15      69 ..      12      66 ..      10      67 .] 0.97

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.9e-08
                                  HHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHH CS
                      Bromo_TP 15 ileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvltLq 69
                                  il++aG +++  +a E L e +++  +e++++a + a ha R +++++D+ l+L+
  gi|15668340|ref|NP_247136.1| 12 ILKKAGAERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALK 66
                                  89**************************************************997 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2   1.8e-08   3.2e-05      24      75 ..      15      66 ..       2      67 .] 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.8e-08
                      CENP-T_C 24 sgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmk 75
                                  ++  ++++++a + l +a ++    ++++    akHa+RKt++ +D+ l +k
  gi|15668340|ref|NP_247136.1| 15 KAGAERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALK 66
                                  356789*****************************************99887 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.4e-07   0.00043      23      66 ..      24      67 .]      14      67 .] 0.91

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.4e-07
                                  HHHHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXXXX CS
                   TFIID-18kDa 23 etvqlledlvrgyliellqqaakvaklrgsrkitlEDllfliRk 66
                                  ++++ l + v++   e+ ++a+++ak+ +++ +++ED++ +++k
  gi|15668340|ref|NP_247136.1| 24 AAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALKK 67
                                  677889999******************************99986 PP

>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.1   1.4e-06    0.0024       1      55 [.       9      63 ..       9      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
                                  HHHHHHHHHS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-- CS
                       DUF1931  1 lerlfreaagLdvdkedlkrisdfVekklydLllvaeenAkangrdviepaDLPi 55
                                  +er++++a    v +  ++ + + Ve++  +++  a e Ak  +r++++++D+ +
  gi|15668340|ref|NP_247136.1|  9 FERILKKAGAERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKL 63
                                  89**************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1090  (0.0607954); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 438.03
//
Query:       gi|15668341|ref|NP_247137.1|  [L=263]
Description: cell division inhibitor MinD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-28   99.9   0.4    2.6e-28   99.1   0.4    1.3  1  AAA_31       AAA domain
    2.3e-24   85.9   0.4    3.2e-24   85.4   0.4    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.9e-21   76.7   4.5    8.8e-21   74.5   4.5    2.0  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.8e-19   70.2   0.0    4.5e-19   68.8   0.0    1.6  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    5.6e-16   58.8   2.5    3.4e-15   56.2   2.5    1.9  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    7.2e-11   41.9   1.3      2e-10   40.4   1.3    1.6  1  MipZ         ATPase MipZ
    1.1e-09   37.9   6.7    2.6e-08   33.4   4.9    2.8  2  ArsA_ATPase  Anion-transporting ATPase
    1.3e-05   25.2   5.3    0.00036   20.4   0.1    2.5  2  AAA_26       AAA domain
    0.00032   20.1   2.1     0.0038   16.6   0.6    2.3  2  VirC1        VirC1 protein
    0.00098   18.8   2.1     0.0047   16.6   1.1    2.1  2  SRP54        SRP54-type protein, GTPase domain
     0.0026   17.4   0.6      0.006   16.2   0.6    1.6  1  AAA_25       AAA domain
  ------ inclusion threshold ------
      0.023   14.5   0.1      0.052   13.3   0.1    1.6  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
      0.032   14.0   0.0      0.057   13.1   0.0    1.4  1  AAA_24       AAA domain
      0.055   11.7   0.3       0.07   11.3   0.3    1.1  1  FTHFS        Formate--tetrahydrofolate ligase
      0.067   13.1   0.1       0.12   12.2   0.1    1.4  1  APS_kinase   Adenylylsulphate kinase
       0.13   11.7   0.0        0.6    9.4   0.0    1.8  2  DUF5581      Family of unknown function (DUF5581)


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1   0.4   2.3e-31   2.6e-28       3     159 ..       5     153 ..       3     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 2.3e-31
                        AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQ.anattglgiekneiektlyevlieeknikeaiiktkvenld 82 
                                   +I+ia  KGGvGKTTts  la+alaklgkkvL +D D   an+ + +++  ++++ +l+evl ee+++++ai+k+k + ++
  gi|15668341|ref|NP_247137.1|   5 IITIASGKGGVGKTTTSASLAVALAKLGKKVLAIDGDISmANLGILFNM--EKKKPSLHEVLSEEADVRDAIYKHK-TGVY 82 
                                   8************************************752677776665..55668*****************666.788* PP

                        AAA_31  83 lipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleq 159
                                   ++p+s++L +++++        + l +++++v d++Dy+iiD+p  L+  + + L+++d+++ +v +e +++  + +
  gi|15668341|ref|NP_247137.1|  83 VLPTSLSLEGYKKS------DIDLLPDVVNEVADDFDYVIIDAPAGLNREMATHLAIADKLLLVVTPEMFSIIDAVR 153
                                   ********999765......4567899*******************************************9876555 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.4   2.8e-27   3.2e-24       1     127 [.       6     212 ..       6     213 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 2.8e-27
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   i+ias+kGGvGKTt++a+La+ala+ g++Vl++D D  + nl il+  e+++                             
  gi|15668341|ref|NP_247137.1|   6 ITIASGKGGVGKTTTSASLAVALAKLGKKVLAIDGDISMANLGILFNMEKKKPSlhevlseeadvrdaiykhktgvyvlpt 86 
                                   79*****************************************97777777777888************************ PP

                                   ...............................................................CCHCCCHHHHHHCHCHHH CS
                                   ...............................................................xxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ...............................................................dlkrllellealgkkkal 72 
                                                                                                  d+ rl+e++e+ g++   
  gi|15668341|ref|NP_247137.1|  87 slslegykksdidllpdvvnevaddfdyviidapaglnremathlaiadklllvvtpemfsiiDAVRLKESAEMAGTP--- 164
                                   ****************************************************************************88... PP

                                   H..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  73 llkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                      ++gvvlnrv+ +   ++ ++ +e l+   + +vl ++p+de+v  a+ ++++
  gi|15668341|ref|NP_247137.1| 165 ---LMGVVLNRVGRD-FGEMGRDEIEMLI---KGKVLVEVPEDENVRSAALKKMS 212
                                   ...8********988.69999999**999...9*************999998876 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   4.5   7.9e-24   8.8e-21       4     244 ..       4     232 ..       1     234 [. 0.86

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 7.9e-24
                          ParA   4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvmSigflle 83 
                                    +i+++SgKGGVGK+t++++lA+aLak g+kv  +D Di   ++  l+++e++kp+ +e      ++ + i     g+ + 
  gi|15668341|ref|NP_247137.1|   4 MIITIASGKGGVGKTTTSASLAVALAKLGKKVLAIDGDISMANLGILFNMEKKKPSLHEVLSEEADVrDAIYKHKTGVYVL 84 
                                   589**************************************************9999984444444467787777777766 PP

                          ParA  84 sedeavvwrGpmksk..aikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkk 162
                                      +++   G +ks   ++ +++++v+ ++ Dy+iiD P G   e  t +     ++ ++V tp+  +++d+ +  e ++ 
  gi|15668341|ref|NP_247137.1|  85 --PTSLSLEGYKKSDidLLPDVVNEVA-DDFDYVIIDAPAGLNREMATHLAIA--DKLLLVVTPEMFSIIDAVRLKESAEM 160
                                   ..5889999999886225778888876.89***********987755544443..68899********************* PP

                          ParA 163 vkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiae 243
                                   + ++++Gvv N  g          + fg+ g +++   ++ ++l e+p d+++r+a+ ++ ++++ +++s+a++a++++a+
  gi|15668341|ref|NP_247137.1| 161 AGTPLMGVVLNRVG----------RDFGEMGRDEIEMLIKGKVLVEVPEDENVRSAALKKMSVIEYRKNSPASQAYMKLAS 231
                                   *********98543..........34999999999999***************************************9987 PP

                          ParA 244 k 244
                                    
  gi|15668341|ref|NP_247137.1| 232 I 232
                                   5 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.0   4.1e-22   4.5e-19       3     231 ..       5     231 ..       3     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 4.1e-22
                      CBP_BcsQ   3 vlalqGvRGGvGttsllaaLawalhelgesvlviD..lspdnlLrlhFnvdieqregwaraeldgapwrqaaleyapgldl 81 
                                   ++++   +GGvG+t+ +a+La al +lg++vl+iD  +s +n L + Fn++ +++ ++ + + ++a+ r+a+++ ++g+ +
  gi|15668341|ref|NP_247137.1|   5 IITIASGKGGVGKTTTSASLAVALAKLGKKVLAIDgdISMAN-LGILFNME-KKKPSLHEVLSEEADVRDAIYKHKTGVYV 83 
                                   56677779**************************73356666.7999****.88899************************ PP

                      CBP_BcsQ  82 lPfGelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdanc...hvrLhqqa 159
                                   lP  +l+ e  +     +++ + l + ++e++ +++++++D pag ++ + + la ad+ llvv+p++ +    vrL++ a
  gi|15668341|ref|NP_247137.1|  84 LPT-SLSLEGYK-----KSDIDLLPDVVNEVADDFDYVIIDAPAGLNREMATHLAIADKLLLVVTPEMFSiidAVRLKESA 158
                                   **5.45554444.....56789999*******************************************9833357999998 PP

                      CBP_BcsQ 160 lpaaellLiNqfeaasqlqqDllqlWlqslrrllP....lvihrDealaEalaakqPlgeyrpdslaaeevktLan 231
                                     a + l+     +  ++ +D+  + +++ + l+     + + +De +  a + k  + eyr +s a+++ ++La+
  gi|15668341|ref|NP_247137.1| 159 EMAGTPLMG---VVLNRVGRDFGEMGRDEIEMLIKgkvlVEVPEDENVRSAALKKMSVIEYRKNSPASQAYMKLAS 231
                                   888877764...4566888899999888877776422216789*****************************9996 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   2.5     3e-18   3.4e-15       6     247 ..      10     236 ..       4     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 3e-18
                     Fer4_NifH   6 yGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkGyggvkcves 86 
                                    GkGG+Gk+tts+ l+ ala+ gkkvl +  D       +l++  +++  l+ + +    e+  v d ++k  +gv+++ +
  gi|15668341|ref|NP_247137.1|  10 SGKGGVGKTTTSASLAVALAKLGKKVLAIDGDISMANLGILFNMEKKKPSLHEVLS----EEADVRDAIYKHKTGVYVLPT 86 
                                   59******************************999999999998776665554443....445799***********9965 PP

                     Fer4_NifH  87 GGPepGvGCaGrgvitaiellee..lgayddlDfvlyDvLGDvvCGGfalPiredkaqevyivtsgelmalyaanniakgi 165
                                             G+     i+ll +  +++ dd+D+v+ D         +a  +    a+++++v++ e+ ++  a ++    
  gi|15668341|ref|NP_247137.1|  87 S-----LSLEGYK-KSDIDLLPDvvNEVADDFDYVIIDAPAGL-NREMATHL--AIADKLLLVVTPEMFSIIDAVRL---- 154
                                   4.....4555555.45688886533567789*******86554.33455555..49****************99886.... PP

                     Fer4_NifH 166 ekyaksggvrlgGliinsrkvddereli..ekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarki 244
                                   ++ a+  g  l G++ n r v ++ + +  +++   ++ kvl  vP de+vr a l+k+ viey ++s+ ++ y +la+ i
  gi|15668341|ref|NP_247137.1| 155 KESAEMAGTPLMGVVLN-R-VGRDFGEMgrDEIEMLIKGKVLVEVPEDENVRSAALKKMSVIEYRKNSPASQAYMKLASII 233
                                   667889999********.5.4444333312566677899***************************************988 PP

                     Fer4_NifH 245 len 247
                                   +  
  gi|15668341|ref|NP_247137.1| 234 AGV 236
                                   765 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   1.3   1.8e-13     2e-10       2     135 ..       5     150 ..       4     156 .. 0.72

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.8e-13
                                   EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHH...........HHT------EEE-SS CS
                          MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraatae...........rkglsLplpealals 71 
                                   +i ++  kGG Gk+tt+  +avaL+k G++v aid d+  + l   ++  ++  +           r  +    + +++l+
  gi|15668341|ref|NP_247137.1|   5 IITIASGKGGVGKTTTSASLAVALAKLGKKVLAIDGDISMANLGILFNMEKKKPSlhevlseeadvRDAIYKHKTGVYVLP 85 
                                   78999********************************99999988776554433300011010111233333444455566 PP

                                   S-HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEE...EEEEESSHHH CS
                          MipZ  72 eaeeaeveeeeeaevaeleelvadleaeldfividtPGsdsalsrlahsladtl...vtPlndsfvd 135
                                   ++ +  +e+ ++ ++  l ++v++++ ++d+++id+P   ++ + +  + ad l   vtP   s++d
  gi|15668341|ref|NP_247137.1|  86 TSLS--LEGYKKSDIDLLPDVVNEVADDFDYVIIDAPAGLNREMATHLAIADKLllvVTPEMFSIID 150
                                   5444..455555555699*******************999999999999999753337887666666 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   4.9   2.3e-11   2.6e-08       4      49 ..       7      53 ..       4     124 .. 0.81
   2 ?    2.8   0.0     0.048        53     209     245 ..     137     173 ..     125     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.3e-11
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT.THHHHHHTS CS
                   ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistDPA.hslsDsfdq 49
                                   + +GKGGVGKtt sa++av l++ gkkvl i  D    +l   f+ 
  gi|15668341|ref|NP_247137.1|  7 TIASGKGGVGKTTTSASLAVALAKLGKKVLAIDGDISmANLGILFNM 53
                                  4679***************************9988542566666666 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.048
                                   EEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE CS
                   ArsA_ATPase 209 frlVvipEklslkEteRaikeLkkygikvdavivNkl 245
                                   + lVv+pE  s+ +  R+ ++ +  g     v+ N++
  gi|15668341|ref|NP_247137.1| 137 LLLVVTPEMFSIIDAVRLKESAEMAGTPLMGVVLNRV 173
                                   579******************************9997 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   1.6    0.0092        10       3      30 ..       6      33 ..       4      37 .. 0.82
   2 !   20.4   0.1   3.2e-07   0.00036      80     196 ..      92     205 ..      60     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0092
                        AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgv 30
                                  i +++   gvGKT++s+ L+ al + g 
  gi|15668341|ref|NP_247137.1|  6 ITIASGKGGVGKTTTSASLAVALAKLGK 33
                                  567888889***********99966555 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 3.2e-07
                        AAA_26  80 rqegedid.lekivkelekdadivvVEGagglgvpiteellnadiaknlgapvilVargglgtinqllltiealrqknvrv 159
                                     ++ did l ++v+e+++d d v++++  gl    +       ia     + +lV++++  +i +++   e++   + ++
  gi|15668341|ref|NP_247137.1|  92 GYKKSDIDlLPDVVNEVADDFDYVIIDAPAGLNREMATH---LAIAD----KLLLVVTPEMFSIIDAVRLKESAEMAGTPL 165
                                   455666766777778999999999999888876554443...34444....679*********99999999999999**** PP

                        AAA_26 160 lGvilNkvrnp...envetlekksgipvlGvvPylpdlea 196
                                   +Gv+lN+v  +     ++++e  ++ +vl +vP ++++++
  gi|15668341|ref|NP_247137.1| 166 MGVVLNRVGRDfgeMGRDEIEMLIKGKVLVEVPEDENVRS 205
                                   *******9777765499999999999********999886 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.6   3.4e-06    0.0038       3      39 ..       5      41 ..       3      46 .. 0.93
   2 ?    2.8   0.0     0.056        63      67     119 ..      96     150 ..      63     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.4e-06
                         VirC1  3 litfcslkGGaGkttalmglcsalasdgkrvalfead 39
                                  +it++s kGG Gktt+  +l  ala  gk+v   ++d
  gi|15668341|ref|NP_247137.1|  5 IITIASGKGGVGKTTTSASLAVALAKLGKKVLAIDGD 41
                                  79*****************************988887 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.056
                         VirC1  67 delplleaayeeaegeGfdyaladtrgGsselnntiiassd.llli..Ptmltpld 119
                                    ++ ll +  +e++ + fdy+++d+  G     +t +a +d lll+  P m++ +d
  gi|15668341|ref|NP_247137.1|  96 SDIDLLPDVVNEVA-DDFDYVIIDAPAGLNREMATHLAIADkLLLVvtPEMFSIID 150
                                   56666666666654.67********9998766666555554244432377776666 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.1   4.2e-06    0.0047       6      39 ..       9      42 ..       4      46 .. 0.88
   2 ?    0.6   0.0      0.33   3.7e+02      74     114 ..     103     143 ..      74     164 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.2e-06
                                  EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                         SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                    G  G+GKTtt a La  l k gkkvl +  D+
  gi|15668341|ref|NP_247137.1|  9 ASGKGGVGKTTTSASLAVALAKLGKKVLAIDGDI 42
                                  56899**********************9988885 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.33
                                   HHHHHHHHTTSSEEEEEE.--SSTTHHHHHHHHHHHHHHHSS CS
                         SRP54  74 eavekakeekidvvlvDT.aGrlqndkelmeelkkikkvvkp 114
                                   + v++  ++++d+v++D  aG +++ +  ++  +k+  vv+p
  gi|15668341|ref|NP_247137.1| 103 DVVNEV-ADDFDYVIIDApAGLNREMATHLAIADKLLLVVTP 143
                                   444444.44789999997577766666665555555555544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.6   5.4e-06     0.006      35     149 ..       6     118 ..       4     126 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.4e-06
                        AAA_25  35 lallaGapgtGKttlaldlalava.tGkpwlg...pvapeqgkVlyvsaEdsedelrrRlravgeal....rddarllvld 107
                                   +++  G +g+GKtt   +la+a+a +Gk++l    ++ + +   l+ + E +   l++ l++    +    +++ +++vl 
  gi|15668341|ref|NP_247137.1|   6 ITIASGKGGVGKTTTSASLAVALAkLGKKVLAidgDISMANLGILF-NMEKKKPSLHEVLSEEADVRdaiyKHKTGVYVLP 85 
                                   57899********************999998877755445555554.5577766666666642211122334444444443 PP

                        AAA_25 108 lagveslpLfakdrggtlltadvdaleaaieeveg.vrlvviD 149
                                       +sl L      +   ++d+d l ++++ev++  + v+iD
  gi|15668341|ref|NP_247137.1|  86 ----TSLSL------EGYKKSDIDLLPDVVNEVADdFDYVIID 118
                                   ....12222......2223455555666666665556777776 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.6e-05     0.052       1      39 [.      11      49 ..      11      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-05
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseisp 39
                                  G+  +GK+T ++ L+  +++ g+k++ +D D+   ++++
  gi|15668341|ref|NP_247137.1| 11 GKGGVGKTTTSASLAVALAKLGKKVLAIDGDISMANLGI 49
                                  66789***************************9998875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.1e-05     0.057       9      72 ..      11     118 ..       5     127 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-05
                        AAA_24   9 GpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.........swedfldevvel.............. 59 
                                   G+ g+GKTt+ ++l       g+k+l id + ++++l      + +           +d++d++ +               
  gi|15668341|ref|NP_247137.1|  11 GKGGVGKTTTSASLavalaklGKKVLAIDGDISMANLGILFNMEKKkpslhevlsEEADVRDAIYKHktgvyvlptslsle 91 
                                   99******************************9998876543333345444444434444444444466666666666666 PP

                        AAA_24  60 ..............aaeladyktlviD 72 
                                                 ++  +d++ ++iD
  gi|15668341|ref|NP_247137.1|  92 gykksdidllpdvvNEVADDFDYVIID 118
                                   666666666666666666666666666 PP

>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   6.3e-05      0.07      59      91 ..       5      37 ..       1      53 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.3e-05
                                  EEESS--TT--SHHHHHHHHHHHHHHTT--EEE CS
                         FTHFS 59 vtaitPtplGeGKttttigLaqalnklgkkava 91
                                  + +i+  + G GKttt+ +La al+klgkk++a
  gi|15668341|ref|NP_247137.1|  5 IITIASGKGGVGKTTTSASLAVALAKLGKKVLA 37
                                  567888899*********************986 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00011      0.12       7      41 ..       9      43 ..       4      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                  EESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHH CS
                    APS_kinase  7 ltGlsgsGKstianalekkLvekgisvylLdGdnv 41
                                   +G  g GK+t +  l+ +L + g++v  +dGd  
  gi|15668341|ref|NP_247137.1|  9 ASGKGGVGKTTTSASLAVALAKLGKKVLAIDGDIS 43
                                  57999***************************965 PP

>> DUF5581  Family of unknown function (DUF5581)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00053       0.6      78     123 ..     127     170 ..     125     197 .. 0.71
   2 ?   -0.4   0.0      0.53     6e+02     198     227 ..     204     233 ..     196     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00053
                       DUF5581  78 lPkhlalgdqnklllpttvfqlidpwkfqrmkkvgtaqtkiqllll 123
                                   +  hla+ d+  l+++ ++f +id+ +++      +a t +  ++l
  gi|15668341|ref|NP_247137.1| 127 MATHLAIADKLLLVVTPEMFSIIDAVRLKESAE--MAGTPLMGVVL 170
                                   678**********************99976543..34444544555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.53
                       DUF5581 198 rlvlstkmPvlfdrkesvahkdwaslrwfv 227
                                   r     km v+  rk+s a + +++l  ++
  gi|15668341|ref|NP_247137.1| 204 RSAALKKMSVIEYRKNSPASQAYMKLASII 233
                                   5555679**************999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1930.87
//
Query:       gi|15668342|ref|NP_247138.1|  [L=350]
Description: hypothetical protein MJ_0170 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-68  230.4   0.4    1.5e-68  230.4   0.4    1.7  2  MS_channel  Mechanosensitive ion channel
    0.00046   20.1   1.5    0.00046   20.1   1.5    2.9  3  TM_helix    Conserved TM helix
  ------ inclusion threshold ------
      0.025   14.5   0.7        2.4    8.2   0.0    3.4  3  RHH_3       Ribbon-helix-helix domain
       0.11   12.8   0.6         27    5.1   0.1    4.1  5  DUF5388     Family of unknown function (DUF5388)
        6.5    5.9  11.0         13    4.9  11.0    1.5  1  CitMHS      Citrate transporter


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.7      0.97   3.5e+03       3      16 ..      10      23 ..       6      37 .. 0.54
   2 !  230.4   0.4   4.2e-72   1.5e-68       1     206 []     135     337 ..     135     337 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.97
                                  HHHHHHHHHHHHHH CS
                    MS_channel  3 ilkiliivvgiliv 16
                                  i +ili+vv++l+ 
  gi|15668342|ref|NP_247138.1| 10 ISNILIFVVITLLG 23
                                  44444444444432 PP

  == domain 2  score: 230.4 bits;  conditional E-value: 4.2e-72
                                   ..HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-S CS
                    MS_channel   1 kkilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedigl 81 
                                   kk++kil+i++gil++ls++g++++alla+lG++glal+la++d+i+n++aGi++l++kpf++G +v+++++eG+Ve+ig+
  gi|15668342|ref|NP_247138.1| 135 KKVVKILTILLGILTALSSVGYDITALLAGLGVGGLALALAMQDTIKNFIAGILILIDKPFSLGHWVKVKGAEGIVEEIGI 215
                                   589****************************************************************************** PP

                                   SEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEE CS
                    MS_channel  82 rttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvlde 162
                                   r+t+irtfd +++tiPns+l++s+ieNl+  +++rr+ ++ig+ty+++v+k++++ e++ke+++++p +l  +++ v++ e
  gi|15668342|ref|NP_247138.1| 216 RSTRIRTFDYTLITIPNSELLDSAIENLTV-RDRRRVLMTIGLTYNTPVEKIKRAKEIIKEIVENHPATL--PPYRVHFRE 293
                                   ******************************.************************************999..7******** PP

                                   E-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                    MS_channel 163 fgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                   +gd+sln++v +fv+++ ++ yl+  +einl+ik+++e+egie+
  gi|15668342|ref|NP_247138.1| 294 YGDWSLNLRVEYFVRNMGFDYYLNAVDEINLKIKEEFEKEGIEM 337
                                   ******************************************96 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.5   1.3e-07   0.00046      14      45 ..      10      41 ..       3      48 .. 0.87
   2 ?   -2.0   0.1         1   3.6e+03      21      36 ..      94     109 ..      91     114 .. 0.83
   3 ?   -1.5   0.4      0.73   2.6e+03      16      25 ..     182     191 ..     178     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.3e-07
                                  HSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      TM_helix 14 lPnLvgAilILlvGwiiAkfvsrlvtkllakt 45
                                  + n++++++I l+G +i+k+v ++v++ l+k+
  gi|15668342|ref|NP_247138.1| 10 ISNILIFVVITLLGIFIGKIVDKIVRNYLKKI 41
                                  77***********************8888774 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1
                                   HHHHHHHHHHHHHHHH CS
                      TM_helix  21 ilILlvGwiiAkfvsr 36 
                                   ++IL   ++  kf+  
  gi|15668342|ref|NP_247138.1|  94 VVILSATYFAVKFIDG 109
                                   7899999999999976 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.73
                                   HHHHHHHHHH CS
                      TM_helix  16 nLvgAilILl 25 
                                   n ++ ilIL+
  gi|15668342|ref|NP_247138.1| 182 NFIAGILILI 191
                                   8899999997 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.081   2.9e+02      25      42 ..      23      40 ..      22      40 .. 0.88
   2 ?    0.3   0.1       0.2   7.1e+02      30      37 ..      85      92 ..      85      95 .. 0.86
   3 ?    8.2   0.0   0.00068       2.4      26      39 ..     230     243 ..     228     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.081
                         RHH_3 25 rIprSklldeAiellLek 42
                                  +I + k++d+ + ++L+k
  gi|15668342|ref|NP_247138.1| 23 GIFIGKIVDKIVRNYLKK 40
                                  677889**********98 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.2
                         RHH_3 30 klldeAie 37
                                  kl+deA++
  gi|15668342|ref|NP_247138.1| 85 KLIDEAVK 92
                                  8*****97 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00068
                         RHH_3  26 IprSklldeAiell 39 
                                   Ip S+lld Aie+l
  gi|15668342|ref|NP_247138.1| 230 IPNSELLDSAIENL 243
                                   9***********99 PP

>> DUF5388  Family of unknown function (DUF5388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0075        27      36      65 ..      28      55 ..      21      59 .. 0.89
   2 ?   -2.0   0.0       1.2   4.3e+03      34      59 ..     103     128 ..      90     131 .. 0.78
   3 ?    2.2   0.0     0.059   2.1e+02      40      56 ..     234     250 ..     232     256 .. 0.88
   4 ?   -1.2   0.0      0.66   2.4e+03      32      49 ..     267     284 ..     264     288 .. 0.79
   5 ?   -3.0   0.0       2.5     9e+03      10      20 ..     299     309 ..     297     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0075
                       DUF5388 36 eavkklveslidsLsesdkkrfkkqleiLE 65
                                  ++v+k+v +++ ++ +++k +f++++  LE
  gi|15668342|ref|NP_247138.1| 28 KIVDKIVRNYLKKIIDKTKTKFDDII--LE 55
                                  689********************984..55 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                       DUF5388  34 qkeavkklveslidsLsesdkkrfkk 59 
                                   + ++++ + e+++  L+e+++ ++++
  gi|15668342|ref|NP_247138.1| 103 AVKFIDGIFEHYLIPLTEKTETELDE 128
                                   55789999999999999998888775 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.059
                       DUF5388  40 klveslidsLsesdkkr 56 
                                   +l++s i++L+  d++r
  gi|15668342|ref|NP_247138.1| 234 ELLDSAIENLTVRDRRR 250
                                   799***********998 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.66
                       DUF5388  32 ksqkeavkklveslidsL 49 
                                   k +ke++k++ve+   +L
  gi|15668342|ref|NP_247138.1| 267 KRAKEIIKEIVENHPATL 284
                                   568999**9999876665 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 2.5
                       DUF5388  10 vnvrvdNHirN 20 
                                    n+rv+  +rN
  gi|15668342|ref|NP_247138.1| 299 LNLRVEYFVRN 309
                                   69***999999 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  11.0    0.0035        13     143     230 ..       5     173 ..       1     201 [. 0.61

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0035
                                   xxxxxxxxxxxxxx..........................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS 143 rpglslpnllllal..........................................llvgllplvllfmfgvalalpvnap 181
                                   ++g+s+ n+l+ ++                                          ++v++++l+++f  g+ + +++++ 
  gi|15668342|ref|NP_247138.1|   5 IFGNSISNILIFVVitllgifigkivdkivrnylkkiidktktkfddiilesidlpIIVLVVTLFFYF--GLRFLILPDYI 83 
                                   67888888888444344444555555555555555555555555555555555555444445555555..33444444443 PP

                                   .......................................xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                        CitMHS 182 .......................................kvkkqkaiieaiarsllpvatillla...ykkveWsvlllfa 220
                                                                          +++  ++ii+ +++ ++++ till +   + +v +++  l+a
  gi|15668342|ref|NP_247138.1|  84 lklideavkvvvilsatyfavkfidgifehylipltektETELDEHIIKPLKK-VVKILTILLGIltaLSSVGYDITALLA 163
                                   56777777777777777777777777777777777566544445555555555.55455555444999************* PP

                                   xxxxxxxxxx RF
                        CitMHS 221 Gvfllvgale 230
                                   G+++++ al 
  gi|15668342|ref|NP_247138.1| 164 GLGVGGLALA 173
                                   *****77764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2297.31
//
Query:       gi|15668343|ref|NP_247139.1|  [L=573]
Description: DNA ligase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-68  228.3   2.5    1.3e-67  227.4   2.5    1.5  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
    2.4e-37  128.9   2.4    7.1e-37  127.4   1.1    2.1  2  DNA_ligase_A_N   DNA ligase N terminus
    7.6e-17   61.7   0.0    3.1e-16   59.8   0.0    2.1  2  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
    6.3e-06   26.6   1.3      1e-05   25.9   1.3    1.4  1  RNA_ligase       RNA ligase
    4.1e-05   23.5   0.8    8.4e-05   22.5   0.8    1.5  1  mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
     0.0076   15.9   0.0      0.059   13.0   0.0    2.0  2  DUF2071          Uncharacterized conserved protein (COG2071)
  ------ inclusion threshold ------
       0.03   14.4   0.4       0.22   11.6   0.1    2.6  2  DNA_ligase_OB_2  DNA ligase OB-like domain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.4   2.5   5.2e-71   1.3e-67       1     204 []     226     440 ..     226     440 .. 0.98

  Alignments for each domain:
  == domain 1  score: 227.4 bits;  conditional E-value: 5.2e-71
                                   -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEE CS
                DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElv 81 
                                   pmLA+ + sie+al ++ ++a+ +E+KyDG+R+q+hk+g+kvk++SRrl+d+t+a+pe+v+a+k+++ ++   +i++GE+v
  gi|15668343|ref|NP_247139.1| 226 PMLAQLTPSIEEALLEM-GRAQ-FETKYDGARVQIHKDGNKVKIYSRRLEDVTNALPEIVEAVKNINVDK---LIVEGECV 301
                                   9****************.5665.7*******************************************996...9******* PP

                                   EEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB................ CS
                DNA_ligase_A_M  82 avdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeil................ 146
                                   a+dk+tg+++pfq++ +r+++k+++ +++ke++l++++FDiLy dg+s++de++++Rrk+Leei+                
  gi|15668343|ref|NP_247139.1| 302 AIDKQTGKPRPFQDILRRFRRKYDIGKMMKEINLRVYLFDILYKDGVSFIDEEFEKRRKVLEEIVgyendwrterkrieke 382
                                   *******************************************************************************99 PP

                                   --BTTTEEE--EEEESSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                DNA_ligase_A_M 147 kesedrvelaeslevkdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                    +s++ ++++++l+++d++e++e++++++s g+EG+++Kn +++Y+pg+r ++++K+K
  gi|15668343|ref|NP_247139.1| 383 LKSDKIIDISYKLVTNDAKEAREFYNWSLSIGHEGVMIKNLKAPYTPGSRVRTMYKFK 440
                                   999******************************************************9 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.4   1.1   2.8e-40   7.1e-37       3     172 ..       4     178 ..       2     179 .. 0.94
   2 ?    1.4   0.0      0.14   3.6e+02      68     102 ..     178     212 ..     177     290 .. 0.72

  Alignments for each domain:
  == domain 1  score: 127.4 bits;  conditional E-value: 2.8e-40
                                   HHHHHHHHHHCC.---HHHHHHHHHHHHHTS-...SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT--HHH CS
                DNA_ligase_A_N   3 aelaelfekieestkkrlekrailanffrkves.agpedlypalrL....llPdydgreygigesllakalaealglskkk 78 
                                   ++++e+f+kie+ t+krlekr+++ +++  v++  +pedl +++++    ++P+yd+re+gige+ll+ a+    g++k++
  gi|15668343|ref|NP_247139.1|   4 RDVCEIFNKIEK-TTKRLEKRDYFIKLIDMVKEkGKPEDLKKICYMaigrVYPEYDERELGIGEKLLINAVTS-IGIKKDE 82 
                                   799*********.999************4444447899********************************985.699*998 PP

                                   HHHHHHHHS-HHHHHHHHHCCHHHH.------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHHHHHHHHCT CS
                DNA_ligase_A_N  79 ikdalakvgDlgevaeevlskrstl.akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEakyliriilk 157
                                   + ++ +++gD+g ++e+++sk +++    +plt++ev+e+L+++ +  g+gs+++k +++++l+ rasp E +yl+r+il+
  gi|15668343|ref|NP_247139.1|  83 LLEKIKETGDIGLAIEQLKSKIKQAsLFFQPLTVDEVYETLKRVGEIeGEGSQKKKLRLISSLFLRASPIECRYLARLILE 163
                                   9888999*************9999999999**************8779********************************* PP

                                   ---SS--HHHHHHHH CS
                DNA_ligase_A_N 158 dlriglsektvldal 172
                                   d+rig+   t+ldal
  gi|15668343|ref|NP_247139.1| 164 DMRIGMNVPTILDAL 178
                                   **************9 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.14
                                   HHHHHT--HHHHHHHHHHHS-HHHHHHHHHCCHHH CS
                DNA_ligase_A_N  68 laealglskkkikdalakvgDlgevaeevlskrst 102
                                   l+ +++++k+k+++ +a ++D+g  ae++l    +
  gi|15668343|ref|NP_247139.1| 178 LSVYFNVPKEKLEKIYAITNDIGLLAEKLLMGDLE 212
                                   5667899999999999999******9998854443 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.7   1.2e+04      28      76 ..     350     395 ..     346     404 .. 0.55
   2 !   59.8   0.0   1.2e-19   3.1e-16       1      99 []     460     551 ..     460     551 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.7
                                   --HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEESE CS
                DNA_ligase_A_C  28 fsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfae 76 
                                   f d+e e+ rk l+e+   ++ ++ + ++ ek+   ++ ++++ ++++ 
  gi|15668343|ref|NP_247139.1| 350 FIDEEFEKRRKVLEEIVGYENDWRTERKRIEKE---LKSDKIIDISYKL 395
                                   566666666666665555555553333333333...5556666666654 PP

  == domain 2  score: 59.8 bits;  conditional E-value: 1.2e-19
                                   GGGSEEEEEEEEEE.TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEESEEECT CS
                DNA_ligase_A_C   1 rgglvgslllgvyd.dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfaeitas 80 
                                   r++++gs+ + v+d +g+l  +g+vgtG+++a+le l+++++++  ++       + e      veP++v+eV+++ei++s
  gi|15668343|ref|NP_247139.1| 460 RKDWYGSFEICVRDeEGNLYPIGHVGTGLTEADLEFLKEEIDKIIIRDLGE----EVE------VEPKIVIEVAYEEIQKS 530
                                   5789**********9**************************9888887766....222......89*************** PP

                                   SSSTT..EECT-EEEEE-TTS CS
                DNA_ligase_A_C  81 gkyka..slRfPrfkrlReDk 99 
                                   +ky++  +lRfPr++r+R Dk
  gi|15668343|ref|NP_247139.1| 531 DKYPCgyALRFPRVVRFRFDK 551
                                   ********************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.3   4.1e-09     1e-05       4     161 .]     246     440 ..     243     440 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.1e-09
                                   EEEEE-SSEEEEEEEETT.EEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES........SS..T CS
                    RNA_ligase   4 vvtEKlDGtnfriylvke.vgvasRsqil.pfgeekfkefkrwaaalrkklkeklaneelilyGElig.......hsikyg 75 
                                   + + K DG++++i+++ + v++ sR+ +  +      +   + ++a +     ++++ +li+ GE +        +     
  gi|15668343|ref|NP_247139.1| 246 QFETKYDGARVQIHKDGNkVKIYSRRLEDvT------NALPEIVEAVK-----NINVDKLIVEGECVAidkqtgkP----- 310
                                   6789************444999999987721......22333333333.....345789*********54433330..... PP

                                   TSS.........................EEEEEEEEEEECTT.....................BECE--HHHH.HHHHHCC CS
                    RNA_ligase  76 glpk........................efyvFdifdirdke.....................eqrylspdev.ealakgl 110
                                                                 y+Fdi+  +                        e+++ + +++ e+ +k+ 
  gi|15668343|ref|NP_247139.1| 311 ---RpfqdilrrfrrkydigkmmkeinlRVYLFDILYKD--GvsfideefekrrkvleeivgyENDWRTERKRiEKELKS- 385
                                   ...2334455556666777788999999********644..255666678889999999988877776666666666663. PP

                                   T.B..EEEEE.SSHHHHHCCC...HHHHTC--EEEEEESSSSBE.TTE.BSEEEEE CS
                    RNA_ligase 111 g.tvpvlyegkflaaeellel..llskgnkrEGlVikpeselyk.nkg.raifKvk 161
                                   + ++ + y+ ++++a+e++e+  + s +   EG+ ik+ ++ y+  ++ r+++K k
  gi|15668343|ref|NP_247139.1| 386 DkIIDISYKLVTNDAKEAREFynW-SLSIGHEGVMIKNLKAPYTpGSRvRTMYKFK 440
                                   247777777777788888888652.556699*************9999***99986 PP

>> mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.8   3.3e-08   8.4e-05      87     195 .]     331     440 ..     324     440 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.3e-08
                                   CEEEEEEEEEEEEEETTEEGTTSBHHHHHHHHHHHTHHHHHHHH.HTTCCCCTTSSSEEEE--EEETTHHHHHHHHCCCCC CS
               mRNA_cap_enzyme  87 kkkelryliyDivaingvtvaeeplskRleilkkelikprneek.ktglletdkepfsvrlKefilleavaklleekfikk 166
                                   k  +lr  ++Di+  +gv++ +e+++kR ++l+ e++   n+ +   +++e++++  ++   ++ l+++ ak   e    +
  gi|15668343|ref|NP_247139.1| 331 KEINLRVYLFDILYKDGVSFIDEEFEKRRKVLE-EIVGYENDWRtERKRIEKELKSDKIIDISYKLVTNDAKEAREFYNWS 410
                                   44678999************************8.56666666554777888877777766666677777777666666778 PP

                                   TTSTEEEEEEEESSSB--SE.EEEEEEEE- CS
               mRNA_cap_enzyme 167 lshesDGLIfqpvkepyvag.rdsdllKwK 195
                                   ls    G +++  k+py++g r + ++K+K
  gi|15668343|ref|NP_247139.1| 411 LSIGHEGVMIKNLKAPYTPGsRVRTMYKFK 440
                                   999999**************8888999988 PP

>> DUF2071  Uncharacterized conserved protein (COG2071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.15   3.9e+02      93     125 ..     240     273 ..     235     297 .. 0.76
   2 !   13.0   0.0   2.3e-05     0.059      60     121 ..     328     394 ..     312     452 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.15
                       DUF2071  93 vlvarllfglpYvtarmrveeeegeveyksrr.s 125
                                     + r+ f+ +Y  ar+++++++++v++ srr +
  gi|15668343|ref|NP_247139.1| 240 LEMGRAQFETKYDGARVQIHKDGNKVKIYSRRlE 273
                                   56789999************999****9999842 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.3e-05
                       DUF2071  60 stfpelNvRtYvrdkegrrGVvFlsldadrllivlvarllfglpYvtarmrveeee.....geveyk 121
                                   + ++e+N+R+Y  d   + GV F+ ++ +++  vl   + ++  ++t r r+e+e       +++yk
  gi|15668343|ref|NP_247139.1| 328 KMMKEINLRVYLFDILYKDGVSFIDEEFEKRRKVLEEIVGYENDWRTERKRIEKELksdkiIDISYK 394
                                   5689********99899***************99999999999999999988833244445555553 PP

>> DNA_ligase_OB_2  DNA ligase OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.7   4.4e+03      36      54 ..     378     399 ..     372     401 .. 0.71
   2 ?   11.6   0.1   8.5e-05      0.22       2      66 .]     456     548 ..     455     548 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                                   H...HHHTT-EEEEEEE-TTSS CS
               DNA_ligase_OB_2  36 n...ppkiGkiitykyqeltsk 54 
                                   +   + k +kii + y+ +t++
  gi|15668343|ref|NP_247139.1| 378 RiekELKSDKIIDISYKLVTND 399
                                   3344667899****99988875 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.5e-05
                                   ...EEEEEEEEE..EEEE.TTEE...EEE-SS--HHHHHH.................HHHTT-EEEEEEE-TTSSSS.... CS
               DNA_ligase_OB_2   2 GkGkykgmlGal..lvetkkgkr...fkiGsGlsdaqRen.................ppkiGkiitykyqeltskgv.... 56 
                                   G Gk k+  G++   v+ ++g+      +G+Gl++a+ e                  +     +i++ y+e+ ++++    
  gi|15668343|ref|NP_247139.1| 456 GMGKRKDWYGSFeiCVRDEEGNLypiGHVGTGLTEADLEFlkeeidkiiirdlgeevEVEPKIVIEVAYEEIQKSDKypcg 536
                                   67777777777631244445554333567888888887666667888888888876634444588********99999*** PP

                                   ..-EEEEEEEE- CS
               DNA_ligase_OB_2  57 ..pRfPsflrvR 66 
                                     +RfP+++r+R
  gi|15668343|ref|NP_247139.1| 537 yaLRFPRVVRFR 548
                                   ***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 4088.33
//
Query:       gi|15668344|ref|NP_247140.1|  [L=215]
Description: protein-L-isoaspartate O-methyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-86  288.3   0.0    4.1e-86  288.1   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.5e-10   41.1   0.0    2.2e-10   40.5   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      2e-06   27.2   0.0    2.7e-06   26.7   0.0    1.2  1  Methyltransf_3   O-methyltransferase
    0.00011   21.4   0.0    0.00014   21.0   0.0    1.2  1  Fibrillarin      Fibrillarin
    0.00033   20.0   0.0    0.00044   19.6   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0012   19.5   0.0     0.0022   18.7   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
      0.002   17.2   0.0     0.0038   16.3   0.0    1.4  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0059   16.3   0.0     0.0095   15.6   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.016   14.9   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
      0.014   16.4   0.1      0.036   15.1   0.0    1.7  2  Methyltransf_24  Methyltransferase domain
      0.044   13.2   0.0      0.079   12.4   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
       0.11   11.8   0.0       0.16   11.3   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family


Domain annotation for each model (and alignments):
>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.1   0.0   2.7e-89   4.1e-86       2     209 ..       6     211 ..       5     212 .. 0.99

  Alignments for each domain:
  == domain 1  score: 288.1 bits;  conditional E-value: 2.7e-89
                                   HHHHHHHHHHHTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES- CS
                          PCMT   2 kkealieelkkkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevGs 82 
                                   +k+a+ie+l+++g+iks++v++al++v+Reef+pe++ke+aY+d+pl+igy++tiSa+hmv++++ell+lk+g++vLe+G+
  gi|15668344|ref|NP_247140.1|   6 QKKAVIEKLIREGYIKSKRVIDALLKVPREEFLPEHLKEYAYVDTPLEIGYGQTISAIHMVGMMCELLDLKPGMKVLEIGT 86 
                                   689****************************************************************************** PP

                                   TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS--HHHHHTE CS
                          PCMT  83 GsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiPealidQL 163
                                   G+Gy++av+a++vge+g+vvsieri+el+e+a+r+l+kl+++nviv+vgDG+ Gye+ aPYd+i+++aa p+iPe+li+QL
  gi|15668344|ref|NP_247140.1|  87 GCGYHAAVTAEIVGEDGLVVSIERIPELAEKAERTLRKLGYDNVIVIVGDGTLGYEPLAPYDRIYTTAAGPKIPEPLIRQL 167
                                   ********************************************************************************* PP

                                   EEEEEEEEEESBSSSEEEEEEEEETTTEEEEEEEEEE---B-BCCC CS
                          PCMT 164 keGGrlvvPvgeeeeQvlklvdkkadgkvvikkleevrfvpltdke 209
                                   k+GG+l++Pvg ++ Q+l l++k++ ++++ik++  v+fvpl++ke
  gi|15668344|ref|NP_247140.1| 168 KDGGKLLMPVG-RYLQRLVLAEKRG-DEIIIKDCGPVAFVPLVGKE 211
                                   ***********.*************.9****************997 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   1.5e-13   2.2e-10       2     113 ..      76     179 ..      75     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.5e-13
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsn 81 
                                   + g++vl++G+G G+ + + ae +g+++ vv+i++ +e  e+A+  ++klg+dnv + +gd +   e l   +++D i + 
  gi|15668344|ref|NP_247140.1|  76 KPGMKVLEIGTGCGYHAAVTAEIVGEDGLVVSIERIPELAEKAERTLRKLGYDNVIVIVGDGTLgYEPL---APYDRIYT- 152
                                   679**********************************************************99976644...89**9777. PP

               Methyltransf_31  82 evlnaladpdkileeiervlkpggilliedpr 113
                                        +a+ +ki e ++r lk+gg ll+   r
  gi|15668344|ref|NP_247140.1| 153 -----TAAGPKIPEPLIRQLKDGGKLLMPVGR 179
                                   .....89999999999999****999986666 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.8e-09   2.7e-06      38     108 ..      65     137 ..      31     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.8e-09
                                   HHHH...HHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-H CS
                Methyltransf_3  38 fLsl...LvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegda 108
                                   ++++   L++l    +vleiG+  Gy +  ta  + eDG +++i+  +e +e a + ++k g+++ i +i+gd+
  gi|15668344|ref|NP_247140.1|  65 MVGMmceLLDLKPGMKVLEIGTGCGYHAAVTAEIVGEDGLVVSIERIPELAEKAERTLRKLGYDNVI-VIVGDG 137
                                   4555111455555669***********************************************9977.555665 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   9.6e-08   0.00014      64     130 ..      71     139 ..      59     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 9.6e-08
                                   S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTT..STTEEEEES-TTS CS
                   Fibrillarin  64 kelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakk..RknivPileDArk 130
                                   + l +k+g kvL +G++ G  ++  ++ivge+g+v ++e  p    +  +  +k    n++ i++D + 
  gi|15668344|ref|NP_247140.1|  71 ELLDLKPGMKVLEIGTGCGYHAAVTAEIVGEDGLVVSIERIPELAEKAERTLRKlgYDNVIVIVGDGTL 139
                                   45679*********************************9888776655544443225899999999875 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.9e-07   0.00044      52      83 ..      67      98 ..      60     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.9e-07
                                  HHHHTTTT--TT-EEEEES-TTSHHHHHHHHH CS
                          CMAS 52 dlileklelkpGmtlLdiGcGWGslvrraver 83
                                   +++e l+lkpGm++L+iG+G G+ +  ++e 
  gi|15668344|ref|NP_247140.1| 67 GMMCELLDLKPGMKVLEIGTGCGYHAAVTAEI 98
                                  6899******************9988777665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.5e-06    0.0022       1      71 [.      81     153 ..      81     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
                                   EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvss 71 
                                   vL++G+G G +++  a+ +g ++ v+ ++  +e+ e+a++ +++ g+ nv +++gd +   ++ + +D ++ +
  gi|15668344|ref|NP_247140.1|  81 VLEIGTGCGYHAAVTAEIVGeDGLVVSIERIPELAEKAERTLRKLGYdNVIVIVGDGTLGYEPLAPYDRIYTT 153
                                   9*****************9769**********************999*********98877788889988875 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.5e-06    0.0038      26      84 ..      73     136 ..      64     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.5e-06
                                   H-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S- CS
                        RrnaAD  26 lnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdeklkvvhqD 84 
                                   l+l++ ++vleig+G G   +  a+++     vv++E  ++La+  + +l+   + ++ v+  D
  gi|15668344|ref|NP_247140.1|  73 LDLKPGMKVLEIGTGCGYHAAVTAEIVgedGLVVSIERIPELAEKAERTLRklGYDNVIVIVGD 136
                                   7999*************99999999998767899************999998878888888777 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   6.4e-06    0.0095       3      83 ..      72     150 ..      70     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.4e-06
                                   HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEE CS
               Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDri 83 
                                   lL+++++ ++l++ ++ G   +  ae++ + g vv +++  e +++ +++l++Lg  n+iv+ +D++   + l+   +Dri
  gi|15668344|ref|NP_247140.1|  72 LLDLKPGMKVLEIGTGCGYHAAVTAEIVGEDGLVVSIERIPELAEKAERTLRKLGYDNVIVIVGDGTLGYEPLAP--YDRI 150
                                   689999999********************************************************9876666654..6766 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.1e-05     0.016      29      95 ..      66     132 ..      52     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                         GCD14  29 isliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvt 95 
                                   + ++   L+lkpG +v+e GtG g  +   a  v+  G + ++e   + aeka   +r+ + ++++ 
  gi|15668344|ref|NP_247140.1|  66 VGMMCELLDLKPGMKVLEIGTGCGYHAAVTAEIVGEDGLVVSIERIPELAEKAERTLRKLGYDNVIV 132
                                   345556799************************************9999999999999988877554 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       7.5   1.1e+04       1      14 [.      52      63 ..      52      67 .. 0.79
   2 ?   15.1   0.0   2.4e-05     0.036       1      53 [.      82     133 ..      82     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.5
               Methyltransf_24  1 vEiGvysGvstlwl 14
                                  +EiG  +G +  ++
  gi|15668344|ref|NP_247140.1| 52 LEIG--YGQTISAI 63
                                  79**..99887665 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.4e-05
               Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrl 53 
                                   +EiG+ +G+ +++ ++ + + g   +v+++  p+ ae+a++ +r++g+d+++ +
  gi|15668344|ref|NP_247140.1|  82 LEIGTGCGYHAAVTAEIVGEDGL--VVSIERIPElAEKAERTLRKLGYDNVIVI 133
                                   7********************98..******99888889999999999998754 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.3e-05     0.079       4      60 ..      80     137 ..      77     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.3e-05
                                   EEEEET-TTSHHHHHHHHHST.TSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                Methyltransf_4   4 vvleiGcGkGeflvalAkknP.dknflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                                    vleiG+G G +    A+    d +++ iE   ++ +k+ ++ ++l++ N+ ++ gd 
  gi|15668344|ref|NP_247140.1|  80 KVLEIGTGCGYHAAVTAEIVGeDGLVVSIERIPELAEKAERTLRKLGYDNVIVIVGDG 137
                                   589**************9987256899***************************9997 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.16      44     108 ..      74     138 ..      62     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                   -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TT CS
               Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanae 108
                                     k+g kvl++ +G g  a+  ++ vge g vv ++  +++ + +e+ l++ g+ n+  +++++ 
  gi|15668344|ref|NP_247140.1|  74 DLKPGMKVLEIGTGCGYHAAVTAEIVGEDGLVVSIERIPELAEKAERTLRKLGYDNVIVIVGDGT 138
                                   56899****************************************************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1329.03
//
Query:       gi|15668345|ref|NP_247141.1|  [L=157]
Description: putative transcriptional regulator [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-31  106.8   1.0    7.7e-31  105.9   1.0    1.5  1  TFX_C          DNA_binding protein, TFX, C-term
    4.4e-09   35.7   0.2    8.4e-09   34.8   0.2    1.4  1  Sigma70_r4     Sigma-70, region 4
    2.5e-07   30.6   3.2    2.6e-07   30.6   2.0    1.8  1  HTH_19         Helix-turn-helix domain
    1.5e-06   28.1   0.5    2.8e-06   27.3   0.5    1.4  1  HTH_3          Helix-turn-helix
    0.00064   19.6   0.0     0.0011   18.8   0.0    1.5  1  HTH_Crp_2      Crp-like helix-turn-helix domain
    0.00076   19.2   0.1     0.0019   18.0   0.1    1.8  1  HTH_23         Homeodomain-like domain
     0.0012   18.4   2.8     0.0013   18.2   1.0    2.1  2  GerE           Bacterial regulatory proteins, luxR family
     0.0016   18.5   0.2     0.0027   17.8   0.2    1.4  1  Trp_repressor  Trp repressor protein
     0.0018   18.0   0.1     0.0036   17.0   0.1    1.5  1  HTH_38         Helix-turn-helix domain
     0.0031   17.4   0.5     0.0094   15.9   0.1    1.9  2  HTH_37         Helix-turn-helix domain
     0.0052   16.8   0.5      0.018   15.1   0.1    1.9  2  KorB           KorB domain
     0.0062   16.2   0.1      0.011   15.4   0.1    1.5  1  Sigma70_r4_2   Sigma-70, region 4
     0.0071   17.0   0.1      0.011   16.5   0.1    1.3  1  Pex14_N        Peroxisomal membrane anchor protein (Pex14p) c
     0.0075   16.5   0.0      0.013   15.8   0.0    1.4  1  KORA           TrfB plasmid transcriptional repressor
  ------ inclusion threshold ------
      0.013   15.5   0.1      0.023   14.7   0.1    1.4  1  HTH_29         Winged helix-turn helix
      0.014   15.7   0.0      0.023   15.0   0.0    1.2  1  HTH_31         Helix-turn-helix domain
      0.023   14.6   0.0      0.034   14.0   0.0    1.3  1  MarR_2         MarR family
      0.045   13.3   0.7       0.22   11.1   0.1    2.4  2  HTH_24         Winged helix-turn-helix DNA-binding
      0.055   13.6   0.1      0.078   13.1   0.1    1.2  1  RepB           RepB plasmid partitioning protein
      0.074   13.0   0.1       0.17   11.9   0.1    1.6  1  MarR           MarR family
       0.14   12.3   0.0        0.3   11.2   0.0    1.5  1  HTH_28         Helix-turn-helix domain
       0.21   11.0   0.6       0.68    9.4   0.2    1.8  2  DUF3335        Peptidase_C39 like family


Domain annotation for each model (and alignments):
>> TFX_C  DNA_binding protein, TFX, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   1.0   9.4e-34   7.7e-31       1      83 []      72     154 ..      72     154 .. 0.99

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 9.4e-34
                                   SS-HHHHHHHH---EEEEE--GGGHHHHHHHHHHHHHHHS-S----HHHHHHHHHHH-SSS-----SSS-EEEEESSSSSE CS
                         TFX_C   1 AreTlaflealdapvlvtieeGtdlfdipkiiyaeadkagikvkydtieLikllreeapeaikgrvvkedlevyitedGei 81 
                                   A +T+++++ ++ap++++ieeGtd+++ip+i++++ad++gikvky+t+eLi+l++e+a+e i++r+vk+++++yi e+G++
  gi|15668345|ref|NP_247141.1|  72 AYNTIKIYNRIMAPLSIEIEEGTDVLEIPDIVFKKADEEGIKVKYNTLELIELIKENASEFIEKRTVKKKFKIYILENGDL 152
                                   789*****************************************************************************9 PP

                                   EE CS
                         TFX_C  82 rv 83 
                                   +v
  gi|15668345|ref|NP_247141.1| 153 DV 154
                                   87 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.2     1e-11   8.4e-09       5      50 .]      27      71 ..      26      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1e-11
                                  S-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                    Sigma70_r4  5 LpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkLRk 50
                                  L++ + +vl+lr  +glT+eEI+++lg Sr  +++iekrA ++++k
  gi|15668345|ref|NP_247141.1| 27 LTDTQIKVLKLRK-KGLTQEEIAKMLGTSRANISMIEKRAKENIKK 71
                                  7889999999997.789***********************999886 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   2.0   3.2e-10   2.6e-07       9      48 ..      38      82 ..      34     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.2e-10
                        HTH_19  9 eelgltqeelaerlgisrskisaiEngkkdvps..aell...lki 48
                                  +++gltqee+a++lg+sr+ is+iE+  k++++  ++++   ++i
  gi|15668345|ref|NP_247141.1| 38 RKKGLTQEEIAKMLGTSRANISMIEKRAKENIKkaYNTIkiyNRI 82
                                  579**********************99777777653433333555 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.5   3.5e-09   2.8e-06       4      31 ..      37      63 ..      33      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.5e-09
                                  HHHHTTHHHHHHHHHHTSSHHHHHHHHT CS
                         HTH_3  4 lRkqlglsqeeLAeklGvsrstisriEn 31
                                  lR ++gl+qee+A++lG sr+ is+iE+
  gi|15668345|ref|NP_247141.1| 37 LR-KKGLTQEEIAKMLGTSRANISMIEK 63
                                  34.6***********************8 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.4e-06    0.0011      21      41 ..      41      61 ..      17      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                                  EHHHHHHHHHTTSSHHHHHHH CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsri 41
                                   ltqee+A mlG++r  +s i
  gi|15668345|ref|NP_247141.1| 41 GLTQEEIAKMLGTSRANISMI 61
                                  59**************99976 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   2.3e-06    0.0019       8      32 ..      32      56 ..      29      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.3e-06
                        HTH_23  8 lrillllaeGlsvreIAreLgvsrr 32
                                  +++l+l ++Gl+++eIA++Lg sr 
  gi|15668345|ref|NP_247141.1| 32 IKVLKLRKKGLTQEEIAKMLGTSRA 56
                                  5799999****************95 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.0   1.6e-06    0.0013       3      41 ..      27      65 ..      25      82 .. 0.90
   2 ?   -2.1   0.0       3.4   2.8e+03      27      36 ..     131     140 ..     129     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-06
                                  S-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHH CS
                          GerE  3 LskRErevLrllaeGksnkeIAeelniSekTVkvhksni 41
                                  L++ + +vL+l  +G++ +eIA+ l+ S  ++++  +++
  gi|15668345|ref|NP_247141.1| 27 LTDTQIKVLKLRKKGLTQEEIAKMLGTSRANISMIEKRA 65
                                  9*****************************999766655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.4
                                   HTS-HHHHHH CS
                          GerE  27 lniSekTVkv 36 
                                    +i ++TVk 
  gi|15668345|ref|NP_247141.1| 131 EFIEKRTVKK 140
                                   5788899985 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   3.3e-06    0.0027      38      76 ..      31      72 ..       5      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-06
                 Trp_repressor 38 RlqvvkeLLkeelsqreIaeelgvSiAtIt....RvsrsLktg 76
                                   ++v+k L k++l+q+eIa++lg+S A I+    R + ++k++
  gi|15668345|ref|NP_247141.1| 31 QIKVLK-LRKKGLTQEEIAKMLGTSRANISmiekRAKENIKKA 72
                                  578999.99********************95555555555554 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   4.4e-06    0.0036      14      38 ..      35      59 ..      27      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.4e-06
                        HTH_38 14 erllaeGlslreIArrLgrspsTIs 38
                                   +l+++Gl++ eIA+ Lg s+  Is
  gi|15668345|ref|NP_247141.1| 35 LKLRKKGLTQEEIAKMLGTSRANIS 59
                                  5799****************98776 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.2e-05    0.0094      27      54 ..      37      64 ..      32      70 .. 0.89
   2 ?   -1.2   0.0       2.5     2e+03       4      29 ..     101     127 ..     100     139 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                                  HHHCT--HHHHHHHHT--HHHHHHHHTT CS
                        HTH_37 27 iekrelsqseaaqllgiaqPkvsrllrg 54
                                  ++k++l+q+e+a++lg++++++s +++ 
  gi|15668345|ref|NP_247141.1| 37 LRKKGLTQEEIAKMLGTSRANISMIEKR 64
                                  6799*******************99975 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.5
                                   XXX--HHHHHHHHHHHHHH.HHHHHHH CS
                        HTH_37   4 DlgeedaeelkaKaqlala.iaeliek 29 
                                   D+ ++ a+e  +K+++    ++eli++
  gi|15668345|ref|NP_247141.1| 101 DIVFKKADEEGIKVKYNTLeLIELIKE 127
                                   566677777777777654447777776 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.2e-05     0.018       2      38 ..      40      74 ..      39      84 .. 0.86
   2 ?   -0.6   0.0       1.8   1.4e+03      27      66 ..      97     133 ..      94     143 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                          KorB  2 kgvkqadIAkaLGksksfvslylklldvpdylrelyd 38
                                  kg++q++IAk LG s++ +s+  k ++  + ++++y+
  gi|15668345|ref|NP_247141.1| 40 KGLTQEEIAKMLGTSRANISMIEKRAK--ENIKKAYN 74
                                  89*******************998766..45888887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.8
                          KorB  27 ldvpdylrelydseviadirtLyeLrraaekhpaevrafv 66 
                                   l++pd +++  d    + i++ y+   + e + +++++f+
  gi|15668345|ref|NP_247141.1|  97 LEIPDIVFKKAD---EEGIKVKYNTLELIELIKENASEFI 133
                                   567777776666...4455555555555566666666666 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.4e-05     0.011      17      43 ..      33      58 ..      27      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                                  HHHHHHHTS---HHHHHHHHT--HHHH CS
                  Sigma70_r4_2 17 eifllryleglsykEIAellgisegtV 43
                                  +++ lr  +gl+++EIA++lg+s +++
  gi|15668345|ref|NP_247141.1| 33 KVLKLRK-KGLTQEEIAKMLGTSRANI 58
                                  6777755.9**************9987 PP

>> Pex14_N  Peroxisomal membrane anchor protein (Pex14p) conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.3e-05     0.011      29      53 ..      37      61 ..      25      85 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-05
                       Pex14_N 29 LesKGLtqeEIeeaLkraereeeas 53
                                  L++KGLtqeEI + L+ ++ + +  
  gi|15668345|ref|NP_247141.1| 37 LRKKGLTQEEIAKMLGTSRANISMI 61
                                  9***************955444333 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-05     0.013      30      71 ..      40      82 ..      26      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                          KORA 30 egkkqadvatelgltkqavsqavkrvwaahaere.epaglerV 71
                                  +g +q+++a+ lg ++ ++s ++kr+ ++ ++   + + ++r+
  gi|15668345|ref|NP_247141.1| 40 KGLTQEEIAKMLGTSRANISMIEKRAKENIKKAYnTIKIYNRI 82
                                  6779**********************99988755455556666 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.8e-05     0.023       2      30 ..      32      59 ..      31      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.8e-05
                        HTH_29  2 aqallllaeGvstvsqiAkllglsrrtvy 30
                                  +++l l ++G+ t  +iAk+lg sr  + 
  gi|15668345|ref|NP_247141.1| 32 IKVLKLRKKGL-TQEEIAKMLGTSRANIS 59
                                  78999*****9.9************8775 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.8e-05     0.023      12      36 ..      39      63 ..      31      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.8e-05
                        HTH_31 12 raGLsqeevAerlgvsestlsrlEq 36
                                  + GL+qee A+ lg s++ +s +E 
  gi|15668345|ref|NP_247141.1| 39 KKGLTQEEIAKMLGTSRANISMIEK 63
                                  57********************997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.2e-05     0.034      17      46 ..      39      66 ..      27      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-05
                                  TTTSEEEHHHHHHHHTSSHHHHHHHHHHHH CS
                        MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLv 46
                                    g  lt+ e+a+ lg s++++s i kr+ 
  gi|15668345|ref|NP_247141.1| 39 KKG--LTQEEIAKMLGTSRANISMIEKRAK 66
                                  445..9*****************9988775 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00026      0.22      15      35 ..      39      59 ..      27      64 .. 0.84
   2 ?   -0.8   0.1       1.4   1.1e+03       4      16 ..     117     129 ..     115     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                        HTH_24 15 nprisqreLAerlglSpstvn 35
                                  + +++q e+A++lg S+++++
  gi|15668345|ref|NP_247141.1| 39 KKGLTQEEIAKMLGTSRANIS 59
                                  569*************99875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.4
                        HTH_24   4 tdrkILelLqknp 16 
                                   ++++++el+++n+
  gi|15668345|ref|NP_247141.1| 117 NTLELIELIKENA 129
                                   6789999999997 PP

>> RepB  RepB plasmid partitioning protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.5e-05     0.078      14      50 ..      34      69 ..      28      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.5e-05
                          RepB 14 aarleerGvdreeiasalgldkqtvskmvaraipegi 50
                                  + +l+++G+++eeia+ lg++++ + +m+ +++ e+i
  gi|15668345|ref|NP_247141.1| 34 VLKLRKKGLTQEEIAKMLGTSRANI-SMIEKRAKENI 69
                                  689**********************.99998888888 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0002      0.17       1      36 [.      27      60 ..      27      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                  --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHH CS
                          MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtr 36
                                  lt tq+++L +  ++ +l++ e+ak+lg+s+++++ 
  gi|15668345|ref|NP_247141.1| 27 LTDTQIKVLKL--RKKGLTQEEIAKMLGTSRANISM 60
                                  67888888876..7899****************995 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00037       0.3       3      30 ..      32      59 ..      31      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                        HTH_28  3 leiikllaaGhsvreaArelgisrrtvy 30
                                  ++++kl ++G ++ e+A+ lg+sr  ++
  gi|15668345|ref|NP_247141.1| 32 IKVLKLRKKGLTQEEIAKMLGTSRANIS 59
                                  5899999*****************8776 PP

>> DUF3335  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00083      0.68      88     138 ..      13      63 ..       3      73 .. 0.85
   2 ?   -0.4   0.0       0.8   6.5e+02     102     125 ..     104     127 ..      89     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00083
                       DUF3335  88 eekkevlelvqedfleeaeeagvevekeelsleeleealakgalvlvList 138
                                   +++  vl +v+++fl++++ + ++++k+ l++ee+++ l + ++ + +i++
  gi|15668345|ref|NP_247141.1|  13 QNNYLVLCMVEDSFLTDTQIKVLKLRKKGLTQEEIAKMLGTSRANISMIEK 63 
                                   455668999**************************************9987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.8
                       DUF3335 102 leeaeeagvevekeelsleeleea 125
                                    ++a+e+g++v++++l+l el ++
  gi|15668345|ref|NP_247141.1| 104 FKKADEEGIKVKYNTLELIELIKE 127
                                   67899999***9999998877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1368  (0.076301); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 998.71
//
Query:       gi|15668346|ref|NP_247142.1|  [L=347]
Description: cell division protein pelota PelA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-32  111.9   0.3    4.1e-32  110.9   0.3    1.6  1  eRF1_1          eRF1 domain 1
    6.4e-27   94.3   2.5      8e-27   94.0   0.8    2.1  2  eRF1_3          eRF1 domain 3
      1e-13   51.7   0.3    2.3e-13   50.6   0.3    1.6  1  eRF1_2          eRF1 domain 2
     0.0084   16.4   4.6      0.078   13.3   0.0    3.2  4  SpoU_sub_bind   RNA 2'-O ribose methyltransferase substrate b
  ------ inclusion threshold ------
       0.06   13.9   0.7        1.1    9.9   0.3    2.5  2  baeRF_family12  Bacterial archaeo-eukaryotic release factor f
      0.088   12.4   0.3       0.33   10.6   0.1    2.0  2  DUF2529         Domain of unknown function (DUF2529)
      0.088   12.7   2.6        1.8    8.4   0.0    2.3  2  TK              Thymidine kinase
       0.13   12.5   1.1        2.9    8.1   0.1    2.2  2  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C


Domain annotation for each model (and alignments):
>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.3   1.8e-35   4.1e-32       1     128 [.       1     125 [.       1     126 [. 0.91

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 1.8e-35
                                   HEEEEECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......-.-CEEEEEEEEEEEEEEECTTSSE CS
                        eRF1_1   1 mkllkrdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsre.servklkLtikvekvdfdkdagv 80 
                                   mk++++  +   ++ ++L+pe+ +dlw lyn+i++gd++ a+t r+vq +      +   + k+ L i+v++v+fd+++++
  gi|15668346|ref|NP_247142.1|   1 MKIIEEIPQ---KNIIKLMPENLDDLWVLYNIIEEGDKIFAVTERRVQDKGDVIRADrGAKRKMFLGIEVKNVEFDENTKR 78 
                                   777777555...669********************************996333222258999******************* PP

                                   EEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                        eRF1_1  81 lrisGkvieenehvklgafhtldlelkrpftiikeewdsfalerLkea 128
                                   +ri G++i++ ++v+lg++ht++++++++++i+k +w+++++er+kea
  gi|15668346|ref|NP_247142.1|  79 VRILGTIIHGPDDVPLGSHHTIEIKPFDELSIEK-NWKKWQIERIKEA 125
                                   **********************************.9***********8 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       6.3   1.4e+04      27      43 ..     182     198 ..     160     199 .. 0.60
   2 !   94.0   0.8   3.5e-30     8e-27       2     113 .]     255     346 ..     254     346 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.3
                                   HHHHHHHHTT-EEEEEE CS
                        eRF1_3  27 eevlkalemgAvetLLv 43 
                                   +e+ k+l    v+++Lv
  gi|15668346|ref|NP_247142.1| 182 HEIAKVLSEYDVDNILV 198
                                   35555555555666655 PP

  == domain 2  score: 94.0 bits;  conditional E-value: 3.5e-30
                                   HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHHTT CS
                        eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenveesg 82 
                                   ++e++l+e++lee+ak  g+avYG++ev+kale++A++tLLvs++l r++     +             ie+++++ ee+g
  gi|15668346|ref|NP_247142.1| 255 AKETQLIEKLLEEIAKK-GLAVYGIDEVKKALEYSAIDTLLVSDSLVRNH-----E-------------IEKIIDTTEEMG 316
                                   79*************99.******************************96.....2.............99********** PP

                                   -EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                        eRF1_3  83 akveiisseseeGeqlvkafgGiaaiLRykv 113
                                   +kv+i+sse+++G+ql ka+gGia++LR+++
  gi|15668346|ref|NP_247142.1| 317 GKVVIVSSEHDAGKQL-KALGGIAGLLRFPI 346
                                   ****************.************96 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.3     1e-16   2.3e-13       2     126 ..     134     242 ..     133     251 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1e-16
                                   EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEEEE CS
                        eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgiil 82 
                                   v ++v+d++eA i+ +++++++ + +i+++  kK        +   ++ ee  +e+++++a+ ++++       +++ i++
  gi|15668346|ref|NP_247142.1| 134 VLVVVMDDEEADIFEVRDYSIKEICSIKSHTSKKLD------Y---KINEELKKEYYHEIAKVLSEY-------DVDNILV 198
                                   568***************************999995......2...367999*************99.......99***** PP

                                   EESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC CS
                        eRF1_2  83 agpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlek 126
                                   agpgf+k+ f++ +  ++ + k++i++  +s++ ++glnev++ 
  gi|15668346|ref|NP_247142.1| 199 AGPGFAKNSFYNFISSQYPELKNKIVVESISTTSRAGLNEVIKR 242
                                   ******************************************97 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.7   3.9e+03      31      52 ..     121     142 ..     103     148 .. 0.50
   2 ?   -1.8   0.0       1.8     4e+03       8      29 ..     122     145 ..     119     172 .. 0.56
   3 ?    5.0   0.2     0.013        30      12      46 ..     240     275 ..     235     276 .. 0.82
   4 !   13.3   0.0   3.5e-05     0.078       2      52 ..     275     325 ..     274     327 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.7
                 SpoU_sub_bind  31 rleellklakkrgikvelvdke 52 
                                   r++e ++  k+ ++ v  +d+e
  gi|15668346|ref|NP_247142.1| 121 RIKEAIESSKRPKVLVVVMDDE 142
                                   3444444444445555555544 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                 SpoU_sub_bind   8 VleaLksgrr..iekllvtegrad 29 
                                   + ea++s +r  +  ++ ++++ad
  gi|15668346|ref|NP_247142.1| 122 IKEAIESSKRpkVLVVVMDDEEAD 145
                                   567777764434555554444333 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.013
                 SpoU_sub_bind  12 Lksgrriekllvteg..radkrleellklakkrgikv 46 
                                   +k g  i++++ ++   ++ + +e+ll++++k+g  v
  gi|15668346|ref|NP_247142.1| 240 IKRGI-INRIYAESRvaKETQLIEKLLEEIAKKGLAV 275
                                   55554.99999999988888889**********9987 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 3.5e-05
                 SpoU_sub_bind   2 iyGlhaVleaLksgrriekllvteg.radkrleellklakkrgikvelvdke 52 
                                   +yG+  V  aL+  + i++llv+++  ++ ++e++++  ++ g kv +v++e
  gi|15668346|ref|NP_247142.1| 275 VYGIDEVKKALEY-SAIDTLLVSDSlVRNHEIEKIIDTTEEMGGKVVIVSSE 325
                                   8************.57*******************************99976 PP

>> baeRF_family12  Bacterial archaeo-eukaryotic release factor family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.3   0.00047       1.1       1      33 [.     133     165 ..     133     177 .. 0.79
   2 ?    2.7   0.1     0.076   1.7e+02     101     135 ..     163     197 ..     159     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00047
                baeRF_family12   1 ktlvvVadgekarffrneegdieelelveefkr 33 
                                   k+lvvV d e+a +f+ ++  i+e+  ++ ++ 
  gi|15668346|ref|NP_247142.1| 133 KVLVVVMDDEEADIFEVRDYSIKEICSIKSHTS 165
                                   79*************999999998877755544 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.076
                baeRF_family12 101 etlgelrkhlhkevkkrlvgeiaknltkhppaeil 135
                                   +t ++l  ++++e+kk   +eiak l++ +++ il
  gi|15668346|ref|NP_247142.1| 163 HTSKKLDYKINEELKKEYYHEIAKVLSEYDVDNIL 197
                                   56666777788888888888888888888887775 PP

>> DUF2529  Domain of unknown function (DUF2529)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.84   1.9e+03      92     127 ..     118     153 ..      93     163 .. 0.60
   2 ?   10.6   0.1   0.00015      0.33      68     120 ..     280     332 ..     248     339 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.84
                                   HHHHHHHHHHHHT--EEEEESS---T..TGGGSSS- CS
                       DUF2529  92 ealklakkleekgievvavsskvkeedalteladvf 127
                                   +++++ +++e  + + v+v   ++ee ++ e+ d  
  gi|15668346|ref|NP_247142.1| 118 QIERIKEAIESSKRPKVLVVVMDDEEADIFEVRDYS 153
                                   555566666666666666666666666565555555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00015
                                   E--TT----TT-EEEEEES-S--HHHHHHHHHHHHHT--EEEEESS---T..T CS
                       DUF2529  68 kleeekeltetDrvllfsresndkealklakkleekgievvavsskvkeedal 120
                                   +++++ e ++ D+ l+  +   ++e++k++++ ee g +vv+vss++++ ++l
  gi|15668346|ref|NP_247142.1| 280 EVKKALEYSAIDTLLVSDSLVRNHEIEKIIDTTEEMGGKVVIVSSEHDAGKQL 332
                                   45555588999*****99999**************************988775 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.7     0.017        37      48     129 ..     102     189 ..      94     199 .. 0.78
   2 ?    8.4   0.0   0.00082       1.8      21      87 ..     212     282 ..     195     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.017
                            TK  48 vvthdgisleak..ksktssleeikeeleeedvdvvlvD..EaqFfe.qd..ivelseklanegkivivagLdtdFerklF 121
                                   ++  d++s+e++  k +++ ++e +e++++ +v vv++D  Ea  fe +d  i e++++  ++ k+ + + ++ + +++ +
  gi|15668346|ref|NP_247142.1| 102 IKPFDELSIEKNwkKWQIERIKEAIESSKRPKVLVVVMDdeEADIFEvRDysIKEICSIKSHTSKK-LDYKINEELKKEYY 181
                                   556677777777667788899999999999999999998778999997543377888877766666.68999999999999 PP

                            TK 122 enilklla 129
                                   ++i k+l+
  gi|15668346|ref|NP_247142.1| 182 HEIAKVLS 189
                                   99999887 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00082
                            TK  21 rvkryqlaekkvvvikaakdnRysegkvvth...dgisleak.ksktssleeikeeleeedvdvvlvDEaq 87 
                                    + +y + + k+vv   +   R + ++v+ +   ++i+ e++  ++t+ +e++ ee++++ + v ++DE++
  gi|15668346|ref|NP_247142.1| 212 ISSQYPELKNKIVVESISTTSRAGLNEVIKRgiiNRIYAESRvAKETQLIEKLLEEIAKKGLAVYGIDEVK 282
                                   45689999999***999*******99999984333455555578899999*******************86 PP

>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.05   1.1e+02     102     160 ..     105     164 ..      94     173 .. 0.73
   2 ?    8.1   0.1    0.0013       2.9      75     132 ..     251     308 ..     205     321 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.05
                CobA_CobO_BtuR 102 lDEinyalklglldeeevlellkkkpeklelvlTGrnapeelleaADl.vtemkkvkHpy 160
                                   +DE+ +  +++  ++e++ e++++ ++   lv+   +++++++e+ D+ + e+ ++k + 
  gi|15668346|ref|NP_247142.1| 105 FDELSIEKNWKKWQIERIKEAIESSKRPKVLVVVMDDEEADIFEVRDYsIKEICSIKSHT 164
                                   799999999999999999999996555555555566777788888887456677766655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0013
                CobA_CobO_BtuR  75 eedaaaakealekakealaseeydlvvlDEinyalklglldeeevlellkkkpeklel 132
                                   e   a+ ++ +ek+ e++a++ + ++ +DE+  al++  +d+  v + l +++e  ++
  gi|15668346|ref|NP_247142.1| 251 ESRVAKETQLIEKLLEEIAKKGLAVYGIDEVKKALEYSAIDTLLVSDSLVRNHEIEKI 308
                                   4556677788999999999999***********************9999874444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2284.09
//
Query:       gi|15668347|ref|NP_247143.1|  [L=222]
Description: haloacid dehalogenase superfamily protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-13   50.5   2.6    3.9e-12   46.6   2.6    2.1  1  Translin        Translin family
  ------ inclusion threshold ------
      0.024   14.8   0.6      0.049   13.8   0.6    1.5  1  CTNNBL          Catenin-beta-like, Arm-motif containing nucle
      0.062   13.6   1.3        2.2    8.6   0.1    3.1  3  Glu-tRNAGln     Glu-tRNAGln amidotransferase C subunit
      0.064   13.9   0.5        1.3    9.7   0.4    2.3  2  Cytochrom_B562  Cytochrome b562
       0.15   12.6   3.1        0.2   12.2   0.5    2.4  3  EF-G-binding_N  Elongation factor G-binding protein, N-termin
        3.3    8.3   8.4          6    7.5   1.1    3.2  2  SF3A3           Pre-mRNA-splicing factor SF3A3, of SF3a compl


Domain annotation for each model (and alignments):
>> Translin  Translin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   2.6   1.3e-15   3.9e-12       2     193 ..      34     194 ..      33     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.3e-15
                                   HHHHHHHHHHHHHHHHHHHHHHHHTTGSSTTTHHHHHHH.HHHHHHHHHHHTTSS..........GHHHHGGGTH.HHHHH CS
                      Translin   2 rreriikasrditaaskkiifllhrvrsekteaqdkkakikkeakeklkeiakllasvaeelqgsnayrYqrqisgglqel 82 
                                   +re+i k+sr+it+    +i  +h+ +           + k+e k+kl+ei+++++++++      + ++   +s   qe+
  gi|15668347|ref|NP_247143.1|  34 VREEILKLSREITRDCAMLIRKIHKSD-----------D-KDEFKDKLNEISEKIKKLNSLA---TFPEFVGYLSTPQQEF 99 
                                   69***********99888776555533...........1.3456677777777774444333...5777888888899*** PP

                                   HHHHHHHHHHHHSS---HHHHHHHTT.---SSSSSS---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHHHHHHHHHH CS
                      Translin  83 iealsfahYletqtLitleevqkilealkeneedafhltpedYllGlfdLtgELmRfainsvalgdkeekplqilkflrel 163
                                   +eals++    ++++ +++e+                +++e Y+lGl+d++gEL R    ++ + +   +  +  kf+++l
  gi|15668347|ref|NP_247143.1| 100 VEALSLYMIKFDNKIPSFKELD--------------FIKEENYILGLADVIGELRREVLEAMKNDNLA-EVERYFKFMEDL 165
                                   *****98555555554444432..............57889**********************99977.9*********** PP

                                   HHHHHTS----HH...HHHHHTTHHHHHHH CS
                      Translin 164 ragfellnlkndsakdlrkKldvlkqsvkK 193
                                   ++ +  ++      ++lr+K+d  +  ++K
  gi|15668347|ref|NP_247143.1| 166 YEFLMNFDYYH-VVDNLRRKQDISRGILEK 194
                                   **888888874.4679******99888877 PP

>> CTNNBL  Catenin-beta-like, Arm-motif containing nuclear
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.6   1.6e-05     0.049      20      88 ..      30     103 ..      16     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                        CTNNBL  20 deaalkklllklekkvkknqel...RikyeddpekfmeSEadLdeeikelsvlaeapel..YpelvelgavesL 88 
                                   +++++++ +lkl +++++   +   +i  +dd + f +   +++e+ik+l+ la+ pe   Y +  +++ ve L
  gi|15668347|ref|NP_247143.1|  30 NKDSVREEILKLSREITRDCAMlirKIHKSDDKDEFKDKLNEISEKIKKLNSLATFPEFvgYLSTPQQEFVEAL 103
                                   67899*************99884423445688999***********************9777766666666665 PP

>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.9   5.8e+03      41      50 ..      31      40 ..      18      46 .. 0.69
   2 ?    8.6   0.1   0.00074       2.2       4      28 ..      60      84 ..      58     103 .. 0.89
   3 ?    2.5   0.0      0.06   1.8e+02       8      37 ..     121     150 ..     118     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.9
                                  -S--HHHHHT CS
                   Glu-tRNAGln 41 eDevreelLk 50
                                  +D vree+Lk
  gi|15668347|ref|NP_247143.1| 31 KDSVREEILK 40
                                  4556788877 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00074
                                  HHHHHHHHHHHHHHHHHTTCGCS-- CS
                   Glu-tRNAGln  4 eEleklakelnsildyveqLqevdt 28
                                  +++++++ +ln+i + +++L+++ t
  gi|15668347|ref|NP_247143.1| 60 DDKDEFKDKLNEISEKIKKLNSLAT 84
                                  6799*****************9986 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.06
                                   HHHHHHHHHHHHHTTCGCS--TT----S.. CS
                   Glu-tRNAGln   8 klakelnsildyveqLqevdttgveplthp 37 
                                   ++ ke n il++ + + e+  +  e + + 
  gi|15668347|ref|NP_247143.1| 121 DFIKEENYILGLADVIGELRREVLEAMKND 150
                                   688899999999999999986666666554 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0084        25      14      74 ..      54      82 ..      17      90 .. 0.68
   2 ?    9.7   0.4   0.00044       1.3       3      92 ..      66     164 ..      47     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0084
                Cytochrom_B562 14 kqvakaddaeelkkalkelraaaedakeatpsklekdseeqkdYqeGldklidqldkaeal 74
                                  +++                                 +s + +++++ l+++ ++++k+++l
  gi|15668347|ref|NP_247143.1| 54 RKIH--------------------------------KSDDKDEFKDKLNEISEKIKKLNSL 82
                                  3344................................5555556666666666666666555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00044
                Cytochrom_B562   3 keeMkqmkkalkqvakaddaeelkkalkelraaaedakeatpsklek........dseeqkdYqeGldklidqld.kaeal 74 
                                   k++ +++++++k++++ ++  e+  +l++ ++ + +a +  + k+++        d  ++++Y  Gl ++i++l  ++ ++
  gi|15668347|ref|NP_247143.1|  66 KDKLNEISEKIKKLNSLATFPEFVGYLSTPQQEFVEALSLYMIKFDNkipsfkelDFIKEENYILGLADVIGELRrEVLEA 146
                                   566778888888888888888888888888888888887777777778888887888999999999999999996368999 PP

                Cytochrom_B562  75 akagkleeakaalkelkd 92 
                                   +k+++l+e++   k ++d
  gi|15668347|ref|NP_247143.1| 147 MKNDNLAEVERYFKFMED 164
                                   999999999888777766 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   6.7e-05       0.2      32      79 ..      29      76 ..      26      80 .. 0.92
   2 ?   -3.1   0.0       4.1   1.2e+04      50      59 ..      94     103 ..      87     110 .. 0.59
   3 ?   -0.7   0.0      0.72   2.1e+03      29      77 ..     143     167 ..     122     173 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                EF-G-binding_N 32 avkalaaekIlelfpelseeqkelLeqiddiktkekaeklLeeLkeyV 79
                                  a k+++ e+Il+l  e + + + l+++i++ ++k +++  L+e+ e +
  gi|15668347|ref|NP_247143.1| 29 ANKDSVREEILKLSREITRDCAMLIRKIHKSDDKDEFKDKLNEISEKI 76
                                  68999*************************************998866 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.1
                EF-G-binding_N  50 eeqkelLeqi 59 
                                   + q+e++e++
  gi|15668347|ref|NP_247143.1|  94 TPQQEFVEAL 103
                                   5555555544 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.72
                EF-G-binding_N  29 vveavkalaaekIlelfpelseeqkelLeqiddiktkekaeklLeeLke 77 
                                   v+ea+k    +++                        e+  k++e+L e
  gi|15668347|ref|NP_247143.1| 143 VLEAMKNDNLAEV------------------------ERYFKFMEDLYE 167
                                   3333333333333........................344444444444 PP

>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.4     0.048   1.4e+02      55      75 ..      66     117 ..       1     121 [. 0.54
   2 ?    7.5   1.1     0.002         6      42      68 ..     145     172 ..     116     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.048
                         SF3A3  55 k...............................eYlkeLleYLesfikrtqpL 75 
                                   k                               e++++L  Y+ +f ++   +
  gi|15668347|ref|NP_247143.1|  66 KdklneisekikklnslatfpefvgylstpqqEFVEALSLYMIKFDNKIPSF 117
                                   2333333344444444445555555555555588888888888887776655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.002
                         SF3A3  42 seip.kkqkkskeYkeYlkeLleYLesf 68 
                                   ++++ ++  + ++Y +++++L+e+L +f
  gi|15668347|ref|NP_247143.1| 145 EAMKnDNLAEVERYFKFMEDLYEFLMNF 172
                                   555534445578*************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1168  (0.0651459); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1394.67
//
Query:       gi|15668348|ref|NP_247144.1|  [L=335]
Description: 50S ribosomal protein L3P [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-94  315.9   0.4    5.9e-94  315.1   0.4    1.4  1  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.1   0.4   3.3e-98   5.9e-94       6     369 .]       5     334 ..       1     334 [. 0.95

  Alignments for each domain:
  == domain 1  score: 315.1 bits;  conditional E-value: 3.3e-98
                                   SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC--EEE CS
                  Ribosomal_L3   6 feaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtvvetppmvi 86 
                                    ++pr+gsl f+prkRa+r +++++s+P++dt   v l+af  yKaGm h   + d p s+  ++ev  ++t++e pp+ +
  gi|15668348|ref|NP_247144.1|   5 INRPRRGSLAFSPRKRAKRPVPRIRSWPEEDT---VRLQAFPVYKAGMSHAFIKEDNPKSPNAGQEVFTPITILEAPPINV 82 
                                   689**************************998...59******************************************** PP

                                   EEEEEEEEETTE.EEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHHHSCSCEEEEEEE CS
                  Ribosomal_L3  87 vgvvgyvetprG.lrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadleeikkeasvvrviaht 166
                                    +++ y   +r  l +l++vwa++l +e++r++             k      +k+++k++e dle++k++   vrv++ht
  gi|15668348|ref|NP_247144.1|  83 CAIRVYGRNERNyLTTLTEVWADNLDKELERKI-------------KLP----KKEDRKTVE-DLEALKDKIEDVRVLVHT 145
                                   ***9998776653899****************9.............233....334444444.78899999999******* PP

                                   ECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT----STTTSS CS
                  Ribosomal_L3 167 virktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGkGfeGvvkRWgvkklprkthr 247
                                     + t  l +Kk+++lEi+++g  i e+l++a+e l k+ ++++vF++gel+D igvtkGkGf+G vkRWgvk + +k++r
  gi|15668348|ref|NP_247144.1| 146 NPKLTC-LPKKKPEILEIRIGGKDIEERLNYAKEILGKQLNITDVFQEGELVDTIGVTKGKGFQGQVKRWGVKIQFGKHAR 225
                                   **9999.************************************************************************** PP

                                   S..SSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS..SS.TTTCTTCB..TSCEEE CS
                  Ribosomal_L3 248 g..lRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdltekeitPmGGfvhyGevkndfil 326
                                   +   R+v++ig+w+p  V+++v+++Gq+Gyh+Rte+nk+i +ig+              ++eitP+GGf hyG+++n++++
  gi|15668348|ref|NP_247144.1| 226 KgvGRHVGSIGPWQPKMVMWSVPMPGQMGYHQRTEYNKRILKIGN-------------NGDEITPKGGFLHYGVIRNNYVV 293
                                   9999*****************************************.............689******************** PP

                                   EES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TTCTSS CS
                  Ribosomal_L3 327 vkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidtaskfg 369
                                   +kGsv Gp krl+ lr+++++q+   + +e+   +i+t+sk+g
  gi|15668348|ref|NP_247144.1| 294 LKGSVQGPAKRLIVLRRAIRPQEPLIKVPEI--TYISTTSKQG 334
                                   *******************************..9*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2092.64
//
Query:       gi|15668349|ref|NP_247145.1|  [L=252]
Description: 50S ribosomal protein L4P [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-46  157.4   0.2      4e-46  157.1   0.2    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.1   0.2   2.2e-50     4e-46       1     192 []      16     250 ..      16     250 .. 0.93

  Alignments for each domain:
  == domain 1  score: 157.1 bits;  conditional E-value: 2.2e-50
                                   EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT......STTSTT---SS CS
                  Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir......spiargGgvah 74 
                                   ++L p+vF++++r+dli+ra+++  ++r q+++s++ a+ ++s+  ++++k  G+GrARv ++       +p+a+gG++ah
  gi|15668349|ref|NP_247145.1|  16 IDL-PAVFEEEYRPDLIKRAFLSAFTARLQPKGSDPlAGLRTSA--KNIGK--GHGRARVDRVPqgwaarVPQAVGGRRAH 91 
                                   578.9***************************************..78998..**********9999999*********** PP

                                   ---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES--.-.-S............S--HHHHHHHHHHTT-........ CS
                  Ribosomal_L4  75 gpkperdystklnkKvrrlAlrsaLsakakqglllvvdnl.eple............esktkelvellkklgl........ 134
                                   +pk+e+  ++++nkK+r +A++sa++a+a+ +l++ ++++ e  e             +ktk++ ++++klg+        
  gi|15668349|ref|NP_247145.1|  92 PPKVEKILWERVNKKERIKAIKSAIAATANPELVKERGHVfE-TEnlpiivessfeeLQKTKDVFAVFEKLGIsddvirak 171
                                   **************************************6544.334457888999999************99988888888 PP

                                   ..................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEEHHHHHHHHHH CS
                  Ribosomal_L4 135 ..................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvitksavekleek 192
                                                     k++s+L+vv++ + n +la+rnlpgv+vi++++l + +l+++      +v+t+sa+ekl+e+
  gi|15668349|ref|NP_247145.1| 172 ngikiragkgkmrgrkykKPRSILVVVGD-KCNAILASRNLPGVDVITAKDLGIIHLAPGGVagrlTVWTESALEKLKER 250
                                   888889898888888888888*******8.99*********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1768.95
//
Query:       gi|15668350|ref|NP_247146.1|  [L=86]
Description: 50S ribosomal protein L23 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-19   68.8   7.3    4.7e-18   65.3   7.3    1.9  1  Ribosomal_L23  Ribosomal protein L23
     0.0024   17.7   0.5     0.0031   17.3   0.5    1.4  1  TusA           Sulfurtransferase TusA
  ------ inclusion threshold ------
      0.013   16.0   0.4      0.019   15.4   0.4    1.4  1  HP0268         HP0268
      0.028   14.3   0.2      0.037   13.9   0.2    1.2  1  Tap-RNA_bind   Tap, RNA-binding
       0.11   12.6   0.1       0.22   11.7   0.0    1.5  2  Tudor_RapA     RapA N-terminal Tudor like domain


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   7.3   1.3e-21   4.7e-18       1      82 [.       5      74 ..       5      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 1.3e-21
                                  SSEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSSEEBE--EEEEEEEESSS- CS
                 Ribosomal_L23  1 dvilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrkvgrrksyKkaiVtLkege 82
                                  dvi++Pv+tEk++++ e+ nk+vF V+++a+K +ik+a+++lF+V+VekVntl+ ++               Kka+V+Lkeg+
  gi|15668350|ref|NP_247146.1|  5 DVIKAPVVTEKTVRMIEEeNKLVFYVDRRATKQDIKRAMKELFDVEVEKVNTLITPK-------------GEKKAYVKLKEGY 74
                                  79**************9988**********************************998.............4566777777665 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.5   8.7e-07    0.0031      15      50 ..      11      46 ..       9      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.7e-07
                                  HHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHH CS
                          TusA 15 lklkkalekleegevlevladdpaatediprfakkl 50
                                  + + k+++ +ee+++l + +d +a+++di+r +k+l
  gi|15668350|ref|NP_247146.1| 11 VVTEKTVRMIEEENKLVFYVDRRATKQDIKRAMKEL 46
                                  6799***************************99986 PP

>> HP0268  HP0268
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.4   5.2e-06     0.019      17      52 ..      11      46 ..       3      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.2e-06
                                  HHHHHHHHHHHH-SEEEEEE--TTTSHHHHHHHHHH CS
                        HP0268 17 islekleekvekegekifYfdkenshKdlkklveff 52
                                  +  ek   ++e+e++ +fY+d+  ++ d+k +++ +
  gi|15668350|ref|NP_247146.1| 11 VVTEKTVRMIEEENKLVFYVDRRATKQDIKRAMKEL 46
                                  567888899********************9877654 PP

>> Tap-RNA_bind  Tap, RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2     1e-05     0.037      40      78 ..      22      60 ..      11      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                  Tap-RNA_bind 40 eknkavFfVedastAsaLkkvsrkItdedgekisilvrp 78
                                  e+nk vF+V+ ++t + +k++ ++  d + ek++ l++p
  gi|15668350|ref|NP_247146.1| 22 EENKLVFYVDRRATKQDIKRAMKELFDVEVEKVNTLITP 60
                                  789******************************999887 PP

>> Tudor_RapA  RapA N-terminal Tudor like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     6e-05      0.22      14      45 ..      14      46 ..       5      47 .. 0.80
   2 ?   -2.2   0.0       1.4   4.9e+03      20      34 ..      51      65 ..      49      73 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6e-05
                    Tudor_RapA 14 kltVeeveeenGlliYlgkredtgee.vslpEt 45
                                  + tV+ +eeen l++Y  +r+ +++  ++++E+
  gi|15668350|ref|NP_247146.1| 14 EKTVRMIEEENKLVFYVDRRATKQDIkRAMKEL 46
                                  5699************99999666556777775 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                    Tudor_RapA 20 veeenGlliYlgkre 34
                                  ve+ n l++  g+++
  gi|15668350|ref|NP_247146.1| 51 VEKVNTLITPKGEKK 65
                                  555566665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 581.15
//
Query:       gi|15668351|ref|NP_247147.1|  [L=242]
Description: 50S ribosomal protein L2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-45  154.9   2.1    1.8e-45  154.2   2.1    1.3  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    6.4e-21   74.1   0.1    3.8e-20   71.6   0.0    2.3  3  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.2   2.1     2e-49   1.8e-45       1     119 [.      93     222 ..      93     227 .. 0.93

  Alignments for each domain:
  == domain 1  score: 154.2 bits;  conditional E-value: 2e-49
                                   SSSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT--- CS
                Ribosomal_L2_C   1 kvGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehkekkl 81 
                                   k+Gn+lpl++ipeG  v+nie+ pg+ggkl+r+ G+ya +++++g+++ vklpSg+++ ++s crAtiGvv++g++kek++
  gi|15668351|ref|NP_247147.1|  93 KPGNILPLGAIPEGIPVFNIETVPGDGGKLVRAGGCYAHILTHDGERTYVKLPSGHIKALHSMCRATIGVVAGGGRKEKPF 173
                                   68******************************************************************************* PP

                                   -STTHHHHT.....TBS----SSSS-TTTSSS--SS....SS..--SSS CS
                Ribosomal_L2_C  82 gkAgrkrwl.....grrpkvrGvamnpvdHphGGGe....Gk..tksrk 119
                                   +kAg+k++       ++p+vrGvamn+vdHp+GGG+    Gk  t+srk
  gi|15668351|ref|NP_247147.1| 174 VKAGKKYHAmkakaVKWPRVRGVAMNAVDHPFGGGRhqhtGKptTVSRK 222
                                   ********9999999*********************7777666444453 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.0   4.2e-24   3.8e-20       1      76 [.      11      85 ..      11      86 .. 0.98
   2 ?   -1.3   0.0      0.25   2.2e+03      51      68 ..     130     147 ..     126     151 .. 0.83
   3 ?   -2.8   0.0      0.73   6.5e+03      48      69 ..     158     180 ..     152     188 .. 0.61

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 4.2e-24
                                  TB-TT.--BSSTT--------EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                  Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                  Gr++s +  ++++r+g  ++kyr +d  ++k+kv gk+v+i +DpgRsAp+A v+ye ge+ +++ peg+kvGd+++
  gi|15668351|ref|NP_247147.1| 11 GRGSSvYTCPSHKRRG--EAKYRRFDELEKKGKVLGKIVDILHDPGRSAPVAKVEYETGEEGLLVVPEGVKVGDIIE 85
                                  9***************..*********************************************************98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.25
                                   EEEEETTTEEEEEE--SS CS
                  Ribosomal_L2  51 Alvkyedgekryiiapeg 68 
                                   A +   dge++y+ +p g
  gi|15668351|ref|NP_247147.1| 130 AHILTHDGERTYVKLPSG 147
                                   667889999999988876 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.73
                                   S-EEEEEETT.TEEEEEE--SS- CS
                  Ribosomal_L2  48 ApiAlvkyed.gekryiiapegl 69 
                                   A i+ v+ +   ek ++ a +++
  gi|15668351|ref|NP_247147.1| 158 ATIGVVAGGGrKEKPFVKAGKKY 180
                                   55666666554444455554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1560.85
//
Query:       gi|15668352|ref|NP_247148.1|  [L=152]
Description: 30S ribosomal protein S19 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-33  112.9   0.1    8.3e-33  112.1   0.1    1.4  1  Ribosomal_S19  Ribosomal protein S19
  ------ inclusion threshold ------
       0.19   10.8   0.0       0.22   10.6   0.0    1.1  1  Citrate_synt   Citrate synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.1   9.3e-37   8.3e-33       3      81 .]      52     135 ..      50     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 9.3e-37
                                   HHSS.TTCCCHHHHHHHHHH....TS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS-- CS
                 Ribosomal_S19   3 lkkg.pfvqesllkkvrkak....aekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTrkp 78 
                                   l +g +  q++l  k++ka+    + k++++i+th+Rd +I+P+mvglt+gVynGk+fv+v++++em+Gh+LgEFs+Trkp
  gi|15668352|ref|NP_247148.1|  52 LLRGlTPQQKKLAMKIKKARrllnKGKEPRIIRTHCRDFVITPDMVGLTFGVYNGKEFVEVKVTPEMIGHYLGEFSLTRKP 132
                                   567766789999999999998986667****************************************************** PP

                                   --S CS
                 Ribosomal_S19  79 vkh 81 
                                   v+h
  gi|15668352|ref|NP_247148.1| 133 VQH 135
                                   **9 PP

>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   2.4e-05      0.22      19      60 ..      19      66 ..       8      94 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.4e-05
                                  TTEEEETTEEHHHHHHHHS-HHHHHHH........HHHSS---HHHHHHH CS
                  Citrate_synt 19 kgelrYRGydieeLaeekssfeevayl........LltgelPtkeelkef 60
                                  k e rYRGy++eeL   + ++ e a l        Ll g  P++++l+  
  gi|15668352|ref|NP_247148.1| 19 KIEFRYRGYTLEELQ--QMPLREFAKLlparqrrtLLRGLTPQQKKLAMK 66
                                  3459*********77..799***999944444444444445555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1029.20
//
Query:       gi|15668353|ref|NP_247149.1|  [L=246]
Description: hypothetical protein MJ_0181 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.067   13.9   0.0       0.92   10.2   0.0    2.1  2  Lumazine_bd_2  Putative lumazine-binding


Domain annotation for each model (and alignments):
>> Lumazine_bd_2  Putative lumazine-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   5.1e-05      0.92       4      48 ..      30      74 ..      28      94 .. 0.82
   2 ?    1.4   0.0     0.029   5.1e+02      17      98 ..     145     224 ..     136     226 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.1e-05
                                  HHHHHHHHHHHHHHHHT-HHHHHHHEEEEEEEEEECTCEEEEEEC CS
                 Lumazine_bd_2  4 aaieavledYfdglaegdaaklrkafhpdaalvgvtkgelremsl 48
                                  ++i++ le++f+++   ++ +l+k++ + a+l+ +++ +  + +l
  gi|15668353|ref|NP_247149.1| 30 DKIAEKLERFFKAINFTNPRHLKKVLNKYAILIEFKNSKIDNERL 74
                                  68999****************************999988766655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.029
                                   HHHT-HHHHHHHEEEEEEEEEECTC.EEEEEECHHHHHHHHHHH..-TT-EE-.EEEEEEEEETTEEEEEEEE.EETTEEE CS
                 Lumazine_bd_2  17 laegdaaklrkafhpdaalvgvtkg.elremsleellalvaerespakegdprekeIesidvagdvAmvkvel.elpdenf 95 
                                   +++ +a+ +++++ + + l+   +  + +e +  ++++lv +re ++k+ +      + ++++ + A ++v++ e++++n+
  gi|15668353|ref|NP_247149.1| 145 IKNRNANDMDRVITNLMLLYSQLGYrYNYEIKGRKFYKLVINREIRDKDYNI----ANELSIELKEAGITVDFwEYIKNNY 221
                                   6677888888888888888874444255666777888888888875443332....2467777777888888888999999 PP

                                   EEE CS
                 Lumazine_bd_2  96 tDy 98 
                                   +D+
  gi|15668353|ref|NP_247149.1| 222 EDL 224
                                   887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1448.29
//
Query:       gi|15668354|ref|NP_247150.1|  [L=194]
Description: hypothetical protein MJ_0182 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-18   66.9   0.7    2.1e-18   66.7   0.7    1.0  1  KAP_NTPase     KAP family P-loop domain
  ------ inclusion threshold ------
      0.018   15.5   0.3      0.026   14.9   0.3    1.2  1  TbpB_B_D       C-lobe and N-lobe beta barrels of Tf-binding p
       0.02   14.8   3.6      0.048   13.6   3.6    1.7  1  ATPase_2       ATPase domain predominantly from Archaea
      0.022   14.1   0.2      0.028   13.7   0.2    1.1  1  DUF4961        Domain of unknown function (DUF4961)
      0.023   15.1   0.4      0.044   14.2   0.3    1.4  1  AAA            ATPase family associated with various cellular
      0.024   14.5   0.1      0.051   13.5   0.0    1.6  2  PriA_3primeBD  3′ DNA-binding domain (3′BD)
      0.038   14.0   2.7      0.044   13.8   0.2    2.0  2  DUF600         Protein of unknown function, DUF600
      0.059   13.7   0.0      0.067   13.6   0.0    1.2  1  AAA_16         AAA ATPase domain
      0.064   13.4   0.4       0.69   10.1   0.1    2.1  2  COG5           Golgi transport complex subunit 5
       0.11   12.2   0.7       0.51   10.0   0.1    2.0  2  HH_signal      Hedgehog amino-terminal signalling domain
       0.11   13.0   4.1        4.1    7.9   0.7    2.2  2  FadA           Adhesion protein FadA
       0.11   12.7   0.2       0.14   12.4   0.2    1.5  1  AAA_22         AAA domain


Domain annotation for each model (and alignments):
>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.7   1.4e-21   2.1e-18      50     203 ..       6     174 ..       1     178 [. 0.84

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 1.4e-21
                    KAP_NTPase  50 pvrflfaefnawsfkggddavaellaaLadaleeeygqlatkllrak.klkalkikgkiklrkacaiplvlilevalflli 129
                                   +++f+  +f+aw++++ d++  +ll+ + d+le++  + +t +   k k+k+l+ k +  ++ +++ ++ ++       + 
  gi|15668354|ref|NP_247150.1|   6 KNEFICLKFDAWLYEKDDNLPYSLLEFIWDELEAKLNKDETITKEIKdKIKKLGKKSVNLWKNMVLGAINATN------IK 80 
                                   679*********************************9998877655405666666666667777777777554......55 PP

                    KAP_NTPase 130 egasllavls....................raaklkeeaplkklqteveelladmektLdalqkrlVvviDdLDrceteev 190
                                   +g s +++ls                     +   +ee++ +k+ +e ++ ++++ ktL+++ k+l+++iD+LDrce e++
  gi|15668354|ref|NP_247150.1|  81 AGTSPITELSgikinasfdgskfvgyvvnaSKEDENEEESYHKKVKELQNCFKELSKTLADNGKKLIIFIDELDRCEAENI 161
                                   5666677777888889999*********7666677899999**************************************** PP

                    KAP_NTPase 191 lqlleavkllfsl 203
                                   l+ll  +kl+fsl
  gi|15668354|ref|NP_247150.1| 162 LNLLASIKLFFSL 174
                                   ***********98 PP

>> TbpB_B_D  C-lobe and N-lobe beta barrels of Tf-binding protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.3   1.7e-05     0.026      30     103 ..      48     127 ..      16     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                                   E-SS-SSCSCEEEEEEETTTTEEEEEEEETT-SSB--S......EEEEEEEETTEEEEEEEETTT-TTSSTT-S-S-CEE CS
                      TbpB_B_D  30 eadkeaeagakaefdvdFgekkltGkLteengeekkkk......vdieakIkgnrFtgkakakdkkkekkensskkkdak 103
                                   +++ +++ ++  + +v+  ++ + G ++++n +  +++      ++i+a+ +g +F+g   +++k++e++e+s +kk ++
  gi|15668354|ref|NP_247150.1|  48 TKEIKDKIKKLGKKSVNLWKNMVLGAINATNIKAGTSPitelsgIKINASFDGSKFVGYVVNASKEDENEEESYHKKVKE 127
                                   566666677788899************99555544444555667***************999998888877776665555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.6   3.2e-05     0.048      77     131 ..     102     157 ..      20     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-05
                      ATPase_2  77 klekalgiavpkaeleeilk.eksklvfkaielllekikkkgkkiiiiiDelqkli 131
                                   k+  ++ +a +++e ee +  +k k++++ +++l + + ++gkk+ii+iDel +  
  gi|15668354|ref|NP_247150.1| 102 KFVGYVVNASKEDENEEESYhKKVKELQNCFKELSKTLADNGKKLIIFIDELDRCE 157
                                   344444777788888777667*******************************8866 PP

>> DUF4961  Domain of unknown function (DUF4961)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   1.9e-05     0.028     119     215 ..      56     151 ..      42     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                       DUF4961 119 kkiGvrG.nllndyewvafksdasysvnatihatvsikiksskdnlkfklsyfvanssdGlssdea.yasvkdaddcfevv 197
                                   kk+G +  nl +++   a ++ +  +  + i     iki++s d  kf ++y+v+ s +    +e  +  vk+ ++cf+  
  gi|15668354|ref|NP_247150.1|  56 KKLGKKSvNLWKNMVLGAINATNIKAGTSPITELSGIKINASFDGSKF-VGYVVNASKEDENEEESyHKKVKELQNCFK-- 133
                                   56665433888888888999999999999999999*************.79******98877777615689*******9.. PP

                       DUF4961 198 eGsGdlidfcstqisqve 215
                                   e s +l d  +  i  ++
  gi|15668354|ref|NP_247150.1| 134 ELSKTLADNGKKLIIFID 151
                                   778888777666666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3     3e-05     0.044      37      70 ..     119     156 ..      88     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                                   SSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGH CS
                           AAA  37 kyvgesekkirelfkeakeka....kpsilfiDEidal 70 
                                   +   ++ k+++++fke+++      k+ i+fiDE+d+ 
  gi|15668354|ref|NP_247150.1| 119 ESYHKKVKELQNCFKELSKTLadngKKLIIFIDELDRC 156
                                   367788899999999976655699888*********97 PP

>> PriA_3primeBD  3′ DNA-binding domain (3′BD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       3.1   4.6e+03      53      76 ..      46      66 ..      35      70 .. 0.56
   2 ?   13.5   0.0   3.4e-05     0.051      23      64 ..      89     134 ..      78     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.1
                 PriA_3primeBD 53 eklkpieevldeepllteellela 76
                                    +k+i++ ++    l ++ ++l+
  gi|15668354|ref|NP_247150.1| 46 TITKEIKDKIK---KLGKKSVNLW 66
                                  44566666655...3455555555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.4e-05
                 PriA_3primeBD  23 kiGsrVlVpfgkrklvGiVvalkeeseve....eeklkpieevlde 64 
                                     G  +  +f ++k vG+Vv+ ++e+e e    ++k+k+++++++e
  gi|15668354|ref|NP_247150.1|  89 LSGIKINASFDGSKFVGYVVNASKEDENEeesyHKKVKELQNCFKE 134
                                   45999999***************99664455668899999988876 PP

>> DUF600  Protein of unknown function, DUF600
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.57   8.5e+02      74      95 ..      46      70 ..      15      80 .. 0.60
   2 ?   13.8   0.2     3e-05     0.044      50      89 ..     106     145 ..      97     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.57
                                  HHHHHHHHHHHHHHS...S--SEEE CS
                        DUF600 74 elikeLreefkkeeq...eaWtnlt 95
                                  ++ ke+++++kk  +   + W+n+ 
  gi|15668354|ref|NP_247150.1| 46 TITKEIKDKIKKLGKksvNLWKNMV 70
                                  3444555544443332225676665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3e-05
                                   EGGGGGGT--S-HHHHHHHHHHHHHHHHHHHHHHHHHHSS CS
                        DUF600  50 ysheipekynvseeeykkllkeLyelikeLreefkkeeqe 89 
                                   y+++ +++ + +ee y+k++keL++++keL ++ +++ ++
  gi|15668354|ref|NP_247150.1| 106 YVVNASKEDENEEESYHKKVKELQNCFKELSKTLADNGKK 145
                                   6667777777899********************9999876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.5e-05     0.067     106     149 ..      60     158 ..       4     183 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.5e-05
                        AAA_16 106 a.................................................avpelagaea......srllellkrllalls 131
                                   +                                                 a++e++ +e+      + l + +k+l + l+
  gi|15668354|ref|NP_247150.1|  60 KksvnlwknmvlgainatnikagtspitelsgikinasfdgskfvgyvvnASKEDENEEEsyhkkvKELQNCFKELSKTLA 140
                                   144444444444444477777777777777777777788888888887776666666666777789788888888884444 PP

                        AAA_16 132 rderplvlvlDdlqwade 149
                                    ++++l++++D+l++ ++
  gi|15668354|ref|NP_247150.1| 141 DNGKKLIIFIDELDRCEA 158
                                   44777*********9877 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.26   3.9e+02      65      90 ..      38      65 ..      30      80 .. 0.68
   2 ?   10.1   0.1   0.00046      0.69       5      52 ..      95     142 ..      94     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.26
                                  XXXXXXXX.XXXXXXXXXXXX.XXXXXX CS
                          COG5 65 skskslss.vlselksslesL.sasyer 90
                                  + ++++++ +++e+k ++++L ++s++ 
  gi|15668354|ref|NP_247150.1| 38 EAKLNKDEtITKEIKDKIKKLgKKSVNL 65
                                  5556666668888888888883334444 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00046
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          COG5   5 epdFdpksfanallkatnnnddteldlstplkrlnydiqeldkrlrql 52 
                                   +++Fd ++f   ++ a ++++++e++   ++k l+ + +el k l ++
  gi|15668354|ref|NP_247150.1|  95 NASFDGSKFVGYVVNASKEDENEEESYHKKVKELQNCFKELSKTLADN 142
                                   789***************************************999875 PP

>> HH_signal  Hedgehog amino-terminal signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00034      0.51      66     104 ..      38      76 ..      30      88 .. 0.87
   2 ?    0.5   0.1      0.29   4.3e+02      37      66 ..     119     152 ..      93     167 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00034
                                   --------EE-HHHHHHHHHHHHHHHHHSTT--EEEEES CS
                     HH_signal  66 eeetgadrlmtkrckekldiLailvmneWpgvklrviea 104
                                   e + ++d  +tk +k+k++ L  +  n W+++ l  i+a
  gi|15668354|ref|NP_247150.1|  38 EAKLNKDETITKEIKDKIKKLGKKSVNLWKNMVLGAINA 76 
                                   45678999***********************99988887 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.29
                                   --------SSSGGGGG-EE....---TTEEE--- CS
                     HH_signal  37 GpaegkikrnderfkeLvt....nanpdiifkde 66 
                                      + k+k+ ++ fkeL +    n  + iif de
  gi|15668354|ref|NP_247150.1| 119 ESYHKKVKELQNCFKELSKtladNGKKLIIFIDE 152
                                   4455577777777776543111166667888777 PP

>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0097        14      28      54 ..      35      61 ..      18      68 .. 0.79
   2 ?    7.9   0.7    0.0027       4.1      61      91 ..     118     148 ..     107     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0097
                          FadA 28 eaaaaklakkkelkakieeklaklead 54
                                  ++ +akl+k ++  ++i++k++kl ++
  gi|15668354|ref|NP_247150.1| 35 DELEAKLNKDETITKEIKDKIKKLGKK 61
                                  556789999999999*****9998765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0027
                          FadA  61 kdeYkellkeyksllkelekeikekekkian 91 
                                   ++ Y +++ke+++  kel k  +++ kk+  
  gi|15668354|ref|NP_247150.1| 118 EESYHKKVKELQNCFKELSKTLADNGKKLII 148
                                   578********************99998755 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   9.7e-05      0.14      54     115 ..     101     168 ..      29     194 .] 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.7e-05
                        AAA_22  54 kdllrellralglelka......erlsseellealeqalraravielliiDEaqhlrs.eealeeLrsl 115
                                   +++   +++a +++ ++      + ++++ +++ l + l + +++ ++ iDE ++  + e++l+ L s+
  gi|15668354|ref|NP_247150.1| 101 SKFVGYVVNASKEDENEeesyhkKVKELQNCFKELSKTLADNGKKLIIFIDELDRC-EaENILNLLASI 168
                                   5555556666666555566755566677888877777777777789999******9.658888888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1899  (0.105918); expected 358.6 (0.02)
Passed bias filter:                      998  (0.055664); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1249.21
//
Query:       gi|15668355|ref|NP_247151.1|  [L=48]
Description: hypothetical protein MJ_0183 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   13.6   0.0      0.056   13.6   0.0    1.1  1  DUF2789   Protein of unknown function (DUF2789)


Domain annotation for each model (and alignments):
>> DUF2789  Protein of unknown function (DUF2789)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.1e-06     0.056       5      32 ..       5      34 ..       1      45 [. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-06
                                  -THHHHH..HHHHTS---HHHHHHHHHHS. CS
                       DUF2789  5 ehtlseL..FeqLGLdsseeaieaFiakhk 32
                                     l++L  +++LG++++ +ai++Fi++  
  gi|15668355|ref|NP_247151.1|  5 DMPLKNLdeYDRLGIKKKADAIARFIENRW 34
                                  55666665589***************9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.32s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 302.32
//
Query:       gi|15668356|ref|NP_247152.1|  [L=77]
Description: hypothetical protein MJ_0184 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.25   11.5   6.1      0.095   12.9   3.1    1.7  2  DUF2985   Protein of unknown function (DUF2985)
        3.3    6.4   5.3        3.5    6.3   5.3    1.0  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> DUF2985  Protein of unknown function (DUF2985)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       0.2   1.8e+03      18      59 ..      20      30 ..       5      36 .. 0.49
   2 ?   12.9   3.1   1.1e-05     0.095       4      37 ..      38      71 ..      36      77 .] 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.2
                       DUF2985 18 vvawgamlfLlLlgaapamninsarkkwieidsqilnALFcv 59
                                  v ++                                n+   +
  gi|15668356|ref|NP_247152.1| 20 VKVFA-------------------------------NGIILI 30
                                  33332...............................232223 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.1e-05
                       DUF2985  4 ktplgflvtiYglnvvawgamlfLlLlgaapamn 37
                                  + p+g l+ +Y+++ v+w ++ +++L ++++ m 
  gi|15668356|ref|NP_247152.1| 38 ELPVGYLIGLYIIMFVVWLLVSMFFLGRLLDFMA 71
                                  569***********************99999987 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.3   0.00039       3.5     371     428 ..       8      63 ..       2      74 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00039
                       DUF2207 371 yfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivll 428
                                    fd+  k +++++ +++ g+i++  + +++ l + ++ l++l+i++++++l++++++l
  gi|15668356|ref|NP_247152.1|   8 QFDRHLKYYTTIVKVFANGIILITAYYLVFELPV-GY-LIGLYIIMFVVWLLVSMFFL 63 
                                   5777766666666666666666665555444333.22.44444444444444333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1115  (0.0621897); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 486.13
//
Query:       gi|15668357|ref|NP_247153.1|  [L=49]
Description: hypothetical protein MJ_0185 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.92    9.6   4.0          1    9.4   4.0    1.1  1  Metaviral_G     Metaviral_G glycoprotein


Domain annotation for each model (and alignments):
>> Metaviral_G  Metaviral_G glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.0   5.6e-05         1       2      24 ..      24      47 ..      23      49 .] 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 5.6e-05
                   Metaviral_G  2 igitt.lsialniyliinytiqkt 24
                                  +gi+  + ia+ iylii+y+i+k 
  gi|15668357|ref|NP_247153.1| 24 VGISImIIIAIGIYLIIEYAIKKI 47
                                  677651568************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 310.61
//
Query:       gi|15668358|ref|NP_247154.1|  [L=402]
Description: bifunctional ornithine acetyltransferase/N-acetylglutamate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.2e-143  477.6   9.4   2.6e-143  477.3   9.4    1.0  1  ArgJ      ArgJ family
  ------ inclusion threshold ------
      0.029   14.5   0.3       0.12   12.5   0.0    2.1  2  Hit1_C    Hit1 C-terminal
      0.069   13.8   0.2        1.4    9.6   0.0    2.7  3  Bcl-2     Apoptosis regulator proteins, Bcl-2 family


Domain annotation for each model (and alignments):
>> ArgJ  ArgJ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  477.3   9.4  4.4e-147  2.6e-143       6     376 .]      16     402 .]      12     402 .] 0.94

  Alignments for each domain:
  == domain 1  score: 477.3 bits;  conditional E-value: 4.4e-147
                                   XXSSS..SXXEEEEEEEEEEEEEEEEEXXSSXXHHHHHHHHHHH.HHSEEEEEEEEEEXXXSXHHHHHHHHHHHHHHHHHH CS
                          ArgJ   6 aagikkkkkdlalivseepasaaavfTknkvkAapvkvsrevlkkkkgaravvvnsgnANavtgeqGledaeemaeavaea 86 
                                   a g k+ k  +a+i+se++a+ a++fT+nkv A+pv +sre +k+++++ra+v+nsgnAN++t  +G+eda+em+++vae+
  gi|15668358|ref|NP_247154.1|  16 ANGYKEGKFGVAIIISEKDAVGAGTFTTNKVVAHPVVLSRELIKNRDKFRAIVANSGNANCFTK-DGMEDAKEMQRLVAEL 95 
                                   468888899***********************************9999***************5.7*************** PP

                                   HTSXGGGEEEEEEEESSXXXXHHHHHHHHHHX....X.....HHHHHHHXSSXSSXXEEEEEEEE.TEEEEEEEEEEXSSS CS
                          ArgJ  87 lgikeeevlvasTGviGerlpmekieagieklvekle.....eeaaeAimTTDtvpKlaavevel.gkevtiagiaKGaGm 161
                                   ++i+e+evlvasTGviG++++m+ i++ i+k+++ ++      +aa+AimTTDt pK++ave+e+ gk+v+++giaKGaGm
  gi|15668358|ref|NP_247154.1|  96 FNINEDEVLVASTGVIGRKMDMNIIKDRINKVYNLIKegnssINAAKAIMTTDTKPKEIAVEFEVnGKTVRVGGIAKGAGM 176
                                   *********************************9776677778**********************889************* PP

                                   XXXXE..E--EEEEEE-----HHHHHHHHHHHHHHTGGGB-SSS---SS-EEEEEE--TTTT..STTHHHHHHHHHHHHHH CS
                          ArgJ 162 ihPnm..aTmLafittDaavsaealqellkeavdksFnsisvDgdtSTnDtvlllAngaaeee.eedleefeealtevlqe 239
                                   i+Pnm  aTmL+fittD+++++e+l+++l+++vdk+Fn+isvDgdtSTnDtv++lAng +  + ee  eefe+al  v++e
  gi|15668358|ref|NP_247154.1| 177 IAPNMlhATMLCFITTDIEIDKESLTNILQKVVDKTFNNISVDGDTSTNDTVFVLANGLSGVNyEECGEEFENALLYVCRE 257
                                   ***********************************************************833448899************* PP

                                   HHHHHHHTSTT-S-EEEEEEEEESSHHHHHHHHHHHHT-HHHHHHHHTT---HHHHHHHHHHSSS---TTS-EE......T CS
                          ArgJ 240 LakqivrDGEGatklveveVkgakseeeAkkvaksvanssLvKtAlfGeDanwGRilaavGyagaeldpekvsv....llg 316
                                   Lak+iv+DGEGatk++ev Vkgak+ee+A k++k+++ns LvKtA+fG D+nwGRi+aavGy+ga+++pe v+v    + +
  gi|15668358|ref|NP_247154.1| 258 LAKMIVKDGEGATKFMEVVVKGAKTEEDAVKASKAIVNSLLVKTAVFGGDPNWGRIVAAVGYSGADFNPEVVDVilsnYKD 338
                                   **************************************************************************7776435 PP

                                   TEEEEETTE...E---..-HHHHHHHHH-SSEEEEEE--SSSEEEEEEEE---HHHHHHHTT-XX CS
                          ArgJ 317 evkvlekge...peev..deerakeilkeeeveievdlgegeeeatvwtcDLsyeYvkiNadYrt 376
                                   ev ++++g    + e   + ++a+ei+k++e++i vdl++ge e  +++cDLsyeYv+iNa+Y+t
  gi|15668358|ref|NP_247154.1| 339 EVYLVKDGIplaD-EGteELKKAEEIMKSDEIKIVVDLKMGEFENVCYGCDLSYEYVRINAEYTT 402
                                   6889999974321.2222568999***************************************98 PP

>> Hit1_C  Hit1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     2e-05      0.12      11      65 ..     111     170 ..     102     174 .. 0.81
   2 ?   -1.3   0.1      0.43   2.6e+03      63      75 ..     236     248 ..     225     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
                        Hit1_C  11 lkellkyntvkfhlakvyrilttsegnggssdt.lsseak.kqlavdy.ln..tlryGGv 65 
                                   +   +  n +k  ++kvy +++  +++ ++ ++ +++++k k++av++ +n  t+r+GG+
  gi|15668358|ref|NP_247154.1| 111 IGRKMDMNIIKDRINKVYNLIKEGNSSINAAKAiMTTDTKpKEIAVEFeVNgkTVRVGGI 170
                                   55667889**************998888888887999998689****9534448999998 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.43
                        Hit1_C  63 GGvhyneaieefC 75 
                                    Gv y e  eef 
  gi|15668358|ref|NP_247154.1| 236 SGVNYEECGEEFE 248
                                   599********96 PP

>> Bcl-2  Apoptosis regulator proteins, Bcl-2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.1   1.2e+04      28      28 ..      83      83 ..      40     106 .. 0.56
   2 ?    0.6   0.0      0.15   9.1e+02      27      56 ..     199     232 ..     183     273 .. 0.60
   3 ?    9.6   0.0   0.00023       1.4      28      59 ..     285     321 ..     268     322 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.1
                                  S CS
                         Bcl-2 28 e 28
                                  e
  gi|15668358|ref|NP_247154.1| 83 E 83
                                  2 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.15
                                   .SSHCHHHHHHHHCCT....TS--SCHHHHHHHH CS
                         Bcl-2  27 eealelfakvaeelfs....dgelnWgrvvalfa 56 
                                   e+  ++++kv+++ f+    dg+++ +  v ++a
  gi|15668358|ref|NP_247154.1| 199 ESLTNILQKVVDKTFNnisvDGDTSTNDTVFVLA 232
                                   4555667777777777666666666665555554 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00023
                                   SSHCHHHHHHHHCCT.....TS--SCHHHHHHHHHHH CS
                         Bcl-2  28 ealelfakvaeelfs.....dgelnWgrvvalfafag 59 
                                   +a+++ ++++++l+       g++nWgr+va + + g
  gi|15668358|ref|NP_247154.1| 285 DAVKASKAIVNSLLVktavfGGDPNWGRIVAAVGYSG 321
                                   44445555555554433334469********987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.47
# Mc/sec: 2572.45
//
Query:       gi|15668359|ref|NP_247155.1|  [L=145]
Description: hypothetical protein MJ_0187 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-09   36.7   0.0    5.9e-09   36.3   0.0    1.2  1  CGI-121         Kinase binding protein CGI-121
  ------ inclusion threshold ------
      0.025   15.1   0.0       0.28   11.7   0.0    2.1  2  EF-G-binding_N  Elongation factor G-binding protein, N-termin


Domain annotation for each model (and alignments):
>> CGI-121  Kinase binding protein CGI-121
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   6.5e-13   5.9e-09      18     138 ..      17     124 ..       4     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 6.5e-13
                                   CHCTT-EEE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT-S-EEEEEEESSS- CS
                       CGI-121  18 raeldfafldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdkttsllvvkvsssea 98 
                                   +  l+f +l+a+++  k+h+l+A+++a +++       k+   Eil++ s++++I ea+k  g +d +   +++  +++  
  gi|15668359|ref|NP_247155.1|  17 NLGLKFQILNADVVATKKHVLHAINQAKTKK----PIAKSFWMEILVRASGQRQIHEAIKIIGAKDGNV--CLICEDEE-- 89 
                                   455788********************98665....69***********************999887655..55554444.. PP

                                   -HHHHHHHHHHHS-SEEE--SHHHHHH--HHHHHHHTT-- CS
                       CGI-121  99 deeevlkslkevvegelvpleeeleeltdwkkikkiYkln 138
                                   +  ++++ +   ++ + ++++e          i++i+k+ 
  gi|15668359|ref|NP_247155.1|  90 TFRKIYELIGGEIDDSVLEINE-----DKERLIREIFKIR 124
                                   6778888888888877778887.....3567889999997 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.074   6.7e+02      49      68 ..      30      49 ..       6      56 .. 0.63
   2 ?   11.7   0.0   3.1e-05      0.28      20      75 ..      81     137 ..      79     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.074
                EF-G-binding_N 49 seeqkelLeqiddiktkeka 68
                                     +k  L++i++ ktk+ +
  gi|15668359|ref|NP_247155.1| 30 VATKKHVLHAINQAKTKKPI 49
                                  33457888888888877655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.1e-05
                EF-G-binding_N  20 ayrsvnDkkvveavkalaaekIlelfpelseeqkelLeqiddik.tkekaeklLeeL 75 
                                   ++  + D+++ + +++l+  +I + + e +e++++l+++i +i+     +e++Le++
  gi|15668359|ref|NP_247155.1|  81 VCLICEDEETFRKIYELIGGEIDDSVLEINEDKERLIREIFKIRgFGNVVERVLEKI 137
                                   666799*************************************97777778888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 942.59
//
Query:       gi|15668360|ref|NP_247156.1|  [L=265]
Description: inosine-5'-monophosphate dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-28   97.5   5.7    1.3e-15   57.6   0.4    2.6  2  CBS       CBS domain
    7.5e-14   51.8   0.3    9.7e-13   48.2   0.0    2.3  2  ParBc     ParB-like nuclease domain
    0.00021   21.4   0.3     0.0011   19.1   0.1    2.2  2  ParBc_2   Putative ParB-like nuclease
     0.0053   16.6   0.1       0.52   10.2   0.0    2.9  2  TusA      Sulfurtransferase TusA
  ------ inclusion threshold ------
      0.072   12.9   0.3       0.12   12.2   0.3    1.4  1  DEAD      DEAD/DEAH box helicase
         10    6.5   7.6         62    3.9   0.1    3.5  4  DUF575    Protein of unknown function (DUF575)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.4   4.2e-19   1.3e-15       1      54 [.       5      57 ..       5      60 .. 0.95
   2 !   41.9   0.7   3.3e-14     1e-10       1      54 [.      63     118 ..      63     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 4.2e-19
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54
                                  V+++mt++vvtv+ d t++++++l++e+g++++PVV e+gkl+Giv+ +D++ +
  gi|15668360|ref|NP_247156.1|  5 VSEYMTKKVVTVSKDNTVKDVIKLLKETGHNSFPVV-ENGKLIGIVSVHDIVGK 57
                                  899**********************9999*******.9*************865 PP

  == domain 2  score: 41.9 bits;  conditional E-value: 3.3e-14
                                   HHHHSBS..SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS   1 Vgdimtr..dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                   V+ +mt+  d+v+ +pd+++ ++ ++m ++g+s lPVVde+++lvGi++ +D++r 
  gi|15668360|ref|NP_247156.1|  63 VENVMTKrkDMVVTTPDANIMDVGRIMFRTGFSKLPVVDEENNLVGIISNMDVIRS 118
                                   667888888*****************76999**********************995 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.19   5.8e+02       5      34 ..     110     139 ..     109     141 .. 0.86
   2 !   48.2   0.0   3.2e-16   9.7e-13       1      83 [.     147     224 ..     147     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.19
                         ParBc   5 lseirpnplqprkdspekieelvasIkkkG 34 
                                   +s+++  + q+ k+ p+k+e ++++ k+ G
  gi|15668360|ref|NP_247156.1| 110 ISNMDVIRSQIEKTTPKKLENIIKTYKSLG 139
                                   57788889999999*********9998877 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 3.2e-16
                         ParBc   1 tevplseirpnplqprkdspekieelvasIkkkGllqPiivrktr.qgryeiiaGerRlrAakrlglkevpvivleiddee 80 
                                   +ev+++++rp++++++   ++++   + ++k kGl +Pii+ kt+ +++y +++G++R  Aa  +g+ +++++v+ +d  +
  gi|15668360|ref|NP_247156.1| 147 EEVDVNKLRPTQNKIH---ADELVGRMYELK-KGLAEPIIAIKTKrGDYYILVDGHHRAVAAYKMGVPKLDAYVIYLD--T 221
                                   5899*****9999999...89**********.*************77777889*********************9999..4 PP

                         ParBc  81 ama 83 
                                   +++
  gi|15668360|ref|NP_247156.1| 222 DKK 224
                                   444 PP

>> ParBc_2  Putative ParB-like nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.67     2e+03      31      54 ..      58      81 ..      48     143 .. 0.70
   2 !   19.1   0.1   3.5e-07    0.0011       2      90 ..     148     225 ..     147     258 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.67
                                  -----.---TT-BEEEEEE-STT- CS
                       ParBc_2 31 kekkkldkflekklvpvVigpdge 54
                                  ++++k+++++ k++  vV  pd +
  gi|15668360|ref|NP_247156.1| 58 DDNEKVENVMTKRKDMVVTTPDAN 81
                                  445566667776666666665544 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.5e-07
                                   EEEGGGCB-SBSEE-HHHHHHHHHHHHT------.---TT-BEEEEEE-STT-EE.E-S-HHHHHHHHHTT-....-EEEE CS
                       ParBc_2   2 eveiadLrPTQlavGldeveyklgeleelkekkkldkflekklvpvVigpdgelY.liDhHHllrallesgvggaekkvlv 81 
                                   ev++++LrPTQ  +  de+  ++ e   lk  k+      ++++ ++  ++g++Y l+D+HH + a ++ gv  ++ +++v
  gi|15668360|ref|NP_247156.1| 148 EVDVNKLRPTQNKIHADELVGRMYE---LK--KG-----LAEPIIAIKTKRGDYYiLVDGHHRAVAAYKMGV--PKLDAYV 216
                                   68999*********99988655555...45..33.....3468888999999988469***********666..6666666 PP

                                   EEEEE-TTS CS
                       ParBc_2  82 kvvadlsal 90 
                                     ++  ++l
  gi|15668360|ref|NP_247156.1| 217 IYLDTDKKL 225
                                   555444444 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00017      0.52      31      62 ..      13      44 ..       2      51 .. 0.80
   2 ?    3.0   0.0     0.029        88      36      61 ..     124     148 ..     114     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                                  EEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC CS
                          TusA 31 evladdpaatediprfakklghelveveeedg 62
                                   v+++   +++d+ +++k++gh+ + v e+++
  gi|15668360|ref|NP_247156.1| 13 VVTVSKDNTVKDVIKLLKETGHNSFPVVENGK 44
                                  58999999**************9887766655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.029
                                   SCHHHHHHHHHHHHHTEEEEEEE-GC CS
                          TusA  36 dpaatediprfakklghelveveeed 61 
                                    p   e+i +  k+lg++ + ve+e+
  gi|15668360|ref|NP_247156.1| 124 TPKKLENIIKTYKSLGYN-LRVEKEE 148
                                   566689************.7776654 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   3.9e-05      0.12      74     154 ..      46     125 ..      13     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.9e-05
                                   ST.SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHC CS
                                   xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  74 id.lrvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqit 153
                                   i+ ++v+ i+g+++ ++  +++ ++ d+vv+tp+  +  + +  +++   ++ V+DE  +l        ++ i +q++++t
  gi|15668360|ref|NP_247156.1|  46 IGiVSVHDIVGKDDNEKVENVMTKRKDMVVTTPDANIMDVGRIMFRTGFSKLPVVDEENNLVGI--ISNMDVIRSQIEKTT 124
                                   3367788999999999999999999********8766666666677888999*****9999886..444444445664444 PP

                                   T CS
                                   x RF
                          DEAD 154 c 154
                                    
  gi|15668360|ref|NP_247156.1| 125 P 125
                                   4 PP

>> DUF575  Protein of unknown function (DUF575)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.042   1.3e+02      37      74 ..       5      42 ..       1      45 [. 0.83
   2 ?    3.9   0.1     0.021        62      56      83 ..      47      74 ..      42      88 .. 0.80
   3 ?    2.5   0.1     0.058   1.7e+02      43      94 ..     118     169 ..      96     174 .. 0.69
   4 ?   -2.3   0.0       1.8   5.4e+03      59      87 ..     220     248 ..     214     256 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.042
                        DUF575 37 vsrilertvkkpeftsdvasivkvekvaGrdhlarvee 74
                                  vs++++++v   +    v++++k+ k +G+++   ve+
  gi|15668360|ref|NP_247156.1|  5 VSEYMTKKVVTVSKDNTVKDVIKLLKETGHNSFPVVEN 42
                                  7888888888888888999999*99*****99988876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.021
                        DUF575 56 sivkvekvaGrdhlarveeilkrlrvai 83
                                   iv v  ++G+d   +ve+++ +++  +
  gi|15668360|ref|NP_247156.1| 47 GIVSVHDIVGKDDNEKVENVMTKRKDMV 74
                                  6999***************998776554 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.058
                        DUF575  43 rtvkkpeftsdvasivkvekvaGrdhlarveei.lkrlrvaieeededkvhGk 94 
                                   ++++k+  +  +++i+k+ k  G++ +   ee+ +++lr + ++   d + G+
  gi|15668360|ref|NP_247156.1| 118 SQIEKT-TPKKLENIIKTYKSLGYNLRVEKEEVdVNKLRPTQNKIHADELVGR 169
                                   444443.4677899*********998877666436666666666666665555 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.8
                        DUF575  59 kvekvaGrdhlarveeilkrlrvaieeed 87 
                                    ++k  G ++ a + +  + + v+i + d
  gi|15668360|ref|NP_247156.1| 220 DTDKKLGIEKTAEIMNLKSLEDVKIVDSD 248
                                   56777888888888776666666655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1158  (0.0645881); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1794.59
//
Query:       gi|15668361|ref|NP_247157.1|  [L=150]
Description: 30S ribosomal protein S13 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-44  150.0   0.2    4.8e-44  149.8   0.2    1.0  1  Ribosomal_S13  Ribosomal protein S13/S18
     0.0054   15.5   0.0     0.0069   15.2   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.016   15.2   0.0    1.2  1  H2TH           Formamidopyrimidine-DNA glycosylase H2TH domai
       0.13   12.2   0.0        0.4   10.6   0.0    1.9  1  HHH            Helix-hairpin-helix motif
       0.13   12.5   0.0       0.25   11.6   0.0    1.4  1  HHH_6          Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.2   1.3e-47   4.8e-44       1     128 []      11     139 ..      11     139 .. 0.99

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 1.3e-47
                 Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdikdGk 80 
                                   R++ td+dg+kk+ +al+ i+G+G+  a++i++ a++d +k +g lteee++kiee+++ +a++ ip+w+ nr+kd+ +G+
  gi|15668361|ref|NP_247157.1|  11 RVSRTDLDGNKKLIMALQDIYGVGEAMARAIVRVAKLDPNKLAGYLTEEEVKKIEEVLADPAKFGIPSWMfNRRKDYVTGE 91 
                                   899*****************************************************************999********** PP

                 Ribosomal_S13  81 dshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                   d+hv+e+dl   ++edi+Rlk+ir+yrG+RH+ Gl++RGQrTk+t R+
  gi|15668361|ref|NP_247157.1|  92 DKHVIESDLMIIKQEDINRLKRIRCYRGIRHELGLPCRGQRTKSTFRR 139
                                   *********************************************996 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.9e-06    0.0069     185     236 ..      19      69 ..       2      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-06
                                   S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHH CS
                          FbpA 185 kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealq 236
                                    +k+l  aL++ + G+++++a+ +++ a+ld+++ a  l+ee+++++ e l 
  gi|15668361|ref|NP_247157.1|  19 GNKKLIMALQDIY-GVGEAMARAIVRVAKLDPNKLAGYLTEEEVKKIEEVLA 69 
                                   5688999999999.********************************998775 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   4.4e-06     0.016      27      75 ..      21      69 ..       2      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.4e-06
                                  HHHHHCTTTSCS--HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHHH CS
                          H2TH 27 ktlLLDqklvaGlGNiyadEvLfrakihPerlakslskeelellhqeik 75
                                  k+l++  + + G+G   a  +   ak++P++la  l++ee++ + + ++
  gi|15668361|ref|NP_247157.1| 21 KKLIMALQDIYGVGEAMARAIVRVAKLDPNKLAGYLTEEEVKKIEEVLA 69
                                  889999999********************************99987665 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011       0.4      13      28 ..      27      42 ..      26      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                  HHTSTT-SHHHHHHHH CS
                           HHH 13 LlalPGVGpktAeaIl 28
                                  L+++ GVG+++A+aI 
  gi|15668361|ref|NP_247157.1| 27 LQDIYGVGEAMARAIV 42
                                  77888**********7 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     7e-05      0.25      20      45 ..      18      43 ..       2      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7e-05
                         HHH_6 20 eedgairlGLaaikglgeaaaeriva 45
                                  + +++++++L+ i g+gea a++iv+
  gi|15668361|ref|NP_247157.1| 18 DGNKKLIMALQDIYGVGEAMARAIVR 43
                                  24577*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 945.48
//
Query:       gi|15668362|ref|NP_247158.1|  [L=187]
Description: 30S ribosomal protein S4 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-19   69.3   3.5    4.8e-18   64.6   0.1    2.5  2  S4            S4 domain
    0.00029   21.7   5.2    0.00053   20.8   4.0    2.0  2  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.5    0.0022        20      16      25 ..      53      62 ..      50      63 .. 0.90
   2 !   64.6   0.1   5.3e-22   4.8e-18       1      47 [.     105     151 ..     105     154 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0022
                                  HHHHHHHHHT CS
                            S4 16 rreArqlIeh 25
                                  rr+Ar+lI++
  gi|15668362|ref|NP_247158.1| 53 RRQARRLISD 62
                                  9*******97 PP

  == domain 2  score: 64.6 bits;  conditional E-value: 5.3e-22
                                   EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCE CS
                            S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDv 47 
                                   rRL+++++r+gla + r+ArqlI hG++ VNG+vv+ psy+V+++++
  gi|15668362|ref|NP_247158.1| 105 RRLQTLVFRKGLARTPRQARQLIVHGHIAVNGRVVTAPSYMVTVEEE 151
                                   8******************************************8765 PP

>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   4.0   5.9e-08   0.00053      36      80 ..      16      61 ..       3     110 .. 0.83
   2 ?   -0.2   0.0      0.22   1.9e+03      11      22 ..     105     124 ..     102     173 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.9e-08
                                  --CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHHH CS
                  Ribosomal_S4 36 lseYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLlq 80
                                    ++ k +++++ +l r+Ygl+ +++++++ +++r++r +++++L+ 
  gi|15668362|ref|NP_247158.1| 16 NHPWIKeRIEREKELCRKYGLRrKREVWKAETILRKYR-RQARRLIS 61
                                  4599999*******************************.****9985 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.22
                                   CHCTS-STSSS........S CS
                  Ribosomal_S4  11 Rrvgfklflkg........r 22 
                                   Rr+++ +f kg        r
  gi|15668362|ref|NP_247158.1| 105 RRLQTLVFRKGlartprqaR 124
                                   78888888888544443331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1268.18
//
Query:       gi|15668363|ref|NP_247159.1|  [L=129]
Description: 30S ribosomal protein S11 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-43  146.1   1.1    6.2e-43  145.7   1.1    1.1  1  Ribosomal_S11  Ribosomal protein S11


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.7   1.1   3.4e-47   6.2e-43       1     108 [.      10     126 ..      10     128 .. 0.98

  Alignments for each domain:
  == domain 1  score: 145.7 bits;  conditional E-value: 3.4e-47
                 Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg........pG 72 
                                   G++hi++s+nntii+ td++Gae++++ +Gg + +++r + sPyaa++aa k ae ++++Gi+++++kv++        pG
  gi|15668363|ref|NP_247159.1|  10 GIVHIYSSYNNTIIHATDITGAETIARVSGGRVTRNQRdEGSPYAAMQAAFKLAEVLKERGIENIHIKVRApggsgqknPG 90 
                                   89************************************9****************************************** PP

                 Ribosomal_S11  73 pGreaalralaraGlkigriedvtPiPhdgirrpkk 108
                                   pG++aa+ralaraGl+igriedvtP+Phdg+ ++k+
  gi|15668363|ref|NP_247159.1|  91 PGAQAAIRALARAGLRIGRIEDVTPVPHDGTTPKKR 126
                                   *******************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 814.56
//
Query:       gi|15668364|ref|NP_247160.1|  [L=191]
Description: DNA-directed RNA polymerase subunit D [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-25   87.9   0.0    1.5e-23   83.3   0.0    2.3  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    3.8e-15   55.1   0.0    5.4e-15   54.6   0.0    1.2  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   0.0   1.6e-27   1.5e-23       1     112 []      46     138 ..      46     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 1.6e-27
                                   EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBESSSSCEESST CS
                 RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkledadveivnp 81 
                                   V+i+en+s++ DE++aHrlglip++ ++ le                 ++ ++++L+++gp +v+++dlk+  ++ e++ +
  gi|15668364|ref|NP_247160.1|  46 VYIYENSSSMDDEILAHRLGLIPIKGKPLLE-----------------NEVITFTLEKEGPCTVYSSDLKS--ENGEVAFK 107
                                   9************************777666.................4569******************8..5778889* PP

                                   TSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                 RNA_pol_A_bac  82 dilIakLrkgqeleleakvkkGiGkehakfs 112
                                   +i+I+kL kgq++++e+++  GiGk+hak++
  gi|15668364|ref|NP_247160.1| 108 NIPIVKLGKGQRIQIECEAIPGIGKVHAKWQ 138
                                   ******************************6 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0     6e-19   5.4e-15       9      68 ..      24     178 ..      17     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 6e-19
                                   xxxxxxxxxxxxxxxxxxxxxx........................................................... RF
                     RNA_pol_L   9 htlgNaLRrillsevpgvaiea........................................................... 30 
                                   +++ Na+Rri++sevp++aie                                                            
  gi|15668364|ref|NP_247160.1|  24 ISFSNAIRRIMISEVPTFAIEDvyiyensssmddeilahrlglipikgkpllenevitftlekegpctvyssdlksengev 104
                                   7999****************************************9999999999999999999998888888888888888 PP

                                   .......................xxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_L  31 .......................pvvkvn.................tdkdklilevetdgslkPeealkeAlkiLkek 68 
                                                          p                        +d+  + vet g++++ee+l+eA+kiLk+k
  gi|15668364|ref|NP_247160.1| 105 afknipivklgkgqriqieceaiP----GigkvhakwqpcnavykqIADDEVEFFVETFGQMEAEEILEEAVKILKNK 178
                                   888884444444444444444440....03444444555555556678999*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1191.92
//
Query:       gi|15668365|ref|NP_247161.1|  [L=121]
Description: 50S ribosomal protein L18e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-16   59.4   0.3    3.3e-16   59.2   0.3    1.0  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    2.7e-09   37.8   1.2    4.3e-09   37.1   1.2    1.4  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
  ------ inclusion threshold ------
       0.05   12.8   0.2      0.063   12.5   0.2    1.2  1  RE_HaeII        HaeII restriction endonuclease


Domain annotation for each model (and alignments):
>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.3   5.5e-20   3.3e-16      27     138 ..      12     120 ..       2     121 .] 0.88

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 5.5e-20
                 Ribosomal_L18  27 LvklyrfLar...RtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPklsvaALrf 104
                                   Lvkl + L +   + ++k  k + +rL + r+ r+ + ls++ +++k    e+ ++ v g+v+   +l +  k+ vaA+ f
  gi|15668365|ref|NP_247161.1|  12 LVKLIEILKQesyKNQAKIWKDIARRLAKPRRRRAEVNLSKINRYTK----EGDVVLVPGKVLGAGKLEH--KVVVAAFAF 86 
                                   6666666666444889999999**********************999....4689************986..9******** PP

                 Ribosomal_L18 105 tetararilkaGGeiltlDqLalraPtGkntvLl 138
                                   +eta++ i +aGGe +t+++L  r+P+G+n+ ++
  gi|15668365|ref|NP_247161.1|  87 SETAKKLIKEAGGEAITIEELIKRNPKGSNVKIM 120
                                   ******************************9765 PP

>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   1.2   7.2e-13   4.3e-09      53     127 ..      26     102 ..       5     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 7.2e-13
                                   EHHHHHHTTTTGTTS------EEEGGGTTTTSSS........SEEEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                Ribosomal_L27A  53 nlkdLdelideerleladeaeeidleelaeaglikk....kdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                   n  ++++ i++   +   +++e++l+++  ++ +k+        Kvlg g+l++k+ v a +fS++Ak+ I++aGG+++
  gi|15668365|ref|NP_247161.1|  26 NQAKIWKDIARRLAKPRRRRAEVNLSKI--NRYTKEgdvvLVPGKVLGAGKLEHKVVVAAFAFSETAKKLIKEAGGEAI 102
                                   5567776666655553368899******..77777777654455********************************987 PP

>> RE_HaeII  HaeII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.1e-05     0.063      29      58 ..      10      38 ..       4      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.1e-05
                      RE_HaeII 29 drvqkdldlldldtyrntskrwrnkitrrl 58
                                   r+ k +++l++++y+n++k w++ i+rrl
  gi|15668365|ref|NP_247161.1| 10 PRLVKLIEILKQESYKNQAKIWKD-IARRL 38
                                  589999****************97.77776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 763.12
//
Query:       gi|15668366|ref|NP_247162.1|  [L=137]
Description: 50S ribosomal protein L13 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-14   53.4   1.0    7.6e-10   39.1   0.2    2.1  2  Ribosomal_L13  Ribosomal protein L13


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.1e-06      0.02       4      25 ..       3      25 ..       1      27 [. 0.86
   2 !   39.1   0.2   4.2e-14   7.6e-10      37     116 ..      24     105 ..      21     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-06
                                  EEEETTSBHHHHHHHHHH.HHHT CS
                 Ribosomal_L13  4 viDAegqvlgrlaskiak.vLrG 25
                                  viDAeg +lgrlas++ak vLrG
  gi|15668366|ref|NP_247162.1|  3 VIDAEGAILGRLASEVAKrVLRG 25
                                  8***************9736888 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 4.2e-14
                                   -S-EEEEEEGGCBB-SSTH.HTT-EEEEE-SSTTSEEEEEHHHHHCCSHHHHHHHHHHCCS-.SSHHHHHHGCTEEEESSS CS
                 Ribosomal_L13  37 cGdyvvvinaekvaltgkk.leqkvyyrhtgypgglkevtakellekkpeeilekaVkgmLp.knklgrrrlkrLkvyage 115
                                    G+ +v++nae v++tg+k +  k+y+++ +     + +++   + ++p+ il++++++mLp k+  gr+ +kr+kvy g+
  gi|15668366|ref|NP_247162.1|  24 RGEEIVIVNAEMVVITGNKdWIIKTYQEEREKKNVANPRRFGPKFPRRPDDILRRTIRKMLPyKKPKGREAFKRVKVYVGN 104
                                   5899*************875999*****9999999***************************5566999999******998 PP

                                   T CS
                 Ribosomal_L13 116 e 116
                                    
  gi|15668366|ref|NP_247162.1| 105 P 105
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 901.64
//
Query:       gi|15668367|ref|NP_247163.1|  [L=136]
Description: 30S ribosomal protein S9 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-27   95.5   1.1    3.6e-27   95.3   1.1    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16
  ------ inclusion threshold ------
      0.089   12.7   0.2        1.2    9.0   0.1    2.2  2  NIL           NIL domain


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.3   1.1     4e-31   3.6e-27       1     121 []       9     136 .]       9     136 .] 0.91

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 4e-31
                                   EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSS..SEEEEEEEESS-HHHHHHHHHHHHHHHHH CS
                  Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllg..kfdvfvkvkgGGlsgqaeAirlgiaraLv 79 
                                   G+rK+++Ar+  +egkg+i++n+ ++e  ++ +++r+k++ep+ l+g++   ++d+ v+vkgGG++gq++A+r++i +a+v
  gi|15668367|ref|NP_247163.1|   9 GKRKRAIARAVAREGKGRIRINKIPIEL-IEPKYKRMKLMEPILLAGEEVisQMDIDVTVKGGGVMGQMDAARTAIGKAIV 88 
                                   8***************************.888**********99999765659**************************** PP

                                   HHHHHHHHHHC......TCCCTS-B--------TTS..SCTTB----S-- CS
                  Ribosomal_S9  80 alekeekkeLk......kaglltrDpRvvErkKtgk..kkARkkyqwskR 121
                                   +++    keL+      +++ll++D+R++E++K+ +  k+ R+k q+s+R
  gi|15668367|ref|NP_247163.1|  89 EFTG--SKELRdkflayDRTLLVSDARRTEPHKPSRstKGPRAKRQKSYR 136
                                   **87..677776666788***************9753389********99 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.03   2.7e+02      44      63 ..       2      21 ..       1      30 [. 0.79
   2 ?    9.0   0.1   0.00013       1.2      19      64 ..      56     104 ..      47     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.03
                                  EEEEEEEES-HHHHHHHHHH CS
                           NIL 44 Gqlvielsgsqesiaaalqy 63
                                  G++vi++   + +ia+a+++
  gi|15668367|ref|NP_247163.1|  2 GKIVITVGKRKRAIARAVAR 21
                                  999****5577899999876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00013
                                   HHHHHHT-EEEEEEEEEE...EETTEEEEEEEEEEES-HHHHHHHHHHH CS
                           NIL  19 hlvrqlglevnIlqGsve...riqgtpfGqlvielsgsqesiaaalqyl 64 
                                   ++++q +++v + +G+v      + t++G+ ++e++gs+e  ++ l+y 
  gi|15668367|ref|NP_247163.1|  56 EVISQMDIDVTVKGGGVMgqmDAARTAIGKAIVEFTGSKELRDKFLAYD 104
                                   5788889999998887742113579***************999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 947.65
//
Query:       gi|15668368|ref|NP_247164.1|  [L=73]
Description: DNA-directed RNA polymerase subunit N [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-26   92.4   0.5    1.9e-26   92.1   0.5    1.2  1  RNA_pol_N       RNA polymerases N / 8 kDa subunit
    0.00046   20.4   0.1    0.00057   20.1   0.1    1.2  1  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.5   2.1e-30   1.9e-26       1      52 [.       1      52 [.       1      65 [. 0.93

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 2.1e-30
                                  ----SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB CS
                     RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllth 52
                                  M++P+rCF+CG+vi+e++eey+e++ kge+pkd+Ld+Lg+k+yCCrrm+++ 
  gi|15668368|ref|NP_247164.1|  1 MMFPIRCFSCGNVIAEVFEEYKERILKGENPKDVLDDLGIKKYCCRRMFISY 52
                                  9*************************************************97 PP

>> Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   6.4e-08   0.00057       1      41 [.       1      46 [.       1      61 [. 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.4e-08
                Chordopox_RPO7  1 mvfplvCstCGrDlse..eryr.LlvkkkkLkdvlat..vkrkCCr 41
                                  m+fp+ C +CG+ ++e  e y+  ++k ++ kdvl+   +k+ CCr
  gi|15668368|ref|NP_247164.1|  1 MMFPIRCFSCGNVIAEvfEEYKeRILKGENPKDVLDDlgIKKYCCR 46
                                  99**********999844478736889999*****97336999**8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 513.30
//
Query:       gi|15668369|ref|NP_247165.1|  [L=57]
Description: DNA-directed RNA polymerase subunit K [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-11   43.2   0.1    3.2e-11   43.0   0.1    1.1  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.1   1.8e-15   3.2e-11       6      49 .]       2      49 ..       1      49 [. 0.85

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.8e-15
                                  S--HHHHHHHHHHHHHHH....HT........SS-SSSSTTCHHHHTT-S-- CS
                  RNA_pol_Rpb6  6 vltrYelvriaakRArQieegesl........etqkpvviAlrEiaegkipi 49
                                  +lt++e++ri+++R +Qi    s+          +  + iA +Ei +gk+p+
  gi|15668369|ref|NP_247165.1|  2 KLTKFEIARILGARSLQI----SSgayatietKCDSSLKIAYEEIKQGKVPL 49
                                  69****************....66666666542579**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 389.99
//
Query:       gi|15668370|ref|NP_247166.1|  [L=314]
Description: hypothetical protein MJ_0198 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-06   29.0   0.0    2.5e-06   27.7   0.0    1.7  1  Enolase_N  Enolase, N-terminal domain


Domain annotation for each model (and alignments):
>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.4e-10   2.5e-06      61     131 .]      42     106 ..      36     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.4e-10
                                   -HHHHHHHHHTHHHHHTTSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                     Enolase_N  61 vekavenvnekiapaligldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                    e+a++ v+++iap+lig+ +td   iD+l++e+    n       +++++S++va+aa++++++pl+++l
  gi|15668370|ref|NP_247166.1|  42 PEEAIADVENVIAPELIGYPATDIDFIDSLICETS--VNN----PTVAMGISISVARAASNSLDIPLFKFL 106
                                   5799****************************988..333....34689*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1977.19
//
Query:       gi|15668371|ref|NP_247167.1|  [L=65]
Description: ferredoxin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-09   37.7  17.4      6e-08   32.2   5.2    3.0  3  Fer4      4Fe-4S binding domain
    3.5e-09   37.1  12.6      7e-09   36.2  12.6    1.5  1  Fer4_7    4Fe-4S dicluster domain
    3.6e-09   36.3  16.1    3.4e-05   23.7   2.6    2.1  2  Fer4_6    4Fe-4S binding domain
    1.7e-07   31.2  10.8    2.3e-07   30.9  10.8    1.2  1  Fer4_9    4Fe-4S dicluster domain
    4.4e-07   29.9  12.2    8.6e-07   29.0  12.3    1.4  1  Fer4_10   4Fe-4S dicluster domain
      4e-06   27.7  10.0    0.00061   20.7   2.6    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    5.2e-06   26.5  10.5    6.9e-06   26.1  10.5    1.2  1  Fer4_21   4Fe-4S dicluster domain
    2.9e-05   23.9  14.7     0.0031   17.5   5.1    2.2  2  Fer4_2    4Fe-4S binding domain
    4.8e-05   23.8   7.4     0.0083   16.6   0.6    2.1  2  Fer4_17   4Fe-4S dicluster domain
    0.00025   21.3  14.1     0.0069   16.8   4.3    2.2  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.015   16.2   5.4      0.015   16.2   5.4    2.3  2  Fer4_3    4Fe-4S binding domain
      0.029   14.8  14.5         15    6.1  14.5    2.1  1  Fer4_8    4Fe-4S dicluster domain
      0.072   13.3  12.3       0.17   12.1   3.5    2.1  2  Fer4_18   4Fe-4S dicluster domain
       0.09   13.5   1.3       0.09   13.5   1.3    2.3  2  Fer4_15   4Fe-4S single cluster domain
       0.12   13.0  13.2       0.39   11.3   2.0    2.2  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.05        60       1      10 [.       6      15 ..       6      15 .. 0.88
   2 !    8.8   2.1    0.0012       1.5      11      22 ..      18      29 ..      16      31 .. 0.87
   3 !   32.2   5.2     5e-11     6e-08       4      23 ..      41      60 ..      38      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.05
                                  EEEETTTSSS CS
                          Fer4  1 vvideekCig 10
                                  v+id+++C g
  gi|15668371|ref|NP_247167.1|  6 VTIDYSLCKG 15
                                  68******87 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                                  -THHHHHSTTTE CS
                          Fer4 11 CGaCvevCPvgA 22
                                  C +Cv+ CP ++
  gi|15668371|ref|NP_247167.1| 18 CAECVNNCPMEV 29
                                  99*******986 PP

  == domain 3  score: 32.2 bits;  conditional E-value: 5e-11
                                  ETTTSSS-THHHHHSTTTEE CS
                          Fer4  4 deekCigCGaCvevCPvgAI 23
                                   +++C++CG C++vCP+gA 
  gi|15668371|ref|NP_247167.1| 41 RPDDCTYCGVCEDVCPTGAV 60
                                  59*****************7 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2  12.6   5.8e-12     7e-09       4      52 .]      17      59 ..      12      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 5.8e-12
                        Fer4_7  4 gCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  +C  Cv++Cp++++e++ +      + v+ +p++C++Cg+C++vCPtga
  gi|15668371|ref|NP_247167.1| 17 ECAECVNNCPMEVFEIEGD------KVVVARPDDCTYCGVCEDVCPTGA 59
                                  7***************765......568899****************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   2.6   2.8e-08   3.4e-05       2      23 ..       6      29 ..       5      30 .. 0.90
   2 !   18.5   5.8   1.2e-06    0.0015       1      23 [.      37      59 ..      37      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.8e-08
                        Fer4_6  2 veidpdkCig..CgdCvrvCPega 23
                                  v+id+++C g  C +Cv++CP+ +
  gi|15668371|ref|NP_247167.1|  6 VTIDYSLCKGaeCAECVNNCPMEV 29
                                  89*******777*********876 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.2e-06
                        Fer4_6  1 vveidpdkCigCgdCvrvCPega 23
                                  vv+  pd C+ Cg C++vCP+ga
  gi|15668371|ref|NP_247167.1| 37 VVVARPDDCTYCGVCEDVCPTGA 59
                                  688899***************99 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9  10.8   1.9e-10   2.3e-07       4      50 ..      17      59 ..      12      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.9e-10
                        Fer4_9  4 gCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                  +C +Cv+ Cp++v++ +  +  ++       +C+ Cg C+++Cp+ga
  gi|15668371|ref|NP_247167.1| 17 ECAECVNNCPMEVFEIEGDKVVVARPD----DCTYCGVCEDVCPTGA 59
                                  6*************9999888887644....5*************97 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0  12.3   7.2e-10   8.6e-07       2      56 .]       6      56 ..       5      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 7.2e-10
                       Fer4_10  2 vvidddtC..irCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  v id + C   +C++Cv+ CP+         e++++++v   +++Ct cg C ++CP
  gi|15668371|ref|NP_247167.1|  6 VTIDYSLCkgAECAECVNNCPM------EVFEIEGDKVVVARPDDCTYCGVCEDVCP 56
                                  6899999*5559**********......7778888888888***************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.9   0.00026      0.32       4      25 ..      17      38 ..      10      43 .. 0.72
   2 !   20.7   2.6   5.1e-07   0.00061       2      20 ..      45      63 ..      44      65 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                       Fer4_16  4 tCgkCaevCPtnaikekkekei 25
                                  +C +C++ CP ++++ + +k++
  gi|15668371|ref|NP_247167.1| 17 ECAECVNNCPMEVFEIEGDKVV 38
                                  6889999999888776655555 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 5.1e-07
                       Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                  C+ Cg C +vCPt+a+k +
  gi|15668371|ref|NP_247167.1| 45 CTYCGVCEDVCPTGAVKVE 63
                                  ***************9866 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1  10.5   5.8e-09   6.9e-06       3      58 ..       8      61 ..       6      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.8e-09
                       Fer4_21  3 idedkC..igCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                  id + C   +C +C+  C+   ++  ei++++v+  + d+C+ C +C +vCP+ ++++
  gi|15668371|ref|NP_247167.1|  8 IDYSLCkgAECAECVNNCP---MEVFEIEGDKVVVARPDDCTYCGVCEDVCPT-GAVK 61
                                  5666663357*********...8999**************************6.8876 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   2.0   0.00013      0.16       3      21 ..       6      26 ..       4      27 .. 0.90
   2 !   17.5   5.1   2.6e-06    0.0031       3      22 .]      38      57 ..      36      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                        Fer4_2  3 vvvdtdrCig..CgaCvsaCP 21
                                  v +d   C g  C  Cv++CP
  gi|15668371|ref|NP_247167.1|  6 VTIDYSLCKGaeCAECVNNCP 26
                                  6799999*9999********* PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.6e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                  vv+ +d C+ Cg C ++CP+
  gi|15668371|ref|NP_247167.1| 38 VVARPDDCTYCGVCEDVCPT 57
                                  5666899************7 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   1.2   0.00033      0.39      47      60 ..      16      29 ..       5      30 .. 0.84
   2 !   16.6   0.6     7e-06    0.0083      44      59 ..      43      58 ..      31      61 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                       Fer4_17 47 ieCgeCerkCPqgl 60
                                  +eC eC+  CP+++
  gi|15668371|ref|NP_247167.1| 16 AECAECVNNCPMEV 29
                                  6899*******986 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 7e-06
                       Fer4_17 44 slCieCgeCerkCPqg 59
                                  ++C+ Cg Ce +CP g
  gi|15668371|ref|NP_247167.1| 43 DDCTYCGVCEDVCPTG 58
                                  6777777777777764 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   2.1   0.00088         1       6      16 ..      17      27 ..      10      30 .. 0.81
   2 !   16.8   4.3   5.8e-06    0.0069       2      17 .]      43      58 ..      42      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00088
                        Fer4_4  6 gCgsCvaaCPq 16
                                  +C  Cv+ CP+
  gi|15668371|ref|NP_247167.1| 17 ECAECVNNCPM 27
                                  8*********7 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 5.8e-06
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  + C+ Cg+C+++CP+g
  gi|15668371|ref|NP_247167.1| 43 DDCTYCGVCEDVCPTG 58
                                  78************86 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.8     0.026        32       1      12 [.      13      26 ..      13      29 .. 0.78
   2 ?   16.2   5.4   1.2e-05     0.015       1      15 []      45      59 ..      45      59 .. 0.98

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.026
                        Fer4_3  1 Ctg..CgaCvevCP 12
                                  C g  C  Cv+ CP
  gi|15668371|ref|NP_247167.1| 13 CKGaeCAECVNNCP 26
                                  55444999****** PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.2e-05
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  Ct Cg C++vCP+gA
  gi|15668371|ref|NP_247167.1| 45 CTYCGVCEDVCPTGA 59
                                  **************9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  14.5     0.012        15       7      64 ..      17      58 ..      11      62 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                        Fer4_8  7 eCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                  eC  C ++Cp      ++ ++ +g++   v +          + Ct cg C++vCp+g
  gi|15668371|ref|NP_247167.1| 17 ECAECVNNCP------MEVFEIEGDKVV-VAR---------PDDCTYCGVCEDVCPTG 58
                                  6778888887......555566666333.222.........36799999999999986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.9    0.0052       6.2      62      75 ..      16      29 ..       7      39 .. 0.81
   2 ?   12.1   3.5   0.00014      0.17      56      74 ..      40      58 ..      28      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0052
                       Fer4_18 62 idcescvkvcPtgi 75
                                   +c  cv+ cP+++
  gi|15668371|ref|NP_247167.1| 16 AECAECVNNCPMEV 29
                                  68999******987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00014
                       Fer4_18 56 kgagdcidcescvkvcPtg 74
                                  +   dc+ c++c +vcPtg
  gi|15668371|ref|NP_247167.1| 40 ARPDDCTYCGVCEDVCPTG 58
                                  5668**************8 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.3   7.5e-05      0.09       1      28 [.       6      36 ..       6      43 .. 0.84
   2 ?    5.3   4.6     0.029        34       6      20 ..      43      57 ..      37      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.5e-05
                       Fer4_15  1 VvvDrdaCig..cglCvaeap.evfeldedg 28
                                  V++D ++C g  c+ Cv ++p evfe+++d 
  gi|15668371|ref|NP_247167.1|  6 VTIDYSLCKGaeCAECVNNCPmEVFEIEGDK 36
                                  89*******98899******64899999875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.029
                       Fer4_15  6 daCigcglCvaeape 20
                                  d C+ cg+C +++p+
  gi|15668371|ref|NP_247167.1| 43 DDCTYCGVCEDVCPT 57
                                  89***********96 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.0   0.00032      0.39       8      32 ..      17      40 ..       8      44 .. 0.80
   2 ?    7.8   4.0    0.0041       4.9       4      17 ..      43      56 ..      41      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                       Fer4_13  8 acgaCvelaP.dvFeeddeggasvva 32
                                  +c+ Cv+ +P +vFe++ +  ++vva
  gi|15668371|ref|NP_247167.1| 17 ECAECVNNCPmEVFEIEGD--KVVVA 40
                                  7*********88*****98..56554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0041
                       Fer4_13  4 dtCiacgaCvelaP 17
                                  d C+ cg+C +++P
  gi|15668371|ref|NP_247167.1| 43 DDCTYCGVCEDVCP 56
                                  78************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 415.72
//
Query:       gi|15668372|ref|NP_247168.1|  [L=82]
Description: hydrogenase expression/formation protein HypC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-21   75.9   0.1    2.3e-21   75.7   0.1    1.1  1  HupF_HypC  HupF/HypC family
  ------ inclusion threshold ------
       0.07   13.4   0.4      0.093   13.0   0.4    1.3  1  DUF3006    Protein of unknown function (DUF3006)


Domain annotation for each model (and alignments):
>> HupF_HypC  HupF/HypC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.1   2.6e-25   2.3e-21       1      65 []       1      70 [.       1      70 [. 0.95

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 2.6e-25
                                  CCEEEEEEEEEEET....TEEEEECTTEEEEEEGTTC.TTB-TT-EEEEETTEEEEEE-HHHHHHHHHHH CS
                     HupF_HypC  1 MCLaiPgkvveied....elAlvdvgGvrrevslalv.eevkvGdyVLvhvGfAiekideeeaeetlell 65
                                  MCLaiP+kvvei +    + A+++++Gv+++++l l+ +evk+Gdy+L+h G+A+e+++ee+a+ +le++
  gi|15668372|ref|NP_247168.1|  1 MCLAIPCKVVEIIEedgeKYAIAEYKGVKQKAKLTLLdKEVKIGDYILIHTGYALEVLSEEDAKLSLEAW 70
                                  ***********98878877******************889***************************987 PP

>> DUF3006  Protein of unknown function (DUF3006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4     1e-05     0.093       8      65 ..      15      76 ..       9      78 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                       DUF3006  8 gd...lAVleledgetidiprsdLpegakeGdvLeiedd.eieldpeetekrk.eriqelldr 65
                                  +d   +A+ e     + + ++++L +++k Gd++ i+ + ++e+  ee +k   e+ +el++ 
  gi|15668372|ref|NP_247168.1| 15 EDgekYAIAEYKG-VKQKAKLTLLDKEVKIGDYILIHTGyALEVLSEEDAKLSlEAWEELFKA 76
                                  4444578887774.44557899***************99889999999988761444666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 635.86
//
Query:       gi|15668373|ref|NP_247169.1|  [L=160]
Description: lipoprotein B LppB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-19   71.1   2.0    1.7e-19   70.4   2.0    1.3  1  SNARE_assoc      SNARE associated Golgi protein
    0.00071   20.2   1.4    0.00071   20.2   1.4    1.6  2  Sm_multidrug_ex  Putative small multi-drug export protein


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   2.0   1.9e-23   1.7e-19       1     110 [.      36     144 ..      36     152 .. 0.93

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 1.9e-23
                   SNARE_assoc   1 lPsevllvaaGvlf.glllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygflallllrllpiv 80 
                                   +P+e++++a+ +l+ ++ l++l++ +++  Ga+++y+l++++g ++l+ kl++e+++k+ ++++++ g+l ++++ ++pi 
  gi|15668373|ref|NP_247169.1|  36 FPTEIFIIAGILLGlDWKLVWLISTIACNFGAVVTYYLAKKYG-EKLMLKLFDEEKIKKGSHYLKKWGILGVIIASFTPI- 114
                                   6899999988888778888************************.888888*****************************7. PP

                   SNARE_assoc  81 PrdlvnyvaGltrvsfkrFflatfiGsipw 110
                                   P+ +++ v+G ++++f r+++a f++ +++
  gi|15668373|ref|NP_247169.1| 115 PFEVICWVCGSFEMPFERYMIAVFLSRLIR 144
                                   8************************99886 PP

>> Sm_multidrug_ex  Putative small multi-drug export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1         2   1.8e+04      69      79 ..      15      25 ..      12      27 .. 0.78
   2 !   20.2   1.4     8e-08   0.00071       6     117 ..      42     143 ..      39     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2
               Sm_multidrug_ex 69 iekygflGLll 79
                                  i+ yg++G++l
  gi|15668373|ref|NP_247169.1| 15 IKDYGYFGIFL 25
                                  56799999987 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 8e-08
               Sm_multidrug_ex   6 iplgillgldpllallvsvlgnllpvplillflrkllellkkkkllkklfekleekaekksekiekygflGLll..FvaiP 84 
                                   i++gillgld+ l+ l+s ++    +++ + +++k  e     kl+ klf+  eek +k s+ ++k+g+lG+++  F +iP
  gi|15668373|ref|NP_247169.1|  42 IIAGILLGLDWKLVWLISTIACNFGAVVTYYLAKKYGE-----KLMLKLFD--EEKIKKGSHYLKKWGILGVIIasFTPIP 115
                                   899********999999999988888888888888777.....34556665..688888888899******9884466666 PP

               Sm_multidrug_ex  85 LpgTGawtGsliasllglkkkkallaillGvli 117
                                   + +   + Gs     +++++ + ++a++l+ li
  gi|15668373|ref|NP_247169.1| 116 FEVICWVCGS-----FEMPFERYMIAVFLSRLI 143
                                   6666555554.....788888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1045.97
//
Query:       gi|15668374|ref|NP_247170.1|  [L=304]
Description: hypothetical protein MJ_0202 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-62  211.1   6.0    2.4e-62  210.9   6.0    1.0  1  DUF89           Protein of unknown function DUF89
  ------ inclusion threshold ------
      0.017   14.9   0.1      0.083   12.7   0.0    1.9  2  Dna2            DNA replication factor Dna2
        1.2    9.7   4.1       0.95   10.0   0.3    2.5  2  EF-G-binding_N  Elongation factor G-binding protein, N-termin


Domain annotation for each model (and alignments):
>> DUF89  Protein of unknown function DUF89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.9   6.0   4.1e-66   2.4e-62       3     352 ..      17     299 ..      15     300 .. 0.94

  Alignments for each domain:
  == domain 1  score: 210.9 bits;  conditional E-value: 4.1e-66
                                   HTHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCTTCGHHH-HHHHT-BTTBSBHHHHHHHHHHHHHHHHTHS CS
                         DUF89   3 eerlpciltqviddlekakdekeeelkkiieelselkeelqtdkpltpledeeekrswfnapwlfaecylyrrllelfgls 83 
                                   +e++ ci++qv+d++++ +d+ e e+ ++i++ +e+ ++++ ++++++                 + + ++r l+++ +  
  gi|15668374|ref|NP_247170.1|  17 PECAICIIRQVVDAANEITDD-EREQFRLIKSTMEVIKDVYGESAVPAW----------------MGTVVHRYLKKISN-- 78 
                                   89***************9999.99*************************................**************.. PP

                                   GGGTTS-TTHHHHHHHHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHCG--CCCHTSHHCHHHHHHHHHHHHHHCTE CS
                         DUF89  84 kelknyDpFkeqKeesnksalkaveelakrleeledekelfkellkislwGNaiDlsllateediqkdqeeearkalekni 164
                                       n+Dp+k++Ke++nk al++++++++  ++  de e++++ + + ++GN+iD+++ +    +  + e+ +++ l+ ++
  gi|15668374|ref|NP_247170.1|  79 ----NNDPYKNLKEKANKIALQYLDKVREM-SNTDDELERLRKKVLATIAGNVIDFGAYS----TGINIEKLIEDTLNGEL 150
                                   ....***********************996.7888888**********************....55555777778888889 PP

                                   SEE-HHHHHHHHCTCHTSEEEEE--BTTHHHHHHHHHHHHHHHCTTTSEEEEEEBSS--TTTB-BHHHHHHHHHHHH-TTT CS
                         DUF89 165 lvddleklweklkkkkakrvdivlDNaGfElvfDlllaeeLlesglatkVvlhvkaiPwfvsDvtpeDfewlleqladsks 245
                                    +d+++kl+++lk+k+ k++++++DNaG E++fD++l+ee+++  + +++v +vk++P +++D+t+eD++           
  gi|15668374|ref|NP_247170.1| 151 KIDNSRKLLNDLKDKNIKKILYICDNAG-EIIFDRVLMEEIKK--YDKDIVAVVKGKP-ILNDATLEDAK----------- 216
                                   9***************************.**************..*************.***********........... PP

                                   SHHHHCHTTHHHHHHTSEEEEESSCGGSSS--CCGSSSHHHHHHHHHC-SEEEEEHHHHHHHHTTSCTTTTTSEHHHHTGT CS
                         DUF89 246 felsalgagldellkegklvlrgssfwttglsysempeapelyeelekadLvifKGdlNyrkLtgdrkwppttpfttalgf 326
                                          a++de    +k++++gs+  ++g+ ++e+  ++e+++e+e+adL+i+KG++Ny++Lt+ +++  + p       
  gi|15668374|ref|NP_247170.1| 217 ------IAKIDE---IAKVITTGSD--IIGIILEEC--SEEFLKEFESADLIIAKGMGNYESLTEYEDKI-DKP------- 276
                                   ......9*****...**********..*********..*************************8777765.555....... PP

                                   SS--EEEEEE--SHHHHHHH.STTTHE CS
                         DUF89 327 spvpvlaLrtvKadvvagll.egegek 352
                                       +++++++K+++va+ + +++g++
  gi|15668374|ref|NP_247170.1| 277 ----IYYILKAKCKPVAENIgVDVGDN 299
                                   ....***************99999887 PP

>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.4e-05     0.083      77     141 ..      54     117 ..      43     129 .. 0.80
   2 ?   -0.3   0.1      0.14   8.1e+02      95     158 ..     141     205 ..     115     236 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                          Dna2  77 kvsgesskamliGtilHelfqkalleeeldkekleelldklleknleelyalglteeeakeeike 141
                                   +v ges  ++ +Gt++H+ + k+ ++ +   ++l+e+++k+  ++l+++ ++  t +e+++  k+
  gi|15668374|ref|NP_247170.1|  54 DVYGESAVPAWMGTVVHRYLKKISNN-NDPYKNLKEKANKIALQYLDKVREMSNTDDELERLRKK 117
                                   567889999***********998655.777899**********9999999999999887654444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.14
                          Dna2  95 lfqkalleeeldkekleelldklleknleel.yalglteeeakee.ikekleeiekwakkyvkksn 158
                                   l+++ l+  el+ ++ ++ll++l +kn++++ y ++   e + ++ ++e+++++ k + ++vk ++
  gi|15668374|ref|NP_247170.1| 141 LIEDTLNG-ELKIDNSRKLLNDLKDKNIKKIlYICDNAGEIIFDRvLMEEIKKYDKDIVAVVKGKP 205
                                   55555543.777788888888888888877614444444444443145556666555555555554 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00016      0.95       4      79 ..      39     118 ..      38     120 .. 0.89
   2 ?   -1.3   0.1      0.56   3.3e+03      53      77 ..     139     164 ..     136     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00016
                EF-G-binding_N   4 pyqYnfIkkqveqllnayrsvnDkkvveavkalaaekIlel...fpelseeq.kelLeqiddiktkekaeklLeeLkeyV 79 
                                    +q+ +Ik+ +e +  +y  +  +  + +v     +kI +     ++l+e++ k  L+ +d++++ ++ +  Le+L++ V
  gi|15668374|ref|NP_247170.1|  39 REQFRLIKSTMEVIKDVYGESAVPAWMGTVVHRYLKKISNNndpYKNLKEKAnKIALQYLDKVREMSNTDDELERLRKKV 118
                                   58************************************998888888888874666999999999999999999999876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.56
                EF-G-binding_N  53 kelLeqiddik.tkekaeklLeeLke 77 
                                   ++l+e+  + + +  ++ klL++Lk 
  gi|15668374|ref|NP_247170.1| 139 EKLIEDTLNGElKIDNSRKLLNDLKD 164
                                   56666666666677777788888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1169  (0.0652016); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2096.64
//
Query:       gi|15668375|ref|NP_247171.1|  [L=350]
Description: phosphoribosylaminoimidazole synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-30  104.1   0.0    1.4e-29  103.3   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain
    2.9e-16   59.9   0.6      5e-16   59.1   0.6    1.4  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.0   1.5e-33   1.4e-29       1     148 [.     166     326 ..     166     332 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 1.5e-33
                                   STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT......TSEHHHHHHHHHHHHHHHHHHHH...HTTECEEEE--TTHH CS
                        AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds......avqlgdvlleptliyvkralaal...kglvkaahDvTgGGL 72 
                                   k+Gdv++++ s+G++++g+sl+rk++ + +  d+      ++ ++++ll+pt+iyvk+ l ++   + +vk+++++Tg G 
  gi|15668375|ref|NP_247171.1| 166 KAGDVIVGLRSSGIHSNGLSLARKVFFDIAKLDIndklsyGKTVAEELLTPTRIYVKPVLEMIrdkDIEVKGLAHITG-GS 245
                                   69**************************9998889****8888***********************************.7* PP

                                   HHHHHHHHHTTTEEEEEECG..THHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEE CS
                        AIRS_C  73 lgalaemapasgvgaeidld..kvpifdele.....splemllsensGrllvavppeea.davlaileeeglpeaavIGev 145
                                      l+++ ++  v+  id     +pif+e++      ++em++++n+G+++++++ ee+ ++v++i++++++p a+vIG+v
  gi|15668375|ref|NP_247171.1| 246 FRKLKRLNDK--VTYYIDNLpePLPIFKEIQrlgnvPDEEMFRTFNMGIGFCVIVDEEDaNKVIKIANKYNIP-AQVIGRV 323
                                   *******887..99999999******************************9988888888************7.******* PP

                                   EES CS
                        AIRS_C 146 tak 148
                                   +++
  gi|15668375|ref|NP_247171.1| 324 VDS 326
                                   *97 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.6   5.5e-20     5e-16       5      90 ..      52     150 ..       6     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 5.5e-20
                                   EEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-EEEEE CS
                          AIRS   5 vvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvplvgG 76 
                                   +v++td+++++++v+++      +G  ++a+n++D ++ GA+P+al+++la++     ++e++ +gl+e+a+e+++++vgG
  gi|15668375|ref|NP_247171.1|  52 LVLSTDGVGSKMIVAEMANkfdtVGIDMIAMNVNDAICIGAEPIALVDYLAVGhiteeIAEQIGKGLNEGAKEANINIVGG 132
                                   699***********665555566********************************************************** PP

                                   EEEEESS....EEEEEEE CS
                          AIRS  77 dtsfsne....ptisvta 90 
                                   +t+  ++    + ++ t+
  gi|15668375|ref|NP_247171.1| 133 ETATLPDmikgIDLAGTV 150
                                   **9887755555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2160.61
//
Query:       gi|15668376|ref|NP_247172.1|  [L=471]
Description: amidophosphoribosyltransferase PurF [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-24   84.1   0.0    1.1e-23   83.5   0.0    1.3  1  GATase_7      Glutamine amidotransferase domain
    1.3e-22   80.4   0.0    2.4e-22   79.5   0.0    1.4  1  GATase_6      Glutamine amidotransferase domain
    1.1e-09   37.6   0.0      1e-08   34.4   0.0    2.3  2  GATase_4      Glutamine amidotransferases class-II
    2.3e-07   30.5   0.1    4.5e-07   29.5   0.1    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
        0.2   11.1   0.0       0.36   10.3   0.0    1.3  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   0.0   3.1e-27   1.1e-23       9     122 ..      83     203 ..      73     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 3.1e-27
                      GATase_7   9 seagaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGmfA 79 
                                     ++ QP+v  s+ g+++i++nG ++N +elr+eLe kgh f++++D+ev+++ll +         e ++++l++l G ++
  gi|15668376|ref|NP_247172.1|  83 AVENCQPFVVkSSFGNIAIAHNGDLVNSDELRRELEMKGHIFTSSTDSEVIAQLLVRellktsdkiEAIKNTLKKLVGAYS 163
                                   55788***99899****************************************99888*********************** PP

                      GATase_7  80 faiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                   ++i+ +++  l+++RD++G+kPL +g+d+ ++++++Se  al+
  gi|15668376|ref|NP_247172.1| 164 LLIMFNDS--LIAVRDPWGFKPLCIGRDE-SNIYISSEDCALT 203
                                   ******99..******************6.7********9996 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.0   6.8e-26   2.4e-22      13     134 .]      68     198 ..      46     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 6.8e-26
                      GATase_6  13 evalaHvRlaivglaeeegaqPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.......eel 84 
                                    ++++HvR +++g ++ e +qPf  +s+ g+++++hNG+  n +elr+el+  kg+ f s +D+ev+++ll       +  
  gi|15668376|ref|NP_247172.1|  68 YIGIGHVRYSTTGGKAVENCQPFvvKSSFGNIAIAHNGDLVNSDELRRELEM-KGHIFTSSTDSEVIAQLLvrellktS-- 145
                                   39*************88888***999999***********************.****************8887666440.. PP

                      GATase_6  85 G.....eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                   +     + +l++l+G+++  i+   ++ li +rd +g kpl+++ des+++++se
  gi|15668376|ref|NP_247172.1| 146 DkieaiKNTLKKLVGAYSLLIMF--NDSLIAVRDPWGFKPLCIGRDESNIYISSE 198
                                   1556889999*****99998876..6788999*********************98 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   2.8e-12     1e-08      14     164 ..      18     160 ..       1     177 [. 0.71
   2 ?   -0.1   0.0     0.097   3.5e+02     233     256 ..     206     229 ..     189     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2.8e-12
                      GATase_4  14 disfsftgfaarggltdahadGwGiafyegkaarvfkdpepsaesplaelvreypiksknvvaHiRkatqGevklenthpF 94 
                                   +i + + ++++rg++      G Gia  +gk +++ k+    ++    e +++  +   + + H+R  t+G  + en++pF
  gi|15668376|ref|NP_247172.1|  18 KIYYGLFALQHRGQE------GAGIATSDGKNIHYYKNIGLVTDVFKNETLQN--LFGYIGIGHVRYSTTGGKAVENCQPF 90 
                                   455555555555544......77777777777777777777777777777766..778889******************** PP

                      GATase_4  95 vRelwgrewifAHnGdlke...ykpkl.egrfePvGsTDsElafCelleelasrfekaepsaeeleralaelak 164
                                   v +    ++ +AHnGdl +   ++ +l  + +    sTDsE++   l++el ++ +k    +e+++++l++l+ 
  gi|15668376|ref|NP_247172.1|  91 VVKSSFGNIAIAHNGDLVNsdeLRRELeMKGHIFTSSTDSEVIAQLLVRELLKTSDK----IEAIKNTLKKLVG 160
                                   **99999**********66222444445334445689*************9999854....5555555555544 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.097
                      GATase_4 233 rdetWkklepGellvfrdGalvat 256
                                   ++e  k++epGe++ ++dG+++  
  gi|15668376|ref|NP_247172.1| 206 DAEFVKDIEPGEIIEIKDGEIISH 229
                                   5778899************99765 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   1.2e-10   4.5e-07      16     120 ..     282     390 ..     271     395 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.2e-10
                                   EETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-.EE-EEEEEE-TTT--EE.................EE----T CS
                  Pribosyltran  16 arlaaeileeyngkpdvvvgiargGvpfakiladeLevp.layvrkvkyrpdgseeaargssdes.........rlledpa 86 
                                    +++a+ +       dvv +i+  Gv+fa   + e ++p +  + k +y + +    +++    +            + ++
  gi|15668376|ref|NP_247172.1| 282 GKILAKEHPV---DADVVSPIPDSGVTFALGFSEESGIPyYEGLIKNRYVGRTFILPSQNE---RelavrlklsPVKSVLE 356
                                   4444444433...678999999999999999999999994446766666666655555433...1246888887899999* PP

                                   TSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEE CS
                  Pribosyltran  87 gkkVliVDDildtGgTllaalelLkekgpeevri 120
                                   gk+V++VDD +  G+T +++++ ++++g++ev++
  gi|15668376|ref|NP_247172.1| 357 GKRVVLVDDSIVRGTTSRRIVNMVRKAGAKEVHL 390
                                   ******************************9985 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   9.9e-05      0.36     118     150 ..     354     386 ..     343     396 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.9e-05
                      PRTase_2 118 laaakelvLvDDEistGktalnliralqeklpr 150
                                   + + k++vLvDD i  G+t  ++++ ++++  +
  gi|15668376|ref|NP_247172.1| 354 VLEGKRVVLVDDSIVRGTTSRRIVNMVRKAGAK 386
                                   456688**************9999998877554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 3680.60
//
Query:       gi|15668377|ref|NP_247173.1|  [L=354]
Description: aspartate-semialdehyde dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-45  153.9   0.0    7.3e-45  153.3   0.0    1.3  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    7.2e-39  133.0   0.0    1.4e-38  132.0   0.0    1.5  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    0.00026   21.7   0.0    0.00066   20.4   0.0    1.7  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
      0.001   19.2   0.0     0.0021   18.2   0.0    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.013   15.8   0.0      0.023   14.9   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.019   14.5   0.1       0.29   10.7   0.0    2.3  2  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
      0.023   14.6   0.0      0.063   13.2   0.0    1.7  1  NAD_binding_10   NAD(P)H-binding
      0.024   15.3   0.0      0.075   13.7   0.0    1.7  2  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   0.0   3.3e-48   7.3e-45       1     183 [.     166     335 ..     166     336 .. 0.97

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 3.3e-48
                                   HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHH CS
               Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkav 81 
                                   LkP++d+ ++le+v +at+qavSGaG+                    +gv++++i++Nlip+i++ee+k+++e+ + l+ +
  gi|15668377|ref|NP_247173.1| 166 LKPIMDK-FGLEAVFIATMQAVSGAGY--------------------NGVPSMAILDNLIPFIKNEEEKMQTESLKLLGTL 225
                                   8*****9.88*****************....................8********************************* PP

                                   HHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCS.......TTEEEEESSHCHHSSHHHHTT CS
               Semialdhyde_dhC  82 aetkkileftekvsatcvrVPvlrGhseavtiklk..lkdveveeveellaaa.......pevkvvvneeedrPtpaavag 153
                                   ++ k++l++++ +sa+c+rV+v++Gh+e++++k+k  ++++e++ev++++            + +v++ee drP+p+++++
  gi|15668377|ref|NP_247173.1| 226 KDGKVELANFK-ISASCNRVAVIDGHTESIFVKTKegAEPEEIKEVMDKFDPLkdlnlptYAKPIVIREEIDRPQPRLDRN 305
                                   **********8.***************************************9999***997888888889**********9 PP

                                   C..SSSEEEEEEEEETTCTTEEEEEEEEETTT CS
               Semialdhyde_dhC 154 g..tnsvsVGRirkdemgdeglklvvvgDNll 183
                                   +  ++s+ VGRirkd+++d  +k++++++N++
  gi|15668377|ref|NP_247173.1| 306 EgnGMSIVVGRIRKDPIFD--VKYTALEHNTI 335
                                   9999***************..*********97 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.0   0.0   6.4e-42   1.4e-38       1     119 [.      10     136 ..      10     138 .. 0.97

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 6.4e-42
                                   EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG......GGTTTECEBEEE..GGGGGCTT-SEEEE- CS
                Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk......aleegkdlkved..vdeeelkevdivfla 73 
                                   kv+++GatG vGq++++lL++hp +el++l++s+rsaGkk+++a+       ++e++kd++v +  ++ ee+++vdivf+a
  gi|15668377|ref|NP_247173.1|  10 KVGVLGATGSVGQRFVQLLADHPMFELTALAASERSAGKKYKDACYwfqdrdIPENIKDMVVIPtdPKHEEFEDVDIVFSA 90 
                                   7************************************************************99867888999********* PP

                                   SCHHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGG CS
                Semialdhyde_dh  74 lpagvskelapklaeagvkviDlssdfRlkddavyvlpevnreaik 119
                                   lp++ +k+++p++a++g  +++++s++R+++d+++v+pevn+++++
  gi|15668377|ref|NP_247173.1|  91 LPSDLAKKFEPEFAKEGKLIFSNASAYRMEEDVPLVIPEVNADHLE 136
                                   *******************************************997 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.9e-07   0.00066       1      36 [.      11      45 ..      11      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.9e-07
                                  EEEESTTSHHHHHHHHHHHHCTTTEEEEEEEESSTH CS
               DXP_reductoisom  1 vviLGsTGSIGtqtLdvieenpdkfevvalaagsnv 36
                                  v +LG+TGS+G+  +++++++p  fe++alaa+++ 
  gi|15668377|ref|NP_247173.1| 11 VGVLGATGSVGQRFVQLLADHP-MFELTALAASERS 45
                                  579*******************.9*******95543 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   9.5e-07    0.0021       1      41 [.       9      47 ..       9     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.5e-07
                                  EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTT CS
                        DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeseleg 41
                                  ikv+v+Ga+G +G++ v+++ +++ +el+a   +++s+  g
  gi|15668377|ref|NP_247173.1|  9 IKVGVLGATGSVGQRFVQLLADHPMFELTALAASERSA--G 47
                                  79***************************998887743..2 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     1e-05     0.023       1      43 [.      11      52 ..      11      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                                  EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCH CS
               Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaak 43
                                  v ++Ga GsvGq +++lla+h  +  e+t    s++++ +  ++
  gi|15668377|ref|NP_247173.1| 11 VGVLGAtGSVGQRFVQLLADHPMF--ELTALAASERSAGKKYKD 52
                                  679******************999..888888887776665554 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.12   2.7e+02       4      25 ..     165     186 ..     162     189 .. 0.88
   2 ?   10.7   0.0   0.00013      0.29      70     109 ..     235     274 ..     230     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.12
                                   HHHHHHHHHEEEEEEEEEEEEC CS
                       Gp_dh_C   4 lakvlndkfgikkglmttvhay 25 
                                   ++k + dkfg++ +++ t  a+
  gi|15668377|ref|NP_247173.1| 165 TLKPIMDKFGLEAVFIATMQAV 186
                                   6899*************99886 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00013
                                   TTEEEEEEEESSSSEEEEEEEEEESSTS-HHHHHHHHHHH CS
                       Gp_dh_C  70 gkldglAvrVPtpnvsvvdlvvelekevtveevnaalkea 109
                                    k++++  rV +++++  ++ v++++ ++ ee+++++++ 
  gi|15668377|ref|NP_247173.1| 235 FKISASCNRVAVIDGHTESIFVKTKEGAEPEEIKEVMDKF 274
                                   6899999******************************985 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.8e-05     0.063       1      33 [.      15      47 ..      15     107 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                                  TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCH CS
                NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpekla 33
                                  GAtG+vG++ v+ l+++  +e+tal+ ++ ++ 
  gi|15668377|ref|NP_247173.1| 15 GATGSVGQRFVQLLADHPMFELTALAASERSAG 47
                                  9**********9888888*******99887764 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.4e-05     0.075       3      85 ..      18     109 ..      17     123 .. 0.83
   2 ?   -2.2   0.0       2.9   6.5e+03      10      41 ..     222     261 ..     220     277 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-05
                                   SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TTHHHHHT--CB---HHHHHHHH.........S-EEEEE-S--HHHH CS
                 NAD_binding_3   3 GaiGsavleqlkrqqseielelvavadrd.sllskdrkallasealtldlddliahl.........dpdvvVEcasseava 73 
                                   G +G++++++l++++  +el+  a  +r+  ++ kd+  ++++ +++++++d++  +         d+d+v  + +s+ ++
  gi|15668377|ref|NP_247173.1|  18 GSVGQRFVQLLADHPM-FELTALAASERSaGKKYKDACYWFQDRDIPENIKDMVVIPtdpkheefeDVDIVFSALPSDLAK 97 
                                   99*************7.45555555555655566668899**************977999*****88****9999999999 PP

                                   TTHHHHHHTTEE CS
                 NAD_binding_3  74 elvlkaLkagkd 85 
                                   ++ +++ k+gk 
  gi|15668377|ref|NP_247173.1|  98 KFEPEFAKEGKL 109
                                   999999999974 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                                   HHHHHH---S.......SEEEEEEEEESS.EEE-TTHHHH CS
                 NAD_binding_3  10 leqlkrqqse.......ielelvavadrd.sllskdrkal 41 
                                   l  lk+++ e       ++++ vav d +   +  ++k+ 
  gi|15668377|ref|NP_247173.1| 222 LGTLKDGKVElanfkisASCNRVAVIDGHtESIFVKTKEG 261
                                   6677888877744444444444445444433333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2569.09
//
Query:       gi|15668378|ref|NP_247174.1|  [L=135]
Description: hypothetical protein MJ_0206 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-56  188.9   2.4    3.7e-56  188.8   2.4    1.0  1  DUF371         Domain of unknown function (DUF371)
  ------ inclusion threshold ------
       0.14   12.2   2.0        2.5    8.2   0.2    2.1  2  Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen r
       0.76    9.9   8.0         85    3.3   8.0    2.1  1  ETRAMP         Malarial early transcribed membrane protein (E


Domain annotation for each model (and alignments):
>> DUF371  Domain of unknown function (DUF371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.8   2.4   6.1e-60   3.7e-56       1     132 [.       5     135 .]       5     135 .] 0.99

  Alignments for each domain:
  == domain 1  score: 188.8 bits;  conditional E-value: 6.1e-60
                                   EEEE--TT-----SSEEEEES-S---TT-TTEEEBS-S--GGGS-HHHHHHHS----EEEEEEE-SS-EEEEEEE--TT-- CS
                        DUF371   1 ikarGHenvkaehksTleitkddeltprgdCIigveadkaaadlseelkealkeeeatitvtlevgeledeitgrGspklt 81 
                                   ika+GH+nv+a+hk+Tleitk+d+ltp+g CIig++adk+++d+see+ke+l++++ +i v++ev++++d+i+g+G+++l 
  gi|15668378|ref|NP_247174.1|   5 IKAKGHKNVSATHKTTLEITKEDYLTPTGHCIIGIDADKSMTDFSEEFKEKLRNAK-KIIVEIEVEGIKDTIIGEGHKDLI 84 
                                   79******************************************************.9*********************** PP

                                   ---SSEEEEESSS---TTEEEBS-S--GGGS-HHHHHHHHTT-EEEEEEEE CS
                        DUF371  82 lenerdlvvRkSdyvddrTllvkadkaaadldrelveaLkkgaeltvelev 132
                                   l++++d+v+RkS+y+++rTl+++a+k+a+d++re+v++Lk+g+el ++++v
  gi|15668378|ref|NP_247174.1|  85 LNHPTDMVIRKSNYICPRTLMINANKSAKDINREIVKKLKEGKELIFKIIV 135
                                   ***********************************************9986 PP

>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2   0.00041       2.5      72     104 ..      40      72 ..      13      76 .. 0.85
   2 ?    4.1   0.1    0.0077        46      42      96 ..      80     131 ..      73     135 .] 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00041
                 Nit_Regul_Hom  72 vdeekvekikeeleeklkderytiieipvekik 104
                                      + +++  ee++ekl++ +  i+ei+ve+ik
  gi|15668378|ref|NP_247174.1|  40 DADKSMTDFSEEFKEKLRNAKKIIVEIEVEGIK 72 
                                   4456688999********************997 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0077
                 Nit_Regul_Hom  42 wkgflleedpesaikiikdlseeavlintvvdeekvekikeeleeklkderytii 96 
                                   +k++ l+   +++i   + +  ++++in+   ++ +++i++e+ +klk+ +  i 
  gi|15668378|ref|NP_247174.1|  80 HKDLILNHPTDMVIRKSNYICPRTLMINA---NKSAKDINREIVKKLKEGKELIF 131
                                   57778888888999999999999999986...56678888888888888775555 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   8.0     0.014        85      32      60 ..      58     133 ..       5     135 .] 0.65

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.014
                        ETRAMP  32 k...............................................ekakkaikkiddkiekkkkkkKliiist 60 
                                   +                                                +a+k+ k+i+ +i kk k  K +i   
  gi|15668378|ref|NP_247174.1|  58 NakkiiveievegikdtiigeghkdlilnhptdmvirksnyicprtlmINANKSAKDINREIVKKLKEGKELIFKI 133
                                   0444555555555556666666666666666666677777777777778899999999999999999999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1078.44
//
Query:       gi|15668379|ref|NP_247175.1|  [L=151]
Description: hypothetical protein MJ_0207 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1050.48
//
Query:       gi|15668380|ref|NP_247176.1|  [L=246]
Description: 4Fe-4S binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-15   55.2   0.0    1.1e-14   54.5   0.0    1.3  1  Flavoprotein  Flavoprotein
    5.6e-14   51.3  13.8    2.5e-07   30.2   2.5    2.4  2  Fer4          4Fe-4S binding domain
    2.4e-11   43.2  11.1    1.4e-06   28.1   1.0    2.4  2  Fer4_6        4Fe-4S binding domain
    6.4e-11   42.2  21.1    4.7e-07   29.8  12.6    2.3  2  Fer4_10       4Fe-4S dicluster domain
    2.3e-10   41.2   7.5      1e-05   26.4   0.5    2.3  2  Fer4_16       4Fe-4S double cluster binding domain
    6.7e-09   36.2  31.4    4.6e-06   27.1  11.5    2.2  3  Fer4_7        4Fe-4S dicluster domain
    8.9e-09   35.4  30.8    1.5e-06   28.3  10.7    1.9  3  Fer4_9        4Fe-4S dicluster domain
    4.5e-08   32.7   8.4     0.0015   18.5   0.8    2.5  2  Fer4_2        4Fe-4S binding domain
    8.9e-07   29.0  10.2    1.7e-06   28.0  10.2    1.4  1  Fer4_21       4Fe-4S dicluster domain
    9.7e-07   29.2   1.6     0.0032   17.9   0.1    2.3  2  Fer4_8        4Fe-4S dicluster domain
      4e-05   23.7   2.4    6.4e-05   23.0   2.4    1.3  1  Fer4_11       4Fe-4S dicluster domain
    0.00071   19.9  12.3      0.017   15.6   2.8    2.4  2  Fer4_4        4Fe-4S binding domain
     0.0012   19.6  17.5      0.047   14.6   5.3    2.5  2  Fer4_3        4Fe-4S binding domain
      0.002   18.6   5.2       0.36   11.4   0.1    2.3  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
     0.0026   18.3  12.3       0.02   15.5   2.3    2.4  4  Fer4_17       4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.19   12.0   9.6        3.1    8.0   9.6    2.2  2  Fer4_18       4Fe-4S dicluster domain
       0.28   12.0  10.6       0.44   11.4   2.3    2.3  3  Fer4_22       4Fe-4S dicluster domain
       0.86   10.4   8.3          6    7.7   1.2    2.5  2  Fer4_15       4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   1.1e-17   1.1e-14       1      99 [.       9     128 ..       9     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.1e-17
                                   EEEEEEE-SSCGGGCH.HHHHHHHHH..TTEEEEEEESCHHHHCCHHG....GS....TCSSHHHHHHCT........... CS
                  Flavoprotein   1 kkillgiTGsvaaika.lellekLkk..egievqvvltkaAkkfiske....klklaaredpilhielrr........... 63 
                                   +ki+++iTG+ + + +  +++++Lk+  e+ +v+  +++a++++++      +l + ++++  ++  l+r           
  gi|15668380|ref|NP_247176.1|   9 MKIVWCITGAGHLLREsFQVMKRLKEeiEDLKVTTLVSRAGEEVVKMYglfgELYNISNGNYYEELILERehpysspitgr 89 
                                   79*************99*********989*****************66555533333356666666666688999999999 PP

                                   ....TESEEEEEEEEHHHHHHHHTT--SSHHHHHHHTHCC CS
                  Flavoprotein  64 ....wadllviaPasantlakianGiadnlltlilratak 99 
                                       ++d l+  Pa+ nt+ak++nGiad+l+t+ + a+a 
  gi|15668380|ref|NP_247176.1|  90 lslgKYDYLICSPATGNTVAKVVNGIADSLVTNAI-AQAG 128
                                   9999*****************************99.3322 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   3.7   3.6e-09   3.6e-06       2      23 ..     153     174 ..     152     175 .. 0.94
   2 !   30.2   2.5   2.6e-10   2.5e-07       2      23 ..     182     203 ..     181     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.6e-09
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                    id+ kC  C +C++vCP+gAI
  gi|15668380|ref|NP_247176.1| 153 AIDKKKCKLCLKCINVCPNGAI 174
                                   69*******************9 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 2.6e-10
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                   +i  +kC gCG+C +vCP++AI
  gi|15668380|ref|NP_247176.1| 182 EILLSKCLGCGNCKKVCPYNAI 203
                                   56679****************9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   3.2   6.2e-07   0.00061       4      24 .]     154     174 ..     153     174 .. 0.95
   2 !   28.1   1.0   1.4e-09   1.4e-06       2      24 .]     181     203 ..     180     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.2e-07
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   id+ kC  C +C++vCP gai
  gi|15668380|ref|NP_247176.1| 154 IDKKKCKLCLKCINVCPNGAI 174
                                   99****************998 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 1.4e-09
                        Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                   vei  +kC+gCg+C +vCP++ai
  gi|15668380|ref|NP_247176.1| 181 VEILLSKCLGCGNCKKVCPYNAI 203
                                   777789****************8 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8  12.6   4.7e-10   4.7e-07       4      56 .]     154     199 ..     152     199 .. 0.94
   2 !   24.7   1.2   1.9e-08   1.9e-05       3      24 ..     182     209 ..     180     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4.7e-10
                       Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   id+++C  C kC ++CP         ++ ++++ v++ ++kC gcg+C ++CP
  gi|15668380|ref|NP_247176.1| 154 IDKKKCKLCLKCINVCPN-------GAIVKRDNFVEILLSKCLGCGNCKKVCP 199
                                   89****************.......788888999999***************9 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.9e-08
                       Fer4_10   3 vidddtCirCgkCvkaCPadl......t 24 
                                   +i  ++C++Cg+C+k+CP+++       
  gi|15668380|ref|NP_247176.1| 182 EILLSKCLGCGNCKKVCPYNAiiegkeI 209
                                   567799*************665555432 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.5   3.8e-06    0.0038       1      20 [.     158     177 ..     158     183 .. 0.87
   2 !   26.4   0.5     1e-08     1e-05       1      40 [.     187     226 ..     187     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.8e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                   +C+ C kC++vCP +ai ++
  gi|15668380|ref|NP_247176.1| 158 KCKLCLKCINVCPNGAIVKR 177
                                   5****************987 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 1e-08
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkd 40 
                                   +C +Cg+C +vCP nai e ke +++ r+  ++nt++  +
  gi|15668380|ref|NP_247176.1| 187 KCLGCGNCKKVCPYNAIIEGKEIKMRVRKIDAENTRKLME 226
                                   5*******************99999999999988877655 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.5   1.4e-05     0.014      31      52 .]     152     173 ..     135     173 .. 0.83
   2 !   27.1  11.5   4.6e-09   4.6e-06       1      52 []     158     202 ..     158     202 .. 0.93
   3 !   18.5   3.3   2.3e-06    0.0023       1      17 [.     187     203 ..     187     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                        Fer4_7  31 veidpekClgCgaCvavCPtga 52 
                                   ++id  kC  C +C++vCP ga
  gi|15668380|ref|NP_247176.1| 152 YAIDKKKCKLCLKCINVCPNGA 173
                                   579999*************997 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 4.6e-09
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C  C +C ++Cp++ai  ++         vei  +kClgCg+C +vCP++a
  gi|15668380|ref|NP_247176.1| 158 KCKLCLKCINVCPNGAIVKRDN-------FVEILLSKCLGCGNCKKVCPYNA 202
                                   7****************99876.......489*****************997 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 2.3e-06
                        Fer4_7   1 rCigCgaCvaaCpvkai 17 
                                   +C gCg+C ++Cp++ai
  gi|15668380|ref|NP_247176.1| 187 KCLGCGNCKKVCPYNAI 203
                                   69999999999998887 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   2.0   2.4e-05     0.024      31      51 .]     155     174 ..     133     174 .. 0.75
   2 !   28.3  10.7   1.5e-09   1.5e-06       1      51 []     158     203 ..     158     203 .. 0.88
   3 !   17.8   2.8   2.7e-06    0.0027       1      25 [.     187     211 ..     187     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                        Fer4_9  31 aseeaCigCgaCveaCpkgai 51 
                                   ++ ++C  C +C+++Cp+gai
  gi|15668380|ref|NP_247176.1| 155 DK-KKCKLCLKCINVCPNGAI 174
                                   22.58*************987 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 1.5e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   kC  C +C+++Cp+g++v++++  ++ l      +C+gCg C ++Cp +ai
  gi|15668380|ref|NP_247176.1| 158 KCKLCLKCINVCPNGAIVKRDNFVEILLS-----KCLGCGNCKKVCPYNAI 203
                                   7****************877777777763.....6*************987 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 2.7e-06
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerk 25 
                                   kC gCg+C ++Cp+++++e +  ++
  gi|15668380|ref|NP_247176.1| 187 KCLGCGNCKKVCPYNAIIEGKEIKM 211
                                   7999999999999999988766554 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.5   2.3e-06    0.0023       2      22 .]     151     171 ..     150     171 .. 0.93
   2 !   18.5   0.8   1.5e-06    0.0015       6      22 .]     184     200 ..     180     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.3e-06
                        Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                   p+++d  +C  C +C+++CP+
  gi|15668380|ref|NP_247176.1| 151 PYAIDKKKCKLCLKCINVCPN 171
                                   6899****************5 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.5e-06
                        Fer4_2   6 dtdrCigCgaCvsaCPa 22 
                                      +C+gCg C ++CP+
  gi|15668380|ref|NP_247176.1| 184 LLSKCLGCGNCKKVCPY 200
                                   5679************5 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0  10.2   1.7e-09   1.7e-06       3      56 ..     154     203 ..     152     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.7e-09
                       Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedc 56 
                                   id++kC  C kC+ +C++    ai +  ++ ++++ ++C GC  C +vCP +  
  gi|15668380|ref|NP_247176.1| 154 IDKKKCKLCLKCINVCPN---GAIVK-RDNFVEILLSKCLGCGNCKKVCPYNAI 203
                                   9****************6...77865.57888******************7544 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00065      0.65      49      64 ..     157     172 ..     122     173 .. 0.88
   2 !   17.9   0.1   3.2e-06    0.0032       3      63 ..     186     200 ..     175     235 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00065
                        Fer4_8  49 wsCttcgaCtevCpvg 64 
                                   ++C  c +C +vCp+g
  gi|15668380|ref|NP_247176.1| 157 KKCKLCLKCINVCPNG 172
                                   6899*********986 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.2e-06
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                   +kC +Cg C++ Cp                                               
  gi|15668380|ref|NP_247176.1| 186 SKCLGCGNCKKVCP----------------------------------------------Y 200
                                   55666666666665..............................................3 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   2.4   6.5e-08   6.4e-05       5      78 ..     154     223 ..     150     243 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.5e-08
                       Fer4_11   5 flpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrknee.tgkvekCdmcldrv 78 
                                   +  ++C+ Cl+  C++++p++aivk++    V +  +++  ++ +++++cPy+++ + +e +++v+k d +  r 
  gi|15668380|ref|NP_247176.1| 154 IDKKKCKLCLK--CINVCPNGAIVKRD--NFVEILLSKCL-GCGNCKKVCPYNAIIEGKEiKMRVRKIDAENTRK 223
                                   56689****95..************99..67777778886.9***********9988776144577777777776 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   2.1    0.0018       1.8       1      16 [.     156     171 ..     156     176 .. 0.90
   2 !   15.6   2.8   1.8e-05     0.017       2      17 .]     186     201 ..     185     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                        Fer4_4   1 qerCigCgsCvaaCPq 16 
                                   +++C  C +C+++CP 
  gi|15668380|ref|NP_247176.1| 156 KKKCKLCLKCINVCPN 171
                                   589************5 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.8e-05
                        Fer4_4   2 erCigCgsCvaaCPqg 17 
                                   ++C+gCg C  +CP++
  gi|15668380|ref|NP_247176.1| 186 SKCLGCGNCKKVCPYN 201
                                   69************86 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   4.3     0.001         1       1      15 []     159     173 ..     159     173 .. 0.95
   2 !   14.6   5.3   4.7e-05     0.047       1      15 []     188     202 ..     188     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.001
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C  C  C +vCP+gA
  gi|15668380|ref|NP_247176.1| 159 CKLCLKCINVCPNGA 173
                                   999*99********9 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.7e-05
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+gCg C +vCP++A
  gi|15668380|ref|NP_247176.1| 188 CLGCGNCKKVCPYNA 202
                                   *************98 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   1.4    0.0026       2.6       1      18 [.     154     171 ..     154     172 .. 0.96
   2 !   11.4   0.1   0.00036      0.36       4      32 ..     186     214 ..     185     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0026
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   +D+++C  c +C +++P+
  gi|15668380|ref|NP_247176.1| 154 IDKKKCKLCLKCINVCPN 171
                                   8****************6 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00036
                       Fer4_13   4 dtCiacgaCvelaPdvFeeddeggasvva 32 
                                   ++C +cg+C +++P    ++ ++ +++v 
  gi|15668380|ref|NP_247176.1| 186 SKCLGCGNCKKVCPYNAIIEGKEIKMRVR 214
                                   58************877777766666665 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.8     0.025        25      45      59 ..     158     172 ..     143     174 .. 0.78
   2 ?    5.4   2.6     0.028        28       1      16 [.     158     173 ..     158     184 .. 0.70
   3 !   15.5   2.3     2e-05      0.02      43      59 ..     185     201 ..     176     205 .. 0.86
   4 !   15.3   2.6   2.2e-05     0.022       1      26 [.     187     212 ..     187     229 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.025
                       Fer4_17  45 lCieCgeCerkCPqg 59 
                                   +C  C +C  +CP+g
  gi|15668380|ref|NP_247176.1| 158 KCKLCLKCINVCPNG 172
                                   677777777777765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.028
                       Fer4_17   1 rCiqCgyClpeCpsye 16 
                                   +C  C  C+++Cp ++
  gi|15668380|ref|NP_247176.1| 158 KCKLCLKCINVCPNGA 173
                                   4777777777777655 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 2e-05
                       Fer4_17  43 aslCieCgeCerkCPqg 59 
                                    s+C++Cg+C+++CP++
  gi|15668380|ref|NP_247176.1| 185 LSKCLGCGNCKKVCPYN 201
                                   58999*********997 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 2.2e-05
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkll 26 
                                   +C +Cg C ++Cp++++++ ++ k++
  gi|15668380|ref|NP_247176.1| 187 KCLGCGNCKKVCPYNAIIEGKEIKMR 212
                                   58888888888888888776655544 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   9.6    0.0031       3.1      57      95 ..     155     198 ..     140     205 .. 0.75
   2 ?    7.7   1.4    0.0039       3.9      58      75 ..     185     202 ..     173     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0031
                       Fer4_18  57 gagdcidcescvkvcPtgidi.rkG....lqleciscllcidac 95 
                                   ++ +c  c +c++vcP g  + r+     l  +c+ c++c   c
  gi|15668380|ref|NP_247176.1| 155 DKKKCKLCLKCINVCPNGAIVkRDNfveiLLSKCLGCGNCKKVC 198
                                   5678************99665154422224568*******9988 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0039
                       Fer4_18  58 agdcidcescvkvcPtgi 75 
                                    ++c+ c+ c kvcP + 
  gi|15668380|ref|NP_247176.1| 185 LSKCLGCGNCKKVCPYNA 202
                                   578************875 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.5     0.073        72      77      94 ..     154     171 ..     140     173 .. 0.75
   2 ?   11.4   2.3   0.00044      0.44      80      94 ..     186     200 ..     173     204 .. 0.77
   3 ?   11.1   2.6   0.00055      0.55       1      21 [.     187     207 ..     187     228 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.073
                       Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                   +++++C  C +Ci++cp+
  gi|15668380|ref|NP_247176.1| 154 IDKKKCKLCLKCINVCPN 171
                                   577788888888888876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00044
                       Fer4_22  80 sgCvGCgRCieacpv 94 
                                   s+C GCg C+++cp 
  gi|15668380|ref|NP_247176.1| 186 SKCLGCGNCKKVCPY 200
                                   578888888888875 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00055
                       Fer4_22   1 rClsCgaCtlvCptCsCfdve 21 
                                   +Cl+Cg+C+ vCp    ++ +
  gi|15668380|ref|NP_247176.1| 187 KCLGCGNCKKVCPYNAIIEGK 207
                                   588888888888866555555 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.2    0.0061         6       3      20 ..     154     171 ..     153     185 .. 0.86
   2 ?    6.5   0.9     0.014        14       6      23 ..     186     203 ..     181     229 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0061
                       Fer4_15   3 vDrdaCigcglCvaeape 20 
                                   +D+++C  c  C+ ++p+
  gi|15668380|ref|NP_247176.1| 154 IDKKKCKLCLKCINVCPN 171
                                   9***************86 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                       Fer4_15   6 daCigcglCvaeapevfe 23 
                                   ++C gcg+C +++p    
  gi|15668380|ref|NP_247176.1| 186 SKCLGCGNCKKVCPYNAI 203
                                   68***********85443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1680.69
//
Query:       gi|15668381|ref|NP_247177.1|  [L=266]
Description: hypothetical protein MJ_0209 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-74  249.6   4.1    1.6e-74  249.2   4.1    1.1  1  PPS_PS         Phosphopantothenate/pantothenate synthetase
  ------ inclusion threshold ------
      0.016   15.5   1.2      0.033   14.5   0.2    1.8  2  D5_N           D5 N terminal like
      0.078   13.1   0.2       0.15   12.2   0.0    1.5  2  vWA-TerF-like  vWA found in TerF C terminus
       0.13   12.0   0.8       0.38   10.5   0.4    1.9  2  TPP_enzyme_M   Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> PPS_PS  Phosphopantothenate/pantothenate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.2   4.1   3.7e-78   1.6e-74       1     176 []      71     254 ..      71     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: 249.2 bits;  conditional E-value: 3.7e-78
                        PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellk.......eagaeevlgleeda.ripel 73 
                                   l+la++pvisvNGNt+aL+ +e+veLa++l++k+evNlfyrt+eR+ +i+++++       e+g+ ++lg+++ + +ip+l
  gi|15668381|ref|NP_247177.1|  71 LILAENPVISVNGNTVALAIDEVVELAKELNGKIEVNLFYRTKERELAIKRAFEekfkddiETGKIKILGIDDANkQIPNL 151
                                   689***************************************************999999999*******988767***** PP

                        PPS_PS  74 eseRakvskeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkske 154
                                   +s R+kvs+eGi++aDvvlvplEDGDRaeaLv+mgKkviaiDLNPlsRtar++titivd+++Ra+p l+++vke+k+k++e
  gi|15668381|ref|NP_247177.1| 152 DSLRGKVSEEGIFTADVVLVPLEDGDRAEALVNMGKKVIAIDLNPLSRTARKSTITIVDELTRAMPLLIKYVKEFKNKDRE 232
                                   ********************************************************************************* PP

                        PPS_PS 155 eleeivkefdnkkvlkealkei 176
                                   el +iv++fdnkk+lk+++++i
  gi|15668381|ref|NP_247177.1| 233 ELLKIVEDFDNKKNLKDMIDYI 254
                                   *****************99876 PP

>> D5_N  D5 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.4   1.8e+03      34      62 ..      90     122 ..      78     139 .. 0.64
   2 ?   14.5   0.2   7.3e-06     0.033      34      94 ..     206     265 ..     188     266 .] 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.4
                          D5_N  34 keaireladkvaeaiaeea....eeaksalkal 62 
                                    + ++ela+++ ++i+ ++    +e++ a+k+ 
  gi|15668381|ref|NP_247177.1|  90 IDEVVELAKELNGKIEVNLfyrtKERELAIKRA 122
                                   566778888888888887775554444444443 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 7.3e-06
                          D5_N  34 keaireladkvaeaiaeeaeeaksalkalkkfakssrskkkvdnvlreaaelprldleide 94 
                                    +++ el+++++ +i+  +e  ++ +++l k ++  ++kk+ +++++++ae +  +l++de
  gi|15668381|ref|NP_247177.1| 206 ITIVDELTRAMPLLIKYVKEFKNKDREELLKIVEDFDNKKNLKDMIDYIAERL-KNLSLDE 265
                                   6778889999999999999******************************9984.5555555 PP

>> vWA-TerF-like  vWA found in TerF C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.2e-05      0.15      21     118 ..      84     180 ..      80     197 .. 0.86
   2 ?   -2.9   0.0       1.4   6.2e+03      95     113 ..     221     240 ..     200     259 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-05
                 vWA-TerF-like  21 gvvqavverllavaaqlDddgelevwlfaskakrlpdvtladleeyvkeeeegllelkklggvneeapvleevlekvrkep 101
                                   ++v+ +++ ++ +a +l  +g++ev lf ++ +r   ++ a  e++ ++ e+g++++  ++ +n++ p l++++ kv +e 
  gi|15668381|ref|NP_247177.1|  84 NTVALAIDEVVELAKEL--NGKIEVNLFYRTKERELAIKRAFEEKFKDDIETGKIKILGIDDANKQIPNLDSLRGKVSEEG 162
                                   5789999*********9..7*********************9************************************866 PP

                 vWA-TerF-like 102 .aelptlvlFitDGgvkk 118
                                     ++ + ++ ++DG+ ++
  gi|15668381|ref|NP_247177.1| 163 iFTADVVLVPLEDGDRAE 180
                                   234445556689998766 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                 vWA-TerF-like  95 ekvrk.epaelptlvlFitD 113
                                   ++v++ ++++   l+  ++D
  gi|15668381|ref|NP_247177.1| 221 KYVKEfKNKDREELLKIVED 240
                                   33333323333333333333 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   8.5e-05      0.38       1      39 [.      64     101 ..      64     109 .. 0.91
   2 ?   -1.7   0.0      0.48   2.2e+03     103     127 ..     186     209 ..     162     218 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.5e-05
                                   HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT CS
                  TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklg 39 
                                   i++aa+ll  a++pvi v g +  + a +e++ela++l+
  gi|15668381|ref|NP_247177.1|  64 IKAAAALLILAENPVISVNGNTV-ALAIDEVVELAKELN 101
                                   789*************9988888.89**********998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.48
                                   T-EEEEEESSCCCCTTCC--SEEEE CS
                  TPP_enzyme_M 103 eakiihididpaeigknyqvdlaiv 127
                                    +k+i id +p +   ++  +++iv
  gi|15668381|ref|NP_247177.1| 186 GKKVIAIDLNPLSRTARK-STITIV 209
                                   248888888886655554.445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1248  (0.0696079); expected 358.6 (0.02)
Passed bias filter:                      779  (0.0434492); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1701.86
//
Query:       gi|15668382|ref|NP_247178.1|  [L=364]
Description: succinyl-CoA synthetase subunit beta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.8e-72  242.1   3.9    3.8e-72  242.1   3.9    1.6  2  ATP-grasp_2  ATP-grasp domain
    2.8e-12   46.7   1.1    4.2e-12   46.1   0.2    1.7  2  Ligase_CoA   CoA-ligase
    1.5e-11   44.2   0.6    5.8e-11   42.3   0.6    1.9  1  ATP-grasp_5  ATP-grasp domain
    1.9e-07   31.0   0.9    4.2e-07   29.9   0.9    1.5  1  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 
     0.0031   17.1   0.2     0.0053   16.3   0.2    1.3  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
  ------ inclusion threshold ------
      0.058   13.1   0.4        1.8    8.4   0.0    3.1  3  HeH          HeH/LEM domain


Domain annotation for each model (and alignments):
>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.1   3.9   1.3e-75   3.8e-72       1     202 []       2     193 ..       2     193 .. 0.98
   2 ?   -2.0   0.0      0.73   2.2e+03     152     171 ..     331     350 ..     311     361 .. 0.60

  Alignments for each domain:
  == domain 1  score: 242.1 bits;  conditional E-value: 1.3e-75
                                   BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE CS
                   ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelv 81 
                                   +lhEy+ak+i++kyg++vpe+++++++++++++  +   ke+v+KaQvl+GGRGKagG+ ++++kee+ ++a+el++ke++
  gi|15668382|ref|NP_247178.1|   2 KLHEYEAKNIFKKYGIPVPESFLVSKEDDLNSINVD---KEVVLKAQVLVGGRGKAGGILFASNKEEFIKKAEELFNKEVK 79 
                                   69******************************9987...778*************************************** PP

                                   -TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB--HHHHHHH CS
                   ATP-grasp_2  82 tkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakglkeeqarei 162
                                          G+kvek+lvee+l+i+kE+Y+si++Dr++kk+++i+S+eGGvdiEeva+k+Pekiik++id++k + ++ ar i
  gi|15668382|ref|NP_247178.1|  80 -------GEKVEKILVEEKLPIEKEYYVSIIIDRDAKKPLIIFSTEGGVDIEEVAEKNPEKIIKYHIDVRKPFLPYIARWI 153
                                   .......************************************************************************** PP

                                   HHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEE CS
                   ATP-grasp_2 163 akklglekelvkkaakiikklyklfveldatlvEiNPLvv 202
                                   +k+++l+++++ k+a++i+klyk+f+eldat+vEiNPLv+
  gi|15668382|ref|NP_247178.1| 154 VKEAKLPSNEIGKVADVIYKLYKIFKELDATMVEINPLVI 193
                                   **************************************96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.73
                                   TB--HHHHHHHHHHCT--CH CS
                   ATP-grasp_2 152 kglkeeqareiakklgleke 171
                                   +g +ee  r+i+++ g++ e
  gi|15668382|ref|NP_247178.1| 331 MGTNEEIGRKILEEHGIPYE 350
                                   56666666666666666654 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.7     8e+03      63      80 ..      72      89 ..      68      92 .. 0.81
   2 !   46.1   0.2   1.4e-15   4.2e-12       3     146 ..     246     356 ..     244     361 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.7
                                  HHHHHHHS-TT-SEEEEE CS
                    Ligase_CoA 63 ealkklaadpevkvilld 80
                                  e ++k+++ ++v+ il++
  gi|15668382|ref|NP_247178.1| 72 ELFNKEVKGEKVEKILVE 89
                                  678899999999999985 PP

  == domain 2  score: 46.1 bits;  conditional E-value: 1.4e-15
                                   SSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEEE CS
                    Ligase_CoA   3 nGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldivl 83 
                                   nG++L+ + md+i++               g +++ ++d+G++a            +++  al+k++++++vk+i+++i +
  gi|15668382|ref|NP_247178.1| 246 NGAGLTLASMDIINNL--------------GRKPACFLDIGGGAD----------AETVKLALRKVLENKNVKGIFINILG 302
                                   899**********999..............*************98..........7************************* PP

                                   SSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHH CS
                    Ligase_CoA  84 GygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqa 146
                                   G+ +++++a+++++ +ke      ++ + +r++Gt+++      ++k+lee g+   +s ++a
  gi|15668382|ref|NP_247178.1| 303 GITRCDEVAKGIVEVLKEHP----NVKFAVRMMGTNEE-----IGRKILEEHGIPYETSMEEA 356
                                   *******************7....9*************.....88899999998877766665 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.6   1.9e-14   5.8e-11      10     221 ..       3     207 ..       1     208 [. 0.84

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.9e-14
                   ATP-grasp_5  10 LteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervke 90 
                                   L e+eak++++ ygipv+e+ l+s++++  ++  +++  vvlK ++  +  + ++gG+ +  +++e +++a e + ++v  
  gi|15668382|ref|NP_247178.1|   3 LHEYEAKNIFKKYGIPVPESFLVSKEDDLNSI--NVDKEVVLKAQVL-VGGRGKAGGILFASNKEEFIKKAEELFNKEV-- 78 
                                   89*************************98888..79999****9964.889*********6666666666666666666.. PP

                   ATP-grasp_5  91 kspeariegvlVqemakr.ggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertkaskllkgv 170
                                     +++++e++lV+e  +  +++ + + + +D+    +i   +GG+ +e +++   +     + ++r+      a  ++k+ 
  gi|15668382|ref|NP_247178.1|  79 --KGEKVEKILVEEKLPIeKEYYVSIIIDRDAKKPLIIFSTEGGVDIEEVAEKNPEKIIKYHIDVRKPFLPYIARWIVKEA 157
                                   ..5689*********886677777777888887655555567***********9888888899999988888888888887 PP

                   ATP-grasp_5 171 rgekkadlaaleellvrlsqLvvdlpeIreldinPllveeeg.vvalDarir 221
                                   +     ++ ++++++ +l ++  +l   + ++inPl+++++g v a+Da++ 
  gi|15668382|ref|NP_247178.1| 158 KLP-SNEIGKVADVIYKLYKIFKELDA-TMVEINPLVITKDGnVYAADAVLH 207
                                   777.99******************765.889*********999******986 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.9   1.4e-10   4.2e-07       6     104 ..       8     108 ..       5     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.4e-10
                                   HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT....-EEEESSHHHHHHHHHHHCTS-TTCCCCSS CS
                        GARS_A   6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagK....gvivakseeealkavkeilekkkfGeagek 82 
                                   ak+++kk+gip +e   +++ ++++++  ++++++ V+Ka+ l +g+    g+  a+++ee +k ++e+++k+  Ge  ek
  gi|15668382|ref|NP_247178.1|   8 AKNIFKKYGIPVPESFLVSKEDDLNSI--NVDKEV-VLKAQVLVGGRgkagGILFASNKEEFIKKAEELFNKEVKGEKVEK 85 
                                   79******************9999987..455666.9******9998334347889************************* PP

                                   EEEEE---.SEEEEEEEEECTTE CS
                        GARS_A  83 vviEelle.GeEvsllalvdgkt 104
                                   +++Ee+l   +E  +  ++d + 
  gi|15668382|ref|NP_247178.1|  86 ILVEEKLPiEKEYYVSIIIDRDA 108
                                   ******97234666666666555 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   1.8e-06    0.0053       4     104 ..       7     107 ..       5     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-06
                                   HHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEE....EESSHHHHHHHHHHHHHHHHHHHST CS
                   CPSase_L_D2   4 sakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmr....varneeelaelvkkalaeakaafgn 80 
                                   +ak++ kk ++pv +s+ +  e+  ++++    +   v++ka + +GG+G      +a+n+ee+++ +++ +++       
  gi|15668382|ref|NP_247178.1|   7 EAKNIFKKYGIPVPESFLVSKEDDLNSIN----VDKEVVLKAQVLVGGRGKAggilFASNKEEFIKKAEELFNKEVKGEKV 83 
                                   689999***********994444444444....444589*********986334449***************999999999 PP

                                   S-EEEEE--SSSEEEEEEEEEETT CS
                   CPSase_L_D2  81 kqvlvekslkgpkeiEvevlrDak 104
                                   +++lve+ l   ke+ v ++ D++
  gi|15668382|ref|NP_247178.1|  84 EKILVEEKLPIEKEYYVSIIIDRD 107
                                   ***************999997764 PP

>> HeH  HeH/LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.32   9.6e+02      10      22 ..       9      21 ..       9      22 .. 0.86
   2 ?    0.2   0.1      0.22   6.5e+02       9      18 ..     284     293 ..     283     294 .. 0.92
   3 ?    8.4   0.0   0.00059       1.8      10      22 ..     339     351 ..     339     353 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.32
                           HeH 10 RriLvehgveyPs 22
                                  + i+ ++g+++P 
  gi|15668382|ref|NP_247178.1|  9 KNIFKKYGIPVPE 21
                                  67999******97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.22
                           HeH   9 LRriLvehgv 18 
                                   LR++L  ++v
  gi|15668382|ref|NP_247178.1| 284 LRKVLENKNV 293
                                   9********9 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00059
                           HeH  10 RriLvehgveyPs 22 
                                   R+iL ehg++y +
  gi|15668382|ref|NP_247178.1| 339 RKILEEHGIPYET 351
                                   99********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2364.94
//
Query:       gi|15668383|ref|NP_247179.1|  [L=172]
Description: hypothetical protein MJ_0210.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.4    8.3  13.2       0.04   14.0   3.8    2.5  3  DUF5367   Family of unknown function (DUF5367)
        2.9    7.7   4.6        4.4    7.1   4.6    1.2  1  Lig_chan  Ligand-gated ion channel
          5    7.1   8.3         13    5.8   0.8    2.3  2  DUF4389   Domain of unknown function (DUF4389)


Domain annotation for each model (and alignments):
>> DUF5367  Family of unknown function (DUF5367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.8   6.7e-06      0.04       7      58 ..      15      66 ..       9      76 .. 0.85
   2 ?   -0.6   1.0      0.24   1.4e+03      12      28 ..      90     106 ..      81     115 .. 0.56
   3 ?   -2.5   0.0      0.95   5.7e+03      24      37 ..     124     137 ..     122     149 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.7e-06
                       DUF5367  7 tllllvlfllviplllvlllpvykykklnkterlkaailialpgmllDvlil 58
                                   ++++++++++i  +l++ + ++ky+k++k+ ++   + i lp ml   +i 
  gi|15668383|ref|NP_247179.1| 15 LIMIVIAIIITIGSFLFIAYLIFKYSKIKKQVKIIREVKINLPKMLKSNMIK 66
                                  46778888999999*******************************9766665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.24
                       DUF5367  12 vlfllviplllvlllpv 28 
                                   ++ +l i +++++++ +
  gi|15668383|ref|NP_247179.1|  90 ISHILFIAICWIVVFLY 106
                                   33444444455444433 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.95
                       DUF5367  24 lllpvykykklnkt 37 
                                   +++++y +k+ +  
  gi|15668383|ref|NP_247179.1| 124 VSGVLYSWKEFKDV 137
                                   56778888887655 PP

>> Lig_chan  Ligand-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.6   0.00074       4.4       7      86 ..      18     108 ..      13     110 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00074
                                   XXXTXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX.............XXXHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Lig_chan   7 svlvalilvsivlflverfspyewrepeea.aet.............veneftlsnslwfslgalvqqGcdesprsvsgRi 73 
                                   +v++++i+++ +lf+   + +y+  +++ +  ++              +n+f +++ l+f +g+l  +G +      +  +
  gi|15668383|ref|NP_247179.1|  18 IVIAIIITIGSFLFIAYLIFKYSKIKKQVKiIREvkinlpkmlksnmIKNSFLIISLLCFYFGMLYIAG-E--LVISHILF 95 
                                   455556666666665555555544433222222245566666777779*******************94.3..33334458 PP

                                   XXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxx RF
                      Lig_chan  74 vvavWwffvlill 86 
                                   ++++W+++ l ++
  gi|15668383|ref|NP_247179.1|  96 IAICWIVVFLYII 108
                                   8899988888665 PP

>> DUF4389  Domain of unknown function (DUF4389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.4    0.0035        21       9      32 ..      15      38 ..      14      41 .. 0.91
   2 ?    5.8   0.8    0.0022        13      22      42 ..      92     113 ..      70     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0035
                       DUF4389  9 llmllfaivlslaslvlwvvvvvq 32
                                  l+m+++ai++ + s+++++ +++ 
  gi|15668383|ref|NP_247179.1| 15 LIMIVIAIIITIGSFLFIAYLIFK 38
                                  68****************999886 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0022
                       DUF4389  22 slv.lwvvvvvqflivLvtgrp 42 
                                   +++ ++++++v+fl++++ g++
  gi|15668383|ref|NP_247179.1|  92 HILfIAICWIVVFLYIIIKGET 113
                                   4441456788999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1338  (0.0746277); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1077.29
//
Query:       gi|15668384|ref|NP_247180.1|  [L=305]
Description: UDP-glucose 4-epimerase GalE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-66  223.1   0.1    4.2e-66  222.8   0.1    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.3e-62  210.8   0.2    1.8e-61  208.4   0.2    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.3e-28   97.6   0.5    8.2e-28   97.2   0.5    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      7e-17   61.5   0.3    9.3e-16   57.8   0.3    2.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.6e-16   60.3   0.0    3.3e-11   42.9   0.0    2.6  2  NAD_binding_4    Male sterility protein
    3.6e-15   55.8   0.0    4.4e-15   55.5   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    5.5e-09   36.2   0.0    7.9e-09   35.7   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    0.00026   20.5   0.1    0.00086   18.8   0.1    1.9  1  adh_short        short chain dehydrogenase
    0.00028   20.9   0.0      0.016   15.1   0.0    2.3  1  KR               KR domain
     0.0012   18.4   0.1     0.0073   15.9   0.1    1.9  2  NmrA             NmrA-like family
     0.0046   17.2   0.2     0.0091   16.3   0.2    1.5  1  TrkA_N           TrkA-N domain


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.8   0.1   2.6e-69   4.2e-66       1     241 []       2     233 ..       2     233 .. 0.97

  Alignments for each domain:
  == domain 1  score: 222.8 bits;  conditional E-value: 2.6e-69
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHH CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaass 81 
                                   ilVtG++GfiGs++v++l e++y+vi ld+l+++++++ ++++e+v++d++d++ l++ ++ +++++vih Aa+ +v++s+
  gi|15668384|ref|NP_247180.1|   2 ILVTGGAGFIGSHIVDKLIENNYDVIILDNLTTGNKNNINPKAEFVNADIRDKD-LDEKINFKDVEVVIHQAAQINVRNSV 81 
                                   8*************************************99999*********98.88889999****************** PP

                                   HSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEE.GGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT CS
                     Epimerase  82 edpadfieknlqgtlnlleaarkagvkrllflsS.sevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyg 161
                                   e+p +  ++n+ gt n+le++rk+++++++f+sS  +vYG+++  p +e+    p++p spY+++K+ ge++++ y++ yg
  gi|15668384|ref|NP_247180.1|  82 ENPVYDGDINVLGTINILEMMRKYDIDKIVFASSgGAVYGEPNYLPVDENH---PINPLSPYGLSKYVGEEYIKLYNRLYG 159
                                   **********************************99*******99999999...*************************** PP

                                   -EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
                     Epimerase 162 lnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                                   +++ ilr++n+yG+r+ ++ +++vi+ +i k+l+++ + +++gdg++ Rdf+yv Dva+a+l++l+      k+ei+niG
  gi|15668384|ref|NP_247180.1| 160 IEYAILRYSNVYGERQDPKGEAGVISIFIDKMLKNQ-SPIIFGDGNQTRDFVYVGDVAKANLMALNW-----KNEIVNIG 233
                                   ***************55555***************9.*****************************9.....46899998 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.4   0.2   1.1e-64   1.8e-61       1     331 [.       3     294 ..       3     295 .. 0.89

  Alignments for each domain:
  == domain 1  score: 208.4 bits;  conditional E-value: 1.1e-64
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   L+TG+aGfiGs+++++L+e++y+v+++++++    tg+ +++         ++ +++++D++D++ l++ ++  +++ v++
  gi|15668384|ref|NP_247180.1|   3 LVTGGAGFIGSHIVDKLIENNYDVIILDNLT----TGNKNNIN--------PKAEFVNADIRDKD-LDEKINFKDVEVVIH 70 
                                   9***********************9987654....45555543........3467********65.899999999****** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEE.EEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHH CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfy.qaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyad 161
                                    AAq  V++s+e+P y  ++nvlGt+++Le++r++ ++   +++  +S   vYG+++  p++E++p++P sPY+ +K + +
  gi|15668384|ref|NP_247180.1|  71 QAAQINVRNSVENPVYDGDINVLGTINILEMMRKYDID---KIVfASSGGAVYGEPNYLPVDENHPINPLSPYGLSKYVGE 148
                                   ***********************************985...4440555579****************************** PP

                                   HHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS- CS
                 GDP_Man_Dehyd 162 wivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkp 242
                                     ++ y++ yg+   + +++n ++ r+ ++     i+ ++ ++++++   +++G+++++Rd+ +v D+++a  ++l+ + +
  gi|15668384|ref|NP_247180.1| 149 EYIKLYNRLYGIEYAILRYSNVYGERQDPKGEAGVISIFIDKMLKNQS-PIIFGDGNQTRDFVYVGDVAKANLMALNWK-N 227
                                   *******************************************99875.5669******************99888865.5 PP

                                   --EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS CS
                 GDP_Man_Dehyd 243 edyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkv 323
                                   e ++i+tg+++sv+e++++   e+g     +g             +      + + r+gev +++ d++ka+  LgWkp++
  gi|15668384|ref|NP_247180.1| 228 EIVNIGTGKETSVNELFDIIKHEIGF----RG-------------E----AIYDKPREGEVYRIYLDIKKAE-SLGWKPEI 286
                                   99****************98777775....33.............1....12346799*************9.9******* PP

                                   -HHHHHHH CS
                 GDP_Man_Dehyd 324 sfeelvre 331
                                   +++e++++
  gi|15668384|ref|NP_247180.1| 287 DLKEGIKR 294
                                   *****997 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.5   5.1e-31   8.2e-28       1     229 [.       3     223 ..       3     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 5.1e-31
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk.viegDvtdkdkleea.legvdvvihlaslvdv 79 
                                   +vtGgaGF+G+++v +L++ +   +v +lD  +  ++    +++n k  ++++D++dkd  e+   ++v+vvih a+ ++v
  gi|15668384|ref|NP_247180.1|   3 LVTGGAGFIGSHIVDKLIENN--YDVIILDNLTTGNK----NNINPKAeFVNADIRDKDLDEKInFKDVEVVIHQAAQINV 77 
                                   69****************999..59999997766666....3444444499******9855443268************** PP

                     3Beta_HSD  80 agkltedeim.kvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlk 159
                                   ++ +++  ++ ++nv GT n+le+ +k ++ ++v+ Ss ++v++   + + l  dE+ +   ++ ++y  sK + E++++ 
  gi|15668384|ref|NP_247180.1|  78 RNSVENPVYDgDINVLGTINILEMMRKYDIDKIVFASSGGAVYG---EPNYLPVDENHP--INPLSPYGLSKYVGEEYIKL 153
                                   **8888877658*******************************9...566666788765..56789*************** PP

                     3Beta_HSD 160 aNgrtlknggrlyTcaLRpagiyGegdk......llvpllkqlaklglalfkigdeevlsdrvYvgNvawahilAa 229
                                    N   l ++       LR + +yGe+++      +++ ++ +++k++ + +  gd +++ d+vYvg va+a ++A 
  gi|15668384|ref|NP_247180.1| 154 YNR--LYGI---EYAILRYSNVYGERQDpkgeagVISIFIDKMLKNQ-SPIIFGDGNQTRDFVYVGDVAKANLMAL 223
                                   **9..5544...6678*********9864444446788999999998.8999*******************99996 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.3   5.7e-19   9.3e-16       1     241 [.       2     245 ..       2     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 5.7e-19
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                   +lvtG++G iGs++v+++++++   iil + +  +  +i+ +        +       v +d+rdk+ l++ ++  +v+vv
  gi|15668384|ref|NP_247180.1|   2 ILVTGGAGFIGSHIVDKLIENNYDVIILDNLTTGNKNNINPKA-------E------FVNADIRDKD-LDEKINFKDVEVV 68 
                                   89*******************9998888777766666666654.......1......23589**987.66667778***** PP

                                   EE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGS...............S--SHHHHHHHHHHH CS
               Polysacc_synt_2  82 fhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAv...............nPtnvmGatKrlaek 147
                                   +h AA  +V    enp+   + Nvlgt n++e+  +++++k+v+ S+  Av               nP + +G++K + e 
  gi|15668384|ref|NP_247180.1|  69 IHQAAQINVRNSVENPVYDGDINVLGTINILEMMRKYDIDKIVFASSGGAVygepnylpvdenhpiNPLSPYGLSKYVGEE 149
                                   ***********99**********************************988744444444444433368889********** PP

                                   HHHHGGG--SSS--EEEEEEE-EETTGT......TSSHHHHHHHH.HTTSSEEES-TT-EEEEE-HHHHHHHHHHHHHH-- CS
               Polysacc_synt_2 148 llqalakeseekktkfvvvRfGNVlgSr......GSviplFkkqi.keggpvtvTdpemtRyfmtieeavqLvlqalalak 221
                                   ++  +++       ++++ R+ NV g r        vi +F +++ k+++p+   d + tR f+ + + ++  l+al+   
  gi|15668384|ref|NP_247180.1| 150 YIKLYNRLY---GIEYAILRYSNVYGERqdpkgeAGVISIFIDKMlKNQSPIIFGDGNQTRDFVYVGDVAKANLMALNW-- 225
                                   ******999...89***********986444422479**99876516669**************999999887777654.. PP

                                   SS-EEEE--.-EEEHHHHHH CS
               Polysacc_synt_2 222 ggeifvldmGepvkivdlak 241
                                   ++ei     G+ +++ +l  
  gi|15668384|ref|NP_247180.1| 226 KNEIVNIGTGKETSVNELFD 245
                                   44566666666666666655 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.9e-06    0.0063       1      28 [.       4      29 ..       4      62 .. 0.68
   2 !   42.9   0.0     2e-14   3.3e-11      59     255 ..      41     217 ..      29     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.9e-06
                                  EE-TTSHHHHHHHHHHHHHS-.TEEEEE CS
                 NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyll 28
                                  +TG+ GF+G++++ kL++++ +v  ++l
  gi|15668384|ref|NP_247180.1|  4 VTGGAGFIGSHIVDKLIENNYDV--IIL 29
                                  7******************9964..443 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 2e-14
                                   TTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--SS-S.STTSSEEH...HHHHHHHHHHHHHHTSSS--.-EEEEEE CS
                 NAD_binding_4  59 aerikvveGDlseprlGLseedlqelaeevdviihsaAtvnfdepykell...rvNveGtrevlelakklkklkvllhvST 136
                                     + ++v++D+ +++l       +   + v+v+ih aA++n+ +++++ +   ++Nv+Gt ++le+ +k      +++ S+
  gi|15668384|ref|NP_247180.1|  41 NPKAEFVNADIRDKDLD-----EKINFKDVEVVIHQAAQINVRNSVENPVydgDINVLGTINILEMMRKYDID-KIVFASS 115
                                   56666666666666642.....22236899*****************9764558****************999.7888888 PP

                                   .GGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST--- CS
                 NAD_binding_4 137 .ayvngeregeveekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwin 216
                                    ++v+ge +                    ++++  +    Y  sK+++E+ ++ ++r  g+  +i+R s+++ge +   ++
  gi|15668384|ref|NP_247180.1| 116 gGAVYGEPNY----------------LPVDENHPINPLSPYGLSKYVGEEYIKLYNRLYGIEYAILRYSNVYGERQD--PK 178
                                   7888888883................3355677778888**********************************8887..77 PP

                                   TTSHHHHHHHHHHHH-EEES-SB---TT--EEEHHHHHH CS
                 NAD_binding_4 217 gsdlgirgllgliakgvlpeilgdkeavldlvpvDyvan 255
                                   g   +i+ ++  + k++ p i+gd +++ d+v v  va+
  gi|15668384|ref|NP_247180.1| 179 GEAGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDVAK 217
                                   777778888888999999999999999888888877766 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   2.7e-18   4.4e-15       3     156 ..       2     175 ..       1     229 [. 0.88

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 2.7e-18
                                   EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHHHHH--SEEEE------HHHHH CS
                 RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre...............eldltdaeavaellkeakpdvvvnaAAytavDkaE 68 
                                   ilvtG+ G +Gs+++++l e++++v+ l++                ++d++d+  ++e ++ ++ +vv++ AA  +v +  
  gi|15668384|ref|NP_247180.1|   2 ILVTGGAGFIGSHIVDKLIENNYDVIILDNLttgnknninpkaefvNADIRDK-DLDEKINFKDVEVVIHQAAQINVRNSV 81 
                                   9**************************977789999********999999986.589999999****************** PP

                                   HSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEG.GGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH....H-SSE CS
                 RmlD_sub_bind  69 seeeaayavnaeavealAeaaaavga.lLihvStD.yVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla....agkka 143
                                   +++  +  +n+ ++ ++ e+ +++++ ++++ S+   V+   +  p  e+++ +Pl+ YG +K+ GE+ ++     +g ++
  gi|15668384|ref|NP_247180.1|  82 ENPVYDGDINVLGTINILEMMRKYDIdKIVFASSGgAVYGEPNYLPVDENHPINPLSPYGLSKYVGEEYIKLynrlYGIEY 162
                                   *************************95578887752666666788899**********************9855556679* PP

                                   EEEEE-SEESSSS CS
                 RmlD_sub_bind 144 livRtswvygekg 156
                                   +i+R s vyge++
  gi|15668384|ref|NP_247180.1| 163 AILRYSNVYGERQ 175
                                   **********954 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   4.8e-12   7.9e-09       1     147 [.       6     171 ..       6     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 4.8e-12
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHH..TT-SEEEES---TCCHHHH.. CS
                NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaeal..kgadaVvsalggggkdeeg.. 77 
                                   G+ G +G+++v++l+++ +++v +   n    ++   ++++e v +d+ d+ dl e +  k++++V+  +++ + ++ +  
  gi|15668384|ref|NP_247180.1|   6 GGAGFIGSHIVDKLIEN-NYDVII-LDNLTTGNKNNINPKAEFVNADIRDK-DLDEKInfKDVEVVIHQAAQINVRNSVen 83 
                                   99***************.6**965.5776666665668**********976.56666612677777777744333222244 PP

                                   ...........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHH...HCCHHHHHHHHHHHHHHHH....SSSEEEE CS
                NAD_binding_10  78 ...........aknivdaakeagvkRfvlvsaigvgdevpgefgewnk...ellkaylaakraaeellra....sgldwTi 140
                                              ++ni++ +++ ++ ++v+ s+ g+    p+ ++   +   + l++y   k+  ee+++      g+++ i
  gi|15668384|ref|NP_247180.1|  84 pvydgdinvlgTINILEMMRKYDIDKIVFASSGGAVYGEPNYLPVDENhpiNPLSPYGLSKYVGEEYIKLynrlYGIEYAI 164
                                   45677778899***********************98777887776665223467889899999999975544557999999 PP

                                   EEE-CEE CS
                NAD_binding_10 141 vrpggLt 147
                                   +r +   
  gi|15668384|ref|NP_247180.1| 165 LRYSNVY 171
                                   9988764 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   5.3e-07   0.00086       3     141 ..       2     120 ..       1     127 [. 0.63

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.3e-07
                                   EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE CS
                     adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvn 83 
                                   +lvtG+++ IG  i+++l++++++v+++d+        ++++   + ka ++++D++d++    l ek+  +++ ++v+++
  gi|15668384|ref|NP_247180.1|   2 ILVTGGAGFIGSHIVDKLIENNYDVIILDNLTTGN---KNNI---NPKAEFVNADIRDKD----LDEKI--NFKDVEVVIH 70 
                                   8**************************88775433...3333...457999999999865....33444..5666667666 PP

                                   ---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTS CS
                     adh_short  84 NAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkv 141
                                    A+  ++++   +++  ++   ++N+ g++++ ++    m k    +Iv+ sS  + +
  gi|15668384|ref|NP_247180.1|  71 QAAQINVRNS--VENPVYD--GDINVLGTINILEM----MRKYDIDKIVFASSGGAVY 120
                                   6666322222..2222222..35666666654433....3444555566666665555 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     1e-05     0.016       3     144 ..       2     123 ..       1     127 [. 0.74

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                                   EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                            KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    l+tGG+G +G ++++ l+e+    ++l   +      +k++       + + e+v+aD+ dkd  e+    i+  ++ ++
  gi|15668384|ref|NP_247180.1|   2 ILVTGGAGFIGSHIVDKLIENNYDVIILDNLT----TGNKNN------INPKAEFVNADIRDKDLDEK----IN--FKDVE 66 
                                   59*******************99999997666....223322......34577899999999886554....43..66788 PP

                                   EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--T CS
                            KR  84 GvihaAgvlr.dklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsa 144
                                    vih A  ++  + +e+   +         v G+ n+ e++++ ++d +v+ SS ++++g++
  gi|15668384|ref|NP_247180.1|  67 VVIHQAAQINvRNSVENPVYD-----GDINVLGTINILEMMRKYDIDKIVFASSGGAVYGEP 123
                                   899988776623444443333.....334577999999999999999999999999999986 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   4.5e-06    0.0073       1      73 [.       2      73 ..       2      88 .. 0.80
   2 ?    0.1   0.0      0.29   4.7e+02     162     226 ..     192     252 ..     150     260 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.5e-06
                                  EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHH.HTT-SEEEE--- CS
                          NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvea.lkgvdvvfsvtg 73
                                  Ilv+G++G +G+++v+ l++++++v +l  d  +   k+  +  +e+v++d+ dk++ +++ +k+v+vv+   +
  gi|15668384|ref|NP_247180.1|  2 ILVTGGAGFIGSHIVDKLIENNYDVIIL--DNLTTGNKNNINPKAEFVNADIRDKDLDEKInFKDVEVVIHQAA 73
                                  9************************887..33333444444566899999999999988866999999997765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.29
                                   TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHH.TTEEEEE-SEEE-HHHHHHHHHHHHT CS
                          NmrA 162 ppedkvtllgpgnpkavlldaeeDiGafvikilkdprkl.kgkriklagntlsgneivelfekkig 226
                                    ++++ ++ g+gn    ++  + D++++ + +l+ ++++ ++     +g++ s+ne+ ++++ +ig
  gi|15668384|ref|NP_247180.1| 192 LKNQSPIIFGDGNQTRDFV-YVGDVAKANLMALNWKNEIvNI----GTGKETSVNELFDIIKHEIG 252
                                   4455778889999888888.8899999888888755544222....24556677777777777666 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   5.6e-06    0.0091       5      67 ..       7      69 ..       2      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.6e-06
                                  S-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEE CS
                        TrkA_N  5 GlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadavi 67
                                  G+G +G++++++L e ++ dv++ d+     ++  + ++e+v++d  d+++ e+++ +++++vi
  gi|15668384|ref|NP_247180.1|  7 GAGFIGSHIVDKLIEnNY-DVIILDNLTTGNKNNINPKAEFVNADIRDKDLDEKINFKDVEVVI 69
                                  89*************555.7******999999999999***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1911.88
//
Query:       gi|15668385|ref|NP_247181.1|  [L=87]
Description: DNA/RNA-binding protein AlbA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-19   68.7   3.9    4.1e-19   68.2   3.9    1.3  1  Alba      Alba
    3.3e-05   23.9   0.4    3.9e-05   23.6   0.4    1.3  1  Rpp20     Rpp20 subunit of nuclear RNase MRP and P


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   3.9   4.6e-23   4.1e-19       1      66 [.       3      64 ..       3      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 4.6e-23
                                  CEEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEE CS
                          Alba  1 neiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltss 66
                                  n++ +++ +p+m+yv ++l++L   +++eV++ka+G+aI+kAv+vae++++rf+k+ ++++++ ++
  gi|15668385|ref|NP_247181.1|  3 NVVLIGK-KPVMNYVVAVLTQL--TSNDEVIIKARGKAINKAVDVAEMIRNRFIKD-IKIKKIEIG 64
                                  7999***.**************..99****************************87.*****9875 PP

>> Rpp20  Rpp20 subunit of nuclear RNase MRP and P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.4   4.4e-09   3.9e-05      58      98 ..      23      68 ..      13      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.4e-09
                         Rpp20 58 elkkeeVfvkatGrAiekalsvgrwfqeke.....eykvrvetgsV 98
                                    +++eV++ka G+Ai+ka+ v++  +++        k+++ t  V
  gi|15668385|ref|NP_247181.1| 23 LTSNDEVIIKARGKAINKAVDVAEMIRNRFikdikIKKIEIGTDKV 68
                                  56799******************99965532322244455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 581.98
//
Query:       gi|15668386|ref|NP_247182.1|  [L=149]
Description: hypothetical protein MJ_0213 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-37  127.2   3.7    3.9e-37  127.2   3.7    1.4  2  RNA_binding  RNA binding
  ------ inclusion threshold ------
      0.063   13.6   0.2       0.11   12.8   0.2    1.3  1  THOC7        Tho complex subunit 7


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.2   3.7   4.3e-41   3.9e-37       2     118 ..       5     126 ..       4     127 .. 0.96
   2 ?   -3.1   0.1         1   9.2e+03      12      23 ..     134     145 ..     130     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 127.2 bits;  conditional E-value: 4.3e-41
                                   EEEEEEE-TTC-HHHHHHHHHTTSTTS....E---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH..HHH CS
                   RNA_binding   2 ievrafvhaTEdeekVlealsnllpee....eveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei..keL 76 
                                   i+++a+vhaTEde+kVlea++ ++pe+    ++++++ e++G++gnpi+i+++++e+k+akk++k++++l++++++  ++L
  gi|15668386|ref|NP_247182.1|   5 IKLSAIVHATEDEDKVLEAIEFFIPENvdeeKIDLDVVETQGYFGNPIKIINVNVEGKEAKKIFKHIIDLIKSDDKniNKL 85 
                                   89***********************99**987788**************************************99999*** PP

                                   HHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEEE CS
                   RNA_binding  77 lkeleervdekgklylrldKQaaylgklslvegddvIkvkik 118
                                   +k+l  rv+ ++k+y+r+dKQ+aylg++++v+gdd+I+ +++
  gi|15668386|ref|NP_247182.1|  86 KKDLHLRVE-DNKFYVRFDKQKAYLGECRVVDGDDIIRAVFN 126
                                   *********.***************************98876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1
                                   C-HHHHHHHHHT CS
                   RNA_binding  12 EdeekVlealsn 23 
                                    +eekV+e ++n
  gi|15668386|ref|NP_247182.1| 134 NKEEKVKEIVAN 145
                                   568888877665 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.2e-05      0.11      11      57 ..      57     101 ..      52     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                         THOC7  11 v..eerplkrltkrllklltslaesteeeleqlkedllldfaafelsie 57 
                                   v  e ++ k++ k +  l++s    +++++ +lk+dl+l+++  ++ ++
  gi|15668386|ref|NP_247182.1|  57 VnvEGKEAKKIFKHIIDLIKS----DDKNINKLKKDLHLRVEDNKFYVR 101
                                   444999***************....69***************9998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 981.20
//
Query:       gi|15668387|ref|NP_247183.1|  [L=124]
Description: hydrogenase expression/formation protein HypA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-30  103.6   1.6    6.5e-30  103.4   1.6    1.0  1  HypA          Hydrogenase/urease nickel incorporation, metall
      0.003   17.3   2.9     0.0042   16.8   0.0    2.6  3  Cys_rich_KTR  Cysteine-rich KTR
  ------ inclusion threshold ------
      0.031   13.8   0.1      0.042   13.4   0.1    1.1  1  DUF4791       Domain of unknown function (DUF4791)
      0.045   13.9   2.8       0.12   12.5   2.8    1.7  1  Zn-ribbon_8   Zinc ribbon domain
      0.089   12.7   0.0      0.089   12.7   0.0    2.1  2  DUF3797       Domain of unknown function (DUF3797)
       0.13   12.0   0.7       0.25   11.2   0.7    1.4  1  HscB_4_cys    Co-chaperone HscB tetracysteine metal binding m


Domain annotation for each model (and alignments):
>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   1.6   2.2e-33   6.5e-30       1     111 [.       1     119 [.       1     120 [. 0.89

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 2.2e-33
                                   XCHHHHHHHHHHHHHHHH.CCTT......EEEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTT CS
                          HypA   1 MHElsiaesivevveeea.keaa....arkvtkvkvevGelsgvepeaLefafellaegtvlegaeLeieevpvkvrCreC 76 
                                   MHEls a++++e++ +++ ke++    ++kvt++++evGel+ ++ e+L+fafe++aegtv+ega++++e ++ k++C +C
  gi|15668387|ref|NP_247183.1|   1 MHELSYANAMLEAILNSIkKEEEkgkkIKKVTEINLEVGELTFINVEQLKFAFEVIAEGTVCEGAKINVEFIKPKCKCLDC 81 
                                   *******9999999988844432455588999************************************************* PP

                                   S-EEECHH.H..HHS-TTTSSS-EEEEESSSEEEEEEE CS
                          HypA  77 gkefelee.k..alrCpkCgsadveivsGeellvksie 111
                                   g+e+e e  +  ++ CpkC+s ++++ +G+e+++k+ +
  gi|15668387|ref|NP_247183.1|  82 GYEGEPEIlDefEVYCPKCKSIRLKLSGGKEFNIKNAT 119
                                   *****7765347789*******************9875 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.45   1.3e+03      37      46 ..      42      51 ..      40      59 .. 0.73
   2 ?   -1.9   0.3      0.99     3e+03      31      34 ..      74      77 ..      67      79 .. 0.82
   3 !   16.8   0.0   1.4e-06    0.0042      22      38 ..      89     105 ..      85     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.45
                  Cys_rich_KTR 37 tlinvkqlki 46
                                  t inv+qlk 
  gi|15668387|ref|NP_247183.1| 42 TFINVEQLKF 51
                                  6799999985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.99
                  Cys_rich_KTR 31 PKCk 34
                                  PKCk
  gi|15668387|ref|NP_247183.1| 74 PKCK 77
                                  8998 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 1.4e-06
                  Cys_rich_KTR  22 vLknfpLfCPKCkqetl 38 
                                   +L +f ++CPKCk   l
  gi|15668387|ref|NP_247183.1|  89 ILDEFEVYCPKCKSIRL 105
                                   799**********8655 PP

>> DUF4791  Domain of unknown function (DUF4791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.4e-05     0.042      21      54 ..      13      47 ..       3      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                       DUF4791 21 Glvralse.deeckkarevtssilevvpLplvNie 54
                                   +++++++ +e+ kk+++vt+  lev  L+ +N+e
  gi|15668387|ref|NP_247183.1| 13 AILNSIKKeEEKGKKIKKVTEINLEVGELTFINVE 47
                                  46778887456669********************8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.8     4e-05      0.12       7      36 ..      77     105 ..      75     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                   Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs.ev 36 
                                   +C +Cg e e+     d+ ++ CP+C+s ++
  gi|15668387|ref|NP_247183.1|  77 KCLDCGYEGEPEI--LDEFEVYCPKCKSiRL 105
                                   7*****9999775..3556677****99776 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.9       0.7   2.1e+03      14      18 ..      76      80 ..      60      84 .. 0.66
   2 ?   12.7   0.0     3e-05     0.089       9      30 ..      90     111 ..      89     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.7
                       DUF3797 14 vqCPe 18
                                  ++C +
  gi|15668387|ref|NP_247183.1| 76 CKCLD 80
                                  44544 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3e-05
                       DUF3797   9 LdekYvqCPeCgNnkvlNsegk 30 
                                   Lde  v+CP+C+ ++   s+gk
  gi|15668387|ref|NP_247183.1|  90 LDEFEVYCPKCKSIRLKLSGGK 111
                                   566669**********999997 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.7   8.2e-05      0.25       2      24 ..      77     101 ..      74     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.2e-05
                                   B-SSS--B--SS-S---..B-TTT- CS
                    HscB_4_cys   2 rCWnCGgpgapgrgdef..FCpqCR 24 
                                   +C  CG  g+p   def  +Cp+C 
  gi|15668387|ref|NP_247183.1|  77 KCLDCGYEGEPEILDEFevYCPKCK 101
                                   5899*******98888777*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 804.35
//
Query:       gi|15668388|ref|NP_247184.1|  [L=159]
Description: hypothetical protein MJ_0215 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-05   25.2   0.0    2.4e-05   24.5   0.0    1.3  1  PTPlike_phytase  Inositol hexakisphosphate
    0.00025   20.7   0.0    0.00038   20.1   0.0    1.3  1  Y_phosphatase    Protein-tyrosine phosphatase
    0.00035   20.4   0.0    0.00051   19.9   0.0    1.4  1  DSPc             Dual specificity phosphatase, catalytic doma


Domain annotation for each model (and alignments):
>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   4.1e-09   2.4e-05     105     151 ..      70     117 ..      61     119 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.1e-09
                                   EEE-TTS---HHHHHHHHHHHHTS.-TT-EEEEE-SSSSHHHHHHHHH CS
               PTPlike_phytase 105 ipitdekapeeedfdalvsilkea.pektalvfnCqmGrgRTTtamvi 151
                                   +pi+d + p+ ed+d +v+++k   ++++ +v++C  G gRT t++++
  gi|15668388|ref|NP_247184.1|  70 VPIEDYGIPTVEDMDLIVDFIKYHvSKEKEVVVSCIGGHGRTGTVLAV 117
                                   79*********************9999***************999875 PP

>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.4e-08   0.00038     145     199 ..      74     126 ..      69     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.4e-08
                                   SSSSG..SCCHHHHHHHHHHHHHHSTTSS-EEEECSSSSHHHHHHHHHHHHHHHHHH CS
                 Y_phosphatase 145 dhgvp..esaksllklirkvekskeaksgpvvVhCsaGvgRtgtfvaldillqqlea 199
                                   d g+p  e+ + ++++i+   +++    + vvV C+ G gRtgt++a+ + l+ +++
  gi|15668388|ref|NP_247184.1|  74 DYGIPtvEDMDLIVDFIKYHVSKE----KEVVVSCIGGHGRTGTVLAVWAGLNGIKN 126
                                   566775566677778888777777....9******************9999988887 PP

>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.6e-08   0.00051      42      94 ..      67     118 ..      54     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.6e-08
                                   EEEECCESSTTSCCGGGHHHHHHHHHHHHHTT-EEEEEESSSSSHHHHHHHHH CS
                          DSPc  42 klripvedehetkiskyleeavefidkakqkgkkvlVHCqaGisRSatliiaY 94 
                                    l +p+ed +   + ++++ +v+fi+   +k+k+v+V C  G  R++t+ + +
  gi|15668388|ref|NP_247184.1|  67 TLYVPIED-YGIPTVEDMDLIVDFIKYHVSKEKEVVVSCIGGHGRTGTVLAVW 118
                                   55677777.8888999*********************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1009.52
//
Query:       gi|15668389|ref|NP_247185.1|  [L=465]
Description: V-type ATP synthase subunit B [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-69  233.7   0.0    2.3e-69  233.3   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    2.8e-14   53.4   2.1    5.6e-14   52.4   2.1    1.6  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
      0.002   18.2   0.7     0.0061   16.7   0.7    1.8  1  HAS-barrel     HAS barrel domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.3   0.0   3.8e-73   2.3e-69       1     213 []     136     354 ..     136     354 .. 0.99

  Alignments for each domain:
  == domain 1  score: 233.3 bits;  conditional E-value: 3.8e-73
                                   SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrtvlva 76 
                                   Gi+++D + ++v+Gq++ i++++g++++++++++++q++ +    + a++++++G  ++e++ ++eef+++++++r v+++
  gi|15668389|ref|NP_247185.1| 136 GISTIDGMNTLVRGQKLPIFSGSGLPHNQLAAQIARQAKVRgegeKfAVVFAAMGITSEEANFFMEEFRKTGALERAVVFI 216
                                   899**********************************9888999868********************************** PP

                                   EETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  77 ntsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagkap 156
                                   n +++p+++r++++++++t+AEy+++ ++++vl+i++++++++eAlreis++ +e+p+++gyp+y++++la++yERag+++
  gi|15668389|ref|NP_247185.1| 217 NLADDPAIERILTPRIALTVAEYLAYeKDMHVLVILTDMTNYCEALREISAARNEVPGRRGYPGYMYTDLATIYERAGRVK 297
                                   *************************9999**************************************************** PP

                                   SSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 157 drtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                    rtG++t++++++++++D+++p+++ t +it+g+ivL+++l++++++P+++vl S+S
  gi|15668389|ref|NP_247185.1| 298 GRTGTITQIPILTMPDDDITHPIPDLTGYITEGQIVLSRELHRKGIYPPVDVLPSLS 354
                                   *******************************************************98 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   2.1   9.4e-18   5.6e-14       2      69 .]      14      79 ..      13      79 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 9.4e-18
                                  EEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBT.TSEEEEES CS
                 ATP-synt_ab_N  2 vqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsr.GteVkrTG 69
                                   ++ Gp+++ve+++g+++g+++ + ++  + g++++g++l+ +e+ ++v+v+++t+Gls   t+V++TG
  gi|15668389|ref|NP_247185.1| 14 KSIAGPLLIVEGVEGAAYGEIVEVICP--D-GEKRMGQVLEAREGLAVVQVFEGTTGLSTkDTRVRFTG 79
                                  689************************..9.*****************************9*******9 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.7     1e-06    0.0061       3      83 ..       8      74 ..       7      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-06
                    HAS-barrel  3 evigests.sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalatedt.. 82
                                  ++++++ s  +++  veg+++  +Ge Ve++ pdge++ G+v+  r+                       +++v++++e+t  
  gi|15668389|ref|NP_247185.1|  8 IEYSSVKSiAGPLLIVEGVEGAAYGEIVEVICPDGEKRMGQVLEARE-----------------------GLAVVQVFEGTtg 67
                                  6788888889*************************************.......................7777777777766 PP

                    HAS-barrel 83 ......g 83
                                        +
  gi|15668389|ref|NP_247185.1| 68 lstkdtR 74
                                  6666662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 2741.99
//
Query:       gi|15668390|ref|NP_247186.1|  [L=594]
Description: V-type ATP synthase subunit A [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-91  306.2   0.0    2.5e-91  305.1   0.0    1.6  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      2e-48  163.2   0.7      2e-48  163.2   0.7    1.7  2  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    2.6e-16   59.9   3.3    2.6e-16   59.9   3.3    3.0  2  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
    4.9e-05   23.2   1.9     0.0035   17.3   0.1    2.6  2  RnfC_N           RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.019   15.2   0.5        1.6    9.0   0.0    2.9  3  Peptidase_M23    Peptidase family M23
      0.081   12.8   0.0       0.22   11.4   0.0    1.7  1  Biotin_lipoyl_2  Biotin-lipoyl like
       0.11   12.7   0.0       0.32   11.3   0.0    1.7  1  AAA_22           AAA domain
       0.18   11.6   0.0       0.38   10.6   0.0    1.5  1  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
        1.4    8.8   7.8         31    4.5   4.9    3.4  2  Myosin_N         Myosin N-terminal SH3-like domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.1   0.0   1.2e-94   2.5e-91       1     213 []     221     444 ..     221     444 .. 0.98

  Alignments for each domain:
  == domain 1  score: 305.1 bits;  conditional E-value: 1.2e-94
                                   SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH.......SSGGGGEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxx RF
                   ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe.......gtimkrtvl 74 
                                   G+rv D++f++++G++ +ipg fg Gktv +++l+k+s++d +++y+g+Gergne++ev+eefp+       +++m+rtvl
  gi|15668390|ref|NP_247186.1| 221 GQRVEDTFFTLAKGGTAAIPGPFGSGKTVTQHQLAKWSDAD-VVVYIGCGERGNEMTEVIEEFPHledirtgNKLMDRTVL 300
                                   89***********************************9888.***********************999988666******* PP

                                   EEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  75 vantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagka 155
                                   +antsn+pvaareas+ytgit+AEyfrd+g+ vll ads+srwaeA+reis+rl+emp+++gypayl+++la++yERag++
  gi|15668390|ref|NP_247186.1| 301 IANTSNMPVAAREASVYTGITIAEYFRDMGYGVLLTADSTSRWAEAMREISGRLEEMPGEEGYPAYLASRLAQFYERAGRV 381
                                   ********************************************************************************* PP

                                   .....TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                   .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 156 .....pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                        ++r+G v iv avsp+ggDfs+pvt++tl+i+++f+ Ld +la+r+hfPain+l+S+S
  gi|15668390|ref|NP_247186.1| 382 itlgkDNRQGFVCIVGAVSPPGGDFSEPVTSNTLRIVKVFWALDANLARRRHFPAINWLQSYS 444
                                   ****9889******************************************************9 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       5.4   1.1e+04      67      97 ..      23      54 ..      16      59 .. 0.62
   2 !  163.2   0.7     1e-51     2e-48       1     121 []      92     212 ..      92     212 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.4
                                  --TT-EEE.EEEE--EEEE-TTSECEEECETT CS
               ATP-synt_ab_Xtn 67 vppkvegk.vkeiaeegeytvedtiaevetee 97
                                  v+ +++g  + e+++ ge +++  i+++++++
  gi|15668390|ref|NP_247186.1| 23 VAEGMKGAqMYEVVKVGEEKLTGEIIQLHDDK 54
                                  55555554466666677777777777766554 PP

  == domain 2  score: 163.2 bits;  conditional E-value: 1e-51
                                   EETTS-BHHHHHHHHTS.BE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEEE-- CS
               ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgs.fierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkvkeiae 80 
                                   yDGiqrpL++i+ek+gs fi+rGv+vpal r+ kwefkp v++gd v++gdi+Gtv+et +i hki+vp +v+gk++ei+ 
  gi|15668390|ref|NP_247186.1|  92 YDGIQRPLTAIEEKTGSiFIPRGVDVPALPRDIKWEFKPVVNEGDYVEEGDIIGTVDETPSIVHKILVPIGVKGKIVEIK- 171
                                   9******************************************************************************9. PP

                                   EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
               ATP-synt_ab_Xtn  81 egeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                   eg++tve+t+a+vete+g++ke+t++qkwPvrkprp+kekl
  gi|15668390|ref|NP_247186.1| 172 EGKFTVEETVAVVETENGERKEITMMQKWPVRKPRPYKEKL 212
                                   ***************************************97 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   3.3   1.3e-19   2.6e-16       1      69 []      14      76 ..      14      76 .. 0.98
   2 ?    0.6   0.5      0.43   8.6e+02       4      31 ..     163     188 ..     161     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 1.3e-19
                                  EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                 ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                  i+++ Gpvv +e+++g   ++y++++v+  e  ++l g++++l++dk++++v+++t+G+++G++V+ TG
  gi|15668390|ref|NP_247186.1| 14 IIKIAGPVVVAEGMKG--AQMYEVVKVG--E--EKLTGEIIQLHDDKAVIQVYEETSGIKPGEPVVGTG 76
                                  6799************..**********..8..9**********************************8 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.43
                                   EETTEEEEESSTSCETCTTEEEEECCET CS
                 ATP-synt_ab_N   4 viGpvvdvefgigrlpgiynalevelve 31 
                                   v G++v+++ g+  + +   ++e+e  +
  gi|15668390|ref|NP_247186.1| 163 VKGKIVEIKEGKFTVEETVAVVETE--N 188
                                   89******99999777777777766..4 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.014        29      38      75 ..      28      65 ..       3      68 .. 0.87
   2 !   17.3   0.1   1.7e-06    0.0035      35      97 ..     121     187 ..     103     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                        RnfC_N 38 iGapakplvkvgdkVlkGqkiaeaegfvsapvhasvsG 75
                                   Ga+   +vkvg++ l+G++i   +     +v+  +sG
  gi|15668390|ref|NP_247186.1| 28 KGAQMYEVVKVGEEKLTGEIIQLHDDKAVIQVYEETSG 65
                                  6899999***************9998779999999999 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.7e-06
                        RnfC_N  35 sqhiGapakplvkvgdkVlkGqkiaeaeg..fvsapvhas..vsGtVkaiekrlvahgsgveavvie 97 
                                    + i  + kp+v++gd+V++G++i++ ++   +  ++  +  v G++++i++ + + +++v  v  e
  gi|15668390|ref|NP_247186.1| 121 PRDIKWEFKPVVNEGDYVEEGDIIGTVDEtpSIVHKILVPigVKGKIVEIKEGKFTVEETVAVVETE 187
                                   566777899*****************998443444555553378*******9999988887776655 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.06   1.2e+02      23      63 ..      34      72 ..      27      79 .. 0.86
   2 ?    9.0   0.0   0.00079       1.6      57      75 ..     132     150 ..     127     158 .. 0.88
   3 ?   -3.4   0.0       6.1   1.2e+04      22      54 ..     165     199 ..     163     204 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.06
                                  EEEEEEEETTTEEEEEEEECTCEEEEEEEESEESS-TTEEE CS
                 Peptidase_M23 23 tVvfagkkegyGnvviidhgdgystlyahlskisvkegqkV 63
                                  +Vv++g+++ +G+++++ +++ ++++y   s   +k+g+ V
  gi|15668390|ref|NP_247186.1| 34 EVVKVGEEKLTGEIIQLHDDKAVIQVYEETSG--IKPGEPV 72
                                  59999998788****************99998..6666654 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00079
                                   S-TTEEE-TTCEEEEEBST CS
                 Peptidase_M23  57 vkegqkVkaGqvIGtvgst 75 
                                   v+eg++V++G++IGtv +t
  gi|15668390|ref|NP_247186.1| 132 VNEGDYVEEGDIIGTVDET 150
                                   99**************877 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6.1
                                   EEEEEEEEET.TT.EEEEEEEECTCEEEEEEEESE CS
                 Peptidase_M23  22 GtVvfagkke.gy.Gnvviidhgdgystlyahlsk 54 
                                   G++v++++ + ++  +v +++ ++g    +  ++k
  gi|15668390|ref|NP_247186.1| 165 GKIVEIKEGKfTVeETVAVVETENGERKEITMMQK 199
                                   77777766331443555555666666666666655 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.22      18      35 ..     132     149 ..     131     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
               Biotin_lipoyl_2  18 VkdGqrVkaGdvLaelDs 35 
                                   V +G++V++Gd++ + D 
  gi|15668390|ref|NP_247186.1| 132 VNEGDYVEEGDIIGTVDE 149
                                   88*************997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016      0.32       6      51 ..     235     272 ..     232     294 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst 51 
                                   g  ++ G+ G+GKT++  +l+++ d         ++vv ++ + + +
  gi|15668390|ref|NP_247186.1| 235 GTAAIPGPFGSGKTVTQHQLAKWSD---------ADVVvYIGCGERG 272
                                   66799******************95.........4444377776666 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019      0.38      49      95 ..     440     486 ..     432     521 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                                   -HHHHHHHHHHHHHHHTSGGGGT-SSSHHHHTTEEEESSHHHHHHHH CS
               Methyltrn_RNA_4  49 leaqrelverilehWtegagaeynpdRkealslvkvvesleealeei 95 
                                   l++    +++++e+W++++g + ++ R ea+sl++  ++l+e+++ +
  gi|15668390|ref|NP_247186.1| 440 LQSYSLYIDDVTEWWNTNTGPDWRQLRDEAMSLLQKEAELQEIVQLV 486
                                   5666677999********************************99866 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.22   4.3e+02      16      30 ..      45      59 ..      43      64 .. 0.87
   2 ?    4.5   4.9     0.016        31      14      29 ..     163     178 ..     163     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.22
                                  EEEEEEESSEEEEEE CS
                      Myosin_N 16 GeIkeeeGdkvtVet 30
                                  GeI+   +dk++++ 
  gi|15668390|ref|NP_247186.1| 45 GEIIQLHDDKAVIQV 59
                                  9**********9997 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.016
                                   EEEEEEEEESSEEEEE CS
                      Myosin_N  14 vkGeIkeeeGdkvtVe 29 
                                   vkG+I+e++ +k+tVe
  gi|15668390|ref|NP_247186.1| 163 VKGKIVEIKEGKFTVE 178
                                   89**********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 3762.60
//
Query:       gi|15668391|ref|NP_247187.1|  [L=98]
Description: V-type ATP synthase subunit F [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-21   75.9   2.3    2.7e-21   75.7   2.3    1.1  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit
     0.0046   16.7   0.2     0.0053   16.5   0.2    1.1  1  LUD_dom     LUD domain


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   2.3     3e-25   2.7e-21       1      89 [.       3      87 ..       3      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 3e-25
                                  EEEEESHHHHHHHHHTTCEEEE.CSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCSSSSEEEEESCSCCGGSH CS
                    ATP-synt_F  1 iavIGdedtvtgfrlaGvgeve.vtdeeeieealkelleredigiilitekiaeeirelideykeealPaileIPskegpyde 82
                                  ++v+Gd++t++gfrlaG+++v+ v+++ee+ +a++el+++e+i+ i+ite+iae i+++++++++    +i+eIP+k+g+ ++
  gi|15668391|ref|NP_247187.1|  3 VGVVGDRETAIGFRLAGLTDVYeVKNDEEAVKAINELANNENIAFIIITERIAESIKDKLKNINK----VIVEIPDKHGKLER 81
                                  79******************998899***************************************....**********8754 PP

                                  HCHHHHH CS
                    ATP-synt_F 83 ekdsvrk 89
                                    d v++
  gi|15668391|ref|NP_247187.1| 82 -IDPVKE 87
                                  .666666 PP

>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   5.9e-07    0.0053      13      70 ..      21      77 ..      17      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.9e-07
                       LUD_dom 13 aevyyaktaeealelilellkeksvvseggstdlgeiglapalhsgreevldlfeekl 70
                                  ++vy++k+ eea+++i el+  +++ +  + ++++e +  + l++ ++ + ++ ++ +
  gi|15668391|ref|NP_247187.1| 21 TDVYEVKNDEEAVKAINELANNENIAFIIITERIAESIK-DKLKNINKVIVEIPDKHG 77
                                  68***********************99999999999988.777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1386  (0.0773049); expected 358.6 (0.02)
Passed bias filter:                      779  (0.0434492); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 657.06
//
Query:       gi|15668392|ref|NP_247188.1|  [L=399]
Description: V-type ATP synthase subunit C [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-79  266.7   5.3    4.7e-79  266.3   5.3    1.1  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit
  ------ inclusion threshold ------
       0.26   11.3   0.9        2.3    8.2   0.1    2.8  3  DUF3926         Protein of unknown function (DUF3926)


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.3   5.3   5.2e-83   4.7e-79       1     335 [.      58     394 ..      58     395 .. 0.96

  Alignments for each domain:
  == domain 1  score: 266.3 bits;  conditional E-value: 5.2e-83
                                   HHHHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H.HHH CS
                vATP-synt_AC39   1 leArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgpsre 81 
                                   ++Ar+r ++++l++++++++L+++ sle+++ +L++tdYg++++++ +e  ++ ++ekal+  la+ +  +++++p+++++
  gi|15668392|ref|NP_247188.1|  58 VNARIRSKEAKLFDDAKLNELIESGSLEELVGLLEDTDYGQYVIEVMNELKDPVAVEKALDMYLADLYGLIYRISPDSAKK 138
                                   69********************************************999*****************************99* PP

                                   HHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SSSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHHHHHCC...- CS
                vATP-synt_AC39  82 fldyllyrydidNvklllrgklsgdldleeleeklhplgelsaldldklieaksveelyeallgtpyakyleealdeleet 162
                                   +l+++ +++di N+k+l+r+k+  +l++ee  + l+plg+++ ++l++l+e k+vee+++ l gt+y k+l+e l+++++t
  gi|15668392|ref|NP_247188.1| 139 VLKVFAKKFDIKNIKTLIRAKFV-GLSAEETYALLIPLGNIPVEKLKELAEVKTVEEVVRGLDGTEYFKILQEELSNYDQT 218
                                   ***********************.5888***************************************************** PP

                                   -SHHHHHHHHHHHHHHHHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T...--SS-.S--HHHHHH CS
                vATP-synt_AC39 163 gdleiienaLdkayledllkfckklggetaeilreilgfeiDlrniniilrskkygelskedrkkllipgg.slypeglea 242
                                    ++  +e aLdk+yle+l k + + g ++++i+re++g+ iD+ n+++il+ k +g ls e+  k+    g +l  ++l++
  gi|15668392|ref|NP_247188.1| 219 SNIIGFELALDKYYLESLRKTIMTEG-KEEDIFREFVGTIIDVENLKVILKGKADG-LSAEELSKYVTLTGyELADWKLKD 297
                                   *********************99555.5559***********************77.666666666666666********* PP

                                   HHTT-G.....GG.GGSSTSSTTGGGTT-...-S.HHHHHHHHHHHHHHHHHT.TTSSSTSTHHHHHHHHHHHHHHHHHHH CS
                vATP-synt_AC39 243 laeaedveellaalkyteygelleealee...agslksledaldealvkllkk.afrqqfsvgvfyaYlklkeqEirnlrw 319
                                   l++a  +e +l+ l+ t+y+e+l+ea+ee   ++s+ ++e+ald+  +++ kk + r++f+vg++++ +  ke E++nl++
  gi|15668392|ref|NP_247188.1| 298 LMSAGGIEGVLSGLEGTSYAEVLAEAMEEyekTKSIYAFEKALDKFVLEKGKKlSTRKPFGVGPIIGLIVSKELEVKNLKA 378
                                   ****************************9**8777********************************************** PP

                                   HHHHHHHT--SHHHHG CS
                vATP-synt_AC39 320 IaegiaqglpkekIre 335
                                   I++g+  +l +e+Ir 
  gi|15668392|ref|NP_247188.1| 379 IIKGKIENLKPEEIRS 394
                                   **************95 PP

>> DUF3926  Protein of unknown function (DUF3926)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.2   1.8e+03      14      21 ..     135     142 ..     133     145 .. 0.85
   2 ?    8.2   0.1   0.00026       2.3      20      31 ..     206     217 ..     203     220 .. 0.86
   3 ?   -1.9   0.0      0.36   3.2e+03      24      34 ..     277     287 ..     275     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.2
                       DUF3926  14 SAkkvLNI 21 
                                   SAkkvL +
  gi|15668392|ref|NP_247188.1| 135 SAKKVLKV 142
                                   9*****86 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00026
                       DUF3926  20 NILQEELSSymq 31 
                                    ILQEELS y q
  gi|15668392|ref|NP_247188.1| 206 KILQEELSNYDQ 217
                                   69*******987 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.36
                       DUF3926  24 EELSSymqEtt 34 
                                   EELS y   t+
  gi|15668392|ref|NP_247188.1| 277 EELSKYVTLTG 287
                                   9***9987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1281  (0.0714485); expected 358.6 (0.02)
Passed bias filter:                      848  (0.0472977); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2586.43
//
Query:       gi|15668393|ref|NP_247189.1|  [L=206]
Description: H+-transporting ATP synthase subunit E AtpE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-55  186.4  20.9    4.4e-55  186.2  20.9    1.0  1  vATP-synt_E     ATP synthase (E/31 kDa) subunit
     0.0049   17.3  17.6     0.0049   17.3  17.6    1.8  2  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
  ------ inclusion threshold ------
      0.078   13.2   1.0        1.6    9.0   0.1    2.5  2  DUF3253         Protein of unknown function (DUF3253)
       0.14   12.3  21.4       0.53   10.4  21.3    1.9  1  ATP-synt_B      ATP synthase B/B' CF(0)
       0.85    8.6   6.6        1.2    8.1   6.6    1.3  1  Emaravirus_P4   P4 movement protein of Emaravirus, and the 30
        1.5    8.2  26.5       0.21   11.0  22.5    1.7  2  DUF3552         Domain of unknown function (DUF3552)
        2.1    8.2   6.9         10    5.9   6.9    1.9  1  HrpE            HrpE/YscL/FliH and V-type ATPase subunit E
        2.2    8.4  23.3       0.16   12.0   8.7    2.6  3  DivIVA          DivIVA protein
        2.7    8.0  15.3        5.3    7.1  15.3    1.5  1  Pinin_SDK_memA  pinin/SDK/memA/ protein conserved region
        4.3    7.9  24.9         40    4.8  24.7    2.3  1  V-ATPase_G      Vacuolar (H+)-ATPase G subunit
          6    7.3  10.0        9.8    6.6  10.0    1.4  1  Bud13           Pre-mRNA-splicing factor of RES complex


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.2  20.9   2.7e-58   4.4e-55       1     199 []      12     206 .]      12     206 .] 0.99

  Alignments for each domain:
  == domain 1  score: 186.2 bits;  conditional E-value: 2.7e-58
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   vATP-synt_E   1 fIrqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevfeea 81 
                                   +I ++A+++A++I+++ae+e++++++k++ee+e++++e+++k eK+ae++k+++iS+a+++a++k+L+a+ee++e++++++
  gi|15668393|ref|NP_247189.1|  12 KILDDAKAEANKIISEAEAEKAKILEKAKEEAEKRKAEILKKGEKEAEMTKSRIISEAKLEAKKKLLEAKEEIIEMAINKL 92 
                                   699****************************************************************************** PP

                                   HHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCT.HCCCCCCHHCCSSSS--SEEEEESSEBTTSS CS
                   vATP-synt_E  82 ekkLaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveea.ldkaaeeykaktkkktvevagdeedfledvl 161
                                   +++L +++e+  eYk+ l kLi++++++l+++e+ivr++k+D+el++++ l+++++e++++tkk+tv+++g+      d++
  gi|15668393|ref|NP_247189.1|  93 KEELVKLPEQP-EYKDKLIKLIKDGAISLGGGELIVRLNKRDMELIDDStLWNLEKEVENATKKVTVLKKGEP----VDIA 168
                                   ***********.**********************************99889**********************....**** PP

                                   SEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                   vATP-synt_E 162 GGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                   GG+++e+adg  +++n+lea+++++l+ ++++i+++LF
  gi|15668393|ref|NP_247189.1| 169 GGCIIETADGLKSLDNSLEAIFNRNLNVIRARITEKLF 206
                                   *************************************9 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3  17.6     3e-06    0.0049      21      97 ..      14      91 ..       8      98 .. 0.85
   2 ?   -3.6   0.0       9.5   1.6e+04      17      26 ..     145     154 ..     143     158 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3e-06
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHCSHHHHHHH CS
                  V-ATPase_G_2 21 lEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqavr.kraearlqqAvel 97
                                  l++A+ ea++ +++Aeae a+il++A+++a++ +ae  ++ ++e ++ + ++ ++a+ ea++   ++ e+ ++ A+++
  gi|15668393|ref|NP_247189.1| 14 LDDAKAEANKIISEAEAEKAKILEKAKEEAEKRKAEILKKGEKEAEMTKSRIISEAKLEAKKKLlEAKEEIIEMAINK 91
                                  689*********************************************************875505555555666655 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.5
                                   HHHHHHHHHH CS
                  V-ATPase_G_2  17 LdqrlEaArk 26 
                                   L++ +E+A k
  gi|15668393|ref|NP_247189.1| 145 LEKEVENATK 154
                                   4555555554 PP

>> DUF3253  Protein of unknown function (DUF3253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.12     2e+02      44      65 ..      34      55 ..      15      62 .. 0.85
   2 ?    9.0   0.1   0.00097       1.6      54      72 ..     152     168 ..     147     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.12
                                  HHHHHHHHHHHTTSEEEEETTE CS
                       DUF3253 44 kvRevavrlaaaGeveilqkGk 65
                                  k+ e a + a++ + eil+kG+
  gi|15668393|ref|NP_247189.1| 34 KILEKAKEEAEKRKAEILKKGE 55
                                  677889999999999*****97 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00097
                                   HTTSEEEEETTEE--TTT- CS
                       DUF3253  54 aaGeveilqkGkvvdpatf 72 
                                   a+ +v++l+kG++vd+  +
  gi|15668393|ref|NP_247189.1| 152 ATKKVTVLKKGEPVDI--A 168
                                   5679***********9..3 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  21.3   0.00032      0.53      50     129 ..      15      94 ..       7      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                    ATP-synt_B  50 aallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqekdralaeLreqvvalavqiaek 129
                                   + ++aea +   eA+ae a+i ++Ak+eaek k+ei ++ e+eae +k+    e + e ++ l e +e++ ++a+++ ++
  gi|15668393|ref|NP_247189.1|  15 DDAKAEANKIISEAEAEKAKILEKAKEEAEKRKAEILKKGEKEAEMTKSRIISEAKLEAKKKLLEAKEEIIEMAINKLKE 94 
                                   56778888888888888888888888888888888888888888888888888888888888888888888888887765 PP

>> Emaravirus_P4  P4 movement protein of Emaravirus, and the 30K superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.6   0.00075       1.2     246     345 ..      20     120 ..       6     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00075
                 Emaravirus_P4 246 isnaliwgsdqglnkvkaklkedtss.stlllidsekrveaiklkliqdeiseakaklsealagidlaiieaakaklvavl 325
                                    +n++i  ++    k+ +k ke+++   + +l+  ek  e  k + i +   eak kl ea   i   +i+  k +lv + 
  gi|15668393|ref|NP_247189.1|  20 EANKIISEAEAEKAKILEKAKEEAEKrKAEILKKGEKEAEMTKSRIISEAKLEAKKKLLEAKEEIIEMAINKLKEELVKLP 100
                                   57899999999999**9**999987625789*******************************9999999999999999877 PP

                 Emaravirus_P4 326 rkynlaenvseeteegyvki 345
                                   ++ +   ++ + +++g + +
  gi|15668393|ref|NP_247189.1| 101 EQPEYKDKLIKLIKDGAISL 120
                                   76666666666666666655 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0  22.5   0.00013      0.21      23     133 ..       8     110 ..       2     115 .. 0.84
   2 ?   -3.0   0.1       2.4   3.9e+03     119     127 ..     146     154 ..     128     162 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                       DUF3552  23 kiaekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreelekelkerrnelqrlekRllqkeetLdrkeeslek 103
                                   ki+ k +++A++eA+kii+eA    ea k ++l +akee+ k ++e+   lk+ ++e +    R+++ e +L+ k++ le 
  gi|15668393|ref|NP_247189.1|   8 KIKSKILDDAKAEANKIISEA----EAEKAKILEKAKEEAEKRKAEI---LKKGEKEAEMTKSRIIS-EAKLEAKKKLLEA 80 
                                   677888999*********875....6778889999*********999...67778888888899996.899********** PP

                       DUF3552 104 keesleekekelkqkeqsleekeeeleelv 133
                                   kee +e   ++lk++  +l e+ e  ++l+
  gi|15668393|ref|NP_247189.1|  81 KEEIIEMAINKLKEELVKLPEQPEYKDKLI 110
                                   *******99999999999888877766665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.4
                       DUF3552 119 eqsleekee 127
                                   e+++e+  +
  gi|15668393|ref|NP_247189.1| 146 EKEVENATK 154
                                   222222222 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   6.9    0.0064        10      33      93 ..      11      67 ..       3      95 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0064
                          HrpE 33 rellaeArlqAeqllaqarekaeellevaveqAeaqFWeqAnalLrglqqeRealeeqllt 93
                                   ++l++A+  A++++ +a+  + ++le+a e+Ae++   +A ++L++  +e e  + ++++
  gi|15668393|ref|NP_247189.1| 11 SKILDDAKAEANKIISEAEAEKAKILEKAKEEAEKR---KA-EILKKGEKEAEMTKSRIIS 67
                                  689****************999999**9***99985...33.4555555555555555554 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   8.7   9.9e-05      0.16      74     116 ..       8      50 ..       2      54 .. 0.88
   2 ?    3.9   4.9     0.033        54      80     117 ..      55      90 ..      48     103 .. 0.73
   3 ?   -3.4   0.0       5.7   9.4e+03      46      54 ..     147     155 ..     139     161 .. 0.44

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.9e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        DivIVA  74 etaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeei 116
                                   ++  ++   ak+ea+ ii+eAe+++ ki+e+a+eea+k ++ei
  gi|15668393|ref|NP_247189.1|   8 KIKSKILDDAKAEANKIISEAEAEKAKILEKAKEEAEKRKAEI 50 
                                   667788899****************************998886 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.033
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        DivIVA  80 kanakkeaeliikeAekkaekiveeaeeeakkiaeeie 117
                                    ++a+   + ii+eA+ +a+k + ea+ee+ ++a+  +
  gi|15668393|ref|NP_247189.1|  55 EKEAEMTKSRIISEAKLEAKKKLLEAKEEIIEMAI--N 90 
                                   45666677778999999999999999998877654..3 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 5.7
                                   HHHHCCCCT CS
                        DivIVA  46 ekvkeleek 54 
                                   ++v+++++k
  gi|15668393|ref|NP_247189.1| 147 KEVENATKK 155
                                   222222222 PP

>> Pinin_SDK_memA  pinin/SDK/memA/ protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  15.3    0.0032       5.3      21      87 ..      17      83 ..      11     109 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0032
                Pinin_SDK_memA 21 fkkeeekqk...ekeerraeiekrleekakeekeeleerkrekreeleeerraeqkelraleeklelkel 87
                                  +k+e++  k   e+e+ +a+i ++++e+a+++k+e+  +k ek++e+++ r + +++l+a+ + le+ke+
  gi|15668393|ref|NP_247189.1| 17 AKAEAN--KiisEAEAEKAKILEKAKEEAEKRKAEI-LKKGEKEAEMTKSRIISEAKLEAKKKLLEAKEE 83
                                  444443..3347888999999999999999999999.566678899999999999999666555544332 PP

>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  24.7     0.025        40      11      94 ..      16      97 ..      10      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.025
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHH CS
                    V-ATPase_G 11 qAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgseeelekkieketeekikelkesvkknkeav 93
                                  +A  eA++i++eA  +kak l +AkeeAek  +e  +k eke +  +++ +++ +  +kk   e++e+i e+  +++k ke+ 
  gi|15668393|ref|NP_247189.1| 16 DAKAEANKIISEAEAEKAKILEKAKEEAEKRKAEILKKGEKEAEMTKSRIISEAKLEAKKKLLEAKEEIIEM--AINKLKEEL 96
                                  6889***************************99999999999999999999998888888888888888665..455666655 PP

                                  H CS
                    V-ATPase_G 94 v 94
                                  v
  gi|15668393|ref|NP_247189.1| 97 V 97
                                  5 PP

>> Bud13  Pre-mRNA-splicing factor of RES complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  10.0     0.006       9.8       8      67 ..      21      80 ..      13     110 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.006
                         Bud13  8 tgrkidleekreaeaekkkkeeeekeekkkewgkGlvqkeekekrleelekekkkp.lary 67
                                    ++i+ +e+++a+  +k+ke e++++k++  +kG+++ e++++r+ +++k ++k+ l + 
  gi|15668393|ref|NP_247189.1| 21 ANKIISEAEAEKAKILEKAKE-EAEKRKAEILKKGEKEAEMTKSRIISEAKLEAKKkLLEA 80
                                  567888888664555554444.44677777899********99998776665554414332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2678  (0.149367); expected 358.6 (0.02)
Passed bias filter:                      873  (0.0486921); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 1291.96
//
Query:       gi|15668394|ref|NP_247190.1|  [L=220]
Description: V-type ATP synthase subunit K [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      5e-49  164.5  50.6    4.7e-17   62.1  10.8    3.2  3  ATP-synt_C  ATP synthase subunit C


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1  10.8   2.6e-21   4.7e-17       2      60 .]      11      69 ..      10      69 .. 0.98
   2 !   57.7  11.7     6e-20   1.1e-15       1      60 []      82     140 ..      82     140 .. 0.98
   3 !   57.2  12.2   8.5e-20   1.5e-15       1      60 []     157     215 ..     157     215 .. 0.99

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 2.6e-21
                                  HHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_C  2 gaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60
                                  gaglavG+++lgsGig G++g++g++ va++p+ f+++++++a++ +++lyg++va+++
  gi|15668394|ref|NP_247190.1| 11 GAGLAVGIAGLGSGIGAGITGASGAGVVAEDPNKFGTAIVFQALPQTQGLYGFLVAILI 69
                                  9********************************************************98 PP

  == domain 2  score: 57.7 bits;  conditional E-value: 6e-20
                                   HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_C   1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60 
                                   ++agla Gl++l s+ig+G+a+sag++ava++ ++f+k++++ +++e++a+ygL++a++l
  gi|15668394|ref|NP_247190.1|  82 FAAGLAAGLAGL-SAIGQGIAASAGLGAVAEDNSIFGKAMVFSVLPETQAIYGLLIAILL 140
                                   79*********9.*********************************************97 PP

  == domain 3  score: 57.2 bits;  conditional E-value: 8.5e-20
                                   HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_C   1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60 
                                   lgag+avG+++l sGig+G++++++i+a+ar+p++++k l++++++e+ a++gL++a+++
  gi|15668394|ref|NP_247190.1| 157 LGAGFAVGFAGL-SGIGQGITAAGAIGATARDPDAMGKGLVLAVMPETFAIFGLLIAILI 215
                                   7**********9.*********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1596.35
//
Query:       gi|15668395|ref|NP_247191.1|  [L=695]
Description: V-type ATP synthase subunit I [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-33  116.0   5.8    6.8e-18   64.0   0.0    2.8  3  V_ATPase_I  V-type ATPase 116kDa subunit family
    0.00034   19.6  14.5    0.00034   19.6  14.5    1.7  2  DctM        Tripartite ATP-independent periplasmic transporte
  ------ inclusion threshold ------
      0.021   14.8   6.7        3.3    7.7   0.2    3.1  3  Laminin_II  Laminin Domain II
       0.38   10.8   5.5        1.3    9.1   0.4    2.6  2  UPF0242     Uncharacterised protein family (UPF0242) N-termin
       0.52   10.8   2.9        4.4    7.8   0.2    2.5  2  DUF16       Protein of unknown function DUF16
       0.62   10.5   9.5       0.12   12.7   1.3    3.2  3  FlaC_arch   Flagella accessory protein C (FlaC)
       0.93    9.9   8.2        2.3    8.7   0.8    2.9  3  V-SNARE     Vesicle transport v-SNARE protein N-terminus
        1.1    9.2   6.6        5.3    7.0   0.2    2.8  3  Takusan     Takusan
        5.7    6.8   8.7        5.3    6.9   0.6    3.1  3  CdvA        CdvA-like coiled-coil domain


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   3.4e-21   6.8e-18      71     452 ..      74     442 ..      20     459 .. 0.75
   2 ?   -4.1   4.1       1.3   2.6e+03     515     560 ..     500     545 ..     495     551 .. 0.85
   3 !   53.4   0.3   5.5e-18   1.1e-14     715     812 ..     596     687 ..     588     688 .. 0.79

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 3.4e-21
                    V_ATPase_I  71 ldeleeelekleeelkelnenleklkkelnelvelkavlekakefleeeeeeeeeeeseeeeeekeeeeeeeseeeeeeel 151
                                   + ++ ++++++e+++k++  n + ++k++ +   +++v+  a+++l+e ++e +   +  + +e ++++++         l
  gi|15668395|ref|NP_247191.1|  74 ILDMFSSVSQKETSIKDIL-NPKPVEKKKVSFNSYQEVIDYAEKVLNEISKEVDGPAE--RLSELDNKKSK---------L 142
                                   4445555556666665554.34556666666677777777777777644222222111..11111111111.........1 PP

                    V_ATPase_I 152 leeeee...................lsfvaGvikrekveaferilwralrgnl.flrqaeieepledpetgekveksvfii 212
                                   l+ +e+                   + + aG +++ek+ +++  l ++  g + +++ +e+e+   d+      +  v i+
  gi|15668395|ref|NP_247191.1| 143 LQLKEQisylkglefdlkylgsgeyVFIGAGSVPKEKLGELKAELDKVADGYIgIFSGSEFEK---DK------KIRVPIV 214
                                   111111223334445666666655433369*********************983445556666...33......4457777 PP

                    V_ATPase_I 213 ffqgeqlkekikkicesfgaklyelpeseeereeklkeveeriedlekvleqteealkevleeiakeleewklkvkkekai 293
                                   f++ ++  e +   +  f+ + y++++ e + +e+l+++e++++ +e+  ++  e+lk++ +++ kel ++   ++ eka 
  gi|15668395|ref|NP_247191.1| 215 FVTLKEKLENVLSEIRKFEFERYDISDVEGTPSEALSKIESELKAIESERNSLIEKLKALAQKWEKELLAVYELLSIEKAR 295
                                   77765555555555678***************************************************************9 PP

                    V_ATPase_I 294 yhtLnlfnldvtkkvliaegWvpkeeleeiqkalkeateessssvpsilneietketpPTyfrtnkfteafQeivdaYGia 374
                                    ++   f   +t+++++ e+Wvp+++ e+ ++ +++     +    +i++  e +e+ P      k+ + f  + + Y+ +
  gi|15668395|ref|NP_247191.1| 296 GDAYSQF--GKTDRTYYIEAWVPARDAEKAKSLIENSA--DGFAFVEITEPDEPEEKIPVLLDNPKVIKPFEMLTEMYALP 372
                                   9999999..78899******************999965..66788889988888999************************ PP

                    V_ATPase_I 375 rYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvlkekklkkkkkdeilemlfsgRYiillmGlfsiYtGli 452
                                   +Y+Ev p+l+ +  F   +++M  D+  Glll++++l++  k  k+         e + +  Yi++l G+  + +G+i
  gi|15668395|ref|NP_247191.1| 373 KYNEVDPTLLLVPGFLLFYGIMLTDAVYGLLLTIIGLFIWKKIGKV--------SEGANKLGYILTLAGISTVIMGII 442
                                   ************************************9976544444........456677888888888888888887 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 1.3
                    V_ATPase_I 515 lsvilGviqMlfgvllslvNalyfkkkldiilefiPqllfllsifg 560
                                   +s+ +G+i++l+g+++ + +++   ++ d +++    +l++lsif+
  gi|15668395|ref|NP_247191.1| 500 FSIFVGLIHLLIGLFVGFKENVKRGNMGDAFINQGVWILLILSIFV 545
                                   699***************9999999999999887777777777775 PP

  == domain 3  score: 53.4 bits;  conditional E-value: 5.5e-18
                    V_ATPase_I 715 gciSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavltvavLllmeglsafLHaLRLhWVE 795
                                   g + n  SY RL AL LA   L+  +  ++++k + +  s+  + ++v ++++ +  t+    +m+gl af+H+LRLh VE
  gi|15668395|ref|NP_247191.1| 596 GFLGNVLSYARLLALCLATGGLAMAV--NIMAKLVGE--SIPVIGIIVAIIILLVGHTFN--FVMNGLGAFIHSLRLHYVE 670
                                   5667888***************9765..566663333..333333345555566667776..68***************** PP

                    V_ATPase_I 796 fqsKFykgdGykFepfs 812
                                   f s Fy+g G kF+pf+
  gi|15668395|ref|NP_247191.1| 671 FFSQFYEGGGKKFSPFK 687
                                   ****************7 PP

>> DctM  Tripartite ATP-independent periplasmic transporter, DctM component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.6      0.73   1.5e+03     175     194 ..     383     402 ..     379     451 .. 0.51
   2 !   19.6  14.5   1.7e-07   0.00034     217     332 ..     536     652 ..     479     657 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.73
                          DctM 175 iipglllavglllavaiaak 194
                                   ++pg+ll+ g++l+ a++  
  gi|15668395|ref|NP_247191.1| 383 LVPGFLLFYGIMLTDAVYGL 402
                                   45666666666655554443 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.7e-07
                          DctM 217 ipalllplii.ligillgiftpteagavavvyalviallvyrrltleevaaallstakttaavlfilaaagifaglltltg 296
                                   +  l+l +++ ++ +++g+ t + +g ++++ +l+i + +y+  + + v++a+l ++ +t+++  +l  a+++a+ l++ g
  gi|15668395|ref|NP_247191.1| 536 WILLILSIFVgIGLMFAGANTMIAGGIIGIFVVLAILASMYKGYKSGGVMEAILGAMDVTGFLGNVLSYARLLALCLATGG 616
                                   334444444438889****************************************************************** PP

                          DctM 297 vplklselllslsggkllfLilvnllvlvlGmfldt 332
                                   +++++  ++  ++++  ++ i+v++++l++G   ++
  gi|15668395|ref|NP_247191.1| 617 LAMAVNIMAKLVGESIPVIGIIVAIIILLVGHTFNF 652
                                   ****987777777777889999********987766 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.17   3.5e+02      56      84 ..      59      87 ..      34      94 .. 0.83
   2 ?    7.4   0.7    0.0021       4.2      43      97 ..     100     154 ..      94     155 .. 0.88
   3 ?    7.7   0.2    0.0017       3.3      22      84 ..     218     280 ..     209     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.17
                                  XXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                    Laminin_II 56 dArrsvkkLeklapqLldklkelkqleea 84
                                  d  r+v  L  +a ++ld ++++ q+e  
  gi|15668395|ref|NP_247191.1| 59 DYVRNVTSLMIKAGRILDMFSSVSQKETS 87
                                  5568999999**************99987 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0021
                                   XXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHH CS
                    Laminin_II  43 tnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseike 97 
                                    +   ++++++i+ A++   ++ k+++   ++l+el++++++   l+++is +k 
  gi|15668395|ref|NP_247191.1| 100 KKVSFNSYQEVIDYAEKVLNEISKEVDGPAERLSELDNKKSKLLQLKEQISYLKG 154
                                   44556799**********************************999*****99986 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0017
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                    Laminin_II  22 lsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                   l+++len+ +++ +++ +   + ++    ++a+   +++ k +e + + L++klk l q+ e+
  gi|15668395|ref|NP_247191.1| 218 LKEKLENVLSEIRKFEFERYDISDVEGTPSEALSKIESELKAIESERNSLIEKLKALAQKWEK 280
                                   67889999999999999988888888899****************************998765 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.7     0.038        76      41     118 ..      67     148 ..      38     157 .. 0.72
   2 ?    9.1   0.4   0.00065       1.3      84     155 ..     215     300 ..     195     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.038
                       UPF0242  41 llaaaGsLl.llllllkwekalkeklekskleekeaklteldeglktkeealeelqeeeeeLkee...ldakeeelerlke 117
                                   l++ aG +l +++++ + e+ +k  l+ + +e+k+    + +e ++  e+ l+e  +e +  +e+   ld+k+++l +lke
  gi|15668395|ref|NP_247191.1|  67 LMIKAGRILdMFSSVSQKETSIKDILNPKPVEKKKVSFNSYQEVIDYAEKVLNEISKEVDGPAERlseLDNKKSKLLQLKE 147
                                   777788776245556666777777778888888888888888889988888888888876555542226666666666666 PP

                       UPF0242 118 e 118
                                   +
  gi|15668395|ref|NP_247191.1| 148 Q 148
                                   5 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00065
                       UPF0242  84 lktkeealeelqeeeeeLkee..............ldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqel 150
                                   + t +e+le++ +e ++ + e              l++ e+el+  + e ++L ekl+a a+  e+ +l++ e L  ++ +
  gi|15668395|ref|NP_247191.1| 215 FVTLKEKLENVLSEIRKFEFErydisdvegtpseaLSKIESELKAIESERNSLIEKLKALAQKWEKELLAVYELLSIEKAR 295
                                   557788899999998888888899999999999999*****************************9999999999888877 PP

                       UPF0242 151 lqeyq 155
                                    + y 
  gi|15668395|ref|NP_247191.1| 296 GDAYS 300
                                   77665 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3     0.092   1.8e+02      44      83 ..      98     137 ..      72     157 .. 0.54
   2 ?    7.8   0.2    0.0022       4.4       2      83 ..     198     304 ..     197     311 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.092
                                   H...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....... CS
                         DUF16  44 dklgeqinkleqkvekqgekikelkveqkaqgeelnkvde 83 
                                   +k+++++n  ++ ++  ++ ++e+++e++   e+l ++d+
  gi|15668395|ref|NP_247191.1|  98 EKKKVSFNSYQEVIDYAEKVLNEISKEVDGPAERLSELDN 137
                                   3444444444444444444444444444444444442222 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0022
                                   XXXXXXXXXXX.X.XTTB-BHHHHHHB-...........................BHHHHHHHHHHHH...HHHHHHHHHH CS
                         DUF16   2 fsGsfneivKkiPvkteYVTrkqlnefkds.........................nkqrLkkieakvdklgeqinkleqkv 57 
                                   fsGs  e  Kki v+  +VT k+  e   s                          + +Lk ie + ++l e++++l+qk 
  gi|15668395|ref|NP_247191.1| 198 FSGSEFEKDKKIRVPIVFVTLKEKLENVLSeirkfeferydisdvegtpsealskIESELKAIESERNSLIEKLKALAQKW 278
                                   566444455666777888888875442222244444556677788888777777677888888888889999999999999 PP

                                   HHHHHHHHHHHHHHHHHHH....... CS
                         DUF16  58 ekqgekikelkveqkaqgeelnkvde 83 
                                   ek    + el    ka+g++  + ++
  gi|15668395|ref|NP_247191.1| 279 EKELLAVYELLSIEKARGDAYSQFGK 304
                                   99999999999999998887665554 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3      0.19   3.8e+02      16      45 ..     111     147 ..      97     153 .. 0.58
   2 ?   -3.6   0.0       7.7   1.5e+04       7      16 ..     220     229 ..     217     240 .. 0.51
   3 ?   12.7   1.3   6.2e-05      0.12       8      48 ..     249     290 ..     247     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.19
                     FlaC_arch  16 letvkkeneelsksveelkenV.......kdllsLYE 45 
                                   ++ ++k ++e+sk+v+   e+         +ll+L E
  gi|15668395|ref|NP_247191.1| 111 IDYAEKVLNEISKEVDGPAERLseldnkkSKLLQLKE 147
                                   5666677777777776544444444443355555555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.7
                     FlaC_arch   7 nklsklstel 16 
                                   +kl+++ +e+
  gi|15668395|ref|NP_247191.1| 220 EKLENVLSEI 229
                                   3333333333 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 6.2e-05
                     FlaC_arch   8 klsklsteletvkkeneelsksveelkenV.kdllsLYEvVs 48 
                                    lsk+++el+ +++e ++l ++++ l ++  k+ll++YE  s
  gi|15668395|ref|NP_247191.1| 249 ALSKIESELKAIESERNSLIEKLKALAQKWeKELLAVYELLS 290
                                   699***************************9********988 PP

>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.8    0.0011       2.3      14      73 ..      91     152 ..      78     154 .. 0.82
   2 ?   -2.0   0.0       2.4   4.7e+03      60      75 ..     177     192 ..     177     194 .. 0.83
   3 ?    4.6   0.3     0.021        43      39      72 ..     248     280 ..     246     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                       V-SNARE  14 rlsslageerkaalreiekkldeaeelldqMelEvrnlps..serasykaklreykselkkl 73 
                                    l++++ e++k   + +++ +d ae++l++ + Ev + +   se ++ k+kl + k ++  l
  gi|15668395|ref|NP_247191.1|  91 ILNPKPVEKKKVSFNSYQEVIDYAEKVLNEISKEVDGPAErlSELDNKKSKLLQLKEQISYL 152
                                   45688889****************************99555799999999999998887655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.4
                       V-SNARE  60 kaklreykselkklkk 75 
                                   k+kl e k+el+k+ +
  gi|15668395|ref|NP_247191.1| 177 KEKLGELKAELDKVAD 192
                                   6899999999999876 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.021
                       V-SNARE  39 elldqMelEvrnlpsserasykaklreykselkk 72 
                                   e l++ e E++ +  ser+s+ +kl+   ++++k
  gi|15668395|ref|NP_247191.1| 248 EALSKIESELKAIE-SERNSLIEKLKALAQKWEK 280
                                   7899999****999.***********99998876 PP

>> Takusan  Takusan
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.3   6.6e+03      16      29 ..     177     190 ..     175     191 .. 0.87
   2 ?    7.0   0.2    0.0027       5.3      15      37 ..     218     240 ..     216     242 .. 0.89
   3 ?    4.8   0.5     0.013        25      17      46 ..     248     277 ..     242     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.3
                       Takusan  16 kkklEeLkleLrki 29 
                                   k+kl eLk eL k+
  gi|15668395|ref|NP_247191.1| 177 KEKLGELKAELDKV 190
                                   7999******9987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0027
                       Takusan  15 akkklEeLkleLrkitreRdELr 37 
                                   +k+klE++++e+rk + eR +  
  gi|15668395|ref|NP_247191.1| 218 LKEKLENVLSEIRKFEFERYDIS 240
                                   689****************8876 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.013
                       Takusan  17 kklEeLkleLrkitreRdELrdiLalyteg 46 
                                   + l ++ +eL+ i++eR+ L + L    ++
  gi|15668395|ref|NP_247191.1| 248 EALSKIESELKAIESERNSLIEKLKALAQK 277
                                   67788999************9999876655 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.5     0.027        53       3      42 ..     115     153 ..     106     155 .. 0.85
   2 ?   -2.5   0.0       2.1   4.2e+03      23      35 ..     218     230 ..     215     235 .. 0.49
   3 ?    6.9   0.6    0.0027       5.3      25      59 ..     251     285 ..     244     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.027
                          CdvA   3 kkALeeLvsegdipkstyeeikekleealkklkekakelk 42 
                                   +k+L+e+++e d+p+++ +e+  k +++l +lke+ + lk
  gi|15668395|ref|NP_247191.1| 115 EKVLNEISKEVDGPAERLSELDNK-KSKLLQLKEQISYLK 153
                                   588999999999999999999988.677888888877665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.1
                          CdvA  23 ikekleealkklk 35 
                                   +kekle+ l++++
  gi|15668395|ref|NP_247191.1| 218 LKEKLENVLSEIR 230
                                   3344444444333 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0027
                          CdvA  25 ekleealkklkekakelkeklkkrlkeledqiksl 59 
                                    k+e++lk+++ +++ l+eklk+  ++ e+++ ++
  gi|15668395|ref|NP_247191.1| 251 SKIESELKAIESERNSLIEKLKALAQKWEKELLAV 285
                                   699********************999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (695 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1228  (0.0684924); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 4570.86
//
Query:       gi|15668396|ref|NP_247192.1|  [L=104]
Description: hypothetical protein MJ_0223 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00017   21.5   7.2     0.0002   21.3   7.2    1.1  1  HrpE            HrpE/YscL/FliH and V-type ATPase subunit E
     0.0026   17.8  30.2       0.12   12.5  17.7    1.9  2  ATP-synt_B      ATP synthase B/B' CF(0)
  ------ inclusion threshold ------
      0.012   15.7  25.9       0.27   11.3   5.0    2.0  2  DivIVA          DivIVA protein
      0.015   15.7  29.8       0.07   13.6  29.8    1.8  1  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
       0.13   12.5  11.8      0.077   13.2   9.5    1.7  2  Ribosomal_L22   Ribosomal protein L22p/L17e
       0.16   11.4  22.0       0.18   11.2  22.0    1.0  1  GBP_C           Guanylate-binding protein, C-terminal domain
       0.26   11.0   4.5       0.27   10.9   4.5    1.0  1  DUF3492         Domain of unknown function (DUF3492)
        0.3   11.0  20.0        0.4   10.6  20.0    1.2  1  RRF             Ribosome recycling factor
       0.42   11.1  16.5        2.2    8.8  16.4    1.9  1  GlutR_dimer     Glutamyl-tRNAGlu reductase, dimerisation doma
       0.54    9.7  31.4        2.9    7.2  17.0    2.3  2  DUF3552         Domain of unknown function (DUF3552)
       0.61    9.1  12.6        1.1    8.2  12.6    1.5  1  RapA_C          RNA polymerase recycling family C-terminal
       0.63    9.9  10.3       0.73    9.6  10.3    1.0  1  PIN_8           PIN like domain
       0.78    9.6   5.5        0.9    9.4   5.5    1.0  1  FdhE            Protein involved in formate dehydrogenase for
       0.92    9.2   9.8        1.1    9.0   9.8    1.2  1  zf-CpG_bind_C   CpG binding protein zinc finger C terminal do
       0.97    8.6  16.1        1.4    8.1  16.1    1.2  1  ISG65-75        Invariant surface glycoprotein
        1.1    9.4  17.2       0.84    9.8   2.9    2.8  2  CinA_KH         Damage-inducible protein CinA KH domain
        1.2    7.7   8.4        1.3    7.7   8.4    1.0  1  Prismane        Prismane/CO dehydrogenase family
        1.6    8.6  13.5        8.4    6.2  12.7    1.9  2  Peptidase_M41   Peptidase family M41
        1.6    6.4   8.8        1.8    6.2   8.8    1.0  1  CobN-Mg_chel    CobN/Magnesium Chelatase
        1.7    7.6   4.7        1.8    7.5   4.7    1.1  1  DUF2252         Uncharacterized protein conserved in bacteria
        2.3    7.4  11.8        2.7    7.2  11.8    1.1  1  TMPIT           TMPIT-like protein
        2.5    8.7  12.7         13    6.4   4.8    2.1  2  DUF883          Bacterial protein of unknown function (DUF883
          3    6.7   8.3        3.3    6.5   8.3    1.0  1  PA26            PA26 p53-induced protein (sestrin)
          3    8.1  19.7         27    5.0  19.7    2.0  1  SMBP            Small metal-binding protein
        3.1    5.9  17.4        3.6    5.6  17.4    1.0  1  HSP70           Hsp70 protein
        3.6    7.3  14.2        4.3    7.1  14.2    1.0  1  RR_TM4-6        Ryanodine Receptor TM 4-6
        5.2    6.1  12.1        6.7    5.7  12.1    1.1  1  Atg14           Vacuolar sorting 38 and autophagy-related sub
          6    6.3   7.1        6.9    6.1   7.1    1.1  1  Z1              Z1 domain
        7.7    6.7  11.0        9.3    6.5  11.0    1.2  1  TSP_NTD         Tail specific protease N-terminal domain
        7.8    6.8  14.2          9    6.6  14.2    1.1  1  Vfa1            AAA-ATPase Vps4-associated protein 1


Domain annotation for each model (and alignments):
>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   7.2   3.4e-07    0.0002      27      87 ..      25      85 ..       4     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.4e-07
                          HrpE 27 aeslrarellaeArlqAeqllaqarekaeellevaveqAeaqFWeqAnalLrglqqeReal 87
                                   ++ ra+++ aeA   A++l+a+a+e a++l+e  +++Ae +  ++A+++L++  +e +++
  gi|15668396|ref|NP_247192.1| 25 EAKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEAKKEAEKILEETEKEIKEI 85
                                  45789***********************************************998775544 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3  16.5   0.00097      0.58      58     103 ..      10      55 ..       5      58 .. 0.71
   2 !   12.5  17.7    0.0002      0.12      51     104 ..      36      93 ..      35      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00097
                    ATP-synt_B  58 qqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaae 103
                                   ++ k A+ +A + i++Ak++ae++k+e+++ea++ ++  +e+A++ 
  gi|15668396|ref|NP_247192.1|  10 KEVKLAEEQAVKEIEEAKNRAEQIKAEAIEEAKKLIAEAEEEAKKL 55 
                                   5667777888888888888888888888888888777777777764 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0002
                    ATP-synt_B  51 allaeaeqqlkeAraeAa....eiiknAkkeaeklkeeieaeaeaeaerlkesAaaeI 104
                                   ++++ea++  +eA+ eA+    e+ik+A++ea+k++e+i +e+e+e++ +++ A+ +I
  gi|15668396|ref|NP_247192.1|  36 EAIEEAKKLIAEAEEEAKklveEMIKKAEEEAKKEAEKILEETEKEIKEIISIAKVKI 93 
                                   788999999999999996222267899************************9999777 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  16.5   0.00088      0.53      53     109 ..       7      63 ..       4      66 .. 0.71
   2 ?   11.3   5.0   0.00045      0.27      73     109 ..      57      93 ..      55     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00088
                                   CTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        DivIVA  53 eklkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeea 109
                                   e++ke k +ee+  k +  a++ ae++ka+a +ea+ +i+eAe++a+k+vee  ++a
  gi|15668396|ref|NP_247192.1|   7 EAIKEVKLAEEQAVKEIEEAKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKA 63 
                                   567777777777777777788888888888888888888888888888877655554 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00045
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        DivIVA  73 qetaeevkanakkeaeliikeAekkaekiveeaeeea 109
                                   +e+ +++ ++akkeae i++e+ek+ ++i++ a+ ++
  gi|15668396|ref|NP_247192.1|  57 EEMIKKAEEEAKKEAEKILEETEKEIKEIISIAKVKI 93 
                                   67889999**********************9998776 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6  29.8   0.00012      0.07       8      87 ..      10      89 ..       4      95 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00012
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  V-ATPase_G_2  8 keLaerEaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqavrkra 87
                                  ke++  E++  + +E+A++ ae+  ++A  eA+++++eAe++ak+l +e  ++ +ee ++++e++ ++ e+e +++   a
  gi|15668396|ref|NP_247192.1| 10 KEVKLAEEQAVKEIEEAKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEAKKEAEKILEETEKEIKEIISIA 89
                                  55555566666667777777777777777777777777777777777777777777777777777777777766665555 PP

>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1       1.1   6.5e+02      25      54 ..       5      30 ..       2      32 .. 0.50
   2 ?   13.2   9.5   0.00013     0.077      13      69 ..      26      85 ..      20      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.1
                                  HHHHHHHHHT-SSTTHHHHHHHHHHHHHHH CS
                 Ribosomal_L22 25 veeAlkyLkfskkkaakfvlklLknaeana 54
                                  v eA+k  k ++++a k++    ++a+++a
  gi|15668396|ref|NP_247192.1|  5 VMEAIKEVKLAEEQAVKEI----EEAKNRA 30
                                  5555555555555554444....4444444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00013
                                  HHHHHHHHTTSBHHHHHHHHHT-SSTTHHHHHHHHHHHHHHHH..HT...-GGGEEEEEE CS
                 Ribosomal_L22 13 lrevarlIrgmkveeAlkyLkfskkkaakfvlklLknaeanaelkgl...dvdslvIeei 69
                                  +++ a++I+   +eeA+k   +++++a k v++++k+ae++a++++    ++++  I+ei
  gi|15668396|ref|NP_247192.1| 26 AKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEAKKEAEkilEETEKEIKEI 85
                                  667799************************************977766675655556555 PP

>> GBP_C  Guanylate-binding protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  22.0    0.0003      0.18     186     269 ..       7      91 ..       3     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                         GBP_C 186 eaveeailqtdkalta.kekeieaeqakaeaaeaekelleekqkeeeqrmeakeksleehvkqLkekleeereklleeqer 265
                                   ea++e +l+ ++a+++ +e +++aeq+kaea+e++k+l +e ++e ++ +e+++k+ ee++k+  ek+ ee ek ++e  +
  gi|15668396|ref|NP_247192.1|   7 EAIKEVKLAEEQAVKEiEEAKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEAKKEAEKILEETEKEIKEIIS 87 
                                   79999********99834567889*******************************************99999999999888 PP

                         GBP_C 266 llek 269
                                   +++ 
  gi|15668396|ref|NP_247192.1|  88 IAKV 91 
                                   7765 PP

>> DUF3492  Domain of unknown function (DUF3492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.5   0.00046      0.27      59     130 ..       8      79 ..       4     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00046
                       DUF3492  59 eveevylveeeeaskapa.srkgekaaaetleellealkepeaeseellkelleelaekekklsledflkske 130
                                    ++ev l ee+  ++  + +++ e+ +ae  ee+ +++ e e+e+++l++e++++ +e++ k ++e++l+  e
  gi|15668396|ref|NP_247192.1|   8 AIKEVKLAEEQAVKEIEEaKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEA-KKEAEKILEETE 79 
                                   578889999977765544477788899999999999999999999999999999999999.777777776543 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6  20.0   0.00067       0.4      96     161 ..      17      82 ..       5      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00067
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           RRF  96 keakkaaekakvairniRrdankklkklekkiseDdvkkaekeiqkltdkyikeidellkakekel 161
                                   ++a k++e+ak++  +i+++a ++ kkl  +  e+ +k +e+ i+k  ++  ke++++l++ eke+
  gi|15668396|ref|NP_247192.1|  17 EQAVKEIEEAKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEAKKEAEKILEETEKEI 82 
                                   578899**********************99988999999999***********************8 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  16.4    0.0037       2.2      16      69 ..      13      63 ..       5      90 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0037
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S..-------.-TTHHHHHHHHH CS
                   GlutR_dimer 16 wlkslevvptIkalrekaeeireeeleralkklaldgedree.lekltrslvnkl 69
                                  +l + ++v+ I + +++ae+i++e +e+a+k +a  +e++++ +e++++    k 
  gi|15668396|ref|NP_247192.1| 13 KLAEEQAVKEIEEAKNRAEQIKAEAIEEAKKLIAEAEEEAKKlVEEMIK----KA 63
                                  5778899************************999444444444555555....44 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  17.0    0.0049       2.9      26      69 ..       9      52 ..       2      54 .. 0.85
   2 ?    5.9  15.7     0.012       7.3     149     185 ..      39      74 ..      39      89 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0049
                       DUF3552 26 ekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreel 69
                                   k+++ Aee+A k ieeAk+ Ae++k ea+ eak  i ++ ee+
  gi|15668396|ref|NP_247192.1|  9 IKEVKLAEEQAVKEIEEAKNRAEQIKAEAIEEAKKLIAEAEEEA 52
                                  578999************************99999888776665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                       DUF3552 149 eeAkeilleeveeelkheaAkmikeieeeakeeAdkk 185
                                   eeAk+++  e+eee+k+ + +mik+ eeeak+eA+k 
  gi|15668396|ref|NP_247192.1|  39 EEAKKLI-AEAEEEAKKLVEEMIKKAEEEAKKEAEKI 74 
                                   4555543.44555666666666666666666666553 PP

>> RapA_C  RNA polymerase recycling family C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  12.6    0.0019       1.1     249     309 ..      26      86 ..      10      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                                   S-STTTSTT-------STTSSTTSSS-SHHHHTTTTTTTTSSSHHHHHHHHHHHHHHHHHH CS
                        RapA_C 249 ekvsfeslnkqlkkvkkklarklvkakrkeiekllkkaeklaeeqaeelieeakaraeqel 309
                                   +k  +e++++++ +  kkl+ +  + ++k +e+++kkae+ a+++ae++ ee+++++++ +
  gi|15668396|ref|NP_247192.1|  26 AKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEAKKEAEKILEETEKEIKEII 86 
                                   4556677777777888888888899999999999999999999999999999999998876 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  10.3    0.0012      0.73      25     110 ..       4      89 ..       2     102 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                         PIN_8  25 kvlekladrlwvPhqvalEfqrnresviskekkayedlekeleklkkaaekkleealkkwakkkaldteelrkelkkqlee 105
                                   +v+e++++      q+++E  + ++++ + +++a+e+++k +++++++a+k +ee++kk +++++ ++e++ +e++k+++e
  gi|15668396|ref|NP_247192.1|   4 SVMEAIKEVKLAEEQAVKEIEEAKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEAKKEAEKILEETEKEIKE 84 
                                   566777775556677777777666666666677788888777888888888888888888888888888888888888877 PP

                         PIN_8 106 lkeel 110
                                   + +  
  gi|15668396|ref|NP_247192.1|  85 IISIA 89 
                                   77665 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.5    0.0015       0.9      39     118 ..      10      86 ..       3     102 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                                   HHHHHHHHHHHCS---..--HHHHHHHHHTT--TT-HHHHHHH-TTHHHHHHHHHT--S-SSHHHHHHHHHHHH--HHHH CS
                          FdhE  39 aalaeaqqkvlaaekplaldaeaieraqehgmpplaakalerdeawqelLqallealkeelpealrealerlrkadaeel 118
                                    ++  a ++++++ ++   +++++e+ ++++++  ++   e++e+ ++l+++++++++ee+++++++ le+ +k  +e +
  gi|15668396|ref|NP_247192.1|  10 KEVKLAEEQAVKEIEE---AKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEAKKEAEKILEETEKEIKEII 86 
                                   3444444444433333...3444445556666666666677788999999999999999999999999999888655544 PP

>> zf-CpG_bind_C  CpG binding protein zinc finger C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   9.8    0.0018       1.1       1      65 [.      26      92 ..       6     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0018
                 zf-CpG_bind_C  1 AkkRileiLpqriqewqsspsvaeeenkkklekirkeqeea..kkklkelekklkkLeeliekakkl 65
                                  Ak+R ++i  + i+e ++  ++aeee kk  e++ k+ ee   k+++k le+  k+++e+i+ ak  
  gi|15668396|ref|NP_247192.1| 26 AKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEakKEAEKILEETEKEIKEIISIAKVK 92
                                  7899999999*******999*****999999887665544401344566999999*****9988755 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  16.1    0.0023       1.4      77     147 ..       9      81 ..       2      93 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0023
                      ISG65-75  77 vekleslleeakekgtltesdaekl.kkaceeAkaknkkarekakkalek.aekaskkakeaakkAlGeelee 147
                                    ++++   e+a ++ +  ++ ae++  +a+eeAk+ +++a+e+akk +e+ ++ka ++ak+ a+k l e+++e
  gi|15668396|ref|NP_247192.1|   9 IKEVKLAEEQAVKEIEEAKNRAEQIkAEAIEEAKKLIAEAEEEAKKLVEEmIKKAEEEAKKEAEKILEETEKE 81 
                                   4444333333333333334444444357889999999999999999766537888889999999888775543 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   6.6      0.06        36      44      69 ..      33      58 ..       5      60 .. 0.93
   2 ?    9.8   2.9    0.0014      0.84      44      67 ..      63      86 ..      60      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.06
                                  ...EEHHHHHHHHH....HHHHHTTT CS
                       CinA_KH 44 akaaneeeaealiapveeeirerlgd 69
                                   ka+  eea++lia++eee ++ + +
  gi|15668396|ref|NP_247192.1| 33 IKAEAIEEAKKLIAEAEEEAKKLVEE 58
                                  589999***************98876 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                                  ...EEHHHHHHHHH....HHHHHT CS
                       CinA_KH 44 akaaneeeaealiapveeeirerl 67
                                  a+ + ++eae++++++e+ei+e++
  gi|15668396|ref|NP_247192.1| 63 AEEEAKKEAEKILEETEKEIKEII 86
                                  77899****************987 PP

>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   8.4    0.0021       1.3      61     155 ..       6      94 ..       1     103 [. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0021
                                   CHTSTTTB-SHHHHHHHHHHHHCHHHCCSSHHHHHHHHCCHHHCGGGS-SSHHHHHHHCCCHHHHHHHHHHHCHHTT-HHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane  61 fktltnvnfddekklkrlaealgieeelkdieelaakvaevaledlskeenedirslkellpkglkglyaehaivlgyade 141
                                    +++++v+  +e+ +k+++ea + +e++  ++e ++++++     ++++e+e  ++++e++ k  ++  +e +++l+++++
  gi|15668396|ref|NP_247192.1|   6 MEAIKEVKLAEEQAVKEIEEAKNRAEQI--KAEAIEEAKK----LIAEAEEEAKKLVEEMIKKAEEEAKKEAEKILEETEK 80 
                                   5677888999999999999988887777..5666666664....4444445567899999999999999999********* PP

                                   HHHHHHHHCCCCTT CS
                                   xxxxxxxxxxxxxx RF
                      Prismane 142 evveflaktlagle 155
                                   e+ e+++ + +++ 
  gi|15668396|ref|NP_247192.1|  81 EIKEIISIAKVKIL 94 
                                   ****9987777665 PP

>> Peptidase_M41  Peptidase family M41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  12.7     0.014       8.4     114     176 ..      12      69 ..       1      85 [. 0.67
   2 ?    6.0   2.9     0.016       9.8     142     174 ..      54      86 ..      53      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                                   --------..----.------SS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHH CS
                 Peptidase_M41 114 vsleeeeeeevflgkelkkekelseetaeeideevkelveeayerakeileekreelealaea 176
                                   v+l ee+       ke++++k+ +e++++e  ee k+l++ea e+ak+++ee  ++ e+ a++
  gi|15668396|ref|NP_247192.1|  12 VKLAEEQ-----AVKEIEEAKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEAKK 69 
                                   3433333.....346899999999999999999999999999999998887766655544433 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHH CS
                 Peptidase_M41 142 eeideevkelveeayerakeileekreeleala 174
                                   + ++e +k+  eea ++a++ilee ++e++++ 
  gi|15668396|ref|NP_247192.1|  54 KLVEEMIKKAEEEAKKEAEKILEETEKEIKEII 86 
                                   568899999999999999999999999999875 PP

>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   8.8     0.003       1.8     610     684 ..      18      85 ..       2      95 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.003
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel 610 alaealgldldeleeksekelrtagdalealeeeaeelveelleeeaeeeeaeaeeleeeeeeeeeeteeEital 684
                                   + +++++   ++ e+ + + +++a+++++++eeea++lvee++++++ee+++e       +e+  eete+Ei+++
  gi|15668396|ref|NP_247192.1|  18 QAVKEIEEAKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEAKKE-------AEKILEETEKEIKEI 85 
                                   223333333444778888899999999999*************9844443322.......222223344555554 PP

>> DUF2252  Uncharacterized protein conserved in bacteria (DUF2252)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.7     0.003       1.8     119     179 ..      24      84 ..       4     100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.003
                       DUF2252 119 rdlaerealdewyeridv.elleeatseeakgvvrkalekarkrtreklldklteleegkrr 179
                                   ++  ++ a++ + e+i++ + l +  +eeak+ v+++++ka++++++++ + l e+e++ + 
  gi|15668396|ref|NP_247192.1|  24 EEA-KNRAEQIKAEAIEEaKKLIAEAEEEAKKLVEEMIKKAEEEAKKEAEKILEETEKEIKE 84 
                                   443.4445666667777778888888999999999999999999877777766666654444 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  11.8    0.0045       2.7      12      77 ..      10      84 ..       2     101 .. 0.37

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0045
                         TMPIT 12 keleetakeykqkleelsklqskcske.ikkqkkrlkelksslkklkks........vkeeeeeeveelkeelke 77
                                  ke++ ++++  +++ee ++  ++++ e i++ kk + e +++ kkl ++        +k+e e+++ee ++e+ke
  gi|15668396|ref|NP_247192.1| 10 KEVKLAEEQAVKEIEEAKNRAEQIKAEaIEEAKKLIAEAEEEAKKLVEEmikkaeeeAKKEAEKILEETEKEIKE 84
                                  333333333333333333333333322123333333333333333333210000000333333333333333333 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.8     0.023        13      27      67 ..      10      50 ..       3      54 .. 0.59
   2 ?    6.3   2.2     0.025        15      12      42 ..      54      84 ..      50      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.023
                        DUF883 27 eeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67
                                  +e++ + e++ +++e+a++r+++ + ++ e+ak+ +++a++
  gi|15668396|ref|NP_247192.1| 10 KEVKLAEEQAVKEIEEAKNRAEQIKAEAIEEAKKLIAEAEE 50
                                  44555556666666666666666666666666666666655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.025
                        DUF883 12 adleellkeaadeageeaeelRerleerler 42
                                  + +ee++k+a++ea++eae++ e+ e+++++
  gi|15668396|ref|NP_247192.1| 54 KLVEEMIKKAEEEAKKEAEKILEETEKEIKE 84
                                  5579999999999999999999988888776 PP

>> PA26  PA26 p53-induced protein (sestrin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   8.3    0.0055       3.3     177     256 ..      10      85 ..       2     102 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0055
                          PA26 177 peldlesskklksasasanekedsseeeeeelerkaaaeaeaevealmermkklqeeedeeeeaseeelserfekeeses 256
                                   +e++l++++++k+  ++ ++++++ ++e  e ++k +aeae+e + l+e+m k  eee ++e    e+  e+ eke +e 
  gi|15668396|ref|NP_247192.1|  10 KEVKLAEEQAVKEIEEA-KNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEAKKE---AEKILEETEKEIKEI 85 
                                   45666666666666655.34566666667777777777888888888887766655555533...233333333333333 PP

>> SMBP  Small metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  19.7     0.045        27      27      84 ..      16      84 ..       1      92 [. 0.36

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.045
                                  HHHHHHHHHHHHHHHHT......T-HHHHHHHHHHHHHHHHHH........-------HHHHHHHHHHH CS
                          SMBP 27 laeAiehaeaAvahgka......ghakalveHaeealkhakaa.....aekakeeekehldegikhLee 84
                                  +++A+++ e+A++ +++      ++ak+l+++aee  k++ ++     +e+ak+e+++ l+e+ k+++e
  gi|15668396|ref|NP_247192.1| 16 EEQAVKEIEEAKNRAEQikaeaiEEAKKLIAEAEEEAKKLVEEmikkaEEEAKKEAEKILEETEKEIKE 84
                                  333444444444444431111112333333333333333222233333333334444444444444444 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  17.4    0.0061       3.6     510     590 ..       6      86 ..       2      95 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0061
                                   HHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHHHHHHHHHHH CS
                         HSP70 510 mvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaekekvesaieeLkeeleeeekeeieakteelkkvv 590
                                   m+  +e   +e+++ ke  eakn+ae++  ++ ++ ++   +++e++k+ ve+ i++ +ee+++e ++ +e+  +e+k+++
  gi|15668396|ref|NP_247192.1|   6 MEAIKEVKLAEEQAVKEIEEAKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEAKKEAEKILEETEKEIKEII 86 
                                   566667778899999999999999999998888888888777888888778888877777765555555555555555544 PP

>> RR_TM4-6  Ryanodine Receptor TM 4-6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  14.2    0.0071       4.3      95     176 ..      15      95 ..       2      97 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0071
                                   XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX..........XXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHH CS
                      RR_TM4-6  95 eaeeekeeeeepeaeaeekadaengekeekekekeeeekeseeeeeekkkkkkakskkkeeaeaeesellkklevyqtkll 175
                                   ++e++ +e ee ++ a e+ +ae  e+++k  +++eee ++ +ee+ kk++++ak++ ++  e+ e e+++ +++ + k+l
  gi|15668396|ref|NP_247192.1|  15 AEEQAVKEIEEAKNRA-EQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEEAKKEAEKILEETEKEIKEIISIAKVKIL 94 
                                   2333334444444444.5555566666555555777788888888999999999999999999999999999999999988 PP

                                   H CS
                      RR_TM4-6 176 n 176
                                   +
  gi|15668396|ref|NP_247192.1|  95 S 95 
                                   6 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  12.1     0.011       6.7      68     143 ..       8      85 ..       4     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                         Atg14  68 kleelksliadlrerlqelkdklsqlk.keieekkkklaklsdklkkRrsd.leslqneleerrkkqiaklqdaikri 143
                                   +++e k   ++  ++++e k + +q k ++iee+kk +a+  ++ kk  ++ ++++++e +++ +k+++++ ++ik+i
  gi|15668396|ref|NP_247192.1|   8 AIKEVKLAEEQAVKEIEEAKNRAEQIKaEAIEEAKKLIAEAEEEAKKLVEEmIKKAEEEAKKEAEKILEETEKEIKEI 85 
                                   566777777888888888888888887346899999999999998876544167777777777777777777777754 PP

>> Z1  Z1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   7.1     0.012       6.9      38     111 ..      25      94 ..       2     102 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                            Z1  38 eqekvaelieelleelkkelkesaeekkeellkeleklwekektstkseeeelsfeevkeelkealekievvvv 111
                                   e ++ ae+i++ + e  k+l ++aee+ ++l++e+ k  e+e     ++e+e  +ee+++e+ke+++  +v+++
  gi|15668396|ref|NP_247192.1|  25 EAKNRAEQIKAEAIEEAKKLIAEAEEEAKKLVEEMIKKAEEE----AKKEAEKILEETEKEIKEIISIAKVKIL 94 
                                   223333333333222222222222333333333333333333....4455555677888888888887777765 PP

>> TSP_NTD  Tail specific protease N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  11.0     0.016       9.3     109     175 ..      20      86 ..       6      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.016
                       TSP_NTD 109 akneaelkelwrkrlkneilaelklk.skkdkeikkskeelekryeeqlkrlsqrlekkksedvfelf 175
                                   +k+ +e+k++  +++k+e+++e k+   + ++e+kk  ee+ k++ee+ k+  +++ +++++++ e++
  gi|15668396|ref|NP_247192.1|  20 VKEIEEAKNRA-EQIKAEAIEEAKKLiAEAEEEAKKLVEEMIKKAEEEAKKEAEKILEETEKEIKEII 86 
                                   57788999998.89999999888888977788999999999999999999999977778888777765 PP

>> Vfa1  AAA-ATPase Vps4-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  14.2     0.015         9      64     134 ..      15      84 ..       3     100 .. 0.42

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.015
                          Vfa1  64 kkkeleeeiekvkkeyeekqkkkkekekkkkekdkkdkdkkkekekdkkkekekeeekkkelkkaeeelee 134
                                   +++++ +eie+ k++ e+ +++  e+ kk   +++++++kk  +e  kk+e+e+++e++k l+++e+e++e
  gi|15668396|ref|NP_247192.1|  15 AEEQAVKEIEEAKNRAEQIKAEAIEEAKKLI-AEAEEEAKKLVEEMIKKAEEEAKKEAEKILEETEKEIKE 84 
                                   3333555555555555555444444443331.222222222222222222222233333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      5195  (0.289754); expected 358.6 (0.02)
Passed bias filter:                     1641  (0.0915277); expected 358.6 (0.02)
Passed Vit filter:                       358  (0.0199677); expected 17.9 (0.001)
Passed Fwd filter:                        69  (0.00384851); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 729.45
//
Query:       gi|15668397|ref|NP_247193.1|  [L=169]
Description: hypothetical protein MJ_0224 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-72  241.5   0.0    5.6e-72  241.4   0.0    1.0  1  DUF531    Protein of unknown function (DUF531)


Domain annotation for each model (and alignments):
>> DUF531  Protein of unknown function (DUF531)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.4   0.0   3.1e-76   5.6e-72       1     169 [.       6     164 ..       6     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 241.4 bits;  conditional E-value: 3.1e-76
                        DUF531   1 mltlglvntYDkkklheaHkRaiARaapicyafdfnLalldFplkkeekelvdvvaekttiGesGkylkelaeknrllvld 81 
                                   +ltl+l+n+YDk+++heaHkRaiARaapicyafd+nLa++dFp+k+     +d+++ kttiG+sG+yl++l+eknr++++d
  gi|15668397|ref|NP_247193.1|   6 RLTLILYNSYDKTRWHEAHKRAIARAAPICYAFDCNLAIMDFPCKM-----EDILNIKTTIGNSGEYLEKLIEKNRFFIVD 81 
                                   68******************************************96.....89**************************** PP

                        DUF531  82 lpkkgfpaqfGevvattskpdekkaitpeevaeeilrkksvllliGlGrkGlPkellklakyhlditekgvslEtctAiga 162
                                       +f +qfG ++a+tskpdekkaitp + a  +l+kk++ +++GlGr+GlPk++++++ yhld+tek+vslEtctAig+
  gi|15668397|ref|NP_247193.1|  82 ----KFLPQFGIPIASTSKPDEKKAITPLDTAY-LLKKKPIGVYVGLGRHGLPKDIMESCVYHLDVTEKRVSLETCTAIGS 157
                                   ....***************************85.799******************************************** PP

                        DUF531 163 iaaviat 169
                                   i+avi++
  gi|15668397|ref|NP_247193.1| 158 IPAVIYC 164
                                   *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1209.59
//
Query:       gi|15668398|ref|NP_247194.1|  [L=263]
Description: hypothetical protein MJ_0225 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   6.4e-119  395.4   0.3   7.3e-119  395.2   0.3    1.0  1  NucS            Endonuclease NucS
    0.00084   19.5   0.2      0.012   15.8   0.1    2.1  2  Cas_Cas4        Domain of unknown function DUF83
     0.0016   18.3   0.0     0.0045   16.9   0.0    1.7  1  PDDEXK_9        PD-(D/E)XK nuclease superfamily
     0.0059   16.8   0.2      0.011   15.9   0.2    1.5  1  PDDEXK_4        PD-(D/E)XK nuclease superfamily
     0.0078   16.1   1.0       0.56   10.2   0.0    2.5  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.043   13.7   0.0    1.6  1  YhcG_C          YhcG PDDEXK nuclease domain
      0.022   14.8   0.0       0.06   13.3   0.0    1.7  2  HSDR_N_2        Type I restriction enzyme R protein N terminu
      0.073   13.0   0.1       0.14   12.0   0.1    1.4  1  HSDR_N          Type I restriction enzyme R protein N terminu


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.2   0.3  3.3e-122  7.3e-119       2     229 .]      28     259 ..      27     259 .. 0.98

  Alignments for each domain:
  == domain 1  score: 395.2 bits;  conditional E-value: 3.3e-122
                          NucS   2 savlvvlarCkvsyeGraksrLeegerlivikpdGaflvhkdrkvePvnWqppkssltaevedgslilksirrkpeeeLkv 82 
                                   +++l++larCkv+yeGraks+Leeg+r+i+ikpdGafl+hkd+k+ePvnWqp++ss+++eved+++ilksirrkp+eeLkv
  gi|15668398|ref|NP_247194.1|  28 KYILILLARCKVFYEGRAKSQLEEGDRVIIIKPDGAFLIHKDKKREPVNWQPSGSSIIWEVEDNFFILKSIRRKPKEELKV 108
                                   589****************************************************************************** PP

                          NucS  83 eieevehasayeledveelvldGseaelaeliiehpdLieeGfkpvareyavaiGivdiLgkdeegklvivelkrrkaevd 163
                                   +i+ev+ha+a+++ed+ee++l+Gse+e+ae+i+++pdLieeGfkp++rey++++GivdiLgkd+e+k+vi+elkrr+a+++
  gi|15668398|ref|NP_247194.1| 109 VISEVYHACAFNCEDYEEINLRGSESEMAEMIFRNPDLIEEGFKPISREYQIPTGIVDILGKDKENKWVILELKRRRADLQ 189
                                   ********************************************************************************* PP

                          NucS 164 aveqLkryvellkedsvldkvrGvlvapsittdaekllkeeglefkeldppkds....krnidskklrvl 229
                                   av+qLkryve++k+++++dkvrG+lv+ps+tt+aekllkee+lefk+l+ppk+s    k+ni++kk++vl
  gi|15668398|ref|NP_247194.1| 190 AVSQLKRYVEYFKNKYGEDKVRGILVSPSLTTGAEKLLKEENLEFKRLNPPKGSkrdlKHNIKTKKTTVL 259
                                   ***************************************************9997788999***999875 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.12   2.6e+02     101     140 ..      60      99 ..      53     121 .. 0.75
   2 !   15.8   0.1   5.2e-06     0.012      47     121 ..     156     230 ..     133     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.12
                      Cas_Cas4 101 keGvleypkekkreevelteelreelekaikeieeiisse 140
                                     G+  ++k kkre v++++   + + ++ ++   + s  
  gi|15668398|ref|NP_247194.1|  60 PDGAFLIHKDKKREPVNWQPSGSSIIWEVEDNFFILKSIR 99 
                                   4599999***********9998888888777755554444 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 5.2e-06
                      Cas_Cas4  47 kevelsesikiDvve.kekeklvvvEvKkskkkeeaaklQllyYlllLe.kkgveikeGvleypkekkreeveltee 121
                                   +e ++  ++ +D++  ++++k+v+ E+K+ +++ +a   Ql+ Y+ +++ k g ++ +G+l  p+     e  l+ee
  gi|15668398|ref|NP_247194.1| 156 REYQI-PTGIVDILGkDKENKWVILELKRRRADLQA-VSQLKRYVEYFKnKYGEDKVRGILVSPSLTTGAEKLLKEE 230
                                   55555.688999999678899********9996655.68**********99****999***9998877666555555 PP

>> PDDEXK_9  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     2e-06    0.0045      22      93 ..     154     215 ..     146     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                      PDDEXK_9  22 vksEdetnkGriDlllkpkektkkkiyifEfKylkekesekekaeealeQikekgyaekykedgkkikkigi 93 
                                   +  E++++ G +D+l k   ++++k  i+E+K        + ++ +a++Q+k++ +  k k+ + k++ i++
  gi|15668398|ref|NP_247194.1| 154 ISREYQIPTGIVDILGK---DKENKWVILELK-------RRRADLQAVSQLKRYVEYFKNKYGEDKVRGILV 215
                                   5679************9...555566678***.......778888*************99999999998877 PP

>> PDDEXK_4  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   4.8e-06     0.011      65     128 ..     153     218 ..      99     257 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.8e-06
                      PDDEXK_4  65 everenasekngriDlll.qenkivvlIEnKva.Akdqk.eQlarYeefakkkakkkdivvvyLtld 128
                                    + re ++ ++g +D+l  ++++  v++E K   A  q  +Ql+rY e+ k+k+++++++ + +++ 
  gi|15668398|ref|NP_247194.1| 153 PISRE-YQIPTGIVDILGkDKENKWVILELKRRrADLQAvSQLKRYVEYFKNKYGEDKVRGILVSPS 218
                                   35566.999999******988899999****988****99**************8888887777554 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2      0.01        23      20      43 ..      48      72 ..      44      74 .. 0.71
   2 !   10.2   0.0   0.00025      0.56      16      45 ..      72     102 ..      72     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.01
                                  CEECTCEEEEEECTT..CCCCCCCHH CS
                MazE_antitoxin 20 gireGdevelevdgd..kiilrplks 43
                                   ++eGd+v++ +++d   +i++ +k+
  gi|15668398|ref|NP_247194.1| 48 QLEEGDRVII-IKPDgaFLIHKDKKR 72
                                  6899*****9.777755666666555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00025
                                   HHHCCEEC.TCEEEEEECTTCCCCCCCHHSX CS
                MazE_antitoxin  16 rfelgire.Gdevelevdgdkiilrplkslp 45 
                                   r++ ++++ G+++++ev+++  il+ ++++p
  gi|15668398|ref|NP_247194.1|  72 REPVNWQPsGSSIIWEVEDNFFILKSIRRKP 102
                                   7899****************99999999877 PP

>> YhcG_C  YhcG PDDEXK nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.9e-05     0.043      70     105 ..     173     208 ..     123     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                        YhcG_C  70 lkcyvvieLKvgefkpedagklnlYlsaldeelkke 105
                                    + +v++eLK ++ + + +++l+ Y+++++++  ++
  gi|15668398|ref|NP_247194.1| 173 ENKWVILELKRRRADLQAVSQLKRYVEYFKNKYGED 208
                                   5679*************************9876544 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.6   5.8e+03      37      57 ..      20      38 ..       8      53 .. 0.60
   2 ?   13.3   0.0   2.7e-05      0.06      37      83 ..     163     206 ..     152     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.6
                      HSDR_N_2 37 kraDivvykkdkkpllivecK 57
                                  + +D+ v+k     +l+++cK
  gi|15668398|ref|NP_247194.1| 20 NFIDMYVFKYI--LILLARCK 38
                                  44566666644..55555555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.7e-05
                      HSDR_N_2  37 kraDivvykkdkkpllivecKapsvkiseevleqlksYlealkaeyl 83 
                                   + +Di+  +k+ + ++i+e+K+ +  ++  +++qlk+Y+e +k +y+
  gi|15668398|ref|NP_247194.1| 163 GIVDILGKDKE-NKWVILELKRRRADLQ--AVSQLKRYVEYFKNKYG 206
                                   56788888877.99***********996..7************9996 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   6.5e-05      0.14     122     164 ..     163     204 ..     151     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.5e-05
                                   --EEEEEEETTEEEEEEEE--TT-HHHHHHHHTSS---.---S CS
                        HSDR_N 122 rrpDivlfvnglplvviElKrpgtieeAinQikryrkeksdvs 164
                                    ++Di+   ++   v++ElKr+++  +A++Q+kry  e+++++
  gi|15668398|ref|NP_247194.1| 163 GIVDILGKDKENKWVILELKRRRADLQAVSQLKRYV-EYFKNK 204
                                   57899999999999*******976689********9.656665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1739.93
//
Query:       gi|15668399|ref|NP_247195.1|  [L=193]
Description: putative deoxyribonucleotide triphosphate pyrophosphatase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-51  175.3   0.2    1.4e-51  175.1   0.2    1.0  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.1   0.2   7.6e-56   1.4e-51       1     186 [.      11     187 ..      11     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 175.1 bits;  conditional E-value: 7.6e-56
                                   EEEC-S-HHHHHHHHHHTTT.ECCCE.EECCCCEE----BSSSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTTTBGG CS
                    Ham1p_like   1 ivfaTgNkgKlrevkeilae.ellevkslkelelpeveEtqgtfeenalkKaraaae.aglpvladDsgLevdaLnglPGv 79 
                                   i+faTgN++K++e++ il++ +++e++++    +  ++E+qgt+ee+a   a+ +++  ++pv+++Dsg++v+aLng+PG 
  gi|15668399|ref|NP_247195.1|  11 IYFATGNPNKIKEANIILKDlKDVEIEQI----KISYPEIQGTLEEVAEFGAKWVYNiLKKPVIVEDSGFFVEALNGFPGT 87 
                                   89************999976655555544....45566******************955888******************* PP

                                   GTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SS.SSTTGGGEEETT- CS
                    Ham1p_like  80 ysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeg.gfGyDpiFvpeeg 159
                                   ys+ ++     ++ +++ +l+ le+ +++r+A+f++v++++d+ +++ +lf+G+v+G++ ee r +g gf yD+iF+pee+
  gi|15668399|ref|NP_247195.1|  88 YSKFVQ-----ETIGNEGILKLLEG-KDNRNAYFKTVIGYCDE-NGV-RLFKGIVKGRVSEEIRSKGyGFAYDSIFIPEEE 160
                                   ***995.....34577888888874.458************96.555.8************9999999**********987 PP

                                   SSBTTTS.CHHHHHHSHHHHHHHHHHH CS
                    Ham1p_like 160 ektfaelskeeknaiShRgkAleklle 186
                                   e+tfae+++eek +iShR+kA+e++++
  gi|15668399|ref|NP_247195.1| 161 ERTFAEMTTEEKSQISHRKKAFEEFKK 187
                                   88**********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1319.88
//
Query:       gi|15668400|ref|NP_247196.1|  [L=193]
Description: hypothetical protein MJ_0226.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.8   9.7      0.099   12.9   0.8    2.5  2  DUF3267   Putative zincin peptidase


Domain annotation for each model (and alignments):
>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.8   5.5e-06     0.099      63     105 ..       5      45 ..       3      48 .. 0.86
   2 ?    6.1   2.2   0.00075        13      37      93 ..      49     105 ..      46     118 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-06
                       DUF3267  63 illlllalllpsstlllllllalnaagsagDlliallllkapk 105
                                   ++ll+++l+l ++  l++l++++n  +++ D+l++++ +ka++
  gi|15668400|ref|NP_247196.1|   5 LILLIVVLFLTPY--LIALFIIFNPPYCILDYLLYKKYRKAKE 45 
                                   6777888887777..9********************9999986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00075
                       DUF3267  37 yatsseallskkqfiiillaPfvll.gilllllalllpsstlllllllalnaagsagD 93 
                                   y+ts++  ++++++i+il+  ++ l +   +l+ +  p+   +l++ l++ +++ + D
  gi|15668400|ref|NP_247196.1|  49 YITSTNMGMNRSRWIFILIVEIIALcSGFYILININRPHD-EILTFSLIFLFIAIIYD 105
                                   889999999************9999454455555554443.37777777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1369.53
//
Query:       gi|15668401|ref|NP_247197.1|  [L=122]
Description: hypothetical protein MJ_0226.2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.065   12.3  23.9      0.076   12.1  23.9    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
        2.6    8.0  14.8        3.2    7.7  14.8    1.2  1  Na_Ca_ex         Sodium/calcium exchanger protein
          4    7.2  18.1        6.1    6.6  18.1    1.3  1  DUF443           Protein of unknown function (DUF443)
        5.9    6.9   9.4          4    7.4   4.3    2.0  2  Halogen_Hydrol   5-bromo-4-chloroindolyl phosphate hydrolysis


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  23.9   1.7e-05     0.076     157     251 ..       4     103 ..       1     104 [. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
               ABC2_membrane_3 157 snvasflvg.liliilifitasfiavsi.veEkesrikelqlvsgvsplq....ywlskilgdflvyllqlllilllafgl 231
                                   +nv+  ++  ++ +++++++++++ ++i  +  e++ ke+++v  v++l+    y++ +il +f++ +++++l++ ++f+ 
  gi|15668401|ref|NP_247197.1|   4 MNVVGLAIYlYAGFLSFIFGFISLYAFIkYSKLERKNKEIIYVY-VDNLKnfspYMFYSILLTFTIVFVIFALFICFVFN- 82 
                                   55666655546666666777776666665455677889999999.999998999**************************. PP

               ABC2_membrane_3 232 gipfg.nlglll.llfllfgla 251
                                    ++ + +l  l+  ++++++++
  gi|15668401|ref|NP_247197.1|  83 -FDLYlGLTMLFsYFLIIYLFC 103
                                   .555554444443444444433 PP

>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  14.8   0.00072       3.2      68     149 ..       3     102 ..       1     104 [. 0.59

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00072
                                   HHHHHHHHHHHHHTHHHHHHHHHH............BTTSSCE................CCHHH.HHHHHHHHHHHHHHHH CS
                      Na_Ca_ex  68 ignvlGsnifnlllviGlialigs............lkvdses................lkldl.gllllvallllllvll 119
                                   + nv+G +i    + +++i+ + s                  +                +++    l++++++++++l+++
  gi|15668401|ref|NP_247197.1|   3 TMNVVGLAIYLYAGFLSFIFGFISlyafikysklerK-----NkeiiyvyvdnlknfspYMFYSiLLTFTIVFVIFALFIC 78 
                                   5666666666666666666666555655445665440.....144466666665566553333324444444444445555 PP

                                   TCHHHHHHTEEHHHHHHHHHHHHHHHHHHH CS
                      Na_Ca_ex 120 lllplfvpgrltvleglvllllYalylvls 149
                                   ++       + ++  gl++l+ Y+l+++l+
  gi|15668401|ref|NP_247197.1|  79 FV------FNFDLYLGLTMLFSYFLIIYLF 102
                                   44......99****************9986 PP

>> DUF443  Protein of unknown function (DUF443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  18.1    0.0014       6.1     123     201 ..      32     110 ..       3     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0014
                        DUF443 123 nevelekkskekiilipkslknfllllfaylfflglvilalvali..etqniiilivlllllfllfllnvltisdgkttvk 201
                                   +  +le+k+ke i++ + +lknf  ++f+ +++ + +++++ al+   + n+ +++ l++l+  ++++ ++++++  ++v+
  gi|15668401|ref|NP_247197.1|  32 KYSKLERKNKEIIYVYVDNLKNFSPYMFYSILLTFTIVFVIFALFicFVFNFDLYLGLTMLFSYFLIIYLFCFKK--YRVE 110
                                   34457799999******************999888777777776658899*********9999999999999874..4444 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.028   1.3e+02      18      46 ..      11      35 ..       1      52 [. 0.52
   2 ?    7.4   4.3   0.00088         4       6      54 ..      65     113 ..      60     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.028
                Halogen_Hydrol 18 sffllgfsfflalliailggilvyvasr..k 46
                                  ++++     fl+   +i+g+i +y++++  k
  gi|15668401|ref|NP_247197.1| 11 IYLY---AGFLS---FIFGFISLYAFIKysK 35
                                  3332...33344...3555665555555321 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00088
                Halogen_Hydrol   6 lsiliavivalvsffllgfsfflalliailggilvyvasrknkkkkhlk 54 
                                    ++++ vi+al++ f+++f++ l l++++  ++++y++  k+ + +++k
  gi|15668401|ref|NP_247197.1|  65 TFTIVFVIFALFICFVFNFDLYLGLTMLFSYFLIIYLFCFKKYRVEIYK 113
                                   4566777778888888999999998888888899999888777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1423  (0.0793686); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 817.07
//
Query:       gi|15668402|ref|NP_247198.1|  [L=308]
Description: hypothetical protein MJ_0227 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-66  223.5   0.0    4.7e-66  223.3   0.0    1.0  1  CitG      ATP:dephospho-CoA triphosphoribosyl transferase


Domain annotation for each model (and alignments):
>> CitG  ATP:dephospho-CoA triphosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.3   0.0   2.6e-70   4.7e-66       3     280 ..      24     294 ..      22     295 .. 0.94

  Alignments for each domain:
  == domain 1  score: 223.3 bits;  conditional E-value: 2.6e-70
                                   XXXXXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHHHH..-- CS
                          CitG   3 lavlAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekamlaa..tg 81 
                                   + + A++lEvs + KPG+V+r++++  +D+++++F++  +a  +++ eaa          ++ r +G  ++ka+ ++  ++
  gi|15668402|ref|NP_247198.1|  24 ASQIACCLEVSSF-KPGNVHRNRDY--RDIKYHHFINAGIAFGNVVYEAA----------QKDRDVGLYIKKAVIESkkWS 91 
                                   6799*********.***********..***********************..........99******************* PP

                                   ----HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--HHHHHHH.HHHHHH--.............---.HH CS
                          CitG  82 gvNThkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltvedavaf.rairlakv.............eel.kd 147
                                    +N ++G+i+l +++a+aag+     e+++ ++l e+++++++++tveda+++ +ai++a +             e + k+
  gi|15668402|ref|NP_247198.1|  92 PTNANLGIIMLHIPIAMAAGKL----ENFDENKLKENLKKIAENTTVEDALNVyDAINIAMAyvnkpkkgpdvtsE-DaKK 167
                                   ********************87....78999*******************************99987766555432.1577 PP

                                   HHHH.TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHHHHHS--HHHHHHHHHHHH CS
                          CitG 148 elvekksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallallaelpDtnilrrgGaega 228
                                   el+e k+ltl++v ++s+++d i++e++++F+++fe +++ l++  ++ +++n a+++++l+lla++pDt+i+r+ G e+a
  gi|15668402|ref|NP_247198.1| 168 ELIE-KGLTLLDVYKISAEWDNISKEWVDNFKISFE-GYNLLKKYYDELNNINLAVTKTFLNLLAKYPDTLIARKRGFETA 246
                                   7777.9******************************.********9888******************************** PP

                                   HHHHHHHH..........H-SHHHHHHHHHHHHHHT..---HHHHHHHHHHHHH CS
                          CitG 229 eevqeeArallaaggvaaeaglealeeldrelvern..isPGgsADllaatlfl 280
                                    +v+++A+++l++        +e+++e+d++l +++  ++PG++ADl+a++l++
  gi|15668402|ref|NP_247198.1| 247 LKVSKMAEDVLNN------FKEEKVKEFDKYLSKEGnkLNPGTTADLIASSLMI 294
                                   ************9......45779**********9999*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2062.15
//
Query:       gi|15668403|ref|NP_247199.1|  [L=577]
Description: glycyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-26   91.8   0.5      7e-26   90.2   0.5    1.9  1  HGTP_anticodon  Anticodon binding domain
    2.7e-11   43.8   0.1    3.1e-09   37.0   0.1    2.6  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
      0.054   12.6   5.4        2.7    7.0   0.2    3.2  3  tRNA-synt_2     tRNA synthetases class II (D, K and N)
       0.12   12.4   0.1       0.22   11.5   0.1    1.5  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.12   12.2   0.2       0.12   12.2   0.2    2.9  3  Rad50_zn_hook   Rad50 zinc hook motif
       0.19   12.2   0.3       0.79   10.2   0.1    2.1  2  E6              Early Protein (E6)
        1.4    9.2   4.2          2    8.7   0.2    2.8  3  DUF2757         Protein of unknown function (DUF2757)


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   0.5   2.7e-29     7e-26       1      93 [.     483     573 ..     483     574 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 2.7e-29
                                   SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEE CS
                HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqer 81 
                                   +++v+pl +k++ + + ak++ + Lr++gi +e+d +++ ig+++ +ad++g+pf+++v+ ++le++tvtvr+r+treq+r
  gi|15668403|ref|NP_247199.1| 483 KAYVLPLVNKDD-MPKIAKEIEQMLRENGIIAEYD-DSGAIGRRYMRADEIGVPFCITVDGQTLEDRTVTVRERNTREQVR 561
                                   689*****9666.*****************99997.699****************************************** PP

                                   EETTHHHHHHHH CS
                HGTP_anticodon  82 vsldelveklke 93 
                                   v++delv++lke
  gi|15668403|ref|NP_247199.1| 562 VKIDELVDYLKE 573
                                   **********98 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.1   1.2e-12   3.1e-09      10      85 ..     158     234 ..     153     237 .. 0.83
   2 ?    3.8   0.0     0.019        49      79     177 ..     275     461 ..     270     463 .. 0.64

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.2e-12
                                   EEEE-SSSHHHHHHHHHHHEE...EBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  10 eyiLkPtneetfvelirdevl...rskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlik 85 
                                     +++P+  +++   +r   +   r+k LP+ ++qi+  yR+E s  +G++R+reF+q + + f+++++ + +  dl+k
  gi|15668403|ref|NP_247199.1| 158 TGYMRPETAQGIFIQFRRL-AqffRNK-LPFGVVQIGKSYRNEISPRQGVIRLREFTQAEIEYFVHPERKEHEKFDLVK 234
                                   5678999999988888854.3233555.****************9566******************9999999888887 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.019
                                   HHHHHHHHHHHHHHHTT.SCEEEEEEGTTSC.................................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................. RF
                  tRNA-synt_2b  79 slrdlikaisriferlglefraiielmsaks.................................................. 109
                                    ++  i +++r++e++g+ + +i+   +  +                                                  
  gi|15668403|ref|NP_247199.1| 275 TIAYFIALTKRFLEAIGIDKDKIRFRQHLPNemahyaidcwdaeiyterfgwiecvgiadrtdydlrshsahsgvelsvfv 355
                                   556678889999999999998888775444445567788888888888888888877777777777777777777777777 PP

                                   .....................................BTTSEEEEEEEEETTTSEEEEEEEEEEEET.HHHHHTTEEEECT CS
                                   .....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                  tRNA-synt_2b 110 .....................................adykdkkefeavsesltkgieigtiqklgt.rlserlgatvlde 152
                                                                        ++ k+k+ef    e  +k+i    i ++++  l +  +++ +++
  gi|15668403|ref|NP_247199.1| 356 eldeereietyeinlnykvvgkifkkdtkaieayinnLSEKEKEEFVKNIENDGKVI--INIDGKEFeILKDYVEIKKVKK 434
                                   777777777777777777777766666666666655555555555555544344444..5555555535667777743333 PP

                                   ..TSSEEEEEEEEEEEEHHHHHHHHHH CS
                                   ..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b 153 ..nnreksvimicaaigveRllsaile 177
                                     ++++  +++i  + g+ R+  ++le
  gi|15668403|ref|NP_247199.1| 435 viKGEKVIPHVIEPSYGIDRITYCLLE 461
                                   124455567777777777777777776 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0022       5.6      25      52 ..      43      71 ..      40      82 .. 0.81
   2 ?   -0.5   0.1       0.2   5.1e+02     104     129 ..      95     120 ..      94     126 .. 0.83
   3 ?    7.0   0.2    0.0011       2.7      79     122 ..     177     218 ..     147     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0022
                                  HHHHHHHHH.HHHHHTT-EE----SEESS CS
                                  xxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 25 rstvtkavr.kyleengfieietPiLsks 52
                                  ++++++ +r +y+ ++gf+eie P+++  
  gi|15668403|ref|NP_247199.1| 43 KNNIISKFReQYIIKEGFYEIESPTVTPY 71
                                  6778888883588999*********9876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.2
                                   S--BTTB-S-CEEEEEEEEET-SCHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 104 EdsrtdrhlaEFtqieaemsfieeed 129
                                   E++r+d+ ++EF+ ++ e + ++e d
  gi|15668403|ref|NP_247199.1|  95 ESFRADHLIEEFVDVDTEGKTLKELD 120
                                   899***************87776655 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0011
                                   SHHHHHHHHHCTHSEEEEEEEEE--S--BTT..B-S-CEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                   tRNA-synt_2  79 pqlylellivagidrvfqiaraFRaEdsrtd..rhlaEFtqieaem 122
                                    q+++  l  +    v qi++++R+E s  +    l EFtq e+e 
  gi|15668403|ref|NP_247199.1| 177 AQFFRNKLPFG----VVQIGKSYRNEISPRQgvIRLREFTQAEIEY 218
                                   56666666666....88*********98655225799*******96 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   8.6e-05      0.22      20      35 ..     123     138 ..     122     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.6e-05
                Zn_ribbon_SprT  20 irrhnYrCrrCkgtLr 35 
                                   ir hn rC++C+g+L+
  gi|15668403|ref|NP_247199.1| 123 IRKHNIRCPKCGGELG 138
                                   788***********97 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   4.9e-05      0.12      10      37 ..     117     145 ..     111     146 .. 0.84
   2 ?   -1.1   0.2      0.69   1.8e+03      31      39 ..     395     403 ..     382     407 .. 0.56
   3 ?   -2.7   0.1       2.2   5.6e+03      35      47 ..     496     508 ..     491     509 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.9e-05
                                   HHHHHHTT-SE.E-TTT--EE-HHHHHHH CS
                 Rad50_zn_hook  10 kkieelkeakg.cCPlCgReldeehrseL 37 
                                   k ++el  +++ +CP Cg el+e ++ +L
  gi|15668403|ref|NP_247199.1| 117 KELDELIRKHNiRCPKCGGELGEVKKFNL 145
                                   778888889999***********998665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.69
                                   HHHHHHHHH CS
                 Rad50_zn_hook  31 eehrseLik 39 
                                   e++++e++k
  gi|15668403|ref|NP_247199.1| 395 EKEKEEFVK 403
                                   333444444 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.2
                                   HHHHHHHHHHHHH CS
                 Rad50_zn_hook  35 seLikelqskler 47 
                                    +++ke++++l++
  gi|15668403|ref|NP_247199.1| 496 PKIAKEIEQMLRE 508
                                   5889999999886 PP

>> E6  Early Protein (E6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00031      0.79      33      88 ..      89     144 ..      82     150 .. 0.76
   2 ?   -2.2   0.0       2.3   5.8e+03      79      94 ..     391     406 ..     350     417 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00031
                                   XXHHHHHHHHHHHH.HHHEEEEEEHHHHHHHHTSTGGGSEEEETTT--B--HHHHHH CS
                            E6  33 vCkkClevlallel.llhlerslkakeleelvgkslsdleiRCvvClklLskeeKee 88 
                                    Ck+Cle   +  l ++++  ++++k+l+e +++ + + +iRC  C+  L +  K +
  gi|15668403|ref|NP_247199.1|  89 ECKNCLESFRADHLiEEFVDVDTEGKTLKE-LDELIRKHNIRCPKCGGELGEVKKFN 144
                                   699**9976655550556666777777665.56999999**********99988865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.3
                                   -B--HHHHHHHHHTTS CS
                            E6  79 klLskeeKeellekke 94 
                                   + Ls++eKee +++ e
  gi|15668403|ref|NP_247199.1| 391 NNLSEKEKEEFVKNIE 406
                                   5688889988777655 PP

>> DUF2757  Protein of unknown function (DUF2757)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       6.5   1.7e+04      55      63 ..      90      98 ..      88     106 .. 0.68
   2 ?    0.7   0.0      0.26   6.6e+02       6      19 ..     129     142 ..     126     147 .. 0.86
   3 ?    8.7   0.2   0.00079         2      12      51 ..     373     413 ..     365     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.5
                                  -HHHHHHHH CS
                       DUF2757 55 CedCqeale 63
                                  C +C e+++
  gi|15668403|ref|NP_247199.1| 90 CKNCLESFR 98
                                  667766665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.26
                                   EETTT--BTT-SST CS
                       DUF2757   6 rCrhCgkkigtlek 19 
                                   rC++Cg ++g+++k
  gi|15668403|ref|NP_247199.1| 129 RCPKCGGELGEVKK 142
                                   7*********9986 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00079
                                   -BTT-SSTTT---SS---SSSSHHHHHHTSSS.-TT-S-EE CS
                       DUF2757  12 kkigtlekkeieeealgfnkLteeerqdmiey.eengdikv 51 
                                   k +g++ kk++++ +  +n+L+e+e++++++  e++g++ +
  gi|15668403|ref|NP_247199.1| 373 KVVGKIFKKDTKAIEAYINNLSEKEKEEFVKNiENDGKVII 413
                                   689***************************86155666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1064  (0.0593452); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3769.01
//
Query:       gi|15668404|ref|NP_247200.1|  [L=95]
Description: arsenical resistance operon repressor [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-16   59.8   0.3    3.9e-16   58.6   0.1    1.7  2  HTH_5      Bacterial regulatory protein, arsR family
    3.6e-11   42.9   0.0      5e-11   42.5   0.0    1.2  1  HTH_20     Helix-turn-helix domain
    2.1e-08   33.9   0.3    3.2e-08   33.3   0.3    1.3  1  TrmB       Sugar-specific transcriptional regulator TrmB
    2.2e-06   27.1   0.2    1.8e-05   24.2   0.2    2.2  1  HTH_24     Winged helix-turn-helix DNA-binding
    1.9e-05   24.5   0.0    3.2e-05   23.8   0.0    1.4  1  MarR       MarR family
      2e-05   24.4   0.1    3.8e-05   23.6   0.1    1.5  1  HTH_11     HTH domain
    2.6e-05   24.0   0.0    3.3e-05   23.7   0.0    1.1  1  MarR_2     MarR family
      3e-05   23.9   0.6    0.00012   22.0   0.6    1.8  1  PadR       Transcriptional regulator PadR-like family
    0.00092   19.0   0.0     0.0012   18.5   0.0    1.2  1  HTH_IclR   IclR helix-turn-helix domain
     0.0017   18.0   0.0     0.0034   17.0   0.0    1.5  1  HTH_41     Helix-turn-helix domain
      0.003   17.9   0.0     0.0047   17.3   0.0    1.3  1  Rrf2       Transcriptional regulator
     0.0034   17.9   0.1     0.0053   17.3   0.0    1.4  1  Mga        Mga helix-turn-helix domain
     0.0038   17.4   0.1     0.0051   17.0   0.1    1.2  1  HTH_34     Winged helix DNA-binding domain
      0.008   16.0   0.3       0.21   11.4   0.0    2.4  2  IF2_N      Translation initiation factor IF-2, N-terminal reg
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.014   15.2   0.1    1.2  1  HxlR       HxlR-like helix-turn-helix
      0.016   14.7   0.1      0.028   14.0   0.0    1.5  1  HTH_CodY   CodY helix-turn-helix domain
      0.025   15.0   0.1      0.033   14.6   0.1    1.2  1  HTH_40     Helix-turn-helix domain
      0.038   13.8   0.0      0.068   13.0   0.0    1.4  1  HTH_10     HTH DNA binding domain
      0.038   13.6   0.0      0.056   13.1   0.0    1.4  1  GntR       Bacterial regulatory proteins, gntR family
       0.14   12.2   0.0       0.19   11.7   0.0    1.2  1  HTH_Crp_2  Crp-like helix-turn-helix domain
       0.15   12.0   0.9       0.28   11.2   0.0    1.8  2  BLACT_WH   Beta-lactamase associated winged helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.1   4.6e-19   3.9e-16       1      47 []      15      61 ..      15      61 .. 0.98
   2 ?   -1.5   0.0       2.7   2.3e+03       6      15 ..      86      95 .]      85      95 .] 0.84

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 4.6e-19
                                  SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  +p R+kIL++L+++++ + ela+el+ls++ v  HL+kL++a+LVe+
  gi|15668404|ref|NP_247200.1| 15 NPIRVKILYILNKQPKNIYELAKELELSRPVVYAHLRKLEDADLVES 61
                                  699******************************************96 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                                  HHHHHHTTSS CS
                         HTH_5  6 kILklLaege 15
                                  +I+k L e+e
  gi|15668404|ref|NP_247200.1| 86 EIIKKLFENE 95
                                  8999999986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   5.8e-14     5e-11       5      56 ..      11      61 ..       5      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 5.8e-14
                                  HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20  5 eALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                  eAL++P R +il  L  +++    ela++l+ls+  ++ HLr+Le+a+Lve+
  gi|15668404|ref|NP_247200.1| 11 EALSNPIRVKILYIL-NKQPKNIYELAKELELSRPVVYAHLRKLEDADLVES 61
                                  8**************.**********************************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.3   3.8e-11   3.2e-08      16      67 ..      23      79 ..      21      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 3.8e-11
                                  HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....TTEEEE--H CS
                          TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.....pklYravdp 67
                                  ++l+++p++++e+a+el+++r+ vY  Lr+Led++lVe          +++Y+a ++
  gi|15668404|ref|NP_247200.1| 23 YILNKQPKNIYELAKELELSRPVVYAHLRKLEDADLVESDLVLegsraKRIYKAKEF 79
                                  689***********************************8764445688889999876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.2   2.1e-08   1.8e-05       3      48 .]      16      60 ..      14      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.1e-08
                        HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   ++ kIL +L k+p+ ++ eLA++l lS++ v ++l++Le++ l++
  gi|15668404|ref|NP_247200.1| 16 PIRVKILYILNKQPK-NIYELAKELELSRPVVYAHLRKLEDADLVE 60
                                  667788888888655.677***********************9996 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   3.7e-08   3.2e-05       7      49 ..      20      61 ..      15      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.7e-08
                                  HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                  +iL+il  ++p ++ eLak l++s++ v   l++Le+++l+e+
  gi|15668404|ref|NP_247200.1| 20 KILYILN-KQPKNIYELAKELELSRPVVYAHLRKLEDADLVES 61
                                  6777665.5678*****************************85 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   4.4e-08   3.8e-05       4      42 ..      20      56 ..      18      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.4e-08
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                  +il +L+++ +  ++ eLA+eL++Sr +v+ ++++Le++
  gi|15668404|ref|NP_247200.1| 20 KILYILNKQPK--NIYELAKELELSRPVVYAHLRKLEDA 56
                                  79999955555..8**********************976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   3.8e-08   3.3e-05       6      61 ..      17      72 ..      12      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.8e-08
                                  HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE...ESSSSSS CS
                        MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr...pgpeDkR 61
                                      +L+ L   p    ++ ela++l ls++ v  +l++L++a Lve     +g+++kR
  gi|15668404|ref|NP_247200.1| 17 IRVKILYILNKQPK---NIYELAKELELSRPVVYAHLRKLEDADLVESDlvlEGSRAKR 72
                                  56678888888887...99***************************9765556666665 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.6   1.3e-07   0.00012       1      64 [.      21      75 ..      21      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.3e-07
                                  HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEE CS
                          PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYr 64
                                  iL++l++qp   ye++kele +           +Y  L++Le+ +lves  + +  ++++++Y+
  gi|15668404|ref|NP_247200.1| 21 ILYILNKQPKNIYELAKELELS--------RPVVYAHLRKLEDADLVESDLVLE-GSRAKRIYK 75
                                  89*******9999999999876........568*****************9996.899999996 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.5e-06    0.0012       7      51 ..      20      62 ..      19      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                                  HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                   iL +l+++p    + elA+++ l+++ v+ +L+ L+   +ve d
  gi|15668404|ref|NP_247200.1| 20 KILYILNKQPKN--IYELAKELELSRPVVYAHLRKLEDADLVESD 62
                                  588888888886..99**************************987 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     4e-06    0.0034       7      36 ..      30      59 ..      28      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4e-06
                        HTH_41  7 ktIeelakeleLSvGlvQkALklLeddkai 36
                                  k I elakeleLS+  v + L +Led+  +
  gi|15668404|ref|NP_247200.1| 30 KNIYELAKELELSRPVVYAHLRKLEDADLV 59
                                  5799**********************9887 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.5e-06    0.0047      11      57 ..      19      61 ..      14      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.5e-06
                                  HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                  +++l++L k+++    ++ e+a++ ++s++++   l+kL+ a+lv+s
  gi|15668404|ref|NP_247200.1| 19 VKILYILNKQPK----NIYELAKELELSRPVVYAHLRKLEDADLVES 61
                                  677777777777....68***************************99 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.2e-06    0.0053      24      65 ..      23      65 ..      12      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.2e-06
                                  HHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH.HCHCCT-EE CS
                           Mga 24 flfeeeevsieelaqelyiSestlkrkikelnk.lLkefdlel 65
                                  ++++++ ++i+ela+el +S+  ++ ++++l+   L e dl l
  gi|15668404|ref|NP_247200.1| 23 YILNKQPKNIYELAKELELSRPVVYAHLRKLEDaDLVESDLVL 65
                                  7899**************************9862466666666 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1     6e-06    0.0051       1      60 [.      17      75 ..      17      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6e-06
                        HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllr 60
                                  +R ++l +L+++ +    el ++le++    ++hl+kLe+a+ +e d+ ++g + + +++
  gi|15668404|ref|NP_247200.1| 17 IRVKILYILNKQPKN-IYELAKELELSRPVVYAHLRKLEDADLVESDLVLEGSRAKRIYK 75
                                  799999999998875.568999**************************999998877775 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00024      0.21       4      26 ..      30      52 ..      28      57 .. 0.86
   2 ?    2.3   0.1      0.18   1.5e+02      18      26 ..      85      93 ..      76      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                         IF2_N  4 irVyeLAkeLgvkskevikkLfk 26
                                  + +yeLAkeL ++   v ++L k
  gi|15668404|ref|NP_247200.1| 30 KNIYELAKELELSRPVVYAHLRK 52
                                  789*********99998888865 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.18
                         IF2_N 18 kevikkLfk 26
                                  +e+ikkLf+
  gi|15668404|ref|NP_247200.1| 85 NEIIKKLFE 93
                                  799999986 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   1.6e-05     0.014       8      56 ..      19      66 ..      13      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                                  HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESS CS
                          HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevype 56
                                  + il+ l k +k   el+++l ++s+ +  ++Lr+Le   l+e + + e
  gi|15668404|ref|NP_247200.1| 19 VKILYILNKQPKNIYELAKEL-ELSRPVVYAHLRKLEDADLVESDLVLE 66
                                  579******************.********************9986654 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.3e-05     0.028      10      37 ..      35      62 ..      32      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.3e-05
                      HTH_CodY 10 iaDriGitrsvivnaLrkLesaGiiesr 37
                                  +a ++ + r v+   LrkLe a ++es 
  gi|15668404|ref|NP_247200.1| 35 LAKELELSRPVVYAHLRKLEDADLVESD 62
                                  68889999******************94 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   3.9e-05     0.033       8      64 ..      25      79 ..      19      94 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-05
                        HTH_40  8 lleeglsieeIAkerglkesTIegHLaelieegeeidlerlvse.eeekeIeeaiekv 64
                                  l ++ ++i e Ake +l++  ++ HL +l  ++  +  ++lv e +++k+I +a e +
  gi|15668404|ref|NP_247200.1| 25 LNKQPKNIYELAKELELSRPVVYAHLRKLEDAD--LVESDLVLEgSRAKRIYKAKE-F 79
                                  558889**********************88885..444666655599999998844.3 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.9e-05     0.068      25      48 ..      31      54 ..      27      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.9e-05
                        HTH_10 25 tlkeLAkelGIskstlsehLrkae 48
                                  ++ eLAkel +s++ ++ hLrk e
  gi|15668404|ref|NP_247200.1| 31 NIYELAKELELSRPVVYAHLRKLE 54
                                  6789*****************977 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.5e-05     0.056      29      56 ..      34      61 ..      10      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                                  HHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          GntR 29 eLaaefgVsrttvReALrrLeaeglver 56
                                  eLa+e++ sr++v   Lr+Le ++lve+
  gi|15668404|ref|NP_247200.1| 34 ELAKELELSRPVVYAHLRKLEDADLVES 61
                                  9*************************86 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00022      0.19      26      52 ..      34      60 ..      24      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                  HHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2 26 elAsmlGltretvsrilseLkreglis 52
                                  elA  l l+r  v   l++L+++ l++
  gi|15668404|ref|NP_247200.1| 34 ELAKELELSRPVVYAHLRKLEDADLVE 60
                                  9************************98 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.1   4.3e+03      14      18 ..      29      33 ..      19      41 .. 0.53
   2 ?   11.2   0.0   0.00033      0.28      25      40 ..      46      61 ..      42      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.1
                      BLACT_WH 14 peslh 18
                                  p++ +
  gi|15668404|ref|NP_247200.1| 29 PKNIY 33
                                  44444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00033
                      BLACT_WH 25 vlahLeKLeeeGkVkr 40
                                  v+ahL+KLe+ ++V++
  gi|15668404|ref|NP_247200.1| 46 VYAHLRKLEDADLVES 61
                                  89**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 718.37
//
Query:       gi|15668405|ref|NP_247201.1|  [L=87]
Description: hypothetical protein MJ_0230 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00027   20.3   0.7    0.00032   20.0   0.7    1.1  1  AgrB             Accessory gene regulator B
     0.0038   17.5   0.4     0.0042   17.4   0.4    1.1  1  MscL             Large-conductance mechanosensitive channel, 
     0.0067   15.5   0.6     0.0067   15.5   0.6    1.0  1  SCFA_trans       Short chain fatty acid transporter
  ------ inclusion threshold ------
      0.012   15.3   1.8      0.013   15.3   1.8    1.1  1  ASFV_J13L        African swine fever virus J13L protein
      0.015   14.9   2.1      0.022   14.3   2.1    1.3  1  4HB_MCP_1        Four helix bundle sensory module for signal 
      0.017   15.2   6.8      0.017   15.2   6.8    1.8  2  DUF3671          Protein of unknown function
       0.02   15.1   1.3      0.027   14.7   1.3    1.2  1  Chordopox_A13L   Chordopoxvirus A13L protein
      0.025   14.3   0.8      0.041   13.6   0.8    1.3  1  Choline_kin_N    Choline kinase N terminus
      0.029   14.8   0.8      0.035   14.5   0.8    1.1  1  Snapin_Pallidin  Snapin/Pallidin
      0.038   14.7   0.2      0.044   14.5   0.2    1.1  1  Chordopox_G3     Chordopoxvirus G3 protein
      0.042   14.1   0.3      0.049   13.9   0.3    1.1  1  DUF4330          Domain of unknown function (DUF4330)
      0.047   13.8   0.5      0.059   13.4   0.5    1.1  1  Peptidase_S49_N  Peptidase family S49 N-terminal
       0.11   12.3   0.2       0.13   12.2   0.2    1.0  1  Pox_LP_H2        Viral late protein H2
       0.27   11.1   3.1       0.36   10.7   3.1    1.3  1  60KD_IMP         60Kd inner membrane protein
       0.35   10.8   4.1        1.1    9.2   4.1    1.8  1  YajC             Preprotein translocase subunit
        2.2    8.8   4.7        3.9    8.0   4.7    1.4  1  FeoB_associated  FeoB-associated Cys-rich membrane protein
        4.1    7.4   6.9       0.26   11.4   1.2    1.8  2  DUF1664          Protein of unknown function (DUF1664)
        9.2    6.1  12.8         17    5.3   0.4    2.1  2  Synaptobrevin    Synaptobrevin


Domain annotation for each model (and alignments):
>> AgrB  Accessory gene regulator B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.7   3.3e-07   0.00032      98     140 ..      23      65 ..       6      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.3e-07
                          AgrB  98 lslslllillliilliisliiilllaPvdtpnkpisskekkkk 140
                                   +++ + +++++i+++ii++ii +l++P ++++  i++++ +k+
  gi|15668405|ref|NP_247201.1|  23 INPFYDILWMIIFVVIIAVIIYILISPLKKQSSSIDNEKLIKI 65 
                                   333377899*****************************98876 PP

>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4   4.2e-06    0.0042      68     120 ..      26      79 ..       3      82 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.2e-06
                          MscL  68 ygafiqavinFliiafviFlivkainkkkke.eeeeeeaeekeeellteirdll 120
                                   +  ++  +i  +iia++i++++ +++k++++ ++e+  + ek++e ++ei + l
  gi|15668405|ref|NP_247201.1|  26 FYDILWMIIFVVIIAVIIYILISPLKKQSSSiDNEKLIKIEKDVEEIKEIVKEL 79 
                                   5566778899999*************9555533333334445555566665554 PP

>> SCFA_trans  Short chain fatty acid transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.6   6.8e-06    0.0067     192     237 ..      27      74 ..       4      87 .] 0.73

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.8e-06
                    SCFA_trans 192 ynliilaili.vvlplitamlaPkkeevksidk.kllkeekeeekklk 237
                                   y+++ ++i++ ++ ++i+ ++ P k++  sid+ kl+k ek+ e+  +
  gi|15668405|ref|NP_247201.1|  27 YDILWMIIFVvIIAVIIYILISPLKKQSSSIDNeKLIKIEKDVEEIKE 74 
                                   6777666655055667778899**********8789998887765443 PP

>> ASFV_J13L  African swine fever virus J13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.8   1.3e-05     0.013      31      71 ..      26      65 ..       9      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                     ASFV_J13L 31 mytiliaivvliiiiivliylfssrkkkaaaaieeediqfi 71
                                  +y il  i ++++ii v+iy++ s  kk +++i++e +  i
  gi|15668405|ref|NP_247201.1| 26 FYDILWMI-IFVVIIAVIIYILISPLKKQSSSIDNEKLIKI 65
                                  57777665.5677888999*999999999999*99986555 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.1   2.2e-05     0.022      12      64 ..      29      82 ..      26      87 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                     4HB_MCP_1 12 flllallliivGvvGlyslkkinknletmYedrllpik.dlgeikanlrelrad 64
                                  +l ++++++i++v+ ++ ++ ++k+++++ +++l++i+ d++eik+ ++el+ +
  gi|15668405|ref|NP_247201.1| 29 ILWMIIFVVIIAVIIYILISPLKKQSSSIDNEKLIKIEkDVEEIKEIVKELKKK 82
                                  6889*********************************53799999888887765 PP

>> DUF3671  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   6.8   1.7e-05     0.017      84     113 ..      22      51 ..       4      53 .. 0.89
   2 ?   -0.4   0.3       1.2   1.2e+03      19      29 ..      69      79 ..      56      86 .. 0.43

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-05
                       DUF3671  84 sieklytiffiilvviillvliYiliKviK 113
                                   +i+  y+i+++i+ v+i+ v+iYili+ +K
  gi|15668405|ref|NP_247201.1|  22 AINPFYDILWMIIFVVIIAVIIYILISPLK 51 
                                   57889*********************9777 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                       DUF3671 19 idkidelakkk 29
                                  +++i+e+ k+ 
  gi|15668405|ref|NP_247201.1| 69 VEEIKEIVKEL 79
                                  22222222222 PP

>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.3   2.7e-05     0.027       4      56 ..      28      81 ..      26      83 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-05
                Chordopox_A13L  4 dlllliiCvaivglivYgiYn..rkketqttnpstveeyeeedniKtgfvdkLks 56
                                  d+l +ii v+i+++i+Y +    +k++++  n + ++  +  ++iK   v +Lk+
  gi|15668405|ref|NP_247201.1| 28 DILWMIIFVVIIAVIIYILISplKKQSSSIDNEKLIKIEKDVEEIK-EIVKELKK 81
                                  7999*************87643344444445554455555555676.56666665 PP

>> Choline_kin_N  Choline kinase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.8   4.1e-05     0.041      28      45 ..      70      86 ..      67      87 .] 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                 Choline_kin_N 28 eeilrLlhtLalkgWrdv 45
                                  eei++++++L+ k+W+ +
  gi|15668405|ref|NP_247201.1| 70 EEIKEIVKELK-KKWEEI 86
                                  79*********.***976 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.8   3.5e-05     0.035      62      89 ..      59      86 ..      50      87 .] 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-05
               Snapin_Pallidin 62 akKLvnikkrmsslnerlqklkkRaekL 89
                                   +KL++i+k++++++e++++lkk+ e++
  gi|15668405|ref|NP_247201.1| 59 NEKLIKIEKDVEEIKEIVKELKKKWEEI 86
                                  58*********************98877 PP

>> Chordopox_G3  Chordopoxvirus G3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   4.4e-05     0.044       2      40 ..      29      66 ..      28      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.4e-05
                  Chordopox_G3  2 llnliffilfllvlyfltyyptnklelavkd.....lesenaii 40
                                  +l +i+f++ ++v  ++ + p+ k   ++++     +       
  gi|15668405|ref|NP_247201.1| 29 ILWMIIFVVIIAVIIYILISPLKKQSSSIDNeklikI------E 66
                                  57799************************99222221......2 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   4.9e-05     0.049      17      59 ..      30      69 ..      27      86 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-05
                       DUF4330 17 lDllailvilavivgiflkpgtsgsvaqaeaaatkpvevdvvv 59
                                  l +++ +vi+avi+ i+++p +++s + ++   +k ++++  v
  gi|15668405|ref|NP_247201.1| 30 LWMIIFVVIIAVIIYILISPLKKQSSSIDN---EKLIKIEKDV 69
                                  5578999***************94443332...3444444444 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   5.9e-05     0.059      13      60 ..      32      79 ..      26      86 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.9e-05
               Peptidase_S49_N 13 lvtlvvailvvvvlivalaakkkkekgelevtkLneeykelkeeleea 60
                                  ++++vv+i+v++ ++++  +k++++ ++ ++ k++++ +e+ke ++e 
  gi|15668405|ref|NP_247201.1| 32 MIIFVVIIAVIIYILISPLKKQSSSIDNEKLIKIEKDVEEIKEIVKEL 79
                                  678899999999888888888876666666666666666665555443 PP

>> Pox_LP_H2  Viral late protein H2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00013      0.13      13      79 ..      13      79 ..       5      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                     Pox_LP_H2 13 leyvrekeaksiraakvstliffvlilaisvlllllqvsdnsvlselakyariknavksWkplvesk 79
                                  ++yv ++  +   +     +i+fv+i+a+ + +l+  + ++s   + +k ++i + v++ k++v++ 
  gi|15668405|ref|NP_247201.1| 13 VHYVGSEGVAINPFYDILWMIIFVVIIAVIIYILISPLKKQSSSIDNEKLIKIEKDVEEIKEIVKEL 79
                                  5666666666666777778899999999999999999999999999*****************9873 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.1   0.00036      0.36       2      50 ..      33      82 ..      29      87 .] 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                      60KD_IMP  2 glaIilltiivrlillpltlkqlk.ssakmqelqPelkeiqekykkdkqk 50
                                  ++ ++++ +i+ +++ pl +++     +k+ +++++++ei+e  k+ k+k
  gi|15668405|ref|NP_247201.1| 33 IIFVVIIAVIIYILISPLKKQSSSiDNEKLIKIEKDVEEIKEIVKELKKK 82
                                  45677888899999999987765414589999999999999988544433 PP

>> YajC  Preprotein translocase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.1    0.0011       1.1       3      28 ..      32      57 ..      30      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                          YajC  3 llplvlifvifyfllirpqqkkqkeh 28
                                  ++++v+i+++++++li p +k+    
  gi|15668405|ref|NP_247201.1| 32 MIIFVVIIAVIIYILISPLKKQSSSI 57
                                  45688899888899999***998665 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.7    0.0039       3.9       2      25 ..      31      54 ..      29      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0039
               FeoB_associated  2 tiIVgliiaaavafvirrlikkkk 25
                                  ++I+ ++i+a++++++++  kk+ 
  gi|15668405|ref|NP_247201.1| 31 WMIIFVVIIAVIIYILISPLKKQS 54
                                  579************999999865 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.5       1.4   1.4e+03       7      21 ..      33      47 ..      29      51 .. 0.81
   2 ?   11.4   1.2   0.00026      0.26      94     121 ..      60      87 .]      46      87 .] 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                       DUF1664  7 ivpaavvgavgYgyv 21
                                  i+ +++++++ Y+ +
  gi|15668405|ref|NP_247201.1| 33 IIFVVIIAVIIYILI 47
                                  567899999999876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00026
                       DUF1664  94 edlseigedvesvkeaveglesklerie 121
                                   e+l +i++dve++ke+v++l++k e+ie
  gi|15668405|ref|NP_247201.1|  60 EKLIKIEKDVEEIKEIVKELKKKWEEIE 87 
                                   68889******************99997 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   6.3     0.019        19      67      86 ..      30      49 ..      26      52 .. 0.71
   2 ?    5.3   0.4     0.017        17       2      21 ..      59      78 ..      58      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.019
                                  XXXXXXXXXXXXXXXXXXXX CS
                 Synaptobrevin 67 kliiililvvlililiiiiv 86
                                   ++ii++++++++i+i+i++
  gi|15668405|ref|NP_247201.1| 30 LWMIIFVVIIAVIIYILISP 49
                                  46777777777777777765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.017
                                  XXHHHHHHHHHHCCCCHHCC CS
                 Synaptobrevin  2 ndklakikaevdevkdimke 21
                                  n+kl ki+++v+e+k+i+ke
  gi|15668405|ref|NP_247201.1| 59 NEKLIKIEKDVEEIKEIVKE 78
                                  78999************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2715  (0.151431); expected 358.6 (0.02)
Passed bias filter:                     1383  (0.0771376); expected 358.6 (0.02)
Passed Vit filter:                       220  (0.0122706); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 594.47
//
Query:       gi|15668406|ref|NP_247202.1|  [L=416]
Description: PmbA protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-53  180.2   1.1    9.3e-53  179.9   1.1    1.1  1  PmbA_TldD        Putative modulator of DNA gyrase
  ------ inclusion threshold ------
       0.12   12.7   0.1       0.27   11.5   0.1    1.6  1  Lipoprotein_Ltp  Host cell surface-exposed lipoprotein


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.9   1.1     1e-56   9.3e-53       2     279 .]      17     290 ..      16     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: 179.9 bits;  conditional E-value: 1e-56
                                   EEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESS....HHHHHHHHHHHHHHCCS---TT-... CS
                     PmbA_TldD   2 aevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsd....ealeeaveraveiaklapedpea... 75 
                                    ev +++s + sv ++ ++v++ ++ +++g+gvrvik+g++gfa++++ ++    +a++++ve+  +  ++a +++++   
  gi|15668406|ref|NP_247202.1|  17 TEVLFVKSYEVSVDLDGKSVDSFQTGISYGIGVRVIKDGKVGFAYANKFDEnivyKAMKNLVED--KYTEFAHPQKYKepk 95 
                                   699****************************************998888876777788888887..333444444444665 PP

                                   .......GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEEEEEEEEEE. CS
                     PmbA_TldD  76 .......eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtrvslslsviad 149
                                           ++++e+  e l  + + + +           ++   s+ +s +++  +++nS+G+dve+++t++s+ +s++ d
  gi|15668406|ref|NP_247202.1|  96 gmfykeiLDLDEEKLLEDLITMRDIALDN----------NAIVLSGGVSKEVGYARLINSNGVDVEEQDTYFSAAISIMYD 166
                                   55555443333333333333333332222..........444566788889999**************************4 PP

                                   .STCSETEEEEEEEE.SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGHHHHHTBHHHHHTT--T CS
                     PmbA_TldD 150 .dggsgdgmgggsgy.edleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllheavghaleadavlegrSf 228
                                    +        + ++  ++ + +d+eei  +a + a++s + k++   k ++vlsp+a+ +ll++++ +a++a++v++ rS+
  gi|15668406|ref|NP_247202.1| 167 gE--------TSYECrTRHNIFDVEEISYRALDLAKKSANGKAISY-KGNIVLSPRALYDLLSYTLMPAFSAENVQRDRSV 238
                                   23........2222242333377888*************9888655.5********************************* PP

                                   TTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                     PmbA_TldD 229 lkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                   lk+k+Ge+++ e++ti+dd+t  ++l+s+  D+EG++tq+tvl+enGvLkny
  gi|15668406|ref|NP_247202.1| 239 LKGKIGEQIFGENITIIDDGTLdYALYSSKCDGEGTATQKTVLVENGVLKNY 290
                                   *99******************99****************************9 PP

>> Lipoprotein_Ltp  Host cell surface-exposed lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1     3e-05      0.27       3      40 ..     194     231 ..     193     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3e-05
               Lipoprotein_Ltp   3 nknAlkkAksYadtmnmSkqglydqLtseyGekFteee 40 
                                   +k+A  kA sY  +  +S+ +lyd L ++    F++e 
  gi|15668406|ref|NP_247202.1| 194 KKSANGKAISYKGNIVLSPRALYDLLSYTLMPAFSAEN 231
                                   7999**********************998887887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2529.14
//
Query:       gi|15668407|ref|NP_247203.1|  [L=427]
Description: phosphopyruvate hydratase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   8.7e-134  445.4   0.2   1.1e-133  445.1   0.2    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    1.9e-58  196.3   0.2    3.2e-58  195.6   0.2    1.4  1  Enolase_N  Enolase, N-terminal domain
    1.6e-11   44.2   0.0    2.4e-11   43.6   0.0    1.2  1  MR_MLE_C   Enolase C-terminal domain-like
    0.00071   18.8   0.1     0.0025   17.0   0.0    1.8  2  MAAL_C     Methylaspartate ammonia-lyase C-terminus
  ------ inclusion threshold ------
       0.15   11.8   0.0       0.39   10.4   0.1    1.6  2  TAF1D      TATA box-binding protein-associated factor 1D


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.1   0.2    3e-137  1.1e-133       2     293 ..     146     424 ..     145     427 .] 0.98

  Alignments for each domain:
  == domain 1  score: 445.1 bits;  conditional E-value: 3e-137
                                   -EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHHHH CS
                     Enolase_C   2 lvlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnkea 82 
                                   +v+PvP++nvinGG+hagn+l+lqefmi+Pvga+s++ea+r+G+evyh lk+v+ +kygk+a nvGdeGGfaP l++++ea
  gi|15668407|ref|NP_247203.1| 146 YVMPVPMMNVINGGKHAGNDLDLQEFMIMPVGATSISEAVRMGSEVYHVLKNVILEKYGKNAVNVGDEGGFAPPLKTSREA 226
                                   89******************************************************************************* PP

                                   HHHHHHHHHHCT-TCTBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEES-S-TT-H CS
                     Enolase_C  83 ldliveaiekaGykgkvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsiedpldeddw 163
                                   ldl++e+++kaGy+++v+ ald+a+sefy  kd+ y +++k+        lt e+l d+yk lv++yPivsiedp+ e+d+
  gi|15668407|ref|NP_247203.1| 227 LDLLTESVKKAGYEDEVVFALDAAASEFY--KDGYYYVEGKK--------LTREELLDYYKALVDEYPIVSIEDPFHEEDF 297
                                   *****************************..78899998887........******************************* PP

                                   HHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEEEE--SC--S--H CS
                     Enolase_C 164 eawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvvvshrsGetedtt 244
                                   e+++++t+el+  +qivGddl+vtn++rl+++ie kaanalllkvnqiG+l+e+++a++la ++gygvvvshrsGetedtt
  gi|15668407|ref|NP_247203.1| 298 EGFAMITKELD--IQIVGDDLFVTNVERLRKGIEMKAANALLLKVNQIGTLSEAVDAAQLAFRNGYGVVVSHRSGETEDTT 376
                                   ***********..******************************************************************** PP

                                   HHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE-GGGCT CS
                     Enolase_C 245 iadlavglsaGqiktGaparserlakynqllrieeelgekakyaGkkvr 293
                                   iadl+v+l++GqiktGapar er akynql+rie+elg  +kyaG+++r
  gi|15668407|ref|NP_247203.1| 377 IADLSVALNSGQIKTGAPARGERTAKYNQLIRIEQELGL-SKYAGRNFR 424
                                   *************************************96.79****997 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.6   0.2     9e-62   3.2e-58       1     131 []      11     140 ..      11     140 .. 0.99

  Alignments for each domain:
  == domain 1  score: 195.6 bits;  conditional E-value: 9e-62
                                   EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHTTSBT CS
                     Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapaligldv 81 
                                   Ik++ are++dSrGnpTvevev+t+ + +g+a+vpsGaStg++ealelrD+ +kr++gkgv+ avenvn++i+p+++g+d+
  gi|15668407|ref|NP_247203.1|  11 IKDIVAREVIDSRGNPTVEVEVITKGNGYGSAIVPSGASTGTHEALELRDK-EKRFGGKGVLMAVENVNSIIRPEILGYDA 90 
                                   89**********************9999**********************8.8**************************** PP

                                   T-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                     Enolase_N  82 tdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                   + q+eiD+++ielDgt+nks+lGaNailavSlAvakaaA+++++ply+yl
  gi|15668407|ref|NP_247203.1|  91 RMQREIDTIMIELDGTPNKSRLGANAILAVSLAVAKAAAATAKIPLYKYL 140
                                   *************************************************8 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   6.8e-15   2.4e-11      26     172 ..     222     385 ..     190     406 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 6.8e-15
                                   HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTT..S............BHHHHHHHHHHH.GGGTESEEESSSSTTTHHHHHH CS
                      MR_MLE_C  26 dvaedvervravreavgpgddvdlmvDanqa..w............dlatAirvarel.eeldllwlEEPvppeddlegla 91 
                                   + +e ++ +++  + +g +d+v +++Da ++  +            ++++ + + ++l +e+ +  +E+P++  +d eg a
  gi|15668407|ref|NP_247203.1| 222 TSREALDLLTESVKKAGYEDEVVFALDAAASefYkdgyyyvegkklTREELLDYYKALvDEYPIVSIEDPFHE-EDFEGFA 301
                                   667888888888888899**********999752677778888888************666***********9.57***** PP

                                   HHHHHH.SSEEEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBS.CS.SHHHHHHHHH CS
                      MR_MLE_C  92 elrara.sipiaagEslys.radfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHs.gs.gglglaaslh 168
                                   +++ ++ +i+i+++    + ++++r+ +e +a+ ++ ++v+++g ++ea++ a+la  +g+ v++ +  + +  +++a l+
  gi|15668407|ref|NP_247203.1| 302 MIT-KElDIQIVGDDLFVTnVERLRKGIEMKAANALLLKVNQIGTLSEAVDAAQLAFRNGYGVVVSHrSGeTEDTTIADLS 381
                                   ***.777*******987666************************************9988887766522225667777777 PP

                                   HHHT CS
                      MR_MLE_C 169 laaa 172
                                   +a  
  gi|15668407|ref|NP_247203.1| 382 VALN 385
                                   7655 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.28     1e+03     191     218 ..      99     126 ..      89     133 .. 0.80
   2 !   17.0   0.0     7e-07    0.0025     135     216 ..     304     386 ..     264     394 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.28
                        MAAL_C 191 vgaylGGscnetdvsarvsvhvalatrp 218
                                   + + l G+ n    +a+++  v+la+  
  gi|15668407|ref|NP_247203.1|  99 IMIELDGTPNKSRLGANAILAVSLAVAK 126
                                   5566789************999999864 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 7e-07
                        MAAL_C 135 ekgikvelvaDe.WcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvsarvsvhval 214
                                   +k  ++++v D+ +  ++e +r+ ++ +aa+++ +k+  +G+++++++a + + ++g g+ +   + et+ ++ +   val
  gi|15668407|ref|NP_247203.1| 304 TKELDIQIVGDDlFVTNVERLRKGIEMKAANALLLKVNQIGTLSEAVDAAQLAFRNGYGVVVSHRSGETEDTTIADLSVAL 384
                                   4566899**998467789***************************************************998877777777 PP

                        MAAL_C 215 at 216
                                     
  gi|15668407|ref|NP_247203.1| 385 NS 386
                                   54 PP

>> TAF1D  TATA box-binding protein-associated factor 1D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         1   3.7e+03      72     106 ..      39      73 ..      34      89 .. 0.78
   2 ?   10.4   0.1   0.00011      0.39     161     214 ..     269     321 ..     262     326 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1
                         TAF1D  72 ykptgrprgrpkgkkntkssqekkkrlkdkgvqfp 106
                                   y +   p g + g++++ + + k+kr+  kgv ++
  gi|15668407|ref|NP_247203.1|  39 YGSAIVPSGASTGTHEALELRDKEKRFGGKGVLMA 73 
                                   66677788888899999999999999999998554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00011
                         TAF1D 161 kedldvrkykylDDegsiSPieesnaedenateleeedecDvklvenscFiiss 214
                                   +e+l    yk l De +i  ie++  e++    +  ++e+D+++v ++ F+ + 
  gi|15668407|ref|NP_247203.1| 269 REEL-LDYYKALVDEYPIVSIEDPFHEEDFEGFAMITKELDIQIVGDDLFVTNV 321
                                   5554.3569***************99888777777789************9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2959.87
//
Query:       gi|15668408|ref|NP_247204.1|  [L=277]
Description: hypothetical protein MJ_0233 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-16   60.7  37.5    1.5e-16   60.7  37.5    2.6  3  DUF4013          Protein of unknown function (DUF4013)
  ------ inclusion threshold ------
       0.75    9.8  19.8        0.4   10.7   0.4    3.1  3  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   5.0     0.022     2e+02      39      98 ..      18      74 ..      10      75 .. 0.49
   2 !   60.7  37.5   1.6e-20   1.5e-16       2     165 ..      65     217 ..      64     219 .. 0.80
   3 ?   -1.5   1.2      0.23     2e+03      83     101 ..     235     252 ..     218     273 .. 0.39

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.022
                       DUF4013 39 dwgkllvdGlkafvvslvYllipliialltllvalaslaagdsaagallvlallglllal 98
                                  +++kl + Gl+ ++v+   ++  ++i l   ++  a ++++   ++ l+ +++++++ ++
  gi|15668408|ref|NP_247204.1| 18 NFKKLCIGGLMSAIVGAMSGVTTAFIDL---FMERANYDIMHIIMSFLIYFGIIFIIGLI 74
                                  5777777777777777776644444423...33333333333333333333333333332 PP

  == domain 2  score: 60.7 bits;  conditional E-value: 1.6e-20
                       DUF4013   2 lsllliiaivlslvllGYlvrvlrdtirgddelPefddwgkllvdGlk....afvvslvYllipliialltllvalaslaa 78 
                                   +++++ii++++s ++ GY vr++++t++g + +P+++++++ll +G+     ++++ +++++ip+i+           + +
  gi|15668408|ref|NP_247204.1|  65 FGIIFIIGLIVSAIIGGYNVRIMKTTVEGLNVAPDWNNITDLLYRGILyivgLVLLNIIFYFIPAIL----------FVFG 135
                                   689********************************************96665566666677799999..........1222 PP

                       DUF4013  79 gdsaagallvlallglllalllvllllllfglllpvalarfartgslsaafnfkeilklikkkigkyiialilllvigivl 159
                                   ++s++   +++a+l+++  +l+++++++ + l++ +a +++  +g +  +f+fkei+k+i    ++yii +i++++i +++
  gi|15668408|ref|NP_247204.1| 136 IFSLYISKIIGAFLIIIS-ILIFIISVISLWLYSKLAEVNYSVKG-FYGFFEFKEIFKMI--G-IRYIILVIIIAIINFII 211
                                   333333333333333333.3335667777999999**********.**************..4.5**************** PP

                       DUF4013 160 sllail 165
                                   sl+++l
  gi|15668408|ref|NP_247204.1| 212 SLIVVL 217
                                   **9876 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.23
                       DUF4013  83 agallvlallglllalllv 101
                                   +++++ + + g+ +al   
  gi|15668408|ref|NP_247204.1| 235 ILTIIYISIKGISYALS-T 252
                                   21122222222222221.2 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4   4.5e-05       0.4      33     105 ..      22      94 ..      18     101 .. 0.54
   2 ?    6.1   5.8    0.0012        11      42      95 ..     115     174 ..     104     178 .. 0.61
   3 ?    1.9   0.9     0.024   2.1e+02      42      83 ..     198     247 ..     185     252 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.5e-05
               Phage_holin_3_6  33 agsgagllgaagvlallalllllval..alalaa.....lwlaalivaavllvla.gvlalvglkklkkakplpertieel 105
                                   + +g+++ ++ g++  ++ +++ +++  a            +++li +++ ++++ +v a++g  +++     ++ t+e l
  gi|15668408|ref|NP_247204.1|  22 LCIGGLMSAIVGAMSGVTTAFIDLFMerA----NydimhIIMSFLIYFGIIFIIGlIVSAIIGGYNVRI----MKTTVEGL 94 
                                   45555555544444444444444444322....023346789****66555555527778888777776....55666665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0012
               Phage_holin_3_6  42 aagvlallalllllval..alalaa......lwlaalivaavllvlagvlalvglkklkkak 95 
                                   +++vl+   +++++ a+  ++++ +         a+li+  +l+ +  v  l+ ++kl++++
  gi|15668408|ref|NP_247204.1| 115 VGLVLL-NIIFYFIPAIlfVFGI-FslyiskIIGAFLIIISILIFIISVISLWLYSKLAEVN 174
                                   233333.2222222222133333.12245689999***999999999999999999998865 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.024
               Phage_holin_3_6  42 aagvlallalllllval.a...lala.a...lwlaalivaavllvlagvl 83 
                                   + +v+ +  + +++ ++ +    +++ +   ++la  i++++++ + g+ 
  gi|15668408|ref|NP_247204.1| 198 IILVIIIAIINFIISLIvVlplNIIDiFisySALANSILTIIYISIKGIS 247
                                   33333333333333333222223333225678888889999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1378  (0.0768587); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 1828.65
//
Query:       gi|15668409|ref|NP_247205.1|  [L=336]
Description: anthranilate synthase component II TrpD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.5e-102  339.9   1.1   1.9e-101  338.9   0.2    1.7  2  Glycos_transf_3  Glycosyl transferase family, a/b domain
    1.5e-19   69.6   3.5    1.5e-19   69.6   3.5    1.9  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.11   9.6e+02     195     221 ..      16      42 ..       8      50 .. 0.81
   2 !  338.9   0.2  2.1e-105  1.9e-101       3     253 .]      74     323 ..      72     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.11
                                   SHHHHHHHHTTHHTSCHHHHHHHHHHH CS
               Glycos_transf_3 195 epkenaeilkavlegkksaakrdlvll 221
                                   ++ke+ +++k++++g+ + ++  ++l+
  gi|15668409|ref|NP_247205.1|  16 DEKEAEAVMKDIMSGNAKPTQIAAILT 42 
                                   56899999*******999987666654 PP

  == domain 2  score: 338.9 bits;  conditional E-value: 2.1e-105
                                   TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEEEHHS CS
               Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgflfape 83 
                                   +l+D++gTGGd+ ntfNiSta+a+vv+a  v+vakhgn++vssksGsaDvLealgvnl++  e+v++++e+ g+gflfap+
  gi|15668409|ref|NP_247205.1|  74 KLLDTCGTGGDNLNTFNISTATAFVVSAY-VPVAKHGNKAVSSKSGSADVLEALGVNLNVPIERVKESIEKIGIGFLFAPH 153
                                   789************************98.9************************************************** PP

                                   SSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHHHHHHHHHHH CS
               Glycos_transf_3  84 yhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldevsllakttva 164
                                   +h+amk ++pvr+elgirTvfn+LGPL+npa++++ql+gvy+++l ekla+vlk+lg + alvvhg+G+de+++++kt + 
  gi|15668409|ref|NP_247205.1| 154 FHPAMKFATPVRKELGIRTVFNVLGPLTNPANANYQLMGVYDEKLTEKLANVLKNLGLKGALVVHGSGMDEITTIGKTKIS 234
                                   ********************************************************************************* PP

                                   HHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHHHHHHHHHH CS
               Glycos_transf_3 165 elkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagkadslkegvakaee 245
                                   el +gei++y +epedfg+k+a+le+++gg+++ena+i+ +++eg++  akrd+v+lna+ al++a++a++++eg++ ae+
  gi|15668409|ref|NP_247205.1| 235 ELRNGEIKSYYIEPEDFGIKKAKLEDIRGGDAEENAKIIGEIFEGEEVGAKRDIVVLNAAFALYIAEEAKDVEEGIKLAEK 315
                                   ********************************************************************************* PP

                                   HHHTSHHH CS
               Glycos_transf_3 246 vidsGkAl 253
                                   +id+GkAl
  gi|15668409|ref|NP_247205.1| 316 SIDEGKAL 323
                                   ******95 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   3.5   1.7e-23   1.5e-19       2      63 .]       4      65 ..       3      65 .. 0.97
   2 ?   -1.8   0.1      0.32   2.9e+03      15      29 ..     266     280 ..     264     309 .. 0.66

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.7e-23
                                  HHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
               Glycos_trans_3N  2 diikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63
                                  +++kk+++ ++L++ e+++++++i++g++++ qiaA L+Alr+kGet eEi+a+a+ mre++
  gi|15668409|ref|NP_247205.1|  4 EALKKVIEFKDLDEKEAEAVMKDIMSGNAKPTQIAAILTALRMKGETIEEITAFAKIMREFS 65
                                  789********************************************************985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.32
                                   HHHHHHHHHHHHTTS CS
               Glycos_trans_3N  15 aeeirfaihgilkge 29 
                                   aee + +i +i++ge
  gi|15668409|ref|NP_247205.1| 266 AEENAKIIGEIFEGE 280
                                   577777788888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2104.06
//
Query:       gi|15668410|ref|NP_247206.1|  [L=82]
Description: hypothetical protein MJ_0235 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.01   15.3   3.6      0.013   15.0   1.2    1.9  2  Cluap1          Clusterin-associated protein-1
      0.023   13.0   2.9      0.027   12.8   2.9    1.0  1  Sucrose_synth   Sucrose synthase
      0.083   12.8   2.4       0.11   12.5   1.8    1.6  1  Type2_restr_D3  Type-2 restriction enzyme D3 domain
      0.095   12.9   3.9       0.14   12.3   3.9    1.2  1  Fib_alpha       Fibrinogen alpha/beta chain family
        9.7    7.3   5.6         23    6.1   0.6    2.1  2  DUF5320         Family of unknown function (DUF5320)


Domain annotation for each model (and alignments):
>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.2   3.5e-06     0.013     220     260 ..       7      45 ..       3      54 .. 0.76
   2 ?    1.9   0.3     0.034   1.2e+02      38      60 ..      47      70 ..      39      82 .] 0.56

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-06
                        Cluap1 220 qsvrPafmdeyekleeeLqelyeeYvekfrnlsylekqlek 260
                                   +s++  f++e ++le+eL++++++Y  k +  + l+k++ +
  gi|15668410|ref|NP_247206.1|   7 NSMKKVFLEELKDLENELNQIFKKYNVKSK--DELKKKIAN 45 
                                   678889*******************76655..455555555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.034
                        Cluap1 38 eip.eeieteqdRVifiksvaefl 60
                                  ei+ e+i+ + +R++f+++  e +
  gi|15668410|ref|NP_247206.1| 47 EIKeEQIKDDLERIEFLEENIERV 70
                                  455466777777777776544433 PP

>> Sucrose_synth  Sucrose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.9   7.5e-06     0.027       3      74 ..       7      79 ..       5      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.5e-06
                 Sucrose_synth  3 esiadkleealkqsreelkrllsryvekgkrllkkkelldele.kviedkkerkkllegllgkvlsstqeaiv 74
                                  +s+++ + e lk+  +el++++++y  k+k  lkkk    e++ + i+d+ er ++le  +++v+++ +e+ v
  gi|15668410|ref|NP_247206.1|  7 NSMKKVFLEELKDLENELNQIFKKYNVKSKDELKKKIANGEIKeEQIKDDLERIEFLEENIERVMKCLREINV 79
                                  79999999***************************99999986267899********************9977 PP

>> Type2_restr_D3  Type-2 restriction enzyme D3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.8     3e-05      0.11      21      60 ..      26      63 ..      22      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                Type2_restr_D3 21 ylleskkrrsleeikayLklagleEdveTIkDDiqglini 60
                                   + ++++++s +e+k++++   ++E+   IkDD++ ++  
  gi|15668410|ref|NP_247206.1| 26 QIFKKYNVKSKDELKKKIANGEIKEE--QIKDDLERIEFL 63
                                  5668999****************996..6****9887765 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.9   3.9e-05      0.14      39     106 ..       8      76 ..       3      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.9e-05
                                   CCCC.CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                     Fib_alpha  39 klen.eleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilrlketidaqesnirv 106
                                   ++++  lee+++ ++e +++ k+ + + +++ k+k  n +   ++++++le +i+ l+e+i + ++ +r+
  gi|15668410|ref|NP_247206.1|   8 SMKKvFLEELKDLENELNQIFKKYNVKSKDELKKKIANgEIKEEQIKDDLE-RIEFLEENIERVMKCLRE 76 
                                   555425889999999999999999999999999988887888899999999.999999999988777665 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.5     0.023        81      74      95 ..       9      30 ..       2      34 .. 0.77
   2 ?    6.1   0.6    0.0063        23      70      98 ..      48      76 ..      28      77 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.023
                       DUF5320 74 ekelLeeqaeaLeeeleaikkr 95
                                   k+++ e+ + Le+el++i k+
  gi|15668410|ref|NP_247206.1|  9 MKKVFLEELKDLENELNQIFKK 30
                                  4667778889999999998776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0063
                       DUF5320 70 skeeekelLeeqaeaLeeeleaikkrlke 98
                                   kee+++   e++e+Lee++e ++k l+e
  gi|15668410|ref|NP_247206.1| 48 IKEEQIKDDLERIEFLEENIERVMKCLRE 76
                                  4455555555799**********999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2962  (0.165207); expected 358.6 (0.02)
Passed bias filter:                      985  (0.0549389); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 549.37
//
Query:       gi|15668411|ref|NP_247207.1|  [L=421]
Description: hypothetical protein MJ_0236 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-57  194.1   0.0    1.8e-57  193.5   0.0    1.3  1  ThiP_synth    Thiamine-phosphate synthase
    2.4e-55  187.6   0.0    2.5e-54  184.3   0.0    2.0  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
     0.0028   17.3   0.1     0.0052   16.4   0.1    1.4  1  PGBA_N        Plasminogen-binding protein pgbA N-terminal
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.026   14.0   0.0    1.4  1  Carb_kinase   Carbohydrate kinase


Domain annotation for each model (and alignments):
>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.5   0.0   4.1e-61   1.8e-57       2     163 ..     251     410 ..     250     412 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.5 bits;  conditional E-value: 4.1e-61
                                   HHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-T.SSEEE-S-EEETS-CHHHHHHHHHHCC-TT- CS
                    ThiP_synth   2 leralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvk.grvkvvgepefgasshvarvllaamkfdpev 81 
                                   l+ a+ ll++++   +liPevgsNia++lp +k+ +Dvaa++GRI++ k g+  +vg++efgas+h+a+++l+a kf+pe+
  gi|15668411|ref|NP_247207.1| 251 LSYAIYLLKKMN--FTLIPEVGSNIAESLPFPKDFKDVAALTGRIIKNKlGGFYIVGDIEFGASEHIAKIILSASKFNPEI 329
                                   566777777777..69***************************************************************** PP

                                   -EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EEEEEESSHHHHHH CS
                    ThiP_synth  82 raainirydekilealeelglkvvefdreeepeevgstmewgvaeaieel.evpdviydeGgvGkEpmiyvlgkdaeevve 161
                                   ra++ni+yd  +++ l+++ + v++fdr+eep++v stmewg++ a+e+  +vpd+iyd+Gg GkEpmi+vlg+da evv+
  gi|15668411|ref|NP_247207.1| 330 RACMNIKYDGGLIKLLKDK-FAVSSFDRKEEPPNV-STMEWGTKIACEKFgGVPDIIYDRGGEGKEPMIRVLGRDAIEVVK 408
                                   ****************996.**************6.**************99***************************** PP

                                   HH CS
                    ThiP_synth 162 kv 163
                                   kv
  gi|15668411|ref|NP_247207.1| 409 KV 410
                                   *8 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.3   0.0   5.6e-58   2.5e-54       1     244 [.      14     239 ..      14     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 184.3 bits;  conditional E-value: 5.6e-58
                                   ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHHH CS
                  Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiievvaek 81 
                                   D+++GAGi+AD+kt+++lgvy+ ++ t+++ qn+k v+e ++lp+e +++q++av+e+++++ vK+G+l ++ +i+++ ++
  gi|15668411|ref|NP_247207.1|  14 DPTSGAGISADIKTAHTLGVYCPTITTSVIPQNNKMVYEKFDLPEENIKNQFKAVFEEFDIEYVKTGVL-TKPAIDTLLKY 93 
                                   9********************************************************************.778889999** PP

                                   HHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEE CS
                  Phos_pyr_kin  82 lkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlik 162
                                   ++ky+++v++DPV+++++  ++++e+ +e++ e L++++ +itPN +E++++++  ik+++ m +    +l++g + +l+k
  gi|15668411|ref|NP_247207.1|  94 IDKYDLKVICDPVLASTTKFSFVDEKLMEKYIE-LFNKSFLITPNKEEYKKIME-FIKNNNLMIRNDLYILATGIDDILMK 172
                                   ********************************8.*******************8.99999*******99999999999999 PP

                                   EGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHH..CG-BSTSS CS
                  Phos_pyr_kin 163 GghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvteaik..ealelgkg 241
                                     +                 ++++++ r++ k+ hGtGC++s+ai+a l+kg++leeA+k+Ak++v +++   ++ ++g +
  gi|15668411|ref|NP_247207.1| 173 NFK----------------PIKTFKGFRVD-KEVHGTGCVYSTAITAFLSKGYDLEEAIKEAKRFVLSSVIyaKKSKFGYN 236
                                   987................4789*******.************************************99985556666665 PP

                                   S-B CS
                  Phos_pyr_kin 242 agp 244
                                    +p
  gi|15668411|ref|NP_247207.1| 237 SNP 239
                                   555 PP

>> PGBA_N  Plasminogen-binding protein pgbA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.2e-06    0.0052      88     121 ..     126     160 ..     117     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-06
                        PGBA_N  88 elydralliaPneeiYekiksavkeitf.ihpDlf 121
                                   el+++++li+Pn+e Y+ki + +k++++ i  Dl+
  gi|15668411|ref|NP_247207.1| 126 ELFNKSFLITPNKEEYKKIMEFIKNNNLmIRNDLY 160
                                   689*******************9977642678876 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.8e-06     0.026      61     239 ..      65     243 ..       7     248 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-06
                                   ..--SSS-SEEEE-TT-SSSHCHHHHCHHHCCCCS-EEEE.....GGGGGSGGGG......TTTTSSEEEE--HHHHHHHC CS
                   Carb_kinase  61 ileklerldavviGpGLgrdekikklleevlekdeplviD.....AdgLnllaqkne...lserkaeviLTPhkkEfkrLl 133
                                     +  e  d+  +  G  ++++i+ ll+++ + d  ++ D        + ++++k     +  +++   +TP+k E+k+++
  gi|15668411|ref|NP_247207.1|  65 FKAVFEEFDIEYVKTGVLTKPAIDTLLKYIDKYDLKVICDpvlasTTKFSFVDEKLMekyIELFNKSFLITPNKEEYKKIM 145
                                   34555667777777777788888887777777777766664441133455555543367788999**************** PP

                                   TTTCHHCCSHHHHHHHHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHH CS
                   Carb_kinase 134 kaivkkeddrlelarelaqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaa 214
                                   + i           ++l  +    +l  g  d++++  +++++ +   + + + G+G v + +i a+L+  ++  ea   a
  gi|15668411|ref|NP_247207.1| 146 EFIK---------NNNLMIRNDLYILATGIDDILMKNFKPIKTFKGFRVDKEVHGTGCVYSTAITAFLSKGYDLEEAIKEA 217
                                   ****.........445666667789*********************************************99766654333 PP

                                   H.HHHHHHHHHHCCCT-TS-HCHHHH CS
                   Carb_kinase 215 a.wlhgaasdeaaekkgvgmlatels 239
                                     ++ +    +++ k g+  ++t++ 
  gi|15668411|ref|NP_247207.1| 218 KrFVLSSVIYAKKSKFGYNSNPTYIN 243
                                   31333333334444444556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2727.83
//
Query:       gi|15668412|ref|NP_247208.1|  [L=566]
Description: arginyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-36  122.9   0.2    7.8e-36  122.9   0.2    3.3  3  DALR_1           DALR anticodon binding domain
    5.1e-33  114.5   2.4    8.2e-33  113.8   2.4    1.3  1  tRNA-synt_1d     tRNA synthetases class I (R)
    3.3e-19   69.2   5.9    2.4e-18   66.5   1.5    3.8  4  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
    1.3e-07   30.9   0.2      0.011   14.7   0.0    3.2  3  tRNA-synt_1f     tRNA synthetases class I (K)
    1.3e-06   27.5   2.0      0.029   13.1   0.1    3.7  4  tRNA-synt_1g     tRNA synthetases class I (M)
    5.3e-05   22.7   2.1    5.8e-05   22.6   0.4    1.9  2  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
     0.0046   15.3   1.2     0.0098   14.2   0.3    2.0  2  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
  ------ inclusion threshold ------
      0.031   13.5   0.0      0.067   12.3   0.0    1.6  1  CAF1             CAF1 family ribonuclease
      0.035   14.6   0.2       0.61   10.6   0.0    2.9  4  RuvA_C           RuvA, C-terminal domain
      0.053   14.0   0.1       0.14   12.6   0.1    1.7  1  RlmM_FDX         RlmM ferredoxin-like domain
       0.13   12.4   0.5          6    7.0   0.0    2.3  2  Nup54            Nucleoporin complex subunit 54


Domain annotation for each model (and alignments):
>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.8      0.27   4.4e+02      29      55 ..     197     228 ..     180     253 .. 0.66
   2 ?    0.4   0.0      0.44   7.2e+02      99     117 ..     342     360 ..     340     362 .. 0.87
   3 !  122.9   0.2   4.8e-39   7.8e-36       1     119 []     448     566 .]     448     566 .] 0.94

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.27
                                   C.....S-SHHHHHHHHHHHTHHHHHHHHHHH CS
                        DALR_1  29 l.....leeeeekeLlkalaqfpevleeaaee 55 
                                   +      + eee+++l  + +++++le+  ++
  gi|15668412|ref|NP_247208.1| 197 InkyleEHPEEEEKILELMRKYEDALENNEDN 228
                                   12333345559999999999999999987665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.44
                                   HHHHHHHHHHHHTT----S CS
                        DALR_1  99 avrqvLangLdlLGieape 117
                                   +++++++ +L+lLG ++pe
  gi|15668412|ref|NP_247208.1| 342 LTAEMVKAALKLLGSKVPE 360
                                   688999********99998 PP

  == domain 3  score: 122.9 bits;  conditional E-value: 4.8e-39
                                   HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHHHCTS CS
                        DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYnkerv 81 
                                   +qyahaR++sil++ae++g k+e+  +    + eekeL+k l +f+++++e+ae++++h la+yl eLa++f++fY ++++
  gi|15668412|ref|NP_247208.1| 448 IQYAHARCCSILKEAENKGVKDEAVFNYE-LTSEEKELIKMLDEFKDIIKESAESRRVHILANYLLELAKAFNRFYANCPI 527
                                   7*********************9999999.999************************************************ PP

                                   TTSC.THHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                        DALR_1  82 lkee.eeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                   l ++ +++ +++RL+Lvk+++ vL++gL+lLGi++p +m
  gi|15668412|ref|NP_247208.1| 528 LMTKvDDDVKKSRLKLVKSTKTVLETGLELLGINCPGRM 566
                                   9854133346**************************999 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8   2.4     5e-36   8.2e-33       9     335 ..     104     420 ..      96     434 .. 0.83

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 5e-36
                                   TTTT.---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTT CS
                  tRNA-synt_1d   9 krklqkksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekll 89 
                                   +++++   ++  k++++++s n   ++h+GhLr +iiGd + r+lef Gydv    +v D G+q+ l++ ++e  + +k  
  gi|15668412|ref|NP_247208.1| 104 GNNYGRGDKKSIKIILEHTSANPNGPLHIGHLRNAIIGDCLKRILEFYGYDVETHYYVNDMGRQMALVVYGIELFGLDKEK 184
                                   4555666667779************************************************************99999944 PP

                                   S-----SCCCHHHHHHHHCC....CSHCCCHHHHHHHHHHHCT-HH.HHHHHHHHHHHHHHHHHHHHHHCT---EC.--CC CS
                  tRNA-synt_1d  90 qeqelqdLeafykeakkdyd....eeeifaerarnyvvkLqsgded.irklwkllvditrtelqklydrldvtlie.rGes 164
                                     ++   + + y++++k ++    eee + e  r+y   L++++++ i+k ++  v+++    +++ ++l++       es
  gi|15668412|ref|NP_247208.1| 185 --KKDHAIAETYVKINKYLEehpeEEEKILELMRKYEDALENNEDNeITKKFEFAVNYALDGIKETLKNLNIKHDTfVWES 263
                                   ..44466788899999877522215677999*********98766559999999999999999999999999886567787 PP

                                   ..CCCCCHHHHHHHHHCTT-EEECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCH CS
                  tRNA-synt_1d 165 ..lykeslneivkelkkkglvkesdGalvvfldefgkrlgvvvqksDGgylytttDiaaakerkeelkadkvlyvidsrqs 243
                                     + + ++++++++l + g v +++ + +++l++fg +  +v+ + +G+ ly t+Dia   +++   k d  + v+ +  +
  gi|15668412|ref|NP_247208.1| 264 syVRNGMVKKVIEKLMETGKVIKEE-TYMLDLSDFGIEKKMVLARANGTSLYSTRDIAYHLDKLS--KCDIGIDVLGADHK 341
                                   678899*************987766.6789****************************9888776..56777777777777 PP

                                   HHHHHHHHHHHCTTSSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCTS-CCCCHCHHH CS
                  tRNA-synt_1d 244 lhlqqiflilkkigyvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkdkvlqadelekva 324
                                   l  + + ++lk +g   ++ ++   +f  +    + +++tr+G  +  ++lL+ea++ra++   e nk         e++a
  gi|15668412|ref|NP_247208.1| 342 LTAEMVKAALKLLGS--KVPEVIFYEFISL---PEGSMSTRRGRFISTDELLEEAIKRAKE---ECNKR-----GVEENIA 409
                                   777778889999995..5555555566555...5679**********************99...77777.....2345688 PP

                                   HHHHHHHHHCC CS
                  tRNA-synt_1d 325 eavgvgaikya 335
                                     +g+ga++y+
  gi|15668412|ref|NP_247208.1| 410 YDIGLGAVRYN 420
                                   88999999885 PP

>> Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   1.5   1.5e-21   2.4e-18       3      85 .]       3      87 ..       1      87 [. 0.88
   2 ?   -2.4   0.0       4.6   7.5e+03      32      44 ..     231     243 ..     196     252 .. 0.64
   3 ?    0.8   0.0      0.46   7.5e+02       8      59 ..     272     322 ..     268     334 .. 0.71
   4 ?    0.2   0.0      0.72   1.2e+03      20      51 ..     489     520 ..     478     545 .. 0.80

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 1.5e-21
                                  HHHHHHHHHHHHH.SS-HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT..EEEEEEETT.EEE CS
               Arg_tRNA_synt_N  3 lkeaiaealkkaa.gadleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei..iekvevagpGFiN 82
                                  +k+ i +alk++  ++   e++i+++k++n + GDy++n++++lak+lkknP+ iAee+++kl++ +i  +++++++  G+iN
  gi|15668412|ref|NP_247208.1|  3 IKSNIINALKEVIsKEICKEIDIKLDKTPNLELGDYSVNICFRLAKELKKNPKIIAEELVDKLKAMNIegVKEIKAVN-GYIN 84
                                  677788888888764455677999999***************************************9889******88.9*** PP

                                  EEE CS
               Arg_tRNA_synt_N 83 ffL 85
                                  f++
  gi|15668412|ref|NP_247208.1| 85 FYI 87
                                  *85 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.6
                                   GGG-SEEEEGGGG CS
               Arg_tRNA_synt_N  32 pkfGDyatnvamq 44 
                                    k+ ++a+n a+ 
  gi|15668412|ref|NP_247208.1| 231 TKKFEFAVNYALD 243
                                   3455666666665 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.46
                                   HHHHHHHHSS-HHHHGGG-E.-.SSGGG-SEEEEGGGG--TT-.....-HHHHHHH CS
               Arg_tRNA_synt_N   8 aealkkaagadleeeeivie.kpknpkfGDyatnvamqlakklkk...nPreiAee 59 
                                   +++++k+      e+  vi+ ++   +  D+ +   m la++ ++   + r+iA  
  gi|15668412|ref|NP_247208.1| 272 KKVIEKL-----METGKVIKeETYMLDLSDFGIEKKMVLARANGTslySTRDIAYH 322
                                   5555555.....22223444356777899*************99988888888865 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.72
                                   HHHGGG-E-.SSGGG-SEEEEGGGG--TT-.. CS
               Arg_tRNA_synt_N  20 eeeeiviekpknpkfGDyatnvamqlakklkk 51 
                                   +e + +i++++++   ++  n  ++lak++++
  gi|15668412|ref|NP_247208.1| 489 DEFKDIIKESAESRRVHILANYLLELAKAFNR 520
                                   34445778889999999999********9875 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   9.1e-05      0.15      24      71 ..     117     164 ..      90     170 .. 0.74
   2 ?    0.8   0.1      0.11   1.9e+02     113     156 ..     243     287 ..     231     293 .. 0.80
   3 !   14.7   0.0   6.5e-06     0.011     235     297 ..     331     389 ..     326     395 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.1e-05
                  tRNA-synt_1f  24 evvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdm 71 
                                    ++  + + p G++HiG lr+ + +d++ r l+  g +v++ ++++dm
  gi|15668412|ref|NP_247208.1| 117 IILEHTSANPNGPLHIGHLRNAIIGDCLKRILEFYGYDVETHYYVNDM 164
                                   334468999*******************************99999998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                  tRNA-synt_1f 113 aelvesLdelgievefisatelY.ksglydeaikealenrekike 156
                                     ++e+L++l+i+ ++   ++ Y ++g+ ++ i++++e  + ike
  gi|15668412|ref|NP_247208.1| 243 DGIKETLKNLNIKHDTFVWESSYvRNGMVKKVIEKLMETGKVIKE 287
                                   557899******988766666664899999999999999888875 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 6.5e-06
                  tRNA-synt_1f 235 VdfEpaGkDhaaaGgSvdvsskiaeilggeaPekvvYelillkggekmssSkGnvltledwle 297
                                   + +   G Dh      +++ ++  ++lg + Pe + Ye+i+l +g  ms  +G +++ +++le
  gi|15668412|ref|NP_247208.1| 331 IGIDVLGADHKL---TAEMVKAALKLLGSKVPEVIFYEFISLPEG-SMSTRRGRFISTDELLE 389
                                   667789999999...888888888********************9.9*************997 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   1.8e-05     0.029      10      39 ..     126     155 ..     120     168 .. 0.90
   2 ?   -1.6   0.0      0.54   8.8e+02     194     237 ..     196     240 ..     181     246 .. 0.66
   3 !    8.8   0.1   0.00036      0.59      72     118 ..     243     289 ..     224     297 .. 0.88
   4 ?    2.2   0.0     0.037        60     313     344 ..     359     390 ..     340     395 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                                   -SS---HHHHHHHHHHHHHHHHHHHTT-EE CS
                  tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeev 39 
                                   +ng+lH+Ghl+++i++D++ R     g++v
  gi|15668412|ref|NP_247208.1| 126 PNGPLHIGHLRNAIIGDCLKRILEFYGYDV 155
                                   69*********************9999997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.54
                                   HHHHHH.HH-TTSHHHHHHHH.HH...HHT----EE-ESS-SSS-EE CS
                  tRNA-synt_1g 194 klkewieeeekeleenvkkivkew...lkegLkdlaisrdldwGipv 237
                                   k+++++ ee++e+ee++ + ++++   l++  +d  i++++++++++
  gi|15668412|ref|NP_247208.1| 196 KINKYL-EEHPEEEEKILELMRKYedaLEN-NEDNEITKKFEFAVNY 240
                                   677888.55556666655555444111555.5889999999998876 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00036
                                   HHHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEE CS
                  tRNA-synt_1g  72 eeikelfkklnisfdkygrttseehkelvqeifkklkekgliyekei 118
                                   + ike++k+lni++d++   +s   + +v+++++kl e g++ ++e+
  gi|15668412|ref|NP_247208.1| 243 DGIKETLKNLNIKHDTFVWESSYVRNGMVKKVIEKLMETGKVIKEET 289
                                   66899***********************************9998775 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.037
                                   S-EEEE--EEE--------------HHHHHHH CS
                  tRNA-synt_1g 313 kkvvaheyltvegkKlSkSrgvvvkakealer 344
                                    +v+  e++ + ++ +S+ rg+++ ++e+le+
  gi|15668412|ref|NP_247208.1| 359 PEVIFYEFISLPEGSMSTRRGRFISTDELLEE 390
                                   4577789*********************9986 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       2.8   4.6e+03      76     110 ..      54      88 ..      39     118 .. 0.58
   2 !   22.6   0.4   3.5e-08   5.8e-05      23     124 ..     130     287 ..     124     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.8
                                   HHHHHHHHHHHHHHTT----SB--BGGGGHHHHHH CS
                  tRNA-synt_1e  76 aekfieefkkdleaLnvlkptleprvsekvdeiie 110
                                   ++ + ee+ ++l+a+n+   +    v  +++  i+
  gi|15668412|ref|NP_247208.1|  54 PKIIAEELVDKLKAMNIEGVKEIKAVNGYINFYID 88 
                                   45555566666666666655555555555554443 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 3.5e-08
                                   -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-................................ CS
                  tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeks................................ 71 
                                    h+Gh R++++ D l+ril+  gYdv+    v D+  ++ +     e++                                
  gi|15668412|ref|NP_247208.1| 130 LHIGHLRNAIIGDCLKRILEFYGYDVETHYYVNDMGRQMALVVYGIELFgldkekkkdhaiaetyvkinkyleehpeeeek 210
                                   7**************************999999999999888888888889999999999********************* PP

                                   .......................HHHHHHHHHHHHHHHHHHTT----SB--BGGGGHHHHH.HHHHHHHHTTSEEE- CS
                  tRNA-synt_1e  72 .......................vkelaekfieefkkdleaLnvlkptleprvsekvdeii.elvekliekgyaYav 124
                                                          ++  +++  +  k+ l++Ln+++ t+    s   + ++ +++ekl+e g   + 
  gi|15668412|ref|NP_247208.1| 211 ilelmrkyedalennedneitkkFEFAVNYALDGIKETLKNLNIKHDTFVWESSYVRNGMVkKVIEKLMETGKVIKE 287
                                   99999999999999999999998888899999999999999999999888887766666652688999998865544 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.3     6e-06    0.0098      20     122 ..     112     215 ..      95     248 .. 0.75
   2 ?   -0.7   0.1      0.19   3.2e+02     301     362 ..     226     294 ..     223     310 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6e-06
                   tRNA-synt_1  20 kekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakve.kklgakekkerkklgree 99 
                                   k+  + il     + +G lHiGh  + ++ d + r+ ++ G++v+    +   G  +  +v   +l   +k+++k+ + +e
  gi|15668412|ref|NP_247208.1| 112 KKSIKIILEHTSANPNGPLHIGHLRNAIIGDCLKRILEFYGYDVETHYYVNDMGRQMALVVYgIELFGLDKEKKKDHAIAE 192
                                   445556777777899*****************************9998888888887777742456566666777777777 PP

                   tRNA-synt_1 100 frekvrewkaeyaeeirkqvkrl 122
                                      k+ ++ +e  ee +k ++ +
  gi|15668412|ref|NP_247208.1| 193 TYVKINKYLEEHPEEEEKILELM 215
                                   77778888777777766666555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.19
                   tRNA-synt_1 301 dDyevgkkynlevinild......edgtlteeaaefeglkvfd.arkkvveelkekglllkaekiehsv 362
                                   +D+e++kk++  v  +ld      ++ ++++++  +e  +v +   kkv+e+l e+g+ +k+e+ ++ +
  gi|15668412|ref|NP_247208.1| 226 EDNEITKKFEFAVNYALDgiketlKNLNIKHDTFVWESSYVRNgMVKKVIEKLMETGKVIKEETYMLDL 294
                                   566666666665555554111111444444444667777665515699999999999999999887765 PP

>> CAF1  CAF1 family ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.1e-05     0.067     167     231 ..     262     527 ..     174     553 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.1e-05
                                   H................................................................................ CS
                                   x................................................................................ RF
                          CAF1 167 e................................................................................ 167
                                   e                                                                                
  gi|15668412|ref|NP_247208.1| 262 Essyvrngmvkkvieklmetgkvikeetymldlsdfgiekkmvlarangtslystrdiayhldklskcdigidvlgadhkl 342
                                   144444444444444455555555555666666666666666666666666666666666666666666666666666666 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CAF1 168 ................................................................................. 167
                                                                                                                    
  gi|15668412|ref|NP_247208.1| 343 taemvkaalkllgskvpevifyefislpegsmstrrgrfistdelleeaikrakeecnkrgveeniaydiglgavryniar 423
                                   666666677777777777777777777777777777777777777777777777777777777788888888888888888 PP

                                   .........................................-S.HHHHHHHHHHHHHHHHHHHHHHSBTHHHHHHHHHC-- CS
                                   .........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CAF1 168 .........................................kskeeeelkeeeklkeeeeekiakqsgfrlvfealvksrk 207
                                                                            k   ++e+  + +l +ee+e i+    f++++++ ++sr+
  gi|15668412|ref|NP_247208.1| 424 ispekpmvfrweealdfekvgcpfiqyaharccsilkeaenK-GVKDEAVFNYELTSEEKELIKMLDEFKDIIKESAESRR 503
                                   888888888888888888888888888888888877544421.1222222233345588888999999************* PP

                                   EEEESSTHHHHHHHHHHHT----S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                          CAF1 208 piVgHNgllDllflyqtfyaeLPe 231
                                   + ++ N+ll l+  ++ fya+ P 
  gi|15668412|ref|NP_247208.1| 504 VHILANYLLELAKAFNRFYANCPI 527
                                   ********************9886 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         6   9.8e+03      37      46 ..     243     252 ..     243     253 .. 0.82
   2 ?   -3.5   0.0       9.7   1.6e+04      24      40 ..     271     286 ..     270     287 .. 0.54
   3 ?   10.6   0.0   0.00038      0.61      15      47 .]     314     355 ..     314     355 .. 0.89
   4 ?   -0.1   0.0      0.84   1.4e+03      34      45 ..     383     394 ..     377     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6
                                   HHHHHHHCCT CS
                        RuvA_C  37 elIraALklL 46 
                                   ++I++ Lk L
  gi|15668412|ref|NP_247208.1| 243 DGIKETLKNL 252
                                   5799999988 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.7
                                   HHHHHC-TTS-HHHHHH CS
                        RuvA_C  24 vakvlanpgasveelIr 40 
                                   v+kv  ++ + +  +I+
  gi|15668412|ref|NP_247208.1| 271 VKKVI-EKLMETGKVIK 286
                                   55555.55566666666 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00038
                                   S-HHHHHHHHHHHHC.-TTS-........HHHHHHHHHCCTT CS
                        RuvA_C  15 YkekeaekAvakvla.npgas........veelIraALklLs 47 
                                   Y+++++++ ++k+++ + g +        ++e+++aALklL+
  gi|15668412|ref|NP_247208.1| 314 YSTRDIAYHLDKLSKcDIGIDvlgadhklTAEMVKAALKLLG 355
                                   999999999****999777777778899************95 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.84
                                   -HHHHHHHHHCC CS
                        RuvA_C  34 sveelIraALkl 45 
                                   s++el+ +A+k 
  gi|15668412|ref|NP_247208.1| 383 STDELLEEAIKR 394
                                   799999999985 PP

>> RlmM_FDX  RlmM ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   8.7e-05      0.14      16      61 ..      57     102 ..      55     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.7e-05
                      RlmM_FDX  16 cAaElqekaaelevaGyvkakknsgyvlfeleeaeaaeellkkldl 61 
                                    A El +k +++++ G  ++k+ +gy+ f ++ ++ a++l++++d 
  gi|15668412|ref|NP_247208.1|  57 IAEELVDKLKAMNIEGVKEIKAVNGYINFYIDYNKFAKNLMEEIDK 102
                                   589****************************999********9985 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0037         6      65     105 ..     188     230 ..     181     263 .. 0.72
   2 ?    3.4   0.1     0.048        78      99     134 ..     471     505 ..     449     511 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0037
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTT-.SS-- CS
                         Nup54  65 khqletsvrlekakkrhvelshRllrllrkle.ilrsr.gyal 105
                                   +  +et v+++k+  +h e ++++l+l+rk e  l++     +
  gi|15668412|ref|NP_247208.1| 188 HAIAETYVKINKYLEEHPEEEEKILELMRKYEdALENNeDNEI 230
                                   55689***************************77755423333 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.048
                                   TT-SS---SSHHHHHHHHHHHHHHHS-HHH.HHHHH CS
                         Nup54  99 rsrgyaldaeEeelrarletleaqlndpaqlkgrvn 134
                                   + ++y l+ eE+el + l++ ++ +++ a+ ++rv 
  gi|15668412|ref|NP_247208.1| 471 AVFNYELTSEEKELIKMLDEFKDIIKESAE-SRRVH 505
                                   45689********************98777.67765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1216  (0.0678231); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3531.31
//
Query:       gi|15668413|ref|NP_247209.1|  [L=197]
Description: anthranilate synthase component II TrpG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-52  177.7   0.0    2.4e-52  177.5   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    2.8e-10   40.3   0.3    2.7e-09   37.1   0.3    2.0  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.5   0.0   2.7e-56   2.4e-52       2     180 ..       8     178 ..       7     187 .. 0.97

  Alignments for each domain:
  == domain 1  score: 177.5 bits;  conditional E-value: 2.7e-56
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEETHHH CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGICLGm 81 
                                   +iDn ds+++nlv+++  lg+kv++v ++ + +ei+  + npd i++s+Gp +p+ ++++i++i+e    +iPiLG+CLG+
  gi|15668413|ref|NP_247209.1|   8 VIDNIDSFVWNLVQYVGTLGYKVKLVDNKITLDEIK--KINPDRIIISPGPKTPKeAGNCIKIIQE---VDIPILGVCLGH 83 
                                   8**********************************5..79*************************8...689********* PP

                                   HHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETT CS
                        GATase  82 QllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekkn 162
                                   Q+++++fg++v ++k + +hg+ + +++d+++++++ +n+++  ++H++ +++   +p++l++taks dd+ +m++++kk 
  gi|15668413|ref|NP_247209.1|  84 QCIVEAFGGEVGRAK-RVMHGKASLINHDGEGIFKDIPNPFYGGRYHSLIAKE---VPKELKITAKSLDDNYIMGVRHKKL 160
                                   ***************.9************************************...************************* PP

                                   TEEEESSBTTSTTSTTHH CS
                        GATase 163 pfvgvQFHPEststpegp 180
                                   p+ gvQFHPEs++t+ ++
  gi|15668413|ref|NP_247209.1| 161 PIEGVQFHPESILTESDN 178
                                   **************9986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.3   3.1e-13   2.7e-09     102     216 .]      70     170 ..      64     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 3.1e-13
                 Peptidase_C26 102 lergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaikela 182
                                    e ++Pilg+C+G+q +  a+GG++ ++ +     + h       ++  ++ + +++++++ +   +    +H+   ke+ 
  gi|15668413|ref|NP_247209.1|  70 QEVDIPILGVCLGHQCIVEAFGGEVGRAKRV----M-H------GKASLINHDGEGIFKDIPN--PFYGGRYHSLIAKEVP 137
                                   5679*******************99877662....2.2......3345678889999999998..89999*********** PP

                 Peptidase_C26 183 eelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                   +el+++A +  D+ i  +++++   ++ gvQ+HPE
  gi|15668413|ref|NP_247209.1| 138 KELKITAKSLdDNYIMGVRHKK--LPIEGVQFHPE 170
                                   *********9899**9999988..67********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1267.51
//
Query:       gi|15668414|ref|NP_247210.1|  [L=164]
Description: hypothetical protein MJ_0239 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.054   13.5   0.1        8.5    6.5   0.0    2.3  2  YpmT             Uncharacterized YmpT-like
       0.14   11.7   0.1        1.6    8.2   0.1    2.0  2  Intg_mem_TP0381  Integral membrane protein (intg_mem_TP0381)


Domain annotation for each model (and alignments):
>> YpmT  Uncharacterized YmpT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0   0.00095       8.5      27      60 ..      31      63 ..      26      65 .. 0.84
   2 ?    4.8   0.1    0.0031        28      23      62 .]      90     129 ..      76     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00095
                          YpmT 27 lvaenmDkvYLnigYCaLFLsimvftldmkdekk 60
                                  l  e++Dkv L++ + ++   ++++++++k++++
  gi|15668414|ref|NP_247210.1| 31 LKKEDLDKVDLDLPWTSI-RDLAIYLYELKKKQQ 63
                                  6789*********99776.689999999999877 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0031
                          YpmT  23 ayqhlvaenmDkvYLnigYCaLFLsimvftldmkdekktd 62 
                                    y  lv e+m   YL     a    i+ + + mk+ ++t+
  gi|15668414|ref|NP_247210.1|  90 NYMGLVTEDMCLTYLSELITARINCIARYYYMMKKPQNTN 129
                                   58899**********9999999999999999999987775 PP

>> Intg_mem_TP0381  Integral membrane protein (intg_mem_TP0381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.022     2e+02      51      88 ..      51      85 ..      45      96 .. 0.69
   2 ?    8.2   0.1   0.00018       1.6     165     200 ..     107     140 ..      98     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.022
               Intg_mem_TP0381 51 iflllwalaagypnlweslPLhlCrlaiillaialitk 88
                                  ++++l+ l +++ n +e   L  C+++ il+ ial+  
  gi|15668414|ref|NP_247210.1| 51 LAIYLYELKKKQQNSKE---LIKCDIVEILVGIALLKP 85
                                  56666666666666666...888999999999999844 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00018
               Intg_mem_TP0381 165 lliflvNlllgtNYfFlnrkpsnlsildeiaellgp 200
                                   l+++ +N +    Y ++++kp+n +i+dei  ++++
  gi|15668414|ref|NP_247210.1| 107 LITARINCIAR--YYYMMKKPQNTNIFDEIILKFPQ 140
                                   78888999985..***************99988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1254.39
//
Query:       gi|15668415|ref|NP_247211.1|  [L=175]
Description: hypothetical protein MJ_0240 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-39  133.5   5.3    8.5e-39  133.3   5.3    1.0  1  CYTH             CYTH domain
     0.0091   15.8   0.4        4.5    7.1   0.0    2.3  2  Cyclophil_like   Cyclophilin-like
  ------ inclusion threshold ------
      0.012   15.4  13.2      0.042   13.7   0.7    4.1  5  UBA_3            Fungal ubiquitin-associated domain
       0.03   14.5   0.5        0.4   10.8   0.0    2.2  2  Glyoxalase_5     Hydroxyphenylpyruvate dioxygenase, HPPD, N-t
      0.031   14.2   1.7      0.045   13.7   0.2    2.1  2  Imm51            Immunity protein 51
       0.04   14.7   1.5       0.04   14.7   1.5    2.7  3  DUF4162          Domain of unknown function (DUF4162)
      0.043   14.1   0.4         18    5.7   0.0    2.8  3  PG_binding_2     Putative peptidoglycan binding domain
      0.077   13.2   2.4       0.36   11.0   0.1    2.7  2  PGM_PMM_IV       Phosphoglucomutase/phosphomannomutase, C-ter
        0.1   12.5   0.0        5.5    6.9   0.0    2.3  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
       0.53   10.3   8.5        1.5    8.8   1.8    2.8  2  PUB              PUB domain
        3.3    7.9   7.2       0.64   10.2   0.7    2.7  3  DUF3567          Protein of unknown function (DUF3567)
          4    7.9   8.2         16    6.0   4.7    2.8  2  Latarcin         Latarcin precursor


Domain annotation for each model (and alignments):
>> CYTH  CYTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.3   5.3   5.7e-42   8.5e-39       1     179 []       1     169 [.       1     169 [. 0.94

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 5.7e-42
                                   EEEEEEEEEE-HHHHHHHHHH.HHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEEEETTTEEE.EEEEEECSSST... CS
                          CYTH   1 miEvEvKflvsaaeyedlelr.laelrakeettveqrdtYydtpdrdlartdeaLRiRraegdgee.ltlKgpgvdge... 76 
                                   miEvE+K++++   +++  ++ l++l++k  ++++q+d+Y++  drd+++tdeaLRiR  ++dg + +t+Kgp+ d+    
  gi|15668415|ref|NP_247211.1|   1 MIEVEIKVKID---DKNKVVEqLKKLGFKFIKKKFQEDIYFNGIDRDFRETDEALRIR--DEDGNFfVTYKGPKIDKIskt 76 
                                   89********4...333345579***********************************..8999999**********7777 PP

                                   EEEEEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEESSHHHHHHHH CS
                          CYTH  77 reevegevsreEyeeplsdaaeaaelldglglepvasvkklRrkyklegvevalDaveflegeevEiElevedeeevkeaa 157
                                   ree+e++++         d +++ +++++lg+++v  ++k R++yk e++e+++D ve+l g ++E+E   +d +e ++++
  gi|15668415|ref|NP_247211.1|  77 REEIEVKIE---------DKEKMRQIFKKLGFKEVPPIRKIREIYKKEDIEASIDDVEGL-GLFLELEKSISDINEKDKVL 147
                                   777777777.........******************************************.******************** PP

                                   HHHHHHHHHTTEEGGGBSCSHH CS
                          CYTH 158 ekllallrelglssaskirrsy 179
                                   e+++++l+ l++s+ + ir+sy
  gi|15668415|ref|NP_247211.1| 148 EEMMEILKALNISKDNIIRKSY 169
                                   ********************99 PP

>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0     0.003       4.5      10      45 ..       4      39 ..       1      61 [. 0.83
   2 !    6.8   0.1    0.0037       5.5       5      51 ..      73     120 ..      69     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.003
                                  EEEEEEEETTHHHHHHHHC-SEEEEEEECTTEEEEE CS
                Cyclophil_like 10 seveveLddtetaraikealPiesrvntWgeEiYfs 45
                                   e++v++dd++ + +  ++l ++   ++ +e+iYf+
  gi|15668415|ref|NP_247211.1|  4 VEIKVKIDDKNKVVEQLKKLGFKFIKKKFQEDIYFN 39
                                  58999*****777777889****************7 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0037
                                   EEETTEEEEEEEETTHHHHHHHHC-SEEEEE.EECTTEEEEE-S---- CS
                Cyclophil_like   5 idiesseveveLddtetaraikealPiesrv.ntWgeEiYfstpvkle 51 
                                   i+    e+ev+++d+e +r+i ++l ++     +   EiY + +++++
  gi|15668415|ref|NP_247211.1|  73 ISKTREEIEVKIEDKEKMRQIFKKLGFKEVPpIRKIREIYKKEDIEAS 120
                                   4555789********************876514556899988888776 PP

>> UBA_3  Fungal ubiquitin-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   2.8e-05     0.042      22      44 ..      12      34 ..      11      38 .. 0.88
   2 ?   -1.2   0.0       1.2   1.8e+03       2      12 ..      35      45 ..      34      48 .. 0.77
   3 ?    5.6   0.2    0.0093        14      22      41 ..      86     105 ..      85     111 .. 0.84
   4 ?    2.1   0.2      0.12   1.7e+02      42      54 ..     139     151 ..     132     152 .. 0.77
   5 ?    1.8   0.8      0.14   2.1e+02      23      35 ..     143     159 ..     138     167 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-05
                                  -HHHHHHHHHHS--SS--SS--H CS
                         UBA_3 22 ekdkvievLkrLgiksldpedne 44
                                  +k+kv+e Lk+Lg k + ++ +e
  gi|15668415|ref|NP_247211.1| 12 DKNKVVEQLKKLGFKFIKKKFQE 34
                                  79*************98877666 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                                  -SS----SHHH CS
                         UBA_3  2 eaqlyGidrdl 12
                                  ++   Gidrd 
  gi|15668415|ref|NP_247211.1| 35 DIYFNGIDRDF 45
                                  56678****95 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0093
                                   -HHHHHHHHHHS--SS--SS CS
                         UBA_3  22 ekdkvievLkrLgiksldpe 41 
                                   +k+k  +++k+Lg k++ p 
  gi|15668415|ref|NP_247211.1|  86 DKEKMRQIFKKLGFKEVPPI 105
                                   799999*********98765 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.12
                                   --HHHHHHHHHHT CS
                         UBA_3  42 dnetankileELL 54 
                                   d ++++k+leE++
  gi|15668415|ref|NP_247211.1| 139 DINEKDKVLEEMM 151
                                   667899****986 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.14
                                   HHHH....HHHHHHS-- CS
                         UBA_3  23 kdkv....ievLkrLgi 35 
                                   kdkv     e+Lk L+i
  gi|15668415|ref|NP_247211.1| 143 KDKVleemMEILKALNI 159
                                   44441111345666665 PP

>> Glyoxalase_5  Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.18   2.7e+02      18      43 ..      11      36 ..       4      42 .. 0.82
   2 ?   10.8   0.0   0.00027       0.4      11      52 ..      78     118 ..      65     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.18
                  Glyoxalase_5 18 peaealeelfeklGftavarhrskdv 43
                                  ++++++ e ++klGf+ + +  + d+
  gi|15668415|ref|NP_247211.1| 11 DDKNKVVEQLKKLGFKFIKKKFQEDI 36
                                  57788889999*****9999888887 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00027
                  Glyoxalase_5  11 efvefaapeaealeelfeklGftavarhrskdvtlyrqGgin 52 
                                   e +e   +++e+++++f+klGf++v   r+   ++y++ +i+
  gi|15668415|ref|NP_247211.1|  78 EEIEVKIEDKEKMRQIFKKLGFKEVPPIRK-IREIYKKEDIE 118
                                   56888999****************987664.44677777775 PP

>> Imm51  Immunity protein 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2     3e-05     0.045      63     102 ..      56      96 ..       9      98 .. 0.86
   2 ?   -1.0   0.1       1.1   1.7e+03      76      86 ..     144     154 ..     113     166 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
                         Imm51  63 DpEagmFvay.sedkealkelaellkelledeeklreliee 102
                                   D +   Fv y +  ++++ +  e ++  +ed+ek+r+++++
  gi|15668415|ref|NP_247211.1|  56 DEDGNFFVTYkGPKIDKISKTREEIEVKIEDKEKMRQIFKK 96 
                                   5555566666999*************************986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                         Imm51  76 kealkelaell 86 
                                    + l+e++e+l
  gi|15668415|ref|NP_247211.1| 144 DKVLEEMMEIL 154
                                   23344444444 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.9   4.3e+03      41      57 ..       5      20 ..       3      28 .. 0.52
   2 ?   14.7   1.5   2.6e-05      0.04       6      68 ..      28     110 ..      24     113 .. 0.76
   3 ?    2.6   0.3      0.15   2.2e+02       3      38 ..     105     145 ..     104     167 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.9
                                  EEEE------------- CS
                       DUF4162 41 elkledeeaanellkal 57
                                  e+k++  +++n++ ++l
  gi|15668415|ref|NP_247211.1|  5 EIKVKI-DDKNKVVEQL 20
                                  444442.3455555555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.6e-05
                                   HHTTS-SSEEE..EE...-------...............---EEEE-TTS-EEEEE--------------.---E.EEEE CS
                       DUF4162   6 iKrsygknrie..ve...adaeellee.............pgveeveeeggelelkledeeaanellkalt.sgve.irsF 66 
                                   iK++++++++   +     + +e+l++             p++ +++++ +e+e+k+ed+e++++++k+l  + v+ ir++
  gi|15668415|ref|NP_247211.1|  28 IKKKFQEDIYFngIDrdfRETDEALRIrdedgnffvtykgPKIDKISKTREEIEVKIEDKEKMRQIFKKLGfKEVPpIRKI 108
                                   8899999999855556663344444445557777777877889999999999******************44777778887 PP

                                   EE CS
                       DUF4162  67 ee 68 
                                   +e
  gi|15668415|ref|NP_247211.1| 109 RE 110
                                   76 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.15
                                   HHHHHTTS-SSEEEEE....-------..--.-EEEE-TTS CS
                       DUF4162   3 leeiKrsygknrieve....adaeelleepg.veeveeegg 38 
                                   +++i++ y+k+ ie +    ++ + +le+++ +++++e+++
  gi|15668415|ref|NP_247211.1| 105 IRKIREIYKKEDIEASiddvEGLGLFLELEKsISDINEKDK 145
                                   67899999999999776343223333344444777766653 PP

>> PG_binding_2  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.012        18      14      31 ..       9      26 ..       3      38 .. 0.72
   2 ?    5.6   0.0     0.013        19       8      41 ..      77     110 ..      72     120 .. 0.81
   3 ?   -1.9   0.1       2.9   4.3e+03      10      28 ..     139     157 ..     130     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
                  PG_binding_2 14 aedvaeevqaaLsrLGyy 31
                                  + d +++v ++L++LG++
  gi|15668415|ref|NP_247211.1|  9 KIDDKNKVVEQLKKLGFK 26
                                  446788999********3 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.013
                  PG_binding_2   8 eeervlaedvaeevqaaLsrLGyydgeaggafre 41 
                                    ee + + + +e++++  ++LG+++ ++ + +re
  gi|15668415|ref|NP_247211.1|  77 REEIEVKIEDKEKMRQIFKKLGFKEVPPIRKIRE 110
                                   45666677778999***********999988887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.9
                  PG_binding_2  10 ervlaedvaeevqaaLsrL 28 
                                   +   ++ v ee+++ L++L
  gi|15668415|ref|NP_247211.1| 139 DINEKDKVLEEMMEILKAL 157
                                   4555667777777777765 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00024      0.36       1      39 [.       5      62 ..       5      77 .. 0.93
   2 ?    1.6   0.3      0.22   3.2e+02       1      24 [.      79     104 ..      79     168 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                  CCCCCHCC-TT..EECCCCCTTH....................HCCCCCCCCGCCEEEE CS
                    PGM_PMM_IV  1 linvrveekakvvaalaallkva....................sikeglkilledGrrl 39
                                  +i+v++++k+kvv++l++l + +                    ++ e+l+i++edG ++
  gi|15668415|ref|NP_247211.1|  5 EIKVKIDDKNKVVEQLKKL-GFKfikkkfqediyfngidrdfrETDEALRIRDEDGNFF 62
                                  89*******9999999988.77799*******************************998 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.22
                                   CCCCCHCC-TT..EECCCCCTTH...H CS
                    PGM_PMM_IV   1 linvrveekakvvaalaallkva...s 24 
                                   +i v++e+k+k ++++ + l+ +   +
  gi|15668415|ref|NP_247211.1|  79 EIEVKIEDKEK-MRQIFKKLGFKevpP 104
                                   56667777644.333333333332331 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.05        75      88     116 ..       7      35 ..       2      42 .. 0.83
   2 ?    6.9   0.0    0.0037       5.5      81     113 ..      74     106 ..      69     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.05
               Acetyltransf_10  88 eltvnaspyavpfYeklGFkavgeeqeen 116
                                   +++++ +++ v+  +klGFk ++++++e+
  gi|15668415|ref|NP_247211.1|   7 KVKIDDKNKVVEQLKKLGFKFIKKKFQED 35 
                                   78889999999999********8888765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0037
               Acetyltransf_10  81 ekdgikleltvnaspyavpfYeklGFkavgeeq 113
                                   +k + ++e++++ + + +++++klGFk+v + +
  gi|15668415|ref|NP_247211.1|  74 SKTREEIEVKIEDKEKMRQIFKKLGFKEVPPIR 106
                                   45555559999999*************997665 PP

>> PUB  PUB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.5     0.016        23      37      62 ..       6      33 ..       3      63 .. 0.75
   2 ?    8.8   1.8     0.001       1.5      25      60 ..      68     103 ..      60     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.016
                           PUB 37 fkekvlplegavelLealGFeekne..e 62
                                  +k k++  +++ve L++lGF+  ++  +
  gi|15668415|ref|NP_247211.1|  6 IKVKIDDKNKVVEQLKKLGFKFIKKkfQ 33
                                  6789999999**********97655552 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.001
                           PUB  25 ekyrrIrleNkafkekvlplegavelLealGFeekn 60 
                                   +k  +I+++ + ++ k+   e++++++++lGF+e  
  gi|15668415|ref|NP_247211.1|  68 PKIDKISKTREEIEVKIEDKEKMRQIFKKLGFKEVP 103
                                   78899***************************9864 PP

>> DUF3567  Protein of unknown function (DUF3567)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.7   0.00043      0.64      15      61 ..       8      52 ..       2      65 .. 0.74
   2 ?    0.4   0.2      0.49   7.3e+02      35      47 ..      84      96 ..      60     133 .. 0.60
   3 ?    0.1   0.5       0.6   8.9e+02      54      74 ..     133     153 ..      86     163 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00043
                       DUF3567 15 leadaeeealaekaargGyEivDKrakkeiyldGslAesfrkevkal 61
                                  +++d++++ + e+ ++ G+  + K+ + +iy +G + ++fr++ +al
  gi|15668415|ref|NP_247211.1|  8 VKIDDKNKVV-EQLKKLGFKFIKKKFQEDIYFNG-IDRDFRETDEAL 52
                                  4444444444.66799*****************9.567788766555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.49
                       DUF3567 35 ivDKrakkeiyld 47
                                  i DK+  ++i+ +
  gi|15668415|ref|NP_247211.1| 84 IEDKEKMRQIFKK 96
                                  4566666666643 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.6
                       DUF3567  54 frkevkalieeepseeevddf 74 
                                   + k+++++ e+++  ee+ ++
  gi|15668415|ref|NP_247211.1| 133 LEKSISDINEKDKVLEEMMEI 153
                                   345555555555555555555 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       2.2   3.3e+03      45      50 ..      18      23 ..      10      37 .. 0.59
   2 ?    6.0   4.7     0.011        16       6      51 ..     114     158 ..      75     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.2
                      Latarcin 45 enlrkv 50
                                  e+l+k+
  gi|15668415|ref|NP_247211.1| 18 EQLKKL 23
                                  444433 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
                      Latarcin   6 seeleaeeLdelergainrklmemvnnlRkvqgRLeemvenlrkve 51 
                                   +e++ea  +d+ e  +++  l + + ++ +  + Leem+e l++++
  gi|15668415|ref|NP_247211.1| 114 KEDIEA-SIDDVEGLGLFLELEKSISDINEKDKVLEEMMEILKALN 158
                                   489999.899999999999999988888888888999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1393  (0.0776954); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1194.21
//
Query:       gi|15668416|ref|NP_247212.1|  [L=145]
Description: hypothetical protein MJ_0241 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-09   36.2   0.9    1.1e-08   35.2   0.1    1.9  2  Rrf2            Transcriptional regulator
    1.5e-06   28.1   0.0    2.5e-06   27.4   0.0    1.4  1  HTH_20          Helix-turn-helix domain
    3.1e-06   26.9   0.7      6e-06   25.9   0.7    1.4  1  ACT             ACT domain
    8.7e-06   26.2   1.4    1.4e-05   25.5   0.7    1.8  1  ACT_4           ACT domain
    5.4e-05   22.8   0.2     0.0001   21.9   0.2    1.4  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
    6.6e-05   22.7   0.4    0.00023   20.9   0.1    2.0  2  HTH_5           Bacterial regulatory protein, arsR family
    0.00047   20.1   0.3      0.013   15.4   0.1    2.5  3  ACT_6           ACT domain
    0.00064   19.6   0.1     0.0015   18.4   0.1    1.7  1  HTH_11          HTH domain
     0.0084   16.0   0.0      0.014   15.3   0.0    1.4  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.012   15.8   0.3      0.084   13.1   0.1    2.2  2  HTH_34          Winged helix DNA-binding domain
      0.013   15.4   0.2       0.85    9.6   0.0    2.4  2  PuR_N           Bacterial purine repressor, N-terminal
      0.018   14.6   0.1      0.047   13.3   0.1    1.8  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.023   14.5   0.1      0.064   13.1   0.1    1.8  1  IF2_N           Translation initiation factor IF-2, N-termina
      0.033   14.2   0.0      0.063   13.3   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.035   14.0   0.0      0.071   13.0   0.0    1.5  1  MarR            MarR family
       0.05   13.6   1.8      0.087   12.8   0.3    2.0  2  HTH_45          Winged helix-turn-helix
      0.067   13.1   1.0       0.26   11.3   1.0    2.0  1  HTH_12          Ribonuclease R winged-helix domain
       0.11   12.5   3.2        9.5    6.3   0.1    3.0  3  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   1.1e-11   1.1e-08      23      70 ..      15      62 ..       6      75 .. 0.92
   2 ?   -1.6   0.0       3.7   3.6e+03      65      82 ..     107     124 ..      97     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.1e-11
                                  CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSH CS
                          Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakp 70
                                  +ep++++e+a++ n++p+ l   ++ Lr  glv++++G++GG+rL+k+
  gi|15668416|ref|NP_247212.1| 15 KEPITIKELAKKLNMHPKNLDVKIRVLRDLGLVETKKGRNGGVRLTKE 62
                                  568******************************************997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.7
                                   EEESSHCCCSBHHHHHHH CS
                          Rrf2  65 yrLakppeeItlldvvra 82 
                                    +L ++ +e+ ++ vv+ 
  gi|15668416|ref|NP_247212.1| 107 TVLEREGDEVIIYLVVEN 124
                                   679999999999998876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   2.5e-09   2.5e-06      14      58 ..       9      51 ..       6      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.5e-09
                                  HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                        HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                  +i+ +L  +e+ t +ela+ l +++++l+  +rvL++ gLve+ +
  gi|15668416|ref|NP_247212.1|  9 KIMEHL--KEPITIKELAKKLNMHPKNLDVKIRVLRDLGLVETKK 51
                                  7999**..**********************************987 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.7     6e-09     6e-06       3      61 ..      79     136 ..      78     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6e-09
                                   EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHH CS
                           ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlea 61 
                                   l + ++Dr GlLa++++ +++ g Ni+s    + +d+ + i+ vv+ vd ++++++le 
  gi|15668416|ref|NP_247212.1|  79 LQIVAKDRIGLLADITSRISKIGGNITSTVLEREGDE-VIIYLVVENVDKDEIKNTLED 136
                                   57899*******************************9.999999999999999999886 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.7   1.4e-08   1.4e-05       8      55 ..      78     123 ..      76     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.4e-08
                         ACT_4   8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitve 55 
                                   +l+++a+dr glLadit+ is+ ++ni+s  ++ +  d  + i + ve
  gi|15668416|ref|NP_247212.1|  78 KLQIVAKDRIGLLADITSRISKIGGNITSTVLEREG-D-EVIIYLVVE 123
                                   79***************************9999854.4.555555555 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.2     1e-07    0.0001      18      70 ..      12      64 ..       3      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1e-07
                  HrcA_DNA-bdg 18 rkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkay 70
                                  ++ k+++  +e+A++l+ ++  +   + +L+ lgLve++ G +GG + t +  
  gi|15668416|ref|NP_247212.1| 12 EHLKEPITIKELAKKLNMHPKNLDVKIRVLRDLGLVETKKGRNGGVRLTKEGL 64
                                  445899999************************************98887765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   2.4e-07   0.00023      13      47 .]      15      49 ..       5      49 .. 0.91
   2 ?   -1.4   0.0       2.1   2.1e+03       8      19 ..      64      75 ..      64      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.4e-07
                                  TSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5 13 egelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  +++ ++ ela++l++ + +++   ++Lr++GLVe+
  gi|15668416|ref|NP_247212.1| 15 KEPITIKELAKKLNMHPKNLDVKIRVLRDLGLVET 49
                                  47889****************************85 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                                  HHHHTTSSEEHH CS
                         HTH_5  8 LklLaegelcvc 19
                                  L+lL++ge + +
  gi|15668416|ref|NP_247212.1| 64 LYLLEKGEITLG 75
                                  899999997766 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.7   2.7e+03      14      25 ..       5      16 ..       3      17 .. 0.86
   2 ?    1.8   0.0      0.23   2.3e+02      54      75 ..      19      40 ..      14      40 .. 0.89
   3 !   15.4   0.1   1.3e-05     0.013       7      50 ..      81     124 ..      77     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.7
                         ACT_6 14 GltasLtsvlae 25
                                  Glt++++++l e
  gi|15668416|ref|NP_247212.1|  5 GLTKKIMEHLKE 16
                                  99*****99976 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.23
                         ACT_6 54 alarlekaLlflakelgltvef 75
                                  ++++l k+L  + k+l++++++
  gi|15668416|ref|NP_247212.1| 19 TIKELAKKLNMHPKNLDVKIRV 40
                                  68899*************9986 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.3e-05
                         ACT_6   7 vtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsg 50 
                                   ++ +dr Gl+a++ts+++++g ni+   + + ++++ + l+v+ 
  gi|15668416|ref|NP_247212.1|  81 IVAKDRIGLLADITSRISKIGGNITSTVLEREGDEVIIYLVVEN 124
                                   6779*********************9999999999999999874 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.5e-06    0.0015       4      53 ..       9      56 ..       7      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..G 53
                                  +i+e L   ++pi+++eLA++Ln+  +     I+ L++lg  +e ++gr  G
  gi|15668416|ref|NP_247212.1|  9 KIMEHL---KEPITIKELAKKLNMHPKNLDVKIRVLRDLG-LVETKKGRngG 56
                                  555555...889****************************.9****999866 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.4e-05     0.014      19      58 ..      17      54 ..      10      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                                  TSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                        MarR_2 19 grdltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                  +  +t++ela++l++ + ++   ++ L + GLve+++g +
  gi|15668416|ref|NP_247212.1| 17 P--ITIKELAKKLNMHPKNLDVKIRVLRDLGLVETKKGRN 54
                                  3..9*******************************99865 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   8.4e-05     0.084      13      67 ..      16      65 ..       9      81 .. 0.88
   2 ?    0.5   0.0      0.69   6.9e+02       6      25 ..     117     135 ..     115     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.4e-05
                        HTH_34 13 deadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGre 67
                                  + ++ +el ++l++   nL v++++L + g +e +k+ +g+     +r+T+eG+ 
  gi|15668416|ref|NP_247212.1| 16 EPITIKELAKKLNMHPKNLDVKIRVLRDLGLVETKKGRNGG-----VRLTKEGLY 65
                                  5678899*******************************999.....888888875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.69
                        HTH_34   6 lsyLasvdeadfvelkeale 25 
                                   + yL +v+++d  e+k++le
  gi|15668416|ref|NP_247212.1| 117 IIYL-VVENVDKDEIKNTLE 135
                                   4555.578899999999987 PP

>> PuR_N  Bacterial purine repressor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.072        71       6      31 ..       3      28 ..       1      33 [. 0.90
   2 ?    9.6   0.0   0.00085      0.85      51      68 ..      42      59 ..      36      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.072
                         PuR_N  6 lvaitkiLlenPnklisltyfaerfe 31
                                  +v +tk ++e+ ++ i+++++a++++
  gi|15668416|ref|NP_247212.1|  3 VVGLTKKIMEHLKEPITIKELAKKLN 28
                                  6789******************9987 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00085
                         PuR_N 51 eglGkletvaGaaGGvky 68
                                  ++lG +et +G++GGv+ 
  gi|15668416|ref|NP_247212.1| 42 RDLGLVETKKGRNGGVRL 59
                                  589*************85 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.7e-05     0.047       6      48 .]       8      48 ..       5      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
                        HTH_24  6 rkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +kI+e L++   i+++eLA++l++ p ++   ++ L + Gl++
  gi|15668416|ref|NP_247212.1|  8 KKIMEHLKE--PITIKELAKKLNMHPKNLDVKIRVLRDLGLVE 48
                                  678888888..9************9999999999999999986 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.5e-05     0.064       2      19 ..      16      33 ..      15      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                         IF2_N  2 skirVyeLAkeLgvkske 19
                                  + i+++eLAk+L++ +k 
  gi|15668416|ref|NP_247212.1| 16 EPITIKELAKKLNMHPKN 33
                                  679**********99986 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.3e-05     0.063      18      59 ..      14      59 ..       5      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-05
                                  EEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E.TEE..EEE CS
                     HTH_Crp_2 18 ielpltqeelAsmlGltretvsrilseLkreglis.r.grr..iri 59
                                  ++ p+t +elA  l++++  +   ++ L++ gl++ + gr+  +r+
  gi|15668416|ref|NP_247212.1| 14 LKEPITIKELAKKLNMHPKNLDVKIRVLRDLGLVEtKkGRNggVRL 59
                                  45699******************************73343235666 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.1e-05     0.071      16      48 ..      16      48 ..      13      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.1e-05
                                  TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR 16 gplsvseLakklgvskstvtrvldrLekkGlie 48
                                  +p++++eLakkl++++ ++   ++ L + Gl+e
  gi|15668416|ref|NP_247212.1| 16 EPITIKELAKKLNMHPKNLDVKIRVLRDLGLVE 48
                                  79****************999999999999998 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   8.8e-05     0.087      12      68 ..      11      69 ..       5      73 .. 0.81
   2 ?   -0.8   0.1       1.5   1.5e+03       4      26 ..      86     108 ..      84     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.8e-05
                        HTH_45 12 LeaisegeakkTkimykanLsykllnkYLdmLvekgli...kkskekYvlTekGlellek 68
                                  +e + ++  +  ++ +k n+  k+l+  +  L + gl+   k +++  +lT++Gl llek
  gi|15668416|ref|NP_247212.1| 11 MEHL-KEPITIKELAKKLNMHPKNLDVKIRVLRDLGLVetkKGRNGGVRLTKEGLYLLEK 69
                                  5555.44555568999**********************6533367789*********997 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                        HTH_45   4 kleIiadILeaisegeakkTkim 26 
                                   ++  +adI + is+ + + T+ +
  gi|15668416|ref|NP_247212.1|  86 RIGLLADITSRISKIGGNITSTV 108
                                   67778999999999999998766 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.0   0.00026      0.26       6      66 .]      10      67 ..       8      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                        HTH_12  6 ilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergl..trrvgyagreltEkGleeL 66
                                  i++  ++pi  ke+a++L+    ++       ++r+l + gl  t++ +++g +lt  Gl +L
  gi|15668416|ref|NP_247212.1| 10 IMEHLKEPITIKELAKKLNMHPKNL-----DVKIRVLRDLGLveTKKGRNGGVRLTKEGLYLL 67
                                  6777789************998888.....45788899999822456677799*****99876 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0095       9.5      13      42 ..      21      52 ..      21      55 .. 0.89
   2 ?    1.1   0.0      0.41   4.1e+02       2      11 ..      50      59 ..      49      59 .. 0.89
   3 ?    5.6   0.2     0.015        15      22      33 ..     111     122 ..     109     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0095
                                  CCCHHHCCEEC.TCEEEEEECTT.CCCCCCCH CS
                MazE_antitoxin 13 kevrfelgire.Gdevelevdgd.kiilrplk 42
                                  ke++++l+  + + +v ++v  d +++ +++ 
  gi|15668416|ref|NP_247212.1| 21 KELAKKLNMHPkNLDVKIRVLRDlGLVETKKG 52
                                  8**********************888877776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.41
                                  EETTEEEEEE CS
                MazE_antitoxin  2 kvGnsgavri 11
                                  k G++g vr+
  gi|15668416|ref|NP_247212.1| 50 KKGRNGGVRL 59
                                  78*******8 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.015
                                   ECTCEEEEEECT CS
                MazE_antitoxin  22 reGdevelevdg 33 
                                   reGdev+++ + 
  gi|15668416|ref|NP_247212.1| 111 REGDEVIIYLVV 122
                                   78******9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 965.06
//
Query:       gi|15668417|ref|NP_247213.1|  [L=22]
Description: 50S ribosomal protein L41E [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00033   20.7  17.9    0.00046   20.2  17.9    1.3  1  Ribosomal_L41  Ribosomal protein L41


Domain annotation for each model (and alignments):
>> Ribosomal_L41  Ribosomal protein L41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2  17.9   2.5e-08   0.00046       1      24 [.       1      22 []       1      22 [] 0.90

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.5e-08
                 Ribosomal_L41  1 MraKWrKKRmrRLKrKRRKmRqRS 24
                                  Mr KW KKR+rRLKr+R   R+RS
  gi|15668417|ref|NP_247213.1|  1 MRWKWYKKRLRRLKRERK--RARS 22
                                  9***************98..5665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (22 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 152.89
//
Query:       gi|15668418|ref|NP_247214.1|  [L=82]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit C [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-08   33.5   1.8    4.2e-08   33.4   1.8    1.1  1  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
  ------ inclusion threshold ------
      0.039   14.5   0.1       0.05   14.1   0.1    1.3  1  YtxH         YtxH-like protein


Domain annotation for each model (and alignments):
>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   1.8   4.7e-12   4.2e-08       2      62 .]       2      75 ..       1      75 [. 0.87

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 4.7e-12
                                  -HHHHHHHHHHHHHHHHHHTTCGC.S--TT----S.......-EB-S-.-......HHHHHTT-SSE.ETTEEEE CS
                   Glu-tRNAGln  2 seeEleklakelnsildyveqLqe.vdttgveplthp.....vlReDe.v......reelLknApet.edgyfvV 62
                                  +e+ +ek++ke ++i++ + ++ e +++ ++e  +++     vlReDe v      re++Lk Ap++ ++gy+vV
  gi|15668418|ref|NP_247214.1|  2 DEKTIEKIKKEAEEIINKFSEVLEkFNL-EMEESYYIidtrnVLREDEaVesnpefREKFLKIAPKVnKEGYVVV 75
                                  68889************99888876885.788889999*********853899************9967888887 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.6e-06      0.05      24      60 ..       3      64 ..       2      78 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.6e-06
                          YtxH 24 ketRkdlkekaddlkekakelleeakeka.........................kekaedlk 60
                                  ++t +++k++a+++ +k+ e+le+++  +                         +ek+ +++
  gi|15668418|ref|NP_247214.1|  3 EKTIEKIKKEAEEIINKFSEVLEKFNLEMeesyyiidtrnvlredeavesnpefREKFLKIA 64
                                  6899******************9998888888888888888885555444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2043  (0.113949); expected 358.6 (0.02)
Passed bias filter:                     1200  (0.0669307); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 610.12
//
Query:       gi|15668419|ref|NP_247215.1|  [L=289]
Description: dihydrodipicolinate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-97  324.7   0.4    3.6e-97  324.6   0.4    1.0  1  DHDPS       Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
      0.042   13.3   0.0      0.062   12.8   0.0    1.3  1  PEP_mutase  Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.6   0.4    4e-101   3.6e-97       2     288 ..       2     285 ..       1     286 [. 0.98

  Alignments for each domain:
  == domain 1  score: 324.6 bits;  conditional E-value: 4e-101
                                   -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SSH CS
                         DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsnst 82 
                                   f+g+ +a++tpf+++ ++d+  l+++i+fli++gv+g+v +GttGEs+tls+ee+++++e++v++++gr++viag+Gsn t
  gi|15668419|ref|NP_247215.1|   2 FKGVYPAIITPFKNK-EVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIEKVVDVVNGRVQVIAGAGSNCT 81 
                                   89**********986.8**************************************************************** PP

                                   HHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHT.STTEEEEEE CS
                         DHDPS  83 seaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLae.lenivgvKe 162
                                   +eai+l+  ae++Gad+vl++tPYYnkp+qegl +hf +++e+ +lp++lYnvpsrt ++l+p+tvk Lae ++ni +vKe
  gi|15668419|ref|NP_247215.1|  82 EEAIELSVFAEDVGADAVLSITPYYNKPTQEGLRKHFGKVAESINLPIVLYNVPSRTAVNLEPKTVKLLAEeYSNISAVKE 162
                                   **********************************************************************99********* PP

                                   -SS-CTHHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHC CS
                         DHDPS 163 avgdleevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaelnekllplikil 243
                                   a  +l++v ++++    +++++sG del+l+++ lG++Gvisv +ni++++  ++++++ eGd+++a+e++ kl pl+k++
  gi|15668419|ref|NP_247215.1| 163 ANPNLSQVSELIHD--AKITVLSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFPLMKAM 241
                                   *********99998..79*************************************************************** PP

                                   CCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHHH CS
                         DHDPS 244 faepnvilvktalellGlvveatlrkPltpleeeekeeleallka 288
                                   f e+n+i+vktal+++G ++++ lr Pl +++ee+k+ le++lk 
  gi|15668419|ref|NP_247215.1| 242 FIETNPIPVKTALNMMGRPAGE-LRLPLCEMSEEHKKILENVLKD 285
                                   **********************.****************999985 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.9e-06     0.062      85     178 ..      21     104 ..      17     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.9e-06
                    PEP_mutase  85 eevaetvrrliaaGvvgvniEDkkkndaerqlldieefaekiaaaraaaeeagfvinARtdalllsagagleeaieRaraY 165
                                   + ++e+++ li+ Gv+g++   +    +e+++l+ ee+ + i+++++       v+n R+ ++  + ++  eeaie     
  gi|15668419|ref|NP_247215.1|  21 DGLEENINFLIENGVSGIVAVGT---TGESPTLSHEEHKKVIEKVVD-------VVNGRVQVIAGAGSNCTEEAIELSVFA 91 
                                   568899************98888...579999*************65.......79******999999999*****99999 PP

                    PEP_mutase 166 aeAGAdgvfvpgl 178
                                    + GAd+v+ +  
  gi|15668419|ref|NP_247215.1|  92 EDVGADAVLSITP 104
                                   99*****987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1691.21
//
Query:       gi|15668420|ref|NP_247216.1|  [L=63]
Description: 30S ribosomal protein S17e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-22   79.5   1.1    1.9e-22   79.4   1.1    1.0  1  Ribosomal_S17e  Ribosomal S17


Domain annotation for each model (and alignments):
>> Ribosomal_S17e  Ribosomal S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   1.1   1.1e-26   1.9e-22       1      62 [.       2      63 .]       2      63 .] 0.99

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 1.1e-26
                                  XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHHTT CS
                Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkriq 62
                                  mgr+r+  +K++a ++i+ky   +t+dF+tnk+v+eeva+i++k+lrn+iaGy+th m+++q
  gi|15668420|ref|NP_247216.1|  2 MGRIRQTLIKRTAMELIKKYRDLFTTDFETNKRVLEEVAQISTKRLRNRIAGYITHKMRQLQ 63
                                  9**********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 403.87
//
Query:       gi|15668421|ref|NP_247217.1|  [L=99]
Description: chorismate mutase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-19   68.4   4.4    6.5e-19   68.1   4.4    1.1  1  CM_2             Chorismate mutase type II
    0.00069   19.6   1.0     0.0013   18.7   1.0    1.5  1  AKAP7_RIRII_bdg  PKA-RI-RII subunit binding domain of A-kinas
     0.0071   16.5   1.5     0.0087   16.3   1.5    1.2  1  DUF313           Domain of unknown function (DUF313)
  ------ inclusion threshold ------
      0.028   14.8   3.0      0.071   13.5   3.0    1.7  1  Syntaxin_2       Syntaxin-like protein
      0.032   14.8   1.5      0.043   14.4   1.5    1.3  1  DUF3800          Protein of unknown function (DUF3800)
      0.034   12.8   5.8      0.036   12.8   5.8    1.0  1  MAP65_ASE1       Microtubule associated protein (MAP65/ASE1 f
       0.55   10.3   8.6       0.72   10.0   8.6    1.2  1  TssO             Type VI secretion system, TssO
        1.8    8.4   9.3      0.059   13.1   1.7    2.0  2  DivIC            Septum formation initiator


Domain annotation for each model (and alignments):
>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   4.4   2.9e-22   6.5e-19       1      75 []       9      87 ..       9      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 2.9e-22
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHH....HHS-HHHHHHHHHHHHHHHHHHHH CS
                          CM_2  1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerlee....galdeeaierifreiisasralqk 75
                                  Rk+IdeiD++il+L+aeR  lak+v+e+K++ g p+ dpeRe+ + +r+++      +de+   +if+ +i++ +alqk
  gi|15668421|ref|NP_247217.1|  9 RKKIDEIDNKILKLIAERNSLAKDVAEIKNQLGIPINDPEREKYIYDRIRKlckeHNVDENIGIKIFQILIEHNKALQK 87
                                  9**************************************************885433********************96 PP

>> AKAP7_RIRII_bdg  PKA-RI-RII subunit binding domain of A-kinase anchor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.0   5.9e-07    0.0013      22      36 ..      83      98 ..      75      99 .] 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.9e-07
               AKAP7_RIRII_bdg 22 KAVq.qYLEETqnkar 36
                                  KA q qYLEETqnk++
  gi|15668421|ref|NP_247217.1| 83 KALQkQYLEETQNKNK 98
                                  788779********98 PP

>> DUF313  Domain of unknown function (DUF313)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.5   3.9e-06    0.0087      15      78 ..      13      76 ..       1      97 [. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.9e-06
                        DUF313 15 ng..aedpkliiektlfktdvkkkqsrlsipfkklirndFLteeElraikeeekkkdedkGvkvil 78
                                  ++  ++  kli e++  + dv + +++l ip++  +r+ ++  +  r++  +e++ de++G+k++ 
  gi|15668421|ref|NP_247217.1| 13 DEidNKILKLIAERNSLAKDVAEIKNQLGIPINDPEREKYIY-DRIRKL-CKEHNVDENIGIKIFQ 76
                                  43334556********************************97.567777.6788888999999753 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.0   3.2e-05     0.071      29      81 ..       6      63 ..       3      97 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                    Syntaxin_2 29 eelreklhelieeinelikktnellkklsqldnsssds.....qqklqkekLkkdfke 81
                                   e+r+k++e+ ++i +li + n+l k++++++n++        ++k++ ++++k +ke
  gi|15668421|ref|NP_247217.1|  6 AEIRKKIDEIDNKILKLIAERNSLAKDVAEIKNQLGIPindpeREKYIYDRIRKLCKE 63
                                  589******************************9943367778555555555554443 PP

>> DUF3800  Protein of unknown function (DUF3800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.5   1.9e-05     0.043      28      77 ..      23      78 ..       1      99 [] 0.61

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                       DUF3800 28 e.eikkleekikelkkky..........krlleriakflkkndliksdeesdesilivldk 77
                                    e+++l + + e+k+++          k++++ri+k +k++     + +++++i+i+   
  gi|15668421|ref|NP_247217.1| 23 IaERNSLAKDVAEIKNQLgipindpereKYIYDRIRKLCKEH-----NVDENIGIKIFQIL 78
                                  245666666666677777**********************95.....44444444444322 PP

>> MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   5.8   1.6e-05     0.036     121     211 ..       3      97 ..       1      99 [] 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT----SHHHHHHHCT-TTTS-....TSHHH.HHHHHHH...HH CS
                    MAP65_ASE1 121 eeleslrkhleelkeekerRleeikelkkqIkslmeeLglepktsieedllkesednskklkpltret.ikkLkll...kk 197
                                   e+l+++rk+++e+ +++ + ++e ++l+k++ ++ ++Lg++ ++  +e+ +     + +k +++++++ ik +++l    k
  gi|15668421|ref|NP_247217.1|   3 EKLAEIRKKIDEIDNKILKLIAERNSLAKDVAEIKNQLGIPINDPEREKYIYDRIRKLCKEHNVDENIgIKIFQILiehNK 83 
                                   7899**********************************************9999999999999998865444444410156 PP

                                   HHHHHHHHHHHHHH CS
                    MAP65_ASE1 198 eleeqksereeklk 211
                                    l++q+ e +++++
  gi|15668421|ref|NP_247217.1|  84 ALQKQYLEETQNKN 97 
                                   67777777777665 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   8.6   0.00032      0.72      60     146 ..       1      95 [.       1      97 [. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00032
                          TssO  60 lkkkvdsiykkIdsL.kpevnavfleneIkkdlndiknty..gknssdeRykmyaqiakfykmlledKkelksvse..... 132
                                   +++k+ +i kkId + ++  + + ++n++ kd+ +ikn+   + n+ ++ + +y+ i k+ k+   d ++ +++ +     
  gi|15668421|ref|NP_247217.1|   1 MIEKLAEIRKKIDEIdNKILKLIAERNSLAKDVAEIKNQLgiPINDPEREKYIYDRIRKLCKEHNVDENIGIKIFQilieh 81 
                                   578999*********9999999*****************943447777778899999999999999999988887777775 PP

                          TssO 133 niklfkkqLeecei 146
                                   n+ l k+ Lee ++
  gi|15668421|ref|NP_247217.1|  82 NKALQKQYLEETQN 95 
                                   66666666777776 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.7   2.6e-05     0.059      18      62 ..       4      58 ..       2      69 .. 0.83
   2 ?   -0.4   1.0      0.45     1e+03      26      41 ..      83      98 ..      75      99 .] 0.54

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX..........XXXXXXXXXX CS
                         DivIC 18 aykqlkqeiaalqaelaklkaeneeLeaevkdLks..........dedyieerAR 62
                                  ++ +++++i+++ +++ kl ae+++L++ v++ k+           e yi  r R
  gi|15668421|ref|NP_247217.1|  4 KLAEIRKKIDEIDNKILKLIAERNSLAKDVAEIKNqlgipindpeREKYIYDRIR 58
                                  5678999************************998877777776666667777776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.45
                                  HHHHHHHHHHHHHHHH CS
                         DivIC 26 iaalqaelaklkaene 41
                                   a +++ l++ +++n+
  gi|15668421|ref|NP_247217.1| 83 KALQKQYLEETQNKNK 98
                                  4444555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1731  (0.0965475); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 634.48
//
Query:       gi|15668422|ref|NP_247218.1|  [L=247]
Description: proliferating-cell nuclear antigen Pol30 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-23   82.2   3.8    3.2e-23   81.8   0.8    2.2  3  PCNA_N           Proliferating cell nuclear antigen, N-termin
    7.9e-18   64.9   0.6    2.6e-14   53.5   0.1    2.3  2  PCNA_C           Proliferating cell nuclear antigen, C-termin
    2.8e-07   29.9   0.5    3.9e-05   22.8   0.5    2.3  1  Rad1             Repair protein Rad1/Rec1/Rad17
    1.3e-05   24.8   0.3    1.6e-05   24.5   0.3    1.2  1  Rad9             Rad9
     0.0002   21.2   2.6     0.0003   20.6   0.3    2.3  3  DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal 
  ------ inclusion threshold ------
      0.034   13.3   0.0      0.052   12.7   0.0    1.4  1  Hus1             Hus1-like protein


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.8   1.1e-26   3.2e-23       1     121 [.       1     117 [.       1     122 [. 0.92
   2 ?   -0.4   0.0       0.3     9e+02      83     108 ..     158     183 ..     141     196 .. 0.60
   3 ?   -0.3   0.0      0.28   8.2e+02      44      68 ..     182     206 ..     162     223 .. 0.69

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 1.1e-26
                                   CEEEEESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTT CS
                        PCNA_N   1 mlearleqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkc 81 
                                   m+   +e a  +kk++++i  l++e++f++d++Gi++ a+D shvaLvsle+   +fe+y  D +  +g++l+++ k++  
  gi|15668422|ref|NP_247218.1|   1 MFRGVMESAKEFKKVVDTISTLLDEICFEVDEEGIKASAMDPSHVALVSLEIPRLAFEEYEADSH-DIGIDLEAFKKVMNR 80 
                                   67777889999****************************************************75.79************* PP

                                   STTTSEEEEEEETTSSEEEEEEEECTSSEEEEEEEEEEEB CS
                        PCNA_N  82 annedsvtlkaedeadtlalvfesekkdkiaeydlklkli 121
                                   a+++d ++l+ ++e+++l+++fe++ k k +   l l +i
  gi|15668422|ref|NP_247218.1|  81 AKAKDRLILELDEEKNKLNVIFENTGKRKFS---LALLDI 117
                                   ************************9998766...555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.3
                                   TTTSEEEEEEETTSSEEEEEEEECTS CS
                        PCNA_N  83 nnedsvtlkaedeadtlalvfesekk 108
                                    +ed+ +++a+ + +    +fe++++
  gi|15668422|ref|NP_247218.1| 158 ADEDKFVIHAKGDLNENEAIFEKDSS 183
                                   34555555555555555555555544 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.28
                                   SSEEEEEEEEGGGSSEEEESS-EEE CS
                        PCNA_N  44 hvaLvslelrsegfekyrCDrnlal 68 
                                     a++sle+++e+ + +  D  + +
  gi|15668422|ref|NP_247218.1| 182 SSAIISLEVKEEAKSAFNLDYLMDM 206
                                   4567888888888888877764444 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00034         1      14      45 ..       8      39 ..       4      53 .. 0.91
   2 !   53.5   0.1   8.8e-18   2.6e-14       1     127 [.     123     244 ..     123     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00034
                                  EHHHHHHHHHHHTTT-SEEEEEEETTEEEEEE CS
                        PCNA_C 14 pssefaricrdlsqlsdsvvisvtkegvkfsa 45
                                  ++ ef++++  +s+l d++   v  eg+k sa
  gi|15668422|ref|NP_247218.1|  8 SAKEFKKVVDTISTLLDEICFEVDEEGIKASA 39
                                  789**************************987 PP

  == domain 2  score: 53.5 bits;  conditional E-value: 8.8e-18
                                   ----SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEE CS
                        PCNA_C   1 gipdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltf 81 
                                   ++p++ey  v+ +    f+   +d   +sd v++++  +     a+Gd+ + + +       +++   + le+ke  +  f
  gi|15668422|ref|NP_247218.1| 123 KVPEIEYPNVIMIKGDAFKEALKDADLFSDYVILKADEDKFVIHAKGDLNENEAIF-----EKDSSAIISLEVKEEAKSAF 198
                                   68***********************************************9984444.....456778899*********** PP

                                   EHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                        PCNA_C  82 alkYlaeftkatsLservtlslssevPlvveykikdvgllayllak 127
                                    l+Yl++++k+ s  + ++++l +++Pl++ey+i+ v l++ l+++
  gi|15668422|ref|NP_247218.1| 199 NLDYLMDMVKGVSSGDIIKIYLGNDMPLKLEYSIAGVNLTFLLAPR 244
                                   ***********************************99998887765 PP

>> Rad1  Repair protein Rad1/Rec1/Rad17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.5   1.3e-08   3.9e-05     111     254 ..      77     211 ..       1     232 [. 0.77

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.3e-08
                          Rad1 111 vasssakatscklsYkgeGsPLvliLee.agvtttcelsTyepeedldleldrqevvlkvilkselLhsalteLdatskkl 190
                                   v++  +++ ++ l+ ++e + L++i+e+  + + +++l    +++    e    e  + +++k++ +++al++ d  s+ +
  gi|15668422|ref|NP_247218.1|  77 VMNRAKAKDRLILELDEEKNKLNVIFENtGKRKFSLALLDISASSVKVPEI---EYPNVIMIKGDAFKEALKDADLFSDYV 154
                                   366777788899999999999999999955555555555555555555555...55556789****************988 PP

                          Rad1 191 kilassekkapvfalsakgelgssevefpneksvlekfevsslsessessYkfallkkaakala 254
                                    + a +      f ++akg+l ++e  f +++s + ++ev+  +e+++  +++ +l  + k ++
  gi|15668422|ref|NP_247218.1| 155 ILKADE----DKFVIHAKGDLNENEAIFEKDSSAIISLEVK--EEAKSA-FNLDYLMDMVKGVS 211
                                   777766....58*****************************..555555.99988888777665 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.3   5.5e-09   1.6e-05       1     165 [.      12     167 ..      12     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 5.5e-09
                          Rad9   1 laralqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvKsvlsvfrslsakektve 81 
                                   + +++ ++s + de+ +e  e+g++ ++++ s+ a +++++ +  F++ye ++     + i + ++ +v+     + k  +
  gi|15668422|ref|NP_247218.1|  12 FKKVVDTISTLLDEICFEVDEEGIKASAMDPSHVALVSLEIPRLAFEEYEADS---HDIGIDLEAFKKVMN----RAKAKD 85 
                                   6799*********************************************5544...456777788888883....446678 PP

                          Rad9  82 kvkisidekksrlivqllCkhgvkkthkisledseslkavfdkettpsklriksrvLsdllehfsssleeitielakervl 162
                                   ++ +++de+k +l v +   +  k++++++l d    ++++ +   p++++ik   ++++l+      + + +++ +++++
  gi|15668422|ref|NP_247218.1|  86 RLILELDEEKNKLNVIFE--NTGKRKFSLALLDISASSVKVPEIEYPNVIMIKGDAFKEALKDADLFSDYVILKADEDKFV 164
                                   999***999999999885..55699***********************************998887777777777777777 PP

                          Rad9 163 lks 165
                                   ++ 
  gi|15668422|ref|NP_247218.1| 165 IHA 167
                                   764 PP

>> DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.77   2.3e+03      16      49 ..       9      38 ..       5      46 .. 0.68
   2 ?   -1.1   0.1      0.54   1.6e+03      12      27 ..      67      82 ..      61     109 .. 0.60
   3 !   20.6   0.3     1e-07    0.0003       8     105 ..     129     228 ..     124     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.77
                                  HHHHHHHHHHHHTTSSTSTGEEEEEEETTEEEEE CS
               DNA_pol3_beta_3 16 lkelkealkRvalladeknrkvrLsleegqlkls 49
                                   ke+k++++ +++l d    ++  +++e+ +k s
  gi|15668422|ref|NP_247218.1|  9 AKEFKKVVDTISTLLD----EICFEVDEEGIKAS 38
                                  6888999998888886....55555666555555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.54
                                  EEEEHHHHHHHHHHHH CS
               DNA_pol3_beta_3 12 vtvdlkelkealkRva 27
                                  + +dl+++k++++R++
  gi|15668422|ref|NP_247218.1| 67 IGIDLEAFKKVMNRAK 82
                                  5577777777777764 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 1e-07
                                   -SEEEEEEHHHHHHHHHHHHTTSSTSTGEEEEEEETTEEEEEEE..ETTSEEEEEEEEEBEE....SS-EEEEEEHHHHHH CS
               DNA_pol3_beta_3   8 fkkkvtvdlkelkealkRvalladeknrkvrLsleegqlklsae..nsevgeaeEevdvnye....GeeleiafNvsYlld 82 
                                   + ++++++ +++kealk ++l +d     v L+++e++  ++a+   +e +   E+ + +++     ee + afN  Yl+d
  gi|15668422|ref|NP_247218.1| 129 YPNVIMIKGDAFKEALKDADLFSD----YVILKADEDKFVIHAKgdLNENEAIFEKDSSAIIslevKEEAKSAFNLDYLMD 205
                                   568899*****************8....999****99988887611456666667555554457789999*********** PP

                                   HHHHH-SSE.EEEEESSTTS-EEE CS
               DNA_pol3_beta_3  83 alkaletee.velqltdstkpvll 105
                                    +k + + + +++ l + + p++l
  gi|15668422|ref|NP_247218.1| 206 MVKGVSSGDiIKIYLGNDM-PLKL 228
                                   ***9987651566666665.7766 PP

>> Hus1  Hus1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05     0.052       3     102 ..       2      94 ..       1     167 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                          Hus1   3 FkaqltdaetlkkvlqslsklgkecilrltpeklrfiiiteaddgvqvwaqlqvdaiFeeyeieSndeneInlevdlaaLl 83 
                                   F+  +++a+++kkv+ ++s l  e+   + +e +    ++ ++    v  ++++   Feeye +S d     + +dl+a+ 
  gi|15668422|ref|NP_247218.1|   2 FRGVMESAKEFKKVVDTISTLLDEICFEVDEEGIKASAMD-PSHVALVSLEIPR-LAFEEYEADSHD-----IGIDLEAFK 75 
                                   9999*******************************99994.7777778888876.59**********.....899****** PP

                          Hus1  84 raLksaeaaksvqlrLtkk 102
                                   +++  a+a+ ++ l L  +
  gi|15668422|ref|NP_247218.1|  76 KVMNRAKAKDRLILELDEE 94 
                                   *******999998888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1484.35
//
Query:       gi|15668423|ref|NP_247219.1|  [L=194]
Description: hypothetical protein MJ_0248 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.64   10.3   4.2        2.8    8.2   0.1    2.4  3  MapZ_EC1  MapZ extracellular domain 1


Domain annotation for each model (and alignments):
>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.4    0.0091   1.6e+02      21      77 ..      13      66 ..      10      76 .. 0.79
   2 ?    8.2   0.1   0.00016       2.8      25      61 ..      82     120 ..      70     130 .. 0.86
   3 ?   -3.7   0.0      0.73   1.3e+04      64      78 ..     167     181 ..     157     190 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.0091
                      MapZ_EC1 21 fekeyaafftddketflknsefaklseLekkLeklkgskeYkklkkkldslkkqisa 77
                                  f+k+ + +f+ +  + lkn  f+++++   kL kl ++  Y+++++ ++++k+ i+ 
  gi|15668423|ref|NP_247219.1| 13 FSKDHKPYFVITMYESLKNYFFEEIKN--DKLLKLPDD-FYDDIREYIKNIKDDIEL 66
                                  777888889999999999999998885..778788765.599999999999999974 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00016
                      MapZ_EC1  25 yaafftddketflknsefaklseLekkLeklk..gskeY 61 
                                   y+a+++d++++ l ++e + ++++e+ + +lk  ++ e+
  gi|15668423|ref|NP_247219.1|  82 YKALYLDNERENLLPEELNIIHAIENIVVELKieETPEF 120
                                   99**************************99995444455 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 0.73
                      MapZ_EC1  64 lkkkldslkkqisai 78 
                                   l +k+ ++ ++ ++i
  gi|15668423|ref|NP_247219.1| 167 LDRKISHILEKHRII 181
                                   444555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1268.29
//
Query:       gi|15668424|ref|NP_247220.1|  [L=94]
Description: 50S ribosomal protein L44e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-28   98.7   1.2    2.8e-28   98.2   1.2    1.2  1  Ribosomal_L44  Ribosomal protein L44
    0.00023   21.5   7.7      0.002   18.5   3.5    2.4  2  Ribosomal_L33  Ribosomal protein L33
  ------ inclusion threshold ------
       0.02   14.9   0.2        3.7    7.6   0.0    2.1  2  HypA           Hydrogenase/urease nickel incorporation, metal
      0.021   14.9   0.9       0.79    9.8   0.1    2.1  2  Elf1           Transcription elongation factor Elf1 like
      0.068   12.9   4.6        3.9    7.3   0.3    2.6  3  zinc_ribbon_2  zinc-ribbon domain
      0.078   13.4   4.0        4.8    7.8   0.5    2.5  2  zf-H2C2_2      Zinc-finger double domain
       0.11   11.9   2.2        1.6    8.2   0.2    2.2  2  zf-ribbon_3    zinc-ribbon domain
       0.33   11.3   4.4        2.7    8.4   0.9    2.4  2  zf-C2H2_jaz    Zinc-finger double-stranded RNA-binding
        0.9    9.4   6.0        5.8    6.9   0.2    2.9  3  TFIIS_C        Transcription factor S-II (TFIIS)


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   1.2   1.4e-31   2.8e-28       1      76 []      16      92 ..      16      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 1.4e-31
                                  EEEEEEEEE-------SSSHHHHHHHH.H-SSSGGGGS----.--SSBB--EEEEETTT--EEE--..--BBS--EEE CS
                 Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaKttKKivlrleCteCkkkrlka..lkRakkfelv 76
                                  kHt+h ve++kkgk sel++g+R+++r ++gygG ++p + + +K+ KKi+lr++CteC+k+++ka  ++R ++fe+v
  gi|15668424|ref|NP_247220.1| 16 KHTIHIVEKAKKGKPSELTWGQRQFRRVTAGYGGFPRPLPDR-SKPVKKIDLRFKCTECGKMHTKAngCFRSGRFEFV 92
                                  8*****************************************.**********************9888*******96 PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   3.5     1e-06     0.002      30      43 ..       7      20 ..       5      24 .. 0.89
   2 ?    4.8   0.1      0.02        39       4      18 ..      67      79 ..      64      91 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1e-06
                                  EEEEETTTTEEEEE CS
                 Ribosomal_L33 30 lkKYcprcrkhtlh 43
                                  +++Ycp+c+kht+h
  gi|15668424|ref|NP_247220.1|  7 VRRYCPYCKKHTIH 20
                                  799*********** PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.02
                                  EEEET......EEEE CS
                 Ribosomal_L33  4 tLeCtecksrnYttt 18
                                  + +Ctec++   +t+
  gi|15668424|ref|NP_247220.1| 67 RFKCTECGKM--HTK 79
                                  679****995..444 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.006        12      87     101 ..       9      23 ..       1      28 [. 0.78
   2 ?    7.6   0.0    0.0019       3.7      64      83 ..      61      80 ..      39      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.006
                                   HS-TTTSSS-EEEEE CS
                          HypA  87 lrCpkCgsadveivs 101
                                     Cp C+++ ++iv+
  gi|15668424|ref|NP_247220.1|   9 RYCPYCKKHTIHIVE 23 
                                   46*********9986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0019
                                  EEEE--EEEETTTS-EEECH CS
                          HypA 64 ieevpvkvrCreCgkefele 83
                                  +++++++++C+eCgk  +++
  gi|15668424|ref|NP_247220.1| 61 VKKIDLRFKCTECGKMHTKA 80
                                  67888999999999766544 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.023        46      24      41 ..      11      27 ..       2      34 .. 0.72
   2 ?    9.8   0.1    0.0004      0.79      10      31 ..      56      77 ..      41      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.023
                          Elf1 24 CpfCnheksvevkldkke 41
                                  Cp+C+++ ++++  + k+
  gi|15668424|ref|NP_247220.1| 11 CPYCKKH-TIHIVEKAKK 27
                                  ****999.6666544444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0004
                          Elf1 10 rkkkkkkklptkFdCpfCnhek 31
                                   + k +kk++ +F+C  C++ +
  gi|15668424|ref|NP_247220.1| 56 DRSKPVKKIDLRFKCTECGKMH 77
                                  56788999**********9875 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3     0.002       3.9      13      19 ..       8      14 ..       2      17 .. 0.76
   2 ?   -2.7   0.0       2.8   5.6e+03       8      14 ..      53      59 ..      52      60 .. 0.79
   3 ?    6.8   0.5    0.0028       5.5       1       8 [.      69      76 ..      69      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.002
                 zinc_ribbon_2 13 akFCpyC 19
                                   ++CpyC
  gi|15668424|ref|NP_247220.1|  8 RRYCPYC 14
                                  579**** PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.8
                 zinc_ribbon_2  8 elqdnak 14
                                  +l+d++k
  gi|15668424|ref|NP_247220.1| 53 PLPDRSK 59
                                  7999987 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0028
                 zinc_ribbon_2  1 fCpnCGae 8 
                                  +C++CG+ 
  gi|15668424|ref|NP_247220.1| 69 KCTECGKM 76
                                  7*****96 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0049       9.8      16      24 ..      10      18 ..       3      23 .. 0.82
   2 ?    7.8   0.5    0.0024       4.8      11      23 ..      61      76 ..      57      79 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0049
                     zf-H2C2_2 16 eCplCdkaF 24
                                   Cp+C+k +
  gi|15668424|ref|NP_247220.1| 10 YCPYCKKHT 18
                                  6*****976 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0024
                     zf-H2C2_2 11 gekp...yeCplCdka 23
                                  ++k+   ++C +C+k 
  gi|15668424|ref|NP_247220.1| 61 VKKIdlrFKCTECGKM 76
                                  5664555*******96 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2   0.00082       1.6       3      11 ..       9      17 ..       8      19 .. 0.80
   2 ?    3.4   0.1     0.027        54      19      24 ..      70      75 ..      68      81 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00082
                   zf-ribbon_3  3 vrCPnCGap 11
                                  ++CP+C+++
  gi|15668424|ref|NP_247220.1|  9 RYCPYCKKH 17
                                  589999985 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.027
                   zf-ribbon_3 19 CpyCGt 24
                                  C+ CG+
  gi|15668424|ref|NP_247220.1| 70 CTECGK 75
                                  555553 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.9    0.0014       2.7       3      11 ..      10      18 ..       8      21 .. 0.86
   2 ?    4.1   0.1     0.031        61       2      10 ..      68      76 ..      67      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0014
                                  BBTTTTBBB CS
                   zf-C2H2_jaz  3 YCvlCdKyF 11
                                  YC++C+K+ 
  gi|15668424|ref|NP_247220.1| 10 YCPYCKKHT 18
                                  *******95 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.031
                                  CBBTTTTBB CS
                   zf-C2H2_jaz  2 fYCvlCdKy 10
                                  f C +C K+
  gi|15668424|ref|NP_247220.1| 68 FKCTECGKM 76
                                  99****996 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.021        41       3      14 ..      11      22 ..       9      25 .. 0.84
   2 ?    0.1   0.0      0.39   7.7e+02      10      20 ..      32      42 ..      29      43 .. 0.83
   3 ?    6.9   0.2    0.0029       5.8      28      36 ..      67      75 ..      65      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.021
                       TFIIS_C  3 CpkCgsreayff 14
                                  Cp C+++ ++ +
  gi|15668424|ref|NP_247220.1| 11 CPYCKKHTIHIV 22
                                  ******998776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.39
                       TFIIS_C 10 eayffqlQtRs 20
                                  e ++ q+Q R+
  gi|15668424|ref|NP_247220.1| 32 ELTWGQRQFRR 42
                                  78899***996 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0029
                       TFIIS_C 28 fykCtkCgh 36
                                   +kCt+Cg+
  gi|15668424|ref|NP_247220.1| 67 RFKCTECGK 75
                                  589999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 610.66
//
Query:       gi|15668425|ref|NP_247221.1|  [L=62]
Description: 30S ribosomal protein S27e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-28   98.3   2.0    1.6e-28   98.2   2.0    1.0  1  Ribosomal_S27e  Ribosomal protein S27
     0.0044   16.5   0.8     0.0057   16.2   0.8    1.3  1  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.021   14.2   1.3        1.6    8.3   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain
      0.027   14.4   1.4        2.5    8.1   0.1    2.4  2  zinc_ribbon_4   zinc-ribbon domain
      0.029   14.1   0.1      0.034   13.8   0.1    1.1  1  TackOD1         Thaumarchaeal output domain 1
      0.036   13.9   4.4        3.4    7.6   4.4    2.2  1  TFIIS_C         Transcription factor S-II (TFIIS)
      0.046   13.7   0.1      0.055   13.5   0.1    1.1  1  Zn_Tnp_IS91     Transposase zinc-binding domain
      0.047   13.6   0.7      0.047   13.6   0.7    1.9  2  DUF3797         Domain of unknown function (DUF3797)
       0.06   13.5   0.3      0.064   13.4   0.3    1.2  1  DUF2614         Zinc-ribbon containing domain
       0.06   13.4   0.2      0.071   13.1   0.2    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.066   13.0   4.3        1.4    8.8   0.1    2.1  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
      0.083   12.8   1.1       0.11   12.4   1.1    1.2  1  eIF-5_eIF-2B    Domain found in IF2B/IF5
       0.18   11.6   0.0       0.18   11.6   0.0    1.1  1  NTF-like        Nucleotidyltransferase-like
       0.35   10.7   2.9       0.44   10.4   0.9    1.8  2  PADR1           PADR1 (NUC008) domain
        0.6   10.0   4.1         19    5.2   2.1    2.2  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
        0.9    9.6   5.7        1.8    8.6   0.2    2.4  2  DUF1610         Domain of unknown function (DUF1610)
        2.1    8.2   7.5          9    6.2   5.1    2.6  2  zinc_ribbon_5   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   2.0   1.5e-31   1.6e-28       1      54 [.       8      61 ..       8      62 .] 0.98

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 1.5e-31
                                  -S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEEE CS
                Ribosomal_S27e  1 prskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqilerl 54
                                  pr+kFl+v+Cp+C+ne++vF+++atvvkC++CgkvLveP+GGk+k+ka+ile+l
  gi|15668425|ref|NP_247221.1|  8 PRTKFLRVQCPECNNEQIVFGSPATVVKCLTCGKVLVEPRGGKGKVKAKILEIL 61
                                  89**************************************************97 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.8   5.4e-06    0.0057       2      34 ..      16      48 ..      15      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.4e-06
                                  EETTTTCEECHEETSTTCEEESSSSBEEEECCC CS
                  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsi 34
                                  +CP+C+++++v+    + + C  CG Vl +   
  gi|15668425|ref|NP_247221.1| 16 QCPECNNEQIVFGSPATVVKCLTCGKVLVEPRG 48
                                  8*************************9977665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0015       1.6       3      12 ..      15      25 ..      14      31 .. 0.83
   2 ?    5.2   0.1     0.014        15       3      14 ..      34      46 ..      32      47 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                   zf-ribbon_3  3 vrCPnCGa.pl 12
                                  v+CP+C++ ++
  gi|15668425|ref|NP_247221.1| 15 VQCPECNNeQI 25
                                  68****99775 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.014
                   zf-ribbon_3  3 vrCPnCGa.plss 14
                                  v+C  CG+ ++++
  gi|15668425|ref|NP_247221.1| 34 VKCLTCGKvLVEP 46
                                  6788888866776 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0023       2.5       2       9 ..      14      21 ..       3      23 .. 0.70
   2 ?    5.3   0.1     0.017        18      24      34 ..      32      42 ..      28      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0023
                 zinc_ribbon_4  2 kitCpsCk 9 
                                  +++Cp+C+
  gi|15668425|ref|NP_247221.1| 14 RVQCPECN 21
                                  45555555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.017
                 zinc_ribbon_4 24 vkvrCskCghv 34
                                  + v+C  Cg+v
  gi|15668425|ref|NP_247221.1| 32 TVVKCLTCGKV 42
                                  579******97 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   3.2e-05     0.034      88     115 ..      15      45 ..       7      52 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                       TackOD1  88 evCpkCkSidi...eeqelihhftCgnvgpe 115
                                     Cp+C+  +i   +  +++++ tCg+v +e
  gi|15668425|ref|NP_247221.1|  15 VQCPECNNEQIvfgSPATVVKCLTCGKVLVE 45 
                                   4566666666633334566666666666544 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   4.4    0.0032       3.4       2      36 ..      16      41 ..      15      43 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0032
                       TFIIS_C  2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCgh 36
                                  +Cp+C++++++f          ++ + +kC++Cg+
  gi|15668425|ref|NP_247221.1| 16 QCPECNNEQIVFG---------SPATVVKCLTCGK 41
                                  8*******99997.........6666677777776 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.2e-05     0.055      37      66 ..      12      42 ..       6      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.2e-05
                   Zn_Tnp_IS91 37 faryeCeeCghekivyfsCksrh.CpsCqkk 66
                                  f r++C+eC++e+iv+ s      C +C+k 
  gi|15668425|ref|NP_247221.1| 12 FLRVQCPECNNEQIVFGSPATVVkCLTCGKV 42
                                  7899**************999999****996 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   4.4e-05     0.047      14      25 ..      15      26 ..       2      35 .. 0.82
   2 ?    1.2   0.1      0.33   3.5e+02      14      30 ..      34      50 ..      29      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.4e-05
                       DUF3797 14 vqCPeCgNnkvl 25
                                  vqCPeC N+++ 
  gi|15668425|ref|NP_247221.1| 15 VQCPECNNEQIV 26
                                  8********986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.33
                       DUF3797 14 vqCPeCgNnkvlNsegk 30
                                  v+C  Cg   v   +gk
  gi|15668425|ref|NP_247221.1| 34 VKCLTCGKVLVEPRGGK 50
                                  78999998888777765 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   6.1e-05     0.064      62      93 ..       9      43 ..       1      55 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.1e-05
                       DUF2614 62 stkavqvvcpeceketkvlGr...vdlcmhcdepl 93
                                   tk ++v+cpec++e  v+G    v  c+ c + l
  gi|15668425|ref|NP_247221.1|  9 RTKFLRVQCPECNNEQIVFGSpatVVKCLTCGKVL 43
                                  68999**************9633366788887766 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   6.7e-05     0.071      69     104 ..      13      51 ..       7      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-05
                                   -EEEETTTS-EEECHH..H.HHS-TTTSSS-EEEEESSS CS
                          HypA  69 vkvrCreCgkefelee..k.alrCpkCgsadveivsGee 104
                                   ++v+C eC++e  +    +  ++C +Cg+  ve  +G++
  gi|15668425|ref|NP_247221.1|  13 LRVQCPECNNEQIVFGspAtVVKCLTCGKVLVEPRGGKG 51 
                                   6899*****98875443335679******9999998874 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0013       1.4       2      12 ..      15      26 ..      14      27 .. 0.80
   2 ?    5.7   0.9     0.012        12       1      19 [.      33      51 ..      33      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                                  EE-SSS-.-EEE CS
                zf-C4_Topoisom  2 ekCPkCg.gdLv 12
                                  ++CP+C+ +++v
  gi|15668425|ref|NP_247221.1| 15 VQCPECNnEQIV 26
                                  68*****77766 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.012
                                  -EE-SSS--EEEEEE-SSS CS
                zf-C4_Topoisom  1 vekCPkCggdLvlkrgkkG 19
                                  v+kC  Cg+ Lv+ rg kG
  gi|15668425|ref|NP_247221.1| 33 VVKCLTCGKVLVEPRGGKG 51
                                  589*********9999888 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.1    0.0001      0.11      88     116 ..      15      41 ..      10      42 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                                   TSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                  eIF-5_eIF-2B  88 VlCkeCkspetelekeerllvlkCkaCga 116
                                   V+C+eC++ ++ +    +  v+kC +Cg+
  gi|15668425|ref|NP_247221.1|  15 VQCPECNNEQIVFGSPAT--VVKCLTCGK 41 
                                   99*****99887765544..46*****97 PP

>> NTF-like  Nucleotidyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00017      0.18      75     101 ..      22      48 ..       7      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                   HHHHHHT--HHHHHHHHHSEEEEESTT CS
                      NTF-like  75 eewlllgsnrrlvdwlleGkilfdrne 101
                                   +e ++ gs   +v++l+ Gk+l+++ +
  gi|15668425|ref|NP_247221.1|  22 NEQIVFGSPATVVKCLTCGKVLVEPRG 48 
                                   6899*******************9876 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.9   0.00042      0.44      15      28 ..      16      29 ..      15      38 .. 0.83
   2 ?    1.2   0.1      0.29   3.1e+02      14      21 ..      34      41 ..      26      52 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00042
                         PADR1 15 kCpeCkegqlvfds 28
                                  +CpeC++ q+vf s
  gi|15668425|ref|NP_247221.1| 16 QCPECNNEQIVFGS 29
                                  7**********976 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.29
                         PADR1 14 ekCpeCke 21
                                   kC +C++
  gi|15668425|ref|NP_247221.1| 34 VKCLTCGK 41
                                  58999985 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   2.1     0.018        19       4       9 ..      17      22 ..      16      24 .. 0.97
   2 ?    4.7   0.0     0.026        27       4      20 ..      36      52 ..      34      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.018
                                  ESTTTS CS
                RNA_POL_M_15KD  4 CpkCgN 9 
                                  Cp+C+N
  gi|15668425|ref|NP_247221.1| 17 CPECNN 22
                                  *****9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.026
                                  ESTTTSBEEEEECSCCC CS
                RNA_POL_M_15KD  4 CpkCgNlLlpkedkegk 20
                                  C +Cg  L  +++ +gk
  gi|15668425|ref|NP_247221.1| 36 CLTCGKVLVEPRGGKGK 52
                                  99***999888777765 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.4     0.097     1e+02      19      22 ..      17      20 ..       2      21 .. 0.73
   2 ?    8.6   0.2    0.0017       1.8       1      11 [.      36      46 ..      36      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.097
                       DUF1610 19 CPNC 22
                                  CP+C
  gi|15668425|ref|NP_247221.1| 17 CPEC 20
                                  **** PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0017
                       DUF1610  1 CtSCGaelapr 11
                                  C +CG++l+++
  gi|15668425|ref|NP_247221.1| 36 CLTCGKVLVEP 46
                                  99******975 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.6   4.9e+03       6      12 ..       6      12 ..       6      12 .. 0.84
   2 ?    6.2   5.1    0.0085         9       1      34 [.      13      42 ..      13      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.6
                 zinc_ribbon_5  6 pdCdtkF 12
                                  p+ +tkF
  gi|15668425|ref|NP_247221.1|  6 PQPRTKF 12
                                  7889999 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0085
                 zinc_ribbon_5  1 LiirCpdCdtkFklvdsklKksgkkVrCakCaev 34
                                  L+++Cp+C+    +  s        V+C  C++v
  gi|15668425|ref|NP_247221.1| 13 LRVQCPECNNEQIVFGSP----ATVVKCLTCGKV 42
                                  89******9988777777....677888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.52
# Mc/sec: 361.80
//
Query:       gi|15668426|ref|NP_247222.1|  [L=147]
Description: ferredoxin II [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-05   25.1   6.7    0.00074   20.1   0.1    2.3  2  Fer4_7    4Fe-4S dicluster domain
    4.2e-05   23.4   2.4    4.2e-05   23.4   2.4    2.4  2  Fer4_2    4Fe-4S binding domain
    5.8e-05   22.7   2.7    5.8e-05   22.7   2.7    2.9  3  Fer4      4Fe-4S binding domain
    0.00049   20.1   2.6    0.00049   20.1   2.6    2.2  2  Fer4_6    4Fe-4S binding domain
    0.00085   19.4  14.1     0.0023   18.0  14.2    1.7  2  Fer4_10   4Fe-4S dicluster domain
     0.0044   17.4   3.1     0.0044   17.4   3.1    2.3  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.01   16.0  14.5      0.024   14.8  14.7    1.6  1  Fer4_9    4Fe-4S dicluster domain
      0.018   16.0   2.0      0.018   16.0   2.0    2.6  3  Fer4_16   4Fe-4S double cluster binding domain
       0.02   15.0  15.3      0.069   13.3  15.4    1.8  1  Fer4_21   4Fe-4S dicluster domain
       0.02   15.3   0.1       0.02   15.3   0.1    2.2  2  Fer4_8    4Fe-4S dicluster domain
        0.1   13.2   2.1        0.1   13.2   2.1    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   4.6e-07   0.00074      31      52 .]      78     103 ..      40     103 .. 0.75
   2 !    7.5   2.5    0.0039       6.4       2      21 ..     119     140 ..     106     147 .] 0.72

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.6e-07
                        Fer4_7  31 v....eidpekClgCgaCvavCPtga 52 
                                   +    +id+++C +C++C++ CP g+
  gi|15668426|ref|NP_247222.1|  78 IswypKIDYNRCKNCEKCISFCPRGV 103
                                   24445899***************986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0039
                        Fer4_7   2 Ci.gCgaCvaaCp.vkaielde 21 
                                   Ci +C+aC  +C  ++ai +++
  gi|15668426|ref|NP_247222.1| 119 CIvNCNACSIMCCeNNAIIFPD 140
                                   5558999998875366665554 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   2.4   2.6e-08   4.2e-05       1      21 [.      80     100 ..      80     101 .. 0.95
   2 ?    2.7   5.1     0.098   1.6e+02       7      20 ..     116     130 ..     109     132 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.6e-08
                        Fer4_2   1 apvvvdtdrCigCgaCvsaCP 21 
                                   +++++d +rC +C++C+s CP
  gi|15668426|ref|NP_247222.1|  80 WYPKIDYNRCKNCEKCISFCP 100
                                   789****************** PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.098
                        Fer4_2   7 tdrCi.gCgaCvsaC 20 
                                   + +Ci +C+aC   C
  gi|15668426|ref|NP_247222.1| 116 PYSCIvNCNACSIMC 130
                                   557966*****6546 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   2.7   3.5e-08   5.8e-05       1      22 [.      82     103 ..      82     105 .. 0.92
   2 ?    2.1   2.6      0.12   1.9e+02       9      18 ..     121     130 ..     121     130 .. 0.91
   3 ?   -1.9   0.1       2.1   3.5e+03      18      23 ..     131     136 ..     131     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.5e-08
                                   EEEETTTSSS-THHHHHSTTTE CS
                          Fer4   1 vvideekCigCGaCvevCPvgA 22 
                                   ++id+++C +C +C++ CP g+
  gi|15668426|ref|NP_247222.1|  82 PKIDYNRCKNCEKCISFCPRGV 103
                                   68*****************997 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                                   SS-THHHHHS CS
                          Fer4   9 igCGaCvevC 18 
                                   ++C+aC  +C
  gi|15668426|ref|NP_247222.1| 121 VNCNACSIMC 130
                                   68*****999 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.1
                                   STTTEE CS
                          Fer4  18 CPvgAI 23 
                                   C ++AI
  gi|15668426|ref|NP_247222.1| 131 CENNAI 136
                                   999999 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   2.6     3e-07   0.00049       2      23 ..      82     103 ..      81     106 .. 0.91
   2 ?    2.7   6.6     0.095   1.5e+02       6      24 .]     116     136 ..     110     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3e-07
                        Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                   + id+++C  C++C++ CP g+
  gi|15668426|ref|NP_247222.1|  82 PKIDYNRCKNCEKCISFCPRGV 103
                                   789****************776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.095
                        Fer4_6   6 pdkCi.gCgdCvrvCPe.gai 24 
                                   p +Ci  C++C + C e +ai
  gi|15668426|ref|NP_247222.1| 116 PYSCIvNCNACSIMCCEnNAI 136
                                   668*879****8777763565 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0  14.2   1.4e-06    0.0023       3      55 ..      83     130 ..      81     131 .. 0.88
   2 ?    3.0   4.2     0.068   1.1e+02       6      19 ..     116     130 ..     111     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg.cgaCveaC 55 
                                   +id ++C +C+kC ++CP       + + a+++++v k +++C+  c aC   C
  gi|15668426|ref|NP_247222.1|  83 KIDYNRCKNCEKCISFCPR------GVYDAENGKVVVKYPYSCIVnCNACSIMC 130
                                   799****************......77778888888888****965****9888 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.068
                       Fer4_10   6 ddtCi.rCgkCvkaC 19 
                                   + +Ci +C++C  +C
  gi|15668426|ref|NP_247222.1| 116 PYSCIvNCNACSIMC 130
                                   5679669******99 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   3.1   2.7e-06    0.0044       1      16 [.      86     101 ..      86     106 .. 0.91
   2 ?   -2.3   6.2       5.8   9.4e+03       3      14 ..     118     130 ..     116     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.7e-06
                        Fer4_4   1 qerCigCgsCvaaCPq 16 
                                   ++rC +C +C+++CP 
  gi|15668426|ref|NP_247222.1|  86 YNRCKNCEKCISFCPR 101
                                   58*************6 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.8
                        Fer4_4   3 rCi.gCgsCvaaC 14 
                                   +Ci +C +C + C
  gi|15668426|ref|NP_247222.1| 118 SCIvNCNACSIMC 130
                                   6855999997766 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8  14.7   1.5e-05     0.024       1      48 [.      88     132 ..      88     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaC.igCgaCveaCpk 48 
                                   +C +C +C++ Cp gv+  ++++  +++      +C + C+aC   C +
  gi|15668426|ref|NP_247222.1|  88 RCKNCEKCISFCPRGVYDAENGKVVVKYPY----SCiVNCNACSIMCCE 132
                                   5**********************9999966....6*889****977754 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   2.0   1.1e-05     0.018       1      21 [.      88     108 ..      88     118 .. 0.83
   2 ?   -2.0   6.5       4.4   7.1e+03      53      65 ..     119     131 ..     110     133 .. 0.71
   3 ?   -1.0   6.4       2.2   3.6e+03       4      20 ..     122     139 ..     118     146 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                       Fer4_16   1 rCgtCgkCaevCPtnaikekk 21 
                                   rC++C+kC++ CP ++ ++++
  gi|15668426|ref|NP_247222.1|  88 RCKNCEKCISFCPRGVYDAEN 108
                                   6*************9987774 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.4
                       Fer4_16  53 aitgCdiCqdvCP 65 
                                    i  C++C  +C 
  gi|15668426|ref|NP_247222.1| 119 CIVNCNACSIMCC 131
                                   4578888888885 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.2
                       Fer4_16   4 tCgkCaevCPt.naikek 20 
                                   +C++C  +C + nai  +
  gi|15668426|ref|NP_247222.1| 122 NCNACSIMCCEnNAIIFP 139
                                   588885555442666655 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  15.4   4.2e-05     0.069       2      57 ..      83     136 ..      82     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.2e-05
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                   +id ++C +C+kC+  C+ + ++a ++  k v+k+  +  v Cn Cs++C  +++i
  gi|15668426|ref|NP_247222.1|  83 KIDYNRCKNCEKCISFCPRGVYDAENG--KVVVKYPYSCIVNCNACSIMCCENNAI 136
                                   699***************999998654..4444454555589********877766 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   1.2e-05      0.02      44      65 .]      70     103 ..      26     103 .. 0.70
   2 ?    1.6   3.8      0.24     4e+02      48      63 ..     116     132 ..     105     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                        Fer4_8  44 e............eealwsCttcgaCtevCpvgi 65 
                                   e            +   ++C +c++C + Cp g+
  gi|15668426|ref|NP_247222.1|  70 EygkkrkdiswypKIDYNRCKNCEKCISFCPRGV 103
                                   12223333444457889**************986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.24
                        Fer4_8  48 lwsC.ttcgaCtevCpv 63 
                                    +sC ++c+aC+  C +
  gi|15668426|ref|NP_247222.1| 116 PYSCiVNCNACSIMCCE 132
                                   56776678888888865 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.1   6.2e-05       0.1       1      31 [.      84     113 ..      84     118 .. 0.76
   2 ?   -3.2   6.3       8.3   1.3e+04       6      18 ..     119     132 ..     116     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.2e-05
                       Fer4_13   1 VDrdtCiacgaCvelaPd.vFeeddeggasvv 31 
                                   +D ++C +c++C +++P  v++ ++  g++vv
  gi|15668426|ref|NP_247222.1|  84 IDYNRCKNCEKCISFCPRgVYDAEN--GKVVV 113
                                   7999*************83555443..56555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.3
                       Fer4_13   6 Ci.acgaCvelaPd 18 
                                   Ci +c+aC  ++ +
  gi|15668426|ref|NP_247222.1| 119 CIvNCNACSIMCCE 132
                                   5448*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1371  (0.0764683); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 881.37
//
Query:       gi|15668427|ref|NP_247223.1|  [L=234]
Description: hypothetical protein MJ_0252 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      6e-45  153.6   2.1    6.9e-45  153.4   2.1    1.0  1  OMPdecase    Orotidine 5'-phosphate decarboxylase / HUMPS fam
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.032   14.2   0.0    1.6  1  Lipocalin_7  Lipocalin / cytosolic fatty-acid binding protein
      0.034   13.8   0.3      0.085   12.5   0.3    1.7  1  SSXT         SSXT protein (N-terminal region)
      0.036   14.2   1.2      0.094   12.8   0.7    2.0  2  DUF2325      Uncharacterized protein conserved in bacteria (D
      0.082   12.3   6.3        1.4    8.3   0.2    3.1  3  PcrB         PcrB family
        1.1   10.0   8.1       0.77   10.5   0.4    2.5  2  PTS_IIB      PTS system, Lactose/Cellobiose specific IIB subu


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.4   2.1   2.3e-48   6.9e-45       2     225 .]      24     228 ..      23     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 153.4 bits;  conditional E-value: 2.3e-48
                                   EEEEEE-SSSHHHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT.SEEEEEEEE-S-HHHHHHHHHSTCH CS
                     OMPdecase   2 nLclalDvatarelleladkvgpsivvlKthydlvegwgfegtgaklaalarkhg.flifeDrKfaDIGntvekqatagsa 81 
                                   +L+lalDv +++++l+++++v+++++ +K++y+lv + g      +++++++k   +++++D+K+aDI++t ek+a+    
  gi|15668427|ref|NP_247223.1|  24 KLMLALDVLDRDRALKIVEDVKDYVDAIKVGYPLVLSTG-----TEIIKEIKKLCnKEVIADFKVADIPATNEKIAK---- 95 
                                   89*************************************.....*********988********************8.... PP

                                   HHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCCHTH CS
                     OMPdecase  82 rikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqetln 162
                                      + ad ++vh+++G++svka+ ++a+k + ++++++++ms++g+ ++ +      ++++++e++++ +v+ +va +t++
  gi|15668427|ref|NP_247223.1|  96 ITLKYADGIIVHGFVGEDSVKAVQDVAKKLN-KKVIMVTEMSHPGAVQFLQ-----PIADKLSEMAKKLKVDAIVAPSTRP 170
                                   467789************************6.9*************99999.....88888888888888*********** PP

                                   .HHHHH..TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHHH CS
                     OMPdecase 163 .ateed..addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaery 225
                                    +++e+    +++++tpg+g+ qgg+ +++ +     + +  + d++ivGR+I+++++p+eea++y
  gi|15668427|ref|NP_247223.1| 171 eRLKEIkeIAELPVITPGVGA-QGGKIEDILN-----ILD--ENDYVIVGRAIYQSQNPKEEAKKY 228
                                   9444445558**********9.9998888884.....344..37********************98 PP

>> Lipocalin_7  Lipocalin / cytosolic fatty-acid binding protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.1e-05     0.032      11      57 ..      14      62 ..       3     133 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                  EEESHHHHHHHHT--HHHHHHHHTS-EEEEEEE..ETTEEEEEEEETTT CS
                   Lipocalin_7 11 seknydefmkrlglpsdviekarnlkiitevkq..dgqnftwsqsysgg 57
                                    kn  + m +l l+ dv+++ r lki+ +vk+  d  +  +    s g
  gi|15668427|ref|NP_247223.1| 14 NAKNCGDRMPKLMLALDVLDRDRALKIVEDVKDyvDAIKVGYPLVLSTG 62
                                  56999999***********************972244444455555554 PP

>> SSXT  SSXT protein (N-terminal region)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   2.9e-05     0.085       7      44 ..     197     234 .]     195     234 .] 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                          SSXT   7 eqIqklLDENsqLIqtIielqnkGraeecdqyqqiLhr 44 
                                   e I ++LDEN+  I+    +q++   ee+++y+++L++
  gi|15668427|ref|NP_247223.1| 197 EDILNILDENDYVIVGRAIYQSQNPKEEAKKYKEMLNK 234
                                   56889*********99999999999***********97 PP

>> DUF2325  Uncharacterized protein conserved in bacteria (DUF2325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   3.2e-05     0.094      11      83 ..      65     136 ..      57     147 .. 0.84
   2 ?   -1.5   0.0      0.92   2.7e+03      15      32 ..     151     168 ..     144     180 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                       DUF2325  11 meeqyrklleklgg.klkvfdgrkekkkkkleskigkaDlvvlftdtvsHkavkkvkkeakkkgkpvvrlhsss 83 
                                   + ++++kl++k  + ++kv d   + ++k  +  ++ aD +++  ++v  ++vk v++ akk +k+v+++   s
  gi|15668427|ref|NP_247223.1|  65 IIKEIKKLCNKEVIaDFKVADIPAT-NEKIAKITLKYADGIIV-HGFVGEDSVKAVQDVAKKLNKKVIMVTEMS 136
                                   67899****999999******9999.44466667788998775.79***********************97655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.92
                       DUF2325  15 yrklleklggklkvfdgr 32 
                                   ++++++kl+++++v    
  gi|15668427|ref|NP_247223.1| 151 LSEMAKKLKVDAIVAPST 168
                                   445555555555554444 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.025        74      17      55 ..      35      73 ..      24      86 .. 0.75
   2 ?    8.3   0.2   0.00046       1.4      19      76 ..      89     149 ..      81     187 .. 0.67
   3 ?    4.1   0.1    0.0094        28     191     216 ..     195     223 ..     162     233 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.025
                                  S-CHHHHHHHHCTT-SEEEEECST.CHHHHHHHHHHHHHC CS
                          PcrB 17 enpdEiveiviesgtDavmigGsq.svtldntvrllkkvs 55
                                  +    ive v +++ Da+ +g     +t  ++++ +kk  
  gi|15668427|ref|NP_247223.1| 35 DRALKIVEDV-KDYVDAIKVGYPLvLSTGTEIIKEIKKLC 73
                                  3444556666.9********98877888888888888874 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00046
                                   CHHHHHHHHCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEE...ESSGGG--TTSS CS
                          PcrB  19 pdEiveiviesgtDavmigGsqsvtldntvrllkkvsriklPivle...psnvegvvryaD 76 
                                   ++E +  ++ +++D++++ G  + +  ++v+ + k  + k+ +v e   p++v+ + + aD
  gi|15668427|ref|NP_247223.1|  89 TNEKIAKITLKYADGIIVHGFVGEDSVKAVQDVAKKLNKKVIMVTEmshPGAVQFLQPIAD 149
                                   67777777799******99987555555555554444555555555001555555555555 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0094
                                   SHHHHHHHHCCSSEEEE-CHHHHHH...H CS
                          PcrB 191 saEkAkevveaADvivvGnvveekd...e 216
                                   + E+  +++   D ++vG ++++++   e
  gi|15668427|ref|NP_247223.1| 195 KIEDILNILDENDYVIVGRAIYQSQnpkE 223
                                   557888889999**********9984431 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   2.0     0.072   2.2e+02      18      77 ..      67     134 ..      56     145 .. 0.59
   2 ?   10.5   0.4   0.00026      0.77      17      86 ..     148     223 ..     146     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.072
                                   HHHHHHHHHCTEEEEETTEE....GGGHHHHHHT-SEEEEEESSGG...CTHHHHTTS.EEEEECTTH CS
                       PTS_IIB  18 eklekaakelgieaegeagv....eleaeeiaddaDlvllapqvrv...kdlarfagk.pvavinikd 77 
                                   + ++k ++++ i    +a +    e+ a+   + aD ++++  v     k +++ a+k + +vi +++
  gi|15668427|ref|NP_247223.1|  67 KEIKKLCNKEVIADFKVADIpatnEKIAKITLKYADGIIVHGFVGEdsvKAVQDVAKKlNKKVIMVTE 134
                                   67788888887444444444344566677777889999999966653332222222222344555555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00026
                                   HHHHHHHHHHCTEEEEETTEE.GGGHHHHHHT-SEEEEEESSGG.....CTHHHHTTSEEEEECTTHHHCCHCHHH CS
                       PTS_IIB  17 aeklekaakelgieaegeagv.eleaeeiaddaDlvllapqvrv.....kdlarfagkpvavinikdalgimdgek 86 
                                   a+kl ++ak+l ++a+++ ++ +   +ei++ a l +++p v       +d+ +  + + +vi  ++++  +++++
  gi|15668427|ref|NP_247223.1| 148 ADKLSEMAKKLKVDAIVAPSTrPERLKEIKEIAELPVITPGVGAqggkiEDILNILDENDYVIVGRAIYQSQNPKE 223
                                   69********************9999999999********999766333333333335678888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1448.33
//
Query:       gi|15668428|ref|NP_247224.1|  [L=154]
Description: coenzyme F420-reducing hydrogenase subunit delta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-39  133.2   1.0    5.6e-39  132.9   1.0    1.1  1  HycI      Hydrogenase maturation protease


Domain annotation for each model (and alignments):
>> HycI  Hydrogenase maturation protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   1.0   3.1e-43   5.6e-39       1     129 [.      23     150 ..      23     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 3.1e-43
                                   HHHHHHHHHHEC--TTEEEEEECT-SGGGHHHHCC..-SEEEEEEE--SSS-TT-EEEEECCHHHHHHTTC.CGCCCHCHH CS
                          HycI   1 vrvvekLkrryefkenvtviDgGtqglelvgtlee..adkliivDavdfglepGevkiikddevpkklkakkmsaHqlpla 79 
                                   ++vv+kL++ ++ ++nv+viD+G++g ++++tl +  ++k+i+vDa+df+lepG++k+i++de+p+++k++ ++aH++pla
  gi|15668428|ref|NP_247224.1|  23 CEVVSKLEK-MNLPDNVEVIDAGASGAYYLMTLVDedIKKIIVVDAIDFDLEPGTIKKIDVDELPNIKKYS-FDAHNVPLA 101
                                   589******.788889***************999989****************************988888.********* PP

                                   HHHHHHHHCCS--SEEEEEEE--S-BST.CCS--HHHHCCHHHHHHHCCC CS
                          HycI  80 evlklleekgeipkevillgvqpesledvgielseevkkavekavelile 129
                                   ++lk l++kg i+++vi+++ ++++++d++ +lseev+kav+ka+e+il 
  gi|15668428|ref|NP_247224.1| 102 PFLKDLHNKG-IEVVVIGCQGKEFTMPDIKPGLSEEVAKAVDKAIEIILG 150
                                   *********6.9************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 999.28
//
Query:       gi|15668429|ref|NP_247225.1|  [L=212]
Description: DNA repair and recombination protein RadB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.3e-26   90.8   0.8    1.1e-25   90.3   0.8    1.2  1  Rad51         Rad51
    5.5e-09   35.9   0.6    6.9e-09   35.6   0.6    1.1  1  RecA          recA bacterial DNA recombination protein
    1.9e-07   31.0   0.3    3.4e-07   30.2   0.3    1.5  1  AAA_24        AAA domain
    1.3e-06   27.9   4.0    3.7e-05   23.2   4.0    2.5  1  ATPase        KaiC
    3.5e-05   23.5   0.0    4.6e-05   23.2   0.0    1.2  1  Zot           Zonular occludens toxin (Zot)
    0.00039   20.0   0.0     0.0075   15.9   0.0    2.5  1  AAA_25        AAA domain
     0.0036   17.7   4.1      0.018   15.5   4.1    2.0  1  AAA           ATPase family associated with various cellular 
     0.0081   16.1   3.4      0.015   15.2   3.4    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.011   15.3   0.1      0.019   14.5   0.1    1.3  1  CobU          Cobinamide kinase / cobinamide phosphate guanyl
      0.013   16.0   0.2      0.043   14.4   0.2    2.0  1  AAA_18        AAA domain
      0.058   12.7   0.0      0.069   12.5   0.0    1.2  1  CN_hydrolase  Carbon-nitrogen hydrolase
      0.093   12.5   0.1       0.22   11.2   0.1    1.8  1  IstB_IS21     IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.8   7.6e-29   1.1e-25      26     252 ..       2     208 ..       1     210 [. 0.79

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 7.6e-29
                                   HHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHH.HHTT--HHHHGGG CS
                         Rad51  26 lDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveia.erykldkeevlen 105
                                   l e+L G  e g it i+G  + Gkt +c   ++ +          gk++yidteg++  er+ +ia + y    + vlen
  gi|15668429|ref|NP_247225.1|   2 LKEILLGNAEKGIITQIYGPPGVGKTNICIINSINA-------VNSGKVIYIDTEGGLSIERIKQIAsNNY----KIVLEN 71 
                                   6789**********************9986555543.......35689*******************5555....569999 PP

                                   EEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHH.HHHHHHHHHHHHHHHHHH--EEEEEEE CS
                         Rad51 106 vayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakR.qqklgkllrtLrkladefevavvitnq 185
                                   + +  a+   +q +++q+    l  ++ +l++vD +t+lyR + s+  + +   ++ lg+ ++tL kla+  ++av+itnq
  gi|15668429|ref|NP_247225.1|  72 MIIYNAFDFYEQDKIIQKELP-LITNNASLIVVDNITSLYRLELSDEANKNIMlNKMLGNQVKTLLKLAKTNNLAVIITNQ 151
                                   99999***********96544.4566789*****************9887765156699********************** PP

                                   -------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EEEEEEETTEE CS
                         Rad51 186 vvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpeleavfaigeeGi 252
                                   v ++v+g    f+a     +gG++l   s+  + l k +g+ R++ + +  +  e+ ++f i e+Gi
  gi|15668429|ref|NP_247225.1| 152 VRETVNG----FEA-----SGGRLLEYWSKCIVRLEKLNGD-RLAILEKHLHAGEERVKFRIVERGI 208
                                   ****999....443.....5666666666666666666553.5555555566666666666666665 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.6   4.6e-12   6.9e-09      47     219 ..       7     179 ..       3     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 4.6e-12
                                   SSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHTT.....--GGG-EEE-.-SSHHHHHH CS
                          RecA  47 iGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakklG.....vdidellvsq.pdtGeqale 121
                                   +G   kG i++iyGp   Gkt +++    +a  ++g + +id+e  l  +  k++      + ++++++ +  d  eq   
  gi|15668429|ref|NP_247225.1|   7 LGNAEKGIITQIYGPPGVGKTNICIINSINAV-NSGKVIYIDTEGGLSIERIKQIAsnnykIVLENMIIYNaFDFYEQDKI 86 
                                   577889****************9976665555.456789******999877666541111166889888652699999998 PP

                                   HHHHH.HTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT--EEEEEEE------------- CS
                          RecA 122 iadal.vrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksntvvifinqirekiGvmfgnpe 201
                                   i + l + ++   livvd +++l  + e+  e +++ +    +++ + ++ l    + +n +vi  nq+re +        
  gi|15668429|ref|NP_247225.1|  87 IQKELpLITNNASLIVVDNITSLY-RLELSDEANKNIM--LNKMLGNQVKTLLKLAKTNNLAVIITNQVRETVN-----GF 159
                                   8887644567789********996.8899888665544..457899999999999999999**********984.....44 PP

                                   ----HHHHHHH-S..EEEEE CS
                          RecA 202 tttGGralkfyas..vrldv 219
                                    ++GGr l +++   vrl+ 
  gi|15668429|ref|NP_247225.1| 160 EASGGRLLEYWSKciVRLEK 179
                                   56899999999873355554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.3   2.3e-10   3.4e-07       5      82 ..      16     114 ..      12     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.3e-10
                        AAA_24   5 iliyGpsgiGKTtlakel......gpkplfidtekGlksldadkfpdieswedfldevvel................aael 63 
                                    +iyGp+g+GKT ++  +        k+++idte+Gl s++ +k    ++++ +l+ +                   +   
  gi|15668429|ref|NP_247225.1|  16 TQIYGPPGVGKTNICIINsinavnSGKVIYIDTEGGL-SIERIKQIASNNYKIVLENMIIYnafdfyeqdkiiqkelPLIT 95 
                                   68***********998888899*************99.6666554444466666655555556667788899999997777 PP

                        AAA_24  64 adyktlviDtideleelcl 82 
                                   ++ + +v+D+i+ l++l l
  gi|15668429|ref|NP_247225.1|  96 NNASLIVVDNITSLYRLEL 114
                                   7789**********99644 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   4.0   2.5e-08   3.7e-05      10     193 ..       4     182 ..       1     212 [] 0.71

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.5e-08
                        ATPase  10 eilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidase 90 
                                   eil g   +g ++ i+G pG GKt ++    i+ +++   +++++ +e      +e++k++  +  k+  e +++i +a+ 
  gi|15668429|ref|NP_247225.1|   4 EILLGNAEKGIITQIYGPPGVGKTNICIINSINAVNS--GKVIYIDTEGGL--SIERIKQIASNNYKIVLE-NMIIYNAFD 79 
                                   677777888999***************9999999777..689999888765..478999999999999988.567778887 PP

                        ATPase  91 saeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeek.........eavaReilrqlvrvlkklgvTailv 161
                                     e+          + + +el  +    +a+ +v+D+it+l   e +         ++++ +++++l++  k +++  i++
  gi|15668429|ref|NP_247225.1|  80 FYEQ------D---KIIQKELPLIT--NNASLIVVDNITSLyRLELSdeanknimlNKMLGNQVKTLLKLAKTNNLAVIIT 149
                                   7655......2...23444555443..47899999999999544333111112222457888999999999********** PP

                        ATPase 162 sekss..seeaaggygveefivdgvivLdlkeie 193
                                   +++++  +  +a+g ++ e+ ++++++L++ ++ 
  gi|15668429|ref|NP_247225.1| 150 NQVREtvNGFEASGGRLLEYWSKCIVRLEK-LNG 182
                                   ****96655567788899**********94.333 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   3.1e-08   4.6e-05       5     124 ..      18     149 ..      14     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.1e-08
                           Zot   5 vtGapGsgKtsgavkkdllpalkegRkiitnid.Glrlerieqvlgekvs..tarliridnpegaetlkefakwat..idk 80 
                                    +G+pG gKt   + + + +a+ +g++i+ + + Gl +eri+q+  ++ +   +++i  +  ++ e+ k ++k  +  +++
  gi|15668429|ref|NP_247225.1|  18 IYGPPGVGKTNICIINSI-NAVNSGKVIYIDTEgGLSIERIKQIASNNYKivLENMIIYNAFDFYEQDKIIQKELPliTNN 97 
                                   58************9976.6999*******8884699******99999888767777666666666666555555542348 PP

                           Zot  81 gallviDEcqeifpvrakegrkd........pevinaftehRhlgwDivllt 124
                                    +l+v+D    ++  +   ++++         + ++ + ++ + +  +v++t
  gi|15668429|ref|NP_247225.1|  98 ASLIVVDNITSLYRLELSDEANKnimlnkmlGNQVKTLLKLAKTNNLAVIIT 149
                                   99************99997555566666665444444444444444444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     5e-06    0.0075      31     190 ..      11     153 ..       2     156 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5e-06
                        AAA_25  31 pagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagv 111
                                    +g ++ ++G+pg+GKt +++  ++  +             gkV+y+++E++     +R++++  ++       ++     
  gi|15668429|ref|NP_247225.1|  11 EKGIITQIYGPPGVGKTNICIINSINAV-----------NSGKVIYIDTEGGL--SIERIKQIASNN-----YKIVL---- 69 
                                   67889999*********99998888877...........4689*********9..667888877765.....33332.... PP

                        AAA_25 112 eslpLfakdrggtlltadvdaleaaieev.egvrlvviDplsralgg..densnsd.....v.galvealeriarrtgaav 183
                                    +++++++ ++    +     +++++  + +++ l+v+D+++++++   + ++n+      + g  v+ l ++a+  + av
  gi|15668429|ref|NP_247225.1|  70 -ENMIIYNAFDFYEQDKI---IQKELPLItNNASLIVVDNITSLYRLelSDEANKNimlnkMlGNQVKTLLKLAKTNNLAV 146
                                   .13344444333332222...333333331359**************7755555556665545777777888888888999 PP

                        AAA_25 184 llvhHvg 190
                                   +++ +v+
  gi|15668429|ref|NP_247225.1| 147 IITNQVR 153
                                   8887775 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   4.1   1.2e-05     0.018       3     111 ..      18     151 ..      16     166 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                                   EESSTTSSHHHHHHHHHHHH....THE............EEEEETTTCSSS......................STTHHHHH CS
                           AAA   3 lyGppGtGKTllakavakel....gve............fleisgsellsk......................yvgesekk 45 
                                   +yGppG+GKT ++   ++++    + +                                               + e+ k 
  gi|15668429|ref|NP_247225.1|  18 IYGPPGVGKTNICI--INSInavnSGKviyidtegglsiE----------RikqiasnnykivlenmiiynafDFYEQDKI 86 
                                   79*********994..444411331222222333333330..........2333444444444444555554444477777 PP

                                   HHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS......SSTEEEEEEESS CS
                           AAA  46 irelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk......eskvivigatnr 111
                                   i++ +  + ++a  s +++D+i +l + +      ++e   n +l+++ g + k      + + + +++tn+
  gi|15668429|ref|NP_247225.1|  87 IQKELPLITNNA--SLIVVDNITSLYRLE-----LSDEANKNIMLNKMLGNQVKtllklaKTNNLAVIITNQ 151
                                   888787777777..***********9999.....55566678888888888776444445333344455555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   3.4     1e-05     0.015      18      96 ..      11     137 ..       2     159 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1e-05
                      ATPase_2  18 epneiyfiYGpegsGKtaL.lkeiienledkdkyviyyialreesiskldefieeeeekkklekal............... 82 
                                   e+  i  iYGp g+GKt + + ++i+  ++   +viy++   + si+++++  + ++ k  le+++               
  gi|15668429|ref|NP_247225.1|  11 EKGIITQIYGPPGVGKTNIcIINSINAVNS--GKVIYIDTEGGLSIERIKQI-ASNNYKIVLENMIiynafdfyeqdkiiq 88 
                                   5677899**********9735666666633..479***************97.5444445566666666666666555555 PP

                      ATPase_2  83 ...................................giavpkaeleeilk 96 
                                                                      ++++  ++++++lk
  gi|15668429|ref|NP_247225.1|  89 kelplitnnaslivvdnitslyrlelsdeanknimLNKMLGNQVKTLLK 137
                                   5556666666666655555555555555555555555555555555555 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.3e-05     0.019      54     146 ..      78     172 ..      74     187 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                          CobU  54 Wetveepldlaealkeeek.kevvLvDcltlwltnllleeeaek..veekleeeveellealkelkatvvlVsnEvglgvv 131
                                   ++ +e+ + +++ l   ++ ++ ++vD +t +    l +e +++   ++ l ++v++ll+ +k+ ++  v+++n v  +v 
  gi|15668429|ref|NP_247225.1|  78 FDFYEQDKIIQKELPLITNnASLIVVDNITSLYRLELSDEANKNimLNKMLGNQVKTLLKLAKT-NNLAVIITNQVRETVN 157
                                   6778888888888877555589***************997766686677777777777776655.6677889**9998888 PP

                          CobU 132 penalgrlfrdllGr 146
                                     +a+g +  +  ++
  gi|15668429|ref|NP_247225.1| 158 GFEASGGRLLEYWSK 172
                                   777777776666555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   2.9e-05     0.043       3      93 ..      18     117 ..      17     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                        AAA_18   3 ltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenss........alee 73 
                                   + G+pGvGKt ++    + +++ + +++ + +e+gl++e+ ++ a +++k++ e++  ++   + e+++           +
  gi|15668429|ref|NP_247225.1|  18 IYGPPGVGKTNICIIN-SINAVnSGKVIYIDTEGGLSIERIKQiASNNYKIVLENMIIYNAFDFYEQDKiiqkelplITNN 97 
                                   78***********544.4333358889999999999999999999999999988888887777777666777888875566 PP

                        AAA_18  74 gknlvidghlaeleseaakd 93 
                                   ++ +v+d + + ++ e   +
  gi|15668429|ref|NP_247225.1|  98 ASLIVVDNITSLYRLELSDE 117
                                   66667777766666555544 PP

>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.6e-05     0.069      51     106 ..     113     180 ..      75     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.6e-05
                                   HHHHHHB......HSSSHHHHHHHHHHHHHTEEEEEEEEEEEC......CTTEEEEEEEEEEEETTSE CS
                  CN_hydrolase  51 hfleaAe......aglgetlallaalarkngiavviglierel......tngklqayntavlldldgk 106
                                   +  + A       ++lg+ ++ l +la++n+ av+i+   re+       +g+l +y++ +++ l++ 
  gi|15668429|ref|NP_247225.1| 113 ELSDEANknimlnKMLGNQVKTLLKLAKTNNLAVIITNQVRETvngfeaSGGRLLEYWSKCIVRLEKL 180
                                   4445555666677899*********************666666678888***********99987665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00015      0.22      52      82 ..      18      47 ..       9     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                     IstB_IS21 52 llGpsGvGKshlaialgveavraglsvlfvr 82
                                  + Gp+GvGK+ + i  + +av++g+ v+++ 
  gi|15668429|ref|NP_247225.1| 18 IYGPPGVGKTNICIINSINAVNSGK-VIYID 47
                                  89*******************9996.55554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 1503.16
//
Query:       gi|15668430|ref|NP_247226.1|  [L=251]
Description: hypothetical protein MJ_0255 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-92  307.6   0.1    6.8e-92  307.3   0.1    1.0  1  ComA             (2R)-phospho-3-sulfolactate synthase (ComA)
  ------ inclusion threshold ------
       0.05   12.9   0.1       0.32   10.2   0.0    2.0  2  Glyco_hydro_97   Glycoside hydrolase 97
       0.13   12.4   0.0       0.23   11.6   0.0    1.3  1  Isochorismatase  Isochorismatase family
       0.22   11.7   0.4       0.51   10.5   0.4    1.6  1  VGCC_beta4Aa_N   Voltage gated calcium channel subunit beta d


Domain annotation for each model (and alignments):
>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.3   0.1   1.5e-95   6.8e-92       9     243 .]      12     246 ..       8     246 .. 0.99

  Alignments for each domain:
  == domain 1  score: 307.3 bits;  conditional E-value: 1.5e-95
                                   SSS-EEEEESS--HHHHHHHHHHHGGG-SEEEE-TTGGGGSTCHHHHHHHHHHHCTT-EEEE-HHHHHHHHHTT-HHHHHH CS
                          ComA   9 ktGlTeviDkGlglreledlletageyiDglKlgggtsallpeeilrekielahehgvyvstGgtlfEaalaqgkvdeyle 89 
                                   ++GlT+v+DkGl+++ +ed+l+++g+yiD++K+g+gtsa++++++++eki+++++ g++v++GgtlfE+a+++gk+de+l+
  gi|15668430|ref|NP_247226.1|  12 QRGLTVVLDKGLPPKFVEDYLKVCGDYIDFVKFGWGTSAVIDRDVVKEKINYYKDWGIKVYPGGTLFEYAYSKGKFDEFLN 92 
                                   68******************************************************************************* PP

                                   HHHHCT-SEEEE--SSS---HHHHHHHHHHHCCTTSEEEEEES-SSHHHHTT--CCHHHHHHHHHHHHTECEEEE--TTT- CS
                          ComA  90 eckelgfdviEvsdgtlelpeeeklrliekakkeglkvlpevgkkdgelesesdveklieeakrdleaGaekviiEaresG 170
                                   ec++lgf+++E+sdg+ +++ ee++++i++ak++g+ vl+evgkk +++++++++++ i+ ++ dl+aGa++viiE+resG
  gi|15668430|ref|NP_247226.1|  93 ECEKLGFEAVEISDGSSDISLEERKNAIKRAKDNGFMVLTEVGKKMPDKDKQLTIDDRIKLINFDLDAGADYVIIEGRESG 173
                                   ********************************************************************************* PP

                                   -SSTTB-TTS-B-HHHHHHHHTTS-GGGEEEE--SHHHHHHHHHHH-TT--EEEEEGGGHHHHHHHHCT-SGG CS
                          ComA 171 itegvydekgevrtdvvekiierlgleklifEApekkqqewfikefGpnVnLgnvdpsevlaLealRlglrgd 243
                                   +++g++d++g+v++++++ ++++++++k+ifEAp+k+qq++fi +fG++VnL+n++ +ev++Le+lR+glrgd
  gi|15668430|ref|NP_247226.1| 174 KGIGLFDKEGKVKENELDVLAKNVDINKVIFEAPQKSQQVAFILKFGSSVNLANIAFDEVISLETLRRGLRGD 246
                                   ************************************************************************8 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.064   2.9e+02     111     129 ..      52      71 ..      43     132 .. 0.68
   2 ?   10.2   0.0   7.1e-05      0.32      24     111 ..     137     228 ..     116     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.064
                Glyco_hydro_97 111 lekq.ldkafklyeklGvkg 129
                                   ++++ +++ +++y+++G+k 
  gi|15668430|ref|NP_247226.1|  52 IDRDvVKEKINYYKDWGIKV 71 
                                   55663477788888888774 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 7.1e-05
                Glyco_hydro_97  24 lkedfkhgantetvkryiDfAaengleyvlvegwdegWee....kkkkekefdftkpypdfdleelvaYakekgvgvelwl 100
                                   + +d+++  + ++  + i+f  + g +yv++eg + g       k+ k ke+++    +++d+++++  a +k  +v ++l
  gi|15668430|ref|NP_247226.1| 137 KMPDKDKQLTIDDRIKLINFDLDAGADYVIIEGRESGKGIglfdKEGKVKENELDVLAKNVDINKVIFEAPQKSQQVAFIL 217
                                   556778889999999******************999986677766667778888888999*****************9999 PP

                Glyco_hydro_97 101 hsetsgnvanl 111
                                   +   s n+an+
  gi|15668430|ref|NP_247226.1| 218 KFGSSVNLANI 228
                                   99887777764 PP

>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.2e-05      0.23     136     172 ..      96     132 ..      90     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.2e-05
               Isochorismatase 136 dlGyevvvvsDAvaalspelhdaalkrlkqafatvit 172
                                   +lG+e v +sD+ +++s e++++a+kr+k+++  v+t
  gi|15668430|ref|NP_247226.1|  96 KLGFEAVEISDGSSDISLEERKNAIKRAKDNGFMVLT 132
                                   68***************************99988876 PP

>> VGCC_beta4Aa_N  Voltage gated calcium channel subunit beta domain 4Aa N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00011      0.51       8      26 ..     105     123 ..     103     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                VGCC_beta4Aa_N   8 SrpsSdlsleedrEalRre 26 
                                   S  sSd+slee + a+ r 
  gi|15668430|ref|NP_247226.1| 105 SDGSSDISLEERKNAIKRA 123
                                   6779************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1623.89
//
Query:       gi|15668431|ref|NP_247229.1|  [L=311]
Description: tRNA-modifying protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-21   76.7   1.0    2.2e-20   73.7   0.3    2.6  2  Radical_SAM   Radical SAM superfamily
    9.2e-20   70.8   0.0    3.5e-19   68.9   0.0    2.0  2  Wyosine_form  Wyosine base formation
  ------ inclusion threshold ------
       0.17   12.3   0.0       0.69   10.3   0.0    1.9  2  HAD           haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.3   3.6e-24   2.2e-20       5     163 ..      60     235 ..      56     239 .. 0.80
   2 ?   -0.6   0.0      0.25   1.5e+03      20      42 ..     259     281 ..     250     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 3.6e-24
                                   SEESS--TTTSCCTT......HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE.......................... CS
                                   xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                   Radical_SAM   5 rgCnlrCsfCarpet......vrregrgrslsveeileevkelkaekgvkevilg.......................... 53 
                                    +C ++C+fC+r          ++ + ++   +e + e++ +++     k +i+g                          
  gi|15668431|ref|NP_247229.1|  60 IWCQQNCIFCWRVLPrdigidISQIKEPKWEEPEVVYEKILAMH-----KRIIMGyagvldrvgekkfkealepkhvaisl 135
                                   58***********999*****66666666666666666666664.....33333334455555555555555555555555 PP

                                   SSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                   Radical_SAM  54 ggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlea 133
                                   +gep+lyp + el++  +k+   g++++v++ng+l      + + + ++++++++l+a+d + ++++++ +++ +e +l++
  gi|15668431|ref|NP_247229.1| 136 SGEPTLYPYLDELIKIFHKN---GFTTFVVSNGILT-----DVIEKIEPTQLYISLDAYDLDSYRRICGgKKEYWESILNT 208
                                   *******************8...************8.....77777777******************************** PP

                                   HHHHHHTTSETEEEEEEEBTTTSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 134 leklreagikrvvdrivglpGendeeleel 163
                                   l++l+e+  + +++r+++++G+nd+ + ++
  gi|15668431|ref|NP_247229.1| 209 LDILKEK-KR-TCIRTTLIRGYNDD-ILKF 235
                                   *******.77.9************8.5555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.25
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  20 vrregrgrslsveeileevkelk 42 
                                   ++r +++ +l+ +eil+++k l 
  gi|15668431|ref|NP_247229.1| 259 QKRLKKEDMLQHDEILKLAKMLD 281
                                   567788999999****9999885 PP

>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.1   6.7e+03      10      26 ..      21      38 ..      21      40 .. 0.76
   2 !   68.9   0.0   5.8e-23   3.5e-19       1      63 []     241     302 ..     241     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                                  EE--------.------- CS
                  Wyosine_form 10 KaytyvGssr.srLtmkn 26
                                  +a+  +G  r + L+ kn
  gi|15668431|ref|NP_247229.1| 21 TAVKLCGWVRkKMLEDKN 38
                                  68889**99966676666 PP

  == domain 2  score: 68.9 bits;  conditional E-value: 5.8e-23
                                   HHT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                  Wyosine_form   1 kaepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                   +a+ +F+E+K+y++vG+s++rL+++++++h+e+++ ak l ++++ Y+l++++++Srv+ll++
  gi|15668431|ref|NP_247229.1| 241 RADVHFIELKSYMHVGYSQKRLKKEDMLQHDEILKLAKMLDENSS-YKLIDDSEDSRVALLQN 302
                                   5889*****************************************.**************986 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00012      0.69      53     111 ..      98     166 ..      61     179 .. 0.86
   2 ?   -0.8   0.0      0.28   1.7e+03      26      68 ..     220     260 ..     201     278 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                           HAD  53 glaelleallaglseelaaelerfvaevirpk..........lldpgalellaahraaGdrvvvvSggl 111
                                   ++ ++  ++  g+++ l++  e+ + e+ +pk          +l+p + el++  +++G+++ vvS+g+
  gi|15668431|ref|NP_247229.1|  98 KILAMHKRIIMGYAGVLDRVGEKKFKEALEPKhvaislsgepTLYPYLDELIKIFHKNGFTTFVVSNGI 166
                                   566778899999999999999999999999999999999988677*9999999666**********994 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.28
                           HAD  26 gaprlwralreklllalfrellrldraglaelleallaglsee 68 
                                    +  l r ++  +l+ +  el ++ + ++ el ++++ g+s++
  gi|15668431|ref|NP_247229.1| 220 IRTTLIRGYNDDILKFV--ELYERADVHFIELKSYMHVGYSQK 260
                                   44444444555544444..888888889999999999999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2066.78
//
Query:       gi|15668432|ref|NP_247230.1|  [L=404]
Description: hypothetical protein MJ_0258 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-09   36.1   0.7    2.9e-08   33.9   0.7    2.1  1  Mur_ligase_M  Mur ligase middle domain


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.7   1.6e-12   2.9e-08       1     190 [.     110     273 ..     110     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.6e-12
                                   EESSS-HHHHHHHHHHHHHCT..EEEEETTCSS-THHHHHHHHHHHHHTT-SEEEEE--HCHHHCTTTCCHCBESEEEE-- CS
                  Mur_ligase_M   1 vTGtnGKTTtteliaaileka..gkvigtvgttnneiglpktlaemekkeaeyavlEvsshglgekrlegllkpdvavitn 79 
                                   vTG +GKTTtt+li++il+++  + ++ +      + ++ k l++++ ++++++++E+s           l+k ++++itn
  gi|15668432|ref|NP_247230.1| 110 VTGVKGKTTTTSLINHILKDKysTYLHNSNFGSIAPPTILKVLNSLDIDKYDFFIFETSLG---------LIKCKYGAITN 181
                                   9********************4444455544555667788888888889**********99.........6889******* PP

                                   -TSTTHHHHSSHHHHHHHHHHHHHTSETTCEEEEETTSC...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEETTEEEE CS
                  Mur_ligase_M  80 ispdHldfhgtlenyaeaKaelferlkeegiavinaddpyakelikklkkakvkvvtfglekeaedlraknieeksegtei 160
                                   + ++     g +++ ++aK   f++lk+ ++ +in  d   +++  +++++  +vv ++ +k  ++        +    ++
  gi|15668432|ref|NP_247230.1| 182 VLEN-YKIAGGRKDALTAK---FSSLKNAELSFINKRDI--NRYDLNINHKCLNVVDVDRAKILDK--------YPL--KF 246
                                   *544.33445555555555...77888888999998887..6888888888888998888775532........222..22 PP

                                   EEEEETTEEEEEEESSCSCHHHHHHHHHHH CS
                  Mur_ligase_M 161 ellevkggeleieipllGkhnvyNalaaia 190
                                      ++ ++ +e++ +++G h v+N l ai 
  gi|15668432|ref|NP_247230.1| 247 ---KYFDEIFEFSKNIFGLHFVENSLFAIE 273
                                   ...233666789999***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2730.68
//
Query:       gi|15668433|ref|NP_247231.1|  [L=202]
Description: hypothetical protein MJ_0259 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1372.99
//
Query:       gi|15668434|ref|NP_247232.1|  [L=203]
Description: signal sequence peptidase I [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-06   26.2   1.1    1.3e-05   25.0   0.3    2.0  2  Peptidase_S24  Peptidase S24-like
  ------ inclusion threshold ------
       0.17   12.0   2.2       0.41   10.7   2.2    1.7  1  UPF0370        Uncharacterised protein family (UPF0370)


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.3   1.5e-09   1.3e-05       2      34 ..      14      52 ..      13      56 .. 0.91
   2 ?   -1.6   0.0       0.3   2.7e+03      41      48 ..     117     124 ..     108     150 .. 0.59

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.5e-09
                                  XXSSTTCCTXXTTXEEEEECTS......---TTSEEEEE CS
                 Peptidase_S24  2 vpGdSMeptlldGdlilVdkfs......epkrGdivvfr 34
                                  v +dSM+p ++ Gdl++V+         +++ Gdivv +
  gi|15668434|ref|NP_247232.1| 14 VVSDSMYPIMKRGDLVIVENAGfefnpnDVDVGDIVVYK 52
                                  78*****************888889999*********87 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.3
                                   EEEEEEEE CS
                 Peptidase_S24  41 ayiKrvig 48 
                                     i+rvi 
  gi|15668434|ref|NP_247232.1| 117 PVIHRVID 124
                                   56777762 PP

>> UPF0370  Uncharacterised protein family (UPF0370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.2   4.5e-05      0.41       3      24 ..     177     199 ..     175     203 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.5e-05
                       UPF0370   3 WLadYWWv.illllvGillngik 24 
                                   WL++YW++ +l +l+    n +k
  gi|15668434|ref|NP_247232.1| 177 WLKEYWYLvVLFVLIYYAYNYLK 199
                                   ******98578888877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1338.37
//
Query:       gi|15668435|ref|NP_247233.1|  [L=220]
Description: hypothetical protein MJ_0261 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-53  179.5   0.0    4.8e-53  179.3   0.0    1.1  1  NTPase_I-T  Protein of unknown function DUF84
  ------ inclusion threshold ------
       0.24   11.6   1.4       0.47   10.7   1.4    1.4  1  CEBP_ZZ     Cytoplasmic polyadenylation element-binding prote


Domain annotation for each model (and alignments):
>> NTPase_I-T  Protein of unknown function DUF84
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.3   0.0   5.4e-57   4.8e-53       1     162 [.      53     212 ..      53     213 .. 0.99

  Alignments for each domain:
  == domain 1  score: 179.3 bits;  conditional E-value: 5.4e-57
                                   S---HHHHHHHHHHHHHHCTTEEEEEEE---SS-SS-BSHHHHHHHHHHHHHHHHHHSTTSSEEEEEEEEEET....TEEE CS
                    NTPase_I-T   1 gSkNpvKveAvkeafeklfkdvevegvsvpsgvsdqPmgdeetlkGAinRaknaleaaeeadygvGlEgGveeleeklldv 81 
                                   gS+NpvK+eAvke fek++  vev gv+v sgvs+ P+g eet+ GA+nRakna+e+++ ++y+vG+E+G+ +++e+++d+
  gi|15668435|ref|NP_247233.1|  53 GSTNPVKIEAVKEGFEKVLGAVEVIGVDVISGVSSHPIGLEETYLGALNRAKNAFEKVQ-CTYAVGIEAGLIKVGEHYIDI 132
                                   8********************************************************99.********************* PP

                                   EEE.EEEESS-EEEEE---EE--HHHHHHHCTT--HHHHHHHHHTHCCHHHTTHHHHHHTTTSS-HHHHHHHHHHHHTHHH CS
                    NTPase_I-T  82 awaavvdkegrvsvgrsasfelPeevveevkegeelgevmdelfgtenikqkeGaigllTkglvtRedlyeqavilAlipf 162
                                   ++++v+d+  +++vg s++fe+P+ v+e+v+eg e g++ +e++g ++i+++ G+ig+lT++ +tR+dl++++vi+Alip+
  gi|15668435|ref|NP_247233.1| 133 HICVVFDG-VNETVGLSQGFEYPKIVAEKVLEGIEGGKIAEEISGIKDIGKNIGLIGYLTDNNITRKDLCRESVIMALIPR 212
                                   ********.799*******************************************************************97 PP

>> CEBP_ZZ  Cytoplasmic polyadenylation element-binding protein ZZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.4   5.3e-05      0.47      10      34 ..       7      34 ..       5      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.3e-05
                       CEBP_ZZ 10 edseCeiCekakar...gpyfCrdlaCf 34
                                  ++++CeiC k++     g+++C++ +C+
  gi|15668435|ref|NP_247233.1|  7 KNKKCEICGKKAEIflfGRFLCKNEKCI 34
                                  5789*****99855999**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 1329.52
//
Query:       gi|15668436|ref|NP_247234.1|  [L=1155]
Description: translation initiation factor IF-2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-29  101.0   0.4    1.2e-28   98.9   0.2    2.4  1  GTP_EFTU_D4      Elongation factor Tu domain 4
    1.4e-27   96.5   0.7    5.1e-24   84.9   0.0    2.9  3  GTP_EFTU         Elongation factor Tu GTP binding domain
    1.4e-23   83.3   0.0      6e-23   81.3   0.0    2.2  1  Intein_splicing  Intein splicing domain
    6.5e-22   77.7   5.9    1.1e-21   77.0   4.5    2.3  1  IF-2             Translation-initiation factor 2
    1.7e-21   76.3   7.3    1.4e-20   73.4   1.9    3.7  3  LAGLIDADG_3      LAGLIDADG-like domain
    6.7e-11   42.4   4.9    3.6e-10   40.1   0.0    3.4  2  GTP_EFTU_D2      Elongation factor Tu domain 2
      8e-08   32.3   5.7    0.00057   19.9   0.4    3.7  3  LAGLIDADG_WhiA   WhiA LAGLIDADG-like domain
    0.00065   19.7   0.5      0.014   15.4   0.1    2.8  2  Phage_Gp17       Gene Product 17
    0.00086   19.3   0.1     0.0035   17.4   0.0    2.2  1  HTH_3            Helix-turn-helix
     0.0016   18.5   0.3     0.0063   16.6   0.0    2.2  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0037   16.9   0.0      0.017   14.7   0.0    2.1  2  Ras              Ras family
     0.0038   17.1   0.0     0.0088   15.9   0.0    1.6  1  ATP_bind_1       Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.015   15.6   1.4      0.029   14.6   0.1    2.2  2  PT-HINT          Pretoxin HINT domain
      0.025   14.5   0.5         12    5.9   0.1    2.7  2  ComZ             ComZ
      0.047   14.2   0.5       0.21   12.1   0.1    2.3  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
       0.28   11.3   4.0          3    8.0   1.9    3.0  2  Exog_C           Endo/exonuclease (EXOG) C-terminal domain


Domain annotation for each model (and alignments):
>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.2     1e-31   1.2e-28       1      86 []    1024    1110 ..    1024    1110 .. 0.99

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 1e-31
                                    S-CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-.TTTS CS
                   GTP_EFTU_D4    1 rPgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegki.vGrq 78  
                                    +P+ i+ilp+++fr++dpai+Gvevl+G++++g +l++edG+++G +++i+d+g++++eakaG+ v+i+i+g++ + r+
  gi|15668436|ref|NP_247234.1| 1024 KPAIIRILPDCIFRQKDPAICGVEVLCGTLRVGAPLMREDGMQLGYVREIKDRGENVKEAKAGKAVSIAIDGRVvLKRH 1102
                                    79************************************************************************889** PP

                                    --TT-EEE CS
                   GTP_EFTU_D4   79 ikegdily 86  
                                    ++egd++y
  gi|15668436|ref|NP_247234.1| 1103 VDEGDYMY 1110
                                    *****998 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00078      0.87       5      54 ..      19      69 ..      15      88 .. 0.67
   2 !   84.9   0.0   4.5e-27   5.1e-24      47     191 ..     589     775 ..     559     778 .. 0.82
   3 ?   -2.9   0.1       3.6     4e+03     130     154 ..     890     936 ..     864     994 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00078
                                  EEEEEESTTSSHHHH.HHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTS CS
                      GTP_EFTU  5 nigiighvDhGKtTL.tdrLlyktgaiskkgekaeeervlDtlkeErergi 54
                                   ++++ghvDhGK  +  +++l++ g+i+ +   + +++++ + +  + r +
  gi|15668436|ref|NP_247234.1| 19 IVCVLGHVDHGKCLMpHEKVLTEYGEIKIEDLFKIGKEIVEKDELKEIRKL 69
                                  79**********876446777777777665555533455555555555555 PP

  == domain 2  score: 84.9 bits;  conditional E-value: 4.5e-27
                                   HHHHHHTSCSSCEEEEEE................TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHH CS
                      GTP_EFTU  47 keErergiTiksaaisle................ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqt 111
                                   ++ ++ giT ++ a ++                 ++ k   + +iDtPGH+ F++   rg + +D+a+lvvd++eG +pqt
  gi|15668436|ref|NP_247234.1| 589 AKREAGGITQHIGASEIPidvikrlcgdllkmlkADLKIPGLLVIDTPGHEAFTSLRKRGGALADIAILVVDINEGFKPQT 669
                                   44556799999999999999999999999998855999999**************************************** PP

                                   HHHHHHHHHTTTEEEEEEESCGST..........HHHHHHHHHHHHHHHHHH..................HHHHHHHHHTT CS
                      GTP_EFTU 112 eevlrlalkegvpiivfiNKmDrl..........kaelkeiveevkqklsrk..................eeklekygekg 164
                                    e ++++++ ++p++v+ NK+D +          + +++e  +  +     +                  +++l + +++ 
  gi|15668436|ref|NP_247234.1| 670 VEAVNILRQCKTPFVVAANKIDLIpgwnskegpfILNFNEKNQHPNALT--EfeirlyeniikplnelgfDADLYSRVQDV 748
                                   *************************999988888555554444444222..134667778888888888877777777777 PP

                                   TTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                      GTP_EFTU 165 ekevpvvfgSalkgegvktllealvel 191
                                   +k+v ++++Sa++geg+ +ll ++  l
  gi|15668436|ref|NP_247234.1| 749 TKTVCIIPVSAVTGEGIPDLLMMVAGL 775
                                   799*******************99865 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.6
                                   ESCGSTHHHHHHHHHHHHHHHHHH......................H CS
                      GTP_EFTU 130 NKmDrlkaelkeiveevkqklsrk......................e 154
                                    K+ ++k+e+ + vee+k +++++                       
  gi|15668436|ref|NP_247234.1| 890 DKIEEAKEEVMKEVEEAKIEVDDEgilikadtlgslealanelrkaG 936
                                   56666666666666666666654466666666666555544444331 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.0   5.4e-26     6e-23      14     134 .]      56     576 ..      38     576 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 5.4e-26
                                   HHCCECT.TEEEEEETTTTEEEEEE......EEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--T CS
                                   xxxxxxx.xxxxxxxxxxxxxxxxx......xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  14 elvekeg.eevlslnledlklevks......vkkliklklk.elyeiklesgrkikaTpeHkllvvrdegivEkradeLke 86 
                                   e+vek++ +e+ +ln++   l+ +          ++klk k +++++kl++ ++i +TpeH++l+   +g+   +a+++k+
  gi|15668436|ref|NP_247234.1|  56 EIVEKDElKEIRKLNIKVHTLNENGeikiinAPYVWKLKHKgKMIKVKLKNWHSITTTPEHPFLTN--NGW--IKAENIKK 132
                                   344433312233444444444443344543377899999999************************..9**..8******* PP

                                   T-EEEEE.......................................................................... CS
                                   xxxxxxx.......................................................................... RF
               Intein_splicing  87 gdliavp.......................................................................... 93 
                                   g ++a+p                                                                          
  gi|15668436|ref|NP_247234.1| 133 GMYVAIPrkiygnedfekfiefinskiltnelivkvnekdlknvelpstkiykkqknvfrsediiehnlniekisfsprih 213
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15668436|ref|NP_247234.1| 214 rcgkpqhyiklpkslnewkaifyfagvmfgdgcvdrianndeevfnklkslnnlgieverikrkssyeiifkngknalinl 294
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15668436|ref|NP_247234.1| 295 lkilfdypsekkshnikipqilyiapkelvaefikgyfdadgyvnlrqnrievisaskefieglsilllrfeitskiyeik 375
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15668436|ref|NP_247234.1| 376 ksyketkkkyyqlnivgkrnlknfknigfsikykeenlnkiieksrksekypinkdmkrlrilfgmtrnevnvsyyakyen 456
                                   ********************************************************************************* PP

                                   ................................................................................H CS
                                   ................................................................................x RF
               Intein_splicing  94 ................................................................................d 94 
                                                                                                                    
  gi|15668436|ref|NP_247234.1| 457 gkeipsyeivkkflnslkpknldkkikvlegkerdvnylkafesdgliengrltklgrealniwknhefgkenidymkslI 537
                                   *******************************************************************************99 PP

                                   SCEEEEEEEEEEEEECEEEEEEEEETTT-EEEECTTEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  95 advvwdkvksievedeeeyVYdltvednhNFvangiivHN 134
                                   +++++ +v+++e  d+++yVYdlt+e +hNF+angi+vHN
  gi|15668436|ref|NP_247234.1| 538 ENIAFVEVEDVEIIDYDGYVYDLTTE-THNFIANGIVVHN 576
                                   99**********************99.************9 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   4.5   9.4e-25   1.1e-21       4     104 ..     899    1003 ..     896    1004 .. 0.89

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 9.4e-25
                                    HHHCCCSCS...SCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHH...ST...EEEEEES CS
                          IF-2    4 lfeeikeeg...kelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasa...sn...aiiigFn 73  
                                    +++e++e +   ++ +++ikaD+ GsleAl++ L+k +     vk+ +++vG++t++Dv  +++   sn   + i++Fn
  gi|15668436|ref|NP_247234.1|  899 VMKEVEEAKievDDEGILIKADTLGSLEALANELRKAG-----VKIKKAEVGDVTKKDVIEVASykqSNplhGAIVAFN 972 
                                    566666655666899*********************95.....9***************9998755544888******* PP

                                    SSCTHHHHHCCCCCTSEEEEESSHHHHHHHH CS
                          IF-2   74 vkvskkakklaekegvkirlynvIYkliddv 104 
                                    vk+ ++a+k++ek ++k++l n+IYkl++d+
  gi|15668436|ref|NP_247234.1|  973 VKILPEAQKEIEKYDIKVFLDNIIYKLVEDF 1003
                                    *****************************97 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.3   1.4e+03      62      82 ..     132     155 ..     122     156 .. 0.74
   2 ?    3.0   0.0      0.11   1.2e+02      28      65 ..     249     280 ..     235     297 .. 0.73
   3 !   73.4   1.9   1.2e-23   1.4e-20       2      80 ..     323     401 ..     322     403 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.3
                                   CCCC...ECCCHCHCTTCGGGTTT CS
                   LAGLIDADG_3  62 rgvy...rlliisgenlkrFleki 82 
                                   +g+y    + i+++e++++F e i
  gi|15668436|ref|NP_247234.1| 132 KGMYvaiPRKIYGNEDFEKFIEFI 155
                                   44444455789**********988 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                                   EEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCC CS
                   LAGLIDADG_3  28 sltssskelledvqrlLlrlGIestiyekkkakgrgvy 65 
                                   +++++++e+ ++++  L++lGIe    ++     + +y
  gi|15668436|ref|NP_247234.1| 249 RIANNDEEVFNKLKS-LNNLGIEVERIKR-----KSSY 280
                                   46799*********9.88****9877776.....4444 PP

  == domain 3  score: 73.4 bits;  conditional E-value: 1.2e-23
                                   HHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEE...EEE-SCCCCECCCHCHCTTCGGG CS
                   LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyek...kkakgrgvyrlliisgenlkrFl 79 
                                    +a+f++G+fdaDG+v+ ++++   i++ s+ske++e+++ lLlr++I+s+iye    +k+ ++ +y+l i++++nlk+F 
  gi|15668436|ref|NP_247234.1| 323 LVAEFIKGYFDADGYVNLRQNR---IEVISASKEFIEGLSILLLRFEITSKIYEIkksYKETKKKYYQLNIVGKRNLKNFK 400
                                   689******************9...******************************99999999*****************6 PP

                                   T CS
                   LAGLIDADG_3  80 e 80 
                                   +
  gi|15668436|ref|NP_247234.1| 401 N 401
                                   5 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   3.2e-13   3.6e-10       1      73 [.     806     884 ..     806     885 .. 0.94
   2 ?    2.8   0.3      0.13   1.5e+02       3      59 ..    1043    1094 ..    1042    1108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 3.2e-13
                                   EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE...........ETTSEEEEEEEESSCCSGSSTT CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededea...........vaganaGvivaikgledaiivG 70 
                                   Gt++++++y+G+ k+Gd+++++  d+     vtr+++l+++ +++de+           ++ a+aGv++a+++l++ +i+G
  gi|15668436|ref|NP_247234.1| 806 GTTIDAIIYDGIAKRGDYLVVGLPDD---VLVTRVKALLKP-KPLDEMrdprdkfkpvnEVTAAAGVKIAAPELDK-VIAG 881
                                   9********************55443...89**********.88********************************.**** PP

                                   CEE CS
                   GTP_EFTU_D2  71 dtl 73 
                                   +++
  gi|15668436|ref|NP_247234.1| 882 CPI 884
                                   987 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                                    EEEEEEEESEEETTEEEEEECTCTTSEE.EEEEEEEEEEETEEESEEETTSEEEEEEE CS
                   GTP_EFTU_D2    3 valgrvysGtlkkGdevrilgndtskke.ivtrissletfhededeavaganaGviva 59  
                                    ++++ v  Gtl++G  ++    d    + +++ ++ +    e+++ea ag ++ + + 
  gi|15668436|ref|NP_247234.1| 1043 ICGVEVLCGTLRVGAPLMR--ED----GmQLGYVREIKDRGENVKEAKAGKAVSIAID 1094
                                    5778899999**9999998..55....4489*****************9999988775 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   0.00013      0.14       4      74 ..     236     298 ..     233     313 .. 0.84
   2 !   19.9   0.4   5.1e-07   0.00057       3      63 ..     326     384 ..     324     402 .. 0.89
   3 ?   -0.2   0.1      0.93     1e+03      29      65 ..     461     499 ..     459     500 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                LAGLIDADG_WhiA   4 flrGaflasGsindpekkyhLEivspdeelaeqlqkllnefeleakilerrkkyvvylKkae.qIvdlLkii 74 
                                   +++G++++ G + +        i+ +dee++++l+  ln++++e + ++r+++y + +K+++ + ++lLki+
  gi|15668436|ref|NP_247234.1| 236 YFAGVMFGDGCVDR--------IANNDEEVFNKLK-SLNNLGIEVERIKRKSSYEIIFKNGKnALINLLKIL 298
                                   78888888888888........8889********8.99*********************9861578888876 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 5.1e-07
                LAGLIDADG_WhiA   3 aflrGaflasGsindpekkyhLEivspdeelaeqlqkllnefeleakilerrkkyvvylKk 63 
                                    f++G f a G +n  ++   +E++s ++e++e l+ ll +fe+++ki e +k+y+ + Kk
  gi|15668436|ref|NP_247234.1| 326 EFIKGYFDADGYVNLRQN--RIEVISASKEFIEGLSILLLRFEITSKIYEIKKSYKETKKK 384
                                   79*************555..5*********************************9877666 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.93
                LAGLIDADG_WhiA  29 pdeelaeqlqklln..efeleakilerrkkyvvylKkae 65 
                                   p+ e++++  + l+  +++ + k+le +++ v ylK  e
  gi|15668436|ref|NP_247234.1| 461 PSYEIVKKFLNSLKpkNLDKKIKVLEGKERDVNYLKAFE 499
                                   566777777777876566778899999*********877 PP

>> Phage_Gp17  Gene Product 17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.3e-05     0.014      86     129 ..     543     586 ..     509     594 .. 0.83
   2 ?    1.0   0.0      0.34   3.9e+02      92     129 ..     946     982 ..     919     992 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                    Phage_Gp17  86 geidrvdyidkdgirfdvpretsphvdksivtfndelldeanki 129
                                    e++ v+ id dg  +d+  et   + + iv  n  lld+  k 
  gi|15668436|ref|NP_247234.1| 543 VEVEDVEIIDYDGYVYDLTTETHNFIANGIVVHNTTLLDKIRKT 586
                                   58999**********************************98875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.34
                    Phage_Gp17  92 dyidkdgirfdvpretsphvdksivtfndelldeanki 129
                                   d   kd i +   +++ p +  +iv+fn ++l ea+k 
  gi|15668436|ref|NP_247234.1| 946 DVTKKDVIEVASYKQSNP-LHGAIVAFNVKILPEAQKE 982
                                   555677777776666655.6789************984 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.1e-06    0.0035       4      48 ..     435     473 ..     432     480 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.1e-06
                                   HHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHH CS
                         HTH_3   4 lRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaL 48 
                                   lR   g+++     +  v +s+++++EnG+ +Ps e++kk ++ L
  gi|15668436|ref|NP_247234.1| 435 LRILFGMTR----NE--VNVSYYAKYENGKEIPSYEIVKKFLNSL 473
                                   555555555....23..468********************98876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.6e-06    0.0063      14     114 .]     578     689 ..     576     689 .. 0.69
   2 ?   -3.2   0.1       7.6   8.5e+03      48      59 ..     916     929 ..     889     989 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.6e-06
                                   HHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE..................EEEEECGGCSSHHHHHH.HHHHHHHHHHC CS
                      MMR_HSR1  14 tLinaltgekaivsdkpgtTrdinegrvklkgke..................ielvDtpGliegaseek.glgkaflalee 75 
                                   tL+ ++ ++++   +  g T++i   ++ ++  +                  + ++DtpG  e       +l+k+      
  gi|15668436|ref|NP_247234.1| 578 TLLDKIRKTRVAKREAGGITQHIGASEIPIDVIKrlcgdllkmlkadlkipgLLVIDTPG-HE----AFtSLRKRGG---A 650
                                   666666666666777778888887777765532234555555555555566699******.44....2212222222...2 PP

                                   .TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  76 .adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                    ad+++lvvd++ e++kp+  e  ++l++ k p+++++nk
  gi|15668436|ref|NP_247234.1| 651 lADIAILVVDIN-EGFKPQTVEAVNILRQCKTPFVVAANK 689
                                   47********99.88**********************998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.6
                                   EEEEECGGCSS..H CS
                      MMR_HSR1  48 ielvDtpGlie..g 59 
                                   ++ +Dt G +e   
  gi|15668436|ref|NP_247234.1| 916 LIKADTLGSLEalA 929
                                   34455555443221 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1         4   4.5e+03      67      97 ..     353     388 ..     348     402 .. 0.60
   2 !   14.7   0.0   1.5e-05     0.017      49     116 ..     629     692 ..     615     712 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4
                                   HHHTTESEEEEEEETTBH.....HHHHTHHHHHHHH CS
                           Ras  67 lyyrdaegillvyditsr.....esfenvkkwveei 97 
                                    ++++ + +ll ++its+     +s+++ kk + ++
  gi|15668436|ref|NP_247234.1| 353 EFIEGLSILLLRFEITSKiyeikKSYKETKKKYYQL 388
                                   566677788888888875222224555555444333 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.5e-05
                                   EEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTG CS
                           Ras  49 kleiwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDl 116
                                    l + DT G e f+slr+     a+ ++lv di++   f+  +    +i r+++  +p+v+ +nK+Dl
  gi|15668436|ref|NP_247234.1| 629 GLLVIDTPGHEAFTSLRKRGGALADIAILVVDINEG--FKPQTVEAVNILRQCK--TPFVVAANKIDL 692
                                   57899***************************9865..6655555668999999..6**********8 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.8e-06    0.0088      92     236 ..     629     773 ..     597     778 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.8e-06
                    ATP_bind_1  92 dyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkek 172
                                    +l++DtPG   +  +++ +           a +++ +vD +          +++ a++++ ++++P+vv+ nk+Dl+   
  gi|15668436|ref|NP_247234.1| 629 GLLVIDTPGHEAFTSLRKRGG--------ALADIAILVVDINEGF-----KPQTVEAVNILRQCKTPFVVAANKIDLIPGW 696
                                   689999999988888888888........5556888888877554.....45556679*******************9866 PP

                    ATP_bind_1 173 lekeleffedvealslllekee.............ekykklaeaiaelleefalvlrflplssekeesiedllslid 236
                                   + ke  f+ ++++ ++  +  +                    +++ + +++++ +  ++p+s+ ++e+i dll ++ 
  gi|15668436|ref|NP_247234.1| 697 NSKEGPFILNFNEKNQHPNALTefeirlyeniikpLNELGFDADLYSRVQDVTKTVCIIPVSAVTGEGIPDLLMMVA 773
                                   77777777766665555444444556888877643222333567888888888888899999999999999988875 PP

>> PT-HINT  Pretoxin HINT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.6e-05     0.029      55      84 ..     104     133 ..      71     138 .. 0.83
   2 ?   -3.4   0.1       9.6   1.1e+04     127     136 ..     567     576 ..     544     577 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                       PT-HINT  55 ignsevlisnkihPfyskgkfieakelkvG 84 
                                   + n + + ++ +hPf ++ ++i+a+++k+G
  gi|15668436|ref|NP_247234.1| 104 LKNWHSITTTPEHPFLTNNGWIKAENIKKG 133
                                   578899**********************99 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.6
                       PT-HINT 127 aeteGvlvhn 136
                                     ++G++vhn
  gi|15668436|ref|NP_247234.1| 567 FIANGIVVHN 576
                                   3468999999 PP

>> ComZ  ComZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.011        12      11      33 ..     900     922 ..     897     931 .. 0.89
   2 ?    5.8   0.0     0.012        14      11      33 ..     973     995 ..     969    1001 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.011
                          ComZ  11 mkylPeakkeLekkGIelsmeel 33 
                                   mk + eak e++++GI ++ ++l
  gi|15668436|ref|NP_247234.1| 900 MKEVEEAKIEVDDEGILIKADTL 922
                                   9***************9999987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
                          ComZ  11 mkylPeakkeLekkGIelsmeel 33 
                                    k lPea+ke+ek  I++ ++++
  gi|15668436|ref|NP_247234.1| 973 VKILPEAQKEIEKYDIKVFLDNI 995
                                   589*************9988875 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00019      0.21      17      45 ..     934     962 ..     921     972 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                   SXXSSTTTSXXEEEEHHHHHHHHHHHGGG CS
                 Ribosomal_L11  17 kgsgkpgketvGtvslkqvyeIAkiKksd 45 
                                   k   k +k  vG+v+ k+v+e+A  K+s+
  gi|15668436|ref|NP_247234.1| 934 KAGVKIKKAEVGDVTKKDVIEVASYKQSN 962
                                   3344446777*****************86 PP

>> Exog_C  Endo/exonuclease (EXOG) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.9    0.0027         3      25      41 ..     897     913 ..     891     918 .. 0.92
   2 ?    1.6   0.0      0.26   2.9e+02      18      37 ..     919     938 ..     915     939 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0027
                        Exog_C  25 ekvmkeLkeagiepDey 41 
                                   e+vmke++ea+ie D++
  gi|15668436|ref|NP_247234.1| 897 EEVMKEVEEAKIEVDDE 913
                                   89*************95 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.26
                        Exog_C  18 ArtlkRLekvmkeLkeagie 37 
                                   A tl  Le   +eL++ag++
  gi|15668436|ref|NP_247234.1| 919 ADTLGSLEALANELRKAGVK 938
                                   88999*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.81u 0.30s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 7085.88
//
Query:       gi|15668437|ref|NP_247235.1|  [L=320]
Description: hypothetical protein MJ_0263 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-33  112.2  25.9      6e-05   22.9   0.5    8.5  8  TPR_2         Tetratricopeptide repeat
    5.5e-33  111.4  36.7      5e-06   26.1   0.9    9.0  9  TPR_1         Tetratricopeptide repeat
    2.8e-29   98.9  35.4      8e-05   22.5   0.5    9.2  9  TPR_8         Tetratricopeptide repeat
    3.6e-28   97.9   0.0    8.5e-08   32.7   0.0    5.1  5  TPR_16        Tetratricopeptide repeat
    1.1e-26   91.2   0.1    0.00015   22.3   0.0    7.8  8  TPR_14        Tetratricopeptide repeat
    2.7e-26   91.9   5.1    5.4e-07   30.0   0.1    5.2  5  TPR_19        Tetratricopeptide repeat
    2.2e-24   85.6   5.7    1.4e-05   25.3   0.0    5.8  5  TPR_12        Tetratricopeptide repeat
    1.6e-20   72.3   9.0     0.0043   17.6   0.0    8.1  7  TPR_6         Tetratricopeptide repeat
    1.5e-19   68.9  12.5    0.00077   19.7   0.1    7.3  7  TPR_17        Tetratricopeptide repeat
      6e-19   68.1  11.2    4.7e-07   29.9   2.0    4.4  4  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    2.5e-18   66.0   0.0    6.9e-06   26.1   0.0    5.1  5  TPR_9         Tetratricopeptide repeat
    2.2e-16   58.6   6.8       0.11   12.6   0.0    8.6  9  TPR_7         Tetratricopeptide repeat
    3.4e-16   58.6  19.5    0.00044   19.9   0.1    7.0  6  TPR_11        TPR repeat
      3e-15   56.1  10.3    1.7e-05   23.9   0.8    4.1  4  NARP1         NMDA receptor-regulated protein 1
    3.3e-11   42.6   2.6       0.16   10.7   0.0    4.9  5  DUF3808       Protein of unknown function (DUF3808)
    3.4e-08   33.2   7.7         24    5.4   0.2    7.9  7  PPR           PPR repeat
    1.2e-07   31.5   0.0      0.014   14.8   0.1    3.8  3  TPR_MalT      MalT-like TPR region
    1.2e-07   31.6   2.9       0.91    9.4   0.0    5.1  7  ATP13         Mitochondrial ATPase expression
    5.1e-07   29.2   1.9     0.0003   20.1   0.7    3.1  3  TPR_15        Tetratricopeptide repeat
    6.4e-07   29.0   8.0        2.5    8.1   0.0    7.6  8  TPR_10        Tetratricopeptide repeat
    9.6e-07   29.0   2.0      0.017   15.2   0.1    4.1  5  DUF3856       Domain of Unknown Function (DUF3856)
    4.9e-06   26.4   2.4       0.27   10.9   0.0    3.8  3  TPR_21        Tetratricopeptide repeat-like domain
    7.9e-06   24.6   7.5    7.2e-05   21.4   0.1    2.5  2  Cohesin_load  Cohesin loading factor
    9.3e-06   25.6   1.9        0.6   10.2   0.2    4.7  4  ANAPC5        Anaphase-promoting complex subunit 5
    1.9e-05   24.6   9.0        2.7    8.1   0.0    5.8  5  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
    4.7e-05   22.3   0.0      0.011   14.4   0.0    2.4  3  PknG_TPR      Protein kinase G tetratricopeptide repeat
    0.00023   21.0   2.3      0.005   16.6   0.1    3.2  4  Leptin        Leptin
    0.00049   19.4   1.3      0.063   12.5   0.5    2.1  2  FAT           FAT domain
     0.0011   19.3   6.9       0.29   11.5   0.1    4.1  5  TPR_20        Tetratricopeptide repeat
     0.0017   18.1  13.7      0.059   13.1   0.8    4.9  4  RPN7          26S proteasome subunit RPN7
     0.0043   17.6   0.0         97    4.1   0.0    5.0  4  TPR_4         Tetratricopeptide repeat
     0.0049   16.9   2.6      0.017   15.1   0.7    2.4  2  DUF4919       Domain of unknown function (DUF4919)
  ------ inclusion threshold ------
      0.012   15.4   3.8       0.69    9.6   0.3    3.3  3  YfiO          Outer membrane lipoprotein
      0.013   15.4   8.6       0.33   11.0   0.1    5.5  6  TPR_3         Tetratricopeptide repeat
      0.015   15.9   0.9         19    6.1   0.0    4.2  4  Sel1          Sel1 repeat
      0.017   15.5   0.0       0.28   11.6   0.0    2.8  3  BTAD          Bacterial transcriptional activator domain
      0.056   13.5   1.0       0.79    9.8   0.1    3.1  3  PTS_IIA       PTS system, Lactose/Cellobiose specific IIA sub
      0.061   13.2   0.7        1.8    8.4   0.1    2.9  2  T6PP_N        Trehalose-6-phosphate phosphatase N-terminal he
      0.062   13.2   1.8       0.21   11.5   1.2    2.5  1  CLTH          CTLH/CRA C-terminal to LisH motif domain
       0.49   10.5  18.8       0.99    9.5   0.0    6.1  6  MIT           MIT (microtubule interacting and transport) dom
       0.96    9.4   7.9        2.1    8.2   0.1    4.0  3  YfdX          YfdX protein


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.6   1.3e-05    0.0056      10      34 .]      21      45 ..      18      45 .. 0.89
   2 !    9.7   0.0    0.0022      0.97       2      25 ..      47      70 ..      46      70 .. 0.93
   3 !   17.3   0.2     8e-06    0.0035       6      33 ..     119     146 ..     118     147 .. 0.93
   4 !   11.5   0.0   0.00058      0.25       4      33 ..     151     180 ..     149     181 .. 0.88
   5 !   22.9   0.5   1.4e-07     6e-05       1      33 [.     182     214 ..     182     215 .. 0.95
   6 !   16.5   0.6   1.5e-05    0.0063       3      34 .]     218     249 ..     216     249 .. 0.92
   7 !   15.6   0.1   2.9e-05     0.013       2      28 ..     251     277 ..     250     279 .. 0.92
   8 !   14.2   0.1   8.3e-05     0.036       6      28 ..     294     316 ..     292     319 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-05
                         TPR_2 10 ayyklgdyeeAleafekAleldPnn 34
                                   ++ +g++++Ale++ekA + d +n
  gi|15668437|ref|NP_247235.1| 21 ECADKGNFDKALEYLEKAQKVDKDN 45
                                  57889***************99987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0022
                         TPR_2  2 ealynlGlayyklgdyeeAleafe 25
                                   +ly  G ++  +gd e+A+++fe
  gi|15668437|ref|NP_247235.1| 47 LVLYVKGIVLKLKGDMEKAEKYFE 70
                                  68999******************8 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 8e-06
                         TPR_2   6 nlGlayyklgdyeeAleafekAleldPn 33 
                                     +l+y++ g++e+Alea+++ l+++Pn
  gi|15668437|ref|NP_247235.1| 119 HKALIYIEFGEFEKALEALDEFLKIYPN 146
                                   6799***********************9 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00058
                         TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                   l + + +++ lg+++eAl++ +k l++  +
  gi|15668437|ref|NP_247235.1| 151 LRQKASILEILGKLDEALDCVNKILSIKKD 180
                                   6778999******************99776 PP

  == domain 5  score: 22.9 bits;  conditional E-value: 1.4e-07
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                   a a+y  G+++ klg+ +eAl+a++ A+ l++n
  gi|15668437|ref|NP_247235.1| 182 AHAWYLKGRILKKLGNIKEALDALKMAINLNEN 214
                                   679****************************87 PP

  == domain 6  score: 16.5 bits;  conditional E-value: 1.5e-05
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                   ++  ++++ +++++yeeAl++  k le  Pn+
  gi|15668437|ref|NP_247235.1| 218 VYKDIAYLELANNNYEEALNYITKYLEKFPND 249
                                   57789999**********************97 PP

  == domain 7  score: 15.6 bits;  conditional E-value: 2.9e-05
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAl 28 
                                   ea ++l+l+y++l++ ++Al+ ++k +
  gi|15668437|ref|NP_247235.1| 251 EAKFYLALIYENLNKVDDALKIYDKII 277
                                   789********************9976 PP

  == domain 8  score: 14.2 bits;  conditional E-value: 8.3e-05
                         TPR_2   6 nlGlayyklgdyeeAleafekAl 28 
                                   n +++++klg+ eeA+e ++kA 
  gi|15668437|ref|NP_247235.1| 294 NKARILEKLGKIEEAVETYNKAF 316
                                   789******************96 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.1   2.1e-06   0.00091       9      34 .]      20      45 ..      18      45 .. 0.91
   2 !   13.7   0.0   9.7e-05     0.042       3      25 ..      48      70 ..      46      71 .. 0.93
   3 ?   -0.3   0.0       2.5   1.1e+03      13      26 ..      92     105 ..      81     105 .. 0.82
   4 !   13.8   0.2   9.1e-05      0.04       6      33 ..     119     146 ..     118     147 .. 0.94
   5 !   14.0   0.0   7.6e-05     0.033       6      33 ..     153     180 ..     149     181 .. 0.88
   6 !   26.1   0.9   1.2e-08     5e-06       3      33 ..     184     214 ..     182     215 .. 0.95
   7 !   11.8   2.3   0.00037      0.16       4      34 .]     219     249 ..     217     249 .. 0.93
   8 !   14.6   0.2   5.1e-05     0.022       2      28 ..     251     277 ..     250     279 .. 0.91
   9 !   17.5   0.1     6e-06    0.0026       6      28 ..     294     316 ..     291     319 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.1e-06
                                  HHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1  9 nayfklgkydeAleyyekALelnPnn 34
                                  + +  +g++d+Aley ekA +++ +n
  gi|15668437|ref|NP_247235.1| 20 LECADKGNFDKALEYLEKAQKVDKDN 45
                                  667899*****************987 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 9.7e-05
                                  HHHHHHHHHHHTT-HHHHHHHHH CS
                         TPR_1  3 alynlGnayfklgkydeAleyye 25
                                  +ly +G ++  +g+ ++A++y+e
  gi|15668437|ref|NP_247235.1| 48 VLYVKGIVLKLKGDMEKAEKYFE 70
                                  7999******************8 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.5
                                   HTT-HHHHHHHHHH CS
                         TPR_1  13 klgkydeAleyyek 26 
                                    +g+y+  l+y ek
  gi|15668437|ref|NP_247235.1|  92 VKGEYERTLKYIEK 105
                                   689***99999887 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 9.1e-05
                                   HHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   6 nlGnayfklgkydeAleyyekALelnPn 33 
                                    ++++y + g++++Ale+ ++ L+++Pn
  gi|15668437|ref|NP_247235.1| 119 HKALIYIEFGEFEKALEALDEFLKIYPN 146
                                   689************************8 PP

  == domain 5  score: 14.0 bits;  conditional E-value: 7.6e-05
                                   HHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   6 nlGnayfklgkydeAleyyekALelnPn 33 
                                   +++ ++  lgk+deAl++ +k L++  +
  gi|15668437|ref|NP_247235.1| 153 QKASILEILGKLDEALDCVNKILSIKKD 180
                                   78999******************99876 PP

  == domain 6  score: 26.1 bits;  conditional E-value: 1.2e-08
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                   a+y +G ++ klg+ +eAl++ + A+ ln+n
  gi|15668437|ref|NP_247235.1| 184 AWYLKGRILKKLGNIKEALDALKMAINLNEN 214
                                   9****************************98 PP

  == domain 7  score: 11.8 bits;  conditional E-value: 0.00037
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                   ++ ++++ + +++y+eAl y  k Le  Pn+
  gi|15668437|ref|NP_247235.1| 219 YKDIAYLELANNNYEEALNYITKYLEKFPND 249
                                   88899999********************996 PP

  == domain 8  score: 14.6 bits;  conditional E-value: 5.1e-05
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekAL 28 
                                   +a + l+++y +l+k d+Al+ y+k +
  gi|15668437|ref|NP_247235.1| 251 EAKFYLALIYENLNKVDDALKIYDKII 277
                                   78899*******************977 PP

  == domain 9  score: 17.5 bits;  conditional E-value: 6e-06
                                   HHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_1   6 nlGnayfklgkydeAleyyekAL 28 
                                   n++ ++ klgk +eA+e y+kA 
  gi|15668437|ref|NP_247235.1| 294 NKARILEKLGKIEEAVETYNKAF 316
                                   99*******************95 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.6   1.9e-05    0.0085      11      34 .]      22      45 ..      19      45 .. 0.90
   2 !   11.3   0.1   0.00075      0.33       4      25 ..      49      70 ..      47      71 .. 0.93
   3 ?    0.3   0.0       2.5   1.1e+03      14      32 ..      93     111 ..      93     113 .. 0.86
   4 !   14.9   0.1   5.2e-05     0.023       5      33 ..     118     146 ..     118     147 .. 0.95
   5 !   13.9   0.1   0.00011     0.048       6      34 .]     153     181 ..     150     181 .. 0.94
   6 !   22.5   0.5   1.8e-07     8e-05       1      33 [.     182     214 ..     182     215 .. 0.95
   7 !    8.7   0.2    0.0051       2.2       6      29 ..     221     244 ..     216     249 .. 0.87
   8 !   10.1   0.3    0.0017      0.76       7      29 ..     256     278 ..     250     281 .. 0.87
   9 !   21.1   0.1   5.5e-07   0.00024       5      28 ..     293     316 ..     290     319 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.9e-05
                                  HHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8 11 ylklgdyeeAkeyyekaleldpdn 34
                                  + ++g++++A ey+eka + d+dn
  gi|15668437|ref|NP_247235.1| 22 CADKGNFDKALEYLEKAQKVDKDN 45
                                  5799*****************986 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00075
                                  HHHHHHHHHHTT-HHHHHHHHH CS
                         TPR_8  4 yynlgsiylklgdyeeAkeyye 25
                                  +y +g +++ +gd+e+A++y+e
  gi|15668437|ref|NP_247235.1| 49 LYVKGIVLKLKGDMEKAEKYFE 70
                                  799999***************8 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.5
                                   TT-HHHHHHHHHHHHHHHH CS
                         TPR_8  14 lgdyeeAkeyyekaleldp 32 
                                   +g+ye   +y+ek  +l++
  gi|15668437|ref|NP_247235.1|  93 KGEYERTLKYIEKLSRLSK 111
                                   68999999*****999886 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 5.2e-05
                                   HHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   +++++iy++ g++e+A e++ + l++ p+
  gi|15668437|ref|NP_247235.1| 118 FHKALIYIEFGEFEKALEALDEFLKIYPN 146
                                   579***********************997 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 0.00011
                                   HHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   +++si++ lg+++eA  + +k l++++d+
  gi|15668437|ref|NP_247235.1| 153 QKASILEILGKLDEALDCVNKILSIKKDD 181
                                   689***********************986 PP

  == domain 6  score: 22.5 bits;  conditional E-value: 1.8e-07
                                   CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   a+a+y++g+i++klg+++eA  +++ a+ l+++
  gi|15668437|ref|NP_247235.1| 182 AHAWYLKGRILKKLGNIKEALDALKMAINLNEN 214
                                   78***************************9986 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.0051
                                   HHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8   6 nlgsiylklgdyeeAkeyyekale 29 
                                    ++++ l  ++yeeA  y+ k+le
  gi|15668437|ref|NP_247235.1| 221 DIAYLELANNNYEEALNYITKYLE 244
                                   68999999*************997 PP

  == domain 8  score: 10.1 bits;  conditional E-value: 0.0017
                                   HHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8   7 lgsiylklgdyeeAkeyyekale 29 
                                   l++iy++l++ + A + y k ++
  gi|15668437|ref|NP_247235.1| 256 LALIYENLNKVDDALKIYDKIIS 278
                                   99******************987 PP

  == domain 9  score: 21.1 bits;  conditional E-value: 5.5e-07
                                   HHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_8   5 ynlgsiylklgdyeeAkeyyekal 28 
                                   +n+++i++klg++eeA+e+y+ka 
  gi|15668437|ref|NP_247235.1| 293 LNKARILEKLGKIEEAVETYNKAF 316
                                   79********************96 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.1e-06   0.00049       9      58 ..      24      70 ..      18      71 .. 0.90
   2 !   16.7   0.0   1.9e-05    0.0085       3      59 ..     120     173 ..     118     181 .. 0.91
   3 !   18.4   0.0     6e-06    0.0026      11      60 ..     162     208 ..     161     213 .. 0.92
   4 !   32.7   0.0     2e-10   8.5e-08       3      60 ..     222     276 ..     220     281 .. 0.93
   5 ?    6.8   0.0     0.024        11       1      27 [.     293     319 ..     293     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.1e-06
                        TPR_16  9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyr 58
                                  + g++d+A+++le a k d++ P+    l+ +g ++  +g++++A+ +++
  gi|15668437|ref|NP_247235.1| 24 DKGNFDKALEYLEKAQKVDKDNPL---VLYVKGIVLKLKGDMEKAEKYFE 70
                                  78*****************66665...*******************9885 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.9e-05
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyra 59 
                                   +a+++++ g++++A++al+++lk +   P     l  ++ ++  +g l+eA++ +++
  gi|15668437|ref|NP_247235.1| 120 KALIYIEFGEFEKALEALDEFLKIY---PNLTSILRQKASILEILGKLDEALDCVNK 173
                                   5899*********************...***********************976666 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 6e-06
                        TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                   g+ d+A+   +  l       d+a+A++l+g+++ ++g+ +eA+++++ a
  gi|15668437|ref|NP_247235.1| 162 GKLDEALDCVNKILSIK---KDDAHAWYLKGRILKKLGNIKEALDALKMA 208
                                   89999999999999999...99**********************998876 PP

  == domain 4  score: 32.7 bits;  conditional E-value: 2e-10
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                    a++ l++++y++A+++ + +l+++   P ++eA ++l++++  ++ +++A+  y++ 
  gi|15668437|ref|NP_247235.1| 222 IAYLELANNNYEEALNYITKYLEKF---PNDVEAKFYLALIYENLNKVDDALKIYDKI 276
                                   68999********************...************************999876 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.024
                        TPR_16   1 lalaraalragdyddAaaaleaalkrd 27 
                                   l++ar++ ++g+ ++A++ ++ a +++
  gi|15668437|ref|NP_247235.1| 293 LNKARILEKLGKIEEAVETYNKAFDNN 319
                                   678999999999999999999988765 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   0.00013     0.057      12      40 ..      23      51 ..      10      55 .. 0.80
   2 ?   -0.0   0.0       5.1   2.2e+03       7      25 ..      52      70 ..      48      70 .. 0.83
   3 !   11.1   0.0    0.0014      0.61       8      40 ..     121     153 ..     119     155 .. 0.86
   4 !   18.0   0.0   8.2e-06    0.0036       4      43 ..     151     190 ..     149     191 .. 0.93
   5 !   13.0   0.1   0.00032      0.14       2      30 ..     183     211 ..     182     215 .. 0.90
   6 !   22.3   0.0   3.4e-07   0.00015       3      42 ..     218     257 ..     216     259 .. 0.94
   7 ?    7.3   0.0     0.023        10       7      29 ..     256     278 ..     254     287 .. 0.88
   8 ?    6.0   0.0     0.058        26       8      28 ..     296     316 ..     293     319 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00013
                        TPR_14 12 lalGdpdeAiallrralalaPddaeawll 40
                                  +  G++d+A+++l++a + + d++ +++ 
  gi|15668437|ref|NP_247235.1| 23 ADKGNFDKALEYLEKAQKVDKDNPLVLYV 51
                                  4679********************99876 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 5.1
                        TPR_14  7 laeallalGdpdeAiallr 25
                                   + +l   Gd ++A+++++
  gi|15668437|ref|NP_247235.1| 52 KGIVLKLKGDMEKAEKYFE 70
                                  57788999********997 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0014
                        TPR_14   8 aeallalGdpdeAiallrralalaPddaeawll 40 
                                   a ++ + G++++A+++l++ l+ +P+   ++++
  gi|15668437|ref|NP_247235.1| 121 ALIYIEFGEFEKALEALDEFLKIYPNLTSILRQ 153
                                   6689999******************97776665 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 8.2e-06
                        TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                   l++ a++l+ lG++deA+++ +++l+   dda aw+l ++
  gi|15668437|ref|NP_247235.1| 151 LRQKASILEILGKLDEALDCVNKILSIKKDDAHAWYLKGR 190
                                   57789*******************************9998 PP

  == domain 5  score: 13.0 bits;  conditional E-value: 0.00032
                        TPR_14   2 eallalaeallalGdpdeAiallrralal 30 
                                    a+++ +++l  lG+ +eA+++l+ a+ l
  gi|15668437|ref|NP_247235.1| 183 HAWYLKGRILKKLGNIKEALDALKMAINL 211
                                   69**********************99865 PP

  == domain 6  score: 22.3 bits;  conditional E-value: 3.4e-07
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                   +++++a ++la+ +++eA+++  ++l+++P+d ea ++la
  gi|15668437|ref|NP_247235.1| 218 VYKDIAYLELANNNYEEALNYITKYLEKFPNDVEAKFYLA 257
                                   68899**********************************9 PP

  == domain 7  score: 7.3 bits;  conditional E-value: 0.023
                        TPR_14   7 laeallalGdpdeAiallrrala 29 
                                   la ++++l + d+A+++++++++
  gi|15668437|ref|NP_247235.1| 256 LALIYENLNKVDDALKIYDKIIS 278
                                   899****************9997 PP

  == domain 8  score: 6.0 bits;  conditional E-value: 0.058
                        TPR_14   8 aeallalGdpdeAiallrral 28 
                                   a++l+ lG+ +eA++ +++a 
  gi|15668437|ref|NP_247235.1| 296 ARILEKLGKIEEAVETYNKAF 316
                                   899***************996 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     2e-06   0.00089       3      46 ..      24      67 ..      23      75 .. 0.94
   2 !    8.8   0.0    0.0053       2.3      32      57 ..     121     146 ..      94     157 .. 0.88
   3 !   25.2   0.1     4e-08   1.7e-05       5      57 ..     162     214 ..     158     221 .. 0.93
   4 !   30.0   0.1   1.2e-09   5.4e-07       2      52 ..     227     277 ..     226     282 .. 0.95
   5 ?    6.2   0.0     0.033        14      29      51 ..     293     315 ..     290     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2e-06
                        TPR_19  3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46
                                  + g+++ Al++le+a + d +n+ +++   ++l   g+ ++Ae+
  gi|15668437|ref|NP_247235.1| 24 DKGNFDKALEYLEKAQKVDKDNPLVLYVKGIVLKLKGDMEKAEK 67
                                  579***************************************98 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0053
                        TPR_19  32 AeallalgqldeAealLdalpeedpd 57 
                                   A ++++ g++++A ++Ld+ ++ +p+
  gi|15668437|ref|NP_247235.1| 121 ALIYIEFGEFEKALEALDEFLKIYPN 146
                                   668***************99988887 PP

  == domain 3  score: 25.2 bits;  conditional E-value: 4e-08
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                   g+++eAl+   ++l+ + ++a a++l  ++l +lg+++eA ++L+ + + + +
  gi|15668437|ref|NP_247235.1| 162 GKLDEALDCVNKILSIKKDDAHAWYLKGRILKKLGNIKEALDALKMAINLNEN 214
                                   89*******************************************99887765 PP

  == domain 4  score: 30.0 bits;  conditional E-value: 1.2e-09
                        TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalp 52 
                                   la+++y+eAl++ ++ l++ p++ ea+ +LA ++ +l+ +d+A ++ d++ 
  gi|15668437|ref|NP_247235.1| 227 LANNNYEEALNYITKYLEKFPNDVEAKFYLALIYENLNKVDDALKIYDKII 277
                                   799*********************************************996 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.033
                        TPR_19  29 llLAeallalgqldeAealLdal 51 
                                   l+ A++l +lg ++eA ++ +++
  gi|15668437|ref|NP_247235.1| 293 LNKARILEKLGKIEEAVETYNKA 315
                                   5679**************98876 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.8e-06    0.0025      15      70 ..      24      71 ..      18      75 .. 0.89
   2 ?    6.7   0.0      0.02       8.6      52      76 ..     121     145 ..     118     146 .. 0.86
   3 !   24.1   0.1   7.2e-08   3.2e-05       5      76 ..     150     213 ..     147     214 .. 0.91
   4 !   18.4   1.6   4.5e-06     0.002       3      73 ..     182     244 ..     180     248 .. 0.90
   5 !   25.3   0.0   3.2e-08   1.4e-05       9      73 ..     256     317 ..     250     319 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.8e-06
                        TPR_12 15 rlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlellee 70
                                    g++d+Ale+leka  +      +d+pl   +l+  g+++ + g+ e+A++++e 
  gi|15668437|ref|NP_247235.1| 24 DKGNFDKALEYLEKAQKVD-----KDNPL---VLYVKGIVLKLKGDMEKAEKYFEC 71
                                  68*************6666.....99999...6*********************96 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.02
                        TPR_12  52 grlyralgryeeAlelleealaiae 76 
                                   + +y ++g++e+Ale+l e l+i++
  gi|15668437|ref|NP_247235.1| 121 ALIYIEFGEFEKALEALDEFLKIYP 145
                                   6789999999999999999999986 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 7.2e-08
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                   +l++ a++l  lg++deAl++ +k l i      +d    a + +  gr++ +lg+ +eAl++l+ a+++ e
  gi|15668437|ref|NP_247235.1| 150 ILRQKASILEILGKLDEALDCVNKILSIK-----KDD---AHAWYLKGRILKKLGNIKEALDALKMAINLNE 213
                                   67789************************.....664...889999*********************99866 PP

  == domain 4  score: 18.4 bits;  conditional E-value: 4.5e-06
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                   a a++  + +l +lg+  eAl+ l+ a+++      + +  ++ ++ +++ l +a ++yeeAl++ ++ l+
  gi|15668437|ref|NP_247235.1| 182 AHAWYLKGRILKKLGNIKEALDALKMAINLN-----E-N--LVHVYKDIAYLELANNNYEEALNYITKYLE 244
                                   789999*********************8888.....3.3..788*********************999987 PP

  == domain 5  score: 25.3 bits;  conditional E-value: 3.2e-08
                        TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                   la+++  l + d+Al++++k +    ++  +d++l  ++  n +r++++lg+ eeA+e +++a +
  gi|15668437|ref|NP_247235.1| 256 LALIYENLNKVDDALKIYDKIISNK-NV--KDKLLIKSSILNKARILEKLGKIEEAVETYNKAFD 317
                                   9********************8888.66..9*******************************976 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.095        42      10      26 ..      23      38 ..      19      41 .. 0.80
   2 ?    1.3   0.0       1.5   6.7e+02       7      24 ..      53      70 ..      48      70 .. 0.73
   3 !   17.6   0.0   9.9e-06    0.0043       5      32 ..     119     146 ..     118     147 .. 0.91
   4 !    9.6   0.0    0.0034       1.5       2      28 ..     184     210 ..     183     212 .. 0.93
   5 !   10.6   0.1    0.0017      0.75       7      32 ..     223     248 ..     221     249 .. 0.85
   6 !   15.6   0.0   4.2e-05     0.018       1      29 [.     251     279 ..     251     279 .. 0.94
   7 !    9.4   0.0     0.004       1.8       4      26 ..     293     315 ..     290     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.095
                                  HHHHHHHHHHHHHHHHH CS
                         TPR_6 10 yrklgdtdkAlealerl 26
                                    k+ + dkAle+le+ 
  gi|15668437|ref|NP_247235.1| 23 ADKG-NFDKALEYLEKA 38
                                  4555.**********96 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.5
                                  HHHHHHHHHHHHHHHHHH CS
                         TPR_6  7 alsyrklgdtdkAleale 24
                                  +  ++  gd +kA +++e
  gi|15668437|ref|NP_247235.1| 53 GIVLKLKGDMEKAEKYFE 70
                                  55556667*******997 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 9.9e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   5 klalsyrklgdtdkAlealerlikeYPd 32 
                                   + al y++ g+ +kAleal++++k YP+
  gi|15668437|ref|NP_247235.1| 119 HKALIYIEFGEFEKALEALDEFLKIYPN 146
                                   56999***66*****************8 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0034
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                   A y+ ++ ++klg+  +Al+al+  i+
  gi|15668437|ref|NP_247235.1| 184 AWYLKGRILKKLGNIKEALDALKMAIN 210
                                   89*********9**********99987 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.0017
                                   HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                   a++ ++ +++++Al +  + ++++P+
  gi|15668437|ref|NP_247235.1| 223 AYLELANNNYEEALNYITKYLEKFPN 248
                                   66666668*****************9 PP

  == domain 6  score: 15.6 bits;  conditional E-value: 4.2e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   1 dAlyklalsyrklgdtdkAlealerlike 29 
                                   +A ++lal y++l++ d+Al++++++i++
  gi|15668437|ref|NP_247235.1| 251 EAKFYLALIYENLNKVDDALKIYDKIISN 279
                                   688*********99************986 PP

  == domain 7  score: 9.4 bits;  conditional E-value: 0.004
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   4 yklalsyrklgdtdkAlealerl 26 
                                   ++ a+ ++klg+ ++A+e++++ 
  gi|15668437|ref|NP_247235.1| 293 LNKARILEKLGKIEEAVETYNKA 315
                                   7889*****99*********997 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00037      0.16       2      34 .]      35      67 ..      34      67 .. 0.94
   2 ?   -1.3   0.0       8.9   3.9e+03      19      33 ..     120     134 ..     118     135 .. 0.74
   3 !   10.7   0.0    0.0013      0.55       3      33 ..     138     168 ..     136     169 .. 0.93
   4 !   15.7   0.0   3.3e-05     0.014       4      33 ..     173     202 ..     170     203 .. 0.91
   5 ?    6.9   1.6      0.02         9       5      33 ..     208     236 ..     204     237 .. 0.92
   6 !   19.7   0.1   1.8e-06   0.00077       3      33 ..     240     270 ..     238     271 .. 0.93
   7 ?    4.2   0.0      0.15        65      17      34 .]     293     310 ..     290     310 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00037
                        TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtArq 34
                                  ++ka + d++n+ +++ ++ +l+ +Gd ++A++
  gi|15668437|ref|NP_247235.1| 35 LEKAQKVDKDNPLVLYVKGIVLKLKGDMEKAEK 67
                                  79*************************999985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 8.9
                        TPR_17  19 LAelllknGdlmtAr 33 
                                   +A ++ + G++++A+
  gi|15668437|ref|NP_247235.1| 120 KALIYIEFGEFEKAL 134
                                   678888888888886 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0013
                        TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtAr 33 
                                    ++l+++Pn    + ++A +l+ +G+l++A+
  gi|15668437|ref|NP_247235.1| 138 DEFLKIYPNLTSILRQKASILEILGKLDEAL 168
                                   689**************************96 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 3.3e-05
                        TPR_17   4 kaleldPnnadaynnLAelllknGdlmtAr 33 
                                   k l + +++a a+++++++l+k+G+ ++A+
  gi|15668437|ref|NP_247235.1| 173 KILSIKKDDAHAWYLKGRILKKLGNIKEAL 202
                                   7788999*******************9996 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.02
                        TPR_17   5 aleldPnnadaynnLAelllknGdlmtAr 33 
                                   a+ l+ n + +y   A+l l n+++++A+
  gi|15668437|ref|NP_247235.1| 208 AINLNENLVHVYKDIAYLELANNNYEEAL 236
                                   8999***********************96 PP

  == domain 6  score: 19.7 bits;  conditional E-value: 1.8e-06
                        TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   +k le+ Pn+++a ++LA +++++++ ++A+
  gi|15668437|ref|NP_247235.1| 240 TKYLEKFPNDVEAKFYLALIYENLNKVDDAL 270
                                   799*************************997 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.15
                        TPR_17  17 nnLAelllknGdlmtArq 34 
                                    n+A++l+k+G+ ++A++
  gi|15668437|ref|NP_247235.1| 293 LNKARILEKLGKIEEAVE 310
                                   69************9975 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0013      0.57       1      55 [.      24      79 ..      24      86 .. 0.85
   2 !   19.5   0.2     2e-06   0.00086       3      81 ..      94     173 ..      92     174 .. 0.86
   3 !   12.2   0.1   0.00038      0.17      54      80 ..     180     206 ..     171     208 .. 0.85
   4 !   29.9   2.0   1.1e-09   4.7e-07       2      81 ..     229     314 ..     228     315 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                                  HTT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC- CS
                        ANAPC3  1 dqnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnsks 55
                                  d++n+++A+ ++e++++ ++++p  +y ++ +l l g+ ++A ++++ + +++++s
  gi|15668437|ref|NP_247235.1| 24 DKGNFDKALEYLEKAQKVDKDNPLVLYVKGIVLKLKGDMEKAEKYFECLeNIEGTS 79
                                  57899999999999999999999999999999999999999999988776666655 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2e-06
                                   T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   + y+  + ++e+l   ++  + + + +Al + + g++++A+e l+++ k++++   ++  +A  l  L+k++eA+++  k
  gi|15668437|ref|NP_247235.1|  94 GEYERTLKYIEKLSRLSKPCYLSPFHKALIYIEFGEFEKALEALDEFlKIYPNLTSILRQKASILEILGKLDEALDCVNK 173
                                   568888899999994444444556667*************************************************9876 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00038
                                   C-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3  54 kslgcrylfAqcllkLkkyeeAiaaLe 80 
                                    +  ++yl+++ l kL++++eA++aL+
  gi|15668437|ref|NP_247235.1| 180 DDAHAWYLKGRILKKLGNIKEALDALK 206
                                   56679********************97 PP

  == domain 4  score: 29.9 bits;  conditional E-value: 1.1e-09
                                   TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT..SHHHC-H....HHHHHHHHHHHHTT-HHHHH CS
                        ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka..klnsksl....gcrylfAqcllkLkkyeeAi 76 
                                   +nny++A+ ++ ++l++ +++ e+ ++lAl + ++++ + A+++++k   ++n k++     + + +A+ l kL+k+eeA+
  gi|15668437|ref|NP_247235.1| 229 NNNYEEALNYITKYLEKFPNDVEAKFYLALIYENLNKVDDALKIYDKIisNKNVKDKllikSSILNKARILEKLGKIEEAV 309
                                   89*********************************************944444444488867777789************* PP

                                   HHH-S CS
                        ANAPC3  77 aaLek 81 
                                    ++ k
  gi|15668437|ref|NP_247235.1| 310 ETYNK 314
                                   99876 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.15        66       9      49 ..      26      66 ..      21      71 .. 0.63
   2 !   18.5   0.0   3.9e-06    0.0017      10      61 ..      95     146 ..      91     162 .. 0.88
   3 !   26.1   0.0   1.6e-08   6.9e-06      10      59 ..     163     212 ..     153     220 .. 0.91
   4 !    9.2   0.0    0.0029       1.3       6      50 ..     227     271 ..     222     281 .. 0.90
   5 ?    1.5   0.0      0.76   3.3e+02      32      54 ..     292     314 ..     290     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.15
                         TPR_9  9 edweralavverllllaPddpeerrdRGlllaqlGclsaAl 49
                                   ++++al+++e    ++ d p  ++  G++l   G++++A 
  gi|15668437|ref|NP_247235.1| 26 GNFDKALEYLEKAQKVDKDNPLVLYVKGIVLKLKGDMEKAE 66
                                  45666666666666666666666666666666666666665 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 3.9e-06
                         TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                   ++er+l+++e l  l        +  +l++ + G +++Al++L+ +l + p+
  gi|15668437|ref|NP_247235.1|  95 EYERTLKYIEKLSRLSKPCYLSPFHKALIYIEFGEFEKALEALDEFLKIYPN 146
                                   689********************************************99994 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 1.6e-08
                         TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                   + ++al +v+ +l ++ dd++ ++  G++l +lG++++Al++L  ++ l+
  gi|15668437|ref|NP_247235.1| 163 KLDEALDCVNKILSIKKDDAHAWYLKGRILKKLGNIKEALDALKMAINLN 212
                                   5789***************************************9888665 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0029
                         TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAla 50 
                                   + ++++e+al ++   l  +P+d+e  +  +l+++ l+ +  Al+
  gi|15668437|ref|NP_247235.1| 227 LANNNYEEALNYITKYLEKFPNDVEAKFYLALIYENLNKVDDALK 271
                                   67899********************************99998886 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.76
                         TPR_9  32 rrdRGlllaqlGclsaAladLea 54 
                                   ++  +++l++lG +++A++  + 
  gi|15668437|ref|NP_247235.1| 292 ILNKARILEKLGKIEEAVETYNK 314
                                   56789************997765 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00083      0.36      10      33 ..      23      44 ..      20      47 .. 0.82
   2 ?    4.1   0.0      0.13        55      12      23 ..      59      70 ..      49      70 .. 0.87
   3 ?   -0.9   0.0         5   2.2e+03       2      24 ..      80     105 ..      79     112 .. 0.67
   4 ?    5.2   0.0     0.056        25       6      24 ..     121     139 ..     118     150 .. 0.86
   5 ?    0.9   0.0       1.4   6.1e+02       7      33 ..     156     182 ..     146     184 .. 0.73
   6 ?    4.9   0.0     0.069        30       1      28 [.     184     209 ..     184     216 .. 0.82
   7 ?    3.9   0.1      0.15        65      12      29 ..     229     244 ..     218     251 .. 0.79
   8 !    9.9   0.0    0.0018      0.79       4      24 ..     255     275 ..     254     281 .. 0.92
   9 !   12.6   0.0   0.00025      0.11       1      29 [.     291     317 ..     291     320 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00083
                         TPR_7 10 srlGdyeeAielyeqsLaltkdpe 33
                                   + G++++A+e++e+  a   d +
  gi|15668437|ref|NP_247235.1| 23 ADKGNFDKALEYLEK--AQKVDKD 44
                                  678************..8777765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.13
                         TPR_7 12 lGdyeeAielye 23
                                   Gd+e+A++++e
  gi|15668437|ref|NP_247235.1| 59 KGDMEKAEKYFE 70
                                  69********98 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 5
                         TPR_7   2 LlnLarl.ysr..lGdyeeAielyeq 24 
                                   Ll L++l +     G+ye+ +++ e+
  gi|15668437|ref|NP_247235.1|  80 LLSLGNLiCLTfvKGEYERTLKYIEK 105
                                   67777773333667888887777777 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.056
                         TPR_7   6 arlysrlGdyeeAielyeq 24 
                                   a +y + G++e+A+e + +
  gi|15668437|ref|NP_247235.1| 121 ALIYIEFGEFEKALEALDE 139
                                   789***********98765 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 1.4
                         TPR_7   7 rlysrlGdyeeAielyeqsLaltkdpe 33 
                                   ++ + lG+ +eA+++  + L + kd+ 
  gi|15668437|ref|NP_247235.1| 156 SILEILGKLDEALDCVNKILSIKKDDA 182
                                   4444499******99888888888876 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.069
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                   a++  +r+  +lG+ +eA++ ++   a+
  gi|15668437|ref|NP_247235.1| 184 AWYLKGRILKKLGNIKEALDALKM--AI 209
                                   567789*************99998..54 PP

  == domain 7  score: 3.9 bits;  conditional E-value: 0.15
                         TPR_7  12 lGdyeeAielyeqsLalt 29 
                                    ++yeeA+ + ++   l+
  gi|15668437|ref|NP_247235.1| 229 NNNYEEALNYITK--YLE 244
                                   589*******999..554 PP

  == domain 8  score: 9.9 bits;  conditional E-value: 0.0018
                         TPR_7   4 nLarlysrlGdyeeAielyeq 24 
                                   +La +y++l++ ++A+++y +
  gi|15668437|ref|NP_247235.1| 255 YLALIYENLNKVDDALKIYDK 275
                                   8******************87 PP

  == domain 9  score: 12.6 bits;  conditional E-value: 0.00025
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                   ++ln ar+ ++lG+ eeA+e y +  a++
  gi|15668437|ref|NP_247235.1| 291 SILNKARILEKLGKIEEAVETYNK--AFD 317
                                   57999*****************99..876 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1     1e-06   0.00044       3      42 .]      21      60 ..      19      60 .. 0.91
   2 ?    6.8   0.0     0.012       5.3       3      27 ..     123     147 ..     121     159 .. 0.85
   3 !   14.1   0.0   6.2e-05     0.027       7      42 .]     161     196 ..     155     196 .. 0.95
   4 !   16.0   0.1   1.6e-05    0.0069       1      31 [.     189     219 ..     189     225 .. 0.90
   5 ?    1.1   3.3      0.74   3.2e+02       5      40 ..     227     262 ..     223     264 .. 0.69
   6 !   13.0   0.1   0.00014     0.061       6      20 ..     301     315 ..     296     317 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1e-06
                        TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                  ++ ++G++++A+e ++kA k d dn+ ++y  G ++  +G
  gi|15668437|ref|NP_247235.1| 21 ECADKGNFDKALEYLEKAQKVDKDNPLVLYVKGIVLKLKG 60
                                  5789**************************9999988776 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.012
                        TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdn 27 
                                   +y e G++e+A+ea+ + lk+ P+ 
  gi|15668437|ref|NP_247235.1| 123 IYIEFGEFEKALEALDEFLKIYPNL 147
                                   89999**********9999998886 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 6.2e-05
                        TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   +Gk++eA+ + +k l ++ d+a a+y  G ++ k+G
  gi|15668437|ref|NP_247235.1| 161 LGKLDEALDCVNKILSIKKDDAHAWYLKGRILKKLG 196
                                   7*******************************9998 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 1.6e-05
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeay 31 
                                   G+++ ++G+++eA+ a+k A++l+++ + +y
  gi|15668437|ref|NP_247235.1| 189 GRILKKLGNIKEALDALKMAINLNENLVHVY 219
                                   899***********************98888 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.74
                        TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                    + ++yeeA++   k l+  P+++ea + L+l+y +
  gi|15668437|ref|NP_247235.1| 227 LANNNYEEALNYITKYLEKFPNDVEAKFYLALIYEN 262
                                   566778888776666666677888888888877765 PP

  == domain 6  score: 13.0 bits;  conditional E-value: 0.00014
                        TPR_11   6 eqGkyeeAieaYkkA 20 
                                   ++Gk+eeA+e Y+kA
  gi|15668437|ref|NP_247235.1| 301 KLGKIEEAVETYNKA 315
                                   79************9 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00057      0.25     205     249 ..      25      69 ..      16      77 .. 0.67
   2 !   15.5   0.0   1.4e-05     0.006     199     255 ..     121     177 ..     108     183 .. 0.72
   3 !   23.9   0.8   3.9e-08   1.7e-05     206     286 ..     162     242 ..     161     249 .. 0.95
   4 !   18.1   0.4   2.3e-06     0.001     194     252 ..     252     315 ..     244     318 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00057
                                   HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                         NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevm 249
                                    g+ +kAley++ka + +     + ++K+ +lk +Gd++kA +  
  gi|15668437|ref|NP_247235.1|  25 KGNFDKALEYLEKAQKVDKDNPLVLYVKGIVLKLKGDMEKAEKYF 69 
                                   345667777777777776666666777777777777777776654 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                         NARP1 199 AqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                   A  y + g+ ekAle +d+ ++  p+l+ +  +Ka il+  G l++A +++++  ++
  gi|15668437|ref|NP_247235.1| 121 ALIYIEFGEFEKALEALDEFLKIYPNLTSILRQKASILEILGKLDEALDCVNKILSI 177
                                   555667777788888888888888888888888888888888888888777765444 PP

  == domain 3  score: 23.9 bits;  conditional E-value: 3.9e-08
                                   T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHTT-HHHHHHHHTTT CS
                         NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyiNskcakymLradeveeAeetvslF 286
                                   g+ ++Al++++k ++ +      ++ K+rilk+ G++k+A ++++ a +l ++  ++    a   L ++++eeA + ++++
  gi|15668437|ref|NP_247235.1| 162 GKLDEALDCVNKILSIKKDDAHAWYLKGRILKKLGNIKEALDALKMAINLNENLVHVYKDIAYLELANNNYEEALNYITKY 242
                                   67899***********************************************************************99886 PP

  == domain 4  score: 18.1 bits;  conditional E-value: 2.3e-06
                                   HHHHHHHHHHHHT-SHHHHHHHHHHHHH-...TT-H..HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                         NARP1 194 vlyflAqhydklgsrekAleyidkaieht...ptlv..elyltKarilkhaGdlkkAaevmeea 252
                                   + ++lA  y++l++++ Al++ dk i+++   ++l+     l+Karil++ G +++A+e+ ++a
  gi|15668437|ref|NP_247235.1| 252 AKFYLALIYENLNKVDDALKIYDKIISNKnvkDKLLikSSILNKARILEKLGKIEEAVETYNKA 315
                                   579***********************98633344432245689****************99987 PP

>> DUF3808  Protein of unknown function (DUF3808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00039      0.17     247     341 ..      24     113 ..       2     133 .. 0.79
   2 !   10.7   0.0   0.00037      0.16     250     297 ..     129     176 ..     114     184 .. 0.89
   3 !    8.4   0.1    0.0018      0.77     275     333 ..     188     241 ..     182     244 .. 0.81
   4 !    9.5   0.0   0.00081      0.35     247     301 ..     228     281 ..     213     289 .. 0.84
   5 ?    5.6   0.0     0.012       5.4     272     296 ..     292     316 ..     288     320 .] 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                       DUF3808 247 lkapleeleelLlksrkrfPksalwllfearieslkgnldeAlelleeiieesqselkqvkhlclfelaltlvylheykea 327
                                    k++ +++ e L+k++k   +  l+l  ++ ++ lkg++++A +++e ++    ++++    l l +l     ++ ey++ 
  gi|15668437|ref|NP_247235.1|  24 DKGNFDKALEYLEKAQKVDKDNPLVLYVKGIVLKLKGDMEKAEKYFE-CL----ENIEGTSLLSLGNLICLTFVKGEYERT 99 
                                   4678889999999999999999*************************.76....67778888999999999999******* PP

                       DUF3808 328 aesfleLlklskwS 341
                                   ++++++L++lsk +
  gi|15668437|ref|NP_247235.1| 100 LKYIEKLSRLSKPC 113
                                   *****999888755 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00037
                       DUF3808 250 pleeleelLlksrkrfPksalwllfearieslkgnldeAlelleeiie 297
                                   + e++ e+L +++k +P+   +l ++a i+++ g+ldeAl+ +++i++
  gi|15668437|ref|NP_247235.1| 129 EFEKALEALDEFLKIYPNLTSILRQKASILEILGKLDEALDCVNKILS 176
                                   5688999*************************************9984 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0018
                       DUF3808 275 earieslkgnldeAlelleeiieesqselkqvkhlclfelaltlvylheykeaaesfle 333
                                   ++ri+   gn++eAl++l+++i     +l +    ++ ++a   + + +y+ea++++++
  gi|15668437|ref|NP_247235.1| 188 KGRILKKLGNIKEALDALKMAI-----NLNENLVHVYKDIAYLELANNNYEEALNYITK 241
                                   89*****************988.....3444445567888889999999****999986 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00081
                       DUF3808 247 lkapleeleelLlksrkrfPksalwllfearieslkgnldeAlelleeiieesqs 301
                                    + + ee+ + + k++++fP+ +   ++ a i++   ++d+Al+++++ii ++++
  gi|15668437|ref|NP_247235.1| 228 ANNNYEEALNYITKYLEKFPNDVEAKFYLALIYENLNKVDDALKIYDKII-SNKN 281
                                   45688999999**************************************9.5544 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.012
                       DUF3808 272 llfearieslkgnldeAlelleeii 296
                                   +l++ari++  g+++eA+e++++++
  gi|15668437|ref|NP_247235.1| 292 ILNKARILEKLGKIEEAVETYNKAF 316
                                   589*******************987 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.075        33      10      25 ..      22      37 ..      22      41 .. 0.86
   2 ?    5.4   0.2     0.056        24      13      26 ..      59      72 ..      55      75 .. 0.87
   3 ?    3.3   0.1      0.28   1.2e+02      10      27 ..     124     141 ..     123     143 .. 0.84
   4 ?    3.1   0.0       0.3   1.3e+02      13      27 ..     161     175 ..     156     178 .. 0.86
   5 ?    2.0   0.0       0.7   3.1e+02      10      25 ..     192     207 ..     190     212 .. 0.82
   6 ?    4.9   0.0      0.08        35      12      29 ..     262     279 ..     259     281 .. 0.84
   7 ?    5.1   0.0     0.071        31      11      25 ..     300     314 ..     297     320 .] 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.075
                           PPR 10 ycknGkleeAlelfke 25
                                  ++ +G++++Ale++++
  gi|15668437|ref|NP_247235.1| 22 CADKGNFDKALEYLEK 37
                                  6789*********998 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.056
                           PPR 13 nGkleeAlelfkeM 26
                                  +G++e+A+++f+ +
  gi|15668437|ref|NP_247235.1| 59 KGDMEKAEKYFECL 72
                                  79*********976 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.28
                           PPR  10 ycknGkleeAlelfkeMk 27 
                                   y   G++e+Ale ++e +
  gi|15668437|ref|NP_247235.1| 124 YIEFGEFEKALEALDEFL 141
                                   6678*********99965 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.3
                           PPR  13 nGkleeAlelfkeMk 27 
                                    Gkl+eAl++ ++++
  gi|15668437|ref|NP_247235.1| 161 LGKLDEALDCVNKIL 175
                                   69*******999876 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.7
                           PPR  10 ycknGkleeAlelfke 25 
                                   + k G+++eAl+ +k 
  gi|15668437|ref|NP_247235.1| 192 LKKLGNIKEALDALKM 207
                                   5699*******98875 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.08
                           PPR  12 knGkleeAlelfkeMkek 29 
                                     +k+++Al+++++++++
  gi|15668437|ref|NP_247235.1| 262 NLNKVDDALKIYDKIISN 279
                                   6789**********9886 PP

  == domain 7  score: 5.1 bits;  conditional E-value: 0.071
                           PPR  11 cknGkleeAlelfke 25 
                                    k Gk+eeA+e +++
  gi|15668437|ref|NP_247235.1| 300 EKLGKIEEAVETYNK 314
                                   599********9997 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.12        54     174     196 ..      25      47 ..      15      76 .. 0.67
   2 !   14.8   0.1   3.3e-05     0.014      78     186 ..     146     241 ..     121     246 .. 0.78
   3 !    8.3   0.0    0.0031       1.3      40     107 ..     250     316 ..     243     318 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.12
                      TPR_MalT 174 qGdleeAetllekaeelaresnf 196
                                   +G+ ++A+++leka+++ + ++ 
  gi|15668437|ref|NP_247235.1|  25 KGNFDKALEYLEKAQKVDKDNPL 47 
                                   68888888888888887666554 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.3e-05
                      TPR_MalT  78 vallallqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlepe 158
                                   +    l+q a il   G+L+eAl+  +++l  +++ + +      ++  l +++l   ++ +eA ++l+ +i l e l   
  gi|15668437|ref|NP_247235.1| 146 NLTSILRQKASILEILGKLDEALDCVNKILS-IKKDDAH-----AWY--LKGRILKKLGNIKEALDALKMAINLNENL--- 215
                                   33345668889*******************9.4444444.....455..4567777777889************9999... PP

                      TPR_MalT 159 aaldayvllarialaqGdleeAetllek 186
                                     ++ y  +a + la ++ eeA++++ k
  gi|15668437|ref|NP_247235.1| 216 --VHVYKDIAYLELANNNYEEALNYITK 241
                                   ..9********************99977 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0031
                      TPR_MalT  40 iaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqal 107
                                   + a + l+ ++   +++++Al+ + ++++     d+l     ++l  a il + G+ +eA+ety++a+
  gi|15668437|ref|NP_247235.1| 250 VEAKFYLALIYENLNKVDDALKIYDKIISNKNVKDKLL-IKSSILNKARILEKLGKIEEAVETYNKAF 316
                                   66778888888888888888888888887776666666.6678999999***************9997 PP

>> ATP13  Mitochondrial ATPase expression
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.031        13      50      83 ..       6      41 ..       2      49 .. 0.81
   2 ?   -2.4   0.0       9.6   4.2e+03      66      82 ..      92     108 ..      85     109 .. 0.81
   3 !    9.4   0.0    0.0021      0.91      63      87 ..     123     147 ..     115     161 .. 0.84
   4 ?   -1.7   0.0       5.8   2.6e+03      61      82 ..     155     176 ..     147     188 .. 0.75
   5 ?   -1.3   0.0       4.2   1.9e+03      55      55 ..     190     190 ..     156     227 .. 0.52
   6 !    9.1   0.2    0.0026       1.1      66      99 ..     228     260 ..     215     263 .. 0.88
   7 ?    3.5   0.1      0.14        61      74     107 ..     263     296 ..     256     303 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.031
                         ATP13 50 lyPtselLkaivssfsynn..eiesAlklvdkfskk 83
                                  ++ t e+Lk +v+++   +  ++++Al++++k +k+
  gi|15668437|ref|NP_247235.1|  6 MVKTLEILKDVVNALECADkgNFDKALEYLEKAQKV 41
                                  666899********9554447**********98875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9.6
                         ATP13  66 ynneiesAlklvdkfsk 82 
                                   +++e+e+ lk+++k+s+
  gi|15668437|ref|NP_247235.1|  92 VKGEYERTLKYIEKLSR 108
                                   46789999999999875 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0021
                         ATP13  63 sfsynneiesAlklvdkfskkYpei 87 
                                   +++  +e+e+Al+ +d+f k+Yp++
  gi|15668437|ref|NP_247235.1| 123 IYIEFGEFEKALEALDEFLKIYPNL 147
                                   566778*****************83 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 5.8
                         ATP13  61 vssfsynneiesAlklvdkfsk 82 
                                   +s++   +++++Al+ v+k+ +
  gi|15668437|ref|NP_247235.1| 155 ASILEILGKLDEALDCVNKILS 176
                                   5666667788999999999876 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 4.2
                         ATP13  55 e 55 
                                   +
  gi|15668437|ref|NP_247235.1| 190 R 190
                                   2 PP

  == domain 6  score: 9.1 bits;  conditional E-value: 0.0026
                         ATP13  66 ynneiesAlklvdkfskkYpeielkkefWeelle 99 
                                   +nn++e+Al++++k  +k+p ++++ +f+  l++
  gi|15668437|ref|NP_247235.1| 228 ANNNYEEALNYITKYLEKFP-NDVEAKFYLALIY 260
                                   799*****************.999****999875 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.14
                         ATP13  74 lklvdkfskkYpeielkkefWeellewaiiltsk 107
                                   l+ vd+  k+Y++i  +k++ ++ll  + il++ 
  gi|15668437|ref|NP_247235.1| 263 LNKVDDALKIYDKIISNKNVKDKLLIKSSILNKA 296
                                   5567777777777777777777777777777654 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.016       7.1     228     269 ..      26      67 ..      15      70 .. 0.87
   2 ?   -0.1   0.0         1   4.4e+02      19      48 ..     125     142 ..     105     166 .. 0.58
   3 !   20.1   0.7     7e-07    0.0003     153     270 ..     155     272 ..     148     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.016
                        TPR_15 228 grpkkALeylrkqakenrkdplwllaYADaleqagradeAwr 269
                                   g+ +kALeyl+k  k  +++pl+l     +l+ +g+ ++A++
  gi|15668437|ref|NP_247235.1|  26 GNFDKALEYLEKAQKVDKDNPLVLYVKGIVLKLKGDMEKAEK 67 
                                   56689*******9999******99988888888888888876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                        TPR_15  19 ykqgdvkkAlevLkeaaqkaapskdteyWr 48 
                                    + g+++kAle+L+e            +++
  gi|15668437|ref|NP_247235.1| 125 IEFGEFEKALEALDE------------FLK 142
                                   444555555555543............333 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 7e-07
                        TPR_15 153 aelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgpla.aAlllLgrp.. 230
                                   a++ +  g+ d+Al ++ + l+ + d  ++ a +l   i l++  +++e+l a+k + + +++L  ++   A+l L ++  
  gi|15668437|ref|NP_247235.1| 155 ASILEILGKLDEALDCVNKILSIKKD--DAHAWYLKGRI-LKKLGNIKEALDALKMAINLNENLVHVYKdIAYLELANNny 232
                                   56666678999999999999999999..66677777777.77777899*******************96468999976422 PP

                        TPR_15 231 kkALeylrkqakenrkdplwllaYADaleqagradeAwrl 270
                                   ++AL+y+ k++++ ++d+  ++  A + e   ++d A ++
  gi|15668437|ref|NP_247235.1| 233 EEALNYITKYLEKFPNDVEAKFYLALIYENLNKVDDALKI 272
                                   89**********************************9987 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.058        25      14      28 ..      24      38 ..      19      38 .. 0.91
   2 ?   -0.7   0.0       3.4   1.5e+03       9      26 ..      53      70 ..      53      70 .. 0.87
   3 ?    1.8   0.0      0.53   2.3e+02       9      32 ..     121     144 ..     120     144 .. 0.85
   4 ?   -0.2   0.0       2.4     1e+03      12      30 ..     158     176 ..     149     180 .. 0.73
   5 ?    5.3   0.0     0.042        18       9      36 ..     189     216 ..     189     221 .. 0.91
   6 ?    1.6   0.3      0.64   2.8e+02       9      24 ..     223     238 ..     218     241 .. 0.80
   7 !    8.1   0.0    0.0058       2.5       8      29 ..     256     277 ..     255     278 .. 0.92
   8 ?    2.5   0.0      0.33   1.4e+02       7      23 ..     294     310 ..     290     319 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.058
                        TPR_10 14 qrgrydeAealleea 28
                                  + g++d+A+++le+a
  gi|15668437|ref|NP_247235.1| 24 DKGNFDKALEYLEKA 38
                                  679**********98 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.4
                        TPR_10  9 analrqrgrydeAealle 26
                                  +++l   g+ ++Ae+++e
  gi|15668437|ref|NP_247235.1| 53 GIVLKLKGDMEKAEKYFE 70
                                  6788888999******97 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.53
                        TPR_10   9 analrqrgrydeAealleealair 32 
                                   a ++ + g++++A++ l+e l i+
  gi|15668437|ref|NP_247235.1| 121 ALIYIEFGEFEKALEALDEFLKIY 144
                                   6789999********999877665 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.4
                        TPR_10  12 lrqrgrydeAealleeala 30 
                                   l  +g++deA++   + l+
  gi|15668437|ref|NP_247235.1| 158 LEILGKLDEALDCVNKILS 176
                                   5568999**9987666655 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.042
                        TPR_10   9 analrqrgrydeAealleealairrrll 36 
                                   +++l ++g+ +eA++ l+ a+++ + l+
  gi|15668437|ref|NP_247235.1| 189 GRILKKLGNIKEALDALKMAINLNENLV 216
                                   7899*****************9988765 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 0.64
                        TPR_10   9 analrqrgrydeAeal 24 
                                   a +  + ++y+eA+++
  gi|15668437|ref|NP_247235.1| 223 AYLELANNNYEEALNY 238
                                   555678899****998 PP

  == domain 7  score: 8.1 bits;  conditional E-value: 0.0058
                        TPR_10   8 LanalrqrgrydeAealleeal 29 
                                   La ++ ++++ d+A++++++ +
  gi|15668437|ref|NP_247235.1| 256 LALIYENLNKVDDALKIYDKII 277
                                   9*****************9976 PP

  == domain 8  score: 2.5 bits;  conditional E-value: 0.33
                        TPR_10   7 NLanalrqrgrydeAea 23 
                                   N a++l ++g+ +eA++
  gi|15668437|ref|NP_247235.1| 294 NKARILEKLGKIEEAVE 310
                                   66777777777777765 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.4   1.1e+03      79     123 ..      29      69 ..       5      76 .. 0.60
   2 ?    0.9   0.0         1   4.4e+02      65      85 ..     124     144 ..     118     158 .. 0.81
   3 !    8.8   0.0    0.0035       1.5      67     129 ..     153     211 ..     142     217 .. 0.83
   4 ?   -2.3   0.0       9.3   4.1e+03      69      83 ..     230     244 ..     214     259 .. 0.63
   5 !   15.2   0.1     4e-05     0.017      65     127 ..     253     316 ..     232     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.4
                                   HHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                       DUF3856  79 dkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkaf 123
                                   dkal+y+++  ++++d+      +++ ++  l+  G  ++a k+f
  gi|15668437|ref|NP_247235.1|  29 DKALEYLEKAQKVDKDNP----LVLYVKGIVLKLKGDMEKAEKYF 69 
                                   456666666666665553....24455555555555555555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1
                                   HHHTT-HHHHHHHHHHHHHHH CS
                       DUF3856  65 laklgrydealesadkalryf 85 
                                   ++++g++++ale+ d+ l+ +
  gi|15668437|ref|NP_247235.1| 124 YIEFGEFEKALEALDEFLKIY 144
                                   6889**********9999754 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0035
                                   HTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                       DUF3856  67 klgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                   +  +  e l   d+al   n+   +++d+ + W    + +++ l++lG+ +eal+a++ma ++
  gi|15668437|ref|NP_247235.1| 153 QKASILEILGKLDEALDCVNKILSIKKDDAHAW----YLKGRILKKLGNIKEALDALKMAINL 211
                                   5555567788889999999999999****9999....689*******************9875 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 9.3
                                   T-HHHHHHHHHHHHH CS
                       DUF3856  69 grydealesadkalr 83 
                                    +y+eal+ + k l+
  gi|15668437|ref|NP_247235.1| 230 NNYEEALNYITKYLE 244
                                   346666665555555 PP

  == domain 5  score: 15.2 bits;  conditional E-value: 4e-05
                                   HHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHH.HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                       DUF3856  65 laklgrydealesadkalryfnrrGeleqdeGklWia.avfsravaleelGrkdealkafrmag 127
                                      l    e l+ +d al+ +++    ++ + kl i+  ++++a+ le+lG+ +ea++++++a 
  gi|15668437|ref|NP_247235.1| 253 KFYLALIYENLNKVDDALKIYDKIISNKNVKDKLLIKsSILNKARILEKLGKIEEAVETYNKAF 316
                                   555666678999***********99999999999996379********************9985 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0056       2.4     124     171 ..      23      70 ..      17      86 .. 0.81
   2 !   10.9   0.0   0.00061      0.27      83     176 ..     121     212 ..     114     222 .. 0.86
   3 ?    5.0   0.4      0.04        18      86     174 ..     226     317 ..     212     319 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0056
                        TPR_21 124 laekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqa 171
                                   ++++++d+Al+ Le++++ ++ + lv  ++G +l  +g++++A + Y +
  gi|15668437|ref|NP_247235.1|  23 ADKGNFDKALEYLEKAQKvDKDNPLVLYVKGIVLKLKGDMEKAEK-YFE 70 
                                   6899*********766552677899******************76.444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00061
                        TPR_21  83 AkaaveagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkl 162
                                   A   +e g++++A ++L++ l+     +l+++ r + a++l   +k+deAl  +++  + ++ +a++  l+G il + g++
  gi|15668437|ref|NP_247235.1| 121 ALIYIEFGEFEKALEALDEFLKIY--PNLTSILRQK-ASILEILGKLDEALDCVNKILSiKKDDAHAWYLKGRILKKLGNI 198
                                   556678899999999999999887..6789999988.999999***********998763667888999************ PP

                        TPR_21 163 deAraaYqaAlaal 176
                                   +eA +a + A++ +
  gi|15668437|ref|NP_247235.1| 199 KEALDALKMAINLN 212
                                   ********999865 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.04
                        TPR_21  86 aveagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLeakkeeafaalvael......rGDilvaqg 160
                                   + +++++++A + +++ lek +++     a+  La ++ + +k+d+Alk  ++  +++       +      +  il + g
  gi|15668437|ref|NP_247235.1| 226 ELANNNYEEALNYITKYLEKFPND---VEAKFYLALIYENLNKVDDALKIYDKIISNKNVKDKLLIkssilnKARILEKLG 303
                                   445566666666666666666665...336666777777777777777766444333333222222000011455677788 PP

                        TPR_21 161 kldeAraaYqaAla 174
                                   k++eA + Y++A++
  gi|15668437|ref|NP_247235.1| 304 KIEEAVETYNKAFD 317
                                   88888888888877 PP

>> Cohesin_load  Cohesin loading factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   1.6e-07   7.2e-05     370     488 ..      22     125 ..       3     178 .. 0.66
   2 ?    2.9   5.5     0.067        29     111     203 ..     227     311 ..     141     319 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.6e-07
                  Cohesin_load 370 afvlknwkkankeleeletasnkleskllkelaplllyLeglyaqskgdlkaAlaqyketaarkskerelyilsllNlviI 450
                                   ++  +n++ka + le   +a++      +++  pl+ly++g+    kgd+++A++++       ++   + +lsl Nl+++
  gi|15668437|ref|NP_247235.1|  22 CADKGNFDKALEYLE---KAQK------VDKDNPLVLYVKGIVLKLKGDMEKAEKYFE----CLENIEGTSLLSLGNLICL 89 
                                   455555544444444...4443......45567************************6....5666777899********9 PP

                  Cohesin_load 451 lesevseddkelnkllsqleplcsnspnknislanall 488
                                   +  +++     + k +++l +l++ +  + +  a  ++
  gi|15668437|ref|NP_247235.1|  90 TFVKGEYER--TLKYIEKLSRLSKPCYLSPFHKALIYI 125
                                   985555333..666666666666666666666665555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.067
                  Cohesin_load 111 lektnpkaAlksldeliedaetyqhnewvylfrllriqlslqtdkdnsaalenlqslaelanrkgdkklfvvlslleallh 191
                                   l ++n+  Al+++++ +e++ +  + e    + l+   ++  +  +   al++++++++ +n  +dk l+    l +a+++
  gi|15668437|ref|NP_247235.1| 227 LANNNYEEALNYITKYLEKFPN--DVEAKFYLALI---YENLN--KVDDALKIYDKIISNKN-VKDKLLIKSSILNKARIL 299
                                   4444555566666666666655..22222222233...22222..44555566666655555.444444444444445555 PP

                  Cohesin_load 192 lrrgspkdvlev 203
                                   ++ g+ +++ e+
  gi|15668437|ref|NP_247235.1| 300 EKLGKIEEAVET 311
                                   555555555544 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       4.4   1.9e+03       4      23 ..      18      37 ..      16      43 .. 0.81
   2 ?    6.8   0.0     0.016       6.9      43      70 ..     116     143 ..      66     146 .. 0.90
   3 ?    2.4   0.0      0.38   1.7e+02      52      70 ..     193     211 ..     182     228 .. 0.85
   4 !   10.2   0.2    0.0014       0.6      17      67 ..     265     315 ..     217     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.4
                        ANAPC5  4 sylnalrakdYqqaldsLhr 23
                                  + l++  + ++++al++L +
  gi|15668437|ref|NP_247235.1| 18 NALECADKGNFDKALEYLEK 37
                                  66788889999999999965 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                        ANAPC5  43 alLnlaslhadfghneeAvkaleeairl 70 
                                   + ++ a +  +fg+ e+A++al e  ++
  gi|15668437|ref|NP_247235.1| 116 SPFHKALIYIEFGEFEKALEALDEFLKI 143
                                   678999*****************98776 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.38
                        ANAPC5  52 adfghneeAvkaleeairl 70 
                                    ++g+ +eA++al+ ai+l
  gi|15668437|ref|NP_247235.1| 193 KKLGNIKEALDALKMAINL 211
                                   67999************97 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.0014
                        ANAPC5  17 aldsLhryFDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleea 67 
                                    +d+  +++D ++s+++ ++k   ++++Ln a++  ++g+ eeAv++ + a
  gi|15668437|ref|NP_247235.1| 265 KVDDALKIYDKIISNKNVKDKLLIKSSILNKARILEKLGKIEEAVETYNKA 315
                                   345555677777777777779999*********************987665 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.33   1.5e+02      15      34 ..      26      45 ..      19      48 .. 0.85
   2 ?    1.0   0.0         1   4.4e+02      15      27 ..      94     106 ..      92     110 .. 0.90
   3 !    8.1   0.0    0.0063       2.7      12      33 ..     125     146 ..     118     156 .. 0.85
   4 ?    4.7   0.0     0.072        32      14      47 ..     161     194 ..     161     202 .. 0.90
   5 !    8.0   0.6     0.007       3.1      15      44 ..     230     259 ..     222     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.33
                                  T-HHHHHHHHHHHHHHTTS- CS
                    Fis1_TPR_C 15 geYseArryvdalLeiEPen 34
                                  g++++A++y++   +++ +n
  gi|15668437|ref|NP_247235.1| 26 GNFDKALEYLEKAQKVDKDN 45
                                  8**********998888777 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1
                                   T-HHHHHHHHHHH CS
                    Fis1_TPR_C  15 geYseArryvdal 27 
                                   geY++ ++y++ l
  gi|15668437|ref|NP_247235.1|  94 GEYERTLKYIEKL 106
                                   8*********987 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0063
                                   HHHT-HHHHHHHHHHHHHHTTS CS
                    Fis1_TPR_C  12 yklgeYseArryvdalLeiEPe 33 
                                   +  ge+++A++ +d +L+i P+
  gi|15668437|ref|NP_247235.1| 125 IEFGEFEKALEALDEFLKIYPN 146
                                   5679***************998 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.072
                                   HT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHH CS
                    Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaqsLkeliedk 47 
                                   lg+ +eA+ +v+ +L+i  +   a  Lk  i +k
  gi|15668437|ref|NP_247235.1| 161 LGKLDEALDCVNKILSIKKDDAHAWYLKGRILKK 194
                                   68999**************999999999998877 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.007
                                   T-HHHHHHHHHHHHHHTTS-HHHHHHHHHH CS
                    Fis1_TPR_C  15 geYseArryvdalLeiEPenrQaqsLkeli 44 
                                    +Y+eA++y+   Le+ P+   a+   +li
  gi|15668437|ref|NP_247235.1| 230 NNYEEALNYITKYLEKFPNDVEAKFYLALI 259
                                   79****************998887655555 PP

>> PknG_TPR  Protein kinase G tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.014       6.2     106     158 ..      24      75 ..       4     143 .. 0.67
   2 ?    1.0   0.0      0.33   1.4e+02     108     218 ..      94     205 ..      81     207 .. 0.71
   3 !   14.4   0.0   2.6e-05     0.011     102     218 ..     190     312 ..     147     317 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.014
                                   HCT-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHS CS
                      PknG_TPR 106 dlGdveearelLdeleeeveedWrldWyrglaeLlegdyeeAaaeFdevlaal 158
                                   d G+ ++a e+L++ ++  +++  + + +g+   l+gd+e+A + F+ + + +
  gi|15668437|ref|NP_247235.1|  24 DKGNFDKALEYLEKAQKVDKDNPLVLYVKGIVLKLKGDMEKAEKYFECLEN-I 75 
                                   78999**********99999999999999*****************97654.3 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.33
                                   T-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT---TT.-HHHHH CS
                      PknG_TPR 108 GdveearelLdeleeeveedWrldWyrglaeLlegdyeeAaaeFdevlaalpGEiaPklaLAataElagetdee.kyYrtV 187
                                   G+ e+  +++++l++ ++  +   ++++l  +  g++e+A ++ de l++ p  ++     A   E+ g+ de+ +  + +
  gi|15668437|ref|NP_247235.1|  94 GEYERTLKYIEKLSRLSKPCYLSPFHKALIYIEFGEFEKALEALDEFLKIYPNLTSILRQKASILEILGKLDEAlDCVNKI 174
                                   677777777777777777777777788888888888888888888888888876666666677777777666543666677 PP

                                   HHH-TT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                      PknG_TPR 188 wrtdrgvvsAaFGlaRqlaaagdraaAvaaL 218
                                    +  +    A +   R l + g+ ++A++aL
  gi|15668437|ref|NP_247235.1| 175 LSIKKDDAHAWYLKGRILKKLGNIKEALDAL 205
                                   7777777777777777777777777777766 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 2.6e-05
                                   HHHHHCT-HHHHHHHHHHHHHHH---HHHHHHHHHH..HHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT---T CS
                      PknG_TPR 102 rahldlGdveearelLdeleeeveedWrldWyrgla..eLlegdyeeAaaeFdevlaalpGEiaPklaLAataElagetde 180
                                   r+   lG+ +ea + L+   + +  +  ++ y+ +a  eL++++yeeA +  ++ l+ +p ++  k+ LA   E  ++ d+
  gi|15668437|ref|NP_247235.1| 190 RILKKLGNIKEALDALKMAINLN--ENLVHVYKDIAylELANNNYEEALNYITKYLEKFPNDVEAKFYLALIYENLNKVDD 268
                                   66667788877777776654433..34567787777447899********************************9988775 PP

                                   T.-HHHHHHHH-TT....-H.HHHHHHHHHHHHTT-HHHHHHHH CS
                      PknG_TPR 181 e.kyYrtVwrtdrg....vv.sAaFGlaRqlaaagdraaAvaaL 218
                                   + k Y+ + ++ +     ++ s     aR l + g+ ++Av++ 
  gi|15668437|ref|NP_247235.1| 269 AlKIYDKIISNKNVkdklLIkSSILNKARILEKLGKIEEAVETY 312
                                   44999999886442122233488899999999999999999976 PP

>> Leptin  Leptin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.3   1.4e+03      53      79 ..       6      32 ..       2      56 .. 0.59
   2 ?    2.1   0.0      0.33   1.5e+02      50      81 ..     134     166 ..      99     212 .. 0.60
   3 ?    0.9   0.1       0.8   3.5e+02      47      67 ..     158     178 ..     147     240 .. 0.70
   4 !   16.6   0.1   1.2e-05     0.005      47      91 ..     260     304 ..     256     315 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.3
                                  HHHHHHHHHHHHHTS--HHHHHHHHHH CS
                        Leptin 53 mdqtLavyqqilsslpseevvqisnDl 79
                                  m +tL++ + ++ +l   +     + l
  gi|15668437|ref|NP_247235.1|  6 MVKTLEILKDVVNALECADKGNFDKAL 32
                                  445555555555555554444433333 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.33
                                   HHHHHHHHHHHHHHHHTS--.HHHHHHHHHHHH CS
                        Leptin  50 lskmdqtLavyqqilsslps.eevvqisnDlen 81 
                                   l  +d+ L++y ++ s l     +  i+  l+ 
  gi|15668437|ref|NP_247235.1| 134 LEALDEFLKIYPNLTSILRQkASILEILGKLDE 166
                                   555566666666555555442233344444432 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.8
                                   -SSHHHHHHHHHHHHHHHHTS CS
                        Leptin  47 leslskmdqtLavyqqilssl 67 
                                   le l+k+d+ L+  ++ils  
  gi|15668437|ref|NP_247235.1| 158 LEILGKLDEALDCVNKILSIK 178
                                   567888999999988888743 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 1.2e-05
                                   -SSHHHHHHHHHHHHHHHHTS--HHHHHHHHHHHHHHHHHHHHHH CS
                        Leptin  47 leslskmdqtLavyqqilsslpseevvqisnDlenLrallkllat 91 
                                   +e+l k+d+ L++y++i+s+  +++   i   + n   +l+ l+ 
  gi|15668437|ref|NP_247235.1| 260 YENLNKVDDALKIYDKIISNKNVKDKLLIKSSILNKARILEKLGK 304
                                   689********************************9999999876 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.017       7.5     157     281 ..      22     150 ..      19     166 .. 0.73
   2 !   12.5   0.5   0.00014     0.063     142     278 ..     177     315 ..     160     319 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.017
                                   HCHHHHCCSTTHHCCCCCHCTT.....TT.TSSCCCHHHHHHHCCHHHHHSSCC..........HHHHCCTSSCCCSS-SS CS
                           FAT 157 arksgrlslAekaLkelleedpeewlprappevvyaylKylwssgeqkealqkL..........reftsellekkeelqsg 227
                                   + ++g+++ A + L +++++d++++l+  +      +lK+  + ++ ++++++L            ++ +l+  k+e+   
  gi|15668437|ref|NP_247235.1|  22 CADKGNFDKALEYLEKAQKVDKDNPLVLYVKG---IVLKLKGDMEKAEKYFECLeniegtsllsLGNLICLTFVKGEYERT 99 
                                   77899*****************8888733333...4577777777778888888665655555555555555555577777 PP

                                   ---..................HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHC CS
                           FAT 228 leaq......keptnleeftkllarcylkkGewqealqkldwseekieeilqsysaatei 281
                                   l+++      ++p  l+ f+k l  +y + Ge+ +al+         +e l+ y   t+i
  gi|15668437|ref|NP_247235.1| 100 LKYIeklsrlSKPCYLSPFHKAL--IYIEFGEFEKALEA-------LDEFLKIYPNLTSI 150
                                   77667788778888888888888..99999999999888.......67777777666666 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                                   CCS-STTCCCCCCCCHCHHHHCCSTTHHCCCCCHCTT.....TT.TSSCCCHHHHHHHCCHHHHHSSCCHHHHCCTSSCCC CS
                           FAT 142 lkgvkaemwlkfanlarksgrlslAekaLkelleedpeewlprappevvyaylKylwssgeqkealqkLreftsellekke 222
                                   +k+ +a++w    ++  k g+++ A +aLk+++  ++   l+    +v+   + +++++++ +eal+ + + +++  +++e
  gi|15668437|ref|NP_247235.1| 177 IKKDDAHAWYLKGRILKKLGNIKEALDALKMAINLNE--NLV----HVYKDIAYLELANNNYEEALNYITKYLEKFPNDVE 251
                                   677799****99********************99999..444....5566666689******************9999998 PP

                                   ..........SS-SS---.......................HH.HHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCC CS
                           FAT 223 ..........elqsgleaq...........keptnleeftkll.arcylkkGewqealqkldwseekieeilqsysaa 278
                                             +                   k  +n++ + kll     l k+  +e+l+k       iee+++ y +a
  gi|15668437|ref|NP_247235.1| 252 akfylaliyeN-------LnkvddalkiydKIISNKNVKDKLLiKSSILNKARILEKLGK-------IEEAVETYNKA 315
                                   87777776642.......02233446888878899999999999999*************.......55555555544 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       9.4   4.1e+03      29      52 ..      19      42 ..      16      46 .. 0.66
   2 ?    5.4   0.0     0.051        22      28      56 ..     120     148 ..     116     176 .. 0.69
   3 ?    0.0   0.1       2.5   1.1e+03      17      50 ..     177     210 ..     163     216 .. 0.75
   4 ?    4.6   0.2     0.095        41       7      50 ..     201     244 ..     198     245 .. 0.85
   5 !   11.5   0.1   0.00066      0.29      14      81 ..     242     312 ..     237     318 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 9.4
                        TPR_20 29 AlallaagryeeAleqLleilkrd 52
                                  Al  + +g+ ++Ale L +  k d
  gi|15668437|ref|NP_247235.1| 19 ALECADKGNFDKALEYLEKAQKVD 42
                                  556667778888887775555544 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.051
                        TPR_20  28 lAlallaagryeeAleqLleilkrdrkwe 56 
                                    Al +++ g+ e+Ale+L e+lk   + +
  gi|15668437|ref|NP_247235.1| 120 KALIYIEFGEFEKALEALDEFLKIYPNLT 148
                                   58999999**************9888773 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 2.5
                        TPR_20  17 anpddldarldlAlallaagryeeAleqLleilk 50 
                                    ++dd  a +   + l + g+ +eAl++L + + 
  gi|15668437|ref|NP_247235.1| 177 IKKDDAHAWYLKGRILKKLGNIKEALDALKMAIN 210
                                   5677788888888888888999999999877665 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.095
                        TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                    l++l+ a++ n + +    d A + la+++yeeAl+ + + l+
  gi|15668437|ref|NP_247235.1| 201 ALDALKMAINLNENLVHVYKDIAYLELANNNYEEALNYITKYLE 244
                                   577888888888888899999***************98877765 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00066
                        TPR_20  14 alaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllk...ifealgsqdplvaky 81 
                                    l++ p+d++a++ lAl +   +++++Al+   +i++++   ++  ++  +l    i+e lg+ +++v++y
  gi|15668437|ref|NP_247235.1| 242 YLEKFPNDVEAKFYLALIYENLNKVDDALKIYDKIISNKNVKDKLLIKSSILNkarILEKLGKIEEAVETY 312
                                   57889************************988888887777777778888774333777777777777766 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.61   2.7e+02      88     154 ..      27      86 ..      22      94 .. 0.54
   2 ?    2.1   0.0      0.33   1.4e+02      42      63 ..     120     141 ..     118     161 .. 0.81
   3 ?    6.1   1.3     0.018       8.1      30      99 ..     176     242 ..     146     259 .. 0.68
   4 !   13.1   0.8   0.00014     0.059       6      64 ..     260     317 ..     256     320 .] 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.61
                                   -HHHHHHHHHHHHCSSS---.HHHHHHHHHH.HHHHHHHTT-HHHHHHHHCTS-GGGT.TTT--HHHH CS
                          RPN7  88 dwdlvskylekakellekggdwerknrlkvy.eGlallairkfkeAaellldilstftskellsyedl 154
                                   ++       +ka e+lek+++++  n l  y +G+ l   +++++A + + ++l+ ++ + lls  +l
  gi|15668437|ref|NP_247235.1|  27 NF-------DKALEYLEKAQKVDKDNPLVLYvKGIVLKLKGDMEKAEKYF-ECLENIEGTSLLSLGNL 86 
                                   34.......45555555555555555544433666666666666665554.44445545555555555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.33
                                   HHHHHHHCT-HHHHHHHHHTCC CS
                          RPN7  42 laehYlkigdleeAlkaysrir 63 
                                   +a  Y++ g++e+Al+a+ + +
  gi|15668437|ref|NP_247235.1| 120 KALIYIEFGEFEKALEALDEFL 141
                                   67789***********999855 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.018
                                   T-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          RPN7  30 lgkeeirrakldlaehYlkigdleeAlkaysrireyctslkhkidmllnlirvaiffndwdlvskyleka 99 
                                   ++k + + a++ +++   k g+++eAl a++ +++     ++ ++++  +  ++++ n+++ + +y+ k 
  gi|15668437|ref|NP_247235.1| 176 SIKKDDAHAWYLKGRILKKLGNIKEALDALKMAINLN---ENLVHVYKDIAYLELANNNYEEALNYITKY 242
                                   5667777777777777777777777777777775544...345666777777777777777777777765 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                          RPN7   6 eelrkknekeleeLdaelkdakenlgkeeirrakldlaehYlkigdleeAlkaysrire 64 
                                    e+ +k+++ l+  d+ + + k+   k  i+   l++a+   k g++eeA+++y+++++
  gi|15668437|ref|NP_247235.1| 260 YENLNKVDDALKIYDKIISN-KNVKDKLLIKSSILNKARILEKLGKIEEAVETYNKAFD 317
                                   56667888888888877776.88899999***************************987 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.35   1.5e+02       8      26 .]     121     139 ..     119     139 .. 0.87
   2 ?   -0.2   0.0       5.3   2.3e+03      14      22 ..     161     169 ..     155     172 .. 0.85
   3 ?    4.1   0.0      0.22        97       1      24 [.     182     205 ..     182     206 .. 0.91
   4 ?    2.0   0.0         1   4.4e+02       6      23 ..     294     311 ..     293     313 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.35
                         TPR_4   8 ArallalGdldeAraller 26 
                                   A  + + G+++ A+++l++
  gi|15668437|ref|NP_247235.1| 121 ALIYIEFGEFEKALEALDE 139
                                   6778899*********986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 5.3
                         TPR_4  14 lGdldeAra 22 
                                   lG ldeA++
  gi|15668437|ref|NP_247235.1| 161 LGKLDEALD 169
                                   799****97 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.22
                         TPR_4   1 arallaLArallalGdldeArall 24 
                                   a+a ++ +r l  lG+  eA+++l
  gi|15668437|ref|NP_247235.1| 182 AHAWYLKGRILKKLGNIKEALDAL 205
                                   6899999**************987 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 1
                         TPR_4   6 aLArallalGdldeAral 23 
                                   + Ar l  lG  +eA ++
  gi|15668437|ref|NP_247235.1| 294 NKARILEKLGKIEEAVET 311
                                   67999**********986 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.98   4.3e+02      67     120 ..      22      75 ..       2      85 .. 0.75
   2 !   15.1   0.7   3.9e-05     0.017      67     117 ..     226     276 ..     200     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.98
                       DUF4919  67 elseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkl 120
                                     ++ ++++++++ e+a k +  ++  l++  +++k++g+ e+a++y + l+++
  gi|15668437|ref|NP_247235.1|  22 CADKGNFDKALEYLEKAQKVDKDNPLVLYVKGIVLKLKGDMEKAEKYFECLENI 75 
                                   556777888888877777666666668889999999999999999998888777 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.9e-05
                       DUF4919  67 elseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrl 117
                                   el +++++e++++ +++l+k+P d+++ ++la +y++l+k + a ++++++
  gi|15668437|ref|NP_247235.1| 226 ELANNNYEEALNYITKYLEKFPNDVEAKFYLALIYENLNKVDDALKIYDKI 276
                                   67889************************************9998888775 PP

>> YfiO  Outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.3   5.6e+02       7      33 ..      48      74 ..      42      80 .. 0.82
   2 ?    4.7   0.0     0.051        22      50      76 ..     124     148 ..      90     153 .. 0.76
   3 ?    9.6   0.3    0.0016      0.69      41      80 ..     215     254 ..     178     301 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.3
                                  HHHHHHHHHHHHT-HHHHHHHHHHHHH CS
                          YfiO  7 elYekgqealqkgdyaeAikklealds 33
                                   lY kg     kgd+++A k++e l++
  gi|15668437|ref|NP_247235.1| 48 VLYVKGIVLKLKGDMEKAEKYFECLEN 74
                                  6788888777899**********9987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.051
                                   HHHHHTT-HHHHHHHHHHHHHH-SSST CS
                          YfiO  50 yAyykdadyaealasaerFlrlyPthk 76 
                                   y   + +++++al+++++Fl+ yP+  
  gi|15668437|ref|NP_247235.1| 124 Y--IEFGEFEKALEALDEFLKIYPNLT 148
                                   3..4557999**************865 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0016
                                   HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-SSSTTHHH CS
                          YfiO  41 aeqaqldliyAyykdadyaealasaerFlrlyPthknvdy 80 
                                     ++  d++y  + +++y+eal ++ ++l+++P+  ++++
  gi|15668437|ref|NP_247235.1| 215 LVHVYKDIAYLELANNNYEEALNYITKYLEKFPNDVEAKF 254
                                   4455567888888888888888888888888887655544 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00075      0.33       8      24 ..      19      35 ..      10      45 .. 0.82
   2 ?    1.2   0.0      0.91     4e+02      13      27 ..      58      70 ..      55      76 .. 0.83
   3 ?   -0.7   0.1       3.4   1.5e+03      15      29 ..     128     141 ..     126     144 .. 0.81
   4 ?   -2.1   0.0       9.5   4.2e+03      15      31 ..     196     210 ..     195     214 .. 0.73
   5 ?   -1.5   0.1       6.3   2.8e+03      16      23 ..     231     238 ..     230     239 .. 0.91
   6 ?    2.9   0.0      0.26   1.1e+02      15      25 ..     303     313 ..     301     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00075
                                  HHHHHHTT-HHHHHHH. CS
                         TPR_3  8 AaefynkkkyqeArelf 24
                                  A e+ +k+++++A+e++
  gi|15668437|ref|NP_247235.1| 19 ALECADKGNFDKALEYL 35
                                  99*************95 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.91
                                  HTT-HHHHHHH..HH CS
                         TPR_3 13 nkkkyqeArelfsYa 27
                                  +k++ ++A+ +  ++
  gi|15668437|ref|NP_247235.1| 58 LKGDMEKAEKY--FE 70
                                  69*********..54 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 3.4
                                   T-HHHHHHH..HHHH CS
                         TPR_3  15 kkyqeArelfsYall 29 
                                   +++++A+e+++ ++l
  gi|15668437|ref|NP_247235.1| 128 GEFEKALEALD-EFL 141
                                   7899****999.777 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 9.5
                                   T-HHHHHHH..HHHHHH CS
                         TPR_3  15 kkyqeArelfsYallai 31 
                                   +++ eA++++    + +
  gi|15668437|ref|NP_247235.1| 196 GNIKEALDALK--MAIN 210
                                   89999999954..5555 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 6.3
                                   -HHHHHHH CS
                         TPR_3  16 kyqeArel 23 
                                   +y+eA+++
  gi|15668437|ref|NP_247235.1| 231 NYEEALNY 238
                                   7*****98 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.26
                                   T-HHHHHHH.. CS
                         TPR_3  15 kkyqeArelfs 25 
                                   +k++eA+e++ 
  gi|15668437|ref|NP_247235.1| 303 GKIEEAVETYN 313
                                   9********54 PP

>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.043        19      20      33 ..      25      38 ..      20      38 .. 0.87
   2 ?    4.0   0.0       0.2        89      15      31 ..      52      70 ..      48      71 .. 0.73
   3 ?   -0.4   0.0       4.9   2.1e+03      12      27 ..     185     202 ..     181     211 .. 0.74
   4 ?   -0.8   0.0       6.5   2.8e+03       2      15 ..     251     262 ..     250     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.043
                          Sel1 20 pkDpekAiewyekA 33
                                  + + +kA+e++ekA
  gi|15668437|ref|NP_247235.1| 25 KGNFDKALEYLEKA 38
                                  4499*********9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.2
                          Sel1 15 nGl.g.vpkDpekAiewye 31
                                  +G    ++ D ekA++++e
  gi|15668437|ref|NP_247235.1| 52 KGIvLkLKGDMEKAEKYFE 70
                                  666433566*********8 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 4.9
                          Sel1  12 lylnGlgvpk..DpekAi 27 
                                   +yl+G+ ++k  ++++A+
  gi|15668437|ref|NP_247235.1| 185 WYLKGRILKKlgNIKEAL 202
                                   458888666677777775 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 6.5
                          Sel1   2 eAmyrLGmfylyln 15 
                                   eA + L+++y  +n
  gi|15668437|ref|NP_247235.1| 251 EAKFYLALIY--EN 262
                                   78999**555..65 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         9     4e+03      10      32 ..      16      38 ..      11      46 .. 0.78
   2 ?   -0.7   0.0         4   1.8e+03      73     116 ..     125     168 ..     118     177 .. 0.67
   3 ?   11.6   0.0   0.00063      0.28      45     122 ..     199     276 ..     179     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 9
                                  HHHHHHHHHTT-HHHHHHHHHHH CS
                          BTAD 10 vaagraalaagdpeeaaelleaA 32
                                  v ++ + + +g +++a+e le+A
  gi|15668437|ref|NP_247235.1| 16 VVNALECADKGNFDKALEYLEKA 38
                                  55677788899999999999988 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4
                                   HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHH CS
                          BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeAL 116
                                   +++G+ e+al+ l++ ++ +P      rq    l  +G+  eAL
  gi|15668437|ref|NP_247235.1| 125 IEFGEFEKALEALDEFLKIYPNLTSILRQKASILEILGKLDEAL 168
                                   56777777777777777777766666666555555555555555 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00063
                                   TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          BTAD  45 eagewleaererleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                   ++   + + +  l+e  +++++++a +el+ + +eeal + ++ +++ P + ++   l + +  +++  +AL+ Y+++
  gi|15668437|ref|NP_247235.1| 199 KEALDALKMAINLNENLVHVYKDIAYLELANNNYEEALNYITKYLEKFPNDVEAKFYLALIYENLNKVDDALKIYDKI 276
                                   4456666777889**************************************************************875 PP

>> PTS_IIA  PTS system, Lactose/Cellobiose specific IIA subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0018      0.79      17      41 ..      16      40 ..      13      44 .. 0.91
   2 ?   -1.4   0.0       5.7   2.5e+03      17      38 ..     118     139 ..     116     142 .. 0.82
   3 ?   -0.6   0.0       3.2   1.4e+03      35      57 ..     224     246 ..     196     260 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0018
                       PTS_IIA 17 ameAlkaakegdfeeaeellkeAee 41
                                  +++Al++a +g+f++a e l++A++
  gi|15668437|ref|NP_247235.1| 16 VVNALECADKGNFDKALEYLEKAQK 40
                                  789********************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.7
                       PTS_IIA  17 ameAlkaakegdfeeaeellke 38 
                                   +++Al  ++ g+fe+a e l+e
  gi|15668437|ref|NP_247235.1| 118 FHKALIYIEFGEFEKALEALDE 139
                                   5789999999999999888765 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.2
                       PTS_IIA  35 llkeAeeelkeAhkaqteliqke 57 
                                    l+ A+++++eA ++ t+ ++k 
  gi|15668437|ref|NP_247235.1| 224 YLELANNNYEEALNYITKYLEKF 246
                                   45667777777777777666665 PP

>> T6PP_N  Trehalose-6-phosphate phosphatase N-terminal helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.37   1.6e+02      75      93 ..      27      45 ..       7      50 .. 0.88
   2 ?    8.4   0.1    0.0041       1.8      52      92 ..     182     234 ..     130     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.37
                        T6PP_N 75 eLekDlkFLefiqsdeven 93
                                  +++k l++Le+ q+ +++n
  gi|15668437|ref|NP_247235.1| 27 NFDKALEYLEKAQKVDKDN 45
                                  6899999999999999887 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0041
                        T6PP_N  52 tevlelrtt............eeekvrldikdEieeLekDlkFLefiqsdeve 92 
                                   ++   l+ +             + k+ +++++ +    kD+++Le  +++ +e
  gi|15668437|ref|NP_247235.1| 182 AHAWYLKGRilkklgnikealDALKMAINLNENLVHVYKDIAYLELANNNYEE 234
                                   4444444446666677777777889********************87776555 PP

>> CLTH  CTLH/CRA C-terminal to LisH motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.2   0.00047      0.21      15      82 ..     162     268 ..       7     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00047
                          CLTH  15 gdlseaiewine.............nkpellesnsnLeFkLkllqfielirgkt...............kdieealeyare 67 
                                   g+l+ea++ +n+             +k ++l++  n++  L  l+    +++ +               +++eeal+y+++
  gi|15668437|ref|NP_247235.1| 162 GKLDEALDCVNKilsikkddahawyLKGRILKKLGNIKEALDALKMAINLNE-NlvhvykdiaylelanNNYEEALNYITK 241
                                   4455555555555555555555555555555555555555555555555553.244455555555555589********** PP

                          CLTH  68 nl.efend...........ehlkelek 82 
                                   +l +f nd           e+l+++ +
  gi|15668437|ref|NP_247235.1| 242 YLeKFPNDveakfylaliyENLNKVDD 268
                                   **6677776666666555555555544 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.14        62      17      30 ..      25      38 ..      13      47 .. 0.58
   2 ?   -1.2   0.0         5   2.2e+03      29      42 ..     132     146 ..     128     168 .. 0.58
   3 ?    0.2   0.0       1.8   7.8e+02      20      32 ..     198     210 ..     194     223 .. 0.59
   4 ?    4.3   0.9     0.099        43      22      41 ..     227     247 ..     222     266 .. 0.73
   5 ?    0.7   0.1       1.3   5.8e+02      11      28 ..     257     274 ..     252     277 .. 0.87
   6 ?    9.5   0.0    0.0023      0.99       7      32 ..     292     317 ..     290     318 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.14
                           MIT 17 agnyeeAlelYkea 30
                                  +gn+++Ale+ ++a
  gi|15668437|ref|NP_247235.1| 25 KGNFDKALEYLEKA 38
                                  55555555543333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5
                           MIT  29 ealelLlqalk.ekn 42 
                                   +ale L + lk   n
  gi|15668437|ref|NP_247235.1| 132 KALEALDEFLKiYPN 146
                                   666666666662233 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.8
                           MIT  20 yeeAlelYkeale 32 
                                   ++eAl++ k a++
  gi|15668437|ref|NP_247235.1| 198 IKEALDALKMAIN 210
                                   5555554444444 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.099
                           MIT  22 eAlelYkealelLlqalke.k 41 
                                    A ++Y+eal+++++ l    
  gi|15668437|ref|NP_247235.1| 227 LANNNYEEALNYITKYLEKfP 247
                                   577788888888888887554 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 1.3
                           MIT  11 AveeDnagnyeeAlelYk 28 
                                   A  ++n ++ ++Al+ Y 
  gi|15668437|ref|NP_247235.1| 257 ALIYENLNKVDDALKIYD 274
                                   67799***********97 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.0023
                           MIT   7 lvkkAveeDnagnyeeAlelYkeale 32 
                                   +++kA  +++ g++eeA+e Y +a +
  gi|15668437|ref|NP_247235.1| 292 ILNKARILEKLGKIEEAVETYNKAFD 317
                                   7899999****************976 PP

>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0049       2.1       2      29 ..      13      40 ..      12      45 .. 0.92
   2 ?   -0.1   0.0       1.8     8e+02      15      33 ..     128     139 ..     118     181 .. 0.68
   3 ?    0.1   2.7       1.6   6.8e+02      26      26 ..     241     241 ..     191     319 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0049
                                  HHHHHHHHHHHCTT-HHHHHHHHHHHHH CS
                          YfdX  2 lrdiqkArlaldqgdtkeAkkllekAqg 29
                                  l+d+++A+   d+g+ ++A++ lekAq+
  gi|15668437|ref|NP_247235.1| 13 LKDVVNALECADKGNFDKALEYLEKAQK 40
                                  7899**********************97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
                                   T-HHHHHHHHHHHHHHHTS CS
                          YfdX  15 gdtkeAkkllekAqgklea 33 
                                   g+ ++A+++l+       +
  gi|15668437|ref|NP_247235.1| 128 GEFEKALEALD-------E 139
                                   33333333333.......3 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.6
                                   H CS
                          YfdX  26 k 26 
                                   k
  gi|15668437|ref|NP_247235.1| 241 K 241
                                   2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1209  (0.0674327); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              41  [number of targets reported over threshold]
# CPU time: 0.81u 0.30s 00:00:01.11 Elapsed: 00:00:00.55
# Mc/sec: 1739.51
//
Query:       gi|15668438|ref|NP_247236.1|  [L=153]
Description: carbon monoxide dehydrogenase iron sulfur subunit CooF1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-17   62.0  36.5    7.8e-08   32.1   3.0    4.3  4  Fer4_6    4Fe-4S binding domain
    6.7e-17   60.5  42.4      8e-10   38.1   3.9    5.8  6  Fer4      4Fe-4S binding domain
    7.2e-14   51.7  28.6    3.7e-08   33.4  10.9    3.5  3  Fer4_21   4Fe-4S dicluster domain
    1.8e-13   50.9  30.2    4.2e-06   27.2  11.9    3.7  3  Fer4_7    4Fe-4S dicluster domain
    7.2e-13   47.8  30.8    4.3e-05   23.4   1.9    4.2  4  Fer4_2    4Fe-4S binding domain
    1.1e-12   47.8  24.7    1.8e-06   28.0  10.0    3.2  3  Fer4_9    4Fe-4S dicluster domain
    2.1e-11   44.6  26.7      0.019   15.9   4.2    4.2  4  Fer4_16   4Fe-4S double cluster binding domain
    5.7e-11   42.4  16.3    1.7e-10   40.9  12.6    2.1  2  Fer4_11   4Fe-4S dicluster domain
      1e-10   41.7  38.7      0.012   16.5   2.2    4.2  4  Fer4_3    4Fe-4S binding domain
    1.9e-09   37.3  34.6    0.00078   19.8   2.0    4.2  4  Fer4_4    4Fe-4S binding domain
    4.5e-09   36.3  32.1     0.0032   17.5  13.0    4.0  5  Fer4_10   4Fe-4S dicluster domain
    7.4e-07   29.6  25.2     0.0025   18.3   0.3    4.2  4  Fer4_17   4Fe-4S dicluster domain
     0.0049   17.3  33.8       0.08   13.4   2.7    4.2  5  Fer4_8    4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.02   15.1  25.5       0.34   11.1   7.6    2.8  2  Fer4_18   4Fe-4S dicluster domain
      0.061   14.2   0.8      0.061   14.2   0.8    4.2  4  Fer4_22   4Fe-4S dicluster domain
        3.7    8.4  23.5         20    6.0  10.8    4.3  3  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   2.8   6.4e-08   7.1e-05       2      20 ..      18      36 ..      17      41 .. 0.90
   2 !   11.6   4.2    0.0002      0.23       8      24 .]      48      66 ..      47      66 .. 0.94
   3 !   32.1   3.0     7e-11   7.8e-08       1      24 []      72      95 ..      72      95 .. 0.97
   4 !   13.8   3.2     4e-05     0.045       8      24 .]     103     124 ..     103     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.4e-08
                        Fer4_6  2 veidpdkCigCgdCvrvCP 20
                                  v+++  +CigC++C+r CP
  gi|15668438|ref|NP_247236.1| 18 VVVNVGSCIGCRRCERSCP 36
                                  89999************** PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0002
                        Fer4_6  8 kCigCgd..CvrvCPegai 24
                                  kC +C++  C  +CPe+ai
  gi|15668438|ref|NP_247236.1| 48 KCMHCDRnpCLYACPENAI 66
                                  79***8889*********8 PP

  == domain 3  score: 32.1 bits;  conditional E-value: 7e-11
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  +v++ +dkC+gCg C+ +CP+gai
  gi|15668438|ref|NP_247236.1| 72 KVVVIKDKCVGCGLCALACPFGAI 95
                                  699********************8 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 4e-05
                        Fer4_6   8 kCigCgd.....CvrvCPegai 24 
                                   kC+gC++     C  vCP+gai
  gi|15668438|ref|NP_247236.1| 103 KCNGCYKrdveiCKEVCPTGAI 124
                                   8****999*************8 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   3.6   4.4e-08   4.9e-05       1      24 []      18      41 ..      18      41 .. 0.92
   2 ?    0.2   0.2       0.7   7.9e+02       7      11 ..      48      52 ..      46      54 .. 0.79
   3 !    8.4   0.7    0.0018         2      14      24 .]      57      67 ..      55      67 .. 0.92
   4 !   38.1   3.9   7.1e-13     8e-10       1      24 []      73      96 ..      73      96 .. 0.95
   5 ?    0.8   1.0      0.42   4.7e+02       7      12 ..     103     108 ..     102     109 .. 0.80
   6 !   14.2   0.6   2.5e-05     0.029      13      23 ..     114     124 ..     113     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.4e-08
                                  EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                  vv++   CigC +C+  CP + It
  gi|15668438|ref|NP_247236.1| 18 VVVNVGSCIGCRRCERSCPINGIT 41
                                  68999**************99875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.7
                                  TSSS- CS
                          Fer4  7 kCigC 11
                                  kC++C
  gi|15668438|ref|NP_247236.1| 48 KCMHC 52
                                  89999 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0018
                                  HHHHSTTTEEE CS
                          Fer4 14 CvevCPvgAIt 24
                                  C  +CP +AI+
  gi|15668438|ref|NP_247236.1| 57 CLYACPENAIE 67
                                  999*******6 PP

  == domain 4  score: 38.1 bits;  conditional E-value: 7.1e-13
                                  EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                  vv++++kC+gCG+C+ +CP+gAI+
  gi|15668438|ref|NP_247236.1| 73 VVVIKDKCVGCGLCALACPFGAIR 96
                                  689********************6 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.42
                                   TSSS-T CS
                          Fer4   7 kCigCG 12 
                                   kC gC 
  gi|15668438|ref|NP_247236.1| 103 KCNGCY 108
                                   799995 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 2.5e-05
                                   HHHHHSTTTEE CS
                          Fer4  13 aCvevCPvgAI 23 
                                   +C evCP+gAI
  gi|15668438|ref|NP_247236.1| 114 ICKEVCPTGAI 124
                                   7*********9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.4   1.2e-07   0.00013      26      57 ..      10      40 ..       3      42 .. 0.85
   2 !   33.4  10.9   3.3e-11   3.7e-08       7      58 ..      48      96 ..      46      97 .. 0.80
   3 !    6.2   3.5    0.0097        11      40      58 ..     103     125 ..      96     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.2e-07
                       Fer4_21 26 ieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                  + id+++++ v   +C+GC  C   CP++  i
  gi|15668438|ref|NP_247236.1| 10 LAIDGEKMVVVNVGSCIGCRRCERSCPIN-GI 40
                                  5789999999999**************94.44 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 3.3e-11
                       Fer4_21  7 kCigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                  kC++C +  Cl aC++++++ i+   + ++ v++d+CvGC lC+  CP  ++i+
  gi|15668438|ref|NP_247236.1| 48 KCMHCDRnpCLYACPENAIERIN---N-KVVVIKDKCVGCGLCALACPF-GAIR 96
                                  7****6555******85555544...4.45899***************7.8886 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0097
                       Fer4_21  40 eCvGC.....nlCssvCPvedcie 58 
                                   +C GC     ++C +vCP+ ++i+
  gi|15668438|ref|NP_247236.1| 103 KCNGCykrdvEICKEVCPT-GAIN 125
                                   799996666679******6.8885 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2  12.7   1.5e-07   0.00016       1      52 []      24      65 ..      24      65 .. 0.95
   2 !   27.2  11.9   3.8e-09   4.2e-06       1      52 []      48      94 ..      48      94 .. 0.90
   3 !   22.9  11.4   8.4e-08   9.4e-05       1      52 []      79     123 ..      79     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.5e-07
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga..CvavCPtga 52
                                  +CigC++C++ Cp + i+++e+            p kC++C++  C  +CP +a
  gi|15668438|ref|NP_247236.1| 24 SCIGCRRCERSCPINGITFNEF------------PIKCMHCDRnpCLYACPENA 65
                                  5******************998............89******99*******987 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 3.8e-09
                        Fer4_7  1 rCigC..gaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  +C++C  + C  aCp +aie  +        kv++  +kC+gCg C+ +CP+ga
  gi|15668438|ref|NP_247236.1| 48 KCMHCdrNPCLYACPENAIERINN-------KVVVIKDKCVGCGLCALACPFGA 94
                                  7****5559**********98654.......68999****************98 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 8.4e-08
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga.....CvavCPtga 52 
                                   +C+gCg C+ aCp +ai++d +            + kC gC++     C +vCPtga
  gi|15668438|ref|NP_247236.1|  79 KCVGCGLCALACPFGAIRIDGV------------AIKCNGCYKrdveiCKEVCPTGA 123
                                   7*****************9765............56788887666688*******98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   2.9   2.1e-06    0.0023       3      21 ..      18      36 ..      15      36 .. 0.92
   2 !   13.9   1.6   3.9e-05     0.044       9      22 .]      48      63 ..      42      63 .. 0.86
   3 !   23.4   1.9   3.8e-08   4.3e-05       3      21 ..      73      91 ..      71      92 .. 0.91
   4 !   10.0   2.0   0.00069      0.77       9      22 .]     103     121 ..      99     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.1e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  vvv+  +CigC+ C  +CP
  gi|15668438|ref|NP_247236.1| 18 VVVNVGSCIGCRRCERSCP 36
                                  8999**************9 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.9e-05
                        Fer4_2  9 rCigC..gaCvsaCPa 22
                                  +C++C  ++C+ aCP+
  gi|15668438|ref|NP_247236.1| 48 KCMHCdrNPCLYACPE 63
                                  7****645*******5 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 3.8e-08
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  vvv  d+C+gCg C  aCP
  gi|15668438|ref|NP_247236.1| 73 VVVIKDKCVGCGLCALACP 91
                                  78999************** PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00069
                        Fer4_2   9 rCigCg.....aCvsaCPa 22 
                                   +C+gC      +C  +CP+
  gi|15668438|ref|NP_247236.1| 103 KCNGCYkrdveICKEVCPT 121
                                   7****556777*******7 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.0   4.5e-06    0.0051       2      17 ..      25      40 ..      24      47 .. 0.83
   2 !   28.0  10.0   1.6e-09   1.8e-06       1      51 []      48      95 ..      48      95 .. 0.90
   3 !   12.6   0.5    0.0001      0.12       1      18 [.     103     125 ..      97     139 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.5e-06
                        Fer4_9  2 CtgCgaCveaCpagvv 17
                                  C+gC++C+++Cp + +
  gi|15668438|ref|NP_247236.1| 25 CIGCRRCERSCPINGI 40
                                  ***********98866 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 1.6e-09
                        Fer4_9  1 kCtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  kC+ C++  C +aCp +++++ +++  +  +     +C+gCg C+ aCp gai
  gi|15668438|ref|NP_247236.1| 48 KCMHCDRnpCLYACPENAIERINNKVVVIKD-----KCVGCGLCALACPFGAI 95
                                  7****8778**********999999888864.....6************9987 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.0001
                        Fer4_9   1 kCtgCga.....CveaCpagvvv 18 
                                   kC+gC +     C e+Cp+g+++
  gi|15668438|ref|NP_247236.1| 103 KCNGCYKrdveiCKEVCPTGAIN 125
                                   57777444455577777777765 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.3     2e-05     0.023       2      20 ..      25      43 ..      23      47 .. 0.86
   2 !   14.1   1.8     6e-05     0.068       1      26 [.      48      75 ..      48      79 .. 0.84
   3 !   15.9   4.2   1.7e-05     0.019       1      20 [.      79      98 ..      79     112 .. 0.82
   4 !   12.0   1.9   0.00028      0.31       6      32 ..     113     137 ..     102     152 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-05
                       Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                  C++C++C  +CP n i+ +
  gi|15668438|ref|NP_247236.1| 25 CIGCRRCERSCPINGITFN 43
                                  99999******99999876 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6e-05
                       Fer4_16  1 rCgtCgk..CaevCPtnaikekkekeie 26
                                  +C  C +  C+ +CP+nai+  ++k++ 
  gi|15668438|ref|NP_247236.1| 48 KCMHCDRnpCLYACPENAIERINNKVVV 75
                                  599**9999**********998777665 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 1.7e-05
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  +C++Cg Ca +CP +ai+ +
  gi|15668438|ref|NP_247236.1| 79 KCVGCGLCALACPFGAIRID 98
                                  5****************976 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00028
                       Fer4_16   6 gkCaevCPtnaikekkekeiearecis 32 
                                   + C evCPt+ai++   +ei +++ ++
  gi|15668438|ref|NP_247236.1| 113 EICKEVCPTGAINNL--EEILNNKIQN 137
                                   46**********988..5555555444 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.042        47      34      62 ..      16      43 ..       3      45 .. 0.82
   2 !   40.9  12.6   1.5e-13   1.7e-10       4      96 ..      43     125 ..      40     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.042
                       Fer4_11 34 GaVlldektkkeevrevveacPykivrkn 62
                                   +V+++  ++  ++r++ ++cP + +  n
  gi|15668438|ref|NP_247236.1| 16 KMVVVNVGSCI-GCRRCERSCPINGITFN 43
                                  47899999996.9*********9877665 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 1.5e-13
                       Fer4_11   4 lflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGllp 84 
                                   + +p +C+hC + pC+ ++p++ai + + + +V++++k +  ++  ++ acP+ ++r +   g++ kC++c++r       
  gi|15668438|ref|NP_247236.1|  43 NEFPIKCMHCDRNPCLYACPENAIERIN-NKVVVIKDKCV--GCGLCALACPFGAIRID---GVAIKCNGCYKRDV----E 113
                                   5599*****************9998777.55666665554..89*************97...5566********87....8 PP

                       Fer4_11  85 acvescptgaln 96 
                                   +c e+cptga+n
  gi|15668438|ref|NP_247236.1| 114 ICKEVCPTGAIN 125
                                   *********987 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.2   1.1e-05     0.012       1      14 [.      25      38 ..      25      40 .. 0.91
   2 !   14.4   4.3   4.9e-05     0.055       1      15 []      49      65 ..      49      65 .. 0.88
   3 !   16.2   6.2   1.3e-05     0.015       1      15 []      80      94 ..      80      94 .. 0.98
   4 !   13.1   2.6   0.00013      0.14       1      15 []     104     123 ..     104     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C+gC++C+++CP +
  gi|15668438|ref|NP_247236.1| 25 CIGCRRCERSCPIN 38
                                  ************75 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.9e-05
                        Fer4_3  1 CtgCg..aCvevCPvgA 15
                                  C++C   +C+ +CP++A
  gi|15668438|ref|NP_247236.1| 49 CMHCDrnPCLYACPENA 65
                                  ****6459*******98 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.3e-05
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gCg+C  +CP gA
  gi|15668438|ref|NP_247236.1| 80 CVGCGLCALACPFGA 94
                                  *************98 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 0.00013
                        Fer4_3   1 CtgCg.....aCvevCPvgA 15 
                                   C+gC+      C evCP+gA
  gi|15668438|ref|NP_247236.1| 104 CNGCYkrdveICKEVCPTGA 123
                                   ****9655544********9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   2.9   1.2e-06    0.0014       3      15 ..      24      36 ..      23      43 .. 0.92
   2 !    8.6   3.1    0.0027         3       3      16 ..      48      63 ..      48      64 .. 0.92
   3 !   19.8   2.0     7e-07   0.00078       1      17 []      77      93 ..      77      93 .. 0.93
   4 !    7.7   3.5    0.0051       5.7       3      17 .]     103     122 ..     103     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-06
                        Fer4_4  3 rCigCgsCvaaCP 15
                                  +CigC++C+++CP
  gi|15668438|ref|NP_247236.1| 24 SCIGCRRCERSCP 36
                                  7***********9 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0027
                        Fer4_4  3 rCigCgs..CvaaCPq 16
                                  +C +C++  C +aCP 
  gi|15668438|ref|NP_247236.1| 48 KCMHCDRnpCLYACPE 63
                                  7**************6 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 7e-07
                        Fer4_4  1 qerCigCgsCvaaCPqg 17
                                  +++C+gCg C  aCP+g
  gi|15668438|ref|NP_247236.1| 77 KDKCVGCGLCALACPFG 93
                                  69*************86 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0051
                        Fer4_4   3 rCigCgs.....CvaaCPqg 17 
                                   +C+gC +     C  +CP+g
  gi|15668438|ref|NP_247236.1| 103 KCNGCYKrdveiCKEVCPTG 122
                                   7*****99999*******86 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   3.2   5.5e-06    0.0062      33      56 .]      13      36 ..      10      36 .. 0.69
   2 !   14.7  13.9   2.2e-05     0.025       2      56 .]      18      62 ..      17      62 .. 0.86
   3 !   17.5  13.0   2.9e-06    0.0032       7      56 .]      47      91 ..      43      91 .. 0.90
   4 !   17.2  11.8   3.8e-06    0.0042       2      56 .]      73     120 ..      72     120 .. 0.70
   5 !    7.7   2.5    0.0033       3.7       8      31 ..     103     129 ..     100     144 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.5e-06
                       Fer4_10 33 seeeavrkkvekCtgcgaCveaCP 56
                                  ++e++v ++v++C+gc  C ++CP
  gi|15668438|ref|NP_247236.1| 13 DGEKMVVVNVGSCIGCRRCERSCP 36
                                  566777777777777777777777 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.2e-05
                       Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg..aCveaCP 56
                                  vv++  +Ci+C++C ++CP             ++ + ++ + kC++c    C  aCP
  gi|15668438|ref|NP_247236.1| 18 VVVNVGSCIGCRRCERSCPI------------NGITFNEFPIKCMHCDrnPCLYACP 62
                                  788999**************............66677777888****7679*****9 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 2.9e-06
                       Fer4_10  7 dtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   +C++C    C  aCP        ++++ ++++v +  +kC gcg C+ aCP
  gi|15668438|ref|NP_247236.1| 47 IKCMHCDrnPCLYACPE-------NAIERINNKVVVIKDKCVGCGLCALACP 91
                                  58****9889*******.......88888888888899*************9 PP

  == domain 4  score: 17.2 bits;  conditional E-value: 3.8e-06
                       Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg..cgaCveaCP 56 
                                   vv+ +d+C++Cg C  aCP+          a +++ v +k+  C +  ++ C e+CP
  gi|15668438|ref|NP_247236.1|  73 VVVIKDKCVGCGLCALACPF---------GAIRIDGVAIKCNGCYKrdVEICKEVCP 120
                                   77889***************.........3344444444455554433369*****9 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0033
                       Fer4_10   8 tCirCg.....kCvkaCPadltsvgakge 31 
                                   +C +C       C+++CP+ +   ++ +e
  gi|15668438|ref|NP_247236.1| 103 KCNGCYkrdveICKEVCPTGA--INNLEE 129
                                   688888666656999****33..222222 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   2.3e-06    0.0025      42      57 ..      21      36 ..       3      39 .. 0.83
   2 ?    4.8   3.1     0.037        42       1      22 [.      48      71 ..      47      79 .. 0.70
   3 !   13.4   1.3   7.4e-05     0.083      44      58 ..      78      92 ..      66      95 .. 0.81
   4 !    8.6   0.5    0.0025       2.8       1      22 [.     103     129 ..     103     151 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.3e-06
                       Fer4_17 42 kaslCieCgeCerkCP 57
                                  ++++Ci+C++Cer+CP
  gi|15668438|ref|NP_247236.1| 21 NVGSCIGCRRCERSCP 36
                                  6799***********9 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.037
                       Fer4_17  1 rCiqCgy..ClpeCpsyeaydnep 22
                                  +C++C    Cl +Cp +++ + ++
  gi|15668438|ref|NP_247236.1| 48 KCMHCDRnpCLYACPENAIERINN 71
                                  588887667888888877755554 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 7.4e-05
                       Fer4_17 44 slCieCgeCerkCPq 58
                                  ++C++Cg+C+ +CP 
  gi|15668438|ref|NP_247236.1| 78 DKCVGCGLCALACPF 92
                                  789999999999996 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0025
                       Fer4_17   1 rCiqCgy.....ClpeCpsyeaydnep 22 
                                   +C++C       C ++Cp++++++ e+
  gi|15668438|ref|NP_247236.1| 103 KCNGCYKrdveiCKEVCPTGAINNLEE 129
                                   699998555556*******99987743 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   3.0   8.2e-05     0.092      48      63 ..      22      37 ..      12      40 .. 0.72
   2 !   13.4   2.7   7.2e-05      0.08       4      17 ..      24      37 ..      21      47 .. 0.64
   3 ?    1.7   3.2      0.32   3.6e+02      50      63 ..      48      63 ..      41      66 .. 0.71
   4 !   13.3   2.8   7.6e-05     0.085       3      17 ..      78      92 ..      77     100 .. 0.88
   5 !    6.7   1.6    0.0088       9.8      50      64 ..     103     122 ..      95     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.2e-05
                        Fer4_8 48 lwsCttcgaCtevCpv 63
                                  ++sC +c++C++ Cp+
  gi|15668438|ref|NP_247236.1| 22 VGSCIGCRRCERSCPI 37
                                  5666677777777765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.2e-05
                        Fer4_8  4 kCieCgaCqsaCpv 17
                                  +Ci+C +C+ +Cp+
  gi|15668438|ref|NP_247236.1| 24 SCIGCRRCERSCPI 37
                                  46666666666654 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.32
                        Fer4_8 50 sCttcga..CtevCpv 63
                                  +C++c +  C  +Cp+
  gi|15668438|ref|NP_247236.1| 48 KCMHCDRnpCLYACPE 63
                                  5666666667777776 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 7.6e-05
                        Fer4_8  3 ekCieCgaCqsaCpv 17
                                  +kC++Cg+C  aCp+
  gi|15668438|ref|NP_247236.1| 78 DKCVGCGLCALACPF 92
                                  69***********97 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.0088
                        Fer4_8  50 sCttcga.....CtevCpvg 64 
                                   +C++c +     C+evCp+g
  gi|15668438|ref|NP_247236.1| 103 KCNGCYKrdveiCKEVCPTG 122
                                   799999999999*****986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   7.6    0.0003      0.34      55      97 ..      19      63 ..       8      77 .. 0.78
   2 ?    9.1  10.3    0.0013       1.4      51      99 ..      70     119 ..      62     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                       Fer4_18 55 ekgagdcidcescvkvcPtgidirkGlqleciscll..cidacdk 97
                                    ++g ci c+ c + cP++    + + ++c+ c +  c+ ac +
  gi|15668438|ref|NP_247236.1| 19 VVNVGSCIGCRRCERSCPINGITFNEFPIKCMHCDRnpCLYACPE 63
                                  56789*************98777899********7555*****53 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                       Fer4_18  51 eerkekgagdcidcescvkvcPtgidirkGlqleciscll.cidacdkvm 99 
                                   +++    + +c+ c+ c   cP g    +G+ ++c  c +  ++ c++v 
  gi|15668438|ref|NP_247236.1|  70 NNKVVVIKDKCVGCGLCALACPFGAIRIDGVAIKCNGCYKrDVEICKEVC 119
                                   4555666789**************8777**********752689998875 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.8   5.5e-05     0.061      78      94 ..      21      37 ..       3      39 .. 0.85
   2 ?    1.1   1.3      0.64   7.2e+02       1      15 [.      48      64 ..      48      79 .. 0.71
   3 ?   10.8   2.4   0.00059      0.66      79      94 ..      77      92 ..      64      94 .. 0.80
   4 ?    4.1   0.7     0.074        83       6      27 ..     113     134 ..     101     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.5e-05
                       Fer4_22 78 gesgCvGCgRCieacpv 94
                                  +  +C+GC RC+++cp 
  gi|15668438|ref|NP_247236.1| 21 NVGSCIGCRRCERSCPI 37
                                  6678***********96 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.64
                       Fer4_22  1 rClsCga..CtlvCptC 15
                                  +C++C +  C ++Cp  
  gi|15668438|ref|NP_247236.1| 48 KCMHCDRnpCLYACPEN 64
                                  68888644488888865 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00059
                       Fer4_22 79 esgCvGCgRCieacpv 94
                                  + +CvGCg C  acp 
  gi|15668438|ref|NP_247236.1| 77 KDKCVGCGLCALACPF 92
                                  5789999999999985 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.074
                       Fer4_22   6 gaCtlvCptCsCfdvedet.kee 27 
                                     C+ vCpt    ++e+   + +
  gi|15668438|ref|NP_247236.1| 113 EICKEVCPTGAINNLEEILnN-K 134
                                   46999****999999988843.3 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.2     0.038        42       1      19 [.      18      36 ..      18      42 .. 0.87
   2 ?    1.3   0.1      0.52   5.9e+02      58      65 ..      60      67 ..      53      68 .. 0.89
   3 ?    6.0  10.8     0.018        20       1      33 [.      73     103 ..      73     125 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.038
                       Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                  Vvv+   Cigc +C + +p
  gi|15668438|ref|NP_247236.1| 18 VVVNVGSCIGCRRCERSCP 36
                                  6778889*******99887 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.52
                       Fer4_15 58 aCPvdAIr 65
                                  aCP+ AI+
  gi|15668438|ref|NP_247236.1| 60 ACPENAIE 67
                                  89*99996 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.018
                       Fer4_15   1 VvvDrdaCigcglCvaeapevfeldedglasvl 33 
                                   Vvv +d+C gcglC+ ++p +  +  dg+a ++
  gi|15668438|ref|NP_247236.1|  73 VVVIKDKCVGCGLCALACP-FGAIRIDGVA-IK 103
                                   56668*************9.7777778888.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 960.80
//
Query:       gi|15668439|ref|NP_247237.1|  [L=166]
Description: carbon monoxide dehydrogenase iron sulfur subunit CooF2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-11   45.2  26.8    0.00017   22.1  12.8    3.4  4  Fer4_7    4Fe-4S dicluster domain
    3.4e-11   43.2  14.4    3.4e-11   43.2  14.4    2.1  2  Fer4_11   4Fe-4S dicluster domain
    1.5e-09   37.2   2.6    1.5e-09   37.2   2.6    5.5  6  Fer4      4Fe-4S binding domain
    4.7e-09   35.8  30.1    6.3e-06   26.0   1.1    4.3  4  Fer4_2    4Fe-4S binding domain
    1.5e-08   34.3  39.6      7e-06   25.9   2.1    4.4  4  Fer4_6    4Fe-4S binding domain
    1.3e-07   31.7  30.3    8.5e-05   22.6   1.1    3.2  3  Fer4_21   4Fe-4S dicluster domain
    1.9e-07   31.1  34.0    0.00046   20.2  11.3    3.5  3  Fer4_10   4Fe-4S dicluster domain
    2.7e-07   30.6  32.6    6.3e-05   23.1   8.8    3.4  5  Fer4_9    4Fe-4S dicluster domain
    9.1e-07   29.4  45.7     0.0035   18.2   5.0    4.3  4  Fer4_3    4Fe-4S binding domain
    1.1e-06   29.5  25.3      0.006   17.5   2.8    4.2  4  Fer4_16   4Fe-4S double cluster binding domain
    0.00061   20.1  33.7     0.0035   17.7   1.7    4.5  4  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.089   13.2   1.9      0.089   13.2   1.9    4.2  3  Fer4_8    4Fe-4S dicluster domain
       0.16   12.5  29.4       0.19   12.3   1.2    4.6  6  Fer4_17   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1  13.7   2.2e-06    0.0031       2      52 .]      13      62 ..      12      62 .. 0.78
   2 !   22.1  12.8   1.2e-07   0.00017       2      52 .]      46      91 ..      46      91 .. 0.91
   3 !   20.5   1.0   3.9e-07   0.00053       2      22 ..      77      97 ..      76      99 .. 0.88
   4 !   13.5   0.3   6.1e-05     0.084       1      23 [.     100     126 ..     100     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.2e-06
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga..CvavCPtga 52
                                  C +Cg Cv+aC+ k    + +      ++ ++ p  C++C +  C +vCP+ a
  gi|15668439|ref|NP_247237.1| 13 CDNCGDCVKACMEKNKVGRIAIM---EKDGKYIPIVCQHCASapCKEVCPVSA 62
                                  ***********955555444422...2456999********999******986 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.2e-07
                        Fer4_7  2 CigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  C +C    C ++Cpv+aie ++        +v+++++ C+gCg C+ +CP+ga
  gi|15668439|ref|NP_247237.1| 46 CQHCAsaPCKEVCPVSAIEHKDG-------YVYLNEDVCIGCGLCALACPFGA 91
                                  99996559***********9773.......89*******************98 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 3.9e-07
                        Fer4_7  2 CigCgaCvaaCpvkaieldee 22
                                  CigCg C+ aCp +ai ++++
  gi|15668439|ref|NP_247237.1| 77 CIGCGLCALACPFGAILMEDK 97
                                  ***************998765 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 6.1e-05
                        Fer4_7   1 rCigCg....aCvaaCpvkaieldeee 23 
                                   +Ci C+    aCv+aC+ +++el +++
  gi|15668439|ref|NP_247237.1| 100 KCILCNgdepACVKACSKRCLELVDVN 126
                                   7****88999**********9998764 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.4     0.054        74       4      33 ..      10      38 ..       6      40 .. 0.69
   2 !   43.2  14.4   2.4e-14   3.4e-11       4      99 ..      40     124 ..      37     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.054
                       Fer4_11  4 lflpeqCrhCleppCvasapseaivkdeet 33
                                  +f  ++C +C++ +C+++ +++ i   e++
  gi|15668439|ref|NP_247237.1| 10 NFNCDNCGDCVK-ACMEKNKVGRIAIMEKD 38
                                  577788889975.79999888844444444 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 2.4e-14
                       Fer4_11   4 lflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGllp 84 
                                    ++p  C+hC ++pC++++p++ai ++  +G V l+e+ +  ++  ++ acP+ ++ +++++    kC +c     +G +p
  gi|15668439|ref|NP_247237.1|  40 KYIPIVCQHCASAPCKEVCPVSAIEHK--DGYVYLNEDVCI-GCGLCALACPFGAILMEDKAY---KCILC-----NGDEP 109
                                   699******************999776..5**********7.****************99877...*****.....6999* PP

                       Fer4_11  85 acvescptgalnfgd 99 
                                   acv++c  ++l++ d
  gi|15668439|ref|NP_247237.1| 110 ACVKACSKRCLELVD 124
                                   ********9998765 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   4.3   0.00053      0.74       8      18 ..      13      23 ..      10      23 .. 0.95
   2 ?   -2.3   0.3       3.4   4.7e+03      11      16 ..      46      51 ..      44      52 .. 0.58
   3 !    9.5   0.9   0.00063      0.87      14      24 .]      54      64 ..      54      64 .. 0.94
   4 !   37.2   2.6   1.1e-12   1.5e-09       1      23 [.      70      92 ..      70      93 .. 0.95
   5 ?    1.5   0.4      0.22     3e+02       7      12 ..     100     105 ..      98     106 .. 0.87
   6 ?    1.5   1.5      0.21   2.9e+02      13      18 ..     110     115 ..     110     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00053
                                  SSS-THHHHHS CS
                          Fer4  8 CigCGaCvevC 18
                                  C +CG Cv++C
  gi|15668439|ref|NP_247237.1| 13 CDNCGDCVKAC 23
                                  *********** PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                                  -THHHH CS
                          Fer4 11 CGaCve 16
                                  C  C++
  gi|15668439|ref|NP_247237.1| 46 CQHCAS 51
                                  666665 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00063
                                  HHHHSTTTEEE CS
                          Fer4 14 CvevCPvgAIt 24
                                  C evCPv AI+
  gi|15668439|ref|NP_247237.1| 54 CKEVCPVSAIE 64
                                  9********96 PP

  == domain 4  score: 37.2 bits;  conditional E-value: 1.1e-12
                                  EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                  v+ +e+ CigCG+C+ +CP+gAI
  gi|15668439|ref|NP_247237.1| 70 VYLNEDVCIGCGLCALACPFGAI 92
                                  578*******************9 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.22
                                   TSSS-T CS
                          Fer4   7 kCigCG 12 
                                   kCi C+
  gi|15668439|ref|NP_247237.1| 100 KCILCN 105
                                   9****5 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.21
                                   HHHHHS CS
                          Fer4  13 aCvevC 18 
                                   aCv++C
  gi|15668439|ref|NP_247237.1| 110 ACVKAC 115
                                   7***** PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   2.3   4.8e-05     0.066       9      20 ..      12      23 ..       6      25 .. 0.90
   2 ?    4.5   3.4     0.032        44       9      21 ..      45      59 ..      39      60 .. 0.76
   3 !   26.0   1.1   4.6e-09   6.3e-06       2      21 ..      69      88 ..      68      89 .. 0.93
   4 !    8.6   1.3    0.0015       2.1       9      20 ..     100     115 ..      93     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-05
                        Fer4_2  9 rCigCgaCvsaC 20
                                  +C +Cg Cv+aC
  gi|15668439|ref|NP_247237.1| 12 NCDNCGDCVKAC 23
                                  5*********** PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.032
                        Fer4_2  9 rCigCg..aCvsaCP 21
                                   C +C   +C  +CP
  gi|15668439|ref|NP_247237.1| 45 VCQHCAsaPCKEVCP 59
                                  57788556******* PP

  == domain 3  score: 26.0 bits;  conditional E-value: 4.6e-09
                        Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                  +v+ ++d CigCg C  aCP
  gi|15668439|ref|NP_247237.1| 69 YVYLNEDVCIGCGLCALACP 88
                                  6899**************** PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0015
                        Fer4_2   9 rCigCg....aCvsaC 20 
                                   +Ci C+    aCv+aC
  gi|15668439|ref|NP_247237.1| 100 KCILCNgdepACVKAC 115
                                   9****7799******* PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   3.6   5.5e-06    0.0076       8      21 ..      12      25 ..      12      33 .. 0.89
   2 ?    5.2   4.8     0.018        25       9      24 .]      46      63 ..      45      63 .. 0.84
   3 !   25.9   2.1   5.1e-09     7e-06       5      24 .]      73      92 ..      70      92 .. 0.94
   4 ?    5.1   5.6     0.019        26       8      20 ..     100     116 ..      97     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.5e-06
                        Fer4_6  8 kCigCgdCvrvCPe 21
                                  +C+ CgdCv++C e
  gi|15668439|ref|NP_247237.1| 12 NCDNCGDCVKACME 25
                                  6***********76 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.018
                        Fer4_6  9 CigCgd..CvrvCPegai 24
                                  C +C    C  vCP  ai
  gi|15668439|ref|NP_247237.1| 46 CQHCASapCKEVCPVSAI 63
                                  88994447*******998 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 5.1e-09
                        Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                  ++d CigCg C+ +CP+gai
  gi|15668439|ref|NP_247237.1| 73 NEDVCIGCGLCALACPFGAI 92
                                  7899***************8 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.019
                        Fer4_6   8 kCigC.gd...CvrvCP 20 
                                   kCi C gd   Cv++C 
  gi|15668439|ref|NP_247237.1| 100 KCILCnGDepaCVKACS 116
                                   8****888********7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1  13.0   2.7e-05     0.037       7      57 ..      12      63 ..       7      65 .. 0.75
   2 !   22.6   1.1   6.2e-08   8.5e-05      31      59 .]      67      94 ..      61      94 .. 0.77
   3 !    6.6   1.7    0.0061       8.5       7      29 ..     100     126 ..      95     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                       Fer4_21  7 kCigCgkCliaCedt...shqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                  +C +Cg C++aC ++   +  ai  ++ +++++v ++C   + C +vCPv  +i
  gi|15668439|ref|NP_247237.1| 12 NCDNCGDCVKACMEKnkvGRIAIMEKDGKYIPIVCQHCAS-APCKEVCPV-SAI 63
                                  799*********8752113345556666899999999976.68******9.666 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 6.2e-08
                       Fer4_21 31 ktvlkvvedeCvGCnlCssvCPvedciem 59
                                  + ++ + ed C+GC lC+  CP  ++i m
  gi|15668439|ref|NP_247237.1| 67 DGYVYLNEDVCIGCGLCALACPF-GAILM 94
                                  4566778999************7.88866 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0061
                       Fer4_21   7 kCigCg....kCliaCedtshqaieid 29 
                                   kCi C+     C++aC++ + + ++++
  gi|15668439|ref|NP_247237.1| 100 KCILCNgdepACVKACSKRCLELVDVN 126
                                   8****966666*****99988888664 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4  15.4   4.5e-05     0.062       3      56 .]       7      59 ..       5      59 .. 0.79
   2 !    8.5   3.3    0.0016       2.2       6      22 ..      43      61 ..      38      68 .. 0.80
   3 !   20.2  11.3   3.3e-07   0.00046       2      55 ..      70     115 ..      69     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                       Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg..aCveaCP 56
                                  +     C +Cg+CvkaC +  +++++  +a  e+  +  +  C++c    C e+CP
  gi|15668439|ref|NP_247237.1|  7 IMTNFNCDNCGDCVKAC-M--EKNKVGRIAIMEKDGKYIPIVCQHCAsaPCKEVCP 59
                                  556678***********.7..666666666666666679*******7779*****9 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0016
                       Fer4_10  6 ddtCirCg..kCvkaCPad 22
                                  +  C +C+   C+++CP++
  gi|15668439|ref|NP_247237.1| 43 PIVCQHCAsaPCKEVCPVS 61
                                  568****9999******94 PP

  == domain 3  score: 20.2 bits;  conditional E-value: 3.3e-07
                       Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg....aCveaC 55 
                                   v++++d Ci+Cg C  aCP+        g++      ++k +kC+ c     aCv+aC
  gi|15668439|ref|NP_247237.1|  70 VYLNEDVCIGCGLCALACPF--------GAILM----EDKAYKCILCNgdepACVKAC 115
                                   6789****************........55444....445667****66778*****9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   4.5   8.9e-05      0.12      34      48 ..      11      25 ..       2      28 .. 0.75
   2 !   14.0  14.7   3.1e-05     0.042       1      51 []      12      63 ..      12      63 .. 0.73
   3 !   23.1   8.8   4.5e-08   6.3e-05       2      51 .]      46      92 ..      45      92 .. 0.90
   4 !   12.5  13.8   9.3e-05      0.13       2      49 ..      77     118 ..      76     120 .. 0.77
   5 ?    4.0   4.9      0.04        56       1      17 [.     100     120 ..     100     135 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.9e-05
                        Fer4_9 34 eaCigCgaCveaCpk 48
                                   +C  Cg+Cv+aC +
  gi|15668439|ref|NP_247237.1| 11 FNCDNCGDCVKACME 25
                                  379999999999976 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.1e-05
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga..CveaCpkgai 51
                                  +C +Cg Cv+aC  +  v++ a  +   +      C +C +  C e+Cp  ai
  gi|15668439|ref|NP_247237.1| 12 NCDNCGDCVKACMEKNKVGRIAIMEKDGKYIP-IVCQHCASapCKEVCPVSAI 63
                                  6***********66655555444444443333.36**************9887 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 4.5e-08
                        Fer4_9  2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  C  C +  C e+Cp  +++ +++  + + +      CigCg C+ aCp gai
  gi|15668439|ref|NP_247237.1| 46 CQHCASapCKEVCPVSAIEHKDGYVYLNEDV-----CIGCGLCALACPFGAI 92
                                  999*8667***********999999988754.....************9987 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 9.3e-05
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga....CveaCpkg 49 
                                   C+gCg C  aCp+g++ ++++++k          Ci C+     Cv+aC k 
  gi|15668439|ref|NP_247237.1|  77 CIGCGLCALACPFGAILMEDKAYK----------CILCNGdepaCVKACSKR 118
                                   ****************77777766..........666766666677777665 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.04
                        Fer4_9   1 kCtgCga....CveaCpagvv 17 
                                   kC+ C+     Cv+aC +   
  gi|15668439|ref|NP_247237.1| 100 KCILCNGdepaCVKACSKRCL 120
                                   466663223336666655554 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   4.1   0.00016      0.22       1      13 [.      13      25 ..      13      27 .. 0.90
   2 !    9.4   6.5    0.0016       2.3       1      15 []      46      62 ..      46      62 .. 0.87
   3 !   18.2   5.0   2.5e-06    0.0035       1      15 []      77      91 ..      77      91 .. 0.98
   4 !    8.2   6.2    0.0039       5.4       1      13 [.     101     117 ..     101     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                        Fer4_3  1 CtgCgaCvevCPv 13
                                  C++Cg Cv++C +
  gi|15668439|ref|NP_247237.1| 13 CDNCGDCVKACME 25
                                  ***********75 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0016
                        Fer4_3  1 CtgCg..aCvevCPvgA 15
                                  C++C   +C evCPv A
  gi|15668439|ref|NP_247237.1| 46 CQHCAsaPCKEVCPVSA 62
                                  ****6568******977 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 2.5e-06
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gCg+C  +CP gA
  gi|15668439|ref|NP_247237.1| 77 CIGCGLCALACPFGA 91
                                  *************98 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0039
                        Fer4_3   1 CtgCg....aCvevCPv 13 
                                   C+ C+    aCv++C +
  gi|15668439|ref|NP_247237.1| 101 CILCNgdepACVKACSK 117
                                   ****88999******76 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   1.5    0.0019       2.6       1      14 [.      12      25 ..      12      38 .. 0.88
   2 !   13.5   1.3   7.5e-05       0.1       2      21 ..      46      67 ..      45      75 .. 0.85
   3 !   17.5   2.8   4.3e-06     0.006       2      20 ..      77      95 ..      76     105 .. 0.85
   4 ?    2.6   1.8       0.2   2.7e+02       2      29 ..     101     133 ..     100     159 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0019
                       Fer4_16  1 rCgtCgkCaevCPt 14
                                  +C +Cg C+++C +
  gi|15668439|ref|NP_247237.1| 12 NCDNCGDCVKACME 25
                                  6***********65 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.5e-05
                       Fer4_16  2 CgtCgk..CaevCPtnaikekk 21
                                  C+ C    C evCP++ai++k 
  gi|15668439|ref|NP_247237.1| 46 CQHCASapCKEVCPVSAIEHKD 67
                                  99999889***********984 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 4.3e-06
                       Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                  C++Cg Ca +CP +ai ++
  gi|15668439|ref|NP_247237.1| 77 CIGCGLCALACPFGAILME 95
                                  ****************988 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.2
                       Fer4_16   2 CgtCg....kCaevCPtnaikek.kekeieare 29 
                                   C+ C+    +C+++C  ++++    ++ i a++
  gi|15668439|ref|NP_247237.1| 101 CILCNgdepACVKACSKRCLELVdVNELIFAKR 133
                                   5555533336*****999998763333344444 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   4.5     0.019        26       3      14 ..      12      23 ..      11      24 .. 0.95
   2 !    8.8   1.3    0.0019       2.6       4      16 ..      46      60 ..      36      67 .. 0.93
   3 !   17.7   1.7   2.5e-06    0.0035       2      17 .]      75      90 ..      74      90 .. 0.91
   4 ?    4.7   3.7     0.037        51       3      15 ..     100     116 ..      98     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.019
                        Fer4_4  3 rCigCgsCvaaC 14
                                  +C +Cg Cv aC
  gi|15668439|ref|NP_247237.1| 12 NCDNCGDCVKAC 23
                                  69********** PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0019
                        Fer4_4  4 CigCgs..CvaaCPq 16
                                  C++C s  C  +CP+
  gi|15668439|ref|NP_247237.1| 46 CQHCASapCKEVCPV 60
                                  **************6 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 2.5e-06
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  + CigCg C  aCP+g
  gi|15668439|ref|NP_247237.1| 75 DVCIGCGLCALACPFG 90
                                  78************86 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.037
                        Fer4_4   3 rCigCg....sCvaaCP 15 
                                   +Ci C     +Cv aC+
  gi|15668439|ref|NP_247237.1| 100 KCILCNgdepACVKACS 116
                                   68855544448*****7 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1  15.0      0.92   1.3e+03       3      64 ..      11      61 ..       9      62 .. 0.69
   2 ?   13.2   1.9   6.5e-05     0.089       5      18 ..      77      90 ..      75      98 .. 0.84
   3 ?    4.3   1.6     0.041        57       2      16 ..      98     116 ..      96     154 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.92
                        Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga..CtevCpvg 64
                                  ++C +Cg C +aC           +++ ++++   e+++   +++   C++c +  C+evCpv+
  gi|15668439|ref|NP_247237.1| 11 FNCDNCGDCVKACME---------KNKVGRIA-IMEKDG---KYIPIVCQHCASapCKEVCPVS 61
                                  689999999999942.........22233333.334444...45677899999999******86 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.5e-05
                        Fer4_8  5 CieCgaCqsaCpvl 18
                                  Ci+Cg+C  aCp+ 
  gi|15668439|ref|NP_247237.1| 77 CIGCGLCALACPFG 90
                                  ************74 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.041
                        Fer4_8   2 lekCieCg....aCqsaCp 16 
                                   ++kCi C     aC +aC 
  gi|15668439|ref|NP_247237.1|  98 AYKCILCNgdepACVKACS 116
                                   5788888767777777773 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.6   0.00063      0.87       1      14 [.      12      25 ..       5      40 .. 0.80
   2 ?    5.1   1.7     0.024        33       2      17 ..      46      63 ..      45      75 .. 0.76
   3 ?   12.3   1.2   0.00014      0.19      46      58 ..      77      89 ..      64      92 .. 0.78
   4 ?   10.1   3.5   0.00066      0.91       2      16 ..      77      91 ..      76     102 .. 0.66
   5 ?    1.5   3.8      0.33   4.6e+02      41      57 ..      96     112 ..      90     124 .. 0.68
   6 ?   -1.3   4.7       2.3   3.2e+03       2      13 ..     101     116 ..     100     152 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00063
                       Fer4_17  1 rCiqCgyClpeCps 14
                                  +C +Cg C+++C  
  gi|15668439|ref|NP_247237.1| 12 NCDNCGDCVKACME 25
                                  58888888888865 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.024
                       Fer4_17  2 CiqCgy..ClpeCpsyea 17
                                  C++C+   C ++Cp  ++
  gi|15668439|ref|NP_247237.1| 46 CQHCASapCKEVCPVSAI 63
                                  99999778*****98655 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00014
                       Fer4_17 46 CieCgeCerkCPq 58
                                  Ci+Cg+C+ +CP 
  gi|15668439|ref|NP_247237.1| 77 CIGCGLCALACPF 89
                                  7777777777775 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00066
                       Fer4_17  2 CiqCgyClpeCpsye 16
                                  Ci+Cg C+ +Cp+++
  gi|15668439|ref|NP_247237.1| 77 CIGCGLCALACPFGA 91
                                  666666666666654 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.33
                       Fer4_17  41 ekaslCieCgeCerkCP 57 
                                   +ka +Ci C++ e +C 
  gi|15668439|ref|NP_247237.1|  96 DKAYKCILCNGDEPACV 112
                                   57888888886444443 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 2.3
                       Fer4_17   2 CiqCgy....ClpeCp 13 
                                   Ci C      C+++C+
  gi|15668439|ref|NP_247237.1| 101 CILCNGdepaCVKACS 116
                                   6666633333666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1073.41
//
Query:       gi|15668440|ref|NP_247238.1|  [L=298]
Description: pyruvate ferredoxin oxidoreductase subunit beta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-29  100.2   0.2    1.4e-28   99.6   0.2    1.3  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
     0.0077   15.5   0.2      0.011   15.0   0.2    1.2  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
  ------ inclusion threshold ------
      0.044   13.5   0.3      0.096   12.5   0.3    1.6  1  HTH_38          Helix-turn-helix domain
       0.15   12.4   0.1       0.37   11.1   0.1    1.6  1  Mur_ligase_C    Mur ligase family, glutamate ligase domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   0.2   3.1e-32   1.4e-28       2     153 .]      45     214 ..      44     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 3.1e-32
                                   SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHH...H.........STTSEEEEEEEHHHHHHT.GGGHHHHH CS
                  TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakl...a.........kpdrevvaivGDGgflmi.lqelatav 69 
                                   +Gcl++++  +    + +s+  + +++++ ++ + A+G+++   a         +++ +v+ai GDGg+++i +q+l+ a+
  gi|15668440|ref|NP_247238.1|  45 TGCLEVMTTPY----PETSWRVPWIHTAFENAAATASGIEAavkAlkrkrgkfaDKKINVIAIGGDGGTADIgFQALSGAM 121
                                   79999955555....77889999*****************966615555555535578*********************** PP

                                   HTT-SEEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB......BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHH CS
                  TPP_enzyme_C  70 rrnlpitvvvlnNegygmtggq...qepfggkrksgpagk.....dlkpvdfaklaealGak.garvekadveeleealke 141
                                   +r+++i++++++Ne+y++tg q   ++pf + ++++pag+     d +++d+ ++++a+G++ +a+   +++e++ +++k+
  gi|15668440|ref|NP_247238.1| 122 ERGHDILYIMYDNEAYMNTGIQrssSTPFMAATTTSPAGSkirgeDRPKKDMTMIMAAHGIPyVATACISYPEDFMRKVKK 202
                                   ***************************************9****88****************9998889999********* PP

                                   HHCSSSEEEEEE CS
                  TPP_enzyme_C 142 alekkgpaliev 153
                                   al+ +gp +i+v
  gi|15668440|ref|NP_247238.1| 203 ALSIEGPKFIQV 214
                                   **********87 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   2.4e-06     0.011     118     177 ..      74     140 ..      64     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-06
                DXP_synthase_N 118 saalGlava........rdlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisk 177
                                   ++a G+ +a         + +++k +v+a+ GDg+ t+ + f+al  + e  +++l i+ dNe  +++
  gi|15668440|ref|NP_247238.1|  74 ATASGIEAAvkalkrkrGKFADKKINVIAIGGDGG-TADIGFQALSGAMERGHDILYIMYDNEAYMNT 140
                                   445555555322211112233347899*******9.99************************987765 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   2.1e-05     0.096       1      21 [.     273     293 ..     273     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                        HTH_38   1 kykhLsleeReeIerllaeGl 21 
                                   +y+hL+ e+ e+I++ ++e++
  gi|15668440|ref|NP_247238.1| 273 RYRHLTDEDIERIQKYIDEKC 293
                                   69**************99875 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   8.3e-05      0.37      20      80 ..      72     134 ..      66     141 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.3e-05
                                   T--SHHHHHHHHHHHHHHSS...SSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEEEEEES CS
                  Mur_ligase_C  20 yahnpdslsaalkalreiap...dkrlilvfgpggelgertrtfhdefgrlasaladslvvlgd 80 
                                    a++  +++aa+kal+       dk++ +++  gg+ g+ ++ f+++ g+++  +++ ++++++
  gi|15668440|ref|NP_247238.1|  72 AAATASGIEAAVKALKRKRGkfaDKKINVIAI-GGDGGTADIGFQALSGAMERGHDILYIMYDN 134
                                   699999*********88755887444444444.556666**************95555666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1933.69
//
Query:       gi|15668441|ref|NP_247239.1|  [L=389]
Description: pyruvate ferredoxin oxidoreductase subunit alpha PorA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-84  282.9   1.1    2.7e-84  282.5   1.1    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    2.2e-34  117.8   0.0    5.1e-34  116.6   0.0    1.6  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    1.9e-07   31.0   0.1    7.5e-07   29.1   0.0    2.0  2  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
      0.017   15.4   0.1      0.036   14.4   0.1    1.6  1  DUF2524          Protein of unknown function (DUF2524)
      0.055   13.4   0.0        0.3   11.0   0.0    2.1  2  MannoseP_isomer  Mannose-6-phosphate isomerase
       0.13   12.0   0.0       0.23   11.1   0.0    1.4  1  DDE_Tnp_ISL3     Transposase


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.5   1.1     9e-88   2.7e-84       1     230 [.      18     243 ..      18     244 .. 0.99

  Alignments for each domain:
  == domain 1  score: 282.5 bits;  conditional E-value: 9e-88
                                   .HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHH CS
                         POR_N   1 eaaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgl 81 
                                   eaa+ a+vdviaaYPITP+++++e+lae++a+ge+ d+e++++esE++a+sa+iGAaa+Gar++TaT++qGl+Lm+e+l++
  gi|15668441|ref|NP_247239.1|  18 EAAKLADVDVIAAYPITPQTTCVEKLAEFVANGEL-DAEYIKVESEHSAMSACIGAAATGARTFTATASQGLALMHEMLFI 97 
                                   58999*****************************9.9******************************************** PP

                                   HHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEEEHHHH.H CS
                         POR_N  82 aageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlfDgfllsh 160
                                   a+g++lP+v++v++Ral+++ ++i++d++D +a rd+g+i++++e++qe  d +++A+++Ae+  v +Pv+v++Dgf+l+h
  gi|15668441|ref|NP_247239.1|  98 ASGMRLPIVMMVANRALSAP-INIWNDHQDSIAERDSGWIQIYVEDNQETLDSIIQAYKIAENedVLLPVMVCLDGFILTH 177
                                   ********************.******************************************9***************** PP

                                   EEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHHH CS
                         POR_N 161 evekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvveeve 230
                                   +ve+v++p+ e     ++e+l  ye+k+++ldp++pi++g+  +pd+++e r++ +ea+++a+kv+++v+
  gi|15668441|ref|NP_247239.1| 178 TVEPVTIPKAE----RVREFLGVYEPKHAYLDPDRPITQGPVGVPDCYMETRKQIEEAMERAKKVIRDVN 243
                                   ***********....***************************************************9986 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.0   1.7e-37   5.1e-34       1     102 []     267     367 ..     267     367 .. 0.99

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 1.7e-37
                                   -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G.-HHHHHHHHHTGG CS
                       PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgse.Gqlveevkaalkk 80 
                                   A++v+vamGsv+gt+k ++del++eg +vGllr+r++rPFP+e++kellk++++++vld+nis+g++ G+l+ e+++ lk+
  gi|15668441|ref|NP_247239.1| 267 ADTVLVAMGSVCGTIKYVIDELKKEGKNVGLLRIRAFRPFPKEDVKELLKDANNIAVLDKNISLGFNkGALGIEMASILKN 347
                                   89******************************************************************************9 PP

                                   GTSEEEEEE--GGG----HHHH CS
                       PFOR_II  81 skvkvvnfvaglgGrditvedi 102
                                   +  kv+n++ glgGrdi+++di
  gi|15668441|ref|NP_247239.1| 348 K--KVCNYIVGLGGRDIKIDDI 367
                                   9..****************997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.4   7.3e+03      11      30 ..      93     112 ..      92     118 .. 0.82
   2 !   29.1   0.0   2.5e-10   7.5e-07       9     104 ..     266     362 ..     261     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.4
                                   SEEEEEETTHHHHHHHHHHH CS
               Transketolase_C  11 dvtlvayGsmveealeAaee 30 
                                   +++++a G+ ++ ++ +a++
  gi|15668441|ref|NP_247239.1|  93 EMLFIASGMRLPIVMMVANR 112
                                   56889999999999999876 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 2.5e-10
                                   TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEES....TTSHHHHHHHHHH CS
               Transketolase_C   9 gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavk....rgGigsevaaala 85 
                                   + d +lva+Gs + +   +++eL+keg ++ ++ +r ++p+ ke+++e++k  + + v++ +       g++g e a++l 
  gi|15668441|ref|NP_247239.1| 266 NADTVLVAMGSVCGTIKYVIDELKKEGKNVGLLRIRAFRPFPKEDVKELLKDANNIAVLDKNISlgfnKGALGIEMASILK 346
                                   7899***************************************************99998765311114566666666666 PP

                                   HCCCTTCSSEEEEEEE-SS CS
               Transketolase_C  86 eeafdgldapvkrvggpdv 104
                                       +++  +++ +gg d+
  gi|15668441|ref|NP_247239.1| 347 N---KKVCNYIVGLGGRDI 362
                                   6...666677777776666 PP

>> DUF2524  Protein of unknown function (DUF2524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.2e-05     0.036       1      31 [.     222     252 ..     222     267 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                       DUF2524   1 Matrqsveellqkceqaieeaeeqfeeakrq 31 
                                   M tr+++ee++++++++i+ ++e+f+e  + 
  gi|15668441|ref|NP_247239.1| 222 METRKQIEEAMERAKKVIRDVNEEFAEWFKR 252
                                   89***********************986665 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0001       0.3       8      55 ..     263     310 ..     256     324 .. 0.88
   2 ?   -0.7   0.0       0.4   1.2e+03      22      40 ..     363     381 ..     355     385 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
               MannoseP_isomer   8 vvetkdavlvadkdkvqdvkkvveelkaegreeaelhrevyrPWGsye 55 
                                    +++ d+vlva  + +  +k v++elk+eg++   l  +++rP+ + +
  gi|15668441|ref|NP_247239.1| 263 NLDNADTVLVAMGSVCGTIKYVIDELKKEGKNVGLLRIRAFRPFPKED 310
                                   57899**************************************97765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.4
               MannoseP_isomer  22 kvqdvkkvveelkaegree 40 
                                   k++d+k ++++++++++++
  gi|15668441|ref|NP_247239.1| 363 KIDDIKTIINHVEKAEDDS 381
                                   789*********9998876 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.8e-05      0.23     180     217 ..     225     263 ..     217     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.8e-05
                  DDE_Tnp_ISL3 180 rsglke.fkklaktlknhreeIlnyfdsrlsngpvEgiN 217
                                   r++++e ++++ k ++   ee  ++f+ ++ ng vE+ N
  gi|15668441|ref|NP_247239.1| 225 RKQIEEaMERAKKVIRDVNEEFAEWFKRKYGNGLVEAYN 263
                                   4556666********************99********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      813  (0.0453455); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2539.15
//
Query:       gi|15668442|ref|NP_247240.1|  [L=86]
Description: pyruvate ferredoxin oxidoreductase subunit delta PorD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-15   55.9  14.8    2.1e-08   33.6   3.3    2.2  2  Fer4      4Fe-4S binding domain
      7e-12   45.3  10.0    9.3e-12   44.9  10.0    1.2  1  Fer4_21   4Fe-4S dicluster domain
    1.6e-10   40.6  13.9    1.8e-05   24.6   2.9    2.2  2  Fer4_6    4Fe-4S binding domain
      2e-10   40.6  31.6    1.7e-06   28.1  12.0    1.8  3  Fer4_9    4Fe-4S dicluster domain
    2.3e-09   37.7  21.4      9e-08   32.6  10.9    1.6  2  Fer4_7    4Fe-4S dicluster domain
    4.5e-09   36.3  11.8    0.00013   22.0   2.3    2.1  2  Fer4_10   4Fe-4S dicluster domain
    8.8e-09   36.2  10.1    0.00012   22.9   0.9    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    6.9e-07   29.0   9.6     0.0028   17.7   1.1    2.2  2  Fer4_2    4Fe-4S binding domain
    6.3e-05   23.4   7.1      0.059   13.9   0.2    2.1  2  Fer4_17   4Fe-4S dicluster domain
    0.00077   19.8  12.6     0.0087   16.5   2.7    2.2  2  Fer4_4    4Fe-4S binding domain
     0.0045   17.5  11.4      0.018   15.5   1.2    2.6  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.012   16.0  13.2       0.13   12.8   2.6    2.1  3  Fer4_8    4Fe-4S dicluster domain
      0.039   13.9   0.1      0.078   12.9   0.1    1.4  1  IceA2     Helicobacter pylori IceA2 protein
      0.048   14.4  11.1        1.4    9.7   3.2    2.6  2  Fer4_15   4Fe-4S single cluster domain
       0.12   12.5   0.0       0.13   12.3   0.0    1.3  1  CH_2      CH-like domain in sperm protein
       0.22   12.5  16.4        1.7    9.8   3.5    2.2  2  Fer4_3    4Fe-4S binding domain
       0.45   11.4  10.2          4    8.3   1.1    2.1  3  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   3.8   9.8e-10     1e-06       2      24 .]      28      50 ..      27      50 .. 0.93
   2 !   33.6   3.3     2e-11   2.1e-08       2      24 .]      58      80 ..      57      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 9.8e-10
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  + d ekC++C +C+  CP gAI+
  gi|15668442|ref|NP_247240.1| 28 ILDNEKCVKCENCYIFCPEGAIQ 50
                                  789******************95 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 2e-11
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  +id++ C gC +C++ CPv+AIt
  gi|15668442|ref|NP_247240.1| 58 KIDYDYCKGCLICMNECPVNAIT 80
                                  79********************7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9  10.0   8.8e-15   9.3e-12       3      58 ..      29      80 ..      27      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 8.8e-15
                       Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                  +d++kC++C++C+i C++    ai+ d++  +k+  d C GC +C++ CPv ++i+
  gi|15668442|ref|NP_247240.1| 29 LDNEKCVKCENCYIFCPE---GAIQEDENGNFKIDYDYCKGCLICMNECPV-NAIT 80
                                  799**************7...8999*************************9.8886 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   2.9   1.8e-08   1.8e-05       5      24 .]      30      49 ..      29      49 .. 0.96
   2 !   21.7   3.4   1.4e-07   0.00015       3      24 .]      58      79 ..      57      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.8e-08
                        Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                  d +kC+ C++C++ CPegai
  gi|15668442|ref|NP_247240.1| 30 DNEKCVKCENCYIFCPEGAI 49
                                  789****************8 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.4e-07
                        Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                   id+d C gC  C++ CP +ai
  gi|15668442|ref|NP_247240.1| 58 KIDYDYCKGCLICMNECPVNAI 79
                                  59******************98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   1.5     2e-07   0.00021      33      51 .]      24      49 ..       6      49 .. 0.71
   2 !   28.1  12.0   1.6e-09   1.7e-06       1      51 []      33      79 ..      33      79 .. 0.94
   3 !   13.6   3.0   5.4e-05     0.057       1      20 [.      63      82 ..      63      86 .] 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2e-07
                        Fer4_9 33 e.......eaCigCgaCveaCpkgai 51
                                          e+C++C+ C+  Cp+gai
  gi|15668442|ref|NP_247240.1| 24 TfrpildnEKCVKCENCYIFCPEGAI 49
                                  2444566789*************997 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 1.6e-09
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  kC++C +C   Cp g+++ed+++++     +    C gC  C++ Cp +ai
  gi|15668442|ref|NP_247240.1| 33 KCVKCENCYIFCPEGAIQEDENGNFKIDYDY----CKGCLICMNECPVNAI 79
                                  7**********************99998765....*************987 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 5.4e-05
                        Fer4_9  1 kCtgCgaCveaCpagvvved 20
                                  +C gC  C++ Cp +++++ 
  gi|15668442|ref|NP_247240.1| 63 YCKGCLICMNECPVNAITKV 82
                                  69999999999999998765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.8   9.2e-06    0.0097      29      52 .]      25      48 ..      11      48 .. 0.79
   2 !   32.6  10.9   8.6e-11     9e-08       1      52 []      33      78 ..      33      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.2e-06
                        Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                   ++ +d ekC+ C++C   CP ga
  gi|15668442|ref|NP_247240.1| 25 FRPILDNEKCVKCENCYIFCPEGA 48
                                  55678999*************997 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 8.6e-11
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  +C++C++C   Cp +ai+ de          +id+++C gC  C+++CP++a
  gi|15668442|ref|NP_247240.1| 33 KCVKCENCYIFCPEGAIQEDEN------GNFKIDYDYCKGCLICMNECPVNA 78
                                  7*****************9885......57899*****************97 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   2.3   1.2e-07   0.00013       3      32 ..      28      52 ..      26      58 .. 0.76
   2 !   20.3   2.1   4.2e-07   0.00045       3      23 ..      58      78 ..      56      86 .] 0.80

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.2e-07
                       Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgea 32
                                  ++d ++C++C++C  +CP      ga++e+
  gi|15668442|ref|NP_247240.1| 28 ILDNEKCVKCENCYIFCPE-----GAIQED 52
                                  7899***************.....443333 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4.2e-07
                       Fer4_10  3 vidddtCirCgkCvkaCPadl 23
                                  +id d C +C  C++ CP+++
  gi|15668442|ref|NP_247240.1| 58 KIDYDYCKGCLICMNECPVNA 78
                                  699****************55 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.9   1.1e-07   0.00012       1      26 [.      33      58 ..      33      62 .. 0.87
   2 !   17.9   2.5   4.2e-06    0.0044       2      22 ..      64      84 ..      63      86 .] 0.88

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.1e-07
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkekeie 26
                                  +C++C++C   CP++ai+e+++ +++
  gi|15668442|ref|NP_247240.1| 33 KCVKCENCYIFCPEGAIQEDENGNFK 58
                                  6*******************777665 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 4.2e-06
                       Fer4_16  2 CgtCgkCaevCPtnaikekke 22
                                  C++C  C++ CP+nai++ +e
  gi|15668442|ref|NP_247240.1| 64 CKGCLICMNECPVNAITKVRE 84
                                  ****************99855 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.8   7.5e-06    0.0079       3      22 .]      27      46 ..      25      46 .. 0.89
   2 !   17.7   1.1   2.7e-06    0.0028       3      21 ..      57      75 ..      55      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.5e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                  +  d ++C+ C+ C+  CP+
  gi|15668442|ref|NP_247240.1| 27 PILDNEKCVKCENCYIFCPE 46
                                  67899**************5 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.7e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  +++d d C gC +C + CP
  gi|15668442|ref|NP_247240.1| 57 FKIDYDYCKGCLICMNECP 75
                                  689**************** PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.2   5.6e-05     0.059      43      59 ..      31      47 ..       5      49 .. 0.83
   2 !   12.7   2.1   0.00013      0.14       2      20 ..      64      82 ..      63      86 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-05
                       Fer4_17 43 aslCieCgeCerkCPqg 59
                                   ++C++C++C   CP+g
  gi|15668442|ref|NP_247240.1| 31 NEKCVKCENCYIFCPEG 47
                                  589************87 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00013
                       Fer4_17  2 CiqCgyClpeCpsyeaydn 20
                                  C +C  C++eCp +++++ 
  gi|15668442|ref|NP_247240.1| 64 CKGCLICMNECPVNAITKV 82
                                  ************9998765 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.7   8.2e-06    0.0087       2      16 ..      32      46 ..      31      53 .. 0.91
   2 !    8.7   2.4    0.0025       2.6       2      17 .]      62      77 ..      61      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.2e-06
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  e+C+ C  C+++CP 
  gi|15668442|ref|NP_247240.1| 32 EKCVKCENCYIFCPE 46
                                  89************5 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0025
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  + C gC  C++ CP++
  gi|15668442|ref|NP_247240.1| 62 DYCKGCLICMNECPVN 77
                                  89************85 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.2   1.7e-05     0.018       2      18 ..      30      46 ..      29      57 .. 0.90
   2 !    6.9   2.5    0.0086         9       1      17 [.      59      75 ..      59      77 .. 0.93
   3 ?    5.5   0.3     0.024        26      48      57 ..      71      80 ..      68      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                       Fer4_13  2 DrdtCiacgaCvelaPd 18
                                  D+++C+ c++C+ ++P+
  gi|15668442|ref|NP_247240.1| 30 DNEKCVKCENCYIFCPE 46
                                  89**************8 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0086
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  +D d C +c +C + +P
  gi|15668442|ref|NP_247240.1| 59 IDYDYCKGCLICMNECP 75
                                  79999***********9 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.024
                       Fer4_13 48 adaCPvesIg 57
                                  +++CPv++I+
  gi|15668442|ref|NP_247240.1| 71 MNECPVNAIT 80
                                  689******7 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.4    0.0027       2.8      49      64 ..      32      47 ..      16      48 .. 0.82
   2 ?    8.8   3.1    0.0021       2.3      50      64 ..      33      47 ..      30      60 .. 0.71
   3 ?   12.8   2.6   0.00012      0.13       3      22 ..      62      81 ..      60      86 .] 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0027
                        Fer4_8 49 wsCttcgaCtevCpvg 64
                                  ++C+ c++C   Cp+g
  gi|15668442|ref|NP_247240.1| 32 EKCVKCENCYIFCPEG 47
                                  5688888888888875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0021
                        Fer4_8 50 sCttcgaCtevCpvg 64
                                  +C+ c++C   Cp+g
  gi|15668442|ref|NP_247240.1| 33 KCVKCENCYIFCPEG 47
                                  566666666666654 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00012
                        Fer4_8  3 ekCieCgaCqsaCpvlrrtk 22
                                  ++C +C  C+++Cpv   tk
  gi|15668442|ref|NP_247240.1| 62 DYCKGCLICMNECPVNAITK 81
                                  68999999999999876665 PP

>> IceA2  Helicobacter pylori IceA2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   7.4e-05     0.078       9      25 ..      46      62 ..      42      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.4e-05
                         IceA2  9 nGkiqeyenGiykRtYd 25
                                   G iqe enG++k  Yd
  gi|15668442|ref|NP_247240.1| 46 EGAIQEDENGNFKIDYD 62
                                  599**********9998 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.0    0.0026       2.7       3      28 ..      29      55 ..      28      56 .. 0.82
   2 ?    9.7   3.2    0.0013       1.4       2      19 ..      58      75 ..      57      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
                       Fer4_15  3 vDrdaCigcglCvaeape.vfeldedg 28
                                  +D ++C  c++C+  +pe  +++de+g
  gi|15668442|ref|NP_247240.1| 29 LDNEKCVKCENCYIFCPEgAIQEDENG 55
                                  79**************75367777766 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                       Fer4_15  2 vvDrdaCigcglCvaeap 19
                                  ++D d C gc  C+ e+p
  gi|15668442|ref|NP_247240.1| 58 KIDYDYCKGCLICMNECP 75
                                  79***************8 PP

>> CH_2  CH-like domain in sperm protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.13      43      68 ..       8      33 ..       3      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                          CH_2 43 nysngsslaaklnNWetLekvlkklg 68
                                   y++g+s+++k   W+t++++l + +
  gi|15668442|ref|NP_247240.1|  8 IYEPGNSIKNKTGTWRTFRPILDNEK 33
                                  59********************6533 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.5    0.0016       1.7       1      15 []      34      48 ..      34      48 .. 0.97
   2 ?    8.7   5.0    0.0035       3.7       1      15 []      64      78 ..      64      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ C+ C   CP+gA
  gi|15668442|ref|NP_247240.1| 34 CVKCENCYIFCPEGA 48
                                  9*************9 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0035
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C gC  C++ CPv+A
  gi|15668442|ref|NP_247240.1| 64 CKGCLICMNECPVNA 78
                                  99**77********9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.3    0.0041       4.4       1      13 [.      33      45 ..      13      49 .. 0.69
   2 ?    7.6   2.5    0.0067       7.1       1      14 [.      33      46 ..      33      58 .. 0.86
   3 ?    8.3   1.1    0.0038         4      76      95 ..      58      77 ..      48      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0041
                       Fer4_22  1 rClsCgaCtlvCp 13
                                  +C++C +C + Cp
  gi|15668442|ref|NP_247240.1| 33 KCVKCENCYIFCP 45
                                  4666666666665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0067
                       Fer4_22  1 rClsCgaCtlvCpt 14
                                  +C++C +C + Cp 
  gi|15668442|ref|NP_247240.1| 33 KCVKCENCYIFCPE 46
                                  7***********96 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0038
                       Fer4_22 76 kfgesgCvGCgRCieacpvk 95
                                  k++   C GC  C++ cpv+
  gi|15668442|ref|NP_247240.1| 58 KIDYDYCKGCLICMNECPVN 77
                                  568899***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 587.05
//
Query:       gi|15668443|ref|NP_247241.1|  [L=178]
Description: pyruvate ferredoxin oxidoreductase subunit gamma [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-41  140.9   1.0    5.8e-41  140.5   1.0    1.1  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.21   11.5   0.0    1.3  1  DUF1425   Protein of unknown function (DUF1425)


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.5   1.0   6.5e-45   5.8e-41       1     176 [.      10     170 ..      10     171 .. 0.94

  Alignments for each domain:
  == domain 1  score: 140.5 bits;  conditional E-value: 6.5e-45
                                   CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGGEEEE CS
                           POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldglkpg 79 
                                   GGqG+vta++ilakaa++ G+ +qa++++g e+rG+++++  ri+d++i+ +++++e+d++++ da++l+  ++++glk++
  gi|15668443|ref|NP_247241.1|  10 GGQGAVTAAQILAKAAFYDGKFCQAFPFFGVERRGAPVMAFTRIDDKKITLRCQIYEPDYVIVQDATLLEsvNVVEGLKKD 90 
                                   9*********************************************9999*******************99********** PP

                                   EEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHHHHHHCCS- CS
                           POR  80 giiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lplealeeaikkrfp 159
                                   g +++n+  +++ +l  +               y++dat ia + +g  +++Nt+m+Ga+a+++g +++e++++ai ++f+
  gi|15668443|ref|NP_247241.1|  91 GAVVINT-VKDDLDLGYK--------------TYTIDATGIALDVLG-VPIVNTAMVGAFAGVTGiVSIESVKKAILDTFK 155
                                   *******.3333333333..............479************.********************************* PP

                                   CH.HHHHHHHHHHHHHH CS
                           POR 160 kkkeviekNlkafragy 176
                                   +k  + ekN ka++ +y
  gi|15668443|ref|NP_247241.1| 156 GK--LGEKNAKAAEVAY 170
                                   95..**********999 PP

>> DUF1425  Protein of unknown function (DUF1425)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.4e-05      0.21      18      56 ..      81     119 ..      72     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.4e-05
                                   EEECCCEEEEEEEEEE-SSS-EEEEEEEEEE-TTS-EE- CS
                       DUF1425  18 lresngllraqvtlsnkskkdltlqYrFyWyDkqGleve 56 
                                   ++ ++gl++  +++ n+ k+dl+l Y+ y +D+ G+ ++
  gi|15668443|ref|NP_247241.1|  81 VNVVEGLKKDGAVVINTVKDDLDLGYKTYTIDATGIALD 119
                                   67789999999************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1139.53
//
Query:       gi|15668444|ref|NP_247242.1|  [L=78]
Description: hypothetical protein MJ_0270 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 522.57
//
Query:       gi|15668445|ref|NP_247243.1|  [L=180]
Description: hypothetical protein MJ_0271 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.12   12.2   0.4       0.12   12.2   0.4    3.5  5  Brr6_like_C_C  Di-sulfide bridge nucleocytoplasmic transport 
       0.17   12.1   0.2       0.17   12.1   0.2    2.0  2  CCSMST1        CCSMST1 family


Domain annotation for each model (and alignments):
>> Brr6_like_C_C  Di-sulfide bridge nucleocytoplasmic transport domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   1.3     0.064   5.7e+02      10     124 ..      28      44 ..       8      53 .. 0.56
   2 ?    0.6   1.2     0.049   4.4e+02       9      28 ..      27      46 ..      19      62 .. 0.58
   3 ?    0.5   1.6     0.055   4.9e+02      95     124 ..      72     101 ..      60     104 .. 0.82
   4 ?   12.2   0.4   1.3e-05      0.12      94     129 ..     105     140 ..     102     144 .. 0.86
   5 ?   -2.4   0.4      0.41   3.7e+03       9      22 ..     159     172 ..     152     177 .. 0.46

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.064
                 Brr6_like_C_C  10 lllvllllylvisfvltikkDiekkleekkaellaeieeCkkeYeeNkCdpetrvpaleekCeewekCmnrdpeskverak 90 
                                   + +vl                                                                            
  gi|15668445|ref|NP_247243.1|  28 FKMVLA--------------------------------------------------------------------------- 33 
                                   223333........................................................................... PP

                 Brr6_like_C_C  91 vsaetlaeiinsfvepislktllfllllllivlf 124
                                                          fll++++i+lf
  gi|15668445|ref|NP_247243.1|  34 -----------------------FLLAVFVIWLF 44 
                                   .......................33333333333 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.049
                 Brr6_like_C_C  9 nlllvllllylvisfvltik 28
                                  n+ +vl +l +v+ ++l i 
  gi|15668445|ref|NP_247243.1| 27 NFKMVLAFLLAVFVIWLFID 46
                                  45555555555555555553 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.055
                 Brr6_like_C_C  95 tlaeiinsfvepislktllfllllllivlf 124
                                    l+ i n+ +  i+l  +++l+l+++++lf
  gi|15668445|ref|NP_247243.1|  72 FLGIIYNEVFLDITLGIFAILILIVMGILF 101
                                   578899999999999999888888887776 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 1.3e-05
                 Brr6_like_C_C  94 etlaeiinsfvepislktllfllllllivlfvsnva 129
                                   +++ e++++fve+++ k+ +++l++++++l+++ v 
  gi|15668445|ref|NP_247243.1| 105 KLIFEVFDEFVEHLKQKSGFLTLISIFGMLLTIYVF 140
                                   67889**************99999999999887654 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 0.41
                 Brr6_like_C_C   9 nlllvllllylvis 22 
                                   +++lv+++ +++i 
  gi|15668445|ref|NP_247243.1| 159 TIMLVITANMFIIE 172
                                   33333333333333 PP

>> CCSMST1  CCSMST1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.9e-05      0.17      34      65 ..      30      59 ..      24      65 .. 0.87
   2 ?   -4.4   1.7         2   1.8e+04      36      49 ..     128     141 ..     124     142 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
                       CCSMST1 34 lvislslaaflvYFcilReendlDeaLeksly 65
                                  +v+++ la+f+++   + + n++ e L+++l+
  gi|15668445|ref|NP_247243.1| 30 MVLAFLLAVFVIW--LFIDKNNINERLYENLL 59
                                  899**********..66699*******99986 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 2
                       CCSMST1  36 islslaaflvYFci 49 
                                   is+  + + +Y + 
  gi|15668445|ref|NP_247243.1| 128 ISIFGMLLTIYVFL 141
                                   67788888888554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1256  (0.0700541); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1187.39
//
Query:       gi|15668446|ref|NP_247244.1|  [L=79]
Description: repressor protein YorfE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-20   70.9   0.0    7.5e-20   70.7   0.0    1.1  1  HTH_3           Helix-turn-helix
    1.2e-11   44.5   0.1    1.3e-11   44.3   0.1    1.1  1  HTH_19          Helix-turn-helix domain
    1.4e-08   35.0   0.0    1.8e-08   34.7   0.0    1.1  1  HTH_26          Cro/C1-type HTH DNA-binding domain
    9.4e-08   32.3   0.0    1.2e-07   32.0   0.0    1.1  1  HTH_31          Helix-turn-helix domain
    7.9e-05   22.1   0.0    0.00016   21.1   0.0    1.5  2  Sigma70_r4      Sigma-70, region 4
     0.0001   22.1   0.0    0.00018   21.4   0.0    1.4  1  HTH_11          HTH domain
     0.0001   22.1   0.0    0.00013   21.8   0.0    1.3  1  HTH_25          Helix-turn-helix domain
     0.0021   18.0   0.0     0.0041   17.1   0.0    1.5  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0054   16.5   0.0      0.014   15.2   0.0    1.6  2  HTH_23          Homeodomain-like domain
     0.0063   16.3   0.0      0.025   14.4   0.0    1.9  2  HTH_10          HTH DNA binding domain
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.018   14.6   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.012   15.4   0.0      0.015   15.1   0.0    1.1  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.014   15.1   0.0      0.072   12.7   0.0    1.9  2  GntR            Bacterial regulatory proteins, gntR family
      0.016   15.2   0.0      0.034   14.1   0.0    1.7  2  HTH_36          Helix-turn-helix domain
      0.017   15.3   0.0      0.028   14.6   0.0    1.5  1  HTH_17          Helix-turn-helix domain
      0.035   13.8   0.0      0.083   12.6   0.0    1.6  2  Sigma70_r4_2    Sigma-70, region 4
      0.036   13.8   0.0      0.067   13.0   0.0    1.4  1  TetR_N          Bacterial regulatory proteins, tetR family
      0.041   13.7   0.0      0.088   12.6   0.0    1.6  2  HTH_38          Helix-turn-helix domain
      0.042   13.9   0.0      0.054   13.6   0.0    1.2  1  Phage_CI_repr   Bacteriophage CI repressor helix-turn-helix d
      0.046   13.5   0.0      0.085   12.6   0.0    1.5  1  HTH_Tnp_4       Helix-turn-helix of DDE superfamily endonucle
      0.047   13.4   0.0      0.066   12.9   0.0    1.2  1  Sigma54_DBD     Sigma-54, DNA binding domain
      0.051   14.0   0.1      0.077   13.4   0.1    1.3  1  SAM_1           SAM domain (Sterile alpha motif)
      0.053   13.5   0.0        0.3   11.0   0.0    1.9  2  MarR            MarR family
      0.079   12.9   0.0       0.11   12.4   0.0    1.2  1  MarR_2          MarR family
      0.095   12.5   0.0        1.3    8.9   0.0    2.2  2  MerR            MerR family regulatory protein
       0.11   12.4   0.0       0.15   11.9   0.0    1.2  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
       0.14   12.4   0.0       0.21   11.8   0.0    1.2  1  HTH_28          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0   1.1e-22   7.5e-20       1      54 [.      18      71 ..      18      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 1.1e-22
                                  HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                         HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54
                                  lk +R  ++l+qe+LA+klGvsr+ti +iE+G+  Psl+ ++k+ak++gv++++
  gi|15668446|ref|NP_247244.1| 18 LKYYRALHNLTQEDLAKKLGVSRQTIIAIEKGKYDPSLKLAFKIAKFFGVKIED 71
                                  899************************************************987 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.1   1.9e-14   1.3e-11       4      60 ..      18      73 ..      16      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.9e-14
                        HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyll 60
                                  Lk +R   +ltqe+la++lg+sr  i+aiE+gk+ +ps +l  kia+++g+ +e ++
  gi|15668446|ref|NP_247244.1| 18 LKYYRALHNLTQEDLAKKLGVSRQTIIAIEKGKY-DPSLKLAFKIAKFFGVKIEDIF 73
                                  77778888*************************9.****************999776 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   2.7e-11   1.8e-08       1      63 []      17      78 ..      17      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.7e-11
                        HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLleyepd 63
                                  kL+   a +++t+ +La+++g+s++t+  + kgk   +sl+   ki++ +g++++D+++ye+d
  gi|15668446|ref|NP_247244.1| 17 KLKYYRALHNLTQEDLAKKLGVSRQTIIAIEKGK-YDPSLKLAFKIAKFFGVKIEDIFIYEDD 78
                                  67778899*************************9.6************************987 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   1.8e-10   1.2e-07       6      57 ..      18      68 ..      17      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.8e-10
                        HTH_31  6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57
                                  L+ +R+ ++L+qe++A+ lgvs+ t+  +E G+ + ps+    ++a  +g+ 
  gi|15668446|ref|NP_247244.1| 18 LKYYRALHNLTQEDLAKKLGVSRQTIIAIEKGKYD-PSLKLAFKIAKFFGVK 68
                                  66789*****************************7.**********999985 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.5e-07   0.00016      17      42 ..      21      48 ..      12      49 .. 0.86
   2 ?   -2.4   0.0       5.4   3.6e+03      26      35 ..      61      70 ..      60      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.5e-07
                                  H..TTT--HHHHHHHHTS-HHHHHHHHH CS
                    Sigma70_r4 17 f..geglTleEIgerlgiSrerVrqiek 42
                                  +  +++lT+e+++++lg+Sr ++  iek
  gi|15668446|ref|NP_247244.1| 21 YraLHNLTQEDLAKKLGVSRQTIIAIEK 48
                                  3469*******************88886 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.4
                                  HHHHHTS-HH CS
                    Sigma70_r4 26 IgerlgiSre 35
                                  I++ +g+  e
  gi|15668446|ref|NP_247244.1| 61 IAKFFGVKIE 70
                                  9999999766 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.7e-07   0.00018       7      33 ..      19      44 ..      14      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.7e-07
                        HTH_11  7 elLleargpisgeeLAeeLnvSrrtvr 33
                                  +  ++ ++ ++ e+LA++L+vSr+t+ 
  gi|15668446|ref|NP_247244.1| 19 KYYRALHN-LTQEDLAKKLGVSRQTII 44
                                  55555565.9***************95 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.9e-07   0.00013       2      36 ..      18      52 ..      17      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.9e-07
                                  HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                        HTH_25  2 LraaRearglsleevaketkIrkdylealEeddfd 36
                                  L+  R   +l+ e++ak++ ++ +++ a+E++++d
  gi|15668446|ref|NP_247244.1| 18 LKYYRALHNLTQEDLAKKLGVSRQTIIAIEKGKYD 52
                                  77779999*************************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.2e-06    0.0041      21      39 ..      26      44 ..       8      47 .. 0.86
   2 ?   -2.5   0.0       7.8   5.2e+03      27      36 ..      61      70 ..      60      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.2e-06
                                  EHHHHHHHHHTTSSHHHHH CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvs 39
                                  +ltqe+lA  lG++r+t+ 
  gi|15668446|ref|NP_247244.1| 26 NLTQEDLAKKLGVSRQTII 44
                                  79***************86 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.8
                                  HHHHTTSSHH CS
                     HTH_Crp_2 27 lAsmlGltre 36
                                  +A + G+  e
  gi|15668446|ref|NP_247244.1| 61 IAKFFGVKIE 70
                                  8999998877 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.1e-05     0.014      16      35 ..      23      44 ..      15      49 .. 0.81
   2 ?   -2.0   0.0       5.2   3.5e+03      22      29 ..      60      67 ..      60      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                        HTH_23 16 e..GlsvreIAreLgvsrrTvy 35
                                      l++++ A++Lgvsr+T+ 
  gi|15668446|ref|NP_247244.1| 23 AlhNLTQEDLAKKLGVSRQTII 44
                                  344799**************95 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.2
                        HTH_23 22 eIAreLgv 29
                                  +IA+ +gv
  gi|15668446|ref|NP_247244.1| 60 KIAKFFGV 67
                                  59***998 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.8e-05     0.025      17      40 ..      20      43 ..      18      46 .. 0.87
   2 ?   -0.1   0.0       1.3   8.4e+02      12      35 ..      45      67 ..      43      71 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-05
                        HTH_10 17 YFdyPRrvtlkeLAkelGIskstl 40
                                  Y+   ++ t ++LAk+lG+s++t+
  gi|15668446|ref|NP_247244.1| 20 YYRALHNLTQEDLAKKLGVSRQTI 43
                                  6666678899************97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                        HTH_10 12 AyemGYFdyPRrvtlkeLAkelGI 35
                                  A+e+G +d + +    ++Ak +G+
  gi|15668446|ref|NP_247244.1| 45 AIEKGKYDPSLKLAF-KIAKFFGV 67
                                  677776765433322.46666665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.7e-05     0.018      18      34 ..      27      43 ..      26      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                        HTH_24 18 isqreLAerlglSpstv 34
                                  ++q +LA++lg+S++t+
  gi|15668446|ref|NP_247244.1| 27 LTQEDLAKKLGVSRQTI 43
                                  8**************98 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.3e-05     0.015      10      51 ..      28      67 ..      26      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-05
                YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqvpaervpeIekatnGeV 51
                                  +q  LA++lgvs+q++    kgk   + +   +I k+ +  V
  gi|15668446|ref|NP_247244.1| 28 TQEDLAKKLGVSRQTIIAIEKGKYDPSLKLAFKIAKFFG--V 67
                                  5899************99998888788888888877766..4 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011     0.072      18      41 ..      21      43 ..      15      45 .. 0.90
   2 ?    0.4   0.0       0.8   5.3e+02      13      37 ..      46      68 ..      43      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                  S-TTSB---HHHHHHHHTS-HHHH CS
                          GntR 18 lrpGdkLPsereLaaefgVsrttv 41
                                  +r+   L ++++La+++gVsr+t+
  gi|15668446|ref|NP_247244.1| 21 YRALHNL-TQEDLAKKLGVSRQTI 43
                                  6778889.***************8 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.8
                                  HHTTSS-TTSB---HHHHHHHHTS- CS
                          GntR 13 IlsgelrpGdkLPsereLaaefgVs 37
                                  I +g + p  kL    ++a+ fgV+
  gi|15668446|ref|NP_247244.1| 46 IEKGKYDPSLKL--AFKIAKFFGVK 68
                                  788888888888..67899999986 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.1e-05     0.034      26      43 ..      27      44 ..      10      48 .. 0.91
   2 ?   -2.3   0.0       6.6   4.4e+03      31      40 ..      61      70 ..      60      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.1e-05
                        HTH_36 26 psqetlakrlglsknTvs 43
                                   +qe+lak+lg+s++T++
  gi|15668446|ref|NP_247244.1| 27 LTQEDLAKKLGVSRQTII 44
                                  589**************8 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.6
                        HTH_36 31 lakrlglskn 40
                                  +ak +g++ +
  gi|15668446|ref|NP_247244.1| 61 IAKFFGVKIE 70
                                  8999999865 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.3e-05     0.028       2      25 ..      27      49 ..      26      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.3e-05
                        HTH_17  2 ltveEaAelLgvsrstvyrlirrg 25
                                  lt e++A+ Lgvsr+t+   i +g
  gi|15668446|ref|NP_247244.1| 27 LTQEDLAKKLGVSRQTIIA-IEKG 49
                                  899*************987.6666 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013     0.083      22      43 ..      22      43 ..      20      43 .. 0.93
   2 ?   -2.7   0.0       7.2   4.8e+03      22      32 ..      62      72 ..      57      72 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                  HHTS---HHHHHHHHT--HHHH CS
                  Sigma70_r4_2 22 ryleglsykEIAellgisegtV 43
                                  r+l++l++++ A++lg+s +t+
  gi|15668446|ref|NP_247244.1| 22 RALHNLTQEDLAKKLGVSRQTI 43
                                  899****************996 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.2
                                  HHTS---HHHH CS
                  Sigma70_r4_2 22 ryleglsykEI 32
                                    ++g ++++I
  gi|15668446|ref|NP_247244.1| 62 AKFFGVKIEDI 72
                                  34556666655 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0    0.0001     0.067      13      33 ..      23      43 ..      19      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                                  HTTT--HHHHHHHHTSSHHHH CS
                        TetR_N 13 GydattvreIAkrAGvskgal 33
                                    +++t +++Ak++Gvs+ ++
  gi|15668446|ref|NP_247244.1| 23 ALHNLTQEDLAKKLGVSRQTI 43
                                  5799***************99 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013     0.088      19      37 ..      25      43 ..      15      44 .. 0.85
   2 ?   -2.7   0.0       7.8   5.2e+03      25      32 ..      60      67 ..      54      68 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                        HTH_38 19 eGlslreIArrLgrspsTI 37
                                   +l++ + A++Lg+s++TI
  gi|15668446|ref|NP_247244.1| 25 HNLTQEDLAKKLGVSRQTI 43
                                  67999*************9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.8
                        HTH_38 25 eIArrLgr 32
                                  +IA+  g+
  gi|15668446|ref|NP_247244.1| 60 KIAKFFGV 67
                                  79987775 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.2e-05     0.054      14      57 ..      28      72 ..      19      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.2e-05
                                  SCHHHHCCTT--HHHHHHHHHSSS--.HHHHHHHHHHH---HHHH CS
                 Phage_CI_repr 14 mqkeLAdlLgiakssvstwvrRdffP.gdvvvtcaletdtsLewL 57
                                  +q++LA+ Lg++++++    +  + P  ++  ++a+  ++++e++
  gi|15668446|ref|NP_247244.1| 28 TQEDLAKKLGVSRQTIIAIEKGKYDPsLKLAFKIAKFFGVKIEDI 72
                                  799************976655555555888888888888888876 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013     0.085      18      37 ..      25      44 ..      18      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                     HTH_Tnp_4 18 lnltyqdLayrFgvsestvs 37
                                  +nlt++dLa   gvs+ t+ 
  gi|15668446|ref|NP_247244.1| 25 HNLTQEDLAKKLGVSRQTII 44
                                  9*****************85 PP

>> Sigma54_DBD  Sigma-54, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.9e-05     0.066      45      93 ..      22      70 ..      10      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.9e-05
                                  XXXXXXXHHHHHTTSSSXHHHHHHHHHHXEEEXSSXEEECSCCXXXCSS CS
                   Sigma54_DBD 45 ealrpltlrevaealelhesTvSRvvsnkyiktprGvfelkafFsssvs 93
                                  +al+ lt +++a++l++++ T+  + ++ky  + +  f++ +fF  +++
  gi|15668446|ref|NP_247244.1| 22 RALHNLTQEDLAKKLGVSRQTIIAIEKGKYDPSLKLAFKIAKFFGVKIE 70
                                  78999***************************************99986 PP

>> SAM_1  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00012     0.077      13      49 ..       2      40 ..       1      46 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                                  HHTTSGGGHHHH.HTTTSSHHHHTTSCHHHHHH.CTTTS CS
                         SAM_1 13 esiglgqYadlF.rageidgdaLlllteddLek.lgvtl 49
                                   si+l+   ++  ++     +aL +lt++dL k lgv++
  gi|15668446|ref|NP_247244.1|  2 SSIHLKSFHSETmKNKLKYYRALHNLTQEDLAKkLGVSR 40
                                  56777555555547888889************99***97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00046       0.3      17      34 ..      26      43 ..      21      46 .. 0.89
   2 ?   -0.0   0.0       1.3   8.5e+02      16      30 ..      53      68 ..      50      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                                  TEEHHHHHHHHTS-HHHH CS
                          MarR 17 plsvseLakklgvskstv 34
                                  +l++ +Lakklgvs+ t+
  gi|15668446|ref|NP_247244.1| 26 NLTQEDLAKKLGVSRQTI 43
                                  7999***********997 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.3
                                  TTEEHH.HHHHHHTS- CS
                          MarR 16 gplsvs.eLakklgvs 30
                                  ++l+++ ++ak++gv+
  gi|15668446|ref|NP_247244.1| 53 PSLKLAfKIAKFFGVK 68
                                  55666689****9986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016      0.11      21      38 ..      26      43 ..      14      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                                  EEEHHHHHHHHTSSHHHH CS
                        MarR_2 21 dltvgelarrlglsksav 38
                                  +lt+ +la++lg+s++++
  gi|15668446|ref|NP_247244.1| 26 NLTQEDLAKKLGVSRQTI 43
                                  48**************97 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0019       1.3       4      17 ..      31      44 ..      30      48 .. 0.88
   2 ?    1.3   0.0      0.45     3e+02       5      20 ..      61      76 ..      60      78 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0019
                                  HHHHHHTTTHHHHH CS
                          MerR  4 evAeltGvsprtLR 17
                                  ++A+++Gvs +t+ 
  gi|15668446|ref|NP_247244.1| 31 DLAKKLGVSRQTII 44
                                  79**********95 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.45
                                  HHHHHTTTHHHHHHHH CS
                          MerR  5 vAeltGvsprtLRyYE 20
                                  +A+++Gv +  +  YE
  gi|15668446|ref|NP_247244.1| 61 IAKFFGVKIEDIFIYE 76
                                  69*****987666555 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00023      0.15      19      35 ..      28      44 ..      26      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                 HTH_AsnC-type 19 syaeLAervGlSestvl 35
                                  + ++LA+++G+S++t++
  gi|15668446|ref|NP_247244.1| 28 TQEDLAKKLGVSRQTII 44
                                  678************86 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00031      0.21       7      29 ..      19      43 ..      18      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                        HTH_28  7 kllaaGh..svreaArelgisrrtv 29
                                  k++ a h  ++ ++A++lg+sr+t+
  gi|15668446|ref|NP_247244.1| 19 KYYRALHnlTQEDLAKKLGVSRQTI 43
                                  6777766579999***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 534.25
//
Query:       gi|15668447|ref|NP_247245.1|  [L=103]
Description: hypothetical protein MJ_0273 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-28   97.0   0.2      6e-28   96.7   0.2    1.1  1  DUF357    Protein of unknown function (DUF357)


Domain annotation for each model (and alignments):
>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   0.2   3.4e-32     6e-28       1      73 []      17      90 ..      17      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 3.4e-32
                                  HHHHHHHHHHHHHH......TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTSTS CS
                        DUF357  1 rYirlleealekvkiap.deesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgll 73
                                  +Y++++eea++ +k  + +++s l+++a+++l m+esY+eDak f e+gd+v+A+as++Ya+Gw+Dag+rlg++
  gi|15668447|ref|NP_247245.1| 17 NYFKRTEEAIKIIKKGMpPKRSLLYDVAKDFLLMIESYFEDAKAFKERGDYVTAFASLNYAYGWIDAGVRLGIF 90
                                  6*************7766******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      795  (0.0443416); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 683.28
//
Query:       gi|15668448|ref|NP_247246.1|  [L=543]
Description: hypothetical protein MJ_0274 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-16   59.8   0.1    8.5e-16   58.8   0.1    1.6  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.1   4.7e-20   8.5e-16       1     156 [.     211     399 ..     211     409 .. 0.80

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 4.7e-20
                                   EEEESEESS-....-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE...............SSTGGGSTT CS
                                   xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlr....CsfCarpetvrregrgrslsveeileevkelkaekgvkevilg...............ggepllypd 62 
                                   ++++rgC+++    CsfC+ p+   r g +++++  +i++e+k l ++ g+k++ +g                  p  + +
  gi|15668448|ref|NP_247246.1| 211 IETYRGCPRAltggCSFCTEPR---RFGLPKFRDEKDIIDEIKVL-YNEGIKYFRIGrqpcmfsyksidsekEEVPKPNVE 287
                                   5789*****9999********7...9*******************.8**********666666655555555444444455 PP

                                   HHHHHHHHHHTC.......CCTEEEEEEECSSCHGHHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHH CS
                                   xxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  63 fvellerlakla.......vpgiritvetngtlpdeeklerllelg..vdrvslgleaaddekvlklmnrghtfeevleal 134
                                    +e+l++ +++         ++ + +v++ +   ++e+++ l+++    ++ ++g+e++d++ v k +n   t+e+vl+a+
  gi|15668448|ref|NP_247246.1| 288 AIEKLFKGIRNVsnpkvlhIDNANPAVIARHEDESREVAKILVKYCtsGNVAAFGVESFDEK-VIKANNLLTTPEDVLKAV 367
                                   55555555555587777777777777777777777***************************.99999988********** PP

                                   HHHHHTTSET..........EEEEEEEBTTTS CS
                                   xxxxxxxxxx..........xxxxxxxxxxxx RF
                   Radical_SAM 135 eklreagikr..........vvdrivglpGen 156
                                   e+l+e+g+kr           ++ ++gl+Ge 
  gi|15668448|ref|NP_247246.1| 368 EILNEVGGKRgetglpyllpGINLLFGLKGER 399
                                   **********8666555555666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 3319.09
//
Query:       gi|15668449|ref|NP_247247.1|  [L=204]
Description: hypothetical protein MJ_0275 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.12   11.5   3.5       0.15   11.2   3.5    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
        8.1    6.6  11.0        6.9    6.8   7.4    2.5  2  ETRAMP           Malarial early transcribed membrane protein 


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.5   1.6e-05      0.15       1      99 [.       5     161 ..       5     200 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.6e-05
               ABC2_membrane_3   1 ksfliitlllPiilvlllglifsnsveddentpiavvdedn..sslsqqlv....................ealeaspsve 59 
                                   k ++i  ++l +il + ++ +f n+ e++++++++v+  +n   ++ ++ +                    +         
  gi|15668449|ref|NP_247247.1|   5 KVSIIVLFILSLILTISICGCFENEKEEVNKPNMTVIEKENikVQN-NKPIenlkeescklnitndenrtnN--------- 75 
                                   568889999********************************96444.4444133334444434433333320......... PP

               ABC2_membrane_3  60 lvyevdseeeakkalkngdidgilvipkgfskdll.............................................. 94 
                                                 + +++  + +  p +++k +l                                              
  gi|15668449|ref|NP_247247.1|  76 --------------ITKTTKKYDFSKPVDMDKMFLnlpyneetdfddkiikkyknitfvvsrkpidlsyayiynevkeype 142
                                   ..............3333333333333333322223333333333333333333333333332222223344444444444 PP

               ABC2_membrane_3  95 ..............kgesa 99 
                                                 k+++ 
  gi|15668449|ref|NP_247247.1| 143 rdifgnyiyyefipKNANL 161
                                   4443333333333333333 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   7.4   0.00077       6.9       1      56 [.       1      54 [.       1      89 [. 0.80
   2 ?   -0.0   0.1       0.1   9.4e+02      40      52 ..     104     116 ..      97     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00077
                        ETRAMP  1 MKvtkvllffafLlavnlltpeslcdevnkkkekakkaikkiddkiekkkkkkKli 56
                                  M   kv+++++f+l++ l ++ + c e++k  e  +k    + +k + k +++K+i
  gi|15668449|ref|NP_247247.1|  1 MSMKKVSIIVLFILSLILTISICGCFENEK--EEVNKPNMTVIEKENIKVQNNKPI 54
                                  556799999999999999999999999998..555555555555555555777765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.1
                        ETRAMP  40 kkiddkiekkkkk 52 
                                   +++ddki kk k+
  gi|15668449|ref|NP_247247.1| 104 TDFDDKIIKKYKN 116
                                   57999*9999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1618  (0.0902449); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1247.29
//
Query:       gi|15668450|ref|NP_247248.1|  [L=148]
Description: hypothetical protein MJ_0275.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.91    9.4   4.3       0.63   10.0   2.1    1.9  1  Deltameth_res  Deltamethrin resistance


Domain annotation for each model (and alignments):
>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.1   3.5e-05      0.63      19      43 ..       9      33 ..       4      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.5e-05
                 Deltameth_res 19 rkYNavLaaGiviligTialakesg 43
                                  r YNa+ ++G vi++++i+++ +  
  gi|15668450|ref|NP_247248.1|  9 RVYNAYKIVGAVIFSMSIIVILYIS 33
                                  89*****************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1221  (0.068102); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 970.39
//
Query:       gi|15668451|ref|NP_247249.1|  [L=366]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-83  278.0   0.1    7.9e-83  277.7   0.1    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    9.7e-25   86.9   0.1    1.9e-24   85.9   0.1    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    4.6e-05   23.3   0.0    0.00012   22.0   0.0    1.7  1  Transketolase_C  Transketolase, C-terminal domain
    6.3e-05   22.7   0.1     0.0002   21.1   0.1    1.9  3  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
  ------ inclusion threshold ------
      0.035   13.8   0.1       0.85    9.4   0.0    2.3  2  DUF835           Protein of unknown function (DUF835)


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.7   0.1   2.2e-86   7.9e-83       1     230 [.      14     245 ..      14     246 .. 0.95

  Alignments for each domain:
  == domain 1  score: 277.7 bits;  conditional E-value: 2.2e-86
                                   .HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHH CS
                         POR_N   1 eaaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgl 81 
                                   ++ai+ag++++a+YPITPs+eiae++a+ l+k++    +++qme+Eig+i+aviGA+++G +a+TaTSg+G++Lm+en+g+
  gi|15668451|ref|NP_247249.1|  14 KGAIKAGCRFFAGYPITPSTEIAEAMARELPKVGG---YYIQMEDEIGSIAAVIGASWGGLKAMTATSGPGFSLMQENIGF 91 
                                   589*******************************5...******************************************* PP

                                   HHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHH CS
                         POR_N  82 aageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgfl 157
                                   a ++e+P+v+v+++R++pstg++++ +q+D+m++r     d+++i+la+++vqe++d++++Afn+Aek+r+Pv+v+ D+++
  gi|15668451|ref|NP_247249.1|  92 AYMTETPCVVVDIQRGGPSTGQPTMASQGDMMQCRwgshgDYEVIALAPSSVQEMYDFTIMAFNYAEKYRIPVFVMADEIV 172
                                   ********************************************************************************* PP

                                   H.HEEEEEEC-SGG.GS-----SBXXXXXXXX.....SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHHH CS
                         POR_N 158 lshevekvelpdeedelklikekleeyerkey.....aldpekpiargtaanpdtglehrekgneaedaaekvveeve 230
                                   + h++ekv l+d+    ++i++k++e+++ ++     +l pe+p++ ++++++ tgl+h+e+g+++++  e++++ v+
  gi|15668451|ref|NP_247249.1| 173 G-HMREKVILHDNI---EIINRKKPEEKPCKKpypfdKLIPEMPVFGEGYNVHITGLTHDERGYPDVS-PETHDKLVR 245
                                   *.********9877...6666666666665555679*******************************9.999998876 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.1   5.4e-28   1.9e-24       1     102 []     268     360 ..     268     360 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 5.4e-28
                                   -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGG CS
                       PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkks 81 
                                   Ae+v+v++Gs ++t+k+av++lRe+g++vG++rl+t++PFP + lk+l  k+kkvvv ++n      Gq++ ev++  kk 
  gi|15668451|ref|NP_247249.1| 268 AEIVFVCYGSPSRTVKHAVRNLREKGLDVGYIRLITVYPFPDDLLKKL--KAKKVVVPEMNL-----GQIYYEVERVCKKA 341
                                   9**********************************************8..69**********.....**********9988 PP

                                   TSEEEEEE--GGG----HHHH CS
                       PFOR_II  82 kvkvvnfvaglgGrditvedi 102
                                     + v +v ++gG+++++e++
  gi|15668451|ref|NP_247249.1| 342 --EEVILVDKIGGELHRPEEL 360
                                   ..****************985 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.3e-08   0.00012       9      66 ..     267     322 ..     260     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.3e-08
                                   TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEE CS
               Transketolase_C   9 gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvv 66 
                                     ++++v+yGs  +++  A+ +L+++g+++  + l+tv p+  ++++++++k  ++vv
  gi|15668451|ref|NP_247249.1| 267 DAEIVFVCYGSPSRTVKHAVRNLREKGLDVGYIRLITVYPFPDDLLKKLKAK--KVVV 322
                                   5789*******************************************66554..4444 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   5.4e-08    0.0002       3     121 ..       8     124 ..       6     172 .. 0.72
   2 ?   -3.6   0.0       2.1   7.4e+03      16      38 ..     271     293 ..     265     301 .. 0.62
   3 ?   -3.7   0.0       2.2   7.8e+03     118     141 ..     329     355 ..     318     356 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.4e-08
                                   HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT..TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHH CS
                  TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeq.girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalta 82 
                                   + +a ++   ++g + + g+p + ++++ +a+++e  ++  +    E   + +A  +  + g + +  +tsgpG+  +  +
  gi|15668451|ref|NP_247249.1|   8 GNQACAKGAIKAGCRFFAGYPITPSTEIAEAMARELpKVGGYYIQMEDEIGSIAAVIGASWGGLKAMTATSGPGFSLMQEN 88 
                                   5566666667889999******************99966666666677777777777778899****************** PP

                                   HHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHC CS
                  TPP_enzyme_N  83 laeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfr 121
                                   +  A+ + +P++v+  +r+  ++gq+++    +q ++++
  gi|15668451|ref|NP_247249.1|  89 IGFAYMTETPCVVVDIQRGGPSTGQPTMA---SQGDMMQ 124
                                   ************************55444...6777755 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.1
                                   --EEEE---CCCHHHHCCHHCT. CS
                  TPP_enzyme_N  16 vehvfgvpGsrilplldalseeq 38 
                                   v +++g p  ++++ ++ l+e  
  gi|15668451|ref|NP_247249.1| 271 VFVCYGSPSRTVKHAVRNLREKG 293
                                   55667777777777777776664 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.2
                                   HH...HCCCSSEEEE-SSGGGHHHHHH CS
                  TPP_enzyme_N 118 al...frpvtkyaervtspeelpealr 141
                                   ++   ++ v+k ae+v  ++ +  +l+
  gi|15668451|ref|NP_247249.1| 329 QIyyeVERVCKKAEEVILVDKIGGELH 355
                                   444446789999999988888776665 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00024      0.85      41      80 ..     219     259 ..     208     265 .. 0.87
   2 ?    1.9   0.0     0.048   1.7e+02      52      85 ..     317     350 ..     311     352 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00024
                        DUF835  41 nvkviwltkve.eentvsPtnlekltetivkflkeaekgvv 80 
                                   nv+++ lt  e ++  vsP+  +kl + iv+++++++++++
  gi|15668451|ref|NP_247249.1| 219 NVHITGLTHDErGYPDVSPETHDKLVRRIVNKIRKNKDEII 259
                                   788999999995699***********************998 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.048
                        DUF835  52 eentvsPt.nlekltetivkflkeaekgvvliDgl 85 
                                    ++ v P+ nl ++  ++++  k+ae+ v+l+D +
  gi|15668451|ref|NP_247249.1| 317 AKKVVVPEmNLGQIYYEVERVCKKAEE-VILVDKI 350
                                   455555643899**************6.*****76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2245.47
//
Query:       gi|15668452|ref|NP_247250.1|  [L=591]
Description: acetolactate synthase catalytic subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-65  217.8   0.0    4.6e-62  208.7   0.0    2.2  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    7.2e-56  187.7   0.0    1.5e-55  186.6   0.0    1.6  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
    4.5e-50  169.4   0.0      2e-49  167.3   0.0    2.2  3  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.7   0.0   7.6e-66   4.6e-62       1     170 [.       1     168 [.       1     170 [. 0.99
   2 !    7.0   0.0   0.00067         4      75     144 ..     449     531 ..     424     544 .. 0.72

  Alignments for each domain:
  == domain 1  score: 208.7 bits;  conditional E-value: 7.6e-66
                                   EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                  TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                   m++aea+++aL+a+gv+ +fg+pG+ +lp++dal +++ + ++l+rhEq+aa+aAdg+ara+g+ gv++ tsgpGatn++t
  gi|15668452|ref|NP_247250.1|   1 MKGAEAIIKALEAEGVKIIFGYPGGAMLPFYDALYDSD-LVHILTRHEQAAAHAADGFARASGEAGVCVSTSGPGATNLVT 80 
                                   79***********************************6.****************************************** PP

                                   HHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHH CS
                  TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkd 162
                                   ++a+A+ d++P+++l+g++pt+l+g +++q e+d+l+lf p+tk+++++++pee+pe++r A+++a++grpgPv+++lpkd
  gi|15668452|ref|NP_247250.1|  81 GIATAYADSSPVIALTGQVPTKLIGNDAFQ-EIDALGLFMPITKHNFQIKKPEEIPETFRAAFEIATTGRPGPVHIDLPKD 160
                                   ******************************.************************************************** PP

                                   HCC-EEEH CS
                  TPP_enzyme_N 163 vlleevde 170
                                   v++ e+d 
  gi|15668452|ref|NP_247250.1| 161 VQDGEIDI 168
                                   *****996 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00067
                                   HHHHCHHHHHHHHHHT--EEEEEEE--CCCHH.............S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHH CS
                  TPP_enzyme_N  75 GatnaltalaeAkvdriPllvlsgdrptslrg.............qgvlqqeldqlalfrpvtkyaervtspeelpealrr 142
                                   G++     la+ +   iP+++   d+ t                 + +l +  d ++l++++   a+r+ sp+e++e l++
  gi|15668452|ref|NP_247250.1| 449 GFLMNSQELATISEYDIPVVICIFDNRTLGMVyqwqnlyygqrqsEVHLGESPDFVKLAESYGVKADRIISPDEIKEKLKE 529
                                   566666667777777777766666665554445666777655554333444559999************************ PP

                                   HH CS
                  TPP_enzyme_N 143 Ai 144
                                   Ai
  gi|15668452|ref|NP_247250.1| 530 AI 531
                                   98 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.6   0.0   2.6e-59   1.5e-55       1     137 []     193     328 ..     193     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 186.6 bits;  conditional E-value: 2.6e-59
                                   HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEE CS
                  TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlv 81 
                                   i+kaa+l+++++rpvil+Gggv+ sgaseel +lae ++iPv+ttlmgkg++pedhpl lgm+g+hg+kaan a+ e+D++
  gi|15668452|ref|NP_247250.1| 193 IKKAAKLIAESERPVILAGGGVIISGASEELLRLAEFVKIPVCTTLMGKGCFPEDHPLALGMVGMHGTKAANYAVTECDVL 273
                                   79******************************************************************************* PP

                                   EEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                  TPP_enzyme_M  82 lalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                   +a+G+rf+d r+tg  + fapeakiihididpaeigkn+++d++ivgd+k++l+ L
  gi|15668452|ref|NP_247250.1| 274 IAIGCRFSD-RVTGDIRYFAPEAKIIHIDIDPAEIGKNVRADIPIVGDAKNVLRDL 328
                                   *********.9***9**************************************987 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0         2   1.2e+04      38      54 ..      80      97 ..      76      97 .. 0.75
   2 ?   -3.0   0.0      0.93   5.5e+03     128     151 ..     129     155 ..     121     156 .. 0.65
   3 !  167.3   0.0   3.3e-53     2e-49       1     153 []     393     541 ..     393     541 .. 0.97

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2
                                  HHHHHHST.TSEEEEEEE CS
                  TPP_enzyme_C 38 iGaklakp.drevvaivG 54
                                  +G++ a+  +++v+a++G
  gi|15668452|ref|NP_247250.1| 80 TGIATAYAdSSPVIALTG 97
                                  688887652579999998 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.93
                                   SSH.HHHHHHHHHHHH.....CSSSEEEE CS
                  TPP_enzyme_C 128 ekadveeleealkeal.....ekkgpali 151
                                   +k+  ee+ e++++a+      + gp+ i
  gi|15668452|ref|NP_247250.1| 129 KKP--EEIPETFRAAFeiattGRPGPVHI 155
                                   445..888888888886664555556555 PP

  == domain 3  score: 167.3 bits;  conditional E-value: 3.3e-53
                                   ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE CS
                  TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvln 81 
                                   d+G++++w+a+++k k prs+l sgglgtmG+g+paAiGak+akp ++v++i+GDGgflm+ qelat+ ++++p+++++++
  gi|15668452|ref|NP_247250.1| 393 DVGQNQMWMAHFFKTKMPRSFLASGGLGTMGFGFPAAIGAKVAKPYANVISITGDGGFLMNSQELATISEYDIPVVICIFD 473
                                   89*******************************************99********************************** PP

                                   -SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  82 NegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                   N+++gm+ ++q+ ++g+r+s+++   ++++df+klae++G+k+ r+ ++  +e++e+lkea+ +++p l+++
  gi|15668452|ref|NP_247250.1| 474 NRTLGMVYQWQNLYYGQRQSEVH--LGESPDFVKLAESYGVKADRIISP--DEIKEKLKEAILSNEPYLLDI 541
                                   *******************9988..69999************8898888..***********999****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3643.67
//
Query:       gi|15668453|ref|NP_247251.1|  [L=157]
Description: peptidyl-prolyl cis-trans isomerase SlyD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-20   73.6   0.1    3.8e-20   72.0   0.1    1.7  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
  ------ inclusion threshold ------
       0.12   12.3   0.7       0.42   10.5   0.0    2.1  3  YajC      Preprotein translocase subunit
       0.24   11.5   7.1       0.89    9.7   0.1    2.9  3  DUF150_C  RimP C-terminal SH3 domain


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.1   6.3e-24   3.8e-20       5      92 ..       5     147 ..       3     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 6.3e-24
                                   B-TTCEEEEEEEEEETTSSEEEEH.............CCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTT CS
                        FKBP_C   5 akegdtVtvhykgkledgkvfdss.............rsrakplefkvGsgqvikGfeealegmkvGekrtltippelaYg 72 
                                   +k+gd V+v+y + + dgkv+d+s              ++++p+ f vG+g++i+Gfeea+ gm+vGe++t+tippe +Yg
  gi|15668453|ref|NP_247251.1|   5 IKKGDYVKVDYILEV-DGKVIDTSieevakenkiyypEREYEPIGFIVGNGELIEGFEEAVIGMEVGEEKTVTIPPEKGYG 84 
                                   589**********99.********999999988876545****************************************** PP

                                   TTTBCTTT.B.TT..........................................SEEEEEEE CS
                        FKBP_C  73 ekglaggv.ippn..........................................atLvFeve 92 
                                    +++   + ip++                                          ++L F+++
  gi|15668453|ref|NP_247251.1|  85 LRDERLIQeIPKEmfadadfepqegmlilasgipakiikvtddtvtldfnhelagKELKFTIK 147
                                   966533223333344444444444444444444444555555555555555555577777666 PP

>> YajC  Preprotein translocase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.26   1.5e+03      31      41 ..       1      11 [.       1      36 [. 0.76
   2 ?   -3.2   0.0       1.3   7.9e+03      59      71 ..      65      77 ..      56      82 .. 0.61
   3 ?   10.5   0.0   7.1e-05      0.42      42      66 ..     112     136 ..     108     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.26
                          YajC 31 mlasLkkGdeV 41
                                  m++ +kkGd V
  gi|15668453|ref|NP_247251.1|  1 MINLIKKGDYV 11
                                  67778888876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.3
                          YajC 59 vtveigesagvki 71
                                  + +e+ge++ v+i
  gi|15668453|ref|NP_247251.1| 65 IGMEVGEEKTVTI 77
                                  5567776666655 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 7.1e-05
                          YajC  42 vtigGivGkvvkvdddevtveiges 66 
                                   ++++Gi +k++kv+dd+vt++++ +
  gi|15668453|ref|NP_247251.1| 112 ILASGIPAKIIKVTDDTVTLDFNHE 136
                                   789***********99999999654 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2    0.0076        46      12      40 ..       8      35 ..       5      38 .. 0.78
   2 ?    0.0   0.1      0.16   9.6e+02      33      57 ..      57      78 ..      53      81 .. 0.71
   3 ?    9.7   0.1   0.00015      0.89      31      63 ..     119     153 ..     116     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0076
                      DUF150_C 12 GelVkvklklpvegrkkftGkivevdeet 40
                                  G +Vkv++ l+v ++k +   i+ev++e+
  gi|15668453|ref|NP_247251.1|  8 GDYVKVDYILEV-DGKVIDTSIEEVAKEN 35
                                  889****77666.5689999999998776 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.16
                      DUF150_C 33 ivevdeetitlevdgkkrkkettip 57
                                  i+ ++e  i  ev ++   k++tip
  gi|15668453|ref|NP_247251.1| 57 IEGFEEAVIGMEVGEE---KTVTIP 78
                                  4445555588998888...888888 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00015
                      DUF150_C  31 Gkivevdeetitlevdgkkrkkett..ipladidk 63 
                                   +ki  v ++t+tl+++ +  +ke++  i++ d++ 
  gi|15668453|ref|NP_247251.1| 119 AKIIKVTDDTVTLDFNHELAGKELKftIKVRDVQP 153
                                   89*********************997777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1076.75
//
Query:       gi|15668454|ref|NP_247252.1|  [L=283]
Description: (s)-2,3-di-O-geranylgeranylglyceryl phosphate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-49  167.6   6.8    3.8e-49  167.3   6.8    1.1  1  UbiA             UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.11   12.9   2.4         16    6.0   0.1    2.8  3  Phage_holin_3_1  Phage holin family (Lysis protein S)
       0.38   11.1  21.7      0.038   14.3   3.3    3.9  4  Sigma_reg_N      Sigma factor regulator N-terminal
       0.66   10.1  10.6        2.3    8.3   1.1    3.4  3  Na_Pi_cotrans    Na+/Pi-cotransporter


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.3   6.8   8.5e-53   3.8e-49       5     249 ..      27     265 ..      23     273 .. 0.92

  Alignments for each domain:
  == domain 1  score: 167.3 bits;  conditional E-value: 8.5e-53
                          UbiA   5 alvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilglllla 85 
                                    ++g++++++  +d+l  ll+++ +++++a++n++Nd+fD+eiD++  ++p RPl+sG+i+ +ea+ f+++llilgl+l+ 
  gi|15668454|ref|NP_247252.1|  27 GIIGYLISSNFEIDILKSLLVFFVVFFVCAYGNVINDIFDIEIDRI--NKPSRPLPSGKIKLNEAKKFSAILLILGLVLS- 104
                                   5789******************************************..********************************. PP

                          UbiA  86 lllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlr 166
                                   l++n +++++++++ l++++Y +  +K++ ++g++++g   g ++l+g +a  +   +++++l+l  +l +w+  +++d++
  gi|15668454|ref|NP_247252.1| 105 LFINIYALIIAVINALFLYLYAK-KYKKYKPIGNFIIGYLTGSVFLFGGVAGKN--VMPVVILFLCSLLSIWGREIVKDFE 182
                                   **********************5.77777777*******************666..5899******9************** PP

                          UbiA 167 dregDrkagiktlpvvlGrkaarillalllavllla.llllllalllllylllalllaalallraarlvrrrdakkaakff 246
                                   d+egD+k g+ +lp+++G+k  ++ +++l+++++++ +l + l  ++ +yl+l ++  +l+++  a l++  ++++a+k+ 
  gi|15668454|ref|NP_247252.1| 183 DMEGDKKEGVISLPIKYGKKSLYF-ATFLVVLAVILsPLPYILKIFGIWYLILIAICDILFIYAMALLLKEPNKETASKVS 262
                                   ******************999999.5555555555569999999*****************************99999988 PP

                          UbiA 247 lfl 249
                                    fl
  gi|15668454|ref|NP_247252.1| 263 KFL 265
                                   555 PP

>> Phage_holin_3_1  Phage holin family (Lysis protein S)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0043        19      59      83 ..       8      32 ..       2      37 .. 0.88
   2 ?    6.0   0.1    0.0035        16      11      59 ..      99     147 ..      90     153 .. 0.86
   3 ?   -2.9   0.0       2.1   9.3e+03      50      63 ..     165     178 ..     161     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0043
               Phage_holin_3_1 59 vrsllellglpaslavviggliGfl 83
                                  ++  lel+ +++ ++  igg+iG+l
  gi|15668454|ref|NP_247252.1|  8 LKTYLELIRVKNCITASIGGIIGYL 32
                                  56789999****************7 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0035
               Phage_holin_3_1  11 lawlqsaspqiiaavlAlviallrviYdgkswkkvlleallCgllalav 59 
                                   l ++ s   +i+a ++A++ al+  +Y +k  k + +  ++ g l+ +v
  gi|15668454|ref|NP_247252.1|  99 LGLVLSLFINIYALIIAVINALFLYLYAKKYKKYKPIGNFIIGYLTGSV 147
                                   56677777889*******************9999999999999998765 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.1
               Phage_holin_3_1  50 llCgllalavrsll 63 
                                   +lC+ll++  r+++
  gi|15668454|ref|NP_247252.1| 165 FLCSLLSIWGREIV 178
                                   68999998888776 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3     0.095   4.3e+02      18      31 ..      43      57 ..      35      73 .. 0.70
   2 ?    5.6   2.8    0.0044        20       7      45 ..      90     132 ..      86     144 .. 0.73
   3 ?   14.3   3.3   8.5e-06     0.038       4      66 ..     197     261 ..     196     272 .. 0.91
   4 ?   -1.1   0.2      0.52   2.3e+03      13      26 ..     265     278 ..     259     281 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.095
                   Sigma_reg_N 18 islivlllifvil.v 31
                                   sl+v++++f+++ +
  gi|15668454|ref|NP_247252.1| 43 KSLLVFFVVFFVCaY 57
                                  466677777766643 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0044
                   Sigma_reg_N   7 akrksilrivlislivlllifvil..vvtllyl..aekegnkl 45 
                                   +k+ +il i  ++l++++ i++++  v+++l+l    k+++k+
  gi|15668454|ref|NP_247252.1|  90 KKFSAILLILGLVLSLFINIYALIiaVINALFLylYAKKYKKY 132
                                   5888999999999999999999997455555447744444443 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 8.5e-06
                   Sigma_reg_N   4 lkkakrksilrivlislivlllifvil..vvtllylaekegnklrevlelaveitsPNvyvdsgs 66 
                                   +k++k+ +++ ++l++l+v+l  ++++  ++++ yl+     ++ + + +a+ + +PN +  s++
  gi|15668454|ref|NP_247252.1| 197 IKYGKKSLYFATFLVVLAVILSPLPYIlkIFGIWYLILIAICDILFIYAMALLLKEPNKETASKV 261
                                   89*************************999999999**********************9975554 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.52
                   Sigma_reg_N  13 lrivlislivllli 26 
                                   l+i++ ++++++++
  gi|15668454|ref|NP_247252.1| 265 LKIIMNIVLLAFIV 278
                                   55555555555554 PP

>> Na_Pi_cotrans  Na+/Pi-cotransporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2       0.1   4.6e+02      77     110 ..      23      55 ..       4      67 .. 0.68
   2 ?    8.3   1.1   0.00051       2.3      90     127 ..     101     142 ..      90     152 .. 0.72
   3 ?    5.7   0.2    0.0034        15       1      41 [.     241     281 ..     241     282 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.1
                 Na_Pi_cotrans  77 aniGttvtaqllslalklsslalllllvgvllll 110
                                   a iG   +  l+s +++++ l  ll+++ v++++
  gi|15668454|ref|NP_247252.1|  23 ASIGGI-IGYLISSNFEIDILKSLLVFFVVFFVC 55 
                                   455543.344555678888888888777777554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00051
                 Na_Pi_cotrans  90 l..alklsslalllllvgvl.lllfskkk.klkklgeillgl 127
                                   l  +l ++ +al+++++ +l l+l++kk  k+k +g++++g 
  gi|15668454|ref|NP_247252.1| 101 LvlSLFINIYALIIAVINALfLYLYAKKYkKYKPIGNFIIGY 142
                                   144777888999999998884445544336********9985 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0034
                 Na_Pi_cotrans   1 LfLfGmkllsegleklageklkkilekltsnrlkgvlvGll 41 
                                   Lf+++m ll ++ +k + +k+ k+l+ +++  l++++vG++
  gi|15668454|ref|NP_247252.1| 241 LFIYAMALLLKEPNKETASKVSKFLKIIMNIVLLAFIVGAI 281
                                   8**************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1103  (0.0615204); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1720.25
//
Query:       gi|15668455|ref|NP_247253.1|  [L=128]
Description: nascent polypeptide-associated complex protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-13   50.7   0.6    1.3e-13   50.7   0.6    2.0  3  NAC          NAC domain
     0.0022   18.0   1.2     0.0038   17.2   1.2    1.4  1  HOIP-UBA     HOIP UBA domain pair
  ------ inclusion threshold ------
      0.019   14.8   0.1      0.038   13.8   0.1    1.5  1  UBA_4        UBA-like domain
      0.037   14.6   1.1      0.037   14.6   1.1    2.2  3  PRESAN       Plasmodium RESA N-terminal
      0.071   13.0   0.2        0.2   11.6   0.2    1.7  1  UBA          UBA/TS-N domain
      0.075   13.1   0.4      0.075   13.1   0.4    2.1  2  Arcadin_1    Arcadin 1
       0.08   12.7   0.1       0.17   11.6   0.1    1.6  1  CUE          CUE domain
       0.56   10.3   8.1      0.082   13.0   2.0    2.4  2  Tk-SP_N-pro  Tk-SP N-propeptide domain
       0.99   10.2   4.0         54    4.7   4.0    2.2  1  DUF4373      Domain of unknown function (DUF4373)


Domain annotation for each model (and alignments):
>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.6   6.6e-17   1.3e-13       2      55 ..      12      67 ..      12      69 .. 0.97
   2 ?   -0.7   0.1      0.71   1.4e+03      21      40 ..      81      99 ..      67     106 .. 0.64
   3 ?   -3.2   0.0       4.3   8.7e+03      18      29 ..     113     124 ..     112     126 .. 0.74

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 6.6e-17
                           NAC  2 kKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeae 55
                                  kK++k++k +g+  +++ ++ +V++ ++d ++ vf++PkVq  +  g +ty ++G+++
  gi|15668455|ref|NP_247253.1| 12 KKMQKMMKDFGMetEDL-DVRKVIFVFDD-EEWVFEEPKVQvmDILGVKTYSITGKPK 67
                                  9************8888.9**********.***************************8 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.71
                           NAC 21 eVtirksdgkvlvfdnPkVq 40
                                  +V i  +d  +lv ++  V 
  gi|15668455|ref|NP_247253.1| 81 KVEITEED-VELVAKQCNVS 99
                                  46666666.88887777776 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.3
                           NAC  18 gieeVtirksdg 29 
                                   +i e++++ ++ 
  gi|15668455|ref|NP_247253.1| 113 DIAEAILKLEEE 124
                                   788888888765 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.2   1.9e-06    0.0038      67      96 ..      83     121 ..      61     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.9e-06
                      HOIP-UBA  67 e.........nevgklsraEakealleagGdvekAvkqc 96 
                                   e         ++  ++s++Ea++al e++Gd+ +A+ ++
  gi|15668455|ref|NP_247253.1|  83 EiteedvelvAKQCNVSKEEARKALEECNGDIAEAILKL 121
                                   033344444578899********************8665 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.9e-05     0.038      12      33 ..      97     118 ..      92     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                         UBA_4  12 GadeekArqlLeannWdLerAi 33 
                                   +++ e+Ar+ Le +n+d+  Ai
  gi|15668455|ref|NP_247253.1|  97 NVSKEEARKALEECNGDIAEAI 118
                                   5688**************9998 PP

>> PRESAN  Plasmodium RESA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.1   2.3e+03      36      44 ..      12      20 ..       4      45 .. 0.64
   2 ?   -1.2   0.1       1.4   2.8e+03      60      71 ..      67      81 ..      55      91 .. 0.53
   3 ?   14.6   1.1   1.8e-05     0.037      50      85 ..      90     125 ..      78     128 .] 0.91

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.1
                                  HHHHHHHHH CS
                        PRESAN 36 kkyknmikk 44
                                  kk+++m+k+
  gi|15668455|ref|NP_247253.1| 12 KKMQKMMKD 20
                                  333333333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                                  HHHHHHH...HHHHH CS
                        PRESAN 60 eeykkkl...wkeck 71
                                  +++kk++    +e+k
  gi|15668455|ref|NP_247253.1| 67 KKIKKEKveeEEEVK 81
                                  444433311133444 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 1.8e-05
                                   HHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        PRESAN  50 eelakkynipeeykkklwkeckneitkelkklekey 85 
                                   e +ak++n+++e++ k ++ec+ +i + + kle+e 
  gi|15668455|ref|NP_247253.1|  90 ELVAKQCNVSKEEARKALEECNGDIAEAILKLEEEK 125
                                   5689*****************************986 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2    0.0001       0.2      16      34 ..     100     118 ..      99     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHHTTTSHHHHH CS
                           UBA  16 reevveALratgnNeErAv 34 
                                   +ee+++AL+ +++++  A+
  gi|15668455|ref|NP_247253.1| 100 KEEARKALEECNGDIAEAI 118
                                   79************99986 PP

>> Arcadin_1  Arcadin 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   3.8e-05     0.075      50      99 ..      10      57 ..       5      70 .. 0.82
   2 ?    0.9   2.0      0.23   4.5e+02      17      31 ..      75      89 ..      60     121 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                                  -----------------.--EEEEEEEEEE-HHHHHHH-.---TT-EEEE CS
                     Arcadin_1 50 evapivqqivrslpllslnkvkvpritLvlteeEleklevklevgdvyei 99
                                  ++ + +q++++ +++ + + + v++++ v+ +eE+   e+k++v d++ +
  gi|15668455|ref|NP_247253.1| 10 MLKK-MQKMMKDFGMET-EDLDVRKVIFVFDDEEWVFEEPKVQVMDILGV 57
                                  4443.677778887776.999**************999999999998776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.23
                                  T--EEEEEEEEEEE- CS
                     Arcadin_1 17 egekgvkielvEere 31
                                  e+e+ vk+e++Ee  
  gi|15668455|ref|NP_247253.1| 75 EEEEEVKVEITEEDV 89
                                  567888889888754 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   8.8e-05      0.17      14      38 ..      97     121 ..      97     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.8e-05
                                   TS-HHHHHHHHHHCTTTHHHHHHHH CS
                           CUE  14 dldeevIravLrasngnvEatinaL 38 
                                   ++++e  r++L++ ng++  +i +L
  gi|15668455|ref|NP_247253.1|  97 NVSKEEARKALEECNGDIAEAILKL 121
                                   6899*****************9776 PP

>> Tk-SP_N-pro  Tk-SP N-propeptide domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.0   4.1e-05     0.082       4      49 ..       4      59 ..       3      65 .. 0.76
   2 ?   -0.0   0.4      0.46   9.2e+02      12      25 ..      67      82 ..      61      99 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
                                  TTB-HHHHHHHHTS-TT.....-EEE...EEEEESSHH..HHHHHHHHHHHCT-EE CS
                   Tk-SP_N-pro  4 glltpgLfkKiqklndn.....eeis...tiivFknka..dkekavkvleilGaki 49
                                  g++ p + kK+qk+ ++     e+++   +i vF+++     e +v+v +ilG+k+
  gi|15668455|ref|NP_247253.1|  4 GKVNPRMLKKMQKMMKDfgmetEDLDvrkVIFVFDDEEwvFEEPKVQVMDILGVKT 59
                                  7889999*******876444335554223699**9986335799*********986 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.46
                                  HHH..HTS-TT-EEEE CS
                   Tk-SP_N-pro 12 kKi..qklndneeist 25
                                  kKi  +k++++ee+++
  gi|15668455|ref|NP_247253.1| 67 KKIkkEKVEEEEEVKV 82
                                  5551144555555555 PP

>> DUF4373  Domain of unknown function (DUF4373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   4.0     0.027        54      34      74 ..      72     110 ..       2     112 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.027
                       DUF4373  34 ekiykekgyyiewdeeqlllladkaklevdeeevkeiveac 74 
                                   ek+ +e++  +e++ee ++l+a+  +++v++ee ++ +e+c
  gi|15668455|ref|NP_247253.1|  72 EKVEEEEEVKVEITEEDVELVAK--QCNVSKEEARKALEEC 110
                                   56667777778888888888888..7888888887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2387  (0.133136); expected 358.6 (0.02)
Passed bias filter:                      838  (0.0467399); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 812.95
//
Query:       gi|15668456|ref|NP_247254.1|  [L=179]
Description: hypothetical protein MJ_0281 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.6e-28   97.5   0.1    1.3e-27   97.0   0.1    1.3  1  Peptidase_M54  Peptidase family M54
    0.00018   21.4   0.0    0.00021   21.2   0.0    1.2  1  Peptidase_M10  Matrixin
  ------ inclusion threshold ------
      0.043   13.7   0.0      0.064   13.2   0.0    1.2  1  Peptidase_M43  Pregnancy-associated plasma protein-A
      0.047   12.3   0.1      0.064   11.9   0.1    1.1  1  Metallopep     Putative peptidase family
       0.25   10.9   0.0        0.4   10.3   0.0    1.2  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like


Domain annotation for each model (and alignments):
>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   0.1   3.7e-31   1.3e-27      65     193 ..      51     171 ..       9     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 3.7e-31
                                   TTEEEHHHHHHHHHT--S--..SEE........EEEESS-EE-TT-S-BSEEE-SSSSEEEEE-T..--.......SHHHH CS
                 Peptidase_M54  65 rleavveallgkLkemkddvndDsitkifgittlplgsrdqyidiykkvlGievsiGnyavlals..ikefyte..dkeLf 141
                                   r+++    +l+ L  ++     D          l++++ d y+d +++v+G +   G+ a+++l+  + efy    +k++ 
  gi|15668456|ref|NP_247254.1|  51 RGQFNSTLILKSLPTVE-----DI--------VLGVTEVDIYADNLNFVFGEAELFGKRALISLArlRPEFYGLppNKDVL 118
                                   55555555554444444.....22........389999***************************98889**8556***** PP

                                   HHHHHHHHHHHHHHHTT----S-.TSTTS--SSHHHHHHS-SS--HHHHHHHH CS
                 Peptidase_M54 142 lervvkevlhelGhlyGLshCke.dCvmnfsndlkdvDrkapkyCksCleklk 193
                                     r +ke +he+Gh++GL hC++  Cvm+fsn++ dvD+k  +yCk+Cl+kl+
  gi|15668456|ref|NP_247254.1| 119 KIRALKEAIHEIGHVLGLIHCENkRCVMSFSNSIIDVDLKDWRYCKKCLKKLQ 171
                                   ***********************99**************************98 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   5.8e-08   0.00021     111     134 ..     124     147 ..      74     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.8e-08
                                   HHHHHHHHHHTTBESXSSTTSTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M10 111 lVaaHEiGHalGLeHssdkdalmy 134
                                     a+HEiGH+lGL H ++k+ +m 
  gi|15668456|ref|NP_247254.1| 124 KEAIHEIGHVLGLIHCENKRCVMS 147
                                   5689****************9996 PP

>> Peptidase_M43  Pregnancy-associated plasma protein-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.8e-05     0.064      73     111 ..     127     165 ..     116     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                 Peptidase_M43  73 thelGhfLgLihtfeggCerGegDkvsDtpsedgkevsa 111
                                    he+Gh LgLih  +  C    ++ + D + +d +  ++
  gi|15668456|ref|NP_247254.1| 127 IHEIGHVLGLIHCENKRCVMSFSNSIIDVDLKDWRYCKK 165
                                   6*****************999889999988886555555 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.8e-05     0.064     319     336 ..     127     146 ..     123     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
                    Metallopep 319 lHEiGHllglpHqed..Gvm 336
                                   +HEiGH+lgl H+e+   vm
  gi|15668456|ref|NP_247254.1| 127 IHEIGHVLGLIHCENkrCVM 146
                                   8************9977777 PP

>> Reprolysin_4  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00011       0.4     141     158 ..     128     145 ..     122     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                  Reprolysin_4 141 HEiGHtfGaaHdlsdege 158
                                   HEiGH +G+ H  ++ + 
  gi|15668456|ref|NP_247254.1| 128 HEIGHVLGLIHCENKRCV 145
                                   ***********7777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1216.30
//
Query:       gi|15668457|ref|NP_247255.1|  [L=149]
Description: hypothetical protein MJ_0282 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-14   51.6   0.0    1.2e-13   51.0   0.0    1.3  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.074   12.8   0.1      0.099   12.4   0.1    1.1  1  DUF1647         Protein of unknown function (DUF1647)


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   1.3e-17   1.2e-13       1      88 []      16     103 ..      16     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.3e-17
                                   HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTT..TEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEE CS
                Putative_PNPOx   1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgr..dgivfatnadsrklrnleenprvallflddelgrgvrieG 79 
                                   l+ee+++ l++ ++v++AT+++dG Pnv ++  ++  +   ++ ++a n + ++l+n+ enp+val+ ++ + +  ++++G
  gi|15668457|ref|NP_247255.1|  16 LTEEMVKSLEN-EIVFIATASKDGVPNVAAMRAIKVLDAekGIVLIADNFMNKTLKNILENPKVALTTANCK-DMPYQYKG 94 
                                   57888888886.9****************99955544444789999**************************.8******* PP

                                   EEEEESCHH CS
                Putative_PNPOx  80 taelvsdge 88 
                                   tae  ++ge
  gi|15668457|ref|NP_247255.1|  95 TAEYYKEGE 103
                                   ***999876 PP

>> DUF1647  Protein of unknown function (DUF1647)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.1e-05     0.099      55     132 ..      21      97 ..       3     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                       DUF1647  55 likneedvvFvsatsddhlkeakksiksirkyypkkklilysldlseeeieklkkdknlevrkFntskYPeyvknlke 132
                                   +++ e+++vF++++s+d + +    +++i+ +  +k ++l   ++ +++++++ +++++ + + n ++ P   k  +e
  gi|15668457|ref|NP_247255.1|  21 VKSLENEIVFIATASKDGVPNVA-AMRAIKVLDAEKGIVLIADNFMNKTLKNILENPKVALTTANCKDMPYQYKGTAE 97 
                                   3456899***********99876.56899*********************************9999999955444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 943.35
//
Query:       gi|15668458|ref|NP_247256.1|  [L=290]
Description: nucleotide-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.3e-102  342.4   1.7   1.6e-102  342.2   1.7    1.0  1  ParA          NUBPL iron-transfer P-loop NTPase
    5.3e-16   58.8   0.0      8e-15   55.0   0.0    2.1  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    2.8e-11   43.7   1.8    1.1e-08   35.2   0.4    2.3  2  AAA_31        AAA domain
    1.8e-07   30.7   0.7    6.4e-07   28.9   0.7    1.8  1  MipZ          ATPase MipZ
      2e-07   30.7   0.7    1.6e-05   24.5   0.2    2.2  2  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    4.6e-06   26.0   4.2    1.5e-05   24.4   0.3    2.6  2  ArsA_ATPase   Anion-transporting ATPase
    0.00028   20.8   1.4     0.0017   18.2   0.2    2.3  2  RsgA_GTPase   RsgA GTPase
    0.00035   20.1   0.0      0.012   15.1   0.1    2.1  2  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
    0.00058   19.8   0.0    0.00092   19.1   0.0    1.3  1  APS_kinase    Adenylylsulphate kinase
    0.00061   19.4   0.0      0.001   18.7   0.0    1.3  1  AAA_25        AAA domain
    0.00097   18.2   0.3      0.002   17.2   0.1    1.6  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.002   18.7   0.2     0.0094   16.5   0.1    2.0  2  AAA_18        AAA domain
     0.0028   17.5   0.5        2.5    7.9   0.4    2.2  2  AAA_26        AAA domain
     0.0069   15.7   0.3      0.014   14.7   0.1    1.6  2  Zeta_toxin    Zeta toxin
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.023   14.0   0.0    1.4  1  VirC1         VirC1 protein
      0.011   15.5   0.0       0.02   14.7   0.0    1.4  1  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
      0.013   15.2   1.0      0.044   13.4   0.3    2.0  2  SRP54         SRP54-type protein, GTPase domain
      0.033   14.4   0.1        1.1    9.6   0.0    3.0  2  Glutaredoxin  Glutaredoxin
      0.042   12.0   0.1      0.071   11.3   0.1    1.4  1  FTHFS         Formate--tetrahydrofolate ligase
       0.06   12.5   0.2       0.11   11.7   0.2    1.4  1  NB-ARC        NB-ARC domain
       0.13   12.0   0.2        0.2   11.3   0.2    1.3  1  AAA_30        AAA domain
       0.13   11.3   0.1       0.22   10.6   0.1    1.3  1  T2SSE         Type II/IV secretion system protein
       0.13   12.6   0.1       0.24   11.7   0.1    1.4  1  AAA_16        AAA ATPase domain
       0.14   12.2   0.4       0.23   11.4   0.4    1.3  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.17   12.1   0.0        2.1    8.6   0.1    2.1  2  AAA_22        AAA domain


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.2   1.7  2.2e-105  1.6e-102       1     245 [.      37     281 ..      37     286 .. 0.95

  Alignments for each domain:
  == domain 1  score: 342.2 bits;  conditional E-value: 2.2e-105
                          ParA   1 kvkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvmSigf 80 
                                   k+k++i++lSgKGGVGKStv+vnlA+aL+ +g+kvg+lDaDi+Gp+ip++lgve+++p++  ++++P+ + +gik+mSig+
  gi|15668458|ref|NP_247256.1|  37 KIKHKIVILSGKGGVGKSTVTVNLAAALNLMGKKVGVLDADIHGPNIPKMLGVENTQPMAGPAGIFPIVTkDGIKTMSIGY 117
                                   69***********************************************************99****998799******** PP

                          ParA  81 llesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvkkaiemf 160
                                   ll++++++v+wrGp++s+ai+q+l+dv wgelDyL+iD+PPGtgDeqlt++q++ +++ga+iVttp+ev++ dvkk+i m+
  gi|15668458|ref|NP_247256.1| 118 LLPDDKTPVIWRGPKVSGAIRQFLSDVVWGELDYLLIDTPPGTGDEQLTIMQSIpDIDGAIIVTTPEEVSVLDVKKSIMMA 198
                                   ******************************************************889************************ PP

                          ParA 161 kkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleei 241
                                   k ++++++G++eNmsgfvcp c++ ++ifg+gggek+a+elgv++lg+ipld + reasd+g p+vl +   +a++++++i
  gi|15668458|ref|NP_247256.1| 199 KMLNIPIIGIIENMSGFVCPYCNKVVDIFGRGGGEKAAKELGVEFLGRIPLDIKAREASDKGIPMVLLD--CKASEEFKKI 277
                                   ****************************************************************99875..4455555555 PP

                          ParA 242 aekv 245
                                   ++++
  gi|15668458|ref|NP_247256.1| 278 VKRI 281
                                   5544 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   1.1e-17     8e-15       1     127 [.      42     262 ..      42     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.1e-17
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   i+i s+kGGvGK+t+++nLa+al+  g++V ++DaD  ++n     g+en + p                           
  gi|15668458|ref|NP_247256.1|  42 IVILSGKGGVGKSTVTVNLAAALNLMGKKVGVLDADIHGPNIPKMLGVENTQ-Pmagpagifpivtkdgiktmsigyllpd 121
                                   79***************************************99455555544.36************************** PP

                                   ....................................................................CCHCCCHHHHHHC CS
                                   ....................................................................xxxxxxxxxxxxx RF
                          CbiA  55 ....................................................................dlkrllellealg 67 
                                                                                                       d+k+ + ++++l 
  gi|15668458|ref|NP_247256.1| 122 dktpviwrgpkvsgairqflsdvvwgeldyllidtppgtgdeqltimqsipdidgaiivttpeevsvlDVKKSIMMAKMLN 202
                                   *************************************************************99999998888777777777 PP

                                   HCHHHH..EEEEEEEEES......S...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                   xxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  68 kkkalllkiagvvlnrvd......geneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                   ++      i+g++ n+ +      ++  +   + + e+  +++gv++lg ip d +  ea  +g p
  gi|15668458|ref|NP_247256.1| 203 IP------IIGIIENMSGfvcpycNKVVDIFGRGGGEKAAKELGVEFLGRIPLDIKAREASDKGIP 262
                                   66......6666666533111111222333344444455555599999999999999888888865 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.4   1.5e-11   1.1e-08       3      41 ..      41      79 ..      39     111 .. 0.88
   2 !    7.6   0.0    0.0047       3.3     115     159 ..     146     193 ..     130     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.5e-11
                        AAA_31  3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQ 41
                                   I+i   KGGvGK+T +vnlaaal  +gkkv + D+D  
  gi|15668458|ref|NP_247256.1| 41 KIVILSGKGGVGKSTVTVNLAAALNLMGKKVGVLDADIH 79
                                  689999*******************************75 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0047
                        AAA_31 115 kdeYDyiiiDcpPsLg...lltenaLvasdsviipvqaeayaleGleq 159
                                     e Dy +iD+pP  g   l  ++++   d  ii++ +e+ ++  +++
  gi|15668458|ref|NP_247256.1| 146 WGELDYLLIDTPPGTGdeqLTIMQSIPDIDGAIIVTTPEEVSVLDVKK 193
                                   4678*********88633356677777789999999999998877665 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.7     9e-10   6.4e-07       1      56 [.      40      97 ..      40     193 .. 0.65

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 9e-10
                                  EEEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHH..HHHHHHHH CS
                          MipZ  1 hvivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryl..enraatae 56
                                  h iv+   kGG Gkst++v +a aL  +G++v+++d d+    + + l  en + +a 
  gi|15668458|ref|NP_247256.1| 40 HKIVILSGKGGVGKSTVTVNLAAALNLMGKKVGVLDADIHGPNIPKMLgvENTQPMAG 97
                                  6799999*******************************98877777642255555544 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.2   2.2e-08   1.6e-05       3      37 ..      43      77 ..      41      92 .. 0.88
   2 ?    4.5   0.0     0.029        21     193     247 ..     232     284 ..     178     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.2e-08
                     Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCD 37
                                  + + GkGG+Gkst + nl+aal  mgkkv ++  D
  gi|15668458|ref|NP_247256.1| 43 VILSGKGGVGKSTVTVNLAAALNLMGKKVGVLDAD 77
                                  6678************************9777655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.029
                     Fer4_NifH 193 iekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilen 247
                                    ek a+elg++ l  +P+d  ++  e+  k +     +++ ++e++++ ++i+e+
  gi|15668458|ref|NP_247256.1| 232 GEKAAKELGVEFLGRIPLD--IKAREASDKGIPMVLLDCKASEEFKKIVKRIVEK 284
                                   578899***********98..566666777777888889999*********9987 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.3     2e-08   1.5e-05       1      38 [.      40      77 ..      40      86 .. 0.93
   2 ?    1.4   0.1       0.2   1.4e+02     209     243 ..     177     211 ..     169     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2e-08
                                  -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                   ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                  +k+++++GKGGVGK+tv   +a+ l  +gkkv ++  D
  gi|15668458|ref|NP_247256.1| 40 HKIVILSGKGGVGKSTVTVNLAAALNLMGKKVGVLDAD 77
                                  589****************************9988776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.2
                                   EEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                   ArsA_ATPase 209 frlVvipEklslkEteRaikeLkkygikvdavivN 243
                                    ++V++pE++s+ + +++i   k ++i +  +i N
  gi|15668458|ref|NP_247256.1| 177 AIIVTTPEEVSVLDVKKSIMMAKMLNIPIIGIIEN 211
                                   579*****************999999999999877 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   2.4e-06    0.0017      84     125 ..      25      66 ..      14      76 .. 0.83
   2 ?    1.0   0.0      0.49   3.5e+02      11      50 ..     169     206 ..     152     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.4e-06
                                   TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT--- CS
                   RsgA_GTPase  84 aktkegleelkellkdktsvlvGqSGvGKStLinallpelel 125
                                   a++ ++++e  +++k+k+++l G+ GvGKSt+  +l+  l+l
  gi|15668458|ref|NP_247256.1|  25 AQQDAKIRENMSKIKHKIVILSGKGGVGKSTVTVNLAAALNL 66 
                                   56677888889999******************9888877655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.49
                                   TTEES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEE CS
                   RsgA_GTPase  11 pkvaNvdqllivvslkepelslnlldrfLvlaeekgiepv 50 
                                   +++  +d ++iv++ +  e+s+  +++ +++a+  +i+++
  gi|15668458|ref|NP_247256.1| 169 QSIPDIDGAIIVTTPE--EVSVLDVKKSIMMAKMLNIPII 206
                                   5588899999999988..9999999999999999999876 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.7e-05     0.012       3      38 ..      42      76 ..      40      96 .. 0.89
   2 ?    2.9   0.0     0.088        63     103     154 ..     135     190 ..     107     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                      CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhelgesvlviDl 38
                                  ++ l+G +GGvG++++++ La al+ +g++v v+D+
  gi|15668458|ref|NP_247256.1| 42 IVILSG-KGGVGKSTVTVNLAAALNLMGKKVGVLDA 76
                                  566777.8***********************99997 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.088
                      CBP_BcsQ 103 eallaalkelk.eqyrwillDlpagasalt...rellaladlvllvvepdanchvr 154
                                   +a+ ++l+ +  ++ +++l+D p g+ + +    + +   d  + v++p+  + + 
  gi|15668458|ref|NP_247256.1| 135 GAIRQFLSDVVwGELDYLLIDTPPGTGDEQltiMQSIPDIDGAIIVTTPEEVSVLD 190
                                   566777777777999********976554400144555678899999998776555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.3e-06   0.00092       3      51 ..      41      89 ..      39      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
                                  EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--S CS
                    APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgf 51
                                   +v l+G  g GKst++++l+ +L+ +g++v +Ld d    ++ k Lg 
  gi|15668458|ref|NP_247256.1| 41 KIVILSGKGGVGKSTVTVNLAAALNLMGKKVGVLDADIHGPNIPKMLGV 89
                                  5899*******************************99766666666665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.4e-06     0.001      29      57 ..      38      64 ..      18      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-06
                        AAA_25 29 llpagelallaGapgtGKttlaldlalav 57
                                  +  ++++++l G +g+GK+t++++la+a+
  gi|15668458|ref|NP_247256.1| 38 I--KHKIVILSGKGGVGKSTVTVNLAAAL 64
                                  3..7999*******************997 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.7e-06     0.002      29      66 ..      40      77 ..      13      84 .. 0.80
   2 ?   -2.5   0.0       2.7   1.9e+03     147     188 ..     153     194 ..     145     204 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.7e-06
                                  SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                          MeaB 29 aqvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                   + v l G  G+Gkst++ +l++ l   Gk+v+vl  D
  gi|15668458|ref|NP_247256.1| 40 HKIVILSGKGGVGKSTVTVNLAAALNLMGKKVGVLDAD 77
                                  4567799***************************9877 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.7
                                   EEEEESSTTTTTTT--CCCHHH-SEEEEE---HHHHHHHHHH CS
                          MeaB 147 vvlllpeaGDelqgikkGileiaDiivvnkaDkkeaekaare 188
                                   ++ + p++GDe  +i + i +i   i+v   ++  +  +++ 
  gi|15668458|ref|NP_247256.1| 153 LIDTPPGTGDEQLTIMQSIPDIDGAIIVTTPEEVSVLDVKKS 194
                                   444556677776666666666666555555554444444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.3e-05    0.0094       1      25 [.      43      72 ..      43      95 .. 0.80
   2 ?   -0.7   0.0       2.7   1.9e+03      96     119 ..     258     286 ..     218     290 .] 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-05
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgf.....g 25
                                  ++l+G+ GvGK+t++ +L+  l++     g
  gi|15668458|ref|NP_247256.1| 43 VILSGKGGVGKSTVTVNLAAALNLmgkkvG 72
                                  79*****************99977755553 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.7
                        AAA_18  96 k.....vvLtaspeelleRlekRgyeeak 119
                                         v L+++ +e ++ + kR  e+ +
  gi|15668458|ref|NP_247256.1| 258 DkgipmVLLDCKASEEFKKIVKRIVEKVE 286
                                   24456689999999999999988877665 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.4    0.0035       2.5       2      34 ..      41      73 ..      40      75 .. 0.91
   2 !    7.8   0.0    0.0036       2.6     132     196 ..     178     255 ..     139     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0035
                        AAA_26  2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgy 34
                                  +i++ +   gvGK++v+  L++al+  g kvg+
  gi|15668458|ref|NP_247256.1| 41 KIVILSGKGGVGKSTVTVNLAAALNLMGKKVGV 73
                                  789999999***************999999997 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0036
                        AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNk....vrnp..e.........nvetlekksgipvlGvvPylpdlea 196
                                   i+V+++++ ++ ++  +i +++  n++++G+i N     +  p  +           e++ k  g++ lG++P + + ++
  gi|15668458|ref|NP_247256.1| 178 IIVTTPEEVSVLDVKKSIMMAKMLNIPIIGIIENMsgfvC--PycNkvvdifgrgGGEKAAKELGVEFLGRIPLDIKARE 255
                                   8899999999999999******99********99855432..234423334444455566666669*******9987765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1     2e-05     0.014      10      68 ..      34      93 ..      25      99 .. 0.84
   2 ?   -3.0   0.0       5.2   3.7e+03     127     141 ..     178     192 ..     177     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                    Zeta_toxin 10 ypsqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelhPeyeeilkad 68
                                  + s+ + k+++l+G  G GKs++   l+++l+ ++++v +ld+D   + +P+  ++++ +
  gi|15668458|ref|NP_247256.1| 34 NMSKIKHKIVILSGKGGVGKSTVTVNLAAALNlMGKKVGVLDADIHGPNIPKMLGVENTQ 93
                                  56788999***********************99999999*****9888888887766655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.2
                    Zeta_toxin 127 vvvavkkelSrlgvl 141
                                   ++v++++e+S+l+v+
  gi|15668458|ref|NP_247256.1| 178 IIVTTPEEVSVLDVK 192
                                   6899******99986 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.2e-05     0.023       4      41 ..      42      79 ..      40      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-05
                         VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfeaden 41
                                  i + s kGG Gk+t  + l +al   gk+v++++ad  
  gi|15668458|ref|NP_247256.1| 42 IVILSGKGGVGKSTVTVNLAAALNLMGKKVGVLDADIH 79
                                  567789*****************************965 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.8e-05      0.02       1      36 [.      47      82 ..      47     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.8e-05
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqse 36
                                  G+  +GKST++ +L+  +  +g+k+ ++D+D+  ++
  gi|15668458|ref|NP_247256.1| 47 GKGGVGKSTVTVNLAAALNLMGKKVGVLDADIHGPN 82
                                  66789**************************98776 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   6.1e-05     0.044       2      39 ..      41      78 ..      40      82 .. 0.93
   2 ?   -0.5   0.0       1.1   8.1e+02      83     121 ..     148     189 ..     134     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.1e-05
                                  EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                         SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                  ++++l G  G+GK t +  Laa l+ +gkkv +  aD+
  gi|15668458|ref|NP_247256.1| 41 KIVILSGKGGVGKSTVTVNLAAALNLMGKKVGVLDADI 78
                                  68999***************************999997 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                                   TSSEEEEEE-.-SSTTHHHHHHHHHHHHHHH..SSSEEEEEE CS
                         SRP54  83 kidvvlvDTa.Grlqndkelmeelkkikkvv..kpdevllvl 121
                                   + d++l+DT  G   ++  +m+ + +i  ++  ++ e + vl
  gi|15668458|ref|NP_247256.1| 148 ELDYLLIDTPpGTGDEQLTIMQSIPDIDGAIivTTPEEVSVL 189
                                   579999999548888888888888888877655333344444 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.76   5.5e+02       7      23 ..      15      28 ..       9      39 .. 0.66
   2 ?    9.6   0.0    0.0015       1.1       9      26 ..     217     243 ..     211     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.76
                                  TSSHHHHHHHHHHHHTT CS
                  Glutaredoxin  7 ptCpyCkkakrlLkelg 23
                                  +t   C+ +k+lL ++ 
  gi|15668458|ref|NP_247256.1| 15 NT---CPDTKKLLAQQD 28
                                  44...555666665555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                                   SHHHHHHHHHH.........HHTTGGE CS
                  Glutaredoxin   9 CpyCkkakrlL.........kelgvkf 26 
                                   CpyC+k+++++         kelgv+f
  gi|15668458|ref|NP_247256.1| 217 CPYCNKVVDIFgrgggekaaKELGVEF 243
                                   *********996666666666666665 PP

>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   9.8e-05     0.071      58      90 ..      44      72 ..      18     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.8e-05
                                  EEEESS--TT--SHHHHHHHHHHHHHHTT--EE CS
                         FTHFS 58 lvtaitPtplGeGKttttigLaqalnklgkkav 90
                                  +       + G GK+t+t+ La aln +gkk+ 
  gi|15668458|ref|NP_247256.1| 44 IL----SGKGGVGKSTVTVNLAAALNLMGKKVG 72
                                  33....34779******************9975 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00015      0.11      15      39 ..      35      59 ..      24      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                                  TTTSCSEEEEEEESTTSSHHHHHHH CS
                        NB-ARC 15 kdelqslvvalvGmgGvGKttlakq 39
                                  + +++  +v l+G+gGvGK+t+  +
  gi|15668458|ref|NP_247256.1| 35 MSKIKHKIVILSGKGGVGKSTVTVN 59
                                  4567777**************9766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00028       0.2       4      51 ..      25      73 ..      22      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                        AAA_30  4 aeQaaavea.lltsgdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                  a+Q a +++ + + ++++++l G  G GK+t+   l++a++  g++v +
  gi|15668458|ref|NP_247256.1| 25 AQQDAKIREnMSKIKHKIVILSGKGGVGKSTVTVNLAAALNLMGKKVGV 73
                                  55655555414555889********************999988888855 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0003      0.22     113     154 ..      26      65 ..      15      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                         T2SSE 113 alkekiaevlrkavrerglilvsGgTgsGKttllyallkein 154
                                   ++++ki+e ++k   +++++++sG  g GK+t++  l + +n
  gi|15668458|ref|NP_247256.1|  26 QQDAKIRENMSKI--KHKIVILSGKGGVGKSTVTVNLAAALN 65 
                                   5677788888887..9***************99865555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00034      0.24      25      48 ..      41      64 ..      22      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00034
                        AAA_16 25 elvllsGesGvGKsslvrellral 48
                                   +v+lsG  GvGKs++   l+ al
  gi|15668458|ref|NP_247256.1| 41 KIVILSGKGGVGKSTVTVNLAAAL 64
                                  79**************97776555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   0.00033      0.23       9      45 ..      30      66 ..      19      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00033
                                  HHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT- CS
                          TsaE  9 algkklakalgdvilLeGdLGaGKTtlvrglakalgv 45
                                  ++ +++ k  +++++L+G+ G+GK+t + +la+al++
  gi|15668458|ref|NP_247256.1| 30 KIRENMSKIKHKIVILSGKGGVGKSTVTVNLAAALNL 66
                                  3444454444789*******************99976 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0029       2.1       5      29 ..      40      64 ..      37      87 .. 0.87
   2 ?    1.0   0.0      0.64   4.6e+02      37      67 ..     255     288 ..     240     290 .] 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
                        AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                  ++i+++ G  G+GK+t+  +l+  l
  gi|15668458|ref|NP_247256.1| 40 HKIVILSGKGGVGKSTVTVNLAAAL 64
                                  6899**************9999877 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.64
                        AAA_22  37 e...erpevvfvtlpsstsskdllrellralgle 67 
                                   e   ++ + v+ ++++s++ k++ ++++++++ +
  gi|15668458|ref|NP_247256.1| 255 EasdKGIPMVLLDCKASEEFKKIVKRIVEKVEGK 288
                                   34446788899*****************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                       133  (0.00741815); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1816.09
//
Query:       gi|15668459|ref|NP_247257.1|  [L=219]
Description: hypothetical protein MJ_0284 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-12   46.0   0.4    6.2e-12   45.5   0.4    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      2e-11   43.9   0.1    2.8e-11   43.5   0.1    1.3  1  Methyltransf_31  Methyltransferase domain
      5e-11   43.2   0.0    8.3e-11   42.5   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.4e-10   41.0   0.2    3.1e-10   39.9   0.2    1.5  1  MTS              Methyltransferase small domain
    8.2e-07   29.6   0.0    1.7e-06   28.6   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    5.8e-06   25.9   0.0    8.7e-06   25.3   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
    1.4e-05   25.0   0.0    1.8e-05   24.6   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    2.6e-05   24.0   0.0    3.6e-05   23.5   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    5.3e-05   23.0   0.2    0.00014   21.7   0.2    1.7  1  UPF0020          Putative RNA methylase family UPF0020
    0.00026   20.6   0.0    0.00038   20.1   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0004   20.2   0.1    0.00049   19.9   0.1    1.2  1  Met_10           Met-10+ like-protein
     0.0005   20.1   0.0    0.00064   19.7   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
    0.00053   20.7   0.2    0.00084   20.0   0.2    1.5  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.017   15.1   0.1    1.3  1  Methyltransf_18  Methyltransferase domain
      0.025   14.3   0.0      0.044   13.5   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.031   13.8   0.0      0.038   13.5   0.0    1.2  1  DOT1             Histone methylation protein DOT1
       0.06   12.7   0.0      0.072   12.4   0.0    1.1  1  Methyltransf_10  RNA methyltransferase
      0.063   12.7   0.1        0.1   12.0   0.1    1.3  1  TehB             Tellurite resistance protein TehB


Domain annotation for each model (and alignments):
>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.4   6.2e-15   6.2e-12     163     213 ..      48      98 ..      41     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 6.2e-15
                          PrmA 163 eevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakl 213
                                   + v+D+G+G+G Lai+++ Lgak+++++DiD  ++++akeNa++ +v+  +
  gi|15668459|ref|NP_247257.1|  48 NVVIDLGCGTGRLAIGSKILGAKRAIGIDIDRESIEAAKENAKKLNVDVDF 98 
                                   569***************************************987777655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.1   2.8e-14   2.8e-11       4      68 ..      47     108 ..      45     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.8e-14
               Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelek 68 
                                   +++v+DlGCGtG+l++     +   ++ +GiDi+ e+ie A+ena+kl++d v F   di + + 
  gi|15668459|ref|NP_247257.1|  47 NNVVIDLGCGTGRLAIGSK--ILGAKRAIGIDIDRESIEAAKENAKKLNVD-VDFYCMDIRDVDD 108
                                   678**********998776..5556789**********************8.9999999988664 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   8.4e-14   8.3e-11       1      60 [.      50     108 ..      50     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 8.4e-14
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpf 60 
                                   v+dlGcGtGrl++      g+++ +g+Di+ e +eaa+e+a++ +++v+f+++d++d++ 
  gi|15668459|ref|NP_247257.1|  50 VIDLGCGTGRLAIGSKIL-GAKRAIGIDIDRESIEAAKENAKKLNVDVDFYCMDIRDVDD 108
                                   89**********999877.79**********************************99873 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.2   3.1e-13   3.1e-10      22     117 ..      37     141 ..      29     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 3.1e-13
                                   HHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-ST.......TTTSTT CS
                           MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdv.......leevee 95 
                                   +L  ++++  ++ v+DlGcG+G l++  +    + +   +d+d +++e+aken+++ +++v+++  d+       l++v  
  gi|15668459|ref|NP_247257.1|  37 ILFFAVNDFYNNVVIDLGCGTGRLAIGSKILGAK-RAIGIDIDRESIEAAKENAKKLNVDVDFYCMDIrdvddefLNNVLG 116
                                   5555555656788*************99888887.56789********************666655541111111445543 PP

                                   S-EE...EEEE---STTTCHCHHHH CS
                           MTS  96 kkfd...livsNPPfhagkatelav 117
                                   ++ d   +++ NPPf a+k+  ++v
  gi|15668459|ref|NP_247257.1| 117 EDRDlkrVVIQNPPFGAQKKHADRV 141
                                   3333223799*******99966554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.7e-09   1.7e-06       2      55 ..      52     106 ..      51     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.7e-09
                                   EET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT CS
               Methyltransf_11   2 dvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaekl 55 
                                   d+GcGtGrla   +  g +r +g+D++ e +++ake+a++ ++ v+f ++d++++
  gi|15668459|ref|NP_247257.1|  52 DLGCGTGRLAIGSKILGaKRAIGIDIDRESIEAAKENAKKLNVDVDFYCMDIRDV 106
                                   9*************8889**********************************985 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   8.7e-09   8.7e-06       3     101 ..      48     148 ..      46     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 8.7e-09
                                   EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C....CCHHHHCS.-TTSEEEEEE CS
                Methyltransf_4   3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda....lkvllell.edgslekifi 78 
                                    vv+++GcG G++ +  +k    k  +Gi+i +++++++ +++++l++  +   + d      ++l+++l ed+ l++++i
  gi|15668459|ref|NP_247257.1|  48 NVVIDLGCGTGRLAIG-SKILGAKRAIGIDIDRESIEAAKENAKKLNVD-VDFYCMDIrdvdDEFLNNVLgEDRDLKRVVI 126
                                   689*********9997.8999999**********************664.445555544444599**99956789****** PP

                                   ES-----SGGGGGGSTTSHHHHH CS
                Methyltransf_4  79 lFPDPwfKkrhhKrRllqpellk 101
                                   + P P+  +++h  R++ ++ l+
  gi|15668459|ref|NP_247257.1| 127 QNP-PFGAQKKHADRVFLDKALE 148
                                   *99.************9888765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.8e-08   1.8e-05       8      78 ..      32     105 ..      21     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.8e-08
               Methyltransf_23   8 elsdklerllpklraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae..kakkaqkdqfdeqeaae 78 
                                   +l++ +++++ +++ ++ v+d+GcGtG+l+   +  g+   +g+D+++e +e a+   +k ++++ f+ +++++
  gi|15668459|ref|NP_247257.1|  32 KLAADILFFAVNDFYNNVVIDLGCGTGRLAIGSKILGAkRAIGIDIDRESIEAAKenAKKLNVDVDFYCMDIRD 105
                                   5667788888889******************99999997899**********9987744444455554444444 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   3.6e-08   3.6e-05      41     150 ..      46     155 ..      36     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.6e-08
                                   CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T..TTEEEEES-HHHHCTS--SS-EEE.EEE CS
                 Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee..etaelkedaleallklakkkeefd.ivf 118
                                    ++ v+Dl +G+G l++     gak+a+ ++ d+e +++ ken ++l+++    +  +++ + e l++  ++++ +  +v 
  gi|15668459|ref|NP_247257.1|  46 YNNVVIDLGCGTGRLAIGSKILGAKRAIGIDIDRESIEAAKENAKKLNVDVdfYCMDIRDVDDEFLNNVLGEDRDLKrVVI 126
                                   45679*******************************************987775555555555666665566666651566 PP

                                   E--SSSTTCH.HHHHHHHHHTT-EEEEEEEEE CS
                 Cons_hypoth95 119 lDPPyakellieevlelleekkllkenalvvv 150
                                    +PP+ +++   +  + +   k+l+ + ++++
  gi|15668459|ref|NP_247257.1| 127 QNPPFGAQK---KHADRVFLDKALEIGDIIYT 155
                                   79***9995...56666666677777777665 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   1.4e-07   0.00014      51     137 ..      69     137 ..      28     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.4e-07
                                   TT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.........STTS-- CS
                       UPF0020  51 aniapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLr.........lkegev 122
                                   a++                          +g+D+dr+ +++a+eNa+k +v+  ++f+++d++++          ++++  
  gi|15668459|ref|NP_247257.1|  69 AKR-------------------------AIGIDIDRESIEAAKENAKKLNVD--VDFYCMDIRDVDdeflnnvlgEDRDLK 122
                                   444.........................59*****************98876..788888888888777668766666677 PP

                                   -EEEE---------- CS
                       UPF0020 123 dvivtnpPYGerlgs 137
                                   +v++ npP+G   ++
  gi|15668459|ref|NP_247257.1| 123 RVVIQNPPFGAQKKH 137
                                   89********87655 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.8e-07   0.00038       2      85 ..      48     135 ..      47     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.8e-07
               Methyltransf_15   2 rvilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfe....llaklkleki.kvdlvf 76 
                                   +v++Dl +G+G  +i  +    ++ i+i+i++e ++ a++Na+    +  +++ + d+ +     l+++  e      +v+
  gi|15668459|ref|NP_247257.1|  48 NVVIDLGCGTGRLAIGSKILgAKRAIGIDIDRESIEAAKENAKKL--NVDVDFYCMDIRDvddeFLNNVLGEDRdLKRVVI 126
                                   689*************99985689*******************99..5568888888888555544444333332566889 PP

               Methyltransf_15  77 lSpPwGGps 85 
                                     pP G  +
  gi|15668459|ref|NP_247257.1| 127 QNPPFGAQK 135
                                   999998655 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1     5e-07   0.00049     101     171 ..      47     123 ..      37     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5e-07
                                   T-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EE..........E CS
                        Met_10 101 gevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqlad..........r 171
                                   ++vV+d+  G G +ai  + ++ akr ++id++ es++  ken k   ++  v  +++D r+v   ++++          r
  gi|15668459|ref|NP_247257.1|  47 NNVVIDLGCGTGRLAIGSKILG-AKRAIGIDIDRESIEAAKENAKK--LNVDVDFYCMDIRDVDD-EFLNnvlgedrdlkR 123
                                   89***************99865.56689***************985..5556788********74.444436666666663 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.5e-07   0.00064      26      78 ..      47      96 ..      32     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.5e-07
               Methyltransf_32 26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78
                                  ++ v+D+G+G g L+   +        + +gid+ +e +e+a++ a+kl+ ++
  gi|15668459|ref|NP_247257.1| 47 NNVVIDLGCGTGRLAIGSKI---LGAKRAIGIDIDRESIEAAKENAKKLNVDV 96
                                  5679**********999888...77899*********************9433 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   8.4e-07   0.00084       2      63 ..      52     111 ..      51     171 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.4e-07
               Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldg 63 
                                   ++GcGtG+l+         ++ +g+Di++++ie+ake  +k  n +++++  + +d++d++ 
  gi|15668459|ref|NP_247257.1|  52 DLGCGTGRLAIGSKIL-GAKRAIGIDIDRESIEAAKENAKKL-NVDVDFYCMDIRDVDDEFL 111
                                   9*******98655333.668999*********6666655554.4566666555555555544 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.7e-05     0.017      15      68 ..      47      97 ..      40     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
               Methyltransf_18 15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkie 68
                                  +++v+D G+  g l+i       ak++i +Di ++++e+aken++k +++   +
  gi|15668459|ref|NP_247257.1| 47 NNVVIDLGCGTGRLAIGSK-ILGAKRAIGIDIDRESIEAAKENAKKLNVDV--D 97
                                  4799***********9875.67789********************988853..3 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.4e-05     0.044      76     124 ..      49      95 ..      38     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.4e-05
                                   EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC CS
                          PCMT  76 rvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle 124
                                    v+++G+G+G l a+ ++++g+k  +++i+  +e +e+ak+n kkl+++
  gi|15668459|ref|NP_247257.1|  49 VVIDLGCGTGRL-AIGSKILGAKR-AIGIDIDRESIEAAKENAKKLNVD 95 
                                   589*******77.789*****997.9******************99875 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.9e-05     0.038      43     110 ..      47     110 ..      36     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-05
                                   T-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTTB----EEEESS-S CS
                          DOT1  43 edvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlklfGkklakiefirksF 110
                                   ++v +DLG G G++ +  +  +g k ++G++i  +  e a+++++ l+  ++++ ++  +++   ++F
  gi|15668459|ref|NP_247257.1|  47 NNVVIDLGCGTGRLAIG-SKILGAKRAIGIDIDRESIEAAKENAKKLNVDVDFYCMDIRDVD---DEF 110
                                   6789*********9875.778999******************************99877765...344 PP

>> Methyltransf_10  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.2e-05     0.072     104     199 ..      48     143 ..      32     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.2e-05
                                   -EEEEES-TTTTHHHHHHHHHH--.EEEEEES-HHHHHHHHHHHHHT.T-TTTEEEEE--T.T-SCCHHSSTTSS.-EEEE CS
               Methyltransf_10 104 vraldiGvGanCiyPllGvteyGW.rfvgsevddvslasakaivesnsklsdaiklrkqke.kkaifdglieene.rydvt 181
                                     ++d+G G+  +   +G +  G  r +g ++d  s++ ak + ++  +++    +   ++   + ++ + +e+     v+
  gi|15668459|ref|NP_247257.1|  48 NVVIDLGCGTGRL--AIGSKILGAkRAIGIDIDRESIEAAKENAKKL-NVDVDFYCMDIRDvDDEFLNNVLGEDRdLKRVV 125
                                   4467777777655..4677766642689*************998774.455444454444313345566666665377899 PP

                                   EE-S---SS--------- CS
               Methyltransf_10 182 lCnPPfhaslaeakagse 199
                                   + nPPf a++++a ++  
  gi|15668459|ref|NP_247257.1| 126 IQNPPFGAQKKHADRVFL 143
                                   9**********9998765 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1    0.0001       0.1      32      89 ..      48     105 ..      32     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                   -EEEEES-TTSHHHHHHHHTT-E.EEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG CS
                          TehB  32 gkvldlgcgqgrnslylsllgyd.vtawdknensiafleeikekenlknistalydine 89 
                                     v+dlgcg gr ++  ++lg +    +d + +si+  +e ++k n++ ++   +di +
  gi|15668459|ref|NP_247257.1|  48 NVVIDLGCGTGRLAIGSKILGAKrAIGIDIDRESIEAAKENAKKLNVD-VDFYCMDIRD 105
                                   5689*****************8725689***********999999998.7777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1409.50
//
Query:       gi|15668460|ref|NP_247258.1|  [L=147]
Description: small heat shock protein Hsp20 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.7e-12   44.6   0.0    1.2e-11   44.0   0.0    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA
    1.6e-11   44.2   0.1      2e-11   44.0   0.1    1.1  1  HSP20       Hsp20/alpha crystallin family
  ------ inclusion threshold ------
      0.069   12.5   0.2      0.079   12.3   0.2    1.1  1  DUF4097     Putative adhesin


Domain annotation for each model (and alignments):
>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0     2e-15   1.2e-11       1      61 [.      51     131 ..      51     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2e-15
                    ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig.....................nfrRqitLPsvlarkevtsAkfedgvLe 60 
                                   d ++++ + LP+v+ke+i l  +gd+L I+++                        R+i LP +++++++ sAkfe+gvL 
  gi|15668460|ref|NP_247258.1|  51 DQHIKVIAWLPGVNKEDIILNAVGDTLEIRAKrsplmiteseriiyseipeeeEIYRTIKLPATVKEENA-SAKFENGVLS 130
                                   689**************************************************99*************99.*********9 PP

                    ArsA_HSP20  61 I 61 
                                   +
  gi|15668460|ref|NP_247258.1| 131 V 131
                                   8 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.1   3.3e-15     2e-11       2      99 ..      47     146 ..      46     147 .] 0.88

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 3.3e-15
                                   --SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--....---TT----SS.---EEEEEE--STTB-TTT-EEEEETT CS
                         HSP20   2 ikeeeeefevkldvpglkkeelkvkvednrvlvkgehe..eeeedekgliker.ssrkFsrkftLPenvdadkvkaslkdG 79 
                                   i+e +++++v + +pg++ke++ ++  ++++ +++++     +e+e+ +++e  ++++  r+++LP  v++++ +a++++G
  gi|15668460|ref|NP_247258.1|  47 IIEGDQHIKVIAWLPGVNKEDIILNAVGDTLEIRAKRSplMITESERIIYSEIpEEEEIYRTIKLPATVKEENASAKFENG 127
                                   78999*********************************9967777777777762678899********************* PP

                                   EEEEEEEBSS--..------ CS
                         HSP20  80 vLtvtvpkkepekkkkerki 99 
                                   vL+v +pk e+  k k ++i
  gi|15668460|ref|NP_247258.1| 128 VLSVILPKAESSIK-KGINI 146
                                   *********99855.55555 PP

>> DUF4097  Putative adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   1.3e-05     0.079       4      95 ..      35     131 ..      32     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                       DUF4097   4 ldisse.sadvtikesddekitveystakklkkqkve.etggtLsitqkekngvstgfik.....elssgekskitiylPk 77 
                                   ++is +   ++ i+e+d + i+v ++  + +k++ +    g tL+i+ k+   ++t   +     e+ + e+ + ti+lP 
  gi|15668460|ref|NP_247258.1|  35 IQISGKgFMPISIIEGD-QHIKVIAWLPGVNKEDIILnAVGDTLEIRAKRSPLMITES-EriiysEIPEEEEIYRTIKLPA 113
                                   77777766789999999.77*************99999***********999998875.4599877888888888****** PP

                       DUF4097  78 ktkledlqvkassGdlsv 95 
                                   + k e+ ++k ++G lsv
  gi|15668460|ref|NP_247258.1| 114 TVKEENASAKFENGVLSV 131
                                   **************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1039.58
//
Query:       gi|15668461|ref|NP_247259.1|  [L=117]
Description: hypothetical protein MJ_0286 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.051   13.6   0.4       0.12   12.4   0.2    1.9  2  TFIID-18kDa  Transcription initiation factor IID, 18kD subuni


Domain annotation for each model (and alignments):
>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   6.7e-06      0.12      46      84 ..      45      83 ..       6      91 .. 0.79
   2 ?    0.4   0.0     0.038   6.9e+02      62      89 ..      76     103 ..      74     107 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.7e-06
                                  -XXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   TFIID-18kDa 46 vaklrgsrkitlEDllfliRkDkkKlnRlkellslkell 84
                                  +  ++++++i++ Dll li+ +k+ +nRl  +l   +  
  gi|15668461|ref|NP_247259.1| 45 LLSQNQKNEIQMSDLLALIKEEKEGINRLFSFLYQTDIP 83
                                  4456679**********************9999887765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.038
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   TFIID-18kDa  62 fliRkDkkKlnRlkellslkellkkakK 89 
                                   fl   D    nR++ l+ lke  k++ K
  gi|15668461|ref|NP_247259.1|  76 FLYQTDIPVENRIEILMLLKEFVKEEIK 103
                                   6666666667899999999999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 737.69
//
Query:       gi|15668462|ref|NP_247260.1|  [L=97]
Description: hypothetical protein MJ_0287 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-28   98.1   1.9    2.5e-28   97.9   1.9    1.1  1  HTH_45        Winged helix-turn-helix
     0.0048   16.6   0.3     0.0064   16.2   0.3    1.2  1  DUF4364       Domain of unknown function (DUF4364)
      0.007   16.8   0.1      0.012   16.1   0.0    1.4  2  HTH_27        Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.025   13.6   0.0      0.035   13.1   0.0    1.2  1  Topoisom_bac  DNA topoisomerase
      0.027   12.9   0.0      0.027   12.8   0.0    1.0  1  DUF505        Protein of unknown function (DUF505)
       0.14   12.2   3.1       0.23   11.5   3.1    1.5  1  DUF1803       Domain of unknown function (DUF1803)


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   1.9   8.4e-32   2.5e-28       1      76 [.      18      93 ..      18      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 8.4e-32
                        HTH_45  1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkeleela 76
                                  +Rs++e+i++IL++i+ege+ kT+imy+anL++++++kY+d+L+++g+ikk+kek++lTe G++l+++l el e++
  gi|15668462|ref|NP_247260.1| 18 KRSQFEVIFEILHIIKEGEQIKTRIMYAANLDWRNFSKYIDFLISNGFIKKNKEKFELTELGKKLYSSLYELFEIM 93
                                  8**********************************************************************99875 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   2.1e-06    0.0064      19      73 ..      36      86 ..      25      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.1e-06
                       DUF4364 19 sqlseiileneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelf 73
                                  +q+   i+    +++ +++++++ L+++g+i++    nk+ +++Te Gk+  + +
  gi|15668462|ref|NP_247260.1| 36 EQIKTRIMYAANLDWRNFSKYIDFLISNGFIKK----NKEKFELTELGKKLYSSL 86
                                  6888888999999999****************5....99**********998776 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       5.3   1.6e+04      54      61 ..      12      19 ..       9      21 .. 0.69
   2 !   16.1   0.0   4.1e-06     0.012       7      65 ..      27      76 ..      24      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.3
                        HTH_27 54 eadrrekr 61
                                   ++rr+kr
  gi|15668462|ref|NP_247260.1| 12 NRNRRYKR 19
                                  57788776 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 4.1e-06
                        HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlT 65
                                   +Lh i+  ++++++++++ + n++  ++s+ ++ L+ +G++++++ +       ++lT
  gi|15668462|ref|NP_247260.1| 27 EILHIIK--EGEQIKTRIMYAANLDWRNFSKYIDFLISNGFIKKNKEK-------FELT 76
                                  69*****..*********************************776655.......5555 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05     0.035     348     387 ..      55      94 ..      52      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                  Topoisom_bac 348 eiieklvergYverkkkslvptelGkalvellekfkdlvs 387
                                   + i+ l++ g+++++k+++  telGk+l++ l ++ ++++
  gi|15668462|ref|NP_247260.1|  55 KYIDFLISNGFIKKNKEKFELTELGKKLYSSLYELFEIMN 94 
                                   67999*********99***************966667665 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.2e-06     0.027       9      72 ..      27      91 ..      18      97 .] 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.2e-06
                        DUF505  9 eiLeklkeeeekkeeeeieveeleeeei...lleLelagLvrleepekielTyaGkklaelldelie 72
                                  eiL+ +ke  e+ +++ + +++l  ++    +  L   g+++ +++ek+elT+ Gkkl   l el e
  gi|15668462|ref|NP_247260.1| 27 EILHIIKE-GEQIKTRIMYAANLDWRNFskyIDFLISNGFIK-KNKEKFELTELGKKLYSSLYELFE 91
                                  55555554.444444444444443333344344577789***.999*************99999854 PP

>> DUF1803  Domain of unknown function (DUF1803)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.1   7.5e-05      0.23      13      64 ..      24      75 ..       9      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.5e-05
                       DUF1803 13 lFkeLieyLaehddviLRelkkeFadqkkldrlldelidaglikRenkrYkl 64
                                  + +e+++ ++e +++  R + ++  d +++++ +d li +g+ik++  +++l
  gi|15668462|ref|NP_247260.1| 24 VIFEILHIIKEGEQIKTRIMYAANLDWRNFSKYIDFLISNGFIKKNKEKFEL 75
                                  33444445555599999*9999999********************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 662.56
//
Query:       gi|15668463|ref|NP_247261.1|  [L=178]
Description: hypothetical protein MJ_0288 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.018   15.6   0.3      0.024   15.1   0.3    1.3  1  LEA_2           Late embryogenesis abundant protein
      0.019   15.1   0.4       0.22   11.7   0.5    2.2  2  Transglut_C     Transglutaminase family, C-terminal ig like d
      0.037   11.4   0.3      0.048   11.0   0.3    1.1  1  TRAPPC9-Trs120  Transport protein Trs120 or TRAPPC9, TRAPP II


Domain annotation for each model (and alignments):
>> LEA_2  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.3   4.1e-06     0.024       4      57 ..      55     108 ..      53     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.1e-06
                                   EEESSSS-EEEEEEEEEEEESSSEEEEEEECE-EEESSSCEEEEEEEEEEEHHH CS
                         LEA_2   4 vrNPNsfgvrydgleldlsyngqrlasgtspqgfsqpargtttlevpvsvsadd 57 
                                   v+NPNsf+v+++ ++   + n +++ ++ + + f+++++ t  ++++ +v+ +d
  gi|15668463|ref|NP_247261.1|  55 VKNPNSFPVKVEMVTTGDLNNSKKVEVKIMKNNFTLKPGETVGVNITFTVKEKD 108
                                   99************98888899********************999998888765 PP

>> Transglut_C  Transglutaminase family, C-terminal ig like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   3.6e-05      0.22       1      76 [.      33     104 ..      33     114 .. 0.82
   2 ?    1.2   0.0     0.069   4.1e+02      71      92 ..     115     136 ..     107     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                                   EEEEEEESSCEBTTSEEEEEEEEEE-SSS-BEEEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE-H CS
                   Transglut_C   1 pelkievlesavlgqdltvsvllkNplseelkdvklnlcaqtveynGvlaaefkkksleltLePkeeksvrlkilp 76 
                                   p+++i v  s  l qd++  +++kNp s +   vk+++ + t   n   + e+k  ++++tL+P+e++ v ++++ 
  gi|15668463|ref|NP_247261.1|  33 PKIDIMVNASNGLPQDINSIIYVKNPNSFP---VKVEM-VTTGDLNNSKKVEVKIMKNNFTLKPGETVGVNITFTV 104
                                   57888998899999************9999...45555.444455555567******************9999975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.069
                                   EEEE-HHSHEEECCEEEEEECS CS
                   Transglut_C  71 rlkilpskyGerkllvelssda 92 
                                    +ki+p+ yG+ k+ v+l+ ++
  gi|15668463|ref|NP_247261.1| 115 LTKISPVDYGDDKKGVNLKASV 136
                                   579********99998877665 PP

>> TRAPPC9-Trs120  Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3     8e-06     0.048     698     752 ..      52     110 ..      47     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8e-06
                TRAPPC9-Trs120 698 kvtLqNPfefeveiesiel....etegvefealkeslvigpkstqkltltgkptesgel 752
                                    + ++NP +f v++e ++     ++++ve++++k++++++p +t  +++t++ +e++++
  gi|15668463|ref|NP_247261.1|  52 IIYVKNPNSFPVKVEMVTTgdlnNSKKVEVKIMKNNFTLKPGETVGVNITFTVKEKDNY 110
                                   5889*************85333356788888*********************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1369.81
//
Query:       gi|15668464|ref|NP_247262.1|  [L=338]
Description: hypothetical protein MJ_0289 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.066   13.8   0.1       0.23   12.1   0.0    1.9  2  DM13      Electron transfer DM13
        1.1    9.1   3.4       0.55   10.1   1.2    1.5  2  DUF4811   Domain of unknown function (DUF4811)


Domain annotation for each model (and alignments):
>> DM13  Electron transfer DM13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.75   6.7e+03      26      33 ..     112     117 ..      88     149 .. 0.55
   2 ?   12.1   0.0   2.5e-05      0.23      18      82 ..     232     296 ..     219     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.75
                          DM13  26 fatdgkgp 33 
                                   ++t  +g 
  gi|15668464|ref|NP_247262.1| 112 LQT--NGA 117
                                   232..222 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.5e-05
                          DM13  18 dktlelegfatdgkgpdlkvwlgkseapsskkgf.kipdedgvtlgplkaykgeq.ytlelpagvdl 82 
                                   ++++ +++++ dg g +  v++++++  +   g+ +ip e+ +    +ka++ +q y+ +l ++v++
  gi|15668464|ref|NP_247262.1| 232 ENVVTIHNIDPDGVGTKIAVFVSATSMTQA-GGTgIIPAENIKAH-VIKANNMTQsYNTHLQNNVKV 296
                                   489999********************9888.89988888886666.*****************9986 PP

>> DUF4811  Domain of unknown function (DUF4811)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.2   6.1e-05      0.55       2      75 ..       6      74 ..       5      79 .. 0.90
   2 ?   -3.5   0.0      0.91   8.2e+03      49      56 ..     290     297 ..     270     304 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.1e-05
                       DUF4811  2 kilrlllglisllllvaSvllivandsdHfGmkkvtttktqkiysaadskdlglllyqeiGtkgkekvylYktk 75
                                  ++ r++l+l+  +++ ++v++ +  +s  +G    tt +  +++++ + +++++++ +  G     kvy Yk++
  gi|15668464|ref|NP_247262.1|  6 NSTRYILSLLLSIIMGVAVMGSTFAISTTYGTG-HTTATVDNLKPVVNCSSYEMVIRTVQGI----KVYEYKNT 74
                                  6789***************************86.57778899***************99999....89999986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.91
                       DUF4811  49 dskdlgll 56 
                                    ++++++l
  gi|15668464|ref|NP_247262.1| 290 LQNNVKVL 297
                                   12234444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2314.71
//
Query:       gi|15668465|ref|NP_247263.1|  [L=211]
Description: hypothetical protein MJ_0290 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-27   95.0   2.8    5.6e-27   93.5   2.8    1.8  1  HTH_45        Winged helix-turn-helix
    2.1e-05   24.6   3.6    3.3e-05   24.0   3.6    1.3  1  Cnd1          non-SMC mitotic condensation complex subunit 1
  ------ inclusion threshold ------
      0.015   15.1   0.6       0.23   11.3   0.3    2.4  2  DUF3116       Protein of unknown function (DUF3116)
      0.031   12.7   0.1       0.04   12.4   0.1    1.1  1  Herpes_pp85   Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV 
      0.032   14.1   1.4       0.48   10.3   0.1    2.5  2  RuvB_C        RuvB C-terminal winged helix domain
       0.16   11.0   0.2       0.32   10.0   0.2    1.3  1  FA_synthesis  Fatty acid synthesis protein
        4.1    7.3   6.0       0.98    9.3   2.9    1.7  2  CLTH          CTLH/CRA C-terminal to LisH motif domain


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   2.8   2.2e-30   5.6e-27       1      75 [.     132     206 ..     132     208 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 2.2e-30
                        HTH_45   1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkeleel 75 
                                   +R+k++Ii++IL+a++++e kkTkimy+anL++k++++Y+ +L+++++i+k+++ Y+lT kG+ llek++e+ +l
  gi|15668465|ref|NP_247263.1| 132 KRDKIMIIFEILKAVKNKELKKTKIMYAANLDWKTFRNYIGYLLDNEFIRKTDGVYTLTPKGELLLEKIEEVFRL 206
                                   8**********************************************************************9987 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   3.6   1.3e-08   3.3e-05      22     134 ..      32     153 ..      22     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.3e-08
                          Cnd1  22 lvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisek.senaiynllpdii 101
                                   l+e+++  Lk +d + + t++ ++ +L+l++ v+  +++++l++ l ++++  + nal++l+ei e  +e+++ ++  ++i
  gi|15668465|ref|NP_247263.1|  32 LLEEIYGFLKSDDIQLKITCLAILGNLYLKGKVQITQLIKHLEEVLLENDKDAILNALLILKEIPEVyQEDLLKRIILKYI 112
                                   67899999***********************************************************87777777766666 PP

                          Cnd1 102 sklsd...alne........csewgqitilefLlsyipkdkqea 134
                                    k  +   +  +        +++++ + i+e+L   ++k+ +  
  gi|15668465|ref|NP_247263.1| 113 GKDIKdceD--DkdkstlpsVKRDKIMIIFEILKAVKNKELK-K 153
                                   554433440..1445555559999999999988888888877.4 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2     0.088   2.3e+02       4      25 ..     134     155 ..     131     170 .. 0.72
   2 ?   11.3   0.3   8.9e-05      0.23      55      84 ..     172     201 ..     140     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.088
                       DUF3116   4 PseelilevLelvkdpnftikn 25 
                                    +  +i+e+L++vk+++ + ++
  gi|15668465|ref|NP_247263.1| 134 DKIMIIFEILKAVKNKELKKTK 155
                                   556789999****999876544 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 8.9e-05
                       DUF3116  55 gyilRkeekannkkrYelTekGellykelk 84 
                                   gy+l +e  +++   Y+lT+kGell+++++
  gi|15668465|ref|NP_247263.1| 172 GYLLDNEFIRKTDGVYTLTPKGELLLEKIE 201
                                   677888888889999************997 PP

>> Herpes_pp85  Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.6e-05      0.04      50     111 ..      31      92 ..      14     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                   Herpes_pp85  50 liiivkfkfskvkdllqevirlgvlinryraskdvlkdlrtqldvlyseelkrrllralirl 111
                                   l +   + f k+ d+  ++  l++l n y  +k ++ +l+  l+ +  e+ k  +l al+ l
  gi|15668465|ref|NP_247263.1|  31 LLLEEIYGFLKSDDIQLKITCLAILGNLYLKGKVQITQLIKHLEEVLLENDKDAILNALLIL 92 
                                   55566688***************************************9**999999999876 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.061   1.6e+02       8      35 ..      48      75 ..      40      86 .. 0.88
   2 ?   10.3   0.1   0.00019      0.48      14      71 ..     142     197 ..     134     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.061
                                  HHHHHHHHHHT.TT--B-HHHHHHHTT- CS
                        RuvB_C  8 dikyLkllkekfkggpvglktlaailge 35
                                   i++L +l + + +g+v ++ l ++l+e
  gi|15668465|ref|NP_247263.1| 48 KITCLAILGNLYLKGKVQITQLIKHLEE 75
                                  578999**************99998875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
                                   HHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEEEE-HHHHHHH CS
                        RuvB_C  14 llkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrGRilTkkglkyl 71 
                                   +lk + k++++  + +  +++++ +t+ + i  yLl +++I++t+   +lT+kg  +l
  gi|15668465|ref|NP_247263.1| 142 ILK-AVKNKELKKTKIMYAANLDWKTFRNYI-GYLLDNEFIRKTDGVYTLTPKGELLL 197
                                   444.347788888889999999999999887.6************9999999997655 PP

>> FA_synthesis  Fatty acid synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00012      0.32     206     273 ..      36      99 ..      16     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00012
                                   EEEEEEGGGCCCTS-SEEE--HHHHHHHHHHHHHHHHHHHHHHHHHHTTT----------HHCHHHHH CS
                  FA_synthesis 206 flGnvegrdildgkvdvivcdgftgNvilktaegvakavksllkeelkkslasklgalllskalkrlk 273
                                    +G++ + di       i+c+ + gN  lk    + + +k+l +  l++ + + l+all+ k++ ++ 
  gi|15668465|ref|NP_247263.1|  36 IYGFLKSDDIQL----KITCLAILGNLYLKGKVQITQLIKHLEEVLLENDKDAILNALLILKEIPEVY 99 
                                   566666666654....389****************************************999887665 PP

>> CLTH  CTLH/CRA C-terminal to LisH motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.9   0.00038      0.98       6      79 ..       8      88 ..       3     118 .. 0.80
   2 ?   -3.4   0.1       3.1     8e+03       7      19 ..     141     153 ..     136     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00038
                          CLTH  6 qkIiklilegdlseaiewinenkpelles.....nsnLeFkLkllqfielirgktkd..ieealeyarenl.efendehlke 79
                                   +I++li++g+++ +++ i+e    l+e+     +++++ k+ +l ++  +  k ++  i++++++  e l e ++d+ l+ 
  gi|15668465|ref|NP_247263.1|  8 GEIKELIKNGKINDVLQLIEEDTLLLEEIygflkSDDIQLKITCLAILGNLYLK-GKvqITQLIKHLEEVLlENDKDAILNA 88
                                  69*******************887777776666669999999999998777632.334589999999888867777754443 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.1
                          CLTH   7 kIiklilegdlse 19 
                                   +I k++++++l++
  gi|15668465|ref|NP_247263.1| 141 EILKAVKNKELKK 153
                                   5777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1021  (0.0569468); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1379.73
//
Query:       gi|15668466|ref|NP_247264.1|  [L=409]
Description: signal recognition particle, receptor [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-78  261.6   2.7    3.8e-78  261.6   2.7    1.9  2  SRP54            SRP54-type protein, GTPase domain
      1e-13   51.3   8.2      1e-13   51.3   8.2    4.4  2  SRP54_N          SRP54-type protein, helical bundle domain
    2.9e-07   30.4   2.0      6e-07   29.4   2.0    1.4  1  AAA_30           AAA domain
    7.9e-07   28.6   0.5    7.9e-07   28.6   0.5    2.3  2  Zeta_toxin       Zeta toxin
    7.1e-06   26.5  16.3    1.1e-05   25.8   0.3    2.7  2  AAA_17           AAA domain
    8.1e-06   25.0   2.0    2.7e-05   23.3   2.0    1.9  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    1.1e-05   25.6   0.1      3e-05   24.2   0.1    1.7  1  AAA_33           AAA domain
    1.6e-05   25.2   0.7    0.00023   21.5   0.1    2.4  2  AAA_28           AAA domain
    2.6e-05   24.2   0.0    6.5e-05   22.9   0.0    1.7  1  APS_kinase       Adenylylsulphate kinase
    4.8e-05   23.7   0.2    0.00018   21.8   0.0    1.9  2  AAA_22           AAA domain
    5.8e-05   22.9   0.3    5.8e-05   22.9   0.3    3.9  3  Thymidylate_kin  Thymidylate kinase
     0.0001   22.3   0.4     0.0001   22.3   0.4    2.7  1  ResIII           Type III restriction enzyme, res subunit
    0.00051   20.1   3.8    0.00051   20.1   3.8    3.5  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00053   19.3   0.7    0.00053   19.3   0.7    2.0  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0008   19.8   1.1     0.0023   18.3   0.1    2.1  2  AAA_16           AAA ATPase domain
     0.0016   18.0   0.3     0.0054   16.3   0.3    2.0  1  PPK2             Polyphosphate kinase 2 (PPK2)
     0.0021   18.6   3.4      0.019   15.4   0.0    2.6  2  ABC_tran         ABC transporter
     0.0032   17.4   8.3      0.047   13.6   0.5    2.7  2  YjeF_N           YjeF-related protein N-terminus
     0.0046   16.3   0.0     0.0095   15.3   0.0    1.5  1  VirC1            VirC1 protein
     0.0048   16.8   0.4     0.0048   16.8   0.4    2.8  2  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0096   15.5   0.1      0.018   14.6   0.1    1.4  1  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.016   15.3   4.8      0.086   12.9   0.0    2.7  2  AAA_14           AAA domain
      0.024   13.9   2.3      0.031   13.6   0.0    2.2  2  6PF2K            6-phosphofructo-2-kinase
      0.031   14.2   0.7      0.031   14.2   0.7    3.3  3  AAA_31           AAA domain
      0.037   14.4   0.7      0.037   14.4   0.7    3.2  3  AAA              ATPase family associated with various cellul
      0.046   13.2   3.7       0.16   11.4   0.1    2.7  2  Arf              ADP-ribosylation factor family
      0.069   13.6   0.0          1    9.8   0.0    2.4  2  Metallophos      Calcineurin-like phosphoesterase
      0.086   12.4   1.6       0.12   11.9   0.1    2.1  2  Glyco_trans_4_5  Glycosyl-transferase family 4
      0.089   12.7   0.2       0.19   11.7   0.2    1.5  1  NACHT            NACHT domain
       0.12   11.2  10.3      0.053   12.3   0.6    2.9  4  Fe-ADH           Iron-containing alcohol dehydrogenase
       0.22   11.3  12.0       0.63    9.8   0.0    2.4  2  AAA_11           AAA domain
       0.35   11.9   7.8       0.52   11.3   2.8    3.3  2  LytR_C           LytR cell envelope-related transcriptional a
       0.37   10.4  10.5      0.014   15.0   2.6    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.62   10.2  14.8      0.037   14.1   1.4    3.2  2  MMR_HSR1         50S ribosome-binding GTPase
       0.66    8.4   3.9        0.8    8.1   3.9    1.1  1  Rrn6             RNA polymerase I-specific transcription-init
        1.6    9.0   5.5       0.29   11.5   1.3    2.0  1  AAA_19           AAA domain
        2.9    6.9   7.2        0.2   10.7   0.2    2.3  3  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
        3.2    7.7   5.7        1.5    8.8   0.1    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
        3.8    7.4   9.8       0.21   11.5   0.6    3.2  4  RsgA_GTPase      RsgA GTPase
        5.8    7.6   6.3        1.6    9.3   0.2    2.6  2  PIG-L            GlcNAc-PI de-N-acetylase
        5.9    6.3   8.1       0.16   11.4   0.5    2.2  3  ParA             NUBPL iron-transfer P-loop NTPase
          7    6.7   6.8        4.9    7.2   0.2    3.3  2  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.6       4.7     2e+03      85     107 ..      67      89 ..      27     124 .. 0.59
   2 !  261.6   2.7   8.9e-81   3.8e-78       1     195 [.     202     396 ..     202     397 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.7
                                   SEEEEEE--SSTTHHHHHHHHHH CS
                         SRP54  85 dvvlvDTaGrlqndkelmeelkk 107
                                   ++v    + + ++ ke ++e+k+
  gi|15668466|ref|NP_247264.1|  67 EIVKTEPSEKVEEAKEEIKEIKE 89 
                                   44444434333333333333333 PP

  == domain 2  score: 261.6 bits;  conditional E-value: 8.9e-81
                                   SEEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHH CS
                         SRP54   1 pnvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekake 81 
                                   p+vi++vG++G+GKTtt+aKLa +lk++g++v+l+a DtfRa+A+eQL+++a+++gv+vik+k +ad+aav+++a+++ak+
  gi|15668466|ref|NP_247264.1| 202 PTVIVFVGINGTGKTTTIAKLAYKLKQKGYSVVLAAGDTFRAGAIEQLEQHAKNVGVKVIKHKPGADSAAVIYDAIQHAKA 282
                                   689****************************************************************************** PP

                                   TTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHH CS
                         SRP54  82 ekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsi 162
                                   ++idvvl DTaGr++++ +lmee+kk+ +v+kpd v++v da+tg++av qa++F++av+i+g+iltk+D+dakgGaalsi
  gi|15668466|ref|NP_247264.1| 283 RGIDVVLADTAGRQATNVNLMEEIKKVVRVTKPDLVIFVGDALTGNDAVYQAEEFNRAVNIDGIILTKVDADAKGGAALSI 363
                                   ********************************************************************************* PP

                                   HHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                         SRP54 163 aaelklPikfigvGekiedleefdperlvsrll 195
                                    +++++Pi ++gvG++++dl efd++++v++l+
  gi|15668466|ref|NP_247264.1| 364 GYAIGKPILYLGVGQRYQDLIEFDADWMVRKLF 396
                                   *******************************98 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   8.2   2.4e-16     1e-13       5      70 ..     104     169 ..     103     173 .. 0.87
   2 ?   -0.2   0.1       2.8   1.2e+03       5      25 ..     174     191 ..     170     195 .. 0.69

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 2.4e-16
                                   HHHHHHHHCCSS.CGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS-HHHHHHHH CS
                       SRP54_N   5 lnsalkklsgks.kideedleealkeleeaLleaDVgvkvvkklienvkkkavgekklkpkqqvkki 70 
                                   l++a+kk+ +k+ +i eed+e++l+ele aLleaDV+++vv+klien+k++ vg +k++p + v++i
  gi|15668466|ref|NP_247264.1| 104 LTRAIKKVLKKEvVILEEDIEDVLEELEIALLEADVALEVVEKLIENIKNELVG-RKISPDDNVEEI 169
                                   455555555555389***************************************.99*****99987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.8
                                   HHHHHHHHCCSSCGHHHHHHH CS
                       SRP54_N   5 lnsalkklsgkskideedlee 25 
                                   +++a+k++ +++kid    ee
  gi|15668466|ref|NP_247264.1| 174 VKNAIKNILSQEKIDI---EE 191
                                   5788888888888873...33 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   2.0   1.4e-09     6e-07      18     125 ..     202     324 ..     193     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.4e-09
                        AAA_30  18 drvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.............grar 85 
                                     v v +G  GtGKtt++++l+  ++++g++v+++A     A +++ +l+ +a+++   + ++k             ++a+
  gi|15668466|ref|NP_247264.1| 202 PTVIVFVGINGTGKTTTIAKLAYKLKQKGYSVVLAAGDTFRAGAIE-QLEQHAKNVGVKVIKHKpgadsaaviydaiQHAK 281
                                   458999*******************************999999998.6777888888777777788889999998875455 PP

                        AAA_30  86 lepgtllivDEagmv..dtkqlaallkaaekag.akvilvGDe 125
                                    +  ++++ D ag    + + ++++ k ++ ++   vi+vGD 
  gi|15668466|ref|NP_247264.1| 282 ARGIDVVLADTAGRQatNVNLMEEIKKVVRVTKpDLVIFVGDA 324
                                   5555*********99334567999999999977699*****96 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.5      0.98   4.2e+02     156     191 ..      70     105 ..      54     112 .. 0.82
   2 !   28.6   0.5   1.8e-09   7.9e-07       8     119 ..     193     308 ..     187     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.98
                    Zeta_toxin 156 keehdeafeglresvealeeekqldrvkikdrdgkt 191
                                   k+e  e +e+++e++++++eek  ++++ +dr g t
  gi|15668466|ref|NP_247264.1|  70 KTEPSEKVEEAKEEIKEIKEEKEEKKITFFDRFGLT 105
                                   556678899999**********99999999987755 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.8e-09
                    Zeta_toxin   8 kk.ypsqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe.lhPeyeeilka.dpkkaseltqkdaselv 84 
                                   +k ++++ +P++i+ +G  G GK++++++l+ +l+ ++ +vv   +D++R+  + + e++ k+  +k       +d+  + 
  gi|15668466|ref|NP_247264.1| 193 IKkNKAEGKPTVIVFVGINGTGKTTTIAKLAYKLKqKGYSVVLAAGDTFRAgAIEQLEQHAKNvGVKVIKHKPGADSAAVI 273
                                   3446799***************************945555666678****8456677777776678888888899****** PP

                    Zeta_toxin  85 ekllqeaiengyniivegtlrspdvvkklaealkk 119
                                     ++q+a  +g+++++  t     +  +l+e++kk
  gi|15668466|ref|NP_247264.1| 274 YDAIQHAKARGIDVVLADTAGRQATNVNLMEEIKK 308
                                   *************9986665555555557777665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  10.2      0.18        76      24     135 ..      39     169 ..      15     170 .. 0.59
   2 !   25.8   0.3   2.6e-08   1.1e-05       1     108 [.     208     321 ..     208     325 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.18
                                   EEHHHHHHHHHHTTTS..HSSHHHHC.....TSHHHHHHHHHHHHHHHHHHHH.HSSEEEEEE-SEEEET....TEEEESS CS
                        AAA_17  24 lsaGdllreeakrggl..akardemr.....klpleekkelqkeaaekiaeea.kkkgvlvdghprikeq....agfldgl 92 
                                   +s+ +l+ +e k+++   +ka++e++     k + +ek e  ke +++i+ee+ +kk   +d +  +++     ++++  l
  gi|15668466|ref|NP_247264.1|  39 ISFTSLFKKEPKKEEVkkEKAEEEIKkseivKTEPSEKVEEAKEEIKEIKEEKeEKKITFFDRFGLTRAIkkvlKKEVVIL 119
                                   666666666666665433444555552222233333333334455567788773445578888865544411225555667 PP

                                   HHHHHHHH..SEEEEEE--HH.HHHHHHHHH.TT..ST-...TS-SHHHH CS
                        AAA_17  93 pkevleelkpdaiilleadpe.eilerrlkd.rt..rgr...dddneesi 135
                                   ++++++ l+   i llead   e++e++++  ++   gr   +ddn e+i
  gi|15668466|ref|NP_247264.1| 120 EEDIEDVLEELEIALLEADVAlEVVEKLIENiKNelVGRkisPDDNVEEI 169
                                   77777777777899999987768888888776433433322577777776 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 2.6e-08
                                   EE-TTSSHHHHHHHHHHHH...TEE.EEEHHHHHHHHHHTTTSHSSHHHHC.TS.HHHHHHHHHHHHHHHHHHHH..HSSE CS
                        AAA_17   1 lGgPGsGKgtqceklveky...gft.hlsaGdllreeakrgglakardemr.kl.pleekkelqkeaaekiaeea..kkkg 73 
                                   +G+ G GK+t ++kl+ k+   g++ +l aGd +r+ a ++ l+++ +++  k+ ++++  +  + + ++i++++  + + 
  gi|15668466|ref|NP_247264.1| 208 VGINGTGKTTTIAKLAYKLkqkGYSvVLAAGDTFRAGAIEQ-LEQHAKNVGvKViKHKPGADSAAVIYDAIQHAKarGIDV 287
                                   79*************988777766626799*****998654.556666665443366666777777777777766324466 PP

                                   EEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                        AAA_17  74 vlvdghprikeqagfldglpkevleelkpdaiill 108
                                   vl d+  r  ++  ++++++k v++  kpd++i++
  gi|15668466|ref|NP_247264.1| 288 VLADTAGRQATNVNLMEEIKK-VVRVTKPDLVIFV 321
                                   999***9*9999999999885.99********997 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   2.0   6.4e-08   2.7e-05      24     153 ..     197     316 ..     176     330 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.4e-08
                                   GG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTTEEEEEE-----HH CS
                          MeaB  24 akaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdegvfiRslpsrGalG 104
                                   +  G+ +v+ + G+ G+Gk t++ +l+ +l+++G+ v + a     +f  G+i     +le++a++ gv +     +    
  gi|15668466|ref|NP_247264.1| 197 KAEGKPTVIVFVGINGTGKTTTIAKLAYKLKQKGYSVVLAAG---DTFRAGAI----EQLEQHAKNVGVKVIKHKPGAD-- 268
                                   456999******************************977664...58999999....5799999888886544333222.. PP

                                   HHHHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESS CS
                          MeaB 105 GlaaktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpe 153
                                     aa   ++++   a G Dvvl +t G    +v+++e ++ +v ++ p+
  gi|15668466|ref|NP_247264.1| 269 -SAAVIYDAIQHAKARGIDVVLADTAGRQATNVNLMEEIKKVVRVTKPD 316
                                   .355678999*******************9****999999999998664 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1     7e-08     3e-05       1      91 [.     204     312 ..     204     322 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7e-08
                        AAA_33   1 lvllvGlpGsGKstlaerllkklg.....avllssdtlrr.rlfgtdqqskt......dytrvldr.....lyqilnelar 64 
                                   ++++vG +G+GK+t + +l+ kl+     +vl + dt+r  +++  +q+ k+      +      +       + + + ++
  gi|15668466|ref|NP_247264.1| 204 VIVFVGINGTGKTTTIAKLAYKLKqkgysVVLAAGDTFRAgAIEQLEQHAKNvgvkviK------HkpgadSAAVIYDAIQ 278
                                   89*****************8777777797777788999996677666666666555442......2233335567779999 PP

                        AAA_33  65 kalsagrnvil......datnlsr.rerarflkl 91 
                                    a ++g++v+l       atn++  +e ++++++
  gi|15668466|ref|NP_247264.1| 279 HAKARGIDVVLadtagrQATNVNLmEEIKKVVRV 312
                                   9*******99954444444455544555555555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.67   2.9e+02      40      83 ..      60     104 ..      42     108 .. 0.54
   2 !   21.5   0.1   5.3e-07   0.00023       2      50 ..     205     258 ..     204     298 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.67
                        AAA_28  40 akgedalpwv..edllafaervleeqleeeaaaaankvlfcDrgll 83 
                                   +++ ++++ v  e   +++e+  ee +e  ++ +++k++f+Dr  l
  gi|15668466|ref|NP_247264.1|  60 EEEIKKSEIVktEPSEKVEEA-KEEIKEIKEEKEEKKITFFDRFGL 104
                                   344444444431222233332.22222334455899******9666 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 5.3e-07
                        AAA_28   2 ivitGgestGKTtlleaLa....argypvvpEaareileeklakgedalpwv.e 50 
                                   iv++G  +tGKTt++++La    ++gy+vv  a+ ++     ++ e++++ v  
  gi|15668466|ref|NP_247264.1| 205 IVFVGINGTGKTTTIAKLAyklkQKGYSVVLAAGDTFRAGAIEQLEQHAKNVgV 258
                                   9******************777555*****999999999999999988886533 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.5e-07   6.5e-05       2      53 ..     202     253 ..     201     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-07
                                   -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSH CS
                    APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfse 53 
                                   ++v+ + G+ g+GK+t   +l+ kL++kg+sv+l  Gd+ R g  ++L +++
  gi|15668466|ref|NP_247264.1| 202 PTVIVFVGINGTGKTTTIAKLAYKLKQKGYSVVLAAGDTFRAGAIEQLEQHA 253
                                   789**************9*************************999998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       5.3   2.3e+03      55      71 ..      82     110 ..      43     180 .. 0.55
   2 !   21.8   0.0   4.2e-07   0.00018       4     117 ..     201     311 ..     198     324 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.3
                        AAA_22  55 dllrellralglelka............e 71 
                                   +  +e+ ++ ++++ +            +
  gi|15668466|ref|NP_247264.1|  82 EEIKEIKEEKEEKKITffdrfgltraikK 110
                                   44444444444433333322222222220 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 4.2e-07
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...sskdllrellralglelka..erlsseell 79 
                                   + +++v +G  GtGKTt++++l+++l+        ++++  v ++++t   +  + l++ ++++g++  +  ++++s +++
  gi|15668466|ref|NP_247264.1| 201 KPTVIVFVGINGTGKTTTIAKLAYKLK--------QKGYSVVLAAGDTfraGAIEQLEQHAKNVGVKVIKhkPGADSAAVI 273
                                   56799*********************4........4444444444444434444445555555555555598888999999 PP

                        AAA_22  80 ealeqalraravielliiDEaqhlr.seealeeLrslln 117
                                       q+++ar+   +++ D a +   + +++ee+++ + 
  gi|15668466|ref|NP_247264.1| 274 YDAIQHAKARGI-DVVLADTAGRQAtNVNLMEEIKKVVR 311
                                   888888888888.9****999885435888888877766 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   4.4         2   8.4e+02     133     180 ..      18      65 ..       9      71 .. 0.79
   2 ?   -0.4   2.0       1.9   7.9e+02     131     182 ..      80     127 ..      67     131 .. 0.58
   3 !   22.9   0.3   1.4e-07   5.8e-05       3     124 ..     209     321 ..     207     354 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2
                                   TSCCTTSS.TTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHH CS
               Thymidylate_kin 133 kRlakrde.ldeeeeeqldflrkvrerylelakederiliidasksiee 180
                                   +++  ++e ++ +ee+++++  +++  ++++ k +e+++  +a+++i++
  gi|15668466|ref|NP_247264.1|  18 EKIYSKGEaEEVKEEKEEKSKISFTSLFKKEPK-KEEVKKEKAEEEIKK 65 
                                   667777774567778888889999999999997.999999999999875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.9
                                   HHTSCCTTSS..TTTSHHHHHHHHHHHHHHHHHHHH.TTSTEEEEETTS-HHHHH CS
               Thymidylate_kin 131 alkRlakrde..ldeeeeeqldflrkvrerylelak.ederiliidasksieevh 182
                                   a + +    +  ++e+ee++++f+ ++     ++ k  +++++i+  ++ ie+v 
  gi|15668466|ref|NP_247264.1|  80 AKEEI----KeiKEEKEEKKITFFDRFGL-TRAIKKvLKKEVVIL--EEDIEDVL 127
                                   33333....23355888999999988854.333333357777777..66666665 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 1.4e-07
                                   ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT-EE CS
               Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkqgktv 83 
                                   G++G+GKtt +++l+ +lk++g++vvl    g+t  +  i +l ++++++  + +     ad +  +++ i+ a ++g  v
  gi|15668466|ref|NP_247264.1| 209 GINGTGKTTTIAKLAYKLKQKGYSVVLA--AGDTFRAGAIEQLEQHAKNVGVKVIKHKPGADSAAVIYDAIQHAKARGIDV 287
                                   9**********************98876..588899999999999999999999999999999999999999999999988 PP

                                   EEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTS.E-SEEEEE CS
               Thymidylate_kin  84 ivdRylfSslaYqgakegvdldlvlslnedvll.kPdltfll 124
                                   +++  +       +a++   ++l+ ++++ v   kPdl++++
  gi|15668466|ref|NP_247264.1| 288 VLADTAG-----RQATN---VNLMEEIKKVVRVtKPDLVIFV 321
                                   8764332.....33333...5666666666655688888876 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.4   2.4e-07    0.0001      12      82 ..     178     257 ..     141     320 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.4e-07
                                   HHHHT.....................TTS.EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGG CS
                        ResIII  12 ienlleklks...............krdk.rglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkk 76 
                                   i+n+l    s               +++   ++++   GtGKT ++akl+++l++kg+    ++l+ + +    ++e++++
  gi|15668466|ref|NP_247264.1| 178 IKNIL----SqekidieeiikknkaEGKPtVIVFVGINGTGKTTTIAKLAYKLKQKGY---SVVLAAGDTFRAGAIEQLEQ 251
                                   44444....1233344666654443444425559**********************99...58899998888888888888 PP

                                   GTGG.. CS
                        ResIII  77 flseay 82 
                                    +++  
  gi|15668466|ref|NP_247264.1| 252 HAKNVG 257
                                   777754 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.9       2.3   9.9e+02      95     118 ..     142     166 ..      42     184 .. 0.63
   2 !   20.1   3.8   1.2e-06   0.00051       9      88 ..     212     355 ..     204     374 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.3
                                   HHHHHHHHHCTS-EEE.EEE--CCH CS
                                   xxxxxxxxxxxxxxxx.xxxxxxxx RF
                          CbiA  95 ealeelkqrygvpvlg.viprdeav 118
                                   e +e+l++ ++++++g +i+ d++v
  gi|15668466|ref|NP_247264.1| 142 EVVEKLIENIKNELVGrKISPDDNV 166
                                   2233333333455555555555555 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.2e-06
                                   TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................... RF
                          CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep................................... 54 
                                   G+GKTt+ a+La  l+++g+ V+l   D+ +       g  +++e+                                   
  gi|15668466|ref|NP_247264.1| 212 GTGKTTTIAKLAYKLKQKGYSVVLAAGDTFR------AGAIEQLEQhaknvgvkvikhkpgadsaaviydaiqhakargid 286
                                   9***********************9999883......34444444455559999999999999999999999999999999 PP

                                   ....................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS.. CS
                                   ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ....................................dlkrllellealgkkkalllkiagvvlnrvdgen 88 
                                                                       d+  +   + +   +++ +++i g++l++vd ++
  gi|15668466|ref|NP_247264.1| 287 vvladtagrqatnvnlmeeikkvvrvtkpdlvifvgDALTGNDAVYQAE-EFNRAVNIDGIILTKVDADA 355
                                   9999999999998888888888888888877777775555555553333.22333888999999999874 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   1.4       3.1   1.3e+03      46      59 ..      58      72 ..      14     102 .. 0.54
   2 !   19.3   0.7   1.2e-06   0.00053       3     129 ..     204     321 ..     202     334 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.1
                       DUF2075 46 vlrealakke.ekkk 59
                                  + +e+++k+e  k++
  gi|15668466|ref|NP_247264.1| 58 KAEEEIKKSEiVKTE 72
                                  333333333333333 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.2e-06
                       DUF2075   3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeek 83 
                                   v++  G  GtGKt    +l+++l   +++ ++v+l     +++   e+l++++  k+ + ++ k +    ++   ++a+++
  gi|15668466|ref|NP_247264.1| 204 VIVFVGINGTGKTTTIAKLAYKL---KQKGYSVVLAAGDTFRAGAIEQLEQHA--KNVGVKVIKHKPGADSAAVIYDAIQH 279
                                   67777******************...88888999999999*********9999..5555555555555555554499**** PP

                       DUF2075  84 keepkedvvivDEAhrlltksdqaekqseenqlkelmkrak..vvval 129
                                   ++ + +dvv+ D A r  t      + +  +++k++++  k  +v+++
  gi|15668466|ref|NP_247264.1| 280 AKARGIDVVLADTAGRQAT------NVNLMEEIKKVVRVTKpdLVIFV 321
                                   ****************999......34446677777777444344444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       2.5   1.1e+03     137     144 ..     116     123 ..      13     190 .. 0.60
   2 !   18.3   0.1   5.4e-06    0.0023      19      88 ..     197     252 ..     183     324 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.5
                        AAA_16 137 lvlvlDdl 144
                                   +v++ +d+
  gi|15668466|ref|NP_247264.1| 116 VVILEEDI 123
                                   22222222 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 5.4e-06
                        AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                    ++g p +++++G  G+GK++ + +l+  l+++g  ++ +  d +              r + ++ql+++
  gi|15668466|ref|NP_247264.1| 197 KAEGKPTVIVFVGINGTGKTTTIAKLAYKLKQKGYSVVLAAGDTF--------------RAGAIEQLEQH 252
                                   567899***************************877777777777..............22333333333 PP

>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   1.3e-05    0.0054       6      63 ..     177     234 ..     172     280 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHHHHHHHHHHHHSGGGGG-EEEEEEEESTTS-HHHHHHHHHTTS-GGG-EEE CS
                          PPK2   6 eyeeelaklqielvklqekvkaegkklvvifegrDaAGKgGaikrvtealnprvarvv 63 
                                   + ++ l +++i++ ++++k kaegk  v++f g ++ GK  +i+++  +l+ +++ vv
  gi|15668466|ref|NP_247264.1| 177 AIKNILSQEKIDIEEIIKKNKAEGKPTVIVFVGINGTGKTTTIAKLAYKLKQKGYSVV 234
                                   55677889999******************************************99987 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.1      0.34   1.5e+02      40     100 ..      75     138 ..       9     149 .. 0.58
   2 !   15.4   0.0   4.6e-05     0.019      12      74 ..     203     271 ..     198     364 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.34
                                   EEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH................HHHTCHHHHHHHSTTGGTTCB CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  40 Geilldgkdlkeqeleslrkeigvlpqepqlfpeltvren................esdeeiekalsklglkelkdt 100
                                   ++++  ++++ke+++e+ +k+i ++              +                  +e+ie++l++l++  l+++
  gi|15668466|ref|NP_247264.1|  75 EKVEEAKEEIKEIKEEKEEKKITFFD-------------RfgltraikkvlkkevvILEEDIEDVLEELEIALLEAD 138
                                   22233334444444444444444444.............23333333333333566666667777777777666655 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.6e-05
                                   SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG...B-HHHCCHCEE..EE-SS--S-TTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx...xxxxxxxxxxx..xxxxxxxxxxxx RF
                      ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke...qeleslrkeig..vlpqepqlfpel 74 
                                   +++++vG nG+GK+t ++ la +lk++  ++ l  g+ ++    ++le+  k++g  v++++p  ++  
  gi|15668466|ref|NP_247264.1| 203 TVIVFVGINGTGKTTTIAKLAYKLKQKGYSVVLAaGDTFRAgaiEQLEQHAKNVGvkVIKHKPGADSAA 271
                                   57899**********999999999877777766645555556665556655555411444445555544 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.5   0.00011     0.047      21     110 ..     183     278 ..     166     286 .. 0.77
   2 !    8.3   0.0    0.0047         2      12      61 ..     302     348 ..     287     363 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                        YjeF_N  21 g.............nspaekkvlvlvGsgnnGgdglaa..ArhLaqegakVtvllleeeekldedaeralellkkaggkvv 86 
                                                 ++  +++v+v+vG + +G    +a  A  L q+g++V +   + +  + + +e+  +++k++g+kv+
  gi|15668466|ref|NP_247264.1| 183 SqekidieeiikknKAEGKPTVIVFVGINGTGKTTTIAklAYKLKQKGYSVVL--AAGDTFRAGAIEQLEQHAKNVGVKVI 261
                                   44455566666666678899************9987644499********998..44555677888888899********* PP

                        YjeF_N  87 eekpeedleeklsapvdlviDAll 110
                                   ++kp +d        + ++ DA++
  gi|15668466|ref|NP_247264.1| 262 KHKPGADS-------AAVIYDAIQ 278
                                   ****9986.......778888876 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0047
                        YjeF_N  12 vaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvlll 61 
                                   ++e +++ +  ++ +++ +++vG+  +G d+++ A +  ++ ++++ ++l
  gi|15668466|ref|NP_247264.1| 302 LMEEIKKVV--RVTKPDLVIFVGDALTGNDAVYQAEEF-NRAVNIDGIIL 348
                                   344455555..89**********************998.77777776444 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.2e-05    0.0095      11      95 ..     211     296 ..     203     329 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                         VirC1  11 GGaGkttalmglcsalasdgkrvalfeadenrP..ltkwkenalrkgawddacevfvadelplleaayeeaegeGfdyala 89 
                                    G+Gktt++  l   l ++g  v l  +d  r   +++  ++a++ g  +       ad  +++ +a ++a+++G d++la
  gi|15668466|ref|NP_247264.1| 211 NGTGKTTTIAKLAYKLKQKGYSVVLAAGDTFRAgaIEQLEQHAKNVG-VKVIKHKPGADSAAVIYDAIQHAKARGIDVVLA 290
                                   389**************************999622444444444443.344445567999********************* PP

                         VirC1  90 dtrgGs 95 
                                   dt g +
  gi|15668466|ref|NP_247264.1| 291 DTAGRQ 296
                                   **9865 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   1.1e-05    0.0048       1      31 [.     204     234 ..     204     241 .. 0.94
   2 ?    2.2   0.4      0.35   1.5e+02      25      94 ..     253     318 ..     237     322 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                          MobB   1 vlgivgksgsGKTtLleklipelkarglrvg 31 
                                   v+ +vg +g+GKTt + kl  +lk++g++v 
  gi|15668466|ref|NP_247264.1| 204 VIVFVGINGTGKTTTIAKLAYKLKQKGYSVV 234
                                   689*************************985 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.35
                          MobB  25 arglrvgtiKhahhgfdvdkpgkDsyrhrkA.GAkevlvaskerlalikeleeaelsleellarlsevDlv 94 
                                   a+++ v +iKh+  g d      D+ +h+kA G + vl  +  r a   +l e   +++++++ + + Dlv
  gi|15668466|ref|NP_247264.1| 253 AKNVGVKVIKHKP-GADSAAVIYDAIQHAKArGIDVVLADTAGRQATNVNLME---EIKKVVRVT-KPDLV 318
                                   4556677899976.567777889999999994555555555556555555433...344444444.45665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   4.2e-05     0.018      22      65 ..     189     234 ..     162     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.2e-05
                         AAA_7  22 ysyllelllknkkp..vllvGptGtGKtviikdllkkldkekylsl 65 
                                   ++ ++++  +++kp  +++vG  GtGKt++i +l  kl+++ y+++
  gi|15668466|ref|NP_247264.1| 189 IEEIIKKNKAEGKPtvIVFVGINGTGKTTTIAKLAYKLKQKGYSVV 234
                                   55566666666666225799*******************9998765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   2.4      0.56   2.4e+02      45      85 ..      76     114 ..      36     122 .. 0.63
   2 ?   12.9   0.0    0.0002     0.086       3      76 ..     203     280 ..     201     324 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.56
                        AAA_14  45 kladpekllelilek.lkeekktylflDEiqevpewekalks 85 
                                   k    e+  e+i+e   ++e+k++ f+D     + ++k+lk+
  gi|15668466|ref|NP_247264.1|  76 KV---EEAKEEIKEIkEEKEEKKITFFDRFGLTRAIKKVLKK 114
                                   11...1233444444222369999****99999888888886 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.0002
                        AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe....kll.elileklke...ekktylflDEiqe 75 
                                    ++v +G+  +GKTt + +l+++l  k  s++  + d+ r  ++++ e    ++  ++i+    +    +   ++ D iq+
  gi|15668466|ref|NP_247264.1| 203 TVIVFVGINGTGKTTTIAKLAYKLKQKGYSVVLAAGDTFRAGAIEQLEqhakNVGvKVIK----HkpgADSAAVIYDAIQH 279
                                   58999****************999966777777777777775555444222122212222....12345677788888887 PP

                        AAA_14  76 v 76 
                                   +
  gi|15668466|ref|NP_247264.1| 280 A 280
                                   7 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.6       1.6   6.7e+02      79     119 ..      78     116 ..      28     183 .. 0.65
   2 ?   13.6   0.0   7.4e-05     0.031       7      43 ..     196     232 ..     190     282 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHHHHTS--SEEEEES---SHHHHHHHHHHH CS
                         6PF2K  79 klalaalkdllaylneeegqvaifDAtNttrerRklilefv 119
                                   + a++ +k+++++  +ee ++  fD    tr  +k+++++v
  gi|15668466|ref|NP_247264.1|  78 EEAKEEIKEIKEE--KEEKKITFFDRFGLTRAIKKVLKKEV 116
                                   3355556666654..56777888888888877777777665 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.4e-05
                                   HHT..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT-- CS
                         6PF2K   7 tnlknsklvivlvGLpargKtyiskkltrylkwlgvr 43 
                                   ++ + +++viv+vG+  +gKt++  kl   lk  g++
  gi|15668466|ref|NP_247264.1| 196 NKAEGKPTVIVFVGINGTGKTTTIAKLAYKLKQKGYS 232
                                   5667899********************9999976654 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   2.2       2.6   1.1e+03      65     116 ..     100     153 ..      29     156 .. 0.68
   2 ?    0.8   0.6      0.93     4e+02      50      84 ..     169     205 ..     159     208 .. 0.76
   3 ?   14.2   0.7   7.3e-05     0.031      12      86 ..     212     290 ..     201     314 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.6
                        AAA_31  65 eeknikeaiiktkvenldlipssid..Laeaeielvelekkeeilkellekvkd 116
                                   ++  +  ai+k   +++ ++  +i+  L e+ei l+e++   e++++l+e++k+
  gi|15668466|ref|NP_247264.1| 100 DRFGLTRAIKKVLKKEVVILEEDIEdvLEELEIALLEADVALEVVEKLIENIKN 153
                                   455555555544455556666666656777777777777777777777777776 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.93
                        AAA_31  50 iekneiektlyevli.eeknikeaiiktkvenl.dli 84 
                                   i+ n +++ + ++l  e+++i+e+i+k+k e   ++i
  gi|15668466|ref|NP_247264.1| 169 ITINAVKNAIKNILSqEKIDIEEIIKKNKAEGKpTVI 205
                                   4456788899999976999*******99966543555 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 7.3e-05
                        AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt.glgiekneiektlyevl..i.eeknikeaiiktkvenldlips 86 
                                   G GKTTt  +la+ l ++g+ v l   D+  + ++ +l+ + +++  ++++    + + + i +ai+++k + +d++ +
  gi|15668466|ref|NP_247264.1| 212 GTGKTTTIAKLAYKLKQKGYSVVLAAGDTFRAGAIeQLEQHAKNVGVKVIKHKpgAdSAAVIYDAIQHAKARGIDVVLA 290
                                   89**********************9999876655513333444454555544344335556666666666666666655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   2.5         5   2.1e+03      28      65 ..      62     100 ..      50     154 .. 0.72
   2 ?    1.1   0.1       1.2     5e+02      25      63 ..     167     207 ..     123     208 .. 0.73
   3 ?   14.4   0.7   8.8e-05     0.037       2      47 ..     206     254 ..     205     326 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 5
                                   EEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEE CS
                           AAA  28 eisgsellskyvgesekkirelfkeakeka.kpsilfiD 65 
                                   ei+ se+++   +e+ ++ +e +ke+ke++ +++i f+D
  gi|15668466|ref|NP_247264.1|  62 EIKKSEIVKTEPSEKVEEAKEEIKEIKEEKeEKKITFFD 100
                                   566666665544444444444455555444445788888 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.2
                                   EEEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTSTS.EEEE CS
                           AAA  25 efleisgsell.skyvgesekkirelfkeakekakp.silf 63 
                                   e ++i++ +   ++++++ + +i+e++k+ k++ kp +i+f
  gi|15668466|ref|NP_247264.1| 167 EEITINAVKNAiKNILSQEKIDIEEIIKKNKAEGKPtVIVF 207
                                   44555555555466888889999999999877778844544 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 8.8e-05
                                   EEESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCSSSSTTHHHHHHH CS
                           AAA   2 llyGppGtGKTllakavakelg...vefleisgsellskyvgesekkir 47 
                                   +++G  GtGKT+++  +a +l+    +++   g +++   +++ e++ +
  gi|15668466|ref|NP_247264.1| 206 VFVGINGTGKTTTIAKLAYKLKqkgYSVVLAAGDTFRAGAIEQLEQHAK 254
                                   799*****************97332445555555555443333333333 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.7      0.32   1.3e+02      91     118 ..      71      98 ..      46     154 .. 0.84
   2 ?   11.4   0.1   0.00038      0.16       3      37 ..     191     225 ..     189     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.32
                                   TT-CTTHHHHHHHHHHHCTSGCCTTSEE CS
                           Arf  91 sadreRleeakeeLkalleeeelkeval 118
                                   +  +e++eeakee+k++ ee+e k++++
  gi|15668466|ref|NP_247264.1|  71 TEPSEKVEEAKEEIKEIKEEKEEKKITF 98 
                                   5567899999999999999999988765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00038
                                   HHHHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHS CS
                           Arf   3 silaklklkkkelrilllGLDnaGKtTilkklkle 37 
                                   +i++k k + k + i+++G+ ++GKtT + kl  +
  gi|15668466|ref|NP_247264.1| 191 EIIKKNKAEGKPTVIVFVGINGTGKTTTIAKLAYK 225
                                   6889999999999***************9999765 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.4     6e+02      23      54 ..     221     250 ..     187     265 .. 0.72
   2 ?    9.8   0.0    0.0024         1       4      51 ..     287     332 ..     287     352 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.4
                                   HHHHHHHHHTTESEEEEESTSSSSSHHHHHHH CS
                   Metallophos  23 kllddllreekpdlvllaGDlvdrgdlekell 54 
                                   kl  +l+++ +  +vl aGD +  g +e+ l+
  gi|15668466|ref|NP_247264.1| 221 KLAYKLKQK-GYSVVLAAGDTFRAGAIEQ-LE 250
                                   444344444.7888888899999996666.44 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0024
                                   EEEESBTBTTCCTHHHHHHHHHHHH...HHHTTESEEEEESTSSSSSHHHH CS
                   Metallophos   4 lvigDlHlalgggqlddllkllddl...lreekpdlvllaGDlvdrgdlek 51 
                                   +v++D+      g+ ++ ++l++++    r  kpdlv+++GD   ++d  +
  gi|15668466|ref|NP_247264.1| 287 VVLADTA-----GRQATNVNLMEEIkkvVRVTKPDLVIFVGDALTGNDAVY 332
                                   5889999.....99999999998884445558**********888884444 PP

>> Glyco_trans_4_5  Glycosyl-transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       5.9   2.5e+03      48      95 ..     109     153 ..      87     160 .. 0.62
   2 ?   11.9   0.1   0.00029      0.12       2      83 ..     200     296 ..     199     318 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.9
               Glyco_trans_4_5  48 keladrgikvleakaeelfklalkaDlvvlntvvaakwidqlleenka 95 
                                   k++ ++++ +le+ +e       ++++ +l + va +++++l+e+ k+
  gi|15668466|ref|NP_247264.1| 109 KKVLKKEVVILEEDIEDV---LEELEIALLEADVALEVVEKLIENIKN 153
                                   455555555555555444...445555566666666666666666555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00029
               Glyco_trans_4_5   2 gkrvllishelsltGaPlvlmelatlLrsvgaevvvltlskkgg.....llkeladrgikvlea............kaeel 65 
                                   gk  ++++   + tG    +  la  L++ g++vv+ + +         l++++++ g+kv+++             ++  
  gi|15668466|ref|NP_247264.1| 200 GKPTVIVFVGINGTGKTTTIAKLAYKLKQKGYSVVLAAGDTFRAgaieqLEQHAKNVGVKVIKHkpgadsaaviydAIQ-- 278
                                   8889999999999*********************999887754448888***************888777775533222.. PP

               Glyco_trans_4_5  66 fklalkaDlvvlntvvaa 83 
                                      a  +D+v++ t+   
  gi|15668466|ref|NP_247264.1| 279 HAKARGIDVVLADTAGRQ 296
                                   235566788888887554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00044      0.19       2      28 ..     204     230 ..     203     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00044
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                         NACHT   2 lvilqGeaGsGKTtLlqklalawaegk 28 
                                   +++  G +G GKTt ++kla +++++ 
  gi|15668466|ref|NP_247264.1| 204 VIVFVGINGTGKTTTIAKLAYKLKQKG 230
                                   68999*******************986 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       7.8   3.3e+03      38      72 ..      23      56 ..      16      69 .. 0.69
   2 ?   -2.6   0.0       4.2   1.8e+03      24      68 ..     113     154 ..      94     160 .. 0.66
   3 ?    5.0   0.1     0.021       8.8      42      89 ..     190     238 ..     177     239 .. 0.85
   4 ?   12.3   0.6   0.00013     0.053       6      89 ..     241     322 ..     240     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.8
                                  H.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHH CS
                        Fe-ADH 38 sglldkvlesleeagievtvfdgvepnptleevee 72
                                   g +++v+e+  e++ ++   + ++++p+ eev++
  gi|15668466|ref|NP_247264.1| 23 KGEAEEVKEEK-EEKSKISFTSLFKKEPKKEEVKK 56
                                  55667777775.55666666677888898888876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.2
                                   .EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HH CS
                        Fe-ADH  24 kralivtdkgslkksglldkvlesleeagievtvfdgvepnptle 68 
                                   k+ +++  + +    ++l++++ +l ea+++++v+++  +n + e
  gi|15668466|ref|NP_247264.1| 113 KKEVVILEEDIE---DVLEELEIALLEADVALEVVEKLIENIKNE 154
                                   455555566644...677777777777777777777766666555 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.021
                                   HHHHHHHHCTT-EEE.E.EEE-S---HHHHHHHHTTS-TT.--EEEEEE CS
                        Fe-ADH  42 dkvlesleeagievt.vfdgvepnptleeveeaaalareegadvviavG 89 
                                   ++++++ +++g   + vf g+++  ++++++++a  ++++g+ vv+a G
  gi|15668466|ref|NP_247264.1| 190 EEIIKKNKAEGKPTViVFVGINGTGKTTTIAKLAYKLKQKGYSVVLAAG 238
                                   5666666666666666*******************************98 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00013
                                   EETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE.-S---HHHHHHHHTTS-TT.--EE CS
                        Fe-ADH   6 fgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgv.epnptleeveeaaalareegadvv 85 
                                   f +ga+e+l++++k+ g+   +i + +g + ++ ++ +++++ ++ gi+v++ d+  ++   +  +ee+ +++r +++d+v
  gi|15668466|ref|NP_247264.1| 241 FRAGAIEQLEQHAKNVGV--KVIKHKPG-ADSAAVIYDAIQHAKARGIDVVLADTAgRQATNVNLMEEIKKVVRVTKPDLV 318
                                   889**************5..56677777.45788999999999***********9966777777888888999******** PP

                                   EEEE CS
                        Fe-ADH  86 iavG 89 
                                   i vG
  gi|15668466|ref|NP_247264.1| 319 IFVG 322
                                   *888 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6  10.6      0.93   3.9e+02     103     176 ..      19      93 ..       5     132 .. 0.49
   2 ?    9.8   0.0    0.0015      0.63       8      44 ..     176     229 ..     170     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.93
                        AAA_11 103 avksvsleekvekrlekeekaqlakeiskeleklakelrafeeeeek.eklkkskekskskleqerrklkkerke 176
                                   ++ s    e+v++++e+++k++ ++  +ke +k++ + ++ eee++k e++k++ +++ +++++e +++k+e++e
  gi|15668466|ref|NP_247264.1|  19 KIYSKGEAEEVKEEKEEKSKISFTSLFKKEPKKEEVKKEKAEEEIKKsEIVKTEPSEKVEEAKEEIKEIKEEKEE 93 
                                   333333334444444444444444444444444444444444443333333333333333333333333333322 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                        AAA_11   8 eaiksalsese........itliqGPP.........GtgKTktivellsqllsr 44 
                                   +aik++ls+++            +G+P         GtgKT+ti++l  +l ++
  gi|15668466|ref|NP_247264.1| 176 NAIKNILSQEKidieeiikKNKAEGKPtvivfvginGTGKTTTIAKLAYKLKQK 229
                                   566666666666655555533334455555555555*************99533 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2       2.2   9.5e+02      19      63 ..      12      64 ..      10      96 .. 0.62
   2 ?   11.3   2.8    0.0012      0.52       7      81 ..     210     289 ..     203     324 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 2.2
                        LytR_C 19 vadaLeerGftvgevgnagnadee.ttivy......reaaa..a.aakalaaalg 63
                                  +a++ +e+ + +ge++++ + +ee ++i +      +  ++  + + ++ +++++
  gi|15668466|ref|NP_247264.1| 12 TASKITEKIYSKGEAEEVKEEKEEkSKISFtslfkkE--PKkeEvKKEKAEEEIK 64
                                  6777788888888877666555556777776665432..2222123334444444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0012
                        LytR_C   7 lNgtgvsGlAarvadaLeerGftvgevgnagnadeettivyreaaaaaakalaaalglgelqedsvkdas........... 76 
                                    Ngtg++   a++a +L+++G+ v+   +ag++      +  ++a ++ ++ a+ +g++ +++++ +d++           
  gi|15668466|ref|NP_247264.1| 210 INGTGKTTTIAKLAYKLKQKGYSVVL--AAGDT-----FR--AGAIEQLEQHAKNVGVKVIKHKPGADSAaviydaiqhak 281
                                   5*********************7776..34444.....22..223345556666666666666666665555555555555 PP

                        LytR_C  77 ...vtvvl 81 
                                      ++vvl
  gi|15668466|ref|NP_247264.1| 282 argIDVVL 289
                                   55555555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   1.1       3.2   1.4e+03     126     168 ..      50      89 ..      18      99 .. 0.61
   2 ?   15.0   2.6   3.2e-05     0.014       2     152 ..     204     353 ..     203     362 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.2
                                   CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHH CS
                          cobW 126 aeeekieekaedqlaaadllvlnKtDlldeeallekleerlrq 168
                                   ++ee ++ekae+++++++++   Kt+  ++++++++  +++++
  gi|15668466|ref|NP_247264.1|  50 KKEEVKKEKAEEEIKKSEIV---KTEPSEKVEEAKEEIKEIKE 89 
                                   56677788888888888877...44444444222333333333 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.2e-05
                                   EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCC...CT.EEEETTTTECCHCTT-HHHHHHHHH CS
                          cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellret...gveivelenGciCctlredllkeleale 77 
                                   v+v++G  G+GKTt + +l    +++g+++ +  ++    +  ++l +++   gv++++ + G    ++  d   ++++ +
  gi|15668466|ref|NP_247264.1| 204 VIVFVGINGTGKTTTIAKLAykLKQKGYSVVLAAGDTFRAGAIEQLEQHAknvGVKVIKHKPGADSAAVIYD---AIQHAK 281
                                   7999****************7767777777777888775443333322221125556666666555553333...333333 PP

                                   HHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHH CS
                          cobW  78 ereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDl 152
                                   +r   +dv+l  t G  a+   ++ + +++ + ++ d v++v Da    ++   ++e++++ ++  d ++l+K+D 
  gi|15668466|ref|NP_247264.1| 282 AR--GIDVVLADTAGrQATNVNLMEEIKKVVRVTKPDLVIFVGDALTG-NDAVYQAEEFNRAVNI-DGIILTKVDA 353
                                   34..5**********777777777778999999999*********554.5666677777777665.999****996 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   5.9       1.6     7e+02      42      87 ..      90     164 ..      32     207 .. 0.60
   2 ?   14.1   1.4   8.6e-05     0.037       2      87 ..     205     328 ..     204     350 .. 0.53

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.6
                                   EETTEEEEEEECGGC..............SSHHHHHHHHHHHHHHHHCTSEEEEEEETT.................T CS
                      MMR_HSR1  42 klkgkeielvDtpGl..............iegaseekglgkaflaleeadlillvvdas.................e 87 
                                   ++++k+i++ D  Gl              + +++ e  l++   al ead++l vv+ +                 +
  gi|15668466|ref|NP_247264.1|  90 EKEEKKITFFDRFGLtraikkvlkkevviL-EEDIEDVLEELEIALLEADVALEVVE-KlieniknelvgrkispdD 164
                                   233478999999997555555444433321.23333344555555667888888887.4355554444444444330 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8.6e-05
                                   EEEEESTTSSHHHHHHHHH..............TSTEEESSSTTSSSSE.EEEEEEETTEE.................... CS
                      MMR_HSR1   2 vaivGrpNvGKStLinalt..............gekaivsdkpgtTrdi.negrvklkgke.................... 47 
                                   +++vG   +GK+t i +l               g           T      ++++    +                    
  gi|15668466|ref|NP_247264.1| 205 IVFVGINGTGKTTTIAKLAyklkqkgysvvlaaG----------DTFRAgAIEQLEQ---Haknvgvkvikhkpgadsaav 272
                                   799***************9444443333333331..........3322212222221...011233333333344445555 PP

                                   ..............EEEEECGGCSSHHHHHH...HHHHHHHHHHCTSEEEEEEETT..T CS
                      MMR_HSR1  48 ..............ielvDtpGliegaseek...glgkaflaleeadlillvvdas..e 87 
                                                 ++l+Dt+G  +   ++    ++ k++ ++ + dl+++v da   +
  gi|15668466|ref|NP_247264.1| 273 iydaiqhakargidVVLADTAG-RQ--ATNVnlmEEIKKVVRVTKPDLVIFVGDALtgN 328
                                   55555555555555********.43..3333123444444445557*******966331 PP

>> Rrn6  RNA polymerase I-specific transcription-initiation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.9    0.0019       0.8     425     555 ..      11     141 ..       9     236 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0019
                          Rrn6 425 dsdlslheslyssstepsrelrspakelrlkdlskssikrkkkekrkktasrkeddfvvpdgle..lkvrkeksaklkrss 503
                                    + ++++e +ys  +   +e++++++e+ ++++   ++  kk++k+++ ++ k+++ ++  ++   +++ k ++ak+++++
  gi|15668466|ref|NP_247264.1|  11 ETASKITEKIYS--KGEAEEVKEEKEEKSKISF---TSLFKKEPKKEEVKKEKAEEEIKKSEIVktEPSEKVEEAKEEIKE 86 
                                   5678999*****..4444444444444444333...233444444444555555555555555544334455555555555 PP

                          Rrn6 504 saslapeqrtldfervy...sassteeaeeqsfqdllyrlseaiqqlllegsese 555
                                   +++++ e++   f r       +++ ++e   +++ ++ ++e+++  lle +   
  gi|15668466|ref|NP_247264.1|  87 IKEEKEEKKITFFDRFGltrAIKKVLKKEVVILEEDIEDVLEELEIALLEADVAL 141
                                   5555555554445555577755555666666666666666666654444444333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.3   0.00068      0.29       9      69 ..     201     271 ..     190     344 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00068
                        AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillv..aftgrAakelrerlaalgae...........a 69 
                                   k +v++ ++  GtGKT+++ +    l++ g      +l++  +f   A ++l++  +++g++           a
  gi|15668466|ref|NP_247264.1| 201 KPTVIVFVGINGTGKTTTIAKLAYKLKQKG-Y--SVVLAAgdTFRAGAIEQLEQHAKNVGVKvikhkpgadsaA 271
                                   44566778889********99999998888.3..3444442245555677888877777766555555555540 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.5       7.2   3.1e+03     208     214 ..      46      52 ..       3      94 .. 0.46
   2 ?   10.7   0.2   0.00048       0.2      37      69 ..     205     234 ..     182     238 .. 0.79
   3 ?   -0.1   0.0      0.92   3.9e+02     132     155 ..     271     293 ..     241     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.2
                                   EEEE.EE CS
                          LpxK 208 rlepkkl 214
                                   + epkk+
  gi|15668466|ref|NP_247264.1|  46 KKEPKKE 52 
                                   2222222 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00048
                                   EEEEEESBSS-HSHHHHHHHHHHHTTTS..-EE CS
                          LpxK  37 VivVGNitvGGtGKTPlvialvkllqarglkvg 69 
                                   ++ VG   + GtGKT +++ l+ +l+++g+ v+
  gi|15668466|ref|NP_247264.1| 205 IVFVG---INGTGKTTTIAKLAYKLKQKGYSVV 234
                                   44444...78********************986 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.92
                                   EEEET-SS-TTB--SEEEEEE..E CS
                          LpxK 132 iilDDGlQhyaLardleivvvdae 155
                                    ++ D++Qh + ar +++v+ d++
  gi|15668466|ref|NP_247264.1| 271 AVIYDAIQHAK-ARGIDVVLADTA 293
                                   45558999998.899999999974 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   2.6         4   1.7e+03      65      97 ..      93     127 ..      52     200 .. 0.66
   2 ?    8.8   0.1    0.0036       1.5       3      32 ..     206     236 ..     204     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4
                                   G-SEEEEE..SGGG--HHHHHHHHHHHHSSEEE.. CS
                         AAA_5  65 egeilvlD..EveraesevlnsLlslleerrllle 97 
                                   e++i+++D  +++ra ++vl++   +lee+  ++ 
  gi|15668466|ref|NP_247264.1|  93 EKKITFFDrfGLTRAIKKVLKKEVVILEEDIEDVL 127
                                   55555555444455555555555555554444433 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0036
                                   EEE--SSSSHHHHHHHGGGGB.S--EEEEE- CS
                         AAA_5   3 lLvGppGtgKselaerlaaal.nreveyvql 32 
                                   + vG  GtgK++ + +la  l ++ + +v+ 
  gi|15668466|ref|NP_247264.1| 206 VFVGINGTGKTTTIAKLAYKLkQKGYSVVLA 236
                                   689******************5555555544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.3       3.2   1.3e+03      58     101 ..      50      95 ..      32     105 .. 0.57
   2 ?   11.5   0.6   0.00049      0.21      68     126 ..     174     229 ..     129     239 .. 0.68
   3 ?   -1.1   0.0       3.7   1.6e+03      51      85 ..     233     266 ..     227     294 .. 0.76
   4 ?   -1.8   0.0       5.8   2.5e+03      83     107 ..     299     323 ..     268     328 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.2
                                   G--HHH..HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSE CS
                   RsgA_GTPase  58 lleeee..eleelkeelealgyevllvsaktkegleelkellkdkt 101
                                     ee +  ++ee  ++ e + +e+    ++ ke+++e+ke+ ++k 
  gi|15668466|ref|NP_247264.1|  50 KKEEVKkeKAEEEIKKSEIVKTEPSEKVEEAKEEIKEIKEEKEEKK 95 
                                   3333332224555555555556666655666777777777777644 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00049
                                   HHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT---- CS
                   RsgA_GTPase  68 lkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpelelk 126
                                   +k++++++ ++  +++   +e +++ k++ k  ++v+vG  G GK+t i +l+ +l++k
  gi|15668466|ref|NP_247264.1| 174 VKNAIKNI-LSQEKID--IEEIIKKNKAEGKPTVIVFVGINGTGKTTTIAKLAYKLKQK 229
                                   33333333.2222222..2245555566667799******************9998876 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.7
                                   EEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TT CS
                   RsgA_GTPase  51 ivlnKiDlleeeeeleelkeelealgyevllvsak 85 
                                   +vl   D       +e+l+++ +++g++v++ +  
  gi|15668466|ref|NP_247264.1| 233 VVLAAGDTFRAGA-IEQLEQHAKNVGVKVIKHKPG 266
                                   5666667777777.999999999999999987554 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 5.8
                                   -TTTHTTHHHHHHHCTTSEEEEECS CS
                   RsgA_GTPase  83 saktkegleelkellkdktsvlvGq 107
                                   +++  e+++++ ++ k +++++vG 
  gi|15668466|ref|NP_247264.1| 299 NVNLMEEIKKVVRVTKPDLVIFVGD 323
                                   3344466666666777777777775 PP

>> PIG-L  GlcNAc-PI de-N-acetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   1.6       2.9   1.2e+03      49     107 ..      82     156 ..      20     189 .. 0.66
   2 ?    9.3   0.2    0.0039       1.6      48     110 ..     224     321 ..     185     329 .. 0.54

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 2.9
                                   -HHHHH.HHHHHHHH..HHHCTE.........EEEEECC..CBTT-STT....S-CHHHHHHHHHHHHHH--SEE CS
                         PIG-L  49 eelaei.RekEaraa..akhlgva.......dedvffld..fpDgsles....ydedellddlaklieryrPdvv 107
                                   ee++ei  ekE+++       g++       +++v++l+  ++D   e      + d +l++++klie+++ ++v
  gi|15668466|ref|NP_247264.1|  82 EEIKEIkEEKEEKKItfFDRFGLTraikkvlKKEVVILEedIEDVLEELeialLEADVALEVVEKLIENIKNELV 156
                                   455555433444433223444554555555555666665553333222244446667777777777777766655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0039
                                   H..................-HHHHHHHHHHHHHHHHCTE..........EEEEECC.............CBTT-STTS-CH CS
                         PIG-L  48 k..................eelaeiRekEaraaakhlgva........dedvffld.............fpDgslesyded 89 
                                                      +       + +++ ak +gv+        d+ +++ d             ++D+  ++ ++ 
  gi|15668466|ref|NP_247264.1| 224 YklkqkgysvvlaagdtfrA----GAIEQLEQHAKNVGVKvikhkpgaDSAAVIYDaiqhakargidvvLADTAGRQATNV 300
                                   12333344444444322221....122222222233333222222443444444444444445555588888888889*** PP

                                   HHHHHHHHHHHHH--SEEEEE CS
                         PIG-L  90 ellddlaklieryrPdvvltl 110
                                   +l ++++k+++ ++Pd+v+ +
  gi|15668466|ref|NP_247264.1| 301 NLMEEIKKVVRVTKPDLVIFV 321
                                   ******************986 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.7         7     3e+03     187     210 ..      19      40 ..      11     102 .. 0.49
   2 ?   -2.5   0.0       6.4   2.7e+03      32      56 ..     129     153 ..     105     180 .. 0.65
   3 ?   11.4   0.5   0.00038      0.16       5      40 ..     203     238 ..     200     262 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7
                          ParA 187 eifgkgggeklaeelgvpllgeip 210
                                   +i++kg++e++ ee + +   +i 
  gi|15668466|ref|NP_247264.1|  19 KIYSKGEAEEVKEEKEEKS--KIS 40 
                                   5666666666655544321..111 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.4
                          ParA  32 glkvgllDaDiyGpsiprllgveee 56 
                                   +l+++ll aD+    + +l++  ++
  gi|15668466|ref|NP_247264.1| 129 ELEIALLEADVALEVVEKLIENIKN 153
                                   4566666666666666666554443 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00038
                          ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDa 40 
                                   +++v  g  G GK+t+ ++lA++L++kg++v l   
  gi|15668466|ref|NP_247264.1| 203 TVIVFVGINGTGKTTTIAKLAYKLKQKGYSVVLAAG 238
                                   678899999**********************88655 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       1.9   8.2e+02      41      90 ..     165     217 ..     148     228 .. 0.57
   2 ?    7.2   0.2     0.012       4.9      39      79 ..     279     319 ..     204     325 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.9
               Glyco_trans_4_2  41 eaegihvhrlkvdrkg..pleylkafkl.kklikkikPDvvhahyakpygllg 90 
                                   + e i++  +k+ +k   + e + + ++ kk  ++ kP v+  + +++ g   
  gi|15668466|ref|NP_247264.1| 165 NVEEITINAVKNAIKNilSQEKIDIEEIiKKNKAEGKPTVIVFVGINGTGKTT 217
                                   44555555555555544444444455433555555567777666666665544 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
               Glyco_trans_4_2  39 eleaegihvhrlkvdrkg.pleylk.afklkklikkikPDvvh 79 
                                   + +a gi v   +  ++g ++++++ + ++kk+++  kPD+v+
  gi|15668466|ref|NP_247264.1| 279 HAKARGIDVVLAD--TAGrQATNVNlMEEIKKVVRVTKPDLVI 319
                                   2233333333333..5556666666345888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3548  (0.197892); expected 358.6 (0.02)
Passed bias filter:                      980  (0.05466); expected 358.6 (0.02)
Passed Vit filter:                       202  (0.0112667); expected 17.9 (0.001)
Passed Fwd filter:                        52  (0.00290033); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.96u 0.35s 00:00:01.31 Elapsed: 00:00:00.52
# Mc/sec: 2368.84
//
Query:       gi|15668467|ref|NP_247265.1|  [L=93]
Description: putative monovalent cation/H+ antiporter subunit G [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.009   16.3   1.8     0.0097   16.2   1.8    1.1  1  YwiC            YwiC-like protein
  ------ inclusion threshold ------
      0.012   15.8   8.1      0.074   13.3   8.1    2.0  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit


Domain annotation for each model (and alignments):
>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.8   1.1e-06    0.0097      28     103 ..      14      88 ..       3      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-06
                          YwiC  28 hllllvawlvgYlaffplllllkarrrarylkplliYgavallllllalllqpa.llwwallflplvavavyeakrk 103
                                    +l+l+a +   la++   l++ ++r++ + + + i g++ +++ l++++l    l +++l+++p++a a++ a+ +
  gi|15668467|ref|NP_247265.1|  14 DILVLIASFGILLASY--RLWIEKDRKNIIYARIHILGVIDCACFLIFIALGETlLAFVYLILAPFLAHAIAHAAYN 88 
                                   5778888888888887..57999999999999999999998888888888877747777888889999888877655 PP

>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   8.1   8.3e-06     0.074       1      79 []      16      87 ..      16      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.3e-06
                PhaG_MnhG_YufB  1 llllGalfvllgaigll....rlpdvytRlhaatkadtlGlllillGlllrfslaaslkllliilfllltaPvaahliaraay 79
                                  l+l++++ +ll+++ l+    r + +y+R+h ++++d   ++li+++l             l++++ l+ aP  ah+ia+aay
  gi|15668467|ref|NP_247265.1| 16 LVLIASFGILLASYRLWiekdRKNIIYARIHILGVIDCA-CFLIFIALGE----------TLLAFVYLILAPFLAHAIAHAAY 87
                                  678888888888888885555556699*******99965.5566666665..........578899999*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 628.83
//
Query:       gi|15668468|ref|NP_247266.1|  [L=188]
Description: thymidylate kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-55  187.1   1.2    2.7e-55  186.9   1.2    1.0  1  Thymidylate_kin  Thymidylate kinase
      3e-08   34.1   0.0    3.7e-08   33.8   0.0    1.1  1  AAA_28           AAA domain
    2.9e-07   30.6   2.1    3.5e-06   27.0   2.1    2.1  1  dNK              Deoxynucleoside kinase
    2.1e-06   28.2   0.5    1.1e-05   25.8   0.1    2.1  2  AAA_17           AAA domain
    6.5e-06   26.3   0.9     0.0015   18.7   0.1    2.3  2  SKI              Shikimate kinase
    4.6e-05   24.0   0.3    0.00023   21.7   0.2    2.3  2  AAA_18           AAA domain
  ------ inclusion threshold ------
       0.01   15.6   1.2       0.46   10.2   0.1    2.4  2  Cytidylate_kin   Cytidylate kinase
      0.013   15.6   0.0      0.022   14.9   0.0    1.6  1  AAA_33           AAA domain
       0.02   14.6   3.3       0.23   11.1   0.3    2.3  2  AAA_24           AAA domain
      0.021   15.0   0.4      0.038   14.1   0.4    1.4  1  ADK              Adenylate kinase
      0.022   14.6   0.5      0.041   13.7   0.4    1.5  1  SLS              Mitochondrial inner-membrane-bound regulator
      0.074   12.7   0.2       0.63    9.6   0.0    2.2  2  SRP54            SRP54-type protein, GTPase domain
      0.093   13.2   1.7       0.31   11.5   1.7    1.8  1  AAA              ATPase family associated with various cellul


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.9   1.2   1.9e-58   2.7e-55       1     185 []       9     179 ..       9     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 186.9 bits;  conditional E-value: 1.9e-58
                                   EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT- CS
               Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkqgk 81 
                                   +EG+DG+GKttq++ll++++++ +     t ep+++ +G+ ire+l+ ++e++++t+allfaadrieh+  +ik++lk+ +
  gi|15668468|ref|NP_247266.1|   9 FEGIDGSGKTTQSKLLAKKMDAFW-----TYEPSNSLVGKIIREILSGKTEVDNKTLALLFAADRIEHTK-LIKEELKK-R 82 
                                   8*********************99.....9***********************************88777.*******9.9 PP

                                   EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHH CS
               Thymidylate_kin  82 tvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylel 162
                                    v++dRyl+Ss+aYq++++ vd ++++s+n+ +l kPd++fll vd e+alkR++++d      +e++dfl+kv+ +ylel
  gi|15668468|ref|NP_247266.1|  83 DVVCDRYLYSSIAYQSVAG-VDENFIKSINRYAL-KPDIVFLLIVDIETALKRVKTKDI-----FEKKDFLKKVQDKYLEL 156
                                   9***************988.*************9.************************.....***************** PP

                                   HHTTSTEEEEETTS-.HHHHHHHH CS
               Thymidylate_kin 163 akederiliidasks.ieevheeI 185
                                   a+ + ++++id++k+ +eevh+eI
  gi|15668468|ref|NP_247266.1| 157 AE-EYNFIVIDTTKKsVEEVHNEI 179
                                   *6.********99988******98 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   2.7e-11   3.7e-08       2     162 ..       7     174 ..       6     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.7e-11
                        AAA_28   2 ivitGgestGKTtlleaLaar.........gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaaaan 73 
                                   iv+ G  ++GKTt ++ La++           + v  + reil+ k++ ++++l+     l fa+ ++e+ +   ++  ++
  gi|15668468|ref|NP_247266.1|   7 IVFEGIDGSGKTTQSKLLAKKmdafwtyepSNSLVGKIIREILSGKTEVDNKTLA-----LLFAADRIEHTKLIKEE-LKK 81 
                                   89*****************7667777554455599************99999775.....46777777666544444.456 PP

                        AAA_28  74 kvlfcDrglldtlaYarayggeaeaeleaaar.ekrydlvfllppapei..dddgeRr..edleereaiderlrealrelg 149
                                   + ++cDr l  ++aY  + g + e+ ++++ r + + d vfll ++ e+  ++ ++ +  e+ +  ++++++ +e+ +e++
  gi|15668468|ref|NP_247266.1|  82 RDVVCDRYLYSSIAYQSVAGVD-ENFIKSINRyALKPDIVFLLIVDIETalKRVKTKDifEKKDFLKKVQDKYLELAEEYN 161
                                   7789******************.8888888777778999****99998855555555432556668889999999999999 PP

                        AAA_28 150 ipviivpsgdvee 162
                                   + vi+  + +vee
  gi|15668468|ref|NP_247266.1| 162 FIVIDTTKKSVEE 174
                                   9999998999887 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   2.1   2.6e-09   3.5e-06       1     178 [.       7     165 ..       7     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.6e-09
                                   EEEEESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSSHHHHHHHHSHHH.HHHHHHHHHHHHHHHHHHCHH..SSS-EE CS
                           dNK   1 ivveGnIgaGKstlvklLskklgvkvfeEpvdkwtnvqknlLekfYkdpsr.wsfalqtyvllsrlkqqleal..atkqvv 78 
                                   iv eG  g+GK+t  klL+kk++    +Ep +  +   +++++ +   +++    +l   + + r++ ++ ++   +k+ v
  gi|15668468|ref|NP_247266.1|   7 IVFEGIDGSGKTTQSKLLAKKMDAFWTYEPSNSLV---GKIIREILSGKTEvDNKTLALLFAADRIEHTKLIKeeLKKRDV 84 
                                   789********************888899888873...3555555554444234455555555555555444222445555 PP

                                   EEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHH CS
                           dNK  79 vleRsiysdryiFakalaekgtlseeelkiykelldnlleelakpdlliYLkasletclerikkRgreeekkieldYlekL 159
                                   v +R  ys+       ++++    +e      ++ + +++++ kpd++  L +++et l+r+k ++  e+    +d+l+k+
  gi|15668468|ref|NP_247266.1|  85 VCDRYLYSSI------AYQSVAGVDE------NFIKSINRYALKPDIVFLLIVDIETALKRVKTKDIFEK----KDFLKKV 149
                                   5555555555......4444333333......344555555557***********************995....5666666 PP

                                   HHHHHHHHTSGGCS-EEEE CS
                           dNK 160 hekyeewlkklnevpvlvi 178
                                   + ky e  +++n +   vi
  gi|15668468|ref|NP_247266.1| 150 QDKYLELAEEYNFI---VI 165
                                   66666666665543...33 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   8.3e-09   1.1e-05       2     121 ..      11     136 ..      10     144 .. 0.75
   2 ?    0.3   0.1      0.61   8.4e+02      85     112 ..     142     169 ..     134     179 .. 0.55

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 8.3e-09
                                   E-TTSSHHHHHHHHHHHH.....TEEEEEH..HHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEE CS
                        AAA_17   2 GgPGsGKgtqceklveky.....gfthlsa..Gdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvl 75 
                                   G+ GsGK+tq++ l++k+       +  +   G ++re  + +  + +++ ++ l   ++ e++k+++e++++    ++v+
  gi|15668468|ref|NP_247266.1|  11 GIDGSGKTTQSKLLAKKMdafwtY-EPSNSlvGKIIREILSGKT-EVDNKTLALLFAADRIEHTKLIKEELKK----RDVV 85 
                                   899*************99766641.2222224999998876665.4466667777777777777777776665....6899 PP

                                   EEE-SEEEETTEEEESSHHHHHH.....HH..SEEEEEE--HHHHHHHHHH CS
                        AAA_17  76 vdghprikeqagfldglpkevle.....elkpdaiilleadpeeilerrlk 121
                                    d +       + ++g+++++++      lkpd+++ll +d e+ l+r++ 
  gi|15668468|ref|NP_247266.1|  86 CDRYLYSSIAYQSVAGVDENFIKsinryALKPDIVFLLIVDIETALKRVKT 136
                                   9999988888888999999998733344666***************99864 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.61
                                   TTEEEESSHHHHHHHH..SEEEEEE--H CS
                        AAA_17  85 qagfldglpkevleelkpdaiilleadp 112
                                   +++fl++++++ le ++   +i++++ +
  gi|15668468|ref|NP_247266.1| 142 KKDFLKKVQDKYLELAEEYNFIVIDTTK 169
                                   4455555555555555555555555544 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1    0.0072        10       2      17 ..      14      29 ..      13      33 .. 0.90
   2 !   18.7   0.1   1.1e-06    0.0015      73     155 ..     106     181 ..      90     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0072
                                  TSSHHHHHHHHHHHHT CS
                           SKI  2 GaGKstvGkllAkklg 17
                                  G+GK+t  kllAkk++
  gi|15668468|ref|NP_247266.1| 14 GSGKTTQSKLLAKKMD 29
                                  9************975 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.1e-06
                                   GGSHHHHHHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCCSSCEEEECTSSHHHHHHHHH CS
                           SKI  73 vlseenrellkekgiviyLdvsleellerlkadkeRPllqekskeeelleelaereplyeeaadvvvdeseeskeevaeei 153
                                   ++++ nr +lk   iv++L v++e+ l+r+k ++    +++k+  +++++   +  +l ee++ +v+d++++s eev +ei
  gi|15668468|ref|NP_247266.1| 106 FIKSINRYALK-PDIVFLLIVDIETALKRVKTKDI---FEKKDFLKKVQD---KYLELAEEYNFIVIDTTKKSVEEVHNEI 179
                                   66788999999.99*****************9999...555555444444...5559***********************9 PP

                                   HH CS
                           SKI 154 le 155
                                   + 
  gi|15668468|ref|NP_247266.1| 180 IG 181
                                   86 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   1.7e-07   0.00023       1     114 [.       7     138 ..       7     155 .. 0.56
   2 ?   -0.8   0.0       1.5   2.1e+03      61      84 ..     154     170 ..     135     187 .. 0.42

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.7e-07
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf..........gvnlrdvakenglllevdpealdeskrldedkldklldaleenss. 69 
                                   I+  G+ G+GKtt +k L+k++ +f          g ++r++++     +evd++ l     +d+  + kl+++  + ++ 
  gi|15668468|ref|NP_247266.1|   7 IVFEGIDGSGKTTQSKLLAKKMdAFwtyepsnslvGKIIREILSG---KTEVDNKTLALLFAADRIEHTKLIKEELKKRDv 84 
                                   8899*****************978899888855553333333333...223333322333333333333333333333334 PP

                        AAA_18  70 .............aleegknlvidghlaeleseaakdikkvvLtaspeelleRlekRg 114
                                                + +  +   i ++    ++++ +    + L ++ e+ l+R+++ +
  gi|15668468|ref|NP_247266.1|  85 vcdrylyssiayqSVAGVDENFIKSINRYALKPDIV----FLLIVDIETALKRVKTKD 138
                                   444444433334322222222444444444444333....888888888888888866 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                        AAA_18  61 ldaleenssaleegknlvidghla 84 
                                   l++ e       e + +vid    
  gi|15668468|ref|NP_247266.1| 154 LELAE-------EYNFIVIDTTKK 170
                                   22222.......223334443333 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.025        34       4      24 ..      10      30 ..       7      41 .. 0.86
   2 ?   10.2   0.1   0.00033      0.46     180     210 ..     154     184 ..     122     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.025
                                  E-STTSSHHHHHHHHHHHHT- CS
                Cytidylate_kin  4 DGPagsGKssvaralaeklgl 24
                                   G  gsGK + +++la+k+++
  gi|15668468|ref|NP_247266.1| 10 EGIDGSGKTTQSKLLAKKMDA 30
                                  67789************9976 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00033
                                   S-S---TT-EEEETTTS-HHHHHHHHHHHHH CS
                Cytidylate_kin 180 gpLklaedaliidtskltieevvekilelik 210
                                    +L    + ++idt+k+++eev ++i+ ++k
  gi|15668468|ref|NP_247266.1| 154 LELAEEYNFIVIDTTKKSVEEVHNEIIGYLK 184
                                   33444456799***************98876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.6e-05     0.022       2      76 ..       7      87 ..       6     168 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                        AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdt.......lrrrlfg.tdqqsktdytrvldrlyqilnelarkalsagrnvild 76
                                  +++ G  GsGK+t ++ l+kk +a+   +++       +r+ l g t++++kt    +l+ + +i +  + k   ++r+v+ d
  gi|15668468|ref|NP_247266.1|  7 IVFEGIDGSGKTTQSKLLAKKMDAFWTYEPSnslvgkiIREILSGkTEVDNKT--LALLFAADRIEHTKLIKEELKKRDVVCD 87
                                  799****************9998554444444555553333333333333333..3344444443333333444445555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.019        27       7      23 ..       9      25 ..       4      87 .. 0.85
   2 ?   11.1   0.3   0.00017      0.23      27      86 ..     123     180 ..     106     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.019
                        AAA_24  7 iyGpsgiGKTtlakelg 23
                                    G  g+GKTt+ k l 
  gi|15668468|ref|NP_247266.1|  9 FEGIDGSGKTTQSKLLA 25
                                  55999*******99883 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00017
                        AAA_24  27 lfidtekGlksldadkfpdieswedfldevvel.aaeladyktlviDtideleelclaevi 86 
                                   l++d+e  lk+++ ++   i   +dfl++v+    +  ++y+ +viDt  + +e + +e+i
  gi|15668468|ref|NP_247266.1| 123 LIVDIETALKRVKTKD---IFEKKDFLKKVQDKyLELAEEYNFIVIDTTKKSVEEVHNEII 180
                                   5669999777777666...568899999998885677788*********999998888876 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   2.8e-05     0.038       3     133 ..      11     154 ..       9     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                                   ESTTSSHHHHHHHHHHHHTS......EEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCH.GTTTE CS
                                   xxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                           ADK   3 GaPgaGKGtqaeklvkkygl......ahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeeleke.dkkkg 76 
                                   G  g+GK tq++ l+kk+ +       +   G ++R+ ++ +te+ ++  +++ +++ + +   +kl+keel+k+    ++
  gi|15668468|ref|NP_247266.1|  11 GIDGSGKTTQSKLLAKKMDAfwtyepSNSLVGKIIREILSGKTEVDNKTLALLFAADRIEH---TKLIKEELKKRdVVCDR 88 
                                   778***********99865411111134457***************999999988887765...79*******99555678 PP

                                   EEEES..B-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT.......GSHHHHHHHHH CS
                                   xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxx RF
                           ADK  77 fllDG..fPRtveqaealeelleeekvkldlvleldvpeevlveRltg.......DneetvkkRle 133
                                   +l     +       e++ + +++++ k d+v+ l v+ e+ ++R+         D  ++v+++  
  gi|15668468|ref|NP_247266.1|  89 YLYSSiaYQSVAGVDENFIKSINRYALKPDIVFLLIVDIETALKRVKTkdifekkDFLKKVQDKYL 154
                                   888762255556667889999*************************98788866655555554433 PP

>> SLS  Mitochondrial inner-membrane-bound regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4     3e-05     0.041      30      91 ..     113     186 ..      97     188 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
                           SLS  30 vklsprefflLltgngklLqnlsri............hgakielnrsenklritAtkstaeyieasineilkni 91 
                                     l+p+ +flL+ + ++ L+ ++ +            +++ +el  + n + i +tk+++e + ++i  +lkni
  gi|15668468|ref|NP_247266.1| 113 YALKPDIVFLLIVDIETALKRVKTKdifekkdflkkvQDKYLELAEEYNFIVIDTTKKSVEEVHNEIIGYLKNI 186
                                   668999999999********996666777777888889**********************************98 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00046      0.63       3      25 ..       6      28 ..       4      35 .. 0.87
   2 ?    0.6   0.1      0.27   3.7e+02      78      95 ..     155     171 ..     125     186 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00046
                                  EEEEEESTTSSHHHHHHHHHHHH CS
                         SRP54  3 villvGlqGaGKTttlaKLaall 25
                                   i++ G+ G+GKTt    La+++
  gi|15668468|ref|NP_247266.1|  6 FIVFEGIDGSGKTTQSKLLAKKM 28
                                  68999*********999999876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.27
                                   HHHHTTSSEEEEEE--SS CS
                         SRP54  78 kakeekidvvlvDTaGrl 95 
                                   +  +e+++++++DT+ ++
  gi|15668468|ref|NP_247266.1| 155 EL-AEEYNFIVIDTTKKS 171
                                   22.346889999997554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.7   0.00023      0.31       2     119 ..       8     179 ..       7     186 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                   EEESSTTSSHHHHHHHHHHHHTHE.............EEEEETTTCSSS................................ CS
                           AAA   2 llyGppGtGKTllakavakelgve.............fleisgsellsk................................ 37 
                                   ++ G  G GKT+  k +ak++++              +                                           
  gi|15668468|ref|NP_247266.1|   8 VFEGIDGSGKTTQSKLLAKKMDAFwtyepsnslvgkiI----------Reilsgktevdnktlallfaadriehtklikee 78 
                                   68899***************975422223333333331..........033333344444566666666666666677777 PP

                                   ....................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                           AAA  38 ....................yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                                       + g  e+ i+ + + a +    + l+i +i+   k+ ++++  e+++ +++   +  ++ +
  gi|15668468|ref|NP_247266.1|  79 lkkrdvvcdrylyssiayqsVAGVDENFIKSINRYALKPD-IVFLLIVDIETALKRVKTKDIFEKKDFLKKVQDKYLELAE 158
                                   8888888888887776666556666666666666655554.5777788888887777444444444444444443333333 PP

                                   SSSTEEEEEEESS.GGGSTHHH CS
                           AAA  99 keskvivigatnr.pdkldpal 119
                                    e ++ivi +t++ ++++ +++
  gi|15668468|ref|NP_247266.1| 159 -EYNFIVIDTTKKsVEEVHNEI 179
                                   .345888888877666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1239.53
//
Query:       gi|15668469|ref|NP_247267.1|  [L=841]
Description: ATP-dependent helicase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-49  168.1   0.0    3.2e-49  167.3   0.0    1.4  1  DEAD_assoc     DEAD/H associated
    1.7e-29  102.8   0.1      1e-28  100.3   0.0    2.1  2  DEAD           DEAD/DEAH box helicase
    9.2e-20   71.1   2.3    3.3e-19   69.3   0.2    2.8  3  Helicase_C     Helicase conserved C-terminal domain
      6e-12   45.9   1.2    1.9e-11   44.2   0.0    2.4  3  ResIII         Type III restriction enzyme, res subunit
    0.00047   19.0   0.3     0.0011   17.8   0.3    1.6  1  SNF2_N         SNF2 family N-terminal domain
    0.00051   20.4   0.0       0.21   11.9   0.0    2.8  3  AAA_19         AAA domain
     0.0031   17.0   0.0     0.0074   15.8   0.0    1.7  1  PhoH           PhoH-like protein
  ------ inclusion threshold ------
       0.02   15.2   2.4       0.12   12.7   0.3    3.3  3  AAA_22         AAA domain
      0.065   13.4   0.0        0.2   11.8   0.0    1.8  1  Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family
       0.12   11.7   0.0        0.5    9.7   0.0    2.0  1  HEM4           Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.3   0.0   1.8e-52   3.2e-49       1     191 []     620     803 ..     620     803 .. 0.95

  Alignments for each domain:
  == domain 1  score: 167.3 bits;  conditional E-value: 1.8e-52
                    DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldellell 81 
                                   +P+d+++l+E+f++e +++++++h ++Grr+neala+++a  +s+  +++v++++nD+g++l+lp++++++    +++el+
  gi|15668469|ref|NP_247267.1| 620 VPDDEKVLIENFDEE-KRRYYIFHFVAGRRANEALARAFANYISKIKKCNVRISVNDYGFALILPKNRKIK--RADITELF 697
                                   8***********665.599*******************************************999999986..45799999 PP

                    DEAD_assoc  82 spdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareyp.dfpllleavrevledqlD 161
                                   + d + + +++++++se++krrFr+vA+r ++++rry +++ ++ +q+++a++Ll+  +  + ++pl++e++re+led lD
  gi|15668469|ref|NP_247267.1| 698 NLD-VVKNVKESIERSEILKRRFRHVATRGFMILRRYMNRKISVDRQQFNAEMLLKYCK--EvNHPLYRETLREILEDSLD 775
                                   988.67889**************************************************..669***************** PP

                    DEAD_assoc 162 lerlaellrriaageirvvevetprpSpfA 191
                                   ++++ ++ ++i++++i   e  +p+pSpfA
  gi|15668469|ref|NP_247267.1| 776 IDNALDYFEKIKRRKIYYLE--LPSPSPFA 803
                                   ********************..*******9 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.0   5.8e-32     1e-28       1     170 [.      36     217 ..      36     225 .. 0.87
   2 ?   -0.3   0.0      0.44   7.8e+02      52      85 ..     256     287 ..     250     335 .. 0.66

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 5.8e-32
                                   -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkkyid.. 75 
                                   t+ Q+ ai++i +g++vl++ +TGsGKTl ++++ ++++++     k +++  +l+v+P+r+L +++ +nlk+ +k+i   
  gi|15668469|ref|NP_247267.1|  36 TPPQRYAIKEIHEGKNVLICSPTGSGKTLSAFLAGINELIKLsmenKLEDRIYILYVSPLRALNNDIERNLKEPLKEIYdv 116
                                   788************************************99999999*****************************64336 PP

                                   ..........SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHH CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  76 ..........lrvlliiggvaardqlskldngvdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdfinr 144
                                             +rv + +++++ +++++ l++ ++i+++tp+ l+  l++ k++  ls ++++++DE++ l ++ ++ +++ 
  gi|15668469|ref|NP_247267.1| 117 akeigieldeIRVAVRTSDTTSSQKQRMLKKPPHILITTPESLAIALNSPKFSqlLSGIKYVIVDEIHALTNK-RGVHLSL 196
                                   66666777777777666666666777777666*************9999998889*****************9.9999**9 PP

                                   HHHHSHHHCTTSTTTSEEEEEESSBS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 145 ilnqlpqitcdgklqrqvivlSATlp 170
                                    l++l++i +        i lSAT++
  gi|15668469|ref|NP_247267.1| 197 SLERLNRIAN-----FIRIGLSATIH 217
                                   99***77644.....447*******9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.44
                                   EEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  52 ivePtreLaeqtlnnlkkfkkyidlrvlliiggv 85 
                                   i +P++e+ +  +n lkk++++ +  + li++++
  gi|15668469|ref|NP_247267.1| 256 IYTPSEEISKRLYNLLKKLIEEHK--TTLIFTNT 287
                                   667888888888888888888644..34443322 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.68   1.2e+03      37      62 ..     123     148 ..      71     170 .. 0.79
   2 !   69.3   0.2   1.8e-22   3.3e-19       4     108 ..     265     371 ..     262     373 .. 0.92
   3 ?   -3.0   0.0       5.1   9.2e+03      21      45 ..     656     680 ..     627     705 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.68
                                   HHTTSTEEEESTTSTHHHHHHHHHHH CS
                    Helicase_C  37 ekkgikvavlhgelpqnereeileqf 62 
                                   e  +i+vav ++++++++++++l++ 
  gi|15668469|ref|NP_247267.1| 123 ELDEIRVAVRTSDTTSSQKQRMLKKP 148
                                   344899*************9999987 PP

  == domain 2  score: 69.3 bits;  conditional E-value: 1.8e-22
                                   HHHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTS CS
                    Helicase_C   4 eallell.kleeeggkilifvntidrlekvklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidi 82 
                                   ++l++ll kl ee++++lif+nt++  e+v + l++    kv ++h++l+ ++r+e+ e+ +kge++v i+++ +e G+di
  gi|15668469|ref|NP_247267.1| 265 KRLYNLLkKLIEEHKTTLIFTNTRSATERVAFYLKQLgVEKVETHHSSLSREHRLEVEEKLKKGEIRVCISSTSLELGVDI 345
                                   67899999999**************8887666666663689**************************************** PP

                                   TTESEEEESSSSSSHHHHHHHHTTSS CS
                    Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtg 108
                                    +++lVi ++ p++v+++ qriGR g
  gi|15668469|ref|NP_247267.1| 346 GSIDLVILLGSPKSVSRALQRIGRSG 371
                                   ************************87 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.1
                                   EEESSHHHHHH..HHHHHHHTTSTEEE CS
                    Helicase_C  21 ifvntidrlek..vklllekkgikvav 45 
                                    f+n+i++++k  v++    +++ +a 
  gi|15668469|ref|NP_247267.1| 656 AFANYISKIKKcnVRIS--VNDYGFAL 680
                                   56666666655333333..34444444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   1.1e-14   1.9e-11       4     169 ..      35     216 ..      13     218 .. 0.80
   2 ?   -1.8   0.1       1.5   2.6e+03      47     118 ..     273     294 ..     249     337 .. 0.50
   3 ?   -2.1   0.1       1.9   3.4e+03      66      85 ..     599     622 ..     593     666 .. 0.61

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.1e-14
                                   E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S...........-EEEEESSHHHHHHHHHHGGGG CS
                        ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkee......kflflvprkslleqtleefkkf 77 
                                   + + Q  ai+++      ++ k++li  +TG+GKTl a ++ i +l k   e+       +l + p ++l +  ++++k+ 
  gi|15668469|ref|NP_247267.1|  35 FTPPQRYAIKEI------HEGKNVLICSPTGSGKTLSAfLAGINELIKLSMENkledriYILYVSPLRALNNDIERNLKEP 109
                                   667777777777......57899***************888899999887777899999999****************999 PP

                                   TGG....GEEE...........ESSS-B--...............-SEEEEEHHHHHHTH........HHHTTT-SEEEEE CS
                        ResIII  78 lseaykeigkk...........vsgdkkka........kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiD 139
                                   l+e y+ ++++                           ++  ++  +il+tt +sl  ++   ++ + ++l + ++++i+D
  gi|15668469|ref|NP_247267.1| 110 LKEIYDVAKEIgieldeirvavR------TsdttssqkQRMLKKPPHILITTPESLAIAL---NSPKFSQLLSGIKYVIVD 181
                                   99998763333333444444332......03334445556678899**************...8899999999999***** PP

                                   TGGGTTS.T......TTHHHHHT---SEEEEEESS- CS
                        ResIII 140 EaHrlgakk......swreilekfkeavllglTATp 169
                                   E H l+ k       s ++ l+ + +++++gl+AT+
  gi|15668469|ref|NP_247267.1| 182 EIHALTNKRgvhlslSLER-LNRIANFIRIGLSATI 216
                                   *******735555567777.788899*********7 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                                   HH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH CS
                        ResIII  47 rllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdstnkkilvttiqsldads 118
                                   +l                                                  ++++++ +++t++ s++++ 
  gi|15668469|ref|NP_247267.1| 273 KL--------------------------------------------------IEEHKTTLIFTNTRSATERV 294
                                   22..................................................23444444444444433332 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.9
                                   HHHHHHHHGGGGTGG........G CS
                        ResIII  66 lleqtleefkkflseayke....i 85 
                                   + e+t +++k++++e++k+     
  gi|15668469|ref|NP_247267.1| 599 IDEKTAKAIKNYMDEQNKFaivpD 622
                                   566666666666666554433331 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.3   5.9e-07    0.0011     123     297 ..     126     318 ..      39     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.9e-07
                                   -EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--T....TSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx RF
                        SNF2_N 123 alrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlkns....tskaaea 199
                                   ++rv v ++++++++k    ++ l +  +++itt + l+   + +k  + l+ +  k+v++DE h l n+     s   e 
  gi|15668469|ref|NP_247267.1| 126 EIRVAVRTSDTTSSQK----QRMLKKPPHILITTPESLAIALNSPKFSQLLSGI--KYVIVDEIHALTNKrgvhLSLSLER 200
                                   4566666665544444....555666789*************999999999876..69************64433777777 PP

                                   HHH---S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHH........HHHHHHHHHHHTT-ST...... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxx...... RF
                        SNF2_N 200 vskLstsnrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpie........aqaekgrsrLlqllqr...... 266
                                   ++++++  r+ l++T     l+++   l   + + +    +++k ++ ++           +e+ ++rL++ll++      
  gi|15668469|ref|NP_247267.1| 201 LNRIANFIRIGLSAT--IHPLTEVAKFLVGNGRDCYIVDVSYKKEIEIKVIspvddfiyTPSEEISKRLYNLLKKlieehk 279
                                   78888999999**99..5567777777777777777777777777777776777777777777999999999998777788 PP

                                   .....TEE---GGGT...--S---EEEEEEEEE--HHHH CS
                                   .....xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 267 .....lmlrrakkdv...eknlPpkteeiiflklskver 297
                                        ++ r+a + v    k+l   ++e+++ +ls ++r
  gi|15668469|ref|NP_247267.1| 280 ttlifTNTRSATERVafyLKQLGVEKVETHHSSLSREHR 318
                                   888888888888888777788888888888888888776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00011      0.21       1     115 [.      39     187 ..      39     210 .. 0.64
   2 ?    5.2   0.0     0.013        24      36      84 ..     272     319 ..     261     474 .. 0.78
   3 ?   -2.0   0.0       2.2     4e+03     105     139 ..     590     624 ..     490     629 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                        AAA_19   1 qreave.alkekvllvtaGpGtGKTrv.....lkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrl 75 
                                   qr a++  ++ k++l+  + G+GKT       +++ ++l  e++ ++   il v++ +   + ++ +l   +++ + i  +
  gi|15668469|ref|NP_247267.1|  39 QRYAIKeIHEGKNVLICSPTGSGKTLSaflagINELIKLSMENKLEDRIYILYVSPLRALNNDIERNL---KEPLKEIYDV 116
                                   88999879999**************6433333566666666666666677888888877778888888...4554444444 PP

                        AAA_19  76 al.................................ldfddlltealelle...........eaeeekklqeee.llivDEf 111
                                   a                                  l                         + + ++ l ++  ++ivDE+
  gi|15668469|ref|NP_247267.1| 117 AKeigieldeirvavrtsdttssqkqrmlkkpphiL-------------IttpeslaialnSPKFSQLL-SGIkYVIVDEI 183
                                   444445666666666544444444444444444431.............04444444545355566666.66669999999 PP

                        AAA_19 112 qdvd 115
                                     ++
  gi|15668469|ref|NP_247267.1| 184 HALT 187
                                   8776 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.013
                        AAA_19  36 elggvkpeeillvaftgrAakelrerlaalgae.atTiHrlalldfddll 84 
                                   +   ++ ++ l+ + t+ A+++++  l++lg+e  +T H+   l  +++l
  gi|15668469|ref|NP_247267.1| 272 KKLIEEHKTTLIFTNTRSATERVAFYLKQLGVEkVETHHSS--LSREHRL 319
                                   3333445899********************99867888865..3333333 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.2
                        AAA_19 105 llivDEfqdvdelqyrLlkallgekkklllvGDpd 139
                                   +  + E  d+de   + +k+ ++e++k+ +v D++
  gi|15668469|ref|NP_247267.1| 590 IEEIREKYDIDEKTAKAIKNYMDEQNKFAIVPDDE 624
                                   44566777888888888888887888788888765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.2e-06    0.0074       6      89 ..      36     119 ..      31     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.2e-06
                                   SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHHHHH CS
                          PhoH   6 tkeQkeylealkkndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelGflpgdleekvdpylrplyda 86 
                                   t  Q+ +++ +++ + v +  p+G+GKt+ a  ++++ l k ++++ +  r  +     l +l+ d+e  ++  l+ +yd 
  gi|15668469|ref|NP_247267.1|  36 TPPQRYAIKEIHEGKNVLICSPTGSGKTLSAFLAGINELIKLSMENKLEDRIYILYVSPLRALNNDIERNLKEPLKEIYDV 116
                                   778999********************************9999888877777777777788888888888888888888776 PP

                                   HTT CS
                          PhoH  87 Lkd 89 
                                    k+
  gi|15668469|ref|NP_247267.1| 117 AKE 119
                                   655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   6.5e-05      0.12       5     120 ..      49     209 ..      44     228 .. 0.69
   2 ?   -1.3   0.0       1.3   2.4e+03     105     135 ..     264     292 ..     252     320 .. 0.70
   3 ?   -2.3   0.0       2.8   4.9e+03      76     105 ..     412     442 ..     386     462 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-05
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka.............. 70 
                                    + ++++ ++G+GKT+++     +  +  + e+  +++   +++   + ++ l +++ r+l+++lk+              
  gi|15668469|ref|NP_247267.1|  49 GKNVLICSPTGSGKTLSAFLAGINELIKLSMENkLEDR---IYILYVSPLRALNNDIERNLKEPLKEiydvakeigielde 126
                                   67789**********99865555544433333353333...333333446799999******999999************* PP

                        AAA_22  71 .....................erlsseellealeqalrarav........................ielliiDEaqhlr.. 104
                                                        +                                            i+ +i+DE++ l+  
  gi|15668469|ref|NP_247267.1| 127 irvavrtsdttssqkqrmlkkP------------------PHilittpeslaialnspkfsqllsgIKYVIVDEIHALTnk 189
                                   **98887777555555554421..................22222223344445555666888889999*********775 PP

                        AAA_22 105 s....eealeeLrsllnlsr 120
                                   +       le L +++n+ r
  gi|15668469|ref|NP_247267.1| 190 RgvhlSLSLERLNRIANFIR 209
                                   26778778888888888633 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                        AAA_22 105 seealeeLrsllnlsrkgvqliLvGtpelrk 135
                                   s+++++ L++l +  +++++li+  t+++ +
  gi|15668469|ref|NP_247267.1| 264 SKRLYNLLKKLIE--EHKTTLIFTNTRSATE 292
                                   4555566666666..6666666665555544 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.8
                        AAA_22  76 eellealeqalraravielliiDEaqhlr.s 105
                                   + +l+ l+q+l   a  ++  +DEa +l+ +
  gi|15668469|ref|NP_247267.1| 412 KNCLDVLAQHLVGMALEKVWDVDEAYNLIkK 442
                                   5677777778877777899999999998652 PP

>> Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011       0.2      37     108 ..     208     294 ..     189     329 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                 Lipase_GDSL_3  37 vnLgfsGnalleaeladvlaevdasvfvldllpN................asaeeirerleyfvktlrkahPktpillved 101
                                   + +g+s      +e+a++l     +++++d+                   + +eei++rl +++k+l ++h kt ++++++
  gi|15668469|ref|NP_247267.1| 208 IRIGLSATIHPLTEVAKFLVGNGRDCYIVDVSYKkeieikvispvddfiyTPSEEISKRLYNLLKKLIEEH-KTTLIFTNT 287
                                   55666665555667777777777777777777667777777777777998889******************.999999999 PP

                 Lipase_GDSL_3 102 lsttkgl 108
                                   +s+t++ 
  gi|15668469|ref|NP_247267.1| 288 RSATERV 294
                                   8887764 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00028       0.5      97     196 ..     258     375 ..     242     382 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00028
                                   E-..SSSHHHHGGGS-.---E.EE.EEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHHHHHHHHHHHTT--..... CS
                          HEM4  97 vpseegtaegLaeelaeslag.kr.vlllrgeiarddlaegLeergaevdevevYetvpaeeepeelkealkagev..... 170
                                   +ps e+ ++ L ++l++ + + k+ +++     a +++a +L++ g  v++ve+ + +  +e++ e++e+lk+ge+     
  gi|15668469|ref|NP_247267.1| 258 TPS-EEISKRLYNLLKKLIEEhKTtLIFTNTRSATERVAFYLKQLG--VEKVETHHSSLSREHRLEVEEKLKKGEIrvcis 335
                                   688.999*********988886663555777788********9888..****************************99999 PP

                                   ..............SEEEESSHHHHHHHHHH-S-HHHHHC CS
                          HEM4 171 ..............davvftSpstvrnllellkdegdelk 196
                                                  ++++ Sp +v + l+++++ g+ l+
  gi|15668469|ref|NP_247267.1| 336 stslelgvdigsidLVILLGSPKSVSRALQRIGRSGHRLH 375
                                   9999999999999778888999999999999998875554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (841 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1272  (0.0709465); expected 358.6 (0.02)
Passed bias filter:                      738  (0.0411624); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 5266.16
//
Query:       gi|15668470|ref|NP_247268.1|  [L=227]
Description: formate dehydrogenase FdhD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.2e-51  172.8   0.0    1.4e-42  146.0   0.0    2.0  2  FdhD-NarQ  FdhD/NarQ family


Domain annotation for each model (and alignments):
>> FdhD-NarQ  FdhD/NarQ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   2.4e-10   4.3e-06       1      63 [.      23      82 ..      23      95 .. 0.74
   2 !  146.0   0.0     8e-47   1.4e-42      96     232 ..      87     221 ..      73     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.4e-10
                                  E--EEEEEEETTEEEEEEEE-SSSHHHHHHHHHHHCTS--SGGGEEEEEEETTTEEEE-S... CS
                     FdhD-NarQ  1 veEepltivvngrelatlmatpadleelalGfllsegliesaediesievdedeasvavatra 63
                                  ++Ee+++i++ng+ + +l ++p+ l+e+a+Gf +seg++++++   ++evd+++ ++  ++++
  gi|15668470|ref|NP_247268.1| 23 AVEESYNIFINGEFVKSLSMSPNFLNEFAVGFAISEGFLNKID---KVEVDKNNINIFGEKND 82
                                  58*************************************9655...55666555444333333 PP

  == domain 2  score: 146.0 bits;  conditional E-value: 8e-47
                                   ----------EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE.TTEEEEEEEESSHHHHHHHHHHHHHT.TSS-SSSEEE CS
                     FdhD-NarQ  96 tlelpesdlklsaeallrlmdalrekqelfketggvHaaalfdadgellavreDvGRHnAlDkviGaallegldlsdkilv 176
                                   ++++ ++++k++ e + ++++  + k++ ++ tg++H a +fd +g+ ++++eD+GRHnA+DkviG+a+l++++l++ il 
  gi|15668470|ref|NP_247268.1|  87 NNKN-NKEIKIDIEIIKKIIS-YEIKAKYWEITGSFHWASMFDLKGNSIIFVEDIGRHNAVDKVIGYAILNNYNLNKLILR 165
                                   3333.4578888888777665.67789****************************************************** PP

                                   ESS-B-HHHHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEEEEETTEEEEEE- CS
                     FdhD-NarQ 177 vsgRlssemvqKaaragipvlvsvsaptslavelAeeagltlvgfvrgkrfnvYtg 232
                                   +sgR++s++v Ka++ g ++++s+s pt++a+elAee ++ l+gf+r+++fn+Yt 
  gi|15668470|ref|NP_247268.1| 166 YSGRIPSDIVKKAINSGLNIIISKSPPTDKAIELAEENNILLIGFARNGKFNIYTS 221
                                   ******************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1459.80
//
Query:       gi|15668471|ref|NP_247269.1|  [L=203]
Description: hypothetical protein MJ_0296 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-18   67.4   0.0    1.4e-13   51.3   0.1    2.1  2  Lactamase_B     Metallo-beta-lactamase superfamily
    3.8e-05   23.3   0.0    4.8e-05   23.0   0.0    1.2  1  Lactamase_B_2   Beta-lactamase superfamily domain
    0.00061   19.7   0.1    0.00088   19.2   0.1    1.2  1  Lactamase_B_3   Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.015   14.9   0.2       0.07   12.7   0.0    2.0  2  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
      0.043   13.9   0.8      0.092   12.8   0.3    1.7  2  G8              G8 domain
        0.2   11.6   4.8       0.37   10.7   0.2    2.2  2  DUF507          Protein of unknown function (DUF507)


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.1   4.7e-17   1.4e-13       5      72 ..      39     106 ..      36     109 .. 0.95
   2 !   14.9   0.0   6.5e-06     0.019     103     193 ..     107     190 ..     103     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 4.7e-17
                                   SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEE CS
                   Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpv 72 
                                   +++s+li +d+ +i++Dt t   ++ + + l  l l p+d+d vi+THlH+DHi +++ +++at +++
  gi|15668471|ref|NP_247269.1|  39 SSSSTLIITDNNNIIVDTSTKDMENIIIKGLSELNLSPNDIDVVINTHLHYDHIENNPIFKNATFYAS 106
                                   589***********************************************************998765 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.5e-06
                                   GCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHH CS
                   Lactamase_B 103 adkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridltlrgaevrdpsdaekyldsll 183
                                   ++  ++ ++ +d+  + +++ +++ +pgh+ g+++v y+  +++++GDa++  ++++        ++   +d + +l+sl+
  gi|15668471|ref|NP_247269.1| 107 PKEFGFNDNFEDFKKFKDKEIEIIETPGHTYGSISVIYK--DYVVVGDASPLKNNILKMI-----PPKLNVDEKLALESLK 180
                                   566677888888888999999999999999999888886..67889*****999999888.....7888888888888888 PP

                                   HHHHHCHSEE CS
                   Lactamase_B 184 klaglkaevl 193
                                   k+++l+  v+
  gi|15668471|ref|NP_247269.1| 181 KIRKLRKNVI 190
                                   8888877665 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.6e-08   4.8e-05       2      63 ..      51     106 ..      50     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.6e-08
                                   EEEES--TT.....HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEE CS
                 Lactamase_B_2   2 riLiDagpd.....lrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyap 63 
                                   +i++D+++      + +  l+ l       ++++id+V+ th HyDH+++ + ++      +++ya+
  gi|15668471|ref|NP_247269.1|  51 NIIVDTSTKdmeniIIKG-LSEL-----NLSPNDIDVVINTHLHYDHIENNPIFKN-----ATFYAS 106
                                   899999999666643333.3333.....55689***************99888887.....456655 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   2.9e-07   0.00088       5      75 ..      38     114 ..      35     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.9e-07
                 Lactamase_B_3   5 lghnsflletagarilvDPf.........kanlgyeppa........eeaDlvlisqaledHahletlkqlaenvkvleeg 68 
                                     ++s l+ t++ +i+vD           k                  ++D+v+ ++ + dH + +++ +   n+++ +++
  gi|15668471|ref|NP_247269.1|  38 ASSSSTLIITDNNNIIVDTStkdmeniiiK--------GlselnlspNDIDVVINTHLHYDHIENNPIFK---NATFYASP 107
                                   66899*************885555444443........155555555*******************9999...99999998 PP

                 Lactamase_B_3  69 eslevgg 75 
                                   +++ +++
  gi|15668471|ref|NP_247269.1| 108 KEFGFND 114
                                   8876653 PP

>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.3e-05      0.07     110     139 ..      35      63 ..       5      94 .. 0.71
   2 ?    0.2   0.0      0.17     5e+02      41      58 ..     184     202 ..     146     203 .] 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                                   E-TETTTTEE-B-TTS-EEEEEESSSBSSS CS
                Rib_5-P_isom_A 110 lReakgkdgpvvTdngnlilDvkfeekied 139
                                   +++a++++  ++Tdn+n+i+D++ +  +e+
  gi|15668471|ref|NP_247269.1|  35 IKKASSSSTLIITDNNNIIVDTSTK-DMEN 63 
                                   3444778899************994.3433 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.17
                                   T.TS-EE--TTS-HHHHHH CS
                Rib_5-P_isom_A  41 e.dlnliKGgGgallrEKi 58 
                                   + ++n+i G  g++++EK+
  gi|15668471|ref|NP_247269.1| 184 KlRKNVITGHEGIVYKEKL 202
                                   4578999999999999997 PP

>> G8  G8 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   3.1e-05     0.092       9      53 ..      39      85 ..      31      98 .. 0.81
   2 ?   -1.5   0.0      0.84   2.5e+03      11      42 ..     138     170 ..     131     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                            G8  9 qegdnvvIpagktvlldvsspklrsllve..GtLifsddksdielna 53
                                  +++++++I+ ++++++d+s+++++ ++++  ++L +s ++ d+++n+
  gi|15668471|ref|NP_247269.1| 39 SSSSTLIITDNNNIIVDTSTKDMENIIIKglSELNLSPNDIDVVINT 85
                                  568899***********************999999977764444443 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.84
                            G8  11 gdnvvIpagktvlldvsspklrsllve.GtLif 42 
                                   g+  vI ++  v+ d s+ k + l     +L +
  gi|15668471|ref|NP_247269.1| 138 GSISVIYKDYVVVGDASPLKNNILKMIpPKLNV 170
                                   677788888888888777766655333355555 PP

>> DUF507  Protein of unknown function (DUF507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.7     0.036   1.1e+02     110     151 ..      46      87 ..      14      93 .. 0.86
   2 ?   10.7   0.2   0.00013      0.37     123     163 ..     154     194 ..     141     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.036
                        DUF507 110 llkedlievsvsenkirnkIfkilkeylkeeeeidkevreki 151
                                   + ++++i v++s +++ n+I+k l+e+    ++id  + + +
  gi|15668471|ref|NP_247269.1|  46 ITDNNNIIVDTSTKDMENIIIKGLSELNLSPNDIDVVINTHL 87 
                                   778999999999999******999999999999998877665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00013
                        DUF507 123 nkirnkIfkilkeylkeeeeidkevrekiknykrklieGte 163
                                     ++n I k++   l+++e++  e  +ki++ ++++i G e
  gi|15668471|ref|NP_247269.1| 154 SPLKNNILKMIPPKLNVDEKLALESLKKIRKLRKNVITGHE 194
                                   569***********************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1545.00
//
Query:       gi|15668472|ref|NP_247270.1|  [L=251]
Description: hypothetical protein MJ_0297 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.5    8.3   9.4         10    6.2   0.1    4.3  4  Imm30     Immunity protein 30


Domain annotation for each model (and alignments):
>> Imm30  Immunity protein 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1   0.00058        10       3      33 ..       9      39 ..       7      44 .. 0.87
   2 ?    2.7   0.3    0.0074   1.3e+02      61      91 ..      95     127 ..      51     143 .. 0.71
   3 ?   -0.6   0.1      0.08   1.4e+03      42      52 ..     193     203 ..     188     211 .. 0.85
   4 ?    2.2   0.0     0.011     2e+02      58      76 ..     229     247 ..     214     251 .] 0.65

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00058
                         Imm30  3 kllrteeevelFesalekllkeqnkdnledl 33
                                   +++ e+e +lF +ale+  k + +d + +l
  gi|15668472|ref|NP_247270.1|  9 DKMNFENENALFKKALEEKEKGNYDDAIYYL 39
                                  68999*************9999999988776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0074
                         Imm30  61 eylkklvealpkllknakeWakil..nyRilns 91 
                                   + ++++ ea++ + ++ ke+  ++  ++Ri+n 
  gi|15668472|ref|NP_247270.1|  95 NIIDEFFEAIEGIEEKDKEFKFVVmaLKRIVNY 127
                                   555666666666666655554443114666664 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.08
                         Imm30  42 edeevmFglvH 52 
                                   e   +mFg++ 
  gi|15668472|ref|NP_247270.1| 193 ERAKMMFGIIE 203
                                   67789***995 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.011
                         Imm30  58 eveeylkklvealpkllkn 76 
                                   + ee+l+k+++++++l+  
  gi|15668472|ref|NP_247270.1| 229 KNEEHLNKIIKTIEDLMID 247
                                   4455566666666655543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1358  (0.0757432); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1605.67
//
Query:       gi|15668473|ref|NP_247271.1|  [L=150]
Description: flavodoxin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-14   52.7   2.0    1.1e-11   44.7   0.2    2.0  2  Flavodoxin_3  Flavodoxin domain
    5.9e-12   46.0   0.0      7e-12   45.8   0.0    1.2  1  Flavodoxin_5  Flavodoxin domain
    0.00039   20.6   0.1     0.0026   18.0   0.1    2.1  1  Flavodoxin_1  Flavodoxin


Domain annotation for each model (and alignments):
>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.2   1.8e-15   1.1e-11       2     112 ..       5     115 ..       4     129 .. 0.84
   2 !    8.1   0.2   0.00032       1.9     145     160 ..     129     144 ..     126     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.8e-15
                  Flavodoxin_3   2 ilysS.ltGNTkkvAeaikealeeekeivsikeakek.veeadvvfvGfwvdkgtadeealkfletlk..nkkillfgTlG 78 
                                   ily+S +  NT+k+A++i+++l++  +i++i++++   +e++d++  G  ++ g+  +++ kfl +++  nkk ++f T+G
  gi|15668473|ref|NP_247271.1|   5 ILYKSiHHKNTEKIAKTIADELNA--DIYNIDKVSPDiIENYDLIGFGSGIYFGKHHKSIFKFLDKISktNKKAFIFSTAG 83 
                                   788884467***************..999*99988777****************************96559********** PP

                  Flavodoxin_3  79 agkdseyakkilekvkallekn.nevlgeflcqGk 112
                                   +   ++ ++k    ++  l+++  e+lgef c+G 
  gi|15668473|ref|NP_247271.1|  84 FPFLKSMFHKE---LRDKLKSKgFEILGEFCCKGY 115
                                   *8666555543...344455544**********96 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00032
                  Flavodoxin_3 145 asHPdeeDlekakevv 160
                                   ++HP+e+D++kake++
  gi|15668473|ref|NP_247271.1| 129 KNHPNEDDIKKAKEFA 144
                                   58************97 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   1.2e-15     7e-12       1      82 [.       4      81 ..       4     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.2e-15
                  Flavodoxin_5  1 lilYsS.rdGqTkkiaeriaeelreegelvdvedvekesedlesydavvigasvyygkllpelakFvekhreaLstkpvalfs 82
                                  lilY+S ++ +T+kia++ia+el   ++++++++v  + + +e+yd + +g+++y gk+++++ kF++k   + ++k +++ +
  gi|15668473|ref|NP_247271.1|  4 LILYKSiHHKNTEKIAKTIADELN--ADIYNIDKV--SPDIIENYDLIGFGSGIYFGKHHKSIFKFLDKIS-KTNKKAFIFST 81
                                  799*9967789*************..779999999..6789***************************855.44445554444 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   4.3e-07    0.0026       1     123 [.       5     108 ..       5     142 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-07
                                   EEEETSSS.HHHHHHHHHHHHHHHTTTEEEEEEEEGTTSCGGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHHHHHCHHG CS
                  Flavodoxin_1   1 ilYgSetG.nteklAkqlaeelgehgfnadvvslsdydeslseieeealllvvtsTfgnGdppengesffqdllelkgdel 80 
                                   ilY S    ntek+Ak++a+el+     ad++++++++  ++ ie+++l+ ++    + G+            +  + d+ 
  gi|15668473|ref|NP_247271.1|   5 ILYKSIHHkNTEKIAKTIADELN-----ADIYNIDKVS--PDIIENYDLIGFGSG-IYFGKHHKS--------IFKFLDKI 69 
                                   6777765428************9.....589*******..679999998877755.777755522........22221211 PP

                                   CCSTTTTEEEEEEEEECTTSSSTT..HHHHHHHHHHHHTTCEEES CS
                  Flavodoxin_1  81 edgdlsgvrfavfglGdsayenFc..aagkkldekleelGaerll 123
                                   +  + +++ f     +++a+ +F   ++ k+l +kl+ +G+e+l+
  gi|15668473|ref|NP_247271.1|  70 S--KTNKKAFI----FSTAGFPFLksMFHKELRDKLKSKGFEILG 108
                                   2..12233332....233333333114566777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 981.98
//
Query:       gi|15668474|ref|NP_247272.1|  [L=389]
Description: hypothetical protein MJ_0299 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.3e-181  602.8   0.0   2.6e-181  602.6   0.0    1.0  1  FBPase_3  Fructose-1,6-bisphosphatase


Domain annotation for each model (and alignments):
>> FBPase_3  Fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  602.6   0.0  1.5e-185  2.6e-181       1     360 [.       8     366 ..       8     367 .. 1.00

  Alignments for each domain:
  == domain 1  score: 602.6 bits;  conditional E-value: 1.5e-185
                      FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafkeate 81 
                                   kvt+svikaDvG+l+Ght + +elle++e vleea ++ +++d+yvt++GDDi+lim+h+ g dne+vh+law af+eat+
  gi|15668474|ref|NP_247272.1|   8 KVTISVIKADVGGLCGHTLAPDELLEACEAVLEEAVDE-IILDYYVTRCGDDIDLIMSHKLGCDNEKVHGLAWRAFEEATK 87 
                                   89**********************************98.****************************************** PP

                      FBPase_3  82 vakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGlvidpklhe 162
                                   vakelklygaGqDlL+d+fsGnv+G+GPg+ae+ef eRksep+vvf++Dkt+p+afn+pl+k+fadpfntaGlv dp++ +
  gi|15668474|ref|NP_247272.1|  88 VAKELKLYGAGQDLLADSFSGNVRGMGPGCAEMEFVERKSEPIVVFCCDKTDPTAFNYPLFKMFADPFNTAGLVFDPSMIS 168
                                   ********************************************************************************* PP

                      FBPase_3 163 GfkfevlDvieekkillsapeelydllallgakeryvikrvyskkdeeiaavvsterlsliaGkYvGkDDPvaivRaqsgl 243
                                   Gfkfev+Dv+ +kk+ l++pee+y llal+g+ e+y+ikrvy+++d+eiaavvste+l+ iaG+YvGkDDPvaivRaqsg+
  gi|15668474|ref|NP_247272.1| 169 GFKFEVHDVVGHKKVFLDTPEEMYMLLALIGDYEKYAIKRVYRRRDNEIAAVVSTEKLNYIAGEYVGKDDPVAIVRAQSGF 249
                                   ********************************************************************************* PP

                      FBPase_3 244 PavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklvgpvDlfddpafdeaRekaaei 324
                                   Pavgevlepfa+ph+v GwmrGsh gplmPv  +da+ptrfdgp r++algfq+++g+l+gp+Dlf+d+ fd+aReka e+
  gi|15668474|ref|NP_247272.1| 250 PAVGEVLEPFANPHFVPGWMRGSHWGPLMPVGEEDATPTRFDGPARIIALGFQVCDGMLIGPNDLFADKGFDKAREKALEM 330
                                   ********************************************************************************* PP

                      FBPase_3 325 adelRrqGpfephrlpeeeleYttlpevleklkerf 360
                                   ad +Rr+Gpf+phrlp+  +eYtt+p+vle l++rf
  gi|15668474|ref|NP_247272.1| 331 ADIIRRMGPFQPHRLPATMMEYTTVPKVLEALEDRF 366
                                   ***********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2491.75
//
Query:       gi|15668475|ref|NP_247273.1|  [L=296]
Description: transcriptional regulator [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-38  132.1   0.0    2.1e-38  131.8   0.0    1.1  1  LysR_substrate  LysR substrate binding domain
    1.1e-17   63.7   0.0    3.1e-17   62.3   0.0    1.8  2  HTH_1           Bacterial regulatory helix-turn-helix protein
    3.8e-09   35.9   0.0    2.4e-07   30.1   0.0    2.2  1  PBP_like        PBP superfamily domain
      4e-05   23.4   0.0    0.00012   21.8   0.0    1.7  1  PBP_like_2      PBP superfamily domain
     0.0016   18.3   0.3     0.0061   16.4   0.0    2.1  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0017   17.9   0.1     0.0097   15.5   0.0    2.4  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.002   18.2   0.0     0.0092   16.0   0.0    2.1  2  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.021   14.8   0.6       0.22   11.5   0.0    2.7  3  HTH_11          HTH domain
      0.025   15.0   0.1      0.053   14.0   0.1    1.7  1  HTH_40          Helix-turn-helix domain
      0.045   13.4   0.2      0.045   13.4   0.2    2.7  3  HTH_50          Helix-turn-helix domain
        0.1   12.1   0.0        0.2   11.2   0.0    1.5  1  Sigma70_r4      Sigma-70, region 4
        0.1   12.5   0.1       0.37   10.7   0.0    2.0  2  MarR            MarR family
       0.13   12.1   0.0        2.2    8.2   0.0    2.5  2  MarR_2          MarR family
       0.17   11.7   0.2         10    6.0   0.0    3.0  3  FtsK_gamma      Ftsk gamma domain
       0.29   10.9   1.0        2.6    7.9   0.1    2.6  3  HTH_38          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.8   0.0   1.7e-41   2.1e-38       2     205 ..      89     294 ..      88     296 .] 0.98

  Alignments for each domain:
  == domain 1  score: 131.8 bits;  conditional E-value: 1.7e-41
                                   TTSCEEEEEEEECCCHHHHHHHHHHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEEESSSCCTTEEEEEEEEEEEEE CS
                LysR_substrate   2 gglrgrLrigapptlaryllppllarfraryPevelelvegdseelldllaegelDlairagppedsglearpLaeeplvl 82 
                                   + ++g +ri a++t ++++lp ++++++  y +v++e++ +dse++ ++l+eg +D+a + g +   ++e++ +++++lvl
  gi|15668475|ref|NP_247273.1|  89 ENPEGIIRIYASTTPGEHILPSIIKEYKSSYKNVDFEITITDSERCFKALDEGLADIAAV-GYLKNKNYEYTIIGKDRLVL 168
                                   6799******************************************************88.99999999************ PP

                                   EEETTSGGGGSSSECGGGGCTSEEEEESTTSTHHHHHHHHHHCTTEEC...EEEEEESSHHHHHHHHHTTS-BEEEEGGGH CS
                LysR_substrate  83 vaspdhpLargepvsledLadeplilleegsglrdlledalreaglkp...rvalevnsleallalvaaGlGiallprsav 160
                                   +++p+hpLa++    led+ +e+ i +eegsg+r+++ +al ++g ++   +v++++ s +a++ +v+ G G++++++  +
  gi|15668475|ref|NP_247273.1| 169 IVPPNHPLAEKGTAKLEDILKEDYIDREEGSGTREAFIKALNDKGYSImdlNVVMRLGSHSAVITAVSEGYGVSVVSEIPA 249
                                   **********99**********************************99999****************************** PP

                                   HCCCHTTTEEEEEESSTTCEEEEEEEEETTCCCHHHHHHHHHHHH CS
                LysR_substrate 161 rdeladgrlvalplpepplprelylvyrkgrelspavrafidflr 205
                                   +++ ++g ++++p+ ++++ r lylv  ++   ++av+ f++f++
  gi|15668475|ref|NP_247273.1| 250 KKAEDAGLIKIVPVVDLDVVRYLYLVKSRRPKNPSAVKSFWEFVT 294
                                   *******************************************97 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   2.6e-20   3.1e-17       4      60 .]       8      64 ..       5      64 .. 0.96
   2 ?   -2.6   0.0       4.6   5.5e+03      35      51 ..     182     198 ..     181     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.6e-20
                                  HHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSEEEE-HHHH CS
                         HTH_1  4 lrlfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfeRtgrglrLTeaGe 60
                                  +++f+   +++sf++AA++Lg++q +vs +i++LE+ ++++Lf Rt  g+ LT++G+
  gi|15668475|ref|NP_247273.1|  8 FQTFIVASKTKSFSKAAKRLGITQGTVSNHISALEKYFDAQLFLRTPEGVDLTPEGK 64
                                  689****************************************************95 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.6
                                   HHHHHHHTS-SEEESSS CS
                         HTH_1  35 krLEeelgvpLfeRtgr 51 
                                   ++LE+ l+++ ++R  +
  gi|15668475|ref|NP_247273.1| 182 AKLEDILKEDYIDREEG 198
                                   58999999998888554 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0     2e-10   2.4e-07       3     192 ..     114     293 ..     112     294 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2e-10
                                   HHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS- CS
                      PBP_like   3 elaeknpgvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkki 83 
                                   e++   ++v ++++ + s   +kal +g adia++  l+ +  ey +                  ++   l+v ++ p++ 
  gi|15668475|ref|NP_247273.1| 114 EYKSSYKNVDFEITITDSERCFKALDEGLADIAAVGYLKNKNYEYTII--G--------------KDRLVLIVPPNHPLAE 178
                                   566667788888888888888888888888888888888755444443..2..............2334456666666655 PP

                                   -BGGGC-S.-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCCETTCCECCCGG-HCCCCCCEC CS
                      PBP_like  84 tnwkdlad.aplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVaagradvgvgieavaeelkgldf 163
                                   ++ ++l d  +  ++ Re+GSGtr  f ++l+++g s ++++ +     sh+av +aV+ g +   v+  +++ ++++ + 
  gi|15668475|ref|NP_247273.1| 179 KGTAKLEDiLKEDYIDREEGSGTREAFIKALNDKGYSIMDLNVVM-RLGSHSAVITAVSEGYGVSVVSEIPAK-KAEDAGL 257
                                   55555533355578*****************************95.9*************9876655544444.4555555 PP

                                   T...TCE-...EEEEEEEECTCCCSH.HHHHHHHHH CS
                      PBP_like 164 v...plae...erydlvvrkealddp.evqaflefl 192
                                   +   p+ +    ry ++v+ ++ + p +v++f ef+
  gi|15668475|ref|NP_247273.1| 258 IkivPVVDldvVRYLYLVKSRRPKNPsAVKSFWEFV 293
                                   422233335556776666666666542677777775 PP

>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     1e-07   0.00012      12     189 ..      95     238 ..      85     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1e-07
                    PBP_like_2  12 ifgaGsttp.apalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangaggliqvpva 91 
                                   i++ +sttp + +l   ++ +++++++++++++ t+S  + kal +g +d+a++   l+++ + +           ++ ++
  gi|15668475|ref|NP_247273.1|  95 IRIYASTTPgEHILPSIIKEYKSSYKNVDFEITITDSERCFKALDEGLADIAAVG-YLKNKNY-E-----------YTIIG 162
                                   55555555516778889999********************************999.8888877.2...........45666 PP

                    PBP_like_2  92 igaialvvnkdnpln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqgpwtasgigasgse 171
                                    + ++l+v+++ pl    ++ L++I++                   ++ r++gsgt+++f +al+++g       +  ++ 
  gi|15668475|ref|NP_247273.1| 163 KDRLVLIVPPNHPLAeKGTAKLEDILKE-----------------DYIDREEGSGTREAFIKALNDKG------YS-IMDL 219
                                   *************************773.................599*****************992......22.2234 PP

                    PBP_like_2 172 gvasav.snngaigyvsva 189
                                    v++++ s+   i+ vs +
  gi|15668475|ref|NP_247273.1| 220 NVVMRLgSHSAVITAVSEG 238
                                   4444444444444444444 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.1e-06    0.0061      13      41 ..      15      43 ..      11      44 .. 0.85
   2 ?   -2.4   0.2       3.8   4.6e+03       6      15 ..      72      81 ..      72      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.1e-06
                                  TSSEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                         HTH_5 13 egelcvcelaeelglsqstvShHLkkLre 41
                                  ++ ++++  a+ lg++q+tvS H ++L++
  gi|15668475|ref|NP_247273.1| 15 SKTKSFSKAAKRLGITQGTVSNHISALEK 43
                                  55677888899****************97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.8
                                  HHHHHHTTSS CS
                         HTH_5  6 kILklLaege 15
                                  kIL lL+e +
  gi|15668475|ref|NP_247273.1| 72 KILDLLNEAK 81
                                  7999999965 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.1e-06    0.0097      24      43 ..      24      43 ..      18      44 .. 0.91
   2 ?   -1.8   0.0       1.9   2.3e+03      39      48 .]     250     259 ..     250     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.1e-06
                        HTH_24 24 AerlglSpstvnrrlkrLee 43
                                  A+rlg++++tv+ ++  Le+
  gi|15668475|ref|NP_247273.1| 24 AKRLGITQGTVSNHISALEK 43
                                  9*****************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.9
                        HTH_24  39 krLeeeGlIk 48 
                                   k+ e++GlIk
  gi|15668475|ref|NP_247273.1| 250 KKAEDAGLIK 259
                                   7889*****7 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.7e-06    0.0092      26      50 ..      19      43 ..      14      49 .. 0.91
   2 ?   -3.0   0.0       6.7     8e+03      49      57 ..     253     261 ..     253     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.7e-06
                                  -HHHHHHHHTS-HHHHHHHHHHHHH CS
                        HTH_20 26 taselaerldlskntlsyHLrvLee 50
                                  ++s  a+rl++++ t+s+H+ +Le+
  gi|15668475|ref|NP_247273.1| 19 SFSKAAKRLGITQGTVSNHISALEK 43
                                  88999******************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.7
                                   HHCTTEEEE CS
                        HTH_20  49 eeagLvevv 57 
                                   e+agL++ v
  gi|15668475|ref|NP_247273.1| 253 EDAGLIKIV 261
                                   78****976 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00018      0.22      22      43 ..      24      45 ..      15      52 .. 0.91
   2 ?   -0.9   0.1       1.4   1.7e+03       1      13 [.      69      81 ..      69      82 .. 0.88
   3 ?   -1.5   0.0       2.1   2.6e+03      36      46 ..     206     216 ..     205     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                        HTH_11 22 AeeLnvSrrtvrrdIkaLeelg 43
                                  A++L+++  tv ++I aLe+  
  gi|15668475|ref|NP_247273.1| 24 AKRLGITQGTVSNHISALEKYF 45
                                  89****************9975 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                        HTH_11  1 RllqilelLlear 13
                                  R+++il lL+ea+
  gi|15668475|ref|NP_247273.1| 69 RAEKILDLLNEAK 81
                                  899******9876 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.1
                        HTH_11  36 IkaLeelgvpI 46 
                                   IkaL+++g+ I
  gi|15668475|ref|NP_247273.1| 206 IKALNDKGYSI 216
                                   89999999877 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.4e-05     0.053       4      63 ..       9      79 ..       6     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                        HTH_40  4 etlelleeglsieeIAkerglkesTIegHLaeliee.........geeidlerl..vseeeekeIeeaiek 63
                                  +t+    + +s+ + Ak+ g++++T+ +H+  l +           e +dl+    +  e++++I + +++
  gi|15668475|ref|NP_247273.1|  9 QTFIVASKTKSFSKAAKRLGITQGTVSNHISALEKYfdaqlflrtPEGVDLTPEgkIFYERAEKILDLLNE 79
                                  6666778899********************99888733333332213344433322455666666665555 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   3.8e-05     0.045      24      43 ..      18      37 ..      13      44 .. 0.88
   2 ?   -1.9   0.1       2.1   2.5e+03      15      26 ..     107     118 ..     105     120 .. 0.73
   3 ?   -0.5   0.0      0.82   9.8e+02      33      42 ..     225     233 ..     221     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-05
                        HTH_50 24 pStRklAkrLGvShtaiank 43
                                  +S+ k+AkrLG+++ ++ n 
  gi|15668475|ref|NP_247273.1| 18 KSFSKAAKRLGITQGTVSNH 37
                                  8999*************986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                        HTH_50  15 likkayekYpSt 26 
                                   ++ + +++Y+S+
  gi|15668475|ref|NP_247273.1| 107 ILPSIIKEYKSS 118
                                   566778899987 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.82
                        HTH_50  33 LGvShtaian 42 
                                   LG Sh+a++ 
  gi|15668475|ref|NP_247273.1| 225 LG-SHSAVIT 233
                                   55.9****96 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00016       0.2      21      41 ..      18      38 ..      10      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                                  --HHHHHHHHTS-HHHHHHHH CS
                    Sigma70_r4 21 lTleEIgerlgiSrerVrqie 41
                                   +++  ++rlgi++++V+ ++
  gi|15668475|ref|NP_247273.1| 18 KSFSKAAKRLGITQGTVSNHI 38
                                  58999************9876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00031      0.37      20      43 ..      20      43 ..      14      44 .. 0.88
   2 ?   -3.1   0.0       6.4   7.7e+03      13      31 ..     177     195 ..     176     196 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                                  HHHHHHHHTS-HHHHHHHHHHHHH CS
                          MarR 20 vseLakklgvskstvtrvldrLek 43
                                   s+ ak+lg++++tv++ + +Lek
  gi|15668475|ref|NP_247273.1| 20 FSKAAKRLGITQGTVSNHISALEK 43
                                  56669******************8 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.4
                                   HHSTTEEHHHHHHHHTS-H CS
                          MarR  13 yeqgplsvseLakklgvsk 31 
                                   +e+g +++ ++ k  ++++
  gi|15668475|ref|NP_247273.1| 177 AEKGTAKLEDILKEDYIDR 195
                                   6777788888877777664 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0019       2.2      24      47 ..      20      43 ..      11      43 .. 0.87
   2 ?    0.6   0.0      0.44   5.3e+02      43      55 ..     250     262 ..     248     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                                  HHHHHHHHTSSHHHHHHHHHHHHH CS
                        MarR_2 24 vgelarrlglsksavsrilkrLva 47
                                   +  a+rlg+++++vs+++  L++
  gi|15668475|ref|NP_247273.1| 20 FSKAAKRLGITQGTVSNHISALEK 43
                                  67789*************999985 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.44
                                   HHHHHTTSEEEEE CS
                        MarR_2  43 krLvaaGLverrp 55 
                                   k++++aGL+  +p
  gi|15668475|ref|NP_247273.1| 250 KKAEDAGLIKIVP 262
                                   89*******8765 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.35   4.2e+02      11      44 ..       9      42 ..       1      44 [. 0.77
   2 ?    6.0   0.0    0.0086        10      30      52 ..      64      86 ..      62      95 .. 0.81
   3 ?    0.7   0.0      0.39   4.6e+02      42      62 ..     186     206 ..     181     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.35
                    FtsK_gamma 11 velvveegkaStSllQRrlriGYnRAarlidqLe 44
                                    ++v +++ S S   +rl i     ++ i +Le
  gi|15668475|ref|NP_247273.1|  9 QTFIVASKTKSFSKAAKRLGITQGTVSNHISALE 42
                                  5789999999***999999998776666666666 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0086
                    FtsK_gamma 30 riGYnRAarlidqLeeeGiVgpa 52
                                  +i Y RA +++d L e+++   a
  gi|15668475|ref|NP_247273.1| 64 KIFYERAEKILDLLNEAKLLMRA 86
                                  577************99887655 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.39
                    FtsK_gamma  42 qLeeeGiVgpaegskpReVli 62 
                                   ++ +e ++  +egs+ Re +i
  gi|15668475|ref|NP_247273.1| 186 DILKEDYIDREEGSGTREAFI 206
                                   5557789**********9776 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0022       2.6      19      41 ..      16      38 ..      12      39 .. 0.89
   2 ?   -3.4   0.0       7.4   8.8e+03      12      25 ..      72      86 ..      71      87 .. 0.60
   3 ?    0.5   0.0      0.44   5.2e+02       5      27 ..     126     146 ..     125     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0022
                        HTH_38 19 eGlslreIArrLgrspsTIsREl 41
                                  + +s+++ A+rLg   +T+s+++
  gi|15668475|ref|NP_247273.1| 16 KTKSFSKAAKRLGITQGTVSNHI 38
                                  558999**************987 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.4
                        HTH_38 12 eIerlla.eGlslre 25
                                  +I +ll+ ++l +r+
  gi|15668475|ref|NP_247273.1| 72 KILDLLNeAKLLMRA 86
                                  788998624455555 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.44
                        HTH_38   5 LsleeReeIerllaeGlslreIA 27 
                                   +++++ e++ + l+eGl  ++IA
  gi|15668475|ref|NP_247273.1| 126 ITITDSERCFKALDEGL--ADIA 146
                                   58889999999999998..6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 1735.70
//
Query:       gi|15668476|ref|NP_247274.1|  [L=294]
Description: hypothetical protein MJ_0301 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-11   43.4   0.0    8.3e-11   42.3   0.0    1.8  1  Lactamase_B    Metallo-beta-lactamase superfamily
      5e-08   32.7   0.0    7.7e-08   32.1   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0017   17.8   0.0     0.0047   16.4   0.0    1.7  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.028   14.3   0.0      0.044   13.7   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
      0.037   14.4   0.0      0.075   13.5   0.0    1.4  1  BAF            Barrier to autointegration factor


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   2.3e-14   8.3e-11       7      83 ..      33     113 ..      30     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 2.3e-14
                                   EEEEEE...ET.TCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHC..CEETCCEHHHHC CS
                   Lactamase_B   7 nsylie...gd.ggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatd..vpvgavaeeapa 81 
                                    s+lie   ++ ++ iL+Dt t +e  ++   +++l ++pk +d +il+H H+DH+Ggl g++++ +  +p++a++ + ++
  gi|15668476|ref|NP_247274.1|  33 LSFLIEvesNGiKKRILFDTATYAEPILFN--MKLLNINPKSIDMIILSHNHFDHTGGLFGIMKEINkeIPIFAHPNIFKV 111
                                   5788888885559****************6..8*******************************98722444444444444 PP

                                   CH CS
                   Lactamase_B  82 lf 83 
                                    f
  gi|15668476|ref|NP_247274.1| 112 SF 113
                                   44 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   2.2e-11   7.7e-08       2      68 ..      47     110 ..      46     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2.2e-11
                                   EEEES--TTHHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH CS
                 Lactamase_B_2   2 riLiDagpdlrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla 68 
                                   riL+D+ +     a++ l + + l  ++++id+++l+h+H+DH+ gl  + +  +k++p++a++ + +
  gi|15668476|ref|NP_247274.1|  47 RILFDTATY----AEPILFNMKlLNINPKSIDMIILSHNHFDHTGGLFGIMKEINKEIPIFAHPNIFK 110
                                   889998888....2444444555778899***********************66788******98766 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-06    0.0047       8      77 ..      47     110 ..      36     135 .. 0.75
   2 ?   -1.9   0.0      0.53   1.9e+03      48      90 ..     232     273 ..     228     287 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-06
                 Lactamase_B_6   8 kiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvk 77 
                                   +iL D ++  + + +   +k l+   +++d+i+Lsh   +h G++  +++    ++ ++ip++a   ++k
  gi|15668476|ref|NP_247274.1|  47 RILFDTATYAEPILF--NMKLLNINPKSIDMIILSHNHFDHTGGLFGIMK----EINKEIPIFAHPNIFK 110
                                   677777777664444..35555556789****************755554....5678999999877766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.53
                 Lactamase_B_6  48 hlGayallyakfksklllnipvyatlpvvkLGrvslldlyask 90 
                                   ++G++  l+ + +++++++i++   l v+k+    ++   a++
  gi|15668476|ref|NP_247274.1| 232 VIGGFH-LIDADNERIVSTIKALKKLGVKKICTGHCTGFKAEN 273
                                   678874.555556778888888888777777665555555544 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05     0.044       9      50 ..      34      86 ..      19     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                 Lactamase_B_3  9 sfllet..ag..arilvDPf.......kanlgyeppaeeaDlvlisqaledHa 50
                                  sfl+e+  +g  +ril D         ++ + ++++++++D++++s+++ dH 
  gi|15668476|ref|NP_247274.1| 34 SFLIEVesNGikKRILFDTAtyaepilFNMKLLNINPKSIDMIILSHNHFDHT 86
                                  5666653235556777775555555543355667777***************6 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.1e-05     0.075      24      65 ..     211     252 ..     208     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                           BAF  24 aGigevlgkkLeekGfdkAyvvlgqfLvlkkdeelFkewlke 65 
                                   +Gi ++++k+++ +G++k y v+g f +++ d+e+  + +k 
  gi|15668476|ref|NP_247274.1| 211 PGIVSMVKKSIKISGINKVYAVIGGFHLIDADNERIVSTIKA 252
                                   89*******************************998888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1923.25
//
Query:       gi|15668477|ref|NP_247275.1|  [L=95]
Description: phosphoribosyl-ATP pyrophosphatase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-21   74.1   1.2      1e-20   74.0   1.2    1.0  1  PRA-PH           Phosphoribosyl-ATP pyrophosphohydrolase
     0.0057   17.0   0.6     0.0075   16.6   0.6    1.2  1  mCpol            minimal CRISPR polymerase domain
     0.0069   16.5   2.8     0.0069   16.5   2.8    2.3  2  MazG             MazG nucleotide pyrophosphohydrolase domain
  ------ inclusion threshold ------
       0.01   15.7   1.9      0.032   14.1   1.9    1.7  1  PIN_8            PIN like domain
       0.01   15.4   0.3      0.011   15.2   0.3    1.0  1  Diphthami_syn_2  Diphthamide synthase


Domain annotation for each model (and alignments):
>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   1.2   2.8e-24     1e-20       1      82 [.       3      93 ..       3      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 2.8e-24
                                  HHHHHHHCT----SS----.-HHHHHH........HHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CHH CS
                        PRA-PH  1 vkefhrligerkpetPeas.taelasl........raaligEEavElleaasegdlaeladelaDllYvtygllvllGidlda 74
                                  ++e++++i++r++e+Pe+s  a+l ++        ++++igEE++El+ aa+++++ e+++e+aDl+++t++ll++++i++++
  gi|15668477|ref|NP_247275.1|  3 LEEVYEIIKQRIKEKPEGSyVAKLTTDdkktainkICEKIGEESTELILAAKDDKKDEIIYEAADLIFHTMVLLAYKNIEFEE 85
                                  5799**********************9******************************************************** PP

                                  HHHHHHHH CS
                        PRA-PH 75 vfeevhra 82
                                  +++e++r+
  gi|15668477|ref|NP_247275.1| 86 LLKEFERR 93
                                  ******98 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.6   2.1e-06    0.0075      10      78 ..      20      88 ..      19      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-06
                         mCpol 10 GkklealllsndeeeleklskevkeaikklkkllkdelgasvifaaGDsilakssleedllvelsrvyq 78
                                  G ++ +l  +++  +++k+ +++ e++ +l  + kd  + ++i++a+D i  +  l + + +e++++++
  gi|15668477|ref|NP_247275.1| 20 GSYVAKLTTDDKKTAINKICEKIGEESTELILAAKDDKKDEIIYEAADLIFHTMVLLAYKNIEFEELLK 88
                                  6778888999999***********************************998877666666666665555 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.4     0.029   1.1e+02      10      20 ..       2      12 ..       1      27 [. 0.79
   2 !   16.5   2.8   1.9e-06    0.0069       6      61 ..      38      89 ..      33      95 .] 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.029
                                  HHHHHHHHHHH CS
                          MazG 10 lleEvgEvaea 20
                                  +leEv+E++ +
  gi|15668477|ref|NP_247275.1|  2 ILEEVYEIIKQ 12
                                  79*****9864 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.9e-06
                                  HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHH CS
                          MazG  6 llaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidledvaet 61
                                  + + + eE  E++ a k +++de+  E +D++++ + l       ++i++e+ +++
  gi|15668477|ref|NP_247275.1| 38 ICEKIGEESTELILAAKDDKKDEIIYEAADLIFHTMVLLAY----KNIEFEELLKE 89
                                  667899*****************************999997....99999987765 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.9   8.8e-06     0.032      88     162 ..      21      94 ..       1      95 [] 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.8e-06
                         PIN_8  88 kaldteelrkelkkqleelkeelkaeleelkksskadkeedpilkkleellegkigealskeeleelvkegekRy 162
                                    ++ ++ + ++ k++++++ e++ +e++el  + k+dk+++ i+++ + +++  +  a+++ e+eel+ke e+R 
  gi|15668477|ref|NP_247275.1|  21 SYV-AKLTTDDKKTAINKICEKIGEESTELILAAKDDKKDEIIYEAADLIFHTMVLLAYKNIEFEELLKEFERRK 94 
                                   233.57788899999********999999999999998877788888888***********************95 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.3   3.2e-06     0.011      78     152 ..      10      87 ..       2      94 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-06
               Diphthami_syn_2  78 kgtlkkldveavviGaieseyqksriervCrelGlksvaPLW...kkdpeelleeiveekfevivvavkaegldeslL 152
                                    ++  k + e+ ++ +++++ +k+ i+++C+++G  s   +    + + +e++ e  +  f+ +v+  +++   e+lL
  gi|15668477|ref|NP_247275.1|  10 IKQRIKEKPEGSYVAKLTTDDKKTAINKICEKIGEESTELILaakDDKKDEIIYEAADLIFHTMVLLAYKNIEFEELL 87 
                                   444344467899999*******************88764433110333456788889999*****9999888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1141  (0.0636399); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 583.26
//
Query:       gi|15668478|ref|NP_247276.1|  [L=141]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-34  118.7   0.7    1.9e-34  118.5   0.7    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.5   0.7   1.1e-38   1.9e-34       3     140 ..       6     136 ..       4     137 .. 0.93

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 1.1e-38
                                   EEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHHHH CS
                 DMRL_synthase   3 riaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfeyva 83 
                                   ++++V a+fn++it  + + a ++++ +g++      + VPG+f++pla+kkl+e+ + +dav+++G+vi+Get+h+e+v+
  gi|15668478|ref|NP_247276.1|   6 NLGFVIAEFNRDITYMMEKVAEEHAEFLGAT--VKYKIVVPGVFDMPLAVKKLLEK-DDVDAVVTIGCVIEGETEHDEIVV 83 
                                   6899*************************75..555667****************5.447********************* PP

                                   HHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHHHHHHHHH CS
                 DMRL_synthase  84 eavskglmrvsldtgvPvifgvltvd.teeqaleraggkagnkGeeaaeaalemanll 140
                                   +++++++++++l++++Pv+ g+  +  t+ qa+er+     ++G++a+eaa++m++ l
  gi|15668478|ref|NP_247276.1|  84 HNAARKIADLALQYDKPVTLGISGPGmTRLQAQERV-----DYGKRAVEAAVKMVKRL 136
                                   **************************9*********.....9************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 959.95
//
Query:       gi|15668479|ref|NP_247277.1|  [L=159]
Description: ferripyochelin binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-23   79.7  24.7    1.1e-11   44.0   2.0    4.2  4  Hexapep      Bacterial transferase hexapeptide (six repeats)
    1.6e-10   40.6  17.0    5.5e-08   32.4   5.5    3.8  4  Hexapep_2    Hexapeptide repeat of succinyl-transferase
     0.0037   16.3   2.1      0.027   13.4   1.6    2.3  2  Fucokinase   L-fucokinase
  ------ inclusion threshold ------
        1.2    7.2   5.4          1    7.4   4.1    1.5  1  DUF4954      Domain of unknown function (DUF4954)


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   1.3   8.9e-11     4e-07       4      36 .]       2      34 ..       1      34 [. 0.95
   2 !    6.6   0.8    0.0015       6.9      20      35 ..      39      54 ..      36      55 .. 0.81
   3 !   15.4   0.8   2.5e-06     0.011      19      36 .]      60      77 ..      58      77 .. 0.87
   4 !   44.0   2.0   2.4e-15   1.1e-11       1      35 [.      77     111 ..      77     112 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 8.9e-11
                                  EETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                       Hexapep  4 IGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36
                                  I +nv I ++avi g+V+IGd++ ++ ++vi+g
  gi|15668479|ref|NP_247277.1|  2 ISKNVRIAKGAVIVGDVTIGDYSSVWYNAVIRG 34
                                  678****************************97 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0015
                                  EEE-TTEEEETTEEEE CS
                       Hexapep 20 VkIGdnvkIgagvvig 35
                                  ++IG+++ I  ++v++
  gi|15668479|ref|NP_247277.1| 39 IIIGNYSNIQDCCVVH 54
                                  7899999999999985 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 2.5e-06
                                  TEEE-TTEEEETTEEEES CS
                       Hexapep 19 nVkIGdnvkIgagvvigg 36
                                  +++IGd+v Ig+g+vi+g
  gi|15668479|ref|NP_247277.1| 60 PTIIGDYVSIGHGAVIHG 77
                                  689999999999999986 PP

  == domain 4  score: 44.0 bits;  conditional E-value: 2.4e-15
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   +++I++nvl+g++a+i++++kIG+n++Iga++ ++
  gi|15668479|ref|NP_247277.1|  77 GCRIEDNVLVGMNATILNGAKIGENCIIGANALVT 111
                                   699*****************************997 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.0     0.012        53       6      23 ..       4      23 ..       2      33 .. 0.78
   2 ?   -0.9   0.8      0.33   1.5e+03      13      21 ..      29      42 ..      18      54 .. 0.56
   3 !   20.5   3.7   6.6e-08    0.0003       1      32 [.      60      92 ..      60      94 .. 0.96
   4 !   32.4   5.5   1.2e-11   5.5e-08       3      33 ..      79     111 ..      77     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.012
                                  TT-EE-TT-EE.S.EEE-TT CS
                     Hexapep_2  6 dnCliGanagi.G.vslGdn 23
                                  +n+ i + a+i G v++Gd 
  gi|15668479|ref|NP_247277.1|  4 KNVRIAKGAVIvGdVTIGDY 23
                                  78888899997755****95 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.33
                                  T-EE.S....EEE- CS
                     Hexapep_2 13 nagi.G....vslG 21
                                  na+i G    +++G
  gi|15668479|ref|NP_247277.1| 29 NAVIrGdvdkIIIG 42
                                  44444333344444 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 6.6e-08
                                  .EEE-TT-EE-TT-EE.SEEE-TT-EE-TT-EE CS
                     Hexapep_2  1 pviIGdnCliGanagi.GvslGdncvvgaGvvi 32
                                  p+iIGd + iG  a+i G  ++dn+ vg++ +i
  gi|15668479|ref|NP_247277.1| 60 PTIIGDYVSIGHGAVIhGCRIEDNVLVGMNATI 92
                                  89****************************988 PP

  == domain 4  score: 32.4 bits;  conditional E-value: 1.2e-11
                                   EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
                     Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvvit 33 
                                   +I+dn+l+G na+i  G ++G+nc++ga+  +t
  gi|15668479|ref|NP_247277.1|  79 RIEDNVLVGMNATIlnGAKIGENCIIGANALVT 111
                                   7****************************9998 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2     0.042   1.9e+02     279     315 ..      12      52 ..       2      59 .. 0.75
   2 !   13.4   1.6     6e-06     0.027     279     326 ..      61     118 ..      36     141 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.042
                    Fucokinase 279 Svlessvsvg.egsviehsslkgnvs...igsnsivsglel 315
                                   +v+ ++v++g  +sv+++  ++g+v+   ig+ s + ++++
  gi|15668479|ref|NP_247277.1|  12 AVIVGDVTIGdYSSVWYNAVIRGDVDkiiIGNYSNIQDCCV 52 
                                   46778888884467889999997666666999999999876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6e-06
                    Fucokinase 279 Svlessvsvgegsviehsslkgnvsigsns.ivsglelessee..........slelpd 326
                                   +++  +vs+g g+vi  +++++nv +g n  i+ g ++ ++ +          + e+p 
  gi|15668479|ref|NP_247277.1|  61 TIIGDYVSIGHGAVIHGCRIEDNVLVGMNAtILNGAKIGEN-CiiganalvtqNKEIPP 118
                                   4789999*********9999999999977515556666543.43444444444444444 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.1   0.00023         1     198     265 ..      40     104 ..       1     121 [. 0.59

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00023
                       DUF4954 198 tiegasklengt.inSskeapveiGegViledfiissGskikdgavi.srcfvGqavklkkqfsaedsll 265
                                    i + s+++++  ++ sk  p+ iG+ V +  + + +G++i+d +++ +++ + ++ k++     e++++
  gi|15668479|ref|NP_247277.1|  40 IIGNYSNIQDCCvVHCSKGYPTIIGDYVSIGHGAVIHGCRIEDNVLVgMNATILNGAKIG-----ENCII 104
                                   344555555554145667778888888888888888888888766542222222222222.....22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 965.91
//
Query:       gi|15668480|ref|NP_247278.1|  [L=395]
Description: hypothetical protein MJ_0305 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-69  233.4  25.2    4.3e-69  233.4  25.2    1.7  2  Voltage_CLC  Voltage gated chloride channel
     0.0088   16.3   5.3       0.52   10.6   0.1    2.9  2  DUF3522      Protein of unknown function (DUF3522)


Domain annotation for each model (and alignments):
>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.4   0.5    0.0081        72     305     351 ..      16      62 ..       4      64 .. 0.73
   2 !  233.4  25.2   4.8e-73   4.3e-69       2     352 ..      55     384 ..      54     386 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0081
                                   HHHHCCTHHHHHCCS-HHHHHHHHHHCC--GCCHHHHHHHHHHHHHH CS
                   Voltage_CLC 305 falvGmaaflagvtrapltaiviviEltgdlelllplmlavliAkav 351
                                   +  +G a++ + v +++  +i+i+iE + + + +l + ++ +iA ++
  gi|15668480|ref|NP_247278.1|  16 IKWIGIASLIGIVGGLSSVIIAIIIEYFPEKHNVLLIPIVFFIAGLF 62 
                                   55678888888888888888888888888777777777777777655 PP

  == domain 2  score: 233.4 bits;  conditional E-value: 4.8e-73
                                   HHHHHHHCCCCC-GGGSC-SHHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHHHTT.- CS
                   Voltage_CLC   2 ggllagllvklvapeaagsGipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsrllkls 82 
                                   ++++agl+v ++  e +gsGi+ v +aln ++ +l++   l+k+l+   +++ G+s+G+eGp+vq +A+++  l rllkl+
  gi|15668480|ref|NP_247278.1|  55 VFFIAGLFVDYI-YELKGSGIDRVLKALNTNE-KLTWIRGLLKVLLAGAVIAVGGSAGKEGPCVQSSASFADELYRLLKLK 133
                                   678999999999.9***************776.599999999*************************************74 PP

                                   -SHHHHHHHHHHHHHHHHHHHT-HHHHHHHHCTT.TSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S-.T---...--GG CS
                   Voltage_CLC  83 rndrdrrlvaaGaAAGiAAaFnaPlgGvlfalEe.vsrefslrallpvfvasvvaalvlrlllgeepafgeveslfalsll 162
                                     + ++ ++++G+A+G++ aF+aPlg +++a+E+  +++f++ +l+p ++asvv++l++ l+ g ++ f+ ++  ++++++
  gi|15668480|ref|NP_247278.1| 134 --N-RELVIITGIAGGLGGAFSAPLGTAILACEIiEHENFNYINLIPPIIASVVGYLIFYLITGRKHLFN-ITLSYTINIH 210
                                   ..3.468***************************66799******************************9.99889***** PP

                                   GHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC.CSSSSCCHHHHHCTT-S-HH CS
                   Voltage_CLC 163 elilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgllvgllglllpasvlgggyeliasllegstlll 243
                                   +++lf+l ++++ l++++++++++k++++f++l   ki+  ++ +++g+lv+++++++p+ v+g+g +l+++l+  +   +
  gi|15668480|ref|NP_247278.1| 211 DFLLFILGAFFCSLIAHCYIKTYRKISSTFDNL---KIPYCIKTLIGGILVAVISYFIPE-VMGMGLTLTKELFIME---F 284
                                   ********************************9...998777******************.*************887...9 PP

                                   HHHH...HHHHHHHHHHHHHCTT-CSBSHHHHHHHHHHHHHHHHHHHHHH-CTSSC...HHHHHHCCTHHHHHCCS-HHHH CS
                   Voltage_CLC 244 sllllllllllkllataltlgsgvpgGifaPsLviGAalGrlvglvlalllpgaassdpgafalvGmaaflagvtraplta 324
                                   sl++l+lll+ k+lat++t+gsg pgG+++Ps+ iGA+ G ++g +++           + ++++G a +l+++t+apl  
  gi|15668480|ref|NP_247278.1| 285 SLVFLVLLLIGKILATSFTVGSGTPGGLVFPSMCIGAISGIIFGSLIGDC--------SAPYIVLGIATTLSATTNAPLGG 357
                                   ********************************************999888........256******************** PP

                                   HHHHHHCC--GCCHHHHHHHHHHHHHHH CS
                   Voltage_CLC 325 iviviEltgdlelllplmlavliAkava 352
                                   +v+ +E++g +++++p  ++++i + ++
  gi|15668480|ref|NP_247278.1| 358 AVLCTEIFG-FDFAVPASIGAVIGYQMT 384
                                   *********.*************99876 PP

>> DUF3522  Protein of unknown function (DUF3522)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   5.8e-05      0.52      97     162 ..      33      99 ..      27     109 .. 0.71
   2 !    5.6   2.0    0.0019        17      86     166 ..     178     255 ..     155     269 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.8e-05
                       DUF3522  97 lllvailqekdrwslantiipilvgllillvswliecvkkrkl.ypsllrrrlkrlnlqqllpglll 162
                                    +++ai++e+ + +  +++ipi++ ++ l+v +++e++ +    + ++l+++ k ++ + ll+ ll+
  gi|15668480|ref|NP_247278.1|  33 SVIIAIIIEYFPEKHNVLLIPIVFFIAGLFVDYIYELKGSGIDrVLKALNTNEKLTWIRGLLKVLLA 99 
                                   6899*****************************9998765432233334444444444444444433 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0019
                       DUF3522  86 eklksllhylglllvailqekdrwslantiipilvgllillvswliecvkkrklypsllrrrlkrlnlqqllpgllllalA 166
                                   + + s++ yl++ l+   +++    l++ti    + l+il +++   c+   ++y +++r+ ++++ + ++ +++ +l+ +
  gi|15668480|ref|NP_247278.1| 178 PIIASVVGYLIFYLITGRKHLFNITLSYTINIHDFLLFILGAFF---CSLIAHCYIKTYRKISSTFDNLKIPYCIKTLIGG 255
                                   33334444444444444444444444444444334444444444...5555556666555555555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 2339.77
//
Query:       gi|15668481|ref|NP_247279.1|  [L=78]
Description: hypothetical protein MJ_0306 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 498.06
//
Query:       gi|15668482|ref|NP_247280.1|  [L=85]
Description: thioredoxin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-18   66.1   1.5    2.4e-18   66.0   1.5    1.0  1  Thioredoxin_3   Thioredoxin domain
    4.5e-13   49.2   0.1    6.5e-13   48.7   0.1    1.2  1  Glutaredoxin    Glutaredoxin
    6.3e-11   42.2   0.1    7.4e-11   42.0   0.1    1.0  1  Thioredoxin     Thioredoxin
    1.4e-09   38.3   0.8    0.00022   21.4   0.2    2.0  2  Thioredoxin_4   Thioredoxin
    3.2e-09   36.9   0.1    0.00067   19.5   0.0    2.0  2  DSBA            DSBA-like thioredoxin domain
    1.7e-06   28.2   0.1    0.00012   22.2   0.1    2.0  2  DUF1223         Protein of unknown function (DUF1223)
    7.3e-06   26.3   0.0    8.2e-06   26.2   0.0    1.1  1  DUF836          Glutaredoxin-like domain (DUF836)
    2.5e-05   23.9   0.0      3e-05   23.6   0.0    1.2  1  KaiB            KaiB domain
     0.0044   17.5   0.3     0.0091   16.4   0.3    1.6  1  Thioredoxin_2   Thioredoxin-like domain
  ------ inclusion threshold ------
      0.037   13.7   0.2       0.74    9.5   0.0    2.0  2  Thioredoxin_5   Thioredoxin
      0.038   13.9   0.0      0.042   13.8   0.0    1.1  1  Thioredoxin_6   Thioredoxin-like domain
      0.046   13.2   0.0      0.046   13.2   0.0    1.1  1  ABC_transp_aux  ABC-type uncharacterized transport system
      0.062   12.9   1.0       0.13   11.8   1.0    1.6  1  DUF953          Eukaryotic protein of unknown function (DUF95
       0.15   12.1   0.1       0.66    9.9   0.0    1.8  2  PTPS            6-pyruvoyl tetrahydropterin synthase


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   1.5   1.8e-21   2.4e-18       1      75 [.       4      81 ..       2      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1.8e-21
                                  EEEEEE.SSSSTTCHHHHHHHHHHCHCC.T.CECEEECC.TTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
                 Thioredoxin_3  1 meikvl.gpgCakCpklekavkeaaaek.g.ikaevekv.tdfeeiekygVmsvPalvidgkvvvsGkvpseeeirkll 75
                                  ++i+ + +p C++Cp+++++v+e+a+e+ + +++e+++v +++++ ++yg+m+vP++vi+g v++ G +p++e + + +
  gi|15668482|ref|NP_247280.1|  4 VKIELFtSPMCPHCPAAKRVVEEVANEMpDaVEVEYINVmENPQKAMEYGIMAVPTIVINGDVEFIG-APTKEALVEAI 81
                                  3556644777******************857********8888888*********************.9****998876 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.1     5e-16   6.5e-13       1      59 [.       6      66 ..       6      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 5e-16
                                  EEEEESTSSHHHHHHHHHHHHTT......GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEE CS
                  Glutaredoxin  1 vvlftkptCpyCkkakrlLkelg......vkfeeidvdkdeeireelkelsgvrtvPqvfidgkh 59
                                  ++lft+p+Cp+C++akr+ +e        v++e+i+v+++++   e     g+++vP+++i+g++
  gi|15668482|ref|NP_247280.1|  6 IELFTSPMCPHCPAAKRVVEEVAnempdaVEVEYINVMENPQKAMEY----GIMAVPTIVINGDV 66
                                  79*****************998888889999*********9888888....************86 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.1   5.8e-14   7.4e-11      25     103 .]       9      83 ..       2      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 5.8e-14
                                   EE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHHHHHHHHH CS
                   Thioredoxin  25 FyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegarekeklaaflkk 103
                                   F++p C+hC a + ++e++a+e+ d v +  ++v en++ a +y++ ++Pt+++  ng+   ++ ga +ke+l++ +kk
  gi|15668482|ref|NP_247280.1|   9 FTSPMCPHCPAAKRVVEEVANEMPDAVEVEYINVMENPQKAMEYGIMAVPTIVI--NGD--VEFIGAPTKEALVEAIKK 83 
                                   99**************************************************55..666..679999999999999985 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   1.8e-07   0.00022      14      61 ..       3      48 ..       1      51 [. 0.90
   2 !   19.0   0.1   9.3e-07    0.0012     126     166 .]      42      83 ..      41      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.8e-07
                                  SEEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE-..---S CS
                 Thioredoxin_4 14 pvtvieyedlrCphCakfeeeveklleeyidtGkvkfiirdfpldkek 61
                                  +v+++++++  CphC + ++ ve++ +e    + v++ +++++ +++k
  gi|15668482|ref|NP_247280.1|  3 KVKIELFTSPMCPHCPAAKRVVEEVANEM--PDAVEVEYINVMENPQK 48
                                  899*************************9..99999999999888776 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 9.3e-07
                                   HHHHHHHHHHHT--SS-EEEETTEE.E-TT--HHHHHHHHT- CS
                 Thioredoxin_4 126 veaeskeakkagiestPtfiingek.veepqtyeelkalida 166
                                   v+++ ++a + gi ++Pt++ing + + +++t e+l ++i++
  gi|15668482|ref|NP_247280.1|  42 VMENPQKAMEYGIMAVPTIVINGDVeFIGAPTKEALVEAIKK 83 
                                   7899999****************999999**********985 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.2e-07   0.00067       1      35 [.       5      40 ..       5      43 .. 0.92
   2 !   16.4   0.0   4.7e-06     0.006     153     193 .]      42      82 ..      41      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.2e-07
                                  EEEEEEBTTBHHHHHHHHHHHHHHHHCCT.EEEEEE CS
                          DSBA  1 tvdeffDvlCPyCylgkerleklaarspd.vkvvlr 35
                                  ++++f + +CP+C ++k+++e++a+  pd v+v + 
  gi|15668482|ref|NP_247280.1|  5 KIELFTSPMCPHCPAAKRVVEEVANEMPDaVEVEYI 40
                                  599************************998*99986 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.7e-06
                                   HHHHHHHHHHTT-SSSSEEEETTCEEEESSSSHHHHHHHHH CS
                          DSBA 153 vrentaaaqslgvtGvPtvvvdgkrmvfGadrldtladala 193
                                   v+en ++a ++g+  vPt+v++g + + Ga+  + l +a++
  gi|15668482|ref|NP_247280.1|  42 VMENPQKAMEYGIMAVPTIVINGDVEFIGAPTKEALVEAIK 82 
                                   7899*******************99***********99985 PP

>> DUF1223  Protein of unknown function (DUF1223)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   9.1e-08   0.00012       2      32 ..       6      36 ..       5      44 .. 0.82
   2 ?    4.7   0.0     0.021        27      72      97 ..      57      83 ..      41      85 .] 0.79

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.1e-08
                                  EEEEE-TT-TT-HHHHHHHHHH.HHHTSSEE CS
                       DUF1223  2 vELFtSqGCssCPpAdallselaaedkdvva 32
                                  +ELFtS  C  CP+A+++++e+a+e +d v 
  gi|15668482|ref|NP_247280.1|  6 IELFTSPMCPHCPAAKRVVEEVANEMPDAVE 36
                                  7*********************777766554 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.021
                                  SSEEEETTTEEEETT-.HHHHHHHHHH CS
                       DUF1223 72 TPqvvvnGreevvgsd.eeeleaaisa 97
                                   P +v+nG  e++g+  +e+l +ai++
  gi|15668482|ref|NP_247280.1| 57 VPTIVINGDVEFIGAPtKEALVEAIKK 83
                                  69************9856777888875 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   6.4e-09   8.2e-06       1      57 [.       5      64 ..       5      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6.4e-09
                                  -EEEEE-TT-HHHHHHHHHHHHHCCCTT..EEEEEEETTT-CCCHCCCCT.TTTEEEECT CS
                        DUF836  1 kltLyskpgChlCeqakekLkelkleeg..leleviDIakdeeleakYgl.eipvlaleg 57
                                  k+ L++ p C+ C  ak +++e++ e    +e+e i++ ++++  ++Yg   +p ++++g
  gi|15668482|ref|NP_247280.1|  5 KIELFTSPMCPHCPAAKRVVEEVANEMPdaVEVEYINVMENPQKAMEYGImAVPTIVING 64
                                  699******************966555468******************962589998888 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.4e-08     3e-05      14      56 ..      20      61 ..       7      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.4e-08
                                  HHHHHHHHCCCHCTTTEEEEEEETTTSHCHHCCTCEESCCCCC CS
                          KaiB 14 alenlkkleeedlgfqyeLqvvdvleqPelaeedrlvatPaLi 56
                                  a+++++++++e +   +e++ ++v e+P++a e+ ++a+P+ +
  gi|15668482|ref|NP_247280.1| 20 AKRVVEEVANE-MPDAVEVEYINVMENPQKAMEYGIMAVPTIV 61
                                  67777788777.8899*************************86 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   7.1e-06    0.0091       8      86 ..       5      62 ..       2      81 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.1e-06
                 Thioredoxin_2  8 vlvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivf 86
                                   + +ft+p Cp C + k++++e+ ++         + +++e +++++  +++k             a +yg+ ++Ptiv+
  gi|15668482|ref|NP_247280.1|  5 KIELFTSPMCPHCPAAKRVVEEVaNE---------MPDAVEVEYINVMENPQK-------------AMEYGIMAVPTIVI 62
                                  5668*******************222.........344456666666666665.............6899******9986 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00058      0.74       2      38 ..       8      44 ..       8      50 .. 0.92
   2 ?    2.9   0.1      0.06        77     150     164 ..      49      63 ..      43      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00058
                 Thioredoxin_5  2 lFidPlcseCweiEpelkklkveygekiklrfillln 38
                                  lF+ P+c++C + ++ +  + +e+ + +++++i +++
  gi|15668482|ref|NP_247280.1|  8 LFTSPMCPHCPAAKRVVEEVANEMPDAVEVEYINVME 44
                                  7******************************998775 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.06
                 Thioredoxin_5 150 akemgvtevPtlvff 164
                                   a e+g+  vPt+v+ 
  gi|15668482|ref|NP_247280.1|  49 AMEYGIMAVPTIVIN 63 
                                   89**********985 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.3e-05     0.042     113     159 ..      20      63 ..      16      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                                   HHHHHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEE CS
                 Thioredoxin_6 113 lkkaiekvakefkdkinfaladaksfkrpleylglsssdlPvivivd 159
                                   +k+++e+va+e++d + + +++++++++   ++g+   ++P+iv ++
  gi|15668482|ref|NP_247280.1|  20 AKRVVEEVANEMPDAVEVEYINVMENPQKAMEYGIM--AVPTIV-IN 63 
                                   68899*******************************..******.55 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.6e-05     0.046      26      94 ..       3      61 ..       1      78 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                ABC_transp_aux 26 pvtikvylsenlalppelkalekevkdlLeeyaaysggkisvefidpspneeeeeeaeaygitpvqisv 94
                                  +v+i+++ s+     p  +a +     + ee a++ ++ ++ve+i++++n+   ++a +ygi +v+  v
  gi|15668482|ref|NP_247280.1|  3 KVKIELFTSPM---CPHCPAAK----RVVEEVANEMPDAVEVEYINVMENP---QKAMEYGIMAVPTIV 61
                                  57777777777...45555444....455555555666799*******888...788889**9988555 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.0   0.00011      0.13      37      68 ..      13      44 ..       9      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                  SSHHHHHHHHHHHHHHHH-SS-EEEEEEE--- CS
                        DUF953 37 WCPdCvkaepvieealkeapedvklvrvdvGd 68
                                   CP C +a  v+ee+ +e+p  v++ +++v +
  gi|15668482|ref|NP_247280.1| 13 MCPHCPAAKRVVEEVANEMPDAVEVEYINVME 44
                                  5******************9977666666554 PP

>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00052      0.66      87     120 ..      20      52 ..      18      54 .. 0.92
   2 ?   -0.1   0.0      0.69   8.8e+02      72      93 ..      66      84 ..      58      85 .] 0.65

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00052
                                   HHHHHHHHHHHHGCCCGCEEEEEEEEETTEEEEE CS
                          PTPS  87 aklifeelkerlqekevklskvrvwEtpnswaey 120
                                   ak ++ee+++++ ++ v+++ ++v+E+p++++ey
  gi|15668482|ref|NP_247280.1|  20 AKRVVEEVANEM-PDAVEVEYINVMENPQKAMEY 52 
                                   677899999999.9*****************999 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.69
                                  -CCHHCCS.--HHHHHHHHHHH CS
                          PTPS 72 dpeleellspTaEnlaklifee 93
                                  ++ +     pT E+l + i ++
  gi|15668482|ref|NP_247280.1| 66 VEFIG---APTKEALVEAIKKR 84
                                  33333...49999999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 553.29
//
Query:       gi|15668483|ref|NP_247281.1|  [L=233]
Description: hypothetical protein MJ_0308 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-62  210.7   0.2    2.4e-62  210.6   0.2    1.0  1  DUF169    Uncharacterised ArCR, COG2043
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.27   11.4   0.0    1.5  1  CwsA      Cell wall synthesis protein CwsA


Domain annotation for each model (and alignments):
>> DUF169  Uncharacterised ArCR, COG2043
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.6   0.2   2.6e-66   2.4e-62       1     205 [.      12     220 ..      12     221 .. 0.97

  Alignments for each domain:
  == domain 1  score: 210.6 bits;  conditional E-value: 2.6e-66
                        DUF169   1 kLaealrlktePVavkfsdekpelpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfk.elpeklksg. 79 
                                   kL+e++ l++  Vavk++++k+e+pe++e+++e+kr+C m+++ar ++k++++t +++ C+gGa+a+G   ++pe l +g 
  gi|15668483|ref|NP_247281.1|  12 KLMELMMLDKPFVAVKLAKSKEEIPEGYETLDEEKRHCEMIQMARLERKKLYATVDKHLCKGGAYAMGVFrNPPEPLATGk 92 
                                   799*****************************************************************9526679****** PP

                        DUF169  80 ....egylkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrlnvsfpgnga 156
                                       +g +k++eaakk+v+++p++e +e++++v+apL++++f Pd++vf+++p  ++rLvq++ly++gg r++++f+g+++
  gi|15668483|ref|NP_247281.1|  93 lyvkLGNFKDEEAAKKTVDAIPKVE-EEIYATVYAPLDETDFIPDSIVFIGEPLYALRLVQAILYHKGG-RFQADFSGIQS 171
                                   **********************996.5669*************************************99.*********** PP

                        DUF169 157 aCadivaypykegepniglgdpgarkfaklkddelafgiPyelleemve 205
                                    Cad+va +y++++pn++lg++g+rk+a++k++e+++++P e+l+++ve
  gi|15668483|ref|NP_247281.1| 172 LCADAVAAVYTRKAPNMTLGCNGSRKYAGIKPEEVVVAFPPEKLKDIVE 220
                                   ***********************************************98 PP

>> CwsA  Cell wall synthesis protein CwsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.1e-05      0.27      48     119 ..      12      87 ..       3      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                          CwsA  48 rlarelaaaqeaiaqelaaaqevvaglPqaleda......rkkrrrkrplllagvavavlaGGavafsivrrssrPeP 119
                                   +l + +   +  +a +la ++e + +  ++l++        +  r  r+ l a+v   +  GGa a+ + r +  PeP
  gi|15668483|ref|NP_247281.1|  12 KLMELMMLDKPFVAVKLAKSKEEIPEGYETLDEEkrhcemIQMARLERKKLYATVDKHLCKGGAYAMGVFRNP--PEP 87 
                                   5555555566678999999999999999999888777776677899999**********************98..666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1871.09
//
Query:       gi|15668484|ref|NP_247282.1|  [L=284]
Description: agmatinase SpeB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-76  254.9   0.0    1.1e-75  254.7   0.0    1.0  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.7   0.0   6.2e-80   1.1e-75       4     278 ..      24     280 ..      21     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 254.7 bits;  conditional E-value: 6.2e-80
                                   EEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHTT CS
                      Arginase   4 allGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeavaeilkag 83 
                                   +++ +P+d+++s++pGar+G +air+as+ le+   y++ l++ l elk++dl+d+++  +++ee++ +i++  +eilk++
  gi|15668484|ref|NP_247282.1|  24 VIFSIPYDETTSFKPGAREGGNAIRTASWGLET---YSPILDRdLAELKYCDLKDLDLY-GSQEEIFGTIHSVSREILKEN 100
                                   89******************************8...7777777799************7.59999**************** PP

                                   CEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STCSHH CS
                      Arginase  84 klpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvqiGirsvdnee 164
                                   k +iv GG+Hsi+++i++a+++ y+ ++ vi+fDAH+Dlr+++  g+++sh++++rr++  +l+  k+++q+Girs d+ee
  gi|15668484|ref|NP_247282.1| 101 KKIIVFGGEHSITYPIIKAVKDIYD-DFIVIQFDAHCDLRDEY-LGNKLSHACVMRRVY--ELT--KNIFQFGIRSGDKEE 175
                                   ***********************98.6****************.8**************..455..6************** PP

                                   HHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHHC.H CS
                      Arginase 165 yelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlrellallrelae.k 244
                                   ++la++ +  +++m+ +++ +l        e++++ ++p+y+++DiDvlDpa+aPGtGtpep G+++rel++ l  l+e k
  gi|15668484|ref|NP_247282.1| 176 WDLARK-NNLYLKMDLMNKDDL--------EYIKSLDKPIYVTIDIDVLDPAYAPGTGTPEPCGFSTRELFNSLYLLEEvK 247
                                   ****96.668999999999887........34444467*********************************9999997778 PP

                                   SEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHHH CS
                      Arginase 245 lnlvgaDvvEvnPaldteaeqtarlaarlvrell 278
                                    +++g+D+vEv+P +d+ a++ta++aa+++rel+
  gi|15668484|ref|NP_247282.1| 248 DKIIGFDIVEVSPIYDI-ANITAITAAKIARELM 280
                                   9****************.55************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2040.44
//
Query:       gi|15668485|ref|NP_247283.1|  [L=114]
Description: hypothetical protein MJ_0310 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.3e-24   83.8   1.2    6.6e-24   83.5   1.2    1.1  1  Robl_LC7    Roadblock/LC7 domain
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.019   14.8   0.0    1.1  1  MAPKK1_Int  Mitogen-activated protein kinase kinase 1 interac


Domain annotation for each model (and alignments):
>> Robl_LC7  Roadblock/LC7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   1.2   7.4e-28   6.6e-24       1      91 []       1      90 [.       1      90 [. 0.97

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 7.4e-28
                                  HHHHHHHHCCHHCTECEEEEEETTS-EEEECCSSSS-HHHHHHHHHHHHHHHHHHHHHCTSSSECEEEEEETTEEEEEEECTT CS
                      Robl_LC7  1 lveelleelqsvpgvrgalvvskdGlviatstldnddadqlAalasgllsaakaaarelgegelkelliegkkgelyltpage 83
                                  +++ +l el++++g++g++vv kdGlvia++ +++ da+ ++a+as++++aa++ a e+g g+l++++ieg++g+ +++ age
  gi|15668485|ref|NP_247283.1|  1 MIDRVLLELNKTEGIKGSMVVGKDGLVIASQLPGSVDAELVGAMASAAFGAAERTAAEIGMGTLEQTMIEGEHGKTLMVDAGE 83
                                  57899****************************************************************************** PP

                                  TEEEEEEE CS
                      Robl_LC7 84 galLvvla 91
                                    +Lvvl+
  gi|15668485|ref|NP_247283.1| 84 -GILVVLT 90
                                  .9999985 PP

>> MAPKK1_Int  Mitogen-activated protein kinase kinase 1 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.1e-06     0.019      11     101 ..       9      99 ..       2     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-06
                    MAPKK1_Int  11 lsevdgllaiivtDrDGvvllkvgddssadsalrpslistfvlatdQasKLdlgknksiislyedyqvvqfnklplilsvi 91 
                                   l++ +g+++ +v  +DG v+++    s + + +     ++f  a   a  +++g  ++++   e+     +++ + il v+
  gi|15668485|ref|NP_247283.1|   9 LNKTEGIKGSMVVGKDGLVIASQLPGSVDAELVGAMASAAFGAAERTAAEIGMGTLEQTMIEGEHGKTLMVDAGEGILVVL 89 
                                   6788999999************999998999999999999****************999999999999999********** PP

                    MAPKK1_Int  92 astecNiGli 101
                                   ++ + N Gli
  gi|15668485|ref|NP_247283.1|  90 TDAKVNLGLI 99 
                                   ********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 767.94
//
Query:       gi|15668486|ref|NP_247284.1|  [L=110]
Description: hypothetical protein MJ_0311 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-16   58.9   0.0    3.6e-16   58.7   0.0    1.0  1  Robl_LC7  Roadblock/LC7 domain


Domain annotation for each model (and alignments):
>> Robl_LC7  Roadblock/LC7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.0     2e-20   3.6e-16       2      91 .]       3      91 ..       2      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 2e-20
                                  HHHHHHHCCHHCTECEEEEEETTS-EEEECCSSSS-HHHHHHHHHHHHHHHHHHHHHCTSSSECEEEEEETTEEEEEEECTTT CS
                      Robl_LC7  2 veelleelqsvpgvrgalvvskdGlviatstldnddadqlAalasgllsaakaaarelgegelkelliegkkgelyltpageg 84
                                  ++e+leel++++ ++g+l++ +dGlv  +s  +++++++l+a +s +l+ ++++++++ ++++++++i++k++ ++l+p ++ 
  gi|15668486|ref|NP_247284.1|  3 QKEILEELKDLDYIHGVLLIKNDGLVEYSSLSEDSNMESLGARLSIILNSISEVIKDIYNEKTECVFIKVKDDGIILIPKDN- 84
                                  6799******************************************************************************. PP

                                  EEEEEEE CS
                      Robl_LC7 85 alLvvla 91
                                   +L++l+
  gi|15668486|ref|NP_247284.1| 85 EILTILF 91
                                  9999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 702.90
//
Query:       gi|15668487|ref|NP_247285.1|  [L=206]
Description: hypothetical protein MJ_0312 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1316.61
//
Query:       gi|15668488|ref|NP_247286.1|  [L=293]
Description: spermidine synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-71  240.2   0.1    1.5e-71  239.7   0.1    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
    1.5e-22   79.3   0.3    2.8e-22   78.3   0.3    1.5  1  Spermine_synt_N  Spermidine synthase tetramerisation domain
    0.00042   19.9   0.0    0.00063   19.3   0.0    1.3  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
     0.0021   18.7   0.0     0.0063   17.2   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
     0.0032   18.2   0.0      0.011   16.4   0.0    2.0  1  Methyltransf_12  Methyltransferase domain
     0.0056   16.6   0.0      0.036   13.9   0.0    2.2  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
     0.0067   16.0   0.0      0.011   15.3   0.0    1.4  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.035   13.8   0.0      0.057   13.1   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.083   12.7   0.0       0.18   11.6   0.0    1.6  1  PRMT5            PRMT5 arginine-N-methyltransferase


Domain annotation for each model (and alignments):
>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.7   0.1   7.7e-75   1.5e-71       1     182 [.      66     247 ..      66     253 .. 0.98

  Alignments for each domain:
  == domain 1  score: 239.7 bits;  conditional E-value: 7.7e-75
                                   THHHHHHHHHHHHCCSSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEEEST CS
                Spermine_synth   1 efaykemiahvplmlhknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklvlgd 81 
                                   ef+y+e+i h+pl++h+np++vL+iGGgDGg++revvkh++ve++++v++D+kvi+ +kk++p+l+++ +++++v+l+++d
  gi|15668488|ref|NP_247286.1|  66 EFIYHELISHIPLFTHPNPRNVLVIGGGDGGTVREVVKHKSVETVDFVELDEKVIEACKKYMPKLSCE-IDNEKVNLIITD 145
                                   79******************************************************************.************ PP

                                   CHHHHCTCSS-EEEEEEECCSTTCSSCGCSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHHHHTTSSCEEEEEE CS
                Spermine_synth  82 gfkflkayekkfdvvivdsldpvgpaenlFskeffdllkkvlkedGviilqaekpelekelvinvdksgkqvfalqvepsa 162
                                   g+k+++++ekk+dv+ivd+ dpvgpa+ lF+kef++++ k+l++dG++++q+e+p+++++l++n+++ +k++ +++++p++
  gi|15668488|ref|NP_247286.1| 146 GIKYVAETEKKYDVIIVDCPDPVGPAKGLFEKEFYKNVFKCLNDDGIMVQQSESPLYNLDLIQNICRYLKDAGFKIIMPYT 226
                                   ********************************************************************************* PP

                                   EETTTSCSCEEEEEEEESS.T CS
                Spermine_synth 163 vlvPtylsgminfvveskk.n 182
                                   +++Pty+sg+++f+++skk n
  gi|15668488|ref|NP_247286.1| 227 YPMPTYPSGFWSFTLASKKyN 247
                                   *****************9953 PP

>> Spermine_synt_N  Spermidine synthase tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.3   1.4e-25   2.8e-22       1      53 []      11      63 ..      11      63 .. 0.99

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 1.4e-25
                                  EEEEEEEETTEEEEEEEEEEEEEEEESSSEEEEEEETTTEEEEEETTEEEEET CS
               Spermine_synt_N  1 gWfteisdpglalelkVekvLyeekSeyQdieifesktfGkvLvLDgvvqltE 53
                                  +Wfte++++++al+++V+++Ly+ekS +Q+iei+++++fGk L+LD+++q+tE
  gi|15668488|ref|NP_247286.1| 11 IWFTEYHNNNVALSVRVKDILYREKSGFQEIEIIDTYDFGKALILDNTFQTTE 63
                                  7***************************************************9 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.2e-07   0.00063      61     158 ..      89     194 ..      65     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.2e-07
               Methyltransf_PK  61 dcGaG.iGrvtknlLlkllskvDlvepvekflekakeelae.....ekkkvgkvyvvglqeftPeegrYdliWiqWcvghL 135
                                    +G G  G v + + +k ++ vD+ve  ek++e+ k+++ +     +++kv  +++ g++  +  e++Yd+i +       
  gi|15668488|ref|NP_247286.1|  89 VIGGGdGGTVREVVKHKSVETVDFVELDEKVIEACKKYMPKlsceiDNEKVNLIITDGIKYVAETEKKYDVIIVDCPDPVG 169
                                   3333314788999999***********************99999999*************99999*******987654444 PP

               Methyltransf_PK 136 tDedlv..aflkrckkalkpnGliv 158
                                   + + l   +f+k + k l+++G++v
  gi|15668488|ref|NP_247286.1| 170 PAKGLFekEFYKNVFKCLNDDGIMV 194
                                   5555542257777777777777777 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.2e-06    0.0063       1      73 [.      87     164 ..      87     191 .. 0.75
   2 ?   -2.5   0.0       4.4   8.7e+03      85      97 .]     206     218 ..     202     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.2e-06
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.....TEEEEESBC.CGBSSSTTTEEEEEEEST CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.....nvefvqgda.edlpfedgsfDlvvssga 73 
                                   vL +G G G +++++ k+ + ++v  v+++e+ +ea+++ + + ++     +v+++  d  + + + ++++D++++  +
  gi|15668488|ref|NP_247286.1|  87 VLVIGGGDGGTVREVVKHKSVETVDFVELDEKVIEACKKYMPKLSCeidneKVNLIITDGiKYVAETEKKYDVIIV-DC 164
                                   899**************96589*******************9866666667888888888344678899****998.45 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.4
                                   HHHHHHHHEEEEE CS
               Methyltransf_25  85 alkeiarvLkpgG 97 
                                   ++++i+r Lk+ G
  gi|15668488|ref|NP_247286.1| 206 LIQNICRYLKDAG 218
                                   7899*****9987 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.6e-06     0.011       1      72 [.      88     162 ..      88     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.6e-06
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.......ssfDlvva 72 
                                   L iG+G+G ++r++ ++ +  ++ +v++++++ie+ k+ + k +     ++++e+ +l+ +dg        +++D++++
  gi|15668488|ref|NP_247286.1|  88 LVIGGGDGGTVREVVKHKSVETVDFVELDEKVIEACKKYMPKLSC----EIDNEKVNLIITDGIkyvaeteKKYDVIIV 162
                                   569**************6666666*********888888888774....6666666666666666677799*****984 PP

>> Methyltransf_30  S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.8e-05     0.036      22      87 ..     128     194 ..     111     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                                   EEEEETTTTEEEEEEES-HHHHHHHC-T-EEEEEE-SS-TTT.SGGGCSHHHHHHHHHHEEEEEEEE CS
               Methyltransf_30  22 qrlelaaeevtlklligdarealkeldekadawFlDgFsPak.nPelwseellkelarllkkkgtla 87 
                                    +l+ + ++ +++l+i d  + + e ++k+d++  D   P   +  l+++e++k+++++l++ g ++
  gi|15668488|ref|NP_247286.1| 128 PKLSCEIDNEKVNLIITDGIKYVAETEKKYDVIIVDCPDPVGpAKGLFEKEFYKNVFKCLNDDGIMV 194
                                   4566666788999**********************99999751446***************999876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.5e-06     0.011      31     167 ..      83     221 ..      70     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.5e-06
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.....EEEEE-STTTTST..TS-EEEEEE- CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.....vevvasdvleeve..ekkfdlivsN 104
                                     ++vl +G G G    ++ k+++  +v++v+ d + +e++k+ + +  +e     v+++ +d+++ v+  ekk+d+i+  
  gi|15668488|ref|NP_247286.1|  83 NPRNVLVIGGGDGGTVREVVKHKSVETVDFVELDEKVIEACKKYMPKLSCEidnekVNLIITDGIKYVAetEKKYDVIIVD 163
                                   5678999*****999999999999999****************999888877788899999999987765579******** PP

                                   --STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHHHHS--EEEEEESSEEE CS
                           MTS 105 PPfhagkatelavaeeliaeAkeaLkegGeLliVanrklgyeslleelfgnvevvaktkkfkv 167
                                    P   g a +    +e+ ++  ++L+++G   +V +++ +  +l  +l++n+    k+++fk+
  gi|15668488|ref|NP_247286.1| 164 CPDPVGPA-KGLFEKEFYKNVFKCLNDDGI--MVQQSESPLYNL--DLIQNICRYLKDAGFKI 221
                                   **999998.777889999999999999995..456665555554..44444444445555555 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.8e-05     0.057      63     160 ..     106     205 ..      83     223 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
                                   T-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--S....SSTTCH.HHHHHHHHHT CS
                 Cons_hypoth95  63 gakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDPP....yakellieevlelleek 139
                                    ++ + +ve d+++++++k+ + +l +e   ++++   ++ ++  a++++++d++ +D P     ak+l+ +e  + +   
  gi|15668488|ref|NP_247286.1| 106 SVETVDFVELDEKVIEACKKYMPKLSCEIDNEKVNLIITDGIKYVAETEKKYDVIIVDCPdpvgPAKGLFEKEFYKNVF-- 184
                                   467889********************9985555655666666666777889*******993332244444344444444.. PP

                                   T-EEEEEEEEEEEECCSSS-- CS
                 Cons_hypoth95 140 kllkenalvvvetekekelpe 160
                                   k+l++++++v ++e+    ++
  gi|15668488|ref|NP_247286.1| 185 KCLNDDGIMVQQSESPLYNLD 205
                                   677777777777766655555 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.2e-05      0.18      65     143 ..      84     162 ..      49     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.2e-05
                                   EEEEEEES-TTSHHHHHHHHHHHHHCCCEEEEEEE.ES-HHHHHHHHHHHHHHTTCCGCEEEES-.CCCCCHCC.-ECEEE CS
                         PRMT5  65 klvilvvGaGRGplvdralkaleetkvtkvkivav.EKnpnavvtLqkkvneekWeekveviksd.mrelkaee.kvdllv 142
                                      +lv+G+G G+ v++++k  + ++   v+ v + EK  +a+     k++ e  +ekv++i +d ++ + ++e k+d+++
  gi|15668488|ref|NP_247286.1|  84 PRNVLVIGGGDGGTVREVVKHKSVET---VDFVELdEKVIEACKKYMPKLSCEIDNEKVNLIITDgIKYVAETEkKYDVII 161
                                   5679************9998776666...4433332677777777777777777789999887774777655444999998 PP

                                   E CS
                         PRMT5 143 s 143
                                    
  gi|15668488|ref|NP_247286.1| 162 V 162
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1902.57
//
Query:       gi|15668489|ref|NP_247287.1|  [L=263]
Description: hypothetical protein MJ_0314 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-17   62.2   4.4    2.3e-08   34.3   0.0    2.8  3  LAGLIDADG_3      LAGLIDADG-like domain
    9.4e-16   57.3   1.7      3e-07   30.1   0.4    2.5  2  HTH_38           Helix-turn-helix domain
    1.9e-15   56.6   0.9    3.8e-07   30.1   0.1    2.7  2  HTH_7            Helix-turn-helix domain of resolvase
      5e-15   54.8   0.3    4.1e-07   29.6   0.1    2.4  2  HTH_23           Homeodomain-like domain
    1.5e-09   37.9   0.1    0.00012   22.1   0.0    2.5  2  HTH_28           Helix-turn-helix domain
    1.6e-08   33.9   0.1      0.003   17.1   0.0    2.5  2  GerE             Bacterial regulatory proteins, luxR family
    2.1e-07   30.7   0.4      0.031   14.1   0.1    2.8  2  Terminase_5      Putative ATPase subunit of terminase (gpP-li
    2.7e-07   30.1   0.1      0.024   14.3   0.0    2.3  2  Sigma70_r4_2     Sigma-70, region 4
    4.7e-07   29.7   0.1      0.035   14.1   0.0    2.4  2  HTH_29           Winged helix-turn helix
    8.1e-07   28.5   0.0    0.00085   18.8   0.0    2.4  2  Sigma70_r4       Sigma-70, region 4
    1.2e-05   25.7   0.2       0.26   11.8   0.0    2.7  2  HTH_40           Helix-turn-helix domain
    2.2e-05   24.4   4.1    6.3e-05   23.0   0.2    3.0  3  LAGLIDADG_WhiA   WhiA LAGLIDADG-like domain
    3.7e-05   23.6   1.9       0.25   11.3   0.1    2.9  2  HTH_36           Helix-turn-helix domain
    7.1e-05   22.3   1.8    0.00044   19.8   0.2    2.9  2  HTH_50           Helix-turn-helix domain
    7.8e-05   22.8   0.2      0.046   13.9   0.0    2.6  2  HTH_17           Helix-turn-helix domain
    0.00012   22.0   0.0      0.085   12.7   0.0    2.2  2  Sigma70_ECF      ECF sigma factor
    0.00013   22.1   0.0       0.13   12.5   0.0    2.4  2  Hom_end          Homing endonuclease
    0.00022   21.1   0.7      0.062   13.2   0.1    2.5  2  Phage_antitermQ  Phage antitermination protein Q
    0.00034   19.7   0.5       0.03   13.3   0.2    2.3  2  TnsD             Tn7-like transposition protein D
    0.00035   20.4   0.1          1    9.3   0.0    2.6  2  HTH_11           HTH domain
    0.00042   19.7   0.0       0.06   12.8   0.0    2.2  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
    0.00051   19.8   0.0       0.18   11.6   0.0    3.1  2  HTH_10           HTH DNA binding domain
    0.00084   19.5   0.4      0.027   14.7   0.2    2.6  2  HTH_Tnp_Tc3_2    Transposase
    0.00085   18.9   0.3       0.11   12.1   0.2    2.4  2  CENP-B_N         CENP-B N-terminal DNA-binding domain
     0.0014   18.7   0.5       0.83    9.9   0.1    2.5  2  DUF3853          Protein of unknown function (DUF3853)
     0.0016   18.7   0.1       0.18   12.1   0.1    2.5  2  ANT              Phage antirepressor protein KilAC domain
     0.0021   18.1   0.4        1.3    9.2   0.1    2.7  2  HTH_3            Helix-turn-helix
     0.0026   17.1   2.9     0.0039   16.6   0.5    2.3  3  DUF1670          Protein of unknown function (DUF1670)
     0.0072   16.4   0.0        3.5    7.7   0.0    2.2  2  RepB             RepB plasmid partitioning protein
  ------ inclusion threshold ------
      0.014   15.1   0.0        1.5    8.6   0.0    2.8  3  UPF0175          Uncharacterised protein family (UPF0175)
      0.024   14.7   0.4         11    6.1   0.1    3.1  4  MerR_1           MerR HTH family regulatory protein
      0.025   14.8  14.9        0.2   12.0   0.1    4.7  4  NUMOD1           NUMOD1 domain
      0.033   14.2   2.2        1.2    9.2   0.1    3.2  3  HTH_Mga          M protein trans-acting positive regulator (M
      0.036   14.0   0.7         36    4.3   0.0    4.0  4  TrmB             Sugar-specific transcriptional regulator Trm
      0.047   13.6   2.5        5.4    7.0   0.0    3.3  3  RepA_N           Replication initiator protein A (RepA) N-ter
       0.06   13.2   0.3       0.26   11.2   0.0    2.1  2  Phage_NinH       Phage NinH protein
      0.066   13.0   0.0       0.29   11.0   0.0    2.0  2  HTH_30           PucR C-terminal helix-turn-helix domain
      0.086   12.7   0.0       0.98    9.3   0.0    2.2  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
        0.2   12.1   0.0       0.39   11.1   0.0    1.5  1  GcrA             GcrA cell cycle regulator


Domain annotation for each model (and alignments):
>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       7.6   3.5e+03      71      78 ..      66      73 ..      27      89 .. 0.57
   2 !   28.8   0.4   2.4e-09   1.1e-06       3      73 ..     103     172 ..     101     182 .. 0.82
   3 !   34.3   0.0   4.9e-11   2.3e-08       4      62 ..     198     259 ..     195     263 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 7.6
                                  CHCTTCGG CS
                   LAGLIDADG_3 71 sgenlkrF 78
                                  s+e ++r 
  gi|15668489|ref|NP_247287.1| 66 SHETIRRI 73
                                  33333332 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 2.4e-09
                                   HHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEE.EEE-SCCCCECCCHCHC CS
                   LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyek.kkakgrgvyrlliisge 73 
                                    +a++ G   +DGsv+k++ + v i+l+ ++k+++e+++r L+++G +       k ++++++y +++++++
  gi|15668489|ref|NP_247287.1| 103 SLAYILGVLNGDGSVNKQESNYV-IELKVTDKDFIEEFKRNLENIGFKYINEYVrKFENKKDQY-VVRVRSK 172
                                   579****************7744.**********************987555446889999999.5555444 PP

  == domain 3  score: 34.3 bits;  conditional E-value: 4.9e-11
                                   HHHHHHHHHHCCECCECSTTTTS...EEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SC CS
                   LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvs...isltssskelledvqrlLlrlGIestiyekkkakgr 62 
                                     +L+G++d++Gsv+ +kk++     +s+++++++l++ +   L++lGIe ++y +k++  +
  gi|15668489|ref|NP_247287.1| 198 ISWLKGFYDSEGSVVINKKGNYVykyVSIANTNRNLIDVCCSFLEKLGIEYSVYCEKNNRYK 259
                                   578***************987779******************************99555444 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.2e-08   5.4e-06      15      37 ..       2      24 ..       1      32 [. 0.94
   2 !   30.1   0.4   6.5e-10     3e-07      12      44 .]      45      77 ..      42      77 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.2e-08
                        HTH_38 15 rllaeGlslreIArrLgrspsTI 37
                                   l+++G+s r+IA++Lg+s+sT+
  gi|15668489|ref|NP_247287.1|  2 ELYKKGYSARTIAKILGCSKSTV 24
                                  59********************8 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 6.5e-10
                        HTH_38 12 eIerllaeGlslreIArrLgrspsTIsRElkRn 44
                                  eI +l++ G++  eIA+++++s+ TI R l+ n
  gi|15668489|ref|NP_247287.1| 45 EIIKLYQNGYTTTEIAKIMKCSHETIRRILRNN 77
                                  8999***************************88 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   4.1e-08   1.9e-05      16      38 ..       2      24 ..       1      30 [. 0.92
   2 !   30.1   0.1   8.2e-10   3.8e-07       5      44 ..      40      76 ..      37      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.1e-08
                                  SSTTTT--STTTSSSS---SSSS CS
                         HTH_7 16 kLleeGisiskIAkevnisRsTv 38
                                  +L+++G+s+++IAk++++s+sTv
  gi|15668489|ref|NP_247287.1|  2 ELYKKGYSARTIAKILGCSKSTV 24
                                  8*********************9 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 8.2e-10
                                  SS-HHHHGGGGSSTTTT--STTTSSSS---SSSS--SS-- CS
                         HTH_7  5 klskndinrvvkLleeGisiskIAkevnisRsTvYRylad 44
                                  +l++   ++++kL+++G++ ++IAk+ ++s +T+ R+l+ 
  gi|15668489|ref|NP_247287.1| 40 DLNP---QEIIKLYQNGYTTTEIAKIMKCSHETIRRILRN 76
                                  6788...9*****************************986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0     1e-07   4.8e-05      13      36 ..       3      27 ..       1      37 [. 0.86
   2 !   29.6   0.1   8.9e-10   4.1e-07       8      40 ..      44      76 ..      44      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1e-07
                        HTH_23 13 llaeGlsvreIAreLgvsrrTvy.r 36
                                  l+++G+s r+IA++Lg+s++Tv+ r
  gi|15668489|ref|NP_247287.1|  3 LYKKGYSARTIAKILGCSKSTVCyR 27
                                  8999******************944 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 8.9e-10
                        HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrwlkr 40
                                  ++i++l+++G++++eIA+++ +s+ T++r+l+ 
  gi|15668489|ref|NP_247287.1| 44 QEIIKLYQNGYTTTEIAKIMKCSHETIRRILRN 76
                                  58****************************997 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00014     0.064       7      34 ..       2      30 ..       1      37 [. 0.93
   2 !   22.1   0.0   2.7e-07   0.00012       4      35 ..      45      76 ..      44      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00014
                        HTH_28  7 kllaaGhsvreaArelgisrrtv.yrWik 34
                                  +l+++G s+r +A++lg+s +tv yr+ k
  gi|15668489|ref|NP_247287.1|  2 ELYKKGYSARTIAKILGCSKSTVcYRLYK 30
                                  689********************999876 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 2.7e-07
                        HTH_28  4 eiikllaaGhsvreaArelgisrrtvyrWikr 35
                                  eiikl+++G + +e+A+++ +s++t++r ++ 
  gi|15668489|ref|NP_247287.1| 45 EIIKLYQNGYTTTEIAKIMKCSHETIRRILRN 76
                                  8****************************986 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.7e-05     0.022      11      37 ..       1      27 [.       1      31 [. 0.87
   2 !   17.1   0.0   6.6e-06     0.003       9      36 ..      45      72 ..      43      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.7e-05
                                  HHHHCTTS-HHHHHHHHTS-HHHHHHH CS
                          GerE 11 LrllaeGksnkeIAeelniSekTVkvh 37
                                  ++l  +G+s   IA++l++S+ TV + 
  gi|15668489|ref|NP_247287.1|  1 MELYKKGYSARTIAKILGCSKSTVCYR 27
                                  677889******************765 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 6.6e-06
                                  HHHHHHCTTS-HHHHHHHHTS-HHHHHH CS
                          GerE  9 evLrllaeGksnkeIAeelniSekTVkv 36
                                  e+ +l  +G++++eIA+++ +S +T++ 
  gi|15668489|ref|NP_247287.1| 45 EIIKLYQNGYTTTEIAKIMKCSHETIRR 72
                                  7889999******************985 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0    0.0001     0.047       7      31 ..       1      25 [.       1      28 [. 0.93
   2 !   14.1   0.1   6.8e-05     0.031       8      30 ..      48      70 ..      44      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                   Terminase_5  7 rlLYwqGyrvaeIAeelglkeatVy 31
                                  ++LY +Gy+ + IA+ lg ++ tV 
  gi|15668489|ref|NP_247287.1|  1 MELYKKGYSARTIAKILGCSKSTVC 25
                                  68*********************96 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.8e-05
                   Terminase_5  8 lLYwqGyrvaeIAeelglkeatV 30
                                   LY +Gy+ +eIA+ +  +++t+
  gi|15668489|ref|NP_247287.1| 48 KLYQNGYTTTEIAKIMKCSHETI 70
                                  79*******************99 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   9.3e-05     0.043      25      49 ..       6      30 ..       2      30 .. 0.90
   2 !   14.3   0.0   5.1e-05     0.024      16      45 ..      44      72 ..      38      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.3e-05
                                  S---HHHHHHHHT--HHHHHHHHHH CS
                  Sigma70_r4_2 25 eglsykEIAellgisegtVksrlsR 49
                                  +g+s + IA++lg+s +tV +rl++
  gi|15668489|ref|NP_247287.1|  6 KGYSARTIAKILGCSKSTVCYRLYK 30
                                  699****************999875 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5.1e-05
                                  HHHHHHHHTS---HHHHHHHHT--HHHHHH CS
                  Sigma70_r4_2 16 reifllryleglsykEIAellgisegtVks 45
                                  +ei+ l y +g+++ EIA+++++s  t+++
  gi|15668489|ref|NP_247287.1| 44 QEIIKL-YQNGYTTTEIAKIMKCSHETIRR 72
                                  789999.89***************999997 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00013     0.062       7      29 ..       3      24 ..       1      27 [. 0.92
   2 !   14.1   0.0   7.7e-05     0.035       3      34 ..      45      75 ..      44      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                        HTH_29  7 llaeGvstvsqiAkllglsrrtv 29
                                  l+++G s  + iAk+lg+s++tv
  gi|15668489|ref|NP_247287.1|  3 LYKKGYS-ARTIAKILGCSKSTV 24
                                  7899**8.**************9 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.7e-05
                        HTH_29  3 qallllaeGvstvsqiAkllglsrrtvyrwlk 34
                                  +++ l+  G  t+ +iAk++ +s  t++r+l+
  gi|15668489|ref|NP_247287.1| 45 EIIKLYQNGY-TTTEIAKIMKCSHETIRRILR 75
                                  5788889998.9*****************986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0079       3.6      18      38 ..       5      25 ..       2      30 .. 0.86
   2 !   18.8   0.0   1.8e-06   0.00085      11      42 ..      45      75 ..      38      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0079
                                  TTT--HHHHHHHHTS-HHHHH CS
                    Sigma70_r4 18 geglTleEIgerlgiSrerVr 38
                                   +g++   I+++lg S+++V 
  gi|15668489|ref|NP_247287.1|  5 KKGYSARTIAKILGCSKSTVC 25
                                  57899999***********97 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.8e-06
                                  HHHHHHHTTT--HHHHHHHHTS-HHHHHHHHH CS
                    Sigma70_r4 11 evlelrfgeglTleEIgerlgiSrerVrqiek 42
                                  e+++l+   g+T  EI++++  S e++r+i++
  gi|15668489|ref|NP_247287.1| 45 EIIKLYQ-NGYTTTEIAKIMKCSHETIRRILR 75
                                  5666654.678*******************97 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00056      0.26       6      36 ..       1      31 [.       1      41 [. 0.89
   2 !   11.3   0.1   0.00076      0.35       4      31 ..      45      72 ..      42     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00056
                        HTH_40  6 lelleeglsieeIAkerglkesTIegHLael 36
                                  +el+++g+s   IAk+ g ++sT+   L +l
  gi|15668489|ref|NP_247287.1|  1 MELYKKGYSARTIAKILGCSKSTVCYRLYKL 31
                                  589*********************8777765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00076
                        HTH_40  4 etlelleeglsieeIAkerglkesTIeg 31
                                  e ++l+++g++  eIAk+ + +  TI +
  gi|15668489|ref|NP_247287.1| 45 EIIKLYQNGYTTTEIAKIMKCSHETIRR 72
                                  5579*********************975 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2       5.8   2.7e+03      39      67 ..      68      96 ..      55      97 .. 0.66
   2 !   23.0   0.2   1.4e-07   6.3e-05       3      49 ..     105     151 ..     103     199 .. 0.84
   3 ?    1.5   0.0      0.67   3.1e+02       4      55 ..     200     255 ..     197     260 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.8
                LAGLIDADG_WhiA 39 kllnefeleakilerrkkyvvylKkaeqI 67
                                  + ++++  + +i  r+++  + +K+ ++I
  gi|15668489|ref|NP_247287.1| 68 ETIRRILRNNNIDIRKSSESLIIKNTKKI 96
                                  45555555666777788888888887777 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.4e-07
                LAGLIDADG_WhiA   3 aflrGaflasGsindpekkyhLEivspdeelaeqlqkllnefeleak 49 
                                   a++ G++ + Gs+n+ e++y +E+ ++d++++e+ +  l+++++++ 
  gi|15668489|ref|NP_247287.1| 105 AYILGVLNGDGSVNKQESNYVIELKVTDKDFIEEFKRNLENIGFKYI 151
                                   7999***********************************98877653 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.67
                LAGLIDADG_WhiA   4 flrGaflasGsindpekk.yhLE...ivspdeelaeqlqkllnefeleakilerrk 55 
                                   +l+G   ++Gs+   +k+ y +    i+ ++ +l++  ++ l+++++e+++   ++
  gi|15668489|ref|NP_247287.1| 200 WLKGFYDSEGSVVINKKGnYVYKyvsIANTNRNLIDVCCSFLEKLGIEYSVYCEKN 255
                                   67888889999876655557654111556677778888889999999988865554 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00083      0.38      20      42 ..       5      24 ..       1      30 [. 0.88
   2 !   11.3   0.1   0.00055      0.25      15      47 ..      47      75 ..      45      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00083
                        HTH_36 20 knggcfpsqetlakrlglsknTv 42
                                  k+g+   s +t+ak lg+sk+Tv
  gi|15668489|ref|NP_247287.1|  5 KKGY---SARTIAKILGCSKSTV 24
                                  6777...99*************8 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00055
                        HTH_36 15 asfanknggcfpsqetlakrlglsknTvsraik 47
                                   +++ +ng+   +   +ak +++s +T++r+++
  gi|15668489|ref|NP_247287.1| 47 IKLY-QNGY---TTTEIAKIMKCSHETIRRILR 75
                                  5666.8999...999****************97 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   9.6e-07   0.00044      19      50 .]       3      34 ..       1      34 [. 0.91
   2 ?    0.2   0.0       1.3     6e+02      16      45 ..      46      75 ..      43      80 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.6e-07
                        HTH_50 19 ayekYpStRklAkrLGvShtaianklrkYgIs 50
                                  +y+k  S+R++Ak LG S++++  +l k gI+
  gi|15668489|ref|NP_247287.1|  3 LYKKGYSARTIAKILGCSKSTVCYRLYKLGIT 34
                                  688888**********************9996 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                        HTH_50 16 ikkayekYpStRklAkrLGvShtaianklr 45
                                  i+k+y++   t  +Ak +  Sh +i + lr
  gi|15668489|ref|NP_247287.1| 46 IIKLYQNGYTTTEIAKIMKCSHETIRRILR 75
                                  555666555566789999999*99988776 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.022        10       4      18 ..      10      24 ..       8      32 .. 0.85
   2 !   13.9   0.0    0.0001     0.046       2      27 ..      54      79 ..      54      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.022
                        HTH_17  4 veEaAelLgvsrstv 18
                                     +A++Lg+s+stv
  gi|15668489|ref|NP_247287.1| 10 ARTIAKILGCSKSTV 24
                                  5568**********8 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.0001
                        HTH_17  2 ltveEaAelLgvsrstvyrlirrgel 27
                                  +t+ E+A++ ++s  t++r +r++ +
  gi|15668489|ref|NP_247287.1| 54 YTTTEIAKIMKCSHETIRRILRNNNI 79
                                  8******************9998866 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.011       5.1     150     171 ..       6      27 ..       2      31 .. 0.87
   2 !   12.7   0.0   0.00018     0.085     148     172 ..      50      74 ..      40      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                   Sigma70_ECF 150 eGlsveEiAeklgvskrtverr 171
                                   +G+s   iA+ lg+sk+tv  r
  gi|15668489|ref|NP_247287.1|   6 KGYSARTIAKILGCSKSTVCYR 27 
                                   7*****************9655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00018
                   Sigma70_ECF 148 kleGlsveEiAeklgvskrtverrl 172
                                   + +G++ +EiA+ +++s+ t++r l
  gi|15668489|ref|NP_247287.1|  50 YQNGYTTTEIAKIMKCSHETIRRIL 74 
                                   668******************9976 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.011       5.1      16      47 ..     105     137 ..      94     171 .. 0.84
   2 !   12.5   0.0   0.00027      0.13      16      68 ..     199     256 ..     191     262 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                       Hom_end  16 aFlaGLvdsdgyvkkeked.satvktedksvme 47 
                                   a+++G   +dg+v+k++++ ++ +k +dk  +e
  gi|15668489|ref|NP_247287.1| 105 AYILGVLNGDGSVNKQESNyVIELKVTDKDFIE 137
                                   8***************99898888888887666 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00027
                       Hom_end  16 aFlaGLvdsdgyvkkeked.....satvktedksvmegivklarsLGikasvktkeek 68 
                                   ++l G+ ds+g+v  +k++      +++  +++++++   ++ ++LGi+ sv  ++++
  gi|15668489|ref|NP_247287.1| 199 SWLKGFYDSEGSVVINKKGnyvykYVSIANTNRNLIDVCCSFLEKLGIEYSVYCEKNN 256
                                   5799*********999988999999**************************9876554 PP

>> Phage_antitermQ  Phage antitermination protein Q
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.028        13      74      99 ..       3      28 ..       1      30 [. 0.88
   2 !   13.2   0.1   0.00013     0.062      71     101 ..      46      76 ..      41      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.028
               Phage_antitermQ 74 yYvfgvskraiarklkisekevrkkl 99
                                   Y +g+s r+ia+ l++s+++v  +l
  gi|15668489|ref|NP_247287.1|  3 LYKKGYSARTIAKILGCSKSTVCYRL 28
                                  6999****************997766 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00013
               Phage_antitermQ  71 lvdyYvfgvskraiarklkisekevrkklqk 101
                                   +++ Y  g+++++ia+ +k+s++++r+ l +
  gi|15668489|ref|NP_247287.1|  46 IIKLYQNGYTTTEIAKIMKCSHETIRRILRN 76 
                                   8899**********************98865 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.023        11     193     223 ..       2      31 ..       1      37 [. 0.83
   2 !   13.3   0.2   6.4e-05      0.03     189     229 ..      43      83 ..      29     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.023
                          TnsD 193 eLveeeglslkeiAkelgvdiktVlryakkl 223
                                   eL++ +g s + iAk+lg++ +tV   + kl
  gi|15668489|ref|NP_247287.1|   2 ELYK-KGYSARTIAKILGCSKSTVCYRLYKL 31 
                                   5777.9******************8666555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.4e-05
                          TnsD 189 erlkeLveeeglslkeiAkelgvdiktVlryakklgllkek 229
                                    + ++ ++++g +  eiAk+++++ +t++r++++++   +k
  gi|15668489|ref|NP_247287.1|  43 PQEIIKLYQNGYTTTEIAKIMKCSHETIRRILRNNNIDIRK 83 
                                   444444555***********************976544322 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0023         1      16      32 ..       8      24 ..       2      31 .. 0.85
   2 !    8.3   0.1    0.0046       2.1       9      34 ..      49      72 ..      44      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0023
                        HTH_11 16 isgeeLAeeLnvSrrtv 32
                                   s+ ++A+ L++S++tv
  gi|15668489|ref|NP_247287.1|  8 YSARTIAKILGCSKSTV 24
                                  69**************9 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0046
                        HTH_11  9 LleargpisgeeLAeeLnvSrrtvrr 34
                                  L+++    +  e+A+ +++S  t+rr
  gi|15668489|ref|NP_247287.1| 49 LYQNG--YTTTEIAKIMKCSHETIRR 72
                                  33555..599***************9 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.043        20      31      44 ..      11      24 ..       2      24 .. 0.90
   2 !   12.8   0.0   0.00013      0.06      21      49 ..      47      75 ..      44      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.043
                  HTH_Tnp_ISL3 31 kavArqlgvSwtTV 44
                                  +++A++lg+S +TV
  gi|15668489|ref|NP_247287.1| 11 RTIAKILGCSKSTV 24
                                  79***********9 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00013
                  HTH_Tnp_ISL3 21 lelllesrsvkavArqlgvSwtTVwrild 49
                                  ++l +++ + +++A+++ +S  T++ril+
  gi|15668489|ref|NP_247287.1| 47 IKLYQNGYTTTEIAKIMKCSHETIRRILR 75
                                  5555666689*****************97 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0    0.0004      0.18      20      45 ..       4      29 ..       4      31 .. 0.88
   2 ?    4.6   0.0     0.061        28      25      46 ..      55      76 ..      50      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0004
                        HTH_10 20 yPRrvtlkeLAkelGIskstlsehLr 45
                                  y +  +++ +Ak+lG skst+ ++L 
  gi|15668489|ref|NP_247287.1|  4 YKKGYSARTIAKILGCSKSTVCYRLY 29
                                  5678899**************99995 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.061
                        HTH_10 25 tlkeLAkelGIskstlsehLrk 46
                                  t+ e+Ak++  s  t+  +Lr+
  gi|15668489|ref|NP_247287.1| 55 TTTEIAKIMKCSHETIRRILRN 76
                                  789*****************97 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.45     2e+02      29      48 ..      18      37 ..       3      44 .. 0.81
   2 !   14.7   0.2   5.9e-05     0.027      29      57 ..      64      92 ..      54     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.45
                 HTH_Tnp_Tc3_2 29 svsreTirrrLrkaglkkrk 48
                                   +s++T+  rL k g+  r+
  gi|15668489|ref|NP_247287.1| 18 GCSKSTVCYRLYKLGITPRR 37
                                  68999999999999987665 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.9e-05
                 HTH_Tnp_Tc3_2 29 svsreTirrrLrkaglkkrkprkkplLsk 57
                                  ++s+eTirr+Lr++++  rk+ +   ++ 
  gi|15668489|ref|NP_247287.1| 64 KCSHETIRRILRNNNIDIRKSSESLIIKN 92
                                  89**************9999887766665 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.061        28      20      39 ..       5      24 ..       2      28 .. 0.87
   2 !   12.1   0.2   0.00024      0.11      14      46 ..      45      77 ..      35      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.061
                                  HCTT-HHHHHHHHT--CCHH CS
                      CENP-B_N 20 eegeSkaelarrfnvpestl 39
                                    g S + +a+ +++ +st+
  gi|15668489|ref|NP_247287.1|  5 KKGYSARTIAKILGCSKSTV 24
                                  5677999************8 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00024
                                  HHHHHHHCTT-HHHHHHHHT--CCHHHHHHHCH CS
                      CENP-B_N 14 evIqrleegeSkaelarrfnvpestlsdilknK 46
                                  e+I+++  g    e+a+   +   t+++il n 
  gi|15668489|ref|NP_247287.1| 45 EIIKLYQNGYTTTEIAKIMKCSHETIRRILRNN 77
                                  89****************************774 PP

>> DUF3853  Protein of unknown function (DUF3853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.015       7.1      46      69 ..       8      32 ..       2      47 .. 0.80
   2 !    9.9   0.1    0.0018      0.83      43      72 ..      51      80 ..      40     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.015
                       DUF3853 46 yGikglarllGislptan.rikksG 69
                                  y  + +a++lG+s +t+  r+ k G
  gi|15668489|ref|NP_247287.1|  8 YSARTIAKILGCSKSTVCyRLYKLG 32
                                  55678***********853666666 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0018
                       DUF3853 43 kfvyGikglarllGislptanrikksGkiD 72
                                  ++ y  +++a+++ +s  t+ ri ++  iD
  gi|15668489|ref|NP_247287.1| 51 QNGYTTTEIAKIMKCSHETIRRILRNNNID 80
                                  5667889******************99999 PP

>> ANT  Phage antirepressor protein KilAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.14        65      24      53 ..       8      37 ..       4      47 .. 0.87
   2 !   12.1   0.1   0.00039      0.18      23      57 ..      53      85 ..      45      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.14
                           ANT 24 ititeiAkllgigenrlfelLrekgilyrq 53
                                  ++ ++iAk+lg ++  +   L + gi  r+
  gi|15668489|ref|NP_247287.1|  8 YSARTIAKILGCSKSTVCYRLYKLGITPRR 37
                                  7899**************999999998775 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00039
                           ANT 23 sititeiAkllgigenrlfelLrekgilyrqkgsg 57
                                   +t+teiAk+++ ++    ++Lr+++i +r++  +
  gi|15668489|ref|NP_247287.1| 53 GYTTTEIAKIMKCSHETIRRILRNNNIDIRKS--S 85
                                  599************************99973..3 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.023        10       7      26 ..       5      24 ..       2      24 .. 0.93
   2 !    9.2   0.1    0.0028       1.3       7      38 ..      51      81 ..      44      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.023
                                  HTTHHHHHHHHHHTSSHHHH CS
                         HTH_3  7 qlglsqeeLAeklGvsrsti 26
                                  ++g+s + +A+ lG s+st+
  gi|15668489|ref|NP_247287.1|  5 KKGYSARTIAKILGCSKSTV 24
                                  69****************97 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0028
                                  HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBH CS
                         HTH_3  7 qlglsqeeLAeklGvsrstisriEnGernPsl 38
                                  q+g++ +e+A+ +  s  ti+ri ++  n+++
  gi|15668489|ref|NP_247287.1| 51 QNGYTTTEIAKIMKCSHETIRRILRN-NNIDI 81
                                  89***********************9.66666 PP

>> DUF1670  Protein of unknown function (DUF1670)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       0.8   3.7e+02     193     214 ..       3      24 ..       1      31 [. 0.84
   2 !   16.6   0.5   8.6e-06    0.0039     154     186 ..      44      76 ..       8      87 .. 0.85
   3 ?   -2.8   0.1       6.9   3.2e+03      17      37 ..     143     163 ..     131     171 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.8
                       DUF1670 193 Lkekkleseeirlitglseklv 214
                                   L++k+++   i++i+g s+++v
  gi|15668489|ref|NP_247287.1|   3 LYKKGYSARTIAKILGCSKSTV 24 
                                   7888999999999999999887 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 8.6e-06
                       DUF1670 154 kkivrlylkgyetteiarrtnHseeaidRYika 186
                                   ++i++ly +gy+tteia+ ++ s+e+i R +++
  gi|15668489|ref|NP_247287.1|  44 QEIIKLYQNGYTTTEIAKIMKCSHETIRRILRN 76 
                                   68***************************9985 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.9
                       DUF1670  17 laedvvelvdeefrepdslee 37 
                                   l +   ++++e+ r+ +++++
  gi|15668489|ref|NP_247287.1| 143 LENIGFKYINEYVRKFENKKD 163
                                   444445555555554444444 PP

>> RepB  RepB plasmid partitioning protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.015       6.8      17      38 ..       3      24 ..       1      34 [. 0.88
   2 !    7.7   0.0    0.0077       3.5      13      41 ..      45      73 ..      42      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.015
                          RepB 17 leerGvdreeiasalgldkqtv 38
                                  l ++G++ ++ia+ lg++k+tv
  gi|15668489|ref|NP_247287.1|  3 LYKKGYSARTIAKILGCSKSTV 24
                                  6789****************99 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0077
                          RepB 13 faarleerGvdreeiasalgldkqtvskm 41
                                  ++ +l + G++ +eia+ + ++ +t+++ 
  gi|15668489|ref|NP_247287.1| 45 EIIKLYQNGYTTTEIAKIMKCSHETIRRI 73
                                  799***********************544 PP

>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.14        66      29      61 ..       4      35 ..       1      45 [. 0.83
   2 ?    8.6   0.0    0.0032       1.5      25      65 ..      46      85 ..      40      89 .. 0.85
   3 ?   -1.6   0.0         5   2.3e+03      59      74 ..     126     140 ..     122     143 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.14
                       UPF0175 29 YeegrlSlgkAaelaglsrveflelLarrgipl 61
                                  Y++g  S    a+++g+s+ ++ + L + gi +
  gi|15668489|ref|NP_247287.1|  4 YKKG-YSARTIAKILGCSKSTVCYRLYKLGITP 35
                                  5554.388889************9999999976 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0032
                       UPF0175 25 AvklYeegrlSlgkAaelaglsrveflelLarrgiplinyd 65
                                  ++klY+ g  +  + a+++ +s  + +++L++++i+++  +
  gi|15668489|ref|NP_247287.1| 46 IIKLYQNGY-TTTEIAKIMKCSHETIRRILRNNNIDIRKSS 85
                                  588999887.667899********************87654 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5
                       UPF0175  59 iplinydeeeleeDle 74 
                                   i  + ++++++ e+++
  gi|15668489|ref|NP_247287.1| 126 IE-LKVTDKDFIEEFK 140
                                   55.4677777777764 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.085        39       1      30 [.       8      37 ..       8      44 .. 0.83
   2 ?    4.3   0.0     0.094        43      48      67 ..      45      64 ..      44      66 .. 0.89
   3 ?    6.1   0.1     0.025        11       1      29 [.      54      82 ..      54      87 .. 0.82
   4 ?   -0.4   0.0       2.7   1.2e+03      19      39 ..     204     222 ..     203     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.085
                                  EEHHHHHHHHTS-HHHHHHHHHHTT-S-EE CS
                        MerR_1  1 ysigevakilgvtthtlrywekegllkpkr 30
                                  ys +  akilg++++t+ y   +  + p r
  gi|15668489|ref|NP_247287.1|  8 YSARTIAKILGCSKSTVCYRLYKLGITPRR 37
                                  788999**********99887777777776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.094
                                  HHHHHHHTT--GGG---XXX CS
                        MerR_1 48 likyLlkrGltlkgikklln 67
                                   i +L ++G+t  +i+k+++
  gi|15668489|ref|NP_247287.1| 45 EIIKLYQNGYTTTEIAKIMK 64
                                  5889999***********97 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.025
                                  EEHHHHHHHHTS-HHHHHHHHHHTT-S-E CS
                        MerR_1  1 ysigevakilgvtthtlrywekegllkpk 29
                                  y+ +e aki  ++  t+r   +  ++ + 
  gi|15668489|ref|NP_247287.1| 54 YTTTEIAKIMKCSHETIRRILRNNNIDIR 82
                                  899***************87776666655 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.7
                                   HHHHHTT-S-EE-TTS-EEEE CS
                        MerR_1  19 ywekegllkpkrteggrryYt 39 
                                   +++ eg +++ + +g+ + Y 
  gi|15668489|ref|NP_247287.1| 204 FYDSEGSVVINK-KGN-YVYK 222
                                   899999999999.455.5554 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0058       2.6      18      33 ..       9      24 ..       8      26 .. 0.91
   2 ?   12.0   0.1   0.00043       0.2      20      37 .]      57      74 ..      54      74 .. 0.90
   3 ?   -0.2   0.3       2.8   1.3e+03       7      21 ..     149     163 ..     148     163 .. 0.80
   4 ?    1.8   0.1      0.66     3e+02       7      20 ..     214     227 ..     211     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0058
                        NUMOD1 18 SireAakyLgishntI 33
                                  S r  ak+Lg+s++t+
  gi|15668489|ref|NP_247287.1|  9 SARTIAKILGCSKSTV 24
                                  8899**********97 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00043
                        NUMOD1 20 reAakyLgishntInkyl 37
                                  +e ak++++sh tI++ l
  gi|15668489|ref|NP_247287.1| 57 TEIAKIMKCSHETIRRIL 74
                                  799************976 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.8
                        NUMOD1   7 DlntktigkFsSire 21 
                                   +++  +++kF+++++
  gi|15668489|ref|NP_247287.1| 149 KYINEYVRKFENKKD 163
                                   677888999999986 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.66
                        NUMOD1   7 DlntktigkFsSir 20 
                                   + ++++++k+ Si 
  gi|15668489|ref|NP_247287.1| 214 NKKGNYVYKYVSIA 227
                                   67899999999997 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.25   1.2e+02      25      37 ..      12      24 ..       5      32 .. 0.86
   2 ?    9.2   0.1    0.0026       1.2      22      45 ..      55      78 ..      48      84 .. 0.87
   3 ?   -2.2   0.0       9.4   4.3e+03      41      59 ..     198     216 ..     197     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.25
                       HTH_Mga 25 elakeLglseltl 37
                                  ++ak Lg+s +t+
  gi|15668489|ref|NP_247287.1| 12 TIAKILGCSKSTV 24
                                  79*******9997 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0026
                       HTH_Mga 22 tldelakeLglseltlqsdiseLn 45
                                  t++e+ak + +s  t++ ++++ n
  gi|15668489|ref|NP_247287.1| 55 TTTEIAKIMKCSHETIRRILRNNN 78
                                  578****************99865 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 9.4
                       HTH_Mga  41 iseLnelFpeelsivikkg 59 
                                   is L+ ++++e s+vi+k 
  gi|15668489|ref|NP_247287.1| 198 ISWLKGFYDSEGSVVINKK 216
                                   6779999999999999996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.078        36      20      40 ..       5      25 ..       3      33 .. 0.80
   2 ?    4.1   0.0     0.092        42      21      45 ..      52      76 ..      48      76 .. 0.88
   3 ?   -1.0   0.0       3.6   1.6e+03       8      55 ..     100     120 ..      94     128 .. 0.53
   4 ?   -0.6   0.1       2.7   1.3e+03      50      66 ..     209     225 ..     206     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.078
                                  HCCCHHCHHCCCTTSSCHCHH CS
                          TrmB 20 lgpatadeiaeelgvprskvY 40
                                  ++  +a++ia++lg ++s+v 
  gi|15668489|ref|NP_247287.1|  5 KKGYSARTIAKILGCSKSTVC 25
                                  566789*************95 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.092
                                  CCCHHCHHCCCTTSSCHCHHHHHHH CS
                          TrmB 21 gpatadeiaeelgvprskvYevLrs 45
                                     t++eia++ + ++ ++ ++Lr+
  gi|15668489|ref|NP_247287.1| 52 NGYTTTEIAKIMKCSHETIRRILRN 76
                                  56799******************86 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3.6
                                   HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                          TrmB   8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55 
                                     E+ +Y+                           L  L   G V+++
  gi|15668489|ref|NP_247287.1| 100 PSESLAYI---------------------------LGVLNGDGSVNKQ 120
                                   55555554...........................4444445555555 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.7
                                   TSEEEESSTTTEEEE-- CS
                          TrmB  50 GlVerekgrpklYravd 66 
                                   G V ++k+  ++Y++v+
  gi|15668489|ref|NP_247287.1| 209 GSVVINKKGNYVYKYVS 225
                                   78889999999999997 PP

>> RepA_N  Replication initiator protein A (RepA) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.27   1.2e+02      53      70 ..       8      25 ..       7      31 .. 0.85
   2 ?    7.0   0.0     0.012       5.4      53      74 ..      54      75 ..      49      76 .. 0.92
   3 ?    1.9   0.3      0.47   2.2e+02      32      62 ..     194     224 ..     178     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.27
                        RepA_N 53 ftieelaellncskqkvi 70
                                  ++   +a++l+csk++v 
  gi|15668489|ref|NP_247287.1|  8 YSARTIAKILGCSKSTVC 25
                                  78899**********997 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                        RepA_N 53 ftieelaellncskqkvikikk 74
                                  +t++e+a++++cs++++ +i++
  gi|15668489|ref|NP_247287.1| 54 YTTTEIAKIMKCSHETIRRILR 75
                                  9****************99986 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.47
                        RepA_N  32 dRlelSiknnwiDeegrvYliftieelaell 62 
                                   ++l++S  +++ D+eg+v ++ + + + +++
  gi|15668489|ref|NP_247287.1| 194 EKLMISWLKGFYDSEGSVVINKKGNYVYKYV 224
                                   68999*************8876666555555 PP

>> Phage_NinH  Phage NinH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       8.9   4.1e+03      22      33 ..      13      24 ..       8      29 .. 0.79
   2 ?   11.2   0.0   0.00056      0.26      19      39 ..      56      76 ..      43      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 8.9
                    Phage_NinH 22 vARrlkcsRatv 33
                                  +A+ l cs++tv
  gi|15668489|ref|NP_247287.1| 13 IAKILGCSKSTV 24
                                  678889999998 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00056
                    Phage_NinH 19 qtEvARrlkcsRatvRkYvrD 39
                                   tE+A+ +kcs  t+R+ +r+
  gi|15668489|ref|NP_247287.1| 56 TTEIAKIMKCSHETIRRILRN 76
                                  59***************9886 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00062      0.29      12      36 ..       7      31 ..       3      51 .. 0.81
   2 ?   -0.7   0.0       2.8   1.3e+03      11      31 ..      52      72 ..      45      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00062
                                  TT-HHHHHHHHTS-HHHHHHHHHHH CS
                        HTH_30 12 ggnisatAkaLhvHrnTlryRLrri 36
                                  g +++  Ak L++++ T+ yRL ++
  gi|15668489|ref|NP_247287.1|  7 GYSARTIAKILGCSKSTVCYRLYKL 31
                                  6788999***************885 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.8
                                  TTT-HHHHHHHHTS-HHHHHH CS
                        HTH_30 11 nggnisatAkaLhvHrnTlry 31
                                  ng   ++ Ak + ++  T+r 
  gi|15668489|ref|NP_247287.1| 52 NGYTTTEIAKIMKCSHETIRR 72
                                  666778888888888888874 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0021      0.98      19      41 ..       9      31 ..       8      31 .. 0.91
   2 ?    0.7   0.0         1   4.7e+02      20      36 ..      56      72 ..      54      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0021
                 HTH_AsnC-type 19 syaeLAervGlSestvlrRvrrL 41
                                  s + +A+ +G+S stv  R+ +L
  gi|15668489|ref|NP_247287.1|  9 SARTIAKILGCSKSTVCYRLYKL 31
                                  6799*************999887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1
                 HTH_AsnC-type 20 yaeLAervGlSestvlr 36
                                   +e+A+   +S +t++r
  gi|15668489|ref|NP_247287.1| 56 TTEIAKIMKCSHETIRR 72
                                  68999999999999987 PP

>> GcrA  GcrA cell cycle regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00084      0.39      13      49 ..       2      37 ..       1      94 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00084
                          GcrA 13 klwleGlSasqiaaqlggvsRnAViGkvhRLglsgra 49
                                  +l+++G Sa+ ia+ lg  s++ V  ++ +Lg++ r 
  gi|15668489|ref|NP_247287.1|  2 ELYKKGYSARTIAKILG-CSKSTVCYRLYKLGITPRR 37
                                  689***********999.9**************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1466  (0.081767); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1635.93
//
Query:       gi|15668490|ref|NP_247288.1|  [L=135]
Description: hypothetical protein MJ_0315 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.7e-39  133.7   0.0    3.2e-39  133.5   0.0    1.0  1  AdoMet_dc  S-adenosylmethionine decarboxylase


Domain annotation for each model (and alignments):
>> AdoMet_dc  S-adenosylmethionine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.5   0.0   1.8e-43   3.2e-39       1     106 []      19     125 ..      19     125 .. 0.99

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 1.8e-43
                                   EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEEEST.H CS
                     AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkfepeGvsvvvliaeShlsiHtwpetgyaaiDvftcge.i 80 
                                   hl+++l+gcdp+ l+d e +e++l + ++a+gat++ v +hkf+p+G+++v+++aeSh++iHt+pe+gyaa+Dvftcge +
  gi|15668490|ref|NP_247288.1|  19 HLILELWGCDPKALDDIEGIEKMLVDSVKACGATLICVRTHKFSPQGATGVAVLAESHIAIHTYPEYGYAALDVFTCGEhT 99 
                                   9******************************************************************************** PP

                                   HHHHHHHHHHHHHT-SEEEEEEEEEE CS
                     AdoMet_dc  81 spekaleylieafkadrvtvdelkRG 106
                                   +p kale+++e +k++++++  lkRG
  gi|15668490|ref|NP_247288.1| 100 DPYKALEVIREFLKPKSIQIIDLKRG 125
                                   ************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 888.82
//
Query:       gi|15668491|ref|NP_247289.1|  [L=165]
Description: pyruvoyl-dependent arginine decarboxylase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-47  159.3   0.0    7.8e-47  159.1   0.0    1.0  1  PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC


Domain annotation for each model (and alignments):
>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.1   0.0   4.3e-51   7.8e-47       2     162 .]      15     163 ..      14     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.1 bits;  conditional E-value: 4.3e-51
                      PvlArgDC   2 PkkvfltkGvgeskeelasFdlALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepgrliaa 82 
                                   P++v l++G++e+++ l++Fd ALl+AgI+n+NL+++SSi+Ppeaeiv+ +++    p+G++v+++++++ s+ pg++i+a
  gi|15668491|ref|NP_247289.1|  15 PNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISSIMPPEAEIVPLPKL----PMGALVPTAYGYIISDVPGETISA 91 
                                   99********************************************9988877....************************ PP

                      PvlArgDC  83 avgvaipkdekkgGyiaEysgfgeseeeaeeeaeelaaemlattrglleekiietkeievaaveakvekygtvlaaavfv 162
                                   a++vaipkd++ +G+i+Ey+g++ s++eae++++e+a+ ++++ rg+      e  +ie+ ave++vek g+++aaa+++
  gi|15668491|ref|NP_247289.1|  92 AISVAIPKDKSLCGLIMEYEGKC-SKKEAEKTVREMAKIGFEM-RGW------ELDRIESIAVEHTVEKLGCAFAAAALW 163
                                   *********************99.******************7.***......999*********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1091.03
//
Query:       gi|15668492|ref|NP_247290.1|  [L=224]
Description: hypothetical protein MJ_0317 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
       0.01   16.2   0.4      0.067   13.5   0.0    2.3  3  DUF5461   Family of unknown function (DUF5461)


Domain annotation for each model (and alignments):
>> DUF5461  Family of unknown function (DUF5461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   3.7e-06     0.067      33      79 ..       8      54 ..       3      64 .. 0.91
   2 ?   -1.2   0.0      0.14   2.5e+03      71      89 ..      96     114 ..      86     118 .. 0.82
   3 ?   -1.7   0.0      0.21   3.7e+03      67      86 ..     190     211 ..     162     217 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-06
                       DUF5461 33 kdyiigrvgiirisktyiGivlvdGvkipfvaevhlnnkidiyldpr 79
                                  ++ +ig   +++  +ty G vl    + p    v +n+k +iy++p 
  gi|15668492|ref|NP_247290.1|  8 RKDMIGEFTLNKSFNTYRGKVLKADFNGPIEGIVMKNKKEHIYFYPL 54
                                  4679*****************************************96 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.14
                       DUF5461  71 kidiyldprkdfylallvG 89 
                                   ++++y +  k  yl  l+G
  gi|15668492|ref|NP_247290.1|  96 TLKVYYETPKTSYLGRLLG 114
                                   6788999889999998887 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.21
                       DUF5461  67 hlnnkidiyldp..rkdfylal 86 
                                     ++k+ +y +    kd yl +
  gi|15668492|ref|NP_247290.1| 190 NIEDKVFVYPYGvvSKDDYLGK 211
                                   4444444443322245555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1456.92
//
Query:       gi|15668493|ref|NP_247291.1|  [L=301]
Description: formylmethanofuran--tetrahydromethanopterin formyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-67  226.1   3.5    2.7e-67  225.4   3.5    1.3  1  FTR_C     FTR, proximal lobe
    4.4e-66  221.2   0.9    1.4e-65  219.6   0.0    2.1  3  FTR       Formylmethanofuran-tetrahydromethanopterin formyltr


Domain annotation for each model (and alignments):
>> FTR_C  FTR, proximal lobe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.4   3.5     3e-71   2.7e-67       1     149 []     148     299 ..     148     299 .. 0.99

  Alignments for each domain:
  == domain 1  score: 225.4 bits;  conditional E-value: 3e-71
                                   EEEEEES-EEEEEEEEEEEEEEEESSHHHHHHHHHHHHHHHHTSTTEE--SGGGEESS-EEES-...S-TT-SEEE-GGG- CS
                         FTR_C   1 geflieeklgvvkgvaGgnllilaedqeaaleaaeaaveaikkvegvitpFpGgivrsgSKvgs...kykflkastNeafc 78 
                                   gef++e k+g++kgvaGgn++i+a+++++al aaeaav+ai++v+gvitpFpGg+v+sgSKvg+   kykf+ a+tN+++c
  gi|15668493|ref|NP_247291.1| 148 GEFITEAKFGIKKGVAGGNFFIMADTNASALIAAEAAVNAIASVDGVITPFPGGVVASGSKVGAsnpKYKFMVATTNHKMC 228
                                   8**************************************************************98999************* PP

                                   TTSTT....----TT--EEEEEEEEESSHHHHHHHHHHHHHHHTTSTTEEEEE---STTSS-SEEEEGGGG CS
                         FTR_C  79 ptlkekveeselpedveavlEiVidgldeeavaeamkagieaavkvegvlkisAgNygGkLGkykfkLkel 149
                                   ptlk+ ve+se+pedv+ v+EiVidg+dee+v+eamk+gi aa++v+gv+ki+AgNygGkLGky+f+L+el
  gi|15668493|ref|NP_247291.1| 229 PTLKGVVEDSEIPEDVNGVYEIVIDGVDEESVKEAMKQGILAATRVKGVKKITAGNYGGKLGKYQFNLREL 299
                                   ********************************************************************996 PP

>> FTR  Formylmethanofuran-tetrahydromethanopterin formyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.6   0.0   1.6e-69   1.4e-65       1     142 []       1     145 [.       1     145 [. 0.98
   2 ?   -1.4   0.1      0.22     2e+03      24      47 ..     168     191 ..     162     207 .. 0.70
   3 ?   -2.0   0.0      0.35   3.1e+03      59      90 ..     234     266 ..     221     276 .. 0.64

  Alignments for each domain:
  == domain 1  score: 219.6 bits;  conditional E-value: 1.6e-69
                                   -EETTEEE-S-EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHSS-S-TTTSS-EEEESEEB-GGGSTTSS-EEEEEEEESSH CS
                           FTR   1 leingveiedtfaEaFeikvtrviiTaatkkwakeaateatgfatsvigceaEagiervlspeetpDgRpGvailifaask 81 
                                   +eingv iedtfaEaF+i+v+rv+iTaatkkwak+aateatgf++svi+c+aEagie++++p++tpDgRpG++i+i++ +k
  gi|15668493|ref|NP_247291.1|   1 MEINGVYIEDTFAEAFPIWVSRVLITAATKKWAKIAATEATGFGCSVIMCPAEAGIEKYVPPSKTPDGRPGFIIQICHPKK 81 
                                   89******************************************************************************* PP

                                   HHHHHHHHHHHHHHTTTSTT-EEEE--...GG-SEEHHHHHHGGGTT--EEEEETTEEEEEEEE CS
                           FTR  82 kklekqlleRigqcvLtapttavfngl...aeekiklgkklrffgDgyeiekelggrkvwriPv 142
                                   ++le+q+leR+gqcvLt+ptta+f+++   a+e++k+g kl+ffgDgye+++el+grkv++iP+
  gi|15668493|ref|NP_247291.1|  82 SELEHQMLERLGQCVLTCPTTAIFDAMgdmADEQLKVGFKLKFFGDGYEKKDELYGRKVYKIPI 145
                                   ***************************76556*******************************8 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.22
                                   EEE-SSHHHHHHHHHHHHSS-S-T CS
                           FTR  24 iiTaatkkwakeaateatgfatsv 47 
                                    i a+t++ a +aa++a    +sv
  gi|15668493|ref|NP_247291.1| 168 FIMADTNASALIAAEAAVNAIASV 191
                                   567777777777777666555554 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.35
                                   EB-GGGSTTSS-EEE.EEEEESSHHHHHHHHHH CS
                           FTR  59 vlspeetpDgRpGva.ilifaaskkklekqlle 90 
                                   v++++e p++  Gv+ i+i  ++++++++ +++
  gi|15668493|ref|NP_247291.1| 234 VVEDSEIPEDVNGVYeIVIDGVDEESVKEAMKQ 266
                                   566777777777765244445666655555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 2325.38
//
Query:       gi|15668494|ref|NP_247292.1|  [L=97]
Description: hypothetical protein MJ_0319 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-41  138.0   4.5    9.6e-41  137.9   4.5    1.0  1  DUF211    Uncharacterized ArCR, COG1888
  ------ inclusion threshold ------
      0.046   13.9   0.0      0.054   13.6   0.0    1.2  1  PilN      Fimbrial assembly protein (PilN)
      0.065   13.6   0.1      0.092   13.1   0.1    1.3  1  BRCT      BRCA1 C Terminus (BRCT) domain
       0.11   13.0   0.1       0.13   12.7   0.1    1.2  1  Rtt106    Histone chaperone Rttp106-like
       0.16   12.5   0.3       0.16   12.5   0.3    1.7  2  HMA       Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.9   4.5   2.7e-44   9.6e-41       2      88 ..       4      90 ..       3      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 137.9 bits;  conditional E-value: 2.7e-44
                                  EEEEEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEEEESS- CS
                        DUF211  2 irrlvLDvlkphepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevvaGkki 84
                                  irr+vLD+lkphep+i+++a kl++l+++dgvnitv+e+Dketen+k+tieG+n+d++ei+e+ie+lgg+ihSiDevvaGkki
  gi|15668494|ref|NP_247292.1|  4 IRRIVLDILKPHEPKITDMALKLTSLSNIDGVNITVYEIDKETENVKVTIEGNNLDFDEIQEIIESLGGTIHSIDEVVAGKKI 86
                                  9********************************************************************************** PP

                                  ---- CS
                        DUF211 85 veev 88
                                  +eev
  gi|15668494|ref|NP_247292.1| 87 IEEV 90
                                  **97 PP

>> PilN  Fimbrial assembly protein (PilN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.5e-05     0.054      23      47 ..      33      72 ..      17      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                          PilN 23 gn...............qltitGsAvsndeVaefmrnLeg 47
                                  ++               ++ti+G+  ++de+ e +++L+g
  gi|15668494|ref|NP_247292.1| 33 DGvnitvyeidketenvKVTIEGNNLDFDEIQEIIESLGG 72
                                  33444444444447788*********************98 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.6e-05     0.092       8      36 ..      48      74 ..      44      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                                  TEEEEEEESTSSHHHHHHHHHHHHTTCEE CS
                          BRCT  8 gckfvitgvldnftrdeleelikehGGkv 36
                                  ++k+ i    +n + de++e+i+++GG++
  gi|15668494|ref|NP_247292.1| 48 NVKVTI--EGNNLDFDEIQEIIESLGGTI 74
                                  778888..8899999*************9 PP

>> Rtt106  Histone chaperone Rttp106-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.5e-05      0.13      31      70 ..      26      65 ..      19      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                        Rtt106 31 fiplediesvsfeRvsvtsrtfdlvvelkkeeveFsmidq 70
                                  + +l++i++v+++ +++ + t +++v++++++++F+ i++
  gi|15668494|ref|NP_247292.1| 26 LTSLSNIDGVNITVYEIDKETENVKVTIEGNNLDFDEIQE 65
                                  568999*******77*************99******9975 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   4.3e-05      0.16      19      60 ..      28      71 ..      26      73 .. 0.88
   2 ?   -1.7   0.1       1.1     4e+03      50      56 ..      84      90 ..      74      92 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.3e-05
                           HMA 19 vLselpgV..esvkvdlatktvtVegdaestklrkiieaiekag 60
                                  +Ls+++gV  + +++d +t  v V+ +   +++ +i+e ie++g
  gi|15668494|ref|NP_247292.1| 28 SLSNIDGVniTVYEIDKETENVKVTIEGNNLDFDEIQEIIESLG 71
                                  789999999888999999999999999999999********988 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                           HMA 50 rkiieai 56
                                  +kiie++
  gi|15668494|ref|NP_247292.1| 84 KKIIEEV 90
                                  5677666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 644.22
//
Query:       gi|15668495|ref|NP_247293.1|  [L=219]
Description: GTP-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-18   64.8   0.0    1.1e-17   64.2   0.0    1.3  1  MMR_HSR1      50S ribosome-binding GTPase
    1.4e-10   40.9   0.1    1.2e-09   37.9   0.1    2.0  1  FeoB_N        Ferrous iron transport protein B
    1.6e-06   28.2   0.5     0.0083   16.1   0.1    2.6  2  RsgA_GTPase   RsgA GTPase
     0.0008   18.9   0.1     0.0019   17.6   0.1    1.7  1  SRPRB         Signal recognition particle receptor beta subun
     0.0065   15.8   0.3      0.019   14.2   0.3    2.0  1  Septin        Septin
     0.0072   15.9   0.2       0.16   11.5   0.0    2.5  3  GTP_EFTU      Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.013   15.5   0.4       0.22   11.6   0.4    2.3  1  Dynamin_N     Dynamin family
      0.039   14.5   0.1      0.062   13.8   0.1    1.4  1  ABC_tran      ABC transporter
      0.041   13.2   0.0      0.077   12.3   0.0    1.4  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.064   13.5   1.3       0.18   12.0   0.1    2.2  2  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.067   13.6   0.0       0.15   12.5   0.0    1.6  1  HTH_26        Cro/C1-type HTH DNA-binding domain
      0.068   12.6   0.0       0.11   12.0   0.0    1.3  1  TniB          Bacterial TniB protein
       0.07   12.7   1.0       0.78    9.3   0.1    2.3  2  Ras           Ras family


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   7.6e-21   1.1e-17       1     114 []      26     155 ..      26     155 .. 0.64

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 7.6e-21
                                   EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGC......SS..HHHHHHHHHHHHHH CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGl......ie..gaseekglgkafla 72 
                                   +v++vGr+NvGKSt+++ +tg+   +v++kpg+T++ine+ +     e++lvD+pG+       +  +++ + ++ + +++
  gi|15668495|ref|NP_247293.1|  26 KVIVVGRSNVGKSTFVRLMTGRkDIRVGKKPGVTLKINEYDMG----EYILVDMPGFgymaglPKkvQEKIKDEIVHYIEE 102
                                   699******************9568***************996....7********4332221111111111123333333 PP

                                   HHC.TSEEEEEEETT...........TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  73 lee.adlillvvdas...........eeklkpldeeleelleeakkplilvlnk 114
                                   + +   +++ ++d +           + +  p+d e+ +++++ k+  ilv+nk
  gi|15668495|ref|NP_247293.1| 103 HADeIAAAVQIIDTKsffeiverwkgR-GEIPIDLEMFDFITDLKISPILVANK 155
                                   333345555555544666665555432.22466777777777677777777776 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.1   8.7e-13   1.2e-09       2     156 .]      26     205 ..      25     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 8.7e-13
                                   EEEEEESTTSSHHHHHHHHHTTS.EEEEESTTSSSEEEEEEEEETTEEEEEEE----SSS..SSSSHHHHHHHHHHH.... CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgak.qkvgNwpGvtvekkegklklkgkeveivDlPGiYsl..sayseeekvardfll.... 75 
                                   +v++vG  nvGk+t++  +tg k  +vg  pGvt + +e  +     e+ +vD+PG   +   +   +ek+  ++++    
  gi|15668495|ref|NP_247293.1|  26 KVIVVGRSNVGKSTFVRLMTGRKdIRVGKKPGVTLKINEYDMG----EYILVDMPGFGYMagLPKKVQEKIKDEIVHyiee 102
                                   6899*****************87469**********9998888....9********9544354566777777776655533 PP

                                   .CTSSSEEEEEEEGGG....HHH.........HHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-..... CS
                        FeoB_N  76 .eeepdvvvnvvdatn....ler.........nLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvp..... 137
                                     +e+ + v+++d+++    +er         +L ++  +++l+++ +l+ n++d+++k++ +  l+ + e L+++     
  gi|15668495|ref|NP_247293.1| 103 hADEIAAAVQIIDTKSffeiVERwkgrgeipiDLEMFDFITDLKISPILVANKMDKIKKEEWDAVLDGICEYLKCQppwhq 183
                                   355666789****986333235544444333357777788899999**************999999999999998656666 PP

                                   ...EEEEBTTTTBTHHHHHHHH CS
                        FeoB_N 138 ...vvktsakkkegieellkai 156
                                      +v+++ k+++giee++k+i
  gi|15668495|ref|NP_247293.1| 184 wkfIVPAILKEGKGIEEIKKKI 205
                                   6668888888888888888875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1     6e-06    0.0083      96     129 ..      21      54 ..       4      82 .. 0.76
   2 !    9.8   0.0    0.0005      0.69      43     103 ..     143     211 ..     137     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6e-06
                                   HCTTSEEEEECSTTSSHHHHHHHHCTT-----S- CS
                   RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallpelelktge 129
                                   + ++  +++vG S vGKSt++  +++++++++g+
  gi|15668495|ref|NP_247293.1|  21 KKTKPKVIVVGRSNVGKSTFVRLMTGRKDIRVGK 54 
                                   334445799******************9999985 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0005
                                   HHTT-EEEEEEE-GGG--HHH.........HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEE CS
                   RsgA_GTPase  43 eekgiepvivlnKiDlleeee.........eleelkeelealgyevllvsaktkegleelkellkdktsv 103
                                    + +i+p++v nK+D +++ee         e+ + +   +++ + v ++  k+++g+ee+k+++ +++ +
  gi|15668495|ref|NP_247293.1| 143 TDLKISPILVANKMDKIKKEEwdavldgicEYLKCQPPWHQWKFIVPAI-LKEGKGIEEIKKKILERVRL 211
                                   6679*****************9999998888888888888888877777.56689999999988877765 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.4e-06    0.0019       2      62 ..      23      81 ..      22     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                                  ---EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT-GCC CS
                         SRPRB  2 skpavllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfPGhekl 62
                                  +kp+v++vG s+ GK + f rL+t+ + +  +  ++ ++lk+++ +  +  l+D+PG   +
  gi|15668495|ref|NP_247293.1| 23 TKPKVIVVGRSNVGKST-FVRLMTGRK-DIRVGKKPGVTLKINEYDMGEYILVDMPGFGYM 81
                                  689************76.889999865.667889********999999*********7543 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.3   1.4e-05     0.019       6      75 ..      26     122 ..      21     178 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                                   EEEEEEBTTSSCCCCCCTTSSSS----.............................--------------S-EEEEEEEEE CS
                        Septin   6 tlmvvGesglGkttlintlfetdliee.............................ekleeasekkkktveikkkkvviee 57 
                                    ++vvG+s +Gk+t+++ +  +++i+                                l+++  ++k + ei ++   iee
  gi|15668495|ref|NP_247293.1|  26 KVIVVGRSNVGKSTFVRLMTGRKDIRVgkkpgvtlkineydmgeyilvdmpgfgymAGLPKKV-QEKIKDEIVHY---IEE 102
                                   699*******************99999777777777777777777777776554332222111.12222233332...333 PP

                                   T..TCEEEEEEEE---BSSS CS
                        Septin  58 d..gvklnltviDtpgfGda 75 
                                   +  ++   +++iDt  f + 
  gi|15668495|ref|NP_247293.1| 103 HadEIAAAVQIIDTKSFFEI 122
                                   21135556677777777555 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.072        99       5      24 ..      26      45 ..      22      67 .. 0.80
   2 ?   -2.8   0.0       2.7   3.7e+03      66      79 ..      64      77 ..      49      78 .. 0.69
   3 !   11.5   0.0   0.00012      0.16     113     148 ..     137     173 ..      93     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.072
                                  EEEEEESTTSSHHHHHHHHH CS
                      GTP_EFTU  5 nigiighvDhGKtTLtdrLl 24
                                  +++++g  + GK+T++  ++
  gi|15668495|ref|NP_247293.1| 26 KVIVVGRSNVGKSTFVRLMT 45
                                  689***********985444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                                  TCSSEEEEEEEESS CS
                      GTP_EFTU 66 etkkylinliDtPG 79
                                  e++  ++ l+D PG
  gi|15668495|ref|NP_247293.1| 64 EYDMGEYILVDMPG 77
                                  34444789999999 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00012
                                   HHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHH CS
                      GTP_EFTU 113 evlrlalkegvpiivfiNKmDrl.kaelkeiveevkq 148
                                   e++  + ++++ +i++ NKmD++ k+e + + + + +
  gi|15668495|ref|NP_247293.1| 137 EMFDFITDLKISPILVANKMDKIkKEEWDAVLDGICE 173
                                   5667788999*************76677766666555 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00016      0.22       1      47 [.      27      74 ..      27     140 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                  EEEEEBTTTTHHHHHHHHHTS--S---SSS.---S-EEEEECCT---C CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnp.tTrrplelqlgeeeeas 47
                                  ++vvG  + GKS+++  ++g++   +g+ p +T +++e  +ge   + 
  gi|15668495|ref|NP_247293.1| 27 VIVVGRSNVGKSTFVRLMTGRKDIRVGKKPgVTLKINEYDMGEYILVD 74
                                  79******************9877777774378888877775544433 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.5e-05     0.062      12      41 ..      25      54 ..      14     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.5e-05
                                  SEEEEEESTTSSHHHHHHHHTTSS--SEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 12 ekvaivGenGaGKStLlkllagllkpteGe 41
                                   kv +vG++  GKSt+++l++g  +   G+
  gi|15668495|ref|NP_247293.1| 25 PKVIVVGRSNVGKSTFVRLMTGRKDIRVGK 54
                                  5899******************99876665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.5e-05     0.077      21      59 ..       6      44 ..       3      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-05
                                  EEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHH CS
                  FtsK_SpoIIIE 21 algkeisgnplvldlkkmashllvaGatgsGKStalntL 59
                                  ++++   + +++ ++kk  + ++v+G++  GKSt+++ +
  gi|15668495|ref|NP_247293.1|  6 DFFERYKNLKEKYEEKKTKPKVIVVGRSNVGKSTFVRLM 44
                                  55666677788888888889****************966 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00013      0.18       1      25 [.      26      49 ..      26      70 .. 0.73
   2 ?   -0.3   0.1      0.84   1.2e+03     109     119 ..     147     157 ..      89     158 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                  EEEEESSTTSSHHHHHHCHCT-CCC CS
                           Roc  1 KvvlvGdsgvGKtsllkrfvedkfs 25
                                  Kv++vG s+vGK+++++ +++++ +
  gi|15668495|ref|NP_247293.1| 26 KVIVVGRSNVGKSTFVR-LMTGRKD 49
                                  9*************985.5555555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.84
                                   S-EEEEEE-TT CS
                           Roc 109 spvilvgnkiD 119
                                   +  ilv+nk+D
  gi|15668495|ref|NP_247293.1| 147 ISPILVANKMD 157
                                   33466677766 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.15      25      54 ..     154     179 ..     149     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                        HTH_26  25 atlsrlvkgkpervsldtLdkiCdaLgctp 54 
                                   +++++++k++       +Ld iC++L+c+p
  gi|15668495|ref|NP_247293.1| 154 NKMDKIKKEE----WDAVLDGICEYLKCQP 179
                                   5666666666....3589***********9 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.6e-05      0.11      23      54 ..      11      43 ..       3      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-05
                          TniB 23 LeeLley.pkrkrmpnlllvGdsnnGKtmivek 54
                                   ++L e+  ++k  p++++vG+sn+GK++ v+ 
  gi|15668495|ref|NP_247293.1| 11 YKNLKEKyEEKKTKPKVIVVGRSNVGKSTFVRL 43
                                  55665551445555***************9875 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00056      0.78       1      17 [.      26      42 ..      26      52 .. 0.89
   2 ?    1.8   0.1      0.12   1.6e+02     102     119 ..     137     161 ..      89     169 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00056
                                  EEEEEESTTSSHHHHHH CS
                           Ras  1 KlvlvGdsavGKtslll 17
                                  K+++vG s+vGK++++ 
  gi|15668495|ref|NP_247293.1| 26 KVIVVGRSNVGKSTFVR 42
                                  99************985 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.12
                                   T.......TTSEEEEEEETTTGGGG CS
                           Ras 102 e.......envpivLvGnKvDleek 119
                                   e        +++ +Lv+nK+D  +k
  gi|15668495|ref|NP_247293.1| 137 EmfdfitdLKISPILVANKMDKIKK 161
                                   2444453445777999999997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 1360.88
//
Query:       gi|15668496|ref|NP_247294.1|  [L=122]
Description: hypothetical protein MJ_0321 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0097   15.3   3.0      0.011   15.1   3.0    1.1  1  Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
  ------ inclusion threshold ------
       0.21   11.3   0.0       0.21   11.3   0.0    2.9  3  MlaE             Permease MlaE
       0.24   11.4   3.7        1.5    8.8   0.1    2.4  3  RseC_MucC        Positive regulator of sigma(E), RseC/MucC
       0.26   11.4   1.4       0.36   11.0   0.1    1.8  2  CcmD             Heme exporter protein D (CcmD)
       0.32   10.6   5.2        0.5   10.0   5.2    1.4  1  Wzy_C            O-Antigen ligase
        0.7   10.1   9.9          1    9.6   9.9    1.3  1  DUF3792          Protein of unknown function (DUF3792)
        3.5    7.9   6.5       0.37   11.0   0.3    2.3  2  Holin_SPP1       SPP1 phage holin


Domain annotation for each model (and alignments):
>> Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   3.0   4.3e-06     0.011     193     265 ..       6      88 ..       1     107 [. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.3e-06
               Cyt_bd_oxida_II 193 lvlalvllvllvvvllwtll.......l.vllllavlalllavlllrk.kr.eglaflasaltvllvvlllavslfPyllp 263
                                   +++a+v+ ++++ ++l +++       + v+ l+ +++++l+++  +k ++ e+   +++++++++ ++l+a+s  P +  
  gi|15668496|ref|NP_247294.1|   6 KIVAIVTSIAVICISLTVIFcdtlvlaVgVPTLVLLWLVFLGWINNKKlDKgEMRRAITGSIVIAFFIILIAISKNPDIYS 86 
                                   45556666666666665555666543323444455555555555544442246678999999999999999***9999987 PP

               Cyt_bd_oxida_II 264 ss 265
                                   ++
  gi|15668496|ref|NP_247294.1|  87 NN 88 
                                   76 PP

>> MlaE  Permease MlaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.2      0.26   6.7e+02     187     209 ..       8      30 ..       2      33 .. 0.69
   2 ?    3.0   0.1     0.026        68     185     205 ..      57      77 ..      50      80 .. 0.83
   3 ?   11.3   0.0   8.1e-05      0.21     162     185 ..      93     116 ..      86     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.26
                          MlaE 187 vgrattravvtsivlilvvdlvl 209
                                   v+  t  av+  +++++++d+++
  gi|15668496|ref|NP_247294.1|   8 VAIVTSIAVICISLTVIFCDTLV 30 
                                   56667777888888888877766 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.026
                          MlaE 185 egvgrattravvtsivlilvv 205
                                    ++ ra+t ++v+++++il++
  gi|15668496|ref|NP_247294.1|  57 GEMRRAITGSIVIAFFIILIA 77 
                                   567899999999999999985 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 8.1e-05
                          MlaE 162 alvfGliialiacyqGltakggae 185
                                   +l+fG+++++i++y G++ +++++
  gi|15668496|ref|NP_247294.1|  93 SLFFGMVTTIIGYYFGYRSGKESK 116
                                   79***************9988765 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.6     0.055   1.4e+02      88     115 ..      23      50 ..       2      64 .. 0.44
   2 ?    5.2   0.4    0.0073        19      67     113 ..      29      78 ..      24      89 .. 0.78
   3 ?    8.8   0.1   0.00057       1.5      83     122 ..      73     119 ..      65     122 .] 0.73

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.055
                     RseC_MucC  88 llgssellaalgallglv.lgflivrlls 115
                                   + +  ++l++++++  lv l ++++ +++
  gi|15668496|ref|NP_247294.1|  23 V-IFCDTLVLAVGVPTLVlLWLVFLGWIN 50 
                                   2.333333333333333303333333444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0073
                     RseC_MucC  67 allvYllPllllilgallgsall...gssellaalgallglvlgflivrl 113
                                    +l+ ++P l+l+  ++lg +      ++e+  a+++ +++++ ++++ +
  gi|15668496|ref|NP_247294.1|  29 LVLAVGVPTLVLLWLVFLGWINNkklDKGEMRRAITGSIVIAFFIILIAI 78 
                                   56777899999999999998877888888888888888888777777655 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00057
                     RseC_MucC  83 llgsall.......gssellaalgallglvlgflivrllskrlkkks 122
                                   ++  a++        ++e+++++++++ +++g+++ ++  k+ k++s
  gi|15668496|ref|NP_247294.1|  73 IILIAISknpdiysNNKEIFSLFFGMVTTIIGYYFGYRSGKESKNSS 119
                                   2222222455677799********************99999876655 PP

>> CcmD  Heme exporter protein D (CcmD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00014      0.36       9      32 ..      31      54 ..      29      61 .. 0.91
   2 ?   -2.1   0.2       1.6   4.2e+03      19      24 ..      70      75 ..      67      80 .. 0.41

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                          CcmD  9 lsYgitllvlagLilwslrdrrrl 32
                                  l++g+  lvl++L+++ ++  ++l
  gi|15668496|ref|NP_247294.1| 31 LAVGVPTLVLLWLVFLGWINNKKL 54
                                  89****************999986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                          CcmD 19 agLilw 24
                                  a  i++
  gi|15668496|ref|NP_247294.1| 70 AFFIIL 75
                                  222222 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.2    0.0002       0.5       2      74 ..      15      93 ..      10     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0002
                         Wzy_C  2 alllsllalflstsRsgiigl..lvalivlliifykrri....pfllllgilvgvilliilfvlstnletlknitkafg 74
                                  a+++++l++++  + +  +g+  lv+l ++++ +++++       ++ + + ++++++iil+++s+n     n++ +f+
  gi|15668496|ref|NP_247294.1| 15 AVICISLTVIFCDTLVLAVGVptLVLLWLVFLGWINNKKldkgEMRRAITGSIVIAFFIILIAISKNPDIYSNNKEIFS 93
                                  55666677777777777777777777777788888888899*988888889999************9998888888776 PP

>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   9.9   0.00039         1      13     111 ..       9     104 ..       6     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00039
                       DUF3792  13 lvitlilllilalllyftslsekvlsililiililsvfigGflagkkakkkgllnGllvGllyflillllsllikksgsaf 93 
                                    ++t i+++ ++l + f   +  vl +++  +++l +++ G++ +kk +k   +  +++G + ++++++l  ++k+    +
  gi|15668496|ref|NP_247294.1|   9 AIVTSIAVICISLTVIFC--DTLVLAVGVPTLVLLWLVFLGWINNKKLDKGE-MRRAITGSIVIAFFIILIAISKNPDIYS 86 
                                   577778888888888887..56678888888888888999**9988776655.8889999999999777777888888889 PP

                       DUF3792  94 slkllikllllllagaiG 111
                                   + k + +l++++++ +iG
  gi|15668496|ref|NP_247294.1|  87 NNKEIFSLFFGMVTTIIG 104
                                   999999999999999998 PP

>> Holin_SPP1  SPP1 phage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   2.9      0.14   3.6e+02      14      53 ..      35      77 ..       6      84 .. 0.64
   2 ?   11.0   0.3   0.00015      0.37       1      55 [.      53     106 ..      53     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.14
                    Holin_SPP1 14 llallnqlltilGk.nplpideealytait..lvftvataiva 53
                                  + +l+   l+ lG+ n    d++++  ait  +v+ +  +++a
  gi|15668496|ref|NP_247294.1| 35 VPTLVLLWLVFLGWiNNKKLDKGEMRRAITgsIVIAFFIILIA 77
                                  4456666667777535556666666666542244444444444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00015
                    Holin_SPP1   1 kldkgtlvrtillllallnqll.tilGknplpideealytaitlvftvataivawy 55 
                                   kldkg + r+i + + +   ++ ++  knp   +++  +++++l f ++t+i+++y
  gi|15668496|ref|NP_247294.1|  53 KLDKGEMRRAITGSIVIAFFIIlIAISKNPDIYSNN--KEIFSLFFGMVTTIIGYY 106
                                   689********9988877655548889999888888..9****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1136  (0.063361); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.58
# Mc/sec: 637.96
//
Query:       gi|15668497|ref|NP_247295.1|  [L=106]
Description: 30S ribosomal protein S10P [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-28   98.9   0.2    1.7e-28   98.7   0.2    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
  ------ inclusion threshold ------
      0.011   16.5   0.1      0.022   15.6   0.0    1.5  2  PriA_C         Primosomal protein N C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.2   1.9e-32   1.7e-28       1      97 [.      10     103 ..      10     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 1.9e-32
                                   EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHHHH CS
                 Ribosomal_S10   1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketidt 80 
                                   ri+l+S+d+k+L++++++i+++a+++g++++gp+plPtk++rv ++ksp ++ + + +++ +++hkRlidi da+++ +++
  gi|15668497|ref|NP_247295.1|  10 RIKLSSTDHKVLDEICRQIKEIAEKTGVDISGPIPLPTKVLRVVTRKSPDGEgSSTFDRWTMKIHKRLIDI-DADERALRH 89 
                                   8**********************************************************************.8******** PP

                                   HS-...S---SS-EEEE CS
                 Ribosomal_S10  81 llkllqlnlpegVsvev 97 
                                   ++k   +++p+ V++e+
  gi|15668497|ref|NP_247295.1|  90 IMK---IRIPDNVQIEI 103
                                   ***...*********98 PP

>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   2.4e-06     0.022       6      52 ..       9      51 ..       6      57 .. 0.88
   2 ?   -2.3   0.0      0.89     8e+03      67      67 ..      85      85 ..      68     103 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-06
                        PriA_C  6 alirvsgkdeekveeaaeelaellkealkleeveilgpapapiakik 52
                                  a+i++s++d + + e +++++e+ ++    ++v+i gp+p p + ++
  gi|15668497|ref|NP_247295.1|  9 ARIKLSSTDHKVLDEICRQIKEIAEK----TGVDISGPIPLPTKVLR 51
                                  89*******************99999....6799******9988776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.89
                        PriA_C 67 k 67
                                  +
  gi|15668497|ref|NP_247295.1| 85 R 85
                                  1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 723.78
//
Query:       gi|15668498|ref|NP_247296.1|  [L=428]
Description: elongation factor 1-alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-56  189.6   0.0    5.8e-56  189.1   0.0    1.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.2e-38  131.0   1.8    3.8e-38  130.2   0.2    2.2  2  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    1.1e-16   60.9   0.4    8.3e-16   58.1   0.5    2.4  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    1.3e-08   34.9   0.3    5.2e-08   33.0   0.3    2.0  1  MMR_HSR1     50S ribosome-binding GTPase
    1.6e-05   24.7   0.6    5.7e-05   22.9   0.6    1.9  1  GTP_EFTU_D4  Elongation factor Tu domain 4
    0.00012   21.5   0.4     0.0002   20.8   0.4    1.3  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
    0.00058   19.4   1.5     0.0037   16.8   0.9    2.4  2  FeoB_N       Ferrous iron transport protein B
     0.0017   18.1   0.5       0.02   14.6   0.3    2.3  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
     0.0025   17.4   0.3     0.0065   16.1   0.3    1.7  1  Ras          Ras family
     0.0037   16.7   0.4      0.021   14.3   0.1    2.3  3  Arf          ADP-ribosylation factor family
      0.004   17.1   0.8       0.17   11.8   0.2    2.4  2  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.028   13.8   0.2       0.11   12.0   0.2    2.0  1  SRPRB        Signal recognition particle receptor beta subuni
      0.034   14.2   0.3        3.3    7.7   0.1    2.7  2  Dynamin_N    Dynamin family
       0.13   11.8   0.8       0.24   11.0   0.3    1.7  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
        1.5    8.7   4.6         16    5.4   1.4    3.1  3  SHOCT        Short C-terminal domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.1   0.0   4.9e-59   5.8e-56       2     191 ..       6     218 ..       5     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 189.1 bits;  conditional E-value: 4.9e-59
                                   CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH...HHHST............HCHSHHHHHHTSCSSCEEEEEETTC CS
                      GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgeka...eeerv............lDtlkeErergiTiksaaisleket 67 
                                   +++n+++ighvD+GK+T+++rLly++gai+ +  ++   e  ++            +D+lkeErerg+Ti++a+ ++e  t
  gi|15668498|ref|NP_247296.1|   6 PVLNVAFIGHVDAGKSTTVGRLLYDSGAIDPQLLEKlkrE--AQergkagfefayvMDNLKEERERGVTIDVAHKKFE--T 82 
                                   789****************************988887442..33567999****************************..* PP

                                   SSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETT...TBSTHHHHHHHHHHHHTTTE.EEEEEESCGST...HHHHHH CS
                      GTP_EFTU  68 kkylinliDtPGHvdFskevirglrvlDgavlvvdav...eGvepqteevlrlalkegvp.iivfiNKmDrl...kaelke 141
                                   +ky+++++D+PGH+dF+k++i+g++++D avlvvd++    G++pqt+e++ la+++g++ i v+iNKmD +   ++e+++
  gi|15668498|ref|NP_247296.1|  83 QKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVDVNdakTGIQPQTREHMFLARTLGIKqIAVAINKMDTVnysQEEYEK 163
                                   **********************************87744489******************999****************** PP

                                   HHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............HHHHHHHHH CS
                      GTP_EFTU 142 iveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............tllealvel 191
                                   ++++++++l      l++ g++ + ++ ++++++lkg++v             tl+eal+++
  gi|15668498|ref|NP_247296.1| 164 MKKMLSEQL------LKVLGYNPD-QIDFIPTASLKGDNVVkrsenmpwykgpTLVEALDKF 218
                                   *********......*******96.*************998788888888888888888875 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.9   2.3e+03       5      55 ..     106     157 ..     102     171 .. 0.58
   2 !  130.2   0.2   3.2e-41   3.8e-38       3     111 ..     317     423 ..     315     424 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                                   ECCEEEEEEESSS...SS-BSTT-EEEEE.SSS-EEEEEEEEEEECCSSTTSB CS
                   GTP_EFTU_D3   5 htkfeAqvyileke.rhtpitagYrpvly.irtadvtgkvveLlskldkktek 55 
                                   +++ +A v+++  +  +t i+ + r  ++ +rt  ++   v++ +k+d  + +
  gi|15668498|ref|NP_247296.1| 106 ASQADAAVLVVDVNdAKTGIQPQTREHMFlARTLGIKQIAVAI-NKMDTVNYS 157
                                   5666778888877767777877776655526887777655555.555533322 PP

  == domain 2  score: 130.2 bits;  conditional E-value: 3.2e-41
                                   EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEEEE- CS
                   GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpiale 83 
                                   + +++f+Aq+++l++  +t+it gY+pv++++ta+v+++++eLl+kld++t++v e++p+f+k+Gd++iv+++++kp+++e
  gi|15668498|ref|NP_247296.1| 317 TVAEEFTAQIVVLQH--PTAITVGYTPVFHAHTAQVACTFIELLKKLDPRTGQVIEENPQFLKTGDAAIVKIKPTKPMVIE 395
                                   6789***********..**************************************************************** PP

                                   -TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                   GTP_EFTU_D3  84 kgseypqlGrFaiReggrTvaaGvvtei 111
                                   ++ e+pqlGrFaiR++g T+aaG+  ++
  gi|15668498|ref|NP_247296.1| 396 NVREIPQLGRFAIRDMGMTIAAGMAIDV 423
                                   ***********************97665 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.3   2.8e+03      19      40 ..      10      29 ..       9      35 .. 0.78
   2 !   58.1   0.5   6.9e-19   8.3e-16       1      73 [.     243     309 ..     243     310 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.3
                                  EEEEC.TCTTSEEEEEEEEEEEE CS
                   GTP_EFTU_D2 19 vrilg.ndtskkeivtrisslet 40
                                  v ++g +d +k+   t++++l+ 
  gi|15668498|ref|NP_247296.1| 10 VAFIGhVDAGKS---TTVGRLLY 29
                                  556677899999...****9986 PP

  == domain 2  score: 58.1 bits;  conditional E-value: 6.9e-19
                                   EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                   Gtv  grv++G+l++Gd+v++   + + +   ++++s+e++he+  +a++g+n+G++v+++  +d i++Gd+ 
  gi|15668498|ref|NP_247296.1| 243 GTVPVGRVETGILRPGDKVVF--EPAGVS---GEVKSIEMHHEQIPQAEPGDNIGFNVRGVSKKD-IKRGDVC 309
                                   99*******************..666678...9********************************.*****95 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.3   4.3e-11   5.2e-08       1     102 [.       9     137 ..       9     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.3e-11
                                   EEEEEESTTSSHHHHHHHHH...................T............STEEESSSTTSSSSEEEEEEEETTEEEEE CS
                      MMR_HSR1   1 evaivGrpNvGKStLinalt...................g............ekaivsdkpgtTrdinegrvklkgkeiel 50 
                                   +va++G+  +GKSt + +l+                   +            ++ + +++ g+T+d+ ++++++++ e+++
  gi|15668498|ref|NP_247296.1|   9 NVAFIGHVDAGKSTTVGRLLydsgaidpqlleklkreaqErgkagfefayvmDNLKEERERGVTIDVAHKKFETQKYEVTI 89 
                                   59*****************977777777766666665550556667666554588999999************999***** PP

                                   EECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT..TTCSHHHHHHHHHHHH CS
                      MMR_HSR1  51 vDtpGliegaseekglgkaflaleeadlillvvdas..eeklkpldeeleelle 102
                                   vD+pG  +    +  +++ +    +ad+++lvvd++  +++++p+ +e   l +
  gi|15668498|ref|NP_247296.1|  90 VDCPG--H----RDFIKNMITGASQADAAVLVVDVNdaKTGIQPQTREHMFLAR 137
                                   *****..4....23456666667779*******988764467777655443333 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.6   4.8e-08   5.7e-05      21      84 ..     247     308 ..     232     309 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.8e-08
                                   EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-E CS
                   GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdi 84 
                                   vG +v +G+++pg k++ e     Ge+++i+ +++++ +a+ G++++  ++g    ++ik gd+
  gi|15668498|ref|NP_247296.1| 247 VG-RVETGILRPGDKVVFEPAGVSGEVKSIEMHHEQIPQAEPGDNIGFNVRGVS-KKDIKRGDV 308
                                   88.9***********998877789***************************976.899999996 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.4   1.6e-07    0.0002      29     144 ..      67     172 ..      56     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.6e-07
                     Gtr1_RagA  29 lrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvliyVfDvesreleedletlkeilealrqys 109
                                   ++ g+tidv ++++  +++ ++ ++Dc+G ++f++++++       ++ ++ + V+Dv+  + ++ ++  ++    l ++ 
  gi|15668498|ref|NP_247296.1|  67 RERGVTIDVAHKKF-ETQKYEVTIVDCPGHRDFIKNMITGA-----SQADAAVLVVDVN--DAKTGIQPQTREHMFLARTL 139
                                   56689*********.58899****************86554.....567888999****..66666666666666666666 PP

                     Gtr1_RagA 110 peakvfvlihKmDliqedereeifeerkeeireei 144
                                      ++ v i+KmD ++ ++  e +e++k+ ++e++
  gi|15668498|ref|NP_247296.1| 140 GIKQIAVAINKMDTVNYSQ--EEYEKMKKMLSEQL 172
                                   7778999********6443..33444444444433 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.67   8.1e+02       2      20 ..       9      27 ..       8      31 .. 0.86
   2 !   16.8   0.9   3.1e-06    0.0037      32     145 ..      70     179 ..      68     189 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.67
                                  EEEEEESTTSSHHHHHHHH CS
                        FeoB_N  2 tvalvGnpnvGkttlfnal 20
                                  +va++G  ++Gk+t + +l
  gi|15668498|ref|NP_247296.1|  9 NVAFIGHVDAGKSTTVGRL 27
                                  699**********987665 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.1e-06
                                   TSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEEEEEEEGGG....HHHHHHHHHHHHHTTSSE CS
                        FeoB_N  32 GvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdvvvnvvdatn....lernLyLtlqllelgvpv 108
                                   Gvt++ ++ k++++++ev+ivD PG  ++ +      ++      + + +vv+v da++      r+ +++++ l + +++
  gi|15668498|ref|NP_247296.1|  70 GVTIDVAHKKFETQKYEVTIVDCPGHRDFIKNM----ITG-ASQADAAVLVVDVNDAKTgiqpQTREHMFLARTLGI-KQI 144
                                   9************************98774322....222.222344445666666653211123444555555554.468 PP

                                   EEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTT CS
                        FeoB_N 109 vlalnmideaekkgieidlkkLsekLgvpvvktsakk 145
                                    +a+n++d+++ ++ e   +k++++L  + +k+ + +
  gi|15668498|ref|NP_247296.1| 145 AVAINKMDTVNYSQEE--YEKMKKMLSEQLLKVLGYN 179
                                   89*******9988776..4567777776666666655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.31   3.7e+02       3      19 ..       9      25 ..       7      31 .. 0.80
   2 !   14.6   0.3   1.7e-05      0.02      30     114 ..      79     160 ..      71     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.31
                     PduV-EutP  3 killiGkvgsGKttLtq 19
                                  ++ +iG+v++GK t   
  gi|15668498|ref|NP_247296.1|  9 NVAFIGHVDAGKSTTVG 25
                                  5789********88654 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.7e-05
                     PduV-EutP  30 ktqaiefsdeviDtPGeylenrklysalivtsaeadvialvqdateeesvfppgf.asvfnkeviGiitkidlaedeenie 109
                                   k  + +++ +++D+PG    +r + + +i+ + +ad  +lv+d+++ ++ + p+   ++f   ++Gi   +   ++++ ++
  gi|15668498|ref|NP_247296.1|  79 KFETQKYEVTIVDCPG----HRDFIKNMITGASQADAAVLVVDVNDAKTGIQPQTrEHMFLARTLGIKQIAVAINKMDTVN 155
                                   544555666789****....79*********************99888777665516799999999844333334444444 PP

                     PduV-EutP 110 aveel 114
                                   +++e+
  gi|15668498|ref|NP_247296.1| 156 YSQEE 160
                                   44433 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.3   5.4e-06    0.0065      11     131 ..      50     168 ..      46     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.4e-06
                                   SHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHH CS
                           Ras  11 GKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvk 91 
                                   GK+ + + +v d+ kee e  + +d   k++e+  ++++++i D  G  +f +   +  ++a++++lv d++++++  + +
  gi|15668498|ref|NP_247296.1|  50 GKAGFEFAYVMDNLKEERERGVTIDVAHKKFET--QKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVDVNDAKTGIQPQ 128
                                   99999***************9999999888765..6677889**********99999****************99866655 PP

                                   .HHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHH CS
                           Ras  92 .kwveeikrvaeenvpivLvGnKvDleekravsteegeela 131
                                    + +  + r+     +i++  nK+D  +  + ++e+ +++ 
  gi|15668498|ref|NP_247296.1| 129 tREHMFLARTLG-IKQIAVAINKMDTVNYSQEEYEKMKKML 168
                                   233333444444.2456666699998886655555555554 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         1   1.2e+03      16      36 ..       9      29 ..       2      34 .. 0.80
   2 !   14.3   0.1   1.8e-05     0.021      40     164 ..      67     196 ..      51     205 .. 0.74
   3 ?   -3.1   0.0       3.7   4.5e+03      45      59 ..     290     304 ..     276     311 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1
                                  EEEEEESTTSSHHHHHHHHHH CS
                           Arf 16 rilllGLDnaGKtTilkklkl 36
                                   + ++G   aGK+T + +l  
  gi|15668498|ref|NP_247296.1|  9 NVAFIGHVDAGKSTTVGRLLY 29
                                  567889999*****9999865 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.8e-05
                                   EECSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGCTTESEEEEEEETT-CT.THHHHHHHHHHHCTSGCCTTSEEE CS
                           Arf  40 vttvPTigfnveeleiknlkftvwDvGGqeklRplWknYfektdavifvvDsadre.RleeakeeLkalleeeelkevall 119
                                    +   Ti    ++ e++++++t+ D  G++   +   +  ++ da + vvD++d +  ++   +e  +++  ++l   ++ 
  gi|15668498|ref|NP_247296.1|  67 RERGVTIDVAHKKFETQKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVDVNDAKtGIQPQTRE--HMFLARTLGIKQIA 145
                                   4455689999999*****************999999999**************987245555554..55556666666777 PP

                                   EEEE-TTSTTSS-HH..HHHHHTTGGGSS....SSSSEEEEEEBTTTTBTH CS
                           Arf 120 vlaNKqDlpealsee..elrellgleelk....gkrkleiqkcsavkgegl 164
                                   v  NK+D+ +  +ee  +++++l+ + lk    +  ++  + ++ +kg+++
  gi|15668498|ref|NP_247296.1| 146 VAINKMDTVNYSQEEyeKMKKMLSEQLLKvlgyNPDQIDFIPTASLKGDNV 196
                                   888****99876664115566666555666655556666677777777665 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.7
                                   SSSEEEEEEEETTEE CS
                           Arf  45 Tigfnveeleiknlk 59 
                                    igfnv+ ++ k++k
  gi|15668498|ref|NP_247296.1| 290 NIGFNVRGVSKKDIK 304
                                   489***999999986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.06        72     102     162 ..      10      96 ..       5      99 .. 0.70
   2 !   11.8   0.2   0.00014      0.17      13      82 ..     106     178 ..      95     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.06
                                   EEEECSTTSSHHHHHHHHCTT.........................-----S--------------SEEEEEETT.TEEEE CS
                   RsgA_GTPase 102 svlvGqSGvGKStLinallpe.........................lelktgevseklgrGkhTTtavellelae.gglli 156
                                   ++++G+  +GKSt + +ll +                             + +++e+ +rG     a + +e ++ + +++
  gi|15668498|ref|NP_247296.1|  10 VAFIGHVDAGKSTTVGRLLYDsgaidpqlleklkreaqergkagfeFAYVMDNLKEERERGVTIDVAHKKFETQKyEVTIV 90 
                                   579999999***999999887677777777777777777777666555566667777777766666666666655566777 PP

                                   SS-SSS CS
                   RsgA_GTPase 157 DtPGfr 162
                                   D PG r
  gi|15668498|ref|NP_247296.1|  91 DCPGHR 96 
                                   777765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00014
                                   EES--EEEEEEESTTTT--HHHHHH.HHHHHHHTT-.EEEEEEE-GGG--HHH.HHHHHHHHHHHTTSEEEE- CS
                   RsgA_GTPase  13 vaNvdqllivvslkepelslnlldr.fLvlaeekgi.epvivlnKiDlleeee.eleelkeelealgyevllv 82 
                                   ++  d +++vv +++ ++  +  +r  ++la + gi ++ +++nK+D ++ ++ e+e++k+ l++  ++vl  
  gi|15668498|ref|NP_247296.1| 106 ASQADAAVLVVDVNDAKTGIQPQTReHMFLARTLGIkQIAVAINKMDTVNYSQeEYEKMKKMLSEQLLKVLGY 178
                                   67899*********999988766663688899999977899*******9977757888888887776666655 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2     9e-05      0.11      40      85 ..      76     118 ..       5     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9e-05
                                   ETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEET CS
                         SRPRB  40 alkvksekgskltliDfPGheklrqklleklkaksslkglvfvvDS 85 
                                   a+k  ++++ ++t++D PGh  + +++++     s++ + v vvD 
  gi|15668498|ref|NP_247296.1|  76 AHKKFETQKYEVTIVDCPGHRDFIKNMITG---ASQADAAVLVVDV 118
                                   33334778999***********99999998...6777788888885 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.041        49       1      19 [.      10      28 ..      10      31 .. 0.86
   2 ?    7.7   0.1    0.0028       3.3      68     139 ..      59     119 ..      35     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.041
                                  EEEEEBTTTTHHHHHHHHH CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLl 19
                                  +a++G++ +GKS+ +  Ll
  gi|15668498|ref|NP_247296.1| 10 VAFIGHVDAGKSTTVGRLL 28
                                  799**********877665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0028
                                   HHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETT CS
                     Dynamin_N  68 vreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikkadiilavtsan 139
                                   v +++++e+e+         ++ + +k+++ ++ ++t+vD PG  +  k+    ++  + +ad+ ++v++ n
  gi|15668498|ref|NP_247296.1|  59 VMDNLKEERERGV-------TIDVAHKKFETQKYEVTIVDCPGHRDFIKNM---ITG-ASQADAAVLVVDVN 119
                                   4444444444444.......3456788999999**********98855543...333.34444444454444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.2   6.2e+03       6      21 ..      13      28 ..      10      35 .. 0.78
   2 ?   11.0   0.3    0.0002      0.24     102     167 ..      99     169 ..      57     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.2
                                  EESTTCCHHHHHHHHH CS
                          cobW  6 tGflGsGKTtLlnhll 21
                                   G + +GK+t + +ll
  gi|15668498|ref|NP_247296.1| 13 IGHVDAGKSTTVGRLL 28
                                  577889***9998887 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0002
                                   TSHHHHHCCCECEEEEEEETTTH.........CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC...HHHHHHHHH CS
                          cobW 102 teeelksdltldavvavvDaknl........eaeeekieekaedqlaaadllvlnKtDlldee.allekleerlr 167
                                    ++ ++ + ++da v vvD++ +         ++    ++++ +q+a+     +nK+D+++++ ++ ek++++l+
  gi|15668498|ref|NP_247296.1|  99 IKNMITGASQADAAVLVVDVNDAktgiqpqtREHMFLARTLGIKQIAV----AINKMDTVNYSqEEYEKMKKMLS 169
                                   46677888999*********8887776554333333344445555554....49********9888888888765 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.082        98       9      17 ..      28      36 ..      26      37 .. 0.88
   2 ?   -2.6   0.0       4.4   5.2e+03       4      14 ..      61      71 ..      60      71 .. 0.81
   3 ?    5.4   1.4     0.013        16      16      25 ..     157     166 ..     157     166 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.082
                         SHOCT  9 LyarGeIte 17
                                  Ly++G+I+ 
  gi|15668498|ref|NP_247296.1| 28 LYDSGAIDP 36
                                  9******95 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.4
                         SHOCT  4 ekLkeLyarGe 14
                                  + Lke ++rG+
  gi|15668498|ref|NP_247296.1| 61 DNLKEERERGV 71
                                  56999999995 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.013
                         SHOCT  16 teEEFeakKa 25 
                                   ++EE+e++K+
  gi|15668498|ref|NP_247296.1| 157 SQEEYEKMKK 166
                                   89*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       967  (0.053935); expected 358.6 (0.02)
Passed bias filter:                      813  (0.0453455); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 2521.65
//
Query:       gi|298575371|ref|YP_003727983.1|  [L=89]
Description: hypothetical protein MJ_0323 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.022   14.6   0.2      0.032   14.1   0.2    1.3  1  Cys_rich_CPCC  Cysteine-rich CPCC


Domain annotation for each model (and alignments):
>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.8e-06     0.032       2      27 ..      61      86 ..      60      89 .] 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-06
                     Cys_rich_CPCC  2 qCpcCgyltleeeegsydiCpvCfWe 27
                                      +Cp+ g   ++++ + +  C+vC W+
  gi|298575371|ref|YP_003727983.1| 61 TCPVLGSNFFNNSMNVHATCAVCAWK 86
                                      8*********999999*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 598.96
//
Query:       gi|15668499|ref|NP_247297.1|  [L=308]
Description: translation factor EF-1 alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-12   46.9   1.3    5.4e-12   45.9   0.3    2.1  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    5.5e-05   23.0   0.6    0.00013   21.7   0.1    1.9  2  GTP_EFTU_D4  Elongation factor Tu domain 4
    0.00046   20.4   1.6    0.00063   19.9   0.2    1.9  2  eIF2_C       Initiation factor eIF2 gamma, C terminal


Domain annotation for each model (and alignments):
>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.3     9e-16   5.4e-12       1      73 [.     157     223 ..     157     224 .. 0.97
   2 ?   -1.8   0.0      0.73   4.4e+03      12      24 ..     227     237 ..     225     268 .. 0.53

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 9e-16
                                   EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                   Gtv+lg+v+sGt+++ d++r+   +t+k      ++s++ + +d +ea ag ++G+ ++++ +++ + +G++l
  gi|15668499|ref|NP_247297.1| 157 GTVILGKVESGTVRVHDNLRV--YPTDKM---AMVRSIQIHDNDFKEAKAGNRVGLALKGITTDE-LDRGMIL 223
                                   9********************..999999...*********************************.9****98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.73
                                   EEETTEEEEEECT CS
                   GTP_EFTU_D2  12 tlkkGdevrilgn 24 
                                   +lk+  e++i  n
  gi|15668499|ref|NP_247297.1| 227 ELKVAKEIEI--N 237
                                   5555555555..3 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   2.3e-08   0.00013      11      74 ..     151     213 ..     143     224 .. 0.85
   2 ?   -2.1   0.0      0.61   3.6e+03      18      24 ..     255     261 ..     230     289 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.3e-08
                                   EEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS- CS
                   GTP_EFTU_D4  11 vvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegki 74 
                                   +  r+   +i G +v +G++++  +l      ++  +++iq +++  +eakaG++v+++++g +
  gi|15668499|ref|NP_247297.1| 151 FTVRSVGTVILG-KVESGTVRVHDNLRVYPTDKMAMVRSIQIHDNDFKEAKAGNRVGLALKGIT 213
                                   45667778999*.**************99*******************************9966 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.61
                                   CEEEEEE CS
                   GTP_EFTU_D4  18 paivGve 24 
                                   ++ivG++
  gi|15668499|ref|NP_247297.1| 255 QIIVGLQ 261
                                   3344443 PP

>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.72   4.3e+03      39      75 ..     154     190 ..     152     192 .. 0.76
   2 !   19.9   0.2   1.1e-07   0.00063      23      84 ..     246     306 ..     227     308 .] 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.72
                                   EEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEET CS
                        eIF2_C  39 stggvvtsvkkdeakvkLkkPvcaekgekialsRrve 75 
                                    ++g+v+  k +  +v+ ++ + +   +k a+ R ++
  gi|15668499|ref|NP_247297.1| 154 RSVGTVILGKVESGTVRVHDNLRVYPTDKMAMVRSIQ 190
                                   5677888778888888888888888888999988886 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.1e-07
                                   ----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSEEEEEEE CS
                        eIF2_C  23 eklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrWrLiGwG 84 
                                   +++k++E+ ++ +G  s+ +vv +v+k+++k++L+k ++ ++g+k+ l    +++ r+ G+G
  gi|15668499|ref|NP_247297.1| 246 KTVKEGENYQIIVGLQSVSCVVEEVNKNKIKLSLQKEIAYDVGDKLCLIDG-SAKIRILGVG 306
                                   67899****************************************998643.4445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2173.24
//
Query:       gi|15668500|ref|NP_247298.1|  [L=436]
Description: hypothetical protein MJ_0326 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-58  196.5  48.7    6.8e-58  196.2  48.7    1.1  1  Xan_ur_permease  Permease family
  ------ inclusion threshold ------
        2.1    8.7   8.9       0.33   11.2   0.3    3.6  3  DUF5464          Family of unknown function (DUF5464)


Domain annotation for each model (and alignments):
>> Xan_ur_permease  Permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.2  48.7   7.6e-62   6.8e-58       4     387 ..      23     396 ..      20     398 .. 0.96

  Alignments for each domain:
  == domain 1  score: 196.2 bits;  conditional E-value: 7.6e-62
                                   HHHHHHHHHHHHHHHHHHHHTTTS-.........H.HHHHHHHHHHHHHHHHHTTT-----EEE-GGGHHHHHGGG-.... CS
               Xan_ur_permease   4 lllglQhllamfaalvvvPllvgdalglaeelrqlisatllasGiatllqllifgirlpillgssfafvtalmialGsaed 84 
                                    l+g++++++m + + v+P +++ a g  +++  ++ at++as+iatl++ l++ ++ +++ g++++++  + ++lG+   
  gi|15668500|ref|NP_247298.1|  23 TLAGITTFMTMAYIIFVNPQILSTA-G--MDFGAVMVATCIASAIATLVMGLYARYPFALAPGMGLNAYFTYGVCLGM--- 97 
                                   689**********************.3..7899**********************************9999******5... PP

                                   HHHHHHHHHHHHHHHHHHHHHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHTTSS-..BTT.B---HHHHHHHH CS
               Xan_ur_permease  85 ieialagllgallvagvlfilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkvgggwaavegltvvslkllllav 165
                                    +i  +++lga++++gvlfi++ lt++r +++ +ip+ + +++ ++iGl++a i++k++g++  + ++  v++++l++ + 
  gi|15668500|ref|NP_247298.1|  98 -GIDWRVALGAVFISGVLFIILTLTKIRTWIFNVIPNAIKYGTAVGIGLFIAFIGLKSAGIIVSS-KATLVTLGNLMEPST 176
                                   .*************************************************************855.5569*********** PP

                                   HHHHHHHHHHHSSSTTTTTHHHHHHHHHHHHHHHHHHHTTSSHHHHS-SS-----------HH...H.HHHHTHHH.HHHH CS
               Xan_ur_permease 166 vvllvilllsvflkglfsqlpiLigiiagwllalfmgivnlspevseapwfqlpsplkfgtpl.fnlgliltvlavalvav 245
                                    + l+++ l+  l   ++ ++iLigii++ l+ +++gi ++ + ++++p    p+ l++     +nlgl+++vla+++v +
  gi|15668500|ref|NP_247298.1| 177 LLALFGIFLTSILVSRNVIGAILIGIIVTSLIGMILGISPFPEGIFSMPPSIAPTFLQLDIMGaLNLGLLTIVLAFFFVDM 257
                                   ******************************************9999999998999999876656***************** PP

                                   HHHHHHHHHHHHHHTS-TII..IIIHHHHHHHHHHHHHHHHHHT---EEE-HHHHHHHHHHTB--HHHHHHHHHHHHHHT- CS
               Xan_ur_permease 246 vesvGdiravakvvgrslkp..kpdlrralladGlatllsgllGalpvttyaeniGvvaltkvasrrvmvtagvilillgl 324
                                   ++++G++ a+a+++g  +k+   p++++al+ad ++t++++llG++ vtty+e++ ++al+    +r++++  v+++l+ l
  gi|15668500|ref|NP_247298.1| 258 FDTLGTLSALASQAGYLDKDgkLPRVEKALMADATGTVVGSLLGTSTVTTYIESASGIALG----GRTGFVSVVVAMLFLL 334
                                   ***************99999999**************************************....**************** PP

                                   -HHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHTTS-SHHHHHHHHHHHHHHHH----- CS
               Xan_ur_permease 325 ipklaallssIPepvlgGvllvvfgmiaasgvsnlqtvdldsarnllivavslvlGlgvatvp 387
                                   + ++ + + +IP ++ ++++lv++g +++ +v+ +++ d+++a  ++i+ +++ l+ ++at+ 
  gi|15668500|ref|NP_247298.1| 335 SLFFYPVVKAIPPYA-TAAALVIVGALMMRSVKYIDFDDYTEAIPAFITLLTIPLTFSIATGL 396
                                   ***************.*******************************************9975 PP

>> DUF5464  Family of unknown function (DUF5464)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   3.7e-05      0.33       9      39 ..      24      53 ..      13      71 .. 0.71
   2 ?    0.7   0.5      0.07   6.3e+02      28      38 ..     352     362 ..     324     366 .. 0.81
   3 ?   -2.3   0.1      0.64   5.8e+03      18      25 ..     419     426 ..     414     433 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.7e-05
                       DUF5464  9 laalaailtlayilavyPqvalvvvGaCyla 39
                                  la +++ +t+ayi+ v Pq+ l   G  + a
  gi|15668500|ref|NP_247298.1| 24 LAGITTFMTMAYIIFVNPQI-LSTAGMDFGA 53
                                  8999999************8.3333333333 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.07
                       DUF5464  28 valvvvGaCyl 38 
                                    alv+vGa  +
  gi|15668500|ref|NP_247298.1| 352 AALVIVGALMM 362
                                   59*****9766 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.64
                       DUF5464  18 layilavy 25 
                                   l y+lav 
  gi|15668500|ref|NP_247298.1| 419 LVYVLAVI 426
                                   66777774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2656.72
//
Query:       gi|15668501|ref|NP_247299.1|  [L=104]
Description: hypothetical protein MJ_0327 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-12   46.2   0.4      7e-12   45.5   0.4    1.4  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.4   3.9e-16     7e-12       3      94 ..      13      94 ..      11      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.9e-16
                                  SCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES-SSB CS
                 Nitro_FeMo-Co  3 srvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykgaggt 85
                                  +++++ F +++yF+i+ ++++evk  ++           ++++ ++++ +e+v+++i+++i ++ ++k++++ ie+y ++g +
  gi|15668501|ref|NP_247299.1| 13 DKISNSFEDCKYFLIVRIDDNEVKSTKVI---------FNDESGKKSIVKENVNAIICKNISEENYKKFSKK-IEIYHAEGDD 85
                                  79*****************9998888888.........555666899*************************.********** PP

                                  HHHHHHHHH CS
                 Nitro_FeMo-Co 86 veealkevl 94
                                  v++ +  ++
  gi|15668501|ref|NP_247299.1| 86 VDKNISLFI 94
                                  ***998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1326  (0.0739584); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 815.68
//
Query:       gi|15668502|ref|NP_247300.1|  [L=146]
Description: hypothetical protein MJ_0328 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.011   15.9   0.3      0.047   13.9   0.3    2.1  1  Clr5         Clr5 domain
      0.012   15.6   3.4      0.019   15.0   1.1    2.4  2  HTH_19       Helix-turn-helix domain
      0.013   16.1   0.0      0.031   14.9   0.0    1.7  1  HTH_32       Homeodomain-like domain
      0.018   15.5   1.4      0.033   14.6   1.4    1.6  1  FadA         Adhesion protein FadA
      0.024   14.5   0.2       0.06   13.3   0.1    1.7  2  Terminase_5  Putative ATPase subunit of terminase (gpP-like)
      0.066   13.7   0.1      0.085   13.3   0.1    1.3  1  DUF1793      Domain of unknown function (DUF1793)


Domain annotation for each model (and alignments):
>> Clr5  Clr5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   1.6e-05     0.047       7      39 ..      16      47 ..      15      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                          Clr5  7 ahkatIrrLYleenrsLkdvmeiMeeehgFkat 39
                                  +h+a+I+ LY  +++  k++ ++++e+++   +
  gi|15668502|ref|NP_247300.1| 16 PHRAEIEALYF-QGWGAKKISKYLKEKYNEDIS 47
                                  6*********5.89**************86655 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.1   6.4e-06     0.019      21      62 ..      56      96 ..      27      98 .. 0.83
   2 ?   -1.4   0.0      0.81   2.4e+03       5      13 ..     123     131 ..     118     137 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.4e-06
                        HTH_19 21 rlgisrskisaiEngkkdvpsaelllkiaealgidleyllqg 62
                                  ++++ +  + aiE + + ++++++++ ia+ +g+ le l+++
  gi|15668502|ref|NP_247300.1| 56 QNHVKPQLLEAIEEETT-EIYSKMYKEIANNFGLALEGLFTM 96
                                  56666999********9.*********************998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.81
                        HTH_19   5 keaReelgl 13 
                                   +++Re++ l
  gi|15668502|ref|NP_247300.1| 123 MAIREMKEL 131
                                   556666544 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     1e-05     0.031      31      71 ..      15      53 ..       2      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                        HTH_32 31 devrariiallreeprWsprqlaarlaeregvkvShstvyr 71
                                    +ra+i al   +  W++++++++l+e++ +++S+s + r
  gi|15668502|ref|NP_247300.1| 15 SPHRAEIEALY-FQ-GWGAKKISKYLKEKYNEDISYSAILR 53
                                  34566666666.33.9**********9999999****9977 PP

>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.4   1.1e-05     0.033      37      92 ..      52     107 ..      31     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                          FadA  37 kkelkakieeklakleadsevrfykdeYkellkeyksllkelekeikekekkianf 92 
                                    + +++ ++ +l ++ +++ +++y++ Yke+++++  +l+ l + ik  +k ++n 
  gi|15668502|ref|NP_247300.1|  52 LRHMQNHVKPQLLEAIEEETTEIYSKMYKEIANNFGLALEGLFTMIKTAKKDLENP 107
                                   567999999999999999****************************9999999985 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     2e-05      0.06       8      27 ..      23      43 ..      17      50 .. 0.84
   2 ?   -3.5   0.0       3.3   9.8e+03      17      25 ..      80      88 ..      78      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                   Terminase_5  8 lLYwqGyrvaeIAeelglk.e 27
                                  +LY+qG+  ++I++ l +k +
  gi|15668502|ref|NP_247300.1| 23 ALYFQGWGAKKISKYLKEKyN 43
                                  7***************99854 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.3
                   Terminase_5 17 aeIAeelgl 25
                                  +eIA+  gl
  gi|15668502|ref|NP_247300.1| 80 KEIANNFGL 88
                                  799998775 PP

>> DUF1793  Domain of unknown function (DUF1793)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.8e-05     0.085      29     111 ..      25     111 ..       9     139 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.8e-05
                       DUF1793  29 yikkweelaidgthlklaYdkedswsllY....nlyaDkllglnlvpqsvyemqsafYktvaqkyGlplDsrht...ytks 102
                                   y++ w +  i ++ lk +Y+++ s+s +     n++  +ll+   ++++  e  s++Yk+ a+++Gl+l+   t   ++k+
  gi|15668502|ref|NP_247300.1|  25 YFQGWGAKKI-SKYLKEKYNEDISYSAILrhmqNHVKPQLLE--AIEEETTEIYSKMYKEIANNFGLALEGLFTmikTAKK 102
                                   5555555555.5678888888888876651111555555665..9************************976552124555 PP

                       DUF1793 103 dWelfaaav 111
                                   d e   a++
  gi|15668502|ref|NP_247300.1| 103 DLENPKATA 111
                                   655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1308  (0.0729544); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 882.86
//
Query:       gi|15668503|ref|NP_247301.1|  [L=616]
Description: hypothetical protein MJ_0329 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-24   85.6   0.0    8.8e-24   84.4   0.0    1.7  1  Phage_Mu_F   Phage Mu protein F like protein
     0.0011   18.8   2.1     0.0038   17.0   2.1    2.0  1  Hydrolase_3  haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.38   11.1   5.6        0.3   11.5   0.8    2.8  3  DUF2924      Protein of unknown function (DUF2924)
        7.1    6.9   6.6         26    5.1   2.3    3.4  3  PAH          Paired amphipathic helix repeat


Domain annotation for each model (and alignments):
>> Phage_Mu_F  Phage Mu protein F like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.0     2e-27   8.8e-24       2     111 ..     510     611 ..     509     612 .. 0.92

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 2e-27
                    Phage_Mu_F   2 kirdavtqaiarGegeeelakelkkrgqlssrsrlrtiartetlraynaarlaqeaaskevkkekwryvavkdsrtrpeHa 82 
                                   ++ d++t++i++G geee+ak+lkk  + ++ srl++ ar+e++++yn +r+++     +  + k+ yv++kd+r+rp+H+
  gi|15668503|ref|NP_247301.1| 510 QFLDVLTEGIQKGLGEEEIAKNLKKVAKDVKGSRLQMRAREEMNKTYNLTRARRFW---N--D-KVIYVTMKDERVRPSHR 584
                                   67899*********************8888**********************7755...2..2.469************** PP

                    Phage_Mu_F  83 aldGkvfkvddpfwqtgappedvnCRCrv 111
                                   +l+G +f  ++++  + +pp +++CRC++
  gi|15668503|ref|NP_247301.1| 585 KLHGLIFVPAERP--ELVPPLGYGCRCTI 611
                                   *************..79**********97 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.1   8.6e-07    0.0038      96     201 ..     432     534 ..     356     539 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.6e-07
                                   CEEEEEESSEEEESTT.THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEEEES-HHHHHHHHHHHHHHCTTTEEEEEEST CS
                   Hydrolase_3  96 veillytedkvyvlnkeksekkkkeeektkkkkeeidseeeledeeiakililkdkekldelekelksklnklltitsssk 176
                                   v+++l+t +++ +++  +++ ++  +e t+++++    +   ++ +  ki  + d++ +d l+++ ++ + +   ++s+s+
  gi|15668503|ref|NP_247301.1| 432 VNWILETYERLGYNEL-MQDWDELLREFTREEVDMFFLDYVAPTLNSLKIYDDLDQQTIDILKQHWEQAFYN--IYSSYSQ 509
                                   5555555555544444.6666666677777777777777788888999999*******************98..9****** PP

                                   TEEEEEETT-SHHHHHHHHHHHCT- CS
                   Hydrolase_3 177 gyleimpkgvsKgtalkklakelni 201
                                   ++l+++ +g++Kg + +++ak+l+ 
  gi|15668503|ref|NP_247301.1| 510 QFLDVLTEGIQKGLGEEEIAKNLKK 534
                                   *********************9986 PP

>> DUF2924  Protein of unknown function (DUF2924)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.35   1.5e+03      21      67 ..     371     417 ..     357     431 .. 0.55
   2 ?   -0.2   0.0      0.27   1.2e+03       5      34 ..     437     466 ..     434     478 .. 0.78
   3 ?   11.5   0.8   6.8e-05       0.3       5     102 ..     482     577 ..     478     589 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.35
                       DUF2924  21 elfgeeapklnkeflekrlayriqelaeggLseearrrleelaeeke 67 
                                   +l+++e +kl k   e +   +   +++ +L e++r+ le++ ++ e
  gi|15668503|ref|NP_247301.1| 371 DLTEKEVEKLLKMAKEGKGGLEYADEEKQKLLEKKRKSLEKIISKLE 417
                                   44444444444433333333344445556677777777777766644 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.27
                       DUF2924   5 aaLkelsvkeLkekwrelfgeeapklnkef 34 
                                   ++ ++l  +eL + w+el++e +++    f
  gi|15668503|ref|NP_247301.1| 437 ETYERLGYNELMQDWDELLREFTREEVDMF 466
                                   566788999*********999988855444 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 6.8e-05
                       DUF2924   5 aaLkelsvkeLkekwrelfgeeapklnkeflekrlayriqelaeggLseearrrleelaee..kekkkkkakkkkeelkpG 83 
                                   ++L++++++ Lk++w++ f +   +++++fl   l+  iq+      +ee  ++l+++a++   ++ + +a+++ +++   
  gi|15668503|ref|NP_247301.1| 482 DDLDQQTIDILKQHWEQAFYNIYSSYSQQFLD-VLTEGIQKG---LGEEEIAKNLKKVAKDvkGSRLQMRAREEMNKTYNL 558
                                   579999************************86.566666654...224556666777777633335556666666666678 PP

                       DUF2924  84 trLvRewkgrehevtvled 102
                                   tr  R w+++ + vt+ ++
  gi|15668503|ref|NP_247301.1| 559 TRARRFWNDKVIYVTMKDE 577
                                   999999******9999876 PP

>> PAH  Paired amphipathic helix repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.065   2.9e+02      15      45 .]      44      73 ..      29      73 .. 0.71
   2 ?    5.1   2.3    0.0058        26      28      42 ..     445     459 ..     285     460 .. 0.86
   3 ?   -2.2   0.0       1.1   4.8e+03       4      11 ..     509     516 ..     509     534 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.065
                           PAH 15 keqidskeVyeqVskLFhdh.pdLlreFnqFL 45
                                  k+   sk+V+ ++s L+  h  dL   F  FL
  gi|15668503|ref|NP_247301.1| 44 KQL--SKDVIDEISGLIDRHiRDLQLAFSDFL 73
                                  444..999*********988679999999997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0058
                           PAH  28 skLFhdhpdLlreFn 42 
                                    +L +d  +LlreF+
  gi|15668503|ref|NP_247301.1| 445 NELMQDWDELLREFT 459
                                   689***********8 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.1
                           PAH   4 keFLdiLh 11 
                                   ++FLd+L 
  gi|15668503|ref|NP_247301.1| 509 QQFLDVLT 516
                                   68***996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1392  (0.0776396); expected 358.6 (0.02)
Passed bias filter:                      764  (0.0426125); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.77u 0.30s 00:00:01.07 Elapsed: 00:00:00.49
# Mc/sec: 3817.45
//
Query:       gi|15668504|ref|NP_247302.1|  [L=549]
Description: hypothetical protein MJ_0330 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.051   13.6   0.5       0.15   12.1   0.1    2.1  2  PA28_alpha  Proteasome activator pa28 alpha subunit


Domain annotation for each model (and alignments):
>> PA28_alpha  Proteasome activator pa28 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.3e-06      0.15      35      60 ..      10      35 ..       3      36 .. 0.88
   2 ?   -3.0   0.0      0.44   7.8e+03      15      24 ..     213     222 ..     213     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.3e-06
                    PA28_alpha 35 eLLkspsfnvsdlsevhadLnIPvPd 60
                                  e Lk+++fn + + e++ +L+IP+P+
  gi|15668504|ref|NP_247302.1| 10 ESLKKKTFNKKIFLELCKKLDIPIPQ 35
                                  669**********************7 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.44
                    PA28_alpha  15 tkeAEeLvsk 24 
                                   +k AE+L+ +
  gi|15668504|ref|NP_247302.1| 213 FKNAEQLFEQ 222
                                   689****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 3342.08
//
Query:       gi|15668505|ref|NP_247303.1|  [L=135]
Description: hypothetical protein MJ_0331 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-07   31.4   0.1    1.7e-07   31.2   0.1    1.1  1  Phage_tail_S    Phage virion morphogenesis family
     0.0058   17.6   1.9      0.033   15.1   0.3    2.5  2  HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-compon
     0.0077   15.9   0.0       0.01   15.5   0.0    1.3  1  YtxC            YtxC-like family


Domain annotation for each model (and alignments):
>> Phage_tail_S  Phage virion morphogenesis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.1   2.9e-11   1.7e-07      21     129 ..      12     112 ..       5     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.9e-11
                  Phage_tail_S  21 rplmraigeeLresqeqrfeaqkdPdGspwkplkdktlaakkgkikrggkilrklg....rlarslkteatsdsvevGsnk 97 
                                   ++l+ +i +eL+ + ++++++  + +   wkpl+++++++k+++++++ k l  +g     + +++k++++  +v+v +n 
  gi|15668505|ref|NP_247303.1|  12 KELAHEIEKELVAEVDDNIQRGFQKKELKWKPLSKDYQKRKEKEGRNT-KGLIYHGallkATDSKVKITSKGLQVKVFNNM 91 
                                   6789999999999999999999989999******77666665555555.777777744445566677777777788***** PP

                  Phage_tail_S  98 iyAaiHQfGgkagrdrvskkgkkvtipaRplL 129
                                   +yA +H fG            kk +ipaRp++
  gi|15668505|ref|NP_247303.1|  92 VYAGVHEFGS-----------KKKNIPARPFI 112
                                   **********...........45678888876 PP

>> HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   5.6e-06     0.033      15      81 .]       7     100 ..       2     100 .. 0.62
   2 ?    0.9   0.1      0.15     9e+02       5      21 ..     117     133 ..     111     134 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.6e-06
                HK97-gp10_like  15 vekaikkalkkaAkevldkakkrtp........................svdtggdLrdsitv........qgkvkkkgge 63 
                                   v++++k+ + +  ke+++++ +++                               +  ++  +         +kvk ++  
  gi|15668505|ref|NP_247303.1|   7 VREFKKELAHEIEKELVAEVDDNIQrgfqkkelkwkplskdyqkrkekeG-----RNTKGLIYhgallkatDSKVKITSKG 82 
                                   55666666666666667777777776666666666666555554322221.....22222222344444443399999999 PP

                HK97-gp10_like  64 yrvevgnnaeyArlvEfG 81 
                                   ++v v+nn  yA   EfG
  gi|15668505|ref|NP_247303.1|  83 LQVKVFNNMVYAGVHEFG 100
                                   *****************9 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.15
                HK97-gp10_like   5 kklek.lserevekaikk 21 
                                   kk++k l++ +vek+ik+
  gi|15668505|ref|NP_247303.1| 117 KKVQKdLPK-IVEKVIKR 133
                                   667777777.67777765 PP

>> YtxC  YtxC-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-06      0.01      17     108 ..      37     132 ..      20     135 .] 0.73

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-06
                          YtxC  17 kkllkkilkenYfyfdeeEkeeIlelale..ilk.eeekkeredekkklnr.knkilekileylkenkeinleGFitFRlk 93 
                                   k+l  k l+++Y   +e+E ++ + l+++  +lk +++k + +++  +++  +n+++  + e+ +++k+i  + Fi+  lk
  gi|15668505|ref|NP_247303.1|  37 KELKWKPLSKDYQKRKEKEGRNTKGLIYHgaLLKaTDSKVKITSKGLQVKVfNNMVYAGVHEFGSKKKNIPARPFIQPALK 117
                                   3344477999999999999888877665411444322233323333333335899999*********************** PP

                          YtxC  94 eyleeLeeivdkavd 108
                                   +  ++L +iv+k++ 
  gi|15668505|ref|NP_247303.1| 118 KVQKDLPKIVEKVIK 132
                                   ************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 902.29
//
Query:       gi|15668506|ref|NP_247304.1|  [L=110]
Description: hypothetical protein MJ_0332 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.1   0.0       0.25   11.2   0.0    1.4  1  HTH_23    Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.4e-05      0.25       8      28 ..      69      89 ..      69      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.4e-05
                        HTH_23  8 lrillllaeGlsvreIAreLg 28
                                  l+++ l+ eG+++++IA+++g
  gi|15668506|ref|NP_247304.1| 69 LKVIELACEGYTKEDIAEAYG 89
                                  5799***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 737.43
//
Query:       gi|15668507|ref|NP_247305.1|  [L=132]
Description: hypothetical protein MJ_0332.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   13.9   2.5      0.054   13.2   2.5    1.3  1  DUF4956   Domain of unknown function (DUF4956)
      0.082   11.9   1.8      0.098   11.7   1.8    1.1  1  ArAE_2_N  Putative ER transporter, 6TM, N-terminal
      0.097   12.3   0.0       0.12   12.1   0.0    1.1  1  DUF4131   Domain of unknown function (DUF4131)
        0.1   13.4   0.1        0.1   13.4   0.1    1.8  2  YMF19     Plant ATP synthase F0
        1.3    9.0   6.5        3.8    7.6   0.1    2.2  2  DUF4227   Protein of unknown function (DUF4227)


Domain annotation for each model (and alignments):
>> DUF4956  Domain of unknown function (DUF4956)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.5   1.5e-05     0.054      23      60 ..      12      48 ..       4      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                       DUF4956 23 vftflllnvgvfavvlllasvevsiglglGLfgvlsil 60
                                  v+ f+ +  +v+ +v+ l++   s++l l++fg++s+l
  gi|15668507|ref|NP_247305.1| 12 VIGFV-VLFCVLELVFYLKKLYQSMALTLAVFGIFSLL 48
                                  44444.45789999999*******************98 PP

>> ArAE_2_N  Putative ER transporter, 6TM, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.8   2.7e-05     0.098     133     194 ..       4      62 ..       1      71 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                      ArAE_2_N 133 gkmltarvsvvyavllcvflffvgrlrakspkfalg.aifgiIaadvfltyapmlPlfapgtl 194
                                   g  ++ + +v+ +v+l++ l +v++l+  ++ +al+ a+fgi+ +  fl y p+l   +++++
  gi|15668507|ref|NP_247305.1|   4 GENMDKQ-TVIGFVVLFCVLELVFYLKKLYQSMALTlAVFGIFSLLFFLLYIPVL---SKKAV 62 
                                   6666654.6***********************666548*******8888877665...34554 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.2e-05      0.12       9      95 ..      12     101 ..       8     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.2e-05
                       DUF4131   9 llalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqlles...gqeviveGvvaslpeltgsgt 86 
                                   ++++++l+++l l++++++  + ++l+l+++ ++ ll+f+l+ p  +++  ++++++    ++ + e +v s   ++ s  
  gi|15668507|ref|NP_247305.1|  12 VIGFVVLFCVLELVFYLKKLYQSMALTLAVFGIFSLLFFLLYIPVLSKKAVPYVINYfkpPHQRVREIKVGSDETTDNSII 92 
                                   556666666666666665888889999999999999******************999998555556789988888777777 PP

                       DUF4131  87 rfvleverv 95 
                                   r+  +++ +
  gi|15668507|ref|NP_247305.1|  93 RLKEKAKTL 101
                                   777776666 PP

>> YMF19  Plant ATP synthase F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3       1.1   3.8e+03      18      36 ..      14      33 ..      11      46 .. 0.57
   2 ?   13.4   0.1   2.9e-05       0.1      16      67 ..      46      96 ..      36     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                         YMF19 18 fFitlYivll.knilpkiar 36
                                   F++l+ vl   + l k+++
  gi|15668507|ref|NP_247305.1| 14 GFVVLFCVLElVFYLKKLYQ 33
                                  56666664432344444444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.9e-05
                         YMF19 16 clfFitlYi.vllknilpkiarilklrkkllsslssevsklkkeqknlivskd 67
                                   l F++lYi vl k+ +p+++  +k + + +++ +  v ++++++++ i  k+
  gi|15668507|ref|NP_247305.1| 46 SLLFFLLYIpVLSKKAVPYVINYFKPPHQRVREIK--VGSDETTDNSIIRLKE 96
                                  4679999**6666**************99999976..4555555555555444 PP

>> DUF4227  Protein of unknown function (DUF4227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   2.7      0.02        70       6      22 ..      12      28 ..       9      33 .. 0.88
   2 ?    7.6   0.1    0.0011       3.8       5      63 ..      34      94 ..      29      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.02
                       DUF4227  6 rlkvflLFtvltllfyy 22
                                  ++ +++LF vl l+fy 
  gi|15668507|ref|NP_247305.1| 12 VIGFVVLFCVLELVFYL 28
                                  6789************6 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0011
                       DUF4227  5 erlkvflLFtvltllfy..yallwlneeyepyhrYdePeGsAVkvfqkeegeaskswleRL 63
                                  ++   + +F +++llf+  y+ ++ ++ +  + +Y +P  + V+ ++  ++e++++++ RL
  gi|15668507|ref|NP_247305.1| 34 SMALTLAVFGIFSLLFFllYIPVLSKKAVPYVINYFKPPHQRVREIKVGSDETTDNSIIRL 94
                                  5666788899999988732344455666777789999999999999888888888877777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1090  (0.0607954); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 865.76
//
Query:       gi|15668508|ref|NP_247306.1|  [L=96]
Description: hypothetical protein MJ_0333 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0086   16.5   0.0      0.015   15.7   0.0    1.4  1  HTH_26    Cro/C1-type HTH DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.013   15.5   0.1    1.0  1  ATPase_2  ATPase domain predominantly from Archaea
      0.015   15.4   0.1      0.026   14.6   0.0    1.5  1  HTH_3     Helix-turn-helix
      0.035   14.1   0.0      0.039   14.0   0.0    1.1  1  TUDOR     Tudor domain


Domain annotation for each model (and alignments):
>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.4e-06     0.015      17      49 ..      53      85 ..      27      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.4e-06
                        HTH_26 17 argtgisaatlsrlvkgkpervsldtLdkiCda 49
                                  ++ tg+ ++tl+++++++ + ++++t  k+ +a
  gi|15668508|ref|NP_247306.1| 53 SKETGLGKGTLHKIKNNELQDPRISTVLKLLKA 85
                                  579**************************9987 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   2.8e-06     0.013      46     126 ..      14      95 ..       9      96 .] 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-06
                      ATPase_2  46 dkdkyviyyialreesiskldefie....eeeekkklekal.......giavpkaeleeilkeksklvfkaielllekikk 115
                                   + +k+ i++i +++++i+++++ ++      +e                + ++k +l++i  ++++l +  i+ +l+ +k 
  gi|15668508|ref|NP_247306.1|  14 SDSKQAIFIIGVQGKEIKNVEQLMQelskIVNE-------GsiyryskETGLGKGTLHKI--KNNELQDPRISTVLKLLKA 85 
                                   567899****************96544432222.......12333333667777777666..8999999************ PP

                      ATPase_2 116 kgkkiiiiiDe 126
                                   +gk+++ii De
  gi|15668508|ref|NP_247306.1|  86 SGKRLVII-DE 95 
                                   ***98765.65 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.8e-06     0.026      16      47 ..      53      85 ..      47      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.8e-06
                                  HHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHH CS
                         HTH_3 16 AeklGvsrstisriEnG.ernPsletlkklaka 47
                                  ++++G+ + t+ +i n+  + P+++t++kl+ka
  gi|15668508|ref|NP_247306.1| 53 SKETGLGKGTLHKIKNNeLQDPRISTVLKLLKA 85
                                  799***************999**********98 PP

>> TUDOR  Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   8.7e-06     0.039       3      60 ..       3      63 ..       1      71 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.7e-06
                                  CCGEEEEEEEEEEETTEEEE..EEGGHHHHHHHHHHHHHHHHTSSCC.TCSSS--TT-EEE CS
                         TUDOR  3 edktievvvsaiespskfyi..qpkeqskkleklteelqeyyaskkk.aellapavgegcv 60
                                  ++k+ + ++++ +s + ++i  ++++  k++e+l++el+++ ++ +  + ++++ +g+g +
  gi|15668508|ref|NP_247306.1|  3 KEKYGDNMMTDSDSKQAIFIigVQGKEIKNVEQLMQELSKIVNEGSIyRYSKETGLGKGTL 63
                                  67888999*********9999********************99988866666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 599.13
//
Query:       gi|15668509|ref|NP_247307.1|  [L=102]
Description: hypothetical protein MJ_0334 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00016   21.4   4.1    0.00016   21.4   4.1    2.1  2  DivIC          Septum formation initiator
    0.00064   19.5   8.6     0.0017   18.2   8.3    1.9  1  PKcGMP_CC      Coiled-coil N-terminus of cGMP-dependent prote
     0.0038   16.2   5.3     0.0045   15.9   5.3    1.0  1  Spc7           Spc7 kinetochore protein
     0.0056   15.6   2.8      0.007   15.3   2.8    1.0  1  VPS38          Vacuolar protein sorting 38
     0.0074   16.9   0.2      0.013   16.1   0.1    1.5  1  SlyX           SlyX
     0.0096   15.9   4.0     0.0096   15.9   4.0    1.9  2  TMF_DNA_bd     TATA element modulatory factor 1 DNA binding
  ------ inclusion threshold ------
      0.011   16.1   1.7      0.013   15.8   1.7    1.1  1  DUF641         Plant protein of unknown function (DUF641)
      0.014   14.3   0.5      0.017   14.0   0.5    1.0  1  DUF2600        Protein of unknown function (DUF2600)
      0.015   15.3   6.1      0.015   15.3   6.1    2.0  2  Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
      0.018   13.7   3.7      0.019   13.6   3.7    1.0  1  AAA_13         AAA domain
      0.022   15.2   3.0      0.029   14.9   3.0    1.1  1  DUF16          Protein of unknown function DUF16
      0.024   14.3   4.5       0.03   14.0   4.5    1.1  1  Syntaxin       Syntaxin
      0.031   13.9   8.5        0.1   12.2   8.5    1.8  1  PEARLI-4       Arabidopsis phospholipase-like protein (PEARLI
      0.044   12.9   1.9      0.051   12.7   1.9    1.1  1  Atg14          Vacuolar sorting 38 and autophagy-related subu
      0.056   13.5   2.2       0.07   13.2   1.6    1.4  1  Vps51          Vps51/Vps67
      0.082   12.3   1.6      0.088   12.1   1.6    1.1  1  FAM76          FAM76 protein
        0.1   12.9   4.2       0.13   12.5   4.2    1.1  1  I_LWEQ         I/LWEQ domain
       0.15   11.9   1.5       0.31   10.8   0.9    1.8  2  ubiquitin      Ubiquitin family
       0.16   12.1   4.4        0.2   11.8   4.4    1.0  1  CREPT          Cell-cycle alteration and expression-elevated 
       0.26   11.7   2.8       0.35   11.3   2.8    1.3  1  DUF4140        N-terminal domain of unknown function (DUF4140
       0.27   10.0   3.5       0.33    9.8   3.5    1.0  1  FemAB          FemAB family
        2.8    8.4  11.2         14    6.1   3.7    3.1  2  FlgM           Anti-sigma-28 factor, FlgM


Domain annotation for each model (and alignments):
>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.59   4.8e+02      53      62 ..      23      32 ..      13      36 .. 0.80
   2 !   21.4   4.1   1.9e-07   0.00016      20      54 ..      56      89 ..      49      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.59
                                  XXXXXXXXXX CS
                         DivIC 53 dedyieerAR 62
                                    dy+e++A 
  gi|15668509|ref|NP_247307.1| 23 KSDYVEKIAQ 32
                                  679****996 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.9e-07
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                         DivIC 20 kqlkqeiaalqaelaklkaeneeLeaevkdLksde 54
                                   +++++ia+l+aelak+ +e+eeL++e++ L +++
  gi|15668509|ref|NP_247307.1| 56 VSQNEKIAELKAELAKKEKEIEELKEEIRGL-KGK 89
                                  589***************************9.465 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   8.3   2.1e-06    0.0017       7      28 ..      59      80 ..      57      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.1e-06
                     PKcGMP_CC  7 DERIRELEkrlaekdeEIqELr 28
                                   E+I+EL + la+k++EI+EL+
  gi|15668509|ref|NP_247307.1| 59 NEKIAELKAELAKKEKEIEELK 80
                                  69*******************9 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   5.3   5.5e-06    0.0045     162     240 ..      13      87 ..       8      93 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.5e-06
                          Spc7 162 eeeldellpeleeekaeleeeleklqe.....aaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekie 237
                                   +  +d+l+p+ + + +++ +e+ +  +     +        k e+e++ +e++ ++++i+e+k+ela++++++eel+e+i 
  gi|15668509|ref|NP_247307.1|  13 NGVIDDLVPKKSDYVEKIAQEAIRKDKvdalvR--------KHEMEQFYHEVS-QNEKIAELKAELAKKEKEIEELKEEIR 84 
                                   445666666666666666666655555333333........555555555543.344555555555555555555555554 PP

                          Spc7 238 elk 240
                                    lk
  gi|15668509|ref|NP_247307.1|  85 GLK 87 
                                   443 PP

>> VPS38  Vacuolar protein sorting 38
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.8   8.6e-06     0.007     185     246 ..      24      84 ..      20      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.6e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHS--S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         VPS38 185 leYtsqveeElqeisekveelikseekkelwslkelqkaieqlkksiekkklklkrLessle 246
                                    +Y +++ +E  +   kv++l++++e ++ ++  + +++i +lk+++ kk+ ++++L+++++
  gi|15668509|ref|NP_247307.1|  24 SDYVEKIAQEAIR-KDKVDALVRKHEMEQFYHEVSQNEKIAELKAELAKKEKEIEELKEEIR 84 
                                   5899999999876.68******************************************9987 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.6e-05     0.013      15      47 ..      58      90 ..      48      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                          SlyX 15 qedtieeLndvvaeqqqqidrlqrqlrllaerl 47
                                  q + i eL +++a+ +++i++l++++r l+ + 
  gi|15668509|ref|NP_247307.1| 58 QNEKIAELKAELAKKEKEIEELKEEIRGLKGKA 90
                                  8899************************99886 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.5   1.2e+03      52      65 ..      19      32 ..       8      51 .. 0.56
   2 !   15.9   4.0   1.2e-05    0.0096      28      57 ..      55      84 ..      53      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.5
                    TMF_DNA_bd 52 lkkkleklekelee 65
                                  l  k++++++++++
  gi|15668509|ref|NP_247307.1| 19 LVPKKSDYVEKIAQ 32
                                  33444444444443 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.2e-05
                    TMF_DNA_bd 28 elklnntikkLrkknkelekeikelkkkle 57
                                  e+ +n++i +L++++++ ekei+elk++++
  gi|15668509|ref|NP_247307.1| 55 EVSQNEKIAELKAELAKKEKEIEELKEEIR 84
                                  677888888888888888888888888775 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   1.7   1.6e-05     0.013      57     118 ..      23      86 ..      10      93 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                        DUF641  57 krlyrkkqkkkas.eaeeseleaeiqeqrsllkt.yeitvkkleaelkakdseieeLkekLeea 118
                                   k+ y++k  ++a  + +  +l ++ + ++   ++ ++  + +l+ael +k++eieeLke+++ +
  gi|15668509|ref|NP_247307.1|  23 KSDYVEKIAQEAIrKDKVDALVRKHEMEQFYHEVsQNEKIAELKAELAKKEKEIEELKEEIRGL 86 
                                   667777766555432334444444444444444313446789*****************99765 PP

>> DUF2600  Protein of unknown function (DUF2600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   2.1e-05     0.017     107     180 ..       7      80 ..       4      82 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                       DUF2600 107 reeqdDggYLaaLvetCqevlkklpsyelvreellelaelysdLqvykhvkkeereerLkewlerekeklpele 180
                                   +++++D+g +++Lv +  + ++k+ + ++ ++++ +l++     q y+ v+++e+ ++Lk+ l++++++++el+
  gi|15668509|ref|NP_247307.1|   7 FKKEKDNGVIDDLVPKKSDYVEKIAQEAIRKDKVDALVRKHEMEQFYHEVSQNEKIAELKAELAKKEKEIEELK 80 
                                   78899*********************9999*************************************9999986 PP

>> Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.7       3.3   2.7e+03      10      10 ..      30      30 ..       8      51 .. 0.63
   2 ?   15.3   6.1   1.8e-05     0.015       1      27 [.      60      86 ..      60      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.3
                 Bap31_Bap29_C 10 L 10
                                  +
  gi|15668509|ref|NP_247307.1| 30 I 30
                                  1 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.8e-05
                 Bap31_Bap29_C  1 keiekLkkeLkkkkkDlealKkQaegl 27
                                  ++i++Lk+eL+kk+k++e lK+ + gl
  gi|15668509|ref|NP_247307.1| 60 EKIAELKAELAKKEKEIEELKEEIRGL 86
                                  689******************988877 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.7   2.4e-05     0.019     383     444 ..      28      88 ..       8      94 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                        AAA_13 383 ekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkklee 444
                                   ek+a+ + +k ++   +++h++e+++ e++  ++k+++l++++ k eke++e ++e++ l++
  gi|15668509|ref|NP_247307.1|  28 EKIAQEAIRKDKVDALVRKHEMEQFYHEVS-QNEKIAELKAELAKKEKEIEELKEEIRGLKG 88 
                                   444444555666666666777777776664.4445666666666666666666666666555 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   3.0   3.5e-05     0.029      12      72 ..      19      84 ..       5      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.5e-05
                                  X.X.XTTB-BHHHHHHB-........BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         DUF16 12 kiPvkteYVTrkqlnefkds......nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqk 72
                                  ++P+k++YV +   +  +++       k +++++ ++v+ ++e+i++l+ +  k++++i+elk+e+ 
  gi|15668509|ref|NP_247307.1| 19 LVPKKSDYVEKIAQEAIRKDkvdalvRKHEMEQFYHEVS-QNEKIAELKAELAKKEKEIEELKEEIR 84
                                  4899999*9887777777666778888888888888887.99*********************9986 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   4.5   3.7e-05      0.03     128     186 ..      30      87 ..      23      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                      Syntaxin 128 vtGkevseeeieelietgesevflqkllqeqrgarealseieeRhkevlelekslkeLh 186
                                   ++ + + +++++ l+ + e+e+f +++ q++++a e  +e  +  ke+ el+++++ L+
  gi|15668509|ref|NP_247307.1|  30 IAQEAIRKDKVDALVRKHEMEQFYHEVSQNEKIA-ELKAELAKKEKEIEELKEEIRGLK 87 
                                   66788999*******************9999998.6778****************9986 PP

>> PEARLI-4  Arabidopsis phospholipase-like protein (PEARLI 4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   8.5   0.00013       0.1     176     245 ..      28      98 ..      13     102 .] 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                      PEARLI-4 176 eEiveavkyydeqetavvEKevke..rdvllkkqEmekqekelaekEKeikevrekvtemaaklgelemkra 245
                                   e i++ +   d+ +  v   e+++  ++v ++ + + + ++ela+kEKei+e++e++  +++k g l + ++
  gi|15668509|ref|NP_247307.1|  28 EKIAQEAIRKDKVDALVRKHEMEQfyHEV-SQNEKIAELKAELAKKEKEIEELKEEIRGLKGKAGGLGIGGS 98 
                                   55666655556666544433333310333.45566788999**********************999877655 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.9   6.2e-05     0.051      71     109 ..      50      88 ..      16      92 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.2e-05
                         Atg14  71 elksliadlrerlqelkdklsqlkkeieekkkklaklsd 109
                                   e+  +  +++e+++elk+ l +  keiee k+++++l+ 
  gi|15668509|ref|NP_247307.1|  50 EQFYHEVSQNEKIAELKAELAKKEKEIEELKEEIRGLKG 88 
                                   555677789999999999999999999999999999875 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.6   8.6e-05      0.07       7      45 ..      48      86 ..      44      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.6e-05
                         Vps51  7 daeayvrellakstlkellkveasllseiraldselkal 45
                                  ++e++++e+ ++++++el++  a+ ++ei++l++e++ l
  gi|15668509|ref|NP_247307.1| 48 EMEQFYHEVSQNEKIAELKAELAKKEKEIEELKEEIRGL 86
                                  689999*****************************9965 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.6   0.00011     0.088     196     255 ..      30      89 ..       3      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                         FAM76 196 laeekesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkae 255
                                   +a+e+ ++++  + + ++  +++ +    +e+ia+lk +l++k++e+ e + +i  lk++
  gi|15668509|ref|NP_247307.1|  30 IAQEAIRKDKVDALVRKHEMEQFYHEVSQNEKIAELKAELAKKEKEIEELKEEIRGLKGK 89 
                                   33444444444556666777777766667999*****************99999999987 PP

>> I_LWEQ  I/LWEQ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   4.2   0.00015      0.13      86     149 ..      17      81 ..      12      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                        I_LWEQ  86 kelvkavkeakekqeeeeseeeeld.isklslvqakrqemeaqvkilklekeLeearkkLaeirk 149
                                   ++lv +  +  ek  +e   ++++d + ++ ++++  +e+ + +ki++l+ eL +++k+++e++ 
  gi|15668509|ref|NP_247307.1|  17 DDLVPKKSDYVEKIAQEAIRKDKVDaLVRKHEMEQFYHEVSQNEKIAELKAELAKKEKEIEELKE 81 
                                   677777777788877777677899988999999999***********************999875 PP

>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.9   0.00038      0.31       9      33 ..      50      74 ..      42      80 .. 0.83
   2 ?    1.3   0.2      0.35   2.9e+02      16      29 ..      71      84 ..      70      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                                  EEEEEEEETTSBHHHHHHHHHHHHT CS
                     ubiquitin  9 kkitleveesdtveelKekiaekeg 33
                                  +++ +ev+++++++elK+ +a+ke+
  gi|15668509|ref|NP_247307.1| 50 EQFYHEVSQNEKIAELKAELAKKEK 74
                                  67889*****************994 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.35
                                  ETTSBHHHHHHHHH CS
                     ubiquitin 16 eesdtveelKekia 29
                                  ++++++eelKe i 
  gi|15668509|ref|NP_247307.1| 71 KKEKEIEELKEEIR 84
                                  56789******996 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   4.4   0.00024       0.2      53     123 ..      16      86 ..       8      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                         CREPT  53 veealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelkshiqsL 123
                                   +++ +   ++Y++++++e     k+  ++++    q  +   ++ek++elk  l+k +++ +elk+ i+ L
  gi|15668509|ref|NP_247307.1|  16 IDDLVPKKSDYVEKIAQEAIRKDKVDALVRKHEMEQFYHEVSQNEKIAELKAELAKKEKEIEELKEEIRGL 86 
                                   556667779************************99999999999**********************99876 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.8   0.00043      0.35      53      93 ..      48      88 ..      23      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                       DUF4140 53 qvervpnreaeeeelkalraeleeledelaaledelaaaea 93
                                  + e+ +++ +++e++++l+ael + e+e+++l++e++ ++ 
  gi|15668509|ref|NP_247307.1| 48 EMEQFYHEVSQNEKIAELKAELAKKEKEIEELKEEIRGLKG 88
                                  44555666666668********************9998875 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.5   0.00041      0.33     242     298 ..      25      83 ..      22      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00041
                         FemAB 242 eylkelqekleklekklakleekleknpe....kkkkkklkelekqlaslekelkeaeefi 298
                                   +y++++++++  ++k  + l +k+e + +     ++++k++el+ +la+ eke++e++e i
  gi|15668509|ref|NP_247307.1|  25 DYVEKIAQEAIRKDKV-DALVRKHEME-QfyheVSQNEKIAELKAELAKKEKEIEELKEEI 83 
                                   7888888844444333.3333333333.235778999********************9966 PP

>> FlgM  Anti-sigma-28 factor, FlgM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   3.7     0.017        14      22      38 ..      53      70 ..      20      72 .. 0.77
   2 ?    3.0   1.1      0.17   1.4e+02      27      38 ..      73      84 ..      71      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
                          FlgM 22 ape.vreekVaelKeaIa 38
                                    e + +ek+aelK+++a
  gi|15668509|ref|NP_247307.1| 53 YHEvSQNEKIAELKAELA 70
                                  34668899*******997 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.17
                          FlgM 27 eekVaelKeaIa 38
                                  e+ ++elKe+I 
  gi|15668509|ref|NP_247307.1| 73 EKEIEELKEEIR 84
                                  678*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2705  (0.150873); expected 358.6 (0.02)
Passed bias filter:                     1259  (0.0702214); expected 358.6 (0.02)
Passed Vit filter:                       205  (0.011434); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 630.16
//
Query:       gi|15668510|ref|NP_247308.1|  [L=247]
Description: hypothetical protein MJ_0335 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.012   15.3   5.9          3    7.4   4.9    2.1  2  Phage_GPO      Phage capsid scaffolding protein (GPO) serine 
       0.07   13.5   0.3       0.29   11.5   0.3    2.0  2  Styelin        Styelin
       0.61   10.1   4.2        1.4    8.9   4.2    1.5  1  DUF1676        Protein of unknown function (DUF1676)


Domain annotation for each model (and alignments):
>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00059       3.5      11      44 ..      12      41 ..       5     102 .. 0.82
   2 ?    7.4   4.9    0.0005         3     164     233 ..     151     223 ..     120     228 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00059
                     Phage_GPO 11 aTtdGreierewleqmaanYdpkvYgArinleHl 44
                                   T+dG ei+ ew++    +Y p++ g  +n++H 
  gi|15668510|ref|NP_247308.1| 12 TTIDGQEITEEWIK----KYGPTLRGKPVNIDHN 41
                                  69**********95....7*************94 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0005
                     Phage_GPO 164 efeeeeeeeegeslferikallskkkksd...darfadveeavelvAeevkelsekveallaleaelaalkke 233
                                   ++++ +eee ++ l e+i+++l+++kk++   d+  ++  ++ve +A+++ el    +++l++ +e+ +++ke
  gi|15668510|ref|NP_247308.1| 151 KIKDMTEEEFEKFLHEKIEQILASHKKENedkDKSDNEDDKVVEILASKMDELVAVNKSVLKQLEEIRKAQKE 223
                                   455555555567789999999987666553335556677899**********999999888888887777765 PP

>> Styelin  Styelin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.91   5.4e+03      25      38 ..      43      56 ..      39      59 .. 0.62
   2 ?   11.5   0.3   4.8e-05      0.29      32      49 ..     152     170 ..     144     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.91
                       Styelin 25 lsiakhlLGDmtDe 38
                                  +s ++ ++GD+ D 
  gi|15668510|ref|NP_247308.1| 43 YSNGNLAVGDVVDV 56
                                  45566677887775 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.8e-05
                       Styelin  32 LGDmtDeefqefmke.veq 49 
                                   + Dmt+eef  f++e +eq
  gi|15668510|ref|NP_247308.1| 152 IKDMTEEEFEKFLHEkIEQ 170
                                   67**********9865888 PP

>> DUF1676  Protein of unknown function (DUF1676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.2   0.00024       1.4      36      90 ..     134     184 ..     118     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00024
                       DUF1676  36 lvrneeaasasskeeeeelsreeeeareeelekllleklerflkshslevklpee 90 
                                   ++r++ ++    k++e++++++ ++  eee ek+l ek+e++l+sh+ e + ++ 
  gi|15668510|ref|NP_247308.1| 134 IKRDSMDT----KTQEKTEPKKIKDMTEEEFEKFLHEKIEQILASHKKENEDKDK 184
                                   44443333....3678899999999999******************866555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2631  (0.146745); expected 358.6 (0.02)
Passed bias filter:                     1071  (0.0597356); expected 358.6 (0.02)
Passed Vit filter:                       145  (0.00808746); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 1508.70
//
Query:       gi|15668511|ref|NP_247309.1|  [L=119]
Description: hypothetical protein MJ_0336 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.047   14.2   0.7       0.11   13.0   0.7    1.7  1  DUF2190   Uncharacterized conserved protein (DUF2190)


Domain annotation for each model (and alignments):
>> DUF2190  Uncharacterized conserved protein (DUF2190)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.7   6.1e-06      0.11      38      88 ..      54     106 ..       6     119 .] 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.1e-06
                       DUF2190  38 a.aaGetvtvaveGvf...veaaaaiavGdkVy..wdasgkvlttttatgnvaGval 88 
                                   +  aG +v ++v+Gv    ++ ++ ia Gd V+   d sgk++ + + +  +aG+ +
  gi|15668511|ref|NP_247309.1|  54 IyTAGMYVDLKVNGVQkveIKEGESIAPGDYVIpsTDGSGKAV-K-SPI--KAGFKV 106
                                   1469*************9999999********96455555553.2.222..234444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 809.10
//
Query:       gi|15668512|ref|NP_247310.1|  [L=262]
Description: hypothetical protein MJ_0337 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1700.40
//
Query:       gi|15668513|ref|NP_247311.1|  [L=104]
Description: hypothetical protein MJ_0338 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 701.20
//
Query:       gi|15668514|ref|NP_247312.1|  [L=107]
Description: hypothetical protein MJ_0339 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00047   20.0   0.2    0.00065   19.5   0.2    1.3  1  DUF2247   Uncharacterized protein conserved in bacteria (DUF2
  ------ inclusion threshold ------
      0.054   13.6   0.2       0.11   12.6   0.1    1.6  1  DUF4840   Domain of unknown function (DUF4840)
      0.099   12.7   0.1       0.33   11.1   0.1    1.8  2  Exog_C    Endo/exonuclease (EXOG) C-terminal domain
       0.12   13.0   0.7       0.66   10.6   0.2    1.9  2  DUF3502   Domain of unknown function (DUF3502)


Domain annotation for each model (and alignments):
>> DUF2247  Uncharacterized protein conserved in bacteria (DUF2247)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   1.4e-07   0.00065      79     155 ..      12      90 ..       6      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-07
                       DUF2247  79 leerkwlyvvL.kelkelskdfeepLeeveeiyadfdyPeeienfirYmppkdgys..pseyseeeninrliekleeyLe 155
                                   +++ k l++++ ++lk++    ++pL ++++++ + d++ eien ++Y  +   ++  p+e    e i+  +  +++yLe
  gi|15668514|ref|NP_247312.1|  12 YANAKALVEKIlEDLKNNGIKVKSPLSKIQDFHCEADFSVEIENRVAYVDATFTFDklPNEDLV-EKIEAVMTTYNSYLE 90 
                                   566677777666************************************8876544322444433.345555555666665 PP

>> DUF4840  Domain of unknown function (DUF4840)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.4e-05      0.11      31      66 ..      53      89 ..      35     103 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                       DUF4840 31 isv.aevkdstltienfPvkdLaksivdeeeelkeai 66
                                  i+      d t+t++++P +dL+++i+  ++  +  +
  gi|15668514|ref|NP_247312.1| 53 IENrVAYVDATFTFDKLPNEDLVEKIEAVMTTYNSYL 89
                                  4443444589****************66555555444 PP

>> Exog_C  Endo/exonuclease (EXOG) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   7.3e-05      0.33      24      44 ..      19      39 ..      12      42 .. 0.82
   2 ?   -1.6   0.0      0.65   2.9e+03      21      29 ..      75      83 ..      68      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.3e-05
                        Exog_C 24 LekvmkeLkeagiepDeyLlk 44
                                  +ek++++Lk+ gi+    L+k
  gi|15668514|ref|NP_247312.1| 19 VEKILEDLKNNGIKVKSPLSK 39
                                  8************98777766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.65
                        Exog_C 21 lkRLekvmk 29
                                  ++++e vm 
  gi|15668514|ref|NP_247312.1| 75 VEKIEAVMT 83
                                  678888885 PP

>> DUF3502  Domain of unknown function (DUF3502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.13     6e+02      97     115 ..      14      32 ..       8      39 .. 0.84
   2 ?   10.6   0.2   0.00015      0.66      57      92 ..      55      90 ..      32     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.13
                       DUF3502  97 DpeetlpkfneklkaaGid 115
                                   + ++ ++k++e+lk+ Gi+
  gi|15668514|ref|NP_247312.1|  14 NAKALVEKILEDLKNNGIK 32 
                                   6778899999999999985 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00015
                       DUF3502 57 eakaspalgFtfDsspvkteiaalsnvveeykkale 92
                                  + +a   + FtfD+ p ++ ++++++v+++y++ le
  gi|15668514|ref|NP_247312.1| 55 NRVAYVDATFTFDKLPNEDLVEKIEAVMTTYNSYLE 90
                                  455577789**********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 720.58
//
Query:       gi|15668515|ref|NP_247313.1|  [L=234]
Description: hypothetical protein MJ_0340 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00022   20.8   0.1    0.00076   19.0   0.1    1.9  2  DUF2460    Conserved hypothetical protein 2217 (DUF2460)
  ------ inclusion threshold ------
      0.083   12.6   0.0       0.27   10.9   0.0    1.7  2  CBM_17_28  Carbohydrate binding domain (family 17/28)
       0.09   12.6   0.1       0.75    9.7   0.1    2.2  2  DUF4183    Domain of unknown function (DUF4183)


Domain annotation for each model (and alignments):
>> DUF2460  Conserved hypothetical protein 2217 (DUF2460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.3e-07   0.00076      94     168 ..      32      97 ..      19     101 .. 0.80
   2 ?   -1.7   0.0      0.28   1.7e+03     123     166 ..     102     140 ..      97     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-07
                       DUF2460  94 vGdgattkFqLvktygsgeesyvrkitkPvagtvrvavdgvelaega.fsvdtttG...lvtfaaapaagasvtagfeF 168
                                   +Gd+++ +F+L+k+ +             v g++ v+v+gv + eg+ ++  +++G   ++ f+++pa+gas+t+ + +
  gi|15668515|ref|NP_247313.1|  32 TGDEQNDTFELTKDDA-------------VLGSEIVKVNGVLQFEGQdYTAIHENGilkKIKFTQPPANGASITVEYLY 97 
                                   4555555555555554.............99*****************77777877333589**************988 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.28
                       DUF2460 123 vagtvrvavdgvelaegafsvdtttGlvtfaaapaagasvtagf 166
                                     g  +++v++ + +e+ ++vd   G+++++    +g+s+t +f
  gi|15668515|ref|NP_247313.1| 102 LGGASELSVKEDKDKEE-LTVDCSYGKIQIE----KGSSITLSF 140
                                   55666667777777765.8888888888765....566666666 PP

>> CBM_17_28  Carbohydrate binding domain (family 17/28)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.28   1.7e+03      45      74 ..      36      65 ..      22      99 .. 0.73
   2 ?   10.9   0.0   4.6e-05      0.27      77     148 ..     156     229 ..     129     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.28
                                  XXXXXXXXXXXXXX........XXXXXXXX CS
                     CBM_17_28 45 ttqGfgvnsdspvksvtvenennaLkieel 74
                                      f++ +d +v + ++ + n++L+ e+ 
  gi|15668515|ref|NP_247313.1| 36 QNDTFELTKDDAVLGSEIVKVNGVLQFEGQ 65
                                  445567777777777777777777777664 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.6e-05
                                   XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXX.XXXXXXXXXX...... CS
                     CBM_17_28  77 sndlseenfwanvrlsadewaekpdilgakelsldvivkepltvsi..aavPqssnhgWanperavavtpddfe 148
                                   s ++ e+n +++ +  a ++a+ + ++ +ke ++   v+ p  + i  +a+P++++ +W+  ++++ +t++ +e
  gi|15668515|ref|NP_247313.1| 156 SGEILEGNTYSKYKNGASKSANIVVLAFSKEATMAYGVEPPKRIVIirGAMPNNLEFDWSGGSKSFDLTAQSYE 229
                                   678889*****************************999999887775589*****************9998775 PP

>> DUF4183  Domain of unknown function (DUF4183)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00013      0.75      13      73 ..      30      94 ..      24      95 .. 0.77
   2 ?    0.1   0.0      0.12     7e+02      54      74 .]     117     140 ..     113     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                       DUF4183 13 sFtdddgaaatalpailtpn.syfnlYINGvLQ.esslytvtpgaltlk...egdsilaGtpiile 73
                                  +Ft d+++  ++l+   ++  ++  + +NGvLQ e++ yt   ++ +lk    ++++ +G +i++e
  gi|15668515|ref|NP_247313.1| 30 TFTGDEQNDTFELTKD-DAVlGSEIVKVNGVLQfEGQDYTAIHENGILKkikFTQPPANGASITVE 94
                                  6777777777776663.33357777889*****556789999999999888889999******998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.12
                       DUF4183  54 galtlk...egdsilaGtpiilei 74 
                                   ++lt++   ++ +i +G++i+l++
  gi|15668515|ref|NP_247313.1| 117 EELTVDcsyGKIQIEKGSSITLSF 140
                                   677777777888999*****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1600.74
//
Query:       gi|15668516|ref|NP_247314.1|  [L=120]
Description: hypothetical protein MJ_0341 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1281  (0.0714485); expected 358.6 (0.02)
Passed bias filter:                      760  (0.0423894); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 803.30
//
Query:       gi|15668517|ref|NP_247315.1|  [L=123]
Description: hypothetical protein MJ_0342 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        5.1    7.2   9.3        4.1    7.5   4.0    2.0  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.0   0.00023       4.1      52      89 ..      18      60 ..       4      63 .. 0.59
   2 ?    3.0   0.2    0.0057     1e+02      48      87 ..      79     117 ..      76     123 .] 0.49

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00023
               Phage_holin_3_6 52 llllval.alala.a...lwlaalivaavllvlagvlalvglk 89
                                  +l++++l + +++ a   l la+++v+a  lvl ++ +l+ +k
  gi|15668517|ref|NP_247315.1| 18 GLIFFGLiMEVIHnAlisLVLAFFVVFAWDLVLSLIYGLRFVK 60
                                  2222222122222223358889999999999999999988776 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0057
               Phage_holin_3_6  48 llalllllvala.....lalaalwlaalivaavllvlagvlalvg 87 
                                   l+a ++l++ ++     l      l  liv ++ + l+  l++  
  gi|15668517|ref|NP_247315.1|  79 LFASTCLSAVIWtytdsL------LLGLIVPVIIVFLGKQLMRGL 117
                                   555556665554222221......334566666555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 859.13
//
Query:       gi|15668518|ref|NP_247316.1|  [L=849]
Description: hypothetical protein MJ_0343 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-06   26.3  20.4    1.3e-05   25.1   7.3    4.1  3  PhageMin_Tail   Phage-related minor tail protein
     0.0034   16.2   2.0     0.0034   16.2   2.0    3.4  3  AAA_32          AAA domain
  ------ inclusion threshold ------
      0.054   13.3   0.2       0.27   11.1   0.2    2.2  1  TMV_coat        Virus coat protein (TMV like)
      0.062   13.4   7.5        0.2   11.8   7.5    1.9  1  Recep_L_domain  Receptor L domain
       0.12   12.9   4.5        2.6    8.6   0.0    3.8  3  YflT            Heat induced stress protein YflT
       0.12   12.8   0.4       0.64   10.5   0.0    2.4  2  Chrome_Resist   Chromate resistance exported protein
       0.45   10.5   4.0       0.61   10.1   0.0    3.1  3  Mor             Mor transcription activator family
        1.7    8.8  10.6       0.87    9.8   4.4    3.3  3  COG5            Golgi transport complex subunit 5
        2.7    8.0   6.0         13    5.8   0.2    3.6  4  HetR_C          Heterocyst differentiation regulator C-termin
        9.8    6.7  24.5         33    5.0  13.9    4.2  4  APG6_N          Apg6 coiled-coil region


Domain annotation for each model (and alignments):
>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   1.0      0.65   1.2e+03     157     186 ..      83     127 ..       3     136 .. 0.57
   2 !   25.1   7.3   7.3e-09   1.3e-05      15     117 ..     251     348 ..     238     365 .. 0.83
   3 !    8.0   0.1    0.0014       2.4      96     190 ..     640     741 ..     579     746 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.65
                 PhageMin_Tail 157 Gist..............kdaq.gkmksldeiledlsealkkltd 186
                                    i++              k+++ +   ++d+il+++++  ++l++
  gi|15668518|ref|NP_247316.1|  83 NINFdydlsklkseleqlKNTKiDIKTNTDQILKQINKIKSELSE 127
                                   222233333333333222222322235666666666665555544 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 7.3e-09
                 PhageMin_Tail  15 atelaealeelasaGvsteeilnll.egaaklataggaddleeaaeilstalnafglsaadaeeaaDvlaaaanngatsve 94 
                                   a+++a ++ +l  +G s+eei++++   ++  ++ g ++ ++ea + +s +++    +    e++a++l +a+ +ga +v+
  gi|15668518|ref|NP_247316.1| 251 ADDIARMISALTAMGKSNEEIMKMVnAEVLE-MKQGHTE-VAEAIREFSITMGDTLDP----EKFASILIQAQAAGAQDVG 325
                                   69**********************9444444.4555524.777777777776555555....7****************** PP

                 PhageMin_Tail  95 dlaealkevgavakaaGlsfeet 117
                                   +laea++ ++   +++G++ e++
  gi|15668518|ref|NP_247316.1| 326 QLAEAINDLALNSRQMGFDVEKA 348
                                   *******************9986 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0014
                 PhageMin_Tail  96 laealkevgavakaaGlsfeetaaalallaaag.ikgseAgtalknllsrltkeaaealkkl..Gis.tkdaq...gkm.. 167
                                    + + + +  ++  +G++ +e+  a+ +la++  + + ++ +a++ ++ ++    ++++++   G++ + +++   +k+  
  gi|15668518|ref|NP_247316.1| 640 WSVVQNTLQEAFEELGMKEDEARQAAENLAQQWqQLPQQILDAFNGFVDNI----KQTFDEWwnGLNeWWSQKieeAKNwg 716
                                   555555566678899999999999999999977799999999999999999....77777777788877666664444466 PP

                 PhageMin_Tail 168 .ksldeiledlsealkkltda.qra 190
                                       ++i++ ++e++++l++a  +a
  gi|15668518|ref|NP_247316.1| 717 sDLIQNIIDGIKEKFSELENAvSQA 741
                                   6667889999999999997774443 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   9.0      0.17   3.1e+02     182     305 ..      56     180 ..      19     184 .. 0.71
   2 !   16.2   2.0   1.9e-06    0.0034     126     247 ..     266     387 ..     256     409 .. 0.89
   3 !    4.7   0.0    0.0062        11     167     246 ..     670     753 ..     639     758 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.17
                        AAA_32 182 ekseeleeeleeilrelrelekeakeklkelerevakeaveplleelkekykdl....ekvleyLeaveedilenlelfle 258
                                   +++ e++++++ i+rel+e+e +a++   + + ++ k  +++ le+lk++  d     +++l+ ++++++++ e+ ++  +
  gi|15668518|ref|NP_247316.1|  56 KSEVEFKSNINMIIRELEEIEADASKMNINFDYDLSK--LKSELEQLKNTKIDIktntDQILKQINKIKSELSEKQTIRAK 134
                                   3455778889999999999999888887777776654..444455554443322222478999999999999988775444 PP

                        AAA_32 259 eeeeeeeeekkkkedelkrYkvnvlvdnsetegaPVvvednptyanL 305
                                    e + +e  +k k++  ++Y++n + d ++   a   + d  +y++L
  gi|15668518|ref|NP_247316.1| 135 VEVDRTE-WDKLKKEWSEKYHINAIADVASVGTAYMGISDAEKYNEL 180
                                   4444443.356789999*********999988888888877777777 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.9e-06
                        AAA_32 126 ekeeelleelekeaeekgfalkrtpegivlvPlkdgkplseeefealpeeerkeleekseeleeeleeilrelrelekeak 206
                                   + +ee+++ +++e+ e +   ++  e i  ++++ g +l++e+f+++  + +++  +++ +l e ++++  + r++  +++
  gi|15668518|ref|NP_247316.1| 266 KSNEEIMKMVNAEVLEMKQGHTEVAEAIREFSITMGDTLDPEKFASILIQAQAAGAQDVGQLAEAINDLALNSRQMGFDVE 346
                                   55666666666666666666666666699999************************************************* PP

                        AAA_32 207 eklkelerevakeaveplleelkekykdlekvleyLeavee 247
                                   ++l+e++++   +++ +l ++   +y++  k+ +yL++v  
  gi|15668518|ref|NP_247316.1| 347 KALREIQKTKDDKTLAELAKKYGLTYEQIVKIHDYLQRVDL 387
                                   *************************************9965 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0062
                        AAA_32 167 eefealpeeerkeleekseeleeeleeilrelrelekeakeklkelerevakeav...eplleelkekykdlek.vleyLe 243
                                   ++ ++lp++  ++++  ++++++ ++e  + l+e+ ++  e+ k++ ++++++++   ++ ++el++  ++ +  + +yL+
  gi|15668518|ref|NP_247316.1| 670 QQWQQLPQQILDAFNGFVDNIKQTFDEWWNGLNEWWSQKIEEAKNWGSDLIQNIIdgiKEKFSELENAVSQAAGiISSYLH 750
                                   567788888888888888888888888888888888888888777777776665411134455555554444333667777 PP

                        AAA_32 244 ave 246
                                   +  
  gi|15668518|ref|NP_247316.1| 751 HTT 753
                                   665 PP

>> TMV_coat  Virus coat protein (TMV like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00015      0.27       7      53 ..      80     124 ..      76     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                   TTTCCCCCTEEECCCHHHHHHHCTTS-TTSCCCCHHHHHHCCCT-B- CS
                      TMV_coat   7 ikkasqakfWirvselksllknlraikfsvassrsvvaealaalgrd 53 
                                    k+ +++++  ++s+lks l++l+ +k++++++ +++++++++++ +
  gi|15668518|ref|NP_247316.1|  80 SKMNINFDY--DLSKLKSELEQLKNTKIDIKTNTDQILKQINKIKSE 124
                                   678899999..*******************************99865 PP

>> Recep_L_domain  Receptor L domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   7.5   0.00011       0.2       4      97 ..       8     111 ..       7     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                   EEESBEEEECCHCTSBGGGGGGGGG--EESS-EEEESET-SSEGCGTT--EEESSSSBTTTEEEEEES-TT.......... CS
                Recep_L_domain   4 vieGnLeitltseneeeellsflsnveeitGyllikntnlkslsflenLrvIrgrelfeskyalaildnkn.......... 74 
                                   ++eG Le++l ++       + l+++e+i+  l+i+++ +  ++ l+ L+ ++++ +f+s++ ++i++ ++          
  gi|15668518|ref|NP_247316.1|   8 KVEGTLELNLDDKD----VRKNLKSLEKIKSKLEIESNINAVIKQLDELKNVKSEVEFKSNINMIIRELEEieadaskmni 84 
                                   599*********99....7899****************99999*************************9997777777777 PP

                                   .....-SBEE-TTTSEESSSEEEEESET CS
                Recep_L_domain  75 .....leeLglpslkeitsgsvviskNp 97 
                                        l++L+ + l+++++ ++ i+ N 
  gi|15668518|ref|NP_247316.1|  85 nfdydLSKLKSE-LEQLKNTKIDIKTNT 111
                                   776555555433.666666777777766 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.6     0.066   1.2e+02      53      89 ..     160     198 ..      90     200 .. 0.60
   2 ?   -3.1   0.0       6.2   1.1e+04      32      83 ..     356     373 ..     328     385 .. 0.61
   3 ?    8.6   0.0    0.0014       2.6      67      93 ..     643     669 ..     622     671 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.066
                          YflT  53 e.eglwdsiknlfrs.kgdelrekleslGltedeaeeye 89 
                                   +  +++++ + +    k +el + l++ Glt+d+ae++ 
  gi|15668518|ref|NP_247316.1| 160 DvASVGTAYMGISDAeKYNELMTILRERGLTKDQAERLI 198
                                   224444444444443566788899************975 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.2
                          YflT  32 kdkdrlerlaentdaetettseeglwdsiknlfrskgdelrekleslGlted 83 
                                   k                                  +++ l+e  +++Glt +
  gi|15668518|ref|NP_247316.1| 356 K----------------------------------DDKTLAELAKKYGLTYE 373
                                   2..................................33333444444454444 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0014
                          YflT  67 kgdelrekleslGltedeaeeyeeeld 93 
                                    ++ l+e++e+lG++edea++ +e l+
  gi|15668518|ref|NP_247316.1| 643 VQNTLQEAFEELGMKEDEARQAAENLA 669
                                   678999****************99886 PP

>> Chrome_Resist  Chromate resistance exported protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       3.2   5.7e+03      80     115 ..      44      80 ..      31     123 .. 0.63
   2 ?   10.5   0.0   0.00036      0.64      40     101 ..     338     399 ..     324     422 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.2
                 Chrome_Resist  80 eivraadvke.eaklapeaagleailaglseelkdde 115
                                   ++++++d  +  +++++  +++++i+++l e+ +d +
  gi|15668518|ref|NP_247316.1|  44 AVIKQLDELKnVKSEVEFKSNINMIIRELEEIEADAS 80 
                                   5555555433123333334555555555555533332 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00036
                 Chrome_Resist  40 eeaipFDiega..elthegerctFevllkkfeledpaLkrlaeivraadvkeeaklapeaagle 101
                                   + +++FD+e+a  e+++++++ t   l kk++l+ +++ ++   ++ +d+++   l+ ++++l+
  gi|15668518|ref|NP_247316.1| 338 SRQMGFDVEKAlrEIQKTKDDKTLAELAKKYGLTYEQIVKIHDYLQRVDLDK--GLPDNTNELD 399
                                   47899***99866899999*******************************96..4444444444 PP

>> Mor  Mor transcription activator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.5   2.8e+03       9      34 ..     106     131 ..      99     137 .. 0.80
   2 ?   10.1   0.0   0.00034      0.61      60      92 ..     346     378 ..     339     390 .. 0.79
   3 ?   -1.1   0.1         1   1.9e+03      13      40 ..     646     672 ..     641     675 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHTS.S-....TTSHH CS
                           Mor   9 dlakhvaaelkrlgeidealaeqige 34 
                                   d+ +++ + lk+ ++i+++l+e+  +
  gi|15668518|ref|NP_247316.1| 106 DIKTNTDQILKQINKIKSELSEKQTI 131
                                   78888999999999999999887655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00034
                                   HHHHHHHHHH--SS-HHHHHHHHT--HHHHHHH CS
                           Mor  60 elrdreifnefkGnnvaeLarkYglseqwiyki 92 
                                   e+  rei +  + + +aeLa+kYgl++++i ki
  gi|15668518|ref|NP_247316.1| 346 EKALREIQKTKDDKTLAELAKKYGLTYEQIVKI 378
                                   555567778888999****************99 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1
                                   HHHHHHHHTS.S-....TTSHHHHHHHH CS
                           Mor  13 hvaaelkrlgeidealaeqigeevadal 40 
                                    ++++ ++lg ++e+ a+q++e++a++ 
  gi|15668518|ref|NP_247316.1| 646 TLQEAFEELG-MKEDEARQAAENLAQQW 672
                                   4566677788.88899999999988875 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.8   3.3e+03      68      84 ..      33      49 ..      19      75 .. 0.50
   2 ?    9.8   4.4   0.00049      0.87      22     100 ..      77     154 ..      66     162 .. 0.87
   3 ?    0.1   0.1      0.46   8.2e+02       9      54 ..     305     354 ..     300     380 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.8
                                  XXXXXXXXXXXXXXXXX CS
                          COG5 68 kslssvlselksslesL 84
                                  ks+ ++ s+++  +++L
  gi|15668518|ref|NP_247316.1| 33 KSKLEIESNINAVIKQL 49
                                  22222222222222222 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00049
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHH CS
                          COG5  22 nnnddteldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepye 100
                                    ++++ ++  +  l++l++ +++l++  + +i++n +++l++++k+ks+ s  ++++ ++e      ++lk++ +e+y 
  gi|15668518|ref|NP_247316.1|  77 ADASKMNINFDYDLSKLKSELEQLKN-TKIDIKTNTDQILKQINKIKSELSEKQTIRAKVEVDRTEWDKLKKEWSEKYH 154
                                   56677788888889999999999865.56789****************************************9999985 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.46
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXX CS
                          COG5   9 dpksfanallkatnnnddteldlstplkrlnydiq....eldkrlrqlit 54 
                                   dp++fa+ l++a+ +  ++   l+ +++ l    +    +++k lr++ +
  gi|15668518|ref|NP_247316.1| 305 DPEKFASILIQAQAAGAQDVGQLAEAINDLALNSRqmgfDVEKALREIQK 354
                                   89999999999666666655555555555444333111123344444444 PP

>> HetR_C  Heterocyst differentiation regulator C-terminal Hood domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       6.3   1.1e+04      41      54 ..      39      52 ..      24      69 .. 0.69
   2 ?   -2.6   0.1         3   5.5e+03      29      45 ..      67      83 ..      52      87 .. 0.75
   3 ?    5.8   0.2     0.007        13      35      65 ..     126     156 ..     111     162 .. 0.82
   4 ?    3.0   0.1     0.055        98      20      53 ..     637     670 ..     630     678 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.3
                        HetR_C 41 pekleqaleeldei 54
                                  + +++  +++lde+
  gi|15668518|ref|NP_247316.1| 39 ESNINAVIKQLDEL 52
                                  34567777777775 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3
                        HetR_C 29 kvlrvleeldippekle 45
                                   ++r lee++  + k++
  gi|15668518|ref|NP_247316.1| 67 MIIRELEEIEADASKMN 83
                                  46788998888777776 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.007
                        HetR_C  35 eeldippekleqaleeldeiirewadkyhqe 65 
                                    e      k+e   +e d++ +ew++kyh +
  gi|15668518|ref|NP_247316.1| 126 SEKQTIRAKVEVDRTEWDKLKKEWSEKYHIN 156
                                   555566778999999**************75 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.055
                        HetR_C  20 mrdwaerkpkvlrvleeldippekleqaleelde 53 
                                     dw+  ++    ++eel + +++  qa e+l +
  gi|15668518|ref|NP_247316.1| 637 TGDWSVVQNTLQEAFEELGMKEDEARQAAENLAQ 670
                                   5699999999999****************99965 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  13.9     0.018        33      18     124 ..      15     137 ..       2     142 .. 0.73
   2 ?   -1.6   0.0         2   3.5e+03      64     106 ..     255     297 ..     248     304 .. 0.82
   3 ?   -2.8   0.1       4.7   8.5e+03      52      61 ..     348     357 ..     325     389 .. 0.63
   4 ?    4.4   0.2     0.028        51      50      84 ..     645     679 ..     639     703 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.018
                        APG6_N  18 leqaekerdaYeeflkklkkekkeeek......qdeeleeleee..........leklekeeeelleeLkelekereelea 82 
                                   l+  +k+ ++ ++ l+k+k++ + e++      q +el++ + e          +++le+ e+++ +   + +   ++l++
  gi|15668518|ref|NP_247316.1|  15 LNLDDKDVRKNLKSLEKIKSKLEIESNinavikQLDELKNVKSEvefksninmiIRELEEIEADASKMNINFDYDLSKLKS 95 
                                   555555555555555555555444444555566555555555557777777777999999999999999999999999999 PP

                        APG6_N  83 elaaleeelealeeeeerfwreynelqlelleleeeldslea 124
                                   el++l++++ +++ + ++ +++ n+ + el+e++  ++++e+
  gi|15668518|ref|NP_247316.1|  96 ELEQLKNTKIDIKTNTDQILKQINKIKSELSEKQTIRAKVEV 137
                                   9999999999999******************99999998886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                        APG6_N  64 eelleeLkelekereeleaelaaleeelealeeeeerfwreyn 106
                                   +++++ L ++ k +ee+ + ++a   e ++ + e ++ +re++
  gi|15668518|ref|NP_247316.1| 255 ARMISALTAMGKSNEEIMKMVNAEVLEMKQGHTEVAEAIREFS 297
                                   6777888888888999999888888888888888888888875 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.7
                        APG6_N  52 leeeleklek 61 
                                   + +e++k+++
  gi|15668518|ref|NP_247316.1| 348 ALREIQKTKD 357
                                   2222222222 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.028
                        APG6_N  50 eeleeeleklekeeeelleeLkelekereeleael 84 
                                   + l+e +e+l  +e+e+ +  ++l ++ ++l +++
  gi|15668518|ref|NP_247316.1| 645 NTLQEAFEELGMKEDEARQAAENLAQQWQQLPQQI 679
                                   45666677777777777777777777777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (849 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2461  (0.137264); expected 358.6 (0.02)
Passed bias filter:                      855  (0.0476881); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.93u 0.25s 00:00:01.18 Elapsed: 00:00:00.47
# Mc/sec: 5482.38
//
Query:       gi|15668519|ref|NP_247317.1|  [L=180]
Description: hypothetical protein MJ_0344 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
        0.4   11.1   7.4        7.7    6.9   3.0    2.3  2  Lipoprotein_17  Lipoprotein associated domain


Domain annotation for each model (and alignments):
>> Lipoprotein_17  Lipoprotein associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0007        13      58      82 ..      83     104 ..      73     106 .. 0.83
   2 ?    6.9   3.0   0.00043       7.7      35      79 ..     114     160 ..     105     165 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0007
                                   TEEEEEEEETTT--EEEEEEEEE-S CS
                Lipoprotein_17  58 GtLkvkvtlsknnksetktititGF 82 
                                   G+L+vkv +++++   tkt++i  F
  gi|15668519|ref|NP_247317.1|  83 GSLTVKVAATLDS---TKTYKIIAF 104
                                   9**********99...677776555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00043
                                   -S..-TTTEEEEE......EEE-THHHHHTEEEEEEEETTT--EEEEEEEE CS
                Lipoprotein_17  35 tfpntkngvsfsi......kivssanDeeGtLkvkvtlsknnksetktiti 79 
                                   t++++++g   +i       +v ++nD+eGt ++++++  ++ se  tit+
  gi|15668519|ref|NP_247317.1| 114 TSIQSQSGTVTEIapgfgiFKV-IYNDTEGTDTLTINYDDGT-SE--TITV 160
                                   4455555555555555542233.39***********986666.33..3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1151.04
//
Query:       gi|15668520|ref|NP_247318.1|  [L=317]
Description: hypothetical protein MJ_0345 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2027.47
//
Query:       gi|15668521|ref|NP_247319.1|  [L=101]
Description: hypothetical protein MJ_0346 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 690.78
//
Query:       gi|15668522|ref|NP_247320.1|  [L=151]
Description: hypothetical protein MJ_0347 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.012   14.2   0.0      0.016   13.8   0.0    1.1  1  Terminase_1  Phage Terminase
      0.021   15.0   0.1      0.048   13.8   0.1    1.7  1  H_lectin     H-type lectin domain


Domain annotation for each model (and alignments):
>> Terminase_1  Phage Terminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.8e-06     0.016     109     154 ..      27      73 ..       7      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-06
                   Terminase_1 109 kplssneDavDGkdps.lvilDElaafkddelletikeglikrknpl 154
                                   +  + n D +DGkd s ++ +D ++ +k+d+ ++++ +gli +  ++
  gi|15668522|ref|NP_247320.1|  27 ANQAGNADKLDGKDASdFLSIDSFKDLKEDNGYIKFPTGLIMQWGKV 73 
                                   456789*******9754************************976555 PP

>> H_lectin  H-type lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.4e-06     0.048       3      67 .]      85     149 ..      83     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.4e-06
                                   EEE-SS--.SS--EEEEEEEEEEEBTT.EEEEEEEEES--SSEEEEEEEE-TT-EEEEEEEEEEEE CS
                      H_lectin   3 tvtFskpF.ssiPkVflslnkidmdkgqnlrvsvqatnitttgFtikfvtwgdtklyslrvsWlAf 67 
                                   +v+F  +F ++  +Vf s+ + +   +  +++ +++ nitt+g+ + ++   +    ++++ W+A+
  gi|15668522|ref|NP_247320.1|  85 PVNFTIEFpNKCLNVFASIYEGSGVDNDYIKCITRIANITTKGCVVCITDI-SGASGDVGFFWFAI 149
                                   79999999999999*****99997666789*****************9999.55777899999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 942.44
//
Query:       gi|15668523|ref|NP_247321.1|  [L=183]
Description: hypothetical protein MJ_0347.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 1177.16
//
Query:       gi|15668524|ref|NP_247322.1|  [L=795]
Description: hypothetical protein MJ_0348 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 5116.43
//
Query:       gi|15668525|ref|NP_247323.1|  [L=105]
Description: hypothetical protein MJ_0349 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0059   16.6   0.1     0.0072   16.3   0.1    1.1  1  DUF999           Protein of unknown function (DUF999)
  ------ inclusion threshold ------
      0.015   14.9   0.4      0.018   14.7   0.4    1.1  1  Vac14_Fig4_bd    Vacuolar protein 14 C-terminal Fig4p binding
      0.018   15.9   0.2      0.023   15.5   0.2    1.1  1  DUF469           Protein with unknown function (DUF469)
      0.044   13.6   1.7      0.059   13.2   1.7    1.2  1  FACT-Spt16_Nlob  FACT complex subunit SPT16 N-terminal lobe d
       0.48   10.7   3.6       0.67   10.2   3.6    1.3  1  MecA_N           NTF2-like N-terminal transpeptidase domain


Domain annotation for each model (and alignments):
>> DUF999  Protein of unknown function (DUF999)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     2e-06    0.0072      30     101 ..      19      87 ..       7      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2e-06
                        DUF999  30 rqsrqslftniikpqk.dklniktnkikeflndlftefskfhnsyypdgristrsklrwvlliiwsiiivlai 101
                                    +  ++l+  ii   k +kl +kt+    + ++l  e++   +  y dg+i   +k     lii ++ii++ai
  gi|15668525|ref|NP_247323.1|  19 EKEAEELYNAIIEIVKeEKLAVKTE----LKDELRGELATKEDIKYLDGKIEMVKKELEYKLIIHTLIILFAI 87 
                                   4556778888888655269999996....5678888888899**********99888888899********98 PP

>> Vac14_Fig4_bd  Vacuolar protein 14 C-terminal Fig4p binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   5.1e-06     0.018       9      93 ..      10      97 ..       5     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.1e-06
                 Vac14_Fig4_bd  9 sliirkLcvllnaekvykelaeiLekeedlefasamvqtLnliLltsselaelRkkLkslkee....eaaelFatLfkswchn 87
                                  +li++k+    +ae++y+++ ei+ kee+l+  + + + L   L t+++++ l  k++ +k+e       ++   Lf   + n
  gi|15668525|ref|NP_247323.1| 10 ELILKKVKDEKEAEELYNAIIEIV-KEEKLAVKTELKDELRGELATKEDIKYLDGKIEMVKKEleykLIIHTLIILFAIIITN 91
                                  79**********************.7999***************************988888844434556667788888888 PP

                 Vac14_Fig4_bd 88 pvatls 93
                                  p a   
  gi|15668525|ref|NP_247323.1| 92 PNAIEL 97
                                  877654 PP

>> DUF469  Protein with unknown function (DUF469)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.2   6.5e-06     0.023      23      85 ..      13      75 ..       7      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.5e-06
                        DUF469 23 lkedlseeeidalvdafievieanglafggsgkeeleglvclaklgsvteedreaveawlkar 85
                                  lk+  +e+e ++l +a+ie++++++la++ + k+el+g +++++  +  + + e v++ l+ +
  gi|15668525|ref|NP_247323.1| 13 LKKVKDEKEAEELYNAIIEIVKEEKLAVKTELKDELRGELATKEDIKYLDGKIEMVKKELEYK 75
                                  556678999**********************999********999999999999998877766 PP

>> FACT-Spt16_Nlob  FACT complex subunit SPT16 N-terminal lobe domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.7   1.6e-05     0.059      99     142 ..      12      55 ..       7      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                                   EEEE-S-HHHHHHHHHHHHHHHHTTTSEEEE-TT----SHHHHH CS
               FACT-Spt16_Nlob  99 llvreKdadenkknfeklieaikeagkkvGvlaKdkseGkfvee 142
                                   +l++ Kd++e +++++++ie++ke++  v +  Kd+ +G+++++
  gi|15668525|ref|NP_247323.1|  12 ILKKVKDEKEAEELYNAIIEIVKEEKLAVKTELKDELRGELATK 55 
                                   56889***********************************9876 PP

>> MecA_N  NTF2-like N-terminal transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.6   0.00019      0.67      18      84 ..       5      65 ..       2      80 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00019
                                  HHHHHCTB--BSSBSS-HHHHHHHHHHHCCCTT-EEEEEEEEEEEEEETTEEEEEEEEEEEETTEEE CS
                        MecA_N 18 ykkaasllseqskkeisekeavekyqaiydglqvkklkieakkvkkdkentaeipykvsmntpagki 84
                                  y+k+++l  +++    +ekea+e y+ai + ++ +kl +   k + ++e   e++ k  ++   gki
  gi|15668525|ref|NP_247323.1|  5 YAKLYELILKKV---KDEKEAEELYNAIIEIVKEEKLAV---KTELKDELRGELATKEDIKYLDGKI 65
                                  667777777777...789*********************...5555566666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1374  (0.0766356); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 744.54
//
Query:       gi|15668526|ref|NP_247324.1|  [L=88]
Description: hypothetical protein MJ_0350 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0011   19.0   1.1     0.0013   18.7   1.1    1.2  1  SIKE      SIKE family
  ------ inclusion threshold ------
      0.025   14.6   3.5      0.036   14.1   0.3    2.2  2  bZIP_2    Basic region leucine zipper
      0.043   13.1   0.2      0.047   13.0   0.2    1.0  1  CorA      CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> SIKE  SIKE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.1   2.1e-07    0.0013      74     139 ..      18      81 ..       6      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.1e-07
                          SIKE  74 qireLqqENreLrasleehqsaLelImsKYReqvskllkakkeekkeavlkkklseevesqeekie 139
                                   +i+ L++EN +Lr+ + +++++L lI  K  + +++llk + e+  ++++   ++e++++++ek+e
  gi|15668526|ref|NP_247324.1|  18 KINHLKRENLKLRNKIADYKRTLYLIRGKGCKLTEELLKIEIENCIKMIKF--NEETIRDLKEKVE 81 
                                   699************************************999988888887..8999999999986 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   6.1e-06     0.036      24      53 ..       9      38 ..       2      39 .. 0.87
   2 ?    1.5   0.2     0.053   3.2e+02      34      51 ..      66      83 ..      53      86 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-06
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_2 24 kakeeeleervkeLeeeNaqLrqkveqLek 53
                                  + + +el  ++++L++eN +Lr+k++ +++
  gi|15668526|ref|NP_247324.1|  9 RTERIELIIKINHLKRENLKLRNKIADYKR 38
                                  667889999****************99875 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.053
                                  HHHHHHHHHHHHHHHHHH CS
                        bZIP_2 34 vkeLeeeNaqLrqkveqL 51
                                  +k+ ee +  L++kve+ 
  gi|15668526|ref|NP_247324.1| 66 IKFNEETIRDLKEKVEMI 83
                                  566677777777777775 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   7.8e-06     0.047     145     224 ..      11      82 ..       6      88 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.8e-06
                          CorA 145 tkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtyss 224
                                   ++ e++ ++  l+r+  klr  +a+ +++l  l++ + + +l++e       l +e+e+ ++m+++  e ++ l++    
  gi|15668526|ref|NP_247324.1|  11 ERIELIIKINHLKRENLKLRNKIADYKRTL-YLIR-GKGCKLTEEL------LKIEIENCIKMIKFNEETIRDLKEKVEM 82 
                                   5668889999********************.9**9.8888888887......999******************9997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 730.03
//
Query:       gi|15668527|ref|NP_247325.1|  [L=150]
Description: hypothetical protein MJ_0351 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.065   11.8   0.0      0.096   11.3   0.0    1.2  1  Ufd2P_core  Ubiquitin elongating factor core


Domain annotation for each model (and alignments):
>> Ufd2P_core  Ubiquitin elongating factor core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.4e-06     0.096     560     608 ..      48     104 ..      43     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.4e-06
                                   HHHHHHHHHHHHHHCTT-........HHHHHHHHH-TTT--HHHHHHHHHHHTTSTS CS
                    Ufd2P_core 560 PkelLssiveiYlnLske........eeFvkavakDgRsYkkelFekavrilkregl 608
                                    ++lL + +++Y+n s+          eF+   a++g  Y+++l++ a  ilk  g+
  gi|15668527|ref|NP_247325.1|  48 LRRLLVNRCQCYINDSETtksktkiiAEFCMDAAENGVRYSPDLVNAALTILKSMGY 104
                                   68899999******988899999*****************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 973.12
//
Query:       gi|15668528|ref|NP_247326.1|  [L=239]
Description: hypothetical protein MJ_0352 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.034   14.5   0.2      0.079   13.3   0.2    1.7  1  NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N


Domain annotation for each model (and alignments):
>> NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   4.4e-06     0.079      60     117 ..      30      87 ..       4      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-06
                    NAPRTase_N  60 eieyLkrklpyfkedfleyLrtfrfkpsevaveeeevvfpgepeirveGpwieaillE 117
                                   ei+   +++   + +f+++L+t+++k++  +++eee+++++  +i+v++    + +lE
  gi|15668528|ref|NP_247326.1|  30 EIRKEHNNWIDESAAFVKWLETLELKDEFKKLREEERMNKNGNSIEVKASNNAMVVLE 87 
                                   333333444448999**************************999*9999877776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1610  (0.0897987); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1490.42
//
Query:       gi|15668529|ref|NP_247327.1|  [L=84]
Description: hypothetical protein MJ_0353 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 597.08
//
Query:       gi|15668530|ref|NP_247328.1|  [L=58]
Description: hypothetical protein MJ_0354 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   13.0   0.0       0.12   13.0   0.0    1.1  1  ArdA      Antirestriction protein (ArdA)


Domain annotation for each model (and alignments):
>> ArdA  Antirestriction protein (ArdA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.6e-06      0.12       6      33 ..      14      40 ..      12      58 .] 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.6e-06
                          ArdA  6 lakYnnGelhGeWldlpadaeelqealk 33
                                  +++YnnG  +G+ l+l+ +++ +++ l+
  gi|15668530|ref|NP_247328.1| 14 WSDYNNGDTVGAILKLEEAEDLIRK-LR 40
                                  899**************87776664.43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 394.78
//
Query:       gi|15668531|ref|NP_247329.1|  [L=109]
Description: hypothetical protein MJ_0355 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 787.44
//
Query:       gi|15668532|ref|NP_247330.1|  [L=97]
Description: hypothetical protein MJ_0356 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.096   12.8   0.2       0.15   12.2   0.2    1.3  1  bPH_4     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_4  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   8.3e-06      0.15       9      37 ..      13      41 ..      10      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-06
                         bPH_4  9 vLliksGfirkkIpiedIkkirktkspls 37
                                   L++k G  +k+I++e+Ik+i++ +s+++
  gi|15668532|ref|NP_247330.1| 13 FLVVKKGSETKRINVEEIKEISNVGSFVI 41
                                  59999**999**************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 718.99
//
Query:       gi|15668533|ref|NP_247331.1|  [L=155]
Description: hypothetical protein MJ_0357 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-14   52.7   0.6    4.9e-14   52.4   0.6    1.1  1  SecB           Preprotein translocase subunit SecB
  ------ inclusion threshold ------
       0.98    9.3  10.9      0.051   13.4   4.5    2.0  2  Orthopox_B11R  Orthopoxvirus B11R protein


Domain annotation for each model (and alignments):
>> SecB  Preprotein translocase subunit SecB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.6   5.4e-18   4.9e-14      35     136 ..      34     136 ..       4     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 5.4e-18
                          SecB  35 qPevkvnlnveakkleeevyevvlkitvtakae.ektlFlvevkyaGiftienipeeqlepllliecPrilFPyaReivsd 114
                                   + +v+++ +++ +k e +++  ++kit+  k++  k    + v+  G f++ +   ++++++  i+  +ilFPy+R+++s+
  gi|15668533|ref|NP_247331.1|  34 RLNVNIDTEIRYNKNEPNKFITIIKITAGEKKDfAKSPVYLSVEVWGFFEVIEEAIDKVRQFAEINSVAILFPYVRALIST 114
                                   2345555566667777889999999999998854444445679999*********************************** PP

                          SecB 115 lvreggfppllLepinFealyq 136
                                   ++ ++++pp++L pin++ + +
  gi|15668533|ref|NP_247331.1| 115 ITANANIPPVILPPINVAGMMA 136
                                   *****************99866 PP

>> Orthopox_B11R  Orthopoxvirus B11R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   4.5   5.7e-06     0.051       4      43 ..      16      55 ..      14      67 .. 0.91
   2 ?   -1.2   0.4      0.21   1.9e+03       6      24 ..     130     148 ..     129     154 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-06
                 Orthopox_B11R  4 vtnvediineidrekeeilknveiennkninknhpsGyir 43
                                  v  +e i+ne+  + e+i  nv+i+ +   nkn p  +i 
  gi|15668533|ref|NP_247331.1| 16 VKHIEFILNEVPEKDEKIRLNVNIDTEIRYNKNEPNKFIT 55
                                  667999*****************************99985 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.21
                 Orthopox_B11R   6 nvediineidrekeeilkn 24 
                                   nv  ++ +i+  kee    
  gi|15668533|ref|NP_247331.1| 130 NVAGMMANIEEVKEENTEK 148
                                   5555666666666665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1007.72
//
Query:       gi|15668534|ref|NP_247332.1|  [L=128]
Description: hypothetical protein MJ_0358 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 939.85
//
Query:       gi|15668535|ref|NP_247333.1|  [L=214]
Description: hypothetical protein MJ_0359 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0012   19.5   0.6      0.018   15.7   0.0    2.3  2  Tox-ART-HYD1  HYD1 signature containing ADP-ribosyltransferas
     0.0043   17.1   0.1      0.012   15.7   0.1    1.7  1  DUF3847       Protein of unknown function (DUF3847)
  ------ inclusion threshold ------
      0.033   13.8   0.2       0.11   12.0   0.0    1.9  2  PARP          Poly(ADP-ribose) polymerase catalytic domain
      0.068   12.9   1.0       0.15   11.7   0.2    1.9  2  DUF3990       Protein of unknown function (DUF3990)


Domain annotation for each model (and alignments):
>> Tox-ART-HYD1  HYD1 signature containing ADP-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     4e-06     0.018       1      37 [.       9      44 ..       9      67 .. 0.93
   2 ?    2.0   0.1     0.077   3.5e+02      23      71 ..     130     178 ..     117     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4e-06
                  Tox-ART-HYD1  1 lyHYTnekgvnaIldskvlklkarnrkdrfgqgqylt 37
                                  lyH T+ k +++I++sk++  ++++ +   g+g y+ 
  gi|15668535|ref|NP_247333.1|  9 LYHGTDRKSAEKIMESKEIL-PSQGDNHWLGDGIYFY 44
                                  8******************8.**************96 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.077
                  Tox-ART-HYD1  23 arnrkdrfgqgqyltdiapgkktkgqlrdavsqlpiarkrlthfieidv 71 
                                     + + rf+  + l  i   k+ k+++r++  + ++  +rlt + ei+v
  gi|15668535|ref|NP_247333.1| 130 ELGYNKRFDIVRALFPIPVKKYQKIENREKNKKYKERTHRLTFMPEIQV 178
                                   5556667777777777777777899999999999988888888777765 PP

>> DUF3847  Protein of unknown function (DUF3847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.8e-06     0.012      22      70 ..     150     197 ..     148     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.8e-06
                       DUF3847  22 kekiLenrlkyleRkeRtHrLitrGaalEsilpeakeLteeevyellek 70 
                                   k + +enr k+ + keRtHrL  +  +++  ++++  + + e y+l + 
  gi|15668535|ref|NP_247333.1| 150 KYQKIENREKNKKYKERTHRLTFM-PEIQVCVKNPSVIKKLEWYDLEKT 197
                                   66889****************766.689999999999999999988766 PP

>> PARP  Poly(ADP-ribose) polymerase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.5e-05      0.11      49     110 ..       6      64 ..       3      99 .. 0.80
   2 ?   -0.9   0.1      0.24   1.1e+03      23      44 ..     146     167 ..     126     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                                   EEEEEEEE-GGGHHHHHHH-S--S-TTS-GGGSTTSSSEEEBSSHHHHHGGG--BSSS-EEE CS
                          PARP  49 rrlLfHGsrltnvasilsqGLriappeapvtGymfGkGiYfAddaskSanYcktsekkgsgl 110
                                   r+ L+HG+  ++ ++i+++   i p+  +     +G GiYf ++   + ++ + +ek++++l
  gi|15668535|ref|NP_247333.1|   6 RMTLYHGTDRKSAEKIMESKE-ILPSQGDN--HWLGDGIYFYEEEFHAFKWIWYKEKNRNRL 64 
                                   789*************98764.43444444..57********99999999999988888877 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.24
                                   EEEEEEEEEEETTHHHHCGCCG CS
                          PARP  23 lkileifrvqregeaerfqekk 44 
                                   + +++ +++++ +++++++e+ 
  gi|15668535|ref|NP_247333.1| 146 IPVKKYQKIENREKNKKYKERT 167
                                   5677778888888888887754 PP

>> DUF3990  Protein of unknown function (DUF3990)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   3.4e-05      0.15       1      53 [.       7      63 ..       7      93 .. 0.69
   2 ?   -1.1   0.0       0.3   1.3e+03     135     151 ..     174     190 ..     148     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                       DUF3990  1 miLYHGsk.....eevekpdls.ksrkkkDFGkGFYlteskeqAkewakrkskrkgkke 53
                                  m+LYHG++     +++e+ ++   + +++  G G+Y  e++ +A +w+  k+k+++   
  gi|15668535|ref|NP_247333.1|  7 MTLYHGTDrksaeKIMESKEILpSQGDNHWLGDGIYFYEEEFHAFKWIWYKEKNRN--R 63
                                  99*****977766555555554144566677*****************88874333..2 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.3
                       DUF3990 135 lgkQyvfktekalkkLk 151
                                   ++ Q+++k+ +++kkL+
  gi|15668535|ref|NP_247333.1| 174 PEIQVCVKNPSVIKKLE 190
                                   57899999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1357.62
//
Query:       gi|15668536|ref|NP_247334.1|  [L=135]
Description: hypothetical protein MJ_0360 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.045   13.5   1.5      0.071   12.8   1.5    1.3  1  DUF3481   C-terminal domain of neuropilin glycoprotein
      0.074   13.2   0.0       0.13   12.5   0.0    1.5  1  DUF3426   Protein of unknown function (DUF3426)


Domain annotation for each model (and alignments):
>> DUF3481  C-terminal domain of neuropilin glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.5   7.9e-06     0.071      23      54 ..       1      35 [.       1      40 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.9e-06
                       DUF3481 23 msalGvll...GaicGvvlycacsqaslsdrnlsa 54
                                  m  lGv+l     +cGvv  c c+ ++ +d ++s+
  gi|15668536|ref|NP_247334.1|  1 MKRLGVFLilaSIVCGVVAICGCTGGGGTDYSSST 35
                                  66789887444579************999999886 PP

>> DUF3426  Protein of unknown function (DUF3426)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.4e-05      0.13      57      99 ..      50      91 ..      40     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                       DUF3426 57 sslrekageanlvlegtlrNradkpqalpaleltLtDaqgqvv 99
                                  + l +k+    + +eg+++N  +k  +++++++ ++Da+g ++
  gi|15668536|ref|NP_247334.1| 50 HHLVRKDYGT-VYVEGVAQNVGNKRLKFVEIKARFYDADGVLI 91
                                  4444444444.799*************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 848.27
//
Query:       gi|15668537|ref|NP_247335.1|  [L=107]
Description: hypothetical protein MJ_0361 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-06   27.5   0.0    1.7e-05   24.7   0.0    2.1  1  PadR         Transcriptional regulator PadR-like family
    5.5e-06   26.3   0.0    1.1e-05   25.3   0.0    1.6  1  HTH_45       Winged helix-turn-helix
      1e-05   25.3   0.0    1.2e-05   25.0   0.0    1.1  1  HxlR         HxlR-like helix-turn-helix
    0.00024   20.9   1.1    0.00037   20.3   0.1    1.9  3  HTH_5        Bacterial regulatory protein, arsR family
    0.00031   20.5   0.0    0.00046   20.0   0.0    1.3  1  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0024   17.7   0.2     0.0029   17.4   0.2    1.2  1  TFIIE_alpha  TFIIE alpha subunit
     0.0028   18.0   0.0     0.0049   17.2   0.0    1.5  1  Rrf2         Transcriptional regulator
     0.0046   17.2   0.0     0.0055   16.9   0.0    1.2  1  CsgF         Type VIII secretion system (T8SS), CsgF protein
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.025   14.5   0.0    1.5  2  MarR         MarR family
      0.024   13.6   0.1      0.024   13.6   0.1    1.0  1  mTERF        mTERF
      0.037   13.8   0.0      0.059   13.1   0.0    1.4  1  DUF4364      Domain of unknown function (DUF4364)
      0.038   13.8   0.1       0.15   11.9   0.0    1.8  2  DUF1495      Winged helix DNA-binding domain (DUF1495)
      0.042   13.7   0.0        3.6    7.5   0.0    2.6  2  HTH_IclR     IclR helix-turn-helix domain
      0.064   13.4   0.0        0.1   12.8   0.0    1.3  1  HTH_34       Winged helix DNA-binding domain
       0.11   13.1   0.1       0.16   12.5   0.1    1.3  1  PCI          PCI domain


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.4e-08   1.7e-05       2      74 ..      15      79 ..      14      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.4e-08
                                  HHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                          PadR  2 LalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                  L+ll+ +++y  e+ k l+ +        +  l  +L++L +eg+ve+++ es  +  + yY +T++G+r+l+
  gi|15668537|ref|NP_247335.1| 15 LKLLNSKDMYFSELQKTLNLH--------PKILDSILSDLVNEGFVEKREGESPYKFGKVYYSITPRGKRALE 79
                                  666666666666666666666........2235579**********************************996 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   9.4e-09   1.1e-05       9      73 ..      12      85 ..       8      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 9.4e-09
                        HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdmLvekgli.........kkskekYvlTekGlelleklkele 73
                                   d+L+ +++++   +++ +  nL  k+l++ L+ Lv++g++         k  k  Y++T +G++ le l+ +e
  gi|15668537|ref|NP_247335.1| 12 KDVLKLLNSKDMYFSELQKTLNLHPKILDSILSDLVNEGFVekregespyKFGKVYYSITPRGKRALEILDLIE 85
                                  699**************************************99999999888999********99988876655 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0     1e-08   1.2e-05       4      81 ..       8      86 ..       5      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1e-08
                                  STTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE..ESSSS-EEEEEE-TCGGGGHHHHHHHHH CS
                          HxlR  4 gkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierev..ypevPpkveYsltekGrslepvlqelkk 81
                                  +k    +l  l ++ + fsel+++l ++  k+L + L  L ++g++e+++   p    kv Ys+t++G+   ++l+ ++ 
  gi|15668537|ref|NP_247335.1|  8 KKHVKDVLKLLNSKDMYFSELQKTL-NLHPKILDSILSDLVNEGFVEKREgeSPYKFGKVYYSITPRGKRALEILDLIET 86
                                  566666788888899**********.9*******************9875114556679***********9999987765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.6   3.1e+03       7      13 ..       2       8 ..       1      12 [. 0.79
   2 !   20.3   0.1   3.1e-07   0.00037       6      47 .]      13      54 ..       8      54 .. 0.96
   3 ?   -3.1   0.0       6.1   7.3e+03       5      10 ..      78      83 ..      76      86 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.6
                                  HHHHHTT CS
                         HTH_5  7 ILklLae 13
                                  ILk+La+
  gi|15668537|ref|NP_247335.1|  2 ILKILAK 8 
                                  8999987 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 3.1e-07
                                  HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  ++LklL+++ ++++el + l+l + +++  L+ L ++G+Vek
  gi|15668537|ref|NP_247335.1| 13 DVLKLLNSKDMYFSELQKTLNLHPKILDSILSDLVNEGFVEK 54
                                  68**************************************97 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 6.1
                                  HHHHHH CS
                         HTH_5  5 lkILkl 10
                                  l+IL l
  gi|15668537|ref|NP_247335.1| 78 LEILDL 83
                                  566665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.8e-07   0.00046      15      62 ..      15      63 ..       8      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.8e-07
                                  HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEE CS
                          TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklY 62
                                  l+Ll+++ +  +e+ + l++      ++L+ L++ G+Ve+++g+ p+++
  gi|15668537|ref|NP_247335.1| 15 LKLLNSKDMYFSELQKTLNLHPKILDSILSDLVNEGFVEKREGEsPYKF 63
                                  6899**************************************8886555 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   2.4e-06    0.0029      13      79 ..       9      73 ..       1      92 [. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.4e-06
                                  HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECC CS
                   TFIIE_alpha 13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinye 79
                                  ++++ vl+ L +k  +   +l+k l++ +++l ++L +L ++++v+ kr+ +   +  k+y+ i+++
  gi|15668537|ref|NP_247335.1|  9 KHVKDVLKLLNSK-DMYFSELQKTLNLHPKILDSILSDLVNEGFVE-KREGESPYKFGKVYYSITPR 73
                                  4566788877755.455578*************************8.677888899999***99975 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.1e-06    0.0049      26      61 ..      23      58 ..       9      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.1e-06
                                  B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                          Rrf2 26 vsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                  +  +e+ +  n++p++l  il+ L ++g+v+ ++G 
  gi|15668537|ref|NP_247335.1| 23 MYFSELQKTLNLHPKILDSILSDLVNEGFVEKREGE 58
                                  77899*****************************97 PP

>> CsgF  Type VIII secretion system (T8SS), CsgF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.6e-06    0.0055      69     120 ..      32      82 ..       6      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.6e-06
                                   HHHHHHHHHHTTTTT.......S---S--EE-SSEEEEEEEETTEEEEEEEE CS
                          CsgF  69 dsLnrqllsrlssklvqqqFgenalkegtytfgsyqieitnsgsgvsititd 120
                                    +L  ++l ++ s lv++ F e    e+ y+fg+++ +it++g+   ++i+d
  gi|15668537|ref|NP_247335.1|  32 LNLHPKILDSILSDLVNEGFVEKREGESPYKFGKVYYSITPRGKRA-LEILD 82 
                                   467889***********************************99863.55555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.1e-05     0.025      11      51 ..      16      56 ..      12      59 .. 0.91
   2 ?   -2.7   0.0         5   5.9e+03       7      19 ..      79      91 ..      76      99 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                                  HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                  +l ++ +++ seL+k l++++  +  +l  L+ +G++e++ 
  gi|15668537|ref|NP_247335.1| 16 KLLNSKDMYFSELQKTLNLHPKILDSILSDLVNEGFVEKRE 56
                                  5778999*******************************986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5
                                  HHHHHHHHSTTEE CS
                          MarR  7 viLrilyeqgpls 19
                                  +iL ++++ + l+
  gi|15668537|ref|NP_247335.1| 79 EILDLIETFDTLR 91
                                  6777777766665 PP

>> mTERF  mTERF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     2e-05     0.024      24     115 ..       2      90 ..       1     100 [. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                         mTERF  24 vlladvekelapklkaLkslgasssdlteilskyPkiLskkleeslsksvdflkeikvdkssigellrslplilgskvenk 104
                                   +l   ++k+++ +lk+L+s+++  s+l ++l+  PkiL+  l++ +++   f+++ + ++  +  ++  ++ + + k   +
  gi|15668537|ref|NP_247335.1|   2 ILKILAKKHVKDVLKLLNSKDMYFSELQKTLNLHPKILDSILSDLVNE--GFVEKREGESPYKFGKV-YYSITPRGKRALE 79 
                                   667778999*****************************9655544433..36666644444444444.3555555555555 PP

                         mTERF 105 iknlvevLrel 115
                                   i  l+e ++ l
  gi|15668537|ref|NP_247335.1|  80 ILDLIETFDTL 90 
                                   55556666655 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     5e-05     0.059      38      73 ..      41      81 ..      38     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5e-05
                       DUF4364 38 qalseLvesglieeeek.....enktlykiTekGketlelf 73
                                  ++ls+Lv++g++e++e       +k +y+iT++Gk++le++
  gi|15668537|ref|NP_247335.1| 41 SILSDLVNEGFVEKREGespykFGKVYYSITPRGKRALEIL 81
                                  789**********9854234445789************987 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.85     1e+03      14      39 ..      11      36 ..       2      40 .. 0.66
   2 ?   11.9   0.0   0.00013      0.15      58      89 ..      45      80 ..      39      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.85
                       DUF1495 14 vllyLysiypeksnlqeisrrvrskp 39
                                  v   L+   ++  + +e+ +  + +p
  gi|15668537|ref|NP_247335.1| 11 VKDVLKLLNSKDMYFSELQKTLNLHP 36
                                  44444444577788888888887766 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00013
                       DUF1495 58 sLielGLveeeeeseglk....lYklteeGieivev 89
                                   L++ G ve++e+++ +k    +Y++t++G++  e+
  gi|15668537|ref|NP_247335.1| 45 DLVNEGFVEKREGESPYKfgkvYYSITPRGKRALEI 80
                                  59*******99998887777779********98876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.003       3.6      19      51 ..      23      55 ..       1      56 [. 0.75
   2 ?    3.9   0.0     0.039        47       4      13 ..      76      85 ..      75      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.003
                                  -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                  + +sel + + l++     +L+ Lv++G+ve+ 
  gi|15668537|ref|NP_247335.1| 23 MYFSELQKTLNLHPKILDSILSDLVNEGFVEKR 55
                                  45777777777777777789**********985 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.039
                                  HHHHHHCT-C CS
                      HTH_IclR  4 RalaiLdala 13
                                  Ral+iLd+++
  gi|15668537|ref|NP_247335.1| 76 RALEILDLIE 85
                                  9*******97 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.6e-05       0.1       7      70 ..      16      79 ..      13      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.6e-05
                        HTH_34  7 syLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefk.gkkprtllriTpeGreafk 70
                                   +L+  + + f+el+++l++    L + l+ L + g++e + + +  k  +  ++iTp G+ a +
  gi|15668537|ref|NP_247335.1| 16 KLLN-SKDMYFSELQKTLNLHPKILDSILSDLVNEGFVEKREGESpYKFGKVYYSITPRGKRALE 79
                                  4444.45689****************************987766515678999********9975 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00013      0.16      57      90 ..      19      52 ..       2      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                  CESEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSS CS
                           PCI 57 iyssislerlaklldlsvdevEkilvklIrdgei 90
                                    +   +++l+k+l+l  + +++il++l+++g++
  gi|15668537|ref|NP_247335.1| 19 NSKDMYFSELQKTLNLHPKILDSILSDLVNEGFV 52
                                  667789**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 827.22
//
Query:       gi|15668538|ref|NP_247336.1|  [L=63]
Description: hypothetical protein MJ_0362 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-24   84.9   0.3    2.6e-24   84.7   0.3    1.1  1  DUF2080   Putative transposon-encoded protein (DUF2080)


Domain annotation for each model (and alignments):
>> DUF2080  Putative transposon-encoded protein (DUF2080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.3   1.5e-28   2.6e-24       1      49 [.       1      49 [.       1      50 [. 0.98

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 1.5e-28
                       DUF2080  1 veIrkktwlkvkeilpffegkVkpfGnSAkvsiPkeylGkkvylvIldd 49
                                  ++Irkktw+++k+++++f+g+Vkp+GnS+++ iPk+y+G+kv+++Ild+
  gi|15668538|ref|NP_247336.1|  1 MKIRKKTWRLPKDATISFKGVVKPIGNSGMILIPKDYVGCKVLVTILDE 49
                                  8**********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 443.78
//
Query:       gi|15668539|ref|NP_247337.1|  [L=759]
Description: cell division control protein 21 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-72  241.4   0.0    8.7e-72  240.8   0.0    1.3  1  MCM              MCM P-loop domain
    3.2e-26   91.5   0.9    7.6e-26   90.4   0.9    1.7  1  MCM_lid          MCM AAA-lid domain
    1.6e-08   34.5   0.0      3e-08   33.5   0.0    1.4  1  MCM_OB           MCM OB domain
    2.2e-06   27.2   0.1     0.0015   17.9   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    5.5e-06   26.4   0.0    1.5e-05   25.0   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00044   20.7   0.0     0.0019   18.7   0.0    2.2  1  AAA              ATPase family associated with various cellul
    0.00097   18.9   0.0     0.0019   17.9   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
     0.0026   18.4   0.0      0.034   14.8   0.0    2.3  2  RPA_C            Replication protein A C terminal
     0.0026   18.2   2.1        1.7    9.1   0.1    3.9  2  AAA_17           AAA domain
     0.0052   16.6   0.0      0.011   15.6   0.0    1.5  1  Dioxygenase_N    Catechol dioxygenase N terminus
  ------ inclusion threshold ------
      0.033   13.9   0.2       0.16   11.7   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.036   13.9   0.0      0.075   12.9   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
      0.067   13.6   0.4        2.1    8.8   0.0    3.1  3  RNA_helicase     RNA helicase
      0.093   12.9   0.0        1.4    9.1   0.0    2.7  2  Mrr_N            Mrr N-terminal domain
       0.11   12.6   0.0       0.53   10.4   0.0    2.3  1  MMR_HSR1         50S ribosome-binding GTPase
       0.13   12.7   0.4         40    4.7   0.0    3.5  3  ABC_tran         ABC transporter


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.8   0.0   7.8e-75   8.7e-72       2     223 ..     340     558 ..     339     559 .. 0.96

  Alignments for each domain:
  == domain 1  score: 240.8 bits;  conditional E-value: 7.8e-75
                                   HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSS CS
                           MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklap 82 
                                   +e i+++ak+k++i+kl+++ +++++g++++k+a+llql+++ ++     + +r++i++l+++dpg++Ks+l++++ + +p
  gi|15668539|ref|NP_247337.1| 340 LELINRIAKDKNVIQKLSDYAFREVTGYDMIKRAVLLQLVSSGTN-----IDMRTSIHILMISDPGVGKSTLMESLIQKFP 415
                                   6789************************************99984.....569**************************** PP

                                   SEEEEESSSSSSSHSSSEEEEESSSSS..EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSS.CEEE CS
                           MCM  83 ravytsgkgssaagLtaavvrdeetge..fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaG.ivat 160
                                       + + +ss+ gL+ +vvr++++    +vl+aG l  ad+Gv+ciDef ++ke   ++l+ +mEqq+i+i+KaG i a+
  gi|15668539|ref|NP_247337.1| 416 FVKKVYAVTSSGPGLVGSVVREKAEFGdsWVLKAGVLTEADGGVVCIDEFSRNKE-VYDYLLGVMEQQKIEINKAGvIDAV 495
                                   **********************9986667************************99.9*******************77899 PP

                                   EE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHH CS
                           MCM 161 LnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivsl 223
                                   L+ar+++laA+np++gr++++ +v+e+inl+++lL+rFDlifv++Dk+d++kDe++a++ +++
  gi|15668539|ref|NP_247337.1| 496 LPARVAILAACNPRFGRFNPDLTVWEQINLPKELLDRFDLIFVIKDKIDKKKDEDIADFSIDN 558
                                   **********************************************************99876 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.9   6.8e-29   7.6e-26       1      86 [.     585     667 ..     585     668 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 6.8e-29
                                   HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHH CS
                       MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeair 81 
                                   ell kY+ yar +i+P +s+ea+++++e+Yv++Rk++e  ++ ++ i++RqL s+iRL+ A+Aklrlsevv++ d+eeair
  gi|15668539|ref|NP_247337.1| 585 ELLLKYVLYAR-QIEPEISDEARKIIKEYYVSVRKMSE--AKGTFGISARQLGSIIRLAVAHAKLRLSEVVKAVDAEEAIR 662
                                   6899*******.***********************995..479************************************** PP

                                   HHHHH CS
                       MCM_lid  82 llkes 86 
                                   l++++
  gi|15668539|ref|NP_247337.1| 663 LVDTC 667
                                   **987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   2.7e-11     3e-08       3      85 ..     175     265 ..     173     299 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.7e-11
                                   GG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE...S----S......B-..TTT-HHH-EEE-GGGSEE CS
                        MCM_OB   3 RdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev...eleePr......kCeekeCeskdpfkletekskf 74 
                                    +l+s+h gklv+ + ++ +a+++k +  k +++c+kcg+t+++      +P+      +C+ + C+  + + ++ + s  
  gi|15668539|ref|NP_247337.1| 175 SELSSAHKGKLVEFRAMILQATKLKLRYAKGFYYCPKCGATKTLdlgFWDKPKevgkslTCPADGCD-CKGLIFDEDLSGK 254
                                   5899************************************9997555344577777777********.799********** PP

                                   EEEEEEEEE-- CS
                        MCM_OB  75 vdfqklklQEs 85 
                                   vdfq++k+Q  
  gi|15668539|ref|NP_247337.1| 255 VDFQEIKVQTP 265
                                   *********64 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0045       5.1      23      49 ..     391     417 ..     361     427 .. 0.78
   2 !   17.9   0.0   1.3e-06    0.0015      92     158 ..     442     508 ..     424     546 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0045
                  Mg_chelatase  23 HnlllvGppGsGKtmlakrlpsllppl 49 
                                    ++l++  pG GK+ l + l + +p +
  gi|15668539|ref|NP_247337.1| 391 IHILMISDPGVGKSTLMESLIQKFPFV 417
                                   589**************9998877765 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.3e-06
                  Mg_chelatase  92 GggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisraka.kvefparfqlvaamNp 158
                                   G +   k G ++ a  Gv+ +DE++  +++v + L   +e+++++i++a   ++  par+ ++aa Np
  gi|15668539|ref|NP_247337.1| 442 GDSWVLKAGVLTEADGGVVCIDEFSR-NKEVYDYLLGVMEQQKIEINKAGViDAVLPARVAILAACNP 508
                                   5555788999*************987.789******************9752789************9 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.3e-08   1.5e-05       1     124 [.     392     510 ..     392     533 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.3e-08
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------....G-SEEEEESGGG- CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar....egeilvlDEvera 77 
                                   ++l++ +pG+gKs+l+e+l + +     +++ t+  +   l+g++    +++++ ds + +a+      g ++++DE+   
  gi|15668539|ref|NP_247337.1| 392 HILMISDPGVGKSTLMESLIQKFPFVKKVYAVTS--SGPGLVGSVV--REKAEFGDSWVLKAGVlteaDGGVVCIDEFS-R 467
                                   6789999****************99999999998..5668999999..68899999999988888889***********.6 PP

                                   -HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                         AAA_5  78 esevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                   ++ev + Ll ++e++++ +++ g    + +      + ++a++np+ 
  gi|15668539|ref|NP_247337.1| 468 NKEVYDYLLGVMEQQKIEINKAGVIDAVLPAR----VAILAACNPRF 510
                                   8*****************99999999888865....99999999975 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.7e-06    0.0019       1     111 [.     393     508 ..     393     539 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                                   EEEESSTTSSHHHHHHHHHHHH....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHHHHHT CS
                           AAA   1 vllyGppGtGKTllakavakel....gvefleisgsellskyvgesekkirelfkeakeka..kpsilfiDEidalaksrs 75 
                                   +l++  pG+GK++l++++++++    +v+ ++ sg+ l+ ++v e+++     + +a      +  ++ iDE+ +      
  gi|15668539|ref|NP_247337.1| 393 ILMISDPGVGKSTLMESLIQKFpfvkKVYAVTSSGPGLVGSVVREKAEFGDSWVLKAGVLTeaDGGVVCIDEFSRN----- 468
                                   578899***************8777779*************9999999999999888666664459******8654..... PP

                                   TCCCHHHHHHHHHHHHHHHHTTTS...........SSTEEEEEEESS CS
                           AAA  76 gseseeeervvnqLlteldgvkkk...........eskvivigatnr 111
                                          ++v + Ll +++++k +            ++v +++a+n 
  gi|15668539|ref|NP_247337.1| 469 -------KEVYDYLLGVMEQQKIEinkagvidavlPARVAILAACNP 508
                                   .......3578888888888888877788888887677777777774 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.7e-06    0.0019      19     142 ..     387     507 ..     369     517 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.7e-06
                                   CTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEEE CS
               Sigma54_activat  19 aktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlfL 99 
                                   ++t++++l+  + G+GK++l +++ ++ +  +k +    +++  + l+ s +   ek  F ++   k+G + +adgG++ +
  gi|15668539|ref|NP_247337.1| 387 MRTSIHILMISDPGVGKSTLMESLIQKFPFVKKVYA---VTSSGPGLVGSVV--REKAEFGDSWVLKAGVLTEADGGVVCI 462
                                   57889***************9999988776666443...3456688999965..899************************ PP

                                   ETGGGS-HHHHHHHHHHHHHSEE..ESBTS.SSEEE--EEEEEEES CS
               Sigma54_activat 100 DeigelplelQekLlrvlqegev..ervGs.skeikvdvriiaatn 142
                                   De ++ + e+   Ll v++++++  ++ G  ++  ++ v i+aa n
  gi|15668539|ref|NP_247337.1| 463 DEFSR-NKEVYDYLLGVMEQQKIeiNKAGViDAVLPARVAILAACN 507
                                   **998.679999******9987511678852456788888888876 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.78   8.7e+02      57      97 ..      13      54 ..       3      58 .. 0.68
   2 !   14.8   0.0     3e-05     0.034      46      99 ..     691     749 ..     671     751 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.78
                                  HHHH.SXSTTTEEHHHHH.HHSTSXHHHHHHHHHHHHHTTSE CS
                         RPA_C 57 likqspeseeGvhvdeia.qklrlsvndvkqavdeLsneGii 97
                                  ++k+ p++++    d +   k  ++ ++v +a  +L++eG+i
  gi|15668539|ref|NP_247337.1| 13 MLKRMPNKQADWDNDLLPtLKAMFNPKSVSNAKSQLISEGVI 54
                                  5555555555555555552333688999************99 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3e-05
                                   XSXHHHHHHHHHHHH..SXSTTTEEHH.HHHHHS...TSXHHHHHHHHHHHHHTTSEEE CS
                         RPA_C  46 gltalaqqvlnlikq.speseeGvhvd.eiaqkl...rlsvndvkqavdeLsneGiiYs 99 
                                   ++ +  + vln+ik+ s  +++G+  + ei ++    +ls+++v+ a+++L   G iYs
  gi|15668539|ref|NP_247337.1| 691 SKRDKVEKVLNIIKEiSNSRDDGLAPEeEIYERAeraGLSEKEVEDAINYLKRVGDIYS 749
                                   56667789********99******9652575433345*********************8 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0015       1.7       4      22 ..     399     417 ..     398     500 .. 0.61
   2 ?    3.5   0.3     0.082        91      17     100 ..     624     703 ..     615     739 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                                   TTSSHHHHHHHHHHHHTEE CS
                        AAA_17   4 PGsGKgtqceklvekygft 22 
                                   PG+GK+t++e l +k+ f 
  gi|15668539|ref|NP_247337.1| 399 PGVGKSTLMESLIQKFPFV 417
                                   9*************99764 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.082
                                   HHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHH CS
                        AAA_17  17 ekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpkevl 97 
                                     +g++  + G+++r  +++ +l +  + ++ ++ ee  +l ++  ++ia + +++ + +d+ + + +    +d+++k vl
  gi|15668539|ref|NP_247337.1| 624 GTFGISARQLGSIIRLAVAHAKL-RLSEVVKAVDAEEAIRLVDTCLKQIAYDPESGSIDIDKIAGTPK--SKRDKVEK-VL 700
                                   5678888899*****88899998.456778889******************99999999999998744..44455554.33 PP

                                   HHH CS
                        AAA_17  98 eel 100
                                   + +
  gi|15668539|ref|NP_247337.1| 701 NII 703
                                   333 PP

>> Dioxygenase_N  Catechol dioxygenase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.6e-06     0.011      17      54 ..     722     759 .]     718     759 .] 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.6e-06
                                   HHHHHTT--HHHHHHHHHHHHHHHH.....TT-HHHHH CS
                 Dioxygenase_N  17 dfirevdlteeEwwaavdfLtrvGqisddkrqEfiLls 54 
                                   + ++   l+e+E + a+++L+rvG i ++k++ ++L+s
  gi|15668539|ref|NP_247337.1| 722 ERAERAGLSEKEVEDAINYLKRVGDIYSPKSGYWQLMS 759
                                   5678889*************************999986 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.3   1.5e+03      72     102 ..     325     355 ..     317     370 .. 0.79
   2 ?   11.7   0.0   0.00014      0.16       7     115 ..     362     486 ..     354     502 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                        RuvB_N  72 agdlaalltnleekdvlfideihrlsravee 102
                                     d+  + +nl+ekd+ +i+ i + +++++ 
  gi|15668539|ref|NP_247337.1| 325 DEDIEEIAKNLNEKDLELINRIAKDKNVIQK 355
                                   4699999*********999999887777665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00014
                        RuvB_N   7 eeyigqekvkek..lkifieaakkreealdhvllyGpPGlGkttlakiiakel....gvklkitsgP.....vleka...g 73 
                                   +e +g + +k    l+++ + ++   ++  h+l++  PG+Gk+tl + + +++    +v   ++sgP     v+ ++   g
  gi|15668539|ref|NP_247337.1| 362 REVTGYDMIKRAvlLQLVSSGTNIDMRTSIHILMISDPGVGKSTLMESLIQKFpfvkKVYAVTSSGPglvgsVVREKaefG 442
                                   566677777765213444445555667788**************9987777652222344556678833332333331223 PP

                        RuvB_N  74 d...l.aalltnleekdvlfideihrlsraveevlysamedfrldi 115
                                   d   l a++lt+  ++ v+ ide  r +++v ++l   me  +++i
  gi|15668539|ref|NP_247337.1| 443 DswvLkAGVLTE-ADGGVVCIDEFSR-NKEVYDYLLGVMEQQKIEI 486
                                   333222445554.4567899999988.6677788888999988887 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.7e-05     0.075       1     112 [.     392     508 ..     392     535 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.7e-05
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke..kefefkkGpvfan...llladeinrapp 76 
                                   h+l+ + PG++k +l+++l +++    k   +t+   P  ++G+ v e++e   ++ +k+G +      ++  de  r + 
  gi|15668539|ref|NP_247337.1| 392 HILMISDPGVGKSTLMESLIQKFPFVKKVYAVTS-SGP-GLVGSVVREKAEfgDSWVLKAGVLTEAdggVVCIDEFSRNK- 469
                                   9*******************99987655555554.445.5899999998888788999999887534459********76. PP

                         AAA_3  77 ktqsalleameerqvtveget...hklpepflvlatqnP 112
                                    +   ll +me++++ ++++      lp    +la+ nP
  gi|15668539|ref|NP_247337.1| 470 EVYDYLLGVMEQQKIEINKAGvidAVLPARVAILAACNP 508
                                   68899**********9998752225799999****9999 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         3   3.3e+03      27      55 ..     263     291 ..     246     296 .. 0.76
   2 ?    8.8   0.0    0.0019       2.1       2      22 ..     394     414 ..     393     430 .. 0.81
   3 ?    0.6   0.0      0.65   7.3e+02      52      88 ..     459     490 ..     455     507 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3
                  RNA_helicase  27 klkkkdsvysrnpeddfwdgYtgqevvvi 55 
                                   +++ ++s+y+++ ++++++ +++++  v+
  gi|15668539|ref|NP_247337.1| 263 QTPLQESIYANKHSTTVFYEFNKPKKAVY 291
                                   56777888888888888888887776665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0019
                  RNA_helicase   2 wlyGpsgeGKStlakeLakal 22 
                                   ++  ++g+GKStl+++L++++
  gi|15668539|ref|NP_247337.1| 394 LMISDPGVGKSTLMESLIQKF 414
                                   667789**********99876 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.65
                  RNA_helicase  52 vvvidDfgqvkdeenpsdlaelirlvsstpyplnmas 88 
                                   vv+id+f+++k+      +  l+++++ +++++n+a 
  gi|15668539|ref|NP_247337.1| 459 VVCIDEFSRNKEV-----YDYLLGVMEQQKIEINKAG 490
                                   89********977.....6666666666666666665 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0         1   1.1e+03      23      79 ..     406     464 ..     392     469 .. 0.73
   2 ?    9.1   0.0    0.0013       1.4      47      77 ..     727     757 ..     692     758 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1
                         Mrr_N  23 irervaerfglseeeraellpsgkq...trfknrvgWartyLkkagllespkrgvwkiTe 79 
                                   + e ++++f + ++  a +  sg     ++++ ++ +  +   kag l++ + gv+ i e
  gi|15668539|ref|NP_247337.1| 406 LMESLIQKFPFVKKVYAVTS-SGPGlvgSVVREKAEFGDSWVLKAGVLTEADGGVVCIDE 464
                                   55666666666666555554.4433457899999999999999*********99999976 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                         Mrr_N  47 qtrfknrvgWartyLkkagllespkrgvwki 77 
                                     + ++ v  a++yLk+ g + spk g+w++
  gi|15668539|ref|NP_247337.1| 727 AGLSEKEVEDAINYLKRVGDIYSPKSGYWQL 757
                                   4467889999*******************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00047      0.53       7      33 ..     398     424 ..     392     496 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
                                   STTSSHHHHHHHHHTSTEEESSSTTSS CS
                      MMR_HSR1   7 rpNvGKStLinaltgekaivsdkpgtT 33 
                                    p vGKStL+ +l+++   v++   +T
  gi|15668539|ref|NP_247337.1| 398 DPGVGKSTLMESLIQKFPFVKKVYAVT 424
                                   699***********9977776666555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.59   6.7e+02      42     109 ..     255     356 ..     247     359 .. 0.60
   2 ?    4.7   0.0     0.036        40      12      34 ..     391     413 ..     381     418 .. 0.77
   3 ?    2.4   0.0      0.19   2.1e+02      35      95 ..     673     744 ..     666     754 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.59
                                   EEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSBHHHH.............................HHHTCHHHHHHH CS
                                   xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................xxxxxxxxxxxx RF
                      ABC_tran  42 illdgkdlke..qeleslrkeigvlpqepqlfpeltvren.............................esdeeiekalsk 91 
                                   + +++ ++++  qe   ++k++ +++ e + +p++ v++                              ++de+ie+++++
  gi|15668539|ref|NP_247337.1| 255 VDFQEIKVQTplQESIYANKHSTTVFYE-FNKPKKAVYSGyvkivgvpivkenkngsvgelyihafyieKDDEDIEEIAKN 334
                                   5444444444433333444444444444.333333344446777777777777888888889999999888888******9 PP

                                   STTGG..TTCBGESTTS..GGS CS
                                   xxxxx..xxxxxxxxxx..xxx RF
                      ABC_tran  92 lglke..lkdtvvkssp..ssL 109
                                   l+ k+  l ++++k++   ++L
  gi|15668539|ref|NP_247337.1| 335 LNEKDleLINRIAKDKNviQKL 356
                                   9999855445555444444555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.036
                                   SEEEEEESTTSSHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  12 ekvaivGenGaGKStLlkllagl 34 
                                     + ++ + G GKStL++ l+++
  gi|15668539|ref|NP_247337.1| 391 IHILMISDPGVGKSTLMESLIQK 413
                                   556667788*********99875 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.19
                                   S--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS.....--S-TTSBHHHH.....HHHTCHHHHHHHSTTG CS
                                   xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.....xxxxxxxxxxxx.....xxxxxxxxxxxxxxxx RF
                      ABC_tran  35 lkpteGeilldgkdlke.qeleslrkeigvlpqe.....pqlfpeltvren.....esdeeiekalsklglk 95 
                                   ++p++G+i +d+   +   ++ +++k + ++++      + l pe +++e+      s++e+e+a++ l+ +
  gi|15668539|ref|NP_247337.1| 673 YDPESGSIDIDKIAGTPkSKRDKVEKVLNIIKEIsnsrdDGLAPEEEIYERaeragLSEKEVEDAINYLKRV 744
                                   789*****9996665555444444444444444332255778888888887899984444455554444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (759 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      730  (0.0407162); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 4777.90
//
Query:       gi|15668540|ref|NP_247338.1|  [L=114]
Description: hypothetical protein MJ_0364 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.042   13.7   0.0      0.066   13.1   0.0    1.3  1  DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain
       0.07   13.0   0.1       0.11   12.4   0.1    1.3  1  GreA_GreB      Transcription elongation factor, GreA/GreB, C-


Domain annotation for each model (and alignments):
>> DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.3e-06     0.066      36      73 ..      22      60 ..      19      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.3e-06
                                  XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX CS
                 DNA_ligase_OB 36 atLhnedeierkdirigdtVvvek.aGdvIPevvgvvle 73
                                   t+ +++++++k++r+gd V +++ +G+   ++vgv ++
  gi|15668540|ref|NP_247338.1| 22 TTIRSKHYLKNKGLRVGDVVKIKHpSGEFPAKIVGVEVK 60
                                  588999****************98578999999999765 PP

>> GreA_GreB  Transcription elongation factor, GreA/GreB, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.2e-05      0.11      52      76 ..      34      58 ..      33      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                                  T--TT-EE---BTTB---EEEEEEX CS
                     GreA_GreB 52 gkkvGdevevkapsgkikveIlkie 76
                                  g +vGd+v++k psg++  +I+ +e
  gi|15668540|ref|NP_247338.1| 34 GLRVGDVVKIKHPSGEFPAKIVGVE 58
                                  789******************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 746.30
//
Query:       gi|15668541|ref|NP_247339.1|  [L=176]
Description: hypothetical protein MJ_0365 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-19   69.7   0.3    3.3e-19   69.5   0.3    1.1  1  RNase_H_2       RNase_H superfamily
      8e-05   21.9   0.9    0.00012   21.4   0.6    1.4  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    0.00013   21.7   0.1    0.00066   19.4   0.1    1.9  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
     0.0085   16.7   0.2      0.019   15.5   0.1    1.7  1  RNase_T         Exonuclease
  ------ inclusion threshold ------
       0.02   14.6   0.0      0.034   13.8   0.0    1.4  1  DNA_pol_A_exo1  3'-5' exonuclease
      0.054   13.7   0.1      0.086   13.1   0.1    1.2  1  Plant_vir_prot  Plant viral movement protein
       0.21   11.2   0.0        0.3   10.7   0.0    1.3  1  BRCA-2_OB3      BRCA2, oligonucleotide/oligosaccharide-bindin


Domain annotation for each model (and alignments):
>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.3   1.3e-22   3.3e-19       2     165 ..       5     168 ..       4     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.3e-22
                     RNase_H_2   2 ffDiEttGlspkknliyliGvldvdekeiekltqllaeepeeekailelflellekkkalvtfngksFDvpflkrlf..kk 80 
                                    +DiEttGl+p +  i+ iGv   d++ i+ l  + ++e     ++++++    e  ++++ fn   FD++flk +   ++
  gi|15668541|ref|NP_247339.1|   5 IIDIETTGLNPMEHRIVAIGVKLGDRD-II-L--MDESEYYLLVNFWDTV--EKEGIEKIIGFN-IDFDWQFLKLRSlyHR 78 
                                   58********************97777.34.2..3356667777777733..5666699*****.579******7774555 PP

                     RNase_H_2  81 yklde..eefrhiDLlkelrkkkl...esysLksvekelgierreedlsGsqavklyqeylrtgdeellekilaYNedDvr 156
                                    k++   + +  +DL ++l+ ++    ++++L +  ++lgi+  e+d++Gs++++l++++ ++gdee+++ki ++ + D+ 
  gi|15668541|ref|NP_247339.1|  79 LKIKHfrKYQGRVDLRQILNGSGGqyrKGTKLVDYCRFLGIDVPEDDANGSEIPELWEKFEEEGDEEAKRKICEHLKRDLE 159
                                   5555576799*******9966544458899*************************************************** PP

                     RNase_H_2 157 alatlyekl 165
                                    ++ ly+ l
  gi|15668541|ref|NP_247339.1| 160 RTWELYKIL 168
                                   ******976 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.6   4.5e-08   0.00012     232     288 ..      33      87 ..      25     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.5e-08
                                   EEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCC CS
                DNA_pol_B_exo1 232 vlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrl 288
                                   +l  +sE+ lL +f +++ ++  + i+g+Ni +FD+++++ R   +  +k++ + + 
  gi|15668541|ref|NP_247339.1|  33 ILMDESEYYLLVNFWDTVEKEGIEKIIGFNI-DFDWQFLKLRSL-YHRLKIKHFRKY 87 
                                   556689************************6.5*****998876.334455544443 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   2.6e-07   0.00066      34      86 ..      36      88 ..      13     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.6e-07
                DNA_pol_B_exo2 34 essekelikkffegvekkk.pqlVsfngrgfDlpvleyralkhgvsapkyfdeg 86
                                  ++se  l+ +f+++vek+   ++++fn   fD   l++r+l+h+++++++ + +
  gi|15668541|ref|NP_247339.1| 36 DESEYYLLVNFWDTVEKEGiEKIIGFN-IDFDWQFLKLRSLYHRLKIKHFRKYQ 88
                                  447899**********88769******.68*****************9997755 PP

>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   7.6e-06     0.019       2      23 ..       5      25 ..       4      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.6e-06
                                  EEEEEESSSTTCTTS-EEEEEE CS
                       RNase_T  2 viDlEttgldakekdeiieiaa 23
                                  +iD+Ettgl++   ++i++i+ 
  gi|15668541|ref|NP_247339.1|  5 IIDIETTGLNP-MEHRIVAIGV 25
                                  7**********.9*******96 PP

>> DNA_pol_A_exo1  3'-5' exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.3e-05     0.034      25      94 ..       6      72 ..       4      96 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                                  EEEEEE-SSSTTSSEEEEEEEEECSSEEEEE.ECTTTTTT-HGHHHHHHHT-TTSEEEESSHHHHHHHHHH CS
                DNA_pol_A_exo1 25 vDtEttsldlisatlvliliqlgekeeayii.dplelgddvalealkrlledenitkvghnakfDlevlar 94
                                  +D Ett+l++++++ v i + lg+++   +  ++++l  +++ +  k+ +e    +++g+n++fD ++l+ 
  gi|15668541|ref|NP_247339.1|  6 IDIETTGLNPMEHRIVAIGVKLGDRDIILMDeSEYYLLVNFWDTVEKEGIE----KIIGFNIDFDWQFLKL 72
                                  79********99999999999999854444202233333334444455555....6789*********986 PP

>> Plant_vir_prot  Plant viral movement protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.3e-05     0.086      43      58 ..     100     115 ..      93     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.3e-05
                Plant_vir_prot  43 hGGkYrDGtksikYns 58 
                                    GG+Yr Gtk ++Y++
  gi|15668541|ref|NP_247339.1| 100 SGGQYRKGTKLVDYCR 115
                                   59************97 PP

>> BRCA-2_OB3  BRCA2, oligonucleotide/oligosaccharide-binding, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00012       0.3      39      67 ..      31      59 ..       5      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                                  EEEEE-TT--EEEEEESS---....SS-. CS
                    BRCA-2_OB3 39 vvyLsdeesnllavkfwsdlkelalediv 67
                                   + L de+  +l v+fw  +++ ++e+i+
  gi|15668541|ref|NP_247339.1| 31 DIILMDESEYYLLVNFWDTVEKEGIEKII 59
                                  47799***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1176.45
//
Query:       gi|15668542|ref|NP_247340.1|  [L=92]
Description: hypothetical protein MJ_0366 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.7e-36  121.8   4.0      1e-35  121.6   4.0    1.1  1  DUF2540    Protein of unknown function (DUF2540)
     0.0015   17.5   1.3     0.0017   17.2   1.3    1.0  1  HTH_micro  HTH-like


Domain annotation for each model (and alignments):
>> DUF2540  Protein of unknown function (DUF2540)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.6   4.0   1.1e-39     1e-35       1      73 [.      14      85 ..      14      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 1.1e-39
                                  EEEESS---HHHHHHHHHHGGG-----HHHHHHHHHS---EEEEEE--HHHHHHHHHHGGGHHHHHHHH.HHH CS
                       DUF2540  1 tlnLiknidarelRYllHklenlenvdvetlkkakeaekktkktltLsdeEkkIvkklGkaanlLlNcvilve 73
                                  t++L+knid+r+lRYllHklen+envd++tl++a+eaekk+k+++tL++eE++I+++lGk+anlLlNc+++ +
  gi|15668542|ref|NP_247340.1| 14 TFYLYKNIDGRKLRYLLHKLENVENVDIDTLRRAIEAEKKYKRSITLTEEEEVIIQRLGKSANLLLNCELV-K 85
                                  79*******************************************************************55.4 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.3   1.9e-07    0.0017     232     309 ..       8      84 ..       3      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.9e-07
                     HTH_micro 232 ieeeedsiktkeefegkikrlkfytvenleklnerkkkrliegddleekeliTsedriealkqllkkkkafvlsketf 309
                                    e++  ++   + ++g+  r++ ++ en e ++   ++r ie ++ + k+ iT  + +e++ q l k+  + l+ e +
  gi|15668542|ref|NP_247340.1|   8 KEKKRATFYLYKNIDGRKLRYLLHKLENVENVDIDTLRRAIEAEK-KYKRSITLTEEEEVIIQRLGKSANLLLNCELV 84 
                                   5667778888999********************999999999998.999********************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 605.82
//
Query:       gi|15668543|ref|NP_247341.1|  [L=330]
Description: integrase/recombinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-36  123.8   0.6    8.9e-36  123.3   0.1    1.5  2  Phage_integrase  Phage integrase family
      2e-13   50.6   0.4    4.8e-13   49.4   0.4    1.6  1  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    0.00081   19.6   1.7      0.012   15.9   0.4    3.1  4  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.038   14.3   8.2        0.3   11.4   1.9    4.0  4  Phage_int_SAM_5  Phage integrase SAM-like domain
       0.12   11.9   0.5         20    4.7   0.0    3.2  3  PrpR_N           Propionate catabolism activator
       0.25   11.6   2.9        7.9    6.8   0.3    2.7  2  GST_C_3          Glutathione S-transferase, C-terminal domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.7   5.2e+03      63      83 ..      94     114 ..      73     138 .. 0.41
   2 !  123.3   0.1     3e-39   8.9e-36      13     170 ..     151     314 ..     139     316 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                                   SSSSEEEEECTHHHHHHHHHH CS
               Phage_integrase  63 Kgskeravplseealellkel 83 
                                   K+s+  +  l +  +++l+++
  gi|15668543|ref|NP_247341.1|  94 KSSQRKYFLLLKVFYRVLRMY 114
                                   333332222223333333332 PP

  == domain 2  score: 123.3 bits;  conditional E-value: 3e-39
                                   HCCGC...HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHHHCHC CS
               Phage_integrase  13 aalee...slkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkellskalee 90 
                                   + + e    + ird+l+++ll++tG R+sE+l+L++kd dl+ng++++  r++K+  er+v  s+  lell+++++ + ++
  gi|15668543|ref|NP_247341.1| 151 KKIIEsgsRTRIRDALIIRLLWDTGCRVSEVLNLKYKDCDLDNGIFKI--RNTKTHEERTVVCSSDTLELLRNYVQFN-VR 228
                                   33333455589*************************************..****************************.99 PP

                                   CTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-S......SC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHHH CS
               Phage_integrase  91 aeksellfaskrgkplsrqtvrkafkraveeagie......kpltpHtlRhsfataLleagvdlrvvqkllGHssisttqi 165
                                   + ++++lf + +g ++ ++ ++++f++av+e + e       ++  H++Rh  a +Ll++gv+++ v+++lGH+s++tt i
  gi|15668543|ref|NP_247341.1| 229 QGSDDYLFQNSQGGRVRKEWISEVFRKAVNELKEEgkipknRRIVIHSIRHGRAVDLLNKGVPIDIVKEYLGHKSMNTTLI 309
                                   ***********9999999999999999999999999999999*************************************** PP

                                   HHCCC CS
               Phage_integrase 166 Ythva 170
                                   Y+h++
  gi|15668543|ref|NP_247341.1| 310 YAHSK 314
                                   ***86 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.4   1.6e-16   4.8e-13       2      76 ..      32     109 ..      31     112 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.6e-16
               Phage_int_SAM_4   2 lerfrealrlaglserTiksYlsaikrflrfl...kkkapeeltkedieaYlnyLanerklsastqknalnalsffyk 76 
                                   l+rf +++r++g++e+Tiks+l  ++ fl+++    +k+peel++ d+  ++nyL + rk+s+s+q+ ++  l++fy+
  gi|15668543|ref|NP_247341.1|  32 LKRFEDERRFDGIKESTIKSDLDRLRVFLDYCinyLGKNPEELKTSDFVKFFNYLDTVRKVSKSSQRKYFLLLKVFYR 109
                                   789*****************************755269***************************************8 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4     4e-06     0.012       1      80 [.      28     111 ..      28     113 .. 0.86
   2 !    9.3   0.4   0.00045       1.3       3      35 ..      81     113 ..      79     132 .. 0.86
   3 ?    0.7   0.0      0.22   6.6e+02      31      69 ..     129     165 ..     117     168 .. 0.79
   4 ?   -2.6   0.0       2.4   7.1e+03      73      84 .]     219     230 ..     214     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4e-06
                                   HHHHHHHHHHTT...-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS-----.-----HHHHHHHHHHHH CS
               Phage_int_SAM_1   1 leqfleyLiker...glspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeg.lsatslarrlsalrsFf 77 
                                   ++++l++ + er   g+ + T+ + +++Lr fl++     +++ e+l+t+d ++f ++l   + +s +s ++++  l+ F+
  gi|15668543|ref|NP_247341.1|  28 IKEYLKRFEDERrfdGIKESTIKSDLDRLRVFLDYCINYLGKNPEELKTSDFVKFFNYLDTVRkVSKSSQRKYFLLLKVFY 108
                                   5677777777773335789****************9999*************99999988877699999999********* PP

                                   HHH CS
               Phage_int_SAM_1  78 qfl 80 
                                   ++l
  gi|15668543|ref|NP_247341.1| 109 RVL 111
                                   988 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00045
                                   HHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH CS
               Phage_int_SAM_1   3 qfleyLikerglspnTlraYrrdLrrflkflae 35 
                                    f++yL ++r +s+ + r Y   L+ f + l+ 
  gi|15668543|ref|NP_247341.1|  81 KFFNYLDTVRKVSKSSQRKYFLLLKVFYRVLRM 113
                                   69*************************999876 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.22
                                   HHHHH.TS--TTT--HHHHHHHHHS----------HHHH CS
               Phage_int_SAM_1  31 kflaergkesleqlttedvraflaeleeeglsatslarr 69 
                                   +f++  ++++ +++++e++  +l++  e+g s+t ++ +
  gi|15668543|ref|NP_247341.1| 129 RFARI-EIQHYDAVDAEMLNMILKKIIESG-SRTRIRDA 165
                                   55566.899999999999999999999988.66666655 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHTT CS
               Phage_int_SAM_1  73 lrsFfqflvreg 84 
                                   lr++ qf vr+g
  gi|15668543|ref|NP_247341.1| 219 LRNYVQFNVRQG 230
                                   899999999987 PP

>> Phage_int_SAM_5  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0026       7.8      53      85 ..      27      65 ..       6      76 .. 0.76
   2 ?   11.4   1.9    0.0001       0.3      11      81 ..      33     109 ..      28     119 .. 0.79
   3 ?   -1.6   0.0       1.2   3.5e+03       3      21 ..     114     132 ..     112     146 .. 0.66
   4 ?    0.2   0.1      0.32   9.4e+02      67      67 ..     238     238 ..     196     274 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0026
                                  HHHHHH......HHTS---HHHHHHHHHHHHHHHHHHHH CS
               Phage_int_SAM_5 53 eFedYL......kkkkglsentiskyfkklkavlnkAik 85
                                  + ++YL      ++  g++e+ti++ + +l+ +l ++i+
  gi|15668543|ref|NP_247341.1| 27 KIKEYLkrfedeRRFDGIKESTIKSDLDRLRVFLDYCIN 65
                                  456666555544466799999999999999999999886 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0001
                                   HHHHTTS.....-HHHHHHHHHHHHHTTTS-...S---TTT--HHHHHHHHHHHHHTS---HHHHHHHHHHHHHHHH CS
               Phage_int_SAM_5  11 ekkkkkg.....skgtlrnykstlkhlkkFl.kkkditfeeidkefleeFedYLkkkkglsentiskyfkklkavln 81 
                                   ++ + ++     +++t+++    l+ + +++ +    + ee+ ++   +F +YL + +++s+++++kyf  lk +++
  gi|15668543|ref|NP_247341.1|  33 KRFEDERrfdgiKESTIKSDLDRLRVFLDYCiNYLGKNPEELKTSDFVKFFNYLDTVRKVSKSSQRKYFLLLKVFYR 109
                                   3333333333477888888888888888888666778999999999999********************99998875 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.2
                                   HHHHHHHTHHHHTTS-HHH CS
               Phage_int_SAM_5   3 ldyfkeyiekkkkkgskgt 21 
                                   +++++e++e++k +++ ++
  gi|15668543|ref|NP_247341.1| 114 YNVIQEFVEESKDRKRFAR 132
                                   4567777777777764433 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.32
                                   H CS
               Phage_int_SAM_5  67 n 67 
                                   n
  gi|15668543|ref|NP_247341.1| 238 N 238
                                   1 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2     0.085   2.5e+02      84     117 ..       4      37 ..       3      41 .. 0.90
   2 ?    2.0   0.0     0.045   1.3e+02      81     132 ..     119     170 ..     115     181 .. 0.81
   3 ?    4.7   0.0    0.0066        20       5      50 ..     182     227 ..     178     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.085
                        PrpR_N  84 kglktlselldldieiytinseeeaeaavkelka 117
                                   k+lk +++ll l+++  +i++++++++ +k+  +
  gi|15668543|ref|NP_247341.1|   4 KELKHIENLLLLKVKKEKIEETDKIKEYLKRFED 37 
                                   68999***********************998765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.045
                        PrpR_N  81 niikglktlselldldieiytinseeeaeaavkelkaegvevvvGdgvvadl 132
                                   +++++ k  +++  ++i++y   ++e +++++k++ ++g ++ + d ++ +l
  gi|15668543|ref|NP_247341.1| 119 EFVEESKDRKRFARIEIQHYDAVDAEMLNMILKKIIESGSRTRIRDALIIRL 170
                                   566677777788899*********************9999888777776665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0066
                        PrpR_N   5 ldievvegdleeavelakeleaegvdviiSrGgtaellrkhvsvPV 50 
                                   l+++ ++ dl++++  +++ ++++ + +++   t ellr+ v+  V
  gi|15668543|ref|NP_247341.1| 182 LNLKYKDCDLDNGIFKIRNTKTHEERTVVCSSDTLELLRNYVQFNV 227
                                   67888999********************************998765 PP

>> GST_C_3  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.015        43      79      97 ..      15      33 ..       3      35 .. 0.80
   2 ?    6.8   0.3    0.0026       7.9      20      88 ..      70     143 ..      53     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.015
                                  HHHHHHHHHTSHHHHHHHC CS
                       GST_C_3 79 lkalyervearpkikaYle 97
                                  lk  +e++e+  kik+Yl+
  gi|15668543|ref|NP_247341.1| 15 LKVKKEKIEETDKIKEYLK 33
                                  5556899***********8 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0026
                                   HHHHHHHHHHHCHHHHHHHHHH..C.HGTSSSSTTS--HHHHHHHHHHHHHHHHTCC.CC-HHHH.HHHHHHHT CS
                       GST_C_3  20 kkkefleerlpkflkyfekvlk..k.kgggylvgdklTyADlalfqvldgleeaeal.kkfpklk.alyervea 88 
                                   + +e++++   kf++y+++v k  k ++ +y++  k+ y  l +++v++ + e +++ k+f ++  ++y++v a
  gi|15668543|ref|NP_247341.1|  70 NPEELKTSDFVKFFNYLDTVRKvsKsSQRKYFLLLKVFYRVLRMYNVIQEFVEESKDrKRFARIEiQHYDAVDA 143
                                   55788899999*********999854667799999999999999999998888744458888766577777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1211  (0.0675442); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1960.12
//
Query:       gi|15668544|ref|NP_247342.1|  [L=106]
Description: hypothetical protein MJ_0368 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.8   0.8       0.55   10.5   0.0    2.3  2  Mrx7      MIOREX complex component 7
      0.016   15.4   0.2       0.02   15.1   0.2    1.2  1  DUF3952   Domain of unknown function (DUF3952)


Domain annotation for each model (and alignments):
>> Mrx7  MIOREX complex component 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1    0.0076        68      29      58 ..      14      43 ..       8      56 .. 0.80
   2 ?   10.5   0.0   6.1e-05      0.55       6      30 ..      75      99 ..      74     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0076
                          Mrx7 29 keteiseekqesellykptrrqklkaFrkl 58
                                  k+ +++e+ +e++  ++p++ +  + F k+
  gi|15668544|ref|NP_247342.1| 14 KNYPPKESIKEEKRVFNPKNIEVGNNFIKI 43
                                  566678899999*********999999876 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 6.1e-05
                          Mrx7  6 rkLLeSpgFhrfVrkihakvngike 30
                                  ++L+e + +++ ++ki++k+n+i++
  gi|15668544|ref|NP_247342.1| 75 YNLIEDEVYKKEIKKIWEKINEIRN 99
                                  78999999***************97 PP

>> DUF3952  Domain of unknown function (DUF3952)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.2   2.2e-06      0.02      54      92 ..      57      97 ..      24     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-06
                       DUF3952 54 edgeh..skviyqtteGiynikekslyGettqkvtsevedk 92
                                   ++e+  + vi  + eGiyn+ e+++y +  +k+  ++++ 
  gi|15668544|ref|NP_247342.1| 57 GEEEYllMDVILSSLEGIYNLIEDEVYKKEIKKIWEKINEI 97
                                  2333222689999***********************99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 692.12
//
Query:       gi|15668545|ref|NP_247343.1|  [L=369]
Description: DNA topoisomerase VI subunit A [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-17   61.8   0.0    7.6e-17   61.1   0.0    1.4  1  TP6A_N          Type IIB DNA topoisomerase
      0.008   15.9   0.0      0.016   14.9   0.0    1.4  1  Acetyltransf_8  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0   8.5e-21   7.6e-17       3      61 ..      76     138 ..      74     139 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 8.5e-21
                                   HHHHHHHHHHHHHHHHTT--EEHHHHHHH....GGGS-SSHHHHHHHHHHHHHHHTS-GGGGT CS
                        TP6A_N   3 faqllkvlelihelleegkvvTkRdiYYr....dvelFksQaesdrliddievllgvsReeLn 61 
                                   faq++k+le+ ++lle++  +T+R+ YY      ++ F++Q++s+++i+d+e++lgv+Re+L+
  gi|15668545|ref|NP_247343.1|  76 FAQTTKMLEFAKQLLETDDFSTLREAYYVsknwGEARFDDQQASNNVIEDLEAALGVLREHLG 138
                                   9****************************88776***************************97 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.8e-06     0.016      27      65 ..     225     262 ..     214     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-06
                                   -HHHHHHHHHHHC.STTEEEEEEEETTEEEEEEEEEEGG CS
                Acetyltransf_8  27 tleevrellakldadphsepliglldgepvgyfeiYwak 65 
                                   +++ +r++ ++l+ ++h  p+++  dg p gy+ iY+  
  gi|15668545|ref|NP_247343.1| 225 PARATRRFIKRLH-EEHDLPVLVFTDGDPYGYLNIYRTL 262
                                   55788999999*8.**********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2425.88
//
Query:       gi|15668546|ref|NP_247344.1|  [L=364]
Description: cell division protein FtsZ [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-44  153.1   1.4    1.7e-44  152.4   1.4    1.4  1  Tubulin    Tubulin/FtsZ family, GTPase domain
    1.2e-34  118.4   1.1    4.6e-34  116.6   1.1    2.0  1  FtsZ_C     FtsZ family, C-terminal domain
     0.0036   16.5   6.5     0.0055   15.9   1.1    2.6  2  Tubulin_2  Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   1.4   2.9e-48   1.7e-44       1     196 [.      39     199 ..      39     200 .. 0.97

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 2.9e-48
                                   EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE--CC CS
                       Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllgke 81 
                                   +i v+g+G++Gn+++++l      e gi             +g ++++    ai+td+q+l ++ka+      +k+l+gk+
  gi|15668546|ref|NP_247344.1|  39 KITVVGCGGAGNNTITRLKM----E-GI-------------EG-AKTV----AINTDAQQLIRTKAD------KKILIGKK 90 
                                   699***************99....8.**.............88.5555....***************......******** PP

                                   CCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG.G CS
                       Tubulin  82 gagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefse 162
                                    ++++gagg+p++g+eaa+e++eei+ +++++d+   +fit +lgGGTG+G +pv++e+ k+   +al+v+vv+lP+ + e
  gi|15668546|ref|NP_247344.1|  91 LTRGLGAGGNPKIGEEAAKESAEEIKAAIQDSDM---VFITCGLGGGTGTGSAPVVAEISKKI--GALTVAVVTLPFVM-E 165
                                   **********************************...**************************..************99.* PP

                                   -HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                       Tubulin 163 vvvepynailalkelieesdavividNdaLlkil 196
                                   ++v+++na+++l++l+++ d+++vi+N++L++i+
  gi|15668546|ref|NP_247344.1| 166 GKVRMKNAMEGLERLKQHTDTLVVIPNEKLFEIV 199
                                   *******************************997 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   1.1   7.8e-38   4.6e-34       1      95 []     247     341 ..     247     341 .. 0.99

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 7.8e-38
                                   EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE-TT- CS
                        FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavideel 81 
                                   G Am+g+Ge+++e+ra+ea+  a++spLLdvd++gA+g+l+++ g +dltl+E+ ev+ t+++++d++a++i+Ga+ide+l
  gi|15668546|ref|NP_247344.1| 247 GLAMIGIGESDSEKRAKEAVSMALNSPLLDVDIDGATGALIHVMGPEDLTLEEAREVVATVSSRLDPNATIIWGATIDENL 327
                                   89******************************************************************************* PP

                                   -SEEEEEEEEES-X CS
                        FtsZ_C  82 edeirvtvvatglk 95 
                                   e+++rv  v+tg++
  gi|15668546|ref|NP_247344.1| 328 ENTVRVLLVITGVQ 341
                                   ************96 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.9   0.4    0.0082        49       2      19 ..      42      59 ..      41      86 .. 0.86
   2 !   15.9   1.1   9.2e-07    0.0055     115     201 ..      95     167 ..      70     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0082
                     Tubulin_2  2 viGLGGtGgkvlaelrrr 19
                                  v+G+GG G +++++l+  
  gi|15668546|ref|NP_247344.1| 42 VVGCGGAGNNTITRLKME 59
                                  7**************975 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 9.2e-07
                     Tubulin_2 115 eGAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllrkilkeekqkvkiig 195
                                    GAG+++ +G  a  +++eei++a++d                vf+ ++L GGTG G++  va + +ki   +   v +++
  gi|15668546|ref|NP_247344.1|  95 LGAGGNPKIGEEAAKESAEEIKAAIQDS-------------DMVFITCGLGGGTGTGSAPVVAEISKKIGALTVA-VVTLP 161
                                   5899999999999999999999888874.............38***************98777776666555554.33444 PP

                     Tubulin_2 196 lvllPd 201
                                   +v+  +
  gi|15668546|ref|NP_247344.1| 162 FVMEGK 167
                                   444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2300.47
//
Query:       gi|15668547|ref|NP_247345.1|  [L=74]
Description: preprotein translocase subunit SecE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-06   26.4   0.1    5.6e-06   26.2   0.1    1.1  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   3.1e-10   5.6e-06       1      45 [.      13      57 ..      13      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.1e-10
                                  HHCHHHHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          SecE  1 kkFfkevkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDl 45
                                  k+F+ e+++ +    +Pt++E+l  ++v+++++ ++g++++++ +
  gi|15668547|ref|NP_247345.1| 13 KEFIEECRRVWLVLKKPTKDEYLAVAKVTALGISLLGIIGYIIHV 57
                                  68****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      779  (0.0434492); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 470.46
//
Query:       gi|15668548|ref|NP_247346.1|  [L=147]
Description: transcription antitermination protein NusG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-23   80.8   0.1    8.7e-23   80.0   0.1    1.4  1  Spt5-NGN  Early transcription elongation factor of RNA pol II
    7.6e-10   38.4   1.3    1.7e-09   37.3   1.3    1.6  1  KOW       KOW motif
  ------ inclusion threshold ------
      0.011   16.2   0.4       0.11   13.0   0.1    2.5  2  NusG      Transcription termination factor nusG
        0.2   11.8   0.3          1    9.5   0.3    2.0  2  GBR2_CC   Gamma-aminobutyric acid type B receptor subunit 2 c


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.1   1.9e-26   8.7e-23       1      84 []       1      80 [.       1      80 [. 0.97

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 1.9e-26
                      Spt5-NGN  1 siwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikEvedl 83
                                  +i+av++  gqE+++a  ++ +    a+ke+l+++S++a ++lkGy++vEA++k +ve++++g+p vrg+v+g++ i+E+e l
  gi|15668548|ref|NP_247346.1|  1 MIFAVRTMVGQEKNIAGLMASR----AEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPL 79
                                  69*****************999....9999**************************************************988 PP

                      Spt5-NGN 84 l 84
                                  l
  gi|15668548|ref|NP_247346.1| 80 L 80
                                  6 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   1.3   3.7e-13   1.7e-09       1      32 []      91     122 ..      91     122 .. 0.96

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 3.7e-13
                                   TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                           KOW   1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32 
                                   +Gd+V++++Gp+kG+ +kV +vd+hk+ V+++
  gi|15668548|ref|NP_247346.1|  91 KGDVVEIIAGPFKGERAKVIRVDKHKEEVTLE 122
                                   7*************************999976 PP

>> NusG  Transcription termination factor nusG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.5e-05      0.11      41      83 ..      24      78 ..       2      90 .. 0.67
   2 ?    0.3   0.1      0.23   1.1e+03      42      44 ..     114     116 ..      81     146 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                                  TEEE...........CSSTTEEEEEE---CHHHHHHHCSTTEEEE-EETT....SSCC CS
                                  xxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx RF
                          NusG 41 gkkk...........klfpgyifikadmndkllmairktpgVtgfvrvgg....eskp 83
                                  +  k             ++gy++++a+ + +   +i+ +p+V g+v  g+    e +p
  gi|15668548|ref|NP_247346.1| 24 E--KeqldvysilasESLKGYVLVEAETKGDVEELIKGMPRVRGIV-PGTiaieEIEP 78
                                  2..1346666777777789**********9****************.33345444444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.23
                                   EEE CS
                                   xxx RF
                          NusG  42 kkk 44 
                                   k k
  gi|15668548|ref|NP_247346.1| 114 KHK 116
                                   222 PP

>> GBR2_CC  Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.35   1.6e+03       8      20 ..      21      33 ..      19      34 .. 0.84
   2 ?    9.5   0.3   0.00023         1      21      38 ..     106     123 ..     105     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.35
                       GBR2_CC  8 SRLeklQaenHsl 20
                                  SR ek Q +  s+
  gi|15668548|ref|NP_247346.1| 21 SRAEKEQLDVYSI 33
                                  99*****998775 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00023
                       GBR2_CC  21 RmkitelDKdLEEVTMQL 38 
                                   R k++ +DK  EEVT+ L
  gi|15668548|ref|NP_247346.1| 106 RAKVIRVDKHKEEVTLEL 123
                                   7899***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1097.69
//
Query:       gi|15668549|ref|NP_247347.1|  [L=161]
Description: 50S ribosomal protein L11 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-25   87.1   2.0      6e-25   86.9   0.9    1.6  2  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
      1e-23   83.6   0.6      1e-23   83.6   0.6    1.6  2  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
  ------ inclusion threshold ------
      0.099   13.0   0.0       0.17   12.2   0.0    1.3  1  DUF3646          DNA polymerase III gamma and tau subunits C 


Domain annotation for each model (and alignments):
>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.9     1e-28     6e-25       6      65 .]       4      64 ..       2      64 .. 0.95
   2 ?   -2.8   0.0      0.99   5.9e+03      33      42 ..     141     150 ..     130     151 .. 0.65

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 1e-28
               Ribosomal_L11_N  6 kvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitv.yqdrsf 65
                                   vv++ v++G+At++PplGpa+GplG+n+++++ke+n++Tkd++g+++pVk+ v  ++r+f
  gi|15668549|ref|NP_247347.1|  4 EVVEVLVTGGRATAGPPLGPAIGPLGVNVMQVVKEINEKTKDYEGMQVPVKVIVdTETRKF 64
                                  699***************************************************8888876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.99
               Ribosomal_L11_N  33 nikkfckefn 42 
                                    +k++ ke+ 
  gi|15668549|ref|NP_247347.1| 141 DPKEVQKEID 150
                                   3788888875 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.1   6.3e+03      35      53 ..      36      54 ..      30      59 .. 0.51
   2 !   83.6   0.6   1.7e-27     1e-23       2      70 .]      70     137 ..      69     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                                  HHHHHHHHGGGHTXS.SHH CS
                 Ribosomal_L11 35 vyeIAkiKksdlnaalsle 53
                                  v+eI +  k+ + ++++++
  gi|15668549|ref|NP_247347.1| 36 VKEINEKTKDYEGMQVPVK 54
                                  5555554443333555555 PP

  == domain 2  score: 83.6 bits;  conditional E-value: 1.7e-27
                                   --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                 Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                    Ppt++l+kk++gie+ + +p +e+vG+++l+qv++IAk+Kk+ + ++ +l++avk++lgt+ smG++V
  gi|15668549|ref|NP_247347.1|  70 IPPTTALIKKELGIETAAHEPRHEVVGNLTLEQVIKIAKMKKDAMLSY-TLKNAVKEVLGTCGSMGVTV 137
                                   5*****************************************666688.******************99 PP

>> DUF3646  DNA polymerase III gamma and tau subunits C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.9e-05      0.17       3      53 ..      99     149 ..      98     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                       DUF3646   3 sfedlvalleekrdiklkvelerdvrlvrfepgrlelalapgapkdlakrL 53 
                                   ++e+++++++ k+d++l ++l+++v+ v  + g++ ++++ + pk++ k++
  gi|15668549|ref|NP_247347.1|  99 TLEQVIKIAKMKKDAMLSYTLKNAVKEVLGTCGSMGVTVEGKDPKEVQKEI 149
                                   689**********************************99999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1056.67
//
Query:       gi|15668550|ref|NP_247348.1|  [L=330]
Description: lipoprotein B LppB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-27   96.5   2.4    2.4e-27   95.4   2.4    1.7  1  PAP2         PAP2 superfamily
    3.1e-18   66.4   6.7    3.1e-18   66.4   6.7    3.1  4  SNARE_assoc  SNARE associated Golgi protein
    5.6e-13   49.0   9.3    3.6e-12   46.4   9.3    2.0  1  PAP2_3       PAP2 superfamily
     0.0012   19.4   2.8     0.0012   19.4   2.8    3.0  2  PAP2_C       PAP2 superfamily C-terminal
  ------ inclusion threshold ------
      0.012   15.8   0.2        1.4    9.1   0.0    2.4  2  DUF212       Divergent PAP2 family
      0.098   12.8   0.1       0.32   11.2   0.1    1.9  1  COX6C        Cytochrome c oxidase subunit VIc
       0.16   11.8   0.2       0.34   10.8   0.2    1.5  1  Pam17        Mitochondrial import protein Pam17


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   2.4   9.2e-31   2.4e-27       3     132 ..     213     324 ..     211     328 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 9.2e-31
                          PAP2   3 lalllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkrkkig 83 
                                   ++l++al+la ++   lK+lv++pRP+ + ++  l  +  ++         +sfPSgH++ af+la+ l ++ +++ +   
  gi|15668550|ref|NP_247348.1| 213 MKLIFALFLAFMIAFSLKYLVNEPRPYLVLDNVHLLCNEGNE---------PSFPSGHTTLAFTLATSLLFYSKKLGIL-- 282
                                   89*******************************999996553.........6***************************.. PP

                          PAP2  84 lvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayrlvq 132
                                          +l +a+ va+sR+y+gvH++ DvlaG++iGi++++l+    +
  gi|15668550|ref|NP_247348.1| 283 -------FLSWAIIVAYSRVYVGVHYPLDVLAGMIIGIFCGCLTRIDIY 324
                                   .......9**********************************9876655 PP

>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.65   1.7e+03      59      80 ..      13      34 ..       4      40 .. 0.78
   2 !   66.4   6.7   1.2e-21   3.1e-18       1     119 [.      38     155 ..      38     156 .. 0.97
   3 ?   -2.4   0.2       2.5   6.4e+03      19      31 ..     215     227 ..     194     234 .. 0.54
   4 ?   -2.0   1.4       1.9   4.8e+03       6       6 ..     303     303 ..     264     321 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.65
                   SNARE_assoc 59 lerlverygflallllrllpiv 80
                                  +e lv++yg + ++++ ++  +
  gi|15668550|ref|NP_247348.1| 13 AEYLVNNYGYIGIFIISFTEAF 34
                                  7889999999999999998766 PP

  == domain 2  score: 66.4 bits;  conditional E-value: 1.2e-21
                   SNARE_assoc   1 lPsevllvaaGvlf.glllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygflallllrllpiv 80 
                                   +P +v+++ a++++ ++++  +v+ +g++lG++++y+lg +lg + +  kl+ ek++++ e+++++yg++ ++++ ++p +
  gi|15668550|ref|NP_247348.1|  38 IPPDVFIIGASFFGlNPIISAIVATIGTTLGGLFGYFLGDKLG-HPIFIKLFGEKYLHKGEEFFNKYGVYGVVIAGFSP-L 116
                                   789999999999999****************************.899999*****************************.7 PP

                   SNARE_assoc  81 PrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                   P+ +++ + G+++++   F+++t+iG +p+ l +ay+G+
  gi|15668550|ref|NP_247348.1| 117 PYKVIAWLSGIFEMHKLLFTVGTIIGRLPRFLAVAYFGD 155
                                   9*************************************8 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.5
                   SNARE_assoc  19 gtlvtslgallGa 31 
                                    +++++l+ +++ 
  gi|15668550|ref|NP_247348.1| 215 LIFALFLAFMIAF 227
                                   3334444444444 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.9
                   SNARE_assoc   6 l 6  
                                   l
  gi|15668550|ref|NP_247348.1| 303 L 303
                                   2 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   9.3   1.4e-15   3.6e-12      40     187 ..     193     315 ..     173     318 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.4e-15
                        PAP2_3  40 hfqvtllvlvllflrrrerlreflttlllatllgllvyalfPaagPrlleeagfvdtvaaaslagalrdgasravllrgti 120
                                    ++++ ++ +++f+++r+ + +++++l+la+++++ + +l+   +P+l+             l++        ++l +++ 
  gi|15668550|ref|NP_247348.1| 193 AYPLIAITSLIIFIKNRKFGMKLIFALFLAFMIAFSLKYLVNEPRPYLV-------------LDN-------VHLLCNEG- 252
                                   5677777888889*********************************999.............333.......33444444. PP

                        PAP2_3 121 englaafPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvDviaGvalalva 187
                                        +fPS H+++a+ +a  l  +++k   ++l+l ++++++++ v+ g HY +Dv+aG+++++ +
  gi|15668550|ref|NP_247348.1| 253 --NEPSFPSGHTTLAFTLATSLLFYSKKL--GILFLSWAIIVAYSRVYVGVHYPLDVLAGMIIGIFC 315
                                   ..5569***************88777777..*******************************99876 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   2.4      0.75   1.9e+03      29      66 ..     186     223 ..     165     232 .. 0.48
   2 !   19.4   2.8   4.5e-07    0.0012       8      69 ..     259     316 ..     257     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.75
                        PAP2_C  29 lailkvillllallglfliiasrkHYtvDVllglyitt 66 
                                   + i++ ++  l ++++++i ++   + +  +++l++++
  gi|15668550|ref|NP_247348.1| 186 MPIISKTAYPLIAITSLIIFIKNRKFGMKLIFALFLAF 223
                                   22444444455555555555555555555555555554 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 4.5e-07
                        PAP2_C   8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlvf 69 
                                   SGHt+  ++++  +l ys+k      ++ l +a++  ++ ++   HY +DVl g++i +++ 
  gi|15668550|ref|NP_247348.1| 259 SGHTTLAFTLATSLLFYSKKLG----ILFLSWAIIVAYSRVYVGVHYPLDVLAGMIIGIFCG 316
                                   9****************99985....8888889999999******************99875 PP

>> DUF212  Divergent PAP2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00053       1.4       5      62 ..     215     277 ..     211     297 .. 0.65
   2 ?    4.4   0.1     0.015        39     113     127 ..     300     314 ..     294     315 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00053
                        DUF212   5 vllaallawlvaqllKvliellkek..kldlkllvstGg...mPSsHsalvtalatavgleeg 62 
                                   +++a +la+++a  lK+l++  +      +++ll+++G    +PS H++l  +lat++ + + 
  gi|15668550|ref|NP_247348.1| 215 LIFALFLAFMIAFSLKYLVNEPRPYlvLDNVHLLCNEGNepsFPSGHTTLAFTLATSLLFYSK 277
                                   67778888888888888888544442223477888888444499************9987443 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.015
                        DUF212 113 HtpleVlvGallGii 127
                                   H pl+Vl+G+++Gi+
  gi|15668550|ref|NP_247348.1| 300 HYPLDVLAGMIIGIF 314
                                   9************97 PP

>> COX6C  Cytochrome c oxidase subunit VIc
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00012      0.32      16      41 ..     212     237 ..     206     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                         COX6C  16 krhlvvafvlslgvaaaykfavaepR 41 
                                     +l+ a+ l++++a+++k++v+epR
  gi|15668550|ref|NP_247348.1| 212 GMKLIFALFLAFMIAFSLKYLVNEPR 237
                                   56799********************9 PP

>> Pam17  Mitochondrial import protein Pam17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00013      0.34      63     117 ..      47     101 ..      21     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                         Pam17  63 qqilglDplvvlglatlas...galGwllGpvlgsavfkllnrkklkqleekekeFle 117
                                   + ++gl+p++ + +at+++   g +G+ lG  lg+ +f  l     +++ +k +eF++
  gi|15668550|ref|NP_247348.1|  47 ASFFGLNPIISAIVATIGTtlgGLFGYFLGDKLGHPIFIKL---FGEKYLHKGEEFFN 101
                                   6789****998888777652226789999999999998544...44455556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2237.48
//
Query:       gi|15668551|ref|NP_247349.1|  [L=254]
Description: hypothetical protein MJ_0375 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-38  130.6   3.8    6.5e-38  130.6   3.8    2.0  2  Cas_Cas6     CRISPR associated protein Cas6
  ------ inclusion threshold ------
      0.012   16.3   0.0      0.048   14.3   0.0    2.0  2  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6


Domain annotation for each model (and alignments):
>> Cas_Cas6  CRISPR associated protein Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.11   9.5e+02      85     111 ..      51      77 ..      20      95 .. 0.46
   2 !  130.6   3.8   7.3e-42   6.5e-38       1     144 [.      97     237 ..      97     239 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.11
                                   .SS---EEEEEEEEE.......TEEEEE CS
                      Cas_Cas6  85 keeklsikpdkkvkkivvkkk.etyirG 111
                                   k++ + ++  + ++k v+ k    +i G
  gi|15668551|ref|NP_247349.1|  51 KFKFFTFSLLQ-IRKRVIRKEgIETIDG 77 
                                   22222233333.5554444444222222 PP

  == domain 2  score: 130.6 bits;  conditional E-value: 7.3e-42
                                   HHHCS-EEEETTEEEEEEEEEE----S--TCEE.EEESS-BBEEEEEEETTCCEEEEE-TTSTTHHHHHHHHHHHHHHHHH CS
                      Cas_Cas6   1 gllknkeirlgnnefkveevellkepeitssevvfktlSPivvrstkkengkkktyylspddeeFsellkenlkkkykaly 81 
                                   gll+++++r+gn+ef v+++++l+ p+++    ++kt+SPi++++ +++++  kty+l p++++F+e+lk+nlkkky+a+y
  gi|15668551|ref|NP_247349.1|  97 GLLEDGKLRVGNVEFFVRKAKILPIPKKF---NILKTISPIYLKTMIETEDGLKTYDLLPNNSKFYENLKNNLKKKYEAFY 174
                                   699************************64...349*********9999********************************* PP

                                   SS..SS---EEEEE.EEEE......TEEEEEEEEEEEEEE-HHHHHHHHHC-SCS-CCCT-S-E CS
                      Cas_Cas6  82 geekeeklsikpdk.kvkkivvkkketyirGylgrfelegdpellklaydaGlGeknsqGFGmv 144
                                   +e+ + ++++++ k + k++ +k+ ++y r++++ f++ gd +l+k++y++G+Gekns+GFGmv
  gi|15668551|ref|NP_247349.1| 175 NEKCDMNFEFEVLKfRPKRMRIKN-DIYCRCSEMVFKVWGDYDLIKFGYECGFGEKNSMGFGMV 237
                                   ***888888888886666655444.89************************************8 PP

>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.4   3.6e+03      26      40 ..      31      55 ..      20     121 .. 0.54
   2 ?   14.3   0.0   5.4e-06     0.048       2      86 .]     129     237 ..     128     237 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.4
                                  HHHHHHHHTSS.............E CS
                   CRISPR_Cas6 26 llrrwnalaglkgk..........p 40
                                  +++++++ +++++k           
  gi|15668551|ref|NP_247349.1| 31 IYNKIHSANPAYAKrlhnyqkfkfF 55
                                  5555555555554433333333330 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5.4e-06
                                   EEEEEE-EE.........TEEESS--HHHHHHH....HHHHHHHHTSS...............EECHHHHH.HEEEEEEEE CS
                   CRISPR_Cas6   2 rfltPtrfk.........krkgllpsprlvfss....llrrwnalaglkgk............ptveeele.gGfvGevky 56 
                                   + ++P ++k         k++ llp+ + +  +    l +++ a+ ++k++            ++++++ +    + e+ +
  gi|15668551|ref|NP_247349.1| 129 KTISPIYLKtmietedglKTYDLLPNNSKFYENlknnLKKKYEAFYNEKCDmnfefevlkfrpKRMRIKNDiYCRCSEMVF 209
                                   567777777777777777777777777777766333345556666666655555555544443222222222255566666 PP

                                   --HHHECCC...HHHHHHHH-SSSTGGGTTT-E CS
                   CRISPR_Cas6  57 sgeleelek...llrfaeylgvGkktafGlGkv 86 
                                        ++++   l++f+  +g G k ++G+G+v
  gi|15668551|ref|NP_247349.1| 210 -----KVWGdydLIKFGYECGFGEKNSMGFGMV 237
                                   .....6666778*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1642.25
//
Query:       gi|15668552|ref|NP_247350.1|  [L=728]
Description: hypothetical protein MJ_0376 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-07   31.1   0.0    7.4e-07   29.1   0.0    2.1  2  DEAD        DEAD/DEAH box helicase
    1.3e-06   28.5   4.1    2.8e-06   27.4   0.0    2.9  3  ResIII      Type III restriction enzyme, res subunit
     0.0001   22.6   0.1    0.00043   20.6   0.1    2.1  1  Helicase_C  Helicase conserved C-terminal domain
     0.0003   20.3   0.0     0.0019   17.7   0.0    2.1  2  PhoH        PhoH-like protein
     0.0019   18.4   0.1      0.036   14.3   0.0    2.7  2  AAA_22      AAA domain
  ------ inclusion threshold ------
       0.03   14.5   0.2       0.11   12.8   0.2    2.0  1  HD          HD domain
       0.06   13.5   0.3       0.14   12.3   0.3    1.6  1  CDC24_OB1   Cell division control protein 24, OB domain 1
      0.084   13.0   0.0       0.14   12.3   0.0    1.3  1  HD_6        HD domain
      0.095   13.0   0.0        0.2   12.0   0.0    1.6  1  AAA_19      AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   3.7e-10   7.4e-07      13     171 ..     218     389 ..     208     394 .. 0.71
   2 ?   -3.2   0.0       3.1   6.1e+03      56      76 ..     568     588 ..     568     595 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.7e-10
                                   TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT...........TSTSEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxx RF
                          DEAD  13 gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk...........yidlrvllii 82 
                                   +++ v++ a+ G GKT+ +l+ +l+++   k+ +++k+++  Pt+   + ++++l k++            +i+lr +  i
  gi|15668552|ref|NP_247350.1| 218 KNKFVMLFAPCGRGKTEGALLWALNAL---KNFKRNKIILAMPTQVTSNAMYDRLVKIFGeenvglfhgksFIKLRDSKEI 295
                                   45779999******************9...78***********************99999454444333222335554444 PP

                                   TTSSHHHHHHHHH....TT....CSEEEEEHHHHHHHH....HCTSSHCTTE..EEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                   xxxxxxxxxxxxx....xx....xxxxxxxxxxxxxxx....xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  83 ggvaardqlskld....ng....vdivvgtpgrlddll....stgklnlsqv..rflVlDEadrlldqgfsdfinrilnql 149
                                   +    +d+l++++    +g      i+++t + ++  +    s+  + l ++  +++++DE++ + +    +++ +++  l
  gi|15668552|ref|NP_247350.1| 296 E---DEDDLEEIRdenfKGnvffKPITITTIDHVIYSFvhgfSQADFALGNIqnSVIIFDEVHYYEKY-TLEHLLTLFDIL 372
                                   4...4555555532223336788899999999988855599988889998886689*********998.444444444444 PP

                                   HHHCTTSTTTSEEEEEESSBS.H CS
                                   xxxxxxxxxxxxxxxxxxxxx.x RF
                          DEAD 150 pqitcdgklqrqvivlSATlp.k 171
                                   +    d +     +++S Tlp +
  gi|15668552|ref|NP_247350.1| 373 R--RMDIP----HLLMSGTLPnF 389
                                   2..22445....89999999855 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.1
                                   SHHHHHHHHHHHHHHTTTSTS CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  56 treLaeqtlnnlkkfkkyidl 76 
                                   ++eL+e+t+n++k + k++d+
  gi|15668552|ref|NP_247350.1| 568 SKELIEKTINHIKFYEKPLDY 588
                                   5899*****999988887765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3      0.19   3.8e+02      56      93 ..      49      88 ..      39     134 .. 0.78
   2 !   27.4   0.0   1.4e-09   2.8e-06      17     153 ..     212     365 ..     183     387 .. 0.68
   3 ?   -2.8   0.1       2.8   5.6e+03      96     112 ..     487     510 ..     433     519 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.19
                                  -EEEEESSHHHHHHHHHHGGGGTGG......GEEEESSS- CS
                        ResIII 56 kflflvprkslleqtleefkkflseayke..igkkvsgdk 93
                                   f +l + ++l++ ++ +++++++ ++    i++++++ k
  gi|15668552|ref|NP_247350.1| 49 VFAILSHHTQLYNNLYADYQQYKKGTFLIeeIKEFIKNSK 88
                                  5778999999*********999999986555444444443 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.4e-09
                                   ......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG...............GE CS
                        ResIII  17 eklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke...........ig 86 
                                   ++l + ++k +++ +++G GKT  a+  + + lk++k++k+++  p++   + +++++ k++ e++              +
  gi|15668552|ref|NP_247350.1| 212 KELYNSKNKFVMLFAPCGRGKTEGALLWALNALKNFKRNKIILAMPTQVTSNAMYDRLVKIFGEENVGlfhgksfiklrDS 292
                                   444447888889********************************9999666666666655555443334433333334433 PP

                                   EEESSS-B--..........-SEEEEEHHHHHHTH..............HHHTTT-SEEEEETGGGTTS.TTTHHH CS
                        ResIII  87 kkvsgdkkka...kekdstnkkilvttiqsldadseee......eeeseellrdrfdviiiDEaHrlgakkswrei 153
                                   k+++++ + +    e+++ n  +  +ti ++d  +         ++++  l++ ++ vii+DE+H + +  + +++
  gi|15668552|ref|NP_247350.1| 293 KEIEDEDDLEeirDENFKGNVFFKPITITTIDHVI--YsfvhgfSQADFALGNIQNSVIIFDEVHYYEK-YTLEHL 365
                                   33443333335554444444443334444444444..12355568888888888888********9988.555555 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.8
                                   -..............-SEEEEEHH CS
                        ResIII  96 a.......kekdstnkkilvttiq 112
                                   +       ++++s+nk ++++ +q
  gi|15668552|ref|NP_247350.1| 487 EdeiftleEMRKSQNKPYVIVATQ 510
                                   122234555555566666555555 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   2.1e-07   0.00043       6     111 .]     435     544 ..     430     544 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                                   HHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTT......STHHHHHHHHHHHHTTSSS..EEEESGGGT CS
                    Helicase_C   6 llellkleeeggkilifvntidrlek.vklllekkgikvavlhge......lpqnereeileqfnkgesd..vLiatdvae 77 
                                   + e++++ ++g    i++nt++r+ +  k +  + ++ ++ +h++       ++++ + +le+++k + +  v++at+v+e
  gi|15668552|ref|NP_247350.1| 435 INEIIENYKKGLSQAIILNTVERAREfYKAV--RDKVPAILYHSQfaykdrVKKEDEIFTLEEMRKSQNKpyVIVATQVIE 513
                                   4455567777777789999999996333444..45899999999955555566666668899998544444799******* PP

                                   SSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                    Helicase_C  78 rGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                    ++d+ +v+++     p  ++ + qr+GR +R g
  gi|15668552|ref|NP_247350.1| 514 ISLDM-SVDVMYSELSP--PDALGQRAGRLHRKG 544
                                   *****.47766554444..899**********75 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   9.3e-07    0.0019      18      58 ..     218     258 ..     205     284 .. 0.89
   2 ?   -0.6   0.0      0.38   7.6e+02     118     141 ..     344     367 ..     342     375 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.3e-07
                                   H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S CS
                          PhoH  18 kndivfaiGpaGtGKtylavalavealkkkkvkriiltrpa 58 
                                   kn++v+ ++p G GKt  a+  a++alk+ k ++iil+ p+
  gi|15668552|ref|NP_247350.1| 218 KNKFVMLFAPCGRGKTEGALLWALNALKNFKRNKIILAMPT 258
                                   899**********************************9997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.38
                                   B-SEEEEE-SGGG--HHHHHHHHT CS
                          PhoH 118 lndafvilDEAQnttkeqmkmflt 141
                                   ++++++i+DE    +k +++ +lt
  gi|15668552|ref|NP_247350.1| 344 IQNSVIIFDEVHYYEKYTLEHLLT 367
                                   689*******99999988888887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.6   3.2e+03      77     112 ..      58      94 ..      53     107 .. 0.77
   2 !   14.3   0.0   1.8e-05     0.036       4     128 ..     218     382 ..     214     386 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.6
                        AAA_22  77 ellealeqalraravielliiDEaqhlr..seealeeL 112
                                   +l++ l+   +++++ + ++i+E+  ++  s+ea+e L
  gi|15668552|ref|NP_247350.1|  58 QLYNNLYADYQQYKK-GTFLIEEIKEFIknSKEAYESL 94 
                                   677888888888889.9999999999776778888877 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.8e-05
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.............. 70 
                                   + ++++++++ G GKT  +   + ++      ++ ++  +   +p + +s  ++ +l++++g+e+ +              
  gi|15668552|ref|NP_247350.1| 218 KNKFVMLFAPCGRGKTEGALLWALNAL-----KNFKRNKIILAMPTQVTSNAMYDRLVKIFGEENVGlfhgksfiklrdsk 293
                                   568899999999999988877777763.....3335555555555555699999999999999999999999999999999 PP

                        AAA_22  71 .........................erlsseell.ealeqalrarav.....ielliiDEaqhlrseealeeLrsllnl.s 119
                                                               + ++++ + ++  ++a ++      +++i DE+++  ++  le+L +l+++ +
  gi|15668552|ref|NP_247350.1| 294 eiededdleeirdenfkgnvffkpiTITTIDHVIySFVHGFSQADFAlgniqNSVIIFDEVHYY-EKYTLEHLLTLFDIlR 373
                                   99999999999999999999998774455555553444444444444888888***********.9999999999999998 PP

                        AAA_22 120 rkgvqliLv 128
                                   r +++++L+
  gi|15668552|ref|NP_247350.1| 374 RMDIPHLLM 382
                                   999998885 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   5.3e-05      0.11      34      93 ..       1      61 [.       1      96 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.3e-05
                                  HTTTTHHHHTS..HHH.HHH.CTCCHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHTTCCHHH CS
                            HD 34 lHDiGkgpfgdafekk.eee.fekflaHekvgaeilrevekrlgld.ledvaklirehheswe 93
                                  +HDiGk+++g ++ ++ +   +   + H  ++  i++++e +  +d   +v ++ ++h+   +
  gi|15668552|ref|NP_247350.1|  1 MHDIGKITEG-FQNNIkK-GkRSNKHPHPLYALPIIKNIEFDYLFDiPIEVFAILSHHTQLYN 61
                                  6*******88.6666643.45778899****************88884447777777765554 PP

>> CDC24_OB1  Cell division control protein 24, OB domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   7.1e-05      0.14      42     113 ..     437     513 ..     414     518 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                     CDC24_OB1  42 klleeYssGvTeaIllseLeqaweeqsregaskkree........kkerrkklkntvtidsiyekkflsldsvleaviid 113
                                   +++e+Y +G+++aI+l+  e+a+e ++   ++ k +          k+r kk ++  t++++ ++++ ++ +++ + +i+
  gi|15668552|ref|NP_247350.1| 437 EIIENYKKGLSQAIILNTVERAREFYK--AVRDKVPAilyhsqfaYKDRVKKEDEIFTLEEMRKSQNKPY-VIVATQVIE 513
                                   58999*****************44332..23333233567788999999999999999999999988777.455555555 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.9e-05      0.14      60      80 ..       1      21 [.       1     103 [. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.9e-05
                                  CCCGGGSSHHHHTTS----TT CS
                          HD_6 60 lHDlGKaspaFqakvpelaek 80
                                  +HD+GK++++Fq++ ++  ++
  gi|15668552|ref|NP_247350.1|  1 MHDIGKITEGFQNNIKKGKRS 21
                                  6*************9665443 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001       0.2       7      82 ..     216     291 ..     211     404 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                        AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae..atTiHrlalldfdd 82 
                                   ++k+k +++ a+ G GKT+   + +  l++l++ k ++i+l+ +t+   + + +rl ++ +e     +H+ +++++ d
  gi|15668552|ref|NP_247350.1| 216 NSKNKFVMLFAPCGRGKTEG--ALLWALNALKNFKRNKIILAMPTQVTSNAMYDRLVKIFGEenVGLFHGKSFIKLRD 291
                                   7899**************95..3344444445555689******************8888776744455544422222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (728 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 5397.33
//
Query:       gi|15668553|ref|NP_247351.1|  [L=170]
Description: hypothetical protein MJ_0377 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-54  185.0   7.3    1.2e-54  184.8   7.3    1.0  1  Cas_Cas4     Domain of unknown function DUF83
    0.00023   21.2   1.5    0.00034   20.6   1.3    1.3  1  PDDEXK_1     PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
       0.45   10.8   6.2       0.32   11.3   3.0    2.1  2  Tox-REase-9  Restriction endonuclease fold toxin 9


Domain annotation for each model (and alignments):
>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.8   7.3     2e-58   1.2e-54       2     162 .]      13     170 .]      12     170 .] 0.99

  Alignments for each domain:
  == domain 1  score: 184.8 bits;  conditional E-value: 2e-58
                      Cas_Cas4   2 gtkiqyyliCkrklwlisheitleensetvelGkllheesyerekkevelsesikiDvvekekeklvvvEvKkskkkeeaa 82 
                                   g++i+y+++Ck+klw++ ++it+e++s+ v+lGk+lhe+sy  e+kev++ +sikiD+++ +++ ++++EvK++k++e+a+
  gi|15668553|ref|NP_247351.1|  13 GIEINYLYVCKTKLWYFVRGITMEQESDFVDLGKFLHEKSYFGEEKEVQI-GSIKIDFIK-KRDVIEIHEVKRGKQMEKAH 91 
                                   899***********************************************.*********.999***************** PP

                      Cas_Cas4  83 klQllyYlllLekkgveikeGvleypkekkreevelteelreelekaikeieeiissekppkvkkkkiCkkCayaelCli 162
                                    +Q+lyY+++L++ g++ k ++l+ypk k+ +e+el+e+++ee+++aikeie i s ++pp++ ++kiCk+Cay+elC+i
  gi|15668553|ref|NP_247351.1|  92 IMQVLYYIYYLNSLGIKSK-AILHYPKLKEIKEIELKENNKEEIKRAIKEIEYIKSLKEPPEPIYQKICKNCAYYELCFI 170
                                   *******************.**********************************************************96 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.3   5.7e-08   0.00034     133     254 ..      66     168 ..      31     169 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.7e-08
                      PDDEXK_1 133 riDrvddkegelriiDyKtgsappkskelaelkegl.QlllYllalaegeelkeegepagalylrleepkvkdeevvkkma 212
                                   +iD + +++  ++i + K g+   + ++      ++ Q+l Y ++l           +++a++         + +++k+++
  gi|15668553|ref|NP_247351.1|  66 KIDFIKKRDV-IEIHEVKRGK---QMEK-----AHImQVLYYIYYLNSLGI------KSKAILHYP------KLKEIKEIE 125
                                   5899988888.*******999...5565.....4555**********9933......444444444......446666666 PP

                      PDDEXK_1 213 lteeeleallqeleel..aeeilagefparpskk..CeyCpyksvC 254
                                   l+e++ e++++ ++e+  +++++    p++p  +  C++C+y ++C
  gi|15668553|ref|NP_247351.1| 126 LKENNKEEIKRAIKEIeyIKSLK---EPPEPIYQkiCKNCAYYELC 168
                                   66777777777777764345555...6666665557*********9 PP

>> Tox-REase-9  Restriction endonuclease fold toxin 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       0.1   6.2e+02      24      45 ..      54      74 ..      41      83 .. 0.67
   2 ?   11.3   3.0   5.3e-05      0.32       6      71 ..      81     146 ..      76     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.1
                   Tox-REase-9 24 vgrekEfklpsgkRiDfvdfet 45
                                   g+ekE++  s ++iDf+   +
  gi|15668553|ref|NP_247351.1| 54 FGEEKEVQIGS-IKIDFIKKRD 74
                                  67889988766.6799987554 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.3e-05
                   Tox-REase-9   6 lklGrqmHkdykaekvlgvgrekEfklpsgkRiDfvdfetkiiyELKPnnpraikrGlkqlevYkq 71 
                                   +k G+qm k++ ++  + + + +     s+    +  +++   +ELK nn+++ikr +k++e  k+
  gi|15668553|ref|NP_247351.1|  81 VKRGKQMEKAHIMQVLYYIYYLNSLGIKSKAILHYPKLKEIKEIELKENNKEEIKRAIKEIEYIKS 146
                                   68899999999888888888888888888888888888887778****************985544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1070.56
//
Query:       gi|15668554|ref|NP_247352.1|  [L=322]
Description: hypothetical protein MJ_0378 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-83  279.7   0.6    2.6e-83  279.4   0.6    1.1  1  Cas_Cas1  CRISPR associated protein Cas1
  ------ inclusion threshold ------
       0.16   12.3   2.9       0.35   11.2   0.1    2.7  3  DUF5603   Domain of unknown function (DUF5603)


Domain annotation for each model (and alignments):
>> Cas_Cas1  CRISPR associated protein Cas1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.4   0.6   2.9e-87   2.6e-83       6     283 .]      11     277 ..       6     277 .. 0.96

  Alignments for each domain:
  == domain 1  score: 279.4 bits;  conditional E-value: 2.9e-87
                                   TEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEESTEEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEE.SSSSTHHHHH CS
                      Cas_Cas1   6 qgaylrkkgerlvvekegeekkeiplediesivifgevslstkalrllaekgipvvflsengkylgrlep.eesgnvelrr 85 
                                   +g yl +k++++++e+ +  kk + +e i +i+i+g+vs+s++al++la+kgi+++f++++g+y g+++p e+  ++ l +
  gi|15668554|ref|NP_247352.1|  11 DG-YLFRKENTIYFENARG-KKPLAIEGIYDIYIYGKVSISSQALHYLAQKGIALHFFNHYGYYDGSFYPrESLHSGYLVV 89 
                                   44.699**********988.9*************************************************9999******* PP

                                   HHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHHHHHHHHHHHHHHH CS
                      Cas_Cas1  86 aQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrgiEGeaakaYfeaf 166
                                   +Q++++ d++krlelak ++ g ++n++++l ++k+++   ++++ iee       l+++++++e++++EG+++ +Y++ +
  gi|15668554|ref|NP_247352.1|  90 NQVEHYLDKDKRLELAKLFIIGGIKNMEWNLLKFKNKT---KFSSYIEE-------LNNCNKITEVMNVEGRVRTEYYRLW 160
                                   ************************************99...55555555.......667********************** PP

                                   HHHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHHHHHHHHHHHCHHHHH CS
                      Cas_Cas1 167 dkllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalDLmEefRpllvDrlvl 247
                                   d+ l+++f++ +R+rrppk+++Nal+sf+++ ly  +++++++++L P++++LHe++++r+sLalDL E+f+p+++Drl+ 
  gi|15668554|ref|NP_247352.1| 161 DETLPDDFKIVKRTRRPPKNEMNALISFLNSRLYPAIITELYNTQLTPTVSYLHEPHERRFSLALDLSEIFKPMIADRLAN 241
                                   ********************************************************************************* PP

                                   HHHHTTSS-GGGEEEETTEEEE-HHHHHHHHHHHHH CS
                      Cas_Cas1 248 slinkrqlkekdFekeengvlLteegrkkfleafee 283
                                   +l++++++++k+F  + ngvlL++eg+k +le+f++
  gi|15668554|ref|NP_247352.1| 242 RLVKQGIIQKKHFRDDLNGVLLNKEGMKVVLEHFNK 277
                                   *********************************985 PP

>> DUF5603  Domain of unknown function (DUF5603)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.54   4.9e+03      73      87 ..      32      46 ..      28      65 .. 0.72
   2 ?   11.2   0.1   3.9e-05      0.35      55      93 ..     128     166 ..      92     170 .. 0.87
   3 ?    0.0   0.2      0.12   1.1e+03       8      33 ..     256     279 ..     251     314 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.54
                                  HHHTTSSEEEEESSH CS
                       DUF5603 73 lslegkielvyygek 87
                                  l++eg +++  yg+ 
  gi|15668554|ref|NP_247352.1| 32 LAIEGIYDIYIYGKV 46
                                  788999999889864 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.9e-05
                                   EE--SHHHHHHHHHHHHHHHHTTSSEEEEESSHHHHHHH CS
                       DUF5603  55 kiygsleeqkkvskvldklslegkielvyygekeealrd 93 
                                   k    +ee     k+ + +++eg++   yy + +e+l d
  gi|15668554|ref|NP_247352.1| 128 KFSSYIEELNNCNKITEVMNVEGRVRTEYYRLWDETLPD 166
                                   5566799*************************9998866 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.12
                                   S-HHHHHHHHHHTT---EE-TTHHHH CS
                       DUF5603   8 gdlnklleelkkeglrveedkekeek 33 
                                    dln +l  l keg++v+ ++ ++e+
  gi|15668554|ref|NP_247352.1| 256 DDLNGVL--LNKEGMKVVLEHFNKEM 279
                                   5666666..77899987644333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1017  (0.0567237); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2015.58
//
Query:       gi|15668555|ref|NP_247353.1|  [L=208]
Description: hypothetical protein MJ_0379 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-11   42.0   0.3    8.6e-11   41.2   0.3    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    2.8e-09   36.8   0.3    4.8e-09   36.0   0.3    1.3  1  MarR             MarR family
    2.7e-08   33.6   0.9    2.7e-08   33.6   0.9    1.8  1  TrmB             Sugar-specific transcriptional regulator Trm
    1.5e-07   31.2   1.2    1.5e-07   31.2   1.2    1.7  2  HTH_5            Bacterial regulatory protein, arsR family
    1.1e-05   25.7   0.6    2.5e-05   24.6   0.6    1.6  1  Penicillinase_R  Penicillinase repressor
    2.9e-05   24.5   0.8    4.5e-05   23.9   0.2    1.6  1  HTH_27           Winged helix DNA-binding domain
    2.9e-05   23.8   0.0    4.4e-05   23.2   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
    3.1e-05   23.8   0.4      7e-05   22.7   0.4    1.5  1  HTH_11           HTH domain
    0.00017   21.4   0.0    0.00025   20.9   0.0    1.2  1  MarR_2           MarR family
    0.00025   20.8   0.6    0.00084   19.2   0.6    1.8  1  RuvB_C           RuvB C-terminal winged helix domain
    0.00032   20.8   0.5    0.00068   19.8   0.5    1.5  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    0.00071   19.6   0.4     0.0012   18.8   0.4    1.3  1  FeoC             FeoC like transcriptional regulator
    0.00078   19.4   0.9     0.0013   18.7   0.9    1.4  1  HTH_Mga          M protein trans-acting positive regulator (M
    0.00092   19.2   0.0     0.0014   18.7   0.0    1.2  1  HTH_20           Helix-turn-helix domain
     0.0011   19.0   1.1     0.0026   17.8   0.7    1.8  1  DUF2250          Uncharacterized protein conserved in archaea
     0.0018   18.3   0.0      0.003   17.6   0.0    1.3  1  HTH_29           Winged helix-turn helix
     0.0022   17.5   0.1      0.015   14.8   0.1    2.1  1  Sigma70_r4       Sigma-70, region 4
     0.0022   17.9   0.4     0.0062   16.5   0.1    1.9  2  HTH_36           Helix-turn-helix domain
     0.0026   17.5   0.0     0.0045   16.7   0.0    1.4  1  HTH_38           Helix-turn-helix domain
     0.0077   16.6   0.2      0.016   15.5   0.2    1.5  1  Rrf2             Transcriptional regulator
  ------ inclusion threshold ------
      0.016   15.3   0.6       0.94    9.6   0.2    2.4  2  FUR              Ferric uptake regulator family
       0.02   14.9   0.5       0.02   14.9   0.5    2.2  2  HTH_45           Winged helix-turn-helix
      0.021   14.5   0.1      0.036   13.8   0.1    1.3  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.024   15.1   0.1      0.047   14.2   0.1    1.5  1  HTH_40           Helix-turn-helix domain
      0.029   14.2   0.0      0.047   13.5   0.0    1.3  1  HTH_23           Homeodomain-like domain
      0.058   13.2   0.0      0.084   12.7   0.0    1.3  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.061   12.9   0.0       0.11   12.1   0.0    1.3  1  HTH_47           winged helix-turn-helix
      0.093   12.3   0.8       0.27   10.8   0.8    1.8  1  GerE             Bacterial regulatory proteins, luxR family
      0.095   12.9   1.7       0.15   12.3   0.2    2.0  2  Sun2_CC2         SUN2 coiled coil domain 2
       0.12   12.6   1.1       0.21   11.8   0.3    1.8  1  HTH_34           Winged helix DNA-binding domain
       0.14   12.1   0.1       0.28   11.1   0.1    1.5  1  HTH_Tnp_Tc3_1    Tc3 transposase
       0.14   12.1   1.1       0.51   10.3   1.1    1.9  1  HTH_12           Ribonuclease R winged-helix domain
       0.15   12.2   0.0       0.23   11.6   0.0    1.3  1  HTH_28           Helix-turn-helix domain
       0.17   11.9   0.1       0.33   10.9   0.1    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.3   1.6e-13   8.6e-11       2      48 .]     148     194 ..     147     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.6e-13
                        HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                    e++ kIL+lL k++ +s + +A +l  S+st+++++ +Le++Gl+k
  gi|15668555|ref|NP_247353.1| 148 TELEMKILNLLDKEGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVK 194
                                   68899****************************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.3   9.1e-12   4.8e-09       1      50 [.     147     196 ..     147     200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 9.1e-12
                                   --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR   1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                   lt+ +++iL +l+ +g++svs +a kl+ s st+++ + +LekkGl+++ 
  gi|15668555|ref|NP_247353.1| 147 LTELEMKILNLLDKEGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVKKL 196
                                   7999*******************************************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.9   5.1e-11   2.7e-08       6      60 ..     147     202 ..     144     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 5.1e-11
                                   HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTT CS
                          TrmB   6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpk 60 
                                   L+e E+k+   L k+g+++++ ia++l+++ s++ e++++Le+kGlV++   gr+k
  gi|15668555|ref|NP_247353.1| 147 LTELEMKILNLLDKEGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVKKLSkGRRK 202
                                   99******99888***********************************97624444 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   1.2   2.8e-10   1.5e-07       6      47 .]     153     195 ..     150     195 .. 0.97
   2 ?   -2.0   0.0       6.6   3.5e+03       2      10 ..     198     206 ..     197     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.8e-10
                                   HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5   6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                   kIL+lL + ge++v+ +a +l+ s st+S++ ++L++ GLV+k
  gi|15668555|ref|NP_247353.1| 153 KILNLLDKeGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVKK 195
                                   8****************************************87 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.6
                                   HHHHHHHHH CS
                         HTH_5   2 ptRlkILkl 10 
                                   ++R+kI+k 
  gi|15668555|ref|NP_247353.1| 198 KGRRKIVKK 206
                                   78****985 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.6   4.8e-08   2.5e-05       1      59 [.     147     201 ..     147     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.8e-08
                                   ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTE CS
               Penicillinase_R   1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegra 59 
                                   l+elE +++++l ++ge++v+++  +le+      sT+   +++L+kKgl+++  +gr+
  gi|15668555|ref|NP_247353.1| 147 LTELEMKILNLLDKEGEMSVSNIAHKLERS----LSTISEYVSQLEKKGLVKKLSKGRR 201
                                   79**************************99....99******************99997 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.2   8.6e-08   4.5e-05       1      60 [.     147     202 ..     147     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 8.6e-08
                        HTH_27   1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrek 60 
                                   lt+++  +L+l+   +++++ + ++ +l ++ s+is+ +++L++kGLv++  ++  +r+k
  gi|15668555|ref|NP_247353.1| 147 LTELEMKILNLLD-KEGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVKKL-SK--GRRK 202
                                   6889999******.**********************************443.33..4554 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   8.4e-08   4.4e-05       7      50 ..     153     195 ..     152     197 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8.4e-08
                                   HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                    iL++l ++++ +++s +A+++  + St + +++ L++ G+v++
  gi|15668555|ref|NP_247353.1| 153 KILNLLDKEGE-MSVSNIAHKLERSLSTISEYVSQLEKKGLVKK 195
                                   79999999999.9*****************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.4   1.3e-07     7e-05       3      43 ..     152     191 ..     151     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.3e-07
                        HTH_11   3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                    +il lL +++g +s + +A +L++S +t+  ++ +Le++g
  gi|15668555|ref|NP_247353.1| 152 MKILNLL-DKEGEMSVSNIAHKLERSLSTISEYVSQLEKKG 191
                                   5899999.99999***************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   4.7e-07   0.00025       7      54 ..     151     196 ..     146     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.7e-07
                                   HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2   7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                   +  +L+ L  +++  ++v+ +a +l  s s++s  +  L+++GLv + 
  gi|15668555|ref|NP_247353.1| 151 EMKILNLLDKEGE--MSVSNIAHKLERSLSTISEYVSQLEKKGLVKKL 196
                                   6778888988888..******************************875 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.6   1.6e-06   0.00084       4      62 ..     147     201 ..     146     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.6e-06
                                   --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEEE CS
                        RuvB_C   4 LdeldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrGRi 62 
                                   L+el++k+L+ll    k+g+++++++a+ l+ + +ti++ +   L k+gl+++ s+GR+
  gi|15668555|ref|NP_247353.1| 147 LTELEMKILNLLD---KEGEMSVSNIAHKLERSLSTISEYV-SQLEKKGLVKKLSKGRR 201
                                   899*********9...89********************777.689************75 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.5   1.3e-06   0.00068      13      53 ..     154     194 ..     150     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.3e-06
                                   HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress  13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53 
                                   I+ l ++++  +++++a  L+ s s++se ++ Lek+G+v+
  gi|15668555|ref|NP_247353.1| 154 ILNLLDKEGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVK 194
                                   78899999999*****************************7 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.4   2.3e-06    0.0012       7      50 ..     156     199 ..     150     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.3e-06
                          FeoC   7 eyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50 
                                   ++l+++g+ s+++++++++ s +++   + q+++kG v+k+ ++
  gi|15668555|ref|NP_247353.1| 156 NLLDKEGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVKKLSKG 199
                                   5789************************************9875 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.9   2.5e-06    0.0013       6      45 ..     150     188 ..     146     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.5e-06
                       HTH_Mga   6 rklkLlelLteneksltldelakeLglseltlqsdiseLn 45 
                                    + k+l+lL + e++++++ +a++L  s +t+ +++s+L 
  gi|15668555|ref|NP_247353.1| 150 LEMKILNLLDK-EGEMSVSNIAHKLERSLSTISEYVSQLE 188
                                   5889****999.**************************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.6e-06    0.0014      13      55 ..     152     194 ..     148     200 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.6e-06
                                   HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20  13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55 
                                   ++il +L  ++++++s +a+ l+ s +t+s  + +Le+ gLv+
  gi|15668555|ref|NP_247353.1| 152 MKILNLLDKEGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVK 194
                                   799**************************************98 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.7   4.9e-06    0.0026       5      57 ..     146     198 ..     143     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.9e-06
                       DUF2250   5 eedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerveg 57 
                                   + +el++k+l+ l+k +     +ia++le +l+ ++e++ +Le+ GL+++ ++
  gi|15668555|ref|NP_247353.1| 146 KLTELEMKILNLLDKEGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVKKLSK 198
                                   5678899********999999***************************99763 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.6e-06     0.003       9      51 ..     160     199 ..     153     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.6e-06
                        HTH_29   9 aeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsg 51 
                                   +eG+++vs+iA+ l  s +t+  ++   e++Gl + l ++  g
  gi|15668555|ref|NP_247353.1| 160 KEGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVKKL-SK--G 199
                                   577789**************************64422.33..2 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   2.8e-05     0.015       4      47 ..     146     194 ..     146     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-05
                                   HS-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHH....HHHHHHHHHHH CS
                    Sigma70_r4   4 sLpererevlelrf.geglTleEIgerlgiSrer....VrqiekrAlrk 47 
                                   +L+e e ++l l   + +++ + I+ +l  S+++    V+q+ek++l k
  gi|15668555|ref|NP_247353.1| 146 KLTELEMKILNLLDkEGEMSVSNIAHKLERSLSTiseyVSQLEKKGLVK 194
                                   69*****************************987333367999998865 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       9.1   4.8e+03      38      47 ..      47      56 ..      44      57 .. 0.83
   2 !   16.5   0.1   1.2e-05    0.0062      19      55 .]     159     193 ..     150     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 9.1
                        HTH_36 38 sknTvsraik 47
                                  ++nTv ++++
  gi|15668555|ref|NP_247353.1| 47 DENTVNSIKN 56
                                  789**99987 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.2e-05
                        HTH_36  19 nknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55 
                                   +k+g+   s++ +a++l+ s +T+s ++  Le++G++
  gi|15668555|ref|NP_247353.1| 159 DKEGE--MSVSNIAHKLERSLSTISEYVSQLEKKGLV 193
                                   46666..69**************************85 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.6e-06    0.0045      12      38 ..     153     181 ..     146     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.6e-06
                        HTH_38  12 eIerll.aeG.lslreIArrLgrspsTIs 38 
                                   +I  ll +eG +s++ IA +L rs sTIs
  gi|15668555|ref|NP_247353.1| 153 KILNLLdKEGeMSVSNIAHKLERSLSTIS 181
                                   5777875799******************8 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   3.1e-05     0.016      16      56 ..     154     194 ..     147     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-05
                                   HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2  16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56 
                                   +L + ++e+ +s+++ia++ + s s ++  +++L+k+glvk
  gi|15668555|ref|NP_247353.1| 154 ILNLLDKEGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVK 194
                                   45555666679*****************************8 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.14        74      74     100 ..      11      36 ..       3      42 .. 0.78
   2 ?    9.6   0.2    0.0018      0.94       4      64 ..     145     199 ..     143     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.14
                                   SSSSEEEEEETTT--EEEE--HHHHHH CS
                           FUR  74 kkehhdhlicekCgkviefkddeieki 100
                                    + h +h+ +++ gk+i ++d++i ++
  gi|15668555|ref|NP_247353.1|  11 FGYHTNHIFDKN-GKIIGIDDEKISNM 36 
                                   466777888877.**********9875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0018
                                   HCHHHHHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET CS
                           FUR   4 lklTkqRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefe 64 
                                   +klT+  +kil++l k+ e +s+ ++ ++l++     sl+T+   + +le+ glvk+l+  
  gi|15668555|ref|NP_247353.1| 145 IKLTELEMKILNLLDKEGE-MSVSNIAHKLER-----SLSTISEYVSQLEKKGLVKKLSKG 199
                                   7999999999999999887.899999999876.....8999999************99865 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.6   1.9e+03      27      40 ..      80      93 ..      79      97 .. 0.90
   2 ?   14.9   0.5   3.7e-05      0.02       8      56 ..     151     201 ..     147     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.6
                        HTH_45 27 ykanLsykllnkYL 40
                                  y+ n + k+++kY+
  gi|15668555|ref|NP_247353.1| 80 YEFNTNVKNFRKYI 93
                                  7889999******8 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.7e-05
                        HTH_45   8 iadILeais.egeakkTkimykanLsykllnkYLdmLvekglikk.skekY 56 
                                    + IL+ ++ ege + ++i  k + s +++++Y+++L +kgl+kk sk+  
  gi|15668555|ref|NP_247353.1| 151 EMKILNLLDkEGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVKKlSKGRR 201
                                   57899999879999*****************************98566555 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.9e-05     0.036       4      47 ..     153     196 ..     151     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.9e-05
                      HTH_DeoR   4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRt 47 
                                   +il ll ++g +sv  ++  l+ S  Ti    ++Le++gl+++ 
  gi|15668555|ref|NP_247353.1| 153 KILNLLDKEGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVKKL 196
                                   8**************************************99986 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   8.8e-05     0.047      10      41 ..     161     192 ..     151     208 .] 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.8e-05
                        HTH_40  10 eeglsieeIAkerglkesTIegHLaelieege 41 
                                   e  +s+  IA++ + + sTI +++ +l ++g 
  gi|15668555|ref|NP_247353.1| 161 EGEMSVSNIAHKLERSLSTISEYVSQLEKKGL 192
                                   4469***********************99985 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.8e-05     0.047       9      46 ..     153     192 ..     148     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.8e-05
                        HTH_23   9 rillllae..GlsvreIAreLgvsrrTvyrwlkryreeGl 46 
                                   +il ll++   +sv+ IA +L +s +T++ +++  +++Gl
  gi|15668555|ref|NP_247353.1| 153 KILNLLDKegEMSVSNIAHKLERSLSTISEYVSQLEKKGL 192
                                   78999998899***********************988997 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00016     0.084       2      38 ..     148     184 ..     147     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                 HTH_AsnC-type   2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRv 38 
                                    e+  kIL++L + + +s++ +A ++  S st+ + v
  gi|15668555|ref|NP_247353.1| 148 TELEMKILNLLDKEGEMSVSNIAHKLERSLSTISEYV 184
                                   57778********************998888877655 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.11      37      77 ..     152     194 ..     145     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                   HHHHHH-E..EEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                        HTH_47  37 lwvLnlaD..GkrsLldiAeriglpfdrvaaiaraLaeaglla 77 
                                   +++Lnl D  G++s+ +iA++++ +  ++ + + +L+++gl++
  gi|15668555|ref|NP_247353.1| 152 MKILNLLDkeGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVK 194
                                   7888998877*******************************97 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.8   0.00051      0.27       3      44 ..     147     190 ..     146     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00051
                                   S-HHHHHHHHHHCT.T.S-HHHHHHHHTS-HHHHHHHHHHHHHH CS
                          GerE   3 LskRErevLrllae.G.ksnkeIAeelniSekTVkvhksnimkK 44 
                                   L++ E+++L ll + G +s+  IA +l+ S  T++ ++s++ kK
  gi|15668555|ref|NP_247353.1| 147 LTELEMKILNLLDKeGeMSVSNIAHKLERSLSTISEYVSQLEKK 190
                                   788899999998542536889******************99887 PP

>> Sun2_CC2  SUN2 coiled coil domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00028      0.15       4      35 ..     146     177 ..     144     180 .. 0.93
   2 ?   -1.3   0.1       5.2   2.7e+03       7      25 ..     186     205 ..     182     207 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00028
                      Sun2_CC2   4 eLqeLEkkILaklaeeqgksardaaasvgvaL 35 
                                   +L eLE kIL+ l +e ++s+ ++a+ +++ L
  gi|15668555|ref|NP_247353.1| 146 KLTELEMKILNLLDKEGEMSVSNIAHKLERSL 177
                                   699**********************9999887 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.2
                      Sun2_CC2   7 eLEkk.ILaklaeeqgksar 25 
                                   +LEkk + +kl++ ++k ++
  gi|15668555|ref|NP_247353.1| 186 QLEKKgLVKKLSKGRRKIVK 205
                                   68888445788888887765 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3    0.0004      0.21       2      45 ..     151     194 ..     150     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0004
                        HTH_34   2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45 
                                   ++++l +L ++ e++ +++  +le + + +s  ++ Lek+g ++
  gi|15668555|ref|NP_247353.1| 151 EMKILNLLDKEGEMSVSNIAHKLERSLSTISEYVSQLEKKGLVK 194
                                   6899*************************************886 PP

>> HTH_Tnp_Tc3_1  Tc3 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00053      0.28      17      41 ..     160     184 ..     146     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00053
                                   HHTT--HHHHHHHHT--HHHHHHHH CS
                 HTH_Tnp_Tc3_1  17 kllnvklsEiarklsRsRnCIrryL 41 
                                   k+   ++s ia kl Rs   I++y 
  gi|15668555|ref|NP_247353.1| 160 KEGEMSVSNIAHKLERSLSTISEYV 184
                                   67789*******************7 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.1   0.00097      0.51       1      59 [.     152     204 ..     152     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00097
                        HTH_12   1 veILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagrelt 59 
                                   ++IL++l ++ + ++  +ia++L+     i+e         le++gl+++ +++ r++ 
  gi|15668555|ref|NP_247353.1| 152 MKILNLLDKEGE-MSVSNIAHKLERSLSTISE-----YVSQLEKKGLVKKLSKGRRKIV 204
                                   58**********.**********987666644.....6899***********9999986 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00044      0.23       4      48 ..     153     197 ..     152     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00044
                        HTH_28   4 eiiklla.aGh.svreaArelgisrrtvyrWikryeegGiagLvpr.r 48 
                                   +i+ ll  +G+ sv+ +A++l  s +t++  ++++e+ G+   v++ +
  gi|15668555|ref|NP_247353.1| 153 KILNLLDkEGEmSVSNIAHKLERSLSTISEYVSQLEKKGL---VKKlS 197
                                   788899966878*************************776...55432 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00063      0.33      22      57 ..     164     203 ..     149     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00063
                                   HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE...ETEE.E CS
                     HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglis...rgrr.i 57 
                                   ++   +A+ l  + +t+s   s+L+++gl++   +grr i
  gi|15668555|ref|NP_247353.1| 164 MSVSNIAHKLERSLSTISEYVSQLEKKGLVKklsKGRRkI 203
                                   677889999999*******************743355545 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1300  (0.0725082); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1499.46
//
Query:       gi|15668556|ref|NP_247354.1|  [L=118]
Description: hypothetical protein MJ_0380 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.013   15.1   0.3      0.014   15.0   0.3    1.0  1  Cas_DxTHG  CRISPR-associated (Cas) DxTHG family


Domain annotation for each model (and alignments):
>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3     8e-07     0.014     163     259 ..       3      91 ..       1     110 [. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8e-07
                     Cas_DxTHG 163 lteflelsdwltaverflktgdaeklaellrekkekkkeklkklkklkeklkkeleefskalelirplellekaekleke. 242
                                   + e+++l++w++ + r+l++    k++e + +   +     + ++k  +  +++le++ k l+l+ +l+   ++ +++ + 
  gi|15668556|ref|NP_247354.1|   3 IDEVIKLENWMKNIGRYLSYLISDKFEEYAYD--II-----DGVAKARN-ANELLEALYKGLRLSPKLKKK-GNIEVPSPe 74 
                                   6789**************************44..22.....22333333.445888888888888854443.233333333 PP

                     Cas_DxTHG 243 iveklkeeleeieslee 259
                                    v+kl+e l+ei ++e+
  gi|15668556|ref|NP_247354.1|  75 DVKKLEETLREIGDNEK 91 
                                   56666666666633333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 914.40
//
Query:       gi|15668557|ref|NP_247355.1|  [L=320]
Description: hypothetical protein MJ_0381 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-79  267.2   0.0    1.4e-79  267.0   0.0    1.0  1  DevR      CRISPR-associated negative auto-regulator DevR/Csa2
  ------ inclusion threshold ------
      0.067   13.5   0.0       0.16   12.3   0.0    1.6  1  PucR      Purine catabolism regulatory protein-like family


Domain annotation for each model (and alignments):
>> DevR  CRISPR-associated negative auto-regulator DevR/Csa2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.0   0.0   1.5e-83   1.4e-79       1     268 [.       5     279 ..       5     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: 267.0 bits;  conditional E-value: 1.5e-83
                                   EEEEEE-------------.------EEEEEE--T..T--EEEEEE-THHHHHHHHHHHHHHHHTS..TTSSBHHHHTT-- CS
                          DevR   1 isgrvvvnveaLNmdesvG.Nytehrkvpvvlkee..ykvrtvpaiSgeslkHayfetlvklaken..nlpvcelckrveg 76 
                                   isgrv++n+++LN++++ G Ny+e++k++v +k++  +++ +vpaiSg+++kH++f+ +v++++e+  + +++e++ r++g
  gi|15668557|ref|NP_247355.1|   5 ISGRVRLNSHSLNAQGGGGtNYVEITKAKVSIKNDdrWEILEVPAISGNMVKHWHFVSFVDFFRETdyKDNLTERALRYNG 85 
                                   79*****************************99999******************************9999*********** PP

                                   ----TT--EEEBTTS..EESS-HHHHHHH-HHHHHH-EEEGGGT..EEE--SEEE--BEE-TTTTTTT....--------- CS
                          DevR  77 dggvikfatekklke..kelkvekeiikecvveDvfGfLitekeksvkRkspvkfsyavpveesekav....vdaqfhary 151
                                    ++  + +++kk++    elk+e+eiik+++ +Dv+GfL+++++  v+R s vk+s+++p+e++ k+v    v a+ h+r+
  gi|15668557|ref|NP_247355.1|  86 ARFGQE-TKAKKADGseVELKDESEIIKNFADADVHGFLAPKTG--VRRVSLVKTSFILPTEDFIKEVderlVYAVKHNRV 163
                                   998855.545555556799**********************888..********************99************* PP

                                   --------------------HHHHHSSEEEEEEEEEGGGTTS-TTS--EE---S-HHHHHHHHHHHHHTHHHHHH------ CS
                          DevR 152 dllenrarkkgeeeekqnifqvEehsalYalsfvlDldriGkpevkkskieyvleeeerkkRikaalkallnlLsgsfgak 232
                                   d +e++a+k+gee+++q++f++E++++lY++ + lDl  +G+p+   s +++v+e++erk+Ri +alkal+++Lsg++ga+
  gi|15668557|ref|NP_247355.1| 164 DIDEKGAIKSGEEQTAQMLFNREYATGLYGFEIILDLGFVGVPQS--SPSNPVIEDDERKARIVSALKALIPMLSGYIGAN 242
                                   *********************************************..********************************** PP

                                   --------EEEEEEEE--SSS------TT.TTHHHHH CS
                          DevR 233 rarllPvfeveslvaavskkpfpvfpirl.edyveee 268
                                    ar +Pvf++e+++a+vs+kp+p++++++ edyve++
  gi|15668557|ref|NP_247355.1| 243 LARSFPVFKLEEMIAVVSEKPIPALVHGFyEDYVEVS 279
                                   ****************************99****987 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.8e-05      0.16      58     116 ..     251     312 ..     240     313 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                          PucR  58 alaelvrelaeagvaaLviklg.r..eipeelieaadelglPlielpeevpfveiieevlea 116
                                   +l+e+++ ++e+ + aLv +   +  e++++++e a++lg+ +  + ++v+f e +++v e 
  gi|15668557|ref|NP_247355.1| 251 KLEEMIAVVSEKPIPALVHGFYeDyvEVSKNVVENAKKLGFEIEDFGYNVDFGESVSSVEEL 312
                                   7899****************953378**************************9988888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2283.47
//
Query:       gi|15668558|ref|NP_247356.1|  [L=245]
Description: hypothetical protein MJ_0382 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-06   28.2   0.0    2.1e-06   27.8   0.0    1.2  1  Cas_Cas5d  CRISPR-associated protein (Cas_Cas5)


Domain annotation for each model (and alignments):
>> Cas_Cas5d  CRISPR-associated protein (Cas_Cas5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.2e-10   2.1e-06       2     171 ..       6     177 ..       5     221 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.2e-10
                                   EEEEEECCEE-EB-TTCCSCCCBESS--HHHHHHHHHHHH...T--TTS-........-CCCCTTEEEEEEEEEEEEEEET CS
                     Cas_Cas5d   2 LllrlegplasfgrpsrkveretydvPtkSavlGllaaal...Girrddd........leelkpalrwgvrvdrrgellrg 71 
                                   L+  l++p+ sfg +s ++ r+++ +P++Sa++G la  +   G +  +         +e            + +++l++ 
  gi|15668558|ref|NP_247356.1|   6 LVALLRFPFYSFGKQS-YQVRQSLLLPSPSALKGALAKGIillGGKKGKSldeiakktVE------------ELENKLIYV 73 
                                   778899********98.7889****************97656765555552233333333............555555553 PP

                                   EEEEECT.....-GGGS--BSSS----CCEEEEEEEEEEEECEEEEEECCSCCHHHHHHHHHHHHHTTSSSSESSSTTSEE CS
                     Cas_Cas5d  72 dyhtvag.....rtlperrkektadrkkraatvlseraYladahfevalegeeegklleelaralrkpvwplyLGrkeciv 147
                                     + +++     + l++r  +  +d+k   +     r+Y++    +++          ee   +l++ + +++LG  ec +
  gi|15668558|ref|NP_247356.1|  74 GAKPYKSsiiktPILLKRL-RNLEDQKNPEKSDAMRREYVFAREILAIYVFRRK-LSEEEKDLMLKAVYLIDQLGDTECVG 152
                                   3333333455432222333.3334666777778888888877776666666644.155555556666666666******99 PP

                                   EECESETTT.CES.SHHHCCHSSCE CS
                     Cas_Cas5d 148 pvepveaekvgee.egledalkelp 171
                                    v   e  +v ee ++l++++k ++
  gi|15668558|ref|NP_247356.1| 153 NVIKTEWVEVKEEkAPLKTYVKFKK 177
                                   8888887444444266666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1909.40
//
Query:       gi|15668559|ref|NP_247357.1|  [L=614]
Description: ATP-dependent RNA helicase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.8e-20   71.4   1.2    1.8e-16   60.4   0.0    2.7  2  DEAD        DEAD/DEAH box helicase
    8.3e-12   45.4   0.1      3e-11   43.6   0.1    2.1  1  Helicase_C  Helicase conserved C-terminal domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0     2e-20   1.8e-16       4     176 .]      19     208 ..      16     208 .. 0.70
   2 !    8.8   0.3   0.00014       1.3      44     128 ..     253     328 ..     237     331 .. 0.77

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 2e-20
                                   HHHHHHHHH....TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                   xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   4 Qaeaiplil....gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                   Q +a++ i      gg v+++++T+ GKT+a++ip l ++++ ++ + p+ ++v Ptr+L+e++++++++++k+i   +  
  gi|15668559|ref|NP_247357.1|  19 QIRAWEKINkimeLGGRVVIEIPTAGGKTEAAIIPYLYQFIS-NDWKVPRLIYVLPTRSLVEKQVERIRNYIKKI--LEIK 96 
                                   5555555554446689*********************99999.99****************************74..2333 PP

                                   EETTSSHHHHHHHH........HTT...CSEEEEEH.HHHHHHH..........HCTSSHCTTE..EEEEEETHHHHHHT. CS
                                   xxxxxxxxxxxxxx........xxx...xxxxxxxx.xxxxxxx..........xxxxxxxxxx..xxxxxxxxxxxxxx. RF
                          DEAD  81 iiggvaardqlskl........dng...vdivvgtp.grlddll..........stgklnlsqv..rflVlDEadrlldq. 136
                                    +++++ ++  +k+        + +   + +vv t+ + +   l          ++ ++ +  +  +++V+DE+++++d+ 
  gi|15668559|ref|NP_247357.1|  97 GYSKDKVEELAKKIvqveygleE-ThafLGFVVLTTwDTF---LyglaahrtvgDRFTFPCGAIaqSLVVFDEIQMYQDEs 173
                                   44555555555555444333321.1233444544442222...2455677665544445555555499************7 PP

                                   .TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSHHHHHH CS
                                   .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 137 .gfsdfinrilnqlpqitcdgklqrqvivlSATlpkdvkkl 176
                                     + + i  ++++l   +++      +++++ATlp+++kk+
  gi|15668559|ref|NP_247357.1| 174 lYMPRLIGLVVKRL--VEAN----VPLVFMTATLPTELKKI 208
                                   66777888888888..3333....45*********999986 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00014
                                   TSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  44 gktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrf 124
                                    ++g+k+li+  t   a ++++++k++++   l +++ ++ +++ ++ +++  +++i+v+t      +++   l+l +v +
  gi|15668559|ref|NP_247357.1| 253 INEGKKVLIIKNTVNSAIEVYEKVKQLGNS--LLLHSRFTVEDRAEKEKDI-DKAEIIVATQ-----VVE-AGLDLTNVGL 324
                                   56889************************7..5555667767777788888.899****998.....222.3345666666 PP

                                   EEEE CS
                                   xxxx RF
                          DEAD 125 lVlD 128
                                   ++ D
  gi|15668559|ref|NP_247357.1| 325 VITD 328
                                   6655 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.1   3.3e-15     3e-11       7     110 ..     246     345 ..     206     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 3.3e-15
                                   HHHH.HHTTTTSEEEEEESSHH.HHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTE CS
                    Helicase_C   7 lell.kleeeggkilifvntid.rlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkv 85 
                                    +++ k  +eg+k+li+ nt++  +e  + +  k+  +++ lh++ + ++r e  ++    +  +++at+v+e G+d+++v
  gi|15668559|ref|NP_247357.1| 246 SNEIkKAINEGKKVLIIKNTVNsAIEVYEKV--KQLGNSLLLHSRFTVEDRAEKEKDID--KAEIIVATQVVEAGLDLTNV 322
                                   445567779*************533323555..556899*******************4..567***************** PP

                                   SEEEESSSSSSHHHHHHHHTTSSST CS
                    Helicase_C  86 nlVinfdlprnvtsyiqriGRtgRa 110
                                    lVi   +p  ++ +iqriGR++R 
  gi|15668559|ref|NP_247357.1| 323 GLVITDLAP--LDALIQRIGRCARR 345
                                   ****98888..779*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1128  (0.0629148); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3789.55
//
Query:       gi|15668560|ref|NP_247358.1|  [L=244]
Description: hypothetical protein MJ_0384 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-08   34.3   0.0    3.2e-08   33.9   0.0    1.1  1  HD_6       HD domain
  ------ inclusion threshold ------
       0.04   14.2   1.4       0.83   10.0   0.1    3.1  3  NAAA-beta  beta subunit of N-acylethanolamine-hydrolyzing aci


Domain annotation for each model (and alignments):
>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   3.6e-12   3.2e-08      14     135 ..      15     139 ..      10     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.6e-12
                                   EEHHHHHHHHHHHHHHHHHHTS-HHHHHC.....TS-HHHHHHHHHHHHHCCCGGGSSHHHHTTS----TTS-.....-GG CS
                          HD_6  14 hpLvaHllDvaavaealldkwlsllarll.r...gleeealrrllaflaalHDlGKaspaFqakvpelaekleeaglelek 90 
                                   ++L+ H+ D     e++  ++l+ ++r+l +   +l+ e++ +++ +l+ lHD+GKas+ +q+   + +ekl + + el +
  gi|15668560|ref|NP_247358.1|  15 QSLIDHVNDMVKYWERIKYRYLKTIKRALeAlniKLDIEKVDEFMKILIKLHDIGKASKIYQRAIINDQEKLMGFRHELVS 95 
                                   689*********************9999966999*******************************9999999866555553 PP

                                   GT----HHHHHHHHHHHHHHHHHHHHHTTTS---HHHHHTSS-HH CS
                          HD_6  91 elekarHdslgaalleevarslaaavggHHGkppkeeeekaekks 135
                                   + + + H  l    +++ a   a  v+ HH      + ++ +kk+
  gi|15668560|ref|NP_247358.1|  96 A-YYTYHILLKKFGDKNLAFIGALTVMLHHEPIIMGQIRNLKKKE 139
                                   3.7777777776666678888888899999844444444433333 PP

>> NAAA-beta  beta subunit of N-acylethanolamine-hydrolyzing acid amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.15   1.3e+03      21      41 ..       6      26 ..       5      32 .. 0.77
   2 ?    0.7   0.0     0.073   6.6e+02      25      57 ..      89     120 ..      86     124 .. 0.80
   3 ?   10.0   0.1   9.3e-05      0.83      20      55 ..     143     178 ..     142     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                     NAAA-beta 21 vakdykpelksliqvlkdllk 41
                                  ++   + + +sli  ++d++k
  gi|15668560|ref|NP_247358.1|  6 IMEVLAFKNQSLIDHVNDMVK 26
                                  566666666889999999986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.073
                     NAAA-beta  25 ykpelksliqvlkdllkslvpgklvdlvdklaa 57 
                                   +++el s+ ++++ llk++ + k ++++ +l+ 
  gi|15668560|ref|NP_247358.1|  89 FRHELVSAYYTYHILLKKF-GDKNLAFIGALTV 120
                                   7789999999999999998.5688888888765 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 9.3e-05
                     NAAA-beta  20 qvakdykpelksliqvlkdllkslvpgklvdlvdkl 55 
                                   +v+ d+ +++  +i+++ dl+k+l++ ++ d++++ 
  gi|15668560|ref|NP_247358.1| 143 EVVLDKLKKFDGMIEDFEDLIKKLIGYSIGDIIKND 178
                                   789999999**********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1667.72
//
Query:       gi|15668561|ref|NP_247359.1|  [L=375]
Description: hypothetical protein MJ_0385 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-128  429.4   2.0   1.4e-128  429.2   2.0    1.0  1  Cas_Csa4  CRISPR-associated protein (Cas_Csa4)
  ------ inclusion threshold ------
       0.32   11.4   1.8         10    6.5   0.1    2.7  3  RTBV_P12  Rice tungro bacilliform virus P12 protein


Domain annotation for each model (and alignments):
>> Cas_Csa4  CRISPR-associated protein (Cas_Csa4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.2   2.0  1.5e-132  1.4e-128       1     354 [.      25     373 ..      25     374 .. 0.99

  Alignments for each domain:
  == domain 1  score: 429.2 bits;  conditional E-value: 1.5e-132
                      Cas_Csa4   1 kelytPghseildtlImygivrslaragvvelrvertGerYvieve..vDvrnkn.leegLrealeevlsghealgrr... 75 
                                   ++++tPg++eild++I+yg+v++l+r+gv++lr++++G++Y+i ve  ++v++kn +e+g+++ale++ls+h+a+g++   
  gi|15668561|ref|NP_247359.1|  25 MLFETPGYNEILDLYIAYGVVECLVREGVENLRFFPIGNKYCIVVEepTNVNIKNrIEKGMLNALEDMLSLHKAIGKYist 105
                                   579*********************************************99999999************************* PP

                      Cas_Csa4  76 ....kiisdadisagafisdlqrlnrvy.....relesilnnleklkasvkselskkkqaeargrkkklltvpltLmPsag 147
                                       kiisd+d+saga      ++n+vy     ++le+i++n++k+k s+ks+                +tvpltLmP+ag
  gi|15668561|ref|NP_247359.1| 106 kediKIISDVDFSAGA------NINNVYwdgipKTLEKIKENIKKGKLSTKSK----------------NTVPLTLMPAAG 164
                                   ****************......*******************************................9*********** PP

                      Cas_Csa4 148 kyllkslkkkeekpyrvcklcyalawlGfhYyastikikdGesvvv..vtlapseevslidllalkdlkeklsvlqpa... 223
                                   ky++k +++k+++p+++++++yalaw+GfhYya++i+i+d++++++  ++++p ee++li++lalkdlk+k++++q     
  gi|15668561|ref|NP_247359.1| 165 KYMPKIYGVKGGNPIKIDDSNYALAWIGFHYYAPYINISDNRATYIhiYAIKPLEELGLIEILALKDLKKKINNYQLGkyk 245
                                   *****************************************************************************99** PP

                      Cas_Csa4 224 .lvnsreallkalllyllslgalellteskftvlvYalefkvgnnqrirsfrevelsklldfiaelkardfastiklvddl 303
                                    +vn+++all ++l++++s++ale++t+++f+v++Y+le +v+nnq+irsf e++lskl+df+++lka+df++ti++vd++
  gi|15668561|ref|NP_247359.1| 246 fFVNKKLALL-YHLTHTESISALEIVTKKNFSVVSYTLE-NVDNNQAIRSFGEYDLSKLMDFLWYLKATDFYNTIQFVDNI 324
                                   **********.****************************.***************************************** PP

                      Cas_Csa4 304 lredleillrLieallygdlrevysalrvlkkagvrldaelvdalaeilae 354
                                   lr dle++l++i+ +ly+dl++vysa+r  k ++vr+++ +++++ e++ +
  gi|15668561|ref|NP_247359.1| 325 LRGDLEVSLTFIDGILYDDLDAVYSAIR--KLKSVRISPLIIQSILEWFGN 373
                                   ****************************..999***************975 PP

>> RTBV_P12  Rice tungro bacilliform virus P12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.011        96      29      89 ..     101     163 ..      76     177 .. 0.77
   2 ?    6.5   0.1    0.0012        10      46      67 ..     219     240 ..     208     253 .. 0.85
   3 ?   -2.4   0.0      0.69   6.2e+03      24      39 ..     271     287 ..     255     295 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.011
                      RTBV_P12  29 nwvftleniksaadvnlaskglvqlyalqeidkkinnlttqvs..klpttsgsssagaivpag 89 
                                   +++ t e+ik  +dv++++   ++    + i k ++++  ++   kl t s  +   +++pa 
  gi|15668561|ref|NP_247359.1| 101 KYISTKEDIKIISDVDFSAGANINNVYWDGIPKTLEKIKENIKkgKLSTKSKNTVPLTLMPAA 163
                                   688999**********99988888877899999998887766422688888777777777764 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0012
                      RTBV_P12  46 askglvqlyalqeidkkinnlt 67 
                                      gl+++ al+++ kkinn  
  gi|15668561|ref|NP_247359.1| 219 EELGLIEILALKDLKKKINNYQ 240
                                   5679****************75 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.69
                      RTBV_P12  24 gkdkfnwv.ftleniks 39 
                                    k +f  v +tlen+  
  gi|15668561|ref|NP_247359.1| 271 TKKNFSVVsYTLENVDN 287
                                   45556555478888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2355.37
//
Query:       gi|15668562|ref|NP_247360.1|  [L=114]
Description: hypothetical protein MJ_0386 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-21   76.1   0.5    1.7e-21   76.1   0.5    1.7  2  CRISPR_Cas2  CRISPR associated protein Cas2
  ------ inclusion threshold ------
      0.042   13.9   0.1      0.089   12.8   0.0    1.5  2  GvpG         Gas vesicle protein G
      0.098   12.2   0.0       0.12   11.8   0.0    1.1  1  DUF4916      Domain of unknown function (DUF4916)
        0.2   11.5   0.4        0.2   11.5   0.4    1.9  2  SHOCT        Short C-terminal domain


Domain annotation for each model (and alignments):
>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.47   2.1e+03      49      56 ..      10      17 ..       3      26 .. 0.50
   2 !   76.1   0.5   3.9e-25   1.7e-21       1      68 [.      28      92 ..      28      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.47
                                  HHHHHHHS CS
                   CRISPR_Cas2 49 kkrlkkii 56
                                   k lkki+
  gi|15668562|ref|NP_247360.1| 10 NKILKKIK 17
                                  33333332 PP

  == domain 2  score: 76.1 bits;  conditional E-value: 3.9e-25
                                  EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEE CS
                   CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykl 68
                                  m+v++vYD+  +  r++k++ +l+k+ +++vQ+SVFege+++a++e++k+ + +iid++eds++iy++
  gi|15668562|ref|NP_247360.1| 28 MYVIIVYDV--NVSRVNKIKSFLRKH-LNWVQNSVFEGEVTKAEFERIKDGILRIIDEDEDSVIIYQF 92
                                  9********..***************.***************************************87 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.5   6.9e+03      60      70 ..      11      21 ..       9      27 .. 0.65
   2 ?   12.8   0.0     2e-05     0.089      31      67 ..      46      82 ..      37      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                          GvpG 60 elLdrLealer 70
                                  ++L +++++++
  gi|15668562|ref|NP_247360.1| 11 KILKKIKNIRN 21
                                  67888877766 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2e-05
                          GvpG 31 enlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrLea 67
                                    lrk+L   q +  +Ge++++eF+r  + +L  +++
  gi|15668562|ref|NP_247360.1| 46 SFLRKHLNWVQNSVFEGEVTKAEFERIKDGILRIIDE 82
                                  5699****************************98886 PP

>> DUF4916  Domain of unknown function (DUF4916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.7e-05      0.12      12      92 ..      17      98 ..      11     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                                  XXX--SSEEEEEEEEEEEE-TTS-EEEEEEEEEE-TTS-EEEE-EEEE--TT..--HHHHHHHHHHHHH-TT--B---SS--- CS
                       DUF4916 12 eevrrrlPilyvevvPvrvddlgevtevGlllraseegelertlvsGrvlyh..etvreallrhiekdlGelalpqlPaslqP 92
                                  +++r+ l    + v+ v   + ++v+++  +lr + +  ++ ++  G v     e++++ +lr i++d  ++ + q+P + +P
  gi|15668562|ref|NP_247360.1| 17 KNIRNLLQDESMYVIIVYDVNVSRVNKIKSFLRKHLN-WVQNSVFEGEVTKAefERIKDGILRIIDEDEDSVIIYQFPLNFMP 98
                                  5555555544444455555567899999999997665.599********9763379**********************99888 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   4.4e-05       0.2      13      28 .]      62      77 ..      61      77 .. 0.88
   2 ?   -2.9   1.2       1.5   6.6e+03      14      19 ..      79      84 ..      79      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.4e-05
                         SHOCT 13 GeIteEEFeakKakLL 28
                                  Ge t++EFe+ K+ +L
  gi|15668562|ref|NP_247360.1| 62 GEVTKAEFERIKDGIL 77
                                  9***********8665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.5
                         SHOCT 14 eIteEE 19
                                  +I+e+E
  gi|15668562|ref|NP_247360.1| 79 IIDEDE 84
                                  79**99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1067  (0.0595125); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 799.39
//
Query:       gi|15668563|ref|NP_247361.1|  [L=99]
Description: DNA-directed RNA polymerase subunit L [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-22   77.4   0.2    6.6e-22   77.1   0.2    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
    1.8e-06   27.3   0.0      4e-06   26.2   0.0    1.6  1  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.2   7.4e-26   6.6e-22       2      74 ..      13      93 ..      12      94 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 7.4e-26
                                  EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTT........SEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHHH CS
                   RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPle........pkmnlriqtkssnnpleaLkkalkdlldicdelee 74
                                  +++e+ +EDh+L nlL+++ll +++V++a+Y+i+HPl         ++ +++i t+++++ple+Lk++l+d++++cd+l +
  gi|15668563|ref|NP_247361.1| 13 VEIELINEDHSLPNLLKDILLTKEGVKMASYSIDHPLLhpetgryiSNPKITIITEEGTDPLEVLKEGLRDIIKMCDTLLD 93
                                  589*********************************7778899999********************************986 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   4.4e-10     4e-06       1      69 []      14      88 ..      14      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.4e-10
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_L  1 efllrgvdhtlgNaLRrillsevpgvaiea..................pvvkvntdkdklilevetdgslkPeealkeAlkiL 65
                                  e +l+++dh+l N L+ ill   +gv +++                  p+           +++ t   ++P e+lke+l+++
  gi|15668563|ref|NP_247361.1| 14 EIELINEDHSLPNLLKDILL-TKEGVKMASysidhpllhpetgryisnPK-----------ITIITEEGTDPLEVLKEGLRDI 84
                                  57899***************.67888888887888777766665555554...........8888889*************** PP

                                  xxxx RF
                     RNA_pol_L 66 kekl 69
                                  ++++
  gi|15668563|ref|NP_247361.1| 85 IKMC 88
                                  *998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 684.77
//
Query:       gi|15668564|ref|NP_247362.1|  [L=207]
Description: hypothetical protein MJ_0388 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-53  178.8   6.3    9.3e-53  178.6   6.3    1.0  1  DUF2067   Uncharacterized protein conserved in archaea (DUF20
    0.00024   21.3   0.0      0.037   14.3   0.0    2.7  3  DUF4777   Domain of unknown function (DUF4777)
  ------ inclusion threshold ------
      0.081   11.7   0.0      0.099   11.4   0.0    1.2  1  XFP_N     XFP N-terminal domain


Domain annotation for each model (and alignments):
>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.6   6.3   1.6e-56   9.3e-53       2     186 .]       8     191 ..       7     191 .. 0.94

  Alignments for each domain:
  == domain 1  score: 178.6 bits;  conditional E-value: 1.6e-56
                       DUF2067   2 klndeeeleeflekise.kiksaeevkievegnrllievyGtekei.....kdiirrikellreklkkekrglfkyslsdl 76 
                                   k++++eel+e++e++s+ +i++++e+    +gnr+++ v+G++k++     ++i++++++++r+ ++k+++gl+ky+l +l
  gi|15668564|ref|NP_247362.1|   8 KVSCDEELLELCERLSRmDIDCTIES----KGNRVRVYVFGYDKDSlkxnyRTIREVMEKVKRK-YQKDDEGLYKYPLFEL 83 
                                   7899****************999888....688************9966666666666666666.**************** PP

                       DUF2067  77 lreagapvppdvLvdaLkllGykaelre.envlktnapleevvelaerlseiykelrfknl.skaakrvvavvsvltgldp 155
                                   +    +pv++++++daLk+lGyk+ + e en++ktn+++++++e++ +l+e+ +elrf+nl sk++k++v++vs++t++++
  gi|15668564|ref|NP_247362.1|  84 K----YPVNKNLIIDALKTLGYKVIYLEdENAIKTNVDINKFNEILGELHELSQELRFSNLgSKPVKNLVVLVSYITKKPV 160
                                   *....**************************************************************************** PP

                       DUF2067 156 devieellekGlLeeeegkivlrkewkkalk 186
                                   d+viee+lekG+++eeeg+ivl+k+++ a+k
  gi|15668564|ref|NP_247362.1| 161 DDVIEEALEKGFFREEEGRIVLNKDINLAKK 191
                                   ***************************9986 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.01        63      21      38 ..      56      73 ..      55      78 .. 0.88
   2 ?   -2.5   0.0       1.1   6.3e+03       5      17 ..      88     100 ..      84     101 .. 0.83
   3 !   14.3   0.0   6.2e-06     0.037      41      63 ..     157     179 ..     153     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.01
                       DUF4777 21 TldEivervaerydlsee 38
                                  T++E++e+v ++y++ +e
  gi|15668564|ref|NP_247362.1| 56 TIREVMEKVKRKYQKDDE 73
                                  9**********9998776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                       DUF4777   5 ngalvlealkvln 17 
                                   n  l++ alk+l+
  gi|15668564|ref|NP_247362.1|  88 NKNLIIDALKTLG 100
                                   6789999999985 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 6.2e-06
                       DUF4777  41 kkvVkntLeaAvrhGFlkkengr 63 
                                   kk+V+++ e+A  +GF+++e gr
  gi|15668564|ref|NP_247362.1| 157 KKPVDDVIEEALEKGFFREEEGR 179
                                   89******************997 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.7e-05     0.099     218     300 ..      92     174 ..      74     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.7e-05
                         XFP_N 218 lkklfeGlGyepafvededteslhkllaevldkaveeihdiqkearsneeasrPkwPmiilrtPkGwt.gPkyvdGkkveg 297
                                   + + ++ lGy++ ++ede+  +++ +  + +++++ e+h++ +e r ++ +s+P   +++l +   +    + ++     g
  gi|15668564|ref|NP_247362.1|  92 IIDALKTLGYKVIYLEDENAIKTN-VDINKFNEILGELHELSQELRFSNLGSKPVKNLVVLVSYITKKpVDDVIEEALEKG 171
                                   55667899*********7776665.566789***************************99976544431444555555566 PP

                         XFP_N 298 sfr 300
                                   +fr
  gi|15668564|ref|NP_247362.1| 172 FFR 174
                                   666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1102  (0.0614647); expected 358.6 (0.02)
Passed bias filter:                      719  (0.0401026); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1508.33
//
Query:       gi|15668565|ref|NP_247363.1|  [L=306]
Description: tyrosyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-49  169.3   0.0    1.3e-49  169.1   0.0    1.1  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
    0.00026   20.0   1.3       0.47    9.3   0.0    3.0  3  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.1   0.0   1.5e-53   1.3e-49       4     293 .]      27     300 ..      24     300 .. 0.91

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 1.5e-53
                                   S--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTTT CS
                  tRNA-synt_1b   4 rplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpek 84 
                                   ++ ++y G++P+gk+HlG+++ +kk+++lq+ag ++++l+aDlhA+++++   e+ ++rk  ++ +++     a gl   k
  gi|15668565|ref|NP_247363.1|  27 DEKSAYIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLNQKG--ELDEIRKIGDYNKKV---FEAMGL---K 99 
                                   56689********************************************99..777777777777777...555666...5 PP

                                   EEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGGHHHHH CS
                  tRNA-synt_1b  85 aevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGsDQkqnie 165
                                   a++v++se +  ++++  + +l+  ++l+r  +  +   r  e  + +++e +Yp++q +Di +l +d+ +gG+ Q+++  
  gi|15668565|ref|NP_247363.1| 100 AKYVYGSEFQLDKDYTLNVYRLALKTTLKRARRSMELIAREDE--NPKVAEVIYPIMQVNDIHYLGVDVAVGGMEQRKIHM 178
                                   69*****************************999996665555..559********************************* PP

                                   HHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC....SHHHHHHHHHT CS
                  tRNA-synt_1b 166 lgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde....evekllklkte 242
                                   l+r+l+++        k++++ +p+ltgldGe KmS+S+gn  I  dd++e++++ki+ka++  +      +    k++ e
  gi|15668565|ref|NP_247363.1| 179 LARELLPK--------KVVCIHNPVLTGLDGEGKMSSSKGN-FIAVDDSPEEIRAKIKKAYCPAGVvegnPIMEIAKYFLE 250
                                   *****986........599**********************.*********************999885567778888888 PP

                                   HHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1b 243 lsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnelle 293
                                    +  +i+r e+++g  + +++eel+  +++k++h++dlk+a+ae+l+++le
  gi|15668565|ref|NP_247363.1| 251 YPL-TIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILE 300
                                   888.***********9999*****************************985 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0   0.00027       2.5       8      43 ..      11      47 ..       7      62 .. 0.81
   2 ?    1.3   0.1     0.014   1.3e+02     132     175 ..     111     155 ..      83     161 .. 0.74
   3 !    9.3   0.0   5.2e-05      0.47     274     295 ..     197     218 ..     158     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00027
                  tRNA-synt_1f  8 aeklieerkkkka.ekdevvvesGispSGliHiGnlr 43
                                    ++i+e++ ++  +kde     G  pSG+iH+G   
  gi|15668565|ref|NP_247363.1| 11 TSEIISEEELREVlKKDEKSAYIGFEPSGKIHLGHYL 47
                                  55677666666667999999999***********865 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.014
                  tRNA-synt_1f 132 telYksglydeaikealenrekikeilekyrgee.reetyspylp 175
                                    + Y+ ++y+ a+k+ l++ ++ +e++++  +++  +e  +p++ 
  gi|15668565|ref|NP_247363.1| 111 DKDYTLNVYRLALKTTLKRARRSMELIAREDENPkVAEVIYPIMQ 155
                                   4569***************99999999988776635555667665 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 5.2e-05
                  tRNA-synt_1f 274 illkggekmssSkGnvltledw 295
                                    +l+g++kmssSkGn+++++d 
  gi|15668565|ref|NP_247363.1| 197 TGLDGEGKMSSSKGNFIAVDDS 218
                                   5689999************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1912.50
//
Query:       gi|15668566|ref|NP_247364.1|  [L=130]
Description: hypothetical protein MJ_0390 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2870  (0.160076); expected 358.6 (0.02)
Passed bias filter:                      857  (0.0477997); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 832.30
//
Query:       gi|15668567|ref|NP_247365.1|  [L=183]
Description: cobalamin biosynthesis precorrin-8W decarboxylase CbiT [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-11   44.4   1.4    1.8e-11   44.1   1.4    1.2  1  Methyltransf_31  Methyltransferase domain
    3.5e-09   37.2   0.1    7.1e-09   36.3   0.1    1.6  1  Methyltransf_25  Methyltransferase domain
    2.6e-07   30.7   1.3    3.8e-07   30.2   1.3    1.2  1  Methyltransf_18  Methyltransferase domain
    8.2e-07   29.6   0.0      2e-06   28.4   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    1.4e-06   28.0   0.1    2.6e-06   27.1   0.1    1.4  1  MTS              Methyltransferase small domain
    2.3e-06   27.3   1.0    3.1e-06   26.9   1.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    2.3e-06   28.2   0.1    3.5e-06   27.7   0.1    1.4  1  Methyltransf_12  Methyltransferase domain
    1.3e-05   24.7   2.6      3e-05   23.6   2.5    1.6  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.6e-05   24.6   0.1    2.9e-05   23.8   0.1    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95
    2.5e-05   23.4   0.2    2.7e-05   23.3   0.2    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
    3.5e-05   23.2   0.6    4.3e-05   22.9   0.6    1.2  1  GidB             rRNA small subunit methyltransferase G
    6.8e-05   22.1   0.0    0.00018   20.7   0.0    1.5  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00015   21.6   0.9    0.00025   20.9   0.8    1.3  1  Met_10           Met-10+ like-protein
    0.00018   21.3   0.0    0.00034   20.4   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00032   20.4   0.0    0.00041   20.0   0.0    1.3  1  NodS             Nodulation protein S (NodS)
    0.00053   19.5   1.0    0.00076   19.0   0.1    1.7  2  Methyltransf_4   Putative methyltransferase
      0.002   17.8   0.1     0.0039   16.9   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0027   17.3   0.7     0.0045   16.5   0.6    1.5  1  DOT1             Histone methylation protein DOT1
      0.004   17.0   0.0     0.0047   16.8   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0044   16.4   0.0     0.0059   15.9   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.012   14.9   0.2      0.023   14.0   0.1    1.4  1  N6_Mtase         N-6 DNA Methylase
      0.029   14.3   0.1      0.038   13.9   0.1    1.1  1  Mtr2             Nuclear pore RNA shuttling protein Mtr2
      0.032   13.7   0.4      0.037   13.5   0.4    1.2  1  Telomere_res     Telomere resolvase
      0.043   13.8   0.1       0.07   13.1   0.1    1.3  1  Methyltransf_32  Methyltransferase domain
      0.049   13.7   0.1       0.07   13.2   0.1    1.3  1  FtsJ             FtsJ-like methyltransferase
      0.061   12.7   0.5      0.085   12.2   0.5    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
       0.12   11.7   0.0       0.16   11.3   0.0    1.2  1  HEM4             Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   1.4   2.7e-14   1.8e-11       2     102 ..      34     142 ..      33     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 2.7e-14
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgldnveFeqgdiee.lekl.led......e 73 
                                   +k+ +v+D+GCG+G  t e+a++     + v+ iD+   aie+ ++n++k +++n++  +g +e+ l+kl +++      +
  gi|15668567|ref|NP_247365.1|  34 NKDDVVVDVGCGSGGMTVEIAKRC----KfVYAIDYLDGAIEVTKQNLAKFNIKNCQIIKGRAEDvLDKLeFNKafiggtK 110
                                   68899****************653....33**************************************9766666665552 PP

               Methyltransf_31  74 kfDl......ilsnevlnaladpdkileeiervlk 102
                                             il++  +n++ ++  +le++ + ++
  gi|15668567|ref|NP_247365.1| 111 ---NiekiieILDKKKINHIVANTIVLENAAKIIN 142
                                   ...04556668999999***********9887765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.1   1.1e-11   7.1e-09       1      60 [.      39      97 ..      39     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.1e-11
                                  EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSS CS
               Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpf 60
                                  v+d+GcG+G +t ++akr+  + v+++D+ ++++e +++++++ ++ n+++++g aed+  
  gi|15668567|ref|NP_247365.1| 39 VVDVGCGSGGMTVEIAKRC--KFVYAIDYLDGAIEVTKQNLAKFNIkNCQIIKGRAEDVLD 97
                                  89****************9..9*******************998889********998543 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   1.3   5.7e-10   3.8e-07      13     117 ..      34     136 ..      27     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 5.7e-10
               Methyltransf_18  13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagled..kievrlsdGleklkeeevdtvviaGm 91 
                                   +k+++v+D+G+  g ++++++  +++k v+a+D  +g++e  k+n++k ++++   i+ r  d l+kl   e++ + i G 
  gi|15668567|ref|NP_247365.1|  34 NKDDVVVDVGCGSGGMTVEIA--KRCKFVYAIDYLDGAIEVTKQNLAKFNIKNcqIIKGRAEDVLDKL---EFNKAFIGGT 109
                                   67899***************9..68999**********************965224555666666666...7999***997 PP

               Methyltransf_18  92 G.gelileILeeakeklkkikklilqp 117
                                      e i+eIL+++k ++  +++++l+ 
  gi|15668567|ref|NP_247365.1| 110 KnIEKIIEILDKKKINHIVANTIVLEN 136
                                   515789999999876666677777764 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0     3e-09     2e-06       1      55 [.      40      95 ..      40     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3e-09
                                  EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCT CS
               Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaekl 55
                                  +dvGcG+G ++ ++akr++ v+++D+ + ++++ k++  + ++ ++++++++ae++
  gi|15668567|ref|NP_247365.1| 40 VDVGCGSGGMTVEIAKRCKFVYAIDYLDGAIEVTKQNLAKFNIkNCQIIKGRAEDV 95
                                  59************************************999989999*****9983 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1     4e-09   2.6e-06      27      94 ..      31     100 ..      25     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4e-09
                                   CHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-STTTTST CS
                           MTS  27 lpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevvasdvleeve 94 
                                   l+ ++++ v+D+GcG G +++++ak+++   v ++d    A+e++k+nl++ +++    ++ +a+dvl+++e
  gi|15668567|ref|NP_247365.1|  31 LNLNKDDVVVDVGCGSGGMTVEIAKRCKF--VYAIDYLDGAIEVTKQNLAKFNIKncqiIKGRAEDVLDKLE 100
                                   55567788*****************9998..9999*999************999996666666777777766 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   1.0   4.7e-09   3.1e-06       3      70 ..      38     104 ..      36     156 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.7e-09
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkleki 70 
                                   v++D+ +G+GG ++++a+  + v+ai++    ++++++N   ++++ + ++++g  +++l kl+++k+
  gi|15668567|ref|NP_247365.1|  38 VVVDVGCGSGGMTVEIAKRCKFVYAIDYLDGAIEVTKQNLAKFNIK-NCQIIKGRAEDVLDKLEFNKA 104
                                   79*****************999*********************886.589999999999999888876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   5.2e-09   3.5e-06       1      78 [.      40     136 ..      40     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 5.2e-09
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg................. 64 
                                   +++GcG+G ++ +++++   + ++++D+   aie +k+ lak + +n++ ++ +a+d+ld+ +                  
  gi|15668567|ref|NP_247365.1|  40 VDVGCGSGGMTVEIAKR--CKFVYAIDYLDGAIEVTKQNLAKFNIKNCQIIKGRAEDVLDKLEFnkafiggtkniekiiei 118
                                   69***************..88888***********************************9988887777777777777777 PP

               Methyltransf_12  65 ...ssfDlvvas.nvlhh 78 
                                      ++   +va+  vl++
  gi|15668567|ref|NP_247365.1| 119 ldkKKINHIVANtIVLEN 136
                                   777777777776555555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   2.5   4.5e-08     3e-05     160     222 ..      34      96 ..      24     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.5e-08
                          PrmA 160 kegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseell 222
                                   ++++ v+DvG+GSG +++  ak   k v+a+D+ + A++v+k+N+++ ++++ ++    +e++l
  gi|15668567|ref|NP_247365.1|  34 NKDDVVVDVGCGSGGMTVEIAK-RCKFVYAIDYLDGAIEVTKQNLAKFNIKNcQIIKGRAEDVL 96 
                                   5677899***********9999.5899*****************99988888666222344444 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   4.3e-08   2.9e-05      42     119 ..      36     106 ..      19     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.3e-08
                                   C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE CS
                 Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivfl 119
                                   +  v+D+ +GsG++ +E + R +k +++++  + a+++ k+nl+++++++ ++++k  a++ l+kl     ef+  f+
  gi|15668567|ref|NP_247365.1|  36 DDVVVDVGCGSGGMTVEIAKR-CKFVYAIDYLDGAIEVTKQNLAKFNIKN-CQIIKGRAEDVLDKL-----EFNKAFI 106
                                   45699************7766.7**************************7.999999999999888.....4555555 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.2   4.1e-08   2.7e-05     201     271 ..      34     105 ..       1     146 [. 0.85

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.1e-08
               tRNA_U5-meth_tr 201 skgd.llelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirlsaeeltealkkkref 271
                                   +k+d ++++ cG G +++ +a++ + v a +    ++e+++ n+a+ +i+n qii+  ae++ + l+ +++f
  gi|15668567|ref|NP_247365.1|  34 NKDDvVVDVGCGSGGMTVEIAKRCKFVYAIDYLDGAIEVTKQNLAKFNIKNCQIIKGRAEDVLDKLEFNKAF 105
                                   4444267999**************************************************999988888777 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.6   6.5e-08   4.3e-05      46     139 ..      33     122 ..      19     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.5e-08
                                   -CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCCTTTTT-EEEEEEC-SSS CS
                          GidB  46 kekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaeekqeeekydvvtsRAlas 126
                                    +k+d v+DvG G G  G+ + ia+  + ++ ++ l   i+  ++  ++++++n +i++ rae+   + +++ + + +  +
  gi|15668567|ref|NP_247365.1|  33 LNKDDVVVDVGCGSG--GMTVEIAKRCKFVYAIDYLDGAIEVTKQNLAKFNIKNCQIIKGRAEDVLDKLEFNKAFIGGTKN 111
                                   344445*********..***********************************************999*********99999 PP

                                   HHHHHHHHCCCEE CS
                          GidB 127 lnelteillkllk 139
                                   +++++eil k  k
  gi|15668567|ref|NP_247365.1| 112 IEKIIEILDK--K 122
                                   9999999987..3 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.7e-07   0.00018      23      60 ..      28      65 ..      21      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.7e-07
                                  HHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S CS
                        RrnaAD 23 ldklnleekltvleigpGkGilTeeLakrakqvvvlEl 60
                                  + klnl++++ v+++g G G +T+e+akr+k v ++  
  gi|15668567|ref|NP_247365.1| 28 IGKLNLNKDDVVVDVGCGSGGMTVEIAKRCKFVYAIDY 65
                                  569****************************9988865 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.8   3.7e-07   0.00025      98     178 ..      33     110 ..      19     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.7e-07
                                   --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE--TT CS
                        Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnlpk 178
                                    ++++vVvdv  G G  ++ iak  + k+v+aid    +++  k+n++  ++++    i++ +++v+ +  +++  ++  k
  gi|15668567|ref|NP_247365.1|  33 LNKDDVVVDVGCGSGGMTVEIAK--RCKFVYAIDYLDGAIEVTKQNLAKFNIKNCQ-IIKGRAEDVLDKLEFNKAFIGGTK 110
                                   6789*******************..9********************9998887753.678888888777777766655543 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.2e-07   0.00034      56     131 ..      18      90 ..      10     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.2e-07
                                   E--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES CS
                          PCMT  56 iSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvg 131
                                   i +  + a+ +  l+l+k + v++vG+GsG  t+ +a+  +    v +i++    +e +k+nl k +++n +++ g
  gi|15668567|ref|NP_247365.1|  18 ITKEEIRAVSIGKLNLNKDDVVVDVGCGSGGMTVEIAKRCKF---VYAIDYLDGAIEVTKQNLAKFNIKNCQIIKG 90 
                                   5666778899999*****************999988876654...55***********************999877 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   6.1e-07   0.00041      33      87 ..      27      79 ..      18     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.1e-07
                          NodS 33 qilrlslaqgsiadalevGcaaGalterlapyckrltvvdvveeaiararervke 87
                                   i +l l++ ++  +++vGc +G +t+++a  ck +  +d ++ ai+ +++ + +
  gi|15668567|ref|NP_247365.1| 27 SIGKLNLNKDDV--VVDVGCGSGGMTVEIAKRCKFVYAIDYLDGAIEVTKQNLAK 79
                                  555556655555..799*******************************9998765 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.1e-06   0.00076       3      66 ..      37      98 ..      35     107 .. 0.89
   2 ?   -2.3   0.1       3.9   2.6e+03      55      63 ..     132     140 ..     109     157 .. 0.44

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                                  EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHH CS
                Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvlle 66
                                   vv+++GcG+G+++v++Ak+   k + +i+     ++   ++ ++ ++kN +i++g a +vl +
  gi|15668567|ref|NP_247365.1| 37 DVVVDVGCGSGGMTVEIAKRC--KFVYAIDYLDGAIEVTKQNLAKFNIKNCQIIKGRAEDVLDK 98
                                  589***************985..7889****999999999999999************888865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.9
                                   EEES-CCCH CS
                Methyltransf_4  55 ilrgdalkv 63 
                                   i+  +a k+
  gi|15668567|ref|NP_247365.1| 132 IVLENAAKI 140
                                   222222232 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.8e-06    0.0039       4      70 ..      31      94 ..      28     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.8e-06
                                  H---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTC CS
               Methyltr_RsmB-F  4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDark 70
                                  L++++++ ++D+ ++ Gg T  ia+     + v+A+d  +  ++  ++nl +++++n +++++ a  
  gi|15668567|ref|NP_247365.1| 31 LNLNKDDVVVDVGCGSGGMTVEIAK---RCKFVYAIDYLDGAIEVTKQNLAKFNIKNCQIIKGRAED 94
                                  8999****************88875...5899****************************9986655 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.6   6.8e-06    0.0045      35      94 ..      28      86 ..      19     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.8e-06
                                  HHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHH.HHHH CS
                          DOT1 35 ldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelk.krlk 94
                                  + k+nl+k+dv vD G G G +++ +a   +ck  + ++  d a e+++++   ++ k ++
  gi|15668567|ref|NP_247365.1| 28 IGKLNLNKDDVVVDVGCGSGGMTVEIAK--RCKFVYAIDYLDGAIEVTKQNLAKFNiKNCQ 86
                                  6799********************9997..6777899*********999987766525555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     7e-06    0.0047      20      62 ..      33      81 ..      17     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7e-06
               Methyltransf_23 20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......k 62
                                  l+++  v+d+GcG+G ++ +++++ + v+++D  + a+e  +      +
  gi|15668567|ref|NP_247365.1| 33 LNKDDVVVDVGCGSGGMTVEIAKRCKFVYAIDYLDGAIEVTKqnlakfN 81
                                  68899**********9999998887778888888877776544444440 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.9e-06    0.0059      53      84 ..      26      57 ..      19     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.9e-06
                                  HHHTTTT--TT-EEEEES-TTSHHHHHHHHHH CS
                          CMAS 53 lileklelkpGmtlLdiGcGWGslvrravery 84
                                  + ++kl+l++ + ++d+GcG G+++++ ++r 
  gi|15668567|ref|NP_247365.1| 26 VSIGKLNLNKDDVVVDVGCGSGGMTVEIAKRC 57
                                  5689**********************999983 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.5e-05     0.023      30     132 ..      19     130 ..      11     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                      N6_Mtase  30 TPrevsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykk.vki 109
                                   T +e+  + +  l+ +++ +v+D  cGsgg+ v+ +k  k          +y  +  + +++++k Nl+  +i++ + +k 
  gi|15668567|ref|NP_247365.1|  19 TKEEIRAVSIGKLNLNKDDVVVDVGCGSGGMTVEIAKRCK---------FVYAIDYLDGAIEVTKQNLAKFNIKNCQiIKG 90 
                                   6677888888889999999***************999764.........66677777777777777777666665541345 PP

                      N6_Mtase 110 rlgdtlekpkfe.................kdkkfdvvvaN 132
                                   r +d l k +f+                 ++kk++ +vaN
  gi|15668567|ref|NP_247365.1|  91 RAEDVLDKLEFNkafiggtkniekiieilDKKKINHIVAN 130
                                   6677777766666666666666666666666666666666 PP

>> Mtr2  Nuclear pore RNA shuttling protein Mtr2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.7e-05     0.038      21      96 ..      68     148 ..      53     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-05
                                   --HCCHHHHHCCB-SSS-EEEE.TTEEESSHHHHHHHHHHHS--EEEEEEEEEEEEET..TTSEEEEEEEEEE..EEBTTS CS
                          Mtr2  21 qdvnkleqflqlFlkpqckivf.ngkPlaqaaaFlkiwlqsvvltqHaltalDfHvip..gtgtliinanckv..rfdesG 96 
                                     ++  +q+l +F+ ++c+i+   ++ + ++ +F k++      +   +  lD   i+   ++t+++  ++k+   f+ +G
  gi|15668567|ref|NP_247365.1|  68 GAIEVTKQNLAKFNIKNCQIIKgRAEDVLDKLEFNKAFIGGTKNIEKIIEILDKKKINhiVANTIVLENAAKIinEFESRG 148
                                   5567889**************835889*****************************9977789999998888733345555 PP

>> Telomere_res  Telomere resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   5.6e-05     0.037      92     179 ..      60     145 ..      18     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                                   ........HHHHHTT-SSHHHHHHHHHHHH---HHHHHHT-EEEEEEETEEEEEEEEEE--SS-TS-TT--EEEE-SS-HH CS
                  Telomere_res  92 vkavevieialellkSrdirlkviglllltGRRheEvlkkgkfdkadktdveknsilfegqaKkkeneaivyeipvlapae 172
                                   v a+++++ a e+ k +     +    ++ G R e+vl k +f+ka+ ++ ++    +e   Kkk n  iv +  vl +a 
  gi|15668567|ref|NP_247365.1|  60 VYAIDYLDGAIEVTKQNLAKFNIKNCQIIKG-RAEDVLDKLEFNKAFIGGTKNIEKIIEILDKKKIN-HIVANTIVLENAA 138
                                   5678888888888888877777777777777.5899************9999999999*********.9999999****** PP

                                   HHHHHHH CS
                  Telomere_res 173 tilnaik 179
                                   +i+n ++
  gi|15668567|ref|NP_247365.1| 139 KIINEFE 145
                                   9999776 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00011      0.07      24      92 ..      34      95 ..      21     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
               Methyltransf_32 24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieea 92
                                  +++  vvDvG+G g ++  +a    +    v++id  +  +e +++  +k++  + k+++ +++  e+ 
  gi|15668567|ref|NP_247365.1| 34 NKDDVVVDVGCGSGGMTVEIAK---R-CKFVYAIDYLDGAIEVTKQNLAKFN--I-KNCQIIKGRAEDV 95
                                  67889************99999...4.4569999999999999999988888..6.7777777766655 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   0.00011      0.07      19      77 ..      33      89 ..      21     154 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                  S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...........HHHTTEEEECS-CCCSSHHH CS
                          FtsJ 19 fkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...........aplpgvttiqgditdpetie 77
                                  +++++ vvD+g++ Gg +  +++r+   + v+a+D   +            +++++++i          +
  gi|15668567|ref|NP_247365.1| 33 LNKDDVVVDVGCGSGGMTVEIAKRC---KFVYAIDYLDGaievtkqnlakFNIKNCQII----------K 89
                                  567889******************6...57******98855555433322222444444..........2 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   0.00013     0.085      47     110 ..      35      95 ..      20     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                   -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT- CS
               Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeL 110
                                   +   v+Dv +G+g +++++++  +  +    +D+ +  ++v+++ l +   +n + +++ ae++
  gi|15668567|ref|NP_247365.1|  35 KDDVVVDVGCGSGGMTVEIAKRCKFVYA---IDYLDGAIEVTKQNLAKFNIKNCQIIKGRAEDV 95 
                                   455799*************998876555...555567788888888888899999999888864 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00024      0.16      83     151 ..      92     159 ..      61     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                                   HHHHHHHTT---SEE-..SSSHHHHGGGS-.---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEE CS
                          HEM4  83 TaraLeelglrvdlvpseegtaegLaeelaeslagkrvlllrgeiarddlaegLeergaevdevevYet 151
                                   + ++L +l++++++++  + + e+ +e+l+++  +  v      +  + + +++e+rg++vd+v+v+  
  gi|15668567|ref|NP_247365.1|  92 AEDVLDKLEFNKAFIGG-TKNIEKIIEILDKKKINHIVANTIVLENAAKIINEFESRGYNVDAVNVFIS 159
                                   6789************9.9********999733332222222223468999**************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1124.21
//
Query:       gi|15668568|ref|NP_247366.1|  [L=339]
Description: hypothetical protein MJ_0392 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-27   96.2   1.1      2e-13   50.6   0.5    2.5  2  CBS             CBS domain
    1.3e-15   57.4  14.5    4.1e-08   32.8   5.4    3.1  3  Peptidase_M50   Peptidase family M50
    2.5e-06   27.3   3.7    2.5e-06   27.3   3.7    2.1  2  Peptidase_M50B  Peptidase M50B-like
    0.00011   22.5   1.1    0.00011   22.5   1.1    3.0  3  DUF3267         Putative zincin peptidase
  ------ inclusion threshold ------
      0.029   14.3   0.3       0.53   10.2   0.0    2.3  2  Rubredoxin_C    Rubredoxin NAD+ reductase C-terminal domain
       0.11   12.9   0.3         18    5.8   0.1    2.6  2  Corona_3        Coronavirus ORF3 protein
        0.2   10.7   2.2       0.38    9.8   2.2    1.4  1  FUSC-like       FUSC-like inner membrane protein yccS
       0.58   10.4  15.0          3    8.1   9.5    2.8  2  DUF456          Protein of unknown function (DUF456)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   1.3e-14     3e-11       1      46 [.     222     266 ..     222     273 .. 0.92
   2 !   50.6   0.5   8.7e-17     2e-13       1      55 [.     278     328 ..     278     330 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.3e-14
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEE CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGiv 46 
                                   ++dimt+++v+v+pd+++ee l+ m ++++ ++PVV e+gklvG +
  gi|15668568|ref|NP_247366.1| 222 AKDIMTPNPVYVTPDMSIEEFLDFMLKHKYFGYPVV-ENGKLVGCI 266
                                   68***************************66*****.9*****987 PP

  == domain 2  score: 50.6 bits;  conditional E-value: 8.7e-17
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   V+d+m ++v +v++dt+++e+l++m  ++ +r++VV e gkl Gi++++D+lra+
  gi|15668568|ref|NP_247366.1| 278 VRDYMEKPV-VVSEDTDIKEILRKM--ANTDRVFVV-EGGKLKGIISKTDILRAM 328
                                   799997777.***************..6699*****.899*************97 PP

>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   5.4   1.8e-11   4.1e-08       2     108 ..      43     112 ..      42     121 .. 0.89
   2 !   29.7   0.9   1.6e-10   3.5e-07     189     242 ..     121     176 ..     111     186 .. 0.73
   3 ?   -1.8   0.1      0.69   1.6e+03      97     109 ..     189     235 ..     178     308 .. 0.59

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.8e-11
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkk 82 
                                   +++ll+++vv+HElGH +vAk+ gvk+e+                    i llp+GG+  m++   +e             
  gi|15668568|ref|NP_247366.1|  43 LFILLFVSVVLHELGHSYVAKKYGVKIEK--------------------ILLLPIGGVAMMDKIP-KE------------- 89 
                                   5799***********************99....................99******66666655.33............. PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50  83 spwqrllivlAGplanfilailvfvv 108
                                       +l+i +AGpl+ fi++i++++v
  gi|15668568|ref|NP_247366.1|  90 ---GELRIGIAGPLVSFIIGIVLLIV 112
                                   ...58*****************9987 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 1.6e-10
                                   X..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 189 s..sflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlv 242
                                       +l++l l+++ Lg +NL+P +++DGg++l+a+l++  +   s++  + + + 
  gi|15668568|ref|NP_247366.1| 121 NgyPLLYTLSLLNLMLGGFNLIPAFPMDGGRILRAILSKKYGYLKSTKIAANIGKS 176
                                   44478999****************************99877666555544443333 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.69
                                   XXXXXXXXXXXX..................................- CS
                                   xxxxxxxxxxxx..................................x RF
                 Peptidase_M50  97 anfilailvfvv..................................p 109
                                   +n+il ++ ++v                                  p
  gi|15668568|ref|NP_247366.1| 189 MNIILILVSLFVyfgaeqesrvvevetifknikakdimtpnpvyvtP 235
                                   67777666666655555555555555444444444444444444441 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   3.7   1.1e-09   2.5e-06       9      89 ..      32     114 ..      17     142 .. 0.75
   2 ?   -0.4   0.2      0.34   7.6e+02     113     133 ..     182     202 ..     154     216 .. 0.60

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.1e-09
                Peptidase_M50B   9 vvlwnk....pllrpfkllvvffHElGHalaalLtGgrvkgielhsdesGvtvtrg.pgglgqiltllaGYlgpallGlll 84 
                                    ++  +    ++l ++  ++v++HElGH  +a+  G ++++i l +  +Gv+++   p+  g   + +aG+l + ++G++l
  gi|15668568|ref|NP_247366.1|  32 SIMN-NsifwAVLFILLFVSVVLHELGHSYVAKKYGVKIEKILLLP-IGGVAMMDKiPKE-GELRIGIAGPLVSFIIGIVL 109
                                   2333.24555566678899***********************9998.58*******9776.6789**************** PP

                Peptidase_M50B  85 illsa 89 
                                   +++s+
  gi|15668568|ref|NP_247366.1| 110 LIVSQ 114
                                   99983 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.34
                Peptidase_M50B 113 nlfglvlllllgallllvlll 133
                                    lfgl+++ ++++l+ l++++
  gi|15668568|ref|NP_247366.1| 182 LLFGLLSMNIILILVSLFVYF 202
                                   234444444444444444444 PP

>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   3.5       1.8   4.1e+03      62      99 ..      20      41 ..       4      48 .. 0.44
   2 !   22.5   1.1   4.7e-08   0.00011       2      92 ..      48     139 ..      47     145 .. 0.85
   3 ?    1.9   0.3      0.12   2.6e+02      46      72 ..     174     200 ..     153     207 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.8
                       DUF3267 62 gilllllalllpsstlllllllalnaagsagDlliall 99
                                  +++l+l                ++ +++s++   i+++
  gi|15668568|ref|NP_247366.1| 20 TFILFL----------------VVIIGLSIMNNSIFWA 41
                                  333333................3333333333222222 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 4.7e-08
                       DUF3267   2 lvlvilHEllHglffklfgkkpkkkvkfgiklliayatsseallskkqfiiillaPfv..llgilllllalllpsstl... 77 
                                   +v v+lHEl H  + k++g+k +k + +    +  +a+  + + +  +  i    P+v  ++gi+ll+++ ++  +++   
  gi|15668568|ref|NP_247366.1|  48 FVSVVLHELGHSYVAKKYGVKIEKILLL---PIGGVAMMDKIP-KEGELRIGIAGPLVsfIIGIVLLIVSQFFDININgyp 124
                                   899***************9998888888...566677777777.99999999999*954388************888899* PP

                       DUF3267  78 llllllalnaagsag 92 
                                   ll+ l++ln++++  
  gi|15668568|ref|NP_247366.1| 125 LLYTLSLLNLMLGGF 139
                                   *********998765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.12
                       DUF3267  46 skkqfiiillaPfvllgilllllalll 72 
                                    k+  +i+ll+ ++ ++i+l+l++l++
  gi|15668568|ref|NP_247366.1| 174 GKSLALIMLLFGLLSMNIILILVSLFV 200
                                   455566777777777777777777664 PP

>> Rubredoxin_C  Rubredoxin NAD+ reductase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00024      0.53      41      68 ..     256     284 ..     233     286 .. 0.79
   2 ?    1.8   0.2       0.1   2.3e+02      26      65 ..     296     333 ..     287     337 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00024
                                   EEETTEEEEEEEES-HHHH.HHHHHHHHT CS
                  Rubredoxin_C  41 fikngklvGAiliGDtkes.aklkkliek 68 
                                   +++ngklvG+i iG++ +   ++++++ek
  gi|15668568|ref|NP_247366.1| 256 VVENGKLVGCIGIGNIHKKeGTVRDYMEK 284
                                   89*************97653667777765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.1
                                   EEEEE-SS-..EEEEEEETTEEEEEEEES-HHHHHHHHHH CS
                  Rubredoxin_C  26 elveedkekgkYkklfikngklvGAiliGDtkesaklkkl 65 
                                   e+ ++ +++   +  +++ gkl G i   D+ +++++++l
  gi|15668568|ref|NP_247366.1| 296 EILRKMANT--DRVFVVEGGKLKGIISKTDILRAMSILEL 333
                                   444444444..378899*********99999999998876 PP

>> Corona_3  Coronavirus ORF3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0078        18       7      34 ..      45      70 ..      41      83 .. 0.75
   2 ?    4.5   0.0     0.021        46      32      44 ..     258     270 ..     237     275 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0078
                      Corona_3  7 idifvdavldeldrayfavtlkvefktG 34
                                  i +fv  vl el  +y a    v     
  gi|15668568|ref|NP_247366.1| 45 ILLFVSVVLHELGHSYVAKKYGVK--IE 70
                                  678*************98655443..33 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.021
                      Corona_3  32 ktGkllvciGfGd 44 
                                     Gkl+ ciG G+
  gi|15668568|ref|NP_247366.1| 258 ENGKLVGCIGIGN 270
                                   47*********97 PP

>> FUSC-like  FUSC-like inner membrane protein yccS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.2   0.00017      0.38       2      47 ..      17      60 ..      16      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00017
                     FUSC-like  2 LavtllcfalaslivqlllpypwlfvlglllstflftmlgalGqry 47
                                  L +t+++f   ++i++l++++  +f+++l+++ f+ ++l  lG  y
  gi|15668568|ref|NP_247366.1| 17 LHITFILF--LVVIIGLSIMNNSIFWAVLFILLFVSVVLHELGHSY 60
                                  77999999..567899**************************9987 PP

>> DUF456  Protein of unknown function (DUF456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   9.5    0.0013         3      14      91 ..      25     107 ..      12     139 .. 0.77
   2 ?    4.3   0.2      0.02        44      49      93 ..     153     196 ..     150     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                        DUF456  14 glllyalltgfaelgwlflavllvlallglvldylapalgakraGaskrgligaivGaivGffllpp........lGlllg 86 
                                    +++++l  ++   + +f+avl++l+ +++vl  l   + ak++G++   ++   +G+++ +  +p         +G l+ 
  gi|15668568|ref|NP_247366.1|  25 LVVIIGL--SIM-NNSIFWAVLFILLFVSVVLHELGHSYVAKKYGVKIEKILLLPIGGVAMMDKIPKegelrigiAGPLVS 102
                                   2222222..222.5689*****************************************98776666344555455444455 PP

                        DUF456  87 pflga 91 
                                   +++g+
  gi|15668568|ref|NP_247366.1| 103 FIIGI 107
                                   55554 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.02
                        DUF456  49 apalgakraGaskrgligaivGaivGffllpplGlllgpflgafl 93 
                                   + a+  k++G  k++ i+a +G  + +++l  +Gll + ++ +++
  gi|15668568|ref|NP_247366.1| 153 LRAILSKKYGYLKSTKIAANIGKSLALIMLL-FGLLSMNIILILV 196
                                   5678899*****************9986554.9998777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1379  (0.0769145); expected 358.6 (0.02)
Passed bias filter:                      724  (0.0403815); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2180.47
//
Query:       gi|15668569|ref|NP_247367.1|  [L=60]
Description: 30S ribosomal protein S27ae [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-21   75.6   5.6    2.9e-21   75.4   5.6    1.1  1  Ribosomal_S27   Ribosomal protein S27a
     0.0038   17.4   0.9     0.0038   17.4   0.9    1.6  2  Ribosomal_L37e  Ribosomal protein L37e
     0.0064   16.8   0.9        1.7    9.0   0.1    2.0  2  GFA             Glutathione-dependent formaldehyde-activating
  ------ inclusion threshold ------
      0.018   14.9   3.5          1    9.3   3.8    2.3  2  Nudix_N_2       Nudix N-terminal
      0.045   14.2   3.3       0.94    9.9   0.1    2.2  2  zf-IS66         zinc-finger binding domain of transposase IS6
       0.35   10.9   4.8        0.5   10.4   4.0    1.8  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.46   10.4   0.1       0.46   10.4   0.1    2.2  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
        1.9    8.1   5.1        3.8    7.1   0.1    2.2  2  zf_C2H2_10      C2H2 type zinc-finger
        4.6    6.9   5.7         17    5.1   1.6    2.4  2  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   5.6   1.5e-24   2.9e-21       2      44 ..      10      50 ..       9      51 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 1.5e-24
                                  SSSCCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTT CS
                 Ribosomal_S27  2 lkyYkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCgl 44
                                  +kyYk+++ +kv rl+k Cpr CG+GvfMAeh +R++CGkCg+
  gi|15668569|ref|NP_247367.1| 10 YKYYKIEG-DKVIRLKKTCPR-CGPGVFMAEHLNRYACGKCGY 50
                                  7*******.9***********.********************8 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       4.1   8.1e+03      43      47 ..       6      10 ..       3      14 .. 0.44
   2 !   17.4   0.9   1.9e-06    0.0038      18      42 ..      26      53 ..      17      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.1
                Ribosomal_L37e 43 klrky 47
                                  k+ ky
  gi|15668569|ref|NP_247367.1|  6 KTAKY 10
                                  33333 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.9e-06
                Ribosomal_L37e 18 lCrrCgkrsy...hvqkktCascGypsa 42
                                  +C rCg   +   h+++  C++cGy + 
  gi|15668569|ref|NP_247367.1| 26 TCPRCGPGVFmaeHLNRYACGKCGYMEW 53
                                  7******99977788899*******654 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1   0.00085       1.7      31      61 ..       3      36 ..       1      39 [. 0.68
   2 !    7.8   0.1    0.0021       4.3      45      65 ..      38      58 ..      36      60 .] 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00085
                           GFA 31 eg.elkeykktadsgnkvtr..sfCpeCgsplys 61
                                  +g ++++yk+ + +g+kv r  + Cp+Cg  +++
  gi|15668569|ref|NP_247367.1|  3 KGkKTAKYKYYKIEGDKVIRlkKTCPRCGPGVFM 36
                                  555555666665566666665789*****99997 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0021
                           GFA 45 nkvtrsfCpeCgsplyseesa 65
                                  ++++r+ C +Cg   + ++++
  gi|15668569|ref|NP_247367.1| 38 EHLNRYACGKCGYMEWKQPQK 58
                                  6789********998876554 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4    0.0068        14      16      29 ..      16      31 ..       6      34 .. 0.73
   2 ?    9.3   3.8   0.00053         1       3      30 ..      27      50 ..      25      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0068
                                  TT-SS-EE..EETTTT CS
                     Nudix_N_2 16 dgDnreRl..vCpaCg 29
                                  +gD+  Rl  +Cp+Cg
  gi|15668569|ref|NP_247367.1| 16 EGDKVIRLkkTCPRCG 31
                                  5777777544799987 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00053
                                  -TTT--B-EEE--TT-SS-EEEETTTTE CS
                     Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgt 30
                                  C+ CG  v +     ++  R+ C +Cg+
  gi|15668569|ref|NP_247367.1| 27 CPRCGPGVFM----AEHLNRYACGKCGY 50
                                  8888887554....4799*********8 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00047      0.94      35      46 .]      20      31 ..      14      31 .. 0.90
   2 ?    5.0   0.4     0.016        32      38      46 .]      41      49 ..      38      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00047
                       zf-IS66 35 hirpkyaCpcCe 46
                                   ir k++Cp+C+
  gi|15668569|ref|NP_247367.1| 20 VIRLKKTCPRCG 31
                                  699********7 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.016
                       zf-IS66 38 pkyaCpcCe 46
                                   +yaC +C+
  gi|15668569|ref|NP_247367.1| 41 NRYACGKCG 49
                                  58******7 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.1     0.011        22      19      25 ..      25      31 ..       7      31 .. 0.88
   2 ?   10.4   4.0   0.00025       0.5      19      45 ..      25      50 ..      17      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                 Zn_Tnp_IS1595 19 fvCPhCg 25
                                   +CP+Cg
  gi|15668569|ref|NP_247367.1| 25 KTCPRCG 31
                                  58****8 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00025
                 Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrk 45
                                   +CP+Cg   ++  ++  ++ C +C++
  gi|15668569|ref|NP_247367.1| 25 KTCPRCG-PGVFMAEHLNRYACGKCGY 50
                                  58*****.5566666689*******97 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.8      0.31   6.2e+02       4       8 ..      27      31 ..      25      32 .. 0.88
   2 ?   10.4   0.1   0.00023      0.46      19      31 ..      41      52 ..      34      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.31
                                  ESTTT CS
                RNA_POL_M_15KD  4 CpkCg 8 
                                  Cp Cg
  gi|15668569|ref|NP_247367.1| 27 CPRCG 31
                                  99998 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00023
                                  CCEEEESSSS-EE CS
                RNA_POL_M_15KD 19 gknfeCrqCgYee 31
                                  + +++C +CgY e
  gi|15668569|ref|NP_247367.1| 41 N-RYACGKCGYME 52
                                  3.49*******76 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.4     0.054   1.1e+02       4       9 ..      26      31 ..      24      33 .. 0.85
   2 ?    7.1   0.1    0.0019       3.8       3      11 ..      43      51 ..      42      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.054
                    zf_C2H2_10  4 sCPKCq 9 
                                   CP+C+
  gi|15668569|ref|NP_247367.1| 26 TCPRCG 31
                                  6****6 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0019
                    zf_C2H2_10  3 fsCPKCqek 11
                                  ++C KC++ 
  gi|15668569|ref|NP_247367.1| 43 YACGKCGYM 51
                                  89*****95 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.6    0.0086        17       3       9 ..      25      31 ..      24      40 .. 0.83
   2 ?    3.8   0.1     0.022        44       2       9 ..      42      49 ..      41      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0086
                        zf_UBZ  3 ylCerCg 9 
                                   +C+rCg
  gi|15668569|ref|NP_247367.1| 25 KTCPRCG 31
                                  59****9 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.022
                        zf_UBZ  2 tylCerCg 9 
                                   y C +Cg
  gi|15668569|ref|NP_247367.1| 42 RYACGKCG 49
                                  699****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 408.28
//
Query:       gi|15668570|ref|NP_247368.1|  [L=101]
Description: 30S ribosomal protein S24e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-22   77.6   0.2    6.2e-22   77.3   0.2    1.1  1  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.2   3.5e-26   6.2e-22       2      78 ..      21      96 ..      20      97 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 3.5e-26
                                  EEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS---S CS
                Ribosomal_S24e  2 vdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekkk 78
                                  + v H+g +tp+ ++++ kla+++++++dl++v ++  + G++++ G+ak Yd++e +k +E++h+l++n+++e+++
  gi|15668570|ref|NP_247368.1| 21 FIVDHDG-PTPTFKDVKLKLAAILNANKDLLIVEKIVEEAGMQRARGYAKLYDNEEMLKLVEREHILRKNKIEEETA 96
                                  7899***.******************************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 695.74
//
Query:       gi|15668571|ref|NP_247369.1|  [L=158]
Description: hypothetical protein MJ_0395 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-38  131.4   0.3    1.6e-38  131.2   0.3    1.1  1  DUF359           Protein of unknown function (DUF359)
  ------ inclusion threshold ------
      0.035   14.1   0.2       0.18   11.8   0.1    2.2  2  DUF4911          Domain of unknown function (DUF4911)
        0.2   11.1   0.1        0.3   10.5   0.1    1.3  1  Astro_capsid_p2  C-terminal tail of astrovirus capsid project


Domain annotation for each model (and alignments):
>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2   0.3   2.7e-42   1.6e-38       1     125 [.      37     155 ..      37     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 2.7e-42
                        DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikeal.eseekvlilVdGEED 80 
                                   vtk+ ++++i+P+l+i+D kt+R+       +  k+++ +k+vi+vkNp+G+i++e+ie ik     +++++++lVdGEED
  gi|15668571|ref|NP_247369.1|  37 VTKTAIENNIIPKLSIFDLKTRRN-------IPVKINHVFKKVIKVKNPPGCISDEAIESIKYLStINDRNIALLVDGEED 110
                                   89**********************.......44467999************************99899************* PP

                        DUF359  81 LavlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellekf 125
                                   L++l +i ++p g++v+YGqpdeG+v++k+++++k+e+ee+l++f
  gi|15668571|ref|NP_247369.1| 111 LLALIVIKYFPIGTYVLYGQPDEGIVVLKINKKLKQEIEEILKQF 155
                                   *******************************************99 PP

>> DUF4911  Domain of unknown function (DUF4911)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.28   1.7e+03      16      30 ..      85      99 ..      85     115 .. 0.71
   2 ?   11.8   0.1     3e-05      0.18      29      55 ..     131     157 ..     129     158 .] 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.28
                       DUF4911 16 EaydgLavvttvdkk 30
                                  Ea + + +++t++ +
  gi|15668571|ref|NP_247369.1| 85 EAIESIKYLSTINDR 99
                                  677777788888543 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3e-05
                       DUF4911  29 kkkGlvrirttpdtkeellelLesLkk 55 
                                   +++G+v++ + + +k+e++e+L+  kk
  gi|15668571|ref|NP_247369.1| 131 PDEGIVVLKINKKLKQEIEEILKQFKK 157
                                   689********************9875 PP

>> Astro_capsid_p2  C-terminal tail of astrovirus capsid projection or spike
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1     5e-05       0.3      77     103 ..     124     150 ..     115     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5e-05
               Astro_capsid_p2  77 tgvlfgqpklgvgviqtmktlkqhikd 103
                                   t vl+gqp  g+ v++  k lkq i++
  gi|15668571|ref|NP_247369.1| 124 TYVLYGQPDEGIVVLKINKKLKQEIEE 150
                                   789*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1118.55
//
Query:       gi|15668572|ref|NP_247370.1|  [L=59]
Description: DNA-directed RNA polymerase subunit E'' [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-14   52.1   0.7    7.6e-14   51.6   0.7    1.3  1  Spt4          Spt4/RpoE2 zinc finger
    0.00013   21.4   2.5    0.00017   21.1   2.5    1.2  1  RecR          RecR protein
  ------ inclusion threshold ------
      0.048   13.7   0.0      0.055   13.5   0.0    1.1  1  CARD          Caspase recruitment domain
      0.049   13.1   1.3      0.073   12.6   1.3    1.3  1  zn-ribbon_14  Zinc-ribbon
      0.095   12.0   0.2        0.1   12.0   0.2    1.1  1  Rtf2          Rtf2 RING-finger


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.7   2.1e-17   7.6e-14       1      77 []       1      58 [.       1      58 [. 0.95

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 2.1e-17
                          Spt4  1 lrACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                  +rACl+Ck++++++      Cp+C            ++ tse++ Gl+++++pekS++Ak+   +  ++g+YAl+v+
  gi|15668572|ref|NP_247370.1|  1 MRACLKCKYLTNDEI-----CPIC------------HSPTSENWIGLLIVINPEKSEIAKK--AGIDIKGKYALSVK 58
                                  69********98776.....****............89***********************..9999********96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   2.5   4.7e-08   0.00017      17      37 ..       2      22 ..       1      23 [. 0.92

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.7e-08
                                  EE-TTT--EESSSS-CCCCST CS
                          RecR 17 rhCsrCgnlteedlCaICsdp 37
                                  r C +C  lt +++C+IC +p
  gi|15668572|ref|NP_247370.1|  2 RACLKCKYLTNDEICPICHSP 22
                                  78****************998 PP

>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.5e-05     0.055      24      64 ..       3      43 ..       1      47 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                                  HHHHTTSS-HHHHHHHHTSSSHHHHHHHHHHHHHTSCHHHH CS
                          CARD 24 yLlekkVLteeeeekikakttrlskareLldlvqkkgekac 64
                                  ++l++k Lt++e++ i++++t+++  + L+ + ++k e a+
  gi|15668572|ref|NP_247370.1|  3 ACLKCKYLTNDEICPICHSPTSENWIGLLIVINPEKSEIAK 43
                                  789************************99999888877665 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.3     2e-05     0.073       2      16 ..       3      17 ..       2      20 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                  zn-ribbon_14  2 kCerCGylSSqkiCk 16
                                   C +C yl++ +iC 
  gi|15668572|ref|NP_247370.1|  3 ACLKCKYLTNDEICP 17
                                  6*************5 PP

>> Rtf2  Rtf2 RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   2.8e-05       0.1     150     177 ..      13      43 ..       2      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                          Rtf2 150 sevClvCgkeykeedv...iplnptkeelel 177
                                   +e C+ C+ + +e+ +   i++np+k+e ++
  gi|15668572|ref|NP_247370.1|  13 DEICPICHSPTSENWIgllIVINPEKSEIAK 43 
                                   789***********66666********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 396.46
//
Query:       gi|15668573|ref|NP_247371.1|  [L=187]
Description: DNA-directed RNA polymerase subunit E' [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-22   78.0   0.3    9.2e-22   77.2   0.3    1.4  1  SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/
    2.8e-12   46.8   1.2    1.2e-11   44.8   1.2    2.0  1  S1           S1 RNA binding domain


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.3     1e-25   9.2e-22       2      70 .]       9      77 ..       8      77 .. 0.99

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 1e-25
                                  EEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                   SHS2_Rpb7-N  2 dtvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                  d+v+++P+ +g++l++ ++++l ekyeg++++++G+++++ d+++++egkv++g+Gs+y+ V+f+ lv+
  gi|15668573|ref|NP_247371.1|  9 DVVKVPPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVY 77
                                  89*****************************************************************97 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   1.2   1.3e-15   1.2e-11       6      71 ..      83     147 ..      79     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.3e-15
                                   CEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEE CS
                            S1   6 evveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrrii 71 
                                   e +eGeV++v+++G fV+lg + +g++++s++++d+  +dp+++  +G+e  ++++  d+ r+ri+
  gi|15668573|ref|NP_247371.1|  83 ELIEGEVVDVVEFGSFVRLG-PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIV 147
                                   568*****************.**************8888888888888887777777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1277.11
//
Query:       gi|15668574|ref|NP_247372.1|  [L=271]
Description: hypothetical protein MJ_0398 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-18   64.8  10.1    2.3e-13   50.3   1.1    3.3  3  LAGLIDADG_3     LAGLIDADG-like domain
     0.0063   16.6   2.1        1.1    9.3   0.0    3.1  3  LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
  ------ inclusion threshold ------
      0.018   15.0   7.6       0.12   12.4   2.4    3.1  3  Spc42p          Spindle pole body component Spc42p
      0.068   13.3   0.0       0.25   11.5   0.0    2.0  2  Hom_end         Homing endonuclease
       0.07   13.7   0.2        0.2   12.3   0.1    1.8  2  HTH_32          Homeodomain-like domain
       0.25   12.0   2.4        2.6    8.8   0.3    2.5  2  DUF2281         Protein of unknown function (DUF2281)


Domain annotation for each model (and alignments):
>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2      0.45   1.3e+03      34      57 ..      13      37 ..       6      55 .. 0.65
   2 !   18.9   0.1   4.8e-07    0.0014       3      80 ..      73     150 ..      71     152 .. 0.92
   3 !   50.3   1.1   7.7e-17   2.3e-13       5      80 ..     166     248 ..     162     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.45
                                  HHHHHHHHHHHHHCT.HSCEEEE.E CS
                   LAGLIDADG_3 34 kelledvqrlLlrlGIestiyek.k 57
                                  +el+++v+ l ++    s+i +k  
  gi|15668574|ref|NP_247372.1| 13 LELINYVKSLRKQNFSYSQISKKiE 37
                                  7888888888776667777777632 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 4.8e-07
                                   HHHHHHHHHHHCCECCECSTTTTS.EEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGGGT CS
                   LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvs.isltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisgenlkrFle 80 
                                   ++ ++ G + +D  +  +kk+g++  +++  +k++++ v++ L ++G++ ti    ++ +++ +  +  s+++l +Fl+
  gi|15668574|ref|NP_247372.1|  73 ELSYIIGVYFGDANIYYRKKTGSYyFRIKVVDKDFVDVVKNSLIKIGLNPTISYVEEKTRSNRW-HVEASSKSLYKFLS 150
                                   67899***************9999*******************************999999999.78889999999987 PP

  == domain 3  score: 50.3 bits;  conditional E-value: 7.7e-17
                                   HHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEE.EEE-SCCCC...............ECCC CS
                   LAGLIDADG_3   5 afLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyek.kkakgrgvy...............rlli 69 
                                    fLrG+fd++G+v+ +k     i l + ++elle  ++lL++l ++sti+   kk+                     rl i
  gi|15668574|ref|NP_247372.1| 166 DFLRGFFDSEGYVTSNK-----IALENYDLELLEFSKELLKKLDVHSTIHIAkKKGT----EsnirgeiyhykddfyRLSI 237
                                   5****************.....******************************33333....22347999************ PP

                                   HCHCTTCGGGT CS
                   LAGLIDADG_3  70 isgenlkrFle 80 
                                    ++e++++F+ 
  gi|15668574|ref|NP_247372.1| 238 HRKESVRNFAI 248
                                   *********85 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.9   8.6e+03      40      47 ..      21      28 ..       8      45 .. 0.53
   2 !    5.4   0.0    0.0062        19       4      58 ..      76     132 ..      74     149 .. 0.82
   3 !    9.3   0.0   0.00038       1.1       3      38 ..     166     204 ..     164     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.9
                LAGLIDADG_WhiA 40 llnefele 47
                                   l++ +++
  gi|15668574|ref|NP_247372.1| 21 SLRKQNFS 28
                                  33333333 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0062
                LAGLIDADG_WhiA   4 flrGaflasGsindpekk..yhLEivspdeelaeqlqkllnefeleakilerrkkyv 58 
                                   ++ G+ ++   i   +k+  y + i + d+++++ +++ l +++l+  i+ + +k++
  gi|15668574|ref|NP_247372.1|  76 YIIGVYFGDANIYYRKKTgsYYFRIKVVDKDFVDVVKNSLIKIGLNPTISYVEEKTR 132
                                   66666666666655533336***************************9999888765 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00038
                LAGLIDADG_WhiA   3 aflrGaflasGsindp...ekkyhLEivspdeelaeqlq 38 
                                    flrG f ++G +++     ++y LE+   ++el+++l 
  gi|15668574|ref|NP_247372.1| 166 DFLRGFFDSEGYVTSNkiaLENYDLELLEFSKELLKKLD 204
                                   69***********99744235599999999999998876 PP

>> Spc42p  Spindle pole body component Spc42p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.4   3.9e-05      0.12      17      72 ..       8      62 ..       2      65 .. 0.85
   2 ?    4.0   0.0     0.017        51       3      20 ..     148     165 ..     146     167 .. 0.86
   3 ?   -1.5   0.1      0.87   2.6e+03       7      15 ..     196     204 ..     191     221 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                        Spc42p 17 kqeEierLnvlvgslRaKLiKYtelnkKLedqlenlersssslekktedandyiqe 72
                                   q+E+ +L   v slR     Y+++ kK+e + +n+++s+s+  +  +++n+ ++ 
  gi|15668574|ref|NP_247372.1|  8 SQNEVLELINYVKSLRKQNFSYSQISKKIEIE-RNIKISKSTIIRWCKNSNNPFNK 62
                                  599***************************99.99999999887777777776655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.017
                        Spc42p   3 likQNKeLnkkldekqeE 20 
                                    ++QNKe  +k+ ek  E
  gi|15668574|ref|NP_247372.1| 148 FLSQNKEELFKVAEKYPE 165
                                   579***********9755 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.87
                        Spc42p   7 NKeLnkkld 15 
                                    KeL kkld
  gi|15668574|ref|NP_247372.1| 196 SKELLKKLD 204
                                   577777776 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.8   2.4e+03      28      72 ..      89     134 ..      75     159 .. 0.60
   2 ?   11.5   0.0   8.3e-05      0.25      14      73 ..     164     220 ..     151     264 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.8
                       Hom_end  28 vkkeked.satvktedksvmegivklarsLGikasvktkeekidak 72 
                                    +k+     + +k +dk  ++ + +   + G++ +++  eek +++
  gi|15668574|ref|NP_247372.1|  89 YRKKTGSyYFRIKVVDKDFVDVVKNSLIKIGLNPTISYVEEKTRSN 134
                                   4444333566677777776666666656666666666544444443 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.3e-05
                       Hom_end  14 REaFlaGLvdsdgyvkkekedsatvktedksvmegivklarsLGikasvktkeekidakg 73 
                                    E Fl G+ ds+gyv+++   +++++  d +++e   +l ++L++  ++   ++k  +++
  gi|15668574|ref|NP_247372.1| 164 PEDFLRGFFDSEGYVTSN---KIALENYDLELLEFSKELLKKLDVHSTIHIAKKKGTESN 220
                                   599***************...888888888888888888888888888777444434333 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   6.7e-05       0.2      33      72 ..      15      52 ..       5      53 .. 0.71
   2 ?   -2.9   0.0       3.6   1.1e+04      37      51 ..     127     140 ..     123     150 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                        HTH_32 33 vrariiallreeprWsprqlaarlaeregvkvShstvyri 72
                                  +  +++ l+ ++  +s++q++++++ ++ +k+S+st+ r+
  gi|15668574|ref|NP_247372.1| 15 LINYVKSLR-KQ-NFSYSQISKKIEIERNIKISKSTIIRW 52
                                  333444444.34.9**********5555999******887 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.6
                        HTH_32  37 iiallreeprWsprq 51 
                                   + + + +  rW+ + 
  gi|15668574|ref|NP_247372.1| 127 VEEKT-RSNRWHVEA 140
                                   55666.434887764 PP

>> DUF2281  Protein of unknown function (DUF2281)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3   0.00087       2.6       5      34 ..       3      33 ..       2      44 .. 0.79
   2 ?    2.5   0.1      0.08   2.4e+02      15      54 ..     190     232 ..     186     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00087
                       DUF2281  5 kiqeLPedlkqEvldFaefLleKy...aakkkk 34
                                  +++eL+ +++ E+ ++++ L +++   +  + +
  gi|15668574|ref|NP_247372.1|  3 NLKELSQNEVLELINYVKSLRKQNfsyS--QIS 33
                                  689********************96431..322 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.08
                       DUF2281  15 qEvldFaefLleKy.......aakkkktlklrlaGilkglltmsdDf 54 
                                    E+l F + Ll+K         akkk+t++  ++G   +     dDf
  gi|15668574|ref|NP_247372.1| 190 LELLEFSKELLKKLdvhstihIAKKKGTESN-IRGEIYHY---KDDF 232
                                   699**********999877775566666665.88876666...5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1815.75
//
Query:       gi|15668575|ref|NP_247373.1|  [L=449]
Description: phosphomannomutase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-27   96.4   0.0    2.4e-27   95.3   0.0    1.6  1  PGM_PMM_I        Phosphoglucomutase/phosphomannomutase, alpha
    2.6e-22   79.4   0.2    5.3e-21   75.2   0.1    2.5  2  PGM_PMM_II       Phosphoglucomutase/phosphomannomutase, alpha
      2e-18   66.6   0.0    3.7e-18   65.8   0.0    1.5  1  PGM_PMM_III      Phosphoglucomutase/phosphomannomutase, alpha
    2.5e-13   50.0   0.0    1.5e-12   47.5   0.0    2.2  2  PGM_PMM_IV       Phosphoglucomutase/phosphomannomutase, C-ter
  ------ inclusion threshold ------
      0.021   14.1   0.9      0.048   13.0   0.9    1.5  1  TcdA_TcdB        TcdA/TcdB catalytic glycosyltransferase doma
        2.6    8.4   8.6        1.3    9.3   0.2    3.8  4  Phage_int_SAM_3  Phage integrase, N-terminal SAM-like domain


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.3   0.0   8.2e-31   2.4e-27       3     135 ..       7     130 ..       5     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 8.2e-31
                                   GBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHH CS
                     PGM_PMM_I   3 kfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavs 83 
                                    f+++++Rg++g  el+++++++lg++i++ +++    kk++vG D R+ s+el   ++ gl +  ++v+ +g ++tP ++
  gi|15668575|ref|NP_247373.1|   7 VFKAYDIRGIYG-RELDENFAYSLGKCIGKKFEN----KKILVGNDVRIGSKELLPYFIVGLKEY-ADVFYAGTISTPLMY 81 
                                   79**********.67******************8....7**********************9888.9************** PP

                                   HHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT- CS
                     PGM_PMM_I  84 fairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekee 135
                                   f ++  k+d g+++taSHnppey+g+K+++++ +p+sp   e+I+ i++k+e
  gi|15668575|ref|NP_247373.1|  82 FGTKG-KYDLGVILTASHNPPEYTGFKMCDKEAIPLSP--IEEIKPIFKKYE 130
                                   ****9.9*************************999998..578888888776 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.1   1.8e-24   5.3e-21      10     103 .]     157     250 ..     151     250 .. 0.93
   2 ?    1.3   0.0      0.17   5.2e+02      16      56 ..     268     315 ..     256     330 .. 0.63

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 1.8e-24
                                   TS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG-SEEEEE- CS
                    PGM_PMM_II  10 kvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkegadlglafD 90 
                                   k+  ++ k s+ k+++d ++Ga+    ke+l+el  + v +n++pd++fp + p+  + e+lk++i++vkk++++lgl+fD
  gi|15668575|ref|NP_247373.1| 157 KFFLKRCKASDKKIAVDFANGATTIAEKEILNELFDNAVFINDYPDGNFPAHQPDTLKMECLKDIIRAVKKNNCELGLIFD 237
                                   344678899999*********************8889999***************************************** PP

                                   TTS-BEEEEETTE CS
                    PGM_PMM_II  91 gDaDRlgvvderG 103
                                   gD+DRlg+vde+G
  gi|15668575|ref|NP_247373.1| 238 GDGDRLGIVDENG 250
                                   ***********98 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.17
                                   HHHHT-EEEEE-TT-TTHHHHHHHHHHTT-.........EEEE.S-----T CS
                    PGM_PMM_II  16 ikksglkvvidplhGaggeilkellkelgv.........dvve.lnaepdp 56 
                                   ++ks+ k+v+d      ++i++e+++++g           +++ l +e d+
  gi|15668575|ref|NP_247373.1| 268 KEKSNAKIVYDLRC---SKIVPEIIEKYGGiaiksrvghYFIKkLMHEIDA 315
                                   45668888888865...6899999999988555555554333334444444 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   1.2e-21   3.7e-18       2     111 ..     255     361 ..     254     364 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 1.2e-21
                                   HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBSS CS
                   PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeatt 82 
                                   gd l a++ak++l+e  k +a++v ++ +s+++ ++++k+g+ +++++vG+ +++++m+e +a ++gE S h++f++  + 
  gi|15668575|ref|NP_247373.1| 255 GDILTAIIAKEILKE--KSNAKIVYDLRCSKIVPEIIEKYGGIAIKSRVGHYFIKKLMHEIDAEFAGELSNHFYFKEIGYF 333
                                   99**********995..55668*********************************************************** PP

                                   --HHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                   PGM_PMM_III  83 kDGilaallvleilaetgkslselleell 111
                                      +la   +l+++ e++kslsel +e +
  gi|15668575|ref|NP_247373.1| 334 ESPLLALNYILKAMDEENKSLSELNKE-F 361
                                   ************************865.4 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.58   1.7e+03       3      39 ..     162     197 ..     160     224 .. 0.73
   2 !   47.5   0.0   5.2e-16   1.5e-12       1      73 [.     369     442 ..     369     443 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.58
                                   CCCHCC-TT..EECCCCCTTHHCCCCCCCCGCCEEEE CS
                    PGM_PMM_IV   3 nvrveekakvvaalaallkvasikeglkilledGrrl 39 
                                   +++  +k k+  ++a  + +  +ke+l  l+ +++++
  gi|15668575|ref|NP_247373.1| 162 RCKASDK-KIAVDFANGATTIAEKEILNELFDNAVFI 197
                                   5666665.44666666666557889999999988877 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 5.2e-16
                                   CCCCCHCC-TT...EECCCCCTTH..HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHHHH CS
                    PGM_PMM_IV   1 linvrveekak.vvaalaallkva..sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevaell 73 
                                   +in+rv+++ k +++++++++k+   ++ +g+ i  ++ ++  +RpS+Tepllr+++Ea++++ +++ +ee+ +l+
  gi|15668575|ref|NP_247373.1| 369 EINFRVKDQ-KyIMEKIKEHFKDCklEELDGISIYCKNFWFN-LRPSNTEPLLRLNLEADDEKTMKEKVEEIKNLI 442
                                   8*******6.66**********97788888888888888887.****************************99887 PP

>> TcdA_TcdB  TcdA/TcdB catalytic glycosyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.9   1.6e-05     0.048      45     102 ..     130     199 ..     126     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHHHHHHHHHHHCCCCCT--HHHHHHHHHHHHHHH.............................H CS
                     TcdA_TcdB  45 klkkilvesasdaalqdlreaidedtkkfvkkrdeliekr............aekdqlkdlldtlvivaq 102
                                   +l + ++e+a++  l+dl+ +i e++kkf+ kr +  +k+            aek+ l +l+d  v++ +
  gi|15668575|ref|NP_247373.1| 130 ELTESIKEEAKNLNLDDLKVNIIEEYKKFFLKRCKASDKKiavdfangattiAEKEILNELFDNAVFIND 199
                                   68899***********************************9*****99999999999*****99987665 PP

>> Phage_int_SAM_3  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.13     4e+02      32      43 ..     121     132 ..     118     137 .. 0.86
   2 ?    1.0   0.2      0.17   5.2e+02      25      55 ..     127     157 ..     126     160 .. 0.84
   3 ?   -2.5   0.1       2.1   6.4e+03      28      45 ..     296     313 ..     295     316 .. 0.79
   4 ?    9.3   0.2   0.00044       1.3      26      53 ..     377     406 ..     373     410 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.13
                                   THHHHTTSSBGG CS
               Phage_int_SAM_3  32 hIlPyFgniklk 43 
                                    I+P F+++ l+
  gi|15668575|ref|NP_247373.1| 121 EIKPIFKKYELT 132
                                   49*******997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.17
                                   HHHHHTTTHHHHTTSSBGGG--HHHHHHHHH CS
               Phage_int_SAM_3  25 yksiiknhIlPyFgniklkkItpadiqkfqn 55 
                                   +k+ +  +I+   +n+ l++++   i ++ +
  gi|15668575|ref|NP_247373.1| 127 KKYELTESIKEEAKNLNLDDLKVNIIEEYKK 157
                                   56777788888899***********999876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.1
                                   HHTTTHHHHTTSSBGGG- CS
               Phage_int_SAM_3  28 iiknhIlPyFgniklkkI 45 
                                   +ik+++  yF ++ + +I
  gi|15668575|ref|NP_247373.1| 296 AIKSRVGHYFIKKLMHEI 313
                                   689999999988888777 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.00044
                                   HHHHTTTHHHHTTSSBGGG--..HHHHHHH CS
               Phage_int_SAM_3  26 ksiiknhIlPyFgniklkkIt..padiqkf 53 
                                   +++i  +I+ +F+++kl+++   ++++++f
  gi|15668575|ref|NP_247373.1| 377 QKYIMEKIKEHFKDCKLEELDgiSIYCKNF 406
                                   5555567*************9888888884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3340.05
//
Query:       gi|15668576|ref|NP_247374.1|  [L=273]
Description: fructose-bisphosphate aldolase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      4e-72  242.6   0.1    4.7e-72  242.4   0.1    1.1  1  DeoC       DeoC/LacD family aldolase
  ------ inclusion threshold ------
      0.012   15.3   0.4      0.022   14.3   0.1    1.6  2  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil
        0.1   12.9   0.0        2.9    8.2   0.0    2.6  3  PucR       Purine catabolism regulatory protein-like family


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.4   0.1   7.9e-76   4.7e-72       1     235 []      27     243 ..      27     243 .. 0.99

  Alignments for each domain:
  == domain 1  score: 242.4 bits;  conditional E-value: 7.9e-76
                                   EEEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEE CS
                          DeoC   1 ivilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvd 81 
                                   +vi+++D++v+n+++++       +d++++v++++++ga+avll++g++++++++y+kd++l+++l+ gt +++++ ++v+
  gi|15668576|ref|NP_247374.1|  27 TVIVPMDHGVSNGPIKGL------IDIRKTVNDVAEGGANAVLLHKGIVRHGHRGYGKDVGLIIHLSGGTAISPNPLKKVI 101
                                   69****************......9******************************************************** PP

                                   TTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHHHHTC CS
                          DeoC  82 evasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeAarvsae 162
                                    v++veea+++GAdav+++v++   gs+e+++ ++++++++e+c+ +g+pli+++y+r+++i++e+ dp+lva+Aar++ae
  gi|15668576|ref|NP_247374.1| 102 -VTTVEEAIRMGADAVSIHVNV---GSDEDWEAYRDLGMIAETCEYWGMPLIAMMYPRGKHIQNER-DPELVAHAARLGAE 177
                                   .*********************...*****************************************.************** PP

                                   CT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEESHHHHTT CS
                          DeoC 163 lGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvlsGRaifqk 235
                                   lGaDi+K++++        +d+++f+dv+k++p p vv++GG+   ++e+fl++++dA+ eaga+Gv++GR+ifq+
  gi|15668576|ref|NP_247374.1| 178 LGADIVKTSYT--------GDIDSFRDVVKGCPAP-VVVAGGPktnTDEEFLQMIKDAM-EAGAAGVAVGRNIFQH 243
                                   ***********........****************.*********99************.**************97 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.1   6.7e+03      66      80 ..      45      59 ..      44      69 .. 0.76
   2 ?   14.3   0.1   3.7e-06     0.022      83     221 ..     109     249 ..      99     253 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.1
                                  -S-HHHHHHHHHSTC CS
                     OMPdecase 66 aDIGntvekqatags 80
                                   DI +tv+  a++g+
  gi|15668576|ref|NP_247374.1| 45 IDIRKTVNDVAEGGA 59
                                  699999999998655 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.7e-06
                                   HHTTESEEEEEGTGHHH....HHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCC CS
                     OMPdecase  83 ikewadivtvhavaGka....svkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqe 159
                                   i  +ad+v +h+ +G++    + + l   ae ++  g+ ++a+m   g+    e   + ++v +a++  ae    G+   +
  gi|15668576|ref|NP_247374.1| 109 IRMGADAVSIHVNVGSDedweAYRDLGMIAETCEYWGMPLIAMMYPRGKHIQNE--RDPELVAHAARLGAE---LGADIVK 184
                                   556666666666666431111233333333333344778888888888888888..788888888888867...6776666 PP

                                   HTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHH......HHHHHTTCSEEEESHHHHTSSSHHHH CS
                     OMPdecase 160 tlnateedaddfihltpgigleqggdgkgqqyntpe......kligiagadiiivGRgIlkagdpvee 221
                                   t      d d f  +++g+ +    +++g + nt e      k++ +aga  + vGR I++ +d v  
  gi|15668576|ref|NP_247374.1| 185 TSY--TGDIDSFRDVVKGCPA-PVVVAGGPKTNTDEeflqmiKDAMEAGAAGVAVGRNIFQHDDVVGI 249
                                   655..34469**********9.77777777777776222222456789**************998765 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.2   7.1e+03      59      78 ..      47      66 ..      46      73 .. 0.80
   2 ?    1.7   0.0     0.048   2.9e+02      60     100 ..     102     151 ..      84     156 .. 0.66
   3 ?    8.2   0.0   0.00049       2.9      45      79 ..     206     239 ..     161     261 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                          PucR 59 laelvrelaeagvaaLvikl 78
                                  ++++v+++ae g+ a+ +  
  gi|15668576|ref|NP_247374.1| 47 IRKTVNDVAEGGANAVLLHK 66
                                  67899999999999988765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.048
                          PucR  60 aelvrelaeagvaaLviklg....r.....eipeelieaadelglPliel 100
                                     +v+e  + g+ a+ i ++    +     +    + e+++ +g+Pli++
  gi|15668576|ref|NP_247374.1| 102 VTTVEEAIRMGADAVSIHVNvgsdEdweayRDLGMIAETCEYWGMPLIAM 151
                                   5667777777777777777544541342221125678999999****998 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00049
                          PucR  45 llttglalkddpealaelvrelaeagvaaLviklg 79 
                                   ++  g   ++++e++ +++++  eag+a+++++ +
  gi|15668576|ref|NP_247374.1| 206 VVAGGPK-TNTDEEFLQMIKDAMEAGAAGVAVGRN 239
                                   4444444.458999*****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1635.79
//
Query:       gi|15668577|ref|NP_247375.1|  [L=66]
Description: hypothetical protein MJ_0401 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0029   17.7   1.0     0.0054   16.8   1.0    1.5  1  Zn-ribbon_8    Zinc ribbon domain
      0.005   16.3   0.2        3.1    7.4   0.0    2.2  2  TF_Zn_Ribbon   TFIIB zinc-binding
     0.0057   16.6   1.0      0.007   16.4   0.3    1.5  2  DZR            Double zinc ribbon
     0.0099   15.8   1.6        3.6    7.6   0.1    2.8  3  Nudix_N_2      Nudix N-terminal
  ------ inclusion threshold ------
      0.016   14.6   4.3       0.11   12.0   0.2    2.7  3  zf-ribbon_3    zinc-ribbon domain
      0.021   14.2   0.2      0.022   14.1   0.2    1.0  1  FAM76          FAM76 protein
      0.046   14.0   0.5      0.068   13.4   0.5    1.4  1  zinc_ribbon_9  zinc-ribbon
      0.069   13.2   0.1      0.082   12.9   0.1    1.1  1  HypA           Hydrogenase/urease nickel incorporation, metal
      0.096   12.3   3.2       0.31   10.7   0.1    2.5  3  zf_UBZ         Ubiquitin-Binding Zinc Finger
       0.28   10.9   0.4       0.28   10.9   0.4    2.5  3  zinc_ribbon_2  zinc-ribbon domain
        2.7    8.0   8.1        4.2    7.4   2.3    2.4  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
        5.5    7.1   6.0       0.79    9.8   0.3    2.3  3  Ogr_Delta      Ogr/Delta-like zinc finger


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.0   3.6e-06    0.0054       6      36 ..       6      34 ..       1      36 [. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.6e-06
                   Zn-ribbon_8  6 YrCeeCghefevlqsisdaplta.CPeCgsev 36
                                  + C +C+++ ev   +    +++ CP Cg+++
  gi|15668577|ref|NP_247375.1|  6 FLCAKCQKVIEVPYGVP---KPDvCPYCGAPA 34
                                  78*********776554...4555*****965 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0025       3.8      20      38 ..       6      24 ..       4      25 .. 0.91
   2 !    7.4   0.0    0.0021       3.1       2      10 ..      26      34 ..      26      44 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0025
                                  EEESSSSBEEEECCCCCCC CS
                  TF_Zn_Ribbon 20 lvCtdCGlVlednsidegp 38
                                  ++C +C  V+e  + +++p
  gi|15668577|ref|NP_247375.1|  6 FLCAKCQKVIEVPYGVPKP 24
                                  89**********9999988 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0021
                                  EETTTTCEE CS
                  TF_Zn_Ribbon  2 kCPnCgstn 10
                                  +CP+Cg + 
  gi|15668577|ref|NP_247375.1| 26 VCPYCGAPA 34
                                  699999865 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   4.7e-06     0.007      14      39 ..       7      35 ..       2      42 .. 0.80
   2 ?   -3.3   0.0       6.5   9.7e+03      18      19 ..      55      56 ..      51      59 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.7e-06
                           DZR 14 fCseCgtklkavaa...edrCpsCgekvd 39
                                   C +C++ ++ +     +d+Cp Cg++++
  gi|15668577|ref|NP_247375.1|  7 LCAKCQKVIEVPYGvpkPDVCPYCGAPAT 35
                                  7*****99875544888********9986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.5
                           DZR 18 Cg 19
                                  Cg
  gi|15668577|ref|NP_247375.1| 55 CG 56
                                  44 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.1    0.0052       7.7      21      31 ..       4      14 ..       2      15 .. 0.86
   2 !    7.6   0.1    0.0024       3.6       3      17 ..      27      43 ..      26      46 .. 0.81
   3 ?   -1.4   0.0       1.5   2.3e+03       5      10 ..      54      59 ..      53      64 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0052
                                  -EEEETTTTEE CS
                     Nudix_N_2 21 eRlvCpaCgti 31
                                   R+ C++C+ +
  gi|15668577|ref|NP_247375.1|  4 KRFLCAKCQKV 14
                                  79******987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0024
                                  -TTT--B-E..EE--TT CS
                     Nudix_N_2  3 CsqCGtpve..lripdg 17
                                  C+ CG+p +  +ri +g
  gi|15668577|ref|NP_247375.1| 27 CPYCGAPATfiHRIDAG 43
                                  999***98767888777 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.5
                                  TT--B- CS
                     Nudix_N_2  5 qCGtpv 10
                                   CG ++
  gi|15668577|ref|NP_247375.1| 54 RCGMRM 59
                                  588775 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.032        48      19      26 .]       8      15 ..       7      15 .. 0.85
   2 ?   12.0   0.2   7.1e-05      0.11       5      11 ..      27      33 ..      25      36 .. 0.62
   3 ?   -1.5   0.0       1.3   1.9e+03      22      25 ..      55      58 ..      54      59 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.032
                   zf-ribbon_3 19 CpyCGtkl 26
                                  C++C++++
  gi|15668577|ref|NP_247375.1|  8 CAKCQKVI 15
                                  ****9986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.1e-05
                   zf-ribbon_3  5 CPnCGap 11
                                  CP+CGap
  gi|15668577|ref|NP_247375.1| 27 CPYCGAP 33
                                  6666665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.3
                   zf-ribbon_3 22 CGtk 25
                                  CG++
  gi|15668577|ref|NP_247375.1| 55 CGMR 58
                                  8876 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.5e-05     0.022      50      79 ..       5      37 ..       1      47 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                         FAM76 50 stiCkkCeknvk.kYG..kPkaCelCniiaaFi 79
                                  + +C kC+k  +  YG  kP  C +C   a+Fi
  gi|15668577|ref|NP_247375.1|  5 RFLCAKCQKVIEvPYGvpKPDVCPYCGAPATFI 37
                                  678*****987637**444557*********98 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   4.6e-05     0.068       5      35 .]       8      40 ..       4      40 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.6e-05
                 zinc_ribbon_9  5 ChqCdrfVsvspd..edsdvlCPhCgg..gFVEei 35
                                  C  C++ ++v p     +dv CP+Cg    F+++i
  gi|15668577|ref|NP_247375.1|  8 CAKCQKVIEV-PYgvPKPDV-CPYCGApaTFIHRI 40
                                  6689999998.552567777.****9533777765 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.5e-05     0.082      70      97 ..       5      35 ..       1      43 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                                  EEEETTTS-EEECHH...HHHS-TTTSSS-E CS
                          HypA 70 kvrCreCgkefelee...kalrCpkCgsadv 97
                                  ++ C +C+k +e+     k   Cp Cg+  +
  gi|15668577|ref|NP_247375.1|  5 RFLCAKCQKVIEVPYgvpKPDVCPYCGAPAT 35
                                  789*********8765433347*****9876 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00021      0.31       2      14 ..       5      17 ..       4      21 .. 0.88
   2 ?    1.6   0.1      0.14   2.1e+02       4      10 ..      26      32 ..      24      34 .. 0.86
   3 ?   -1.4   0.1       1.2   1.8e+03       7      12 ..      54      59 ..      53      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                        zf_UBZ  2 tylCerCgkeipe 14
                                   +lC++C+k i++
  gi|15668577|ref|NP_247375.1|  5 RFLCAKCQKVIEV 17
                                  599********87 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.14
                        zf_UBZ  4 lCerCgk 10
                                  +C+ Cg+
  gi|15668577|ref|NP_247375.1| 26 VCPYCGA 32
                                  7****97 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.2
                        zf_UBZ  7 rCgkei 12
                                  rCg ++
  gi|15668577|ref|NP_247375.1| 54 RCGMRM 59
                                  9**886 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.16   2.5e+02       2       6 ..       8      12 ..       5      19 .. 0.71
   2 ?   10.9   0.4   0.00019      0.28      16      22 ..      27      33 ..      21      33 .. 0.90
   3 ?   -2.1   0.1       2.3   3.5e+03       4       6 ..      54      56 ..      53      57 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.16
                 zinc_ribbon_2  2 CpnCG 6 
                                  C +C 
  gi|15668577|ref|NP_247375.1|  8 CAKCQ 12
                                  66665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00019
                 zinc_ribbon_2 16 CpyCGtp 22
                                  CpyCG+p
  gi|15668577|ref|NP_247375.1| 27 CPYCGAP 33
                                  9999997 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.3
                 zinc_ribbon_2  4 nCG 6 
                                  +CG
  gi|15668577|ref|NP_247375.1| 54 RCG 56
                                  455 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.3     0.033        50      36      45 ..       4      13 ..       2      14 .. 0.82
   2 ?    7.4   2.3    0.0028       4.2      19      34 ..      25      39 ..      19      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.033
                 Zn_Tnp_IS1595 36 glfqCkeCrk 45
                                  ++f C++C+k
  gi|15668577|ref|NP_247375.1|  4 KRFLCAKCQK 13
                                  7899999986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0028
                 Zn_Tnp_IS1595 19 fvCPhCgsrkayrikt 34
                                   vCP+Cg + a++i +
  gi|15668577|ref|NP_247375.1| 25 DVCPYCG-APATFIHR 39
                                  58*****.55555555 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.93   1.4e+03       2       8 ..       8      14 ..       7      17 .. 0.78
   2 ?    9.8   0.3   0.00053      0.79       2      10 ..      27      35 ..      26      39 .. 0.88
   3 ?   -1.1   0.1       1.3     2e+03       5      13 ..      55      63 ..      54      66 .] 0.73

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.93
                     Ogr_Delta  2 CPhCgap 8 
                                  C +C++ 
  gi|15668577|ref|NP_247375.1|  8 CAKCQKV 14
                                  9999976 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00053
                     Ogr_Delta  2 CPhCgapaa 10
                                  CP+Cgapa+
  gi|15668577|ref|NP_247375.1| 27 CPYCGAPAT 35
                                  *******96 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.3
                     Ogr_Delta  5 Cgapaaart 13
                                  Cg ++  r 
  gi|15668577|ref|NP_247375.1| 55 CGMRMMGRF 63
                                  999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 424.70
//
Query:       gi|15668578|ref|NP_247376.1|  [L=106]
Description: hypothetical protein MJ_0402 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00012   23.1  14.5       0.02   15.9  14.5    2.2  1  DUF5320     Family of unknown function (DUF5320)
  ------ inclusion threshold ------
       0.01   15.2   4.2      0.012   15.0   4.2    1.1  1  DUF2353     Uncharacterized coiled-coil protein (DUF2353)
      0.024   15.0   0.0      0.028   14.8   0.0    1.1  1  DUF4140     N-terminal domain of unknown function (DUF4140)
      0.038   14.0   5.1      0.045   13.8   5.1    1.1  1  TPR_MLP1_2  TPR/MLP1/MLP2-like protein
      0.069   12.4   4.8       0.08   12.2   4.8    1.0  1  FmiP_Thoc5  Fms-interacting protein/Thoc5


Domain annotation for each model (and alignments):
>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9  14.5   5.7e-06      0.02      37      99 .]       2     103 ..       1     103 [. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.7e-06
                       DUF5320  37 fGrgrggrglgrgfgrrrraggarla.......................................aaetaeaskeeekelL 78 
                                   fG+grg++g+grgf+r +  + ++++                                       a+  ++   ee+++ L
  gi|15668578|ref|NP_247376.1|   2 FGWGRGWFGRGRGFWRYFPVSTVGGRyryvgpcrcglgphafyvdektgalvhawdlyrgyvpgyAEVDERRYLEETIKEL 82 
                                   56666888888888886665555555777899999999999999999999999999999999997777888899999**** PP

                       DUF5320  79 eeqaeaLeeeleaikkrlkel 99 
                                   ee++++Leeel+ ikkrl+el
  gi|15668578|ref|NP_247376.1|  83 EEEKRMLEEELARIKKRLDEL 103
                                   ******************997 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   4.2   3.4e-06     0.012     196     231 ..      70     105 ..      67     106 .] 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.4e-06
                       DUF2353 196 lENrYlkerlkqleeEkelakqtlskYksllekkkn 231
                                    E rYl+e +k+leeEk +++++l++ k+ l++ k+
  gi|15668578|ref|NP_247376.1|  70 DERRYLEETIKELEEEKRMLEEELARIKKRLDELKK 105
                                   699***************************987665 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   7.8e-06     0.028      65      96 ..      70     101 ..      39     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.8e-06
                       DUF4140  65 eelkalraeleeledelaaledelaaaearla 96 
                                   +e + l+++++ele+e++ le+ela++++rl+
  gi|15668578|ref|NP_247376.1|  70 DERRYLEETIKELEEEKRMLEEELARIKKRLD 101
                                   34677777777777777777777777777765 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   5.1   1.3e-05     0.045      86     117 ..      74     105 ..      68     106 .] 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                    TPR_MLP1_2  86 eleeseesweeqkeelekelselekriedlne 117
                                    lee  +++ee+k +le+el+ ++kr+++l++
  gi|15668578|ref|NP_247376.1|  74 YLEETIKELEEEKRMLEEELARIKKRLDELKK 105
                                   58888899**********************97 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   4.8   2.2e-05      0.08      99     137 ..      67     105 ..      66     106 .] 0.95

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                    FmiP_Thoc5  99 wEleqRkelaeqlkeleekkkkleqeieekkkfLssLpp 137
                                    E ++R+ l+e++kelee+k+ le+e +  kk+L++L++
  gi|15668578|ref|NP_247376.1|  67 AEVDERRYLEETIKELEEEKRMLEEELARIKKRLDELKK 105
                                   599*********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1476  (0.0823247); expected 358.6 (0.02)
Passed bias filter:                     1011  (0.0563891); expected 358.6 (0.02)
Passed Vit filter:                       221  (0.0123264); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 667.48
//
Query:       gi|15668579|ref|NP_247377.1|  [L=287]
Description: hypothetical protein MJ_0403 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   6.5e-102  340.3   0.1   7.4e-102  340.1   0.1    1.0  1  Memo        Memo-like protein
     0.0014   17.7   0.0     0.0022   17.1   0.0    1.4  1  LigB        Catalytic LigB subunit of aromatic ring-opening d
  ------ inclusion threshold ------
      0.021   14.8   0.1      0.049   13.6   0.1    1.6  1  Mo-nitro_C  Mo-dependent nitrogenase C-terminus
      0.038   13.9   0.1      0.093   12.6   0.1    1.6  1  LeuA_dimer  LeuA allosteric (dimerisation) domain


Domain annotation for each model (and alignments):
>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.1   0.1  1.6e-105  7.4e-102       2     270 ..       7     284 ..       6     285 .. 0.96

  Alignments for each domain:
  == domain 1  score: 340.1 bits;  conditional E-value: 1.6e-105
                          Memo   2 aavAGsfYpedeeelkkqleeflekntgkkei.....arviis...PHagyvysgevaakayaeles....skvervvilG 70 
                                   +avAG+fYp++++el +++e+++++++g+k++     +++ i    PHagyvysg+++a++y+el++     ++++vvilG
  gi|15668579|ref|NP_247377.1|   7 PAVAGLFYPSHPDELIDMIEQCYLHKFGPKSMpvhgtYEKPIGllcPHAGYVYSGPIQAHSYYELSKrvdaLEETTVVILG 87 
                                   89****************************99*9999666544455*******************9987766899****** PP

                          Memo  71 psHtilgskvsvlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkek..kfkivPilvs 149
                                   p+Ht+lgs+vsv++ ++++TPlGd+k+Dee+veeL++k+ei+dldeta+l+EHS+EvqlpfLk+l   +  kfkivPi+++
  gi|15668579|ref|NP_247377.1|  88 PNHTGLGSGVSVMD-GIWRTPLGDVKCDEEFVEELWRKCEIVDLDETAHLNEHSIEVQLPFLKHLELLNiaKFKIVPICMM 167
                                   **************.*************************************************9999999********** PP

                          Memo 150 aqseetakevgealakvikdes..nlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelkeylektnnticGe 228
                                   +q++eta evg+++ak++k+ +  ++vi+SsDl+Hy+     pqeia+++ D++vik++ e+ne+el+e ++++n+++cG+
  gi|15668579|ref|NP_247377.1| 168 FQDYETAVEVGYFIAKIAKELNrrIVVIASSDLTHYE-----PQEIASKK-DAIVIKDILEMNEKELYEDVVNYNISMCGY 242
                                   *********************9999************.....********.****************************** PP

                          Memo 229 kpiavilkalkklgakkakllkYaqssdvtsdtdsvVsyasl 270
                                   +p++++lka+k+lga+kakll+Ya+s+d+t+d+++vV+yas+
  gi|15668579|ref|NP_247377.1| 243 GPVIAMLKAMKTLGAEKAKLLAYATSGDITGDYSAVVGYASA 284
                                   ****************************************98 PP

>> LigB  Catalytic LigB subunit of aromatic ring-opening dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.9e-07    0.0022     126     195 ..     153     215 ..      64     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.9e-07
                          LigB 126 lmlpdeakvpvikvslntvaypllsferlykLGeAlrkaveeldknvlilgsGglsHqlegdeaakadaq 195
                                   l++   ak + +++ ++     + + e   ++G  ++k+ +el++++++++s +l+H+ +++ a k+da 
  gi|15668579|ref|NP_247377.1| 153 LLNI--AKFKIVPICMM-----FQDYETAVEVGYFIAKIAKELNRRIVVIASSDLTHYEPQEIASKKDAI 215
                                   3333..34444444444.....69**********************************999998888874 PP

>> Mo-nitro_C  Mo-dependent nitrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.1e-05     0.049      13      63 ..     126     177 ..     116     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                    Mo-nitro_C  13 eikd.kklakllckliPaqCPFerdiklfgrkllhiPplCklnPlyeelval 63 
                                   ei d +++a+l  + i +q PF ++++l++   ++i p+C +   ye  v++
  gi|15668579|ref|NP_247377.1| 126 EIVDlDETAHLNEHSIEVQLPFLKHLELLNIAKFKIVPICMMFQDYETAVEV 177
                                   54442678999999****************************9999988876 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.1e-05     0.093      50      82 ..     227     266 ..     197     277 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                                   E.......EEEEEE-SSHHHHHHHHHHHHHHHT-EEEEEE CS
                    LeuA_dimer  50 e.......keasaeGnGpvdAllnAlrkalgvdikLldYs 82 
                                   e       +++s  G Gpv A+l+A++ +  +++kLl Y 
  gi|15668579|ref|NP_247377.1| 227 ElyedvvnYNISMCGYGPVIAMLKAMKTLGAEKAKLLAYA 266
                                   2455555589999***************8888******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1793.69
//
Query:       gi|15668580|ref|NP_247378.1|  [L=150]
Description: hypothetical protein MJ_0404 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-65  218.9   0.1    2.9e-65  218.6   0.1    1.0  1  DUF2112   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
       0.15   12.3   0.0       0.27   11.4   0.0    1.3  1  VF530     DNA-binding protein VF530


Domain annotation for each model (and alignments):
>> DUF2112  Uncharacterized protein conserved in archaea (DUF2112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.6   0.1   3.3e-69   2.9e-65       2     143 .]       3     144 ..       2     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 218.6 bits;  conditional E-value: 3.3e-69
                       DUF2112   2 kvaviPdnsliladlverfgheplslakeikekvktaeldspplniteedpkkGlkyaavevPsGvrGRlsligplieeae 82 
                                   k++++P+nslil+dlverfgh+pl+l+  i + v+++e+dspp+nit+e+pkkGlkyaavevPsGvrGR++ligplieeae
  gi|15668580|ref|NP_247378.1|   3 KIFIYPPNSLILTDLVERFGHKPLNLNIVIGKLVRNPEIDSPPMNITDEEPKKGLKYAAVEVPSGVRGRMALIGPLIEEAE 83 
                                   9******************************************************************************** PP

                       DUF2112  83 aaiiveeadilfgcvGCartnelvkalirkkdiPileleyPkseeeaielvkkineFLksl 143
                                   aaii+++a+i+fgc+GC+rtnel+ +l+r+k+iPil ++yP++eeea  lv+ki++FLksl
  gi|15668580|ref|NP_247378.1|  84 AAIIMDDAPIAFGCIGCQRTNELTLYLVRRKNIPILRVKYPTNEEEAEILVNKIANFLKSL 144
                                   **********************************************************986 PP

>> VF530  DNA-binding protein VF530
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.1e-05      0.27      13      43 ..      13      43 ..      10      45 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                                  HHHHHHHHT-HHHHHHHTTSSSTTSS--HHH CS
                         VF530 13 ileeLveeygweeLaerinircFksnpsikS 43
                                  il++Lve++g++ L+ +i i  +  np+i+S
  gi|15668580|ref|NP_247378.1| 13 ILTDLVERFGHKPLNLNIVIGKLVRNPEIDS 43
                                  9****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1078.98
//
Query:       gi|15668581|ref|NP_247379.1|  [L=131]
Description: hypothetical protein MJ_0405 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-33  114.3   3.1    2.5e-33  114.0   3.1    1.1  1  DUF2111   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2111  Uncharacterized protein conserved in archaea (DUF2111)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   3.1   1.4e-37   2.5e-33       1      83 []      23     104 ..      23     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 1.4e-37
                       DUF2111   1 vhelvgklPvtirsknkkGvriekgkvvdedYtgpvLeevleegkvikkvpkeGaYkGvpvvvaPikekegkviaaiGvVD 81 
                                   vh lv+klPv++rsknk+Gvr+ekg+vvd++Y+g+vL+ ++e+g+v++++p  G+Y+G+pv+vaPik+  ++v++aiGvVD
  gi|15668581|ref|NP_247379.1|  23 VHILVNKLPVAMRSKNKPGVRLEKGEVVDTNYEGYVLKVAIEKGEVVRATPIIGPYAGLPVIVAPIKD-GDNVLGAIGVVD 102
                                   8*******************************************************************.9*********** PP

                       DUF2111  82 it 83 
                                   it
  gi|15668581|ref|NP_247379.1| 103 IT 104
                                   97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 987.57
//
Query:       gi|15668582|ref|NP_247380.1|  [L=302]
Description: ribokinase RbsK [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-68  231.4   0.0    1.7e-68  231.2   0.0    1.0  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.2   0.0   9.2e-73   1.7e-68       1     301 [.       5     289 ..       5     290 .. 0.97

  Alignments for each domain:
  == domain 1  score: 231.2 bits;  conditional E-value: 9.2e-73
                                   EEEEEEEEEEEEEEEEECSSH.TTSEE.EESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEE CS
                          PfkB   1 mtkvvviGealidliavsekl.egelv.evktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdt 79 
                                   m+k+ ++G++  d i ++ek+ e++++ + ++ +k++GGa+aN+Av++++lg+++ ++++vG D+  + ++++lk   +++
  gi|15668582|ref|NP_247380.1|   5 MEKITCVGHTALDYIFNVEKFpEPNTSiQIPSARKYYGGAAANTAVGIKKLGVNSELLSCVGYDFKNSGYERYLKNLDINI 85 
                                   789*******************999999***************************************************** PP

                                   TTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTE CS
                          PfkB  80 dyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggt 160
                                   ++++ +e+++t +a+i++d+d +++i+f+++ aa+ +ke      +   + ++++i++    ++pe +l+ +++a  n+  
  gi|15668582|ref|NP_247380.1|  86 SKLYYSEEEETPKAWIFTDKD-NNQITFFLWGAAKHYKE----LNPPNFNTEIVHIAT----GDPEFNLKCAKKAYGNNLV 157
                                   *******************98.88888888888888885....68************9....******************* PP

                                   .EEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEE CS
                          PfkB 161 .fdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdge 240
                                    fdp +  p  +  ke+lle+++++++l++n +E+e+ ++  + +i++ l+++ +        ++vt+G++G+++++kd++
  gi|15668582|ref|NP_247380.1| 158 sFDPGQDLPQYS--KEMLLEIIEHTNFLFMNKHEFERASNLLNFEIDDYLERVDA--------LIVTKGSKGSVIYTKDKK 228
                                   ***********8..9*************************************866........****************** PP

                                   EEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCSCC CS
                          PfkB 241 lkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiaslpt 301
                                   +++p +++ kv+D+tGAGDs+ +gfl+a+++g +le++  ++ a+A++vv+ kg++++lpt
  gi|15668582|ref|NP_247380.1| 229 IEIPCIKAGKVIDPTGAGDSYRAGFLSAYVKGYDLEKCGLIGAATASFVVEAKGCQTNLPT 289
                                   **********************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2028.22
//
Query:       gi|15668583|ref|NP_247381.1|  [L=307]
Description: quinolinate synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   6.2e-111  370.3   0.5     7e-111  370.1   0.5    1.0  1  NadA            Quinolinate synthetase A protein
     0.0059   16.5   1.3     0.0059   16.5   1.3    1.8  2  DNA_pol3_a_NII  DNA polymerase III polC-type N-terminus II
  ------ inclusion threshold ------
      0.026   14.6   0.4       0.06   13.4   0.2    1.7  2  RNA_pol_RpbG    DNA-directed RNA polymerase, subunit G


Domain annotation for each model (and alignments):
>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.1   0.5  1.2e-114    7e-111       1     298 [.       7     305 ..       7     306 .. 0.93

  Alignments for each domain:
  == domain 1  score: 370.1 bits;  conditional E-value: 1.2e-114
                                   HHHHHHHHHHTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHSTTSEEE-SSTT-.--H CS
                          NadA   1 eeikelkkeknavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLspekkvllpdlea.gCs 80 
                                   e+i++lk+eknavilaHnYq +eiq+iadf+GDSleL+ ka+et+a++ivfcGV+FM+e+akiL+pekkvl+p++e  +C+
  gi|15668583|ref|NP_247381.1|   7 ERINKLKEEKNAVILAHNYQPKEIQKIADFLGDSLELCIKAKETDADIIVFCGVDFMGESAKILNPEKKVLMPEIEGtQCP 87 
                                   68************************************************************************87549** PP

                                   HHCT--HHHHHHHHHHSTTS-EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS-SEEEEES-HHHHHHHHHHH.SEEEEES CS
                          NadA  81 ladmitaeeveelkeelpdaavvtYvNssaevKalsdivcTSsnavkvvealkekkilflPDqnLgryvakklgekkiilw 161
                                   +a++++ e +++++e +p+a++v+YvN++ae+Kal+di+cTS+na++vv++l+ +++lf PD+nL+ yv+k++++k +i +
  gi|15668583|ref|NP_247381.1|  88 MAHQLPPEIIKKYRELYPEAPLVVYVNTTAETKALADITCTSANADRVVNSLDADTVLFGPDNNLAYYVQKRTDKK-VIAI 167
                                   ************************************************************************9776.5555 PP

                                   S..SS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-THHHHHHHHH-T CS
                          NadA 162 k..gaCsvHeefkaeeveelkeehpdakvlvHPEckeevveaadvvgSTsqiikavkeseakefiigTelglverlkkeap 240
                                   +  g C+vH++f+ ++++++k+++p+akvl+HPEc++e+ ++ad++ STs+i+++v es+++efiigTe+g+++rl+ e +
  gi|15668583|ref|NP_247381.1| 168 PegGGCYVHKKFTIDDLKRVKSKYPNAKVLIHPECSPELQDNADYIASTSGILRIVLESDDEEFIIGTEVGMINRLEIELE 248
                                   44699**********************************************************************998654 PP

                                   T....SEEE.....ECSSSSSTTGGG--HHHHHHHHHHT-S.B----HHHHHHHHHHHHHHH CS
                          NadA 241 e....kefialsaeaaeeavCetMkkitleklleaLeeleeeeikvdeevaekAkkalerml 298
                                   +    k++i       ++a+C++Mk+itlek+ ++L e+++ eik+++e++ekA+ka+erml
  gi|15668583|ref|NP_247381.1| 249 KlgkkKTLI----PLRKDAICHEMKRITLEKIEKCLLEERY-EIKLEKEIIEKAQKAIERML 305
                                   322114444....2234899******************999.*******************9 PP

>> DNA_pol3_a_NII  DNA polymerase III polC-type N-terminus II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.5       1.6   9.4e+03      89     109 ..      11      31 ..       8      34 .. 0.58
   2 !   16.5   1.3   9.9e-07    0.0059      31      83 ..     253     302 ..     237     306 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.6
                DNA_pol3_a_NII  89 keeeeekaikeaieakekkea 109
                                   k +ee++a+  a + ++k+ +
  gi|15668583|ref|NP_247381.1|  11 KLKEEKNAVILAHNYQPKEIQ 31 
                                   566777666665555555544 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 9.9e-07
                DNA_pol3_a_NII  31 nkliikvpneiiaealkkkkldklleeyikfgFgklkidvevdedesseeeie 83 
                                   +k +i +++++i++ +k+  l+k+++ ++++++  +k++ e+ e+   ++ ie
  gi|15668583|ref|NP_247381.1| 253 KKTLIPLRKDAICHEMKRITLEKIEKCLLEERYE-IKLEKEIIEKA--QKAIE 302
                                   34459*****************************.*********54..44445 PP

>> RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2     1e-05      0.06      32     104 ..       2      74 ..       1      80 [. 0.83
   2 ?   -2.7   0.0      0.99   5.9e+03      56      68 ..     203     215 ..     180     242 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                  RNA_pol_RpbG  32 elDiiselnifkeedkveviisrekPeyld.gkdFcghGylvtekeeenkiitliSlfGllvkisskkdllnel 104
                                   ++Di++ +n++kee +  +   + +P+ ++ + dF g    +  k + ++ +++i + G+ +  +s k l +e+
  gi|15668583|ref|NP_247381.1|   2 SMDIVERINKLKEEKNAVILAHNYQPKEIQkIADFLGDSLELCIKAK-ETDADIIVFCGVDFMGESAKILNPEK 74 
                                   79************9999999999**9876368*****998888875.79999999999988877776666655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.99
                  RNA_pol_RpbG  56 kPeyldgkdFcgh 68 
                                    Pe +d  d+++ 
  gi|15668583|ref|NP_247381.1| 203 SPELQDNADYIAS 215
                                   5666666666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1977.53
//
Query:       gi|15668584|ref|NP_247382.1|  [L=121]
Description: hypothetical protein MJ_0408 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-39  132.7   0.0    9.2e-39  132.3   0.0    1.1  1  DHNA      Dihydroneopterin aldolase
  ------ inclusion threshold ------
        0.1   12.5   0.0       0.14   12.1   0.0    1.2  1  Fae       Formaldehyde-activating enzyme (Fae)


Domain annotation for each model (and alignments):
>> DHNA  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.3   0.0     1e-42   9.2e-39       1     108 []      17     117 ..      17     117 .. 0.96

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 1e-42
                                   -HHHHHHHHHHHHHHHHHHHHTT-EESTTTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-STS-EE--TTTEEEEE CS
                          DHNA   1 tdrerAvFEagiklgalyHqfvGtPvseesaeslekaieesielQPfvedvkvkidrekleekleefgYteLtgemldvei 81 
                                   tdrerAvFE+gi+lgal+HqfvGtPvs+ ++esle+aiee++++QP+v d+kvki++          +Y++L+g+mldv++
  gi|15668584|ref|NP_247382.1|  17 TDRERAVFEGGITLGALFHQFVGTPVSKYNKESLERAIEEAMKNQPCVYDIKVKIRNV---G----EKYVSLDGKMLDVDL 90 
                                   89*****************************************************874...2....36************* PP

                                   EEEETTEEEEEEEEEETTTTEEEEEEE CS
                          DHNA  82 tvkyeeaevkarleyieeldYplmkve 108
                                   ++k++++ ++ +leyi e dYplm+v+
  gi|15668584|ref|NP_247382.1|  91 KIKINKTVAHLKLEYIPEIDYPLMYVK 117
                                   *************************95 PP

>> Fae  Formaldehyde-activating enzyme (Fae)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.6e-05      0.14     122     150 ..      42      70 ..      39      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                           Fae 122 iyeynyeAtklAikrAlkeePsidevlee 150
                                   + +yn+e+ ++Ai++A+k++P + ++  +
  gi|15668584|ref|NP_247382.1|  42 VSKYNKESLERAIEEAMKNQPCVYDIKVK 70 
                                   568******************99888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 780.38
//
Query:       gi|15668585|ref|NP_247383.1|  [L=703]
Description: hypothetical protein MJ_0409 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (703 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 4559.62
//
Query:       gi|15668586|ref|NP_247384.1|  [L=264]
Description: hypothetical protein MJ_0410 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-16   58.8   0.0    2.1e-15   56.9   0.0    2.0  2  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.7e-15   57.4   1.3    1.8e-15   57.3   0.2    1.7  2  AAA_31       AAA domain
      2e-11   43.8   1.2    1.7e-10   40.8   0.5    2.4  2  ParA         NUBPL iron-transfer P-loop NTPase
    8.9e-06   25.3   1.7    0.00012   21.7   1.7    2.1  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    0.00017   20.9   1.8      0.017   14.3   0.0    3.2  3  ArsA_ATPase  Anion-transporting ATPase
     0.0017   17.7   0.0     0.0047   16.3   0.0    1.7  1  MipZ         ATPase MipZ
     0.0049   16.4   0.0      0.034   13.6   0.0    2.2  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
  ------ inclusion threshold ------
      0.059   13.0   0.2        0.4   10.3   0.1    2.1  2  SRP54        SRP54-type protein, GTPase domain
       0.15   11.9   2.6       0.19   11.5   0.3    2.1  2  AAA_26       AAA domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   1.1e-18   2.1e-15       4     121 ..       6     200 ..       3     207 .. 0.92
   2 ?   -2.7   0.0       2.8   5.6e+03      94     118 ..     231     252 ..     210     258 .. 0.52

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 1.1e-18
                                   EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.............................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
                          CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.............................. 54 
                                    +  GG+GKTt+aan+a +l++   +++l+D+D  +  +a+l+gle ++++                              
  gi|15668586|ref|NP_247384.1|   6 YNIQGGTGKTTVAANFAYILSQ-SVKTILIDCDIYGGTTAVLFGLEDKEHNlntylagdsaiediiyhyddlaiihtdvss 85 
                                   5789******************.********************************************************** PP

                                   .................................................................CCHCCCHHHHHHCHCH CS
                                   .................................................................xxxxxxxxxxxxxxxx RF
                          CbiA  55 .................................................................dlkrllellealgkkk 70 
                                                                                                    +  + +el+ +lg++ 
  gi|15668586|ref|NP_247384.1|  86 kvfgyksdlnrfetlvkeleeeydviiydfppnitednpligyvgefelvnkvvvvgedsipsivNSLKTIELITDLGIG- 165
                                   ***********************************************************999999666779999999988. PP

                                   HHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  71 alllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaea 121
                                        + g+++n+++g    t ++e +        + v+gv+p+d++v + 
  gi|15668586|ref|NP_247384.1| 166 -----LTGIIVNKYRGL---TDISEII--------DDVIGVLPYDQNVERQ 200
                                   .....89********96...4444444........4589999999999665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.8
                                   HHHHHHHHHHCTS-EEEEEE--CCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  94 kealeelkqrygvpvlgviprdeav 118
                                   +++l+ l    ++++ + i++ ++v
  gi|15668586|ref|NP_247384.1| 231 EKDLASLR---ALRLAKAISELTEV 252
                                   33333333...55555555555555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.2     9e-19   1.8e-15       4     129 ..       3     119 ..       1     158 [. 0.89
   2 ?   -2.0   0.1       1.5     3e+03      88     110 ..     240     262 ..     204     264 .] 0.64

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 9e-19
                        AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkvenldli 84 
                                   I ++n  GG GKTT + n+a+ l+++  k++l+D+D  + +t  l +  +++e++l++ l+ ++ i+++i+  ++++l +i
  gi|15668586|ref|NP_247384.1|   3 IGFYNIQGGTGKTTVAANFAYILSQS-VKTILIDCDIYGGTTAVL-FGLEDKEHNLNTYLAGDSAIEDIIY--HYDDLAII 79 
                                   899********************875.78889******9999854.56788899*****************..55677777 PP

                        AAA_31  85 pssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsL 129
                                    +     +++ ++++ ++  +++++l++++++eYD+ii D pP++
  gi|15668586|ref|NP_247384.1|  80 HT-----DVSSKVFGYKSDLNRFETLVKELEEEYDVIIYDFPPNI 119
                                   64.....4567899999999***********************97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                        AAA_31  88 idLaeaeielvelekkeeilkel 110
                                   + La+a  el+e+ek+e+ ++++
  gi|15668586|ref|NP_247384.1| 240 LRLAKAISELTEVEKSEKDFEDY 262
                                   45666667777777776666655 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.5   8.6e-14   1.7e-10      12     173 ..       9     172 ..       2     183 .. 0.75
   2 ?   -0.3   0.0      0.29   5.8e+02     204     245 ..     186     225 ..     173     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 8.6e-14
                          ParA  12 KGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvmSigf.llesedeavv 90 
                                    GG GK+tva+n+A+ L++  +k+ l+D DiyG   + l+g+e+++ + ++  l   +a ++i     ++ +++++ ++ v
  gi|15668586|ref|NP_247384.1|   9 QGGTGKTTVAANFAYILSQ-SVKTILIDCDIYGGTTAVLFGLEDKEHNLNT-YLAGDSAiEDIIYHYDDLaIIHTDVSSKV 87 
                                   6****************75.67888*******************8665554.44433333554444333303333445555 PP

                          ParA  91 wrGpmkskaikqllkdvewgelDyLiiDlPPG.tgDeql.tvaqkl.plagaviVttpqevaladvkkaiemfkkvkvkvl 168
                                   +      +  + l+k+ e +e D++i D+PP  t D  l   + ++  ++++v+V      ++ +  k+ie+++++ + + 
  gi|15668586|ref|NP_247384.1|  88 FGYKSDLNRFETLVKELE-EEYDVIIYDFPPNiTEDNPLiGYVGEFeLVNKVVVVGEDSIPSIVNSLKTIELITDLGIGLT 167
                                   555556667778888777.88**********967898873456666256677777777777899999************** PP

                          ParA 169 GvveN 173
                                   G++ N
  gi|15668586|ref|NP_247384.1| 168 GIIVN 172
                                   **988 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.29
                          ParA 204 pllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                                   +++g +p d+++ ++  e +p+v+ +  ++ +k+++++a+++
  gi|15668586|ref|NP_247384.1| 186 DVIGVLPYDQNVERQWVESTPIVKIK--TKFTKEMTALANEI 225
                                   68999***********9999999776..66777777777765 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   1.7   5.9e-08   0.00012       2     246 ..       2     227 ..       1     235 [. 0.75

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5.9e-08
                     Fer4_NifH   2 kiaiyG.kGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkGyggv 81 
                                   ki +y  +GG Gk+t ++n +  l++  k +l + CD    +t +l+g   +e  l+t    ++     +ed++++ y ++
  gi|15668586|ref|NP_247384.1|   2 KIGFYNiQGGTGKTTVAANFAYILSQSVKTIL-IDCDIYGGTTAVLFGLEDKEHNLNTYLAGDS----AIEDIIYH-YDDL 76 
                                   67778648****************99998876.68************99999999998877665....89*****9.**** PP

                     Fer4_NifH  82 kcvesGGPepGvGCaGrgvitaielleelgayddlDfvlyDvLGDvvCG....GfalPiredkaqevyivtsgelmalyaa 158
                                     + +       G    +  + +e l ++   +++D+++yD+  ++       G+      +  ++v++v +  + ++   
  gi|15668586|ref|NP_247384.1|  77 AIIHTDVSSKVFGYK--SDLNRFETLVKE-LEEEYDVIIYDFPPNITEDnpliGYVGEF--ELVNKVVVVGEDSIPSIV-- 150
                                   *99987666555543..334455544332.3468*******877766441111554444..488999999998888775.. PP

                     Fer4_NifH 159 nniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyre 239
                                    n  k+ie  +   g++l+G+i+n+      r+l +  ++e+  +v+ v+P d++v+++ ++   +++ +++    ke  +
  gi|15668586|ref|NP_247384.1| 151 -NSLKTIELIT-DLGIGLTGIIVNKY-----RGLTD--ISEIIDDVIGVLPYDQNVERQWVESTPIVKIKTKFT--KEMTA 220
                                   .4456776655.4579********33.....23322..344556799***************999999988766..89999 PP

                     Fer4_NifH 240 larkile 246
                                   la++i++
  gi|15668586|ref|NP_247384.1| 221 LANEIAS 227
                                   9999875 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   8.5e-06     0.017       5      34 ..       5      34 ..       1      37 [. 0.82
   2 ?    3.3   0.0     0.019        37     112     134 ..      96     117 ..      76     120 .. 0.80
   3 ?    0.3   0.0      0.16   3.1e+02     211     245 ..     140     174 ..     134     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.5e-06
                                  EEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                   ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvll 34
                                  +    GG GKttv+a +a+ ls++ k +l+
  gi|15668586|ref|NP_247384.1|  5 FYNIQGGTGKTTVAANFAYILSQSVKTILI 34
                                  55568******************9887765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.019
                                   HHHHHHHHHHCSSSSEEEEESBS CS
                   ArsA_ATPase 112 sfeellkyvkeeeydvvvlDtaP 134
                                    fe+l+k++ eeeydv++ D +P
  gi|15668586|ref|NP_247384.1|  96 RFETLVKEL-EEEYDVIIYDFPP 117
                                   344555544.789*******999 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.16
                                   EEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE CS
                   ArsA_ATPase 211 lVvipEklslkEteRaikeLkkygikvdavivNkl 245
                                   +V      s+  + + i+ ++ +gi    +ivNk+
  gi|15668586|ref|NP_247384.1| 140 VVGEDSIPSIVNSLKTIELITDLGIGLTGIIVNKY 174
                                   444444558999999999999************96 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.3e-06    0.0047       4     110 ..       4     118 ..       1     128 [. 0.65

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.3e-06
                                   EE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHH.HHHHHH.........HT------EEE-SSS-H CS
                          MipZ   4 vlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenr.aataer.........kglsLplpealalseae 74 
                                    + n +GG+Gk+t+a   a  L++  ++   id d+   t a  ++   ++ + +         +++     +   +++  
  gi|15668586|ref|NP_247384.1|   4 GFYNIQGGTGKTTVAANFAYILSQ-SVKTILIDCDIYGGTTAVLFGLEdKEHNLNtylagdsaiEDIIYHYDDLAIIHTDV 83 
                                   577999***********9988765.56677899999988888776532022222301111101123333334444444444 PP

                                   HHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS CS
                          MipZ  75 eaeveeeeeaevaeleelvadleaeldfividtPGs 110
                                   +++v +  + + +++e+lv++le+e+d+i+ d P +
  gi|15668586|ref|NP_247384.1|  84 SSKVFGY-KSDLNRFETLVKELEEEYDVIIYDFPPN 118
                                   4555554.45569*******************9965 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   1.7e-05     0.034       4     127 ..       3     119 ..       1     126 [. 0.76
   2 ?   -2.6   0.0       1.6   3.1e+03      81     119 ..     190     228 ..     184     248 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                      CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhelgesvlviDlsp.dnlLrlhFnvdieqregwaraeldgapwrqaaleyapgldllP 83 
                                   + +  + GG+G+t+++a  a+ l +  + + +iD        ++ F ++ ++++ +   ++ +  +++ +++y ++l+++ 
  gi|15668586|ref|NP_247384.1|   3 IGFYNIQGGTGKTTVAANFAYILSQSVKTI-LIDCDIyGGTTAVLFGLE-DKEHNLNTYLAGDSAIEDIIYHY-DDLAII- 79 
                                   5667799****************9877665.566654156778889988.77777777777777788877777.567776. PP

                      CBP_BcsQ  84 fGelnveekenlqqlaekaeallaalkelkeqyrwillDlpaga 127
                                       +++  +++  ++++ +++ + +kel+e+y+ i++D p + 
  gi|15668586|ref|NP_247384.1|  80 ----HTDVSSKVFGYKSDLNRFETLVKELEEEYDVIIYDFPPNI 119
                                   ....344444566799999999999**************99865 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                      CBP_BcsQ  81 llPfGelnveekenlqqlaekaeallaalkelkeqyrwi 119
                                   +lP+ +  + +  + + + + + ++++++++l+++   i
  gi|15668586|ref|NP_247384.1| 190 VLPYDQNVERQWVESTPIVKIKTKFTKEMTALANEIASI 228
                                   677777666666666667777777777777777665554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1    0.0002       0.4      11      40 ..      11      39 ..       4      44 .. 0.80
   2 ?    0.1   0.0      0.26   5.1e+02      73      91 ..      97     115 ..      73     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                                  TSSHHHHHHHHHHHHHHTTS-EEEEEESTS CS
                         SRP54 11 GaGKTttlaKLaallkkegkkvllvaaDtf 40
                                  G+GKTt +a  a +l++   k++l+ +D++
  gi|15668586|ref|NP_247384.1| 11 GTGKTTVAANFAYILSQ-SVKTILIDCDIY 39
                                  8***********77665.566677777876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.26
                                   HHHHHHHHHTTSSEEEEEE CS
                         SRP54  73 keavekakeekidvvlvDT 91 
                                   +e++ k+ ee++dv++ D 
  gi|15668586|ref|NP_247384.1|  97 FETLVKELEEEYDVIIYDF 115
                                   4556666778999999995 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       0.6   1.2e+03      11      28 ..      11      28 ..       8      34 .. 0.81
   2 ?   11.5   0.3   9.6e-05      0.19     130     195 ..     137     198 ..     133     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.6
                        AAA_26 11 gvGKTvvslgLvralkrk 28
                                  g GKT+v++  +++l++ 
  gi|15668586|ref|NP_247384.1| 11 GTGKTTVAANFAYILSQS 28
                                  78******9999999664 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.6e-05
                        AAA_26 130 pvilVargglgtinqllltiealrqknvrvlGvilNkvrnpenvetlekksgipvlGvvPylpdle 195
                                   +v++V+     +i + l tie+  + ++ ++G+i+Nk r  +++ ++      +v+Gv+Py++++e
  gi|15668586|ref|NP_247384.1| 137 KVVVVGEDSIPSIVNSLKTIELITDLGIGLTGIIVNKYRGLTDISEIID----DVIGVLPYDQNVE 198
                                   677777777789*************************655555555544....5999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 1829.51
//
Query:       gi|15668587|ref|NP_247385.1|  [L=272]
Description: imidazole glycerol phosphate synthase subunit HisF [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-93  311.4   1.6    3.9e-93  311.1   1.6    1.0  1  His_biosynth  Histidine biosynthesis protein
    6.1e-08   32.1   0.0      4e-05   22.9   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
    7.5e-08   32.1   0.0    0.00069   19.1   0.0    2.2  2  NMO           Nitronate monooxygenase
    4.4e-07   29.5   0.3    0.00093   18.6   0.1    2.2  2  ThiG          Thiazole biosynthesis protein ThiG
    3.9e-05   23.1   0.2       0.11   11.9   0.1    2.3  2  TMP-TENI      Thiamine monophosphate synthase
    5.8e-05   22.6   0.2      0.023   14.1   0.1    2.4  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
     0.0016   17.5   0.5       0.97    8.4   0.1    2.2  2  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0019   17.5   0.1      0.028   13.7   0.0    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
     0.0023   17.4   1.4       0.02   14.4   0.1    2.4  2  PcrB          PcrB family


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.1   1.6   1.9e-96   3.9e-93       1     229 []       5     254 ..       5     254 .. 0.97

  Alignments for each domain:
  == domain 1  score: 311.1 bits;  conditional E-value: 1.9e-96
                                   EEEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESS CS
                  His_biosynth   1 riipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGG 81 
                                   riip+lD+kdG+vV   kG++f +lr+agdpvela++y++egadel+++D++a++e+r++ +d+ve++ae+vfip++vGGG
  gi|15668587|ref|NP_247385.1|   5 RIIPCLDIKDGRVV---KGTKFLNLRDAGDPVELAQYYDDEGADELVFLDITASAEKRDIIIDVVERTAEKVFIPLTVGGG 82 
                                   8*************...**************************************************************** PP

                                   SSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE........C...............EEEEET CS
                  His_biosynth  82 IrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr........g...............ykvaik 139
                                   I+s+ed++++l+agadkv+i+taavknp+like++e fgsq++vvaiDa+r        +               ++v+i+
  gi|15668587|ref|NP_247385.1|  83 IKSIEDFRRILRAGADKVSINTAAVKNPNLIKEASEIFGSQCVVVAIDAKRhyvnedeiDkinknvvkvedgycwFEVYIY 163
                                   ***************************************************887766550566778888899**9****** PP

                                   TTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTC.SEEEE CS
                  His_biosynth 140 gwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegv.daviv 219
                                   g+r+etg+da+++akk+eelgageillt+id+dGt+sG+dl ltke++++vk+pviasGG+g++e+++e++  g+ da+++
  gi|15668587|ref|NP_247385.1| 164 GGRKETGIDAINWAKKVEELGAGEILLTSIDKDGTKSGYDLILTKEISKSVKLPVIASGGCGKPEHVYEAFVYGKaDAALM 244
                                   ********************************************************************************* PP

                                   SHHHHTTSS- CS
                  His_biosynth 220 gsalyegelt 229
                                   + +l+++e+t
  gi|15668587|ref|NP_247385.1| 245 AGILHYREYT 254
                                   ******9986 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     2e-08     4e-05     170     228 ..      61     118 ..      27     159 .. 0.78
   2 !    7.8   0.0   0.00079       1.6     135     212 ..     168     244 ..     136     265 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2e-08
                                   --CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHH CS
                           Dus 170 adweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.sta 228
                                   + ++ ++   ++v ip+ + G+Ik++ed ++il+  Gad v i  +a +nP+l++e s +
  gi|15668587|ref|NP_247385.1|  61 IIIDVVERTAEKVFIPLTVGGGIKSIEDFRRILRA-GADKVSINTAAVKNPNLIKEaS-E 118
                                   45566777788899********************9.******************9733.3 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00079
                                   TTTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEE CS
                           Dus 135 deeenalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmi 212
                                   ++  +a++ ak+ve+ Ga ++ +     +++ +   d+   ke+ ++v++pvia G++ ++e + ++  +  ad+ ++
  gi|15668587|ref|NP_247385.1| 168 ETGIDAINWAKKVEELGAGEILLTS-IDKDGTKSGYDLILTKEISKSVKLPVIASGGCGKPEHVYEAFVYGKADAALM 244
                                   6667788888888888888888843.3444444466677779********************9999988877776544 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   9.9e-05       0.2     182     224 ..      63     105 ..      20     111 .. 0.89
   2 !   19.1   0.0   3.5e-07   0.00069     143     237 ..     171     259 ..     166     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.9e-05
                           NMO 182 faLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                   + +v++ ++ v iP+   GGi   ++   +L++GA  v i t+
  gi|15668587|ref|NP_247385.1|  63 IDVVERTAEKVFIPLTVGGGIKSIEDFRRILRAGADKVSINTA 105
                                   456666666677****************************998 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.5e-07
                           NMO 143 issvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigt 223
                                   i +++ a+kve++Ga  + ++  ++ G +    +     + L +++ + v++PviA GG  + + v  a+ +G + +++ +
  gi|15668587|ref|NP_247385.1| 171 IDAINWAKKVEELGAGEILLTSIDKDGTKS--GY----DLILTKEISKSVKLPVIASGGCGKPEHVYEAFVYGKADAALMA 245
                                   678889999999999999999998888776..45....5899*******************************77777777 PP

                           NMO 224 rfLltkesdakdah 237
                                     L   e + +++ 
  gi|15668587|ref|NP_247385.1| 246 GILHYREYTIEEIK 259
                                   77777777777665 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00017      0.35     169     217 ..      68     116 ..      55     120 .. 0.86
   2 !   18.6   0.1   4.7e-07   0.00093      85     204 ..     116     245 ..     110     252 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                                   HHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHH CS
                          ThiG 169 iiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamA 217
                                      e++ +P+ v  Gi s +d    +  Gad v +nta  +  + ++ A
  gi|15668587|ref|NP_247385.1|  68 RTAEKVFIPLTVGGGIKSIEDFRRILRAGADKVSINTAAVKNPNLIKEA 116
                                   45678889*****************************988877776655 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 4.7e-07
                                   HHHTTS-SEEEE--BCETTTTEB-HHHHHHHHHHHHHTT...-EEEEE.....E.-S-HHHHHHHHHTT-SEBEEBS.SST CS
                          ThiG  85 arevletdliklEviadektLlPdvvetlkaaeiLvkeG...FevlpY.....v.sdDlvlarrleevGcaavmPla.api 155
                                   a e+++++ + + + a+++++  d ++ ++   + v++G   Fev  Y     +  d +  a+++ee+G+  ++  +    
  gi|15668587|ref|NP_247385.1| 116 ASEIFGSQCVVVAIDAKRHYVNEDEIDKINKNVVKVEDGycwFEVYIYggrkeTgIDAINWAKKVEELGAGEILLTSiDKD 196
                                   7889999999999**************************6666777773333321345678*********88765541566 PP

                                   TS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT.-SEEEES CS
                          ThiG 156 GsglGllnkealkiiieeakvPvivDAGigspsdaaqamelG.adavlln 204
                                   G+  G       k i +++k+Pvi   G g+p+++ +a+ +G ada l++
  gi|15668587|ref|NP_247385.1| 197 GTKSGYD-LILTKEISKSVKLPVIASGGCGKPEHVYEAFVYGkADAALMA 245
                                   8888864.567789999************************966888876 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00037      0.74     137     178 ..      61     103 ..      32     106 .. 0.79
   2 !   11.9   0.1   5.3e-05      0.11     117     180 ..     180     246 ..     169     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00037
                      TMP-TENI 137 lgleglkelaealeiPvvaiGGitl.envaevleagadgvavv 178
                                   + ++ ++++ae++ iP+ + GGi+  e+  ++l+agad v++ 
  gi|15668587|ref|NP_247385.1|  61 IIIDVVERTAEKVFIPLTVGGGIKSiEDFRRILRAGADKVSIN 103
                                   55788999999999*********8549************9875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.3e-05
                      TMP-TENI 117 adYigvGpifpTdtKkdaeplglegl..kelaealeiPvvaiGGi.tlenvaevleagadgvavvsa 180
                                   +  +g+G i  T+  kd +  g +++  ke+++++++Pv+a GG  ++e+v e++ +g +  a++ +
  gi|15668587|ref|NP_247385.1| 180 VEELGAGEILLTSIDKDGTKSGYDLIltKEISKSVKLPVIASGGCgKPEHVYEAFVYGKADAALMAG 246
                                   5557999999999988886666665555****************84578888888777777666655 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   1.1e-05     0.023     127     169 ..      62     104 ..      60     107 .. 0.91
   2 !    6.1   0.0    0.0034       6.7     131     161 ..     207     237 ..     203     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                   GHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE-- CS
                  G3P_antiterm 127 vpkvikeikkelkipiiaGGLietkedveealkaGaiavstsn 169
                                   + +v++++ +++ ip+  GG i++ ed +++l+aGa+ vs  +
  gi|15668587|ref|NP_247385.1|  62 IIDVVERTAEKVFIPLTVGGGIKSIEDFRRILRAGADKVSINT 104
                                   678999*********************************9865 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0034
                                   HCTSTTS...EEEEESS--SHHHHHHHCTT. CS
                  G3P_antiterm 131 ikeikkelkipiiaGGLietkedveealkaG 161
                                   +kei+k++k+p+ia+G   + e+v ea+  G
  gi|15668587|ref|NP_247385.1| 207 TKEISKSVKLPVIASGGCGKPEHVYEAFVYG 237
                                   689*********************9998665 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1   0.00048      0.97     196     235 ..      62     102 ..      32     151 .. 0.82
   2 !    7.8   0.0   0.00072       1.4     197     238 ..     205     247 ..     168     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00048
                                   HHHHHH.HHCTCT-EEEEES---SHHHHHHHHHTT-SEEEE CS
                                   xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 196 vaevae.aakkagvpviaDGGikysgdivkAlaaGadavml 235
                                   +++v+e +a+k  +p+   GGik+ +d  + l aGad v +
  gi|15668587|ref|NP_247385.1|  62 IIDVVErTAEKVFIPLTVGGGIKSIEDFRRILRAGADKVSI 102
                                   44444425666677888888888888888888888877754 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00072
                                   HHHHHHHCTCT-EEEEES---SHHHHHHHHHTT.-SEEEESCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         IMPDH 197 aevaeaakkagvpviaDGGikysgdivkAlaaG.adavmlGsl 238
                                   + + e+ k+ + pvia GG  + +++  A++ G ada ++  +
  gi|15668587|ref|NP_247385.1| 205 ILTKEISKSVKLPVIASGGCGKPEHVYEAFVYGkADAALMAGI 247
                                   5567888999**********************97777666554 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.4e-05     0.028     228     280 ..      60     110 ..      55     119 .. 0.83
   2 ?    1.5   0.0     0.069   1.4e+02     236     274 ..     209     245 ..     202     263 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHG CS
                        DHO_dh 228 dialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfeg 280
                                   di + v+ + ++++   ip+   GGi+s eD    ++aGA  v + ta v++ 
  gi|15668587|ref|NP_247385.1|  60 DIIIDVVERTAEKVF--IPLTVGGGIKSIEDFRRILRAGADKVSINTAAVKNP 110
                                   666777777777777..999999*************************97654 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.069
                                   HHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESH CS
                        DHO_dh 236 elykrlkkeipiIgvGGiesgeDalekieaGAslvqvyt 274
                                   e++k +k  +p+I++GG    e ++e +  G +  ++ +
  gi|15668587|ref|NP_247385.1| 209 EISKSVK--LPVIASGGCGKPEHVYEAFVYGKADAALMA 245
                                   5556666..9*******9999999998877754444444 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   9.9e-06      0.02     158     215 ..      49     110 ..      45     120 .. 0.69
   2 ?    1.9   0.1     0.063   1.3e+02     171     222 ..     207     258 ..     126     262 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.9e-06
                                   EEE-TTSSS-HHHHHHHHHHHSSSE...EEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH CS
                          PcrB 158 YlEasGaledveevialkkklekar...livGGGirsaEkAkevvea.ADvivvGnvveekd 215
                                   +l+     e+ + +i+++ +  ++    l vGGGi+s E+ +++++a AD + + ++  +++
  gi|15668587|ref|NP_247385.1|  49 FLDITASAEKRDIIIDVVERTAEKVfipLTVGGGIKSIEDFRRILRAgADKVSINTAAVKNP 110
                                   555555555556666666666554411277********************997776655554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.063
                                   HHHHHHHHSSSEEEEESS--SHHHHHHHHCC..SSEEEE-CHHHHHHHCHHHHH CS
                          PcrB 171 vialkkklekarlivGGGirsaEkAkevvea..ADvivvGnvveekderkidai 222
                                   +++++k + k  +i  GG  ++E+ +e   +  AD+ ++  +++  +  +i++i
  gi|15668587|ref|NP_247385.1| 207 TKEISKSV-KLPVIASGGCGKPEHVYEAFVYgkADAALMAGILHYRE-YTIEEI 258
                                   45555544.45577888888999988887766788766655554333.455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 2109.07
//
Query:       gi|15668588|ref|NP_247386.1|  [L=267]
Description: nitrate transporter protein CmpC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-32  112.1   0.0    4.7e-32  111.4   0.0    1.4  1  ABC_tran     ABC transporter
    5.2e-08   33.1   0.0     0.0031   17.4   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.6e-06   28.6   0.6    1.6e-05   25.3   0.6    2.2  1  AAA          ATPase family associated with various cellular a
    4.1e-05   23.6   0.1     0.0015   18.5   0.0    2.2  2  ATPase_2     ATPase domain predominantly from Archaea
    6.5e-05   22.5   0.1      0.028   13.9   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00032   20.5   0.1       0.46   10.1   0.0    2.3  2  AAA_15       AAA ATPase domain
    0.00033   20.6   0.0    0.00057   19.8   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
    0.00052   20.0   0.0      0.001   19.0   0.0    1.4  1  Rad17        Rad17 P-loop domain
    0.00058   20.4   0.3       0.58   10.7   0.1    2.4  2  AAA_18       AAA domain
     0.0011   19.2   0.1     0.0029   17.9   0.1    1.9  1  AAA_22       AAA domain
     0.0062   16.9   0.0       0.01   16.2   0.0    1.6  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.012   15.6   0.5       0.33   11.0   0.0    2.8  3  AAA_14       AAA domain
      0.013   15.7   0.4       0.32   11.2   0.1    2.3  2  AAA_28       AAA domain
      0.023   15.0   0.0        1.7    9.0   0.0    2.9  3  AAA_19       AAA domain
      0.033   13.9   0.2        0.3   10.8   0.0    2.5  3  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
      0.035   12.8   0.0        4.2    5.9   0.0    2.0  2  AAA_13       AAA domain
      0.039   13.9   0.2       0.15   12.0   0.1    2.0  2  NACHT        NACHT domain
      0.056   12.6   0.0       0.11   11.7   0.0    1.4  1  NB-ARC       NB-ARC domain
      0.065   12.3   0.0      0.097   11.7   0.0    1.3  1  T2SSE        Type II/IV secretion system protein
      0.088   13.3   0.9       0.18   12.3   0.0    1.9  2  AAA_23       AAA domain
        0.1   12.3   0.0       0.54   10.0   0.0    1.9  2  AAA_30       AAA domain
       0.11   12.3   0.0       0.22   11.3   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
       0.15   11.9   0.0       0.28   11.0   0.0    1.4  1  HTH_30       PucR C-terminal helix-turn-helix domain
       0.18   12.1   0.1       0.45   10.8   0.1    1.6  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.22   11.7   0.4       0.69   10.1   0.4    1.9  1  AAA_33       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   0.0   6.6e-35   4.7e-32       1     137 []      36     176 ..      36     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 6.6e-35
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+n++l+++e+e + ++G++G+GK+tLl+++agl  pteG++lldgk++k        +  gv++q+ +l p  tv +n  
  gi|15668588|ref|NP_247386.1|  36 LDNINLEVYENEFLTVMGPSGCGKTTLLRIIAGLDYPTEGKVLLDGKEVKG-----PGADRGVVFQQYTLMPWRTVLKNvt 111
                                   79**********************************************999.....999********************** PP

                                   ........HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ........xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ........esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                            ++e+   ++k+++ +gl++++d       ++LSgG++qrva+ar+l+++p+++l+DEp+a
  gi|15668588|ref|NP_247386.1| 112 fglelkgiPKNERieiAKKFIKMVGLEGFEDAYP----YQLSGGMQQRVAIARTLANDPEIVLMDEPFA 176
                                   *******944444445888899999999888887....*****************************85 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   5.7e-05     0.041       4      22 ..      51      69 ..      48      99 .. 0.80
   2 !   17.4   0.0   4.3e-06    0.0031     232     298 ..     143     207 ..     103     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-05
                        AAA_21  4 liGpNgsGKSnLLdaldll 22
                                  + Gp g+GK++LL+++ +l
  gi|15668588|ref|NP_247386.1| 51 VMGPSGCGKTTLLRIIAGL 69
                                  66**************998 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 4.3e-06
                        AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll..ellkelsrngaQviltTHS 298
                                     +++lS G+++  a++  l+ ++    ++l DEp + L+   +r +l  ellk+ ++++  v+++THS
  gi|15668588|ref|NP_247386.1| 143 AYPYQLSGGMQQRVAIARTLANDP---EIVLMDEPFAALDA-QTRNILqnELLKIWQKEKKTVFFVTHS 207
                                   45799*******988888888877...9*************.8888889999999999999*******9 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.6   2.2e-08   1.6e-05       3     110 ..      51     208 ..      49     236 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.2e-08
                                   EESSTTSSHHHHHHHHHHH.........HTHE................................................. CS
                           AAA   3 lyGppGtGKTllakavake.........lgve................................................. 25 
                                   ++Gp G+GKT+l + +a           l  +                                                 
  gi|15668588|ref|NP_247386.1|  51 VMGPSGCGKTTLLRIIAGLdyptegkvlL--Dgkevkgpgadrgvvfqqytlmpwrtvlknvtfglelkgipknerieiak 129
                                   79****************96554444431..14444455666666666777777777777777777777777777777777 PP

                                   .EEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTE CS
                           AAA  26 .fleisgsell.skyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskv 103
                                    f+++ g e + + y  + +  +++ ++ a++ a +p i+++DE  a   ++       ++ ++n+Ll+ ++++kk    v
  gi|15668588|ref|NP_247386.1| 130 kFIKMVGLEGFeDAYPYQLSGGMQQRVAIARTLAnDPEIVLMDEPFAALDAQ------TRNILQNELLKIWQKEKKT---V 201
                                   7777777777755588888888888888899999889*******99999999......8999*************95...4 PP

                                   EEEEEES CS
                           AAA 104 ivigatn 110
                                   ++++ + 
  gi|15668588|ref|NP_247386.1| 202 FFVTHSV 208
                                   4443332 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.2e-06    0.0015       3      40 ..      31      66 ..      30      74 .. 0.87
   2 ?    3.0   0.0      0.11        81     121     161 ..     168     204 ..     124     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-06
                      ATPase_2  3 dRekelkeleeilerepneiyfiYGpegsGKtaLlkei 40
                                  +R+k+l++++  + +  ne++ + Gp g+GKt+Ll+ i
  gi|15668588|ref|NP_247386.1| 31 NRVKALDNINLEVYE--NEFLTVMGPSGCGKTTLLRII 66
                                  899999999855555..9*****************976 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                      ATPase_2 121 iiiiDelqklidlglngaellvkeLlnliesltkekhlcvv 161
                                   i+++De + + d + +  + l +eLl+++++  ++k +++v
  gi|15668588|ref|NP_247386.1| 168 IVLMDEPFAALDAQTR--NILQNELLKIWQK--EKKTVFFV 204
                                   8999999999966666..9999999999988..33333333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0058       4.2      22      42 ..      44      64 ..      24      68 .. 0.80
   2 !   13.9   0.0   3.9e-05     0.028     135     213 ..     140     223 ..      92     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0058
                                  TTSSEEEEEESTTSSHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 22 fsksftaivGpNGSGKsnlld 42
                                  ++++f  ++Gp G+GK+ ll 
  gi|15668588|ref|NP_247386.1| 44 YENEFLTVMGPSGCGKTTLLR 64
                                  578899***********9976 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.9e-05
                                   T......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHH.HHH..HHCTTSEEEEE-SSHHHCCC-S CS
                                   x......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx..xxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 135 e......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvae.llk..eksknaQfivislreemlekad 206
                                          +LSgG ++ va+a  +A    +   ++l+De  aaLD++ ++++ + llk  +k+k++ f+v+   +e +  +d
  gi|15668588|ref|NP_247386.1| 140 FedaypyQLSGGMQQRVAIARTLA----NDPEIVLMDEPFAALDAQTRNILQNeLLKiwQKEKKTVFFVTHSVDEAVYLSD 216
                                   055555589***999999998877....344599****************9872555668888899999988888888888 PP

                                   CEEEEEE CS
                                   xxxxxxx RF
                         SMC_N 207 klvgvtk 213
                                   ++v +t 
  gi|15668588|ref|NP_247386.1| 217 RVVVLTA 223
                                   8887766 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0018       1.3      13      43 ..      35      66 ..      34     133 .. 0.87
   2 !   10.1   0.0   0.00064      0.46     321     365 ..     163     207 ..     103     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
                        AAA_15 13 slkdveidlsee.ltvliGkNnsGKSsileal 43
                                  +l+++ +++ e+ + ++ G+ ++GK+++l+++
  gi|15668588|ref|NP_247386.1| 35 ALDNINLEVYENeFLTVMGPSGCGKTTLLRII 66
                                  6777777776667999**************99 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00064
                        AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                    +++ i+l++EP a L  q  ++l + l+++ +++k+ v++ THS
  gi|15668588|ref|NP_247386.1| 163 ANDPEIVLMDEPFAALDAQTRNILQNELLKIWQKEKKTVFFVTHS 207
                                   45789***************************************9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   7.9e-07   0.00057      55     121 ..       3      68 ..       1      81 [. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.9e-07
                                   -GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  55 KiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                   K D +++++   ++k ++e+l ++++  + ++ ++l++++ ++ + ++ +++G+SG GK+tL+  +++
  gi|15668588|ref|NP_247386.1|   3 KDDEVKKRD-RMKVKLKVENL-TKIFEFNGNRVKALDNINLEVYEnEFLTVMGPSGCGKTTLLRIIAG 68 
                                   667777777.66777777777.89999999999******8766555*****************98876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.5e-06     0.001      34      66 ..      35      67 ..      28      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-06
                         Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                  +l+   Le  +++ L + GPsGCgk+t +++++
  gi|15668588|ref|NP_247386.1| 35 ALDNINLEVYENEFLTVMGPSGCGKTTLLRIIA 67
                                  6788889999999*****************987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00082      0.58       3      19 ..      51      67 ..      49      98 .. 0.86
   2 !    7.8   0.0    0.0063       4.5      33     106 ..     164     228 ..     127     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00082
                        AAA_18  3 ltGtpGvGKttlakeLs 19
                                  ++G++G+GKttl + ++
  gi|15668588|ref|NP_247386.1| 51 VMGPSGCGKTTLLRIIA 67
                                  89**********99886 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0063
                        AAA_18  33 kenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlaeleseaakdikkvvLtaspeel 106
                                    + +++l+++p+       ld + ++ l+++l ++   ++++k  v+   ++  e  ++ d++ vvLta+p   
  gi|15668588|ref|NP_247386.1| 164 NDPEIVLMDEPF-----AALDAQTRNILQNELLKI---WQKEKKTVFFVTHSVDEAVYLSDRV-VVLTARPGRI 228
                                   444444444444.....788888888999999998...9999*********************.*****99755 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1     4e-06    0.0029       6      68 ..      47     118 ..      42     219 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4e-06
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsstsskdllrellralglel 68 
                                    +l+v+G+sG+GKTtllr ++  +    +++e              ++++vvf + +    ++++l+++   l+l++
  gi|15668588|ref|NP_247386.1|  47 EFLTVMGPSGCGKTTLLRIIAGLD----YPTEgkvlldgkevkgpgADRGVVFQQYTLMP-WRTVLKNVTFGLELKG 118
                                   699**************9888765....23333466666666666555555555554444.6666666666666554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.4e-05      0.01      25      46 ..      47      68 ..      33     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-05
                        AAA_16 25 elvllsGesGvGKsslvrellr 46
                                  e + + G+sG+GK++l+r ++ 
  gi|15668588|ref|NP_247386.1| 47 EFLTVMGPSGCGKTTLLRIIAG 68
                                  6789*************98874 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00046      0.33       2      23 ..      46      67 ..      45      83 .. 0.82
   2 ?   -1.1   0.0       2.4   1.7e+03      52      96 ..     186     203 ..     156     224 .. 0.55
   3 ?    1.2   0.1      0.49   3.5e+02      31      59 ..     229     257 ..     213     265 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                        AAA_14  2 rkilvitGaRrvGKTtllkqli 23
                                  ++ l+++G+  +GKTtll+ ++
  gi|15668588|ref|NP_247386.1| 46 NEFLTVMGPSGCGKTTLLRIIA 67
                                  67899************98776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.4
                        AAA_14  52 llelileklkeekktylflDEiqevpewekalkslvdegknldvi 96 
                                   l +++l+                             +++k+  ++
  gi|15668588|ref|NP_247386.1| 186 LQNELLKI---------------------------WQKEKKTVFF 203
                                   22333333...........................3333333333 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.49
                        AAA_14  31 esilyinldderdkkladpekllelilek 59 
                                   ++i+ i+l+++rd+++ ++ ++ + il+ 
  gi|15668588|ref|NP_247386.1| 229 KEIVKIDLERPRDRTSIEFLEYRKKILNI 257
                                   7899*********8877664344444443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00044      0.32       4      25 ..      51      72 ..      49      79 .. 0.86
   2 ?    2.4   0.0      0.23   1.7e+02      58      92 ..     184     217 ..     152     252 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00044
                        AAA_28  4 itGgestGKTtlleaLaargyp 25
                                  ++G++++GKTtll+ +a  +yp
  gi|15668588|ref|NP_247386.1| 51 VMGPSGCGKTTLLRIIAGLDYP 72
                                  78************99976666 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.23
                        AAA_28  58 rvleeqleeeaaa...aankvlfcDrglldtlaYaray 92 
                                    +l+++l         +++k++f+ + ++d+++Y+  +
  gi|15668588|ref|NP_247386.1| 184 NILQNELL----KiwqKEKKTVFFVTHSVDEAVYLSDR 217
                                   33333332....23335788899999999999998654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0024       1.7       9      30 ..      45      66 ..      38      75 .. 0.86
   2 ?    1.7   0.0      0.41     3e+02     111     135 ..     180     204 ..     132     206 .. 0.76
   3 ?    0.0   0.0       1.3   9.6e+02       3      21 ..     210     227 ..     208     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
                        AAA_19  9 kekvllvtaGpGtGKTrvlkhi 30
                                  +++ l v+++ G+GKT++l+ i
  gi|15668588|ref|NP_247386.1| 45 ENEFLTVMGPSGCGKTTLLRII 66
                                  678899***********99876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.41
                        AAA_19 111 fqdvdelqyrLlkallgekkklllv 135
                                   +q  + lq++Llk + +ekk++++v
  gi|15668588|ref|NP_247386.1| 180 AQTRNILQNELLKIWQKEKKTVFFV 204
                                   4555578999***999999889887 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.3
                        AAA_19   3 eavealkekvllvtaGpGt 21 
                                   eav +l+++v+++ta pG 
  gi|15668588|ref|NP_247386.1| 210 EAV-YLSDRVVVLTARPGR 227
                                   788.999**********96 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00042       0.3       5      24 ..      50      69 ..      47      88 .. 0.87
   2 ?   -1.8   0.0       3.2   2.3e+03     104     121 ..     121     138 ..     115     141 .. 0.85
   3 ?   -1.1   0.0         2   1.4e+03      57     103 ..     191     238 ..     182     253 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                     PduV-EutP  5 lliGkvgsGKttLtqalkge 24
                                   ++G++g+GKttL + + g 
  gi|15668588|ref|NP_247386.1| 50 TVMGPSGCGKTTLLRIIAGL 69
                                  58***********9998875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.2
                     PduV-EutP 104 deenieaveelLksaGae 121
                                   ++e+ie++++++k++G e
  gi|15668588|ref|NP_247386.1| 121 KNERIEIAKKFIKMVGLE 138
                                   678999****99999976 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2
                     PduV-EutP  57 livtsaeadvialvqdateeesvfppgfasvfnke.viGiitkidlae 103
                                   l++   e + + +v+++++e  ++++ ++ + +++  i  i kidl +
  gi|15668588|ref|NP_247386.1| 191 LKIWQKEKKTVFFVTHSVDEAVYLSDRVVVLTARPgRIKEIVKIDLER 238
                                   556667778888899999999999999988888874577788888864 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0058       4.2       3      40 ..      24      70 ..      23      97 .. 0.82
   2 ?    5.0   0.0     0.011       7.8     525     572 ..     164     209 ..     155     253 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0058
                        AAA_13  3 rifdfrgaeledfkriNl.........iYGwNGaGKTtLSrllrsle 40
                                  +if+f+g++++ +  iNl         + G  G GKTtL r+++ l 
  gi|15668588|ref|NP_247386.1| 24 KIFEFNGNRVKALDNINLevyenefltVMGPSGCGKTTLLRIIAGLD 70
                                  58899999999999999874444444456**************9984 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
                        AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnle 572
                                   +  +iv +D P   LD++  +i  + + +    +k+ k +f  TH+++
  gi|15668588|ref|NP_247386.1| 164 NDPEIVLMDEPFAALDAQTRNILQNELLKIW--QKEKKTVFFVTHSVD 209
                                   5679*********************999998..8999********986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00021      0.15       3      21 ..      49      67 ..      47      69 .. 0.87
   2 ?   -1.2   0.0       2.3   1.7e+03     117     134 ..     213     230 ..     172     252 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                                  EEEEC-TTTCHHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqkla 21
                                  + + G++G+GKTtLl+ +a
  gi|15668588|ref|NP_247386.1| 49 LTVMGPSGCGKTTLLRIIA 67
                                  5689***********9886 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.3
                                   TTT--EEEEEEECCCHHH CS
                         NACHT 117 llpeasllltvrpralrd 134
                                   +l+   ++lt+rp++ ++
  gi|15668588|ref|NP_247386.1| 213 YLSDRVVVLTARPGRIKE 230
                                   455556777777777766 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00015      0.11      17      40 ..      45      66 ..      31      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                                  TSCSEEEEEEESTTSSHHHHHHHH CS
                        NB-ARC 17 elqslvvalvGmgGvGKttlakqi 40
                                  e +  +++++G  G+GKttl++ i
  gi|15668588|ref|NP_247386.1| 45 ENE--FLTVMGPSGCGKTTLLRII 66
                                  444..9**************9865 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014     0.097      96     151 ..      10      68 ..       2     110 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                         T2SSE  96 Rkksakeltlddlgaeealk...ekiaevlrkavrerglilvsGgTgsGKttllyallk 151
                                   R++ + +l++++l +  +++    k  + ++  v e+  + v G+ g GKttll ++  
  gi|15668588|ref|NP_247386.1|  10 RDRMKVKLKVENLTKIFEFNgnrVKALDNINLEVYENEFLTVMGPSGCGKTTLLRIIAG 68 
                                   555556665555554444442224556678889999******************87754 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00025      0.18      15      39 ..      39      66 ..      14      72 .. 0.73
   2 ?   -1.6   0.2       4.4   3.2e+03      71      84 ..     228     241 ..     179     265 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00025
                        AAA_23 15 idF...skgltlItGpNGaGKTTildAi 39
                                  i++   ++ +  + Gp G+GKTT+l+ i
  gi|15668588|ref|NP_247386.1| 39 INLevyENEFLTVMGPSGCGKTTLLRII 66
                                  44455666777789***********988 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.4
                        AAA_23  71 vkayveltfenkdg 84 
                                    k++v++++e+ ++
  gi|15668588|ref|NP_247386.1| 228 IKEIVKIDLERPRD 241
                                   33334444433333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00075      0.54      19      42 ..      47      70 ..      40      83 .. 0.80
   2 ?   -0.6   0.0       1.2   8.9e+02      39      66 ..     191     218 ..     184     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00075
                        AAA_30 19 rvavltGpAGtGKttalkalreaw 42
                                   + ++ Gp G GKtt+l+ ++ + 
  gi|15668588|ref|NP_247386.1| 47 EFLTVMGPSGCGKTTLLRIIAGLD 70
                                  477899************998765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                        AAA_30  39 reaweaaggrviglAptgkaAkvLaeel 66 
                                    ++w++++++v+ ++++   A  L++ +
  gi|15668588|ref|NP_247386.1| 191 LKIWQKEKKTVFFVTHSVDEAVYLSDRV 218
                                   5677777777777777777776666554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0003      0.22      17      39 ..      41      63 ..      33      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                        AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                  +e+ ++++  ++GpsG GK+Tll
  gi|15668588|ref|NP_247386.1| 41 LEVYENEFLTVMGPSGCGKTTLL 63
                                  555556678899**********8 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00039      0.28      31      54 ..     223     246 ..     220     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
                                   HHHHHHHHHHS--TTSHHHHHHHH CS
                        HTH_30  31 yRLrrieellgldlddpddrlaLy 54 
                                    R  ri+e+ ++dl++p+dr++++
  gi|15668588|ref|NP_247386.1| 223 ARPGRIKEIVKIDLERPRDRTSIE 246
                                   6678****************9986 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00062      0.45      57      82 ..     159     184 ..     145     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00062
                       SbcCD_C  57 aegrepalrlvfLDEAFsklDeesia 82 
                                   a++  +++++v++DE F+ lD+++++
  gi|15668588|ref|NP_247386.1| 159 ARTLANDPEIVLMDEPFAALDAQTRN 184
                                   44446789**************9875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.4   0.00096      0.69       4      19 ..      51      66 ..      49     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00096
                        AAA_33  4 lvGlpGsGKstlaerl 19
                                  + G++G+GK+tl++ +
  gi|15668588|ref|NP_247386.1| 51 VMGPSGCGKTTLLRII 66
                                  68**********9855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 1614.32
//
Query:       gi|15668589|ref|NP_247387.1|  [L=267]
Description: nitrate transporter protein CmpB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-24   84.9  13.9    5.6e-24   84.9  13.9    1.6  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        7.6    6.6   7.1       0.76    9.8   0.2    2.5  2  SecE          SecE/Sec61-gamma subunits of protein translocat


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2      0.44   3.9e+03      95     117 ..      15      37 ..      12      44 .. 0.67
   2 !   84.9  13.9   6.2e-28   5.6e-24       1     182 [.      89     258 ..      89     261 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.44
                  BPD_transp_1  95 wqifrkvvlPnalppiitglila 117
                                   ++++ k+ lP+++ +i  +l++ 
  gi|15668589|ref|NP_247387.1|  15 KELVLKISLPALAVVIWELLAIY 37 
                                   56677777777777776666665 PP

  == domain 2  score: 84.9 bits;  conditional E-value: 6.2e-28
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpk 81 
                                   +i+lGil++  + ++++ l ++li++l+ +P++++++l +       ++g + +++i++++++a++++++++ ++++ +p+
  gi|15668589|ref|NP_247387.1|  89 AIPLGILMG--YYRTVNSLCDTLIELLRPIPPLAWVPLSL------AWFGLGEMSMIFIIFIGAFFPILINTISGVKGVPT 161
                                   69*******..778**************************......9********************************** PP

                  BPD_transp_1  82 dlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtllleailgydyseisnggvlal 161
                                    l+eaa++lGa+ + i+ kvv+P++ p+i+tgl++ +g+++   v++e+l s+++ lg+l++ a++ + ++     +v+a+
  gi|15668589|ref|NP_247387.1| 162 PLIEAALTLGAKGRDILIKVVIPASSPSILTGLRVGAGIAWMCVVAAEMLPSSNAgLGYLIMYAYSLSRMD-----VVIAC 237
                                   **************************************************998877***************.....99999 PP

                  BPD_transp_1 162 viavlllnlvadilqrlldpr 182
                                    i++ l+ lv+d   r+++ +
  gi|15668589|ref|NP_247387.1| 238 MIIIGLIGLVLDRGLRYIEDK 258
                                   999999999999999999876 PP

>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   2.3      0.42   3.7e+03      30      40 ..     136     146 ..     134     149 .. 0.75
   2 ?    9.8   0.2   8.5e-05      0.76      28      49 ..     233     254 ..     232     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.42
                                   HHHHHHHHHHH CS
                          SecE  30 lvfvvimglfl 40 
                                   ++f++++g+f+
  gi|15668589|ref|NP_247387.1| 136 MIFIIFIGAFF 146
                                   67888888886 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 8.5e-05
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                          SecE  28 vVlvfvvimglflflvDlvfsk 49 
                                   vV+++++i+gl++ ++D ++ +
  gi|15668589|ref|NP_247387.1| 233 VVIACMIIIGLIGLVLDRGLRY 254
                                   8****************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1758.24
//
Query:       gi|15668590|ref|NP_247388.1|  [L=395]
Description: hypothetical protein MJ_0414 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-38  130.1   2.1    8.9e-38  129.1   2.1    1.5  1  Lig_C           Ligase Pab1020 C-terminal region
    7.1e-21   75.2   0.3    1.7e-20   74.0   0.3    1.6  1  RNA_ligase      RNA ligase
    1.3e-07   31.5   0.3    8.4e-07   28.8   0.3    2.2  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
  ------ inclusion threshold ------
       0.74   10.3   3.5        4.9    7.7   0.2    3.1  3  KELK            KELK-motif containing domain of MRCK Ser/Thr 


Domain annotation for each model (and alignments):
>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.1   2.1     2e-41   8.9e-38       2     124 ..     265     391 ..     264     392 .. 0.95

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 2e-41
                                   HCCSCCGS-STSCHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHHHHHHH CS
                         Lig_C   2 afsylfelgrdFlfsRviReafqavefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvrfkdeenieelle 82 
                                   af+++f+lg dFlfsRv+Re+f ++ef+e+ ee+++rak+LGe+iL pmveti+kv+ +e+v+e+f++ f++ee+++e+l+
  gi|15668590|ref|NP_247388.1| 265 AFTFFFDLGMDFLFSRVVREGFMSYEFKETLEERKNRAKDLGEAILLPMVETINKVASGERVSEDFELIFDSEEDFDEFLD 345
                                   8******************************************************************************** PP

                                   HHHCTT--EEEEEEE..TTEEEEE......EE-HHHHHHHHHHHTT CS
                         Lig_C  83 hLrrlgvkaeveekekedgelvvkfk....kiaqsttdkikslLeG 124
                                   ++r++++ +++++ ek+d e  vk+k    ki+++t+dki s+L+G
  gi|15668590|ref|NP_247388.1| 346 FMRKMKMVITIKNIEKIDTEEGVKIKavigKIYNKTNDKIISYLNG 391
                                   ***************998887777654445***************9 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.3   3.7e-24   1.7e-20       2     149 ..      94     246 ..      93     253 .. 0.70

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 3.7e-24
                                   EEEEEEE-SSEEEEEEEETT.EEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH...ECCEEEEEEEES...SS..... CS
                    RNA_ligase   2 evvvtEKlDGtnfriylvke.vgvasRsqil.pfgeekfkefkrwaaalrkklkekla.neelilyGElig..hsi...ky 74 
                                   +vv++EKl+G+n+ri++ ++ v++ +Rs+++ p        f+++++++  +  e+l+   e++l+GE+ig  +++   +y
  gi|15668590|ref|NP_247388.1|  94 KVVIEEKLNGYNIRIVKIDGeVYALTRSGYIcP--------FTTKKVKKFLN-LEILDdYSEYMLCGEMIGinNPYtpyYY 165
                                   79****************556**********54........44444444333.455557567*********7533364233 PP

                                   TTSS......EEEEEEEEEEECTTBECE--HHHHHHHHHCCT..B..EEEEE.SS.HHHHHCCC..HHHHTC--EEEEEES CS
                    RNA_ligase  75 gglpk.....efyvFdifdirdkeeqrylspdevealakglg..tvpvlyegkfl.aaeellell.lskgnkrEGlVikpe 146
                                   +   +     e + F+ifdi+++e+++ l+ +e+  l+++++  +v+ l   +++ a+ +++e++ + +++ rEG+V+k++
  gi|15668590|ref|NP_247388.1| 166 K---EvdrgfENLGFYIFDIKERETNKSLPIKERINLCEKYNlpYVKPLAVVDKDeAHIHVREIIeKLNKEGREGVVLKDP 243
                                   3...23456855556666666888**********8888878788777776666655545555553237888********98 PP

                                   SSS CS
                    RNA_ligase 147 sel 149
                                   ++ 
  gi|15668590|ref|NP_247388.1| 244 DMA 246
                                   874 PP

>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.3   1.9e-10   8.4e-07      15     189 ..      88     245 ..      79     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.9e-10
                                   HHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEEEETTTTCBEHHHH CS
                DNA_ligase_A_M  15 kkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElvavdketgeilpfqk 95 
                                   kk+  +++++E+K++G+ +++ k +++v+ ++R++   + + +++ k+l+  + +d ++++l GE++ +++      p+  
  gi|15668590|ref|NP_247388.1|  88 KKHFIDKVVIEEKLNGYNIRIVKIDGEVYALTRSGYICPFTTKKVKKFLNLEILDDYSEYMLCGEMIGINNP---YTPYYY 165
                                   444467888*****************************99**********9*****************8444...444443 PP

                                   HCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEESSHHHHHHHHHHHHH CS
                DNA_ligase_A_M  96 lasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslevkdveeleelleeais 176
                                        ++ +         +l +++FDi   +      +p+keR +l e++  +  + + ++++ e +   +++e++e+  +
  gi|15668590|ref|NP_247388.1| 166 KEV--DRGF--------ENLGFYIFDIKERET--NKSLPIKERINLCEKYNLPYVKPLAVVDKDEAHI--HVREIIEKLNK 232
                                   111..2223........3799******95555..5699*************99999999999998877..9********** PP

                                   TTECEEEEEETT- CS
                DNA_ligase_A_M 177 eglEGlvvKnpds 189
                                   eg EG+v+K+pd 
  gi|15668590|ref|NP_247388.1| 233 EGREGVVLKDPDM 245
                                   **********986 PP

>> KELK  KELK-motif containing domain of MRCK Ser/Thr protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0011       4.9      22      55 ..      12      45 ..       8      51 .. 0.92
   2 ?   -0.0   0.0      0.27   1.2e+03      15      36 ..     215     236 ..     211     244 .. 0.84
   3 ?    0.6   0.1      0.17   7.8e+02      22      40 ..     290     308 ..     284     310 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                          KELK 22 elaeaqErlksqkkeLkdaisqrklamqefsevn 55
                                  +l+ + E+l  + k+L  a s++ l  +e++e++
  gi|15668590|ref|NP_247388.1| 12 DLNKIAEKLNLSIKDLNKAFSRKILREDEYKEIK 45
                                  78999***************************97 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.27
                          KELK  15 EkeelqkelaeaqErlksqkke 36 
                                   +k+e++  + e+ E+l ++++e
  gi|15668590|ref|NP_247388.1| 215 DKDEAHIHVREIIEKLNKEGRE 236
                                   7999999999****99988776 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.17
                          KELK  22 elaeaqErlksqkkeLkda 40 
                                   e++e+ E  k+++k+L +a
  gi|15668590|ref|NP_247388.1| 290 EFKETLEERKNRAKDLGEA 308
                                   5666666667766666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2497.86
//
Query:       gi|15668591|ref|NP_247389.1|  [L=162]
Description: hypothetical protein MJ_0415 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1099.75
//
Query:       gi|15668592|ref|NP_247390.1|  [L=190]
Description: hypothetical protein MJ_0416 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-21   73.2  20.6    2.1e-09   36.5   1.1    3.2  3  zf-ribbon_3      zinc-ribbon domain
    1.8e-18   66.2  15.3    3.7e-13   49.3  10.2    2.2  2  DZR              Double zinc ribbon
      8e-18   63.5  16.6    6.3e-07   28.9   1.9    3.3  3  zinc_ribbon_2    zinc-ribbon domain
      8e-12   45.7  12.8     0.0018   19.0   2.2    3.2  3  zinc_ribbon_15   zinc-ribbon family
    2.2e-05   24.4  14.0     0.0064   16.5   2.6    3.1  3  UPF0547          Uncharacterised protein family UPF0547
      8e-05   22.5  15.1      0.013   15.4   2.0    3.4  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0022   18.0  17.1         21    5.2   0.9    3.0  2  zinc-ribbons_6   zinc-ribbons
     0.0027   17.4  21.7      0.012   15.3   3.3    4.1  4  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
     0.0079   16.1   1.3     0.0079   16.1   1.3    3.4  3  C1_1             Phorbol esters/diacylglycerol binding domain
  ------ inclusion threshold ------
      0.015   15.4   1.1      0.024   14.8   0.2    1.8  1  DUF4734          Domain of unknown function (DUF4734)
      0.016   15.3   4.8      0.016   15.3   4.8    5.2  5  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.016   15.1  19.6       0.11   12.4   2.1    3.8  4  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
      0.018   15.7  10.5        5.1    7.9   1.1    3.3  3  zinc-ribbon_6    zinc-ribbon domain
      0.024   14.3   1.7      0.024   14.3   1.7    4.7  4  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
      0.037   13.4   1.9      0.037   13.4   1.9    4.0  4  zf-TFIIB         Transcription factor zinc-finger
      0.039   14.1  21.9       0.14   12.3   2.4    4.6  4  Zn-ribbon_8      Zinc ribbon domain
      0.042   13.5  12.4        0.7    9.5   1.6    2.6  2  TackOD1          Thaumarchaeal output domain 1
      0.043   13.6   2.5      0.043   13.6   2.5    3.1  3  zf-RING_4        RING/Ubox like zinc-binding domain
       0.06   13.4   1.2       0.06   13.4   1.2    3.0  3  DUF1451          Zinc-ribbon containing domain
       0.19   11.9   0.6       0.19   11.9   0.6    5.5  6  zf-RING_7        C4-type zinc ribbon domain
       0.27   11.2  22.2        2.7    8.0   4.3    5.0  5  Nudix_N_2        Nudix N-terminal
       0.33   11.0  19.6        4.1    7.5   5.2    3.4  2  HypA             Hydrogenase/urease nickel incorporation, met
        1.2    9.3  13.1        1.5    8.9   1.3    3.2  3  DHHC             DHHC palmitoyltransferase
        2.1    8.7  13.8       0.58   10.5   3.7    2.8  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
        2.8    8.0  13.7        9.1    6.4  11.8    2.5  1  Mut7-C           Mut7-C RNAse domain
          4    7.3  15.0       0.11   12.3   2.6    3.5  3  DUF4187          Domain of unknown function (DUF4187)
          4    7.8  15.2       0.59   10.4   3.0    3.4  3  Ribosomal_L32p   Ribosomal L32p protein family
        4.3    7.4  18.4        5.8    7.0   5.3    4.0  4  YhfH             YhfH-like protein
        4.4    7.9  17.3         16    6.1   0.4    4.7  4  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
        4.6    7.6  24.3        9.6    6.6   0.2    5.2  5  zf-LITAF-like    LITAF-like zinc ribbon domain
        5.1    6.8  11.8         12    5.6   0.5    3.2  3  Zn_ribbon_17     Zinc-ribbon, C4HC2 type
        5.7    7.2  17.3        3.3    7.9   6.7    3.4  3  zf-C3HC4_4       zinc finger of C3HC4-type, RING
        5.8    6.5  28.3        1.4    8.5   1.8    4.9  3  TF_Zn_Ribbon     TFIIB zinc-binding
        9.8    6.0  23.2        2.3    8.0   0.3    5.1  5  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   3.1   1.8e-06   0.00094       5      26 .]     101     122 ..     101     122 .. 0.95
   2 !   29.2   1.9   7.7e-10     4e-07       3      26 .]     132     155 ..     130     155 .. 0.91
   3 !   36.5   1.1   3.9e-12   2.1e-09       4      26 .]     164     186 ..     161     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.8e-06
                   zf-ribbon_3   5 CPnCGaplssddnvCpyCGtkl 26 
                                   C++C++p++ +++ C++CG+++
  gi|15668592|ref|NP_247390.1| 101 CNSCKSPIDLGWTYCTNCGAEI 122
                                   ******99***********976 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 7.7e-10
                   zf-ribbon_3   3 vrCPnCGa.plssddnvCpyCGtkl 26 
                                    rCPnC++ + s++++ C++CG+kl
  gi|15668592|ref|NP_247390.1| 132 ERCPNCNNyI-SDSWKYCAHCGAKL 155
                                   69******66.***********997 PP

  == domain 3  score: 36.5 bits;  conditional E-value: 3.9e-12
                   zf-ribbon_3   4 rCPnCGaplssddnvCpyCGtkl 26 
                                   rCPnC+ p++++++vCpyCG++l
  gi|15668592|ref|NP_247390.1| 164 RCPNCKRPVQPEWIVCPYCGYRL 186
                                   9******99************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   9.9e-07   0.00052      31      49 .]     101     119 ..      82     133 .. 0.71
   2 !   49.3  10.2   7.1e-16   3.7e-13       1      49 []     134     183 ..     134     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.9e-07
                           DZR  31 CpsCgekvdpearfCpeCG 49 
                                   C sC++++d+++++C +CG
  gi|15668592|ref|NP_247390.1| 101 CNSCKSPIDLGWTYCTNCG 119
                                   5555555555555555555 PP

  == domain 2  score: 49.3 bits;  conditional E-value: 7.1e-16
                           DZR   1 CpqCgeelppdarfCseCgtklkavaa.edrCpsCgekvdpearfCpeCG 49 
                                   Cp+C++ ++++ ++C +Cg+klk++++   rCp+C+++v+pe+ +Cp+CG
  gi|15668592|ref|NP_247390.1| 134 CPNCNNYISDSWKYCAHCGAKLKEEEEeVLRCPNCKRPVQPEWIVCPYCG 183
                                   ***********************8888899*******************9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.8   1.8e-06   0.00095       2      22 ..     101     121 ..     100     122 .. 0.95
   2 !   28.9   1.9   1.2e-09   6.3e-07       1      23 []     133     155 ..     133     155 .. 0.96
   3 !   25.5   0.8   1.4e-08   7.6e-06       1      23 []     164     186 ..     164     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.8e-06
                 zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtp 22 
                                   C +C  +++ + ++C++CG++
  gi|15668592|ref|NP_247390.1| 101 CNSCKSPIDLGWTYCTNCGAE 121
                                   *******************98 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 1.2e-09
                 zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                                   +CpnC + ++d  k+C +CG++l
  gi|15668592|ref|NP_247390.1| 133 RCPNCNNYISDSWKYCAHCGAKL 155
                                   6********************97 PP

  == domain 3  score: 25.5 bits;  conditional E-value: 1.4e-08
                 zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                                   +CpnC +++q++   CpyCG+ l
  gi|15668592|ref|NP_247390.1| 164 RCPNCKRPVQPEWIVCPYCGYRL 186
                                   6*******************976 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   5.3e-05     0.028      64      86 .]      93     119 ..      67     119 .. 0.76
   2 !   19.0   2.2   3.4e-06    0.0018      63      86 .]     129     152 ..     120     152 .. 0.84
   3 !   18.2   0.7   5.8e-06    0.0031      59      86 .]     156     183 ..     153     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.3e-05
                zinc_ribbon_15  64 e....kkeCknCgkeveeefkyCpkCg 86 
                                   +    +  C++C++ ++   +yC++Cg
  gi|15668592|ref|NP_247390.1|  93 KfstfVPLCNSCKSPIDLGWTYCTNCG 119
                                   14455889******************9 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 3.4e-06
                zinc_ribbon_15  63 sekkeCknCgkeveeefkyCpkCg 86 
                                   +e+++C+nC++ ++++ kyC +Cg
  gi|15668592|ref|NP_247390.1| 129 EEVERCPNCNNYISDSWKYCAHCG 152
                                   4489*******************9 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 5.8e-06
                zinc_ribbon_15  59 kkessekkeCknCgkeveeefkyCpkCg 86 
                                   k+e++e+ +C+nC++ v++e   Cp+Cg
  gi|15668592|ref|NP_247390.1| 156 KEEEEEVLRCPNCKRPVQPEWIVCPYCG 183
                                   45667799*******************9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.8       5.9   3.1e+03      16      21 ..     114     119 ..     101     123 .. 0.59
   2 !   15.3   0.1   3.1e-05     0.016       2      21 ..     133     152 ..     133     152 .. 0.97
   3 !   16.5   2.6   1.2e-05    0.0064       2      23 ..     164     185 ..     164     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5.9
                       UPF0547  16 fCphCG 21 
                                    C  CG
  gi|15668592|ref|NP_247390.1| 114 YCTNCG 119
                                   465665 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.1e-05
                       UPF0547   2 vCPeCeakvPvaaqfCphCG 21 
                                   +CP C   ++ + + C+hCG
  gi|15668592|ref|NP_247390.1| 133 RCPNCNNYISDSWKYCAHCG 152
                                   6******************9 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.2e-05
                       UPF0547   2 vCPeCeakvPvaaqfCphCGyv 23 
                                   +CP C ++v     +Cp+CGy+
  gi|15668592|ref|NP_247390.1| 164 RCPNCKRPVQPEWIVCPYCGYR 185
                                   6********************6 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   1.8    0.0015      0.77      30      55 ..     114     140 ..     113     144 .. 0.91
   2 !   15.4   2.0   2.4e-05     0.013      29      53 ..     146     169 ..     141     176 .. 0.93
   3 ?    4.4   0.1     0.066        35      30      40 ..     178     188 ..     176     190 .] 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                OrfB_Zn_ribbon  30 tCseCgsknke.alsgrtfkCpnCgfe 55 
                                    C +Cg++ k+ + ++++ +CpnC+ +
  gi|15668592|ref|NP_247390.1| 114 YCTNCGAEIKNmTFEEEVERCPNCNNY 140
                                   6***********************976 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.4e-05
                OrfB_Zn_ribbon  29 ktCseCgsknkealsgrtfkCpnCg 53 
                                   k C++Cg+k+ke  ++++++CpnC+
  gi|15668592|ref|NP_247390.1| 146 KYCAHCGAKLKE-EEEEVLRCPNCK 169
                                   78**********.***********7 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.066
                OrfB_Zn_ribbon  30 tCseCgsknke 40 
                                    C+ Cg+++k+
  gi|15668592|ref|NP_247390.1| 178 VCPYCGYRLKR 188
                                   59999999987 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.9     0.039        21      19      39 ..     101     122 ..      90     124 .. 0.63
   2 ?    4.1  17.3     0.085        45       2      38 ..     147     185 ..      99     189 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.039
                                   -TTT--EEEE.EEE-SSS-S-- CS
                zinc-ribbons_6  19 CeaCqedlkk.ealCpeCeqel 39 
                                   C++C++ ++   ++C +C+ e+
  gi|15668592|ref|NP_247390.1| 101 CNSCKSPIDLgWTYCTNCGAEI 122
                                   6666665554235666666655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.085
                                   --SSS-S--E.E-SSEEE-TTT--EEEEE.EE-SSS-S- CS
                zinc-ribbons_6   2 kCpeCqqele.krgeqyhCeaCqedlkke.alCpeCeqe 38 
                                   +C +C ++l+ +++e ++C +C++ ++ e  +Cp C+ +
  gi|15668592|ref|NP_247390.1| 147 YCAHCGAKLKeEEEEVLRCPNCKRPVQPEwIVCPYCGYR 185
                                   455666666544445556666666555431456666655 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.4      0.16        82       3      25 ..     101     120 ..     100     123 .. 0.71
   2 ?    3.9   3.3     0.081        43       3      23 ..     115     137 ..     113     141 .. 0.77
   3 !   15.3   3.3   2.2e-05     0.012       3      23 ..     148     168 ..     147     170 .. 0.97
   4 !    7.6   0.1    0.0058       3.1      16      27 ..     175     186 ..     171     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.16
                                   -SSS--B----SSS----SSS-- CS
                DNA_RNApol_7kD   3 CgeCgaevslkkgdpiRCkeCGh 25 
                                   C  C+++  l  +    C++CG 
  gi|15668592|ref|NP_247390.1| 101 CNSCKSPIDLGWT---YCTNCGA 120
                                   6667777776666...7999997 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.081
                                   -SSS--B--..--SSS----SSS CS
                DNA_RNApol_7kD   3 CgeCgaevs..lkkgdpiRCkeC 23 
                                   C +Cgae +    ++++ RC +C
  gi|15668592|ref|NP_247390.1| 115 CTNCGAEIKnmTFEEEVERCPNC 137
                                   9999999988344556669*999 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 2.2e-05
                                   -SSS--B----SSS----SSS CS
                DNA_RNApol_7kD   3 CgeCgaevslkkgdpiRCkeC 23 
                                   C+ Cga+ + ++++++RC +C
  gi|15668592|ref|NP_247390.1| 148 CAHCGAKLKEEEEEVLRCPNC 168
                                   ********************* PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0058
                                   S----SSS---- CS
                DNA_RNApol_7kD  16 dpiRCkeCGhRi 27 
                                   + i C +CG+R+
  gi|15668592|ref|NP_247390.1| 175 EWIVCPYCGYRL 186
                                   6799*******6 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   4.3     0.045        23      12      35 ..     113     138 ..      92     144 .. 0.65
   2 !   16.1   1.3   1.5e-05    0.0079      11      36 ..     145     170 ..     139     173 .. 0.89
   3 ?   -1.3   0.1       4.1   2.2e+03      14      21 ..     179     186 ..     175     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.045
                                   -B-TTT-SB-.-S.SSS-EEEETTT- CS
                          C1_1  12 tfCkhCgefl.wg.kekqglkCswCk 35 
                                   t+C+ Cg  +  + +e    +C +C+
  gi|15668592|ref|NP_247390.1| 113 TYCTNCGAEIkNMtFEEEVERCPNCN 138
                                   56666666665334666666666665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.5e-05
                                   --B-TTT-SB--SSSS-EEEETTT-- CS
                          C1_1  11 ptfCkhCgeflwgkekqglkCswCkl 36 
                                    ++C+hCg  l+++e   l+C +Ck+
  gi|15668592|ref|NP_247390.1| 145 WKYCAHCGAKLKEEEEEVLRCPNCKR 170
                                   579********88***********97 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.1
                                   -TTT-SB- CS
                          C1_1  14 CkhCgefl 21 
                                   C +Cg  l
  gi|15668592|ref|NP_247390.1| 179 CPYCGYRL 186
                                   77777665 PP

>> DUF4734  Domain of unknown function (DUF4734)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   4.5e-05     0.024       2      56 ..     131     184 ..     130     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.5e-05
                       DUF4734   2 ilelpevqslinealsystalmyedkeeglsalleklekekpqeReWiydegcpy 56 
                                   + ++p+ +++i ++ +y+  + ++ kee+ ++ l+  + + p++ eWi+++ c y
  gi|15668592|ref|NP_247390.1| 131 VERCPNCNNYISDSWKYCAHCGAKLKEEE-EEVLRCPNCKRPVQPEWIVCPYCGY 184
                                   56799*********************997.99*********************98 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.7      0.83   4.4e+02       4      10 ..     101     107 ..     101     108 .. 0.84
   2 ?   15.3   4.8     3e-05     0.016       1      26 []     112     137 ..     112     137 .. 1.00
   3 ?    6.0   1.1     0.024        13       1      15 [.     145     159 ..     145     161 .. 0.85
   4 ?    1.8   0.3       0.5   2.6e+02       4       8 ..     165     169 ..     163     172 .. 0.71
   5 ?    3.5   0.5      0.15        79       1       8 [.     176     183 ..     176     189 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.83
                        zf-ACC   4 CpsCgem 10 
                                   C+sC++ 
  gi|15668592|ref|NP_247390.1| 101 CNSCKSP 107
                                   ****985 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3e-05
                        zf-ACC   1 WtKCpsCgemlykkeLernlyVCPkC 26 
                                   Wt C+ Cg+ + +  +e+  + CP+C
  gi|15668592|ref|NP_247390.1| 112 WTYCTNCGAEIKNMTFEEEVERCPNC 137
                                   ************************** PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.024
                        zf-ACC   1 WtKCpsCgemlykke 15 
                                   W  C +Cg+ l  +e
  gi|15668592|ref|NP_247390.1| 145 WKYCAHCGAKLKEEE 159
                                   99******9887665 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.5
                        zf-ACC   4 CpsCg 8  
                                   Cp C+
  gi|15668592|ref|NP_247390.1| 165 CPNCK 169
                                   77776 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.15
                        zf-ACC   1 WtKCpsCg 8  
                                   W+ Cp Cg
  gi|15668592|ref|NP_247390.1| 176 WIVCPYCG 183
                                   66677666 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2       1.5     8e+02      39      47 ..     100     108 ..      94     111 .. 0.71
   2 ?   12.3   1.0   0.00022      0.11      24      49 ..     113     143 ..     110     144 .. 0.90
   3 ?   12.4   2.1   0.00021      0.11      25      48 ..     147     173 ..     145     174 .. 0.91
   4 ?    0.4   0.1       1.1   5.9e+02      40      44 ..     179     183 ..     176     189 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.5
                                   B-TTT--B- CS
                    zf-C3HC4_3  39 kCpiCrrpi 47 
                                    C  C++pi
  gi|15668592|ref|NP_247390.1| 100 LCNSCKSPI 108
                                   466677776 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00022
                                   EE-HHHHHHHHH.....TT-B-TTT--B--E CS
                    zf-C3HC4_3  24 vlCeeCaekllk.....rkkkCpiCrrpiek 49 
                                    +C +C  ++++     + ++Cp C+  i++
  gi|15668592|ref|NP_247390.1| 113 TYCTNCGAEIKNmtfeeEVERCPNCNNYISD 143
                                   48********9999*9999*******99986 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00021
                                   E-HHHHHHHHH...TT-B-TTT--B-- CS
                    zf-C3HC4_3  25 lCeeCaekllk...rkkkCpiCrrpie 48 
                                   +C +C  kl++   +  +Cp C+rp++
  gi|15668592|ref|NP_247390.1| 147 YCAHCGAKLKEeeeEVLRCPNCKRPVQ 173
                                   7********98999999********97 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.1
                                   -TTT- CS
                    zf-C3HC4_3  40 CpiCr 44 
                                   Cp+C 
  gi|15668592|ref|NP_247390.1| 179 CPYCG 183
                                   66664 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3     0.011       5.9       4      28 ..     101     125 ..      98     133 .. 0.84
   2 ?    7.9   1.1    0.0096       5.1       3      25 ..     133     155 ..     131     163 .. 0.90
   3 ?    6.0   0.1     0.038        20       3      25 ..     164     186 ..     162     190 .] 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.011
                 zinc-ribbon_6   4 CeqCgqllffenssClkCgaalgfa 28 
                                   C++C++++    + C++Cga++  +
  gi|15668592|ref|NP_247390.1| 101 CNSCKSPIDLGWTYCTNCGAEIKNM 125
                                   *******************998654 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0096
                 zinc-ribbon_6   3 eCeqCgqllffenssClkCgaal 25 
                                   +C +C++ +    + C++Cga+l
  gi|15668592|ref|NP_247390.1| 133 RCPNCNNYISDSWKYCAHCGAKL 155
                                   6*******************998 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.038
                 zinc-ribbon_6   3 eCeqCgqllffenssClkCgaal 25 
                                   +C +C++++  e   C  Cg +l
  gi|15668592|ref|NP_247390.1| 164 RCPNCKRPVQPEWIVCPYCGYRL 186
                                   8******************9987 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.24   1.3e+02      24      30 ..     115     121 ..     113     123 .. 0.70
   2 ?    3.1   0.6      0.14        75      23      29 ..     133     139 ..     133     141 .. 0.87
   3 ?   14.3   1.7   4.5e-05     0.024       4      29 ..     146     170 ..     143     172 .. 0.87
   4 ?    3.2   0.1      0.13        71      24      30 ..     179     185 ..     177     190 .] 0.57

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.24
                 zf-NADH-PPase  24 CpaCgle 30 
                                   C +Cg+e
  gi|15668592|ref|NP_247390.1| 115 CTNCGAE 121
                                   7777776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.14
                 zf-NADH-PPase  23 vCpaCgl 29 
                                   +Cp+C++
  gi|15668592|ref|NP_247390.1| 133 RCPNCNN 139
                                   7****97 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 4.5e-05
                 zf-NADH-PPase   4 rFCgrCGaptepaeggwarvCpaCgl 29 
                                   ++C++CGa+ + +e +  ++Cp+C++
  gi|15668592|ref|NP_247390.1| 146 KYCAHCGAKLKEEEEE-VLRCPNCKR 170
                                   69********999886.89*****85 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.13
                 zf-NADH-PPase  24 CpaCgle 30 
                                   Cp Cg++
  gi|15668592|ref|NP_247390.1| 179 CPYCGYR 185
                                   5555544 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.9     7e-05     0.037       1      25 [.     114     137 ..     114     138 .. 0.97
   2 ?   -1.4   5.6       2.8   1.5e+03       2      25 ..     148     168 ..     147     169 .. 0.62
   3 ?    1.7   1.4       0.3   1.6e+02       2       8 ..     165     171 ..     164     174 .. 0.74
   4 ?   -1.4   0.1       2.8   1.5e+03       2       6 ..     179     183 ..     178     187 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-05
                      zf-TFIIB   1 kCPkCqdeleeserggveidyCpqC 25 
                                   +C +C++e + + + + e+++Cp+C
  gi|15668592|ref|NP_247390.1| 114 YCTNCGAEIKNMTFEE-EVERCPNC 137
                                   7***************.******** PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.8
                      zf-TFIIB   2 CPkCqdeleeserggveidyCpqC 25 
                                   C  C++ l+e    + e+ +Cp+C
  gi|15668592|ref|NP_247390.1| 148 CAHCGAKLKEE---EEEVLRCPNC 168
                                   66666666654...4577788888 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.3
                      zf-TFIIB   2 CPkCqde 8  
                                   CP+C+ +
  gi|15668592|ref|NP_247390.1| 165 CPNCKRP 171
                                   9999876 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.8
                      zf-TFIIB   2 CPkCq 6  
                                   CP C+
  gi|15668592|ref|NP_247390.1| 179 CPYCG 183
                                   77776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       1.5     8e+02      29      34 ..     101     106 ..      91     109 .. 0.68
   2 ?   12.3   2.4   0.00026      0.14       8      33 ..     115     138 ..     114     142 .. 0.77
   3 ?    5.4   4.2     0.038        20       8      37 ..     148     173 ..     140     175 .. 0.75
   4 ?    4.5   0.1     0.071        37      27      38 ..     177     188 ..     173     190 .] 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.5
                   Zn-ribbon_8  29 CPeCgs 34 
                                   C +C+s
  gi|15668592|ref|NP_247390.1| 101 CNSCKS 106
                                   777766 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00026
                   Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCg 33 
                                   C++Cg e   +   ++++ + CP+C+
  gi|15668592|ref|NP_247390.1| 115 CTNCGAEIKNMT--FEEEVERCPNCN 138
                                   *****8888665..3666666****7 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.038
                   Zn-ribbon_8   8 CeeCghefevlqsisdaplta.CPeCgsevr 37 
                                   C  Cg +  +     +++++  CP+C+ +v+
  gi|15668592|ref|NP_247390.1| 148 CAHCGAKLKE-----EEEEVLrCPNCKRPVQ 173
                                   8888855443.....4556777****98875 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.071
                   Zn-ribbon_8  27 taCPeCgsevrr 38 
                                   ++CP Cg +++r
  gi|15668592|ref|NP_247390.1| 177 IVCPYCGYRLKR 188
                                   56****999988 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.6    0.0013       0.7      67     130 ..      92     138 ..      32     142 .. 0.60
   2 ?    6.7   8.2    0.0099       5.2      68     111 ..     126     170 ..     120     189 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                       TackOD1  67 eelvdrirlCpsCksghlnvrevCpkCkSidieeqelihhftCgnvgpeeeflkegkleCpkCk 130
                                   +++   + lC+sCks                        + +Cg+  ++ +f +e    Cp+C+
  gi|15668592|ref|NP_247390.1|  92 TKFSTFVPLCNSCKSPIDLGWT----------------YCTNCGAEIKNMTFEEEV-ERCPNCN 138
                                   4444444444444444444444................466666666666665444.4566665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0099
                       TackOD1  68 elvdrirlCpsCksghlnvrevCpkCkSi.dieeqelihhftCgn 111
                                   ++ +++  Cp+C+ +     ++C +C++  + ee+e++ + +C +
  gi|15668592|ref|NP_247390.1| 126 TFEEEVERCPNCNNYISDSWKYCAHCGAKlKEEEEEVLRCPNCKR 170
                                   566777788888888888888888887642556677778877743 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.1    0.0031       1.7       1      44 [.      98     138 ..      98     140 .. 0.77
   2 ?   13.6   2.5   8.2e-05     0.043      22      46 ..     145     171 ..     144     173 .. 0.82
   3 ?   -0.9   0.2       2.8   1.5e+03      40      43 ..     179     182 ..     175     188 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0031
                     zf-RING_4   1 cplCdeeldetdkdlkpC.eCgyqiClfCyhrileeeegrCPaCr 44 
                                   +plC ++ +  d   ++C +Cg +i    ++    ee +rCP+C 
  gi|15668592|ref|NP_247390.1|  98 VPLCNSCKSPIDLGWTYCtNCGAEIKNMTFE----EEVERCPNCN 138
                                   6788888888888888887788888777766....6788*****6 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 8.2e-05
                     zf-RING_4  22 yqiClfCyhrile..eeegrCPaCree 46 
                                   ++ C  C  +++e  ee  rCP+C+++
  gi|15668592|ref|NP_247390.1| 145 WKYCAHCGAKLKEeeEEVLRCPNCKRP 171
                                   578*********94345779*****97 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.8
                     zf-RING_4  40 CPaC 43 
                                   CP C
  gi|15668592|ref|NP_247390.1| 179 CPYC 182
                                   5555 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       3.8     2e+03     125     139 ..      91     105 ..      53     108 .. 0.72
   2 ?   13.4   1.2   0.00011      0.06     112     140 ..     110     139 ..     107     141 .. 0.85
   3 ?    5.7   2.8     0.027        14     116     139 ..     147     169 ..     140     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.8
                       DUF1451 125 alkkteeippCpkCg 139
                                     k ++ +p C++C+
  gi|15668592|ref|NP_247390.1|  91 GTKFSTFVPLCNSCK 105
                                   445566677788886 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00011
                       DUF1451 112 lGtlvCekCgkela.lkkteeippCpkCga 140
                                   lG   C++Cg+e++ ++  ee+++Cp+C++
  gi|15668592|ref|NP_247390.1| 110 LGWTYCTNCGAEIKnMTFEEEVERCPNCNN 139
                                   68889*******963788899*******86 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.027
                       DUF1451 116 vCekCgkelalkkteeippCpkCg 139
                                    C++Cg++l+ +  ee+ +Cp+C+
  gi|15668592|ref|NP_247390.1| 147 YCAHCGAKLKEE-EEEVLRCPNCK 169
                                   6********955.567779****8 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       5.4   2.8e+03      23      29 ..      98     104 ..      82     106 .. 0.66
   2 ?    1.1   0.7      0.86   4.6e+02      25      31 ..     114     120 ..     112     120 .. 0.86
   3 ?    9.5   0.4     0.002       1.1      16      30 ..     121     138 ..     120     138 .. 0.79
   4 ?   -0.7   0.3       3.1   1.7e+03      25      31 ..     147     153 ..     146     153 .. 0.85
   5 ?   11.9   0.6   0.00036      0.19      17      31 ..     155     170 ..     153     170 .. 0.79
   6 ?    3.2   0.2      0.19     1e+02      25      30 ..     178     183 ..     175     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.4
                                   -EE-TTT CS
                     zf-RING_7  23 vvtCpeC 29 
                                   v+ C +C
  gi|15668592|ref|NP_247390.1|  98 VPLCNSC 104
                                   7889999 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.86
                                   E-TTT-- CS
                     zf-RING_7  25 tCpeCGR 31 
                                   +C +CG+
  gi|15668592|ref|NP_247390.1| 114 YCTNCGA 120
                                   8****96 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.002
                                   HHCCS...TB-EE-TTT- CS
                     zf-RING_7  16 elrag...devvtCpeCG 30 
                                   e+++    +ev +Cp+C+
  gi|15668592|ref|NP_247390.1| 121 EIKNMtfeEEVERCPNCN 138
                                   6666677789*******7 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 3.1
                                   E-TTT-- CS
                     zf-RING_7  25 tCpeCGR 31 
                                   +C +CG+
  gi|15668592|ref|NP_247390.1| 147 YCAHCGA 153
                                   799**96 PP

  == domain 5  score: 11.9 bits;  conditional E-value: 0.00036
                                   HCCS.TB-EE-TTT-- CS
                     zf-RING_7  17 lrag.devvtCpeCGR 31 
                                   l+   +ev +Cp+C R
  gi|15668592|ref|NP_247390.1| 155 LKEEeEEVLRCPNCKR 170
                                   5555588*******98 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.19
                                   E-TTT- CS
                     zf-RING_7  25 tCpeCG 30 
                                    Cp+CG
  gi|15668592|ref|NP_247390.1| 178 VCPYCG 183
                                   6****9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       2.6   1.4e+03       3       9 ..     101     107 ..     100     111 .. 0.68
   2 ?    7.3   2.8    0.0084       4.5       2      29 ..     114     138 ..     113     141 .. 0.78
   3 ?    8.0   4.3    0.0052       2.7       1      28 [.     146     168 ..     146     170 .. 0.75
   4 ?    1.3   0.4      0.64   3.4e+02       3      11 ..     165     173 ..     164     176 .. 0.77
   5 ?    3.2   0.1      0.16        86       3      10 ..     179     186 ..     177     189 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.6
                                   -TTT--B CS
                     Nudix_N_2   3 CsqCGtp 9  
                                   C++C +p
  gi|15668592|ref|NP_247390.1| 101 CNSCKSP 107
                                   7777666 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0084
                                   B-TTT--B-EEE--TT-SS-EEEETTTT CS
                     Nudix_N_2   2 FCsqCGtpvelripdgDnreRlvCpaCg 29 
                                   +C++CG++++  +  +++ eR  Cp+C+
  gi|15668592|ref|NP_247390.1| 114 YCTNCGAEIKNMTF-EEEVER--CPNCN 138
                                   9*******998775.455555..88885 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0052
                                   -B-TTT--B-EEE--TT-SS-EEEETTT CS
                     Nudix_N_2   1 kFCsqCGtpvelripdgDnreRlvCpaC 28 
                                   k+C +CG++++     ++++e l+Cp+C
  gi|15668592|ref|NP_247390.1| 146 KYCAHCGAKLK-----EEEEEVLRCPNC 168
                                   8********76.....455566678887 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.64
                                   -TTT--B-E CS
                     Nudix_N_2   3 CsqCGtpve 11 
                                   C++C  pv+
  gi|15668592|ref|NP_247390.1| 165 CPNCKRPVQ 173
                                   888888876 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.16
                                   -TTT--B- CS
                     Nudix_N_2   3 CsqCGtpv 10 
                                   C+ CG ++
  gi|15668592|ref|NP_247390.1| 179 CPYCGYRL 186
                                   55566555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.2    0.0077       4.1      71      94 ..     113     139 ..      73     146 .. 0.87
   2 ?    7.4   6.3    0.0081       4.3      73      94 ..     148     170 ..     143     189 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0077
                                   EEETTTS-EEECHH.H..HHS-TTTSS CS
                          HypA  71 vrCreCgkefelee.k..alrCpkCgs 94 
                                   ++C++Cg+e++  + +   +rCp+C++
  gi|15668592|ref|NP_247390.1| 113 TYCTNCGAEIKNMTfEeeVERCPNCNN 139
                                   58*******997664334569****87 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0081
                                   ETTTS-EEECHHH.HHS-TTTSS CS
                          HypA  73 CreCgkefeleek.alrCpkCgs 94 
                                   C +Cg++ ++ee+  lrCp+C++
  gi|15668592|ref|NP_247390.1| 148 CAHCGAKLKEEEEeVLRCPNCKR 170
                                   77777777766544667777765 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2      0.14        72       7      30 ..     100     123 ..      97     127 .. 0.88
   2 ?    8.9   1.3    0.0028       1.5       6      26 ..     132     152 ..     128     155 .. 0.89
   3 ?    3.9   0.8       0.1        54       7      27 ..     164     184 ..     158     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.14
                          DHHC   7 fCstcniykpprskHcrvCnrcvl 30 
                                    C+ c+ +    + +c  C+  + 
  gi|15668592|ref|NP_247390.1| 100 LCNSCKSPIDLGWTYCTNCGAEIK 123
                                   5******************97766 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0028
                          DHHC   6 kfCstcniykpprskHcrvCn 26 
                                   + C++cn y  + +k+c +C+
  gi|15668592|ref|NP_247390.1| 132 ERCPNCNNYISDSWKYCAHCG 152
                                   67******************7 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.1
                          DHHC   7 fCstcniykpprskHcrvCnr 27 
                                    C++c+++++p++  c  C+ 
  gi|15668592|ref|NP_247390.1| 164 RCPNCKRPVQPEWIVCPYCGY 184
                                   5******************86 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.7    0.0011      0.58       4      42 ..     133     173 ..     129     178 .. 0.83
   2 ?    4.9   0.8     0.063        33       4      12 ..     178     186 ..     175     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0011
                       zf-Di19   4 tCPyCgke.ltvkeLveHvedeHrveskevv.CPvCaekvt 42 
                                    CP C++   +  + ++H+ ++ ++e++ev  CP C+  v+
  gi|15668592|ref|NP_247390.1| 133 RCPNCNNYiSDSWKYCAHCGAKLKEEEEEVLrCPNCKRPVQ 173
                                   6******6367789********9999998755****97665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.063
                       zf-Di19   4 tCPyCgkel 12 
                                    CPyCg  l
  gi|15668592|ref|NP_247390.1| 178 VCPYCGYRL 186
                                   6****9765 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  11.8     0.017       9.1      84     131 ..     125     170 ..      73     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.017
                        Mut7-C  84 lslkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrk 131
                                   +++++e++rC +Cn+ ++   k  +  +  +k++ee++e+ rC++C++
  gi|15668592|ref|NP_247390.1| 125 MTFEEEVERCPNCNNYISDSWKYCA--HCGAKLKEEEEEVLRCPNCKR 170
                                   5667788999999999988887766..788999999999999999987 PP

>> DUF4187  Domain of unknown function (DUF4187)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.7       0.7   3.7e+02      26      38 ..     112     124 ..     111     139 .. 0.69
   2 ?   12.3   2.6   0.00021      0.11      13      47 ..     132     166 ..     120     170 .. 0.78
   3 ?    0.8   0.2       0.8   4.2e+02      29      35 ..     179     185 ..     174     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.7
                       DUF4187  26 ylYCfwCgtkYed 38 
                                   + YC  Cg + ++
  gi|15668592|ref|NP_247390.1| 112 WTYCTNCGAEIKN 124
                                   58******98765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00021
                       DUF4187  13 erLeklleyLReeylYCfwCgtkYedeedLeenCP 47 
                                   er  ++++y+ ++++YC +Cg k ++ee+    CP
  gi|15668592|ref|NP_247390.1| 132 ERCPNCNNYISDSWKYCAHCGAKLKEEEEEVLRCP 166
                                   55556789999*************99998555787 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.8
                       DUF4187  29 CfwCgtk 35 
                                   C +Cg++
  gi|15668592|ref|NP_247390.1| 179 CPYCGYR 185
                                   9****97 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.4       1.2   6.5e+02      40      46 ..     113     119 ..      97     130 .. 0.63
   2 ?    3.9   1.0      0.12        64      25      46 ..     130     152 ..     123     163 .. 0.70
   3 ?   10.4   3.0    0.0011      0.59      25      51 ..     161     188 ..     149     190 .] 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.2
                                   C-BTTTT CS
                Ribosomal_L32p  40 rvcpscG 46 
                                   + c++cG
  gi|15668592|ref|NP_247390.1| 113 TYCTNCG 119
                                   4455554 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.12
                                   -EEEETTTCCEEC.TTC-BTTTT CS
                Ribosomal_L32p  25 nlvecpncgelkl.pHrvcpscG 46 
                                    + +cpnc++++  +   c +cG
  gi|15668592|ref|NP_247390.1| 130 EVERCPNCNNYISdSWKYCAHCG 152
                                   5789*****87541455666665 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0011
                                   -EEEETTTCCEECTT.C-BTTTTBSSSB CS
                Ribosomal_L32p  25 nlvecpncgelklpH.rvcpscGyYkgr 51 
                                    + +cpnc+ +  p   vcp+cGy   r
  gi|15668592|ref|NP_247390.1| 161 EVLRCPNCKRPVQPEwIVCPYCGYRLKR 188
                                   5679*****999997479****997655 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   3.2     0.068        36      15      26 ..     114     125 ..     109     137 .. 0.84
   2 ?   -1.5   0.1       4.8   2.5e+03      16      23 ..     134     141 ..     130     143 .. 0.72
   3 ?    7.0   5.3     0.011       5.8      14      28 ..     146     160 ..     144     168 .. 0.86
   4 ?    0.3   0.0       1.4   7.3e+02      16      22 ..     179     185 ..     178     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.068
                          YhfH  15 kCteCGkeieEq 26 
                                    Ct+CG ei+ +
  gi|15668592|ref|NP_247390.1| 114 YCTNCGAEIKNM 125
                                   6********977 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.8
                          YhfH  16 CteCGkei 23 
                                   C++C + i
  gi|15668592|ref|NP_247390.1| 134 CPNCNNYI 141
                                   88886665 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.011
                          YhfH  14 KkCteCGkeieEqae 28 
                                   K C++CG +++E +e
  gi|15668592|ref|NP_247390.1| 146 KYCAHCGAKLKEEEE 160
                                   99*********9987 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 1.4
                          YhfH  16 CteCGke 22 
                                   C+ CG  
  gi|15668592|ref|NP_247390.1| 179 CPYCGYR 185
                                   *****76 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   2.4      0.82   4.3e+02       6      19 ..     113     126 ..     110     144 .. 0.57
   2 ?    5.6   0.1     0.045        24       7      16 ..     147     156 ..     146     159 .. 0.89
   3 ?    2.9   0.1       0.3   1.6e+02       5      15 ..     162     172 ..     160     176 .. 0.85
   4 ?    6.1   0.4      0.03        16       6      18 ..     177     189 ..     175     190 .] 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.82
               Zn_ribbon_recom   6 lrCgeCGspmtrrk 19 
                                    +C +CG+  ++ +
  gi|15668592|ref|NP_247390.1| 113 TYCTNCGAEIKNMT 126
                                   68889988766654 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.045
               Zn_ribbon_recom   7 rCgeCGspmt 16 
                                   +C++CG++++
  gi|15668592|ref|NP_247390.1| 147 YCAHCGAKLK 156
                                   8******985 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.3
               Zn_ribbon_recom   5 llrCgeCGspm 15 
                                   +lrC +C +p 
  gi|15668592|ref|NP_247390.1| 162 VLRCPNCKRPV 172
                                   69*****9986 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.03
               Zn_ribbon_recom   6 lrCgeCGspmtrr 18 
                                   ++C +CG +++r+
  gi|15668592|ref|NP_247390.1| 177 IVCPYCGYRLKRK 189
                                   89*******9987 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.7     0.098        52      44      67 ..      97     123 ..      89     126 .. 0.61
   2 ?    6.6   0.2     0.018       9.6      54      67 ..     129     142 ..     124     145 .. 0.78
   3 ?    4.2   4.5     0.099        52      46      67 ..     135     156 ..     134     159 .. 0.86
   4 ?    3.7   0.5      0.14        76      58      64 ..     164     170 ..     156     173 .. 0.64
   5 ?    4.4   0.1     0.088        46       2      13 ..     173     184 ..     172     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.098
                 zf-LITAF-like  44 liPfcvdslkdve...hyCpnCgallg 67 
                                   ++P+c ++   ++    yC+nCga ++
  gi|15668592|ref|NP_247390.1|  97 FVPLCNSCKSPIDlgwTYCTNCGAEIK 123
                                   556444333333322359****99986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.018
                 zf-LITAF-like  54 dvehyCpnCgallg 67 
                                   +   +CpnC++++ 
  gi|15668592|ref|NP_247390.1| 129 EEVERCPNCNNYIS 142
                                   55678*****9985 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.099
                 zf-LITAF-like  46 PfcvdslkdvehyCpnCgallg 67 
                                   P c +   d   yC +Cga+l+
  gi|15668592|ref|NP_247390.1| 135 PNCNNYISDSWKYCAHCGAKLK 156
                                   889999999999*****99986 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.14
                 zf-LITAF-like  58 yCpnCga 64 
                                   +CpnC++
  gi|15668592|ref|NP_247390.1| 164 RCPNCKR 170
                                   5666665 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.088
                 zf-LITAF-like   2 eptqvdCpaCqq 13 
                                   +p+ + Cp+C+ 
  gi|15668592|ref|NP_247390.1| 173 QPEWIVCPYCGY 184
                                   69999*****85 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5     0.041        22       7      25 ..     101     119 ..      96     122 .. 0.93
   2 ?    3.0   0.4      0.14        76       4      25 ..     131     152 ..     128     158 .. 0.84
   3 ?    5.6   0.5     0.023        12       6      25 ..     164     183 ..     159     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.041
                  Zn_ribbon_17   7 CayCelavkgrvvlcgvCe 25 
                                   C+ C+ ++    ++c++C+
  gi|15668592|ref|NP_247390.1| 101 CNSCKSPIDLGWTYCTNCG 119
                                   ******************6 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                  Zn_ribbon_17   4 lksCayCelavkgrvvlcgvCe 25 
                                    + C  C+  +  +  +c  C+
  gi|15668592|ref|NP_247390.1| 131 VERCPNCNNYISDSWKYCAHCG 152
                                   5679999999999999999996 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.023
                  Zn_ribbon_17   6 sCayCelavkgrvvlcgvCe 25 
                                    C  C+ +v+   ++c+ C+
  gi|15668592|ref|NP_247390.1| 164 RCPNCKRPVQPEWIVCPYCG 183
                                   799****************7 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   4.3      0.12        66      16      42 .]     110     137 ..      99     137 .. 0.75
   2 ?    7.9   6.7    0.0063       3.3       1      42 []     134     168 ..     134     168 .. 0.89
   3 ?   -1.3   0.1       4.7   2.5e+03      39      42 .]     179     182 ..     173     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.12
                    zf-C3HC4_4  16 CGhsfClsCisslqkepdgeq.llCplC 42 
                                    G ++C +C  ++ +   +e+  +Cp C
  gi|15668592|ref|NP_247390.1| 110 LGWTYCTNCGAEIKNMTFEEEvERCPNC 137
                                   499******877776655544369**99 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0063
                    zf-C3HC4_4   1 CPiCldYLekPvsleCGhsfClsCisslqkepdgeqllCplC 42 
                                   CP C +Y+++         +C +C  +l +e++++ l+Cp C
  gi|15668592|ref|NP_247390.1| 134 CPNCNNYISD------SWKYCAHCGAKLKEEEEEV-LRCPNC 168
                                   8888888877......579*********9999887.****** PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.7
                    zf-C3HC4_4  39 CplC 42 
                                   Cp C
  gi|15668592|ref|NP_247390.1| 179 CPYC 182
                                   4444 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.8    0.0027       1.4      17      39 ..     110     132 ..     100     133 .. 0.82
   2 ?    3.6   4.0     0.089        47       2      31 ..     133     157 ..     132     161 .. 0.74
   3 ?    2.5   7.4       0.2     1e+02       2      27 ..     164     184 ..     163     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0027
                                   TTCEEESSSSBEEEECCCCCCCH CS
                  TF_Zn_Ribbon  17 rgelvCtdCGlVlednsidegpe 39 
                                    g ++Ct+CG+ + ++  +e++e
  gi|15668592|ref|NP_247390.1| 110 LGWTYCTNCGAEIKNMTFEEEVE 132
                                   57789*********999999988 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.089
                                   EETTTTCEECHEETSTTCEEESSSSBEEEE CS
                  TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVled 31 
                                   +CPnC+++  + D      +C  CG+ l +
  gi|15668592|ref|NP_247390.1| 133 RCPNCNNY--ISDSW---KYCAHCGAKLKE 157
                                   6****985..66633...478888888876 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.2
                                   EETTTTCEECHEETSTTCEEESSSSB CS
                  TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGl 27 
                                   +CPnC+ +  v + e   +vC+ CG+
  gi|15668592|ref|NP_247390.1| 164 RCPNCKRP--VQP-E--WIVCPYCGY 184
                                   7*****98..444.3..589999996 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3     0.023        12      22      29 ..     113     120 ..     111     122 .. 0.83
   2 ?    8.0   0.3    0.0044       2.3       2      13 ..     129     140 ..     128     145 .. 0.75
   3 ?    5.2   0.2     0.033        17      23      30 ..     147     154 ..     146     155 .. 0.83
   4 ?    0.5   0.5      0.97   5.1e+02       3      10 ..     161     168 ..     159     170 .. 0.80
   5 ?    0.3   0.7       1.1   5.9e+02       6      11 ..     178     183 ..     177     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.023
                       zf-RRN7  22 yyCrrCht 29 
                                   +yC++C+ 
  gi|15668592|ref|NP_247390.1| 113 TYCTNCGA 120
                                   8*****97 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0044
                       zf-RRN7   2 ekgppCgvCgcr 13 
                                   e +++C+ C+++
  gi|15668592|ref|NP_247390.1| 129 EEVERCPNCNNY 140
                                   6689******94 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.033
                       zf-RRN7  23 yCrrChtq 30 
                                   yC +C+ +
  gi|15668592|ref|NP_247390.1| 147 YCAHCGAK 154
                                   9****975 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.97
                       zf-RRN7   3 kgppCgvC 10 
                                    + +C+ C
  gi|15668592|ref|NP_247390.1| 161 EVLRCPNC 168
                                   6789**** PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1.1
                       zf-RRN7   6 pCgvCg 11 
                                   +C+ Cg
  gi|15668592|ref|NP_247390.1| 178 VCPYCG 183
                                   566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                        67  (0.00373696); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.68u 0.26s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 1153.12
//
Query:       gi|15668593|ref|NP_247391.1|  [L=237]
Description: hypothetical protein MJ_0417 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-14   53.2   0.0    3.5e-14   52.3   0.0    1.4  1  PHP_C     PHP-associated


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.0   1.9e-18   3.5e-14       3      47 ..     133     178 ..     132     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 1.9e-18
                         PHP_C   3 aNrrArrfAeklglpgtgGSDAHrleeVGrayTef.eepiatpdel 47 
                                    N +A+++Aek+++++  GSDAH+++eVG+ay+ f e +i++pd+l
  gi|15668593|ref|NP_247391.1| 133 PNLKALEYAEKYDFAMAFGSDAHFIWEVGNAYIKFsELNIEKPDDL 178
                                   699********************************97777755554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1627.46
//
Query:       gi|15668594|ref|NP_247392.1|  [L=257]
Description: hypothetical protein MJ_0418 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-07   29.3   0.0    8.3e-07   28.4   0.0    1.4  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   4.6e-11   8.3e-07     142     231 ..      36     119 ..      20     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 4.6e-11
                                   TT-EEES-HHHHHHHHHHHT.TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTTEEEEEEEETTEEEEEE-TT--SSS CS
                Regulator_TrmB 142 ekpitfssirlavedikkllraglkveaeveGrdtetgeevtieGrvveatlnstpgvaslvvetedgevtVGGlgAvlED 222
                                   +++ + +++  + ++ +k+l+++ +++a++ G++t +++++   G+v      +++   +l+  +++ ++t+GG  A+ ED
  gi|15668594|ref|NP_247392.1|  36 DYEFDGNQMYKCAWVCEKILNKNFPLNATIIGKWTLSKKPF--NGEVKI----YDAKGGTLYAIYNGTPITIGGELAYQED 110
                                   4444446778899*********************8888886..688888....445566888889999************* PP

                                   EEEEEEEEE CS
                Regulator_TrmB 223 ieaeeitle 231
                                   i+a++i+l+
  gi|15668594|ref|NP_247392.1| 111 IAAKKIILH 119
                                   ******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1719.85
//
Query:       gi|15668595|ref|NP_247393.1|  [L=354]
Description: hypothetical protein MJ_0419 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-92  310.0  45.7    2.4e-92  309.8  45.7    1.1  1  O_anti_polymase  Putative O-antigen polymerase
  ------ inclusion threshold ------
      0.011   15.0   2.8      0.031   13.6   2.2    1.9  1  YdjM             LexA-binding, inner membrane-associated puta


Domain annotation for each model (and alignments):
>> O_anti_polymase  Putative O-antigen polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.8  45.7   2.7e-96   2.4e-92       1     335 []      11     336 ..      11     336 .. 0.95

  Alignments for each domain:
  == domain 1  score: 309.8 bits;  conditional E-value: 2.7e-96
               O_anti_polymase   1 dlfspliivlllilfiilsaiavsslliili..llglisfilgalllsklvlsieellvknnkkkleikfnekkvekigli 79 
                                   +++ ++++v+l+++++i+s i+++s++++l+  ++++isf++g++l+  + +            k ++k+n kk++++g++
  gi|15668595|ref|NP_247393.1|  11 KIELHHVFVMLSCIYLIFSDISINSAVVFLFssIFFYISFTAGKRLYYLIGI-----------DKENLKINLKKHYNFGIF 80 
                                   6899******************************************332222...........4567899999******** PP

               O_anti_polymase  80 lvliGillfiinllivggiPlfdpslraklntkltalsylflpsiailvakvarlrnlilfiiglv...llallgYrttvl 157
                                   l+++G+++++ +l++v+++Plf+p +r++ln+ +t+ls+lfl+++ai+va++ +++++++++++++   l++llgYrt+vl
  gi|15668595|ref|NP_247393.1|  81 LMIVGLIAVTSDLIWVKDVPLFNPLSRKFLNVYFTTLSHLFLVGWAIVVASS-NIDKKKILLYTIIfsiLIMLLGYRTNVL 160
                                   **************************************************77.8888888888888788************ PP

               O_anti_polymase 158 aillsilitlYytkkikikeivllilllvllllgigylrsiseqawsl..nplelllyRadftlsvldkivkglqgvthGk 236
                                   ++l+s+  +lYy++ki+++ei+ + +l++++llg+++l   + +a+++  np   +++R+++t+s++d+i+++++gv++G+
  gi|15668595|ref|NP_247393.1| 161 VLLISVGAILYYKNKISNREILKYGILVFVILLGLSIL---RLYALGVegNP---ITSRISLTMSIYDIIFNNFNGVFNGY 235
                                   ************************************99...99999998899...************************** PP

               O_anti_polymase 237 lllsaits.l.sssgprvligklilgrevsiTsTlfGpvllDFGllgvliqmlilgllLgilykiikklkdvllalYsill 315
                                   +++sa++s l  ++g+r++i+k++++++vsiT+T++G+v+ D+G+l+++++++ilg++Lg++yk++k+ k+++l++Y+il+
  gi|15668595|ref|NP_247393.1| 236 IHYSAVFSyLgLCNGARTVIAKTLGIYNVSITPTIVGAVIGDYGTLAIIPYFGILGIFLGFFYKLAKDVKGIYLGIYGILF 316
                                   ********5599********************************************************************* PP

               O_anti_polymase 316 aytiigietGildlvvllly 335
                                   ayt+igie Gild++v+l+y
  gi|15668595|ref|NP_247393.1| 317 AYTLIGIESGILDIDVILYY 336
                                   *******************9 PP

>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.2   3.4e-06     0.031      73     162 ..      44     150 ..      32     170 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.4e-06
                          YdjM  73 llflallalvlllllrlfgrsa..................lrlglllllgvlsHlllDlltkyGvpllwPfskkkvrlsll 135
                                   ++f + ++++ +                              +g+ l++  l+ +  Dl++ + vpl+ P+s  +++l++ 
  gi|15668595|ref|NP_247393.1|  44 IFFYISFTAGKR---------LyyligidkenlkinlkkhYNFGIFLMIVGLIAVTSDLIWVKDVPLFNPLS--RKFLNVY 113
                                   333333333333.........34444455557888888777788888999999******************9..9****** PP

                          YdjM 136 fiiidplltll..........srrglvalelvllvly 162
                                   f++ + l++            ++++ +  ++++++l+
  gi|15668595|ref|NP_247393.1| 114 FTTLSHLFLVGwaivvassniDKKKILLYTIIFSILI 150
                                   **88886666477777776653333333444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2499.92
//
Query:       gi|15668596|ref|NP_247394.1|  [L=380]
Description: O-antigen polymerase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-74  251.4  63.6    2.4e-74  250.6  63.6    1.4  1  O_anti_polymase  Putative O-antigen polymerase


Domain annotation for each model (and alignments):
>> O_anti_polymase  Putative O-antigen polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.6  63.6   1.3e-78   2.4e-74       1     335 []      14     363 ..      14     363 .. 0.92

  Alignments for each domain:
  == domain 1  score: 250.6 bits;  conditional E-value: 1.3e-78
               O_anti_polymase   1 dlfspliivlllilfiilsaia......vsslliili..llglisfilgall............................. 44 
                                   dlf+p++iv++++l+i+++a++      ++sl++il   +++++ f+l++++                             
  gi|15668596|ref|NP_247394.1|  14 DLFHPVSIVIIGHLMIFILAFPylddigLYSLFKILGvlSIFIVGFFLPFIFpmqikfnrhilylsflllsflsifgafki 94 
                                   79********************99999988888888877888999999999888889999999999999999888777777 PP

               O_anti_polymase  45 lsklvlsieellvknnkkkleikfnekkvekiglilvliGillfiinllivggiPlfdpslraklntkltalsylflpsia 125
                                    ++l+lsi++ll+     +l +kf   k++ ++ il+ iGi++f++ +li+g+iPlf++++r+++n+++     l+l+s++
  gi|15668596|ref|NP_247394.1|  95 THSLFLSIAYLLFILIIAELFVKFY--KKKIFVDILFSIGIIAFLLIVLIYGAIPLFNYEVRMTINSEP-----LRLISMG 168
                                   5666666666555555445544444..455789************************************.....******* PP

               O_anti_polymase 126 ilvakvarlrnlilfiiglvllallgYrttvlaillsilitlYytkkikikeivllilllvllllgigyl..rsiseqaws 204
                                   +l++  a ++n+++fii++++l+llgY++ vl+++++++i++Y  ++i +k++vll+++l++ +lgi+ +  + +s+q+w+
  gi|15668596|ref|NP_247394.1| 169 ALIY--AGIENKVYFIIAFMILVLLGYKAGVLMLFIAYIIYRY--RNILFKYMVLLAFALLI-FLGIMGKiiLLSSNQNWD 244
                                   ****..89***********************************..9************9999.*****99999******** PP

               O_anti_polymase 205 lnplelllyRadftlsvldkivkglqgvthGklllsaitslsssgprvligklilgrevsiTsTlfGpvllDFGllgvliq 285
                                   lnp+ell+yRa+f+l+vl+kiv+  +++t Gk++l+       ++++++ig+l+++++++iT+TlfG+++lDFG++g+   
  gi|15668596|ref|NP_247394.1| 245 LNPIELLCYRAYFDLYVLSKIVE-SNILTLGKITLT-------PNGEHFIGELLFKYPHNITTTLFGTIYLDFGIFGG--- 314
                                   ***********************.*********998.......9**********************************... PP

               O_anti_polymase 286 mlilgllLgilykiikklkdvllalY.sillaytiigietGildlvvllly 335
                                     ++++lLg+++k+i++ + +l+a+Y s+llay++igi++G+l++  llly
  gi|15668596|ref|NP_247394.1| 315 --LFAMLLGVISKYIYEGDKKLYAIYaSLLLAYCEIGINYGFLVVLSLLLY 363
                                   ..9**************777****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 2569.04
//
Query:       gi|15668597|ref|NP_247395.1|  [L=360]
Description: hypothetical protein MJ_0421 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-81  271.1   0.3    4.5e-81  270.3   0.3    1.4  1  SPOUT_MTase_2    AF2226-like SPOUT RNA Methylase fused to THU
    7.4e-31  107.2   4.4    2.1e-30  105.7   4.4    1.8  1  THUMP            THUMP domain
  ------ inclusion threshold ------
      0.035   14.0   0.0      0.088   12.7   0.0    1.6  2  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
      0.048   13.9   0.6      0.048   13.9   0.6    2.1  2  YnfE             Uncharacterized YnfE-like
      0.063   13.2   0.3        0.3   11.0   0.2    2.3  1  Spt5-NGN         Early transcription elongation factor of RNA
        0.1   12.7   0.0        3.4    7.8   0.0    2.6  2  SpoU_methylase   SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.3   0.3   1.5e-84   4.5e-81       1     172 [.     168     340 ..     168     341 .. 0.99

  Alignments for each domain:
  == domain 1  score: 270.3 bits;  conditional E-value: 1.5e-84
                 SPOUT_MTase_2   1 kvvlvqlpYlgdlkaakelgeriGRavqafevkeliiapkekvdayelaeflrgvreGqesRyeiqkksygrevrkvpvlv 81 
                                   kvv+vq+pYlg++ ++k++ge iGRa+q fevkeliiapkekvdayel+ef++gv+ Gq+sRyeiqk++y+ e++ vpv+v
  gi|15668597|ref|NP_247395.1| 168 KVVIVQMPYLGEKIVCKRFGEAIGRAAQGFEVKELIIAPKEKVDAYELMEFIKGVKIGQHSRYEIQKRAYPFEIKLVPVTV 248
                                   89******************************************************************************* PP

                 SPOUT_MTase_2  82 qdlyqlvr.krrkkellivtdPeGeeisevkeelaealrkakevvvlvGsReGiPkGlfrfadfvvDlaPgvtlateyaia 161
                                   qdlyq+vr krr+++lli+tdP+G+e+s++k++la +lrk++e++v++GsReGiP+Glfrfad++vDlaP++t+ate+ai+
  gi|15668597|ref|NP_247395.1| 249 QDLYQVVRdKRRDNRLLIITDPKGDELSKIKDKLAYDLRKKREIIVFCGSREGIPRGLFRFADYIVDLAPHMTFATEHAIP 329
                                   ********************************************************************************* PP

                 SPOUT_MTase_2 162 aalialvtvle 172
                                   aalial+ v++
  gi|15668597|ref|NP_247395.1| 330 AALIALWGVYS 340
                                   ********996 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   4.4     7e-34   2.1e-30       3     143 ..      19     147 ..      17     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 7e-34
                                   HHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT CS
                         THUMP   3 ieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeek 83 
                                   ++e+    + n+ + ++g+++iv++++       +e +++++ +++ ++rv+ v  ++e+d+++i ++a++i+   +e+e 
  gi|15668597|ref|NP_247395.1|  19 LKEI--VDDFNYIVSPDGYQGIVIVES-------DEDIEDKILQIPEVERVLKVYFETETDFDKIVNLAEKIKDYIKEDE- 89 
                                   5556..566788899999999999997.......7789************************************888777. PP

                                   -EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                         THUMP  84 etFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisid 143
                                    tFaV++k+rgkh +f+s +in ++G+ i+++t+++Vdl+nPd+vv+ve++k+k+y+si 
  gi|15668597|ref|NP_247395.1|  90 -TFAVETKKRGKH-DFSSTDINIVLGAKIKDLTNASVDLNNPDKVVHVEVFKNKTYVSIT 147
                                   .************.********************************************97 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.8   5.5e+03      87     105 ..      46      64 ..       9      98 .. 0.54
   2 ?   12.7   0.0   2.9e-05     0.088      31     155 ..     190     314 ..     188     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.8
                                   SHHHHHHHHHHHHSS--EE CS
               Methyltrn_RNA_4  87 sleealeeiekeegkkplv 105
                                   ++e+ + +i + e    + 
  gi|15668597|ref|NP_247395.1|  46 DIEDKILQIPEVERVLKVY 64 
                                   4444444444333333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.9e-05
                                   HHHHHHHTT-SEEEEE---H.HHHHHHHHHHHHHHTSGGGGT-SSSHHHHTTEEEESSHHHHHHHHHHHHSS--EEEE--S CS
               Methyltrn_RNA_4  31 iaRsartygvkkyyvvtple.aqrelverilehWtegagaeynpdRkealslvkvvesleealeeiekeegkkplvvatsA 110
                                   i+R+a+ ++vk++ +    + +  el+e i      ++ +   ++R+  +++  v  ++++ ++ +++++ ++ l+++t+ 
  gi|15668597|ref|NP_247395.1| 190 IGRAAQGFEVKELIIAPKEKvDAYELMEFIKGVKIGQHSRYEIQKRAYPFEIKLVPVTVQDLYQVVRDKRRDNRLLIITDP 270
                                   89**********988755542556777777666666666666678999999999999************************ PP

                                   S--SS-B-HHHHHHHHHH--S-EEEEE--TT---HHHHTT-SEEB CS
               Methyltrn_RNA_4 111 rkkentvsyeelrelleeeekpvlllfGtgwGlaeevlekadyiL 155
                                   +  e +   ++l   l ++++++++  G   G+ + +++ adyi+
  gi|15668597|ref|NP_247395.1| 271 KGDELSKIKDKLAYDL-RKKREIIVFCGSREGIPRGLFRFADYIV 314
                                   *887777777888888.7888888899**************9997 PP

>> YnfE  Uncharacterized YnfE-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   1.6e-05     0.048      26      60 ..      44      78 ..      16      92 .. 0.84
   2 ?   -3.6   0.1       4.9   1.5e+04      37      56 ..     150     169 ..     150     171 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                          YnfE 26 eeDlekqkeqlelYekqLkqesssdedfDevvdav 60
                                  +eD+e +  q+   e+ Lk  + ++ dfD++v+ +
  gi|15668597|ref|NP_247395.1| 44 DEDIEDKILQIPEVERVLKVYFETETDFDKIVNLA 78
                                  79******************************966 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.9
                          YnfE  37 elYekqLkqesssdedfDev 56 
                                   e+++k+ k++  + e f +v
  gi|15668597|ref|NP_247395.1| 150 EKFKKYTKEKRNARELFKKV 169
                                   67778888888777777766 PP

>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2    0.0001       0.3       3      70 ..       3      60 ..       1      74 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                      Spt5-NGN  3 wavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgv 70
                                  +++k+++g E  v+ +l + + +           ++ pd+ +G ++vE+d+  ++e+ + +ip+v +v
  gi|15668597|ref|NP_247395.1|  3 FIIKTQKGFENIVVNNLKEIVDDF--------NYIVSPDGYQGIVIVESDE--DIEDKILQIPEVERV 60
                                  789999999999999995552222........24888************96..677777777777665 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.6   4.9e+03      63      91 ..      76     103 ..      45     140 .. 0.58
   2 ?    7.8   0.0    0.0011       3.4      54     121 ..     242     315 ..     187     321 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.6
                                   SHHHHHHHHCCCTEEEEEESTT-SEGCCS CS
                SpoU_methylase  63 sleealkelkeegfalvatslkgkslsei 91 
                                   +l+e +k+  +e  +++a+++k++  +++
  gi|15668597|ref|NP_247395.1|  76 NLAEKIKDYIKE-DETFAVETKKRGKHDF 103
                                   444444444333.3444444433333333 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0011
                                   HHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGCCSHHH.......TTEEEEEEBTTTBS-HHHHCTSSEEEE CS
                SpoU_methylase  54 evlelkvvdsleealkelkeegfalvatslkgkslseidlk.......ekvalvfGnEdkGlsnelleladrlvk 121
                                   ++++ ++v++l +++++ ++ +  l+ t++kg++ls+i+ k       ++ ++vf   ++G+++ l + ad++v 
  gi|15668597|ref|NP_247395.1| 242 KLVP-VTVQDLYQVVRDKRRDNRLLIITDPKGDELSKIKDKlaydlrkKREIIVFCGSREGIPRGLFRFADYIVD 315
                                   2333.3568999999999999888899999999999773333455667888888888889999999888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2340.93
//
Query:       gi|15668598|ref|NP_247396.1|  [L=290]
Description: dihydrodipicolinate reductase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-43  146.2   0.1    8.1e-43  145.3   0.1    1.4  1  DapB_C           Dihydrodipicolinate reductase, C-terminus
    2.7e-39  134.1   3.2    4.8e-39  133.3   3.2    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    3.2e-05   24.2   0.6    5.3e-05   23.5   0.6    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00054   20.4   0.3     0.0014   19.1   0.3    1.8  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0013   19.3   0.5     0.0027   18.3   0.5    1.5  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
      0.004   16.7   0.0     0.0076   15.7   0.0    1.6  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0074   15.3   0.6      0.017   14.1   0.5    1.7  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
  ------ inclusion threshold ------
      0.063   13.4   0.5       0.35   11.0   0.1    2.2  2  DUF531           Protein of unknown function (DUF531)
      0.072   12.2   0.1       0.17   11.0   0.1    1.7  1  RmlD_sub_bind    RmlD substrate binding domain


Domain annotation for each model (and alignments):
>> DapB_C  Dihydrodipicolinate reductase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.3   0.1   4.1e-46   8.1e-43       1     121 []     150     283 ..     150     283 .. 0.94

  Alignments for each domain:
  == domain 1  score: 145.3 bits;  conditional E-value: 4.1e-46
                                   HHHHHHHHHHHHCCCSTTT-EEEEEEEESTT--SSS-HHHHHHHHHHH....................-S-ETTCCCEEEE CS
                        DapB_C   1 GvnlllklveeaakllkeaydveiiEkHhnkKaDaPSGTAlalaeaia..egke..............arkkkeigihsvR 65 
                                   Gvn+++k +e +ak l + yd+eiiE+Hh+ K+DaPSGTAl+ ae i+                    +rkk+eigih++R
  gi|15668598|ref|NP_247396.1| 150 GVNIFFKTLEFLAKKLGD-YDIEIIEMHHRYKKDAPSGTALRAAEIIKanR--GiesvfvygrygmtgERKKEEIGIHALR 227
                                   9***************99.*****************************551..2556677777777789************ PP

                                   TTT--CCCCEEEECTTEEEEEEEEEESCHHHHHHHHHHHHHH.HCTSSEESHHHHH CS
                        DapB_C  66 gggvvgehevlfagegevieikhealsreiFaeGallaaewlakkkkglysmedvL 121
                                   gg+vvg+h+v+fag+ge+ie++h+a+sr+ F++G++la++++a+kk+g+y+  dvL
  gi|15668598|ref|NP_247396.1| 228 GGDVVGDHTVIFAGDGERIELTHRASSRQAFVNGVILAIRYIADKKEGIYNTFDVL 283
                                   ****************************************************9997 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.3   3.2   2.4e-42   4.8e-39       1     124 []      18     147 ..      18     147 .. 0.98

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 2.4e-42
                                   EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEB..SSHHHHHHH..-SEEEE-S-H CS
                        DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavt..ddleevlek..advliDFTtp 77 
                                   ikvav+Ga GrmG++++k+++++ed+++v+a++ ++++ +g+d+gel+g+gk+gv+++  d+l++vl++   dvl+DFT  
  gi|15668598|ref|NP_247396.1|  18 IKVAVTGALGRMGSNIIKTITQQEDMKVVCAFEVPNHPKKGEDVGELIGIGKIGVPLStaDELDKVLKEtkPDVLVDFTIA 98 
                                   79******************************************************99999*******9999********* PP

                                   HHHHHHHHHHHHTT-EEEE--SS--HHHHHHHHHHTTT..SEEEE-S-- CS
                        DapB_N  78 eavlenlklalekgvklViGTTGlseeelaeleelakk..igvviapNf 124
                                   +a++en+k+a+++gv+lViGTTG++ee++ae+e++ k+  +++vi++Nf
  gi|15668598|ref|NP_247396.1|  99 HACVENVKIAAKNGVNLVIGTTGFTEEQKAEIEKAIKEnnVAAVISQNF 147
                                   **********************************999999********8 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.6   2.7e-08   5.3e-05       1     126 [.      20     138 ..      20     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.7e-08
                                   EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS..SEEEE-SS CS
               Sacchrp_dh_NADP   1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg..dlvvnlsp 78 
                                   v + Ga G++G+ +++ + +++d+  ++++a    ++ ++  +    + + +i +  +  ++ L+++lke+  d++v+ + 
  gi|15668598|ref|NP_247396.1|  20 VAVTGAlGRMGSNIIKTITQQEDM--KVVCAFEVPNHPKKGEDVGELIGIGKIGVPLSTADE-LDKVLKETkpDVLVDFTI 97 
                                   5678********************..9*9999999998888777799***************.****************** PP

                                   GGGHHHHHHHHHHHT-EEEE..SS-BCGCCSCHCCSHHHHHTHHHHHHCT CS
               Sacchrp_dh_NADP  79 pissldvlkaCietgvhyvd..tsiskeertnyalreavlklkekakeag 126
                                    +   + +k+++++gv+ v   t +          +e+  + +++ ke++
  gi|15668598|ref|NP_247396.1|  98 AHACVENVKIAAKNGVNLVIgtTGF---------TEEQKAEIEKAIKENN 138
                                   *****************99766777.........4444444444444444 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.3     7e-07    0.0014       1      93 [.      19     116 ..      19     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7e-07
                                   EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTT..TTTSBHHHHSGGGTTTECEBEEE.GGGGGC..TT-SEEEE-SCH CS
                Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssr..saGkklaeavkaleegkdlkved.vdeeel..kevdivflalpa 76 
                                   kva+ Ga G +G+++++ + ++ ++++v+++   +  ++G+ + e+ ++ + g  l+  d   ++ l   + d+++  + a
  gi|15668598|ref|NP_247396.1|  19 KVAVTGALGRMGSNIIKTITQQEDMKVVCAFEVPNhpKKGEDVGELIGIGKIGVPLSTADeL-DKVLkeTKPDVLVDFTIA 98 
                                   7******************************9999889999999999988888888888843.333346889999999999 PP

                                   HHHHHHHHHHHHTTS.EE CS
                Semialdhyde_dh  77 gvskelapklaeagv.kv 93 
                                    ++ e ++ +a++gv  v
  gi|15668598|ref|NP_247396.1|  99 HACVENVKIAAKNGVnLV 116
                                   9*******9999999445 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.5   1.4e-06    0.0027       2     112 ..      26     139 ..      25     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.4e-06
                                   -SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TT......HHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTT CS
                 NAD_binding_3   2 lGaiGsavleqlkrqqseielelvavadrd.sllskd......rkallasealtldlddliahldpdvvVEcasseavael 75 
                                   lG  Gs +++ +++q++     ++a+ + + +++ +d      + +   +  + ++ld+++++ +pdv+V+ +   a  e 
  gi|15668598|ref|NP_247396.1|  26 LGRMGSNIIKTITQQEDM--KVVCAFEVPNhPKKGEDvgeligIGKIGVPLSTADELDKVLKETKPDVLVDFTIAHACVEN 104
                                   699999999999999995..44555555554566666778877666666777888999999999***************** PP

                                   HHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS-- CS
                 NAD_binding_3  76 vlkaLkagkdvvtankgaladealyeeLreaaeanga 112
                                   v  a k+g+++v+   g     ++ +e+ +a ++n++
  gi|15668598|ref|NP_247396.1| 105 VKIAAKNGVNLVIGTTGFTE--EQKAEIEKAIKENNV 139
                                   *************9888777..777777777777765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.8e-06    0.0076       2      74 ..      21      98 ..      20     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.8e-06
                                  EEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE--S- CS
                     Epimerase  2 lVtGatGfiGsalvkallekg.yevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihlAav 74
                                   VtGa G +Gs+++k + ++   +v++    ++  +++++  +        + + l  +++l++++ke++pd+ + +   
  gi|15668598|ref|NP_247396.1| 21 AVTGALGRMGSNIIKTITQQEdMKVVCAFEVPNHPKKGED--VgeligiGKIGVPLSTADELDKVLKETKPDVLVDFTIA 98
                                  7****************99997776665555444444443..3447999889999*******************998442 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.5   8.7e-06     0.017       1      68 [.      21      88 ..      21     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.7e-06
                     3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvd 68
                                  +vtG+ G +G++++k++ + e++k v ++ + ++p++ e++ ++  +  i + +  +d+l+++l++ +
  gi|15668598|ref|NP_247396.1| 21 AVTGALGRMGSNIIKTITQQEDMKVVCAFEVPNHPKKGEDVGELIGIGKIGVPLSTADELDKVLKETK 88
                                  69***************************************999888899999999999999999865 PP

>> DUF531  Protein of unknown function (DUF531)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00017      0.35      85     142 ..      23      81 ..       6     109 .. 0.76
   2 ?   -0.1   0.0      0.44   8.7e+02      99     122 ..     126     149 ..     104     176 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                        DUF531  85 kgfpaqfGevva.ttskpdekkaitpeevaeeilrkksvllliGlGrkGlPkellklak 142
                                    g   ++G+ ++ t ++ ++ k + + ev ++ ++++ v  liG+G+ G+P +  +  +
  gi|15668598|ref|NP_247396.1|  23 TGALGRMGSNIIkTITQQEDMKVVCAFEVPNHPKKGEDVGELIGIGKIGVPLSTADELD 81 
                                   555667887665155677788899999************************87766555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.44
                        DUF531  99 skpdekkaitpeevaeeilrkksv 122
                                   +k++ +kai++++va  i ++ ++
  gi|15668598|ref|NP_247396.1| 126 QKAEIEKAIKENNVAAVISQNFAI 149
                                   456667778888887776665444 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   8.5e-05      0.17       2      60 ..      19      97 ..      18     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.5e-05
                                  EEEEESTTSHHHHHHHHHCTT.TSEEEEEE.-TT..................T--TTSHHHHHHHHHHH--SEEEE--- CS
                 RmlD_sub_bind  2 kilvtGanGqlGseLakqlae.eglevlal.tre..................eldltdaeavaellkeakpdvvvnaAA 60
                                  k+ vtGa G +Gs+++k +++ e+++v+   + +                   + l+ a++++++lke+kpdv+v+   
  gi|15668598|ref|NP_247396.1| 19 KVAVTGALGRMGSNIIKTITQqEDMKVVCAfEVPnhpkkgedvgeligigkiGVPLSTADELDKVLKETKPDVLVDFTI 97
                                  789************9998763666665441555999*************999999*****************998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2005.07
//
Query:       gi|15668599|ref|NP_247397.1|  [L=59]
Description: hypothetical protein MJ_0423 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-11   43.7   1.0      3e-11   43.7   1.0    1.0  1  ATPase_2     ATPase domain predominantly from Archaea
    6.1e-05   23.5   0.0    6.5e-05   23.4   0.0    1.0  1  AAA_16       AAA ATPase domain
    6.8e-05   22.9   0.2    8.8e-05   22.5   0.2    1.2  1  AAA_14       AAA domain
    0.00017   21.0   0.1     0.0002   20.8   0.1    1.0  1  TniB         Bacterial TniB protein
    0.00061   20.1   0.0    0.00065   20.0   0.0    1.2  1  AAA_22       AAA domain
     0.0047   17.1   0.2     0.0082   16.3   0.1    1.4  2  Roc          Ras of Complex, Roc, domain of DAPkinase
  ------ inclusion threshold ------
      0.015   14.5   0.0      0.015   14.5   0.0    1.0  1  DUF815       Protein of unknown function (DUF815)
      0.022   14.7   0.0      0.025   14.6   0.0    1.0  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
      0.031   13.5   0.0      0.032   13.4   0.0    1.1  1  DAP3         Mitochondrial ribosomal death-associated protein
      0.089   12.7   0.0      0.098   12.6   0.0    1.0  1  RsgA_GTPase  RsgA GTPase
      0.099   12.4   0.0       0.12   12.0   0.0    1.2  1  AAA_24       AAA domain


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   1.0   1.8e-14     3e-11       1      48 [.       7      54 ..       7      59 .] 0.92

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.8e-14
                      ATPase_2  1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkd 48
                                  F++R++el+ le+  ++++++ + +YG++++GKt L+k+++en++ k 
  gi|15668599|ref|NP_247397.1|  7 FVNRKEELEFLERKWNENKANLIILYGRRRVGKTMLIKKFLENKKIKR 54
                                  9******************************************96544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0     4e-08   6.5e-05       2      46 ..       7      48 ..       6      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4e-08
                        AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellr 46
                                  +v R+eele L++ ++   ++  +l++l+G + vGK+ l++++l+
  gi|15668599|ref|NP_247397.1|  7 FVNRKEELEFLERKWN---ENKANLIILYGRRRVGKTMLIKKFLE 48
                                  7889999988888665...66679*******************97 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.2   5.4e-08   8.8e-05       3      33 ..      27      57 ..      25      59 .] 0.87

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.4e-08
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesi 33
                                  +++++ G RrvGKT+l+k++++++ +k+ si
  gi|15668599|ref|NP_247397.1| 27 NLIILYGRRRVGKTMLIKKFLENKKIKRASI 57
                                  6799*****************9998887776 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.2e-07    0.0002      21      61 ..      12      52 ..       8      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.2e-07
                          TniB 21 erLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhpp 61
                                  e+Le L ++ ++++ + ++l+G+  +GKtm+++kF ++++ 
  gi|15668599|ref|NP_247397.1| 12 EELEFLERKWNENKANLIILYGRRRVGKTMLIKKFLENKKI 52
                                  678999999999999999******************99875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     4e-07   0.00065       4      31 ..      25      52 ..      10      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4e-07
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleqlde 31
                                  +a++++++G   +GKT+l++++le++++
  gi|15668599|ref|NP_247397.1| 25 KANLIILYGRRRVGKTMLIKKFLENKKI 52
                                  7899*******************99864 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.3   5.3e+03      93      95 ..      15      17 ..       3      27 .. 0.41
   2 !   16.3   0.1   5.1e-06    0.0082       2      24 ..      29      51 ..      28      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.3
                                  HCH CS
                           Roc 93 enl 95
                                  e l
  gi|15668599|ref|NP_247397.1| 15 EFL 17
                                  222 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 5.1e-06
                                  EEEESSTTSSHHHHHHCHCT-CC CS
                           Roc  2 vvlvGdsgvGKtsllkrfvedkf 24
                                  ++l G  +vGKt l+k+f+e+k 
  gi|15668599|ref|NP_247397.1| 29 IILYGRRRVGKTMLIKKFLENKK 51
                                  7899***************9986 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   9.3e-06     0.015      45      77 ..      18      50 ..       6      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.3e-06
                        DUF815 45 eqfleglpannvLLwGarGtGKSslvkallney 77
                                  e+  + ++an ++L+G r +GK  l+k  l++ 
  gi|15668599|ref|NP_247397.1| 18 ERKWNENKANLIILYGRRRVGKTMLIKKFLENK 50
                                  45567899*******************998764 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.5e-05     0.025       4      46 ..      11      53 ..       8      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                                  HHHHHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                          TsaE  4 eeetealgkklakalgdvilLeGdLGaGKTtlvrglakalgve 46
                                  +ee+e l +k  ++ +++i+L+G   +GKT+l+++++++ +++
  gi|15668599|ref|NP_247397.1| 11 KEELEFLERKWNENKANLIILYGRRRVGKTMLIKKFLENKKIK 53
                                  667777777777766889*******************998776 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     2e-05     0.032      12      41 ..      15      44 ..       7      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                                  HHHTTS-SSS---EEEEE-SSSSSTTTTHH CS
                          DAP3 12 kklkkadkkkkvkrlvltGekgsGKSvlLl 41
                                  + l+++ +++k++ ++l+G++ +GK++l+ 
  gi|15668599|ref|NP_247397.1| 15 EFLERKWNENKANLIILYGRRRVGKTMLIK 44
                                  5678888999*****************975 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     6e-05     0.098      81     128 ..       7      55 ..       2      58 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6e-05
                                   E--TTTHTTHHHHHHHCTT...SEEEEECSTTSSHHHHHHHHCTT-----S CS
                   RsgA_GTPase  81 lvsaktkegleelkellkd...ktsvlvGqSGvGKStLinallpelelktg 128
                                   +v  ++ke+le l++++++   ++++l G   vGK+ Li+++l+++++k +
  gi|15668599|ref|NP_247397.1|   7 FV--NRKEELEFLERKWNEnkaNLIILYGRRRVGKTMLIKKFLENKKIKRA 55 
                                   33..4456777777666543347899****************999887755 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.6e-05      0.12       4      24 ..      28      48 ..      25      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-05
                        AAA_24  4 kiliyGpsgiGKTtlakelgp 24
                                   i++yG   +GKT+l+k++ +
  gi|15668599|ref|NP_247397.1| 28 LIILYGRRRVGKTMLIKKFLE 48
                                  589***************933 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 416.42
//
Query:       gi|15668600|ref|NP_247398.1|  [L=103]
Description: hypothetical protein MJ_0424 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-06   27.3   0.1    3.6e-06   27.1   0.1    1.1  1  ATPase_2  ATPase domain predominantly from Archaea
     0.0024   18.2   0.1     0.0032   17.8   0.1    1.3  1  AAA_22    AAA domain
     0.0056   16.7   0.1     0.0063   16.5   0.1    1.1  1  AAA_14    AAA domain
  ------ inclusion threshold ------
        0.1   11.6   0.1       0.12   11.3   0.1    1.1  1  DUF684    Protein of unknown function (DUF684)


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1     8e-10   3.6e-06      88     166 ..      20      92 ..       3     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 8e-10
                      ATPase_2  88 kaeleeilkeksklvfkaielllekikkkgkk..iiiiiDelqklidlglngaellvkeLlnliesltkekhlcvviclsS 166
                                   + +++    e  k+++  + +l++ ++++ k   ++i +De+q+l   +ln  + +++ ++++++  +++++++++ic+sS
  gi|15668600|ref|NP_247398.1|  20 SLTGK----EYFKNLDVGLVDLFRYLRDEIKDekVVIALDEFQYLM--QLN--RGVLSIFQKIWDGILADTKVFLIICGSS 92 
                                   22222....3335555555566666666665555************..999..99*************************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   7.1e-07    0.0032      74     130 ..      33      89 ..       3      95 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.1e-07
                        AAA_22  74 sseellealeqalraravielliiDEaqhlr..seealeeLrsllnlsrkgvqliLvGt 130
                                    + +l+++l++ +++ +v  ++ +DE+q+l+  +  +l+ + ++++    +++++L+++
  gi|15668600|ref|NP_247398.1|  33 GLVDLFRYLRDEIKDEKV--VIALDEFQYLMqlNRGVLSIFQKIWDGILADTKVFLIIC 89 
                                   567899999******999..*********986669999999999998445555555544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.4e-06    0.0063      30     101 ..      13      92 ..       1      99 [. 0.66

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-06
                        AAA_14  30 kesilyinldderdkkladpe..kllelileklkeekktylflDEiqevpewekalkslvd.......egknldvivtGSn 101
                                   + + ++ +l  +++ k+ d    +l +++++++k+ +k ++ lDE q++ ++ + + s+++        ++++ +i+ GS+
  gi|15668600|ref|NP_247398.1|  13 ELKRVFSSLTGKEYFKNLDVGlvDLFRYLRDEIKD-EKVVIALDEFQYLMQLNRGVLSIFQkiwdgilADTKVFLIICGSS 92 
                                   44555555555555554433255888999999888.9************77777766666644444443347888888887 PP

>> DUF684  Protein of unknown function (DUF684)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   2.7e-05      0.12      14      56 ..       4      49 ..       2      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.7e-05
                        DUF684 14 sdkmsekfddLk...afiveqeFykniasaasvLmkymqdtlespg 56
                                  +d+m+e++++Lk   ++ + +e++kn+ + +  L++y++d ++ ++
  gi|15668600|ref|NP_247398.1|  4 NDSMNENLNELKrvfSSLTGKEYFKNLDVGLVDLFRYLRDEIKDEK 49
                                  699*********544467889*******************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.33s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 646.91
//
Query:       gi|15668601|ref|NP_247399.1|  [L=140]
Description: hypothetical protein MJ_0425 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-24   83.8   2.5    1.2e-23   83.4   2.5    1.2  1  DUF234    Archaea bacterial proteins of unknown function
    1.2e-06   28.7   0.5    1.6e-06   28.3   0.5    1.2  1  DUF4143   Domain of unknown function (DUF4143)


Domain annotation for each model (and alignments):
>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   2.5   1.4e-27   1.2e-23       3      99 .]       3      94 ..       1      94 [. 0.94

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 1.4e-27
                        DUF234  3 rfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnkagklpfrftkvGrwWkkeeeiDivaldeeekkalfg 85
                                  ++vypn++++e+g+++ev++ki ++lney+gk+FE+lv e+l+     + ++f  ++v +wW+k+eeiD++a+++++  ++++
  gi|15668601|ref|NP_247399.1|  3 QVVYPNMADLEIGNVKEVYNKILASLNEYYGKMFENLVFEMLK----LKIIDFGQKSVAKWWHKGEEIDVLAYNNNK--MIAF 79
                                  78****************************************9....67899**********************999..9*** PP

                        DUF234 86 EvKwkn.sekeakki 99
                                  EvKwk+ s keak+i
  gi|15668601|ref|NP_247399.1| 80 EVKWKDlSFKEAKGI 94
                                  ******988888765 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.5   1.8e-10   1.6e-06      64     121 ..      27      83 ..       9      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.8e-10
                                   xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  64 edsenkGallEnlVaqeLlky..sekegaklyyyrdkngaEvDfvielkggkivpiEvKs 121
                                   + +e++G+++EnlV+++L  +     ++    +++  +g E+D++   +++k++++EvK+
  gi|15668601|ref|NP_247399.1|  27 SLNEYYGKMFENLVFEMLKLKiiDFGQKSVAKWWH--KGEEIDVLAY-NNNKMIAFEVKW 83 
                                   44599*************99986333233444444..49*******8.699********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 951.70
//
Query:       gi|15668602|ref|NP_247400.1|  [L=180]
Description: hypothetical protein MJ_0426 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   13.2   0.2      0.094   12.5   0.2    1.4  1  RICTOR_M  Rapamycin-insensitive companion of mTOR, middle dom


Domain annotation for each model (and alignments):
>> RICTOR_M  Rapamycin-insensitive companion of mTOR, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   5.2e-06     0.094      37      92 ..       7      64 ..       3      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-06
                      RICTOR_M 37 lklLekwkiftllyklvelks.rdd.llklilssldysvdghiRiilskaLtnsseki 92
                                  +k+L++++i++ + k+++ +   d  + +li + l+   +++i +il+++L+n + ki
  gi|15668602|ref|NP_247400.1|  7 IKILKQFGIYSEYLKILDVELdGDRyITILIPTTLNWIEEEEIEEILEEMLKNVRVKI 64
                                  79**************7777633333777777889****************9876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1196  (0.0667076); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1225.91
//
Query:       gi|15668603|ref|NP_247401.1|  [L=160]
Description: hypothetical protein MJ_0427 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   18.5   3.1     0.0017   18.3   2.7    1.3  1  WbqC      WbqC-like protein family


Domain annotation for each model (and alignments):
>> WbqC  WbqC-like protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   2.7   9.7e-08    0.0017      31     126 ..      59     154 ..      40     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.7e-08
                          WbqC  31 rgwinRnriltpngeqw.ltvPvekkasqqklineveidddekwrkkhlksleqaYkkapffeevlpllesvyeaeeenla 110
                                   ++w+n+ r ++ +++   + + ++  ++ +  i   +++ + k  ++h++ ++++Y k +ff+    l +++y+ ++++l+
  gi|15668603|ref|NP_247401.1|  59 EDWHNKDRYANFSKKIRnFLMDLKLYRHASDYILSPRLE-HGKHYEEHWEEFKESYLKLKFFHYLHILRQELYSYRHNQLI 138
                                   578888888876666666777776666666668888887.56889************************************ PP

                          WbqC 111 elniallealakyLgi 126
                                    ++i+ le + k+L++
  gi|15668603|ref|NP_247401.1| 139 AIIIEKLEIIEKLLKL 154
                                   *************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1097.10
//
Query:       gi|15668604|ref|NP_247402.1|  [L=427]
Description: UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-59  201.0   0.9    1.2e-59  201.0   0.9    1.7  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    2.2e-27   95.1   0.3    1.3e-26   92.6   0.0    2.3  2  UDPG_MGDP_dh     UDP-glucose/GDP-mannose dehydrogenase family
    9.7e-25   87.0   2.7    1.7e-24   86.2   0.3    2.6  3  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase family
    2.5e-09   37.5   0.3    5.9e-07   29.8   0.0    3.3  3  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    4.5e-07   29.4   0.5    0.00015   21.2   0.1    2.4  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    6.6e-06   25.8   0.3    6.1e-05   22.7   0.0    2.6  3  ApbA             Ketopantoate reductase PanE/ApbA
     0.0001   22.5   4.5     0.0024   18.1   0.0    3.8  4  TrkA_N           TrkA-N domain
    0.00019   21.3   0.2    0.00065   19.5   0.0    2.0  2  Methyltransf_31  Methyltransferase domain
    0.00028   20.8   0.2      0.001   19.0   0.0    2.0  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00098   18.7   0.4        1.1    8.8   0.0    3.5  3  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.001   18.4   0.0     0.0024   17.2   0.0    1.6  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0062   16.4   0.1      0.025   14.5   0.1    2.1  1  UPF0146          Uncharacterised protein family (UPF0146)
  ------ inclusion threshold ------
      0.012   16.1   2.7        1.3    9.7   0.1    3.8  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.014   15.1   0.1       0.25   11.0   0.0    2.3  2  Bombinin         Bombinin
      0.015   15.3   0.0       0.06   13.3   0.0    2.0  2  ADH_zinc_N       Zinc-binding dehydrogenase
      0.031   14.3   0.1        2.5    8.1   0.0    3.1  3  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.031   14.1   0.0      0.094   12.6   0.0    1.8  2  Methyltransf_23  Methyltransferase domain
      0.045   14.0   0.0       0.18   12.1   0.0    2.2  1  OKR_DC_1_N       Orn/Lys/Arg decarboxylase, N-terminal domain
      0.051   12.7   0.2       0.13   11.4   0.1    1.7  2  ALAD             Delta-aminolevulinic acid dehydratase
       0.75    8.9   6.1         14    4.8   0.1    3.5  4  CofC             Guanylyl transferase CofC like


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.0   0.9   1.3e-62   1.2e-59       2     186 ..      12     187 ..      11     188 .. 0.95
   2 ?   -3.7   0.0       8.2   7.3e+03      70      86 ..     360     376 ..     357     398 .. 0.54

  Alignments for each domain:
  == domain 1  score: 201.0 bits;  conditional E-value: 1.3e-62
                                   EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvifi 82 
                                   +i+viGlGY+Gl+ta +la +g++vigvDi+e++v+++++ +++ +e++L++lvk a+     s++++v++++e+adv++i
  gi|15668604|ref|NP_247402.1|  12 RICVIGLGYIGLPTASMLAIQGFDVIGVDINEKRVKEIKELSFKTTEKDLMTLVKGAI----NSGNLKVQTKPEKADVFII 88 
                                   9*********************************************************....6888899999999****** PP

                                   -----B-T..TTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE------TTSH CS
                UDPG_MGDP_dh_N  83 aVgTPskk..kgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvsnPEflregsa 161
                                   +V+TP+ +   +k++Dl+y+++a++si+++l++g++++++ST+p+gt+++++kk+++      +++++v+++PE++++gs+
  gi|15668604|ref|NP_247402.1|  89 CVPTPCIEcdGEKKCDLTYLNKAIESIKPYLENGNLIIIESTIPPGTTDDIYKKLSK------DKKIYVAHCPERVLPGSI 163
                                   *******998899************************************88877766......3579************** PP

                                   HHHHHS-S-EEEEESSCHHHHHHHH CS
                UDPG_MGDP_dh_N 162 vkdllnpdrvviGveekkaeaalee 186
                                   +k+l+++drv++Gv+ek+ae +++e
  gi|15668604|ref|NP_247402.1| 164 LKELVENDRVIGGVDEKSAE-MAKE 187
                                   ******************99.7666 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8.2
                                   HHHHHHC-SEEEE---- CS
                UDPG_MGDP_dh_N  70 vekaveeadvifiaVgT 86 
                                   +++ave ad+i+i    
  gi|15668604|ref|NP_247402.1| 360 LDEAVEGADIIVILAEH 376
                                   56677777777775543 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.7   1.5e+03       1      20 [.     180     199 ..     180     202 .. 0.86
   2 !   92.6   0.0   1.5e-29   1.3e-26       1      93 [.     203     289 ..     203     290 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.7
                  UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsf 20 
                                   ++AE++K +  +f + kI +
  gi|15668604|ref|NP_247402.1| 180 KSAEMAKEIYETFVTGKIYL 199
                                   58********9999999866 PP

  == domain 2  score: 92.6 bits;  conditional E-value: 1.5e-29
                  UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeelgle 81 
                                   +tAE++Kl++N++++++I+++Ne+a+++e++gi+v+e ie ++++pr   ++lkpg+GvGG+c+  D++++v+++++    
  gi|15668604|ref|NP_247402.1| 203 KTAEMVKLMENTYRDVNIALANEFAKIAEEIGINVWEAIELANKHPR--VNILKPGPGVGGHCISIDPWFIVEKSKN---- 277
                                   59*********************************************..5************************988.... PP

                  UDPG_MGDP_dh  82 aelleavrevNe 93 
                                   a+l++++re N+
  gi|15668604|ref|NP_247402.1| 278 AKLIRTARELND 289
                                   699999999997 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.4   3.9e+03      61      77 ..      77      93 ..      27     104 .. 0.63
   2 ?   -1.4   0.1       3.4     3e+03      22      67 ..     163     218 ..     162     231 .. 0.65
   3 !   86.2   0.3   1.9e-27   1.7e-24       1     104 [.     311     407 ..     311     408 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.4
                                  HHHHTT-SEEEE-S--G CS
                UDPG_MGDP_dh_C 61 eealkgadaiviltehd 77
                                  ++  ++ad+ +i+++ +
  gi|15668604|ref|NP_247402.1| 77 QTKPEKADVFIICVPTP 93
                                  45557778888877765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.4
                                   HHHHHHHCTSEEEEE-SSTHHCCCCHHGG..........BTCCEEES-CHHHHTT- CS
                UDPG_MGDP_dh_C  22 iieeLleegaevkiyDPkvkeeaveaele..........ekgvevvdsleealkga 67 
                                   i++eL e++  +  +D k  e a+e + +          +k++e+v+ +e++ +++
  gi|15668604|ref|NP_247402.1| 163 ILKELVENDRVIGGVDEKSAEMAKEIYETfvtgkiyltdAKTAEMVKLMENTYRDV 218
                                   67778888888888888887777777655666666666645555555445555554 PP

  == domain 3  score: 86.2 bits;  conditional E-value: 1.9e-27
                                   EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGG CS
                UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefke 81 
                                   ai+G+++K ++dD+ReSpa +++ +L +eg evk yD ++++              ++sl+ea++gad+ivil ehde+k+
  gi|15668604|ref|NP_247402.1| 311 AIFGVTYKGNVDDTRESPAEKVVSKLIDEGFEVKCYDKYARDFIYP----------LNSLDEAVEGADIIVILAEHDEYKN 381
                                   89***************************************97765..........4799********************* PP

                                   S...-HHHHHHCCSS-EEEESSS-CC CS
                UDPG_MGDP_dh_C  82 l...dlaklkelmkpavvfDgrnvld 104
                                   +   d++++++++k+++++D++n+l+
  gi|15668604|ref|NP_247402.1| 382 FdkeDIKNIASKVKNKIILDTKNILN 407
                                   9555555566666***********97 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   6.5e-10   5.9e-07       1     108 [.      12     147 ..      12     155 .. 0.79
   2 ?   -3.1   0.0       8.5   7.6e+03      24      44 ..     196     221 ..     181     237 .. 0.52
   3 ?    3.6   0.0     0.074        66      16      71 ..     334     381 ..     328     410 .. 0.61

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 6.5e-10
                                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-S.SHHHHHHHC...............SEEEE-SSS CS
                 NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaae.sieelvasl...............dvvitmvka 65 
                                   +i +iGlG +G + a+ l+ +g++v++++ ++++v+e+ +  +k++e ++  lv+++               dv i++v+ 
  gi|15668604|ref|NP_247402.1|  12 RICVIGLGYIGLPTASMLAIQGFDVIGVDINEKRVKEIKELSFKTTEkDLMTLVKGAinsgnlkvqtkpekaDVFIICVPT 92 
                                   589************************************999544431455666666777777777788888*******97 PP

                                   H.......HHHHHHHHS.....HCCC--TT-EEEE-S---HHHHHHHHHHHHHTT CS
                 NAD_binding_2  66 g.......kavdevieg.....llealkkgdilidgstsspedtrelakelkekg 108
                                           k+ d ++ +     ++++l++g+++i  st+ p +t +++k+l++ +
  gi|15668604|ref|NP_247402.1|  93 PciecdgeKKCDLTYLNkaiesIKPYLENGNLIIIESTIPPGTTDDIYKKLSKDK 147
                                   5222222245555555577777****************************98865 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.5
                                   EEEEE-SSHHHHHHHHHTT.....EE CS
                 NAD_binding_2  24 kvavynrtkekveelvaeg.....ak 44 
                                   k+++ + +++++ +l+++      + 
  gi|15668604|ref|NP_247402.1| 196 KIYLTDAKTAEMVKLMENTyrdvnIA 221
                                   45555556666666665554444333 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.074
                                   HHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHH CS
                 NAD_binding_2  16 lnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavde 71 
                                   ++l+++g++v +y+       + + + + +++s+ e+v+++d+++++ ++++  ++
  gi|15668604|ref|NP_247402.1| 334 SKLIDEGFEVKCYD-------KYARDFIYPLNSLDEAVEGADIIVILAEHDE-YKN 381
                                   55566666666666.......3344557999***********9987665543.333 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   1.7e-07   0.00015      36      85 ..      10      59 ..       2      68 .. 0.86
   2 !    6.1   0.0    0.0071       6.4      52     106 ..     333     379 ..     329     399 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.7e-07
                                  TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSH CS
                  2-Hacid_dh_C 36 gktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsl 85
                                  gk++++iGlG IG  +a +l+  g++vi++d ++k+ +e +el ++ ++ 
  gi|15668604|ref|NP_247402.1| 10 GKRICVIGLGYIGLPTASMLAIQGFDVIGVDINEKRVKEIKELSFKTTEK 59
                                  89*********************************999888888866543 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0071
                                   HHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTT CS
                  2-Hacid_dh_C  52 akrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetr 106
                                     +l   g++v +yd++ +      +  + l sl+e+++ +Di+++ +    + +
  gi|15668604|ref|NP_247402.1| 333 VSKLIDEGFEVKCYDKYAR------DFIYPLNSLDEAVEGADIIVILAEH--DEY 379
                                   5555666889999999966......4566789*************99874..334 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   6.8e-08   6.1e-05       1      78 [.      13      92 ..      13      96 .. 0.83
   2 ?   -1.9   0.0       2.5   2.3e+03      82     100 ..     109     127 ..     106     131 .. 0.82
   3 ?   -1.4   0.0       1.8   1.6e+03      20      58 ..     365     405 ..     359     417 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.8e-08
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCH...SCCCCS-ESEEEE-SSG CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsae...ekselepidlvivtvKa 78
                                  i+++G+G iG   a +La +g dv+ ++ ++ r++++k+  ++ t+++     +++ a+++     + + e++d++i++v++
  gi|15668604|ref|NP_247402.1| 13 ICVIGLGYIGLPTASMLAIQGFDVIGVDINEkRVKEIKELSFKTTEKD--LMTLVKGAINSGnlkVQTKPEKADVFIICVPT 92
                                  89***************99********************999999999..33333333333344555679**********86 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                                   HHHHHHHGGGECTCEEEEE CS
                          ApbA  82 eealeeikplldpntvvll 100
                                    +a+e+ikp+l++   +++
  gi|15668604|ref|NP_247402.1| 109 NKAIESIKPYLENGNLIII 127
                                   5799********9976664 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.8
                                   HTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEECEEE CS
                          ApbA  20 agadvtlilrsr.rlealkknGlrltseg.geeilrppeal 58 
                                    gad+++il +  +++++ k++++   ++ +++i+++++++
  gi|15668604|ref|NP_247402.1| 365 EGADIIVILAEHdEYKNFDKEDIKNIASKvKNKIILDTKNI 405
                                   57887777777778999888887644444477777777766 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.7e-06    0.0024       1      71 [.      13      91 ..      13      97 .. 0.78
   2 ?   -0.2   0.1       1.3   1.2e+03      34      57 ..     185     210 ..     161     238 .. 0.47
   3 ?   -2.2   0.0       5.5     5e+03      75      90 ..     276     291 ..     271     307 .. 0.65
   4 ?    3.3   0.1       0.1        92      32     109 ..     331     415 ..     327     421 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.7e-06
                                  EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSE........EEES-TTSHHHHHHTTGGGESEEEE-SS CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreegle........vvvgdatdeevLeeagiekadaviaatg 71
                                  i +iGlG +G   a  L  +g dv+++d +e+rv+e++e  ++         v+g   + ++  + + ekad++i++++
  gi|15668604|ref|NP_247402.1| 13 ICVIGLGYIGLPTASMLAIQGFDVIGVDINEKRVKEIKELSFKttekdlmtLVKGAINSGNLKVQTKPEKADVFIICVP 91
                                  68***************997768*************9877755334444446777777777777777888887777765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.3
                                   HHHHHHTTSE..EEES-TTSHHHHHH CS
                        TrkA_N  34 veelreegle..vvvgdatdeevLee 57 
                                   ++e+ e +++  ++  da   e+++ 
  gi|15668604|ref|NP_247402.1| 185 AKEIYETFVTgkIYLTDAKTAEMVKL 210
                                   44444444333344455544444443 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.5
                                   HHHHHHHHHHHHTSSS CS
                        TrkA_N  75 anilavllakelnpkk 90 
                                   +n+ ++ +a+eln+  
  gi|15668604|ref|NP_247402.1| 276 KNAKLIRTARELNDSM 291
                                   6777777777777763 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.1
                                   HHHHHHHHTTSEEEES-TTSHHHH.....HHTTGGGESEEEE-SSSHHHHHHHHHHHHHHTSS..SEEEEEESSGGGHHHH CS
                        TrkA_N  32 erveelreeglevvvgdatdeevL.....eeagiekadaviaatgddeanilavllakelnpk..kkiiaraqdpehaell 105
                                   ++v +l +eg+ev + d   ++++      +  +e ad++++++++de + +  + +k++ +k   kii  +++  + el 
  gi|15668604|ref|NP_247402.1| 331 KVVSKLIDEGFEVKCYDKYARDFIyplnsLDEAVEGADIIVILAEHDEYKNFDKEDIKNIASKvkNKIILDTKNILNRELW 411
                                   566666667766666666666664222223456899999999999998876666666666655555566666666666666 PP

                                   HHHT CS
                        TrkA_N 106 kklg 109
                                   +k g
  gi|15668604|ref|NP_247402.1| 412 EKEG 415
                                   6666 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   7.2e-07   0.00065      14     133 ..      18     156 ..      17     196 .. 0.74
   2 ?   -3.5   0.0       8.9     8e+03      43      67 ..     366     391 ..     361     400 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.2e-07
               Methyltransf_31  14 tGeltfelae.elgpkaevvGiDiseeaielAre.naqklgldnveFeqgdiee.lekl.ledekfDl.ilsnevl..... 84 
                                    G++++  a+ +++++ +v+G+Di+e+ ++  +e   +  + d +++ +g i++   k   ++ek D+ i++         
  gi|15668604|ref|NP_247402.1|  18 LGYIGLPTASmLAIQGFDVIGVDINEKRVKEIKElSFKTTEKDLMTLVKGAINSgNLKVqTKPEKADVfIICV--Ptpcie 96 
                                   588888888888888999****************54455566689*********755555666*****64444..233566 PP

               Methyltransf_31  85 ......naladpdkileeiervlkpggilliedpr...llaelpakveeeskay..evve 133
                                         ++l+ ++k++e+i+ +l++g  ++ie+     + ++  +k++++ k y   ++e
  gi|15668604|ref|NP_247402.1|  97 cdgekkCDLTYLNKAIESIKPYLENGNLIIIESTIppgTTDDIYKKLSKDKKIYvaHCPE 156
                                   666666******************888888777667777777778888888877664443 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.9
               Methyltransf_31  43 lAre...naqklgldnveFeqgdieele 67 
                                    A      a++ +++  +F ++di ++ 
  gi|15668604|ref|NP_247402.1| 366 GADIiviLAEHDEYK--NFDKEDIKNIA 391
                                   555544456777777..57777777744 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.1e-06     0.001       2      47 ..      13      58 ..      12      84 .. 0.85
   2 ?   -2.8   0.0       5.7   5.1e+03      70      90 ..     161     181 ..     137     220 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                                  EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHH CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksle 47
                                  + viG G +G   a+++a +g++V  vdi+e+++++ +e   k++e
  gi|15668604|ref|NP_247402.1| 13 ICVIGLGYIGLPTASMLAIQGFDVIGVDINEKRVKEIKELSFKTTE 58
                                  78********************************998886665444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.7
                                   ES-HHHHHC-SEEEE-S-SSH CS
                       3HCDH_N  70 ttdleeavdadlviEavvEnl 90 
                                    + l+e+v+ d vi  v E+ 
  gi|15668604|ref|NP_247402.1| 161 GSILKELVENDRVIGGVDEKS 181
                                   445555555555555555542 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0012       1.1       4      53 ..      10      58 ..       9      92 .. 0.89
   2 ?    0.0   0.0      0.62   5.5e+02      27      69 ..     215     255 ..     203     257 .. 0.80
   3 ?    5.4   0.0     0.014        13      44      87 ..     350     393 ..     307     421 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0012
                                  TS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEE CS
                          IlvN  4 gkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevlt 53
                                  gk+i+viG G  G   a  l  +g+dv +g+  ++k vk+ ke +f++++
  gi|15668604|ref|NP_247402.1| 10 GKRICVIGLGYIGLPTASMLAIQGFDV-IGVDINEKRVKEIKELSFKTTE 58
                                  79************************8.5888888899999999988765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.62
                                   T--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S- CS
                          IlvN  27 gldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliP 69 
                                     dv ++l ++   +k A+e g++v ++ e+++k   v il P
  gi|15668604|ref|NP_247402.1| 215 YRDVNIALANEF--AKIAEEIGINVWEAIELANKHPRVNILKP 255
                                   457888888776..8899************9999999999887 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.014
                                   HHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTGGG--T CS
                          IlvN  44 AkeegfevltvaeavkkadvvmiliPDelqkevyeeeiepnlke 87 
                                   A++  +   +++eav+ ad+++il+     k+  +e+i++  ++
  gi|15668604|ref|NP_247402.1| 350 ARDFIYPLNSLDEAVEGADIIVILAEHDEYKNFDKEDIKNIASK 393
                                   444555667899************99888888888888765544 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.7e-06    0.0024      30     100 ..      12      91 ..       3      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.7e-06
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE.........HCHHHHHHHHHHHH-SEEEE--- CS
                   AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev.........lksqeellaeavkeadvvigtvl 100
                                   ++ viG G  Gl  +++ +  g +V  +D++++r +++++l  k+ e          ++s + +++ + ++adv i +v 
  gi|15668604|ref|NP_247402.1|  12 RICVIGLGYIGLPTASMLAIQGFDVIGVDINEKRVKEIKELSFKTTEKdlmtlvkgaINSGNLKVQTKPEKADVFIICVP 91 
                                   789*************************************7766444466779999988899999999999999987765 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   2.8e-05     0.025      11      52 ..       6      49 ..       1      63 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.8e-05
                                  HS-SS.EEEEET-TT-.-HHHHHHHHHS-EEEEE-SS-S....S CS
                       UPF0146 11 enarg.kvvEvGiGrk.ldvaealakrgvdlvatDikekkakeg 52
                                  +n+ g ++  +G+G   l  a++la +g+d++ +Di+ek++ke 
  gi|15668604|ref|NP_247402.1|  6 KNGIGkRICVIGLGYIgLPTASMLAIQGFDVIGVDINEKRVKEI 49
                                  4555449999****753789********************9974 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0014       1.3       1      71 [.      12      92 ..      12      96 .. 0.74
   2 ?   -0.6   0.0       2.2     2e+03      14      63 ..     163     206 ..     161     214 .. 0.59
   3 ?    3.4   0.1      0.13   1.1e+02      55      94 ..     360     402 ..     350     404 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...............-EEECECHHHHHHH-SEEEE- CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...............vkvtavdneeaaeeadvvvla 68
                                  +i++iG G +g   as l+ +g    +++ + + n+++++e++e l+               ++    + ++  e+adv +++
  gi|15668604|ref|NP_247402.1| 12 RICVIGLGYIGLPTASMLAIQG---FDVI-GVDINEKRVKEIKE-LSfkttekdlmtlvkgaINSGNLKVQTKPEKADVFIIC 89
                                  799*******************...9999.87888888888864.34356677888887555444444555555678888888 PP

                                  S-H CS
                 F420_oxidored 69 vkp 71
                                  v++
  gi|15668604|ref|NP_247402.1| 90 VPT 92
                                  876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.2
                                   HHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-S CS
                 F420_oxidored  14 lasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeead 63 
                                   +++ l++++     ++ +   ++++ae ++e ++  vt++ + + a+ a+
  gi|15668604|ref|NP_247402.1| 163 ILKELVEND----RVI-G-GVDEKSAEMAKEIYETFVTGKIYLTDAKTAE 206
                                   666677776....555.4.6677777777777775555444444444444 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.13
                                   HHHHHHH-SEEEE-S-HHHHHHHHHHC...GHHHHTTSEEEEE CS
                 F420_oxidored  55 neeaaeeadvvvlavkpedveevlsel...akdalkgklvisv 94 
                                     ea+e ad++v+      ++++ +e     +++ k+k+++++
  gi|15668604|ref|NP_247402.1| 360 LDEAVEGADIIVILAEHDEYKNFDKEDiknIASKVKNKIILDT 402
                                   579**********999999998876654444666777887776 PP

>> Bombinin  Bombinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00028      0.25      47     121 ..     171     248 ..     155     264 .. 0.81
   2 ?    1.4   0.0      0.26   2.3e+02     101     125 ..     375     399 ..     298     407 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                      Bombinin  47 rkllggvktalkgavkelaskyvngk...rtaeehevmkrleavmrdldsldypeeaseretrgfnqeeianlftkke 121
                                    +++ggv      ++ke+ +++v gk     a+  e++k +e   rd++     e a   e  g+n  e  +l  k+ 
  gi|15668604|ref|NP_247402.1| 171 DRVIGGVDEKSAEMAKEIYETFVTGKiylTDAKTAEMVKLMENTYRDVNIALANEFAKIAEEIGINVWEAIELANKHP 248
                                   46889999999999************443469999**************99999999999999999988888877764 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.26
                      Bombinin 101 seretrgfnqeeianlftkkekril 125
                                      e + f++e+i n+ +k +++i+
  gi|15668604|ref|NP_247402.1| 375 EHDEYKNFDKEDIKNIASKVKNKII 399
                                   4568899*********999655543 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.7e-05      0.06       2      66 ..      21      90 ..      21      96 .. 0.73
   2 ?   -2.4   0.0       4.8   4.3e+03      78      96 ..     302     321 ..     296     334 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.7e-05
                                  HHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEET.....TTCHHHHHHHHHTTTSSEEEEEESS CS
                    ADH_zinc_N  2 vGlaavqlAkalGaeviavdsseeklelakklGadeviny.....keadlverikeltggegvdvvfecv 66
                                  +Gl +  ++++ G+ vi+vd++e++++  k+l  + +        k a  +  +k  t++e++dv + cv
  gi|15668604|ref|NP_247402.1| 21 IGLPTASMLAIQGFDVIGVDINEKRVKEIKELSFKTTEKDlmtlvKGAINSGNLKVQTKPEKADVFIICV 90
                                  688889999**********************965555444444433322345666667777888887777 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.8
                                   CEEEE.EEEEECSCTSSEEE CS
                    ADH_zinc_N  78 llkpg.GrlvvvGggkgeee 96 
                                   ++k++ G+++++G+ +++++
  gi|15668604|ref|NP_247402.1| 302 IIKKDiGKVAIFGVTYKGNV 321
                                   56666699999999776664 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0027       2.5       2      81 ..      13      94 ..      12     127 .. 0.76
   2 ?   -2.3   0.1       4.3   3.9e+03      95     126 ..     276     307 ..     272     321 .. 0.75
   3 ?    2.5   0.0      0.15   1.3e+02      61      93 ..     358     390 ..     347     416 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0027
                                  EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-H..HHHHTT--EEEE---HHH CS
                NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdl..aealkgadiivlvvPsqa 81
                                  i+v+G G  G   A +la +g +v     +e+ ++ei+e    ++  + ++l +    + +l  ++  ++ad+ ++ vP+  
  gi|15668604|ref|NP_247402.1| 13 ICVIGLGYIGLPTASMLAIQGFDVIGVDINEKRVKEIKELSFKTTEKDLMTLVKGAINSGNLkvQTKPEKADVFIICVPTPC 94
                                  9******************************999988876555544444445444444444411334456788888888765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.3
                                   TT-EEEE---SEET.TTEEHHHHHHHHH-S-- CS
                NAD_Gly3P_dh_N  95 kkailvsliKGieegtlkllsevieeelkeek 126
                                   k+a+l+ +++ +++++  ++ e i++++k++ 
  gi|15668604|ref|NP_247402.1| 276 KNAKLIRTARELNDSMPLFVVEKIKKIIKKDI 307
                                   67777888888888888888888888888874 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.15
                                   S-HHHHHTT--EEEE---HHHHHHHHHHHCCC- CS
                NAD_Gly3P_dh_N  61 tdlaealkgadiivlvvPsqalrevlkklkgll 93 
                                   + l+ea++gadiiv+   +   +++ k+  + +
  gi|15668604|ref|NP_247402.1| 358 NSLDEAVEGADIIVILAEHDEYKNFDKEDIKNI 390
                                   6799***********998888887765544444 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001     0.094      35      99 ..      24     119 ..       7     136 .. 0.70
   2 ?   -2.9   0.0       5.8   5.2e+03     147     164 ..     222     239 ..     199     240 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
               Methyltransf_23  35 illevlrengfsvtgvDlspeaveiae..................kakkaqkdqfdeqeaae.............pqgkfd 84 
                                    +++ l+ +gf+v+gvD++++ v++++                    + + k+q+  ++a++              ++k+d
  gi|15668604|ref|NP_247402.1|  24 PTASMLAIQGFDVIGVDINEKRVKEIKelsfkttekdlmtlvkgaINSGNLKVQTKPEKADVfiicvptpciecdGEKKCD 104
                                   46777899***********99999888887777777777777766233333333322233334444444555555666*** PP

               Methyltransf_23  85 lIvlrevlehvpdpp 99 
                                   l +l+  +e+++++ 
  gi|15668604|ref|NP_247402.1| 105 LTYLNKAIESIKPYL 119
                                   ***********9765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.8
               Methyltransf_23 147 sarslkelleeaGlevve 164
                                    a ++++++ee G +v e
  gi|15668604|ref|NP_247402.1| 222 LANEFAKIAEEIGINVWE 239
                                   567899999999999876 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00021      0.18       9      76 ..     229     300 ..     223     336 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                    OKR_DC_1_N   9 laealekegfevvgvtstdDllsvieqnsriaavvlsvd.......deaaelldeirernedlPvFllaetrtse 76 
                                   +ae++  +  e +++++    +++++  + +++  +s+d        ++a+l++ +re+n  +P+F++ +    +
  gi|15668604|ref|NP_247402.1| 229 IAEEIGINVWEAIELANKHPRVNILKPGPGVGGHCISIDpwfivekSKNAKLIRTARELNDSMPLFVVEK---IK 300
                                   5555555555666666666667777777888899999999999999999******************987...33 PP

>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.1   4.5e+03      28      62 ..     188     227 ..     170     237 .. 0.53
   2 ?   11.4   0.1   0.00015      0.13      28      85 ..     266     323 ..     264     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.1
                                   EEEEEEESS.....-SS-EE-TTSTT-EEEEGGGHHHHHH CS
                          ALAD  28 ilplfvkeg.....eeekeeiksmpgvyrlsvdelvkeve 62 
                                   i+  fv+ +      ++ e +k m+++yr     l++e +
  gi|15668604|ref|NP_247402.1| 188 IYETFVTGKiyltdAKTAEMVKLMENTYRDVNIALANEFA 227
                                   4555554332221145667777777777654444443333 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00015
                                   EEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE-SS-BSS- CS
                          ALAD  28 ilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvpeekdeeg 85 
                                   i p f++e++++ + i++  +        +v+++++++k++i +v++Fgv+ + + + 
  gi|15668604|ref|NP_247402.1| 266 IDPWFIVEKSKNAKLIRTARELNDSMPLFVVEKIKKIIKKDIGKVAIFGVTYKGNVDD 323
                                   6699******************9999999*********************95522222 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.5   1.3e+03      71     101 ..      57      95 ..      30     105 .. 0.50
   2 ?    4.3   0.0     0.022        20      74     122 ..     107     155 ..      99     164 .. 0.83
   3 ?    4.8   0.1     0.015        14      57     103 ..     200     246 ..     183     255 .. 0.78
   4 ?    0.1   0.1      0.42   3.7e+02      37      68 ..     360     390 ..     345     420 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.5
                          CofC  71 kekdlntaveka........feeieekeviiipsdiPli 101
                                   +ekdl t v+ a         +++e+++v ii    P i
  gi|15668604|ref|NP_247402.1|  57 TEKDLMTLVKGAinsgnlkvQTKPEKADVFIICVPTPCI 95 
                                   233443333322111121115667777777777666665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.022
                          CofC  74 dlntavekafeeieekeviiipsdiPlikkedvkdllelekradvviaP 122
                                    ln+a+e +    e+ ++iii s iP  + +d+ + l ++k+  v   P
  gi|15668604|ref|NP_247402.1| 107 YLNKAIESIKPYLENGNLIIIESTIPPGTTDDIYKKLSKDKKIYVAHCP 155
                                   589****997778*************99999999888888876666555 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.015
                          CofC  57 eyaldelgvevvkekekdlntavekafeeieekeviiipsdiPlikk 103
                                     a+  + v++++++++d+n a+ + f +i e+  i +   i l +k
  gi|15668604|ref|NP_247402.1| 200 TDAKTAEMVKLMENTYRDVNIALANEFAKIAEEIGINVWEAIELANK 246
                                   557778999******************99988766656556666555 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.42
                          CofC  37 vidalkrld.vlvvsedeevleyaldelgvevv 68 
                                   + +a+++ d +++++e +e  +++++  +   +
  gi|15668604|ref|NP_247402.1| 360 LDEAVEGADiIVILAEHDEYKNFDKEDIK--NI 390
                                   45677888866667777777777764433..22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 2822.53
//
Query:       gi|15668605|ref|NP_247403.1|  [L=395]
Description: argininosuccinate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.4e-189  630.4   0.4   1.5e-189  630.2   0.4    1.0  1  Arginosuc_synth  Arginosuccinate synthase
    3.7e-06   26.6   0.1    1.4e-05   24.7   0.1    1.9  1  QueC             Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.068   11.9   0.1       0.11   11.2   0.1    1.3  1  tRNA_Me_trans    tRNA methyl transferase
      0.089   12.7   0.9         14    5.6   0.1    2.4  2  Rep_1B           Replicase polyprotein 1ab


Domain annotation for each model (and alignments):
>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  630.2   0.4  3.4e-193  1.5e-189       1     387 [.       6     388 ..       6     389 .. 0.99

  Alignments for each domain:
  == domain 1  score: 630.2 bits;  conditional E-value: 3.4e-193
               Arginosuc_synth   1 vLaysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikanalYedr 81 
                                   vLaysGGlDts+++kll++k+g++v++v+vdvGq+ee+++ev+eka+klg +k++++Dakeefv+dyif+aikana+Ye+ 
  gi|15668605|ref|NP_247403.1|   6 VLAYSGGLDTSCCLKLLEDKYGYKVVSVCVDVGQPEEEIKEVEEKAKKLGVLKHYTIDAKEEFVKDYIFRAIKANAMYEG- 85 
                                   8*******************************************************************************. PP

               Arginosuc_synth  82 YllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeieyakekgipve 162
                                   Y+l+talaRPlia+k+ve+a++ gaeavahGctGkGnDq+Rfe++ir +aP+lk+iaP+R+l+ltR eeieyakekgip++
  gi|15668605|ref|NP_247403.1|  86 YPLSTALARPLIAHKVVEIAEEVGAEAVAHGCTGKGNDQFRFETTIRIKAPHLKIIAPIRDLNLTRAEEIEYAKEKGIPIP 166
                                   ********************************************************************************* PP

               Arginosuc_synth 163 vtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeelsvlelieklneia 243
                                   +++kk ysiDenl+grsie++ Le+p+++ppe+iy++tk+p +++ e+e+veief++GvPva++ge+l+++eli+k+neia
  gi|15668605|ref|NP_247403.1| 167 TESKK-YSIDENLWGRSIEGSELENPDFVPPEEIYAWTKNPVEDK-EEEIVEIEFKEGVPVAINGEKLEPVELIKKANEIA 245
                                   99766.**************************************9.89********************************* PP

               Arginosuc_synth 244 gkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvYkGlwfsPlkealdafie 324
                                   gkhGvGRiDi+edR++glksRe+Ye+p+a++L++ahk+le+l+l+r++++fk+iv++ y+el+YkGlwf+Pl+e+ldafi+
  gi|15668605|ref|NP_247403.1| 246 GKHGVGRIDIIEDRIIGLKSRENYECPGAVLLLTAHKALEQLVLTRDELRFKEIVDSLYGELIYKGLWFDPLREDLDAFID 326
                                   ********************************************************************************* PP

               Arginosuc_synth 325 ktqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGfikihglqakly 387
                                   ktqervtGtv+vklf G+++v+gR+s+++lY++el+s+d e+e+dqke +G++k+hglqa+ly
  gi|15668605|ref|NP_247403.1| 327 KTQERVTGTVKVKLFGGTARVVGRDSPYALYSKELVSFD-EKEIDQKELAGMVKYHGLQAMLY 388
                                   ***************************************.99******************998 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   3.2e-09   1.4e-05       2     122 ..       5     118 ..       4     177 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.2e-09
                                   EEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG--------- CS
                          QueC   2 avvllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeeievpk 81 
                                   av+  SGGlD + +l l ++++ ++v  + +d gq + +e++ +++ ak+lgv +h ++d +  +e+ +  ++++   ++ 
  gi|15668605|ref|NP_247403.1|   5 AVLAYSGGLDTSCCLKLLEDKYgYKVVSVCVDVGQPE-EEIKEVEEKAKKLGVLKHYTIDAK--EEFVKDYIFRA---IKA 79 
                                   78999**********99988766***********975.689999999******999999998..77777777766...333 PP

                                   --...--------TTHHHHHHHHHHHHHHHHT-SEEEE--- CS
                          QueC  82 eeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvn 122
                                    ++  e+ p +   aR li   + +  ae++gaea++ G++
  gi|15668605|ref|NP_247403.1|  80 -NAMYEGYPLSTALARPLIAHKV-VEIAEEVGAEAVAHGCT 118
                                   .4556777777777777766555.45577777777777765 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   2.5e-05      0.11       4      81 ..       6      75 ..       2      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.5e-05
                 tRNA_Me_trans  4 vvalSgGVDSsvaaallkeqg.yevigvflklweeedeegkeccaeedlkdaervaeklgi.plevvdfekeykekvfee 81
                                  v a SgG D s  + ll++++ y+v+ v + + +           ee++k++e+ a+klg+ +++++d ++e+ ++ + +
  gi|15668605|ref|NP_247403.1|  6 VLAYSGGLDTSCCLKLLEDKYgYKVVSVCVDVGQP----------EEEIKEVEEKAKKLGVlKHYTIDAKEEFVKDYIFR 75
                                  4589*************98755****999876554..........56788999999999986899999999998876544 PP

>> Rep_1B  Replicase polyprotein 1ab
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0031        14      22      35 ..      25      38 ..      22      40 .. 0.92
   2 ?    5.2   0.1    0.0043        19      23      42 ..      97     117 ..      90     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0031
                                  ESSSSEEEEE--TS CS
                        Rep_1B 22 kvGhkvvavvadvG 35
                                  k G+kvv+v  dvG
  gi|15668605|ref|NP_247403.1| 25 KYGYKVVSVCVDVG 38
                                  78***********9 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0043
                                   SSSSEEEEE--TSSEEE.BSS CS
                        Rep_1B  23 vGhkvvavvadvGGniv.fGc 42 
                                   + hkvv +  +vG + v  Gc
  gi|15668605|ref|NP_247403.1|  97 IAHKVVEIAEEVGAEAVaHGC 117
                                   78***********98663788 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2603.32
//
Query:       gi|15668606|ref|NP_247404.1|  [L=204]
Description: deoxycytidine triphosphate deaminase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-09   36.4   0.0    1.4e-08   34.5   0.0    1.9  3  dUTPase   dUTPase
    4.9e-08   32.2   0.0    0.00042   19.2   0.0    2.9  2  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.39   3.5e+03      59      77 ..      15      31 ..      13      36 .. 0.81
   2 ?   -1.8   0.0      0.26   2.3e+03      16      31 ..      32      47 ..      18      59 .. 0.74
   3 !   34.5   0.0   1.5e-12   1.4e-08      31     107 ..      95     172 ..      82     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.39
                                  HHEEEEEEEEETTBTSEEE CS
                       dUTPase 59 kglivvpgvidsdyrGevk 77
                                  k +i++p   ++d+ G+++
  gi|15668606|ref|NP_247404.1| 15 KRIIIKP--FNKDFVGPCS 31
                                  7789999..9999999886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.26
                                  EEEE-SSSEEEETTEE CS
                       dUTPase 16 yDlsaakdltvkpget 31
                                  yD+ + ++++++ +e 
  gi|15668606|ref|NP_247404.1| 32 YDVTLGDEFIIYDDEV 47
                                  8888888888877655 PP

  == domain 3  score: 34.5 bits;  conditional E-value: 1.5e-12
                                   EEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEE..EEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEEEEEEBECG CS
                       dUTPase  31 tvlvptdisiklpdglaalilpRSglaakglivvp..gvidsdyrGevkvvlfnltkkdvkikkgdRiAqLifarilta 107
                                    vl +t+ +i+lp+++ a   +RS+l +  l+++   g id+ ++G++ + ++++ k +v + k++Ri qLif ++l +
  gi|15668606|ref|NP_247404.1|  95 GVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQtaGWIDAGFKGKITLEIVAFDK-PVILYKNQRIGQLIFSKLLSP 172
                                   577799**************************99889*********99999999999.***************999883 PP

>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   0.00011         1      84     111 ..      90     123 ..       1     130 [. 0.47
   2 !   19.2   0.0   4.7e-08   0.00042     287     353 ..     131     189 ..     127     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00011
                           DCD  84 Yivp......lleslaLpadlsaaanpksstGRl 111
                                   Y+v+       +e ++Lp+d+sa+ + +ss GR+
  gi|15668606|ref|NP_247404.1|  90 YVVEggvlgtTNEYIELPNDISAQYQGRSSLGRV 123
                                   4443222222579999999999999999999997 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 4.7e-08
                           DCD 287 aGffDpGFGlaeaggegsravLevRsrevPFiledgqivgrlvyermaekpealYGeelgsnYqgqg 353
                                   aG++D+GF          +  Le+ + + P il + q +g+l++ ++ + ++  Y e+ +s+Y  q+
  gi|15668606|ref|NP_247404.1| 131 AGWIDAGF--------KGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADVGYSERKTSKYAYQK 189
                                   55555555........35789******************************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 1539.69
//
Query:       gi|15668607|ref|NP_247405.1|  [L=75]
Description: hypothetical protein MJ_0431 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-09   37.3   2.6      3e-09   36.6   2.6    1.4  1  Class_IIIsignal  Class III signal peptide
  ------ inclusion threshold ------
      0.039   14.2   0.6      0.043   14.0   0.6    1.1  1  DUF4330          Domain of unknown function (DUF4330)
      0.072   13.3   0.6        0.1   12.8   0.6    1.2  1  DUF347           Repeat of Unknown Function (DUF347)


Domain annotation for each model (and alignments):
>> Class_IIIsignal  Class III signal peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   2.6     5e-13     3e-09       1      27 []      13      39 ..      13      39 .. 0.98

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 5e-13
               Class_IIIsignal  1 kKGQiSlEyiLLilavlviaiiaiyyy 27
                                  kKGQ+S+E ++L++a++++aiia y+y
  gi|15668607|ref|NP_247405.1| 13 KKGQLSMEVGVLVAAAVLVAIIAAYFY 39
                                  8************************98 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   7.2e-06     0.043       4      55 ..      11      60 ..       8      71 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.2e-06
                       DUF4330  4 iDskgrlfgkvnilDllailvilavivgiflkpgtsgsvaqaeaaatkpvev 55
                                  + +kg+l   v +  l+a++v++a+i++ f++++ + +va a++++++ ++v
  gi|15668607|ref|NP_247405.1| 11 LSKKGQLSMEVGV--LVAAAVLVAIIAAYFYVKNAKSAVASAGNKSAAFINV 60
                                  5556666655555..5788899999999999999998888888877666555 PP

>> DUF347  Repeat of Unknown Function (DUF347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.6   1.7e-05       0.1      20      50 ..      11      41 ..      10      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.7e-05
                        DUF347 20 lsqglglgyavgaaifgalllvvvlaqfltk 50
                                  ls+   l+  vg ++ +a+l+++++a+f  k
  gi|15668607|ref|NP_247405.1| 11 LSKKGQLSMEVGVLVAAAVLVAIIAAYFYVK 41
                                  7787889999999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1297  (0.0723409); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 491.14
//
Query:       gi|15668608|ref|NP_247406.1|  [L=92]
Description: hypothetical protein MJ_0432 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-21   74.3   0.3    7.6e-21   74.1   0.3    1.1  1  HTH_34    Winged helix DNA-binding domain
    2.1e-08   33.9   0.1      4e-08   33.0   0.1    1.5  1  HTH_5     Bacterial regulatory protein, arsR family
      4e-07   30.0   0.0    5.3e-07   29.6   0.0    1.2  1  HTH_20    Helix-turn-helix domain
    0.00035   20.5   0.0    0.00046   20.1   0.0    1.2  1  MarR      MarR family
     0.0012   18.8   0.1     0.0017   18.2   0.1    1.3  1  PadR      Transcriptional regulator PadR-like family
     0.0017   17.8   0.0     0.0038   16.7   0.0    1.7  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.013   16.0   0.0      0.017   15.6   0.0    1.2  1  HTH_27    Winged helix DNA-binding domain
       0.03   14.2   0.1      0.046   13.6   0.1    1.6  1  TrmB      Sugar-specific transcriptional regulator TrmB
      0.047   13.6   0.0       0.07   13.0   0.0    1.3  1  MarR_2    MarR family
      0.062   13.3   0.4       0.26   11.3   0.2    1.9  2  BLACT_WH  Beta-lactamase associated winged helix domain
      0.066   13.1   0.1      0.076   12.9   0.1    1.1  1  HxlR      HxlR-like helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.3   4.7e-24   7.6e-21       1      76 [.       8      83 ..       8      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 4.7e-24
                        HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaL 76
                                  vR ++l++L+  +  +f++lke+l++tdgnL  hlkkLe+ g++e +k++ +++ +t+++iT++Gr afk+y+ ++
  gi|15668608|ref|NP_247406.1|  8 VRVKILALLYGLEYCEFNYLKEKLNLTDGNLEHHLKKLEECGFVETKKSVIKGRVKTIIKITNKGRVAFKNYIYEI 83
                                  89**********************************************************************9776 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.1   2.5e-11     4e-08       3      47 .]       8      53 ..       6      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.5e-11
                                  HHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  3 tRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                   R+kIL lL   + + +  l e+l+l+ +++ hHLkkL+e+G+Ve+
  gi|15668608|ref|NP_247406.1|  8 VRVKILALLYGlEYCEFNYLKEKLNLTDGNLEHHLKKLEECGFVET 53
                                  69*********55599****************************85 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   3.3e-10   5.3e-07       9      58 ..       6      55 ..       2      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.3e-10
                                  -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                        HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                  + vR +il++L + e   ++ l+e l l++ +l +HL++Lee g+ve+ +
  gi|15668608|ref|NP_247406.1|  6 SVVRVKILALLYGLEYCEFNYLKEKLNLTDGNLEHHLKKLEECGFVETKK 55
                                  569********************************************976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.8e-07   0.00046       5      52 ..       9      56 ..       6      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.8e-07
                                  HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                          MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                  +++iL++ly  + +    L +kl+++ +++   l++Le+ G++e +ks
  gi|15668608|ref|NP_247406.1|  9 RVKILALLYGLEYCEFNYLKEKLNLTDGNLEHHLKKLEECGFVETKKS 56
                                  689****************************************98877 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.1e-06    0.0017      25      74 ..      29      77 ..      15      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.1e-06
                                  T-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                          PadR 25 gllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                  + l+l +G+l   Lk+Le+ g+ve++++   +g+ + + ++T++Gr +++
  gi|15668608|ref|NP_247406.1| 29 EKLNLTDGNLEHHLKKLEECGFVETKKSV-IKGRVKTIIKITNKGRVAFK 77
                                  45678899999***************998.59**************9876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.3e-06    0.0038      25      48 .]      29      52 ..       8      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.3e-06
                        HTH_24 25 erlglSpstvnrrlkrLeeeGlIk 48
                                  e+l+l+ +++  +lk+Lee G+++
  gi|15668608|ref|NP_247406.1| 29 EKLNLTDGNLEHHLKKLEECGFVE 52
                                  89*******************996 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.1e-05     0.017      24      68 .]      27      72 ..      23      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                        HTH_27 24 lcgrlnvedshisyslkkLtekGLvertgdeadrre.krvrlTdkG 68
                                  l ++ln++d +    lkkL+e G+ve++++   +r  + +++T kG
  gi|15668608|ref|NP_247406.1| 27 LKEKLNLTDGNLEHHLKKLEECGFVETKKSVIKGRVkTIIKITNKG 72
                                  6789**************************9999986778899888 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.8e-05     0.046      27      58 ..      26      57 ..      10      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                                  HHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 27 eiaeelgvprskvYevLrsLedkGlVerekgr 58
                                   + e+l++   +    L++Le++G+Ve++k+ 
  gi|15668608|ref|NP_247406.1| 26 YLKEKLNLTDGNLEHHLKKLEECGFVETKKSV 57
                                  5778999999999999***********99875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.3e-05      0.07      25      56 ..      25      56 ..       8      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                                  HHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2 25 gelarrlglsksavsrilkrLvaaGLverrpg 56
                                  + l ++l+l+ +++  +lk+L++ G+ve++++
  gi|15668608|ref|NP_247406.1| 25 NYLKEKLNLTDGNLEHHLKKLEECGFVETKKS 56
                                  568899***********************976 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00016      0.26      24      43 ..      37      56 ..      35      61 .. 0.83
   2 ?   -0.5   0.0       0.8   1.3e+03      29      40 ..      65      76 ..      59      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                      BLACT_WH 24 gvlahLeKLeeeGkVkregd 43
                                  ++ +hL+KLee G V+ +++
  gi|15668608|ref|NP_247406.1| 37 NLEHHLKKLEECGFVETKKS 56
                                  899********999987665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.8
                      BLACT_WH 29 LeKLeeeGkVkr 40
                                   +K  + G+V+ 
  gi|15668608|ref|NP_247406.1| 65 IIKITNKGRVAF 76
                                  568889999976 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.7e-05     0.076      20      71 ..      23      74 ..       9      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-05
                                  EHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEE.EESSSS-EEEEEE-TCGGG CS
                          HxlR 20 RfselkralpkisqkmLaqrLreLeqdgliere.vypevPpkveYsltekGrs 71
                                   f+ lk++l +++   L ++L++Le+ g++e +  + +  +k   ++t+kGr 
  gi|15668608|ref|NP_247406.1| 23 EFNYLKEKL-NLTDGNLEHHLKKLEECGFVETKkSVIKGRVKTIIKITNKGRV 74
                                  588899999.9*******************96515667778999999**9994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 574.40
//
Query:       gi|15668609|ref|NP_247407.1|  [L=175]
Description: hypothetical protein MJ_0433 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00019   21.3   1.9    0.00019   21.3   1.9    2.1  2  TrbL            TrbL/VirB6 plasmid conjugal transfer protein
  ------ inclusion threshold ------
          3    8.1   9.4         18    5.7   4.7    3.0  2  PhaG_MnhG_YufB  Na+/H+ antiporter subunit


Domain annotation for each model (and alignments):
>> TrbL  TrbL/VirB6 plasmid conjugal transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.9   2.1e-08   0.00019     100     177 ..      24     104 ..       2     106 .. 0.74
   2 ?   -6.3  10.0         2   1.8e+04     105     166 ..     110     171 ..     106     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.1e-08
                          TrbL 100 ggilagllawlgvlllflvaavvl.llakialalllalgpifIaf..llFkaTrdlFenWlgqvlsyalllvllavivglg 177
                                   + +++ +++  ++++l+ + + +  +  ++ + lll++g i+I+    l+k+Tr +F++ + +++ y+++ v+l+ +++l 
  gi|15668609|ref|NP_247407.1|  24 KVYFISYFLSSLIFVLIHISIKYWnFNILFIVSLLLIIGSILIVRqqKLYKKTRCYFDKIFEKIVKYGMIAVVLSSVITLY 104
                                   445555555555555555555544588899999**********96336*****************************9985 PP

  == domain 2  score: -6.3 bits;  conditional E-value: 2
                          TrbL 105 gllawlgvlllflvaavvlllakialalllalgpifIafllFkaTrdlFenWlgqvlsyall 166
                                     +a++g++ ++lv+ ++l+ +k    l l+  +  I++ +F   ++l  ++++++++ ++l
  gi|15668609|ref|NP_247407.1| 110 SGVAIAGIFGFLLVIDGILFKSKKRKFLGLLMMFSSIPMFIFHEYQFLIFAFVQFLVALCFL 171
                                   56788899999999999999999999999999999999999999999999999988888876 PP

>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1    0.0076        68       3      25 ..      53      75 ..      31      79 .. 0.77
   2 ?    5.7   4.7     0.002        18      22      53 ..     105     144 ..      87     173 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0076
                PhaG_MnhG_YufB  3 llGalfvllgaigllrlpdvytR 25
                                  ++ +l+ ++g+i ++r +++y +
  gi|15668609|ref|NP_247407.1| 53 FIVSLLLIIGSILIVRQQKLYKK 75
                                  45567777888888888887766 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.002
                PhaG_MnhG_YufB  22 vytRlhaatkadtlGlllillGlllrf.slaa.......s 53 
                                   +y R+  +++a  +G+ll++ G+l++  +          s
  gi|15668609|ref|NP_247407.1| 105 TYPRISGVAIAGIFGFLLVIDGILFKSkKRKFlgllmmfS 144
                                   799*****************99999774443344433330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1169  (0.0652016); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1072.58
//
Query:       gi|15668610|ref|NP_247408.1|  [L=222]
Description: hypothetical protein MJ_0434 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-23   82.1   1.0    4.6e-23   81.3   1.0    1.4  1  DUF86     Protein of unknown function DUF86
    2.5e-10   41.0   1.2    4.5e-10   40.2   1.2    1.4  1  GGACT     Gamma-glutamyl cyclotransferase, AIG2-like


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   1.0   5.1e-27   4.6e-23       1     116 [.      12     105 ..      12     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 5.1e-27
                                   HHHHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHTTSS-HHHHHHHHH CS
                         DUF86   1 ikealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdyifeilaekgviaeepeepwrk 81 
                                   i+e++e+++e+t++++e++f  ++  +dav+r +++igEa+++++ +                      +++++ ++pw++
  gi|15668610|ref|NP_247408.1|  12 ILESIELIEEYTKDKTEDDFFTSKFLQDAVIRRIEIIGEAIKNLPME----------------------FREKYNHIPWKE 70 
                                   689********************************************......................************ PP

                                   HHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHH CS
                         DUF86  82 miglRNrLvHgYlgidpeivwsiikenlpdleefl 116
                                    + +R++L+ +Y+g+d+   w+++k+++p+l+e +
  gi|15668610|ref|NP_247408.1|  71 FAEMRDILIRKYFGVDLGLTWEVVKKDIPKLKEEI 105
                                   ********************************977 PP

>> GGACT  Gamma-glutamyl cyclotransferase, AIG2-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   1.2     5e-14   4.5e-10       1     103 [.     122     221 ..     122     222 .] 0.86

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 5e-14
                                   EEESSTTSTTSCCCHHHHCSECEEEEEEEECCTBEEEE..ET.TTEEEETTSSE.EEE.EEEEE-HHHHHHHHHCT.TTTT CS
                         GGACT   1 vFvYGtLkrgepnhqrlllgarflesgpatlkgyrlyd.lgg.kypalvpgdgekVkG.elyevddeelarLDelEpeeps 78 
                                   vF+YG L+++e+ +   l++ r++++ + ++ gy+ +    + +y ++ +++g+ + G  l++++d+el   D++E + + 
  gi|15668610|ref|NP_247408.1| 122 VFAYGELMKKERLLE--LIN-RVPKMIEGRVYGYEKFFdE-TiGYYGARKKEGSYIDGiILLDITDKELGIFDDYE-DLDV 197
                                   8*******6655554..557.9*************88743.359********************************.999* PP

                                   SEEEEEEEE.EC.TTS-EEEEEEEEE CS
                         GGACT  79 eYereevkv.evledgeqveawvYvy 103
                                   +Y+re  k  +v+edg+++++++Y+ 
  gi|15668610|ref|NP_247408.1| 198 YYIRE--KTtAVSEDGRKYDVYIYLR 221
                                   *****..553568******9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1515.34
//
Query:       gi|15668611|ref|NP_247409.1|  [L=93]
Description: hypothetical protein MJ_0435 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-18   66.4   0.2      2e-18   66.3   0.2    1.0  1  Polbeta         Polymerase beta, Nucleotidyltransferase
    3.2e-16   59.4   0.5    3.7e-16   59.2   0.5    1.0  1  NTP_transf_2    Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.023   14.9   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm
      0.034   14.3   0.0       0.04   14.0   0.0    1.2  1  PUFD            BCORL-PCGF1-binding domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.2   4.4e-22     2e-18       2      84 ..       9      89 ..       8      93 .] 0.97

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 4.4e-22
                                  STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS- CS
                       Polbeta  2 kikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeilkeg 84
                                  ki+ il k+ +++ a +FGS+a+++++e SDiD+ v + e ++l + ++l+ ele++ lgk+vD++++n+ +pll+ +il+e 
  gi|15668611|ref|NP_247409.1|  9 KIIPILLKH-GVKRASIFGSYARNEQKETSDIDILVEFGEGKSLLDLVRLKYELEEV-LGKEVDVLTYNSIHPLLKDRILNEA 89
                                  9********.***********************************************.9********************9975 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.5   8.3e-20   3.7e-16       3      93 ..       9      90 ..       7      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 8.3e-20
                                  HHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCTEE CS
                  NTP_transf_2  3 klleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpllv 85
                                  k++ +l +  +v+++ +fGSyar++ +++SDiD+lv + e        ++l++l++  ++lee+lg evd++t+++++ pll+
  gi|15668611|ref|NP_247409.1|  9 KIIPILLKH-GVKRASIFGSYARNEQKETSDIDILVEFGEG-------KSLLDLVRLKYELEEVLGKEVDVLTYNSIH-PLLK 82
                                  566666654.49*****************************.......678***************************.**** PP

                                  EEEECEEE CS
                  NTP_transf_2 86 ksileerp 93
                                  + il+e++
  gi|15668611|ref|NP_247409.1| 83 DRILNEAV 90
                                  ****9986 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   5.1e-06     0.023      26      67 ..      21      69 ..       3      91 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.1e-06
                                  EEEE-HHHHTT.-SEESSEEEEEEBTTBSTT......SS--HHHHHHHH CS
                DNA_pol_B_palm 26 evivcGSYRRg.aessGDvDvlitkkdakse......skklkklleklv 67
                                  ++ + GSY R+ ++++ D+D+l+   ++ks       + +l+++l k v
  gi|15668611|ref|NP_247409.1| 21 RASIFGSYARNeQKETSDIDILVEFGEGKSLldlvrlKYELEEVLGKEV 69
                                  46799***886257899******99999886555544333444444444 PP

>> PUFD  BCORL-PCGF1-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   8.9e-06      0.04      84     113 ..      40      73 ..      13      75 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.9e-06
                          PUFD  84 d...e.pdskelveLvelepelqslLGssvefle 113
                                   d   e  + k l++Lv+l+ el+++LG +v++l+
  gi|15668611|ref|NP_247409.1|  40 DilvEfGEGKSLLDLVRLKYELEEVLGKEVDVLT 73 
                                   25543367899*******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 593.35
//
Query:       gi|15668612|ref|NP_247410.1|  [L=550]
Description: 7-cyano-7-deazaguanine tRNA-ribosyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-64  218.7   0.0    1.8e-64  218.1   0.0    1.3  1  TGT       Queuine tRNA-ribosyltransferase
    2.1e-17   63.0   0.0    6.8e-17   61.4   0.0    2.0  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    4.2e-16   58.7   0.2    1.2e-15   57.2   0.1    1.9  2  PUA       PUA domain
      2e-07   31.2   2.1      0.006   16.9   0.3    2.7  2  TGT_C1    C1 domain of tRNA-guanine transglycosylase dimerisa
     0.0001   22.2   0.3    0.00022   21.1   0.3    1.6  1  DUF5591   Domain of unknown function (DUF5591)
    0.00036   20.7   0.2     0.0013   19.0   0.0    2.0  2  UPF0113   UPF0113 PUA domain
     0.0017   18.1   0.5       0.35   10.7   0.0    3.0  3  PUA_3     PUA-like domain


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.1   0.0     7e-68   1.8e-64     115     349 ..       2     237 ..       1     238 [. 0.96

  Alignments for each domain:
  == domain 1  score: 218.1 bits;  conditional E-value: 7e-68
                                   HHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHHHHHHHH.....SE.EEEEE--TT-HHHHHHHHHHHHHH- CS
                           TGT 115 esieiqeklgsDiimalddvvpspaskkrveksverTlrwldrcleah.....qa.lfgivqGglyedlreesaeelakrd 189
                                   e+ie+qe++g D+ ++ld ++p++ +++r+ek++e+Tl++++ ++e +     +  l g vqG++y dlr++sa+e+ak++
  gi|15668612|ref|NP_247410.1|   2 EIIEFQERIGVDVGTILDIPTPPDVDRERAEKELEETLKRAKASIELKeergfKLlLNGTVQGSTYLDLRQKSAKEMAKLG 82 
                                   79*******************************************8778899*888************************* PP

                                   -SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEE CS
                           TGT 190 fdgyaigG.lsvge..ekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegel 267
                                   fd y+ig+ ++++e  +++++ e++ +++ +lp++kp++l+G+g+P+ ++ avalG+D+fd+++++++a+++r+lt++g+l
  gi|15668612|ref|NP_247410.1|  83 FDIYPIGAvVPLMEqyRYRDVAEIIINSKMYLPTNKPVHLFGCGHPMFFALAVALGCDLFDSAAYALYAKDDRYLTERGTL 163
                                   ********888***8999*************************************************************** PP

                                   ETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           TGT 268 nlknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarky 348
                                   +l++ k  + f p    CsC++C++yt+++l +l k+++    +Ll++HNl++++e+++ri++aI++g+++e+vee++r +
  gi|15668612|ref|NP_247410.1| 164 HLEEIKDLKAF-P----CSCPVCSSYTPKELASLNKKER---ERLLAEHNLYVTFEEINRIKQAIRDGSLWELVEERVRCH 236
                                   **988777664.7....*****************98888...**********************************99877 PP

                                   T CS
                           TGT 349 e 349
                                   +
  gi|15668612|ref|NP_247410.1| 237 P 237
                                   6 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.0   2.6e-20   6.8e-17       2      71 .]     400     471 ..     399     471 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 2.6e-20
                        TGT_C2   2 rlraiadYqFGagagdaLfpedvtitrs.atgrirqvlv.dgerlatlraqdgrltLsleGarrlheslppP 71 
                                   r+r++++Yq+G  + d+  ++++++ rs +tgr+rqvl+ +ge l+++r +d++l++s +Ga++l + +p+P
  gi|15668612|ref|NP_247410.1| 400 RIRKMLQYQYGFDIIDDELMNKIKVVRSkTTGRLRQVLDeNGEILFSVRSNDNLLIPSEKGAKLLWKKIPFP 471
                                   79**************999999*****************99**************************99987 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.3   8.6e+03      53      66 ..     183     196 ..     181     200 .. 0.82
   2 !   57.2   0.1   4.8e-19   1.2e-15       2      72 ..     474     544 ..     473     546 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.3
                                   SS-HHHHHHHCTSE CS
                           PUA  53 nysseelakikggk 66 
                                    y+ +ela+ +++ 
  gi|15668612|ref|NP_247410.1| 183 SYTPKELASLNKKE 196
                                   7999*****99876 PP

  == domain 2  score: 57.2 bits;  conditional E-value: 4.8e-19
                                   EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                           PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                   rvvv+++A ++ ++g++++a++v+++++++++ ++V +v+ed+el+a G + +++ el++++ g +v+++ 
  gi|15668612|ref|NP_247410.1| 474 RVVVNKEAEEFAREGRNVFAKFVIDCDEELRPYEEVLVVNEDDELLAYGTTILNGIELREFNYGLAVKVRG 544
                                   8*******************************************************************986 PP

>> TGT_C1  C1 domain of tRNA-guanine transglycosylase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   2.8e-05     0.072       1      32 [.     258     289 ..     258     302 .. 0.91
   2 !   16.9   0.3   2.3e-06     0.006      31      70 .]     313     352 ..     292     352 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                        TGT_C1   1 pvtkksaffkvseealkwpiverakeraekvk 32 
                                   pvtkksaff    e++  p v r k+r ++++
  gi|15668612|ref|NP_247410.1| 258 PVTKKSAFFYTGIESMFRPEVLRHKKRLKRLR 289
                                   9**************************99987 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.3e-06
                        TGT_C1  31 vkakfpesishpifGeipkylslsypfaqseseedftvek 70 
                                   v +     i  p+fG ip y+   yp++q e  e f  ek
  gi|15668612|ref|NP_247410.1| 313 VETDVDILIKDPVFGFIPYYIDTVYPLSQHEIPELFDYEK 352
                                   55566667999*********************99999887 PP

>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   8.7e-08   0.00022      28     114 ..     302     380 ..     278     406 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.7e-08
                                   SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT----------------HHH.HHHHHHHHHHHHHHHT-S CS
                       DUF5591  28 akkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqYdiavtgewseee.iefvaellakylektkye 107
                                    +kP         ++e+++  +++v+ +i    +G +P  +++vYP++q++i+   ++++e  ++fv e +    +k  ++
  gi|15668612|ref|NP_247410.1| 302 IEKP---------YHEHLNVVETDVDILIKDPVFGFIPYYIDTVYPLSQHEIPELFDYEKEInKRFVDEFIDWLKKKIGED 373
                                   4444.........44555556667*******************************99999961456666665555555555 PP

                                   EEEE--- CS
                       DUF5591 108 kviahle 114
                                   +++  + 
  gi|15668612|ref|NP_247410.1| 374 NILDIMT 380
                                   5655555 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.1   5.5e+03      28      46 ..     426     444 ..     409     452 .. 0.63
   2 !   19.0   0.0   4.9e-07    0.0013       2      55 ..     475     528 ..     474     537 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.1
                       UPF0113  28 esvkenqvvvVlnengepl 46 
                                   +s+ ++    Vl+enge+l
  gi|15668612|ref|NP_247410.1| 426 RSKTTGRLRQVLDENGEIL 444
                                   4555566667888888876 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 4.9e-07
                       UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt 55 
                                   vvv+++ae+    Gr+v+ + ++  +e+++  + v+V+ne++e+l++G ++ ++
  gi|15668612|ref|NP_247410.1| 475 VVVNKEAEEFAREGRNVFAKFVIDCDEELRPYEEVLVVNEDDELLAYGTTILNG 528
                                   5677777777777************************************97765 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00014      0.35       4      42 ..     194     232 ..     191     235 .. 0.84
   2 ?   -1.8   0.0       1.1   2.8e+03      24      46 ..     423     444 ..     410     444 .. 0.71
   3 ?    4.1   0.0     0.016        40       4      49 ..     478     522 ..     475     524 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                         PUA_3   4 kkkaekrlrqGhPwvfsneiasvegeledGdvVdvfsek 42 
                                   kk++e+ l  + + v  +ei++++++++dG++ ++++e+
  gi|15668612|ref|NP_247410.1| 194 KKERERLLAEHNLYVTFEEINRIKQAIRDGSLWELVEER 232
                                   44557778888899*********************9975 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                         PUA_3  24 asvegeledGdvVdvfsekgkfl 46 
                                   + v+   ++G + +v +e+g+ l
  gi|15668612|ref|NP_247410.1| 423 KVVR-SKTTGRLRQVLDENGEIL 444
                                   3344.348999999999999865 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.016
                         PUA_3   4 kkkaekrlrqGhPwvfsneiasvegeledGdvVdvfsekgkflGtG 49 
                                   +k+ + ++ +    vf++ + + ++el++ + V v++e+++ l++G
  gi|15668612|ref|NP_247410.1| 478 NKE-AEEFAREGRNVFAKFVIDCDEELRPYEEVLVVNEDDELLAYG 522
                                   444.4444444457999999999999******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3365.82
//
Query:       gi|15668613|ref|NP_247411.1|  [L=79]
Description: hypothetical protein MJ_0437 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-18   64.1   3.9    1.1e-17   63.9   3.9    1.1  1  DUF4040          Domain of unknown function (DUF4040)
     0.0011   19.4   1.7     0.0013   19.1   1.7    1.0  1  Caps_synth_CapC  Capsule biosynthesis CapC


Domain annotation for each model (and alignments):
>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   3.9   1.3e-21   1.1e-17       2      67 .]      11      76 ..      10      76 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.3e-21
                       DUF4040  2 llvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrlpr 67
                                  +++l++la +l+rd+++++il+g +Gl++a l++ l APDvAlT+a+++ ++ ++l+++++rr++r
  gi|15668613|ref|NP_247411.1| 11 MTLLSSLASLLQRDLIKCIILSGFAGLCMAYLYYALLAPDVALTEAILGGAILPALFAFTVRRTQR 76
                                  7899***********************************************************986 PP

>> Caps_synth_CapC  Capsule biosynthesis CapC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.7   1.5e-07    0.0013      46     114 ..       7      75 ..       3      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-07
               Caps_synth_CapC  46 tylivrllsrflilyGrrrfvavlllgvlvklllelllllllpaelveeleviGlivpgLiAndferqg 114
                                   +++i++lls+++ l  r+ +  ++l g++  ++  l + ll p+  ++e  + G i+p+L A+++ r +
  gi|15668613|ref|NP_247411.1|   7 IVIIMTLLSSLASLLQRDLIKCIILSGFAGLCMAYLYYALLAPDVALTEAILGGAILPALFAFTVRRTQ 75 
                                   5678888********999999999999998888888899999999999*****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 488.41
//
Query:       gi|15668614|ref|NP_247412.1|  [L=381]
Description: hypothetical protein MJ_0438 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-74  248.5   0.0    5.3e-74  248.2   0.0    1.1  1  UPF0020          Putative RNA methylase family UPF0020
      9e-32  110.2   2.7      9e-32  110.2   2.7    1.9  2  THUMP            THUMP domain
    4.6e-06   27.2   0.1    3.6e-05   24.4   0.0    2.5  2  Methyltransf_25  Methyltransferase domain
    1.2e-05   24.9   0.0    4.5e-05   23.1   0.0    1.9  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    1.9e-05   24.7   0.9    0.00016   21.7   1.1    2.2  2  Methyltransf_18  Methyltransferase domain
    1.9e-05   24.3   0.1    5.6e-05   22.8   0.1    1.7  2  MTS              Methyltransferase small domain
    4.8e-05   23.2   0.1    0.00085   19.1   0.1    2.7  2  N6_N4_Mtase      DNA methylase
    0.00014   21.7   0.4    0.00076   19.3   0.3    2.1  2  Methyltransf_31  Methyltransferase domain
    0.00021   20.7   1.0     0.0032   16.8   0.2    3.4  2  N6_Mtase         N-6 DNA Methylase
    0.00046   20.7   0.3     0.0042   17.6   0.0    2.3  2  Eco57I           Eco57I restriction-modification methylase
    0.00067   19.1   0.1     0.0011   18.3   0.1    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0025   18.4   0.0     0.0084   16.7   0.0    1.8  1  Methyltransf_11  Methyltransferase domain
     0.0035   16.8   0.0       0.15   11.5   0.0    2.7  3  AviRa            RRNA methyltransferase AviRa
  ------ inclusion threshold ------
      0.019   13.8   0.0      0.027   13.3   0.0    1.2  1  UTP25            Utp25, U3 small nucleolar RNA-associated SSU
      0.036   13.2   0.1       0.06   12.5   0.1    1.3  1  Methyltransf_3   O-methyltransferase


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.2   0.0   4.4e-77   5.3e-74       1     196 [.     166     374 ..     166     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 248.2 bits;  conditional E-value: 4.4e-77
                                   -SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SS..........HHHHHHH CS
                       UPF0020   1 RgyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvle..........lkaeaee 71 
                                   RgyR+fn+pa+L++t+A++lv+l++wk++e+llDPmCGsGti+IE+al+++ni+pg++re+++           l++++++
  gi|15668614|ref|NP_247412.1| 166 RGYRVFNHPAHLNATIASSLVYLSDWKDDEMLLDPMCGSGTIPIEGALMKRNIPPGKFRENKYGfkfidifgyeLLDKIKK 246
                                   9**************************************************************99*********8999988 PP

                                   HHH...HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHH CS
                       UPF0020  72 ear...aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYsefl 149
                                   e+    + +k++g+D+++++++ga++Na++a+v d+ief + da+kL++k +e dvi++npPYG+r+gsk++++kLY+efl
  gi|15668614|ref|NP_247412.1| 247 EIVenkNIYKIIGLDKNQKYLDGAKDNAKNAEVLDTIEFICGDATKLHEKFNESDVIIANPPYGIRIGSKRSVKKLYDEFL 327
                                   8776668899*********************************************************************** PP

                                   HHHHHH-TT..-EEEEEESSHHHHHCC---ESEEEEEEETTEEEEEE CS
                       UPF0020 150 relkrvlrgggrlvlltsenkalekaleeralrkvkeknvklglllk 196
                                   +++k++++g++rl+++t+e+k++++a+++++++ ++e+nv++g+l++
  gi|15668614|ref|NP_247412.1| 328 SSAKEIMHGSSRLIVITAEDKMFKDAIAKNNFEVKEEFNVMFGGLMT 374
                                   *******************************************9986 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   2.7   7.5e-35     9e-32       2     144 .]      18     157 ..      16     157 .. 0.96
   2 ?   -2.2   0.1       3.4     4e+03      40      72 ..     327     354 ..     310     368 .. 0.49

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 7.5e-35
                                   HHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEE...EEEEESSHHHHHHHHHHHHHHHH CS
                         THUMP   2 eieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipv...cevceadledileaakeivkkkf 79 
                                   eie++    ++++++++++kgri+++        d +l+ ++++ +r+i+r+ +    +e+++ +l+di++ +++i+++++
  gi|15668614|ref|NP_247412.1|  18 EIESF----GGKIKEIRENKGRIFFSG-------DLKLIPKINYLSRTIERMNILlhrEEIPNIALDDIYKRVYNIDWTEW 87 
                                   56666....899*************96.......9********************************************** PP

                                   HHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT......-EE-SSS-SEEEEEEEETTEEEEEEEC CS
                         THUMP  80 eeeketFaVrvkrrgkhfeftsreinrevGkaivektg......lkVdlenPdivvrveiikdkayisidr 144
                                   ++e+++Fa+r  r g+h  fts +i r+ G+a+ ++++      lkV+l++Pd++vrve+i d++ ++id+
  gi|15668614|ref|NP_247412.1|  88 IKENQSFAIRPLRAGEH-NFTSIDIGRVAGEAVIKSYQrdknirLKVNLDEPDVIVRVEVIFDELIVGIDT 157
                                   *****************.***************************************************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.4
                                   HHHHHHTSTTECEEEEEEEEEESSHHHHHHHHH CS
                         THUMP  40 lkealekargiqrvipvcevceadledileaak 72 
                                   l +a e+  g +r+i++     ++ +++++ a 
  gi|15668614|ref|NP_247412.1| 327 LSSAKEIMHGSSRLIVI-----TAEDKMFKDAI 354
                                   44444444455555555.....44444444433 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.1   3.8e+03      17      49 ..     100     130 ..      93     138 .. 0.71
   2 !   24.4   0.0     3e-08   3.6e-05      20      71 ..     253     306 ..     240     332 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.1
                                   CTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEE CS
               Methyltransf_25  17 krlgkakvtgvDiseemleaareraeeeglnve 49 
                                   ++ g++++t +Di   + ea+ + +++++ n++
  gi|15668614|ref|NP_247412.1| 100 RA-GEHNFTSIDIGRVAGEAVIKSYQRDK-NIR 130
                                   34.5799999**99999888888876643.443 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 3e-08
                                   TSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEE CS
               Methyltransf_25  20 gkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvss 71 
                                   + +k++g+D ++++l+ a+ +a+++++   +ef++gda++l+++ ++ D+++++
  gi|15668614|ref|NP_247412.1| 253 NIYKIIGLDKNQKYLDGAKDNAKNAEVldTIEFICGDATKLHEKFNESDVIIAN 306
                                   4689********************9999***********************994 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.1   2.5e+03       3      13 ..     196     206 ..     195     216 .. 0.81
   2 !   23.1   0.0   3.8e-08   4.5e-05      19      82 ..     252     310 ..     247     329 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
               Methyltransf_15   3 vilDlfsGaGG 13 
                                   ++lD+++G+G 
  gi|15668614|ref|NP_247412.1| 196 MLLDPMCGSGT 206
                                   78*******95 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 3.8e-08
               Methyltransf_15  19 alvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpPwG 82 
                                   ++ + k+i++++n++ l  a+ Na+  +v d i +++gd ++l +k  +++   d++++ pP G
  gi|15668614|ref|NP_247412.1| 252 KNIY-KIIGLDKNQKYLDGAKDNAKNAEVLDTIEFICGDATKLHEK--FNES--DVIIANPPYG 310
                                   4555.9**********************************998776..5666..88******98 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.2   5.1e+03      69      84 ..       5      20 ..       3      22 .. 0.83
   2 !   21.7   1.1   1.3e-07   0.00016      30     140 ..     246     366 ..     243     374 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.2
               Methyltransf_18 69 vrlsdGleklkeeevd 84
                                  v+ls Glek++++e++
  gi|15668614|ref|NP_247412.1|  5 VTLSPGLEKISKNEIE 20
                                  67999*****999876 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.3e-07
               Methyltransf_18  30 iylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvvia....G..mGge.....lileI 99 
                                    ++v+++++ k+i  D n++ l+ ak+n+++a++ d ie++++d  +  ++ + + v+ia    G  +G++     l  e 
  gi|15668614|ref|NP_247412.1| 246 KEIVENKNIYKIIGLDKNQKYLDGAKDNAKNAEVLDTIEFICGDATKLHEKFNESDVIIAnppyGirIGSKrsvkkLYDEF 326
                                   6789*****************************************999987776777777455554457751111144456 PP

               Methyltransf_18 100 LeeakeklkkikklilqpnseaeelRkylvengfkiedEel 140
                                   L++ake+++  ++li+   +  + +++ +++n+f++++E  
  gi|15668614|ref|NP_247412.1| 327 LSSAKEIMHGSSRLIVITAE-DKMFKDAIAKNNFEVKEEFN 366
                                   77778888888888877654.56789999999999998865 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         2   2.4e+03      32      50 ..     194     212 ..     183     218 .. 0.74
   2 !   22.8   0.1   4.7e-08   5.6e-05      57     151 ..     256     356 ..     244     367 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2
                                   CSEEEEET-TTSHHHHHHH CS
                           MTS  32 sgkvlDlGcGaGvlgaala 50 
                                   ++ +lD  cG G + ++ a
  gi|15668614|ref|NP_247412.1| 194 DEMLLDPMCGSGTIPIEGA 212
                                   45689999****9987655 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 4.7e-08
                                   EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTT.S-EEEEEE---..STTTC.HCHHHHHHHHHHHHHHHEEE CS
                           MTS  57 evtlvdvdarAlesakenleankle..vevvasdvleevee.kkfdlivsNPP..fhagk.atelavaeeliaeAkeaLke 131
                                   ++  +d++ + l+ ak n+++ ++   +e++  d+++  e+ ++ d+i+ NPP  ++ g+    +++ +e++ +Ake+++ 
  gi|15668614|ref|NP_247412.1| 256 KIIGLDKNQKYLDGAKDNAKNAEVLdtIEFICGDATKLHEKfNESDVIIANPPygIRIGSkRSVKKLYDEFLSSAKEIMHG 336
                                   57789**************99998779*******99877742789********444666624567899************* PP

                                   EEEEEEEEETTSCHHHHHHH CS
                           MTS 132 gGeLliVanrklgyesllee 151
                                   + +L++++ +    ++++++
  gi|15668614|ref|NP_247412.1| 337 SSRLIVITAEDKMFKDAIAK 356
                                   *******9998888887654 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   7.1e-07   0.00085     169     230 ..     170     271 ..      17     272 .. 0.78
   2 ?    0.3   0.0      0.39   4.6e+02       2      39 ..     301     334 ..     300     370 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.1e-07
                                   ----SS---HHHHHHHHHHHS-T.T-EEEETT-TTTHHHHHHHHTT-E................................. CS
                   N6_N4_Mtase 169 kkkHpaqkPvallerlIklstkk.gdivlDpFaGSGtTavaakelgrk................................. 215
                                     +Hpa  ++ ++  l+ ls  k +++ lDp +GSGt+ ++ + ++r+                                 
  gi|15668614|ref|NP_247412.1| 170 VFNHPAHLNATIASSLVYLSDWKdDEMLLDPMCGSGTIPIEGALMKRNippgkfrenkygfkfidifgyelldkikkeive 250
                                   578**************77755528899***************************************************** PP

                                   ......EEEEESSHHHHHHHH CS
                   N6_N4_Mtase 216 ......fiGieieeeyvelae 230
                                          iG +++++y++ a+
  gi|15668614|ref|NP_247412.1| 251 nkniykIIGLDKNQKYLDGAK 271
                                   *****99*******9998665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.39
                                   EEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHH CS
                   N6_N4_Mtase   2 dlivtdpPYntgkdyendeqyeeedsyeeyleflekvl 39 
                                   d+i++ pPY++        +   ++ y+e+l+  ++++
  gi|15668614|ref|NP_247412.1| 301 DVIIANPPYGIRIG----SKRSVKKLYDEFLSSAKEIM 334
                                   67899999998876....44444444555555444444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.87     1e+03       5      20 ..     195     210 ..     192     221 .. 0.79
   2 !   19.3   0.3   6.4e-07   0.00076      30     111 ..     253     344 ..     236     371 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.87
               Methyltransf_31   5 lrvlDlGCGtGeltfe 20 
                                     +lD+ CG+G++ +e
  gi|15668614|ref|NP_247412.1| 195 EMLLDPMCGSGTIPIE 210
                                   5689*******98665 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 6.4e-07
               Methyltransf_31  30 e...vvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsnevl.naladpdkile.......eie 98 
                                   +   ++G+D +++ +  A+ na++ ++   +eF  gd+++l +++  +  D+i++n +    + ++ ++ +       +++
  gi|15668614|ref|NP_247412.1| 253 NiykIIGLDKNQKYLDGAKDNAKNAEVLdTIEFICGDATKLHEKF--NESDVIIANPPYgIRIGSKRSVKKlydeflsSAK 331
                                   3444*******************998654***********88654..469*****96656333333333331111111444 PP

               Methyltransf_31  99 rvlkpggillied 111
                                   + ++  ++l++ +
  gi|15668614|ref|NP_247412.1| 332 EIMHGSSRLIVIT 344
                                   4444444444444 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.76     9e+02      89     115 ..      52      76 ..      47      93 .. 0.72
   2 !   16.8   0.2   2.7e-06    0.0032      31     138 ..     174     312 ..     164     332 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.76
                      N6_Mtase  89 tyrLakmNlllhgieykkvkirlgdtl 115
                                   ++ + +mN+llh  e  +  i+l+d +
  gi|15668614|ref|NP_247412.1|  52 SRTIERMNILLHREEIPN--IALDDIY 76 
                                   566779999999888874..5555544 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.7e-06
                      N6_Mtase  31 Prevsklivell....epksgesvyDpacGsggllvqaekvlkee...............................dgktk 76 
                                   P ++  +i++ l    + k++e  +Dp cGsg + ++ +  +k++                                ++++
  gi|15668614|ref|NP_247412.1| 174 PAHLNATIASSLvylsDWKDDEMLLDPMCGSGTIPIEGAL-MKRNippgkfrenkygfkfidifgyelldkikkeiVENKN 253
                                   555555665555566699****************999876.6777899999999888888888888888777644433444 PP

                      N6_Mtase  77 elsiyGqeknettyrLakmNlllhgieykkvkirlgd.tlekpkfekdkkfdvvvaNppfnqk 138
                                     +i G++kn++    ak N    ++    ++   gd t  ++   k ++ dv++aNpp++++
  gi|15668614|ref|NP_247412.1| 254 IYKIIGLDKNQKYLDGAKDNAKNAEVLDT-IEFICGDaTKLHE---KFNESDVIIANPPYGIR 312
                                   44444888888888888888644444333.5544444033444...45699*********987 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.78   9.3e+02      61      87 ..     240     266 ..     230     275 .. 0.80
   2 !   17.6   0.0   3.5e-06    0.0042       4      51 ..     301     342 ..     296     365 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.78
                        Eco57I  61 glkefrekllkdkklkklvefedskev 87 
                                    l++++++++++k++ k++ + ++++ 
  gi|15668614|ref|NP_247412.1| 240 LLDKIKKEIVENKNIYKIIGLDKNQKY 266
                                   678999999999999999998888765 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.5e-06
                        Eco57I   4 dviiGNPPYqeseakkelkaleekakdiyqkFvekalkledkylalii 51 
                                   dvii NPPY          + +++ k++y +F+  a+++ ++ + li+
  gi|15668614|ref|NP_247412.1| 301 DVIIANPPYGIRI------GSKRSVKKLYDEFLSSAKEIMHGSSRLIV 342
                                   9********9888......2357889*************977776664 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   9.3e-07    0.0011      48     128 ..     229     313 ..     213     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.3e-07
                                   TTEEEEES-TT-HHHHHHHHHHHHHH.......EEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEE CS
               Ubie_methyltran  48 gakvlDvagGtgDlafklsdsvgekg.......kvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvv 120
                                   g k++D+ g       +l+d+++++        k+++lD n++ L+ +++ +k+  +   ief++++a +L ++ +  Dv+
  gi|15668614|ref|NP_247412.1| 229 GFKFIDIFGY------ELLDKIKKEIvenkniyKIIGLDKNQKYLDGAKDNAKNAEVLdTIEFICGDATKLHEKFNESDVI 303
                                   5555555543......33333333333333577*********************998879**************9999998 PP

                                   EEE..S-GGG CS
               Ubie_methyltran 121 tvs..fGlrn 128
                                        +G+r 
  gi|15668614|ref|NP_247412.1| 304 IANppYGIRI 313
                                   7644488885 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   7.1e-06    0.0084      17      68 ..     253     306 ..     243     307 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.1e-06
                                   TTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEE CS
               Methyltransf_11  17 rgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvss 68 
                                   + ++++g+D +++ l+ ak++a+++++  ++ef+++da+kl  + n  D+++++
  gi|15668614|ref|NP_247412.1| 253 NIYKIIGLDKNQKYLDGAKDNAKNAEVldTIEFICGDATKLHEKFNESDVIIAN 306
                                   3489*************************************9999999999875 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.38   4.6e+02      54      67 ..     194     207 ..     171     218 .. 0.71
   2 ?    0.9   0.0      0.21   2.6e+02      74      98 ..     249     273 ..     246     278 .. 0.90
   3 !   11.5   0.0   0.00013      0.15     149     216 ..     283     349 ..     271     367 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.38
                         AviRa  54 pltlyDpCCGgayL 67 
                                      l Dp CG++ +
  gi|15668614|ref|NP_247412.1| 194 DEMLLDPMCGSGTI 207
                                   45799******965 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.21
                         AviRa  74 lhgkkikkvlasDvdeevlelakkN 98 
                                   + +k+i k+++ D +++ l+ ak+N
  gi|15668614|ref|NP_247412.1| 249 VENKNIYKIIGLDKNQKYLDGAKDN 273
                                   56799******************99 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00013
                         AviRa 149 ievfkaditekeeeaekevdivitDlPYGelvswqgeseepvkqlleslaavldpeesvvaviadkkk 216
                                   ie +  d t+ +e +++e d++i+  PYG     + + ++  +++l+s +++++ ++ +++++a+ k 
  gi|15668614|ref|NP_247412.1| 283 IEFICGDATKLHE-KFNESDVIIANPPYGIRIGSKRSVKKLYDEFLSSAKEIMHGSSRLIVITAEDKM 349
                                   5666678885555.55569**********************************988888888877653 PP

>> UTP25  Utp25, U3 small nucleolar RNA-associated SSU processome protein 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.3e-05     0.027     150     192 ..     288     330 ..     243     337 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.3e-05
                         UTP25 150 rkslklyskfyssdiiiaS.PlglrliieeedkkkrdtdfLsSi 192
                                    ++ kl +kf++sd+iia  P g+r+  +    kk  ++fLsS 
  gi|15668614|ref|NP_247412.1| 288 GDATKLHEKFNESDVIIANpPYGIRIGSK-RSVKKLYDEFLSSA 330
                                   5789**************8359**99666.666999999***95 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     5e-05      0.06      74     119 ..     256     301 ..     235     337 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-05
                                   EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSS CS
                Methyltransf_3  74 kilaididreayeialkfiqkagvaekieliegdalkvLeelvkdk 119
                                   ki+ +d+++++ + a++  + a v + ie+i gda+k  e++ + +
  gi|15668614|ref|NP_247412.1| 256 KIIGLDKNQKYLDGAKDNAKNAEVLDTIEFICGDATKLHEKFNESD 301
                                   8999**********************************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2273.36
//
Query:       gi|15668615|ref|NP_247413.1|  [L=361]
Description: hypothetical protein MJ_0439 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-93  312.4   9.1    2.3e-93  312.4   9.1    1.9  2  ATPase_2      ATPase domain predominantly from Archaea
    1.4e-07   32.1   0.0      4e-07   30.6   0.0    1.8  2  AAA_16        AAA ATPase domain
    1.5e-07   31.7   0.0    1.1e-06   28.9   0.0    2.2  3  AAA_22        AAA domain
      1e-05   26.0   1.8    0.00035   21.0   0.1    3.0  2  AAA           ATPase family associated with various cellular 
    1.8e-05   24.8  12.1     0.0038   17.3   0.1    3.6  3  AAA_14        AAA domain
    2.7e-05   23.1   0.6      0.014   14.2   0.0    2.9  3  RNA12         RNA12 protein
     0.0025   17.0   0.2       0.39    9.9   0.0    3.0  2  NB-ARC        NB-ARC domain
     0.0071   17.0   0.7        0.2   12.4   0.1    2.7  2  Pre-PUA       Pre-PUA-like domain
  ------ inclusion threshold ------
      0.017   14.7   0.8      0.033   13.7   0.1    1.7  2  Cas9_a        Cas9 alpha-helical lobe domain
       0.04   13.5   0.0       0.13   11.9   0.0    1.8  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.068   13.0   1.6       0.76    9.6   0.0    2.7  3  TK            Thymidine kinase
      0.074   12.6   0.0       0.25   10.8   0.0    1.9  2  AAA_7         P-loop containing dynein motor region
      0.086   13.2   0.1       0.83   10.1   0.0    2.6  3  RNA_helicase  RNA helicase
       0.23   11.3   1.9         12    5.7   0.0    3.2  3  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.57    9.9   2.9        2.2    8.0   1.3    2.1  2  FTCD_C        Formiminotransferase-cyclodeaminase
       0.77   10.3   3.9        4.2    8.0   0.0    3.3  3  RPAP3_C       Potential Monad-binding region of RPAP3


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.4   9.1     2e-96   2.3e-93       1     233 []      15     263 ..      15     263 .. 0.96
   2 ?    0.3   0.8      0.49   5.5e+02      94     119 ..     275     300 ..     264     343 .. 0.56

  Alignments for each domain:
  == domain 1  score: 312.4 bits;  conditional E-value: 2e-96
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...eeeekkkl 78 
                                   Ff+Reke+ e+++ile +p+ +yf+YGp +sGKtaL+ eii+n+ dk+kyv++yi+lr+++isk+++fie   ee+e+++ 
  gi|15668615|ref|NP_247413.1|  15 FFNREKEITEILSILEGNPDLVYFVYGPLNSGKTALISEIINNRIDKNKYVVFYINLRGIFISKYKDFIEvlfEEYEEDRK 95 
                                   9************************************************************************77666655 PP

                      ATPase_2  79 ekal............giavpkaeleeilk.eksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLl 146
                                      +            gi++pk++leeilk +++k+vfk+i+++l++ikk+gk++iiiiDelqk++d+++n  ++l++eL+
  gi|15668615|ref|NP_247413.1|  96 PVEIikslikdvpslcGIPTPKNTLEEILKkKTTKNVFKYITNVLMDIKKEGKQPIIIIDELQKIGDMKIN--GFLIYELF 174
                                   444459************************9****************************************..******** PP

                      ATPase_2 147 nliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkel..eelskedfeeiyryvGG 225
                                   n++++ltke hlc+v+clsS++lfie+vy+e++l++r++yilvdd+dketal+f++++++e+  ++ls++++e+iy+yvGG
  gi|15668615|ref|NP_247413.1| 175 NYFVDLTKELHLCHVFCLSSDSLFIEQVYSEAMLKDRVDYILVDDFDKETALKFMDFLAEEIlnKKLSDDEKELIYSYVGG 255
                                   **************************************************************87777************** PP

                      ATPase_2 226 kPkalvel 233
                                   kP+ ++++
  gi|15668615|ref|NP_247413.1| 256 KPILIIKV 263
                                   *****987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.49
                      ATPase_2  94 ilkeksklvfkaielllekikkkgkk 119
                                    l+e  ++  ++++++le+ik+k  +
  gi|15668615|ref|NP_247413.1| 275 TLDEMLRDEMQKLKYFLEDIKEKDEE 300
                                   44444455555555555555554433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   3.6e-10     4e-07       1     150 [.      14     163 ..      14     175 .. 0.71
   2 ?   -2.7   0.1       6.1   6.9e+03     138     159 ..     214     233 ..     206     253 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.6e-10
                        AAA_16   1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellr.alekdggiflrgkcdqlesaipysalaqalare 79 
                                   r++ Re+e+ ++ls+le    g p  + +++G+  +GK++l+ e+ + ++ k++ ++++ + +       y  ++++l +e
  gi|15668615|ref|NP_247413.1|  14 RFFNREKEITEILSILE----GNPdLVYFVYGPLNSGKTALISEIINnRIDKNKYVVFYINLRGI-FISKYKDFIEVL-FE 88 
                                   6999********99999....77779****************88885488888755555555555.001134455555.33 PP

                        AAA_16  80 ellrqlldeaesaeleawrekleealaavpelagaea....srllellkrllallsrderplvlvlDdlqwadea 150
                                   e+ ++ +  +  ++l  +   l++  ++ + l+  ++    + ++  +++ l+ +++++++ ++++D+lq++ ++
  gi|15668615|ref|NP_247413.1|  89 EYEEDRKPVEIIKSLIKDVPSLCGIPTPKNTLEEILKkkttKNVFKYITNVLMDIKKEGKQPIIIIDELQKIGDM 163
                                   4444444444444444444444444445555555555888899999******999999999*********98765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.1
                        AAA_16 138 vlvlDdlqwadeaslqllaaLl 159
                                   ++++Dd++  +e+ l+++++L+
  gi|15668615|ref|NP_247413.1| 214 YILVDDFD--KETALKFMDFLA 233
                                   57888888..344444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0     1e-09   1.1e-06       7     123 ..      36     186 ..      32     198 .. 0.84
   2 ?   -0.5   0.0       1.2   1.3e+03      85     110 ..     205     230 ..     178     259 .. 0.55
   3 ?   -0.3   0.1         1   1.2e+03      43      70 ..     215     242 ..     198     315 .. 0.57

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1e-09
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka............... 70 
                                   + +v+G+  +GKT l+ ++ ++      +++++  v++++l +    + kd+ + l++++++++k                
  gi|15668615|ref|NP_247413.1|  36 VYFVYGPLNSGKTALISEIINNR-----IDKNKYVVFYINLRGIFisKYKDFIEVLFEEYEEDRKPveiikslikdvpslc 111
                                   6789*****************97.....33445555599999999*9***************9999*************** PP

                        AAA_22  71 .............erlsseellealeqalrarav...ielliiDEaqhlr..s......eealeeLrsllnlsrkgv 123
                                                + ++++ +++++++ l + ++   ++++iiDE q++   +       e+++++++l +  + ++
  gi|15668615|ref|NP_247413.1| 112 giptpkntleeilKKKTTKNVFKYITNVLMDIKKegkQPIIIIDELQKIGdmKingfliYELFNYFVDLTK--ELHL 186
                                   *****************************999999*************96442555555666666666655..4444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                        AAA_22  85 alraravielliiDEaqh.lrseeale 110
                                    +  ++++  +++D++++     + + 
  gi|15668615|ref|NP_247413.1| 205 EAMLKDRVDYILVDDFDKeT-ALKFMD 230
                                   33333334556666665522.222222 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1
                        AAA_22  43 vfvtlpsstsskdllrellralglelka 70 
                                   ++v+   +++  +++  l++++ +++ +
  gi|15668615|ref|NP_247413.1| 215 ILVDDFDKETALKFMDFLAEEILNKKLS 242
                                   4444444444444444444444433333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   3.1e-07   0.00035       2     111 ..      38     195 ..      37     218 .. 0.77
   2 ?    0.0   0.3      0.95   1.1e+03      38      58 ..     252     275 ..     219     314 .. 0.54

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.1e-07
                                   EEESSTTSSHHHHHHHHHHHH....THEEEEEETTTCS.SS........................................ CS
                           AAA   2 llyGppGtGKTllakavakel....gvefleisgsell.sk........................................ 37 
                                    +yGp   GKT+l++ ++++     +  ++ i++  ++ sk                                        
  gi|15668615|ref|NP_247413.1|  38 FVYGPLNSGKTALISEIINNRidknKYVVFYINLRGIFiSKykdfievlfeeyeedrkpveiikslikdvpslcgiptpkn 118
                                   58*****************944443455788888888877788888889999999999*********************** PP

                                   .........STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEE CS
                           AAA  38 .........yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigat 109
                                            + ++  k i +++ ++k++ k+ i++iDE+ +++  +       +  ++ +L++ + +++k+ + + v + +
  gi|15668615|ref|NP_247413.1| 119 tleeilkkkTTKNVFKYITNVLMDIKKEGKQPIIIIDELQKIGDMK------INGFLIYELFNYFVDLTKELHLCHVFCLS 193
                                   **99988888888888899999999998877***********8777......56666666666666666666655555555 PP

                                   SS CS
                           AAA 110 nr 111
                                    +
  gi|15668615|ref|NP_247413.1| 194 SD 195
                                   55 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.95
                                   STTHHHHHHHHHHHHHHHTS...T CS
                           AAA  38 yvgesekkirelfkeakeka...k 58 
                                   yvg ++  i +++k++k k    +
  gi|15668615|ref|NP_247413.1| 252 YVGGKPILIIKVIKKLKIKGlkeT 275
                                   555555555555555444433221 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   3.3e-06    0.0038       4      64 ..      36      94 ..      34     101 .. 0.81
   2 !   12.8   1.0   7.9e-05     0.088      43     120 ..     129     215 ..     103     224 .. 0.65
   3 ?    0.4   2.6      0.55   6.1e+02      19      67 ..     199     248 ..     196     317 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.3e-06
                        AAA_14  4 ilvitGaRrvGKTtllkqlikell.vkkesilyinldderdkkladpekllelileklkeek 64
                                  ++++ G+  +GKT l+ ++i++++  +k  ++yinl     +k++d+   +e+++e+++e++
  gi|15668615|ref|NP_247413.1| 36 VYFVYGPLNSGKTALISEIINNRIdKNKYVVFYINLRGIFISKYKDF---IEVLFEEYEEDR 94
                                  68999******************988888899*****9999998887...556666554434 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.9e-05
                        AAA_14  43 dkkladpekllelileklkeekktylflDEiqev..........pewekalkslvd...egknldvivtGSnskllskeia 110
                                   +k+   ++ + +++++  ke k+ ++++DE q++              +  +++vd   e + ++v++  S s+++ +  +
  gi|15668615|ref|NP_247413.1| 129 TKN--VFKYITNVLMDIKKEGKQPIIIIDELQKIgdmkingfliY---ELFNYFVDltkELHLCHVFCLSSDSLFIEQVYS 204
                                   111..22234455555434468899*********88888774443...455555552214466899999999999988655 PP

                        AAA_14 111 .tslagrvaei 120
                                      l +rv++i
  gi|15668615|ref|NP_247413.1| 205 eAMLKDRVDYI 215
                                   14567777766 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.55
                        AAA_14  19 lkqlikellvkkesilyin...ldderdkkladpekllelilek.lkeekkty 67 
                                   ++q+++e +  k+++ yi    +d+e+  k+ d+  l e+il+k l++++k++
  gi|15668615|ref|NP_247413.1| 199 IEQVYSEAM-LKDRVDYILvddFDKETALKFMDF--LAEEILNKkLSDDEKEL 248
                                   556665555.344444444001444444444444..44555555444434433 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0097        11       1      47 [.      18      68 ..      18      84 .. 0.78
   2 !   14.2   0.0   1.2e-05     0.014     141     232 ..     141     235 ..     113     248 .. 0.77
   3 ?    1.8   0.2     0.068        76     270     361 ..     240     331 ..     230     340 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0097
                         RNA12  1 RkekiedlkewleEnvntFivvkGPrGSGkkeLvldrvlkdrkk.....vlv 47
                                  R+++i+++ + le n++    v GP  SGk+ L+  +++++r +     v++
  gi|15668615|ref|NP_247413.1| 18 REKEITEILSILEGNPDLVYFVYGPLNSGKTALI-SEIINNRIDknkyvVFY 68
                                  78899999999999***999*************9.77777654333444455 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.2e-05
                         RNA12 141 yleahpeakPvvvidnflakaek..ngvvykklaeWaasLvqs.niahViflted.vsaskaLskaLpnqvfktislgDas 217
                                   +  +++ ++P+++id+ ++  +   ng++  +l ++   L+++  + hV  l++d   ++++ s+a+ +     i + D +
  gi|15668615|ref|NP_247413.1| 141 MDIKKEGKQPIIIIDELQKIGDMkiNGFLIYELFNYFVDLTKElHLCHVFCLSSDsLFIEQVYSEAMLKDRVDYILVDDFD 221
                                   334566688*********98876679**************987589********956679999****************** PP

                         RNA12 218 eesarkyVlsklkee 232
                                   +e+a k+  + l+ee
  gi|15668615|ref|NP_247413.1| 222 KETALKFM-DFLAEE 235
                                   ******95.555555 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.068
                         RNA12 270 kdlkeldeal.eklGGRltDLealvrrvksgetpkeAveeiieqsaeeilkmflldseeakkakwtk.eqaWklikklskk 348
                                   k++++ +e + + +GG+ + +  +++++k+ +  ke ++e+++   +++ k fl d +e+++++++k ++a ++ k   + 
  gi|15668615|ref|NP_247413.1| 240 KLSDDEKELIySYVGGKPILIIKVIKKLKI-KGLKETLDEMLRDEMQKL-KYFLEDIKEKDEESYNKiADALEIFKDSYEI 318
                                   444444444436789998888899999998.457999999998877665.7899977777777776536777777766666 PP

                         RNA12 349 gsieynellleel 361
                                   + i+  + + e l
  gi|15668615|ref|NP_247413.1| 319 EDIKIPKNIREFL 331
                                   6666655555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00034      0.39       3      49 ..      20      61 ..      18     146 .. 0.76
   2 ?    3.3   0.1     0.034        38     188     248 ..     247     311 ..     204     339 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00034
                                  HHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC CS
                        NB-ARC  3 ksvekviekLlekdelqslvvalvGmgGvGKttlakqilnksdeveg 49
                                  k++ ++   L   ++++ lv +++G   +GKt l+++i+n+   +++
  gi|15668615|ref|NP_247413.1| 20 KEITEILSILE--GNPD-LVYFVYGPLNSGKTALISEIINN--RIDK 61
                                  55555555555..8899.999******************99..4443 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.034
                                   HHHHHHCTT-HHHH.HHHHHHHC-T...CSCCHH.HHHHHHHHCTGCCTS--SSSSSSSHHHHHHH CS
                        NB-ARC 188 keivekckGlPlal.kvlggllstk...ktveew.kkvlekleskllevekstskslesvasilql 248
                                   + i +  +G P+ + kv+ +l + k   +t++e+ +  ++kl+  l  ++ + ++s++++a +l++
  gi|15668615|ref|NP_247413.1| 247 ELIYSYVGGKPILIiKVIKKL-KIKglkETLDEMlRDEMQKLKYFLEDIKEKDEESYNKIADALEI 311
                                   334556788886541555443.33323378877724456778766666999999999999999876 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.27     3e+02      34      55 ..     117     137 ..      96     158 .. 0.73
   2 !   12.4   0.1   0.00018       0.2      22      85 ..     295     355 ..     292     356 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.27
                       Pre-PUA  34 eeqleellpkkeevkvvklqge 55 
                                   +++lee+l+kk+  +v+k+  +
  gi|15668615|ref|NP_247413.1| 117 KNTLEEILKKKTTKNVFKYI-T 137
                                   479*********99999987.3 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00018
                       Pre-PUA  22 raklleqfpslseeqleellpkkeevkvvklqgehvelyvvdgeplffqdregellPtlytlwk 85 
                                   ++k  e+++++   +  e+++   e++ +k+  +++  ++v++++lf+++++g+l P  y++w+
  gi|15668615|ref|NP_247413.1| 295 KEKDEESYNKI--ADALEIFKDSYEIEDIKIP-KNIREFLVKKNILFLNPQKGTLKPQSYLVWN 355
                                   55566888888..5666999999*********.******************************7 PP

>> Cas9_a  Cas9 alpha-helical lobe domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         4   4.5e+03      46      64 ..     121     139 ..     117     150 .. 0.77
   2 ?   13.7   0.1     3e-05     0.033      31      82 ..     260     312 ..     258     317 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4
                        Cas9_a  46 erkLtveekqkvfdfLlsl 64 
                                   e+ L+++++++vf++++++
  gi|15668615|ref|NP_247413.1| 121 EEILKKKTTKNVFKYITNV 139
                                   6778888899999988775 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3e-05
                        Cas9_a  31 ivavlanLrir.ekgeerkLtveekqkvfdfLlslkskeeltWedvaekLgie 82 
                                   i+ v+++L+i+  k++ +++  +e qk+  fL + k+k+e +++++a++L+i 
  gi|15668615|ref|NP_247413.1| 260 IIKVIKKLKIKgLKETLDEMLRDEMQKLKYFLEDIKEKDEESYNKIADALEIF 312
                                   899********87778889999****************************995 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.13       2      31 ..      36      65 ..      35      68 .. 0.84
   2 ?   -2.2   0.0       2.3   2.6e+03      23      39 ..     144     160 ..     136     218 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                  EEEEEESTTCCHHHHHHHHHCT--SS-EEE CS
                          cobW  2 vtvltGflGsGKTtLlnhllenraglklav 31
                                  v+ + G+l sGKT+L++++++nr +++  v
  gi|15668615|ref|NP_247413.1| 36 VYFVYGPLNSGKTALISEIINNRIDKNKYV 65
                                  67899***************9988776555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.3
                                   T--SS-EEEEESS-SSC CS
                          cobW  23 nraglklavivNefgev 39 
                                   +++g++  +i+ e++++
  gi|15668615|ref|NP_247413.1| 144 KKEGKQPIIIIDELQKI 160
                                   45666666776666542 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00068      0.76       3      35 ..      36      67 ..      34      72 .. 0.74
   2 ?    1.5   0.1      0.21   2.3e+02      60      87 ..     134     158 ..      73     168 .. 0.56
   3 ?   -3.6   0.1         8     9e+03      69      85 ..     203     219 ..     195     235 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00068
                            TK  3 ielilgpmfaGKsteLlrrvkryqlaekkvvvi 35
                                  +++++gp+++GK++ L+ ++ + ++ + k vv+
  gi|15668615|ref|NP_247413.1| 36 VYFVYGPLNSGKTA-LISEIINNRIDKNKYVVF 67
                                  689*********86.676666666666666654 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                            TK  60 ksktssleeikeeleeedvdvvlvDEaq 87 
                                   k  t+ l   +++++e +  ++++DE q
  gi|15668615|ref|NP_247413.1| 134 KYITNVL---MDIKKEGKQPIIIIDELQ 158
                                   2223333...344444455899****98 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 8
                            TK  69 ikeeleeedvdvvlvDE 85 
                                   ++e++ ++ vd +lvD+
  gi|15668615|ref|NP_247413.1| 203 YSEAMLKDRVDYILVDD 219
                                   45566677788888886 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00022      0.25      37      70 ..      38      72 ..      25      96 .. 0.88
   2 ?   -3.5   0.0       5.5   6.2e+03     100     118 ..     285     303 ..     283     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                         AAA_7 37 llvGptGtGKtviikd.llkkldkekylsltinfs 70
                                  +++Gp  +GKt++i++ + +++dk+ky++  in+ 
  gi|15668615|ref|NP_247413.1| 38 FVYGPLNSGKTALISEiINNRIDKNKYVVFYINLR 72
                                  578*************99999***********986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.5
                         AAA_7 100 kklvvFvDDlnmpakekyg 118
                                   +kl +F+ D+     e y+
  gi|15668615|ref|NP_247413.1| 285 QKLKYFLEDIKEKDEESYN 303
                                   6888999999999888887 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00074      0.83       2      64 ..      38      96 ..      37     139 .. 0.75
   2 ?   -0.4   0.0       1.3   1.5e+03      49      66 ..     148     166 ..      99     186 .. 0.74
   3 ?   -1.8   0.0       3.7   4.1e+03      14      34 ..     228     249 ..     211     258 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00074
                  RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkde 64
                                  ++yGp + GK+ l+ e++++      +k+k  v++ n +  f ++Y++   v++++  ++++ 
  gi|15668615|ref|NP_247413.1| 38 FVYGPLNSGKTALISEIINNRI----DKNKYVVFYINLRGIFISKYKDFIEVLFEEYEEDRKP 96
                                  79**************666555....4445666778999999999999888888888777755 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
                  RNA_helicase  49 gqevvvidDfgqvkdee.n 66 
                                   +q++++id++ ++ d + n
  gi|15668615|ref|NP_247413.1| 148 KQPIIIIDELQKIGDMKiN 166
                                   6889999998887766544 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.7
                  RNA_helicase  14 lakeLakall.kklklkkkdsv 34 
                                   +++ La+++l kkl +++k+ +
  gi|15668615|ref|NP_247413.1| 228 FMDFLAEEILnKKLSDDEKELI 249
                                   3444555555233344444444 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.011        12       4      24 ..      39      59 ..      36      70 .. 0.75
   2 ?    2.0   0.1      0.16   1.8e+02      87     107 ..     207     228 ..     192     253 .. 0.71
   3 ?    0.6   0.2      0.43   4.8e+02      11      29 ..     255     273 ..     247     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                          MobB  4 ivgksgsGKTtLleklipelk 24
                                  + g  +sGKT+L++++i+   
  gi|15668615|ref|NP_247413.1| 39 VYGPLNSGKTALISEIINNRI 59
                                  567889**********98644 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.16
                          MobB  87 rl.sevDlvlvEGfkkealpki 107
                                   +l ++vD +lv  f ke+  k 
  gi|15668615|ref|NP_247413.1| 207 MLkDRVDYILVDDFDKETALKF 228
                                   44356*********99987774 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.43
                          MobB  11 GKTtLleklipelkarglr 29 
                                   GK  L+ k+i++lk +gl+
  gi|15668615|ref|NP_247413.1| 255 GKPILIIKVIKKLKIKGLK 273
                                   9*************99997 PP

>> FTCD_C  Formiminotransferase-cyclodeaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.31   3.5e+02      88     135 ..     116     162 ..     112     166 .. 0.85
   2 ?    8.0   1.3    0.0019       2.2      42      93 ..     265     317 ..     262     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.31
                                   .........S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS- CS
                        FTCD_C  88 pketeeekaareeaiqealkkavevPlelarkalellelleelaekgn 135
                                   pk+t ee   ++++ ++ +k  ++v +++ ++ ++ + +++el ++g 
  gi|15668615|ref|NP_247413.1| 116 PKNTLEEI-LKKKTTKNVFKYITNVLMDIKKEGKQPIIIIDELQKIGD 162
                                   88886655.678888*******************99999999999886 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0019
                                   T-TT-GGGHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHTTTT....... CS
                        FTCD_C  42 gkkkyedveeemeell.ekleelrkellelideDaeaFnevmeayklpketee 93 
                                   +k k++ ++e+++e+l +++++l+  l ++ ++D+e +n++++a+++ k++ e
  gi|15668615|ref|NP_247413.1| 265 KKLKIKGLKETLDEMLrDEMQKLKYFLEDIKEKDEESYNKIADALEIFKDSYE 317
                                   67788888999977652678999999999****************99998755 PP

>> RPAP3_C  Potential Monad-binding region of RPAP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.7   6.3e+03      49      76 ..      81     103 ..      66     109 .. 0.78
   2 ?    8.0   0.0    0.0037       4.2      29      83 ..     115     164 ..      87     170 .. 0.84
   3 ?    0.8   1.2      0.64   7.2e+02      46      74 ..     275     310 ..     192     319 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.7
                       RPAP3_C  49 dildalnerlqeekaedsslvleiLdrL 76 
                                   d++++l e+++e++++     +ei ++L
  gi|15668615|ref|NP_247413.1|  81 DFIEVLFEEYEEDRKP-----VEIIKSL 103
                                   7888888888887655.....6776666 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0037
                       RPAP3_C  29 inpkqlpkiFknsledeilsdildalnerlqeekaedsslvleiLdrLskvkRFd 83 
                                   +++++l++i+k++ + +++  i ++l + ++e k++     + i d+L+k+  ++
  gi|15668615|ref|NP_247413.1| 115 TPKNTLEEILKKKTTKNVFKYITNVLMDIKKEGKQP-----IIIIDELQKIGDMK 164
                                   66799***************************9877.....88999999987766 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.64
                       RPAP3_C  46 ilsdild.......alnerlqeekaedsslvleiLd 74 
                                   +l ++l+       ++ e ++e+++e+ +++++ L+
  gi|15668615|ref|NP_247413.1| 275 TLDEMLRdemqklkYFLEDIKEKDEESYNKIADALE 310
                                   333333333333445555555555555556655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1336  (0.0745161); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 2110.51
//
Query:       gi|15668616|ref|NP_247414.1|  [L=299]
Description: hypothetical protein MJ_0440 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-85  288.2  23.2    1.3e-85  287.9  23.2    1.1  1  DUF63        Membrane protein of unknown function DUF63
  ------ inclusion threshold ------
          1    7.6  17.5        1.5    7.0  17.5    1.3  1  DUF2070      Predicted membrane protein (DUF2070)
        1.1    8.4  33.7      0.026   13.9  12.8    2.5  2  EpsG         EpsG family
        8.7    6.0  13.7      3e+03   -2.3  13.7    2.4  1  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.9  23.2   2.9e-89   1.3e-85       1     272 []      37     299 .]      37     299 .] 0.99

  Alignments for each domain:
  == domain 1  score: 287.9 bits;  conditional E-value: 2.9e-89
                         DUF63   1 iseFiykyYidpivykegYnivntltyaiiLivavyliykllkklkikidekfvlatipyvilgsslRvveDagllkppls 81 
                                   i++FiykyYi+p ++++gYniv+++ty+iiL++a+yl+yk+l+kl+i+idekf++  i++++l++++R+++D+g++  ++s
  gi|15668616|ref|NP_247414.1|  37 IKNFIYKYYIEPAEKGTGYNIVQEITYGIILALALYLFYKALRKLNINIDEKFAIPGIVFTVLIALMRALVDCGYI--ERS 115
                                   89**************************************************************************..*** PP

                         DUF63  82 yllitPliyflvflitlavlliskklekklkkdykklyaavGvvlvlvvlllLllteevvnlevlllvlllaavltalvll 162
                                   +l+itP+i+fl++ ++++++l++  +   +k++y+k +a++G++l+l++l+++l  +++++le++l+v +l+ ++++lv +
  gi|15668616|ref|NP_247414.1| 116 FLTITPGIVFLIGGFFILTILTTGLV---FKEKYYKASAVIGLILLLYFLFVFL--QHITHLEAILYVGILVGIFYYLVKF 191
                                   **************************...*************************..************************* PP

                         DUF63 163 llrklklellsdklnlllllahllDasatfvgidllgYvEqHvvpsfLidltGtalvmyplkllvlipvlyildkevkeee 243
                                   l ++lkl+++++k++ ++++++l+Dasat++gi ++gY+EqH++p+fL++++G  + ++p+kll+++++lyil+kev++e+
  gi|15668616|ref|NP_247414.1| 192 LDKTLKLNIIQSKIDDYVVIGQLIDASATTIGIGVYGYWEQHPIPRFLMETFG-VYAFIPFKLLIILLALYILNKEVEDEN 271
                                   *****************************************************.*************************** PP

                         DUF63 244 elrnlvklailvlGlaPgiRnllrmvlgv 272
                                    ++n++kl+i++lGlaPg+R+l+r+v+gv
  gi|15668616|ref|NP_247414.1| 272 -IKNIIKLCIMALGLAPGLRDLFRTVMGV 299
                                   .**************************97 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  17.5   0.00034       1.5       5     182 ..       3     199 ..       1     205 [. 0.64

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00034
                       DUF2070   5 skyifrlPswkvsllliillalligllaflssk.....................lfgillfglpalvaflltlpvlrilgg 64 
                                   +k++ +  s   +l+ i l+  li +l  ++++                     + + + +g+ + +a+ l++++lr l++
  gi|15668616|ref|NP_247414.1|   3 YKLVLSHYSKTSTLINITLIKHLINILRERMIQeiknfiykyyiepaekgtgynIVQEITYGIILALALYLFYKALRKLNI 83 
                                   566666555555666666666666666666666777777777778888888877777777888888888888888877765 PP

                       DUF2070  65 rltykrs...lflalltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllai 142
                                   +++ k +   +++ +l++l+ ++++   i  s+l    ++  +v+ +   f+l++l + +v++e++ ka+++  +++ll  
  gi|15668616|ref|NP_247414.1|  84 NIDEKFAipgIVFTVLIALMRALVDCGYIERSFL---TITPGIVFLIGGFFILTILTTGLVFKEKYYKASAVIGLILLL-- 159
                                   5433333222222222222222222222222222...334445555777899999999999999999999665555554.. PP

                       DUF2070 143 lllvlyfspesfllllllslifalavylfivvvdrplkrn 182
                                    +l+++++  ++l ++l++ i++ ++y +++++d+ lk n
  gi|15668616|ref|NP_247414.1| 160 YFLFVFLQHITHLEAILYVGILVGIFYYLVKFLDKTLKLN 199
                                   45555556899***********************998865 PP

>> EpsG  EpsG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3  19.2      0.12   5.3e+02     166     310 ..      14     166 ..       1     171 [. 0.50
   2 ?   13.9  12.8   5.7e-06     0.026     148     261 ..     155     289 ..     149     297 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
                          EpsG 166 llllllafi.llllllldlilsllslllliseryesYlesdeysggtig..gvqlaillfilfllllkkileekkkeklkl 243
                                    +l+++ +i  l+ +l +++++ ++++      y++Y+e  e++ g  +   +   i+l+++++l++k +++ + + + k+
  gi|15668616|ref|NP_247414.1|  14 STLINITLIkHLINILRERMIQEIKNF-----IYKYYIEPAEKGTGYNIvqEITYGIILALALYLFYKALRKLNINIDEKF 89 
                                   444444444344444444444444443.....8999999999888766666333334444444344444444444444477 PP

                          EpsG 244 flnllliglallllllsls.........vilsRlslyflifqiillppllkk...lfkrkkrrl.illiliillflflfv 310
                                       +++ +++ l+    +         +i+  +   fli  + +++ +l     +++++++   ++ ++++l+flf+f 
  gi|15668616|ref|NP_247414.1|  90 AIPGIVFTVLIALMRALVDcgyiersflTITPGI--VFLIGGF-FILTILTTglvFKEKYYKASaVIGLILLLYFLFVFL 166
                                   7777777777777776666755555444333333..3333333.444444444424555555553444444455555554 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.7e-06
                          EpsG 148 aiiflplyfllklklklkllllllafillllllldlilsllslllliseryesYlesdeysggtig............... 213
                                    i++l ++f+    ++ +  +l+++++++++++l+++l+  ++l +i++++++Y+  ++  +  +                
  gi|15668616|ref|NP_247414.1| 155 LILLLYFLFVFLQHITHLEAILYVGILVGIFYYLVKFLDKTLKLNIIQSKIDDYVVIGQLIDASATtigigvygyweqhpi 235
                                   3566666777778888999***************************************99887766789************ PP

                          EpsG 214 ........gvqlaillfilfllllkkileekkkeklklflnllliglallllllsl 261
                                           gv  +i + +l++ll  +il+++ ++  +++ n++ ++++ l l++ l
  gi|15668616|ref|NP_247414.1| 236 prflmetfGVYAFIPFKLLIILLALYILNKEVED--ENIKNIIKLCIMALGLAPGL 289
                                   ****999866666666666655555666555554..66666666666666665555 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3  13.7      0.67     3e+03      18     107 ..      65     151 ..      55     282 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.67
                                   XXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin  18 vllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcigalkenkcllltfsllllvlfllelaagi 98 
                                   ++la++++l     ++al++l+ + +e++ai     iv+ vl++l+  l  +g + ++   ++  +++l+  f+++ +++ 
  gi|15668616|ref|NP_247414.1|  65 IILALALYL----FYKALRKLNINIDEKFAIP---GIVFTVLIALMRALVDCGYIERSFLTITPGIVFLIGGFFILTILTT 138
                                   567777777....4555666656666666666...9999999999999999999999999999988888888887777555 PP

                                   XXX--HHH...... CS
                                   xxxxxxxx.....x RF
                   Tetraspanin  99 lgfvfsdk.....a 107
                                    g+vf++k     a
  gi|15668616|ref|NP_247414.1| 139 -GLVFKEKyykasA 151
                                   .8888888444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1146  (0.0639188); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1785.46
//
Query:       gi|15668617|ref|NP_247415.1|  [L=267]
Description: hypothetical protein MJ_0441 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-49  169.0  27.1    1.6e-49  168.7  27.1    1.0  1  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
        2.1    8.7   3.1        1.8    9.0   0.4    2.1  2  DUF1689   Protein of unknown function (DUF1689)
        7.7    6.4   7.2          3    7.7   0.5    2.7  2  DUF3767   Protein of unknown function (DUF3767)


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.7  27.1   2.7e-53   1.6e-49       1     236 []      16     265 ..      16     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 168.7 bits;  conditional E-value: 2.7e-53
                          TauE   1 lllagllaGfvagllGiGggliavPlLll.l..l....ppavavatsllavvatslsgalahrrrgnvdwrlllllllgsl 74 
                                   l+++g+++G++++l+GiGgg+++ P+L++ +  +      + av+tsl++v+++s++++++h + +n++w++ +++++ sl
  gi|15668617|ref|NP_247415.1|  16 LIIVGFIVGILGSLFGIGGGFLVAPILTFiFdyFgipdGVKFAVGTSLFVVFINSIISIFRHAKIKNINWKASITIGIISL 96 
                                   589**************************6664399877788**********************99*************** PP

                          TauE  75 iGall.GallllllpsellkllfgvlllllallmllrkkrsrakgrerrptaillvligglvGllsGllGiGgGfllvpll 154
                                   + +++ G+l+++ ++s++lk lfg++l++ a++m+ ++++ + + re++  +   +l+g+++G+lsGl+GiGgG++++p+l
  gi|15668617|ref|NP_247415.1|  97 VFSYFsGFLVVNFIDSAILKKLFGIFLIANAIYMAKSHHIDKISDREDKLEPF--ILCGVITGFLSGLFGIGGGIVIIPIL 175
                                   ***997888889**********************9888765555444555555..677777*******************9 PP

                          TauE 155 llllglplkkavatslllilvislagalgyal.........agavdwpllllllpgallGallGarlarrlsertlrrlfa 226
                                     + ++p+k+ava s+ +i ++s+ g+++y+           g+v++p++l+++++++  + lG ++++++s+++lr+++ 
  gi|15668617|ref|NP_247415.1| 176 A-MAKYPVKRAVAISVGVIPLTSIGGLISYLTantegyiynIGYVSIPIALIMAIPIIYSSKLGIKINQKISPKHLRIMLS 255
                                   8.69*************************944556666678**************************************** PP

                          TauE 227 llllvlgvkl 236
                                   ++l v+g+ +
  gi|15668617|ref|NP_247415.1| 256 SILGVMGLFM 265
                                   *******987 PP

>> DUF1689  Protein of unknown function (DUF1689)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4    0.0003       1.8      38      78 ..      59      99 ..      53     106 .. 0.88
   2 ?   -0.3   0.1      0.22   1.3e+03      44      44 ..     226     226 ..     119     266 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0003
                       DUF1689 38 wlgfsavflaptayrryktgaikgvkvprsfllGlvalvvs 78
                                  +++ + v+++  ++  +++ +ik+++ ++s+ +G+++lv+s
  gi|15668617|ref|NP_247415.1| 59 VGTSLFVVFINSIISIFRHAKIKNINWKASITIGIISLVFS 99
                                  56677788899999999********************9987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.22
                       DUF1689  44 v 44 
                                   +
  gi|15668617|ref|NP_247415.1| 226 I 226
                                   1 PP

>> DUF3767  Protein of unknown function (DUF3767)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.3     0.073   4.4e+02      64      64 ..      65      65 ..      26     100 .. 0.51
   2 ?    7.7   0.5    0.0005         3      28      68 ..     160     200 ..     159     203 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.073
                       DUF3767 64 g 64
                                  +
  gi|15668617|ref|NP_247415.1| 65 V 65
                                  2 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0005
                       DUF3767  28 slltGigagavvGglrfvlkknvakaaNWavgafllgsiva 68 
                                   s+l+Gig g+v+  + ++ k +v++a+  +vg++ l+si++
  gi|15668617|ref|NP_247415.1| 160 SGLFGIGGGIVIIPILAMAKYPVKRAVAISVGVIPLTSIGG 200
                                   789***********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1639.25
//
Query:       gi|15668618|ref|NP_247416.1|  [L=221]
Description: hydrogenase expression/formation protein HypB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-31  106.7   1.9    1.2e-30  106.4   1.9    1.1  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      2e-08   33.5   1.3    5.5e-07   28.8   1.3    2.1  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    0.00012   22.0   0.2      0.058   13.3   0.1    2.2  2  RsgA_GTPase      RsgA GTPase
    0.00017   21.5   0.4    0.00073   19.4   0.2    2.2  2  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0002   21.1   0.1    0.00044   19.9   0.1    1.7  1  SRP54            SRP54-type protein, GTPase domain
     0.0068   16.3   0.0      0.016   15.1   0.0    1.7  2  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.036   14.1   1.7       0.14   12.2   0.2    2.2  2  MMR_HSR1_Xtn     C-terminal region of MMR_HSR1 domain
       0.05   13.6   0.1        0.1   12.6   0.1    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.057   12.3   0.0      0.082   11.8   0.0    1.1  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.082   12.4   0.0       0.12   11.8   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
        0.1   12.9   0.0       0.28   11.5   0.0    1.8  1  AAA_22           AAA domain
       0.15   12.2   0.0       0.97    9.6   0.0    2.1  2  AAA_33           AAA domain
       0.38    9.7   2.1        0.4    9.6   0.1    1.8  2  IMPDH            IMP dehydrogenase / GMP reductase domain
        1.5    8.7   4.7         16    5.5   0.0    3.8  4  Arg_repressor_C  Arginine repressor, C-terminal domain


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.4   1.9   9.6e-34   1.2e-30       5     176 ..      38     196 ..      34     197 .. 0.93

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 9.6e-34
                                   EEESTTCCHHHHHHHHH.CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHHHTT-S CS
                          cobW   5 ltGflGsGKTtLlnhll.enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelealeereerld 84 
                                   + G +GsGKT L+++l+ + ++++k+a i +++   + Dae+++++g+++v l++G+ C+  ++ +  +le+l  +e  +d
  gi|15668618|ref|NP_247416.1|  38 FMGAIGSGKTLLIEKLIdNLKDKYKIACIAGDVI-AKFDAERMEKHGAKVVPLNTGKECHLDAHLVGHALEDLNLDE--ID 115
                                   5799*************888999***********.**************************6666666666666655..** PP

                                   EEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC...HHHHH CS
                          cobW  85 viliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldee.allekle 163
                                   +++iE++G l +Pa           dl     ++v++     +e++++ ek +  +++adl+v+nK+Dl+d++ a+++k+e
  gi|15668618|ref|NP_247416.1| 116 LLFIENVGnLICPADF---------DLGTHKRIVVIST----TEGDDTIEKHPGIMKTADLIVINKIDLADAVgADIKKME 183
                                   ****************.........*************....99************************************* PP

                                   HHHHHHHTTS-EE CS
                          cobW 164 erlrqlnpeakvl 176
                                   ++++++np+a+v+
  gi|15668618|ref|NP_247416.1| 184 NDAKRINPDAEVV 196
                                   **********986 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   1.3   4.3e-10   5.5e-07      34     229 ..      38     217 ..      25     221 .] 0.79

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 4.3e-10
                                   EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTTEEEEEE-----HHHHHHHHHHHH CS
                          MeaB  34 ltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdegvfiRslpsrGalGGlaaktrevv 114
                                   + G  G+Gk  l+e+l+ +l+++ +++a +a D  ++f       D  R+e++    g+ + +l ++ +    a+  ++++
  gi|15668618|ref|NP_247416.1|  38 FMGAIGSGKTLLIEKLIDNLKDK-YKIACIAGDVIAKF-------DAERMEKH----GAKVVPLNTGKECHLDAHLVGHAL 106
                                   67889999999999999999887.89999999988887.......77899877....455677777666655666777888 PP

                                   HHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTTTTTTT--CCCHHH-SEEEEE---HHHHHHHHHHHHHHHHH CS
                          MeaB 115 llleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpeaGDelqgikkGileiaDiivvnkaDkkeaekaarelraalel 195
                                   + l+    D + ie vG      d    ++  +v++ +  GD+      Gi+  aD+iv+nk D+++a  a    +++ + 
  gi|15668618|ref|NP_247416.1| 107 EDLNLDEIDLLFIENVGNLICPADFDLGTHKRIVVISTTEGDDTIEKHPGIMKTADLIVINKIDLADAVGADI--KKMEN- 184
                                   88888889*********999999999999999***9999****999******************998876543..33322. PP

                                   CSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHH CS
                          MeaB 196 eeekekeWrpkvlktsavegeGidelvdaieehr 229
                                    + k+ +  ++v+  s ++ eG d++++ ie+  
  gi|15668618|ref|NP_247416.1| 185 -DAKRINPDAEVVLLSLKTMEGFDKVLEFIEKSV 217
                                   .233444567788888888888888888887765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0     0.005       6.5      91     125 ..      25      59 ..       7      70 .. 0.69
   2 !   13.3   0.1   4.5e-05     0.058      49     101 ..     162     217 ..     154     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.005
                                   HHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT--- CS
                   RsgA_GTPase  91 eelkellkdktsvlvGqSGvGKStLinallpelel 125
                                   ++l ++       ++G  G GK+ Li++l+ +l+ 
  gi|15668618|ref|NP_247416.1|  25 RKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDNLKD 59 
                                   44444444444459***************998654 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.5e-05
                                   EEEEEE-GGG--HHH.HHHHHHHHHHHTT..SEEEE--TTTHTTHHHHHHHCTTSE CS
                   RsgA_GTPase  49 pvivlnKiDlleeee.eleelkeelealg..yevllvsaktkegleelkellkdkt 101
                                    +iv+nKiDl++    ++++++++ ++++   ev+l+s kt eg++++ e +++++
  gi|15668618|ref|NP_247416.1| 162 DLIVINKIDLADAVGaDIKKMENDAKRINpdAEVVLLSLKTMEGFDKVLEFIEKSV 217
                                   58**********98888999999999997557899************999988765 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   5.7e-07   0.00073       3      70 ..      37      97 ..      35     161 .. 0.72
   2 ?   -0.5   0.0      0.85   1.1e+03      65      96 ..     136     166 ..     130     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.7e-07
                          MobB  3 givgksgsGKTtLleklipelkarglrvgtiKhah.hgfdvdkpgkDsyrhrkAGAkevlvaskerlal 70
                                   ++g  gsGKT L+ekli  lk+ ++++++i  ++  +f       D+ r++k GAk v + + +++ l
  gi|15668618|ref|NP_247416.1| 37 DFMGAIGSGKTLLIEKLIDNLKD-KYKIACIAGDViAKF-------DAERMEKHGAKVVPLNTGKECHL 97
                                  689999***************86.699999976541233.......45556666666666666666555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.85
                          MobB  65 kerlalikeleeaelsleellarlsevDlvlv 96 
                                   ++r+ +i+ + e + ++e++   ++++Dl+++
  gi|15668618|ref|NP_247416.1| 136 HKRIVVISTT-EGDDTIEKHPGIMKTADLIVI 166
                                   5666666664.336677777888888888876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   3.5e-07   0.00044       6      95 ..      38     125 ..      33     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.5e-07
                                   EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSE CS
                         SRP54   6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakeekidv 86 
                                   ++G  G+GKT  + KL + lk+ ++k++ +a D+     +e ++ ++ k+  p+ + ke +  a+++ +a+e  + ++id+
  gi|15668618|ref|NP_247416.1|  38 FMGAIGSGKTLLIEKLIDNLKD-KYKIACIAGDVIAKFDAERMEKHGAKVV-PLNTGKECHLDAHLVGHALEDLNLDEIDL 116
                                   789**************99875.699**********************996.98889999999****************** PP

                                   EEEEE--SS CS
                         SRP54  87 vlvDTaGrl 95 
                                   +++   G l
  gi|15668618|ref|NP_247416.1| 117 LFIENVGNL 125
                                   ***988865 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.3e-05     0.016       6      61 ..      40      98 ..      37     127 .. 0.83
   2 ?   -3.8   0.1       8.2   1.1e+04      93     102 ..     158     167 ..     148     171 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                                  --TTSSHHHHHHHHHHHH......GGGEEEEEEEEE-------EEEEEET.T--EEEEE CS
                      NTPase_1  6 GppGvGKtTlvkkvlellkss...gvkvgGfyteevreggrrigFkivdlasgeegiLa 61
                                  G  G+GKt l++k++++lk++    +  g ++++   e+ ++ g k+v l++g+e  L 
  gi|15668618|ref|NP_247416.1| 40 GAIGSGKTLLIEKLIDNLKDKykiACIAGDVIAKFDAERMEKHGAKVVPLNTGKECHLD 98
                                  889***************98733223334466666679999************998775 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.2
                                   HHHH-EEEE- CS
                      NTPase_1  93 lseadviviD 102
                                   +++ad+ivi 
  gi|15668618|ref|NP_247416.1| 158 MKTADLIVIN 167
                                   3677888875 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.36   4.6e+02      42      72 ..      50      81 ..      41     122 .. 0.59
   2 ?   12.2   0.2   0.00011      0.14      58     100 ..     162     213 ..     135     218 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.36
                  MMR_HSR1_Xtn 42 vDdlidviegnrvYipcly..vlNKiDlislee 72
                                  +++lid ++++ + i c+   v+ K D+ ++e+
  gi|15668618|ref|NP_247416.1| 50 IEKLIDNLKDKYK-IACIAgdVIAKFDAERMEK 81
                                  5666666665443.4444434556666543333 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00011
                  MMR_HSR1_Xtn  58 clyvlNKiDl.....isleeldelare....pnsvviSaekelnldeLkeki 100
                                    l+v+NKiDl     ++++++++ a++     ++v +S ++  ++d+++e i
  gi|15668618|ref|NP_247416.1| 162 DLIVINKIDLadavgADIKKMENDAKRinpdAEVVLLSLKTMEGFDKVLEFI 213
                                   489*******66555444444443333665469999***********99977 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   7.8e-05       0.1      15      48 ..      25      63 ..      10     125 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.8e-05
                                  HHCH...TEE..EEEEESTTSSHHHHHHHHHHHTT--.-- CS
                          TsaE 15 akal...gdv..ilLeGdLGaGKTtlvrglakalgve.ev 48
                                   k l   g v  + + G +G+GKT l+ +l+ +l+ + ++
  gi|15668618|ref|NP_247416.1| 25 RKLLnkhG-VvaFDFMGAIGSGKTLLIEKLIDNLKDKyKI 63
                                  33223322.2346789****************99876666 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.4e-05     0.082      20      60 ..      38      75 ..      29      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.4e-05
                 TrwB_AAD_bind 20 ivGttGsGKtqalekllrairargdraivlDltGafvsrfy 60
                                  ++G++GsGKt  +ekl+++++ + + a ++   G+++++f 
  gi|15668618|ref|NP_247416.1| 38 FMGAIGSGKTLLIEKLIDNLKDKYKIACIA---GDVIAKFD 75
                                  68******************9988877664...66666665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.7e-05      0.12      38      67 ..      38      66 ..      25      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.7e-05
                         AAA_7 38 lvGptGtGKtviikdllkkldkekylslti 67
                                  ++G  G+GKt++i++l+++l+ +ky+++ i
  gi|15668618|ref|NP_247416.1| 38 FMGAIGSGKTLLIEKLIDNLK-DKYKIACI 66
                                  89******************9.99988776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00022      0.28      11      38 ..      39      74 ..      38     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                        AAA_22 11 tGesGtGKTtllrrlleqldeeakaee........e 38
                                  +G  G+GKT+l+++l ++l+  +k++          
  gi|15668618|ref|NP_247416.1| 39 MGAIGSGKTLLIEKLIDNLKDKYKIACiagdviakF 74
                                  6999**************976666555544444440 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00076      0.97       4      31 ..      38      69 ..      36     100 .. 0.83
   2 ?    0.1   0.0      0.65   8.3e+02      99     141 ..     162     204 ..     156     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00076
                        AAA_33  4 lvGlpGsGKstlaerllkklg....avllssd 31
                                  + G+ GsGK+ l+e+l+ +l+       ++ d
  gi|15668618|ref|NP_247416.1| 38 FMGAIGSGKTLLIEKLIDNLKdkykIACIAGD 69
                                  78**************9999877665555555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.65
                        AAA_33  99 vrivvvetdeetlkeRlakRaangddrsevpeealdrqkarfe 141
                                   ++iv+ + d + +     k+++n  +r++++ e++   ++++e
  gi|15668618|ref|NP_247416.1| 162 DLIVINKIDLADAVGADIKKMENDAKRINPDAEVVLLSLKTME 204
                                   6778888888888888899999999999999999988888776 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00031       0.4     126     172 ..      44      89 ..      16      94 .. 0.84
   2 ?   -0.6   0.3       0.4   5.1e+02     102     164 ..     147     211 ..     132     220 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00031
                                   TSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 126 hghsekvleavkeikkkveeveviaGnvataegakaLieagadavkv 172
                                    g++  + + ++++k+k+ ++  iaG+v  +  a+++ ++ga++v  
  gi|15668618|ref|NP_247416.1|  44 SGKTLLIEKLIDNLKDKY-KIACIAGDVIAKFDAERMEKHGAKVVPL 89 
                                   5666777899********.7**********************99865 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.4
                                   STTHHHHHHHHHHTT-SEEE...EE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 102 kedalervkalveagvdvlv...vdsahghsekvleavkeikkkveeveviaGnvataegakaLie 164
                                    +d++e+   +++  +d++v   +d a++  + + ++ +  k+  ++ ev+  ++ t eg+ +++e
  gi|15668618|ref|NP_247416.1| 147 GDDTIEKHPGIMK-TADLIVinkIDLADAVGADIKKMENDAKRINPDAEVVLLSLKTMEGFDKVLE 211
                                   4556666665554.3666662335778888888888888888777778888888888888777665 PP

>> Arg_repressor_C  Arginine repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.012        16      26      46 ..      49      69 ..      42      70 .. 0.86
   2 ?    1.5   0.0      0.21   2.6e+02      24      39 ..      99     114 ..      86     115 .. 0.93
   3 ?   -0.1   0.2      0.68   8.8e+02      39      49 ..     141     151 ..     135     151 .. 0.64
   4 ?   -1.1   0.1       1.3   1.7e+03      22      36 ..     170     184 ..     158     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.012
                                  HHHHHHHH-..TTEEEEEE-S CS
               Arg_repressor_C 26 avAaaiDslelpeilGtiAGd 46
                                  ++  +iD+l+ +  + +iAGd
  gi|15668618|ref|NP_247416.1| 49 LIEKLIDNLKDKYKIACIAGD 69
                                  67789***************9 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                                   HHHHHHHHHH-..TTE CS
               Arg_repressor_C  24 AqavAaaiDslelpei 39 
                                   A++v+ a+ +l+l+ei
  gi|15668618|ref|NP_247416.1|  99 AHLVGHALEDLNLDEI 114
                                   99************98 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.68
                                   EEEEEE-SSEE CS
               Arg_repressor_C  39 ilGtiAGdDTi 49 
                                   +++t  GdDTi
  gi|15668618|ref|NP_247416.1| 141 VISTTEGDDTI 151
                                   45555677776 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.3
                                   THHHHHHHHHHH-.. CS
               Arg_repressor_C  22 GaAqavAaaiDslel 36 
                                     A+av+a i ++e 
  gi|15668618|ref|NP_247416.1| 170 DLADAVGADIKKMEN 184
                                   579999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1403.73
//
Query:       gi|15668619|ref|NP_247417.1|  [L=227]
Description: putative RNA-processing protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-17   62.3   4.7    4.9e-09   35.9   0.3    2.6  2  KH_1          KH domain
      7e-07   29.3   0.1    2.2e-06   27.7   0.1    1.9  2  KH_8          Krr1 KH1 domain
    6.5e-06   25.9   6.6    0.00081   19.2   1.9    2.9  2  KH_2          KH domain
  ------ inclusion threshold ------
      0.097   13.4   2.0       0.41   11.4   0.5    2.5  2  Ribosomal_L6  Ribosomal protein L6
       0.23   11.3  10.1       0.76    9.7   0.4    3.4  3  KH_4          KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.3   1.4e-12   4.9e-09       3      56 ..      17      64 ..      15      79 .. 0.81
   2 !   27.8   0.6   4.7e-10   1.7e-06       9      65 ..     116     164 ..     114     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.4e-12
                                  EE.EEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHH CS
                          KH_1  3 ri.lvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspea 56
                                  +i ++P++ vg +IGk+G++ k I++e g+k  ++        + +vti G+ ++
  gi|15668619|ref|NP_247417.1| 17 EIlKIPKDRVGVLIGKKGNVKKTIEKELGVKLEID-A------DGTVTIYGTDKQ 64
                                  4449**********************88*****76.3......469*****5543 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 4.7e-10
                                   GHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
                          KH_1   9 slvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkelie 65 
                                   +l gr+IGk G++ + I++ tga++ v  +       ++v i G+ e v+ Ake++e
  gi|15668619|ref|NP_247417.1| 116 RLKGRVIGKEGKSRRYIESLTGANVSVY-G-------NTVAIVGEHEPVQIAKEAVE 164
                                   567***********************87.4.......59**************9985 PP

>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   6.1e-10   2.2e-06      15      81 .]      29      95 ..      16      95 .. 0.83
   2 ?   -2.7   0.0       1.8   6.4e+03      59      79 ..     159     179 ..     157     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 6.1e-10
                          KH_8 15 lkeveekikkll.eekklklevdlkerslkvsTtekTrDPyiilkardlikLisrgvpleeakkvleD 81
                                  l +++ ++kk++ +e  +kle+d  ++++++  t+k  DP  + kard+++ i+rg + e a k++ D
  gi|15668619|ref|NP_247417.1| 29 LIGKKGNVKKTIeKELGVKLEIDA-DGTVTIYGTDKQKDPLAVWKARDIVRAIGRGFNPEIALKLVSD 95
                                  556667778888345578888886.6899*********************************999877 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.8
                          KH_8  59 ardlikLisrgvpleeakkvl 79 
                                   a++ ++++ rg++  +  k l
  gi|15668619|ref|NP_247417.1| 159 AKEAVEMLLRGASHAKTYKFL 179
                                   678899999999888877766 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.9   2.3e-07   0.00081      28      68 ..      18      58 ..       9      67 .. 0.87
   2 !    8.1   0.2   0.00064       2.3      36      65 ..     118     146 ..     116     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.3e-07
                                  EEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
                          KH_2 28 iiviresqpgivIGkgGsnikkigkelrkdieklegkkVkl 68
                                  i+ i + + g++IGk+G   k+i+kel+ ++e+  ++ V +
  gi|15668619|ref|NP_247417.1| 18 ILKIPKDRVGVLIGKKGNVKKTIEKELGVKLEIDADGTVTI 58
                                  6778899************************9888888876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00064
                                   HHHHHTGGGHHHHHHHHHHHHHHHHHHTTC CS
                          KH_2  36 pgivIGkgGsnikkigkelrkdieklegkk 65 
                                   +g+vIGk+G+  + i++  + ++  + g  
  gi|15668619|ref|NP_247417.1| 118 KGRVIGKEGKSRRYIESLTGANVS-VYGNT 146
                                   8*********99999999998885.55555 PP

>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00011      0.41      17      73 ..      29      84 ..      20      86 .. 0.77
   2 ?    0.6   0.0      0.26   9.4e+02       4      24 ..     137     156 ..     120     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                  EEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH.HHHHHHHHHHHHHHHHH CS
                  Ribosomal_L6 17 vlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv.AligtvrslinnmikGV 73
                                   +G+kg ++ +i +++ v+++  ++ +tv ++ g+dk+k    + ++r +++  ++G+
  gi|15668619|ref|NP_247417.1| 29 LIGKKGNVKKTIEKELGVKLE-IDADGTV-TIYGTDKQKDpLAVWKARDIVRAIGRGF 84
                                  57*************999976.4556665.7899999987756666777777777766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.26
                                   TEEEEEETTTEEEEEESSEEE CS
                  Ribosomal_L6   4 gvrvsikggqlvlvlGpkgel 24 
                                   g +vs+ g ++v ++G+  ++
  gi|15668619|ref|NP_247417.1| 137 GANVSVYG-NTVAIVGEHEPV 156
                                   45566665.667777766665 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4   0.00021      0.76      32      50 ..      18      36 ..       5      42 .. 0.80
   2 ?    6.3   0.1    0.0024       8.7      40      49 ..     118     127 ..     113     149 .. 0.84
   3 ?   -0.4   0.5       0.3   1.1e+03       4      26 ..     200     222 ..     197     226 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00021
                          KH_4 32 elnvegedlGrvIGkrGrt 50
                                   l++ ++ +G++IGk+G +
  gi|15668619|ref|NP_247417.1| 18 ILKIPKDRVGVLIGKKGNV 36
                                  57899999*********75 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0024
                          KH_4  40 lGrvIGkrGr 49 
                                   +GrvIGk+G+
  gi|15668619|ref|NP_247417.1| 118 KGRVIGKEGK 127
                                   6********8 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.3
                          KH_4   4 vedilkalvddpeevevteeeee 26 
                                   v ++ +++  + ee+e++e+e+e
  gi|15668619|ref|NP_247417.1| 200 VDELYEKMNPNYEEIEIEEDEDE 222
                                   66777788777888888888544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1486.66
//
Query:       gi|15668620|ref|NP_247418.1|  [L=290]
Description: hypothetical protein MJ_0444 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-61  204.9   0.5    8.2e-61  204.9   0.5    1.6  2  RIO1            RIO1 family
    0.00019   21.5   0.0    0.00053   20.0   0.0    1.6  1  APH             Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.013   14.8   0.2      0.029   13.8   0.2    1.6  1  Pkinase         Protein kinase domain
      0.015   14.9   0.1      0.089   12.4   0.0    2.1  2  Choline_kinase  Choline/ethanolamine kinase
      0.029   13.1   0.0      0.055   12.2   0.0    1.4  1  Pkinase_fungal  Fungal protein kinase
       0.15   12.3   0.6       0.78    9.9   0.1    2.0  2  Imm5            Immunity protein Imm5


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2      0.56   1.7e+03      47      68 ..      33      54 ..      11      59 .. 0.65
   2 !  204.9   0.5   2.7e-64   8.2e-61       2     184 ..      90     266 ..      89     270 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.56
                                  HHHHHHHHHHHHHHHHHHHHHT CS
                          RIO1 47 prklvklwaekEfrnLkrleea 68
                                   r+  k + ekE + L+ l++a
  gi|15668620|ref|NP_247418.1| 33 DREYQKEILEKERKFLEDLKTA 54
                                  4566666777777777777665 PP

  == domain 2  score: 204.9 bits;  conditional E-value: 2.7e-64
                                   EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTE CS
                          RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhv 82 
                                   V++a++ +    a+K+y+++t +Fk+++ky++g++rf+ r  k+++r+++++w+ekEfrnL+r++e+ +++Pk+   +++v
  gi|15668620|ref|NP_247418.1|  90 VFKARKGKF-YRAVKVYRVATCDFKTMSKYIQGDPRFHLR--KSSRRQIIHAWVEKEFRNLRRASEI-INAPKARLRRENV 166
                                   777766444.69**************************99..9************************.************* PP

                                   EEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHH.HHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHHH CS
                          RIO1  83 lvmefigedgvaapklkdveeeeeaeelyeevle.emrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnale 162
                                   lvm+f+g +g++apklkd++  + + e y ++++ +m+kly+e +lvH+DLSeyN+lv++d++v+ID+sQ+v ++hp a+ 
  gi|15668620|ref|NP_247418.1| 167 LVMDFVGYRGIPAPKLKDMQ--DLDWEKYFKIIKeSMKKLYEEGELVHGDLSEYNILVKDDEPVFIDFSQSVITQHPLAHP 245
                                   ********************..55556666666559********************************************* PP

                                   HHHHHHHHHHHHHHTTC----- CS
                          RIO1 163 fLerDveniikfFrrkgvekvd 184
                                   +L rD+ ni++fFrrk v+ ++
  gi|15668620|ref|NP_247418.1| 246 LLIRDCINICNFFRRKRVD-CN 266
                                   ****************998.44 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.8e-07   0.00053     164     196 ..     206     235 ..     175     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-07
                                   S-EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                           APH 164 lptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                                   ++  l+HgDl+  N+lv+ dd +v  +iDf  +
  gi|15668620|ref|NP_247418.1| 206 EEGELVHGDLSEYNILVK-DDEPV--FIDFSQS 235
                                   55669*************.99999..****655 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   9.6e-06     0.029      73     144 ..     165     234 ..      79     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.6e-06
                                   EEEEEE--TTEBHHHHHH.HHSS--HHHHHHHHHHHHHHHHHHHHTT.EE-SS-SGGGEEEETTTEEEE-SGTT CS
                       Pkinase  73 lylvleyveggeladlle.rkgslseeeakkiakqilegleylHskg.iiHrDlKpeNiLidekgelKitDFGl 144
                                    +lv+++v       +   + + +++ + +k++k i e+++ l+++g ++H Dl   NiL++ ++e   +DF  
  gi|15668620|ref|NP_247418.1| 165 NVLVMDFVGYR---GIPApKLKDMQDLDWEKYFKIIKESMKKLYEEGeLVHGDLSEYNILVK-DDEPVFIDFSQ 234
                                   44577777633...2222122348888999**************8887**************.77777788865 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.25   7.4e+02      91     127 ..     109     144 ..      74     169 .. 0.77
   2 ?   12.4   0.0     3e-05     0.089     118     171 ..     184     232 ..     177     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.25
                                   -HHHHHHHHHHHCCS.TT..ECHHGGCCHCCCTHHHH CS
                Choline_kinase  91 pslwktmqkwllnkeaqtkakkekkkkqlklinledl 127
                                   ++ +ktm k+ ++++ + + +k+++++ ++ +  +++
  gi|15668620|ref|NP_247418.1| 109 TCDFKTMSKY-IQGDPRFHLRKSSRRQIIHAWVEKEF 144
                                   5668999999.77777788888887777776654444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3e-05
                                   CHCCCTHHHHHHHHHTHHHHHHCHGG-EEEE-S--SGGGEEE.-CTTEEEE--G CS
                Choline_kinase 118 qlklinledlekelekleklleelespvvfcHnDlqegNillnkeekklvlIDF 171
                                    ++ +++e++ k ++   + +++l+++  + H Dl e Nil+  ++++ v+IDF
  gi|15668620|ref|NP_247418.1| 184 DMQDLDWEKYFKIIK---ESMKKLYEEGELVHGDLSEYNILV--KDDEPVFIDF 232
                                   455555555555555...5555667777888***********..888889***9 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.9e-05     0.055     320     344 ..     202     226 ..     196     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                Pkinase_fungal 320 rsLflkagiLHrDiSenNilitdsk 344
                                   ++L+++++++H D Se+Nil+ d++
  gi|15668620|ref|NP_247418.1| 202 KKLYEEGELVHGDLSEYNILVKDDE 226
                                   79*******************9764 PP

>> Imm5  Immunity protein Imm5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00026      0.78      40     119 ..       1      81 [.       1      95 [. 0.79
   2 ?    0.4   0.1      0.22   6.5e+02       4      27 ..     115     138 ..     112     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00026
                          Imm5  40 ecvkkvlplweevfaedqsplrlLekaedylyektdkeeiekeadklsndlen.dsgeeaeetvalaglaAlkvivtliys 119
                                   + + kv+p++++   e  ++++lL++ e++ +++  ++ei ++  k+ +dl+  +++ ++++ + l  l A k +++ i  
  gi|15668620|ref|NP_247418.1|   1 MSCYKVMPIAKNIDDELYELNKLLSEKEEFQLDREYQKEILEKERKFLEDLKTaNEVFDKRTLMTLFSLLAGKHLTEYIGI 81 
                                   5799*******98888899**************888888888888899999887777777777777778888887776644 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.22
                          Imm5   4 lkeeveqspkGhLsLplRvkllra 27 
                                     + ++ +p  hL  ++R++++ a
  gi|15668620|ref|NP_247418.1| 115 MSKYIQGDPRFHLRKSSRRQIIHA 138
                                   6788999**************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1902.63
//
Query:       gi|15668621|ref|NP_247419.1|  [L=102]
Description: translation initiation factor IF-1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-22   78.7   2.6    2.7e-22   78.3   1.5    1.7  2  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.13   2.3e+03      24      34 ..       7      17 ..       3      19 .. 0.71
   2 !   78.3   1.5   1.5e-26   2.7e-22       1      64 []      20      83 ..      20      83 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.13
                                  SSBEEEEE-HH CS
                        eIF-1a 24 gkevlaeipgk 34
                                  ++++ ++ip+k
  gi|15668621|ref|NP_247419.1|  7 EQQIRVRIPRK 17
                                  56777888876 PP

  == domain 2  score: 78.3 bits;  conditional E-value: 1.5e-26
                                  EEEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-.TTEEEEES- CS
                        eIF-1a  1 gevigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspyd.ltkGrIvyr 64
                                  +e+ g+++++lg +++rV++ d gk++l++ipg+++n+iw+++Gd+V+V++++ + ++k++I++r
  gi|15668621|ref|NP_247419.1| 20 NEILGIIEQMLGASRVRVRCLD-GKTRLGRIPGRLKNRIWVREGDVVIVKPWEVQgDQKCDIIWR 83
                                  6899****************96.*******************************9555*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 739.08
//
Query:       gi|15668622|ref|NP_247420.1|  [L=361]
Description: FO synthase subunit 1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-12   48.6   0.1      2e-12   47.8   0.1    1.5  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.1   1.1e-16     2e-12       2     164 ..      47     217 ..      46     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.1e-16
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC....... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla....... 74 
                                   + +++C+++C +C+++e     +++  + + e++e++ ++  + g  + ++ +g +++ ++++ e l+ +           
  gi|15668622|ref|NP_247420.1|  47 PLSKWCRNKCGYCIFRE-----DKPSLMKPNEVKEILLKG-DRLGcREALFTFGEHVDENKEIKEQLKSMGYDNileylyd 121
                                   6789************5.....9*****************.7***777777778888888999999999888889999999 PP

                                   .....CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH....HHHHHHTCTSHHHHHHHHHHHHHHTTSETEE CS
                                   .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  75 .....vpgiritvetngtlpdeeklerllelgvdrvslgleaadde....kvlklmnrghtfeevlealeklreagikrvv 146
                                         ++ ++   tn + ++ + l+ l++ +   + l le a+++      +k+  +g+ ++ ++e +e++ ++ i+  +
  gi|15668622|ref|NP_247420.1| 122 leewtLNNTSLLPHTNCGILNYDELKMLKDVN-ASMGLMLENASERlmntIAHKHS-PGKHPKLRIEMIENAGKLKIP-FT 199
                                   9999999*********99999*********99.***************96666666.*********************.** PP

                                   EEEEEBTTTSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 147 drivglpGendeeleell 164
                                   ++++++ Ge+ ee+++ l
  gi|15668622|ref|NP_247420.1| 200 TGLLIGIGETNEEIVDSL 217
                                   **************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2403.85
//
Query:       gi|15668623|ref|NP_247421.1|  [L=161]
Description: hypothetical protein MJ_0447 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.099   11.0   0.4       0.12   10.7   0.4    1.1  1  Glyco_hydro_1  Glycosyl hydrolase family 1
       0.12   12.2   1.2       0.17   11.7   0.2    1.8  2  FrhB_FdhB_C    Coenzyme F420 hydrogenase/dehydrogenase, beta 


Domain annotation for each model (and alignments):
>> Glyco_hydro_1  Glycosyl hydrolase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4   1.4e-05      0.12     270     363 ..      58     154 ..      36     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.4e-05
                                   ..S----HHHHHHHTT--SEEEEEEEEEEEEEE--...-STT---SSGGGGG-SBSS-B-SSSS-B-.HHHHHHHHHHHHH CS
                 Glyco_hydro_1 270 galpeiteedkellkgkadflglnyYtsrlvknkeseeaslskteekkleeevdpslpktdigwiie.peglrkllellkk 349
                                    +++ i+++d + +++ + f g n Y ++l     s++ + s t +   + ++ +++++ + +  +   ++ +k l++lk+
  gi|15668623|ref|NP_247421.1|  58 KIKQLIEDKDIKEIAKLNLFCGNNVYEEMLKDILSSNKFI-SLTISFDENIAYVKYMERGKEEVVYLdGKSAYKALQILKN 137
                                   567889***********99***999998887776644443.3333334444444566665555555459************ PP

                                   TS--...--EEEEE--- CS
                 Glyco_hydro_1 350 eYqk...lpiyiteNGl 363
                                   +Y++   ++i i e  +
  gi|15668623|ref|NP_247421.1| 138 RYENilkKQISIIEDAI 154
                                   ***97767788887665 PP

>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.18   1.6e+03      53      76 ..       9      32 ..       3      53 .. 0.58
   2 ?   11.7   0.2   1.8e-05      0.17      11      76 ..      54     124 ..      49     153 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.18
                   FrhB_FdhB_C 53 gvdpedvkklefrgkgkfrvelkd 76
                                  + + ++ k+ e+r+kgk ++e + 
  gi|15668623|ref|NP_247421.1|  9 KQKINEWKNREWRWKGKGKIEIRF 32
                                  344455555666544777776555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.8e-05
                   FrhB_FdhB_C  11 CqiaalrklqkkklkekilltiglfCggnfspealrklleelgvdpe......dvkklefrgkgkfrvelkd 76 
                                   C+ + +++l + k+ ++    + lfCg n++ e+l+++l ++++ +       ++  +++++ gk +v + d
  gi|15668623|ref|NP_247421.1|  54 CEYEKIKQLIEDKDIKE-IAKLNLFCGNNVYEEMLKDILSSNKFISLtisfdeNIAYVKYMERGKEEVVYLD 124
                                   55555555555344444.899****************88776643222334448888888855655554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1287  (0.0717831); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1208.04
//
Query:       gi|15668624|ref|NP_247422.1|  [L=256]
Description: hypothetical protein MJ_0448 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-09   38.1   0.0    2.1e-09   37.7   0.0    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.6e-07   30.3   0.0    3.8e-07   29.8   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00012   22.0   0.0    0.00018   21.4   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.082   12.3   0.0       0.13   11.7   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   4.6e-13   2.1e-09       6      98 ..      19     109 ..      16     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 4.6e-13
                                   SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHH CS
                   Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmee 86 
                                   ++s lie +++ iL+D+G  + + r+ l   +l  + +  d+++l+H+H+DH+ gl++++e   ++  + a++++ l + +
  gi|15668624|ref|NP_247422.1|  19 GFSALIEINNKRILFDAGQNSITLRENL---RLFNEKEGFDYIVLSHGHYDHCDGLKYVIENDLINGKVIAHKDAFLDKYA 96 
                                   6899**********************98...999999***********************998888888888888887777 PP

                                   HHHHHHHCCHH.T CS
                   Lactamase_B  87 addaasrkgll.l 98 
                                   ++++ + ++ +  
  gi|15668624|ref|NP_247422.1|  97 GNRYIGIDEEIkE 109
                                   7776666555553 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   8.4e-11   3.8e-07       2      66 ..      30      90 ..      29     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 8.4e-11
                                  EEEES--TT...HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EEEEEEEEHHH CS
                 Lactamase_B_2  2 riLiDagpd...lrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkklplyapkgv 66
                                  riL+Dag +   lr++ lr+       +  +  d ++l+h+HyDH+ gl  + e   +   + +++a+k+ 
  gi|15668624|ref|NP_247422.1| 30 RILFDAGQNsitLREN-LRLF----NEK--EGFDYIVLSHGHYDHCDGLKYVIEndlI---NGKVIAHKDA 90
                                  9********8877777.7776....334..59*****************999994422...2457777655 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0     4e-08   0.00018       9      51 ..      21      69 ..      18     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4e-08
                 Lactamase_B_3  9 sflletagarilvDPf......kanlgyeppaeeaDlvlisqaledHah 51
                                  s l+e++++ril D +      ++nl + +++e  D +++s+++ dH++
  gi|15668624|ref|NP_247422.1| 21 SALIEINNKRILFDAGqnsitlRENLRLFNEKEGFDYIVLSHGHYDHCD 69
                                  789***********997777665577888888****************7 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.9e-05      0.13       1      58 [.      23      77 ..      23      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.9e-05
                 Lactamase_B_6  1 lLeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyak 58
                                  l+e++n +iL D G+++ ++  ++ l+ l +  +  d i+Lsh   +h  ++ +++ +
  gi|15668624|ref|NP_247422.1| 23 LIEINNKRILFDAGQNSITL--RENLR-LFNEKEGFDYIVLSHGHYDHCDGLKYVIEN 77
                                  799*************9865..55665.4556689***************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1611.14
//
Query:       gi|15668625|ref|NP_247423.1|  [L=283]
Description: hypothetical protein MJ_0449 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-48  163.7  17.3    4.8e-48  163.5  17.3    1.0  1  Cation_efflux  Cation efflux family
    1.1e-15   57.5   3.7    2.1e-15   56.6   3.7    1.5  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
       0.13   12.3   0.4       0.54   10.4   0.0    2.2  2  RinB           Transcriptional activator RinB
        2.2    8.1  15.9       0.38   10.5   1.0    3.9  3  PAP2           PAP2 superfamily


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.5  17.3   1.1e-51   4.8e-48       1     198 [.       8     200 ..       8     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 163.5 bits;  conditional E-value: 1.1e-51
                 Cation_efflux   1 lilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllgl 81 
                                   lils++ n++l l+++i g++  S +l++d++hslsd+++++++++++k+++kppde +p+G+ r+e l++++ gl l+++
  gi|15668625|ref|NP_247423.1|   8 LILSIVGNILLGLIKIIIGYVYSSISLISDGIHSLSDVITSIIGIIGVKIASKPPDESHPYGHSRFECLFSFFIGLALFFT 88 
                                   79******************************************************************************* PP

                 Cation_efflux  82 avfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalvill 162
                                   a+ +   a++++i  ge  + ++++++va++s+vv+ ++ ++  ++g+kl+s++l a+a+h+++Dal+s++vlv++l++++
  gi|15668625|ref|NP_247423.1|  89 AYEIGKFAVERII-YGEVIEVNAIMVGVAILSIVVKELMTRYSLFVGKKLNSQVLIADAYHHRSDALSSVVVLVGLLLQKF 168
                                   *************.9****************************************************************** PP

                 Cation_efflux 163 fnlksgplaDpvaslligliilysalkllkeslseL 198
                                   + ++     D++a+++++l+i++ a++++ +++  L
  gi|15668625|ref|NP_247423.1| 169 GIYY----GDAIAGIIVALMIAKVAFDICLTNIDYL 200
                                   8555....7********************9999877 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   3.7   4.8e-19   2.1e-15       4      77 ..     208     280 ..     205     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 4.8e-19
                                   .HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEE CS
                      ZT_dimer   4 eeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHve 77 
                                   +  e i++ +++v++v+gvhd++++++G++i+v+lh+ev+ ++s ke H+i  +v++r++ ++++v++ ++Hv+
  gi|15668625|ref|NP_247423.1| 208 KFFELIEKEALNVDKVIGVHDIKAHYVGPRIHVELHVEVPSNISAKEMHDIEVAVKNRLE-SLENVERAYVHVD 280
                                   556778999999***********************************************5.889*********8 PP

>> RinB  Transcriptional activator RinB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00012      0.54       4      23 ..      81     100 ..      80     105 .. 0.88
   2 ?   -2.2   0.1         1   4.6e+03      11      25 ..     127     143 ..     122     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                          RinB   4 lkLlfllaaleLvKkvvEsl 23 
                                   + L ++ +a+e++K +vE +
  gi|15668625|ref|NP_247423.1|  81 IGLALFFTAYEIGKFAVERI 100
                                   56889*************87 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                          RinB  11 aaleL..vKkvvEsllv 25 
                                   + + L  +Kk   ++l+
  gi|15668625|ref|NP_247423.1| 127 TRYSLfvGKKLNSQVLI 143
                                   44444338999999998 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.0   8.6e-05      0.38      91     121 ..      23      52 ..      14      60 .. 0.81
   2 ?    3.8   1.6      0.01        47      54     116 ..      64     156 ..      56     168 .. 0.48
   3 ?    0.5   0.5      0.11   4.8e+02     111     129 ..     173     191 ..     170     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.6e-05
                          PAP2  91 llllavlvalsRlylgvHflsDvlaGlliGi 121
                                   +++  v+ ++s +++g+H lsDv+++ +iGi
  gi|15668625|ref|NP_247423.1|  23 IIIGYVYSSISLISDGIHSLSDVITS-IIGI 52 
                                   567778889****************9.4554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.01
                          PAP2  54 esfPSgHs....afafalalllalllrrkrkkig..........................lvllalillllavlvalsRly 104
                                   es P gHs    +f+f++ l+l+++  +  k+                             +++   l++   l +   ++
  gi|15668625|ref|NP_247423.1|  64 ESHPYGHSrfecLFSFFIGLALFFTAYEIGKFAVeriiygevievnaimvgvailsivvkELMTRYSLFVGKKLNSQVLIA 144
                                   555556663333233332222222222222222244555555555555555555444444444444444444455555556 PP

                          PAP2 105 lgvHflsDvlaG 116
                                   + +H++sD l +
  gi|15668625|ref|NP_247423.1| 145 DAYHHRSDALSS 156
                                   666666666655 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.11
                          PAP2 111 sDvlaGlliGialaalayr 129
                                    D +aG+++++++a +a+ 
  gi|15668625|ref|NP_247423.1| 173 GDAIAGIIVALMIAKVAFD 191
                                   699********99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 2044.67
//
Query:       gi|15668626|ref|NP_247424.1|  [L=186]
Description: inosine monophosphate dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.8e-18   65.7   6.4    2.8e-13   50.1   0.2    2.4  2  CBS          CBS domain
  ------ inclusion threshold ------
      0.013   15.0   0.1      0.018   14.6   0.1    1.2  1  m04gp34like  Immune evasion protein
      0.056   12.9   0.1      0.085   12.3   0.1    1.3  1  DUF99        Protein of unknown function DUF99


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.5   4.9e-07     0.003       3      55 ..       4      62 ..       2      64 .. 0.83
   2 !   50.1   0.2   4.7e-17   2.8e-13       1      54 [.      74     126 ..      74     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.9e-07
                                  HH....SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHHHH CS
                           CBS  3 di....mtrdvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllral 55
                                  +i      +++++v+ d ++ ++++lm+e +v +++VV    +++ + + t++D+++++
  gi|15668626|ref|NP_247424.1|  4 EIpvllIMKKPIVVSGDVSVYDVAKLMVEQDVPCVLVVceRPNHESIEVATDKDIIKKV 62
                                  544445446777************************999844668***********986 PP

  == domain 2  score: 50.1 bits;  conditional E-value: 4.7e-17
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                   V+di + ++vt+pp+tt+ eale+m +++ + l++V +dgk+vG++t++Dl++ 
  gi|15668626|ref|NP_247424.1|  74 VEDISSGKLVTIPPNTTIDEALEIMNKYKTNELFIV-DDGKIVGVITEEDLIKI 126
                                   78998999*****************88889******.6*************985 PP

>> m04gp34like  Immune evasion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1     3e-06     0.018     146     195 ..      18      65 ..      14     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-06
                                   ST-EEE-TTS-.HHHHTTEEEEEEEEEEES-TT--..S--HHHHHHTHHH CS
                   m04gp34like 146 tGnLyvysnatreksaddvrCrLrvClwttkdslsdrsddeeavknlsev 195
                                   +G++ vy+ a+    ++dv C+L vC + +++s+   ++d++++k+    
  gi|15668626|ref|NP_247424.1|  18 SGDVSVYDVAK-LMVEQDVPCVLVVCERPNHESIE-VATDKDIIKKVLIR 65 
                                   49999999999.699*************9999999.66788888876544 PP

>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.4e-05     0.085      79     163 ..      21     102 ..       5     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                                   TEE--HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT.....EEEEEESS-HHHHHHH CS
                         DUF99  79 FNvvDlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevek.tgeelyvravGieleeaakl 158
                                     v+D+ +l+ e ++P++ v+ e+p+ +++e a     +++  +  li+kl++   +ve+ ++++l+      + +ea ++
  gi|15668626|ref|NP_247424.1|  21 VSVYDVAKLMVEQDVPCVLVVCERPNHESIEVAT----DKDIIKKVLIRKLPPDKVKVEDiSSGKLVTIPPNTTIDEALEI 97 
                                   4689**********************77666555....4566666778888666655555577778888888888888888 PP

                                   HHHC- CS
                         DUF99 159 vrklt 163
                                   ++k+ 
  gi|15668626|ref|NP_247424.1|  98 MNKYK 102
                                   88775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1221.20
//
Query:       gi|15668627|ref|NP_247425.1|  [L=226]
Description: phosphoribosylanthranilate isomerase TrpF [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-32  112.3   0.3      3e-32  112.0   0.3    1.1  1  PRAI      N-(5'phosphoribosyl)anthranilate (PRA) isomerase


Domain annotation for each model (and alignments):
>> PRAI  N-(5'phosphoribosyl)anthranilate (PRA) isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   0.3   1.7e-36     3e-32       1     193 [.       8     221 ..       8     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 1.7e-36
                                   TCE----SHHHHHHHHHHTSSEEEEE--.TTBTTB--HHHHHHHCCCS--E..EEEEESSS-HHHHHHHHHHCTECEEEE- CS
                          PRAI   1 akicgltrasdvkaavkagadelglifa.esskrevseeqaqellekvpak..lVGVfvNqpieevlriaqelgldvvQLH 78 
                                   +kicg+t+ +d++ ++k+  + + ++++ ++++r++s  +a el+++v +   lV V + ++ieevl+i++ l+ +++QLH
  gi|15668627|ref|NP_247425.1|   8 VKICGITNEEDIAYISKKVHAVGVIVDVpVKTPRKISLDKAIELKKYVAPFtsLVTVLMPNSIEEVLEIYNALKPNAIQLH 88 
                                   69***********9999888554444442579***************984447**************************** PP

                                   CGG.-...HHHHHHHHH...HS-TTSEEEEEEE-S.....SS--S-SSTT-.SEEEEE....SSS-SSSXXXXGGGGTTSX CS
                          PRAI  79 Gdede...qeyeellkt...elpvikalkvaesvd.....evkearradhv.dllllD....sgaGGtGelldwsliskll 143
                                   G e+    +e+ +l++t   +  +ik ++ +++ +       + a+++++  +++l+D    s    +G++ +w + +kl+
  gi|15668627|ref|NP_247425.1|  89 GFESLdfvKELNKLKNTgelNAHIIKVIHIPKDEEidfktLLNTAKEYEKYvEAILVDtkieS-IKLEGKTHNWAVSKKLR 168
                                   *9943112344444443222578888888777655547665666777766559*****99854.44499**********99 PP

                                   X...TTEEEESSXXTTTHHHHHT.TXXSEEEEXGGGEEE.TEEXHHHHHHHHH CS
                          PRAI 144 ks..lkviLAGGLtpeNvaeaiklegvlgvDvssGVEtn.GvkDlekirkfvq 193
                                   +s  +++iLAGGL+ +Nv eaik+ +++++Dvss+ E++ G+kDl+k+ +f++
  gi|15668627|ref|NP_247425.1| 169 ESleKPLILAGGLNKDNVLEAIKTVKPYAIDVSSSLEAYgGKKDLKKVDEFLE 221
                                   9999**********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1312.96
//
Query:       gi|15668628|ref|NP_247426.1|  [L=148]
Description: hypothetical protein MJ_0452 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-46  157.4   0.0    3.2e-46  157.2   0.0    1.0  1  DUF1890   Domain of unknown function (DUF1890)
  ------ inclusion threshold ------
       0.13   12.3   0.0        0.2   11.7   0.0    1.4  1  PAS_8     PAS domain


Domain annotation for each model (and alignments):
>> DUF1890  Domain of unknown function (DUF1890)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.2   0.0   3.6e-50   3.2e-46       1     139 []       5     144 ..       5     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: 157.2 bits;  conditional E-value: 3.6e-50
                                   EEE---S-STTHHHHHHHHHHHHHCTTEEEEEEE-HHHHHHHHHHSTT-SS-SEE..EEHHHHHHH--TTS-SEEEEEESS CS
                       DUF1890   1 lillGCPevPvqtplalylanklkkkgievvvagnpaalkLlkvaDpekhYvkel..vdldkaleeieekdvdlllgfvhn 79 
                                   l+++GCPe+P+ +p++lyl+n+lkkkg++v++a+npaalkLl+vaD++k+Y+k +  vd+d  l+ ie   ++ +++fvhn
  gi|15668628|ref|NP_247426.1|   5 LVIVGCPEPPALIPSVLYLTNQLKKKGFNVIIAANPAALKLLEVADDDKYYLKGVgaVDIDGGLRGIE--GINKIISFVHN 83 
                                   79****************************************************999***********..9********** PP

                                   HHHHHHHHHHHHHH-.SEEEEEEE-S-HHHHHHHHHH....--EEEEE--SS--HHHHHHHHHH CS
                       DUF1890  80 Dagvsyavtlkavlnkakliaivfgkdaeelaelief....daeviaaravHnpkplkkkldev 139
                                   D+gvsy+vt+ka +n + ++aivfg+++++  +++e+    ++ v++ara+Hnp+p++++++e+
  gi|15668628|ref|NP_247426.1|  84 DGGVSYTVTYKAKYN-KPTYAIVFGRQINK--DYVETlknsNIGVYTARAFHNPMPIVNRIKEI 144
                                   ************999.**********9987..444444545********************986 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.2e-05       0.2      22      42 ..      34      54 ..       6      77 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                         PAS_8 22 rivdvNqaalellGysadlkg 42
                                   i+ +N+aal+ll + +d+k 
  gi|15668628|ref|NP_247426.1| 34 VIIAANPAALKLLEVADDDKY 54
                                  4************98866554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 958.90
//
Query:       gi|15668629|ref|NP_247427.1|  [L=107]
Description: hypothetical protein MJ_0453 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-32  109.2   2.0    1.2e-31  108.9   2.0    1.1  1  DUF1894   Domain of unknown function (DUF1894)


Domain annotation for each model (and alignments):
>> DUF1894  Domain of unknown function (DUF1894)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.9   2.0   6.5e-36   1.2e-31       1      83 [.       1      81 [.       1      91 [. 0.93

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 6.5e-36
                                  B---HHH--S-SS-EEESSHHHHHHHHTTSEEEEES--EEES.SS---SS----EEEE--S-EEEE---SS-EEEEE-SS-GG CS
                       DUF1894  1 maCleklkyeillkeasfkeceeyikkkakevyevepgykil.gvrliGvppipvgideekilfpytkPCyGtfvlkvkesee 82
                                  m+C++kl+yeil k  +fkec+eyi+k++k++ e+e+gy+i+ g+ liG+ppipv+++++ ++fpytkPCyGtfvlk++   +
  gi|15668629|ref|NP_247427.1|  1 MGCIDKLNYEILYK-GGFKECAEYIRKNFKNIKEMEAGYEIFeGIFLIGIPPIPVAYEDNYVIFPYTKPCYGTFVLKINL--D 80
                                  89***********9.99*************************************************************43..3 PP

                                  G CS
                       DUF1894 83 e 83
                                  e
  gi|15668629|ref|NP_247427.1| 81 E 81
                                  3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 706.53
//
Query:       gi|15668630|ref|NP_247428.1|  [L=329]
Description: translation initiation factor aIF-2B subunit delta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-88  296.2   0.0    2.5e-88  295.9   0.0    1.1  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.9   0.0   1.4e-92   2.5e-88       2     282 .]      49     319 ..      48     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 295.9 bits;  conditional E-value: 1.4e-92
                                   S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHHH CS
                         IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksliek 82 
                                   vrG+pai+++a+++l+ +  + +         ++ ka+++Lk++rPtav+l++a++r+l+            +  ks++++
  gi|15668630|ref|NP_247428.1|  49 VRGAPAIGVSAAYGLALAEINGD---------DIYKAYEVLKNTRPTAVNLFWALDRCLT----------AYKEGKSILDE 110
                                   89*************99988888.........9***************************..........5678899**** PP

                                   HHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH.HTHHHHH CS
                         IF-2B  83 ikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG.rltakeL 154
                                   +k++++e+ e+++kig i+++li+dgdtilT+cn+++        +l+v+r a  ++kk++Vi+ E+rPrlqG +lta eL
  gi|15668630|ref|NP_247428.1| 111 AKKIHEEDIETCKKIGMIGEKLIEDGDTILTHCNAGAlatsaygtALSVIRFAFYNGKKIRVIADETRPRLQGaKLTAFEL 191
                                   ********************************************************************************* PP

                                   HHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSX CS
                         IF-2B 155 vqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedifi 234
                                   +++gipv++itd++++++m++ e+dk+ivGAdril++G+++nkiGT+slAvlAk ++ip++v+a++++f+ r + +ed++i
  gi|15668630|ref|NP_247428.1| 192 NYEGIPVKVITDNTAGFLMQKgEIDKIIVGADRILADGTVYNKIGTYSLAVLAKYHRIPFYVAAPLSTFDLR-SSEEDVII 271
                                   ************************************************************************.99999*** PP

                                   XBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                         IF-2B 235 eerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                   eerd++e+++i+g+ri++e + ++n+afD tPp+lIt+iITe+G+++p
  gi|15668630|ref|NP_247428.1| 272 EERDEKEVAYIDGVRIVPEGVGCYNYAFDKTPPDLITAIITEKGIVKP 319
                                   *********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2611.40
//
Query:       gi|15668631|ref|NP_247429.1|  [L=193]
Description: hypothetical protein MJ_0455 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-62  207.7   6.0    9.2e-62  207.3   6.0    1.1  1  DUF1847         Protein of unknown function (DUF1847)
  ------ inclusion threshold ------
       0.16   12.3   4.4      0.071   13.4   2.0    1.7  2  T3RM_EcoP15I_C  Type III R-M EcoP15I C-terminal domain


Domain annotation for each model (and alignments):
>> DUF1847  Protein of unknown function (DUF1847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.3   6.0     1e-65   9.2e-62       6     157 .]      18     165 ..      12     165 .. 0.96

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 1e-65
                       DUF1847   6 ekeileealeeykdeeekkiakaaaeveaegyakltRveeiiefakrmgykkiGiafCvglleeakalakileakgfevvs 86 
                                   +k+i+++++eeyk+ee+ kia+++a +ea++y+k+tR+eeiief+k m+ykkiGiafC+gl +eak+lakil+++ fev+s
  gi|15668631|ref|NP_247429.1|  18 KKDITQKIIEEYKKEENLKIAEVSAYIEATYYMKKTRLEEIIEFCKLMEYKKIGIAFCIGLENEAKILAKILSKH-FEVYS 97 
                                   57899*******************************************************************765.***** PP

                       DUF1847  87 viCkvgsvdkeelgieeeekvkkkkkeamCnPilQAellneaktdlnvvlGLCvGhDslfikyseapvttL 157
                                   v+Ckv+++dk+ ++ ++ +   k++keamCnPi QAe+lne +tdln+++GLC+GhD+lf kys+ap+tt+
  gi|15668631|ref|NP_247429.1|  98 VCCKVCGIDKDVFKFKKIN---KGEKEAMCNPIGQAEILNEIGTDLNIIVGLCIGHDILFQKYSKAPTTTF 165
                                   ************9998866...7**********************************************96 PP

>> T3RM_EcoP15I_C  Type III R-M EcoP15I C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.0   7.9e-06     0.071      32      89 ..       3      60 ..       1      70 [. 0.87
   2 ?   -3.1   0.0       1.1     1e+04       8      22 ..     163     177 ..     162     190 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-06
                T3RM_EcoP15I_C 32 ayliekkLYliekglesealkaLiekldedkefniekivlfgysfeskelreleenlk 89
                                  +  ++kkL    k+++++ ++++ie+++++++++i ++ ++ ++  + ++  lee ++
  gi|15668631|ref|NP_247429.1|  3 CSQCNKKLCYTGKDCKKDITQKIIEEYKKEENLKIAEVSAYIEATYYMKKTRLEEIIE 60
                                  67899999999******************************99988888888887665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.1
                T3RM_EcoP15I_C   8 ttwlvkDgygltekv 22 
                                   tt++vkD +  ++++
  gi|15668631|ref|NP_247429.1| 163 TTFIVKDRVLSHNTA 177
                                   567777755444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1339  (0.0746835); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1290.36
//
Query:       gi|15668632|ref|NP_247430.1|  [L=352]
Description: hypothetical protein MJ_0456 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-24   85.9  25.1    2.7e-24   85.9  25.1    2.0  2  CitMHS    Citrate transporter


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9  25.1   1.5e-28   2.7e-24      14     274 ..      12     284 ..       5     290 .. 0.75
   2 ?   -0.5   5.3     0.031   5.5e+02     118     168 ..     292     341 ..     287     351 .. 0.62

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.5e-28
                                   xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS  14 vallvlvll..vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrdllvllvlltallsafvsnd 92 
                                   +++ +l+ll  ++ ++e++  + + +i+ l+ +m+i++++ +t + d+++ k+l+++++   ++++l++lt +ls++++nd
  gi|15668632|ref|NP_247430.1|  12 ISIGILLLLlnIINPMEVFHIVEWKTIFSLFYLMVIINIMRDTKFLDYISLKILKKSKR---IFIALIFLTLFLSSLITND 89 
                                   44544455578***********************************************9...8****************** PP

                                   xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                        CitMHS  93 gvvlimipivlslakrlkklppl....lliplalaaniggaltpiGtpttraaarpglslpnlll................ 153
                                   + + ++ip++l + +  +++p      l+i  +++anig+ ltpiG+p            +nl l                
  gi|15668632|ref|NP_247430.1|  90 VSLFVIIPLTLIIHR-YTNMPFKdlekLIIFEGVSANIGSGLTPIGNP------------QNLFLfhfynigtlefiinmi 157
                                   ************999.6*****9*************************............777777777766666655555 PP

                                   .................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS 154 .................................lalllvgllplvllfmfgvalalpvnapkvkkqkaiieaiarsllpva 201
                                                                    +  +l ++l+l+++f          n+                +lp +
  gi|15668632|ref|NP_247430.1| 158 pfeifgilailpflefkkydtkinidikfkkewIFYILSFILVLLCVF-------GYLNF--------------IYILPLI 217
                                   455444333333333333333333333333333222333333333333.......11222..............3466666 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS 202 tilllaykkveWsvlllfaGvfll..vgaleqtGilealadllgaggplvalalvlgliallsafisnvavaalm 274
                                   +++ l+yk+v+ + l+l++ +fl+   ++l++ Gi++ ++      g+ v   ++++  +lls++isnv++++l+
  gi|15668632|ref|NP_247430.1| 218 LAI-LMYKRVKVDYLFLLTFIFLFvdIEGLKRIGIINIFSIKC---GN-V---MLMIYASLLSQIISNVPATVLL 284
                                   666.558888888888888888886689**********98555...34.2...56888999**********9887 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.031
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxx RF
                        CitMHS 118 iplalaaniggaltpiGtpttraaarpglslpnlll...............lalllvgllplvllf 168
                                   +p+a++ nigg  t+i                nl+                +     g+++++ l+
  gi|15668632|ref|NP_247430.1| 292 LPIAYGVNIGGNGTLIASF------------ANLITlrlsngnvrvgrfllI----GGIIYIMHLI 341
                                   69************99999............776665555555555543331....3333322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2167.64
//
Query:       gi|15668633|ref|NP_247431.1|  [L=410]
Description: diaminopimelate aminotransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-36  125.9   0.0    2.1e-36  125.6   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    3.8e-16   58.9   0.4      2e-15   56.7   0.0    2.2  3  M20_dimer      Peptidase dimerisation domain
    7.3e-05   22.5   0.0    0.00013   21.8   0.0    1.4  1  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.6   0.0   3.5e-40   2.1e-36       2     205 ..      84     409 ..      83     410 .] 0.89

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 3.5e-40
                                   EEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.THHHH CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                 Peptidase_M20   2 lgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.gGaka 80 
                                   + sHlD+Vpe++ + w t p+++ ++dGk+yGrG+ d+  g+++ l +l+ + +++i+pk+++ l+f+ dEE g+  G k+
  gi|15668633|ref|NP_247431.1|  84 IISHLDTVPEGDISLWGTnPYEPVIKDGKIYGRGSEDNHKGIVSSLLLLKMIFENNIEPKYNLSLIFVSDEEDGSeYGLKY 164
                                   569******9999***********************************************************7777***** PP

                                   HHHHHH.TTTCESEEEEEEEESSSBTCHSTETEEEE............................................. CS
                                   xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
                 Peptidase_M20  81 llegle.erekvdavfelhieepgileagklaigvv............................................. 115
                                   ll+++e e +k d +  +++ + g +  g+  + ++                                             
  gi|15668633|ref|NP_247431.1| 165 LLNNFEdEIFKKDDL--IIVPDFGTPT-GE-FVEIGekgilwikfnikgkqchgstpenglnadivafnfanelynglyek 241
                                   ***999775555553..3555555555.33.344445577777788889999999999999999999************** PP

                                   .............................................................................EEEE CS
                                   .............................................................................xxxx RF
                 Peptidase_M20 116 .............................................................................kvev 119
                                                                                                                ++++
  gi|15668633|ref|NP_247431.1| 242 fdeinsiflpeystfeptilknkvenpntipgyvevvfdcrilptykieevlefinkfiknfefkkyikhydnsikaEITY 322
                                   ***************************************************************************876788 PP

                                   EEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEESSGGCTTSTTTEEEHHHHHHH CS
                                   xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 120 elleggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff..agiptvmifgpgsglaHspnEyvdledlekg 197
                                   e l +++p  ++ +++++k l++a++++++++ +l  +g ggt a+f+  +g  +v + g g+++aH+pnE++++edl+k 
  gi|15668633|ref|NP_247431.1| 323 EILKSENPNYTDeNAEIIKELKKAIKNVLNRDAKLCGMG-GGTVAAFLryKGY-NVAVWGIGEETAHQPNEHIKIEDLVKM 401
                                   8778899999999***************99899999999.********88777.6666777789***************** PP

                                   HHHHHHHH CS
                                   xxxxxxxx RF
                 Peptidase_M20 198 ikvlarll 205
                                   ++v++++l
  gi|15668633|ref|NP_247431.1| 402 AEVFYEIL 409
                                   *****998 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       2.6   1.5e+04      88     103 ..      31      46 ..      30      49 .. 0.77
   2 !   56.7   0.0   3.3e-19     2e-15       1     103 [.     195     302 ..     195     307 .. 0.86
   3 ?   -0.8   0.1      0.24   1.4e+03      88     106 ..     334     352 ..     317     355 .. 0.71

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 2.6
                                   HHHHHHHHHHHHHHTS CS
                     M20_dimer  88 edpeevleeieeilek 103
                                   e++e v++++ e++e+
  gi|15668633|ref|NP_247431.1|  31 EKAEYVKKKLMEYVES 46 
                                   6778889999988875 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 3.3e-19
                                   SEB-EEEEEEEEEE-B-EEGG-TTTTB-....HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-C.CCCEESSEE CS
                     M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaN....AieklarllaeledeegdiaeerslprttlnvtgiegGs.aknvipdea 76 
                                   ig+kG+++ k  +kgk++H++ p++g N    A++ + +l + l ++ ++i+  + + ++t+++t+++    ++n+ip+++
  gi|15668633|ref|NP_247431.1| 195 IGEKGILWIKFNIKGKQCHGSTPENGLNadivAFNFANELYNGLYEKFDEINSIFLPEYSTFEPTILKNKVeNPNTIPGYV 275
                                   699*************************555555555555555555544455999999***********99********** PP

                                   EEEEEEEHHHHHHHHHHHHHHHHHHTS CS
                     M20_dimer  77 eakidiRllpgedpeevleeieeilek 103
                                   e+ +d+R+lp+ + eevle i++++++
  gi|15668633|ref|NP_247431.1| 276 EVVFDCRILPTYKIEEVLEFINKFIKN 302
                                   **********************99986 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.24
                                   HHHHHHHHHHHHHHTSCCS CS
                     M20_dimer  88 edpeevleeieeilekeap 106
                                   ++ +e+++e+++++++++ 
  gi|15668633|ref|NP_247431.1| 334 DENAEIIKELKKAIKNVLN 352
                                   4567778888888777665 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.1e-08   0.00013       1      82 [.      69     166 ..      69     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.1e-08
                                   EEEEEESTTCESEEEEEEEE--B-TTT...............TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEE CS
                 Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvg...............rgp.ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrf 65 
                                   N++ ++  +  d++l + +H+D+v++g               +g+    G  Dn  g+++ L l++++ +++ +pk+++ +
  gi|15668633|ref|NP_247431.1|  69 NIVFKIDFGR-DKTLHIISHLDTVPEGdislwgtnpyepvikDGKiYGRGSEDNHKGIVSSLLLLKMIFENNIEPKYNLSL 148
                                   8888888888.99********************9999999876666668******************999999******** PP

                                   EEESSCSG.SSHHHHHHH CS
                 Peptidase_M28  66 lffdaEEa.gllGSkafa 82 
                                   +f++ EE  + +G k++ 
  gi|15668633|ref|NP_247431.1| 149 IFVSDEEDgSEYGLKYLL 166
                                   *******94456766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1126  (0.0628033); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2816.90
//
Query:       gi|15668634|ref|NP_247432.1|  [L=216]
Description: delta 1-pyrroline-5-carboxylate synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-15   57.0   0.7    1.6e-13   50.8   0.7    2.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.7   8.8e-18   1.6e-13       4     217 ..       3     174 ..       1     198 [. 0.71

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 8.8e-18
                                   EEEE-TTCCCCTCCHHHHHHHHHHHHH.HHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC....E..HHHHHHHHHHH CS
                     AA_kinase   4 VvKlGGssltdkeeaslrrlaeqiaal.kesgnklvvVhGggsftdgllal..ksglssgelaaglrstleeagevatrda 81 
                                   +vK+GGs+  d++      l++ ++++ ke+++k+v++ Ggg f++   ++  + ++s + +                 + 
  gi|15668634|ref|NP_247432.1|   3 IVKIGGSLTYDAKP-----LLKALKNYaKENNKKIVIIPGGGEFANVVRKIdkALNISNSLS-----------------HK 61 
                                   8******8888888.....5555555533467899*******99999999933333333333.................45 PP

                                   HHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE-HHH CS
                     AA_kinase  82 laslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgssDt 162
                                   la+   +l  +++a+     g+  +a+d+  + +        +++++e+i+ ll + ++   t ++     ++++ ++sD 
  gi|15668634|ref|NP_247432.1|  62 LAIKCMDLIGEVYAEI----GY-IKAYDTLFDLK--------REIEKEKIAILLPS-KILLSTDIA-----EHSWAITSDS 123
                                   5555555555555555....54.34444444444........799*********88.465555555.....7799****** PP

                                   HHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTT CS
                     AA_kinase 163 iaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatg 217
                                   ++ +++++l+++++ii+tdVdG+yd+ p      +ll+ i++++++  +s + t+
  gi|15668634|ref|NP_247432.1| 124 LSLYIGKLLDVREVIIATDVDGIYDKFPGG----KLLNIINANDIKGLTSVDETF 174
                                   ***************************966....8*********99955555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1525.18
//
Query:       gi|15668635|ref|NP_247433.1|  [L=57]
Description: hypothetical protein MJ_0458.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-14   54.1  15.8    1.3e-14   53.8   6.0    2.3  2  DUF1610          Domain of unknown function (DUF1610)
    0.00062   19.6  13.6      0.083   12.8   5.5    3.1  3  zf-HIT           HIT zinc finger
    0.00093   19.6   7.3     0.0013   19.2   7.3    1.2  1  zf-CHY           CHY zinc finger
     0.0011   18.6  12.9        1.1    9.1   0.1    3.8  3  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
     0.0017   18.7  12.7       0.31   11.6   0.8    3.9  4  zf-H2C2_2        Zinc-finger double domain
     0.0033   17.0  13.7        3.4    7.4   0.2    4.0  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
     0.0047   16.6  20.0      0.016   14.9   3.8    3.5  2  zinc_ribbon_2    zinc-ribbon domain
      0.009   15.9  14.5        1.4    8.9   2.6    4.0  3  zinc_ribbon_4    zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.7   3.5      0.011   15.7   3.5    2.1  2  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
      0.011   15.9   1.1      0.011   15.9   1.1    2.5  2  zinc_ribbon_9    zinc-ribbon
      0.013   15.5  13.7       0.12   12.4   2.6    2.3  2  DZR              Double zinc ribbon
      0.016   15.2  12.3      0.018   15.0   1.3    2.0  2  HypA             Hydrogenase/urease nickel incorporation, met
      0.031   14.4  16.4      0.034   14.3   4.5    2.8  2  Zn-ribbon_8      Zinc ribbon domain
        0.1   12.7   4.3       0.51   10.4   0.0    2.4  2  DUF2752          Protein of unknown function (DUF2752)
        0.1   12.7   0.6        0.1   12.7   0.6    2.2  2  Zn_Tnp_IS91      Transposase zinc-binding domain
       0.16   12.0  11.1       0.18   11.9   6.5    2.6  2  Elf1             Transcription elongation factor Elf1 like
       0.23   11.3   6.8       0.35   10.7   6.8    1.3  1  MCM_OB           MCM OB domain
        0.3   11.4  14.0        4.7    7.6   7.9    2.9  2  C1_2             C1 domain
       0.38   10.7  11.5        0.5   10.3   1.0    2.3  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
        0.4   10.9  10.5       0.44   10.7   4.6    2.1  2  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
        0.5   10.5   9.9        1.9    8.6   3.7    2.3  2  zf-MYND          MYND finger
       0.56   10.0  14.3        2.5    7.9   0.2    3.9  4  Rubredoxin_2     Rubredoxin metal binding domain
       0.58    8.0   6.6       0.63    7.8   6.6    1.0  1  PolC_DP2         DNA polymerase II large subunit DP2
       0.85    9.1  17.8       0.45   10.0   1.2    3.6  4  zf-ribbon_3      zinc-ribbon domain
       0.92    9.7  13.0        3.1    8.0   4.3    2.6  3  zf-AN1           AN1-like Zinc finger
       0.92    9.6  13.2         12    6.1   3.1    2.7  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        1.5    8.6  13.4        4.3    7.2   0.3    3.7  4  A2L_zn_ribbon    A2L zinc ribbon domain
        1.6    8.7  16.8        7.9    6.4   0.4    3.9  4  TFIIS_C          Transcription factor S-II (TFIIS)
        1.7    8.8  16.1         15    5.8   1.6    4.1  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
          3    8.2   7.8        2.3    8.6   0.1    2.2  2  DUF3268          zinc-finger-containing domain
        3.1    7.9   9.3        8.5    6.5   0.5    3.0  3  Ribosomal_L37ae  Ribosomal L37ae protein family
        4.3    6.9  18.2       0.97    9.0   1.5    3.3  4  TF_Zn_Ribbon     TFIIB zinc-binding
        5.4    6.6  14.2        2.7    7.6   0.5    3.0  3  zf_C2H2_10       C2H2 type zinc-finger
        5.7    6.9  17.1    1.8e+04   -4.2  17.1    3.8  0  Zn_ribbon_SprT   SprT-like zinc ribbon domain
        6.2    6.6  17.5        4.3    7.1   1.8    3.3  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
        6.4    6.8  11.2       0.17   11.9   2.7    2.2  2  DUF1451          Zinc-ribbon containing domain
        8.5    6.5  15.2    4.8e+02    0.9  15.2    3.0  1  DUF1272          Protein of unknown function (DUF1272)


Domain annotation for each model (and alignments):
>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   6.0   2.7e-17   1.3e-14       1      24 []       8      31 ..       8      31 .. 0.99
   2 ?    5.8   2.2     0.027        13      18      23 ..      48      53 ..      46      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 2.7e-17
                       DUF1610  1 CtSCGaelaprEravvFpCPNCGE 24
                                  C+SC+ae+aprE++++FpCPNCGE
  gi|15668635|ref|NP_247433.1|  8 CISCNAEIAPREKSTKFPCPNCGE 31
                                  ***********************9 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.027
                       DUF1610 18 pCPNCG 23
                                   CP+CG
  gi|15668635|ref|NP_247433.1| 48 KCPKCG 53
                                  5****9 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.016         8      13      21 ..       5      13 ..       2      15 .. 0.86
   2 ?    5.0   0.2     0.045        22      13      21 ..      23      31 ..      19      32 .. 0.80
   3 !   12.8   5.5   0.00017     0.083       4      20 ..      36      53 ..      35      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.016
                                  SEE-TTT-- CS
                        zf-HIT 13 kYkCpkCnt 21
                                  kY C  Cn+
  gi|15668635|ref|NP_247433.1|  5 KYVCISCNA 13
                                  9******97 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.045
                                  SEE-TTT-- CS
                        zf-HIT 13 kYkCpkCnt 21
                                  k  Cp+C++
  gi|15668635|ref|NP_247433.1| 23 KFPCPNCGE 31
                                  667****95 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00017
                                  B-TTT-S.B-SEE-TTT- CS
                        zf-HIT  4 lCgvCgf.pakYkCpkCn 20
                                   C+ C +    YkCpkC+
  gi|15668635|ref|NP_247433.1| 36 RCERCRKlNNPYKCPKCG 53
                                  699**************8 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   7.3   2.7e-06    0.0013      19      73 ..       5      53 ..       2      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.7e-06
                        zf-CHY 19 lyaCreCHeeledhelerlevkevlcllCeteqekavlCkkCkkefaeyfCpiCk 73
                                   y C +C +    + + r + +++ c +C ++  + v C++C+k  + y+Cp+C 
  gi|15668635|ref|NP_247433.1|  5 KYVCISCNA----EIAPREKSTKFPCPNCGEV--EIVRCERCRKLNNPYKCPKCG 53
                                  599****99....666788889999*****98..8899****************7 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0022       1.1      42      52 ..       3      13 ..       1      15 [. 0.87
   2 !    8.9   0.1    0.0025       1.2      41      53 ..      20      32 ..      16      33 .. 0.83
   3 ?    3.2   5.1      0.15        71      43      52 ..      45      54 ..      34      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0022
                zinc_ribbon_10 42 evkyrCpkCga 52
                                  e+ky+C +C+a
  gi|15668635|ref|NP_247433.1|  3 EMKYVCISCNA 13
                                  689******98 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0025
                zinc_ribbon_10 41 eevkyrCpkCgal 53
                                  + +k+ Cp+Cg++
  gi|15668635|ref|NP_247433.1| 20 KSTKFPCPNCGEV 32
                                  6789******985 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.15
                zinc_ribbon_10 43 vkyrCpkCga 52
                                    y+CpkCg+
  gi|15668635|ref|NP_247433.1| 45 NPYKCPKCGF 54
                                  4799999995 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.051        25      11      21 ..       2      12 ..       1      14 [. 0.88
   2 ?    7.2   0.5     0.015       7.3      13      21 ..      22      30 ..      18      32 .. 0.79
   3 ?    0.9   0.1       1.5   7.1e+02      15      22 ..      35      42 ..      33      43 .. 0.84
   4 !   11.6   0.8   0.00063      0.31      13      21 ..      45      53 ..      44      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.051
                     zf-H2C2_2 11 gekpyeCplCd 21
                                  ge +y C +C+
  gi|15668635|ref|NP_247433.1|  2 GEMKYVCISCN 12
                                  8899******8 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.015
                     zf-H2C2_2 13 kpyeCplCd 21
                                  +++ Cp C+
  gi|15668635|ref|NP_247433.1| 22 TKFPCPNCG 30
                                  67******8 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.5
                     zf-H2C2_2 15 yeCplCdk 22
                                  + C+ C+k
  gi|15668635|ref|NP_247433.1| 35 VRCERCRK 42
                                  68****98 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00063
                     zf-H2C2_2 13 kpyeCplCd 21
                                  +py+Cp+C+
  gi|15668635|ref|NP_247433.1| 45 NPYKCPKCG 53
                                  7*******8 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.2     0.008       3.9       3      17 ..       6      20 ..       5      22 .. 0.88
   2 ?    6.5   0.3     0.013       6.3       2      10 ..      23      31 ..      22      32 .. 0.86
   3 ?    4.6   0.3     0.051        25       4      10 ..      36      42 ..      33      43 .. 0.83
   4 !    7.4   0.2     0.007       3.4       3      10 ..      47      54 ..      45      57 .] 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.008
                        zf_UBZ  3 ylCerCgkeipesel 17
                                  y+C  C++ei + e+
  gi|15668635|ref|NP_247433.1|  6 YVCISCNAEIAPREK 20
                                  9*********99876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                        zf_UBZ  2 tylCerCgk 10
                                   ++C+ Cg+
  gi|15668635|ref|NP_247433.1| 23 KFPCPNCGE 31
                                  69*****97 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.051
                        zf_UBZ  4 lCerCgk 10
                                   CerC k
  gi|15668635|ref|NP_247433.1| 36 RCERCRK 42
                                  7****87 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.007
                        zf_UBZ  3 ylCerCgk 10
                                  y C++Cg 
  gi|15668635|ref|NP_247433.1| 47 YKCPKCGF 54
                                  99****96 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   3.8   3.3e-05     0.016       2      21 ..       8      31 ..       7      32 .. 0.93
   2 ?    3.9   8.4     0.097        47      12      22 ..      44      55 ..      36      56 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-05
                 zinc_ribbon_2  2 CpnCGaelqdnakF....CpyCGt 21
                                  C +C ae+ +++k     Cp+CG+
  gi|15668635|ref|NP_247433.1|  8 CISCNAEIAPREKStkfpCPNCGE 31
                                  99******999999999******7 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.097
                 zinc_ribbon_2 12 nakF.CpyCGtp 22
                                  n+++ Cp+CG++
  gi|15668635|ref|NP_247433.1| 44 NNPYkCPKCGFE 55
                                  666668888876 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   2.6     0.003       1.4       1      34 [.       4      32 ..       4      32 .. 0.85
   2 ?    6.4   0.5     0.018       8.7      26      32 ..      35      41 ..      34      43 .. 0.55
   3 ?    5.4   0.2     0.037        18      27      32 ..      48      53 ..      47      55 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.003
                 zinc_ribbon_4  1 MkitCpsCkakyeiddeklpakgvkvrCskCghv 34
                                  Mk +C sC+a  ei++   ++k +k  C++Cg+v
  gi|15668635|ref|NP_247433.1|  4 MKYVCISCNA--EIAP---REKSTKFPCPNCGEV 32
                                  8999999999..5888...58999999****986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.018
                 zinc_ribbon_4 26 vrCskCg 32
                                  vrC +C+
  gi|15668635|ref|NP_247433.1| 35 VRCERCR 41
                                  5566665 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.037
                 zinc_ribbon_4 27 rCskCg 32
                                  +C+kCg
  gi|15668635|ref|NP_247433.1| 48 KCPKCG 53
                                  566665 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   3.5   2.3e-05     0.011       8      50 ..       3      43 ..       1      46 [. 0.88
   2 ?   -0.5   5.0       2.5   1.2e+03      31      37 ..      47      53 ..      37      56 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-05
                                  HCEEE-TTTTTTSEETTE......E-TTTTTSSEEE-HHHHHH CS
                     Anti-TRAP  8 eLEtkCdaCngsGkiepeeprasleCPkCsGkglipTaqGqkL 50
                                  e+   C  Cn   +i+p e+ + ++CP+C+ + ++  +  +kL
  gi|15668635|ref|NP_247433.1|  3 EMKYVCISCNA--EIAPREKSTKFPCPNCGEVEIVRCERCRKL 43
                                  56678999996..8******************99999988887 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.5
                                  .E-TTTT CS
                     Anti-TRAP 31 leCPkCs 37
                                   +CPkC+
  gi|15668635|ref|NP_247433.1| 47 YKCPKCG 53
                                  5799997 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   1.1   2.4e-05     0.011       5      28 ..       8      30 ..       5      36 .. 0.89
   2 ?    2.8   2.8      0.29   1.4e+02      17      28 ..      43      53 ..      36      56 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-05
                 zinc_ribbon_9  5 ChqCdrfVsvspdedsdvlCPhCg 28
                                  C +C+ ++ ++++++  + CP+Cg
  gi|15668635|ref|NP_247433.1|  8 CISCNAEIAPREKSTKFP-CPNCG 30
                                  889********999999*.****8 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.29
                 zinc_ribbon_9 17 dedsdvlCPhCg 28
                                   +++ + CP Cg
  gi|15668635|ref|NP_247433.1| 43 LNNPYK-CPKCG 53
                                  466777.****7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.6   0.00025      0.12      28      49 .]       5      30 ..       2      30 .. 0.79
   2 ?   10.8  14.1   0.00077      0.37       1      49 []       8      53 ..       8      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00025
                           DZR 28 edrCpsCgekvdpearf....CpeCG 49
                                  +++C sC++++ p+++     Cp+CG
  gi|15668635|ref|NP_247433.1|  5 KYVCISCNAEIAPREKStkfpCPNCG 30
                                  47899999997777666688999998 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00077
                           DZR  1 CpqCgeelppdar....fCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49
                                  C +C++e+ p+ +     C++Cg+         rC +C + ++p    Cp+CG
  gi|15668635|ref|NP_247433.1|  8 CISCNAEIAPREKstkfPCPNCGEVEI-----VRCERCRKLNNPY--KCPKCG 53
                                  9******99888877767*****9976.....8999999998887..699998 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.3   3.8e-05     0.018      68      96 ..       3      33 ..       1      36 [. 0.81
   2 ?    6.8   3.6     0.014       6.8      71      93 ..      35      53 ..      33      56 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.8e-05
                                  --EEEETTTS-EEECHHH..HHS-TTTSSS- CS
                          HypA 68 pvkvrCreCgkefeleek..alrCpkCgsad 96
                                  ++k+ C +C++e+  +ek  ++ Cp+Cg+ +
  gi|15668635|ref|NP_247433.1|  3 EMKYVCISCNAEIAPREKstKFPCPNCGEVE 33
                                  57899*********66643799******854 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.014
                                  EEETTTS-EEECHHHHHS-TTTS CS
                          HypA 71 vrCreCgkefeleekalrCpkCg 93
                                  vrC++C+k  +     ++CpkCg
  gi|15668635|ref|NP_247433.1| 35 VRCERCRKLNNP----YKCPKCG 53
                                  79****944442....58****9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   4.5     7e-05     0.034       6      38 ..       6      36 ..       5      37 .. 0.86
   2 ?    2.0   6.8      0.46   2.2e+02      27      33 ..      46      53 ..      31      55 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7e-05
                   Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs.evrr 38
                                  Y C +C+ e  ++ ++++ p   CP+Cg+ e  r
  gi|15668635|ref|NP_247433.1|  6 YVCISCNAEIAPREKSTKFP---CPNCGEvEIVR 36
                                  9************9988555...*****988776 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.46
                   Zn-ribbon_8 27 ta.CPeCg 33
                                  +  CP+Cg
  gi|15668635|ref|NP_247433.1| 46 PYkCPKCG 53
                                  34477776 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0011      0.51       5      15 ..      20      30 ..      17      33 .. 0.87
   2 ?    3.9   0.2      0.12        57       9      15 ..      47      53 ..      44      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                       DUF2752  5 altGipCPGCG 15
                                  + t +pCP CG
  gi|15668635|ref|NP_247433.1| 20 KSTKFPCPNCG 30
                                  5699******9 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.12
                       DUF2752  9 ipCPGCG 15
                                  ++CP CG
  gi|15668635|ref|NP_247433.1| 47 YKCPKCG 53
                                  68***** PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6   0.00021       0.1      35      67 ..       1      33 [.       1      36 [. 0.87
   2 ?    3.7   1.8      0.13        64      27      46 ..      34      53 ..      32      56 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
                   Zn_Tnp_IS91 35 lGfaryeCeeCghekivyfsCksrh.CpsCqkka 67
                                  +G ++y C +C+  +i +     ++ Cp+C++ +
  gi|15668635|ref|NP_247433.1|  1 MGEMKYVCISCNA-EIAPREKSTKFpCPNCGEVE 33
                                  7999*******86.889999999999****9875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.13
                   Zn_Tnp_IS91 27 ilrCrtaalGfaryeCeeCg 46
                                  i rC++ +   + y+C++Cg
  gi|15668635|ref|NP_247433.1| 34 IVRCERCRKLNNPYKCPKCG 53
                                  45555555556778888887 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.73   3.5e+02      21      30 ..       5      14 ..       2      18 .. 0.77
   2 ?   11.9   6.5   0.00037      0.18      18      52 ..      20      53 ..      15      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.73
                          Elf1 21 kFdCpfCnhe 30
                                  k+ C  Cn+e
  gi|15668635|ref|NP_247433.1|  5 KYVCISCNAE 14
                                  6778899887 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00037
                          Elf1 18 lptkFdCpfCnheksvevkldkkekiaevsCkvCg 52
                                   +tkF Cp+C++ + v+++  +k ++   +C +Cg
  gi|15668635|ref|NP_247433.1| 20 KSTKFPCPNCGEVEIVRCERCRKLNN-PYKCPKCG 53
                                  579****************9999765.56999997 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   6.8   0.00072      0.35      24      60 ..      13      53 ..       7      57 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00072
                                  ---EEEEEEEEEEETTT-.-EEE......S----SB-..TTT- CS
                        MCM_OB 24 sevkpklkkavfeckkcgktvev......eleePrkCeekeCe 60
                                   e+ p+ k+++f c++cg+++ v      +l++P kC  ++C+
  gi|15668635|ref|NP_247433.1| 13 AEIAPREKSTKFPCPNCGEVEIVrcercrKLNNPYKC--PKCG 53
                                  67899999**********865566777766777****..99*8 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.088        43      31      40 ..       4      13 ..       1      18 [. 0.73
   2 ?    7.6   7.9    0.0098       4.7      18      40 ..      34      54 ..      15      55 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.088
                          C1_2 31 ffYsCseCdf 40
                                  ++Y C  C+ 
  gi|15668635|ref|NP_247433.1|  4 MKYVCISCNA 13
                                  4499988986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0098
                          C1_2 18 sfnCsaCgrkidgffYsCseCdf 40
                                    +C+ C++   ++ Y+C++C f
  gi|15668635|ref|NP_247433.1| 34 IVRCERCRKL--NNPYKCPKCGF 54
                                  4578888777..344******98 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.0     0.001       0.5      31      55 ..       8      32 ..       5      36 .. 0.88
   2 ?    5.7   8.6     0.029        14      31      55 ..      26      55 ..      26      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.001
                OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfe 55
                                  C  C ++  ++ ++ +f CpnCg +
  gi|15668635|ref|NP_247433.1|  8 CISCNAEIAPREKSTKFPCPNCGEV 32
                                  8889999999999*********976 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.029
                OrfB_Zn_ribbon 31 CseCgsknke.....alsgrtfkCpnCgfe 55
                                  C++Cg++        ++ ++ +kCp+Cgfe
  gi|15668635|ref|NP_247433.1| 26 CPNCGEVEIVrcercRKLNNPYKCPKCGFE 55
                                  9****9988778889999999*******97 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.6   0.00091      0.44      10      38 ..       7      38 ..       3      40 .. 0.75
   2 ?    3.3   3.4      0.19        91       8      30 ..      34      53 ..      33      55 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00091
                  NOB1_Zn_bind 10 rChaCfkvt...kdmtkkFCpkCGnktLkrva 38
                                   C +C   +   +++tk  Cp+CG+  + r++
  gi|15668635|ref|NP_247433.1|  7 VCISCNAEIaprEKSTKFPCPNCGEVEIVRCE 38
                                  6999998665635566666******9999985 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.19
                  NOB1_Zn_bind  8 vlrChaCfkvtkdmtkkFCpkCG 30
                                  ++rC  C k+ +  +   CpkCG
  gi|15668635|ref|NP_247433.1| 34 IVRCERCRKLNNPYK---CPKCG 53
                                  578999988765444...****9 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.7     0.004       1.9       1      18 [.      26      42 ..       8      44 .. 0.79
   2 ?    4.7   4.4     0.065        32       1      16 [.      37      52 ..      37      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.004
                                  -TTT--.B-SCE-TTTS- CS
                       zf-MYND  1 CavCgkaealkkCagCks 18
                                  C +Cg+  +  +C++C++
  gi|15668635|ref|NP_247433.1| 26 CPNCGE-VEIVRCERCRK 42
                                  788888.77778888875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.065
                                  -TTT--.B-SC.E-TTT CS
                       zf-MYND  1 CavCgkaealk.kCagC 16
                                  C+ C+k ++   kC++C
  gi|15668635|ref|NP_247433.1| 37 CERCRKLNN-PyKCPKC 52
                                  9*****444.46***** PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.094        45       1       9 [.       6      14 ..       6      16 .. 0.86
   2 ?    5.3   0.4     0.034        16      17      22 ..      26      31 ..      24      33 .. 0.80
   3 ?    1.5   0.5      0.51   2.5e+02      16      21 ..      36      41 ..      36      44 .. 0.62
   4 ?    7.9   0.2    0.0052       2.5       1      10 [.      47      56 ..      47      57 .] 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.094
                  Rubredoxin_2  1 YvCsqCGfe 9 
                                  YvC +C++e
  gi|15668635|ref|NP_247433.1|  6 YVCISCNAE 14
                                  999999976 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.034
                  Rubredoxin_2 17 CpsCgs 22
                                  Cp+Cg+
  gi|15668635|ref|NP_247433.1| 26 CPNCGE 31
                                  888885 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.51
                  Rubredoxin_2 16 rCpsCg 21
                                  rC  C+
  gi|15668635|ref|NP_247433.1| 36 RCERCR 41
                                  566665 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0052
                  Rubredoxin_2  1 YvCsqCGfes 10
                                  Y C +CGfe 
  gi|15668635|ref|NP_247433.1| 47 YKCPKCGFEG 56
                                  8999999986 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.6    0.0013      0.63     626     662 ..      19      53 ..       2      56 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0013
                      PolC_DP2 626 ketlearCeeCgekteeklvCkkceeeveeekcekce 662
                                   ++++++ C++Cge      +C++c++ ++  kc+kc+
  gi|15668635|ref|NP_247433.1|  19 EKSTKFPCPNCGEVEIV--RCERCRKLNNPYKCPKCG 53 
                                   45667777777776554..777777777777777776 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1       0.2        96       3      15 ..       6      18 ..       4      21 .. 0.73
   2 ?   10.0   1.2   0.00094      0.45       4      11 ..      25      32 ..      23      34 .. 0.75
   3 ?   -1.3   0.3       3.4   1.6e+03       3       8 ..      35      40 ..      33      42 .. 0.80
   4 ?    7.9   0.9    0.0044       2.1       4       9 ..      48      53 ..      47      55 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.2
                   zf-ribbon_3  3 vrCPnCGa.plssd 15
                                  + C +C+a + +++
  gi|15668635|ref|NP_247433.1|  6 YVCISCNAeI-APR 18
                                  6788999966.665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00094
                   zf-ribbon_3  4 rCPnCGap 11
                                   CPnCG++
  gi|15668635|ref|NP_247433.1| 25 PCPNCGEV 32
                                  59999875 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.4
                   zf-ribbon_3  3 vrCPnC 8 
                                  vrC +C
  gi|15668635|ref|NP_247433.1| 35 VRCERC 40
                                  688887 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0044
                   zf-ribbon_3  4 rCPnCG 9 
                                  +CP+CG
  gi|15668635|ref|NP_247433.1| 48 KCPKCG 53
                                  455555 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.6      0.02       9.7       5      21 ..      10      31 ..       8      33 .. 0.74
   2 ?    5.1   3.3     0.054        26       1      21 [.      26      42 ..      26      43 .. 0.86
   3 ?    8.0   4.3    0.0064       3.1       1      20 [.      37      53 ..      36      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.02
                        zf-AN1  5 sCkkkd.....flpfkCryCgk 21
                                  sC+ ++     ++ f C++Cg+
  gi|15668635|ref|NP_247433.1| 10 SCNAEIaprekSTKFPCPNCGE 31
                                  68877766654566******97 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.054
                        zf-AN1  1 CsfksCkkkdflpfkCryCgk 21
                                  C   +C++ +   ++C++C+k
  gi|15668635|ref|NP_247433.1| 26 CP--NCGEVEI--VRCERCRK 42
                                  44..8*****9..******97 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0064
                        zf-AN1  1 CsfksCkkkdflpfkCryCg 20
                                  C+  +C+k+ + p+kC++Cg
  gi|15668635|ref|NP_247433.1| 37 CE--RCRKLNN-PYKCPKCG 53
                                  55..8999998.*******8 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   6.5     0.056        27      11      23 ..      18      30 ..       2      40 .. 0.77
   2 ?    6.1   3.1     0.025        12      12      24 ..      42      54 ..      36      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.056
                      zf-Mss51 11 apkhvdfeCpdCG 23
                                   +k+ +f Cp+CG
  gi|15668635|ref|NP_247433.1| 18 REKSTKFPCPNCG 30
                                  58999*******9 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.025
                      zf-Mss51 12 pkhvdfeCpdCGi 24
                                  + +  ++Cp+CG+
  gi|15668635|ref|NP_247433.1| 42 KLNNPYKCPKCGF 54
                                  55778*******7 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.015         7      22      30 ..       6      14 ..       4      16 .. 0.83
   2 ?    3.2   0.3      0.15        73      24      29 ..      26      31 ..      24      35 .. 0.84
   3 ?   -0.7   0.2       2.7   1.3e+03       5      10 ..      36      41 ..      33      42 .. 0.73
   4 ?    7.2   0.3    0.0089       4.3      22      30 ..      47      55 ..      44      57 .] 0.63

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.015
                 A2L_zn_ribbon 22 lvCieCgas 30
                                  +vCi C+a+
  gi|15668635|ref|NP_247433.1|  6 YVCISCNAE 14
                                  899999985 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.15
                 A2L_zn_ribbon 24 CieCga 29
                                  C++Cg 
  gi|15668635|ref|NP_247433.1| 26 CPNCGE 31
                                  ****95 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.7
                 A2L_zn_ribbon  5 vCsvCg 10
                                   C+ C+
  gi|15668635|ref|NP_247433.1| 36 RCERCR 41
                                  599997 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0089
                 A2L_zn_ribbon 22 lvCieCgas 30
                                  + C++Cg++
  gi|15668635|ref|NP_247433.1| 47 YKCPKCGFE 55
                                  447777765 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.054        26      28      36 ..       5      13 ..       3      15 .. 0.84
   2 ?    5.9   1.9     0.025        12       1      12 [.      24      35 ..      24      39 .. 0.82
   3 ?    1.4   0.6      0.59   2.9e+02       2       8 ..      36      42 ..      35      45 .. 0.71
   4 ?    6.4   0.4     0.016       7.9       2       7 ..      48      53 ..      46      56 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.054
                       TFIIS_C 28 fykCtkCgh 36
                                   y+C++C+ 
  gi|15668635|ref|NP_247433.1|  5 KYVCISCNA 13
                                  59*****86 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.025
                       TFIIS_C  1 akCpkCgsreay 12
                                  ++Cp+Cg+ e++
  gi|15668635|ref|NP_247433.1| 24 FPCPNCGEVEIV 35
                                  68*****98876 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.59
                       TFIIS_C  2 kCpkCgs 8 
                                  +C++C++
  gi|15668635|ref|NP_247433.1| 36 RCERCRK 42
                                  6888865 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.016
                       TFIIS_C  2 kCpkCg 7 
                                  kCpkCg
  gi|15668635|ref|NP_247433.1| 48 KCPKCG 53
                                  566666 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.14        69       4       8 ..       8      12 ..       4      18 .. 0.68
   2 ?    5.5   0.3     0.038        18       4      10 ..      26      32 ..      24      32 .. 0.83
   3 ?    3.1   0.1      0.21     1e+02       2       8 ..      35      41 ..      35      44 .. 0.81
   4 ?    5.8   1.6     0.031        15       3       8 ..      48      53 ..      47      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                        zf-ACC  4 CpsCg 8 
                                  C sC+
  gi|15668635|ref|NP_247433.1|  8 CISCN 12
                                  55665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.038
                        zf-ACC  4 CpsCgem 10
                                  Cp Cge+
  gi|15668635|ref|NP_247433.1| 26 CPNCGEV 32
                                  9999985 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.21
                        zf-ACC  2 tKCpsCg 8 
                                  ++C++C 
  gi|15668635|ref|NP_247433.1| 35 VRCERCR 41
                                  68****7 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.031
                        zf-ACC  3 KCpsCg 8 
                                  KCp+Cg
  gi|15668635|ref|NP_247433.1| 48 KCPKCG 53
                                  999998 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0048       2.3      27      47 ..       2      22 ..       1      25 [. 0.80
   2 ?    2.2   3.7      0.45   2.2e+02       4      37 ..      25      53 ..      22      55 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0048
                       DUF3268 27 gkllylCpkCdayvgvhkgtk 47
                                  g++ y+C +C+a +  +++++
  gi|15668635|ref|NP_247433.1|  2 GEMKYVCISCNAEIAPREKST 22
                                  789*********998776654 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.45
                       DUF3268  4 rCpyCGekvilvsaseiYkerskgkllylCpkCd 37
                                   Cp CGe  i++ ++       k +  y CpkC+
  gi|15668635|ref|NP_247433.1| 25 PCPNCGEVEIVRCER-CR----KLNNPYKCPKCG 53
                                  599999876665543.33....334689999997 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.7     0.018       8.7      32      59 ..       4      31 ..       2      32 .. 0.85
   2 ?    6.5   0.5     0.017       8.5      30      54 ..      20      37 ..      14      44 .. 0.71
   3 ?    4.1   0.3       0.1        51      31      40 ..      44      53 ..      41      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.018
                                  S-BEESSSSSSEEEEEETTEEEETTTTE CS
               Ribosomal_L37ae 32 akytCpfcgktkvkRkavgiwkCkkcgk 59
                                   ky C +c+ +   R+    + C +cg+
  gi|15668635|ref|NP_247433.1|  4 MKYVCISCNAEIAPREKSTKFPCPNCGE 31
                                  6899999999999999999999999986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.017
                                  HHS-BEESSSSSSEEEEEETTEEEE CS
               Ribosomal_L37ae 30 qhakytCpfcgktkvkRkavgiwkC 54
                                  + +k+ Cp+cg+ ++ R       C
  gi|15668635|ref|NP_247433.1| 20 KSTKFPCPNCGEVEIVR-------C 37
                                  56789999999866555.......4 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.1
                                  HS-BEESSSS CS
               Ribosomal_L37ae 31 hakytCpfcg 40
                                  ++ y+Cp+cg
  gi|15668635|ref|NP_247433.1| 44 NNPYKCPKCG 53
                                  578******9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.3      0.24   1.1e+02      19      25 ..       5      11 ..       2      19 .. 0.81
   2 ?    8.1   4.5    0.0037       1.8       1      28 [.       6      32 ..       6      33 .. 0.82
   3 ?    9.0   1.5     0.002      0.97       2      12 ..      25      35 ..      24      39 .. 0.79
   4 ?    6.1   1.1     0.016       7.9       1       7 [.      47      53 ..      47      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.24
                                  CEEESSS CS
                  TF_Zn_Ribbon 19 elvCtdC 25
                                   +vC +C
  gi|15668635|ref|NP_247433.1|  5 KYVCISC 11
                                  589*999 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0037
                                  EEETTTTCEECHEETSTTCEEESSSSBE CS
                  TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGlV 28
                                  y+C  C+ + +   ++++ + C++CG+V
  gi|15668635|ref|NP_247433.1|  6 YVCISCNAE-IAPREKSTKFPCPNCGEV 32
                                  678888865.77789999999*****99 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.002
                                  EETTTTCEECH CS
                  TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                   CPnCg  ++v
  gi|15668635|ref|NP_247433.1| 25 PCPNCGEVEIV 35
                                  59999998876 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.016
                                  EEETTTT CS
                  TF_Zn_Ribbon  1 ykCPnCg 7 
                                  ykCP+Cg
  gi|15668635|ref|NP_247433.1| 47 YKCPKCG 53
                                  89****8 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2       2.2   1.1e+03       3      13 ..       6      17 ..       5      17 .. 0.60
   2 ?    7.6   0.5    0.0056       2.7       2      11 ..      23      32 ..      22      33 .. 0.89
   3 ?    6.5   2.5     0.012       5.9       3      12 ..      47      56 ..      46      57 .] 0.76

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.2
                    zf_C2H2_10  3 fsCPKCq.eklP 13
                                  + C  C+ e++P
  gi|15668635|ref|NP_247433.1|  6 YVCISCNaEIAP 17
                                  667778735555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0056
                    zf_C2H2_10  2 efsCPKCqek 11
                                  +f CP C+e+
  gi|15668635|ref|NP_247433.1| 23 KFPCPNCGEV 32
                                  799****996 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.012
                    zf_C2H2_10  3 fsCPKCqekl 12
                                  + CPKC+   
  gi|15668635|ref|NP_247433.1| 47 YKCPKCGFEG 56
                                  56****9765 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.8    0.0089       4.3       1      24 [.       6      30 ..       6      31 .. 0.91
   2 ?    2.3   2.6      0.28   1.3e+02      16      23 ..      33      40 ..      31      42 .. 0.88
   3 ?    6.6   0.3     0.012         6      15      25 ..      44      54 ..      41      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0089
                                  -B-SSS--B--.--SSS----SSS- CS
                DNA_RNApol_7kD  1 YiCgeCgaevs.lkkgdpiRCkeCG 24
                                  Y C  C+ae    +k+    C +CG
  gi|15668635|ref|NP_247433.1|  6 YVCISCNAEIApREKSTKFPCPNCG 30
                                  99*******99888888999****9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.28
                                  S----SSS CS
                DNA_RNApol_7kD 16 dpiRCkeC 23
                                  +++RC  C
  gi|15668635|ref|NP_247433.1| 33 EIVRCERC 40
                                  78****99 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                                  SS----SSS-- CS
                DNA_RNApol_7kD 15 gdpiRCkeCGh 25
                                  + p +C +CG+
  gi|15668635|ref|NP_247433.1| 44 NNPYKCPKCGF 54
                                  56779999997 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.7   0.00034      0.17     114     145 ..       5      36 ..       1      38 [. 0.89
   2 ?   -1.3   3.4       4.2     2e+03     133     139 ..      47      53 ..      35      56 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00034
                       DUF1451 114 tlvCekCgkelalkkteeippCpkCgateFrR 145
                                   ++vC +C++e+a ++ ++  pCp+Cg+ e  R
  gi|15668635|ref|NP_247433.1|   5 KYVCISCNAEIAPREKSTKFPCPNCGEVEIVR 36 
                                   689***********************988777 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.2
                       DUF1451 133 ppCpkCg 139
                                    +CpkCg
  gi|15668635|ref|NP_247433.1|  47 YKCPKCG 53 
                                   3577776 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9  15.2         1   4.8e+02       3      48 ..       3      53 ..       1      55 [. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1
                       DUF1272  3 elrpnCecCdkdlppdseeari.c....syEctFCaeCaeevlenvCPncg 48
                                  e++  C  C++++ p +++++  c      E   C++C +      CP cg
  gi|15668635|ref|NP_247433.1|  3 EMKYVCISCNAEIAPREKSTKFpCpncgEVEIVRCERCRKLNNPYKCPKCG 53
                                  8999*********999887765232112357789****9999899*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        58  (0.00323498); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.61
# Mc/sec: 282.55
//
Query:       gi|15668636|ref|NP_247434.1|  [L=89]
Description: elongation factor 1-beta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-16   59.4   1.3    3.3e-16   59.2   1.3    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain
  ------ inclusion threshold ------
       0.06   13.7   0.0       0.06   13.7   0.0    1.2  1  MAP       MAP domain


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   1.3   3.7e-20   3.3e-16       3      88 ..       7      87 ..       5      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 3.7e-20
                                  EEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEESSS-GGGGHHHHHHTTS-S.....SEEEEE CS
                       EF1_GNE  3 vlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvieddkvstdeleekieeiegeledlVqsvei 84
                                   ++++P + e++ e+l++k+k++  ++ + +      ep+afGl+++   + +e+ +++t+ +e++++ei++     V+sve+
  gi|15668636|ref|NP_247434.1|  7 KIKIMPTSPEVNKEKLKEKIKEVLEKQdVAIR-GLFDEPLAFGLYAIYTVIEMEEREGGTEPIENALAEIDE-----VESVET 83
                                  79********************4444448888.5**************************************.....999999 PP

                                  EEEE CS
                       EF1_GNE 85 vsfn 88
                                  v+++
  gi|15668636|ref|NP_247434.1| 84 VEVS 87
                                  9886 PP

>> MAP  MAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.7e-06      0.06      20      61 ..      11      56 ..       1      85 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.7e-06
                           MAP 20 fsnkskisykdlsskvKsvlksd....rGiteedlklakkAvYtvy 61
                                  ++  ++++ ++l++k+K vl+++    rG+ +e l +   A Ytv 
  gi|15668636|ref|NP_247434.1| 11 MPTSPEVNKEKLKEKIKEVLEKQdvaiRGLFDEPLAFGLYAIYTVI 56
                                  567899**************98778889****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 603.27
//
Query:       gi|15668637|ref|NP_247435.1|  [L=156]
Description: 50S ribosomal protein L22 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-32  112.3   0.7    1.3e-32  112.0   0.7    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   0.7   7.4e-37   1.3e-32       1     102 [.      21     152 ..      21     153 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 7.4e-37
                                   EEEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST............................THHHHHHHHHHHH CS
                 Ribosomal_L22   1 akgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk............................aakfvlklLknae 51 
                                   a+g+n+++s k++re+++ I+gmk++eA+k+L++  + ++                            aak +lk+L++a+
  gi|15668637|ref|NP_247435.1|  21 AMGRNIPISRKHAREICKSINGMKLDEAIKFLEDviAMRRpvlfrrhckkvghrkgklgwpagrypvkAAKAILKILQHAK 101
                                   689********************************877779**************************************** PP

                                   HHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEE CS
                 Ribosomal_L22  52 anaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvl 102
                                   anae+kgl+ ++l I++i  nkg ++kr+++rA Gr++p  ++++hi+v+l
  gi|15668637|ref|NP_247435.1| 102 ANAEYKGLNTEKLRIKHISTNKGITIKRYMPRAFGRATPKFQETVHIQVIL 152
                                   **************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1110.05
//
Query:       gi|15668638|ref|NP_247436.1|  [L=208]
Description: 30S ribosomal protein S3 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-26   91.0   1.9    9.9e-26   90.1   1.9    1.5  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    1.8e-17   62.9   0.6    6.8e-17   61.1   0.1    2.2  2  KH_2            KH domain
     0.0033   17.2   0.1      0.011   15.6   0.1    1.9  1  KH_1            KH domain
  ------ inclusion threshold ------
      0.028   14.5   0.0      0.084   13.0   0.0    1.8  1  KH_5            NusA-like KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   1.9   2.2e-29   9.9e-26       1      83 []      98     181 ..      98     181 .. 0.99

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 2.2e-29
                                   HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTEEEEE CS
                Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyGiiGv 79 
                                   +a++le++++fRr+ ++a+rr+m+agakG+ +++sG+L+ +e+ar+ek+++G++++  +++++ +d++ a aktk G+iGv
  gi|15668638|ref|NP_247436.1|  98 VAQSLERGLHFRRVGHTAVRRVMNAGAKGVIVIISGKLT-GERARTEKFMAGYMKHcgEPAEELVDKGRAIAKTKPGVIGV 177
                                   699************************************.9**************************************** PP

                                   EEEE CS
                Ribosomal_S3_C  80 kVwI 83 
                                   +V+I
  gi|15668638|ref|NP_247436.1| 178 TVKI 181
                                   **98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.1   1.5e-20   6.8e-17       2      75 ..      16      86 ..      15      89 .. 0.92
   2 ?   -1.0   0.1      0.35   1.6e+03      15      40 ..     103     129 ..      92     130 .. 0.63

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.5e-20
                                  HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETT CS
                          KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkk 75
                                  i+e++++e++kag+s+++I++t+ +++i+i++++pg vIG++Gs+i++++++l k+++ +e+ ++ +  + V++
  gi|15668638|ref|NP_247436.1| 16 IDEYFKKELSKAGYSHCDIRKTPIGTKIIIYAEKPGFVIGRRGSRIRELTETLAKEFG-VEKPQIDV--KPVEN 86
                                  889****************99************************************8.99999995..55555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.35
                                   EEEEEEEC.CSCEEEEEEEESCHHHHH CS
                          KH_2  15 vskveIer.tanrviiviresqpgivI 40 
                                    ++++ +r  + +v+ v+ ++ +g+++
  gi|15668638|ref|NP_247436.1| 103 ERGLHFRRvGHTAVRRVMNAGAKGVIV 129
                                   555555553337788888888888886 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.4e-06     0.011       4      29 ..      43      67 ..      40      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-06
                                  EEEGGGHHHHHHTGGGHHHHHHHHHH CS
                          KH_1  4 ilvPsslvgriIGkgGsnIkeIreet 29
                                  i++ +++ g++IG++Gs+I+e+ e t
  gi|15668638|ref|NP_247436.1| 43 IIIYAEKPGFVIGRRGSRIRELTE-T 67
                                  555566679*************99.6 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.9e-05     0.084       5      40 ..      41      71 ..      39      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                          KH_5  5 tkvaVkshnpnvdpvGaivgkkGsrikavsseLkge 40
                                  tk+++++++      G ++g++Gsri+++ + L++e
  gi|15668638|ref|NP_247436.1| 41 TKIIIYAEK-----PGFVIGRRGSRIRELTETLAKE 71
                                  799999999.....9****************99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1336.70
//
Query:       gi|15668639|ref|NP_247437.1|  [L=70]
Description: 50S ribosomal protein L29 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-22   79.6   2.2    1.4e-22   79.4   2.2    1.1  1  Ribosomal_L29   Ribosomal L29 protein
  ------ inclusion threshold ------
      0.097   12.9   0.5       0.14   12.4   0.5    1.3  1  DUF3213         Protein of unknown function (DUF3213)
          1    9.5   5.0       0.18   11.9   0.6    1.9  2  DUF1192         Protein of unknown function (DUF1192)


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   2.2   2.3e-26   1.4e-22       2      57 .]       8      64 ..       7      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 2.3e-26
                                  HHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHHH CS
                 Ribosomal_L29  2 elrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlrer 57
                                  elr++s eeLkekl+elk+eL++ r  ka+  +++np+r+r++R++IARi+T+++e+
  gi|15668639|ref|NP_247437.1|  8 ELRGMSMEELKEKLVELKRELLKERASKAVAgAPSNPGRMREIRRTIARILTIMNEK 64
                                  9****************************887************************8 PP

>> DUF3213  Protein of unknown function (DUF3213)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   2.3e-05      0.14      46      66 ..      12      32 ..       2      37 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                                  -SHHHHHHHT...TT-SS--- CS
                       DUF3213 46 vnieelkkkleelkgevveek 66
                                  +++eelk+kl elk e+++e+
  gi|15668639|ref|NP_247437.1| 12 MSMEELKEKLVELKRELLKER 32
                                  679***************997 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   2.9e-05      0.18      13      40 ..       5      32 ..       2      42 .. 0.78
   2 ?   -0.9   0.3      0.29   1.7e+03      35      43 ..      49      57 ..      46      68 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.9e-05
                       DUF1192 13 igqDLslLSveELeerIalLeaEIaRle 40
                                    ++L  +S+eEL+e   +L+ E  + +
  gi|15668639|ref|NP_247437.1|  5 RADELRGMSMEELKEKLVELKRELLKER 32
                                  5678999****************85433 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.29
                       DUF1192 35 EIaRleaai 43
                                  EI R+ a i
  gi|15668639|ref|NP_247437.1| 49 EIRRTIARI 57
                                  444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 559.76
//
Query:       gi|15668640|ref|NP_247438.1|  [L=103]
Description: translation initiation factor Sui1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-22   79.4   1.3    2.7e-22   79.1   1.3    1.1  1  SUI1      Translation initiation factor SUI1
    0.00025   20.8   0.8    0.00036   20.3   0.8    1.2  1  DTW       DTW domain
     0.0076   16.5   0.2      0.011   16.1   0.2    1.3  1  Img2      Mitochondrial large subunit ribosomal protein (Img2
  ------ inclusion threshold ------
        0.1   12.5   0.0       0.17   11.8   0.0    1.3  1  DUF1421   UBA-like domain (DUF1421)


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   1.3     6e-26   2.7e-22       2      76 ..      25      95 ..      24      96 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 6e-26
                          SUI1  2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygv 76
                                  ++ki+i + +r+ +K +T+++g+++  idlk+lak+lk  +ac+g+v kd+   i++QGd+rkkvae L+++ g+
  gi|15668640|ref|NP_247438.1| 25 EQKIKIYVTKRRFGKLMTIIEGFDTSVIDLKELAKKLKDICACGGTV-KDN--TIELQGDHRKKVAEELVKM-GF 95
                                  79********************************************9.888..8*****************9.87 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.8     8e-08   0.00036       2      33 ..       4      34 ..       3      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8e-08
                           DTW  2 elCerCllpaevclcsslppleklpikvlilq 33
                                  e+C+rC lp+e+c+c+++ + e+++ik+++ +
  gi|15668640|ref|NP_247438.1|  4 EICPRCGLPKELCVCEEIAK-EEQKIKIYVTK 34
                                  58******************.88889998876 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   2.4e-06     0.011      15      80 .]      30      95 ..      20      95 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.4e-06
                          Img2 15 VYtdvkrggtkkltvirkieGDiaalredLrkalee..lvkvnevtgkieikGdrveevkkfLeskgF 80
                                  +Y   +r   k +t+i   + ++ +l+ +L+k l++  ++  + + ++ie++Gd++++v + L + gF
  gi|15668640|ref|NP_247438.1| 30 IYVTKRRF-GKLMTIIEGFDTSVIDLK-ELAKKLKDicACGGTVKDNTIELQGDHRKKVAEELVKMGF 95
                                  66655554.445888888887666654.3555555533377788999******************999 PP

>> DUF1421  UBA-like domain (DUF1421)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.8e-05      0.17       4      19 ..      86     101 ..      84     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.8e-05
                       DUF1421   4 lidkvasMGfrrDqVr 19 
                                   +++ +++MGf+rD ++
  gi|15668640|ref|NP_247438.1|  86 VAEELVKMGFSRDSIE 101
                                   89***********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1105  (0.061632); expected 358.6 (0.02)
Passed bias filter:                      729  (0.0406604); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 653.44
//
Query:       gi|15668641|ref|NP_247439.1|  [L=95]
Description: ribonuclease P protein component 1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-25   88.3   0.9    2.6e-25   88.1   0.9    1.0  1  UPF0086   Domain of unknown function UPF0086
  ------ inclusion threshold ------
       0.54   10.1   5.7       0.11   12.3   2.3    1.6  2  Myosin_N  Myosin N-terminal SH3-like domain


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.9     3e-29   2.6e-25       2      84 .]       6      87 ..       5      87 .. 0.97

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 3e-29
                                  HHCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHHHHCH CS
                       UPF0086  2 kLlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpadRaer 84
                                  ++l+++l+G++ve+v++kn++++gikG Vv+Et+ntl+i++++ r  ++pK+ +vF f++ + ++v+vdG+ l+ rp++R ++
  gi|15668641|ref|NP_247439.1|  6 NILRHELIGLKVEIVEAKNKAMIGIKGKVVDETRNTLVIEKEDGREVVIPKDIAVFLFQL-KGCKVKVDGRLLIGRPEERLKK 87
                                  799*********************************************************.699****************986 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.63   5.7e+03      15      22 ..      16      23 ..      15      25 .. 0.68
   2 ?   12.3   2.3   1.3e-05      0.11      14      40 .]      30      56 ..      30      56 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.63
                                  EEEEEEEE CS
                      Myosin_N 15 kGeIkeee 22
                                  k eI+e +
  gi|15668641|ref|NP_247439.1| 16 KVEIVEAK 23
                                  67888765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.3e-05
                                  EEEEEEEEESSEEEEEETTSEEEEEEG CS
                      Myosin_N 14 vkGeIkeeeGdkvtVetedGktvtVkk 40
                                  +kG++++e+ +++++e edG++v ++k
  gi|15668641|ref|NP_247439.1| 30 IKGKVVDETRNTLVIEKEDGREVVIPK 56
                                  89*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 607.09
//
Query:       gi|15668642|ref|NP_247440.1|  [L=117]
Description: 30S ribosomal protein S17 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-26   91.8   5.1    2.7e-26   91.4   5.1    1.1  1  Ribosomal_S17    Ribosomal protein S17
     0.0082   16.5   0.4      0.019   15.4   0.0    1.8  2  Ribosomal_S17_N  Ribosomal_S17 N-terminal
  ------ inclusion threshold ------
      0.053   14.0   0.0      0.084   13.4   0.0    1.3  1  DUF2535          Protein of unknown function (DUF2535)


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   5.1   4.5e-30   2.7e-26       1      68 []      37     105 ..      37     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 4.5e-30
                                   EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
                 Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                                   GvVvsdk +kTv++++e  ++++ky++y++r++k+ ah+++++ ++vGDiVr++ecrP+Sktk fvvve
  gi|15668642|ref|NP_247440.1|  37 GVVVSDKPHKTVIIKREVVKYIKKYERYERRTTKLAAHNPPCIhARVGDIVRVMECRPISKTKAFVVVE 105
                                   9******************************************************************97 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.1e-06     0.019      34      67 ..       4      33 ..       2      35 .. 0.77
   2 ?   -2.2   0.1      0.93   5.6e+03      23      24 ..      58      59 ..      42      72 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.1e-06
                                  ----TT----GGGGS-----TTSSSSSS----S- CS
               Ribosomal_S17_N 34 knvglgfktPkeAiegtYiDkKCPFtGnvsirGr 67
                                  +n+g+  k+P+   +    Dk CPF Gn  +rG+
  gi|15668642|ref|NP_247440.1|  4 RNIGIQVKAPEVECD----DKNCPFHGNLPVRGQ 33
                                  566666666655444....**************7 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.93
                                  -- CS
               Ribosomal_S17_N 23 kk 24
                                   k
  gi|15668642|ref|NP_247440.1| 58 IK 59
                                  22 PP

>> DUF2535  Protein of unknown function (DUF2535)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.084      11      72 ..       5      66 ..       2      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                       DUF2535 11 adGqkvkvteiPvLeedepyffmvklrLeafikkvykskkkkkvYsfreylkrvlkWkdyeq 72
                                    G++vk  e+   +++ p+   + +r + f+  v ++k +k+v   re +k   k++ ye+
  gi|15668642|ref|NP_247440.1|  5 NIGIQVKAPEVECDDKNCPFHGNLPVRGQSFVGVVVSDKPHKTVIIKREVVKYIKKYERYER 66
                                  679********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 747.90
//
Query:       gi|15668643|ref|NP_247441.1|  [L=132]
Description: 50S ribosomal protein L14 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-35  122.4   1.3    1.3e-35  122.2   1.3    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e
  ------ inclusion threshold ------
       0.14   11.9   0.1       0.15   11.8   0.1    1.2  1  SBP_bac_11     Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.2   1.3   1.4e-39   1.3e-35       5     121 ..      15     131 ..      12     132 .] 0.94

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 1.4e-39
                                   S-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-EEEESS CS
                 Ribosomal_L14   5 ktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsvirfdd 81 
                                   ++r  +aDN+gakeve+i+v ++k    + ++a+vGd+++v+vkk++p   +++++v+ avv+r++ke+rr+dG+ ++f d
  gi|15668643|ref|NP_247441.1|  15 GARCICADNTGAKEVEIIAVRNYKgvarRLPTARVGDMVIVTVKKGTP---EMRKQVLPAVVIRQRKEIRRPDGTRVKFAD 92 
                                   67888****************999777555******************...99**************************** PP

                                   -EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE CS
                 Ribosomal_L14  82 naaVllnkkgeplGtrifgpvarelrekkflkivslApev 121
                                   na+V+++ +g+p+G+ i+gpva+e++e+ ++ i+ +A+ +
  gi|15668643|ref|NP_247441.1|  93 NAVVIVTPDGNPKGSDIKGPVAKEAAER-WPGIARIAKII 131
                                   ***************************9.******99876 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.7e-05      0.15      39      93 ..      41     109 ..      23     129 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.7e-05
                                   HHHHHHH..-SEEEESSH.HHHHHHHH....GGGGG...........GG-EEEEEEEEEEEESTT-TT..-- CS
                    SBP_bac_11  39 arqiadgarpDvwipassawlellaaa....glvqa...........esavplassplviavpkgnpk..ki 93 
                                   ar++   +  D++i +  +   +++++                    +++v +a + +vi++p gnpk  +i
  gi|15668643|ref|NP_247441.1|  41 ARRLPTARVGDMVIVTVKKGTPEMRKQvlpaV---VirqrkeirrpdGTRVKFADNAVVIVTPDGNPKgsDI 109
                                   56666666666666666555555554433211...1345666777889******************994344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 839.33
//
Query:       gi|15668644|ref|NP_247442.1|  [L=120]
Description: 50S ribosomal protein L24 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-29  102.3   0.8    1.7e-29  102.1   0.8    1.1  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    1.7e-09   37.3   1.7    1.7e-09   37.3   1.7    1.6  2  KOW            KOW motif
     0.0095   16.3   0.7      0.093   13.1   0.1    2.3  2  ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L
  ------ inclusion threshold ------
      0.079   12.3   0.0       0.11   11.9   0.0    1.3  1  AAL_decarboxy  Alpha-acetolactate decarboxylase
      0.091   12.8   0.1       0.18   11.8   0.1    1.5  1  DUF2187        Uncharacterized protein conserved in bacteria 


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.8   4.6e-33   1.7e-29       1      80 [.       6     118 ..       6     120 .] 0.97

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 4.6e-33
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xxxxxx RF
                 Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................gvtrek 49 
                                   s+++rkqrKa+fnap+h rrk+msa LskeL+ek g +++p+r                                g+++++
  gi|15668644|ref|NP_247442.1|   6 SKQPRKQRKALFNAPLHLRRKVMSAMLSKELKEKLGKNAIPVRkgdvvrimrgdfkglegevikvdlkryriyveGANNKR 86 
                                   89******************************************************************************* PP

                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                 Ribosomal_L26  50 angttvpvgihpSkvvItklkl.DkdrkkiLe 80 
                                   ++g++vp++ihpS+v+I+kl+  D++r k ++
  gi|15668644|ref|NP_247442.1|  87 QDGREVPYPIHPSNVMIIKLYDkDEKRFKHIK 118
                                   ********************998999988776 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   1.7   4.6e-13   1.7e-09       1      32 []      49      80 ..      49      80 .. 0.98
   2 ?   -3.1   0.0       2.4   8.8e+03      18      25 ..     102     109 ..     100     111 .. 0.66

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 4.6e-13
                                  TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                           KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                  +Gd+V++++G +kG +G+V kvd +++r++v+
  gi|15668644|ref|NP_247442.1| 49 KGDVVRIMRGDFKGLEGEVIKVDLKRYRIYVE 80
                                  7*****************************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                                   EEEEEETT CS
                           KOW  18 kVvkvdqh 25 
                                   ++ k +++
  gi|15668644|ref|NP_247442.1| 102 MIIKLYDK 109
                                   77777765 PP

>> ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.082   2.9e+02      23      58 ..      18      56 ..       3      68 .. 0.73
   2 !   13.1   0.1   2.6e-05     0.093      20      46 ..      90     116 ..      69     120 .] 0.77

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.082
                 ribosomal_L24 23 EapIhv.SnVmlvdpkcgkptrvgfrlk..edgkkvRvs 58
                                   ap+h+  +Vm    +++ + ++g      ++g  vR+ 
  gi|15668644|ref|NP_247442.1| 18 NAPLHLrRKVMSAMLSKELKEKLGKNAIpvRKGDVVRIM 56
                                  689999999998777777777777744244567777776 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.6e-05
                 ribosomal_L24  20 iekEapIhvSnVmlvdpkcgkptrvgf 46 
                                    e   pIh SnVm++   ++   r ++
  gi|15668644|ref|NP_247442.1|  90 REVPYPIHPSNVMIIKLYDKDEKRFKH 116
                                   58899*********9877777777666 PP

>> AAL_decarboxy  Alpha-acetolactate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.9e-05      0.11      33      70 ..      58      95 ..      48     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.9e-05
                 AAL_decarboxy 33 GTfeeldGEliildgkvYqlksdgsvrevddeektPFa 70
                                  G f++l+GE+i +d k Y++  +g  ++ +d +++P+ 
  gi|15668644|ref|NP_247442.1| 58 GDFKGLEGEVIKVDLKRYRIYVEGANNKRQDGREVPYP 95
                                  6799*******************************995 PP

>> DUF2187  Uncharacterized protein conserved in bacteria (DUF2187)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1     5e-05      0.18       5      26 ..      49      71 ..      47      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5e-05
                       DUF2187  5 vGdiieFkkgdlk.ltGiVekvn 26
                                   Gd+++ ++gd+k l+G V+kv 
  gi|15668644|ref|NP_247442.1| 49 KGDVVRIMRGDFKgLEGEVIKVD 71
                                  7********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 805.56
//
Query:       gi|15668645|ref|NP_247443.1|  [L=244]
Description: 30S ribosomal protein S4e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-25   88.2   0.8    4.6e-25   87.3   0.8    1.5  1  Ribosomal_S4e  Ribosomal family S4e
    1.9e-14   53.4   6.1    3.1e-14   52.8   6.1    1.3  1  RS4NT          RS4NT (NUC023) domain
    3.9e-09   36.1   2.0    1.6e-08   34.2   0.2    2.4  2  S4             S4 domain
     0.0002   21.2   0.3     0.0002   21.2   0.3    2.0  2  KOW            KOW motif
     0.0081   15.9   0.5      0.033   14.0   0.1    2.1  2  S4_2           S4 domain
  ------ inclusion threshold ------
      0.033   14.0   0.0      0.054   13.4   0.0    1.2  1  zf-ZPR1        ZPR1 zinc-finger domain


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   0.8   1.5e-28   4.6e-25       2      75 .]      97     176 ..      96     176 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 1.5e-28
                                   TEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEES........STT-STTEEEEEETTTTE CS
                 Ribosomal_S4e   2 genyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtiryp........dpdikvnDtvkidleenk 74 
                                   +enyr+l+d+kgr++l++   e+ ++KLcKik+kt++k+g++ql++hdGr+i ++        ++ +k++Dt++i+++e++
  gi|15668645|ref|NP_247443.1|  97 NENYRVLFDRKGRIKLKPT--ENPDVKLCKIKNKTVIKGGHIQLNLHDGRNIVIKvsdptkaeEDVYKTGDTLLISIPEQE 175
                                   8****************99..9999***************************99999999999555**************9 PP

                                   E CS
                 Ribosomal_S4e  75 I 75 
                                   I
  gi|15668645|ref|NP_247443.1| 176 I 176
                                   8 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   6.1     1e-17   3.1e-14       1      36 [.       4      39 ..       4      40 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 1e-17
                                  -S----EETTTS-TTS---SSSSSEE----SSSS-T CS
                         RS4NT  1 rGpkkHLKrlaAPkhWpldkkegvfavkPspGPHkl 36
                                  +Gpk+HLKrlaAP  W l++k ++f+v+P pG+H++
  gi|15668645|ref|NP_247443.1|  4 KGPKRHLKRLAAPVRWELPRKIHKFTVRPLPGAHPM 39
                                  7*********************************98 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.2   5.2e-12   1.6e-08       9      48 .]      52      91 ..      43      91 .. 0.92
   2 ?    0.8   0.1      0.13     4e+02      21      31 ..     129     139 ..     128     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 5.2e-12
                                  HTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                            S4  9 rlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                   l++a   reA+++I+ G+VlV+G+v+k  + +V+ +Dv+
  gi|15668645|ref|NP_247443.1| 52 ILKYADNAREAKKIIKMGKVLVDGRVRKEEKLPVGLMDVV 91
                                  5899**********************************98 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.13
                                   HHHHTTTEEET CS
                            S4  21 qlIehGrVlVN 31 
                                     I++G++++N
  gi|15668645|ref|NP_247443.1| 129 TVIKGGHIQLN 139
                                   57******998 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.3   6.7e-08    0.0002       1      31 [.     184     217 ..     184     218 .. 0.90
   2 ?   -3.2   0.2       3.3   9.8e+03       2       9 ..     229     236 ..     228     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.7e-08
                                   TTSEEEESSSTTTTCEEEEEEEETTT...TEEEE CS
                           KOW   1 pGdhVkVvsGphkGktGkVvkvdqhk...vrVfv 31 
                                   +G+  ++++G+h G+ +k+v++++     ++V++
  gi|15668645|ref|NP_247443.1| 184 VGKLAYITGGKHVGDFAKIVEIERRGiypDIVTL 217
                                   799*********************9988887776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.3
                                   TSEEEESS CS
                           KOW   2 GdhVkVvs 9  
                                    d+V Vv+
  gi|15668645|ref|NP_247443.1| 229 KDYVFVVG 236
                                   68999985 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.1e-05     0.033      24      64 ..      60     102 ..      50     103 .. 0.76
   2 ?   -1.1   0.0      0.56   1.7e+03      27      38 ..     128     139 ..     123     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                          S4_2  24 geaKafiaegeVkvNGevetrRgkKlraG..dvVei..dgetiev 64 
                                    eaK +i+ g+V+v+G v  r+  Kl  G  dvV++  ++e+++v
  gi|15668645|ref|NP_247443.1|  60 REAKKIIKMGKVLVDGRV--RKEEKLPVGlmDVVSLpdANENYRV 102
                                   59**************99..6777777776688988644666665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.56
                          S4_2  27 KafiaegeVkvN 38 
                                   K++i+ g++++N
  gi|15668645|ref|NP_247443.1| 128 KTVIKGGHIQLN 139
                                   788888888887 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.8e-05     0.054      36      89 ..     123     180 ..     120     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                       zf-ZPR1  36 Cgyknnevksageie...ekGkritlkveseedlnrqvlkS.etatveipeleleipp 89 
                                   C+ kn+ v  +g+i+   + G++i++kv+++++ + +v+k  +t  ++ipe e++ + 
  gi|15668645|ref|NP_247443.1| 123 CKIKNKTVIKGGHIQlnlHDGRNIVIKVSDPTKAEEDVYKTgDTLLISIPEQEIKAHI 180
                                   ***************99989********************74677899**98887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1644.23
//
Query:       gi|15668646|ref|NP_247444.1|  [L=190]
Description: 50S ribosomal protein L5 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-26   92.4   0.1    7.4e-26   90.2   0.1    2.1  3  Ribosomal_L5_C  ribosomal L5P family C-terminus
    5.2e-21   74.7   0.1    9.5e-21   73.9   0.1    1.5  1  Ribosomal_L5    Ribosomal protein L5


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.49   4.4e+03      40      51 ..      53      64 ..      38      66 .. 0.75
   2 !   90.2   0.1   8.3e-30   7.4e-26       1      94 []      67     169 ..      67     169 .. 0.93
   3 ?    2.7   0.0     0.016   1.4e+02       7      28 ..     160     181 ..     154     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.49
                Ribosomal_L5_C 40 dgrGnvsfGike 51
                                   ++ n sfGi++
  gi|15668646|ref|NP_247444.1| 53 AKQTNPSFGIRK 64
                                  567889999986 PP

  == domain 2  score: 90.2 bits;  conditional E-value: 8.3e-30
                Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivttak... 78 
                                   piG+kvtLrg+k++efl++++e+  ++ +    + ++sfd+ Gn+sfGi+e+i+fp+ +yd+ +gifGmd++++++++   
  gi|15668646|ref|NP_247444.1|  67 PIGLKVTLRGKKAEEFLKNAFEAFQKEGK---KLYDYSFDDYGNFSFGIHEHIDFPGQKYDPMIGIFGMDVCVTLERPgfr 144
                                   8***********************99999...788*******************************************988 PP

                Ribosomal_L5_C  79 tde..........earallkelgipf 94 
                                   +++          ++r l++e++i+f
  gi|15668646|ref|NP_247444.1| 145 VKRrkrcrakiprRHR-LTREEAIEF 169
                                   4446788899997888.999999998 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.016
                Ribosomal_L5_C   7 tLrgekmyefldkllevvlprl 28 
                                    L++e++ ef++k + v++ r+
  gi|15668646|ref|NP_247444.1| 160 RLTREEAIEFIEKTFGVKVERV 181
                                   68999********999988876 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.1   1.1e-24   9.5e-21       1      57 []      10      63 ..      10      63 .. 0.99

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 1.1e-24
                                  SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                  Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                  N+M +Pr+eK+v+n gvGe+g++   l+k a++++e+tGQkP++t+ak++ ++F+iR
  gi|15668646|ref|NP_247444.1| 10 NPMLKPRIEKVVVNFGVGESGDR---LTKGAQVIEELTGQKPIRTRAKQTNPSFGIR 63
                                  9**********************...******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1166.70
//
Query:       gi|15669881|ref|NP_247445.1|  [L=53]
Description: 30S ribosomal protein S14 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-11   42.6   2.1    4.2e-11   42.4   2.1    1.0  1  Ribosomal_S14  Ribosomal protein S14p/S29e
  ------ inclusion threshold ------
      0.088   12.4   2.1       0.45   10.1   0.1    2.0  2  RecR           RecR protein


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   2.1   4.7e-15   4.2e-11       4      52 ..       3      51 ..       1      52 [. 0.90

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 4.7e-15
                                  ----SS..CTTT---SSS--.SSSEE-GGG-..EHHHHHHHTTT...TT-EE CS
                 Ribosomal_S14  4 klprnssptrirnrCrvtGr.prGvirkfgL..sRicfRelAlkgelpGvkK 52
                                  k p +++ + + + C+ +G+ + G+irk+gL  +R+cfRe A+k    G+kK
  gi|15669881|ref|NP_247445.1|  3 KKPWKKKYGYGIRPCQRCGHvGPGLIRKYGLnlCRQCFREIAHK---LGFKK 51
                                  66667777889999******99**********************...***99 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1     5e-05      0.45      15      25 ..      13      23 ..      12      25 .. 0.89
   2 ?    2.0   0.2     0.017   1.5e+02      16      23 ..      33      40 ..      30      41 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5e-05
                                  H-EE-TTT--E CS
                          RecR 15 kvrhCsrCgnl 25
                                  ++r+C+rCg++
  gi|15669881|ref|NP_247445.1| 13 GIRPCQRCGHV 23
                                  59*******96 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.017
                                  -EE-TTT- CS
                          RecR 16 vrhCsrCg 23
                                  +  C++C+
  gi|15669881|ref|NP_247445.1| 33 LNLCRQCF 40
                                  56899997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 347.09
//
Query:       gi|15668647|ref|NP_247446.1|  [L=130]
Description: 30S ribosomal protein S8 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-28   99.7   0.0    1.3e-28   99.5   0.0    1.0  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.5   0.0     7e-33   1.3e-28       1     127 []       5     130 .]       5     130 .] 0.89

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 7e-33
                                   -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCC..EEEEE-BSSS-SBSSSEEEE-SB CS
                  Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkk..ikielkynkkkksvikklkrvsk 77 
                                   Dp+a++l++i N e+++k+ v++ paskl+ ++lkv++++Gyi +fe+  + +  +  +++ +k+nk  +++ik    v+k
  gi|15668647|ref|NP_247446.1|   5 DPLANALNHISNCERVGKKVVYIkPASKLIGRVLKVMQDNGYIGEFEFIeDGRAGIfkVELIGKINK--CGAIKPRFPVKK 83 
                                   9***********************************************8444445544777778877..************ PP

                                   TTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                  Ribosomal_S8  78 pgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                    g + +  ++ lp   + +Gi+ivsT++Gvm+++eA+k+++GG++layv+
  gi|15668647|ref|NP_247446.1|  84 FGYEKFE-KRYLP--ARDFGILIVSTTQGVMSHEEAKKRGLGGRLLAYVY 130
                                   9999544.34555..689*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 899.65
//
Query:       gi|15668648|ref|NP_247447.1|  [L=182]
Description: 50S ribosomal protein L6 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-35  119.7  12.8    2.6e-17   63.3   3.6    2.1  2  Ribosomal_L6  Ribosomal protein L6
  ------ inclusion threshold ------
          5    7.3   7.6        9.2    6.5   1.0    3.2  4  HSP20         Hsp20/alpha crystallin family


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   3.6   2.9e-21   2.6e-17       1      76 []      13      85 ..      13      85 .. 0.98
   2 !   62.1   1.8   6.6e-21   5.9e-17       1      76 []      97     171 ..      97     171 .. 0.99

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 2.9e-21
                                  CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                  Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                  iP++v+v+i++ + v v+   +el+r++ +  ++ +k+eg++++  +    +k k+ ++gt+r++innmikGVteg
  gi|15668648|ref|NP_247447.1| 13 IPENVQVEINN-NEVVVKSGGKELRRRFEHP-KIVIKKEGDEIVIFCEYPRRKDKA-MVGTIRAHINNMIKGVTEG 85
                                  8*********5.*******************.9999********************.*****************98 PP

  == domain 2  score: 62.1 bits;  conditional E-value: 6.6e-21
                                   CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHHHTC CS
                  Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGVteg 76 
                                   +P++v+v+++++ ++++lG+k++++++i egvtv+++     +++++v+gidkekv    A+i+++++++  + +++++g
  gi|15668648|ref|NP_247447.1|  97 FPMKVSVKGNEVIIENFLGEKHPRRARIMEGVTVKIS-----GEDVIVTGIDKEKVgqtaANIEQATRIKGRDPRVFQDG 171
                                   8************************************.....9***********************************98 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.0     0.001       9.2      20      39 ..      14      33 ..       9      51 .. 0.77
   2 ?   -0.2   0.0      0.13   1.1e+03      18      47 ..      39      67 ..      36      74 .. 0.76
   3 ?   -1.0   0.0      0.21   1.9e+03      23      35 ..      99     111 ..      85     125 .. 0.77
   4 ?    2.6   0.2     0.016   1.5e+02      22      45 ..     127     149 ..     124     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.001
                                  CCCEEEEEETTEEEEEEE-- CS
                         HSP20 20 keelkvkvednrvlvkgehe 39
                                  +e+++v++++n+v+vk++ +
  gi|15668648|ref|NP_247447.1| 14 PENVQVEINNNEVVVKSGGK 33
                                  89*************98876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.13
                                  --CCCEEEEEETTEEEEEEE--..---TT- CS
                         HSP20 18 lkkeelkvkvednrvlvkgeheeeeedekg 47
                                  +++  + +k e++++++  e + +++d+ +
  gi|15668648|ref|NP_247447.1| 39 FEHPKIVIKKEGDEIVIFCEYP-RRKDKAM 67
                                  5666789999999999999998.5555544 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.21
                                   EEEEEETTEEEEE CS
                         HSP20  23 lkvkvednrvlvk 35 
                                   +kv+v++n+v+++
  gi|15668648|ref|NP_247447.1|  99 MKVSVKGNEVIIE 111
                                   5788888888876 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.016
                                   CEEEEEETTEEEEEEE--..---T CS
                         HSP20  22 elkvkvednrvlvkgeheeeeede 45 
                                    ++vk+ ++ v+v+g  + e+ ++
  gi|15668648|ref|NP_247447.1| 127 GVTVKISGEDVIVTGIDK-EKVGQ 149
                                   689************999.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1427.79
//
Query:       gi|15668649|ref|NP_247448.1|  [L=146]
Description: 50S ribosomal protein L32e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-40  136.1   0.4    8.7e-40  135.5   0.4    1.3  1  Ribosomal_L32e  Ribosomal protein L32


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.5   0.4   4.9e-44   8.7e-40       1     108 []      15     120 ..      15     120 .. 0.99

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 4.9e-44
                                   ------TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE..EE CS
                Ribosomal_L32e   1 tkkFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenksyaa 81 
                                   +++Fir++ +r ++l+e+wr+p+G ++++r ++k+++++++iGY+spk++rgl+psG+++vlV+nvk+Le+l++e++   a
  gi|15668649|ref|NP_247448.1|  15 KPDFIRQEAHRHKRLGEKWRRPKGRHSKMRLKWKEKPPVVEIGYRSPKAVRGLHPSGLEDVLVYNVKDLEKLNPETQ--GA 93 
                                   589**************************************************************************..** PP

                                   EE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                Ribosomal_L32e  82 eiahsVsskkrkeiverAaelgikVtN 108
                                   +ia++V+++k++ei+ rA+elgi+++N
  gi|15668649|ref|NP_247448.1|  94 RIASTVGKRKKIEIIIRARELGIRILN 120
                                   *************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1028.14
//
Query:       gi|15668650|ref|NP_247449.1|  [L=151]
Description: 50S ribosomal protein L19e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-57  191.7  10.5    7.1e-57  191.5  10.5    1.0  1  Ribosomal_L19e  Ribosomal protein L19e
  ------ inclusion threshold ------
      0.066   12.7   1.6      0.079   12.5   1.6    1.1  1  ORC5_C          Origin recognition complex (ORC) subunit 5 C-
        1.6    9.0   6.5        1.1    9.6   0.1    2.6  3  pXO2-72         Uncharacterized protein pXO2-72


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.5  10.5   1.2e-60   7.1e-57       2     143 ..       6     147 ..       5     148 .. 0.98

  Alignments for each domain:
  == domain 1  score: 191.5 bits;  conditional E-value: 1.2e-60
                                   THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGGG--S- CS
                Ribosomal_L19e   2 lklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsGkrkGt 82 
                                   ++ q+r+aa++lk+G +rvw+dp++l+++++A++++dir+lik+g+I+kk+kkg s ar++++ke+++kgrrrg+G+r+G+
  gi|15668650|ref|NP_247449.1|   6 VSVQRRMAAEILKCGIERVWIDPTQLDRVKMAMSKDDIRALIKEGVIKKKQKKGISSARVKKLKEQRKKGRRRGPGSRRGA 86 
                                   689****************************************************************************** PP

                                   HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT-X CS
                Ribosomal_L19e  83 keaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiekk 143
                                   ++aR+p ke+W+ +iRalR++Lk+lr+++kid+k Yr+lYr+akGg+f+++++L  y++++
  gi|15668650|ref|NP_247449.1|  87 AGARTPPKERWMATIRALRKTLKQLRDSGKIDRKVYRKLYRMAKGGAFRSRSHLFLYMREH 147
                                   *******************************************************999876 PP

>> ORC5_C  Origin recognition complex (ORC) subunit 5 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.6   1.3e-05     0.079     150     236 ..      40     126 ..      36     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                        ORC5_C 150 rlDlrlFsktsgkskkrrkrrkgssqkskekakskkrk.......isqkllgPkaFpLeRllAIfqailpeeeaepseees 223
                                   + D+r   k+      ++k++kg s+++++k k++++k        ++   g+++ p eR++A  +a+++  ++  +++ +
  gi|15668650|ref|NP_247449.1|  40 KDDIRALIKEGV---IKKKQKKGISSARVKKLKEQRKKgrrrgpgSRRGAAGARTPPKERWMATIRALRKTLKQ-LRDSGK 116
                                   567777777762...23445556666666665545555667788788889*******************87644.444333 PP

                        ORC5_C 224 setlsvdvlsqia 236
                                      ++ +v++++ 
  gi|15668650|ref|NP_247449.1| 117 ---IDRKVYRKLY 126
                                   ...7777777765 PP

>> pXO2-72  Uncharacterized protein pXO2-72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.6     0.033     2e+02      35      49 ..      40      54 ..      25      68 .. 0.72
   2 ?   -2.4   0.5      0.99   5.9e+03      46      55 ..      67      76 ..      53      81 .. 0.57
   3 ?    9.6   0.1   0.00018       1.1      16      40 ..      95     119 ..      91     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.033
                       pXO2-72 35 selldkLikeGklky 49
                                   + +  LikeG +k 
  gi|15668650|ref|NP_247449.1| 40 KDDIRALIKEGVIKK 54
                                  355789*****8874 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.99
                       pXO2-72 46 klkyykPiek 55
                                  klk  + +++
  gi|15668650|ref|NP_247449.1| 67 KLKEQRKKGR 76
                                  4444444444 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00018
                       pXO2-72  16 drWeitleaLrmkLkrlkdselldk 40 
                                   +rW  t  aLr  Lk+l+ds  +d+
  gi|15668650|ref|NP_247449.1|  95 ERWMATIRALRKTLKQLRDSGKIDR 119
                                   6*******************98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1043.46
//
Query:       gi|15668651|ref|NP_247450.1|  [L=195]
Description: 50S ribosomal protein L18 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-31  108.7   5.6    2.2e-19   70.0   1.6    2.9  3  Ribosomal_L5e    Ribosomal large subunit proteins 60S L5, and
    1.2e-13   51.8   1.4    1.2e-13   51.8   1.4    1.5  2  Ribosomal_L18_c  Ribosomal L18 C-terminal region
    2.1e-07   31.3   0.1    2.9e-07   30.9   0.1    1.3  1  Ribosomal_L18p   Ribosomal L18 of archaea, bacteria, mitoch. 


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   1.6   3.7e-23   2.2e-19       3      99 ..       7      96 ..       5     100 .. 0.95
   2 !   39.5   0.1   9.1e-14   5.4e-10     129     162 ..      99     132 ..      95     133 .. 0.93
   3 ?   -0.3   0.0      0.16   9.3e+02     115     140 ..     153     178 ..     137     194 .. 0.62

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 3.7e-23
                 Ribosomal_L5e  3 fqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvgltnyaaa 85
                                  ++vkfrrrre+ktdY++r +l+        + k Rlv r t +++i+qi+    +gdk++++a+s+el k+g+k    n  +a
  gi|15668651|ref|NP_247450.1|  7 YRVKFRRRREAKTDYRKRLKLLL-------SRKPRLVARRTLNHCIAQIVLYDEKGDKTVVSAHSRELIKLGYKGHTGNLPSA 82
                                  9********************98.......5688****************************************9999***** PP

                 Ribosomal_L5e 86 Yatglllarrllkk 99
                                  Y+tg+ll++++l+k
  gi|15668651|ref|NP_247450.1| 83 YLTGYLLGKKALAK 96
                                  **********9987 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 9.1e-14
                 Ribosomal_L5e 129 fkaiLdvGLartttgakvfgalkgavdgglsiph 162
                                    +a+Ld+GL+r+t+g+ +f+ lkga+d+g++iph
  gi|15668651|ref|NP_247450.1|  99 TEAVLDIGLHRATKGNAIFAILKGALDAGMEIPH 132
                                   689******************************9 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.16
                 Ribosomal_L5e 115 eeynveeideekrafkaiLdvGLart 140
                                   e+ + ++++  k+ f  +L+ GL+  
  gi|15668651|ref|NP_247450.1| 153 EMLKEQDEERYKKQFSKYLEKGLEPE 178
                                   33344444556688999999998755 PP

>> Ribosomal_L18_c  Ribosomal L18 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1         3   1.8e+04      74      79 ..      18      23 ..       6      36 .. 0.51
   2 !   51.8   1.4     2e-17   1.2e-13       5      57 ..     140     192 ..     138     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3
               Ribosomal_L18_c 74 eskkyk 79
                                  ++ + k
  gi|15668651|ref|NP_247450.1| 18 KTDYRK 23
                                  222223 PP

  == domain 2  score: 51.8 bits;  conditional E-value: 2e-17
               Ribosomal_L18_c   5 rkrIfgkhvaeYmeeLkeedeekykkqFskyikkgieaddleelykkahaaIr 57 
                                   ++rI g+h++ Y e+Lke+dee+ykkqFsky++kg+e+++l e ++++ a+I 
  gi|15668651|ref|NP_247450.1| 140 EERIRGEHIKAYAEMLKEQDEERYKKQFSKYLEKGLEPEKLPEHFEEIKAKID 192
                                   579***********************************************995 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.1   4.9e-11   2.9e-07       6      96 ..      11     108 ..       6     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 4.9e-11
                                   HHCHHHHH..HTTT--.TTSSS-EEEEEE-SS-EEEEEE..-TTT--EEEEECS-SC.CCT.S-SSSCHHHHHHHHHHHHH CS
                Ribosomal_L18p   6 arkrRhkR..irkkls.gtaerprlvvfrsnrhiyaQvi..ddvkgktlasastlek.elk.lkstknkeaakkvgeliAe 79 
                                    r+rR+++   rk+l+   + +prlv  r+ +h  aQ++  d++ +kt++sa + e  +l  + +t+n  +a   g l+ +
  gi|15668651|ref|NP_247450.1|  11 FRRRREAKtdYRKRLKlLLSRKPRLVARRTLNHCIAQIVlyDEKGDKTVVSAHSRELiKLGyKGHTGNLPSAYLTGYLLGK 91 
                                   4555554411578888777889***************976699999******99986244467889999************ PP

                                   HHCHHCHTC-EE--TTS CS
                Ribosomal_L18p  80 rakekgiekvvfDrggy 96 
                                   +a++kg +++v D g +
  gi|15668651|ref|NP_247450.1|  92 KALAKGYTEAVLDIGLH 108
                                   *************8755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1332.00
//
Query:       gi|15668652|ref|NP_247451.1|  [L=217]
Description: 30S ribosomal protein S5 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-27   93.7   5.8    1.4e-26   92.2   5.8    1.8  2  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
      9e-24   82.7   0.1    1.4e-23   82.1   0.1    1.3  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.49   4.4e+03      13      23 ..      16      26 ..      14      29 .. 0.82
   2 !   92.2   5.8   1.6e-30   1.4e-26       1      65 []      49     113 ..      49     113 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.49
                                  EEETTEEEEEE CS
                  Ribosomal_S5 13 kvtkgGrrtsf 23
                                  +++k G++t +
  gi|15668652|ref|NP_247451.1| 16 RMVKEGQITDI 26
                                  599****9875 PP

  == domain 2  score: 92.2 bits;  conditional E-value: 1.6e-30
                                   XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                  Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                   l+ekvl++k vq++ k+Grr +f+a+vvvG++nG+vG+G gkakev  AirkAi +Akkn+++v+
  gi|15668652|ref|NP_247451.1|  49 LEEKVLDVKLVQRMHKSGRRARFRATVVVGNRNGYVGVGKGKAKEVGPAIRKAIAQAKKNIIRVK 113
                                   79************************************************************995 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.1   1.6e-27   1.4e-23       2      67 ..     135     201 ..     134     206 .. 0.94

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 1.6e-27
                                   EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT-. CS
                Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrspee 67 
                                   gk+g++ + + pap+G G++ag++++avl laGikDv++k+ g +r+++n++ AtfeALk+l+  ++
  gi|15668652|ref|NP_247451.1| 135 GKCGSTAIEILPAPKGVGLVAGDVAKAVLGLAGIKDVWTKTFGeTRTTYNFAMATFEALKSLNFTRT 201
                                   9************************************************************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1456.31
//
Query:       gi|15668653|ref|NP_247452.1|  [L=154]
Description: 50S ribosomal protein L30 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-17   61.2   2.2    8.5e-17   60.8   0.3    2.0  2  Ribosomal_L30  Ribosomal protein L30p/L7e


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.3   4.7e-21   8.5e-17       1      51 []       3      53 ..       3      53 .. 0.92
   2 ?   -0.7   0.1     0.077   1.4e+03       6      21 ..      73      88 ..      62      90 .. 0.68

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 4.7e-21
                                  EEEEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHHHCCCGE CS
                 Ribosomal_L30  1 lfVtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLkkVkhlV 51
                                  ++V+rir+ +gv  ++ +tL++L+L+k+n+ v+ + t + +GmL+kVk++V
  gi|15668653|ref|NP_247452.1|  3 YAVIRIRGRVGVRRDIADTLKMLRLHKVNHCVIIPETETFKGMLQKVKDYV 53
                                  58***************************66666666*************9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.077
                                  -S-STTS-HHHHHHHH CS
                 Ribosomal_L30  6 irsiigvppkvrktLq 21
                                    +  +v+p + k L 
  gi|15668653|ref|NP_247452.1| 73 LPGNKKVNPEIIKELT 88
                                  4457778888777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 982.33
//
Query:       gi|15668654|ref|NP_247453.1|  [L=143]
Description: 50S ribosomal protein L15 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-25   88.5   0.4    8.4e-25   87.9   0.4    1.3  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
  ------ inclusion threshold ------
      0.025   14.0   0.0      0.041   13.3   0.0    1.4  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.4   9.3e-29   8.4e-25       2     127 ..      29     141 ..      28     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 9.3e-29
                                   GGGTSSTTTTTTTTT-..S--........S--.........---.GGG..---EEEEHHHHHHTTTTGTTS.--.----EE CS
                Ribosomal_L27A   2 GktgGrGhkGqkkrsg..vkk.kpg.feGGqmplyrrlpkrGfk.nskfkkeykvvnlkdLdelideerle.la.deaeei 75 
                                   G++gGrG++G +k+++  + k  p+ f  G++         Gfk +    k+ +++n+++L+e++ ++  + ++ d++ ++
  gi|15668654|ref|NP_247453.1|  29 GNKGGRGMAGGHKHKWtwIIKyCPDyF--GKY---------GFKrHPSLVKRLETINVGELEEIVLKNPDKfEKeDDKFVV 98 
                                   9***************98555577779..***.........***765567999************999877444799**** PP

                                   EGGGTTTTSSS....SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                Ribosomal_L27A  76 dleelaeaglikkkdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                   d+ el          g+ Kvlgkg++t +++vka ++S+kA+ekIea+GG+v+
  gi|15668654|ref|NP_247453.1|  99 DVIEL----------GYeKVLGKGKVTIPMIVKAVEVSEKAREKIEAVGGEVV 141
                                   *****..........************************************97 PP

>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.6e-06     0.041      97     120 ..     118     141 ..      85     143 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-06
                 Ribosomal_L18  97 lsvaALrftetararilkaGGeil 120
                                   + v A++++e+ar++i++ GGe++
  gi|15668654|ref|NP_247453.1| 118 MIVKAVEVSEKAREKIEAVGGEVV 141
                                   6799******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1088.56
//
Query:       gi|15668655|ref|NP_247454.1|  [L=436]
Description: preprotein translocase subunit SecY [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-64  216.5  26.1    6.9e-64  216.0  26.1    1.2  1  SecY             SecY translocase
    1.1e-06   28.3   1.7    9.9e-05   22.1   0.2    3.6  3  Plug_translocon  Plug domain of Sec61p


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.0  26.1   7.7e-68   6.9e-64       1     306 []      69     415 ..      69     415 .. 0.83

  Alignments for each domain:
  == domain 1  score: 216.0 bits;  conditional E-value: 7.7e-68
                                   BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS.-S.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.......HH.HHH CS
                          SecY   1 sifaLGImPyitasIilqLl.tvvipkleelk.ke.geegrkkinqitryltvvlalvqalgialslg.......lallli 71 
                                   ++++LGI+P++ta+Ii+qLl ++      +++ +   +e+r+++++++++l++++++v+a+ ++ ++g       l ++l+
  gi|15668655|ref|NP_247454.1|  69 TLITLGIGPIVTAGIIMQLLvGS-----GIIQmDLsIPENRALFQGCQKLLSIIMCFVEAVLFV-GAGafgiltpLLAFLV 143
                                   799*****************999.....667755569***********************9966.3346779999789*** PP

                                   HHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHC.CHSS..-.HHHHSS........THHHHHHHHHHHHHHHHH CS
                          SecY  72 vlqltagtvllmwLgEqitekGiGnGisllifagivarlp.kals..g.lielale......gilallllllvtllvillv 142
                                   ++q+ +g+++l++L+E ++++GiG+Gi l+i+ag++++++ +al   g l+++ ++      + +  ++ ++ t++v+l+v
  gi|15668655|ref|NP_247454.1| 144 IIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIFvGALGpeGyLWKFLNSliqgvpN-IEYIAPIIGTIIVFLMV 223
                                   ****************************************88888873344442223446744.799************** PP

                                   CHHHHBEEEECBBBSTT....S.S-EEEEETTCCCSCHHHHHHHHHH.................................. CS
                          SecY 143 vyveeaerripvqyakrgrkggqssylPlklnyagviPiIfasslla.................................. 189
                                   vy e ++++ip+ + +    +g+ +++P+k++y ++iP+I+a +l+a                                  
  gi|15668655|ref|NP_247454.1| 224 VYAECMRVEIPLAHGRI---KGAVGKYPIKFVYVSNIPVILAAALFAniqlwglalyrmgipilghyeggravdgiayyls 301
                                   *************9965...699************************5555555555555555555555544444333333 PP

                                   HHHCCCCS.TCCCS..THHHHHHHHHHHHHHHHHHHHTCT.THHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHH CS
                          SecY 190 lpstiaqfllalls..psvlyvvlyvlliifFayfyteit.fnpkevaenlkksggfipgir.pgketakyLekvlsritl 266
                                   +p  + ++++   +  + ++y++ +++  ++F +f++e+t ++pk++a+ +   g+ i+g+r ++k++++ L+++++ +t+
  gi|15668655|ref|NP_247454.1| 302 TPYGLSSVIS---DpiHAIVYMIAMIITCVMFGIFWVETTgLDPKSMAKRIGSLGMAIKGFRkSEKAIEHRLKRYIPPLTV 379
                                   3444433332...233345566666666666*******************************99***************** PP

                                   HHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
                          SecY 267 iGalflaliavlpdllgasligafggtslLivVgvaletv 306
                                   ++++f++++a++++++ga  +g  ggt++L++V+++++++
  gi|15668655|ref|NP_247454.1| 380 MSSAFVGFLATIANFIGA--LG--GGTGVLLTVSIVYRMY 415
                                   ******************..87..************9875 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   1.1e-08   9.9e-05       1      35 []      35      68 ..      35      68 .. 0.92
   2 ?    0.8   0.0     0.052   4.7e+02       4      14 ..     265     274 ..     265     278 .. 0.88
   3 ?    1.9   0.0     0.022     2e+02      12      26 ..     304     317 ..     302     323 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-08
                                  HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
               Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                  +lY+++++i +y   +++++ +f+++++i As  G
  gi|15668655|ref|NP_247454.1| 35 VLYFIMGCIDVY-TAGAQIPAIFEFWQTITASRIG 68
                                  79**********.4478***************987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.052
                                   HHHCCSB-TT- CS
               Plug_translocon   4 lvlsqiPLyGi 14 
                                   l+ ++i L+G+
  gi|15668655|ref|NP_247454.1| 265 LF-ANIQLWGL 274
                                   67.9******9 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.022
                                   TT--SSS-TCCHTTT CS
               Plug_translocon  12 yGissssssDpfywl 26 
                                   yG+s s +sDp+   
  gi|15668655|ref|NP_247454.1| 304 YGLS-SVISDPIHAI 317
                                   9**9.89****9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2720.48
//
Query:       gi|15668656|ref|NP_247455.1|  [L=195]
Description: adenylate kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-40  137.8   0.2    3.9e-40  137.4   0.2    1.2  1  AAA_17      AAA domain
      3e-09   37.5   0.1    7.4e-09   36.2   0.1    1.6  1  AAA_18      AAA domain
    7.7e-05   22.1   0.6    0.00011   21.6   0.1    1.5  2  6PF2K       6-phosphofructo-2-kinase
    0.00057   19.6   0.0    0.00067   19.3   0.0    1.2  1  SRP54       SRP54-type protein, GTPase domain
     0.0036   17.2   1.1     0.0049   16.8   0.3    1.7  2  NTPase_1    NTPase
     0.0049   17.0   0.0       0.01   16.0   0.0    1.5  1  AAA_33      AAA domain
     0.0068   16.8   1.2      0.011   16.1   1.2    1.9  1  AAA_19      AAA domain
      0.007   15.9   0.3      0.007   15.9   0.3    1.5  2  AAA_7       P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.012   14.6   0.2      0.022   13.7   0.2    1.4  1  MeaB        Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.019   15.2   2.7       0.13   12.5   1.0    2.4  2  DUF1884     Domain of unknown function (DUF1884)
       0.03   14.2   0.1      0.067   13.1   0.1    1.6  1  MobB        Molybdopterin guanine dinucleotide synthesis prot
      0.032   14.6   0.0      0.044   14.1   0.0    1.3  1  AAA_16      AAA ATPase domain
      0.035   14.0   0.7      0.045   13.7   0.5    1.3  1  ATPase_2    ATPase domain predominantly from Archaea
      0.036   13.5   0.1      0.049   13.1   0.1    1.4  1  KTI12       Chromatin associated protein KTI12
      0.044   13.0   0.1      0.057   12.6   0.1    1.3  1  NB-ARC      NB-ARC domain
      0.068   12.9   0.3       0.19   11.5   0.1    1.8  2  ATP_bind_1  Conserved hypothetical ATP binding protein
      0.077   12.7   0.2       0.12   12.0   0.2    1.5  1  AAA_30      AAA domain
       0.11   12.8   0.1       0.16   12.3   0.1    1.5  1  AAA_22      AAA domain
       0.11   11.8   0.1       0.37   10.0   0.1    1.8  1  DUF1611     Domain of unknown function (DUF1611_C) P-loop dom
       0.11   12.4   0.0       0.29   11.0   0.0    1.7  1  APS_kinase  Adenylylsulphate kinase
       0.11   12.4   0.0       0.16   11.9   0.0    1.3  1  NACHT       NACHT domain


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.4   0.2   4.6e-43   3.9e-40       1     135 [.      12     151 ..      12     152 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 4.6e-43
                                   EE-TTSSHHHHHHHHHHHH.....TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEE CS
                        AAA_17   1 lGgPGsGKgtqceklveky.....gfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlv 76 
                                   +G+PG+G +t+ +k  e++     +++++++G +++e ak++gl+++rd++rklp ee+k++qk+a +kiae+ak+ +++v
  gi|15668656|ref|NP_247455.1|  12 VGVPGVGSTTVTNKAIEELkkegiEYKIVNFGTVMFEIAKEEGLVEHRDQLRKLPPEEQKRIQKLAGKKIAEMAKEFNIVV 92 
                                   7**************9988777779******************************************************** PP

                                   EE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHHH CS
                        AAA_17  77 dghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddneesi 135
                                   d+h +ik+++g+l+glp++vleel+pd+i+l+ea+++eil rrlkd+tr+rd ++ e+i
  gi|15668656|ref|NP_247455.1|  93 DTHSTIKTPKGYLPGLPAWVLEELNPDIIVLVEAENDEILMRRLKDETRQRDFESTEDI 151
                                   *********************************************************98 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.1   8.6e-12   7.4e-09       1     116 [.       9     142 ..       9     152 .. 0.66

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 8.6e-12
                        AAA_18   1 IlltGtpGvGKttlakeL....skrl.gf.....gvnlrdvakenglllevdpe......aldeskrldedkldklldale 65 
                                   +++ G+pGvG tt+++      +k++ ++     g++  ++ake+gl++ +d+       + ++ ++l  +k ++  ++++
  gi|15668656|ref|NP_247455.1|   9 VVIVGVPGVGSTTVTNKAieelKKEGiEYkivnfGTVMFEIAKEEGLVEHRDQLrklppeEQKRIQKLAGKKIAEMAKEFN 89 
                                   789***********97663332555444499999********************555444333333333333333333333 PP

                        AAA_18  66 enss...aleegknlvidghlaeleseaakdikkvvLtasp.eelleRlekRgye 116
                                      +   +   +k  ++ g++a+ ++e + di  v ++a++ e+l++Rl++  ++
  gi|15668656|ref|NP_247455.1|  90 IVVDthsTIKTPKG-YLPGLPAWVLEELNPDII-VLVEAENdEILMRRLKDETRQ 142
                                   33335432223333.788888888888888888.******989999999997633 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   1.3e-07   0.00011      13      93 ..       6      89 ..       1      98 [. 0.89
   2 ?   -2.1   0.0       2.2   1.9e+03     134     169 ..     127     160 ..     113     188 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.3e-07
                                  -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS...---GGGGSTT-HHHHHHHHHHHHHHHHHHHHHH CS
                         6PF2K 13 klvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaska...lsdaeffrpdneealklreklalaalkdllayl 92
                                  + v+v+vG p  g t++++k +  lk  g++ k+ n+g +  e++k+    +  +  r+  +e +k  +kla + + ++++++
  gi|15668656|ref|NP_247455.1|  6 NKVVVIVGVPGVGSTTVTNKAIEELKKEGIEYKIVNFGTVMFEIAKEeglVEHRDQLRKLPPEEQKRIQKLAGKKIAEMAKEF 88
                                  45899**************************************9999888777788888888888989999999999999988 PP

                                  H CS
                         6PF2K 93 n 93
                                  n
  gi|15668656|ref|NP_247455.1| 89 N 89
                                  6 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                                   -HHHHHHHHHHHHTTTSGGGTTS-HHHHHHHHHHHH CS
                         6PF2K 134 sdeeiikeNikevklsspDYkdketeeaikdflkRl 169
                                   ++ ei+ + +k+ + +  D++  +++ + + f++R 
  gi|15668656|ref|NP_247455.1| 127 ENDEILMRRLKDETRQ-RDFES-TEDIGEHIFMNRC 160
                                   4555555555555555.55543.3334445555553 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   7.8e-07   0.00067       2     106 ..       7     109 ..       6     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.8e-07
                                   EEEEEEESTTSSHHHHHHHHHHHHHHT..TS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHH CS
                         SRP54   2 nvillvGlqGaGKTttlaKLaallkke..gkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekak 80 
                                   +v+++vG+ G+G Tt + K  + lkke  ++k++   + +f +a  e L ++ ++l+   +  +e++   ++a +++ ++ 
  gi|15668656|ref|NP_247455.1|   7 KVVVIVGVPGVGSTTVTNKAIEELKKEgiEYKIVNFGTVMFEIAKEEGLVEHRDQLR--KLPPEEQKRIQKLAGKKIAEMA 85 
                                   699************************66677777778889***********99999..4567778888889988888887 PP

                                   HTTSSEEEEEE--SSTTHHHHHHHHH CS
                         SRP54  81 eekidvvlvDTaGrlqndkelmeelk 106
                                   +e    ++vDT    ++ k ++  l 
  gi|15668656|ref|NP_247455.1|  86 KEF--NIVVDTHSTIKTPKGYLPGLP 109
                                   765..578999888777777776665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   5.7e-06    0.0049       2      30 ..       9      37 ..       8      53 .. 0.92
   2 ?   -3.0   0.0         7     6e+03     129     147 ..     121     139 ..     112     151 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.7e-06
                                  EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                  v+i G pGvG tT+ +k++e+lk++g+++
  gi|15668656|ref|NP_247455.1|  9 VVIVGVPGVGSTTVTNKAIEELKKEGIEY 37
                                  7899*********************9876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7
                                   EEE--SS--SHHHHHHHT- CS
                      NTPase_1 129 lavihrrkdlalveeirer 147
                                   ++ +  ++d+ l+++++++
  gi|15668656|ref|NP_247455.1| 121 IVLVEAENDEILMRRLKDE 139
                                   3333333355555555544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.2e-05      0.01       1     128 [.       8     151 ..       8     165 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                        AAA_33   1 lvllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfg..tdqqsktdytrvldrlyqilnelarkal...sagr 71 
                                   +v++vG+pG+G +t+  + +++l+     + +++  t+++ +++    +++  ++ ++ ++  +++++la k+    ++++
  gi|15668656|ref|NP_247455.1|   8 VVVIVGVPGVGSTTVTNKAIEELKkegieYKIVNFGTVMFEIAKeeGLVEHRDQLRKLPPEEQKRIQKLAGKKIaemAKEF 88 
                                   89*****************99999888999999999999988885533445555556777788888888888772213345 PP

                        AAA_33  72 nvildatnlsrrer.....arflklarrlgvpvrivvvetdeetl.keRlak..Raangddrsev 128
                                   n+++  t  + ++          +++++l+ p+ iv ve+ ++++  +Rl+   R+++ ++  + 
  gi|15668656|ref|NP_247455.1|  89 NIVV-DTHSTIKTPkgylpGLPAWVLEELN-PDIIVLVEAENDEIlMRRLKDetRQRDFESTEDI 151
                                   5555.4444433331224445556778888.9999999998776514444431133333444445 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.2   1.3e-05     0.011       8      38 ..       4      34 ..       1     190 [. 0.94

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                        AAA_19  8 lkekvllvtaGpGtGKTrvlkhivallvelg 38
                                  +k+kv+++++ pG G T+v+++++++l+++g
  gi|15668656|ref|NP_247455.1|  4 MKNKVVVIVGVPGVGSTTVTNKAIEELKKEG 34
                                  689************************9998 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   8.2e-06     0.007      29      70 ..       2      43 ..       1      51 [. 0.93
   2 ?   -3.6   0.1         8   6.9e+03       5      21 ..      83      99 ..      80     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.2e-06
                         AAA_7 29 llknkkpvllvGptGtGKtviikdllkkldkekylsltinfs 70
                                  ++ ++k v++vG  G+G t+++++ +++l+ke + ++++nf 
  gi|15668656|ref|NP_247455.1|  2 MMMKNKVVVIVGVPGVGSTTVTNKAIEELKKEGIEYKIVNFG 43
                                  7889999*********************************95 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8
                         AAA_7  5 eeakfseilVptvdtvr 21
                                  e ak ++i+V t  t++
  gi|15668656|ref|NP_247455.1| 83 EMAKEFNIVVDTHSTIK 99
                                  56667789999988876 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   2.6e-05     0.022      29      62 ..       6      39 ..       2      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                                  SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEE CS
                          MeaB 29 aqvvGltGvPGaGkstlvealglelrrrGkrvav 62
                                   +vv + GvPG+G  t++++ ++el+++G    +
  gi|15668656|ref|NP_247455.1|  6 NKVVVIVGVPGVGSTTVTNKAIEELKKEGIEYKI 39
                                  67899***********************976655 PP

>> DUF1884  Domain of unknown function (DUF1884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.0   0.00015      0.13      11      42 ..      23      54 ..      19     103 .. 0.67
   2 ?    1.8   0.0      0.33   2.8e+02      21      46 ..     114     140 ..     110     155 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                  HHHHHHHHHHTT----EEEE-HHHHHHHHHHH CS
                       DUF1884 11 ieekineLkleGfePdiiLvGkeaieflkeal 42
                                   +++i+eLk+eG+e  i+ +G  ++e  ke+ 
  gi|15668656|ref|NP_247455.1| 23 TNKAIEELKKEGIEYKIVNFGTVMFEIAKEEG 54
                                  5689**********************999863 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.33
                                   TT----EE.EE-HHHHHHHHHHHHHHH CS
                       DUF1884  21 eGfePdii.LvGkeaieflkealkkel 46 
                                   e ++Pdii Lv  e  e l   lk+e 
  gi|15668656|ref|NP_247455.1| 114 EELNPDIIvLVEAENDEILMRRLKDET 140
                                   678999762666777777777777654 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.9e-05     0.067       1      43 [.       8      50 ..       8      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.9e-05
                          MobB  1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvd 43
                                  v+ ivg  g G Tt  +k i+elk++g++  ++   +  f++ 
  gi|15668656|ref|NP_247455.1|  8 VVVIVGVPGVGSTTVTNKAIEELKKEGIEYKIVNFGTVMFEIA 50
                                  689************************9988887766666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.2e-05     0.044      26     106 ..       8      78 ..       3     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.2e-05
                        AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrekleeal 105
                                   +v+++G +GvG +++ +++ ++l+k+g   ++ k + +       +   +++++e+l++  ++    +++++ ++++++ +
  gi|15668656|ref|NP_247455.1|   8 VVVIVGVPGVGSTTVTNKAIEELKKEG---IEYKIVNF------GTvMFEIAKEEGLVEHRDQL--RKLPPEEQKRIQKLA 77 
                                   799***********************8...77777777......44477888777777777666..335666666666655 PP

                        AAA_16 106 a 106
                                   +
  gi|15668656|ref|NP_247455.1|  78 G 78 
                                   5 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   5.3e-05     0.045      19      89 ..       5      84 ..       1     124 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.3e-05
                      ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienledkdk........yviyyialreesiskldefie.eeeekkklekalgiavpka 89
                                  +n++++i G  g+G t++ +++ie+l++ +          v++ ia +e   ++ d+  +   ee+k+++k +g+++ + 
  gi|15668656|ref|NP_247455.1|  5 KNKVVVIVGVPGVGSTTVTNKAIEELKKEGIeykivnfgTVMFEIAKEEGLVEHRDQLRKlPPEEQKRIQKLAGKKIAEM 84
                                  689***********************988877777777778888888888888877764475555566666665555443 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.7e-05     0.049       4      46 ..       9      53 ..       7     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-05
                                  EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH...TTSS CS
                         KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg..iekds 46
                                  vv+ G+P +G +t++++  ++l++e+++  +++  ++   i+k++
  gi|15668656|ref|NP_247455.1|  9 VVIVGVPGVGSTTVTNKAIEELKKEGIEYKIVNFGTVMfeIAKEE 53
                                  9******************************99888874434443 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   6.7e-05     0.057      20      56 ..       6      42 ..       1      92 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.7e-05
                                  SEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEE CS
                        NB-ARC 20 slvvalvGmgGvGKttlakqilnksdevegrFdsvaw 56
                                    vv +vG +GvG tt+ +++++++++   ++ +v +
  gi|15668656|ref|NP_247455.1|  6 NKVVVIVGVPGVGSTTVTNKAIEELKKEGIEYKIVNF 42
                                  459*********************7776668887755 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00023      0.19       1      32 [.      11      42 ..      11      50 .. 0.95
   2 ?   -1.5   0.0       2.1   1.8e+03     182     215 ..      58      92 ..      46     100 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNL 32
                                  +vG++G+G tt +++ +e l+++g ++++vN 
  gi|15668656|ref|NP_247455.1| 11 IVGVPGVGSTTVTNKAIEELKKEGIEYKIVNF 42
                                  79*****************************6 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                    ATP_bind_1 182 dvealslllekeeekykkla.eaiaelleefalvl 215
                                   + ++l++l  +e+++ +kla ++iae+ +ef++v 
  gi|15668656|ref|NP_247455.1|  58 HRDQLRKLPPEEQKRIQKLAgKKIAEMAKEFNIVV 92 
                                   44555666666665555544277888888888774 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00014      0.12      16      50 ..       4      40 ..       1     102 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                        AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaag..grvi 50
                                   +++v+v++G++G G tt+ +++ e ++++g  ++++
  gi|15668656|ref|NP_247455.1|  4 MKNKVVVIVGVPGVGSTTVTNKAIEELKKEGieYKIV 40
                                  4567*****************9999999888555444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00018      0.16       4      51 ..       5      53 ..       2     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsst 51
                                  + +++v++G +G+G Tt+ ++  e+l++e  +e+   + ++v +++++++
  gi|15668656|ref|NP_247455.1|  5 KNKVVVIVGVPGVGSTTVTNKAIEELKKE-GIEYkiVNFGTVMFEIAKEE 53
                                  56899********************9543.33335655666655555555 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00043      0.37      10     129 ..       4     130 ..       2     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00043
                       DUF1611  10 vkakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgili.agegvvldavvvdfvaGaveglvkkaae..... 84 
                                   +k+k+v++vG    vG  t + +  e+l+++G++ ++v  g ++  i  +eg+v  +      +++ ++ ++k+a      
  gi|15668656|ref|NP_247455.1|   4 MKNKVVVIVGVP-GVGSTTVTNKAIEELKKEGIEYKIVNFGTVMFEIaKEEGLVEHRDQLRKLPPEEQKRIQKLAGkkiae 83 
                                   578999999975.79********************************8888988877777777777666666555411111 PP

                       DUF1611  85 eeepdlilveGQgsLthpay..sgvtlglLlGsqPdalvLchrpgrk 129
                                     +   i+v+  + +  p +  +g+ + +L   +Pd +vL+ +++ +
  gi|15668656|ref|NP_247455.1|  84 MAKEFNIVVDTHSTIKTPKGylPGLPAWVLEELNPDIIVLVEAENDE 130
                                   22223477888888876654225677778888888888888777655 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00034      0.29       3      53 ..       7      57 ..       5      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                                  EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSH CS
                    APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfse 53
                                   vv + G+ g G +t++n+  ++L+++gi+ ++++  +v +++ k+ g  e
  gi|15668656|ref|NP_247455.1|  7 KVVVIVGVPGVGSTTVTNKAIEELKKEGIEYKIVNFGTVMFEIAKEEGLVE 57
                                  68999**************************99999999999988877643 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.16       2      98 ..       8     103 ..       7     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C.CHHHHCCSCC CS
                         NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse.vwavllelpe 81 
                                   +v++ G +G+G Tt   k +++++++  + +   + F   + e+ +++     +d+l++  pe+++++++   + ++e ++
  gi|15668656|ref|NP_247455.1|   8 VVVIVGVPGVGSTTVTNKAIEELKKEGIEYK--IVNFGTVMFEIAKEEGLVEHRDQLRKLPPEEQKRIQKlAGKKIAEMAK 86 
                                   89*************************9995..688888888999988889999999999999999999954566777777 PP

                                   CEEEEEE-STT-SS-TC CS
                         NACHT  82 rlLlilDglDelvtdlg 98 
                                      +++D    ++t  g
  gi|15668656|ref|NP_247455.1|  87 EFNIVVDTHSTIKTPKG 103
                                   77777777777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1081  (0.0602934); expected 358.6 (0.02)
Passed bias filter:                      780  (0.0435049); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1241.00
//
Query:       gi|15668657|ref|NP_247456.1|  [L=198]
Description: hypothetical protein MJ_0480 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-28  100.1   8.5    1.3e-28   99.9   8.5    1.0  1  EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
    0.00055   19.9   8.2    0.00086   19.3   8.2    1.4  1  60KD_IMP    60Kd inner membrane protein
     0.0046   16.6   0.8     0.0077   15.9   0.8    1.3  1  Bac_transf  Bacterial sugar transferase
     0.0078   16.4   0.3      0.024   14.8   0.2    1.7  1  DUF4079     Protein of unknown function (DUF4079)
  ------ inclusion threshold ------
      0.013   14.9   0.3      0.017   14.5   0.3    1.1  1  V-ATPase_C  V-ATPase subunit C
      0.024   14.7   0.5      0.044   13.9   0.0    1.6  2  COX6C       Cytochrome c oxidase subunit VIc
      0.059   13.5   0.9      0.087   13.0   0.9    1.1  1  Uds1        Up-regulated During Septation
      0.074   13.0   0.4      0.074   13.0   0.4    2.1  2  T2SSF       Type II secretion system (T2SS), protein F
        2.1    8.4   6.6          3    7.9   6.6    1.1  1  FlxA        FlxA-like protein
          4    7.8  12.1       0.14   12.5   5.5    1.9  2  DUF4199     Protein of unknown function (DUF4199)


Domain annotation for each model (and alignments):
>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   8.5   7.1e-32   1.3e-28       2     168 ..      15     197 ..      14     198 .] 0.92

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 7.1e-32
                    EMC3_TMCO1   2 lvldplirdwvllPivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqeelme 82 
                                    +++p i+  vl P  + il+++i+++l++++ +kll+d+k++ + +k  +e+q +++++ kn +  + +kl+++q+++m+
  gi|15668657|ref|NP_247456.1|  15 AIFMPIIK--VLHPA-LAILIIAIIVSLIINIATKLLVDQKRVAELKKEIQEFQVKFKKMSKNPE--MMEKLQEEQQRIMQ 90 
                                   57889999..88888.9*****************************************9987665..99************ PP

                    EMC3_TMCO1  83 dqsemmmdqmkpmivtmipqiliffwlnsffs...................gfvvaklp.fpltgrfksllqrgl.esldv 142
                                    + e+m+++++pmi+t +p+ilif++l++++                     +++ k++ + +++++ s+  +g  + +  
  gi|15668657|ref|NP_247456.1|  91 LNAELMKMSFRPMIYTWVPIILIFIYLRHVYGfggvyqelnpgwngvvvylPIILSKILfIDFWHWLGSIFYKGGfKIVSN 171
                                   *********************************************66666655668888579********999988***** PP

                    EMC3_TMCO1 143 rfvssiswYflcsfglsqiirklLge 168
                                   +   ++ wY+lcsf++s ++rk+Lg+
  gi|15668657|ref|NP_247456.1| 172 TALGWLGWYILCSFATSTVLRKILGI 197
                                   ************************98 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   8.2   4.8e-07   0.00086       3     114 ..      28     152 ..      26     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.8e-07
                      60KD_IMP   3 laIilltiivrlillpltlkqlkssakmqelqPelkeiqekyk...kdk...qklqqemmklYkkegvnplaGclplLiql 77 
                                   laI+++ iiv li + +++k l  +++++el++e++e q k+k   k++   +klq+e++++ + +   + +++ p++ ++
  gi|15668657|ref|NP_247456.1|  28 LAILIIAIIVSLI-INIATKLLVDQKRVAELKKEIQEFQVKFKkmsKNPemmEKLQEEQQRIMQLNAELMKMSFRPMIYTW 107
                                   8999999999876.57899999********************98883423448899999999998888888899****999 PP

                      60KD_IMP  78 pifialyrvlrslasf..wikdLsapd......lpillavttflq 114
                                   + +i ++  lr++  f  + ++L+         lpi+l+ + f+ 
  gi|15668657|ref|NP_247456.1| 108 VPIILIFIYLRHVYGFggVYQELNPGWngvvvyLPIILSKILFID 152
                                   989999999999776665566666522456666666666666655 PP

>> Bac_transf  Bacterial sugar transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.8   4.3e-06    0.0077      13      89 ..      28      99 ..      11     104 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.3e-06
                    Bac_transf 13 lillsplllviallikle.ssggpvffkqkRvGkngkpFk..iyKFRsmvkdaekklgavvklkndpritkvGrflRkts 89
                                  l+     +l+ia+++ l  +  ++++  qkRv + +k+++   +KF+ m k+ e +   +  +++++ri+++ + l k+s
  gi|15668657|ref|NP_247456.1| 28 LA-----ILIIAIIVSLIiNIATKLLVDQKRVAELKKEIQefQVKFKKMSKNPEMM---EKLQEEQQRIMQLNAELMKMS 99
                                  22.....223444433333334579********98876653347*****9988875...666777889998887777766 PP

>> DUF4079  Protein of unknown function (DUF4079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   1.4e-05     0.024       2      82 ..      22     136 ..      21     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                       DUF4079   2 allHPvlmvllvfpllgavaylG..wqtrqrrlqsk................................aerkekipkkvrd 48 
                                   ++lHP+l++l++++++++ ++ +  + + q+r ++                                 + + e+++ ++r 
  gi|15668657|ref|NP_247456.1|  22 KVLHPALAILIIAIIVSLIINIAtkLLVDQKRVAELkkeiqefqvkfkkmsknpemmeklqeeqqrimQLNAELMKMSFRP 102
                                   689***************999997777888888888999999999999999999999999999999999999999999999 PP

                       DUF4079  49 eHvklgslllllvvlgaigglvllylrrgklfps 82 
                                     +++  ++l++++l  + g+ ++y + +  + +
  gi|15668657|ref|NP_247456.1| 103 MIYTWVPIILIFIYLRHVYGFGGVYQELNPGWNG 136
                                   999999999****999999999999777666655 PP

>> V-ATPase_C  V-ATPase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   9.7e-06     0.017     238     308 ..      54     124 ..      46     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.7e-06
                    V-ATPase_C 238 arekkfivReFsydeeeleeekeeltkleaekkkqegelvrllkvnFsevfvawiHlkalrvFvEsvLRYG 308
                                   + e k  ++eF+++ ++++++ e ++kl++e+++  +   +l+k++F  ++ +w+ +  + ++   v  +G
  gi|15668657|ref|NP_247456.1|  54 VAELKKEIQEFQVKFKKMSKNPEMMEKLQEEQQRIMQLNAELMKMSFRPMIYTWVPIILIFIYLRHVYGFG 124
                                   55778899************************************************999999987776665 PP

>> COX6C  Cytochrome c oxidase subunit VIc
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       7.6   1.4e+04      48      54 ..       9      15 ..       7      15 .. 0.84
   2 ?   13.9   0.0   2.5e-05     0.044      18      64 ..      30      80 ..      23      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.6
                         COX6C 48 FYknYDa 54
                                  +Yk+ Da
  gi|15668657|ref|NP_247456.1|  9 YYKTLDA 15
                                  89*9996 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.5e-05
                         COX6C 18 hlvvafvlslgvaaaykfavaepR....KkayadFYknYDaekefeemrka 64
                                   l++a+++sl++ +a k +v ++R    Kk++++F  ++  + +  em+++
  gi|15668657|ref|NP_247456.1| 30 ILIIAIIVSLIINIATKLLVDQKRvaelKKEIQEFQVKFKKMSKNPEMMEK 80
                                  689********************98888999*********99999999985 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.9   4.8e-05     0.087      20      62 ..      51      93 ..      48     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.8e-05
                          Uds1 20 leeVeelkkelkaLeerlealrkkLaletklrdaarsLsrlys 62
                                  ++ V+elkke++  + + ++++k+ ++  kl++  +++++l++
  gi|15668657|ref|NP_247456.1| 51 QKRVAELKKEIQEFQVKFKKMSKNPEMMEKLQEEQQRIMQLNA 93
                                  688***********************************99994 PP

>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   3.4       2.8     5e+03     105     120 ..      26      41 ..      15      45 .. 0.61
   2 ?   13.0   0.4   4.1e-05     0.074      78     120 ..      75     117 ..      70     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.8
                                   TXXXXXXXXXXXXXXX CS
                         T2SSF 105 pllllvvallvllill 120
                                   p+l ++++++++++++
  gi|15668657|ref|NP_247456.1|  26 PALAILIIAIIVSLII 41 
                                   4444444444444443 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.1e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXX CS
                         T2SSF  78 aevLerlaeyleeerelrrkllaallepllllvvallvllill 120
                                   +e++e+l+e++++  +l ++l+++++ p+++ +v +++++i+l
  gi|15668657|ref|NP_247456.1|  75 PEMMEKLQEEQQRIMQLNAELMKMSFRPMIYTWVPIILIFIYL 117
                                   69********************************999999975 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.6    0.0017         3      17      67 ..      52      97 ..      47      99 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                          FlxA 17 sqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaq 67
                                  +++a+L+k+i++ q + k++s++      e +++ q+ q+ I ql+a++ +
  gi|15668657|ref|NP_247456.1| 52 KRVAELKKEIQEFQVKFKKMSKN-----PEMMEKLQEEQQRIMQLNAELMK 97
                                  34555555555555555555555.....24568888889999999999866 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   5.5     8e-05      0.14      63     151 ..      17     113 ..       2     123 .. 0.65
   2 ?   -0.4   1.5      0.75   1.4e+03      11      44 ..     112     146 ..     107     193 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8e-05
                       DUF4199  63 fisfgqafgfgflislvagllsavfqyiyfnfidpdfienyiaeilekleeakeesae.eenaemseeei.....keales 137
                                   f+++ + +  +++i ++a ++s+++++++  ++d+  ++++++ei+e   + k++s+  e +++++ee+      +++l++
  gi|15668657|ref|NP_247456.1|  17 FMPIIKVLHPALAILIIAIIVSLIINIATKLLVDQKRVAELKKEIQEFQVKFKKMSKNpEMMEKLQEEQQrimqlNAELMK 97 
                                   777778888889999999999999998888899**********99988777777666655555444444332222222223 PP

                       DUF4199 138 ls..piivalqsflgn 151
                                   +s  p+i+++  ++ +
  gi|15668657|ref|NP_247456.1|  98 MSfrPMIYTWVPIILI 113
                                   3355544333333332 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.75
                       DUF4199  11 ilifll.ilyllglhqi.lstgpllgllallllllv 44 
                                   +++++l ++y++g   +   +  + g+++ l ++l+
  gi|15668657|ref|NP_247456.1| 112 LIFIYLrHVYGFGGV-YqELNPGWNGVVVYLPIILS 146
                                   555566666666653.32233344444443333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2574  (0.143566); expected 358.6 (0.02)
Passed bias filter:                     1236  (0.0689386); expected 358.6 (0.02)
Passed Vit filter:                       195  (0.0108762); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 1390.64
//
Query:       gi|15668658|ref|NP_247457.1|  [L=240]
Description: hypothetical protein MJ_0482 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-26   94.0   0.1    1.8e-26   93.4   0.1    1.3  1  NYN       NYN domain


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4   0.1     1e-30   1.8e-26       1     146 [.      71     202 ..      71     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 1e-30
                           NYN   1 rvavfiDgenlpvpakgkevdyrklleeirskgelvraraygnwedeeqnkfqdalsstgikvkhkplkkrggsgkkavDv 81 
                                   r+a++iDg n+    k+ ++d++k++e +++ g++v+ r+y+n++++   k+ +a  ++g++ k          + ++vDv
  gi|15668658|ref|NP_247457.1|  71 RIALLIDGPNMLR--KEFNIDLDKIREVLSEFGDIVIGRVYLNQYAS--DKLIEAVINQGFEPKI---------SAGDVDV 138
                                   89***********..6668************************4444..6788888888996644.........5699*** PP

                           NYN  82 elavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaadefisl 146
                                   e+avda+el++++++dti  v++D+DF p+++k++ergk+V+v++ae +  s++L++ ad++i++
  gi|15668658|ref|NP_247457.1| 139 EMAVDATELVFNPNIDTIAYVTRDADFLPAIRKAKERGKKVIVIGAE-PGFSTALQNIADYVIKI 202
                                   *********************************************65.9*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1496  (0.0834402); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1497.20
//
Query:       gi|15668659|ref|NP_247458.1|  [L=98]
Description: zinc finger protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00053   19.3  15.2       0.18   11.3   0.5    3.4  3  zf-ribbon_3      zinc-ribbon domain
     0.0016   19.1   9.6        0.8   10.7   0.7    3.4  3  zf-C2H2_4        C2H2-type zinc finger
     0.0016   18.5   8.4       0.12   12.6   0.1    3.2  3  zf-RING_7        C4-type zinc ribbon domain
     0.0026   17.6   4.7     0.0059   16.5   0.4    2.5  2  Prok-RING_1      Prokaryotic RING finger family 1
     0.0037   17.6  13.1       0.44   11.1   1.0    3.5  3  zf-C2H2          Zinc finger, C2H2 type
     0.0049   16.9  11.8      0.023   14.7   5.6    2.3  2  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.013   15.7  13.7       0.51   10.5   0.3    3.3  3  zf-AN1           AN1-like Zinc finger
      0.015   15.2   3.8        4.4    7.3   0.1    3.2  3  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.032   13.8   8.3        1.6    8.4   0.1    3.3  3  Sgf11            Sgf11 (transcriptional regulation protein)
      0.036   13.8   1.7      0.036   13.8   1.7    2.4  2  Ribosomal_S27e   Ribosomal protein S27
      0.037   14.0   9.4       0.11   12.5   0.5    3.2  3  DUF1610          Domain of unknown function (DUF1610)
       0.05   13.5  13.9        2.1    8.3   0.7    3.3  3  Cys_rich_CPXG    Cysteine-rich CPXCG
      0.055   13.6   8.9      0.047   13.8   7.9    1.5  1  zf-RRPl_C4       Putative ribonucleoprotein zinc-finger pf C4
      0.062   13.6  14.0       0.84   10.0   0.5    3.2  3  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
      0.091   12.9   0.7       0.12   12.5   0.7    1.5  1  Arv1             Arv1-like family
       0.12   12.6  10.7        5.8    7.3   0.1    3.3  3  zinc_ribbon_9    zinc-ribbon
       0.13   11.8  13.6      0.094   12.2   4.4    2.6  3  TF_Zn_Ribbon     TFIIB zinc-binding
       0.14   12.1  10.0        9.3    6.3   0.0    3.1  3  zf-C2HC5         Putative zinc finger motif, C2HC5-type
       0.15   12.5   6.5        1.9    9.0   2.4    2.4  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.19   11.5  17.0       0.37   10.6   0.1    3.7  4  zinc_ribbon_2    zinc-ribbon domain
       0.22   11.6   5.0        1.6    8.9   0.1    2.5  2  Ribosomal_L37ae  Ribosomal L37ae protein family
       0.26   11.2   5.7       0.36   10.8   1.4    2.3  2  C1_1             Phorbol esters/diacylglycerol binding domain
        0.3   11.1  10.7          3    7.9   0.2    3.0  3  CpXC             CpXC protein
       0.39   11.4  11.1        5.2    7.8   1.4    3.3  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.54   10.4  12.3       0.25   11.5   4.5    2.7  3  Zn-ribbon_8      Zinc ribbon domain
       0.85   10.0  11.0       0.36   11.2   0.8    2.9  3  DUF3268          zinc-finger-containing domain
       0.97    9.7   5.5         13    6.1   0.0    3.1  3  HNH              HNH endonuclease
        1.1    9.3  12.6        9.4    6.3   1.0    3.3  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        1.1    9.3   8.6        1.1    9.3   2.8    2.7  2  HypA             Hydrogenase/urease nickel incorporation, met
        1.1    9.8  19.5        2.2    8.8   2.3    3.6  3  zf-H2C2_2        Zinc-finger double domain
        1.3    9.0  10.4         41    4.3  10.4    2.7  1  zinc-ribbons_6   zinc-ribbons
          2    7.8   7.9       0.37   10.2   1.5    2.5  2  zf-TFIIB         Transcription factor zinc-finger
        2.3    8.7   4.2        3.3    8.2   0.3    2.4  2  Evr1_Alr         Erv1 / Alr family
        2.5    7.9  12.6         13    5.6   0.4    3.2  3  YacG             DNA gyrase inhibitor YacG
        2.8    8.0   7.6       0.99    9.4   2.8    2.5  3  zf-DNL           DNL zinc finger
          3    8.0   9.8        1.3    9.2   2.5    2.4  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        3.6    7.7  13.5        1.1    9.4   0.6    3.2  3  zf-C2H2_6        C2H2-type zinc finger
        4.6    7.2   9.6        7.5    6.6   4.9    2.9  2  zinc_ribbon_4    zinc-ribbon domain
        6.1    7.4  10.3         15    6.2   8.9    2.3  2  zf-CHY           CHY zinc finger
        9.2    6.8  10.9        1.7    9.1   0.5    3.3  3  Zn-C2H2_12       Autophagy receptor zinc finger-C2H2 domain
        9.8    5.9  13.1        7.3    6.3   0.2    3.3  3  zf_UBZ           Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   1.9    0.0012      0.53      18      24 ..       3       9 ..       1      14 [. 0.64
   2 ?    6.7   0.6     0.011         5      19      25 ..      61      67 ..      59      69 .. 0.63
   3 !   11.3   0.5    0.0004      0.18       3      10 ..      79      86 ..      77      95 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                   zf-ribbon_3 18 vCpyCGt 24
                                  +CpyCG+
  gi|15668659|ref|NP_247458.1|  3 NCPYCGK 9 
                                  4555554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                   zf-ribbon_3 19 CpyCGtk 25
                                  CpyC ++
  gi|15668659|ref|NP_247458.1| 61 CPYCKKP 67
                                  6666554 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0004
                   zf-ribbon_3  3 vrCPnCGa 10
                                  ++CPnCG+
  gi|15668659|ref|NP_247458.1| 79 ITCPNCGE 86
                                  56777776 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1    0.0033       1.5       1      15 [.       2      16 ..       2      24 .. 0.78
   2 !   10.7   0.7    0.0018       0.8       1      14 [.      59      72 ..      59      75 .. 0.85
   3 ?    3.3   0.4      0.42   1.9e+02       2      10 ..      80      88 ..      79      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0033
                     zf-C2H2_4  1 fkCpiCgksFsskka 15
                                  + Cp+Cgk + +  a
  gi|15668659|ref|NP_247458.1|  2 YNCPYCGKDCVNEAA 16
                                  79******9987766 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0018
                     zf-C2H2_4  1 fkCpiCgksFsskk 14
                                  + Cp+C+k+F+ ++
  gi|15668659|ref|NP_247458.1| 59 YLCPYCKKPFKAYY 72
                                  78********8665 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.42
                     zf-C2H2_4  2 kCpiCgksF 10
                                  +Cp Cg++ 
  gi|15668659|ref|NP_247458.1| 80 TCPNCGETL 88
                                  6****9987 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3     0.068        30      25      30 ..       3       8 ..       1       9 [. 0.85
   2 ?    5.3   0.4     0.051        22      20      29 ..      55      64 ..      45      66 .. 0.79
   3 !   12.6   0.1   0.00027      0.12      21      30 ..      76      85 ..      69      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.068
                                  E-TTT- CS
                     zf-RING_7 25 tCpeCG 30
                                   Cp+CG
  gi|15668659|ref|NP_247458.1|  3 NCPYCG 8 
                                  7****9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.051
                                  STB-EE-TTT CS
                     zf-RING_7 20 gdevvtCpeC 29
                                  g+ +  Cp+C
  gi|15668659|ref|NP_247458.1| 55 GGRIYLCPYC 64
                                  47899***** PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00027
                                  TB-EE-TTT- CS
                     zf-RING_7 21 devvtCpeCG 30
                                  ++v+tCp+CG
  gi|15668659|ref|NP_247458.1| 76 KVVITCPNCG 85
                                  568******9 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.4      0.35   1.5e+02       6      13 ..       3      10 ..       1      18 [. 0.72
   2 !   16.5   0.4   1.4e-05    0.0059       6      27 ..      60      85 ..      57      88 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.35
                   Prok-RING_1  6 kCpvCgke 13
                                  +Cp Cgk 
  gi|15668659|ref|NP_247458.1|  3 NCPYCGKD 10
                                  68888876 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.4e-05
                   Prok-RING_1  6 kCpvCgkelkee...dD.iVvCpeCg 27
                                   Cp C+k++k     d  +++Cp+Cg
  gi|15668659|ref|NP_247458.1| 60 LCPYCKKPFKAYyekDKvVITCPNCG 85
                                  6********975553442446****9 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.6    0.0043       1.9       1      11 [.       2      12 ..       2      17 .. 0.85
   2 !   11.1   1.0     0.001      0.44       1      13 [.      59      71 ..      59      73 .. 0.84
   3 ?    4.7   0.3      0.11        49       2       9 ..      80      87 ..      79      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0043
                                  EEETTTTEEES CS
                       zf-C2H2  1 ykCpdCgksFk 11
                                  y Cp+Cgk + 
  gi|15668659|ref|NP_247458.1|  2 YNCPYCGKDCV 12
                                  89******876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.001
                                  EEETTTTEEESSH CS
                       zf-C2H2  1 ykCpdCgksFkrk 13
                                  y Cp+C+k+Fk  
  gi|15668659|ref|NP_247458.1| 59 YLCPYCKKPFKAY 71
                                  66********976 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.11
                                  EETTTTEE CS
                       zf-C2H2  2 kCpdCgks 9 
                                  +Cp Cg++
  gi|15668659|ref|NP_247458.1| 80 TCPNCGET 87
                                  8*****87 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4     0.026        11      29      41 ..       2      14 ..       1      20 [. 0.68
   2 !   14.7   5.6   5.2e-05     0.023      13      38 ..      59      89 ..      49      98 .] 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.026
                           DZR 29 drCpsCgekvdpe 41
                                  ++Cp Cg+++ +e
  gi|15668659|ref|NP_247458.1|  2 YNCPYCGKDCVNE 14
                                  5677777776555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.2e-05
                           DZR 13 rfCseCgtklkavaa....edrCpsCgek.v 38
                                    C++C+++ ka+ +     ++Cp+Cge  +
  gi|15668659|ref|NP_247458.1| 59 YLCPYCKKPFKAYYEkdkvVITCPNCGETlC 89
                                  57*********99999***********9843 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.9      0.38   1.7e+02      14      21 ..       2       9 ..       1      11 [. 0.84
   2 ?    9.9   0.4    0.0019      0.81       4      23 ..      49      68 ..      47      68 .. 0.90
   3 ?   10.5   0.3    0.0012      0.51       9      25 ..      74      90 ..      72      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.38
                        zf-AN1 14 fkCryCgk 21
                                  ++C+yCgk
  gi|15668659|ref|NP_247458.1|  2 YNCPYCGK 9 
                                  78****98 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0019
                        zf-AN1  4 ksCkkkdflpfkCryCgkvF 23
                                   +Ck+    ++ C+yC+k F
  gi|15668659|ref|NP_247458.1| 49 GECKETGGRIYLCPYCKKPF 68
                                  57***************987 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0012
                        zf-AN1  9 kdflpfkCryCgkvFCl 25
                                  kd ++++C++Cg++ Cl
  gi|15668659|ref|NP_247458.1| 74 KDKVVITCPNCGETLCL 90
                                  77788***********7 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.43   1.9e+02      20      26 ..       2       8 ..       1      10 [. 0.70
   2 ?    5.8   0.0     0.032        14      16      26 ..      55      65 ..      34      68 .. 0.81
   3 ?    7.3   0.1      0.01       4.4      15      26 ..      74      85 ..      69      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.43
                PhnA_Zn_Ribbon 20 lvCpeCa 26
                                  + Cp C+
  gi|15668659|ref|NP_247458.1|  2 YNCPYCG 8 
                                  6688886 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.032
                PhnA_Zn_Ribbon 16 dgallvCpeCa 26
                                  +g +++Cp C+
  gi|15668659|ref|NP_247458.1| 55 GGRIYLCPYCK 65
                                  5789******7 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.01
                PhnA_Zn_Ribbon 15 edgallvCpeCa 26
                                   d+ +  Cp+C+
  gi|15668659|ref|NP_247458.1| 74 KDKVVITCPNCG 85
                                  6899999****8 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.3     0.044        19       5      14 ..       2      11 ..       1      13 [. 0.86
   2 ?    3.8   0.1       0.1        44       6      13 ..      60      67 ..      55      70 .. 0.80
   3 ?    8.4   0.1    0.0037       1.6       2      11 ..      76      85 ..      75      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.044
                                  EE-TTTSSEE CS
                         Sgf11  5 vtCpnCgRqi 14
                                  ++Cp+Cg+++
  gi|15668659|ref|NP_247458.1|  2 YNCPYCGKDC 11
                                  68*****987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.1
                                  E-TTTSSE CS
                         Sgf11  6 tCpnCgRq 13
                                   Cp+C+++
  gi|15668659|ref|NP_247458.1| 60 LCPYCKKP 67
                                  6*****86 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0037
                                  C-EEE-TTTS CS
                         Sgf11  2 seyvtCpnCg 11
                                  ++ +tCpnCg
  gi|15668659|ref|NP_247458.1| 76 KVVITCPNCG 85
                                  6789*****8 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.4         2   8.9e+02      10      16 ..       4      10 ..       2      17 .. 0.63
   2 ?   13.8   1.7   8.3e-05     0.036      10      39 ..      61      91 ..      57      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2
                                  -TTTS-E CS
                Ribosomal_S27e 10 CpdCene 16
                                  Cp C++ 
  gi|15668659|ref|NP_247458.1|  4 CPYCGKD 10
                                  5555543 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.3e-05
                                  -TTTS-E.EEEESS-SS-EEESSSTCEEEEE CS
                Ribosomal_S27e 10 CpdCene.tvvFshaatvvkCisCgkvLveP 39
                                  Cp C++  +  +++ + v++C  Cg++L+ P
  gi|15668659|ref|NP_247458.1| 61 CPYCKKPfKAYYEKDKVVITCPNCGETLCLP 91
                                  999988526778899999***********99 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.7     0.094        41      18      24 .]       3       9 ..       1       9 [. 0.86
   2 ?    1.6   0.1      0.65   2.9e+02      16      22 ..      58      64 ..      53      64 .. 0.83
   3 ?   12.5   0.5   0.00025      0.11      18      24 .]      80      86 ..      76      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.094
                       DUF1610 18 pCPNCGE 24
                                   CP CG+
  gi|15668659|ref|NP_247458.1|  3 NCPYCGK 9 
                                  5*****8 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.65
                       DUF1610 16 vFpCPNC 22
                                  +++CP C
  gi|15668659|ref|NP_247458.1| 58 IYLCPYC 64
                                  689**99 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00025
                       DUF1610 18 pCPNCGE 24
                                   CPNCGE
  gi|15668659|ref|NP_247458.1| 80 TCPNCGE 86
                                  6*****9 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.7    0.0047       2.1       1       9 [.       2      10 ..       2      22 .. 0.85
   2 ?    6.4   0.5     0.019       8.5       2      11 ..      60      69 ..      59      73 .. 0.82
   3 ?    7.1   0.9     0.011       4.9       1      10 [.      79      88 ..      79      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0047
                 Cys_rich_CPXG  1 iqCPyCgee 9 
                                  ++CPyCg+ 
  gi|15668659|ref|NP_247458.1|  2 YNCPYCGKD 10
                                  68*****86 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
                 Cys_rich_CPXG  2 qCPyCgeeie 11
                                   CPyC ++++
  gi|15668659|ref|NP_247458.1| 60 LCPYCKKPFK 69
                                  6****99886 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.011
                 Cys_rich_CPXG  1 iqCPyCgeei 10
                                  i+CP+Cge++
  gi|15668659|ref|NP_247458.1| 79 ITCPNCGETL 88
                                  79******86 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   7.9   0.00011     0.047       1      73 [.       1      84 [.       1      97 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
                    zf-RRPl_C4  1 mkkCkyClskklknlnetvyCeaCeiyfkvknekqkv..elvpik.e...lekislrdkLCtkCke....knekeke.ircet 72
                                  m++C+yC +  +++   ++y +  e +fk++n+   +  e+ p   e   ++    r  LC +Ck+    ++ek+k  i+c +
  gi|15668659|ref|NP_247458.1|  1 MYNCPYCGKDCVNEAAVNIYLKMVEKFFKYQNKGSDItfEKYPTVgEvgeCKETGGRIYLCPYCKKpfkaYYEKDKVvITCPN 83
                                  789**************************998754321133333224333777778889*****9733335667776788876 PP

                    zf-RRPl_C4 73 f 73
                                   
  gi|15668659|ref|NP_247458.1| 84 C 84
                                  5 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5    0.0019      0.84       3      12 ..       2      11 ..       1      18 [. 0.77
   2 ?    7.9   1.3    0.0088       3.9       3      13 ..      59      69 ..      57      72 .. 0.83
   3 ?    3.9   0.4      0.15        65       3      12 ..      79      88 ..      77      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0019
                       zf-Di19  3 ftCPyCgkel 12
                                  ++CPyCgk+ 
  gi|15668659|ref|NP_247458.1|  2 YNCPYCGKDC 11
                                  79*****973 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0088
                       zf-Di19  3 ftCPyCgkelt 13
                                  + CPyC+k ++
  gi|15668659|ref|NP_247458.1| 59 YLCPYCKKPFK 69
                                  78*****9776 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.15
                       zf-Di19  3 ftCPyCgkel 12
                                  +tCP Cg++l
  gi|15668659|ref|NP_247458.1| 79 ITCPNCGETL 88
                                  69****9865 PP

>> Arv1  Arv1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   0.00027      0.12      20      45 ..      55      80 ..      17      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00027
                          Arv1 20 nirltkCknCkkvaDkYvEfdnvilf 45
                                    r+  C+ Ckk+   Y+E d+v+++
  gi|15668659|ref|NP_247458.1| 55 GGRIYLCPYCKKPFKAYYEKDKVVIT 80
                                  668999******************96 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.1      0.13        56      24      33 ..       4      13 ..       2      15 .. 0.81
   2 ?    6.6   0.5     0.022       9.5      23      31 ..      60      68 ..      50      68 .. 0.81
   3 ?    7.3   0.1     0.013       5.8      20      28 ..      76      85 ..      71      87 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.13
                 zinc_ribbon_9 24 CPhCgggFVE 33
                                  CP+Cg + V 
  gi|15668659|ref|NP_247458.1|  4 CPYCGKDCVN 13
                                  *****98665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.022
                 zinc_ribbon_9 23 lCPhCgggF 31
                                  lCP+C+  F
  gi|15668659|ref|NP_247458.1| 60 LCPYCKKPF 68
                                  7****9988 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.013
                 zinc_ribbon_9 20 sdv.lCPhCg 28
                                    v +CP+Cg
  gi|15668659|ref|NP_247458.1| 76 KVViTCPNCG 85
                                  33459****8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.9     0.032        14       1      10 [.       2      11 ..       2      19 .. 0.76
   2 ?   12.2   4.4   0.00022     0.094       3      27 ..      61      86 ..      59      89 .. 0.92
   3 ?    7.2   2.2    0.0079       3.4       2       9 ..      80      87 ..      79      98 .] 0.70

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.032
                                  EEETTTTCEE CS
                  TF_Zn_Ribbon  1 ykCPnCgstn 10
                                  y CP+Cg + 
  gi|15668659|ref|NP_247458.1|  2 YNCPYCGKDC 11
                                  56*****864 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00022
                                  ETTTTCEE.CHEETSTTCEEESSSSB CS
                  TF_Zn_Ribbon  3 CPnCgstn.lveDpergelvCtdCGl 27
                                  CP+C+ ++  +++ +   ++C++CG+
  gi|15668659|ref|NP_247458.1| 61 CPYCKKPFkAYYEKDKVVITCPNCGE 86
                                  ********99***************7 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0079
                                  EETTTTCE CS
                  TF_Zn_Ribbon  2 kCPnCgst 9 
                                  +CPnCg t
  gi|15668659|ref|NP_247458.1| 80 TCPNCGET 87
                                  79999987 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.048        21      36      48 ..       3      15 ..       1      19 [. 0.78
   2 ?    6.3   0.0     0.021       9.3      28      52 ..      51      76 ..      49      78 .. 0.74
   3 ?    5.6   2.2     0.037        16      16      30 ..      77      91 ..      75      98 .] 0.75

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.048
                      zf-C2HC5 36 pCsfCgspllsse 48
                                  +C++Cg++ ++++
  gi|15668659|ref|NP_247458.1|  3 NCPYCGKDCVNEA 15
                                  7999999987765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.021
                      zf-C2HC5 28 Cakegls.kpCsfCgspllsseerqe 52
                                  C+  g     C++C++p+    e+++
  gi|15668659|ref|NP_247458.1| 51 CKETGGRiYLCPYCKKPFKAYYEKDK 76
                                  6666666688******9876666655 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.037
                      zf-C2HC5 16 aapnClnCGkiiCak 30
                                  ++  C nCG  +C  
  gi|15668659|ref|NP_247458.1| 77 VVITCPNCGETLCLP 91
                                  56789******9965 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.056        24       4      12 ..       2      10 ..       1      24 [. 0.83
   2 ?    9.0   2.4    0.0042       1.9       3      36 ..      58      86 ..      56      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.056
               Lar_restr_allev  4 kpCPfCggr 12
                                  + CP Cg++
  gi|15668659|ref|NP_247458.1|  2 YNCPYCGKD 10
                                  79*****86 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0042
               Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCga 36
                                  ++ CP C+++ +   ++++v     +++C +Cg 
  gi|15668659|ref|NP_247458.1| 58 IYLCPYCKKPFKAYYEKDKV-----VITCPNCGE 86
                                  678******99999999999.....8******96 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.1     0.016       7.2       2       8 ..       4      10 ..       3      16 .. 0.61
   2 ?    3.4   1.3      0.16        68      16      21 ..      61      66 ..      59      68 .. 0.75
   3 ?   10.6   0.1   0.00085      0.37      16      21 ..      81      86 ..      73      88 .. 0.62
   4 ?   -1.8   0.0       6.7   2.9e+03      12      16 ..      94      98 .]      90      98 .] 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.016
                 zinc_ribbon_2  2 CpnCGae 8 
                                  Cp CG+ 
  gi|15668659|ref|NP_247458.1|  4 CPYCGKD 10
                                  5555555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.16
                 zinc_ribbon_2 16 CpyCGt 21
                                  CpyC  
  gi|15668659|ref|NP_247458.1| 61 CPYCKK 66
                                  999955 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00085
                 zinc_ribbon_2 16 CpyCGt 21
                                  Cp+CG+
  gi|15668659|ref|NP_247458.1| 81 CPNCGE 86
                                  555554 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 6.7
                 zinc_ribbon_2 12 nakFC 16
                                  n +FC
  gi|15668659|ref|NP_247458.1| 94 NRTFC 98
                                  67899 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0036       1.6      34      52 ..       2      20 ..       1      32 [. 0.93
   2 ?    3.9   1.4      0.13        56      34      60 ..      59      87 ..      45      92 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0036
                                  BEESSSSSSEEEEEETTEE CS
               Ribosomal_L37ae 34 ytCpfcgktkvkRkavgiw 52
                                  y+Cp cgk+ v+  av i+
  gi|15668659|ref|NP_247458.1|  2 YNCPYCGKDCVNEAAVNIY 20
                                  9***************996 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.13
                                  BEESSSSSS..EEEEEETTEEEETTTTEE CS
               Ribosomal_L37ae 34 ytCpfcgkt..kvkRkavgiwkCkkcgkt 60
                                  y Cp c+k   +   k   + +C +cg+t
  gi|15668659|ref|NP_247458.1| 59 YLCPYCKKPfkAYYEKDKVVITCPNCGET 87
                                  66666666543333334445566666665 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2       0.3   1.3e+02      13      22 ..       3      12 ..       1      31 [. 0.77
   2 ?   10.8   1.4   0.00082      0.36      13      37 ..      60      87 ..      50      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.3
                                  B-TTT-SB-- CS
                          C1_1 13 fCkhCgeflw 22
                                   C +Cg+ + 
  gi|15668659|ref|NP_247458.1|  3 NCPYCGKDCV 12
                                  6999999883 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00082
                                  B-TTT-SB-...-SSSS-EEEETTT--E CS
                          C1_1 13 fCkhCgefl...wgkekqglkCswCkll 37
                                   C +C++++   ++k k+ ++C +C+++
  gi|15668659|ref|NP_247458.1| 60 LCPYCKKPFkayYEKDKVVITCPNCGET 87
                                  6*********9777***********975 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0068         3      38      65 ..       2      30 ..       1      54 [. 0.79
   2 ?    2.6   0.2      0.31   1.4e+02      40      49 ..      61      70 ..      57      74 .. 0.59
   3 ?    7.2   0.9     0.011         5      37      50 ..      78      91 ..      69      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0068
                          CpXC 38 atCpkCgatakleapll.yhdpekellil 65
                                  + Cp+Cg++   ea +  y ++ ++++ +
  gi|15668659|ref|NP_247458.1|  2 YNCPYCGKDCVNEAAVNiYLKMVEKFFKY 30
                                  78*******99998875377777777655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.31
                          CpXC 40 CpkCgatakl 49
                                  Cp+C + +k+
  gi|15668659|ref|NP_247458.1| 61 CPYCKKPFKA 70
                                  6666555544 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.011
                          CpXC 37 eatCpkCgatakle 50
                                   +tCp+Cg+t  l+
  gi|15668659|ref|NP_247458.1| 78 VITCPNCGETLCLP 91
                                  68999999998776 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.081        36       5      12 ..       4      11 ..       3      32 .. 0.87
   2 ?    4.4   0.3      0.14        61       5      14 ..      61      71 ..      59      78 .. 0.73
   3 ?    7.8   1.4     0.012       5.2       3      11 ..      79      87 ..      77      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.081
                       zf-ISL3  5 CPnCgskt 12
                                  CP+Cg+  
  gi|15668659|ref|NP_247458.1|  4 CPYCGKDC 11
                                  *****974 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.14
                       zf-ISL3  5 CPnCgsk.tvv 14
                                  CP+C+++ +++
  gi|15668659|ref|NP_247458.1| 61 CPYCKKPfKAY 71
                                  *****998654 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.012
                       zf-ISL3  3 hrCPnCgsk 11
                                  ++CPnCg++
  gi|15668659|ref|NP_247458.1| 79 ITCPNCGET 87
                                  89*****97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.9      0.24   1.1e+02      29      35 ..       4      10 ..       1      14 [. 0.70
   2 ?    2.5   0.8      0.36   1.6e+02       6      15 ..      59      68 ..      37      71 .. 0.75
   3 ?   11.5   4.5   0.00057      0.25       6      35 ..      59      87 ..      50      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.24
                   Zn-ribbon_8 29 CPeCgse 35
                                  CP Cg++
  gi|15668659|ref|NP_247458.1|  4 CPYCGKD 10
                                  8888875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.36
                   Zn-ribbon_8  6 YrCeeCghef 15
                                  Y C  C++ f
  gi|15668659|ref|NP_247458.1| 59 YLCPYCKKPF 68
                                  4455554444 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00057
                   Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgse 35
                                  Y C  C++ f +  + +d+  ++CP+Cg++
  gi|15668659|ref|NP_247458.1| 59 YLCPYCKKPFKAYYE-KDKVVITCPNCGET 87
                                  89*********9986.4667788*****85 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.8   0.00083      0.36       4      24 ..       3      23 ..       1      42 [. 0.79
   2 ?    3.9   0.5      0.15        65      24      38 ..      52      66 ..      41      78 .. 0.75
   3 ?    1.0   0.2       1.1     5e+02       3      14 ..      79      90 ..      76      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00083
                       DUF3268  4 rCpyCGekvilvsaseiYker 24
                                  +CpyCG+  +   a +iY + 
  gi|15668659|ref|NP_247458.1|  3 NCPYCGKDCVNEAAVNIYLKM 23
                                  8*****************443 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.15
                       DUF3268 24 rskgkllylCpkCda 38
                                  +++g  +ylCp C  
  gi|15668659|ref|NP_247458.1| 52 KETGGRIYLCPYCKK 66
                                  667888999998864 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.1
                       DUF3268  3 trCpyCGekvil 14
                                  ++Cp CGe+  l
  gi|15668659|ref|NP_247458.1| 79 ITCPNCGETLCL 90
                                  579999988765 PP

>> HNH  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.4      0.14        60       1      10 [.       4      13 ..       4      20 .. 0.82
   2 ?    6.1   0.0     0.029        13       1      11 [.      61      71 ..      61      79 .. 0.84
   3 ?    1.0   0.2       1.1     5e+02      35      40 ..      79      84 ..      71      88 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.14
                           HNH  1 CeyCgrkfhk 10
                                  C yCg+ +  
  gi|15668659|ref|NP_247458.1|  4 CPYCGKDCVN 13
                                  ******9865 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.029
                           HNH  1 CeyCgrkfhks 11
                                  C yC+++f+ +
  gi|15668659|ref|NP_247458.1| 61 CPYCKKPFKAY 71
                                  ********877 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.1
                           HNH 35 llCksC 40
                                    C++C
  gi|15668659|ref|NP_247458.1| 79 ITCPNC 84
                                  567776 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3      0.04        17      20      27 ..       3      10 ..       2      21 .. 0.83
   2 ?    4.9   0.4      0.06        26      21      30 ..      61      71 ..      54      77 .. 0.76
   3 ?    6.3   1.0     0.022       9.4      19      27 ..      79      87 ..      74      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.04
                 Zn_Tnp_IS1595 20 vCPhCgsr 27
                                   CP+Cg++
  gi|15668659|ref|NP_247458.1|  3 NCPYCGKD 10
                                  5*****86 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.06
                 Zn_Tnp_IS1595 21 CPhCgsr.kay 30
                                  CP+C++  kay
  gi|15668659|ref|NP_247458.1| 61 CPYCKKPfKAY 71
                                  ****9877666 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.022
                 Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                   +CP+Cg +
  gi|15668659|ref|NP_247458.1| 79 ITCPNCGET 87
                                  47*****65 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.8      0.79   3.5e+02      88      97 ..       3      12 ..       1      26 [. 0.73
   2 ?    9.3   2.8    0.0025       1.1      71      94 ..      59      86 ..       9      97 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.79
                                  S-TTTSSS-E CS
                          HypA 88 rCpkCgsadv 97
                                  +Cp Cg+  v
  gi|15668659|ref|NP_247458.1|  3 NCPYCGKDCV 12
                                  6999998655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0025
                                  EEETTTS-EEECHH..H..HHS-TTTSS CS
                          HypA 71 vrCreCgkefelee..k..alrCpkCgs 94
                                  + C  C+k f+     +   ++Cp+Cg+
  gi|15668659|ref|NP_247458.1| 59 YLCPYCKKPFKAYYekDkvVITCPNCGE 86
                                  4577777777743322234448888887 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.5    0.0094       4.1      15      25 ..       2      12 ..       1      13 [. 0.84
   2 ?    8.8   2.3    0.0051       2.2      10      25 ..      54      69 ..      50      70 .. 0.86
   3 ?    4.4   0.2      0.12        55      15      22 ..      79      86 ..      71      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0094
                     zf-H2C2_2 15 yeCplCdkaFk 25
                                  y+Cp+C+k  +
  gi|15668659|ref|NP_247458.1|  2 YNCPYCGKDCV 12
                                  99*****9766 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0051
                     zf-H2C2_2 10 tgekpyeCplCdkaFk 25
                                  tg ++y Cp+C+k Fk
  gi|15668659|ref|NP_247458.1| 54 TGGRIYLCPYCKKPFK 69
                                  78899*******9776 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.12
                     zf-H2C2_2 15 yeCplCdk 22
                                   +Cp C+ 
  gi|15668659|ref|NP_247458.1| 79 ITCPNCGE 86
                                  69****85 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  10.4     0.093        41       3      39 ..       4      88 ..       2      98 .] 0.65

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.093
                                  -SSS-S--EE-S.........................................SEEE-TTT--.......EEEEEEE-SSS-S CS
                zinc-ribbons_6  3 CpeCqqelekrg.........................................eqyhCeaCqe.......dlkkealCpeCeq 37
                                  Cp C +  +++                                          + y C  C++       + k++ +Cp+C++
  gi|15668659|ref|NP_247458.1|  4 CPYCGKDCVNEAavniylkmvekffkyqnkgsditfekyptvgevgecketggRIYLCPYCKKpfkayyeKDKVVITCPNCGE 86
                                  55555555544445555555555555555555555555555555555555555889999999988887765667788999998 PP

                                  -- CS
                zinc-ribbons_6 38 el 39
                                   l
  gi|15668659|ref|NP_247458.1| 87 TL 88
                                  87 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.6      0.84   3.7e+02       1       7 [.       3       9 ..       3      18 .. 0.78
   2 ?   10.2   1.5   0.00085      0.37       2      26 ..      61      85 ..      60      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.84
                      zf-TFIIB 1 kCPkCqd 7
                                 +CP C+ 
  gi|15668659|ref|NP_247458.1| 3 NCPYCGK 9
                                 6999975 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00085
                      zf-TFIIB  2 CPkCqdeleeserggveidyCpqCr 26
                                  CP C+ +++ +   +  + +Cp+C+
  gi|15668659|ref|NP_247458.1| 61 CPYCKKPFKAYYEKDKVVITCPNCG 85
                                  *********9999888899*****7 PP

>> Evr1_Alr  Erv1 / Alr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.5      0.72   3.1e+02      39      52 ..       1      14 [.       1      33 [. 0.73
   2 ?    8.2   0.3    0.0075       3.3      36      57 ..      55      76 ..      29      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.72
                                  HSSCHHHHHHHHHH CS
                      Evr1_Alr 39 fypCeeCaehfekv 52
                                  +y+C +C ++  + 
  gi|15668659|ref|NP_247458.1|  1 MYNCPYCGKDCVNE 14
                                  79999999998773 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0075
                                  HHHHSSCHHHHHHHHHHHHHCH CS
                      Evr1_Alr 36 iakfypCeeCaehfekvlaenp 57
                                    ++y C +C++ f++++++++
  gi|15668659|ref|NP_247458.1| 55 GGRIYLCPYCKKPFKAYYEKDK 76
                                  5689************877665 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4      0.03        13       2      13 ..       3      14 ..       2      19 .. 0.79
   2 ?    5.3   0.1     0.038        17       3      11 ..      61      69 ..      59      76 .. 0.82
   3 ?    3.6   2.3      0.13        57       1      16 [.      79      94 ..      79      98 .] 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.03
                          YacG  2 kCPtCkkevews 13
                                  +CP C+k+ + +
  gi|15668659|ref|NP_247458.1|  3 NCPYCGKDCVNE 14
                                  8*****987655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.038
                          YacG  3 CPtCkkeve 11
                                  CP Ckk+++
  gi|15668659|ref|NP_247458.1| 61 CPYCKKPFK 69
                                  ******987 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.13
                          YacG  1 vkCPtCkkevewseen 16
                                  ++CP C+++    ++n
  gi|15668659|ref|NP_247458.1| 79 ITCPNCGETLCLPATN 94
                                  58*****988776644 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2       1.9   8.2e+02       4      13 ..       2      11 ..       1      26 [. 0.63
   2 ?   -0.7   0.1       3.1   1.4e+03      28      36 ..      58      66 ..      51      69 .. 0.73
   3 ?    9.4   2.8    0.0023      0.99      19      36 ..      69      86 ..      57      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.9
                        zf-DNL  4 ftCkaCetrs 13
                                  + C  C++  
  gi|15668659|ref|NP_247458.1|  2 YNCPYCGKDC 11
                                  5666666554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.1
                        zf-DNL 28 ivqCpgCkn 36
                                  i  Cp Ck+
  gi|15668659|ref|NP_247458.1| 58 IYLCPYCKK 66
                                  455888875 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0023
                        zf-DNL 19 kkaYekGvVivqCpgCkn 36
                                  k  Yek  V+++Cp+C +
  gi|15668659|ref|NP_247458.1| 69 KAYYEKDKVVITCPNCGE 86
                                  7789************76 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.8      0.27   1.2e+02      17      23 ..       2       8 ..       1      15 [. 0.89
   2 ?    9.2   2.5     0.003       1.3       1      23 [.      60      85 ..      60      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.27
                      zf-Mss51 17 feCpdCG 23
                                  ++Cp CG
  gi|15668659|ref|NP_247458.1|  2 YNCPYCG 8 
                                  89****9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.003
                      zf-Mss51  1 lCPvpkhkqt...apkhvdfeCpdCG 23
                                  lCP +k+  +   ++ +v ++Cp+CG
  gi|15668659|ref|NP_247458.1| 60 LCPYCKKPFKayyEKDKVVITCPNCG 85
                                  59999876668899***********9 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2     0.012       5.2       2       9 ..       2       9 ..       1      10 [. 0.93
   2 ?    9.4   0.6    0.0025       1.1       2      15 ..      59      72 ..      58      73 .. 0.86
   3 ?   -0.8   0.1       3.8   1.6e+03       4      10 ..      81      87 ..      80      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.012
                     zf-C2H2_6 2 heCsvCsk 9
                                 ++C++C+k
  gi|15668659|ref|NP_247458.1| 2 YNCPYCGK 9
                                 9******9 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0025
                     zf-C2H2_6  2 heCsvCsksFpslq 15
                                  + C++C+k F+ ++
  gi|15668659|ref|NP_247458.1| 59 YLCPYCKKPFKAYY 72
                                  89*******99776 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3.8
                     zf-C2H2_6  4 CsvCsks 10
                                  C+ C+++
  gi|15668659|ref|NP_247458.1| 81 CPNCGET 87
                                  999*987 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.6   7.1e+02       5      10 ..       4       9 ..       2      10 .. 0.69
   2 ?    6.6   4.9     0.017       7.5       5      34 ..      61      87 ..      57      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.6
                 zinc_ribbon_4  5 CpsCka 10
                                  Cp C++
  gi|15668659|ref|NP_247458.1|  4 CPYCGK 9 
                                  777765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.017
                 zinc_ribbon_4  5 CpsCkakyeiddeklpakgvkvrCskCghv 34
                                  Cp Ck+ ++   e   +++v ++C++Cg++
  gi|15668659|ref|NP_247458.1| 61 CPYCKKPFKAYYE---KDKVVITCPNCGET 87
                                  7777777765554...78999999999975 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   8.9     0.035        15      26      73 ..       8      85 ..       1      87 [. 0.69
   2 ?    3.3   0.6      0.26   1.2e+02      50      63 ..      74      87 ..      68      98 .] 0.68

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.035
                        zf-CHY 26 H.......................eeledhelerlevkevlcllCeteqekavlCkkCkkefaey........fCpiCk 73
                                                          ++ +d ++e++ +    + +C+++     lC  Ckk f++y        +Cp+C 
  gi|15668659|ref|NP_247458.1|  8 GkdcvneaavniylkmvekffkyqNKGSDITFEKYPTVG-EVGECKETGGRIYLCPYCKKPFKAYyekdkvviTCPNCG 85
                                  444445555555555554444443334566777877664.4799***99999**********999999999988***96 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.26
                        zf-CHY 50 eqekavlCkkCkke 63
                                  +++++++C +C+++
  gi|15668659|ref|NP_247458.1| 74 KDKVVITCPNCGET 87
                                  45677888888874 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.5       1.1   4.8e+02       3       8 ..       4       9 ..       3      19 .. 0.90
   2 ?    9.1   0.5     0.004       1.7       3      18 ..      61      76 ..      60      78 .. 0.92
   3 ?    1.9   0.3      0.76   3.3e+02       2       9 ..      80      87 ..      80      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.1
                    Zn-C2H2_12 3 CPlCse 8
                                 CP C++
  gi|15668659|ref|NP_247458.1| 4 CPYCGK 9
                                 ****97 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.004
                    Zn-C2H2_12  3 CPlCseqFpknvdqde 18
                                  CP C++ F++ +++d+
  gi|15668659|ref|NP_247458.1| 61 CPYCKKPFKAYYEKDK 76
                                  **********999986 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.76
                    Zn-C2H2_12  2 eCPlCseq 9 
                                  +CP C+e+
  gi|15668659|ref|NP_247458.1| 80 TCPNCGET 87
                                  6****995 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.9      0.45     2e+02       2      10 ..       1       9 [.       1      11 [. 0.89
   2 ?    6.3   0.2     0.017       7.3       3      14 ..      59      70 ..      58      75 .. 0.84
   3 ?    4.6   0.4     0.056        25       3      11 ..      79      87 ..      78      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.45
                        zf_UBZ  2 tylCerCgk 10
                                  +y C+ Cgk
  gi|15668659|ref|NP_247458.1|  1 MYNCPYCGK 9 
                                  599*****8 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.017
                        zf_UBZ  3 ylCerCgkeipe 14
                                  ylC+ C+k++  
  gi|15668659|ref|NP_247458.1| 59 YLCPYCKKPFKA 70
                                  99******9975 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.056
                        zf_UBZ  3 ylCerCgke 11
                                  ++C+ Cg++
  gi|15668659|ref|NP_247458.1| 79 ITCPNCGET 87
                                  59*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        56  (0.00312343); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              41  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 576.00
//
Query:       gi|15668660|ref|NP_247459.1|  [L=340]
Description: hypothetical protein MJ_0483 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-58  197.4   1.0    8.9e-56  189.5   1.0    2.2  1  Diphthamide_syn  Putative diphthamide synthesis protein
  ------ inclusion threshold ------
      0.019   14.8   0.2      0.019   14.8   0.2    2.5  3  DSPc             Dual specificity phosphatase, catalytic doma
      0.085   12.4   1.5        1.4    8.4   0.1    2.7  3  MS_channel       Mechanosensitive ion channel
       0.11   12.4   1.8        1.3    9.0   0.1    2.7  3  DUF3854          Domain of unknown function (DUF3854)
       0.12   12.0   0.0       0.36   10.5   0.0    1.7  2  Arnt_C           Aminoarabinose transferase C-terminal domain


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.5   1.0   2.5e-59   8.9e-56       2     295 ..      45     326 ..      44     335 .. 0.89

  Alignments for each domain:
  == domain 1  score: 189.5 bits;  conditional E-value: 2.5e-59
               Diphthamide_syn   2 Pegllpdsaeiadileef......gaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvd.rlpvlYvfveield 75 
                                   Pegl+   ++ +++++++      ++e++++g+t++GaC++ +  +++l++dl++HyGh++ls  + ++++l++++ + ++
  gi|15668660|ref|NP_247459.1|  45 PEGLKLKVEKEIEKIKQYfkqkniNIEIYLWGNTCFGACDLIDNHVKNLNVDLIIHYGHEKLSYANpEIKTLFIPAYHIFN 125
                                   9**************776699988899************************************8778*******9999885 PP

               Diphthamide_syn  76 ...vehlvetlkknf....kekkkivlvstiqyahaleevkeeleeegyevvkvpqsekplspgevlgctspklkeeeeev 149
                                       e++++ +k+ +    + +kk+++++tiqy++ l+        + +    +p        + +lgc  +       e 
  gi|15668660|ref|NP_247459.1| 126 kdeEEKILNDIKNFIekhkSGGKKVAIATTIQYKKLLK--------D-F----NP--------SIILGCRGEVK-----EG 180
                                   445889999999888876555788*********99855........3.3....23........449***88775.....57 PP

               Diphthamide_syn 150 dailyigdgrfhllslmlsnpklpvyrydpyskklt.eesydakkllrrRyaaiekak..dakkvGiivgtlgvqgrlelv 227
                                   d+il++g+grfh+l ++++++k +v+ y+p sk ++  ++++++k++++R  ai+k+   + kkvG++++t+++q r ++ 
  gi|15668660|ref|NP_247459.1| 181 DVILFVGTGRFHPLMIAYKYQK-EVFIYNPLSKCFDkISEEEINKFIKKRILAISKLLlnKPKKVGVVLSTKKGQCRKRVF 260
                                   9*******************88.9*********9995677899*************87435899***************** PP

               Diphthamide_syn 228 erlkkllkeagkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalge 295
                                   +++ kll+e++ ++  +lv++++p+ L  f ++d++++vaCpr+ +dd   ++kP+ tp E+++ l++
  gi|15668660|ref|NP_247459.1| 261 DEIIKLLEENDVNYLPILVDNISPDIL--FYDVDCYIIVACPRIVLDDYILYKKPIYTPEEFKLFLKN 326
                                   *************************99..77***********************************93 PP

>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.3      0.43   1.5e+03      20      46 ..      16      45 ..       6      71 .. 0.42
   2 ?   14.8   0.2   5.3e-06     0.019      13      78 ..      89     152 ..      80     155 .. 0.90
   3 ?   -1.7   0.0      0.63   2.3e+03      50      78 ..     217     246 ..     191     247 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.43
                                  SEEEEESSSSSEC...ECCTTTTSEEEEEC CS
                          DSPc 20 tlvinvtkevpna...nalkkseieklrip 46
                                  t  +n+ +e+  +   n+ k++ +  ++ p
  gi|15668660|ref|NP_247459.1| 16 TTLFNLETERVIReieNLNKNNPKVIFQAP 45
                                  444444443333232223333333333333 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5.3e-06
                                   HHHHHTCSEEEEESSSSSECECCTTTTSEEEEEC.CESSTTSCCGGGHHHHHHHHHHHHHTT-EEEE CS
                          DSPc  13 llsklgitlvinvtkevpnanalkkseieklrip.vedehetkiskyleeavefidkakqkgkkvlV 78 
                                     ++l+++l+i   +e+     +++ ei+ l ip  + +++++ +k l+++++fi+k k+ gkkv++
  gi|15668660|ref|NP_247459.1|  89 HVKNLNVDLIIHYGHEKLS---YANPEIKTLFIPaYHIFNKDEEEKILNDIKNFIEKHKSGGKKVAI 152
                                   578999*****99988886...889*********777799*************************98 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.63
                                   STTSCCGGGHHHHHHHHHHH.HHTT-EEEE CS
                          DSPc  50 ehetkiskyleeavefidka.kqkgkkvlV 78 
                                    +e++i k++++ +  i+k+  +k kkv V
  gi|15668660|ref|NP_247459.1| 217 ISEEEINKFIKKRILAISKLlLNKPKKVGV 246
                                   678888999999888888776777777766 PP

>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0004       1.4     133     178 ..      23      78 ..      10      94 .. 0.91
   2 ?    2.0   0.0     0.036   1.3e+02      35      68 ..     151     184 ..     145     189 .. 0.90
   3 ?   -2.1   0.0      0.63   2.3e+03     183     205 ..     251     273 ..     242     274 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0004
                                   HHHHHHHHHHHHHH-TTB-T..........TS-EEEEEEEE-SSSEEEEEEEEEET CS
                    MS_channel 133 lekvleelkealkekpevlk..........dkellvvldefgdsslnfevrvfvkt 178
                                    e+v++e+ +  k++p+v+           +ke +++ + f+++++n+e++ + +t
  gi|15668660|ref|NP_247459.1|  23 TERVIREIENLNKNNPKVIFqapeglklkvEKEIEKIKQYFKQKNINIEIYLWGNT 78 
                                   689999*************99********************************999 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.036
                                   HHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEE CS
                    MS_channel  35 glalglalkdlisnlvaGiillfekpfkiGDlve 68 
                                   ++a ++  k+l++++  +iil     +k GD++ 
  gi|15668660|ref|NP_247459.1| 151 AIATTIQYKKLLKDFNPSIILGCRGEVKEGDVIL 184
                                   67888899************************96 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.63
                                   THHHHHHHHHHHHHHHHHHHT-- CS
                    MS_channel 183 eylsvqseinlrikkileeegie 205
                                   ++ + ++ ++++i+k lee++++
  gi|15668660|ref|NP_247459.1| 251 KKGQCRKRVFDEIIKLLEENDVN 273
                                   55678899999999999999875 PP

>> DUF3854  Domain of unknown function (DUF3854)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00036       1.3      54     127 ..      22      90 ..       5      93 .. 0.78
   2 ?   -1.4   0.0      0.59   2.1e+03      73      94 ..     121     142 ..     104     159 .. 0.72
   3 ?    1.6   0.0     0.071   2.5e+02      75     110 ..     213     248 ..     200     265 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00036
                       DUF3854  54 ekkklipeleklakegreiliaFDqDtkpktiknVraaikrlgklleergckvkvikwepeeekGvDDlivakG 127
                                   e ++ i+e+e+l k++ +++  F + +  k   +V+++i+++ + +++++ ++++  w  +   G  Dli ++ 
  gi|15668660|ref|NP_247459.1|  22 ETERVIREIENLNKNNPKVI--FQAPEGLKL--KVEKEIEKIKQYFKQKNINIEIYLW-GNTCFGACDLIDNHV 90 
                                   45577888888887777665..445555555..99***********************.688899999998876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.59
                       DUF3854  73 liaFDqDtkpktiknVraaikr 94 
                                   +  F +D+++k+ +++++ i++
  gi|15668660|ref|NP_247459.1| 121 YHIFNKDEEEKILNDIKNFIEK 142
                                   5568888888887777665554 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.071
                       DUF3854  75 aFDqDtkpktiknVraaikrlgklleergckvkvik 110
                                   +FD+ +++++ k +++ i  ++kll ++  kv v+ 
  gi|15668660|ref|NP_247459.1| 213 CFDKISEEEINKFIKKRILAISKLLLNKPKKVGVVL 248
                                   9************************99999998875 PP

>> Arnt_C  Aminoarabinose transferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0001      0.36      46      85 ..     125     164 ..     121     172 .. 0.89
   2 ?   -3.8   0.0       2.7   9.6e+03       8      21 ..     281     294 ..     278     294 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                   HHHSGGGSB-SHHHHHHHHHCS-S-EEEE-HHHHHHHTT. CS
                        Arnt_C  46 lkqepekwiptleaFaarWredkkalalmspetyeeLkaq 85 
                                    k e+ek++ ++++F+++ +++ k++a+ ++ +y++L ++
  gi|15668660|ref|NP_247459.1| 125 NKDEEEKILNDIKNFIEKHKSGGKKVAIATTIQYKKLLKD 164
                                   57899*******************************9875 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.7
                                   T--TTS-EEEES-- CS
                        Arnt_C   8 klkpdtplysvgty 21 
                                   +++pd  +y v++y
  gi|15668660|ref|NP_247459.1| 281 NISPDILFYDVDCY 294
                                   67899999*99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1969.18
//
Query:       gi|15668661|ref|NP_247460.1|  [L=495]
Description: cobyric acid synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-50  171.4   0.1    2.8e-50  170.7   0.1    1.3  1  GATase_3      CobB/CobQ-like glutamine amidotransferase domai
    5.7e-27   94.3   0.1    1.3e-26   93.2   0.0    1.6  2  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    2.5e-23   82.9   0.4      2e-22   80.0   0.4    2.0  1  AAA_26        AAA domain
    0.00011   22.0   0.1     0.0009   19.1   0.0    2.2  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
     0.0018   17.6   0.0      0.044   13.1   0.1    2.4  2  DUF1611       Domain of unknown function (DUF1611_C) P-loop d
     0.0069   16.2   0.0      0.017   14.9   0.0    1.6  2  DJ-1_PfpI     DJ-1/PfpI family
     0.0069   16.3   0.0      0.017   14.9   0.0    1.6  2  SNO           SNO glutamine amidotransferase family
  ------ inclusion threshold ------
      0.018   14.3   0.2      0.056   12.8   0.2    1.8  1  P53_tetramer  P53 tetramerisation motif
       0.02   14.5   0.2       0.61    9.7   0.1    2.3  2  SRP54         SRP54-type protein, GTPase domain
       0.02   14.8   0.3      0.072   13.0   0.3    1.9  1  AAA_31        AAA domain
      0.057   12.5   0.0        0.1   11.7   0.0    1.3  1  GATase_5      CobB/CobQ-like glutamine amidotransferase domai
       0.11   11.8   0.0       0.18   11.1   0.0    1.4  1  VirC1         VirC1 protein


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.7   0.1   1.9e-53   2.8e-50       1     195 [.     257     446 ..     257     447 .. 0.93

  Alignments for each domain:
  == domain 1  score: 170.7 bits;  conditional E-value: 1.9e-53
                      GATase_3   1 kiavirlpaisnytdldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgi 81 
                                   +i v+r ++isn+tdldpL++ +   ++f++  d++++   d++i+pG+++ ++++ +l+++++de++ e++++gg v+gi
  gi|15668661|ref|NP_247460.1| 257 EINVVRFSKISNFTDLDPLRYDA--FIKFID-FDDDIT--GDILIFPGTRSSTKEAYYLKQHNFDEKVLEFLKDGGIVIGI 332
                                   599******************65..888999.788994..6**************************************** PP

                      GATase_3  82 CGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevelaaegeevkGyEiHsGrtilkekakpllkvk 162
                                   CGG+q+LG+e++d+e++e+++g +egl ++d++t f+++k++++++g +e  +++ +vkGyEiH+G t++  k+kpl+k++
  gi|15668661|ref|NP_247460.1| 333 CGGYQVLGKELIDKEKKESDVGDIEGLKIFDAKTYFGNDKVVKNSCGFLEIDNKTFNVKGYEIHEGFTYS--KEKPLIKIE 411
                                   ****************************************************9*************7775..679*****9 PP

                      GATase_3 163 v.ggnng..ekdGavkksedgnvlGtYlHglfdnrn 195
                                   +   +n   + dG +kk  dg  +GtY+Hg+f+n +
  gi|15668661|ref|NP_247460.1| 412 RgF-GNCgnGFDGSIKKFGDGLAIGTYFHGIFENYE 446
                                   963.44447************************976 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   0.0   8.5e-30   1.3e-26       1     119 [.       8     234 ..       8     242 .. 0.95
   2 ?   -2.8   0.0       4.1   6.2e+03      76     116 ..     447     459 ..     341     490 .. 0.68

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 8.5e-30
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   i++++t++++GKTt++a+L+r+la++g++V++++ ++++ n+++  +  ++i+                            
  gi|15668661|ref|NP_247460.1|   8 IMVVGTSSNSGKTTITAGLCRILANKGYKVAPFKSQNMSLNSRV-AKEDGEIAIaqytqslacrvepsvhfnpillkpkgn 87 
                                   89*****************************************5.44444444455************************* PP

                                   ................................................................................C CS
                                   ................................................................................x RF
                          CbiA  55 ................................................................................d 55 
                                                                                                                   d
  gi|15668661|ref|NP_247460.1|  88 fisqvivhgrpykdmnyneyrknkdfflkkikesleildreydyvimegagscceinllkddianlriaelvnakailvaD 168
                                   ********************************************************************************* PP

                                   CHCCCHHHHHHCHCHHHH.......EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHC CS
                                   xxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  56 lkrllellealgkkkall.....lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeava 119
                                   ++r ++++++++++ +ll      +i+g+++n+++g+   + lke++e++++ +g+pvlg++p+de+++
  gi|15668661|ref|NP_247460.1| 169 IDR-GGVFASIYGTIKLLpenwrKLIKGIIINKFRGN--VEVLKEGIEKIEELTGIPVLGIVPYDENLV 234
                                   ***.************99*******************..***********9999************985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.1
                                   EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--C CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  76 iagvvlnrvdgeneetllkealeelkqrygvpvlgviprde 116
                                   +                            ++ ++++i++++
  gi|15668661|ref|NP_247460.1| 447 F----------------------------RNYIINLIRKRK 459
                                   2............................333333333333 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.4   1.4e-25     2e-22       3     195 ..       8     234 ..       6     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 1.4e-25
                        AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie.....ede...dselikellgldqtyelpeplalsap... 72 
                                   i+v+gt+ ++GKT++++gL+r+l +kg+kv+ fK  +  ++     ed+    ++ +++l++  +++ + +p++l+     
  gi|15668661|ref|NP_247460.1|   8 IMVVGTSSNSGKTTITAGLCRILANKGYKVAPFKSQNMSLNsrvakEDGeiaIAQYTQSLACRVEPSVHFNPILLKPKgnf 88 
                                   9**********************************8888777776633334333333446666666666777777632111 PP

                        AAA_26  73 lspelaarqegedidlekiv..............kelekdadivvVEGagglgvp.itee.llnadiaknlgapvilVarg 137
                                   +s+ +   +  +d   +++               + l  ++d v+ EGag+ ++  ++++   n +ia+  +a+ ilVa +
  gi|15668661|ref|NP_247460.1|  89 ISQVIVHGRPYKDMNYNEYRknkdfflkkikeslEILDREYDYVIMEGAGSCCEInLLKDdIANLRIAELVNAKAILVADI 169
                                   23333333333444444444455555555557755577899************6535555588****************** PP

                        AAA_26 138 gl.gtinqllltiealrqknvr.vlGvilNkvrnp.....envetlekksgipvlGvvPylpdle 195
                                   ++ g ++ ++ ti++l ++  + ++G+i+Nk+r       e +e++e+ +gipvlG+vPy+++l 
  gi|15668661|ref|NP_247460.1| 170 DRgGVFASIYGTIKLLPENWRKlIKGIIINKFRGNvevlkEGIEKIEELTGIPVLGIVPYDENLV 234
                                   994589**********8764445*********999878877********************9985 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   6.1e-07    0.0009       2      40 ..       8      47 ..       7      56 .. 0.83
   2 ?    0.1   0.0      0.48   7.1e+02      80      98 ..     117     136 ..      99     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.1e-07
                          MobB  2 lgivgk.sgsGKTtLleklipelkarglrvgtiKhahhgf 40
                                  + +vg+ s+sGKTt+   l ++l+++g++v+  K ++ ++
  gi|15668661|ref|NP_247460.1|  8 IMVVGTsSNSGKTTITAGLCRILANKGYKVAPFKSQNMSL 47
                                  45666548************************99987665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.48
                          MobB  80 sleellarlse.vDlvlvEG 98 
                                   +++e l+ l++ +D v++EG
  gi|15668661|ref|NP_247460.1| 117 KIKESLEILDReYDYVIMEG 136
                                   6788888995459******9 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1     3e-05     0.044      13      51 ..       6      44 ..       3      54 .. 0.87
   2 ?    2.0   0.0     0.073   1.1e+02     154     192 ..     190     227 ..     125     234 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
                       DUF1611 13 krvlvvGTdcavGKrttaleleealeerGlkaafvaTgq 51
                                  + ++vvGT+++ GK t +  l + l ++G+k+a +    
  gi|15668661|ref|NP_247460.1|  6 EFIMVVGTSSNSGKTTITAGLCRILANKGYKVAPFKSQN 44
                                  679***************************998766555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.073
                       DUF1611 154 akkkvvgislNtknlseeeakealeeleeelglpvvdpv 192
                                   +k  + gi +N+   + e +ke +e++ee +g+pv  +v
  gi|15668661|ref|NP_247460.1| 190 RKL-IKGIIINKFRGNVEVLKEGIEKIEELTGIPVLGIV 227
                                   444.7899999999999999**************98765 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.3     5e+03      56      75 ..     123     142 ..     100     163 .. 0.75
   2 !   14.9   0.0   1.1e-05     0.017      48     115 ..     275     347 ..     237     374 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.3
                                   GCTCCG-SEEEE--BHHHHH CS
                     DJ-1_PfpI  56 dvkaaeyDalvlpGGragpe 75 
                                   ++ + eyD +++ G  + +e
  gi|15668661|ref|NP_247460.1| 123 EILDREYDYVIMEGAGSCCE 142
                                   36677899999998766555 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.1e-05
                                   EE-SEEGG..GCTCC.G-SEEEE--BHHHHH...HHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTT CS
                     DJ-1_PfpI  48 vtvdasld..dvkaa.eyDalvlpGGragpe...rlrenekvvelvkefaekgklvaaICagpqlLaaagvlkg 115
                                   ++ da ++  d +++ + D+l+ pG r++ +   +l++ + + e v ef+++g++v  IC g q+L ++ + k 
  gi|15668661|ref|NP_247460.1| 275 LRYDAFIKfiDFDDDiTGDILIFPGTRSSTKeayYLKQ-HNFDEKVLEFLKDGGIVIGICGGYQVLGKELIDKE 347
                                   445555554466677788*******9986442214555.599************************98766555 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       7.7   1.2e+04     148     169 ..      52      73 ..      47      77 .. 0.77
   2 !   14.9   0.0   1.2e-05     0.017      35     102 ..     293     365 ..     278     391 .. 0.73

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 7.7
                                   EECTTEEEEEEETTEEEESS-G CS
                           SNO 148 yeldgeivvakqkkilatsfhP 169
                                    + dgei  a+  + la+   P
  gi|15668661|ref|NP_247460.1|  52 AKEDGEIAIAQYTQSLACRVEP 73 
                                   5678999888888999998877 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.2e-05
                                   SEEEE-SS-HHH.HHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB.....SS-SS--CCEEEET CS
                           SNO  35 daliiPGGesta.mskliertglyedllefvknsekvvlGtCaGlillskelene.....lvktlellkvkvkr 102
                                   d li PG  s +  +  +++ ++ e++lef+k++  +v+G C G  +l kel  +     +v  +e lk+   +
  gi|15668661|ref|NP_247460.1| 293 DILIFPGTRSSTkEAYYLKQHNFDEKVLEFLKDG-GIVIGICGGYQVLGKELIDKekkesDVGDIEGLKIFDAK 365
                                   89*****98755156789999*************.7899*********99987662333344455555555555 PP

>> P53_tetramer  P53 tetramerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   3.7e-05     0.056      24      38 ..     114     128 ..     113     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                  P53_tetramer  24 mLkKineaLELkdav 38 
                                   +LkKi+e+LE++d +
  gi|15668661|ref|NP_247460.1| 114 FLKKIKESLEILDRE 128
                                   79**********975 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0004      0.61       3      33 ..       7      38 ..       5      41 .. 0.90
   2 ?    2.6   0.0      0.06        90      70     125 ..     116     171 ..      89     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0004
                                  EEEEEESTT.SSHHHHHHHHHHHHHHTTS-EE CS
                         SRP54  3 villvGlqG.aGKTttlaKLaallkkegkkvl 33
                                   i++vG+   +GKTt +a L ++l ++g+kv+
  gi|15668661|ref|NP_247460.1|  7 FIMVVGTSSnSGKTTITAGLCRILANKGYKVA 38
                                  69****97659******************996 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.06
                                   HHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHH.SSSEEEEEEETTB CS
                         SRP54  70 avakeavekakeekidvvlvDTaGrlqndkelmeelkkikkvv.kpdevllvldatt 125
                                   + +ke++e  ++ ++d+v++  aG   + + l +++++++ +   +++ +lv d   
  gi|15668661|ref|NP_247460.1| 116 KKIKESLEILDR-EYDYVIMEGAGSCCEINLLKDDIANLRIAElVNAKAILVADIDR 171
                                   445566665555.89**********99999999999987655446888899988655 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   4.8e-05     0.072      13     124 ..      17     135 ..       6     147 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.8e-05
                        AAA_31  13 vGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevl......i.eeknikeaiiktkvenl.dlip 85 
                                    GKTT +  l+  la++g+kv      + +n++ + ++ k++ e  + +        +  +++ + ++ k k + + ++i+
  gi|15668661|ref|NP_247460.1|  17 SGKTTITAGLCRILANKGYKVAPF--KS-QNMSLNSRVAKEDGEIAIAQYTqslacrVePSVHFNPILLKPKGNFIsQVIV 94 
                                   69******************9754..44.5999999999999999888885333333324555555666555333356666 PP

                        AAA_31  86 ssidLaeaeielvelekk..eeilkellekvkdeYDyiiiD 124
                                         +++ +  +++k    + +ke le ++ eYDy+i+ 
  gi|15668661|ref|NP_247460.1|  95 HGRPYKDMNYNEYRKNKDffLKKIKESLEILDREYDYVIME 135
                                   666666655555444444554457999************86 PP

>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.7e-05       0.1      75     109 ..     312     344 ..     300     356 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.7e-05
                      GATase_5  75 neklrealekflnredtlaLGiCnGfqlLvklglv 109
                                   +++  e++ +fl++ +++++GiC G q+L k +l+
  gi|15668661|ref|NP_247460.1| 312 QHNFDEKVLEFLKD-GGIVIGICGGYQVLGK-ELI 344
                                   6788999*******.*************987.355 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.18      10      40 ..      14      44 ..       2      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                         VirC1 10 kGGaGkttalmglcsalasdgkrvalfeade 40
                                     +Gktt   glc  la++g +va f++ +
  gi|15668661|ref|NP_247460.1| 14 SSNSGKTTITAGLCRILANKGYKVAPFKSQN 44
                                  4568***********************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2977.84
//
Query:       gi|15668662|ref|NP_247461.1|  [L=337]
Description: hypothetical protein MJ_0485 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-15   55.8   0.0    1.1e-13   51.3   0.0    2.2  1  ATP_bind_3      PP-loop family
    0.00025   19.9   0.0    0.00034   19.5   0.0    1.2  1  tRNA_Me_trans   tRNA methyl transferase
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.32   11.2   0.0    1.6  1  YwqJ-deaminase  YwqJ-like deaminase


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   1.9e-17   1.1e-13       2     167 ..      80     281 ..      79     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 1.9e-17
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SS...S..TCHHHHHHHHHHHHHHTT-EEEEEE--H......... CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhgl...r..eeskeeaelvkelckklnikleiekvdv......... 68 
                                   v+v++SgG DS++Ll+ll   ++k gikl+a++vd ++   r  +e  e  +l+k+ c++ln++++i k d+         
  gi|15668662|ref|NP_247461.1|  80 VIVGLSGGKDSLLLLHLLEVYRRKYGIKLIAVTVDVNIggiRpwKEDTEGVKLIKHHCEMLNVPHIILKNDLdvvelseil 160
                                   69*********************************97533375567788899****************9999889999998 PP

                                   .......HHCTTSTCCCHHHHHHHHHHHHCHHCCT.CE....EE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEE... CS
                    ATP_bind_3  69 .......akkkgknleeaARelRYevlkealkkegiev....lllAhhadDqaEtfllrlargsglaglagikeasei... 135
                                          + +   +     R+l  ++ ke++++e+i +    l+ +h+ dD   t+l ++++g+ l+ +  + + +     
  gi|15668662|ref|NP_247461.1| 161 tkhskgmEFSPCFSCSVIKRHLLGKLAKEIAENENIPYekvkLAYGHNLDDNSDTILANIFKGERLKFMRPLTRFKYNevd 241
                                   7433222111233445677888888999999999875333349999*****************998666555544433779 PP

                                   ........TTCCEE-CCCT--HHHHHHHHHHTT---B--C CS
                    ATP_bind_3 136 ........asirlvRPlLkvskeeleeylkekkikwveDe 167
                                           ++  ++RP+L +   ++ + l+e +i++++D+
  gi|15668662|ref|NP_247461.1| 242 yqsfkiplEECIIIRPMLPILERDIIKALEECGIEYYKDK 281
                                   9999999999****************************96 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.7e-08   0.00034       3     118 ..      80     194 ..      78     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.7e-08
                 tRNA_Me_trans   3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaerv...aeklgiplevvdfekeykekvfe 80 
                                   v+v+lSgG DS + ++ll e ++   g+ l  ++ + + g   +++ed++ ++ +   +e l++p+ +++   +     ++
  gi|15668662|ref|NP_247461.1|  80 VIVGLSGGKDSLLLLHLL-EVYRRKYGIKLIAVTVDVNIGGIRPWKEDTEGVKLIkhhCEMLNVPHIILKNDLDV--VELS 157
                                   99********98877766.678888899999998888888888999998887655444********998665554..4479 PP

                 tRNA_Me_trans  81 efleeyeeGrTPnPdvlCNkeiKfgallekakeelgad 118
                                   e+l+++++G   +P+ +C   iK ++l + ake ++++
  gi|15668662|ref|NP_247461.1| 158 EILTKHSKGMEFSPCFSCS-VIKRHLLGKLAKEIAENE 194
                                   ******************5.688777777776633333 PP

>> YwqJ-deaminase  YwqJ-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.3e-05      0.32     110     128 ..     159     178 ..     131     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.3e-05
                YwqJ-deaminase 110 p.kkpekGtaappCpnCtai 128
                                     +k+ kG+++ pC++C+ i
  gi|15668662|ref|NP_247461.1| 159 IlTKHSKGMEFSPCFSCSVI 178
                                   3489*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2035.39
//
Query:       gi|15668663|ref|NP_247462.1|  [L=322]
Description: hypothetical protein MJ_0486 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      8e-22   77.1   0.3    1.5e-21   76.2   0.3    1.4  1  Radical_SAM_C  Radical_SAM C-terminal domain
    1.7e-20   74.1   0.1    2.7e-20   73.4   0.1    1.3  1  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
       0.14   11.5   0.0       0.22   10.8   0.0    1.2  1  DUF3083        Protein of unknown function (DUF3083)


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.3   2.4e-25   1.5e-21       2      76 ..     227     305 ..     226     311 .. 0.92

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.4e-25
                 Radical_SAM_C   2 dgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkell.iagpwh.knlrel..i 76 
                                   + vK+ypl+v+kgT+L+e+y +gey+ l++++y++lv+d+le+l+p + ++Rl  d  +e++ ++++w  + l+++  +
  gi|15668663|ref|NP_247462.1| 227 EAVKIYPLVVVKGTKLEEMYWKGEYRTLDENQYISLVCDFLEHLSPYVLIQRLSKDKVPESIkVSPEWYlGRLKIMnkV 305
                                   689*****************************************************9999998*****99999887654 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.1   4.5e-24   2.7e-20       4     165 ..      47     219 ..      44     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 4.5e-24
                                   ESEESS-....-TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                   xxxxxxx....xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   4 trgCnlr....CsfCarpet..vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpg 77 
                                   + gC+++    C+fC+      + ++  +++  +e+i+++++   ++kg +k+ i +    + y++ ++l e       + 
  gi|15668663|ref|NP_247462.1|  47 GLGCPHKknggCIFCPEMGRpiSVKYCSAKIPLKEQIKKQMENQ-KKKGfKKFYIYFYPGTNTYAPAEKLKEIWDFS-LSY 125
                                   56899999999*****9998988888888888899999999999.69999888777776677778887777777777.599 PP

                                   EEEEEEECSSCHG...HHHHHHHHHTT....-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                   xxxxxxxxxxxxx...xxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  78 iritvetngtlpd...eeklerllelg....vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivg 151
                                    ++   + gt+pd   +ekl+ l+e+       ++ lg+++ + + +l+++nrgh+++++++a++ ++++gik++ ++i+g
  gi|15668663|ref|NP_247462.1| 126 KEVIGLSIGTRPDcleKEKLDILAEYVengyDIWIDLGVQSMHQK-TLEILNRGHDVSDIIKAIKDCHKRGIKVCGHVILG 205
                                   999999999999999999999999999999***************.*********************************** PP

                                   BTTTSHHHHHHHHH CS
                                   xxxxxxxxxxxxxx RF
                   Radical_SAM 152 lpGendeeleelle 165
                                   lpGe+++e+ e+++
  gi|15668663|ref|NP_247462.1| 206 LPGESWKEMMETAK 219
                                   ***********987 PP

>> DUF3083  Protein of unknown function (DUF3083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.7e-05      0.22     160     205 ..      69     113 ..      64     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.7e-05
                       DUF3083 160 altYvvvslpvsrrlkkqleadensdeysklYqkledafikaakkk 205
                                   ++ Y  +++p++ ++kkq+e+++++  ++k+Y ++    ++ a ++
  gi|15668663|ref|NP_247462.1|  69 SVKYCSAKIPLKEQIKKQMENQKKKG-FKKFYIYFYPGTNTYAPAE 113
                                   678*****************999988.*****99876555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2093.27
//
Query:       gi|15668664|ref|NP_247463.1|  [L=480]
Description: phenylalanyl-tRNA synthetase subunit alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-99  331.6   0.0    5.2e-99  330.7   0.0    1.5  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    7.3e-12   45.2   0.0    4.3e-08   32.9   0.0    3.1  3  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    2.5e-07   30.1   0.5    0.00018   20.7   0.1    3.6  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)
     0.0042   17.2   1.0     0.0042   17.2   1.0    2.3  2  KIP1             KIP1-like protein
  ------ inclusion threshold ------
      0.015   14.6   0.0       0.77    9.0   0.0    2.4  2  tRNA-synt_His    Histidyl-tRNA synthetase
      0.016   15.2   0.1      0.048   13.6   0.1    1.8  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
      0.067   13.2   3.8       0.36   10.8   3.8    2.4  1  HTH_45           Winged helix-turn-helix
       0.15   12.3   1.8        1.2    9.3   0.0    2.9  3  DUF1858          Domain of unknown function (DUF1858)
        0.2   12.0   0.1        0.2   12.0   0.1    2.9  3  Mnd1             Mnd1 HTH domain
       0.58   10.8   5.0        1.2    9.9   0.4    2.6  2  SecA_PP_bind     SecA preprotein cross-linking domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.7   0.0  2.9e-102   5.2e-99       2     244 ..     213     479 ..     212     480 .] 0.99

  Alignments for each domain:
  == domain 1  score: 330.7 bits;  conditional E-value: 2.9e-102
                                   .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-...... CS
                  tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka...... 76 
                                   +dv++p+k+i+++k+hplt++++e+kei+l++gf+ev++p ve+ef+nfd+L+ pqdhpaR+mqdtF+lk p++       
  gi|15668664|ref|NP_247463.1| 213 YDVKVPTKPIYPAKVHPLTRIIREVKEILLAMGFKEVKSPIVETEFWNFDMLFEPQDHPAREMQDTFFLKYPNEGdipedl 293
                                   9***********************************************************************999****** PP

                                   ...................ECESEEE-SSTHHHHHHHH.....TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEE CS
                  tRNA-synt_2d  77 ...................veekllLRthttavqirtl.....ekkkppikiisigrvfRrdavDathlaeFhqveglvvd 133
                                                      v+++l+LRthtta +ir+l     e+k++p+k+++i+rvfR++a+D++hl+eF+q+eg+++d
  gi|15668664|ref|NP_247463.1| 294 lskvkevhercwkykfdenVSRRLILRTHTTASSIRYLaslsdEEKNKPHKVFCIDRVFRNEAIDYKHLPEFYQCEGIIMD 374
                                   *******************9**********************99999********************************** PP

                                   TT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEE CS
                  tRNA-synt_2d 134 envsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsgfaf 214
                                   +nv++++l+gvl+e+l++l g+e kvrfrp+yfpftePs+e++vyl  ++k+wlE+lgaG++rpevle++gi  e++++a+
  gi|15668664|ref|NP_247463.1| 375 DNVNFNNLIGVLKEFLNRL-GFE-KVRFRPAYFPFTEPSLEAEVYL--EGKGWLEILGAGIFRPEVLEPIGI--EKPVLAW 449
                                   *******************.***.**********************..************************..******* PP

                                   EEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                  tRNA-synt_2d 215 GlGveRlamlkygieDiRelvendlrflrq 244
                                   G+G+ Rlaml+yg++DiR+l++ndl++l++
  gi|15668664|ref|NP_247463.1| 450 GIGFSRLAMLRYGLTDIRDLHKNDLDWLKR 479
                                   ***************************986 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.15   2.8e+02     107     161 ..      86     140 ..      70     163 .. 0.85
   2 !    7.4   0.0    0.0014       2.6       4      39 ..     216     251 ..     214     285 .. 0.84
   3 !   32.9   0.0   2.4e-11   4.3e-08      93     209 ..     339     448 ..     314     453 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.15
               tRNA_synthFbeta 107 lkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiek 161
                                   +k+ ++ lp+ee + a+++  ++  + +++ +  +d  d k + e+ll++++ +k
  gi|15668664|ref|NP_247463.1|  86 IKNLKDILPKEEINAALGAIKRKGIARIEKGKIIFDNLDYKDVEEQLLQKIKENK 140
                                   55666778***************9************************9988655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0014
               tRNA_synthFbeta   4 tlPkapttegelnkeqklrrklrdllagaGlnEvit 39 
                                   ++P+ p+ +++ ++  ++ r+++++l ++G+ Ev +
  gi|15668664|ref|NP_247463.1| 216 KVPTKPIYPAKVHPLTRIIREVKEILLAMGFKEVKS 251
                                   579999999999*********************976 PP

  == domain 3  score: 32.9 bits;  conditional E-value: 2.4e-11
               tRNA_synthFbeta  93 gnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepaehpal 172
                                   +n+  ++F i +vf+++  + +   e  +  ++++ ++           v+f +l g+++++l++lg+ekv+f+pa  p+ 
  gi|15668664|ref|NP_247463.1| 339 KNKPHKVFCIDRVFRNEaIDYKHLPEFYQCEGIIMDDN-----------VNFNNLIGVLKEFLNRLGFEKVRFRPAYFPFT 408
                                   45558999999999999766667888899999999999...........******************************** PP

               tRNA_synthFbeta 173 hpgrsAeikvdgk...evGvlGelhpevleafdlkqrvyv 209
                                   +p   Ae++++gk   e+  +G + pevle  +++++v +
  gi|15668664|ref|NP_247463.1| 409 EPSLEAEVYLEGKgwlEILGAGIFRPEVLEPIGIEKPVLA 448
                                   *************99*9999*****************987 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.057     1e+02      27      51 ..     232     256 ..     219     276 .. 0.91
   2 !   20.7   0.1     1e-07   0.00018      92     138 ..     343     390 ..     340     402 .. 0.77
   3 ?    3.1   0.0     0.023        42     287     307 ..     449     469 ..     444     471 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.057
                                   HHHHHHHHHHHHTT-EE----SEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  27 tvtkavrkyleengfieietPiLsk 51 
                                   ++++ v+++l   gf e++ Pi+ +
  gi|15668664|ref|NP_247463.1| 232 RIIREVKEILLAMGFKEVKSPIVET 256
                                   79999****************9865 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1e-07
                                   SEEEEEEEEE--S--BTTB-S-CEEEEEEEE..ET-SCHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  92 drvfqiaraFRaEdsrtdrhlaEFtqieaem..sfieeedimqvleeli 138
                                   ++vf+i r+FR+E ++ ++ + EF+q+e  +    +++++++ vl+e++
  gi|15668664|ref|NP_247463.1| 343 HKVFCIDRVFRNEAIDYKHLP-EFYQCEGIImdDNVNFNNLIGVLKEFL 390
                                   69**************99999.*****9544234566666666666655 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.023
                                   EEEEHHHHHHHHCT-SSGGGC CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 287 lglGldRlvmlllgsesIrdv 307
                                   +g+G++Rl ml  g+++Ird+
  gi|15668664|ref|NP_247463.1| 449 WGIGFSRLAMLRYGLTDIRDL 469
                                   79*****************97 PP

>> KIP1  KIP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.0   2.3e-06    0.0042      13      52 ..      40      78 ..      30      89 .. 0.78
   2 ?   -3.1   0.5       4.9   8.7e+03      20      36 ..     142     158 ..     132     177 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-06
                          KIP1 13 skwLq.etlseldekvkemlklieedadsfakraemyykkr 52
                                  s wL+ ++l e +ekvk+++kli+e++  f +r+ ++y k+
  gi|15668664|ref|NP_247463.1| 40 SLWLKgKNLVETEEKVKKIIKLIKEEE--FPERKIANYLKQ 78
                                  77998569***************8875..555555555554 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.9
                          KIP1  20 lseldekvkemlkliee 36 
                                   l++  e  k+++ ++++
  gi|15668664|ref|NP_247463.1| 142 LDDFSEEEKKIIDILKK 158
                                   45555556666666654 PP

>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.03        55       5      39 ..     222     256 ..     219     262 .. 0.92
   2 ?    9.0   0.0   0.00043      0.77      43     148 ..     293     399 ..     288     405 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.03
                                   EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEE CS
                 tRNA-synt_His   5 llpeeaekieelrrrlldlfeswGYelVspPllEy 39 
                                   ++p++++  +++ r++ +++ + G+++V++P++E 
  gi|15668664|ref|NP_247463.1| 222 IYPAKVHPLTRIIREVKEILLAMGFKEVKSPIVET 256
                                   5799999999***********************96 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00043
                                   HCTTSTCCHHHS-EE.E-T.TSSEEEE-SSSHHHHHHHHHHHHH..TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEE CS
                 tRNA-synt_His  43 lltgagedldqtfkl.vDq.sgrllglRaDiTpqvaRiaahrln..rerplRlcYaGsvlrtrpdglgrsreplQvGaEli 119
                                   ll++++e  ++ +k  +D+   r l lR  +T++  R+ a +    +++p+++  + +v+r ++ + +   e++Q+  E i
  gi|15668664|ref|NP_247463.1| 293 LLSKVKEVHERCWKYkFDEnVSRRLILRTHTTASSIRYLASLSDeeKNKPHKVFCIDRVFRNEAIDYKHLPEFYQC--EGI 371
                                   6666666666665554676699999****************9966899***************************6..666 PP

                                   SS-SHHHHHHHHHHHHHHHHHHCTSSSEE CS
                 tRNA-synt_His 120 GaegleadlEvlslllealeaaagvkelr 148
                                     ++  +  +++ +l e l+  +g +++r
  gi|15668664|ref|NP_247463.1| 372 IMDDNVNFNNLIGVLKEFLN-RLGFEKVR 399
                                   66666666777777777774.77777665 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.7e-05     0.048       1     123 [.     307     419 ..     307     435 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                                   EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslr 81 
                                   Yk++++  r++iL+   ++  ++        +k+ P k++ i +++R+E+ d +    + eF q +g ++  +      ++
  gi|15668664|ref|NP_247463.1| 307 YKFDENVSRRLILRTHTTASSIRYLASLSDEEKNKPHKVFCIDRVFRNEAIDYKH---LPEFYQCEGIIMDDNV----NFN 380
                                   88888889******999999998887665677889***************97776...679***9999987755....799 PP

                                   HHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  82 dlikaisriferlglefraiielmsaksadykdkkefeavse 123
                                   +li + +++++rlg+e+   +       ++ ++++e e++ e
  gi|15668664|ref|NP_247463.1| 381 NLIGVLKEFLNRLGFEKVRFRPAYF---PFTEPSLEAEVYLE 419
                                   999**********988654443333...45666666666655 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.8    0.0002      0.36       6      74 ..     117     190 ..     111     193 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                        HTH_45   6 eIiadILeaisegeakkTkimykanLs.y.kllnkYLdmLvekgli...kkskekYvlTekGlelleklkelee 74 
                                   +Ii+d L++ + +e+   ki  + +L+ + +  +k +d+L ++g++   ++++ k +lTekG+e++++  e+ee
  gi|15668664|ref|NP_247463.1| 117 KIIFDNLDYKDVEEQLLQKIKENKYLDdFsEEEKKIIDILKKRGYVdfdEEKEIKIKLTEKGKEFIKNPIEIEE 190
                                   5666666666666666666666666652313457899*********99888999***********998777765 PP

>> DUF1858  Domain of unknown function (DUF1858)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.31   5.5e+02       1      29 [.     136     164 ..     136     171 .. 0.80
   2 ?    9.3   0.0   0.00069       1.2       8      33 ..     228     253 ..     225     257 .. 0.84
   3 ?   -3.2   0.0       5.7     1e+04      17      29 ..     386     398 ..     385     399 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.31
                                   CETTSBHHHHHHH-GGGHHHHHHTTGGGG CS
                       DUF1858   1 ItkdttIgelleeyPelaevLvelGfhcl 29 
                                   I++++ + +  ee  +++++L++ G+ ++
  gi|15668664|ref|NP_247463.1| 136 IKENKYLDDFSEEEKKIIDILKKRGYVDF 164
                                   66777888888999999999999998766 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00069
                                   HHHHHH-GGGHHHHHHTTGGGGGSCC CS
                       DUF1858   8 gelleeyPelaevLvelGfhclgcps 33 
                                   + l +   e++e+L+++Gf++++ p+
  gi|15668664|ref|NP_247463.1| 228 HPLTRIIREVKEILLAMGFKEVKSPI 253
                                   556777789****************8 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5.7
                                   GHHHHHHTTGGGG CS
                       DUF1858  17 laevLvelGfhcl 29 
                                   l+e+L +lGf+++
  gi|15668664|ref|NP_247463.1| 386 LKEFLNRLGFEKV 398
                                   58999999**976 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00011       0.2       1      25 [.      10      35 ..      10      41 .. 0.85
   2 ?   -1.7   0.1       2.1   3.8e+03      14      20 ..      86      92 ..      75     100 .. 0.51
   3 ?   -2.3   0.1       3.2   5.8e+03      27      45 ..     182     201 ..     167     203 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                          Mnd1  1 ileifqes.kefytlKeleklapkek 25
                                  +l+ifq++ ++ ++l+elek +pkek
  gi|15668664|ref|NP_247463.1| 10 LLKIFQDNnRDEFNLNELEKFMPKEK 35
                                  6899999879**************65 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                          Mnd1 14 lKelekl 20
                                  +K l+ +
  gi|15668664|ref|NP_247463.1| 86 IKNLKDI 92
                                  3333344 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.2
                          Mnd1  27 ivs.qsVkdvlqsLvdDglv 45 
                                   i++  ++++ +++L+ D ++
  gi|15668664|ref|NP_247463.1| 182 IKNpIEIEEEITQLTRDIII 201
                                   43337889999999988766 PP

>> SecA_PP_bind  SecA preprotein cross-linking domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.5      0.16   2.8e+02       6      68 ..      14      77 ..      10     138 .. 0.75
   2 ?    9.9   0.4   0.00065       1.2       8      54 ..     148     195 ..     137     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.16
                                  HHHHHHHHCCCHTTCCECCCTTTSEEEESHHHHHHHHHCCT-SSSTT...SCCHCCHHHHHHHHHH CS
                  SecA_PP_bind  6 yekanklvkklkeeedyevdekkktveltekGvekvekllkvkeely...deenlelvhhvnqaLk 68
                                  ++  n+ + +l+e e+++ +ek  +v+l  kG++ ve++ kv ++++   +ee+    +++ + Lk
  gi|15668664|ref|NP_247463.1| 14 FQDNNRDEFNLNELEKFMPKEKILRVSLWLKGKNLVETEEKV-KKIIkliKEEE-FPERKIANYLK 77
                                  556666677799999999999999999999999999998666.33321113222.22233444444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00065
                                   HHHHHHCCCHTTCCECCCT.TTSEEEESHHHHHHHHHCCT-SSSTTSC CS
                  SecA_PP_bind   8 kanklvkklkeeedyevde.kkktveltekGvekvekllkvkeelyde 54 
                                   + +k++  lk++ +   de k+ +++ltekG+e +++ ++++ee+++ 
  gi|15668664|ref|NP_247463.1| 148 EEKKIIDILKKRGYVDFDEeKEIKIKLTEKGKEFIKNPIEIEEEITQL 195
                                   555666668888777777615679**************9998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1208  (0.0673769); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3359.24
//
Query:       gi|15668665|ref|NP_247464.1|  [L=158]
Description: hypothetical protein MJ_0488 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-71  238.5   4.6    2.6e-71  238.3   4.6    1.0  1  DUF3236          Protein of unknown function (DUF3236)
  ------ inclusion threshold ------
       0.01   15.9   2.0      0.015   15.4   2.0    1.2  1  CRISPR_Cas9_WED  CRISPR-Cas9 WED domain
      0.054   14.1   0.6      0.091   13.3   0.6    1.4  1  DUF4844          Domain of unknown function (DUF4844)
      0.061   13.5   0.1       0.28   11.3   0.0    1.9  2  DUF2620          Protein of unknown function DUF2620
        1.2    7.9   5.5        1.6    7.5   5.5    1.2  1  DUF4781          Domain of unknown function (DUF4781)


Domain annotation for each model (and alignments):
>> DUF3236  Protein of unknown function (DUF3236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.3   4.6   7.2e-75   2.6e-71       1     153 []       4     156 ..       4     156 .. 0.99

  Alignments for each domain:
  == domain 1  score: 238.3 bits;  conditional E-value: 7.2e-75
                                   HHHHHHHHHHHHHTT---S--HHHHHHHHHHHHT-SEEEES-SSHHHHHHHHHHHTTTT--EEEEESSTGGGGGGSSSHHH CS
                       DUF3236   1 leelikkayleslegaRkGDkeeeveaireyiknakkivvatknkkkvkvinkvlsklglkeiekleietnsaDltriPal 81 
                                   +ee+ikka++es++++R+GDkeee+++i+e+i nakkivvat+n+kk+kvi++++ +++++ei++l+i+t++aDltr+Pal
  gi|15668665|ref|NP_247464.1|   4 MEEIIKKAFIESINNIRRGDKEEELKKIQEKIVNAKKIVVATNNQKKFKVIRDIMLRVCNAEIKMLDIDTRFADLTRMPAL 84 
                                   79******************************************************************************* PP

                                   HHHHHHHHHS--SEEEEEEESSSTTS-EEEEEEETTS-EEEEEEE--TTTS---HHHHHHHHHHHHHHTTT- CS
                       DUF3236  82 skalialdisdadlviaRGRLGvpGsGsllvildekgriltaalsPshvihkksveeavkkelleaLkriGl 153
                                   +k+lialdi++adl+iaRGRLG+pGsGs+lvildekgr+lta+lsPs+vihk+++ee++kkel+eaL+riG+
  gi|15668665|ref|NP_247464.1|  85 TKGLIALDIEKADLYIARGRLGAPGSGSMLVILDEKGRVLTASLSPSSVIHKEDIEERIKKELIEALSRIGI 156
                                   ***********************************************************************7 PP

>> CRISPR_Cas9_WED  CRISPR-Cas9 WED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   2.0   4.1e-06     0.015      18      70 ..      10      64 ..       5      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.1e-06
               CRISPR_Cas9_WED 18 eyviekikniydkkeakkvkkllkk..dkekflmakkdpktfeklkkilkeysdk 70
                                  +  ie i+ni+  ++ +++kk+ +k  + +k ++a +++k f+ +++i+ +  + 
  gi|15668665|ref|NP_247464.1| 10 KAFIESINNIRRGDKEEELKKIQEKivNAKKIVVATNNQKKFKVIRDIMLRVCNA 64
                                  6789*******************999999*******************9766555 PP

>> DUF4844  Domain of unknown function (DUF4844)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   2.5e-05     0.091      14      83 ..       8      74 ..       3      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
                       DUF4844 14 akkKFiedvaelypgasddklrvalekkiNevakklleavsenlteeklqkklkltlerldkqylelDtE 83
                                   kk Fie ++++  g  +++l+++ ek++N  akk++ a++ n  + k+ + + l + +++ + l++Dt 
  gi|15668665|ref|NP_247464.1|  8 IKKAFIESINNIRRGDKEEELKKIQEKIVN--AKKIVVATN-NQKKFKVIRDIMLRVCNAEIKMLDIDTR 74
                                  4789**************************..688888875.56677999******99999999999996 PP

>> DUF2620  Protein of unknown function DUF2620
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       0.3   1.1e+03      85     103 ..      29      47 ..       8      73 .. 0.60
   2 ?   11.3   0.0   7.9e-05      0.28      41      93 ..      92     145 ..      82     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.3
                       DUF2620  85 eeikkaveeGkkaFgftae 103
                                   ++i++++ + kk+   t +
  gi|15668665|ref|NP_247464.1|  29 KKIQEKIVNAKKIVVATNN 47 
                                   4444444444443333333 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.9e-05
                       DUF2620  41 ksgeaDyylGaCntGaGgalalaiallGkekcltvs.kpgkvkkeeeikkavee 93 
                                      +aD+y+   + Ga g+ ++++ l  k++ lt s +p++v ++e+i++ +++
  gi|15668665|ref|NP_247464.1|  92 DIEKADLYIARGRLGAPGSGSMLVILDEKGRVLTASlSPSSVIHKEDIEERIKK 145
                                   5579******************************994569999******99986 PP

>> DUF4781  Domain of unknown function (DUF4781)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.5   0.00045       1.6     256     309 ..       4      57 ..       1      58 [. 0.92

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00045
                       DUF4781 256 AskiIekaqnqkikdyretlrsnrsrkaFkkilketakkneekeskkldiirtl 309
                                    ++iI+ka  + i+++r+  ++++ +k  +ki++ ++     +++kk+++ir++
  gi|15668665|ref|NP_247464.1|   4 MEEIIKKAFIESINNIRRGDKEEELKKIQEKIVNAKKIVVATNNQKKFKVIRDI 57 
                                   589*****************9************9999999999999******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1592  (0.0887947); expected 358.6 (0.02)
Passed bias filter:                      810  (0.0451782); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1021.84
//
Query:       gi|15668666|ref|NP_247465.1|  [L=268]
Description: hypothetical protein MJ_0489 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-94  315.0   2.6    3.8e-94  314.9   2.6    1.0  1  DUF1188   Protein of unknown function (DUF1188)
  ------ inclusion threshold ------
      0.033   13.5   0.1      0.052   12.9   0.1    1.4  1  DUF3638   Protein of unknown function (DUF3638)
      0.068   13.0   0.1       0.19   11.6   0.0    1.7  1  3HCDH_N   3-hydroxyacyl-CoA dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.9   2.6   6.3e-98   3.8e-94       1     248 []       7     265 ..       7     265 .. 0.98

  Alignments for each domain:
  == domain 1  score: 314.9 bits;  conditional E-value: 6.3e-98
                                   EBSSSTTSEEEE-SSBHHHHHHHHHHHHHHHHHHHHTT--E..EEEEEES-CCCHHHHHHHHCCC.EEEEEEESSGGGGGG CS
                       DUF1188   1 etGiTetvkTikskvklvdivkeiaekKaeavleyleeeeleeknvlviGaYltGaaiakkLskk.eevtlvDiephlkel 80 
                                   ++GiTe+vkTi++k+++vd+++eia+kK++a++++le+ee+  k+v+++G+Yl+G+++a++Lsk+ ++v+lvDi++ +k +
  gi|15668666|ref|NP_247465.1|   7 KYGITEMVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEF--KEVVIFGVYLWGNYTAQMLSKYaDKVYLVDIHEFMKGF 85 
                                   69***************************************..************************************** PP

                                   SSST........HHHHHHHHTTS---SEEEE---TT-S-HHHHTT---SEEEEE--B-S.--HHHHHH--HHHHHG.GTTT CS
                       DUF1188  81 lekd........vefklsleevernadlviDltGlGGvdpeklsklnakvlivEdPksegsDklikeanntekrle.svea 152
                                   ++++        +efkl++ + e+n+dl++DltGlGG++pe l+k+n+kv+ivEdPk+  +D +i+ea+nt+kr++ ++e+
  gi|15668666|ref|NP_247465.1|  86 VPNNnsikflnlNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGV-FDVDIYEADNTYKRTApFIEK 165
                                   ***********************************************************.**************9989*** PP

                                   SEEEEEEE..TTS--SB--HHHHHHHHHHHHHHHHHTSTTEEEEEEBB--HHHHHHTS--HHHHHHHHTSBSEEEEESS.. CS
                       DUF1188 153 ekkgiLkt..kglesKTSGtmTLtvdvlrdalneaeelegvLYavpnleffErilFkekdiekfleelekpAltvSslk.. 229
                                   +k g+Lkt  k+  sKTSGtmTLt+d+++da +e+++l+gvLYa+pnl+++E+ilF+e+di+kfl+e+++pA+t+S+l+  
  gi|15668666|ref|NP_247465.1| 166 AKVGVLKTyrKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNdv 246
                                   ********999********************************************************************76 PP

                                   HHHHHHHHHHHHHTEEEEE CS
                       DUF1188 230 evdvdeilkknldkiksev 248
                                     +++eil++n++ i+s+v
  gi|15668666|ref|NP_247465.1| 247 LDEAEEILSNNINLIYSFV 265
                                   679**************97 PP

>> DUF3638  Protein of unknown function (DUF3638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   8.6e-06     0.052     169     194 ..     238     263 ..     170     267 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.6e-06
                       DUF3638 169 wldessrdilDEsDellsvkfeLiYt 194
                                   +  ++  d+lDE+ e+ls +++LiY+
  gi|15668666|ref|NP_247465.1| 238 ITISTLNDVLDEAEEILSNNINLIYS 263
                                   3346789******************7 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.2e-05      0.19       6      49 ..       2      45 ..       1      52 [. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.2e-05
                                  --SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCC CS
                       3HCDH_N  6 GaGtmGagiaavfasagleVvlvdiseealekalekiekslekl 49
                                  G+G+m  gi++++   + ++++vd+++e+++k  ++i++ le  
  gi|15668666|ref|NP_247465.1|  2 GCGIMKYGITEMVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGE 45
                                  9************************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1810.26
//
Query:       gi|15668667|ref|NP_247466.1|  [L=313]
Description: malate dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-34  117.0   0.3    1.2e-33  116.2   0.3    1.4  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
    1.6e-26   93.2   0.0    2.9e-26   92.4   0.0    1.4  1  Ldh_1_C          lactate/malate dehydrogenase, alpha/beta C-t
    9.9e-05   22.0   0.2    0.00017   21.2   0.2    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00013   22.4   0.0    0.00023   21.6   0.0    1.5  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0019   18.4   0.2      0.037   14.3   0.0    2.3  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0028   18.2   0.1     0.0064   17.0   0.1    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.017   15.2   0.1      0.055   13.6   0.0    1.8  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.042   13.5   0.0        0.2   11.3   0.0    2.1  2  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.3   5.2e-37   1.2e-33       1     141 []       1     145 [.       1     145 [. 0.92

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 5.2e-37
                                   EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHH..HHHHHHHHHHHCHCCSTS-EEEEE...SSGGGGTTESEEEE- CS
                       Ldh_1_N   1 vkvavvGaaGgiGqslalllankkladelaLlDiake..kleGvaldlshistflsvkvkvse...keeealkdadvvvit 76 
                                   +kv+++Ga+G +G+++allla++++ ++l+L+  +++  kleG   d+ ++ + + ++++++    ++  ++ ++dvv+it
  gi|15668667|ref|NP_247466.1|   1 MKVTIIGASGRVGSATALLLAKEPFMKDLVLIGREHSinKLEGLREDIYDALAGTRSDANIYVesdENLRIIDESDVVIIT 81 
                                   69******************************9999888***********99888777666553245566889******** PP

                                   -S-SS-TTTTHHHHHHHHHHHHHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
                       Ldh_1_N  77 agvprkpGetRddLlkvNakIvkeiveaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                                   +gvprk+G++R dL k+NakIv + +++ia+++++ ++ v++NPvd++t+ +   s++++++v+g
  gi|15668667|ref|NP_247466.1|  82 SGVPRKEGMSRMDLAKTNAKIVGKYAKKIAEICDT-KIFVITNPVDVMTYKALVDSKFERNQVFG 145
                                   *********************************65.6789***********************98 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.0   1.3e-29   2.9e-26       1     165 [.     148     312 ..     148     313 .] 0.95

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 1.3e-29
                                   THHHHHHHHHHHHHHHTS-GGGEE--EEBSSST..........ETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHHHHH CS
                       Ldh_1_C   1 TtLDivRaktflaekagvtprsvkvtViGgHsg..........vtiipllsqvkellklsekqleeliervqnggdevvka 71 
                                   T+LD+ R+k+++a+ +gv+ ++v+  +iG+H++          +++ip+    ++  +++e  ++e+ie+v+ +g++++  
  gi|15668667|ref|NP_247466.1| 148 THLDSLRFKVAIAKFFGVHIDEVRTRIIGEHGDsmvpllsatsIGGIPI----QKFERFKELPIDEIIEDVKTKGEQIIRL 224
                                   99**************************************988888888....66689*********************** PP

                                   HTTSSSS-HHHHHHHHHHHHHHHTTHTEEEEEEEEEESC.CCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHHHH CS
                       Ldh_1_C  72 kkGagsatlsmAvAgakfveallrdtkeilsagvyldge.vglkdqeieyfsvPvvlgknGvekvleilklndfeeeklek 151
                                   k   g +  + A+A+ ++v+ +++++k+ l+ ++y dge  g+ d   + ++vPv +g++G+e+v++ ++l++ e  +++k
  gi|15668667|ref|NP_247466.1| 225 K---GGSEFGPAAAILNVVRCIVNNEKRLLTLSAYVDGEfDGIRD---VCIGVPVKIGRDGIEEVVS-IELDKDEIIAFRK 298
                                   *...89999******************************667777...9******************.************* PP

                                   HHHHHHHHHHHHHC CS
                       Ldh_1_C 152 svkeLkkeiekgle 165
                                   s++ +kk  e++++
  gi|15668667|ref|NP_247466.1| 299 SAEIIKKYCEEVKN 312
                                   *******9999875 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   7.5e-08   0.00017       1     136 [.       1     138 [.       1     159 [. 0.71

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.5e-08
                                   SEEEEE--.STTHHHHHHHHHHCT..SEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-S CS
                UDPG_MGDP_dh_N   1 mkisviGl.GYvGlvtaavlaeig..hevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveead 78 
                                   mk+++iG+ G vG  ta++la+    ++++++   e+ ++kl+  +  iy+    +   +++    +  + +  + ++e+d
  gi|15668667|ref|NP_247466.1|   1 MKVTIIGAsGRVGSATALLLAKEPfmKDLVLIG-REHSINKLEGLREDIYDALAGTRSDANI----YVESDENLRIIDESD 76 
                                   89*****66*************98656777776.5789********99*9875555555555....44444455669**** PP

                                   EEEE-----B-TTTTCB-T.....HHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHH CS
                UDPG_MGDP_dh_N  79 vifiaVgTPskkkgkaaDl.....kyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkil 136
                                   v++i+ g P k+  + +Dl     k v + a++iae+ +  k+ v+   v v t + lv++  
  gi|15668667|ref|NP_247466.1|  77 VVIITSGVPRKEGMSRMDLaktnaKIVGKYAKKIAEICD-TKIFVITNPVDVMTYKALVDSKF 138
                                   ************555545411111445555555555554.56666666777777776666555 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0     1e-07   0.00023       1      72 [.       2      80 ..       2     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1e-07
                                  EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG.......GGTTTECEBEEE.GGGGGCTT-SEEEE CS
                Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk.......aleegkdlkved.vdeeelkevdivfl 72
                                  kv i+Ga+G vG++ + lL+++p ++ +vl+++++s  k l+ + +        +++ +++ ve+  +  +++e d+v+ 
  gi|15668667|ref|NP_247466.1|  2 KVTIIGASGRVGSATALLLAKEPFMKDLVLIGREHSINK-LEGLREdiydalaGTRSDANIYVESdENLRIIDESDVVII 80
                                  799********************************5544.4333333556777777778888888667777788888875 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.7e-05     0.037       1      36 [.       3      38 ..       3      96 .. 0.76
   2 ?    1.9   0.0      0.11   2.5e+02      26      64 ..      99     134 ..      90     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                                  EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHH CS
               Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskek 36
                                  v iiGa G+vG+a+a lla++  + +++++++r+++ 
  gi|15668667|ref|NP_247466.1|  3 VTIIGAsGRVGSATALLLAKEPFM-KDLVLIGREHSI 38
                                  679*****************9877.599999998764 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                                   EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHH CS
               Sacchrp_dh_NADP  26 eitvadrskeklealaakalgvrfeaialdaenyeavLa 64 
                                   +  +++++ +k +++++  +++ +++  +d++ y+a L+
  gi|15668667|ref|NP_247466.1|  99 NAKIVGKYAKKIAEICD--TKIFVITNPVDVMTYKA-LV 134
                                   66799999999999998..7899************9.54 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   2.9e-06    0.0064       1      68 [.       2      81 ..       2     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.9e-06
                                  EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...........-EEECECHHHHHHH-SEEEE- CS
                 F420_oxidored  1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...........vkvtavdneeaaeeadvvvla 68
                                  k+ ii ++G++g+a a+ l+++ + +  ++++ + + +k+e l+e+++           + v++ +n   ++e+dvv+++
  gi|15668667|ref|NP_247466.1|  2 KVTIIgASGRVGSATALLLAKEPFMKDLVLIGREHSINKLEGLREDIYdalagtrsdanIYVESDENLRIIDESDVVIIT 81
                                  689**668**************99**********************999**********9999999************97 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.4e-05     0.055       1      72 [.       1      79 [.       1      85 [. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                                  EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC..STTTT..TBHH.HHSSSS.--S-BEB.SSHHHHHHH-SEEE CS
                        DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrke..seleg..kdag.ellglg.klgvavt.ddleevlekadvli 72
                                  +kv+++GasGr+G++ + ++ +++ ++    + r++  ++leg  +d+   l+g++   ++ v+ d+  ++++++dv+i
  gi|15668667|ref|NP_247466.1|  1 MKVTIIGASGRVGSATALLLAKEPFMKDLVLIGREHsiNKLEGlrEDIYdALAGTRsDANIYVEsDENLRIIDESDVVI 79
                                  89*****************999988877777777663323322114444344444445555555455556677788877 PP

>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.1e-05       0.2      50      96 ..      56     104 ..      43     118 .. 0.81
   2 ?   -1.4   0.0      0.76   1.7e+03      33      60 ..     231     260 ..     211     267 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.1e-05
                                   SEEEEEEE-SSS..----TT-EEEEE.E--......BTTSTTEEEEBET CS
               Ribosom_S12_S23  50 gkevtafipgegalnfldEhdevlvr.Girrk.gkavkDlpGvrykvvk 96 
                                   + + + ++ +++ l  +dE d+v++  G+ rk g +  Dl+  + k+v 
  gi|15668667|ref|NP_247466.1|  56 RSDANIYVESDENLRIIDESDVVIITsGVPRKeGMSRMDLAKTNAKIVG 104
                                   5667789****************9963777777*******999999986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.76
                                   TT--S-EEEEEEEET.TSE..EEEEEE-SS CS
               Ribosom_S12_S23  33 kPnsAlRkvvrvrLikngk..evtafipge 60 
                                    P +A+  vvr  ++++++  ++ a++ ge
  gi|15668667|ref|NP_247466.1| 231 GPAAAILNVVRCIVNNEKRllTLSAYVDGE 260
                                   588888899987776333322456887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1998.06
//
Query:       gi|15668668|ref|NP_247467.1|  [L=167]
Description: hypothetical protein MJ_0491 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-46  155.6   3.1    7.6e-46  155.6   3.1    1.4  2  DUF2120   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
      0.022   14.6   0.9          4    7.2   0.1    2.2  2  DUF724    Protein of unknown function (DUF724)
       0.16   12.0   0.0       0.38   10.7   0.0    1.6  2  PSDC      Phophatidylserine decarboxylase


Domain annotation for each model (and alignments):
>> DUF2120  Uncharacterized protein conserved in archaea (DUF2120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.86   5.2e+03     102     115 ..       8      21 ..       2      28 .. 0.39
   2 !  155.6   3.1   1.3e-49   7.6e-46       3     135 ..      31     161 ..      29     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.86
                       DUF2120 102 leveYklgkkddla 115
                                    +++ ++ k+++  
  gi|15668668|ref|NP_247467.1|   8 KSLKNTVKKLKTYN 21 
                                   23333333334444 PP

  == domain 2  score: 155.6 bits;  conditional E-value: 1.3e-49
                       DUF2120   3 agkimkeldaFkGSkplldkeeiLivrgvsrkkeeleeleskleellekldaeevdlese..eakkliekldesireveei 81 
                                   +g++m++l+aFkGSkpl++++e+L+v+gv+r++e +e++ s++++l++kl++e ++++++  e++k++++++e ++e +++
  gi|15668668|ref|NP_247467.1|  31 IGRLMHALNAFKGSKPLFETDEMLMVKGVCRDEE-VEKYGSIKDYLVKKLEKEGFEIVEDikEIDKFVSRINEILKE-NPL 109
                                   589******************************9.*************************99*************99.888 PP

                       DUF2120  82 eeevdafglerlkeslEalgleveYklgkkddlavfvvlwkdksgvgPlfvEvv 135
                                   +  +d+fg+er+kes+E++g+e++Y ++kk++++v+v+++ dk++++P+fvEvv
  gi|15668668|ref|NP_247467.1| 110 Y--PDTFGFERMKESFEMIGCECDYVIAKKRNIMVGVCMYFDKKMKNPKFVEVV 161
                                   8..**************************************************8 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1    0.0016       9.3      68      99 ..       5      36 ..       2      44 .. 0.90
   2 ?    7.2   0.1   0.00067         4      58      99 ..      56      98 ..      51     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0016
                        DUF724 68 seleslkeslaeLekhGFdVkalqsrlnkLls 99
                                  + l+slk+++++L+++ F V + +  + +L++
  gi|15668668|ref|NP_247467.1|  5 NLLKSLKNTVKKLKTYNFGVSMWKVNIGRLMH 36
                                  6799*******************999999986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00067
                        DUF724 58 vkklsiddsrseleslkesl.aeLekhGFdVkalqsrlnkLls 99
                                  vk ++ d+++++  s+k+ l ++Lek+GF++    + ++k +s
  gi|15668668|ref|NP_247467.1| 56 VKGVCRDEEVEKYGSIKDYLvKKLEKEGFEIVEDIKEIDKFVS 98
                                  56677788888999999876268*******9998888888776 PP

>> PSDC  Phophatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.52   3.1e+03      46      62 ..      30      46 ..       3      56 .. 0.52
   2 ?   10.7   0.0   6.3e-05      0.38      42     100 ..      88     152 ..      70     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.52
                          PSDC 46 dyeellellnhilttap 62
                                  ++  l+++ln+   + p
  gi|15668668|ref|NP_247467.1| 30 NIGRLMHALNAFKGSKP 46
                                  33445555555544444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6.3e-05
                          PSDC  42 kqirdyeellellnhilttapef......sdkeeevglvgvPlnalLdwpmgtpsGyalFldpev 100
                                   + i++++++++ +n+il++ p +      ++ +e+ +++g+    ++    +   G+ ++ d+++
  gi|15668668|ref|NP_247467.1|  88 EDIKEIDKFVSRINEILKENPLYpdtfgfERMKESFEMIGCECDYVIAKKRNIMVGVCMYFDKKM 152
                                   7899*******************9999999999***********************999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1146  (0.0639188); expected 358.6 (0.02)
Passed bias filter:                      846  (0.0471861); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1110.48
//
Query:       gi|15668669|ref|NP_247468.1|  [L=95]
Description: hypothetical protein MJ_0492 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0072   16.5   0.3      0.012   15.8   0.3    1.3  1  Pox_A14   Poxvirus virion envelope protein A14
     0.0072   16.8   3.0     0.0084   16.5   3.0    1.1  1  DUF3972   Protein of unknown function (DUF3972)
  ------ inclusion threshold ------
      0.013   16.1   3.4      0.032   14.8   3.4    1.6  1  DUF643    Protein of unknown function (DUF643)
      0.031   14.2   0.4      0.047   13.6   0.4    1.3  1  DUF4006   Family of unknown function (DUF4006)
        1.9    9.2   5.9        3.5    8.4   5.9    1.6  1  DUF3139   Protein of unknown function (DUF3139)


Domain annotation for each model (and alignments):
>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   3.3e-06     0.012      12      45 ..       2      35 ..       1      39 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.3e-06
                       Pox_A14 12 stvliaGiiLLilacifafvdfskststtdkawr 45
                                  + v+i+ i+LL +++i+af  + ks+s+t  a++
  gi|15668669|ref|NP_247468.1|  2 NFVIIIAILLLGISLILAFTVLNKSKSKTTMAYK 35
                                  6799***********************9888887 PP

>> DUF3972  Protein of unknown function (DUF3972)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.0   2.4e-06    0.0084      48     104 ..      25      83 ..      15      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.4e-06
                       DUF3972  48 kevvseetnsksldaefvEktigtilsLhekvld.akdetiea.lknenkfLKealism 104
                                   k+ +++ ++ k +++e ++  i+++ +L + v + a de i+  l +en+ LKeal ++
  gi|15668669|ref|NP_247468.1|  25 KSKSKTTMAYKRAQEEKIDTEIKMLKNLKNNVCSgASDEIIDNiLNSENNILKEALKNN 83 
                                   3334446899999*******************95499**99763789********9765 PP

>> DUF643  Protein of unknown function (DUF643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   3.4     9e-06     0.032      20      76 ..      28      83 ..      15      93 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9e-06
                        DUF643 20 nklyeteqltleqkkqlysavkkiqeykiktGksveeiindiiepekefikdvlkdk 76
                                  +k   + + ++e+k +    + k  + ++ +G s +eii++i+++e +++k+ lk+ 
  gi|15668669|ref|NP_247468.1| 28 SKTTMAYKRAQEEKIDTEIKMLKNLKNNVCSGAS-DEIIDNILNSENNILKEALKNN 83
                                  4444444445555555544444445555666666.6*******************85 PP

>> DUF4006  Family of unknown function (DUF4006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   1.3e-05     0.047      18      56 ..       5      43 ..       3      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                       DUF4006 18 liavvLLLsilavLtvlaikvqqaeatnyYkledldsvk 56
                                  +i+ +LLL+i  +L +  ++  +++ t  Yk  + +++ 
  gi|15668669|ref|NP_247468.1|  5 IIIAILLLGISLILAFTVLNKSKSKTTMAYKRAQEEKID 43
                                  78999**************************66665553 PP

>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.9   0.00096       3.5       1      54 [.       1      57 [.       1      88 [. 0.65

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00096
                       DUF3139  1 mkkiiiililliillvivkvflglvgskpikkylan.....kkldkylqekgykeddIk 54
                                  m+ +iii ill+ +++i+++ + l++sk   + +a+     +k+d+ ++  +  ++++ 
  gi|15668669|ref|NP_247468.1|  1 MNFVIIIAILLLGISLILAFTV-LNKSKSK-TTMAYkraqeEKIDTEIKMLKNLKNNVC 57
                                  6788888888888888866666.3333332.2222222345777777766666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2007  (0.111942); expected 358.6 (0.02)
Passed bias filter:                      910  (0.0507558); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 653.76
//
Query:       gi|15668670|ref|NP_247469.1|  [L=283]
Description: nicotinate-nucleotide pyrophosphorylase NadC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-68  228.1   0.9    6.5e-68  227.8   0.9    1.1  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
    1.3e-25   89.2   0.0    2.4e-25   88.4   0.0    1.5  1  QRPTase_N       Quinolinate phosphoribosyl transferase, N-ter
    0.00056   19.9   0.4     0.0049   16.9   0.1    2.3  2  B12-binding     B12 binding domain
     0.0055   16.1   0.0      0.016   14.6   0.0    1.7  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
  ------ inclusion threshold ------
      0.067   12.5   0.0       0.12   11.6   0.0    1.4  1  TMP-TENI        Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.8   0.9   1.8e-71   6.5e-68       1     169 []     105     278 ..     105     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: 227.8 bits;  conditional E-value: 1.8e-71
                                   HHHHHHHHHHHHHCT..SSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHHHTT CS
                     QRPTase_C   1 iAtltarmveaaksa..kvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvreavdk 79 
                                   iAt+t+r+v++aks+  +vr+++TRkt+P l +l+kyAv+iGGgd+hr++L+d+vlikdnhia++g ++ea+++++e+v++
  gi|15668670|ref|NP_247469.1| 105 IATMTNRIVKKAKSVnkNVRVACTRKTLPLLSPLQKYAVYIGGGDTHRFRLDDCVLIKDNHIAIVG-VKEAIRRAKENVSF 184
                                   9*************9999************************************************.************** PP

                                   TSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT....SEEEEESS--TTTHHHHHCTT-SEEEECH CS
                     QRPTase_C  80 evkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkr....vlievSGgvtlenveeyaksgvdvisvga 156
                                   ++kievev++l+el+e+le++adiimLDnf++ee+++a+++++e +++     +ievSGg++++n+ eyak++vdvis+ga
  gi|15668670|ref|NP_247469.1| 185 TKKIEVEVSNLKELREALEERADIIMLDNFKPEEIEEALKIIDEFERKtnfkPIIEVSGGIKEDNILEYAKYNVDVISMGA 265
                                   ******************************************99888888889**************************** PP

                                   HCHTB----EEEE CS
                     QRPTase_C 157 lthsvkalDislk 169
                                   lthsvk++D+sl+
  gi|15668670|ref|NP_247469.1| 266 LTHSVKSVDMSLD 278
                                   ***********97 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.0   6.8e-29   2.4e-25       1      89 []      18     103 ..      18     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 6.8e-29
                                   CTT--HHHHHHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHH CS
                     QRPTase_N   1 igrgDlttealipeekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERva 81 
                                   +g+gD+tt+++ipe+ kak++i+ake+++v+G++++ ++fe + g++++ l++DGe++     +le+eG+ar++l+ ER+a
  gi|15668670|ref|NP_247469.1|  18 VGFGDITTNSIIPEGVKAKGVIKAKEKCIVCGIDFIVAFFEEY-GIKCKKLFNDGEEAYG--NILEFEGDARTILMLERTA 95 
                                   589****************************************.************9865..5****************** PP

                                   HHHHHHHH CS
                     QRPTase_N  82 LnllqrlS 89 
                                   Lnll++lS
  gi|15668670|ref|NP_247469.1|  96 LNLLMHLS 103
                                   *******8 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.15   5.4e+02       8      37 ..      41      70 ..      36     127 .. 0.48
   2 !   16.9   0.1   1.4e-06    0.0049      16     117 ..     167     270 ..     164     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.15
                   B12-binding  8 vggdlhplGlavlaaalrdagfeVqllgan 37
                                  ++ ++   G++ + a++++ g++++ l  +
  gi|15668670|ref|NP_247469.1| 41 AKEKCIVCGIDFIVAFFEEYGIKCKKLFND 70
                                  556666667777777777766666554333 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.4e-06
                   B12-binding  16 GlavlaaalrdagfeVqll...ganvenedivaairaekpdvvglSalltsqleavkelvel..lkrirprvkvvvGGahp 91 
                                   ++  +++a+r+a  +V+++   +++v+n + ++++ +e++d+++l      ++e++ +++++  +k++ + ++ v GG   
  gi|15668670|ref|NP_247469.1| 167 AIVGVKEAIRRAKENVSFTkkiEVEVSNLKELREALEERADIIMLDNFKPEEIEEALKIIDEfeRKTNFKPIIEVSGG--- 244
                                   667789999999999998887799999977788889999********9999************888888888888888... PP

                   B12-binding  92 sldpeetleak.lgiddvvvgegedal 117
                                    + ++ +le++   +d++ +g  ++ +
  gi|15668670|ref|NP_247469.1| 245 -IKEDNILEYAkYNVDVISMGALTHSV 270
                                   .67999999999888999988777765 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.4e-06     0.016     149     195 ..     218     265 ..     212     267 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.4e-06
                                   HHHHHHHHHHHHH.HHT---EEEEESS--TTTCHHHHHHT--EEEESH CS
                Ribul_P_3_epim 149 vlekikkvrklid.ekeldlkievDGGvkldnieqiaeagadvlVags 195
                                    +e+  k+   ++ +++++  iev GG+k+dni + a+ ++dv+ +g 
  gi|15668670|ref|NP_247469.1| 218 EIEEALKIIDEFErKTNFKPIIEVSGGIKEDNILEYAKYNVDVISMGA 265
                                   444333333333303458899***********************9985 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.5e-05      0.12      85     177 ..     174     263 ..     157     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.5e-05
                      TMP-TENI  85 pvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgleglkelaeale.iPvv.aiGGitlen 163
                                   ++++a+e +   + i + v++l+e++ea ++ ad i++  +     K+++    l+ + e  ++++ +P++ + GGi+++n
  gi|15668670|ref|NP_247469.1| 174 AIRRAKENVSFTKKIEVEVSNLKELREALEERADIIMLDNF-----KPEEIEEALKIIDEFERKTNfKPIIeVSGGIKEDN 249
                                   5677888888889999999*******************999.....8888888899999999999987887578******* PP

                      TMP-TENI 164 vaevleagadgvav 177
                                   + e +++++d +++
  gi|15668670|ref|NP_247469.1| 250 ILEYAKYNVDVISM 263
                                   **********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1810.14
//
Query:       gi|15668671|ref|NP_247470.1|  [L=134]
Description: hypothetical protein MJ_0494 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-22   78.8   0.0    3.8e-22   78.5   0.0    1.1  1  RNase_P_Rpp14  Rpp14/Pop5 family


Domain annotation for each model (and alignments):
>> RNase_P_Rpp14  Rpp14/Pop5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   2.1e-26   3.8e-22       1     102 [.      17     111 ..      17     112 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 2.1e-26
                                   EEEEEEEEESS......-HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT--EETT CS
                 RNase_P_Rpp14   1 RYllveilypdeeeelteksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtlitkieg 81 
                                   RY++++ily++   el+e +++++ir++v e++G +g++k++   +++y++     +i+Rc+r+++++v a+L li+++++
  gi|15668671|ref|NP_247470.1|  17 RYIAFKILYDE---ELKEGEVVNLIRKAVLEYYGSWGTSKANP--WLVYYDF--PYGILRCQRDNVDYVKASLILIREFKE 90 
                                   9**********...589**************************..9****99..89************************* PP

                                   EEEEEEEEEEESSHHHHHHHT CS
                 RNase_P_Rpp14  82 rpvvfrvvrvsGTikkaeeea 102
                                   +pv + +++vsGTi+ka+ ++
  gi|15668671|ref|NP_247470.1|  91 KPVNIICLGVSGTIRKAKIKF 111
                                   *****************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 835.35
//
Query:       gi|15668672|ref|NP_247471.1|  [L=469]
Description: EF-1 alpha family translation factor [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.7e-36  123.5   0.9    1.4e-35  122.7   0.9    1.3  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    3.5e-11   43.3   7.4    3.6e-11   43.3   0.3    3.8  4  GTP_EFTU_D2   Elongation factor Tu domain 2
    2.2e-08   34.2   0.1    4.6e-08   33.1   0.1    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
    6.6e-08   31.9   0.3    2.6e-07   29.9   0.1    1.9  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
    9.8e-07   28.4   0.9    4.8e-06   26.2   0.9    2.1  1  FeoB_N        Ferrous iron transport protein B
    6.8e-06   26.1   1.9    1.1e-05   25.4   0.6    1.9  2  RsgA_GTPase   RsgA GTPase
     0.0002   21.1   0.8      0.012   15.3   0.2    2.4  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
    0.00061   19.3   1.2     0.0016   17.9   0.8    1.9  2  SRPRB         Signal recognition particle receptor beta subun
    0.00077   19.5   0.4     0.0023   17.9   0.4    1.7  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0022   18.2   0.1     0.0036   17.5   0.1    1.3  1  MnmE_helical  MnmE helical domain
     0.0051   16.3   0.1      0.009   15.5   0.1    1.5  1  Arf           ADP-ribosylation factor family
     0.0064   16.1   0.1      0.015   14.9   0.1    1.6  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
       0.11   12.3   0.0        0.4   10.4   0.1    1.8  3  ATP_bind_1    Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.9   9.9e-39   1.4e-35       3     192 ..       9     177 ..       7     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 9.9e-39
                                   EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGG CS
                      GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvdF 83 
                                    +n+g+ gh+DhGKt L  +L+    +i++       +++lD+ ke ++rgiTi+    s+    ++y+i+l+D+PGH + 
  gi|15668672|ref|NP_247471.1|   9 NVNVGLFGHIDHGKTQLAKQLT----EIAS-------TSALDKPKESQKRGITIDLGFSSFT--LDRYRITLVDAPGHSEL 76 
                                   68*******************9....3333.......2359*********************..***************** PP

                                   HHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      GTP_EFTU  84 skevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygek 163
                                   +++ i + +++D a+lvvda+eG+++qt e+l ++  +++p+iv+iNK+D + ++e+k++   +kq l       + +  k
  gi|15668672|ref|NP_247471.1|  77 IRTAIGAGNIIDAALLVVDAKEGPKTQTGEHLLVLDLLNIPTIVVINKIDIAnDEEIKRTEMFMKQIL------NSTINLK 151
                                   ****************************************************8888888888888888......2223333 PP

                                   TTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
                      GTP_EFTU 164 gekevpvvfgSalkgegvktllealvell 192
                                      + +++ +Sa++geg+ +l + l +ll
  gi|15668672|ref|NP_247471.1| 152 ---NSKIIKISAKTGEGIGELKKELKNLL 177
                                   ...468**********9998877776655 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1         1   1.4e+03      27      44 ..     128     142 ..     118     145 .. 0.70
   2 !   43.3   0.3   2.6e-14   3.6e-11       1      74 []     204     271 ..     204     271 .. 0.96
   3 ?   -1.3   0.0       2.1   2.9e+03      13      24 ..     354     365 ..     353     396 .. 0.79
   4 ?    1.0   0.1      0.42   5.8e+02      12      29 ..     398     415 ..     391     462 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1
                                   TSEEEEEEEEEEEEETEE CS
                   GTP_EFTU_D2  27 skkeivtrissletfhed 44 
                                     +   ++i+++e+f+++
  gi|15668672|ref|NP_247471.1| 128 AND---EEIKRTEMFMKQ 142
                                   445...89*******985 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 2.6e-14
                                   EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                   Gtv++g++  G++++Gd++ril+ n+   +   ++++s++ f++d+ +a+ag+++G  + +++ e+ + +G++lt
  gi|15668672|ref|NP_247471.1| 204 GTVVTGTIHKGKVEVGDNLRILPiNH---E---VKVKSIQCFKQDVSIAYAGDRVGMALMGVEPES-LFRGCILT 271
                                   9********************99886...4...*********************************.9***9986 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.1
                                   EETTEEEEEECT CS
                   GTP_EFTU_D2  13 lkkGdevrilgn 24 
                                   + +Gd++ i+++
  gi|15668672|ref|NP_247471.1| 354 VDEGDKILIMRL 365
                                   668999999774 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.42
                                   EEETTEEEEEEC.TCTTSE CS
                   GTP_EFTU_D2  12 tlkkGdevrilg.ndtskk 29 
                                   ++kk d+++i g   +sk+
  gi|15668672|ref|NP_247471.1| 398 VVKKKDKIYIEGlA-SSKT 415
                                   58999*****8854.4444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   3.3e-11   4.6e-08       1     114 []      11     124 ..      11     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 3.3e-11
                                   EEEEEESTTSSHHHHHHHHHT.......STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHH CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltg.......ekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflale 74 
                                   +v+++G+   GK+ L ++lt+       +k + s+k g T+d  +  ++l++ +i+lvD pG  +      +l ++     
  gi|15668672|ref|NP_247471.1|  11 NVGLFGHIDHGKTQLAKQLTEiastsalDKPKESQKRGITIDLGFSSFTLDRYRITLVDAPG-HS------ELIRTAIGAG 84 
                                   599*****************877766444889*****************999**********.33......4666666666 PP

                                   C.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  75 e.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                   +  d++llvvda+ e+ k +  e   +l+  ++p+i+v+nk
  gi|15668672|ref|NP_247471.1|  85 NiIDAALLVVDAK-EGPKTQTGEHLLVLDLLNIPTIVVINK 124
                                   647********88.5566655555555555789******98 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   1.9e-10   2.6e-07     113     232 ..      64     180 ..      51     189 .. 0.80
   2 ?   -1.3   0.0       0.6   8.3e+02      52      83 ..     244     277 ..     232     285 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.9e-10
                                   HHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTTTTTTT--C....CCHHH-SEEEEE---HHHHHHHHHHH CS
                          MeaB 113 vvllleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpeaGDelqgikk....GileiaDiivvnkaDkkeaekaarel 189
                                    ++l++a G+  ++   +G+G        ++d  ++++ ++ G + q+  +     +l+i  i+v+nk D ++ e+ +r+ 
  gi|15668672|ref|NP_247471.1|  64 RITLVDAPGHSELIRTAIGAGN-------IIDAALLVVDAKEGPKTQTGEHllvlDLLNIPTIVVINKIDIANDEEIKRTE 137
                                   5789999999999999999995.......455555555555555555433311116899********************** PP

                                   HHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHH CS
                          MeaB 190 raaleleeekekeWrpkvlktsavegeGidelvdaieehrevl 232
                                   +++ ++++++ +  ++k++k+sa++geGi el +++++  + l
  gi|15668672|ref|NP_247471.1| 138 MFMKQILNSTINLKNSKIIKISAKTGEGIGELKKELKNLLDSL 180
                                   *********************************9998877665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.6
                                   HHHCTT--E..EEEEE------------------ CS
                          MeaB  52 elrrrGkrv..avlavDPsspftGGsilGDklRl 83 
                                   +++ +G rv  a++ v+P s f G  +  + ++l
  gi|15668672|ref|NP_247471.1| 244 SIAYAGDRVgmALMGVEPESLFRGCILTSEDTKL 277
                                   5667788874456889999999987766666665 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.9   3.5e-09   4.8e-06       2     155 ..      11     172 ..      10     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.5e-09
                                   EEEEEESTTSSHHHHHHHHHTTSE.......EEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakq.......kvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll 75 
                                   +v l G  + Gkt l  +lt+  +       k +   G+t++    +++l+++++++vD PG  +l  ++        + +
  gi|15668672|ref|NP_247471.1|  11 NVGLFGHIDHGKTQLAKQLTEIAStsaldkpKESQKRGITIDLGFSSFTLDRYRITLVDAPGHSELIRTA--------IGA 83 
                                   5778999999999999999987651111111446778*************************87775543........333 PP

                                   CTSSSEEEEEEEGGGHHH....HHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHT.......S-EEEEBTTT CS
                        FeoB_N  76 eeepdvvvnvvdatnler....nLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLg.......vpvvktsakk 145
                                    + +d+ + vvda++  +    + +L+l+l  l++p+++++n+id a++++i+  +  ++++L+        +++k+sak+
  gi|15668672|ref|NP_247471.1|  84 GNIIDAALLVVDAKEGPKtqtgEHLLVLDL--LNIPTIVVINKIDIANDEEIKRTEMFMKQILNstinlknSKIIKISAKT 162
                                   444578888888876544111134455565..578*****************9998888888862222222479******* PP

                                   TBTHHHHHHH CS
                        FeoB_N 146 kegieellka 155
                                   +egi el+k+
  gi|15668672|ref|NP_247471.1| 163 GEGIGELKKE 172
                                   *******986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       0.4   5.5e+02     102     163 ..      12      75 ..       3      79 .. 0.77
   2 !   25.4   0.6   7.9e-09   1.1e-05       5      99 ..      73     175 ..      69     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.4
                                   EEEECSTTSSHHHHHHHHCT.T-----S--------------SEEEEEETT.TEEEESS-SSSS CS
                   RsgA_GTPase 102 svlvGqSGvGKStLinallp.elelktgevseklgrGkhTTtavellelae.gglliDtPGfre 163
                                   + l G+   GK+ L ++l++   + +  + +e+++rG       + + l++   +l+D+PG +e
  gi|15668672|ref|NP_247471.1|  12 VGLFGHIDHGKTQLAKQLTEiASTSALDKPKESQKRGITIDLGFSSFTLDRyRITLVDAPGHSE 75 
                                   5577888889999999999966688888889999999887777777777765677899999776 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 7.9e-09
                                   S-EETTTT..EES.--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH.......HHHHHHHHHHHT CS
                   RsgA_GTPase   5 knelvrpk..vaN.vdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee.......eleelkeeleal 75 
                                   ++el+r++  + N +d +l+vv +k +  ++++ +  L+++   +i+ ++v+nKiD++++ee         + l+++++  
  gi|15668672|ref|NP_247471.1|  73 HSELIRTAigAGNiIDAALLVVDAK-EGPKTQTGE-HLLVLDLLNIPTIVVINKIDIANDEEikrtemfMKQILNSTINLK 151
                                   5788888876666369999999988.555555555.56667999******************9987773333344455556 PP

                                   TSEEEE--TTTHTTHHHHHHHCTT CS
                   RsgA_GTPase  76 gyevllvsaktkegleelkellkd 99 
                                   + +++++sakt+eg+ elk++lk+
  gi|15668672|ref|NP_247471.1| 152 NSKIIKISAKTGEGIGELKKELKN 175
                                   789******************997 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.026        36       4      23 ..      12      31 ..       7      46 .. 0.87
   2 !   15.3   0.2   8.9e-06     0.012      85     142 ..     111     174 ..      60     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.026
                     PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                  + l+G+++ GKt L+++l++
  gi|15668672|ref|NP_247471.1| 12 VGLFGHIDHGKTQLAKQLTE 31
                                  5689************9976 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 8.9e-06
                     PduV-EutP  85 asvfnkeviGiitkidlaedeenieaveelLksa.......Gaekifevsavekegieellkyle 142
                                     ++n ++i +i kid+a ++e+i+ +e ++k+          +ki+++sa + egi el+k l+
  gi|15668672|ref|NP_247471.1| 111 LDLLNIPTIVVINKIDIA-NDEEIKRTEMFMKQIlnstinlKNSKIIKISAKTGEGIGELKKELK 174
                                   4678999***********.778888887777654211121145799***************9987 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.8   1.2e-06    0.0016       6     142 ..      12     149 ..       7     179 .. 0.71
   2 ?   -2.7   0.0       2.4   3.3e+03     117     127 ..     236     246 ..     199     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.2e-06
                                   EEEE-STTSSHHHHHHHHHHS....S---B---SS-EEETTG.......GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEE CS
                         SRPRB   6 vllvGlsdsGKTslftrLttd....svkktvtSqessaalkv....ksekgskltliDfPGheklrqklleklkaksslkg 78 
                                   v l G  d GKT l ++Lt+     +  k   Sq+  ++ ++     + +  ++tl+D PGh +l    +      + + +
  gi|15668672|ref|NP_247471.1|  12 VGLFGHIDHGKTQLAKQLTEIastsALDKPKESQKRGITIDLgfssFTLDRYRITLVDAPGHSELIRTAIGA---GNIIDA 89 
                                   557899************97655557788899999999999877544568899*********9885444333...566999 PP

                                   EEEEEETTS-HHHHHHHHHHHHHHHHHHHHH.TT---EEEEEE-TTSTT---HHHHHHHHHHHHH CS
                         SRPRB  79 lvfvvDStidpkevkevAEllyeillitekl.kdavdiliACnKqelflakspklikdaLEkEln 142
                                    + vvD+   pk  +    l+ ++l i ++   +++di      ++  + +++  +k+ L + +n
  gi|15668672|ref|NP_247471.1|  90 ALLVVDAKEGPKTQTGEHLLVLDLLNIPTIVvINKIDIA-----NDEEIKRTEMFMKQILNSTIN 149
                                   999***999999655555555566655333226666652.....344456777777777777665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.4
                                   EEEE-TTSTT- CS
                         SRPRB 117 iACnKqelfla 127
                                   i C Kq++++a
  gi|15668672|ref|NP_247471.1| 236 IQCFKQDVSIA 246
                                   78999999988 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.4   1.6e-06    0.0023      56     100 ..     116     173 ..     107     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.6e-06
                  MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare.............pnsvviSaekelnldeLkeki 100
                                   ip+++v+NKiD +++ee+++ +               ++++ iSa+++ ++ eLk+++
  gi|15668672|ref|NP_247471.1| 116 IPTIVVINKIDIANDEEIKRTEMFmkqilnstinlknSKIIKISAKTGEGIGELKKEL 173
                                   89****************998773457889999998668999************9986 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.6e-06    0.0036      70     133 ..      24     179 ..      15     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.6e-06
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx...................................................... RF
                  MnmE_helical  70 kleelkeelekllatakrgellreGik...................................................... 96 
                                   +l++  +e+ ++ a  k +e  + Gi+                                                      
  gi|15668672|ref|NP_247471.1|  24 QLAKQLTEIASTSALDKPKESQKRGITidlgfssftldryritlvdapghselirtaigagniidaallvvdakegpktqt 104
                                   444444444444444455555555555555555999999999999999999999999999999999999999999999999 PP

                                   .....................xxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                  MnmE_helical  97 .....................Dllkeke................ekeeeevlkiSaktgegieeLeeaike.lel 133
                                                        D+++++e                + ++++++kiSaktgegi eL++++k+ l +
  gi|15668672|ref|NP_247471.1| 105 gehllvldllniptivvinkiDIANDEEikrtemfmkqilnstiNLKNSKIIKISAKTGEGIGELKKELKNlLDS 179
                                   9999999999999999999996666666667777888888888889999999*****************994444 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   6.5e-06     0.009      58     173 ..      63     175 ..       4     177 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.5e-06
                                   EEEEEEEE-SSGGGGGGGGGGCTTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTS..S-HHHH CS
                           Arf  58 lkftvwDvGGqeklRplWknYfektdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpea..lseeel 136
                                   +++t+ D  G+++l +      + +da + vvD+ +  + ++ ++    ll   +l +++ +v+ NK+D++++  ++++e+
  gi|15668672|ref|NP_247471.1|  63 YRITLVDAPGHSELIRTAIGAGNIIDAALLVVDAKEGPKTQTGEH----LL-VLDLLNIPTIVVINKIDIANDeeIKRTEM 138
                                   555555555555555555555556666666666666555443322....22.23577899*********987611445555 PP

                                   HHHTTGGGSSSSSSEEEEEEBTTTTBTHHHHHHHHHH CS
                           Arf 137 rellgleelkgkrkleiqkcsavkgeglkeglewlse 173
                                     +  l++  + ++ +i+k sa +geg+ e  + l +
  gi|15668672|ref|NP_247471.1| 139 FMKQILNSTINLKNSKIIKISAKTGEGIGELKKELKN 175
                                   444445554458999**************99888765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.1e-05     0.015     111     169 ..      86     143 ..      68     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                   CECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHH CS
                          cobW 111 tldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerlrql 169
                                    +da + vvDak+  + ++ ++ ++ d l+   ++v+nK+D +++e+  ++ e  ++q+
  gi|15668672|ref|NP_247471.1|  86 IIDAALLVVDAKEGPKTQTGEHLLVLDLLNIPTIVVINKIDIANDEEI-KRTEMFMKQI 143
                                   579999********999****************************965.7777666665 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.6   3.5e+03       3      23 ..      16      36 ..      14      39 .. 0.83
   2 ?   -3.9   0.0       6.6   9.2e+03      94     106 ..      66      78 ..      61      89 .. 0.78
   3 ?   10.4   0.1   0.00029       0.4     155     201 ..     114     170 ..     103     197 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.6
                    ATP_bind_1  3 GpaGsGKttfvgalseilelr 23
                                  G+   GKt + ++l+ei++++
  gi|15668672|ref|NP_247471.1| 16 GHIDHGKTQLAKQLTEIASTS 36
                                  66667***********99876 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.6
                    ATP_bind_1  94 llfDtPGQielft 106
                                    l+D PG  el  
  gi|15668672|ref|NP_247471.1|  66 TLVDAPGHSELIR 78 
                                   799****999865 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00029
                    ATP_bind_1 155 lelPhvvvlnkfDllkeklekeleffedvealslllekee...........ekykkla 201
                                   l++P++vv+nk+D++++++ k+ e+f   + l+ ++++++           e   +l+
  gi|15668672|ref|NP_247471.1| 114 LNIPTIVVINKIDIANDEEIKRTEMFM-KQILNSTINLKNskiikisaktgEGIGELK 170
                                   799***********9877555555555.334444444444334544444443333334 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2856.76
//
Query:       gi|15668673|ref|NP_247472.1|  [L=141]
Description: hypothetical protein MJ_0496 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 953.30
//
Query:       gi|15668674|ref|NP_247473.1|  [L=133]
Description: hypothetical protein MJ_0497 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.6e-30  102.4   0.0    1.5e-29  101.9   0.0    1.2  1  Hjc         Archaeal holliday junction resolvase (hjc)
    2.6e-05   24.2   0.0    3.8e-05   23.7   0.0    1.2  1  Mrr_cat     Restriction endonuclease
  ------ inclusion threshold ------
      0.017   14.7   0.4        9.6    5.9   0.0    3.0  3  FlbD        Flagellar and Swarming motility proteins
      0.026   14.6   0.1      0.048   13.7   0.1    1.5  1  HicA_toxin  HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.9   0.0   3.3e-33   1.5e-29       2      88 ..      11      91 ..      10      95 .. 0.94

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 3.3e-33
                                  HHHHHHHHHHHTT-EEEEBSCSSSSSSSS-SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHHTCEEEEEEEETTT CS
                           Hjc  2 yERelvkiLrergfavvRsagSggatkplpDviAirgdvvlviEvKsskkeriylkkeqvekllefarkaggelllavklqgk 84
                                  +ERel+++L+++gfav+RsagS+g+     D+iA+r+++vl++E+K+s+k+++y++ke++ekl++f++ +gg+++la+k++g 
  gi|15668674|ref|NP_247473.1| 11 FERELKRLLEKEGFAVIRSAGSKGV-----DLIAGRKGEVLIFECKTSSKTKFYINKEDIEKLISFSEIFGGKPYLAIKFNG- 87
                                  8************************.....*************************************************954. PP

                                  EEEE CS
                           Hjc 85 ewkl 88
                                  e+ +
  gi|15668674|ref|NP_247473.1| 88 EMLF 91
                                  5555 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   8.5e-09   3.8e-05       6      71 ..       8      70 ..       5      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 8.5e-09
                                  TTCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-...B-HHHHHHHHH CS
                       Mrr_cat  6 pkeFeklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKryknk...vgvkeVqelig 71
                                  + +Fe+ +++lle++G+  v ++  +g +g+Dlia +++   e ++ ++K ++++   ++++++++li+
  gi|15668674|ref|NP_247473.1|  8 GSSFERELKRLLEKEGFA-VIRS--AGSKGVDLIAGRKG---EVLIFECKTSSKTkfyINKEDIEKLIS 70
                                  678**************9.6555..699*******9865...89********75435599999999986 PP

>> FlbD  Flagellar and Swarming motility proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0054        24       9      22 ..      55      68 ..      49      73 .. 0.84
   2 ?    1.4   0.0     0.054   2.4e+02       6      19 ..      84      97 ..      83      99 .. 0.86
   3 ?    5.9   0.0    0.0021       9.6      33      47 ..      99     113 ..      95     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0054
                          FlbD  9 geefvlNadlIeti 22
                                  +++f++N + Ie+ 
  gi|15668674|ref|NP_247473.1| 55 KTKFYINKEDIEKL 68
                                  689*********86 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.054
                          FlbD  6 rlngeefvlNadlI 19
                                  ++nge +++N+ l 
  gi|15668674|ref|NP_247473.1| 84 KFNGEMLFINPFLL 97
                                  79********9886 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0021
                          FlbD  33 tnGkkyvVkEsvdev 47 
                                   tnGk yv+ E ++ +
  gi|15668674|ref|NP_247473.1|  99 TNGKNYVIDERIKAI 113
                                   8**********9988 PP

>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.1e-05     0.048       2      21 ..      13      32 ..      13      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                                  HCHHHHHHHTT-EEEEEETT CS
                    HicA_toxin  2 reviklLeklGfevvrqkGS 21
                                  re+ +lLek Gf v+r+ GS
  gi|15668674|ref|NP_247473.1| 13 RELKRLLEKEGFAVIRSAGS 32
                                  89*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 853.45
//
Query:       gi|15668675|ref|NP_247474.1|  [L=156]
Description: hypothetical protein MJ_0498 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-39  132.0   0.0    8.6e-39  131.4   0.0    1.2  1  DUF2102   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
      0.046   13.8   0.0      0.099   12.8   0.0    1.5  1  BLUF      Sensors of blue-light using FAD


Domain annotation for each model (and alignments):
>> DUF2102  Uncharacterized protein conserved in archaea (DUF2102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.4   0.0   9.6e-43   8.6e-39       2     103 .]       8     110 ..       7     110 .. 0.98

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 9.6e-43
                       DUF2102   2 vvieseaevtpselvrkvyeleedvtiketCfGllvegeeeevekvveevrkldpnkifvkeRgfppgderrCRakr.gga 81 
                                   +v++++a +tp +lvr +++l+++v +ketCfG+++egeee v+k+++e+r++++n+if+k+Rg++++d+rrCRa r gg+
  gi|15668675|ref|NP_247474.1|   8 IVLAENALTTPGKLVRYINTLNQPVIVKETCFGAYIEGEEELVDKLAQEIRNYERNRIFCKDRGYAIWDKRRCRAFRgGGP 88 
                                   89999999*********************************************************************99** PP

                       DUF2102  82 RpGfhqlekEvelleliskaLe 103
                                   R+Gfhqle+E ++l++i+ aL+
  gi|15668675|ref|NP_247474.1|  89 REGFHQLEAEQAVLDKIGLALD 110
                                   ******************9996 PP

>> BLUF  Sensors of blue-light using FAD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.1e-05     0.099      40      71 ..      33      64 ..      26      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                                  EEETTEEEEEEEEEHHHHHHHHHHHHT-TTEE CS
                          BLUF 40 lydegvflQvLEGeeeaveelyerIkkDpRhk 71
                                  +++e++f  ++EGeee v++l ++I++ +R +
  gi|15668675|ref|NP_247474.1| 33 IVKETCFGAYIEGEEELVDKLAQEIRNYERNR 64
                                  67889999******************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1000.75
//
Query:       gi|15668676|ref|NP_247475.1|  [L=424]
Description: 3-isopropylmalate dehydratase large subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.3e-98  329.0   7.2    1.3e-64  218.9   2.5    2.1  2  Aconitase  Aconitase family (aconitate hydratase)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.9   2.5   7.4e-69   1.3e-64      13     301 ..      22     286 ..       7     292 .. 0.86
   2 !  113.6   0.3   6.4e-37   1.1e-32     330     461 .]     287     416 ..     282     416 .. 0.93

  Alignments for each domain:
  == domain 1  score: 218.9 bits;  conditional E-value: 7.4e-69
                     Aconitase  13 g.iayv.pdrvllqdvtgvqalvdlaaar.eavrrlggtlatidhlvpvdlvidhsvgaeealeknledefernkeryefL 90 
                                   g i +   d  +++d+tg+ ++++l++ + e+v+++++ +   dh+vp+d     s+          + +    +e+   +
  gi|15668676|ref|NP_247475.1|  22 GdIVMAnIDVAMVHDITGPLTVNTLKEYGiEKVWNPEKIVILFDHQVPAD-----SI----------K-A----AENHILM 82 
                                   2322224699***************98872566*****************.....66..........2.1....2445677 PP

                     Aconitase  91 ksaakafgirv.vppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipkvvgvk 170
                                   +++ k+ gi++ +++ +G++Hqv +E+g + pg++vvg DSHT+++g++G++a+G+G++++++v+++ +l++k+p+++ ++
  gi|15668676|ref|NP_247475.1|  83 RKFVKEQGIKYfYDIREGVCHQVLPEKGHVAPGEVVVGADSHTCTHGAFGAFATGIGSTDMAHVFATGKLWFKVPETIYFN 163
                                   8899999997548999***************************************************************** PP

                     Aconitase 171 ltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdektleYLkatgree 251
                                   +tG+l++ vt+kD++l +ig+++++g++ k+  f Ge+v+++s++ r+T++NMa+E+G +tg++++dekt++Y+k + +++
  gi|15668676|ref|NP_247475.1| 164 ITGDLQPYVTSKDVILSIIGEVGVDGATYKACQFGGETVKKMSIASRMTMTNMAIEMGGKTGIIEPDEKTIQYVKEAMKKH 244
                                   ***************************************************************************444433 PP

                     Aconitase 252 aavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdav 301
                                    +   e+  +      ++ dedae+++v+e++++++ep  a p++++++ 
  gi|15668676|ref|NP_247475.1| 245 GT---ERPFE-----VIKGDEDAEFAEVYEIEADKIEPVFACPHNVDNVK 286
                                   33...33222.....4679*************************999865 PP

  == domain 2  score: 113.6 bits;  conditional E-value: 6.4e-37
                     Aconitase 330 egtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkayleaeGlleiLekaGfevvga 410
                                   +  ++   ++d+++igSCTN+++ed+r+a ++++   ++g  ++++v+++v+P+S++   ++ +eG+ e++ k G+ v+++
  gi|15668676|ref|NP_247475.1| 287 QAREVAGKPIDQVFIGSCTNGRLEDLRMAIKIIE---KHG-GIADDVRVVVTPASREEYLKALKEGIIEKFLKYGCVVTNP 363
                                   556677789*************************...556.79999*********************************** PP

                     Aconitase 411 gCstCig.nsdrleegeaivsssNRNFegRqgpntra.yLaSPelvvaaAlaG 461
                                    Cs C+g   + l +ge++vs+sNRNF+gRqg+     yLaSP  ++a A++G
  gi|15668676|ref|NP_247475.1| 364 SCSACMGsLYGVLGPGEVCVSTSNRNFRGRQGSLEAEiYLASPITAAACAVKG 416
                                   *******999*********************9666666*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2477.79
//
Query:       gi|15668677|ref|NP_247476.1|  [L=259]
Description: hypothetical protein MJ_0500 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-39  134.9   0.0    2.4e-39  134.3   0.0    1.3  1  DUF364    Putative heavy-metal chelation
    6.6e-14   51.9   0.0    1.3e-13   50.9   0.0    1.5  1  DUF4213   Putative heavy-metal chelation


Domain annotation for each model (and alignments):
>> DUF364  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.3   0.0   2.6e-43   2.4e-39       1     146 [.     111     256 ..     111     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 2.6e-43
                        DUF364   1 daldl.leikkgkkVvvVGyfapvlkklk.ekgaeltvlelnpnlleeeegdlpdeaaeellpeadvviitGstLvngtle 79 
                                   da +l l+ ++ kk+++VG++ pv+++lk +++ +++v+e++p+ll +    l+d+++++llpe+d+v+i+G+tL+n+tl+
  gi|15668677|ref|NP_247476.1| 111 DAAELvLNRDDIKKIAFVGNMIPVVNMLKkSEKFDIYVFERSPSLLMDGV--LSDAFEYRLLPEMDAVFISGTTLLNDTLD 189
                                   67899999*********************88999*********9999976..5**************************** PP

                        DUF364  80 rllelakkaaevvlvGPsapllpevlfdyGvdviagvvvtdpdkllraiaeGggtkhlkrkgakkiv 146
                                    +l++ak+a+ ++lvGP+a+ lpe+++++G+++ia+++++d dk+l +++ + + + +k+ ++k+++
  gi|15668677|ref|NP_247476.1| 190 FVLDRAKNAKLKILVGPTAQSLPELFKGFGITHIASTKIIDVDKALLYLKFASSSMLFKGASKKYTM 256
                                   *************************************************************999876 PP

>> DUF4213  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.0   1.5e-17   1.3e-13       4      74 .]      16      99 ..      12      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 1.5e-17
                       DUF4213  4 lieaapedltVedvviGlnwtlVelsdg...gaGlAyt......eagkl.......vgkparelaelllswnplersvGlAai 70
                                  l+++ +ed +V d+ + l +++V ++++    +G+A+t      +           ++k+++e+++++ s +++er++G+Aai
  gi|15668677|ref|NP_247476.1| 16 LLSEKEEDFKVIDFSFALPYSYVLIESNgkkALGVAMTlleeyrG---HgnrkdlnINKNLEEFINMADSFDIVERTLGVAAI 95
                                  5556679*******************98788*******7754441...0333444566************************* PP

                       DUF4213 71 NAll 74
                                  NA++
  gi|15668677|ref|NP_247476.1| 96 NAVS 99
                                  **96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2033.87
//
Query:       gi|15668678|ref|NP_247477.1|  [L=202]
Description: hypothetical protein MJ_0501 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-69  233.4   5.3    1.4e-69  233.2   5.3    1.0  1  DUF2119   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2119  Uncharacterized protein conserved in archaea (DUF2119)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.2   5.3     8e-74   1.4e-69       2     187 ..      12     198 ..      11     199 .. 0.96

  Alignments for each domain:
  == domain 1  score: 233.2 bits;  conditional E-value: 8e-74
                       DUF2119   2 egpvrlfvgGlHGdEgkdtskileklk....eedlsegllvipnlek.skYiSTldkeyyeseegkklidlveklkpeiYv 77 
                                   +g+++lf+gGlHG+Egk t+ il+++     e+++ ++++vip+l + skYiSTl+++yyes+egk+li++++k+kp++Y+
  gi|15668678|ref|NP_247477.1|  12 NGVKKLFIGGLHGNEGKFTEIILKDFVnslkECNYIGDIVVIPKLVEnSKYISTLSEKYYESDEGKTLINIIKKYKPKVYF 92 
                                   789****************99998876555599*********998766********************************* PP

                       DUF2119  78 ElHsYskenykkLtdedRlkktgvPplvdlengvLigSvsplirkkyfkkealcltlEipklkskesleevlkileliaes 158
                                   ElH+Y+kenykkLt+++R   ++vPpl+d++n+vLi+S+sp++r k+f+ke++c+t+Eip++k+ e+++e+lkil++ aes
  gi|15668678|ref|NP_247477.1|  93 ELHAYKKENYKKLTSNNR---KKVPPLIDIGNNVLIASISPILR-KRFSKEDFCMTIEIPSWKVYEVKDEILKILKIGAES 169
                                   ******************...99*********************.************************************ PP

                       DUF2119 159 ksreelieklkkkYpeqvekakeyakkfy 187
                                    +ree+ieklkk Ype++eka+   kk++
  gi|15668678|ref|NP_247477.1| 170 LRREEIIEKLKKIYPEHIEKAEYFSKKYN 198
                                   ***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1442.56
//
Query:       gi|15668679|ref|NP_247478.1|  [L=429]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.2e-145  484.5   0.0   2.5e-145  484.4   0.0    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin
  ------ inclusion threshold ------
      0.091   13.3   0.4        6.6    7.3   0.0    2.7  3  Soc            Small outer capsid protein


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.4   0.0  2.8e-149  2.5e-145       2     417 .]       7     419 ..       6     419 .. 0.97

  Alignments for each domain:
  == domain 1  score: 484.4 bits;  conditional E-value: 2.8e-149
                                   ECSS--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE-H CS
                 EPSP_synthase   2 ekgkrlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeape 82 
                                   +k++rleg vk+p+sks+++ra++ A+La+g+s+i n+L+++D++s+++ +r+Lga +i+ld+ek+++iv+g  g++++p 
  gi|15668679|ref|NP_247478.1|   7 KKTDRLEGIVKAPPSKSYTHRAVIGASLADGVSRIINPLWGADCLSSVHGCRMLGA-NIELDKEKDEWIVKG--GELKTP- 83 
                                   7889***************************************************6.66999**********..******. PP

                                   HHHTT-GGGGGGHHHHHHHHSEES.SEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET..SS-BEEEEE CS
                 EPSP_synthase  83 elvldlgnsgtalrlLtallalas.gevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg..lklkgveik 160
                                   ++++d+gnsgt+lr+Lt+++++++ g+ +LtGd+sirkRP+++lldaL+ql++e  +++ +++ap++vk+    ++ v+i+
  gi|15668679|ref|NP_247478.1|  84 DNIIDIGNSGTTLRILTSIASQIPkGYAILTGDDSIRKRPMQPLLDALKQLNIEAFSSKLDGTAPIIVKSgkIYGNVVKIR 164
                                   8*********************666*********************************************9999******* PP

                                   TSSTTHHHHHHHHHHHTTSBS.EEEEES.-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE--B-HHHH CS
                 EPSP_synthase 161 aevsSqqvtsllllaallaeg.ttelee.lasepsiddtlkmlkkfgikietsgteesitvkGkeklpgteyvvegDassA 239
                                   +++sSq++tsl++l ++ +e+ +++l+  l+s+p+id+tl++l+kfgiki++  t++ + v G++k +  +y+vegD+ssA
  gi|15668679|ref|NP_247478.1| 165 GDISSQFITSLMMLLPFNKEDtEIILTSpLKSKPYIDITLDILNKFGIKIDK--TDNGFLVYGNQKYKPIDYIVEGDYSSA 243
                                   *********************9999**9************************..9999********8888*********** PP

                                   HHHHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSEEEEEETTS--BEEEEEBGSTTSBHGGGHHHHH CS
                 EPSP_synthase 240 ayflvaAaitggevtvenvginslqGdiealdeilekmgaeitqeedasivvgpsglklkdvdietlpdeaptlavlaafa 320
                                   +y+++a+++ ++++t+en+++ns qGd+++++ i+++mga+i+ ++d++i++g+++lk++dvd++++pd++pt+avl +fa
  gi|15668679|ref|NP_247478.1| 244 SYLIAAGVLINSNITIENLFANSKQGDKAIIN-IVKEMGADIKVKKDKVIIEGEYSLKGIDVDVKDIPDLVPTIAVLGCFA 323
                                   ***************************77777.************************************************ PP

                                   HHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTTHHHHHHHHHSBSEEEEE CS
                 EPSP_synthase 321 egttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRiamalalaglvaegeveid 401
                                   eg+t+i + +++r ke+drl a+a eL+k+Ga++ee++dglii++++k lkga++++y+DhR+ ma+++agl aege++i+
  gi|15668679|ref|NP_247478.1| 324 EGKTEIYNGEHVRLKECDRLRACAVELKKMGADIEEKPDGLIIRGVKK-LKGAKLNTYHDHRLVMAFTIAGLKAEGETIIE 403
                                   *****************************************9888776.******************************** PP

                                   TTHHHHHHSSSHHHHH CS
                 EPSP_synthase 402 diectdksfpefeekL 417
                                     e++++sfp+f++++
  gi|15668679|ref|NP_247478.1| 404 GEEAVKISFPNFVDVM 419
                                   *************986 PP

>> Soc  Small outer capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.013   1.2e+02       3      38 ..     134     165 ..     132     174 .. 0.74
   2 ?   -3.9   0.0         2   1.8e+04      33      44 ..     369     380 ..     367     384 .. 0.72
   3 ?    7.3   0.0   0.00073       6.6      11      40 ..     395     425 ..     386     428 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.013
                                   EEEEE--BEESTTEEE--EEEEEEHHHHHHS---SS CS
                           Soc   3 vniktfeqkldgnkkiegkeisvafplysdvhkisg 38 
                                   +ni +f  kldg   i  k       +y +v ki g
  gi|15668679|ref|NP_247478.1| 134 LNIEAFSSKLDGTAPIIVKS----GKIYGNVVKIRG 165
                                   69**********98886553....345666666665 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2
                                   S---SSSSEEEE CS
                           Soc  33 vhkisgahyqtf 44 
                                   v+k+ ga+ +t+
  gi|15668679|ref|NP_247478.1| 369 VKKLKGAKLNTY 380
                                   678888887776 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00073
                                   EESTTEEE--EE.EEEEHHHHHHS---SSSS CS
                           Soc  11 kldgnkkiegke.isvafplysdvhkisgah 40 
                                   k +g+  ieg e + ++fp + dv k  ga 
  gi|15668679|ref|NP_247478.1| 395 KAEGETIIEGEEaVKISFPNFVDVMKSLGAN 425
                                   7789999***985789**********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2734.81
//
Query:       gi|15668680|ref|NP_247479.1|  [L=406]
Description: trans-homoaconitate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-84  282.9   0.4    3.7e-84  282.4   0.4    1.2  1  HMGL-like       HMGL-like
  ------ inclusion threshold ------
      0.082   12.3   0.0       0.19   11.1   0.0    1.5  2  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.4   0.4   4.1e-88   3.7e-84       2     264 .]      32     291 ..      31     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 282.4 bits;  conditional E-value: 4.1e-88
                                   -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHH CS
                     HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaav 82 
                                   ++i dttLRDGeq++++ ++ e+kl+ia++Lde+g+++iE+gfp  se + + v++ia+++ +a+ilal+ra +kdi++a+
  gi|15668680|ref|NP_247479.1|  32 IYIYDTTLRDGEQTPGVCFTKEQKLEIARKLDELGLKQIEAGFPIVSEREADIVKTIANEGLNADILALCRALKKDIDKAI 112
                                   79******************************************************************************* PP

                                   H....TT-SEEEEEEES-HHHHHHHHS.STHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-SE CS
                     HMGL-like  83 ealkgagakrvhvfiatselhlkaklk.kdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGatr 162
                                   e    + ++ + +fiats lhlk+k++ k+ +e++++ +eav++a+++g  v++s+eda+rt++e+l++v +aaeeaGa+r
  gi|15668680|ref|NP_247479.1| 113 E----CDVDGIITFIATSPLHLKYKFNnKSLDEILEMGVEAVEYAKEHGLFVAFSAEDATRTPIEDLIKVHKAAEEAGADR 189
                                   *....*********************64899************************************************** PP

                                   EEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHHHH CS
                     HMGL-like 163 iniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelvaal 243
                                   + iaDt G++tP+++  + ++lke++k k+ + vHcHnd+G Av n++ ++  Ga+ v++tvnG+GeraGnaaleel++al
  gi|15668680|ref|NP_247479.1| 190 VHIADTTGCATPQSMEFICKTLKENLK-KAHIGVHCHNDFGFAVINSIYGLIGGAKAVSTTVNGIGERAGNAALEELIMAL 269
                                   ***************************.***************************************************** PP

                                   HHTT.-B----HHHHHHHHHHH CS
                     HMGL-like 244 ealg.vdtgldlqklrsiaalv 264
                                    +l  vd gl+l+ l ++ ++v
  gi|15668680|ref|NP_247479.1| 270 TVLYdVDLGLNLEVLPELCRMV 291
                                   **999********999987776 PP

>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.37   3.3e+03      20      38 ..      50      68 ..      36      70 .. 0.74
   2 ?   11.1   0.0   2.2e-05      0.19      14      50 ..     165     200 ..     155     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.37
                Bac_luciferase 20 aslrylvelaraaEelGfd 38
                                  ++ ++ +e+ar+++elG+ 
  gi|15668680|ref|NP_247479.1| 50 FTKEQKLEIARKLDELGLK 68
                                  67778899*********86 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 2.2e-05
                Bac_luciferase  14 algaasaslrylvelaraaEelGfdavwvaehhggpg 50 
                                   ++ +   ++++l+++ +aaEe+G d+v +a++ g++ 
  gi|15668680|ref|NP_247479.1| 165 EDATR-TPIEDLIKVHKAAEEAGADRVHIADTTGCAT 200
                                   33333.489************************9954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2812.94
//
Query:       gi|15668681|ref|NP_247480.1|  [L=196]
Description: hypothetical protein MJ_0504 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-18   65.5   0.1    7.1e-18   64.9   0.1    1.2  1  PK_C      Pyruvate kinase, alpha/beta domain


Domain annotation for each model (and alignments):
>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.1   3.9e-22   7.1e-18       1     117 []      13     165 ..      13     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 3.9e-22
                                   HHHHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TS....SEEEEEES..............HHHH............. CS
                          PK_C   1 eaiakaaveaaeelgakaIvvltesGetArliskyrpk....vpiiavtp..............nelt............. 50 
                                   ++++k ave+a++ ++k Ivv++++G+tA+++  + +k    +++++vt+              +  +             
  gi|15668681|ref|NP_247480.1|  13 DETLKIAVERAKKGDIKSIVVASSTGYTAKKLLDLLEKegldLNVVVVTYhqgfhgedtismdkE--Veeelkkrgakvfr 91 
                                   57899******************************9999999********888887777776550..15566677888888 PP

                                   ........HHHHH.HCTTEEHHH.HHHHH...TTSHHHHH...HHHHHH.......TTSS-STSEEEEEE-SSSS..SS-- CS
                          PK_C  51 ........arqla.lyrGvypvlvekaktaestdellrea...vkvake.......aglvkkgdevvvtaGtpkgesgttN 112
                                           +r ++ +++G+ pv+v+ a+t       lr++   vkv+ e       agl+k+++ev++++Gt +g    ++
  gi|15668681|ref|NP_247480.1|  92 gshalsgvERGISnKLGGYGPVQVI-AET-------LRTFgqgVKVCYEitimacdAGLIKAKEEVIAIGGTGRG----AD 160
                                   88888899999999********975.555.......44444449999999999999*******************....9* PP

                                   EEEEE CS
                          PK_C 113 tlrVv 117
                                   t+ V+
  gi|15668681|ref|NP_247480.1| 161 TAMVI 165
                                   99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1349.29
//
Query:       gi|15668682|ref|NP_247481.1|  [L=251]
Description: hypothetical protein MJ_0505 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-36  123.7   4.3    8.9e-36  123.5   4.3    1.0  1  DUF2334          Uncharacterized protein conserved in bacteri
     0.0013   18.6   0.0      0.002   18.0   0.0    1.2  1  Polysacc_deac_1  Polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> DUF2334  Uncharacterized protein conserved in bacteria (DUF2334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   4.3     1e-39   8.9e-36       2     208 ..      39     247 ..      38     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 1e-39
                       DUF2334   2 alirleDvspgedleklkeiadyldkegi..pfsvavIPrykdpktgskvnlsenpefvevLkylqakGgeialHGYtHqy 80 
                                    +i ++Dvsp  ++++lkei++++dk+++  + ++++I ++ ++     +nl+++pefv++L++l+++G++i  H Y+H +
  gi|15668682|ref|NP_247481.1|  39 PIILIHDVSP-VYFKELKEIVKIIDKYHYqnRSYLFLIVNHANK-----YNLKNYPEFVDYLHKLEKEGYHIEFHAYNHID 113
                                   689*******.******************999************.....******************************** PP

                       DUF2334  81 gtvksevsgegfeflseseakeriekGieilkklgi...kpkgFeaPhyaaseetykalkky.fsiiyer..ykeykgq.. 153
                                   ++++          ++++ a+e+++k+ +il+++g+   k+k+F++P+y+ se+++k +  + ++ii+e+  ++e++g+  
  gi|15668682|ref|NP_247481.1| 114 DEFN----------CNKTVAEEKLNKSFKILEECGFnpkKIKYFIPPRYKLSEDAEKLFLGRnITIILENkmITEKDGKiv 184
                                   9666..........89*******************9777899******************777*******97666663345 PP

                       DUF2334 154 ......kegltyipenlgyveedeeienaea.l.kvrdglasffyHpyl..tysgrselkellee 208
                                         +e+++y+p++l +v+e  +i+++++ l   ++  + +++Hp+   ++sg ++l+++l+e
  gi|15668682|ref|NP_247481.1| 185 eisitnREYTWYLPKPLVKVAE--KIATTDYkLsIKENRKFFLSIHPKAvnYGSGLEFLDYFLNE 247
                                   666777**************88..6644454354555999*********9999999999999986 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.2e-07     0.002      19     112 ..      52     158 ..      32     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-07
                                   SCHHHHHHHHHHCT-..-EEEEE-HHHHCH-........HHHHHHHHHTTEEEEE--SS--EG.GGSHHHHHHHHHHHHHH CS
               Polysacc_deac_1  19 dntteilpvLkkykv..katffvigglvedy........pdevremaasGveignHtinhsnl.krlseeevrreierakd 88 
                                   +  +ei+++ +ky+   +  +f+i +++++y         d + ++ ++G +i+ H +nh +  +++ +  +++ ++++ +
  gi|15668682|ref|NP_247481.1|  52 KELKEIVKIIDKYHYqnRSYLFLIVNHANKYnlknypefVDYLHKLEKEGYHIEFHAYNHIDDeFNCNKTVAEEKLNKSFK 132
                                   55678899999988733456778888888889999999999*******************976488888899999999999 PP

                                   HHHHH.HS-.---EEE-GGGEE-HHH CS
               Polysacc_deac_1  89 alrka.lgr.eprlfryPygsasatv 112
                                   +l++  +++ + ++f +P  + s+++
  gi|15668682|ref|NP_247481.1| 133 ILEECgFNPkKIKYFIPPRYKLSEDA 158
                                   99999655569999999988877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1179  (0.0657594); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1673.56
//
Query:       gi|15668683|ref|NP_247482.1|  [L=198]
Description: imidazole glycerol phosphate synthase subunit HisH [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-27   95.6   0.0    3.9e-27   95.3   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    6.7e-07   29.1   0.1      1e-06   28.5   0.1    1.5  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    1.5e-06   28.2   0.1      3e-06   27.2   0.1    1.5  1  SNO            SNO glutamine amidotransferase family
    0.00051   19.9   0.2      0.035   13.9   0.1    2.6  2  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
       0.16   12.1   0.0        0.3   11.2   0.0    1.4  1  WI12           Wound-induced protein WI12


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.3   0.0   1.1e-30   3.9e-27      11     186 ..      15     194 ..       6     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 1.1e-30
                                   HHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHH CS
                        GATase  11 enlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllai 86 
                                   +++ +a+   + kv + +++   e    +l  +d+i++ +G+g+ g          e+i ++ + ++P+LGICLGmQ+l++
  gi|15668683|ref|NP_247482.1|  15 RSIQKAVELYD-KVIITNNS---E----ELLACDKIIL-PGVGNFGsamenLAPLKETIYKIVDDRVPFLGICLGMQILFE 86 
                                   44444443333.45444444...2....3567888876.68999999856666666777777889**************** PP

                                   HTTT............EEE....EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETT CS
                        GATase  87 efgr............kvv....kekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtaksedd 151
                                   e+ +            +v+     ek  +h+g+++    +++ l++g kn  + ++ H+y vnp     ++  +++k+e +
  gi|15668683|ref|NP_247482.1|  87 ESEEkrgikglgiikgNVIkfkdVEK-LPHMGWNSVKIVKDCPLFEGIKNNSYFYFVHSYHVNP-----DEDCIVGKTEYG 161
                                   ****8888888888886667776555.99*******9999***********************8.....555788****** PP

                                   EEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHH CS
                        GATase 152 eelmeiiekknpfvgvQFHPEststpegpellfnf 186
                                    e+  +i+k+n ++++QFHPE++ + +  ++++nf
  gi|15668683|ref|NP_247482.1| 162 REFPSVINKDN-VFATQFHPEKSGKIG-LKIIENF 194
                                   **********9.*********988766.8888877 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.1   2.8e-10     1e-06      27     115 ..      27     104 ..       6     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.8e-10
                      GATase_3  27 vrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageveg 107
                                   v++ + + e+l + +d +ilpG  +  ++++ l+   l+e i + + + +p lgiC G+q+L ee e++ g+       +g
  gi|15668683|ref|NP_247482.1|  27 VIITN-NSEELLA-CDKIILPGVGNFGSAMENLAP--LKETIYKIVDDRVPFLGICLGMQILFEESEEKRGI-------KG 96 
                                   44444.7777756.**********99988877776..****************************9988765.......99 PP

                      GATase_3 108 lglLdiet 115
                                   lg+++ ++
  gi|15668683|ref|NP_247482.1|  97 LGIIKGNV 104
                                   99998765 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   8.2e-10     3e-06      24     184 ..      29     196 ..      11     198 .] 0.71

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 8.2e-10
                                   EE-SGGGGCC-SEEEE-S.S-.HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB.SS-SS--CCEEE. CS
                           SNO  24 tvkrkedlaevdaliiPG.Ge.stamskliertglyedllefvknsekvvlGtCaGlillskelene.lvktlellkvkv. 100
                                      + e+l  +d +i+PG G+   am+ l+    l e++++ v +   + lG C G+ +l +e e++  +k l+++k +v 
  gi|15668683|ref|NP_247482.1|  29 ITNNSEELLACDKIILPGvGNfGSAMENLAP---LKETIYKIVDDR-VPFLGICLGMQILFEESEEKrGIKGLGIIKGNVi 105
                                   3467899**********94332456777765...556899888877.9*********999999888778999999986552 PP

                                   .....ET.TTT-SCCGEEEEEEE.ETTTCSEEEEEESS--EEEEE-.TTTCEEEEECTTEEEEEE.ETTEEEESS-GGGST CS
                           SNO 101 .....kr.nafGrqvdsfekeld.fknliekftavfiraPvieeilddeavkvlyeldgeivvak.qkkilatsfhPelae 173
                                        ++    G       k++  f++++++ +  f+ + +++   d ++ k  y  +    ++  +++++at fhPe + 
  gi|15668683|ref|NP_247482.1| 106 kfkdvEKlPHMGWNSVKIVKDCPlFEGIKNNSYFYFVHSYHVNPDEDCIVGKTEYGRE--FPSVInKDNVFATQFHPEKSG 184
                                   22212332467888888889996478888**********9998766655555555554..444442679*********986 PP

                                   T.HCHHHHHHHH CS
                           SNO 174 d.dirvhdyfve 184
                                   + + ++ + fve
  gi|15668683|ref|NP_247482.1| 185 KiGLKIIENFVE 196
                                   547788888876 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   9.7e-06     0.035      98     118 ..      64      84 ..      11      87 .. 0.95
   2 ?    3.8   0.0     0.012        43     197     216 .]     163     181 ..     103     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.7e-06
                 Peptidase_C26  98 iraalergvPilgiCrGlqll 118
                                   i+++++ +vP lgiC+G+q+l
  gi|15668683|ref|NP_247482.1|  64 IYKIVDDRVPFLGICLGMQIL 84 
                                   788999*************98 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.012
                 Peptidase_C26 197 EaieseeakafvlgvQwHPE 216
                                   E+ ++++++  v++ Q+HPE
  gi|15668683|ref|NP_247482.1| 163 EFPSVINKD-NVFATQFHPE 181
                                   666777755.899******9 PP

>> WI12  Wound-induced protein WI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.3e-05       0.3      19      58 ..     119     160 ..     110     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.3e-05
                          WI12  19 rsvdafgstviaeGtdetrklyWvhaWtvk..dGvitqvrey 58 
                                   +sv+ ++++ + eG ++ +  y+vh + v+  +  i    ey
  gi|15668683|ref|NP_247482.1| 119 NSVKIVKDCPLFEGIKNNSYFYFVHSYHVNpdEDCIVGKTEY 160
                                   699**************************8754555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1333.48
//
Query:       gi|15668684|ref|NP_247483.1|  [L=183]
Description: transcription factor [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-62  206.0   0.1    3.1e-30  104.0   0.0    2.0  2  TBP             Transcription factor TFIID (or TATA-binding p
    1.9e-08   34.3   0.0    0.00021   21.3   0.0    2.4  2  DUF3378         Domain of unknown function (DUF3378)
     0.0064   16.2   2.8        1.6    8.6   0.1    2.2  2  Arm-DNA-bind_4  Arm DNA-binding domain
  ------ inclusion threshold ------
      0.018   15.1   2.9       0.31   11.1   1.5    2.7  2  Sigma70_r1_1    Sigma-70 factor, region 1.1
       0.13   11.9   0.0        7.1    6.4   0.0    2.4  2  NdhS            NAD(P)H dehydrogenase subunit S
       0.55   10.2   3.1        7.2    6.6   0.6    2.3  2  DUF5633         Family of unknown function (DUF5633)


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.1   1.3e-32   3.9e-29       2      84 ..       8      88 ..       7      89 .. 0.97
   2 !  104.0   0.0     1e-33   3.1e-30       2      84 ..      99     179 ..      98     180 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 1.3e-32
                                  EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHHH CS
                           TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilkk 84
                                  +ki+Nvv s+++g ++dLe++a+ +  +naeYepe+fpglv+rl+ pkv++liF+sGkv +tGaks+ee++ a+kki++ lk+
  gi|15668684|ref|NP_247483.1|  8 IKIVNVVVSTKIGDNIDLEEVAMIL--ENAEYEPEQFPGLVCRLSVPKVALLIFRSGKVNCTGAKSKEEAEIAIKKIIKELKD 88
                                  89*******************9887..****************************************************9986 PP

  == domain 2  score: 104.0 bits;  conditional E-value: 1e-33
                                   EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHH CS
                           TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapil 82 
                                   +kiqN+va+a+lg+e +L+ +al +  +++eYepe+fpglvyrl++pkv++liF sGkvvitG ksee++++a+kki++ +
  gi|15668684|ref|NP_247483.1|  99 IKIQNMVATADLGIEPNLDDIALMV--EGTEYEPEQFPGLVYRLDDPKVVVLIFGSGKVVITGLKSEEDAKRALKKILDTI 177
                                   89*******************9887..*****************************************************9 PP

                                   HH CS
                           TBP  83 kk 84 
                                   k+
  gi|15668684|ref|NP_247483.1| 178 KE 179
                                   97 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00014      0.43      22      61 ..      37      76 ..      21      89 .. 0.86
   2 !   21.3   0.0     7e-08   0.00021      23      62 ..     129     168 ..     120     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                       DUF3378 22 lrskkppyavfaakkndttItaYtSgKVlFQGknaeaeAs 61
                                   + ++ p+ v +  ++++   +++SgKV   G++ ++eA+
  gi|15668684|ref|NP_247483.1| 37 YEPEQFPGLVCRLSVPKVALLIFRSGKVNCTGAKSKEEAE 76
                                  356789******************************9997 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 7e-08
                       DUF3378  23 rskkppyavfaakkndttItaYtSgKVlFQGknaeaeAsk 62 
                                   + ++ p+ v++ +++++++ ++ SgKV++ G + e++A++
  gi|15668684|ref|NP_247483.1| 129 EPEQFPGLVYRLDDPKVVVLIFGSGKVVITGLKSEEDAKR 168
                                   46789*******************************9986 PP

>> Arm-DNA-bind_4  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.5     0.001       3.1      25      43 ..      70      88 ..      65      91 .. 0.88
   2 !    8.6   0.1   0.00053       1.6      22      43 ..     158     179 ..     154     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.001
                Arm-DNA-bind_4 25 ktKkEAekaeaeflkkink 43
                                  k+K EAe a + ++k+++ 
  gi|15668684|ref|NP_247483.1| 70 KSKEEAEIAIKKIIKELKD 88
                                  9**************9875 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00053
                Arm-DNA-bind_4  22 rGFktKkEAekaeaeflkkink 43 
                                    G k++ +A+ a++ +l +i++
  gi|15668684|ref|NP_247483.1| 158 TGLKSEEDAKRALKKILDTIKE 179
                                   699**************99975 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.052   1.6e+02      19      40 ..      22      43 ..       9      54 .. 0.84
   2 ?   11.1   1.5    0.0001      0.31      38      59 ..      78     100 ..      69     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.052
                                  CEEHHHHHHHGCCSS--HHHHH CS
                  Sigma70_r1_1 19 yLtyeEindaLpddeldseqie 40
                                  ++  eE++  L++ e ++eq+ 
  gi|15668684|ref|NP_247483.1| 22 NIDLEEVAMILENAEYEPEQFP 43
                                  57889***************85 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHHCCT-EEE-SS-.. CS
                  Sigma70_r1_1  38 qiediiemLedmgIdvveeae.d 59 
                                   +i +ii+ L+d+gIdv+e+ e +
  gi|15668684|ref|NP_247483.1|  78 AIKKIIKELKDAGIDVIENPEiK 100
                                   799***************87722 PP

>> NdhS  NAD(P)H dehydrogenase subunit S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.024        72      17      34 ..      40      57 ..      28      63 .. 0.81
   2 ?    6.4   0.0    0.0024       7.1      18      37 ..     132     151 ..     120     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.024
                          NdhS 17 ygfeGlvQrvsdgkaaVl 34
                                   +f Glv r+s  k+a l
  gi|15668684|ref|NP_247483.1| 40 EQFPGLVCRLSVPKVALL 57
                                  589************987 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0024
                          NdhS  18 gfeGlvQrvsdgkaaVlFeG 37 
                                   +f Glv r+ d k+ Vl  G
  gi|15668684|ref|NP_247483.1| 132 QFPGLVYRLDDPKVVVLIFG 151
                                   799*************9766 PP

>> DUF5633  Family of unknown function (DUF5633)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.6    0.0024       7.2       4      19 ..      70      85 ..      67      96 .. 0.80
   2 ?    3.7   0.1     0.019        56      10      23 ..     163     178 ..     158     181 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0024
                       DUF5633  4 atkeeAekAAkkALen 19
                                  ++keeAe A kk ++ 
  gi|15668684|ref|NP_247483.1| 70 KSKEEAEIAIKKIIKE 85
                                  79*********98876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.019
                       DUF5633  10 ekAAkkALen..dpiN 23 
                                   e+ Ak AL++  d i+
  gi|15668684|ref|NP_247483.1| 163 EEDAKRALKKilDTIK 178
                                   4457777777668887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1150.86
//
Query:       gi|15668685|ref|NP_247484.1|  [L=102]
Description: 50S ribosomal protein L12 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-19   70.4  22.1    1.7e-19   70.2  22.1    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
     0.0069   16.6   3.5      0.012   15.8   3.5    1.4  1  TetR_C_31      Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.017   15.3   0.1      0.066   13.4   0.0    1.9  2  PhetRS_B1      Phe-tRNA synthetase beta subunit B1 domain
      0.017   15.2   4.7      0.078   13.1   0.1    2.4  2  VIGSSK         Helicase-associated putative binding domain, C
      0.024   14.6   8.1      0.038   13.9   8.1    1.3  1  Auxin_canalis  Auxin canalisation
      0.026   14.5  10.0        2.6    8.1   0.0    2.2  2  PepSY_2        Peptidase propeptide and YPEB domain
       0.03   13.6   1.1      0.029   13.6   1.1    1.1  1  GCH_III        GTP cyclohydrolase III
      0.071   12.7   0.4      0.076   12.6   0.4    1.1  1  LD_cluster3    SLOG cluster3 family
       0.21   10.9   6.7       0.24   10.7   6.7    1.1  1  ThiG           Thiazole biosynthesis protein ThiG
        4.3    8.0   8.0        6.6    7.4   8.0    1.4  1  DUF3824        Domain of unknwon function (DUF3824)


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2  22.1   9.4e-23   1.7e-19       1      88 []      16     101 ..      16     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 9.4e-23
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX--S CS
                 Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEeedd 81 
                                   e+t++ ik+vl+aagvev++arvk+lv+ leg+diee++an+a    ++aaa+aaaa+aaaa++++ee+kkee++eE+   
  gi|15668685|ref|NP_247484.1|  16 EITEDAIKAVLSAAGVEVDDARVKALVAGLEGVDIEEAIANAA-M--PVAAAPAAAAPAAAAEEKKEEEKKEEKKEEDTAA 93 
                                   79****************************************6.4..68899999999**********9999999444444 PP

                                   S--.STTT CS
                 Ribosomal_60s  82 dmG.fgLF 88 
                                    +G  +LF
  gi|15668685|ref|NP_247484.1|  94 VAGlAALF 101
                                   77877777 PP

>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   3.5   6.7e-06     0.012      51      94 ..      18      66 ..       8      76 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.7e-06
                                  HHHHHHHHHHHHCS.S-HHHHHHHHHHHHHHHHHHHHHSG.....TS-HH CS
                     TetR_C_31 51 lrealaallaalGl.pdpeeaarllvaaldGllldrLagp.....aadpr 94
                                   ++a+ a+l a+G+   +++++ +lva l+G+ ++  +       aa+p+
  gi|15668685|ref|NP_247484.1| 18 TEDAIKAVLSAAGVeV-DDARVKALVAGLEGVDIEEAIANaampvAAAPA 66
                                  467999********55.555************999887653444433332 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.7e-05     0.066       7      40 ..       5      38 ..       3      69 .. 0.87
   2 ?   -0.5   0.4      0.84   1.5e+03      40      52 ..      78      88 ..      70      96 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.7e-05
                     PhetRS_B1  7 kkeaLfkalgkelteeeledllfefGlElDeive 40
                                   ++ L++  gke+te+ ++ +l   G+E+D++  
  gi|15668685|ref|NP_247484.1|  5 YAALLLHSAGKEITEDAIKAVLSAAGVEVDDARV 38
                                  567899999**********************865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.84
                     PhetRS_B1 40 eeeekkkadkkse 52
                                  +eee  k+++k+e
  gi|15668685|ref|NP_247484.1| 78 KEEE--KKEEKKE 88
                                  2222..2222322 PP

>> VIGSSK  Helicase-associated putative binding domain, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.4e-05     0.078      23      39 ..      16      32 ..       9      33 .. 0.85
   2 ?    3.1   1.2     0.057     1e+02      10      27 ..      73      90 ..      65      99 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                        VIGSSK 23 kkksDaiqAILasaGVe 39
                                  +  +Dai+A+L++aGVe
  gi|15668685|ref|NP_247484.1| 16 EITEDAIKAVLSAAGVE 32
                                  5578************8 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.057
                        VIGSSK 10 eakekkkeakkstkkksD 27
                                   a+ekk+e+kk++kk +D
  gi|15668685|ref|NP_247484.1| 73 AAEEKKEEEKKEEKKEED 90
                                  333444444443333333 PP

>> Auxin_canalis  Auxin canalisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   8.1   2.1e-05     0.038     135     184 ..      51     100 ..      45     102 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                 Auxin_canalis 135 qnAqvhAavSvAgvAAAvAAvaaataassssskdeqaaktdaAvASAaaL 184
                                   ++A + Aa+ vA+  AA A  aaa+ ++++++k+e++++  aAvA  aaL
  gi|15668685|ref|NP_247484.1|  51 EEAIANAAMPVAAAPAAAAPAAAAEEKKEEEKKEEKKEEDTAAVAGLAAL 100
                                   578889******9999999999999999999999999999*****99988 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0015       2.6      27      51 ..      14      38 ..      10      51 .. 0.86
   2 ?    7.2   7.3    0.0027       4.9       5      35 ..      61      91 ..      53     100 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0015
                       PepSY_2 27 adwlpreklvakleaqGykvkkiev 51
                                   +++++++++a l a+G +v++++v
  gi|15668685|ref|NP_247484.1| 14 GKEITEDAIKAVLSAAGVEVDDARV 38
                                  67899*****************998 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0027
                       PepSY_2  5 alalallaaaAlAgrrdtdspkadwlprekl 35
                                  ++a+ ++aa+A A++++++++k+++ ++e+ 
  gi|15668685|ref|NP_247484.1| 61 VAAAPAAAAPAAAAEEKKEEEKKEEKKEEDT 91
                                  4555566666666788888888887776654 PP

>> GCH_III  GTP cyclohydrolase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.1   1.6e-05     0.029      57     119 ..      27      88 ..       4     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                                   E-TT--HHHHHHHHHHHHHHSSS-EEEEEEEESSHHHHHHHHHHHHHHH--TT-TT----EEE CS
                       GCH_III  57 itngidleehkRiqesirnrypvtvsmgigaaetPldaleaaseaLreagsaqdeeRkevlsv 119
                                    ++g+++   +R++  ++++  v +  +i+ a  P+ a  aa+     a+++++ee+ke  + 
  gi|15668685|ref|NP_247484.1|  27 SAAGVEVD-DARVKALVAGLEGVDIEEAIANAAMPVAAAPAAAAPAAAAEEKKEEEKKEEKKE 88 
                                   45566654.58*****************************99999999999999999994333 PP

>> LD_cluster3  SLOG cluster3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   4.2e-05     0.076     103     159 ..      35      90 ..      12     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.2e-05
                   LD_cluster3 103 kfkaavfiGGmeGveeefelfrklqPnakilPvastGgaalelakklgeakedlled 159
                                   + +   ++ G+eGv  e ++ +   P a++   a++ +aa+e  +  ++ +e++ ed
  gi|15668685|ref|NP_247484.1|  35 DARVKALVAGLEGVDIEEAIANAAMPVAAAPAAAAPAAAAEEKKE-EEKKEEKKEED 90 
                                   444455899*****************9987666666666665544.44444444444 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   6.7   0.00013      0.24     172     240 ..      19      87 ..       8      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                                   HH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHHHHHHH------S CS
                          ThiG 172 eeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafklaveaGrlaylagriekre 240
                                   e+a   v+  AG+ +    ++a+  G+++v ++ a+a+a+ pva A a ++   a  +  + ++ e+++
  gi|15668685|ref|NP_247484.1|  19 EDAIKAVLSAAGVEVDDARVKALVAGLEGVDIEEAIANAAMPVAAAPAAAAPAAAAEEKKEEEKKEEKK 87 
                                   55555677789***********************************99887766666655555544443 PP

>> DUF3824  Domain of unknwon function (DUF3824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   8.0    0.0037       6.6       9      45 ..      54      90 ..      50      99 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0037
                       DUF3824  9 lAeaalaaggaglAaheyakrrerkkaerererrree 45
                                  +A+aa+  ++a  Aa  +a   e+k++e+++e+++e+
  gi|15668685|ref|NP_247484.1| 54 IANAAMPVAAAPAAAAPAAAAEEKKEEEKKEEKKEED 90
                                  5666665555555555555555555544444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1793  (0.100006); expected 358.6 (0.02)
Passed bias filter:                      883  (0.0492498); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 682.02
//
Query:       gi|15668686|ref|NP_247485.1|  [L=338]
Description: acidic ribosomal protein P0 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-22   78.3   0.3    7.4e-22   77.4   0.3    1.5  1  Ribosomal_L10  Ribosomal protein L10
    6.9e-20   70.8   0.6      2e-19   69.4   0.1    1.9  2  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    7.5e-06   26.4  12.6    2.3e-05   24.9  12.6    1.9  1  Ribosomal_60s  60s Acidic ribosomal protein
  ------ inclusion threshold ------
      0.033   14.3   0.4      0.033   14.3   0.4    3.0  3  7TMR-HDED      7TM-HD extracellular
       0.71    8.4   6.2          1    7.9   6.2    1.2  1  THOC2_N        THO complex subunit 2 N-terminus
          2    8.5   5.2        2.5    8.2   3.4    2.2  2  Chorein_N      N-terminal region of Chorein or VPS13


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.3   2.5e-25   7.4e-22       4      98 ..      11     110 ..       8     112 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 2.5e-25
                                   CCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.S......SCGCCSSS CS
                 Ribosomal_L10   4 ekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeek......lkellkgp 78 
                                    +K+e vk lk l+k+  +v++vd+ ++++ qlqe+R k+r++ ++l++ +ntl+ rAl+e++ee +      l+++++  
  gi|15668686|ref|NP_247485.1|  11 PWKIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRDK-VKLRMSRNTLIIRALKEAAEELNnpklaeLANYVERG 90 
                                   69****************************************9.*******************9833466777******** PP

                                   EEEEEESS-TCHHHHCCCCC CS
                 Ribosomal_L10  79 valvftnedpvalakvleef 98 
                                    a+++t+++p++l+k+lee+
  gi|15668686|ref|NP_247485.1|  91 AAILVTDMNPFKLYKLLEEN 110
                                   ******************99 PP

>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.1   6.5e-23     2e-19       2      71 .]     117     186 ..     116     186 .. 0.99
   2 ?   -1.6   0.0      0.93   2.8e+03      54      67 ..     269     282 ..     258     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 6.5e-23
                  RL10P_insert   2 raGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                   r G+iA++d+ +++g +++ Pg++  eL+++g+p+ ++kGki ++ed++v+kkGe+++++ a++L +Lgi
  gi|15668686|ref|NP_247485.1| 117 RGGQIAPCDIKVEKGSTGMPPGPFLGELKSVGIPAAIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLGI 186
                                   89*******************************************************************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.93
                  RL10P_insert  54 kGetltseqaqlLk 67 
                                   +G++l + qaq L 
  gi|15668686|ref|NP_247485.1| 269 AGDILAKAQAQALA 282
                                   7999*****99885 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9  12.6   7.6e-09   2.3e-05       2      85 ..     238     334 ..     237     338 .] 0.76

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 7.6e-09
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...............XXXXXXXXXXXXXXXXXXXX CS
                 Ribosomal_60s   2 ptaenikkvlkaagveveaarvkllvkalegkdieellangaakla...............aaaaaaaaaaaaaaaaaaae 67 
                                   p +e ++ ++++a++  +a +++++ +++++++  ++la+++a+++                a+ ++   +aa aa++++e
  gi|15668686|ref|NP_247485.1| 238 PAKEVLPFLIQKAFI--NARALSVETAFVTKETAGDILAKAQAQALalasklpdealdediKAKLSSVEVSAAPAAEEEKE 316
                                   66777888999****..5566666779*****************98************99966666666666666777777 PP

                                   XXXXXXXX.XX--SS--S CS
                 Ribosomal_60s  68 ekkkeeeeeEeedddmGf 85 
                                   e+kkeee++Ee+  ++G 
  gi|15668686|ref|NP_247485.1| 317 EEKKEEEKKEEDTGAAGL 334
                                   777777775444447773 PP

>> 7TMR-HDED  7TM-HD extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.079   2.4e+02     100     144 ..      35      83 ..      12     106 .. 0.68
   2 ?   14.3   0.4   1.1e-05     0.033     182     215 ..     152     185 ..     149     187 .. 0.91
   3 ?   -0.4   0.6      0.34     1e+03     110     141 ..     275     305 ..     206     329 .. 0.43

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.079
                     7TMR-HDED 100 llelsdeeleelqqgieqilerilsq...gipedeearekvke.qlqaa 144
                                   +++    +l+e++++i++ ++  +s+    i++ +ea+e++++ +l + 
  gi|15668686|ref|NP_247485.1|  35 MMDVPAPQLQEIRDKIRDKVKLRMSRntlIIRALKEAAEELNNpKLAEL 83 
                                   5555568889999999998888887743223333677777777666444 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.1e-05
                     7TMR-HDED 182 aVepvyvkikkGevIVrkGervteeqlekLealg 215
                                   a+e+  + ik++ v+V+kGe+v+++  ++L+ lg
  gi|15668686|ref|NP_247485.1| 152 AIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLG 185
                                   67778899***********************998 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.34
                     7TMR-HDED 110 elqqgieqilerilsqgipedeearekvke.ql 141
                                   ++q ++ +++ ++ ++ +   e++++k+++ ++
  gi|15668686|ref|NP_247485.1| 275 KAQAQALALASKLPDEALD--EDIKAKLSSvEV 305
                                   2222222222222222111..223333333333 PP

>> THOC2_N  THO complex subunit 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.2   0.00035         1     315     370 ..     266     325 ..     256     337 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00035
                       THOC2_N 315 keleekssekgsanaLamagaLsdddDtep............kkekeakkkekakkkeeeekeeepep 370
                                   ke + ++  k++a aLa+a+ L+d+    +            +      ++++a++++eeek+ee+++
  gi|15668686|ref|NP_247485.1| 266 KETAGDILAKAQAQALALASKLPDE--ALDedikaklssvevS------AAPAAEEEKEEEKKEEEKK 325
                                   56666666779************44..4444567776543321......1122221111111111111 PP

>> Chorein_N  N-terminal region of Chorein or VPS13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         3     9e+03      72      88 ..      24      40 ..      22      61 .. 0.66
   2 ?    8.2   3.4   0.00084       2.5      74     108 ..     293     327 ..     229     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3
                     Chorein_N 72 lkskpvvieiedvylla 88
                                  +kskpvv+ ++ + + a
  gi|15668686|ref|NP_247485.1| 24 IKSKPVVAIVDMMDVPA 40
                                  67888888888777666 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00084
                     Chorein_N  74 skpvvieiedvyllaeprseseeedeekeekreqa 108
                                    + ++++++ v++ a p  e+e+e+e+kee+++++
  gi|15668686|ref|NP_247485.1| 293 DEDIKAKLSSVEVSAAPAAEEEKEEEKKEEEKKEE 327
                                   5889***********99998877777665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1532  (0.0854482); expected 358.6 (0.02)
Passed bias filter:                      889  (0.0495845); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 2321.77
//
Query:       gi|15668687|ref|NP_247486.1|  [L=232]
Description: 50S ribosomal protein L1P [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-43  149.1   1.2    1.7e-43  148.8   1.2    1.1  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.8   1.2   9.3e-48   1.7e-43       7     204 .]      33     220 ..      21     220 .. 0.96

  Alignments for each domain:
  == domain 1  score: 148.8 bits;  conditional E-value: 9.3e-48
                                   SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT-HHHH CS
                  Ribosomal_L1   7 kkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyksfeak 87 
                                   ++f++s e + +l+ ++++k+++r++ +++Lph+ gke+ki++i  ++ a+   +a+e g   +vi  +++++  k++++ 
  gi|15668687|ref|NP_247486.1|  33 RNFTQSFEFIATLKEIDMRKPENRIKTEVVLPHGRGKEAKIAVIGTGDLAK---QAEELG--LTVIRKEEIEELGKNKRKL 108
                                   5899***********************************************...******..******************* PP

                                   HHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEEEEETTSSH CS
                  Ribosomal_L1  88 rkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvkvGklsfta 168
                                   rk++k +d+f+a+ ++mpl+++ +G ++g+r+kmP pv     +++++k  ve+++k tvv+ ++++  ++v vG+ ++t+
  gi|15668687|ref|NP_247486.1| 109 RKIAKAHDFFIAQADLMPLIGRYMGVILGPRGKMPKPV--P--ANANIKPLVERLKK-TVVINTRDKPYFQVLVGNEKMTD 184
                                   **************************************..4..3579**********.*********************** PP

                                   HHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS- CS
                  Ribosomal_L1 169 eelaeNieavvkalvekvpkkwkniksiylkttmsp 204
                                   e++++Nieav++ + +k +k+   ik  y+k tm+p
  gi|15668687|ref|NP_247486.1| 185 EQIVDNIEAVLNVVAKKYEKGLYHIKDAYVKLTMGP 220
                                   ***********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1583.26
//
Query:       gi|15668688|ref|NP_247487.1|  [L=222]
Description: thymidylate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-17   61.6   0.0    8.1e-17   61.2   0.0    1.3  1  Thymidylat_synt  Thymidylate synthase
  ------ inclusion threshold ------
      0.045   13.8   1.5        8.9    6.5   0.1    2.6  3  Erf4             Golgin subfamily A member 7/ERF4 family
       0.11   12.5   0.0       0.28   11.2   0.0    1.7  1  L51_S25_CI-B8    Mitochondrial ribosomal protein L51 / S25 / 


Domain annotation for each model (and alignments):
>> Thymidylat_synt  Thymidylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   1.3e-20   8.1e-17      94     215 ..      81     205 ..       1     214 [. 0.75

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1.3e-20
                                   HHHHHHHBTST.TTSSB-HHHHHHHHHHHSTT-ST-EEE---GGG.GG....GSSS--SEEEEEEEE..SEETEEEEEEEE CS
               Thymidylat_synt  94 YGkqwrkfkae.egkkidqlakvidqlkenpdsRriivsawnpae.ld....kmaLppChvlfqfyvkdkkegkLslqlyq 168
                                   Y ++ r f+ +  ++ki+q++++i++l+++ +sRr +   wnp+  ++    +    pC  l+qf ++   +gkL  ++  
  gi|15668688|ref|NP_247487.1|  81 YDYHQRLFEYPyADEKINQIDYIIEKLNQQKNSRRAVAITWNPKIdIEvsrdERGSVPCLQLVQFLIR---NGKLYQTVIF 158
                                   3444444443368999**************************974353333235699**********4...457******* PP

                                   EEEETTTHHHHHHHHHHHHHHHHHHHHT-EEEEEEEEEEEEEEEGGG CS
               Thymidylat_synt 169 RSaDvflGvpFNiasyalLthmlaqvtglkpgelihtigdaHiYsnh 215
                                   RS+D +l++  N +   +L + +a+ +g+  g+++h    +HiY+++
  gi|15668688|ref|NP_247487.1| 159 RSNDALLAFVSNAIGLITLGEYIAKKVGVGYGTYTHHAISMHIYVDR 205
                                   ********************************************975 PP

>> Erf4  Golgin subfamily A member 7/ERF4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0015       8.9      14      54 ..      10      50 ..       5      57 .. 0.87
   2 ?    6.0   0.1    0.0021        13      76     106 ..      91     121 ..      61     125 .. 0.77
   3 ?   -2.2   0.0       0.7   4.2e+03      58      69 ..     168     181 ..     160     214 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0015
                          Erf4 14 apqFstllppeLsgy.iseeefeeiinkiNeilaeafspysv 54
                                  a  F +l+p++L++  + e+efee  ++i + ++e  +p + 
  gi|15668688|ref|NP_247487.1| 10 ASAFNELIPKILKDGeVVETEFEERTKEIRNTIIEITNP-KL 50
                                  568*********9888*************9999999998.54 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0021
                          Erf4  76 thykkklkklekyieelNeelfkerglkiis 106
                                    ++++k+++++ +ie+lN++  ++r ++i++
  gi|15668688|ref|NP_247487.1|  91 PYADEKINQIDYIIEKLNQQKNSRRAVAITW 121
                                   46678999************99999888865 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.7
                          Erf4  58 ldnvlglltly..l 69 
                                   + n++gl+tl+  +
  gi|15668688|ref|NP_247487.1| 168 VSNAIGLITLGeyI 181
                                   56666666664223 PP

>> L51_S25_CI-B8  Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.6e-05      0.28      15      33 ..     121     140 ..     119     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.6e-05
                                   T-TTSEEEEEE.SS-SS-EE CS
                 L51_S25_CI-B8  15 kNPavpivvrr.rsgdgPal 33 
                                   +NP++ i+v+r  +g+ P+l
  gi|15668688|ref|NP_247487.1| 121 WNPKIDIEVSRdERGSVPCL 140
                                   9***************9*97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1410.06
//
Query:       gi|15668689|ref|NP_247488.1|  [L=237]
Description: hypothetical protein MJ_0512 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.085   13.2   0.0       0.43   10.9   0.0    2.0  2  LAGLIDADG_3     LAGLIDADG-like domain
        8.3    6.4   8.1        8.9    6.3   1.8    2.3  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.19   1.7e+03      47      79 ..      16      53 ..       5      57 .. 0.52
   2 ?   10.9   0.0   4.8e-05      0.43      26      62 ..     168     215 ..     159     237 .] 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.19
                                  CT.HSCEEEE.....EEE-SCCCCECCCHCHCTTCGGG CS
                   LAGLIDADG_3 47 lGIestiyek.....kkakgrgvyrlliisgenlkrFl 79
                                    I ++++        +++g+  y  + ++++ + +F 
  gi|15668689|ref|NP_247488.1| 16 SQILTKVKIVdirrkESEEGSIFYIGTMVDKDGVANFI 53
                                  44555444443322136666666666666666666665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.8e-05
                                   SEEEEES-..........HHHHHHHHHHHHHCT.HSCEEEE..EEE-SC CS
                   LAGLIDADG_3  26 sisltsss..........kelledvqrlLlrlGIestiyek..kkakgr 62 
                                   +i++++ss          ++++ ++  +L++ GI  ti+e   k  +g+
  gi|15668689|ref|NP_247488.1| 168 KIHFGTSSkrcyippatlEQFMPGILDMLEEYGIDDTIREIclK-LNGK 215
                                   399999999999999999**********************9743.3333 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.8     0.001       8.9      24      32 ..     125     133 ..     118     138 .. 0.88
   2 ?    3.6   0.5     0.007        62      25      31 ..     146     152 ..     135     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.001
                Zn_ribbon_SprT  24 nYrCrrCkg 32 
                                   nY+C++C+g
  gi|15668689|ref|NP_247488.1| 125 NYYCKICRG 133
                                   7******98 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.007
                Zn_ribbon_SprT  25 YrCrrCk 31 
                                   Y+Cr C+
  gi|15668689|ref|NP_247488.1| 146 YICRNCG 152
                                   9999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1472.42
//
Query:       gi|15668690|ref|NP_247489.1|  [L=241]
Description: hypothetical protein MJ_0513 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1514.88
//
Query:       gi|15668691|ref|NP_247490.1|  [L=250]
Description: polyferredoxin MvhB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-49  161.5  68.3    9.3e-11   41.1   4.4    6.2  6  Fer4      4Fe-4S binding domain
      1e-32  112.4  87.1    4.6e-09   36.7  12.2    4.4  5  Fer4_7    4Fe-4S dicluster domain
    1.5e-32  110.3  63.0    8.2e-09   35.2   4.2    6.2  6  Fer4_6    4Fe-4S binding domain
    4.3e-31  106.8  58.6    1.1e-11   44.7  14.0    3.8  4  Fer4_21   4Fe-4S dicluster domain
    2.9e-28   98.6  48.8    3.9e-05   24.5   1.9    6.2  6  Fer4_16   4Fe-4S double cluster binding domain
    7.7e-28   94.9  48.3    3.1e-06   26.9   2.4    6.3  6  Fer4_2    4Fe-4S binding domain
    1.2e-25   89.4  88.5    1.3e-08   34.8  11.5    5.2  6  Fer4_10   4Fe-4S dicluster domain
    1.6e-23   82.6  54.1    2.3e-08   34.1  10.5    4.0  4  Fer4_9    4Fe-4S dicluster domain
      9e-15   55.0  42.6    3.1e-05   24.4   6.8    5.4  6  Fer4_17   4Fe-4S dicluster domain
    8.5e-14   51.8  49.1    5.2e-05   23.6   6.8    5.4  6  Fer4_8    4Fe-4S dicluster domain
    2.8e-11   43.0  60.2    0.00048   20.4   3.3    6.2  6  Fer4_4    4Fe-4S binding domain
    4.7e-11   43.1  54.2      0.036   14.6   2.4    6.6  6  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    2.1e-10   41.1  49.9      0.015   16.1   1.6    6.7  6  Fer4_15   4Fe-4S single cluster domain
    1.4e-09   38.2  71.8     0.0012   19.7   4.5    6.2  6  Fer4_3    4Fe-4S binding domain
    2.4e-09   37.9  43.0       0.12   13.3   1.3    6.1  7  Fer4_22   4Fe-4S dicluster domain
    1.5e-05   25.2  51.5       0.25   11.6  10.7    5.3  4  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   2.9   1.6e-11   1.8e-08       2      24 .]      41      63 ..      40      63 .. 0.95
   2 !   29.4   5.8   4.1e-10   4.6e-07       2      24 .]      72      94 ..      71      94 .. 0.95
   3 !   33.0   2.7     3e-11   3.3e-08       2      24 .]     127     149 ..     126     149 .. 0.93
   4 !   29.4   7.2   4.1e-10   4.6e-07       1      24 []     156     179 ..     156     179 .. 0.94
   5 !   26.7   5.9   2.9e-09   3.2e-06       1      24 []     193     216 ..     193     216 .. 0.94
   6 !   41.1   4.4   8.3e-14   9.3e-11       1      24 []     222     245 ..     222     245 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.6e-11
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  +i+e kCi+C++C++ CPv+AI+
  gi|15668691|ref|NP_247490.1| 41 YINETKCIRCNLCYKECPVDAIE 63
                                  8*********************6 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 4.1e-10
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  +i+e+kC++C +C++ CPvgAI+
  gi|15668691|ref|NP_247490.1| 72 KIIEDKCVKCEICAQTCPVGAIY 94
                                  79********************6 PP

  == domain 3  score: 33.0 bits;  conditional E-value: 3e-11
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   + de+ Ci+CG+C+  CP++AI+
  gi|15668691|ref|NP_247490.1| 127 ELDENTCIKCGICARFCPTNAIK 149
                                   679*******************6 PP

  == domain 4  score: 29.4 bits;  conditional E-value: 4.1e-10
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                   ++++ ++C+gCGaC+evCP  +I+
  gi|15668691|ref|NP_247490.1| 156 IEVNLDLCMGCGACAEVCPKKCIK 179
                                   579******************996 PP

  == domain 5  score: 26.7 bits;  conditional E-value: 2.9e-09
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                   +++d+++C+gC  C+e CP +AI+
  gi|15668691|ref|NP_247490.1| 193 IEVDKNLCVGCLVCIEECPINAID 216
                                   589*******************95 PP

  == domain 6  score: 41.1 bits;  conditional E-value: 8.3e-14
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                   v+i+++kCi CG+Cv+vCP++AI+
  gi|15668691|ref|NP_247490.1| 222 VKINKDKCILCGRCVDVCPTNAIK 245
                                   68*********************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7  12.9   7.3e-11   8.2e-08       1      52 []      46      92 ..      46      92 .. 0.95
   2 !   31.3  14.7     2e-10   2.3e-07       1      52 []      77     147 ..      77     147 .. 0.72
   3 !   35.6  16.1   9.6e-12   1.1e-08       1      51 [.     132     176 ..     132     177 .. 0.93
   4 !   36.7  12.2   4.1e-12   4.6e-09       2      52 .]     163     214 ..     162     214 .. 0.89
   5 !   27.1   0.7   4.2e-09   4.7e-06      32      52 .]     223     243 ..     215     250 .] 0.59

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 7.3e-11
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  +Ci C+ C + Cpv+aie  ++     +++++i ++kC+ C+ C+++CP+ga
  gi|15668691|ref|NP_247490.1| 46 KCIRCNLCYKECPVDAIEKAKV-----KKSAKIIEDKCVKCEICAQTCPVGA 92
                                  7******************998.....56799******************98 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 2e-10
                        Fer4_7   1 rCigCgaCvaaCpvkaielde....eenek..................gtekveidpekClgCgaCvavCPtga 52 
                                   +C++C+ C+++Cpv+ai++ e        +                  + +k+e+d+++C+ Cg C++ CPt+a
  gi|15668691|ref|NP_247490.1|  77 KCVKCEICAQTCPVGAIYVIEgraeI---EdsevhytikeksiphrkiRLKKYELDENTCIKCGICARFCPTNA 147
                                   7*****************77532220...123334444444444444444999*******************97 PP

  == domain 3  score: 35.6 bits;  conditional E-value: 9.6e-12
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                   +Ci+Cg C++ Cp++ai+   +      +++e++ + C+gCgaC++vCP++
  gi|15668691|ref|NP_247490.1| 132 TCIKCGICARFCPTNAIKAVRR------KSIEVNLDLCMGCGACAEVCPKK 176
                                   6******************876......789******************86 PP

  == domain 4  score: 36.7 bits;  conditional E-value: 4.1e-12
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenek.gtekveidpekClgCgaCvavCPtga 52 
                                   C+gCgaC+++Cp k+i+++ e  e  +t+++e+d + C+gC +C+++CP +a
  gi|15668691|ref|NP_247490.1| 163 CMGCGACAEVCPKKCIKVERELGEViKTRDIEVDKNLCVGCLVCIEECPINA 214
                                   ******************987555446699*******************886 PP

  == domain 5  score: 27.1 bits;  conditional E-value: 4.2e-09
                        Fer4_7  32 eidpekClgCgaCvavCPtga 52 
                                   +i+ +kC+ Cg+Cv+vCPt+a
  gi|15668691|ref|NP_247490.1| 223 KINKDKCILCGRCVDVCPTNA 243
                                   555555555555555555554 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   2.7     5e-08   5.6e-05       4      24 .]      42      62 ..      40      62 .. 0.94
   2 !   19.9   4.3   4.8e-07   0.00054       2      24 .]      71      93 ..      70      93 .. 0.94
   3 !   23.1   2.8   4.9e-08   5.5e-05       5      24 .]     129     148 ..     127     148 .. 0.96
   4 !   20.3   5.5   3.7e-07   0.00041       2      22 ..     156     176 ..     155     178 .. 0.90
   5 !   20.1   4.3   4.2e-07   0.00047       2      24 .]     193     215 ..     193     215 .. 0.96
   6 !   35.2   4.2   7.3e-12   8.2e-09       1      24 []     221     244 ..     221     244 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5e-08
                        Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                  i++ kCi C+ C++ CP +ai
  gi|15668691|ref|NP_247490.1| 42 INETKCIRCNLCYKECPVDAI 62
                                  89****************998 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 4.8e-07
                        Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                  + i +dkC+ C+ C+  CP gai
  gi|15668691|ref|NP_247490.1| 71 AKIIEDKCVKCEICAQTCPVGAI 93
                                  5799******************8 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 4.9e-08
                        Fer4_6   5 dpdkCigCgdCvrvCPegai 24 
                                   d++ Ci Cg C+r CP++ai
  gi|15668691|ref|NP_247490.1| 129 DENTCIKCGICARFCPTNAI 148
                                   89*****************8 PP

  == domain 4  score: 20.3 bits;  conditional E-value: 3.7e-07
                        Fer4_6   2 veidpdkCigCgdCvrvCPeg 22 
                                   +e++ d+C gCg+C+ vCP +
  gi|15668691|ref|NP_247490.1| 156 IEVNLDLCMGCGACAEVCPKK 176
                                   79*****************76 PP

  == domain 5  score: 20.1 bits;  conditional E-value: 4.2e-07
                        Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                   +e+d+++C+gC  C+  CP +ai
  gi|15668691|ref|NP_247490.1| 193 IEVDKNLCVGCLVCIEECPINAI 215
                                   79*****************9998 PP

  == domain 6  score: 35.2 bits;  conditional E-value: 7.3e-12
                        Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                   +v i++dkCi Cg+Cv+vCP++ai
  gi|15668691|ref|NP_247490.1| 221 KVKINKDKCILCGRCVDVCPTNAI 244
                                   699********************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7  14.0   9.6e-15   1.1e-11       3      57 ..      42      93 ..      41      95 .. 0.89
   2 !   41.3  14.0   1.1e-13   1.2e-10       3      58 ..     128     179 ..     127     180 .. 0.91
   3 !   17.7   3.6   2.6e-06    0.0029      30      57 ..     189     215 ..     186     217 .. 0.85
   4 !   31.6  14.8   1.2e-10   1.3e-07       3      59 .]     195     246 ..     193     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 9.6e-15
                       Fer4_21  3 idedkCigCgkCliaCedtshqaieid.aktvlkvvedeCvGCnlCssvCPvedci 57
                                  i+e kCi C++C++ C+   ++aie++  k+ +k++ed+Cv C++C++ CPv ++i
  gi|15668691|ref|NP_247490.1| 42 INETKCIRCNLCYKECP---VDAIEKAkVKKSAKIIEDKCVKCEICAQTCPV-GAI 93
                                  99***************...8***765156788999***************9.887 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 1.1e-13
                       Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                   +de++Ci+Cg C+  C++   +ai+   ++ ++v  d C+GC  C++vCP ++ci+
  gi|15668691|ref|NP_247490.1| 128 LDENTCIKCGICARFCPT---NAIKAVRRKSIEVNLDLCMGCGACAEVCP-KKCIK 179
                                   699**************5...77777778999******************.7***8 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 2.6e-06
                       Fer4_21  30 aktvlkvvedeCvGCnlCssvCPvedci 57 
                                   + + ++v ++ CvGC +C++ CP+ ++i
  gi|15668691|ref|NP_247490.1| 189 KTRDIEVDKNLCVGCLVCIEECPI-NAI 215
                                   55678999***************9.777 PP

  == domain 4  score: 31.6 bits;  conditional E-value: 1.2e-10
                       Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                   +d++ C+gC  C+  C+   ++ai+ d+++v k+ +d+C+ C  C++vCP+ ++i+m
  gi|15668691|ref|NP_247490.1| 195 VDKNLCVGCLVCIEECP---INAIDQDGDKV-KINKDKCILCGRCVDVCPT-NAIKM 246
                                   89***************...8****999887.99****************6.***98 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   2.8   2.9e-06    0.0033       1      24 [.      46      67 ..      46      76 .. 0.79
   2 !   23.2   1.2   8.8e-08   9.8e-05       1      49 [.      77     124 ..      77     130 .. 0.77
   3 !   24.5   1.9   3.5e-08   3.9e-05       1      27 [.     132     158 ..     132     161 .. 0.89
   4 !   19.6   3.0   1.2e-06    0.0013       2      21 ..     163     182 ..     162     197 .. 0.82
   5 !   17.1   3.1   7.2e-06    0.0081       2      30 ..     200     229 ..     199     230 .. 0.80
   6 !   24.4   1.9   3.8e-08   4.3e-05       1      20 [.     228     247 ..     228     250 .] 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.9e-06
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkeke 24
                                  +C++C+ C + CP++ai++ k  +
  gi|15668691|ref|NP_247490.1| 46 KCIRCNLCYKECPVDAIEKAK--V 67
                                  5*****************982..2 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 8.8e-08
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekck 49 
                                   +C++C+ Ca++CP++ai    e ++e+++++   t+++k++++++ + k
  gi|15668691|ref|NP_247490.1|  77 KCVKCEICAQTCPVGAIYVI-EGRAEIEDSEVHYTIKEKSIPHRKIRLK 124
                                   6***************9987.5666666655555888888887776655 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 3.5e-08
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiea 27 
                                   +C++Cg Ca  CPtnaik+ ++k+ie 
  gi|15668691|ref|NP_247490.1| 132 TCIKCGICARFCPTNAIKAVRRKSIEV 158
                                   5*****************998888875 PP

  == domain 4  score: 19.6 bits;  conditional E-value: 1.2e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikekk 21 
                                   C +Cg+CaevCP ++ik ++
  gi|15668691|ref|NP_247490.1| 163 CMGCGACAEVCPKKCIKVER 182
                                   ****************9883 PP

  == domain 5  score: 17.1 bits;  conditional E-value: 7.2e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikek.kekeiearec 30 
                                   C++C  C+e CP nai+++  + +i++++c
  gi|15668691|ref|NP_247490.1| 200 CVGCLVCIEECPINAIDQDgDKVKINKDKC 229
                                   *****************9944455666665 PP

  == domain 6  score: 24.4 bits;  conditional E-value: 3.8e-08
                       Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                   +C+ Cg+C++vCPtnaik+ 
  gi|15668691|ref|NP_247490.1| 228 KCILCGRCVDVCPTNAIKMW 247
                                   5****************975 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.1   1.3e-06    0.0015       3      21 ..      40      58 ..      38      59 .. 0.91
   2 !   17.1   2.3   3.8e-06    0.0043       4      21 ..      72      89 ..      69      90 .. 0.90
   3 !   21.5   1.6   1.5e-07   0.00017       2      22 .]     125     145 ..     124     145 .. 0.92
   4 !   24.5   1.5   1.7e-08   1.9e-05       3      21 ..     156     174 ..     153     175 .. 0.92
   5 !   15.1   2.5   1.7e-05     0.019       3      21 ..     193     211 ..     191     211 .. 0.93
   6 !   26.9   2.4   2.8e-09   3.1e-06       2      22 .]     221     241 ..     220     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                   ++++ +Ci+C+ C++ CP
  gi|15668691|ref|NP_247490.1| 40 LYINETKCIRCNLCYKECP 58
                                  5899*************** PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.8e-06
                        Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                  ++ +d+C+ C++C + CP
  gi|15668691|ref|NP_247490.1| 72 KIIEDKCVKCEICAQTCP 89
                                  6889************** PP

  == domain 3  score: 21.5 bits;  conditional E-value: 1.5e-07
                        Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                   +++ d+++Ci Cg+C   CP+
  gi|15668691|ref|NP_247490.1| 125 KYELDENTCIKCGICARFCPT 145
                                   5789****************7 PP

  == domain 4  score: 24.5 bits;  conditional E-value: 1.7e-08
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   ++v+ d C+gCgaC  +CP
  gi|15668691|ref|NP_247490.1| 156 IEVNLDLCMGCGACAEVCP 174
                                   789***************9 PP

  == domain 5  score: 15.1 bits;  conditional E-value: 1.7e-05
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   ++vd + C+gC  C+  CP
  gi|15668691|ref|NP_247490.1| 193 IEVDKNLCVGCLVCIEECP 211
                                   789***************9 PP

  == domain 6  score: 26.9 bits;  conditional E-value: 2.8e-09
                        Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                   +v+++ d+Ci Cg Cv++CP+
  gi|15668691|ref|NP_247490.1| 221 KVKINKDKCILCGRCVDVCPT 241
                                   689*****************7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3  15.0   6.2e-10   6.9e-07       2      56 .]      40      89 ..      39      89 .. 0.97
   2 !   17.6   2.8   2.8e-06    0.0031       3      33 ..      72      97 ..      70     116 .. 0.69
   3 !   34.8  11.5   1.1e-11   1.3e-08       3      56 .]     127     174 ..     125     174 .. 0.94
   4 !   18.0   3.2     2e-06    0.0023       3      22 ..     157     176 ..     155     190 .. 0.76
   5 !   30.3  12.9   3.1e-10   3.4e-07       2      56 .]     193     240 ..     192     240 .. 0.90
   6 !   24.5   3.5     2e-08   2.2e-05       1      22 [.     221     242 ..     221     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 6.2e-10
                       Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  ++i++ +CirC+ C k CP+     +a+++a+ ++  ++  +kC +c+ C++ CP
  gi|15668691|ref|NP_247490.1| 40 LYINETKCIRCNLCYKECPV-----DAIEKAKVKKSAKIIEDKCVKCEICAQTCP 89
                                  5799****************.....*****************************9 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.8e-06
                       Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeas 33
                                  +i +d+C++C+ C + CP+ +     ++ ++
  gi|15668691|ref|NP_247490.1| 72 KIIEDKCVKCEICAQTCPVGA-----IYVIE 97
                                  6789***************44.....22222 PP

  == domain 3  score: 34.8 bits;  conditional E-value: 1.1e-11
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   ++d++tCi+Cg C ++CP+      +  +a + + ++++++ C+gcgaC+e+CP
  gi|15668691|ref|NP_247490.1| 127 ELDENTCIKCGICARFCPT------NAIKAVRRKSIEVNLDLCMGCGACAEVCP 174
                                   6899***************......88899999999*****************9 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 2e-06
                       Fer4_10   3 vidddtCirCgkCvkaCPad 22 
                                   +++ d C++Cg+C ++CP +
  gi|15668691|ref|NP_247490.1| 157 EVNLDLCMGCGACAEVCPKK 176
                                   678999************84 PP

  == domain 5  score: 30.3 bits;  conditional E-value: 3.1e-10
                       Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +++d++ C++C  C + CP        ++++ ++++v+++ +kC+ cg Cv++CP
  gi|15668691|ref|NP_247490.1| 193 IEVDKNLCVGCLVCIEECPI-------NAIDQDGDKVKINKDKCILCGRCVDVCP 240
                                   57899***************.......77777788888899*************9 PP

  == domain 6  score: 24.5 bits;  conditional E-value: 2e-08
                       Fer4_10   1 kvvidddtCirCgkCvkaCPad 22 
                                   kv+i++d+Ci Cg+Cv++CP++
  gi|15668691|ref|NP_247490.1| 221 KVKINKDKCILCGRCVDVCPTN 242
                                   689*****************94 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1  13.7   3.6e-10   4.1e-07       1      51 []      46      93 ..      46      93 .. 0.94
   2 !   19.9   1.6   5.4e-07   0.00061      23      51 .]     118     148 ..     108     148 .. 0.74
   3 !   27.8  15.1   1.8e-09     2e-06       2      51 .]     133     178 ..     132     178 .. 0.88
   4 !   34.1  10.5   2.1e-11   2.3e-08       2      51 .]     200     244 ..     199     244 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.6e-10
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  kC++C+ C + Cp +++++ ++++ a++ ++   +C++C+ C++ Cp gai
  gi|15668691|ref|NP_247490.1| 46 KCIRCNLCYKECPVDAIEKAKVKKSAKIIED---KCVKCEICAQTCPVGAI 93
                                  7*************************99654...8*************987 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 5.4e-07
                        Fer4_9  23 erkarlraase..eaCigCgaCveaCpkgai 51 
                                   +rk+rl++++   + Ci+Cg C+  Cp++ai
  gi|15668691|ref|NP_247490.1| 118 HRKIRLKKYELdeNTCIKCGICARFCPTNAI 148
                                   455555555447789*************997 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 1.8e-09
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   C++Cg C + Cp+++++  + + +  +       C+gCgaC+e+Cpk++i
  gi|15668691|ref|NP_247490.1| 133 CIKCGICARFCPTNAIKAVRRKSIEVNLD----LCMGCGACAEVCPKKCI 178
                                   ****************9888888777643....6*************987 PP

  == domain 4  score: 34.1 bits;  conditional E-value: 2.1e-11
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   C+gC  C+e Cp +++ +d  + k++ +     +Ci Cg+Cv++Cp++ai
  gi|15668691|ref|NP_247490.1| 200 CVGCLVCIEECPINAIDQDGDKVKINKD-----KCILCGRCVDVCPTNAI 244
                                   ****************999999998864.....6*************997 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   4.4e-05     0.049      45      58 ..      46      59 ..      20      75 .. 0.75
   2 !   24.4   6.8   2.8e-08   3.1e-05       1      59 [.      77     146 ..      77     147 .. 0.60
   3 !   13.6   4.2   6.5e-05     0.073      40      58 ..     157     175 ..     146     177 .. 0.77
   4 !    8.3   2.0     0.003       3.4      44      57 ..     198     211 ..     182     214 .. 0.71
   5 !    9.5   1.5    0.0013       1.5       2      19 ..     200     217 ..     199     226 .. 0.79
   6 !   15.1   1.3   2.2e-05     0.025      41      59 ..     224     242 ..     212     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-05
                       Fer4_17 45 lCieCgeCerkCPq 58
                                  +Ci C++C ++CP 
  gi|15668691|ref|NP_247490.1| 46 KCIRCNLCYKECPV 59
                                  45566666666653 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2.8e-08
                       Fer4_17   1 rCiqCgyClpeCpsyea......ydnepkkllraakl....glleeaekee.kaslCieCgeCerkCPqg 59 
                                   +C +C+ C++ Cp +++       + e  ++ + +k     +++ + +k e   ++Ci+Cg C+r CP +
  gi|15668691|ref|NP_247490.1|  77 KCVKCEICAQTCPVGAIyviegrAEIEDSEVHYTIKEksipHRKIRLKKYElDENTCIKCGICARFCPTN 146
                                   6************988833333311123334444333323322222223233679*************86 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 6.5e-05
                       Fer4_17  40 eekaslCieCgeCerkCPq 58 
                                   e + +lC++Cg C+++CP+
  gi|15668691|ref|NP_247490.1| 157 EVNLDLCMGCGACAEVCPK 175
                                   35789*************8 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.003
                       Fer4_17  44 slCieCgeCerkCP 57 
                                   +lC++C  C ++CP
  gi|15668691|ref|NP_247490.1| 198 NLCVGCLVCIEECP 211
                                   56777777777776 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0013
                       Fer4_17   2 CiqCgyClpeCpsyeayd 19 
                                   C +C  C++eCp +++ +
  gi|15668691|ref|NP_247490.1| 200 CVGCLVCIEECPINAIDQ 217
                                   999999999999987755 PP

  == domain 6  score: 15.1 bits;  conditional E-value: 2.2e-05
                       Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                    + ++Ci Cg+C+ +CP +
  gi|15668691|ref|NP_247490.1| 224 INKDKCILCGRCVDVCPTN 242
                                   4668999999999999976 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3  13.5   0.00032      0.36       4      64 ..      46      91 ..      44      91 .. 0.72
   2 !   23.6   6.8   4.6e-08   5.2e-05       3      64 ..      76     146 ..      74     148 .. 0.70
   3 !   14.0  13.4   4.7e-05     0.053       4      64 ..     132     176 ..     131     177 .. 0.76
   4 !    7.8   2.1     0.004       4.5      49      63 ..     198     212 ..     181     215 .. 0.72
   5 !    7.6   2.0    0.0045         5       5      63 ..     200     212 ..     196     226 .. 0.70
   6 !   14.3   2.6   3.7e-05     0.042      49      63 ..     227     241 ..     214     243 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                        Fer4_8  4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                  kCi+C +C ++Cpv   +k     a+ ++++ +  e         ++C+ c+ C++ Cpvg
  gi|15668691|ref|NP_247490.1| 46 KCIRCNLCYKECPVDAIEK-----AKVKKSA-KIIE---------DKCVKCEICAQTCPVG 91
                                  8************755543.....3333333.2222.........56************96 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 4.6e-08
                        Fer4_8   3 ekCieCgaCqsaCp.................vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   +kC++C+ C ++Cp                 v  + k+ +   r+ + + + e ++       ++C  cg C++ Cp++
  gi|15668691|ref|NP_247490.1|  76 DKCVKCEICAQTCPvgaiyviegraeiedseVHYTIKEKSIPHRKIRLK-KYELDE-------NTCIKCGICARFCPTN 146
                                   69************66666555555555443222233444455555555.777777.......9*************87 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 4.7e-05
                        Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                    Ci+Cg C   Cp+     + ++  r + +e      +      l+ C++cgaC+evCp++
  gi|15668691|ref|NP_247490.1| 132 TCIKCGICARFCPT-----NAIKAVRRKSIE-----VN------LDLCMGCGACAEVCPKK 176
                                   6***********94.....333444555444.....33......899************97 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.004
                        Fer4_8  49 wsCttcgaCtevCpv 63 
                                   + C++c  C e+Cp+
  gi|15668691|ref|NP_247490.1| 198 NLCVGCLVCIEECPI 212
                                   556666666666665 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.0045
                        Fer4_8   5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                   C++C  C ++Cp                                              +
  gi|15668691|ref|NP_247490.1| 200 CVGCLVCIEECP----------------------------------------------I 212
                                   666666666666..............................................3 PP

  == domain 6  score: 14.3 bits;  conditional E-value: 3.7e-05
                        Fer4_8  49 wsCttcgaCtevCpv 63 
                                   ++C  cg+C++vCp+
  gi|15668691|ref|NP_247490.1| 227 DKCILCGRCVDVCPT 241
                                   566666666666665 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   3.5   0.00054       0.6       3      16 ..      46      59 ..      44      60 .. 0.91
   2 ?    6.5   4.7     0.013        14       2      17 .]      76      91 ..      75      91 .. 0.92
   3 !   14.2   3.6   4.4e-05     0.049       2      17 .]     131     146 ..     130     146 .. 0.91
   4 !   11.7   5.0   0.00027       0.3       2      16 ..     161     175 ..     160     181 .. 0.91
   5 !    9.6   1.3    0.0013       1.4       2      15 ..     198     211 ..     197     219 .. 0.87
   6 !   20.4   3.3   4.3e-07   0.00048       1      17 []     226     242 ..     226     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00054
                        Fer4_4  3 rCigCgsCvaaCPq 16
                                  +Ci+C  C+  CP+
  gi|15668691|ref|NP_247490.1| 46 KCIRCNLCYKECPV 59
                                  8************7 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  ++C+ C  C  +CP+g
  gi|15668691|ref|NP_247490.1| 76 DKCVKCEICAQTCPVG 91
                                  89************86 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 4.4e-05
                        Fer4_4   2 erCigCgsCvaaCPqg 17 
                                   ++Ci Cg C ++CP++
  gi|15668691|ref|NP_247490.1| 131 NTCIKCGICARFCPTN 146
                                   78************86 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00027
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   + C gCg+C  +CP 
  gi|15668691|ref|NP_247490.1| 161 DLCMGCGACAEVCPK 175
                                   78************5 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.0013
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   + C+gC +C+  CP
  gi|15668691|ref|NP_247490.1| 198 NLCVGCLVCIEECP 211
                                   78***********9 PP

  == domain 6  score: 20.4 bits;  conditional E-value: 4.3e-07
                        Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                   +++Ci Cg+Cv++CP++
  gi|15668691|ref|NP_247490.1| 226 KDKCILCGRCVDVCPTN 242
                                   69*************86 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   2.4    0.0005      0.56       1      17 [.      42      58 ..      42      63 .. 0.94
   2 !   11.9   1.6   0.00023      0.25       2      17 ..      75      89 ..      74     104 .. 0.91
   3 !   14.6   2.4   3.2e-05     0.036       2      18 ..     129     145 ..     128     146 .. 0.93
   4 !   11.7   3.9   0.00026      0.29       1      18 [.     158     175 ..     158     179 .. 0.94
   5 !   10.1   2.3   0.00081      0.91       1      17 [.     195     211 ..     195     222 .. 0.91
   6 !   13.5   3.3   7.4e-05     0.083       1      18 [.     224     241 ..     224     242 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0005
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  +++ +Ci c++C++ +P
  gi|15668691|ref|NP_247490.1| 42 INETKCIRCNLCYKECP 58
                                  7889************9 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00023
                       Fer4_13  2 DrdtCiacgaCvelaP 17
                                  + d+C+ c++C++++P
  gi|15668691|ref|NP_247490.1| 75 E-DKCVKCEICAQTCP 89
                                  5.9************9 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 3.2e-05
                       Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                   D++tCi cg+C+ ++P 
  gi|15668691|ref|NP_247490.1| 129 DENTCIKCGICARFCPT 145
                                   89**************6 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00026
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   V+ d C++cgaC+e++P+
  gi|15668691|ref|NP_247490.1| 158 VNLDLCMGCGACAEVCPK 175
                                   78999************6 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.00081
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   VD++ C++c +C e +P
  gi|15668691|ref|NP_247490.1| 195 VDKNLCVGCLVCIEECP 211
                                   9***************9 PP

  == domain 6  score: 13.5 bits;  conditional E-value: 7.4e-05
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   +++d+Ci cg Cv+++P 
  gi|15668691|ref|NP_247490.1| 224 INKDKCILCGRCVDVCPT 241
                                   79***************6 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  13.4     0.024        27       2      66 .]      41      95 ..      40      95 .. 0.83
   2 ?    3.1   3.9      0.15   1.7e+02       6      64 ..      76      93 ..      72     108 .. 0.68
   3 !   10.7   1.0   0.00062       0.7       3      20 ..     128     145 ..     127     152 .. 0.90
   4 !   15.3   1.7   2.3e-05     0.026       1      20 [.     156     175 ..     156     191 .. 0.84
   5 !   14.1   2.5   5.2e-05     0.058       1      28 [.     193     219 ..     193     221 .. 0.83
   6 !   16.1   1.6   1.3e-05     0.015       1      20 [.     222     241 ..     222     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.024
                       Fer4_15  2 vvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                  ++++++Ci c+lC++e+p     d   +a+v+      +++ + +d+  + +  a++CPv+AI v
  gi|15668691|ref|NP_247490.1| 41 YINETKCIRCNLCYKECP----VDAIEKAKVK------KSAKIIEDKCVKCEICAQTCPVGAIYV 95
                                  6899*************9....3434466555......3688999999999************87 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.15
                       Fer4_15  6 daCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAI 64
                                  d+C  c+ C++ +                                         Pv+AI
  gi|15668691|ref|NP_247490.1| 76 DKCVKCEICAQTC-----------------------------------------PVGAI 93
                                  5555555555555.........................................55555 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00062
                       Fer4_15   3 vDrdaCigcglCvaeape 20 
                                   +D+++Ci cg C++ +p+
  gi|15668691|ref|NP_247490.1| 128 LDENTCIKCGICARFCPT 145
                                   8*************9986 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 2.3e-05
                       Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                   ++v+ d+C+gcg+C++++p+
  gi|15668691|ref|NP_247490.1| 156 IEVNLDLCMGCGACAEVCPK 175
                                   78999*************97 PP

  == domain 5  score: 14.1 bits;  conditional E-value: 5.2e-05
                       Fer4_15   1 VvvDrdaCigcglCvaeapevfeldedg 28 
                                   ++vD+++C gc +C++e+p +  +d+dg
  gi|15668691|ref|NP_247490.1| 193 IEVDKNLCVGCLVCIEECP-INAIDQDG 219
                                   79****************9.55566555 PP

  == domain 6  score: 16.1 bits;  conditional E-value: 1.3e-05
                       Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                   V++++d+Ci cg+Cv+++p+
  gi|15668691|ref|NP_247490.1| 222 VKINKDKCILCGRCVDVCPT 241
                                   89****************96 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   2.8   0.00023      0.25       1      15 []      47      61 ..      47      61 .. 0.97
   2 !    8.7   6.3    0.0033       3.7       1      15 []      78      92 ..      78      92 .. 0.98
   3 !   10.8   3.7   0.00071       0.8       1      15 []     133     147 ..     133     147 .. 0.98
   4 !   11.9  10.9   0.00032      0.35       1      14 [.     163     176 ..     163     177 .. 0.94
   5 ?    6.5   4.3     0.017        19       1      15 []     200     214 ..     200     214 .. 0.94
   6 !   19.7   4.5     1e-06    0.0012       1      15 []     229     243 ..     229     243 .. 0.98

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ C++C + CPv+A
  gi|15668691|ref|NP_247490.1| 47 CIRCNLCYKECPVDA 61
                                  *************98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0033
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ C+ C + CPvgA
  gi|15668691|ref|NP_247490.1| 78 CVKCEICAQTCPVGA 92
                                  9*************9 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00071
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ Cg C + CP++A
  gi|15668691|ref|NP_247490.1| 133 CIKCGICARFCPTNA 147
                                   *************98 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00032
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   C+gCgaC evCP++
  gi|15668691|ref|NP_247490.1| 163 CMGCGACAEVCPKK 176
                                   ************97 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.017
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+gC  C e CP +A
  gi|15668691|ref|NP_247490.1| 200 CVGCLVCIEECPINA 214
                                   ****88******998 PP

  == domain 6  score: 19.7 bits;  conditional E-value: 1e-06
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ Cg+Cv+vCP++A
  gi|15668691|ref|NP_247490.1| 229 CILCGRCVDVCPTNA 243
                                   *************98 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0025       2.9      60      94 ..      22      59 ..      11      61 .. 0.76
   2 !    7.4   2.1    0.0072       8.1       1      24 [.      77     100 ..      77     115 .. 0.76
   3 !   11.6   1.3   0.00035      0.39      69      94 ..     120     145 ..      94     148 .. 0.73
   4 !    9.2   2.4     0.002       2.2       1      17 [.     132     148 ..     131     159 .. 0.81
   5 !   10.5   4.1   0.00077      0.86      76      95 ..     157     176 ..     147     177 .. 0.79
   6 !   11.4   0.8   0.00041      0.45      73      94 ..     191     212 ..     178     214 .. 0.79
   7 !   13.3   1.3    0.0001      0.12      76      95 ..     223     242 ..     217     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0025
                       Fer4_22 60 erlrqrllhklsefkekf...gesgCvGCgRCieacpv 94
                                  +++ + + +k++ ++ k    +e++C+ C+ C + cpv
  gi|15668691|ref|NP_247490.1| 22 KKYINEVAKKITPITYKLlyiNETKCIRCNLCYKECPV 59
                                  5666677777776665555569999***********97 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0072
                       Fer4_22   1 rClsCgaCtlvCptCsCfdvedet 24 
                                   +C++C  C+ +Cp    + +e ++
  gi|15668691|ref|NP_247490.1|  77 KCVKCEICAQTCPVGAIYVIEGRA 100
                                   79**********998877776655 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00035
                       Fer4_22  69 klsefkekfgesgCvGCgRCieacpv 94 
                                   k++  k + +e++C+ Cg C + cp+
  gi|15668691|ref|NP_247490.1| 120 KIRLKKYELDENTCIKCGICARFCPT 145
                                   55555566678888888888888876 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.002
                       Fer4_22   1 rClsCgaCtlvCptCsC 17 
                                   +C++Cg C+  Cpt   
  gi|15668691|ref|NP_247490.1| 132 TCIKCGICARFCPTNAI 148
                                   5************9765 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.00077
                       Fer4_22  76 kfgesgCvGCgRCieacpvk 95 
                                   +++   C+GCg C e+cp+k
  gi|15668691|ref|NP_247490.1| 157 EVNLDLCMGCGACAEVCPKK 176
                                   457789***********986 PP

  == domain 6  score: 11.4 bits;  conditional E-value: 0.00041
                       Fer4_22  73 fkekfgesgCvGCgRCieacpv 94 
                                      +++++ CvGC  Cie cp 
  gi|15668691|ref|NP_247490.1| 191 RDIEVDKNLCVGCLVCIEECPI 212
                                   44567999************96 PP

  == domain 7  score: 13.3 bits;  conditional E-value: 0.0001
                       Fer4_22  76 kfgesgCvGCgRCieacpvk 95 
                                   k+++ +C+ CgRC+++cp++
  gi|15668691|ref|NP_247490.1| 223 KINKDKCILCGRCVDVCPTN 242
                                   56889999999999999975 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   1.1    0.0015       1.7      34      74 ..      20      60 ..       5      65 .. 0.71
   2 !    9.8   3.7   0.00075      0.84      51      74 ..      68      91 ..      60     100 .. 0.73
   3 !   11.6  10.7   0.00022      0.25      50     102 ..     122     180 ..      93     189 .. 0.70
   4 !    8.4  15.4    0.0021       2.3      55      96 ..     194     240 ..     176     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                       Fer4_18 34 GekiagrkkekkalkekeerkekgagdcidcescvkvcPtg 74
                                  G+k++ ++ +kk +  + +    ++++ci c+ c k cP++
  gi|15668691|ref|NP_247490.1| 20 GDKKYINEVAKKITPITYKLLYINETKCIRCNLCYKECPVD 60
                                  555555555555555555555667899************85 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00075
                       Fer4_18 51 eerkekgagdcidcescvkvcPtg 74
                                  ++ ++  + +c++ce c + cP+g
  gi|15668691|ref|NP_247490.1| 68 KKSAKIIEDKCVKCEICAQTCPVG 91
                                  3344456788************97 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00022
                       Fer4_18  50 keerkekgagdcidcescvkvcPtg.id.i.rkGlqle...ciscllcidacdkvmekl 102
                                   + ++ e +++ ci+c+ c + cPt+ i  + rk + ++   c+ c+ c + c k   k+
  gi|15668691|ref|NP_247490.1| 122 RLKKYELDENTCIKCGICARFCPTNaIKaVrRKSIEVNldlCMGCGACAEVCPKKCIKV 180
                                   33344567899************9734323377777655579********998755555 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0021
                       Fer4_18  55 ekgagdcidcescvkvcPtgidirkGlql.....eciscllcidacd 96 
                                   e +++ c+ c +c++ cP++   ++G ++     +ci c++c+d c 
  gi|15668691|ref|NP_247490.1| 194 EVDKNLCVGCLVCIEECPINAIDQDGDKVkinkdKCILCGRCVDVCP 240
                                   456778************98655666554223336***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 1647.40
//
Query:       gi|15668692|ref|NP_247491.1|  [L=163]
Description: polyferredoxin MvhB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-29   98.6  40.2    2.6e-09   36.5   4.2    4.3  4  Fer4      4Fe-4S binding domain
    1.5e-22   78.7  35.2    8.8e-07   28.7   5.0    4.4  4  Fer4_6    4Fe-4S binding domain
    6.4e-19   68.3  27.0    1.1e-10   41.9  10.9    3.2  3  Fer4_7    4Fe-4S dicluster domain
    7.3e-18   64.5  27.5    2.2e-10   40.6  10.4    2.3  2  Fer4_9    4Fe-4S dicluster domain
    2.6e-17   63.5  27.1    2.2e-05   25.3   1.1    4.2  4  Fer4_16   4Fe-4S double cluster binding domain
    5.7e-17   61.6  33.6    6.4e-07   29.4  10.6    3.1  3  Fer4_10   4Fe-4S dicluster domain
    1.1e-15   57.5  33.1    4.1e-10   39.6  13.5    3.3  3  Fer4_21   4Fe-4S dicluster domain
      4e-15   54.9  28.1    5.6e-05   23.0   1.6    4.5  4  Fer4_2    4Fe-4S binding domain
    1.3e-08   34.6  37.0     0.0031   17.9   3.4    4.3  4  Fer4_4    4Fe-4S binding domain
    2.1e-06   28.2  39.4      0.011   16.6   3.6    4.3  4  Fer4_3    4Fe-4S binding domain
    3.6e-06   27.3  35.5      0.064   13.7   2.5    4.0  5  Fer4_8    4Fe-4S dicluster domain
    5.1e-06   26.9  35.5       0.35   11.5   3.3    4.1  5  Fer4_17   4Fe-4S dicluster domain
    2.3e-05   24.8  28.7      0.019   15.5   2.9    4.4  4  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    9.7e-05   23.0  23.6       0.22   12.3   0.5    4.9  5  Fer4_15   4Fe-4S single cluster domain
    0.00043   21.1  26.9      0.031   15.1   0.1    4.1  5  Fer4_22   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.15   12.2  30.7        0.2   11.9   2.6    4.0  4  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   6.4     1e-11   1.2e-08       2      24 .]      33      55 ..      32      55 .. 0.93
   2 !   36.5   4.2   2.3e-12   2.6e-09       1      23 [.      63      85 ..      63      86 .. 0.95
   3 !   20.0   1.6   3.9e-07   0.00044       3      24 .]     111     132 ..     109     132 .. 0.91
   4 !   26.2   4.7   4.2e-09   4.8e-06       2      23 ..     139     160 ..     138     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1e-11
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  ++ e+kCi CG+C+e+CPv+AIt
  gi|15668692|ref|NP_247491.1| 33 IVKEDKCISCGKCIEICPVNAIT 55
                                  788*******************7 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 2.3e-12
                                  EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                  ++i++ekC++CG+C +vCP++AI
  gi|15668692|ref|NP_247491.1| 63 ITINKEKCVFCGKCKKVCPTNAI 85
                                  68********************9 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 3.9e-07
                                   EETTTSSS-THHHHHSTTTEEE CS
                          Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                   ++ e+C  C  C   CP++AI+
  gi|15668692|ref|NP_247491.1| 111 YISERCASCLVCLRNCPFNAIE 132
                                   6789*****************6 PP

  == domain 4  score: 26.2 bits;  conditional E-value: 4.2e-09
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                    id +kC  CG+C+e+CP +AI
  gi|15668692|ref|NP_247491.1| 139 RIDINKCELCGKCEEICPLNAI 160
                                   7999*****************9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   5.0   7.9e-10   8.8e-07       3      24 .]      33      54 ..      31      54 .. 0.93
   2 !   26.4   2.5   4.2e-09   4.7e-06       2      24 .]      63      85 ..      62      85 .. 0.96
   3 !   17.9   1.8   2.1e-06    0.0024       4      24 .]     111     131 ..     108     131 .. 0.90
   4 !   23.5   2.9   3.6e-08     4e-05       1      23 [.     137     159 ..     137     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 7.9e-10
                        Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                   +++dkCi+Cg+C+ +CP +ai
  gi|15668692|ref|NP_247491.1| 33 IVKEDKCISCGKCIEICPVNAI 54
                                  689*****************98 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 4.2e-09
                        Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                  ++i+++kC+ Cg+C +vCP++ai
  gi|15668692|ref|NP_247491.1| 63 ITINKEKCVFCGKCKKVCPTNAI 85
                                  79********************8 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 2.1e-06
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   +  ++C +C  C r+CP++ai
  gi|15668692|ref|NP_247491.1| 111 YISERCASCLVCLRNCPFNAI 131
                                   6789****************8 PP

  == domain 4  score: 23.5 bits;  conditional E-value: 3.6e-08
                        Fer4_6   1 vveidpdkCigCgdCvrvCPega 23 
                                   +++id +kC  Cg+C+ +CP +a
  gi|15668692|ref|NP_247491.1| 137 KIRIDINKCELCGKCEEICPLNA 159
                                   689*****************655 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9  10.9   9.8e-14   1.1e-10       1      52 []      38      84 ..      38      84 .. 0.95
   2 !   16.1   1.4   1.1e-05     0.012      29      52 .]     107     130 ..      88     130 .. 0.76
   3 !   28.2   9.1   1.9e-09   2.1e-06       1      52 []     115     159 ..     115     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 9.8e-14
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  +Ci Cg+C + Cpv+ai++  +    g  +++i+ ekC++Cg+C +vCPt+a
  gi|15668692|ref|NP_247491.1| 38 KCISCGKCIEICPVNAITYSSD----G-LYITINKEKCVFCGKCKKVCPTNA 84
                                  7******************887....4.89********************97 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.1e-05
                        Fer4_7  29 ekveidpekClgCgaCvavCPtga 52 
                                   e +++ +e+C +C +C + CP++a
  gi|15668692|ref|NP_247491.1| 107 EFIDYISERCASCLVCLRNCPFNA 130
                                   34577789*************997 PP

  == domain 3  score: 28.2 bits;  conditional E-value: 1.9e-09
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   rC  C  C ++Cp +aie           k++id +kC  Cg+C++ CP +a
  gi|15668692|ref|NP_247491.1| 115 RCASCLVCLRNCPFNAIEEYG-------SKIRIDINKCELCGKCEEICPLNA 159
                                   7****************9754.......58*******************886 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6  10.4   1.9e-13   2.2e-10       1      51 []      38      85 ..      35      85 .. 0.95
   2 !   29.8   9.1   4.4e-10   4.9e-07       1      51 []     115     160 ..     115     160 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.9e-13
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  kC++Cg+C+e Cp +++++++ + ++ ++++   +C++Cg+C ++Cp++ai
  gi|15668692|ref|NP_247491.1| 38 KCISCGKCIEICPVNAITYSSDGLYITINKE---KCVFCGKCKKVCPTNAI 85
                                  7**************************9874...8*************997 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 4.4e-10
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   +C++C  C + Cp+++++e  ++  + ++     +C  Cg+C+e+Cp +ai
  gi|15668692|ref|NP_247491.1| 115 RCASCLVCLRNCPFNAIEEYGSKIRIDIN-----KCELCGKCEEICPLNAI 160
                                   5*********************9999995.....5************9987 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   1.1     2e-08   2.2e-05       1      20 [.      38      57 ..      38      68 .. 0.88
   2 !   21.2   1.6   3.6e-07   0.00041       1      19 [.      69      87 ..      69     112 .. 0.80
   3 !   18.3   2.5     3e-06    0.0034       1      30 [.     115     145 ..     115     146 .. 0.91
   4 !   15.8   2.4   1.8e-05      0.02       1      18 [.     144     161 ..     144     163 .] 0.90

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2e-08
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  +C++CgkC+e+CP+nai+  
  gi|15668692|ref|NP_247491.1| 38 KCISCGKCIEICPVNAITYS 57
                                  6****************976 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 3.6e-07
                       Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                  +C+ CgkC +vCPtnai  
  gi|15668692|ref|NP_247491.1| 69 KCVFCGKCKKVCPTNAIVI 87
                                  5***************974 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 3e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikek.kekeiearec 30 
                                   rC +C  C+  CP nai+e  ++ +i++++c
  gi|15668692|ref|NP_247491.1| 115 RCASCLVCLRNCPFNAIEEYgSKIRIDINKC 145
                                   6*****************9988889999998 PP

  == domain 4  score: 15.8 bits;  conditional E-value: 1.8e-05
                       Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                   +C  CgkC e+CP nai 
  gi|15668692|ref|NP_247491.1| 144 KCELCGKCEEICPLNAII 161
                                   59**************95 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   2.7     1e-07   0.00011       2      23 ..      32      53 ..      31      64 .. 0.79
   2 !   23.5   4.1   3.9e-08   4.4e-05       2      24 ..      63      94 ..      62     113 .. 0.72
   3 !   29.4  10.6   5.7e-10   6.4e-07       5      56 .]     112     156 ..     108     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1e-07
                       Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                  +++ +d+Ci CgkC + CP+++
  gi|15668692|ref|NP_247491.1| 32 IIVKEDKCISCGKCIEICPVNA 53
                                  57789***************65 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 3.9e-08
                       Fer4_10  2 vvidddtCirCgkCvkaCPadl.........t 24
                                  + i++++C+ CgkC+k+CP+++          
  gi|15668692|ref|NP_247491.1| 63 ITINKEKCVFCGKCKKVCPTNAiviirlrceI 94
                                  679*****************766665555440 PP

  == domain 3  score: 29.4 bits;  conditional E-value: 5.7e-10
                       Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    +++C  C  C + CP+       ++++++++++r+++ kC+ cg+C e+CP
  gi|15668692|ref|NP_247491.1| 112 ISERCASCLVCLRNCPF-------NAIEEYGSKIRIDINKCELCGKCEEICP 156
                                   5689*************.......9999***********************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6  13.5   3.7e-13   4.1e-10       3      57 ..      34      85 ..      32      88 .. 0.88
   2 !   30.3  11.7     3e-10   3.3e-07       3      58 ..      65     132 ..      64     133 .. 0.88
   3 !    9.7   3.2   0.00083      0.93      36      57 ..     140     160 ..     133     162 .. 0.68

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 3.7e-13
                       Fer4_21  3 idedkCigCgkCliaCedtshqaieidakt.vlkvvedeCvGCnlCssvCPvedci 57
                                  ++edkCi+CgkC+  C+   ++ai+++++  ++++ +++Cv C  C +vCP+ ++i
  gi|15668692|ref|NP_247491.1| 34 VKEDKCISCGKCIEICP---VNAITYSSDGlYITINKEKCVFCGKCKKVCPT-NAI 85
                                  899**************...8***998775277889***************7.666 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 3e-10
                       Fer4_21   3 idedkCigCgkCliaCedtshqai.............eidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                   i+++kC+ CgkC ++C+++++  i             e+d+ + + +++++C  C +C+  CP  ++ie
  gi|15668692|ref|NP_247491.1|  65 INKEKCVFCGKCKKVCPTNAIVIIrlrceinedariiEVDKYEFIDYISERCASCLVCLRNCPF-NAIE 132
                                   99****************999999999988887777667777788999***************7.8875 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00083
                       Fer4_21  36 vvedeCvGCnlCssvCPvedci 57 
                                   +  ++C  C  C ++CP+ ++i
  gi|15668692|ref|NP_247491.1| 140 IDINKCELCGKCEEICPL-NAI 160
                                   445678888888888886.444 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   1.6     5e-08   5.6e-05       3      21 ..      32      50 ..      30      51 .. 0.90
   2 !   18.1   1.3   1.8e-06     0.002       2      22 .]      62      82 ..      61      82 .. 0.93
   3 !   16.0   1.2   8.6e-06    0.0096       5      21 ..     111     127 ..     107     128 .. 0.89
   4 !   15.5   1.0   1.2e-05     0.014       3      21 ..     138     156 ..     136     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5e-08
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  + v +d+Ci+Cg+C+  CP
  gi|15668692|ref|NP_247491.1| 32 IIVKEDKCISCGKCIEICP 50
                                  67899************** PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.8e-06
                        Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                  ++ ++ ++C+ Cg+C ++CP+
  gi|15668692|ref|NP_247491.1| 62 YITINKEKCVFCGKCKKVCPT 82
                                  5789****************7 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 8.6e-06
                        Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                   + ++rC +C  C+ +CP
  gi|15668692|ref|NP_247491.1| 111 YISERCASCLVCLRNCP 127
                                   6789************* PP

  == domain 4  score: 15.5 bits;  conditional E-value: 1.2e-05
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   + +d ++C  Cg+C   CP
  gi|15668692|ref|NP_247491.1| 138 IRIDINKCELCGKCEEICP 156
                                   678999************9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   3.4   2.8e-06    0.0031       2      17 .]      37      52 ..      36      53 .. 0.93
   2 !   12.1   5.2   0.00019      0.22       1      17 []      67      83 ..      67      83 .. 0.93
   3 !    9.4   2.7    0.0014       1.6       1      17 []     113     129 ..     113     129 .. 0.92
   4 !   13.2   2.4   9.1e-05       0.1       2      16 ..     143     157 ..     142     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  ++Ci Cg+C+ +CP++
  gi|15668692|ref|NP_247491.1| 37 DKCISCGKCIEICPVN 52
                                  89************75 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00019
                        Fer4_4  1 qerCigCgsCvaaCPqg 17
                                  +e+C+ Cg+C  +CP++
  gi|15668692|ref|NP_247491.1| 67 KEKCVFCGKCKKVCPTN 83
                                  699************86 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0014
                        Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                   +erC  C +C + CP++
  gi|15668692|ref|NP_247491.1| 113 SERCASCLVCLRNCPFN 129
                                   69*************86 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 9.1e-05
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   ++C  Cg+C+ +CP 
  gi|15668692|ref|NP_247491.1| 143 NKCELCGKCEEICPL 157
                                   78999*********6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   3.6   9.9e-06     0.011       1      15 []      39      53 ..      39      53 .. 0.98
   2 !   13.8   5.5   7.6e-05     0.085       1      15 []      70      84 ..      70      84 .. 0.98
   3 ?    3.2   3.8      0.18   2.1e+02       3      15 .]     118     130 ..     115     130 .. 0.78
   4 !   13.1   3.0   0.00014      0.15       1      15 []     145     159 ..     145     159 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.9e-06
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ Cg C e CPv+A
  gi|15668692|ref|NP_247491.1| 39 CISCGKCIEICPVNA 53
                                  *************99 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.6e-05
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ Cg C +vCP++A
  gi|15668692|ref|NP_247491.1| 70 CVFCGKCKKVCPTNA 84
                                  *************98 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.18
                        Fer4_3   3 gCgaCvevCPvgA 15 
                                    C  C++ CP +A
  gi|15668692|ref|NP_247491.1| 118 SCLVCLRNCPFNA 130
                                   4656******998 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 0.00014
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C  Cg C+e CP +A
  gi|15668692|ref|NP_247491.1| 145 CELCGKCEEICPLNA 159
                                   999*********987 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   2.5   5.7e-05     0.064       3      18 ..      37      52 ..      35      63 .. 0.75
   2 !   11.8   3.5   0.00023      0.25      49      64 ..      68      83 ..      55      84 .. 0.81
   3 !    9.9  15.5   0.00085      0.96       3      64 ..      68     129 ..      66     130 .. 0.70
   4 !    8.3   2.6    0.0029       3.2       3      17 ..     114     128 ..     112     141 .. 0.84
   5 !   12.9   2.2    0.0001      0.12      47      64 ..     141     158 ..     129     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-05
                        Fer4_8  3 ekCieCgaCqsaCpvl 18
                                  +kCi Cg C + Cpv 
  gi|15668692|ref|NP_247491.1| 37 DKCISCGKCIEICPVN 52
                                  5788888888888864 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00023
                        Fer4_8 49 wsCttcgaCtevCpvg 64
                                  ++C+ cg+C++vCp++
  gi|15668692|ref|NP_247491.1| 68 EKCVFCGKCKKVCPTN 83
                                  5788888888888876 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00085
                        Fer4_8   3 ekCieCgaCqsaCp....vlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   ekC+ Cg C++ Cp    v+ r + + + dar    e v + +    +++ ++C +c  C ++Cp +
  gi|15668692|ref|NP_247491.1|  68 EKCVFCGKCKKVCPtnaiVIIRLRcEINEDARII--E-VDKYEF--IDYISERCASCLVCLRNCPFN 129
                                   69***********988754444443444444444..4.333333..25789**************75 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0029
                        Fer4_8   3 ekCieCgaCqsaCpv 17 
                                   e+C  C  C  +Cp+
  gi|15668692|ref|NP_247491.1| 114 ERCASCLVCLRNCPF 128
                                   689999999999996 PP

  == domain 5  score: 12.9 bits;  conditional E-value: 0.0001
                        Fer4_8  47 alwsCttcgaCtevCpvg 64 
                                    +++C  cg+C+e Cp +
  gi|15668692|ref|NP_247491.1| 141 DINKCELCGKCEEICPLN 158
                                   578999999999999965 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   2.7   0.00035      0.39      44      58 ..      37      51 ..      14      54 .. 0.75
   2 !    9.1  13.7    0.0017         2       1      59 [.      38      83 ..      38      85 .. 0.77
   3 !    9.1   3.1    0.0017       1.9      44      58 ..     114     128 ..      91     130 .. 0.73
   4 !   10.2   2.3   0.00079      0.88       1      17 [.     115     131 ..     115     141 .. 0.80
   5 !   11.5   3.3   0.00031      0.35      42      58 ..     141     157 ..     130     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                       Fer4_17 44 slCieCgeCerkCPq 58
                                  ++Ci+Cg+C + CP 
  gi|15668692|ref|NP_247491.1| 37 DKCISCGKCIEICPV 51
                                  567777777777774 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                       Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                  +Ci+Cg C++ Cp ++++ +               +     + ++C+ Cg+C+++CP +
  gi|15668692|ref|NP_247491.1| 38 KCISCGKCIEICPVNAITYSSD-------------GLYITINKEKCVFCGKCKKVCPTN 83
                                  6*************99966522.............2222334579************86 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0017
                       Fer4_17  44 slCieCgeCerkCPq 58 
                                   ++C++C  C r CP 
  gi|15668692|ref|NP_247491.1| 114 ERCASCLVCLRNCPF 128
                                   567777777777764 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00079
                       Fer4_17   1 rCiqCgyClpeCpsyea 17 
                                   rC++C  Cl++Cp++++
  gi|15668692|ref|NP_247491.1| 115 RCASCLVCLRNCPFNAI 131
                                   69999999999998765 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00031
                       Fer4_17  42 kaslCieCgeCerkCPq 58 
                                    +++C  Cg+Ce+ CP 
  gi|15668692|ref|NP_247491.1| 141 DINKCELCGKCEEICPL 157
                                   789*************6 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   2.9   1.7e-05     0.019       3      17 ..      36      50 ..      34      55 .. 0.91
   2 !   12.1   1.6    0.0002      0.22       1      18 [.      65      82 ..      65      83 .. 0.94
   3 !    6.7   0.7    0.0097        11       4      17 ..     114     127 ..     109     136 .. 0.90
   4 !    6.8   2.1    0.0091        10       1      17 [.     140     156 ..     140     158 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                       Fer4_13  3 rdtCiacgaCvelaP 17
                                  +d+Ci+cg+C e++P
  gi|15668692|ref|NP_247491.1| 36 EDKCISCGKCIEICP 50
                                  69************9 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0002
                       Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                  +++++C+ cg+C +++P 
  gi|15668692|ref|NP_247491.1| 65 INKEKCVFCGKCKKVCPT 82
                                  79***************6 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0097
                       Fer4_13   4 dtCiacgaCvelaP 17 
                                   ++C +c +C   +P
  gi|15668692|ref|NP_247491.1| 114 ERCASCLVCLRNCP 127
                                   89**********99 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0091
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   +D ++C  cg+C e++P
  gi|15668692|ref|NP_247491.1| 140 IDINKCELCGKCEEICP 156
                                   6889************9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.5    0.0002      0.22       2      19 ..      33      50 ..      32      62 .. 0.76
   2 !    8.9   1.9    0.0022       2.5       1      20 [.      63      82 ..      63      84 .. 0.93
   3 ?    3.3   0.1      0.13   1.4e+02      57      66 .]      78      87 ..      77      87 .. 0.89
   4 !    6.8   0.3    0.0099        11       6      19 ..     114     127 ..     108     137 .. 0.78
   5 !    8.6   1.1    0.0027         3       1      19 [.     138     156 ..     138     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                       Fer4_15  2 vvDrdaCigcglCvaeap 19
                                   v +d+Ci+cg C++ +p
  gi|15668692|ref|NP_247491.1| 33 IVKEDKCISCGKCIEICP 50
                                  6778*************7 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0022
                       Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                  +++++++C  cg C +++p+
  gi|15668692|ref|NP_247491.1| 63 ITINKEKCVFCGKCKKVCPT 82
                                  79****************96 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.13
                       Fer4_15 57 raCPvdAIrv 66
                                  ++CP+ AI++
  gi|15668692|ref|NP_247491.1| 78 KVCPTNAIVI 87
                                  68******97 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0099
                       Fer4_15   6 daCigcglCvaeap 19 
                                   ++C +c +C++++p
  gi|15668692|ref|NP_247491.1| 114 ERCASCLVCLRNCP 127
                                   89***********8 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0027
                       Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                   +++D ++C+ cg C + +p
  gi|15668692|ref|NP_247491.1| 138 IRIDINKCELCGKCEEICP 156
                                   789***********99998 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.7e-05     0.031      78      95 ..      35      52 ..       8      53 .. 0.74
   2 !   11.3   3.3   0.00044      0.49      78      94 ..      66      82 ..      56      84 .. 0.75
   3 !    9.4   4.2    0.0016       1.8       1      15 [.      69      83 ..      69     104 .. 0.80
   4 ?    0.6   3.1      0.93     1e+03      81      93 ..     115     127 ..      89     131 .. 0.72
   5 !    8.3   1.2    0.0037       4.1      76      94 ..     139     157 ..     128     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-05
                       Fer4_22 78 gesgCvGCgRCieacpvk 95
                                  +e +C+ Cg+Cie cpv+
  gi|15668692|ref|NP_247491.1| 35 KEDKCISCGKCIEICPVN 52
                                  788999999999999986 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00044
                       Fer4_22 78 gesgCvGCgRCieacpv 94
                                  ++++Cv Cg+C+++cp+
  gi|15668692|ref|NP_247491.1| 66 NKEKCVFCGKCKKVCPT 82
                                  67778888888888876 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0016
                       Fer4_22  1 rClsCgaCtlvCptC 15
                                  +C+ Cg+C+ vCpt 
  gi|15668692|ref|NP_247491.1| 69 KCVFCGKCKKVCPTN 83
                                  689999999999985 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.93
                       Fer4_22  81 gCvGCgRCieacp 93 
                                    C  C  C ++cp
  gi|15668692|ref|NP_247491.1| 115 RCASCLVCLRNCP 127
                                   4555555555555 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0037
                       Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                   +++ ++C  Cg+C+e cp 
  gi|15668692|ref|NP_247491.1| 139 RIDINKCELCGKCEEICPL 157
                                   5678899999999999986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.6   0.00018       0.2      57      74 ..      35      52 ..      18      65 .. 0.81
   2 ?    9.3   3.3    0.0011       1.3      58      74 ..      67      83 ..      57      93 .. 0.84
   3 ?   -2.1  10.3       3.8   4.2e+03      58      92 ..     113     152 ..      89     155 .. 0.63
   4 ?    5.8   1.1     0.014        16      55      74 ..     139     158 ..     128     163 .] 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                       Fer4_18 57 gagdcidcescvkvcPtg 74
                                  ++ +ci+c++c+++cP++
  gi|15668692|ref|NP_247491.1| 35 KEDKCISCGKCIEICPVN 52
                                  5678************86 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
                       Fer4_18 58 agdcidcescvkvcPtg 74
                                  + +c+ c++c kvcPt+
  gi|15668692|ref|NP_247491.1| 67 KEKCVFCGKCKKVCPTN 83
                                  678************97 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.8
                       Fer4_18  58 agdcidcescvkvcPtgidirkGlql.....eciscllci 92 
                                   +  c +c +c++ cP +     G ++     +c  c++c 
  gi|15668692|ref|NP_247491.1| 113 SERCASCLVCLRNCPFNAIEEYGSKIridinKCELCGKCE 152
                                   56799**********8754444544311111344444444 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.014
                       Fer4_18  55 ekgagdcidcescvkvcPtg 74 
                                   + + ++c  c++c ++cP +
  gi|15668692|ref|NP_247491.1| 139 RIDINKCELCGKCEEICPLN 158
                                   556789************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       957  (0.0533772); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1070.24
//
Query:       gi|15668693|ref|NP_247492.1|  [L=408]
Description: polyferredoxin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-40  133.5  87.9    8.2e-07   28.6   5.6    8.3  8  Fer4      4Fe-4S binding domain
    1.2e-30  105.8  59.7    1.8e-08   34.9  10.6    5.4  6  Fer4_7    4Fe-4S dicluster domain
    2.4e-27   93.8  80.8      2e-05   24.5   3.2    8.3  8  Fer4_6    4Fe-4S binding domain
    9.7e-27   93.7  58.3    2.6e-06   28.3   7.7    7.5  7  Fer4_16   4Fe-4S double cluster binding domain
      1e-25   89.6  68.6    1.1e-08   35.1   9.1    5.2  5  Fer4_21   4Fe-4S dicluster domain
    3.3e-25   88.0  70.4    1.1e-06   28.6  13.1    7.0  7  Fer4_10   4Fe-4S dicluster domain
    3.7e-24   84.6  59.8      7e-08   32.5  11.6    5.5  5  Fer4_9    4Fe-4S dicluster domain
    5.8e-20   70.1  77.0    0.00084   19.3   3.6    8.3  8  Fer4_2    4Fe-4S binding domain
    9.8e-14   51.7  60.0    7.8e-06   26.3   4.3    7.4  9  Fer4_17   4Fe-4S dicluster domain
    1.3e-11   44.8  63.9     0.0066   16.9   7.4    6.9  7  Fer4_8    4Fe-4S dicluster domain
    2.5e-08   34.1  64.9    5.7e-06   26.5   9.8    6.2  6  Fer4_18   4Fe-4S dicluster domain
    4.5e-07   29.9  73.5      0.019   15.4   2.3    8.3  8  Fer4_4    4Fe-4S binding domain
    0.00046   20.7  67.2      0.074   13.6   1.6    8.5  8  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0077   17.1  67.3       0.12   13.2   0.5    8.3  9  Fer4_22   4Fe-4S dicluster domain
  ------ inclusion threshold ------
          2    9.5  89.7       0.64   11.1   2.7    8.3  8  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   3.5   6.5e-07   0.00078       2      24 .]      46      68 ..      45      68 .. 0.91
   2 !   25.3   5.7   7.7e-09   9.2e-06       1      23 [.      80     102 ..      80     103 .. 0.94
   3 !   28.6   5.6   6.8e-10   8.2e-07       2      24 .]     125     147 ..     124     147 .. 0.95
   4 !   20.4   4.4   2.7e-07   0.00032       1      20 [.     153     172 ..     153     173 .. 0.93
   5 !   12.7   4.1   7.1e-05     0.085       3      18 ..     216     231 ..     214     231 .. 0.89
   6 !   15.6   4.0   8.6e-06      0.01       7      23 ..     244     260 ..     243     261 .. 0.90
   7 !   28.4   3.8     8e-10   9.5e-07       1      24 []     275     298 ..     275     298 .. 0.96
   8 !   27.4   2.0   1.6e-09   1.9e-06       1      24 []     306     329 ..     306     329 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.5e-07
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  v  +ekCi C  C e CP  AI+
  gi|15668693|ref|NP_247492.1| 46 VKFPEKCISCEGCKESCPAFAIE 68
                                  6789***************9996 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 7.7e-09
                                   EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                   +vide  C++C +C+evCP+g++
  gi|15668693|ref|NP_247492.1|  80 PVIDEGSCVACANCIEVCPTGVL 102
                                   69*******************97 PP

  == domain 3  score: 28.6 bits;  conditional E-value: 6.8e-10
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   +idee C++CG+C+ +CP ++I+
  gi|15668693|ref|NP_247492.1| 125 IIDEEVCVRCGNCERACPINVIE 147
                                   79*******************96 PP

  == domain 4  score: 20.4 bits;  conditional E-value: 2.7e-07
                                   EEEETTTSSS-THHHHHSTT CS
                          Fer4   1 vvideekCigCGaCvevCPv 20 
                                   +vi++ +Ci C++C++vCP 
  gi|15668693|ref|NP_247492.1| 153 YVINMALCISCKECIKVCPI 172
                                   69*****************6 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 7.1e-05
                                   EETTTSSS-THHHHHS CS
                          Fer4   3 ideekCigCGaCvevC 18 
                                   i   +C+ CG+C +vC
  gi|15668693|ref|NP_247492.1| 216 IVSGLCVSCGICKDVC 231
                                   77889*********** PP

  == domain 6  score: 15.6 bits;  conditional E-value: 8.6e-06
                                   TSSS-THHHHHSTTTEE CS
                          Fer4   7 kCigCGaCvevCPvgAI 23 
                                    C++CG+C+evC + AI
  gi|15668693|ref|NP_247492.1| 244 ECVKCGLCIEVCSTTAI 260
                                   5***********98888 PP

  == domain 7  score: 28.4 bits;  conditional E-value: 8e-10
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                   +vide++CigC +C +vC  gAI+
  gi|15668693|ref|NP_247492.1| 275 YVIDEDLCIGCRICQKVCGSGAIK 298
                                   69********************96 PP

  == domain 8  score: 27.4 bits;  conditional E-value: 1.6e-09
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                   ++i +e+C++ GaC+  CPvgAI+
  gi|15668693|ref|NP_247492.1| 306 PYIVPELCVRGGACARECPVGAIK 329
                                   689********************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9  10.6   1.5e-11   1.8e-08       1      52 []      51     101 ..      51     101 .. 0.89
   2 !   32.0  12.1   1.2e-10   1.4e-07       2      50 ..     131     172 ..     130     175 .. 0.93
   3 !   10.8   0.1   0.00047      0.57      36      48 ..     219     231 ..     183     241 .. 0.71
   4 !   31.2  10.3     2e-10   2.4e-07       2      52 .]     245     296 ..     244     296 .. 0.89
   5 !   31.4   7.8   1.7e-10   2.1e-07       2      52 .]     282     327 ..     281     327 .. 0.95
   6 !   14.5   0.7   3.3e-05     0.039       2      36 ..     313     347 ..     312     349 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.5e-11
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +Ci C+ C + Cp+ aie+ + e e  ++ ++id+ +C+ C +C++vCPtg+
  gi|15668693|ref|NP_247492.1|  51 KCISCEGCKESCPAFAIEMIYNE-EYNKKLPVIDEGSCVACANCIEVCPTGV 101
                                   7******************8864.44457789******************96 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 1.2e-10
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                   C+ Cg+C++aCp ++ie +e        k++i++  C++C++C++vCP 
  gi|15668693|ref|NP_247492.1| 131 CVRCGNCERACPINVIERKE-------GKYVINMALCISCKECIKVCPI 172
                                   *****************977.......489******************5 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00047
                        Fer4_7  36 ekClgCgaCvavC 48 
                                     C++Cg C +vC
  gi|15668693|ref|NP_247492.1| 219 GLCVSCGICKDVC 231
                                   5555555555555 PP

  == domain 4  score: 31.2 bits;  conditional E-value: 2e-10
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekv.eidpekClgCgaCvavCPtga 52 
                                   C++Cg C ++C++ ai++ +   +k+++ + +id++ C+gC+ C++vC +ga
  gi|15668693|ref|NP_247492.1| 245 CVKCGLCIEVCSTTAIRIYKPIIPKRKDICyVIDEDLCIGCRICQKVCGSGA 296
                                   *******************99888888776256999************9987 PP

  == domain 5  score: 31.4 bits;  conditional E-value: 1.7e-10
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   CigC+ C+++C ++ai++ +e     t+ ++i+pe C+  gaC+++CP+ga
  gi|15668693|ref|NP_247492.1| 282 CIGCRICQKVCGSGAIKISKE-----TKLPYIVPELCVRGGACARECPVGA 327
                                   ******************997.....67799******************98 PP

  == domain 6  score: 14.5 bits;  conditional E-value: 3.3e-05
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpe 36 
                                   C+  gaC++ Cpv+ai++ + e++++  kv+i ++
  gi|15668693|ref|NP_247492.1| 313 CVRGGACARECPVGAIKVVKPEEAEEAVKVRIIED 347
                                   9999***************9999998888887665 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.7   2.6e-05     0.032       5      24 .]      48      67 ..      44      67 .. 0.87
   2 !   23.0   3.4     5e-08   5.9e-05       2      24 .]      80     102 ..      79     102 .. 0.95
   3 !   19.6   4.5   5.5e-07   0.00066       4      24 .]     126     146 ..     124     146 .. 0.93
   4 !   20.9   4.1   2.2e-07   0.00027       3      24 .]     154     176 ..     154     176 .. 0.92
   5 !    9.5   4.2   0.00091       1.1       1      19 [.     213     231 ..     213     232 .. 0.91
   6 !    9.9   4.2   0.00068      0.81       9      23 ..     245     259 ..     245     260 .. 0.88
   7 !   24.5   3.2   1.6e-08     2e-05       3      24 .]     276     297 ..     276     297 .. 0.96
   8 !   14.5   0.7   2.4e-05     0.029       2      24 .]     306     328 ..     305     328 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-05
                        Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                   p+kCi+C+ C   CP+ ai
  gi|15668693|ref|NP_247492.1| 48 FPEKCISCEGCKESCPAFAI 67
                                  69**************9776 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 5e-08
                        Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                   ++id+ +C+ C +C+ vCP+g++
  gi|15668693|ref|NP_247492.1|  80 PVIDEGSCVACANCIEVCPTGVL 102
                                   89******************986 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 5.5e-07
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   id++ C+ Cg+C+r+CP ++i
  gi|15668693|ref|NP_247492.1| 126 IDEEVCVRCGNCERACPINVI 146
                                   89***************8876 PP

  == domain 4  score: 20.9 bits;  conditional E-value: 2.2e-07
                        Fer4_6   3 eidpdkCigCgdCvrvCP.egai 24 
                                   +i+  +Ci+C +C++vCP e+ai
  gi|15668693|ref|NP_247492.1| 154 VINMALCISCKECIKVCPiENAI 176
                                   6999**************88987 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.00091
                        Fer4_6   1 vveidpdkCigCgdCvrvC 19 
                                   +++i   +C++Cg C +vC
  gi|15668693|ref|NP_247492.1| 213 IPHIVSGLCVSCGICKDVC 231
                                   5788899************ PP

  == domain 6  score: 9.9 bits;  conditional E-value: 0.00068
                        Fer4_6   9 CigCgdCvrvCPega 23 
                                   C+ Cg C+ vC + a
  gi|15668693|ref|NP_247492.1| 245 CVKCGLCIEVCSTTA 259
                                   ***********9755 PP

  == domain 7  score: 24.5 bits;  conditional E-value: 1.6e-08
                        Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                   +id+d+CigC+ C +vC  gai
  gi|15668693|ref|NP_247492.1| 276 VIDEDLCIGCRICQKVCGSGAI 297
                                   69******************98 PP

  == domain 8  score: 14.5 bits;  conditional E-value: 2.4e-05
                        Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                   + i p++C+  g+C+r CP gai
  gi|15668693|ref|NP_247492.1| 306 PYIVPELCVRGGACARECPVGAI 328
                                   67889*****************8 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.4   4.9e-05     0.059       1      25 [.      51      75 ..      51      82 .. 0.82
   2 !   21.2   0.3   3.4e-07   0.00041       2      26 ..      87     110 ..      86     129 .. 0.80
   3 !   17.7   1.7   4.3e-06    0.0052       2      24 ..     131     152 ..     130     158 .. 0.83
   4 !   28.3   7.7   2.2e-09   2.6e-06       2      65 ..     160     232 ..     159     234 .. 0.62
   5 !   15.4   3.0   2.3e-05     0.027       2      28 ..     245     270 ..     244     280 .. 0.77
   6 !   13.7   1.4   7.5e-05     0.089       2      23 ..     282     303 ..     281     307 .. 0.84
   7 !   15.1   0.7   2.8e-05     0.033       2      37 ..     313     346 ..     312     395 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-05
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkekei 25
                                  +C++C+ C e+CP+ ai++  ++e+
  gi|15668693|ref|NP_247492.1| 51 KCISCEGCKESCPAFAIEMIYNEEY 75
                                  5****************98755544 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 3.4e-07
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeie 26 
                                   C+ C +C+evCPt++++++k  ++e
  gi|15668693|ref|NP_247492.1|  87 CVACANCIEVCPTGVLEMDK-HRVE 110
                                   ******************94.4444 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 4.3e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikekkeke 24 
                                   C++Cg+C  +CP n+i+ k e +
  gi|15668693|ref|NP_247492.1| 131 CVRCGNCERACPINVIERK-EGK 152
                                   *****************99.444 PP

  == domain 4  score: 28.3 bits;  conditional E-value: 2.2e-09
                       Fer4_16   2 CgtCgkCaevCPt.naikekkekeiearecisy.........ntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                   C++C++C++vCP  nai    ek+++ + +++          + + k++++e++ +    + +  C+iC+dvC+
  gi|15668693|ref|NP_247492.1| 160 CISCKECIKVCPIeNAIVVVDEKTLKEKIDKAFeiknkkitgKLEIKENVIEKIPHIV-SGLCVSCGICKDVCV 232
                                   ************6599997766666554443333333433322222333333333333.3778**********6 PP

  == domain 5  score: 15.4 bits;  conditional E-value: 2.3e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiear 28 
                                   C++Cg C+evC t ai+   ++ i +r
  gi|15668693|ref|NP_247492.1| 245 CVKCGLCIEVCSTTAIRIY-KPIIPKR 270
                                   ****************976.4555555 PP

  == domain 6  score: 13.7 bits;  conditional E-value: 7.5e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikekkek 23 
                                   C++C+ C +vC ++aik  ke+
  gi|15668693|ref|NP_247492.1| 282 CIGCRICQKVCGSGAIKISKET 303
                                   99*************9977655 PP

  == domain 7  score: 15.1 bits;  conditional E-value: 2.8e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntae 37 
                                   C++ g+Ca  CP++aik  k +e+e  e ++ + +e
  gi|15668693|ref|NP_247492.1| 313 CVRGGACARECPVGAIKVVKPEEAE--EAVKVRIIE 346
                                   9999*************88444433..333333333 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   9.1   9.1e-12   1.1e-08       6      59 .]      50     104 ..      47     104 .. 0.86
   2 !   30.1  14.6   3.3e-10     4e-07       2      57 ..     125     176 ..     124     178 .. 0.88
   3 !    9.4   1.1   0.00093       1.1      35      51 ..     215     231 ..     198     237 .. 0.80
   4 !   22.3  15.9   8.6e-08    0.0001       7      52 ..     244     293 ..     238     297 .. 0.74
   5 !   29.4   7.6   5.4e-10   6.5e-07       2      58 ..     276     329 ..     275     330 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 9.1e-12
                       Fer4_21   6 dkCigCgkCliaCedtshqai.eidaktvlkvv.edeCvGCnlCssvCPvedciem 59 
                                   +kCi+C+ C  +C+  +++ i + + +++l+v+ e +Cv+C+ C++vCP+ +++em
  gi|15668693|ref|NP_247492.1|  50 EKCISCEGCKESCPAFAIEMIyNEEYNKKLPVIdEGSCVACANCIEVCPT-GVLEM 104
                                   89*******************5455677889983669************6.88877 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 3.3e-10
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                   +ide+ C+ Cg+C  aC+   ++ ie ++ ++  +    C+ C+ C++vCP+e++i
  gi|15668693|ref|NP_247492.1| 125 IIDEEVCVRCGNCERACP---INVIERKEGKY-VINMALCISCKECIKVCPIENAI 176
                                   59****************...89998776665.56789****************99 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00093
                       Fer4_21  35 kvvedeCvGCnlCssvC 51 
                                   ++v+  Cv C +C +vC
  gi|15668693|ref|NP_247492.1| 215 HIVSGLCVSCGICKDVC 231
                                   567889**********9 PP

  == domain 4  score: 22.3 bits;  conditional E-value: 8.6e-08
                       Fer4_21   7 kCigCgkCliaCedtshqai...eidaktvlkvv.edeCvGCnlCssvCP 52 
                                   +C++Cg+C+ +C++t++        + k +  v+ ed C+GC +C +vC 
  gi|15668693|ref|NP_247492.1| 244 ECVKCGLCIEVCSTTAIRIYkpiIPKRKDICYVIdEDLCIGCRICQKVCG 293
                                   7************9887665321233344444543999***********6 PP

  == domain 5  score: 29.4 bits;  conditional E-value: 5.4e-10
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCPvedcie 58 
                                   +ided CigC  C ++C      ai+i+++t+l+++  + Cv    C+  CPv ++i+
  gi|15668693|ref|NP_247492.1| 276 VIDEDLCIGCRICQKVCG---SGAIKISKETKLPYIvPELCVRGGACARECPV-GAIK 329
                                   69***************9...599********998649**************9.9997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6  13.1   9.6e-10   1.1e-06       5      56 .]      48      98 ..      44      98 .. 0.88
   2 !   18.8   2.4   1.1e-06    0.0013       2      23 ..      80     101 ..      79     116 .. 0.78
   3 !   20.9   2.8   2.3e-07   0.00028       2      23 ..     124     145 ..     123     153 .. 0.80
   4 !   21.3  12.4   1.8e-07   0.00021       2      55 ..     153     231 ..     152     232 .. 0.96
   5 !   10.7  13.2   0.00037      0.44       5      55 ..     217     255 ..     213     256 .. 0.79
   6 !   24.7   9.1   1.6e-08   1.9e-05       3      56 .]     276     324 ..     274     324 .. 0.96
   7 !   15.8   0.3   9.6e-06     0.011       3      39 ..     307     343 ..     305     348 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9.6e-10
                       Fer4_10  5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   +++Ci C+ C+++CPa +     ++e+ +++   ++ ++C +c +C+e+CP
  gi|15668693|ref|NP_247492.1| 48 FPEKCISCEGCKESCPA-FAIEMIYNEEYNKKLPVIDEGSCVACANCIEVCP 98
                                  579**************.77778888888888888899*************9 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.1e-06
                       Fer4_10   2 vvidddtCirCgkCvkaCPadl 23 
                                   +vid+ +C+ C++C ++CP+ +
  gi|15668693|ref|NP_247492.1|  80 PVIDEGSCVACANCIEVCPTGV 101
                                   689****************944 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 2.3e-07
                       Fer4_10   2 vvidddtCirCgkCvkaCPadl 23 
                                   ++id++ C+rCg+C +aCP ++
  gi|15668693|ref|NP_247492.1| 124 LIIDEEVCVRCGNCERACPINV 145
                                   589****************943 PP

  == domain 4  score: 21.3 bits;  conditional E-value: 1.8e-07
                       Fer4_10   2 vvidddtCirCgkCvkaCPadl.........................tsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                    vi+   Ci C++C k+CP  +                         t++  ++e+ +e+  +++++ C  cg C ++C
  gi|15668693|ref|NP_247492.1| 153 YVINMALCISCKECIKVCPIENaivvvdektlkekidkafeiknkkiTGKLEIKENVIEKIPHIVSGLCVSCGICKDVC 231
                                   68999***************99************************99999999************************9 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00037
                       Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                    +  C+ Cg C+++C +        ge++ +e   kkv +C +cg C+e+C
  gi|15668693|ref|NP_247492.1| 217 VSGLCVSCGICKDVC-V--------GEIDLNE---KKVVECVKCGLCIEVC 255
                                   5668***********.5........5555555...55569*********** PP

  == domain 6  score: 24.7 bits;  conditional E-value: 1.6e-08
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   vid+d Ci+C+ C+k+C     ++ga+++ +e +   +++e C + gaC+++CP
  gi|15668693|ref|NP_247492.1| 276 VIDEDLCIGCRICQKVC-----GSGAIKISKETKLPYIVPELCVRGGACARECP 324
                                   89***************.....67*****************************9 PP

  == domain 7  score: 15.8 bits;  conditional E-value: 9.6e-06
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavr 39 
                                   +i ++ C+r g+C + CP+ + +v++ +ea+e  +vr
  gi|15668693|ref|NP_247492.1| 307 YIVPELCVRGGACARECPVGAIKVVKPEEAEEAVKVR 343
                                   68899**************887777777777666555 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   9.6   3.7e-09   4.4e-06       1      50 [.      51     101 ..      51     102 .. 0.80
   2 !   32.5  11.6   5.8e-11     7e-08       2      48 ..     131     172 ..     130     176 .. 0.93
   3 !   10.6   0.5   0.00042       0.5      33      46 ..     208     231 ..     182     235 .. 0.69
   4 !    9.9  13.2    0.0007      0.84       2      51 .]     221     260 ..     221     260 .. 0.81
   5 !   24.8   5.3   1.5e-08   1.8e-05       2      51 .]     282     328 ..     281     328 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.7e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkar.lraaseeaCigCgaCveaCpkga 50 
                                   kC++C  C e+Cpa ++++  +e++++ l   +e +C+ C  C+e+Cp+g+
  gi|15668693|ref|NP_247492.1|  51 KCISCEGCKESCPAFAIEMIYNEEYNKkLPVIDEGSCVACANCIEVCPTGV 101
                                   7*************9997666666665044455589************985 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 5.8e-11
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                                   C++Cg+C++aCp +v++++++++ +++       Ci+C++C+++Cp 
  gi|15668693|ref|NP_247492.1| 131 CVRCGNCERACPINVIERKEGKYVINMA-----LCISCKECIKVCPI 172
                                   **************************95.....5***********95 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00042
                        Fer4_9  33 e..........eaCigCgaCveaC 46 
                                   +            C++Cg C ++C
  gi|15668693|ref|NP_247492.1| 208 NviekiphivsGLCVSCGICKDVC 231
                                   245555556666899999999999 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0007
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   C++Cg C ++C  ++   d +e+k+        +C++Cg C+e+C ++ai
  gi|15668693|ref|NP_247492.1| 221 CVSCGICKDVCVGEI---DLNEKKVV-------ECVKCGLCIEVCSTTAI 260
                                   9********998775...44445555.......3************9987 PP

  == domain 5  score: 24.8 bits;  conditional E-value: 1.5e-08
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   C+gC+ C+++C +g+++ ++ ++   +  +    C+  gaC+  Cp gai
  gi|15668693|ref|NP_247492.1| 282 CIGCRICQKVCGSGAIKISKETKLPYIVPE---LCVRGGACARECPVGAI 328
                                   *********************999999774...8*************987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   3.1   0.00018      0.22       3      22 .]      45      64 ..      43      64 .. 0.83
   2 !   17.0   3.6   3.7e-06    0.0044       3      22 .]      80      99 ..      78      99 .. 0.94
   3 !   19.3   3.6   7.1e-07   0.00084       5      21 ..     126     142 ..     123     142 .. 0.94
   4 !   16.7   1.6   4.7e-06    0.0056       2      21 ..     152     171 ..     151     171 .. 0.94
   5 !   13.3   2.0   5.5e-05     0.066       3      20 ..     214     231 ..     211     231 .. 0.91
   6 !    7.9   2.9     0.003       3.6      10      21 ..     245     256 ..     240     257 .. 0.90
   7 !   16.6   6.5   5.1e-06    0.0061       3      20 ..     275     292 ..     273     292 .. 0.95
   8 !    8.7   0.7    0.0016       1.9       3      21 ..     306     324 ..     304     325 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                        Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                  +v  +++Ci+C+ C  +CPa
  gi|15668693|ref|NP_247492.1| 45 IVKFPEKCISCEGCKESCPA 64
                                  445589*****99******8 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.7e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                  +v+d+ +C++C  C+ +CP+
  gi|15668693|ref|NP_247492.1| 80 PVIDEGSCVACANCIEVCPT 99
                                  89*****************7 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 7.1e-07
                        Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                   +d++ C++Cg C  aCP
  gi|15668693|ref|NP_247492.1| 126 IDEEVCVRCGNCERACP 142
                                   8***************9 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 4.7e-06
                        Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                   ++v++ + Ci+C+ C+++CP
  gi|15668693|ref|NP_247492.1| 152 KYVINMALCISCKECIKVCP 171
                                   6899***************9 PP

  == domain 5  score: 13.3 bits;  conditional E-value: 5.5e-05
                        Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                   +++++  C++Cg+C ++C
  gi|15668693|ref|NP_247492.1| 214 PHIVSGLCVSCGICKDVC 231
                                   899999************ PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.003
                        Fer4_2  10 CigCgaCvsaCP 21 
                                   C+ Cg C+ +C 
  gi|15668693|ref|NP_247492.1| 245 CVKCGLCIEVCS 256
                                   ***********6 PP

  == domain 7  score: 16.6 bits;  conditional E-value: 5.1e-06
                        Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                   +v+d+d CigC++C+++C
  gi|15668693|ref|NP_247492.1| 275 YVIDEDLCIGCRICQKVC 292
                                   689*************** PP

  == domain 8  score: 8.7 bits;  conditional E-value: 0.0016
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   ++++++ C++ gaC   CP
  gi|15668693|ref|NP_247492.1| 306 PYIVPELCVRGGACARECP 324
                                   8999*****989******* PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   2.3   0.00012      0.15      41      58 ..      47      64 ..       7      66 .. 0.64
   2 !   10.6  12.9   0.00054      0.65       1      60 [.      51     101 ..      51     102 .. 0.85
   3 !   12.0  12.9    0.0002      0.23       2      59 ..      87     144 ..      86     146 .. 0.70
   4 !   12.2   2.0   0.00017      0.21      41      57 ..     155     171 ..     144     175 .. 0.77
   5 !   26.3   4.3   6.6e-09   7.8e-06       2      61 .]     160     236 ..     159     236 .. 0.65
   6 !    6.9   2.8    0.0077       9.2      45      57 ..     244     256 ..     237     259 .. 0.63
   7 ?    4.2  13.1     0.054        64       1      58 [.     244     294 ..     244     297 .. 0.80
   8 ?    4.8   7.6     0.034        41       2      57 ..     282     324 ..     281     328 .. 0.72
   9 ?    6.5   0.3      0.01        12       2      23 ..     313     334 ..     312     357 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                       Fer4_17 41 ekaslCieCgeCerkCPq 58
                                  +  ++Ci+C++C+++CP+
  gi|15668693|ref|NP_247492.1| 47 KFPEKCISCEGCKESCPA 64
                                  56789***********95 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00054
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60 
                                   +Ci+C+ C ++Cp +++   +++++ +++ +  ++e       ++C+ C +C ++CP g+
  gi|15668693|ref|NP_247492.1|  51 KCISCEGCKESCPAFAIEMIYNEEYNKKLPV--IDE-------GSCVACANCIEVCPTGV 101
                                   6****************88888888777555..445.......79************986 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.0002
                       Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                   C  C+ C+++Cp++    ++ +   + + + + ++ +     + C+ Cg+Cer+CP +
  gi|15668693|ref|NP_247492.1|  87 CVACANCIEVCPTGVLEMDKHRVETEGLFFDKPKYSNLIIDEEVCVRCGNCERACPIN 144
                                   *************9885554444344444444444433345578************76 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00017
                       Fer4_17  41 ekaslCieCgeCerkCP 57 
                                    ++ lCi+C+eC ++CP
  gi|15668693|ref|NP_247492.1| 155 INMALCISCKECIKVCP 171
                                   47999*******99999 PP

  == domain 5  score: 26.3 bits;  conditional E-value: 6.6e-09
                       Fer4_17   2 CiqCgyClpeCpsyea................ydnepkkllraaklglleeaeke...ekaslCieCgeCerkCPqgld 61 
                                   Ci+C+ C+++Cp  +a                 + ++kk+  +++++  e+++++    + +lC++Cg C+ +C  ++d
  gi|15668693|ref|NP_247492.1| 160 CISCKECIKVCPIENAivvvdektlkekidkaFEIKNKKITGKLEIK--ENVIEKiphIVSGLCVSCGICKDVCVGEID 236
                                   ************97665555444333333322333555666665553..444444443599*************98886 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.0077
                       Fer4_17  45 lCieCgeCerkCP 57 
                                   +C++Cg+C ++C 
  gi|15668693|ref|NP_247492.1| 244 ECVKCGLCIEVCS 256
                                   6666666666664 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.054
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                   +C +Cg C+++C++ +++  +p  + r+    ++ ++++    +lCi+C+ C+++C +
  gi|15668693|ref|NP_247492.1| 244 ECVKCGLCIEVCSTTAIRIYKPIIPKRK----DICYVID---EDLCIGCRICQKVCGS 294
                                   6*************99988777777777....4445433...389***********76 PP

  == domain 8  score: 4.8 bits;  conditional E-value: 0.034
                       Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57 
                                   Ci+C+ C ++C s+++  +++ kl +              + +lC+  g C+r+CP
  gi|15668693|ref|NP_247492.1| 282 CIGCRICQKVCGSGAIKISKETKLPYI-------------VPELCVRGGACARECP 324
                                   999999999999988866666665554.............4457777777777777 PP

  == domain 9  score: 6.5 bits;  conditional E-value: 0.01
                       Fer4_17   2 CiqCgyClpeCpsyeaydnepk 23 
                                   C + g+C++eCp +++   +p+
  gi|15668693|ref|NP_247492.1| 313 CVRGGACARECPVGAIKVVKPE 334
                                   6666777777777666555554 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  12.7   1.1e-05     0.013       3      65 .]      50     101 ..      49     101 .. 0.74
   2 !   11.1   3.3   0.00036      0.43       5      17 ..     131     143 ..     127     156 .. 0.72
   3 !   12.1   1.7   0.00017       0.2      47      64 ..     156     173 ..     144     174 .. 0.82
   4 !   16.9   7.4   5.6e-06    0.0066       4      62 ..     159     232 ..     156     235 .. 0.65
   5 !   10.1  11.9   0.00074      0.89       4      62 ..     244     293 ..     241     296 .. 0.78
   6 !    7.0   2.3    0.0068       8.1       5      16 ..     282     293 ..     278     311 .. 0.75
   7 !    9.0   0.2    0.0016       1.9       5      21 ..     313     329 ..     309     385 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                   ekCi C+ C+++Cp++  + +  ++ +++ +      ++       +sC++c +C evCp+g+
  gi|15668693|ref|NP_247492.1|  50 EKCISCEGCKESCPAFAIE-MIYNEEYNK-KL--PVIDE-------GSCVACANCIEVCPTGV 101
                                   69************99887.333333333.33..22334.......68************986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00036
                        Fer4_8   5 CieCgaCqsaCpv 17 
                                   C++Cg C+ aCp+
  gi|15668693|ref|NP_247492.1| 131 CVRCGNCERACPI 143
                                   7777777777774 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00017
                        Fer4_8  47 alwsCttcgaCtevCpvg 64 
                                   ++  C +c++C +vCp++
  gi|15668693|ref|NP_247492.1| 156 NMALCISCKECIKVCPIE 173
                                   5889************86 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 5.6e-06
                        Fer4_8   4 kCieCgaCqsaCp......vlrrtk.khlldargeaae......dvqeeqvlee..........eealwsCttcgaCtevC 61 
                                    Ci C  C + Cp      v+ ++  k++ d+  e ++               e          +   + C++cg C++vC
  gi|15668693|ref|NP_247492.1| 159 LCISCKECIKVCPienaivVVDEKTlKEKIDKAFEIKNkkitgkL--------EikenviekipHIVSGLCVSCGICKDVC 231
                                   5***********977776533333335555544444443333331........123455567889999************* PP

                        Fer4_8  62 p 62 
                                    
  gi|15668693|ref|NP_247492.1| 232 V 232
                                   5 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.00074
                        Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62 
                                   +C++Cg+C + C +   +   +  ++ + + +v +e+          C +c+ C++vC 
  gi|15668693|ref|NP_247492.1| 244 ECVKCGLCIEVCSTTAIRIYKPIIPKRKDICYVIDEDL---------CIGCRICQKVCG 293
                                   7***********87777776666666665665777666.........***********6 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.0068
                        Fer4_8   5 CieCgaCqsaCp 16 
                                   Ci+C  Cq+ C 
  gi|15668693|ref|NP_247492.1| 282 CIGCRICQKVCG 293
                                   888888888884 PP

  == domain 7  score: 9.0 bits;  conditional E-value: 0.0016
                        Fer4_8   5 CieCgaCqsaCpvlrrt 21 
                                   C++ gaC  +Cpv   +
  gi|15668693|ref|NP_247492.1| 313 CVRGGACARECPVGAIK 329
                                   88888888888865554 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   2.1       0.1   1.2e+02      60      73 ..      51      64 ..      45      71 .. 0.79
   2 !   14.3   3.1     3e-05     0.035      57      75 ..      83     101 ..      66     111 .. 0.83
   3 !    8.4  11.9     0.002       2.4      59      95 ..     129     170 ..     117     171 .. 0.76
   4 !   11.2   3.3   0.00026      0.31      50      74 ..     149     173 ..     144     185 .. 0.80
   5 !   26.5   9.8   4.8e-09   5.7e-06      19     102 ..     178     262 ..     174     271 .. 0.74
   6 ?    4.3   6.3     0.036        44      58      93 ..     279     315 ..     264     328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.1
                       Fer4_18 60 dcidcescvkvcPt 73
                                  +ci+ce c + cP 
  gi|15668693|ref|NP_247492.1| 51 KCISCEGCKESCPA 64
                                  68888888888885 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3e-05
                       Fer4_18  57 gagdcidcescvkvcPtgi 75 
                                   ++g c++c  c++vcPtg+
  gi|15668693|ref|NP_247492.1|  83 DEGSCVACANCIEVCPTGV 101
                                   6899*************98 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.002
                       Fer4_18  59 gdcidcescvkvcPtgidirk.Glql.e...ciscllcidac 95 
                                     c+ c+ c + cP+++  rk G  + +   cisc +ci  c
  gi|15668693|ref|NP_247492.1| 129 EVCVRCGNCERACPINVIERKeGKYViNmalCISCKECIKVC 170
                                   56************99766652543221335********999 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00026
                       Fer4_18  50 keerkekgagdcidcescvkvcPtg 74 
                                   ke +   +++ ci+c+ c+kvcP++
  gi|15668693|ref|NP_247492.1| 149 KEGKYVINMALCISCKECIKVCPIE 173
                                   55566667889************86 PP

  == domain 5  score: 26.5 bits;  conditional E-value: 4.8e-09
                       Fer4_18  19 lydeetllvvydakrGekiag.rkkekkalkekeerkekgagdcidcescvkvcPtgidirkGlqleciscllcidacdkv 98 
                                   ++de+tl+   d++   k ++ + k + + +  e+  +  +g c++c+ c +vc  +id+ +   +ec++c+lci+ c++ 
  gi|15668693|ref|NP_247492.1| 178 VVDEKTLKEKIDKAFEIKNKKiTGKLEIKENVIEKIPHIVSGLCVSCGICKDVCVGEIDLNEKKVVECVKCGLCIEVCSTT 258
                                   5666666666665543333320334444555666777778999***********************************987 PP

                       Fer4_18  99 mekl 102
                                     ++
  gi|15668693|ref|NP_247492.1| 259 AIRI 262
                                   6555 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.036
                       Fer4_18  58 agdcidcescvkvcPtg.idirkGlqleciscllcid 93 
                                   +  ci c+ c kvc  g i i k  +l  i   lc+ 
  gi|15668693|ref|NP_247492.1| 279 EDLCIGCRICQKVCGSGaIKISKETKLPYIVPELCVR 315
                                   556***********98659********9999999994 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   2.1   0.00024      0.29       1      15 [.      49      63 ..      49      73 .. 0.92
   2 !    6.8   4.0    0.0091        11       3      17 .]      86     100 ..      84     100 .. 0.92
   3 !   15.4   2.3   1.6e-05     0.019       2      15 ..     129     142 ..     128     153 .. 0.91
   4 !   13.1   0.8   9.1e-05      0.11       3      15 ..     159     171 ..     156     185 .. 0.90
   5 ?    4.4   4.8     0.057        68       3      14 ..     220     231 ..     218     231 .. 0.92
   6 !    6.8   2.9    0.0095        11       4      16 ..     245     257 ..     239     258 .. 0.90
   7 !    7.0   3.5    0.0078       9.3       2      14 ..     280     292 ..     279     295 .. 0.88
   8 ?    4.9   0.8     0.037        44       2      17 .]     311     326 ..     310     326 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                        Fer4_4  1 qerCigCgsCvaaCP 15
                                  +e+Ci C  C  +CP
  gi|15668693|ref|NP_247492.1| 49 PEKCISCEGCKESCP 63
                                  69************* PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0091
                        Fer4_4   3 rCigCgsCvaaCPqg 17 
                                   +C+ C  C+ +CP+g
  gi|15668693|ref|NP_247492.1|  86 SCVACANCIEVCPTG 100
                                   7************86 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.6e-05
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   e C++Cg C++aCP
  gi|15668693|ref|NP_247492.1| 129 EVCVRCGNCERACP 142
                                   67***********9 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 9.1e-05
                        Fer4_4   3 rCigCgsCvaaCP 15 
                                    Ci C+ C+ +CP
  gi|15668693|ref|NP_247492.1| 159 LCISCKECIKVCP 171
                                   5***********9 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.057
                        Fer4_4   3 rCigCgsCvaaC 14 
                                    C+ Cg C ++C
  gi|15668693|ref|NP_247492.1| 220 LCVSCGICKDVC 231
                                   5*********** PP

  == domain 6  score: 6.8 bits;  conditional E-value: 0.0095
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   C+ Cg C+ +C++
  gi|15668693|ref|NP_247492.1| 245 CVKCGLCIEVCST 257
                                   ***********85 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.0078
                        Fer4_4   2 erCigCgsCvaaC 14 
                                   + CigC+ C  +C
  gi|15668693|ref|NP_247492.1| 280 DLCIGCRICQKVC 292
                                   78*********** PP

  == domain 8  score: 4.9 bits;  conditional E-value: 0.037
                        Fer4_4   2 erCigCgsCvaaCPqg 17 
                                   e C++ g+C + CP+g
  gi|15668693|ref|NP_247492.1| 311 ELCVRGGACARECPVG 326
                                   789999********86 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   1.3    0.0007      0.83       4      18 ..      50      64 ..      49      76 .. 0.91
   2 !   13.6   1.6   6.2e-05     0.074       1      22 [.      82     104 ..      82     110 .. 0.82
   3 !    8.5   3.4    0.0024       2.9       1      19 [.     126     144 ..     126     156 .. 0.76
   4 !    7.3   3.8    0.0056       6.7       2      17 ..     156     171 ..     155     192 .. 0.90
   5 ?    3.8   1.0     0.071        85       6      16 ..     221     231 ..     218     240 .. 0.92
   6 ?    4.1   2.7     0.057        68       5      17 ..     244     256 ..     242     258 .. 0.89
   7 !    8.5   3.1    0.0024       2.8       1      16 [.     277     292 ..     277     294 .. 0.94
   8 ?    2.8   0.2      0.14   1.7e+02      48      58 .]     320     330 ..     311     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0007
                       Fer4_13  4 dtCiacgaCvelaPd 18
                                  ++Ci+c+ C e +P 
  gi|15668693|ref|NP_247492.1| 50 EKCISCEGCKESCPA 64
                                  79************7 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.2e-05
                       Fer4_13   1 VDrdtCiacgaCvelaPd.vFee 22 
                                   +D+ +C+ac++C e++P  v e+
  gi|15668693|ref|NP_247492.1|  82 IDEGSCVACANCIEVCPTgVLEM 104
                                   7999*************635555 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0024
                       Fer4_13   1 VDrdtCiacgaCvelaPdv 19 
                                   +D++ C+ cg+C  ++P  
  gi|15668693|ref|NP_247492.1| 126 IDEEVCVRCGNCERACPIN 144
                                   899**************55 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0056
                       Fer4_13   2 DrdtCiacgaCvelaP 17 
                                   +   Ci+c+ C +++P
  gi|15668693|ref|NP_247492.1| 156 NMALCISCKECIKVCP 171
                                   6678***********9 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.071
                       Fer4_13   6 CiacgaCvela 16 
                                   C++cg+C +++
  gi|15668693|ref|NP_247492.1| 221 CVSCGICKDVC 231
                                   ********999 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.057
                       Fer4_13   5 tCiacgaCvelaP 17 
                                   +C+ cg+C e++ 
  gi|15668693|ref|NP_247492.1| 244 ECVKCGLCIEVCS 256
                                   7**********96 PP

  == domain 7  score: 8.5 bits;  conditional E-value: 0.0024
                       Fer4_13   1 VDrdtCiacgaCvela 16 
                                   +D+d Ci+c +C +++
  gi|15668693|ref|NP_247492.1| 277 IDEDLCIGCRICQKVC 292
                                   89************99 PP

  == domain 8  score: 2.8 bits;  conditional E-value: 0.14
                       Fer4_13  48 adaCPvesIgv 58 
                                   a +CPv +I+v
  gi|15668693|ref|NP_247492.1| 320 ARECPVGAIKV 330
                                   56899999986 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   2.2     0.023        27       1      17 [.      51      67 ..      51      84 .. 0.78
   2 !    7.8   2.9     0.005         6      81      94 ..      86      99 ..      68     101 .. 0.64
   3 ?    6.5   3.9     0.013        15       2      15 ..      87     100 ..      86     113 .. 0.83
   4 !   13.2   0.5    0.0001      0.12      65      95 ..     114     144 ..     101     145 .. 0.79
   5 !    9.3   1.1    0.0017       2.1       2      25 ..     160     185 ..     159     200 .. 0.77
   6 ?    6.4   2.4     0.014        16      78      96 .]     217     235 ..     193     235 .. 0.71
   7 ?    4.0   4.3     0.075        90       1      15 [.     244     258 ..     244     264 .. 0.80
   8 ?    6.8   3.1      0.01        12      61      93 ..     261     293 ..     256     296 .. 0.81
   9 ?    2.4   0.4      0.24   2.9e+02       2      24 ..     313     335 ..     312     400 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.023
                       Fer4_22  1 rClsCgaCtlvCptCsC 17
                                  +C+sC  C+  Cp+   
  gi|15668693|ref|NP_247492.1| 51 KCISCEGCKESCPAFAI 67
                                  7***********98654 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.005
                       Fer4_22 81 gCvGCgRCieacpv 94
                                  +Cv C  Cie+cp+
  gi|15668693|ref|NP_247492.1| 86 SCVACANCIEVCPT 99
                                  55555555555554 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.013
                       Fer4_22   2 ClsCgaCtlvCptC 15 
                                   C++C++C  vCpt 
  gi|15668693|ref|NP_247492.1|  87 CVACANCIEVCPTG 100
                                   99999999999995 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.0001
                       Fer4_22  65 rllhklsefkekfgesgCvGCgRCieacpvk 95 
                                    +++k ++ +  ++e++Cv Cg C++acp +
  gi|15668693|ref|NP_247492.1| 114 LFFDKPKYSNLIIDEEVCVRCGNCERACPIN 144
                                   46778888888889**************976 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.0017
                       Fer4_22   2 ClsCgaCtlvCptCsCfdvedet..k 25 
                                   C+sC +C  vCp    + v+de+  k
  gi|15668693|ref|NP_247492.1| 160 CISCKECIKVCPIENAIVVVDEKtlK 185
                                   ************99999999888442 PP

  == domain 6  score: 6.4 bits;  conditional E-value: 0.014
                       Fer4_22  78 gesgCvGCgRCieacpvki 96 
                                    +  Cv Cg C+++c  +i
  gi|15668693|ref|NP_247492.1| 217 VSGLCVSCGICKDVCVGEI 235
                                   4567999999999998765 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.075
                       Fer4_22   1 rClsCgaCtlvCptC 15 
                                   +C++Cg C  vC+t 
  gi|15668693|ref|NP_247492.1| 244 ECVKCGLCIEVCSTT 258
                                   588888888888875 PP

  == domain 8  score: 6.8 bits;  conditional E-value: 0.01
                       Fer4_22  61 rlrqrllhklsefkekfgesgCvGCgRCieacp 93 
                                   r+ + ++ k +++   ++e  C+GC  C+++c 
  gi|15668693|ref|NP_247492.1| 261 RIYKPIIPKRKDICYVIDEDLCIGCRICQKVCG 293
                                   5566677788888889999*************6 PP

  == domain 9  score: 2.4 bits;  conditional E-value: 0.24
                       Fer4_22   2 ClsCgaCtlvCptCsCfdvedet 24 
                                   C++ gaC+  Cp      v+ e 
  gi|15668693|ref|NP_247492.1| 313 CVRGGACARECPVGAIKVVKPEE 335
                                   77788888888876655555444 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.2     0.077        92       1      12 [.      52      63 ..      52      66 .. 0.93
   2 ?    8.2   6.3    0.0045       5.3       1      14 [.      87     100 ..      87     101 .. 0.93
   3 ?    9.7   5.0    0.0015       1.8       1      14 [.     131     144 ..     131     145 .. 0.92
   4 ?   11.1   2.7   0.00053      0.64       1      15 []     160     175 ..     160     175 .. 0.86
   5 ?   -1.7   5.6       6.5   7.7e+03       1      11 [.     221     231 ..     221     233 .. 0.94
   6 ?    8.9   4.4    0.0026       3.1       1      12 [.     245     256 ..     245     259 .. 0.90
   7 ?    7.2   4.4    0.0092        11       1      15 []     282     296 ..     282     296 .. 0.94
   8 ?    5.8   2.9     0.027        32       4      15 .]     313     327 ..     312     327 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.077
                        Fer4_3  1 CtgCgaCvevCP 12
                                  C+ C+ C e+CP
  gi|15668693|ref|NP_247492.1| 52 CISCEGCKESCP 63
                                  9***99*****9 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0045
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   C+ C  C evCP+g
  gi|15668693|ref|NP_247492.1|  87 CVACANCIEVCPTG 100
                                   999*9*******98 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0015
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   C+ Cg C+++CP +
  gi|15668693|ref|NP_247492.1| 131 CVRCGNCERACPIN 144
                                   99**********76 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00053
                        Fer4_3   1 CtgCgaCvevCP.vgA 15 
                                   C+ C  C +vCP ++A
  gi|15668693|ref|NP_247492.1| 160 CISCKECIKVCPiENA 175
                                   ************4465 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 6.5
                        Fer4_3   1 CtgCgaCvevC 11 
                                   C+ Cg C +vC
  gi|15668693|ref|NP_247492.1| 221 CVSCGICKDVC 231
                                   99*******99 PP

  == domain 6  score: 8.9 bits;  conditional E-value: 0.0026
                        Fer4_3   1 CtgCgaCvevCP 12 
                                   C+ Cg+C evC 
  gi|15668693|ref|NP_247492.1| 245 CVKCGLCIEVCS 256
                                   9**********6 PP

  == domain 7  score: 7.2 bits;  conditional E-value: 0.0092
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+gC+ C +vC +gA
  gi|15668693|ref|NP_247492.1| 282 CIGCRICQKVCGSGA 296
                                   ***********8887 PP

  == domain 8  score: 5.8 bits;  conditional E-value: 0.027
                        Fer4_3   4 C...gaCvevCPvgA 15 
                                   C   gaC + CPvgA
  gi|15668693|ref|NP_247492.1| 313 CvrgGACARECPVGA 327
                                   43337*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1685  (0.0939818); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 2444.65
//
Query:       gi|15668694|ref|NP_247493.1|  [L=380]
Description: carbon monoxide dehydrogenase hydrogenase subunit CooH [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-47  159.9   1.5    4.8e-38  130.8   0.5    2.1  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    3.9e-13   49.2   2.8    3.9e-13   49.2   2.8    3.2  4  NiFeSe_Hases    Nickel-dependent hydrogenase
  ------ inclusion threshold ------
       0.12   12.5   0.1       0.23   11.5   0.1    1.5  1  NAD1            Novel AID APOBEC clade 1


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.8   0.5   8.1e-42   4.8e-38       5     166 ..     123     285 ..     120     291 .. 0.94
   2 !   28.4   0.0   1.4e-10   8.2e-07     205     271 .]     295     362 ..     283     362 .. 0.89

  Alignments for each domain:
  == domain 1  score: 130.8 bits;  conditional E-value: 8.1e-42
                                   HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSSSS- CS
                Complex1_49kDa   5 ltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkgvgv 85 
                                    t+ +++++ Re i+dl+e++tG+R+++ y  iGGv+rD++++++++i++ l+ +e++l+++ +++ + +++  R k++g+
  gi|15668694|ref|NP_247493.1| 123 ETLAMWLLNVREIIMDLMEMITGNRVNMGYNVIGGVRRDINREMMDEIYKKLDIFEDELKNIIEVFETGPLIALRSKEIGI 203
                                   6999***************************************************************************** PP

                                   BSHHHHHHHTT-SSSSGGGT-.TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--...S- CS
                Complex1_49kDa  86 lskeealelgltGpvlRasGv.kyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpe..gp 163
                                   l  +e+++  ++Gp+ R+sG+ + D R     + Y+el+f+ +++eegD ++R++vr eE+ +S+++i+ ale+++e  g+
  gi|15668694|ref|NP_247493.1| 204 LPYHEVMRTRAVGPICRGSGLpESDWRLR--HSTYQELKFKPVWREEGDNFARMMVRHEEIIESVRLIREALEHYEEcsGD 282
                                   ********************944799987..68*****************************************9876666 PP

                                   SB- CS
                Complex1_49kDa 164 vla 166
                                   + +
  gi|15668694|ref|NP_247493.1| 283 IRV 285
                                   655 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.4e-10
                                   EEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS.-SGGGTHHHHTT---HHHHH- CS
                Complex1_49kDa 205 yaavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkge.llaDvvailgsldivlgevDR 271
                                     + Eap+Ge+++ +   ++    r+ ir+p+ +nl+a++++lk + ++aD+v ++ s+d+++++++R
  gi|15668694|ref|NP_247493.1| 295 EWRNEAPRGEVTYRMEITDGGIIKRIMIRTPTVMNLEAYKYMLKTCpTVADAVSAYTSIDPCVSCTER 362
                                   5578*************999***********************98758***************99887 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   2.8   6.5e-17   3.9e-13       1      68 [.      44     111 ..      44     121 .. 0.95
   2 ?   -1.1   0.0      0.11   6.7e+02     157     202 ..     130     175 ..     120     189 .. 0.73
   3 ?    1.8   0.0     0.015        87     420     447 ..     290     317 ..     251     334 .. 0.70
   4 ?   -1.3   0.7      0.12   7.4e+02     494     503 ..     351     360 ..     338     361 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 6.5e-17
                                   --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHH CS
                  NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhiv 68 
                                   RG+E+i++g+  +   +l++R+CG+C +vH+++ ++++e+  +i+ip++a+++r +    + +h+h++
  gi|15668694|ref|NP_247493.1|  44 RGIEKIMEGKHCHKGIHLAERVCGICSYVHTMTFAECIEHISKIEIPDKAKYLRVVTCELERIHSHLI 111
                                   9*****************************************************************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.11
                                   HHHHHHHTHHHHHHHSSSSS--.EBTTBESSGBGSBSHHHHHHHHH CS
                  NiFeSe_Hases 157 LelqrkaakivaifggknPhpqslvvGGvtcaidllnaerlaevks 202
                                   L++++ ++ ++ +++g   ++   v+GGv   i+   ++++ +  +
  gi|15668694|ref|NP_247493.1| 130 LNVREIIMDLMEMITGNRVNMGYNVIGGVRRDINREMMDEIYKKLD 175
                                   7888899999999999999999999****99966644444433333 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.015
                                   SEEEEEEEEEETTEEEEEEEEEETTEEE CS
                  NiFeSe_Hases 420 keakGvglveapRGaLsHwikikdgkie 447
                                   k  kG    eapRG  +  ++i dg i 
  gi|15668694|ref|NP_247493.1| 290 KGGKGEWRNEAPRGEVTYRMEITDGGII 317
                                   347888899*************998664 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.12
                                   HHT--BHHHH CS
                  NiFeSe_Hases 494 hSfDPClACa 503
                                    S DPC++C+
  gi|15668694|ref|NP_247493.1| 351 TSIDPCVSCT 360
                                   699******5 PP

>> NAD1  Novel AID APOBEC clade 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.8e-05      0.23      56     104 ..     330     378 ..     314     380 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                          NAD1  56 lnkikslklldpsqkykvtwylswSPCseCasklaeflkerpnvtLrIf 104
                                   l+ +k +  ++p+    v  y+s  PC +C+++ +  +k+ +++ ++I+
  gi|15668694|ref|NP_247493.1| 330 LEAYKYMLKTCPTVADAVSAYTSIDPCVSCTERCIVAVKDGKEIPISIK 378
                                   56677777778999999****************9999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2336.42
//
Query:       gi|15668695|ref|NP_247494.1|  [L=148]
Description: carbon monoxide dehydrogenase hydrogenase subunit CooL [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-30  105.7   0.5    1.8e-30  105.4   0.5    1.1  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.5     1e-34   1.8e-30       1     130 [.      21     130 ..      21     131 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 1e-34
                                   -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESH CS
                   Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGt 81 
                                   C+Gc+i++ a+  + +d+     ++y++ ++++++         eadvl+v+G+vt + +e+l+ ++e ++++k+v+avG+
  gi|15668695|ref|NP_247494.1|  21 CNGCDIEIVACLAPRYDI-----EQYGIYVHNNPR---------EADVLLVTGPVTLQWAERLKEIYEKTPEPKIVVAVGA 87 
                                   ******************.....************.........9************************************ PP

                                   HHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHH CS
                   Oxidored_q6  82 CAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetlla 130
                                   CA +GGi++ ++    +  vg++++v+pvd +ipGCPp+p +i+et+l+
  gi|15668695|ref|NP_247494.1|  88 CALSGGIFKEGH----V--VGGVDKVIPVDAKIPGCPPRPSEIIETILK 130
                                   ********6555....5..78*************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1152.87
//
Query:       gi|15668696|ref|NP_247495.1|  [L=140]
Description: hypothetical protein MJ_0517 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-51  172.3   1.4    4.2e-51  171.9   1.4    1.2  1  DUF1959   Domain of unknown function (DUF1959)


Domain annotation for each model (and alignments):
>> DUF1959  Domain of unknown function (DUF1959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.9   1.4   2.4e-55   4.2e-51       1     116 []      22     138 ..      22     138 .. 0.99

  Alignments for each domain:
  == domain 1  score: 171.9 bits;  conditional E-value: 2.4e-55
                                   HHHHHTSHHH.HHHTTTTTTTTGGGTHHHHHHHHHHHS-HHHHHHHHHHHHTTHHHHHHHHHHHHTTHHHHTTTS--S-HH CS
                       DUF1959   1 klrilksfry.eedvivPlskelkisveeledilvkklDmasleelhatvesakkeclkrkldiDLrlcWlsDvleliske 80 
                                   k+++lk++r+ ++dv++P++k+lki+vee+++i++kklD+as++elha++e+ak++cl+rk+diDL+lcWlsD+++li+ke
  gi|15668696|ref|NP_247495.1|  22 KMNVLKDNRFlMDDVFIPIAKALKIEVEEVIEIFAKKLDFASCYELHAYAEQAKMGCLGRKVDIDLGLCWLSDFFGLIKKE 102
                                   89******************************************************************************* PP

                                   HHHHHHHHHHHHHH.TT--HHHHHHHHHHHHHHHHT CS
                       DUF1959  81 dadeikkkvveevllkkkeYeealeeGRkllvellk 116
                                   +ad i+kkvve++ll kk+Y+ealeeGR+++++llk
  gi|15668696|ref|NP_247495.1| 103 EADLIRKKVVESYLLYKKPYKEALEEGRQMIIKLLK 138
                                   **********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 962.61
//
Query:       gi|15668697|ref|NP_247496.1|  [L=94]
Description: hypothetical protein MJ_0518 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-31  108.5   5.0    2.1e-31  108.1   5.0    1.1  1  DUF2104    Predicted membrane protein (DUF2104)
  ------ inclusion threshold ------
       0.66    8.8   6.0       0.27   10.0   3.4    1.6  1  LptF_LptG  Lipopolysaccharide export system permease LptF/Lpt


Domain annotation for each model (and alignments):
>> DUF2104  Predicted membrane protein (DUF2104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   5.0   2.3e-35   2.1e-31       2      99 ..       5      92 ..       4      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 2.3e-35
                       DUF2104  2 illlaviafivGsilGLlysYkkysepyvekkidklalvlaviGwllllnvsllvlvpsyilitigllliglvlgmRpGYGri 84
                                  +l+la+i fi+G+++GL+ysY+kys+pyvek idk+al ++v+G++l        + p    +++g+llig++lgmRpGYGr+
  gi|15668697|ref|NP_247496.1|  5 ELNLAIILFIIGNFIGLEYSYRKYSSPYVEKGIDKFALAISVFGGIL-------INSPL---YMLGCLLIGFPLGMRPGYGRV 77
                                  6889*******************************************.......56774...569****************** PP

                       DUF2104 85 etviGiivallvyll 99
                                  e+v+G+ val++y+l
  gi|15668697|ref|NP_247496.1| 78 EFVVGLAVALFLYFL 92
                                  *************98 PP

>> LptF_LptG  Lipopolysaccharide export system permease LptF/LptG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.4     3e-05      0.27     277     317 ..      53      91 ..      50      93 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3e-05
                     LptF_LptG 277 alplaclvfaliaaplglvkrrggrglrlliaillfvlyyv 317
                                     pl++l  +li++plg+++  +gr+  ++++++++++ y+
  gi|15668697|ref|NP_247496.1|  53 NSPLYMLGCLLIGFPLGMRP-GYGRVE-FVVGLAVALFLYF 91 
                                   579****************9.555554.6666666666444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 625.93
//
Query:       gi|15668698|ref|NP_247497.1|  [L=84]
Description: hypothetical protein MJ_0519 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.38   10.5   3.8       0.14   11.8   1.5    1.6  2  ISK_Channel  Slow voltage-gated potassium channel
          2    8.0  11.1        2.4    7.8  11.1    1.0  1  PRA1         PRA1 family protein
        3.8    7.1   5.2       0.28   10.8   0.3    1.5  2  SARAF        SOCE-associated regulatory factor of calcium hom
        6.3    6.7   6.6        1.7    8.5   2.2    2.0  2  DUF5337      Family of unknown function (DUF5337)


Domain annotation for each model (and alignments):
>> ISK_Channel  Slow voltage-gated potassium channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.61   2.7e+03      51      62 ..       9      20 ..       4      26 .. 0.67
   2 ?   11.8   1.5   3.2e-05      0.14      29      52 ..      52      75 ..      23      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.61
                   ISK_Channel 51 gfftlGimlsyi 62
                                   fft+  +++ i
  gi|15668698|ref|NP_247497.1|  9 YFFTIACIIAVI 20
                                  577777766655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.2e-05
                   ISK_Channel 29 laarseddklevlyillllgffgf 52
                                   +  ++ +++evl++ll+l+ff++
  gi|15668698|ref|NP_247497.1| 52 KKIAHKMEDIEVLFMLLVLAFFAY 75
                                  4445567899************98 PP

>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  11.1   0.00053       2.4      42     108 ..      11      77 ..       3      82 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00053
                          PRA1  42 Ylivvllvlllslltnplslivllllvlawlflyf..lr.seplvlfgrelsdrvvlivllvvsvlllfl 108
                                   ++i  ++++++++l+n l++ v+ ++++  l+l +  ++ ++++    ++++d +vl++llv+++++  +
  gi|15668698|ref|NP_247497.1|  11 FTIACIIAVIYCVLVNLLQINVIPVVLAFSLILILtiSTiNKKI---AHKMEDIEVLFMLLVLAFFAYAI 77 
                                   23444777888999999999888777776666665323367777...8999999********99998665 PP

>> SARAF  SOCE-associated regulatory factor of calcium homoeostasis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.6      0.73   3.3e+03     160     177 ..       7      24 ..       2      32 .. 0.57
   2 ?   10.8   0.3   6.2e-05      0.28     154     181 ..      55      82 ..      42      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.73
                         SARAF 160 asllfvvlvllviayivy 177
                                     ++f+++ ++ ++y v 
  gi|15668698|ref|NP_247497.1|   7 YIYFFTIACIIAVIYCVL 24 
                                   445566666666666554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 6.2e-05
                         SARAF 154 ksssssasllfvvlvllviayivykafl 181
                                   +++ +++++lf++lvl+++ay +yk+++
  gi|15668698|ref|NP_247497.1|  55 AHKMEDIEVLFMLLVLAFFAYAIYKLYI 82 
                                   5667889******************986 PP

>> DUF5337  Family of unknown function (DUF5337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2     0.082   3.7e+02      43      64 ..       7      29 ..       2      32 .. 0.69
   2 ?    8.5   2.2   0.00038       1.7      12      63 ..      29      81 ..      26      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.082
                       DUF5337 43 yalLfdLaAlAaliwa.lvvtyq 64
                                  y  +f +a + a i+  lv+ +q
  gi|15668698|ref|NP_247497.1|  7 YIYFFTIACIIAVIYCvLVNLLQ 29
                                  56678888888888862455555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00038
                       DUF5337 12 kgrlvalviavtmllwlgaqwigeqlgls.nRyalLfdLaAlAaliwalvvty 63
                                  ++ ++ +v+a + +l l ++ i +++    + +++Lf L +lA +++a+ + y
  gi|15668698|ref|NP_247497.1| 29 QINVIPVVLAFSLILILTISTINKKIAHKmEDIEVLFMLLVLAFFAYAIYKLY 81
                                  6678899999999999999999998865415689**************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1318  (0.0735122); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 538.47
//
Query:       gi|15668699|ref|NP_247498.1|  [L=295]
Description: NADH-ubiquinone oxidoreductase subunit 1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-31  108.1  19.7    6.4e-31  107.8  19.7    1.0  1  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.8  19.7   3.6e-35   6.4e-31       7     271 ..      15     264 ..       9     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 3.6e-35
                                   HHHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTTS- CS
                        NADHdh   7 lvvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallafaviP 87 
                                   ++ ++lv  ll +l Rk++Ariq R GP      +++q l  +lK+ +Ke ++p +a + l+++  +l +++ l+a ++i 
  gi|15668699|ref|NP_247498.1|  15 TIHAFLVGSLLLGLHRKIMARIQGRPGP------PIIQYLLHTLKFYVKEITFPITAGNPLYIFVALLDIAIWLAA-LIIA 88 
                                   4445556669******************......9****************************9988877666554.5555 PP

                                   SSSSSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHCCCT CS
                        NADHdh  88 fgevladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagslslseiveaqee 168
                                        +d++ +ll+i+ +  l+ ++    G++s+s+Y  +G++Rs+    + Ev+l+ ++ a+ l+++s+ +s+i ++qe 
  gi|15668699|ref|NP_247498.1|  89 -----IDFKSSLLIIIGIYVLQKIVEHGCGLSSGSPYGKIGGVRSVFS-AAAEVPLFAVVAAIYLTTHSVLISDILSYQEI 163
                                   .....57999**********************************9976.678***************************86 PP

                                   T.-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHHHHHHHCT.SS-HCCS CS
                        NADHdh 169 i.wfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlvsalavllFlgGwllpfs 248
                                   +  +++ +++ +++f+i l+ ++   PF ++ + +++v+G++tE+ g+  a++++ae ++ +++  l++++F+g     ++
  gi|15668699|ref|NP_247498.1| 164 HgSLLFKMPICAFAFFILLVSKAPNSPFGIVKG-KDIVSGYMTEHYGLLGAIIYIAEAIAYFVLLWLFIAVFIGPL--VIN 241
                                   64458999**********************998.69*************************************864..233 PP

                                   HHHHHHHHHHHHHHHHHHHHHC- CS
                        NADHdh 249 gllwfllKvllllflfiwiratl 271
                                   + +++l+ ++++ +++++++   
  gi|15668699|ref|NP_247498.1| 242 SPVLTLAVMVVMTVILAFVNGLT 264
                                   44444444444444444555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2022.92
//
Query:       gi|15668700|ref|NP_247499.1|  [L=69]
Description: hypothetical protein MJ_0521 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.022   14.6   1.2      0.027   14.2   1.2    1.1  1  IncD          Inclusion membrane protein D
      0.024   13.4   0.3      0.024   13.4   0.3    1.1  1  DUF2206       Predicted membrane protein (DUF2206)
       0.05   12.4   0.5      0.052   12.3   0.5    1.0  1  DUF2207       Predicted membrane protein (DUF2207)
       0.25   11.7   1.1        1.8    8.9   1.1    1.9  1  Orf78         Orf78 (ac78)
       0.49   10.5   4.2        2.8    8.0   0.7    2.1  2  CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit


Domain annotation for each model (and alignments):
>> IncD  Inclusion membrane protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.2   7.6e-06     0.027      46      82 ..      15      53 ..      12      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.6e-06
                          IncD 46 lavallvvagl.lfsgvlcspvsvlaa.slffgvgafll 82
                                  l + ll v g+ ++ g++c  + ++a  sl++g+gaf++
  gi|15668700|ref|NP_247499.1| 15 LIIGLLCVIGIvMLNGLICYVLYIIAVpSLLYGIGAFII 53
                                  567889888862579******99998659********97 PP

>> DUF2206  Predicted membrane protein (DUF2206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   6.8e-06     0.024     170     203 ..       2      35 ..       1      51 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-06
                       DUF2206 170 salntaRlyqilliflapffiiGgialiklikkv 203
                                   ++++ +R y +  ++++ +++iG+++l +li  v
  gi|15668700|ref|NP_247499.1|   2 KNMDEERKYGLYSLIIGLLCVIGIVMLNGLICYV 35 
                                   689*************************999776 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   1.4e-05     0.052     381     438 ..       8      59 ..       1      64 [. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                       DUF2207 381 kklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrt 438
                                    k+++++l++++l++i+i+++++l+   ++ l+i+++  ll +i++++++++   rr+
  gi|15668700|ref|NP_247499.1|   8 RKYGLYSLIIGLLCVIGIVMLNGLI---CYVLYIIAVPSLLYGIGAFIIPKT---RRK 59 
                                   4556666666666666666655554...888888888888888888888854...344 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.1   0.00049       1.8      63      95 ..      28      60 ..       1      66 [. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00049
                         Orf78 63 lnillisllavvcvlvllyviyYfvilrerqks 95
                                  ln l+ ++l +++v  lly i  f+i + r+k 
  gi|15668700|ref|NP_247499.1| 28 LNGLICYVLYIIAVPSLLYGIGAFIIPKTRRKD 60
                                  455677777888888888888888888887776 PP

>> CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.013        48      17      37 ..      20      40 ..      14      43 .. 0.86
   2 ?    8.0   0.7   0.00078       2.8      26      37 ..      43      54 ..      40      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.013
                  CytB6-F_Fe-S 17 vGaialtaaaaLyPvvkFFiP 37
                                  + +i+ + +  L  +v ++i+
  gi|15668700|ref|NP_247499.1| 20 LCVIGIVMLNGLICYVLYIIA 40
                                  56899999999********97 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00078
                  CytB6-F_Fe-S 26 aaLyPvvkFFiP 37
                                  ++Ly+ ++F+iP
  gi|15668700|ref|NP_247499.1| 43 SLLYGIGAFIIP 54
                                  79*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 521.09
//
Query:       gi|15668701|ref|NP_247500.1|  [L=218]
Description: NADH dehydrogenase I [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.1e-104  346.7  14.8   4.6e-104  346.6  14.8    1.0  1  NADHdeh_related  NADH dehydrogenase I, subunit N related prot


Domain annotation for each model (and alignments):
>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.6  14.8  2.6e-108  4.6e-104       1     219 []       1     218 []       1     218 [] 0.99

  Alignments for each domain:
  == domain 1  score: 346.6 bits;  conditional E-value: 2.6e-108
               NADHdeh_related   1 mlesisgellfvipfGdivaylseftlilfvvalifvilvilskpekqveiefgkdaiklkvvsldelkirrllaivcgla 81 
                                   m+esi+g+l++++pfGdiv+ +sef++i f++a+if+i+v+l+kpekq+e++++k+++kl+vv+l+elkirr++aivcg+a
  gi|15668701|ref|NP_247500.1|   1 MIESITGYLFGIVPFGDIVFGFSEFSIIGFITAVIFTIIVYLTKPEKQLEAQKFKIEDKLEVVTLNELKIRRMMAIVCGIA 81 
                                   89******************************************************************************* PP

               NADHdeh_related  82 tlgavvtgdvfnftlflaliGianiGivaavkkefvleaafnyGlvaliatlplfggaalilastGtlsifelaklagdvl 162
                                   t+ga++t+d+f+++lfl+l+GianiGiv+avk+e+vl+a+++yGl+a+iatlplfg+a++ila+tGtlsifel k++++ l
  gi|15668701|ref|NP_247500.1|  82 TAGAMLTYDLFDYALFLTLVGIANIGIVSAVKREWVLNASYQYGLIAMIATLPLFGSAGMILAKTGTLSIFELPKIQTS-L 161
                                   ******************************************************************************7.* PP

               NADHdeh_related 163 liaklllvlGvvGetGvaPfyaakaeifrapgapyillihlsslllivrvveilltv 219
                                   l++k+++++G++GetG+aPfyaakae+frapg+pyil+ihlsslllivr+veillt+
  gi|15668701|ref|NP_247500.1| 162 LFEKIIFAAGMAGETGIAPFYAAKAEMFRAPGSPYILMIHLSSLLLIVRTVEILLTI 218
                                   *******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1628.38
//
Query:       gi|15668702|ref|NP_247501.1|  [L=234]
Description: hypothetical protein MJ_0523 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-88  294.9  12.8    3.2e-88  294.7  12.8    1.0  1  DUF2105   Predicted membrane protein (DUF2105)
  ------ inclusion threshold ------
       0.19   11.9   0.0       0.41   10.8   0.0    1.5  1  AnkUBD    Ankyrin ubiquitin-binding domain
        1.9    9.0   4.7        7.1    7.1   0.3    2.4  2  DUF4231   Protein of unknown function (DUF4231)


Domain annotation for each model (and alignments):
>> DUF2105  Predicted membrane protein (DUF2105)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.7  12.8   5.4e-92   3.2e-88       2     199 ..       9     230 ..       8     231 .. 0.98

  Alignments for each domain:
  == domain 1  score: 294.7 bits;  conditional E-value: 5.4e-92
                       DUF2105   2 sslykkailvglivgiisllaisrekedlealiltdlveiamlvivaavgtdLaealiLPGLvvelaellavseilisree 82 
                                   +s+y+++ilvg+++gi+sllai ++k+dl+aliltd+ve+aml+i+a vgtdLaealiLPGLvv+laellavse+li+r+ 
  gi|15668702|ref|NP_247501.1|   9 YSIYHPTILVGFAIGILSLLAIGFQKNDLHALILTDVVECAMLIIIAGVGTDLAEALILPGLVVSLAELLAVSEVLITRKY 89 
                                   689****************************************************************************** PP

                       DUF2105  83 lkkelpvkkk...................lklevlktaPkflalvLvvyGiilsGftGGavaasGlllyllskrvrekevs 144
                                   lk++ p++k+                   +++e+lkt+Pkfla++L+vyG+ilsGftGGav+a+Gll+y+ls+rv+++e+s
  gi|15668702|ref|NP_247501.1|  90 LKSKRPKPKSyklfeefklplytgelkydIHMEILKTSPKFLAIILIVYGAILSGFTGGAVIATGLLFYALSQRVIGVEIS 170
                                   ****99999999******************************************************************999 PP

                       DUF2105 145 .....efegiegvsGiaWalWilgfliffllPqkwllalllaalgllikvasklgLiGtl 199
                                        ++egi+g+sGiaWalWi+gf++ff++P+kwll+ll+a+lgl+ikv+sklgLiG++
  gi|15668702|ref|NP_247501.1| 171 eelktMWEGISGLSGIAWALWIFGFIGFFVFPDKWLLCLLMAGLGLVIKVGSKLGLIGYI 230
                                   99999*****************************************************87 PP

>> AnkUBD  Ankyrin ubiquitin-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.9e-05      0.41      71      93 ..      25      47 ..       6      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.9e-05
                        AnkUBD 71 lvhlairfqrqdmlavlltevsq 93
                                  l  lai fq++d+ a++lt+v +
  gi|15668702|ref|NP_247501.1| 25 LSLLAIGFQKNDLHALILTDVVE 47
                                  5679****************976 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.5      0.02   1.2e+02      13      64 ..       4      85 ..       1      94 [. 0.66
   2 ?    7.1   0.3    0.0012       7.1       6      73 ..     117     205 ..     115     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.02
                       DUF4231 13 akrrfrllrlitivlgallpilvs..............................sklgagvsvlkiltallsalvailaale 64
                                  + ++ +++   ti++g+ + il+                               +++ a++ +l+ l++ l+ l+a+++ l+
  gi|15668702|ref|NP_247501.1|  4 MENIIYSIYHPTILVGFAIGILSLlaigfqkndlhaliltdvvecamliiiagvGTDLAEALILPGLVVSLAELLAVSEVLI 85
                                  5667777777799999999999998887766666666666666666666665565556666666666666666666666655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0012
                       DUF4231   6 yekkasrakrrfrllrlitivlgallpilvs....................sklgagvsvlkiltallsalvai.laalee 65 
                                   y+ ++++ k++ ++l++i+iv ga+l+ +                      ++++   +++  ++ l +++ a+ + ++++
  gi|15668702|ref|NP_247501.1| 117 YDIHMEILKTSPKFLAIILIVYGAILSGFTGgaviatgllfyalsqrvigvEISEELKTMWEGISGLSGIAWALwIFGFIG 197
                                   6667888899999************99888888888888999998888888888888888888888888888887778888 PP

                       DUF4231  66 ffrykerW 73 
                                   ff++ ++W
  gi|15668702|ref|NP_247501.1| 198 FFVFPDKW 205
                                   88888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1529.64
//
Query:       gi|15668703|ref|NP_247502.1|  [L=158]
Description: hypothetical protein MJ_0524 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-73  243.3   0.3    7.1e-73  243.1   0.3    1.0  1  DUF2106   Predicted membrane protein (DUF2106)


Domain annotation for each model (and alignments):
>> DUF2106  Predicted membrane protein (DUF2106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.1   0.3     4e-77   7.1e-73       1     150 [.       8     156 ..       8     157 .. 0.99

  Alignments for each domain:
  == domain 1  score: 243.1 bits;  conditional E-value: 4e-77
                       DUF2106   1 klkklsnalakpenlprlyalllavvlivgllvplslnedqlypkpapqsqidaksplaPydrGGvpleepaevkaqyPen 81 
                                   kl+k++n+l+kpe +pr+++++la+v+i+gll+p+ ln +qlypkp p+sq+  k+plaPydrGG+pl+epae+kaqyP++
  gi|15668703|ref|NP_247502.1|   8 KLGKIWNYLSKPEIVPRIFSVFLALVFIFGLLMPHYLNPNQLYPKPIPHSQT-LKTPLAPYDRGGIPLKEPAELKAQYPQY 87 
                                   689************************************************9.9*************************** PP

                       DUF2106  82 epalGlvtayltPlsellaettlylGttivssPGGiideilyytrGldtvlessillvafviasflvlr 150
                                   ep+lG++tayltP++e+++++t+y+Gttivs+PGGi+deilyytrG+dtvlessill++f+i+s+l+ +
  gi|15668703|ref|NP_247502.1|  88 EPNLGKITAYLTPIAEWIKDKTYYFGTTIVSTPGGILDEILYYTRGMDTVLESSILLISFIIFSWLFFN 156
                                   ******************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1104.87
//
Query:       gi|15668704|ref|NP_247503.1|  [L=53]
Description: hypothetical protein MJ_0525 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.4e-18   64.3   4.8    9.1e-18   64.1   4.8    1.0  1  DUF2107     Predicted membrane protein (DUF2107)
  ------ inclusion threshold ------
       0.04   12.6   0.1      0.045   12.4   0.1    1.0  1  SNF         Sodium:neurotransmitter symporter family
      0.085   12.9   0.2      0.092   12.8   0.2    1.1  1  MitoNEET_N  Iron-containing outer mitochondrial membrane prot


Domain annotation for each model (and alignments):
>> DUF2107  Predicted membrane protein (DUF2107)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   4.8   1.5e-21   9.1e-18      28      70 ..       1      43 [.       1      46 [. 0.97

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.5e-21
                       DUF2107 28 llnlEvpavGvllilLaynetlALlTfiavtaiitlvlvraii 70
                                  +ln+Evp++Gv+li+Lay+e lAL+Tfiav+a++ l+l+ra+i
  gi|15668704|ref|NP_247503.1|  1 MLNVEVPTIGVSLIFLAYDEALALMTFIAVNAVLSLILIRAVI 43
                                  69***************************************97 PP

>> SNF  Sodium:neurotransmitter symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   7.6e-06     0.045     321     362 ..       5      46 ..       3      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.6e-06
                           SNF 321 evaeeGpgLaFiaypealtklplsplwsvlFFlmlillglds 362
                                   ev + G +L+F+ay eal+ + +  + +vl  + + ++ ld+
  gi|15668704|ref|NP_247503.1|   5 EVPTIGVSLIFLAYDEALALMTFIAVNAVLSLILIRAVILDA 46 
                                   57778*******************999999888877777776 PP

>> MitoNEET_N  Iron-containing outer mitochondrial membrane protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.5e-05     0.092      31      61 ..      16      46 ..       3      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
                    MitoNEET_N 31 LslkdwLalvpfaavtaalgYlaykaflpkk 61
                                  L + + Lal++f av a+l  ++ +a+++ +
  gi|15668704|ref|NP_247503.1| 16 LAYDEALALMTFIAVNAVLSLILIRAVILDA 46
                                  8899******************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 367.72
//
Query:       gi|15668705|ref|NP_247504.1|  [L=92]
Description: hypothetical protein MJ_0526 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-28   96.5   9.5    7.5e-28   96.3   9.5    1.1  1  DUF2108   Predicted membrane protein (DUF2108)


Domain annotation for each model (and alignments):
>> DUF2108  Predicted membrane protein (DUF2108)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   9.5   4.2e-32   7.5e-28       1      70 []       3      72 ..       3      72 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 4.2e-32
                       DUF2108  1 llllvalalaliGaigvillkkpldKlimlalleaGlillivakgYLDVaiavallePvstiilllaiik 70
                                  +l+lv+++++++G+igvil+++p++K+imlalle G+i+liv+++YLD+ai+++l+eP++t+illl+++k
  gi|15668705|ref|NP_247504.1|  3 VLPLVSGICCILGGIGVILHTNPINKIIMLALLEIGMIGLIVSCYYLDIAIVSSLCEPICTVILLLGYLK 72
                                  589***************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 615.42
//
Query:       gi|15668706|ref|NP_247505.1|  [L=82]
Description: hypothetical protein MJ_0526.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      8e-36  121.9   4.6    8.9e-36  121.8   4.6    1.0  1  DUF2109       Predicted membrane protein (DUF2109)
     0.0056   16.3   1.1     0.0059   16.3   1.1    1.1  1  DUF4131       Domain of unknown function (DUF4131)
  ------ inclusion threshold ------
      0.034   14.3   1.7       0.27   11.4   1.7    2.0  1  DUF4040       Domain of unknown function (DUF4040)
       0.26   10.2   1.2       0.26   10.2   1.2    1.0  1  DUF3488       Domain of unknown function (DUF3488)
       0.29   10.4   4.3       0.35   10.1   4.3    1.0  1  Peptidase_U4  Sporulation factor SpoIIGA


Domain annotation for each model (and alignments):
>> DUF2109  Predicted membrane protein (DUF2109)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   4.6   2.5e-39   8.9e-36       1      75 [.       5      79 ..       5      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 2.5e-39
                       DUF2109  1 veliigiiailaairilleknraekLlylnvlnFaiaalialliktplgliaAiayFvgsTlesNAiAstlakle 75
                                  ve+iig+ia+l+++ri+le++ra+kLlyl++l+F+i+alial++++p+g i+Ai+yF++sT++sNAiA+t+++++
  gi|15668706|ref|NP_247505.1|  5 VEIIIGFIALLMTARIFLERSRARKLLYLCCLSFCISALIALYVDSPMGGIVAITYFICSTISSNAIAYTIEQTK 79
                                  789*********************************************************************987 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.1   1.6e-06    0.0059       8      64 ..       7      63 ..       4      81 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-06
                       DUF4131  8 vllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqlle 64
                                  +++++++ll+ ++++l r+r r+   l++l +++ al+ +++ +p  +   + +++ 
  gi|15668706|ref|NP_247505.1|  7 IIIGFIALLMTARIFLERSRARKLLYLCCLSFCISALIALYVDSPMGGIVAITYFIC 63
                                  578888888888888885566666666666666666666666666666666666665 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.7   7.5e-05      0.27       2      65 ..      12      78 ..      11      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.5e-05
                       DUF4040  2 llvlaalaavlardrlaavillgvvGllvallfvll.gAPD...vAlTqaavveglttvllllalrrl 65
                                  +++l+++ + l r+r + +++l+ +++++++l +l+ + P    vA+T++ + ++++   +++++ ++
  gi|15668706|ref|NP_247505.1| 12 IALLMTARIFLERSRARKLLYLCCLSFCISALIALYvDSPMggiVAITYF-ICSTISSNAIAYTIEQT 78
                                  56788999999****************99877766525553444888888.88888877777777665 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.2   7.2e-05      0.26      73     137 ..       6      71 ..       1      81 [. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.2e-05
                       DUF3488  73 dagvalLvlllalKl.lElrsrRDalvllllgffllatsflfsqsllfalylllalllllaalval 137
                                   + ++ +++ll++ ++ lE  + R +l l++l+f + a+ +l+  s++  ++++ ++++ +++  a+
  gi|15668706|ref|NP_247505.1|   6 EIIIGFIALLMTARIfLERSRARKLLYLCCLSFCISALIALYVDSPMGGIVAITYFICSTISSNAI 71 
                                   6778888888888852788888************************99999999999888876555 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.3   9.7e-05      0.35      10      83 ..       5      79 ..       2      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.7e-05
                  Peptidase_U4 10 vNllmdyllLlltakllklkikklrlllaAllGalyvvlvlflpklesillsillkilvsllmv.liafgpkslk 83
                                  v +++ ++ Ll+ta+++  + + ++ll   +l   +++l+ ++    +     ++++++s++    ia+ +++ k
  gi|15668706|ref|NP_247505.1|  5 VEIIIGFIALLMTARIFLERSRARKLLYLCCLSFCISALIALYVDSPMGGIVAITYFICSTISSnAIAYTIEQTK 79
                                  678999****************99999999999888888888865555666778899999998878888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 556.80
//
Query:       gi|15668707|ref|NP_247506.1|  [L=164]
Description: hypothetical protein MJ_0527 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1302.38
//
Query:       gi|15668708|ref|NP_247507.1|  [L=98]
Description: hypothetical protein MJ_0528 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-31  107.8   4.2    2.6e-31  107.6   4.2    1.0  1  NiFe_hyd_3_EhaA  NiFe-hydrogenase-type-3 Eha complex subunit 
  ------ inclusion threshold ------
      0.032   13.9   2.8       0.19   11.5   0.6    2.2  2  FeoB_C           Ferrous iron transport protein B C terminus


Domain annotation for each model (and alignments):
>> NiFe_hyd_3_EhaA  NiFe-hydrogenase-type-3 Eha complex subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6   4.2   2.9e-35   2.6e-31       2      97 .]       6      98 .]       5      98 .] 0.96

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 2.9e-35
               NiFe_hyd_3_EhaA  2 iilvnvldllisYlvaiivsiivaliLrlPllp.ekParqsftisvifPtavlalGllalvfk.lgveiydGlllaiiiGvls 82
                                  ++lv+v+d++i Yl+a+i+s+ival+L+lP++p ekP+r+sf++s+ifPt++lalG++a++++ +g +    ++la+++G+++
  gi|15668708|ref|NP_247507.1|  6 SLLVRVMDIIILYLIALITSVIVALVLKLPIIPkEKPIRFSFETSIIFPTPILALGIEAIFRNlFGDY----ISLAFFAGLFG 84
                                  67899****************************9*****************************78888....9********** PP

               NiFe_hyd_3_EhaA 83 alfskyllekvfpkp 97
                                  al+sky+ +k+f++p
  gi|15668708|ref|NP_247507.1| 85 ALLSKYA-DKLFGEP 98
                                  *******.9999886 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6   2.1e-05      0.19       2      27 ..      15      40 ..      14      48 .. 0.79
   2 ?    2.8   0.1     0.011        98       2      22 ..      70      90 ..      69      98 .] 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.1e-05
                        FeoB_C  2 fslYllgilvallvalllkktt.lkge 27
                                  ++lYl+ ++  ++val+lk    +++e
  gi|15668708|ref|NP_247507.1| 15 IILYLIALITSVIVALVLKL-PiIPKE 40
                                  78****************87.555554 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.011
                        FeoB_C  2 fslYllgilvallvalllkkt 22
                                  f+ Y+   ++a l + ll+k+
  gi|15668708|ref|NP_247507.1| 70 FGDYISLAFFAGLFGALLSKY 90
                                  566888888999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 663.40
//
Query:       gi|15668709|ref|NP_247508.1|  [L=232]
Description: repressor protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-10   39.6   0.2    8.1e-10   38.6   0.2    1.6  1  HTH_3           Helix-turn-helix
    2.4e-07   30.7   1.2    7.1e-07   29.2   0.1    2.3  2  HTH_19          Helix-turn-helix domain
    2.6e-05   24.5   0.0    5.1e-05   23.5   0.0    1.4  1  HTH_31          Helix-turn-helix domain
    2.8e-05   24.0   1.0    5.1e-05   23.1   0.3    1.8  2  HTH_37          Helix-turn-helix domain
     0.0034   17.2   0.2      0.022   14.6   0.1    2.4  2  HTH_25          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   15.9   0.0      0.025   15.2   0.0    1.3  1  HNF-1_N         Hepatocyte nuclear factor 1 (HNF-1), N termin
      0.019   14.8   0.0      0.045   13.6   0.0    1.6  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.028   14.5   0.0      0.064   13.4   0.0    1.6  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
      0.036   14.5   0.7      0.066   13.7   0.1    1.7  2  HTH_26          Cro/C1-type HTH DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.2   4.1e-13   8.1e-10       1      37 [.      39      75 ..      39      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 4.1e-13
                                  HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSB CS
                         HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPs 37
                                  +++ R++l+++q +LA+++G+s+s++s++E+G+r  +
  gi|15668709|ref|NP_247508.1| 39 IQAFREKLKITQSKLAKESGISQSHLSMLEKGKRPAT 75
                                  6789****************************99554 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1   3.6e-10   7.1e-07       3      37 ..      38      72 ..      37      87 .. 0.86
   2 ?   -1.3   0.1       1.2   2.3e+03      25      34 ..     125     136 ..     114     165 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 3.6e-10
                        HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkk 37
                                   ++++Re+l++tq +la++ gis+s +s++E+gk+
  gi|15668709|ref|NP_247508.1| 38 YIQAFREKLKITQSKLAKESGISQSHLSMLEKGKR 72
                                  6899*****************************86 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                        HTH_19  25 s..rskisaiEn 34 
                                      +++++ iEn
  gi|15668709|ref|NP_247508.1| 125 KgdKGYLRLIEN 136
                                   445677777776 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.5e-08   5.1e-05       5      54 ..      38      84 ..      37      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.5e-08
                        HTH_31  5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54
                                  + +a+Re+  ++q  +A+ +g+s+s+ls lE G+r+      l a a  l
  gi|15668709|ref|NP_247508.1| 38 YIQAFREKLKITQSKLAKESGISQSHLSMLEKGKRP---ATKLIATAVTL 84
                                  6799*******************************6...55555555555 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.3   2.6e-08   5.1e-05      22      55 ..      38      71 ..      16      84 .. 0.87
   2 ?   -2.7   0.0       2.9   5.9e+03      67      79 ..     198     210 ..     196     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.6e-08
                                  HHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT- CS
                        HTH_37 22 aiaeliekrelsqseaaqllgiaqPkvsrllrgk 55
                                   i++++ek++++qs++a+  gi+q+++s l++gk
  gi|15668709|ref|NP_247508.1| 38 YIQAFREKLKITQSKLAKESGISQSHLSMLEKGK 71
                                  3*******************************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.9
                                   HHHHTTEEEEEEE CS
                        HTH_37  67 lltalGqkveivv 79 
                                   + +++G+kv i+v
  gi|15668709|ref|NP_247508.1| 198 FMKKTGKKVIIQV 210
                                   67899****9987 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.16   3.1e+02       6      29 ..      18      41 ..      16      42 .. 0.89
   2 !   14.6   0.1   1.1e-05     0.022       3      34 ..      40      71 ..      38      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.16
                                  HHTTT--HHHHHHHSS--HHHHHH CS
                        HTH_25  6 RearglsleevaketkIrkdylea 29
                                  Re +   le +++ + + ++y++a
  gi|15668709|ref|NP_247508.1| 18 RENMYKKLEIIERAILLNPQYIQA 41
                                  888899999**************9 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.1e-05
                                  HHHHHTTT--HHHHHHHSS--HHHHHHHHCT- CS
                        HTH_25  3 raaRearglsleevaketkIrkdylealEedd 34
                                  +a Re+++++  ++ake  I++++l  lE+++
  gi|15668709|ref|NP_247508.1| 40 QAFREKLKITQSKLAKESGISQSHLSMLEKGK 71
                                  788**************************985 PP

>> HNF-1_N  Hepatocyte nuclear factor 1 (HNF-1), N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.2e-05     0.025     144     172 ..      38      66 ..      18      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                       HNF-1_N 144 eikaflqqhrIsQrevvdvTGlsQShlSq 172
                                    i+af ++ +I Q   ++  G+sQShlS 
  gi|15668709|ref|NP_247508.1|  38 YIQAFREKLKITQSKLAKESGISQSHLSM 66 
                                   6999***********************94 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.3e-05     0.045       9      35 ..      48      74 ..      44      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                YdaS_antitoxin  9 GgqkaLAealgvsqqaVsqWlkgkkqv 35
                                   +q++LA++ g+sq++ s++ kgk+++
  gi|15668709|ref|NP_247508.1| 48 ITQSKLAKESGISQSHLSMLEKGKRPA 74
                                  57******************9998874 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.2e-05     0.064      66     111 ..      31      75 ..      12      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                MqsA_antitoxin  66 aelvdpafiarvrkkleldqreaaeifGgGvnafsryekGkvrppl 111
                                   a l +p++i+  r+kl+++q+++a+  G     +s  ekGk  p +
  gi|15668709|ref|NP_247508.1|  31 AILLNPQYIQAFREKLKITQSKLAKESGISQSHLSMLEKGKR-PAT 75 
                                   44569***********************************95.433 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.3e-05     0.066       9      38 ..      46      73 ..      39      82 .. 0.86
   2 ?   -3.3   0.0       6.5   1.3e+04       9      18 ..     158     167 ..     150     171 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                        HTH_26  9 rgitkseLargtgisaatlsrlvkgkperv 38
                                   +it+s+La+ +gis++ ls l kgk  r+
  gi|15668709|ref|NP_247508.1| 46 LKITQSKLAKESGISQSHLSMLEKGK--RP 73
                                  589*********************98..54 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.5
                        HTH_26   9 rgitkseLar 18 
                                   ++i + eL+r
  gi|15668709|ref|NP_247508.1| 158 MDIERIELSR 167
                                   4444555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1440.34
//
Query:       gi|15668710|ref|NP_247509.1|  [L=198]
Description: hypothetical protein MJ_0530 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-38  131.2   0.0    3.5e-38  131.0   0.0    1.1  1  zf-ZPR1          ZPR1 zinc-finger domain
     0.0015   18.8   0.7     0.0031   17.7   0.7    1.5  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
     0.0072   16.7   0.1      0.012   16.0   0.1    1.3  1  DnaJ_CXXCXGXG    DnaJ central domain
  ------ inclusion threshold ------
      0.025   15.0   0.1      0.061   13.7   0.1    1.7  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.041   14.1   0.5      0.063   13.5   0.5    1.3  1  DUF3727          Protein of unknown function (DUF3727)


Domain annotation for each model (and alignments):
>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.0   0.0   9.8e-42   3.5e-38       2     158 ..       8     162 ..       7     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 131.0 bits;  conditional E-value: 9.8e-42
                       zf-ZPR1   2 lCpsCgkengetrlllt..kiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetatvei 80 
                                   +Cp Cg  +g+  ++    +iPyf+ v+ +++ Ce+C+++ ++v +++  e+  k++ lk+ese+dln++v++S++a ++i
  gi|15668710|ref|NP_247509.1|   8 DCPVCG-GKGTFVITSHqiDIPYFGPVLETTMICEKCNFRRSDVFPLEVREP--KKYILKIESERDLNKRVVRSSSAYIQI 85 
                                   6****8.667766665546*********************************..*************************** PP

                       zf-ZPR1  81 peleleippg.tlegrlttvEGlLeqikeelekeegdqaeredeekekieeflekleeliegeepftlildDpagnSfi 158
                                   pel++ei+pg   eg++++vEG+L+++ + l++     +++  e+k+k+ee+ e++++l+eg+e+ tlil Dp+g+S+i
  gi|15668710|ref|NP_247509.1|  86 PELGVEIKPGpLAEGFVSNVEGVLNRVDNILQTLIRWAETE--EQKKKAEELRERIKKLKEGKEEATLILIDPLGHSAI 162
                                   **********9********************5332333333..679*******************************98 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.7   8.7e-07    0.0031       4      31 ..       7      43 ..       5      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.7e-07
                                  E--TTTT-TTTEEETT.............S-EEETTT CS
                Prim_Zn_Ribbon  4 spCPvCGGrDrFrfddkdgr.........GtwfCrqC 31
                                    CPvCGG++ F ++  +            t +C +C
  gi|15668710|ref|NP_247509.1|  7 LDCPVCGGKGTFVITSHQIDipyfgpvleTTMICEKC 43
                                  57***********888777789999999999***999 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   3.3e-06     0.012      15      48 ..       7      44 ..       1      50 [. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.3e-06
                 DnaJ_CXXCXGXG 15 ktCktCkGsG.v.vreeqkt...lgpfvqqsqstCpeCe 48
                                   +C+ C+G+G   ++++q     +gp+  ++++ C++C+
  gi|15668710|ref|NP_247509.1|  7 LDCPVCGGKGtFvITSHQIDipyFGPVL-ETTMICEKCN 44
                                  57********532355554346778866.66899****8 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.7e-05     0.061       4      36 ..       7      45 ..       5      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
               Lar_restr_allev  4 kpCPfCggravlersqrvvaeigq.......cvyCadCga 36
                                  ++CP Cgg+++ + +      i +       +++C++C+ 
  gi|15668710|ref|NP_247509.1|  7 LDCPVCGGKGTFVITSHQID-IPYfgpvletTMICEKCNF 45
                                  58********9876644443.4446789**********98 PP

>> DUF3727  Protein of unknown function (DUF3727)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   1.8e-05     0.063      12      91 ..     104     184 ..      98     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                       DUF3727  12 tveGeLpplee..eeileleeeedeeeleeEelqllasFyheeqeYsiytpldPlllvakldeegelellspeeleklqpl 90 
                                    veG L+ +++  + +++  e+e++ + ++Eel+   +  +e++e +  + +dPl   a   e  e e+ls+ee+ekl++ 
  gi|15668710|ref|NP_247509.1| 104 NVEGVLNRVDNilQTLIRWAETEEQ-KKKAEELRERIKKLKEGKEEATLILIDPLGHSAIIGEGVEEEILSEEEVEKLKEG 183
                                   5667776555422333444444444.89999**9999999**************************************984 PP

                       DUF3727  91 l 91 
                                   +
  gi|15668710|ref|NP_247509.1| 184 I 184
                                   4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1849  (0.103129); expected 358.6 (0.02)
Passed bias filter:                     1053  (0.0587317); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1232.57
//
Query:       gi|15668711|ref|NP_247510.1|  [L=170]
Description: hypothetical protein MJ_0531 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-41  139.7   0.5      1e-40  139.5   0.5    1.0  1  Usp              Universal stress protein family
      0.009   15.5   0.1      0.014   14.8   0.1    1.3  1  AP_endonuc_2     Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.015   14.8   0.1      0.028   14.0   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
      0.049   14.4   0.2      0.076   13.7   0.2    1.5  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
      0.077   13.7   0.5       0.29   11.8   0.1    2.0  2  PTS_IIB          PTS system, Lactose/Cellobiose specific IIB 


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.5   0.5   2.8e-44     1e-40       2     141 .]      26     165 ..      25     165 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.5 bits;  conditional E-value: 2.8e-44
                                   -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEE CS
                           Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkv 82 
                                   yk+I++++Dgs+ s +A+++A++ ak+++ae+++++v+d +++   +++ + +  +el +ee ++++++ k++ae+ gvk 
  gi|15668711|ref|NP_247510.1|  26 YKKIVIPTDGSDVSLEAAKHAINIAKEFDAEVYAIYVVDVSPFVGLPAEGSWELISELLKEEGQEALKKVKKMAEEWGVKI 106
                                   9*********************************************************99999999999************ PP

                                   EEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                           Usp  83 evvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                   +++ +eg pa ei+e+ae+++adliV+G++g++gl+r+llGSv+e+v+++a+cpVlvV+
  gi|15668711|ref|NP_247510.1| 107 HTEMLEGVPANEIVEFAEKKKADLIVMGTTGKTGLERILLGSVAERVIKNAHCPVLVVK 165
                                   **********************************************************8 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   3.9e-06     0.014      67     137 ..      38     116 ..      21     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.9e-06
                                   HHHHHHHHHHHHHHHHTBSEEEEEBCC....GBCTTTSGHH....HHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTS CS
                  AP_endonuc_2  67 esvdalkraielaaaLGapllvlhpGt....agagpkgsee....eawerlaeslneladyaekegvklalEtlagsgv 137
                                    s++a+k+ai +a++++a++  + + +     g +++gs+e       e   e+l+++ ++ae+ gvk+  E l g ++
  gi|15668711|ref|NP_247510.1|  38 VSLEAAKHAINIAKEFDAEVYAIYVVDvspfVGLPAEGSWEliseLLKEEGQEALKKVKKMAEEWGVKIHTEMLEGVPA 116
                                   369*****************9999888777655666666665554455556679******************9988776 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.7e-06     0.028      55      98 ..      88     133 ..      41     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.7e-06
                                   .STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHC..ESEEEE CS
               Glycos_transf_1  55 ngeeekelkklaeelelsdnviflgevsredleellkn..adifvl 98 
                                   ++e +k++kk+aee +++ ++++l  v+ +++ e+ ++  ad++v+
  gi|15668711|ref|NP_247510.1|  88 GQEALKKVKKMAEEWGVKIHTEMLEGVPANEIVEFAEKkkADLIVM 133
                                   48999******************************98877999887 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   2.1e-05     0.076      56     108 ..      89     145 ..      44     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                                   HHHHHHHHHHHHH..TTSSSEEEES..HHHHHHHHCHTT-SEEEE--SSGGGHHHHH CS
               DXP_reductoisom  56 eeaaeelkealke..kelktevlvG..eealkelaeeeeadvvvaaivGaaGLkptl 108
                                   +ea +++k++ +e   +++te+l G   + ++e ae+++ad++v + +G +GL+  l
  gi|15668711|ref|NP_247510.1|  89 QEALKKVKKMAEEwgVKIHTEMLEGvpANEIVEFAEKKKADLIVMGTTGKTGLERIL 145
                                   556666666666633466899999933467899********************9776 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.54   1.9e+03      53      78 ..      41      68 ..      22      73 .. 0.54
   2 ?   11.8   0.1   8.2e-05      0.29      18      63 ..      93     142 ..      90     163 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.54
                                  EEESSGGCTHHHHTT..SEEEEECTTHH CS
                       PTS_IIB 53 lapqvrvkdlarfag..kpvavinikda 78
                                   a+  +++  ++f +    ++v++++++
  gi|15668711|ref|NP_247510.1| 41 EAAKHAINIAKEFDAevYAIYVVDVSPF 68
                                  4444444222333332113555555554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.2e-05
                                   HHHHHHHHHCT..EEEEETTEE....GGGHHHHHHT-SEEEEEESSGGCTHH CS
                       PTS_IIB  18 eklekaakelg..ieaegeagv....eleaeeiaddaDlvllapqvrvkdla 63 
                                   +k++k+a+e g  i +e+ +gv     +e +e+++ aDl++ ++  +   l+
  gi|15668711|ref|NP_247510.1|  93 KKVKKMAEEWGvkIHTEMLEGVpaneIVEFAEKKK-ADLIVMGTTGKT-GLE 142
                                   89*********886666667777774455555555.******998774.555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1125.60
//
Query:       gi|15668712|ref|NP_247511.1|  [L=391]
Description: bacteriochlorophyll synthase 43 kDa subunit ChlP [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-14   54.3   0.2    3.7e-13   49.4   0.2    2.4  1  FAD_binding_3   FAD binding domain
    2.5e-10   39.8   0.1    1.4e-06   27.5   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
      2e-09   37.3   4.6    8.2e-09   35.3   4.6    2.2  1  FAD_oxidored    FAD dependent oxidoreductase
    6.1e-07   28.5   0.1    1.6e-06   27.1   0.1    1.7  1  HI0933_like     HI0933-like protein
    9.6e-07   28.2   0.0    9.6e-07   28.2   0.0    2.2  3  GIDA            Glucose inhibited division protein A
    1.7e-06   27.4   1.1    7.8e-06   25.2   0.4    2.1  2  FAD_binding_2   FAD binding domain
    2.9e-06   27.1   2.9       0.07   12.7   0.0    3.0  3  DAO             FAD dependent oxidoreductase
    7.1e-06   25.5   5.2    0.00031   20.1   0.2    2.6  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.6e-05   23.4   0.0    0.00015   20.9   0.0    1.9  1  Lycopene_cycl   Lycopene cyclase protein
    5.5e-05   23.3   0.0    0.00013   22.1   0.0    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    8.4e-05   21.9   0.1    0.00049   19.4   0.1    2.1  2  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.018   14.1   0.0       0.03   13.4   0.0    1.3  1  SE              Squalene epoxidase
       0.08   12.7   0.2       0.79    9.5   0.1    2.4  3  Big_3_4         Domain of unknown function
       0.19   10.9   1.7       0.26   10.5   0.1    1.9  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.2   2.9e-16   3.7e-13       2     308 ..       8     296 ..       7     327 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 2.9e-16
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCC CS
                 FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynelsd 82 
                                   +dV++VGaGp G m++   ++ G +++l+ek ++  +  r      + + ++++ Gl+ + +   +  ++   +l  +   
  gi|15668712|ref|NP_247511.1|   8 YDVVVVGAGPGGSMASYASAKNGAKTLLIEKSQEIGEPVRCA----EAIPSIEEFGLKPEPEFVRNIIKG--GILFSP--- 79 
                                   59*****************************99988888874....78999******9987777755554..444444... PP

                                   CCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--G CS
                 FAD_binding_3  83 tpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDG 163
                                      +  ++++ +   + +v+  + ++++L+ +a+++g++v  kt   +le+d++  +  v     gee+ ++ k +++aDG
  gi|15668712|ref|NP_247511.1|  80 ---SGKKVTVTQDKAQGYVVERKIFDKYLAIRAAKAGAKVAVKTTAIGLERDGDYWNVIVEFL--GEEYVIKTKVVIAADG 155
                                   ...3566666788999999************************************88877776..9*************** PP

                                   TT-HHHHHHTGG.EEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEE..EEEECCETEEEEEEEEECCE-GGGSCC CS
                 FAD_binding_3 164 grStvrktlgie.fegeetvyeagvldvlfdadlsdiveplvlilsaesrgv..mviPlentlerfyvqvearaekeerse 241
                                   + S +++ +g++  + + ++      ++++ + l++ + + ++ +++  +g    + P  +t +   v + +r+ k+++  
  gi|15668712|ref|NP_247511.1| 156 VESNIAEYAGLKaKKKPLEICSCAEYEMTNVELLDKNMME-FYFGNEVAPGGyvWIFPKGETAN---VGLGVRD-KKKKAI 231
                                   ************5555566666666666666555544445.55555554444347888888222...4444443.445566 PP

                                   CHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHHHH CS
                 FAD_binding_3 242 kfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNtai 308
                                   ++ ee + + l +   +++++ e+ +v  ++v+  + ++y++g ++++GDAa   +P +G G+ +a+
  gi|15668712|ref|NP_247511.1| 232 EYLEEFIENGLAKDRLKDATPIEF-KVGGAPVSGPIEKTYTDG-LLVVGDAAGQISPLTGGGIYLAM 296
                                   666666666666666666666665.567788888888888765.99****************99998 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.2   0.00017      0.22       1      52 [.       9      58 ..       9      78 .. 0.79
   2 !   27.5   0.0   1.1e-09   1.4e-06     145     367 ..      90     327 ..      76     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00017
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE.-SSS---SS-EE--THHHHT CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve.seeigtvgvGeatipsirkl 52
                                  ++v+vG+G+ G++a  a ak +   ++ +l+e s+eig       +ipsi+++
  gi|15668712|ref|NP_247511.1|  9 DVVVVGAGPGGSMASYASAKNG---AKTLLIEkSQEIGEPVRCAEAIPSIEEF 58
                                  69**************999999...7788888356788765555568888775 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 1.1e-09
                                   S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT...S-EEE-SEEEE-SGGG-IIIIIIT---E CS
                Trp_halogenase 145 lsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled...greveadlfiDcsGfrgllieqaLktgf 222
                                    + +y ++++ ++k+L   a ++G ++   +   + l+ dg+  ++ +e    + +++   +i + G ++ + e a   g 
  gi|15668712|ref|NP_247511.1|  90 KAQGYVVERKIFDKYLAIRAAKAGAKVAVKTT-AIGLERDGDYWNVIVEFlgeEYVIKTKVVIAADGVESNIAEYA---GL 166
                                   567899******************99876655.777888777777766544338899*****************98...88 PP

                                   EE-TTT----EEEEEEEE--H.....---SSEEEEE-SSEEEEEEEETTEEEEEEEE-TTTS-HHHHHHHHHHHCT--TTT CS
                Trp_halogenase 223 edwsdvLltdrAlavqvesee.....lvepytrataekaGWtWkiPLqhrlgnGyvyssahadddeAlaellaeldgklea 298
                                   +  ++ L + +    +++++e      +e y +      G +W  P  +++  G+ ++ +  ++ e l+e++++  +k + 
  gi|15668712|ref|NP_247511.1| 167 KAKKKPLEICSCAEYEMTNVElldknMMEFYFGNEVAPGGYVWIFPKGETANVGLGVRDKKKKAIEYLEEFIENGLAKDRL 247
                                   8888888777777777777777777799******************9999999*********9999999999886666655 PP

                                   S-.EEEE---EE......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BTT--HHHHHHHHHHH CS
                Trp_halogenase 299 ep.rkirfttGr......rkqawvknvvalGlasgfvePlestsihliqa....alrrLlallpdksdepaaiaefnrev 367
                                   ++   i+f++G        ++++  +++ +G+a+g + Pl + +i+l++     a +   + +  +  ++ +++e++r+ 
  gi|15668712|ref|NP_247511.1| 248 KDaTPIEFKVGGapvsgpIEKTYTDGLLVVGDAAGQISPLTGGGIYLAMDcgliAGEVASKAIKLNDWSEETLKEYERRW 327
                                   555********99999999****************************987655544444555555555666666666665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   4.6   6.4e-12   8.2e-09       1     154 [.       9     166 ..       9     361 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 6.4e-12
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll.tsglvatdignkaee..qvvtgiareflerlrqrgga..... 73 
                                   DvvVvG+gp+G +A +a+a++Gak+lL+e+++ +G  +  +++ ++++++  +   +        f++++ + gg      
  gi|15668712|ref|NP_247511.1|   9 DVVVVGAGPGGSMASYASAKNGAKTLLIEKSQEIGEPVrCAEAIPSIEEFGLKPepE--------FVRNIIK-GGIlfsps 80 
                                   9*********************************96441455566666654443342........3333322.11112211 PP

                  FAD_oxidored  74 ....rlkkrskw.ntfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg.dGdl 148
                                         ++++++  ++e +++ + l    a+ag +v  +t++++ e++g + + v+ve   ++++i+ kv+i A g +  +
  gi|15668712|ref|NP_247511.1|  81 gkkvTVTQDKAQgYVVERKIFDKYLAIRAAKAGAKVAVKTTAIGLERDG-DYWNVIVEFLGEEYVIKTKVVIAADGvESNI 160
                                   1111112222222467777777777777799999999999999999998.8999999877679999999999886546666 PP

                  FAD_oxidored 149 aalaGv 154
                                   a+ aG 
  gi|15668712|ref|NP_247511.1| 161 AEYAGL 166
                                   666666 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   1.3e-09   1.6e-06       1      40 [.       8      47 ..       8      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.3e-09
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40
                                  +dv+v+G+G+ G ma+ + ak+g+++ll+ek +++g+ ++
  gi|15668712|ref|NP_247511.1|  8 YDVVVVGAGPGGSMASYASAKNGAKTLLIEKSQEIGEPVR 47
                                  59**********************************8766 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   7.5e-10   9.6e-07       1      47 [.       9      55 ..       9     102 .. 0.88
   2 ?   -3.5   0.3       3.3   4.2e+03      15      29 ..     106     120 ..     104     125 .. 0.83
   3 ?   -2.6   0.4       1.7   2.2e+03     360     388 ..     280     310 ..     280     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 7.5e-10
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--S.SSSEEE-T CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaels.Cnpsiggi 47
                                  dv+V+G+G  G+ A++a+a+ Gak+lLi +k ++i+e + C ++i +i
  gi|15668712|ref|NP_247511.1|  9 DVVVVGAGPGGSMASYASAKNGAKTLLI-EKSQEIGEPVrCAEAIPSI 55
                                  79**************************.8888998854488888766 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.3
                                   HHHHHHTT--EEEEE CS
                          GIDA  15 AlaaarlGakvlLit 29 
                                   A+ aa++Gakv+  t
  gi|15668712|ref|NP_247511.1| 106 AIRAAKAGAKVAVKT 120
                                   8999******99765 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.7
                                   E-CGGGTB-S...HHHHHHHHHHHHHHHHHHH CS
                          GIDA 360 lAGqinGteG...YeEaaaqGllAGinaarka 388
                                   +AGqi+  +G   Y+ a+  Gl+AG  a++ +
  gi|15668712|ref|NP_247511.1| 280 AAGQISPLTGggiYL-AMDCGLIAGEVASKAI 310
                                   599999998866555.6668*****9998766 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.4   6.1e-09   7.8e-06       1      35 [.       9      43 ..       9      52 .. 0.91
   2 ?    0.2   0.0      0.24     3e+02      15      27 ..     106     118 ..      71     174 .. 0.63

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.1e-09
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                  Dv+V+G+G +G +A+++ a++G+k++++ek qe g
  gi|15668712|ref|NP_247511.1|  9 DVVVVGAGPGGSMASYASAKNGAKTLLIEKSQEIG 43
                                  9******************************9976 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.24
                                   HHHHHHTTT-EEE CS
                 FAD_binding_2  15 AleaaeaGlkvav 27 
                                   A++aa+aG+kvav
  gi|15668712|ref|NP_247511.1| 106 AIRAAKAGAKVAV 118
                                   4444444444444 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   5.5e-05      0.07       1      33 [.       9      43 ..       9      46 .. 0.95
   2 !   12.2   0.1   7.6e-05     0.097     148     210 ..     101     166 ..      88     296 .. 0.67
   3 ?    1.4   0.1      0.15   1.9e+02      42     112 ..     299     368 ..     278     386 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-05
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                  dvv++G+G  G+ + y+ a+ g  ++l+ek+ ++g
  gi|15668712|ref|NP_247511.1|  9 DVVVVGAGPGGSMASYASAKNGakTLLIEKSQEIG 43
                                  9********************9********98887 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.6e-05
                                   HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.EEEEE..EEE--GGGHHHH..HTT CS
                           DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttp.gen.daada..vVnaaGawsdll..gll 210
                                   + ++la +a+++G+++  +t++ gle+ dg+ w+v  ++  ge+ + +++  v+ a G+ s+++  ++l
  gi|15668712|ref|NP_247511.1| 101 FDKYLAIRAAKAGAKVAVKTTAIGLER-DGDYWNVI-VEFlGEEyV-IKTkvVIAADGVESNIAeyAGL 166
                                   66889********************66.78999995.344466633.3444377777999885533333 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.15
                                   EEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEES..SHHHHHHHHHHHHHHHHTTTT CS
                           DAO  42 gllhsglrylpeaselarlslealeelreleeelgididyrrtGllslaa..deeelealdkllallleagld 112
                                   gl+++ +++++   +l ++s+e+l+e+++  +e + +       +  + +  +++el+al++ l++ l  g+d
  gi|15668712|ref|NP_247511.1| 299 GLIAGEVASKA--IKLNDWSEETLKEYERRWKEKHYEYLMSHLKYRKILEkmSDDELDALAEALGESL-DGID 368
                                   67777776444..3678**********77777767776666666666654444445666666555544.4544 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   2.4e-07   0.00031       1      32 [.       8      39 ..       8      59 .. 0.85
   2 !    7.1   0.4    0.0022       2.8     164     251 ..      80     167 ..      71     187 .. 0.81
   3 ?   -3.7   0.0       4.1   5.3e+03     246     278 ..     249     281 ..     220     286 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.4e-07
                                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEETT CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvele 32
                                  +dvvv+G+Gp+G  a+   a++gak++l+e+ 
  gi|15668712|ref|NP_247511.1|  8 YDVVVVGAGPGGSMASYASAKNGAKTLLIEKS 39
                                  69***************************733 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0022
                                   HT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE...EEEEEETTSCEEEESEEEE-S-EEES- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 164 lgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge...klevvledgeeidadlvvvavGvrpst 241
                                    gk+vt+ ++  + +    k + ++l+ +  k G +v ++t++  ++++g+    +   l+++ +i+++ v+ a Gv+ + 
  gi|15668712|ref|NP_247511.1|  80 SGKKVTVTQDKAQGYVVERKIFDKYLAIRAAKAGAKVAVKTTAIGLERDGDywnVIVEFLGEEYVIKTKVVIAADGVESNI 160
                                   588899988888888666777888888888888******************88544478899999**************98 PP

                                   HHCSHCCT-E CS
                                   xxxxxxxxxx RF
                   Pyr_redox_2 242 elleeklgle 251
                                   + +   +gl+
  gi|15668712|ref|NP_247511.1| 161 AEY---AGLK 167
                                   654...5554 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.1
                                   HCCT-EEEETTEEE--TTSBESSTTEEE-GGGC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 246 eklglelderggivvdeflrtnvpgiyaiGDva 278
                                   ++  +e + +g+ v  +  +t  +g+ ++GD a
  gi|15668712|ref|NP_247511.1| 249 DATPIEFKVGGAPVSGPIEKTYTDGLLVVGDAA 281
                                   455555533444444444456678888888887 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.2e-07   0.00015       1     284 [.       9     300 ..       9     360 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.2e-07
                 Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsl...lfpnnyvWsdefedlgaleecvehsWsgtivylddgkkillg 78 
                                   Dvvv+GaGp g s+A    +ak g k +lie s+++   ++ ++   s e+ +l+   e+v    +g i+  + gkk++++
  gi|15668712|ref|NP_247511.1|   9 DVVVVGAGPGG-SMASYA-SAKNGAKTLLIEKSQEIgepVRCAEAIPSIEEFGLKPEPEFVRNIIKGGILFSPSGKKVTVT 87 
                                   9********88.677665.7*************97622266777788888888888899******************9999 PP

                 Lycopene_cycl  79 ....raYgrvsskrlkeellerlvengvkl.leakvesveeeea.geslvvleggr.kirarlvvdarglaslkkarrlgl 152
                                         Y  v++k + + l+ r +++g+k  ++ ++   e + +  ++ v   g++  i+ ++v+ a g+ s+ ++++ + 
  gi|15668712|ref|NP_247511.1|  88 qdkaQGY-VVERKIFDKYLAIRAAKAGAKVaVKTTAIGLERDGDyWNVIVEFLGEEyVIKTKVVIAADGVESNIAEYAGLK 167
                                   7763444.69**************8888753789999999999978888988888889***********777775555555 PP

                 Lycopene_cycl 153 QtfyGvevevdnppfdldkmvlMDfr.....veqklkgltFlYalPldsdrllvEeTelaskpeLpadalkkrlaaylral 228
                                    +   +e+ + ++ +++++++l+D       + +++    ++++ P +++          +k++   + l++ + + l++ 
  gi|15668712|ref|NP_247511.1| 168 AKKKPLEICSCAE-YEMTNVELLDKNmmefyFGNEVAPGGYVWIFPKGETANV-G-LGVRDKKKKAIEYLEEFIENGLAKD 245
                                   5555566655555.666666666655322224444455556666666554432.2.2233444456666777777777777 PP

                 Lycopene_cycl 229 glkvkevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeap 284
                                    lk ++ +e   g  Pv   g+++++     l +G aag + P TG  +  ++    
  gi|15668712|ref|NP_247511.1| 246 RLKDATPIEFKVGGAPV--SGPIEKTYTDgLLVVGDAAGQISPLTGGGIYLAMDCGL 300
                                   77777777777777777..66666666554666777777777777766666665554 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     1e-07   0.00013       1      32 [.      12      43 ..      12      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1e-07
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                  +vGaG +G+ a y+ ak+g++ ll+ek++ +G
  gi|15668712|ref|NP_247511.1| 12 VVGAGPGGSMASYASAKNGAKTLLIEKSQEIG 43
                                  8*****************************99 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   3.8e-07   0.00049      18      54 ..       8      43 ..       2      47 .. 0.92
   2 ?   -1.3   0.0       0.8     1e+03     156     179 ..     144     167 ..     140     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.8e-07
                                  EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                          Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                   Dvv+vGaG+ G  a+y  ak+ + k++++e+s  +G
  gi|15668712|ref|NP_247511.1|  8 YDVVVVGAGPGGSMASYASAKN-GAKTLLIEKSQEIG 43
                                  6*********************.********998777 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.8
                                   EEEEEEEEE--GSSSTTTTHHHHH CS
                          Thi4 156 virakvvvdatGhdgeivavvvkk 179
                                   vi++kvv+ a G +++i + +  k
  gi|15668712|ref|NP_247511.1| 144 VIKTKVVIAADGVESNIAEYAGLK 167
                                   89999****999999998766544 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.4e-05      0.03     125     175 ..     267     317 ..     254     351 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                            SE 125 sknekkGlillGDalnmRHPltggGmtvalnDivllskllkpledlsdeek 175
                                   +k+ + Gl+++GDa     PltggG+  a+   ++  ++ ++   l+d ++
  gi|15668712|ref|NP_247511.1| 267 EKTYTDGLLVVGDAAGQISPLTGGGIYLAMDCGLIAGEVASKAIKLNDWSE 317
                                   566789********************9998766666666666666766443 PP

>> Big_3_4  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       7.5   9.6e+03      25      39 ..      83      97 ..      82     102 .. 0.79
   2 ?    9.5   0.1   0.00061      0.79      16      44 ..     125     154 ..     115     167 .. 0.73
   3 ?   -0.3   0.0      0.67   8.5e+02      68     101 ..     228     261 ..     223     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.5
                       Big_3_4 25 nvpvPldedGeyvve 39
                                  +v+v  d+   yvve
  gi|15668712|ref|NP_247511.1| 83 KVTVTQDKAQGYVVE 97
                                  688888888888887 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00061
                       Big_3_4  16 fdrseGdiWnvpvPldedGeyvve...llaed 44 
                                   ++r +Gd+Wnv v ++ + eyv++   ++a d
  gi|15668712|ref|NP_247511.1| 125 LER-DGDYWNVIVEFLGE-EYVIKtkvVIAAD 154
                                   544.8**********965.9**9733344544 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.67
                       Big_3_4  68 vrpldylsekleteftieavapkitiellvtgkr 101
                                    + ++yl e +e +++ +++     ie +v+g  
  gi|15668712|ref|NP_247511.1| 228 KKAIEYLEEFIENGLAKDRLKDATPIEFKVGGAP 261
                                   57899**************999999999999975 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0002      0.26       1      34 [.      11      44 ..      11      48 .. 0.86
   2 ?   -1.4   0.1      0.83   1.1e+03      89     163 ..     107     182 ..      79     187 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0002
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nign 34
                                  +++GaGP G  a ++  k+g  + l +Ek  +ig+
  gi|15668712|ref|NP_247511.1| 11 VVVGAGPGGSMASYASAKNGA-KTLLIEKSqEIGE 44
                                  79********999*******9.6799999867776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.83
                   Pyr_redox_3  89 evaksfelpiklfeeVesvkkedegfevets..ke..tyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkya 163
                                     a++   ++  +++   ++++++  +v  +   e  ++++k vi A G     n  ++ G +  +k   ++ ++++y+
  gi|15668712|ref|NP_247511.1| 107 IRAAKAGAKVAVKTTAIGLERDGDYWNVIVEflGEeyVIKTKVVIAADGV--ESNIAEYAGLK-AKKKPLEICSCAEYE 182
                                   44444444555555555555554444444321112225666667777666..55666666665.555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 2348.24
//
Query:       gi|15668713|ref|NP_247512.1|  [L=56]
Description: ferredoxin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-13   48.8  15.0    2.6e-07   30.1   3.0    2.1  2  Fer4      4Fe-4S binding domain
    3.8e-09   36.1  11.1    6.5e-06   25.9   1.6    2.1  2  Fer4_2    4Fe-4S binding domain
    7.1e-09   35.7   9.3    3.1e-05   24.0   1.4    2.0  2  Fer4_10   4Fe-4S dicluster domain
    2.9e-08   33.4  12.3    1.5e-05   24.8   2.8    2.1  2  Fer4_6    4Fe-4S binding domain
    1.7e-07   31.3  12.2    2.3e-07   30.9  12.2    1.2  1  Fer4_21   4Fe-4S dicluster domain
    7.8e-07   29.6  22.7    1.1e-05   25.9  12.3    1.9  2  Fer4_7    4Fe-4S dicluster domain
      1e-05   26.3  10.6     0.0071   17.2   2.2    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    6.8e-05   23.0  12.2    0.00053   20.1  12.6    1.8  2  Fer4_9    4Fe-4S dicluster domain
    0.00014   22.5   6.9      0.025   15.3   0.7    2.1  2  Fer4_15   4Fe-4S single cluster domain
    0.00025   21.3  13.5    0.00097   19.5   2.7    2.3  2  Fer4_4    4Fe-4S binding domain
      0.003   18.0  14.1       0.09   13.2   4.0    2.0  2  Fer4_8    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.021   15.4  13.0       0.37   11.4   3.9    2.1  2  Fer4_17   4Fe-4S dicluster domain
      0.064   13.8  10.2       0.45   11.1   2.5    2.1  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.11   13.5  17.3       0.12   13.3   4.0    2.2  2  Fer4_3    4Fe-4S binding domain
        2.4    8.4  12.3        1.4    9.1   2.6    2.0  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   4.4   9.7e-09   1.2e-05       1      23 [.       2      24 ..       2      25 .. 0.92
   2 !   30.1   3.0   2.2e-10   2.6e-07       1      24 []      31      54 ..      31      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 9.7e-09
                                  EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                  v+id+ kC +CGaCv vC   AI
  gi|15668713|ref|NP_247512.1|  2 VKIDYKKCGYCGACVGVCEKLAI 24
                                  68****************98887 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 2.2e-10
                                  EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                  +vide kC +C++C  vCP +A++
  gi|15668713|ref|NP_247512.1| 31 IVIDEKKCNNCKLCTIVCPLNALE 54
                                  69********************85 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   2.5   9.8e-06     0.012       3      20 ..       2      19 ..       1      20 [. 0.93
   2 !   25.9   1.6   5.5e-09   6.5e-06       3      21 ..      31      49 ..      28      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.8e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                  v++d  +C  CgaCv +C
  gi|15668713|ref|NP_247512.1|  2 VKIDYKKCGYCGACVGVC 19
                                  689*************** PP

  == domain 2  score: 25.9 bits;  conditional E-value: 5.5e-09
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  +v+d+ +C++C+ C+ +CP
  gi|15668713|ref|NP_247512.1| 31 IVIDEKKCNNCKLCTIVCP 49
                                  89****************9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.3   4.4e-06    0.0052       2      19 ..       2      19 ..       1      28 [. 0.84
   2 !   24.0   1.4   2.6e-08   3.1e-05       2      21 ..      31      50 ..      30      56 .] 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.4e-06
                       Fer4_10  2 vvidddtCirCgkCvkaC 19
                                  v+id ++C  Cg+Cv +C
  gi|15668713|ref|NP_247512.1|  2 VKIDYKKCGYCGACVGVC 19
                                  788999999999999999 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 2.6e-08
                       Fer4_10  2 vvidddtCirCgkCvkaCPa 21
                                  +vid+++C +C+ C+ +CP 
  gi|15668713|ref|NP_247512.1| 31 IVIDEKKCNNCKLCTIVCPL 50
                                  89*****************9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.1   2.7e-05     0.032       2      21 ..       2      21 ..       1      24 [. 0.88
   2 !   24.8   2.8   1.3e-08   1.5e-05       1      20 [.      30      49 ..      30      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                        Fer4_6  2 veidpdkCigCgdCvrvCPe 21
                                  v id+ kC  Cg+Cv vC  
  gi|15668713|ref|NP_247512.1|  2 VKIDYKKCGYCGACVGVCEK 21
                                  789***************86 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.3e-08
                        Fer4_6  1 vveidpdkCigCgdCvrvCP 20
                                  +++id+ kC+ C  C++vCP
  gi|15668713|ref|NP_247512.1| 30 IIVIDEKKCNNCKLCTIVCP 49
                                  69****************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9  12.2   1.9e-10   2.3e-07       2      55 ..       3      51 ..       2      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.9e-10
                       Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPved 55
                                  +id +kC  Cg C+ +Ce+ +++ ie    +++ + e++C  C+lC++vCP+ +
  gi|15668713|ref|NP_247512.1|  3 KIDYKKCGYCGACVGVCEKLAINLIE----HIIVIDEKKCNNCKLCTIVCPL-N 51
                                  6999**************87666665....45677899*************7.5 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   2.7   3.4e-05      0.04      31      49 ..       2      20 ..       1      23 [. 0.85
   2 !   25.9  12.3   9.3e-09   1.1e-05       1      52 []       8      52 ..       8      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                        Fer4_7 31 veidpekClgCgaCvavCP 49
                                  v+id+ kC +CgaCv vC 
  gi|15668713|ref|NP_247512.1|  2 VKIDYKKCGYCGACVGVCE 20
                                  5789999********9996 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 9.3e-09
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  +C  CgaCv +C   ai+l e+        ++id+ kC +C+ C  vCP +a
  gi|15668713|ref|NP_247512.1|  8 KCGYCGACVGVCEKLAINLIEH-------IIVIDEKKCNNCKLCTIVCPLNA 52
                                  7******************886.......79******************886 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   3.3   4.8e-05     0.057       1      30 [.       8      38 ..       8      40 .. 0.77
   2 !   17.2   2.2     6e-06    0.0071       1      19 [.      37      55 ..      37      56 .] 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-05
                       Fer4_16  1 rCgtCgkCaevCPtnaikek.kekeiearec 30
                                  +Cg Cg+C+ vC   ai+   +  +i+ ++c
  gi|15668713|ref|NP_247512.1|  8 KCGYCGACVGVCEKLAINLIeHIIVIDEKKC 38
                                  6***************997634456666666 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 6e-06
                       Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                  +C +C+ C+ vCP na+++
  gi|15668713|ref|NP_247512.1| 37 KCNNCKLCTIVCPLNALEG 55
                                  6***************986 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   2.6   6.5e-05     0.077      34      51 .]       7      24 ..       1      24 [. 0.79
   2 !   20.1  12.6   4.4e-07   0.00053       1      50 [.       8      52 ..       8      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.5e-05
                        Fer4_9 34 eaCigCgaCveaCpkgai 51
                                  ++C  CgaCv +C+k ai
  gi|15668713|ref|NP_247512.1|  7 KKCGYCGACVGVCEKLAI 24
                                  58999********98665 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 4.4e-07
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                  kC  CgaCv +C++ +++  +    +  +     +C  C+ C+ +Cp +a
  gi|15668713|ref|NP_247512.1|  8 KCGYCGACVGVCEKLAINLIEHIIVIDEK-----KCNNCKLCTIVCPLNA 52
                                  7999**************99988888864.....6************886 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.7   2.1e-05     0.025       1      21 [.       2      22 ..       2      29 .. 0.92
   2 !   11.0   0.8   0.00047      0.56       1      19 [.      31      49 ..      31      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                       Fer4_15  1 VvvDrdaCigcglCvaeapev 21
                                  V++D ++C  cg+Cv +++++
  gi|15668713|ref|NP_247512.1|  2 VKIDYKKCGYCGACVGVCEKL 22
                                  89***************9876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00047
                       Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                  +v+D+++C  c lC  ++p
  gi|15668713|ref|NP_247512.1| 31 IVIDEKKCNNCKLCTIVCP 49
                                  89************99987 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   3.2    0.0057       6.8       7      15 ..      12      20 ..       6      23 .. 0.82
   2 !   19.5   2.7   8.2e-07   0.00097       2      16 ..      36      50 ..      35      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0057
                        Fer4_4  7 CgsCvaaCP 15
                                  Cg+Cv +C+
  gi|15668713|ref|NP_247512.1| 12 CGACVGVCE 20
                                  ********8 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 8.2e-07
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  ++C++C+ C+++CP 
  gi|15668713|ref|NP_247512.1| 36 KKCNNCKLCTIVCPL 50
                                  79************6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   2.2   0.00025       0.3       3      16 ..       7      20 ..       5      37 .. 0.72
   2 !   13.2   4.0   7.6e-05      0.09      50      64 ..      37      51 ..      31      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                        Fer4_8  3 ekCieCgaCqsaCp 16
                                  +kC+ CgaC   C 
  gi|15668713|ref|NP_247512.1|  7 KKCGYCGACVGVCE 20
                                  68999999999995 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.6e-05
                        Fer4_8 50 sCttcgaCtevCpvg 64
                                  +C++c+ Ct vCp +
  gi|15668713|ref|NP_247512.1| 37 KCNNCKLCTIVCPLN 51
                                  799999999999975 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.6   0.00088       1.1       1      19 [.       8      26 ..       8      35 .. 0.83
   2 ?   11.4   3.9   0.00031      0.37      45      58 ..      37      50 ..      32      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00088
                       Fer4_17  1 rCiqCgyClpeCpsyeayd 19
                                  +C  Cg+C+ +C  ++++ 
  gi|15668713|ref|NP_247512.1|  8 KCGYCGACVGVCEKLAINL 26
                                  6999********9887765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00031
                       Fer4_17 45 lCieCgeCerkCPq 58
                                  +C++C++C+ +CP 
  gi|15668713|ref|NP_247512.1| 37 KCNNCKLCTIVCPL 50
                                  79999999999985 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.0    0.0043       5.1       1      17 [.       4      20 ..       4      22 .. 0.89
   2 ?   11.1   2.5   0.00038      0.45       1      17 [.      33      49 ..      33      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0043
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  +D ++C  cgaCv ++ 
  gi|15668713|ref|NP_247512.1|  4 IDYKKCGYCGACVGVCE 20
                                  7999*********9996 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00038
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  +D+++C +c++C  ++P
  gi|15668713|ref|NP_247512.1| 33 IDEKKCNNCKLCTIVCP 49
                                  89**************9 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   5.4      0.02        24       3      11 ..      11      19 ..       9      23 .. 0.80
   2 ?   13.3   4.0    0.0001      0.12       1      15 []      38      52 ..      38      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.02
                        Fer4_3  3 gCgaCvevC 11
                                   CgaCv vC
  gi|15668713|ref|NP_247512.1| 11 YCGACVGVC 19
                                  49******* PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.0001
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C++C +C  vCP +A
  gi|15668713|ref|NP_247512.1| 38 CNNCKLCTIVCPLNA 52
                                  ************987 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.0     0.011        13      60      72 ..       8      20 ..       2      30 .. 0.69
   2 ?    9.1   2.6    0.0012       1.4      57      73 ..      34      50 ..      20      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                       Fer4_18 60 dcidcescvkvcP 72
                                  +c  c++cv vc 
  gi|15668713|ref|NP_247512.1|  8 KCGYCGACVGVCE 20
                                  5667777777774 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0012
                       Fer4_18 57 gagdcidcescvkvcPt 73
                                  ++ +c +c+ c  vcP 
  gi|15668713|ref|NP_247512.1| 34 DEKKCNNCKLCTIVCPL 50
                                  5779************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 385.16
//
Query:       gi|15668714|ref|NP_247513.1|  [L=391]
Description: flavoprotein FprA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-13   51.2   0.0    2.2e-13   50.6   0.0    1.3  1  Flavodoxin_1  Flavodoxin
    0.00054   20.2   0.0     0.0009   19.5   0.0    1.4  1  Flavodoxin_5  Flavodoxin domain
  ------ inclusion threshold ------
      0.019   15.0   0.6      0.042   13.9   0.6    1.6  1  YmzC          YmzC-like protein
      0.042   13.6   0.0       0.13   12.1   0.0    1.8  1  UBA_3         Fungal ubiquitin-associated domain
       0.13   12.2   0.0       0.34   10.9   0.0    1.7  1  CSN7a_helixI  COP9 signalosome complex subunit 7a helix I dom


Domain annotation for each model (and alignments):
>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   6.1e-17   2.2e-13       1     132 [.     249     371 ..     249     382 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 6.1e-17
                                   EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSC.GGGGGTHSEEEEEEEEETTTBEEGGGH.HHHHHHHHHHCHH CS
                  Flavodoxin_1   1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydes.lseieeealllvvtsTfgnGdppenge.sffqdllelkgde 79 
                                   i+Y++ + +tek+Ak+l+e+l+e+g++   v  +++d s l+ i++++l +++++   +G+p+ n++ ++++  l  +   
  gi|15668714|ref|NP_247513.1| 249 IVYATIYSSTEKIAKALGEGLSEEGVD---VIYHRLDTSpLNIIMRDILDAKYVL---VGSPTINMNvHPKVGMLLTYI-- 321
                                   89********************99974...44667776679**************...********************5.. PP

                                   GCCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEES.SSEEEETTS CS
                  Flavodoxin_1  80 ledgdlsgvrfavfglGdsayenFcaagkkldekleelGaerll.kllegdedn 132
                                    e g     +   +++G++++++  +a kk+ e +++lG++++  k l+   ++
  gi|15668714|ref|NP_247513.1| 322 -E-GLKPSNKKIGVAFGSYGWKE--CATKKIIEAFKRLGFKIVDdKILTFRFAP 371
                                   .4.44455555699*********..*****************986556555555 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.5e-07    0.0009       2      67 ..     249     319 ..     248     361 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.5e-07
                  Flavodoxin_5   2 ilYsSrdGqTkkiaeriaeelree.....gelvdvedvekesedlesydavvigasvyygkllpelakFve 67 
                                   i+Y++ + +T+kia+++ e l+ee      + +d ++++  + d+ +++ v++g++  +++++p++  +++
  gi|15668714|ref|NP_247513.1| 249 IVYATIYSSTEKIAKALGEGLSEEgvdviYHRLDTSPLNIIMRDILDAKYVLVGSPTINMNVHPKVGMLLT 319
                                   9***********************7777667778888777889*********************9977666 PP

>> YmzC  YmzC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   1.2e-05     0.042      32      54 ..     360     382 ..     356     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                   ETTEEEEEEEETTTTEEEEEEEE CS
                          YmzC  32 kDdeikiykfdedenEvkLiKef 54 
                                    Dd+i  ++f ++en++k iKef
  gi|15668714|ref|NP_247513.1| 360 VDDKILTFRFAPKENDIKKIKEF 382
                                   599*******************9 PP

>> UBA_3  Fungal ubiquitin-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.6e-05      0.13      23      39 ..     345     361 ..     334     365 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
                                   HHHHHHHHHHS--SS-- CS
                         UBA_3  23 kdkvievLkrLgiksld 39 
                                   + k+ie++krLg k +d
  gi|15668714|ref|NP_247513.1| 345 TKKIIEAFKRLGFKIVD 361
                                   68************987 PP

>> CSN7a_helixI  COP9 signalosome complex subunit 7a helix I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   9.4e-05      0.34      15      48 ..     144     178 ..     142     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.4e-05
                  CSN7a_helixI  15 sCeaiLs.ciEtqverANaeknkaikhkekieqEv 48 
                                    Ce  L  c+E+ +   N  +++++  keki++++
  gi|15668714|ref|NP_247513.1| 144 KCEYMLTyCVEDKILFSNDLFSQHVVYKEKIDSDI 178
                                   58888865*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2573.29
//
Query:       gi|15668715|ref|NP_247514.1|  [L=343]
Description: acetylpolyamine aminohydrolase AphA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.8e-65  219.2   0.0    1.5e-64  218.4   0.0    1.3  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.4   0.0   8.6e-69   1.5e-64       1     293 [.      23     291 ..      23     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 218.4 bits;  conditional E-value: 8.6e-69
                                   SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSSSSST CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiasklldddt 81 
                                   h+enp+R+  il+sl+++ g +d+      + + t +e+l++Hs++Y+ ++ +ls++ +                 +d+dt
  gi|15668715|ref|NP_247514.1|  23 HVENPERVLTILNSLKSN-G-FDDIV--LIEGKSTINEILEIHSRDYVYSIINLSKSFNY----------------YDGDT 83 
                                   89**************97.6.45544..4577888999**********999987654433................4799* PP

                                   HCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-.BTTB-B.....TTBSS-HHHHHHHHHHHCC-SS-EEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl  82 pvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHa.kaseas.....GFClvNnvaiaikylqakhelkrvai 156
                                   +++++tl+aal+a   + eav++ l++  +  f+l rPpgHHa  +++a      GFC++Nn+a a++ +++   +k+v+i
  gi|15668715|ref|NP_247514.1|  84 YLCDRTLDAALTAFKLAKEAVKLALKD-RDLYFALTRPPGHHAgISGRALgamsnGFCIFNNIAGAARLAKN--YMKKVII 161
                                   *************************88.5999***********888885455567*************9998..458**** PP

                                   EE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl 157 lDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvleef 237
                                   +D+DvHhGnGt+e+f++d++v+++++H+  +++yPgtg++ d+g +++kg+++n+p++++++d++y+ +++ei++p+l+ f
  gi|15668715|ref|NP_247514.1| 162 IDFDVHHGNGTQEIFWNDNRVIHIDFHQ--RGIYPGTGDILDIGGEEAKGTKINLPFPAHSTDADYIFAWNEIVEPILNYF 240
                                   ****************************..899************************************************ PP

                                   --SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S---H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl 238 kPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkvkkvvllleGGYnl 293
                                   +Pd +lvsaGfDa  +d l++++l++  y  +  kl   +     v ++leGGY++
  gi|15668715|ref|NP_247514.1| 241 SPDTVLVSAGFDAFINDGLASMDLTETFYRFVGAKLSGYS-----VTAVLEGGYSI 291
                                   **************************99999999998877.....589******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2422.66
//
Query:       gi|15668716|ref|NP_247515.1|  [L=187]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit gamma [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-37  128.3   0.0    3.7e-37  128.1   0.0    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.1   0.0   2.1e-41   3.7e-37       1     177 []      18     182 ..      18     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 2.1e-41
                                   CTSTHHHHHHHHHHHH.HHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEE CS
                           POR   1 GGqGvvtagkilakaa.araGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpgg 80 
                                   GGqG+++ag il++aa  +  ++++++++yg+e rGg+s s+v isde +++ ++v ++d+lv+l +++++++ d++k+gg
  gi|15668716|ref|NP_247515.1|  18 GGQGIILAGVILGRAAaLYDNKEAVQTQSYGPEARGGASKSEVVISDE-PIDFPKVIKPDILVCLSQQAYDKYKDDIKEGG 97 
                                   9***************88999***************************.89****************************** PP

                                   EEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHHHHHHCCS-C CS
                           POR  81 iiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lplealeeaikkrfpk 160
                                   +++++++ +++d +++ +             +y++++t+ia e    +++aN+vmlGal +l++ ++ e++e+ai +++pk
  gi|15668716|ref|NP_247515.1|  98 VVLVDEDLVSTDKMPEVDV-----------TMYKIPFTRIASEEIKLPIVANIVMLGALTRLTNiVSKESMEKAILDSVPK 167
                                   ******9999999999887...........58*********977777*********************************9 PP

                                   H.HHHHHHHHHHHHHHH CS
                           POR 161 kkeviekNlkafragye 177
                                        ekNl af +gye
  gi|15668716|ref|NP_247515.1| 168 G--TEEKNLLAFSKGYE 182
                                   6..89***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1268.73
//
Query:       gi|15668717|ref|NP_247516.1|  [L=270]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit beta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-38  130.1   0.2    8.4e-38  129.6   0.2    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.6   0.2   4.7e-42   8.4e-38       2     153 .]      50     197 ..      49     197 .. 0.95

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 4.7e-42
                                   SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE CS
                  TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvln 81 
                                   iGc+++          p+ ++ +++++t+G+ +++A+G+k+a+pd++vv+++GDG+++ i ++++++ +rrn+++tv+++n
  gi|15668717|ref|NP_247516.1|  50 IGCSSR---------VPGYLYCDSLHTTHGRPIAFATGIKIARPDKHVVVFTGDGDLAAIgGNHFIHGCRRNIDLTVICIN 121
                                   677776.........366666699********************************************************* PP

                                   -SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  82 Negygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                   N++ygmtggq   ++p+g+k +++p+g++++ +d++k+a a+Ga+ +ar ++a++ +l + +k+ ++kkg+a+iev
  gi|15668717|ref|NP_247516.1| 122 NNIYGMTGGQvspTTPYGKKATTAPYGSIENTMDLCKMAIAAGATyVARWTTAHPIQLVRSIKKGIQKKGFAFIEV 197
                                   *********************************************999**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1642.64
//
Query:       gi|15668718|ref|NP_247517.1|  [L=260]
Description: hypothetical protein MJ_0538 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   15.1   0.0      0.031   14.3   0.0    1.4  1  WYL       WYL domain


Domain annotation for each model (and alignments):
>> WYL  WYL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.7e-06     0.031     118     162 ..      42      90 ..       6      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-06
                           WYL 118 qkieeedddgsv.....rvelpvesleellswllsfgdeveVlePaeLre 162
                                   ++iee d++ ++     ++e+++++ ++ + + l +g+++eV++P++L+ 
  gi|15668718|ref|NP_247517.1|  42 EDIEE-DENLKFytkigEFEINFDNFKDYINFCLKYGADIEVIKPEKLKL 90 
                                   44554.444444455557999999***********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1574  (0.0877907); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1676.40
//
Query:       gi|15668719|ref|NP_247518.1|  [L=530]
Description: tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     2e-139  464.5   0.1   2.8e-139  464.0   0.1    1.2  1  tRNA-synt_1f    tRNA synthetases class I (K)
    4.7e-05   22.3   2.2     0.0024   16.7   0.0    2.7  3  tRNA-synt_1g    tRNA synthetases class I (M)
     0.0011   18.8   1.4      0.088   12.7   0.2    2.6  2  eIF-5_eIF-2B    Domain found in IF2B/IF5
     0.0016   17.9   0.4        1.7    7.9   0.0    2.9  4  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.039   13.7   1.6      0.084   12.6   1.6    1.5  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
       0.14   12.0   1.4          8    6.3   0.1    3.2  3  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
        1.7    8.6   7.7        2.4    8.2   0.4    3.1  3  DUF4298         Domain of unknown function (DUF4298)


Domain annotation for each model (and alignments):
>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.0   0.1  1.1e-142  2.8e-139       1     359 [.       1     360 [.       1     361 [. 0.98

  Alignments for each domain:
  == domain 1  score: 464.0 bits;  conditional E-value: 1.1e-142
                  tRNA-synt_1f   1 kaWadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvpenl 81 
                                   ++Wad++aeklieer k+    d+++v+sGi+pSG+iH+Gn+re+ltad++++ l ++g e++li+i+D++D+lRk++++l
  gi|15668719|ref|NP_247518.1|   1 MHWADVIAEKLIEER-KA----DKYIVASGITPSGHIHVGNARETLTADAIYKGLINKGVEAELIFIADTYDPLRKLYPFL 76 
                                   69**********888.33....79********************************************************* PP

                  tRNA-synt_1f  82 pekllekylgkpltsiPdpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenrekikeilekyr 162
                                   p++ +e+y+g+pl++iP+p+g++esyaehf ++++esLd+lg+e+++++a e Yk+glyde+ik+al+nreki+eil+k+r
  gi|15668719|ref|NP_247518.1|  77 PKE-FEQYIGMPLSEIPCPEGCCESYAEHFLRPYLESLDDLGVELTTYRADENYKKGLYDEKIKIALDNREKIMEILNKFR 156
                                   ***.***************************************************************************** PP

                  tRNA-synt_1f 163 geereetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeeevdiregngKLqWkvdwamrWaalgVdfEpaGkD 243
                                    +++ ++++p+++vce+cg+ ++t+v+++d+e+eei+Y+ce cG+e++v+  +g++KL+W+vdw++rW++++V++Ep+GkD
  gi|15668719|ref|NP_247518.1| 157 ANPLPDDWWPINIVCENCGK-LKTKVIKYDSEKEEITYRCEICGFENTVKPYKGRAKLPWRVDWPARWSIFNVTIEPMGKD 236
                                   ********************.8*********************************************************** PP

                  tRNA-synt_1f 244 haaaGgSvdvsskia.eilggeaPekvvYelillkgge...kmssSkGnvltledwlevaepevlrflilrrkPkkakkld 320
                                   haaaGgS+d++  ia ei+++ +P+kvvYe+i+lk g+    mssSkG+v++++dw+++a+pe+lrfl+lr+kP+k++++d
  gi|15668719|ref|NP_247518.1| 237 HAAAGGSYDTGVLIAkEIYNYIPPKKVVYEWIQLKVGDkaiPMSSSKGVVFAVKDWTNIAHPEILRFLLLRSKPTKHIDFD 317
                                   ***********************************9997788*************************************** PP

                  tRNA-synt_1f 321 ldleilrlvdeYdklerkyf.....aeqeeeeekekrvyelsav 359
                                   l+ +i++lvdeYd+le+ yf     +e +eee+++ r+yels++
  gi|15668719|ref|NP_247518.1| 318 LK-KIPDLVDEYDRLEDFYFnnkdkDELSEEEQEKIRIYELSTP 360
                                   **.*****************999888889999*********986 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0047        12      10      39 ..      28      57 ..      20      67 .. 0.73
   2 !   16.7   0.0   9.2e-07    0.0024     287     370 ..     232     320 ..     208     329 .. 0.75
   3 ?   -3.8   0.1       1.5   3.9e+03     266     283 ..     451     466 ..     443     493 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0047
                                  -SS---HHHHHHHHHHHHHHHHHHHTT-EE CS
                  tRNA-synt_1g 10 angklHlGhllevisaDifaRykrlrgeev 39
                                  ++g++H+G+++e++ aD++++    +g e 
  gi|15668719|ref|NP_247518.1| 28 PSGHIHVGNARETLTADAIYKGLINKGVEA 57
                                  5799**************998766665553 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 9.2e-07
                                   EEEGGGHHHHHTHHHHHHHH...TT----S-EEEE--EEE-.---...----------HHHHHHHH-HHHHHHHHHHHS-T CS
                  tRNA-synt_1g 287 figkdiikFHtifwPaillg...aelklpkkvvaheyltve.gkK...lSkSrgvvvkakealerldadllRYylaaeape 360
                                    +gkd       + + +l++    ++  pkkv + e+++++ g+K   +S+S+gvv  +k++++  ++++lR+ l++++p+
  gi|15668719|ref|NP_247518.1| 232 PMGKDHAAAGGSYDTGVLIAkeiYNYIPPKKV-VYEWIQLKvGDKaipMSSSKGVVFAVKDWTNIAHPEILRFLLLRSKPT 311
                                   56777777777777777888544455556665.678888764666677****************************98886 PP

                                   TS-EEE-HHH CS
                  tRNA-synt_1g 361 kkDldfswed 370
                                   k  +df +++
  gi|15668719|ref|NP_247518.1| 312 K-HIDFDLKK 320
                                   4.56666665 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.5
                                   .TTSGGGG.G--S..... CS
                  tRNA-synt_1g 266 kgeeekwkeyWakdkeve 283
                                   k+++++w +y+a+  + +
  gi|15668719|ref|NP_247518.1| 451 KDKQKEWIKYFAE--KLK 466
                                   3444455555522..222 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.2   3.4e-05     0.088      88     116 ..     169     200 ..     135     201 .. 0.90
   2 ?    4.6   0.1     0.011        28      30      57 ..     442     469 ..     413     485 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                                   TSTSSSTSTCEEECC...SSSCEEEEESSSTC CS
                  eIF-5_eIF-2B  88 VlCkeCkspetelek...eerllvlkCkaCga 116
                                   ++C++C++  t+++k   e++ ++ +C+ Cg 
  gi|15668719|ref|NP_247518.1| 169 IVCENCGKLKTKVIKydsEKEEITYRCEICGF 200
                                   79*************998566666******96 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                                   THHHHHHHHTTSHHHHHHHHHHHHTSEE CS
                  eIF-5_eIF-2B  30 NfeeiakaLnrdpehvlkyllkelgtqg 57 
                                     +ei ++L+ +++  +ky+  +l t+ 
  gi|15668719|ref|NP_247518.1| 442 EAKEIYEKLKDKQKEWIKYFAEKLKTAE 469
                                   5789********************9874 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00065       1.7       7      49 ..      14      58 ..       9     127 .. 0.78
   2 ?   -3.5   0.0         2   5.1e+03     251     274 ..     135     158 ..     133     160 .. 0.81
   3 !    6.9   0.0    0.0013       3.4     254     296 ..     279     321 ..     265     325 .. 0.90
   4 ?   -2.7   0.1       1.1   2.8e+03     117     154 ..     424     462 ..     385     476 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00065
                                  TTEEEEEE..EEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEE CS
                  tRNA-synt_1e  7 ekkvtlYv..CGptvydashlGhaRslvafDilrrilqalgYdvq 49
                                  e+k + Y+   G+t   ++h+G+aR++++ D + + l ++g + +
  gi|15668719|ref|NP_247518.1| 14 ERKADKYIvaSGITPSGHIHVGNARETLTADAIYKGLINKGVEAE 58
                                  555555542269*******************99888877665544 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2
                                   TBE--TTTT---BHHHHHTTS-HH CS
                  tRNA-synt_1e 251 gekmsksLknfitikdvlkkfdpr 274
                                   +ek+  +L+n  +i ++l+kf+++
  gi|15668719|ref|NP_247518.1| 135 DEKIKIALDNREKIMEILNKFRAN 158
                                   578888899999999999999875 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0013
                                   --TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHH CS
                  tRNA-synt_1e 254 msksLknfitikdvlkkfdprqlRllllsahyrsqldfkeell 296
                                   ms s + ++ +kd  +  +p++lR+lll  +  +++df+ +++
  gi|15668719|ref|NP_247518.1| 279 MSSSKGVVFAVKDWTNIAHPEILRFLLLRSKPTKHIDFDLKKI 321
                                   9************************************986655 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.1
                                   HTTSEEE-TTS-EEE-.GGG-TTTTTTTT--HHHHHHT- CS
                  tRNA-synt_1e 117 ekgyaYavsdgdvyfd.vskkeeYgklskqnleelelga 154
                                   ++++a +  +  v  +  ++ke Y kl+ +++e ++  a
  gi|15668719|ref|NP_247518.1| 424 ARNWALKYGEKLVIISeDEAKEIYEKLKDKQKEWIKYFA 462
                                   444444444433333302334445555555555554444 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.6   3.3e-05     0.084      22      54 .]     168     202 ..     165     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.3e-05
                zinc_ribbon_10  22 alICskChshnGlap..keeleevkyrCpkCgaln 54 
                                    ++C++C +    +    +e+ee++yrC  Cg+ n
  gi|15668719|ref|NP_247518.1| 168 NIVCENCGKLKTKVIkyDSEKEEITYRCEICGFEN 202
                                   69*****9877777768999***********9865 PP

>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.052   1.3e+02      27      46 ..      51      71 ..      46      85 .. 0.87
   2 ?   -0.9   0.6      0.53   1.3e+03      36      61 ..     169     193 ..     167     199 .. 0.89
   3 ?    6.3   0.1    0.0031         8      32      56 ..     433     464 ..     428     478 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.052
                                  HHTT.TESEEEEETTSSSGGH CS
                Ribosomal_L7Ae 27 lerg.eaklvilAedvepeek 46
                                  +++g ea+l+++A+  +p +k
  gi|15668719|ref|NP_247518.1| 51 INKGvEAELIFIADTYDPLRK 71
                                  77888***********99876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.53
                                   EEETTSSSGGHHHHHHHHHHHTTEEE CS
                Ribosomal_L7Ae  36 ilAedvepeekkkllealckekevpy 61 
                                   i++e++ + + k  +++ +++ e+ y
  gi|15668719|ref|NP_247518.1| 169 IVCENCGKLKTKV-IKYDSEKEEITY 193
                                   799*****99999.999999999987 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0031
                                   ESEEEEETTSSSGGHHH.......HHHHHHHH CS
                Ribosomal_L7Ae  32 aklvilAedvepeekkk.......llealcke 56 
                                    klvi++ed  +e ++k       ++++++++
  gi|15668719|ref|NP_247518.1| 433 EKLVIISEDEAKEIYEKlkdkqkeWIKYFAEK 464
                                   59***************889999999999986 PP

>> DUF4298  Domain of unknown function (DUF4298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.99   2.5e+03      55      76 ..      31      52 ..      27      58 .. 0.80
   2 ?    8.2   0.4   0.00095       2.4      16      56 ..     312     352 ..     307     358 .. 0.84
   3 ?    0.9   2.9      0.18   4.6e+02      18      86 ..     392     459 ..     380     462 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.99
                                  .....--SSTTSSSHHHHHHHH CS
                       DUF4298 55 elpqelkysvLSEDgiynalgd 76
                                  ++   + +  L+ D+iy  l++
  gi|15668719|ref|NP_247518.1| 31 HIHVGNARETLTADAIYKGLIN 52
                                  56677788899******98876 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00095
                                   HHHHHHHHHHHHTHHHHHHHHHHHTSHHHHHHHTS--SS.. CS
                       DUF4298  16 qqLeealeqwkklqkklakLdeYYqseqwredleasnkgel 56 
                                   + ++  l+++ +l ++++ L+++Y  ++ ++ l + +++++
  gi|15668719|ref|NP_247518.1| 312 KHIDFDLKKIPDLVDEYDRLEDFYFNNKDKDELSEEEQEKI 352
                                   56677899****************99988888888777765 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHTHHHHHHHHHHHTSHHHHHHHTS--SS.....--SSTTSSSHHHHHHHHHHHHHHHHHH CS
                       DUF4298  18 LeealeqwkklqkklakLdeYYqseqwredleasnkgelpqelkysvLSEDgiynalgdakelakellk 86 
                                   +e++ e ++++   ++++de+  ++   + l a n   l+  +k  ++SED   +++++ k+ +ke++k
  gi|15668719|ref|NP_247518.1| 392 MERVFEILRRNNYSIDDIDEFSMKKLKDRLLMARNW-ALKYGEKLVIISEDEAKEIYEKLKDKQKEWIK 459
                                   566677777778888888888888877777777776.599999999*****877777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1235  (0.0688828); expected 358.6 (0.02)
Passed bias filter:                      775  (0.0432261); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 3481.30
//
Query:       gi|15668720|ref|NP_247519.1|  [L=85]
Description: hypothetical protein MJ_0540 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-18   67.2   8.5    1.4e-18   66.9   8.5    1.1  1  DUF2097   Uncharacterized protein conserved in archaea (DUF20
  ------ inclusion threshold ------
      0.048   13.5   0.1       0.08   12.8   0.1    1.4  1  SHD1      SLA1 homology domain 1, SHD1
      0.054   13.5   3.4       0.75    9.9   0.1    2.3  2  DUF3791   Protein of unknown function (DUF3791)
       0.11   12.6   0.0       0.17   12.0   0.0    1.4  1  SAM_2     SAM domain (Sterile alpha motif)


Domain annotation for each model (and alignments):
>> DUF2097  Uncharacterized protein conserved in archaea (DUF2097)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   8.5   3.2e-22   1.4e-18       5      87 .]       8      81 ..       4      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 3.2e-22
                       DUF2097  5 ltaeelieYiknnvkegdileisynrvfvpGevlsiekkeslrltlkldgelinqlvevdleeikddliElrHipkdgekviv 87
                                   +++e+ieY+ nn+++++++ei+++rv+v+G+++++++       ++l +e ++ ++ev++e+i ddl+El+H  ++gek++v
  gi|15668720|ref|NP_247519.1|  8 KNPKEVIEYL-NNIDVDEYVEIYFGRVHVEGRLMHYND-----GLIRLVHEKYG-IIEVEIEKILDDLLELVH--SNGEKRVV 81
                                  689*******.***************************.....9**********.******************..69988875 PP

>> SHD1  SLA1 homology domain 1, SHD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.8e-05      0.08      19      61 ..      32      74 ..      30      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                          SHD1 19 sFkVeAeflglkdgkirLhkvnGvkiaVpvekmskeDleyvek 61
                                  + +Ve  ++ ++dg irL      +i+V +ek+  + le+v +
  gi|15668720|ref|NP_247519.1| 32 RVHVEGRLMHYNDGLIRLVHEKYGIIEVEIEKILDDLLELVHS 74
                                  6689**************9999999********9888888876 PP

>> DUF3791  Protein of unknown function (DUF3791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00017      0.75      17      46 ..       9      38 ..       8      44 .. 0.91
   2 ?    4.5   0.9    0.0083        37      29      58 ..      45      73 ..      38      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00017
                       DUF3791 17 sgkevykllkksgvldylidcYevlHtqSk 46
                                  ++kev+++l++ +v +y++ ++   H +++
  gi|15668720|ref|NP_247519.1|  9 NPKEVIEYLNNIDVDEYVEIYFGRVHVEGR 38
                                  689*********************999886 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0083
                       DUF3791 29 gvldylidcYevlHtqSkeyivedideylk 58
                                  g++++++++Y +   + +e i++d+ e+++
  gi|15668720|ref|NP_247519.1| 45 GLIRLVHEKYGIIEVE-IEKILDDLLELVH 73
                                  5569999999999876.8999999999876 PP

>> SAM_2  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.8e-05      0.17       2      24 ..       6      28 ..       5      45 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                                  GGHHHHHHHHHHHHTTTGGGHHH CS
                         SAM_2  2 eswsledvaeWLrsiglkqytdn 24
                                  +++++++v e+L +i+  +y+++
  gi|15668720|ref|NP_247519.1|  6 DVKNPKEVIEYLNNIDVDEYVEI 28
                                  6899*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 599.84
//
Query:       gi|15668721|ref|NP_247520.1|  [L=168]
Description: nicotinamide-nucleotide adenylyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-18   65.9   0.0    1.3e-17   64.4   0.0    1.7  1  CTP_transf_like  Cytidylyltransferase-like
    0.00035   19.9   0.1      0.044   13.0   0.1    2.1  2  HIGH_NTase1      HIGH Nucleotidyl Transferase
     0.0043   16.6   0.0        1.1    8.7   0.0    2.1  2  ATP-sulfurylase  ATP-sulfurylase
  ------ inclusion threshold ------
       0.13   11.9   0.0       0.74    9.5   0.0    2.1  2  Citrate_ly_lig   Citrate lyase ligase C-terminal domain


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   2.8e-21   1.3e-17       2     143 .]       5     132 ..       4     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 2.8e-21
                                   EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTTT CS
               CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevlkklkp 82 
                                   + G+F+p+H+GHl+++++++++++e +i+g+ s+++++   +++++a eR+ m+ +  ++ + ++  p+      +k+++ 
  gi|15668721|ref|NP_247520.1|   5 IIGRFQPFHKGHLEVIKKIAEEVDE-IIIGIGSAQKSHTL-ENPFTAGERILMITQSLKDYD-LTYYPIP-----IKDIEF 77 
                                   68***********************.************99.****************77777.3333333.....444444 PP

                                   TEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHHH CS
               CTP_transf_like  83 dklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkirer 143
                                   +  ++v   ++l+       ++ +++ ++lv v ++e+ ++v+ +++ +++++S+t+ir+r
  gi|15668721|ref|NP_247520.1|  78 N-SIWVSYVESLTP-----PFDIVYSGNPLVRVLFEERGYEVKRPEMFNRKEYSGTEIRRR 132
                                   3.599999999998.....7***************************************97 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   9.8e-06     0.044       6      34 ..       5      32 ..       3      38 .. 0.81
   2 !    5.0   0.0    0.0026        12     201     237 ..     121     154 ..     101     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.8e-06
                   HIGH_NTase1  6 iIaEYNPfHnGHlyhlekakeltgadvvi 34
                                  iI  + PfH+GHl  ++k+ e+++ +++i
  gi|15668721|ref|NP_247520.1|  5 IIGRFQPFHKGHLEVIKKIAEEVD-EIII 32
                                  788899**************9854.4444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0026
                   HIGH_NTase1 201 eeiaSAtaiRkalkeekkleelkklvPestleilkee 237
                                   ++  S t iR+ + +    e+ ++lvP+++++++ke 
  gi|15668721|ref|NP_247520.1| 121 RKEYSGTEIRRRMLNG---EKWEHLVPKAVVDVIKEI 154
                                   35679*******9666...78***********99875 PP

>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0014       6.4      29      52 ..      10      32 ..       4      61 .. 0.85
   2 !    8.7   0.0   0.00025       1.1     176     211 ..     119     153 ..      92     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0014
                                  S---HHHHHHHHHHHHHTSEEEEE CS
               ATP-sulfurylase 29 nplHraHeellkraleeeadglll 52
                                  +p+H++H e++k+++e e+d +++
  gi|15668721|ref|NP_247520.1| 10 QPFHKGHLEVIKKIAE-EVDEIII 32
                                  79**************.6875555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00025
                                   GGEEE--HHHHHCCHHTT----TTTS-HHHHHHHHH CS
               ATP-sulfurylase 176 eevesisgtelrkllregeeipewfsrpevlkvLre 211
                                    +++++sgte+r+++ +ge+  e+++ + v++v++e
  gi|15668721|ref|NP_247520.1| 119 FNRKEYSGTEIRRRMLNGEKW-EHLVPKAVVDVIKE 153
                                   57899**************98.77888889988875 PP

>> Citrate_ly_lig  Citrate lyase ligase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00017      0.74       8      56 ..       9      62 ..       3      69 .. 0.81
   2 ?   -1.6   0.0      0.41   1.8e+03     149     177 ..     120     146 ..     103     151 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00017
                Citrate_ly_lig  8 anPftlGhryLvekaakendvvhlfvvkedksl.....fsyeerlklvkkGikd 56
                                    Pf +Gh  +++k a+e d +++ + + +ks+     f++ er+ ++++ +kd
  gi|15668721|ref|NP_247520.1|  9 FQPFHKGHLEVIKKIAEEVDEIIIGIGSAQKSHtlenpFTAGERILMITQSLKD 62
                                  57************************9999986444446777888888887776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.41
                Citrate_ly_lig 149 eeelisaskvrkllkeknleklaelvPkt 177
                                   + +  s +++r+ + ++  ek ++lvPk+
  gi|15668721|ref|NP_247520.1| 120 NRKEYSGTEIRRRMLNG--EKWEHLVPKA 146
                                   45566777777665543..4455677765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1128.37
//
Query:       gi|15668722|ref|NP_247521.1|  [L=1188]
Description: phosphoenolpyruvate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.6e-124  414.8   0.5   5.3e-124  413.7   0.5    1.5  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    4.3e-89  298.5   0.3      1e-88  297.3   0.3    1.6  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    5.9e-23   80.4   1.5    6.2e-12   45.1   0.1    2.6  2  PEP-utilizers    PEP-utilising enzyme, mobile domain
    1.6e-07   31.5   6.4      0.028   14.7   5.1    3.8  2  LAGLIDADG_3      LAGLIDADG-like domain
      1e-06   28.7   2.4      1e-06   28.7   2.4    2.4  2  Intein_splicing  Intein splicing domain
     0.0033   16.6   0.0     0.0085   15.3   0.0    1.7  1  HpcH_HpaI        HpcH/HpaI aldolase/citrate lyase family
  ------ inclusion threshold ------
       0.04   14.2   1.2       0.17   12.2   0.1    2.6  3  SepF             Cell division protein SepF
      0.046   13.9   0.4        2.5    8.3   0.0    3.1  2  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
       0.16   12.1   0.0       0.58   10.3   0.0    1.9  1  FokI_N           Restriction endonuclease FokI, recognition d


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.7   0.5  2.7e-127  5.3e-124       2     324 ..      27     343 ..      26     347 .. 0.98

  Alignments for each domain:
  == domain 1  score: 413.7 bits;  conditional E-value: 2.7e-127
                        PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelPeele 82 
                                   ++ GGKga+L+e+ n ag+pvPp f++tada+r+f++e+gl +ki+e+l+ ldv+d+d+l++ask+ir+li +ae+Pe+l+
  gi|15668722|ref|NP_247521.1|  27 DIAGGKGASLGEMWN-AGLPVPPAFVVTADAYRHFIKETGLMDKIREILSGLDVNDTDALTNASKKIRKLIEEAEMPEDLR 106
                                   679**********66.***************************************************************** PP

                        PPDK_N  83 eaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYrkekgldhe 163
                                    ai eay++l++ +g++e+ vaVRSSataEDlp+asfaGqqdtyLn++g+e+v++ ++++f+Slf++rAi+Yr+++g+dh+
  gi|15668722|ref|NP_247521.1| 107 LAIIEAYNKLCEMCGEDEVTVAVRSSATAEDLPEASFAGQQDTYLNIKGAENVVKYVQKCFSSLFTPRAIFYREQQGFDHF 187
                                   ********************************************************************************* PP

                        PPDK_N 164 evalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilekkigekeikivyd 244
                                   +vala+vvqk+vn++  ++GV+f+++p + + de++i+a++GlGe VV+G v+pd+++v+k+t +i++k+i++ke+++v d
  gi|15668722|ref|NP_247521.1| 188 KVALAAVVQKLVNAE--KAGVMFTVNPISENYDELVIEAAWGLGEGVVSGSVSPDTYIVNKKTLEIVDKHIARKETMFVKD 266
                                   ***************..**************************************************************** PP

                        PPDK_N 245 ekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaideeegklyllQaRpetrtsekkekkaaetl 324
                                   ek+ +tk vevp++ +ek++Lsd+e++eLa+i+ +iekhyg+pmd+E+a++  +gk+y+lQaRp+t+ ++ k++k+a+++
  gi|15668722|ref|NP_247521.1| 267 EKG-ETKVVEVPDDMKEKQVLSDDEIKELAKIGLNIEKHYGKPMDVEWAYE--KGKFYMLQARPITTLKKGKKEKKAKEE 343
                                   *99.66*******************************************99..***************999988887765 PP

>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.3   0.3   5.1e-92     1e-88       3     293 ..     875    1172 ..     871    1173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 297.3 bits;  conditional E-value: 5.1e-92
                                    HSTSCCCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCC.HHHHHH..........HHHHHHH CS
               PEP-utilizers_C    3 esgklktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmaree.lpteee..........qaeaykk 70  
                                    ++++++ ++a++ + +  +v +N+++pe ae+a+++ga+G+GLlR+E++++   + + ++ e          ++e ++k
  gi|15668722|ref|NP_247521.1|  875 KKQEVVVQQAPIITAT--EVKVNVSMPEVAERAAATGADGVGLLRAEHMILGLGKhPRKILEeegeealieaLMEGIRK 951 
                                    3444555555555555..5555******************************966344433358*************** PP

                                    HHHHTTTSEEEEEXXXSSCC..GGSGGCHHHH.XSXGGGSSXTHHHHCCSHHHHHHHHHHHHHHCCCC..EEEEEESSX CS
               PEP-utilizers_C   71 vleamngrpvvvRtlDiggd..kelpelkeepeevNPmlGfRgirlglsepelfetqlrAllrasaag..kleimlPmv 145 
                                    v++a+++rpv++RtlD+++d  + l+ +++ep e NPmlG+Rgir+ l+e ++++ +l+A++r +++g  ++eim+P+v
  gi|15668722|ref|NP_247521.1|  952 VADAFYPRPVTYRTLDAPTDefRGLEGGENEPIEHNPMLGWRGIRRDLDEVDILKCELKAIKRLREEGykNIEIMIPLV 1030
                                    ********************8889******************************************5555********* PP

                                    XSHHHHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTT.SSEEEEXHHHHHHHHHTXXCCCHCHH CS
               PEP-utilizers_C  146 asveeleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklake.vdFfSiGtNDLtQytlavdRdneeva 223 
                                    ++++e+++ k+i++ev       g++  k++ +GiM+E+p+aal++++++ke ++F+S+GtNDLtQyt+a+dR+ne v+
  gi|15668722|ref|NP_247521.1| 1031 THPDEVRRVKEIMREV-------GLEPCKDIPFGIMVETPAAALIIEDFIKEgINFVSLGTNDLTQYTIAIDRNNELVS 1102
                                    ****************.......89999***********************99************************** PP

                                    HHSXTTTCHHCCCHHHHHHHHHHCCXEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
               PEP-utilizers_C  224 klydplepavlrlikevikaaeekglkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqve 293 
                                    k y + +pavl+l+++vik+++++g+k++iCG++++ p++ve lv+ G+d++S++ ++v ++r+++a++e
  gi|15668722|ref|NP_247521.1| 1103 KYYKEDHPAVLKLVEHVIKTCKKHGIKTSICGQAGSRPHIVEKLVEWGIDSVSANIDAVETIRRVVARTE 1172
                                    *****************************************************************99875 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1     1e-11     2e-08       1      36 [.     376     411 ..     376     412 .. 0.96
   2 !   45.1   0.1   3.1e-15   6.2e-12      35      73 .]     822     860 ..     821     860 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1e-11
                                   G--S-EEEEES---HHHHTTS-GEEEEEES--TTHH CS
                 PEP-utilizers   1 kleegvILvaeetspsdiagldkaaGivterGGmtS 36 
                                   k++eg+ILv+e+t+p+++++++kaa+ivt++GG t+
  gi|15668722|ref|NP_247521.1| 376 KVKEGDILVTEMTTPDMVPAMKKAAAIVTDEGGLTC 411
                                   5799*****************************997 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 3.1e-15
                                   HHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                 PEP-utilizers  35 tSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                   ++HaAiv+relg P+Vvg+++at++lk+g ++tvDg++G
  gi|15668722|ref|NP_247521.1| 822 NCHAAIVSRELGTPCVVGTKKATKVLKDGMIVTVDGEKG 860
                                   79***********************************99 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   7.6e-05      0.15       4      41 ..     533     574 ..     531     581 .. 0.89
   2 !   14.7   5.1   1.4e-05     0.028       2      79 ..     625     709 ..     624     771 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.6e-05
                                   HHHHHHHHHHCCECCECSTTTTSEEEEES-....HHHHHHHH CS
                   LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvsisltsss....kelledvq 41 
                                    ++L G   +DG+++ +++k  ++++t+++    k+++e+v+
  gi|15668722|ref|NP_247521.1| 533 VMYLGGAVLSDGHIVRRNGKPIRVRFTQKDteekKDFIEKVK 574
                                   58999***************999*******888888888876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHHHHHHCCECCECSTTTTSEEEEES-..HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCC..........ECCCH CS
                   LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvsisltsss..kelledvqrlLlrlGIestiyekkkakgrgvy..........rllii 70 
                                   ++a +++G+ d+DG+ s++++    ++++++s   + +e++   L rlGI+ +++ k +++  ++y          r ++i
  gi|15668722|ref|NP_247521.1| 625 EIADLIAGFVDGDGCLSGKRR----VEIYQNSshIKKIEGLIVGLYRLGIIPRLRYK-RSSTATIYfnnnletilqRTRRI 700
                                   57889***************6....6666666448889999999*************.44444445588888877766666 PP

                                   CHCTTCGGG CS
                   LAGLIDADG_3  71 sgenlkrFl 79 
                                   + + lk F 
  gi|15668722|ref|NP_247521.1| 701 KLDKLKEFK 709
                                   666666665 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   2.4   5.1e-10     1e-06      11     131 ..     426     810 ..     418     814 .. 0.93
   2 ?   -3.3   0.5       3.9   7.9e+03      90     113 ..     852     878 ..     838     883 .. 0.53

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 5.1e-10
                                   EHHHHCC....ECTTEEEEEETTTTEEEEEEEEEEEEEEEE....EEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC CS
                                   xxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  11 kieelve....kegeevlslnledlklevksvkkliklklk....elyeiklesgrkikaTpeHkllvvrdegivEkrade 83 
                                   k++e+++     e  +vl+ln e+lk e+k++  + k + +     +y+ + +   +ik+Tp+Hk+ v+ ++++  +++ +
  gi|15668722|ref|NP_247521.1| 426 KMKEVYKlvknGEKLKVLGLNAETLKTEWKEIIDAQKREARryeiGVYRKNKNTKDTIKITPDHKFPVFVNGELSKVQLCD 506
                                   455555555344555899*************9988887766666889999999999**********999899998899999 PP

                                   --TT-EEEEE....................................................................... CS
                                   xxxxxxxxxx....................................................................... RF
               Intein_splicing  84 Lkegdliavp....................................................................... 93 
                                   +  ++l +++                                                                       
  gi|15668722|ref|NP_247521.1| 507 IIDNNLSVLSidyipmieekyeslaevmylggavlsdghivrrngkpirvrftqkdteekkdfiekvkgdvkliggnfiei 587
                                   98888887779********************************************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15668722|ref|NP_247521.1| 588 snrnnvieyqtsrkipseilgfievnintiplyatkdeiadliagfvdgdgclsgkrrveiyqnsshikkieglivglyrl 668
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15668722|ref|NP_247521.1| 669 giiprlrykrsstatiyfnnnletilqrtrrikldklkefkkpvedkklidisqilpelkefdykgylyktykeklfigin 749
                                   ********************************************************************************* PP

                                   .........................HSCEEEEEEEEEEEEECEEEEEEEEETTT-EEEECTTE CS
                                   .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  94 .........................dadvvwdkvksievedeeeyVYdltvednhNFvangii 131
                                                            ++d++  ++k++ + d+ e VY +tv+ ++ F  n ++
  gi|15668722|ref|NP_247521.1| 750 kleeylskidkdgierikqkikllkESDIYSIRIKKVGE-DYGE-VYNITVKAENEFNHNYVV 810
                                   ************************************975.5555.9*****987666555554 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.9
                                   EEEEHSC..EEEE.EEEEEEEEECEEE CS
                                   xxxxxxx..xxxx.xxxxxxxxxxxxx RF
               Intein_splicing  90 iavpdad..vvwd.kvksievedeeey 113
                                   i+++d++  +v++ ++k++e+++++++
  gi|15668722|ref|NP_247521.1| 852 IVTVDGEkgIVYEgEIKKVEEKEKKQE 878
                                   333333334444336777777766654 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.2e-06    0.0085      87     186 ..    1024    1129 ..    1009    1165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.2e-06
                                    EEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEEEE-HHHHHH.HTT-TT.. CS
                     HpcH_HpaI   87 vvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgvflGaeDlsa.dlgtkr.. 162 
                                     +++P v+ ++e++ v++++re+  +     k ++  + +E+ ++ + +e+ +  eg+  v lG++Dl+  ++   r  
  gi|15668722|ref|NP_247521.1| 1024 EIMIPLVTHPDEVRRVKEIMREVGLE---PCKDIPFGIMVETPAAALIIEDFI-KEGINFVSLGTNDLTQyTIAIDRnn 1098
                                    48********************9944...4689*************9999987.58***********985333333300 PP

                                    .......STTSHHHHHHHHHHHHTTHCEEEE CS
                     HpcH_HpaI  163 .......spegtevldareriltaaraagia 186 
                                           +++++ vl+  e+++ ++++ gi+
  gi|15668722|ref|NP_247521.1| 1099 elvskyyKEDHPAVLKLVEHVIKTCKKHGIK 1129
                                    111111146677788**************93 PP

>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.8   5.7e+03      16      33 ..     374     391 ..     367     417 .. 0.78
   2 ?   12.2   0.1   8.5e-05      0.17      20      61 ..     549     590 ..     547     595 .. 0.93
   3 ?   -2.9   0.0       4.2   8.4e+03      14      28 ..     842     856 ..     840     859 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.8
                                   HHHHHTT-EEEEE-CCCT CS
                          SepF  16 adalkegkiVilnledld 33 
                                   +d +keg+i++ +++  d
  gi|15668722|ref|NP_247521.1| 374 IDKVKEGDILVTEMTTPD 391
                                   488999999999988655 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 8.5e-05
                                   HTT-EEEEE-CCCTCHHHHHHHHHHHHHHHHCT-EEEEECTT CS
                          SepF  20 kegkiVilnledldkeeakrivdflsgvvyaldGdiqkvgkk 61 
                                   ++gk++ + +++ d+ee k ++++++g v+ ++G++ +++++
  gi|15668722|ref|NP_247521.1| 549 RNGKPIRVRFTQKDTEEKKDFIEKVKGDVKLIGGNFIEISNR 590
                                   79**************************************96 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.2
                                   HHHHHHHTT-EEEEE CS
                          SepF  14 eiadalkegkiViln 28 
                                   ++ + lk+g iV ++
  gi|15668722|ref|NP_247521.1| 842 KATKVLKDGMIVTVD 856
                                   677889******998 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.11   2.2e+02      65     108 ..      56      99 ..      51     119 .. 0.61
   2 ?    8.3   0.0    0.0013       2.5       1      28 [.     352     381 ..     352     438 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                                   HHHHHHT-HHHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHT CS
               PEP-utilisers_N  65 ahlmlleDpelleeveerIregglnaeaAveevveefaaqfeal 108
                                   a++++++  +l+++++e +    +n   A+  + +++++  e++
  gi|15668722|ref|NP_247521.1|  56 AYRHFIKETGLMDKIREILSGLDVNDTDALTNASKKIRKLIEEA 99 
                                   66666666666666666666666666666666666666555544 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0013
                                   E-EEEE-SEEEEEEE......---.-----G.GG CS
               PEP-utilisers_N   1 kGiaaspGiaiGkav......eveveeeeveaed 28 
                                   kGi+aspGia G +       e     ++v++ d
  gi|15668722|ref|NP_247521.1| 352 KGIGASPGIATGVVKiihdvsE----IDKVKEGD 381
                                   7***********9998764331....34444444 PP

>> FokI_N  Restriction endonuclease FokI, recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00029      0.58       6     109 ..      61     162 ..      58     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                        FokI_N   6 vqepssleslkkvvaifvegskvhrelveeklpklvsekdGkkel.leelearelsiayaelkGkgtpkgesrskakcsGi 85 
                                   ++e+  +++++++++ ++ + +   + +++k++kl++e +  + l l  +ea +   + +e+ G+   +   rs+a  + +
  gi|15668722|ref|NP_247521.1|  61 IKETGLMDKIREILSGLDVNDTDALTNASKKIRKLIEEAEMPEDLrLAIIEAYN---KLCEMCGEDEVTVAVRSSATAEDL 138
                                   67777899999999988877777777899********98876655134444443...56888999988889********** PP

                        FokI_N  86 vqaavkGqrkeyiddWpadsflrW 109
                                     a+  Gq+  y +   a++ +++
  gi|15668722|ref|NP_247521.1| 139 PEASFAGQQDTYLNIKGAENVVKY 162
                                   *************99999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.86u 0.32s 00:00:01.18 Elapsed: 00:00:00.51
# Mc/sec: 6983.61
//
Query:       gi|15668723|ref|NP_247522.1|  [L=174]
Description: 50S ribosomal protein L10e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-37  126.4   0.2    7.7e-37  126.2   0.2    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.2   0.2   4.3e-41   7.7e-37       3     132 .]      15     164 ..      13     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 4.3e-41
                                   SSXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSXXXXE CS
                 Ribosomal_L16   3 rkkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwirvfphh 71 
                                   +++y++++  y++gv+ +k  ++ +g+        ++Lva+ + q++++aleaar+a+n+yl+k +g+   k+ irv+ph+
  gi|15668723|ref|NP_247522.1|  15 KPPYTRKE--YVKGVPqPKVVHFIMGNlsaefpvkVNLVATRPIQIRHNALEAARVAANKYLTKMCGRmgyKFQIRVYPHQ 93 
                                   789*****..***********************9999****************************9999************ PP

                                   EEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE...TTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                 Ribosomal_L16  72 pvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei...kagvneeiakealrraasKlpiktkiv 132
                                   +++++     ag+dR+++G+    Gkp g++arvk+gq i+++    +  +   akealrraa+Klp++++iv
  gi|15668723|ref|NP_247522.1|  94 ILREHkmatgAGADRISDGMrlafGKPIGTAARVKEGQAILTVwvnPD--KFPAAKEALRRAAMKLPVPCRIV 164
                                   *******************************************75433..67799****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1160.48
//
Query:       gi|15668724|ref|NP_247523.1|  [L=229]
Description: dolichyl-phosphate mannose synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-29  102.7   0.2    1.9e-29  102.7   0.2    1.4  2  Glycos_transf_2  Glycosyl transferase family 2
    2.7e-07   30.7   0.0    3.5e-07   30.3   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    4.6e-06   27.1   0.0    8.8e-06   26.2   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2
    0.00024   20.7   0.7     0.0003   20.3   0.7    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0077   15.8   0.1      0.013   15.1   0.1    1.4  1  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
      0.082   12.6   1.9       0.23   11.1   1.9    1.8  1  CLN5             Ceroid-lipofuscinosis neuronal protein 5
      0.094   12.4   0.1       0.25   11.0   0.1    1.7  2  CAP59_mtransfer  Cryptococcal mannosyltransferase 1
       0.26   11.0   0.7       0.45   10.2   0.2    1.6  2  Fe-ADH_2         Iron-containing alcohol dehydrogenase


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.7   0.2   8.4e-33   1.9e-29       2     120 ..       3     122 ..       2     164 .. 0.91
   2 ?   -3.6   0.0       3.7   8.2e+03      44      62 ..     192     213 ..     191     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 8.4e-33
                                   EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHHHH--SS CS
               Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak.edprvrvirreenvGkagalnaglraatgd 81 
                                   ++ip++Neek++l++l+ l +     +++ +vvDDgS+D+t +i+ee+ak  + +v +ir+e+n+Gka+a+ +g + a + 
  gi|15668724|ref|NP_247523.1|   3 AIIPAFNEEKNILKVLKDLEKL----RVDAVVVDDGSKDNTSKIVEEFAKkAKINVYLIRNEKNEGKAKAIEKGTKFALSL 79 
                                   59*******************9....****************************************************999 PP

                                   ....EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEE CS
               Glycos_transf_2  82 ....yilflDaDdepdpdwleklvealekdgadvvlgqrprif 120
                                       yi+++D D +++p +++kl+++le+++ad+v+g r ++ 
  gi|15668724|ref|NP_247523.1|  80 nkykYIIYIDGDYQHKPMDIPKLLKKLEDTNADAVFGIRKYKH 122
                                   9999*********************************998765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.7
                                   HHHGGGCH...C-TTEEEEEES CS
               Glycos_transf_2  44 eileelak...edprvrvirre 62 
                                   +i+ee+++    d+ v +i+ +
  gi|15668724|ref|NP_247523.1| 192 KIVEEYVSveyHDEAVSYITTK 213
                                   6888998888888888888865 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.6e-10   3.5e-07       6     121 ..       3     115 ..       1     165 [. 0.85

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.6e-10
               Glyco_tranf_2_3   6 vlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealra. 85 
                                    ++p+fnee+ +++vl +l +    rv+ vvv+d+s++ t + +ee+a++ +   v +++n++n g   k+ a++ + +  
  gi|15668724|ref|NP_247523.1|   3 AIIPAFNEEKNILKVLKDLEK---LRVDAVVVDDGSKDNTSKIVEEFAKKAKI-NVYLIRNEKNEG---KAKAIEKGTKFa 76 
                                   69****************999...69*********************999965.799999999765...666777776642 PP

               Glyco_tranf_2_3  86 ...vksdlvllvDdDtvvePdtlkrllqffltpkvgavg 121
                                       k+++++ +D+D    P  +++ll  +++ +++av 
  gi|15668724|ref|NP_247523.1|  77 lslNKYKYIIYIDGDYQHKPMDIPKLLKKLEDTNADAVF 115
                                   22266************9999999999888666666665 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   3.9e-09   8.8e-06       2      81 ..       9      91 ..       8      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.9e-09
               Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailke...lpevkllhvdksyed.errqvellkallaryaeadwvlvvDa 80
                                  ne++ + ++l+ +++l++d  +v+d++s+D+t++i++e    ++++++ ++++ ++ ++ ++e  ++++ + ++ ++++++D 
  gi|15668724|ref|NP_247523.1|  9 NEEKNILKVLKDLEKLRVD-AVVVDDGSKDNTSKIVEEfakKAKINVYLIRNEKNEgKAKAIEKGTKFALSLNKYKYIIYIDG 90
                                  99999***********999.899*************994333557788888766552556688888888899999*******8 PP

               Glyco_tranf_2_4 81 D 81
                                  D
  gi|15668724|ref|NP_247523.1| 91 D 91
                                  8 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.7   1.4e-07    0.0003       3     112 ..       4     107 ..       2     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.4e-07
               Glyco_tranf_2_2   3 viplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidl.nllvylkdeddkayslaaarNrGaskaes 82 
                                   +ip  ++e++  i   ++   k     ++ +vvddgS +++ + v+ + ++ + +vyl  + +k  ++a+a  +G++ a s
  gi|15668724|ref|NP_247523.1|   4 IIPAFNEEKN--ILKVLKDLEKL---RVDAVVVDDGSKDNTSKIVEEFAKKaKINVYLIRN-EKNEGKAKAIEKGTKFALS 78 
                                   7888888888..88777777777...8999*****************97651555676555.8999**********99976 PP

               Glyco_tranf_2_2  83 ....dlvlFlDaDcfissDkfekilklitikklr 112
                                        +++++D+D    +  + k+lk     kl+
  gi|15668724|ref|NP_247523.1|  79 lnkyKYIIYIDGDYQHKPMDIPKLLK-----KLE 107
                                   55558********9999988999888.....443 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   5.7e-06     0.013      34     142 ..      14     120 ..       3     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.7e-06
                                   THHHHHHHHHTT-SEEEEEE..ETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTE CS
               NTP_transferase  34 iqatlsrlansgieeiivvl..tqehsflveeqlkegskfgvevlialepegkgtAdAvalaaelledeksdelvlvLggD 112
                                   i ++l+ l + ++++ +vv   ++++   + e+++++  ++++v  +  ++++g A+A+ ++ +++   ++ ++++++ gD
  gi|15668724|ref|NP_247523.1|  14 ILKVLKDLEKLRVDA-VVVDdgSKDNTSKIVEEFAKK--AKINVYLIRNEKNEGKAKAIEKGTKFALSLNKYKYIIYIDGD 91 
                                   556666666666666.444211233344444444444..45779999999999************99999999******** PP

                                   EEEST.THHHHHHHHHTHSSTTSEEEEEEES CS
               NTP_transferase 113 hlikd.ayeeavkkaiekaakgtvtfgivpv 142
                                      k  ++ +++kk ++++a  +++fgi + 
  gi|15668724|ref|NP_247523.1|  92 YQHKPmDIPKLLKKLEDTNA--DAVFGIRKY 120
                                   999988**************..788888765 PP

>> CLN5  Ceroid-lipofuscinosis neuronal protein 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.9    0.0001      0.23     242     294 ..     117     168 ..      66     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                          CLN5 242 irkfyskfkphqslkelllslleildkvvlekkfylfynleywflplkspyik 294
                                   irk y+++  h+ +++++ s+l  l  ++ +k+fy+f +++  f  +k+ ++k
  gi|15668724|ref|NP_247523.1| 117 IRK-YKHIPLHRQISNFFASILTSLAVLIYSKRFYFFRDVQCGFRIIKAEFLK 168
                                   444.788999*******************************999999999987 PP

>> CAP59_mtransfer  Cryptococcal mannosyltransferase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00011      0.25      20      83 ..      12      72 ..       2      95 .. 0.83
   2 ?   -1.7   0.0      0.85   1.9e+03     114     145 ..      81     114 ..      75     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
               CAP59_mtransfer 20 eallelirfLgpenvfvSiyesgskdgtkeaLraleaelealgversivlneeteleldelesg 83
                                  +++l++++ L++ +v   ++++gskd+t+++++++    ++++++ ++  ne++e +++ +e+g
  gi|15668724|ref|NP_247523.1| 12 KNILKVLKDLEKLRVDAVVVDDGSKDNTSKIVEEF---AKKAKINVYLIRNEKNEGKAKAIEKG 72
                                  579999999*999**********************...77888888887777777777777764 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.85
               CAP59_mtransfer 114 kfdkvlFln.DvvftaedileLleq.qngeydaa 145
                                   k++ +++++ D   ++ di +Ll++ +++++da+
  gi|15668724|ref|NP_247523.1|  81 KYKYIIYIDgDYQHKPMDIPKLLKKlEDTNADAV 114
                                   6777888875777889999999999755566665 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2    0.0002      0.45      10      80 ..      14      86 ..       8      90 .. 0.81
   2 ?   -2.8   0.0       1.9   4.2e+03     180     212 ..     181     213 ..     167     221 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                      Fe-ADH_2 10 lgellkelel.kkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklveal.reketdlvv 80
                                  + ++lk+le  +  ++v+d + k+ + + vee  k+a+i+v +++++++e + +++ek  + + + ++++ ++
  gi|15668724|ref|NP_247523.1| 14 ILKVLKDLEKlRVDAVVVDDGSKDNTSKIVEEFAKKAKINVYLIRNEKNEGKAKAIEKGTKFAlSLNKYKYII 86
                                  56777887651455899***************************9999999*****99988662457777666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                      Fe-ADH_2 180 plaklsaamvqeaaeklvedkketealeellea 212
                                   ++a++ a++  + +e+ v+ + ++ea++ ++++
  gi|15668724|ref|NP_247523.1| 181 FIALQLAKKGAKIVEEYVSVEYHDEAVSYITTK 213
                                   444455555555555555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1383.87
//
Query:       gi|15668725|ref|NP_247524.1|  [L=251]
Description: hypothetical protein MJ_0545 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.034   12.9   0.0      0.034   12.9   0.0    1.1  1  ResB          ResB-like family
      0.084   13.0   0.0       0.12   12.5   0.0    1.2  1  Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
       0.51   11.1   2.6       0.49   11.1   0.3    2.1  3  E1_UFD        Ubiquitin fold domain
          2    8.8   7.1        1.2    9.4   4.8    1.8  2  Aconitase_C   Aconitase C-terminal domain
        7.1    7.0  13.3       0.25   11.7   1.3    3.0  3  DUF5383       Family of unknown function (DUF5383)
        7.2    7.0  10.1       0.16   12.3   2.5    2.3  3  DUF4064       Protein of unknown function (DUF4064)


Domain annotation for each model (and alignments):
>> ResB  ResB-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.1e-05     0.034     401     459 ..     177     245 ..      50     247 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                          ResB 401 feqeqln.al.....srygsplllq..ldd.fe.qrqasgLqvsrdpgknlvllgalllvlGlvlslyv 459
                                   + q++ n ++     +  ++    q  +++ f+ +   +  +v++d+g+n+++ g l l++G+v+ ++v
  gi|15668725|ref|NP_247524.1| 177 ITQNKTNiSKnidigNITKANTTSQekITQkFNnTSTQTIENVQKDKGNNWLMYGILGLIIGIVFGFVV 245
                                   333333321122232222222222244222366555556668************************987 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.9e-05      0.12      95     164 ..     170     240 ..     126     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                                   HHGGGS---HHHHHHHHHH.HHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXX CS
                  Spore_III_AB  95 kllkklaLkkedkeilkel.geslgysdregqlkalelaleeleeeieeareeakkkeklyrtlGvlaGlf 164
                                     +++++++++  +i k++   ++ + + ++q+k  + + +  ++ ie  ++++ ++  +y  lG+++G++
  gi|15668725|ref|NP_247524.1| 170 AIINETNITQNKTNISKNIdIGNITKANTTSQEKITQKFNNTSTQTIENVQKDKGNNWLMYGILGLIIGIV 240
                                   444456666666666666656788999******************************************97 PP

>> E1_UFD  Ubiquitin fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.6   1.4e+04      29      41 ..      66      78 ..      56      84 .. 0.63
   2 ?   11.1   0.3   0.00016      0.49      19      82 ..     114     179 ..      98     190 .. 0.84
   3 ?   -1.6   0.1       1.5   4.5e+03      44      66 ..     201     223 ..     192     231 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.6
                        E1_UFD 29 mislgvsllYasf 41
                                   +++++s lY + 
  gi|15668725|ref|NP_247524.1| 66 AVVFKNSTLYYAG 78
                                  4677777777554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                        E1_UFD  19 fkekkklevsmisl..gvsllYasflpkkkdkerlklklselveevtkkkipphqkyldlevsved 82 
                                   +k+k+ l++s+++l  + ++ Y++ +++++++  l  +++++ e+ t+   p+++++++ e  +++
  gi|15668725|ref|NP_247524.1| 114 IKKKFLLNISILTLpeNIYVSYNNTYNRDEENTSLLENITKIFENTTNVTTPNSTNAIINETNITQ 179
                                   788888999999884345688******9999999***************99999999988877775 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.5
                        E1_UFD  44 kkkdkerlklklselveevtkkk 66 
                                   ++k  ++ + + ++ +e+v+k+k
  gi|15668725|ref|NP_247524.1| 201 QEKITQKFNNTSTQTIENVQKDK 223
                                   45556666666666677666665 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.99     3e+03      27      47 ..     103     123 ..      95     152 .. 0.54
   2 ?    9.4   4.8   0.00042       1.2       2      78 ..     154     229 ..     153     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.99
                                   CHHHCCCGGTTTCCCCTTTSB CS
                   Aconitase_C  27 kqfegtianiglgnelveekr 47 
                                   +q++ +i+ + ++++++ ++ 
  gi|15668725|ref|NP_247524.1| 103 VQMSYIIDGTLIKKKFLLNIS 123
                                   555555555555555444333 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00042
                                   CCCCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTT.TEEEEHHHHHHHHHHTT--EEE CS
                   Aconitase_C   2 ekllklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdldd.gekedvvdaaerykkegaklvv 78 
                                   +++++ +++tt++  +++  + +i ++  ++++ni++gn+   +   ++++ ++  +  ++ ++++++ k  g ++++
  gi|15668725|ref|NP_247524.1| 154 KIFENTTNVTTPNSTNAIINETNITQNKTNISKNIDIGNITKANTTSQEKITQKFnNTSTQTIENVQKDK--GNNWLM 229
                                   689999**********************************999887777666543033335555555544..777765 PP

>> DUF5383  Family of unknown function (DUF5383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   1.4       0.3   8.8e+02     105     120 ..       8      23 ..       6      26 .. 0.82
   2 ?    1.6   1.0      0.11   3.4e+02      49      83 ..     150     186 ..     138     189 .. 0.76
   3 ?   11.7   1.3   8.2e-05      0.25      54     118 ..     184     249 ..     174     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.3
                       DUF5383 105 livllivvllivliPk 120
                                   +i+ l++ l+i+liP 
  gi|15668725|ref|NP_247524.1|   8 VIIPLLISLFIFLIPN 23 
                                   577788999******7 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.11
                       DUF5383  49 elkesLfassek..esntiaakakelgLfseekesvk 83 
                                   e + + f ++++  + n+++a  +e ++++++++++k
  gi|15668725|ref|NP_247524.1| 150 ENITKIFENTTNvtTPNSTNAIINETNITQNKTNISK 186
                                   445568888887778999999********99999876 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 8.2e-05
                       DUF5383  54 LfassekesntiaakakelgLfseekesvkqsateqeseeksnlLpi.llillivllivvllivli 118
                                    +++    + t a++ ++ +++++ ++ ++q++++ ++++  n+L+  +l+l+i +++  +++++i
  gi|15668725|ref|NP_247524.1| 184 ISKNIDIGNITKANTTSQEKITQKFNNTSTQTIENVQKDKGNNWLMYgILGLIIGIVFGFVVMYII 249
                                   5555666678999999**********************9****99975777777777777777776 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       1.3   3.8e+03      14      26 ..       9      21 ..       7      33 .. 0.62
   2 ?   -2.9   0.0       2.8   8.3e+03      43      57 ..      87     101 ..      58     114 .. 0.55
   3 ?   12.3   2.5   5.4e-05      0.16      29      83 ..     193     250 ..     131     251 .] 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                       DUF4064 14 ilgillglllllf 26
                                  i+ +l++l+++l+
  gi|15668725|ref|NP_247524.1|  9 IIPLLISLFIFLI 21
                                  4444445544444 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.8
                       DUF4064  43 qalsgedasavlefl 57 
                                   ++++ge+++   + +
  gi|15668725|ref|NP_247524.1|  87 HIFEGEAVTPGNHTI 101
                                   444455555544555 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 5.4e-05
                       DUF4064  29 llssgefsqeltee..qalsgedasavl.eflstllivlgvialiaivlgivgalllk 83 
                                   +++++ +sqe  ++  +++s++  ++v  +  ++ l++ +++++i iv+g+v ++++k
  gi|15668725|ref|NP_247524.1| 193 ITKANTTSQEKITQkfNNTSTQTIENVQkDKGNNWLMYGILGLIIGIVFGFVVMYIIK 250
                                   4455555555555566677777777777344445555555559999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2310  (0.128842); expected 358.6 (0.02)
Passed bias filter:                      717  (0.0399911); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1554.82
//
Query:       gi|15668726|ref|NP_247525.1|  [L=56]
Description: hypothetical protein MJ_0546 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0036   17.2   1.1     0.0038   17.1   1.1    1.0  1  Ninjurin   Ninjurin
     0.0093   16.2   0.5       0.01   16.0   0.5    1.1  1  DUF948     Bacterial protein of unknown function (DUF948)
  ------ inclusion threshold ------
        0.1   13.0   2.5        0.2   12.1   2.5    1.4  1  FlaC_arch  Flagella accessory protein C (FlaC)
       0.21   11.7   1.8       0.22   11.7   0.6    1.7  2  GBR2_CC    Gamma-aminobutyric acid type B receptor subunit 2 
        3.7    6.8   6.5       0.84    8.9   3.2    1.6  2  DUF4191    Domain of unknown function (DUF4191)


Domain annotation for each model (and alignments):
>> Ninjurin  Ninjurin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.1   1.1e-06    0.0038      42      83 ..       2      46 ..       1      52 [. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                      Ninjurin 42 allvLislSllLqvvvgilliliasklnlekekker.....rlnkln 83
                                  +l +++ +S+lL +++gi +i++  +++le+ kk++     +++kln
  gi|15668726|ref|NP_247525.1|  2 ILYIIVAISILLNIILGIKVIML--QKELEEVKKATrltkeEVEKLN 46
                                  67789****************96..5888888885523333555555 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.5   2.9e-06      0.01       3      49 ..       4      49 ..       2      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-06
                        DUF948  3 glIaAiAFvvLviflivvllklkktldeaaatieelekqvdpilkev 49
                                  ++I+Ai++++ +i+ i+v++ l+k l+e++++ + ++++v+++ + +
  gi|15668726|ref|NP_247525.1|  4 YIIVAISILLNIILGIKVIM-LQKELEEVKKATRLTKEEVEKLNERI 49
                                  58*******99999999987.99****************99987665 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.5   5.5e-05       0.2       9      40 ..      21      52 ..      17      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.5e-05
                     FlaC_arch  9 lsklsteletvkkeneelsksveelkenVkdl 40
                                  +  l+ ele vkk     +++ve+l+e++++l
  gi|15668726|ref|NP_247525.1| 21 VIMLQKELEEVKKATRLTKEEVEKLNERIRKL 52
                                  5567789999999999999**********997 PP

>> GBR2_CC  Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   6.1e-05      0.22      20      34 ..      17      31 ..      13      35 .. 0.90
   2 ?   -1.1   0.0      0.59   2.1e+03       9      16 ..      36      43 ..      32      54 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.1e-05
                       GBR2_CC 20 lRmkitelDKdLEEV 34
                                  l +k++ l K+LEEV
  gi|15668726|ref|NP_247525.1| 17 LGIKVIMLQKELEEV 31
                                  569***********9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.59
                       GBR2_CC  9 RLeklQae 16
                                  RL k  +e
  gi|15668726|ref|NP_247525.1| 36 RLTKEEVE 43
                                  55554444 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.6     0.079   2.8e+02      44      62 ..       5      23 ..       1      28 [. 0.47
   2 ?    8.9   3.2   0.00024      0.84     168     198 ..      21      53 ..      16      56 .] 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.079
                       DUF4191 44 glllgslilllilgillgl 62
                                   +++ s++l +ilgi + +
  gi|15668726|ref|NP_247525.1|  5 IIVAISILLNIILGIKVIM 23
                                  2222345555555555444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00024
                       DUF4191 168 lkkLqktlkklprn..ltkaeveevekRLkald 198
                                   +  Lqk+l  ++++  ltk+eve++++R++ l+
  gi|15668726|ref|NP_247525.1|  21 VIMLQKELEEVKKAtrLTKEEVEKLNERIRKLK 53 
                                   5668888888887777*************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2377  (0.132579); expected 358.6 (0.02)
Passed bias filter:                     1429  (0.0797033); expected 358.6 (0.02)
Passed Vit filter:                       188  (0.0104858); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 351.03
//
Query:       gi|15668727|ref|NP_247526.1|  [L=264]
Description: cell division inhibitor MinD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-29  102.7   0.8    2.2e-29  102.1   0.8    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    4.8e-27   95.0   6.6    4.2e-26   91.9   6.6    2.2  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.4e-22   80.5   0.8    2.3e-22   79.7   0.8    1.3  1  AAA_31       AAA domain
    2.8e-13   49.9   3.0    8.7e-07   28.6   0.2    2.0  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    1.2e-11   44.6   0.0    3.7e-11   42.9   0.0    1.7  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    2.8e-11   43.2   0.8    2.1e-10   40.3   0.6    2.1  1  MipZ         ATPase MipZ
      1e-09   38.0   2.3    2.1e-07   30.5   0.4    2.3  2  ArsA_ATPase  Anion-transporting ATPase
    8.5e-08   32.3   5.0    1.7e-06   28.0   0.5    2.3  2  AAA_26       AAA domain
     0.0012   18.2   0.8     0.0021   17.4   0.8    1.4  1  VirC1        VirC1 protein
     0.0023   17.4   2.1       0.17   11.3   1.9    2.2  2  PhoH         PhoH-like protein
     0.0036   17.2   0.0     0.0054   16.6   0.0    1.4  1  APS_kinase   Adenylylsulphate kinase
     0.0045   16.6   3.3      0.016   14.8   3.3    1.8  1  AAA_25       AAA domain
     0.0052   16.5   1.9      0.017   14.8   0.9    2.1  2  AAA_30       AAA domain
     0.0061   16.2   1.8      0.017   14.7   1.8    1.9  1  SRP54        SRP54-type protein, GTPase domain
     0.0069   16.2   0.2      0.018   14.9   0.0    1.7  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
  ------ inclusion threshold ------
      0.035   13.1   0.2      0.076   12.0   0.2    1.5  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.074   13.2   0.0       0.21   11.8   0.0    1.8  2  AAA_33       AAA domain
      0.077   13.0   0.1        1.3    9.0   0.2    2.2  2  ResIII       Type III restriction enzyme, res subunit
       0.13   12.0   0.1       0.26   11.0   0.1    1.6  2  AAA_24       AAA domain
       0.23   10.6   0.9        3.3    6.8   0.4    2.2  2  NB-ARC       NB-ARC domain
       0.33   10.3   1.6        1.8    7.9   1.6    2.2  1  DnaB_C       DnaB-like helicase C terminal domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.8   2.6e-32   2.2e-29       1     127 [.       9     215 ..       9     216 .. 0.95

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 2.6e-32
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   iaias+kGG+GKTt++anLa+ala+ g++V+++DaD  + nl++++gle++  +                           
  gi|15668727|ref|NP_247526.1|   9 IAIASGKGGTGKTTISANLAVALAKFGKKVAVLDADIAMANLELIMGLEGKPVTlndvlagkadikdaiyegpegvlvipa 89 
                                   89******************************************************************************* PP

                                   ...............................................................CCHCCCHHHHHHCHCHHH CS
                                   ...............................................................xxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ...............................................................dlkrllellealgkkkal 72 
                                                                                                  d+ +++ + ++lg     
  gi|15668727|ref|NP_247526.1|  90 gvslekfrrakpekleevlkaihdlveiliidcpagigketliaissadglivvvnpeissisDALKIIAITKRLG----- 165
                                   *********************************************************6666666666666666666..... PP

                                   H..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  73 llkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                     +i+g ++nrv +e +++l  +a+e+++   +vpv+gv+p+d +v +a+a g p
  gi|15668727|ref|NP_247526.1| 166 -TDIIGAIVNRVSNE-STELGVKAIETIL---EVPVIGVVPEDPHVRKAAAFGTP 215
                                   .56*********998.8999********9...******************99987 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   6.6   4.9e-29   4.2e-26       5     245 ..       8     236 ..       5     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 4.9e-29
                          ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqs.....ekkli.Pvea..kgikvmS 77 
                                    ia++SgKGG GK+t+++nlA+aLak g+kv++lDaDi   ++  ++g+e++ ++ +     ++ +   ++   +g+ v+ 
  gi|15668727|ref|NP_247526.1|   8 AIAIASGKGGTGKTTISANLAVALAKFGKKVAVLDADIAMANLELIMGLEGKPVTLNdvlagKADIKdAIYEgpEGVLVIP 88 
                                   599************************************************877666343333344423333677888888 PP

                          ParA  78 igfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaie 158
                                    g+ le       +r + k + ++++lk + ++ +++LiiD+P G g e+l  +++   +g ++V  p+  +++d+ k i+
  gi|15668727|ref|NP_247526.1|  89 AGVSLE------KFRRA-KPEKLEEVLKAI-HDLVEILIIDCPAGIGKETLIAISSA--DGLIVVVNPEISSISDALKIIA 159
                                   888887......45544.445567777654.57899*************99998887..7********************* PP

                          ParA 159 mfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakale 239
                                   ++k++ ++++G + N      +          + g++++ + l+vp++g +p dp++r+a+  g+plv+  p+s+aa+a++
  gi|15668727|ref|NP_247526.1| 160 ITKRLGTDIIGAIVNRVSNEST----------ELGVKAIETILEVPVIGVVPEDPHVRKAAAFGTPLVIMYPDSPAAQAIM 230
                                   ***********99885433322..........45788999999************************************** PP

                          ParA 240 eiaekv 245
                                   eia+k+
  gi|15668727|ref|NP_247526.1| 231 EIAAKL 236
                                   ***987 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.8   2.8e-25   2.3e-22       4     166 ..       9     163 ..       6     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 2.8e-25
                        AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp.Qanattglgiekneiektlyevlieeknikeaiiktkvenldl 83 
                                   Iaia  KGG GKTT s nla+alak gkkv + D+D   an+   +g+e +    tl++vl+ +++ik+ai+ +  e + +
  gi|15668727|ref|NP_247526.1|   9 IAIASGKGGTGKTTISANLAVALAKFGKKVAVLDADIaMANLELIMGLEGKP--VTLNDVLAGKADIKDAIY-EGPEGVLV 86 
                                   9***********************************6257889999986555..6*****************.445999** PP

                        AAA_31  84 ipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllkti 164
                                   ip+ ++L ++         k e l+e+l++++d   + iiDcp  +g  t  a+ ++d +i++v++e  +++ + +++   
  gi|15668727|ref|NP_247526.1|  87 IPAGVSLEKFRR------AKPEKLEEVLKAIHDLVEILIIDCPAGIGKETLIAISSADGLIVVVNPEISSISDALKIIAIT 161
                                   *******98764......4567789*****************************************999988877777666 PP

                        AAA_31 165 ee 166
                                   ++
  gi|15668727|ref|NP_247526.1| 162 KR 163
                                   55 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.2     1e-09   8.7e-07       6      87 ..      13      90 ..       7      93 .. 0.82
   2 !   21.9   0.2   1.2e-07    0.0001     139     248 ..     135     240 ..     112     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1e-09
                     Fer4_NifH  6 yGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqe.tvldtlrekgavedvkvedvvkkGyggvkcvesG 87
                                   GkGG Gk+t s+nl+ ala++gkkv ++  D       l++g   ++ t+ d+l+ k       ++d +++G +gv ++ +G
  gi|15668727|ref|NP_247526.1| 13 SGKGGTGKTTISANLAVALAKFGKKVAVLDADIAMANLELIMGLEGKPvTLNDVLAGKA-----DIKDAIYEGPEGVLVIPAG 90
                                  5*********************************9999999876666515555665554.....5789999999999888776 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.2e-07
                     Fer4_NifH 139 dkaqevyivtsgelmalyaanniakgiekyaksggvrlgGliinsrkvdderel.iekfaeelgtkvlevvPrdeivrkae 218
                                   + a+ +++v++ e+ ++  a +i +     +k+ g  + G i+n r  ++ +el ++++ + l+++v+ vvP d +vrka 
  gi|15668727|ref|NP_247526.1| 135 SSADGLIVVVNPEISSISDALKIIA----ITKRLGTDIIGAIVN-RVSNESTELgVKAIETILEVPVIGVVPEDPHVRKAA 210
                                   5788889999999999888877754....456677889999***.7666667773566667789***************** PP

                     Fer4_NifH 219 lrkktvieyapeseqakeyrelarkilenk 248
                                   +    ++ + p+s+ a+   e+a k++ +k
  gi|15668727|ref|NP_247526.1| 211 AFGTPLVIMYPDSPAAQAIMEIAAKLIGAK 240
                                   **99999999**************998776 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   4.4e-14   3.7e-11       4     230 ..       9     233 ..       5     237 .. 0.71

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 4.4e-14
                      CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspd.nlLrlhFnvdieqregwaraeldgapwrqaaleyapgldllP 83 
                                   +a+   +GG+G+t+++a La al + g++v v+D+  +   L+l   ++  +  ++   ++ +a++++a++e  +g+ ++P
  gi|15668727|ref|NP_247526.1|   9 IAIASGKGGTGKTTISANLAVALAKFGKKVAVLDADIAmANLELIMGLE-GKPVTLNDVLAGKADIKDAIYEGPEGVLVIP 88 
                                   5666669*************************99864314578888888.678899999********************** PP

                      CBP_BcsQ  84 fGelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdanchv.rLhqqalpa. 162
                                    G   ++        ++k+e+l + lk+++   + +++D+pag  + t  +++ ad  + vv+p+ ++    L+  a+++ 
  gi|15668727|ref|NP_247526.1|  89 AGVSLEKF------RRAKPEKLEEVLKAIHDLVEILIIDCPAGIGKETLIAISSADGLIVVVNPEISSISdALKIIAITKr 163
                                   *9754433......357899999999999999*********************************8774312333333221 PP

                      CBP_BcsQ 163 .aellLiNqfeaasqlqqDllqlWlqslrrllPl..vihrDealaEalaakqPlgeyrpdslaaeevktLa 230
                                     + ++    +  s+  ++l    +++  ++ P+  v+ +D  +  a a   Pl    pds aa++++ +a
  gi|15668727|ref|NP_247526.1| 164 lGTDIIGAIVNRVSNESTELGVKAIETILEV-PVigVVPEDPHVRKAAAFGTPLVIMYPDSPAAQAIMEIA 233
                                   1233333333333333344444444433332.332456666666666666666666666666666666655 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.6   2.5e-13   2.1e-10       3     130 ..       9     145 ..       7     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2.5e-13
                                   EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHH..HH.......HH.HHHHHT------E.EE-SSS CS
                          MipZ   3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryle..nr.......aa.taerkglsLplpe.alalse 72 
                                   i ++  kGG+Gk+t++  +avaL+k G++va++d d+  + l+  ++   +       +a  a+ k+   + pe +l+++ 
  gi|15668727|ref|NP_247526.1|   9 IAIASGKGGTGKTTISANLAVALAKFGKKVAVLDADIAMANLELIMGleGKpvtlndvLAgKADIKDAIYEGPEgVLVIPA 89 
                                   788999*******************************99999887652122111110111122223333445552345555 PP

                                   -HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEE CS
                          MipZ  73 aeeaeveeeeeaevaeleelvadleaeldfividtPGsdsalsrlahsladtlvtPln 130
                                   + + e  + ++   ++lee++++++  +++++id+P    + + +a s ad l+  +n
  gi|15668727|ref|NP_247526.1|  90 GVSLEKFRRAK--PEKLEEVLKAIHDLVEILIIDCPAGIGKETLIAISSADGLIVVVN 145
                                   55445455444..459*************************************99888 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.4   2.4e-10   2.1e-07       5      40 ..      11      46 ..       7      67 .. 0.90
   2 !    7.3   0.1    0.0027       2.3     208     251 ..     139     182 ..     127     193 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.4e-10
                                  EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT CS
                   ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvllistDPA 40
                                  + +GKGG GKtt+sa +av l++ gkkv ++  D A
  gi|15668727|ref|NP_247526.1| 11 IASGKGGTGKTTISANLAVALAKFGKKVAVLDADIA 46
                                  679****************************99977 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0027
                                   EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE-TTCSS CS
                   ArsA_ATPase 208 sfrlVvipEklslkEteRaikeLkkygikvdavivNkllpeeeq 251
                                    +++Vv+pE  s+ +  + i+  k++g ++   ivN++ +e+++
  gi|15668727|ref|NP_247526.1| 139 GLIVVVNPEISSISDALKIIAITKRLGTDIIGAIVNRVSNESTE 182
                                   5789*********************************9988765 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.4    0.0094         8       3      34 ..       9      40 ..       8      42 .. 0.86
   2 !   28.0   0.5     2e-09   1.7e-06     131     196 ..     140     208 ..      96     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0094
                        AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgy 34
                                  i +++   g GKT++s+ L+ al + g kv++
  gi|15668727|ref|NP_247526.1|  9 IAIASGKGGTGKTTISANLAVALAKFGKKVAV 40
                                  678888999**************888888876 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 2e-09
                        AAA_26 131 vilVargglgtinqllltiealrqknvrvlGvilNkvrnpe...nvetlekksgipvlGvvPylpdlea 196
                                    i+V++++ ++i ++l  i++ ++ +  ++G i+N+v n+     v+++e+  ++pv+GvvP +p++++
  gi|15668727|ref|NP_247526.1| 140 LIVVVNPEISSISDALKIIAITKRLGTDIIGAIVNRVSNEStelGVKAIETILEVPVIGVVPEDPHVRK 208
                                   58999999*****************************999556799*******************9986 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.8   2.5e-06    0.0021       4      39 ..       9      44 ..       5      50 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.5e-06
                         VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfead 39
                                  i+++s kGG+Gktt    l  ala  gk+va+++ad
  gi|15668727|ref|NP_247526.1|  9 IAIASGKGGTGKTTISANLAVALAKFGKKVAVLDAD 44
                                  7899*******************************9 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   1.9    0.0002      0.17      16      46 ..       4      34 ..       1      43 [. 0.85
   2 ?    4.2   0.0     0.031        26       9      40 ..     104     137 ..      98     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                  HHH-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                          PhoH 16 lkkndivfaiGpaGtGKtylavalavealkk 46
                                  l++  i +a G+ GtGKt ++  lav++ k 
  gi|15668727|ref|NP_247526.1|  4 LMAIAIAIASGKGGTGKTTISANLAVALAKF 34
                                  6677899******************998765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.031
                                   HHHHHHHHH.H-SEEEEE--TTSST.THHHHHHH CS
                          PhoH   9 Qkeylealk.kndivfaiGpaGtGK.tylavala 40 
                                    +e+l+a++   +i+++  paG GK t++a++ a
  gi|15668727|ref|NP_247526.1| 104 LEEVLKAIHdLVEILIIDCPAGIGKeTLIAISSA 137
                                   5678889987789************888888765 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.4e-06    0.0054       7      47 ..      12      52 ..       6     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.4e-06
                                  EESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTT CS
                    APS_kinase  7 ltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnk 47
                                   +G  g+GK+ti+ +l+ +L + g++v +Ld d    +L+ 
  gi|15668727|ref|NP_247526.1| 12 ASGKGGTGKTTISANLAVALAKFGKKVAVLDADIAMANLEL 52
                                  57999***************************988777765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   3.3   1.8e-05     0.016      34     149 ..       8     121 ..       3     125 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                        AAA_25  34 elallaGapgtGKttlaldlalava.tGkpwlg...pvapeqgkVlyvsaEdsedelrrRlravgeal.....rddarllv 105
                                   ++a+  G +gtGKtt+  +la+a+a  Gk+++    ++a+ +   l+  +E++  +l+  l+   +++     + ++++lv
  gi|15668727|ref|NP_247526.1|   8 AIAIASGKGGTGKTTISANLAVALAkFGKKVAVldaDIAMANLE-LIMGLEGKPVTLNDVLAGK-ADIkdaiyEGPEGVLV 86 
                                   578999*******************8455443344644444444.5666777776666666532.2223335566666666 PP

                        AAA_25 106 ldlagveslpLfakdrggtlltadvdaleaaieeveg.vrlvviD 149
                                   +  agv         + ++ + a+ ++le++++++++ v+ ++iD
  gi|15668727|ref|NP_247526.1|  87 IP-AGV---------SLEKFRRAKPEKLEEVLKAIHDlVEILIID 121
                                   65.454.........233445566677888888888878888887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.9     2e-05     0.017      20      77 ..       9      67 ..       3     121 .. 0.79
   2 ?    0.5   0.0       0.5   4.3e+02      19      36 ..     116     133 ..      98     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                        AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Laeelgieastiakll 77
                                  +a++ G  GtGKtt+ + l+ a+++ g++v++l    ++A+  L  +l+ +  t++ +l
  gi|15668727|ref|NP_247526.1|  9 IAIASGKGGTGKTTISANLAVALAKFGKKVAVLDADIAMANLeLIMGLEGKPVTLNDVL 67
                                  68999**************************9966666665436666666666666666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.5
                        AAA_30  19 rvavltGpAGtGKttalk 36 
                                    + ++  pAG GK t+++
  gi|15668727|ref|NP_247526.1| 116 EILIIDCPAGIGKETLIA 133
                                   5789999******99986 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.8     2e-05     0.017       7      39 ..      13      45 ..       7     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                                  EESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                         SRP54  7 vGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                   G  G+GKTt  a La  l k gkkv++  aD+
  gi|15668727|ref|NP_247526.1| 13 SGKGGTGKTTISANLAVALAKFGKKVAVLDADI 45
                                  6889************************99997 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.1e-05     0.018       1      36 [.      14      49 ..      14      53 .. 0.91
   2 ?   -2.2   0.0       3.6   3.1e+03     104     127 ..     116     136 ..     102     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqse 36
                                  G+  +GK+T++++L+  +++ g+k++++D+D+   +
  gi|15668727|ref|NP_247526.1| 14 GKGGTGKTTISANLAVALAKFGKKVAVLDADIAMAN 49
                                  66789**************************98765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.6
                        CLP1_P 104 sgliIntpGwvkglgaelllelie 127
                                   ++liI++p    g+g+e+l ++ +
  gi|15668727|ref|NP_247526.1| 116 EILIIDCP---AGIGKETLIAISS 136
                                   56788888...4777777766554 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   8.8e-05     0.076      35      66 ..      13      44 ..       5      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
                                  EE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                          MeaB 35 tGvPGaGkstlvealglelrrrGkrvavlavD 66
                                   G  G+Gk t+  +l++ l++ Gk+vavl  D
  gi|15668727|ref|NP_247526.1| 13 SGKGGTGKTTISANLAVALAKFGKKVAVLDAD 44
                                  5889************************9877 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00024      0.21       4      37 ..      12      50 ..       9      85 .. 0.84
   2 ?   -2.7   0.0         7     6e+03      92     116 ..     209     233 ..     203     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                        AAA_33  4 lvGlpGsGKstlaerllkklg.....avllssdtlrrrl 37
                                    G  G+GK+t + +l+ +l+     + +l+ d+++ +l
  gi|15668727|ref|NP_247526.1| 12 ASGKGGTGKTTISANLAVALAkfgkkVAVLDADIAMANL 50
                                  56999***********99998888999999999988766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7
                        AAA_33  92 arrlgvpvrivvvetdeetlkeRla 116
                                   a  +g p  i++ +++ +++   +a
  gi|15668727|ref|NP_247526.1| 209 AAAFGTPLVIMYPDSPAAQAIMEIA 233
                                   4458888999999988887765555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2    0.0015       1.3      33      59 ..      16      40 ..       8      48 .. 0.83
   2 ?    1.3   0.0      0.35     3e+02       4      43 ..      96     135 ..      93     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                                  TTSTHHHHHHHHHHHH-S.....-EEE CS
                        ResIII 33 TGtGKTlvaaklierllkkgkeekflf 59
                                   GtGKT ++a+l+ +l+k gk  k+ +
  gi|15668727|ref|NP_247526.1| 16 GGTGKTTISANLAVALAKFGK--KVAV 40
                                  59***************9987..4444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.35
                                   E-HHHHHHHHHHT......TTSEEEEEESTTSTH.HHHHHH CS
                        ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGK.Tlvaak 43 
                                   +r    e +e++l++++ +  + ++i  + G GK Tl+a++
  gi|15668727|ref|NP_247526.1|  96 FRRAKPEKLEEVLKAIH-DLVEILIIDCPAGIGKeTLIAIS 135
                                   67777788899999998.7888889*********6666655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00031      0.26       8      39 ..      13      51 ..       5      82 .. 0.89
   2 ?   -2.6   0.0       4.6   3.9e+03      10      19 ..     123     132 ..      91     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                        AAA_24  8 yGpsgiGKTtlakel.......gpkplfidtekGlksld 39
                                   G+ g+GKTt+ ++l       g+k++++d +  +++l+
  gi|15668727|ref|NP_247526.1| 13 SGKGGTGKTTISANLavalakfGKKVAVLDADIAMANLE 51
                                  499***************************998777665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.6
                        AAA_24  10 psgiGKTtla 19 
                                   p+giGK tl+
  gi|15668727|ref|NP_247526.1| 123 PAGIGKETLI 132
                                   5666666555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.4    0.0039       3.3      25      40 ..      12      27 ..       3      37 .. 0.80
   2 ?    2.1   0.0      0.11        90       7      38 ..     103     133 ..      97     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0039
                                  EEESTTSSHHHHHHHH CS
                        NB-ARC 25 lvGmgGvGKttlakqi 40
                                   +G+gG GKtt++++ 
  gi|15668727|ref|NP_247526.1| 12 ASGKGGTGKTTISANL 27
                                  47**********9986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                                   HHHHHHHCTTTSCSEEEEEEESTTSSHHHHHH CS
                        NB-ARC   7 kviekLlekdelqslvvalvGmgGvGKttlak 38 
                                   k+ e L   ++l   ++ +   +G+GK tl++
  gi|15668727|ref|NP_247526.1| 103 KLEEVLKAIHDLV-EILIIDCPAGIGKETLIA 133
                                   5555555533443.4999999********975 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.6    0.0021       1.8      21      67 ..       9      54 ..       2     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0021
                                  EEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C 21 liiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRl 67
                                  + i  ++ ++Gkt++  n+a + a+   ++vav   + +  +l   +
  gi|15668727|ref|NP_247526.1|  9 IAIASGKGGTGKTTISANLAVALAK-FGKKVAVLDADIAMANLELIM 54
                                  5677899*************99885.455677766665555544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 1587.20
//
Query:       gi|15668728|ref|NP_247527.1|  [L=293]
Description: hypothetical protein MJ_0548 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-71  238.7   7.7    6.2e-71  238.0   7.7    1.3  1  DUF2121     Uncharacterized protein conserved in archaea (DUF
  ------ inclusion threshold ------
      0.027   14.4   0.5       0.11   12.5   0.5    1.9  2  PUA         PUA domain
      0.055   13.9   0.1       0.25   11.8   0.0    1.9  2  DUF3037     Protein of unknown function (DUF3037)
      0.063   13.4   0.7       0.43   10.7   0.7    2.1  2  ApoLp-III   Apolipophorin-III precursor (apoLp-III)
        0.4   10.4   5.4         35    4.1   0.1    3.8  3  DUF4264     Protein of unknown function (DUF4264)
        2.7    6.6   7.8       0.95    8.1   0.7    2.0  2  MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family


Domain annotation for each model (and alignments):
>> DUF2121  Uncharacterized protein conserved in archaea (DUF2121)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.0   7.7   2.1e-74   6.2e-71       1     196 []       1     194 [.       1     194 [. 0.99

  Alignments for each domain:
  == domain 1  score: 238.0 bits;  conditional E-value: 2.1e-74
                       DUF2121   1 MslviayigkkgaviagDkReiafrgdeeerekLEeeLYsGeiktdeeLkkkaeelgvkikitddreKvrkv.gdvlvGEV 80 
                                   Msl+i+y+gk+gavi+gD+R+i+frg+ee+r++LEe+LYsGeik++eeL+k ae+l++ki i+ddreKvrk+ ++v++GEV
  gi|15668728|ref|NP_247527.1|   1 MSLIICYYGKNGAVIGGDRRQIFFRGSEENRKILEEKLYSGEIKSEEELYKLAEKLNIKIIIEDDREKVRKIsDSVVCGEV 81 
                                   9***********************************************************************99******* PP

                       DUF2121  81 keisaketkrrRiYatkgayaivelegsevtkkkkgess.livfGnkvtkeiankllkkevk..kklslkeiekllkeile 158
                                   ++ +  ++krrR+Yatkg++aiv++ +++vt+++++e+  ++v+Gn+++k+ a+++lk+++k  +++++++ie+++kei+e
  gi|15668728|ref|NP_247527.1|  82 RSLGI-DAKRRRVYATKGKCAIVDILNDTVTNQTIKEGFgIVVLGNRFLKKKAEEELKRTAKlfPMMPIQQIEDAIKEIFE 161
                                   *****.********************************************************99***************** PP

                       DUF2121 159 evaektasvskeydllkkkkkldkkeaalekaikkDie 196
                                   +++ ++++vskeyd+++++k+++    ++e++ikkDie
  gi|15668728|ref|NP_247527.1| 162 KLK-WHPTVSKEYDIYSVNKYEK----NFEEVIKKDIE 194
                                   **9.*******************....9********96 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.3   6.9e+03       6      21 ..     130     145 ..     128     146 .. 0.82
   2 ?   12.5   0.5   3.6e-05      0.11      24      43 ..     255     274 ..     253     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                                   -HHHHHHHHTT-EEEG CS
                           PUA   6 ddgAvkallsgasLla 21 
                                   ++ A + l++ a+L++
  gi|15668728|ref|NP_247527.1| 130 KKKAEEELKRTAKLFP 145
                                   6789999999999997 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.6e-05
                                   EEEEETT--TTSEEEEEETT CS
                           PUA  24 vvevegdfeegdvVaivded 43 
                                   vv+veg+f+ gd+V+i ++d
  gi|15668728|ref|NP_247527.1| 255 VVDVEGNFKDGDIVVIENGD 274
                                   9***************9886 PP

>> DUF3037  Protein of unknown function (DUF3037)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.72   2.2e+03      30      53 ..      58      81 ..      50     106 .. 0.72
   2 ?   11.8   0.0   8.5e-05      0.25      19     103 ..     120     218 ..     119     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.72
                       DUF3037 30 lkvrleldeaRlralfpeldleal 53
                                  +k+ +e+d++++r++++ + + ++
  gi|15668728|ref|NP_247527.1| 58 IKIIIEDDREKVRKISDSVVCGEV 81
                                  455677788888888877654444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.5e-05
                       DUF3037  19 GVvlfskkegflkvrleldeaRlralfpeldlealeeelkaleeic................egekaagpiakldlaerfr 83 
                                   G+v+    ++flk + e++ +R  +lfp + ++++e+++k++ e +                + ek++++  k+d++++f+
  gi|15668728|ref|NP_247527.1| 120 GIVVL--GNRFLKKKAEEELKRTAKLFPMMPIQQIEDAIKEIFEKLkwhptvskeydiysvnKYEKNFEEVIKKDIESLFK 198
                                   67777..78999*****999*******************999999999***********99877888999999******** PP

                       DUF3037  84 wltaprstviqtsevhtglt 103
                                     ++ r+++i +++v   + 
  gi|15668728|ref|NP_247527.1| 199 YREQLRKQLIDFGKVMSIVN 218
                                   *************9988765 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.7   0.00014      0.43      20     100 ..     108     193 ..     101     209 .. 0.76
   2 ?    2.6   0.2     0.043   1.3e+02      37      67 ..     177     207 ..     170     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                     ApoLp-III  20 qeevvetiKensenlvdqlkqvikslqeelkkksdeleea.lkevkkkieetadklseenPevkkk.....aqelqekvQs 94 
                                   +  +++tiKe+   +v   + + k+++eelk++   +  + ++++ ++i+e+++kl+  +P v k+     ++++++++ +
  gi|15668728|ref|NP_247527.1| 108 DTVTNQTIKEGFGIVVLGNRFLKKKAEEELKRTAKLFPMMpIQQIEDAIKEIFEKLKW-HPTVSKEydiysVNKYEKNFEE 187
                                   4457899*********999*************99666543489**************9.9**9996333336777777766 PP

                     ApoLp-III  95 gvqslv 100
                                    +++ +
  gi|15668728|ref|NP_247527.1| 188 VIKKDI 193
                                   665544 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.043
                     ApoLp-III  37 qlkqvikslqeelkkksdeleealkevkkki 67 
                                   +++++ k+++e +kk ++ l +  ++++k++
  gi|15668728|ref|NP_247527.1| 177 SVNKYEKNFEEVIKKDIESLFKYREQLRKQL 207
                                   6889999999999999988888888888876 PP

>> DUF4264  Protein of unknown function (DUF4264)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.012        37       8      24 ..      41      57 ..      36      60 .. 0.86
   2 ?    2.2   0.2     0.047   1.4e+02      19      30 ..     102     113 ..      99     123 .. 0.84
   3 ?    4.1   0.1     0.012        35       5      22 ..     241     258 ..     239     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.012
                       DUF4264  8 kefeknddlYkvVDfLN 24
                                   e++  ++lYk+   LN
  gi|15668728|ref|NP_247527.1| 41 GEIKSEEELYKLAEKLN 57
                                  5899********99999 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.047
                       DUF4264  19 vVDfLNktLKdk 30 
                                   +VD+LN t  ++
  gi|15668728|ref|NP_247527.1| 102 IVDILNDTVTNQ 113
                                   9*****997665 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.012
                       DUF4264   5 iatkefeknddlYkvVDf 22 
                                   ia  ++ +n  ++kvVD+
  gi|15668728|ref|NP_247527.1| 241 IAIDKIDPNPKVFKVVDV 258
                                   88999************5 PP

>> MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.3     0.018        53     250     282 ..      46      76 ..      28      82 .. 0.86
   2 ?    8.1   0.7   0.00032      0.95     143     203 ..     148     207 ..     126     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.018
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                    MAP65_ASE1 250 eeEleRLeeLKkknlkklIedlRqeIeelWdkl 282
                                   eeEl +L e  k n+k +Ied R++++++ d++
  gi|15668728|ref|NP_247527.1|  46 EEELYKLAE--KLNIKIIIEDDREKVRKISDSV 76 
                                   677777776..88****************9986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00032
                                   HHHHHHHHHHHHHHHHT----SHHHHHHHCT-TTTS-....TSHHHHHHHHHHHHHHHHHH CS
                    MAP65_ASE1 143 eikelkkqIkslmeeLglepktsieedllkesednskklkpltretikkLkllkkeleeqk 203
                                    i++++++Ik+++e+L   p+ s e+d+   ++ + k+++++ ++ i++L +  ++l++q 
  gi|15668728|ref|NP_247527.1| 148 PIQQIEDAIKEIFEKLKWHPTVSKEYDIYSVNKYE-KNFEEVIKKDIESLFKYREQLRKQL 207
                                   58999**********************97555555.45889****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1231  (0.0686597); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1974.87
//
Query:       gi|15668729|ref|NP_247528.1|  [L=141]
Description: nickel responsive regulator [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-33  115.3   5.2    1.9e-33  114.5   5.2    1.4  1  NikR_C           NikR C terminal nickel binding domain
    2.7e-12   46.2   1.9    2.7e-12   46.2   1.9    2.0  2  RHH_1            Ribbon-helix-helix protein, copG family
     0.0034   17.5   0.1     0.0084   16.2   0.0    1.7  2  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
     0.0084   16.3   0.1      0.012   15.8   0.1    1.4  1  RHH_8            Ribbon-Helix-Helix transcriptional regulator
  ------ inclusion threshold ------
       0.04   14.0   0.0      0.052   13.6   0.0    1.2  1  RRM_3            RNA binding motif
      0.075   12.8   0.1        0.1   12.4   0.1    1.2  1  ChuX_HutX        Haem utilisation ChuX/HutX


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.5   5.2   6.3e-37   1.9e-33       1      76 [.      57     132 ..      57     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 6.3e-37
                                   EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEE CS
                        NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltl 76 
                                   +G i+++y+hh ++++e++t+iqh+y d+i+++lh hldhd+cLe+i+++G+a++i+el+++l+alkgVk+vkl++
  gi|15668729|ref|NP_247528.1|  57 AGSISVIYNHHASDVMEKITEIQHNYTDIIVATLHLHLDHDHCLETILVRGDAKRIRELTDRLTALKGVKQVKLSV 132
                                   699***********************************************************************97 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   1.9     9e-16   2.7e-12       1      37 [.       6      43 ..       6      45 .. 0.97
   2 ?   -1.6   0.1         1     3e+03      11      20 ..     109     118 ..     108     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 9e-16
                                  EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                         RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                  r+si+l+++ll+++de++++rg  SrSe+IR+A+r+y+
  gi|15668729|ref|NP_247528.1|  6 RISISLPSKLLREFDEIIAERGyASRSEAIRDAIRDYI 43
                                  8************************************8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                                   HHHHHHHHHH CS
                         RHH_1  11 lerLdelarr 20 
                                   ++r++el +r
  gi|15668729|ref|NP_247528.1| 109 AKRIRELTDR 118
                                   6889998876 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.8e-06    0.0084      88     120 ..       3      36 ..       1      39 [. 0.88
   2 ?   -1.7   0.0         1   3.1e+03      34      78 ..      79      90 ..      64     117 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.8e-06
               HicB_lk_antitox  88 kaeriNitlpervlkriDaavkaag.esRSgfla 120
                                   +  ri i+lp+++l++ D++++++g  sRS  + 
  gi|15668729|ref|NP_247528.1|   3 EMDRISISLPSKLLREFDEIIAERGyASRSEAIR 36 
                                   568*********************967***8775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
               HicB_lk_antitox 34 ianakeaielhlegliedgeeipepssieellanpeyaggiwalv 78
                                                                    ++y+++i+a+ 
  gi|15668729|ref|NP_247528.1| 79 Q---------------------------------HNYTDIIVATL 90
                                  2.................................33444444333 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   3.8e-06     0.012       2      84 ..       3      87 ..       2     116 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.8e-06
                         RHH_8  2 etekvtinlgvvDLgqiDlLveeGfYsnRtDlirtairaqLakhddalkqavkrkslvlGvtkls.raeleevqa.enkqlel 82
                                  e ++++i l    L + D ++ e  Y++R++ ir air+ + kh+   +   +r  +   + + +  + +e++++ +++  ++
  gi|15668729|ref|NP_247528.1|  3 EMDRISISLPSKLLREFDEIIAERGYASRSEAIRDAIRDYIIKHKWIHSLEGERAGSISVIYNHHaSDVMEKITEiQHNYTDI 85
                                  56889999999999999*9999999****************999865444444443333333333033344443313444444 PP

                         RHH_8 83 kv 84
                                   v
  gi|15668729|ref|NP_247528.1| 86 IV 87
                                  44 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.7e-05     0.052      15      89 ..      32     106 ..      22     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                                   HHHHHHHCHCCS.-ECEEEE-TTSSEEEEEESSHHHHHHHHHHHHHC-B-CCTSSEEEEE--HHHHHHHHHHHHHH CS
                         RRM_3  15 redikellsklg.evayvdyekgdkegevrFkedeeakkalekateaklkikdaevtlelLeGeeEkeywkkiled 89 
                                    e i+++++ +  + +++   +g+  g++    ++ a  ++ek te++ +  d +v    L+ ++  + +++il++
  gi|15668729|ref|NP_247528.1|  32 SEAIRDAIRDYIiKHKWIHSLEGERAGSISVIYNHHASDVMEKITEIQHNYTDIIVATLHLHLDHD-HCLETILVR 106
                                   5677777777766779***********999888888***********9888888887776766664.355555555 PP

>> ChuX_HutX  Haem utilisation ChuX/HutX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.4e-05       0.1      46      97 ..      66     110 ..      49     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                                   EESSEEEEEEEE....--EEEEE..EESCTSEEEEEEGGGEEEEEEEEEEE. CS
                     ChuX_HutX  46 rnegavhEkkGkyenvlpeyynlagvlgeseldlhLfldhwahifaveeptk 97 
                                   ++++ v+Ek  ++++    y  +  +++   l+lhL +dh+ + ++v+ + k
  gi|15668729|ref|NP_247528.1|  66 HHASDVMEKITEIQHN---YTDI--IVAT--LHLHLDHDHCLETILVRGDAK 110
                                   3455588888886666...8888..6666..****************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 899.77
//
Query:       gi|15668730|ref|NP_247529.1|  [L=365]
Description: hypothetical protein MJ_0550 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-10   39.9   0.2    3.3e-09   37.3   0.1    2.1  2  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.011   15.2   0.1       0.23   10.9   0.1    2.2  2  His_biosynth  Histidine biosynthesis protein
      0.013   15.1   0.5      0.026   14.1   0.1    1.7  2  KdgM          Oligogalacturonate-specific porin protein (KdgM
        4.3    7.6   6.2        6.2    7.1   0.9    3.0  2  SRP54_N       SRP54-type protein, helical bundle domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.1   7.4e-13   3.3e-09       5     144 ..      58     211 ..      54     231 .. 0.78
   2 ?   -0.4   0.0       0.3   1.4e+03      12      41 ..     247     286 ..     242     300 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 7.4e-13
                                   SEESS-....-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE.........SSTGGGSTTHHHHHHHHHH CS
                                   xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   5 rgCnlr....CsfCarpetvrregrgrslsveeileevkelkaekgvkevilg.........ggepllypdfvellerlak 72 
                                   +gC ++    C  C+          ++ ++ e+i++++ ++  ek ++ +  +         +g  l++++  +++++++ 
  gi|15668730|ref|NP_247529.1|  58 EGCYYAkeggCLMCSYLM----DSSPEKITAENIINQFNYA-IEKYKEKIKDLkdfsvkiftSGSFLDDREVPKEARNYIF 133
                                   566555555588888885....5566666666666666555.33334444444444444444999**************** PP

                                   TC....CCTEEEEEEECSSCHGHHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                   xx....xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  73 la....vpgiritvetngtlpdeeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr 144
                                   ++    ++  ++++e+ +  +de+kl +++++      + +g+e++++e   k +n+g t+e++++a+e++++++i  
  gi|15668730|ref|NP_247529.1| 134 KKlsefDNLKEVAIESRPEFIDEDKLNEIRKYLdvNVEIGVGIESFNEEIREKAINKGITNEQIIRAIELAKNYNIGI 211
                                   **********************************99*************8888999*****************99985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.3
                                   TTTSCCTT..........HHHHHHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  12 sfCarpet..........vrregrgrslsveeileevkel 41 
                                   sfC+ + +          + +++++   s+ eil+evk+ 
  gi|15668730|ref|NP_247529.1| 247 SFCPATVHkgsvmefffnKNQYRPPFLWSIIEILKEVKKS 286
                                   5888888888888888888888888888999999999875 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   5.1e-05      0.23      61     114 ..     155     206 ..     140     212 .. 0.89
   2 ?    1.4   0.0      0.04   1.8e+02     147     178 ..     274     305 ..     255     320 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.1e-05
                                   HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHH CS
                  His_biosynth  61 nldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelike 114
                                   + d ++ei++ ++++v++G GI s++  ee+ e  ++k i +   ++  el k+
  gi|15668730|ref|NP_247529.1| 155 DEDKLNEIRKYLDVNVEIGVGIESFN--EEIREKAINKGITNEQIIRAIELAKN 206
                                   5577899*******************..***************99999988775 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.04
                                   EEHHHHHHHHHHTT-SEEEEEETTTTTTSS-- CS
                  His_biosynth 147 ldavelakkleelgageilltdidrdGtlsGp 178
                                   ++++e++k++++ + +++++ d + +G++ G 
  gi|15668730|ref|NP_247529.1| 274 WSIIEILKEVKKSNPKALIMCDTSGVGSERGA 305
                                   6899*************************996 PP

>> KdgM  Oligogalacturonate-specific porin protein (KdgM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.9e-06     0.026       5      95 ..     142     229 ..     139     235 .. 0.85
   2 ?   -3.1   0.0       1.1   4.9e+03     190     209 ..     341     360 ..     334     362 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.9e-06
                                   XXX-EEEEEEEEE------EEEEEEEEEE-TTSEEEEEEEEEEE------.---------EEEEEEEEEE-EESSSSEEEE CS
                          KdgM   5 vlAvyvdyRheyadaskaGnkdrlliserfanGvGlaveakvksggadke.nnkrlnelkangnElevsylfKvtdklaiq 84 
                                   +  v ++ R e+ d+ k  n+ r ++  +++ GvG+ +   +++   +k  n+   ne+   ++El   y+  +   l i+
  gi|15668730|ref|NP_247529.1| 142 LKEVAIESRPEFIDEDKL-NEIRKYLDVNVEIGVGIES---FNEEIREKAiNKGITNEQIIRAIELAKNYNIGIKAYLLIK 218
                                   56699*************.9****************98...4444444440555789************************ PP

                                   EEEEEEEESS- CS
                          KdgM  85 PGfvlesgsst 95 
                                   P f+ e+  ++
  gi|15668730|ref|NP_247529.1| 219 PLFITEKEAIY 229
                                   ****9998876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.1
                                   SSEEEEEEEEEEE------- CS
                          KdgM 190 kswkPyvEvgnvsvneetde 209
                                   + w+ y+Ev n +     de
  gi|15668730|ref|NP_247529.1| 341 NIWNAYIEVENKNIVPLGDE 360
                                   56999999999766555555 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.4     0.066     3e+02      46      65 ..      11      30 ..       9      35 .. 0.85
   2 ?    7.1   0.9    0.0014       6.2      18      70 ..     154     201 ..     131     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.066
                                  HHHHHHHHHHHCTTSS-HHH CS
                       SRP54_N 46 klienvkkkavgekklkpkq 65
                                  +++++++++ ++++k+k+k 
  gi|15668730|ref|NP_247529.1| 11 EFLKKLRERHLKKRKVKDKN 30
                                  79999***999999999875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0014
                                   GHHHHHHHHHHHHHHHHHHTT--HHH...HHHHHHHHHHHHHCTTSS-HHHHHHHH CS
                       SRP54_N  18 ideedleealkeleeaLleaDVgvkv...vkklienvkkkavgekklkpkqqvkki 70 
                                   ide+ l+e    +++ L   DV+v++    +++ e++++ka++ k +++ q ++ i
  gi|15668730|ref|NP_247529.1| 154 IDEDKLNE----IRKYL---DVNVEIgvgIESFNEEIREKAIN-KGITNEQIIRAI 201
                                   78888888....99988...99999865569************.999888877754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2260.50
//
Query:       gi|15668731|ref|NP_247530.1|  [L=275]
Description: nitrite reductase NirA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-27   94.4   0.5    6.9e-27   93.9   0.5    1.2  1  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    3.2e-15   55.7   0.0    1.2e-14   53.9   0.0    1.9  2  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
    0.00046   19.9   3.4    0.00046   19.9   3.4    2.9  2  Fer4          4Fe-4S binding domain
     0.0053   16.8   8.0      0.019   15.1   8.0    2.0  1  Fer4_21       4Fe-4S dicluster domain
     0.0059   16.6   2.3     0.0059   16.6   2.3    3.4  3  Fer4_2        4Fe-4S binding domain
  ------ inclusion threshold ------
       0.05   13.7   3.1       0.05   13.7   3.1    3.4  4  Fer4_6        4Fe-4S binding domain
      0.064   13.8  16.5       0.17   12.5   3.8    3.4  3  Fer4_4        4Fe-4S binding domain
       0.47   10.6  17.8      0.061   13.4  11.5    2.6  3  Fer4_10       4Fe-4S dicluster domain
        1.2    9.8  13.1       0.13   12.8   7.2    2.4  2  Fer4_7        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   0.5   3.5e-30   6.9e-27       2     153 ..      88     272 ..      87     275 .] 0.96

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 3.5e-30
                                   SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei... 79 
                                   g+++r+v++c+g + c++a+ D+ +la++i+    +e++  ++PrK+Ki+vsgcpn c  +++ Dig++  +k  ++    
  gi|15668731|ref|NP_247530.1|  88 GNRVRQVVSCIGLE-CYNAIGDSVSLARRIH----EEFEGVWVPRKVKINVSGCPNSCTFHRFCDIGICYRYKITINKeic 163
                                   899**********9.****************....**************************************8888899* PP

                                   ...........................................EEEEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHH CS
                                   ...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR  80 ...........................................gfnilvGGglgrthgakktsarlgfvpeeevlevveai 117
                                                                               ++i+vGG+ gr  +++k++++    +e++vl v++++
  gi|15668731|ref|NP_247530.1| 164 tncgkckdfcdlnaidwerkiikdnctgegkctglcnafkaerVISIFVGGKGGRIYKEGKHLID--LKNEDDVLFVIDEL 242
                                   ****************************************************************7..466668******** PP

                                   HHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR 118 vevyrdhgdrknrkkeRlkylverlGvekFrekvee 153
                                   + +y+      +  k R++++ve++G+e++r++++e
  gi|15668731|ref|NP_247530.1| 243 ISLYA------KFGKGRMADFVENYGIENLRNNIKE 272
                                   *****......9********************9976 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   5.8e-18   1.2e-14       7      68 ..      19      79 ..      16      80 .. 0.94
   2 ?   -1.7   0.0       1.4   2.7e+03      29      42 ..     254     267 ..     251     267 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 5.8e-18
                  NIR_SIR_ferr  7 kgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLae 68
                                  k +y++r++++ G i+aeql+a+a ++e +g+  +++TtrQ++++  +++e+lee++++L++
  gi|15668731|ref|NP_247530.1| 19 KDCYTLRISLKPGFINAEQLKAIAYVIENFGDNKAHITTRQGIEFK-ISPEHLEEVEKILNN 79
                                  3568*****************************************9.************986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                  NIR_SIR_ferr  29 ladiaekygsgeir 42 
                                   +ad++e yg+  +r
  gi|15668731|ref|NP_247530.1| 254 MADFVENYGIENLR 267
                                   79*******87665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   3.4   2.3e-07   0.00046       1      23 [.     156     178 ..     156     179 .. 0.94
   2 ?   -1.0   2.1      0.89   1.8e+03       3      16 ..     184     197 ..     182     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.3e-07
                                   EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                   ++i++e C++CG+C + C  +AI
  gi|15668731|ref|NP_247530.1| 156 ITINKEICTNCGKCKDFCDLNAI 178
                                   689******************99 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.89
                                   EETTTSSS-THHHH CS
                          Fer4   3 ideekCigCGaCve 16 
                                   i+++ C+g G+C  
  gi|15668731|ref|NP_247530.1| 184 IIKDNCTGEGKCTG 197
                                   78899998666655 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   8.0   9.7e-06     0.019       2      51 ..     157     199 ..     156     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.7e-06
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvC 51 
                                   +i+++ C +CgkC   C+    +ai+ +     k+++d+C+G   C+  C
  gi|15668731|ref|NP_247530.1| 157 TINKEICTNCGKCKDFCD---LNAIDWE----RKIIKDNCTGEGKCTGLC 199
                                   599***************...7999986....45789*****99999999 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.2       1.4   2.8e+03       4      13 ..     130     140 ..     127     152 .. 0.56
   2 !   16.6   2.3   2.9e-06    0.0059       2      20 ..     155     173 ..     154     173 .. 0.92
   3 ?    3.0   0.3     0.066   1.3e+02       5      20 ..     184     199 ..     180     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.4
                        Fer4_2   4 vvdtdrC.igC 13 
                                   +++   C ++C
  gi|15668731|ref|NP_247530.1| 130 KINVSGCpNSC 140
                                   56666664455 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.9e-06
                        Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                   ++ ++ ++C++Cg+C + C
  gi|15668731|ref|NP_247530.1| 155 KITINKEICTNCGKCKDFC 173
                                   6899***********9999 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.066
                        Fer4_2   5 vdtdrCigCgaCvsaC 20 
                                   +  d+C+g g+C+  C
  gi|15668731|ref|NP_247530.1| 184 IIKDNCTGEGKCTGLC 199
                                   5568888757777777 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2       4.9   9.7e+03       9      13 ..      97     103 ..      96     104 .. 0.62
   2 ?   -3.3   1.8         6   1.2e+04       6      16 ..     137     152 ..     135     153 .. 0.57
   3 ?   13.7   3.1   2.5e-05      0.05       1      19 [.     155     173 ..     155     178 .. 0.90
   4 ?    1.7   0.8      0.15     3e+02       4      15 ..     184     199 ..     183     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.9
                        Fer4_6   9 Cig..Cg 13 
                                   Cig  C+
  gi|15668731|ref|NP_247530.1|  97 CIGleCY 103
                                   8865576 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6
                        Fer4_6   6 pdkCi.....gCgdCv 16 
                                   p++C+     + g C+
  gi|15668731|ref|NP_247530.1| 137 PNSCTfhrfcDIGICY 152
                                   5667665444445566 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 2.5e-05
                        Fer4_6   1 vveidpdkCigCgdCvrvC 19 
                                   +++i+++ C+ Cg+C + C
  gi|15668731|ref|NP_247530.1| 155 KITINKEICTNCGKCKDFC 173
                                   69*************8877 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.15
                        Fer4_6   4 idpdkCig...C.gdC 15 
                                   i +d+C+g   C g C
  gi|15668731|ref|NP_247530.1| 184 IIKDNCTGegkCtGLC 199
                                   67899*9644476666 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3       2.8   5.6e+03      13      15 ..     135     137 ..     133     141 .. 0.47
   2 ?   12.5   3.8   8.3e-05      0.17       2      14 ..     161     173 ..     160     175 .. 0.91
   3 ?    8.9   0.6    0.0012       2.3       1      14 [.     186     199 ..     186     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.8
                        Fer4_4  13 aCP 15 
                                    CP
  gi|15668731|ref|NP_247530.1| 135 GCP 137
                                   444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8.3e-05
                        Fer4_4   2 erCigCgsCvaaC 14 
                                   e C++Cg+C ++C
  gi|15668731|ref|NP_247530.1| 161 EICTNCGKCKDFC 173
                                   66*********** PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0012
                        Fer4_4   1 qerCigCgsCvaaC 14 
                                   +++C+g g+C+  C
  gi|15668731|ref|NP_247530.1| 186 KDNCTGEGKCTGLC 199
                                   69********9888 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.5       1.6   3.2e+03      39      47 ..     134     142 ..     125     152 .. 0.57
   2 ?   13.4  11.5   3.1e-05     0.061       1      55 [.     155     199 ..     155     200 .. 0.82
   3 ?    4.6   0.9     0.017        34       4      22 ..     184     200 ..     181     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.6
                       Fer4_10  39 rkkvekCtg 47 
                                   ++ + +Ct+
  gi|15668731|ref|NP_247530.1| 134 SGCPNSCTF 142
                                   334445554 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.1e-05
                       Fer4_10   1 kvvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                   k+ i+++ C++CgkC+++C          + + ++ + ++  ++Ctg g+C+  C
  gi|15668731|ref|NP_247530.1| 155 KITINKEICTNCGKCKDFC----------DLNAIDWERKIIKDNCTGEGKCTGLC 199
                                   5789***************..........56666666666667999999999888 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.017
                       Fer4_10   4 idddtCirCgkCvkaCPad 22 
                                   i +d C++ gkC+  C  +
  gi|15668731|ref|NP_247530.1| 184 IIKDNCTGEGKCTGLC--N 200
                                   6678999999999999..3 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   7.7    0.0088        17      29      50 ..     154     175 ..     115     177 .. 0.75
   2 ?   12.8   7.2   6.8e-05      0.13       2      48 ..     163     199 ..     162     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0088
                        Fer4_7  29 ekveidpekClgCgaCvavCPt 50 
                                    k++i+ e C++Cg+C + C  
  gi|15668731|ref|NP_247530.1| 154 YKITINKEICTNCGKCKDFCDL 175
                                   6788999999999999998865 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.8e-05
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavC 48 
                                   C++Cg+C + C  +ai+++ +          i  ++C+g g+C   C
  gi|15668731|ref|NP_247530.1| 163 CTNCGKCKDFCDLNAIDWERK----------IIKDNCTGEGKCTGLC 199
                                   ******************664..........7889999999998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1697.65
//
Query:       gi|15668732|ref|NP_247531.1|  [L=249]
Description: cobalamin biosynthesis protein CbiJ [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-67  227.5   0.0    1.8e-67  227.3   0.0    1.0  1  CbiJ           Precorrin-6x reductase CbiJ/CobK
      0.006   16.7   0.2      0.006   16.7   0.2    1.9  2  RTT107_BRCT_6  Regulator of Ty1 transposition protein 107 BRC
  ------ inclusion threshold ------
      0.057   13.5   0.6        9.1    6.4   0.1    2.4  2  MGDG_synth     Monogalactosyldiacylglycerol (MGDG) synthase
        0.1   12.8   0.1       0.38   10.9   0.0    2.0  3  DapB_N         Dihydrodipicolinate reductase, N-terminus
       0.16   11.4   0.1       0.39   10.1   0.1    1.7  1  AP_endonuc_2   Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> CbiJ  Precorrin-6x reductase CbiJ/CobK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.3   0.0   4.9e-71   1.8e-67       2     235 ..       3     244 ..       2     245 .. 0.97

  Alignments for each domain:
  == domain 1  score: 227.3 bits;  conditional E-value: 4.9e-71
                                   EEEE-SSHHHHHHHHHHHHT.T--EEEEE---SSS----S..S-EEES--SHHHHHHHHHHHT--EEEE-S-TT-HHHHHH CS
                          CbiJ   2 ililgGTsearelaeaLaea.gievvvsvateygaellpekklevrvgrlgeeglaellreekidlvvDATHPfAaeisan 81 
                                   +l++gGT+++ e+ ++L +  ++ ++++ +t+yg +l +e + +v++++l++++l+e++++ +id++vDATHPfA ++s+n
  gi|15668732|ref|NP_247531.1|   3 LLLMGGTKDSVEIGKKLRDLgDLFILYTSTTDYGGKLGEEFANKVITKPLDKNELKEVIKKYNIDILVDATHPFAINASKN 83 
                                   79******************89999******************************************************** PP

                                   HHHHHHHHT-EEEEE-------...EEEEESSHHHHH........EEEESTSTTGGGGSTT...SEEEEEESS--SS.--S CS
                          CbiJ  82 aaeackelgipylrleRpswea...kiievdsleeaaella....vllttGskelaafaealkkerllaRvlptpesleka 155
                                   a+e+ckel+i+y+r+eR++++    +ii+v+++eeaa+l++    v+   G k+l+ ++++  k++++aRvlp + s  +a
  gi|15668732|ref|NP_247531.1|  84 AIEVCKELNIKYVRFERKEEKInhpNIIYVKDFEEAARLAKkankVFHMAGIKNLKMVVDIVGKDKVIARVLPISVS--EA 162
                                   *******************9989**************9999********************999*********9655..78 PP

                                   SS....SEEEEE--SS--HHHHHHHHHHTT--EEEEES--SS.TTTHHHHHHHHTT-EEEEE---..--EE.E-SHHHHHH CS
                          CbiJ 156 lplglkakeiiamrGpfskelerallreykidvlVtKeSGgaGgteeKleaArelgipvivikRp..evee.vsdveelle 233
                                   l+  l++k+i+am G fskel++ l+r+y++dv++tK+SG++Gg++eK+  A e++++viv++Rp  +++  ++d++el++
  gi|15668732|ref|NP_247531.1| 163 LK-ILPQKQIVAMYGTFSKELNKYLIRDYNCDVIITKDSGESGGFKEKVYGALEAEAKVIVVERPkiDYPVcFDDIDELIK 242
                                   99.69**************************************************************99999********9 PP

                                   HH CS
                          CbiJ 234 wl 235
                                   ++
  gi|15668732|ref|NP_247531.1| 243 YI 244
                                   87 PP

>> RTT107_BRCT_6  Regulator of Ty1 transposition protein 107 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.3      0.73   2.6e+03      52      67 ..      97     112 ..      46     126 .. 0.54
   2 !   16.7   0.2   1.7e-06     0.006       1      95 [.     128     224 ..     128     226 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.73
                 RTT107_BRCT_6  52 ekkkkkekkkspeyvl 67 
                                   + ++k+ek ++p++++
  gi|15668732|ref|NP_247531.1|  97 RFERKEEKINHPNIIY 112
                                   3334444445555555 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.7e-06
                 RTT107_BRCT_6   1 kvFerakikkiNlvsdipggtevissiLkahGikevkvlskklkiedlvknekkkkkekkkspeyvliatkas.qvkkfkk 80 
                                   kvF+ a+ik++ +v di g+ +vi+++L     + +k+l++k       + +k+ +k   ++ ++ +i+tk+s +   fk 
  gi|15668732|ref|NP_247531.1| 128 KVFHMAGIKNLKMVVDIVGKDKVIARVLPISVSEALKILPQKQIVAMYGTFSKELNKYLIRDYNCDVIITKDSgESGGFKE 208
                                   8****************************9999999999964333222222344455555555554555555414557875 PP

                 RTT107_BRCT_6  81 .llkeekenkkvlvve 95 
                                    +  + + ++kv+vve
  gi|15668732|ref|NP_247531.1| 209 kVYGALEAEAKVIVVE 224
                                   1444448888888886 PP

>> MGDG_synth  Monogalactosyldiacylglycerol (MGDG) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0025       9.1      78     102 ..      54      79 ..      27     117 .. 0.85
   2 ?    5.5   0.1    0.0047        17      65      95 ..     167     197 ..     147     198 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0025
                                   HHHHHHHHHHH--SEEE.E-STTTTH CS
                    MGDG_synth  78 akelaalleeeqPDiii.sthplvae 102
                                    +el++++++++ Di++ +thp++ +
  gi|15668732|ref|NP_247531.1|  54 KNELKEVIKKYNIDILVdATHPFAIN 79 
                                   579*************9669**9654 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0047
                                   -------------HHHHHH.HHHHH--SEEEE CS
                    MGDG_synth  65 qkksilaklatflakelaa.lleeeqPDiiis 95 
                                   ++k+i+a++ t + kel + l++++++D+ii+
  gi|15668732|ref|NP_247531.1| 167 PQKQIVAMYGT-FSKELNKyLIRDYNCDVIIT 197
                                   34555555555.556665527899******96 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.38      44      92 ..      39      93 ..      26      98 .. 0.66
   2 ?   -2.1   0.0       1.1   4.1e+03      68      68 ..     147     147 ..     113     185 .. 0.53
   3 ?   -2.5   0.0       1.4   5.2e+03      69      69 ..     193     193 ..     158     225 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                  HHHHSSSS--S-BEB.SSHHHHHHH..-SEEEE-S-H...HHHHHHHHHHHHTT- CS
                        DapB_N 44 agellglgklgvavt.ddleevlek..advliDFTtp...eavlenlklalekgv 92
                                  +ge    + +  ++  ++l+ev++k   d+l+D T+p   +a+++ ++++ e ++
  gi|15668732|ref|NP_247531.1| 39 LGEEFANKVITKPLDkNELKEVIKKynIDILVDATHPfaiNASKNAIEVCKELNI 93
                                  444444444444444589*******999*********333344555666666555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                                   - CS
                        DapB_N  68 a 68 
                                    
  gi|15668732|ref|NP_247531.1| 147 K 147
                                   2 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.4
                                   S CS
                        DapB_N  69 d 69 
                                   d
  gi|15668732|ref|NP_247531.1| 193 D 193
                                   2 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00011      0.39      33      99 ..      57     102 ..      42     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
                                   HHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTT CS
                  AP_endonuc_2  33 lrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvlhpGtagagpk 99 
                                   l++ ++++++ i           +++  +     ++++a k+aie +++L+++++ +       + +
  gi|15668732|ref|NP_247531.1|  57 LKEVIKKYNIDI-----------LVDATHP----FAINASKNAIEVCKELNIKYVRFE------RKE 102
                                   555555555552...........2222223....45999****************998......333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1542.99
//
Query:       gi|15668733|ref|NP_247532.1|  [L=153]
Description: hypothetical protein MJ_0553 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-16   59.9   0.1      5e-16   58.9   0.1    1.5  1  Acylphosphatase  Acylphosphatase


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.1   2.8e-20     5e-16       1      78 [.       5      86 ..       5      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 2.8e-20
               Acylphosphatase  1 vrllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekf.leelks..gppk..arvdeveveeleeee 78
                                  ++l+++GrVQ vgFR  + ++ + lg++G v N++dg+V+i+a  ++e+++++ ++ +k+  ++    ++++++e +el++  
  gi|15668733|ref|NP_247532.1|  5 YELIIYGRVQHVGFRDRIEHIGRGLGISGVVYNHKDGTVRILANFDDEEIKELfKKSIKAleKK-DklIKIEKIEEKELNAYI 86
                                  6899*********************************************998624456654322.246********9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1597  (0.0890736); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 925.06
//
Query:       gi|15668734|ref|NP_247533.1|  [L=152]
Description: hypothetical protein MJ_0554 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-70  236.4  23.8    1.4e-70  236.3  23.8    1.0  1  DUF5418      Family of unknown function (DUF5418)
  ------ inclusion threshold ------
       0.15   11.7   2.6        0.2   11.3   2.6    1.2  1  HCV_NS2      Hepatitis C virus non-structural protein NS2
       0.19   10.1   7.2        0.2   10.0   6.7    1.3  1  Mem_trans    Membrane transport protein
        4.4    7.5  10.5       0.32   11.2   2.9    2.1  2  L_HMGIC_fpl  Lipoma HMGIC fusion partner-like protein
        6.1    6.5   6.2       0.77    9.4   1.0    1.8  2  DUF4131      Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF5418  Family of unknown function (DUF5418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.3  23.8   3.8e-74   1.4e-70       1     151 []       1     151 [.       1     151 [. 1.00

  Alignments for each domain:
  == domain 1  score: 236.3 bits;  conditional E-value: 3.8e-74
                       DUF5418   1 mvnehkahasfilkvilalvsysialilaiiiysiffkieenlfllcillalpiiyflilillGlthreleylsiydkykl 81 
                                   mvnehkahasf++k+i+++vs++++lil+i+iy+iff+i+enl+++cil+a+pii+flilil+G++h+el+yl+iydkykl
  gi|15668734|ref|NP_247533.1|   1 MVNEHKAHASFMFKIINVFVSFGFNLILGILIYDIFFNIDENLVVACILIAMPIIAFLILILTGGVHKELTYLQIYDKYKL 81 
                                   9******************************************************************************** PP

                       DUF5418  82 lckfvreltlsllasalatiatlvlyqiqhPlktiefvllvglvlivglvvikllikkyliiikklkkle 151
                                   +c+f+re+t+s+++s+latiat++lyq+q+P+kti+f+ll++++l++gl+++klli++y+i++kklk+l+
  gi|15668734|ref|NP_247533.1|  82 MCEFIREITISTITSELATIATMILYQLQNPIKTITFLLLLIAFLAFGLIFTKLLIDAYFITLKKLKSLK 151
                                   *******************************************************************996 PP

>> HCV_NS2  Hepatitis C virus non-structural protein NS2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.6   5.5e-05       0.2       8     104 ..      49     143 ..      40     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.5e-05
                       HCV_NS2   8 lgaavlvllllltltpaykgllakllwylqyliaraearlrvlvpplgarggrdavilltlllaPelvfevtkiLlailgp 88 
                                   l+a+ ++++l+l+lt   ++ l+ l +y +y +  +e  +++++++++ + ++ a ++l  l  P   ++   +L+a l++
  gi|15668734|ref|NP_247533.1|  49 LIAMPIIAFLILILTGGVHKELTYLQIYDKYKL-MCEFIREITISTITSELATIATMILYQLQNPIKTITFLLLLIAFLAF 128
                                   445556777788888888888889999999966.578888999999999999999999999999****999999******9 PP

                       HCV_NS2  89 lylLeasLlrvpylvR 104
                                     ++ ++L+  +y++ 
  gi|15668734|ref|NP_247533.1| 129 GLIFTKLLID-AYFIT 143
                                   9999998875.46655 PP

>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   6.7   5.7e-05       0.2      56     140 ..       4     105 ..       2     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5.7e-05
                     Mem_trans  56 pyemllrfiladvlvklivlillllgallskifkgslewtitlfslstlpNtlvlgipllkalyge............... 121
                                    ++  ++f++ +++v++ +++ l+lg l++ if    e+  ++ +l+++p +++l ++l+ ++ +e               
  gi|15668734|ref|NP_247533.1|   4 EHKAHASFMFKIINVFVSFGFNLILGILIYDIFFNIDENLVVACILIAMPIIAFLILILTGGVHKEltylqiydkyklmce 84 
                                   5677789999********************************************************999999988888888 PP

                     Mem_trans 122 ..ygvslmvqvvvlqciiiyt 140
                                     +++++ ++ + l  i  ++
  gi|15668734|ref|NP_247533.1|  85 fiREITISTITSELATIATMI 105
                                   884444444444444433332 PP

>> L_HMGIC_fpl  Lipoma HMGIC fusion partner-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.9     9e-05      0.32      62     122 ..       5      62 ..       1      69 [. 0.81
   2 ?    1.2   0.8       0.1   3.6e+02      60     127 ..      96     128 ..      67     145 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9e-05
                   L_HMGIC_fpl  62 flaipssawkaaavlvalgilllllvlllslltlcrqsilkksvfkicallqlvaglllll 122
                                    +a +s ++k+  v+v  g+ l+l +l+  +++ + ++++   v  i+ ++ ++a+l+l+l
  gi|15668734|ref|NP_247533.1|   5 HKAHASFMFKIINVFVSFGFNLILGILIYDIFFNIDENLV---VACILIAMPIIAFLILIL 62 
                                   567899****************************996665...445566677777777776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.1
                   L_HMGIC_fpl  60 ldflaipssawkaaavlvalgilllllvlllslltlcrqsilkksvfkicallqlvaglllllgllly 127
                                   +++++                                   i +  ++++   ++++++llll+++l +
  gi|15668734|ref|NP_247533.1|  96 SELAT-----------------------------------IATMILYQLQNPIKTITFLLLLIAFLAF 128
                                   33333...................................3333344444444444444444444433 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3      0.19     7e+02      11      19 ..      51      59 ..      18      83 .. 0.57
   2 ?    9.4   1.0   0.00021      0.77      12      49 ..      96     133 ..      86     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.19
                       DUF4131 11 allllllll 19
                                  a+ ++++l+
  gi|15668734|ref|NP_247533.1| 51 AMPIIAFLI 59
                                  111111111 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00021
                       DUF4131  12 lllllllllllllrrrprrrvllllllllllallgfal 49 
                                   + l+++++ +l+++++p +++ +llll+++la++ ++ 
  gi|15668734|ref|NP_247533.1|  96 SELATIATMILYQLQNPIKTITFLLLLIAFLAFGLIFT 133
                                   557888888888888******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1126  (0.0628033); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1041.58
//
Query:       gi|15668735|ref|NP_247534.1|  [L=350]
Description: endoglucanase CelM [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.8e-112  375.2   3.9     2e-112  374.9   3.9    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
    1.8e-09   37.6   0.1    3.3e-09   36.7   0.1    1.5  1  Peptidase_M20  Peptidase family M20/M25/M40
    6.2e-07   29.3   0.0    0.00014   21.7   0.0    2.5  2  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  374.9   3.9  3.4e-116    2e-112       1     292 []      44     338 ..      44     338 .. 0.99

  Alignments for each domain:
  == domain 1  score: 374.9 bits;  conditional E-value: 3.4e-116
                                   S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGCHHHH CS
                 Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHllkeee 81 
                                   Gnliak+ +  k++k+miaAHmDeiG+mVk I+++Gfl+f+k+GG+++ ++ +q+v ++++kg++ Gv+gskppH +keee
  gi|15668735|ref|NP_247534.1|  44 GNLIAKRGN--KGKKIMIAAHMDEIGLMVKYIDDNGFLKFTKIGGIYDPTILNQKVVVHGSKGDLIGVLGSKPPHRMKEEE 122
                                   899997776..9********************************************************************* PP

                                   HHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS-SSEEEEEE CS
                 Peptidase_M42  82 rkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeeeleatvylva 162
                                   ++k ++++++fiDiga+s+eea e+G+++G++v+f +e+  l+++++++ka+Ddr+g+avlle++k+l+ee+++++vy+v+
  gi|15668735|ref|NP_247534.1| 123 KTKIIKYEDMFIDIGAESREEAIEMGVNIGTWVSFLSEVYDLGKNRLTGKAFDDRVGCAVLLEVMKRLSEEDIDCQVYAVG 203
                                   ********************************************************************************* PP

                                   ESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETT...CCSHHHHHHHHHHHHHHTT- CS
                 Peptidase_M42 163 tvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDas...giyhpklrkkllelAkknni 238
                                   tvqEEvGl+Ga++sa+ki+pd+aia+Dvt+agd+pg k+++a   lgkGpv+ ++Das   +i+hpk+ ++++++ +k++i
  gi|15668735|ref|NP_247534.1| 204 TVQEEVGLKGARVSAFKINPDVAIALDVTIAGDHPGIKKEDAPvdLGKGPVVGIVDASgrgLIAHPKVLDMIKAVSEKYKI 284
                                   *****************************************999*************99989******************* PP

                                   -EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                 Peptidase_M42 239 pyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                   ++q+ev +gg+tDA+aihlt+eg+pt++is+p+ryiH+pvev++++dle+tv+L
  gi|15668735|ref|NP_247534.1| 285 DVQWEVGEGGTTDATAIHLTREGIPTGVISVPARYIHTPVEVIDKRDLEKTVEL 338
                                   ***************************************************997 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   5.6e-13   3.3e-09      29     206 ..     168     344 ..     156     345 .. 0.74

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 5.6e-13
                                   EEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEE....EESSSBT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx RF
                 Peptidase_M20  29 klyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelh....ieepgil 105
                                   +l G  a d+  g++ +le++++l +e i  +  +  + ++ EE+g +Ga+  +     + ++d +++l        pgi+
  gi|15668735|ref|NP_247534.1| 168 RLTGK-AFDDRVGCAVLLEVMKRLSEEDI--DCQVYAVGTVQEEVGLKGARVSAF----KINPDVAIALDvtiaGDHPGIK 241
                                   56666.89*******************99..56***********88899988888....4555554433311112233333 PP

                                   CHSTETEEEE......EEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEE.EESSSBHTHHHH....TTTEEEEEE CS
                                   xxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx....xxxxxxxxx RF
                 Peptidase_M20 106 eagklaigvv......kvevelleggapvtlndsplvkalaeaaeelfgekveli.vsgpggtdarff....agiptvmif 175
                                   + +      v       v +    ++    + ++++ + ++++ e++ + +v+ +   g g+tda  +    +gipt +i 
  gi|15668735|ref|NP_247534.1| 242 K-EDAP---VdlgkgpVVGIV--DASGRGLIAHPKVLDMIKAVSEKY-KIDVQWEvGEG-GTTDATAIhltrEGIPTGVIS 314
                                   3.3333...244454324444..333444444589999998888884.77777775666.*********999999***999 PP

                                   ESSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 176 gpgsglaHspnEyvdledlekgikvlarlle 206
                                   +p    +H+p E +d +dlek ++++++ ++
  gi|15668735|ref|NP_247534.1| 315 VPA-RYIHTPVEVIDKRDLEKTVELVYNCIK 344
                                   999.9*********************99887 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0    0.0029        17       1      39 [.      45      77 ..      45      79 .. 0.72
   2 !   21.7   0.0   2.3e-08   0.00014      35     188 ..     173     336 ..     163     346 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0029
                                  EEEEEESTTCESEEEEEEEE--B-TTTTCCT---TTTTH CS
                 Peptidase_M28  1 NviatlegkatdevlllgAHyDsvgvgrgpifvGAdDnA 39
                                  N+ia+  g++  + ++++AH+D +g   +     +dDn+
  gi|15668735|ref|NP_247534.1| 45 NLIAKR-GNK-GKKIMIAAHMDEIGLMVK----YIDDNG 77
                                  788887.444.589********9998433....366665 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.3e-08
                                   TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHHHHCCCTTEEEEEEECS-SSSS--EEE...... CS
                 Peptidase_M28  35 AdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafakakpelkkiaavlnlDmvgsggkellf...... 109
                                   A D+ +g+a+lLe+++ l +  ++ + +v  + +  EE gl G++  a     + + ++ + lD + +g+   +       
  gi|15668735|ref|NP_247534.1| 173 AFDDRVGCAVLLEVMKRLSE--EDIDCQVYAVGTVQEEVGLKGARVSA----FKINPDVAIALDVTIAGDHPGIKkedapv 247
                                   78999**************8..579********************999....45555666666666665555555566666 PP

                                   ..............HHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHH..TTT--EEEECTSSS-TTT.T CS
                 Peptidase_M28 110 ..............esgdkssselekelkalakpvgraaaedpfdersgrgrsDhspfl..kagvpvldlaetgfpevy.H 173
                                                  +g   ++++     + +k+v+++++ d++ e +  g++D+++++  ++g+p+  +     p +y H
  gi|15668735|ref|NP_247534.1| 248 dlgkgpvvgivdasGRGLIAHPKVL----DMIKAVSEKYKIDVQWEVGEGGTTDATAIHltREGIPTGVI---SVPARYiH 321
                                   9999998866544333333444444....44555555444477667777888999887776999**9999...67777779 PP

                                   STTSSGGGB-HHHHH CS
                 Peptidase_M28 174 tprDtldnidkdtla 188
                                   tp   +d+ d +++ 
  gi|15668735|ref|NP_247534.1| 322 TPVEVIDKRDLEKTV 336
                                   999888887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2089.51
//
Query:       gi|15668736|ref|NP_247535.1|  [L=185]
Description: hypothetical protein MJ_0556 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-21   74.7   3.6    2.6e-11   43.8   1.2    2.5  3  CBS       CBS domain
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.42   10.6   0.0    1.8  2  LAMTOR5   Ragulator complex protein LAMTOR5
       0.13   12.7   1.1        7.8    6.9   0.2    2.5  2  CM_2      Chorismate mutase type II


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         3   1.8e+04       2       9 ..       9      16 ..       9      19 .. 0.66
   2 !   43.8   1.2   4.4e-15   2.6e-11       1      55 [.      35      90 ..      35      92 .. 0.95
   3 !   30.9   0.0   4.6e-11   2.8e-07       1      56 [.      98     161 ..      98     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3
                                  HHHSBSSC CS
                           CBS  2 gdimtrdv 9 
                                  gdim++ v
  gi|15668736|ref|NP_247535.1|  9 GDIMSKFV 16
                                  57887754 PP

  == domain 2  score: 43.8 bits;  conditional E-value: 4.4e-15
                                  HHHHSBS.SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS  1 Vgdimtr.dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                  V+d+m + dv+  +p+ t++e++++m+++++s++PVVd+ g  +G +tlr + +++
  gi|15668736|ref|NP_247535.1| 35 VKDVMISgDVIITTPEKTIKEIFDEMIKHNISGMPVVDDRGVMIGFITLREIRKYM 90
                                  89998888*********************************999********9986 PP

  == domain 3  score: 30.9 bits;  conditional E-value: 4.6e-11
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHT..SSEEEEE......ETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 Vgdimtrdvvtvppdttleealelmrekg..vsrlPVV......dedgklvGivtlrDllrall 56 
                                   Vg++m +++++ + d+++  a+e+m+e++  +++lPV+         gkl Gi+ ++D++++l 
  gi|15668736|ref|NP_247535.1|  98 VGEVMLKNPPYTTADEDIITAFEKMIESNkkLDQLPVIntkypeKILGKLEGIIFMEDIIKLLY 161
                                   89***********************976667*******76654433347***********9985 PP

>> LAMTOR5  Ragulator complex protein LAMTOR5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     7e-05      0.42       2      32 ..      50      79 ..      49      81 .. 0.88
   2 ?   -2.0   0.0       0.6   3.6e+03      45      65 ..     119     135 ..     110     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7e-05
                       LAMTOR5  2 ekqleevldevmskegvvGvlcaDeqGLclg 32
                                  ek+++e++de+  k++++G+ ++D+ G+ +g
  gi|15668736|ref|NP_247535.1| 50 EKTIKEIFDEM-IKHNISGMPVVDDRGVMIG 79
                                  7999******6.6777***********9876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.6
                       LAMTOR5  45 itallklAskLesesseaPvi 65 
                                   + ++++  +kL+    + Pvi
  gi|15668736|ref|NP_247535.1| 119 FEKMIESNKKLD----QLPVI 135
                                   556777778887....66776 PP

>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1    0.0085        51      54      70 ..      48      64 ..      17      66 .. 0.73
   2 ?    6.9   0.2    0.0013       7.8      26      71 ..     124     169 ..     112     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0085
                                  S-HHHHHHHHHHHHHHH CS
                          CM_2 54 ldeeaierifreiisas 70
                                   +e++i++if e+i++ 
  gi|15668736|ref|NP_247535.1| 48 TPEKTIKEIFDEMIKHN 64
                                  6899**********976 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0013
                                   HHHHHHCTSGSS-HHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHH CS
                          CM_2  26 geyKkeeglpvydpeReaevlerleegaldeeaierifreiisasr 71 
                                      Kk  +lpv +++  +++l +le   + e+ i+ ++++ii++ +
  gi|15668736|ref|NP_247535.1| 124 ESNKKLDQLPVINTKYPEKILGKLEGIIFMEDIIKLLYENIIKELK 169
                                   556877888*****************889*************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1164.32
//
Query:       gi|15668737|ref|NP_247536.1|  [L=205]
Description: ribosome biogenesis protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-46  157.8   0.9      3e-46  157.5   0.9    1.1  1  EMG1      EMG1/NEP1 methyltransferase


Domain annotation for each model (and alignments):
>> EMG1  EMG1/NEP1 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.5   0.9   1.7e-50     3e-46       1     192 [.       5     202 ..       5     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 157.5 bits;  conditional E-value: 1.7e-50
                                   EEEEEES--B--GG.........SCGGSB--HHHHCGG.TTSTTGGGSS-CHHHHHHHHHHHCSCHHCTT.EEEEEEETTS CS
                          EMG1   1 ivLeeasLelvkvk.........kkseqLLnsddhkkilkklkreakeaRpDIvHqcLlalldspLnkagllqvyihttkn 72 
                                   i+L++++Lel++++          +++ +L+s++h+k+++klk+++ ++RpDI+H +Ll++ldsp+n++++l++yiht+++
  gi|15668737|ref|NP_247536.1|   5 IILAKSALELIPEEiknkirksrVYKYDILDSNYHYKAMEKLKDKEMRGRPDIIHISLLNILDSPINHEKKLNIYIHTYDD 85 
                                   89***********999*****9999******************************************************** PP

                                   EEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEECS-HHHHCCC..SEEEEE-TTSEE-............ CS
                          EMG1  73 vlIevnpqtRiPrtfkrFagLmvqLLkklsirategeekLlkviknpitdhlpp.gskiillsesaekklvdleefvvkpv 152
                                   +++++np+tR+Pr++ rF g+m+++Lk         +++L+k+ +++++d+l++ ++k+i++ ++   k  +  +++++  
  gi|15668737|ref|NP_247536.1|  86 KVLKINPETRLPRNYFRFLGVMEKVLKGE-------RNHLIKMEEKTLEDLLNEiNAKKIAIMTKTG-K-LTHPKLLKEYD 157
                                   *************************9854.......358***************9777777666655.2.35688889999 PP

                                   .EEEE-SSSS....---HH.....EEESSSS---HHHHHHHHHHH CS
                          EMG1 153 vfvigamskgsvkidykee.....eisisnypLsaavvcskilta 192
                                   +f+ig+++ g+ ki+ ++      eisi+n+ L a++vc  i+ +
  gi|15668737|ref|NP_247536.1| 158 TFIIGGFPYGKLKINKEKVfgdikEISIYNKGLMAWTVCGIICYS 202
                                   9*********77765544255666******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1285.81
//
Query:       gi|15668738|ref|NP_247537.1|  [L=261]
Description: hypothetical protein MJ_0558 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-15   55.2   0.1    7.4e-15   54.2   0.1    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    8.3e-09   35.2   0.0    1.5e-08   34.4   0.0    1.3  1  MarR_2          MarR family
    1.8e-07   31.0   0.0    3.6e-07   30.0   0.0    1.5  1  MarR            MarR family
    8.2e-06   25.7   0.1    1.7e-05   24.7   0.1    1.5  1  HTH_11          HTH domain
    9.6e-06   25.5   0.0      2e-05   24.5   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    1.7e-05   24.6   0.2    3.9e-05   23.4   0.1    1.7  1  HTH_5           Bacterial regulatory protein, arsR family
    1.9e-05   24.6   0.1    4.7e-05   23.3   0.1    1.7  1  HTH_45          Winged helix-turn-helix
    2.9e-05   24.5   0.1    6.8e-05   23.3   0.0    1.7  1  HTH_27          Winged helix DNA-binding domain
    0.00013   21.7   0.0    0.00029   20.6   0.0    1.5  1  DUF4423         Domain of unknown function (DUF4423)
    0.00027   21.1   0.0    0.00071   19.7   0.0    1.7  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00035   20.9   0.2     0.0015   18.9   0.1    2.0  2  Rrf2            Transcriptional regulator
    0.00042   20.3   0.0    0.00075   19.5   0.0    1.3  1  HTH_20          Helix-turn-helix domain
      0.001   18.9   0.4     0.0026   17.6   0.1    1.8  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0021   18.5   0.1     0.0064   16.9   0.0    1.8  1  HTH_40          Helix-turn-helix domain
     0.0025   17.6   0.0     0.0054   16.5   0.0    1.5  1  HTH_10          HTH DNA binding domain
     0.0036   17.1   0.0     0.0058   16.4   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
     0.0039   17.2   0.0     0.0095   16.0   0.0    1.6  1  HTH_3           Helix-turn-helix
     0.0052   16.9   0.2      0.027   14.6   0.1    2.0  2  Mrr_N           Mrr N-terminal domain
     0.0065   16.6   0.0      0.025   14.7   0.0    2.0  1  HTH_34          Winged helix DNA-binding domain
      0.008   16.2   0.1      0.072   13.1   0.0    2.1  2  HTH_Mga         M protein trans-acting positive regulator (MG
     0.0085   15.7   0.1      0.015   14.9   0.1    1.4  1  GntR            Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.037   14.0   0.0    1.6  1  HTH_36          Helix-turn-helix domain
      0.019   14.9   0.2      0.043   13.8   0.2    1.6  1  HTH_12          Ribonuclease R winged-helix domain
      0.024   14.2   0.1      0.055   13.0   0.1    1.6  1  GerE            Bacterial regulatory proteins, luxR family
      0.027   13.5   0.1      0.044   12.8   0.1    1.3  1  Topoisom_bac    DNA topoisomerase
      0.028   14.7   0.1       0.13   12.6   0.0    2.3  1  Mnd1            Mnd1 HTH domain
      0.047   13.3   0.1       0.11   12.1   0.1    1.6  1  SMC_ScpB        Segregation and condensation complex subunit 
      0.051   13.4   0.0       0.15   11.8   0.0    1.8  1  LexA_DNA_bind   LexA DNA binding domain
      0.054   13.2   0.1        0.1   12.3   0.1    1.5  1  Sigma70_r4_2    Sigma-70, region 4
      0.056   13.6   0.0       0.13   12.4   0.0    1.7  1  HTH_28          Helix-turn-helix domain
      0.061   12.7   0.1       0.14   11.6   0.1    1.6  1  RepL            Firmicute plasmid replication protein (RepL)
      0.081   13.2   0.1       0.19   12.0   0.1    1.7  1  KORA            TrfB plasmid transcriptional repressor
      0.095   12.4   0.0       0.16   11.6   0.0    1.4  1  PLDc_3          PLD-like domain
       0.11   12.3   0.0       0.26   11.2   0.0    1.6  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
       0.12   12.2   0.0       0.31   10.9   0.0    1.7  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
       0.15   11.6   0.7       0.28   10.7   0.1    1.8  1  Sigma70_r4      Sigma-70, region 4
       0.16   11.8   0.0       0.48   10.3   0.0    1.8  1  HTH_23          Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.1   1.5e-17   7.4e-15       1      48 []       4      52 ..       4      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.5e-17
                        HTH_24  1 ldetdrkIL.elLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +++t++++L e+++k+p+i q+e+Ae lg+++++v++++++L++eG++k
  gi|15668738|ref|NP_247537.1|  4 RNITEFQVLsEIIRKQPHIKQKEIAENLGITVQAVSEHIRNLVKEGYVK 52
                                  689******888888********************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0     3e-11   1.5e-08       5      54 ..       6      54 ..       4      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3e-11
                                  HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   ++++vL ++ r  +  + ++e+a+ lg++ +avs +++ Lv+ G+v  r
  gi|15668738|ref|NP_247537.1|  6 ITEFQVLSEIIRKQPH-IKQKEIAENLGITVQAVSEHIRNLVKEGYVKSR 54
                                  69*******9999986.8*****************************866 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   7.4e-10   3.6e-07       2      49 ..       5      53 ..       5      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 7.4e-10
                                  -HHHHHHHH.HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR  2 tltqfviLr.ilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                  + t+f +L  i++ q+ ++++e+a+ lg++  +v++ ++ L+k+G++++
  gi|15668738|ref|NP_247537.1|  5 NITEFQVLSeIIRKQPHIKQKEIAENLGITVQAVSEHIRNLVKEGYVKS 53
                                  57999999724566666*****************************986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   3.5e-08   1.7e-05       2      45 ..       8      50 ..       7      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.5e-08
                        HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                  ++q+l  +++++++i  +e+Ae L+++ ++v  +I+ L + g  
  gi|15668738|ref|NP_247537.1|  8 EFQVLSEIIRKQPHIKQKEIAENLGITVQAVSEHIRNLVKEG-Y 50
                                  5799999*******************************9999.4 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   4.1e-08     2e-05      21      65 ..      21      66 ..       7      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.1e-08
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEEEEES-HHHH CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rgrririldleaL 65
                                  ++ q+e+A+ lG+t + vs  ++ L +eg+++ rgr+  +   ++L
  gi|15668738|ref|NP_247537.1| 21 HIKQKEIAENLGITVQAVSEHIRNLVKEGYVKsRGRGEYVVTEKGL 66
                                  789*****************************77765444455555 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1     8e-08   3.9e-05      19      47 .]      25      53 ..      11      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8e-08
                                  HHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5 19 celaeelglsqstvShHLkkLreaGLVek 47
                                   e+ae lg++  +vS+H + L ++G+V++
  gi|15668738|ref|NP_247537.1| 25 KEIAENLGITVQAVSEHIRNLVKEGYVKS 53
                                  69*************************86 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   9.7e-08   4.7e-05       4      68 ..       8      71 ..       3      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.7e-08
                        HTH_45  4 kleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikk.skekYvlTekGlellek 68
                                  +++++++I +  ++ + k+ +i  +  ++ + +++ +  Lv++g++k    ++Yv+TekGl+ l++
  gi|15668738|ref|NP_247537.1|  8 EFQVLSEIIR--KQPHIKQKEIAENLGITVQAVSEHIRNLVKEGYVKSrGRGEYVVTEKGLRKLKN 71
                                  6778888888..678889999*************************76589*********988775 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.4e-07   6.8e-05      11      68 .]      14      65 ..       7      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.4e-07
                        HTH_27 11 lirhrrrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                   i  r  + ++ +++++ l ++ +++s+ ++ L++ G+v      ++r++  + +T+kG
  gi|15668738|ref|NP_247537.1| 14 EII-RKQPHIKqKEIAENLGITVQAVSEHIRNLVKEGYV------KSRGRGEYVVTEKG 65
                                  555.455566669**************************......99***********9 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   6.1e-07   0.00029      25      90 ..      11      73 ..       7      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.1e-07
                       DUF4423 25 virellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevk 90
                                  v+ e+++ ++   + +e+a+ l+  i+++ v++ ++ L+k g +k  + g+y++tek l   +++ 
  gi|15668738|ref|NP_247537.1| 11 VLSEIIRKQPH-IKQKEIAENLG--ITVQAVSEHIRNLVKEGYVKSRGRGEYVVTEKGLRKLKNWI 73
                                  56666666666.7889*******..********************************998666555 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.5e-06   0.00071      22      55 ..      21      54 ..      12      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-06
                                  SB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                Fe_dep_repress 22 vvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                   +k+k++ae L++    Vse ++ L k+Gyv+  
  gi|15668738|ref|NP_247537.1| 21 HIKQKEIAENLGITVQAVSEHIRNLVKEGYVKSR 54
                                  689****************************976 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1     3e-06    0.0015      20      61 ..      18      56 ..       4      65 .. 0.82
   2 ?   -1.3   0.0       6.1     3e+03      39      53 ..     234     248 ..     231     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3e-06
                                  SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                          Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                  ++   +++ +eiae+ +i  + ++  +++L k+g+vks+ G+
  gi|15668738|ref|NP_247537.1| 18 KQP--HIKQKEIAENLGITVQAVSEHIRNLVKEGYVKSR-GR 56
                                  333..4899****************************95.44 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.1
                                   HHHHHHHHHHHHHTT CS
                          Rrf2  39 psylekilakLrkag 53 
                                    +++ek+++kL +a+
  gi|15668738|ref|NP_247537.1| 234 GKMAEKVIKKLDNAK 248
                                   57899******9987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.6e-06   0.00075      29      60 ..      26      57 ..      25      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-06
                                  HHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20 29 elaerldlskntlsyHLrvLeeagLvevvreg 60
                                  e+ae l+++ + +s H+r L++ g+v++++ g
  gi|15668738|ref|NP_247537.1| 26 EIAENLGITVQAVSEHIRNLVKEGYVKSRGRG 57
                                  9***************************9987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   5.3e-06    0.0026       9      57 ..       7      56 ..       5      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.3e-06
                                  HCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                          TrmB  9 yEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                  +E++v   ++ k+   + +eiae+lg+  + v e +r+L++ G+V+ + +
  gi|15668738|ref|NP_247537.1|  7 TEFQVLSEIIrKQPHIKQKEIAENLGITVQAVSEHIRNLVKEGYVKSRGR 56
                                  588899999978888999***************************98754 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.3e-05    0.0064      16      76 ..      25      87 ..      19      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.3e-05
                        HTH_40 16 eeIAkerglkesTIegHLaelieegeeidl....erlvseeeekeIeeaiekvgseklkpikeal 76
                                  +eIA++ g++++ + +H+ +l++eg+ ++     e +v+e+  +++++ i +++ + l +i  a+
  gi|15668738|ref|NP_247537.1| 25 KEIAENLGITVQAVSEHIRNLVKEGY-VKSrgrgEYVVTEKGLRKLKNWISEFK-DYLDEINTAV 87
                                  89***********************9.888777566679999999999999987.5577776665 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.1e-05    0.0054      24      47 ..      22      45 ..      20      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                        HTH_10 24 vtlkeLAkelGIskstlsehLrka 47
                                  ++ ke+A+ lGI+ +++seh+r+ 
  gi|15668738|ref|NP_247537.1| 22 IKQKEIAENLGITVQAVSEHIRNL 45
                                  6779******************85 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-05    0.0058       7      50 ..      10      53 ..       9      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                                  HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  ++L  + + ++  + +e+A+++g++  +v+ +++ Lv++Gyv+ 
  gi|15668738|ref|NP_247537.1| 10 QVLSEIIRKQPHIKQKEIAENLGITVQAVSEHIRNLVKEGYVKS 53
                                  67777777778899****************************97 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     2e-05    0.0095       4      28 ..      16      40 ..      14      45 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-05
                                  HHHHTTHHHHHHHHHHTSSHHHHHH CS
                         HTH_3  4 lRkqlglsqeeLAeklGvsrstisr 28
                                  +Rkq  + q+e+Ae lG++++++s 
  gi|15668738|ref|NP_247537.1| 16 IRKQPHIKQKEIAENLGITVQAVSE 40
                                  7**********************95 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.4   1.2e+03      24      42 ..      24      42 ..       8      44 .. 0.73
   2 !   14.6   0.1   5.6e-05     0.027      60      86 ..      44      70 ..      41      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.4
                         Mrr_N 24 rervaerfglseeeraell 42
                                  ++++ae++g++ ++++e +
  gi|15668738|ref|NP_247537.1| 24 QKEIAENLGITVQAVSEHI 42
                                  5789999999999988865 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.6e-05
                         Mrr_N 60 yLkkagllespkrgvwkiTekGrevlk 86
                                  +L+k+g+++s  rg + +TekG + lk
  gi|15668738|ref|NP_247537.1| 44 NLVKEGYVKSRGRGEYVVTEKGLRKLK 70
                                  79********************99986 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   5.3e-05     0.025       3      77 ..       9      77 ..       7      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.3e-05
                        HTH_34  3 lavlsyLas.vdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLk 77
                                  ++vls  +  +  ++ +e+ e l++t  + s h++ L k gY++ +    g   r  + +T++G+ + k+ +++ k
  gi|15668738|ref|NP_247537.1|  9 FQVLSEIIRkQPHIKQKEIAENLGITVQAVSEHIRNLVKEGYVKSR----G---RGEYVVTEKGLRKLKNWISEFK 77
                                  6677766665788999**************************9854....2...2456677777777776666665 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00015     0.072      11      45 ..      12      46 ..       3      52 .. 0.82
   2 ?    0.2   0.0       1.7     8e+02      35      52 ..      67      84 ..      66      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                       HTH_Mga 11 lelLteneksltldelakeLglseltlqsdiseLn 45
                                  l+ ++  +++++ +e+a++Lg++  ++ + i++L 
  gi|15668738|ref|NP_247537.1| 12 LSEIIRKQPHIKQKEIAENLGITVQAVSEHIRNLV 46
                                  5445555*************************996 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.7
                       HTH_Mga 35 ltlqsdiseLnelFpeel 52
                                  ++l++ ise+++ ++e +
  gi|15668738|ref|NP_247537.1| 67 RKLKNWISEFKDYLDEIN 84
                                  678999999998888765 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   3.1e-05     0.015      24      60 ..      22      57 ..       8      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                                  ---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                          GntR 24 LPsereLaaefgVsrttvReALrrLeaeglverrqgr 60
                                  + +++e+a+ +g++ + v e +r+L+ eg+v +r ++
  gi|15668738|ref|NP_247537.1| 22 I-KQKEIAENLGITVQAVSEHIRNLVKEGYVKSRGRG 57
                                  5.789***************************99875 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.7e-05     0.037      27      55 .]      23      51 ..      13      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.7e-05
                        HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                   q+ +a++lg+ ++ vs +i++L++ Gy+
  gi|15668738|ref|NP_247537.1| 23 KQKEIAENLGITVQAVSEHIRNLVKEGYV 51
                                  5899***********************96 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   8.8e-05     0.043      14      66 .]      22      69 ..      10      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.8e-05
                        HTH_12 14 igakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGleeL 66
                                  i  keiae+L   g  i  +av  ++r l ++g+++  g++   +tEkGl  L
  gi|15668738|ref|NP_247537.1| 22 IKQKEIAENL---G--ITVQAVSEHIRNLVKEGYVKSRGRGEYVVTEKGLRKL 69
                                  6777777777...3..55599****************************9876 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00011     0.055      20      43 ..      24      47 ..       7      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                                  HHHHHHHHTS-HHHHHHHHHHHHH CS
                          GerE 20 nkeIAeelniSekTVkvhksnimk 43
                                   keIAe+l+i  + V+ h++n+ k
  gi|15668738|ref|NP_247537.1| 24 QKEIAENLGITVQAVSEHIRNLVK 47
                                  69*******************976 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     9e-05     0.044     346     392 ..      38      86 ..      15      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-05
                  Topoisom_bac 346 raeiieklvergYverkk.kslvptelGk.alvellekfkdlvspelTa 392
                                    +e+i++lv++gYv++++ +++v+te+G  +l + +++fkd+ ++  Ta
  gi|15668738|ref|NP_247537.1|  38 VSEHIRNLVKEGYVKSRGrGEYVVTEKGLrKLKNWISEFKDYLDEINTA 86 
                                   579**************889********625666669999998887776 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00027      0.13      19      47 ..      25      53 ..      12      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00027
                          Mnd1 19 klapkekgivsqsVkdvlqsLvdDglvev 47
                                  k+++ + gi+ q V +++ +Lv++g v++
  gi|15668738|ref|NP_247537.1| 25 KEIAENLGITVQAVSEHIRNLVKEGYVKS 53
                                  7778889*******************986 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00022      0.11      86     131 ..       9      58 ..       3      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                      SMC_ScpB  86 letLaiIaykqp.vtraeieeiRGvn...sdsvvrtLlerglieekgrke 131
                                    ++L+ I  kqp + ++ei+e  G +   +++++r+L+++g ++++gr e
  gi|15668738|ref|NP_247537.1|   9 FQVLSEIIRKQPhIKQKEIAENLGITvqaVSEHIRNLVKEGYVKSRGRGE 58 
                                   68999999999868899****999653358899*************9754 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00032      0.15      29      57 ..      25      52 ..       5      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
                                  HHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                 LexA_DNA_bind 29 reiaralglkSpsaveehLkaLerKGyie 57
                                  +eia++lg++  +av eh + L + Gy++
  gi|15668738|ref|NP_247537.1| 25 KEIAENLGIT-VQAVSEHIRNLVKEGYVK 52
                                  79********.9***************97 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00021       0.1      28      48 ..      23      43 ..      21      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                                  -HHHHHHHHT--HHHHHHHHH CS
                  Sigma70_r4_2 28 sykEIAellgisegtVksrls 48
                                  ++kEIAe lgi++++V  +++
  gi|15668738|ref|NP_247537.1| 23 KQKEIAENLGITVQAVSEHIR 43
                                  58**************98886 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00026      0.13      13      51 ..      21      57 ..       9      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00026
                        HTH_28 13 h.svreaArelgisrrtvyrWikryeegGiagLvprrrrp 51
                                  h  ++e+A+ lgi+ + v+  i+ + ++G    v+ r+r+
  gi|15668738|ref|NP_247537.1| 21 HiKQKEIAENLGITVQAVSEHIRNLVKEGY---VKSRGRG 57
                                  56899*******************999664...7777775 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00029      0.14      77     117 ..      23      63 ..       2      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                          RepL  77 tnRelaeetgislktvsetlkileeanilkkkanGvlvinP 117
                                    ++e+ae+ gi ++ vse ++ l + +++k +  G +v+  
  gi|15668738|ref|NP_247537.1|  23 KQKEIAENLGITVQAVSEHIRNLVKEGYVKSRGRGEYVVTE 63 
                                   479**********************************9965 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1    0.0004      0.19      32      58 ..      22      48 ..      10      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0004
                          KORA 32 kkqadvatelgltkqavsqavkrvwaa 58
                                   kq+++a++lg+t qavs+ +++  + 
  gi|15668738|ref|NP_247537.1| 22 IKQKEIAENLGITVQAVSEHIRNLVKE 48
                                  69****************988876654 PP

>> PLDc_3  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00032      0.16      60     139 ..     153     233 ..     124     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                        PLDc_3  60 sksqvfvsdsPklflgkyrsldvdlvlsviedaklsvdlalldylPviktatkveywPdlidkllealvl...rsvkvrll 137
                                    k++v v   P   +g  r++d +l+ + i++   +v  ++  +  v   a k    Pd+  ++ ea+v+   r+  v  l
  gi|15668738|ref|NP_247537.1| 153 PKGKVIVFRIPPEVVGGSRAVDFNLIKENIDNLDDYVIATMGTVAYV--VACKLGLKPDIRFAVPEAIVNacnRGCNVIAL 231
                                   5788999999999***********************96665555444..478999999*9999999988533377777777 PP

                        PLDc_3 138 is 139
                                   i+
  gi|15668738|ref|NP_247537.1| 232 IT 233
                                   76 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00053      0.26      11      41 ..      15      45 ..      12      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00053
                 HTH_AsnC-type 11 aLqedaRisyaeLAervGlSestvlrRvrrL 41
                                  ++++++ i  +e+Ae +G++ ++v + +r L
  gi|15668738|ref|NP_247537.1| 15 IIRKQPHIKQKEIAENLGITVQAVSEHIRNL 45
                                  677889999***************9988876 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00065      0.31      10      29 ..      23      42 ..      16      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00065
                YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWl 29
                                   qk+ Ae+lg++ qaVs  +
  gi|15668738|ref|NP_247537.1| 23 KQKEIAENLGITVQAVSEHI 42
                                  59***************876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00058      0.28      23      43 ..      24      44 ..      20      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00058
                                  HHHHHHHHTS-HHHHHHHHHH CS
                    Sigma70_r4 23 leEIgerlgiSrerVrqiekr 43
                                  ++EI+e lgi+  +V+ ++++
  gi|15668738|ref|NP_247537.1| 24 QKEIAENLGITVQAVSEHIRN 44
                                  89*************998876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0     0.001      0.48      18      45 ..      22      49 ..      10      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.001
                        HTH_23 18 lsvreIAreLgvsrrTvyrwlkryreeG 45
                                  + ++eIA+ Lg++ + v+  ++  ++eG
  gi|15668738|ref|NP_247537.1| 22 IKQKEIAENLGITVQAVSEHIRNLVKEG 49
                                  5789*************95555555666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1082  (0.0603492); expected 358.6 (0.02)
Passed bias filter:                      847  (0.0472419); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 1604.08
//
Query:       gi|15668739|ref|NP_247538.1|  [L=276]
Description: stationary phase survival protein SurE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-53  179.5   0.0    7.1e-53  179.3   0.0    1.1  1  SurE      Survival protein SurE


Domain annotation for each model (and alignments):
>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.3   0.0     4e-57   7.1e-53       1     194 [.      13     208 ..      13     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 179.3 bits;  conditional E-value: 4e-57
                                   EEEE-SS-TT-HHHHHHHHHHT..TTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHHHH CS
                          SurE   1 iLltNDDGieapgiralveala..aaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvklale 79 
                                   iL++NDDGi +p + al++al+    ++++++vaP +++Sgig+a++l eplr+++++  ++   yavsGtP+dcv l++ 
  gi|15668739|ref|NP_247538.1|  13 ILIVNDDGIYSPSLIALYNALKekFSDANITIVAPTNQQSGIGRAISLFEPLRMTKVKLAKDIVGYAVSGTPTDCVILGIY 93 
                                   8*********************8755789**************************88888********************* PP

                                   TTTTTS.SSEEEEEEEES---GGGGGG-HHHHHHHHHHHTTSEEEEEEEESSS.....SS-SSS---HHHHHHHHHHHHTT CS
                          SurE  80 ellkekkpdlVvSGiNhGaNlgtdvlySGTvgAaleaalegipaiAvSlaskk.....eeekkeedtfeaaakvaaklvek 155
                                   ++lk+  pdlV+SGiN G+Nlgt++++SGT+gAa+eaa++g ++iA Sl++++     +e  +   +fe  ak++ak++ek
  gi|15668739|ref|NP_247538.1|  94 QILKK-VPDLVISGINIGENLGTEIMTSGTLGAAFEAAHHGAKSIASSLQITSdhlkfKEL-DIPINFEIPAKITAKIAEK 172
                                   ***86.6*******************************************99966554222.2333477777777777777 PP

                                   ETTS-...SS-EEEEEEESS.GCG-SEEEE-B--CCSCE CS
                          SurE 156 lieklllekvellnvNvPeleeeeikgvkvtrlgrrrys 194
                                   +++       ++ln+N+Pe+ + e   +++trl+r++y+
  gi|15668739|ref|NP_247538.1| 173 YLDYD--MPCDVLNINIPENATLET-PIEITRLARKMYT 208
                                   76665..599********7555553.488******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1884.63
//
Query:       gi|15668740|ref|NP_247539.1|  [L=138]
Description: hypothetical protein MJ_0560 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00065   19.2   0.0    0.00085   18.9   0.0    1.2  1  CheR      CheR methyltransferase, SAM binding domain


Domain annotation for each model (and alignments):
>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.7e-08   0.00085      88     153 ..      40     107 ..      36     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.7e-08
                                   CHHTTS-HHHHHHHEEEEETTCEEE-HHHHTTEEEEE--TTT..-SGGG--EEEEEE-SSGGGC-CHH CS
                          CheR  88 eeleglseelleryfekseddsykvkkeikelvkFeklnlle..kksvlgklDvifcrnvliYfdeet 153
                                     +++++ e+++ yf+++++ ++++ +++ + ++F++ n+    k   + k D+i+     +Yf++++
  gi|15668740|ref|NP_247539.1|  40 AIVKSINWEYIKGYFQEEDELGMEILPNLIDCIDFKNVNVEMekKGYKPIKYDIIVYAGAWSYFNPKK 107
                                   567999**********************************884333345589************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 867.89
//
Query:       gi|15668741|ref|NP_247540.1|  [L=345]
Description: adenylosuccinate synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-90  303.5   5.7    2.8e-44  151.7   0.1    3.0  3  Adenylsucc_synt  Adenylosuccinate synthetase
  ------ inclusion threshold ------
      0.082   11.9   0.0       0.11   11.5   0.0    1.1  1  CytochromB561_N  Cytochrome B561, N terminal


Domain annotation for each model (and alignments):
>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.3     2e-40   1.8e-36       1     151 [.      10     157 ..      10     161 .. 0.93
   2 !  151.7   0.1   3.1e-48   2.8e-44     191     333 ..     155     295 ..     148     298 .. 0.94
   3 !   31.8   0.1   7.9e-12   7.1e-08     373     419 .]     293     339 ..     291     339 .. 0.94

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 2e-40
                                   .EEEE-SSS-S-HHHHHHHHHT..T-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHHH CS
               Adenylsucc_synt   1 vvvvGaqwGDEGKGkivDllae..eadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealleE 79 
                                   +++vG qwGDEGKGki+ ++++  +  +++R   G nAGHtv ++gk+y ++++p G  +++++  iG+gv+vdpe+ll+E
  gi|15668741|ref|NP_247540.1|  10 TIIVGGQWGDEGKGKIISYICDkdKPSIIARGGVGPNAGHTVNIGGKSYGIRMIPTGFPYKEAKLAIGAGVLVDPEVLLKE 90 
                                   68******************7622689****************************************************** PP

                                   HTTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGS CS
               Adenylsucc_synt  80 ieeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlld 151
                                   +e+l++ +v   kerl+++ r+ ++ + hk +D+  e+ +  k+iGtT++G Gpa  d+v r   +++d+ +
  gi|15668741|ref|NP_247540.1|  91 VEMLKDFNV---KERLIVDYRCGIIEEKHKIMDRKDEHLA--KEIGTTGSGCGPANVDRVLRILKQAKDIEE 157
                                   *****9887...57***********************976..59******************9888888755 PP

  == domain 2  score: 151.7 bits;  conditional E-value: 3.1e-48
                                   HHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSSTTSS-SS--SHHHHHHHTT--GGGEEEEEEEEESSEEESS CS
               Adenylsucc_synt 191 aerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGtYPfvTsSnttaggaltglglapkkidevlgvvKAyttrvG 271
                                    e+lk+++ d+++++n+al++g++vL+EG qgtll++ +GtYP+vTs  tta++ ++  g++p+k+dev+ v+K++ trvG
  gi|15668741|ref|NP_247540.1| 155 IEELKEFLGDVSEEVNNALDRGENVLIEGTQGTLLSLYYGTYPYVTSKDTTASSFAADVGIGPTKVDEVIVVFKTFPTRVG 235
                                   6899***************************************************************************** PP

                                   SS--TTB--SHHHHHHHHHTT.-B-TTT--B-EEE-EEHHHHHHHHHHHT-SEEEEE-GGGGT CS
               Adenylsucc_synt 272 eGpfptelkdevgeklrekGk.EfgtttgrpRrcGwlDlvllryavrvngvtelaltklDvld 333
                                   +Gpfpte++ e++e l   G  E+gt+tgr+Rr+G++D  l+r+a+r+ng+t++alt lD  d
  gi|15668741|ref|NP_247540.1| 236 AGPFPTEMSLEEAESL---GIvEYGTVTGRRRRVGYFDFELARKACRLNGATQIALTGLDKYD 295
                                   *******988999999...434**************************************876 PP

  == domain 3  score: 31.8 bits;  conditional E-value: 7.9e-12
                                   --.S--TT---GGGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-EE CS
               Adenylsucc_synt 373 gWkedisgvrsfedlpenakkyvefieellgvpvkiisvGpereqti 419
                                    +++++ gv+++++l e+ak++++ iee++gvpv+iis+Gpe +qti
  gi|15668741|ref|NP_247540.1| 293 KYDKECYGVTEYNKLSEKAKEFINKIEEVTGVPVTIISTGPEMHQTI 339
                                   67788999************************************997 PP

>> CytochromB561_N  Cytochrome B561, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.2e-05      0.11     227     323 ..     142     253 ..     131     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.2e-05
               CytochromB561_N 227 srkraksakeirtekqLerflaevdekitesa..................fgkaspsnvagslnrSgsarstplrsvrmsp 289
                                   +++   + k+ ++ + L++fl +v+e+++++                      + p   ++ +++S  a   ++ + ++++
  gi|15668741|ref|NP_247540.1| 142 VDRVLRILKQAKDIEELKEFLGDVSEEVNNALdrgenvliegtqgtllslYYGTYPYVTSKDTTASSFAADVGIGPTKVDE 222
                                   566667778888889************99998***************998677778877789999999************* PP

               CytochromB561_N 290 gs.qkkttppkkgegdlPskmsmeeaieafeelgi 323
                                        kt p + g g +P  ms+eea    e+lgi
  gi|15668741|ref|NP_247540.1| 223 VIvVFKTFPTRVGAGPFPTEMSLEEA----ESLGI 253
                                   **7777888999*************9....67776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.50
# Mc/sec: 2092.94
//
Query:       gi|15668742|ref|NP_247541.1|  [L=74]
Description: hypothetical protein MJ_0562 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.043   14.0   4.0      0.055   13.7   4.0    1.1  1  DUF2654   Protein of unknown function (DUF2654)
       0.05   13.5   0.2      0.074   13.0   0.2    1.4  1  Pox_L5    Poxvirus L5 protein family


Domain annotation for each model (and alignments):
>> DUF2654  Protein of unknown function (DUF2654)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   4.0   6.2e-06     0.055       5      50 ..      20      69 ..      18      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.2e-06
                       DUF2654  5 ankllkkn..kRelkRLrkhaekalie..nnkaqYvYaikklRdilkqtv 50
                                  a+k  +kn  +++l+RL+k   k +i+  n  a Y Y  kk + i+k +v
  gi|15668742|ref|NP_247541.1| 20 AKKEYEKNpiEKNLNRLKKAEAKLMINypNTNATYIYKNKKYKIIIKDSV 69
                                  7888889944577******9999999866789*************99876 PP

>> Pox_L5  Poxvirus L5 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   8.3e-06     0.074       5      42 ..      17      52 ..      12      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.3e-06
                        Pox_L5  5 lfsrkakiskdpidkllktsLaCegdkllilglpnsgt 42
                                   f+ k++ +k+pi+k l+ +L+ ++ kl+i + pn++ 
  gi|15668742|ref|NP_247541.1| 17 YFNAKKEYEKNPIEKNLN-RLKKAEAKLMI-NYPNTNA 52
                                  7999***********886.7999*******.8997443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1336  (0.0745161); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 479.09
//
Query:       gi|15668743|ref|NP_247542.1|  [L=310]
Description: type II R/M system modification methyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-47  163.0   1.0    4.8e-31  108.3   1.3    2.0  2  DNA_methylase    C-5 cytosine-specific DNA methylase
     0.0033   17.0   0.2     0.0069   16.0   0.0    1.8  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
      0.071   13.1   0.2       0.21   11.6   0.0    1.8  2  NCD1             NAB conserved region 1 (NCD1)


Domain annotation for each model (and alignments):
>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3   1.3   8.1e-35   4.8e-31       1     203 [.       1     216 [.       1     230 [. 0.86
   2 !   54.6   0.0   1.7e-18     1e-14     240     335 .]     212     308 ..     202     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 8.1e-35
                                   -EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-..-SEEEES-TTTS-...GS--...-SEEEE---GGGTE CS
                 DNA_methylase   1 lkfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk.kvsigDitkidkk...klpe.d.iDlLvgGfPCqpfS 75 
                                   +++idLf+G+GGf+ g+   +f++  a+e+ k ++ktY  n+k  v   Di+ i  k   ++ + + +D+++g++PC pf 
  gi|15668743|ref|NP_247542.1|   1 MNVIDLFSGCGGFSKGFLDENFRILGAIENFKPVVKTYLYNIKaPVWMDDIKRIPPKafdEFIKnEkVDVIIGSPPCEPFT 81 
                                   789****************************************9999**********9995555445************** PP

                                   CTSE.......E--TTSGGGHHHHHHHHHH....HHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEEEEEEEEGG CS
                 DNA_methylase  76 vaGk.......qkgfedtrgtLffeiirii....kekkPkvfllENVkgLlkhdkgktlkvilekleelGYevsykllnas 145
                                   +a k        +  +d+ g L  ++i ++    + ++  +f++ENV+++++ +     +++ + + ++G +v++++l+a+
  gi|15668743|ref|NP_247542.1|  82 KANKlikdnplDRLYKDKVGRLVLYYIDYVnyftQRNDDLIFVMENVPQIKEIK-----DELKKLFGDIGHKVYFNILRAE 157
                                   ****99999999999**********999982222456699**********9885.....588899**************** PP

                                   GTT-SB--EEEEEEEEEGGG---.-------SS---GGG.....TSGGGTTS-EE.BTTT CS
                 DNA_methylase 146 dyGvpQnReRvfivgirkdleln.vlvkvkefrfpkkkdleasktlrdlleekse.ldee 203
                                   dyG p +R R+fi  i+ + ++  +lv v+e  + ++kd ++++++++l++ek+e +++ 
  gi|15668743|ref|NP_247542.1| 158 DYGNPSKRARMFISNIKLKPKKVdKLVVVEEALKDIPKD-AKNHEIKKLSKEKVEmISKL 216
                                   ***************986543336777777777777775.789********988764443 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 1.7e-18
                                   -TTS...-B----S-STT-.-B-TTS---EEEETTEEE--T.TTGGG--B-BHHHHHHHHT--TT-----SBHHHHHHHHT CS
                 DNA_methylase 240 kveelkglsatrrksgrge.klekelaeagklqknkerfkpviekkriRrLtprEaarlqGfPddfefgskksaaykqiGn 319
                                    + +lk   a++r  g+++   +++  +  kl  +++   ++i++++ R Lt+rE arl+++Pddf f + +  +y qiG+
  gi|15668743|ref|NP_247542.1| 212 MISKLKWGEALYRYRGKKKlMFNWYKLHPKKLAPTVKGRSRFIHPYEDRLLTVREQARLMSYPDDFVFFGGRDVQYNQIGE 292
                                   444444444444444443445667777778888888877779*************************************** PP

                                   S--HHHHHHHHHHHHH CS
                 DNA_methylase 320 sVpvpvieaiakeikk 335
                                   sVp+ + +aiakeikk
  gi|15668743|ref|NP_247542.1| 293 SVPPILGRAIAKEIKK 308
                                   *************986 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.2e-06    0.0069       4      81 ..       3      77 ..       1     155 [. 0.85
   2 ?   -2.7   0.0      0.64   3.8e+03      96     109 ..     195     208 ..     167     233 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-06
               Methyltransf_15  4 ilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpPw 81
                                  ++DlfsG+GG +  f  + f+   aie  +  ++    N ++    d i+ +  + f+ +  +k ek+  d+++ SpP+
  gi|15668743|ref|NP_247542.1|  3 VIDLFSGCGGFSKGFLDEnFRILGAIENFKPVVKTYLYNIKAPVWMDDIKRIPPKAFDEF--IKNEKV--DVIIGSPPC 77
                                  89************98776999999**999999999999999877999999999999855..556777..********6 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.64
               Methyltransf_15  96 kklkplkleqllke 109
                                   k+ k+ ++++l ke
  gi|15668743|ref|NP_247542.1| 195 KDAKNHEIKKLSKE 208
                                   23333333333333 PP

>> NCD1  NAB conserved region 1 (NCD1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.4   8.6e+03      34      40 ..     111     117 ..     102     134 .. 0.50
   2 ?   11.6   0.0   3.6e-05      0.21       9      36 ..     260     287 ..     256     293 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.4
                          NCD1  34 veqllea 40 
                                   v+++++ 
  gi|15668743|ref|NP_247542.1| 111 VNYFTQR 117
                                   3333322 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.6e-05
                          NCD1   9 qlyrvLqranLlqYydvliaqGGDdveq 36 
                                   +l+ v ++a L++Y d ++  GG dv++
  gi|15668743|ref|NP_247542.1| 260 RLLTVREQARLMSYPDDFVFFGGRDVQY 287
                                   689999********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1968.14
//
Query:       gi|15668744|ref|NP_247543.1|  [L=892]
Description: alanyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     1e-164  549.1   1.3   1.7e-164  548.4   1.3    1.4  1  tRNA-synt_2c  tRNA synthetases class II (A)
    2.4e-14   53.9   4.4    1.2e-13   51.7   4.4    2.3  1  DHHA1         DHHA1 domain
    1.1e-11   44.6   1.4    3.8e-11   42.9   1.4    2.0  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
  ------ inclusion threshold ------
        1.4    8.9   0.0        1.4    8.9   0.0    4.9  7  DUF327        Protein of unknown function (DUF327)
        3.5    7.7   6.9        1.1    9.3   0.7    3.0  3  DUF2680       Protein of unknown function (DUF2680)


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.4   1.3  4.7e-168  1.7e-164       1     552 []      61     582 ..      61     582 .. 0.98

  Alignments for each domain:
  == domain 1  score: 548.4 bits;  conditional E-value: 4.7e-168
                                   HHHHHHHHHHHCTT-EEE----SS-S.SSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTTTSS CS
                  tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpe.ndptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVGkta 80 
                                   e+ ++F++fF+++gH+++k+++v ++ +++++l+++A++a f+p+++++  kpk++++v++Q+ciR++    D++nVG+t+
  gi|15668744|ref|NP_247543.1|  61 EMVKEFINFFKEHGHEPIKRAPVTARrWRDDILLTIASIAVFQPWITKGIVKPKANPLVIAQPCIRLN----DIDNVGRTG 137
                                   7899*********************99*****************************************....********* PP

                                   S--SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGEEEE-HHH CS
                  tRNA-synt_2c  81 rHhTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeerilrfgekd 154
                                   rH+T+F+M G+++f+     +Y+++e++e+++++++ +lg+d+++++++++++++  +a++++e +++++e ++l+f   +
  gi|15668744|ref|NP_247543.1| 138 RHLTCFTMGGHHAFNreddfKYWQDETVELCFNFFK-KLGIDEKSITFIESWWEGggNAGPCYEVITHGVELATLVF---M 214
                                   ***********************************9.9****************999********************...* PP

                                   HEEESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEESTTSHEEEEEEEEEEEEEEHHHHHHHH CS
                  tRNA-synt_2c 155 nfwemgdtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnreedgtlkpLpkksidtGmglerlvavL 235
                                   +++++gd+++++p +++++++g e++++++++e++++d+++ +i+n+++++++++ d+++++L+k + ++G+++ + v +L
  gi|15668744|ref|NP_247543.1| 215 QYEKVGDNYKEIPLKIVDTGYGIERFVWASTGEPTIYDAIFKNIVNKLKEDAGVK-DIDKEILAKITEVAGLMDVKDVGDL 294
                                   *******************************************************.************************* PP

                                   TTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHHHHHHHHHHHHHHHHTT CS
                  tRNA-synt_2c 236 qevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvvpsnegrgYvlRrllRravrhakkLg 316
                                   +++r+++++++ +pv+e+ + is+         +e++++i DH+ralaf+l+dG+vpsn+++gY++R+l+R+++rh+++L+
  gi|15668744|ref|NP_247543.1| 295 RKLREEVANKVNIPVEELDKLISP---------YEDIYAIVDHTRALAFMLGDGIVPSNVKDGYLVRMLIRKTLRHMDRLN 366
                                   ************************.........699********************************************* PP

                                   -SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCSEEXHHHHHHHHHCHXXX CS
                  tRNA-synt_2c 317 lkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklkkkkelsgedafkLydtyGfP 397
                                   l+++ ++++va+++++l+d+ypel ++e++++ei+e E++++++T+erG+ ++e+l+k+   kke+++e++++Lyd++G+P
  gi|15668744|ref|NP_247543.1| 367 LSTP-ITEIVAMQLNELKDLYPELLDMEDYIMEILEIETNKYRQTIERGKGIVERLLKS---KKEIDLENLIELYDSHGLP 443
                                   ****.*****************************************************8...78***************** PP

                                   HHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXXTTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEEE CS
                  tRNA-synt_2c 398 vdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvealkelkkteeflgyeeleaeakvlallkdkefvee 478
                                   ++++k++a++ g +v+i++++++ +++r+++kke+kek           +++kte  l+ye+           k+kef+++
  gi|15668744|ref|NP_247543.1| 444 PEIVKDVAKSLGKDVKIPDNFYTIVAERHENKKEVKEKI-----KLPEVNVDKTE-LLFYEY----------PKMKEFEAK 508
                                   *******************************99999987.....34445555555.599*99..........899****** PP

                                   EEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHHH CS
                  tRNA-synt_2c 479 veegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevdeer 552
                                   + ++ +++v+LdrT+fY+e+GGq++D+G+i k +++frv+dvqk++++v+hk+++ +++lk+gd vk+++d++r
  gi|15668744|ref|NP_247543.1| 509 ILRIVDDYVILDRTAFYPEGGGQKADTGYIIKGDKKFRVVDVQKENNIVYHKIENLNDELKEGDIVKGVIDWKR 582
                                   ***********************************************************************986 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   4.4   3.3e-17   1.2e-13       2     138 .]     766     889 ..     765     889 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 3.3e-17
                                   HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEECTE CS
                         DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvakeegdk 82 
                                   +++ ee+ke +k++eel++++ +lk+ el++k e++ ++kvlv +v  e++++ + ++ad+l +  +++++v++      k
  gi|15668744|ref|NP_247543.1| 766 KRFFEEWKEQRKKIEELEKKIGELKKFELINKFETIGNYKVLVEKV--EANPKEMLNIADNLAT--ENAIVVLLND----K 838
                                   6789*******************************99******999..****************..6666666653....6 PP

                                   EEEEEEESSH.SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHHHHHHHH CS
                         DHHA1  83 vkvsarskkd.gvdagelakeaaaklgggGGGH.dlAaGagipaekleealealeeai 138
                                    ++ ++  ++ +++++el++      + +GGG+ +lA+G     +++ee+ +++ e+i
  gi|15668744|ref|NP_247543.1| 839 GNILCKRGENvDIKMNELIRY-----IAKGGGReHLAQGKYE--GDVEEIKKKVIEFI 889
                                   78999988889**********.....*************999..46999999999986 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   1.4   1.1e-14   3.8e-11       1      43 [.     681     728 ..     681     729 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.1e-14
                                   EEEEEETT......EEEEESS---SBGGGC-SEEEECCECCCTCEEEE CS
                      tRNA_SAD   1 vrvvsiGd.....isvelCgGtHvpnTgeIgafkilseesiakglrRI 43 
                                   +r+v i+d     ++v++CgGtH++nTge+g +ki++ e++++g+ R+
  gi|15668744|ref|NP_247543.1| 681 LRIVIIEDengniVDVQACGGTHCQNTGEVGFIKIIKTERVQDGVERL 728
                                   589999888999*********************************996 PP

>> DUF327  Protein of unknown function (DUF327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00039       1.4      67     107 ..      58      99 ..      51     123 .. 0.82
   2 ?   -0.8   0.0      0.38   1.4e+03     127     139 ..     274     286 ..     253     309 .. 0.87
   3 ?   -3.0   0.2       1.8   6.3e+03     109     129 ..     380     400 ..     357     402 .. 0.71
   4 ?   -1.5   0.0      0.62   2.2e+03      44      91 ..     556     603 ..     543     619 .. 0.70
   5 ?   -1.4   0.0      0.59   2.1e+03      51      96 ..     610     661 ..     586     668 .. 0.64
   6 ?   -1.2   0.4      0.49   1.8e+03      37      69 ..     774     805 ..     738     828 .. 0.63
   7 ?   -0.7   0.1      0.35   1.2e+03      37      77 ..     848     890 ..     838     891 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00039
                                   HHHHHHHHHHHHHHHHHHHHHT..-----H.HHHHHHHHHHH CS
                        DUF327  67 kYkklvkeflkevvknslklkkersldrkg.rsrvykivkei 107
                                    Yk++vkef+++  +++++  k+  ++ +  r +++ ++  i
  gi|15668744|ref|NP_247543.1|  58 TYKEMVKEFINFFKEHGHEPIKRAPVTARRwRDDILLTIASI 99 
                                   6*****************988877777666688888888776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.38
                                   HHHHHHHHHHHHH CS
                        DUF327 127 dilakideIkGLL 139
                                   +ilaki e+ GL+
  gi|15668744|ref|NP_247543.1| 274 EILAKITEVAGLM 286
                                   5889999999884 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.8
                                   HHHHHHHHHHHTTSTTCHHHH CS
                        DUF327 109 ekldeLteellkeekealdil 129
                                   ++l++L+ ell+ e   ++il
  gi|15668744|ref|NP_247543.1| 380 NELKDLYPELLDMEDYIMEIL 400
                                   678888889999998888887 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.62
                                   HHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHT..- CS
                        DUF327  44 elleeidkqgerLaesrtiedlkkYkklvkeflkevvknslklkkers 91 
                                    + ++i++  ++L+e   ++ + ++k+  + + ++++++ ++   ++ 
  gi|15668744|ref|NP_247543.1| 556 IVYHKIENLNDELKEGDIVKGVIDWKRRLSLMRNHTATHIINAAAQKV 603
                                   455677777777777777777777777777777777777776666655 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 0.59
                                   HHHHHHHHH--HHHHHHHH.......HHHHHHHHHHHHHHHHHHT..-----H CS
                        DUF327  51 kqgerLaesrtiedlkkYk.......klvkeflkevvknslklkkersldrkg 96 
                                   ++g+++  ++   d+ +Yk       k + +  +e+v n++++k+  ++dr++
  gi|15668744|ref|NP_247543.1| 610 QAGSDVDVDKARLDITHYKrisreelKDIERVANEIVLNNYNIKS-IFMDRNE 661
                                   555555556666666666622222223477788888888888885.5666665 PP

  == domain 6  score: -1.2 bits;  conditional E-value: 0.49
                                   HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHH CS
                        DUF327  37 eseeelkelleeidkqgerLaesrtiedlkkYk 69 
                                   e++++++el ++i +  ++++   ++e++ +Yk
  gi|15668744|ref|NP_247543.1| 774 EQRKKIEELEKKIGEL-KKFELINKFETIGNYK 805
                                   3333344444444332.2333344444444444 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 0.35
                                   HHHHHHHHHHHHHHHHH..HHHHHH--HHHHHHHHHHHHHHHH CS
                        DUF327  37 eseeelkelleeidkqg..erLaesrtiedlkkYkklvkeflk 77 
                                   +   +++el++ i k g  e La+ +   d+++ kk+v ef+k
  gi|15668744|ref|NP_247543.1| 848 NVDIKMNELIRYIAKGGgrEHLAQGKYEGDVEEIKKKVIEFIK 890
                                   55567889999999988456699999999*********99997 PP

>> DUF2680  Protein of unknown function (DUF2680)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.22   7.8e+02       5      20 ..     378     393 ..     376     398 .. 0.84
   2 ?    9.3   0.7    0.0003       1.1       3      27 ..     773     798 ..     773     803 .. 0.89
   3 ?   -3.6   0.1       3.3   1.2e+04      15      25 ..     877     887 ..     874     887 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.22
                       DUF2680   5 QkkeleaLyqqiaelr 20 
                                   Q +el++Ly + ++++
  gi|15668744|ref|NP_247543.1| 378 QLNELKDLYPELLDME 393
                                   9********9988865 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0003
                       DUF2680   3 deQkkeleaLyqqiaelrK.qivdKy 27 
                                   +eQ k++e+L+++i el+K ++++K+
  gi|15668744|ref|NP_247543.1| 773 KEQRKKIEELEKKIGELKKfELINKF 798
                                   59*****************8899996 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.3
                       DUF2680  15 qiaelrKqivd 25 
                                   ++ e++K++++
  gi|15668744|ref|NP_247543.1| 877 DVEEIKKKVIE 887
                                   67799999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (892 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1114  (0.062134); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.83u 0.27s 00:00:01.10 Elapsed: 00:00:00.48
# Mc/sec: 5573.77
//
Query:       gi|15668745|ref|NP_247544.1|  [L=147]
Description: hypothetical protein MJ_0565 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.8    7.3  11.6       0.57    9.6   2.6    2.2  2  TMEM215   TMEM215 family
        3.1    8.2  26.5       0.41   11.0   4.5    3.2  3  DUF308    Short repeat of unknown function (DUF308)


Domain annotation for each model (and alignments):
>> TMEM215  TMEM215 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.6   6.4e-05      0.57      16      32 ..      10      26 ..       5      32 .. 0.88
   2 ?    2.1   3.0     0.012   1.1e+02      16      51 ..      30      65 ..      26      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 6.4e-05
                       TMEM215 16 lvsvflvfGfmftvsGl 32
                                  +vs+ lvfG++ftvsG+
  gi|15668745|ref|NP_247544.1| 10 IVSLSLVFGLLFTVSGI 26
                                  79**************8 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.012
                       TMEM215 16 lvsvflvfGfmftvsGlkGetlGdiPllaiGPaicl 51
                                  ++ ++ ++Gf   +  + G+ +G + lla+G a +l
  gi|15668745|ref|NP_247544.1| 30 IIGLYSILGFKIELPLFVGDVFGGLALLAVGIAYFL 65
                                  56678899************************9988 PP

>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.5   4.6e-05      0.41      20      44 ..       9      33 ..       4      48 .. 0.85
   2 ?    7.5   5.2   0.00057       5.1      29      72 ..      53      96 ..      43      97 .. 0.83
   3 ?    2.0   4.2      0.03   2.7e+02      27      72 ..      93     133 ..      93     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.6e-05
                        DUF308 20 allalvllfGilllvsGivqiiaaf 44
                                  +++ l+l+fG+l+ vsGi++ii ++
  gi|15668745|ref|NP_247544.1|  9 VIVSLSLVFGLLFTVSGIIEIIIGL 33
                                  68899****************8655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00057
                        DUF308 29 GilllvsGivqiiaafaarkknrggrwlglllGilyliaGllll 72
                                  G+ ll+ Gi+++++  +a ++  ++  + ++ +i+ l +G++++
  gi|15668745|ref|NP_247544.1| 53 GLALLAVGIAYFLGVKKAVDRDIKAVSYLFTASIIGLGIGVIAF 96
                                  88999*******977777776666666999************97 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.03
                        DUF308  27 lfGilllvsGivqiiaafaarkknrggrwlglllGilyliaGllll 72 
                                   ++++l+l+s +++++ +f+ ++ ++  +  +l    +yl++G+l++
  gi|15668745|ref|NP_247544.1|  93 VIAFLILISDAIGFLLGFEDWADWGFFN--DL---TVYLVLGMLAI 133
                                   6899999999999999997776666544..33...44555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 906.55
//
Query:       gi|15668746|ref|NP_247545.1|  [L=668]
Description: ferrous iron transport protein FeoB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-68  228.5   1.0    3.9e-68  227.9   1.0    1.3  1  FeoB_N        Ferrous iron transport protein B
    4.9e-51  171.7  15.0    8.3e-34  116.2   3.4    3.4  3  Gate          Nucleoside recognition
    1.8e-21   76.3   0.1    4.3e-21   75.1   0.1    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
    1.3e-18   66.4   1.6    1.3e-18   66.4   1.6    3.4  4  FeoB_C        Ferrous iron transport protein B C terminus
    5.6e-15   55.7   2.8    1.3e-14   54.5   2.8    1.7  1  FeoB_Cyto     FeoB cytosolic helical domain
    4.7e-06   26.6   1.6      0.008   16.1   0.3    2.7  3  RsgA_GTPase   RsgA GTPase
    1.6e-05   24.3   0.0    3.2e-05   23.3   0.0    1.4  1  AIG1          AIG1 family
    2.5e-05   23.9   0.3    0.00078   19.0   0.2    2.5  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    4.7e-05   22.9   0.0    0.00011   21.7   0.0    1.6  1  SRPRB         Signal recognition particle receptor beta subun
    0.00073   19.6   0.1      0.097   12.7   0.0    2.7  2  Dynamin_N     Dynamin family
     0.0054   16.2   0.1      0.011   15.2   0.1    1.5  1  Arf           ADP-ribosylation factor family
  ------ inclusion threshold ------
      0.012   15.6   0.1      0.048   13.7   0.1    2.0  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
        9.5    6.3   8.4       0.67   10.0   0.4    3.0  3  DUF3927       Protein of unknown function (DUF3927)


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.9   1.0   2.9e-71   3.9e-68       2     156 .]       5     159 ..       4     159 .. 0.99

  Alignments for each domain:
  == domain 1  score: 227.9 bits;  conditional E-value: 2.9e-71
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEE CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdvv 82 
                                   ++al+GnpnvGk+t+fnaltg + ++gNwpGvtvekkeg+++++g+++++vDlPG+Ysl+a s++e +ard++++e+pd+v
  gi|15668746|ref|NP_247545.1|   5 EIALIGNPNVGKSTIFNALTGENVYIGNWPGVTVEKKEGEFEYNGEKFKVVDLPGVYSLTANSIDEIIARDYIINEKPDLV 85 
                                   79******************************************************************************* PP

                                   EEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                        FeoB_N  83 vnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellkai 156
                                   vn+vdat lernLyLtlql+e+g++++laln++d a++ gieid++kL+++Lgv+vv++sa+kk gie+l+kai
  gi|15668746|ref|NP_247545.1|  86 VNIVDATALERNLYLTLQLMEMGANLLLALNKMDLAKSLGIEIDVDKLEKILGVKVVPLSAAKKMGIEDLKKAI 159
                                   ***********************************************************************986 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.37   5.1e+02      35      68 ..     298     331 ..     289     351 .. 0.71
   2 !   60.8   1.3   9.8e-20   1.4e-16       2     111 ..     348     442 ..     347     443 .. 0.97
   3 !  116.2   3.4     6e-37   8.3e-34       1     111 [.     509     639 ..     509     640 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.37
                          Gate  35 faplg.qeldwkatvslltgfaakevvvgtlgtly 68 
                                   f+     +++  a++  ++gf+  evv +++++ +
  gi|15668746|ref|NP_247545.1| 298 FKFTFdVSKPFSAMIEYFFGFL-SEVVKSSISNKF 331
                                   5553346788999*********.999999998776 PP

  == domain 2  score: 60.8 bits;  conditional E-value: 9.8e-20
                          Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtp 82 
                                   l ++pi++++++ i+fl++s++++ri ++ + +++++g  l++ka++s+++gf+   ++v++++ ++         +++++
  gi|15668746|ref|NP_247545.1| 348 LVFFPILAFLFFAISFLEDSGYMARIPFITDRIMNKFG--LPGKAVISMVMGFG---CNVPAIMATR---------TIEDE 414
                                   6789**********************************..**************...*********9.........***** PP

                          Gate  83 ksalafllfvllytpcvatlavivrelgs 111
                                   k+++ ++l++ l + c a+l++++ ++g+
  gi|15668746|ref|NP_247545.1| 415 KDRILTILINPLLS-CSARLPIYALFAGA 442
                                   ************98.********999886 PP

  == domain 3  score: 116.2 bits;  conditional E-value: 6e-37
                          Gate   1 llkagpiillasiliwflss...................ssllgrigkllepvfaplgqeldwkatvslltgfaakevvvg 62 
                                   l+kag+ii++++il+w+ls                    +s+++ igk l+p+f+p+g   dw+a+ +l++g++akevvvg
  gi|15668746|ref|NP_247545.1| 509 LRKAGTIIVFGVILVWVLSVygpsgylgeevfenpqliaNSWVAVIGKTLAPLFSPMG--WDWRACSALVFGIIAKEVVVG 587
                                   689*******************************************************..********************* PP

                          Gate  63 tlgtly...tsalgellqgfdtpksalafllfvllytpcvatlavivrelgs 111
                                   +l++ly   +++l+++++++++p+sa+af+ f+l+y pc+atlavi++e+g+
  gi|15668746|ref|NP_247545.1| 588 SLAMLYgtgEENLSSVIAHAFSPVSAYAFMAFSLIYLPCIATLAVIKQEIGW 639
                                   **************************************************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.1   3.1e-24   4.3e-21       1     114 []       5     117 ..       5     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 3.1e-24
                                   EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHCTSEE CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflaleeadli 79 
                                   e+a++G+pNvGKSt++naltge++ ++++pg+T + +eg+++++g+++++vD+pG+++   +s ++ +++++  +e+ dl+
  gi|15668746|ref|NP_247545.1|   5 EIALIGNPNVGKSTIFNALTGENVYIGNWPGVTVEKKEGEFEYNGEKFKVVDLPGVYSltANSIDEIIARDYIINEKPDLV 85 
                                   69*****************************************************986667788889******9999**** PP

                                   EEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  80 llvvdaseeklkpldeeleelleeakkplilvlnk 114
                                   + +vda+ + l+++   l   l e + +l+l+lnk
  gi|15668746|ref|NP_247545.1|  86 VNIVDAT-A-LERN-LYLTLQLMEMGANLLLALNK 117
                                   *****77.3.3332.22222222345667777766 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.3   4.5e+03      17      33 ..     379     396 ..     375     396 .. 0.78
   2 !   66.4   1.6   9.6e-22   1.3e-18       1      53 []     452     504 ..     452     504 .. 0.97
   3 ?   -3.5   0.9       6.3   8.6e+03       9      20 ..     516     527 ..     514     530 .. 0.67
   4 ?   -3.9   0.7       8.8   1.2e+04      11      20 ..     652     661 ..     650     665 .. 0.44

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.3
                        FeoB_C  17 lllkktt.lkgep.spfvm 33 
                                   ++++k + l+g++  ++vm
  gi|15668746|ref|NP_247545.1| 379 RIMNK-FgLPGKAvISMVM 396
                                   79999.9999999777776 PP

  == domain 2  score: 66.4 bits;  conditional E-value: 9.6e-22
                        FeoB_C   1 lfslYllgilvallvalllkktt.lkgepspfvmELPpYrlPslknvliktweR 53 
                                   ++s+Y+lg+++al++a+l++k + +k  ps+++ ELPpY++P+l  vl++tweR
  gi|15668746|ref|NP_247545.1| 452 ILSMYALGVVLALITAFLFRK-LiFKTSPSYLIVELPPYHIPHLNVVLKNTWER 504
                                   689******************.77*****************************9 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.3
                        FeoB_C   9 ilvallvalllk 20 
                                   i++ +++ ++l+
  gi|15668746|ref|NP_247545.1| 516 IVFGVILVWVLS 527
                                   677777777775 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 8.8
                        FeoB_C  11 vallvalllk 20 
                                   +a +val+++
  gi|15668746|ref|NP_247545.1| 652 LAYVVALVIS 661
                                   3344444433 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   2.8   9.6e-18   1.3e-14       5      91 .]     176     264 ..     173     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 9.6e-18
                     FeoB_Cyto   5 iEkaiekleellkesnlkaklppRwlAlklLegDeelleelkedp...elraeveearkeleaelgedledvIvdarykfi 82 
                                    E  i+k++++l++++  +k++ R+lA+klLe+D++++e +k+++   el+  ++ +++el +++g ++e  Iv++ryk i
  gi|15668746|ref|NP_247545.1| 176 FEPYIKKITSILQKDEDLKKYNLRYLAIKLLENDKYVEEIVKNSKvwnELKPVLDSIINELSKKYG-EAELGIVEERYKVI 255
                                   6899***********99*************************974444999999999999999998.58************ PP

                     FeoB_Cyto  83 egilrevvk 91 
                                   ++i++ev+k
  gi|15668746|ref|NP_247545.1| 256 DKIVKEVMK 264
                                   ******986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0011       1.5     102     123 ..       6      27 ..       1      44 [. 0.86
   2 !   16.1   0.3   5.8e-06     0.008      35      98 ..      94     160 ..      76     164 .. 0.79
   3 ?   -3.2   0.0       5.1     7e+03     123     142 ..     255     273 ..     223     275 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                                   EEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase 102 svlvGqSGvGKStLinallpel 123
                                   ++l+G+  vGKSt+ nal++e+
  gi|15668746|ref|NP_247545.1|   6 IALIGNPNVGKSTIFNALTGEN 27 
                                   6899**************9984 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5.8e-06
                                   HHHHH...HHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHH.TTSEEEE--TTTHTTHHHHHHHCT CS
                   RsgA_GTPase  35 ldrfL...vlaeekgiepvivlnKiDlleeeeeleelkeelea.lgyevllvsaktkegleelkellk 98 
                                   l+r L   +++ e g++++++lnK+Dl+++   +e   ++le+ lg++v+ +sa +k g+e+lk++++
  gi|15668746|ref|NP_247545.1|  94 LERNLyltLQLMEMGANLLLALNKMDLAKSLG-IEIDVDKLEKiLGVKVVPLSAAKKMGIEDLKKAIS 160
                                   5554411134678899****************.777777766626*******************9875 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5.1
                                   -----S-------------- CS
                   RsgA_GTPase 123 lelktgevseklgrGkhTTt 142
                                    +  ++ev +k  +Gk TTt
  gi|15668746|ref|NP_247545.1| 255 IDKIVKEVMKK-TSGKLTTT 273
                                   44455666554.66787777 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   2.3e-08   3.2e-05       3      93 ..       6      91 ..       4     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.3e-08
                                  EEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHHHCTT-ES CS
                          AIG1  3 ivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrclllseegih 85
                                  i l+G   +GkS+  N++ g++++  +    +vt + ++ + + +g+k +V+D Pg+ +l +  ++i + i r + ++e+ ++
  gi|15668746|ref|NP_247545.1|  6 IALIGNPNVGKSTIFNALTGENVYIGNW--PGVTVEKKEGEFEYNGEKFKVVDLPGVYSLTA--NSIDEIIARDYIINEK-PD 83
                                  88***********************996..99999999********************9975..3455666676777776.77 PP

                                  EEEEEEET CS
                          AIG1 86 alllvlsl 93
                                   ++ ++++
  gi|15668746|ref|NP_247545.1| 84 LVVNIVDA 91
                                  66655544 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   5.6e-07   0.00078      53     188 ..      35     159 ..       2     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.6e-07
                                   TSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEE.....EEEETTTB.STHHHHHHHHHHHHTTTEEEE CS
                      GTP_EFTU  53 giTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgav.....lvvdaveG.vepqteevlrlalkegvpiiv 127
                                   g+T++ +  ++e  ++  +++++D PG  + + + i  + + D+ +     lvv +v+    ++   +  ++ ++g ++ +
  gi|15668746|ref|NP_247545.1|  35 GVTVEKKEGEFE--YNGEKFKVVDLPGVYSLTANSIDEIIARDYIInekpdLVVNIVDAtALERNLYLTLQLMEMGANLLL 113
                                   89**********..****************999999996666666655555566666552344555667788899****** PP

                                   EEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHH CS
                      GTP_EFTU 128 fiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktlleal 188
                                   ++NKmD +    ++  v+++++ l                 v+vv+ Sa k+ g+++l +a+
  gi|15668746|ref|NP_247545.1| 114 ALNKMDLAkSLGIEIDVDKLEKIL----------------GVKVVPLSAAKKMGIEDLKKAI 159
                                   ********7677777788888666................2567888888888777665555 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   7.9e-08   0.00011       5     139 ..       5     135 ..       1     177 [. 0.69

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.9e-08
                                   EEEEE-STTSSHHHHHHHHHHS....S---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGG.EEE.. CS
                         SRPRB   5 avllvGlsdsGKTslftrLttd....svkktvtSqessaalkvksekgskltliDfPGheklrqklleklkakss.lkg.. 78 
                                    + l+G  + GK ++f+ Lt +       + vt  +++   ++   +g+k++++D+PG  +l  + +++++a++  +    
  gi|15668746|ref|NP_247545.1|   5 EIALIGNPNVGKSTIFNALTGEnvyiGNWPGVTVEKKEGEFEY---NGEKFKVVDLPGVYSLTANSIDEIIARDYiINEkp 82 
                                   6789****************99433323344555555555566...99*********************999987332233 PP

                                   ..EEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---HHHHHHHHHH CS
                         SRPRB  79 ..lvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflakspklikdaLEk 139
                                     +v +vD+t+ ++++  +  l+          + + ++l+A nK +l+ +   ++  d+LEk
  gi|15668746|ref|NP_247545.1|  83 dlVVNIVDATALERNLYLTLQLM----------EMGANLLLALNKMDLAKSLGIEIDVDKLEK 135
                                   448999****9999975443222..........234556666666666555555555555555 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   7.1e-05     0.097       1      24 [.       6      29 ..       6      37 .. 0.91
   2 ?    3.8   0.0     0.038        52     101     139 ..      50      92 ..      44     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.1e-05
                                  EEEEEBTTTTHHHHHHHHHTS--S CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedil 24
                                  ia++G+ + GKS++ naL+ge++ 
  gi|15668746|ref|NP_247545.1|  6 IALIGNPNVGKSTIFNALTGENVY 29
                                  89*******************975 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.038
                                   -SEEEEE---B-S..SSGTTSHHHHHHH..STTEEEEEEEETT CS
                     Dynamin_N 101 kgltlvDlPGlds..vnkrdqelvkeyi..kkadiilavtsan 139
                                   ++ ++vDlPG+ s   n  d+ +++ yi  +k d+++ +++a 
  gi|15668746|ref|NP_247545.1|  50 EKFKVVDLPGVYSltANSIDEIIARDYIinEKPDLVVNIVDAT 92 
                                   67789*******9433334447778888766778888888775 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   7.8e-06     0.011      13     166 ..       2     154 ..       1     163 [. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.8e-06
                                   TEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSS..SSSEEEEEEEETTEEEEEEEE-SSGGGGG......GGGGGC..TTE CS
                           Arf  13 kelrilllGLDnaGKtTilkklkleelvt.tvP..TigfnveeleiknlkftvwDvGGqeklRp......lWknYf..ekt 82 
                                   k++ i l+G  n GK+Ti + l+ e++     P  T+  +  e e+++ kf+v D+ G  +l        + ++Y   ek 
  gi|15668746|ref|NP_247545.1|   2 KSYEIALIGNPNVGKSTIFNALTGENVYIgNWPgvTVEKKEGEFEYNGEKFKVVDLPGVYSLTAnsideiIARDYIinEKP 82 
                                   6788999****************9998765677335666667899*************88775422222256889733567 PP

                                   SEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBT CS
                           Arf  83 davifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkgeg 163
                                   d v+ +vD++  eR      +L ++        + ll+  NK+Dl+++l  e     +++++l++   ++++  sa k++g
  gi|15668746|ref|NP_247545.1|  83 DLVVNIVDATALERNLYLTLQLMEM-------GANLLLALNKMDLAKSLGIE-----IDVDKLEKILGVKVVPLSAAKKMG 151
                                   8999999999998855554444443.......68899999*****9987543.....223333333355566666666666 PP

                                   HHH CS
                           Arf 164 lke 166
                                   +++
  gi|15668746|ref|NP_247545.1| 152 IED 154
                                   665 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.5e-05     0.048      58     100 ..     111     159 ..     105     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-05
                  MMR_HSR1_Xtn  58 clyvlNKiDl.......isleeldelare..pnsvviSaekelnldeLkeki 100
                                    l++lNK+Dl       i   ++d+l++    ++v++Sa+k++++++Lk++i
  gi|15668746|ref|NP_247545.1| 111 LLLALNKMDLakslgieI---DVDKLEKIlgVKVVPLSAAKKMGIEDLKKAI 159
                                   5889******66654333...566666644469****************987 PP

>> DUF3927  Protein of unknown function (DUF3927)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4   0.00048      0.67      25      46 ..     332     354 ..     311     356 .. 0.76
   2 ?   -2.8   0.2       4.7   6.5e+03      25      40 ..     452     467 ..     450     477 .. 0.72
   3 ?   -0.2   0.1      0.75     1e+03       3      17 ..     647     662 ..     645     665 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00048
                       DUF3927  25 IlSVLsDGvLVA.vvVvlvfPlL 46 
                                   I S L+DG++   ++V + fP+L
  gi|15668746|ref|NP_247545.1| 332 IASLLADGIISGvGAVLVFFPIL 354
                                   88*******98625888889**9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.7
                       DUF3927  25 IlSVLsDGvLVAvvVv 40 
                                   IlS  + Gv  A +  
  gi|15668746|ref|NP_247545.1| 452 ILSMYALGVVLALITA 467
                                   7888888888876654 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.75
                       DUF3927   3 kaklIlAlvF.lvlsv 17 
                                    + +IlA+v  lv+sv
  gi|15668746|ref|NP_247545.1| 647 TYEMILAYVVaLVISV 662
                                   6899***985356666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1335  (0.0744604); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 4375.13
//
Query:       gi|15668747|ref|NP_247546.1|  [L=82]
Description: hypothetical protein MJ_0567 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-18   64.9   0.1    6.5e-18   64.8   0.1    1.0  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.1   3.6e-22   6.5e-18       2      73 ..       3      71 ..       2      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 3.6e-22
                                  EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                          FeoA  2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                  pL+++keGe++++++i d++   ++rL +mG++ G++++v+ r++ +gp+++  +++++a+gr++A++I+Ve
  gi|15668747|ref|NP_247546.1|  3 PLAFAKEGEEVIVKKI-DAGCGAMQRLVSMGINIGSKLKVI-RNQ-NGPVIISTKGSNIAIGRGLAMKIMVE 71
                                  9***************.566999******************.555.6************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 536.03
//
Query:       gi|15668748|ref|NP_247547.1|  [L=125]
Description: iron dependent repressor [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-19   70.3   3.0    3.7e-19   68.6   1.9    2.1  3  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    7.8e-19   67.6   0.0    2.2e-18   66.2   0.1    1.7  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    1.2e-07   31.5   0.0    1.7e-06   27.9   0.0    2.1  2  MarR            MarR family
    2.7e-06   26.9   0.0    5.6e-06   25.8   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.4e-05   24.9   0.0    2.7e-05   24.0   0.0    1.5  1  MarR_2          MarR family
    0.00015   21.4   0.0    0.00025   20.6   0.0    1.4  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
    0.00015   21.5   0.0    0.00024   20.8   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
     0.0013   18.6   0.0     0.0026   17.7   0.0    1.5  1  HTH_11          HTH domain
     0.0014   19.0   0.0     0.0026   18.1   0.0    1.5  1  Rrf2            Transcriptional regulator
      0.005   16.8   0.0      0.011   15.7   0.0    1.6  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0056   16.6   0.1      0.016   15.1   0.1    1.8  1  HTH_12          Ribonuclease R winged-helix domain
     0.0068   16.9   0.0      0.015   15.8   0.0    1.6  1  HTH_27          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.016   15.4   0.1    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.017   15.0   0.0      0.039   13.8   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
      0.026   14.7   0.3       0.51   10.6   0.0    2.9  4  HTH_17          Helix-turn-helix domain
      0.043   13.7   0.1      0.086   12.7   0.1    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.07   13.1   0.0       0.12   12.3   0.0    1.4  1  HTH_37          Helix-turn-helix domain
      0.085   12.8   0.3       0.18   11.7   0.1    1.7  2  CtsR            CtsR N-terminal HTH domain
        0.1   12.4   0.0       0.22   11.3   0.0    1.5  1  LexA_DNA_bind   LexA DNA binding domain
       0.11   12.8   1.0       0.35   11.2   0.1    2.2  3  TFIIE_beta      TFIIE beta subunit core domain


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.5   2.3e+03      45      62 ..       2      19 ..       1      25 [. 0.60
   2 ?   -0.4   0.0       1.4   1.2e+03      22      40 ..      28      46 ..      10      49 .. 0.69
   3 !   68.6   1.9   4.1e-22   3.7e-19       1      60 [.      63     122 ..      63     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.5
                                  -HHHHHHHHHHCT-.SB- CS
                 Fe_dep_repr_C 45 seelierldellgfpeec 62
                                  s+ +++ l+++  f++e+
  gi|15668748|ref|NP_247547.1|  2 SQSIEDYLERIYLFIKEN 19
                                  555666666666665554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                                  HHHHCT--CCCHHHHCCCC CS
                 Fe_dep_repr_C 22 LvdvlgvdweeaheeAerl 40
                                  L++ l+++++ + + A++l
  gi|15668748|ref|NP_247547.1| 28 LAKLLNIKPSAVTNMAKKL 46
                                  7788888888888888776 PP

  == domain 3  score: 68.6 bits;  conditional E-value: 4.1e-22
                                   -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.S CS
                 Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpe 60 
                                   TekG e+Ak+++++h++++ fLv++lg+d++ a eeA++lEhals+e++erl  ++++++
  gi|15668748|ref|NP_247547.1|  63 TEKGIEEAKKILDKHKTIKIFLVEFLGLDEKTASEEACKLEHALSDEILERLKIFMEKFK 122
                                   9*******************************************************9887 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.1   2.5e-21   2.2e-18       3      59 ..       2      59 ..       1      60 [. 0.95
   2 ?   -1.6   0.0       3.6   3.2e+03      29      47 ..      85     103 ..      75     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 2.5e-21
                                  -HHHHHHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE CS
                Fe_dep_repress  3 vestEdYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykg 59
                                  ++s+EdYLe IY   + ++ ++kt++la+ Ln++ps V+ m kkL++ Gyv+ye+y g
  gi|15668748|ref|NP_247547.1|  2 SQSIEDYLERIYLFIKeNNRPIKTTELAKLLNIKPSAVTNMAKKLHRLGYVNYEPYIG 59
                                  789*********9988799*************************************87 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.6
                                   HHHHTS-HHHHHHHHHHHH CS
                Fe_dep_repress  29 aerLnvspssVsemlkkLe 47 
                                    e+L+    ++se   kLe
  gi|15668748|ref|NP_247547.1|  85 VEFLGLDEKTASEEACKLE 103
                                   5788888889998877776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.9e-09   1.7e-06      13      48 ..      18      53 ..      13      56 .. 0.90
   2 ?    1.5   0.0      0.33   2.9e+02      22      43 ..      83     104 ..      73     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.9e-09
                                  HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR 13 yeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                  +++ p++ +eLak l++++s+vt+++++L + G+++
  gi|15668748|ref|NP_247547.1| 18 ENNRPIKTTELAKLLNIKPSAVTNMAKKLHRLGYVN 53
                                  68899**************************99996 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.33
                                   HHHHHHTS-HHHHHHHHHHHHH CS
                          MarR  22 eLakklgvskstvtrvldrLek 43 
                                    L ++lg++  t+++ + +Le+
  gi|15668748|ref|NP_247547.1|  83 FLVEFLGLDEKTASEEACKLEH 104
                                   7999********9998888886 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   6.2e-09   5.6e-06       6      47 ..      10      52 ..       5      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 6.2e-09
                        HTH_24  6 rkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   +I+  +++n r i  +eLA+ l++ ps+v+   k+L + G++
  gi|15668748|ref|NP_247547.1| 10 ERIYLFIKENNRpIKTTELAKLLNIKPSAVTNMAKKLHRLGYV 52
                                  6899*****9999*****************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0     3e-08   2.7e-05      16      55 ..      18      56 ..      11      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3e-08
                                  CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2 16 rrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                   + ++ +  +ela+ l++++sav+++ k+L + G+v ++p
  gi|15668748|ref|NP_247547.1| 18 ENNRP-IKTTELAKLLNIKPSAVTNMAKKLHRLGYVNYEP 56
                                  55544.7899**************************9876 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.8e-07   0.00025       8      55 ..       7      54 ..       1      59 [. 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.8e-07
                  HrcA_DNA-bdg  8 eilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLveg 55
                                  + l+ +    ++++r++K++e+A++l+ ++  v N+ + L+ lg v+ 
  gi|15668748|ref|NP_247547.1|  7 DYLERIYLFIKENNRPIKTTELAKLLNIKPSAVTNMAKKLHRLGYVNY 54
                                  5555555556778*******************************9975 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.7e-07   0.00024      12      51 ..      16      55 ..      12      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.7e-07
                                  -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                  + e +++ + +elA+ + + +S+v ++ + L++lGyv ++
  gi|15668748|ref|NP_247547.1| 16 IKENNRPIKTTELAKLLNIKPSAVTNMAKKLHRLGYVNYE 55
                                  6789999******************************876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.9e-06    0.0026       3      44 ..      10      51 ..       9      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.9e-06
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                  + i+ +++e++ pi   eLA+ Ln+  ++v +  k+L  lg+
  gi|15668748|ref|NP_247547.1| 10 ERIYLFIKENNRPIKTTELAKLLNIKPSAVTNMAKKLHRLGY 51
                                  689999*********************************994 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.9e-06    0.0026      15      56 ..      12      53 ..       8      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.9e-06
                                  HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                  +yL  +e+++p++++e+a+  ni+ps +  + +kL + g+v+
  gi|15668748|ref|NP_247547.1| 12 IYLFIKENNRPIKTTELAKLLNIKPSAVTNMAKKLHRLGYVN 53
                                  5777889999******************************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-05     0.011      20      57 ..      21      58 ..       7      65 .. 0.83
   2 ?   -3.1   0.0       9.1   8.2e+03      29      46 ..      86     103 ..      84     105 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                                  EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET.EEE CS
                     HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrg.rri 57
                                   p+  +elA +l++ ++ v+ + ++L r g++  + + i
  gi|15668748|ref|NP_247547.1| 21 RPIKTTELAKLLNIKPSAVTNMAKKLHRLGYVNYEpY-I 58
                                  489999*************************995423.3 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.1
                                   HHTTSSHHHHHHHHHHHH CS
                     HTH_Crp_2  29 smlGltretvsrilseLk 46 
                                   ++lGl   t s +  +L+
  gi|15668748|ref|NP_247547.1|  86 EFLGLDEKTASEEACKLE 103
                                   577888788777766665 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.8e-05     0.016       3      65 ..      12      69 ..      10      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                        HTH_12  3 ILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGlee 65
                                  I   ++e+++pi   e+a+ L+     i+  av    +kl + g+++   y g +ltEkG+ee
  gi|15668748|ref|NP_247547.1| 12 IYLFIKENNRPIKTTELAKLLN-----IKPSAVTNMAKKLHRLGYVNYEPYIGITLTEKGIEE 69
                                  556799***************7.....5556677778***********************997 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.7e-05     0.015      12      50 ..      16      54 ..       8      66 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                        HTH_27 12 irhrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                  i++++r+ k ++l++ ln+  s++ ++ kkL++ G+v  
  gi|15668748|ref|NP_247547.1| 16 IKENNRPIKTTELAKLLNIKPSAVTNMAKKLHRLGYVNY 54
                                  3346777777***************************43 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1   1.8e-05     0.016      21      55 ..      25      70 ..      23      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                B-block_TFIIIC 21 qsdLakeskqdprslfyrlksLekkgLIvkqsii...........d 55
                                  +++Lak+++++p+ ++   k+L + g++   ++i            
  gi|15668748|ref|NP_247547.1| 25 TTELAKLLNIKPSAVTNMAKKLHRLGYVNYEPYIgitltekgieeA 70
                                  789*************************999988776666655542 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.4e-05     0.039      14      47 .]      21      54 ..      12      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-05
                                  SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5 14 gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  ++ + +ela+ l++ +s+v    kkL+ +G+V++
  gi|15668748|ref|NP_247547.1| 21 RPIKTTELAKLLNIKPSAVTNMAKKLHRLGYVNY 54
                                  77889***************************96 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.1   3.7e+03      42      49 ..       4      11 ..       3      12 .. 0.86
   2 ?   10.6   0.0   0.00057      0.51       3      23 ..      24      44 ..      23      52 .. 0.90
   3 ?   -2.3   0.0         6   5.4e+03       4      15 ..      67      78 ..      66      79 .. 0.77
   4 ?    0.0   0.0       1.1   9.8e+02       9      19 ..      86      96 ..      84     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.1
                        HTH_17 42 dleewlek 49
                                  ++e++le+
  gi|15668748|ref|NP_247547.1|  4 SIEDYLER 11
                                  89****97 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00057
                        HTH_17  3 tveEaAelLgvsrstvyrlir 23
                                  ++ E+A+lL++++s v ++++
  gi|15668748|ref|NP_247547.1| 24 KTTELAKLLNIKPSAVTNMAK 44
                                  689***************996 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6
                        HTH_17  4 veEaAelLgvsr 15
                                  +eEa ++L+ ++
  gi|15668748|ref|NP_247547.1| 67 IEEAKKILDKHK 78
                                  799999998665 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 1.1
                        HTH_17  9 elLgvsrstvy 19
                                  e+Lg+ ++t+ 
  gi|15668748|ref|NP_247547.1| 86 EFLGLDEKTAS 96
                                  78999999986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   9.6e-05     0.086      19      55 ..      19      55 ..       5      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.6e-05
                                  HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                          TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                  ++ p +++e+a+ l++  s v ++ ++L + G+V+ e
  gi|15668748|ref|NP_247547.1| 19 NNRPIKTTELAKLLNIKPSAVTNMAKKLHRLGYVNYE 55
                                  678999****************************876 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.12      29      57 ..      20      47 ..       7      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                  HCT--HHHHHHHHT--HHHHHHHHTT--T CS
                        HTH_37 29 krelsqseaaqllgiaqPkvsrllrgkls 57
                                   r ++++e+a+ll+i+ + v+++ + kl 
  gi|15668748|ref|NP_247547.1| 20 NRPIKTTELAKLLNIKPSAVTNMAK-KLH 47
                                  467899*****************97.665 PP

>> CtsR  CtsR N-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00021      0.18       2      41 ..       1      40 [.       1      47 [. 0.91
   2 ?   -2.8   0.0       6.8   6.1e+03       2      16 ..     106     120 ..     105     124 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                          CtsR  2 lsdlieeyikelleeseeeeveikRnelaekfecvPsQin 41
                                  +s++ie+y++++    +e++  ik +ela+ +++ Ps ++
  gi|15668748|ref|NP_247547.1|  1 MSQSIEDYLERIYLFIKENNRPIKTTELAKLLNIKPSAVT 40
                                  7999*******9988888999****************875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.8
                          CtsR   2 lsdlieeyikellee 16 
                                   lsd i e +k  +e+
  gi|15668748|ref|NP_247547.1| 106 LSDEILERLKIFMEK 120
                                   788888888877765 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.22      12      60 ..       9      56 ..       3      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                  HHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GG CS
                 LexA_DNA_bind 12 ldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyierdp 60
                                  l+ i  +i+e+  p    e+a+ l++k psav +  k+L+r Gy++ +p
  gi|15668748|ref|NP_247547.1|  9 LERIYLFIKENNRPIKTTELAKLLNIK-PSAVTNMAKKLHRLGYVNYEP 56
                                  566777899999999999*********.*****************9876 PP

>> TFIIE_beta  TFIIE beta subunit core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00039      0.35       6      47 ..      10      48 ..       5      59 .. 0.70
   2 ?   -2.0   0.0       5.2   4.6e+03      39      51 ..      68      80 ..      55      86 .. 0.65
   3 ?   -1.0   0.0       2.5   2.3e+03      22      30 ..     108     116 ..     100     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                    TFIIE_beta  6 akiveylKkkdgplsleeIlsylslqldlsdknwllleaLkn 47
                                   +i  ++K++++p++  e+++ l++  +  +   ++++ L  
  gi|15668748|ref|NP_247547.1| 10 ERIYLFIKENNRPIKTTELAKLLNI--KP-SAVTNMAKKLHR 48
                                  567789******************9..32.322334444444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.2
                    TFIIE_beta 39 wllleaLknnpki 51
                                  ++  ++L +++ i
  gi|15668748|ref|NP_247547.1| 68 EEAKKILDKHKTI 80
                                  4556677777655 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.5
                    TFIIE_beta  22 eeIlsylsl 30 
                                   +eIl++l++
  gi|15668748|ref|NP_247547.1| 108 DEILERLKI 116
                                   899999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 973.10
//
Query:       gi|15668749|ref|NP_247548.1|  [L=292]
Description: porphobilinogen deaminase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-67  227.6   0.0    1.3e-67  227.3   0.0    1.1  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    1.1e-21   76.9   0.4    2.5e-21   75.8   0.4    1.6  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.3   0.0   1.4e-71   1.3e-67       1     203 [.       2     204 ..       2     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: 227.3 bits;  conditional E-value: 1.4e-71
                Porphobil_deam   1 irigtRkSkLAlaqaelvaeaLke.eeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKDlpte 80 
                                   irigtR+SkLAl qa+ vae Lk+   +vei++ikt+GD++ldk+L++i g g+Ftkel+ a+l++eid+aVhSlKD+pt 
  gi|15668749|ref|NP_247548.1|   2 IRIGTRGSKLALYQANKVAELLKNlGYKVEIKIIKTTGDRVLDKKLSDI-GIGVFTKELDLAMLNNEIDIAVHSLKDIPTI 81 
                                   89********************7667779********************.69***************************** PP

                Porphobil_deam  81 lpeglelaavlkredprDvlvvksslee.lpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldegeydaiiLA 160
                                    +e+l+++avl+r++ +D+l+++++++   ++++v+gTsS+RR+a lk ++p+++++ lRGnvdtRlrkl+eg ydai+L+
  gi|15668749|ref|NP_247548.1|  82 WNENLMVGAVLERDSYHDLLIWNKDIDFnEDSKIVIGTSSMRRRAFLKFIYPNAKFELLRGNVDTRLRKLKEGLYDAIVLS 162
                                   *********************9775543145689*********************************************** PP

                Porphobil_deam 161 aAGLkRlgleerisevlspeellpavgQGalavevrkedeell 203
                                   +AG+ Rlg++ +  +  +  ++lpa++QG++av ++++dee++
  gi|15668749|ref|NP_247548.1| 163 EAGIIRLGVSLEDFN-YKRLDILPAPAQGIIAVACKRDDEEMK 204
                                   ********6554433.455689*****************9986 PP

>> Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.4   2.7e-25   2.5e-21       2      75 .]     217     292 .]     216     292 .] 0.96

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 2.7e-25
                                   HHHHHHHHHHHHTT--TTSSEEEEEEEE.TTE.EEEEEEEE-TTS..S-EEEEEEEE.-GGGHHHHHHHHHHHHHH CS
               Porphobil_deamC   2 levlaERallkeLeGGCsvPiGvyaeve.aneelkLkglvlsldglksaveeaeakg.eleeaeelGkklaeella 75 
                                   le l+ER+ l+e++GGCsvP+G+ a+++ +ne lkLk++v+++d+lk+a  e+++k+ e+++a+elGkk++ +l++
  gi|15668749|ref|NP_247548.1| 217 LESLCERTALNEFGGGCSVPFGALAVYDeKNELLKLKAAVVTNDELKNASGEVKCKIdEIDKAVELGKKIGLKLKN 292
                                   7899************************8888*************************99**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1926.77
//
Query:       gi|15668750|ref|NP_247549.1|  [L=223]
Description: hypothetical protein MJ_0570 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.2e-111  370.6   3.2   2.4e-111  370.5   3.2    1.0  1  Diphthami_syn_2  Diphthamide synthase
     0.0067   15.9   0.0       0.02   14.4   0.0    1.8  2  QueC             Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.019   13.8   0.0      0.027   13.3   0.0    1.4  1  tRNA_Me_trans    tRNA methyl transferase
      0.029   14.9   0.0      0.083   13.4   0.0    1.7  1  DUF1878          Protein of unknown function (DUF1878)
      0.089   12.4   0.0        0.2   11.2   0.0    1.6  1  ThiI             Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.5   3.2  6.8e-115  2.4e-111       1     218 [.       1     218 [.       1     219 [. 0.99

  Alignments for each domain:
  == domain 1  score: 370.5 bits;  conditional E-value: 6.8e-115
               Diphthami_syn_2   1 mkvavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLkgt 80 
                                   mkvavlysGGkDs++aLy+alke ++v++Lv+v+senkesymfh++nvhl+el+ae+vGiplikl+t+Ge+ekevedLk+ 
  gi|15668750|ref|NP_247549.1|   1 MKVAVLYSGGKDSNYALYWALKEgFDVKYLVNVESENKESYMFHIPNVHLTELSAEAVGIPLIKLYTKGEKEKEVEDLKKG 81 
                                   9******************************************************************************** PP

               Diphthami_syn_2  81 lkkldveavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGrridkkli 161
                                   l+kldve++v+Ga++s+yqksri+rvC+elGlks+aPLW+kdp e+++++v+e f+v++v+v+a+gl++++LG+ri+k++i
  gi|15668750|ref|NP_247549.1|  82 LEKLDVEGIVTGAVASIYQKSRIDRVCEELGLKSFAPLWHKDP-EWILRTVSELFNVRIVGVYAYGLGKEWLGKRITKENI 161
                                   *******************************************.************************************* PP

               Diphthami_syn_2 162 delkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyldierak 218
                                   d+l +++ekygi+ka+egGeaet+v+DaP+fkkr+ev+e+e++w+e++g+++i++ak
  gi|15668750|ref|NP_247549.1| 162 DKLLNICEKYGIHKAFEGGEAETFVFDAPMFKKRIEVVEAEIEWHETWGIYHIKKAK 218
                                   *******************************************************97 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.7e-06      0.02       2      29 ..       3      30 ..       2      56 .. 0.85
   2 ?   -2.4   0.0      0.77   2.7e+03     145     159 ..     178     192 ..     155     217 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.7e-06
                                  EEEE--SSHHHHHHHHHHHHH-SEEEEE CS
                          QueC  2 avvllSGGlDSttvlalakkegkeveal 29
                                  + vl SGG DS  +l++a+keg  v+ l
  gi|15668750|ref|NP_247549.1|  3 VAVLYSGGKDSNYALYWALKEGFDVKYL 30
                                  56999*****************999765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.77
                                   HHHHTS--EEE-TTT CS
                          QueC 145 nlgedkkieieaPli 159
                                   + ge++++   aP+ 
  gi|15668750|ref|NP_247549.1| 178 EGGEAETFVFDAPMF 192
                                   444555555555543 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.5e-06     0.027       1      72 [.       1      69 [.       1     104 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.5e-06
                 tRNA_Me_trans  1 kkvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfek 72
                                  +kv+v+ SgG DS +a++   ++g++v+  +l ++e+e++e+    +  +++  e  ae +gipl ++ ++ 
  gi|15668750|ref|NP_247549.1|  1 MKVAVLYSGGKDSNYALYWALKEGFDVK--YLVNVESENKES-YMFHIPNVHLTELSAEAVGIPLIKLYTKG 69
                                  69*************************8..667777766666.77888888888889999999988876655 PP

>> DUF1878  Protein of unknown function (DUF1878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.3e-05     0.083      36      88 ..     154     208 ..     149     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.3e-05
                                   TT--HHHHHHHHHHHHH..HHHHHHHHHHTT----HHHHHHHHHHS-TTS-HHHH CS
                       DUF1878  36 kklskeeveeilklCek..LseeleeqkaegfvlFdkllakFakkLhekLeveet 88 
                                   k+++ke+++++l++Cek  + + +e   ae fv+  ++++k  + ++ ++e +et
  gi|15668750|ref|NP_247549.1| 154 KRITKENIDKLLNICEKygIHKAFEGGEAETFVFDAPMFKKRIEVVEAEIEWHET 208
                                   789*************94457999*****************99999999999988 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.5e-05       0.2       5      34 ..       2      31 ..       1      53 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.5e-05
                          ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvh 34
                                  kv +L SgG DS  a y +lk G+ v+++ 
  gi|15668750|ref|NP_247549.1|  2 KVAVLYSGGKDSNYALYWALKEGFDVKYLV 31
                                  678899********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1446.50
//
Query:       gi|15668751|ref|NP_247550.1|  [L=473]
Description: aspartate kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-56  191.3   0.3      2e-56  191.3   0.3    1.6  2  AA_kinase        Amino acid kinase family
    5.7e-20   70.9   2.0    8.6e-11   41.5   0.3    2.9  2  ACT_7            ACT domain
    7.2e-20   70.5   4.0    7.8e-10   38.4   0.1    3.2  3  ACT              ACT domain
  ------ inclusion threshold ------
      0.039   14.4   0.3      0.097   13.2   0.3    1.5  1  AAA_23           AAA domain
        1.5    9.1   5.6        0.8   10.0   1.1    2.8  2  Antimicrobial_8  Uperin family
          2    8.1   7.8         11    5.7   0.1    3.0  3  DUF1131          Protein of unknown function (DUF1131)


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.3   0.3   6.8e-60     2e-56       1     241 []       1     287 [.       1     287 [. 0.92
   2 ?   -1.9   0.1      0.66     2e+03      39      39 ..     351     351 ..     295     445 .. 0.60

  Alignments for each domain:
  == domain 1  score: 191.3 bits;  conditional E-value: 6.8e-60
                                   TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHH.TCCCCCHHHC................ CS
                     AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllal.ksglssgelaa............... 64 
                                   +++V+K+GG+s++++e+  +r++a+++ + k+++ ++vvV+++ + +t++l+++ ++ l+ + +a+               
  gi|15668751|ref|NP_247550.1|   1 MTTVMKFGGTSVGSGER--IRHVAKIVTKRKKEDDDVVVVVSAmSEVTNALVEIsQQALDVRDIAKvgdfikfirekhyka 79 
                                   789**************..************************99*********988899998887777777766555544 PP

                                   ........E..HHHHHHHHH....................................HHHHHHHHHHHHHHHHTTHGEEEE- CS
                     AA_kinase  65 .....glrstleeagevatr....................................dalaslgerlvaallaaglpavgls 104
                                        +             +                                    d+++s+gerl++ +l+ ++++ g +
  gi|15668751|ref|NP_247550.1|  80 ieeaiK-------------SeeikeevkkiidsrieelekvligvaylgeltpksrDYILSFGERLSSPILSGAIRDLGEK 147
                                   433332.............14445555666777999********************************************* PP

                                   GGGTCEECCCE......HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHCTSSEEEE CS
                     AA_kinase 105 aaaldateagr....degsdgnvesvdaeaieelleagvvpvltgfigldeege...lgrgssDtiaallAealgAdklii 178
                                   + al   eag+    ++gs+++ +   +e +  ll++g++pv+tgfig +eeg    lgrg+sD++aal+++ l+Ad ++i
  gi|15668751|ref|NP_247550.1| 148 SIALEGGEAGIitdnNFGSARVKRLEVKERLLPLLKEGIIPVVTGFIGTTEEGYittLGRGGSDYSAALIGYGLDADIIEI 228
                                   **************999999999999******************************************************* PP

                                   EESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
                     AA_kinase 179 ltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvItn 241
                                   +tdV+GVy+ dp+ vp+ar++p++s+ ea+e    la++G+kv+hp+++++a+++gip+ ++n
  gi|15668751|ref|NP_247550.1| 229 WTDVSGVYTTDPRLVPTARRIPKLSYIEAME----LAYFGAKVLHPRTIEPAMEKGIPILVKN 287
                                   *******************************....*************************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.66
                                   E CS
                     AA_kinase  39 v 39 
                                   +
  gi|15668751|ref|NP_247550.1| 351 L 351
                                   2 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.3   2.9e-14   8.6e-11       3      64 ..     315     378 ..     313     379 .. 0.95
   2 !   28.1   0.1   4.4e-10   1.3e-06       2      65 .]     400     465 ..     399     465 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.9e-14
                                   EEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHH CS
                         ACT_7   3 edgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLh 64 
                                    ++++ +++ g+g+ + v+G +a+++++L e+ +++  iS   +++ ++++V eed++kA++aL+
  gi|15668751|ref|NP_247550.1| 315 IKNVALINIFGAGMVG-VSGTAARIFKALGEEEVNVILISqgsSETNISLVVSEEDVDKALKALK 378
                                   578999********88.***********************************************7 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 4.4e-10
                                   EEEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHHH CS
                         ACT_7   2 sedgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLhe 65 
                                   +++++ ++svvg+g+++ + Gi+ k++++ +e g +i +i+   ++  ++++++e+dl + v+ Lhe
  gi|15668751|ref|NP_247550.1| 400 VDKDVCVISVVGAGMRG-AKGIAGKIFTAVSESGANIKMIAqgsSEVNISFVIDEKDLLNCVRKLHE 465
                                   678999***********.**********************9999****************9999996 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.67     2e+03      45      64 ..      67      86 ..      42      89 .. 0.73
   2 !   38.4   0.1   2.6e-13   7.8e-10       6      66 ..     327     381 ..     322     382 .. 0.93
   3 !   32.0   0.0   2.5e-11   7.4e-08       3      63 ..     410     464 ..     408     467 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.67
                                  EEEEEEEHHHHHHHHHHHHT CS
                           ACT 45 fvvivvdeedleevlealkk 64
                                  +++  + e++ ++++ea+k+
  gi|15668751|ref|NP_247550.1| 67 DFIKFIREKHYKAIEEAIKS 86
                                  56666778899999999987 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 2.6e-13
                                   EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                           ACT   6 gvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                   g+ ++ G++ar+f al++  +N++ i+q+ss      ++++ +vv+eed++++l+alk+ +
  gi|15668751|ref|NP_247550.1| 327 GMVGVSGTAARIFKALGEEEVNVILISQGSS------ETNISLVVSEEDVDKALKALKREF 381
                                   677899*************************......99******************9865 PP

  == domain 3  score: 32.0 bits;  conditional E-value: 2.5e-11
                                   EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHH CS
                           ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealk 63 
                                   +  g+++ +G+++++f+a+++ g Ni +i q+ss      +v++ +v+de+dl + +++l+
  gi|15668751|ref|NP_247550.1| 410 VGAGMRGAKGIAGKIFTAVSESGANIKMIAQGSS------EVNISFVIDEKDLLNCVRKLH 464
                                   66789999**************************......889999999998877666665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   3.2e-05     0.097      92     181 ..      17     106 ..       8     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-05
                        AAA_23  92 rerelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkkerleelekeleeledekkll 172
                                   r r+++k  +k++k+++   + +++  + ++ l++++++ l++ ++ + ++f +f +++  +++ee++k+ e +e++kk +
  gi|15668751|ref|NP_247550.1|  17 RIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVRDIAKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKII 97 
                                   556777777777788888888889********************************************************* PP

                        AAA_23 173 ekleqekek 181
                                   + +++e+ek
  gi|15668751|ref|NP_247550.1|  98 DSRIEELEK 106
                                   *99988775 PP

>> Antimicrobial_8  Uperin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.63   1.9e+03       2       7 ..      65      70 ..      65      72 .. 0.88
   2 ?   10.0   1.1   0.00027       0.8       4      17 .]     306     319 ..     305     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.63
               Antimicrobial_8  2 VGDliR 7 
                                  VGD+i+
  gi|15668751|ref|NP_247550.1| 65 VGDFIK 70
                                  9***96 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00027
               Antimicrobial_8   4 DliRKiVsaIKNVV 17 
                                   D i K++s+IKNV+
  gi|15668751|ref|NP_247550.1| 306 DSIVKAISTIKNVA 319
                                   5678*********7 PP

>> DUF1131  Protein of unknown function (DUF1131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.7     0.009        27      64     124 ..      28      88 ..      11     106 .. 0.79
   2 ?    5.7   0.1    0.0037        11      50     112 ..     326     388 ..     298     409 .. 0.73
   3 ?    1.0   0.1       0.1   3.1e+02      50      88 ..     412     450 ..     390     467 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.009
                       DUF1131  64 qalkddkvklvisGqekgkveridvldkeiktewgvkiGtpfsdlyskafgaCkkgsedde 124
                                   +  +dd+v +v+s  ++ + + +++++++++  + +k+G+  + + +k ++a +++ +++e
  gi|15668751|ref|NP_247550.1|  28 RKKEDDDVVVVVSAMSEVTNALVEISQQALDVRDIAKVGDFIKFIREKHYKAIEEAIKSEE 88 
                                   4567899*******9************************9988777777777776655443 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0037
                       DUF1131  50 sGmetenGkivsifqalkddkvklvi..sGqekgkveridvldkeiktewgvkiGtpfsdlyska 112
                                    Gm    G+  +if+al +++v++ +  +G+++++++ + v++++++ +    +  +f d  +k+
  gi|15668751|ref|NP_247550.1| 326 AGMVGVSGTAARIFKALGEEEVNVILisQGSSETNIS-LVVSEEDVDKAL-KALKREFGDFGKKS 388
                                   6999999**************9988722455555555.445666665443.33455565555555 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.1
                       DUF1131  50 sGmetenGkivsifqalkdd..kvklvisGqekgkveridv 88 
                                    Gm+  +G   +if a+++   ++k+  +G+++ +++   v
  gi|15668751|ref|NP_247550.1| 412 AGMRGAKGIAGKIFTAVSESgaNIKMIAQGSSEVNIS--FV 450
                                   6999999999999999988611555555665544443..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1101  (0.0614089); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3052.46
//
Query:       gi|15668752|ref|NP_247551.1|  [L=86]
Description: hypothetical protein MJ_0572 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-17   61.1   5.9    4.4e-08   32.6   1.3    2.6  3  TPR_1       Tetratricopeptide repeat
    2.7e-14   52.1   1.0    7.1e-07   29.0   0.3    2.2  2  TPR_8       Tetratricopeptide repeat
    1.2e-13   50.0   5.7      2e-06   27.5   0.7    2.7  3  TPR_2       Tetratricopeptide repeat
    6.3e-09   36.3   0.3    8.6e-09   35.9   0.3    1.3  1  TPR_16      Tetratricopeptide repeat
    1.9e-08   33.8   1.2    4.3e-05   23.1   0.1    3.0  3  TPR_11      TPR repeat
    1.9e-07   31.0   0.5    2.5e-06   27.5   0.2    2.2  2  TPR_17      Tetratricopeptide repeat
    9.5e-07   29.0   0.8      0.022   15.0   0.1    2.9  3  TPR_12      Tetratricopeptide repeat
    1.2e-05   25.8   0.2     0.0091   16.7   0.0    2.3  2  TPR_14      Tetratricopeptide repeat
    4.7e-05   23.1   0.7       0.11   12.6   0.1    2.6  3  TPR_7       Tetratricopeptide repeat
    0.00013   22.4   0.0    0.00019   21.9   0.0    1.2  1  TPR_19      Tetratricopeptide repeat
    0.00014   22.3   0.5       0.17   12.6   0.0    2.2  2  TPR_6       Tetratricopeptide repeat
    0.00078   19.5   0.0     0.0011   19.1   0.0    1.1  1  TPR_9       Tetratricopeptide repeat
     0.0015   18.6   0.1     0.0016   18.5   0.1    1.3  1  DUF3856     Domain of Unknown Function (DUF3856)
     0.0024   16.8   0.0     0.0026   16.7   0.0    1.1  1  NARP1       NMDA receptor-regulated protein 1
     0.0027   17.9   0.6        0.8   10.1   0.0    2.8  3  PPR         PPR repeat
     0.0033   18.0   6.9      0.068   13.9   0.0    3.3  4  Sel1        Sel1 repeat
     0.0082   16.3   0.2      0.015   15.5   0.2    1.5  1  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
     0.0097   15.8   0.5        1.1    9.2   0.1    2.6  3  TPR_10      Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.011   15.8   3.4       0.23   11.6   1.4    2.7  2  MIT         MIT (microtubule interacting and transport) domai
       0.04   13.7   0.4       0.12   12.2   0.2    1.7  2  DUF5113     Domain of unknown function (DUF5113)
        0.1   12.6   1.8          4    7.5   0.2    2.9  3  Ubiq-assoc  Ubiquitin-associated
       0.12   13.0   0.2       0.31   11.8   0.1    1.7  1  TPR_4       Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.018        14      16      29 ..       4      17 ..       3      18 .. 0.86
   2 !   32.6   1.3   5.4e-11   4.4e-08       1      33 [.       8      40 ..       8      41 .. 0.95
   3 !   30.2   0.1   3.2e-10   2.6e-07       2      31 ..      43      72 ..      43      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.018
                                  -HHHHHHHHHHHHH CS
                         TPR_1 16 kydeAleyyekALe 29
                                  + ++A+ yy+k +e
  gi|15668752|ref|NP_247551.1|  4 NIKKAEYYYKKGVE 17
                                  789********887 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 5.4e-11
                                  HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPn 33
                                  a+ +y +G+   ++g+ ++Aley++kA+elnP 
  gi|15668752|ref|NP_247551.1|  8 AEYYYKKGVEVGNKGDVEKALEYFNKAIELNPF 40
                                  789*****************************6 PP

  == domain 3  score: 30.2 bits;  conditional E-value: 3.2e-10
                                  HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                         TPR_1  2 kalynlGnayfklgkydeAleyyekALeln 31
                                  +a++n+++a++ lg+y+eA e++ + L ++
  gi|15668752|ref|NP_247551.1| 43 DAWFNKALALRILGRYEEARECFFRGLAVE 72
                                  69***********************99875 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.3   8.7e-10   7.1e-07       1      33 [.       8      40 ..       8      41 .. 0.96
   2 !   21.9   0.0   1.6e-07   0.00013       2      24 ..      43      65 ..      43      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 8.7e-10
                                  CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33
                                  ae+yy++g    ++gd e+A ey++ka+el+p 
  gi|15668752|ref|NP_247551.1|  8 AEYYYKKGVEVGNKGDVEKALEYFNKAIELNPF 40
                                  799****************************96 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.6e-07
                                  CHHHHHHHHHHHTT-HHHHHHHH CS
                         TPR_8  2 eayynlgsiylklgdyeeAkeyy 24
                                  +a++n++++++ lg+yeeA e++
  gi|15668752|ref|NP_247551.1| 43 DAWFNKALALRILGRYEEARECF 65
                                  59********************8 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.11        87      16      29 ..       4      17 ..       2      19 .. 0.81
   2 !   27.5   0.7   2.5e-09     2e-06       1      32 [.       8      39 ..       8      41 .. 0.95
   3 !   24.3   0.3   2.4e-08     2e-05       2      24 ..      43      65 ..      42      73 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.11
                         TPR_2 16 dyeeAleafekAle 29
                                  + ++A+ +++k +e
  gi|15668752|ref|NP_247551.1|  4 NIKKAEYYYKKGVE 17
                                  77899999999765 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 2.5e-09
                         TPR_2  1 aealynlGlayyklgdyeeAleafekAleldP 32
                                  ae++y  G    ++gd e+Ale+f+kA+el+P
  gi|15668752|ref|NP_247551.1|  8 AEYYYKKGVEVGNKGDVEKALEYFNKAIELNP 39
                                  799****************************9 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 2.4e-08
                         TPR_2  2 ealynlGlayyklgdyeeAleaf 24
                                  +a++n +la++ lg+yeeA+e+f
  gi|15668752|ref|NP_247551.1| 43 DAWFNKALALRILGRYEEARECF 65
                                  69********************9 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.3   1.1e-11   8.6e-09       9      55 ..      20      64 ..       6      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.1e-11
                        TPR_16  9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.a 55
                                  + gd ++A+++++ a++++   P+ ++A++++++a+  +gr++eA+  
  gi|15668752|ref|NP_247551.1| 20 NKGDVEKALEYFNKAIELN---PFYRDAWFNKALALRILGRYEEAReC 64
                                  679****************...***********************944 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.47   3.8e+02      27      35 ..       7      15 ..       5      16 .. 0.77
   2 !   23.1   0.1   5.3e-08   4.3e-05       7      38 ..      21      52 ..      20      53 .. 0.95
   3 !    9.3   0.0    0.0011      0.91       3      17 ..      51      65 ..      49      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.47
                        TPR_11 27 naeayynLG 35
                                   ae yy+ G
  gi|15668752|ref|NP_247551.1|  7 KAEYYYKKG 15
                                  588899877 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 5.3e-08
                        TPR_11  7 qGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                                  +G+ e+A+e ++kA++l+P + +a++n +la+
  gi|15668752|ref|NP_247551.1| 21 KGDVEKALEYFNKAIELNPFYRDAWFNKALAL 52
                                  7**************************99985 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0011
                        TPR_11  3 ayyeqGkyeeAieaY 17
                                  a++ +G+yeeA e++
  gi|15668752|ref|NP_247551.1| 51 ALRILGRYEEARECF 65
                                  8999********997 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.48   3.9e+02      19      33 ..       7      28 ..       4      29 .. 0.67
   2 !   27.5   0.2     3e-09   2.5e-06       1      34 []      30      63 ..      30      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.48
                        TPR_17 19 LAelll.......knGdlmtAr 33
                                  +Ae+++       ++Gd ++A+
  gi|15668752|ref|NP_247551.1|  7 KAEYYYkkgvevgNKGDVEKAL 28
                                  5666665666666778888776 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 3e-09
                        TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtArq 34
                                  ++ ka+el+P + da++n+A +l+ +G++++Ar+
  gi|15668752|ref|NP_247551.1| 30 YFNKAIELNPFYRDAWFNKALALRILGRYEEARE 63
                                  589*****************************96 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.26   2.1e+02      60      73 ..       4      17 ..       1      21 [. 0.79
   2 !    9.4   0.0    0.0015       1.2      17      32 ..      22      37 ..      19      39 .. 0.72
   3 !   15.0   0.1   2.7e-05     0.022       5      26 ..      44      65 ..      40      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.26
                        TPR_12 60 ryeeAlelleeala 73
                                  + ++A++++++ ++
  gi|15668752|ref|NP_247551.1|  4 NIKKAEYYYKKGVE 17
                                  67899999999877 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0015
                        TPR_12 17 grydeAlellekalei 32
                                  g+ ++Ale+++ka+e+
  gi|15668752|ref|NP_247551.1| 22 GDVEKALEYFNKAIEL 37
                                  7777777777777775 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2.7e-05
                        TPR_12  5 alnnlaavlrrlgrydeAlell 26
                                  a+ n a++lr lgry+eA+e++
  gi|15668752|ref|NP_247551.1| 44 AWFNKALALRILGRYEEARECF 65
                                  6669999999999999999998 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-05    0.0091      14      42 ..      21      49 ..       8      51 .. 0.90
   2 !   10.7   0.2   0.00099      0.81       2      29 ..      43      70 ..      42      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                        TPR_14 14 lGdpdeAiallrralalaPddaeawllla 42
                                   Gd ++A++++++a++l+P  ++aw+  a
  gi|15668752|ref|NP_247551.1| 21 KGDVEKALEYFNKAIELNPFYRDAWFNKA 49
                                  69*****************9999998776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00099
                        TPR_14  2 eallalaeallalGdpdeAiallrrala 29
                                  +a+   a al+ lG+++eA++++ r la
  gi|15668752|ref|NP_247551.1| 43 DAWFNKALALRILGRYEEARECFFRGLA 70
                                  68888999*************9988877 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       5.7   4.7e+03      16      24 ..       6      14 ..       3      18 .. 0.73
   2 !    8.5   0.0    0.0027       2.2      12      31 ..      21      38 ..      19      41 .. 0.82
   3 !   12.6   0.1   0.00014      0.11       1      30 [.      44      71 ..      44      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.7
                         TPR_7 16 eeAielyeq 24
                                  ++A+ +y++
  gi|15668752|ref|NP_247551.1|  6 KKAEYYYKK 14
                                  677778887 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0027
                         TPR_7 12 lGdyeeAielyeqsLaltkd 31
                                   Gd e+A+e++ +  a++  
  gi|15668752|ref|NP_247551.1| 21 KGDVEKALEYFNK--AIELN 38
                                  69***********..66554 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00014
                         TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltk 30
                                  a++n a + + lG+yeeA e++ +  +l+ 
  gi|15668752|ref|NP_247551.1| 44 AWFNKALALRILGRYEEARECFFR--GLAV 71
                                  57788888888*************..5553 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.3e-07   0.00019       5      48 ..      22      65 ..      20      73 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.3e-07
                        TPR_19  5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealL 48
                                  gd + Al+++ +a++ +p + +a+ + A al  lg+++eA+++ 
  gi|15668752|ref|NP_247551.1| 22 GDVEKALEYFNKAIELNPFYRDAWFNKALALRILGRYEEARECF 65
                                  99***************************************986 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0    0.0002      0.17       7      31 ..       8      39 ..       6      40 .. 0.82
   2 !    8.0   0.1    0.0059       4.8       1      23 [.      43      65 ..      43      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                                  HHHHHH.H......HHHHHHHHHHHHHHHH-T CS
                         TPR_6  7 alsyrk.l......gdtdkAlealerlikeYP 31
                                  a+ y+k +      gd +kAle++++ i+  P
  gi|15668752|ref|NP_247551.1|  8 AEYYYKkGvevgnkGDVEKALEYFNKAIELNP 39
                                  556777458888889*************9887 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0059
                                  HHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6  1 dAlyklalsyrklgdtdkAleal 23
                                  dA ++ al++r lg++++A+e +
  gi|15668752|ref|NP_247551.1| 43 DAWFNKALALRILGRYEEARECF 65
                                  79999999999677*******88 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.3e-06    0.0011       8      58 ..      21      71 ..      20      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
                         TPR_9  8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylal 58
                                  + d e+al++ +  + l+P   + ++  +l+l  lG++++A++++ + la+
  gi|15668752|ref|NP_247551.1| 21 KGDVEKALEYFNKAIELNPFYRDAWFNKALALRILGRYEEARECFFRGLAV 71
                                  5799****************************************9987765 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1     2e-06    0.0016      78     123 ..      24      65 ..       6      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-06
                                   HHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                       DUF3856  78 adkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkaf 123
                                   ++kal+yfn+  el+      W    f++a al  lGr++ea + f
  gi|15668752|ref|NP_247551.1|  24 VEKALEYFNKAIELNPFYRDAW----FNKALALRILGRYEEARECF 65 
                                   79************98766666....99**************9876 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.2e-06    0.0026     205     248 ..      21      64 ..       6      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.2e-06
                                   HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
                         NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaev 248
                                    g++ekAley +kaie +p   + + +Ka  l+  G  ++A e+
  gi|15668752|ref|NP_247551.1|  21 KGDVEKALEYFNKAIELNPFYRDAWFNKALALRILGRYEEAREC 64 
                                   57899*******************************99999875 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       4.5   3.7e+03      15      25 ..       4      14 ..       2      20 .. 0.72
   2 !   10.1   0.0   0.00098       0.8      12      28 ..      20      36 ..      18      38 .. 0.85
   3 ?    5.3   0.1     0.032        26      13      24 ..      55      66 ..      48      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.5
                           PPR 15 kleeAlelfke 25
                                  ++++A+ ++k+
  gi|15668752|ref|NP_247551.1|  4 NIKKAEYYYKK 14
                                  57888888876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00098
                           PPR 12 knGkleeAlelfkeMke 28
                                   +G++e+Ale+f++ +e
  gi|15668752|ref|NP_247551.1| 20 NKGDVEKALEYFNKAIE 36
                                  68***********9776 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.032
                           PPR 13 nGkleeAlelfk 24
                                   G++eeA e+f 
  gi|15668752|ref|NP_247551.1| 55 LGRYEEARECFF 66
                                  69********96 PP

>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2     0.011       9.3      21      34 ..       3      16 ..       1      20 [. 0.81
   2 !   13.9   0.0   8.4e-05     0.068      20      37 ..      21      38 ..      14      39 .. 0.82
   3 ?   -0.3   0.3       2.5     2e+03      29      35 ..      45      51 ..      44      53 .. 0.81
   4 ?   -1.6   0.0       6.4   5.2e+03      26      30 ..      61      65 ..      55      73 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                          Sel1 21 kDpekAiewyekAA 34
                                   +++kA+++y+k  
  gi|15668752|ref|NP_247551.1|  3 ENIKKAEYYYKKGV 16
                                  5899*******975 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.4e-05
                          Sel1 20 pkDpekAiewyekAAeqG 37
                                  + D+ekA+e++ kA e++
  gi|15668752|ref|NP_247551.1| 21 KGDVEKALEYFNKAIELN 38
                                  459***********9986 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.5
                          Sel1 29 wyekAAe 35
                                  w+ kA +
  gi|15668752|ref|NP_247551.1| 45 WFNKALA 51
                                  9***976 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 6.4
                          Sel1 26 Aiewy 30
                                  A+e++
  gi|15668752|ref|NP_247551.1| 61 ARECF 65
                                  55444 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.8e-05     0.015      35      80 ..      20      66 ..       2      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                                  HTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3 35 lngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80
                                  + g+ ++A+e+++ka +ln+    +++ +A +l  L++yeeA+ +++
  gi|15668752|ref|NP_247551.1| 20 NKGDVEKALEYFNKAiELNPFYRDAWFNKALALRILGRYEEARECFF 66
                                  5799***********99999999********************9987 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.4   2.8e+03      19      30 ..       6      17 ..       3      20 .. 0.74
   2 ?    4.2   0.0     0.052        42      15      31 ..      21      37 ..      19      38 .. 0.88
   3 !    9.2   0.1    0.0013       1.1       8      24 ..      48      64 ..      47      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.4
                        TPR_10 19 deAealleeala 30
                                  ++Ae ++++ ++
  gi|15668752|ref|NP_247551.1|  6 KKAEYYYKKGVE 17
                                  678888887665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.052
                        TPR_10 15 rgrydeAealleealai 31
                                   g+ ++A++++ +a+++
  gi|15668752|ref|NP_247551.1| 21 KGDVEKALEYFNKAIEL 37
                                  6999**********986 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0013
                        TPR_10  8 LanalrqrgrydeAeal 24
                                   a alr +gry+eA++ 
  gi|15668752|ref|NP_247551.1| 48 KALALRILGRYEEAREC 64
                                  589***********986 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.4   0.00028      0.23       2      33 ..       6      37 ..       5      38 .. 0.89
   2 ?    3.4   0.0     0.098        80      17      31 ..      55      69 ..      44      85 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                           MIT  2 dkAlelvkkAveeDnagnyeeAlelYkealel 33
                                  +kA  + kk ve  n+g+ e+Ale++ +a+el
  gi|15668752|ref|NP_247551.1|  6 KKAEYYYKKGVEVGNKGDVEKALEYFNKAIEL 37
                                  5677788999********************96 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.098
                           MIT 17 agnyeeAlelYkeal 31
                                   g yeeA e++  +l
  gi|15668752|ref|NP_247551.1| 55 LGRYEEARECFFRGL 69
                                  577777777765555 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00014      0.12       2      43 ..       2      42 ..       1      62 [. 0.84
   2 ?    1.0   0.0       0.4   3.3e+02      11      47 ..      45      82 ..      41      86 .] 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                       DUF5113  2 ddllqiandYanlayylnvegeyeeALeyldsaleylNahye 43
                                  d+  ++a+ Y + + ++  +g+ e+ALey+++a+e lN +y+
  gi|15668752|ref|NP_247551.1|  2 DENIKKAEYYYKKGVEVGNKGDVEKALEYFNKAIE-LNPFYR 42
                                  56778999**************************8.677776 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.4
                       DUF5113 11 YanlayylnvegeyeeALeyldsaleylNah..yekYak 47
                                  + n a +l + g+yeeA e++   l +  +h  ++kY +
  gi|15668752|ref|NP_247551.1| 45 WFNKALALRILGRYEEARECFFRGLAV-EKHltHKKYNS 82
                                  667777888889999999888887754.44433555654 PP

>> Ubiq-assoc  Ubiquitin-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2     0.005         4      19      31 ..       4      16 ..       3      20 .. 0.90
   2 ?    2.2   0.0      0.22   1.8e+02      19      31 ..      23      35 ..      22      43 .. 0.86
   3 ?    0.8   0.0      0.61   4.9e+02      20      41 ..      58      79 ..      55      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.005
                                  -SHHHHHHHHHH- CS
                    Ubiq-assoc 19 sidkAneyYekGi 31
                                  +i kA+ yY+kG+
  gi|15668752|ref|NP_247551.1|  4 NIKKAEYYYKKGV 16
                                  699*********8 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.22
                                  -SHHHHHHHHHH- CS
                    Ubiq-assoc 19 sidkAneyYekGi 31
                                  +++kA ey++k i
  gi|15668752|ref|NP_247551.1| 23 DVEKALEYFNKAI 35
                                  689******9987 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.61
                                  SHHHHHHHHHH-SSHHHHHHHH CS
                    Ubiq-assoc 20 idkAneyYekGilYedllekrk 41
                                  +++A e + +G   e+ l ++k
  gi|15668752|ref|NP_247551.1| 58 YEEARECFFRGLAVEKHLTHKK 79
                                  6899999999999999888776 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00038      0.31       4      23 ..      45      64 ..      43      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00038
                         TPR_4  4 llaLArallalGdldeAral 23
                                    + A al  lG+++eAr+ 
  gi|15668752|ref|NP_247551.1| 45 WFNKALALRILGRYEEAREC 64
                                  6788**************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 648.26
//
Query:       gi|15668753|ref|NP_247552.1|  [L=189]
Description: hypothetical protein MJ_0573 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-16   61.1   0.0    2.2e-16   60.2   0.0    1.4  1  OsmC      OsmC-like protein
  ------ inclusion threshold ------
      0.059   13.2   2.1       0.26   11.1   0.4    2.4  2  S4_2      S4 domain
      0.082   13.1   3.1        3.2    8.0   0.1    2.3  2  SRI       SRI (Set2 Rpb1 interacting) domain


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.0   3.7e-20   2.2e-16       5      96 ..      94     183 ..      87     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 3.7e-20
                                   SB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECTCEEEEEEEEEEE-SS-H..HHHHHHHHHHHHHS CS
                          OsmC   5 gpsPeelllaalasCfaitlravakkkgikledleveveaerdpegakgiteirlkvevkipgadseeklkkllekaekrC 85 
                                   ++sP++l+la+l++C++i++   +k+++i+  +++v+ ++e++ e  k i+++ ++++vk++g+ ++eklkkl+ +  k+C
  gi|15668753|ref|NP_247552.1|  94 KISPMDLFLAGLCGCVCIAVGNTLKANNIDA-EIKVDGKVEKSFEEGK-IKKVIINIYVKVDGDIDKEKLKKLVLEGSKKC 172
                                   78*************************8877.8888888888888777.******************************** PP

                                   HHHHHHCT-SS CS
                          OsmC  86 pvsntlkngvk 96 
                                    +sn++  +++
  gi|15668753|ref|NP_247552.1| 173 LISNSISCEIE 183
                                   ******88776 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.068   4.1e+02      32      43 ..     123     134 ..     110     135 .. 0.77
   2 ?   11.1   0.4   4.4e-05      0.26      24      50 ..     139     165 ..     137     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.068
                          S4_2  32 egeVkvNGevet 43 
                                   + e+kv+G+ve+
  gi|15668753|ref|NP_247552.1| 123 DAEIKVDGKVEK 134
                                   568999999996 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.4e-05
                          S4_2  24 geaKafiaegeVkvNGevetrRgkKlr 50 
                                   g+ K +i +  Vkv+G +++++ kKl+
  gi|15668753|ref|NP_247552.1| 139 GKIKKVIINIYVKVDGDIDKEKLKKLV 165
                                   789**********************97 PP

>> SRI  SRI (Set2 Rpb1 interacting) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1   0.00054       3.2      11      51 ..      22      62 ..      13      83 .. 0.83
   2 ?    5.7   0.4    0.0028        17       3      38 ..     131     167 ..     129     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00054
                           SRI 11 elakvVvnvlnkYrkklkkedfKklakeltkklvekElkkd 51
                                   + k+++  l+k+ + +++ + K++  +++ ++v+k+  k 
  gi|15668753|ref|NP_247552.1| 22 MMPKMMPLALEKFLQYIPENERKEFIARIVDIIVSKDENKE 62
                                  56677888999*************************96553 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0028
                           SRI   3 kqekkfkk.elakvVvnvlnkYrkklkkedfKklake 38 
                                   k+ek f++ ++ kv++n+  k   +++ke++Kkl+ e
  gi|15668753|ref|NP_247552.1| 131 KVEKSFEEgKIKKVIINIYVKVDGDIDKEKLKKLVLE 167
                                   567777644899*********************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1285.73
//
Query:       gi|15668754|ref|NP_247553.1|  [L=93]
Description: hypothetical protein MJ_0574 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-09   37.9   8.9    1.2e-09   37.9   8.9    2.3  2  PLDc_N           Phospholipase_D-nuclease N-terminal
     0.0013   17.7   7.4     0.0014   17.6   7.4    1.0  1  AA_permease_2    Amino acid permease
  ------ inclusion threshold ------
       0.16   12.0   0.1       0.16   12.0   0.1    2.4  2  FixQ             Cbb3-type cytochrome oxidase component FixQ
        0.2   11.7   3.3       0.25   11.4   3.3    1.2  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
       0.33   11.1   0.1       0.33   11.1   0.1    2.1  2  DUF4870          Domain of unknown function (DUF4870)
        0.8    8.5   4.6       0.82    8.5   4.6    1.1  1  TraG_N           TraG-like protein, N-terminal region
       0.82    8.9   3.2        2.1    7.6   3.2    1.6  1  7tm_1            7 transmembrane receptor (rhodopsin family)
        1.6    8.0   4.6        1.9    7.8   4.6    1.1  1  DUF3810          Protein of unknown function (DUF3810)
        4.6    7.6   9.3        4.6    7.6   8.3    1.5  2  2TM              2TM domain
        5.2    6.2   6.6        6.3    5.9   6.6    1.2  1  Herpes_LMP1      Herpesvirus latent membrane protein 1 (LMP1)


Domain annotation for each model (and alignments):
>> PLDc_N  Phospholipase_D-nuclease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   3.1       1.1   1.9e+03      29      36 ..      13      20 ..       8      20 .. 0.79
   2 !   37.9   8.9   6.7e-13   1.2e-09       1      40 [.      33      74 ..      33      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                        PLDc_N 29 lPvlGail 36
                                  +P++G+++
  gi|15668754|ref|NP_247553.1| 13 FPIFGFFF 20
                                  9****975 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 6.7e-13
                        PLDc_N  1 ilwiialidiir.d.rnpssklaWllvilflPvlGailYllf 40
                                  i+ ii+++di++ d  ++  k++W+lv+ fl ++Gai+Y+l+
  gi|15668754|ref|NP_247553.1| 33 IIIIITIVDILKrDaLDTLEKILWILVVWFLGIIGAIIYYLL 74
                                  689*********44777777********************98 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   7.4   7.7e-07    0.0014      97     179 ..       5      83 ..       2      93 .] 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.7e-07
                 AA_permease_2  97 svaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilglitvdgggfsslst 177
                                   ++++++  + ++++++   +++++ia++i+i+++++ i+    ++++ +il il++  +l i+ ++ +++++++ + s+  
  gi|15668754|ref|NP_247553.1|   5 PIGFGMVGFPIFGFFFMGLFFVIGIAVFIIIIITIVDILKRDALDTLEKILWILVV-WFLGIIGAIIYYLLSKRNSKSK-- 82 
                                   566677777777766666789***********************************.699****999999988766644.. PP

                 AA_permease_2 178 et 179
                                    +
  gi|15668754|ref|NP_247553.1|  83 -G 83 
                                   .2 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   7.4       1.7     3e+03      13      26 ..      16      29 ..      13      37 .. 0.73
   2 ?   12.0   0.1   8.9e-05      0.16      12      35 ..      56      80 ..      48      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                          FixQ 13 wgllflvllfygvv 26
                                  +g +f+ l+f++ +
  gi|15668754|ref|NP_247553.1| 16 FGFFFMGLFFVIGI 29
                                  67777777777655 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.9e-05
                          FixQ 12 swgllflvllfygvviyafrpgn.r 35
                                  +++ ++++++  ++++y++ ++n +
  gi|15668754|ref|NP_247553.1| 56 WILVVWFLGIIGAIIYYLLSKRNsK 80
                                  4566778888888888888888843 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.3   0.00014      0.25      38      91 ..      17      79 ..       6      85 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
               Phage_holin_3_6 38 gllgaagvlallalllllval..a.....lala.a.lwlaalivaavllvlagvlalvglkkl 91
                                  g++++++++++  ++++++ +  +      al+ +   l+ l+v  + ++ a++  l+ +++ 
  gi|15668754|ref|NP_247553.1| 17 GFFFMGLFFVIGIAVFIIIIItiVdilkrDALDtLeKILWILVVWFLGIIGAIIYYLLSKRNS 79
                                  344444444444333333333213544552333337777778886666666666666666544 PP

>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   9.8      0.26   4.7e+02      59      92 ..      10      42 ..       4      52 .. 0.56
   2 ?   11.1   0.1   0.00019      0.33      13      46 ..      55      89 ..      47      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.26
                       DUF4870 59 iilivlsllvligflllllllllllnlvlviiaa 92
                                  ++++ ++ ++++g+ ++++++++ + ++++i+ +
  gi|15668754|ref|NP_247553.1| 10 MVGFPIFGFFFMGL-FFVIGIAVFIIIIITIVDI 42
                                  45555555566665.4444444444445555544 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                       DUF4870 13 lsklliplgniilPlviwllkkdksef.vdeqgke 46
                                  l+ l++ +++ii++++ +ll+k +s+   d++gk+
  gi|15668754|ref|NP_247553.1| 55 LWILVVWFLGIIGAIIYYLLSKRNSKSkGDNNGKN 89
                                  5788999************9998876414666665 PP

>> TraG_N  TraG-like protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.6   0.00046      0.82     335     394 ..      20      80 ..       6      93 .] 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00046
                        TraG_N 335 mqaflemliyalfPlvlllslyplk..glkilkgylfllvwlqlWwplaailnsllldaayg 394
                                   ++++++++ +a+f+++++ ++  lk  +l +l ++l++lv + +++++ ai+ +ll  + + 
  gi|15668754|ref|NP_247553.1|  20 FMGLFFVIGIAVFIIIIITIVDILKrdALDTLEKILWILVVW-FLGIIGAIIYYLLSKRNSK 80 
                                   688888888899988888888777788**********99976.89*******9999887543 PP

>> 7tm_1  7 transmembrane receptor (rhodopsin family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   3.2    0.0012       2.1      85     130 ..      37      82 ..       7      89 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0012
                                   HHHHSTTTHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHCEECC.CT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                         7tm_1  85 laivkplkykrkrtkrravllillvWvlslllsvpllvletvet.na 130
                                   ++iv+ lk  +  t ++ +l il+vW+l ++ ++++++l++++  ++
  gi|15668754|ref|NP_247553.1|  37 ITIVDILKRDALDTLEK-ILWILVVWFLGIIGAIIYYLLSKRNSkSK 82 
                                   46777788888777655.7899***************9999954333 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.6     0.001       1.9      20      72 ..      11      63 ..       6      84 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.001
                       DUF3810 20 fpFSvgellivllillvilylvlaiklkkrkkkkkrllkvllrvllvllvvyf 72
                                  + F +  ++ + l++++ ++++++i+++     k+ +l +l ++l++l+v ++
  gi|15668754|ref|NP_247553.1| 11 VGFPIFGFFFMGLFFVIGIAVFIIIIITIVDILKRDALDTLEKILWILVVWFL 63
                                  55555555555444444444444442333333344566666666665543322 PP

>> 2TM  2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.86   1.5e+03      37      45 ..      18      26 ..       5      30 .. 0.49
   2 ?    7.6   8.3    0.0026       4.6      13      54 ..      25      71 ..      17      86 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.86
                           2TM 37 flwpilfWg 45
                                  f+++ lf  
  gi|15668754|ref|NP_247553.1| 18 FFFMGLFFV 26
                                  233333333 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0026
                           2TM 13 FyrhlvvYlivniflilinl......gsswflwpilfWgiglllhalk 54
                                  F + ++v++i++i ++ i l      + + +lw++++W +g++   + 
  gi|15668754|ref|NP_247553.1| 25 FVIGIAVFIIIIITIVDI-LkrdaldTLEKILWILVVWFLGIIGAIIY 71
                                  444455555555555555.267778988889*********99987776 PP

>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   6.6    0.0035       6.3      52      94 ..      23      65 ..      14      80 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0035
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Herpes_LMP1 52 llvlysfallliiiiliififrrdllcplgalcllllmitlll 94
                                  l+ +  +a+++iiii i+ i++rd l  l  +  +l++  l +
  gi|15668754|ref|NP_247553.1| 23 LFFVIGIAVFIIIIITIVDILKRDALDTLEKILWILVVWFLGI 65
                                  4455678888999999999999999988887665555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1350  (0.075297); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 727.40
//
Query:       gi|15668755|ref|NP_247554.1|  [L=229]
Description: hypothetical protein MJ_0575 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-64  217.0   1.3    2.6e-64  216.8   1.3    1.0  1  DUF166    Domain of unknown function
  ------ inclusion threshold ------
      0.025   14.8   0.3       0.94    9.7   0.0    2.4  2  DUF1858   Domain of unknown function (DUF1858)
      0.089   13.1   0.0       0.26   11.6   0.0    1.7  2  TrkA_N    TrkA-N domain


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.8   1.3   4.3e-68   2.6e-64       1     218 [.       5     226 ..       5     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 216.8 bits;  conditional E-value: 4.3e-68
                        DUF166   1 lvltsgeyGervvenilnepdferslivavvevpe..eldefiedpeelLpelkeaDiviaytlhpDlllelaekake.kk 78 
                                   lv+t+g+yG r+ ++i++ +++++++ +++++ p+   +d+ ie+p+elL+++keaDi++ yt+hpD +++l+ +a++ +k
  gi|15668755|ref|NP_247554.1|   5 LVVTDGAYGYRIKGTINSFGKKNKFIGIYKINKPDdlIVDD-IEFPDELLEKIKEADILLLYTQHPDNTYYLCYEARRlNK 84 
                                   599**********************9999999999899999.************************************99* PP

                        DUF166  79 vkalivpaeapkaglrkelkekleelgievavpkpfCslee.......egkpkideFleefGkPelevevkdgkikkVeVl 152
                                     a+iv++++++     + k++l+++  ++++p+++C l+e       +++pk++eFleefG+P+++v+vkd+k+ +VeVl
  gi|15668755|ref|NP_247554.1|  85 DIAIIVATWSGE-----GEKKELKKF--DAICPEEMCLLDEnevgsliDKYPKLKEFLEEFGTPKVKVYVKDNKVIDVEVL 158
                                   ************.....999999998..5**************************************************** PP

                        DUF166 153 rsapCGstwyvakklkGkeveeaeeka...geahqsYpClAsmerdfelketklhkAgyihkeavekAl 218
                                   r+++CGst ++ak +kG+ev+++ee+a   ++ +q+YpC+A+++++f+ ++++++kA +ihkeav +++
  gi|15668755|ref|NP_247554.1| 159 RTSICGSTLFMAKLMKGMEVNDIEEFAkksAMLIQRYPCVAGKIKIFR-GDCRKQKALNIHKEAVLEGI 226
                                   *************************999999****************9.****************9987 PP

>> DUF1858  Domain of unknown function (DUF1858)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00016      0.94       7      25 ..     121     139 ..     118     145 .. 0.91
   2 ?    2.6   0.1     0.026   1.6e+02      35      58 ..     158     181 ..     151     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00016
                                   HHHHHHH-GGGHHHHHHTT CS
                       DUF1858   7 IgelleeyPelaevLvelG 25 
                                   +g l+++yP+l+e+L e+G
  gi|15668755|ref|NP_247554.1| 121 VGSLIDKYPKLKEFLEEFG 139
                                   899*************998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.026
                                   HTTHHHHSBHHHHHHHHT--HHHH CS
                       DUF1858  35 lktvakvetleqaakvhgidldeL 58 
                                   l+t   + tl +a  ++g++++++
  gi|15668755|ref|NP_247554.1| 158 LRTSICGSTLFMAKLMKGMEVNDI 181
                                   66667788999**********985 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.3e-05      0.26      59     107 ..      55     104 ..      37     109 .. 0.80
   2 ?   -2.4   0.0      0.91   5.4e+03      27      46 ..     125     144 ..     116     159 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.3e-05
                                   TGGGESEEEE-SSSHHHHHHHHHHHHHHTSSSEEE.EEESSGGGHHHHHH CS
                        TrkA_N  59 giekadaviaatgddeanilavllakelnpkkkii.araqdpehaellkk 107
                                   +i++ad+++  t++ + + +++  a+ ln+++ ii a  + + +++ lkk
  gi|15668755|ref|NP_247554.1|  55 KIKEADILLLYTQHPDNTYYLCYEARRLNKDIAIIvATWSGEGEKKELKK 104
                                   799****************************6665166666666666666 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.91
                                   EESSHHHHHHHHHTTSEEEE CS
                        TrkA_N  27 idkdeerveelreeglevvv 46 
                                   idk ++  e l+e g++ v+
  gi|15668755|ref|NP_247554.1| 125 IDKYPKLKEFLEEFGTPKVK 144
                                   56655555555555544222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1477.80
//
Query:       gi|15668756|ref|NP_247555.1|  [L=347]
Description: malic acid transport protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-70  237.6  53.2    2.3e-70  237.4  53.2    1.0  1  SLAC1     Voltage-dependent anion channel
  ------ inclusion threshold ------
      0.016   15.1   4.2      0.016   15.1   4.2    2.5  3  WCOR413   Cold acclimation protein WCOR413


Domain annotation for each model (and alignments):
>> SLAC1  Voltage-dependent anion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.4  53.2   2.6e-74   2.3e-70       1     323 [.      14     334 ..      14     335 .. 0.90

  Alignments for each domain:
  == domain 1  score: 237.4 bits;  conditional E-value: 2.6e-74
                         SLAC1   1 hftpawFaivMGtgila..lllka..lparglriislilfllalvlfllllvlyllrfilypeavrkelrhpveslflgtf 77 
                                   +f p+wFa+vMGtgila   ll+   l  + l+ +++ lf+++++lf+++lv ++lr+i++++++ ++l+hpv s f++t+
  gi|15668756|ref|NP_247555.1|  14 NFVPSWFAAVMGTGILAvdSLLYSsyL--PILKDVAVGLFYFNVLLFFIFLVPWVLRWIMFKDNALADLKHPVLSAFYPTI 92 
                                   699**************7645532234..58899*********************************************** PP

                         SLAC1  78 pmglltilnglllvl.pgewlatlalvllW.igvllslltavvvvfllftek.eekleeitpawllpvvgllvvallgall 155
                                   ++++l++ +  +++  +    + +  v +W +g++ ++l++++v+f++f+++   kl++++p w++p+vgl+v++++g+l+
  gi|15668756|ref|NP_247555.1|  93 AVSCLVLGADFINIGhN----MFWGGV-FWtLGAIGMFLFSLIVPFYMFKSEsI-KLDHVNPGWYIPPVGLIVIPIAGSLI 167
                                   ***98888666666633....445677.**88*****************99745.5************************* PP

                         SLAC1 156 aesqnpslqllgilvvslllwglGlllalvlfvlylyrlithklppaelrptlfiplGplgqgalallllgkaapk..aae 234
                                   +++ +  ++ l ++++ ++ wg G++l+l+l+++++yr+i+h+++p++++pt++i+lGp+g g++al+++ +++p   ++e
  gi|15668756|ref|NP_247555.1| 168 MPHLTGVWHEL-TVLINYFGWGAGFFLYLALLAVVIYRFILHHPLPSAMAPTVWINLGPIGAGIVALINMVNNSPFitIKE 247
                                   ***77776778.9*****************************999*****************************9977777 PP

                         SLAC1 235 vlkvlalllalflwglglfwllvavlsvls......lpvrlkfslswWaftFPlgalalatielgkaleseafkvlgtill 309
                                    +++++++    +wg+gl+w l+a++++l       l     + +swWaf+FPlga++++++ ++k ++ + + ++g++l+
  gi|15668756|ref|NP_247555.1| 248 PFYIFSFI----FWGFGLWWSLMAIIMTLYyvkklkL----PYAMSWWAFIFPLGAYVASSHLVYKIFKFSIIDYIGFGLY 320
                                   77777777....******************6665544....6**********************999999999******** PP

                         SLAC1 310 vllvlvwllvlvgt 323
                                   +ll+++w+++l+ t
  gi|15668756|ref|NP_247555.1| 321 WLLFFFWAITLIKT 334
                                   ***********988 PP

>> WCOR413  Cold acclimation protein WCOR413
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.82   7.4e+03      69      81 ..     127     139 ..     124     147 .. 0.75
   2 ?   -1.8   1.4      0.29   2.6e+03      82     108 ..     179     207 ..     160     221 .. 0.62
   3 ?   15.1   4.2   1.8e-06     0.016      74     116 ..     241     279 ..     234     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.82
                       WCOR413  69 tsllvPyialslP 81 
                                    sl+vP+ +++  
  gi|15668756|ref|NP_247555.1| 127 FSLIVPFYMFKSE 139
                                   6899999998765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.29
                       WCOR413  82 svifsllrgevG..kWiafiavvlrLFfp 108
                                   +v+++++    G   ++a++avv+  F+ 
  gi|15668756|ref|NP_247555.1| 179 TVLINYFGWGAGffLYLALLAVVIYRFIL 207
                                   56667666555522467999998866653 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.8e-06
                       WCOR413  74 PyialslPsvifsllrgevGkWiafiavvlrLFfpkefpdele 116
                                   P+i ++ P  ifs++   +G W +++a+++ L++ k++     
  gi|15668756|ref|NP_247555.1| 241 PFITIKEPFYIFSFIFWGFGLWWSLMAIIMTLYYVKKL----K 279
                                   9*********************************7765....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2475.48
//
Query:       gi|15668757|ref|NP_247556.1|  [L=162]
Description: hypothetical protein MJ_0577 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-35  120.8   0.3    9.4e-35  120.2   0.3    1.3  1  Usp             Universal stress protein family
  ------ inclusion threshold ------
      0.014   14.2   0.1      0.018   13.8   0.1    1.2  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
      0.023   14.7   0.1      0.053   13.5   0.1    1.6  2  Ribonuc_L-PSP   Endoribonuclease L-PSP
      0.026   14.6   0.8      0.026   14.6   0.8    1.7  2  DUF4363         Domain of unknown function (DUF4363)
      0.035   13.8   0.1      0.057   13.1   0.1    1.4  1  DCB             Dimerisation and cyclophilin-binding domain o
      0.046   13.8   0.1       0.16   12.0   0.0    1.8  2  B12-binding     B12 binding domain
      0.047   13.2   0.0      0.078   12.5   0.0    1.4  1  ANAPC4          Anaphase-promoting complex, cyclosome, subuni


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   0.3   3.7e-38   9.4e-35       1     141 []       4     158 ..       4     158 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 3.7e-38
                                   S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH........... CS
                           Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada........... 70 
                                   myk+Il+++D+se+++ Al++  ++   +  e+illhvid+r+ ++++      + + l ++ +e e++            
  gi|15668757|ref|NP_247556.1|   4 MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKSVEEFENELknklteeaknk 84 
                                   9***********************88888899****************************99999999989********** PP

                                   ...HHHHHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                           Usp  71 ...akaaaeaggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       k+++e+ g kv+ ++++g p eei+++ae+e++d+i++Gs+g+++l+++llGSv+e+v++++++pVlvV+
  gi|15668757|ref|NP_247556.1|  85 menIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
                                   *************************************************************************8 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     7e-06     0.018     290     355 ..      65     133 ..      53     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7e-06
                                   HHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT.....SEEEES.CHHHHHHHHHHHT-SEEEE-CCHHHH CS
                Oxidored_nitro 290 llkelGmevvaagtetahrddeerlkaeleeg....epeviddadleeleelikelkpdlllggskeryi 355
                                    ++e + e    +te+a+++ e  +k+ele+     ++ ++++  +ee+ ++++++++d+++ gs+++  
  gi|15668757|ref|NP_247556.1|  65 SVEEFENELKNKLTEEAKNKME-NIKKELEDVgfkvKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTN 133
                                   5556666666667777766655.788888888999988****************************9865 PP

>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.9   4.8e+03      39      54 ..      12      27 ..       5      43 .. 0.56
   2 ?   13.5   0.1   2.1e-05     0.053      33      74 ..      70     110 ..      55     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.9
                                  SSHHHHHHHHHHHHHH CS
                 Ribonuc_L-PSP 39 gdveeqtrqalenlka 54
                                  +d+ e ++ al+ +ka
  gi|15668757|ref|NP_247556.1| 12 TDFSETAEIALKHVKA 27
                                  4455555555554443 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.1e-05
                                   TSCB.-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEES CS
                 Ribonuc_L-PSP  33 tgelvegdveeqtrqalenlkavLaaagaslsdvVkvtvFla 74 
                                   ++el +++++e++++ +en+k+ L+ +g++++d++ v + ++
  gi|15668757|ref|NP_247556.1|  70 ENEL-KNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHE 110
                                   5666.88999***********************998877555 PP

>> DUF4363  Domain of unknown function (DUF4363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       2.1   5.5e+03      39      59 ..      26      46 ..      15      50 .. 0.52
   2 ?   14.6   0.8     1e-05     0.026      14      64 ..      62     116 ..      59     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.1
                       DUF4363 39 elekeWekkkkklsifiehde 59
                                  ++ k+ + ++ +l  +i+ +e
  gi|15668757|ref|NP_247556.1| 26 KAFKTLKAEEVILLHVIDERE 46
                                  344444555555555555555 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1e-05
                       DUF4363  14 lsekleeleeaienedweeakekleelekeWe....kkkkklsifiehdeldeie 64 
                                   l++++ee e++++n+  eeak+k+e+++ke e    k k++  + i h+e+ +i 
  gi|15668757|ref|NP_247556.1|  62 LNKSVEEFENELKNKLTEEAKNKMENIKKELEdvgfKVKDIIVVGIPHEEIVKIA 116
                                   7899***************************944444677778888888887775 PP

>> DCB  Dimerisation and cyclophilin-binding domain of Mon2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.2e-05     0.057       4      71 ..      63     131 ..      60     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                           DCB   4 skllealqsdl.kalsseskrkhskvkeasekgilkLktikssseeeeqslaeaseeilkPlllacetk 71 
                                   +k++e+ +++l ++l +e+k+k +++k++ e +  k+k i      +e+ ++ a +e +  ++++++ k
  gi|15668757|ref|NP_247556.1|  63 NKSVEEFENELkNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGK 131
                                   6889999****789***********************99988774444444555567777777777665 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.53   1.4e+03      11      35 ..      16      40 ..       7      74 .. 0.75
   2 ?   12.0   0.0   6.3e-05      0.16      22      83 ..      90     155 ..      81     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.53
                   B12-binding 11 dlhplGlavlaaalrdagfeVqllg 35
                                  ++ +++l+ ++a++  +  eV+ll 
  gi|15668757|ref|NP_247556.1| 16 ETAEIALKHVKAFKTLKAEEVILLH 40
                                  5667888888888888888888774 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.3e-05
                   B12-binding  22 aalrdagfeVq.llganvenedivaairaekpdvvglSalltsqleav..kelvel.lkrirprvk 83 
                                     l+d gf+V+ ++ + +++e+iv+ +++e +d++ + ++  ++l ++    ++e  +k+ ++ v 
  gi|15668757|ref|NP_247556.1|  90 KELEDVGFKVKdIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEIllGSVTENvIKKSNKPVL 155
                                   55889999999666889999**************99988888888877555555556555555555 PP

>> ANAPC4  Anaphase-promoting complex, cyclosome, subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.1e-05     0.078      34     108 ..      62     152 ..      50     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                        ANAPC4  34 inetlkeiseewke.alelldrklrnledelkeeg..............eeeksisaeLldllltGli.spalkdfLvnql 98 
                                   +n++++e ++e k+ + e+  +k++n+++el++ g              e  k +++e  d++++G     +lk+ L+ ++
  gi|15668757|ref|NP_247556.1|  62 LNKSVEEFENELKNkLTEEAKNKMENIKKELEDVGfkvkdiivvgipheEIVKIAEDEGVDIIIMGSHgKTNLKEILLGSV 142
                                   7889999999**999******************999999999999999866678888999999888777999999999999 PP

                        ANAPC4  99 gerglkkwek 108
                                   +e  +kk  k
  gi|15668757|ref|NP_247556.1| 143 TENVIKKSNK 152
                                   9999999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2218  (0.12371); expected 358.6 (0.02)
Passed bias filter:                     1056  (0.058899); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1007.80
//
Query:       gi|15668758|ref|NP_247557.1|  [L=276]
Description: iron-sulfer cluster binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-18   65.0   0.0    9.2e-18   64.5   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    4.3e-15   55.8   0.1    7.1e-11   42.0   0.0    2.3  2  ParA         NUBPL iron-transfer P-loop NTPase
    2.7e-11   42.8  14.6    1.5e-05   24.6   3.3    2.7  2  Fer4         4Fe-4S binding domain
    3.8e-07   30.2   5.0     0.0024   18.0   0.6    2.4  2  Fer4_9       4Fe-4S dicluster domain
    5.2e-07   29.7   0.0    0.00019   21.4   0.0    2.3  2  AAA_31       AAA domain
    2.8e-06   26.8   0.5    4.7e-05   22.7   0.0    2.5  3  ArsA_ATPase  Anion-transporting ATPase
    3.3e-06   27.6   6.9      0.011   16.3   0.8    2.4  3  Fer4_7       4Fe-4S dicluster domain
    3.1e-05   23.8   9.3     0.0037   17.3   1.8    2.6  2  Fer4_2       4Fe-4S binding domain
    0.00017   22.4   6.4       0.04   14.9   0.9    2.5  2  Fer4_16      4Fe-4S double cluster binding domain
    0.00017   21.5  17.6     0.0061   16.6   2.4    2.7  2  Fer4_6       4Fe-4S binding domain
     0.0009   19.7   2.5       0.17   12.5   0.1    2.5  2  Fer4_17      4Fe-4S dicluster domain
     0.0012   19.1  13.1       0.24   12.0   3.3    2.6  2  Fer4_4       4Fe-4S binding domain
     0.0074   16.1   0.0      0.023   14.5   0.0    1.8  2  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0096   16.0  12.2       0.33   11.1  13.5    2.4  2  Fer4_10      4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   15.1   0.2      0.028   13.9   0.1    1.8  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
      0.018   16.0  12.9        0.3   12.1   2.3    2.6  2  Fer4_3       4Fe-4S binding domain
      0.022   14.7   0.0      0.072   13.1   0.0    1.8  1  AAA_5        AAA domain (dynein-related subfamily)
      0.032   14.6   0.1        0.1   13.0   0.0    1.8  2  AAA_16       AAA ATPase domain
      0.039   14.4   8.2       0.52   10.8   2.2    2.4  2  Fer4_8       4Fe-4S dicluster domain
      0.045   13.9  14.7       0.17   12.0  12.6    2.6  2  Fer4_21      4Fe-4S dicluster domain
      0.047   14.2   0.1       0.14   12.7   0.0    1.7  2  AAA_18       AAA domain
      0.081   13.8   3.9        5.2    8.0   0.1    2.4  2  Fer4_22      4Fe-4S dicluster domain
      0.084   12.1   0.0       0.14   11.5   0.0    1.3  1  Zeta_toxin   Zeta toxin
       0.16   11.8   0.0       0.31   10.8   0.0    1.5  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
       0.22   11.7   4.5       0.43   10.8   4.5    1.5  1  Fer4_18      4Fe-4S dicluster domain
       0.97    9.3   3.1       0.71    9.8   0.3    2.1  2  RsgA_GTPase  RsgA GTPase
        1.4    8.8   2.7        7.7    6.3   0.5    2.4  2  AAA_29       P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   1.4e-20   9.2e-18       1     126 [.      10     252 ..      10     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 1.4e-20
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   iai+s+kGGvGK++++++La+++++ +++++++D+D++a+n ++ + +++d++                            
  gi|15668758|ref|NP_247557.1|  10 IAIISGKGGVGKSSISTSLAKLFSK-EFNIVALDCDVDAPNFNL-MFDVKDKKLleviyreiyeinddcircgkcldvcqf 88 
                                   89***********************.*****************5.44444554457888899******************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|15668758|ref|NP_247557.1|  89 daigdfkinpilcegcgacelicefdaiepikresgyiyegfvgfpliwgelevgesgsgkiiehiknhakkykaelgiid 169
                                   ********************************************************************************* PP

                                   ..............CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCC CS
                                   ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ..............dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaea 121
                                                 d++  l+++e  + ++++ l+++   ln ++ e  + + k+++ ++++  + +++++ip+d +v+++
  gi|15668758|ref|NP_247557.1| 170 gppgvgcplistvkDVDLALCIVEPTKSSVNDCLRLIE-TLNFFNVEYLIVENKKGMNNINY--PFKIFHSIPFDFDVPKL 247
                                   **************************999765455555.58*******************95..****************9 PP

                                   CHHTS CS
                                   xxxxx RF
                          CbiA 122 parge 126
                                   +a++ 
  gi|15668758|ref|NP_247557.1| 248 IANKI 252
                                   99875 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   1.1e-13   7.1e-11       4      58 ..       8      61 ..       5      79 .. 0.87
   2 !   11.5   0.0   0.00022      0.14     113     178 ..     164     226 ..     146     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.1e-13
                          ParA  4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekp 58
                                   +ia++SgKGGVGKS+++++lA  L +k++++  lD D+  p+   +++v+++k 
  gi|15668758|ref|NP_247557.1|  8 MKIAIISGKGGVGKSSISTSLAK-LFSKEFNIVALDCDVDAPNFNLMFDVKDKKL 61
                                  589******************96.5577899999*****************9876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00022
                          ParA 113 DyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfv 178
                                   ++ iiD PPG g   ++ ++ ++l  a+ +  p + +++d  + ie ++  +v+ l +veN +g+ 
  gi|15668758|ref|NP_247557.1| 164 ELGIIDGPPGVGCPLISTVKDVDL--ALCIVEPTKSSVNDCLRLIETLNFFNVEYL-IVENKKGMN 226
                                   5569****************9975..667779*********************998.899977765 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   3.3   2.3e-08   1.5e-05       4      23 ..      72      91 ..      69      92 .. 0.91
   2 !   23.3   3.5   5.7e-08   3.8e-05       2      24 .]      95     117 ..      94     117 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.3e-08
                                  ETTTSSS-THHHHHSTTTEE CS
                          Fer4  4 deekCigCGaCvevCPvgAI 23
                                  + ++Ci+CG+C +vC ++AI
  gi|15668758|ref|NP_247557.1| 72 INDDCIRCGKCLDVCQFDAI 91
                                  6799***************9 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 5.7e-08
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   +i++ +C gCGaC+ +C ++AI+
  gi|15668758|ref|NP_247557.1|  95 KINPILCEGCGACELICEFDAIE 117
                                   69999*****************6 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.6   3.6e-06    0.0024      33      51 .]      68      91 ..      42      91 .. 0.73
   2 !   13.7   0.3     8e-05     0.053       2      21 ..     101     120 ..      99     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.6e-06
                        Fer4_9 33 e.....eaCigCgaCveaCpkgai 51
                                  e     ++Ci Cg+C+++C+ +ai
  gi|15668758|ref|NP_247557.1| 68 EiyeinDDCIRCGKCLDVCQFDAI 91
                                  13445568***********99887 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8e-05
                        Fer4_9   2 CtgCgaCveaCpagvvveda 21 
                                   C gCgaC+  C+++++++ +
  gi|15668758|ref|NP_247557.1| 101 CEGCGACELICEFDAIEPIK 120
                                   99999999999999887765 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.9e-07   0.00019       3      69 ..       9      72 ..       7      91 .. 0.66
   2 ?    6.0   0.0     0.015        10     110     168 ..     153     213 ..     138     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.9e-07
                        AAA_31  3 vIaianqKGGvGKTTtsvnlaaala.klgkkvLlvDlD.pQanattglgiekneiektlyevli.eekni 69
                                   Iai+  KGGvGK+  s+ la+ ++ + +   L +D+D p  n+ +  +++    +k+l+ev+  e ++i
  gi|15668758|ref|NP_247557.1|  9 KIAIISGKGGVGKSSISTSLAKLFSkEFNIVALDCDVDaPNFNLMF--DVK----DKKLLEVIYrEIYEI 72
                                  59*******************9888444555566666633344444..443....344444443233334 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.015
                        AAA_31 110 llekvkdeY..DyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktieevk 168
                                   ++++  ++Y   + iiD pP +g+ +++ +   d  + +v++++ +++   +l++t++ ++
  gi|15668758|ref|NP_247557.1| 153 HIKNHAKKYkaELGIIDGPPGVGCPLISTVKDVDLALCIVEPTKSSVNDCLRLIETLNFFN 213
                                   445555555334679***************************************9998765 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   7.1e-08   4.7e-05       1      50 [.       8      57 ..       8      75 .. 0.73
   2 ?    1.5   0.1       0.2   1.3e+02     210     237 ..     189     216 ..     178     228 .. 0.82
   3 ?   -2.2   0.0       2.8   1.9e+03     234     252 ..     241     260 ..     238     274 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.1e-08
                                  -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S.TTTHHHHHHTS- CS
                   ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistD.PAhslsDsfdqk 50
                                  +k+ +++GKGGVGK+++s+++a   s++ + v  +  D  A++   +fd k
  gi|15668758|ref|NP_247557.1|  8 MKIAIISGKGGVGKSSISTSLAKLFSKEFNIV-ALDCDvDAPNFNLMFDVK 57
                                  7999******************8888764433.333332466666666665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.2
                                   EEEEESSHHHHHHHHHHHHHHHHTT-EE CS
                   ArsA_ATPase 210 rlVvipEklslkEteRaikeLkkygikv 237
                                    ++v p k s+++  R+i+ L+ ++++ 
  gi|15668758|ref|NP_247557.1| 189 LCIVEPTKSSVNDCLRLIETLNFFNVEY 216
                                   6899******************998864 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.8
                                   T-EEEEEEEEE.E-TTCSSS CS
                   ArsA_ATPase 234 gikvdavivNk.llpeeeqe 252
                                   +++v ++i Nk ll +++++
  gi|15668758|ref|NP_247557.1| 241 DFDVPKLIANKiLLCDSNSK 260
                                   67888888888444444442 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.8   1.6e-05     0.011      29      52 .]      67      90 ..      41      90 .. 0.61
   2 !   13.9   1.5   9.4e-05     0.062       2      17 ..      76      91 ..      75      98 .. 0.87
   3 !   13.4   1.0   0.00014     0.091       2      22 ..     101     121 ..     100     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-05
                        Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                  ++++   ++C+ Cg+C +vC ++a
  gi|15668758|ref|NP_247557.1| 67 REIYEINDDCIRCGKCLDVCQFDA 90
                                  566777899999999999998876 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 9.4e-05
                        Fer4_7  2 CigCgaCvaaCpvkai 17
                                  Ci Cg+C ++C  +ai
  gi|15668758|ref|NP_247557.1| 76 CIRCGKCLDVCQFDAI 91
                                  9999999999999887 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.00014
                        Fer4_7   2 CigCgaCvaaCpvkaieldee 22 
                                   C gCgaC+  C  +aie  ++
  gi|15668758|ref|NP_247557.1| 101 CEGCGACELICEFDAIEPIKR 121
                                   99***********99987665 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.8   5.6e-06    0.0037       3      20 ..      70      86 ..      68      88 .. 0.84
   2 !   10.5   1.0   0.00079      0.53       4      20 ..      95     111 ..      92     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.6e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                  ++++ d Ci+Cg+C+++C
  gi|15668758|ref|NP_247557.1| 70 YEINDD-CIRCGKCLDVC 86
                                  567777.*********** PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00079
                        Fer4_2   4 vvdtdrCigCgaCvsaC 20 
                                   ++++  C gCgaC   C
  gi|15668758|ref|NP_247557.1|  95 KINPILCEGCGACELIC 111
                                   678889*******9988 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.9     6e-05      0.04       2      19 ..      76      93 ..      75      98 .. 0.88
   2 !    9.9   0.5    0.0021       1.4       2      20 ..     101     119 ..     100     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6e-05
                       Fer4_16  2 CgtCgkCaevCPtnaike 19
                                  C++CgkC++vC  +ai  
  gi|15668758|ref|NP_247557.1| 76 CIRCGKCLDVCQFDAIGD 93
                                  ************999975 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0021
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C +Cg+C  +C  +ai+  
  gi|15668758|ref|NP_247557.1| 101 CEGCGACELICEFDAIEPI 119
                                   9999999999999999865 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   3.5   7.2e-05     0.048       7      24 .]      74      91 ..      72      91 .. 0.89
   2 !   16.6   2.4   9.2e-06    0.0061       4      24 .]      96     116 ..      94     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.2e-05
                        Fer4_6  7 dkCigCgdCvrvCPegai 24
                                  d Ci Cg+C +vC ++ai
  gi|15668758|ref|NP_247557.1| 74 DDCIRCGKCLDVCQFDAI 91
                                  67***********98887 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9.2e-06
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   i+p +C gCg+C+ +C ++ai
  gi|15668758|ref|NP_247557.1|  96 INPILCEGCGACELICEFDAI 116
                                   66669*************998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00025      0.17      41      57 ..      71      87 ..      47      93 .. 0.74
   2 ?    6.7   0.3     0.016        11       2      17 ..     101     116 ..      99     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00025
                       Fer4_17 41 ekaslCieCgeCerkCP 57
                                  e  ++Ci Cg+C  +C 
  gi|15668758|ref|NP_247557.1| 71 EINDDCIRCGKCLDVCQ 87
                                  45678888888888885 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.016
                       Fer4_17   2 CiqCgyClpeCpsyea 17 
                                   C +Cg+C+  C + ++
  gi|15668758|ref|NP_247557.1| 101 CEGCGACELICEFDAI 116
                                   8888888887776555 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   3.3   0.00036      0.24       2      15 ..      74      87 ..      73      89 .. 0.87
   2 !   11.7   2.3   0.00045       0.3       4      16 ..     101     113 ..     100     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00036
                        Fer4_4  2 erCigCgsCvaaCP 15
                                  + Ci+Cg+C ++C 
  gi|15668758|ref|NP_247557.1| 74 DDCIRCGKCLDVCQ 87
                                  56***********6 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00045
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   C gCg+C+ +C++
  gi|15668758|ref|NP_247557.1| 101 CEGCGACELICEF 113
                                   99*********97 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.4e-05     0.023       1      49 [.      13      58 ..      13      75 .. 0.92
   2 ?   -2.6   0.0       5.7   3.8e+03     219     238 ..     190     209 ..     177     228 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdire 49
                                  + G  G+GK+++  +l+++++++   +++v LD  +++ +++ + d+++
  gi|15668758|ref|NP_247557.1| 13 ISGKGGVGKSSISTSLAKLFSKE---FNIVALDCDVDAPNFNLMFDVKD 58
                                  57999****************99...*********************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.7
                    ATP_bind_1 219 plssekeesiedllslidea 238
                                   ++   +++s++d l+li+++
  gi|15668758|ref|NP_247557.1| 190 CIVEPTKSSVNDCLRLIETL 209
                                   44444445555554444433 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1  13.5   0.00049      0.33       5      55 ..      72     111 ..      68     112 .. 0.80
   2 !    8.5   1.4    0.0032       2.2       3      19 ..      95     111 ..      93     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00049
                       Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                     d CirCgkC ++C           + + ++  ++++  C+gcgaC  +C
  gi|15668758|ref|NP_247557.1|  72 INDDCIRCGKCLDVC-----------QFDAIGDFKINPILCEGCGACELIC 111
                                   4689***********...........34555666677889*******9999 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0032
                       Fer4_10   3 vidddtCirCgkCvkaC 19 
                                   +i++  C +Cg+C   C
  gi|15668758|ref|NP_247557.1|  95 KINPILCEGCGACELIC 111
                                   57788899999998888 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.3e-05     0.028       2      59 ..       9      65 ..       8     124 .. 0.82
   2 ?   -2.9   0.0       5.4   3.6e+03     201     242 ..     231     270 ..     226     274 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-05
                     Fer4_NifH  2 kia.iyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtl 59
                                  kia i GkGG+Gks  s+ l++ l ++   ++ + CD  a   +l+++ k +  +l+++
  gi|15668758|ref|NP_247557.1|  9 KIAiISGKGGVGKSSISTSLAK-LFSKEFNIVALDCDVDAPNFNLMFDVKDK-KLLEVI 65
                                  566257********99998876.55566789999****99999999988876.566655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.4
                     Fer4_NifH 201 gtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelar 242
                                   + k+++ +P d +v k  ++k  + + +++  +++  +el +
  gi|15668758|ref|NP_247557.1| 231 PFKIFHSIPFDFDVPKLIANKILLCDSNSK--VSESIKELYE 270
                                   567888899888888877766666554443..3344444444 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.3   0.00045       0.3       1      15 []      76      90 ..      76      90 .. 0.94
   2 ?    8.8   3.0    0.0051       3.4       1      13 [.     101     113 ..     101     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00045
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ Cg C++vC  +A
  gi|15668758|ref|NP_247557.1| 76 CIRCGKCLDVCQFDA 90
                                  ***********9887 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0051
                        Fer4_3   1 CtgCgaCvevCPv 13 
                                   C gCgaC+  C  
  gi|15668758|ref|NP_247557.1| 101 CEGCGACELICEF 113
                                   99*********55 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.072       3      38 ..      12      47 ..      11      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                  EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--H CS
                         AAA_5  3 lLvGppGtgKselaerlaaalnreveyvqltrdtte 38
                                  ++ G+ G+gKs+++ +la+++ +e+++v+l  d  +
  gi|15668758|ref|NP_247557.1| 12 IISGKGGVGKSSISTSLAKLFSKEFNIVALDCDVDA 47
                                  6789************************99877665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00015       0.1      26      63 ..      10      46 ..       6      75 .. 0.78
   2 ?   -1.5   0.1       4.3   2.9e+03      31      37 ..     143     149 ..     142     175 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                        AAA_16 26 lvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                  + ++sG  GvGKss+ ++l++ ++k+ +  ++ +cd  
  gi|15668758|ref|NP_247557.1| 10 IAIISGKGGVGKSSISTSLAKLFSKE-FNIVALDCDVD 46
                                  678*****************999998.44466666655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.3
                        AAA_16  31 GesGvGK 37 
                                   GesG+GK
  gi|15668758|ref|NP_247557.1| 143 GESGSGK 149
                                   7777777 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.2   0.00079      0.52       3      16 ..      74      87 ..      72     100 .. 0.83
   2 ?    6.9   0.4     0.013       8.5       5      16 ..     101     112 ..      97     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00079
                        Fer4_8  3 ekCieCgaCqsaCp 16
                                  ++Ci+Cg C + C 
  gi|15668758|ref|NP_247557.1| 74 DDCIRCGKCLDVCQ 87
                                  57*********996 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.013
                        Fer4_8   5 CieCgaCqsaCp 16 
                                   C +CgaC+  C 
  gi|15668758|ref|NP_247557.1| 101 CEGCGACELICE 112
                                   667777777773 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0  12.6   0.00026      0.17       5      57 ..      73     116 ..      70     118 .. 0.82
   2 ?    8.3   1.7    0.0037       2.4       3      26 ..      96     119 ..      94     128 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                       Fer4_21   5 edkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                   +d+Ci CgkCl +C+    +ai       +k+    C GC  C  +C   d+i
  gi|15668758|ref|NP_247557.1|  73 NDDCIRCGKCLDVCQ---FDAIG-----DFKINPILCEGCGACELICEF-DAI 116
                                   489************...78885.....35666778***********86.766 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0037
                       Fer4_21   3 idedkCigCgkCliaCedtshqai 26 
                                   i++  C gCg C + Ce  +++ i
  gi|15668758|ref|NP_247557.1|  96 INPILCEGCGACELICEFDAIEPI 119
                                   677778899999999996555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00021      0.14       2      44 ..      12      52 ..      12      82 .. 0.69
   2 ?   -2.3   0.0       9.3   6.1e+03       2      10 ..     167     175 ..     144     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
                        AAA_18  2 lltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44
                                  +++G+ GvGK++++  L+k+   + + + va + +   ++++ 
  gi|15668758|ref|NP_247557.1| 12 IISGKGGVGKSSISTSLAKLF--SKEFNIVALDCDVDAPNFNL 52
                                  699**************9996..55555555554444444444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.3
                        AAA_18   2 lltGtpGvG 10 
                                   ++ G+pGvG
  gi|15668758|ref|NP_247557.1| 167 IIDGPPGVG 175
                                   466888887 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0079       5.2      80      93 ..      74      87 ..      49      90 .. 0.77
   2 ?    6.5   0.7     0.023        16      79      93 ..      98     112 ..      92     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0079
                       Fer4_22 80 sgCvGCgRCieacp 93
                                    C+ Cg+C ++c+
  gi|15668758|ref|NP_247557.1| 74 DDCIRCGKCLDVCQ 87
                                  46888888888776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.023
                       Fer4_22  79 esgCvGCgRCieacp 93 
                                      C GCg C+  c 
  gi|15668758|ref|NP_247557.1|  98 PILCEGCGACELICE 112
                                   567999999999886 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.14      18      76 ..      10      65 ..       8      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                    Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaselt 76
                                  + +++G  G GKs++++ l++ + ++ n+v ld D      P+++ +++ ++kk  e++
  gi|15668758|ref|NP_247557.1| 10 IAIISGKGGVGKSSISTSLAKLFSKEFNIVALDCDV---DAPNFNLMFDVKDKKLLEVI 65
                                  7899*****************************995...45566666665666555555 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00046      0.31       1      37 [.      15      50 ..      15      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqsei 37
                                  G+  +GKS++++ L+   ++k+ ++v +D+Dv  +++
  gi|15668758|ref|NP_247557.1| 15 GKGGVGKSSISTSLAKL-FSKEFNIVALDCDVDAPNF 50
                                  66789********9965.8*************88876 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.5   0.00064      0.43      56      99 ..      71     111 ..      51     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00064
                       Fer4_18  56 kgagdcidcescvkvcPtgidirkGlqleciscllcidacdkvm 99 
                                   + + dci c++c++vc    d    ++++ i c  c  ac+ + 
  gi|15668758|ref|NP_247557.1|  71 EINDDCIRCGKCLDVCQ--FDAIGDFKINPILCEGC-GACELIC 111
                                   56789***********6..56677788888888777.5676654 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3    0.0011      0.71     100     121 ..       9      30 ..       5      42 .. 0.85
   2 ?   -1.7   0.1       3.6   2.4e+03     118     118 ..     153     153 ..     142     197 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                                   SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase 100 ktsvlvGqSGvGKStLinallp 121
                                   k++++ G+ GvGKS++  +l+ 
  gi|15668758|ref|NP_247557.1|   9 KIAIISGKGGVGKSSISTSLAK 30 
                                   7899***********9988875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.6
                                   H CS
                   RsgA_GTPase 118 a 118
                                   +
  gi|15668758|ref|NP_247557.1| 153 H 153
                                   2 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.5     0.012       7.7      25      39 ..      11      25 ..       5      38 .. 0.81
   2 ?    1.6   0.1      0.34   2.3e+02      28      35 ..     142     149 ..     135     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.012
                        AAA_29 25 tlltGpsGsGKSTll 39
                                   +++G+ G+GKS++ 
  gi|15668758|ref|NP_247557.1| 11 AIISGKGGVGKSSIS 25
                                  689*********985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.34
                        AAA_29  28 tGpsGsGK 35 
                                   +G+sGsGK
  gi|15668758|ref|NP_247557.1| 142 VGESGSGK 149
                                   7******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1748.90
//
Query:       gi|15668759|ref|NP_247558.1|  [L=269]
Description: cell division inhibitor MinD-like protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-19   68.9   0.0    2.6e-18   66.3   0.0    1.9  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    8.4e-14   51.6   0.0    9.8e-09   35.0   0.0    2.5  3  ParA          NUBPL iron-transfer P-loop NTPase
    1.2e-08   35.1   0.3    8.9e-08   32.2   0.3    2.2  1  AAA_31        AAA domain
     0.0087   15.3   0.4      0.083   12.1   0.1    2.1  2  ArsA_ATPase   Anion-transporting ATPase
  ------ inclusion threshold ------
      0.023   14.5   0.0      0.038   13.8   0.0    1.3  1  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
      0.078   12.9   0.8        3.3    7.6   0.1    2.4  2  RsgA_GTPase   RsgA GTPase
      0.082   13.7   0.0       0.15   12.9   0.0    1.4  1  GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fol
       0.34   11.1   4.3       0.83    9.9   0.9    2.4  2  Tat           Transactivating regulatory protein (Tat)


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   1.1e-21   2.6e-18       1     126 [.       7     247 ..       7     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 1.1e-21
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.......HTTEB-HHHH.................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxx.................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.......leglendiep.................... 54 
                                   +a++++kGG+GK+tl+anL +++ + +++++l+D+D++++nl +       +                             
  gi|15668759|ref|NP_247558.1|   7 VAVTGGKGGTGKSTLSANLFFYFIE-NYKTALIDCDVETPNLPYltgcedlFL-------Arevfievpnieegktynynn 79 
                                   69***********************.*****************9766666422.......2334444588888******** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|15668759|ref|NP_247558.1|  80 vckegallkvgdklifiedlcsgckacginsnitfkkksigkiyekkfdngylivgksnlgerktakivtetkkyglsknc 160
                                   ********************************************************************************* PP

                                   .....................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHH CS
                                   .....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 .....................................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkeale 98 
                                                                        d+kr+++++e+l ++         +vlnr++ ++    lk    
  gi|15668759|ref|NP_247558.1| 161 einivdtaagthcnvvralinadkvlivteptpfgvsDAKRIIKVVEKLNIP-------YKIVLNRYGISD----LKI--- 227
                                   ***************************************************9.......569****99872....222... PP

                                   HHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  99 elkqrygvpvlgviprdeavaeaparge 126
                                         g ++  +ip+d++++e++++ge
  gi|15668759|ref|NP_247558.1| 228 ------GYNF--KIPYDKRIVECYCKGE 247
                                   ......5555..6777777777777776 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   4.4e-12   9.8e-09       5      55 ..       6      55 ..       3      79 .. 0.89
   2 !   13.7   0.1   1.4e-05     0.031     116     168 ..     164     214 ..     145     228 .. 0.82
   3 ?   -2.6   0.0       1.4     3e+03     203     230 ..     227     254 ..     222     266 .. 0.69

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 4.4e-12
                          ParA  5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee 55
                                  ++av+ gKGG GKSt+++nl + +  +++k++l+D D+  p++p l+g+e+
  gi|15668759|ref|NP_247558.1|  6 IVAVTGGKGGTGKSTLSANLFFYFI-ENYKTALIDCDVETPNLPYLTGCED 55
                                  799*****************99995.68********************998 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.4e-05
                          ParA 116 iiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvkkaiemfkkvkvkvl 168
                                   i+D+  Gt   +  v+  l + ++++iVt p    ++d+k+ i++++k++++  
  gi|15668759|ref|NP_247558.1| 164 IVDTAAGT---HCNVVRALiNADKVLIVTEPTPFGVSDAKRIIKVVEKLNIPYK 214
                                   56666555...555666555999***************************9964 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.4
                          ParA 203 vpllgeipldpeireasdegkplvlkep 230
                                   + +  +ip d++i+e+  +g+++++ ++
  gi|15668759|ref|NP_247558.1| 227 IGYNFKIPYDKRIVECYCKGESFLKYND 254
                                   5556689999999999999998887653 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.3     4e-11   8.9e-08       2     168 ..       5     210 ..       4     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 4e-11
                        AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa.natt......................glgiekneiektl 59 
                                    ++a++  KGG GK+T s nl   +  +++k+ l+D+D  + n+                        g            
  gi|15668759|ref|NP_247558.1|   5 MIVAVTGGKGGTGKSTLSANLFFYFI-ENYKTALIDCDVETpNLPYltgcedlflarevfievpnieeG------------ 72 
                                   689******************87776.589999*****9874666655566666666554444443331............ PP

                        AAA_31  60 yev......................................li.eeknikeaiiktkvenldlipssidLaeaeielvele 101
                                                                            ++ ++k+i +++  +k++n +li+++ +L e ++  + +e
  gi|15668759|ref|NP_247558.1|  73 --KtynynnvckegallkvgdklifiedlcsgckacginsnITfKKKSIGKIYE-KKFDNGYLIVGKSNLGERKTAKIVTE 150
                                   ..0222233344444444477777777777777777766655547888877666.8899**********998777665555 PP

                        AAA_31 102 kkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktieevk 168
                                   +k++        ++++  + i+D+     + ++ aL+ +d+v+i+++++++ ++ +++++k +e+++
  gi|15668759|ref|NP_247558.1| 151 TKKYG-------LSKNCEINIVDTAAGTHCNVVRALINADKVLIVTEPTPFGVSDAKRIIKVVEKLN 210
                                   55555.......66778899*******************************************9875 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   3.7e-05     0.083       5      33 ..       9      37 ..       4      42 .. 0.77
   2 ?    1.1   0.0     0.081   1.8e+02     196     243 ..     174     218 ..     139     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                                  EEEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                   ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvl 33
                                  + gGKGG GK+t+sa +  +  e+ k  l
  gi|15668759|ref|NP_247558.1|  9 VTGGKGGTGKSTLSANLFFYFIENYKTAL 37
                                  579************99887777665554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.081
                                   HHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                   ArsA_ATPase 196 kveeiltdpertsfrlVvipEklslkEteRaikeLkkygikvdavivN 243
                                   +v   l++ ++  + +V+ p    + + +R ik ++k++i  + v  N
  gi|15668759|ref|NP_247558.1| 174 NVVRALINADK--VLIVTEPTPFGVSDAKRIIKVVEKLNIPYKIV-LN 218
                                   55566666666..899999999999999*****999999998755.45 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.7e-05     0.038       1      36 [.      12      46 ..      12      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqse 36
                                  G+  +GKSTl+++L  y ++++ k++++D+Dv  ++
  gi|15668759|ref|NP_247558.1| 12 GKGGTGKSTLSANLFFYFIENY-KTALIDCDVETPN 46
                                  66789************87665.889******8876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.026        58     102     119 ..       8      25 ..       3      35 .. 0.84
   2 ?    7.6   0.1    0.0015       3.3      13      58 ..     179     222 ..     163     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.026
                                   EEEECSTTSSHHHHHHHH CS
                   RsgA_GTPase 102 svlvGqSGvGKStLinal 119
                                   +v  G+ G GKStL  +l
  gi|15668759|ref|NP_247558.1|   8 AVTGGKGGTGKSTLSANL 25 
                                   466799********7665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0015
                                   EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG CS
                   RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDl 58 
                                     N d++liv+  +   + ++  +r++ ++e+ +i+  ivln+  +
  gi|15668759|ref|NP_247558.1| 179 LINADKVLIVTEPT--PFGVSDAKRIIKVVEKLNIPYKIVLNRYGI 222
                                   5699******9887..9*************************9765 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.7e-05      0.15      61     112 ..     158     209 ..     130     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.7e-05
                                   TTESEEEE-S-GGGHHHHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHH CS
                  GFO_IDH_MocA  61 peidavivatpngtheelakaaleagkhvllEKPlattveeakelvelaekk 112
                                   +++++ iv t +gth ++++a+++a k +++  P  + v++ak++++ +ek 
  gi|15668759|ref|NP_247558.1| 158 KNCEINIVDTAAGTHCNVVRALINADKVLIVTEPTPFGVSDAKRIIKVVEKL 209
                                   4799999****************************************99986 PP

>> Tat  Transactivating regulatory protein (Tat)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.9   0.00037      0.83      26      49 ..     103     126 ..      97     129 .. 0.92
   2 ?    1.6   0.1      0.14   3.2e+02      22      31 ..     240     249 ..     233     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00037
                                   SCCHHTSSHHHHHHCTT---S-XX CS
                           Tat  26 ckkcsfhcqvcfikkalGisyerk 49 
                                   ck c     + f kk++G  ye+k
  gi|15668759|ref|NP_247558.1| 103 CKACGINSNITFKKKSIGKIYEKK 126
                                   9*********************98 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.14
                                   -S--SCCHHT CS
                           Tat  22 tncyckkcsf 31 
                                    +cyck  sf
  gi|15668759|ref|NP_247558.1| 240 VECYCKGESF 249
                                   57****8777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1700.34
//
Query:       gi|15668760|ref|NP_247559.1|  [L=118]
Description: hypothetical protein MJ_0580 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-24   86.1   0.1    1.8e-24   85.9   0.1    1.1  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
  ------ inclusion threshold ------
      0.079   12.3   0.1      0.085   12.2   0.1    1.1  1  AnfO_nitrog    Iron only nitrogenase protein AnfO (AnfO_nitro


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.1     2e-28   1.8e-24       1      94 [.      17     110 ..      17     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 2e-28
                                   STSCB-STCCC-SEEEEEEESSSCEE...EEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEE CS
                 Nitro_FeMo-Co   1 dgsrvdqhFGrapyFaiyeveegevk...ivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagiev 78 
                                   d++r+++hFGr++ F+i+e+e+ge+k   i+en    a ++ +g g + a+l+a+ gv+++iv++iGp+a+  +++ gi+v
  gi|15668760|ref|NP_247559.1|  17 DNNRLSPHFGRCEKFMIVEIENGEIKnkeIIENT---ARNGMHGVGTTSASLIANMGVNAIIVQNIGPKAYSVFKQLGIDV 94 
                                   5789*****************8876644466666...888888888888888888************************** PP

                                   EES-SSBHHHHHHHHH CS
                 Nitro_FeMo-Co  79 ykgaggtveealkevl 94 
                                   yk+  ++++e +k +l
  gi|15668760|ref|NP_247559.1|  95 YKANTTSIDECIKLFL 110
                                   ************9886 PP

>> AnfO_nitrog  Iron only nitrogenase protein AnfO (AnfO_nitrog)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   9.5e-06     0.085       1      93 [.      11     100 ..      11     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.5e-06
                   AnfO_nitrog   1 kIAvlvneegetasleekgivkvyekekgkWkvkreiefeleeekglaeirekleelveeLgdckifvakevsGilyslLe 81 
                                   kIA  ++++    ++    ++++ e e+g  ++k++  +e ++ +g++ + ++ ++l++++g  + ++++++   +ys+++
  gi|15668760|ref|NP_247559.1|  11 KIALPIDNNRLSPHFGRCEKFMIVEIENG--EIKNKEIIENTARNGMHGVGTTSASLIANMGV-NAIIVQNIGPKAYSVFK 88 
                                   68888888888888999999999999999..67777778888999****************95.6667799********** PP

                   AnfO_nitrog  82 kagfsiweiegk 93 
                                   + g+++++ + +
  gi|15668760|ref|NP_247559.1|  89 QLGIDVYKANTT 100
                                   *******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 784.41
//
Query:       gi|15668761|ref|NP_247560.1|  [L=86]
Description: hypothetical protein MJ_0581 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-22   78.5   1.4    3.4e-22   78.3   1.4    1.0  1  Thioredoxin_3  Thioredoxin domain
    0.00034   21.2   0.3    0.00041   21.0   0.3    1.1  1  PTS_IIB        PTS system, Lactose/Cellobiose specific IIB su
     0.0022   18.2   2.6      0.014   15.6   0.8    2.4  2  Glutaredoxin   Glutaredoxin
  ------ inclusion threshold ------
      0.035   14.5   0.0      0.042   14.2   0.0    1.2  1  DUF836         Glutaredoxin-like domain (DUF836)
      0.084   12.9   0.0       0.11   12.4   0.0    1.3  1  FlpD           Methyl-viologen-reducing hydrogenase, delta su


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   1.4   9.4e-26   3.4e-22       2      74 ..       7      78 ..       6      80 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 9.4e-26
                                  EEEEESSSSTTCHHHHHHHHHHCHCCTCECEEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHH CS
                 Thioredoxin_3  2 eikvlgpgCakCpklekavkeaaaekgikaevekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirkl 74
                                   i+++g+gC+kC++++++vk+a++e+gi+ae++kvtd++ei++  V  +P+++ d+++v++Gk+ps+eei++ 
  gi|15668761|ref|NP_247560.1|  7 VIRIFGTGCPKCNQTYENVKKAVEELGIDAEIVKVTDVNEIAEW-VFVTPGVAFDDVIVFEGKIPSVEEIKEE 78
                                  599**************************************998.*************************985 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.3   1.1e-07   0.00041      18      70 ..      23      72 ..      20      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.1e-07
                                  HHHHHHHHHCTEEEEETTEEGGGHHHHHHT-SEEEEEESSGGCTHHHHTTS.E.E CS
                       PTS_IIB 18 eklekaakelgieaegeagveleaeeiaddaDlvllapqvrvkdlarfagk.p.v 70
                                  e+++ka++elgi+ae+++ +  +++ei   a  v+++p v+++d+  f+gk p v
  gi|15668761|ref|NP_247560.1| 23 ENVKKAVEELGIDAEIVKVT--DVNEI---AEWVFVTPGVAFDDVIVFEGKiPsV 72
                                  789*****************..55554...66******************32323 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.8     4e-06     0.014       7      41 ..      13      51 ..       4      64 .. 0.81
   2 ?    2.5   0.1     0.048   1.7e+02      23      45 ..      56      83 ..      51      86 .] 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4e-06
                                  TSSHHHH....HHHHHHHHTTGGEEEEEGCCSHHHHHHH CS
                  Glutaredoxin  7 ptCpyCk....kakrlLkelgvkfeeidvdkdeeireel 41
                                  ++Cp C+    ++k++ +elg++ e++ v++  ei e++
  gi|15668761|ref|NP_247560.1| 13 TGCPKCNqtyeNVKKAVEELGIDAEIVKVTDVNEIAEWV 51
                                  89****83333478899**************99999876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.048
                                  TGGEEEEEGCCSH.....HHHHHHHHHH CS
                  Glutaredoxin 23 gvkfeeidvdkde.....eireelkels 45
                                  gv+f+ + v + +     ei+eelk+++
  gi|15668761|ref|NP_247560.1| 56 GVAFDDVIVFEGKipsveEIKEELKSYL 83
                                  5666666665554555559999*99986 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.2e-05     0.042       8      58 ..      13      62 ..       7      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                  TT-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CCCHCCCCTTTTEEEECTT CS
                        DUF836  8 pgChlCeqakekLkelkleegleleviDIakdeeleakYgleipvlalegv 58
                                   gC+ C q +e +k++ +e g++ e + +++ +e  a++   +p +a+++v
  gi|15668761|ref|NP_247560.1| 13 TGCPKCNQTYENVKKAVEELGIDAEIVKVTDVNE-IAEWVFVTPGVAFDDV 62
                                  49**************9*****999999997444.6677777777777764 PP

>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.2e-05      0.11      69     101 ..      13      45 ..      10      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                          FlpD  69 kGnekaerrveklkelleelgiepeRvrleevs 101
                                   +G  k+++++e++k+++eelgi+ e v+++ v+
  gi|15668761|ref|NP_247560.1|  13 TGCPKCNQTYENVKKAVEELGIDAEIVKVTDVN 45 
                                   678899**********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 539.15
//
Query:       gi|15668762|ref|NP_247561.1|  [L=128]
Description: hypothetical protein MJ_0582 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-28   96.9   4.5    9.4e-28   96.5   4.5    1.1  1  CGGC      CGGC domain


Domain annotation for each model (and alignments):
>> CGGC  CGGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   4.5   5.2e-32   9.4e-28       1     106 []       2     111 ..       2     111 .. 0.93

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 5.2e-32
                          CGGC   1 kiaiirCekved.vCpgv....kClkalkerkgaFeeyeeevelvgfvtCggCpgkkvveklkelk.kegvdvihlssCik 75 
                                   k+aii+C+k+ + +Cpg     +C+ka++e++gaFe+y+ +velv+f+tCggCpg+++ +++k lk   g+++ih+++C+ 
  gi|15668762|ref|NP_247561.1|   2 KVAIIACQKMVEmGCPGKeacvSCFKAINEKSGAFERYK-DVELVAFTTCGGCPGRRFPMRVKLLKtAAGAEAIHIANCT- 80 
                                   8********9555***95456689***************.**************************889**********7. PP

                          CGGC  76 tkkakkeCpei..eeikeaieeklgievvegth 106
                                       ++eCp+i  +ei++++ e+l+i++v gth
  gi|15668762|ref|NP_247561.1|  81 --FLQPECPYInfDEICKKLMEELEIPIVFGTH 111
                                   ..5789****9999******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 810.06
//
Query:       gi|15668763|ref|NP_247562.1|  [L=57]
Description: hypothetical protein MJ_0583 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-05   22.7   2.6       0.19   11.6   0.3    2.3  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
    0.00094   18.5   6.2       0.24   10.9   0.5    2.4  2  zf-ribbon_3      zinc-ribbon domain
     0.0021   17.7   4.4       0.28   11.0   0.6    2.3  2  zinc_ribbon_2    zinc-ribbon domain
     0.0022   17.9   0.5          1    9.4   0.1    2.4  2  Ogr_Delta        Ogr/Delta-like zinc finger
      0.003   17.5   0.6       0.92    9.5   0.1    2.2  2  YhfH             YhfH-like protein
     0.0049   16.8   3.5       0.52   10.3   0.5    2.4  2  Nudix_N_2        Nudix N-terminal
     0.0066   16.4   7.4       0.54   10.3   1.5    2.4  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0069   16.0   1.6        1.7    8.3   0.1    2.3  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
  ------ inclusion threshold ------
      0.013   15.5   4.8      0.032   14.3   4.8    1.6  1  DZR              Double zinc ribbon
      0.013   15.5   3.0          1    9.4   0.1    2.5  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.014   15.1   0.3        3.2    7.5   0.0    2.3  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
      0.016   15.7   6.4       0.16   12.5   0.2    2.1  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.019   15.1   1.0      0.023   14.8   1.0    1.2  1  TerY_C           TerY-C metal binding domain
      0.025   14.6   2.8       0.23   11.4   0.7    2.1  2  zf-C2HC5         Putative zinc finger motif, C2HC5-type
      0.036   13.9   1.0        3.4    7.6   0.1    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.042   13.8   2.7        1.6    8.7   0.6    2.2  2  Cys_rich_CPXG    Cysteine-rich CPXCG
      0.045   13.9   7.9        4.5    7.5   8.4    2.3  1  Zn-ribbon_8      Zinc ribbon domain
      0.052   13.6   2.8        2.8    8.0   0.4    2.1  2  CpXC             CpXC protein
      0.057   13.4   4.0       0.11   12.5   3.7    1.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.07   13.1   5.4       0.16   11.9   5.1    1.8  1  zinc-ribbons_6   zinc-ribbons
       0.08   13.6   9.0       0.28   11.9   0.2    2.4  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        0.1   12.4   3.9        5.6    6.8   0.1    2.2  2  PADR1            PADR1 (NUC008) domain
       0.13   12.6   4.0        1.9    8.8   0.9    2.3  2  zinc_ribbon_9    zinc-ribbon
       0.14   12.1   6.5       0.26   11.2   1.1    2.2  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.23   12.0   3.9        5.3    7.7   0.5    2.4  2  zf-C2H2          Zinc finger, C2H2 type
       0.24   11.5   4.2       0.56   10.3   4.2    1.6  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.26   11.0   4.9       0.29   10.9   1.4    2.1  2  YdjO             Cold-inducible protein YdjO
       0.29   11.5   4.5        1.9    8.9   0.1    2.3  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.34   11.9   3.8         10    7.2   0.6    2.4  2  zf-C2H2_4        C2H2-type zinc finger
       0.37   10.3   8.3        1.4    8.5   0.3    2.4  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.44   10.6   2.1       0.83    9.7   0.4    1.8  2  PDCD2_C          Programmed cell death protein 2, C-terminal 
       0.51   10.4   3.3        1.3    9.1   3.3    1.5  1  DUF1451          Zinc-ribbon containing domain
       0.55    9.6   8.8          1    8.7   8.8    1.7  1  zf-TFIIB         Transcription factor zinc-finger
       0.86    9.6   7.5         35    4.4   7.5    2.1  2  Prok-RING_1      Prokaryotic RING finger family 1
       0.99    9.4  10.5        2.2    8.3   0.1    2.6  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
        1.1    9.3   7.4        3.2    7.8   0.3    2.9  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
        4.9    7.6  11.3        3.7    8.0   0.6    2.7  2  zf-IS66          zinc-finger binding domain of transposase IS
        5.4    5.7   5.0        8.1    5.1   5.0    1.5  1  NRDD             Anaerobic ribonucleoside-triphosphate reduct


Domain annotation for each model (and alignments):
>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.3    0.0004      0.19       3      14 ..       7      18 ..       6      21 .. 0.90
   2 !   11.3   0.1   0.00048      0.23       3      13 ..      33      43 ..      32      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0004
                                  E-SSS--EEEEE CS
                zf-C4_Topoisom  3 kCPkCggdLvlk 14
                                   CPkCg+ L +k
  gi|15668763|ref|NP_247562.1|  7 ICPKCGKRLRYK 18
                                  5********998 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00048
                                  E-SSS--EEEE CS
                zf-C4_Topoisom  3 kCPkCggdLvl 13
                                   CP Cg+++v 
  gi|15668763|ref|NP_247562.1| 33 NCPDCGEKMVH 43
                                  5********97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.5   0.00051      0.24      18      26 .]       7      15 ..       5      15 .. 0.75
   2 !   10.3   0.1   0.00078      0.37      17      25 ..      32      40 ..      29      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00051
                   zf-ribbon_3 18 vCpyCGtkl 26
                                  +Cp+CG++l
  gi|15668763|ref|NP_247562.1|  7 ICPKCGKRL 15
                                  688888876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00078
                   zf-ribbon_3 17 nvCpyCGtk 25
                                  ++Cp CG+k
  gi|15668763|ref|NP_247562.1| 32 PNCPDCGEK 40
                                  59****998 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.6   0.00059      0.28       2       9 ..       8      15 ..       7      23 .. 0.74
   2 !    8.3   0.2    0.0039       1.9       2       8 ..      34      40 ..      33      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00059
                 zinc_ribbon_2  2 CpnCGael 9 
                                  Cp+CG+ l
  gi|15668763|ref|NP_247562.1|  8 CPKCGKRL 15
                                  99999877 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0039
                 zinc_ribbon_2  2 CpnCGae 8 
                                  Cp CG++
  gi|15668763|ref|NP_247562.1| 34 CPDCGEK 40
                                  8888887 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.012       5.6       2      10 ..       8      16 ..       7      19 .. 0.85
   2 !    9.4   0.1    0.0022         1       1      10 [.      33      42 ..      33      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.012
                     Ogr_Delta  2 CPhCgapaa 10
                                  CP+Cg++ +
  gi|15668763|ref|NP_247562.1|  8 CPKCGKRLR 16
                                  *****9876 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0022
                     Ogr_Delta  1 rCPhCgapaa 10
                                  +CP Cg++++
  gi|15668763|ref|NP_247562.1| 33 NCPDCGEKMV 42
                                  6*******96 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.018       8.5      16      23 ..       8      15 ..       7      20 .. 0.87
   2 !    9.5   0.1    0.0019      0.92      15      23 ..      33      41 ..      29      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.018
                          YhfH 16 CteCGkei 23
                                  C++CGk +
  gi|15668763|ref|NP_247562.1|  8 CPKCGKRL 15
                                  *****986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0019
                          YhfH 15 kCteCGkei 23
                                   C++CG+++
  gi|15668763|ref|NP_247562.1| 33 NCPDCGEKM 41
                                  5*******9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.5    0.0011      0.52       3      14 ..       8      19 ..       7      23 .. 0.92
   2 !    7.4   0.1    0.0084         4       3      13 ..      34      44 ..      33      56 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                                  -TTT--B-EEE- CS
                     Nudix_N_2  3 CsqCGtpvelri 14
                                  C++CG+++++++
  gi|15668763|ref|NP_247562.1|  8 CPKCGKRLRYKV 19
                                  *********997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0084
                                  -TTT--B-EEE CS
                     Nudix_N_2  3 CsqCGtpvelr 13
                                  C+ CG+++ + 
  gi|15668763|ref|NP_247562.1| 34 CPDCGEKMVHD 44
                                  ******98764 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   1.2    0.0028       1.3      20      31 ..       7      18 ..       3      22 .. 0.81
   2 !   10.3   1.5    0.0012      0.54      19      37 ..      32      53 ..      20      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0028
                 Zn_Tnp_IS1595 20 vCPhCgsrkayr 31
                                  +CP+Cg+r  y+
  gi|15668763|ref|NP_247562.1|  7 ICPKCGKRLRYK 18
                                  7*****996665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0012
                 Zn_Tnp_IS1595 19 fvCPhCgsr...kayriktrgl 37
                                  + CP Cg +    ++++k+r++
  gi|15668763|ref|NP_247562.1| 32 PNCPDCGEKmvhDYTSLKGRRR 53
                                  78******97766777777665 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0036       1.7       4      11 ..       7      14 ..       5      16 .. 0.84
   2 !    7.0   0.1    0.0092       4.3       5      13 ..      34      42 ..      32      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0036
                        zf_UBZ  4 lCerCgke 11
                                  +C++Cgk+
  gi|15668763|ref|NP_247562.1|  7 ICPKCGKR 14
                                  8*****98 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0092
                        zf_UBZ  5 CerCgkeip 13
                                  C++Cg+++ 
  gi|15668763|ref|NP_247562.1| 34 CPDCGEKMV 42
                                  ******985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   4.8   6.8e-05     0.032      15      38 ..       8      41 ..       5      48 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.8e-05
                           DZR 15 CseCgtklkavaa..........edrCpsCgekv 38
                                  C++Cg++l+   +            +Cp Cgek+
  gi|15668763|ref|NP_247562.1|  8 CPKCGKRLRYKVDvcpcmaseveLPNCPDCGEKM 41
                                  6666666653333555555555589999999984 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.017       7.9       2       9 ..       8      15 ..       7      21 .. 0.86
   2 ?    9.4   0.1    0.0022         1       1      10 [.      33      42 ..      33      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.017
                DNA_ligase_ZBD  2 CPvCGsav 9 
                                  CP CG  +
  gi|15668763|ref|NP_247562.1|  8 CPKCGKRL 15
                                  *****877 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0022
                DNA_ligase_ZBD  1 hCPvCGsavv 10
                                  +CP CG + v
  gi|15668763|ref|NP_247562.1| 33 NCPDCGEKMV 42
                                  6*****9877 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0067       3.2       6      12 ..       8      14 ..       4      19 .. 0.76
   2 ?    5.6   0.1     0.026        12       6      14 ..      34      42 ..      34      44 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0067
                 zf-NADH-PPase  6 CgrCGap 12
                                  C++CG +
  gi|15668763|ref|NP_247562.1|  8 CPKCGKR 14
                                  8888876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.026
                 zf-NADH-PPase  6 CgrCGapte 14
                                  C+ CG +++
  gi|15668763|ref|NP_247562.1| 34 CPDCGEKMV 42
                                  888888876 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.6     0.033        16       6      18 ..       6      18 ..       5      24 .. 0.89
   2 ?   12.5   0.2   0.00034      0.16       8      26 ..      34      53 ..      31      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.033
               Zn_ribbon_recom  6 lrCgeCGspmtrr 18
                                  l+C +CG++++++
  gi|15668763|ref|NP_247562.1|  6 LICPKCGKRLRYK 18
                                  79*******9875 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00034
               Zn_ribbon_recom  8 CgeCGspmtrrkrk.gkrhy 26
                                  C +CG +m++ +++ ++r++
  gi|15668763|ref|NP_247562.1| 34 CPDCGEKMVHDYTSlKGRRR 53
                                  **********9988866554 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.0   4.8e-05     0.023      77     120 ..       8      49 ..       3      57 .] 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.8e-05
                        TerY_C  77 CPhCgnalafavCeCgkllCidgeeeatCpwCgkevkfgeasee 120
                                   CP Cg +l   v  C  +   ++ e   Cp Cg+++  +++s +
  gi|15668763|ref|NP_247562.1|   8 CPKCGKRLRYKVDVCPCM--ASEVELPNCPDCGEKMVHDYTSLK 49 
                                   *****9876655555433..3688999*******9998875544 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.14        66      17      25 ..       5      13 ..       1      18 [. 0.74
   2 ?   11.4   0.7    0.0005      0.23       3      25 ..      21      39 ..      19      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.14
                      zf-C2HC5 17 apnClnCGk 25
                                    +C +CGk
  gi|15668763|ref|NP_247562.1|  5 NLICPKCGK 13
                                  567888887 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0005
                      zf-C2HC5  3 kCnCqatrHpLleaapnClnCGk 25
                                   C C+a++ +L    pnC  CG 
  gi|15668763|ref|NP_247562.1| 21 VCPCMASEVEL----PNCPDCGE 39
                                  6*********9....******96 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0072       3.4       3      10 ..       8      15 ..       6      21 .. 0.75
   2 ?    5.2   0.1      0.04        19       3      11 ..      34      42 ..      32      47 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0072
                       TFIIS_C  3 CpkCgsre 10
                                  CpkCg+r 
  gi|15668763|ref|NP_247562.1|  8 CPKCGKRL 15
                                  99999875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.04
                       TFIIS_C  3 CpkCgsrea 11
                                  Cp Cg++ +
  gi|15668763|ref|NP_247562.1| 34 CPDCGEKMV 42
                                  999999876 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.6    0.0034       1.6       2      16 ..       7      21 ..       6      30 .. 0.90
   2 ?    5.5   0.1     0.033        16       2      10 ..      33      41 ..      33      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0034
                 Cys_rich_CPXG  2 qCPyCgeeievlvDl 16
                                  +CP Cg++++  vD+
  gi|15668763|ref|NP_247562.1|  7 ICPKCGKRLRYKVDV 21
                                  6************97 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.033
                 Cys_rich_CPXG  2 qCPyCgeei 10
                                  +CP Cge++
  gi|15668763|ref|NP_247562.1| 33 NCPDCGEKM 41
                                  5******97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   8.4    0.0096       4.5       8      36 ..       8      41 ..       8      44 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0096
                   Zn-ribbon_8  8 CeeCghefe......vlqsis.dapltaCPeCgsev 36
                                  C +Cg++        +   ++ + +l+ CP+Cg+++
  gi|15668763|ref|NP_247562.1|  8 CPKCGKRLRykvdvcPC--MAsEVELPNCPDCGEKM 41
                                  99999999998864333..333666778*****954 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4     0.006       2.8      38      52 ..       6      20 ..       3      31 .. 0.79
   2 ?    6.7   0.2     0.015         7      39      52 ..      33      46 ..      24      53 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.006
                          CpXC 38 atCpkCgatakleap 52
                                    CpkCg++ +++ +
  gi|15668763|ref|NP_247562.1|  6 LICPKCGKRLRYKVD 20
                                  579999999988765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.015
                          CpXC 39 tCpkCgatakleap 52
                                   Cp+Cg++   ++ 
  gi|15668763|ref|NP_247562.1| 33 NCPDCGEKMVHDYT 46
                                  79999998877775 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.7   0.00023      0.11      30      61 ..       7      46 ..       6      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00023
                OrfB_Zn_ribbon 30 tCseCgsknke........alsgrtfkCpnCgfeadrDvn 61
                                   C++Cg+++++        a + ++ +Cp+Cg ++  D+ 
  gi|15668763|ref|NP_247562.1|  7 ICPKCGKRLRYkvdvcpcmASEVELPNCPDCGEKMVHDYT 46
                                  5********************************9988876 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   5.1   0.00035      0.16       2      39 ..       7      41 ..       6      47 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00035
                                  --SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S-- CS
                zinc-ribbons_6  2 kCpeCqqelekrgeqyhCeaCqedlkkealCpeCeqel 39
                                  +Cp+C + l+ + +   C  C ++  + + Cp+C++++
  gi|15668763|ref|NP_247562.1|  7 ICPKCGKRLRYKVD--VCP-CMASEVELPNCPDCGEKM 41
                                  7********96663..565.4455556799*****987 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.6     0.022        10       5      15 ..       8      18 ..       5      22 .. 0.83
   2 ?   11.9   0.2    0.0006      0.28       3      16 ..      32      45 ..      30      56 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.022
                       zf-ISL3  5 CPnCgsktvvk 15
                                  CP+Cg++ ++k
  gi|15668763|ref|NP_247562.1|  8 CPKCGKRLRYK 18
                                  ******97665 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0006
                       zf-ISL3  3 hrCPnCgsktvvkh 16
                                  + CP Cg+k+v++ 
  gi|15668763|ref|NP_247562.1| 32 PNCPDCGEKMVHDY 45
                                  56*******87553 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.8     0.012       5.7      16      30 ..       8      21 ..       6      29 .. 0.78
   2 ?    6.8   0.1     0.012       5.6      13      24 ..      31      41 ..      30      49 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                         PADR1 16 CpeCkegqlvfdssg 30
                                  Cp+C+  +l+++ + 
  gi|15668763|ref|NP_247562.1|  8 CPKCG-KRLRYKVDV 21
                                  *****.999998774 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.012
                         PADR1 13 lekCpeCkegql 24
                                  l++Cp C+e  +
  gi|15668763|ref|NP_247562.1| 31 LPNCPDCGEK-M 41
                                  89******54.3 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.069        32      23      29 ..       7      13 ..       4      14 .. 0.81
   2 ?    8.8   0.9    0.0041       1.9      12      34 ..      19      44 ..      16      45 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.069
                 zinc_ribbon_9 23 lCPhCgg 29
                                  +CP Cg 
  gi|15668763|ref|NP_247562.1|  7 ICPKCGK 13
                                  6****96 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0041
                 zinc_ribbon_9 12 Vsvspdedsd...vlCPhCgggFVEe 34
                                  V+v+p   s+   + CP+Cg   V+ 
  gi|15668763|ref|NP_247562.1| 19 VDVCPCMASEvelPNCPDCGEKMVHD 44
                                  666666666634437*****998876 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.1   0.00056      0.26      14      31 ..       8      24 ..       7      31 .. 0.88
   2 ?    3.9   1.0       0.1        49      14      18 ..      34      38 ..      24      40 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00056
                       DUF35_N 14 CpdCGtvqfPPravCphC 31
                                  Cp+CG+   ++  vCp C
  gi|15668763|ref|NP_247562.1|  8 CPKCGKRLRYKVDVCP-C 24
                                  ***************9.6 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.1
                       DUF35_N 14 CpdCG 18
                                  CpdCG
  gi|15668763|ref|NP_247562.1| 34 CPDCG 38
                                  88887 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.5     0.011       5.3       3      13 ..       8      18 ..       6      23 .. 0.82
   2 ?    5.7   0.2     0.049        23       3       8 ..      34      39 ..      33      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.011
                                  ETTTTEEESSH CS
                       zf-C2H2  3 CpdCgksFkrk 13
                                  Cp+Cgk+ + k
  gi|15668763|ref|NP_247562.1|  8 CPKCGKRLRYK 18
                                  ******98776 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.049
                                  ETTTTE CS
                       zf-C2H2  3 CpdCgk 8 
                                  CpdCg+
  gi|15668763|ref|NP_247562.1| 34 CPDCGE 39
                                  *****5 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   4.2    0.0012      0.56      71      98 ..       6      43 ..       2      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0012
                                  EEETTTS-EEECHHHHH...........S-TTTSSS-EE CS
                          HypA 71 vrCreCgkefeleekal...........rCpkCgsadve 98
                                  + C +Cgk+ + + + +           +Cp+Cg++ v+
  gi|15668763|ref|NP_247562.1|  6 LICPKCGKRLRYKVD-VcpcmasevelpNCPDCGEKMVH 43
                                  78*******997765.23567788899999999988664 PP

>> YdjO  Cold-inducible protein YdjO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.0      0.71   3.3e+02      42      51 ..       8      17 ..       5      25 .. 0.76
   2 ?   10.9   1.4   0.00062      0.29      38      56 ..      30      48 ..      18      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.71
                          YdjO 42 CplCkseMvk 51
                                  Cp C++++  
  gi|15668763|ref|NP_247562.1|  8 CPKCGKRLRY 17
                                  9***998765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00062
                          YdjO 38 eePtCplCkseMvkevrmL 56
                                  e P+Cp C+ +Mv++  +L
  gi|15668763|ref|NP_247562.1| 30 ELPNCPDCGEKMVHDYTSL 48
                                  67***********987665 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.5      0.16        76       6      12 ..       8      14 ..       5      25 .. 0.88
   2 ?    8.9   0.1     0.004       1.9       2      17 ..      30      45 ..      29      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.16
               Lar_restr_allev  6 CPfCggr 12
                                  CP Cg+r
  gi|15668763|ref|NP_247562.1|  8 CPKCGKR 14
                                  ****987 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.004
               Lar_restr_allev  2 eLkpCPfCggravler 17
                                  eL  CP Cg++ v+  
  gi|15668763|ref|NP_247562.1| 30 ELPNCPDCGEKMVHDY 45
                                  799*******988765 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.6     0.022        10       2      13 ..       7      18 ..       6      22 .. 0.81
   2 ?    5.7   0.0     0.071        33       2      16 ..      33      48 ..      32      54 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.022
                     zf-C2H2_4  2 kCpiCgksFssk 13
                                  +Cp Cgk+ + k
  gi|15668763|ref|NP_247562.1|  7 ICPKCGKRLRYK 18
                                  7******98765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.071
                     zf-C2H2_4  2 kCpiC.gksFsskkaL 16
                                   Cp C  k  +++++L
  gi|15668763|ref|NP_247562.1| 33 NCPDCgEKMVHDYTSL 48
                                  5****54444477666 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   2.6      0.04        19       2       9 ..       7      14 ..       6      29 .. 0.78
   2 ?    8.5   0.3     0.003       1.4       3      16 ..      34      46 ..      32      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.04
                                  EETTTTCE CS
                  TF_Zn_Ribbon  2 kCPnCgst 9 
                                  +CP+Cg +
  gi|15668763|ref|NP_247562.1|  7 ICPKCGKR 14
                                  57777765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.003
                                  ETTTTCEECHEETS CS
                  TF_Zn_Ribbon  3 CPnCgstnlveDpe 16
                                  CP+Cg ++ v D+ 
  gi|15668763|ref|NP_247562.1| 34 CPDCGEKM-VHDYT 46
                                  99999875.88875 PP

>> PDCD2_C  Programmed cell death protein 2, C-terminal putative domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.048        23     109     130 ..       8      29 ..       5      31 .. 0.89
   2 ?    9.7   0.4    0.0018      0.83      83     119 ..      15      44 ..      12      46 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.048
                       PDCD2_C 109 CsnCgskrvFEfQlmPqlinvL 130
                                   C++Cg++  + + + P + +++
  gi|15668763|ref|NP_247562.1|   8 CPKCGKRLRYKVDVCPCMASEV 29 
                                   ****************998776 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0018
                       PDCD2_C  83 lRYelggkPLwlsskkspeeesdipkCsnCgskrvFE 119
                                   lRY+++  P ++s       e ++p+C+ Cg+k+v++
  gi|15668763|ref|NP_247562.1|  15 LRYKVDVCPCMAS-------EVELPNCPDCGEKMVHD 44 
                                   7888888787777.......458**********9975 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.3    0.0027       1.3     114     141 ..       5      40 ..       2      43 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0027
                       DUF1451 114 tlvCekCgkelalk........kteeippCpkCgat 141
                                   +l+C kCgk+l++k        +  e+p+Cp+Cg++
  gi|15668763|ref|NP_247562.1|   5 NLICPKCGKRLRYKvdvcpcmaSEVELPNCPDCGEK 40 
                                   699*******9876222222226789*******986 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   8.8    0.0022         1       2      26 ..       8      38 ..       7      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0022
                      zf-TFIIB  2 CPkCqdele.eser.....ggveidyCpqCr 26
                                  CPkC+  l+ ++++     ++ve+  Cp+C+
  gi|15668763|ref|NP_247562.1|  8 CPKCGKRLRyKVDVcpcmaSEVELPNCPDCG 38
                                  **********777777777***********7 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   7.5     0.075        35       5      23 ..       6      24 ..       3      41 .. 0.81
   2 ?    3.7   0.4      0.12        58       7      13 ..      34      40 ..      28      45 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.075
                   Prok-RING_1  5 kkCpvCgkelkeedDiVvC 23
                                   +Cp Cgk+l+ + D+  C
  gi|15668763|ref|NP_247562.1|  6 LICPKCGKRLRYKVDVCPC 24
                                  68***********887655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.12
                   Prok-RING_1  7 CpvCgke 13
                                  Cp Cg++
  gi|15668763|ref|NP_247562.1| 34 CPDCGEK 40
                                  5555555 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0047       2.2      19      26 ..       5      12 ..       4      13 .. 0.86
   2 ?    7.4   1.2    0.0088       4.2       1       9 [.      30      38 ..      30      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0047
                PhnA_Zn_Ribbon 19 llvCpeCa 26
                                  +l+Cp+C+
  gi|15668763|ref|NP_247562.1|  5 NLICPKCG 12
                                  59*****8 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0088
                PhnA_Zn_Ribbon  1 tlpkCplCa 9 
                                  +lp+Cp C+
  gi|15668763|ref|NP_247562.1| 30 ELPNCPDCG 38
                                  6999**995 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0067       3.2      25      37 ..       6      18 ..       4      19 .. 0.77
   2 ?    3.7   1.9      0.13        59       7      14 ..      34      41 ..      33      57 .] 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0067
                Zn_ribbon_SprT 25 YrCrrCkgtLrgk 37
                                   +C++C+ +Lr+k
  gi|15668763|ref|NP_247562.1|  6 LICPKCGKRLRYK 18
                                  6899998888865 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.13
                Zn_ribbon_SprT  7 CtgCgrey 14
                                  C++Cg++ 
  gi|15668763|ref|NP_247562.1| 34 CPDCGEKM 41
                                  9****875 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   4.4      0.17        79       3      10 ..       7      15 ..       5      32 .. 0.74
   2 ?    8.0   0.6    0.0079       3.7       3      12 ..      33      42 ..      32      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.17
                       zf-IS66  3 tCpcCGg.l 10
                                  +Cp+CG+ l
  gi|15668763|ref|NP_247562.1|  7 ICPKCGKrL 15
                                  7*****944 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0079
                       zf-IS66  3 tCpcCGgllk 12
                                  +Cp+CG +++
  gi|15668763|ref|NP_247562.1| 33 NCPDCGEKMV 42
                                  7*****9754 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   5.0     0.017       8.1     506     531 ..      18      42 ..       5      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.017
                                   -EEEETT.--EESSSB-TTT--BE.E CS
                          NRDD 506 kidvCnecgykgeiekCpkCgseeev 531
                                   k+dvC+    + e  +Cp Cg++  v
  gi|15668763|ref|NP_247562.1|  18 KVDVCPCMASEVELPNCPDCGEKM-V 42 
                                   7899998888888899*****543.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 327.45
//
Query:       gi|15668764|ref|NP_247563.1|  [L=365]
Description: hypothetical protein MJ_0584 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     8e-103  343.6  28.1   9.8e-103  343.3  28.1    1.0  1  ArsP_1      Predicted permease
  ------ inclusion threshold ------
      0.011   15.4   0.2      0.011   15.4   0.2    3.2  4  DUF2208     Predicted membrane protein (DUF2208)


Domain annotation for each model (and alignments):
>> ArsP_1  Predicted permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.3  28.1  1.1e-106  9.8e-103       4     293 ..      16     361 ..      14     362 .. 0.99

  Alignments for each domain:
  == domain 1  score: 343.3 bits;  conditional E-value: 1.1e-106
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ArsP_1   4 ealtlfasilleallaLvlgflisgaiqvfvkeekiielLg.prnrlisllvaallGfllpvCscsavPlarrllkkGapl 83 
                                   +++t++++++++++laL+++fl++g+i++++++++ii+++g +++++is++vaa++G+ll+vCsc+++Pl+++++k+Ga++
  gi|15668764|ref|NP_247563.1|  16 MINTIIDYLNVNRVLALLMAFLMAGGIASMINKNFIIKYFGsNTPKYISYTVAAVSGSLLAVCSCTILPLFASIYKRGAGI 96 
                                   699****************************************************************************** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                        ArsP_1  84 gaavaFlvaaPainiiaiiltlillgwqllvarivlalivaiviglvleylfkeeelekaarevaeaglek.......... 154
                                   g+a++Fl+++Pain++ai+++++llgw+++++r+v+a++v+i+igl++e++fk++e+++a r v++a++++          
  gi|15668764|ref|NP_247563.1|  97 GPATTFLFSGPAINVLAIFYSAALLGWDIGFLRAVFAVVVSILIGLSMEIIFKSHEKKRALR-VPKADKISdrplyqtitf 176
                                   **********************************************************9997.999999999********* PP

                                   ......................................xxxxxxxxxxxxxxxxxxxxx.xxxx.......xxxxxxxxxx RF
                        ArsP_1 155 ......................................ltlkpklealkafaknevkew.lelg.......kyLiiGvaia 189
                                                                         l+++ +++++++f+++e+k+w +e++       ++LiiGvaia
  gi|15668764|ref|NP_247563.1| 177 falqfimllvitaspklfptlsmplydgfllkhllfiiLGIILAVTTKIWFKDEEIKNWlRESFtllkivfPLLIIGVAIA 257
                                   ***********************************************************999999**************** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ArsP_1 190 gviqaflpesvllsllggnsvsssllamligvvlyvcslgevpfiaalfesglalGsalAfLlagpllslpellillkvlk 270
                                   g+i+a++p s++++++ggns++++++a++ig+++y+++l+evp+i+al+e+g+++G+a+A+Llagp+ls+p++l+++kvl+
  gi|15668764|ref|NP_247563.1| 258 GAIKAIIPPSYIATYVGGNSITANFIASFIGALMYFATLTEVPIIKALMELGMGVGPAMALLLAGPSLSIPTVLTISKVLG 338
                                   ********************************************************************************* PP

                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                        ArsP_1 271 kklvavllglvvvsvvlaglvin 293
                                   k++++++lglvv++++++g++++
  gi|15668764|ref|NP_247563.1| 339 KTKALTYLGLVVIFSTICGYIAG 361
                                   *********************87 PP

>> DUF2208  Predicted membrane protein (DUF2208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   1.1     0.084   7.6e+02     105     143 ..       7      46 ..       3      69 .. 0.57
   2 ?    0.7   0.4     0.038   3.4e+02     104     143 ..     145     186 ..     125     202 .. 0.46
   3 ?    0.6   0.3      0.04   3.6e+02      67     115 ..     154     202 ..     142     218 .. 0.67
   4 ?   15.4   0.2   1.2e-06     0.011      69     151 ..     222     307 ..     220     327 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.084
                       DUF2208 105 fllyryiiplassllgev.leeklarflaflalFealfli 143
                                   +++ ++i  +++++++ + ++++la ++afl+  ++  +i
  gi|15668764|ref|NP_247563.1|   7 SFIMNIINVMINTIIDYLnVNRVLALLMAFLMAGGIASMI 46 
                                   4455556666666665555566666666666554443333 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.038
                       DUF2208 104 ffllyryiipla..ssllgevleeklarflaflalFealfli 143
                                    +++ +   ++a  +  +++++++ l++ ++f+al  +++l+
  gi|15668764|ref|NP_247563.1| 145 EIIFKSHEKKRAlrVPKADKISDRPLYQTITFFALQFIMLLV 186
                                   444333333322112234444555555555555443333332 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.04
                       DUF2208  67 knalkliekDeelqkelkeqlkasmitllllliviilffllyryiipla 115
                                   k al + + D+   + l + ++++ +++++ll++ +   l+  + +pl+
  gi|15668764|ref|NP_247563.1| 154 KRALRVPKADKISDRPLYQTITFFALQFIMLLVITASPKLFPTLSMPLY 202
                                   4567777888888888888888888887777776665555555555555 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 1.2e-06
                       DUF2208  69 alkliekDeelqkelkeqlkasmitllllliviilffllyryiiplassllgev.....leeklarflaflalFealflis 144
                                   ++k+  kDee+ + l+e ++ + i + ll+i+ +++  +  +i+p +  +++ v     + +++a f+  l++F++l+ + 
  gi|15668764|ref|NP_247563.1| 222 TTKIWFKDEEIKNWLRESFTLLKIVFPLLIIGVAIAGAIKAIIPPSY--IATYVggnsiTANFIASFIGALMYFATLTEVP 300
                                   578999*************************************9944..33333434567788888888999999998887 PP

                       DUF2208 145 mflrlla 151
                                   ++  l+ 
  gi|15668764|ref|NP_247563.1| 301 IIKALME 307
                                   7766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2281.73
//
Query:       gi|15668765|ref|NP_247564.1|  [L=205]
Description: hypothetical protein MJ_0585 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0007   19.7   3.1     0.0016   18.6   3.1    1.6  1  DUF4337          Domain of unknown function (DUF4337)
     0.0071   16.3   6.2      0.014   15.4   6.2    1.4  1  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
     0.0085   15.7   2.2      0.012   15.3   2.2    1.1  1  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
  ------ inclusion threshold ------
      0.012   16.0   5.1      0.015   15.6   5.1    1.1  1  OmpH             Outer membrane protein (OmpH-like)
      0.013   15.5   4.0      0.019   14.9   4.0    1.2  1  FlxA             FlxA-like protein
      0.013   14.7   5.1      0.017   14.4   5.1    1.1  1  Tho2             Transcription factor/nuclear export subunit 
      0.046   13.0   2.3      0.062   12.6   0.3    1.9  2  ABC2_membrane_2  ABC-2 family transporter protein
       0.13   12.9   2.7       0.22   12.2   2.7    1.4  1  Sas10_Utp3       Sas10/Utp3/C1D family
       0.13   12.7   6.9      0.096   13.1   2.9    2.0  2  Snapin_Pallidin  Snapin/Pallidin
       0.17   12.4   3.5       0.23   12.0   3.5    1.1  1  DUF2115          Uncharacterized protein conserved in archaea
       0.52   10.0   9.5        1.2    8.9   9.5    1.8  1  EMC3_TMCO1       Integral membrane protein EMC3/TMCO1-like
        0.7    8.4   6.8       0.88    8.1   6.8    1.0  1  FapA             Flagellar Assembly Protein A
       0.74   10.1   2.6        5.7    7.3   0.1    2.6  3  Viral_Beta_CD    Viral Beta C/D like family
       0.99    9.5  10.6        3.1    7.9   0.3    3.0  3  DUF4315          Domain of unknown function (DUF4315)
        1.7    9.0   9.8        4.7    7.6   4.0    2.4  2  TSC22            TSC-22/dip/bun family
        2.1    9.0   8.5        9.2    7.0   8.4    1.8  2  YabA             Initiation control protein YabA
        9.6    6.3  14.8        9.8    6.3   1.1    2.2  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding


Domain annotation for each model (and alignments):
>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   3.1   1.5e-06    0.0016      56     148 ..      32     137 ..      24     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                       DUF4337  56 eleqlelllkak..aeelaaavdkkiakykkkiarykkekkeikk...............kAkeleaerdeaneasdkfdl 119
                                   e ++l+++lk+   ++++++    +i++yk+k ++  ++++e+k                +  ++++e  e+n +  k+ +
  gi|15668765|ref|NP_247564.1|  32 EINELTVKLKELesKNPNDE----RIEEYKEKLKQLIEKQHELKSqnlkynetlayiqseEYWKMQEEIWEYNNKVMKWFI 108
                                   45666666655533444444....555555555555555555555445588888888666666777777888888888*** PP

                       DUF4337 120 asalLqiaIvlaaialltkkklllylslv 148
                                   a  +L ++I+la + +l k k ll+l+++
  gi|15668765|ref|NP_247564.1| 109 AISILILGIILATLWILRKDKFLLFLAIF 137
                                   ***********************999986 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   6.2   1.3e-05     0.014      98     179 ..      45     127 ..      19     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                   EMP24_GP25L  98 gseasdykdsakkekletleselkkleekldsikreqkylrere.erlrdtnestnsrvvwwsilqllvlvlvavlqvyyL 177
                                   +++ +d+  +  kekl++l ++ ++l+++  +  +++ y++  e  ++++ + + n++v++w i+  ++++++ +  +++L
  gi|15668765|ref|NP_247564.1|  45 SKNPNDERIEEYKEKLKQLIEKQHELKSQNLKYNETLAYIQSEEyWKMQEEIWEYNNKVMKWFIAISILILGIILATLWIL 125
                                   2222334445569999999999999999999999999999987747*********************************** PP

                   EMP24_GP25L 178 kr 179
                                   ++
  gi|15668765|ref|NP_247564.1| 126 RK 127
                                   96 PP

>> HAUS6_N  HAUS augmin-like complex subunit 6 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.2   1.1e-05     0.012     131     216 ..      15      98 ..       9     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                       HAUS6_N 131 alevreaaskkaqdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelkaekeaakkekke 211
                                   +l++++a++++ +++sk + +  v+l+++   k+  d+ +++y+e+++ l +k+ el++++ ++++ l   +++ +  k++
  gi|15668765|ref|NP_247564.1|  15 NLSLVNAIDDNISNYSKEINELTVKLKELE-SKNPNDERIEEYKEKLKQLIEKQHELKSQNLKYNETLAYIQSE-EYWKMQ 93 
                                   56788899999999*******999998765.66666789**************************999754444.444554 PP

                       HAUS6_N 212 aseda 216
                                   +++++
  gi|15668765|ref|NP_247564.1|  94 EEIWE 98 
                                   45544 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   5.1   1.5e-05     0.015      24     107 ..      22     105 ..      12     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.....-HHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHH CS
                          OmpH  24 lekkfkklqaeleakekelqklqeelqkkakkle....keekeqelqkkeqelqqkqqqka.qelqkkqqellkpildkin 99 
                                   +++ ++++ +e++++  +l++l+ +     ++ e     +ek ++l +k+ el+  q+ k+ + l+  q e++ +++++i 
  gi|15668765|ref|NP_247564.1|  22 IDDNISNYSKEINELTVKLKELESKN----PNDErieeYKEKLKQLIEKQHELKS-QNLKYnETLAYIQSEEYWKMQEEIW 97 
                                   45555666666665555555555444....443246678999999**********.88888899***************** PP

                                   HHHHHHHH CS
                          OmpH 100 kaikevak 107
                                   +  ++v+k
  gi|15668765|ref|NP_247564.1|  98 EYNNKVMK 105
                                   99999997 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   4.0   1.8e-05     0.019      13      57 ..      20      67 ..      14     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                          FlxA 13 sgsasqiasLqkQiknlqkqLkelses...deltkeekkkqqqliqaQ 57
                                  + ++++i++  k+i++l+ +Lkel ++   de  +e k+k +qli++Q
  gi|15668765|ref|NP_247564.1| 20 NAIDDNISNYSKEINELTVKLKELESKnpnDERIEEYKEKLKQLIEKQ 67
                                  568999*******************99896666666666888888888 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   5.1   1.6e-05     0.017      10      91 ..      11      88 ..       7     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                          Tho2 10 vtFWslslyD.iyvpkeqYekeieklkseieelakdrsderaaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLkeek 91
                                   +F +lsl + i  + ++Y kei++l+ +++el++++     + ++ ++ k++lk+liek ++E+k+q  +++++++++++e 
  gi|15668765|ref|NP_247564.1| 11 IVFSNLSLVNaIDDNISNYSKEINELTVKLKELESKNP----NDERIEEYKEKLKQLIEK-QHELKSQNLKYNETLAYIQSEE 88
                                  56777776543777889****************44443....356667777777777888.899999***********99875 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   5.9e-05     0.062      18      97 ..       4     124 ..       2     148 .. 0.88
   2 ?   -0.9   0.8      0.75   7.9e+02     213     277 ..     136     197 ..     129     202 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
               ABC2_membrane_2  18 llltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasde.aedtdqdlkv..................... 76 
                                   l++ +ll+++   l  +++++++ +++ k+i e+t++l+ +e  ++ de +e+++++lk+                     
  gi|15668765|ref|NP_247564.1|   4 LAFLILLIVF-SNLSLVNAIDDNISNYSKEINELTVKLKELESKNPNDErIEEYKEKLKQliekqhelksqnlkynetlay 83 
                                   4667777777.999*******************************998835667777888********************* PP

               ABC2_membrane_2  77 ....................vstimavlipviaalfgadai 97 
                                                       ++ ++a+ i +++++++   i
  gi|15668765|ref|NP_247564.1|  84 iqseeywkmqeeiweynnkvMKWFIAISILILGIILATLWI 124
                                   ****************9999778888888888888877665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.75
               ABC2_membrane_2 213 lygvaellagpavpqeindflsllsptsayntllneilagsdlnalgstatnllilllllavllv 277
                                    +g++ +++ +++ +++  +++ l+ ++++++++ e  +gs      +  t  +++ +++++ l+
  gi|15668765|ref|NP_247564.1| 136 IFGLIVPFLQFKI-PNWLFNILALPLFVYIKFIVPECAEGSFYY--SPLITIPISMYGWILIGLA 197
                                   3345556666666.667777788888888888888888888544..4444555666666665554 PP

>> Sas10_Utp3  Sas10/Utp3/C1D family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.7   0.00021      0.22       3      55 ..      28      86 ..      26     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                    Sas10_Utp3  3 slsksldelqeslepllskakaee.....kkslsd....eklsegisllslKnelllaYlln 55
                                  + sk+++el+ +l++l sk+ ++e     k+   +     ++++ +  + lK++  laY+++
  gi|15668765|ref|NP_247564.1| 28 NYSKEINELTVKLKELESKNPNDErieeyKE---KlkqlIEKQHELKSQNLKYNETLAYIQS 86
                                  67899*************9666666655422...13457666666999************97 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.6    0.0081       8.6      33      65 ..      30      60 ..      17      61 .. 0.88
   2 ?   13.1   2.9   9.1e-05     0.096      14      67 ..      52     105 ..      48     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0081
               Snapin_Pallidin 33 leqldrlnekLkeleeaqeaevlpdlkeyakKL 65
                                  ++++++l+ kLkele  ++    ++++ey++KL
  gi|15668765|ref|NP_247564.1| 30 SKEINELTVKLKELESKNP--NDERIEEYKEKL 60
                                  57899*************9..6689******99 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.1e-05
               Snapin_Pallidin  14 kldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvn 67 
                                    ++e +eklk+l+++Q eL++q  + ne L+ ++ ++  ++ +++ ey +K+++
  gi|15668765|ref|NP_247564.1|  52 RIEEYKEKLKQLIEKQHELKSQNLKYNETLAYIQSEEYWKMQEEIWEYNNKVMK 105
                                   5899***************************88887779999******999976 PP

>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.5   0.00022      0.23       4      95 ..      17     102 ..      14     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                       DUF2115   4 eLleilkkeaskisieDlmkisarlekeikklpekyrkelseslteylfeaykelknkrsgdkseykeevideeelkefle 84 
                                    L++++ +++s++s e + +++++l++  +k p+++r e  ++  ++l+e+ +elk+    ++ +y+ e++   + +e+++
  gi|15668765|ref|NP_247564.1|  17 SLVNAIDDNISNYSKE-INELTVKLKELESKNPNDERIEEYKEKLKQLIEKQHELKS----QNLKYN-ETLAYIQSEEYWK 91 
                                   6999*********965.**********99999*99999999999999**********....556665.3444445668888 PP

                       DUF2115  85 mleeqceeeke 95 
                                   m ee  e +++
  gi|15668765|ref|NP_247564.1|  92 MQEEIWEYNNK 102
                                   88877666554 PP

>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   9.5    0.0011       1.2      35     131 ..      45     145 ..       6     205 .] 0.67

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                    EMC3_TMCO1  35 qkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqeelmedqsem...mmdqmkpmivtmipqiliffwlnsf 112
                                   +k++ + ++ e+++++ k+l +++ el++++ k ++     ++ee+ + q+e+     + mk  i++ i+++ i++   ++
  gi|15668765|ref|NP_247564.1|  45 SKNP-NDERIEEYKEKLKQLIEKQHELKSQNLKYNETLAYIQSEEYWKMQEEIweyNNKVMKWFIAISILILGIILATLWI 124
                                   4444.3344777777777777777777777776666666666666666666668888888999999999999999888888 PP

                    EMC3_TMCO1 113 fs..gfvvaklpfpltgrfks 131
                                   +   +f +   +f l+  f +
  gi|15668765|ref|NP_247564.1| 125 LRkdKFLLFLAIFGLIVPFLQ 145
                                   888844444444444444443 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.8   0.00084      0.88     339     421 ..      19     101 ..       7     108 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00084
                          FapA 339 lkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkeeakikv 419
                                   ++++++++ ++ +e+++l+ k+k+l++++ +++  +e ke+lk+l+e++ +lk++  + +e l+++++e   k +e++++ 
  gi|15668765|ref|NP_247564.1|  19 VNAIDDNISNYSKEINELTVKLKELESKNPNDERIEEYKEKLKQLIEKQHELKSQNLKYNETLAYIQSEEYWKMQEEIWEY 99 
                                   477888888888888888888888888333555555566666666666666666666666666655554333334445555 PP

                          FapA 420 nk 421
                                   n+
  gi|15668765|ref|NP_247564.1| 100 NN 101
                                   55 PP

>> Viral_Beta_CD  Viral Beta C/D like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0       0.2   2.1e+02      65      99 ..       6      42 ..       2      57 .. 0.67
   2 ?   -2.2   0.0       4.5   4.8e+03      55      72 ..     117     134 ..      98     141 .. 0.64
   3 ?    7.3   0.1    0.0054       5.7      56      91 ..     148     182 ..     140     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.2
                 Viral_Beta_CD 65 alllcvylk..sikteedavltyfyqdlnsveiklgk 99
                                   l+l + ++  s+ +  d +++++ +++n + +kl +
  gi|15668765|ref|NP_247564.1|  6 FLILLIVFSnlSLVNAIDDNISNYSKEINELTVKLKE 42
                                  34444444412445677778999*******9999865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.5
                 Viral_Beta_CD  55 lllaflfviaalllcvyl 72 
                                   ++la l ++    + ++l
  gi|15668765|ref|NP_247564.1| 117 IILATLWILRKDKFLLFL 134
                                   455666666555555555 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0054
                 Viral_Beta_CD  56 llaflfviaalllcvylksikteedavltyfyqdln 91 
                                   +  +lf i+al l+vy+k i +e +   + +y  l 
  gi|15668765|ref|NP_247564.1| 148 IPNWLFNILALPLFVYIKFIVPECAE-GSFYYSPLI 182
                                   5679****************999887.566666665 PP

>> DUF4315  Domain of unknown function (DUF4315)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3    0.0029       3.1       5      35 ..      22      52 ..      19      54 .. 0.85
   2 ?    5.8   2.8     0.013        14      13      33 ..      50      70 ..      47      75 .. 0.89
   3 ?    1.4   0.1      0.32   3.3e+02       7      23 ..      87     103 ..      84     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0029
                       DUF4315  5 ieaeieKakeKiselqarlkelekqktEaEN 35
                                  i+  i    + i+el  +lkele++    E 
  gi|15668765|ref|NP_247564.1| 22 IDDNISNYSKEINELTVKLKELESKNPNDER 52
                                  7788889999**************9877775 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                       DUF4315 13 keKiselqarlkelekqktEa 33
                                   e+i+e++++lk+l ++++E+
  gi|15668765|ref|NP_247564.1| 50 DERIEEYKEKLKQLIEKQHEL 70
                                  699***********9999986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.32
                       DUF4315   7 aeieKakeKiselqarl 23 
                                   +e+ K++e i e+++++
  gi|15668765|ref|NP_247564.1|  87 EEYWKMQEEIWEYNNKV 103
                                   7999**********997 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3     0.037        39      11      37 ..      21      47 ..      18      49 .. 0.80
   2 ?    7.6   4.0    0.0045       4.7      14      42 ..      51      79 ..      50      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.037
                         TSC22 11 AVrEeVevLkekIkeLeernseleeEN 37
                                  A+ + + +  ++I eL+ + +ele+ N
  gi|15668765|ref|NP_247564.1| 21 AIDDNISNYSKEINELTVKLKELESKN 47
                                  666666777789***********9998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0045
                         TSC22 14 EeVevLkekIkeLeernseleeENslLka 42
                                  E +e+ kek k L+e+ +el+++N  + +
  gi|15668765|ref|NP_247564.1| 51 ERIEEYKEKLKQLIEKQHELKSQNLKYNE 79
                                  789********************976654 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.082        87      10      38 ..      19      47 ..      15      51 .. 0.85
   2 ?    7.0   8.4    0.0087       9.2       4      60 ..      34      89 ..      31     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.082
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA 10 leeleeqleelleeleelkeelaelleen 38
                                  ++++++++++ ++e++el  +l+el  +n
  gi|15668765|ref|NP_247564.1| 19 VNAIDDNISNYSKEINELTVKLKELESKN 47
                                  77889999999999999999999999888 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0087
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXX CS
                          YabA  4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkek 60
                                  +el+ kl+ele++     e++ee ke+l++l+e+ +eL+ +n k  e+l+  +++e 
  gi|15668765|ref|NP_247564.1| 34 NELTVKLKELESKN-PNDERIEEYKEKLKQLIEKQHELKSQNLKYNETLAYIQSEEY 89
                                  68899999999875.56789***********************99999943333333 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.1    0.0093       9.8      47      69 ..      24      46 ..      19      51 .. 0.79
   2 ?    4.7   7.1     0.028        30       5      36 ..      51      82 ..      47     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0093
                    TMF_DNA_bd 47 keikelkkkleklekeleeleer 69
                                   +i++++k++++l+ +l+ele++
  gi|15668765|ref|NP_247564.1| 24 DNISNYSKEINELTVKLKELESK 46
                                  57888888888888888888875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.028
                    TMF_DNA_bd  5 kklkeKDeqIaqLmeEGekLskkelklnntik 36
                                  + ++e  e+++qL e   +L++++lk n+t+ 
  gi|15668765|ref|NP_247564.1| 51 ERIEEYKEKLKQLIEKQHELKSQNLKYNETLA 82
                                  56788889*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3061  (0.170729); expected 358.6 (0.02)
Passed bias filter:                     1099  (0.0612973); expected 358.6 (0.02)
Passed Vit filter:                       180  (0.0100396); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 1310.18
//
Query:       gi|15668766|ref|NP_247565.1|  [L=170]
Description: hypothetical protein MJ_0586 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-11   44.5   5.2    3.7e-11   42.9   3.7    2.1  2  HTH_3       Helix-turn-helix
    1.1e-07   31.6   1.5    1.7e-07   31.0   1.2    1.5  1  HTH_25      Helix-turn-helix domain
    1.2e-06   28.7   0.0    2.4e-06   27.8   0.0    1.5  1  HTH_31      Helix-turn-helix domain
    1.1e-05   25.4   2.6      2e-05   24.5   2.6    1.5  1  HTH_19      Helix-turn-helix domain
     0.0028   17.5   1.6     0.0051   16.7   1.6    1.5  1  zf-C4_ClpX  ClpX C4-type zinc finger
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.037   14.0   0.0    1.3  1  HTH_37      Helix-turn-helix domain
      0.043   13.6   0.0       0.52   10.2   0.0    2.2  2  HTH_23      Homeodomain-like domain
      0.087   12.4   0.5       0.28   10.8   0.0    2.1  2  HTH_24      Winged helix-turn-helix DNA-binding
       0.13   12.6   0.1       0.24   11.7   0.1    1.4  1  DUF3268     zinc-finger-containing domain
       0.16   12.3   0.0        2.5    8.5   0.0    2.0  2  DrsE        DsrE/DsrF-like family
       0.19   11.8   0.0       0.34   11.0   0.0    1.4  1  HTH_20      Helix-turn-helix domain
       0.45    9.9   5.0       0.16   11.4   1.1    1.9  2  NMD3        NMD3 family


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.35   5.2e+02      18      29 ..      37      48 ..      35      58 .. 0.90
   2 !   42.9   3.7   2.5e-14   3.7e-11       1      54 [.      90     143 ..      90     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.35
                                  HHTSSHHHHHHH CS
                         HTH_3 18 klGvsrstisri 29
                                  k G s+ t+sr+
  gi|15668766|ref|NP_247565.1| 37 KFGKSPKTYSRL 48
                                  7899******96 PP

  == domain 2  score: 42.9 bits;  conditional E-value: 2.5e-14
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                         HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54 
                                   ++e+R+++gls+eeLA+kl ++ st+++ E+ e +P+ + +k l+k L++sl+e
  gi|15668766|ref|NP_247565.1|  90 IREAREKRGLSIEELAKKLKMKASTLQKFERYELEPNEKEIKILEKELKISLTE 143
                                   8**************************************************987 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   1.2   1.1e-10   1.7e-07       2      35 ..      90     123 ..      89     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.1e-10
                                   HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                        HTH_25   2 LraaRearglsleevaketkIrkdylealEeddf 35 
                                    r+aRe+rgls+ee+ak++k+++++l+++E+ ++
  gi|15668766|ref|NP_247565.1|  90 IREAREKRGLSIEELAKKLKMKASTLQKFERYEL 123
                                   59****************************8665 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.6e-09   2.4e-06       2      46 ..      86     129 ..      85     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.6e-09
                        HTH_31   2 LGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspav 46 
                                    G+  r++Re++GLs ee+A+ l + +stl + E+ +  +p +  
  gi|15668766|ref|NP_247565.1|  86 YGDVIREAREKRGLSIEELAKKLKMKASTLQKFERYEL-EPNEKE 129
                                   5999******************************9887.676655 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   2.6   1.4e-08     2e-05       1      56 [.      87     141 ..      87     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.4e-08
                        HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidl 56 
                                   G+ ++eaRe++gl++eela++l++  s + ++E  +  +p+ ++++ + ++l+i+l
  gi|15668766|ref|NP_247565.1|  87 GDVIREAREKRGLSIEELAKKLKMKASTLQKFERYEL-EPNEKEIKILEKELKISL 141
                                   6779*****************************4333.344555555555566665 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.6   3.4e-06    0.0051       3      31 ..       9      37 ..       7      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.4e-06
                    zf-C4_ClpX  3 CSFCgksesevkklI.agpngvyICdeCve 31
                                  C  Cgk  ++  k+I +g++ +++C+eC +
  gi|15668766|ref|NP_247565.1|  9 CELCGKLTDKLYKVIiEGSE-MNVCKECAK 37
                                  **********9999978886.9******87 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.5e-05     0.037      22      56 ..      89     123 ..      77     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                                   HHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT-- CS
                        HTH_37  22 aiaeliekrelsqseaaqllgiaqPkvsrllrgkl 56 
                                    i+e +ekr+ls +e+a++l+++ + + + +r++l
  gi|15668766|ref|NP_247565.1|  89 VIREAREKRGLSIEELAKKLKMKASTLQKFERYEL 123
                                   599*************************9999876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.35   5.2e+02      24      37 ..      35      48 ..      35      52 .. 0.87
   2 ?   10.2   0.0   0.00035      0.52      10      36 ..      89     117 ..      88     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.35
                        HTH_23 24 AreLgvsrrTvyrw 37
                                  ++++g s+ T++r 
  gi|15668766|ref|NP_247565.1| 35 CAKFGKSPKTYSRL 48
                                  7899*******995 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00035
                        HTH_23  10 illllae..GlsvreIAreLgvsrrTvyr 36 
                                   +++ ++e  Gls++e A++L +  +T+++
  gi|15668766|ref|NP_247565.1|  89 VIREAREkrGLSIEELAKKLKMKASTLQK 117
                                   688889889*****************986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00019      0.28       8      34 ..      89     115 ..      87     117 .. 0.89
   2 ?   -2.2   0.1       2.1   3.1e+03       2      10 ..     126     134 ..     126     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                        HTH_24   8 ILelLqknprisqreLAerlglSpstv 34 
                                   ++++ +++ ++s+ eLA++l +  st+
  gi|15668766|ref|NP_247565.1|  89 VIREAREKRGLSIEELAKKLKMKASTL 115
                                   6788999***************99997 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                        HTH_24   2 detdrkILe 10 
                                   +e+++kILe
  gi|15668766|ref|NP_247565.1| 126 NEKEIKILE 134
                                   678899995 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00016      0.24       3      72 ..       7      79 ..       5      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                       DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkC.......dayvgvhkgtkiplGtlA.naelrklrkeahaaFdkl 72
                                  ++C+ CG+ +     +++Yk   +g+ + +C++C        +y ++ k+t i +Gt+  n++++k  k+ +++Fd l
  gi|15668766|ref|NP_247565.1|  7 QMCELCGKLT-----DKLYKVIIEGSEMNVCKECakfgkspKTYSRLGKKTIIGKGTITtNKQVKKPIKRRRDIFDTL 79
                                  6899999875.....56776666777777887773333333689999*********9963788999999999999987 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.26   3.8e+02      60      82 ..      15      37 ..      12      40 .. 0.82
   2 ?    8.5   0.0    0.0017       2.5      38     107 ..      53     121 ..      52     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.26
                                  -GGGGGGCGGGT-EEEEEHHHHH CS
                          DrsE 60 laellkalkeygvklyvCgqaak 82
                                  l+++l +++ +g ++ vC+++ak
  gi|15668766|ref|NP_247565.1| 15 LTDKLYKVIIEGSEMNVCKECAK 37
                                  56677777888999*******97 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0017
                                   E-GGGGGGGBS---TGGGTS---GGGGGGCGG.GT-EEEEEHHHHHHTT--GGGE-..T--EEEE-HHHHHHH CS
                          DrsE  38 fygdGvllllkgqtanpadeknlaellkalke.ygvklyvCgqaakargldededl..gvgvevsglgelael 107
                                   ++g+G+   +k+ +++ ++ +++ ++l +l+e yg    v ++a ++rgl+ + +l  +++++ s+l  + ++
  gi|15668766|ref|NP_247565.1|  53 IIGKGTITTNKQVKKPIKRRRDIFDTLPMLREdYG---DVIREAREKRGLSIE-ELakKLKMKASTLQKFERY 121
                                   6899*******9999999**************999...899**********66.5546569999999888766 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023      0.34      12      41 ..      72     115 ..      70     117 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                                   HHHHHHHH..............STCTTB-HHHHHHHHTS-HHHH CS
                        HTH_20  12 RrrilraL..............araegltaselaerldlskntl 41 
                                   Rr+i++ L              ++++gl+ +ela+ l ++ +tl
  gi|15668766|ref|NP_247565.1|  72 RRDIFDTLpmlredygdvireaREKRGLSIEELAKKLKMKASTL 115
                                   9************************************9999998 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.1   0.00011      0.16      11      46 ..       4      40 ..       1      72 [. 0.84
   2 ?   -0.0   0.1      0.33   4.9e+02      72      88 ..      98     114 ..      80     150 .. 0.43

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                          NMD3 11 linglCedCllkevditegiek.ievevCkeCgrylp 46
                                  +i ++Ce C + + ++ ++i +  e++vCkeC ++ +
  gi|15668766|ref|NP_247565.1|  4 SIMQMCELCGKLTDKLYKVIIEgSEMNVCKECAKFGK 40
                                  5668***************9999**********9973 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.33
                          NMD3  72 gLkvseeveevkvelvd 88 
                                   gL+++e +++ k++  +
  gi|15668766|ref|NP_247565.1|  98 GLSIEELAKKLKMKAST 114
                                   33333333333332111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1104.97
//
Query:       gi|15668767|ref|NP_247566.1|  [L=153]
Description: hypothetical protein MJ_0587 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-72  242.4  23.1      2e-72  242.2  23.1    1.0  1  DUF5418   Family of unknown function (DUF5418)


Domain annotation for each model (and alignments):
>> DUF5418  Family of unknown function (DUF5418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.2  23.1   1.1e-76     2e-72       1     151 []       1     151 [.       1     151 [. 1.00

  Alignments for each domain:
  == domain 1  score: 242.2 bits;  conditional E-value: 1.1e-76
                       DUF5418   1 mvnehkahasfilkvilalvsysialilaiiiysiffkieenlfllcillalpiiyflilillGlthreleylsiydkykl 81 
                                   mvne+kah+sfilkv+++l++y+ia+ilaiiiys+ffkie+n+fllc+ll++pii+f+ili++Glt+r++e+l+iydk+kl
  gi|15668767|ref|NP_247566.1|   1 MVNEYKAHSSFILKVVITLIGYWIASILAIIIYSMFFKIETNTFLLCLLLPTPIIWFNILIGMGLTYRCMENLTIYDKHKL 81 
                                   9******************************************************************************** PP

                       DUF5418  82 lckfvreltlsllasalatiatlvlyqiqhPlktiefvllvglvlivglvvikllikkyliiikklkkle 151
                                   +c+fvr+ltl++la++lat++t++lyqi+hPlk+iefv++vglvlivg+++i++li+kyl+iik+lkk++
  gi|15668767|ref|NP_247566.1|  82 WCVFVRDLTLTILATILATLTTMELYQIEHPLKPIEFVFIVGLVLIVGFTIITTLIIKYLKIIKNLKKIS 151
                                   ********************************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1190  (0.0663729); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 994.38
//
Query:       gi|15668768|ref|NP_247567.1|  [L=430]
Description: hypothetical protein MJ_0588 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     8e-114  380.7   0.3    3.8e-92  309.3   0.1    2.2  2  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.3   0.1   2.1e-96   3.8e-92       2     298 ..      41     339 ..      40     342 .. 0.93
   2 !   70.3   0.0   7.4e-24   1.3e-19     329     416 .]     340     425 ..     338     425 .. 0.95

  Alignments for each domain:
  == domain 1  score: 309.3 bits;  conditional E-value: 2.1e-96
                          TruD   2 lgielyvtdtegigGrlrespeDFiVeEieef........sgeeeade........geylvlrvekrnwdtldlvrelara 66 
                                   l+++ y+td+  +gG +++ peDFiVeEi+          s      e        g+y+ +++ekrnw+tld++re+a++
  gi|15668768|ref|NP_247567.1|  41 LNMNKYLTDA-YTGGIIKKYPEDFIVEEITPEgiilevgkSI-----EfkdeenwkGNYIHFTLEKRNWTTLDAIREIANR 115
                                   799*****76.69****************7666655533322.....022234566************************* PP

                          TruD  67 lgisrkrvgfaGtKDkrAvTtQlisirkvepeelealeikdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakra 147
                                   +g +rk +gfaG KDk+AvTtQ + + +v+ e+l +++ik++ l+++++++rk+rlGdL+GN+F+irvr+ +e +   k++
  gi|15668768|ref|NP_247567.1| 116 VGKQRKHFGFAGNKDKYAVTTQRVGCFNVKLEDLMKVKIKGIILRDFQKTNRKIRLGDLWGNRFTIRVRE-PELK--GKEL 193
                                   **********************************************************************.6555..489* PP

                          TruD 148 eeileeleekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelp 228
                                   ee l++l + + + Ny+GvQRFG++rp+th+vG+ i+++d+e+A+++y+g+p + ++++++ are+v ++++++ea++++p
  gi|15668768|ref|NP_247567.1| 194 EEALNKLCKLKYFLNYYGVQRFGTTRPITHIVGRFIIERDWEGAFHAYCGTPLPYDDKKSKLARELV-DEENFKEAYKKFP 273
                                   *********999*******************************************************.9************ PP

                          TruD 229 kslryErallkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifa 298
                                   k + yEr ++k+++e +++y+kA+  lp+ L+ +F++AyqSylFN+++++R+e g+   ep+eGD++i++
  gi|15668768|ref|NP_247567.1| 274 KAFFYERRMIKAYIE-TGSYQKAFMILPPYLRCMFINAYQSYLFNEIINRRFEYGF---EPMEGDILIDN 339
                                   ***************.***************************************4...7******9976 PP

  == domain 2  score: 70.3 bits;  conditional E-value: 7.4e-24
                          TruD 329 fvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaillrvedlelsaeedeltleFsLpkGsYA 409
                                   ++++ l+G++t++a+g +geiere+ e+e+l++edFk+ +    s+ G+rRa++ ++ ++++  e+d+++l+F L kG+YA
  gi|15668768|ref|NP_247567.1| 340 VPSGALFGYKTRFASGIQGEIEREIYERENLSPEDFKIGE--FGSFIGDRRAMIGKIYNMKYWIEDDSYVLQFCLKKGNYA 418
                                   57899********************************987..45689********************************** PP

                          TruD 410 TvvlrEi 416
                                   T+vlrE+
  gi|15668768|ref|NP_247567.1| 419 TSVLREF 425
                                   ******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2576.07
//
Query:       gi|15668769|ref|NP_247568.1|  [L=102]
Description: hypothetical protein MJ_0589 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 666.33
//
Query:       gi|15668770|ref|NP_247570.1|  [L=704]
Description: hypothetical protein MJ_0590 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-53  178.2   0.1    6.1e-52  175.1   0.0    2.4  3  Succ_CoA_lig    Succinyl-CoA ligase like flavodoxin domain
      9e-53  179.0   0.0    1.5e-52  178.2   0.0    1.3  1  ATP-grasp_5     ATP-grasp domain
    8.6e-29  100.4   0.1    7.1e-28   97.4   0.1    2.7  4  CoA_binding_2   CoA binding domain
    7.5e-18   65.0   0.6    3.3e-17   62.9   0.6    2.2  1  CoA_binding     CoA binding domain
    3.7e-06   26.6   0.1    9.1e-06   25.4   0.1    1.7  1  ATP-grasp_2     ATP-grasp domain
  ------ inclusion threshold ------
      0.035   14.1   0.0       0.12   12.4   0.0    1.8  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.12   12.2   0.0       0.63    9.8   0.0    2.2  2  Ligase_CoA      CoA-ligase
       0.13   12.6   3.0        3.6    8.0   2.6    2.5  2  TSNAXIP1_N      Translin-associated factor X-interacting N-te


Domain annotation for each model (and alignments):
>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.1   0.0   2.7e-55   6.1e-52       1     138 []     153     289 ..     153     289 .. 0.98
   2 ?    0.1   0.0      0.28   6.3e+02       3      31 ..     299     327 ..     297     330 .. 0.92
   3 ?   -4.0   0.0       5.1   1.2e+04      43      61 ..     361     379 ..     353     382 .. 0.79

  Alignments for each domain:
  == domain 1  score: 175.1 bits;  conditional E-value: 2.7e-55
                  Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarraark 81 
                                   +G++++isqSGa++ a+ld a   ++gfskvvs+Gn+ad++++dlley+ +d++tk+++ly+E+++d ++fl++a+++++k
  gi|15668770|ref|NP_247570.1| 153 KGGVSIISQSGAVLNAILDIAPLLNIGFSKVVSIGNKADIQESDLLEYFLDDEDTKIVVLYIEGLKD-KRFLKVAKKLSKK 232
                                   699***************************************************************9.68*********** PP

                  Succ_CoA_lig  82 kpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                   kp+++lksGr+e g++aa+shtg+lag+d +++aaf++aG++r++++eel+d+++l+
  gi|15668770|ref|NP_247570.1| 233 KPIIALKSGRTEVGKKAAKSHTGSLAGEDVIYEAAFKEAGIIRAYTFEELVDLIHLF 289
                                   ****************************************************99875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.28
                  Succ_CoA_lig   3 kialisqSGalalalldwaasrglgfskv 31 
                                   +i++i+  G++++  +d++ + ++++s++
  gi|15668770|ref|NP_247570.1| 299 EIGIITNAGGFGVLAADSCVDYNMKLSNF 327
                                   69**********************99987 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 5.1
                  Succ_CoA_lig  43 adlleylaedpetkvilly 61 
                                   + ++e laed+++k +l+ 
  gi|15668770|ref|NP_247570.1| 361 KKVIEVLAEDSNVKGLLVI 379
                                   6789999999999987765 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.2   0.0   6.8e-56   1.5e-52      11     220 ..     490     702 ..     481     703 .. 0.91

  Alignments for each domain:
  == domain 1  score: 178.2 bits;  conditional E-value: 6.8e-56
                   ATP-grasp_5  11 teaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervkek 91 
                                   +e+ ak+ll+ yg+pv++  la++++ea+e+++++g ++v+Kivsp+i+hKt++gGv +   ++++ ++a+++++e++ke+
  gi|15668770|ref|NP_247570.1| 490 NEYTAKKLLSIYGLPVPKGYLAKNEDEALEYCKKLG-KCVMKIVSPQIIHKTEAGGVII---NPKNPKEAFKKLIENAKEY 566
                                   799********************************9.9*********************...5666677888888888888 PP

                   ATP-grasp_5  92 s.....peariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertkaskll 167
                                   +      +  iegvlV+e  +++ +E+i+g+++D +FG v+++GlGG+ vevlkdv++++ p+++  a+e+++++k++k+l
  gi|15668770|ref|NP_247570.1| 567 AkrmgiDNLIIEGVLVEEFIEKDMMEIIIGAKRDDIFGSVVMVGLGGVFVEVLKDVSFGISPITRDFAHEMLRELKSYKVL 647
                                   8444444456899999999777*********************************************************** PP

                   ATP-grasp_5 168 kgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllvee..egvvalDari 220
                                   +gvrg++k d++ ++++l+++   ++ ++eI+eld+nP++v +  eg ++ Dari
  gi|15668770|ref|NP_247570.1| 648 EGVRGRPKRDINFIVDTLIKIGVFMDIHKEIKELDLNPVFVFNekEGGCIGDARI 702
                                   ****************************************965336699999998 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   0.1   3.2e-31   7.1e-28       1     115 [.      15     137 ..      15     138 .. 0.96
   2 ?   -3.5   0.0       6.6   1.5e+04      18      44 ..     224     249 ..     217     260 .. 0.76
   3 ?   -2.8   0.0         4     9e+03      78     100 ..     540     562 ..     528     573 .. 0.60
   4 ?   -3.1   0.0         5   1.1e+04       7      25 ..     625     643 ..     624     655 .. 0.81

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 3.2e-31
                                   --EEEET--S-TTSHHHHHHHHHHH.HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH-- CS
                 CoA_binding_2   1 rtiaVvGasdnpgkfgykvlrylle.hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalga 80 
                                   +++a++Gas+++gk gy ++++l++ +g +++p+npk++ei+g k+y+s+ + + ++dl+++++p  ++p++++e++++g+
  gi|15668770|ref|NP_247570.1|  15 KSVAIIGASKTEGKVGYAIMKNLKDfNG-KIYPINPKYDEIFGIKCYKSVLDVEDDIDLAVIVVPNIVVPKVLEECGKKGV 94 
                                   79***********************777.**********************7469************************** PP

                                   SEEEE-TT........---HHHHHHHHHTT-EEE.ES-HHHHH CS
                 CoA_binding_2  81 kavwlqpg........sedeeaaelaeeagirvvgdrCilveg 115
                                   k++++  +        + ++++ e+a++++ir++g++C+++++
  gi|15668770|ref|NP_247570.1|  95 KGAVIITAgfsevgnyELENKIKEIAKRYNIRIIGPNCLGIMN 137
                                   *99999888*******************************986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.6
                                   HHHHHHHHHT--EEEESSS-SEETTEE CS
                 CoA_binding_2  18 kvlryllehglpvvpVnpkeeeilgek 44 
                                   kv++ l +++ p+++    ++e+  + 
  gi|15668770|ref|NP_247570.1| 224 KVAKKLSKKK-PIIALKSGRTEVGKKA 249
                                   6888888888.9999888888887644 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4
                                   H--SEEEE-TT---HHHHHHHHH CS
                 CoA_binding_2  78 lgakavwlqpgsedeeaaelaee 100
                                    +a +v+++p   +e++ +l e+
  gi|15668770|ref|NP_247570.1| 540 TEAGGVIINPKNPKEAFKKLIEN 562
                                   35666777776555555544444 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 5
                                   T--S-TTSHHHHHHHHHHH CS
                 CoA_binding_2   7 Gasdnpgkfgykvlrylle 25 
                                   G s+ +  f++ +lr l++
  gi|15668770|ref|NP_247570.1| 625 GISPITRDFAHEMLRELKS 643
                                   8888899999999999987 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.6   1.5e-20   3.3e-17       3      96 .]      14     103 ..      12     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.5e-20
                                   TEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHH CS
                   CoA_binding   3 dtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelv 83 
                                   +++v++iGa++++++++y + ++lk  + +++++np+  ++e+ g+++yksv ++e++  +d avi+vP+  + ++ +e+ 
  gi|15668770|ref|NP_247570.1|  14 PKSVAIIGASKTEGKVGYAIMKNLKDFNGKIYPINPK--YDEIFGIKCYKSVLDVEDD--IDLAVIVVPNIVVPKVLEECG 90 
                                   689**************999999996777********..*******************..********************* PP

                                   HTT-SEEEEESST CS
                   CoA_binding  84 eagikgiviiteg 96 
                                   ++g+kg+viit+g
  gi|15668770|ref|NP_247570.1|  91 KKGVKGAVIITAG 103
                                   ***********86 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   4.1e-09   9.1e-06       3     102 ..     490     587 ..     488     619 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 4.1e-09
                                   -HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSE.EEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTS.EEE CS
                   ATP-grasp_2   3 hEyqakeilakygvkvpegevaesaeeaeeaakklgekel.vvKaQvlaGGRGKagGvklvkskeeakeaakellgk.elv 81 
                                    Ey ak++l+ yg++vp+g +a++++ea e  kklg+ ++ +v  Q+    +  agGv +   +++ kea k+l+ + +  
  gi|15668770|ref|NP_247570.1| 490 NEYTAKKLLSIYGLPVPKGYLAKNEDEALEYCKKLGKCVMkIVSPQIIH--KTEAGGVIIN--PKNPKEAFKKLIENaKEY 566
                                   59**********************************9876378889986..6789999764..666666667766431445 PP

                                   -TTS-TT-EEE--EEEEE--- CS
                   ATP-grasp_2  82 tkqtgkeGkkvekvlveeald 102
                                   +k+ g +  ++e vlvee ++
  gi|15668770|ref|NP_247570.1| 567 AKRMGIDNLIIEGVLVEEFIE 587
                                   678888888888888888554 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.1e-05      0.12      58     134 ..      58     131 ..      52     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-05
                                   EEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SEET.TTEEHHHHHHHHH-S--EEEEESS- CS
                NAD_Gly3P_dh_N  58 vattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGieegtlkllsevieeelkeekvavlsGps 134
                                   + ++ + ++ ++ d+ v+vvP  ++ +vl+++ ++    + +v+++ G++e ++  l++ i+e+ k++++  + Gp+
  gi|15668770|ref|NP_247570.1|  58 KCYKSVLDVEDDIDLAVIVVPNIVVPKVLEECGKKG--VKGAVIITAGFSEVGNYELENKIKEIAKRYNIR-IIGPN 131
                                   5666777888899*******************9965..556677788**999999************9665.55887 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.64   1.4e+03      64     117 ..     197     241 ..     191     266 .. 0.58
   2 ?    9.8   0.0   0.00028      0.63      33     136 ..     342     431 ..     303     445 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.64
                                   HHHHHHS-TT-SEEEEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEEC CS
                    Ligase_CoA  64 alkklaadpevkvilldivlGygahedpaaellkaikeakaegrelpvvarvaG 117
                                    l+ ++ d+ +k+++l i++    ++   + +lk +k++    +++p++a   G
  gi|15668770|ref|NP_247570.1| 197 LLEYFLDDEDTKIVVLYIEGL---KD---KRFLKVAKKLS---KKKPIIALKSG 241
                                   566777788888777777632...22...23334444443...55566666665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00028
                                   T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEEESSSEHHHHHHHHHHHHHHTT...--S-EE. CS
                    Ligase_CoA  33 gseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldivlGygahedpaaellkaikeakaegrelpvv. 112
                                   +++ ++ +d+ +da+          p+++ + ++ la+d++vk++l+ +    +++  ++a+ + ++k+ ++e +++p++ 
  gi|15668770|ref|NP_247570.1| 342 TANISNPLDIIGDAT----------PERYKKVIEVLAEDSNVKGLLVILTPQEMTKPLEVAKSIIEVKNSHKEFKNKPLIt 412
                                   566778899999999..........8**********************999888888888877777777777666666661 PP

                                   EEEECTTHH.....HHHHHHHTTT CS
                    Ligase_CoA 113 arvaGteadpqelseqakaleeag 136
                                   ++v G ++      +++  l++ g
  gi|15668770|ref|NP_247570.1| 413 SFVGGVSVK-----GAKSYLRKNG 431
                                   555566555.....6666666655 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.6    0.0016       3.6      38      79 ..     447     490 ..     443     502 .. 0.75
   2 ?    1.9   0.0      0.13   2.9e+02      27      42 ..     553     568 ..     552     571 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                    TSNAXIP1_N  38 kaYkdlLseIKkEYelyiahllesqreaqylkakl..ktlsess 79 
                                     Yk  L ++K++Y++y++ ++e+  +   +++++  ++ls++ 
  gi|15668770|ref|NP_247570.1| 447 HLYKYSLMKVKEDYDEYLENIKEEFIKITEENKEIikELLSNPN 490
                                   569999****************9987777664444455555554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.13
                    TSNAXIP1_N  27 revFedlieefkaYkd 42 
                                   +e+F++lie++k+Y++
  gi|15668770|ref|NP_247570.1| 553 KEAFKKLIENAKEYAK 568
                                   79************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (704 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.50
# Mc/sec: 4258.04
//
Query:       gi|15668771|ref|NP_247571.1|  [L=261]
Description: proteasome subunit alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.8e-69  230.6   0.3    1.7e-68  229.9   0.3    1.4  1  Proteasome      Proteasome subunit
    4.2e-14   51.9   0.7    1.2e-13   50.4   0.1    2.0  2  Proteasome_A_N  Proteasome subunit A N-terminal signature
  ------ inclusion threshold ------
      0.099   12.7   0.7       0.51   10.4   0.9    2.0  2  ROS_MUCR        ROS/MUCR transcriptional regulator protein


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.9   0.3   2.8e-72   1.7e-68       1     190 []      32     215 ..      32     215 .. 0.98

  Alignments for each domain:
  == domain 1  score: 229.9 bits;  conditional E-value: 2.8e-72
                                   HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCH CS
                    Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipv 81 
                                   v++Gtt++Gi++kdgvvla+d+r+t  skl++ +++eKif+iddh+++a++Gl+aDar+l++rar eaq yrl+yg++i++
  gi|15668771|ref|NP_247571.1|  32 VRRGTTAIGIACKDGVVLAVDRRIT--SKLVKIRSIEKIFQIDDHVAAATSGLVADARVLIDRARLEAQIYRLTYGEEISI 110
                                   679**********************..****************************************************** PP

                                   HHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHH CS
                    Proteasome  82 erlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltlee 162
                                   e+l++++++ +qaytq++g+rpfgvslliag+d+++  +L+++dpsG++ie+k a+aiGsg+ +++++lekey++d+tl+e
  gi|15668771|ref|NP_247571.1| 111 EMLAKKICDIKQAYTQHGGVRPFGVSLLIAGIDKNE-ARLFETDPSGALIEYK-ATAIGSGRPVVMELLEKEYRDDITLDE 189
                                   *********************************777.8**************8.*************************** PP

                                   HHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                    Proteasome 163 avelavkalkealerdklsgknievavi 190
                                   ++ela+ al +a e   ++++n++v++i
  gi|15668771|ref|NP_247571.1| 190 GLELAITALTKANE--DIKPENVDVCII 215
                                   *************9..59********97 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.1     2e-17   1.2e-13       1      23 []       9      31 ..       9      31 .. 0.99
   2 ?   -1.0   0.0      0.24   1.4e+03      13      18 ..      67      72 ..      67      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2e-17
                Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                  YDr++t+FSP+GRL+QVEYA +A
  gi|15668771|ref|NP_247571.1|  9 YDRAITVFSPEGRLYQVEYAREA 31
                                  *********************99 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.24
                Proteasome_A_N 13 RLfQVE 18
                                  ++fQ++
  gi|15668771|ref|NP_247571.1| 67 KIFQID 72
                                  79**97 PP

>> ROS_MUCR  ROS/MUCR transcriptional regulator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.27   1.6e+03      83     111 ..      89     117 ..      85     139 .. 0.77
   2 ?   10.4   0.9   8.6e-05      0.51      17      52 ..     223     258 ..     213     261 .] 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.27
                      ROS_MUCR  83 LasahgltpeeYrakwglpkdyPlvApny 111
                                   L ++  l+ + Yr  +g + +  + A++ 
  gi|15668771|ref|NP_247571.1|  89 LIDRARLEAQIYRLTYGEEISIEMLAKKI 117
                                   66777888888999998888888888765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 8.6e-05
                      ROS_MUCR  17 nkveaeelpslikevhaalkalseaeeeeaaeeeek 52 
                                   +k++ ee+++li++v ++l++ +++eee+++e++ek
  gi|15668771|ref|NP_247571.1| 223 KKIPVEEIKKLIEKVKKKLNEENKKEEENREETKEK 258
                                   7899***************99988887777554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2907  (0.16214); expected 358.6 (0.02)
Passed bias filter:                     1103  (0.0615204); expected 358.6 (0.02)
Passed Vit filter:                       131  (0.0073066); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 1570.81
//
Query:       gi|15668772|ref|NP_247572.1|  [L=240]
Description: putative RNA-associated protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-23   83.1   0.3    1.1e-23   83.1   0.3    1.7  2  SBDS             Shwachman-Bodian-Diamond syndrome (SBDS) pro
    5.7e-23   81.1   0.8      9e-23   80.5   0.8    1.3  1  SBDS_C           SBDS protein C-terminal domain
  ------ inclusion threshold ------
      0.055   13.5   0.0       0.13   12.3   0.0    1.6  1  EFG_C            Elongation factor G C-terminus
      0.064   12.3   0.5      0.079   12.0   0.5    1.1  1  hDGE_amylase     Glycogen debranching enzyme, glucanotransfer
      0.072   13.2   0.2       0.12   12.5   0.2    1.3  1  UPF0262          Uncharacterised protein family (UPF0262)
      0.073   13.2   0.1       0.12   12.5   0.1    1.3  1  Ribonucleas_3_3  Ribonuclease-III-like


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   0.3   3.7e-27   1.1e-23       2      87 ..      12      97 ..      11      98 .. 0.98
   2 ?   -3.7   0.1       4.4   1.3e+04      28      74 ..     102     112 ..      99     117 .. 0.47

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 3.7e-27
                                  -EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE--H CS
                          SBDS  2 vsivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiqvsa 84
                                  ++i+ry +++++Fei+v++  + + +eg+++d +e l++e +F++askGe+a+++ l+k+fgt++++ei+k+I+ kG++q++a
  gi|15668772|ref|NP_247572.1| 12 AVIARYTSHGEKFEILVDPYLAAKLKEGQNVDFDELLAIEVVFRDASKGEKAPEELLSKIFGTTDVKEIAKKIILKGQVQLTA 94
                                  6899******************************************************************************* PP

                                  HHH CS
                          SBDS 85 eer 87
                                  ++r
  gi|15668772|ref|NP_247572.1| 95 KQR 97
                                  *98 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.4
                                   CTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHH CS
                          SBDS  28 egkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeI 74 
                                   e+                                    +k +ii++I
  gi|15668772|ref|NP_247572.1| 102 EQ------------------------------------KKRQIITII 112
                                   33....................................444444444 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.8     3e-26     9e-23       2     104 ..     105     211 ..     104     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 3e-26
                                   HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CCCHHH CS
                        SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikdkilk 82 
                                   +++ii+i++++++npqt +p+++ +Ieka++el++++++ ksa++Q+ e++k+L++ +pi++++  +++++p + ++k+ +
  gi|15668772|ref|NP_247572.1| 105 KRQIITIISRNTINPQTDTPHPPHRIEKAMEELRINIDIYKSAEEQVPEIVKKLKKVLPIRFEKRDIAVKIPAEFASKAYN 185
                                   799*********************************************************************777777777 PP

                                   HHHHHHH.....S.EE.....EEEE.EE CS
                        SBDS_C  83 lieqvesqkvaekewe.....vvvl.ie 104
                                   ++ q  +  v+++ew+     +v + i+
  gi|15668772|ref|NP_247572.1| 186 ALYQFGA--VKQEEWQpdgslIVLIeIP 211
                                   7777644..5556776666653333233 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.3e-05      0.13       9      71 ..     171     232 ..     169     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                                   EEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EE CS
                         EFG_C   9 veievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsf 71 
                                   + +++p e+ +k+++ l +  +  ++  q  +g  i+  eiP+    +f+  L+++TkG+ + 
  gi|15668772|ref|NP_247572.1| 171 IAVKIPAEFASKAYNALYQFGAVKQEEWQP-DGSLIVLIEIPSGIEAEFYAHLNKITKGNVQT 232
                                   6799***************99977777777.7999999*****9999************8765 PP

>> hDGE_amylase  Glycogen debranching enzyme, glucanotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5   2.6e-05     0.079     215     299 ..      75     161 ..      31     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHHHS-SSTTS--STT---B-HHHHHHHHHHHT-SS.TTT....THHHHHHHHHHH..HHHHHHHHHHHHHHHHH CS
                  hDGE_amylase 215 keeaklvkekalkeakkllerfsakidlevaaallkalleeekkeeeeeeevaeklkkilde..lNlelykeldedvkail 293
                                   ++  ++ k+  lk + +l+ + +++i+ ++  ++++ ++ ++ + ++++ +  ++++k+++e  +N ++yk+++e+v +i+
  gi|15668772|ref|NP_247572.1|  75 TDVKEIAKKIILKGQVQLTAKQREEIREQKKRQIITIISRNTINPQTDTPHPPHRIEKAMEElrINIDIYKSAEEQVPEIV 155
                                   3334444455567788999999*****************99999999999999*******98446**************** PP

                                   HHHHHH CS
                  hDGE_amylase 294 eqllnr 299
                                   ++l++ 
  gi|15668772|ref|NP_247572.1| 156 KKLKKV 161
                                   *99874 PP

>> UPF0262  Uncharacterised protein family (UPF0262)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2     4e-05      0.12      15      78 ..      94     158 ..      80     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                       UPF0262  15 grasaeveqerkvAifDlleensfaleg.eeegpyklklsleekrlvldireeeeeelaelilsl 78 
                                   +++++e+++++k  i+ ++  n+ ++++ + + p++++ ++ee r+ +di +++ee++ e++  l
  gi|15668772|ref|NP_247572.1|  94 AKQREEIREQKKRQIITIISRNTINPQTdTPHPPHRIEKAMEELRINIDIYKSAEEQVPEIVKKL 158
                                   4455677778889999***********967999********************999998776555 PP

>> Ribonucleas_3_3  Ribonuclease-III-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     4e-05      0.12      35      96 ..      47     109 ..      18     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
               Ribonucleas_3_3  35 lsvseyllekaekdegeltklraslvseeslaeiAkelgLgkvlrl.rkgeeetegsgrekvl 96 
                                   l+ +e+++++a+k e++  +l++++  ++ ++eiAk++ L+  + l  k+ ee +++++++++
  gi|15668772|ref|NP_247572.1|  47 LLAIEVVFRDASKGEKAPEELLSKIFGTTDVKEIAKKIILKGQVQLtAKQREEIREQKKRQII 109
                                   56789999**************************************86667777777776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1106  (0.0616878); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1541.47
//
Query:       gi|15668773|ref|NP_247573.1|  [L=92]
Description: 50S ribosomal protein L37Ae [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-33  114.6   3.2    1.8e-33  114.5   3.2    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
    0.00089   18.7   0.3     0.0015   18.0   0.3    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0048   16.8   2.6      0.015   15.2   2.6    1.8  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
     0.0061   16.2   2.8        1.7    8.5   0.3    2.2  2  zinc_ribbon_2    zinc-ribbon domain
     0.0097   15.8   0.6      0.017   15.0   0.6    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.026   14.9   0.4       0.04   14.3   0.4    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.031   14.2   0.7      0.049   13.6   0.7    1.2  1  Prok-RING_1      Prokaryotic RING finger family 1
      0.033   14.7   0.0       0.04   14.5   0.0    1.2  1  RPA_interact_C   Replication protein A interacting C-terminal
      0.045   13.4   2.6        1.8    8.3   0.1    2.3  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.047   13.4   2.9        2.2    8.0   0.1    2.2  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
      0.068   12.9   1.2       0.16   11.7   1.2    1.6  1  A2L_zn_ribbon    A2L zinc ribbon domain
       0.11   12.6   0.2       0.11   12.6   0.2    2.0  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.14   12.0   0.9       0.22   11.4   0.9    1.3  1  Cys_rich_CPCC    Cysteine-rich CPCC
       0.15   12.0   2.2       0.41   10.6   2.2    1.8  1  DUF4428          Domain of unknown function (DUF4428)
       0.25   11.5   2.3        0.9    9.7   2.2    1.9  2  Zn-ribbon_8      Zinc ribbon domain
       0.26   11.3   3.0       0.41   10.7   3.0    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.29   10.8   0.5        6.1    6.5   0.0    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.73    9.9   4.4       0.77    9.8   0.2    2.1  2  zf-BED           BED zinc finger
       0.83    9.7   6.0          3    7.9   0.6    2.6  2  Rubredoxin       Rubredoxin
       0.87    9.6   3.4         22    5.1   0.1    2.2  2  ADK_lid          Adenylate kinase, active site lid
        1.1    8.8   7.2         21    4.7   7.1    2.2  1  zf-ribbon_3      zinc-ribbon domain
        1.2    9.1   6.3        7.4    6.5   6.3    2.0  1  zf-HIT           HIT zinc finger
        6.1    7.2   9.0         94    3.4   9.0    2.2  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
        7.2    7.2   6.6        2.4    8.8   1.7    2.3  2  zf-H2C2_2        Zinc-finger double domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.5   3.2   2.4e-36   1.8e-33       1      84 [.       4      87 ..       4      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 2.4e-36
                                  XXXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH-XXXX CS
               Ribosomal_L37ae  1 rtkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsaktvksairrl 83
                                  +tkkvg +G++g+rYG ++r rv+++ei+ ++ky+Cp cg  k+kR ++ iw C+kcg+++aGgAytpet ++k+v +airr+
  gi|15668773|ref|NP_247573.1|  4 HTKKVGPTGRFGPRYGLKIRVRVRDVEIKAKKKYKCPVCGFPKLKRASTSIWVCGKCGAKIAGGAYTPETGAGKAVMKAIRRI 86
                                  79*******************************************************************************97 PP

                                  X CS
               Ribosomal_L37ae 84 k 84
                                   
  gi|15668773|ref|NP_247573.1| 87 V 87
                                  5 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   2.1e-06    0.0015       1      29 [.      37      64 ..      37      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.1e-06
                                  EEETTTTCEECHEETSTTCEEESSSSBEE CS
                  TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGlVl 29
                                  ykCP+Cg ++ +  +++   vC++CG+ +
  gi|15668773|ref|NP_247573.1| 37 YKCPVCGFPK-LKRASTSIWVCGKCGAKI 64
                                  8******998.899999999******987 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.6     2e-05     0.015       4      34 ..      36      64 ..      34      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                Zn_ribbon_SprT  4 vYrCtgCgreythhlsirrhnYrCrrCkgtL 34
                                  +Y+C+ Cg  ++   +  +  + C++C+ ++
  gi|15668773|ref|NP_247573.1| 36 KYKCPVCG--FPKLKRASTSIWVCGKCGAKI 64
                                  7*******..99999999999******9765 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.2    0.0026         2       9      22 ..      31      45 ..      29      47 .. 0.75
   2 !    8.5   0.3    0.0023       1.7       2      10 ..      57      65 ..      56      69 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0026
                 zinc_ribbon_2  9 lqdnakF.CpyCGtp 22
                                  ++ + k+ Cp CG+p
  gi|15668773|ref|NP_247573.1| 31 IKAKKKYkCPVCGFP 45
                                  556667779999987 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0023
                 zinc_ribbon_2  2 CpnCGaelq 10
                                  C +CGa++ 
  gi|15668773|ref|NP_247573.1| 57 CGKCGAKIA 65
                                  888888885 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.6   2.3e-05     0.017      30      55 ..      38      63 ..      27      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                                  +C++Cg  + ++ s+  ++C +Cg++
  gi|15668773|ref|NP_247573.1| 38 KCPVCGFPKLKRASTSIWVCGKCGAK 63
                                  7******99999************97 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   5.3e-05      0.04       4      41 ..      37      69 ..      34      86 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.3e-05
               Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCga...stpwf 41
                                  + CP Cg ++ +  s++ +        C +Cga   +   +
  gi|15668773|ref|NP_247573.1| 37 YKCPVCGFPKLKRASTSIWV-------CGKCGAkiaG-GAY 69
                                  89*******99999998885.......******7632.222 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   6.5e-05     0.049       2      28 ..      34      62 ..      33      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
                   Prok-RING_1  2 ytgkkCpvCgk.elkee.dDiVvCpeCgt 28
                                  +++ kCpvCg  +lk +   i vC +Cg+
  gi|15668773|ref|NP_247573.1| 34 KKKYKCPVCGFpKLKRAsTSIWVCGKCGA 62
                                  6899*****96256665589********8 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.4e-05      0.04       2      27 ..      39      66 ..      38      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.4e-05
                RPA_interact_C  2 CPvCkkrklkets.evifCe.Cglrlet 27
                                  CPvC   klk+ s ++ +C+ Cg +++ 
  gi|15668773|ref|NP_247573.1| 39 CPVCGFPKLKRAStSIWVCGkCGAKIAG 66
                                  ***********9957778*99***9987 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0024       1.8       8      25 ..      27      44 ..      26      47 .. 0.92
   2 ?    5.1   0.3     0.024        18       2       9 ..      56      63 ..      55      65 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0024
                                  -B----SSS----SSS-- CS
                DNA_RNApol_7kD  8 aevslkkgdpiRCkeCGh 25
                                   +v++k++   +C  CG+
  gi|15668773|ref|NP_247573.1| 27 RDVEIKAKKKYKCPVCGF 44
                                  589**************8 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.024
                                  B-SSS--B CS
                DNA_RNApol_7kD  2 iCgeCgae 9 
                                   Cg+Cga+
  gi|15668773|ref|NP_247573.1| 56 VCGKCGAK 63
                                  58999887 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4     0.012       9.3      41      52 ..      33      44 ..      26      46 .. 0.80
   2 ?    8.0   0.1     0.003       2.2      40      53 ..      50      63 ..      44      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                zinc_ribbon_10 41 eevkyrCpkCga 52
                                  ++ ky+Cp Cg+
  gi|15668773|ref|NP_247573.1| 33 AKKKYKCPVCGF 44
                                  5569******96 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.003
                zinc_ribbon_10 40 leevkyrCpkCgal 53
                                  +++  ++C kCga+
  gi|15668773|ref|NP_247573.1| 50 ASTSIWVCGKCGAK 63
                                  56669*******97 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.2   0.00022      0.16       2      29 ..      35      62 ..      34      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                 A2L_zn_ribbon  2 nlkvCsvCggngilnseqgylvCieCga 29
                                  + ++C vCg +++  +  ++ vC +Cga
  gi|15668773|ref|NP_247573.1| 35 KKYKCPVCGFPKLKRASTSIWVCGKCGA 62
                                  789***********999**********7 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00014      0.11      11      26 ..      31      46 ..       3      55 .. 0.84
   2 ?    0.4   0.1      0.93     7e+02      17      24 ..      55      62 ..      46      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                      zf-Mss51 11 apkhvdfeCpdCGipt 26
                                   +++ +++Cp CG+p 
  gi|15668773|ref|NP_247573.1| 31 IKAKKKYKCPVCGFPK 46
                                  47899*********95 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.93
                      zf-Mss51 17 feCpdCGi 24
                                    C +CG 
  gi|15668773|ref|NP_247573.1| 55 WVCGKCGA 62
                                  57999986 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.9   0.00029      0.22       1      24 [.      37      60 ..      37      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                 Cys_rich_CPCC  1 yqCpcCgyltleeeegsydiCpvC 24
                                  y+Cp+Cg+  l++ ++s+ +C  C
  gi|15668773|ref|NP_247573.1| 37 YKCPVCGFPKLKRASTSIWVCGKC 60
                                  79***********999999**988 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.2   0.00055      0.41       1      32 [.      38      66 ..      38      84 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00055
                       DUF4428  1 iCaiCgkKigllkrlkleDgyvCkdClkKlse 32
                                  +C++Cg   ++lk  +    +vC +C  K+ +
  gi|15668773|ref|NP_247573.1| 38 KCPVCGF--PKLK-RASTSIWVCGKCGAKIAG 66
                                  6999995..4555.335568*********944 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0028       2.1      25      38 ..      34      49 ..      26      51 .. 0.71
   2 ?    9.7   2.2    0.0012       0.9       6      35 ..      37      63 ..      35      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0028
                   Zn-ribbon_8 25 plta.CPeCgs.evrr 38
                                  +++  CP Cg  +++r
  gi|15668773|ref|NP_247573.1| 34 KKKYkCPVCGFpKLKR 49
                                  3455599999888877 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                   Zn-ribbon_8  6 YrCeeCghefevlqsisdaplta.CPeCgse 35
                                  Y+C  Cg  f +l ++s    +  C +Cg++
  gi|15668773|ref|NP_247573.1| 37 YKCPVCG--FPKLKRAST--SIWvCGKCGAK 63
                                  9******..888887773..5556****985 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.0   0.00054      0.41      19      45 ..      37      62 ..      32      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00054
                 Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrk 45
                                    CP Cg  k+ r +t   + C +C++
  gi|15668773|ref|NP_247573.1| 37 YKCPVCGFPKLKRAST-SIWVCGKCGA 62
                                  67*************9.********86 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.15   1.1e+02       2       9 ..      36      43 ..      35      47 .. 0.86
   2 ?    6.5   0.0    0.0082       6.1       3      13 ..      55      65 ..      53      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.15
                        zf_UBZ  2 tylCerCg 9 
                                   y C+ Cg
  gi|15668773|ref|NP_247573.1| 36 KYKCPVCG 43
                                  69*****9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0082
                        zf_UBZ  3 ylCerCgkeip 13
                                  ++C +Cg++i 
  gi|15668773|ref|NP_247573.1| 55 WVCGKCGAKIA 65
                                  79******995 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.6       0.2   1.5e+02      12      24 ..      32      44 ..      26      54 .. 0.74
   2 ?    9.8   0.2     0.001      0.77      15      29 ..      53      67 ..      44      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.2
                                  GGSS--EETTTTE CS
                        zf-BED 12 lkeqkavCryCgk 24
                                  + ++k +C  Cg+
  gi|15668773|ref|NP_247573.1| 32 KAKKKYKCPVCGF 44
                                  468999*****98 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.001
                                  S--EETTTTEE---- CS
                        zf-BED 15 qkavCryCgkilsrg 29
                                    +vC  Cg+++++g
  gi|15668773|ref|NP_247573.1| 53 SIWVCGKCGAKIAGG 67
                                  679*********998 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.6     0.004         3      34      44 ..      36      46 ..      34      48 .. 0.76
   2 ?    4.0   0.4      0.07        52      35      43 ..      55      63 ..      53      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.004
                                  T-BBTTTB-BG CS
                    Rubredoxin 34 dWvCPdCgvek 44
                                  +++CP+Cg +k
  gi|15668773|ref|NP_247573.1| 36 KYKCPVCGFPK 46
                                  67888888877 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.07
                                  -BBTTTB-B CS
                    Rubredoxin 35 WvCPdCgve 43
                                  WvC +Cg++
  gi|15668773|ref|NP_247573.1| 55 WVCGKCGAK 63
                                  ******986 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.029        22      16      30 ..      31      45 ..      22      50 .. 0.79
   2 ?    5.1   0.7      0.03        22       2       9 ..      55      62 ..      55      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.029
                                  B--SSTTB-TTT--. CS
                       ADK_lid 16 npPkveglCDkCGep 30
                                  ++ k++ +C +CG p
  gi|15668773|ref|NP_247573.1| 31 IKAKKKYKCPVCGFP 45
                                  5679999*****976 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.03
                                  EE-TTT-- CS
                       ADK_lid  2 rvCpkCGr 9 
                                  +vC kCG+
  gi|15668773|ref|NP_247573.1| 55 WVCGKCGA 62
                                  9*****97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   7.1     0.028        21       2      26 .]      36      64 ..      35      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.028
                   zf-ribbon_3  2 tvrCPnCGa.plssddn...vCpyCGtkl 26
                                  +++CP CG  +l+   +   vC +CG+k+
  gi|15668773|ref|NP_247573.1| 36 KYKCPVCGFpKLKRASTsiwVCGKCGAKI 64
                                  689*****955877777556899999986 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   6.3    0.0098       7.4      11      22 ..      34      45 ..      32      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0098
                                  B-SEE-TTT--E CS
                        zf-HIT 11 pakYkCpkCntr 22
                                  ++kYkCp C+ +
  gi|15668773|ref|NP_247573.1| 34 KKKYKCPVCGFP 45
                                  79*******977 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   9.0      0.13        94       2      33 ..      35      61 ..      34      68 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
                                  EEE--TTTT-TTTEEETT....S-EEETTTTB CS
                Prim_Zn_Ribbon  2 khspCPvCGGrDrFrfddkdgrGtwfCrqCgg 33
                                  k+  CPvCG    F   +++ ++ w+C +C g
  gi|15668773|ref|NP_247573.1| 35 KKYKCPVCG----FPKLKRASTSIWVCGKC-G 61
                                  6778****9....55334466699******.5 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.7    0.0032       2.4      12      21 ..      34      43 ..      32      44 .. 0.87
   2 ?    0.1   0.0       1.7   1.3e+03      14      21 ..      54      61 ..      47      63 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0032
                     zf-H2C2_2 12 ekpyeCplCd 21
                                  +k+y+Cp+C+
  gi|15668773|ref|NP_247573.1| 34 KKKYKCPVCG 43
                                  789******7 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.7
                     zf-H2C2_2 14 pyeCplCd 21
                                  ++ C +C+
  gi|15668773|ref|NP_247573.1| 54 IWVCGKCG 61
                                  56788886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 596.12
//
Query:       gi|15668774|ref|NP_247575.1|  [L=169]
Description: ribosomal biogenesis protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1143.07
//
Query:       gi|15668775|ref|NP_247577.1|  [L=76]
Description: 50S ribosomal protein LXA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-10   39.0   0.0    1.1e-09   38.5   0.0    1.3  1  Ribosomal_L18A   Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18
  ------ inclusion threshold ------
      0.083   12.3   0.0      0.083   12.3   0.0    1.1  1  PI3Ka            Phosphoinositide 3-kinase family, accessory 
       0.11   11.9   0.0       0.12   11.7   0.0    1.0  1  Hexose_dehydrat  NDP-hexose 2,3-dehydratase


Domain annotation for each model (and alignments):
>> Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   1.8e-13   1.1e-09      80     121 .]      17      58 ..       3      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.8e-13
                                   EEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEEE CS
                Ribosomal_L18A  80 gthnfykeyrdlteegaveqvYselgsrhrakrssIqIekve 121
                                   +   f+key++l+ e+a+e +Yse+g+r+++krs+I+I+++e
  gi|15668775|ref|NP_247577.1|  17 DPLYFRKEYKALKPEDALEILYSEFGGRYKVKRSRIKILNIE 58 
                                   456799*********************************996 PP

>> PI3Ka  Phosphoinositide 3-kinase family, accessory domain (PIK domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.4e-05     0.083      58     102 ..      11      56 ..       1      75 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                                   SHHHHHHHHHHHTTSHHTTHHHHTTTTSTTS--.HHHHHHHHHHHH CS
                         PI3Ka  58 eesevkealelldsWaeididdaLeLLdskfkd.esvreyavkvLe 102
                                    +++ k+ l   ++ + ++++daLe+L s+f    +v++  +k+L+
  gi|15668775|ref|NP_247577.1|  11 MSKKGKDPLYFRKEYKALKPEDALEILYSEFGGrYKVKRSRIKILN 56 
                                   45556677777888999***************98999998888885 PP

>> Hexose_dehydrat  NDP-hexose 2,3-dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.1e-05      0.12     120     169 ..      13      62 ..       7      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
               Hexose_dehydrat 120 hkgrkppyldefleaerervlvdvlqSEeGgrFyrkrnrnliveveedve 169
                                   +kg++p y+++  +a + +  ++ l SE Ggr+  kr+r  i+++ee  +
  gi|15668775|ref|NP_247577.1|  13 KKGKDPLYFRKEYKALKPEDALEILYSEFGGRYKVKRSRIKILNIEEIKP 62 
                                   6788999999988888889999**********************977555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 550.62
//
Query:       gi|15668776|ref|NP_247578.1|  [L=141]
Description: hypothetical protein MJ_0596 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-66  220.6  11.5    7.5e-66  220.4  11.5    1.0  1  DUF2666       Protein of unknown function (DUF2666)
     0.0051   16.0   0.4     0.0096   15.1   0.4    1.6  1  dCache_2      Cache domain
  ------ inclusion threshold ------
      0.023   14.8   0.1       0.24   11.5   0.0    2.1  2  P_C10         Protein C10
      0.023   15.1   0.8       0.11   12.9   0.3    2.2  2  Phage_TAC_12  Phage tail assembly chaperone protein, TAC
      0.066   12.9   0.0       0.16   11.7   0.0    1.7  2  DUF2717       Protein of unknown function (DUF2717)


Domain annotation for each model (and alignments):
>> DUF2666  Protein of unknown function (DUF2666)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.4  11.5   2.1e-69   7.5e-66       1     135 []       2     136 ..       2     136 .. 0.99

  Alignments for each domain:
  == domain 1  score: 220.4 bits;  conditional E-value: 2.1e-69
                                   SSEEEEEEEETTEEEEEEEE--TTS-HHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHTTT--S--S....HHHHHHHHH CS
                       DUF2666   1 edkieftakkgkWivvkklkiDektedleiarlLasieetvskkikdylpfDlekleeiadeikkkkkgrvkeedisevle 81 
                                   edkief+ak++kW+vvkklkiDe+ted+eiarlLasi+etv +ki++ylpfD++kl+eiad+i++kkkgr++ee+i+evl+
  gi|15668776|ref|NP_247578.1|   2 EDKIEFMAKHKKWFVVKKLKIDENTEDIEIARLLASIDETVLNKIPEYLPFDMNKLYEIADGIYQKKKGRITEEEIAEVLK 82 
                                   8******************************************************************************** PP

                                   HHHT-.............---HHHHHHHHHHHHHTTT--SS--HHHHHHHH-XX CS
                       DUF2666  82 klkspattkklnkitdskegkeilkvilarivLerlGiktkveskllekyleks 135
                                   klkspatt+kln+it+skegkeilk+il++i+LerlGi+t+v++k++eky+e+s
  gi|15668776|ref|NP_247578.1|  83 KLKSPATTRKLNEITESKEGKEILKAILNNIILERLGIQTRVSPKVIEKYIENS 136
                                   ****************************************************96 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   2.7e-06    0.0096      33      84 ..      33      84 ..       8     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-06
                      dCache_2 33 elieyeknsleeslkesLksrveeaysiaeeiyekyknelseeeakklikea 84
                                   l+++  +++ +++ e+L   +++ y+ia  iy+k k +++eee+ + +k++
  gi|15668776|ref|NP_247578.1| 33 RLLASIDETVLNKIPEYLPFDMNKLYEIADGIYQKKKGRITEEEIAEVLKKL 84
                                  44556668889999999999***************999******99988876 PP

>> P_C10  Protein C10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.11   4.1e+02      15      97 ..      18      43 ..       9      60 .. 0.59
   2 ?   11.5   0.0   6.7e-05      0.24       8      59 ..      75     132 ..      70     134 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.11
                         P_C10 15 ealeqpenaakleeakesagndmlkvmqlvlPvvvqiqmevikkyGFaedreGvvkfaqlvrelekedkevarlaselrslfl 97
                                  ++l+  en++ +e a+                                                         l + + +++l
  gi|15668776|ref|NP_247578.1| 18 KKLKIDENTEDIEIAR---------------------------------------------------------LLASIDETVL 43
                                  5555555555555554.........................................................4444443333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.7e-05
                         P_C10   8 aaleevlealeqpenaakleeakes.agndmlkvm.....qlvlPvvvqiqmevikky 59 
                                   + ++evl++l++p+++ kl+e+ es  g+++lk++        l + +++  +vi+ky
  gi|15668776|ref|NP_247578.1|  75 EEIAEVLKKLKSPATTRKLNEITESkEGKEILKAIlnniiLERLGIQTRVSPKVIEKY 132
                                   5689*****************9876157777775411000334566666666666666 PP

>> Phage_TAC_12  Phage tail assembly chaperone protein, TAC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   3.2e-05      0.11      46      89 ..      50      93 ..      21     115 .. 0.76
   2 ?    0.8   0.0      0.18   6.4e+02      64      80 ..     120     136 ..     103     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                  Phage_TAC_12 46 esgdpevLvevlyaalshkkkrpsrdeieealekvdeekdlekl 89
                                     d++ L e+ +   ++kk+r++++ei e+l+k+++ + + kl
  gi|15668776|ref|NP_247578.1| 50 LPFDMNKLYEIADGIYQKKKGRITEEEIAEVLKKLKSPATTRKL 93
                                  556889999999999999****************9666544443 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.18
                  Phage_TAC_12  64 kkkrpsrdeieealekv 80 
                                    + r+s + ie+++e+ 
  gi|15668776|ref|NP_247578.1| 120 IQTRVSPKVIEKYIENS 136
                                   477999999****9964 PP

>> DUF2717  Protein of unknown function (DUF2717)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.6e-05      0.16      22      76 ..      46     101 ..      37     102 .. 0.83
   2 ?   -2.7   0.0       1.4   4.9e+03       3      13 ..     127     137 ..     127     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.6e-05
                       DUF2717  22 aaeYLqvrfnasYliasGlidalrkaGysesyiaGfldGlnla..sevldeielrke 76 
                                   + eYL   +n+ Y ia G++++ +k    e  ia +l+ l+    ++ l+ei   ke
  gi|15668776|ref|NP_247578.1|  46 IPEYLPFDMNKLYEIADGIYQK-KKGRITEEEIAEVLKKLKSPatTRKLNEITESKE 101
                                   579****************997.556689999******9986545888999877776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                       DUF2717   3 kpikkllknPd 13 
                                   k+i+k+++n +
  gi|15668776|ref|NP_247578.1| 127 KVIEKYIENSQ 137
                                   68999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1162  (0.0648112); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1049.27
//
Query:       gi|15668777|ref|NP_247579.1|  [L=357]
Description: hypothetical protein MJ_0597 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-10   41.3   1.0      3e-09   37.5   0.4    2.8  2  Radical_SAM     Radical SAM superfamily
  ------ inclusion threshold ------
      0.064   13.4   1.2       0.18   12.0   1.2    1.8  1  T3SchapCesA     Type III secretion system filament chaperone 
       0.27   11.2   2.3       0.35   10.8   0.5    2.2  2  Arm-DNA-bind_2  Arm DNA-binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.13   7.7e+02      27      46 ..       6      24 ..       2      34 .. 0.62
   2 !   37.5   0.4     5e-13     3e-09       7     167 .]      44     197 ..      42     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.13
                                  HHHHHHHHHHHHHHHHHHTT CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 27 rslsveeileevkelkaekg 46
                                  + + veeile ++++ ++  
  gi|15668777|ref|NP_247579.1|  6 EKMKVEEILENARKA-FKLT 24
                                  556677777777666.5543 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 5e-13
                                   ESS-..-TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEE CS
                                   xxxx..xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   7 Cnlr..CsfCarpet..vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritve 83 
                                   Cnl+  C+fC+  +   + + +r + + +e++l+e+  + ++ g k  +++gg     +++ +++e+ a       +++  
  gi|15668777|ref|NP_247579.1|  44 CNLKqpCKFCYMATQknKIKDPRKARRRLESVLAEAILM-KRIGWKLEFISGGYGYTPKEINDIAEMVAY----VQKCRQY 119
                                   999999*******9999999*******************.7***88888899989998888888888888....5677777 PP

                                   ECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  84 tngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleell 164
                                    n +++    l+ +    +  v   +e+++++  ++++++g+ +++++++l k++e+g+k + ++i+++ Ge +e++e+ll
  gi|15668777|ref|NP_247579.1| 120 LNVGVI---DLDNINLDVIEGVVGAVETVSKD--RDWICPGKPLDKIKDNLLKAKELGLK-TGITIILGLGEKEEDIEKLL 194
                                   777777...344444434889***********..55666*********************.*******************9 PP

                                   HHH CS
                                   xxx RF
                   Radical_SAM 165 ell 167
                                   +l+
  gi|15668777|ref|NP_247579.1| 195 NLI 197
                                   986 PP

>> T3SchapCesA  Type III secretion system filament chaperone CesA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.2     3e-05      0.18      10      70 ..     294     354 ..     289     357 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                   T3SchapCesA  10 kelldkkirseieaikkiiaefdvvkesvnilsekaktdpqaaeklnkliegytygeerkl 70 
                                   +ell      +i a kk++ +   + e++ni se+ k   +  e++n  ie y     rk+
  gi|15668777|ref|NP_247579.1| 294 RELLGTFTDIDILAGKKVLEKTPYIEEEINISSENIKRVEELRENINERIESYVSKVLRKI 354
                                   677777777889999**************************************97777765 PP

>> Arm-DNA-bind_2  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       1.8     1e+04      29      44 ..      62      77 ..      53      78 .. 0.61
   2 ?   10.8   0.5   5.9e-05      0.35      20      51 ..     308     344 ..     305     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.8
                Arm-DNA-bind_2 29 lpdtpanrKkaerlla 44
                                  ++d ++ r+++e +la
  gi|15668777|ref|NP_247579.1| 62 IKDPRKARRRLESVLA 77
                                  4555666666666665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 5.9e-05
                Arm-DNA-bind_2  20 Gkrcresl.....glpdtpanrKkaerllaeIeeeIa 51 
                                   Gk++ e++     ++ +  +n+K++e+l+++I+e+I+
  gi|15668777|ref|NP_247579.1| 308 GKKVLEKTpyieeEINISSENIKRVEELRENINERIE 344
                                   6777777754444488899*****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.21s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2603.36
//
Query:       gi|15668778|ref|NP_247580.1|  [L=289]
Description: type II R/M system modification methyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-82  276.7  12.1    2.5e-82  276.5  12.1    1.0  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
  ------ inclusion threshold ------
      0.024   14.7   2.0      0.036   14.1   0.7    1.9  2  DUF600           Protein of unknown function, DUF600
      0.035   14.2   0.2      0.079   13.0   0.2    1.6  1  Complex1_LYR     Complex 1 protein (LYR family)
        2.1    8.5   8.4        2.6    8.2   4.6    2.5  2  EKAL             EMP3-KAHRP-like N-terminal domain


Domain annotation for each model (and alignments):
>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.5  12.1   5.5e-86   2.5e-82       1     260 []       9     270 ..       9     270 .. 0.97

  Alignments for each domain:
  == domain 1  score: 276.5 bits;  conditional E-value: 5.5e-86
                                   STTTSCTTHHHHHCCS-......--SEEEETT-TTSCCHHCS.....SSCEEEEES-HHHHHHHHHHCCHSHHHHHHHHH. CS
               MethyltransfD12   1 YiGgKrkllpeIkelipkd....kgktfvepFaGggaVffeakk..qgkkvlinDinedlinlykaliknnveelikelek 75 
                                   ++GgK+++l++I+e++pk+    ++k+++epF+GggaV f++++  ++kkv+i+Dinedl+ +yk ++kn+v++li+el +
  gi|15668778|ref|NP_247580.1|   9 WAGGKTQILSQIEENLPKElkegNIKKYIEPFVGGGAVLFYLLQkyEFKKVIISDINEDLMLCYK-VVKNDVDRLIEELSS 88 
                                   9*******************************************9********************.99999********** PP

                                   T....CTTGGC.TSHHHHHHHHHHHH...HHH-HHHHHHHHHHHHCCBGGG---B-TTS-B---B-S-SS-....HHHHHH CS
               MethyltransfD12  76 l....lekeelenereyfyelreefnkkidaireaeeaidflylnrllfsglervnkkgnfnvpygaykkpkkvaekelkl 152
                                   l    l + ++e+++e++y++r++fnk++++++e++++++f++ln+++++gl+rvnkkg+fnvpyg+yk+pk+++e++lk+
  gi|15668778|ref|NP_247580.1|  89 LrdefL-SLDEEKRKEFYYKVRDDFNKNKNDCDEVKRVAQFIFLNKTCYNGLYRVNKKGEFNVPYGRYKNPKIFDEQNLKN 168
                                   999854.455668******************************************************************** PP

                                   HHHHHHHCCEEEC-CHHHHTT--TTE.EEEE--S-T.S...TS--GGGG.CS-HHHHHHHHHHHHHH.HHTT-EEEEEEES CS
               MethyltransfD12 153 rseklknakiecgdfdavllkakieddivYlDPPYnprqytanytlyetlafsdedevrlaevlkslsskfgvkvllsnsf 233
                                   +s+ lkn+ki+cgdf+ v++ +++e+ +vY+DPPY+p+++t+++t+y++ +f+d+d++rla+++++l+ k+g k +lsns 
  gi|15668778|ref|NP_247580.1| 169 VSKLLKNVKILCGDFEIVDEYVDAES-FVYFDPPYKPLNKTSSFTSYTKYDFNDDDQIRLAKFYRKLD-KRGAKLMLSNS- 246
                                   **********************9999.****************************************7.***********. PP

                                   EESHHHHHHCTT...SEEEEECCCCHH CS
               MethyltransfD12 234 kdtklfrelyksYnnesileveelrai 260
                                    ++++f +ly+    ++i++v ++r i
  gi|15668778|ref|NP_247580.1| 247 YNVDFFGKLYEG---FNIKKVVAKRMI 270
                                   ************...******999976 PP

>> DUF600  Protein of unknown function, DUF600
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.7     8e-06     0.036       8      97 ..      16     107 ..      14     127 .. 0.81
   2 ?   -2.5   0.0       1.1   4.9e+03      98     110 ..     142     154 ..     131     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8e-06
                                   HHHHHHHH--S-EEEEEEEEEE-T..T--EEEEEEEEETTT-EEEGGGGGGT--S-HHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DUF600   8 iaekildmiPeeWekvylyaevle..dsgevyFyylkkesekliysheipekynvseeeykkllkeLyelikeLreefkke 86 
                                   i  +i + +P+e ++  +  +++   ++g v+Fy l+k + k +  ++i e+  +  ++ k+ +++L e +++Lr+ef   
  gi|15668778|ref|NP_247580.1|  16 ILSQIEENLPKELKEGNIKKYIEPfvGGGAVLFYLLQKYEFKKVIISDINEDLMLCYKVVKNDVDRLIEELSSLRDEFLSL 96 
                                   6667777777777665555555545489999**99999997888899*******************************999 PP

                                   HSS--SEEEEE CS
                        DUF600  87 eqeaWtnltlt 97 
                                   ++e+ +++  +
  gi|15668778|ref|NP_247580.1|  97 DEEKRKEFYYK 107
                                   88877666555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                                   EETTS-EEEEEE- CS
                        DUF600  98 lkksGklkieydy 110
                                   ++k+G++++ y  
  gi|15668778|ref|NP_247580.1| 142 VNKKGEFNVPYGR 154
                                   6778888888853 PP

>> Complex1_LYR  Complex 1 protein (LYR family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   1.8e-05     0.079      20      45 ..      98     123 ..      87     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                  Complex1_LYR  20 yntreyfrrriRdeFrknkhvtDpek 45 
                                   + +r++f  ++Rd F knk+  D++k
  gi|15668778|ref|NP_247580.1|  98 EEKRKEFYYKVRDDFNKNKNDCDEVK 123
                                   4469****************999887 PP

>> EKAL  EMP3-KAHRP-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.11   4.9e+02       2      14 ..      26      38 ..      25      41 .. 0.88
   2 ?    8.2   4.6   0.00058       2.6      20      52 ..     105     137 ..      97     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.11
                          EKAL  2 eEitpgGlKeYeE 14
                                  +E+++g +K+Y E
  gi|15668778|ref|NP_247580.1| 26 KELKEGNIKKYIE 38
                                  699********98 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00058
                          EKAL  20 hfklkEsvdngkkdCDEKYEaaqYGFrEkcPYe 52 
                                    +k+++  +  k dCDE    aq+ F +k+ Y+
  gi|15668778|ref|NP_247580.1| 105 YYKVRDDFNKNKNDCDEVKRVAQFIFLNKTCYN 137
                                   69***************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1841.13
//
Query:       gi|15668779|ref|NP_247581.1|  [L=199]
Description: hypothetical protein MJ_0599 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   13.4   0.1       0.14   12.3   0.1    1.6  1  HSR       HSR domain
       0.13   12.5   1.9       0.45   10.8   0.1    2.3  2  DUF2197   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> HSR  HSR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.6e-05      0.14      21      75 ..     132     185 ..     113     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                           HSR  21 kkpfpflegLrDkslitekmykesleacrnlvpvqkvvYnvLseLektfslslle 75 
                                   ++   +l+ +  +++i +++y + +     +++v  + Y+vL+eL +++++  l 
  gi|15668779|ref|NP_247581.1| 132 NDLRALLYYFWHRAIIEDRIYSQKKGYN-GRKQVIGATYEVLKELRNNQNRVYLY 185
                                   566678999999**********999987.999999***********999987765 PP

>> DUF2197  Uncharacterized protein conserved in bacteria (DUF2197)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1     0.086   7.7e+02      29      38 ..      98     107 ..      86     113 .. 0.86
   2 ?   10.8   0.1     5e-05      0.45      20      39 ..     171     190 ..     160     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.086
                       DUF2197  29 ihtYmCkeCe 38 
                                   i+ ++C+ C+
  gi|15668779|ref|NP_247581.1|  98 INKFLCHLCK 107
                                   7889999996 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 5e-05
                       DUF2197  20 laKrLrNrpihtYmCkeCee 39 
                                     K LrN+  ++Y+ ++C+e
  gi|15668779|ref|NP_247581.1| 171 VLKELRNNQNRVYLYEKCDE 190
                                   569***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1531.16
//
Query:       gi|15668780|ref|NP_247582.1|  [L=290]
Description: type II R/M system restriction enzyme 2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.7e-105  351.3  26.2   4.1e-105  351.1  26.2    1.0  1  DpnII     DpnII restriction endonuclease


Domain annotation for each model (and alignments):
>> DpnII  DpnII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.1  26.2  2.3e-109  4.1e-105       1     279 [.       2     285 ..       2     286 .. 0.97

  Alignments for each domain:
  == domain 1  score: 351.1 bits;  conditional E-value: 2.3e-109
                         DpnII   1 dfekflktlketiatydyyvdfekvlknvekikielniLnsLigkknieeefkelikkypevlkvlplLlAvrekeikvld 81 
                                   +fe+++++l eti+ty+++vd+ek+ +n++ki+++l+iLn+Ligk+n++eef el+k+ypev++v+p+L+Avr+++i++l+
  gi|15668780|ref|NP_247582.1|   2 NFEYIINSLLETIKTYNFFVDWEKIENNIKKIEKRLHILNYLIGKENFKEEFFELLKEYPEVITVFPILIAVRDNKITILN 82 
                                   699****************************************************************************** PP

                         DpnII  82 ekekevllnfkklel.lkeevekyveFlektGLkellknkkiknlvdYvlGvevGlDsnaRKNRsGklmeklvekllkkag 161
                                   e+ +  +l+fk++++ ++ee+e+y++F+++tGL++llkn+kiknlvdYv+GvevG+D+naRKNR G+lme++v+k++++++
  gi|15668780|ref|NP_247582.1|  83 ENMELETLEFKEKKYlTDEEIERYYKFFKETGLEDLLKNRKIKNLVDYVFGVEVGMDTNARKNRIGDLMENIVKKYIENLC 163
                                   ***************559*************************************************************** PP

                         DpnII 162 lkke..kylkevklkeikekfgidlsaidkaekrfDfvikkk..kklylievnfYssgGSKlnevarsYkelaeelk.eie 237
                                   ++++  +y+ ++++++ik+k+gi+l+  dk++++fDf++++k  kklylievnfYs+gGSKl+++a++Y++l+e +k +++
  gi|15668780|ref|NP_247582.1| 164 KQNKnlDYIFQATKDKIKQKWGINLTL-DKTNRKFDFAVFNKntKKLYLIEVNFYSGGGSKLKATAGEYRSLNEFIKnNNN 243
                                   *99559*******************66.***********998789*******************************95678 PP

                         DpnII 238 gleFvwiTDGkgWksaknkLeeafeeidkllnlkdleegvle 279
                                   +++F+wiTDGkgW++akn L+e+f++   +lnlk+++eg+l+
  gi|15668780|ref|NP_247582.1| 244 NVQFIWITDGKGWNTAKNPLKESFNSGVVILNLKMVKEGLLK 285
                                   9**************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1408  (0.078532); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1974.13
//
Query:       gi|15668781|ref|NP_247583.1|  [L=267]
Description: ribulose-1,5-biphosphate synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-96  320.5   2.5    6.2e-96  320.2   2.5    1.1  1  Thi4            Thi4 family
    9.3e-13   48.5   5.3    4.6e-09   36.3   1.3    2.3  2  DAO             FAD dependent oxidoreductase
    3.3e-10   39.6   6.4    1.2e-06   27.9   0.2    3.0  3  FAD_binding_2   FAD binding domain
    3.6e-10   39.9   0.3    1.3e-09   38.1   0.3    2.0  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      5e-08   32.7   1.3    9.2e-08   31.9   1.3    1.4  1  FAD_oxidored    FAD dependent oxidoreductase
    1.2e-07   31.4   0.3    2.1e-07   30.5   0.3    1.4  1  FAD_binding_3   FAD binding domain
    6.4e-07   28.9   1.1    1.9e-06   27.3   0.8    1.9  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.2e-06   26.1   2.3      4e-06   25.8   0.1    1.9  2  HI0933_like     HI0933-like protein
    3.1e-05   23.4   0.1    7.5e-05   22.1   0.1    1.6  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00021   21.8   1.1     0.0027   18.3   0.3    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00027   20.4   0.2     0.0026   17.1   0.1    2.1  2  Amino_oxidase   Flavin containing amine oxidoreductase
    0.00081   18.5   0.7     0.0024   17.0   0.7    1.9  1  Lycopene_cycl   Lycopene cyclase protein
     0.0011   18.9   1.9     0.0043   17.1   0.6    2.4  3  NAD_binding_9   FAD-NAD(P)-binding
     0.0057   15.8   0.3     0.0057   15.8   0.3    1.6  2  GIDA            Glucose inhibited division protein A
     0.0094   16.0   0.0      0.025   14.6   0.0    1.7  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.027   14.9   0.1      0.045   14.2   0.1    1.5  1  NAD_binding_7   Putative NAD(P)-binding
       0.03   13.2   0.3       0.21   10.4   0.0    1.9  2  Trp_halogenase  Tryptophan halogenase
      0.047   12.8   0.0      0.071   12.2   0.0    1.2  1  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.2   2.5   6.2e-99   6.2e-96       1     235 []      20     245 ..      20     245 .. 0.99

  Alignments for each domain:
  == domain 1  score: 320.2 bits;  conditional E-value: 6.2e-99
                                   HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHTT CS
                          Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelLdelg 81 
                                   ++ai++++f+++l+++e+DvvivGaG+sGLt+a+ylak+ ++kv++ler++++GGG+w+GG+ f +ivv++pa+elL+e+g
  gi|15668781|ref|NP_247583.1|  20 TKAILKASFDMWLDIVEADVVIVGAGPSGLTCARYLAKE-GFKVVVLERHLAFGGGTWGGGMGFPYIVVEEPADELLREVG 99 
                                   79*************************************.***************************************** PP

                                   ---EEESSEEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTC..TTTSS.-B-EEEEEE CS
                          Thi4  82 ikyedegdyvvvkdaalftstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvela..hdtqscvDPlvirak 160
                                   ik+ d+gd+++v+d++++ ++l++++++ a++k+l++++veDli+re +gvaGvvin++++e+a  h     +DPl+ir+k
  gi|15668781|ref|NP_247583.1| 100 IKLIDMGDGYYVADSVEVPAKLAVAAMD-AGAKILTGIVVEDLILRE-DGVAGVVINSYAIERAglH-----IDPLTIRSK 173
                                   ****************************.******************.9***************888.....********* PP

                                   EEEE--GSSSTTTTHHHHHHHHCTTTS-----ECB-HHHHHHHHHHHECEEETTEEE-THHHHHHHT-EB--SB- CS
                          Thi4 161 vvvdatGhdgeivavvvkkikleakiekvkgeksldaekaedaivkktrevvpnlyvaGmevaevdganRmGpif 235
                                   vvvdatGh+++iv+++vkk+klea   +v+geks++aek+e+a++++trev+pnl+v+Gm++++++g++RmG+if
  gi|15668781|ref|NP_247583.1| 174 VVVDATGHEASIVNILVKKNKLEA---DVPGEKSMWAEKGENALLRNTREVYPNLFVCGMAANASHGGYRMGAIF 245
                                   **********************99...9**********************************************9 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   1.3   4.6e-12   4.6e-09       1      40 [.      38      79 ..      38      95 .. 0.89
   2 !   13.9   0.1     3e-05     0.029     150     213 ..     119     189 ..      91     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 4.6e-12
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrn 40
                                  dvvi+G+G  Gl++A++La++g  V++le++  +g g+ g+ 
  gi|15668781|ref|NP_247583.1| 38 DVVIVGAGPSGLTCARYLAKEGfkVVVLERHLAFGGGTWGGG 79
                                  9******************************99996666554 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3e-05
                                   HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE......EECT.EEEE....EEEE..EEE--GGGHHHHHTTCTT CS
                           DAO 150 aalaraaealGveilegtevtgleeedgkvwgve......rttp.gend....aada..vVnaaGawsdllgllkel 213
                                   a la aa ++G++il+g  v++l  ++++v+gv       +  + g  +    +++   vV a+G+ ++++   ++l
  gi|15668781|ref|NP_247583.1| 119 AKLAVAAMDAGAKILTGIVVEDLILREDGVAGVVinsyaiE--RaGL-HidplTIRSkvVVDATGHEASIV---NIL 189
                                   678999****************8666667888877666431..2243.14577334456********9866...333 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.2   1.2e-09   1.2e-06       1      38 [.      38      75 ..      38      85 .. 0.91
   2 !    8.3   0.1    0.0011       1.1     147     200 ..     121     180 ..     105     199 .. 0.80
   3 !    5.9   0.1    0.0057       5.6     385     415 ..     215     244 ..     207     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.2e-09
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38
                                  Dv+++G+G +GL++A  +a++G kv+v+e   +fgg t
  gi|15668781|ref|NP_247583.1| 38 DVVIVGAGPSGLTCARYLAKEGFKVVVLERHLAFGGGT 75
                                  9*****************************99999865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0011
                                   HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET..TTTCEE....EEEESEEEE--- CS
                 FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenp..esgrev....rirakavvlatg 200
                                   l+ +a +ag ++++ + +++Li ++++v G+v++    e  + +    +ir+k vv+atg
  gi|15668781|ref|NP_247583.1| 121 LAVAAMDAGAKILTGIVVEDLILREDGVAGVVINSYaiERAGLHidplTIRSKVVVDATG 180
                                   4555667789**********************9966763333336677888888888887 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0057
                                   STTEEESSBTEEE-STCEESSSSTTS--TTH CS
                 FAD_binding_2 385 ldadgqpipGLYAaGevaaggvhganrlgGn 415
                                   l+++ ++ p+L+ +G +a    hg +r+g++
  gi|15668781|ref|NP_247583.1| 215 LRNTREVYPNLFVCGMAA-NASHGGYRMGAI 244
                                   6889999***********.999*****9987 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.3   1.3e-12   1.3e-09       1      33 [.      41      73 ..      41      76 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.3e-12
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                  IvGaG sGl++A++Lak+gf+v++le++  +GG
  gi|15668781|ref|NP_247583.1| 41 IVGAGPSGLTCARYLAKEGFKVVVLERHLAFGG 73
                                  9***************************99998 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   1.3   9.2e-11   9.2e-08       1     144 [.      38     180 ..      38     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 9.2e-11
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrgga.rlkkrsk 80 
                                   Dvv+vG+gp+G+++A   a++G kv+++e++   GG + +g+++ +   +    vv+  a+e+l+++    +  ++++ + 
  gi|15668781|ref|NP_247583.1|  38 DVVIVGAGPSGLTCARYLAKEGFKVVVLERHLAFGGGTWGGGMGFP---Y---IVVEEPADELLREVGI--KLiDMGDGYY 110
                                   9******************************999988777774333...3...4666667777777733..1112222222 PP

                  FAD_oxidored  81 wntfepevakavleemlaeagvtvllntrlvevekegkr.....iesvtveske.g..rktirAkvfiDATg 144
                                    ++  +ev ++++ + ++  g ++l++ ++++ + +++      i+s  +e+   +    tir+kv++DATg
  gi|15668781|ref|NP_247583.1| 111 -VADSVEVPAKLAVAAMDA-GAKILTGIVVEDLILREDGvagvvINSYAIERAGlHidPLTIRSKVVVDATG 180
                                   .334556666666666655.8888888888888875433123346666666666556689***********8 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.3   2.1e-10   2.1e-07       1      33 [.      36      68 ..      36      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.1e-10
                                  EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                 FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                  e+dV+IVGaGp+Gl+ a+ L++ G +vv++e++
  gi|15668781|ref|NP_247583.1| 36 EADVVIVGAGPSGLTCARYLAKEGFKVVVLERH 68
                                  579*****************************9 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.8   1.9e-09   1.9e-06       2      45 ..      38      85 ..      37     188 .. 0.79
   2 ?    0.5   0.1       0.3   2.9e+02     195     252 ..     127     197 ..      96     238 .. 0.66

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.9e-09
                                  SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx RF
                   Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllska 45
                                  dvv++G+Gp Gl++a++la+ g+kv+++e     +g + +gg+  +++
  gi|15668781|ref|NP_247583.1| 38 DVVIVGAGPSGLTCARYLAKEGFKVVVLErhlaFGGGTWGGGMGFPYI 85
                                  8***************************76666444444444444444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.3
                                   HTTEEEEESCEEEEEEETTEEEE.EEETTSCE...........EEESEEEE-S-EEES-HHCS.HCCT-EE CS
                                   xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx...........xxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                   Pyr_redox_2 195 keGvevklgtsvkeidgngekle.vvledgee...........idadlvvvavGvrpstelle.eklglel 252
                                   + G ++ +g +v++++ +++ +  vv ++              i  + vv a+G ++s   +  +k +le 
  gi|15668781|ref|NP_247583.1| 127 DAGAKILTGIVVEDLILREDGVAgVVINSYAIeraglhidpltIRSKVVVDATGHEASIVNILvKKNKLEA 197
                                   55666666666666666666333333333222344445555558888888888888887666566655555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1     4e-09     4e-06       2      37 ..      38      73 ..      37      98 .. 0.87
   2 ?   -0.3   0.3      0.34   3.4e+02     375     408 ..     222     253 ..     217     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4e-09
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37
                                  dv+++G+G++Gl +A  +ak+g +V++le+  ++g 
  gi|15668781|ref|NP_247583.1| 38 DVVIVGAGPSGLTCARYLAKEGFKVVVLERHLAFGG 73
                                  8****************************9988875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.34
                                   STTEEE-GGGBSEEE-TTTHHHHHHHHHHHHHHH CS
                   HI0933_like 375 vpgLffaGEvlDvegvtGGynlqaAwasgyaAGk 408
                                    p+Lf++G  +  ++  GGy + a +   y+ Gk
  gi|15668781|ref|NP_247583.1| 222 YPNLFVCG--MAANASHGGYRMGAIFGGMYLSGK 253
                                   799*****..8899*******9999988887775 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   7.6e-08   7.5e-05       1      30 [.      40      68 ..      40      73 .. 0.93
   2 ?   -2.0   0.0       1.7   1.7e+03     280     305 .]     205     229 ..     168     229 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.6e-08
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                  +I+GaGP Gl++a  l k g+ ++++lE++
  gi|15668781|ref|NP_247583.1| 40 VIVGAGPSGLTCARYLAKEGF-KVVVLERH 68
                                  7********************.79****97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                   Pyr_redox_3 280 eldedgrpvlteeteetnvpglflaG 305
                                    ++e+g+ +l  +t e  +p+lf++G
  gi|15668781|ref|NP_247583.1| 205 MWAEKGENALLRNTREV-YPNLFVCG 229
                                   45667777777777776.78888887 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   2.7e-06    0.0027       2      31 ..      39      68 ..      38      75 .. 0.93
   2 ?    1.3   0.0      0.51   5.1e+02      51      79 ..     126     154 ..     115     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.7e-06
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                  vv+vG+G +gl +A +la+ g kV v+er+
  gi|15668781|ref|NP_247583.1| 39 VVIVGAGPSGLTCARYLAKEGFKVVVLERH 68
                                  8***************************97 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.51
                                   HHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                     Pyr_redox  51 ekngievllntkveeiegsedgvesvklk 79 
                                    + g ++l++ +ve +   edgv +v+++
  gi|15668781|ref|NP_247583.1| 126 MDAGAKILTGIVVEDLILREDGVAGVVIN 154
                                   567999****************9999985 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   2.6e-06    0.0026       2      28 ..      47      73 ..      46      83 .. 0.92
   2 ?    1.1   0.0      0.19   1.9e+02     412     449 ..     216     257 ..     202     260 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.6e-06
                                  HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                 Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGG 28
                                  +GL++Ar+L+  Gf+V+vlE    +GG
  gi|15668781|ref|NP_247583.1| 47 SGLTCARYLAKEGFKVVVLERHLAFGG 73
                                  9*******************9888888 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.19
                                   HHHCHHCSTTEEE.SGGGCTTTTTS.H....HHHHHHHHHHHH CS
                 Amino_oxidase 412 plakpegdprlffAGehtsreypgt.v....egAilSGlraAa 449
                                   +  ++  +p+lf++G +   ++ g+ +     g +lSG+  A+
  gi|15668781|ref|NP_247583.1| 216 RNTRE-VYPNLFVCGMAANASHGGYrMgaifGGMYLSGKLCAE 257
                                   33344.79*********99999988552222355667766666 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.7   2.5e-06    0.0024       1      31 [.      38      66 ..      38     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.5e-06
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                  Dvv++GaGp gl  A  l  ak g kvv++e
  gi|15668781|ref|NP_247583.1| 38 DVVIVGAGPSGLTCARYL--AKEGFKVVVLE 66
                                  9*****************..*********96 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       7.7   7.6e+03      52      74 ..       5      33 ..       3      36 .. 0.65
   2 !   17.1   0.6   4.3e-06    0.0043       1      42 [.      40      76 ..      40      82 .. 0.89
   3 ?   -0.1   0.0      0.83   8.3e+02      33      55 ..     197     219 ..     164     227 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.7
                 NAD_binding_9 52 lNvpasemslftddp......ptfaeWlr 74
                                  +N++  ++++ + ++       +f+ Wl+
  gi|15668781|ref|NP_247583.1|  5 MNIKDIKLNADETKTtkailkASFDMWLD 33
                                  66655555555554488888888888875 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.3e-06
                 NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvw 42
                                  +ivGaGp+Gl++++ L+++      +++ + +++ + g g+ w
  gi|15668781|ref|NP_247583.1| 40 VIVGAGPSGLTCARYLAKE-----GFKVVVLERHLAfG-GGTW 76
                                  7****************99.....5********87747.9999 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.83
                 NAD_binding_9  33 psepgagrvwrtdqseelllNvp 55 
                                    + pg++++w ++ +++ll N++
  gi|15668781|ref|NP_247583.1| 197 ADVPGEKSMWAEKGENALLRNTR 219
                                   34456666666666666666665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   5.7e-06    0.0057       1      31 [.      38      68 ..      38      75 .. 0.91
   2 ?   -2.0   0.1       1.4   1.4e+03     111     150 ..     141     181 ..     131     199 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.7e-06
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                                  dv+++G+G +G+ +A  +a+ G+kv+ +  +
  gi|15668781|ref|NP_247583.1| 38 DVVIVGAGPSGLTCARYLAKEGFKVVVLERH 68
                                  79***********************998555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                                   EEEEES-EEEEEECTTEEEEEEET.TS-EEEECEEEE--TT CS
                          GIDA 111 leiieeeveeliveekkvkgvvte.dgetikakavviatGt 150
                                   l ++e+ v+ +++++  ++   ++ d  ti++k+vv atG 
  gi|15668781|ref|NP_247583.1| 141 LILREDGVAGVVINSYAIERAGLHiDPLTIRSKVVVDATGH 181
                                   44555555555555555555433314567777788888886 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.5e-05     0.025       9      46 ..      33      69 ..      23      71 .. 0.88
   2 ?   -3.0   0.0       6.8   6.8e+03      77      91 ..     173     187 ..     168     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                                  ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSH CS
                  Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtl 46
                                  ++ e+ v+++GaG  +   a++L+++g+k vvv+ R l
  gi|15668781|ref|NP_247583.1| 33 DIVEADVVIVGAGPSGLTCARYLAKEGFK-VVVLERHL 69
                                  566899**********************9.99999975 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.8
                                   SEEEE-SSSSS-SB- CS
                  Shikimate_DH  77 dvvisataseepile 91 
                                    vv+ at++e  i++
  gi|15668781|ref|NP_247583.1| 173 KVVVDATGHEASIVN 187
                                   688899998888875 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.6e-05     0.045       3      39 ..      32      68 ..      30     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-05
                 NAD_binding_7  3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvape 39
                                  ld+ +  v++vG+G+ +++ +r l+++g kv+v+   
  gi|15668781|ref|NP_247583.1| 32 LDIVEADVVIVGAGPSGLTCARYLAKEGFKVVVLERH 68
                                  6888999**************************8765 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00021      0.21       1      32 [.      38      66 ..      38      72 .. 0.89
   2 ?    0.7   0.0      0.18   1.8e+02     152     216 ..     113     188 ..     108     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve 32
                                  ++vivG+G++G + A +lak +   ++v ++e
  gi|15668781|ref|NP_247583.1| 38 DVVIVGAGPSGLTCARYLAKEG---FKVVVLE 66
                                  69******************99...7788877 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.18
                                   -HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT...........S-EEE-SEEEE-SGGG-IIIII CS
                Trp_halogenase 152 daalyakfLrrvaearGvtrvegkvvevqldedgrveslrled...........greveadlfiDcsGfrgllieq 216
                                   d  ++   L   a ++G +++ g vve  +  ++ v+++ +++             ++    ++D++G+++ +++ 
  gi|15668781|ref|NP_247583.1| 113 DSVEVPAKLAVAAMDAGAKILTGIVVEDLILREDGVAGVVINSyaieraglhidPLTIRSKVVVDATGHEASIVNI 188
                                   5555556666677777777777777776666666677777776666666555444567788899999999888765 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.1e-05     0.071       4      46 ..      38      81 ..      36      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.1e-05
                   K_oxygenase  4 DligiGiGpsnLsLailleevkkelkalflerqpefa...Whpgml 46
                                  D++++G+Gps L+ a  l++    +k+++ler+ +f+   W  gm 
  gi|15668781|ref|NP_247583.1| 38 DVVIVGAGPSGLTCARYLAKEG--FKVVVLERHLAFGggtWGGGMG 81
                                  9******************999..********99984333666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 1633.40
//
Query:       gi|15668782|ref|NP_247584.1|  [L=261]
Description: hypothetical protein MJ_0602 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1230  (0.0686039); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1768.86
//
Query:       gi|161579526|ref|NP_247585.2|  [L=422]
Description: glutamate-1-semialdehyde aminotransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-75  253.1   0.0    4.6e-75  252.8   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
    3.3e-06   26.5   0.0    4.3e-06   26.2   0.0    1.2  1  Aminotran_1_2  Aminotransferase class I and II
     0.0021   16.5   0.1     0.0034   15.8   0.1    1.2  1  Peptidase_S80  Bacteriophage T4-like capsid assembly protein 
  ------ inclusion threshold ------
      0.011   15.9   0.1        2.4    8.3   0.0    2.4  2  DUF167         Uncharacterised ACR, YggU family COG1872


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.8   0.0     1e-78   4.6e-75       9     377 ..      29     391 ..      22     417 .. 0.90

  Alignments for each domain:
  == domain 1  score: 252.8 bits;  conditional E-value: 1e-78
                                    SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..S CS
                    Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgld 88 
                                     +++++ka+ +yl dvdg+ y+D   ++ ++ lGha+ +v+kavkeq++  s   +g  t++++  la++++k +p   +
  gi|161579526|ref|NP_247585.2|  29 YPFFVEKAKDCYLFDVDGNCYIDYCLAYGPMVLGHANDAVIKAVKEQLELGSA--YGCPTEKEI-ILAKEVVKRVPC-AE 104
                                    5699*******************************************998843..345555555.566666666666.6* PP

                                    EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGT CS
                    Aminotran_3  89 kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevl 168
                                    +v ++nsG+eA+++A++lar        t ++kii+f+ga+HG   + l  +gs  +  t  +p++p+++    + ++ +
  gi|161579526|ref|NP_247585.2| 105 MVRFVNSGTEATMSAIRLARG------VTGRKKIIKFDGAYHGAHDYVLVKSGS--GALTHGHPNSPGIPEETTKNTILI 176
                                    *********************......9**************************..88888999**************** PP

                                    B-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT..TTTSSSSG CS
                    Aminotran_3 169 keneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGf..GrTGklfA 246
                                    ++n+      + ++++ +++ kde+a +ivEpi g+ G + +++++l+ lre+++++d+lli+DEv tGf  +  G   A
  gi|161579526|ref|NP_247585.2| 177 PFND------EDAVKKAINENKDEIACIIVEPIMGNVGCILPKEGYLEFLREITEENDILLIFDEVITGFrlAKGG---A 247
                                    ****......6678888889**************************************************877888...* PP

                                    GGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHH CS
                    Aminotran_3 247 lehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiieeekllenaqelgaa 323
                                     e++gv pD+ tl+K l+gG+p+ a+++++e+m++++p +   +++Tf Gnp+   + +a+l+ + +  + ++++++ ++
  gi|161579526|ref|NP_247585.2| 248 QEYFGVVPDIATLGKILGGGFPIGAIVGRRELMEQFSPLGaiyQAGTFNGNPISITAGIATLKQLDDR-FYKETARTAKI 326
                                    **************************************99999*********************9876.567788999** PP

                                    HHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC...........HHHHHHHHHCTEE-EEE CS
                    Aminotran_3 324 lkegLeelqkkyevikevRgkGlmiaielkeeaevke...........keilkkakekGvlilsa 377
                                    l + L+el++k++  ++v +   m+ i + +++ v+             +++ +++ekGv + ++
  gi|161579526|ref|NP_247585.2| 327 LADTLRELADKHNIKAKVYNIASMFQIYFNDKEVVNYeiakqsdtekfMKYFWRLLEKGVFVPPS 391
                                    ************9999***********88888887778999999988888889999999988665 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   9.5e-10   4.3e-06     130     341 ..     179     398 ..     118     413 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 9.5e-10
                                    E-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHH.HHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGST CS
                  Aminotran_1_2 130 ldlealeealkeapegnkktkvilvesphNPtGtvatleelek.lldlakkynlllfvDeaYagfvfgsldavatranve 208
                                    +d +a+++a++e++ +  ++ +i+ve +  + G ++++e + + l ++++++ +ll++De+  gf + + +a++ +++v 
  gi|161579526|ref|NP_247585.2| 179 NDEDAVKKAINENK-D--EIACIIVEPIMGNVGCILPKEGYLEfLREITEENDILLIFDEVITGFRLAKGGAQE-YFGVV 254
                                    68889999999843.3..447****************998666156778888***************9778888.99999 PP

                                    TSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHH CS
                  Aminotran_1_2 209 eepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqs..eleemrqrlqkrr 285
                                    ++++     +l+K +G  G+ +G+i+g  ++ +q   l + +   +  + ++  +a  ++l+  +  + +e++++ + ++
  gi|161579526|ref|NP_247585.2| 255 PDIA-----TLGKILG-GGFPIGAIVGRRELMEQFSPLGAIYQAgTFNGNPISITAGIATLKQLDdrFYKETARTAKILA 328
                                    9999.....******9.599**************9999999988877777777777777766666679999999999999 PP

                                    HHHHHHHHHSTEEEECCS.CSSEEEEEETHH..........CHHHHHHH...HHHTCTEEEEEGGGGTS..T CS
                  Aminotran_1_2 286 kelrdeLaelglkvlasq.sgmflltdlsae..........takelskk...Lleevgvyvtpgtsftv..p 341
                                    ++lr+  ++ ++k    + + mf +   ++e          + +++ k    Lle+ gv v p ++f++  +
  gi|161579526|ref|NP_247585.2| 329 DTLRELADKHNIKAKVYNiASMFQIYFNDKEvvnyeiakqsDTEKFMKYfwrLLEK-GVFVPP-SQFECcfT 398
                                    9999998888888888887899999999999988888888655555555888****.****99.88887543 PP

>> Peptidase_S80  Bacteriophage T4-like capsid assembly protein (Gp20)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   7.5e-07    0.0034      60     116 ..     317     373 ..     301     383 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.5e-07
                                    XXXXXXXXXHHHHHHHTTSSSTTHHHHHHHHHHHHS---SSS-SSEE---S--S-HH CS
                  Peptidase_S80  60 yepgtktvkelidsyralaeyyevddavseivdeaivyeddkevvalnldksdfsek 116
                                    y+   +t+k l d+ r+la+++++   v +i +   +y +dkevv  ++ k   +ek
  gi|161579526|ref|NP_247585.2| 317 YKETARTAKILADTLRELADKHNIKAKVYNIASMFQIYFNDKEVVNYEIAKQSDTEK 373
                                    77788999*************************************999887655554 PP

>> DUF167  Uncharacterised ACR, YggU family COG1872
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.006        27      38      56 ..      60      78 ..      47      81 .. 0.89
   2 ?    8.3   0.0   0.00054       2.4      44      75 ..     103     134 ..     103     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.006
                                   IIIIHHHHHHHHHHHHHS. CS
                         DUF167 38 vdGkANkalikfLakalgv 56
                                   v G AN+a+ik + ++l++
  gi|161579526|ref|NP_247585.2| 60 VLGHANDAVIKAVKEQLEL 78
                                   679***********99986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00054
                                    HHHHHHHHHHHS...SEEEE-S-GGGSEEEEE CS
                         DUF167  44 kalikfLakalgvpksdveivsGeksreKvvr 75 
                                    +++++f+ +  +   s++++ +G + r+K+++
  gi|161579526|ref|NP_247585.2| 103 AEMVRFVNSGTEATMSAIRLARGVTGRKKIIK 134
                                    58999999999*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2833.62
//
Query:       gi|15668784|ref|NP_247586.1|  [L=100]
Description: hypothetical protein MJ_0604 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-15   56.9   0.8    2.4e-15   56.6   0.8    1.1  1  NTP_transf_2    Nucleotidyltransferase domain
    1.3e-11   44.5   0.7    1.8e-11   44.0   0.7    1.3  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0041   17.3   0.0     0.0055   16.9   0.0    1.2  1  SMODS           Second Messenger Oligonucleotide or Dinucleot
  ------ inclusion threshold ------
       0.01   16.0   0.1      0.011   16.0   0.1    1.3  1  DNA_pol_B_palm  DNA polymerase beta palm
       0.05   13.1   0.0      0.072   12.6   0.0    1.2  1  ANAPC4          Anaphase-promoting complex, cyclosome, subuni
       0.07   13.9   0.0        0.1   13.4   0.0    1.3  1  GnHR_trans      Gonadotropin hormone receptor transmembrane r


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.8   8.1e-19   2.4e-15       1      93 [.       7      97 ..       7      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 8.1e-19
                                  HHHHHHHHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEE......C CS
                  NTP_transf_2  1 lkklleelkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlv......t 75
                                  +k++ ++lk+++   ++k++lfGSyarG+++++SDiD+l+v++ +++         + +  + +l +  g+ +  +      +
  gi|15668784|ref|NP_247586.1|  7 IKEFVNALKSKYRgrIKKIILFGSYARGDYTEESDIDILIVGDVDFD---------YVIDLCTKLLLKYGVVINAIveseelF 80
                                  7899*****************************************54.........566666666666677777775666655 PP

                                  EEECCCCTEEEEEECEEE CS
                  NTP_transf_2 76 rekledpllvksileerp 93
                                  ++k+  ++  +++lee++
  gi|15668784|ref|NP_247586.1| 81 NKKIN-WSFHRNVLEEGR 97
                                  55555.777777777665 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.7   5.9e-15   1.8e-11       9      88 ..      17     100 .]       5     100 .] 0.72

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 5.9e-15
                                   HH.HHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH....SSSEEEEEE.TT.TS-HHHHHHHHHS CS
                       Polbeta   9 ke.keielaylFGSrakgkareeSDiDlavllkekldleeelelaaeledi...klgkkvDlvd.ln.eapplllyeilke 83 
                                   k+   i+ ++lFGS+a+g+++eeSDiD+ ++ + +  +++ ++l ++l       ++  v+  + +n + +  + +++l+e
  gi|15668784|ref|NP_247586.1|  17 KYrGRIKKIILFGSYARGDYTEESDIDILIVGDVD--FDYVIDLCTKLLLKygvVINAIVESEElFNkKINWSFHRNVLEE 95 
                                   33348****************************99..55555555555444344244444444434457889********* PP

                                   -EEEE CS
                       Polbeta  84 gklly 88 
                                   g++ly
  gi|15668784|ref|NP_247586.1|  96 GRVLY 100
                                   ***98 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.8e-06    0.0055      28      80 ..       4      55 ..       1      62 [. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-06
                         SMODS 28 vkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllvv 80
                                   kai++++n+ +++++ +i++ +l+GSyar+   +  sd d+l   dvd+  v
  gi|15668784|ref|NP_247586.1|  4 EKAIKEFVNALKSKYRGRIKKIILFGSYARGDYTE-ESDIDILIVGDVDFDYV 55
                                  589***************************98776.66777888888887555 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   0.1   3.6e-06     0.011       6      49 ..       3      48 ..       1      94 [. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.6e-06
                                  HHHHHHHHHHHHHHHH-TT-.EEEE-HHHHTT-.SEESSEEEEEEB CS
                DNA_pol_B_palm  6 Evealealvkkaakeldpev.evivcGSYRRga.essGDvDvlitk 49
                                  E +a++++v++  ++   ++ ++i  GSY Rg  ++  D+D+li  
  gi|15668784|ref|NP_247586.1|  3 EEKAIKEFVNALKSKYRGRIkKIILFGSYARGDyTEESDIDILIVG 48
                                  67788888888888888776257789*****9735678*****975 PP

>> ANAPC4  Anaphase-promoting complex, cyclosome, subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.4e-05     0.072     158     193 ..      51      86 ..      35      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                        ANAPC4 158 eidelletakslllkaeellqviseelkqfkaFinW 193
                                   ++d +++++ +lllk+  ++  i e++++f++ inW
  gi|15668784|ref|NP_247586.1|  51 DFDYVIDLCTKLLLKYGVVINAIVESEELFNKKINW 86 
                                   68899******************************* PP

>> GnHR_trans  Gonadotropin hormone receptor transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.4e-05       0.1      34      58 ..      33      60 ..      11      63 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                    GnHR_trans 34 eedlissyskeed.igeveFdY..DLCn 58
                                   +d+  +++++   +g+v+FdY  DLC 
  gi|15668784|ref|NP_247586.1| 33 RGDYTEESDIDILiVGDVDFDYviDLCT 60
                                  6788888888865258***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 622.12
//
Query:       gi|15668785|ref|NP_247587.1|  [L=134]
Description: hypothetical protein MJ_0605 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.7e-27   95.3   3.5    3.3e-27   95.0   3.5    1.1  1  HEPN       HEPN domain
  ------ inclusion threshold ------
      0.042   14.0   1.7      0.048   13.8   0.8    1.6  2  HEPN_AbiV  AbiV
      0.062   13.3   0.0      0.096   12.7   0.0    1.4  1  ODC_AZ     Ornithine decarboxylase antizyme


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.0   3.5   5.4e-31   3.3e-27       2     117 ..      14     128 ..      13     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 95.0 bits;  conditional E-value: 5.4e-31
                                   HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHC..CHHHT...-HHHHHHHHHH CS
                          HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLle..elkkelkeseelreeleeL 80 
                                   ++++++Aee+l+aA+ l+e++ y++a+ +a++a+++++KAlll+k+ +p+k+ +++++++  ++ ++ + +e + +++++ 
  gi|15668785|ref|NP_247587.1|  14 QALIEIAEENLSAAKILFENKLYRDAVARAYYAIFHSAKALLLTKNLNPKKHAGVIKMFGlyFVNEGYI-EEIYGRIITKS 93 
                                   789**********************************************************99999999.*********** PP

                                   HCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHHH CS
                          HEPN  81 ekayiesrYpdakeeyteedaeealkdaeevlelvee 117
                                    +++ +++Y  +k+  tee+ae+++  ae +++ +++
  gi|15668785|ref|NP_247587.1|  94 YNLRWKADYTTDKP--TEEEAESIIYEAEMFVDRIKK 128
                                   **************..****************99765 PP

>> HEPN_AbiV  AbiV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.8   8.1e-06     0.048       2      50 ..       9      57 ..       8      78 .. 0.91
   2 ?   -1.9   0.0      0.56   3.4e+03      11      23 ..     110     122 ..      92     129 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.1e-06
                     HEPN_AbiV  2 lregakalleNAeeLledAelLaengsyarAysLlilaiEElgKallly 50
                                  +re ++al+e Aee l  A++L+en+ y  A++ ++ ai  ++Kalll 
  gi|15668785|ref|NP_247587.1|  9 IREEIQALIEIAEENLSAAKILFENKLYRDAVARAYYAIFHSAKALLLT 57
                                  78999*********************************99999999886 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.56
                     HEPN_AbiV  11 eNAeeLledAelL 23 
                                   e Ae+ + +Ae+ 
  gi|15668785|ref|NP_247587.1| 110 EEAESIIYEAEMF 122
                                   3455555555554 PP

>> ODC_AZ  Ornithine decarboxylase antizyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.6e-05     0.096      37      63 ..       4      30 ..       1      49 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                        ODC_AZ 37 vlsedlkegLvaLlelAeeklecehlv 63
                                   l++d++e + aL+e+Aee+l++ +++
  gi|15668785|ref|NP_247587.1|  4 LLNKDIREEIQALIEIAEENLSAAKIL 30
                                  6899******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 871.46
//
Query:       gi|15668786|ref|NP_247588.1|  [L=91]
Description: hypothetical protein MJ_0606 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-49  163.6   9.0    1.1e-48  163.4   9.0    1.0  1  DUF5379          Family of unknown function (DUF5379)
  ------ inclusion threshold ------
       0.43   11.0   9.5       0.56   10.6   9.5    1.1  1  DUF4199          Protein of unknown function (DUF4199)
        1.2    8.8   6.7        2.6    7.7   6.5    1.6  1  Cation_ATPase_C  Cation transporting ATPase, C-terminus
        9.5    6.4  10.7        5.4    7.2   0.2    2.5  3  Osw5             Outer spore wall 5


Domain annotation for each model (and alignments):
>> DUF5379  Family of unknown function (DUF5379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   9.0   2.5e-52   1.1e-48       1      90 []       1      90 [.       1      90 [. 0.99

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 2.5e-52
                       DUF5379  1 ldlegkvailhaiggiifgylanyvytlglgllsglatllflfiglvilghlsakvlgeesltqkqwlgsgvlpfflvaivvw 83
                                  +dlegk++++haiggiifgylanyvyt+glg++sg+atl+flfig+vi+gh+sak++geesltqkqwlg+gvlpfflvaivvw
  gi|15668786|ref|NP_247588.1|  1 MDLEGKCCLIHAIGGIIFGYLANYVYTAGLGIFSGIATLIFLFIGAVIFGHISAKTFGEESLTQKQWLGCGVLPFFLVAIVVW 83
                                  89********************************************************************************* PP

                       DUF5379 84 ilkyngv 90
                                  +lk+ng+
  gi|15668786|ref|NP_247588.1| 84 VLKFNGL 90
                                  *****95 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   9.5   0.00012      0.56      11      87 ..      16      85 ..       7      88 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                       DUF4199 11 ilifll..ilyllglhqilstgpllglla.llllllvpflvylalkkyrkknlgGfisfgqafgfgflislvagllsavf 87
                                  i++ +l  ++y  gl+      ++ g+ + ++l++  ++++ ++ k +     +++++ +q +g+g+l++++ ++++ v+
  gi|15668786|ref|NP_247588.1| 16 IIFGYLanYVYTAGLG------IFSGIATlIFLFIGAVIFGHISAKTF----GEESLTQKQWLGCGVLPFFLVAIVVWVL 85
                                  3333322455555554......34444444555555566666666666....4559******************998776 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   6.5   0.00057       2.6     130     178 ..      35      84 ..      16      87 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00057
               Cation_ATPase_C 130 laillslllqvlivyvpglnavfgtaplsleewlialllalvvllv.del 178
                                   ++++l++l++ ++++  + ++ fg ++l+ ++wl++ +l+++++++ + +
  gi|15668786|ref|NP_247588.1|  35 GIATLIFLFIGAVIFGHISAKTFGEESLTQKQWLGCGVLPFFLVAIvVWV 84 
                                   33444555555666666678889999**********99999888773444 PP

>> Osw5  Outer spore wall 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0012       5.4      30      54 ..       9      33 ..       6      40 .. 0.86
   2 ?    6.7   0.7    0.0017       7.6      31      47 ..      41      57 ..      36      62 .. 0.80
   3 ?   -2.8   0.6       1.6   7.1e+03      30      35 ..      76      81 ..      72      87 .. 0.45

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0012
                          Osw5 30 fifatgvvvfgFlSnltfklaqlly 54
                                  +i a+g ++fg+l n  +  ++ ++
  gi|15668786|ref|NP_247588.1|  9 LIHAIGGIIFGYLANYVYTAGLGIF 33
                                  899**************99988777 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0017
                          Osw5 31 ifatgvvvfgFlSnltf 47
                                  ++ +g v+fg +S +tf
  gi|15668786|ref|NP_247588.1| 41 FLFIGAVIFGHISAKTF 57
                                  3347899*********9 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.6
                          Osw5 30 fifatg 35
                                  f+ a+ 
  gi|15668786|ref|NP_247588.1| 76 FLVAIV 81
                                  222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 591.56
//
Query:       gi|15668787|ref|NP_247589.1|  [L=79]
Description: hypothetical protein MJ_0607 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 531.92
//
Query:       gi|15668788|ref|NP_247590.1|  [L=307]
Description: putative manganese-dependent inorganic pyrophosphatase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-25   89.0   0.0    3.6e-25   88.1   0.0    1.4  1  DHH       DHH family
    2.6e-23   82.8   0.3    4.2e-23   82.1   0.3    1.3  1  DHHA2     DHHA2 domain


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.0     4e-29   3.6e-25       3     101 .]       3     144 ..       2     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 4e-29
                                   EEE-ECSSSHHHHHHHHHHHH.......................................CECS--TCGGCGCCHHCCCSE CS
                                   xxxxxxxxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxxxxxxxx RF
                           DHH   3 livghknpDtDsigSaialan.......................................llvDhneksqavegeakeeae 44 
                                   ++vghknpDtDsi+Sai+la+                                       +lvDh+eksq+ ++   ee++
  gi|15668788|ref|NP_247590.1|   3 YVVGHKNPDTDSIASAIVLAYfldcyparlgdinpetefvlrkfgvmepeliesakgkeiILVDHSEKSQSFDD--LEEGK 81 
                                   799******************8888888888877777777777777777777777777777*************..***** PP

                                   EEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHH........TT----HHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxx RF
                           DHH  45 dviiiDHHrlgeefetlapilflnepvgstaeivaellee........kkeeiskeiaellllgi 101
                                    + iiDHH++g  ++t +pil+  +pvgsta+++ael+ +        kk+e+++++a+lll++i
  gi|15668788|ref|NP_247590.1|  82 LIAIIDHHKVG--LTTTEPILYYAKPVGSTATVIAELYFKdaidliggKKKELKPDLAGLLLSAI 144
                                   **********9..99999********************99********999************98 PP

>> DHHA2  DHHA2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.3   4.7e-27   4.2e-23       1     143 []     181     304 ..     181     304 .. 0.92

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 4.7e-27
                                   HHHHHHHT-STTS-HHHHTTTTEEEEE.ETTEEEEEEEEEES-HHHHHT.THHHHHHHHHHHH.HHT-SEEEEEEE..... CS
                         DHHA2   1 kelkkaksdlsglsledllrrDyKeftgeggvkvgiasvpvslsewleekrkgellaalekfaeerkldllvlmttfeeeg 81 
                                   +e+ kaks + +l +e+++++D+K f+  +g+kvgi++v+v + +++e+ +k+++ + le+  +++++dl+v+++t     
  gi|15668788|ref|NP_247590.1| 181 MEILKAKSVVGKLKPEEIINMDFKNFD-FNGKKVGIGQVEVIDVSEVES-KKEDIYKLLEEKLKNEGYDLIVFLIT----- 254
                                   5899***********************.*********************.7788*********9999*********..... PP

                                   ETTT..EEEEEE...STT..HHHHHT---B.T.EEET...............T---HHHHTHHHHHHH CS
                         DHHA2  82 dirr..elllaaldaaek..laealekase.e.leLeewkegaewrrvykqgnvkasRKqvaPllrea 143
                                   di++  +++l++   ++k  +++a++ + e + + Le               +v++++Kqv+P l++a
  gi|15668788|ref|NP_247590.1| 255 DIMKegSEALVV---GNKemFEKAFNVKVEgNsVFLE---------------GVMSRKKQVVPPLERA 304
                                   99999*788887...33347********99888****...............*************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2077.30
//
Query:       gi|15668789|ref|NP_247591.1|  [L=435]
Description: amino acid transporter [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-37  127.0  60.0    1.3e-36  126.4  60.0    1.3  1  AA_permease_2  Amino acid permease
    1.4e-24   86.6  50.9    1.4e-24   86.6  50.9    2.3  2  AA_permease    Amino acid permease
    9.6e-05   21.6  26.3    9.6e-05   21.6  26.3    2.2  2  Trp_Tyr_perm   Tryptophan/tyrosine permease family


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.4  60.0   2.1e-40   1.3e-36       1     418 [.       8     408 ..       8     429 .. 0.85

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 2.1e-40
                 AA_permease_2   1 lsllsafalvigsvigsgifvknlaas..ggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkva.f 78 
                                   lsl+ a+ +++g++ig+ if   ++++  +g  l  ++++ ++i+ l v++ y  l++++ ++ G + + ++a+g  +   
  gi|15668789|ref|NP_247591.1|   8 LSLWEAVSMAVGVMIGASIFSIFGVGAkiAGRNLPETFIL-SGIYALLVAYSYTKLGAKIVSNAGPIAFIHKAIGDNIItG 87 
                                   79************99666543214443466666665555.555669*********999***************8666559 PP

                 AA_permease_2  79 lsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliil 159
                                     ++++w++yv+++a+ +  +a+y+l +++  +  nt+ + +  i+i+++++++n +g k ++++ ++++++k+ l+l ++
  gi|15668789|ref|NP_247591.1|  88 ALSILLWMSYVISIALFAKGFAGYFLPLINAPI--NTFNIAITEIGIVAFFTALNFFGSKAVGRAEFFIVLVKL-LILGLF 165
                                   999**************************9655..778888889******************************.799*** PP

                 AA_permease_2 160 iilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvsee..vkkkdvpkaifigllivlvlyllvn 238
                                   i +glit+++++            p+  +g++++ +i+++s+ Gf +++n se   ++kk+vp+aifi++liv+++y++v+
  gi|15668789|ref|NP_247591.1| 166 IFAGLITIHPSYVI------PDLAPSAVSGMIFASAIFFLSYMGFGVITNASEHieNPKKNVPRAIFISILIVMFVYVGVA 240
                                   **********9997......4789999999***********************9667779********************* PP

                 AA_permease_2 239 iaflgvvpddei.anlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvnkf 318
                                   i+++g +p+de+ + ++n   ++a+ ++ + g  ++ +++i++ +s+  a+n+ ++g + v+++la+dg+lP+ff +   f
  gi|15668789|ref|NP_247591.1| 241 ISAIGNLPIDELiKASEN---ALAVAAKPFLGNLGFLLISIGALFSISSAMNATIYGGANVAYSLAKDGELPEFFERKVWF 318
                                   ***********8355555...45666666667899****************************************999889 PP

                 AA_permease_2 319 gspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkrpgkilvaiigalfllfll 399
                                   +s+ +  i++a+ + +++llf       +  ++s++s  ++++yl++i++  il +   + +r+ ++++++i +l++++ll
  gi|15668789|ref|NP_247591.1| 319 KSTEGLYITSALGV-LFALLFN------MEGVASITSAVFMVIYLFVILSHYILIDE--VGGRKEIVIFSFIVVLGVFLLL 390
                                   88888888877777.8887774......57899999999999999999999999988..5567777888888888887777 PP

                 AA_permease_2 400 valffppkgpatqssliyt 418
                                       +++++ + + ++i t
  gi|15668789|ref|NP_247591.1| 391 LYYQWITNRFVFY-GIIAT 408
                                   7666666665554.34444 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6  50.9   2.3e-28   1.4e-24       2     383 ..      13     366 ..      12     367 .. 0.92
   2 ?   -0.5   4.0     0.057   3.4e+02     341     388 ..     376     423 ..     373     432 .. 0.72

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 2.3e-28
                   AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgp.elGfviGln 81 
                                   ++ +a+g +iG+ +f   gv +  aG  ++   ++l+g+  +lv++s   +  ++ +++g  +++++ +g+    ++ +++
  gi|15668789|ref|NP_247591.1|  13 AVSMAVGVMIGASIFSIFGVGAKIAGR-NLPETFILSGIYALLVAYSYTKLGAKIVSNAGPIAFIHKAIGDnIITGALSIL 92 
                                   6789**********************9.999***************************************9678999**** PP

                   AA_permease  82 ylfswitvlal.eltaasiliqfwel.vtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiil 160
                                   +++s+++ +al + + a++++ +++  +   + + +t + ++++++++n++g k+ g+aef++ l+k++++  fi  g i+
  gi|15668789|ref|NP_247591.1|  93 LWMSYVISIALfAKGFAGYFLPLINApINTFN-IAITEIGIVAFFTALNFFGSKAVGRAEFFIVLVKLLILGLFIFAGLIT 172
                                   ******999973668899******99555555.9999999**************************************766 PP

                   AA_permease 161 laggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvvi 241
                                   +      ++                l p+       a++++i++ +i++++++G++ ++++++ +++P+k++P+ai   ++
  gi|15668789|ref|NP_247591.1| 173 IHPSYVIPD----------------LAPS-------AVSGMIFASAIFFLSYMGFGVITNASEHIENPKKNVPRAIFISIL 230
                                   665555555................4455.......699****************************************** PP

                   AA_permease 242 ritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdg 322
                                   +++++Yv+++++++  +p +   l+++s +a  + v +  ++g+ ++  li ++ l ++ s++n+ +y +  v yslakdg
  gi|15668789|ref|NP_247591.1| 231 IVMFVYVGVAISAIGNLPIDE--LIKASENA--LAVAAKPFLGNLGF-LLISIGALFSISSAMNATIYGGANVAYSLAKDG 306
                                   ************999999998..88888888..99999999999998.799****************************** PP

                   AA_permease 323 laPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlli 383
                                    +P ++++   +     ++++++++++l+ ll ++   a i++++++ i+ +++l+ ++li
  gi|15668789|ref|NP_247591.1| 307 ELPEFFERK-VWFKSTEGLYITSALGVLFALLFNMEGVASITSAVFMVIYLFVILSHYILI 366
                                   ***888763.4555578***************************************99987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.057
                   AA_permease 341 illsmiisllalllaslnlaapivfnfllaisaliglivwlliilsyl 388
                                   +++s+i++l ++ll  ++   ++ f f+  i+++ig++++ +i+ + +
  gi|15668789|ref|NP_247591.1| 376 VIFSFIVVLGVFLLLLYYQWITNRFVFYGIIATFIGVLIFEIIYRKVT 423
                                   567777777777777777766888888888888888888877766555 PP

>> Trp_Tyr_perm  Tryptophan/tyrosine permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6  26.3   1.6e-08   9.6e-05       2     255 ..       7     259 ..       6     286 .. 0.82
   2 ?   -6.7   9.1         3   1.8e+04     126     168 ..     325     369 ..     255     409 .. 0.53

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.6e-08
                  Trp_Tyr_perm   2 tksllggvlliagtviGaGmlalPvatagagfipsllllilswvlmlasgllllEvllaakeeasfttlakkllGkkgnii 82 
                                   + sl+ +v++  g++iGa ++++  + a++   +    +ils +++l+ ++ +  +  ++ ++a+   + +k +G ++ + 
  gi|15668789|ref|NP_247591.1|   7 KLSLWEAVSMAVGVMIGASIFSIFGVGAKIAGRNLPETFILSGIYALLVAYSYTKLGAKIVSNAGPIAFIHKAIGDNIITG 87 
                                   5699****************999887777665544444555666666677778888889999999***********99999 PP

                  Trp_Tyr_perm  83 valvllfllyiLlvAyisgg..Gsilselleeasgialsarlavliftlvlgalvvlstkavdrinrvllflklvafvlll 161
                                   +   ll ++y++ +A +++g  G  l   ++  +  +++  +  + +++++ al  +++kav r   +++ +kl+ + l++
  gi|15668789|ref|NP_247591.1|  88 ALSILLWMSYVISIALFAKGfaGYFLPL-INAPI-NTFNIAITEIGIVAFFTALNFFGSKAVGRAEFFIVLVKLLILGLFI 166
                                   9999999**********98632444444.44433.35556666677889999999************************** PP

                  Trp_Tyr_perm 162 alllskvksdvLlsaksdtskvslvlsalPvlllsf.GFhgivpslvkyldknvkkvkkailiGtliaLvlyllWelivlG 241
                                   + +l  ++ +  +     +s+vs ++ a  +++ls+ GF  ++    + +++ +k+v +ai+i  li + +y+   ++ +G
  gi|15668789|ref|NP_247591.1| 167 FAGLITIHPSYVIP-DLAPSAVSGMIFASAIFFLSYmGFG-VITNASEHIENPKKNVPRAIFISILIVMFVYVGVAISAIG 245
                                   *************9.5578999999999999999985775.556667888889**************************** PP

                  Trp_Tyr_perm 242 nlpreelariiakg 255
                                   nlp  el+++ +++
  gi|15668789|ref|NP_247591.1| 246 NLPIDELIKASENA 259
                                   ********998877 PP

  == domain 2  score: -6.7 bits;  conditional E-value: 3
                  Trp_Tyr_perm 126 iftlvlgal..vvlstkavdrinrvllflklvafvlllalllskv 168
                                    +t  lg+l  ++++ + v  i++ ++++  ++++l+ ++l+ +v
  gi|15668789|ref|NP_247591.1| 325 YITSALGVLfaLLFNMEGVASITSAVFMVIYLFVILSHYILIDEV 369
                                   344444433112233334444444433333333334444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 2597.37
//
Query:       gi|15668790|ref|NP_247592.1|  [L=434]
Description: hypothetical protein MJ_0610 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.7e-175  582.3   0.1   4.3e-175  582.1   0.1    1.0  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
      3e-10   39.9   0.0    3.8e-10   39.5   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    6.3e-05   21.9   0.0    0.00016   20.5   0.0    1.5  2  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
  ------ inclusion threshold ------
       0.11   12.8   0.1       0.19   11.9   0.1    1.4  1  DHquinase_I      Type I 3-dehydroquinase
       0.12   12.6   0.2       0.34   11.1   0.2    1.8  1  MGS              MGS-like domain
       0.18   10.9   0.0       0.39    9.7   0.0    1.5  1  Dus              Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  582.1   0.1  1.4e-178  4.3e-175       1     388 [.      57     434 .]      57     434 .] 0.99

  Alignments for each domain:
  == domain 1  score: 582.1 bits;  conditional E-value: 1.4e-178
                                   TBGGGSSS----SS-S---S-HHHHHCCCCHHCTBSBTTBTTS-CCCCCCCCCHCCCCCHHHHHHHHHTTHCCHHEECCCS CS
                       SepSecS   1 mDtdkdvdtvgiGerearvlselkeesvfdfiHgvGrsGnlvdvqPKalGasvlakltNklvkdilkllGlrevknafvvP 81 
                                   mDtdkd+++v+iGerearv+++l+++ vfdf+HgvGrsGnl+d+qPKa+Gasv++kltNkl++++lk+lGl+  +na+++P
  gi|15668790|ref|NP_247592.1|  57 MDTDKDPNVVQIGEREARVYTKLQRDGVFDFCHGVGRSGNLIDPQPKAPGASVMYKLTNKLLESFLKALGLK--VNAIATP 135
                                   8***********************************************************************..78***** PP

                                   S-HHHHHHHHHHHHHHHCC--CCEEEEEETCHHHHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHH.HCCTCCCEEEEEE CS
                       SepSecS  82 latGlslaLClsalrkrskakkviwvridekSslkavelaGleialvekvlegDelitdvedveeii.ekkreevilavls 161
                                   +atG+slaLClsa+rk++++++vi++++++kS++ka++++G++++lve+vl+gD+++++v+d+e++i ++++e+++++vls
  gi|15668790|ref|NP_247592.1| 136 VATGMSLALCLSAARKKYNSNVVIYPYAAHKSPIKATSFIGMRMRLVETVLDGDIVKVEVSDIEDAIrKEINENNNPVVLS 216
                                   *******************************************************************99************ PP

                                   CSSTTTTB----HHHHHHHHHCCT--EEEEGCCCCT-HHHHHHHHHHHHHTTC-EECCCHCHCCCEECCHCCCCESSCHCC CS
                       SepSecS 162 tlsffaprspDdvkeiakiCaeydvPhlvNgAYaiqsekyieklkkalkvGRvdvvvksldknllvpvGgaiiaasdesfi 242
                                   tl+ff+pr++Dd+keiakiC++yd+Ph++NgAYaiq+++yieklkkalk+ R+d+vv+s+dknl++p+Gg+ii+++desf+
  gi|15668790|ref|NP_247592.1| 217 TLTFFPPRKSDDIKEIAKICQDYDIPHIINGAYAIQNFYYIEKLKKALKY-RIDAVVSSSDKNLFTPIGGGIIYTKDESFL 296
                                   **************************************************.****************************** PP

                                   CCCHCCCHCHCTSCHCCCCCCCHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCEEESSSTT-SSEEEEE-CCCHCCC CS
                       SepSecS 243 keiskeypgrasaapskdvlisllllGskaykkllkeqkesfkllreklkklaeeveekllevpeNpissaltletldeik 323
                                   keis +ypgrasa+p++++lisll++G+k+y++l+keqke++kll+e+l++la++++ek+l+v eNpiss++t++      
  gi|15668790|ref|NP_247592.1| 297 KEISLTYPGRASANPIVNILISLLAIGTKDYLNLMKEQKECKKLLNELLEDLAKKKGEKVLNV-ENPISSCITTK------ 370
                                   ************************************************************998.**********9...... PP

                                   CTHHHHHHHHHHHTTECSSE.EE-SSTCECTTSSS-SSSEEEEEE-TT--HHHHHHHHHHHHHHH CS
                       SepSecS 324 kkarldlaseLfsrkvtGargvrasdsklTshlkeyhsrYlkiasaiGlkdedvdkvlerldeil 388
                                    k++ld+a++L++ +vtG+rgvr++d+++T++lkey+++Y++++saiG+k+ed++kv+e+lde+l
  gi|15668790|ref|NP_247592.1| 371 -KDPLDVAGKLYNLRVTGPRGVRRNDKFGTCYLKEYPYDYIVVNSAIGVKKEDIYKVIEKLDEVL 434
                                   .789**********************************************************986 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   1.3e-13   3.8e-10      83     220 ..     165     329 ..     112     397 .. 0.70

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.3e-13
                                   HHSSTTHHHHC.C--EEEEE-EBTT...TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHH CS
               Beta_elim_lyase  83 hfdetgaiael.agvklrdlknkea...GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakk 159
                                   h    +a +++     +r +++  +    k+++ ++e+ai+++ + e++ ++++ t T       + + + ++e+a+i+++
  gi|15668790|ref|NP_247592.1| 165 HKSPIKATSFIgMR--MRLVETVLDgdiVKVEVSDIEDAIRKEIN-ENNNPVVLSTLTFF----PPRKSDDIKEIAKICQD 238
                                   44444555444222..3333322222257899**********555.9999*********9....5**************** PP

                                   CT-EEEEEETTHHHHHHHHTS-CHHHHTT.SSEEEEESSSTT--SS-EEEEE-HH.......................... CS
               Beta_elim_lyase 160 ygiplhlDgARfanaakslgeivkemfsy.vDsvtmslkKdllanvGgvlafrddel........................ 215
                                   y+ip ++ gA  + +   + e++k+ ++y +D v+ s  K+l++++Gg ++  +de                         
  gi|15668790|ref|NP_247592.1| 239 YDIPHIINGAYAIQNFYYI-EKLKKALKYrIDAVVSSSDKNLFTPIGGGIIYTKDESflkeisltypgrasanpivnilis 318
                                   ****************666.5666666666*****************5555555533366666666666666666666666 PP

                                   ........HHH CS
               Beta_elim_lyase 216 ......edyla 220
                                         +dyl+
  gi|15668790|ref|NP_247592.1| 319 llaigtKDYLN 329
                                   66666644444 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   5.4e-08   0.00016     144     287 ..     155     298 ..     146     306 .. 0.82
   2 ?   -2.3   0.0      0.45   1.4e+03     325     354 ..     317     346 ..     305     361 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.4e-08
                                   CCEEEEEETTS-HHHHHHHHHHT-EEEEE--BTTT...BB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHH CS
                 Pyridoxal_deC 144 dklvlytsdqahssvekaalvlgvklrvipldeng...klrgaalekaieedkekGlipffvvatlGttvlgaFddlkelg 221
                                      v+y  + ah s  ka   +g+++r++++  +g   k+ +++ e ai +++++   p +v  tl      + dd+ke++
  gi|15668790|ref|NP_247592.1| 155 SNVVIYPYA-AHKSPIKATSFIGMRMRLVETVLDGdivKVEVSDIEDAIRKEINENNNP-VVLSTLTFFPPRKSDDIKEIA 233
                                   556667666.999999*************98655411267799**********9999**.9******************** PP

                                   HHHHHCT-EEEEE-TTGGGGGGSGGGGGGGTTGG.GESEEEEECCCCTS--SS-EEEEESSCCGCHH CS
                 Pyridoxal_deC 222 dicekydlwlHvDAAyaGsaficpeirhllkgie.radSitvnphKlllvlldcsalivkdkealqq 287
                                   +ic+ yd++  +  Aya   f   e  +l k +  r+d +  +  K l  +++ + ++ kd++ l++
  gi|15668790|ref|NP_247592.1| 234 KICQDYDIPHIINGAYAIQNFYYIE--KLKKALKyRIDAVVSSSDKNLFTPIGGGIIYTKDESFLKE 298
                                   *********99******87775433..233444325777888999999999*999999999999876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.45
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Pyridoxal_deC 325 fvlralGveglqnqirksvelakyleklir 354
                                     l a G++ + n ++++ e  k l++l++
  gi|15668790|ref|NP_247592.1| 317 ISLLAIGTKDYLNLMKEQKECKKLLNELLE 346
                                   445566777776666666666655555554 PP

>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.5e-05      0.19      79     169 ..     179     261 ..     148     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.5e-05
                                   HHHHHHHHHCT-SEEEEEGG-.HHGHHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSH CS
                   DHquinase_I  79 lellrtaielgadyvDvElteapeeskkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksi 159
                                   ++l++t+++   d+v vE+++++    +++++e++e++  v++S   f    + +++k++ + +q+++  i+ i+  a  i
  gi|15668790|ref|NP_247592.1| 179 MRLVETVLDG--DIVKVEVSDIE----DAIRKEINENNNPVVLSTLTFFPPRKSDDIKEIAKICQDYD--IPHIINGAYAI 251
                                   5566666664..99999996444....69***********************************9775..88888777777 PP

                                   HHHHHHHHHH CS
                   DHquinase_I 160 eDvlrllslt 169
                                   ++ + + +l+
  gi|15668790|ref|NP_247592.1| 252 QNFYYIEKLK 261
                                   7766666665 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00011      0.34      38      94 ..     183     244 ..     169     245 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                   CCHSTGSGGTHCH.....HHHHHHHTTSCCEEEEE--THHHHHHCHHHHHHHHHHHTTSHEE CS
                           MGS  38 ektgegerlggrv.....eildaikngeidlvintlypfkatvakdgykirraaenidIplp 94 
                                   e + +g++ + +v      i ++i++++  +v  tl+ f  ++++d ++i++++ ++dIp +
  gi|15668790|ref|NP_247592.1| 183 ETVLDGDIVKVEVsdiedAIRKEINENNNPVVLSTLTFFPPRKSDDIKEIAKICQDYDIPHI 244
                                   555555555544477777888999999999**********999999999***********76 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00013      0.39     169     211 ..     226     272 ..     223     282 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                                   G--CHHHHHHHHH-SS-EEEESS..--SH...HHHHHHHHHH--SEEE CS
                           Dus 169 tadweaIkevkqavsipviaNGd..Ikda...edaqaileetGadgvm 211
                                    +d+++I++++q+  ip i+NG+  I+++   e+++++l++  +d+v+
  gi|15668790|ref|NP_247592.1| 226 SDDIKEIAKICQDYDIPHIINGAyaIQNFyyiEKLKKALKY-RIDAVV 272
                                   6899******************6334433444888888888.677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2582.64
//
Query:       gi|15668791|ref|NP_247594.1|  [L=191]
Description: hypothetical protein MJ_0611 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-06   28.1  12.5     0.0033   16.7   0.5    3.2  3  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.4   6.6e-05       1.2       3      26 ..      39      62 ..      35      87 .. 0.89
   2 !   10.2   1.0   1.8e-05      0.32      85     108 ..     103     126 ..      98     141 .. 0.87
   3 !   16.7   0.5   1.8e-07    0.0033     196     220 ..     144     168 ..     131     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 6.6e-05
                                  XXXXXXXXXXXXXXXXXXXXXXXX CS
                                  xxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50  3 illlgilvvvHElGHflvAklcgv 26
                                  ++++g   ++HEl+H  vA++ g 
  gi|15668791|ref|NP_247594.1| 39 LIAVGSGFIFHELMHRTVARKYGA 62
                                  68889999************9885 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 1.8e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50  85 wqrllivlAGplanfilailvfvv 108
                                    +   i+lAGpl+n+ la+++f++
  gi|15668791|ref|NP_247594.1| 103 EENGKIALAGPLTNVALAFVFFIL 126
                                   56778****************987 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 1.8e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 196 alisvnLgilNLlPipvLDGghllf 220
                                   + i++ L+ +N+lPip++DG ++l+
  gi|15668791|ref|NP_247594.1| 144 FHINLFLAGFNMLPIPPFDGEKVLK 168
                                   5699******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1200.34
//
Query:       gi|15668792|ref|NP_247595.1|  [L=197]
Description: hypothetical protein MJ_0611.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-05   22.9  22.4     0.0055   16.5  22.4    2.8  1  PAP2      PAP2 superfamily
  ------ inclusion threshold ------
      0.059   13.3   1.1       0.11   12.5   0.6    1.7  1  Sec20     Sec20


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5  22.4   6.2e-07    0.0055      83     128 ..     131     194 ..      34     197 .] 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.2e-07
                          PAP2  83 g..................lvllalillllavlvalsRlylgvHflsDvlaGlliGialaalay 128
                                   +                   ++l +i+l+l++ ++++R+yl  H++s+v+aG+++Gi++ +++ 
  gi|15668792|ref|NP_247595.1| 131 SmhnyglsamayliyaftnSIWLSTIYLILVIITGYARIYLKKHTVSQVIAGTILGISVNYILL 194
                                   344444555555555555556778*********************************9988765 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   1.2e-05      0.11      69      92 .]      52      75 ..      49      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                         Sec20 69 dkllvflalglflacvvyvvkkRi 92
                                   k+++ l+l++f  cv+++ + +i
  gi|15668792|ref|NP_247595.1| 52 SKFDISLSLAFFFPCVFWICWAKI 75
                                  6999***************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1343  (0.0749066); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1228.70
//
Query:       gi|15668793|ref|NP_247596.1|  [L=446]
Description: prephenate dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-91  305.9   0.9      2e-91  305.6   0.2    1.5  2  PDH             Prephenate dehydrogenase
    5.7e-12   46.1   0.2    1.7e-11   44.5   0.2    1.8  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      1e-07   32.3   0.0    2.8e-07   30.8   0.0    1.8  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    5.7e-07   29.3   0.1    1.4e-06   28.0   0.1    1.6  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    1.2e-05   25.6   0.1    4.6e-05   23.7   0.1    2.0  1  FDX-ACB         Ferredoxin-fold anticodon binding domain
      4e-05   23.2   0.2    0.00012   21.6   0.1    2.0  2  adh_short       short chain dehydrogenase
    0.00011   22.6   0.1    0.00053   20.4   0.0    2.2  2  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
     0.0002   21.4   0.1    0.00064   19.8   0.1    1.9  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
     0.0021   17.5   0.1      0.016   14.6   0.0    2.2  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0059   16.6   1.4      0.013   15.5   0.4    2.2  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.037   13.9   0.0    1.7  1  KR              KR domain
      0.015   15.9   0.0        1.7    9.2   0.0    2.8  3  TIR_2           TIR domain
      0.015   15.3   0.0      0.071   13.1   0.0    2.2  2  ADH_zinc_N      Zinc-binding dehydrogenase
      0.022   14.6   0.4        0.1   12.4   0.0    2.2  2  DUF2642         Protein of unknown function (DUF2642)
      0.024   14.3   0.6      0.053   13.2   0.1    1.9  2  ApbA            Ketopantoate reductase PanE/ApbA
        0.1   13.0   0.0       0.35   11.2   0.0    1.9  1  DUF2935         Domain of unknown function (DUF2935)


Domain annotation for each model (and alignments):
>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.6   0.2   1.8e-94     2e-91       1     258 []      21     272 ..      21     272 .. 0.99
   2 ?   -3.0   0.0       2.6     3e+03     218     239 ..     417     438 ..     413     440 .. 0.64

  Alignments for each domain:
  == domain 1  score: 305.6 bits;  conditional E-value: 1.8e-94
                                   HHHHHHHTT--SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S- CS
                           PDH   1 laralrrkgfkvtvigydideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitDvgsv 81 
                                   +ar+l++kgf+v+v+g+di+++k++++ elg+++++++ iea+k++div++avP++v+++v+ke+aph++e++l++D++s+
  gi|15668793|ref|NP_247596.1|  21 FARYLKNKGFNVIVTGRDIEKGKNVEK-ELGVEFTNNN-IEAAKKGDIVIVAVPINVTERVIKEVAPHVREGCLLMDITSI 99 
                                   79*************************.**********.****************************************** PP

                                   -CHHHHHHHHHCC..GCEEEEEES---S-SSGGG--TTTTTT-EEEEEE-TT.S-HHHHHHHHHHHHHCT-EEEE--HHHH CS
                           PDH  82 KekvvreleellkegksfvgghPmaGteksGvdaareelfenavviLtPtek.tdkealekvkelleevgarvilmspeeH 161
                                   Ke +++++ee++keg++++++hPm+G+        ++ ++ ++vviLtP+ek +++e+++kv+++l++ ga+vi+++pe+H
  gi|15668793|ref|NP_247596.1| 100 KEIPSKAMEEHVKEGVTVIPTHPMFGP--------STPSLLRQVVILTPSEKhKNTEWFNKVYNFLKKEGAKVIVIPPEKH 172
                                   ***************************........99**************989*************************** PP

                                   HHHHHHHTHHHHHHHHHHHHHHHCHHCCCCHHHHCGTCCHHHHH....CGGGS-HHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                           PDH 162 Drvvavvshlphvvaialaatlkekkndekeirklasggfrdvt....RiaksnPelwadilleNkeavlealdkfikelk 238
                                   Dr++++v++l+h+++i+l atlke ++d+ke+rk+as+++++++    Ri+++nP+l+adi+++N + ++e++++fi+++k
  gi|15668793|ref|NP_247596.1| 173 DRIMGIVQGLTHFAFISLGATLKELNVDIKESRKFASPIYELMIsiigRIIGQNPYLYADIQMFNPR-IKEIHETFINQCK 252
                                   *******************************************************************.************* PP

                                   HHHHHHHTT-HHHHHHHHHH CS
                           PDH 239 klkelienedaeeLvellke 258
                                   +++e+++n+d+e +v+++ke
  gi|15668793|ref|NP_247596.1| 253 EISEIVKNKDREGFVKIMKE 272
                                   ******************96 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.6
                                   HHHHTHHHHHHHHHHHHHHHHH CS
                           PDH 218 illeNkeavlealdkfikelkk 239
                                   i  +Nk++++++ ++f k +k+
  gi|15668793|ref|NP_247596.1| 417 IYGYNKDELKNIEKEFLKIIKN 438
                                   5566777777777777666655 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.2   1.6e-14   1.7e-11       2      95 ..       8      97 ..       7      98 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.6e-14
                                  EEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGH CS
                 F420_oxidored  2 igii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlselak 83
                                  i ii G+  +g+ +a+ l ++g    +++v+  r+ ek +  ++elgv+ t  +n eaa++ d+v++av+ +++e v++e+a+
  gi|15668793|ref|NP_247596.1|  8 ISIIgGTDGLGKWFARYLKNKG---FNVIVT-GRDIEKGKNVEKELGVEFTN-NNIEAAKKGDIVIVAVPINVTERVIKEVAP 85
                                  899988889*************...****55.********************.****************************** PP

                                  HHHTTSEEEEES CS
                 F420_oxidored 84 dalkgklvisvl 95
                                  +  +g l+ +++
  gi|15668793|ref|NP_247596.1| 86 HVREGCLLMDIT 97
                                  *99999999987 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.5e-10   2.8e-07       7     106 ..      14     113 ..       7     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.5e-10
                                   -SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHT.TEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EE CS
                 NAD_binding_2   7 lGvMGsnmalnllkagykvavynrtkekveelvae.gakaaesieelvasldvvitmvkagkavdeviegllealkkgdil 86 
                                   +  +G+ +a+ l+++g++v+v  r+ ek +++ +e g++ +++  e++++ d+vi+ v+  + ++ vi+++++++++g +l
  gi|15668793|ref|NP_247596.1|  14 TDGLGKWFARYLKNKGFNVIVTGRDIEKGKNVEKElGVEFTNNNIEAAKKGDIVIVAVPI-NVTERVIKEVAPHVREGCLL 93 
                                   556899**************************9996699999999**************8.789***************** PP

                                   EE-S---HHHHHHHHHHHHH CS
                 NAD_binding_2  87 idgstsspedtrelakelke 106
                                   +d ++++   ++ +++ +ke
  gi|15668793|ref|NP_247596.1|  94 MDITSIKEIPSKAMEEHVKE 113
                                   *******9999999998876 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   1.2e-09   1.4e-06       5      92 ..       6      94 ..       3     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.2e-09
                                  S-EEEES.-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHH.HHHHT-SEEEE-S-HHHHHHHHHHHTGGG- CS
                          IlvN  5 kkiaviG.yGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltva.eavkkadvvmiliPDelqkevyeeeiepnl 85
                                   +i++iG     G+  a+ l++ g++v+v+ r+ +k  +  ke g+e ++ + ea+kk d+v++ +P ++ ++v+ +e++p++
  gi|15668793|ref|NP_247596.1|  6 LTISIIGgTDGLGKWFARYLKNKGFNVIVTGRDIEKGKNVEKELGVEFTNNNiEAAKKGDIVIVAVPINVTERVI-KEVAPHV 87
                                  6899997134467889*****************999999999999997765449*********************.99***** PP

                                  -TT-EEE CS
                          IlvN 86 kegkala 92
                                  +eg  l+
  gi|15668793|ref|NP_247596.1| 88 REGCLLM 94
                                  *998764 PP

>> FDX-ACB  Ferredoxin-fold anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   4.1e-08   4.6e-05       8      61 ..     370     418 ..     365     442 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.1e-08
                                   EEEEEEEESSS-HHHHHHHHHHHH-TTEEEEEEEEEEESTTS-SSEEEEEEEEE CS
                       FDX-ACB   8 rDlalvvdekveaaelleavreaagellesvqlfDvYrgkklaegkkSlalrlt 61 
                                    D++++ +++v ++ +l+++++       +++++DvY+g+k++eg kS+++r+ 
  gi|15668793|ref|NP_247596.1| 370 IDVSVLFKKDVDEEVILNLLKKMF-----DIEIIDVYEGEKIEEGYKSITFRIY 418
                                   599****************99988.....9**********************84 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   1.1e-07   0.00012       3      48 ..       8      55 ..       6      87 .. 0.83
   2 ?   -3.5   0.0       5.2   5.8e+03     158     182 ..     301     325 ..     297     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-07
                                  EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..T CS
                     adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..g 48
                                  + ++G+++G+G+ +a+ l ++G++v+v++r  ek ++v kel+ e  +
  gi|15668793|ref|NP_247596.1|  8 ISIIGGTDGLGKWFARYLKNKGFNVIVTGRDIEKGKNVEKELGVEftN 55
                                  789**************************************9976543 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.2
                                   HHHHHHHHHHGGGTEEEEEEEESSB CS
                     adh_short 158 gltrslakelaptgirvnavaPGlv 182
                                   +l + + k++a ++i+ n+v+ G++
  gi|15668793|ref|NP_247596.1| 301 KLNKLIGKDVAVKNINSNVVHFGVL 325
                                   5667788899999999999988865 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.7e-07   0.00053       2      98 ..       8      98 ..       7     122 .. 0.86
   2 ?   -1.9   0.0       3.9   4.3e+03      15      37 ..     385     408 ..     383     433 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.7e-07
                                  EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHH CS
                Semialdhyde_dh  2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvskelap 84
                                  ++i+G+t   G+ ++r+L++ + ++++v ++++ ++Gk++++  +       +++++ ++e+ k+ div+ a+p +v++ + +
  gi|15668793|ref|NP_247596.1|  8 ISIIGGTDGLGKWFARYLKN-KGFNVIV-TGRDIEKGKNVEKELG-------VEFTNNNIEAAKKGDIVIVAVPINVTERVIK 81
                                  79*****************9.4566666.556666********77.......7888888999*******************99 PP

                                  HH...HHTTSEEEESSS CS
                Semialdhyde_dh 85 kl...aeagvkviDlss 98
                                  ++   + +g+ + D +s
  gi|15668793|ref|NP_247596.1| 82 EVaphVREGCLLMDITS 98
                                  99777788999999887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.9
                                   HHHHHHCTSSEEEEEEEESTT.TT CS
                Semialdhyde_dh  15 llrlLeehpevelvvllsssr.sa 37 
                                   +l+lL++ +++e++ ++  ++ ++
  gi|15668793|ref|NP_247596.1| 385 ILNLLKKMFDIEIIDVYEGEKiEE 408
                                   688999999999988876655333 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   5.8e-07   0.00064      15     117 ..       8     102 ..       2     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.8e-07
                                   EEEES.-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHH CS
                  Shikimate_DH  15 vlliG.aGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilekee 94 
                                   + +iG +  +++  a++L +kg++ v+v++R++e+ k++ +el+ e ++     ++ e+ ++ d+vi+a+    + ++++ 
  gi|15668793|ref|NP_247596.1|   8 ISIIGgTDGLGKWFARYLKNKGFN-VIVTGRDIEKGKNVEKELGVE-FTNN---NI-EAAKKGDIVIVAVP---INVTERV 79 
                                   55665144589999*********9.******************544.4433...33.46789******985...3466666 PP

                                   HHCCHHH.S..EEEEE--SS-SB CS
                  Shikimate_DH  95 veealkkrkkplllvDiavPRdv 117
                                   ++e+  + ++  ll+Di+  +++
  gi|15668793|ref|NP_247596.1|  80 IKEVAPHVREGCLLMDITSIKEI 102
                                   77776666678899998866666 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.4e-05     0.016      37     103 ..       6      75 ..       2      95 .. 0.85
   2 ?   -0.3   0.0      0.52   5.9e+02     132     162 ..     380     409 ..     378     417 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                                   SEEEEE.S-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEEC.SHHHHHHH-SEEEE-S--ST CS
                  2-Hacid_dh_C  37 ktvGii.GlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelv.sleellaesDivslhlpltp 103
                                    t+ ii G+  +G+ +a++lk  g++vi++ r  +k +  e+elgve++ +  e+ ++ Div++++p++ 
  gi|15668793|ref|NP_247596.1|   6 LTISIIgGTDGLGKWFARYLKNKGFNVIVTGRDIEKGKnVEKELGVEFTnNNIEAAKKGDIVIVAVPINV 75 
                                   56777625788****************99999988888789999**99967779*************875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.52
                                   B-HHHHHHHHHTTSCCEEEES--SSSSSGTC CS
                  2-Hacid_dh_C 132 vdeeaLleaLksgkiagaalDvfeeeplped 162
                                   vdee +l+ Lk+       +Dv+e e+++e 
  gi|15668793|ref|NP_247596.1| 380 VDEEVILNLLKK-MFDIEIIDVYEGEKIEEG 409
                                   677777776665.7777899******99876 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   1.1e-05     0.013      54     120 ..      48     113 ..       8     130 .. 0.80
   2 ?   -3.1   0.0       6.1   6.8e+03      29      50 ..     351     372 ..     334     382 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                                   -TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SEET.TTEEHHHHHHH CS
                NAD_Gly3P_dh_N  54 penlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGieegtlkllseviee 120
                                   +  +++t++  ea+k+ di++++vP +++++v+k++++++++   l+ ++  i+e   k ++e ++e
  gi|15668793|ref|NP_247596.1|  48 ELGVEFTNNNIEAAKKGDIVIVAVPINVTERVIKEVAPHVREGCLLMDIT-SIKEIPSKAMEEHVKE 113
                                   55688999999*****************************9998877654.3444444555555554 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.1
                                   -S-HHHHHHHHHHSSBTTTBTT CS
                NAD_Gly3P_dh_N  29 vreeelieeineehenvkyLpg 50 
                                   v+  +++ +++++h ++ky++ 
  gi|15668793|ref|NP_247596.1| 351 VFAGDELSKLKKKHLEKKYIDV 372
                                   3444777888888888888764 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.3e-05     0.037       4      62 ..       9      75 ..       7      88 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                                  EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHH.........HHHHHHHTT-EEEE----T CS
                            KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedska.........liaelealgaevevvaaDv 62
                                   i+GG+ gLG+ +ar l +kg  ++++++R+ ++ ++ ++         +i++ ++ ++ + +v++ v
  gi|15668793|ref|NP_247596.1|  9 SIIGGTDGLGKWFARYLKNKGF-NVIVTGRDIEKGKNVEKelgveftnnNIEAAKKGDIVIVAVPINV 75
                                  599******************7.67889**97655555543344443335555555555555555555 PP

>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0015       1.7      14      44 ..      19      49 ..      12      76 .. 0.90
   2 ?    3.3   0.0      0.11   1.2e+02       6      29 ..     143     166 ..     138     183 .. 0.82
   3 ?   -2.9   0.0         9     1e+04      82     107 ..     340     373 ..     329     384 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                         TIR_2 14 eklaeaLeaagirvwldrwdlkpgedweeei 44
                                  +++a++L+++g++v +  +d+++g+++e+e+
  gi|15668793|ref|NP_247596.1| 19 KWFARYLKNKGFNVIVTGRDIEKGKNVEKEL 49
                                  79************99999*******99987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.11
                         TIR_2   6 ssedkewaeklaeaLeaagirvwl 29 
                                    +++ ew  k+++ L+++g +v +
  gi|15668793|ref|NP_247596.1| 143 KHKNTEWFNKVYNFLKKEGAKVIV 166
                                   46789****************953 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 9
                         TIR_2  82 gkkrlipvlle....pekppl....aslqyidls 107
                                   +++++  +++e    +e  +l     +++yid+s
  gi|15668793|ref|NP_247596.1| 340 KEQKFNILRVEvfagDELSKLkkkhLEKKYIDVS 373
                                   4455666777754321222234322333477766 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.3e-05     0.071       1      43 [.      16      59 ..      16      86 .. 0.87
   2 ?   -2.5   0.0       4.2   4.7e+03       9      24 ..     156     171 ..     149     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.3e-05
                                  HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTESEEEETTT CS
                    ADH_zinc_N  1 gvGlaavqlAkalGaeviavdsseeklelakk.lGadevinyke 43
                                  g+G +   ++k  G++vi++ ++ ek + ++k lG++++ n+ e
  gi|15668793|ref|NP_247596.1| 16 GLGKWFARYLKNKGFNVIVTGRDIEKGKNVEKeLGVEFTNNNIE 59
                                  89****************************999*****999832 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.2
                                   HHHHTT-EEEEEESSH CS
                    ADH_zinc_N   9 lAkalGaeviavdsse 24 
                                   ++k  Ga+vi++ + +
  gi|15668793|ref|NP_247596.1| 156 FLKKEGAKVIVIPPEK 171
                                   4455566666665544 PP

>> DUF2642  Protein of unknown function (DUF2642)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.1   3.5e+03       7      16 ..     226     235 ..     223     238 .. 0.84
   2 ?   12.4   0.0   9.4e-05       0.1      11      49 ..     299     339 ..     298     349 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.1
                       DUF2642   7 dPyvyqtlqs 16 
                                   +Py+y  +q 
  gi|15668793|ref|NP_247596.1| 226 NPYLYADIQM 235
                                   8****99985 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9.4e-05
                       DUF2642  11 yqtlqsllgqevvvqttrgsv..rGiLkdvkPDHivveign 49 
                                   ++ l++l+g+ v+v+  + +v   G+Lkd+  D++ ++ ++
  gi|15668793|ref|NP_247596.1| 299 IEKLNKLIGKDVAVKNINSNVvhFGVLKDIEDDYLILNKNG 339
                                   5789************99998777***********998773 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   4.7e-05     0.053       3      96 ..      11      91 ..       8     118 .. 0.80
   2 ?   -3.0   0.1       4.5   5.1e+03      52      90 ..     347     391 ..     326     396 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.7e-05
                                  EES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETT.CEEEEEECEEECCHSCCCCS-ESEEEE-SSGGGHHHH CS
                          ApbA  3 ilGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseg.geeilrppealsaeekselepidlvivtvKayqteea 84
                                  i G+ ++G  +a +L+++g +v++ +r+       ++G ++++e   e+++ + ea        +++ d+viv+v+   te +
  gi|15668793|ref|NP_247596.1| 11 IGGTDGLGKWFARYLKNKGFNVIVTGRDI------EKGKNVEKELgVEFTNNNIEA--------AKKGDIVIVAVPINVTERV 79
                                  55788999999999999999999999988......778888877722222222333........4567*************** PP

                                  HHHHGGGECTCE CS
                          ApbA 85 leeikplldpnt 96
                                  ++e++p++ + +
  gi|15668793|ref|NP_247596.1| 80 IKEVAPHVREGC 91
                                  ********9875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.5
                                   EEECEEECCH......SCCCCS-ESEEEE-SSGGGHHHHHHHHGG CS
                          ApbA  52 lrppealsae......ekselepidlvivtvKayqteealeeikp 90 
                                   lr+++ + +e      +  e++ id+ +++ K  + e  l+ +k+
  gi|15668793|ref|NP_247596.1| 347 LRVEVFAGDElsklkkKHLEKKYIDVSVLFKKDVDEEVILNLLKK 391
                                   444444444455555555566677888887777777776666665 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00031      0.35      17     115 ..     184     282 ..     180     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                       DUF2935  17 Halfiealldpke.kdlikeakefkkeFekllaeavelseglvrasseleeavakLneealkltreliqFkkellekvlsc 96 
                                   H  fi+ + + ke +  ike+++f+ +  +l+ + +   ++++ +++ l  +++++n ++ +  + +i+  ke+ e v+++
  gi|15668793|ref|NP_247596.1| 184 HFAFISLGATLKElNVDIKESRKFASPIYELMISII---GRIIGQNPYLYADIQMFNPRIKEIHETFINQCKEISEIVKNK 261
                                   88999999999997888**********999999984...57779********************************99986 PP

                       DUF2935  97 klf..siiypllidHilrEae 115
                                          i    ++H   Ea+
  gi|15668793|ref|NP_247596.1| 262 DREgfVKIMKEAAKHFGSEAK 282
                                   543115666777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3221.66
//
Query:       gi|15668794|ref|NP_247597.1|  [L=344]
Description: endonuclease III [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-29   99.8   0.2    3.1e-28   98.1   0.1    1.9  2  DUF123    Domain of unknown function DUF123
    3.9e-28   98.0   0.0    8.4e-28   97.0   0.0    1.6  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
    6.3e-10   38.4   0.0    1.6e-09   37.1   0.0    1.7  1  HHH       Helix-hairpin-helix motif
    2.7e-05   24.7   0.3       0.12   13.0   0.0    2.4  2  HHH_5     Helix-hairpin-helix domain
     0.0061   16.6   0.1          5    7.3   0.0    2.7  2  HHH_2     Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.095   11.9   0.1       0.15   11.2   0.1    1.2  1  DUF763    Protein of unknown function (DUF763)


Domain annotation for each model (and alignments):
>> DUF123  Domain of unknown function DUF123
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.3   1.3e+04      59      73 ..     151     166 ..     139     187 .. 0.67
   2 !   98.1   0.1     1e-31   3.1e-28       3      94 .]     255     341 ..     254     341 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.3
                        DUF123  59 aseerlEcalaeal.e 73 
                                   +++e++E +l ++l +
  gi|15668794|ref|NP_247597.1| 151 ETPEETEFELRKKLpK 166
                                   4677777777777743 PP

  == domain 2  score: 98.1 bits;  conditional E-value: 1e-31
                        DUF123   3 lkkgvylYvGsalgsg.glasRvkrHaslskkkekklhWhiDyLleseeaelaevvvaseerlEcalaeal.eaeapvagf 81 
                                   +kkg+y+Y+Gsa+g++ +l++R++rH+  ++  +kk+hWhiDyLl  ++ +++e+++ ++er+Ec++a+++ ++ + v++f
  gi|15668794|ref|NP_247597.1| 255 FKKGYYFYIGSAFGNSmNLKNRIERHL--KD--DKKMHWHIDYLL--KYGKIEEIYI-TNERVECEVANEFiKKFDFVENF 328
                                   89************9978********4..33..479*********..6778899988.89***********555569**** PP

                        DUF123  82 GasDckcesHLlk 94 
                                   G+sDckc+sHL++
  gi|15668794|ref|NP_247597.1| 329 GCSDCKCKSHLFY 341
                                   ***********96 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   0.0   2.8e-31   8.4e-28       1     107 [.      31     165 ..      31     166 .. 0.97

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 2.8e-31
                                   HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                       HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv............... 66 
                                   +s+i+s++t+de+++++ ++lf++++  +++dl+++deekL++li+++Gfy++Kak++k+lA+il                
  gi|15668794|ref|NP_247597.1|  31 ISTIISARTKDEVTEEVSKKLFKEIK--DVDDLLNIDEEKLADLIYPAGFYKNKAKNLKKLAKILKenyngkvpdsleell 109
                                   79**********************88..***************************************************** PP

                                   ................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                   ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD  67 ................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                   ++++ +i+vD+hv+ri++r+ ++++ +t++++e++l++ l+
  gi|15668794|ref|NP_247597.1| 110 klpgvgrktanlvitlAFNKDGICVDTHVHRICNRWEIVDT-ETPEETEFELRKKLP 165
                                   ****************666779*******************.7*********99887 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   5.3e-13   1.6e-09       2      28 ..      97     123 ..      96     124 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 5.3e-13
                                   HHHHHTSSHHHHHTSTT-SHHHHHHHH CS
                           HHH   2 leglipasreeLlalPGVGpktAeaIl 28 
                                   ++g +p+s+eeLl+lPGVG+ktA+ ++
  gi|15668794|ref|NP_247597.1|  97 YNGKVPDSLEELLKLPGVGRKTANLVI 123
                                   899*********************885 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00053       1.6      11      52 ..      44      87 ..      41      92 .. 0.84
   2 !   13.0   0.0     4e-05      0.12      34      52 ..     105     123 ..      87     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00053
                                  -HHHHHHHHTTT--SHHHHHHS-HHHHHTS...TTS-HHHHHHHH CS
                         HHH_5 11 GpktAlallsaGiesvedlaaadveeLaki...pGiGkktAerii 52
                                   +++ ++l +  i+ v+dl++ d+e+La++    G+ k +A++++
  gi|15668794|ref|NP_247597.1| 44 TEEVSKKLFKE-IKDVDDLLNIDEEKLADLiypAGFYKNKAKNLK 87
                                  6678899****.*****************8788888888887775 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4e-05
                                   HHHHHTSTTS-HHHHHHHH CS
                         HHH_5  34 veeLakipGiGkktAerii 52 
                                    eeL k+pG+G ktA  +i
  gi|15668794|ref|NP_247597.1| 105 LEELLKLPGVGRKTANLVI 123
                                   6899999999999998776 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.1    0.0029       8.8      11      38 ..      43      70 ..      41      73 .. 0.91
   2 !    7.3   0.0    0.0017         5      33      53 ..     104     124 ..      87     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0029
                         HHH_2 11 VGektAklLakrFksldaLkkasleeLl 38
                                  V e+++k+L k+ k++d L + ++e+L+
  gi|15668794|ref|NP_247597.1| 43 VTEEVSKKLFKEIKDVDDLLNIDEEKLA 70
                                  66899********************997 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0017
                         HHH_2  33 sleeLlevddiGeeiAqsive 53 
                                   sleeLl+++++G ++A+ +++
  gi|15668794|ref|NP_247597.1| 104 SLEELLKLPGVGRKTANLVIT 124
                                   79**************98875 PP

>> DUF763  Protein of unknown function (DUF763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1     5e-05      0.15     191     275 ..      40     119 ..       8     129 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5e-05
                        DUF763 191 eeevlnlvskeseearkaildlvkekpekllkelkelkallkgekkl............klpakhevlekvlekaye.lqp 258
                                   ++ev                   +e  +kl ke+k++++ll+ ++++            +  ++ + l k+l++ y+ + p
  gi|15668794|ref|NP_247597.1|  40 KDEVT------------------EEVSKKLFKEIKDVDDLLNIDEEKladliypagfykNKAKNLKKLAKILKENYNgKVP 102
                                   22233..................3333555555555555555544445666666666542233444588999988872568 PP

                        DUF763 259 edfeellllkgvGpktl 275
                                   +++eell l+gvG+kt 
  gi|15668794|ref|NP_247597.1| 103 DSLEELLKLPGVGRKTA 119
                                   99************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1219  (0.0679904); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2197.34
//
Query:       gi|15668795|ref|NP_247598.1|  [L=130]
Description: hypothetical protein MJ_0614 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-17   63.2   0.6    1.9e-17   62.9   0.6    1.1  1  DUF22            Domain of unknown function DUF22
  ------ inclusion threshold ------
      0.021   14.8   0.1        7.5    6.6   0.0    2.2  2  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a


Domain annotation for each model (and alignments):
>> DUF22  Domain of unknown function DUF22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.6   2.1e-21   1.9e-17      14     101 ..      17     105 ..       6     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 2.1e-21
                         DUF22  14 rekvevepfgyt..rstvakwelliAdedvevkkGevkkikikeielpentivvplsimrhalgtvldvvekgkpkkveee 92 
                                   +++++ e+++y   +++ ak+e+++A+ed+e+k+G++k i+ik+i++p+ +++  +   rh +g v+ v+e + p +++ e
  gi|15668795|ref|NP_247598.1|  17 EKEIKEEEAKYDliIKNEAKIEPIVAEEDMEFKQGDIKPIRIKKIKIPPMSVLLICPYGRHRVGHVVAVGE-EVPMPIDVE 96 
                                   466666666664227899****************************************************9.********* PP

                         DUF22  93 reiteavfl 101
                                   re++ a+f 
  gi|15668795|ref|NP_247598.1|  97 REVDMAMFA 105
                                   *******97 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0   0.00097       8.7      23      60 ..      34      70 ..       8      88 .. 0.61
   2 ?    6.6   0.0   0.00084       7.5      33      46 ..     107     120 ..      92     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00097
               ParE-like_toxin 23 dkavkeiiedPelGeeKkGDLsgvfvykfklnkqltll 60
                                  +++++ i+++    e K+GD++ +++ k+k+    +ll
  gi|15668795|ref|NP_247598.1| 34 EAKIEPIVAEED-MEFKQGDIKPIRIKKIKIPPMSVLL 70
                                  334444444432.367*************998777776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00084
               ParE-like_toxin  33 PelGeeKkGDLsgv 46 
                                     +Ge KkGDL g+
  gi|15668795|ref|NP_247598.1| 107 GFEGEVKKGDLIGM 120
                                   578********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 1027.69
//
Query:       gi|15668796|ref|NP_247599.1|  [L=216]
Description: V-type ATP synthase subunit D [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-64  215.3  13.9    8.1e-64  215.1  13.9    1.0  1  ATP-synt_D    ATP synthase subunit D
  ------ inclusion threshold ------
       0.55   10.3  11.2       0.46   10.6   0.5    3.9  4  Exonuc_VII_S  Exonuclease VII small subunit
       0.89    8.8   6.8          2    7.7   2.1    2.1  2  CorA          CorA-like Mg2+ transporter protein
        4.4    6.8   9.3        6.9    6.2   0.9    2.3  2  DUF4795       Domain of unknown function (DUF4795)
        6.4    6.8  10.8       0.32   11.0   4.7    1.8  2  CFAP91        Cilia- and flagella-associated protein 91


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.1  13.9   2.2e-67   8.1e-64       1     195 [.      10     203 ..      10     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 215.1 bits;  conditional E-value: 2.2e-67
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-..TSS CS
                    ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvklakvv 81 
                                   eL++lk+++kla++gh+lLk+KrdaLi+ef++i++++ +lr+++e +l eay+ l +a++++g  ++++a+l+ ++   ++
  gi|15668796|ref|NP_247599.1|  10 ELLKLKNKIKLAEKGHKLLKQKRDALIMEFFQIIEQASDLRDKVEAKLAEAYKDLIMAQTVMGTLAVKEAALAAKN--DKL 88 
                                   79**********************************************************************8888..88* PP

                                   -SEEEEEEBTTSEEEEEEE-...S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_D  82 kvelktenvaGVkvpvfeleee.ksdstelygllrtgaqldeavealrellellvelasletslelLdeeikktnrRvNaL 161
                                   +v++ t+n++GV+vp+fe+++  ++  ++ y+ ++ +++ldea+++++e+lel+ ela++ets++lL+eei +t+rRvNaL
  gi|15668796|ref|NP_247599.1|  89 EVDMDTKNIMGVTVPTFEIYNVrRKVGERGYSPYGVSSKLDEAAKKFEEALELITELAEIETSIKLLAEEIITTKRRVNAL 169
                                   ******************999873344566888888********************************************* PP

                                   HTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_D 162 ekvvIPrleetikyIkseLdEqereeffrlkkvk 195
                                   e+v+IPrl++  kyI+++LdE+ere+ffrlk +k
  gi|15668796|ref|NP_247599.1| 170 EYVIIPRLKSLKKYISMRLDEMERENFFRLKLIK 203
                                   *********************************9 PP

>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.3      0.02        70      21      43 ..      13      35 ..      10      37 .. 0.82
   2 ?    1.2   0.1      0.11     4e+02      26      48 ..      40      62 ..      36      65 .. 0.84
   3 ?   10.6   0.5   0.00013      0.46      21      39 ..     127     145 ..     125     155 .. 0.90
   4 ?   -2.0   0.0       1.1     4e+03      35      48 ..     180     193 ..     179     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.02
                  Exonuc_VII_S 21 sLeeslklyeeGvkLlkeCekkL 43
                                   L   +kl e+G kLlk+ ++ L
  gi|15668796|ref|NP_247599.1| 13 KLKNKIKLAEKGHKLLKQKRDAL 35
                                  5667799**********977765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                  Exonuc_VII_S 26 lklyeeGvkLlkeCekkLdeaeq 48
                                  ++  e++  L  + e+kL ea +
  gi|15668796|ref|NP_247599.1| 40 FQIIEQASDLRDKVEAKLAEAYK 62
                                  778899999*********99976 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00013
                  Exonuc_VII_S  21 sLeeslklyeeGvkLlkeC 39 
                                    L+e+ k++ee+ +L+ e+
  gi|15668796|ref|NP_247599.1| 127 KLDEAAKKFEEALELITEL 145
                                   59*************9876 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.1
                  Exonuc_VII_S  35 LlkeCekkLdeaeq 48 
                                   L k+ + +Lde e+
  gi|15668796|ref|NP_247599.1| 180 LKKYISMRLDEMER 193
                                   67888889999986 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2    0.0088        32     107     148 ..      23      65 ..       3      88 .. 0.71
   2 ?    7.7   2.1   0.00055         2     122     202 ..     127     207 ..     122     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0088
                          CorA 107 spgellyrlldeivdrlfellekleeeldeledel.edstkke 148
                                   +  +ll +  d+++ ++f+++e+ ++ +d++e  l e +++  
  gi|15668796|ref|NP_247599.1|  23 KGHKLLKQKRDALIMEFFQIIEQASDLRDKVEAKLaEAYKDLI 65 
                                   4556666777888888999999999999999988844444433 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00055
                          CorA 122 rlfellekleeeldeledel.edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldel 201
                                   +l+e+ +k ee l+ + +    + + k +++e+++ +rr+  l+ ++ p  + lk++++  + +++++e+  +l+ + +++
  gi|15668796|ref|NP_247599.1| 127 KLDEAAKKFEEALELITELAeIETSIKLLAEEIITTKRRVNALEYVIIPRLKSLKKYIS-MRLDEMERENFFRLKLIKSRI 206
                                   6677777777777777777755555688999***************************9.777777777756666666666 PP

                          CorA 202 e 202
                                   e
  gi|15668796|ref|NP_247599.1| 207 E 207
                                   5 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.6    0.0031        11      87     132 ..      33      91 ..      10     118 .. 0.69
   2 ?    6.2   0.9    0.0019       6.9      64     134 ..     124     196 ..     104     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0031
                       DUF4795  87 DeakkeLekmleellekleeqeealkkaldtLq.............eelkekldrlele 132
                                   D+ ++e+ +++e++ +  +++e++l +a+++L               +l  k+d+le++
  gi|15668796|ref|NP_247599.1|  33 DALIMEFFQIIEQASDLRDKVEAKLAEAYKDLImaqtvmgtlavkeAALAAKNDKLEVD 91 
                                   45555555666666666667777777777777777777777777766677777766654 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0019
                       DUF4795  64 veeelaekadk..eaLatkvsrdqfDeakkeLekmleellekleeqeealkkaldtLqeelkekldrlelepL 134
                                   v+ +l+e+a k  eaL+  ++  ++++++k+L + +     ++++ e  +   l+ L++ +  +ld++e e++
  gi|15668796|ref|NP_247599.1| 124 VSSKLDEAAKKfeEALELITELAEIETSIKLLAEEIITTKRRVNALEYVIIPRLKSLKKYISMRLDEMERENF 196
                                   5566666666544899999999999999999999999999999999999999999999********9998876 PP

>> CFAP91  Cilia- and flagella-associated protein 91
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3      0.56     2e+03     101     101 ..      38      38 ..       2      89 .. 0.59
   2 ?   11.0   4.7   8.9e-05      0.32      58     137 ..     133     211 ..     128     215 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.56
                        CFAP91 101 e 101
                                   e
  gi|15668796|ref|NP_247599.1|  38 E 38 
                                   1 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.9e-05
                        CFAP91  58 raleaslpplsdaaslekrkkileelElkewaereeeiqelqeeRlellkkllkkreeeqeeanekrleklkeklekeke 137
                                   +++e++l+ +++ a++e   k+l e E+   + r + ++ +   Rl+ lkk ++ r +e+e++n  rl+ +k+++ek+++
  gi|15668796|ref|NP_247599.1| 133 KKFEEALELITELAEIETSIKLLAE-EIITTKRRVNALEYVIIPRLKSLKKYISMRLDEMERENFFRLKLIKSRIEKREA 211
                                   789******************9987.777779*******************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1027  (0.0572815); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1331.59
//
Query:       gi|15668797|ref|NP_247600.1|  [L=157]
Description: phosphoribosylaminoimidazole carboxylase catalytic subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-59  199.5   1.2    2.1e-59  199.4   1.2    1.0  1  AIRC          AIR carboxylase
    0.00069   19.4   0.1      0.001   18.8   0.1    1.2  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
       0.01   16.1   0.1      0.051   13.8   0.0    2.1  2  Glutaredoxin  Glutaredoxin


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.4   1.2   3.5e-63   2.1e-59       2     147 ..       2     143 ..       1     144 [. 0.97

  Alignments for each domain:
  == domain 1  score: 199.4 bits;  conditional E-value: 3.5e-63
                                   EEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-EEE CS
                          AIRC   2 VgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlPVig 82 
                                   ++iimGS+sDl++++ka++ilke+gve+evrv+Sahrtpe ++e++++ +    +v+Ia+AG aahLpgvvasltt PVi+
  gi|15668797|ref|NP_247600.1|   2 ICIIMGSESDLKIAEKAVNILKEFGVEFEVRVASAHRTPELVEEIVKNSK---ADVFIAIAGLAAHLPGVVASLTTKPVIA 79 
                                   78********************************************9876...58************************** PP

                                   EEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                          AIRC  83 vPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkdeelaekleeyreelke 147
                                   vPv++ +l+gld+llS+vqmP+g+pvatv+i++++nAa+lA++ilalkde++a+kl eyre++k+
  gi|15668797|ref|NP_247600.1|  80 VPVDA-KLDGLDALLSSVQMPPGIPVATVGIDRGENAAILALEILALKDENIAKKLIEYREKMKK 143
                                   *****.9*******************************************************987 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.7e-07     0.001      22     122 ..       2      97 ..       1     107 [. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-07
                      Fe-ADH_2  22 vllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvsaklnvpy 102
                                   + ++++++    ++ek  + lke g++ ev+  ++++++ e ve++v++    ++d+++a+ +G +  +  +v++ + +p+
  gi|15668797|ref|NP_247600.1|   2 ICIIMGSESDLKIAEKAVNILKEFGVEFEVRV-ASAHRTPELVEEIVKNS---KADVFIAI-AGLAAHLPGVVASLTTKPV 77 
                                   568888888888999999***********776.77788888888888655...6*******.899999************* PP

                      Fe-ADH_2 103 vsvpTaaSvDGfaspgaslv 122
                                   ++vp  a  DG  +  +s+ 
  gi|15668797|ref|NP_247600.1|  78 IAVPVDAKLDGLDALLSSVQ 97 
                                   ***********999888876 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   8.6e-06     0.051      14      45 ..      17      50 ..      15      81 .. 0.87
   2 ?   -0.3   0.0      0.21   1.2e+03      32      46 ..     125     139 ..     114     148 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.6e-06
                                  HHHHHHHHTTGGEEEEEGCCSH..HHHHHHHHHH CS
                  Glutaredoxin 14 kakrlLkelgvkfeeidvdkde..eireelkels 45
                                  ka+++Lke+gv+fe++  +++   e+ ee+ ++s
  gi|15668797|ref|NP_247600.1| 17 KAVNILKEFGVEFEVRVASAHRtpELVEEIVKNS 50
                                  89*******************6669999998887 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.21
                                   CCSHHHHHHHHHHHT CS
                  Glutaredoxin  32 dkdeeireelkelsg 46 
                                   +kde+i ++l e+ +
  gi|15668797|ref|NP_247600.1| 125 LKDENIAKKLIEYRE 139
                                   566666666655543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1073.91
//
Query:       gi|15668798|ref|NP_247601.1|  [L=195]
Description: tartrate dehydratse subunit beta TtdB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      6e-52  176.0   0.0    7.3e-52  175.7   0.0    1.0  1  Fumerase_C  Fumarase C-terminus
  ------ inclusion threshold ------
      0.096   12.2   0.1       0.14   11.8   0.1    1.1  1  DUF316      Chymotrypsin family Peptidase-S1
       0.19   11.3   0.0       0.27   10.8   0.0    1.2  1  CitG        ATP:dephospho-CoA triphosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Fumerase_C  Fumarase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.7   0.0   1.2e-55   7.3e-52      35     205 ..       7     180 ..       2     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 1.2e-55
                    Fumerase_C  35 keteeelskykvgtrlllsGkllvaRDaaHkrlkerlekgeelpeyvklkdrviYyaGPv..ktpedeavgsaGPTTatRm 113
                                   k t+++++k+kvg+ + l+Gk+++aRD aH ++ e+l+++e+lp  ++l++++iY+aGP+  k ++++++ s+GPTT+ Rm
  gi|15668798|ref|NP_247601.1|   7 KLTKKDVKKLKVGDIVYLNGKIYTARDEAHLKIIEMLKSNEKLP--FDLNESIIYHAGPImkKVNDSWVCVSIGPTTSARM 85 
                                   4899****************************************..**************87778899************* PP

                    Fumerase_C 114 dkyvekllkktgllimlaKgnrskkvleaikkhggvYLgaiGGaAilakkaikkvevvef.eelGm.EAiyeievedf.pa 191
                                   ++  e+++k t++ ++++Kg++ k+ l++ +++g vYL a GG A l ++++k+v+ v f  elGm EA++e+ev++f p 
  gi|15668798|ref|NP_247601.1|  86 NDVEEEFIKLTNISAIVGKGGMKKELLKTFEDYGVVYLAAPGGCAALLANSVKRVDNVYFlDELGMpEAVWELEVNNFgPL 166
                                   *******************************************99999***********9889***************889 PP

                    Fumerase_C 192 fvvvddkGndlfke 205
                                   +v++d++Gn++++e
  gi|15668798|ref|NP_247601.1| 167 IVAMDSHGNSIYEE 180
                                   99**********97 PP

>> DUF316  Chymotrypsin family Peptidase-S1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.3e-05      0.14     185     272 ..      13      99 ..       9     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                        DUF316 185 stslkkgdavdvygldssgelkhrklkieavssaeasiktsqylskkddggslikkvsgkntvlGfgatgnlesnandelF 265
                                    ++lk gd+v++ g        +  lki+++ +  +++  + + s    +g++ kkv++ ++ + +g t +   n  +e F
  gi|15668798|ref|NP_247601.1|  13 VKKLKVGDIVYLNGK-IYTARDEAHLKIIEMLKSNEKLPFDLNESIIYHAGPIMKKVNDSWVCVSIGPTTSARMNDVEEEF 92 
                                   567788888888887.8888899999*****999*****************************999999999998899*** PP

                        DUF316 266 fnlkkls 272
                                   ++l ++s
  gi|15668798|ref|NP_247601.1|  93 IKLTNIS 99 
                                   **99865 PP

>> CitG  ATP:dephospho-CoA triphosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.6e-05      0.27     153     277 ..      14     136 ..       3     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.6e-05
                                   TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHH CS
                          CitG 153 ksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallallaelpDtnilrrgGaegaeevqe 233
                                   k+l++g++++l+ ++  +r+ea      +++       +  +   dln+++++    ++ +++D+ +    G+ + +++ +
  gi|15668798|ref|NP_247601.1|  14 KKLKVGDIVYLNGKIYTARDEAHLKIIEMLK-------SNEKLPFDLNESIIYHAGPIMKKVNDSWVCVSIGPTTSARMND 87 
                                   4678888888888888888888766555555.......444456899********************************** PP

                                   HHH..............H-.SHHHHHHHHHHHHHHT---HHHHHHHHHH CS
                          CitG 234 eArallaa....ggvaaea.glealeeldrelvernisPGgsADllaat 277
                                     +++++     + v++    +e l+ ++++ v     PGg+A lla +
  gi|15668798|ref|NP_247601.1|  88 VEEEFIKLtnisAIVGKGGmKKELLKTFEDYGVVYLAAPGGCAALLANS 136
                                   *****999888844555555678999********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1248.69
//
Query:       gi|15668799|ref|NP_247602.1|  [L=98]
Description: hypothetical protein MJ_0618 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-21   75.9   1.3    2.7e-21   75.5   1.3    1.2  1  DUF167    Uncharacterised ACR, YggU family COG1872
  ------ inclusion threshold ------
       0.16   11.4   0.0       0.21   11.1   0.0    1.2  1  MdcE      Malonate decarboxylase gamma subunit (MdcE)


Domain annotation for each model (and alignments):
>> DUF167  Uncharacterised ACR, YggU family COG1872
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   1.3     3e-25   2.7e-21       1      76 [.      12      82 ..      12      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 3e-25
                                  EEEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEEE CS
                        DUF167  1 gvilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvri 76
                                  gv++++ v+ +akk++i+  + +e+r++l ++++ap+ +GkANk++ikf+ ++++   +dveivsG+ + +K+v+i
  gi|15668799|ref|NP_247602.1| 12 GVLIDIDVQANAKKNEIV--GINEWRKRLSIKIKAPATEGKANKEIIKFFKEIFK---KDVEIVSGKLNPQKTVLI 82
                                  689***************..9999******************************9...****************98 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.3e-05      0.21      69      90 ..      13      34 ..       1      51 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.3e-05
                                  EEEEE--B--SHHHHHHTHHHH CS
                          MdcE 69 vlvDvasQrlgrrdEllGihea 90
                                  vl+D + Q+ ++++E++Gi+e+
  gi|15668799|ref|NP_247602.1| 13 VLIDIDVQANAKKNEIVGINEW 34
                                  689*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 665.71
//
Query:       gi|15668800|ref|NP_247603.1|  [L=506]
Description: hypothetical protein MJ_0619 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-21   76.7   3.6    2.1e-20   73.8   0.0    2.7  3  Radical_SAM  Radical SAM superfamily
    1.9e-08   34.7   1.2    8.4e-08   32.6   0.0    2.3  2  Fer4_12      4Fe-4S single cluster domain
      1e-07   32.1   0.3    1.4e-06   28.5   0.0    2.5  2  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.15   11.2   0.0       0.24   10.5   0.0    1.2  1  CAF1         CAF1 family ribonuclease


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.3     0.045     2e+02       4      19 ..      70      85 ..      67      94 .. 0.81
   2 !   73.8   0.0   4.6e-24   2.1e-20       3     165 ..      94     253 ..      92     255 .. 0.95
   3 ?   -2.0   0.0      0.91   4.1e+03      32     112 ..     362     441 ..     337     454 .. 0.49

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.045
                                  ESEESS--TTTSCCTT CS
                                  xxxxxxxxxxxxxxxx RF
                   Radical_SAM  4 trgCnlrCsfCarpet 19
                                   +gC+++C  C+++++
  gi|15668800|ref|NP_247603.1| 70 KNGCPYDCGLCPNHKS 85
                                  68***********985 PP

  == domain 2  score: 73.8 bits;  conditional E-value: 4.6e-24
                                   EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiritv 82 
                                   vt+ Cnl+C+ C  +    + g++++ s e+i++ ++ l++e   +  + + ggep++++d+ el++ ++      +++ +
  gi|15668800|ref|NP_247603.1|  94 VTNRCNLNCPICFANAN--KSGKVYEPSFEDIKRMMENLRKEIPpTPAIQFAGGEPTVRSDLPELIKLARDM--GFLHVQL 170
                                   899************96..*********************77777***************************..9****** PP

                                   EECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHH CS
                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpd.eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeelee 162
                                    tng+++    +l++l+e+g+ +++l  + ++++++l    +++ +    +++e+++++g+++vv + ++++G+nd e+  
  gi|15668800|ref|NP_247603.1| 171 ATNGIKLKnINYLKKLKEAGLSTIYLQFDGISEKPYLVAR-GKNLLPIKQKVIENCKKVGFDSVVLVPTLVRGVNDNEVGG 250
                                   ****************************************.999999999***************************9876 PP

                                   HHH CS
                                   xxx RF
                   Radical_SAM 163 lle 165
                                   +++
  gi|15668800|ref|NP_247603.1| 251 IIR 253
                                   665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.91
                                   HHHHHHHHHHHHHTTSEEEEEE..SSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEB CS
                                   xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  32 eeileevkelkaekgvkevilg..ggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgle 110
                                   e  le+vke  +e g+  ++ +   ge  l  +   +l+++ k    +i+  +     ++ +    +l+el+   + ++  
  gi|15668800|ref|NP_247603.1| 362 EGFLEIVKEKIEEIGKSKMHDVkvLGEIALKLPSLIDLDKAPKS--VNIKKIIDLILSVL-KSDYSALAELHYHMLMISCM 439
                                   44444444443333333322222233344444444444444444..44444444444444.55555555555555555555 PP

                                   SS CS
                                   xx RF
                   Radical_SAM 111 aa 112
                                   ++
  gi|15668800|ref|NP_247603.1| 440 HF 441
                                   55 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.7      0.34   1.5e+03      13      28 ..      71      86 ..      68      95 .. 0.83
   2 !   32.6   0.0   1.9e-11   8.4e-08      13     100 ..      96     181 ..      88     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.34
                       Fer4_12 13 sgCnlsCkgCfnketw 28
                                  +gC+  C  C n +  
  gi|15668800|ref|NP_247603.1| 71 NGCPYDCGLCPNHKST 86
                                  69********999875 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 1.9e-11
                       Fer4_12  13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk..esiegltllGGEPllpenaeallelvkevkeekpekdiwly 91 
                                   ++Cnl+C+ Cf+++ +s k  ++  +e +++++e+l k  +  + + + GGEP +++  ++l++l++ +   ++  + +++
  gi|15668800|ref|NP_247603.1|  96 NRCNLNCPICFANANKSGKVYEPS-FEDIKRMMENLRKeiPPTPAIQFAGGEPTVRSDLPELIKLARDM---GFLHVQLAT 172
                                   68*********8877776665554.778889999997745666************66666666666554...444456788 PP

                       Fer4_12  92 tgytleels 100
                                   +g +l++++
  gi|15668800|ref|NP_247603.1| 173 NGIKLKNIN 181
                                   888777775 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3      0.17   7.5e+02       6      20 ..      71      85 ..      69      89 .. 0.85
   2 !   28.5   0.0     3e-10   1.4e-06       5     100 ..      95     185 ..      93     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                       Fer4_14  6 sgCnlsCkgCdnket 20
                                  +gC+  C  C n+++
  gi|15668800|ref|NP_247603.1| 71 NGCPYDCGLCPNHKS 85
                                  79********98875 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 3e-10
                       Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwl 85 
                                   +++Cnl+C+ C+ +++++ ++ +p+ e ++++++++l k+      + + GGeP      ++l +l+k  ++ +  ++++l
  gi|15668800|ref|NP_247603.1|  95 TNRCNLNCPICFANANKSGKVYEPSFE-DIKRMMENLRKEIPPTPAIQFAGGEPTVR---SDLPELIKLARDMG-FLHVQL 170
                                   79**********999888888888765.566888877777666667********966...77777777777777.789999 PP

                       Fer4_14  86 etngtleielektpd 100
                                    tng   ++++  ++
  gi|15668800|ref|NP_247603.1| 171 ATNGIKLKNINYLKK 185
                                   999987767663333 PP

>> CAF1  CAF1 family ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.3e-05      0.24     100     132 ..     432     464 ..     416     498 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.3e-05
                                   EEEEHHHHHHHHHTT--HHHHHTT-B-B--HHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CAF1 100 fsvspsslqFLakngfdfnkliseGipYlsrke 132
                                    ++ +s+++F+  ++fd+ ++++ +i+Y++ ++
  gi|15668800|ref|NP_247603.1| 432 HMLMISCMHFMDAYNFDVKRVMRCCIHYATPDD 464
                                   577899***********************9883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3677.53
//
Query:       gi|15668801|ref|NP_247604.1|  [L=291]
Description: 30S ribosomal protein S6 modification protein RimK [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-35  121.9   0.1      3e-35  121.5   0.1    1.1  1  RimK            RimK-like ATP-grasp domain
    1.3e-19   70.3   0.1    1.7e-19   69.9   0.1    1.1  1  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
      7e-11   42.4   0.8    1.7e-10   41.2   0.8    1.6  1  ATP-grasp_3     ATP-grasp domain
    4.5e-10   39.2   0.1      3e-07   29.9   0.1    2.9  1  ATPgrasp_YheCD  YheC/D like ATP-grasp
    2.2e-06   27.1   0.1      0.018   14.3   0.0    3.0  2  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
  ------ inclusion threshold ------
      0.013   14.4   0.0      0.022   13.7   0.0    1.3  1  DUF3326         Protein of unknown function (DUF3326)
      0.017   14.9   0.1       0.26   11.0   0.1    2.2  2  ATPgrasp_TupA   TupA-like ATPgrasp
      0.024   13.8   0.0       0.17   11.0   0.0    1.9  2  GSP_synth       Glutathionylspermidine synthase preATP-grasp
       0.14   12.1   0.0       0.23   11.5   0.0    1.3  1  R2K_3           ATP-grasp domain, R2K clade family 3


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.5   0.1   1.5e-38     3e-35       1     188 []      94     285 ..      94     285 .. 0.91

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 1.5e-38
                                   HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH...GGG--.. CS
                          RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea...lkeai.. 76 
                                   a++K+++   L  ++++ p+t ++++ ++a   i+k++     v+K ++g  G ++v  kke  +   l+     ke+   
  gi|15668801|ref|NP_247604.1|  94 ASNKFLTSVFLELNNLPQPKTVVTESINEAIVWIDKFE---EAVLKPIFGCGGEGIVRVKKELPISTKLKIlneFKEKYnt 171
                                   789**********************************6...78******************97776555552223333355 PP

                                   .EEEEE--SS-S..EEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEEEEE CS
                          RimK  77 .lvqeyieeaen..ediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDllra 154
                                     +qe+i+   n  +diR +vvddevvaa+ r++ e +++ n+ +Gg +ek +++ee ++lA+ka +a++l++aGvDl+++
  gi|15668801|ref|NP_247604.1| 172 fYIQEFIKPVRNehRDIRAFVVDDEVVAAMYRIGGE-NWKNNVSQGGRVEKCEITEEIEKLALKAKNALGLFYAGVDLIES 251
                                   59******8877679******************999.9******************************************* PP

                                   TTEEEEEEEESS--SHHHHHHHT--HHHHHHHHH CS
                          RimK 155 krgllvlEvnsspglekiektlgidiakklieai 188
                                   ++gl vlEvns p   +++k ++++ia kl+e i
  gi|15668801|ref|NP_247604.1| 252 EDGLKVLEVNSTPSWIGLSKVSEVNIADKLLEKI 285
                                   ******************************9976 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.1   8.6e-23   1.7e-19      12     171 ..     111     273 ..      96     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 8.6e-23
                                   S--EEEES-HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT...-TTHHHHHHHHTTTTTS-EEEEE--GGGGG..-EEE CS
                     GSH-S_ATP  12 ipktlvskdkeeirafleeqgdvilKPldgkgGegvfrvkks...dpnlksilellteegkepviaqrylpeike..GDkR 87 
                                    pkt+v+++ +e   ++++ ++++lKP+ g gGeg++rvkk+   +++lk + e+   e+ +++ +q++++ +++   D R
  gi|15668801|ref|NP_247604.1| 111 QPKTVVTESINEAIVWIDKFEEAVLKPIFGCGGEGIVRVKKElpiSTKLKILNEFK--EKYNTFYIQEFIKPVRNehRDIR 189
                                   59***************************************864444555555543..44556999*****997522699* PP

                                   EEEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETT....EEEEEE-S.S CS
                     GSH-S_ATP  88 illvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigd....kltEinvt.s 163
                                    ++vd e +  a+ R+   ++ ++n++ ggr+e+ e+te+ +++a + +++L   Gl+++G+D+i++    k+ E+n t s
  gi|15668801|ref|NP_247604.1| 190 AFVVDDEVVA-AMYRIGG-ENWKNNVSQGGRVEKCEITEEIEKLALKAKNAL---GLFYAGVDLIESedglKVLEVNSTpS 265
                                   *********9.*****85.679***********************9999887...**********7533337889997745 PP

                                   ---HHHHH CS
                     GSH-S_ATP 164 Ptgireie 171
                                     g+++++
  gi|15668801|ref|NP_247604.1| 266 WIGLSKVS 273
                                   55666665 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.8   8.6e-14   1.7e-10       1     156 [.      94     262 ..      94     265 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 8.6e-14
                                   HTSHHHHHHHHTTT.S---....-EESS--......SSSEEEEESS-------B--SS--TTE................EE CS
                   ATP-grasp_3   1 asdKlktykkLkeagvkvPtkleaeeleee......ekklvvKprdGaggesvrvveekeeaeaaieeve.........lv 66 
                                   as+K+ t  +L+ ++++ P+++  e+++e+       ++ v+Kp+ G+gge+++ v+++    ++++ ++          +
  gi|15668801|ref|NP_247604.1|  94 ASNKFLTSVFLELNNLPQPKTVVTESINEAivwidkFEEAVLKPIFGCGGEGIVRVKKELPISTKLKILNefkekyntfYI 174
                                   79*****************776666666667788889******************99986555555555466699999999 PP

                                   EE---...SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEE CS
                   ATP-grasp_3  67 qefie...GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvl 144
                                   qefi+    ++  + + +   +  v+a    + + ++k++v +G+ ++   e +ee+++la ++ ++l gl+ y+GvDl+ 
  gi|15668801|ref|NP_247604.1| 175 QEFIKpvrNEHRDIRAFVV--DDEVVAAMYRIGGENWKNNVSQGGRVEKC-EITEEIEKLALKAKNAL-GLF-YAGVDLIE 250
                                   ***9722245556655442..23344444444445566688888888765.78999999999999999.887.9******* PP

                                   SS.SEEEEEEES CS
                   ATP-grasp_3 145 kdeepyviEvNP 156
                                   +++++ v+EvN+
  gi|15668801|ref|NP_247604.1| 251 SEDGLKVLEVNS 262
                                   ***********7 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   1.5e-10     3e-07      30     254 ..     112     290 ..      96     291 .] 0.86

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.5e-10
                ATPgrasp_YheCD  30 PetellesledleemlekyksvylKpanGskGkgilriekeekellllsrekkkkkkkrlaslselesllkkllkkkrylv 110
                                   P+t+  es+++   +++k+++ +lKp+ G++G+gi+r++k            +   +++l+ l+e++++ +      ++ +
  gi|15668801|ref|NP_247604.1| 112 PKTVVTESINEAIVWIDKFEEAVLKPIFGCGGEGIVRVKK------------ELPISTKLKILNEFKEKYN------TFYI 174
                                   999*************************************............3344444444444444444......488* PP

                ATPgrasp_YheCD 111 QqgidlatidgrpfDfRvlvqKngkgkWevtgiaaRiagkgsittnlsrGGtalpleellkkafgeekaekileeleelal 191
                                   Q+ i+  +  +++ D+R++v  +     ev++++ Ri+g++    n+s+GG++ +               +i+ee+e+lal
  gi|15668801|ref|NP_247604.1| 175 QEFIKPVR--NEHRDIRAFVVDD-----EVVAAMYRIGGEN-WKNNVSQGGRVEKC--------------EITEEIEKLAL 233
                                   ****9988..7778******966.....699*******887.889******98764..............58899****** PP

                ATPgrasp_YheCD 192 elaealeesfgrlgElGlDlgidkegkvWllEvNskpgrsifkeagdkeaarksvkrpleYak 254
                                   ++ +al      l+  G+Dl i++e  + +lEvNs p+    +++++ ++a k+++++++Y k
  gi|15668801|ref|NP_247604.1| 234 KAKNALG-----LFYAGVDL-IESEDGLKVLEVNSTPSWIGLSKVSEVNIADKLLEKIIQYVK 290
                                   **99998.....5556***8.899999**********************************87 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0     9e-06     0.018       5      81 ..      80     151 ..      78     225 .. 0.75
   2 !    8.7   0.0   0.00047      0.94     226     268 ..     226     266 ..     218     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9e-06
                   ATPgrasp_ST   5 rlirkyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvite 81 
                                   ++i+ +Np   +    +K++++ +++ + l+ pk++++    ++i+e+   + ++ee  v+Kp+ g gG+Gi+ +++
  gi|15668801|ref|NP_247604.1|  80 HYIPVINPPDGIDRASNKFLTSVFLELNNLPQPKTVVT----ESINEAIVWIDKFEE-AVLKPIFGCGGEGIVRVKK 151
                                   589999999999**********************6555....677777788888855.99************98855 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00047
                   ATPgrasp_ST 226 eevlelaakaaeklpglgylGwDivldeekgplllElNarpgl 268
                                   ee+ +la ka +  +gl y G+D+   e++ + +lE+N +p+ 
  gi|15668801|ref|NP_247604.1| 226 EEIEKLALKAKN-ALGLFYAGVDLIESEDG-LKVLEVNSTPSW 266
                                   5778999**999.9*********9655555.********9975 PP

>> DUF3326  Protein of unknown function (DUF3326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.1e-05     0.022     219     285 ..      84     151 ..      74     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                       DUF3326 219 evspraaaeelgytfLpcvLvgLsraPqlvekkeelsaaealsaedv.davvvPasalGgsavlalae 285
                                    ++p +  +  +  fL++v   L++ Pq  +  +e+ ++  +++++  +av+ P   +Gg++++ +++
  gi|15668801|ref|NP_247604.1|  84 VINPPDGIDRASNKFLTSVFLELNNLPQPKTVVTESINEAIVWIDKFeEAVLKPIFGCGGEGIVRVKK 151
                                   5677777888999****************9999998999999**998459999**********99875 PP

>> ATPgrasp_TupA  TupA-like ATPgrasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00013      0.26      41      90 ..     114     164 ..      97     188 .. 0.75
   2 ?    1.3   0.0      0.13   2.5e+02     173     221 ..     215     265 ..     200     274 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                 ATPgrasp_TupA  41 lsvetdl.etidfevikesiViKpthdsGsrgvlevkneldilkvkskllk 90 
                                     v + + e i ++ + e++V+Kp  + G+ g++ vk+el i  + + l +
  gi|15668801|ref|NP_247604.1| 114 TVVTESInEAIVWIDKFEEAVLKPIFGCGGEGIVRVKKELPISTKLKILNE 164
                                   445444426799***************************998766544444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.13
                 ATPgrasp_TupA 173 yegevekpgvleemielAetisse..ipfvRvDlyksgdkvyfGElTfkpg 221
                                   ++g+vek + +ee  +lA +  +   + +  vDl  s+d++ + E   +p+
  gi|15668801|ref|NP_247604.1| 215 QGGRVEKCEITEEIEKLALKAKNAlgLFYAGVDLIESEDGLKVLEVNSTPS 265
                                   567889999999888888765444558999**********99988877775 PP

>> GSP_synth  Glutathionylspermidine synthase preATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.4e-05      0.17     289     368 ..     130     211 ..      83     216 .. 0.75
   2 ?    1.0   0.0     0.094   1.9e+02      61     113 ..     218     267 ..     207     284 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.4e-05
                     GSP_synth 289 gkkyvkKplfgREGanveivee....gsevaeekegeygeekviyQeyaelpkfdgsypvlgswlvgdeaaGlgiRedrgl 365
                                    ++ v Kp+fg  G+ +  v++     ++ +  +e + + +++ +Qe+++  +  +++  + +++v+de ++   R + + 
  gi|15668801|ref|NP_247604.1| 130 FEEAVLKPIFGCGGEGIVRVKKelpiSTKLKILNEFKEKYNTFYIQEFIKPVR--NEHRDIRAFVVDDEVVAAMYRIGGEN 208
                                   56889***********9999774554333333334445556899999998776..6788999**********999988665 PP

                     GSP_synth 366 itd 368
                                     +
  gi|15668801|ref|NP_247604.1| 209 WKN 211
                                   555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.094
                     GSP_synth  61 llarlgipeellelireSwerrepsLygRfDlaydGkgpakllEyNaDTPTsL 113
                                   ++++++i ee+ +l  ++  +    +y+ +Dl+ + ++ +k+lE+N+ TP  +
  gi|15668801|ref|NP_247604.1| 218 RVEKCEITEEIEKLALKAK-NALGLFYAGVDLIES-EDGLKVLEVNS-TPSWI 267
                                   5666666666666555544.445578999***955.789*******7.77665 PP

>> R2K_3  ATP-grasp domain, R2K clade family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.23     111     183 ..     180     262 ..     159     281 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                         R2K_3 111 evvrfsaEwRvFvvdGevvaasrYr....kanddpdl.........epdlaafaeavralvgappfyvlDvavtadGrwkV 178
                                   +v + +   R Fvvd+evvaa  Yr    +++++ ++          ++++++a  ++++   +    +D+  ++dG +kV
  gi|15668801|ref|NP_247604.1| 180 PVRNEHRDIRAFVVDDEVVAAM-YRiggeNWKNNVSQggrvekceiTEEIEKLALKAKNAL-GLFYAGVDLIESEDG-LKV 257
                                   344668899********99875.77788844444444454444444444444443333333.466678*********.*** PP

                         R2K_3 179 VEvnd 183
                                    Evn 
  gi|15668801|ref|NP_247604.1| 258 LEVNS 262
                                   ***95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1919.37
//
Query:       gi|15668802|ref|NP_247605.1|  [L=172]
Description: hypothetical protein MJ_0621 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-07   31.3   0.1    3.3e-07   30.3   0.1    1.6  1  HTH_3           Helix-turn-helix
     0.0015   18.0   0.0     0.0024   17.4   0.0    1.2  1  AbiJ_NTD3       AbiJ N-terminal domain 3
     0.0039   16.8   1.6     0.0073   15.9   0.6    1.7  1  PrpR_N          Propionate catabolism activator
     0.0057   17.1   0.0      0.012   16.0   0.0    1.6  1  HTH_26          Cro/C1-type HTH DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.029   14.3   0.0    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.012   15.7   0.2      0.031   14.4   0.0    1.7  2  HTH_17          Helix-turn-helix domain
      0.023   14.4   1.2       0.08   12.7   0.0    2.4  3  HTH_psq         helix-turn-helix, Psq domain
       0.12   12.4   0.8       0.22   11.6   0.6    1.5  1  CTP-dep_RFKase  Domain of unknown function DUF120


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.1   1.5e-10   3.3e-07       2      47 ..      22      66 ..      21      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.5e-10
                                  HHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHH CS
                         HTH_3  2 kelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklaka 47
                                  k+++++lgl+++e++e +G+++st+++ + G+   +++tl+k++k+
  gi|15668802|ref|NP_247605.1| 22 KRILLELGLTLKEFSEISGIPYSTLYKVIQGKD-FRVSTLIKILKT 66
                                  78899**************************66.*********997 PP

>> AbiJ_NTD3  AbiJ N-terminal domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.1e-06    0.0024     101     155 ..      12      66 ..       7      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
                     AbiJ_NTD3 101 eeqrrlveaiNelLrkdGyeLvetgeisgrpvysvrrigagvagrpknlifasag 155
                                   e q+++ve++ ++L + G+ L+e +eisg p  ++ ++ +g+  r++ li+ +++
  gi|15668802|ref|NP_247605.1|  12 ESQEKFVEEFKRILLELGLTLKEFSEISGIPYSTLYKVIQGKDFRVSTLIKILKT 66 
                                   679***********************************************98765 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.6   3.3e-06    0.0073      13      66 ..     112     165 ..     107     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.3e-06
                        PrpR_N  13 dleeavelakeleaegvdviiSrGgtaellrkhvsvPVveikvsgyDilralkq 66 
                                   +lee + +a ++e+egv+ i+++    + ++k v+vPV  i ++    ++al+ 
  gi|15668802|ref|NP_247605.1| 112 SLEECIVAAVRAEREGVKGIVCAPIVSATIEKIVNVPVAVIIPEKDAFMKALEI 165
                                   79999999*********************************9998888888875 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.4e-06     0.012       4      49 ..      23      66 ..      20      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.4e-06
                        HTH_26  4 elmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCda 49
                                  +++ + g+t +e+++ +gi  +tl++  +gk    + +tL ki ++
  gi|15668802|ref|NP_247605.1| 23 RILLELGLTLKEFSEISGIPYSTLYKVIQGK--DFRVSTLIKILKT 66
                                  67778899**********************9..**********886 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-05     0.029      17      44 ..      24      51 ..      17      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                  HHHHCCCHHCHHCCCTTSSCHCHHHHHH CS
                          TrmB 17 LlklgpatadeiaeelgvprskvYevLr 44
                                  +l +  +t +e +e++g+p+s+ Y+v++
  gi|15668802|ref|NP_247605.1| 24 ILLELGLTLKEFSEISGIPYSTLYKVIQ 51
                                  566667999*****************98 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.4e-05     0.031       2      31 ..      30      59 ..      30      69 .. 0.86
   2 ?   -2.7   0.0       3.1   6.9e+03      32      39 ..      99     106 ..      89     107 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                        HTH_17  2 ltveEaAelLgvsrstvyrlirrgelpaak 31
                                  lt +E++e+ g+  st+y+ i+ +++++  
  gi|15668802|ref|NP_247605.1| 30 LTLKEFSEISGIPYSTLYKVIQGKDFRVST 59
                                  8*************************9874 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.1
                        HTH_17  32 iGrrwrip 39 
                                    G++++i+
  gi|15668802|ref|NP_247605.1|  99 NGKSYLIK 106
                                   57779987 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.6e-05      0.08      27      40 ..      40      53 ..      29      56 .. 0.87
   2 ?   -2.2   0.1       1.6   3.6e+03       2      15 ..     114     127 ..     113     128 .. 0.74
   3 ?   -1.2   0.1      0.78   1.7e+03       3      13 ..     157     167 ..     155     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.6e-05
                       HTH_psq 27 giPrsTLwrrkrgk 40
                                  giP+sTL+++++gk
  gi|15668802|ref|NP_247605.1| 40 GIPYSTLYKVIQGK 53
                                  9***********97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                       HTH_psq   2 pealaaAleavvnG 15 
                                   +e + aA++a ++G
  gi|15668802|ref|NP_247605.1| 114 EECIVAAVRAEREG 127
                                   56788999986666 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.78
                       HTH_psq   3 ealaaAleavv 13 
                                   +a+ +Ale + 
  gi|15668802|ref|NP_247605.1| 157 DAFMKALEIIA 167
                                   89*****9886 PP

>> CTP-dep_RFKase  Domain of unknown function DUF120
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6    0.0001      0.22      61     103 ..     125     169 ..      96     170 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                   EETTEEE--EEEEEEEECCE...EEEEEEESS-SS.TTEEEEE-SS CS
                CTP-dep_RFKase  61 edeertfgavkvypakieki...kaavvvperthyeedvlEiiape 103
                                   +++ +    + ++ a+ieki   ++av++pe+  +  + lEiia++
  gi|15668802|ref|NP_247605.1| 125 REGVKGIVCAPIVSATIEKIvnvPVAVIIPEKDAF-MKALEIIAKK 169
                                   33334444455566777655455999*********.899****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1109.37
//
Query:       gi|15668803|ref|NP_247606.1|  [L=403]
Description: cell division protein FtsZ [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-43  149.4   1.8    2.5e-43  148.6   1.8    1.4  1  Tubulin      Tubulin/FtsZ family, GTPase domain
      4e-38  129.6   4.0    2.7e-37  127.0   0.2    3.3  3  FtsZ_C       FtsZ family, C-terminal domain
     0.0052   16.2   0.0       0.01   15.2   0.0    1.5  1  ThiF         ThiF family
  ------ inclusion threshold ------
      0.015   14.6   2.6      0.032   13.5   2.6    1.6  1  AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
      0.024   14.9   1.6       0.96    9.7   0.5    2.9  2  TrkA_N       TrkA-N domain
        4.3    6.4   9.2        7.3    5.7   4.0    2.5  2  Tubulin_2    Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.6   1.8   8.2e-47   2.5e-43       1     196 [.      62     221 ..      62     222 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.6 bits;  conditional E-value: 8.2e-47
                                   EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE--CC CS
                       Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllgke 81 
                                   +i+v+g+G++Gn+++n+l+e      gi             +g +e+i    ai+td+q+l+ i+a+      +k+l+g +
  gi|15668803|ref|NP_247606.1|  62 RIVVVGCGGAGNNTINRLME-----IGI-------------QG-AETI----AINTDKQHLEVIQAD------KKILIGAT 113
                                   59******************.....599.............88.7787....***************......******** PP

                                   CCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG.G CS
                       Tubulin  82 gagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefse 162
                                    ++++gaggype+g++aae  +++++++++++d+   +f+ta++gGGTG+G +pv++ev+ke+  +a+vv+vv++P+++  
  gi|15668803|ref|NP_247606.1| 114 LTRGLGAGGYPEIGRKAAEMAKNILEEQLKGADL---VFVTAGMGGGTGTGSAPVVAEVAKEN--GAIVVGVVTYPFKI-- 187
                                   **********************************...**************************..*************9.. PP

                                   -HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                       Tubulin 163 vvvepynailalkelieesdavividNdaLlkil 196
                                   +  ++++a +++ +++e +d+vi+idN++Ll+++
  gi|15668803|ref|NP_247606.1| 188 ERARMKKADEGIARMSEVCDTVIIIDNNKLLDLV 221
                                   899***************************9976 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.55   1.6e+03      26      42 ..      77      93 ..      70     108 .. 0.81
   2 ?    1.6   0.1      0.11   3.4e+02      20      48 ..     131     155 ..     111     184 .. 0.63
   3 !  127.0   0.2     9e-41   2.7e-37       1      95 []     269     366 ..     269     366 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.55
                                  SGGGT--GGG-SEEEEE CS
                        FtsZ_C 26 spLLdvdlsgAkgvlvn 42
                                  + L+++ ++gA+++ +n
  gi|15668803|ref|NP_247606.1| 77 NRLMEIGIQGAETIAIN 93
                                  5699999****999888 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.11
                                   HHHHHTSGGGT--GGG-SEEEEEEEE-TT CS
                        FtsZ_C  20 aeaaisspLLdvdlsgAkgvlvnitggsd 48 
                                   ae  +++++L+ +l+gA   lv +t+g+ 
  gi|15668803|ref|NP_247606.1| 131 AE--MAKNILEEQLKGAD--LVFVTAGMG 155
                                   44..45789999999997..555666654 PP

  == domain 3  score: 127.0 bits;  conditional E-value: 9e-41
                                   EEEEEEEEEEESTTHHH...HHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE- CS
                        FtsZ_C   1 GvAmmgvGeasgedrae...eaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavid 78 
                                   GvAm+gvGe++++dr++   +++++++s+pLLdvd++gAkg+l++itgg+dltlkE+++++e i++e+d+eanvi+Ga+id
  gi|15668803|ref|NP_247606.1| 269 GVAMIGVGEVDSSDRGDrvqNVVRETLSCPLLDVDYRGAKGALIHITGGPDLTLKEANDIGEGITKELDPEANVIWGARID 349
                                   99********996654333399*********************************************************** PP

                                   TT--SEEEEEEEEES-X CS
                        FtsZ_C  79 eeledeirvtvvatglk 95 
                                   +e+e++irv++++tg+k
  gi|15668803|ref|NP_247606.1| 350 PEMEGCIRVMAIITGVK 366
                                   ***************96 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.4e-06      0.01      17      44 ..      55      98 ..      31     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.4e-06
                                  HT....SEEEEE--SHHHHHHHHHHHHHTTT............E CS
                                  xx....xxxxxxxxxxxxxxxxxxxxxxxxx............x RF
                          ThiF 17 rd....skvllvGaGglGsellknLalsGvg............k 44
                                  +d    +++++vG+Gg G++ +  L+ +G++            +
  gi|15668803|ref|NP_247606.1| 55 KDefgeARIVVVGCGGAGNNTINRLMEIGIQgaetiaintdkqH 98
                                  4444449**********************986665555555555 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.6   1.1e-05     0.032      28     103 ..      60     156 ..      56     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                                   --EEEEESTSHHHHHHHHHHHHT...T-EEEEEESSHHHHHHHHHTTTCECEE..................HCHHHHHHHH CS
                   AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakgl...gakVtvlDvrparleqleslgakfvev..................lksqeellae 87 
                                   +a+++v+G G aG + i+  +++   ga++ +++++++ le +++ ++  + +                   +  ++ l+e
  gi|15668803|ref|NP_247606.1|  60 EARIVVVGCGGAGNNTINRLMEIgiqGAETIAINTDKQHLEVIQADKKILIGAtltrglgaggypeigrkaAEMAKNILEE 140
                                   69****************9999833458999999999999999985555454466679***********9888889999** PP

                                   HHHH-SEEEE---BTT CS
                   AlaDh_PNT_C  88 avkeadvvigtvlipG 103
                                   ++k ad+v  t+ + G
  gi|15668803|ref|NP_247606.1| 141 QLKGADLVFVTAGMGG 156
                                   ********99987665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.5   0.00032      0.96       1      40 [.      63     105 ..      63     115 .. 0.86
   2 ?    2.8   0.0     0.046   1.4e+02      33      80 ..     165     212 ..     161     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00032
                                   EEEES-SHHHHHHHHHHHH.TT..EEEEEEESSHHHHHHHHHT CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.gg..kdvvvidkdeerveelree 40 
                                   i+++G+G  G + +++L+e g    + ++i +d++++e ++++
  gi|15668803|ref|NP_247606.1|  63 IVVVGCGGAGNNTINRLMEiGIqgAETIAINTDKQHLEVIQAD 105
                                   89*****************76589569*******999987754 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.046
                                   HHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHH CS
                        TrkA_N  33 rveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilav 80 
                                   +v+e+++e+  +vvg +t +  +e+a ++kad  ia +++  ++++++
  gi|15668803|ref|NP_247606.1| 165 VVAEVAKENGAIVVGVVTYPFKIERARMKKADEGIARMSEVCDTVIII 212
                                   5788888999999******************99888887766666655 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.014        43       1      18 [.      64      81 ..      64     103 .. 0.89
   2 ?    5.7   4.0    0.0025       7.3     115     174 ..     118     164 ..      84     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.014
                     Tubulin_2  1 lviGLGGtGgkvlaelrr 18
                                  +v+G+GG G +++++l++
  gi|15668803|ref|NP_247606.1| 64 VVVGCGGAGNNTINRLME 81
                                  69************9986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0025
                     Tubulin_2 115 eGAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGifl 174
                                    GAG+++ +GR a    +e +++ l++++k +           vfV  ++ GGTG G++ 
  gi|15668803|ref|NP_247606.1| 118 LGAGGYPEIGRKA----AEMAKNILEEQLKGADL---------VFVTAGMGGGTGTGSAP 164
                                   5777777777765....34445555555555444.........**************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2600.45
//
Query:       gi|15668804|ref|NP_247607.1|  [L=192]
Description: hypothetical protein MJ_0623 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-30  106.8   0.0    1.7e-30  106.4   0.0    1.2  1  Metallophos_2    Calcineurin-like phosphoesterase superfamily
    3.9e-08   34.0   1.9    3.7e-05   24.3   0.7    2.2  2  Metallophos      Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
       0.13   12.8   0.4       0.27   11.8   0.4    1.4  1  Antimicrobial_2  Frog antimicrobial peptide


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.4   0.0   2.9e-34   1.7e-30       1     162 [.      34     179 ..      34     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 2.9e-34
                 Metallophos_2   1 MklaiiSDlH...snldaleavlealkevgvdaiihaGDleeeepevleellelapvlaVrGNnDeevveedvlreaaelg 78 
                                   M +++iSD+H   +++++++av++++++v  d+iih+GD+  ++ e+l+ l++la+v+aV+GN+D                
  gi|15668804|ref|NP_247607.1|  34 MLIGVISDTHlydRAFELPKAVFDEFSNV--DLIIHCGDV--TDKEILDSLKDLAKVVAVKGNMD---------------Y 95 
                                   99***************************..********9..999********************...............8 PP

                 Metallophos_2  79 tdlpeeaelelagekvlliHgdpl...gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgdpet 156
                                    +lp ++ le+++ k+++iHgd     g++ +l+ l ke  +g+dv+++GHtH+p +++++++l++nPGs++ pr   + +
  gi|15668804|ref|NP_247607.1|  96 LNLPRKEILEINDIKIGVIHGDVVyprGDRLKLRLLGKE--MGVDVLISGHTHTPFIDDCRDILLLNPGSPTVPRCPLK-S 173
                                   99*******************966988888888888888..********************************997776.6 PP

                 Metallophos_2 157 yaildt 162
                                   ++ l++
  gi|15668804|ref|NP_247607.1| 174 IMKLSV 179
                                   655555 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.7   6.3e-09   3.7e-05       3      76 ..      36      97 ..      34     121 .. 0.79
   2 !    9.4   0.1   0.00023       1.4     178     204 .]     121     148 ..     102     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.3e-09
                                  EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS..C CS
                   Metallophos  3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe..g 76
                                  i vi+D+H  l +  ++  ++++d++   +++dl++++GD++d       +l+ l+ l k    v++++GN +  +
  gi|15668804|ref|NP_247607.1| 36 IGVISDTH--LYDRAFELPKAVFDEF---SNVDLIIHCGDVTDKE-----ILDSLKDLAK----VVAVKGNMDylN 97
                                  89******..8889999999999999...799********99998.....6666777777....899******331 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00023
                                   SCCHHHHHHH.HHHTTESEEEEESSSSE CS
                   Metallophos 178 lfgdealedl.lkkygvdlvisGHtHvy 204
                                   + gd+   +l  k+ gvd+ isGHtH++
  gi|15668804|ref|NP_247607.1| 121 PRGDRLKLRLlGKEMGVDVLISGHTHTP 148
                                   4455555566689999**********85 PP

>> Antimicrobial_2  Frog antimicrobial peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   4.5e-05      0.27       2      16 ..      76      91 ..      76      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.5e-05
               Antimicrobial_2  2 iLstlKgvAKgvA.Kg 16
                                  iL++lK++AK vA Kg
  gi|15668804|ref|NP_247607.1| 76 ILDSLKDLAKVVAvKG 91
                                  9***********9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1303.29
//
Query:       gi|15668805|ref|NP_247608.1|  [L=58]
Description: ferredoxin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-16   59.1  16.4    2.5e-08   33.4   5.1    2.1  2  Fer4      4Fe-4S binding domain
    2.3e-10   39.9  12.4    3.8e-05   23.5   2.9    2.2  2  Fer4_2    4Fe-4S binding domain
    2.4e-10   40.0  16.1    2.6e-05   24.1   5.3    2.1  2  Fer4_6    4Fe-4S binding domain
      1e-09   38.4  22.3    5.2e-07   29.7  12.1    1.6  2  Fer4_9    4Fe-4S dicluster domain
    4.9e-09   36.7  26.4    1.5e-06   28.7  15.2    2.0  2  Fer4_7    4Fe-4S dicluster domain
    2.5e-08   34.7  11.3    0.00034   21.5   3.2    2.0  2  Fer4_16   4Fe-4S double cluster binding domain
    6.2e-08   32.6  11.2    8.2e-05   22.8   1.8    2.1  2  Fer4_4    4Fe-4S binding domain
    7.6e-08   32.4  12.7    1.5e-07   31.4  12.7    1.5  1  Fer4_21   4Fe-4S dicluster domain
    3.4e-07   30.3  13.5    8.7e-05   22.6  14.2    2.0  2  Fer4_10   4Fe-4S dicluster domain
    0.00013   22.4  11.8      0.068   13.7   3.9    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    0.00016   22.0  13.0      0.012   16.0   2.1    2.1  2  Fer4_8    4Fe-4S dicluster domain
    0.00034   21.1  14.1      0.064   13.8   2.5    2.1  2  Fer4_17   4Fe-4S dicluster domain
    0.00047   20.9  18.0      0.021   15.7   6.1    2.2  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.028   15.2  12.9       0.92   10.3   3.0    2.5  2  Fer4_15   4Fe-4S single cluster domain
      0.039   13.8   1.6      0.039   13.8   1.6    3.0  2  RLI       Possible Fer4-like domain in RNase L inhibitor, RLI
      0.083   13.7  15.2       0.58   11.0   5.0    2.1  2  Fer4_22   4Fe-4S dicluster domain
        0.4   10.9  12.0        2.6    8.2   2.0    2.0  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   3.5   6.7e-11     7e-08       4      24 .]       5      25 ..       3      25 .. 0.92
   2 !   33.4   5.1   2.4e-11   2.5e-08       2      24 .]      31      53 ..      30      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 6.7e-11
                                  ETTTSSS-THHHHHSTTTEEE CS
                          Fer4  4 deekCigCGaCvevCPvgAIt 24
                                  + ekC+gCG+Cv  CP  AI+
  gi|15668805|ref|NP_247608.1|  5 ILEKCVGCGNCVVFCPRRAIK 25
                                  679****************96 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 2.4e-11
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  ++de+kC +CG+C+  CP +AI+
  gi|15668805|ref|NP_247608.1| 31 IVDENKCSNCGICARYCPINAIK 53
                                  79********************6 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   2.1   1.1e-07   0.00011       8      21 ..       7      20 ..       3      21 .. 0.91
   2 !   23.5   2.9   3.6e-08   3.8e-05       3      21 ..      30      48 ..      28      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.1e-07
                        Fer4_2  8 drCigCgaCvsaCP 21
                                  ++C+gCg Cv  CP
  gi|15668805|ref|NP_247608.1|  7 EKCVGCGNCVVFCP 20
                                  89************ PP

  == domain 2  score: 23.5 bits;  conditional E-value: 3.6e-08
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  + vd+++C +Cg+C   CP
  gi|15668805|ref|NP_247608.1| 30 AIVDENKCSNCGICARYCP 48
                                  679***************9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   3.0   1.2e-07   0.00012       7      24 .]       7      24 ..       5      24 .. 0.91
   2 !   24.1   5.3   2.4e-08   2.6e-05       2      24 .]      30      52 ..      29      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-07
                        Fer4_6  7 dkCigCgdCvrvCPegai 24
                                  +kC+gCg+Cv+ CP  ai
  gi|15668805|ref|NP_247608.1|  7 EKCVGCGNCVVFCPRRAI 24
                                  79************8876 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 2.4e-08
                        Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                  + +d++kC  Cg C+r CP +ai
  gi|15668805|ref|NP_247608.1| 30 AIVDENKCSNCGICARYCPINAI 52
                                  679****************9998 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   2.5   7.9e-07   0.00083      34      51 .]       7      24 ..       3      24 .. 0.85
   2 !   29.7  12.1   4.9e-10   5.2e-07       1      51 []       8      52 ..       8      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.9e-07
                        Fer4_9 34 eaCigCgaCveaCpkgai 51
                                  e+C+gCg Cv  Cp+ ai
  gi|15668805|ref|NP_247608.1|  7 EKCVGCGNCVVFCPRRAI 24
                                  579999999999999887 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 4.9e-10
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  kC+gCg+Cv  Cp  +++   ++  +++      +C  Cg C+  Cp +ai
  gi|15668805|ref|NP_247608.1|  8 KCVGCGNCVVFCPRRAIKTYGVAIVDEN------KCSNCGICARYCPINAI 52
                                  7************************998......7************9887 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7  15.2   1.4e-09   1.5e-06       1      52 []       8      51 ..       8      51 .. 0.92
   2 !   18.9   3.4   1.6e-06    0.0017       1      20 [.      36      55 ..      36      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.4e-09
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  +C+gCg+Cv+ Cp +ai++  +        + +d++kC++Cg C++ CP +a
  gi|15668805|ref|NP_247608.1|  8 KCVGCGNCVVFCPRRAIKTYGV--------AIVDENKCSNCGICARYCPINA 51
                                  7*****************9665........678999*************987 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.6e-06
                        Fer4_7  1 rCigCgaCvaaCpvkaield 20
                                  +C +Cg C+++Cp +ai++d
  gi|15668805|ref|NP_247608.1| 36 KCSNCGICARYCPINAIKVD 55
                                  7****************987 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   3.2   3.2e-07   0.00034       1      31 [.       8      38 ..       8      39 .. 0.89
   2 !   19.6   2.8   1.3e-06    0.0013       1      20 [.      36      55 ..      36      58 .] 0.91

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.2e-07
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkekeieareci 31
                                  +C++Cg+C+  CP +aik+   + ++ ++c 
  gi|15668805|ref|NP_247608.1|  8 KCVGCGNCVVFCPRRAIKTYGVAIVDENKCS 38
                                  6*****************9977888888885 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.3e-06
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  +C +Cg Ca  CP naik +
  gi|15668805|ref|NP_247608.1| 36 KCSNCGICARYCPINAIKVD 55
                                  5****************987 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   1.8   7.8e-08   8.2e-05       2      16 ..       7      21 ..       6      28 .. 0.90
   2 !   15.4   2.2   1.8e-05     0.019       2      15 ..      35      48 ..      34      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.8e-08
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  e+C+gCg Cv +CP 
  gi|15668805|ref|NP_247608.1|  7 EKCVGCGNCVVFCPR 21
                                  89************5 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.8e-05
                        Fer4_4  2 erCigCgsCvaaCP 15
                                  ++C +Cg C ++CP
  gi|15668805|ref|NP_247608.1| 35 NKCSNCGICARYCP 48
                                  79***********9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4  12.7   1.4e-10   1.5e-07       6      58 ..       7      53 ..       3      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.4e-10
                       Fer4_21  6 dkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                  +kC+gCg+C++ C+     ai++ +  v+ v e++C  C +C+  CP+ ++i+
  gi|15668805|ref|NP_247608.1|  7 EKCVGCGNCVVFCP---RRAIKTYG--VAIVDENKCSNCGICARYCPI-NAIK 53
                                  79************...59999765..45599***************9.9987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6  14.2   8.2e-08   8.7e-05       6      56 .]       6      48 ..       2      48 .. 0.78
   2 !   17.9   3.1   2.4e-06    0.0026       3      25 ..      31      53 ..      29      58 .] 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.2e-08
                       Fer4_10  6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   ++C++Cg+Cv +CP      +a++ +    +++    kC +cg C++ CP
  gi|15668805|ref|NP_247608.1|  6 LEKCVGCGNCVVFCPR-----RAIKTYGVAIVDE---NKCSNCGICARYCP 48
                                  689*************.....4454444444444...59999********9 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.4e-06
                       Fer4_10  3 vidddtCirCgkCvkaCPadlts 25
                                  ++d+++C +Cg C + CP ++ +
  gi|15668805|ref|NP_247608.1| 31 IVDENKCSNCGICARYCPINAIK 53
                                  7899**************96544 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.8   7.7e-05     0.081       4      18 ..       7      21 ..       6      22 .. 0.92
   2 !   13.7   3.9   6.4e-05     0.068       1      17 [.      32      48 ..      32      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-05
                       Fer4_13  4 dtCiacgaCvelaPd 18
                                  ++C++cg+Cv ++P 
  gi|15668805|ref|NP_247608.1|  7 EKCVGCGNCVVFCPR 21
                                  79************5 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.4e-05
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  VD+++C++cg+C+  +P
  gi|15668805|ref|NP_247608.1| 32 VDENKCSNCGICARYCP 48
                                  9***************9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   2.1   1.1e-05     0.012      46      63 ..       4      21 ..       1      24 [. 0.81
   2 !   11.7   3.5   0.00025      0.26      49      63 ..      35      49 ..      26      51 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                        Fer4_8 46 ealwsCttcgaCtevCpv 63
                                  ++l++C++cg+C++ Cp 
  gi|15668805|ref|NP_247608.1|  4 KILEKCVGCGNCVVFCPR 21
                                  568889999999999996 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00025
                        Fer4_8 49 wsCttcgaCtevCpv 63
                                  ++C++cg C++ Cp+
  gi|15668805|ref|NP_247608.1| 35 NKCSNCGICARYCPI 49
                                  456666666666665 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   2.5   6.1e-05     0.064      43      58 ..       6      21 ..       2      23 .. 0.86
   2 !   13.5   3.8   7.5e-05      0.08      44      58 ..      35      49 ..      22      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.1e-05
                       Fer4_17 43 aslCieCgeCerkCPq 58
                                   ++C++Cg+C+  CP 
  gi|15668805|ref|NP_247608.1|  6 LEKCVGCGNCVVFCPR 21
                                  579***********96 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.5e-05
                       Fer4_17 44 slCieCgeCerkCPq 58
                                  ++C++Cg C+r+CP 
  gi|15668805|ref|NP_247608.1| 35 NKCSNCGICARYCPI 49
                                  678888888888884 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   6.1     2e-05     0.021       1      15 []       9      23 ..       9      23 .. 0.96
   2 !   11.3   4.0   0.00052      0.54       1      15 []      37      51 ..      37      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-05
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gCg Cv+ CP +A
  gi|15668805|ref|NP_247608.1|  9 CVGCGNCVVFCPRRA 23
                                  ************987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00052
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C +Cg C + CP +A
  gi|15668805|ref|NP_247608.1| 37 CSNCGICARYCPINA 51
                                  99**********998 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.4   0.00092      0.97       6      21 ..       7      22 ..       6      31 .. 0.83
   2 ?   10.3   3.0   0.00087      0.92       3      19 ..      32      48 ..      30      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00092
                       Fer4_15  6 daCigcglCvaeapev 21
                                  ++C gcg+Cv  +p++
  gi|15668805|ref|NP_247608.1|  7 EKCVGCGNCVVFCPRR 22
                                  68***********964 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00087
                       Fer4_15  3 vDrdaCigcglCvaeap 19
                                  vD+++C  cg C++ +p
  gi|15668805|ref|NP_247608.1| 32 VDENKCSNCGICARYCP 48
                                  9**************98 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.9     0.073        77      21      32 ..      15      26 ..       7      28 .. 0.88
   2 ?   13.8   1.6   3.7e-05     0.039       3      31 ..      29      53 ..      27      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.073
                                  HHHTTSEEEESS CS
                           RLI 21 carfcpvrlvrt 32
                                  c+ fcp r+++t
  gi|15668805|ref|NP_247608.1| 15 CVVFCPRRAIKT 26
                                  999*****9998 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.7e-05
                                  EEEES---------TTHHHHHTTSEEEES CS
                           RLI  3 lAivdadqCdPKKCtgkkcarfcpvrlvr 31
                                  +Aivd+++C  + C    car+cp+ +++
  gi|15668805|ref|NP_247608.1| 29 VAIVDENKC--SNCGI--CARYCPINAIK 53
                                  8********..78**9..*******7766 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   5.0   0.00055      0.58      81      94 ..       8      21 ..       4      24 .. 0.84
   2 ?    8.9   2.5    0.0025       2.6      78      94 ..      33      49 ..      23      51 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00055
                       Fer4_22 81 gCvGCgRCieacpv 94
                                  +CvGCg C+  cp 
  gi|15668805|ref|NP_247608.1|  8 KCVGCGNCVVFCPR 21
                                  79999999999986 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0025
                       Fer4_22 78 gesgCvGCgRCieacpv 94
                                  +e++C  Cg C + cp 
  gi|15668805|ref|NP_247608.1| 33 DENKCSNCGICARYCPI 49
                                  67778888888888875 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  11.7     0.012        12      59      95 ..       7      47 ..       3      47 .. 0.79
   2 ?    8.2   2.0    0.0025       2.6      57      74 ..      33      50 ..      24      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                       Fer4_18 59 gdcidcescvkvcPtgidirkGlql....eciscllcidac 95
                                   +c+ c+ cv  cP       G+ +    +c +c+ c   c
  gi|15668805|ref|NP_247608.1|  7 EKCVGCGNCVVFCPRRAIKTYGVAIvdenKCSNCGICARYC 47
                                  58************9876667776544448*******8776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0025
                       Fer4_18 57 gagdcidcescvkvcPtg 74
                                  ++++c +c+ c + cP++
  gi|15668805|ref|NP_247608.1| 33 DENKCSNCGICARYCPIN 50
                                  5789************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 382.59
//
Query:       gi|15668806|ref|NP_247609.1|  [L=336]
Description: hypothetical protein MJ_0625 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-66  223.5   7.9    3.3e-66  223.5   7.9    2.0  2  ATPase_2      ATPase domain predominantly from Archaea
    2.1e-11   44.5   0.0    3.1e-11   44.0   0.0    1.3  1  AAA_16        AAA ATPase domain
    3.7e-10   40.2   0.0    7.8e-10   39.2   0.0    1.5  1  AAA_22        AAA domain
    1.4e-07   31.6  10.8    1.4e-05   25.1   0.1    3.4  3  AAA_14        AAA domain
    1.2e-06   28.9   0.1    8.2e-06   26.3   0.1    2.2  1  AAA           ATPase family associated with various cellular 
     0.0028   16.4   0.2       0.45    9.2   0.0    2.5  3  RNA12         RNA12 protein
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.025   14.1   0.0    1.5  1  AAA_7         P-loop containing dynein motor region
      0.013   15.8   0.0      0.064   13.7   0.0    2.2  2  RNA_helicase  RNA helicase
      0.019   15.1   0.0      0.077   13.1   0.0    2.0  3  AAA_33        AAA domain
      0.044   13.7   0.2       0.21   11.5   0.1    2.2  2  NTPase_1      NTPase
      0.054   12.9   0.6        6.6    6.1   0.0    2.6  3  TniB          Bacterial TniB protein
      0.094   12.6   0.0          1    9.2   0.0    2.2  1  NACHT         NACHT domain
       0.19   11.8   1.0        7.6    6.7   0.0    2.9  2  MMR_HSR1      50S ribosome-binding GTPase
       0.19   11.5   0.0       0.39   10.5   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
        2.3    8.0   8.3        5.1    6.9   0.2    4.0  3  DnaB_2        Replication initiation and membrane attachment


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.5   7.9   2.8e-69   3.3e-66       1     233 []       3     236 ..       3     236 .. 0.97
   2 ?    0.6   1.7      0.37   4.5e+02      37      94 ..     250     301 ..     248     331 .. 0.61

  Alignments for each domain:
  == domain 1  score: 223.5 bits;  conditional E-value: 2.8e-69
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...eeeekkkl 78 
                                   F++Rekel++l+++++ +pn+i+f+YGp++sGK+++++++i++led++  v++y++lr++++ +++ef++   e++ekk+l
  gi|15668806|ref|NP_247609.1|   3 FYNREKELNYLKTYCQLDPNSILFVYGPKSSGKSTVMRRVIKELEDSN-IVFFYYNLRKYATYSKEEFLRvffEKSEKKYL 82 
                                   9*******************************************9976.7******************************* PP

                      ATPase_2  79 ekal..giavpkaeleeilk...eksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltk 154
                                    ++l  +  v k+ +ee ++    k ++vf++i++ ++++ ++gkk+++iiDelqkl+++++ng ++l++eL+nl++sltk
  gi|15668806|ref|NP_247609.1|  83 LNKLelNLGVFKFGVEENFDfnnLKLNDVFAKINESINAVVEDGKKPVLIIDELQKLKNIYFNGGKSLLNELFNLFVSLTK 163
                                   **997778899999*****9988899******************************************************* PP

                      ATPase_2 155 ekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkeleelskedfeeiyryvGGkPkalvel 233
                                    +hlc+vicl+S++lfie++y++s+le+++ky+l+d+l+k t++n+lke     e++s+e+++++ +y+ + P+++v+l
  gi|15668806|ref|NP_247609.1| 164 MEHLCHVICLTSDTLFIEEIYQSSTLENTSKYYLIDWLRKGTIRNILKE-----EGFSEEEINYCLDYL-SLPYEIVDL 236
                                   *************************************************.....799************.9***99976 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.37
                      ATPase_2  37 lkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleei 94 
                                   +++ i+  +dk ky i  ++l ee++ k+ +++     k+k++    ++v+k e+ + 
  gi|15668806|ref|NP_247609.1| 250 IRQWINIEKDKIKYLIDTTDLDEEELYKVLSKF-----KDKIKISYEKEVKKEEM-KY 301
                                   678888888888888888888877777665553.....33333333334444444.23 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   2.6e-14   3.1e-11       1     156 [.       2     152 ..       2     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.6e-14
                        AAA_16   1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy.sa.laqalar 78 
                                   +++ Re+el    ++l++ ++ +p ++++++G++ +GKs+++r++ ++le+++++f++ + +++   ++y    +++++++
  gi|15668806|ref|NP_247609.1|   2 KFYNREKEL----NYLKTYCQLDPnSILFVYGPKSSGKSTVMRRVIKELEDSNIVFFYYNLRKY---ATYsKEeFLRVFFE 75 
                                   6899****8....6667677777779******************************99999999...88853359999988 PP

                        AAA_16  79 eellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwade....aslqll 155
                                   ++  + ll+++e  +l+ ++   ee++   ++l+    +++++++++ ++   +d+++ vl++D+lq+++     +  +ll
  gi|15668806|ref|NP_247609.1|  76 KSEKKYLLNKLEL-NLGVFKFGVEENFD-FNNLKL---NDVFAKINESINAVVEDGKKPVLIIDELQKLKNiyfnGGKSLL 151
                                   8888888888666.88888888888877.333333...89999999999555555777*********98765555555555 PP

                        AAA_16 156 a 156
                                    
  gi|15668806|ref|NP_247609.1| 152 N 152
                                   4 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   6.5e-13   7.8e-10       5     126 ..      22     170 ..      19     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 6.5e-13
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsst..sskdllrellralglelka........... 70 
                                    +il+v+G++ +GK+t++rr+ ++l+        ++ +v  +++l +    s +++lr ++++ + +  +           
  gi|15668806|ref|NP_247609.1|  22 NSILFVYGPKSSGKSTVMRRVIKELE--------DSNIVffYYNLRKYAtySKEEFLRVFFEKSEKK--Yllnklelnlgv 92 
                                   589**********************6........555556799999988999999999999999943..356899999999 PP

                        AAA_22  71 ...........erlsseellealeqalrarav...ielliiDEaqhlr....s......eealeeLrsllnlsrkgvqli 126
                                              ++l++ ++++++++ ++a      +++liiDE q+l     +      +e+++ ++sl +    ++ ++
  gi|15668806|ref|NP_247609.1|  93 fkfgveenfdfNNLKLNDVFAKINESINAVVEdgkKPVLIIDELQKLKniyfNggksllNELFNLFVSLTK--MEHLCHV 170
                                   99*********9999999999999999999889999***********655551663344444444455555..4444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   1.2e-08   1.4e-05       2      68 ..      22      82 ..      21      84 .. 0.72
   2 !   11.6   0.6   0.00018      0.21      38      77 ..     101     152 ..      84     201 .. 0.62
   3 ?   -0.4   0.6       0.9   1.1e+03      25      67 ..     252     301 ..     244     323 .. 0.54

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.2e-08
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktyl 68
                                  + il++ G++ +GK+t+++++ikel   +++i+++  +  ++++++++ ++l++++ek    +k+yl
  gi|15668806|ref|NP_247609.1| 22 NSILFVYGPKSSGKSTVMRRVIKELE--DSNIVFFYYNLRKYATYSKE-EFLRVFFEKS---EKKYL 82
                                  5799******************9988..66666555555555555544.4799999973...44554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00018
                        AAA_14  38 ldderdkkladpekllelileklkeekktylflDEiqev............p 77 
                                   +d +++k ++ ++k++e i + +++ kk +l++DE q++            +
  gi|15668806|ref|NP_247609.1| 101 FDFNNLKLNDVFAKINESINAVVEDGKKPVLIIDELQKLkniyfnggksllN 152
                                   33333332333445555555555457999**********4444444433333 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.9
                        AAA_14  25 ell.vkkesilyi....nldderdkk.ladpekllelilek.lkeekkty 67 
                                   + + ++k++i y+    +ld+e+++k l+++++ +++  ek +k+e+++y
  gi|15668806|ref|NP_247609.1| 252 QWInIEKDKIKYLidttDLDEEELYKvLSKFKDKIKISYEKeVKKEEMKY 301
                                   44455555665543322555555544233444444444444344444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   6.8e-09   8.2e-06       2     111 ..      26     176 ..      25     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.8e-09
                                   EEESSTTSSHHHHHHHHHHHHTHE.......................EEEEETTTCS.SS..................... CS
                           AAA   2 llyGppGtGKTllakavakelgve.......................fleisgsell.sk..................... 37 
                                    +yGp+  GK+++++ v+kel+ +                       f+e s ++ l +k                     
  gi|15668806|ref|NP_247609.1|  26 FVYGPKSSGKSTVMRRVIKELEDSnivffyynlrkyatyskeeflrvFFEKSEKKYLlNKlelnlgvfkfgveenfdfnnl 106
                                   68******************9522233333444444455555555554444444444455999999999999995555555 PP

                                   STTHHHHHHHHHHHHHHHTS.......TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                           AAA  38 yvgesekkirelfkeakeka.......kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                           ++++f+++ e+        k+ +l+iDE+ +l +       + +++++n+L++ +  ++k e+ + vi+ t +
  gi|15668806|ref|NP_247609.1| 107 K-------LNDVFAKINESInavvedgKKPVLIIDELQKLKNIY----FNGGKSLLNELFNLFVSLTKMEHLCHVICLTSD 176
                                   2.......4444444433333444444569**********7666....667899*****************9****99986 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00038      0.45       1      43 [.       6      47 ..       6      56 .. 0.86
   2 ?    4.2   0.0     0.012        15     145     198 ..     124     182 ..     105     194 .. 0.77
   3 ?   -2.8   0.2       1.6   1.9e+03     329     359 ..     266     296 ..     234     308 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00038
                         RNA12  1 RkekiedlkewleEnvntFivvkGPrGSGkkeLvldrvlkdrk 43
                                  R+++ + lk++ +  +n+ + v GP+ SGk+  v+ rv+k+ +
  gi|15668806|ref|NP_247609.1|  6 REKELNYLKTYCQLDPNSILFVYGPKSSGKST-VMRRVIKELE 47
                                  77889999**********************86.77***99865 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.012
                         RNA12 145 hpeakPvvvidnflakaek....ngvvykklaeWaasLvqs.niahVifltedvsaska 198
                                    + +kPv++id+ ++ ++      + + ++l +   sL+++  + hVi lt+d+ +  +
  gi|15668806|ref|NP_247609.1| 124 EDGKKPVLIIDELQKLKNIyfngGKSLLNELFNLFVSLTKMeHLCHVICLTSDTLFIEE 182
                                   45689*******99877655644678999999999999997258********9876655 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.6
                         RNA12 329 kkakwtkeqaWklikklskkgsieynellle 359
                                   +++++++e+ +k+++k  +k +i+y++ +++
  gi|15668806|ref|NP_247609.1| 266 DTTDLDEEELYKVLSKFKDKIKISYEKEVKK 296
                                   2344455555555666655556666555555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.1e-05     0.025      36      91 ..      25      79 ..       9      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                         AAA_7 36 vllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrk 91
                                  ++++Gp+ +GK++++++++k+l+++++++   n+ ++ + ++  +++   +ek +k
  gi|15668806|ref|NP_247609.1| 25 LFVYGPKSSGKSTVMRRVIKELEDSNIVFFYYNLRKYATYSK-EEFLRVFFEKSEK 79
                                  4567*************************9999998876544.4455555555444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.4e-05     0.064       1      27 [.      25      56 ..      25      82 .. 0.77
   2 ?   -1.9   0.0       3.6   4.3e+03      51      76 ..     129     157 ..     126     180 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl.....k 27
                                  +++yGp+  GKSt++++++k+l+++       
  gi|15668806|ref|NP_247609.1| 25 LFVYGPKSSGKSTVMRRVIKELEDSNivffyY 56
                                  589*******************9765455542 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
                  RNA_helicase  51 evvvidDfgqvkdee.nps..dlaelirl 76 
                                   +v++id++ + k+ + n     l+el++l
  gi|15668806|ref|NP_247609.1| 129 PVLIIDELQKLKNIYfNGGksLLNELFNL 157
                                   67788888877776654322244444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.5e-05     0.077       2      25 ..      25      51 ..      24     123 .. 0.86
   2 ?   -2.2   0.0       3.5   4.1e+03      25      53 ..     170     202 ..     158     226 .. 0.62
   3 ?   -2.0   0.0       3.1   3.7e+03      66      90 ..     256     280 ..     227     288 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                        AAA_33  2 vllvGlpGsGKstlaerllkklg...a 25
                                  +++ G++ sGKst+ +r++k+l     
  gi|15668806|ref|NP_247609.1| 25 LFVYGPKSSGKSTVMRRVIKELEdsnI 51
                                  6889****************9986541 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.5
                        AAA_33  25 avllssdtlrr.rlfg...tdqqsktdytrvld 53 
                                   ++ l+sdtl+   ++     +++sk +++++l 
  gi|15668806|ref|NP_247609.1| 170 VICLTSDTLFIeEIYQsstLENTSKYYLIDWLR 202
                                   677888885443555555444445555555554 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.1
                        AAA_33  66 alsagrnvildatnlsrrerarflk 90 
                                     + ++ +++d t l+++e  ++l+
  gi|15668806|ref|NP_247609.1| 256 IEKDKIKYLIDTTDLDEEELYKVLS 280
                                   4567788888888888877766555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00018      0.21       2      29 ..      25      52 ..      24     143 .. 0.67
   2 ?   -1.8   0.0       2.1   2.5e+03      47      81 ..     231     270 ..     214     289 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                  EEEE--TTSSHHHHHHHHHHHH...GGG CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvk 29
                                  +f+ Gp  +GK+T++++v+++l++s++ 
  gi|15668806|ref|NP_247609.1| 25 LFVYGPKSSGKSTVMRRVIKELEDSNIV 52
                                  5899******************998764 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.1
                                   EEEEET.T--EEEEEETT.....---SSEETTEEE-HHHH CS
                      NTPase_1  47 FkivdlasgeegiLarve.....akreprvgkyvvdvesf 81 
                                   ++ivdl ++++  L+ +e      + e    ky +d++++
  gi|15668806|ref|NP_247609.1| 231 YEIVDLIENKKLGLSVEEtirqwINIEKDKIKYLIDTTDL 270
                                   6777777777777777765443322222333455555554 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.021        25      23      57 ..      10      44 ..       5      50 .. 0.75
   2 ?    6.1   0.0    0.0055       6.6     101     146 ..     109     154 ..     103     167 .. 0.80
   3 ?   -2.3   0.0       2.1   2.5e+03      82     126 ..     271     314 ..     263     328 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.021
                          TniB 23 LeeLleypkrkrmpnlllvGdsnnGKtmivekFar 57
                                  L+ L +y + +  + l ++G+   GK++++++  +
  gi|15668806|ref|NP_247609.1| 10 LNYLKTYCQLDPNSILFVYGPKSSGKSTVMRRVIK 44
                                  5555555555555678899***********99765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0055
                          TniB 101 rarvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnal 146
                                   ++  +k+++ + ++ ++ k  vLiiDE+++l +   +  + +ln l
  gi|15668806|ref|NP_247609.1| 109 NDVFAKINESINAVVEDGKKPVLIIDELQKLKNIYFNGGKSLLNEL 154
                                   556677788888899999999*********9988777777777766 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.1
                          TniB  82 dekrlyaaiLealgaplkararvskleqqvlrllrelkvrvLiiD 126
                                   de++ly+ +L +++ ++k + + + +++++  +   +k ++L  D
  gi|15668806|ref|NP_247609.1| 271 DEEELYK-VLSKFKDKIKISYEKEVKKEEMKYFKFLIKNEILFYD 314
                                   6677774.6778877777666555444443222223455555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00087         1       3      99 ..      25     145 ..      23     218 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00087
                                   EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C............ CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse............ 71 
                                   +++ G+  sGK+t +++++ ++ +++       ++F+ +lr+  + +++  l+ +  +  ++   +  e            
  gi|15668806|ref|NP_247609.1|  25 LFVYGPKSSGKSTVMRRVIKELEDSN------IVFFYYNLRKYATYSKEEFLRVFFEKSEKKYLLNKLElnlgvfkfgvee 99 
                                   78999999**************9998......5778888888777666622222222222222222222444444455666 PP

                                   ..................CHHHHCCSCCCEEEEEE-STT-SS-TCH CS
                         NACHT  72 ..................vwavllelperlLlilDglDelvtdlgq 99 
                                                      ++ ++e  ++ +li+D l +l+++  +
  gi|15668806|ref|NP_247609.1| 100 nfdfnnlklndvfakineSINAVVEDGKKPVLIIDELQKLKNIYFN 145
                                   6666666666644444444444444444444677766666665444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0063       7.6       4      22 ..      27      45 ..      24      62 .. 0.85
   2 ?    2.2   0.8      0.15   1.8e+02      48     103 ..     231     281 ..     143     308 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0063
                                  EEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1  4 ivGrpNvGKStLinaltge 22
                                  ++G   +GKSt++++ ++e
  gi|15668806|ref|NP_247609.1| 27 VYGPKSSGKSTVMRRVIKE 45
                                  7899***********9986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                                   EEEEECGGCSSHHHHHHHHHHHHHH..HHCTSEEEEEEETTTTCSHHHHHHHHHHHHH CS
                      MMR_HSR1  48 ielvDtpGliegaseekglgkafla..leeadlillvvdaseeklkpldeeleellee 103
                                   +e+vD+   ie+++ + ++++++++  ++e d i +++d + + l  ++eel ++l++
  gi|15668806|ref|NP_247609.1| 231 YEIVDL---IENKKLGLSVEETIRQwiNIEKDKIKYLIDTT-D-L--DEEELYKVLSK 281
                                   334442...44556666666666664333458888888844.2.3..33344444443 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00032      0.39      17      39 ..      17      39 ..      11      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00032
                        AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                   ++d++++ ++ Gp  sGKST++
  gi|15668806|ref|NP_247609.1| 17 CQLDPNSILFVYGPKSSGKSTVM 39
                                  56788889999**********86 PP

>> DnaB_2  Replication initiation and membrane attachment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2    0.0043       5.1      19      41 ..     205     227 ..     201     253 .. 0.79
   2 ?    1.2   2.2      0.26   3.1e+02      15      42 ..     256     283 ..     236     308 .. 0.79
   3 ?    1.2   0.4      0.25     3e+02       7      42 ..     289     324 ..     284     336 .] 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0043
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                        DnaB_2  19 tilywlddlglspevilllleya 41 
                                   ti+++l++ g+s+e i++ l y 
  gi|15668806|ref|NP_247609.1| 205 TIRNILKEEGFSEEEINYCLDYL 227
                                   57777777777777777777774 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.26
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DnaB_2  15 seletilywlddlglspevilllleyav 42 
                                   +e ++i+y++d+  l++e +  +l +  
  gi|15668806|ref|NP_247609.1| 256 IEKDKIKYLIDTTDLDEEELYKVLSKFK 283
                                   5888999999999999888777776665 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.25
                                   TS-.S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DnaB_2   7 efgrplspseletilywlddlglspevilllleyav 42 
                                    + + + + e++ ++ ++++  l ++vi+  ++ + 
  gi|15668806|ref|NP_247609.1| 289 SYEKEVKKEEMKYFKFLIKNEILFYDVINGIIKPTS 324
                                   566778899***********99999**999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1585  (0.0884043); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 2045.45
//
Query:       gi|15668807|ref|NP_247610.1|  [L=209]
Description: IMP cyclohydrolase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-71  237.5   1.4      1e-70  237.2   1.4    1.0  1  IMP_cyclohyd  IMP cyclohydrolase-like protein
  ------ inclusion threshold ------
      0.025   14.8   0.4      0.055   13.8   0.4    1.6  1  MapZ_C2       MapZ extracellular C-terminal domain 2


Domain annotation for each model (and alignments):
>> IMP_cyclohyd  IMP cyclohydrolase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.2   1.4   1.2e-74     1e-70       1     190 [.       9     200 ..       9     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 237.2 bits;  conditional E-value: 1.2e-74
                                   ---SEEEEEEETTEE.EEEEEEE-SS---EEEEEETT.EEEEEE-TGGGGGT-TTSSEEEEEEETTEEEEESSTHHHHHHH CS
                  IMP_cyclohyd   1 YvGRfivvgksedgkavaaYrvssRSfpnrnrvfred.kirveptdeeklednpyiiYncvrvlddkavvtNGsqtdtiae 80 
                                   Y+GRf+vvgk+++gk++aaYrvssRSfpnr++++++d ++++ p+d +++++npyi+Ync++v+d+++vv+NG++td+iae
  gi|15668807|ref|NP_247610.1|   9 YIGRFLVVGKTKEGKPFAAYRVSSRSFPNREAKKMDDnTVAIIPKDLNEMFKNPYITYNCIKVIDKTIVVSNGTHTDFIAE 89 
                                   9**********************************877******************************************* PP

                                   HHHTSB-HHHHHHHHHHHH-S--STT---EEEEEE-SS.EEEEEEETTEEEEEE--..TTS-EEEESSS-...-S-EE--- CS
                  IMP_cyclohyd  81 klekgltardalalsLlaldyEkDdynTPRiagvvkeeeaalgivksdallvekvelkagegtliatYek...gepkevel 158
                                   kl+ g+  rdala++L ++dyEkDdy+TPRia++++e+e+++g+v++d+++v+kvelk+g+g+++ +Y+    +e++ +++
  gi|15668807|ref|NP_247610.1|  90 KLHFGK--RDALAYVLAVMDYEKDDYKTPRIAAILDENECYMGYVAHDDIRVKKVELKDGKGYYLGVYNAckiDENQIIDI 168
                                   ***996..7************************************************************999********* PP

                                   --SSHHHHHHHHHHGGGSS-EEEEEEEEESSS CS
                  IMP_cyclohyd 159 eaedaeeaaeelweslefenkVslavavidek 190
                                   + e+aee+a+++++++efe++V++avavid++
  gi|15668807|ref|NP_247610.1| 169 KGETAEEIADYILNYEEFEHPVACAVAVIDKD 200
                                   *****************************976 PP

>> MapZ_C2  MapZ extracellular C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   6.1e-06     0.055      35      65 ..     129     163 ..     113     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.1e-06
                       MapZ_C2  35 rGyiveggyilervriengegyY....nlyatdnk 65 
                                    Gy+++++  +++v++++g+gyY    n  + d++
  gi|15668807|ref|NP_247610.1| 129 MGYVAHDDIRVKKVELKDGKGYYlgvyNACKIDEN 163
                                   6*********************8422244455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1349.68
//
Query:       gi|15668808|ref|NP_247611.1|  [L=117]
Description: hypothetical protein MJ_0627 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.017   15.3   0.3      0.024   14.8   0.3    1.2  1  BRAP2            BRCA1-associated protein 2
      0.085   12.0   0.1       0.11   11.6   0.1    1.1  1  APG17            Autophagy protein Apg17
      0.091   11.9   0.6       0.11   11.6   0.6    1.3  1  Thymidylat_synt  Thymidylate synthase


Domain annotation for each model (and alignments):
>> BRAP2  BRCA1-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   4.1e-06     0.024      25      75 ..      47     100 ..      40     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-06
                         BRAP2  25 lkFvgsvlekvseiriirdgken...rymvLikfkdqesadeFykefngkkFss 75 
                                    +F++++ ++++ei+++ d++++   +  v+ikfk++e+  +  ++ ++k +++
  gi|15668808|ref|NP_247611.1|  47 ERFLKIYDNHIKEIKLLIDSENHpepHLIVVIKFKNKENIFKISEQIENKIYEN 100
                                   589999***********9988877889***********9999999999888865 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.8e-05      0.11     306     342 ..      25      61 ..       6      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.8e-05
                                   ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         APG17 306 weeekekieekleeleeLrefYegFlsaYdklllEve 342
                                   ++ ++e++++k+e ++ L +  e+Fl++Yd+ ++E++
  gi|15668808|ref|NP_247611.1|  25 KSIFEESLDNKFEIIQYLMKILERFLKIYDNHIKEIK 61 
                                   567899*****************************85 PP

>> Thymidylat_synt  Thymidylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   1.8e-05      0.11     210     247 ..      51      90 ..      28     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.8e-05
                                   EEEGGGHHHHHHHHTS---S--EEEE-..-SSTHSGGG-- CS
               Thymidylat_synt 210 HiYsnhveqvkeqlereprelpkleln..kekkvsiedfe 247
                                    iY+nh++++k  +  e+++ p+l +    ++k++i++++
  gi|15668808|ref|NP_247611.1|  51 KIYDNHIKEIKLLIDSENHPEPHLIVVikFKNKENIFKIS 90 
                                   7******************999886541023333677764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 951.50
//
Query:       gi|15668809|ref|NP_247612.1|  [L=166]
Description: hypothetical protein MJ_0628 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00025   21.2   4.4       0.14   12.3   4.4    2.9  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   4.4   7.6e-06      0.14      10      95 ..      15     115 ..      13     166 .] 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.6e-06
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--...SSCCHHHHHHC......CHHHT................ CS
                          HEPN  10 edleaAellleegdydlacfhaqqaaekalKAlllkkgge..ppkthdlreLle......elkkelke............. 69 
                                   e+le+++++ +e + +  + ++++a ++ l+++l ++ ++  +++    + L+e                           
  gi|15668809|ref|NP_247612.1|  15 EFLEESKVDKKEAKNRTIIGRYYYASFLFLRGILKENLKNynSKEAKEFLYLIElsnshkI------Ildflnvlkkedgk 89 
                                   7899999999999999999999999999999999995555114455555555553322220......12244444444444 PP

                                   -HHHHHHHHHHHCCCHHCCCTSS--S CS
                          HEPN  70 seelreeleeLekayiesrYpdakee 95 
                                   ++++ + l+ L++++  s+Y+   + 
  gi|15668809|ref|NP_247612.1|  90 FRRVYNALSILRDLRNASDYELESPA 115
                                   99999999************987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1193  (0.0665402); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1062.69
//
Query:       gi|15668810|ref|NP_247613.1|  [L=214]
Description: hypothetical protein MJ_0629 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-68  228.9  16.0    4.7e-68  228.7  16.0    1.0  1  PhoU_div  Protein of unknown function DUF47
     0.0034   17.2   0.1      0.013   15.3   0.0    1.9  2  HTH_51    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.095   13.2  14.3        1.4    9.4   1.0    2.9  3  PhoU      PhoU domain


Domain annotation for each model (and alignments):
>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.7  16.0   7.9e-72   4.7e-68       2     214 .]       8     212 ..       7     212 .. 0.99

  Alignments for each domain:
  == domain 1  score: 228.7 bits;  conditional E-value: 7.9e-72
                      PhoU_div   2 lflfgsspekslqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRedlle 82 
                                   +flf++++eks++d+l+++++++lk+iellk++++   +k+e++lkei+++E+e+De++++ir++lek +flP++R++l++
  gi|15668810|ref|NP_247613.1|   8 IFLFERDNEKSVIDNLRLLIQMSLKSIELLKDYMN---SKDEKILKEIIKIEEEGDETTKNIRINLEK-AFLPNMRRELSR 84 
                                   89*********************************...******************************.************ PP

                      PhoU_div  83 lveslDeildvlediamlvtlrkvefpeelkdeflallkktveaiealaevieeleklletalskkdiveeieslEdeiDq 163
                                   ++e lDe+ld+l+++aml++l k+ef+e+lk+e++ +l++tv+++++l++v++++ek  +++l++  i++ei+++E++iD+
  gi|15668810|ref|NP_247613.1|  85 SAELLDETLDSLKHAAMLYELLKEEFDEYLKNEIDLVLMITVDMFQHLDRVLDVIEK--GGDLDP--IIKEIKDKEKFIDD 161
                                   ********************************************************9..*****7..************** PP

                      PhoU_div 164 lqrklikklfsredasnplevlllveiieklenvsdraedvadrisiille 214
                                   +++++i+k++++ ++++++e ++l+++i++++n+sd++edvad+++ii+l+
  gi|15668810|ref|NP_247613.1| 162 VYQNRIYKYLINLEVESFWEGKILCDFIDNIVNISDYIEDVADELHIIYLH 212
                                   ************************************************986 PP

>> HTH_51  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.59   3.5e+03      69      78 ..      99     108 ..      94     110 .. 0.78
   2 !   15.3   0.0   2.3e-06     0.013      23      74 ..     112     164 ..     106     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.59
                        HTH_51  69 vdylYevLee 78 
                                   + +lYe+L+e
  gi|15668810|ref|NP_247613.1|  99 AAMLYELLKE 108
                                   6789***976 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.3e-06
                        HTH_51  23 evlpkqteLvvalvveAFekLgcdlrsakpGqklpri.khlpkhkrlvdylYe 74 
                                   e l+++  Lv+ ++v+ F++L+  l+ +++G  l++i k +++ ++++d +Y+
  gi|15668810|ref|NP_247613.1| 112 EYLKNEIDLVLMITVDMFQHLDRVLDVIEKGGDLDPIiKEIKDKEKFIDDVYQ 164
                                   55677889***************************999***********9997 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.8   0.00038       2.3       3      57 ..      25      81 ..      23     104 .. 0.71
   2 ?    1.2   0.5     0.085   5.1e+02       8      35 ..      85     108 ..      77     145 .. 0.46
   3 ?    9.4   1.0   0.00024       1.4      12      87 ..     132     204 ..     122     209 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00038
                                  HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HGG CS
                          PhoU  3 rmaeiveemlddalealeekdtelarevierddeidrlekeiersllealak...rqp 57
                                   + +++++ ++++ +   +kd+++++e+i+ ++e d+  k+i+   le+++    r +
  gi|15668810|ref|NP_247613.1| 25 LLIQMSLKSIELLKDYMNSKDEKILKEIIKIEEEGDETTKNIRIN-LEKAFLpnmRRE 81
                                  56678888888888899999*9999*****************888.555543122222 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.085
                                   HHHHHHHHHHHHHCT-HHHHHHHHHHHH CS
                          PhoU   8 veemlddalealeekdtelarevierdd 35 
                                   + e ld++l++l++    ++ e++   +
  gi|15668810|ref|NP_247613.1|  85 SAELLDETLDSLKHA--AMLYELL--KE 108
                                   334444444444432..2222221..22 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00024
                                   HHHHHHHHHCT.-HHHH.HHHHHHHHHHHHHHH.HHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU  12 lddalealeek.dtela.revierddeidrlek.eiersllealakrqplaedlrellsllriardlERigDhavniae 87 
                                   ld++l+++e++ d + + +e+ ++++ id+ ++ +i+++l+++   ++ ++   ++   l + + ++  i+D+++++a+
  gi|15668810|ref|NP_247613.1| 132 LDRVLDVIEKGgDLDPIiKEIKDKEKFIDDVYQnRIYKYLINLE-VESFWEG--KI---LCDFIDNIVNISDYIEDVAD 204
                                   677888887776765555************97614566644433.2344433..22...56677777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1602.46
//
Query:       gi|15668811|ref|NP_247614.1|  [L=297]
Description: putative phosphate permease [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-46  156.9  35.6    7.4e-45  153.4  35.6    1.9  1  PHO4             Phosphate transporter family
     0.0074   16.2   2.1     0.0074   16.2   2.1    3.8  3  Phage_holin_8    Putative phage holin


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.4  35.6   8.3e-49   7.4e-45       2     336 ..      23     289 ..      22     290 .. 0.92

  Alignments for each domain:
  == domain 1  score: 153.4 bits;  conditional E-value: 8.3e-49
                          PHO4   2 GanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselmlgmlaallgaavwlllatv 82 
                                   Gan vana++t+ +s+a t+r  +il +i  ++G++++ ++V +t+++                +l al+ +a++++l t+
  gi|15668811|ref|NP_247614.1|  23 GANNVANAIGTAYASRATTYRNLLILFSISVIIGSLFA-KNVGSTVNSLSS------------DALTALIISALVMTLSTY 90 
                                   9************************************9.*********775............48999999********** PP

                          PHO4  83 lglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklknalralpvlvlv 163
                                    ++P+S    ++ +liG  + + +    +   +++i+lsw+lsP+++++ia++l+ + +++ +                  
  gi|15668811|ref|NP_247614.1|  91 KKVPISLHTVIICSLIGLNFNS-S----NLYVFGEILLSWILSPIIAVVIAYILYSAYEKIDI------------------ 148
                                   ******************9994.2....345689***************************33.................. PP

                          PHO4 164 tiailalsilfkgeskkddeeteklfkflqvvsaalvsfahGanDvanaiGpllaalisiykaskevplwvlllgglaial 244
                                          sil           + +++++++++saa+v+f  G+nD   + G ++               ++ ++g++ ++l
  gi|15668811|ref|NP_247614.1| 149 -------SILK----------KITMIRYFLLISAAVVAFNLGSNDLPTVLGTFTT------------SQIIYIIGAIFLCL 200
                                   .......2222..........23679***************************44............35799********* PP

                          PHO4 245 GlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgavvGvGlakkresavnwklvrnivla 325
                                   G +l+G rv +t+++ it +l+ s++f a+l++ l v ++++lg+PvStT+++vg+++GvGl+k + + v+wk+++ni++ 
  gi|15668811|ref|NP_247614.1| 201 GAYLYGNRVSETLSM-IT-NLSVSSAFIAQLSGGLAVTIFTALGMPVSTTQAIVGGILGVGLTK-GIKTVRWKVLKNIIFW 278
                                   *************86.99.5********************************************.79************** PP

                          PHO4 326 WvlTlpvsall 336
                                   Wv+  +++ ++
  gi|15668811|ref|NP_247614.1| 279 WVVAPIIALII 289
                                   *****999887 PP

>> Phage_holin_8  Putative phage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.1   8.3e-07    0.0074      46     104 ..      37      89 ..      20      92 .. 0.84
   2 ?    1.5   3.0     0.031   2.8e+02      54     105 ..     188     240 ..     153     243 .. 0.62
   3 ?    0.9   0.1     0.046   4.1e+02       4      26 ..     244     266 ..     241     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.3e-07
                 Phage_holin_8  46 akdltlltrlayflvSfiaGvlaaglaaaklatllpatdrvldalgAlvasalavkvll 104
                                   ++  t  + l++f +S+i+G l a+ +++ +++l++       al Al++sal++++ +
  gi|15668811|ref|NP_247614.1|  37 SRATTYRNLLILFSISVIIGSLFAKNVGSTVNSLSSD------ALTALIISALVMTLST 89 
                                   55667777899********************998876......***********99865 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.031
                 Phage_holin_8  54 rlayflvSfiaGvlaaglaaaklatllpa..tdrvldalgAlvasalavkvlll 105
                                   +++y++ ++    l+a l +++++++l++  +  v+ a+ A ++ +lav++ ++
  gi|15668811|ref|NP_247614.1| 188 QIIYIIGAIFL-CLGAYLYGNRVSETLSMitNLSVSSAFIAQLSGGLAVTIFTA 240
                                   34444433322.345556666666666665556677777777777777777665 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.046
                 Phage_holin_8   4 pvsatsaaaaavtgvglagllpg 26 
                                   pvs+t a+ ++++gvgl   +  
  gi|15668811|ref|NP_247614.1| 244 PVSTTQAIVGGILGVGLTKGIKT 266
                                   999****9*******99876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1904.22
//
Query:       gi|15668812|ref|NP_247615.1|  [L=169]
Description: hydrogenase maturation protease HycI [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-33  112.9   2.7      9e-33  112.9   1.5    1.5  2  HycI      Hydrogenase maturation protease


Domain annotation for each model (and alignments):
>> HycI  Hydrogenase maturation protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.17   3.1e+03      29      42 ..       5      18 ..       2      22 .. 0.80
   2 !  112.9   1.5     5e-37     9e-33       1     129 [.      32     160 ..      32     161 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.17
                                  GHHHHCC-SEEEEE CS
                          HycI 29 lvgtleeadkliiv 42
                                  l+++l++++kl+i+
  gi|15668812|ref|NP_247615.1|  5 LLDKLKNCKKLVIM 18
                                  77888999999885 PP

  == domain 2  score: 112.9 bits;  conditional E-value: 5e-37
                                   HHHHHHHHHHEC--T......TEEEEEECT-SGGGHHHHCC..-SEEEEEEE--SSS-TT-EEEEECCHHHHHHTTC.CGC CS
                          HycI   1 vrvvekLkrryefke......nvtviDgGtqglelvgtlee..adkliivDavdfglepGevkiikddevpkklkakkmsa 73 
                                   ++vv+kL+r++ +++      n+++i++Gt+++ ++++l+e  +++++i+D++++++++Gevkiik+de+++    +++s+
  gi|15668812|ref|NP_247615.1|  32 IYVVKKLMRYFGEEKefinikNLYLINAGTVPDFFTDILKEikPTHILIIDCALMDKDVGEVKIIKEDEIIN----YSFST 108
                                   68*********99999*******************************************************8....56*** PP

                                   CCHCHHHHHHHHHHCCS--SEEEEEEE--S-BST.CCS--HHHHCCHHHHHHHCCC CS
                          HycI  74 Hqlplaevlklleekgeipkevillgvqpesledvgielseevkkavekavelile 129
                                   H+lpl+ ++k+l+++  i++e+i+lg+qp+++++  +++seevk + +k+v++++e
  gi|15668812|ref|NP_247615.1| 109 HTLPLSIIVKYLKKF--INAEIIILGIQPKIIDF--CPISEEVKLSGDKLVNTLIE 160
                                   ***************..56***************..****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1046.13
//
Query:       gi|15668813|ref|NP_247616.1|  [L=363]
Description: replication initiator protein DnaA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-95  317.4   9.6    6.8e-95  317.4   9.6    1.9  2  ATPase_2       ATPase domain predominantly from Archaea
    1.9e-06   28.0  10.4    0.00056   20.0   0.4    3.2  3  AAA_14         AAA domain
    2.3e-06   28.1   0.0    7.5e-06   26.4   0.0    1.8  2  AAA_16         AAA ATPase domain
    9.6e-06   25.9   0.0    6.8e-05   23.2   0.0    2.3  2  AAA_22         AAA domain
  ------ inclusion threshold ------
      0.011   16.2   0.1       0.36   11.3   0.0    2.8  2  AAA            ATPase family associated with various cellular
      0.019   15.1   1.2      0.084   13.0   0.0    2.5  3  MMR_HSR1       50S ribosome-binding GTPase
      0.021   14.9   2.3      0.071   13.1   0.2    2.5  2  Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen r
      0.096   12.3   0.0       0.32   10.5   0.0    1.9  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.097   13.6   0.4      0.097   13.6   0.4    2.6  3  DUF2624        Protein of unknown function (DUF2624)
       0.13   12.0   0.9        1.1    9.0   1.3    2.0  2  FTCD_C         Formiminotransferase-cyclodeaminase


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.4   9.6   3.8e-98   6.8e-95       1     233 []       3     265 ..       3     265 .. 0.99
   2 ?    0.4   0.5      0.28   5.1e+02      46      70 ..     285     309 ..     267     361 .. 0.55

  Alignments for each domain:
  == domain 1  score: 317.4 bits;  conditional E-value: 3.8e-98
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...eeeekkkl 78 
                                   Ff+Reke++e+++i+e+ep++i fi+G+++sGKtaL++eii+n+++kdkyv++y++lre++isk+d+fie   ee+e+ ++
  gi|15668813|ref|NP_247616.1|   3 FFNREKEIEEILHIIESEPQRINFIFGSINSGKTALINEIINNRLNKDKYVVFYFDLREIFISKYDDFIEvlfEEYEEPFI 83 
                                   9******************************************************************************** PP

                      ATPase_2  79 ekal...........................giavpkaeleeilk.eksklvfkaielllekikkkgkkiiiiiDelqkli 131
                                   +k++                           +i++pk++l+e+lk ++ k+vf++i+++l kik++gk++iiiiDelqk++
  gi|15668813|ref|NP_247616.1|  84 DKVKrlflslikdypdviksyallnitgvvdSIPIPKNTLNELLKkRNVKNVFRYITSVLIKIKREGKQPIIIIDELQKIG 164
                                   ***9*****************************************9*********************************** PP

                      ATPase_2 132 dlglngaellvkeLlnliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkel.eel 211
                                   dl+ln  ++l++eL+n+++sltk+khlc+v+clsS++lfiervyne++legr+kyilvdd+d+etal+f+++++ke+ ++l
  gi|15668813|ref|NP_247616.1| 165 DLKLN--GFLIYELFNYFVSLTKHKHLCHVFCLSSDSLFIERVYNEAMLEGRCKYILVDDFDRETALKFMDFLAKENnINL 243
                                   *****..************************************************************************** PP

                      ATPase_2 212 skedfeeiyryvGGkPkalvel 233
                                   ++ed+e+iy+yvGGkP++++++
  gi|15668813|ref|NP_247616.1| 244 TNEDKELIYNYVGGKPIDIIYV 265
                                   *******************986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.28
                      ATPase_2  46 dkdkyviyyialreesiskldefie 70 
                                   + +k + ++ +++ee+++ +++ ++
  gi|15668813|ref|NP_247616.1| 285 ETQKLKYFLENVKEEDEELYKKVVD 309
                                   2223333333333333333333322 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.4   3.1e-07   0.00056       3      76 ..      23      89 ..      21     110 .. 0.72
   2 !   13.3   0.3   3.5e-05     0.064      45     120 ..     128     218 ..     102     229 .. 0.73
   3 ?    0.1   0.3      0.44   7.8e+02      34      62 ..     270     298 ..     247     325 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.1e-07
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76
                                  +i +i G   +GKT l++++i+++l +k++++ + +d  +    +++++++e+++e+++e      f+D ++++
  gi|15668813|ref|NP_247616.1| 23 RINFIFGSINSGKTALINEIINNRL-NKDKYVVFYFDLREIFI-SKYDDFIEVLFEEYEE-----PFIDKVKRL 89
                                  788999999****************.88888888887766653.4455678888887655.....355555544 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.5e-05
                        AAA_14  45 kladpekllelilek.lke....ekktylflDEiqev..........pewekalkslvdegknldvivtGSnskllskeia 110
                                   k+++ +++ ++i +  + +     k+ ++++DE q++           e++++  sl ++++ ++v++  S s+++ +  +
  gi|15668813|ref|NP_247616.1| 128 KKRNVKNVFRYITSVlI-KikreGKQPIIIIDELQKIgdlklngfliYELFNYFVSLTKHKHLCHVFCLSSDSLFIERVYN 207
                                   33444445555555432.2234568899*********999999999988888888888888899*********99998665 PP

                        AAA_14 111 .tslagrvaei 120
                                      l gr ++i
  gi|15668813|ref|NP_247616.1| 208 eAMLEGRCKYI 218
                                   14567777766 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.44
                        AAA_14  34 lyinldderdkkladpekllelileklke 62 
                                    y +l+d  +++l+++++ l+++le++ke
  gi|15668813|ref|NP_247616.1| 270 KYKKLEDILTSMLKEETQKLKYFLENVKE 298
                                   34444444444444444455555555433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   4.2e-09   7.5e-06       1     151 [.       2     167 ..       2     190 .. 0.69
   2 ?   -2.1   0.0       2.4   4.3e+03     138     160 ..     217     237 ..     203     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.2e-09
                        AAA_16   1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellr.alekdggiflrgkcdqlesaipysalaqalare 79 
                                   +++ Re+e+e++l+++e  +  +p ++ ++ G   +GK++l++e+ + +l+kd+ ++++ + ++         +++     
  gi|15668813|ref|NP_247616.1|   2 KFFNREKEIEEILHIIE--S--EPqRINFIFGSINSGKTALINEIINnRLNKDKYVVFYFDLREI--------FISKY-D- 68 
                                   6899**********999..3..4449****************99986599999777777777777........44444.2. PP

                        AAA_16  80 ellrqlldeaesaeleawrekleeala.....................avpelagaea......srllellkrllallsrd 133
                                   ++++ l +e e+   +  ++ +++ ++                     ++p+ +  e       + +++ +++ l +++r+
  gi|15668813|ref|NP_247616.1|  69 DFIEVLFEEYEEPFIDKVKRLFLSLIKdypdviksyallnitgvvdsiPIPKNTLNELlkkrnvKNVFRYITSVLIKIKRE 149
                                   344444444333333333333333333333444455557777777787444444444466777988888889999899998 PP

                        AAA_16 134 erplvlvlDdlqwadeas 151
                                   +++ ++++D+lq++ +  
  gi|15668813|ref|NP_247616.1| 150 GKQPIIIIDELQKIGDLK 167
                                   999*********987754 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                        AAA_16 138 vlvlDdlqwadeaslqllaaLlr 160
                                   ++++Dd++  +e+ l+++++L++
  gi|15668813|ref|NP_247616.1| 217 YILVDDFD--RETALKFMDFLAK 237
                                   68999999..5555666666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   3.8e-08   6.8e-05       4     128 ..      21     194 ..      17     201 .. 0.87
   2 ?   -2.1   0.0       2.4   4.4e+03      88     109 ..     212     232 ..     195     266 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.8e-08
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsst..sskdllrellralglelka.......... 70 
                                    ++i +++G   +GKT l++++ ++  +       ++++v  +++l +    + +d+ + l+++++++  +          
  gi|15668813|ref|NP_247616.1|  21 PQRINFIFGSINSGKTALINEIINNRLN-------KDKYVvfYFDLREIFisKYDDFIEVLFEEYEEPFIDkvkrlflsli 94 
                                   578889******************9976.......4444446999999999999999*********9988899******** PP

                        AAA_22  71 .................................erlsseellealeqalrarav...ielliiDEaqhlr..s......ee 107
                                                                    +  + + ++++++  l + ++   ++++iiDE q++   +       e
  gi|15668813|ref|NP_247616.1|  95 kdypdviksyallnitgvvdsipipkntlnellKKRNVKNVFRYITSVLIKIKRegkQPIIIIDELQKIGdlKlngfliYE 175
                                   *********************************999999999999999999999999************655266777788 PP

                        AAA_22 108 aleeLrsllnlsrkgvqliLv 128
                                   ++++++sl +  +k++ ++++
  gi|15668813|ref|NP_247616.1| 176 LFNYFVSLTK--HKHLCHVFC 194
                                   8888888888..888888876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                        AAA_22  88 aravielliiDEaqh.lrseeal 109
                                   + +  + +++D++++     + +
  gi|15668813|ref|NP_247616.1| 212 EGRC-KYILVDDFDReT-ALKFM 232
                                   3444.778888888732.33333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0002      0.36       4      74 ..      28     167 ..      26     221 .. 0.67
   2 ?   -2.3   0.0       3.2   5.7e+03      31      57 ..     274     300 ..     256     308 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                   ESSTTSSHHHHHHHHHHH.H...THEEEEEETTTCS.SS.......................................... CS
                           AAA   4 yGppGtGKTllakavake.l...gvefleisgsell.sk.......................................... 37 
                                   +G    GKT+l++ ++++ l   +  ++ +++ e++ sk                                          
  gi|15668813|ref|NP_247616.1|  28 FGSINSGKTALINEIINNrLnkdKYVVFYFDLREIFiSKyddfievlfeeyeepfidkvkrlflslikdypdviksyalln 108
                                   677788888888888888433333445666666666555666666777777777777788888888888888888888888 PP

                                   ......................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                           AAA  38 ......................yvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                                          v++  + i  ++ ++k++ k+ i++iDE+ +++  +
  gi|15668813|ref|NP_247616.1| 109 itgvvdsipipkntlnellkkrNVKNVFRYITSVLIKIKREGKQPIIIIDELQKIGDLK 167
                                   88888888888887766665566666666666666666666677*********998666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.2
                                   TTTCSSSSTTHHHHHHHHHHHHHHHTS CS
                           AAA  31 gsellskyvgesekkirelfkeakeka 57 
                                   + ++l ++++e  +k++ +++++ke+ 
  gi|15668813|ref|NP_247616.1| 274 LEDILTSMLKEETQKLKYFLENVKEED 300
                                   445556677788888888888777765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.7e-05     0.084       4      25 ..      27      48 ..      25      74 .. 0.88
   2 ?   -2.7   0.0       3.5   6.2e+03      76      76 ..     132     132 ..      85     158 .. 0.56
   3 ?   -0.7   0.3      0.79   1.4e+03      90     107 ..     271     288 ..     244     342 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-05
                                  EEESTTSSHHHHHHHHHTSTEE CS
                      MMR_HSR1  4 ivGrpNvGKStLinaltgekai 25
                                  i+G  N+GK+ Lin +++++  
  gi|15668813|ref|NP_247616.1| 27 IFGSINSGKTALINEIINNRLN 48
                                  89***************98655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.5
                                   T CS
                      MMR_HSR1  76 a 76 
                                   +
  gi|15668813|ref|NP_247616.1| 132 V 132
                                   1 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.79
                                   SHHHHHHHHHHHHHTTSE CS
                      MMR_HSR1  90 lkpldeeleelleeakkp 107
                                   +k+l+  l ++l+e++++
  gi|15668813|ref|NP_247616.1| 271 YKKLEDILTSMLKEETQK 288
                                   444444444444432222 PP

>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2     4e-05     0.071      44     105 ..       3      64 ..       1      66 [. 0.93
   2 ?    0.6   0.2      0.31   5.5e+02      49      91 ..     246     285 ..     230     299 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                 Nit_Regul_Hom  44 gflleedpesaikiikdlseeavlintvvdeekvekikeeleeklkderytiieipvekikv 105
                                    f+ e ++e +++ii+ + ++  +i   +++ k   i+e ++++l++++y +   ++++i +
  gi|15668813|ref|NP_247616.1|   3 FFNREKEIEEILHIIESEPQRINFIFGSINSGKTALINEIINNRLNKDKYVVFYFDLREIFI 64 
                                   5778899*************************************************999977 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.31
                 Nit_Regul_Hom  49 edpesaikiikdlseeavlintvvdeekvekikeeleeklkde 91 
                                   ed e +++ +     + + i  v++e k +k+++ l+  lk+e
  gi|15668813|ref|NP_247616.1| 246 EDKELIYNYVG---GKPIDIIYVINEMKYKKLEDILTSMLKEE 285
                                   55555555544...34455667777777777777777777665 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00018      0.32       4      30 ..      26      52 ..      23      66 .. 0.79
   2 ?   -3.5   0.0       3.8   6.7e+03     118     148 ..     307     342 ..     297     346 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00018
                                  EEEESTTCCHHHHHHHHHCT--SS-EE CS
                          cobW  4 vltGflGsGKTtLlnhllenraglkla 30
                                   + G++ sGKT+L+n++++nr +++  
  gi|15668813|ref|NP_247616.1| 26 FIFGSINSGKTALINEIINNRLNKDKY 52
                                  5789999***********887665544 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.8
                                   EEETTTH......CCHCCHHHHHHHHHHTSSEEEEE CS
                          cobW 118 vvDaknl.....eaeeekieekaedqlaaadllvln 148
                                   vvDa ++     e e+ ki++k+++ l + ++l ln
  gi|15668813|ref|NP_247616.1| 307 VVDALKIfkdsyEIEDIKIPKKLREFLVKKNILFLN 342
                                   777776666666556667777777777777777776 PP

>> DUF2624  Protein of unknown function (DUF2624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       4.5   8.1e+03       3      13 ..      38      48 ..      36      49 .. 0.84
   2 ?   13.6   0.4   5.4e-05     0.097      23      59 ..     235     274 ..     227     297 .. 0.72
   3 ?   -1.6   0.0         3   5.4e+03      56      80 ..     289     312 ..     281     315 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.5
                       DUF2624  3 iiqqlVnqkln 13
                                  +i++++n++ln
  gi|15668813|ref|NP_247616.1| 38 LINEIINNRLN 48
                                  78999**9998 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.4e-05
                       DUF2624  23 yakqygveltksqAekivkilrekkidif...nkeerkkl 59 
                                   +ak+++++lt+++ e i +++ +k idi+   n+ + kkl
  gi|15668813|ref|NP_247616.1| 235 LAKENNINLTNEDKELIYNYVGGKPIDIIyviNEMKYKKL 274
                                   79*************************9622144444443 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3
                       DUF2624  56 rkkllkelakitspqtakkvneLlk 80 
                                    k  l++++++ +++++kkv + lk
  gi|15668813|ref|NP_247616.1| 289 LKYFLENVKEE-DEELYKKVVDALK 312
                                   34455555555.9999999887665 PP

>> FTCD_C  Formiminotransferase-cyclodeaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.47   8.4e+02      81     135 ..     112     165 ..     108     169 .. 0.84
   2 ?    9.0   1.3   0.00062       1.1      42      93 ..     267     319 ..     263     333 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.47
                                   HHTTTT..........S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS- CS
                        FTCD_C  81 vmeayklpketeeekaareeaiqealkkavevPlelarkalellelleelaekgn 135
                                   v++++ +pk+t +e   +++++++ ++  ++v +++ r+ ++ + +++el ++g 
  gi|15668813|ref|NP_247616.1| 112 VVDSIPIPKNTLNE-LLKKRNVKNVFRYITSVLIKIKREGKQPIIIIDELQKIGD 165
                                   67778889999765.57888899****************9999999999999886 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00062
                                   T-TT-GGGHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHTTTT....... CS
                        FTCD_C  42 gkkkyedveeemeell.ekleelrkellelideDaeaFnevmeayklpketee 93 
                                   +  ky+++e+ + ++l e++++l+  l ++ +eD+e +++v++a+k+ k++ e
  gi|15668813|ref|NP_247616.1| 267 NEMKYKKLEDILTSMLkEETQKLKYFLENVKEEDEELYKKVVDALKIFKDSYE 319
                                   56789999997766661556888888899999***************998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1400  (0.0780858); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2181.30
//
Query:       gi|15668814|ref|NP_247617.1|  [L=942]
Description: leucyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-69  233.7   1.3    8.3e-68  229.1   1.3    2.5  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    2.5e-27   95.7   0.1    5.4e-12   45.2   0.1    3.4  2  tRNA-synt_1g   tRNA synthetases class I (M)
    2.6e-26   92.4   0.6      8e-26   90.8   0.6    1.9  1  Anticodon_1    Anticodon-binding domain of tRNA
    6.4e-12   45.4   0.5    1.7e-11   44.0   0.1    1.9  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
     0.0033   16.8   0.1       0.02   14.3   0.0    2.3  3  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.074   13.4   2.8         19    5.6   0.0    3.7  3  FKS1_dom1      1,3-beta-glucan synthase subunit FKS1, domain-
       0.35   10.9   6.0       0.18   11.9   2.7    2.2  2  Pkip-1         Pkip-1 protein


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.1   1.3   3.3e-71   8.3e-68       1     599 [.      13     670 ..      13     673 .. 0.86

  Alignments for each domain:
  == domain 1  score: 229.1 bits;  conditional E-value: 3.3e-71
                   tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlai..... 76 
                                   k++++Wee+++f+++    +++++f +++  Py +G lH Gh  + t+ ++v r++rmk k+vl+++G+   G +i     
  gi|15668814|ref|NP_247617.1|  13 KWQKRWEEAKIFEAN---PDDREKFFITAAFPYLNGVLHAGHLRTFTIPEVVARFQRMKNKNVLWTFGYHVTGTPIlglae 90 
                                   5899*********99...8899***************************************************99822221 PP

                   tRNA-synt_1  77 ..eakvekklgakekkerkklgreefrekv..rewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladk 153
                                     +   ek+++a  +   + + +ee  e +   +++++++++ ++++kr+G s+D+ r+ +T dk +++ +++ f +l +k
  gi|15668814|ref|NP_247617.1|  91 liKNRDEKTIWAYTE--LHGIPKEELLELTtpEKIVEYFSKKAEEAFKRMGFSLDWRRNFKTDDKVFNKFIEWQFHKLKEK 169
                                   113344556665554..78888999998763358999******************************************** PP

                   tRNA-synt_1 154 gliyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv....... 227
                                   gli +g+++v +++++  ++ + ++   ++   + ++  +++ ++   + +aT +PeT++g t v vnpe  yv       
  gi|15668814|ref|NP_247617.1| 170 GLIVKGSHPVRYCPRCDNPVEDHDILVGENATLVEYILIKFTTEDGCIMPMATLRPETVFGVTNVWVNPEATYVkakvyle 250
                                   *************************8877776665555555555555699******************************* PP

                   tRNA-synt_1 228 .........itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahd 299
                                            i++  +i+a+   ++l +++ + +i e+++g++L+ k+v++p++++++pi+  ++v+++ GtG+V   Pah 
  gi|15668814|ref|NP_247617.1| 251 ketengielIENGIWIMAKECAEKLKHQDRKIEIIEEFKGEQLINKKVKNPVTGKEVPILPAKFVKTNIGTGCVMSVPAHA 331
                                   ****99999999999*********99999999************************************************* PP

                   tRNA-synt_1 300 edDyevgkkynl..................evinildedgtlteea................................... 327
                                   + Dy + ++ +l                  +                                                  
  gi|15668814|ref|NP_247617.1| 332 PYDYIALRDLGLvdeigliplinvpgygkyPAK------------Eivekmgiksqeeedkleeatkkiykdefhkgvlne 400
                                   *****9999998888877655555555555222............134444555555577788888888888888888888 PP

                   tRNA-synt_1 328 ..aefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..ladaalkavekvqfvpks 404
                                      ++eg+ v + ++k++++l +kgl   + +++ +  +c  +   i+ +++ qWf++ ++   ++ a k ++k++f+p+ 
  gi|15668814|ref|NP_247617.1| 401 ncLDYEGIPVREIKDKLTKDLIDKGLAEIMYEFSEEKVICRCGTPCIVKMVKGQWFIKYSDekWKELAHKCIDKMRFIPEN 481
                                   88**********************************99**8888889999999*****986558889999999******** PP

                   tRNA-synt_1 405 kekryaswleniqdWciSRqrwWGhripl...fvsketeevvvreelkelvagreeeeaekkalekeakdklkkekgelek 482
                                    ++ +++ +  ++d +  R r  G++ p+   +v ++  + ++      +++ +++++ + ++l+ e  d +  +kg++ k
  gi|15668814|ref|NP_247617.1| 482 LRQVFHEKIDWMKDKACVRRRGLGTKFPFeegWVIESLSDSTIYPAYYTVAKYINQHNIKPEQLTLELFDYVFLGKGDVDK 562
                                   ****************************8888**99999988877777777778888888888888999988677777666 PP

                   tRNA-synt_1 483 dedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePf.kevlvhglvrdeeGr 562
                                   +        + g +p  +++     ++e+  ++p d   +  D i   ++  i+  +a++ +e + + ++v+g v+  eG+
  gi|15668814|ref|NP_247617.1| 563 IAK------ETG-IPKDIIE---GMRKEFIYYYPVDWRCSAKDLIPNHLTFYIFNHVAIFPEEFWpRGIVVNGYVT-IEGK 632
                                   654......555.5666666...3479*********************************9996636799999987.58** PP

                   tRNA-synt_1 563 KmSKslgNvidpldvikkygadalRltli.lsdvgrdi 599
                                   K+SKs+g v+  l+v++k gad+ R+++   ++  +d 
  gi|15668814|ref|NP_247617.1| 633 KLSKSKGPVLPVLEVAEKFGADVGRFYITtCAELPQDA 670
                                   ****************************9666666665 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.1   2.1e-15   5.4e-12       2     134 ..      35     193 ..      34     198 .. 0.78
   2 !   38.2   0.0   2.7e-13   6.9e-10     289     375 ..     593     683 ..     587     697 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 2.1e-15
                                   EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHH...............HTTS...... CS
                  tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAe...............kegv...... 61 
                                   ++t+a+pY ng+lH Ghl++  +  ++aR++r+++++vl+  g    Gtpi   Ae                +g+      
  gi|15668814|ref|NP_247617.1|  35 FITAAFPYLNGVLHAGHLRTFTIPEVVARFQRMKNKNVLWTFGYHVTGTPILGLAEliknrdektiwayteLHGIpkeell 115
                                   8*************************************9999998889888755542222222222222211222222223 PP

                                   ...-HHHHHHHHHHHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG CS
                  tRNA-synt_1g  62 ...tpeelvekvheeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdry 134
                                      tpe++ve ++++ +e fk+++ s d     +t+++  +++ +  f+klkekgli +++  + ycp++++   d  
  gi|15668814|ref|NP_247617.1| 116 eltTPEKIVEYFSKKAEEAFKRMGFSLDwrRNFKTDDKVFNKFIEWQFHKLKEKGLIVKGSHPVRYCPRCDNPVEDHD 193
                                   33389999**************888877335678999*********************************98877765 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 2.7e-13
                                   EGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHH..HS-TTS-EE CS
                  tRNA-synt_1g 289 gkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaa..eapekkDld 365
                                   +kd i+ H  f+     +   e   p+ +v+++y+t+egkKlSkS+g v  + e++e++ ad+ R+y+++  e p++ D++
  gi|15668814|ref|NP_247617.1| 593 AKDLIPNHLTFYIFNHVAifPEEFWPRGIVVNGYVTIEGKKLSKSKGPVLPVLEVAEKFGADVGRFYITTcaELPQDADIK 673
                                   6999999999888777777666778*******************************************9855677777777 PP

                                   E-HHHHHHHH CS
                  tRNA-synt_1g 366 fswedfverv 375
                                   f++ + +++v
  gi|15668814|ref|NP_247617.1| 674 FKEMENTKKV 683
                                   7777766666 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.6   3.1e-29     8e-26       1     151 [.     709     838 ..     709     839 .. 0.91

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 3.1e-29
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfm 81 
                                   d+w+ls+l+k+vk+++e++e+++++ka   ly+ +++dl +wy +   + +            +vl e+le +++l+ Pf+
  gi|15668814|ref|NP_247617.1| 709 DKWLLSRLYKAVKQYDEYMENFELRKAGILLYQ-LLDDL-KWYRRRGGNNI------------RVLEEFLEVIIKLMMPFT 775
                                   9********************************.59***.******99999............9***************** PP

                   Anticodon_1  82 PfitEelwqreeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselkvv 151
                                   P+++Ee+w    e lgk+ +++la++pe k+e+ ++e+ e+  e+   +  +++++++++++++ ++++++
  gi|15668814|ref|NP_247617.1| 776 PHLCEEMW----EILGKEGFVSLAKFPEvKEEFINDEI-EKGEEY---LKAVMEDIKEIINVAKVQPKRIY 838
                                   ********....9***************7777777777.778888...77788888888888888888876 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.1   6.7e-15   1.7e-11      13     126 ..     209     335 ..     204     346 .. 0.72
   2 ?   -2.6   0.1       1.3   3.4e+03      65     174 ..     375     411 ..     361     421 .. 0.45

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 6.7e-15
                 tRNA-synt_1_2  13 efkveeseeklevfttrpdtlfGvtfvalapehplvekl....aekkke...laa....fieevkkk.sesereletke.k 80 
                                   +f+ e+    + + t rp+t+fGvt v + pe   v++     +e+++    +++      +e+++k ++++r++e  e  
  gi|15668814|ref|NP_247617.1| 209 KFTTEDGC-IMPMATLRPETVFGVTNVWVNPEATYVKAKvyleKETENGielIENgiwiMAKECAEKlKHQDRKIEIIEeF 288
                                   55555443.5667799******************99987787633333211123222113455554414445555544435 PP

                 tRNA-synt_1_2  81 eGv.ftglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDf 126
                                   +G    + k+ +P+tg+++pi  a++v ++ gtg+vm+vPah   D+
  gi|15668814|ref|NP_247617.1| 289 KGEqLINKKVKNPVTGKEVPILPAKFVKTNIGTGCVMSVPAHAPYDY 335
                                   66648899**********************************98887 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                 tRNA-synt_1_2  65 vkkksesereletkekeGvftglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpede 145
                                    +++++ e+++++  k+ + +g+   + +                                                    
  gi|15668814|ref|NP_247617.1| 375 QEEEDKLEEATKKIYKDEFHKGVLNENCL---------------------------------------------------- 403
                                   22333333333333333333333333333.................................................... PP

                 tRNA-synt_1_2 146 ekkleeseeayteegilvnsgefdglksk 174
                                                        +++g+ ++
  gi|15668814|ref|NP_247617.1| 404 ---------------------DYEGIPVR 411
                                   .....................55555555 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.1   2.8e+03      22      48 ..      46      72 ..      41      76 .. 0.82
   2 !   14.3   0.0   7.7e-06      0.02     208     282 ..     587     662 ..     576     682 .. 0.81
   3 ?   -2.3   0.2      0.85   2.2e+03      99     131 ..     817     847 ..     799     894 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                                  --BHHHHHHHHHHHHHHHHHHHTT-EE CS
                  tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdv 48
                                    h Gh R++ + ++++r+ ++++ +v
  gi|15668814|ref|NP_247617.1| 46 VLHAGHLRTFTIPEVVARFQRMKNKNV 72
                                  6799******99999999988776666 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.7e-06
                                   EEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                  tRNA-synt_1e 208 idihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                                   +d  +  +DL+  h    +  + a f  + + +  + ng+++ieg+k+sks + ++ + +v +kf + + R+++++
  gi|15668814|ref|NP_247617.1| 587 VDWRCSAKDLIPNHLTFYIFNHVAIFPeEFWPRGIVVNGYVTIEGKKLSKSKGPVLPVLEVAEKFGADVGRFYITT 662
                                   6667777888888888888889999984567788999********************************9*99876 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.85
                                   -BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE CS
                  tRNA-synt_1e  99 prvsekvdeiielvekliekgyaYavsdgdvyf 131
                                     v+e ++eii++ +   ++ y Y+++d   ++
  gi|15668814|ref|NP_247617.1| 817 KAVMEDIKEIINVAKVQPKRIYLYTADD--WKY 847
                                   3456666666666665556666666553..333 PP

>> FKS1_dom1  1,3-beta-glucan synthase subunit FKS1, domain-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0073        19      18      44 ..     474     500 ..     469     538 .. 0.87
   2 ?    0.6   0.1      0.26   6.7e+02      41      91 ..     676     725 ..     659     752 .. 0.61
   3 ?    4.7   0.1     0.014        35      16      90 ..     754     833 ..     745     849 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0073
                     FKS1_dom1  18 nvRflpeclcyifkcaadyleseeake 44 
                                   ++Rf+pe l  +f+  +d+++ +++ +
  gi|15668814|ref|NP_247617.1| 474 KMRFIPENLRQVFHEKIDWMKDKACVR 500
                                   79*****************99988764 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.26
                     FKS1_dom1  41 eakeeeeelkeleeileekvseaaaseeeesfLkk.vitPlyevlrkqeaek 91 
                                   e++++++ l+ l+  ++e +++  ++ ee s+++k +++ ly+ +++  +++
  gi|15668814|ref|NP_247617.1| 676 EMENTKKVLERLYLFAKEIAERRGETGEEFSYIDKwLLSRLYKAVKQ--YDE 725
                                   23344444444555566666667888899999988467899999943..333 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.014
                     FKS1_dom1  16 aanvRflpeclcyifkcaadyleseeak......eeeeelkeleeileekvse....aaaseeeesfLkkvitPlyevlrk 86 
                                    +n+R l e l  i k ++ ++ +  ++      +  e   +l++  e    +    + + e+ e++Lk v++ + e+++ 
  gi|15668814|ref|NP_247617.1| 754 GNNIRVLEEFLEVIIKLMMPFTPHLCEEmweilgK--EGFVSLAKFPEV---KeefiNDEIEKGEEYLKAVMEDIKEIINV 829
                                   589***************97776655543333221..112223333332...13445677788999***********9965 PP

                     FKS1_dom1  87 qeae 90 
                                   ++++
  gi|15668814|ref|NP_247617.1| 830 AKVQ 833
                                   5554 PP

>> Pkip-1  Pkip-1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1         2   5.1e+03      77     122 ..     109     154 ..      91     162 .. 0.57
   2 ?   11.9   2.7   6.8e-05      0.18      75     160 ..     816     903 ..     793     905 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2
                        Pkip-1  77 lsneeieslletkendeflkkkykaaklleaiqkifdknakkflkv 122
                                   + +ee+ +l   +++ e+++kk++ a +    +  +++n k   kv
  gi|15668814|ref|NP_247617.1| 109 IPKEELLELTTPEKIVEYFSKKAEEAFKRMGFSLDWRRNFKTDDKV 154
                                   5566666666666666666666665555444444444444444444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.8e-05
                        Pkip-1  75 LdlsneeieslletkendeflkkkykaaklleaiqkifdknakkflkvleqFvdkrnayrk..nendklleeLvllKsnlI 153
                                   L+   e+i+++++ ++ +      y a++ + +i ki+++n  k +k l   + k   +rk  +e  kl+++L++l +++I
  gi|15668814|ref|NP_247617.1| 816 LKAVMEDIKEIINVAKVQPKRIYLYTADDWKYEILKIIKENEGKTIKELMPIIMKNPEFRKygKEIPKLVNQLIKLNAEII 896
                                   5666799999**99999999999**************************************666668************** PP

                        Pkip-1 154 khlcvle 160
                                       vle
  gi|15668814|ref|NP_247617.1| 897 NEVEVLE 903
                                   9877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (942 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.87u 0.32s 00:00:01.19 Elapsed: 00:00:00.56
# Mc/sec: 5046.15
//
Query:       gi|15668815|ref|NP_247618.1|  [L=620]
Description: hypothetical protein MJ_0634 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-12   46.9   0.1      8e-11   42.6   0.1    3.1  2  Radical_SAM  Radical SAM superfamily
    0.00015   21.9   0.0    0.00034   20.7   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
      0.004   17.4   0.0      0.011   16.1   0.0    1.7  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.43   2.6e+03     118     143 ..     236     260 ..     211     275 .. 0.72
   2 !   42.6   0.1   1.3e-14     8e-11       2     166 ..     333     523 ..     332     524 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.43
                                   HHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 118 lklmnrghtfeevlealeklreagik 143
                                   ++ +n + + e++ e +ek+ ++gi+
  gi|15668815|ref|NP_247618.1| 236 REVTNFKISDEDL-EIIEKAVKNGIP 260
                                   4555544444444.888888888888 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 1.3e-14
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC....... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla....... 74 
                                    +++ C++ C++C+r+++v++ +  ++  +e++++ +++++ e++   e++++gg+p+  +d+  + ++l ++a       
  gi|15668815|ref|NP_247618.1| 333 KPYESCPQICVYCQRNWMVQDFDAKAFPGWEKVEKALDWFA-EHDsMIEILITGGDPFSLSDK-AIEKMLNRIAemnhvvg 411
                                   57789***********************************5.6666*************9666.44455555555678777 PP

                                   ............................CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH CS
                                   ............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  75 ............................vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtf 127
                                                               +  i+++ve+++    +e++e+ ++l+++ +++  +++  + v ++      f
  gi|15668815|ref|NP_247618.1| 412 vrfgtrtivtapmritdelaellgsfekSLMISTHVESCYEIT-PEVAEAVKKLRTNNIYIYNQHVFHRYVSRR------F 485
                                   7777777777777777777777777777789999999999997.999999999999999999999988844444......4 PP

                                   HHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 128 eevlealeklreagikrvvdrivglpGendeeleellel 166
                                   e v   + +l+++gi + +++++ ++ e ++ l+ +++l
  gi|15668815|ref|NP_247618.1| 486 ENVALRI-ALKKVGIIPYYTFYPKGKMEHKDYLVPIARL 523
                                   5553334.4788998889999999999999988887776 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   5.8e-08   0.00034       7      94 ..     337     423 ..     334     446 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.8e-08
                       Fer4_14   7 gCnlsCkgCd.nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwle 86 
                                   +C+  C+ C  n   ++++++     e +e+ l+ + ++++ i+ + +tGG+P+   ++k++ k+++r+ e  + + +++ 
  gi|15668815|ref|NP_247618.1| 337 SCPQICVYCQrNWMVQDFDAKAFPGWEKVEKALDWFAEHDSMIE-ILITGGDPF-SLSDKAIEKMLNRIAEMNHVVGVRFG 415
                                   79*******966677788999999999999***98888888677.*********.66***************999999998 PP

                       Fer4_14  87 tngtleie 94 
                                   t   +   
  gi|15668815|ref|NP_247618.1| 416 TRTIVTAP 423
                                   87766654 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.8e-06     0.011      14      83 ..     337     407 ..     327     435 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-06
                       Fer4_12  14 gCnlsCkgCfnketwsfksgkeft..kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeek 83 
                                    C+  C +C  + + +    k f+  +++++ +   ++++s +++ ++GG+P+    ++a+ ++++++ e +
  gi|15668815|ref|NP_247618.1| 337 SCPQICVYCQRNWMVQDFDAKAFPgwEKVEKALDWFAEHDSMIEILITGGDPFS-LSDKAIEKMLNRIAEMN 407
                                   69999****988877777788887766666666666677999***********9.8999******9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (620 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4098.17
//
Query:       gi|15668816|ref|NP_247619.1|  [L=283]
Description: hypothetical protein MJ_0635 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0066   16.2   4.8        1.2    8.9   0.2    2.8  3  DUF3242   Protein of unknown function (DUF3242)
  ------ inclusion threshold ------
      0.016   15.2   0.3      0.074   13.1   0.3    2.2  1  ETRAMP    Malarial early transcribed membrane protein (ETRAMP
      0.047   13.7   0.0       0.11   12.5   0.0    1.6  1  DUF1971   Domain of unknown function (DUF1971)


Domain annotation for each model (and alignments):
>> DUF3242  Protein of unknown function (DUF3242)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.2   0.00026       1.6      51     122 ..      51     122 ..      33     125 .. 0.81
   2 ?   -1.9   0.0      0.42   2.5e+03      86     120 ..     137     169 ..     128     175 .. 0.65
   3 !    8.9   0.2    0.0002       1.2      31      69 ..     207     248 ..     193     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00026
                                   EEESTTHHHHHHHHHT-------EEEEE-SSEEEEEEEETTEEEEEEEETTEEEEEEESS-HHHHHHHHHHH CS
                       DUF3242  51 kykdeeakksWkkivkkvgivskrkyldlldsGlfsvkkegkdivvWwkdnWlfivegkedveefvkevnev 122
                                    +k+ e  k+ ++ + k+ + +++   +  ++G++  k++         d++++i+eg+ d ++f ++++e+
  gi|15668816|ref|NP_247619.1|  51 NFKNIEDSKYSSEYRSKILNALRLGNANGEKTGIYINKTKRMIFSGSGYDRFVIIIEGDYDFDKFKNHLKEI 122
                                   5666677777788888888888888888899999999988887777788******************99886 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.42
                                   EEEETTEEEEEEEETTEEEEEEESS-HHHHHHHHH CS
                       DUF3242  86 svkkegkdivvWwkdnWlfivegkedveefvkevn 120
                                   +  +++k  ++++kd  ++i+ +k++v + ++ +n
  gi|15668816|ref|NP_247619.1| 137 TKPNDDKIALTFYKD--MIIAGTKQGVYDCINVIN 169
                                   444455555677777..677777777777777665 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0002
                                   EEEEEEEEEEEETTE..EEEEEEEESTT.HHHHHHHHHT--- CS
                       DUF3242  31 vegkGvvavfdnkng..llyvfkykdee.akksWkkivkkvg 69 
                                     ++G+  +f+n++   ++ v kykdee ak++++++ kk +
  gi|15668816|ref|NP_247619.1| 207 TVAEGMSISFENNDRvkVVRVEKYKDEEtAKEKYEELLKKKD 248
                                   46899999**888751257789******9*******999864 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   1.2e-05     0.074       1      33 [.       1     231 [.       1     261 [. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                        ETRAMP   1 MKvtkvllffafLlavnlltpeslcdevnkkk................................................. 32 
                                   MK+++++ ++a+Lla+ + t+ + c +  k++                                                 
  gi|15668816|ref|NP_247619.1|   1 MKFMRIVRILAILLALIIGTSLCGCLNDSKSEadelikmlpvdyngfvyvnfkniedskysseyrskilnalrlgnangek 81 
                                   ***************999998888877776666788888888888888888888887777777777777777777777777 PP

                        ETRAMP  33 ................................................................................. 32 
                                                                                                                    
  gi|15668816|ref|NP_247619.1|  82 tgiyinktkrmifsgsgydrfviiiegdydfdkfknhlkeigvnpveeyggfkiytkpnddkialtfykdmiiagtkqgvy 162
                                   777777777777777777777777766666666666666666666666666666666666666666666666666666666 PP

                        ETRAMP  33 ....................................................................e 33 
                                                                                                       +
  gi|15668816|ref|NP_247619.1| 163 dcinvingemdsllknrevmeiydrlpsdacvyevsgtyspwyktvaegmsisfenndrvkvvrvekyK 231
                                   666666666666666666666666666666666666666666666666666666666666666666653 PP

>> DUF1971  Domain of unknown function (DUF1971)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.9e-05      0.11      20      39 ..     156     175 ..     147     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                                   TSSTTEEEEEEEEESEEEEE CS
                       DUF1971  20 nTkaGvwgklrVleGelkfy 39 
                                    Tk+Gv+ +++V++Ge++  
  gi|15668816|ref|NP_247619.1| 156 GTKQGVYDCINVINGEMDSL 175
                                   5***************9855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1365  (0.0761336); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2050.27
//
Query:       gi|15668817|ref|NP_247620.1|  [L=397]
Description: dihydrolipoamide dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-34  119.4   0.0    8.9e-29  100.6   0.0    2.1  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      2e-12   47.5   2.6    7.7e-09   36.0   0.0    3.4  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    4.4e-09   36.0   0.2    6.4e-09   35.5   0.2    1.3  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.1e-08   34.2   0.2      0.025   14.5   0.0    3.0  3  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    4.1e-08   33.3   0.9    2.4e-07   30.9   0.1    2.4  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.4e-06   27.9   0.3     0.0016   18.9   0.0    3.1  3  NAD_binding_7   Putative NAD(P)-binding
    5.9e-06   25.6   0.0     0.0013   17.9   0.1    2.4  2  GIDA            Glucose inhibited division protein A
    3.9e-05   23.3   0.2       0.26   10.9   0.0    2.8  3  ApbA            Ketopantoate reductase PanE/ApbA
      7e-05   22.3   0.0     0.0071   15.7   0.0    2.4  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    0.00018   20.9   0.1    0.00068   19.0   0.0    1.9  2  FAD_binding_3   FAD binding domain
    0.00019   21.5   0.0       0.17   11.9   0.0    2.5  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    0.00031   20.5   1.0      0.001   18.7   0.1    2.0  2  DAO             FAD dependent oxidoreductase
    0.00094   18.5   0.0     0.0024   17.2   0.0    1.7  1  Thi4            Thi4 family
     0.0014   17.4   0.4     0.0043   15.8   0.0    1.9  2  HI0933_like     HI0933-like protein
     0.0015   17.9   0.0       0.16   11.2   0.0    2.3  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0056   15.8   0.1      0.018   14.2   0.0    1.8  2  FAD_binding_2   FAD binding domain
  ------ inclusion threshold ------
      0.013   15.5   0.2        9.5    6.3   0.0    3.1  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.013   15.0   0.2        1.2    8.6   0.0    2.6  3  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.026   15.0   0.0        3.1    8.3   0.0    2.3  2  XdhC_C          XdhC Rossmann domain
      0.033   13.0   0.1       0.09   11.6   0.0    1.8  2  Trp_halogenase  Tryptophan halogenase
      0.047   13.0   0.0      0.067   12.5   0.0    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
      0.061   12.9   0.3       0.62    9.6   0.1    2.2  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.068   13.3   0.4          1    9.4   0.0    2.3  2  NAD_binding_6   Ferric reductase NAD binding domain
       0.12   13.0   9.1       0.66   10.7   1.2    3.9  4  PglD_N          PglD N-terminal domain
       0.31   10.6   4.8       0.22   11.1   0.5    2.1  2  Mfa2            Fimbrillin-A associated anchor proteins Mfa1 
        0.5   11.4   8.7       0.17   12.9   4.6    2.2  2  PdaC            Deacetylase PdaC


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.0   1.3e-31   8.9e-29       2     195 ..      10     211 ..       9     217 .. 0.83
   2 !   16.8   0.0   4.4e-06     0.003     250     279 ..     234     266 ..     220     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 1.3e-31
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH...................HHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx...................xxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias...................evv 60 
                                   +++v+G+GpAG + a++la++g++v l+e    +gtcln gc + + l+++a+  + +s                   e++
  gi|15668817|ref|NP_247620.1|  10 KIAVVGAGPAGRTSAMFLAKNGFDVDLFEkdrVGGTCLNYGCTYITGLREMADIINNLSilkgekvhleeiisfkelqEKI 90 
                                   799*************************9999*****************9999999999*******999998887777555 PP

                                   HCHHHHCCCCHCCT..CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCS CS
                                   xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  61 kklnqgielllgee..vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklk 139
                                   +k++  i++ l++e   +++  + k++       ++++k +yd+++ AtG ++   +  G         + l++++  +l 
  gi|15668817|ref|NP_247620.1|  91 NKIQDRIRNKLEKEtkELGVNIKYKEF-------KNKHKNDYDYIIYATG-RNYPSNYNGY--------EVLTHKDIPNLR 155
                                   555555555555331123333333344.......4566779*********.6666688888........78********** PP

                                   S-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 140 llpkrivvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleealek 195
                                   +lp++i+++GgG++++E+A+ ++++g++v+ ++ r+++l +  d+e++++l++++ +
  gi|15668817|ref|NP_247620.1| 156 ELPENILIIGGGVVATEYASIFSDFGCNVV-LYTRSKILkEIKDEEIRDYLMKKVIN 211
                                   *****************************8.6666666669999******9998766 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.4e-06
                                   -EEEETTEEE--TTSBE.SSTTEEE-GGGC..T CS
                                   xxxxxxxxxxxxxxxxx.xxxxxxxxxxxx..x RF
                   Pyr_redox_2 250 lelderggivvdeflrt.nvpgiyaiGDva..g 279
                                   l++  +g++++d++lr+ n +++ya+GD+   g
  gi|15668817|ref|NP_247620.1| 234 LAIGGNGRFKTDDYLRVlNEEKVYACGDCLinG 266
                                   567789**********967**********9652 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0074       5.1       1      30 [.      10      39 ..      10      43 .. 0.93
   2 ?    2.0   0.2      0.45   3.1e+02      37      61 ..      92     116 ..      60     126 .. 0.83
   3 !   36.0   0.0   1.1e-11   7.7e-09       1      50 [.     160     209 ..     160     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0074
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvver 30
                                  k++vvG+G  g   A +la+ g +V ++e 
  gi|15668817|ref|NP_247620.1| 10 KIAVVGAGPAGRTSAMFLAKNGFDVDLFEK 39
                                  79********************99999985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.45
                                   TSSHHHHHHHHHHHHHTTEEEECSE CS
                     Pyr_redox  37 llDeeaskilqeklekngievllnt 61 
                                   ++ + +++ l+++ +++g+++ +++
  gi|15668817|ref|NP_247620.1|  92 KIQDRIRNKLEKETKELGVNIKYKE 116
                                   5556789999999999999998875 PP

  == domain 3  score: 36.0 bits;  conditional E-value: 1.1e-11
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHH CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqekl 50 
                                   +++++GgG+++ E+A++++++g++V +  rs+ l    Dee++++l++k+
  gi|15668817|ref|NP_247620.1| 160 NILIIGGGVVATEYASIFSDFGCNVVLYTRSKILKEIKDEEIRDYLMKKV 209
                                   589**************************999999************997 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.2   9.3e-12   6.4e-09       2     204 ..      13     198 ..      12     260 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 9.3e-12
                   Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkgnignsiyrypkemtfispsftsekleipdlnaiseetspafslkeeklsrke 82 
                                   ++GaGPaG ++a+ l k+g+ d+   Ek+++g +  +y    t i+     e  +i++  +i ++++      ee +s ke
  gi|15668817|ref|NP_247620.1|  13 VVGAGPAGRTSAMFLAKNGF-DVDLFEKDRVGGTCLNYGC--TYITG--LREMADIINNLSILKGEKV---HLEEIISFKE 85 
                                   8*******************.89***************76..67884..3566677776677777774...35889999** PP

                   Pyr_redox_3  83 aleYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkya 163
                                   + e  +++ ++ + + +++++   v+ + ++f+   +k++   +++i AtG+ ++P   n++G e  v  ++ +++++++ 
  gi|15668817|ref|NP_247620.1|  86 LQEKINKIQDRIRNKLEKETKELGVNIKYKEFK---NKHKNDYDYIIYATGR-NYPS--NYNGYE--VLTHKDIPNLREL- 157
                                   **********99999999999999999999998...55555668********.7776..689998..5556678888666. PP

                   Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekees 204
                                    +++++iGg+  a ++A  + + g++V ++tr++ +++ ++
  gi|15668817|ref|NP_247620.1| 158 PENILIIGGGVVATEYASIFSDFGCNVVLYTRSKILKEIKD 198
                                   689*****************************998777542 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.6e-05     0.025       1      31 [.      10      40 ..      10      45 .. 0.93
   2 ?    1.7   0.0      0.31   2.1e+02      10      51 ..      60     106 ..      53     129 .. 0.66
   3 !   14.5   0.0   3.6e-05     0.025       2      61 ..     161     222 ..     160     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                                  EEEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdis 31
                                  k+av+GaG  G+  a+ +a++g++V l++ +
  gi|15668817|ref|NP_247620.1| 10 KIAVVGAGPAGRTSAMFLAKNGFDVDLFEKD 40
                                  69************************99875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.31
                                   CHHHHHHHHHHTT-EEEEE-S.....-HHHHHHHHHHHHHHHHCCTT CS
                       3HCDH_N  10 mGagiaavfasagleVvlvdi.....seealekalekieksleklve 51 
                                   m   i ++ + +g +V+l +i      +e+++k +++i+++lek  +
  gi|15668817|ref|NP_247620.1|  60 MADIINNLSILKGEKVHLEEIisfkeLQEKINKIQDRIRNKLEKETK 106
                                   77778888899999999999874444445555555555555555444 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.6e-05
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTT.TSS-.HHHHC CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvek.gklk.eeeve 61 
                                   + +iG G++ ++ a++f   g++Vvl+ +s+   e   e+i++ l k v + + ++ +ee e
  gi|15668817|ref|NP_247620.1| 161 ILIIGGGVVATEYASIFSDFGCNVVLYTRSKILKEIKDEEIRDYLMKKVINfKIINdKEELE 222
                                   679**************************999999999999996665554404444344444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.1   3.4e-10   2.4e-07       1      38 [.      13      49 ..      13      59 .. 0.93
   2 ?   -0.1   0.1       1.6   1.1e+03       1      25 [.     163     187 ..     163     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3.4e-10
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                  +vGaG +G + A +Lak+gfdv+l+ek dr+GG +  y
  gi|15668817|ref|NP_247620.1| 13 VVGAGPAGRTSAMFLAKNGFDVDLFEK-DRVGGTCLNY 49
                                  8*************************9.6****99765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.6
                                   EE--SHHHHHHHHHHHCCTEEEEEE CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlll 25 
                                   I+G+G+ +  +A+  ++ g++v+l+
  gi|15668817|ref|NP_247620.1| 163 IIGGGVVATEYASIFSDFGCNVVLY 187
                                   89***99999998888888888887 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.029        20       8      40 ..       9      41 ..       2     141 .. 0.70
   2 !   18.9   0.0   2.3e-06    0.0016       8      78 ..     159     224 ..     156     237 .. 0.75
   3 ?   -2.3   0.0       8.6   5.9e+03      10      23 ..     262     275 ..     260     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.029
                 NAD_binding_7  8 kkvlvvGgGevAarkvrklleagakvtvvapev 40
                                   k+ vvG+G+ + + +  l+++g +v +  ++ 
  gi|15668817|ref|NP_247620.1|  9 LKIAVVGAGPAGRTSAMFLAKNGFDVDLFEKDR 41
                                  6899**********************9988874 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.3e-06
                 NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatddrelneri 78 
                                   +++l++GgG vA++ ++ + ++g++v++++    ++l+e   +++ee+++ l +  + + +++d+e+ e++
  gi|15668817|ref|NP_247620.1| 159 ENILIIGGGVVATEYASIFSDFGCNVVLYTRS--KILKE---IKDEEIRDYLMKKVINFKIINDKEELENL 224
                                   589**************************999..34333...66666666666666666666666665555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8.6
                 NAD_binding_7  10 vlvvGgGevAarkv 23 
                                   +l+ GgG+   +++
  gi|15668817|ref|NP_247620.1| 262 CLINGGGNTPISRM 275
                                   89999998766665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   1.9e-06    0.0013       1      46 [.      10      57 ..      10      89 .. 0.79
   2 ?    5.3   0.0     0.013       8.7       2      30 ..     161     189 ..     160     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.9e-06
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE- CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsigg 46
                                  ++ V+G+G AG   A+ +a+ G++v L+      +t+++ +C    g 
  gi|15668817|ref|NP_247620.1| 10 KIAVVGAGPAGRTSAMFLAKNGFDVDLFekDRVGGTCLNYGCTYITGL 57
                                  589*************************65556788888888765555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.013
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                          GIDA   2 viViGgGhAGceAAlaaarlGakvlLith 30 
                                   + +iGgG   +e A   +  G++v+L+t 
  gi|15668817|ref|NP_247620.1| 161 ILIIGGGVVATEYASIFSDFGCNVVLYTR 189
                                   78*************************75 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0012      0.84       1      31 [.      11      41 ..      11      53 .. 0.92
   2 ?   -1.2   0.1       2.1   1.4e+03      48      75 ..     104     131 ..      65     132 .. 0.55
   3 !   10.9   0.0   0.00038      0.26       1      43 [.     161     203 ..     161     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                  ia++GaG  G++ a  Lak+g dv l  ++r
  gi|15668817|ref|NP_247620.1| 11 IAVVGAGPAGRTSAMFLAKNGFDVDLFEKDR 41
                                  89**********************9987665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                                   CEEEEEECEEECCH...........SCCCCS-ESEEEE- CS
                          ApbA  48 geeilrppealsae...........ekselepidlvivt 75 
                                   +            +           +++++ ++d++i +
  gi|15668817|ref|NP_247620.1| 104 ET-----------KelgvnikykefKNKHKNDYDYIIYA 131
                                   22...........12333344445577888888888866 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00038
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEE CS
                          ApbA   1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrl 43 
                                   i+i+G G + + +a   +  g++v+l++rs+ l+++k++ +r 
  gi|15668817|ref|NP_247620.1| 161 ILIIGGGVVATEYASIFSDFGCNVVLYTRSKILKEIKDEEIRD 203
                                   89*****************************999999998875 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.04        28      37     100 ..       9      69 ..       3      90 .. 0.70
   2 !   15.7   0.0     1e-05    0.0071      38      80 ..     160     201 ..     144     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.04
                                   SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S- CS
                  2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlp 100
                                    +++++G+G  G++ a  l++ g++v  +++ +   + + ++g++   +  l + +Di+ +   
  gi|15668817|ref|NP_247620.1|   9 LKIAVVGAGPAGRTSAMFLAKNGFDVDLFEKDRVGGT-CLNYGCT--YITGLREMADIINNLSI 69 
                                   5799****************99999888877766444.6666663..34444455566555555 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1e-05
                                   EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC CS
                  2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv 80 
                                    + iiG G ++++ a +++ fg++v+ y rsk  +e  +++++
  gi|15668817|ref|NP_247620.1| 160 NILIIGGGVVATEYASIFSDFGCNVVLYTRSKILKE-IKDEEI 201
                                   688***************************987665.444444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   9.8e-07   0.00068       3      33 ..      10      40 ..       8      43 .. 0.91
   2 ?   -2.6   0.0       3.5   2.4e+03       4      31 ..     161     188 ..     160     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.8e-07
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                  ++++VGaGpaG ++a++L++ G +v l ek 
  gi|15668817|ref|NP_247620.1| 10 KIAVVGAGPAGRTSAMFLAKNGFDVDLFEKD 40
                                  689**********************999987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.5
                                   EEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                 FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlve 31 
                                   +lI+G+G +    a++ s  G +vvl +
  gi|15668817|ref|NP_247620.1| 161 ILIIGGGVVATEYASIFSDFGCNVVLYT 188
                                   79*****999999999999998888755 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00025      0.17       1      33 [.      10      55 ..      10     130 .. 0.81
   2 !    7.3   0.0     0.006       4.1       2      57 ..     161     215 ..     160     236 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                                  -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H.............H CS
                NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvree.............e 33
                                  kiav+GaG  G + A+ la+ng +v l+ +++              
  gi|15668817|ref|NP_247620.1| 10 KIAVVGAGPAGRTSAMFLAKNGFDVDLFEKDRvggtclnygctyiT 55
                                  7**************************9998866655555555553 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.006
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTE CS
                NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenl 57 
                                   i ++G+G   t  A ++++ g++v+l++r++  ++ei++e+     ++++   + +
  gi|15668817|ref|NP_247620.1| 161 ILIIGGGVVATEYASIFSDFGCNVVLYTRSK-ILKEIKDEEIRDYLMKKVINFKII 215
                                   789************************9875.666676665554444444333333 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.5e-06     0.001       1      36 [.      10      45 ..      10      56 .. 0.92
   2 ?   -0.1   0.1      0.77   5.3e+02       2      10 ..     161     169 ..     160     190 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                  +++++G+G +G + A++La+ g  V l+ek+ ++g g+
  gi|15668817|ref|NP_247620.1| 10 KIAVVGAGPAGRTSAMFLAKNGfdVDLFEKD-RVG-GT 45
                                  59*****************************.777.54 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.77
                                   EEEECTSHH CS
                           DAO   2 vviiGGGii 10 
                                   ++iiGGG++
  gi|15668817|ref|NP_247620.1| 161 ILIIGGGVV 169
                                   99*****98 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.5e-06    0.0024      17      55 ..       8      44 ..       3      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.5e-06
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                     +++vGaG++G t+a  lak+ ++ v ++e+    GG
  gi|15668817|ref|NP_247620.1|  8 TLKIAVVGAGPAGRTSAMFLAKN-GFDVDLFEKDRV-GG 44
                                  56799******************.********8743.33 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.2e-06    0.0043       2      33 ..      10      41 ..       9      49 .. 0.91
   2 ?   -1.9   0.1       1.5   1.1e+03     321     342 ..      96     117 ..      75     134 .. 0.48

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.2e-06
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                  +++v+G+G+AG   A+ +ak+g +V l+ek +
  gi|15668817|ref|NP_247620.1| 10 KIAVVGAGPAGRTSAMFLAKNGFDVDLFEKDR 41
                                  689**************************985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                                   BGGG--HHHHHHHHHHHHSEEE CS
                   HI0933_like 321 klaqlskkelkklaealkaltv 342
                                   ++++  +ke k+l  ++k  ++
  gi|15668817|ref|NP_247620.1|  96 RIRNKLEKETKELGVNIKYKEF 117
                                   3333333333333333333333 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.03        21      30      60 ..      10      40 ..       2      58 .. 0.90
   2 !   11.2   0.0   0.00024      0.16      28      76 ..     158     211 ..     136     232 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.03
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                  k+ v+G+G aG  ++   ++ g +V +++++
  gi|15668817|ref|NP_247620.1| 10 KIAVVGAGPAGRTSAMFLAKNGFDVDLFEKD 40
                                  899*************999999999999876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00024
                                   --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH......TTTCECE CS
                   AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles......lgakfve 76 
                                   p ++l+iGgGv+ ++ +++ + +g +V+++  r++ l+++++      l +k+++
  gi|15668817|ref|NP_247620.1| 158 PENILIIGGGVVATEYASIFSDFGCNVVLYT-RSKILKEIKDeeirdyLMKKVIN 211
                                   5689***********************8875.55555555553533344444444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.5e-05     0.018       2      33 ..      11      42 ..      10      54 .. 0.89
   2 ?   -2.6   0.0       3.2   2.2e+03     378     414 ..     244     277 ..     242     279 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                  EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                 FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                  + V+G+G AG ++A+ +a++G +v + ek  +
  gi|15668817|ref|NP_247620.1| 11 IAVVGAGPAGRTSAMFLAKNGFDVDLFEKDRV 42
                                  67**************************9886 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.2
                                   BETTSBESTTEEESSBTEEE-STCE..ESSSSTTS--TT CS
                 FAD_binding_2 378 tdengrvldadgqpipGLYAaGeva..aggvhganrlgG 414
                                   td+ +rv      + +  YA+G ++  +gg  ++ r++G
  gi|15668817|ref|NP_247620.1| 244 TDDYLRV-----LNEEKVYACGDCLinGGGNTPISRMEG 277
                                   6666666.....333457*****9977777777777666 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.032        22       7      37 ..       3      33 ..       1      94 [. 0.83
   2 ?    0.5   0.0      0.82   5.7e+02      41      85 ..      93     134 ..      72     139 .. 0.76
   3 ?    6.3   0.0     0.014       9.5      13      45 ..     159     190 ..     146     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.032
                                  HS..TT-EEEEES-SHHHHHHHHHHHCCT-C CS
                  Shikimate_DH  7 leslkekkvlliGaGemaelvakhLlakgvk 37
                                  +++  + k+ ++GaG  ++  a  L+++g++
  gi|15668817|ref|NP_247620.1|  3 FGESMTLKIAVVGAGPAGRTSAMFLAKNGFD 33
                                  55666889**************999998876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.82
                                   EEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSS CS
                  Shikimate_DH  41 vaNRtlerakelaeelkgeeiealkleelkellaeadvvisatas 85 
                                   +  R +++ ++  +el g++i+++++++  ++ +++d +i at+ 
  gi|15668817|ref|NP_247620.1|  93 IQDRIRNKLEKETKEL-GVNIKYKEFKN--KHKNDYDYIIYATGR 134
                                   6677777778888888.66688888886..456899999999986 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.014
                                   -EEEEES-SHHHHHHHHHHHCCT-CEEEEEESS CS
                  Shikimate_DH  13 kkvlliGaGemaelvakhLlakgvkkvvvaNRt 45 
                                   +++l+iG G +a++ a+ +++ g++ vv   R+
  gi|15668817|ref|NP_247620.1| 159 ENILIIGGGVVATEYASIFSDFGCN-VVLYTRS 190
                                   689*********************9.7777775 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0018       1.2       6      32 ..      10      36 ..       7      67 .. 0.91
   2 ?   -3.4   0.1       8.9   6.1e+03      80     108 ..      96     121 ..      80     127 .. 0.60
   3 ?    3.8   0.0     0.057        39       6      38 ..     160     192 ..     157     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
                                  -EEEES-SHHHHHHHHHHHHTT--EEE CS
                          IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvv 32
                                  kiav+G G  G++ a+ l  +g+dv +
  gi|15668817|ref|NP_247620.1| 10 KIAVVGAGPAGRTSAMFLAKNGFDVDL 36
                                  8***********************965 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.9
                                   HTGGG--TT-EEEESSSHHHHTTSS---T CS
                          IlvN  80 eiepnlkegkalafahGfnihfglikppk 108
                                   +i+++l++++      G ni+++  k+++
  gi|15668817|ref|NP_247620.1|  96 RIRNKLEKETK---ELGVNIKYKEFKNKH 121
                                   44444444332...347788887777665 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.057
                                   -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT- CS
                          IlvN   6 kiaviGyGsqGhaqalnlrdsgldvvvglregs 38 
                                   +i +iG G  +   a  + d g++vv+  r++ 
  gi|15668817|ref|NP_247620.1| 160 NILIIGGGVVATEYASIFSDFGCNVVLYTRSKI 192
                                   689**********************98766554 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.07        49       2      30 ..      12      40 ..      11      62 .. 0.92
   2 ?    8.3   0.0    0.0044       3.1       2      66 ..     162     226 ..     161     257 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.07
                                  EEE--STTHHHHHHHHHHHTEEEEEEES- CS
                        XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpr 30
                                  +++Gag+ ++  a ++a+ gf+v +++++
  gi|15668817|ref|NP_247620.1| 12 AVVGAGPAGRTSAMFLAKNGFDVDLFEKD 40
                                  79*********************999876 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0044
                                   EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE...-EEEE--S-HHHHHHHHHHHSS CS
                        XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade...tavvvlthdhklDaealeaalr 66 
                                   +i+G+g va + a++ + +g++v+++   + +++ ++ +        +  v+  +   D+e le++l+
  gi|15668817|ref|NP_247620.1| 162 LIIGGGVVATEYASIFSDFGCNVVLYTRSKILKEIKDEE---IrdyLMKKVINFKIINDKEELENLLK 226
                                   89**********************998887544322222...12123333555555566666666664 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.09       1      37 [.      10      43 ..      10      65 .. 0.89
   2 ?   -2.1   0.0       1.8   1.3e+03       1      22 [.     160     181 ..     160     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeig 37
                                  ki +vG+G+aG ++A+ lak +   ++v l e++ +g
  gi|15668817|ref|NP_247620.1| 10 KIAVVGAGPAGRTSAMFLAKNG---FDVDLFEKDRVG 43
                                  799*****************99...9*******9997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                                   EEEEE--SHHHHHHHHHHHHHT CS
                Trp_halogenase   1 kivivGGGtaGwlaAaalakal 22 
                                   +i+i+GGG  +   A++++  +
  gi|15668817|ref|NP_247620.1| 160 NILIIGGGVVATEYASIFSDFG 181
                                   599*****99888887777665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.7e-05     0.067       2      53 ..      11      61 ..      10     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.7e-05
                  FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee 53
                                  + VvG+gpaG + A+  a++G  v L e++ ++GG+  + + + ++g +  +
  gi|15668817|ref|NP_247620.1| 11 IAVVGAGPAGRTSAMFLAKNGFDVDLFEKD-RVGGTCLNYGCTYITGLREMA 61
                                  78*************************986.579998888888887766444 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0009      0.62       2      34 ..      10      42 ..       9      69 .. 0.83
   2 ?    0.9   0.0      0.41   2.8e+02       2      28 ..     160     186 ..     159     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0009
                                  EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HH CS
                UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDidee 34
                                  ki+v+G+G  G ++a+ la+ g++v +  +d+ 
  gi|15668817|ref|NP_247620.1| 10 KIAVVGAGPAGRTSAMFLAKNGFDVDLFEKDRV 42
                                  8***********************987777665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.41
                                   EEEEE--STTHHHHHHHHHHCTSEEEE CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevig 28 
                                   +i +iG G v    a +++  g +v++
  gi|15668817|ref|NP_247620.1| 160 NILIIGGGVVATEYASIFSDFGCNVVL 186
                                   799********************9996 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.39   2.7e+02      21      73 ..      61     117 ..      46     156 .. 0.71
   2 ?    9.4   0.0    0.0015         1       2      42 ..     159     215 ..     158     234 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.39
                                   xxxxxxxxxxxxxxxxxxx..xxxxxx.xxxxxxxxxxx.xxxxxxxxx..xxxxxxxx RF
                 NAD_binding_6  21 kdllkkskkealktkkikl..iwvvre.ssslewfkdvL.neleeekse..gnieihiY 73 
                                    d++++++   lk +k++l  i++++e +++++ ++d + n+le+e++e   ni+++ +
  gi|15668817|ref|NP_247620.1|  61 ADIINNLS--ILKGEKVHLeeIISFKElQEKINKIQDRIrNKLEKETKElgVNIKYKEF 117
                                   56777777..6666666665567777734567777777778888888877667776655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0015
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxx RF
                 NAD_binding_6   2 envllvagGiGitpfisilkdllkksk................kealktkkikliwv 42 
                                   en+l+++gG+ +t ++si+ d++ +                     l +k i++ ++
  gi|15668817|ref|NP_247620.1| 159 ENILIIGGGVVATEYASIFSDFGCNVVlytrskilkeikdeeiRDYLMKKVINFKII 215
                                   79********************99988776666666666665555555555555555 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.25   1.7e+02       1      29 [.      10      37 ..      10      75 .. 0.78
   2 ?    1.6   0.3      0.65   4.5e+02      34      68 ..     103     135 ..      58     137 .. 0.59
   3 ?    0.8   0.0       1.1   7.9e+02      20      46 ..     121     148 ..     116     159 .. 0.66
   4 ?   10.7   1.2   0.00096      0.66       1      68 [.     160     239 ..     160     241 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.25
                        PglD_N  1 kivIiGaGGhgkvvadiieangeyeiigf 29
                                  ki+++GaG  g+  a  + +ng +++  f
  gi|15668817|ref|NP_247620.1| 10 KIAVVGAGPAGRTSAMFLAKNG-FDVDLF 37
                                  79**********9999999998.666555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.65
                        PglD_N  34 kktevegypvlgkaiellkslseeeyevvi.AIGnn 68 
                                   k+t++ g+++  k  e  k+ ++++y+++i A G n
  gi|15668817|ref|NP_247620.1| 103 KETKELGVNIKYK--E-FKNKHKNDYDYIIyATGRN 135
                                   1223333333333..3.3444467888777688877 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.1
                        PglD_N  20 angeye.iigflDdnkktevegypvlgk 46 
                                   ++++y+ ii  +  n++++ +gy+vl  
  gi|15668817|ref|NP_247620.1| 121 HKNDYDyIIYATGRNYPSNYNGYEVLTH 148
                                   4556662445667789999999999975 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00096
                        PglD_N   1 kivIiGaGGhgkvvadiieangeyeiigflDdnkkteveg.............ypvlgkaiellkslseeeyevviAIGnn 68 
                                   +i+IiG G  + + a i  + g  +++ ++ ++  +e+++             ++++ +  el++ l+ e+y  + AIG n
  gi|15668817|ref|NP_247620.1| 160 NILIIGGGVVATEYASIFSDFG-CNVVLYTRSKILKEIKDeeirdylmkkvinFKIINDKEELENLLKDESYTKILAIGGN 239
                                   799***************9999.566555555432222111223345556666*****9999999999999*99*****87 PP

>> Mfa2  Fimbrillin-A associated anchor proteins Mfa1 and Mfa2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   0.00032      0.22     130     178 ..      92     142 ..      80     156 .. 0.89
   2 ?    1.3   0.3      0.31   2.2e+02     133     201 ..     199     270 ..     185     325 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                                   CCGEEEEEEEEESEEEEEEEEEESTCCEEEGGGEEEEEEESSSEE..ETTS CS
                          Mfa2 130 dektevtvnLirntnklrvilqgdtgeslditdfkfeitatngrl..dydn 178
                                   + + +++ +L++ t+ l v ++  + ++ + +d+++ i+at  ++  +y++
  gi|15668817|ref|NP_247620.1|  92 KIQDRIRNKLEKETKELGVNIKYKEFKNKHKNDYDYIIYATGRNYpsNYNG 142
                                   56778899************************************9888876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.31
                                   EEEEEEEEESEEEEEEEEEE.STCCEEEGGGEE.EEEEESSSEEETTSEB.TSSEEEEEEESEEEECCCSTT CS
                          Mfa2 133 tevtvnLirntnklrvilqg.dtgeslditdfk.feitatngrldydntl.gddksvtylpystelngntgd 201
                                   +e++  L++++ ++++i ++ +  + l++++++ +  ++ ngr++ d  l   ++++ y      +ng +++
  gi|15668817|ref|NP_247620.1| 199 EEIRDYLMKKVINFKIINDKeELENLLKDESYTkILAIGGNGRFKTDDYLrVLNEEKVYACGDCLINGGGNT 270
                                   555556999999****99998555555555554488888899997777776666677776665555555555 PP

>> PdaC  Deacetylase PdaC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.6   0.00024      0.17      12      78 ..      81     146 ..      71     149 .. 0.86
   2 ?   -1.0   0.1       5.1   3.5e+03      23      44 ..     199     228 ..     188     251 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00024
                                   EEEEEE-S-S-HHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHTT---S-EEEEEEEEEEEE-SSEE CS
                          PdaC  12 ikyPvisglknkevqdkinkkiekdadkflkeyekeakeeakkndfpkrpyelevdyevkynsekil 78 
                                   i++ ++++ k++++qd+i +k+ek+ +++  ++++++ +++ knd+ +  y    +y   yn  ++l
  gi|15668817|ref|NP_247620.1|  81 ISFKELQE-KINKIQDRIRNKLEKETKELGVNIKYKEFKNKHKNDYDYIIYATGRNYPSNYNGYEVL 146
                                   45555566.99**********************999999*************999999999988776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 5.1
                                   HHHHHHHHHHH........HHHHHHHHHHH CS
                          PdaC  23 kevqdkinkki........ekdadkflkey 44 
                                   +e+ d + kk+        +++++++lk+ 
  gi|15668817|ref|NP_247620.1| 199 EEIRDYLMKKVinfkiindKEELENLLKDE 228
                                   444444444422223344456666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1581  (0.0881812); expected 358.6 (0.02)
Passed bias filter:                      878  (0.0489709); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2996.98
//
Query:       gi|15668818|ref|NP_247621.1|  [L=272]
Description: prephenate dehydratase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-56  189.7   0.0      5e-56  189.4   0.0    1.1  1  PDT       Prephenate dehydratase
    3.4e-11   42.7   0.0    7.4e-11   41.6   0.0    1.6  1  ACT       ACT domain
    0.00018   22.0   0.0    0.00073   20.1   0.0    2.0  3  ACT_4     ACT domain
  ------ inclusion threshold ------
      0.044   13.7   0.0       0.12   12.3   0.0    1.7  1  Utp13     Utp13 specific WD40 associated domain
      0.065   13.2   0.2      0.065   13.2   0.2    3.0  4  DUF4974   Domain of unknown function (DUF4974)


Domain annotation for each model (and alignments):
>> PDT  Prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.4   0.0   1.4e-59     5e-56       3     181 ..       7     180 ..       5     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 189.4 bits;  conditional E-value: 1.4e-59
                                   EES-TTSHHHHHHCCCS.......EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEEEEEEE CS
                           PDT   3 ylGpegtyshqAalkvf..kaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkivgEvvlp 81 
                                   y  p+gtys++A++k++   + d ++  ++si +vfe v+++   ++vvPiENs+eGsV+ t DlLl+ +d+ki gE+ l+
  gi|15668818|ref|NP_247621.1|   7 YTLPKGTYSEKATKKFLdyIDGDYKIDYCNSIYDVFERVDNNG--LGVVPIENSIEGSVSLTQDLLLQFKDIKILGELALD 85 
                                   5559************99889999*****************98..9**********************99*********** PP

                                   ---EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHHHHTT-EEEE CS
                           PDT  82 iehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaaelyglkvle 162
                                   i+h+L++  k+   +ik+v+Shpqal+Qcr+++++h  ++ + avesta+A+k+v++s+d++  ai+s++ ae+y+lk+l+
  gi|15668818|ref|NP_247621.1|  86 IHHNLIGYDKN---KIKTVISHPQALAQCRNYIKKH--GWDVKAVESTAKAVKIVAESKDETLGAIGSKESAEHYNLKILD 161
                                   *****999887...9*********************..******************************************* PP

                                   CS-SS-S--EEEEEEEEET CS
                           PDT 163 eniedkknntTRFlvlake 181
                                   enied+knn TRF++++k+
  gi|15668818|ref|NP_247621.1| 162 ENIEDYKNNKTRFILIGKK 180
                                   ****************987 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   2.1e-14   7.4e-11       2      63 ..     193     256 ..     192     258 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.1e-14
                                   EEEEEEE.SSTTHHHHHHHHHHHTTSEEEEEEEEEESTT.ECEEEEEEEEEEHHHHHHHHHHHH CS
                           ACT   2 vlrvgvp.DrPGlLarvfgaladrgiNidsieqrssedk.vagivfvvivvdeedleevlealk 63 
                                   ++ ++++ D+PG+L  ++  +a+r+iN+++ie+r+s+ + +  i+ + ++ + e lee+l+ l+
  gi|15668818|ref|NP_247621.1| 193 SIVFELKeDKPGALYHILKEFAERNINLTRIESRPSKKRlGTYIFYIDFENNKEKLEEILKSLE 256
                                   67788888******************************87777777777777777777777665 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         2   7.3e+03      20      42 ..     108     130 ..     101     143 .. 0.68
   2 ?   -2.7   0.0       2.6   9.4e+03      10      33 ..     133     156 ..     130     176 .. 0.61
   3 !   20.1   0.0     2e-07   0.00073       3      71 ..     188     257 ..     186     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2
                         ACT_4  20 Laditqviseekanivsvnaktr 42 
                                   La+  + i++++ ++++v+++++
  gi|15668818|ref|NP_247621.1| 108 LAQCRNYIKKHGWDVKAVESTAK 130
                                   56666677777777777777664 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.6
                         ACT_4  10 eveaedrkglLaditqviseekan 33 
                                   +++ae ++  L+ i +  s+e+ n
  gi|15668818|ref|NP_247621.1| 133 KIVAESKDETLGAIGSKESAEHYN 156
                                   566666666666666555555333 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 2e-07
                         ACT_4   3 esytvrlevea.edrkglLaditqviseekanivsvnaktrkk.dglaeikitveVkdvehLsrviakLra 71 
                                   ++y+v++  e  ed++g+L  i++ ++e ++n++ ++++  kk  g+  + i++e ++ e+L++++++L++
  gi|15668818|ref|NP_247621.1| 188 KNYKVSIVFELkEDKPGALYHILKEFAERNINLTRIESRPSKKrLGTYIFYIDFE-NNKEKLEEILKSLER 257
                                   68********999***************************998777888888888.889999999999986 PP

>> Utp13  Utp13 specific WD40 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05      0.12       9      64 ..     186     259 ..     180     267 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                                   HCCHHHHHHHHHHHSSSTHHHHHHHHHHHS-SS-....................-STSSSSSHHHHHHHHC--HHH CS
                         Utp13   9 rkkdyreAiaLAlkldqpkrllkllkevleseee....................eeesitgskevdevlkslskeq 64 
                                   + k+y+  i + lk d+p+ l+++lke++e++ +                    +   ++++++++e+lksl++++
  gi|15668818|ref|NP_247621.1| 186 HPKNYKVSIVFELKEDKPGALYHILKEFAERNINltriesrpskkrlgtyifyiDF--ENNKEKLEEILKSLERHT 259
                                   6699*************************887779999999999999988885433..333346899999998765 PP

>> DUF4974  Domain of unknown function (DUF4974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         3   1.1e+04      47      61 ..      20      34 ..      12      39 .. 0.71
   2 ?   -2.1   0.1       1.1     4e+03      19      30 ..     154     166 ..     150     174 .. 0.56
   3 ?    0.4   0.0      0.18   6.4e+02      32      43 ..     188     199 ..     178     219 .. 0.63
   4 ?   13.2   0.2   1.8e-05     0.065      28      57 ..     229     259 ..     221     263 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3
                                  HHHHHHHHHHH--EE CS
                       DUF4974 47 eevLelLektggiky 61
                                   ++L+++   ++i+y
  gi|15668818|ref|NP_247621.1| 20 KKFLDYIDGDYKIDY 34
                                  567888887777777 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                                   HHT--EEE-T.TS CS
                       DUF4974  19 wYnveivien.ee 30 
                                   +Yn +i  en e+
  gi|15668818|ref|NP_247621.1| 154 HYNLKILDENiED 166
                                   5666554444333 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.18
                                   ---EEEEEES-. CS
                       DUF4974  32 knyrftgtfsrn 43 
                                   kny++++ f+ +
  gi|15668818|ref|NP_247621.1| 188 KNYKVSIVFELK 199
                                   456666655333 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 1.8e-05
                                   TTS----EEEEEE.S-.-.HHHHHHHHHHHH CS
                       DUF4974  28 neelknyrftgtf.srnesleevLelLektg 57 
                                   +++l +y f++ f +++e+lee+L++Le+ +
  gi|15668818|ref|NP_247621.1| 229 KKRLGTYIFYIDFeNNKEKLEEILKSLERHT 259
                                   477999*********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1720.57
//
Query:       gi|15668819|ref|NP_247622.1|  [L=225]
Description: hypothetical protein MJ_0638 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-17   63.9   0.0    2.9e-17   63.1   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    2.7e-12   47.2   0.0    5.4e-12   46.3   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    5.3e-11   42.6   0.0    7.7e-11   42.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    4.1e-09   37.1   0.0    1.3e-08   35.5   0.1    1.7  2  Methyltransf_12  Methyltransferase domain
    4.7e-08   33.2   0.9    7.1e-08   32.6   0.5    1.4  2  Methyltransf_8   Hypothetical methyltransferase
    1.3e-07   31.6   2.5      2e-06   27.7   2.4    2.5  2  Methyltransf_31  Methyltransferase domain
    3.5e-07   29.6   0.2    4.2e-07   29.3   0.2    1.2  1  DREV             DREV methyltransferase
    6.1e-07   29.0   0.3      1e-06   28.2   0.1    1.6  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0057   16.2   0.6       0.15   11.6   0.6    2.3  1  MTS              Methyltransferase small domain
     0.0058   15.9   0.0     0.0097   15.2   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.0   1.6e-20   2.9e-17       1      96 []      51     136 ..      51     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 1.6e-20
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekal 81 
                                   Ld+GcG G++ +  +  + +++ +D+s ++lk+ k k ++       ++a++ +lpf+dn+fDlv++ +vl+hv +  kal
  gi|15668819|ref|NP_247622.1|  51 LDCGCGFGAFYNLTK-DF-NTIYLDISLNLLKRFKLKERK-------ICANILHLPFKDNTFDLVLCINVLEHV-NYLKAL 121
                                   8**********9999.44.6999********999766665.......9**************************.5999** PP

                                   HHHHHHEEEEEEEEE CS
               Methyltransf_11  82 keiaRvLkpgGllvi 96 
                                   +ei+R+Lk+ G+l++
  gi|15668819|ref|NP_247622.1| 122 NEIRRILKNKGKLIV 136
                                   ************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0     3e-15   5.4e-12       1      97 []      50     132 ..      50     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 3e-15
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                   vLd+GcG G +  +l k     + + +Dis ++l++ + +        + +++++ +lpf+d++fDlv+++++l+h++   
  gi|15668819|ref|NP_247622.1|  50 VLDCGCGFGAF-YNLTKD---FNTIYLDISLNLLKRFKLKE-------RKICANILHLPFKDNTFDLVLCINVLEHVN--- 116
                                   9********76.456666...589***********998887.......569*******************999***97... PP

                                   HHHHHHHHHHHEEEEE CS
               Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                   + kal+ei+r+Lk++G
  gi|15668819|ref|NP_247622.1| 117 YLKALNEIRRILKNKG 132
                                   789**********998 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   4.3e-14   7.7e-11       9     124 ..      31     143 ..      23     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 4.3e-14
               Methyltransf_23   9 lsdklerllpk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIv 87 
                                   + +++  ll+k  ++++  vLd GcG G + ++ ++  f+ +  D+s ++ ++   + k +k +++    ++++++fdl+ 
  gi|15668819|ref|NP_247622.1|  31 IFEEISLLLKKfeNKKDFLVLDCGCGFGAFYNLTKD--FNTIYLDISLNLLKR--FKLKERKICANILHLPFKDNTFDLVL 107
                                   5567777776644666669*********99997755..699*******98888..59999999999999999********* PP

               Methyltransf_23  88 lrevlehvpdppellrqiatllkpgGylllseplasl 124
                                   +++vlehv +  ++l+ i+++lk  G l++ ++++++
  gi|15668819|ref|NP_247622.1| 108 CINVLEHVNY-LKALNEIRRILKNKGKLIVVVVNKDS 143
                                   ********88.889*******************9986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.1   7.1e-12   1.3e-08       1      99 []      51     134 ..      51     134 .. 0.73
   2 ?   -2.6   0.0       5.3   9.4e+03      70      91 ..     191     212 ..     189     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 7.1e-12
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                   L+ GcG G  +++ l k  d + +++Dis + +  ++ kl++r+     + ++ +l   d    ++fDlv+++nvl+h+ +
  gi|15668819|ref|NP_247622.1|  51 LDCGCGFG--AFYNLTK--DFNTIYLDISLNLL--KRFKLKERKI----CANILHLPFKD----NTFDLVLCINVLEHV-N 116
                                   67788888..5555667..88************..4444444443....22333333222....39************9.7 PP

               Methyltransf_12  82 irevldnirklLkpgGrl 99 
                                     ++l++ir+ Lk+ G+l
  gi|15668819|ref|NP_247622.1| 117 YLKALNEIRRILKNKGKL 134
                                   7789**********9986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.3
               Methyltransf_12  70 vvasnvlhhlkdirevldnirk 91 
                                   +++s  ++++k++++ l++i k
  gi|15668819|ref|NP_247622.1| 191 IILSKIIEYWKPVDKKLSKIFK 212
                                   7889999999999988888765 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.5     4e-11   7.1e-08      37     183 ..      12     170 ..       2     190 .. 0.70
   2 ?   -2.5   0.0       2.1   3.8e+03     130     158 ..     193     221 ..     190     223 .. 0.70

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 4e-11
                                   -HHHHHHHHHHHHHHHCTSSS-HHHHHHHHHCTS-TTS-EEEES-TT-HHHHH--S-..E...EEEESS...-SSTTEEES CS
                Methyltransf_8  37 dpeafdlyhkgfrsqvkkWPenPldviirklkkkkdnlvvadlGcGeakiaeavrekekv...rsfdlv...avnervvac 111
                                   +pe f  y k+  +   +   + +  +++k+++kkd   v d GcG     +  ++++ +   +s++l     ++er +  
  gi|15668819|ref|NP_247622.1|  12 EPEDFPNYIKLLMNFADELIFEEISLLLKKFENKKD-FLVLDCGCGFGAFYNLTKDFNTIyldISLNLLkrfKLKERKICA 91 
                                   566666666666666666666667777777777765.5688*****99988777777666333477765222578999999 PP

                                   -TTS-S--TT-EEEEEEES---SS-HHHHHHHHHHHEEEEEEEEEEEEG..GG-S.....-HHHHHHHHHCTTEEEEEE CS
                Methyltransf_8 112 dlakvPledesvdvavfclslmgtnladflkeanrvlkvGGllkvaevk..srfe.....svklfaraltklGfevksk 183
                                   ++ ++P +d++ d++++   l   n+ + l+e++r+lk+ G l v  v+  s ++     + k+f + l+   fe++  
  gi|15668819|ref|NP_247622.1|  92 NILHLPFKDNTFDLVLCINVLEHVNYLKALNEIRRILKNKGKLIVVVVNkdSLIKeeifnDFKIFHKPLSIKDFEIDGF 170
                                   **************9988889999******************9998775223222222236777777666666666544 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.1
                                   S---SS-HHHHHHHHHHHEEEEEEEEEEE CS
                Methyltransf_8 130 lslmgtnladflkeanrvlkvGGllkvae 158
                                   ls + + ++   k   +++k+ G + + e
  gi|15668819|ref|NP_247622.1| 193 LSKIIEYWKPVDKKLSKIFKNKGQFLIIE 221
                                   56666667777777788888888777766 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   2.4   1.1e-09     2e-06       3     113 ..      46     140 ..      44     159 .. 0.79
   2 ?   -0.8   0.0      0.66   1.2e+03      74     111 ..     169     221 ..     150     224 .. 0.54

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.1e-09
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                   k+  vlD+GCG G++          + + + +Dis + +++ + +  + ++       ++i +l+  ++d++fDl+l+ +v
  gi|15668819|ref|NP_247622.1|  46 KDFLVLDCGCGFGAFYNLTK-----DFNTIYLDISLNLLKRFKLK--ERKI------CANILHLP--FKDNTFDLVLCINV 111
                                   56679*******98866555.....55678889998888877663..3333......389*****..************** PP

               Methyltransf_31  84 lnaladpdkileeiervlkpggilliedpr 113
                                   l +++   k+l+ei r lk++g l++  ++
  gi|15668819|ref|NP_247622.1| 112 LEHVN-YLKALNEIRRILKNKGKLIVVVVN 140
                                   *8876.5689***************98777 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.66
               Methyltransf_31  74 kfDlilsnevl...naladpdkile...................eiervlkpggillied 111
                                    f ++ sn+v            i++                   ++++ +k++g +li +
  gi|15668819|ref|NP_247622.1| 169 GFKIVYSNSVYflpS-------IFKisppiilskiieywkpvdkKLSKIFKNKGQFLIIE 221
                                   555555554443331.......22222222334444455555557777777777777765 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.2   2.3e-10   4.2e-07      92     189 ..      44     139 ..      26     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.3e-10
                          DREV  92 dqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkkkynvlsale.lqetdvkldlilclnlldrcfdplkll 171
                                   +++d  +ld G G G    ++++ f+ +y  ++s ++ +r+k k+ ++ +++  l   d  +dl+lc+n+l+ + + lk l
  gi|15668819|ref|NP_247622.1|  44 NKKDFLVLDCGCGFGAFY-NLTKDFNTIYL-DISLNLLKRFKLKERKICANILhLPFKDNTFDLVLCINVLE-HVNYLKAL 121
                                   467889*********986.5778899***5.89**********999998766448889*************8.6789**** PP

                          DREV 172 edirsalepngrvivalv 189
                                   ++ir +l+ +g+ iv +v
  gi|15668819|ref|NP_247622.1| 122 NEIRRILKNKGKLIVVVV 139
                                   **************9887 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   5.8e-10     1e-06      68     156 ..      62     141 ..      18     160 .. 0.73
   2 ?   -3.5   0.0       2.8   5.1e+03     137     154 ..     205     222 ..     202     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 5.8e-10
                                   HHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEE CS
               Ubie_methyltran  68 svgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGr 148
                                   ++ + ++ + lDi+ n+Lk  + k  e      + ++an  +Lpf+d++fD+v     +    ++lkaL+e++r+lk  G+
  gi|15668819|ref|NP_247622.1|  62 NLTKDFNTIYLDISLNLLKRFKLK--E------RKICANILHLPFKDNTFDLVLC-INVLEHVNYLKALNEIRRILKNKGK 133
                                   445566677777777777754433..3......3479**************9865.55666778***************** PP

                                   EEEEEE-- CS
               Ubie_methyltran 149 lvvlefsk 156
                                   l+v+ + k
  gi|15668819|ref|NP_247622.1| 134 LIVVVVNK 141
                                   99887665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.8
                                   HHHHHHEEEEEEEEEEEE CS
               Ubie_methyltran 137 keayrvlkpGGrlvvlef 154
                                   k++ +++k  G+++++e+
  gi|15668819|ref|NP_247622.1| 205 KKLSKIFKNKGQFLIIEM 222
                                   556678899999999987 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.6   8.6e-05      0.15      21     138 ..      36     137 ..      26     167 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.6e-05
                                   HHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEE CS
                           MTS  21 klLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdli 101
                                   +lLl++++++++  vlD GcG+G+     ++     +   +d++ + l+     l++ k+     a+ +   ++++ fdl+
  gi|15668819|ref|NP_247622.1|  36 SLLLKKFENKKDFLVLDCGCGFGAFYNLTKD----FNTIYLDISLNLLKR--FKLKERKI----CANILHLPFKDNTFDLV 106
                                   699******99999*********86443333....233355665554432..22333333....33333334555556666 PP

                                   EE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEE CS
                           MTS 102 vsNPPfhagkatelavaeeliaeAkeaLkegGeLliV 138
                                   ++   +   ++       + ++e +++Lk++G+L++V
  gi|15668819|ref|NP_247622.1| 107 LC---INVLEH---VNYLKALNEIRRILKNKGKLIVV 137
                                   65...333222...22233445556666666666554 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.4e-06    0.0097      51     167 ..      35     139 ..      26     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.4e-06
                                   HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEE CS
                          CMAS  51 ldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrv 131
                                   + l+l+k e k+   +Ld GcG+G+       + d + + l +S +  k+ k      + +  ++++ l ++d  + +d v
  gi|15668819|ref|NP_247622.1|  35 ISLLLKKFENKKDFLVLDCGCGFGAFYN--LTK-DFNTIYLDISLNLLKRFKL----KERKICANILHLPFKD--NTFDLV 106
                                   67899999999999**********9765..566.88999999**998876554....3444457788888876..79**** PP

                                   EEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEE CS
                          CMAS 132 vsvgafehvgkenydtffkklkkllkedGllllhti 167
                                     ++++ehv   ny +  +++ ++lk+ G l++  +
  gi|15668819|ref|NP_247622.1| 107 LCINVLEHV---NYLKALNEIRRILKNKGKLIVVVV 139
                                   ********9...7999999**********9987554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1389.19
//
Query:       gi|15668820|ref|NP_247623.1|  [L=109]
Description: hypothetical protein MJ_0639 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 738.82
//
Query:       gi|15668821|ref|NP_247624.1|  [L=324]
Description: hypothetical protein MJ_0640 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-16   59.7   1.0    1.8e-15   57.3   0.9    2.0  2  AIRS      AIR synthase related protein, N-terminal domain
    3.7e-13   49.9   0.0    5.5e-13   49.3   0.0    1.3  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.9     2e-19   1.8e-15       1      93 [.      46     151 ..      46     152 .. 0.80
   2 ?   -0.3   0.0       0.2   1.8e+03      19      44 ..     200     228 ..     162     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 2e-19
                                   SSSEEEEEEEEEE.EECC.TCCCC.........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC...HHHHHHHHHHHHHHH CS
                          AIRS   1 dDaavvvttdshnrpvlv.epvhf.........iGakavavnlsDlaamGArPlalllslalp...wleevvrglaeaaee 68 
                                   dDaa v+ +d+ n  +l  +++ +         +G+ +v vn++D+aamG++ +++++ ++++   +++ev++g+++++++
  gi|15668821|ref|NP_247624.1|  46 DDAA-VIGIDGDNAILLAaDGIWGklleadpwwAGYCSVLVNCKDIAAMGGKCVGMTNIISIKdkdICREVLKGVKDGVKK 125
                                   7999.66666555544443444446666666678*********************************************** PP

                                   TT-EEEEEEEEEESS.EEEEEEEEEE CS
                          AIRS  69 lgvplvgGdtsfsne.ptisvtavGl 93 
                                   +gvp+vgG+t+ +    ++ v+++G+
  gi|15668821|ref|NP_247624.1| 126 FGVPMVGGHTHPDAMcNVLDVSITGI 151
                                   ***********985555555555554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.2
                                   TCCCC...HHHHHHHHHHHHHHTTTEEEE CS
                          AIRS  19 epvhf...iGakavavnlsDlaamGArPl 44 
                                   ++++    i++  +a+ ++D+   GA  +
  gi|15668821|ref|NP_247624.1| 200 AQMDAlvqIAENKLANSCKDISNPGAIGT 228
                                   33344556799999999999998888655 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   6.2e-17   5.5e-13      41     154 ..     195     305 ..     175     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 6.2e-17
                                   HHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEH CS
                        AIRS_C  41 vlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdelesplemllsensGrllvavpp 121
                                     l++ ++++   +a++ +l+++++D+++ G +g+l ++++ s+ g ++d+ k+p  +e+  +l  +l  + G ++v+ ++
  gi|15668821|ref|NP_247624.1| 195 KKLVRAQMDALVQIAEN-KLANSCKDISNPGAIGTLGMLLEVSRKGGVVDITKIPKPEEI--DLIHWLKVYPGSGYVLTAK 272
                                   55566666666677776.**********************************99999998..9****************** PP

                                   GGH.HHHHHHHHHTTCCCEEEEEEEEESSSEEEE CS
                        AIRS_C 122 eea.davlaileeeglpeaavIGevtakeelsvi 154
                                   ee+ +++++i+e+ +  +a++ Gev+a+++l+++
  gi|15668821|ref|NP_247624.1| 273 EENfKEIKDIFEDVEM-TAEICGEVIAEKKLYIT 305
                                   ***************9.7***********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2108.93
//
Query:       gi|15668822|ref|NP_247625.1|  [L=417]
Description: phosphoglycerate kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.7e-121  405.7   2.4     2e-121  405.5   2.4    1.0  1  PGK       Phosphoglycerate kinase


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.5   2.4  1.1e-125    2e-121       1     377 [.       7     398 ..       7     399 .. 0.91

  Alignments for each domain:
  == domain 1  score: 405.5 bits;  conditional E-value: 1.1e-125
                                   GGGS--TT-EEEEEE-----EECT.TEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHHHT CS
                           PGK   1 vkdldlkgkrvlvRvDfNvplkke.gkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsellg 80 
                                   ++d+++++krv++RvD+N+p++ + g+i dd+rir+  +Ti +l++kgakvv+l+H++rp g+k+ ++lk++a+ Ls+++g
  gi|15668822|ref|NP_247625.1|   7 LDDFNFEDKRVVLRVDINCPIDPNtGEILDDKRIREIKSTITELINKGAKVVILAHQSRP-GKKDFTTLKNHAKVLSDVIG 86 
                                   589******************9888***********************************.89****************** PP

                                   T-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTT.............TT-H..HHHHHHHHT-SEEEE--GGGTTS CS
                           PGK  81 keVkfvedvvgeeveeaiaelkegevllLeNvrfykeEe.............knde..elakklasladvyVnDAFgtahr 146
                                   keV+++++v+g++++eai ++k g+v+lLeNvrfy+eE              k ++  +l k+la l+d++VnDAF++ahr
  gi|15668822|ref|NP_247625.1|  87 KEVEYIDEVIGSTAREAIINMKCGDVILLENVRFYSEEVlsdwkkwenitpkK-QAetNLIKRLAPLFDYFVNDAFAAAHR 166
                                   **************************************666777777776642.22347********************** PP

                                   --TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHHHHHHHTT CS
                           PGK 147 ahaStvgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgmantFlkaqg 225
                                   a+ S+vg++ +++ +aG+lme+E+ +lskvlenpe+p+v++lGGak +d i+v++n+le+   dk+++ G +an+Fl a g
  gi|15668822|ref|NP_247625.1| 167 AQPSLVGFSYYMPMIAGRLMEREVGVLSKVLENPEKPCVYVLGGAKADDSIRVMKNVLENGtaDKVLTSGIVANIFLVAMG 247
                                   ************99********************************************98777****************** PP

                                   -B-TTSS-..-G....GGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EEEEE-HHHHHHHHHH CS
                           PGK 226 leigkslv..ee....dklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipedemalDigpktielfaea 300
                                   +++g ++   e+    +++e+akell+k++   +ki++pvDv+++ +e++ ea + +  + + ++ + Dig+ktiel++e+
  gi|15668822|ref|NP_247625.1| 248 YDLGVNMDiiENlglkSQIEIAKELLNKFE---DKIVVPVDVALNINEERVEADLNK--DEKVEHLINDIGEKTIELYSEI 323
                                   **9954433344444478***********9...89**********844333333334..4455889*************** PP

                                   HCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSSHHHHHHHCT CS
                           PGK 301 ikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGGgAsLelLeg 377
                                   i+eakt+v nGp+Gvfe e+fakGT++++ka+a+++   +s++GGg+  aa+e +g+adk++hvStGGgA+L++L g
  gi|15668822|ref|NP_247625.1| 324 INEAKTIVANGPAGVFEKEAFAKGTEELLKAIANSKG--FSVIGGGHLSAAAELFGIADKIDHVSTGGGATLDFLAG 398
                                   **********************************855..************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2742.91
//
Query:       gi|15668823|ref|NP_247626.1|  [L=333]
Description: hypothetical protein MJ_0642 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-14   53.4   0.0    4.6e-14   52.6   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   2.5e-18   4.6e-14      31     237 ..      84     294 ..      65     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2.5e-18
                                   GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHHHS-EEE----TTS..HHHHHHHHHHHHHTT CS
                  Peripla_BP_2  31 pldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedeellksgiptvivessntg..eslkeqiralgellg 109
                                   pl +d l+ +i +vg+dg i++ ++++  PD+++l      +   + l+k++ip+    + ++    +  e+i+ ++  ++
  gi|15668823|ref|NP_247626.1|  84 PLYSDYLKGKISNVGTDGKINYGEILNINPDMIFLIDWNIFNPLSKWLDKNNIPYTKTGNYKEPkfLGKMEWIKFYASFYN 164
                                   4444444448999********************9986442355566677777877765554433569************** PP

                                   -HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHH CS
                  Peripla_BP_2 110 ledeaeklvaeidsklaaaksaidse..kpkpvlvfggadeggyvvagsnsyigdlldalgieniaaeskkseyeeisaEq 188
                                   + ++aek++++i ++ +++ ++++s   k kpv+ f g  +  +++ g ++yi   ++++++++++++  + +y  i++  
  gi|15668823|ref|NP_247626.1| 165 KYKKAEKVFNKIIEEKRRILKSLNSRsiKYKPVVAFFGYHKNQPYIYGKSHYIPNWIREIKGNYLFENVEGTNYHYIDRKI 245
                                   *************************99*9999999999999999999********************999*********** PP

                                   HHH..H--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-HH CS
                  Peripla_BP_2 189 ila..sdpdvifvsgraeadnktgleflkenpllaelpAvkngrVyaldss 237
                                   +++    +dv++ +++   +   ++e lk+np + ++ A+kn+r+y + ++
  gi|15668823|ref|NP_247626.1| 246 FNSraKYADVCILDTM--GEDIDIKELLKNNPHFLKFRAYKNKRFYITTKD 294
                                   ***9899*********..777789999*******************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2303.54
//
Query:       gi|15668824|ref|NP_247627.1|  [L=335]
Description: delta-aminolevulinic acid dehydratase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     1e-149  498.0   0.0   1.1e-149  497.8   0.0    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.8   0.0  6.4e-154  1.1e-149       3     316 ..      13     329 ..      11     330 .. 0.98

  Alignments for each domain:
  == domain 1  score: 497.8 bits;  conditional E-value: 6.4e-154
                                   -GGGGGSSHHHHHHC-S----GGGEEEEEEEESS..-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE-SS- CS
                          ALAD   3 rlrrlrksealrelvretrlsasdlilplfvkeg..eeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvpeek 81 
                                   r+rrlrk++++r+lvret l+++dli+p+fv+e+   +ek+ei+smp++yr+sv+ +++e++e+++lgi+av+lFg+p++k
  gi|15668824|ref|NP_247627.1|  13 RPRRLRKNQKIRDLVRETILTKNDLIMPIFVDENlkGNEKKEISSMPNQYRFSVEGAIEEAKEIADLGIPAVILFGIPKHK 93 
                                   9*******************************984457999**************************************** PP

                                   BSS-GGGGSTTSHHHHHHHHHHHH-.TTSEEEEEE-STTTBSS-SSSEEESS.EEHHHHHHHHHHHHHHHHHCT-SEEEE- CS
                          ALAD  82 deegsealnedglvqrairaikeev.pelvvitDvclceytshGhcgileekevdndetlellakvavsqaeaGadivapS 161
                                   de +s+a++++g+vqr+ir ikee+ +el+vi+D clceytshGhcgi+++++++nd+tl +lak+a+s+a+aG+divapS
  gi|15668824|ref|NP_247627.1|  94 DEIASSAYDKNGVVQRTIRGIKEELgDELLVIADCCLCEYTSHGHCGIVKDGKILNDATLPILAKIALSYADAGVDIVAPS 174
                                   ************************9788***************************************************** PP

                                   S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHHHHHHHHHHHHTT-SBEE CS
                          ALAD 162 dmmDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansrealreveldleeGADivm 242
                                   dmmDgrv+aire L+e+g+++vai+sYsaKyaS+fYgPFr+aaesap+fgdrk+Yqmd+ n+real+e++ld+eeGAD+++
  gi|15668824|ref|NP_247627.1| 175 DMMDGRVRAIREILEENGYDDVAIMSYSAKYASSFYGPFREAAESAPKFGDRKSYQMDIGNAREALKEIALDIEEGADLIL 255
                                   ********************************************************************************* PP

                                   EES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHTT-SEEEETTHHHHHH CS
                          ALAD 243 vKPalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEsllsikRAGadliltYfakevak 316
                                   vKPal+ylDiir +k++fd+p+  y vSGEYam++aaa+ngwld++kv++E llsikRAGad+i+tY+akeva+
  gi|15668824|ref|NP_247627.1| 256 VKPALPYLDIIRMAKDRFDVPIGGYCVSGEYAMVEAAARNGWLDREKVIYEILLSIKRAGADFIITYWAKEVAE 329
                                   ************************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2273.54
//
Query:       gi|15668825|ref|NP_247628.1|  [L=208]
Description: S-adenosylmethionine:2-demethylmenaquinone methyltransferase MenG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-37  128.3   0.6    3.3e-37  128.0   0.6    1.1  1  RraA-like  Aldolase/RraA


Domain annotation for each model (and alignments):
>> RraA-like  Aldolase/RraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   0.6   1.8e-41   3.3e-37       2     150 .]      22     168 ..      21     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 1.8e-41
                                   HHHHHHCEE-SSBSTB.TT..EES.EE.EEEEEEEESS.BGHHHHHHHTS--TTEEEEEESTT.SSSSSECE-HHHHHHHH CS
                     RraA-like   2 advsDalkklggrsggirp.lers.fv.GpavTvkvveadnslvkealeeagpgdvlVvdgggdeslraallGgllataak 79 
                                   ++++Da     +  +gi+p le++ +v G+a+Tvk+  +d+ ++ ++++   +++++V +  g+ + ++a++Ggl +  ak
  gi|15668825|ref|NP_247628.1|  22 PNLCDAGA---KPLNGIKPiLENQkLVfGEAITVKISYNDWGTLIKTISF-AKNKFIVAEVVGEGKYETAVWGGLASLNAK 98 
                                   57899844...35558***888855555********999*********97.567778875555545555555********* PP

                                   HTTBSEEEEEEEES-HHHHTTSSSEEEEEEE-SSB-B-S.STSEESS-EEETTEEE-TTSEEEEETTEEEE CS
                     RraA-like  80 angvaGvvvdGavRDvaelreldfpvfargvtprkkpkkkgkgevnvpveiggvtvkpgdlivaDedGvvv 150
                                    +gv+Gvv+dG+vRDv+++++l+fpvfa++ +p++ +k  + ge+nv+v+++gv v+pgd+iv+D +Gvvv
  gi|15668825|ref|NP_247628.1|  99 IKGVRGVVIDGCVRDVEDIKALKFPVFAKNFCPNA-GKPLNLGEINVAVNCCGVIVEPGDIIVGDCNGVVV 168
                                   **********************************8.66669*****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1274.72
//
Query:       gi|15668826|ref|NP_247629.1|  [L=191]
Description: hypothetical protein MJ_0645 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-17   62.0  18.0    3.1e-10   40.3   6.6    2.0  2  VIT1      VIT family
  ------ inclusion threshold ------
       0.16   12.2   4.7       0.26   11.4   4.7    1.3  1  IspA      Intracellular septation protein A
        2.4    7.4   5.2        2.4    7.4   4.7    1.3  1  DUF3810   Protein of unknown function (DUF3810)


Domain annotation for each model (and alignments):
>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   3.2   2.2e-10   1.3e-06       2      69 ..      22      87 ..      21     101 .. 0.86
   2 !   40.3   6.6   5.1e-14   3.1e-10     133     213 ..     108     187 ..      89     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.2e-10
                          VIT1  2 rdavlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserdlekaerkr 69
                                  r +v G+ DG +s +++v+G s+ s  ++++++ aGl + +A  +S  +G++ + k++ + e+ ++++
  gi|15668826|ref|NP_247629.1| 22 RYIVRGLIDGSLSALGVVIGASG-S-ADASVIIAAGLGGGIANGLSNILGAFTAEKASLERERIQKEK 87
                                  67899*****************6.4.4899*************************9988777665554 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 5.1e-14
                          VIT1 133 splkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaaayli 213
                                   + +  +l+ ++s +iG+++P++p+++++  ++al+v+i++t+++l+++G++ +++++ ++++s+++m+++ ++ a++ ++i
  gi|15668826|ref|NP_247629.1| 108 ETMICGLIDGISTTIGSALPVVPFFLFD-IKTALYVAIGITIAILFILGVFIGKISKENVIISGIKMVAGALAVAILCFMI 187
                                   4566899999*****************9.9**************************************9998888887765 PP

>> IspA  Intracellular septation protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.7   4.4e-05      0.26       9      67 ..     127     181 ..     121     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.4e-05
                          IspA   9 PlilFfvayklagillAtavlivatvlqiailklrtrkvekmqlislvlvvvfGgltll 67 
                                   P++ Ff    l++i +A +v+i +t++ ++il +  +k++k ++i+ ++ +v G+l+++
  gi|15668826|ref|NP_247629.1| 127 PVVPFF----LFDIKTALYVAIGITIAILFILGVFIGKISKENVIISGIKMVAGALAVA 181
                                   555555....67999999*************************************9886 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.7    0.0004       2.4       4      76 ..     113     187 ..     110     191 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0004
                       DUF3810   4 gvypviskilsrlsglfpFSvgellivllillvilylvlai..klkkrkkkkkrllkvllrvllvllvvyflftl 76 
                                   g+   is+++++ + ++pF + ++  +l +++ i + +l+i  ++  + +k++ +++ ++ v+ +l+v++++f++
  gi|15668826|ref|NP_247629.1| 113 GLIDGISTTIGSALPVVPFFLFDIKTALYVAIGITIAILFIlgVFIGKISKENVIISGIKMVAGALAVAILCFMI 187
                                   5677899*****************999999888888888888866667778899999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1216.23
//
Query:       gi|15668827|ref|NP_247630.1|  [L=164]
Description: hypothetical protein MJ_0646 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-50  170.3   8.2    5.3e-50  170.2   8.2    1.0  1  DUF2115         Uncharacterized protein conserved in archaea 
     0.0097   16.0   0.5       0.12   12.5   0.4    2.3  2  Rsbr_N          Rsbr N terminal
  ------ inclusion threshold ------
      0.015   15.2   0.8      0.021   14.8   0.8    1.2  1  rRNA_proc-arch  rRNA-processing arch domain
      0.024   14.5   6.4        0.6   10.0   0.4    2.7  2  DUF3781         Protein of unknown function (DUF3781)
      0.074   12.8   0.5      0.079   12.7   0.5    1.1  1  HGD-D           2-hydroxyglutaryl-CoA dehydratase, D-componen
          2    8.4   5.2        2.6    8.1   1.8    2.4  2  Ribosomal_L29   Ribosomal L29 protein


Domain annotation for each model (and alignments):
>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.2   8.2   1.8e-53   5.3e-50       2     163 ..       3     159 ..       2     160 .. 0.96

  Alignments for each domain:
  == domain 1  score: 170.2 bits;  conditional E-value: 1.8e-53
                       DUF2115   2 kgeLleilkkeaskisieDlmkisarlekeikklpekyrkelseslteylfeaykelknkrsgdkseykeevideeelkef 82 
                                    +eL+e+lkke++++si+D+m+i++++ek++k+lp++y++++ e++++yl+e+++e+++ +s d++++  e idee+l+e+
  gi|15668827|ref|NP_247630.1|   3 ARELFEKLKKELNNFSIYDIMMIRSFIEKDAKYLPPQYKNHYVEAMMKYLIETFNEIRK-KSVDEIQD--EEIDEEKLNEM 80 
                                   689*******************************************************9.77777776..57********* PP

                       DUF2115  83 lemleeqceeekeekeerlrklyylvslYliFvleePlHpvgtpfPGgfkveekdgeyYCPvkdkqkdvekalCkfCiakq 163
                                   l+++e+  + ++++ eer+ +l +++++Yl+F++++PlHp   +fPG+ k+ +k+++yYCPvk+kq + e++lC+fC++k 
  gi|15668827|ref|NP_247630.1|  81 LNRIERFRKYYTPD-EERFINLSKILCPYLAFIAKKPLHPEYLTFPGNVKIIKKGNNYYCPVKNKQLN-EYSLCEFCVCKS 159
                                   ************98.****************************************************9.**********95 PP

>> Rsbr_N  Rsbr N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.4   3.9e-05      0.12      73     113 ..      49      87 ..       3     100 .. 0.88
   2 ?    1.2   0.0      0.12   3.5e+02     104     126 ..     128     150 ..     118     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                                   HHHHHHHHHHHHHHHHHHHHH..T--TT--HHHHHHHHHHH CS
                        Rsbr_N  73 LkyltkgLqefrkvvlellseeddvvkeeqslelleeieew 113
                                   +kyl +  +e+rk  ++++++e+  ++ee+  e+l++ie++
  gi|15668827|ref|NP_247630.1|  49 MKYLIETFNEIRKKSVDEIQDEE--IDEEKLNEMLNRIERF 87 
                                   89*******************77..7888888888888887 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                        Rsbr_N 104 lelleeieewidpivnelvneYs 126
                                   ++++++ +++  p++n+ +neYs
  gi|15668827|ref|NP_247630.1| 128 VKIIKKGNNYYCPVKNKQLNEYS 150
                                   6789999999************9 PP

>> rRNA_proc-arch  rRNA-processing arch domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.8   7.1e-06     0.021     165     231 ..      18      89 ..       9     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.1e-06
                                   GEEEEEEEEE---SS..TTSTTHHHHHHHHHHH.HHHHSS..---B--TTTTS----HHHHHHHHHHHHHHH CS
                rRNA_proc-arch 165 cieaiSsvrlklpkd..lrkseareevakavqe.lkrrfp..giplldpikdmkikdeefkkllkkieales 231
                                   +i++i  +r +++kd    +++ ++++++a+ + l + f+    + +d i+d +i++e++ ++l++ie++ +
  gi|15668827|ref|NP_247630.1|  18 SIYDIMMIRSFIEKDakYLPPQYKNHYVEAMMKyLIETFNeiRKKSVDEIQDEEIDEEKLNEMLNRIERFRK 89 
                                   79999**********6533999999999999998888887566679**********************9865 PP

>> DUF3781  Protein of unknown function (DUF3781)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3    0.0014       4.2      14      54 ..       7      47 ..       4      60 .. 0.86
   2 ?   10.0   0.4    0.0002       0.6      40      58 ..     127     145 ..     120     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0014
                       DUF3781 14 ieRIkknLs.lseddvveyckeiildknakiekkGKnyYvea 54
                                  +e++kk L+ +s  d++  +++ i++  + +  + Kn+Yvea
  gi|15668827|ref|NP_247630.1|  7 FEKLKKELNnFSIYDIM-MIRSFIEKDAKYLPPQYKNHYVEA 47
                                  6899****999999987.69*******************875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0002
                       DUF3781  40 nakiekkGKnyYveaknii 58 
                                   n ki+kkG nyY+ +kn +
  gi|15668827|ref|NP_247630.1| 127 NVKIIKKGNNYYCPVKNKQ 145
                                   679*********9988865 PP

>> HGD-D  2-hydroxyglutaryl-CoA dehydratase, D-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   2.6e-05     0.079      68     132 ..       4      92 ..       2     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHTTT.S-EEEE--..............-........HHHHHHHHHHHH.HHHHHHHHHHT----HHHHHHHHHHH CS
                         HGD-D  68 kkilenlaki.ipytvldi..............P........eeavkyledele.nliaaleeitgkrideesleaaikea 124
                                   ++++e l+k+  ++ + di              P        e++ kyl + ++   ++ + ei+ ++idee+l + +++ 
  gi|15668827|ref|NP_247630.1|   4 RELFEKLKKElNNFSIYDImmirsfiekdakylPpqyknhyvEAMMKYLIETFNeIRKKSVDEIQDEEIDEEKLNEMLNRI 84 
                                   57778888886445556665667777777777745888889999*********945578899******************* PP

                                   HHHHHHHH CS
                         HGD-D 125 netrellk 132
                                   ++ r+++ 
  gi|15668827|ref|NP_247630.1|  85 ERFRKYYT 92 
                                   *9777654 PP

>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.14   4.1e+02      13      25 ..       5      17 ..       3      23 .. 0.77
   2 ?    8.1   1.8   0.00086       2.6       1      19 [.      57      76 ..      57      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.14
                                  HHHHHHHHHHHHH CS
                 Ribosomal_L29 13 eklkelkkeLfnL 25
                                  e  ++lkkeL n 
  gi|15668827|ref|NP_247630.1|  5 ELFEKLKKELNNF 17
                                  5668899999875 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00086
                                  HHHHHS-HHHHHH.HHHHHH CS
                 Ribosomal_L29  1 kelrelsdeeLke.klkelk 19
                                  +e+r++s++e+++ +++e+k
  gi|15668827|ref|NP_247630.1| 57 NEIRKKSVDEIQDeEIDEEK 76
                                  69**********95555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1863  (0.10391); expected 358.6 (0.02)
Passed bias filter:                      919  (0.0512577); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1080.74
//
Query:       gi|15668828|ref|NP_247631.1|  [L=71]
Description: hypothetical protein MJ_0647 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-06   28.2   3.6    1.5e-06   28.1   3.6    1.1  1  Prefoldin_2    Prefoldin subunit
  ------ inclusion threshold ------
      0.029   14.3   8.2       0.06   13.3   0.1    2.1  2  Prefoldin      Prefoldin subunit
      0.045   14.2   0.0      0.056   13.9   0.0    1.2  1  ILEI           Interleukin-like EMT inducer
      0.072   12.6   0.2      0.075   12.6   0.2    1.1  1  Leu_Phe_trans  Leucyl/phenylalanyl-tRNA protein transferase
       0.12   12.4   0.8       0.15   12.1   0.6    1.4  1  Xpo1           Exportin 1-like protein


Domain annotation for each model (and alignments):
>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   3.6   4.3e-10   1.5e-06       7      74 ..       1      69 [.       1      71 [] 0.92

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.3e-10
                                  HHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHH CS
                   Prefoldin_2  7 fqqlqqqlqqlaqqikqletqlk.elelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketl 74
                                  +q+l++ l++ +q++k+++++l+ e ++v++ l++l+e ++vy  + ++ ++++kee+++ L+ ++++ 
  gi|15668828|ref|NP_247631.1|  1 MQKLNKHLKKKKQKRKKMKKKLNnEFQEVIDFLKSLPEGRRVYIEMSGIWIEVTKEEAINYLKSKINEK 69
                                  589*************999998538**************************************998765 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   3.7     0.012        41      80     108 ..       6      34 ..       1      38 [. 0.77
   2 ?   13.3   0.1   1.7e-05      0.06      67      88 ..      47      68 ..      35      71 .] 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  80 ellkkkleelekqlekleeeleklkdqit 108
                                   + lkkk+++ +k+ +kl++e ++  d ++
  gi|15668828|ref|NP_247631.1|   6 KHLKKKKQKRKKMKKKLNNEFQEVIDFLK 34 
                                   56888888888888888888888777665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.7e-05
                                  TTEEEEEEHHHHHHHHHHHHHH CS
                     Prefoldin 67 agyyveksleeAiellkkklee 88
                                  +g+ +e+++eeAi +lk k++e
  gi|15668828|ref|NP_247631.1| 47 SGIWIEVTKEEAINYLKSKINE 68
                                  6999****************98 PP

>> ILEI  Interleukin-like EMT inducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.6e-05     0.056      25      66 ..      23      64 ..       3      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                          ILEI 25 eeeskrlveflksipdgsiVlvavkdeassnlsdearkales 66
                                  ++e ++ ++flks+p+g+ V +  ++ + +  ++ea++ l+s
  gi|15668828|ref|NP_247631.1| 23 NNEFQEVIDFLKSLPEGRRVYIEMSGIWIEVTKEEAINYLKS 64
                                  3556699*********************99*******99987 PP

>> Leu_Phe_trans  Leucyl/phenylalanyl-tRNA protein transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   2.1e-05     0.075      40      82 ..       4      54 ..       1      66 [. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                 Leu_Phe_trans 40 isrslrkt.lrkkefevtidkaFeeVieacaekkrre.......gtWitee 82
                                  ++++l+k+  ++k+++ +++++F+eVi+  ++ ++ +       g Wi+ +
  gi|15668828|ref|NP_247631.1|  4 LNKHLKKKkQKRKKMKKKLNNEFQEVIDFLKSLPEGRrvyiemsGIWIEVT 54
                                  56667654156799**************99988743324455556777655 PP

>> Xpo1  Exportin 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   4.2e-05      0.15      61      90 ..       7      36 ..       2      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.2e-05
                                  TTTSCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Xpo1 61 rskleqerrndlkdllrsnvqkilelllqi 90
                                  + k+++++r+++k+ l++++q+++++l ++
  gi|15668828|ref|NP_247631.1|  7 HLKKKKQKRKKMKKKLNNEFQEVIDFLKSL 36
                                  5678999*******************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3410  (0.190195); expected 358.6 (0.02)
Passed bias filter:                     1330  (0.0741815); expected 358.6 (0.02)
Passed Vit filter:                       159  (0.00886831); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 402.02
//
Query:       gi|15668829|ref|NP_247632.1|  [L=147]
Description: prefoldin subunit alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-28   97.2   6.0    7.1e-28   96.9   6.0    1.1  1  Prefoldin        Prefoldin subunit
  ------ inclusion threshold ------
      0.086   13.0   3.1        1.7    8.8   1.9    2.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
       0.19   12.2   3.4         13    6.4   1.9    2.9  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.21   12.1  15.2         11    6.6   0.0    2.1  2  APG6_N           Apg6 coiled-coil region
       0.24   11.5   0.3       0.24   11.5   0.3    2.7  3  DUF1192          Protein of unknown function (DUF1192)
       0.25   12.0   9.9         41    4.9   0.0    3.0  2  YabA             Initiation control protein YabA
       0.33   11.6  12.1         15    6.3   0.1    3.1  3  SlyX             SlyX
       0.47   10.7  13.2        2.2    8.6   0.0    2.6  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.61   10.6  13.6        1.9    9.0   0.2    2.5  2  ZapB             Cell division protein ZapB
       0.76    9.8   4.6       0.35   10.9   2.1    1.7  2  DUF2076          Uncharacterized protein conserved in bacteri
       0.86    9.5   9.9        1.3    9.0   8.0    1.9  2  Ax_dynein_light  Axonemal dynein light chain
        1.6    9.2   9.1        8.9    6.8   6.8    2.2  2  CENP-H           Centromere protein H (CENP-H)
        4.9    7.4   8.4         22    5.4   0.1    2.4  2  Spc24            Spc24 subunit of Ndc80
        7.4    7.1   9.9        3.2    8.3   0.1    2.7  2  DUF4140          N-terminal domain of unknown function (DUF41


Domain annotation for each model (and alignments):
>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   6.0   5.5e-31   7.1e-28       1     118 [.      15     132 ..      15     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 5.5e-31
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHH CS
                     Prefoldin   1 lkeeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiel 81 
                                   + +++e l+ae+++l+++i +l+++l+tlk+lk+ +egk+vlvp+g+ ++v+++v+++dkv+v++G+++++e+++eeA ++
  gi|15668829|ref|NP_247632.1|  15 YIAQIEGLRAEIGRLDATIATLRQSLATLKSLKTLGEGKTVLVPVGSIAQVEMKVEKMDKVVVSVGQNISAELEYEEALKY 95 
                                   5689***************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanlaqly 118
                                   +++++++l   + +le+++++l+++i+ l a+++q +
  gi|15668829|ref|NP_247632.1|  96 IEDEIKKLLTFRLVLEQAIAELYAKIEDLIAEAQQTS 132
                                   **********************************987 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0038       4.9      87     129 ..       3      44 ..       1      46 [. 0.89
   2 ?    8.8   1.9    0.0013       1.7      34     134 ..      30     130 ..      28     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0038
                                   HHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  87 eeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqke 129
                                   + e+++++e + a + +i+ L+  + +++  i+ L+q  ++++
  gi|15668829|ref|NP_247632.1|   3 N-EVIDINEAVRAYIAQIEGLRAEIGRLDATIATLRQSLATLK 44 
                                   4.8999******************************9988775 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0013
                                   CHHHCCCCCCCCCCCCHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHH CS
                     Fib_alpha  34 kkdlekleneleeisnstk..eaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvle 112
                                   + ++++l+++l+++++ ++  e +++ + + ++ + + k +k  d+v+ ++ +++    l+++e ++  e +i++L +   
  gi|15668829|ref|NP_247632.1|  30 DATIATLRQSLATLKSLKTlgEGKTVLVPVGSIAQVEMKVEK-MDKVVVSVGQNIS-AELEYEEALKYIEDEIKKLLTFRL 108
                                   678999999999999877622555666666777777777776.79**********9.88999******************* PP

                                   HHHHHHHHHHHHHHHHHHHTTS CS
                     Fib_alpha 113 sneqkiqkLeqdidqkerkCke 134
                                    +eq i++L  +i+ ++++ ++
  gi|15668829|ref|NP_247632.1| 109 VLEQAIAELYAKIEDLIAEAQQ 130
                                   ************9999887665 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.06        77      20      59 ..      12      41 ..       2      58 .. 0.45
   2 ?    6.4   1.9    0.0099        13      12      56 ..      61     105 ..      53     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.06
                       NPV_P10 20 VdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59
                                  V a  +q++ ++++          + ++ a++a+l +++ 
  gi|15668829|ref|NP_247632.1| 12 VRAYIAQIEGLRAE----------IGRLDATIATLRQSLA 41
                                  33333333333333..........3333333333333222 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0099
                       NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                    i++v+ kV+ +++ v +v +n+    e +e L  + +++++l t
  gi|15668829|ref|NP_247632.1|  61 SIAQVEMKVEKMDKVVVSVGQNISAELEYEEALKYIEDEIKKLLT 105
                                   5999******************99988888999988888888766 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0085        11      55      96 ..       4      45 ..       2      49 .. 0.86
   2 ?    6.3  12.6      0.01        13      45     100 ..      89     144 ..      61     147 .] 0.54

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0085
                        APG6_N 55 eleklekeeeelleeLkelekereeleaelaaleeelealee 96
                                  e+ +++++ ++ +++++ l +e  +l+a +a+l++ l+ l+ 
  gi|15668829|ref|NP_247632.1|  4 EVIDINEAVRAYIAQIEGLRAEIGRLDATIATLRQSLATLKS 45
                                  55677788889999********************99999986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.01
                        APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeer 100
                                    +e l+ +e+e++kl   +  l++ ++el ++ e+l ae ++ +ee++a eee+e+
  gi|15668829|ref|NP_247632.1|  89 YEEALKYIEDEIKKLLTFRLVLEQAIAELYAKIEDLIAEAQQTSEEEKAEEEENEE 144
                                   34455555555555555555555555555555555555555555555555444444 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00018      0.24      28      51 ..      18      41 ..      13      46 .. 0.86
   2 ?   -2.5   0.1       4.2   5.4e+03      27      38 ..      91     102 ..      80     104 .. 0.64
   3 ?   -1.2   8.1       1.7   2.2e+03      22      49 ..     114     141 ..     111     147 .] 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                       DUF1192 28 rIalLeaEIaRleaaiakkkasra 51
                                   I+ L+aEI Rl+a+ia+ ++s a
  gi|15668829|ref|NP_247632.1| 18 QIEGLRAEIGRLDATIATLRQSLA 41
                                  6999*************9888876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.2
                       DUF1192  27 erIalLeaEIaR 38 
                                   e  +  e+EI++
  gi|15668829|ref|NP_247632.1|  91 EALKYIEDEIKK 102
                                   444555666665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.7
                       DUF1192  22 veELeerIalLeaEIaRleaaiakkkas 49 
                                   ++EL + I++L aE + ++++ ++ ++ 
  gi|15668829|ref|NP_247632.1| 114 IAELYAKIEDLIAEAQQTSEEEKAEEEE 141
                                   79*************9999887776654 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.032        41       8      48 ..       3      43 ..       1      55 [. 0.64
   2 ?    3.0   8.6      0.13   1.6e+02      11      65 ..      63     138 ..      53     146 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.032
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA  8 dkleeleeqleelleeleelkeelaelleenaeLelenekl 48
                                  +++ +++e +++  +++e l++e+ +l    a+L+    +l
  gi|15668829|ref|NP_247632.1|  3 NEVIDINEAVRAYIAQIEGLRAEIGRLDATIATLRQSLATL 43
                                  56667777777777777777777766666655555554444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH........................XXXXXXXXXXXXX CS
                          YabA  11 eeleeqleelleeleelkeelaelleenaeLeleneklrerl........................eeeekkekekkke 65 
                                   +++e ++e++ + + ++ +++++ le +++L+   ++++++l                        +   ++++e+k+e
  gi|15668829|ref|NP_247632.1|  63 AQVEMKVEKMDKVVVSVGQNISAELEYEEALKYIEDEIKKLLtfrlvleqaiaelyakiedliaeaQ---QTSEEEKAE 138
                                   5666666666666666666666666666666666666666666666666666666666665554321...111111111 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.012        15      21      55 ..       7      41 ..       3      49 .. 0.77
   2 ?    2.4   0.0      0.19   2.4e+02      12      34 ..      62      84 ..      61      88 .. 0.85
   3 ?    5.2   6.1     0.026        34       9      61 ..      90     142 ..      85     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.012
                                  HHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                          SlyX 21 eLndvvaeqqqqidrlqrqlrllaerlkeleessg 55
                                  + n++v +   qi+ l++++ +l   +++l++s +
  gi|15668829|ref|NP_247632.1|  7 DINEAVRAYIAQIEGLRAEIGRLDATIATLRQSLA 41
                                  67888888888888888888888888888877654 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.19
                                  HHHHHHHHHHHHHHHHHHHHHHH CS
                          SlyX 12 lafqedtieeLndvvaeqqqqid 34
                                  +a  e  +e++++vv+   q i+
  gi|15668829|ref|NP_247632.1| 62 IAQVEMKVEKMDKVVVSVGQNIS 84
                                  67889999999**9999988885 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.026
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXX CS
                          SlyX   9 EiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseaee 61 
                                   E+ l + ed i++L       +q i++l ++++ l  + ++ +e+++a+e+e+
  gi|15668829|ref|NP_247632.1|  90 EEALKYIEDEIKKLLTFRLVLEQAIAELYAKIEDLIAEAQQTSEEEKAEEEEN 142
                                   88999999999999999999999999999999999999988888887766644 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0017       2.2      28      66 ..       2      40 ..       1      55 [. 0.82
   2 ?    3.6   0.3     0.059        76      62     101 ..      65     104 ..      59     108 .. 0.69
   3 ?    2.9   9.2     0.095   1.2e+02      30      92 ..      85     144 ..      78     147 .] 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT CS
                  Seryl_tRNA_N 28 vdelleldekrrelqveleelqaerNelskeIgkakkkk 66
                                  v e+++++e+ r+ ++++e l+ae  +l ++I+ + ++ 
  gi|15668829|ref|NP_247632.1|  2 VNEVIDINEAVRAYIAQIEGLRAEIGRLDATIATLRQSL 40
                                  789999999999999999999999999999999887765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.059
                                   CCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  62 akkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                      k e+ ++++ +v ++     ++e++lk +e+e++kll
  gi|15668829|ref|NP_247632.1|  65 VEMKVEKMDKVVVSVGQNISAELEYEEALKYIEDEIKKLL 104
                                   444445666666665555444457999*********9998 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.095
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  30 elleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelke 92 
                                   + le +e+ + ++ e+ +l + r  l ++I+++ +k   +e+liae+++ +ee ka e+e +e
  gi|15668829|ref|NP_247632.1|  85 AELEYEEALKYIEDEIKKLLTFRLVLEQAIAELYAK---IEDLIAEAQQTSEEEKAEEEENEE 144
                                   557889999999999999999999**********85...899**********99998888766 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2    0.0015       1.9      13      46 ..      12      51 ..       1     107 [. 0.72
   2 ?    2.5  10.8      0.15     2e+02      19      50 ..     113     144 ..      90     147 .] 0.50

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                          ZapB 13 iqkaidtitlLqmeieeLkeeneelkeenrele......e 46
                                  + + i +i+ L+ ei +L +  ++l +  + l+      e
  gi|15668829|ref|NP_247632.1| 12 VRAYIAQIEGLRAEIGRLDATIATLRQSLATLKslktlgE 51
                                  678899*******************999988885555550 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.15
                          ZapB  19 titlLqmeieeLkeeneelkeenreleeeneq 50 
                                    i++L  +ie+L +e ++ +ee ++ eeene+
  gi|15668829|ref|NP_247632.1| 113 AIAELYAKIEDLIAEAQQTSEEEKAEEEENEE 144
                                   34455555555555555555555555555443 PP

>> DUF2076  Uncharacterized protein conserved in bacteria (DUF2076)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.5   1.9e+03      52      74 ..       7      29 ..       1      50 [. 0.59
   2 ?   10.9   2.1   0.00027      0.35      51      81 ..     108     138 ..      90     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
                       DUF2076 52 vqeaaLkqanariqeLeaqlqql 74
                                    ++a ++  a+i+ L+a++ +l
  gi|15668829|ref|NP_247632.1|  7 DINEAVRAYIAQIEGLRAEIGRL 29
                                  55666666677777777776332 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00027
                       DUF2076  51 lvqeaaLkqanariqeLeaqlqqlqqqaqea 81 
                                   lv e+a+ ++ a+i++L a++qq++++++++
  gi|15668829|ref|NP_247632.1| 108 LVLEQAIAELYAKIEDLIAEAQQTSEEEKAE 138
                                   9********************7664333332 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.44   5.7e+02     125     153 ..      16      44 ..       3      49 .. 0.71
   2 ?    9.0   8.0   0.00099       1.3      99     170 ..      72     142 ..      61     147 .] 0.75

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.44
               Ax_dynein_light 125 ekkikeLeeekeelekqvaelkakleale 153
                                    ++i+ L++e  +l   +a+l++ l++l+
  gi|15668829|ref|NP_247632.1|  16 IAQIEGLRAEIGRLDATIATLRQSLATLK 44 
                                   55677788888888888888888777665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00099
               Ax_dynein_light  99 yktlyessvaFgmrkalqaeqgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekkheee 170
                                    ++++  sv  ++  +l+ e+  + +e++ik+L + +  le+ +ael ak+e+l +++++  +ee+ ++ee+
  gi|15668829|ref|NP_247632.1|  72 MDKVVV-SVGQNISAELEYEEALKYIEDEIKKLLTFRLVLEQAIAELYAKIEDLIAEAQQTSEEEKAEEEEN 142
                                   555554.5666777889999999*********99999999999*9999999998877776666655555443 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.085   1.1e+02      18      55 ..       8      45 ..       1      85 [. 0.61
   2 ?    6.8   6.8     0.007       8.9      16      73 ..      87     144 ..      68     147 .] 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.085
                        CENP-H 18 lsqelrelqeeltevekenlrlkrknrelaaellelak 55
                                  +++++r+  ++++ +++e+ rl ++ ++l ++l+ l++
  gi|15668829|ref|NP_247632.1|  8 INEAVRAYIAQIEGLRAEIGRLDATIATLRQSLATLKS 45
                                  55555555555555555555555555555555544443 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.007
                        CENP-H  16 lklsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeeleklea 73 
                                   l+ +++l+ +++e+ ++   +l l+++ +el a+++ l  e+++++e++k+e e+ e+
  gi|15668829|ref|NP_247632.1|  87 LEYEEALKYIEDEIKKLLTFRLVLEQAIAELYAKIEDLIAEAQQTSEEEKAEEEENEE 144
                                   567788999999***********************88888888888554444444333 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.017        22       9      43 ..       8      42 ..       1     107 [. 0.67
   2 ?    3.3   5.6     0.074        95      16      48 ..     110     142 ..      95     147 .] 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.017
                         Spc24  9 iakelsdleselesleselaelkeeleeleeesee 43
                                  i ++++   +++e l++e  +l +++++l ++   
  gi|15668829|ref|NP_247632.1|  8 INEAVRAYIAQIEGLRAEIGRLDATIATLRQSLAT 42
                                  55555555555555555555555555555544433 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.074
                         Spc24  16 leselesleselaelkeeleeleeeseekeser 48 
                                   le+++ +l ++ ++l +e ++ +ee++++e+e 
  gi|15668829|ref|NP_247632.1| 110 LEQAIAELYAKIEDLIAEAQQTSEEEKAEEEEN 142
                                   899999999999999999999999888844443 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0025       3.2      66      98 .]      11      43 ..       2      43 .. 0.84
   2 ?    0.2   5.7      0.79     1e+03      65      93 ..      99     140 ..      61     145 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0025
                       DUF4140 66 elkalraeleeledelaaledelaaaearlafl 98
                                  +++a  a++e l++e+ +l++++a+++++la l
  gi|15668829|ref|NP_247632.1| 11 AVRAYIAQIEGLRAEIGRLDATIATLRQSLATL 43
                                  4899999********************999875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.79
                       DUF4140  65 e.............elkalraeleeledelaaledelaaaea 93 
                                   e             ++++l a++e l +e ++ ++e +a e+
  gi|15668829|ref|NP_247632.1|  99 EikklltfrlvleqAIAELYAKIEDLIAEAQQTSEEEKAEEE 140
                                   144455555555545888888888888888888888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2167  (0.120866); expected 358.6 (0.02)
Passed bias filter:                      757  (0.0422221); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 854.36
//
Query:       gi|15668830|ref|NP_247633.1|  [L=463]
Description: NADH oxidase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-65  218.9   2.4      1e-64  218.6   2.4    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.4e-26   92.8   4.8    1.3e-20   73.7   0.2    3.5  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      9e-17   61.3   8.0    5.9e-06   25.8   0.0    4.0  4  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.2e-16   60.1   0.1    1.6e-15   57.3   0.0    2.4  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    2.3e-10   40.1   0.8     0.0016   17.6   0.0    4.1  4  FAD_binding_2   FAD binding domain
    5.7e-10   39.3   1.8     0.0063   16.1   0.6    4.0  4  DAO             FAD dependent oxidoreductase
    5.9e-10   39.2   0.6    0.00085   19.5   0.0    2.6  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.2e-09   37.4   2.2      0.044   12.5   0.1    4.3  5  HI0933_like     HI0933-like protein
    2.5e-06   27.9   3.7      0.011   16.2   0.2    3.2  3  NAD_binding_7   Putative NAD(P)-binding
    3.7e-06   26.3   0.0     0.0003   20.1   0.0    2.7  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    7.2e-06   25.3   2.8        2.5    7.1   0.1    4.3  4  GIDA            Glucose inhibited division protein A
    9.8e-06   25.0   5.0      0.023   13.9   0.0    3.5  4  Thi4            Thi4 family
    5.3e-05   22.4   0.4        0.2   10.7   0.3    2.5  2  Lycopene_cycl   Lycopene cyclase protein
    5.9e-05   23.3   0.2       0.69   10.2   0.0    3.0  2  TrkA_N          TrkA-N domain
    0.00011   21.6   0.5        0.2   10.9   0.2    2.3  2  FAD_binding_3   FAD binding domain
    0.00012   22.0   0.7    0.00028   20.8   0.1    1.9  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    0.00018   21.5   1.6        2.3    8.2   0.0    4.0  4  NAD_binding_9   FAD-NAD(P)-binding
    0.00049   19.5   0.3      0.097   12.0   0.1    2.7  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    0.00062   19.9   0.1       0.96    9.6   0.0    3.4  3  Response_reg    Response regulator receiver domain
      0.002   17.7   0.3       0.87    9.1   0.1    2.4  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0027   17.1   0.0        3.7    6.7   0.0    2.8  3  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0063   15.4   2.1       0.21   10.4   0.0    2.6  3  Trp_halogenase  Tryptophan halogenase
     0.0083   15.8   0.2       0.65    9.6   0.1    2.5  2  ApbA            Ketopantoate reductase PanE/ApbA
      0.009   15.6   2.2        0.1   12.2   0.0    2.7  3  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
  ------ inclusion threshold ------
      0.016   14.5   0.4        2.1    7.6   0.1    2.3  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.026   14.4   0.1       0.35   10.8   0.0    2.3  2  LpxI_N          LpxI N-terminal domain
      0.052   13.4   0.3       0.22   11.4   0.0    2.2  2  UPF0146         Uncharacterised protein family (UPF0146)
      0.074   12.5   3.4        8.2    5.9   0.1    3.7  4  Glu_dehyd_C     Glucose dehydrogenase C-terminus
      0.075   13.2   0.2       0.22   11.7   0.0    1.9  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
       0.25   11.4   3.0        1.8    8.6   0.2    3.0  3  PepSY_2         Peptidase propeptide and YPEB domain
        9.2    5.5   6.4         19    4.5   0.0    3.1  4  FAD_oxidored    FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.6   2.4   1.8e-67     1e-64       2     294 .]      17     321 ..      16     321 .. 0.93

  Alignments for each domain:
  == domain 1  score: 218.6 bits;  conditional E-value: 1.8e-67
                                   SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.....HHHHCHHHHCCCCHCCTC CS
                                   xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias.....evvkklnqgielllgeev 75 
                                   + ++iG+G+AGl++a t+++  + ++++++ +e+++ +  c ++++++g+ +  + +      +   k + +i+ l++++v
  gi|15668830|ref|NP_247633.1|  17 RAIIIGSGAAGLTTASTIRKynKDMEIVVITKEKEIAYSPCAIPYVIEGAIKSFDDIImhtpeD--YKRERNIDILTETTV 95 
                                   579*****************8779***************************9999888999753..467889******99* PP

                                   EEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T...SEEEEES-SHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
                   Pyr_redox_2  76 vkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp...krivvvGgGyi 153
                                   +++d ++ k+k+ + k+g+e+++ yd+lvlAtG++p++++i+G   ++++ vrt+++ +a+ +   +   k+++vvG+G+i
  gi|15668830|ref|NP_247633.1|  96 IDVDSKNNKIKCVD-KDGNEFEMNYDYLVLATGAEPFIPPIEGKDLDGVFKVRTIEDGRAILKYIEEngcKKVAVVGAGAI 175
                                   ************66.559**************************88888999********998888899************ PP

                                   HHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 154 GvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvv 233
                                   G+E+A  l+  g +v +ve ++++l r ld++++++++++lekeG++v+l +  ++i g+++ +e v  dg+ +d+d+v++
  gi|15668830|ref|NP_247633.1| 176 GLEMAYGLKCRGLDVLVVEMAPQVLpRFLDPDMAEIVQKYLEKEGIKVMLSKPLEKIVGKEK-VEAVYVDGKLYDVDMVIM 255
                                   *************************************************************8.99**************** PP

                                   -S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.......TECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 234 avGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.......ggkggpelaqaAvqqG 294
                                   a+Gvrp+ el+ +k+g+++  + +i+v+e+++t++p+iya+GD++       g+k+     +aAv+qG
  gi|15668830|ref|NP_247633.1| 256 ATGVRPNIELA-KKAGCKI-GKFAIEVNEKMQTSIPNIYAVGDCVevidfitGEKTLSPFGTAAVRQG 321
                                   ***********.*******.78889********************77777776666666667776665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1    0.0014      0.81       1      30 [.      17      46 ..      17      55 .. 0.86
   2 !    9.0   0.1    0.0036       2.1      37      73 ..      69     105 ..      62     111 .. 0.85
   3 !   73.7   0.2   2.2e-23   1.3e-20       1      78 [.     166     243 ..     166     246 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0014
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvver 30
                                  +++++G+G  gl  A+++++++k+  +v+ 
  gi|15668830|ref|NP_247633.1| 17 RAIIIGSGAAGLTTASTIRKYNKDMEIVVI 46
                                  579*******************98877764 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0036
                                   TSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSE CS
                     Pyr_redox  37 llDeeaskilqeklekngievllntkveeiegsedgv 73 
                                    +D+ +    +++ ++++i++l++t+v  ++ +++++
  gi|15668830|ref|NP_247633.1|  69 SFDDIIMHTPEDYKRERNIDILTETTVIDVDSKNNKI 105
                                   6888888888999******************988873 PP

  == domain 3  score: 73.7 bits;  conditional E-value: 2.2e-23
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedgvesvkl 78 
                                   kv+vvG+G iglE+A  l+  g +V vve+++++l r lD+++++i+q++lek+gi+v+l++ +e+i+g+e+ ve+v +
  gi|15668830|ref|NP_247633.1| 166 KVAVVGAGAIGLEMAYGLKCRGLDVLVVEMAPQVLpRFLDPDMAEIVQKYLEKEGIKVMLSKPLEKIVGKEK-VEAVYV 243
                                   79********************************************************************99.898865 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00056      0.32       1      30 [.      19      49 ..      19      61 .. 0.80
   2 !   11.9   0.0   0.00017     0.098     219     275 ..      79     136 ..      39     156 .. 0.76
   3 !   16.5   0.4   6.9e-06     0.004       2      30 ..     169     196 ..     168     204 .. 0.91
   4 !   25.8   0.0     1e-08   5.9e-06     210     305 .]     204     295 ..     198     295 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00056
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagl.edylilEkg 30
                                  iIiG G+aGl++a +++k +   +++++ k+
  gi|15668830|ref|NP_247633.1| 19 IIIGSGAAGLTTASTIRKYNKdMEIVVITKE 49
                                  8***************998772356666665 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00017
                   Pyr_redox_3 219 eelvkeekikvlfnaevkeikekeeeykvktedgkkvev.kddvvlatGykpdlsflk 275
                                   e++ +e++i++l++++v +++ k++++k   +dg+++e  +d  vlatG +p + +++
  gi|15668830|ref|NP_247633.1|  79 EDYKRERNIDILTETTVIDVDSKNNKIKCVDKDGNEFEMnYDYLVLATGAEPFIPPIE 136
                                   344455779********************9*****999945666778**998766665 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 6.9e-06
                   Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkg 30 
                                   ++GaG++Gl++a+ lk  gl d+l++E +
  gi|15668830|ref|NP_247633.1| 169 VVGAGAIGLEMAYGLKCRGL-DVLVVEMA 196
                                   8*******************.8*****86 PP

  == domain 4  score: 25.8 bits;  conditional E-value: 1e-08
                   Pyr_redox_3 210 lkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlt 290
                                   l pd+ + +++++++e ikv+  + +++i  ke +++    dgk  +v d v++atG +p++++ kk++ ++   ++    
  gi|15668830|ref|NP_247633.1| 204 LDPDMAEIVQKYLEKEGIKVMLSKPLEKIVGKE-KVEAVYVDGKLYDV-DMVIMATGVRPNIELAKKAGCKI--GKFAIEV 280
                                   789************99*************975.56777777766655.899***************99999..4445555 PP

                   Pyr_redox_3 291 eeteetnvpglflaG 305
                                   +e+++t +p+++ +G
  gi|15668830|ref|NP_247633.1| 281 NEKMQTSIPNIYAVG 295
                                   67899*******998 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       4.7   2.7e+03      19      43 ..     264     286 ..     256     290 .. 0.82
   2 !   57.3   0.0   2.8e-18   1.6e-15       6     106 ..     346     444 ..     341     448 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.7
                                   HHHHHHHSGEEEEEEEEECGHHHCH CS
                 Pyr_redox_dim  19 eeAkaagieikvgkfpfkangrala 43 
                                   e Ak+ag  +k+gkf ++ n+++++
  gi|15668830|ref|NP_247633.1| 264 ELAKKAG--CKIGKFAIEVNEKMQT 286
                                   5688888..9999999999988876 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 2.8e-18
                                   ESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEEC.TTHHHHHHHHHHHHH CS
                 Pyr_redox_dim   6 ftdpevasvGlteeeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivG.pgageliqelavaik 84 
                                     d+e++ +Glt  +A+ ++i+i++g+++  a++ra++y+  +++ +K+++++ +gkv+G++ivG ++++e+i+++++ai 
  gi|15668830|ref|NP_247633.1| 346 IGDLEIGGTGLTAFSANLKRIPIVIGRAK--ALTRARYYPGgKEIEIKMIFNE-DGKVVGCQIVGgERVAERIDAMSIAIF 423
                                   5689****************999999875..6*********9********998.**********989************** PP

                                   TTSBHH.HHHTSBSSSSSTGGGG CS
                 Pyr_redox_dim  85 agltve.dladtihihPtlseal 106
                                   +++++e +++++++++P++s  +
  gi|15668830|ref|NP_247633.1| 424 KKVSAEeLANMEFCYAPPVS--M 444
                                   ******77999*******99..3 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.8e-06    0.0016       2      33 ..      18      51 ..      17      64 .. 0.86
   2 ?   -0.3   0.0      0.76   4.4e+02     143     201 ..      74     128 ..      70     135 .. 0.85
   3 !   12.1   1.3   0.00013     0.073       2      33 ..     167     198 ..     166     200 .. 0.94
   4 ?    4.3   0.0      0.03        17     376     402 ..     278     298 ..     207     304 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.8e-06
                                  EEEE--SHHHHHHHHHHHHTTT..-EEEEESSSG CS
                 FAD_binding_2  2 viViGsGlAGLaAAleaaeaGl..kvavvekeqe 33
                                  +i+iGsG+AGL+ A ++++ ++  +++v++ke+e
  gi|15668830|ref|NP_247633.1| 18 AIIIGSGAAGLTTASTIRKYNKdmEIVVITKEKE 51
                                  69****************95554599****9987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.76
                                   HHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE---- CS
                 FAD_binding_2 143 llarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgG 201
                                   ++++  ++ r++++d++++t + ++  +++++    v   ++g+e++++ + +vlatg+
  gi|15668830|ref|NP_247633.1|  74 IMHTPEDYKRERNIDILTETTVIDVDSKNNKIKC--VD--KDGNEFEMNYDYLVLATGA 128
                                   6777777888999************998998887..46..8999999999999999996 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00013
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                   v V+G+G+ GL  A+ ++ +Gl+v+vve +++
  gi|15668830|ref|NP_247633.1| 167 VAVVGAGAIGLEMAYGLKCRGLDVLVVEMAPQ 198
                                   89*************************98775 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.03
                                   EEBETTSBESTTEEESSBTEEE-STCE CS
                 FAD_binding_2 376 vetdengrvldadgqpipGLYAaGeva 402
                                   +e++e++++       ip+ YA+G + 
  gi|15668830|ref|NP_247633.1| 278 IEVNEKMQT------SIPNIYAVGDCV 298
                                   678888888......*********997 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0     0.001      0.58       2      33 ..      18      53 ..      17      55 .. 0.84
   2 !    8.4   0.0    0.0024       1.4     158     203 ..      84     129 ..      80     148 .. 0.80
   3 !   16.1   0.6   1.1e-05    0.0063       1      30 [.     166     197 ..     166     199 .. 0.92
   4 ?    0.7   0.0      0.53   3.1e+02     154     207 ..     214     265 ..     205     289 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.001
                                  EEEECTSHHHHHHHHHHHHTT....EEEEESSSSTT CS
                           DAO  2 vviiGGGiiGlstAyeLarrg....Vtllekgdiag 33
                                   +iiG+G +Gl+tA    + +    ++++ k+++++
  gi|15668830|ref|NP_247633.1| 18 AIIIGSGAAGLTTASTIRKYNkdmeIVVITKEKEIA 53
                                  58***************6654579999999987766 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0024
                                   HTT-EEEESECEEEEEEEETCEEEEEEECTEEE.E.EEEEEEE--GGG CS
                           DAO 158 alGveilegtevtgleeedgkvwgverttpgen.d.aadavVnaaGaw 203
                                   ++ ++il++t+v +++ +++k++ v  +++g++ +  +d++V+a+Ga 
  gi|15668830|ref|NP_247633.1|  84 ERNIDILTETTVIDVDSKNNKIKCV--DKDGNEfEmNYDYLVLATGAE 129
                                   6789***********9988898888..6666553356799******86 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.1e-05
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                   +v+++G+G iGl  Ay L  rg  V+++e+++
  gi|15668830|ref|NP_247633.1| 166 KVAVVGAGAIGLEMAYGLKCRGldVLVVEMAP 197
                                   59****************9999*******985 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.53
                                   HHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEEEEEEEEEE--GGGHH.HH CS
                           DAO 154 raaealGveilegtevtgleeedgkvwgve.rttpgendaadavVnaaGawsd.ll 207
                                   + +e+ G+++ +  + +++    +kv  v+ +   g    +d v++a+G+  + +l
  gi|15668830|ref|NP_247633.1| 214 KYLEKEGIKVMLSKPLEKIVG-KEKVEAVYvD---GKLYDVDMVIMATGVRPNiEL 265
                                   458999999999999999833.2467777433...65533577******9876633 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.5e-06   0.00085       1      25 [.      20      46 ..      20      53 .. 0.80
   2 !   17.5   0.2   6.4e-06    0.0037       1      30 [.     169     198 ..     169     200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.5e-06
                                  EE--SHHHHHHHHHHHCCTE..EEEEE CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagf..dvlll 25
                                  I+G+G++Gl++A++++k+++  +++++
  gi|15668830|ref|NP_247633.1| 20 IIGSGAAGLTTASTIRKYNKdmEIVVI 46
                                  9****************9662256665 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 6.4e-06
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                   +vGaG+ Gl +Ay L+ +g+dvl++e++++
  gi|15668830|ref|NP_247633.1| 169 VVGAGAIGLEMAYGLKCRGLDVLVVEMAPQ 198
                                   8*************************9986 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   9.3e-05     0.054       2      34 ..      17      51 ..      16      54 .. 0.75
   2 !    6.4   0.0    0.0053         3     120     165 ..      83     129 ..      71     135 .. 0.85
   3 !   12.5   0.1   7.5e-05     0.044       2      37 ..     166     201 ..     165     205 .. 0.91
   4 ?    2.6   0.0     0.075        43     113     163 ..     210     258 ..     206     275 .. 0.86
   5 ?   -4.0   0.0       7.7   4.5e+03     369     387 ..     283     300 ..     278     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.3e-05
                                  SEEEE--SHHHHHHHHHHHHTT-..-EEEE-SSSS CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgk..rVlllekakk 34
                                  + i+iG GaAGl +A +++k +k  +++++ k+k+
  gi|15668830|ref|NP_247633.1| 17 RAIIIGSGAAGLTTASTIRKYNKdmEIVVITKEKE 51
                                  579**************976655116677777766 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0053
                                   HHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE----S CS
                   HI0933_like 120 keagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtGGl 165
                                   +e+++++ +et+v +v+++++++  v+   +e e++ d+lvlAtG +
  gi|15668830|ref|NP_247633.1|  83 RERNIDILTETTVIDVDSKNNKIKCVDKdGNEFEMNYDYLVLATGAE 129
                                   6899**************99999999993455588999*******75 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 7.5e-05
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37 
                                   +v+v+G+Ga Gl  A  ++ rg +Vl++e a++++ 
  gi|15668830|ref|NP_247633.1| 166 KVAVVGAGAIGLEMAYGLKCRGLDVLVVEMAPQVLP 201
                                   79***************************9999875 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.075
                                   HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                   ++ +k l+++g+k++l++ ++++   ++++  v + +++ +  d +++AtG
  gi|15668830|ref|NP_247633.1| 210 EIVQKYLEKEGIKVMLSKPLEKI-VGKEKVEAVYV-DGKLYDVDMVIMATG 258
                                   6778899****************.45666578888.99************9 PP

  == domain 5  score: -4.0 bits;  conditional E-value: 7.7
                                   T-BBTTSTTEEE-GGGBSE CS
                   HI0933_like 369 tmeskkvpgLffaGEvlDv 387
                                    m   ++p+++ +G +++v
  gi|15668830|ref|NP_247633.1| 283 KM-QTSIPNIYAVGDCVEV 300
                                   35.5789*******98876 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00096      0.56       7      72 ..      15      81 ..      12     155 .. 0.69
   2 !   16.2   0.2   1.9e-05     0.011       8      71 ..     165     259 ..     158     280 .. 0.69
   3 ?    0.1   0.2       1.9   1.1e+03      10      21 ..     403     414 ..     398     423 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00096
                 NAD_binding_7  7 gkkvlvvGgGevAarkvrklleag..akvtvvapevkeele.........elvklaeeelekdlegad.lviaatddr 72
                                  + + +++G G  +++ ++++ +++   +++v+++e  +e+                    e+ ++ +d +++ +++d 
  gi|15668830|ref|NP_247633.1| 15 EMRAIIIGSGAAGLTTASTIRKYNkdMEIVVITKE--KEIAyspcaipyvI---------EGAIKSFDdIIMHTPEDY 81
                                  67899*****************8833566777777..33332333333330.........444444442222222222 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.9e-05
                 NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtv..vapev..keele.elvklaeeelekd......................... 58 
                                   kkv vvG+G ++++ ++ l   g +v v  +ap+v    +l+ +  ++ +++lek+                         
  gi|15668830|ref|NP_247633.1| 165 KKVAVVGAGAIGLEMAYGLKCRGLDVLVveMAPQVlpR-FLDpDMAEIVQKYLEKEgikvmlskplekivgkekveavyvd 244
                                   89**************************5547776641.333444445555544333444444444444444444444433 PP

                 NAD_binding_7  59 ..legadlviaatdd 71 
                                     l ++d+vi+at  
  gi|15668830|ref|NP_247633.1| 245 gkLYDVDMVIMATGV 259
                                   33888*******975 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.9
                 NAD_binding_7  10 vlvvGgGevAar 21 
                                   + +vGg +vA+r
  gi|15668830|ref|NP_247633.1| 403 CQIVGGERVAER 414
                                   789******987 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.097        56       5      39 ..      18      52 ..       8      59 .. 0.79
   2 !   20.1   0.0   5.1e-07    0.0003     126     251 ..     100     226 ..      86     238 .. 0.67
   3 ?   -1.7   0.0       2.1   1.2e+03     329     341 ..     248     260 ..     243     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.097
                   K_oxygenase  5 ligiGiGpsnLsLailleevkkelkalflerqpef 39
                                   i+iG G++ L+ a ++++ +k+++++++ +++e 
  gi|15668830|ref|NP_247633.1| 18 AIIIGSGAAGLTTASTIRKYNKDMEIVVITKEKEI 52
                                  47888888888888888888888888888877765 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 5.1e-07
                   K_oxygenase 126 eeeeeelltveskdaegeeeelearnlvlgvGtepkiPevlekle....gkervvHsseylerkeellakkriaVvGsGqS 202
                                   +++     ++++ d++g+e e++   lvl++G ep iP++  k      +  r +   ++  +  e++  k++aVvG+G  
  gi|15668830|ref|NP_247633.1| 100 SKN----NKIKCVDKDGNEFEMNYDYLVLATGAEPFIPPIEGKDLdgvfK-VRTIEDGRAILKYIEENGCKKVAVVGAGAI 175
                                   322....256666789**********************986543323323.4444444444444479999*********** PP

                   K_oxygenase 203 aaeifedllrrqkk.velklvtrs.ealeplddspfvneifsPeyvdyfys 251
                                   + e+++ l  r  +   +++  +  +++   d +++v+++++ e ++ + s
  gi|15668830|ref|NP_247633.1| 176 GLEMAYGLKCRGLDvLVVEMAPQVlPRFLDPDMAEIVQKYLEKEGIKVMLS 226
                                   ******999885441444444332255666666666666666666666655 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.1
                   K_oxygenase 329 levdavvlATGYr 341
                                    +vd+v++ATG r
  gi|15668830|ref|NP_247633.1| 248 YDVDMVIMATGVR 260
                                   589********76 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0094       5.4       3      40 ..      19      57 ..      17      60 .. 0.86
   2 ?    4.9   0.0      0.02        11     106     150 ..      82     128 ..      74     144 .. 0.81
   3 !    7.1   0.1    0.0044       2.5       1      29 [.     166     194 ..     166     203 .. 0.89
   4 ?    4.4   0.1     0.028        16      99     169 ..     210     274 ..     205     301 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0094
                                  EEE-SSHHHHHHHHHHHHTT--EEEE.ES-GGGTT--SS CS
                          GIDA  3 iViGgGhAGceAAlaaarlGakvlLi.thkldtiaelsC 40
                                  i+iG G AG+  A ++ + + +  ++   k ++ia  +C
  gi|15668830|ref|NP_247633.1| 19 IIIGSGAAGLTTASTIRKYNKDMEIVvITKEKEIAYSPC 57
                                  8*****************999998886677788888888 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.02
                                   HTSTTEEEE.ES-EEEEEECTTEEEEEEETTS-.EEEECEEEE--TT CS
                          GIDA 106 enepnleii.eeeveeliveekkvkgvvtedge.tikakavviatGt 150
                                   ++e n++i+ e +v +++ +++k+k v ++ +e +++ +  v+atG+
  gi|15668830|ref|NP_247633.1|  82 KRERNIDILtETTVIDVDSKNNKIKCVDKDGNEfEMNYDYLVLATGA 128
                                   567899987256799****99****99877655267778*******8 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0044
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLit 29 
                                   +v V+G+G  G+e A+ ++ +G++vl + 
  gi|15668830|ref|NP_247633.1| 166 KVAVVGAGAIGLEMAYGLKCRGLDVLVVE 194
                                   699**********************9874 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.028
                                   HHHHHHHHTSTTEEEEES-.EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEESSCTT CS
                          GIDA  99 kevteklenepnleiieee.veeliveekkvkgvvtedgetikakavviatGtflkgkihigekelsaGrlg 169
                                   + v+++le+ + ++++  +  e++ v ++kv++v+  dg+ +  + v++atG     ++ i   + +  ++g
  gi|15668830|ref|NP_247633.1| 210 EIVQKYLEK-EGIKVMLSKpLEKI-VGKEKVEAVY-VDGKLYDVDMVIMATGV----RPNIELAKKAGCKIG 274
                                   567788887.88888755515666.7688888877.58999***********9....555655555555555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0     4e-05     0.023      17      49 ..      15      48 ..       4     106 .. 0.84
   2 !   11.0   0.1   0.00032      0.18      18      49 ..     165     195 ..     149     198 .. 0.83
   3 ?   -0.4   0.1      0.95   5.5e+02     100     135 ..     208     246 ..     207     267 .. 0.72
   4 ?   -2.6   0.1       4.7   2.7e+03      79     124 ..     387     431 ..     386     435 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
                                  EEEEEEE--SHHHHHHHHHHHHC.TTS-EEEEES CS
                          Thi4 17 esDvvivGaGssGLtaayylakk.pdlkvailer 49
                                  e+  +i+G+G++GLt+a ++ k   d++++++ +
  gi|15668830|ref|NP_247633.1| 15 EMRAIIIGSGAAGLTTASTIRKYnKDMEIVVITK 48
                                  67789****************9889*****9954 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00032
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                          Thi4  18 sDvvivGaGssGLtaayylakkpdlkvailer 49 
                                     v++vGaG+ GL  ay l  + +l v+++e 
  gi|15668830|ref|NP_247633.1| 165 KKVAVVGAGAIGLEMAYGLKCR-GLDVLVVEM 195
                                   569****************999.******995 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.95
                                   HHHHHHHHHTSTTEEEEESEEEEEEEEET..B.TEEEEE CS
                          Thi4 100 tstllskvlqlanvkllnavaveDlivre..g.egvaGv 135
                                   +++++ k l++ ++k++ +  +e ++ +e  + + v G 
  gi|15668830|ref|NP_247633.1| 208 MAEIVQKYLEKEGIKVMLSKPLEKIVGKEkvEaVYVDGK 246
                                   578999999999999999999999999993312334444 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 4.7
                                   HTT---EEESSEEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEE CS
                          Thi4  79 elgikyedegdyvvvkdaalftstllskvlqlanvkllnavaveDl 124
                                   e++ik+  ++d+ vv   +    +++ + ++   + +++ v++e+l
  gi|15668830|ref|NP_247633.1| 387 EIEIKMIFNEDGKVVGCQIVGGERVAER-IDAMSIAIFKKVSAEEL 431
                                   6777777777777776655555555544.55588899999998887 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0     0.001       0.6       3      38 ..      19      54 ..      18      81 .. 0.82
   2 !   10.7   0.3   0.00034       0.2       2      37 ..     167     200 ..     166     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.001
                 Lycopene_cycl  3 vviGaGpAglslAarlteakpglkvvlieaspsllf 38
                                  ++iG+G+Agl  A  + + ++++++v+i   +++ +
  gi|15668830|ref|NP_247633.1| 19 IIIGSGAAGLTTASTIRKYNKDMEIVVITKEKEIAY 54
                                  8***************99999*****9977666655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00034
                 Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsll 37 
                                   v+v+GaG+ gl +A  l  +  gl v+++e +p++l
  gi|15668830|ref|NP_247633.1| 167 VAVVGAGAIGLEMAYGL--KCRGLDVLVVEMAPQVL 200
                                   89***************..99*********999874 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0014      0.79       2      33 ..      19      52 ..      18      87 .. 0.89
   2 !   10.2   0.0    0.0012      0.69       1      41 [.     167     207 ..     167     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                                  EEES-SHHHHHHHHHHHHTT..EEEEEEESSHHH CS
                        TrkA_N  2 iiiGlGrvGrslaeeLsegg..kdvvvidkdeer 33
                                  iiiG G  G + a ++++++  +++vvi k++e 
  gi|15668830|ref|NP_247633.1| 19 IIIGSGAAGLTTASTIRKYNkdMEIVVITKEKEI 52
                                  9*****************555966****998765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0012
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg 41 
                                   ++++G+G +G ++a  L+ +g dv+v++  ++++ ++ +  
  gi|15668830|ref|NP_247633.1| 167 VAVVGAGAIGLEMAYGLKCRGLDVLVVEMAPQVLPRFLDPD 207
                                   68****************97757********9998876555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0017      0.96       3      37 ..      17      53 ..      15      59 .. 0.79
   2 !   10.9   0.2   0.00035       0.2       3      32 ..     166     195 ..     165     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                                  EEEEE--SHHHHHHHHHHHHTTHH..EEEEESSSSSC CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvr..vvlvekrsttv 37
                                    +I+G+G aGl++a+  +++  +   v+++k ++ +
  gi|15668830|ref|NP_247633.1| 17 RAIIIGSGAAGLTTASTIRKYNKDmeIVVITKEKEIA 53
                                  679***************9997765567777776655 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00035
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvek 32 
                                   +V++VGaG  Gl  a  L+ +G +v++ve 
  gi|15668830|ref|NP_247633.1| 166 KVAVVGAGAIGLEMAYGLKCRGLDVLVVEM 195
                                   69**************************96 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       6.9     4e+03       4      30 ..      20      48 ..      18      55 .. 0.64
   2 !   20.8   0.1   4.8e-07   0.00028       1      75 [.     166     240 ..     166     268 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.9
                                  EE--SCCHHHHHHHHHHT..T-EEEEE-S CS
                       3HCDH_N  4 viGaGtmGagiaavfasa..gleVvlvdi 30
                                  +iG+G  G   a+ + +   ++e+v++  
  gi|15668830|ref|NP_247633.1| 20 IIGSGAAGLTTASTIRKYnkDMEIVVITK 48
                                  79999999998888766511444544444 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 4.8e-07
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH.HHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHH CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekale.kieksleklvekgklkeeeveaalarisfttdlee 75 
                                   kvav+GaG +G ++a+ +  +gl+V +v+++++ l + l+  +++ ++k  ek+ +k    ++ l++i  ++++e+
  gi|15668830|ref|NP_247633.1| 166 KVAVVGAGAIGLEMAYGLKCRGLDVLVVEMAPQVLPRFLDpDMAEIVQKYLEKEGIK-VMLSKPLEKIVGKEKVEA 240
                                   79****************************999999887634666777777777777.444444444444444443 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.045        26       2      33 ..      20      48 ..      19      57 .. 0.82
   2 !    8.2   0.0    0.0041       2.3     120     155 ..      91     128 ..      71     129 .. 0.81
   3 ?    1.0   0.2      0.66   3.8e+02       1      32 [.     168     194 ..     168     210 .. 0.79
   4 ?    3.7   0.0     0.093        54     131     154 ..     235     258 ..     198     260 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.045
                 NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdp 33
                                  i+G G++Gl+++  + +     +++ei ++ +
  gi|15668830|ref|NP_247633.1| 20 IIGSGAAGLTTASTIRKY---NKDMEIVVITK 48
                                  9***********999998...58888888866 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0041
                 NAD_binding_9 120 hraevvdleeradgqavlladgas..laadaVvLAlGh 155
                                    +++v+d++ ++++ + + +dg++  + +d++vLA+G 
  gi|15668830|ref|NP_247633.1|  91 TETTVIDVDSKNNKIKCVDKDGNEfeMNYDYLVLATGA 128
                                   3679******************9833599*******95 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.66
                 NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfd 32 
                                   a+vGaG+ Gl ++  L  r      l++ +++
  gi|15668830|ref|NP_247633.1| 168 AVVGAGAIGLEMAYGLKCR-----GLDVLVVE 194
                                   89********999988666.....36666666 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.093
                 NAD_binding_9 131 adgqavlladgaslaadaVvLAlG 154
                                   +++++ +  dg+ +++d V++A+G
  gi|15668830|ref|NP_247633.1| 235 KEKVEAVYVDGKLYDVDMVIMATG 258
                                   455677789**************9 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.037        21      32     101 ..      11      79 ..       3      90 .. 0.70
   2 !   12.0   0.1   0.00017     0.097      32      70 ..     160     198 ..     147     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.037
                                   S-GTTSEEEEES-SHHHHHHHHHHHHT..T-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S-- CS
                  2-Hacid_dh_C  32 kelsgktvGiiGlGrIGqavakrlkaf..gmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpl 101
                                   k+ ++++  iiG G+ G ++a ++++   +m+++++ + k+    + +  +    +e ++++ D +++h+p 
  gi|15668830|ref|NP_247633.1|  11 KNGEEMRAIIIGSGAAGLTTASTIRKYnkDMEIVVITKEKE--I-AYSPCAIPYVIEGAIKSFDDIIMHTPE 79 
                                   556788999***************96611566666655533..3.333333455788888888888888885 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00017
                                   S-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                  2-Hacid_dh_C  32 kelsgktvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                   +e   k+v+++G+G+IG ++a  lk  g++v++++  ++
  gi|15668830|ref|NP_247633.1| 160 EENGCKKVAVVGAGAIGLEMAYGLKCRGLDVLVVEMAPQ 198
                                   566789*************************99987765 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0017      0.96      56      88 ..      25      57 ..      22      71 .. 0.84
   2 ?    0.9   0.0      0.87   5.1e+02      14      39 ..     155     180 ..     141     196 .. 0.62
   3 ?    4.8   0.0     0.053        31       7      54 ..     205     253 ..     205     274 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0017
                                  SEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHH CS
                  Response_reg 56 mdGlellkeireedpelpviiltahseeedave 88
                                    Gl+++++ir+ +++++++++t ++e ++   
  gi|15668830|ref|NP_247633.1| 25 AAGLTTASTIRKYNKDMEIVVITKEKEIAYSPC 57
                                  67**********************999887655 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.87
                                   HHHHHHHTTEEEEEEESSHHHHHHHH CS
                  Response_reg  14 lrqlleeegyeevaeaedgkealell 39 
                                   + +++ee+g+++va++  g+  le++
  gi|15668830|ref|NP_247633.1| 155 ILKYIEENGCKKVAVVGAGAIGLEMA 180
                                   33556677777777777777666665 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.053
                                   SHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHH..ESEEEEESSCS CS
                  Response_reg   7 dplvrellrqlleeegyeevaeaedgkealellkeek..vdlillDinmp 54 
                                   dp+++e+++++le+eg+ +v+  +  ++ + + k e+  vd  l D++m 
  gi|15668830|ref|NP_247633.1| 205 DPDMAEIVQKYLEKEGI-KVMLSKPLEKIVGKEKVEAvyVDGKLYDVDMV 253
                                   6899*************.99988888877766555555577777777775 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.014       7.9       7      74 ..      18      83 ..      14      98 .. 0.83
   2 !    9.1   0.1    0.0015      0.87       5      33 ..     165     193 ..     163     200 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.014
                                  EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHH CS
                          IlvN  7 iaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqk 74
                                    +iG G+ G + a  +r    d+ + + +++   + A +     + ++ a+k+ d +++ +P+ +++
  gi|15668830|ref|NP_247633.1| 18 AIIIGSGAAGLTTASTIRKYNKDMEIVVITKE--KEIAYSPCAIPYVIEGAIKSFDDIIMHTPEDYKR 83
                                  579***************98888777766665..4678888899999999999999999999988776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0015
                                   S-EEEES-SHHHHHHHHHHHHTT--EEEE CS
                          IlvN   5 kkiaviGyGsqGhaqalnlrdsgldvvvg 33 
                                   kk+av+G G+ G   a  l+  gldv v 
  gi|15668830|ref|NP_247633.1| 165 KKVAVVGAGAIGLEMAYGLKCRGLDVLVV 193
                                   8*************************985 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0064       3.7     219     261 ..      83     127 ..      74     136 .. 0.90
   2 ?   -0.6   0.0         1   6.1e+02       3      24 ..     176     197 ..     176     199 .. 0.88
   3 !    6.5   0.0    0.0074       4.3     213     262 ..     212     259 ..     202     264 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0064
                                   TTTTEEEETSEEEEEEEEETTCEEEEETTSTEE..EESEEEE-S- CS
                 Amino_oxidase 219 elrgldirlntrVkeikregdgvtvtledgevv..eaDaVvvTvp 261
                                   ++r+ di+++t V +++  +++++   +dg+++  ++D+ v+++ 
  gi|15668830|ref|NP_247633.1|  83 RERNIDILTETTVIDVDSKNNKIKCVDKDGNEFemNYDYLVLATG 127
                                   467789************************************986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                                   HHHHHHHHHHTTEEEEEEESSS CS
                 Amino_oxidase   3 GLaaArqLlsaGfdVtvlEard 24 
                                   GL  A+ L+ +G+dV+v+E  +
  gi|15668830|ref|NP_247633.1| 176 GLEMAYGLKCRGLDVLVVEMAP 197
                                   78899**************866 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0074
                                   HHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-H CS
                 Amino_oxidase 213 pealaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvpl 262
                                   ++   e + g ++ l++++ +i  ++++v   ++dg+ +++D V++++ +
  gi|15668830|ref|NP_247633.1| 212 VQKYLE-KEGIKVMLSKPLEKIV-GKEKVEAVYVDGKLYDVDMVIMATGV 259
                                   444444.7888999********9.5**********************976 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00036      0.21       3      35 ..      19      50 ..      17      56 .. 0.89
   2 ?   -2.5   0.3         3   1.7e+03       1      33 [.     166     195 ..     166     197 .. 0.88
   3 ?    3.9   0.0     0.033        19     156     211 ..     208     261 ..     204     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
                                  EEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                Trp_halogenase  3 vivGGGtaGwlaAaalakalkgklevtlvesee 35
                                  +i+G G aG ++A++++k+  +++e+ ++ +e+
  gi|15668830|ref|NP_247633.1| 19 IIIGSGAAGLTTASTIRKYN-KDMEIVVITKEK 50
                                  7******************9.55******9885 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlves 33 
                                   k+ +vG+G  G   A  l+  +   l+v++ve 
  gi|15668830|ref|NP_247633.1| 166 KVAVVGAGAIGLEMAYGLKCRG---LDVLVVEM 195
                                   799*********9999999888...89999985 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.033
                                   HHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG- CS
                Trp_halogenase 156 yakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrg 211
                                   +a++ +++ e++G++++  k  e ++  +++ve++ + dg+ +++d++i ++G r 
  gi|15668830|ref|NP_247633.1| 208 MAEIVQKYLEKEGIKVMLSKPLE-KIVGKEKVEAVYV-DGKLYDVDMVIMATGVRP 261
                                   588999999********999955.566789*****99.***************985 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.083        48       2      30 ..      19      49 ..      18      55 .. 0.74
   2 !    9.6   0.1    0.0011      0.65       1      27 [.     167     193 ..     167     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.083
                                  EEES-SHHHHHHHHHHHHHTHC..EEEE-SC CS
                          ApbA  2 ailGaGaiGsllaakLakagad..vtlilrs 30
                                   i+G+Ga G + a ++ k + d  +++i+++
  gi|15668830|ref|NP_247633.1| 19 IIIGSGAAGLTTASTIRKYNKDmeIVVITKE 49
                                  59**************886555225555554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE CS
                          ApbA   1 iailGaGaiGsllaakLakagadvtli 27 
                                   +a++GaGaiG  +a+ L+  g dv ++
  gi|15668830|ref|NP_247633.1| 167 VAVVGAGAIGLEMAYGLKCRGLDVLVV 193
                                   69***************88***99887 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.17        98       1      32 [.      16      47 ..      16      56 .. 0.77
   2 ?   -2.7   0.1       6.5   3.8e+03      25      42 ..      94     111 ..      90     117 .. 0.72
   3 !   12.2   0.0   0.00018       0.1       2      34 ..     166     198 ..     165     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.17
                                  SEEEEE--STTHHHHHHHHHHCTSEEEEE-S- CS
                UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDid 32
                                  m+  +iG+G  Gl+ta  + +  +++ +v i 
  gi|15668830|ref|NP_247633.1| 16 MRAIIIGSGAAGLTTASTIRKYNKDMEIVVIT 47
                                  67789************999988655444443 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.5
                                   EEEEE-S-HHHHHHHCTT CS
                UDPG_MGDP_dh_N  25 evigvDideekvdklnsg 42 
                                   +vi vD  ++k++ + ++
  gi|15668830|ref|NP_247633.1|  94 TVIDVDSKNNKIKCVDKD 111
                                   677888888888876655 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00018
                                   EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HH CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDidee 34 
                                   k++v+G+G +Gl +a  l  +g +v++v +  +
  gi|15668830|ref|NP_247633.1| 166 KVAVVGAGAIGLEMAYGLKCRGLDVLVVEMAPQ 198
                                   89**************************98765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.029        17      29      57 ..      16      44 ..      11      57 .. 0.82
   2 ?    7.6   0.1    0.0036       2.1      30      97 ..     166     255 ..     152     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.029
                                  -EEEEESTSHHHHHHHHHHHHTT-EEEEE CS
                   AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvl 57
                                   + ++iG G aGl  ++t ++ + + +++
  gi|15668830|ref|NP_247633.1| 16 MRAIIIGSGAAGLTTASTIRKYNKDMEIV 44
                                  5789*************999888777665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0036
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH..TTTCECEE.....................HCHHHHHHHH CS
                   AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles..lgakfvev.....................lksqeellae 87 
                                   kv v+G+G  Gl+ +   k  g +V v+++ p++l ++ +  + a++v+                       k ++  ++ 
  gi|15668830|ref|NP_247633.1| 166 KVAVVGAGAIGLEMAYGLKCRGLDVLVVEMAPQVLPRFLDpdM-AEIVQKylekegikvmlskplekivgkEKVEAVYVDG 245
                                   8********************************9988877643.3334444555666667777766666665666666666 PP

                                   HHHH-SEEEE CS
                   AlaDh_PNT_C  88 avkeadvvig 97 
                                   ++ ++d+vi 
  gi|15668830|ref|NP_247633.1| 246 KLYDVDMVIM 255
                                   6666666665 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.71   4.1e+02       3      41 ..      18      56 ..      16      74 .. 0.80
   2 ?   10.8   0.0    0.0006      0.35      52     122 ..     150     226 ..     123     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.71
                        LpxI_N  3 gliAGsGrlPllvaeaakaagrevvvvalegeadeelek 41
                                  ++i GsG+  l  a  +++ ++++ +v +++e + ++++
  gi|15668830|ref|NP_247633.1| 18 AIIIGSGAAGLTTASTIRKYNKDMEIVVITKEKEIAYSP 56
                                  7999***************88777777777777666665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0006
                        LpxI_N  52 gqlgklikaLkregvtevvm..aGkvekpkll..dlrp.Dlralkllak.lkdrgddalLravveelekeGikvlga 122
                                   ++   ++k+++++g+++v    aG++  + ++  + r  D+ ++++ ++ l++  d  + + v ++lekeGikv+ +
  gi|15668830|ref|NP_247633.1| 150 EDGRAILKYIEENGCKKVAVvgAGAIGLEMAYglKCRGlDVLVVEMAPQvLPRFLDPDMAEIVQKYLEKEGIKVMLS 226
                                   5556799*********97662267899999996655556*********98778899999999999*********865 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0        10   5.8e+03      18      44 ..      19      46 ..      11      55 .. 0.56
   2 ?   11.4   0.0   0.00037      0.22       7      47 ..     157     198 ..     153     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 10
                                  EEET-TT-.-HHHHHHHHHS-EEEEE-S CS
                       UPF0146 18 vEvGiGrk.ldvaealakrgvdlvatDi 44
                                  + +G G+  l  a++++k+  d+ ++ i
  gi|15668830|ref|NP_247633.1| 19 IIIGSGAAgLTTASTIRKYNKDMEIVVI 46
                                  5566665425667777777655444433 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00037
                                   HHHHHS-SSEEEEET-TT-.-HHHHHHHHHS-EEEEE-SS-S CS
                       UPF0146   7 kiaeenargkvvEvGiGrk.ldvaealakrgvdlvatDikek 47 
                                   k +een+++kv+ vG+G+  l++a  l+ rg+d++++++ ++
  gi|15668830|ref|NP_247633.1| 157 KYIEENGCKKVAVVGAGAIgLEMAYGLKCRGLDVLVVEMAPQ 198
                                   5688*************86489*************9998877 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.014       8.2      32      64 ..      16      48 ..       9      94 .. 0.82
   2 ?    1.1   0.0      0.39   2.3e+02      68     112 ..      82     130 ..      61     153 .. 0.75
   3 ?    3.6   0.1     0.068        39      32      64 ..     165     194 ..     147     214 .. 0.82
   4 ?   -1.0   0.0       1.8     1e+03      78     109 ..     237     258 ..     226     266 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                   Glu_dehyd_C 32 esalvlGaGslGLLalalleaeerglervyvlg 64
                                   +a+++G+G+ GL ++ ++++ ++++e v ++ 
  gi|15668830|ref|NP_247633.1| 16 MRAIIIGSGAAGLTTASTIRKYNKDMEIVVITK 48
                                  579*****************9999998554443 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.39
                   Glu_dehyd_C  68 rpdptidlveelGatYvdsretpvdeipea....seemdlvvEaTGsak 112
                                   + +++id++ e     vds++++++ + +     + + d++v aTG+ +
  gi|15668830|ref|NP_247633.1|  82 KRERNIDILTETTVIDVDSKNNKIKCVDKDgnefEMNYDYLVLATGAEP 130
                                   4578899999999999***999999886551111455677888999765 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.068
                   Glu_dehyd_C  32 esalvlGaGslGLLalalleaeerglervyvlg 64 
                                   +++ v+GaG++GL ++  l+   rgl+ v v++
  gi|15668830|ref|NP_247633.1| 165 KKVAVVGAGAIGLEMAYGLKC--RGLD-VLVVE 194
                                   6789*********99888876..7776.55555 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.8
                   Glu_dehyd_C  78 elGatYvdsretpvdeipeaseemdlvvEaTG 109
                                   ++ a+Yvd +  +vd          +v+ aTG
  gi|15668830|ref|NP_247633.1| 237 KVEAVYVDGKLYDVD----------MVIMATG 258
                                   556666666555555..........5555555 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00038      0.22       1      42 [.     166     207 ..     166     243 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00038
                                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT CS
                 NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg 42 
                                   k++++G G +G +ma  l+ +g +v v++  ++ + ++++  
  gi|15668830|ref|NP_247633.1| 166 KVAVVGAGAIGLEMAYGLKCRGLDVLVVEMAPQVLPRFLDPD 207
                                   699***************************999998888765 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2     0.003       1.8      49      75 ..      96     121 ..      92     127 .. 0.82
   2 ?   -1.0   0.4       3.1   1.8e+03      36      71 ..     213     250 ..     208     253 .. 0.53
   3 ?    1.3   0.1      0.58   3.4e+02      43      77 ..     234     269 ..     224     274 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.003
                       PepSY_2  49 ievddggcyEvegldkdGkkveikldp 75 
                                   i+vd+    +++ +dkdG+++e+++d+
  gi|15668830|ref|NP_247633.1|  96 IDVDSK-NNKIKCVDKDGNEFEMNYDY 121
                                   677444.589***************97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.1
                       PepSY_2  36 vakleaqGykvkkievddg..gcyEvegldkdGkkvei 71 
                                   ++ le++G kv+  +  +   g+ +ve+++ dGk +++
  gi|15668830|ref|NP_247633.1| 213 QKYLEKEGIKVMLSKPLEKivGKEKVEAVYVDGKLYDV 250
                                   55566666666544322220012456777777777666 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.58
                       PepSY_2  43 Gy.kvkkievddggcyEve.gldkdGkkveikldpat 77 
                                   G  kv+ + v dg+ y+v+ ++++ G +  i+l ++ 
  gi|15668830|ref|NP_247633.1| 234 GKeKVEAVYV-DGKLYDVDmVIMATGVRPNIELAKKA 269
                                   6668888999.99899999999999999888888765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       3.3   1.9e+03       3      19 ..      19      35 ..      18      52 .. 0.78
   2 ?    4.5   0.0     0.032        19      87     125 ..      64     110 ..      33     127 .. 0.76
   3 ?   -0.2   1.0      0.84   4.9e+02       2      31 ..     167     196 ..     166     199 .. 0.92
   4 ?    1.9   0.0       0.2   1.1e+02      89     144 ..     208     258 ..     198     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.3
                  FAD_oxidored  3 vVvGGgpaGvaAAiaAa 19
                                  +++G+g+aG++ A +  
  gi|15668830|ref|NP_247633.1| 19 IIIGSGAAGLTTASTIR 35
                                  79********9997655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.032
                  FAD_oxidored  87 evakavleeml........aeagvtvllntrlvevekegkriesvtv 125
                                   e a + +++++        +e ++++l++t++++v+ ++++i+ v  
  gi|15668830|ref|NP_247633.1|  64 EGAIKSFDDIImhtpedykRERNIDILTETTVIDVDSKNNKIKCVDK 110
                                   555566666666677777799****************9988887765 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.84
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveer 31 
                                   v VvG+g+ G+  A+  + +G  vl+ve  
  gi|15668830|ref|NP_247633.1| 167 VAVVGAGAIGLEMAYGLKCRGLDVLVVEMA 196
                                   89*************************965 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.2
                  FAD_oxidored  89 akavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                   +++++++ l+++g++v+l + l++++ ++ ++e+v v     +k +  +++i ATg
  gi|15668830|ref|NP_247633.1| 208 MAEIVQKYLEKEGIKVMLSKPLEKIVGKE-KVEAVYVD----GKLYDVDMVIMATG 258
                                   457889999999************99986.9***9995....67777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 2772.42
//
Query:       gi|15668831|ref|NP_247634.1|  [L=692]
Description: hypothetical protein MJ_0650 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (692 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 4233.52
//
Query:       gi|15668832|ref|NP_247635.1|  [L=311]
Description: protease IV SppA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-60  201.5   0.5    8.5e-60  201.2   0.5    1.1  1  Peptidase_S49  Peptidase family S49
    8.6e-08   32.3   0.0    0.00019   21.4   0.0    2.3  2  CLP_protease   Clp protease
    0.00022   20.3   0.1    0.00041   19.5   0.1    1.4  1  SDH_sah        Serine dehydrogenase proteinase
     0.0008   18.8   0.5       0.48    9.7   0.0    2.4  3  ECH_1          Enoyl-CoA hydratase/isomerase
     0.0059   16.4   0.0     0.0099   15.7   0.0    1.3  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
  ------ inclusion threshold ------
      0.026   14.3   0.0      0.055   13.3   0.0    1.5  1  Ligase_CoA     CoA-ligase
      0.029   14.3   0.2      0.099   12.6   0.0    1.8  2  DUF2150        Uncharacterized protein conserved in archaea (


Domain annotation for each model (and alignments):
>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.2   0.5   3.3e-63   8.5e-60       2     153 ..     111     262 ..     110     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 201.2 bits;  conditional E-value: 3.3e-63
                                   HHHTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEESSTTCCCCCTTSS--H CS
                 Peptidase_S49   2 akkakkPvvasaenvaaSggYylasaadkivanpstivgsiGvitqllnlenlldklgvevqvvkaGeyksavslrrelte 82 
                                   ++++kkPvv+++e+++aSg+Y++++ ad+iva++++ivgsiGv ++l+++ +l++klg++v+++kaG+yk+++s++r++t+
  gi|15668832|ref|NP_247635.1| 111 ELAKKKPVVVYVEGLDASGAYMVSAPADYIVAEKHSIVGSIGVRMDLMHYYGLMKKLGINVTTIKAGKYKDIGSPFRPMTK 191
                                   5789***************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHCHC CS
                 Peptidase_S49  83 eereilqrlldetyqqFvqtVaknRnlsveqvdkiAegrvltgqqAlklgLvdelgtvddavaeleelakv 153
                                   ee+e+lq++++ety++Fv++Va++R+ls++++ kiA+g++++g++A+k+gLvde+gt +da+++le+la+v
  gi|15668832|ref|NP_247635.1| 192 EEKEYLQKMINETYMDFVKWVAEHRHLSINYTLKIADGKIYSGEDAKKVGLVDEVGTEEDALKKLEQLANV 262
                                   *********************************************************************98 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   7.3e-08   0.00019      27      97 ..      66     138 ..      59     146 .. 0.87
   2 !    8.7   0.0   0.00056       1.4     134     181 ..     203     249 ..     157     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.3e-08
                                   HHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHS..SS-EEEEEEEEEETHHHHHHHTS- CS
                  CLP_protease  27 devankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyi..kpdvsticlGlaaSmgslllaage 97 
                                   ++ a+  i+ L  Le+ d+ k +ll++nspGG+v a+  ++  ++ +  k +v++++ Gl aS + ++ a ++
  gi|15668832|ref|NP_247635.1|  66 KKDARYYINLLDDLEKDDSVKGVLLVVNSPGGEVIASEKLARKVEELakKKPVVVYVEGLDASGAYMVSAPAD 138
                                   5667777888889****************************99998876788999999*****9999887665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00056
                                   HHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHHHHHTSSSEE-SS CS
                  CLP_protease 134 kikerlneilakhtgqslekiekdldrdtflsaeeAveyGLideviek 181
                                   ++  + ++ +a+h + s++   k +   ++ s e+A++ GL+dev ++
  gi|15668832|ref|NP_247635.1| 203 ETYMDFVKWVAEHRHLSINYTLK-IADGKIYSGEDAKKVGLVDEVGTE 249
                                   44444455555555555555444.44567889*************876 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.6e-07   0.00041      93     159 ..      87     155 ..      75     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-07
                       SDH_sah  93 pidliihtpGGlvlaatqiakalke..hkaktrvivphyamsGGtlialaadeiildenavlGpvdpql 159
                                    + l++ +pGG v+a++++a+ ++e  +k ++ v v     sG  +++  ad i+ ++++++G +  ++
  gi|15668832|ref|NP_247635.1|  87 GVLLVVNSPGGEVIASEKLARKVEElaKKKPVVVYVEGLDASGAYMVSAPADYIVAEKHSIVGSIGVRM 155
                                   56799****************99972245556667788899**********************976554 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.3   3.2e+03      31      47 ..      75      91 ..      73     104 .. 0.82
   2 !    7.0   0.1    0.0013       3.3      87     132 ..     114     159 ..      93     189 .. 0.79
   3 !    9.7   0.0   0.00019      0.48     156     186 ..     229     259 ..     223     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                                  HHHHHHHSTTECEEEEE CS
                         ECH_1 31 alekleddksvravvLt 47
                                   l +le+d sv++v L 
  gi|15668832|ref|NP_247635.1| 75 LLDDLEKDDSVKGVLLV 91
                                  5889999******9884 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0013
                                   SSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS-- CS
                         ECH_1  87 vpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlip 132
                                    +kpv+  v+G  + G   +   +D+++a +++  g   +++ l+ 
  gi|15668832|ref|NP_247635.1| 114 KKKPVVVYVEGLDASGAYMVSAPADYIVAEKHSIVGSIGVRMDLMH 159
                                   489**********9999999999********999887766665555 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00019
                                   T-EEEHHHHHHCTSSSEEESGGGHHHHHHHH CS
                         ECH_1 156 gkkisaqealkvGlvdkvvpeeqlleealel 186
                                   gk +s+++a+kvGlvd+v  ee+ l++  +l
  gi|15668832|ref|NP_247635.1| 229 GKIYSGEDAKKVGLVDEVGTEEDALKKLEQL 259
                                   7889**************9998877665544 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.9e-06    0.0099      45     100 ..      75     134 ..      72     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.9e-06
                  Succ_CoA_lig  45 lleylaedpetkvillylEsird....grkflsaarraarkkpvvvlksGrseagaraaa 100
                                   ll+ l++d+++k +ll++ s +      +k+++ ++++a+kkpvvv+  G  ++ga +++
  gi|15668832|ref|NP_247635.1|  75 LLDDLEKDDSVKGVLLVVNSPGGeviaSEKLARKVEELAKKKPVVVYVEGLDASGAYMVS 134
                                   79999*************9977655558*********************99998887665 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.1e-05     0.055      57     121 ..      68     128 ..      56     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                                   .HHHHHHHHHHHHS-TT-SEEEEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH CS
                    Ligase_CoA  57 DptkriealkklaadpevkvilldivlGygahedpaaellkaikeakaegrelpvvarvaGtead 121
                                   D + +i+ l +l +d++vk++ll +    g +    ++l+++++e+    +++pvv++v+G +a 
  gi|15668832|ref|NP_247635.1|  68 DARYYINLLDDLEKDDSVKGVLLVVNSP-GGEVIASEKLARKVEELA---KKKPVVVYVEGLDAS 128
                                   77889999*************9988876.777888889999999998...***********8876 PP

>> DUF2150  Uncharacterized protein conserved in archaea (DUF2150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.9e-05     0.099     112     181 ..      65     134 ..      58     138 .. 0.88
   2 ?   -1.9   0.0       1.1   2.7e+03      58      77 ..     248     267 ..     242     279 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.9e-05
                       DUF2150 112 kekdieelvkaaaeaeaeedleaaleivaqiGakvidgeklpekvledl.eyglvaewldgidslaaamss 181
                                   ++kd + +++   + e+++ +   l +v + G +vi+ ekl++kv e+l ++  v  +++g+d+  a m+s
  gi|15668832|ref|NP_247635.1|  65 QKKDARYYINLLDDLEKDDSVKGVLLVVNSPGGEVIASEKLARKV-EELaKKKPVVVYVEGLDASGAYMVS 134
                                   567888888888999****************************99.66669************98877765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                       DUF2150  58 skeeAleeleevreivleev 77 
                                   ++e+Al++le+  ++   e+
  gi|15668832|ref|NP_247635.1| 248 TEEDALKKLEQLANVSNPEI 267
                                   68899999999888766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1056  (0.058899); expected 358.6 (0.02)
Passed bias filter:                      820  (0.045736); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 1865.30
//
Query:       gi|15668833|ref|NP_247636.1|  [L=134]
Description: hypothetical protein MJ_0652 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-17   63.5   2.4    2.9e-17   62.6   2.4    1.5  1  CRS1_YhbY  CRS1 / YhbY (CRM) domain
     0.0091   16.2   3.0      0.014   15.6   0.5    2.0  2  Toprim     Toprim domain
  ------ inclusion threshold ------
      0.035   14.1   0.0        1.1    9.4   0.0    2.5  2  UPF0154    Uncharacterised protein family (UPF0154)


Domain annotation for each model (and alignments):
>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   2.4   4.8e-21   2.9e-17       1      84 []      13      97 ..      13      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 4.8e-21
                     CRS1_YhbY  1 LtekelrrLrhlairlkpkvkiGkaGvtkevvdeiheklkteelvkvkc..egppalnmkrmaeiLeektgglviqrsgtsiv 81
                                  Lt k +r+Lr++a++l+p+v +Gk+G  ++v++e++++lk++ l+kvk+       ++  ++ae+L+++++++v+++ g++i+
  gi|15668833|ref|NP_247636.1| 13 LTGKMKRMLRAKAHHLEPVVWVGKEGS-EKVIKEVDRQLKERGLIKVKVrkAALLYEDKYEIAEKLAKACDAEVVSVVGHVIT 94
                                  78999*********************8.88*******************76334566799*********************** PP

                     CRS1_YhbY 82 LYR 84
                                  L+R
  gi|15668833|ref|NP_247636.1| 95 LFR 97
                                  **9 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.085   5.1e+02      38      62 ..      27      52 ..       5      62 .. 0.71
   2 !   15.6   0.5   2.3e-06     0.014       7      63 ..      70     131 ..      68     134 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.085
                                  TTEEEEE.ECTTTHHHHHHHHHHHHH CS
                        Toprim 38 efkpvye.eiedkkkvlkalkelakr 62
                                   ++pv +  +e+ +kv+k++++++k+
  gi|15668833|ref|NP_247636.1| 27 HLEPVVWvGKEGSEKVIKEVDRQLKE 52
                                  44555556888999999998888765 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.3e-06
                                   SHHHHHHHHHTHTSTEEEEEEESSSSEEEHS...TTEEEEE.....ECTTTHHHHHHHHHHHHHH CS
                        Toprim   7 gpsdaktiakalgsgfqavtaslGhildlet...efkpvye.....eiedkkkvlkalkelakra 63 
                                   ++  a+++aka   ++ +v++++Gh+++l      +k+ +      ++++++k+++ +++ +k+a
  gi|15668833|ref|NP_247636.1|  70 KYEIAEKLAKA---CDAEVVSVVGHVITLFRpreGWKKYLAkkpkkKVKKDEKIIELFEKFKKKA 131
                                   56779999999...99***************9995555555666689999999999999998776 PP

>> UPF0154  Uncharacterised protein family (UPF0154)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.038   2.2e+02      43      59 ..      35      51 ..      33      52 .. 0.87
   2 ?    9.4   0.0   0.00018       1.1       4      29 ..      86     111 ..      84     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.038
                       UPF0154 43 GrkPSekqikqvmrsmk 59
                                  G+  Sek ik+v r++k
  gi|15668833|ref|NP_247636.1| 35 GKEGSEKVIKEVDRQLK 51
                                  8999********99987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00018
                       UPF0154   4 alivGlvlGffiarkymkkqlkenPp 29 
                                   + +vG v++ f  r   kk+l+++P 
  gi|15668833|ref|NP_247636.1|  86 VSVVGHVITLFRPREGWKKYLAKKPK 111
                                   679*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1101  (0.0614089); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 853.16
//
Query:       gi|15668834|ref|NP_247637.1|  [L=194]
Description: inosine-5'-monophosphate dehydrogenase GuaB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-32  110.6   4.6    4.3e-17   62.3   0.2    2.3  2  CBS             CBS domain
  ------ inclusion threshold ------
      0.016   15.1   0.1      0.025   14.5   0.1    1.4  1  UvrC_HhH_N      UvrC Helix-hairpin-helix N-terminal
      0.064   13.3   0.1        0.1   12.6   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.082   12.8   0.2       0.16   11.9   0.2    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        0.3   11.1   3.4         12    5.9   0.3    2.3  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.68    9.9   0.1       0.68    9.9   0.1    2.9  3  zf-C4_ClpX      ClpX C4-type zinc finger


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.8   1.2e-16   3.6e-13       1      55 [.       9      62 ..       9      64 .. 0.94
   2 !   62.3   0.2   1.4e-20   4.3e-17       2      55 ..      75     127 ..      74     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.2e-16
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                  V+++m+ +v+ ++ ++++ +++++m+e++++++ +V e++k++Givt+rD+++ +
  gi|15668834|ref|NP_247637.1|  9 VSEVMSFPVIKATKNMSIYDIANIMTENNIGAVVIV-ENNKPIGIVTERDIVKRV 62
                                  89*******************************668.89************9976 PP

  == domain 2  score: 62.3 bits;  conditional E-value: 1.4e-20
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   +++m+++++t+p ++++ ea+++m+ +g+ rlPVV +dg+lvGivt++D++r+ 
  gi|15668834|ref|NP_247637.1|  75 EEVMSKKIITIPQNASITEAAKIMATHGIKRLPVV-KDGELVGIVTQSDIVRVS 127
                                   79**********************9999*******.8**************975 PP

>> UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   8.3e-06     0.025       8      38 ..      19      49 ..      13      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.3e-06
                                  S---EEEEEEEEEETTTEEEEEEEEEETTEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    UvrC_HhH_N  8 ekpkriecyDiShiqgtntvgsmvvfedgkp 38
                                  ++ k++ +yDi++i+ +n++g++v++e++kp
  gi|15668834|ref|NP_247637.1| 19 KATKNMSIYDIANIMTENNIGAVVIVENNKP 49
                                  56899***********************987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.5e-05       0.1      36      94 ..     123     187 ..      89     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                                   TCT--HHHHHHHHHHHH....CC.TTTT-EEEEEEE--EEEETTTS-EEECHH.H.HHS-TTTSS CS
                          HypA  36 lsgvepeaLefafella....egtvlegaeLeieevpvkvrCreCgkefelee.k.alrCpkCgs 94 
                                   +  v+pe Le + e ++    e++v++  + e++e+ ++  C++Cg++++++  + ++ C +C +
  gi|15668834|ref|NP_247637.1| 123 IVRVSPELLEIVIEYASitpeEKEVISLDTDEFSEEYINGICENCGYQGRVRLyQgRYLCDECIE 187
                                   556888888888888874343333333333348899999**********9776447889****65 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   5.3e-05      0.16      22      55 ..     155     188 ..     145     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-05
                OrfB_Zn_ribbon  22 vnpayTSktCseCgsknkealsgrtfkCpnCgfe 55 
                                    +++y    C +Cg++++ +l + ++ C++C  e
  gi|15668834|ref|NP_247637.1| 155 FSEEYINGICENCGYQGRVRLYQGRYLCDECIEE 188
                                   556666668**********************776 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3    0.0046        14      21      28 ..     163     170 ..     157     170 .. 0.91
   2 ?    5.9   0.3     0.004        12      20      30 .]     180     190 ..     178     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0046
                PhnA_Zn_Ribbon  21 vCpeCahE 28 
                                   +C++C+++
  gi|15668834|ref|NP_247637.1| 163 ICENCGYQ 170
                                   9*****98 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.004
                PhnA_Zn_Ribbon  20 lvCpeCahEwe 30 
                                   ++C+eC +E+e
  gi|15668834|ref|NP_247637.1| 180 YLCDECIEEFE 190
                                   79******996 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.77   2.3e+03      13      25 ..      79      91 ..      75      91 .. 0.81
   2 ?   -0.3   0.7      0.34     1e+03      25      29 ..     163     167 ..     157     170 .. 0.87
   3 ?    9.9   0.1   0.00023      0.68      23      34 ..     179     190 ..     173     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.77
                    zf-C4_ClpX 13 vkklIagpngvyI 25
                                   kk+I+ p+++ I
  gi|15668834|ref|NP_247637.1| 79 SKKIITIPQNASI 91
                                  6899*99998877 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.34
                    zf-C4_ClpX  25 ICdeC 29 
                                   IC++C
  gi|15668834|ref|NP_247637.1| 163 ICENC 167
                                   9**** PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00023
                    zf-C4_ClpX  23 vyICdeCvelcn 34 
                                    y CdeC+e+  
  gi|15668834|ref|NP_247637.1| 179 RYLCDECIEEFE 190
                                   499******876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1191.82
//
Query:       gi|15668835|ref|NP_247638.1|  [L=306]
Description: dihydroorotate dehydrogenase 1B [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-98  329.7   3.2    1.7e-98  329.5   3.2    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
    1.8e-15   56.8   0.8    1.6e-11   43.9   0.1    2.0  2  Dus           Dihydrouridine synthase (Dus)
     0.0004   19.9   4.7    0.00083   18.8   2.6    2.2  3  NMO           Nitronate monooxygenase
     0.0023   17.4   0.4      0.034   13.6   0.0    2.5  2  His_biosynth  Histidine biosynthesis protein
     0.0033   16.5   4.3      0.033   13.2   3.1    2.6  2  FMN_dh        FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.023   15.1   0.0        2.7    8.3   0.0    2.3  2  Radical_SAM   Radical SAM superfamily
      0.035   13.1   5.7      0.053   12.5   1.0    2.4  2  IMPDH         IMP dehydrogenase / GMP reductase domain
       0.11   11.9   2.7        2.5    7.5   0.1    2.9  3  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
       0.16   11.8   0.3       0.73    9.8   0.1    1.9  2  PapG_C        PapG chaperone-binding domain
       0.17   11.3   4.2        1.1    8.7   0.2    2.8  3  PcrB          PcrB family
        0.2   11.0   2.5        0.6    9.4   2.5    1.7  1  ThiG          Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.5   3.2    1e-101   1.7e-98       1     295 []       5     290 ..       5     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 329.5 bits;  conditional E-value: 1e-101
                                   GG-EEETTEEESSSEEE-TTSSTTSSSHHHHHCTT.SSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHHH CS
                        DHO_dh   1 slatkvlglkfknpiglAaGfdkegeeilkllklg.fgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGldav 80 
                                   +l+t+++g++fknp++lA+G+++e+ ++lk +++g +ga++++s++++p++G+++P++++++ +  +lN++Gl+n+G+d++
  gi|15668835|ref|NP_247638.1|   5 MLKTNICGIEFKNPVFLASGIMGETGSALKRIAKGgAGAVTTKSIGLNPNPGHKNPTIVEVYGG--FLNAMGLPNPGVDEY 83 
                                   79**************************99999999****************************..*************** PP

                                   HHHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGGESEEEEES-SCTCC.TSCCCGCHHHHHHHHHHHHHHH CS
                        DHO_dh  81 lekllkrrkeqeekkelginlskakktenavddyvevvrkigpfadilelNvSsPntp.glrdlqekeelkaillkvvkev 160
                                   le+++k+r+e ++ ++++i+ s+++k+   +++++ev++k+++++di+elN+S+P+++ ++++++++++l+++++k+vk++
  gi|15668835|ref|NP_247638.1|  84 LEEIEKVRDELNR-MDVRIIGSIYGKD---EEEFAEVAKKMERYVDIIELNISCPHAKgYGATIGQNPDLSYDVCKAVKKA 160
                                   **********998.99**********9...****************************889******************** PP

                                   HSSEEEEEE-SSSSHHHHHHHHHHHH.HHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHHHH CS
                        DHO_dh 161 skvpvlvKlaPdltdeekkdiadvll.elkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdialkvirelykr 240
                                    k+pv++Kl+P++td+ ++++a+v +  ++l +i+    tv+++aid++++k++ ank+GGlsGka+k+i++kv+++ly++
  gi|15668835|ref|NP_247638.1| 161 VKIPVFAKLTPNVTDIIEIAQAVVDAgVDGLVAIN----TVRGMAIDIRAKKPILANKFGGLSGKAIKSIGIKVVWDLYEN 237
                                   *******************9999999888999988....9***************************************** PP

                                   TTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
                        DHO_dh 241 lkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                                   ++  +piIgvGGi+sgeDa+e+++aGAs+vq++++++++g+ i+kk+++e+ ++L
  gi|15668835|ref|NP_247638.1| 238 FD--VPIIGVGGIMSGEDAIEYMMAGASAVQIGSGVYYRGYDIFKKVCDEIISFL 290
                                   **..***********************************************9876 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.1   9.9e-15   1.6e-11      60     155 ..     105     191 ..      81     205 .. 0.90
   2 !   11.7   0.1   6.3e-05       0.1     173     219 ..     229     274 ..     217     292 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 9.9e-15
                                   EE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.H CS
                           Dus  60 lggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeena 140
                                   ++g+d ++ ae Ak+ +  ++d+I+lN+ CP      +g+Ga+  ++pdl +++ kav+kav+iPv +k    +     ++
  gi|15668835|ref|NP_247638.1| 105 IYGKDEEEFAEVAKKMER-YVDIIELNISCPHA----KGYGATIGQNPDLSYDVCKAVKKAVKIPVFAKLTPNVT----DI 176
                                   899*************99.************86....69*****************************9987766....78 PP

                                   HHHHHHHHHCT-SEE CS
                           Dus 141 lelakiveaaGaqal 155
                                   +e+a++v +aG++ l
  gi|15668835|ref|NP_247638.1| 177 IEIAQAVVDAGVDGL 191
                                   99*********9866 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.3e-05
                                   HHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCS CS
                           Dus 173 eaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgn 219
                                   + + ++ +++ +p+i+ G+I + eda + +   Ga +v ig g +++
  gi|15668835|ref|NP_247638.1| 229 KVVWDLYENFDVPIIGVGGIMSGEDAIEYMMA-GASAVQIGSGVYYR 274
                                   56778999**********************99.*********99976 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.43     7e+02     183     198 ..     152     167 ..     139     169 .. 0.82
   2 ?    0.2   0.3      0.23   3.8e+02      10      62 ..     161     212 ..     154     219 .. 0.64
   3 !   18.8   2.6   5.1e-07   0.00083     168     223 ..     216     269 ..     177     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.43
                           NMO 183 aLvpqvldavdiPviA 198
                                    + + v++av+iPv A
  gi|15668835|ref|NP_247638.1| 152 DVCKAVKKAVKIPVFA 167
                                   5778999*******98 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.23
                           NMO  10 ikppvvqpgmggisk.arLaaavsnaGgLGvlasgyltaDrlakeirkvkaltd 62 
                                   +k pv++     ++   ++a av +aG  G++a  + t   +a +ir+ k + +
  gi|15668835|ref|NP_247638.1| 161 VKIPVFAKLTPNVTDiIEIAQAVVDAGVDGLVA--INTVRGMAIDIRAKKPILA 212
                                   456666666666554247788888888888887..6666667777777666555 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 5.1e-07
                           NMO 168 GGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigt 223
                                   GG  G  +++    +++v    +  d+P+i  GGi+ +++    + +GAs+vqig+
  gi|15668835|ref|NP_247638.1| 216 GGLSG-KAIK-SIGIKVVWDLYENFDVPIIGVGGIMSGEDAIEYMMAGASAVQIGS 269
                                   66667.3332.344677778888999*****************************7 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.16   2.5e+02      92     157 ..      94     161 ..      83     188 .. 0.56
   2 !   13.6   0.0   2.1e-05     0.034      62     117 ..     228     284 ..     218     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.16
                                   HHCT-SEEEESHHHHH-THHHHHHHHHHCGGG..EEEEEEEEE..CEEEEETTTTEEEEEEHHHHHHHHH CS
                  His_biosynth  92 leagadkviigtaavknpelikelaekfgsqk..ivvaiDarr..gykvaikgwreetgldavelakkle 157
                                   l++ +d  iig+ + k+ e + e+a+k+++    i + i + +  g   a+ g + + ++d+ + +kk+ 
  gi|15668835|ref|NP_247638.1|  94 LNR-MDVRIIGSIYGKDEEEFAEVAKKMERYVdiIELNISCPHakG-YGATIGQNPDLSYDVCKAVKKAV 161
                                   544.556677777777777777777766553200222223222333.33333444444444444444444 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.1e-05
                                   HHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHH.H-THHHHHHHH CS
                  His_biosynth  62 ldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaav.knpelikelae 117
                                   +++v  + e++++p+   GGI s ed+ e++ aga+ v ig+ +  +  +++k++++
  gi|15668835|ref|NP_247638.1| 228 IKVVWDLYENFDVPIIGVGGIMSGEDAIEYMMAGASAVQIGSGVYyRGYDIFKKVCD 284
                                   677888889999999999999999999999999999999998754255666666666 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.41   6.7e+02      46      67 ..       4      25 ..       1      44 [. 0.79
   2 !   13.2   3.1     2e-05     0.033     200     306 ..     146     274 ..      98     303 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.41
                                  -B--EEETTEEESSSEEE--BS CS
                        FMN_dh 46 vdlsttllGqklslPvliaPvg 67
                                  + l+t++ G +++ Pv++a+  
  gi|15668835|ref|NP_247638.1|  4 CMLKTNICGIEFKNPVFLASGI 25
                                  56899************99854 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2e-05
                                   -TC--HHHHHHHHHHHSSEEEEEEE-SHHH....HHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH........ CS
                        FMN_dh 200 dpsltwddikwlreqtklplvvKGvltaed....akraveaGvdgivvSNHGGRqldgapatidvLpeiveav........ 268
                                   +p+l++d  k +++++k+p+  K   ++ d    a+ +v+aGvdg+v  N     ++g+   i++   i ++         
  gi|15668835|ref|NP_247638.1| 146 NPDLSYDVCKAVKKAVKIPVFAKLTPNVTDiieiAQAVVDAGVDGLVAINT----VRGMAIDIRAKKPILANKfgglsgka 222
                                   567777777777777777777776655555333355666777777665553....22222223333222111123333333 PP

                                   ................SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHH CS
                        FMN_dh 269 .............gg.rievlvDgGirrGsDvlkAlalGAdavllGRpflyg 306
                                                ++ +++++  gGi++G+D++  +  GA+av +G  + y 
  gi|15668835|ref|NP_247638.1| 223 iksigikvvwdlyENfDVPIIGVGGIMSGEDAIEYMMAGASAVQIGSGVYYR 274
                                   333344444444322489****************************998875 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0017       2.7      94     165 ..      33     118 ..      16     120 .. 0.70
   2 ?    5.3   0.0     0.015        24      53     105 ..     132     191 ..     109     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0017
                                   HHHHHHTT.....-SEEEEEEBSSSHH........HHHHHHT.CTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTTTSHHH CS
                                   xxxxxxxx.....xxxxxxxxxxxxxx........xxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                   Radical_SAM  94 lerllelg.....vdrvslgleaadde........kvlklmn.rghtfeevlealeklreagikr.vvdrivglpGendee 159
                                   l+r+++ g     +  + l+ + +++          +l+ m+ ++++++e+le +ek r+  ++r  v +i  + G  +ee
  gi|15668835|ref|NP_247638.1|  33 LKRIAKGGagavtTKSIGLNPNPGHKNptivevygGFLNAMGlPNPGVDEYLEEIEKVRDE-LNRmDVRIIGSIYGKDEEE 112
                                   5666665544444444444444444447777777779999*********************.9985344444477778888 PP

                                   HHHHHH CS
                                   xxxxxx RF
                   Radical_SAM 160 leelle 165
                                   + e+++
  gi|15668835|ref|NP_247638.1| 113 FAEVAK 118
                                   887765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                                   E...........SSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEE CS
                                   x...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  53 g...........ggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrv 105
                                   +           g++p+l +d  +++++++k+    +   ++ n t +  e++++ +++gvd +
  gi|15668835|ref|NP_247638.1| 132 ScphakgygatiGQNPDLSYDVCKAVKKAVKI---PVFAKLTPNVTDI-IEIAQAVVDAGVDGL 191
                                   33444444444499999999999999999999...9999999999999.999999999999876 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3     0.041        67      93     136 ..     100     143 ..      75     202 .. 0.49
   2 ?   12.5   1.0   3.2e-05     0.053     196     237 ..     228     269 ..     220     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.041
                                   B-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH  93 llvgaavgvkedalervkalveagvdvlvvdsahghsekvleav 136
                                    ++g+  g  e+++++v++ +e  vd++ ++++  h ++   ++
  gi|15668835|ref|NP_247638.1| 100 RIIGSIYGKDEEEFAEVAKKMERYVDIIELNISCPHAKGYGATI 143
                                   34566667777777777777777777777776665555443333 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.2e-05
                                   HHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 196 vaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGs 237
                                   +  v +  ++++vp+i  GGi + +d +  + aGa+av +Gs
  gi|15668835|ref|NP_247638.1| 228 IKVVWDLYENFDVPIIGVGGIMSGEDAIEYMMAGASAVQIGS 269
                                   55667788999******************************8 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.1   1.8e+03     142     167 ..      20      46 ..      10      50 .. 0.66
   2 ?    3.4   0.0     0.028        46      19      59 ..     163     203 ..     147     215 .. 0.77
   3 ?    7.5   0.1    0.0015       2.5     129     167 ..     229     267 ..     224     270 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.1
                                   EEEESS-.-SHHHHHHHCTT.SSEEEE CS
                  G3P_antiterm 142 iiaGGLi.etkedveealkaGaiavst 167
                                   ++a+G++ et + ++++ k Ga av+t
  gi|15668835|ref|NP_247638.1|  20 FLASGIMgETGSALKRIAKGGAGAVTT 46 
                                   467776624445667777777777776 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.028
                                   SSEEEE--EETTTHHHHHHHHHHTT-EEEEEGGGEET--SS CS
                  G3P_antiterm  19 vevvfllegdilnlkeiveklkkagkkvfvhiDlieGlskd 59 
                                   + v   l+ +++++ ei + + +ag   +v i+ ++G++ d
  gi|15668835|ref|NP_247638.1| 163 IPVFAKLTPNVTDIIEIAQAVVDAGVDGLVAINTVRGMAID 203
                                   344555778999999999*****************999876 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0015
                                   HHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                  G3P_antiterm 129 kvikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                   kv+ ++ +++++pii  G i + ed  e + aGa+av  
  gi|15668835|ref|NP_247638.1| 229 KVVWDLYENFDVPIIGVGGIMSGEDAIEYMMAGASAVQI 267
                                   777788999*******9999****************975 PP

>> PapG_C  PapG chaperone-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.92   1.5e+03      24      63 ..     157     198 ..     140     209 .. 0.70
   2 ?    9.8   0.1   0.00045      0.73      55      86 ..     241     272 ..     221     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.92
                        PapG_C  24 vpvsvkisllsntqpaynn.qkfs.vglgngwdsiisldgve 63 
                                   v  +vki +++  +p  ++  +++   +  g d ++ ++ v 
  gi|15668835|ref|NP_247638.1| 157 VKKAVKIPVFAKLTPNVTDiIEIAqAVVDAGVDGLVAINTVR 198
                                   566777888877777766654444134567889999988886 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00045
                        PapG_C  55 siisldgverseetlrwytagsktvtigsrly 86 
                                    ii + g+  +e+ + +  ag+ +v+igs +y
  gi|15668835|ref|NP_247638.1| 241 PIIGVGGIMSGEDAIEYMMAGASAVQIGSGVY 272
                                   4999*************************998 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.56   9.1e+02     170     223 ..      86     117 ..      74     128 .. 0.47
   2 ?    2.8   0.1     0.042        69      10      35 ..     167     192 ..     158     208 .. 0.85
   3 ?    8.7   0.2   0.00066       1.1     183     220 ..     242     280 ..     225     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.56
                                   HHHHHHHHHSSSEEEEESS--SHHHHHHHHCCSSEEEE-CHHHHHHHCHHHHHH CS
                          PcrB 170 evialkkklekarlivGGGirsaEkAkevveaADvivvGnvveekderkidail 223
                                   e+                     Ek ++ ++  Dv ++G + + kde+ + +++
  gi|15668835|ref|NP_247638.1|  86 EI---------------------EKVRDELNRMDVRIIGSI-YGKDEEEFAEVA 117
                                   33.....................344444444444444432.333333333333 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.042
                                   EEE-TTSS-CHHHHHHHHCTT-SEEE CS
                          PcrB  10 tklDPeeenpdEiveiviesgtDavm 35 
                                    kl P+ + + Ei+++v++ g D+++
  gi|15668835|ref|NP_247638.1| 167 AKLTPNVTDIIEIAQAVVDAGVDGLV 192
                                   6999*******************976 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00066
                                   EEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHHCHHH CS
                          PcrB 183 livGGGirsaEkAkevvea.ADvivvGnvveekderkid 220
                                   +i  GGi s+E+A e++ a A ++ +G  v+  + + ++
  gi|15668835|ref|NP_247638.1| 242 IIGVGGIMSGEDAIEYMMAgASAVQIGSGVYYRGYDIFK 280
                                   55669***********************99988744444 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.5   0.00037       0.6     104     207 ..     168     271 ..     153     275 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00037
                                   TTEB-HHHHHHHHHHHHHTT-EEEEEE-S-HHHHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES-- CS
                          ThiG 104 tLlPdvvetlkaaeiLvkeGFevlpYvsdDlvlarrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDAGi 184
                                    L P+v+++++ a+++v+ G   l+ ++    +a  ++         ++   G +      +++  + e+++vP+i   Gi
  gi|15668835|ref|NP_247638.1| 168 KLTPNVTDIIEIAQAVVDAGVDGLVAINTVRGMAIDIRAKKPILANKFGGLSGKAIKSIGIKVVWDLYENFDVPIIGVGGI 248
                                   467777777777777777777777766655555544443333333333333333333344455666899************ PP

                                   -SHHHHHHHHHTT-SEEEESHHH CS
                          ThiG 185 gspsdaaqamelGadavllntav 207
                                    s +da++ m  Ga+av + + v
  gi|15668835|ref|NP_247638.1| 249 MSGEDAIEYMMAGASAVQIGSGV 271
                                   *****************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 1985.52
//
Query:       gi|15668836|ref|NP_247639.1|  [L=89]
Description: 50S ribosomal protein L34e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-29  100.4   3.9    5.7e-29  100.3   3.9    1.0  1  Ribosomal_L34e  Ribosomal protein L34e
     0.0066   16.3   1.4       0.64   10.0   0.0    2.2  2  DUF4428         Domain of unknown function (DUF4428)


Domain annotation for each model (and alignments):
>> Ribosomal_L34e  Ribosomal protein L34e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   3.9   6.3e-33   5.7e-29      10      92 ..       3      85 ..       1      87 [. 0.97

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 6.3e-33
                Ribosomal_L34e 10 rlsYntrsnkvrvvktpggklvyqykkkkgkapkCgdckkkLqGipalrpkelsrlsktkktvsRaYGgslcakcvkerivra 92
                                  +++Y++rs ++ + +tpgg++v++yk++k+ +pkC+ c+++L+G+p+ rp e+++l+k++++++R+YGg+lc++c+k+ ++++
  gi|15668836|ref|NP_247639.1|  3 APRYRSRSYRRIYRRTPGGRIVIHYKRRKPGKPKCAICGAELHGVPRGRPVEIRKLPKSQRRPERPYGGYLCPRCLKRLMIQK 85
                                  679**************************************************************************999876 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.3    0.0018        17       1       9 [.      36      44 ..      36      46 .. 0.88
   2 !   10.0   0.0   7.1e-05      0.64      20      30 ..      71      81 ..      69      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0018
                       DUF4428  1 iCaiCgkKi 9 
                                  +CaiCg ++
  gi|15668836|ref|NP_247639.1| 36 KCAICGAEL 44
                                  7*****986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 7.1e-05
                       DUF4428 20 gyvCkdClkKl 30
                                  gy+C+ Clk+l
  gi|15668836|ref|NP_247639.1| 71 GYLCPRCLKRL 81
                                  8********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 592.06
//
Query:       gi|15668837|ref|NP_247640.1|  [L=178]
Description: cytidylate kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-28   97.7   1.2    5.4e-26   91.8   1.2    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
      2e-15   57.4   0.2    3.7e-15   56.5   0.2    1.5  1  AAA_17           AAA domain
    5.9e-14   52.7   0.2    7.9e-14   52.3   0.2    1.2  1  AAA_18           AAA domain
    7.2e-12   45.5   1.1    3.6e-07   30.1   0.3    2.0  2  Cytidylate_kin   Cytidylate kinase
    4.3e-07   30.2   0.4    1.2e-05   25.5   0.4    2.2  1  ADK              Adenylate kinase
    2.9e-06   27.5   0.0    4.5e-06   26.9   0.0    1.3  1  AAA_33           AAA domain
    3.2e-05   24.1   1.0    5.3e-05   23.4   1.0    1.4  1  SKI              Shikimate kinase
    3.8e-05   23.5   1.5     0.0044   16.7   0.1    2.2  2  Thymidylate_kin  Thymidylate kinase
     0.0013   18.7   4.9      0.072   12.9   1.1    3.0  2  dNK              Deoxynucleoside kinase
     0.0015   19.0   0.0     0.0025   18.2   0.0    1.4  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.027   14.7   0.1      0.056   13.7   0.1    1.4  1  AAA_28           AAA domain
      0.035   13.8   0.6        5.1    6.7   0.0    2.1  2  CoaE             Dephospho-CoA kinase


Domain annotation for each model (and alignments):
>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   1.2   3.6e-29   5.4e-26       1     179 []       2     159 ..       2     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 3.6e-29
               Cytidylate_kin2   1 iITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldekldde 80 
                                   iITI++  G+g +ti++++Aek++l+ +    i++e+ake+g++ +e+ ++ e                     ++++d+e
  gi|15668837|ref|NP_247640.1|   2 IITIGGLPGTGTTTIAKMIAEKYNLRHVCAgFIFREMAKEMGMDLQEFSKYAE--Q------------------HKEIDEE 62 
                                   8************************9998879*********************..2..................4567777 PP

               Cytidylate_kin2  81 lfeaqervirelaaeesvVivGRgad.liLkd.rpnvlrvfltapledrvkrvaereglseeearekiketDkrrakyykk 159
                                   + ++q     e+a++ +vV+ GR a+ ++Lk+ ++  l +++ aple+r++r+++re+++++ a +k+ e++  ++k+yk+
  gi|15668837|ref|NP_247640.1|  63 IDRRQV----EIAKQGNVVLEGRLAAwMLLKNgIKPDLTIWFKAPLEVRAERISKRENIDKDVALKKMIEREASEKKRYKE 139
                                   666665....556556*******8761555658778********************************************* PP

               Cytidylate_kin2 160 ytgqdwgdaenYdlvlntsk 179
                                   +++ d++d + Ydlv++tsk
  gi|15668837|ref|NP_247640.1| 140 IYNIDLDDLSIYDLVIDTSK 159
                                   ******************97 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.2   2.5e-18   3.7e-15       2     126 ..       7     118 ..       6     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.5e-18
                                   E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEE CS
                        AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghpri 82 
                                   G+PG G +t+++ ++eky++ h+ aG ++re+ak+ g+  + +e++k   e+ ke+++e+ ++  e ak+++v+++g    
  gi|15668837|ref|NP_247640.1|   7 GLPGTGTTTIAKMIAEKYNLRHVCAGFIFREMAKEMGM--DLQEFSKYA-EQHKEIDEEIDRRQVEIAKQGNVVLEGRLAA 84 
                                   9************************************8..788887766.5566789999999999999*********974 PP

                                   EETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST CS
                        AAA_17  83 keqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrg 126
                                   +        l    ++ +kpd+ i ++a+ e+  er  k+++ +
  gi|15668837|ref|NP_247640.1|  85 W------M-LL---KNGIKPDLTIWFKAPLEVRAERISKRENID 118
                                   2......2.23...3799************98888888876544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.2   5.3e-17   7.9e-14       1     122 [.       3     128 ..       3     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 5.3e-17
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegkn 76 
                                   I + G pG+G tt+ak ++++ ++     g++ r++ake g+ l ++ +  +++k++de+ + + +++ ++        +n
  gi|15668837|ref|NP_247640.1|   3 ITIGGLPGTGTTTIAKMIAEKYNLrhvcaGFIFREMAKEMGMDLQEFSKYAEQHKEIDEEIDRRQVEIAKQ--------GN 75 
                                   89*******************87799***********************9999999999998888887777........89 PP

                        AAA_18  77 lvidghlaeleseaakdikk..vvLtaspeelleRlekRgyeeakik.....e 122
                                   +v++g+la +   ++ ++    ++ +a+ e+++eR++kR++ +++ +     e
  gi|15668837|ref|NP_247640.1|  76 VVLEGRLAAWMLLKNGIKPDltIWFKAPLEVRAERISKRENIDKDVAlkkmiE 128
                                   9*****9988866555333367******************9888776665552 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.6e-05     0.023       1      37 [.       3      39 ..       3      48 .. 0.94
   2 !   30.1   0.3   2.4e-10   3.6e-07      90     209 ..      50     173 ..      43     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                                  EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
                Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRala 37
                                  i+i G  g+G  ++a+++aek +l+ + +g ++R +a
  gi|15668837|ref|NP_247640.1|  3 ITIGGLPGTGTTTIAKMIAEKYNLRHVCAGFIFREMA 39
                                  899999****************************998 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 2.4e-10
                                   HHHT.TSHHHHHHHHHHHHTT-BSSBEEEEESSIIIIISTT-...SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHH CS
                Cytidylate_kin  90 Sava.aipavRailvkklrelvkkarvvveGRDigtvvfpda...elKifldAsveeRakRRlkqlkakgtsvsleellae 166
                                   S++a +++++ +++ +++ e++k+++vv+eGR  + +++++    +l i+ +A  e+Ra+R  k       + +++  l++
  gi|15668837|ref|NP_247640.1|  50 SKYAeQHKEIDEEIDRRQVEIAKQGNVVLEGRLAAWMLLKNGikpDLTIWFKAPLEVRAERISKR-----ENIDKDVALKK 125
                                   444415789************************9999999854449**************98887.....34678889999 PP

                                   HHHHHHHHHCTSSS-S---TT-.....EEEETTTS-HHHHHHHHHHHH CS
                Cytidylate_kin 167 ikeRDklDkerevgpLklaeda.....liidtskltieevvekileli 209
                                   ++eR +  k+r  +  ++  d      l+idtsk  +e v + + ++i
  gi|15668837|ref|NP_247640.1| 126 MIEREASEKKRYKEIYNIDLDDlsiydLVIDTSKWDVEGVFNIVSSAI 173
                                   *******99998888777776522222689****99999998887665 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.4     8e-09   1.2e-05       3     130 ..       7     125 ..       5     150 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 8e-09
                                   ESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEEEEESB- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ADK   3 GaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgfllDGfP 83 
                                   G Pg+G  t a+ +++ky+l h+ +G ++R+  k+     +e +++ ++ + + +e+  + v    e  +k+ + +l+G  
  gi|15668837|ref|NP_247640.1|   7 GLPGTGTTTIAKMIAEKYNLRHVCAGFIFREMAKEMGMDLQEFSKYAEQHKEIDEEIDRRQV----EI-AKQGNVVLEG-- 80 
                                   99*****************************9998877778888888888877777654433....22.2445666766.. PP

                                   SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT....GSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxx RF
                           ADK  84 RtveqaealeelleeekvkldlvleldvpeevlveRltg....Dneetvkk 130
                                   R ++       +l ++++k dl + +++p ev  eR+++    D+  ++kk
  gi|15668837|ref|NP_247640.1|  81 R-LAAW-----MLLKNGIKPDLTIWFKAPLEVRAERISKreniDKDVALKK 125
                                   2.2222.....2334577777777777777777777777666644444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0     3e-09   4.5e-06       3     128 ..       4     124 ..       2     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3e-09
                        AAA_33   3 llvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnlsrr 83 
                                    + GlpG+G +t a+ +++k    ++    ++r ++++   +++   ++  + y+ +++ +++   +++  i+ ++n+  +
  gi|15668837|ref|NP_247640.1|   4 TIGGLPGTGTTTIAKMIAEKYNLRHVCAGFIFREMAKEMGMDLQ---EF--SKYAEQHKEIDEEIDRRQVEIAKQGNVVLE 79 
                                   5679********************************87666554...44..44555668999999999999********87 PP

                        AAA_33  84 er.arflklarrlgvpvrivvvetdeetlkeRlakRaangddrsev 128
                                    r a+++ l + ++ p++ ++++++ e+ +eR+ kR++  +d +  
  gi|15668837|ref|NP_247640.1|  80 GRlAAWMLLKNGIK-PDLTIWFKAPLEVRAERISKRENIDKDVALK 124
                                   77366666666666.***********************86544333 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.0   3.6e-08   5.3e-05       1     136 [.       9     142 ..       9     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.6e-08
                                   TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGSHH..HH CS
                           SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsevlkelleeeglViatGGGavlsee..nr 79 
                                   +G+G +t++k++A+k++l+ + +  ++ + ++ ++   ++e   +++ e+ +e+ +e+ ++ ++ ia  G +vl+ +  ++
  gi|15668837|ref|NP_247640.1|   9 PGTGTTTIAKMIAEKYNLRHVCAGFIFREMAK-EMGMDLQE--FSKYAEQHKEIDEEIDRR-QVEIAKQGNVVLEGRlaAW 85 
                                   69*******************88877655554.44444443..367888888877777666.6667777777777763244 PP

                                   HHHH...HHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCCSSC CS
                           SKI  80 ellk...ekgiviyLdvsleellerlkadkeRPllqekskeeelleelaereplyeeaad 136
                                    llk   +  ++i+ +++le+ +er++++++   + ++   +++ e +a++++ y+e+ +
  gi|15668837|ref|NP_247640.1|  86 MLLKngiKPDLTIWFKAPLEVRAERISKREN---IDKDVALKKMIEREASEKKRYKEIYN 142
                                   44446666667********************...56666667777777778888887644 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1    0.0051       7.6       2      26 ..       6      30 ..       5      63 .. 0.74
   2 !   16.7   0.1   2.9e-06    0.0044     108     164 ..      85     142 ..      71     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0051
                                  EESTTSSHHHHHHHHHHHHHHTTE. CS
               Thymidylate_kin  2 EGlDGaGKttqaellkerlkeegik 26
                                   Gl G+G tt+a++++e+++ ++  
  gi|15668837|ref|NP_247640.1|  6 GGLPGTGTTTIAKMIAEKYNLRHVC 30
                                  6999**************9977754 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.9e-06
                                   HHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSS..TTTSHHHHHHHHHHHHHHHHHHHH CS
               Thymidylate_kin 108 lslnedvllkPdltflldvdpevalkRlakrde..ldeeeeeqldflrkvrerylelak 164
                                   + l ++ + kPdlt+ ++ + ev+++R++kr+   +d + ++ ++   + ++ry+e+++
  gi|15668837|ref|NP_247640.1|  85 WMLLKNGI-KPDLTIWFKAPLEVRAERISKRENidKDVALKKMIEREASEKKRYKEIYN 142
                                   55666645.************************55444444444445555667777765 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.031        46       1      26 [.       3      28 ..       3      32 .. 0.89
   2 !   12.9   1.1   4.8e-05     0.072     122     154 ..      81     125 ..      26     174 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.031
                                  EEEEESTTSSHHHHHHHHHCCSTCEE CS
                           dNK  1 ivveGnIgaGKstlvklLskklgvkv 26
                                  i++ G  g G +t++k++++k++  +
  gi|15668837|ref|NP_247640.1|  3 ITIGGLPGTGTTTIAKMIAEKYNLRH 28
                                  7899****************999765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.8e-05
                                   H............-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HH CS
                           dNK 122 k............pdlliYLkasletclerikkRgreeekkield 154
                                   +            pdl i+ ka+le+  eri kR++ ++    ++
  gi|15668837|ref|NP_247640.1|  81 RlaawmllkngikPDLTIWFKAPLEVRAERISKRENIDKDVALKK 125
                                   0444444444445*********************99886543333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.7e-06    0.0025       4      57 ..       6      57 ..       3      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
                                  ESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS CS
                           AAA  4 yGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka 57
                                   G pGtG T++ak +a++   ++  + +  ++ ++ +e+ ++++e+ k a++++
  gi|15668837|ref|NP_247640.1|  6 GGLPGTGTTTIAKMIAEK--YNLRHVCAGFIFREMAKEMGMDLQEFSKYAEQHK 57
                                  599***************..5666777777778999999999999999998876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.7e-05     0.056       2      66 ..       3      70 ..       2      85 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
                        AAA_28  2 ivitGgestGKTtlleaLaar...gypvvpEaareileeklakgedalpwvedllafaervleeqlee 66
                                  i i G ++tG+Tt+++ +a++    +++   ++re+ +e + + ++ ++++e+  ++ e++ + q+e 
  gi|15668837|ref|NP_247640.1|  3 ITIGGLPGTGTTTIAKMIAEKynlRHVCAGFIFREMAKEMGMDLQEFSKYAEQHKEIDEEIDRRQVEI 70
                                  556677*************9875445555666777776666666555555556666666544444443 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0034       5.1       1      65 [.       1      65 [.       1      71 [. 0.81
   2 ?    5.9   0.3    0.0061       9.1     124     165 ..      96     138 ..      55     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0034
                                  EEEEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCTHHHHHHHHHHHGGGCB.TTSSE-H CS
                          CoaE  1 livgltGgiasGKstvanlfad.lgvpivDaDlvArqvvepgsealkkiveeFgeeildedGeLdR 65
                                  +i+ + G  ++G +t+a+++a+ +++  v a  + r++ ++    l++  +++ e+  + d e+dR
  gi|15668837|ref|NP_247640.1|  1 MIITIGGLPGTGTTTIAKMIAEkYNLRHVCAGFIFREMAKEMGMDLQEF-SKYAEQHKEIDEEIDR 65
                                  588899999************99**************999999998888.5555555455555555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0061
                                   EEEEEE--HHHHHHHHHHCCTSTHHHH.HHHHHHS--HHHHHH CS
                          CoaE 124 rvlvvdvelelqveRlvardgvseeev.kaiiaaQlseeerla 165
                                    ++  +++le + eR+ +r++++++ + k++i+  +se++r +
  gi|15668837|ref|NP_247640.1|  96 LTIWFKAPLEVRAERISKRENIDKDVAlKKMIEREASEKKRYK 138
                                   466678999*************998662567778888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1086.61
//
Query:       gi|15668838|ref|NP_247641.1|  [L=80]
Description: 50S ribosomal protein L14e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-05   23.0   1.3    8.4e-05   22.4   1.3    1.3  1  KOW             KOW motif
    0.00024   21.5   0.0    0.00031   21.2   0.0    1.1  1  Ribosomal_L14e  Ribosomal protein L14


Domain annotation for each model (and alignments):
>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.3   9.4e-09   8.4e-05       1      32 []       6      36 ..       6      36 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.4e-09
                                  TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                           KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                  +G++++ ++G+ +Gk++++v++ +++ +V+vd
  gi|15668838|ref|NP_247641.1|  6 VGRVCIKTAGREAGKVCVIVDILDKN-FVIVD 36
                                  799***********************.88887 PP

>> Ribosomal_L14e  Ribosomal protein L14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.5e-08   0.00031       1      38 [.      40      77 ..      40      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.5e-08
                Ribosomal_L14e  1 pRqaiplkrlkLtkivlklprgartgavkkawekadve 38
                                  +R   ++k+l+ t+ ++++p+ga+t+ vk a+++a++ 
  gi|15668838|ref|NP_247641.1| 40 KRRRCNIKHLEPTEKKVDIPKGASTEEVKLALDAAGLL 77
                                  59999*****************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 516.55
//
Query:       gi|15668839|ref|NP_247642.1|  [L=318]
Description: hypothetical protein MJ_0658 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-15   56.7   6.7    1.5e-08   34.5   1.0    2.3  2  GXGXG     GXGXG motif


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.5   6.1e-10   1.1e-05      86     168 ..      57     135 ..      45     151 .. 0.80
   2 !   34.5   1.0   8.2e-13   1.5e-08      88     168 ..     205     289 ..     188     307 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 6.1e-10
                                   GGSB-S-SSTTTT--SEEEEESSB--SSTTTT-SS-EEEESEB-SSTTTT-EEEEEEE-S-B-SSBTTT--EEEEEEE-SS CS
                         GXGXG  86 eeniivGnvvlygatgGklfirgkageRfavrnsgatavvegvgdhgceYmtGGvvvvLgktgrnfaaGmsgGiayvlded 166
                                   +eni     v +   gG ++i+g++g+Rf+  + +      g g    e +  G+v+v g++ + f+ +m  G++y+ +++
  gi|15668839|ref|NP_247642.1|  57 KENITFKTLVEHLKNGGVVYIKGNVGKRFCSSMGVDLKYFSGSG----ERIKVGTVIVDGDVDTRFGISMLSGTVYINEKN 133
                                   5555555666677889****************999988888876....66899************************8776 PP

                                   ST CS
                         GXGXG 167 ek 168
                                   + 
  gi|15668839|ref|NP_247642.1| 134 KI 135
                                   54 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 8.2e-13
                                   SB-S-SSTTTT...--SEEEEESSB--SSTTTT-SS-EEEESEB.-SSTTTT-EEEEEEE-S-B-SSBTTT--EEEEEEE- CS
                         GXGXG  88 niivGnvvlyg...atgGklfirgkageRfavrnsgatavvegv.gdhgceYmtGGvvvvLgktgrnfaaGmsgGiayvld 164
                                    ++ G+v l     +++Gk+ ++g+ag+ ++   +g t++++g+  d+++  m  G++vv g+ g++++a  + G++y +d
  gi|15668839|ref|NP_247642.1| 205 IVVNGDVDLSTgilMRKGKVIVNGNAGKNTGAVLNGGTVIINGNtNDFTGFEMRDGIIVVDGNAGKYLGAKKKEGVIYARD 285
                                   3445777554323389**************99999999***99989999999***************************99 PP

                                   SSST CS
                         GXGXG 165 edek 168
                                    +e 
  gi|15668839|ref|NP_247642.1| 286 GKEV 289
                                   7764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2037.60
//
Query:       gi|15668840|ref|NP_247643.1|  [L=138]
Description: hypothetical protein MJ_0659 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-05   22.9   0.2     0.0002   21.5   0.1    1.7  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    0.00016   22.1   0.5      0.005   17.3   0.0    2.8  3  TPR_19           Tetratricopeptide repeat
     0.0015   18.4   0.2      0.009   15.9   0.2    2.4  1  ATP13            Mitochondrial ATPase expression
     0.0025   17.9   2.3        2.4    8.6   0.0    4.2  4  PPR              PPR repeat
     0.0037   17.2   0.3        2.7    8.3   0.0    3.2  3  TPR_2            Tetratricopeptide repeat
      0.005   17.5   0.0       0.59   11.1   0.0    2.9  3  TPR_14           Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.022   15.0   2.7        6.2    7.1   0.1    3.4  4  SgrR_N           Sugar transport-related sRNA regulator N-ter
      0.029   13.8   1.9      0.037   13.5   1.6    1.3  1  SPO22            Meiosis protein SPO22/ZIP4 like
      0.046   13.7   5.2       0.52   10.3   5.2    2.2  1  SRP_TPR_like     Putative TPR-like repeat
       0.22   11.8   4.4         26    5.4   0.1    3.5  3  TPR_8            Tetratricopeptide repeat
       0.28   11.4   1.1         77    3.6   0.0    3.6  4  PPR_2            PPR repeat family
       0.61    9.4   2.2        1.2    8.5   0.3    1.9  2  Lipase_GDSL_lke  GDSL-like Lipase/Acylhydrolase
       0.67    9.8   3.0        2.8    7.8   2.7    2.3  1  CLTH             CTLH/CRA C-terminal to LisH motif domain


Domain annotation for each model (and alignments):
>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.085   1.2e+02      45      81 ..      17      52 ..       9      53 .. 0.77
   2 !   21.5   0.1   1.5e-07    0.0002       4      81 ..      42     114 ..      39     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.085
                                  HHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3 45 llrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                  +l+k  ++ k  + + ++A +l++ +  +eA+++ ek
  gi|15668840|ref|NP_247643.1| 17 VLKKV-EEIKGDAQLEIIALTLIEKGYCDEAVKVAEK 52
                                  44555.4458889999999999999999999998877 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.5e-07
                                   -HHHHHHHHHHHH.HHH--HHHHHH..HHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3   4 nyknAiflaerllaaetespedayl..lAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                     ++A+ +ae++    +  ++d  l   A ++ +ng+ ++A+ l++k     k++  +  +A  l+++kky eA+++ ek
  gi|15668840|ref|NP_247643.1|  42 YCDEAVKVAEKIS---SFGLKDEVLrkVAIAYIENGEIDKAMALVEKI----KTETDLEKIAMKLIEIKKYREALKVAEK 114
                                   568999*******...777777777335********************....99999*******************9887 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.078   1.1e+02       2      51 ..       9      53 ..       8      65 .. 0.74
   2 !   17.3   0.0   3.6e-06     0.005       8      56 ..      44      91 ..      37     102 .. 0.75
   3 ?   -0.1   0.0         1   1.4e+03       5      17 ..     103     115 ..      99     134 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.078
                        TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51
                                  ++eg+ +e l+  e++     ++a + +  A  l++ g  deA ++ +++
  gi|15668840|ref|NP_247643.1|  9 IEEGKIEEVLKKVEEI----KGDAQLEI-IALTLIEKGYCDEAVKVAEKI 53
                                  6666666666666665....55566666.688999999999999988777 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.6e-06
                        TPR_19  8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56
                                  +eA++  e++ +     +e++   A+a++++g++d+A+al++++  e+ 
  gi|15668840|ref|NP_247643.1| 44 DEAVKVAEKI-SSFGLKDEVLRKVAIAYIENGEIDKAMALVEKIKTETD 91
                                  5666666664.4444566777779*******************988876 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1
                        TPR_19   5 gdyaeAlalleqa 17 
                                   ++y eAl+  e++
  gi|15668840|ref|NP_247643.1| 103 KKYREALKVAEKI 115
                                   5677787777775 PP

>> ATP13  Mitochondrial ATPase expression
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   6.5e-06     0.009      48      83 ..      54      89 ..      13     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.5e-06
                         ATP13 48 splyPtselLkaivssfsynneiesAlklvdkfskk 83
                                  s++  + e+L  ++ +++ n+ei++A+ lv+k+ ++
  gi|15668840|ref|NP_247643.1| 54 SSFGLKDEVLRKVAIAYIENGEIDKAMALVEKIKTE 89
                                  45556789************************9876 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.25   3.5e+02      12      27 ..      10      25 ..       5      27 .. 0.81
   2 ?    2.8   0.0      0.12   1.7e+02      13      30 ..      40      57 ..      37      58 .. 0.82
   3 !    8.6   0.0    0.0017       2.4       9      27 ..      69      87 ..      66      89 .. 0.90
   4 ?    1.0   0.0      0.46   6.3e+02      15      29 ..     104     118 ..      99     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.25
                           PPR 12 knGkleeAlelfkeMk 27
                                   +Gk+ee+l+  +e+k
  gi|15668840|ref|NP_247643.1| 10 EEGKIEEVLKKVEEIK 25
                                  589*****99888877 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                           PPR 13 nGkleeAlelfkeMkekG 30
                                  +G+++eA+++ +++ + G
  gi|15668840|ref|NP_247643.1| 40 KGYCDEAVKVAEKISSFG 57
                                  799******988887776 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0017
                           PPR  9 gycknGkleeAlelfkeMk 27
                                  +y  nG++++A+ l +++k
  gi|15668840|ref|NP_247643.1| 69 AYIENGEIDKAMALVEKIK 87
                                  899*************988 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.46
                           PPR  15 kleeAlelfkeMkek 29 
                                   k++eAl++ +++k++
  gi|15668840|ref|NP_247643.1| 104 KYREALKVAEKIKSR 118
                                   899****99988876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.4     2e+03       9      26 ..      35      52 ..      30      53 .. 0.65
   2 !    8.3   0.0     0.002       2.7       2      26 ..      61      85 ..      60      87 .. 0.88
   3 ?    5.0   0.1     0.022        31       7      26 ..      95     114 ..      91     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.4
                         TPR_2  9 layyklgdyeeAleafek 26
                                  l ++++g  +eA++  ek
  gi|15668840|ref|NP_247643.1| 35 LTLIEKGYCDEAVKVAEK 52
                                  556666666788777665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.002
                         TPR_2  2 ealynlGlayyklgdyeeAleafek 26
                                  e+l   + ay+++g+ ++A ++ ek
  gi|15668840|ref|NP_247643.1| 61 EVLRKVAIAYIENGEIDKAMALVEK 85
                                  678889*************998876 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.022
                         TPR_2   7 lGlayyklgdyeeAleafek 26 
                                   +++ +++ ++y eAl+  ek
  gi|15668840|ref|NP_247643.1|  95 IAMKLIEIKKYREALKVAEK 114
                                   56777888899999998887 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.045        62       8      38 ..      34      64 ..      27      66 .. 0.81
   2 !   11.1   0.0   0.00043      0.59       2      29 ..      61      87 ..      60     102 .. 0.79
   3 ?   -1.0   0.0       3.4   4.7e+03      16      26 ..     104     114 ..      95     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.045
                        TPR_14  8 aeallalGdpdeAiallrralalaPddaeaw 38
                                  a  l + G  deA+++++++ + + +d++++
  gi|15668840|ref|NP_247643.1| 34 ALTLIEKGYCDEAVKVAEKISSFGLKDEVLR 64
                                  6778899999**********99988888776 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00043
                        TPR_14  2 eallalaeallalGdpdeAiallrrala 29
                                  e+l++ a a+ ++G+ d+A+al +++ +
  gi|15668840|ref|NP_247643.1| 61 EVLRKVAIAYIENGEIDKAMALVEKI-K 87
                                  567889****************9987.4 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3.4
                        TPR_14  16 dpdeAiallrr 26 
                                   +++eA++++++
  gi|15668840|ref|NP_247643.1| 104 KYREALKVAEK 114
                                   46677777765 PP

>> SgrR_N  Sugar transport-related sRNA regulator N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.099   1.4e+02      79      98 ..       7      26 ..       2      41 .. 0.76
   2 ?   -0.1   0.0      0.77   1.1e+03      75      94 ..      32      51 ..      23      62 .. 0.81
   3 ?    7.1   0.1    0.0045       6.2      69      98 ..      59      88 ..      51      95 .. 0.84
   4 ?    4.3   0.1     0.033        46      72      97 ..      91     116 ..      85     131 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.099
                        SgrR_N 79 klleqgkiekalalldkdka 98
                                  kl+e+gkie++l+ +++ k 
  gi|15668840|ref|NP_247643.1|  7 KLIEEGKIEEVLKKVEEIKG 26
                                  89**********98885444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.77
                        SgrR_N 75 qlaeklleqgkiekalalld 94
                                    a +l+e+g +++a+++++
  gi|15668840|ref|NP_247643.1| 32 IIALTLIEKGYCDEAVKVAE 51
                                  56778999******999987 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0045
                        SgrR_N 69 peelqeqlaeklleqgkiekalalldkdka 98
                                  ++e+ +++a  ++e+g+i+ka+al++k k 
  gi|15668840|ref|NP_247643.1| 59 KDEVLRKVAIAYIENGEIDKAMALVEKIKT 88
                                  56889999*****************96554 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.033
                        SgrR_N  72 lqeqlaeklleqgkiekalalldkdk 97 
                                     e+ a kl+e  k+++al++++k k
  gi|15668840|ref|NP_247643.1|  91 DLEKIAMKLIEIKKYREALKVAEKIK 116
                                   5678899**************99543 PP

>> SPO22  Meiosis protein SPO22/ZIP4 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.6   2.7e-05     0.037      80     152 ..      56     130 ..      38     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                         SPO22  80 selrlsvlrllarayleldqeesyekalkavellqkeygkkehpsllllklkill.....kreadeeeiee.aleemid 152
                                     l+  vlr +a ay+e   + +++ka+++ve +++e    e++++ l+++k+ +     ++++++ +i+e +l+++i+
  gi|15668840|ref|NP_247643.1|  56 FGLKDEVLRKVAIAYIE---NGEIDKAMALVEKIKTETD-LEKIAMKLIEIKKYRealkvAEKIKSRAIKEgILMAIIN 130
                                   579999**********6...**************74444.467777777777777999998888888887635666665 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   5.2   0.00038      0.52      15      77 ..      61     122 ..       3     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00038
                  SRP_TPR_like  15 elkkfkvvaliklekyeeaLkllkkgsalsedvrfEk.aYvlYklkkykkalkilkkveaee.kv 77 
                                   e+ +  ++a+i+ +  + a+ l++k +    ++  Ek a  l  +kky++alk+ +k+++   k 
  gi|15668840|ref|NP_247643.1|  61 EVLRKVAIAYIENGEIDKAMALVEKIK---TETDLEKiAMKLIEIKKYREALKVAEKIKSRAiKE 122
                                   333445788888888888888888887...66777775777888999999999999998875454 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.035        48       7      27 ..      33      53 ..      30      56 .. 0.89
   2 ?    5.4   0.1     0.019        26      10      26 ..      69      85 ..      65      88 .. 0.87
   3 ?    1.6   0.4       0.3   4.1e+02      11      26 ..      99     114 ..      93     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.035
                                  HHHHHHHTT-HHHHHHHHHHH CS
                         TPR_8  7 lgsiylklgdyeeAkeyyeka 27
                                  ++++++++g  +eA+++ ek 
  gi|15668840|ref|NP_247643.1| 33 IALTLIEKGYCDEAVKVAEKI 53
                                  7999*************9995 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.019
                                  HHHHTT-HHHHHHHHHH CS
                         TPR_8 10 iylklgdyeeAkeyyek 26
                                  +y++ g++++A++  ek
  gi|15668840|ref|NP_247643.1| 69 AYIENGEIDKAMALVEK 85
                                  8***********98887 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.3
                                   HHHTT-HHHHHHHHHH CS
                         TPR_8  11 ylklgdyeeAkeyyek 26 
                                   +++ ++y eA ++ ek
  gi|15668840|ref|NP_247643.1|  99 LIEIKKYREALKVAEK 114
                                   5667888888888777 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.9   2.6e+03      13      29 ..       8      24 ..       5      26 .. 0.77
   2 ?   -0.4   0.0      0.96   1.3e+03      14      28 ..      38      52 ..      34      59 .. 0.74
   3 ?    3.6   0.0     0.055        77      12      30 ..      69      87 ..      68      90 .. 0.89
   4 ?    3.2   0.1     0.076   1.1e+02      16      34 ..     102     120 ..      98     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.9
                         PPR_2 13 lckkgkveeAfklfneM 29
                                  l ++gk+ee +k  +e 
  gi|15668840|ref|NP_247643.1|  8 LIEEGKIEEVLKKVEEI 24
                                  56799999999876665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.96
                         PPR_2 14 ckkgkveeAfklfne 28
                                   +kg  +eA+k+ ++
  gi|15668840|ref|NP_247643.1| 38 IEKGYCDEAVKVAEK 52
                                  568888999998776 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.055
                         PPR_2 12 glckkgkveeAfklfneMk 30
                                  ++ ++g++++A+ l ++ k
  gi|15668840|ref|NP_247643.1| 69 AYIENGEIDKAMALVEKIK 87
                                  6999**********99877 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.076
                         PPR_2  16 kgkveeAfklfneMkkrgl 34 
                                    +k++eA+k+ ++ k+r +
  gi|15668840|ref|NP_247643.1| 102 IKKYREALKVAEKIKSRAI 120
                                   5899***********9987 PP

>> Lipase_GDSL_lke  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.3   0.00085       1.2     145     196 ..       4      55 ..       2      62 .. 0.93
   2 ?    0.9   0.1      0.18   2.5e+02     143     194 ..      65     115 ..      55     123 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00085
               Lipase_GDSL_lke 145 eiyfllnselseevtesvrticrhyqidcielkdidkksghpsvkgmkqise 196
                                   ei  l++++  eev + v++i    q++ i l  i+k +   +vk  ++is+
  gi|15668840|ref|NP_247643.1|   4 EIIKLIEEGKIEEVLKKVEEIKGDAQLEIIALTLIEKGYCDEAVKVAEKISS 55 
                                   789999***************************************9999985 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
               Lipase_GDSL_lke 143 nveiyfllnselseevtesvrticrhyqidcielkdidkksghpsvkgmkqi 194
                                   +v i ++ n e+++ +   v++i    +++ i +k i+ k    ++k  ++i
  gi|15668840|ref|NP_247643.1|  65 KVAIAYIENGEIDKAM-ALVEKIKTETDLEKIAMKLIEIKKYREALKVAEKI 115
                                   5666677777766554.35677777777777777777766666666666666 PP

>> CLTH  CTLH/CRA C-terminal to LisH motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.7     0.002       2.8       6      28 ..       3      25 ..       1     119 [. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.002
                          CLTH  6 qkIiklilegdlseaiewinenk 28
                                   +Iikli+eg+++e++++++e k
  gi|15668840|ref|NP_247643.1|  3 SEIIKLIEEGKIEEVLKKVEEIK 25
                                  68*****************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1125  (0.0627475); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 921.07
//
Query:       gi|15668841|ref|NP_247644.1|  [L=77]
Description: hypothetical protein MJ_0660 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-17   62.2   1.7    4.3e-17   61.9   1.7    1.1  1  TRAM      TRAM domain
  ------ inclusion threshold ------
      0.042   13.7   0.5        8.7    6.3   0.2    2.3  2  DUF824    Salmonella repeat of unknown function (DUF824)


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   1.7   4.8e-21   4.3e-17       2      61 ..      21      76 ..      20      77 .] 0.96

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 4.8e-21
                                  XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                          TRAM  2 syvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61
                                  +++G+t++V++e+ + + g+gi+r++ g+vvfvp +++  G++V+VkIt vk++++++e 
  gi|15668841|ref|NP_247644.1| 21 VKEGETYTVTIEDMG-RGGDGIARVE-GFVVFVPETQK--GETVNVKITAVKSKFAFAEK 76
                                  689************.**********.***********..******************96 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0016        14       5      19 ..      17      31 ..      13      34 .. 0.88
   2 ?    6.3   0.2   0.00097       8.7      11      21 ..      56      66 ..      52      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0016
                        DUF824  5 naAkaKkGEsiplti 19
                                  +++ +K GE+ ++ti
  gi|15668841|ref|NP_247644.1| 17 RNVPVKEGETYTVTI 31
                                  6889*******9999 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00097
                        DUF824 11 kGEsipltitv 21
                                  kGE+++++it 
  gi|15668841|ref|NP_247644.1| 56 KGETVNVKITA 66
                                  9********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 528.23
//
Query:       gi|15668842|ref|NP_247645.1|  [L=182]
Description: hypothetical protein MJ_0661 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-18   66.9   1.4    2.9e-18   66.3   1.4    1.3  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   1.4   1.6e-22   2.9e-18       1      81 [.      27     124 ..      27     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 1.6e-22
                      CxxCxxCC   1 eCkeCgaCCkelkvklteedlerlkaaevaeeeeeskkiak...........adgrCvfldeetklCkiYeeRpkicrlfp 70 
                                   +C +Cg CC    +++t++dl++++ + ++  +e  k++++           ++g+C+fld++tk+CkiY+ Rp+icrl p
  gi|15668842|ref|NP_247645.1|  27 HCIKCGFCCD--APTVTKKDLAKIAGYLKIPFDEVLKRYVRffngyigelkeVGGKCIFLDKKTKKCKIYKVRPLICRLRP 105
                                   6*********..9******************************************************************** PP

                      CxxCxxCC  71 as........ekeellara 81 
                                    s        + ++  ++ 
  gi|15668842|ref|NP_247645.1| 106 YSvqvrngklTLTYDIWFL 124
                                   9966666555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1402.73
//
Query:       gi|15668843|ref|NP_247646.1|  [L=239]
Description: hypothetical protein MJ_0662 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-11   43.5   6.1    4.9e-11   42.7   6.1    1.4  1  PAP2_3          PAP2 superfamily
    1.1e-08   34.9   3.3    1.1e-08   34.9   3.3    2.5  2  PAP2            PAP2 superfamily
  ------ inclusion threshold ------
      0.033   14.7   1.5      0.033   14.7   1.5    2.3  2  PAP2_C          PAP2 superfamily C-terminal


Domain annotation for each model (and alignments):
>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   6.1   8.1e-15   4.9e-11      21     189 ..      51     202 ..      40     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 8.1e-15
                        PAP2_3  21 lllahpa.lavilalaYaslhfqvtllvlv.llf.lrrrerlreflttlllatllgllvyalfPaagPrlleeagfvdtva 98 
                                   +l++ p+ +  +++++Y + +  +++  ++ +lf  r++ + + +l+ l+l +l + l+y+++ +  P+ +          
  gi|15668843|ref|NP_247646.1|  51 FLQSLPNiVIEFFKIIYLYGFSSMIIGGIAyYLFiKRDFLKSDIILIDLALGWLFAGLIYTFVVVKSPFQV--------GV 123
                                   566666656667788877666555554433044457788888899999********************444........22 PP

                        PAP2_3  99 aaslagalrdgasravllrgtienglaafPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvDvia 179
                                   a +      +  ++++++   ++++ + +PSlH+a+++l+al    +++ + l ++  +l++l+ ++t+  g H +vDvi 
  gi|15668843|ref|NP_247646.1| 124 AKD------LINMHYFWI---FTKPTYEIPSLHTAYSFLLALH---FKDEKPLNYIYFALAILIPISTLIMGMHWIVDVIT 192
                                   222......333555554...5579******************...*********************************** PP

                        PAP2_3 180 Gvalalvaia 189
                                   Gv++++++++
  gi|15668843|ref|NP_247646.1| 193 GVLYGYIIYK 202
                                   *****99975 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   1.1      0.11   6.6e+02     117     131 ..      99     113 ..      48     119 .. 0.69
   2 !   34.9   3.3   1.9e-12   1.1e-08      40     124 ..     134     201 ..     117     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.11
                          PAP2 117 lliGialaalayrlv 131
                                   l++G+++a l+y++v
  gi|15668843|ref|NP_247646.1|  99 LALGWLFAGLIYTFV 113
                                   566777777666655 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 1.9e-12
                          PAP2  40 qvstletseskeakesfPSgHsafafalalllalllrrkrkkiglvllalillllavlvalsRlylgvHflsDvlaGlliG 120
                                   + +       +++++  PS H+a +f+lal   ++  +k  +        i+++la+l+ +s l+ g+H+  Dv++G+l+G
  gi|15668843|ref|NP_247646.1| 134 WIF-------TKPTYEIPSLHTAYSFLLAL---HFKDEKPLN-------YIYFALAILIPISTLIMGMHWIVDVITGVLYG 197
                                   333.......4566899*****99987654...566666666.......799***************************** PP

                          PAP2 121 iala 124
                                   +++ 
  gi|15668843|ref|NP_247646.1| 198 YIIY 201
                                   9986 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.7      0.53   3.2e+03      56      69 ..      97     110 ..      50     115 .. 0.71
   2 ?   14.7   1.5   5.5e-06     0.033      10      70 ..     147     202 ..     143     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.53
                        PAP2_C  56 vDVllglyittlvf 69 
                                   +D  lg++++ l++
  gi|15668843|ref|NP_247646.1|  97 IDLALGWLFAGLIY 110
                                   45566666666665 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.5e-06
                        PAP2_C  10 HtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlvfl 70 
                                   Ht++ +   l++l++  +k   l++i++ la+l+ ++ ++   H+ vDV+ g++   +++ 
  gi|15668843|ref|NP_247646.1| 147 HTAYSF---LLALHFKDEKP--LNYIYFALAILIPISTLIMGMHWIVDVITGVLYGYIIYK 202
                                   444444...44444445554..889****************************99998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1535.71
//
Query:       gi|15668844|ref|NP_247647.1|  [L=494]
Description: acetolactate synthase large subunit IlvB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-38  131.9   0.0    2.5e-38  131.4   0.0    1.3  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    1.1e-26   93.4   0.4    4.3e-23   81.8   0.1    3.2  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    2.3e-09   37.1   0.0    5.2e-09   35.9   0.0    1.5  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
     0.0014   18.6   0.6     0.0014   18.6   0.6    2.5  2  DUF4957       Domain of unknown function (DUF4957)


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.4   0.0   5.5e-42   2.5e-38       4     169 ..       8     164 ..       5     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 5.5e-42
                                   HHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHH CS
                  TPP_enzyme_N   4 aealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltala 84 
                                    ea+v+ L++ +v+++f +pG++ilpl+++++ + +i+ +++r+E+ga+f+Adgyar+t+ +gv+l+t+gpGatn++t +a
  gi|15668844|ref|NP_247647.1|   8 LEAMVDFLER-NVKTIFSYPGEQILPLYNEIEGS-SIKNIMVRDERGAGFMADGYARITNYIGVCLATAGPGATNLTTPIA 86 
                                   589*******.***********************.6********************************************* PP

                                   HHHHHT--EEEEEEE--CCCHHS..TC--T.-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHHHC CS
                  TPP_enzyme_N  85 eAkvdriPllvlsgdrptslrgqgvlqqel.dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkdvl 164
                                   +A++d++ +l+++g+ +++++g++++q++  d l++++ ++     v+++e  ++++++A++ +   ++ Pv l++p d+ 
  gi|15668844|ref|NP_247647.1|  87 TAYKDNSSVLAITGRCQRKYIGKNYFQEVNmDFLNFYKGYF-----VDKAE--VSYIAKAFADC-LFNKKPVQLNIPVDLY 159
                                   ***************************55489999999777.....66666..58899******.99999*********** PP

                                   C-EEE CS
                  TPP_enzyme_N 165 leevd 169
                                   +ee++
  gi|15668844|ref|NP_247647.1| 160 KEEAK 164
                                   *9987 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0082        37      74     151 ..      84     152 ..      76     154 .. 0.76
   2 !   81.8   0.1   9.6e-27   4.3e-23       1     153 []     345     482 ..     345     482 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0082
                                   SEEEEEEE-SBCCCHHHH.HHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEE CS
                  TPP_enzyme_C  74 pitvvvlnNegygmtggq.qepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpali 151
                                   pi +   +N++  ++ g  q+++ gk++++     + ++df ++ +++      v+ka+v+ +++a++++l +k+p+ +
  gi|15668844|ref|NP_247647.1|  84 PIATAYKDNSSVLAITGRcQRKYIGKNYFQ-----EVNMDFLNFYKGY-----FVDKAEVSYIAKAFADCLFNKKPVQL 152
                                   666667788665555555488888888887.....5699********9.....77788899999999999988888866 PP

  == domain 2  score: 81.8 bits;  conditional E-value: 9.6e-27
                                   ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH....STTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEE CS
                  TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla....kpdrevvaivGDGgflmilqelatavrrnlpitv 77 
                                   d+G +t+ +  l  +  pr++++s  +gtmG+glpa+iG+k+     + drevv i+GDGgflm+++el  ++++nl+i++
  gi|15668844|ref|NP_247647.1| 345 DAGKHTVFTCLLKTCVIPRNIISSHSFGTMGFGLPASIGVKFGtidfNIDREVVLISGDGGFLMNVEELQVVAENNLKILM 425
                                   89*****8888888888*************************43444569******************************* PP

                                   EEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  78 vvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                   vv+ N++++   +                  k+++f k+a a++++ +++e+   +e+   +k  l+k++p l++v
  gi|15668844|ref|NP_247647.1| 426 VVMKNNSLAEFCK-----------------IKNPNFNKIADAFEIDNCYIENV--DEIGSEIKGYLKKNKPLLVVV 482
                                   ********43222.................67889***********9997777..****************99986 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   1.2e-12   5.2e-09      12     110 ..     191     290 ..     189     305 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.2e-12
                                   SSEEEEE-CHHCHTTGHHHHH...HHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEEEES-SSS CS
                  TPP_enzyme_M  12 krpvilvGggvarsgaseelr...elaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlvlalGarfd 89 
                                   k+p++l+G+g+      +e++   + +ek+++P++tt+ ++gvi+e+ ++++g +g    +   + l eaD ++++G+ ++
  gi|15668844|ref|NP_247647.1| 191 KKPLFLIGQGIFGTLSYKEIVkisKILEKINCPIATTFPARGVINEKLENCIGLVGR---RGDLKSLLEADKIINIGSSLS 268
                                   89*******9988777776651116789*********************99777665...555667789***********9 PP

                                   TCCCTT.TTT.TTTTT-EEEEEE CS
                  TPP_enzyme_M  90 dirttg.sep.efapeakiihid 110
                                     +t+  s + +  ++++ i++ 
  gi|15668844|ref|NP_247647.1| 269 Y-NTYVeSVReKLLSKTENIQLK 290
                                   9.554435554444443445544 PP

>> DUF4957  Domain of unknown function (DUF4957)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3      0.11   4.8e+02      81     111 ..     333     364 ..     259     389 .. 0.75
   2 !   18.6   0.6   3.1e-07    0.0014      30      85 ..     408     462 ..     386     468 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                       DUF4957  81 ikdvnkgliy.dnnkkyviesivinnclvkni 111
                                   ik++++  i  +++ k+++ +++++ c++  +
  gi|15668844|ref|NP_247647.1| 333 IKNIPEDAIIvTDAGKHTVFTCLLKTCVIPRN 364
                                   77887776663666689999999999988554 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.1e-07
                       DUF4957  30 lgkgnasistgasLkiknldldgsasdssfialsetpdetikdtltiqnCeikdvn 85 
                                   ++ ++ ++ +++ Lki  ++++ ++s ++f ++++ + ++i d ++i+nC i++v 
  gi|15668844|ref|NP_247647.1| 408 MNVEELQVVAENNLKILMVVMK-NNSLAEFCKIKNPNFNKIADAFEIDNCYIENVD 462
                                   556678899999*********9.799****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3007.91
//
Query:       gi|15668845|ref|NP_247648.1|  [L=301]
Description: hypothetical protein MJ_0664 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-15   54.9   3.8    1.1e-14   53.9   3.8    1.5  1  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
     0.0033   16.8   0.2     0.0067   15.8   0.2    1.5  1  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   3.8   1.2e-18   1.1e-14       2      39 .]     264     301 .]     263     301 .] 0.96

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.2e-18
                                   EE-SSS--EEEEEE-SSSEEEEESST.T----EEB-GG CS
                zf-C4_Topoisom   2 ekCPkCggdLvlkrgkkGkFvGCsnYPeCkftkklkkn 39 
                                   ++CP+Cg++L + r+kkG+F+GC+nYP+C + ++ kkn
  gi|15668845|ref|NP_247648.1| 264 NTCPWCGAKLRVVRTKKGEFLGCTNYPNCLYRRFPKKN 301
                                   79*******************************99986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   7.5e-07    0.0067      13      26 .]     260     273 ..     259     273 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.5e-07
                   zf-ribbon_3  13 ssddnvCpyCGtkl 26 
                                   + ddn+Cp+CG+kl
  gi|15668845|ref|NP_247648.1| 260 KIDDNTCPWCGAKL 273
                                   579********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2164.02
//
Query:       gi|15668846|ref|NP_247649.1|  [L=341]
Description: hypothetical protein MJ_0665 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     3e-186  618.3   3.9   3.4e-186  618.2   3.9    1.0  1  DUF354       Protein of unknown function (DUF354)
    0.00046   19.1   0.0    0.00069   18.6   0.0    1.3  1  Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
     0.0052   15.7   0.0     0.0094   14.8   0.0    1.3  1  LpxB         Lipid-A-disaccharide synthetase


Domain annotation for each model (and alignments):
>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.2   3.9  5.6e-190  3.4e-186       1     340 []       4     341 .]       4     341 .] 0.99

  Alignments for each domain:
  == domain 1  score: 618.2 bits;  conditional E-value: 5.6e-190
                        DUF354   1 ldvwidltnaphvryfrdlikkfekeGievlltardsGdlaklvklynfvfksiGkhGvtlkekliesakrvinlskliae 81 
                                   ldvwidltnaphv+yf++likkfekeGie+llt+rdsG+laklv++ynfv+k+iGkhG+tlk+kli++a+rvi+l++li++
  gi|15668846|ref|NP_247649.1|   4 LDVWIDLTNAPHVHYFCQLIKKFEKEGIEYLLTFRDSGNLAKLVEIYNFVGKCIGKHGNTLKDKLIFYAERVIGLTELISN 84 
                                   89******************************************************************************* PP

                        DUF354  82 vkpdvalakhsvelprvafGlnipvvyvldnehaeaankltlpladeiikpividendlkktGadpnrirryeGtsevinv 162
                                   vkp+va+akhsvelprvafGlnipv++v+dnehaea+nkltlpladeiikpi++den+lk++G++ n+i+ +eGt+ev+nv
  gi|15668846|ref|NP_247649.1|  85 VKPKVAIAKHSVELPRVAFGLNIPVIFVVDNEHAEAQNKLTLPLADEIIKPIATDENKLKEFGGR-NFIS-FEGTCEVANV 163
                                   *****************************************************************.****.********** PP

                        DUF354 163 qs.....yeideeilkdlnlkledektilmrpepslasyldadchkdvltkiveklkdrid..ilviprdeeqkeiyeevd 236
                                   +s     y+id+eilk+l+ +++d++ti+mrp+p ++sy+++  hkd+l+ki+ekl++rid  i+v+prde+qkeiy+ev+
  gi|15668846|ref|NP_247649.1| 164 NSrlkgyYPIDNEILKKLG-ICDDNPTIVMRPCP-NSSYCNG--HKDILPKIIEKLQKRIDcnIVVFPRDEHQKEIYREVN 240
                                   *******************.**************.*******..****************999*****************9 PP

                        DUF354 237 nviviketvdalsllkrsdlviGaGGtmnreaallGipvvscypqkllsvdkyliekdlmirstdvdeivntalrllvdkl 317
                                    +iv+ket+dalsll++sd++iGaGGtmnre+a+lGip+vscypq+ll+vdkyliekd+mi+++d++ei+n    +++d+l
  gi|15668846|ref|NP_247649.1| 241 -AIVPKETIDALSLLYNSDFMIGAGGTMNRESAILGIPTVSCYPQELLGVDKYLIEKDRMIHTNDIKEIIN----YVEDNL 316
                                   .**********************************************************************....****** PP

                        DUF354 318 ekkk.lie.edltdlivervyealk 340
                                   +k++ +ie ed+tdl++erv+++lk
  gi|15668846|ref|NP_247649.1| 317 GKRMgVIElEDPTDLMFERVCNYLK 341
                                   *****9999**************86 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.2e-07   0.00069     205     284 ..     210     281 ..     172     318 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-07
                                   HHHHHHHHHH--EEEEE--..HHHHHHHHHHHHH-TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEES CS
                   Epimerase_2 205 ealkalakekdvevvvpvhnnprtrkrlleeleelenvtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvnl 284
                                   +++++l+k+ d+++vv     ++ +k++++      +v +i p ++ d lsll n++++++  g++ +E+++lg+p+v  
  gi|15668846|ref|NP_247649.1| 210 KIIEKLQKRIDCNIVVFPR--DEHQKEIYR------EVNAIVPKETIDALSLLYNSDFMIGAGGTMNRESAILGIPTVSC 281
                                   6778888887787777766..888888874......78899************************************976 PP

>> LpxB  Lipid-A-disaccharide synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.6e-06    0.0094     173     287 ..     175     282 ..     166     299 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-06
                                   HHHHHHHT--TTS-EEEEE--SSHHHHHHHHHHHHHHHHHHHHH-TT-EEEEEESSHHHHHHHHHHHHHH-TT---EEEES CS
                          LpxB 173 akakellgidedervlallpgsRkseirrllksllkaaqqlkkqlenlkllvplvnkkyeeqileikaeenldvqllllsg 253
                                   ++  ++lgi +d++++ + p    s  + +  +l k++++l+k ++   +++p    ++++   ei  e+n  v   +++ 
  gi|15668846|ref|NP_247649.1| 175 NEILKKLGICDDNPTIVMRPCPNSSYCNGHKDILPKIIEKLQKRIDCNIVVFPR--DEHQK---EIYREVNAIVPKETID- 249
                                   556677889899999999999999999999888889999999888766555554..33333...4556666656666666. PP

                                   -HHHHHHH-SEEEESSTTHHHHHHHTT--EEE-- CS
                          LpxB 254 ealealaaadlaliksGTaaLEaalaktPmvvay 287
                                    al +l  +d+ + + GT++ E a+++ P+v  y
  gi|15668846|ref|NP_247649.1| 250 -ALSLLYNSDFMIGAGGTMNRESAILGIPTVSCY 282
                                   .9999**************************888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1969.97
//
Query:       gi|15668847|ref|NP_247650.1|  [L=398]
Description: molybdenum cofactor biosynthesis protein MoeA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-41  141.5   0.0    2.7e-41  140.9   0.0    1.3  1  MoeA_N         MoeA N-terminal region (domain I and II)
    1.7e-33  115.3   0.3    1.8e-32  112.0   0.1    2.1  2  MoCF_biosynth  Probable molybdopterin binding domain
    8.2e-19   67.6   0.0    3.2e-18   65.7   0.0    2.0  2  MoeA_C         MoeA C-terminal region (domain IV)
    1.7e-05   25.0   0.6     0.0056   16.8   0.1    3.1  3  7TMR-HDED      7TM-HD extracellular
  ------ inclusion threshold ------
      0.039   13.5   0.0       0.32   10.5   0.0    2.1  2  TrmK           tRNA (adenine(22)-N(1))-methyltransferase


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.9   0.0   7.7e-45   2.7e-41      10     157 .]      17     169 ..       8     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 140.9 bits;  conditional E-value: 7.7e-45
                                   HHHH-.HH.....-EEEEEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--...........-S---TT-.E CS
                        MoeA_N  10 ilaal.el.....eeeevplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeepsaageeperllpgg.a 83 
                                   + ++l e      + +ev++ +eal+r++aed++Ap+d+P f+++amDGYAv ae++ gase++p+  + +++ +++ g a
  gi|15668847|ref|NP_247650.1|  17 VFEKLsEYldenkKVKEVDI-VEALNRISAEDIKAPIDLPYFNKAAMDGYAVIAEDTFGASETNPIILNLADGDEITYGeA 96 
                                   44444333555534445***.9*******************************************777777777777777* PP

                                   EEE-TTSB--TT--EEEEGGGE.E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHHHHHHCT CS
                        MoeA_N  84 vrimTGaplPegadaVvpvEdteeeeaketvev.kavkpgenvrraGedikaGevllragtrltpaeigllasvG 157
                                    +i+TG++lP++a+aVv+ E ++  e+++ vev k+v+p+env r+Ged+k+G+v+l++g++++p ++ +las+G
  gi|15668847|ref|NP_247650.1|  97 KKIFTGDKLPKNANAVVMKEFCN--EVDDFVEVyKTVHPNENVSRIGEDVKKGDVVLKKGEIINPYHLNMLASLG 169
                                   **********************5..33444455799*************************************98 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.075   2.7e+02       6      61 ..      88     151 ..      85     154 .. 0.76
   2 !  112.0   0.1   5.1e-36   1.8e-32       1     139 [.     181     321 ..     181     326 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.075
                                   -HHHHTTSS..........GBHHHHHHHHHHHT..TSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEE CS
                 MoCF_biosynth   6 Gdellsgki..........eDtngpllaellke..lgvevskytvvpDdeeeikeallaaleeadvii 61 
                                   Gde++ g++          +++n+ +++e ++e    vev+k+ +  ++ ++i e +++     dv++
  gi|15668847|ref|NP_247650.1|  88 GDEITYGEAkkiftgdklpKNANAVVMKEFCNEvdDFVEVYKTVHPNENVSRIGEDVKKG----DVVL 151
                                   7788866666666666677999**********8545579999999999999999999444....6665 PP

  == domain 2  score: 112.0 bits;  conditional E-value: 5.1e-36
                                   EEEEE-HHHH...............TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS- CS
                 MoCF_biosynth   1 avitvGdell...............sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGt 66 
                                   ++i++Gdel+                gki ++n+++l+ l+k+lg++++ y +v+Dd+e++k+a+++al+e+d++++tGGt
  gi|15668847|ref|NP_247650.1| 181 GIISTGDELInldeirdieedisklDGKIINSNSYMLYGLVKNLGFNAKIYDIVKDDKEKLKKAIKTALSENDALLITGGT 261
                                   69***************************************************************9999************ PP

                                   SSSTT--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHH CS
                 MoCF_biosynth  67 GptpdDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeill 139
                                   +++++D+t+e++++l++       +++++v+ +pgkp+g++ +   +++   ++++L G+p+a+++ +e++++
  gi|15668847|ref|NP_247650.1| 262 SVSERDITVETVRELGD-------VIVHGVNIRPGKPFGFGII---NDK---PVFMLSGYPVASAVQFELFIQ 321
                                   *****************.......8**************9999...654...8******************94 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.5   5.5e+03      49      59 ..      63      73 ..      60      77 .. 0.82
   2 !   65.7   0.0   8.9e-22   3.2e-18       2      72 .]     332     397 ..     331     397 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.5
                                  -EEEEE-TT-- CS
                        MoeA_C 49 nglivipegte 59
                                  +g++vi e+t 
  gi|15668847|ref|NP_247650.1| 63 DGYAVIAEDTF 73
                                  9******9985 PP

  == domain 2  score: 65.7 bits;  conditional E-value: 8.9e-22
                                   EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                        MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                   ++l+++++s+ gr +f+Rv+++     +++ep++ +gSg++ssl +++g+i ipe++eg+e+Ge V+v+ll
  gi|15668847|ref|NP_247650.1| 332 LPLKRNMASELGRVDFVRVKVD-----IEVEPIRITGSGVISSLIKSDGYILIPENVEGYEKGELVDVYLL 397
                                   7899******************.....9*****************************************97 PP

>> 7TMR-HDED  7TM-HD extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.021        76       3      23 ..      41      61 ..      39      65 .. 0.88
   2 !   16.8   0.1   1.6e-06    0.0056     182     216 ..     136     170 ..     134     172 .. 0.87
   3 ?    1.4   0.0     0.084     3e+02     100     150 ..     189     254 ..     183     281 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.021
                     7TMR-HDED  3 GqiApqdIvAprdfeieDeea 23
                                  + i+ +dI+Ap d+ + +++a
  gi|15668847|ref|NP_247650.1| 41 NRISAEDIKAPIDLPYFNKAA 61
                                  789***********9999987 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.6e-06
                     7TMR-HDED 182 aVepvyvkikkGevIVrkGervteeqlekLealgl 216
                                   +V+ +   +kkG+v+ +kGe++++ +l +L +lg+
  gi|15668847|ref|NP_247650.1| 136 NVSRIGEDVKKGDVVLKKGEIINPYHLNMLASLGI 170
                                   566666679**********************9985 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.084
                     7TMR-HDED 100 llelsdeeleelqqgieqilerilsq......giped...........eearekvkeqlqaalseear 150
                                   l++l  +e+++++++i+++  +i ++      g++++           ++ +ek+k  +++alse++ 
  gi|15668847|ref|NP_247650.1| 189 LINL--DEIRDIEEDISKLDGKIINSnsymlyGLVKNlgfnakiydivKDDKEKLKKAIKTALSENDA 254
                                   6666..77777777777777777766556666555556666666666655555555555555544444 PP

>> TrmK  tRNA (adenine(22)-N(1))-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.9e-05      0.32     116     190 ..      64     137 ..      57     148 .. 0.84
   2 ?    0.1   0.0      0.13   4.8e+02      78     101 ..     228     251 ..     209     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.9e-05
                          TrmK 116 syeikaEkileekkkiYeilvvektkkeeallsekdlrlgplLlkeksalfkkkwkkeleklkkilsklsseeae 190
                                   +y+++aE  +  ++    il ++ +++ + + ++k+++ g++L k+ +a+++k++ +e++ + ++++++  +e+ 
  gi|15668847|ref|NP_247650.1|  64 GYAVIAEDTFGASETNPIILNLADGDEIT-YGEAKKIFTGDKLPKNANAVVMKEFCNEVDDFVEVYKTVHPNENV 137
                                   68888888888877777788888888877.799***********************************9855544 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.13
                          TrmK  78 alIaeILeegkekLkkvkrliLQp 101
                                   a+I +I+++ kekLkk+ +  L  
  gi|15668847|ref|NP_247650.1| 228 AKIYDIVKDDKEKLKKAIKTALSE 251
                                   579999999999998877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2604.37
//
Query:       gi|15668848|ref|NP_247651.1|  [L=503]
Description: thymidine phosphorylase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-18   64.1   1.1    1.1e-16   60.2   0.2    2.7  2  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    7.9e-17   60.9   0.7    2.7e-16   59.2   0.2    2.1  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
    4.3e-16   59.3   0.1    8.5e-16   58.3   0.1    1.5  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    0.00011   21.9   0.9      0.016   15.0   0.0    3.4  3  Biotin_lipoyl_2  Biotin-lipoyl like
      0.001   18.0   0.0     0.0016   17.4   0.0    1.2  1  DUF2254          Predicted membrane protein (DUF2254)
     0.0012   18.9   0.5     0.0053   16.8   0.1    2.2  2  Mucin_bdg        Putative mucin or carbohydrate-binding modul
     0.0014   18.7   0.1     0.0041   17.3   0.1    1.8  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
  ------ inclusion threshold ------
      0.011   15.5   5.3          1    9.2   0.0    3.5  3  Biotin_lipoyl    Biotin-requiring enzyme
      0.042   13.8   0.2        1.1    9.2   0.2    2.9  2  DNA_ligase_OB    NAD-dependent DNA ligase OB-fold domain
      0.091   12.2   0.0       0.18   11.3   0.0    1.4  1  UFD1             Ubiquitin fusion degradation protein UFD1
       0.14   12.1   0.7       0.42   10.6   0.1    2.1  2  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial a
       0.16   11.7   0.0       0.36   10.5   0.0    1.5  1  Mic1             Colon cancer-associated protein Mic1-like


Domain annotation for each model (and alignments):
>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.15   2.2e+02      44      69 ..      72      97 ..      59     100 .. 0.84
   2 !   60.2   0.2   7.5e-20   1.1e-16       1      74 [.     424     490 ..     424     491 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.15
                                  EBTTSEEEEEEESSSCHHHHHHHHHH CS
                        PYNP_C 44 VkkGeplatiYankeekleeavkklk 69
                                  Vk+G+++   +a+k+++l+++ kk++
  gi|15668848|ref|NP_247651.1| 72 VKEGDIVTIKHAEKPKSLPYIRKKMD 97
                                  9***************9999999886 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 7.5e-20
                                   EEEEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHHHHHHEEE CS
                        PYNP_C   1 yvseidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkklkkaiki 74 
                                   yv++i++  i+++a e+GA       p d+++Gi+l++k+G+kV+kG++l+tiY+++ee+l++a+k ++  + i
  gi|15668848|ref|NP_247651.1| 424 YVTRISNAGITKIAKEAGA-------PNDKKAGIYLNVKVGNKVEKGDVLYTIYSDSEERLKSAIKLARILYPI 490
                                   89*****************.......****************************************99988877 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.2   1.8e-19   2.7e-16       2      62 ..      90     150 ..      89     151 .. 0.96
   2 ?   -1.3   0.0       1.4   2.1e+03      10      23 ..     212     225 ..     208     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.8e-19
                                   HHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHH CS
               Glycos_trans_3N   2 diikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmres 62 
                                   ++i+k++dg++L +eei ++i+++++g++t ++i+Af ++l+++G++ +Ei a++  m e 
  gi|15668848|ref|NP_247651.1|  90 PYIRKKMDGNKLKKEEIFEIIDEMVDGKLTNIEISAFVTSLYINGMDMDEIEAMTIRMAET 150
                                   69*****************************************************999886 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                                   T.---HHHHHHHHH CS
               Glycos_trans_3N  10 geeLtaeeirfaih 23 
                                   + +Lt eei+ +++
  gi|15668848|ref|NP_247651.1| 212 RVDLTIEEIKRVVK 225
                                   568999**999886 PP

>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.1   5.7e-19   8.5e-16       3     252 ..     159     387 ..     157     388 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 5.7e-19
                                   TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE..EH CS
               Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl..fa 81 
                                   ++ D+++ GG+  n     +   ++vA+aG+k++k + r+++s +G+aDv+e l  +++lt ee++++++e++ +++  +a
  gi|15668848|ref|NP_247651.1| 159 HIFDVHSIGGVPGNK--YALLVVPIVASAGLKIPKTSSRAITSAAGTADVVEVL-TRVDLTIEEIKRVVKETNGCMVwgGA 236
                                   789********9888..588999*****************************99.58999*********997766652235 PP

                                   HSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHHHHHHHHH CS
               Glycos_transf_3  82 peyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldevsllaktt 162
                                       +a +  ++v r lgi   +    PL+ +        +v++k+la ++ ++l +++++ ++ v++    e+s la   
  gi|15668848|ref|NP_247651.1| 237 LDLAPADDITINVERPLGI---DPE--PLLLS--------SVMAKKLAMGVNKLLIDIPTGYGAKVKS--IKEASSLARKF 302
                                   5566666778899****99...666..99999........****************************..**********9 PP

                                   HHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHHHHHHH CS
               Glycos_transf_3 163 vaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagkadslkegvak 242
                                   +   +    +te +++   ++++ra + ale    ke++ +l++  + ++s   ++  + +ag +l + g +    eg + 
  gi|15668848|ref|NP_247651.1| 303 IELSDrLRIVTECAITYGGQPIGRAIGPALEA---KEALLALEDYTQAPTSL--VEKSISLAGILLEMGG-VAPTGEGKEL 377
                                   9999977899*********************9...*********98888887..5777788898888877.88999***** PP

                                   HHHHHHTSHH CS
               Glycos_transf_3 243 aeevidsGkA 252
                                   ae+++  GkA
  gi|15668848|ref|NP_247651.1| 378 AEDLLARGKA 387
                                   *********9 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.23   3.4e+02      13      24 ..      67      78 ..      66      79 .. 0.87
   2 ?    1.5   0.0      0.18   2.7e+02       4      16 ..     416     428 ..     409     429 .. 0.87
   3 !   15.0   0.0   1.1e-05     0.016      16      33 ..     452     469 ..     451     483 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.23
               Biotin_lipoyl_2 13 VaqlnVkdGqrV 24
                                  V++l Vk+G+ V
  gi|15668848|ref|NP_247651.1| 67 VKELGVKEGDIV 78
                                  89999****998 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.18
               Biotin_lipoyl_2   4 sIaapvsGrVaql 16 
                                    I++p++G V+++
  gi|15668848|ref|NP_247651.1| 416 DIHSPIDGYVTRI 428
                                   79*********98 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 1.1e-05
               Biotin_lipoyl_2  16 lnVkdGqrVkaGdvLael 33 
                                   lnVk G  V++GdvL+++
  gi|15668848|ref|NP_247651.1| 452 LNVKVGNKVEKGDVLYTI 469
                                   89***************9 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     1e-06    0.0016     184     258 ..     406     481 ..     385     489 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1e-06
                       DUF2254 184 eeeseeeeatpiraersGylqaidveaLvklaeeh......dlvielevrpGdfvvkgeplakvwgeeddeelaeklreaf 258
                                   +e +  + +  i+++ +Gy+++i+ + + k+a+e+      ++ i+l+v++G+ v kg++l ++++++     +e+l++a+
  gi|15668848|ref|NP_247651.1| 406 DEIEVGKYKADIHSPIDGYVTRISNAGITKIAKEAgapndkKAGIYLNVKVGNKVEKGDVLYTIYSDS-----EERLKSAI 481
                                   44456678899*********************986222222578*********************988.....34444444 PP

>> Mucin_bdg  Putative mucin or carbohydrate-binding module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   3.6e-06    0.0053      67     110 ..      67     109 ..      38     112 .. 0.79
   2 ?   -0.5   0.0      0.82   1.2e+03      49      89 ..     431     477 ..     389     487 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.6e-06
                     Mucin_bdg  67 ekeisfkeGdvlkiyHaEpknrl..ilskkqeeilksksktntyev 110
                                    ke+ +keGd+++i HaE  ++l  i +k++ ++lk   k++ +e+
  gi|15668848|ref|NP_247651.1|  67 VKELGVKEGDIVTIKHAEKPKSLpyIRKKMDGNKLK---KEEIFEI 109
                                   3799*******************7455556666665...6666666 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.82
                     Mucin_bdg  49 dGneklrkeieGtekqtae......keisfkeGdvlkiyHaEpknrl 89 
                                    G +k+ ke+ + + ++a          ++++Gdvl+    + ++rl
  gi|15668848|ref|NP_247651.1| 431 AGITKIAKEAGAPNDKKAGiylnvkVGNKVEKGDVLYTIYSDSEERL 477
                                   55555555555533333432322222234667777766666666666 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.7e-06    0.0041      13      84 ..      13      84 ..       4      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.7e-06
                                  STTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE- CS
                       CDC48_N 13 grgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrkae 84
                                    + v i++ed+++ + +p d v +e k k v  ++ + +   ++g I + + + k +gv+ Gd Vt++ ae
  gi|15668848|ref|NP_247651.1| 13 LENLVLINSEDLKSSQYFPQDRVVVEFKGKEVIGILHSSTTLINRGEIGLPQKVVKELGVKEGDIVTIKHAE 84
                                  6799*****************88888888867777777777689************************9886 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.3      0.85   1.3e+03      52      65 ..      66      79 ..      64      82 .. 0.80
   2 ?    6.5   0.2     0.005       7.5      35      57 ..     407     429 ..     386     438 .. 0.84
   3 ?    9.2   0.0   0.00068         1      17      39 ..     450     472 ..     439     473 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.85
                                  EEEEESSTTTEEE- CS
                 Biotin_lipoyl 52 vvkeilvkeGdtve 65
                                  vvke+ vkeGd v+
  gi|15668848|ref|NP_247651.1| 66 VVKELGVKEGDIVT 79
                                  68888889888875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.005
                                   EEECTTEEEEEEBSSSEEEEEES CS
                 Biotin_lipoyl  35 eveamKmemeieapkaGvvkeil 57 
                                   e+e+ K + +i +p +G+v+ i 
  gi|15668848|ref|NP_247651.1| 407 EIEVGKYKADIHSPIDGYVTRIS 429
                                   79******************997 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00068
                                   CSESSSTTCEE-TTSEEEEEECT CS
                 Biotin_lipoyl  17 vevlvkvGdkVkagqvlaeveam 39 
                                   +   vkvG kV++g+vl ++ ++
  gi|15668848|ref|NP_247651.1| 450 IYLNVKVGNKVEKGDVLYTIYSD 472
                                   56789************998765 PP

>> DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.046        68      26      64 ..       6      45 ..       3      50 .. 0.85
   2 ?    9.2   0.2   0.00074       1.1      20      61 ..      36      84 ..      34     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.046
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX CS
                 DNA_ligase_OB 26 velaGttVsratLhnedeierkdirigdtVvvekaG.dvI 64
                                  v++ +   ++  L n + +++ +   +d+Vvve  G +vI
  gi|15668848|ref|NP_247651.1|  6 VRVLDIDLENLVLINSEDLKSSQYFPQDRVVVEFKGkEVI 45
                                  788888999999********************98773555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00074
                                  XXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXXX CS
                 DNA_ligase_OB 20 vAeLepvelaGttVsratLhnedei.......erkdirigdtVvvekaG 61
                                  v e++  e+ G   s  tL n  ei       ++++++ gd V++++a 
  gi|15668848|ref|NP_247651.1| 36 VVEFKGKEVIGILHSSTTLINRGEIglpqkvvKELGVKEGDIVTIKHAE 84
                                  66778888899999999**************9**************996 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.18      67      98 ..      56      87 ..      43      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                          UFD1 67 eegtvylPewmmenlgleegdlveiesvslpk 98
                                  + g++ lP+ ++++lg++egd+v+i++++ pk
  gi|15668848|ref|NP_247651.1| 56 NRGEIGLPQKVVKELGVKEGDIVTIKHAEKPK 87
                                  5799***********************99988 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00028      0.42      11      29 ..      62      80 ..      62      81 .. 0.94
   2 ?   -3.4   0.0       7.1   1.1e+04      19      28 ..     452     461 ..     452     461 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                                  E-CCCHHHCCEECTCEEEE CS
                MazE_antitoxin 11 iPkevrfelgireGdevel 29
                                  +P  v++elg++eGd v++
  gi|15668848|ref|NP_247651.1| 62 LPQKVVKELGVKEGDIVTI 80
                                  7999*************98 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.1
                                   CCEECTCEEE CS
                MazE_antitoxin  19 lgireGdeve 28 
                                   l++++G++ve
  gi|15668848|ref|NP_247651.1| 452 LNVKVGNKVE 461
                                   5788888876 PP

>> Mic1  Colon cancer-associated protein Mic1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00024      0.36      52      98 ..     351     399 ..     338     402 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                          Mic1  52 vledskelAclLLslenvypp..alqlalDmLkrlkaneeivevLLskg 98 
                                   ++e s +lA +LL+++ v p+     la D+L+r ka+++ +e+++ +g
  gi|15668848|ref|NP_247651.1| 351 LVEKSISLAGILLEMGGVAPTgeGKELAEDLLARGKAHDKFMEIIVAQG 399
                                   688999**********9999722579******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 3100.76
//
Query:       gi|15668849|ref|NP_247652.1|  [L=85]
Description: hypothetical protein MJ_0668 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0058   16.5   1.5     0.0067   16.3   1.5    1.1  1  PH_16     PH domain


Domain annotation for each model (and alignments):
>> PH_16  PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.5   3.7e-07    0.0067      43     106 ..       8      70 ..       2      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.7e-07
                         PH_16  43 vlvllqkqdeklvlkslataskdkk.vlspiikLskllvrevAadkkalflistsesgpqmyelv 106
                                   +lv++ ++dek++     + +++ k v   i+ ++  ++ +  +dkk+++ i  s+++ ++y+l+
  gi|15668849|ref|NP_247652.1|   8 FLVVIMENDEKIIEDLK-IINSKAKfVGIKILMIR-HIIESHMKDKKSIYKILESTKNTELYKLI 70 
                                   5888999****998887.66667774556666555.56788899*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 562.83
//
Query:       gi|15668850|ref|NP_247653.1|  [L=367]
Description: DEAD/DEAH box helicase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-50  169.5   0.2      2e-49  167.7   0.0    1.8  2  DEAD           DEAD/DEAH box helicase
    2.6e-34  117.9   2.3    6.9e-32  110.1   0.1    3.2  3  Helicase_C     Helicase conserved C-terminal domain
    1.7e-12   47.7   0.1    2.9e-12   46.9   0.1    1.3  1  ResIII         Type III restriction enzyme, res subunit
    1.4e-06   27.9   0.0    2.7e-06   26.9   0.0    1.4  1  CMS1           U3-containing 90S pre-ribosomal complex subuni
     0.0016   18.2   0.0     0.0041   16.9   0.0    1.6  2  AAA_30         AAA domain
     0.0077   15.5   0.2      0.012   14.8   0.2    1.3  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
     0.0098   16.2   0.0       0.92    9.8   0.0    2.3  2  AAA_19         AAA domain
  ------ inclusion threshold ------
      0.089   13.1   0.7       0.47   10.7   0.3    2.5  2  AAA_22         AAA domain
        0.1   12.6   0.0       0.22   11.5   0.0    1.8  1  Flavi_DEAD     Flavivirus DEAD domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.7   0.0     1e-52     2e-49       1     173 [.      30     192 ..      30     195 .. 0.95
   2 ?   -1.0   0.0      0.64   1.3e+03      69     104 ..     256     295 ..     247     307 .. 0.60

  Alignments for each domain:
  == domain 1  score: 167.7 bits;  conditional E-value: 1e-52
                                   -HHHHHHHHHHHTTC.EEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                   xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   1 tdiQaeaiplilggg.dvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                   tdiQ ++ipl+l+++ +++++a+TGsGKT+ f+ip+++ v   ++++g  a+i++PtreLa q++++++++k + +l++  
  gi|15668850|ref|NP_247653.1|  30 TDIQMKVIPLFLNDEyNIVAQARTGSGKTASFAIPLIELV---NENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAK 107
                                   89**********7766*********************999...47****************************999***** PP

                                   EETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  81 iiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrq 161
                                   i+gg+a   q+++l ++++ivvgtpgr++d++++g+lnl++v++++lDEad++l++gf +++++iln++       +++++
  gi|15668850|ref|NP_247653.1| 108 IYGGKAIYPQIKAL-KNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNAC-------NKDKR 180
                                   **************.******************************************************.......55667 PP

                                   EEEEESSBSHHH CS
                                   xxxxxxxxxxxx RF
                          DEAD 162 vivlSATlpkdv 173
                                   ++++SAT+p+++
  gi|15668850|ref|NP_247653.1| 181 ILLFSATMPREI 192
                                   *********876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.64
                                   HHTTTSTSEEEEEETTSSHHHHHHHH....HTTCSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                          DEAD  69 kfkkyidlrvlliiggvaardqlskl....dngvdivvgt 104
                                   +++  i+ ++ +i g+ ++++  +++    +++++i+++t
  gi|15668850|ref|NP_247653.1| 256 SMLRDIGFKAGAIHGDLSQSQREKVIrlfkQKKIRILIAT 295
                                   4445566666666554444333333344533669998888 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.011        23       6      57 ..      65     119 ..      61     152 .. 0.79
   2 ?    1.0   0.1      0.26   5.2e+02       6      28 ..     168     194 ..     163     233 .. 0.51
   3 !  110.1   0.1   3.4e-35   6.9e-32       2     111 .]     226     333 ..     225     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.011
                                   HHHHHHHTTTTSEEEEEESSHH...HHHH...HHHHHHHTTSTEEEESTTSTHHHHHH CS
                    Helicase_C   6 llellkleeeggkilifvntid...rlek...vklllekkgikvavlhgelpqneree 57 
                                   l+el+ +e++g +++i ++t++   +      ++ l+ +k++k+a+++g      +++
  gi|15668850|ref|NP_247653.1|  65 LIELV-NENNGIEAIILTPTRElaiQ--VadeIESLKGNKNLKIAKIYGGKAIYPQIK 119
                                   66777.899999**********8663..233689999999********9765555554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.26
                                   HHHHHHHTTTTSEEEEEESSHH....H CS
                    Helicase_C   6 llellkleeeggkilifvntid....r 28 
                                   + ++l+  +++++il+f+ t      +
  gi|15668850|ref|NP_247653.1| 168 VEKILNACNKDKRILLFSATMPreilN 194
                                   455555668888888888887754331 PP

  == domain 3  score: 110.1 bits;  conditional E-value: 3.4e-35
                                   HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTS CS
                    Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidi 82 
                                   ++eal++ll  ++++   l+f++t+++ +++  +l+  g+k+ ++hg+l+q++re++++ f+++++++Liatdv++rGid+
  gi|15668850|ref|NP_247653.1| 226 RFEALCRLL--KNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDV 304
                                   678899998..6777778********997756666777******************************************* PP

                                   TTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                    Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtgRag 111
                                   +++n+Vin++lp+n++sy++riGRtgRag
  gi|15668850|ref|NP_247653.1| 305 NDLNCVINYHLPQNPESYMHRIGRTGRAG 333
                                   ***************************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.1   1.5e-15   2.9e-12      15     170 ..      17     189 ..       9     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.5e-15
                                   HT........................TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGG CS
                        ResIII  15 lleklks..................krdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkk 76 
                                   +l+++ +                  +++ +++ ++ TG+GKT    + lie + +++++ ++++l p+++l  q  +e+++
  gi|15668850|ref|NP_247653.1|  17 ILNAIRNkgfekptdiqmkviplflNDEYNIVAQARTGSGKTASFaIPLIELVNENNGI-EAIILTPTRELAIQVADEIES 96 
                                   55444445555677777777788879999**************9868888888888776.99******************* PP

                                   GTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHH CS
                        ResIII  77 flseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreil 154
                                   ++ +++ +i k++ g+   ++ k+ +n++i+v t  ++  ++     ++ +l  ++ +++i DEa  +  +   k +++il
  gi|15668850|ref|NP_247653.1|  97 LKGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHI-----NRGTLNLKNVKYFILDEADEMLNMgfiKDVEKIL 172
                                   ***************9999999999*****************.....77888888999************97777899987 PP

                                   HT-.--SEEEEEESS-S CS
                        ResIII 155 ekf.keavllglTATpe 170
                                   +++ k++ +l ++AT++
  gi|15668850|ref|NP_247653.1| 173 NACnKDKRILLFSATMP 189
                                   7653779********87 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   1.3e-09   2.7e-06     117     209 ..      65     155 ..      57     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.3e-09
                          CMS1 117 lvksaksngsPelLvltlaalRaaDlaralkklq.tkdskvakLFakhikleesvtylkksrigiavGtpgRildLleees 196
                                   l++  + n   e ++lt +   a+ +a  + +l+ +k+ k+ak+++    +  +++ lk++ i   vGtpgRild ++ ++
  gi|15668850|ref|NP_247653.1|  65 LIELVNENNGIEAIILTPTRELAIQVADEIESLKgNKNLKIAKIYGGK-AIYPQIKALKNANI--VVGTPGRILDHINRGT 142
                                   555556666667788888877888888899988889*********865.46799*****9875..689************* PP

                          CMS1 197 lsvdeLkrivlDa 209
                                   l+++++k+ +lD 
  gi|15668850|ref|NP_247653.1| 143 LNLKNVKYFILDE 155
                                   ***********96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     2e-06    0.0041       6     120 ..      33     182 ..      30     185 .. 0.73
   2 ?   -2.6   0.0       1.9   3.8e+03      65      81 ..     260     276 ..     243     295 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                        AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalkal.reaweaa.ggrviglAptgkaAkvLaeelgi....eastiakllkrl 80 
                                   Q +++  +l+++    v++++ G+GKt + +    e+++++ g + i+l+pt + A ++a+e++     +   iak+    
  gi|15668850|ref|NP_247653.1|  33 QMKVIPLFLNDEY-NIVAQARTGSGKTASFAIPlIELVNENnGIEAIILTPTRELAIQVADEIESlkgnKNLKIAKIYGGK 112
                                   5666666666665.67899********988753377777666******************987644333444555555444 PP

                        AAA_30  81 k...........................grarlepgtllivDEagmv....dtkqlaallkaaekagakvi 120
                                   +                           g+ +l++ + +i DEa  +     +k+++++l+a++k + +++
  gi|15668850|ref|NP_247653.1| 113 AiypqikalknanivvgtpgrildhinrGTLNLKNVKYFILDEADEMlnmgFIKDVEKILNACNK-DKRIL 182
                                   48888888889999999999999999887788888899999999644344456777777777776.55555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                        AAA_30  65 elgieastiakllkrlk 81 
                                   ++g++a  i+  l++ +
  gi|15668850|ref|NP_247653.1| 260 DIGFKAGAIHGDLSQSQ 276
                                   45555555554444333 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   6.2e-06     0.012      45     151 ..     226     332 ..     194     348 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.2e-06
                 ERCC3_RAD25_C  45 kfracefLikyhekrgDkiivfsDnvfaLkeyakkl.....kkpyiyGetseaerlkilqkfkknpkvntiflskvgDtsi 120
                                   +f+a+  L+k +e      +vf+      ke+a++l     k   i+G+ s+++r k+++ fk++ k++ ++   v    i
  gi|15668850|ref|NP_247653.1| 226 RFEALCRLLKNKEF---YGLVFCKTKRDTKELASMLrdigfKAGAIHGDLSQSQREKVIRLFKQK-KIRILIATDVMSRGI 302
                                   44444444444443...34778777777777777761111144579****************986.899999********* PP

                 ERCC3_RAD25_C 121 DlPeanvliqisshfgsrrqeaqrlGriLra 151
                                   D+ + n++i     +        r+Gr  ra
  gi|15668850|ref|NP_247653.1| 303 DVNDLNCVINYHLPQNP-ESYMHRIGRTGRA 332
                                   ********976544332.2334566666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00046      0.92      13      69 ..      47     111 ..      38     184 .. 0.63
   2 ?    4.2   0.0     0.025        49      34      84 ..     230     278 ..     223     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00046
                        AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae..........a 69 
                                   ++  a  G+GKT      + +lv++++    e +++++t+  a ++++++++l+++           
  gi|15668850|ref|NP_247653.1|  47 IVAQARTGSGKTASFAIPLIELVNENNG--IEAIILTPTRELAIQVADEIESLKGNknlkiakiygG 111
                                   5556788******998877777666644..7999**************9999887766665444440 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.025
                        AAA_19  34 lvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddll 84 
                                   l +l + k    l+ + t+r +kel+  l+ +g +a  iH+   l   +++
  gi|15668850|ref|NP_247653.1| 230 LCRLLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGD--LSQSQRE 278
                                   55555556667789999***********************54..4333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00024      0.47       8     125 ..      47     181 ..      42     195 .. 0.54
   2 ?   -2.3   0.0       2.5     5e+03      46      60 ..     246     261 ..     214     296 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee........erpevvfvtlpsstsskdllrellralglelka.......... 70 
                                   +v  + +G+GKT + +  l +l++e++  e        e                +++ e+ +  g+++ +          
  gi|15668850|ref|NP_247653.1|  47 IVAQARTGSGKTASFAIPLIELVNENNGIEaiiltptrE------------L-AIQVADEIESLKGNKNLKiakiyggkai 114
                                   555677888888888877777765543333333432221............2.2222222222222222224444444445 PP

                        AAA_22  71 ............erlsseellealeqalrarav....ielliiDEaqh.lrseealeeLrsllnlsrkgvql 125
                                                 ++  ++l+++++           ++ +i+DEa+  l ++  ++++ ++ln   k+ ++
  gi|15668850|ref|NP_247653.1| 115 ypqikalknaniVVGTPGRILDHINRGT----LnlknVKYFILDEADEmL-NMGFIKDVEKILNACNKDKRI 181
                                   5777766333333344444555555555....455559**********77.899999998888873343333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.5
                        AAA_22  46 tlpsst.sskdllrel 60 
                                   + + +t +++++lr++
  gi|15668850|ref|NP_247653.1| 246 KTKRDTkELASMLRDI 261
                                   3333333333333333 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.22       8      56 ..      48      97 ..      41     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                  EEE--TTS-TTTTHHHHHHH.HHHHTT--EEEEESSHHHHHHHHHHTTTS CS
                    Flavi_DEAD  8 vldlhPGaGktrkvlpelvk.eaierrlrtlvLaPtrvvlaemeealkgl 56
                                  v ++  G+Gkt  +   l++  + ++ + +++L+Ptr  +  +++ ++ l
  gi|15668850|ref|NP_247653.1| 48 VAQARTGSGKTASFAIPLIElVNENNGIEAIILTPTRELAIQVADEIESL 97
                                  567789*****99866666515667889*********8887777655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2776.77
//
Query:       gi|15668851|ref|NP_247654.1|  [L=356]
Description: hypothetical protein MJ_0670 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-37  125.9   0.0    1.6e-36  124.9   0.0    1.5  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
  ------ inclusion threshold ------
      0.012   15.0   1.7      0.055   12.9   0.1    2.6  3  Spermine_synth   Spermine/spermidine synthase domain
       0.02   14.4   0.0      0.047   13.2   0.0    1.5  1  MTS              Methyltransferase small domain
      0.053   14.2   0.0       0.86   10.4   0.0    2.4  1  Methyltransf_25  Methyltransferase domain
        5.3    7.5   9.2       0.18   12.2   1.5    2.5  3  DUF4208          Domain of unknown function (DUF4208)


Domain annotation for each model (and alignments):
>> Methyltransf_30  S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.9   0.0   4.4e-40   1.6e-36       2     124 .]     134     253 ..     133     253 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 4.4e-40
                                   GGHHHHHHHHHHTS-S-SEEEEEEETTTTEEEEEEES-HHHHHHHC-T-EEEEEE-SS-TTTSGGGCSHHHHHHHHHHEEE CS
               Methyltransf_30   2 eleelakallkeyllalaglqrlelaaeevtlklligdarealkeldekadawFlDgFsPaknPelwseellkelarllkk 82 
                                   +++e++k+ ++ey+l++ g   +e+++++ +++l++gdar+++ ++d+k++++F+D+FsP+++P+l+++++lke+++++++
  gi|15668851|ref|NP_247654.1| 134 KEHEIIKDKVREYFLNKIG---IEYKSDYDNINLYVGDARKFIIKSDKKYNVVFHDAFSPKRDPTLYTYDFLKEIYKRMED 211
                                   6899************999...99********************************************************* PP

                                   EEEEEES---HHHHHHHHHTT-EEEEEE-CTCSSEEEEEESS CS
               Methyltransf_30  83 kgtlatyssAgavrrgLkeaGfkvekrkgfgrKremlkaske 124
                                   +g+l++yssA+++r++L+++Gf +++++++grKr+++ a+k+
  gi|15668851|ref|NP_247654.1| 212 NGVLISYSSAIPFRSALVDCGFVISEKESVGRKRGITLAYKN 253
                                   ***************************************985 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.15   5.4e+02      53      84 ..       9      51 ..       7      76 .. 0.65
   2 ?   -1.9   0.0      0.53   1.9e+03      32      54 ..     100     122 ..      59     125 .. 0.69
   3 ?   12.9   0.1   1.5e-05     0.055      61     134 ..     147     220 ..     137     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.15
                                  HHHHHHHHHSHHHHTT...........CGGCTTEEEEESTCHH CS
                Spermine_synth 53 kvidfskkflpslais...........afndarvklvlgdgfk 84
                                  k++++ +k+++  +++            ++++ v +  +dg  
  gi|15668851|ref|NP_247654.1|  9 KALEIIRKYMKIYNGKnekdikerlikELKEEHVLVETEDGTY 51
                                  7888899999998888444444444444444444444444444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.53
                                   HHHHHTTSTT-SEEEEEES-HHH CS
                Spermine_synth  32 vlrevvkhntvekitlvdiDqkv 54 
                                    +   + +n   +i++v+i ++v
  gi|15668851|ref|NP_247654.1| 100 NAIAALHYNKNAEIDMVEICEEV 122
                                   44455667777889999987776 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 1.5e-05
                                   HSHHHHTT.CGGCTTEEEEESTCHHHHCTCSS-EEEEEEECCSTTCSSCGCSSHHHHHHHHHTEEEEEEEEEEEE CS
                Spermine_synth  61 flpslais.afndarvklvlgdgfkflkayekkfdvvivdsldpvgpaenlFskeffdllkkvlkedGviilqae 134
                                   fl ++ i+   + + ++l +gd+ kf+ +  kk+ vv  d   p     +l++ +f++ ++k ++++Gv+i+ + 
  gi|15668851|ref|NP_247654.1| 147 FLNKIGIEyKSDYDNINLYVGDARKFIIKSDKKYNVVFHDAFSPK-RDPTLYTYDFLKEIYKRMEDNGVLISYSS 220
                                   456666663334478999************************975.34569******************998665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.047      32      63 ..      87     118 ..      80     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                                   CSEEEEET-TTSHHHHHHHHHTTC.EEEEEES CS
                           MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdv 63 
                                   + +vlDl++G+G+ ++a+++ +++ae+++v++
  gi|15668851|ref|NP_247654.1|  87 NPRVLDLCSGMGYNAIAALHYNKNAEIDMVEI 118
                                   568***************************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00024      0.86       1      94 [.      90     210 ..      90     213 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHH.............HHHHHHHHH...TTT.........TEEEEESBCC CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseeml.............eaareraee...egl.........nvefvqgdae 56 
                                   vLdl+ G G +++a+++  ++a++ +v+i ee l             e+++ +++e   +++         n+++++gda+
  gi|15668851|ref|NP_247654.1|  90 VLDLCSGMGYNAIAALHYNKNAEIDMVEICEEVLfltlfldipykehEIIKDKVREyflNKIgieyksdydNINLYVGDAR 170
                                   8*************9988779*********999866666666666665555555444442223344445567777777777 PP

                                   GBS.SSTTTEEEEEEESTGGGSSHHHH..HHHHHHHHHHEE CS
               Methyltransf_25  57 dlp.fedgsfDlvvssgalhhlsdedl..ekalkeiarvLk 94 
                                   ++    d+++++v+   a++   d+ l   ++lkei++ ++
  gi|15668851|ref|NP_247654.1| 171 KFIiKSDKKYNVVFH-DAFSPKRDPTLytYDFLKEIYKRME 210
                                   754246667777776.4555444443312346666666555 PP

>> DUF4208  Domain of unknown function (DUF4208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2      0.95   3.4e+03      18      31 ..       7      20 ..       2      44 .. 0.46
   2 ?   -2.8   0.0       2.6   9.2e+03       4      30 ..      55      81 ..      52      86 .. 0.70
   3 ?   12.2   1.5   5.1e-05      0.18      28      57 ..     285     315 ..     280     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.95
                       DUF4208 18 vkksLkrLkkltke 31
                                   kk+L+ ++k  k 
  gi|15668851|ref|NP_247654.1|  7 NKKALEIIRKYMKI 20
                                  45555544444332 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.6
                       DUF4208  4 esmdeeeckellrpvkksLkrLkkltk 30
                                  ++++ee+++++   +k++  ++ k++k
  gi|15668851|ref|NP_247654.1| 55 AEDEEEMMHSKVGALKEAIYKFAKPSK 81
                                  456677788887777777777777654 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 5.1e-05
                       DUF4208  28 ltkekl.lskkerakilkkeLlkiGdfIdel 57 
                                   ltk+k+  +++er ++lk++L+kiG+ +++ 
  gi|15668851|ref|NP_247654.1| 285 LTKDKIiEDREERREKLKEKLIKIGKYLSTK 315
                                   56778889******************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1032  (0.0575604); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2331.48
//
Query:       gi|15668852|ref|NP_247655.1|  [L=224]
Description: 5-amino-6-(5-phosphoribosylamino)uracil reductase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-67  225.4   0.1    6.4e-67  225.3   0.1    1.0  1  RibD_C    RibD C-terminal domain
  ------ inclusion threshold ------
      0.057   12.8   0.3       0.14   11.6   0.1    1.7  2  Aldolase  KDPG and KHG aldolase
      0.093   12.8   0.2       0.15   12.2   0.2    1.2  1  DHR10     Designed helical repeat protein 10 domain
       0.15   12.2   0.1       0.67   10.1   0.1    1.9  1  DUF382    Domain of unknown function (DUF382)


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.3   0.1   1.4e-70   6.4e-67       1     200 []       9     218 ..       9     218 .. 0.97

  Alignments for each domain:
  == domain 1  score: 225.3 bits;  conditional E-value: 1.4e-70
                                   -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHHHTT.GSS-EEEE CS
                        RibD_C   1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreaeadaearqpvrvV 81 
                                   py+i+++ ++lDGkla+ +++s+ i++ee+  +vh++ra++d+i+vG+gtvl+d+p+ltv+  k++        r+pvr+V
  gi|15668852|ref|NP_247655.1|   9 PYIISNVGMTLDGKLATINNDSR-ISCEEDLIRVHKIRANVDGIMVGIGTVLKDDPRLTVHKIKSD--------RNPVRIV 80 
                                   8**********************.*****************************************9........******* PP

                                   EETTS-S-TTSHHHHSSS-EEEEESSCSCHHHHHHCC......E........SE-HHHHHHHHHHTT--EEEEEETHHHHH CS
                        RibD_C  82 vdstlrvpldakvltddaptlvatteeadkekveklk......v........rvdlkelleeLkergirsllveGGatLag 148
                                   vds+lrvpl+a+vl++da+t++atte++++ek++k+k      v        +vdlk+l+ +L+++gi+s+l+eGG+tL++
  gi|15668852|ref|NP_247655.1|  81 VDSKLRVPLNARVLNKDAKTIIATTEDTNEEKEKKIKiledmgVevvkcgrgKVDLKKLMDILYDKGIKSILLEGGGTLNW 161
                                   *************************************777766266899******************************** PP

                                   HHHHTTT-SEEEEEEESCE--T.TSBCSSSSST-SS....EEEEEEEEEEETTEEEE CS
                        RibD_C 149 sllraglvDelrlyiaPkllGg.agktlfdgegfka....lklklvksealgegvvl 200
                                    ++++glvDe+ +yiaPk++Gg +++t++dgegfk+    +kl+l+++++lgeg+vl
  gi|15668852|ref|NP_247655.1| 162 GMFKEGLVDEVSVYIAPKIFGGkEAPTYVDGEGFKTvdecVKLELKNFYRLGEGIVL 218
                                   ******************************************************996 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1     3e-05      0.14      13      71 ..       2      62 ..       1      73 [. 0.85
   2 ?   -1.5   0.0      0.32   1.5e+03      19      35 ..     133     149 ..      95     158 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3e-05
                                  EE--SSGGGHHHHHHHHHHTT--EEEEETTSTTHHHHHHH..HHHH-TTSEEEEES--SHH CS
                      Aldolase 13 vivikdkedalplaeaLvagGlrvlevtlrteaaldairv..lrkerpdllvgaGtvlnae 71
                                  v+v+++k  ++  +   ++g l +++   r  +  d irv  +r+++++++vg Gtvl+ +
  gi|15668852|ref|NP_247655.1|  2 VMVMEKKPYIISNVGMTLDGKLATINNDSRISCEEDLIRVhkIRANVDGIMVGIGTVLKDD 62
                                  67788888888888888899999999999999*****99765899*************865 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.32
                                   GGGHHHHHHHHHHTT-- CS
                      Aldolase  19 kedalplaeaLvagGlr 35 
                                   k d ++l++ L ++G++
  gi|15668852|ref|NP_247655.1| 133 KVDLKKLMDILYDKGIK 149
                                   34555566666666665 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   3.2e-05      0.15      19      74 ..      96     151 ..      94     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-05
                         DHR10  19 relqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielr 74 
                                   ++ ++ i++ ++  ++ ++ ik+le+  +e+ k+   k +lk+l+d l +k+i++ 
  gi|15668852|ref|NP_247655.1|  96 KDAKTIIATTEDTNEEKEKKIKILEDMGVEVVKCGRGKVDLKKLMDILYDKGIKSI 151
                                   677888999999999************************************99875 PP

>> DUF382  Domain of unknown function (DUF382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00015      0.67      61     119 ..      99     156 ..      52     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                        DUF382  61 eTgieelrealeekeeekslkekarekvqpklgkldidykkLhdaFfklqtkPkllkfG 119
                                   +T i++  ++ eeke++ ++ e +   v  k+g+ ++d kkL d+ +  + k  ll+ G
  gi|15668852|ref|NP_247655.1|  99 KTIIATTEDTNEEKEKKIKILEDMGVEV-VKCGRGKVDLKKLMDILYDKGIKSILLEGG 156
                                   4555555555455555555555554444.699******************999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1331.22
//
Query:       gi|15668853|ref|NP_247656.1|  [L=432]
Description: membrane bound transport protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-45  156.3  34.1      2e-45  155.7  34.1    1.2  1  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    2.2e-39  135.5  38.0    2.5e-38  132.0  34.2    2.1  2  CitMHS         Citrate transporter


Domain annotation for each model (and alignments):
>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.7  34.1   2.2e-49     2e-45      35     464 ..      31     430 ..      24     432 .] 0.86

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 2.2e-49
                 Na_sulph_symp  35 aifiaaivglileplplavialialsllavligvlaakalsevlsgfssdttlLvfaalliaaavektgLgkRiAlvlvki 115
                                    i+i+a   +  e lpl+v++l++ ++ + l+++     l+e+l  f   +++L+++++++a+a+   +L+k iA+ l++ 
  gi|15668853|ref|NP_247656.1|  31 VILIVAGCLWFFELLPLPVTSLAIPIMAVFLGIFN----LKEALTYFAHPIIFLFLGGFMLAQALKNHNLDKFIAYKLLNY 107
                                   56777778899**********97666665555555....5*************************************9975 PP

                 Na_sulph_symp 116 vGk..rtliLgyalvladlllapatpsntAraggivfpvikslssafgsepekqserkigaylmltvvqsasitsiaflTa 194
                                    Gk  +t      l + +l+++++++s+t    +i+     +l +     ++ +   k+  +l+l v++sasi++ia++ +
  gi|15668853|ref|NP_247656.1| 108 -GKdfKTTCFLMFLSAYFLSMWISNTSATLILLPIA----LGLLH-----KKTG---KLRDFLLLGVAYSASIGGIATIIG 175
                                   .76234555556677899*********997666666....33322.....2222...3779******************** PP

                 Na_sulph_symp 195 mApNllllglinsilgveitwasWflaaiptgvillllvplllyvlyppeikkkeeakavaktelkelGpltarekallil 275
                                     pN+++++ ++        + sWf++ +p++++l+l+  l ly+ ++  i k      +++++++    l+++  +ll++
  gi|15668853|ref|NP_247656.1| 176 SPPNAIASSYLD------YGFFSWFKVGFPISLLLFLICTLTLYIYFKKWIPKE---DIAIQARME----LSRNAYKLLVI 243
                                   *******99988......78***********************99999888777...455666654....6899999**** PP

                 Na_sulph_symp 276 fvlllllWifge......slnidattvaivvlvillllrvldWkDivkqktaWntllllgglialakllersgliewlgnk 350
                                   fvl+ +lWi ++      +++  ++++ai+++++l++ ++++ +D   +k  W+tl+l+gg + l  +  +sg   +l++k
  gi|15668853|ref|NP_247656.1| 244 FVLIASLWIISDylseifNVQYFDSVIAIFAIILLFVFNLVEVNDF--KKIDWGTLILFGGALCLGGVIVKSGANTFLSEK 322
                                   ************6665443336699*******************86..6799***************************** PP

                 Na_sulph_symp 351 lttslsglspavaiiiilslfvlvhylfaSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpi 431
                                   l+ +l +l p v+++ ++++ + + + f S+t +t +++pil  v+ +i   p+++++l+++++ s   f+lp++t+pn+i
  gi|15668853|ref|NP_247656.1| 323 LIAILGNLTPIVLLFLVVTITI-ILTNFISNTGLTGIIVPILFGVSLGI---PKEILILAVGMSASCS-FILPVGTPPNAI 398
                                   *********9999998888876.56899***************999888...888***********99.************ PP

                 Na_sulph_symp 432 vfgagylkvkdywrlGfilsiigllillllgal 464
                                   v++ g +k +++ ++G+ilsi++ +++ l   l
  gi|15668853|ref|NP_247656.1| 399 VYSEG-VKKEEMMKIGMILSILSAAVITLYSIL 430
                                   **987.78899*************999887655 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.0  34.2   2.7e-42   2.5e-38       3     286 ..      39     371 ..      37     380 .. 0.85
   2 !    6.7   0.6   0.00041       3.7     116     168 ..     375     427 ..     367     432 .] 0.69

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 2.7e-42
                                   xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS   3 llileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrdllvllv 79 
                                   l+ +e l+l+v++l + +++    ++ ++eal+ +a pii+l+lg++++++al+  +l +++a kll+ ++  ++  +l++
  gi|15668853|ref|NP_247656.1|  39 LWFFELLPLPVTSLAIPIMAvflgIFNLKEALTYFAHPIIFLFLGGFMLAQALKNHNLDKFIAYKLLNYGKDFKTTCFLMF 119
                                   899999********7777778999999999*****************************************9877999999 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                        CitMHS  80 lltallsafvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaarpglslpnlll...... 153
                                   l + +ls+++sn+ ++li++pi+l l ++++++ +  ll+ +a++a+igg++t+iG p            pn ++      
  gi|15668853|ref|NP_247656.1| 120 LSAYFLSMWISNTSATLILLPIALGLLHKKTGKLRDfLLLGVAYSASIGGIATIIGSP------------PNAIAssyldy 188
                                   ****************************966666659*********************............*****999999 PP

                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                        CitMHS 154 ..........lalllvgllplvllfmfgvalalpvnapkvkkqkaiieaiarsllpvatillla................. 207
                                             ++ ll +l++ ++l+     + ++  +pk +   +    ++r++ +  +i++l+                 
  gi|15668853|ref|NP_247656.1| 189 gffswfkvgfPISLLLFLICTLTLY-----IYFKKWIPKEDIAIQARMELSRNAYKLLVIFVLIaslwiisdylseifnvq 264
                                   9999988776333333333333333.....455666777777777777778888888777777788899999999999999 PP

                                   ........................xxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS 208 ........................ykkveWsvlllfaGvfllvgaleqtG....ilealadllgaggplvalalvlglial 260
                                                           +kk++W++l+lf+G++ l+g++ ++G    ++e l+++lg+  p+v+l+lv+ ++ +
  gi|15668853|ref|NP_247656.1| 265 yfdsviaifaiillfvfnlvevndFKKIDWGTLILFGGALCLGGVIVKSGantfLSEKLIAILGNLTPIVLLFLVVTITII 345
                                   9999999999999999**************************************999999999764676888999999999 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS 261 lsafisnvavaalmapialgmapalg 286
                                   l++fisn+ ++ +++pi++g++ ++ 
  gi|15668853|ref|NP_247656.1| 346 LTNFISNTGLTGIIVPILFGVSLGIP 371
                                   ********************766433 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00041
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxx.xxxxxxx RF
                        CitMHS 116 lliplalaaniggaltpiGtpttraaarpglslpnlll............lalllvgl.lplvllf 168
                                   l+++++++a+    ++p+Gtp            pn ++            ++++l +l +++++l+
  gi|15668853|ref|NP_247656.1| 375 LILAVGMSASCSF-ILPVGTP------------PNAIVysegvkkeemmkIGMILSILsAAVITLY 427
                                   6667777777766.99*****............999999999999999996665555543333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2944.49
//
Query:       gi|15668854|ref|NP_247657.1|  [L=129]
Description: 30S ribosomal protein S8e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-37  128.9   3.6    1.7e-37  128.7   3.6    1.1  1  Ribosomal_S8e  Ribosomal protein S8e
  ------ inclusion threshold ------
      0.089   12.8   0.0       0.11   12.4   0.0    1.2  1  Ntox46         Bacterial toxin 46


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.7   3.6   1.9e-41   1.7e-37       4     137 .]       3     127 ..       1     127 [. 0.96

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 1.9e-41
                                   BXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEES..SHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEEEE CS
                 Ribosomal_S8e   4 srdskhkrkltGgkakllrkkrkielgrkekatklg..aervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlgVk 82 
                                    +++++ rk tGg  ++ rkkrk+e+gr++ +t+++  a ++k+vr+rgG+ k++ +r+  anv +pe++++kk+kI++V 
  gi|15668854|ref|NP_247657.1|   3 VWQGRSRRKPTGGLYRPARKKRKYEMGREPIETHVAeeAFKIKKVRTRGGNLKVKVVRTGFANVLDPETGTCKKVKIITVR 83 
                                   689********************************844557899************************************* PP

                                   CSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                 Ribosomal_S8e  83 knpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                   +n++n +yvr++v+tKgaiie++++            A+vtsrPgqdG vna+l+
  gi|15668854|ref|NP_247657.1|  84 ENKANIHYVRRNVITKGAIIETEIGL-----------AKVTSRPGQDGTVNAILI 127
                                   *************************9...........****************96 PP

>> Ntox46  Bacterial toxin 46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05      0.11      66     131 ..       3      68 ..       1      83 [. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                                   EEEEE-TT----SEEBS-TT--TGGGTS-SEEEETTTTEEEE-EEEEEEESS-EEEEEEEE---EE CS
                        Ntox46  66 lwqyqvpgarqgnwyslspdvvptelginplgtirkaetivpkvlnvyrstekvellrstaapvdd 131
                                   +wq ++   + g  y ++ +    e+g +p+ t  + e+ + k + +     kv+++r+  a v+d
  gi|15668854|ref|NP_247657.1|   3 VWQGRSRRKPTGGLYRPARKKRKYEMGREPIETHVAEEAFKIKKVRTRGGNLKVKVVRTGFANVLD 68 
                                   79**********************************************************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 829.81
//
Query:       gi|15668855|ref|NP_247658.1|  [L=338]
Description: pyruvate formate lyase-activating enzyme PflX [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-11   43.4   0.5    4.4e-11   43.4   0.5    2.6  3  Radical_SAM   Radical SAM superfamily
    2.5e-06   27.8   0.2    2.5e-06   27.8   0.2    1.8  2  Fer4_12       4Fe-4S single cluster domain
    8.9e-06   25.8   0.2    8.9e-06   25.8   0.2    2.0  2  Fer4_14       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.046   13.9   0.0       0.09   13.0   0.0    1.5  1  Rad21_Rec8_N  N terminus of Rad21 / Rec8 like protein


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   1.6       2.9   1.3e+04      10      15 ..      79      84 ..      76      93 .. 0.78
   2 !   43.4   0.5   9.9e-15   4.4e-11       2     166 ..     124     284 ..     123     285 .. 0.81
   3 ?    1.1   0.0       0.1   4.7e+02     121     142 ..     312     333 ..     292     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.9
                                  --TTTS CS
                                  xxxxxx RF
                   Radical_SAM 10 rCsfCa 15
                                  +C+fC 
  gi|15668855|ref|NP_247658.1| 79 NCHFCE 84
                                  788885 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 9.9e-15
                                   EEESEESS--TTTSCCTT...HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                   xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpet...vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgi 78 
                                   +++ gCn++C+fC+++       +   + +  + + +e +k++k++++  k+v ++gg+p+ +   + +++ +  +   +i
  gi|15668855|ref|NP_247658.1| 124 IFFCGCNFKCVFCQNWDIsqvYFDKTIPNHCIPYNPKEMAKIIKHKRDySKNVNFVGGDPTPHLLSILKTLSYLDK---NI 201
                                   5788************998875555566666677777777888766667*************88666666666665...** PP

                                   EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGende 158
                                    ++  +n +l   e + +l+    d++  + + +++e + +++   ++ f+ ++++  ++++   + v++r++++p+  d 
  gi|15668855|ref|NP_247658.1| 202 PVVWNSNMYLT-VEGMHLLKGVV-DVYLTDFKFGNNE-CGERLSkVKNYFDIIKRNHLLIKDE--E-VIIRHLVMPNHLDC 276
                                   **********8.********955.*************.5555554888888888888888888..4.88******998887 PP

                                   HHHHHHHH CS
                                   xxxxxxxx RF
                   Radical_SAM 159 eleellel 166
                                     e+++++
  gi|15668855|ref|NP_247658.1| 277 CTEKIFDF 284
                                   77777776 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.1
                                   HTCTSHHHHHHHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 121 mnrghtfeevlealeklreagi 142
                                   +nr+ t+ee+ +ale++ ++++
  gi|15668855|ref|NP_247658.1| 312 INRRLTYEEIEKALELAEKYNL 333
                                   458899*********9998876 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.6       3.5   1.6e+04      14      27 ..      82      93 ..      76      97 .. 0.70
   2 !   27.8   0.2   5.6e-10   2.5e-06       9      98 ..     123     214 ..     113     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.5
                       Fer4_12 14 gCnlsCkgCfnket 27
                                   C+++C    n+et
  gi|15668855|ref|NP_247658.1| 82 FCEHRCYV--NRET 93
                                  58888865..5555 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 5.6e-10
                       Fer4_12   9 slfvsgCnlsCkgCfnketw.......sfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkee 82 
                                   ++f+ gCn++C +C n ++         +++  +++ + +++ii++   ++ + + ++GG+P    +   +l+ + ++ ++
  gi|15668855|ref|NP_247658.1| 123 TIFFCGCNFKCVFCQNWDISqvyfdktIPNHCIPYNPKEMAKIIKHK-RDYSKNVNFVGGDPTP--HLLSILKTLSYLDKN 200
                                   79**************9999444444334466677888889999775.788899********99..777777777777777 PP

                       Fer4_12  83 kpekdiwlytgytlee 98 
                                    p  ++w ++ y  +e
  gi|15668855|ref|NP_247658.1| 201 IP--VVWNSNMYLTVE 214
                                   76..889888887665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.5      0.92   4.1e+03       7      20 ..      82     103 ..      76     117 .. 0.63
   2 !   25.8   0.2     2e-09   8.9e-06       2      95 ..     125     215 ..     124     225 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.92
                       Fer4_14   7 gCnlsCk........gCdnket 20 
                                    C++ C         +C  ke+
  gi|15668855|ref|NP_247658.1|  82 FCEHRCYvnretergFCRIKES 103
                                   4777776666666666654444 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 2e-09
                       Fer4_14   2 fvrlsgCnlsCkgCd....nketwks...elgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlk 75 
                                   f  + gCn++C++C      +  +++   +   p++ +++ +i+  ++k++++++ + ++GG+P  +    ++lk +++l 
  gi|15668855|ref|NP_247658.1| 125 F--FCGCNFKCVFCQnwdiSQVYFDKtipNHCIPYNPKEMAKII--KHKRDYSKN-VNFVGGDPTPH--LLSILKTLSYLD 198
                                   4..48**********66553333333665555677777888999..455555455.99******955..666666666666 PP

                       Fer4_14  76 eeypekkiwletngtleiel 95 
                                   +++   ++  ++n  l +e 
  gi|15668855|ref|NP_247658.1| 199 KNI---PVVWNSNMYLTVEG 215
                                   666...78788887777665 PP

>> Rad21_Rec8_N  N terminus of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     2e-05      0.09      50      94 ..     208     253 ..     188     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                  Rad21_Rec8_N  50 plaLrlsg.qLllGvvriyskkvkyllsDceealekikkafksike 94 
                                   ++ L + g +Ll Gvv +y +  k+  ++c e l+k+k+ f  ik+
  gi|15668855|ref|NP_247658.1| 208 NMYLTVEGmHLLKGVVDVYLTDFKFGNNECGERLSKVKNYFDIIKR 253
                                   5666666647*****************************9997763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2098.94
//
Query:       gi|15668856|ref|NP_247659.1|  [L=391]
Description: hypothetical protein MJ_0675 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.3e-103  345.5   0.1   1.8e-103  345.0   0.1    1.2  1  DUF43            Branched-chain polyamine synthase A C-termin
    2.5e-05   24.0   0.0    4.7e-05   23.1   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00014   21.7   0.0    0.00024   21.0   0.0    1.4  1  N6-adenineMlase  Probable N6-adenine methyltransferase
     0.0042   16.9   0.8       0.16   11.9   0.4    2.5  2  RuvB_C           RuvB C-terminal winged helix domain
     0.0089   16.7   0.0      0.018   15.7   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
     0.0095   15.5   0.0      0.016   14.7   0.0    1.3  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.024   14.5   0.2      0.069   13.1   0.2    1.7  1  MarR             MarR family
      0.063   13.9   0.0        3.7    8.3   0.0    2.3  2  RPA_C            Replication protein A C terminal
      0.093   13.0   3.6       0.26   11.5   3.6    1.8  1  DUF2072          Zn-ribbon containing protein
       0.62   10.2   3.2        1.5    9.0   0.1    2.5  3  FUR              Ferric uptake regulator family
       0.62   10.2   2.6        2.4    8.3   1.3    2.2  2  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> DUF43  Branched-chain polyamine synthase A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.0   0.1  1.1e-106  1.8e-103       1     242 [.     129     378 ..     129     379 .. 0.99

  Alignments for each domain:
  == domain 1  score: 345.0 bits;  conditional E-value: 1.1e-106
                                   HHHHHHHHHHTT-----GGGT---B-HHHHHHHHHHHHHTT-STT-EEEEES-TT-HHHHHHHHT--SEEEEE-S-HHHHH CS
                         DUF43   1 dllekfreiakdRPeaieeyDqgfvtpettvaRvallyerGDLegkeilvlGdDDLtslalaLtglpkkvvvvDiDeRlik 81 
                                   d+l+k+r++ak+RP +++++Dq+f+tpet+++R+al+yerGDLegk+il++GdDDLtsl++aLt+++++++vvDiDeR++k
  gi|15668856|ref|NP_247659.1| 129 DILNKVRVWAKRRPLVDTTIDQSFATPETSTYRAALMYERGDLEGKRILFVGDDDLTSLPTALTNMAEEIAVVDIDERILK 209
                                   89******************************************************************************* PP

                                   HHHHHHHHHT--EEEE---TTS---TTTSS-BSEEEE---SSHHHHHHHHHHHHHTB-STT-EEEEEE-TTT--HHHHHHH CS
                         DUF43  82 fiervakelglkieaivyDlrkplpeelkekFdvfitDPpetvealkaFlgRGiaaLkgegcagYlgltrressldkWkei 162
                                   +ie++++++g+ki++i++Dlr+plp++lke+Fdv++tDPp+tv++lk+Fl+RGi+aL++eg ++Yl++++++  +d+W +i
  gi|15668856|ref|NP_247659.1| 210 LIEKFSQKEGVKIKTIKHDLRNPLPQDLKERFDVISTDPPYTVDGLKLFLSRGIEALGKEG-IAYLSYSHKP--IDEWLSI 287
                                   *************************************************************.**********..******* PP

                                   HHHHHTS--EEEEEEEEEEEB---S-GGGSHHHHHSSS--......--SS---EEEEEEEE--T....T-.---SSS--S. CS
                         DUF43 163 qklllemgvvitdlirnFneYenweykeetraikllpvkk......kpekiwyksalfrietlk....gk.rkveeevkkv 232
                                   qk++++mg+vi++li+nFn+Ye++e++++t++i++l+ k+      ++eki++ +++++i+++k    gk +kv+eevkkv
  gi|15668856|ref|NP_247659.1| 288 QKAITNMGFVISELIPNFNYYEGSEIIANTTFIARLVGKNlkinigDTEKIYTGLVKPVIRYYKclkcGKiHKVGEEVKKV 368
                                   *****************************************************************999777********** PP

                                   S-S--XXXXX CS
                         DUF43 233 edlykdeess 242
                                   edl+++++++
  gi|15668856|ref|NP_247659.1| 369 EDLVCECGGK 378
                                   *******997 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.9e-08   4.7e-05      59     152 ..     190     276 ..     188     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.9e-08
                                   HHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--SSSTTCH.HHHHHHHHHT CS
                 Cons_hypoth95  59 AlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDPPyakellieevlelleek 139
                                   Al   a+++ +v+ d++ +k++++  ++ +++  ++++k+d  + l++    ke+fd++  DPPy  + l +  l+     
  gi|15668856|ref|NP_247659.1| 190 ALTNMAEEIAVVDIDERILKLIEKFSQKEGVK--IKTIKHDLRNPLPQD--LKERFDVISTDPPYTVDGL-KLFLSRGI-- 263
                                   666779999***************99999966..8************99..4679***********9976.44444332.. PP

                                   T-EEEEEEEEEEE CS
                 Cons_hypoth95 140 kllkenalvvvet 152
                                   ++l ++++ ++ +
  gi|15668856|ref|NP_247659.1| 264 EALGKEGIAYLSY 276
                                   4666777666666 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.4e-07   0.00024      42     116 ..     190     268 ..     149     333 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
               N6-adenineMlase  42 alkkekkkekvlLleiDkrFealyge........ekfvfYdlnnpeelpeelkgkfdviviDPPFlseeclkklaktakll 114
                                   al+++   e++ + +iD+r  +l+++         k++  dl+np+  p++lk+ fdvi +DPP+ ++ +   l++ ++ l
  gi|15668856|ref|NP_247659.1| 190 ALTNMA--EEIAVVDIDERILKLIEKfsqkegvkIKTIKHDLRNPL--PQDLKERFDVISTDPPYTVDGLKLFLSRGIEAL 266
                                   444444..8999*******66666666666666745999*****95..599**************8877766666555555 PP

               N6-adenineMlase 115 lk 116
                                    k
  gi|15668856|ref|NP_247659.1| 267 GK 268
                                   55 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.4   9.8e-05      0.16      14      70 ..      43      98 ..      38     100 .. 0.88
   2 ?    2.8   0.0     0.067   1.1e+02       7      33 ..     203     229 ..     200     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.8e-05
                                  HHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEEEE-HHHHHH CS
                        RuvB_C 14 llkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrGRilTkkglky 70
                                  ++   ++ +p++ k +a+ ++++   +  ++  +L +e+ ++rt+rG +lT+ g+++
  gi|15668856|ref|NP_247659.1| 43 IIRVIYRHQPISTKKIAQKTRLPLPIVA-KVRTILEREKILKRTERGAELTDLGKEF 98
                                  45556899**************987766.8999********************9986 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.067
                                   HHHHHHHHHHHT.TT--B-HHHHHHHT CS
                        RuvB_C   7 ldikyLkllkekfkggpvglktlaail 33 
                                   +d ++Lkl+ +  +++ v +kt+ + l
  gi|15668856|ref|NP_247659.1| 203 IDERILKLIEKFSQKEGVKIKTIKHDL 229
                                   7999*****754455569999998765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05     0.018      21      69 ..     195     245 ..     183     265 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                                   SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG.BSS.STTTEEEEE CS
               Methyltransf_25  21 kakvtgvDiseemleaareraeeeglnvefvqgdaed.lpf.edgsfDlvv 69 
                                   ++++  vDi+e+ l+ +++  ++eg++++ +++d+++ lp+  +++fD++ 
  gi|15668856|ref|NP_247659.1| 195 AEEIAVVDIDERILKLIEKFSQKEGVKIKTIKHDLRNpLPQdLKERFDVIS 245
                                   58999******************************98788636779**996 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     1e-05     0.016      51     109 ..     191     252 ..     184     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                                   HHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST...TS-EEEEEE---STT CS
                           MTS  51 kespeaevtlvdvdarAlesakenleanklevevvasdvleeve...ekkfdlivsNPPfha 109
                                     +   e+ +vd+d r l++ ++  ++++++++++++d+ + ++   +++fd+i + PP+  
  gi|15668856|ref|NP_247659.1| 191 LTNMAEEIAVVDIDERILKLIEKFSQKEGVKIKTIKHDLRNPLPqdlKERFDVISTDPPYTV 252
                                   45556679******************************99988754559**********865 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   4.3e-05     0.069       8      50 ..      43      85 ..      42      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-05
                                  HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                  i+r +y+++p+s +++a k  +  + v +v + Le++  ++R+
  gi|15668856|ref|NP_247659.1| 43 IIRVIYRHQPISTKKIAQKTRLPLPIVAKVRTILEREKILKRT 85
                                  8899********************************9999987 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.075   1.2e+02      47      91 ..      33      76 ..       8      82 .. 0.74
   2 ?    8.3   0.0    0.0023       3.7      47      81 ..     200     233 ..     180     247 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.075
                                  SXHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHH CS
                         RPA_C 47 ltalaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeL 91
                                  + + ++ v ++i+  + + + ++ + iaqk+rl+   v ++   L
  gi|15668856|ref|NP_247659.1| 33 IAEGKRAVEDIIRV-IYRHQPISTKKIAQKTRLPLPIVAKVRTIL 76
                                  66667778888888.888899*************99888876555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0023
                                   SXHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXH CS
                         RPA_C  47 ltalaqqvlnlikqspeseeGvhvdeiaqklrlsv 81 
                                   + + ++++l li + + ++eGv+++ i+  lr + 
  gi|15668856|ref|NP_247659.1| 200 VVDIDERILKLIEK-FSQKEGVKIKTIKHDLRNPL 233
                                   5677899******9.****************7664 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.6   0.00016      0.26       3      39 ..     351     389 ..     349     391 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                       DUF2072   3 kCtkCekvfedgsk..eilkGCpsCGgkkFlyvkeeekk 39 
                                   kC kC+k+ + g++  ++ +   +CGgkkF+ +k e+ k
  gi|15668856|ref|NP_247659.1| 351 KCLKCGKIHKVGEEvkKVEDLVCECGGKKFKMIKREKLK 389
                                   9********99986225778899***********99866 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.6   9.2e+03      53      62 ..      77      86 ..      70     124 .. 0.58
   2 ?    0.8   0.1      0.31     5e+02      92     116 ..     203     226 ..     194     230 .. 0.80
   3 ?    9.0   0.1   0.00089       1.5      60     109 ..     329     377 ..     323     386 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.6
                                  HHTTSEEEEE CS
                           FUR 53 eeaglvkele 62
                                  e+++++k++e
  gi|15668856|ref|NP_247659.1| 77 EREKILKRTE 86
                                  4444444443 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.31
                                   E--HHHHHHHHHHHHHTT-EEEEEE CS
                           FUR  92 fkddeiekiqeeiaekegfklvshr 116
                                   + d+ i k+ e++++keg+k+++++
  gi|15668856|ref|NP_247659.1| 203 I-DERILKLIEKFSQKEGVKIKTIK 226
                                   4.456999999*********99875 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00089
                                   EEEETTSEEEEEESSSSSEEEEEETTT--EEEE--HHHHHHHHHHHHHTT CS
                           FUR  60 elefedgesryelakkehhdhlicekCgkviefkddeiekiqeeiaekeg 109
                                   ++++ d+e+ y    k  +    c kCgk++++ ++ ++k+++ ++e  g
  gi|15668856|ref|NP_247659.1| 329 KINIGDTEKIYTGLVKPVIRYYKCLKCGKIHKVGEE-VKKVEDLVCECGG 377
                                   57888999999999999999************9876.8888888876544 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.48   7.8e+02      25      34 ..     109     118 ..      95     122 .. 0.68
   2 ?    8.3   1.3    0.0015       2.4       6      34 ..     350     377 ..     349     383 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.48
                   Zn-ribbon_8  25 pltaCPeCgs 34 
                                   +  +C++C++
  gi|15668856|ref|NP_247659.1| 109 KSLTCKTCNG 118
                                   4456999976 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0015
                   Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgs 34 
                                   Y+C +Cg+ + v  ++++ ++ +C eCg+
  gi|15668856|ref|NP_247659.1| 350 YKCLKCGKIHKVGEEVKKVEDLVC-ECGG 377
                                   9*********98888887778889.8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2461.30
//
Query:       gi|15668857|ref|NP_247660.1|  [L=335]
Description: hydrogenase expression/formation protein HypE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-35  122.0   0.6    3.8e-35  121.3   0.6    1.3  1  AIRS_C    AIR synthase related protein, C-terminal domain
    2.5e-19   69.7   0.1    5.8e-19   68.5   0.1    1.6  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.3   0.6   4.2e-39   3.8e-35       1     153 [.     163     313 ..     163     315 .. 0.96

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 4.2e-39
                                   STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHH CS
                        AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemap 81 
                                   ++Gd++i+ g++G +g++++l+r+++++e+       ++dv+  ++li+ ++++     +++a++D T+GGL+ al+ema+
  gi|15668857|ref|NP_247660.1| 163 QEGDAIIVSGNIGEHGLAILLSREGFDFETNI-----KSDVAPINKLIERVLEEGI---QINAMKDPTRGGLADALNEMAE 235
                                   69***************************964.....************9999888...7********************* PP

                                   TTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTC.CCEEEEEEEEESSSEEE CS
                        AIRS_C  82 asgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeegl.peaavIGevtakeelsv 153
                                   +s++g++i +dk+pi de++     ++l++l ++n+G++++av++e+a+++l+il+e+ l ++a++IG +t+++++ +
  gi|15668857|ref|NP_247660.1| 236 KSNIGITIFEDKIPISDEVQsicdiLGLDPLTIANEGKVVMAVKKEDAERCLEILREHPLgKNAEIIGYATKEHKGVI 313
                                   *************************************************************99*********987665 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.1   6.5e-23   5.8e-19       1      94 []      41     151 ..      41     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 6.5e-23
                                   SSSE........EEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHH CS
                          AIRS   1 dDaa........vvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleevvrgla 63 
                                   dD a        +v+t+d       v+p+ f    iG++av ++++Dla+mGA+Plal+lsl++p      +le++v++++
  gi|15668857|ref|NP_247660.1|  41 DDSAtipigdkeIVFTVD----GHTVKPIFFpggdIGRLAVSGTVNDLAVMGAKPLALSLSLIIPegfnleDLEKIVKSIN 117
                                   677755555555699***....7788898889999********************************************** PP

                                   HHHHHTT-EEEEEEEEEESS...EEEEEEEEEEE CS
                          AIRS  64 eaaeelgvplvgGdtsfsne...ptisvtavGlv 94 
                                   e  +e++v++++Gdt++s++   ++is++ +G+v
  gi|15668857|ref|NP_247660.1| 118 ETSKEAEVAIITGDTKVSDGvddIIISTAGIGIV 151
                                   *****************999999*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2378.45
//
Query:       gi|15668858|ref|NP_247661.1|  [L=330]
Description: pyridoxal biosynthesis lyase PdxS [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.9e-101  337.5   8.2    3.1e-97  324.4   7.1    2.3  3  SOR_SNZ         SOR/SNZ family
    1.2e-08   34.6   6.2    1.7e-05   24.3   0.0    2.7  3  ThiG            Thiazole biosynthesis protein ThiG
    0.00039   19.9   7.0      0.032   13.6   0.0    2.6  3  NMO             Nitronate monooxygenase
    0.00048   19.4   1.0       0.18   10.9   0.0    2.5  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
    0.00055   19.6   0.1     0.0012   18.5   0.1    1.6  1  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
    0.00096   18.3   0.2        1.5    7.8   0.0    2.6  2  Dus             Dihydrouridine synthase (Dus)
    0.00097   19.2   0.1      0.072   13.2   0.0    2.7  2  TetR_C_27       Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.029   14.9   0.0      0.073   13.6   0.0    1.6  1  Peptidase_S66C  LD-carboxypeptidase C-terminal domain
      0.054   12.9   1.8        1.4    8.3   0.1    2.9  3  His_biosynth    Histidine biosynthesis protein
       0.25   11.3   2.0         23    5.1   0.1    2.9  3  DUF438          Family of unknown function (DUF438)


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.4   7.1  1.7e-100   3.1e-97       3     202 ..       7     207 ..       5     212 .. 0.97
   2 !   12.3   0.0   6.1e-05      0.11     177     207 .]     218     248 ..     207     248 .. 0.86
   3 ?   -4.1   0.0       6.2   1.1e+04     124     134 ..     304     314 ..     300     316 .. 0.81

  Alignments for each domain:
  == domain 1  score: 324.4 bits;  conditional E-value: 1.7e-100
                                   HHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEETT-HH CS
                       SOR_SNZ   3 kvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvriGhfv 83 
                                    +k+g+a+m+k+Gv+mdv+n+eqa+iaeeaGavavmalervpadir++ggvarmsdp+li+ei++avsipvmak+riGh++
  gi|15668858|ref|NP_247661.1|   7 LLKKGFAKMVKHGVVMDVTNVEQAQIAEEAGAVAVMALERVPADIRAAGGVARMSDPALIEEIMDAVSIPVMAKCRIGHTT 87 
                                   579****************************************************************************** PP

                                   HHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHHHHHHHHHH CS
                       SOR_SNZ  84 eaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveavrhvrkike 164
                                   ea +lea+gvd+iDesevlt+ad  +hi kkkf+vpfvcGarnlgea+rri eGaamirtkGeagtG++veavrh+r ++e
  gi|15668858|ref|NP_247661.1|  88 EALVLEAIGVDMIDESEVLTQADPFFHIYKKKFNVPFVCGARNLGEAVRRIWEGAAMIRTKGEAGTGNIVEAVRHMRLMNE 168
                                   ********************************************************************************* PP

                                   HHHHHTTS-HHHHHHHHHHHHGGG.HHHHHHHHHTTS-S CS
                       SOR_SNZ 165 eirklkslseeelvalakelkapl.elvkevaelgrlpv 202
                                    i++l+++++ee++ +ak ++  + el k+v+e   lp 
  gi|15668858|ref|NP_247661.1| 169 AIAQLQRMTDEEVYGVAKFYANRYaELAKTVREGMGLPA 207
                                   ******************999988588888898888886 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6.1e-05
                                   HHHHHHHHHGGGHHHHHHHHHTTS-S---T. CS
                       SOR_SNZ 177 lvalakelkaplelvkevaelgrlpvvnfaa 207
                                    ++la+ ++  +e++ ev++lgrlpvvnfaa
  gi|15668858|ref|NP_247661.1| 218 GFTLAEIIDGLYEVLLEVKKLGRLPVVNFAA 248
                                   56788889999******************98 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 6.2
                                   ESSHHHHHHHH CS
                       SOR_SNZ 124 arnlgealrri 134
                                   ++nlgea++ i
  gi|15668858|ref|NP_247661.1| 304 SKNLGEAMKGI 314
                                   58999999876 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   3.0   0.00017       0.3     119     201 ..       7     100 ..       1     115 [. 0.71
   2 ?   -1.7   0.0       0.8   1.4e+03      70      89 ..     151     170 ..     137     199 .. 0.77
   3 !   24.3   0.0   9.4e-09   1.7e-05     175     224 ..     240     291 ..     227     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                                   HHHTT-EEEEE..E-S-HH...HHHHHHHTT-SEBEEB...SSSTTS----S...-HHHHHHHHHH-SS-BEEES---SHH CS
                          ThiG 119 LvkeGFevlpY..vsdDlv...larrleevGcaavmPl...aapiGsglGll...nkealkiiieeakvPvivDAGigsps 188
                                   L+k+GF+ ++   v  D+     a+  ee+G+ avm l    a i ++ G++   +++ ++ i++ +++Pv+    ig+++
  gi|15668858|ref|NP_247661.1|   7 LLKKGFAKMVKhgVVMDVTnveQAQIAEEAGAVAVMALervPADIRAAGGVArmsDPALIEEIMDAVSIPVMAKCRIGHTT 87 
                                   5566666554312333333111567789********97333588988888752226789********************** PP

                                   HHHHHHHTT-SEE CS
                          ThiG 189 daaqamelGadav 201
                                   +a     +G+d +
  gi|15668858|ref|NP_247661.1|  88 EALVLEAIGVDMI 100
                                   *998888899865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.8
                                   TT-SSHHHHHHHHHHHHHTT CS
                          ThiG  70 aGaktaeeAvriarlarevl 89 
                                   aG+ +  eAvr  rl  e++
  gi|15668858|ref|NP_247661.1| 151 AGTGNIVEAVRHMRLMNEAI 170
                                   67777788888888877766 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 9.4e-09
                                   SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHH CS
                          ThiG 175 kvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklav 224
                                   ++Pv+  A  G+ +p daa  m+lG d+v++ + + ++++p + Ara+  a+
  gi|15668858|ref|NP_247661.1| 240 RLPVVNFAagGVATPADAALMMQLGSDGVFVGSGIFKSENPLERARAIVEAT 291
                                   67877543349************************************98886 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   2.9    0.0013       2.3     140     200 ..      21      81 ..       9     100 .. 0.69
   2 ?   -2.3   0.0       1.2   2.2e+03      43      73 ..     159     190 ..     148     206 .. 0.66
   3 !   13.6   0.0   1.8e-05     0.032     179     263 ..     226     314 ..     216     328 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0013
                           NMO 140 iptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaG 200
                                   ++ ++ v++a+++e++Ga a+ +        +    v+  +  aL+++++dav+iPv+A  
  gi|15668858|ref|NP_247661.1|  21 VMDVTNVEQAQIAEEAGAVAVMALERVPADIRAAGGVARMSDPALIEEIMDAVSIPVMAKC 81 
                                   55678888888888888777766444333333333344456789***************65 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                           NMO  43 gyltaDrlakeirkvkaltdk.Pfgvnlflpk 73 
                                   ++     ++++i++++++td+  +gv  f+ +
  gi|15668858|ref|NP_247661.1| 159 AVRHMRLMNEAIAQLQRMTDEeVYGVAKFYAN 190
                                   55555567788888888888766777766654 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 1.8e-05
                           NMO 179 kglfaLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrfLltke..sdakdahkkklleaklddteltsav 255
                                    gl +++ +v++   +Pv+  AaGG+ +  + a ++ lG  gv +g+     ++    a++++++ +   k d++  +s+ 
  gi|15668858|ref|NP_247661.1| 226 DGLYEVLLEVKKLGRLPVVnfAAGGVATPADAALMMQLGSDGVFVGSGIFKSENplERARAIVEATYNYDKPDIVAEVSKN 306
                                   678888888999999***877*************************98765544222455666666666666666555555 PP

                           NMO 256 sGrpaRal 263
                                    G  ++++
  gi|15668858|ref|NP_247661.1| 307 LGEAMKGI 314
                                   55555555 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.3    0.0023       4.1      96     180 ..      21     110 ..       6     121 .. 0.70
   2 !   10.9   0.0    0.0001      0.18     137     181 ..     235     279 ..     224     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0023
                                   EEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-......SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SEE CS
                          NanE  96 maDistleeglvakklGvdivGttlsGytkeeek.....aepDfalvkalsea.glkviaeGrintPekakkaieiGvdav 170
                                   + D+ ++e++ +a+++G+  v + l     + +         D al++++++a  + v+a  ri    +a     iGvd++
  gi|15668858|ref|NP_247661.1|  21 VMDVTNVEQAQIAEEAGAVAVMA-LERVPADIRAaggvaRMSDPALIEEIMDAvSIPVMAKCRIGHTTEALVLEAIGVDMI 100
                                   45788888888888888765543.333333333223344678999***999884688********99*****99****999 PP

                                   EE-HHHH-HH CS
                          NanE 171 vvGsaitrle 180
                                        +t+ +
  gi|15668858|ref|NP_247661.1| 101 DESEVLTQAD 110
                                   8777777665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0001
                                   HHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHH CS
                          NanE 137 vkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrlee 181
                                   vk+l    +   a G + tP+ a+ ++++G d v vGs i + e+
  gi|15668858|ref|NP_247661.1| 235 VKKLGRLPVVNFAAGGVATPADAALMMQLGSDGVFVGSGIFKSEN 279
                                   56666666777899************************9987765 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   6.7e-07    0.0012      79     225 .]     134     287 ..     128     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.7e-07
                                   TCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCC CS
                     OMPdecase  79 gsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqe 159
                                   ++ ri e+a ++   + aG++ + ++++ ++ ++   + +l +m+ ++ + +++  y+   +e a+   +    mG+ a  
  gi|15668858|ref|NP_247661.1| 134 AVRRIWEGAAMIRTKGEAGTGNIVEAVRHMRLMN-EAIAQLQRMTDEEVYGVAK-FYANRYAELAKTVRE---GMGLPATV 209
                                   467999***************************6.9******************.566666666666553...58888777 PP

                                   HTH.......HHHHHTTCSCEEEHHHTT.....EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHHH CS
                     OMPdecase 160 tln.......ateedaddfihltpgigl.....eqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaery 225
                                    +n       ++ e+ d +  +   ++       +   ++g+      +l+ + g+d + vG gI+k+++p e a+++
  gi|15668858|ref|NP_247661.1| 210 LENepiyegfTLAEIIDGLYEVLLEVKKlgrlpVVNFAAGGVATPADAALMMQLGSDGVFVGSGIFKSENPLERARAI 287
                                   777657777544444344444444443366668777788888888888999999********************9985 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00083       1.5      98     134 ..      54      86 ..      47     100 .. 0.76
   2 !    7.7   0.0   0.00091       1.6     181     224 ..     240     282 ..     228     324 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00083
                                   EEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESS CS
                           Dus  98 gaGaaLlrkpdlvaqivkavvkaveiPvtvkirigid 134
                                    +G a + +p+l+    +++ +av+iPv +k rig  
  gi|15668858|ref|NP_247661.1|  54 AGGVARMSDPALI----EEIMDAVSIPVMAKCRIGHT 86 
                                   5666667777665....5667899**********976 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00091
                                   H-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHH CS
                           Dus 181 avsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfa 224
                                   +++++ +a G++ ++ da  +++  G dgv +g g  +  + ++
  gi|15668858|ref|NP_247661.1| 240 RLPVVNFAAGGVATPADAALMMQL-GSDGVFVGSGIFKSENPLE 282
                                   355666899*********999998.********99865433333 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.067   1.2e+02      17      60 ..     160     203 ..     154     205 .. 0.88
   2 !   13.2   0.0     4e-05     0.072      61      97 ..     271     307 ..     266     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.067
                                   HHHHHH-HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH CS
                     TetR_C_27  17 rrkarddpelFatyvvlieeelevvekhieeleeqlaeIireGv 60 
                                   +r++r  +e  a ++++++ee+  v+k+ ++  + la+ +reG+
  gi|15668858|ref|NP_247661.1| 160 VRHMRLMNEAIAQLQRMTDEEVYGVAKFYANRYAELAKTVREGM 203
                                   566777788899999****************************8 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4e-05
                                   HCT-STT--HHHHHHHHHHHSGGGTSHHHHHHHGGG- CS
                     TetR_C_27  61 aaGeFkaadpeaaaravfdatarfhhPalaaewsdpe 97 
                                    +G Fk+++p + ara+++at ++ +P ++ae s++ 
  gi|15668858|ref|NP_247661.1| 271 GSGIFKSENPLERARAIVEATYNYDKPDIVAEVSKNL 307
                                   689*****************************99875 PP

>> Peptidase_S66C  LD-carboxypeptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.1e-05     0.073      47     116 ..      24      92 ..      17      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                                   HHHHCTSTTGGG--EEEEEE--..G......CC...---HHHHHHHHHT-GGGTTS-EEEEESESSSBS---E CS
                Peptidase_S66C  47 LtqlkeagvldkvkGivlGrftkpeek...eeeeekeeykealeevlaeiledlkiPvlynldiGHtspnltl 116
                                   +t+ ++a++ +++ ++++   ++++ +   +  +++ +   ++ee++    +   iPv++++ iGHt++ l+l
  gi|15668858|ref|NP_247661.1|  24 VTNVEQAQIAEEAGAVAVMALERVPADiraAGGVARMSDPALIEEIM----DAVSIPVMAKCRIGHTTEALVL 92 
                                   57788899999999999998888833334556667777778888887....5889************998876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.071   1.3e+02      50      77 ..      50      78 ..       8     107 .. 0.63
   2 ?    8.3   0.1    0.0008       1.4     186     226 ..     235     277 ..     228     280 .. 0.78
   3 ?    3.5   0.1     0.024        43      76     132 ..     268     318 ..     266     329 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.071
                                  EHHHHC.TTHHHHHHHHHHHHHH-SSEEE CS
                  His_biosynth 50 Dldaak.egreanldlveeiaeevfipvq 77
                                  D+ aa    r  + +l+eei+++v+ipv+
  gi|15668858|ref|NP_247661.1| 50 DIRAAGgVARMSDPALIEEIMDAVSIPVM 78
                                  44444322233333455555555555554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0008
                                   HHHHHSSEE..EEESS--SHHHHHHHHHTTCSEEEESHHHHTT CS
                  His_biosynth 186 laeavkipv..iasGGvgsledlkelksegvdavivgsalyeg 226
                                   +++  ++pv   a+GGv++++d + + + g d+v vgs +++ 
  gi|15668858|ref|NP_247661.1| 235 VKKLGRLPVvnFAAGGVATPADAALMMQLGSDGVFVGSGIFKS 277
                                   55555555522599***********************988876 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.024
                                   EEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE CS
                  His_biosynth  76 vqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr 132
                                   v vG+GI + e   + le+ a+ ++ +t   ++p+++ e++++ g+   + +iD+ +
  gi|15668858|ref|NP_247661.1| 268 VFVGSGIFKSE---NPLER-ARAIVEATYNYDKPDIVAEVSKNLGE--AMKGIDITQ 318
                                   67999999988...78888.899999******************99..888888766 PP

>> DUF438  Family of unknown function (DUF438)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.019        34      15      44 ..       6      35 ..       2      50 .. 0.84
   2 ?   -3.5   0.0       5.7     1e+04      37      50 ..     211     224 ..     209     230 .. 0.80
   3 ?    5.1   0.1     0.013        23      13      38 ..     299     324 ..     295     325 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.019
                        DUF438 15 eevkeefkellkevsaeEIsqaEqeLieeG 44
                                  + +k+ f++++k+  + +++++Eq+ i+e 
  gi|15668858|ref|NP_247661.1|  6 DLLKKGFAKMVKHGVVMDVTNVEQAQIAEE 35
                                  56899*******************999775 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.7
                        DUF438  37 EqeLieeGipveei 50 
                                   E+e i eG++  ei
  gi|15668858|ref|NP_247661.1| 211 ENEPIYEGFTLAEI 224
                                   77778899998887 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.013
                        DUF438  13 sleevkeefkellkevsaeEIsqaEq 38 
                                    ++ev +++ e +k+++ + Is+aE+
  gi|15668858|ref|NP_247661.1| 299 IVAEVSKNLGEAMKGIDITQISEAEK 324
                                   5789********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2064.15
//
Query:       gi|15668859|ref|NP_247662.1|  [L=320]
Description: hypothetical protein MJ_0678 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-30  106.2  16.5    1.4e-30  106.2  16.5    1.8  2  DUF389    Domain of unknown function (DUF389)
  ------ inclusion threshold ------
       0.11   12.9   3.8       0.24   11.7   1.4    2.6  2  CRCB      CrcB-like protein, Camphor Resistance (CrcB)


Domain annotation for each model (and alignments):
>> DUF389  Domain of unknown function (DUF389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2  16.5   1.5e-34   1.4e-30       1     142 []     138     273 ..     138     273 .. 0.98
   2 ?   -3.5   0.0       1.1   9.9e+03      36      80 ..     305     313 ..     278     317 .. 0.54

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 1.5e-34
                        DUF389   1 MlisPlmgpilaiafglvigdrkllrrglknlliglllallvgflfglllplkvlgeeelptsemlsrtepnlvdllvAla 81 
                                   M+i+Pl+gp +a+++++++ d kl+ +++k+l++ l++++++++++g  lp++      l ++++ sr++++++++++Al 
  gi|15668859|ref|NP_247662.1| 138 MIIAPLLGPNIALSLSITVADYKLALKSIKTLIAELIFVIILSMIAGHYLPIS------LDNPQIHSRITLDFWSIIIALS 212
                                   ***********************************************877885......889******************* PP

                        DUF389  82 sGaagalallsgnssslvGvaIaaaLlPPavnaGlglalgewalalgslllllvNivgIvl 142
                                   +G+ag l+++s+ ss  vGv+Ia+aLlPP++++Gl++++g ++  + +l+l+l+N+++I+l
  gi|15668859|ref|NP_247662.1| 213 AGIAGSLSTVSNISSIAVGVMIAIALLPPLAVFGLLIGAGYVEQSFSALILFLINMIAINL 273
                                   ***********************************************************86 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.1
                        DUF389  36 lllallvgflfglllplkvlgeeelptsemlsrtepnlvdllvAl 80 
                                   l                                    +v l++A+
  gi|15668859|ref|NP_247662.1| 305 L------------------------------------WVTLFIAI 313
                                   2....................................33344433 PP

>> CRCB  CrcB-like protein, Camphor Resistance (CrcB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   2.7e-05      0.24      25      67 ..     165     232 ..     135     278 .. 0.74
   2 ?    0.2   0.5       0.1   9.3e+02      57      91 ..     279     313 ..     242     318 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                                   BHHHHHHHHHHHHHHHHHHH.........................HHTTTHHHHHS-SHHHHHHHHHH CS
                          CRCB  25 plgtlavNvlGsfllgllla.........................llttGflGglTTfStfvlelvsl 67 
                                    ++tl++ ++  ++l ++++                         +l+ G+ G+l+T+S ++  +v +
  gi|15668859|ref|NP_247662.1| 165 SIKTLIAELIFVIILSMIAGhylpisldnpqihsritldfwsiiiALSAGIAGSLSTVSNISSIAVGV 232
                                   34889999998889988888777777666666666665555555559************987766654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                                   SHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHH CS
                          CRCB  57 fStfvlelvslleegellaallyvllsvvlgllav 91 
                                   fS++ +  ++ ++++e+ + +ly++l +v+ ++a+
  gi|15668859|ref|NP_247662.1| 279 FSAYGISPYRWWKKEEARKYTLYAILLWVTLFIAI 313
                                   55555555555555555555566655555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1321  (0.0736795); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 1842.06
//
Query:       gi|15668860|ref|NP_247663.1|  [L=316]
Description: transketolase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-44  151.4   0.1    3.1e-44  150.7   0.1    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
    4.9e-34  116.9   0.2    1.5e-33  115.3   0.2    1.8  2  Transketolase_C  Transketolase, C-terminal domain
     0.0072   16.6   0.1       0.43   10.9   0.0    2.5  2  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.7   0.1   5.3e-48   3.1e-44       5     174 ..      11     171 ..       9     173 .. 0.98

  Alignments for each domain:
  == domain 1  score: 150.7 bits;  conditional E-value: 5.3e-48
                                   HHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHHH CS
                  Transket_pyr   5 wrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviveaqFgdFa 85 
                                   +rk+++e+l el+k+ +++v+++aD++g+t ++++++++++   r+++ g++Eq+++g+a+G+a++g  ++++   F++Fa
  gi|15668860|ref|NP_247663.1|  11 MRKGYGETLIELGKKYENLVVLDADLSGSTQTAMFAKEFPE---RFFNAGVAEQNMIGMAAGLATTG--KIVFASSFSMFA 86 
                                   89***************************************...***********************..9*********** PP

                                   GGGHHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSSS.SE CS
                  Transket_pyr  86 ngAqiyadqairsgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairredrkP 165
                                   +    +a++ ir+++a  kl+v+ v t+++i vgedG++hq +e++a++r+ip++ v++P+d ++tk+++r+ ++  +++P
  gi|15668860|ref|NP_247663.1|  87 S---GRAWEIIRNLVAYPKLNVKiVATHAGITVGEDGASHQMCEDIAIMRAIPNMVVIAPTDYYHTKNVIRTIAE--YKGP 162
                                   *...9**********************************************************************..779* PP

                                   EEEEE-SSE CS
                  Transket_pyr 166 vvlrlpksl 174
                                   v++r+p++ 
  gi|15668860|ref|NP_247663.1| 163 VYVRMPRRD 171
                                   *******86 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.37   2.2e+03      52      72 ..      17      37 ..      15      68 .. 0.67
   2 !  115.3   0.2   2.6e-37   1.5e-33       1     124 []     187     305 ..     187     305 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.37
                                  HHHHHHHHHHSEEEEEEEEES CS
               Transketolase_C 52 etilesvkktgrlvvveeavk 72
                                  et+ e+ kk++ lvv++ +  
  gi|15668860|ref|NP_247663.1| 17 ETLIELGKKYENLVVLDADLS 37
                                  567788899999998876654 PP

  == domain 2  score: 115.3 bits;  conditional E-value: 2.6e-37
                                   TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHH CS
               Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigseva 81 
                                   gk++il +g+d+t++a+G +v+eal+A e L+++gisae+v + t+kp+D+e i+   k+++ +v+ve+++++gG+g +va
  gi|15668860|ref|NP_247663.1| 187 GKGKILVDGEDLTIIATGEEVPEALRAGEILKENGISAEIVEMATIKPIDEEIIK---KSKDFVVTVEDHSIIGGLGGAVA 264
                                   899****************************************************...99********************* PP

                                   HHHHHCCCTTCSSEEEEEEE-SS.SSSSGHHHHHHHTT-SHHHH CS
               Transketolase_C  82 aalaeeafdgldapvkrvggpdv.iepgsaeelekafgldaeki 124
                                   +++a    +gl+++ +r+g+ dv +++g+a+el+k++gld e+i
  gi|15668860|ref|NP_247663.1| 265 EVIAS---NGLNKKLLRIGINDVfGRSGKADELLKYYGLDGESI 305
                                   *****...9*******************************9987 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.018   1.1e+02      44      92 ..      18      67 ..      16      77 .. 0.71
   2 !   10.9   0.0   7.3e-05      0.43       2      81 ..     197     273 ..     196     294 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.018
                                  HHHHHSTT-SEEEEEE-S--TT-G.-HHHHHHHHHTGGGTSEEEEEE--G CS
                       PFOR_II 44 elkellkkvkkvvvldrnisfgse.Gqlveevkaalkkskvkvvnfvagl 92
                                   l el kk++++vvld + s +++  + ++e  +   +  v+  n+++ +
  gi|15668860|ref|NP_247663.1| 18 TLIELGKKYENLVVLDADLSGSTQtAMFAKEFPERFFNAGVAEQNMIGMA 67
                                  5778999************8666666667777766666655555555544 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.3e-05
                                   SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGG CS
                       PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkks 81 
                                   +  i+a+G  + +a +a + l+e+gi++ ++ + t+ P  ee +k+     + vv+++    +g  G  v ev a+   +
  gi|15668860|ref|NP_247663.1| 197 DLTIIATGEEVPEALRAGEILKENGISAEIVEMATIKPIDEEIIKKSK---DFVVTVEDHSIIGGLGGAVAEVIASNGLN 273
                                   6789************************************99999964...55666666555888877777776665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1940.00
//
Query:       gi|15668861|ref|NP_247664.1|  [L=234]
Description: pentose-5-phosphate-3-epimerase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-82  273.6   2.6    8.4e-82  273.4   2.6    1.1  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
  ------ inclusion threshold ------
      0.023   14.0   0.1       0.23   10.8   0.1    2.2  2  TMP-TENI        Thiamine monophosphate synthase
      0.078   12.7   0.1       0.16   11.7   0.1    1.5  1  Vta1_C          Vta1 C-terminal domain


Domain annotation for each model (and alignments):
>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.4   2.6   1.4e-85   8.4e-82       1     198 []       3     198 ..       3     198 .. 0.99

  Alignments for each domain:
  == domain 1  score: 273.4 bits;  conditional E-value: 1.4e-85
                                   EEEEBGGGS-GGGHHHHHHHHHHTT-SEEEEEEEBSSSSS-B-B-HHHHHHHGGGE-S-EEEEEESSSHHHCHHHHHHCT- CS
                Ribul_P_3_epim   1 kiapSllsadfarlgeevkaveeagadllHvDvmDghfvpNltigplvvealrkltelpldvHLmveevdrivpefaeaga 81 
                                   ki +S+lsadf +l+ee+k++eeag+d++HvD+mDghfvpN+++g+ ++++++kltelp++vHLmve+vd +v+ef+e++ 
  gi|15668861|ref|NP_247664.1|   3 KIGASILSADFGHLREEIKKAEEAGVDFFHVDMMDGHFVPNISMGIGIAKHVKKLTELPVEVHLMVENVDLFVNEFEEMD- 82 
                                   6899**************************************************************************99. PP

                                   SEEEEE-ST-TTHHHHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-SEEEEESS-TT-SS----CCHHHHHHHHHHHHHH CS
                Ribul_P_3_epim  82 siisvHaEalehlkrtiqeikeaGakaglvlnpatplealeyllekldlvllmsvePgfgGQkFipevlekikkvrklide 162
                                    +i++H+Ea++ + r+i++ik++Gak++++lnpatpl+a+ey+l ++++vl+m+vePgf+GQkFip +++ki+k++++i e
  gi|15668861|ref|NP_247664.1|  83 -YITFHIEAVKFPFRIINRIKSIGAKPIVALNPATPLDAIEYILGDVYAVLVMTVEPGFSGQKFIPVMTKKIRKLKSMIVE 162
                                   .******************************************************************************** PP

                                   HT---EEEEESS--TTTCHHHHHHT--EEEESHHHH CS
                Ribul_P_3_epim 163 keldlkievDGGvkldnieqiaeagadvlVagsavf 198
                                   +++d+ki+vDGG++++++  +++agadvlVa+sa+f
  gi|15668861|ref|NP_247664.1| 163 NGYDTKIFVDGGINVETAPLAVKAGADVLVAASAIF 198
                                   ***********************************9 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.03   1.8e+02     104     122 ..      15      33 ..       3      64 .. 0.82
   2 ?   10.8   0.1   3.9e-05      0.23     137     181 .]     148     197 ..      80     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.03
                      TMP-TENI 104 hsleeaeeaealgadYigv 122
                                   h +ee+++ae++g+d++ v
  gi|15668861|ref|NP_247664.1|  15 HLREEIKKAEEAGVDFFHV 33 
                                   4567899999999999865 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 3.9e-05
                      TMP-TENI 137 lgleglkelaeale.....iPvvaiGGitlenvaevleagadgvavvsai 181
                                   +  +++++l++++        +++ GGi+ e+++ +++agad +   sai
  gi|15668861|ref|NP_247664.1| 148 VMTKKIRKLKSMIVengydTKIFVDGGINVETAPLAVKAGADVLVAASAI 197
                                   555666677666666777789**********************9999997 PP

>> Vta1_C  Vta1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.6e-05      0.16      21      33 ..     201     213 ..     198     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.6e-05
                        Vta1_C  21 eDvetAiknLqeA 33 
                                   +Dv+tA+knL+eA
  gi|15668861|ref|NP_247664.1| 201 DDVKTAVKNLREA 213
                                   8*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1445.18
//
Query:       gi|15668862|ref|NP_247665.1|  [L=274]
Description: transketolase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-61  208.4   0.1    2.6e-61  207.5   0.1    1.3  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    2.5e-13   49.9   0.0    2.2e-09   36.9   0.0    2.2  2  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    2.1e-06   26.9   0.0    2.7e-06   26.6   0.0    1.1  1  E1_dh            Dehydrogenase E1 component
    7.9e-06   25.7   0.3    0.00033   20.5   0.3    2.4  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    3.5e-05   22.8   0.1    7.3e-05   21.7   0.1    1.5  1  XFP_N            XFP N-terminal domain


Domain annotation for each model (and alignments):
>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.5   0.1   7.2e-65   2.6e-61       4     273 ..      12     270 ..      10     273 .. 0.94

  Alignments for each domain:
  == domain 1  score: 207.5 bits;  conditional E-value: 7.2e-65
                                   HHHHHHHHHHHHHHHHHT-S--HHHHHHHHHHHHHHHHT--B-TTBTT-TTS-EEEESSGGGHHHHHHHHHHTTSS--HHH CS
               Transketolase_N   4 kavnaiRvLavDavekaksGhPGaplgladiaevlfkkllkhnPndpkwidRDRfvLsnGhaslllYsllhLtGydlsled 84 
                                   k+++ +R   v +v  aksGhPG +l++ di  +l+ kl+++ P++p   dRDRfvLs Gha+  lY++l  +G  ++ e+
  gi|15668862|ref|NP_247665.1|  12 KIAKKVRYNIVKMVGLAKSGHPGGSLSATDIIVALYFKLMNYSPDNPYKKDRDRFVLSKGHAAPALYAVLSELGI-IEEEE 91 
                                   6789999999************************************************************99998.7889* PP

                                   HTTTTSTT-SS-SS--TTTSTT--S---STTHHHHHHHHHHHHHHHHHHHH-BTTB-S----EEEEEEHHHHHSHHHHHHH CS
               Transketolase_N  85 lksfrqlgsktpGhPelghtagvevttGPLGqGianavglalaektlaatynkpgfdivdhytyvilgDgclmeGvsseas 165
                                   l ++r l+ k  GhP   +t+gve+ tG LGqG ++avg+al  +           d +++y+yv+lgDg  +eG+  ea+
  gi|15668862|ref|NP_247665.1|  92 LWKLRRLEGKLQGHPS-MDTPGVEICTGSLGQGFSAAVGMALGCRL----------DKLNNYVYVLLGDGECQEGIVWEAA 161
                                   ***************9.89**********************98764..........45679******************** PP

                                   HHHHHTT-TTEEEEEEESSEETTEEGGGT--.S-HHHHHHHTT-EEEEETTTT-HHHHHHHHHHHHH-TT.S-EEEEEE-- CS
               Transketolase_N 166 slagtlkLgkLivlyDdnkisidGeteisft.edvakrfeaygWhvievedgedveaikaaieeakaekd.kPsliklrtv 244
                                     a++ kL++Li++ D nk+ idG te  ++  d++++fea+gW+v e  dg++ e+i + +e+ak+ k+ kP +i   tv
  gi|15668862|ref|NP_247665.1| 162 MAAAHYKLDNLIAFIDRNKLQIDGCTEDVMSlGDIKAKFEAFGWDVFE-IDGHNFEEIINTVEKAKSMKNgKPKMIIAYTV 241
                                   **************************9776538**************9.9****************97744********** PP

                                   TTTTSTTTTTSGGGTSS---HHHHHHHHH CS
               Transketolase_N 245 iGygspakagtedvhGapLgedevaalkk 273
                                    G g    +++ + hG + +e++++++ +
  gi|15668862|ref|NP_247665.1| 242 KGKGVSFMENNVAFHGKAPNEEQLKQALE 270
                                   ******************99999998755 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   6.1e-13   2.2e-09      12     175 ..       4     183 ..       3     192 .. 0.81
   2 !   10.7   0.0   5.9e-05      0.21     233     269 ..     199     236 ..     185     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 6.1e-13
                DXP_synthase_N  12 klskeeleelaeelrefliesvs.ktggHlasnLgvveLtlalh.........yvfdtpkDklvwDvgHqaYv.hKiltg. 80 
                                   +l+ ++le++a+++r  ++++v  +++gH + +L++ ++ +al+         + +++++D++v   gH a + + +l++ 
  gi|15668862|ref|NP_247665.1|   4 NLEIKDLEKIAKKVRYNIVKMVGlAKSGHPGGSLSATDIIVALYfklmnyspdNPYKKDRDRFVLSKGHAAPAlYAVLSEl 84 
                                   68899*****************74689****************84333322222477889*********996437788763 PP

                DXP_synthase_N  81 ...RkdkfktlrqkgG.lsgfpkrsEseyDafeagHsstsisaalGlavardlkgekkkvvaviGDgaltgGmafealnni 157
                                       ++++ +lr+ +G l+g+p+++    + + +g  +   saa+G+a   +l++ ++ v  ++GDg    G+ +ea   +
  gi|15668862|ref|NP_247665.1|  85 giiEEEELWKLRRLEGkLQGHPSMDTPGVE-ICTGSLGQGFSAAVGMALGCRLDKLNNYVYVLLGDGECQEGIVWEAAMAA 164
                                   343579999999998879999998877766.56788999****************9999999**************97777 PP

                DXP_synthase_N 158 gelk.kkllvilNdNemsi 175
                                   ++ k ++l+  +  N+  i
  gi|15668862|ref|NP_247665.1| 165 AHYKlDNLIAFIDRNKLQI 183
                                   7766266776777777665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.9e-05
                DXP_synthase_N 233 lfeelgfkYlGpidGhdleelikvleevkklkg..pvll 269
                                    fe++g + +  idGh++ee+i+++e++k++k+  p+++
  gi|15668862|ref|NP_247665.1| 199 KFEAFGWDVF-EIDGHNFEEIINTVEKAKSMKNgkPKMI 236
                                   5888888866.7******************975236665 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   7.5e-10   2.7e-06     102     224 ..     119     240 ..      86     268 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 7.5e-10
                                   STTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--E.EEEEEEESEETTEEHHHH-S---GGG. CS
                         E1_dh 102 ivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpv.ifvveNNkygisTeaekasaskeladr 181
                                    +g   + + G+al ++ ++ ++ + +l GDg   +G+v+ea+  aa +kl   i ++  Nk  i   +e   +  ++ ++
  gi|15668862|ref|NP_247665.1| 119 SLGQGFSAAVGMALGCRLDKLNNYVYVLLGDGECQEGIVWEAAMAAAHYKLDNlIAFIDRNKLQIDGCTEDVMSLGDIKAK 199
                                   4455555677*****************************************987*************************** PP

                                   .TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE CS
                         E1_dh 182 argvgipglrVdgnDplavyeAvkfAaeraregkgpllielvt 224
                                     ++g   +++dg  ++++ + v  A+    ++ +p +i + t
  gi|15668862|ref|NP_247665.1| 200 FEAFGWDVFEIDGHNFEEIINTVEKAKSM--KNGKPKMIIAYT 240
                                   ***********************999875..344666665555 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.3   9.1e-08   0.00033      26     151 ..     116     236 ..     100     238 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 9.1e-08
                                   TTS-TTTHHHHHHHHHH...HST.TSEEEEEEEHHHHHHT..GGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTT CS
                  TPP_enzyme_C  26 glgtmGyglpaAiGakl...akp.drevvaivGDGgflmi..lqelatavrrnlpitvvvlnNegygmtggqqepfggkrk 100
                                    +g++G g++aA+G++l   +++ ++ v+++ GDG ++     ++ + a+ ++l+ ++  ++ + ++ + g +e       
  gi|15668862|ref|NP_247665.1| 116 CTGSLGQGFSAAVGMALgcrLDKlNNYVYVLLGDGECQEGivWEAAMAAAHYKLDNLIAFIDRNKLQ-IDGCTEDVM---- 191
                                   5799*************765333478************87645777788888995555555544442.333333222.... PP

                                   TTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH..CSSSEEEE CS
                  TPP_enzyme_C 101 sgpagkdlkpvdfaklaealGakgarvekadveeleealkeal..ekkgpali 151
                                          +   d+ +  ea+G +++ ++ ++ ee+ +++++a   ++++p +i
  gi|15668862|ref|NP_247665.1| 192 -------SLG-DIKAKFEAFGWDVFEIDGHNFEEIINTVEKAKsmKNGKPKMI 236
                                   .......233.777788888888888888888888888888866666677666 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1     2e-08   7.3e-05     120     241 ..      98     219 ..      88     247 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2e-08
                         XFP_N 120 fPGGipshvaaetPGsiheGGelGyalshayGav....ldnPdlivacvvGdGeaetGPlatswhsnkflnPaedGavlPi 196
                                   + G +  h + +tPG     G lG  +s a+G +    ld+ +  v  ++GdGe++ G +   w++       +   ++  
  gi|15668862|ref|NP_247665.1|  98 LEGKLQGHPSMDTPGVEICTGSLGQGFSAAVGMAlgcrLDKLNNYVYVLLGDGECQEGIV---WEAAMAAAHYKLDNLIAF 175
                                   6788999********99999***9988877654422228******************965...88888888888889999* PP

                         XFP_N 197 lelnGykisnptilarisdeelkklfeGlGyepafvededteslh 241
                                   ++ n  +i   t    +s  ++k+ fe +G+++  +++++ e++ 
  gi|15668862|ref|NP_247665.1| 176 IDRNKLQIDGCT-EDVMSLGDIKAKFEAFGWDVFEIDGHNFEEII 219
                                   ********8877.578999*******************9877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1661.36
//
Query:       gi|15668863|ref|NP_247666.1|  [L=968]
Description: hypothetical protein MJ_0682 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.7e-186  618.4   0.2   8.1e-186  618.1   0.2    1.1  1  RtcB             tRNA-splicing ligase RtcB
    2.5e-24   85.4   6.8    4.8e-21   74.9   0.1    3.4  3  LAGLIDADG_3      LAGLIDADG-like domain
    5.6e-14   52.2   2.6    7.5e-14   51.8   0.6    2.2  2  Intein_splicing  Intein splicing domain


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.1   0.2  1.4e-189  8.1e-186       1     412 []      46     968 .]      46     968 .] 1.00

  Alignments for each domain:
  == domain 1  score: 618.1 bits;  conditional E-value: 1.4e-189
                                   HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.............................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.............................. RF
                          RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.............................. 48 
                                   q++nva+lpgi+k+++amPDvH+G+g++iG+V+a++   gvi+P++VG+DI                              
  gi|15668863|ref|NP_247666.1|  46 QIANVACLPGIYKYSIAMPDVHYGYGFAIGGVAAFDqreGVISPGGVGFDIncltsnskiltddgyyikleklkekldlhi 126
                                   89******************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          RtcB  49 ................................................................................. 48 
                                                                                                                    
  gi|15668863|ref|NP_247666.1| 127 kiynteegekssnilfvseryadekiiriktesgrvlegskdhpvltlngyvpmgmlkegddvivypyegveyeepsdeii 207
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          RtcB  49 ................................................................................. 48 
                                                                                                                    
  gi|15668863|ref|NP_247666.1| 208 ldeddfaeydkqiikylkdrgllplrmdnknigiiarllgfafgdgsivkengdrerlyvafygkretlikiredleklgi 288
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          RtcB  49 ................................................................................. 48 
                                                                                                                    
  gi|15668863|ref|NP_247666.1| 289 kasriysrkreveirnaygdeytslcednsikitskafalfmhklgmpigkkteqiykipewikkapkwvkrnflaglfga 369
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          RtcB  49 ................................................................................. 48 
                                                                                                                    
  gi|15668863|ref|NP_247666.1| 370 dgsravfknytplpinltmskseelkenileflneiklllaefdiesmiyeiksldgrvsyrlaivgeesiknflgrinye 450
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          RtcB  49 ................................................................................. 48 
                                                                                                                    
  gi|15668863|ref|NP_247666.1| 451 ysgekkvigllayeylrrkdiakeirkkcikrakelykkgvtvsemlkmdefrnefiskrlieravyenldeddvristkf 531
                                   ********************************************************************************* PP

                                   ......................................................-EEEEEEEEEEHHHHGGGHHHHHHHHH CS
                                   ......................................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB  49 ......................................................CGvrllktnltaeeleeklkelvkele 75 
                                                                                         CGvrl++tnlt+ee+++k+kel+k+l+
  gi|15668863|ref|NP_247666.1| 532 pkfeefiekygviggfvidkikeieeisydsklydvgivskehnfiansivvhnCGVRLIRTNLTKEEVQSKIKELIKTLF 612
                                   ********************************************************************************* PP

                                   HHS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT---STT-EE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB  76 kavpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlGsGNHFi 156
                                   k+vp+glgsk+ +k+sk+ +++vleeg++wav+eg+g++edle iee+g+lk+ad+++vs+kaker+r qlG+lGsGNHF+
  gi|15668863|ref|NP_247666.1| 613 KNVPSGLGSKGILKFSKSVMDDVLEEGVRWAVKEGYGWKEDLEFIEEHGCLKDADASYVSDKAKERGRVQLGSLGSGNHFL 693
                                   ********************************************************************************* PP

                                   EEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB 157 EvqlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagseegqaYlkamq 237
                                   Evq+ve+++deeaa+++g+ee+qvvv++H+GSRglGhqi++dyl+i++ka+k++giklpdr+La++p++seegq+Y+kam+
  gi|15668863|ref|NP_247666.1| 694 EVQYVEKVFDEEAAEIYGIEENQVVVLVHTGSRGLGHQICTDYLRIMEKAAKNYGIKLPDRQLACAPFESEEGQSYFKAMC 774
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-EE-............ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxxxx............ RF
                          RtcB 238 aaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAtrA............ 302
                                   ++anyA+aNRq+it++vre++e+v+k ++edle+++v+dvaHNiakkEeh  d    kv+VhRKGAtrA            
  gi|15668863|ref|NP_247666.1| 775 CGANYAWANRQMITHWVRESFEEVFKIHAEDLEMNIVYDVAHNIAKKEEHIiDgrkVKVIVHRKGATRAfppkheaipkey 855
                                   ***************************************************966889************************ PP

                                   .TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCCT-EEEE------------ CS
                                   .xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB 303 .kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeqgigvearkkegvleEape 380
                                    +vgqpviipG+mgt+Sy+++G++ a+  +fgSt+HGAGR++sRaka k +k++e++++l+e+gi++++++k++++eEape
  gi|15668863|ref|NP_247666.1| 856 wSVGQPVIIPGDMGTASYLMRGTEIAMkeTFGSTAHGAGRKLSRAKALKLWKGKEIQRRLAEMGIVAMSDSKAVMAEEAPE 936
                                   ************************99999**************************************************** PP

                                   ------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB 381 aYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                   aYK++d V++++++ag++ +var++p++v+kg
  gi|15668863|ref|NP_247666.1| 937 AYKSVDLVADTCHKAGISLKVARMRPLGVIKG 968
                                   *******************************8 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       2.4   1.4e+04      43      73 ..     118     146 ..     114     158 .. 0.64
   2 !   13.1   0.3   1.5e-05     0.091       4      66 ..     242     317 ..     240     334 .. 0.73
   3 !   74.9   0.1     8e-25   4.8e-21       1      83 []     357     448 ..     357     448 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.4
                                   HHHHCT.HSCEEEEEEE-SCCCCECCCHCHC CS
                   LAGLIDADG_3  43 lLlrlGIestiyekkkakgrgvyrlliisge 73 
                                   l ++l ++ +iy++ +++ + +  +l +s++
  gi|15668863|ref|NP_247666.1| 118 LKEKLDLHIKIYNT-EEGEKSS-NILFVSER 146
                                   55678888888888.3333333.35666655 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHCCECCECSTTTTS..EEEEES-HHHHHHHHHHHHHCT.H.SCEEEE.EEE-SCCCC..........E CS
                   LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvs..isltssskelledvqrlLlrlGIe.stiyek.kkakgrgvy..........r 66 
                                    a L G+  +DGs++k+++ + +  + ++ +  e l ++++ L++lGI+ s+iy + ++ + r+ y           
  gi|15668863|ref|NP_247666.1| 242 IARLLGFAFGDGSIVKENGDRERlyVAFYGKR-ETLIKIREDLEKLGIKaSRIYSRkREVEIRNAYgdeytslcedN 317
                                   58899**************9999977777665.555578888******83578888777777777766655555544 PP

  == domain 3  score: 74.9 bits;  conditional E-value: 8e-25
                                   HHHHHHHHHHHHHCCECCECSTTTTS.EEEEES-........HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCH CS
                   LAGLIDADG_3   1 evkaafLrGlfdaDGsvskskkkgvs.isltsss........kelledvqrlLlrlGIestiyekkkakgrgvyrlliisg 72 
                                   +vk++fL+Glf aDGs  ++k++++  i+lt+s+        +e+l++++ lL+++ Ies+iye k+ +gr++yrl i+++
  gi|15668863|ref|NP_247666.1| 357 WVKRNFLAGLFGADGSRAVFKNYTPLpINLTMSKseelkeniLEFLNEIKLLLAEFDIESMIYEIKSLDGRVSYRLAIVGE 437
                                   799****************************************************************************** PP

                                   CTTCGGGTTTX CS
                   LAGLIDADG_3  73 enlkrFlekig 83 
                                   e++k+Fl +i+
  gi|15668863|ref|NP_247666.1| 438 ESIKNFLGRIN 448
                                   ********995 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.6   1.3e-17   7.5e-14       2     134 .]     105     585 ..     104     585 .. 0.95
   2 ?   -1.2   0.0       0.3   1.8e+03      34      64 ..     694     724 ..     673     817 .. 0.59

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.3e-17
                                   EECTTCEEEEHHHHCCECTTEEEEEETTTTEEEEEEEEEEEEEEEE..EEEEEEETTS-EEEEETT-EEEECCTTEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing   2 iledgeekvkieelvekegeevlslnledlklevksvkkliklklk..elyeiklesgrkikaTpeHkllvvrdegivEkr 80 
                                   il d+++  k+e+l ek +  +++++  +++++ +++  +++ +++  ++++ik+esgr +  +++H++l++  +g   + 
  gi|15668863|ref|NP_247666.1| 105 ILTDDGYYIKLEKLKEKLDL-HIKIYNTEEGEKSSNIL-FVSERYAdeKIIRIKTESGRVLEGSKDHPVLTL--NGY--VP 179
                                   67888889999999765544.45555555555566644.444555456************************..899..89 PP

                                   CCC--TT-EEEEE.................................................................... CS
                                   xxxxxxxxxxxxx.................................................................... RF
               Intein_splicing  81 adeLkegdliavp.................................................................... 93 
                                   +  Lkegd ++v                                                                     
  gi|15668863|ref|NP_247666.1| 180 MGMLKEGDDVIVYpyegveyeepsdeiildeddfaeydkqiikylkdrgllplrmdnknigiiarllgfafgdgsivkeng 260
                                   ********999889******************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15668863|ref|NP_247666.1| 261 drerlyvafygkretlikiredleklgikasriysrkreveirnaygdeytslcednsikitskafalfmhklgmpigkkt 341
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15668863|ref|NP_247666.1| 342 eqiykipewikkapkwvkrnflaglfgadgsravfknytplpinltmskseelkenileflneiklllaefdiesmiyeik 422
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15668863|ref|NP_247666.1| 423 sldgrvsyrlaivgeesiknflgrinyeysgekkvigllayeylrrkdiakeirkkcikrakelykkgvtvsemlkmdefr 503
                                   ********************************************************************************* PP

                                   ........................................HSCEEEEEEEEEEEEECEEEEEEEE.ETTT-EEEECTTEEE CS
                                   ........................................xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
               Intein_splicing  94 ........................................dadvvwdkvksievedeeeyVYdlt.vednhNFvangiivH 133
                                                                            +  v dk+k+ie+ +++ + Yd+  v ++hNF+an i+vH
  gi|15668863|ref|NP_247666.1| 504 nefiskrlieravyenldeddvristkfpkfeefiekygvIGGFVIDKIKEIEEISYDSKLYDVGiVSKEHNFIANSIVVH 584
                                   **************************************998889********************736899*********** PP

                                   - CS
                                   x RF
               Intein_splicing 134 N 134
                                   N
  gi|15668863|ref|NP_247666.1| 585 N 585
                                   9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.3
                                   EEEEEEEEEEEEEEEEEEEEETTS-EEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  34 evksvkkliklklkelyeiklesgrkikaTp 64 
                                   ev+ v+k++  + +e+y i+ ++   +  T+
  gi|15668863|ref|NP_247666.1| 694 EVQYVEKVFDEEAAEIYGIEENQVVVLVHTG 724
                                   5555555555555555555544443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (968 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 6507.09
//
Query:       gi|15668864|ref|NP_247667.1|  [L=259]
Description: hypothetical protein MJ_0683 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-08   35.6   0.0    1.9e-08   34.9   0.0    1.4  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   1.1e-12   1.9e-08       5     154 ..      32     183 ..      28     191 .. 0.84
   2 ?   -3.5   0.0      0.65   1.2e+04      87     129 ..     233     241 ..     203     251 .. 0.54

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.1e-12
                                   SEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...CCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
                   Radical_SAM   5 rgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla...vpgiritv 82 
                                    gC ++C++C+ +++ +++ +g+  s+  ++e +  l ++k +k+ i ++   ++y++++++ +  + +    ++  ++++
  gi|15668864|ref|NP_247667.1|  32 IGCQYACKYCYARFMCKWYNYGKWGSWVVVKENLPDLIKNKHIKGKIYMSSVSDAYRPIEKDFKLTRNILkniDKRAELSI 112
                                   59*************88888888888888888888886555566666666669999888888777777778899******* PP

                                   EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpG 154
                                    t   l+  + ++++++     v l+++ +     +k ++   +++e++++al++l e+gik+  ++ +++p 
  gi|15668864|ref|NP_247667.1| 113 LTKSDLV-LRDMDLFKKFSSIEVGLTINNFEGN-LKKDIEpFSPSNEKRIDALKTLYENGIKNYAFISPIIPD 183
                                   ******9.*********8888888888888888.*******99*******************98888888876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.65
                                   SCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  87 tlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfee 129
                                   t                                    +  ++e
  gi|15668864|ref|NP_247667.1| 233 TAF----------------------------------KRYIDE 241
                                   222..................................222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1727.37
//
Query:       gi|15668865|ref|NP_247668.1|  [L=370]
Description: aspartate aminotransferase AspB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-56  190.8   0.0    4.5e-56  190.6   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    9.1e-07   27.7   0.0    1.3e-06   27.2   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0011   18.3   0.0     0.0017   17.7   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.017   15.6   0.0       0.04   14.4   0.0    1.6  1  DUF4600          Domain of unknown function (DUF4600)
       0.11   12.9   0.1        4.4    7.7   0.1    2.8  2  Radical_SAM      Radical SAM superfamily
       0.13   12.4   0.0       0.26   11.4   0.0    1.5  1  Cytidylate_kin2  Cytidylate kinase-like family


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.6   0.0   1.5e-59   4.5e-56       1     363 []      29     364 ..      29     364 .. 0.93

  Alignments for each domain:
  == domain 1  score: 190.6 bits;  conditional E-value: 1.5e-59
                                   SEEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                 Aminotran_1_2   1 tdvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                   ++vi L ++e+++     t++ ++ + ++  + +++ + y++++g  el+e++ +++++++k ++ ++ +++ ++G++ ++
  gi|15668865|ref|NP_247668.1|  29 KKVIHLEIGEPDFN----TPKPIVDEGIK--SLKEGKTHYTDSRGILELREKISELYKDKYKADIIPD-NIIITGGSSLGL 102
                                   589***********....88888888888..66678889*****************************.*********999 PP

                                   HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT- CS
                 Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtG 162
                                     +   + ++ gde+l+ +p y+ ykn +r  g++ v +          ++e+leeal++      ktk i+++sp+NP G
  gi|15668865|ref|NP_247668.1| 103 FFALSSI-IDDGDEVLIQNPCYPCYKNFIRFLGAKPVFCD--------FTVESLEEALSD------KTKAIIINSPSNPLG 168
                                   9999999.9*******************************........89**********......*************** PP

                                   -B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHH CS
                 Aminotran_1_2 163 tvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsql 243
                                    v+++e    ++++a+++  ++++De+Y g+v++ +  ++++ + e+  ++++ +++sK ++++G+R+Gy+++n+++++++
  gi|15668865|ref|NP_247668.1| 169 EVIDRE----IYEFAYENIPYIISDEIYNGLVYEGK-CYSAIEFDENLEKTILINGFSKLYAMTGWRIGYVISNDEIIEAI 244
                                   ****86....7777899899**************65.56634444444459**************************9999 PP

                                   HHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHH CS
                 Aminotran_1_2 244 rklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelsk 322
                                    kl++++ +  +++ q+a+++a +++ ++  e++ m +++ +rr+ + +  ++ g++v  + ++++++  + +    e++ 
  gi|15668865|ref|NP_247668.1| 245 LKLQQNLFIsaPTISQYAALKAFEKETER--EINSMIKEFDRRRRLVLKYVKDFGWEVNNPIGAYYVFPNIGED-GREFAY 322
                                   9998887777***************9988..********************999******************99.****** PP

                                   HHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                 Aminotran_1_2 323 kLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                   kLl+e+ v++tpg  f+   ++ +Ri++ + + e+++e +e++
  gi|15668865|ref|NP_247668.1| 323 KLLKEKFVALTPGIGFGSkgKNYIRISY-ANSYENIKEGLERI 364
                                   ********************9*******.999*******9998 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   4.4e-10   1.3e-06      80     165 ..     102     181 ..      75     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.4e-10
                                   HHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHH CS
               Cys_Met_Meta_PP  80 iaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvDiekia 160
                                   ++ a+ +++  Gde+++++ +Y + +++++     lg +  f+d   +e+le+a++++tk++ + +p+npl +v+D ++i 
  gi|15668865|ref|NP_247668.1| 102 LFFALSSIIDDGDEVLIQNPCYPCYKNFIRF----LGAKPVFCDF-TVESLEEALSDKTKAIIINSPSNPLGEVID-REIY 176
                                   5678999***************998888776....5788899999.6899**************************.4566 PP

                                   HHHHH CS
               Cys_Met_Meta_PP 161 klakk 165
                                   ++a +
  gi|15668865|ref|NP_247668.1| 177 EFAYE 181
                                   66655 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.8e-07    0.0017      50     117 ..     101     160 ..      88     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.8e-07
                                   HHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEE CS
               DegT_DnrJ_EryC1  50 AlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlp 117
                                   +l  aL+   +++gdeV++    +    n ++ lgakpvf+D +       ++++e+a+  +tkaI++
  gi|15668865|ref|NP_247668.1| 101 GLFFALSS-IIDDGDEVLIQNPCYPCYKNFIRFLGAKPVFCDFT-------VESLEEALSDKTKAIII 160
                                   44444444.3779*****************************98.......9999***********96 PP

>> DUF4600  Domain of unknown function (DUF4600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.3e-05      0.04      22      89 ..     243     309 ..     229     318 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                       DUF4600  22 qiailkeklekirgnpsdrlasirvleklteeelnqllkqLekekkslenqlkdlelrleqEsKayhk 89 
                                    i  l++ l         + a ++++ek te+e+n+++k+ ++ ++ + + +kd+ + +++   ay+ 
  gi|15668865|ref|NP_247668.1| 243 AILKLQQNLFISA-PTISQYAALKAFEKETEREINSMIKEFDRRRRLVLKYVKDFGWEVNNPIGAYYV 309
                                   5555555554333.344567899***********************************9999988885 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0015       4.4      31      96 ..      14      77 ..       8      88 .. 0.75
   2 ?    2.5   0.0     0.057   1.7e+02     133     133 ..     289     289 ..     126     369 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
                                  HHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG.HHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                   Radical_SAM 31 veeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpd.eekler 96
                                  v +il+++++l ++ g+k+++l  gep+++ ++    e ++ l+ +g +    + g+l + +ek+ +
  gi|15668865|ref|NP_247668.1| 14 VMDILALAQKL-ESEGKKVIHLEIGEPDFNTPKPIVDEGIKSLK-EGKTHYTDSRGIL-ElREKISE 77
                                  668********.9*****************99988888777774.4444444444444.33666655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.057
                                   H CS
                                   x RF
                   Radical_SAM 133 a 133
                                   +
  gi|15668865|ref|NP_247668.1| 289 V 289
                                   1 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.6e-05      0.26     117     165 ..     250     298 ..     241     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.6e-05
               Cytidylate_kin2 117 rvfltapledrvkrvaereglseeearekiketDkrrakyykkytgqdw 165
                                   + f++ap  +    +++ e+ +e+e++++ike D+rr+   k++ +  w
  gi|15668865|ref|NP_247668.1| 250 NLFISAPTISQYAALKAFEKETEREINSMIKEFDRRRRLVLKYVKDFGW 298
                                   5799999999999*************************99999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2220.68
//
Query:       gi|15668866|ref|NP_247669.1|  [L=253]
Description: nitrogenase reductase NifH2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-25   87.4   0.2      1e-24   87.0   0.2    1.2  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    3.5e-16   59.6   0.2    5.4e-16   59.0   0.2    1.3  1  AAA_31        AAA domain
    2.2e-13   50.3   2.2    8.3e-07   28.7   0.3    2.1  2  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    1.3e-12   47.7   1.5    2.3e-11   43.6   1.5    2.4  1  ParA          NUBPL iron-transfer P-loop NTPase
    1.2e-09   37.8   1.4    3.9e-09   36.1   1.4    2.0  1  ArsA_ATPase   Anion-transporting ATPase
    1.4e-09   37.8   0.0    3.7e-05   23.3   0.0    2.1  2  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
     0.0004   20.2   0.0     0.0007   19.5   0.0    1.3  1  ATP_bind_1    Conserved hypothetical ATP binding protein
     0.0007   19.4   0.4       0.02   14.6   0.1    2.4  2  AAA_24        AAA domain
      0.001   18.4   0.4       0.42    9.8   0.0    2.5  2  MipZ          ATPase MipZ
     0.0011   18.7   0.4      0.045   13.5   0.0    2.3  2  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
     0.0013   18.6   5.2       0.29   10.9   0.3    3.0  2  AAA_26        AAA domain
     0.0013   18.0   0.1      0.003   16.9   0.0    1.6  2  KAP_NTPase    KAP family P-loop domain
     0.0051   17.2   0.0     0.0075   16.7   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0086   16.3   1.0        6.3    7.1   0.1    2.8  3  TrkA_N        TrkA-N domain
  ------ inclusion threshold ------
      0.012   15.7   1.3      0.012   15.7   1.3    2.0  2  DUF87         Helicase HerA, central domain
      0.013   15.0   0.1       0.31   10.5   0.0    2.2  2  GTP_EFTU      Elongation factor Tu GTP binding domain
       0.03   14.7   0.0       0.14   12.5   0.0    2.1  2  RNA_helicase  RNA helicase
      0.036   13.6   0.4        4.2    6.9   0.1    2.5  2  Ras           Ras family
       0.04   13.4   0.3       0.11   12.0   0.0    1.9  2  KTI12         Chromatin associated protein KTI12
       0.04   13.8   0.9        3.2    7.6   0.2    2.3  2  RsgA_GTPase   RsgA GTPase
      0.044   14.0   0.1       0.15   12.3   0.1    2.1  2  Toprim        Toprim domain
      0.049   13.6   1.6      0.061   13.3   0.3    2.0  1  PDDEXK_10     PD-(D/E)XK nuclease superfamily
      0.065   12.7   0.0        6.1    6.2   0.0    2.5  2  Pox_A32       Poxvirus A32 protein
      0.068   12.2   0.3       0.13   11.3   0.4    1.5  1  T2SSE         Type II/IV secretion system protein
        0.1   13.1   0.3       0.51   10.9   0.1    2.1  2  Toprim_4      Toprim domain
       0.24   11.0   3.9        1.1    8.9   0.4    2.6  2  SRP54         SRP54-type protein, GTPase domain
       0.36   10.9   3.9        5.1    7.2   0.1    2.5  2  MMR_HSR1      50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.2   1.5e-27     1e-24       1     127 [.       2     227 ..       2     228 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 1.5e-27
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH....................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx....................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep....................... 54 
                                   i+++s+kGGvGKT +++ L++al+++ + +l+vDaDp++n+ ++    +e++++di++                       
  gi|15668866|ref|NP_247669.1|   2 IIAVSGKGGVGKTAFTTLLIKALSKKTNSILVVDADPDSNLPETlgveVEKTVGDIREelkklverdeipagmtkldylrs 82 
                                   7899***************************************777777777777777*********************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|15668866|ref|NP_247669.1|  83 kifeilvetkyydllvmgrpegsgcycsvnnwlrqiidnlakdyefvvidteaglehlsrrttqnvdvmivitdaskrglg 163
                                   **************************************************************************9999999 PP

                                   CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                   ++kr+++l+++l  k    +k + vv+n+v++e  +++l++++++++   g++++g++p+++++ae + +g p
  gi|15668866|ref|NP_247669.1| 164 TAKRIKKLANELEVK----FKDIYVVANKVKPE--YEELIDNYAKEL---GLNLIGKLPYNKEIAEYDLKGIP 227
                                   999999999999999....889***********..999999999999...*****************999987 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.2   8.1e-19   5.4e-16       4     169 ..       2     177 ..       1     185 [. 0.75

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 8.1e-19
                        AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevl...ieeknikeaiiktkvenl 81 
                                   I  +  KGGvGKT+ ++ l +al+k+ + +L+vD+Dp +n+  +lg+e +++  ++ e l   +e+ +i        +++l
  gi|15668866|ref|NP_247669.1|   2 IIAVSGKGGVGKTAFTTLLIKALSKKTNSILVVDADPDSNLPETLGVEVEKTVGDIREELkklVERDEIPA-----GMTKL 77 
                                   445678*************************************9999666544444444311133444444.....45567 PP

                        AAA_31  82 dlipssid..Laeaei.elvelekk..........eeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqa 149
                                   d + s+i   L+e +  +l+ +  +          ++ l+++++++ ++Y +++iD+   L+ l +      d +i++++a
  gi|15668866|ref|NP_247669.1|  78 DYLRSKIFeiLVETKYyDLLVMG-RpegsgcycsvNNWLRQIIDNLAKDYEFVVIDTEAGLEHLSRRTTQNVDVMIVITDA 157
                                   77777775223333321232232.24568888877777******************************************* PP

                        AAA_31 150 eayaleGleqllktieevkk 169
                                   +++ l +++++ k  +e++ 
  gi|15668866|ref|NP_247669.1| 158 SKRGLGTAKRIKKLANELEV 177
                                   99999988887777776655 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   1.9e-07   0.00013       2      62 ..       2      61 ..       1      78 [. 0.84
   2 !   28.7   0.3   1.2e-09   8.3e-07     145     248 ..     152     252 ..     139     253 .] 0.83

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.9e-07
                     Fer4_NifH  2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrek 62
                                   ia+ GkGG+Gk+  ++ l +al+++ + +l+v  DP ++    +lg  +++tv d+ +e 
  gi|15668866|ref|NP_247669.1|  2 IIAVSGKGGVGKTAFTTLLIKALSKKTNSILVVDADPDSNLP-ETLGVEVEKTVGDIREEL 61
                                  79***********************************99876.567888888888776654 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 1.2e-09
                     Fer4_NifH 145 yivtsgelmalyaanniakgiekyaksggvrlgGliinsrkvdde.reliekfaeelgtkvlevvPrdeivrkaelrkktv 224
                                   +++t++    l +    ak i+k a++ +v++  + + + kv+ e +eli+++a+elg++++ ++P ++++ + +l+   +
  gi|15668866|ref|NP_247669.1| 152 IVITDASKRGLGT----AKRIKKLANELEVKFKDIYVVANKVKPEyEELIDNYAKELGLNLIGKLPYNKEIAEYDLKGIPL 228
                                   5555555555554....56678999999999999866666777662679******************************** PP

                     Fer4_NifH 225 ieyapeseqakeyrelarkilenk 248
                                    +  +++e+ k+ +e+a+ki+++k
  gi|15668866|ref|NP_247669.1| 229 WNLPENNEVYKKVEEIAEKIINKK 252
                                   ********************9976 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   1.5   3.5e-14   2.3e-11       6     245 ..       2     248 ..       1     249 [. 0.80

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 3.5e-14
                          ParA   6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee........ekpeqs.ekkliPvea...kgik 74 
                                   i+ +SgKGGVGK+ +++ l  aL+kk  ++ ++DaD    ++p+ lgve         e+ ++  e+  iP  +   + ++
  gi|15668866|ref|NP_247669.1|   2 IIAVSGKGGVGKTAFTTLLIKALSKKTNSILVVDADP-DSNLPETLGVEVektvgdirEELKKLvERDEIPAGMtklDYLR 81 
                                   6778********************************5.5789999999885566555422222245557788773344455 PP

                          ParA  75 vmSigfllesedeavvwrG.p.......mkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqe 147
                                      +++l+e++   ++  G p        +++ ++q++ + + ++ ++++iD+    g e+l+   + +++ ++++t   +
  gi|15668866|ref|NP_247669.1|  82 SKIFEILVETKYYDLLVMGrPegsgcycSVNNWLRQIIDNLA-KDYEFVVIDTEA--GLEHLSRRTTQNVDVMIVITDASK 159
                                   566788999887666665522222333357888999988776.789*******75..56899999999999********** PP

                          ParA 148 valadvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlk 228
                                     l  +k+  +++++++vk   +     ++v +k + ++    ++  +++a+elg++l+g++p ++ei+e   +g pl   
  gi|15668866|ref|NP_247669.1| 160 RGLGTAKRIKKLANELEVKFKDI-----YVVANKVKPEY----EELIDNYAKELGLNLIGKLPYNKEIAEYDLKGIPLWNL 231
                                   ******************99876.....55555555553....4668899******************************* PP

                          ParA 229 epeseaakaleeiaekv 245
                                    +++e+ k++eeiaek+
  gi|15668866|ref|NP_247669.1| 232 PENNEVYKKVEEIAEKI 248
                                   99*************98 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   1.4   5.8e-12   3.9e-09       3      64 ..       2      63 ..       1     204 [. 0.83

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 5.8e-12
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEE CS
                   ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsa 64
                                  +i v+GKGGVGKt+  + +   ls+k +++l++  DP  +l   +  +++k++  ++e L  
  gi|15668866|ref|NP_247669.1|  2 IIAVSGKGGVGKTAFTTLLIKALSKKTNSILVVDADPDSNLPETLGVEVEKTVGDIREELKK 63
                                  799*****************************************************998863 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   5.6e-08   3.7e-05       3      65 ..       2      63 ..       1      85 [. 0.87
   2 !   12.8   0.0   9.4e-05     0.063     102     147 ..     112     157 ..      86     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.6e-08
                      CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqregwaraeldg 65
                                  ++a++G +GGvG+t+ ++ L +al +  +s+lv+D+ pd  L     v++e++ g +r el++
  gi|15668866|ref|NP_247669.1|  2 IIAVSG-KGGVGKTAFTTLLIKALSKKTNSILVVDADPDSNLPETLGVEVEKTVGDIREELKK 63
                                  677787.8**********************************999999999998888777765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.4e-05
                      CBP_BcsQ 102 aeallaalkelkeqyrwillDlpagasaltrellaladlvllvvep 147
                                   ++ l + +++l+++y+++++D  ag ++l r+++++ d+++ ++ +
  gi|15668866|ref|NP_247669.1| 112 NNWLRQIIDNLAKDYEFVVIDTEAGLEHLSRRTTQNVDVMIVITDA 157
                                   555667789**************************88888887765 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0     1e-06    0.0007       1     127 [.       5     131 ..       5     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1e-06
                    ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmed....lglgpngalvvaleflre 77 
                                   v G  G+GKt f+  l++ l+++  s+ vv  DP ++ lp    v++++++    + e+     +  +  a ++ l++lr+
  gi|15668866|ref|NP_247669.1|   5 VSGKGGVGKTAFTTLLIKALSKKTNSILVVDADPDSN-LPETLGVEVEKTVGD--IREElkklVERDEIPAGMTKLDYLRS 82 
                                   78999*****************************987.888999999998853..333331236666677999******** PP

                    ATP_bind_1  78 sldwldeelekeeddyllfDtPGQielfths.eslakiveeLesefalvvv 127
                                   ++  ++  +e +  d+l+++ P    ++  + + l++i+++L++++++vv+
  gi|15668866|ref|NP_247669.1|  83 KI--FEILVETKYYDLLVMGRPEGSGCYCSVnNWLRQIIDNLAKDYEFVVI 131
                                   *9..4444433466********7777776551679*********9998876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1     3e-05      0.02       5      73 ..       3     133 ..       1     141 [. 0.87
   2 !    7.6   0.0    0.0043       2.8      24      62 ..     126     178 ..     117     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
                        AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.swedfldevvel.................. 59 
                                   i++ G+ g+GKT + + l       ++++l++d +    +l  + ++++e ++ d+++e+++l                  
  gi|15668866|ref|NP_247669.1|   3 IAVSGKGGVGKTAFTTLLikalskkTNSILVVDADPD-SNLPETLGVEVEkTVGDIREELKKLverdeipagmtkldylrs 82 
                                   8899************998888888888888888884.46666666666689999999999999999999999999999** PP

                        AAA_24  60 .....................................aaeladyktlviDt 73 
                                                                        +   +dy+ +viDt
  gi|15668866|ref|NP_247669.1|  83 kifeilvetkyydllvmgrpegsgcycsvnnwlrqiiDNLAKDYEFVVIDT 133
                                   ************************************9999999*******9 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0043
                        AAA_24  24 pkplfidtekGlksldadkfpdie..............swedfldevvelaae 62 
                                   +++++idte+Gl +l  +  +++               + + +++ ++el+ +
  gi|15668866|ref|NP_247669.1| 126 YEFVVIDTEAGLEHLSRRTTQNVDvmivitdaskrglgTAKRIKKLANELEVK 178
                                   699**************999999877777777777777666666666666444 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.2    0.0077       5.1       3      38 ..       2      37 ..       1      42 [. 0.89
   2 !    9.8   0.0   0.00064      0.42      89     127 ..     115     153 ..     107     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0077
                                  EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE-- CS
                          MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidld 38
                                  i+    kGG Gk++ +  ++ aL+kk  ++ ++d d
  gi|15668866|ref|NP_247669.1|  2 IIAVSGKGGVGKTAFTTLLIKALSKKTNSILVVDAD 37
                                  556678**************************9988 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00064
                                   HHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEE CS
                          MipZ  89 leelvadleaeldfividtPGsdsalsrlahsladtlvt 127
                                   l++++++l+++++f+vidt    ++lsr + +  d ++ 
  gi|15668866|ref|NP_247669.1| 115 LRQIIDNLAKDYEFVVIDTEAGLEHLSRRTTQNVDVMIV 153
                                   78999***************************9999875 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   6.8e-05     0.045       1      33 [.       7      39 ..       7      61 .. 0.90
   2 ?    3.6   0.1     0.076        50      92     151 ..     138     201 ..     116     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.8e-05
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                  G+  +GK+++++lL+  + +k++++++vD+D+ 
  gi|15668866|ref|NP_247669.1|  7 GKGGVGKTAFTTLLIKALSKKTNSILVVDADPD 39
                                  66789************999999999*****96 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.076
                        CLP1_P  92 eekleenkkakasgliIntpGwvkglg.aellleliealep...dvvvvldq.eellnelkrdlp 151
                                   e +l+ +  ++ +++i+ t+   +glg a+ +++l++ le+   d+ vv  + + +++el ++  
  gi|15668866|ref|NP_247669.1| 138 E-HLSRRTTQNVDVMIVITDASKRGLGtAKRIKKLANELEVkfkDIYVVANKvKPEYEELIDNYA 201
                                   3.566666778999999999999999967999999999999998788888888999999888776 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.7    0.0042       2.8      10      31 ..       9      30 ..       1      34 [. 0.82
   2 !   10.9   0.3   0.00044      0.29      88     194 ..     115     218 ..     110     221 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0042
                        AAA_26 10 tgvGKTvvslgLvralkrkgvk 31
                                   gvGKT+ +++L++al++k+ +
  gi|15668866|ref|NP_247669.1|  9 GGVGKTAFTTLLIKALSKKTNS 30
                                  58**************998765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00044
                        AAA_26  88 lekivkelekdadivvVEGagglgvpiteellnadiaknlgapvilVarg..glgtinqllltiealrqknvrvlGvilNk 166
                                   l +i++ l+kd+++vv++   gl   + +++ n+d++      +++  ++  glgt +++   ++ l  k  + + v++Nk
  gi|15668866|ref|NP_247669.1| 115 LRQIIDNLAKDYEFVVIDTEAGLEHLSRRTTQNVDVM------IVITDASkrGLGTAKRIKKLANELEVK-FKDIYVVANK 188
                                   5678888899999999988777766666666555543......343333323556655554444444443.334679**** PP

                        AAA_26 167 vrnp..envetlekksgipvlGvvPylpdl 194
                                   v+++  e ++++ k  g++++G +Py++++
  gi|15668866|ref|NP_247669.1| 189 VKPEyeELIDNYAKELGLNLIGKLPYNKEI 218
                                   87667779999999999**********986 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.5e-06     0.003      22      60 ..       2      38 ..       1      67 [. 0.95
   2 ?   -2.5   0.0       3.4   2.2e+03     286     320 ..     142     176 ..     109     182 .. 0.50

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.5e-06
                    KAP_NTPase 22 vvgLygkWGsGKssllnkledelkefakpvrflfaefna 60
                                  +++++gk G+GK+++ ++l+++l+++  ++++l++++++
  gi|15668866|ref|NP_247669.1|  2 IIAVSGKGGVGKTAFTTLLIKALSKK--TNSILVVDADP 38
                                  6899**********************..9*******997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.4
                    KAP_NTPase 286 ksnlqlaldlskilltedfsdvnpRemkrlinals 320
                                   + + q+ + +  i +  ++   + + +k+l+n l+
  gi|15668866|ref|NP_247669.1| 142 RRTTQNVDVMIVITDASKRGLGTAKRIKKLANELE 176
                                   33444444444444444455555555555555544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-05    0.0075      26      78 ..       2      58 ..       1     153 [. 0.63

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                        AAA_16 26 lvllsGesGvGKsslvrellralekd..ggiflrgkcdql...esaipysalaqalar 78
                                  ++ +sG  GvGK++  + l +al+k+   ++++ ++ d++   + +++    +  + r
  gi|15668866|ref|NP_247669.1|  2 IIAVSGKGGVGKTAFTTLLIKALSKKtnSILVVDADPDSNlpeTLGVEVEKTVGDI-R 58
                                  688***********************744888999999993322222222233333.3 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.011       7.6       5      33 ..      12      40 ..       3      60 .. 0.78
   2 !    7.1   0.1    0.0094       6.3      11      52 ..     116     160 ..     109     171 .. 0.70
   3 ?    1.6   0.1      0.49   3.2e+02      60      96 ..     145     188 ..     137     203 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                                  S-SHHHHHHHHHHHHTTEEEEEEESSHHH CS
                        TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkdeer 33
                                  G   +++ l++ Ls++ ++++v+d d++ 
  gi|15668866|ref|NP_247669.1| 12 GKTAFTTLLIKALSKKTNSILVVDADPDS 40
                                  4455777899999996668*******974 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0094
                                   HHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.....SEEEES-TTSH CS
                        TrkA_N  11 rslaeeLseggkdvvvidkdeerveelreeg.....levvvgdatde 52 
                                   r+++++L ++++ +vvid++   +e+l+++      +++v+ da+++
  gi|15668866|ref|NP_247669.1| 116 RQIIDNLAKDYE-FVVIDTEA-GLEHLSRRTtqnvdVMIVITDASKR 160
                                   899******995.******65.5555554442223344888888765 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.49
                                   GGGESEEEE-SSSHHHHHHHHHHHHHHTSS.......SEEEEEE CS
                        TrkA_N  60 iekadaviaatgddeanilavllakelnpk.......kkiiara 96 
                                    +++d++i+ t+  +  + +++ +k+l ++       ++++a  
  gi|15668866|ref|NP_247669.1| 145 TQNVDVMIVITDASKRGLGTAKRIKKLANElevkfkdIYVVANK 188
                                   57788888888888888888877777776644434223344444 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   1.3   1.9e-05     0.012      26      61 ..       3      37 ..       2      88 .. 0.95
   2 ?   -0.8   0.1       2.1   1.4e+03     131     131 ..     156     156 ..     109     228 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-05
                         DUF87 26 lAilgsTGsGKSntvavLleellekkgatililDpH 61
                                  +A+ g+ G+GK+ ++ +L++ l  kk  +il++D++
  gi|15668866|ref|NP_247669.1|  3 IAVSGKGGVGKTAFTTLLIKALS-KKTNSILVVDAD 37
                                  6999*******************.9999******86 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
                         DUF87 131 k 131
                                   +
  gi|15668866|ref|NP_247669.1| 156 D 156
                                   1 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.13        84      79     106 ..      12      39 ..       3      99 .. 0.74
   2 ?   10.5   0.0   0.00047      0.31      68     150 ..     124     204 ..     104     249 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.13
                                   SSGGGHHHHHHHHHT-SEEEEEEETTTB CS
                      GTP_EFTU  79 GHvdFskevirglrvlDgavlvvdaveG 106
                                   G   F+   i++l++    +lvvda+ +
  gi|15668866|ref|NP_247669.1|  12 GKTAFTTLLIKALSKKTNSILVVDADPD 39 
                                   7778899999999999999999999844 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00047
                                   SSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE...EEEEEESCGSTHHHHHHHHHH CS
                      GTP_EFTU  68 kkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp...iivfiNKmDrlkaelkeivee 145
                                   k+y++ +iDt    +      r+++ +D+++++ da++      +++ +la++++v+   i v+ NK+   k e++e++++
  gi|15668866|ref|NP_247669.1| 124 KDYEFVVIDTEAGLE--HLSRRTTQNVDVMIVITDASKRGLGTAKRIKKLANELEVKfkdIYVVANKV---KPEYEELIDN 199
                                   666677777632222..233567899************999***************999999****97...6666666666 PP

                                   HHHHH CS
                      GTP_EFTU 146 vkqkl 150
                                   + ++l
  gi|15668866|ref|NP_247669.1| 200 YAKEL 204
                                   66666 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00022      0.14       1      26 [.       3      28 ..       3      45 .. 0.85
   2 ?   -1.5   0.0       4.9   3.2e+03      13      35 ..     166     188 ..     157     206 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                  i ++G+ g+GK+ +++ L+kal+kk 
  gi|15668866|ref|NP_247669.1|  3 IAVSGKGGVGKTAFTTLLIKALSKKT 28
                                  5689******************9776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.9
                  RNA_helicase  13 tlakeLakallkklklkkkdsvy 35 
                                     +k+La++l+ k+k++      
  gi|15668866|ref|NP_247669.1| 166 KRIKKLANELEVKFKDIYVVANK 188
                                   45556666666555443332222 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.039        26       3      21 ..       4      22 ..       2      41 .. 0.81
   2 ?    6.9   0.1    0.0064       4.2      87     141 ..     108     182 ..     103     206 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.039
                                  EEEESTTSSHHHHHHHHHH CS
                           Ras  3 vlvGdsavGKtslllrfvk 21
                                   + G+++vGKt++++  +k
  gi|15668866|ref|NP_247669.1|  4 AVSGKGGVGKTAFTTLLIK 22
                                  567*********9987776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0064
                                   HHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG...................G-SS.-HHHHHHHHHHHTSEEEEE CS
                           Ras  87 fenvkkwveeikrvaeenvpivLvGnKvDlee...................krav.steegeelakelglkflet 141
                                   + +v++w+++i +   +++++v++ + + le+                   kr + ++++ ++la+el++kf ++
  gi|15668866|ref|NP_247669.1| 108 YCSVNNWLRQIIDNLAKDYEFVVIDTEAGLEHlsrrttqnvdvmivitdasKRGLgTAKRIKKLANELEVKFKDI 182
                                   667788888888888888888888888888887777777777777777776555413345566666666666554 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.11       3      67 ..       2      68 ..       1      86 [. 0.88
   2 ?   -2.9   0.0       5.6   3.7e+03      13      37 ..     163     187 ..     150     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                  EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-.THHHH.TTSS.S--GGGHHHHHHHHHHHHHHH CS
                         KTI12  3 LvvltGlPssGKstrakeLakaleeekrsvvvid.deslgiekds.ykdsakekalRsslrsavkrd 67
                                  ++ ++G   +GK+ ++  L kal+++  s+ v+d d   ++ +   ++ +++  ++R++l++ v+rd
  gi|15668866|ref|NP_247669.1|  2 IIAVSGKGGVGKTAFTTLLIKALSKKTNSILVVDaDPDSNLPETLgVEVEKTVGDIREELKKLVERD 68
                                  578999999************************95555666666569999**************996 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.6
                                   SHHHHHHHHHHHHHHTT--EEEE-T CS
                         KTI12  13 GKstrakeLakaleeekrsvvvidd 37 
                                   G  +r k+La++le + ++++v+ +
  gi|15668866|ref|NP_247669.1| 163 GTAKRIKKLANELEVKFKDIYVVAN 187
                                   4556677777777777777777755 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0049       3.2     102     130 ..       3      31 ..       1      37 [. 0.90
   2 ?    4.6   0.0     0.041        27       7      62 ..     139     195 ..     133     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0049
                                   EEEECSTTSSHHHHHHHHCTT-----S-- CS
                   RsgA_GTPase 102 svlvGqSGvGKStLinallpelelktgev 130
                                   +++ G+ GvGK+++   l+  l+ kt+++
  gi|15668866|ref|NP_247669.1|   3 IAVSGKGGVGKTAFTTLLIKALSKKTNSI 31 
                                   6789****************999999987 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.041
                                   EETTTTEES--EEEEEEESTTTT--H.HHHHHHHHHHHHTT-EEEEEEE-GGG--HH CS
                   RsgA_GTPase   7 elvrpkvaNvdqllivvslkepelsl.nlldrfLvlaeekgiepvivlnKiDlleee 62 
                                    l+r++  Nvd +++++ +++  l + ++++++  ++e k  ++ +v nK+    ee
  gi|15668866|ref|NP_247669.1| 139 HLSRRTTQNVDVMIVITDASKRGLGTaKRIKKLANELEVKFKDIYVVANKVKPEYEE 195
                                   689999999999999998887776541567776667777777888888887655444 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.2   5.4e+03      57      74 ..      22      38 ..      13      41 .. 0.54
   2 ?   12.3   0.1   0.00022      0.15      38     100 ..     121     184 ..      21     187 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.2
                                  HHHHHHHSEEEEECSSSH CS
                        Toprim 57 kelakradeiilatDpDr 74
                                  k l+k+ +  il  D+D 
  gi|15668866|ref|NP_247669.1| 22 KALSKKTN-SILVVDADP 38
                                  44444444.455555554 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00022
                                   TTEEEEE.ECTTTHHHHHHHHHHH.HHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEE CS
                        Toprim  38 efkpvye.eiedkkkvlkalkela.kradeiilatDpDreGeaiawellevlkellenkigrvef 100
                                   ++ + ye ++ d++  l+ l ++  +++d  i+ tD+ + G  +a+++ +++ el   k++ +++
  gi|15668866|ref|NP_247669.1| 121 NLAKDYEfVVIDTEAGLEHLSRRTtQNVDVMIVITDASKRGLGTAKRIKKLANELEV-KFKDIYV 184
                                   5556666888888888888888888************************77774433.3666665 PP

>> PDDEXK_10  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   9.2e-05     0.061      15      73 ..     150     206 ..     144     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.2e-05
                     PDDEXK_10  15 ilvEiksslkrgDlavikrkkelYekakgvkvdrlivvtpfiddrnpervkavAerlgi 73 
                                   +++ i+ + krg l + kr+k+l + + +vk + ++vv+  +  +++e + + A++lg+
  gi|15668866|ref|NP_247669.1| 150 VMIVITDASKRG-LGTAKRIKKLANEL-EVKFKDIYVVANKVKPEYEELIDNYAKELGL 206
                                   677788888887.9999*****98776.6888*************************97 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0092       6.1      16      46 ..       3      33 ..       1      41 [. 0.87
   2 ?    3.8   0.0     0.052        34      13      59 ..     149     197 ..     137     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0092
                       Pox_A32 16 lalvGgsGsGktvyLlsLlrtlvkkykhifL 46
                                  +a+ G+ G Gkt++   L++ l kk   i++
  gi|15668866|ref|NP_247669.1|  3 IAVSGKGGVGKTAFTTLLIKALSKKTNSILV 33
                                  6889******************999877765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.052
                       Pox_A32  13 pFrlalvG..gsGsGktvyLlsLlrtlvkkykhifLltpvknseYdkyv 59 
                                   +  ++++   + G G    ++ L ++l  k+k i+++     +eY++ +
  gi|15668866|ref|NP_247669.1| 149 DVMIVITDasKRGLGTAKRIKKLANELEVKFKDIYVVANKVKPEYEELI 197
                                   55555554114588888899******************99999998866 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4    0.0002      0.13     131     182 ..       2      53 ..       1      82 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                         T2SSE 131 lilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnak 182
                                   +i vsG  g GKt ++  l+k + k+++ i++v      +l +   v++++ 
  gi|15668866|ref|NP_247669.1|   2 IIAVSGKGGVGKTAFTTLLIKALSKKTNSILVVDADPDSNLPETLGVEVEKT 53 
                                   688***********************99999998777777777777766665 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.4   2.3e+03      45      64 ..      18      37 ..       4      62 .. 0.75
   2 ?   10.9   0.1   0.00076      0.51      35      84 ..     135     178 ..     127     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.4
                      Toprim_4 45 enlveaekkvkevilaldgD 64
                                  + l++a++k ++ il++d+D
  gi|15668866|ref|NP_247669.1| 18 TLLIKALSKKTNSILVVDAD 37
                                  35666777778899999988 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00076
                      Toprim_4  35 dgirpeklktenlveaekkvkevilaldgDaeGeataerlaellleegvk 84 
                                   +g++ ++++t      +++v+ +i+ +d++++G  ta+r+++l +e +vk
  gi|15668866|ref|NP_247669.1| 135 AGLEHLSRRT------TQNVDVMIVITDASKRGLGTAKRIKKLANELEVK 178
                                   4444334444......5789**********************55444444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.4    0.0016       1.1       3      38 ..       2      37 ..       1      38 [. 0.93
   2 ?    2.4   0.2      0.16     1e+02      83     113 ..     125     156 ..     108     207 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  +i++ G  G+GKT  ++ L + l+k+ +++l+v aD
  gi|15668866|ref|NP_247669.1|  2 IIAVSGKGGVGKTAFTTLLIKALSKKTNSILVVDAD 37
                                  68899***************************9988 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.16
                                   TSSEEEEEE.--SSTTHHHHHHHHHHHHHHHS CS
                         SRP54  83 kidvvlvDT.aGrlqndkelmeelkkikkvvk 113
                                   ++++v++DT aG  +  ++  ++++ +  +++
  gi|15668866|ref|NP_247669.1| 125 DYEFVVIDTeAGLEHLSRRTTQNVDVMIVITD 156
                                   45555555544554444444444444433333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.7     0.073        49       2      27 ..       3      28 ..       2      40 .. 0.79
   2 ?    7.2   0.1    0.0077       5.1      45     114 .]     125     188 ..     107     188 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.073
                                  EEEEESTTSSHHHHHHHHHTSTEEES CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltgekaivs 27
                                  +a+ G+  vGK+ +   l+++ ++ +
  gi|15668866|ref|NP_247669.1|  3 IAVSGKGGVGKTAFTTLLIKALSKKT 28
                                  7899999****999999998855433 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0077
                                   TEEEEEEEC.GGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT......TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  45 gkeielvDt.pGliegaseekglgkaflaleeadlillvvdas......eeklkpldeeleelleeakkplilvlnk 114
                                   + e++++Dt +G +e       l+++  +  ++d+++++ das           +  ++l++ le + k++ +v+nk
  gi|15668866|ref|NP_247669.1| 125 DYEFVVIDTeAG-LE------HLSRRTTQ--NVDVMIVITDASkrglgtA----KRIKKLANELEVKFKDIYVVANK 188
                                   567788888556.66......45555554..789*******994443321....22233333333356788888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1157  (0.0645323); expected 358.6 (0.02)
Passed bias filter:                      829  (0.0462379); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 1500.11
//
Query:       gi|15668867|ref|NP_247670.1|  [L=580]
Description: hypothetical protein MJ_0686 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-32  111.8   3.0    5.2e-32  111.8   3.0    2.6  2  DUF262        Protein of unknown function DUF262
  ------ inclusion threshold ------
      0.028   14.2   1.8      0.056   13.3   0.2    2.3  2  T6PP_N        Trehalose-6-phosphate phosphatase N-terminal he
        0.1   12.7   0.9         21    5.2   1.1    2.7  2  Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
       0.12   11.7   0.1       0.22   10.8   0.1    1.3  1  MCH           Cyclohydrolase (MCH)
       0.32   10.9   1.9       0.54   10.2   0.2    2.3  2  HNH_4         HNH endonuclease


Domain annotation for each model (and alignments):
>> DUF262  Protein of unknown function DUF262
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   3.0   1.4e-35   5.2e-32       2     220 ..      11     246 ..      10     247 .. 0.75
   2 ?   -3.0   6.3       1.8   6.5e+03     103     157 ..     495     563 ..     347     579 .. 0.64

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 1.4e-35
                        DUF262   2 edllskskrg.lriPdfQRpyvWeeeqveeLiedllalkgyplGsivlw.....................skaadsagele 60 
                                    dl++k  +g   +PdfQR++vW+++ +eeLi++l  l+++++G+++++                     ++ +  +++ +
  gi|15668867|ref|NP_247670.1|  11 LDLVKKAYEGeVALPDFQRNFVWTRQDIEELIKSL--LENMFIGTFLIQeinpenppfgtiyirgaeelnPNITLRKPRIL 89 
                                   5788888888899**********************..*****************************8876666666***** PP

                        DUF262  61 viDGQQRltTltlllaatkeesekriknleaeiek..ekeeededrlkrreresdkellqkllrseklsleekeelaelns 139
                                   v+DGQQRlt+l+ +++            l++   +  +++  d ++l  +  + +   l+k +r++k+ l+e+ +++++ +
  gi|15668867|ref|NP_247670.1|  90 VLDGQQRLTSLFYAIYS-------PNFPLKNT--TkpYAFFIDLNKLVEDDIDNSVFSLSKDCRQYKALLNED-NSFDIEK 160
                                   *****************.......22222222..134666666666666666677777777777776654442.3333333 PP

                        DUF262 140 ltkkdl.akeekrneeknlikayevieeilksa....llsalktklslieieleseddedqayeiFerlNsrGvpLtasel 215
                                   l++k + + +  +n++k ++  y+++ ei+ ++    + + l++k+  + + l+  d+++q+  +Fer+N++G +L++++l
  gi|15668867|ref|NP_247670.1| 161 LKEKRFfPLTFLSNSNKFYKIWYKHFSEIFPEEvfnyMHNILEYKVPTLILGLSYNDKPEQVVVLFERINKTGIKLSPYDL 241
                                   33333357778889999999999999988888755433333333334444444466************************* PP

                        DUF262 216 lkall 220
                                   l a++
  gi|15668867|ref|NP_247670.1| 242 LVARF 246
                                   **998 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.8
                        DUF262 103 drlkrreresdkellqkllrseklslee.keelaeln......sltkkdl.......akeekrneeknl 157
                                   ++++ + + +  + + +++++++ls+ e  ++ +e+       +  +++l       +k+e +++ +++
  gi|15668867|ref|NP_247670.1| 495 KKISKKSPSKYVKEMIEIQKNKGLSEDEaVNKVKEILkghfinEEMFEILrntddslSKDEIEENFNRF 563
                                   222222222222222222222222222211111111111111111111112222111332223333333 PP

>> T6PP_N  Trehalose-6-phosphate phosphatase N-terminal helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.1   3.8e+03      65      83 ..     128     146 ..     111     161 .. 0.63
   2 ?   13.3   0.2   1.6e-05     0.056      20      60 ..     527     567 ..     525     575 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                        T6PP_N  65 vrldikdEieeLekDlkFL 83 
                                   v+ di++ +  L kD++  
  gi|15668867|ref|NP_247670.1| 128 VEDDIDNSVFSLSKDCRQY 146
                                   5556666666666665433 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.6e-05
                        T6PP_N  20 vervLkgieirehfvesLknakesLeadcetgtevlelrtt 60 
                                   v+++Lkg  i+e++ e+L+n+ +sL++d+ ++++ + ++ +
  gi|15668867|ref|NP_247670.1| 527 VKEILKGHFINEEMFEILRNTDDSLSKDEIEENFNRFIELR 567
                                   89************************988877776655554 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.012        42      30      72 ..     401     443 ..     390     453 .. 0.84
   2 ?    5.2   1.1    0.0057        21      48     136 ..     486     570 ..     481     577 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHHHHH CS
                  Spore_III_AB  30 leelkralellegeirygatpLpealeklaeksesplseffee 72 
                                    +++ +++e l+ ei+yga +L+++ ++ ++k+++ ++ +f++
  gi|15668867|ref|NP_247670.1| 401 NNKIPEVVENLKIEIQYGAYSLKKVKSSGSSKYKGVFNLIFKN 443
                                   5666778899**************9999999999998888875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0057
                                   SS-.HHHHHHHHHHCS-TTHHHHHHHHHHHHH.STSS-HHHHHHHHHHHHGGGS---HHHHHHHHHHHHHHT--SHHHHHH CS
                  Spore_III_AB  48 atp.LpealeklaeksesplseffeevaerleekegesfeeaweeavekllkklaLkkedkeilkelgeslgysdregqlk 127
                                   +tp L e  +k+++ks s   ++++e+ e  ++++g s  ea ++ v++ lk   +++e  eil++  +sl + ++e++ +
  gi|15668867|ref|NP_247670.1| 486 KTPiLDETNKKISKKSPS---KYVKEMIEI-QKNKGLSEDEAVNK-VKEILKGHFINEEMFEILRNTDDSLSKDEIEENFN 561
                                   566578889999999998...666666653.44588888888776.56668999*****************9999998887 PP

                                   HHHHHHHHH CS
                  Spore_III_AB 128 alelaleel 136
                                    +  ++e+l
  gi|15668867|ref|NP_247670.1| 562 RFIELREKL 570
                                   776666655 PP

>> MCH  Cyclohydrolase (MCH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   6.1e-05      0.22     246     278 ..     421     453 ..     407     457 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.1e-05
                                   HHHHSSGGGSTTTTS-HHHHHHHTTTTGGGS-G CS
                           MCH 246 lakklpssaskdygkpFaeifkeaeydfykidk 278
                                    +kk+ ss s++y   F+ ifk+  +dfyk d+
  gi|15668867|ref|NP_247670.1| 421 SLKKVKSSGSSKYKGVFNLIFKNKPMDFYKPDN 453
                                   5799*************************9875 PP

>> HNH_4  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1         2   7.2e+03      32      40 ..     308     316 ..     300     320 .. 0.71
   2 ?   10.2   0.2   0.00015      0.54      10      54 ..     451     502 ..     447     503 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2
                                   -BSGGGEEE CS
                         HNH_4  32 dDsvsNkVL 40 
                                    D  +N+V+
  gi|15668867|ref|NP_247670.1| 308 NDESWNRVV 316
                                   577788885 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00015
                                   GGGGGG...SEEEESSTTTT---........BSGGGEEEES-GGGGTSSSSSS CS
                         HNH_4  10 iedlsdtkeydiDHilPrsrskd........DsvsNkVLvlrdaNqeKsnrtP 54 
                                   ++++    +++  Hi+P+ +           Dsv Nk+  l ++N++ s++ P
  gi|15668867|ref|NP_247670.1| 451 PDNIAY-YKLEDHHIFPKGFLRNkgisneyiDSVLNKTPILDETNKKISKKSP 502
                                   555553.566678********999**********************9555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3569.80
//
Query:       gi|15668868|ref|NP_247671.1|  [L=335]
Description: hypothetical protein MJ_0687 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-10   40.5   5.2    5.6e-07   29.1   4.2    3.5  2  DUF2092      Predicted periplasmic protein (DUF2092)
    1.8e-09   38.0   1.6    1.8e-09   38.0   1.6    3.3  3  DUF4367      Domain of unknown function (DUF4367)
    3.8e-08   33.3   5.5    2.8e-07   30.4   1.9    2.4  2  LolA_like    Outer membrane lipoprotein-sorting protein
      4e-07   29.9   0.2    9.4e-07   28.7   0.2    1.6  1  LolA         Outer membrane lipoprotein carrier protein LolA
  ------ inclusion threshold ------
      0.016   14.8   0.1      0.031   13.8   0.1    1.5  1  MucB_RseB    MucB/RseB N-terminal domain
       0.66   10.5   5.5        0.5   10.9   3.1    2.0  2  Phage_Gp111  Streptococcus thermophilus bacteriophage Gp111 p


Domain annotation for each model (and alignments):
>> DUF2092  Predicted periplasmic protein (DUF2092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   4.2   1.9e-10   5.6e-07       1     207 [.      27     203 ..      27     206 .. 0.81
   2 ?   -2.2   0.0       0.7   2.1e+03     146     185 ..     219     258 ..     211     266 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.9e-10
                       DUF2092   1 AeeiLkamsdylkalksfsvtadttydsvlasgqklqfsasrevkvqrPdklrvdtsgdekdrefyyDGktftlydkaenv 81 
                                   A+ei k+m++ ++a+ks++ ++ +t+  + +++     + + +   ++P+k++++    + d+ +++DGkt  +ydk++n 
  gi|15668868|ref|NP_247671.1|  27 ADEIAKKMQEKYEAMKSMEADVLITTNIMGQTE-----TMQYKYAFEKPNKFYME----NDDVLIVCDGKTYYMYDKKKNQ 98 
                                   78999********************99998885.....66678999*******97....789******************* PP

                       DUF2092  82 YaqapapgtidelldklqekygielPladlllsdpyedlteevksakyvgtskvngqecehl...afrnkdvdwqlWIsqg 159
                                   Y++++ +g+++++ +  + k          +++++ e++     +++y+g+++++g +c++l     +n + ++ + + ++
  gi|15668868|ref|NP_247671.1|  99 YTKMEIKGELNNMFNPDYGK----------FIKSMLEKF-----NVSYLGEKTYDGRKCYVLeliSKENPEEKMKMYV-DE 163
                                   ********776665433332..........344444443.....579***************5444456667777887.56 PP

                       DUF2092 160 dkpLprkivityktdpgapqytaefsdWnldpeipedtFrftpPkgAr 207
                                   ++  p+ki +           t+e+++ +++ ++p+d F+f+pP+gA+
  gi|15668868|ref|NP_247671.1| 164 EYWQPLKIEM--------DGVTIEYKNVKFNVDVPDDRFKFVPPEGAK 203
                                   6656667655........4678999*********************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.7
                       DUF2092 146 rnkdvdwqlWIsqgdkpLprkivityktdpgapqytaefs 185
                                   ++kdv + + + +    L ++  +++k++ ++  +++++ 
  gi|15668868|ref|NP_247671.1| 219 VQKDVSFKILVPKYTAGLELQNAMATKQNANNEESETVIL 258
                                   5788888888888888888888888888888888777775 PP

>> DUF4367  Domain of unknown function (DUF4367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   7.7      0.69   2.1e+03      10      82 ..      33     100 ..      24     127 .. 0.66
   2 !    6.2   0.3    0.0047        14      28      74 ..     136     181 ..     123     187 .. 0.89
   3 !   38.0   1.6   6.1e-13   1.8e-09      11     110 .]     242     333 ..     223     333 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.69
                       DUF4367  10 GykfkktnisedsesalleYkd.engelisfsiskqskeesqklsidtedaevekieingikatyyekedgeyv 82 
                                   ++++k + ++  + ++l++     + e+++   +k   e+ +k++++++d     i ++g++++ y+k++++y+
  gi|15668868|ref|NP_247671.1|  33 KMQEKYEAMKSMEADVLITTNImGQTETMQ---YKYAFEKPNKFYMENDDV---LIVCDGKTYYMYDKKKNQYT 100
                                   555555555555555555442223333333...346677778888888887...89999999999999998643 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0047
                       DUF4367  28 eYkdengelisfs.iskqskeesqklsidtedaevekieingikatyy 74 
                                   +Y  +  +++++  isk++ ee+ k+++d e+ +  kie +g +++y 
  gi|15668868|ref|NP_247671.1| 136 TY--DGRKCYVLElISKENPEEKMKMYVDEEYWQPLKIEMDGVTIEYK 181
                                   57..89999***********************************9996 PP

  == domain 3  score: 38.0 bits;  conditional E-value: 6.1e-13
                       DUF4367  11 ykfkktnisedsesalleYkdengelisfsiskqskeesqklsidtedaevekieingikatyyekedgeyvlvwedegvv 91 
                                   + +k++  +e+se+++l+Y  engel ++       ++++ l i  e+     + +ng ka + +++d  ++l++e++g+ 
  gi|15668868|ref|NP_247671.1| 242 MATKQNANNEESETVILTY-GENGELAIIE-----SKDNKPLTIP-ENGSNLITLKNGVKALISDSGDV-KMLMFEYNGIK 314
                                   467889999**********.4555555555.....6777777777.5555556778*************.9********** PP

                       DUF4367  92 ytlsgniskeelikiaesi 110
                                   + + g+++k+elikia+s+
  gi|15668868|ref|NP_247671.1| 315 VIIAGKLDKNELIKIANSM 333
                                   *****************98 PP

>> LolA_like  Outer membrane lipoprotein-sorting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   1.9   9.4e-11   2.8e-07      26     119 ..      85     173 ..      61     175 .. 0.89
   2 ?    3.9   0.1     0.013        38     159     177 ..     177     195 ..     174     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 9.4e-11
                                   STTEEEEEETTTTCEEEE-GGGTTSECCTTC.EHHHHC--SCCCEEEEEEEEEEETTEEEEEEEEEESS.TTSSECEEEEE CS
                     LolA_like  26 kdddlWlYlPalkrvrrisssdksqsfmGsdfsyeDlssrevedythellgeeevggkdcyvleltpkdaadvsYskivlw 106
                                   +++ +++Y+ + ++  ++  + + +++ + d  y+ + ++ +e++++++lge++++g++cyvlel+ k++     +k++++
  gi|15668868|ref|NP_247671.1|  85 DGKTYYMYDKKKNQYTKMEIKGELNNMFNPD--YGKFIKSMLEKFNVSYLGEKTYDGRKCYVLELISKEN---PEEKMKMY 160
                                   5678899999999999999999999999999..99999******************************95...457***** PP

                                   EETTT--EEEEEE CS
                     LolA_like 107 vdketylplkvef 119
                                   vd+e + plk+e+
  gi|15668868|ref|NP_247671.1| 161 VDEEYWQPLKIEM 173
                                   ***********97 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.013
                                   EEEEEEEEE--.--GGGCS CS
                     LolA_like 159 vleisevefdkglpdklFt 177
                                   ++e+++v+f+ ++pd+ F+
  gi|15668868|ref|NP_247671.1| 177 TIEYKNVKFNVDVPDDRFK 195
                                   689**************96 PP

>> LolA  Outer membrane lipoprotein carrier protein LolA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.2   3.1e-10   9.4e-07      28     164 ..      64     196 ..      51     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.1e-10
                                   EEEEETTTEEEEEE-TTS-EEEEEETTEEEEEETTTTEEEEEEHHHHTTT-GGGGGGS-HHHHTTTEEEE...EEEETTEE CS
                          LolA  28 klaikrPgkfrweytsPdeqlivsdgktvwlydpdleqvtieslkqalsktplvlLledkaklskdynvs...vkkeqdld 105
                                   k a+++P+kf++e +     liv dgkt  +yd++ +q+t +++k +l++       +  +++ +++nvs   +k  ++ +
  gi|15668868|ref|NP_247671.1|  64 KYAFEKPNKFYMENDD---VLIVCDGKTYYMYDKKKNQYTKMEIKGELNNMFNPDYGKFIKSMLEKFNVSylgEKTYDGRK 141
                                   56899*******9887...*********************99999999988777677777888889999986667778889 PP

                                   EEEEEESSS-SSECEEEEEE.ETTEEEEEEEEETT--EEEEEEEEEEES----GGGG-- CS
                          LolA 106 tltlkpkakdanlsritigfdkkgllkqlkvvdaqGqrttitfsnvkenakladdlFkf 164
                                   +++l+  +k++  +++++++d++   + lk    + +  ti+ +nvk n +++dd+Fkf
  gi|15668868|ref|NP_247671.1| 142 CYVLELISKENPEEKMKMYVDEEY-WQPLK---IEMDGVTIEYKNVKFNVDVPDDRFKF 196
                                   999999999***********8777.44444...44445788889**************9 PP

>> MucB_RseB  MucB/RseB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     1e-05     0.031      66     147 ..      88     173 ..      34     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1e-05
                     MucB_RseB  66 scfepeskavsvesrkikdslpallpadle....aleehYefrllGreRvAgreaqvvrilPkDqlRYgyrlwiDeetgLl 142
                                   ++++ ++k+   ++ +ik++l ++++ d      ++ e ++++ lG++   gr++ v+++++k++   ++++ +Dee   +
  gi|15668868|ref|NP_247671.1|  88 TYYMYDKKKNQYTKMEIKGELNNMFNPDYGkfikSMLEKFNVSYLGEKTYDGRKCYVLELISKENPEEKMKMYVDEEYWQP 168
                                   344445555555555555666666655555555599********************************************* PP

                     MucB_RseB 143 Lksdl 147
                                   Lk+++
  gi|15668868|ref|NP_247671.1| 169 LKIEM 173
                                   **998 PP

>> Phage_Gp111  Streptococcus thermophilus bacteriophage Gp111 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.1   0.00017       0.5      46     113 ..      39     103 ..      18     109 .. 0.74
   2 ?   -1.8   0.0       1.5   4.3e+03      51      81 ..     154     184 ..     128     195 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                   Phage_Gp111  46 elkadvrkfrawvaeivgkgkkyklkrelenaaegkkdkvgekvfdvesgkeYeiavdkesrrfiavk 113
                                   e  ++++    + ++i+g++++++ k  +e+ +  k+   +++v  v++gk+Y ++ dk+++++++++
  gi|15668868|ref|NP_247671.1|  39 EAMKSMEADVLITTNIMGQTETMQYKYAFEKPN--KFYMENDDVLIVCDGKTYYMY-DKKKNQYTKME 103
                                   4444444444455899****************9..77777789999*********9.88888887643 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                   Phage_Gp111  51 vrkfrawvaeivgkgkkyklkrelenaaegk 81 
                                    +k++++v e+  +  k++++ +  + +++k
  gi|15668868|ref|NP_247671.1| 154 EEKMKMYVDEEYWQPLKIEMDGVTIEYKNVK 184
                                   4566666666666666666655555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1455  (0.0811534); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2146.78
//
Query:       gi|15668869|ref|NP_247672.1|  [L=147]
Description: hypothetical protein MJ_0688 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-56  187.2   0.3    1.1e-55  187.0   0.3    1.0  1  UPF0146   Uncharacterised protein family (UPF0146)
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.035   14.4   0.0    1.4  1  TrkA_N    TrkA-N domain


Domain annotation for each model (and alignments):
>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.0   0.3   1.2e-59   1.1e-55       1     129 []      16     145 ..      16     145 .. 0.98

  Alignments for each domain:
  == domain 1  score: 187.0 bits;  conditional E-value: 1.2e-59
                                   HHHHHHHHHHHS-SSEEEEET-TT--HHHHHHHHHS-EEEEE-SS-S........STTEE---SSS--HHHHTTEEEEEEE CS
                       UPF0146   1 lvelakkiaeenargkvvEvGiGrkldvaealakrgvdlvatDikek...kak.egvrivrDDvtdPnleiYkgadliYsl 77 
                                   +ve++kk+aeen+++k++E+GiG+k+dva++l+k+ +dl+a+Di+ek   kak +g+++++DD+++Pn+++Yk++dliYs+
  gi|15668869|ref|NP_247672.1|  16 IVEFIKKFAEENNCKKIAEIGIGFKFDVARELSKY-FDLIAIDINEKaieKAKlLGLNAYKDDLFNPNISLYKNIDLIYSI 95 
                                   689********************************.***********99999999************************** PP

                                   S--TTSHHHHHHHHHHHT-EEEEE-BTTB-----TT-EEEEETTEEEEEEE- CS
                       UPF0146  78 RpPaelqsaildvakkvgAaliikpLlgedvvvekelklvnykgalFyikea 129
                                   RpP++lq++ild++kkv+A+lii+pLl+e++  +kelkl+nykg++Fyike+
  gi|15668869|ref|NP_247672.1|  96 RPPRDLQPYILDLSKKVNANLIIRPLLNEMP--IKELKLKNYKGEVFYIKEK 145
                                   ******************************9..9***************986 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.9e-06     0.035      13      54 ..      43      83 ..      39      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-06
                                  HHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHH CS
                        TrkA_N 13 laeeLseggkdvvvidkdeerveelreeglevvvgdatdeev 54
                                  +a+eLs++  d ++id +e+++e+++  gl++++ d  ++++
  gi|15668869|ref|NP_247672.1| 43 VARELSKYF-DLIAIDINEKAIEKAKLLGLNAYKDDLFNPNI 83
                                  89*****99.6***********************99988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1126.11
//
Query:       gi|15668870|ref|NP_247673.1|  [L=52]
Description: 50S ribosomal protein L39e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-19   68.8  10.4    2.6e-19   68.5  10.4    1.1  1  Ribosomal_L39  Ribosomal L39 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5  10.4   1.5e-23   2.6e-19       1      42 []      10      51 ..      10      51 .. 0.99

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 1.5e-23
                 Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkLk 42
                                  kK+rLaKalkqNr+vP +v++kt+ +vr +pk+R WRr+kLk
  gi|15668870|ref|NP_247673.1| 10 KKVRLAKALKQNRRVPLFVIVKTRGRVRFHPKMRYWRRKKLK 51
                                  7****************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.51
# Mc/sec: 309.23
//
Query:       gi|15668871|ref|NP_247674.1|  [L=200]
Description: hypothetical protein MJ_0690 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00024   20.7   0.0    0.00074   19.1   0.0    1.7  2  QueC           Queuosine biosynthesis protein QueC
     0.0013   18.5   0.0     0.0018   18.0   0.0    1.2  1  Asn_synthase   Asparagine synthase
     0.0057   15.5   0.0     0.0078   15.0   0.0    1.3  1  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
      0.029   14.4   0.0      0.049   13.7   0.0    1.4  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.6e-07   0.00074       4      65 ..       8      64 ..       5      80 .. 0.85
   2 ?   -1.3   0.0      0.27   1.2e+03     142     170 ..     119     147 ..     109     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-07
                                  EE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGG CS
                          QueC  4 vllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllk 65
                                  vl+SGG DS+  +++ kk g++ +++t+++g   +   + a++ ak lg  +hk+++ld  +
  gi|15668871|ref|NP_247674.1|  8 VLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPS--YKLAEETAKILGF-KHKVITLD--R 64
                                  89*****************************8755..5778999999999.99998887..3 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.27
                                   HHHHHHHTS--EEE-TTTT--HHHHHHHH CS
                          QueC 142 kalnlgedkkieieaPlidlsKaeivklg 170
                                   ++ +l + k+i+  +Pl+ +  +   +l+
  gi|15668871|ref|NP_247674.1| 119 EIQSLEMRKNIQYITPLMGFGYKTLRHLA 147
                                   45566688999999999987666555555 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     4e-07    0.0018      20      94 ..       6      77 ..       1      84 [. 0.89

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4e-07
                  Asn_synthase 20 vGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyh 94
                                  v +l+SGG DSSl a ++++    + +  +i f     +  k a+e+a+ lg +h  + l+++ +++a + +i+h
  gi|15668871|ref|NP_247674.1|  6 VHVLFSGGKDSSLSAVILKKLGY-NPHLITINF--GVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADMIIEH 77
                                  6789****************985.99*******..99******************99999998777777766665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.7e-06    0.0078       2      33 ..       5      36 ..       4      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-06
                 tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigvflk 33
                                   v v++SgG DSs++a++lk+ gy+   ++++
  gi|15668871|ref|NP_247674.1|  5 DVHVLFSGGKDSSLSAVILKKLGYNPHLITIN 36
                                  799*********************98777665 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.1e-05     0.049       3     126 ..       7     126 ..       5     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                                   EEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHC.HH CS
                   PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyee.aa 82 
                                    v++sgGkds+    ++ k  ++ +++ ++ g   +  +++ +e+++ +g++ kv + ++++ ek +   + +++y   a+
  gi|15668871|ref|NP_247674.1|   7 HVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPS--YKLAEETAKILGFKHKVITLDRKIVEKAADMII-EHKYPGpAI 84 
                                   689********************99*****998765..99*********9998888888877776666553.344444799 PP

                                   HHHHTHHHHHHHHHCTTECEEE----CCCTT.TTTTSSSEEECTT CS
                   PAPS_reduct  83 eriaKveplkkaLekldedalltGaRrdesk.sraklpiveided 126
                                   +++ K++      ++++  +l  G Rrd+   + +  +i++ + +
  gi|15668871|ref|NP_247674.1|  85 QYVHKTVLEIL-ADEYS--ILADGTRRDDRVpKLSYSEIQSLEMR 126
                                   99999875554.58888..*********97644444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1233.82
//
Query:       gi|15668872|ref|NP_247675.1|  [L=109]
Description: hypothetical protein MJ_0691 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.4e-24   84.6  14.1    6.4e-24   84.4  14.1    1.0  1  dsDNA_bind  Double-stranded DNA-binding domain
  ------ inclusion threshold ------
      0.072   12.4   1.0      0.088   12.1   1.0    1.1  1  DnaB_C      DnaB-like helicase C terminal domain


Domain annotation for each model (and alignments):
>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4  14.1   7.1e-28   6.4e-24       1     111 []       6     109 .]       6     109 .] 0.89

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 7.1e-28
                                   XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--SS CS
                    dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGql 81 
                                   i++++l elq++  +++      +q+e+    ++e +k+a+L++iL+peAreRL+rirl++pe aeave +Liqlaq G+l
  gi|15668872|ref|NP_247675.1|   6 IKRKKLLELQKKLAEQQ------QQEEALL--EAEMQKRALLRKILTPEARERLERIRLARPEFAEAVEVQLIQLAQLGRL 78 
                                   89999999999876433......3333433..4899********************************************* PP

                                   -----HHHHHHHHHHHS-.--XXXXX..XXX CS
                    dsDNA_bind  82 rskvteeqLkeLLeqvae.kkketkivisrr 111
                                      +++e++k LLe+++  +k++ +i+i r+
  gi|15668872|ref|NP_247675.1|  79 PIPLSDEDFKALLERISAlTKRKREIKIVRK 109
                                   *******************999999998875 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.0   9.8e-06     0.088      37     121 ..      12      98 ..       7     107 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.8e-06
                                   HHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHTTSXHHHHHHHHH.HHHHHHHSEEEEEEXS.SXCHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxx RF
                        DnaB_C  37 lniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtgklkeedweklte.aieelseaklfiddtp.altvs 115
                                   l++ ++ a++++++ a+   em+++ l++++l+ ea+ +++++r ++ + ++  +++  ++++l ++++ + d+  +  ++
  gi|15668872|ref|NP_247675.1|  12 LELQKKLAEQQQQEEALLEAEMQKRALLRKILTPEARERLERIRLARPEFAEAVEVQLiQLAQLGRLPIPLSDEDfKALLE 92 
                                   567788888888999**********************99999998877644444443326789999999998876233334 PP

                                   HHHHHH CS
                                   xxxxxx RF
                        DnaB_C 116 eirska 121
                                   +i + +
  gi|15668872|ref|NP_247675.1|  93 RISALT 98 
                                   444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1599  (0.0891851); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 735.53
//
Query:       gi|15668873|ref|NP_247676.1|  [L=148]
Description: 30S ribosomal protein S19e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-59  199.4   0.0    1.9e-59  199.3   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
    0.00036   20.4   0.0     0.0086   15.9   0.0    2.4  2  RuvB_C          RuvB C-terminal winged helix domain
     0.0027   17.6   0.0     0.0046   16.9   0.0    1.4  1  HTH_45          Winged helix-turn-helix
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.022   14.8   0.0    1.5  1  HemN_C          HemN C-terminal domain
      0.027   14.1   0.1        0.1   12.3   0.0    1.9  2  GntR            Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.3   0.0   5.3e-63   1.9e-59       1     135 [.       3     135 ..       3     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 199.3 bits;  conditional E-value: 5.3e-63
                                   TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS---- CS
                Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGgkkrr 81 
                                   tv+dVpa++li++ ae+Lk+  ++ vPew+d+vKtg+++e+ p+++dW+y+R+AsilRk+y+ gpvGv+rlr++YGg+k+r
  gi|15668873|ref|NP_247676.1|   3 TVYDVPADKLIQKTAEKLKEM-NIGVPEWVDFVKTGVSRERRPDQDDWWYIRCASILRKIYIYGPVGVSRLRTAYGGRKNR 82 
                                   79*****************98.7********************************************************** PP

                                   ---THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXX CS
                Ribosomal_S19e  82 gvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeeva 135
                                   g++p+hf k+sg++irk+lq+Leklglv+k+ + gr++t+kG+++ld+ia+ev 
  gi|15668873|ref|NP_247676.1|  83 GHEPEHFYKGSGNIIRKALQELEKLGLVEKTPE-GRVVTPKGRSFLDNIAKEVR 135
                                   ****************************88856.******************96 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.057   2.1e+02      11      34 ..      54      77 ..      46      82 .. 0.81
   2 !   15.9   0.0   2.4e-06    0.0086      50      71 ..     106     127 ..      95     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.057
                                  HHHHHHHT.TT--B-HHHHHHHTT CS
                        RuvB_C 11 yLkllkekfkggpvglktlaailg 34
                                  + ++l + +  gpvg++ l ++ g
  gi|15668873|ref|NP_247676.1| 54 CASILRKIYIYGPVGVSRLRTAYG 77
                                  557899999*******99987765 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.4e-06
                                   HTTSEEEETTEEEE-HHHHHHH CS
                        RuvB_C  50 keglIertsrGRilTkkglkyl 71 
                                   k gl+e+t+ GR +T+kg ++l
  gi|15668873|ref|NP_247676.1| 106 KLGLVEKTPEGRVVTPKGRSFL 127
                                   789***************9998 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.3e-06    0.0046      35      71 ..      96     132 ..      93     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.3e-06
                        HTH_45  35 llnkYLdmLvekglikkskekYvlTekGlelleklke 71 
                                   +++k L+ L + gl++k+ e  v+T kG+ +l+++ +
  gi|15668873|ref|NP_247676.1|  96 IIRKALQELEKLGLVEKTPEGRVVTPKGRSFLDNIAK 132
                                   56788****************************9864 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   6.3e-06     0.022      37      65 ..      96     124 ..      79     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.3e-06
                        HemN_C  37 llaaaleklqeqGLLeldggrlrltprGr 65 
                                   + ++al++l++ GL+e + ++ ++tp+Gr
  gi|15668873|ref|NP_247676.1|  96 IIRKALQELEKLGLVEKTPEGRVVTPKGR 124
                                   56899***********************9 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.8e-05       0.1      34      58 ..      90     114 ..      88     119 .. 0.85
   2 ?   -2.1   0.0      0.88   3.2e+03       4      15 ..     129     140 ..     128     143 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.8e-05
                                   HTS-HHHHHHHHHHHHHTTSEEEET CS
                          GntR  34 fgVsrttvReALrrLeaeglverrq 58 
                                   ++ s + +R+AL++Le  glve  +
  gi|15668873|ref|NP_247676.1|  90 YKGSGNIIRKALQELEKLGLVEKTP 114
                                   6778899**************9665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.88
                                   HHHHHHHHHHHT CS
                          GntR   4 qvyerLredIls 15 
                                   +++ ++r++I++
  gi|15668873|ref|NP_247676.1| 129 NIAKEVRDEIIN 140
                                   577777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1032.05
//
Query:       gi|15668874|ref|NP_247677.1|  [L=241]
Description: hypothetical protein MJ_0693 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-09   35.5   0.1    8.8e-09   35.1   0.1    1.2  1  ThiF          ThiF family
  ------ inclusion threshold ------
       0.13   11.6   0.3       0.88    8.9   0.3    1.9  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1   9.8e-13   8.8e-09      13     152 ..      43     180 ..      29     240 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 9.8e-13
                                   HHHHHT.SEEEEE--SHHHHHHHHHHH...HHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT-TTSE CS
                                   xxxxxx.xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  13 qekLrd.skvllvGaGglGsellknLa...lsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealqeinpdve 89 
                                    +kL+   +v ++G+G lG  ++ +L    + Gv+k+ ++Dn kie  + +   l    ++G++K++ ++++  +      
  gi|15668874|ref|NP_247677.1|  43 ERKLKPkGEVSIIGCGRLGVRVAFDLLevhRGGVEKVYVFDNAKIEENDIVHRRL--GGKVGEYKVDFIKRFFGN-----R 116
                                   4566655899*************999733368*****************988878..689*******99987654.....6 PP

                                   EEEEES-CCGCCS-HHHHTT.-SEEEEE.SSSHHHHHHHHHHHHHHT-EEEE.EEEETTEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                          ThiF  90 veavteritdetvleelles.vDlVvda.lDniearrlvnracvkkgiplie.agtlgfegqvvvi 152
                                   vea++e+it+++ l +l+++ v +++ a  D+i++ +++ ++c ++gi+ i   g+ g+e ++ v 
  gi|15668874|ref|NP_247677.1| 117 VEAFRENITKDN-L-HLIKGdVAVICIAgGDTIPTTKAIINYCKERGIKTIGtNGVFGIEEKIKVC 180
                                   89********87.4.677651454433349*****************9999844666666666665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3   9.8e-05      0.88      38     150 ..      51     166 ..      36     178 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 9.8e-05
                                   EEEEES-SHHHHHHHHHHH...HTT-.EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S-.-STTTTTSBSHHH CS
                  2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlk...afgm.kviaydrskkkeeeeeelgvelvsleellaesDivslhlp.ltpetrhlinaee 113
                                   +v iiG+Gr+G +va  l      g+ kv+++d  k +e+   +   +    +    + D++        ++ r+ i++++
  gi|15668874|ref|NP_247677.1|  51 EVSIIGCGRLGVRVAFDLLevhRGGVeKVYVFDNAKIEEN---DIVHRRLGGKVGEYKVDFIKRFFGnRVEAFRENITKDN 128
                                   689***********98776222335567888888866444...33334444444445778887665415566788888888 PP

                                   HHCSTTTEEEEESS-GGGB.-HHHHHHHHHTTSCCEEE CS
                  2-Hacid_dh_C 114 lakmkkgailiNtaRGglv.deeaLleaLksgkiagaa 150
                                   l ++k ++ +i +a G+++  ++a+++  k++ i+ ++
  gi|15668874|ref|NP_247677.1| 129 LHLIKGDVAVICIAGGDTIpTTKAIINYCKERGIKTIG 166
                                   88888888888888888773567888888888877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1701.25
//
Query:       gi|15668875|ref|NP_247678.1|  [L=414]
Description: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-68  228.0   0.1    1.8e-67  227.2   0.1    1.4  1  Nop              snoRNA binding domain, fibrillarin
  ------ inclusion threshold ------
        5.9    7.2  20.9         14    5.9  20.9    1.7  1  Vfa1             AAA-ATPase Vps4-associated protein 1


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.2   0.1     2e-71   1.8e-67       2     229 ..     133     356 ..     132     361 .. 0.89

  Alignments for each domain:
  == domain 1  score: 227.2 bits;  conditional E-value: 2e-71
                                   HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT.HHHHHHHHHHHHCHHHH-SSS-S-H CS
                           Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkeedeelakevimaakvtastsmgaelse 82 
                                   + ++dk++n l++r+rewYs +FpEL++lv+++  Ya+++ ++g +r++++k++ ++ l+++    +  +a++smg el++
  gi|15668875|ref|NP_247678.1| 133 ISDLDKTLNLLSERLREWYSLYFPELDHLVNKHEVYANLITKLG-KRKNFTKSQLKKILPSKLAGKIAEAAKNSMGGELED 212
                                   579*****************************************.8899977743333666666666666777******** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HHHHCCCH CS
                           Nop  83 edlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaekalfral 163
                                    dl+ i ++++++ +l+e+rkel++Yle+ m++ APN+++L G +++arLi+ aGgL++LakmPastiq+lGaekalf +l
  gi|15668875|ref|NP_247678.1| 213 YDLDVIVKFAEEINHLYEKRKELYNYLEKLMNEEAPNITKLAGVSLGARLIGLAGGLEKLAKMPASTIQVLGAEKALFAHL 293
                                   ********************************************************************************* PP

                                   H.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHHHH CS
                           Nop 164 k.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekklk 229
                                   + + + pk+G+iy+++l+q + p ++++kiaR+la+K+a+aaR D  +   + + ++l e+++k+++
  gi|15668875|ref|NP_247678.1| 294 RmGVEPPKHGIIYNHPLIQGS-PHWQRGKIARALACKLAIAARADYVG---DYIADELLEKLNKRVE 356
                                   *777***************77.***********************874...3444455555555544 PP

>> Vfa1  AAA-ATPase Vps4-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  20.9    0.0016        14      66     123 ..     349     405 ..     333     414 .] 0.55

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0016
                          Vfa1  66 keleeeiekvkkeyeekqkkkkekekkkkekdkkdkdkkkekekdkkkekekeeekkk 123
                                   ++l++++e+++++y +  kkkk+++ k k+k+kk k++k++k+kdkkk+k+  ++++k
  gi|15668875|ref|NP_247678.1| 349 EKLNKRVEEIRRKYPKPPKKKKKEKPKAKKKEKKGKKEKSKKKKDKKKDKK-GKKERK 405
                                   457778888888888777666655555555554444433333333333333.222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3025  (0.168721); expected 358.6 (0.02)
Passed bias filter:                      999  (0.0557198); expected 358.6 (0.02)
Passed Vit filter:                       203  (0.0113224); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.45
# Mc/sec: 2747.85
//
Query:       gi|15668876|ref|NP_247679.1|  [L=108]
Description: hypothetical protein MJ_0695 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 767.60
//
Query:       gi|15668877|ref|NP_247680.1|  [L=182]
Description: hypothetical protein MJ_0696 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-06   27.6  10.7    6.8e-06   26.2  10.7    1.9  1  DUF986    Protein of unknown function (DUF986)
    0.00069   19.3   0.6      0.002   17.8   0.6    1.8  1  YcxB      YcxB-like protein
  ------ inclusion threshold ------
      0.011   15.4   1.5       0.47   10.1   0.2    2.2  2  DUF3341   Protein of unknown function (DUF3341)


Domain annotation for each model (and alignments):
>> DUF986  Protein of unknown function (DUF986)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2  10.7   1.1e-09   6.8e-06      50     129 ..      71     149 ..       3     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.1e-09
                        DUF986  50 liviliyqnvteegesltlyLLavlillaiYlafiRspklllKeeGffyanifieYkkikainlsedgilvidlekrrll 129
                                    i++ +++n+  +++s+   +L+++ +++i+ af ++  ++l ++G++y+n fi++k+i++++ ++dg++v+  +k+++l
  gi|15668877|ref|NP_247680.1|  71 NILLYVVYNCPVSITSIIAEILIIISMIIIWKAFNKEISVYLCDDGIYYSNKFISWKNIENVK-KDDGFIVLFGKKKKIL 149
                                   3567788899999999999******************************************98.5777777777776665 PP

>> YcxB  YcxB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.6   3.4e-07     0.002       4      40 ..     115     147 ..     114     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.4e-07
                          YcxB   4 dgievdsgggesiipWdsiekvkEtkdyfyLflsggs 40 
                                   dgi + s++    i W++ie+vk+++ +++Lf ++++
  gi|15668877|ref|NP_247680.1| 115 DGIYY-SNK---FISWKNIENVKKDDGFIVLFGKKKK 147
                                   77744.566...8*******************88876 PP

>> DUF3341  Protein of unknown function (DUF3341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0036        22     101     156 ..       4      56 ..       2      61 .. 0.85
   2 ?   10.1   0.2   7.9e-05      0.47      85     148 ..      83     146 ..      56     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0036
                                   HHHHHHHHHHTTTTTT-S-----TTTT-TTGGG.TTTS---EE--S-SS---HHHH CS
                       DUF3341 101 vLfaalatvlgllllnglprlyhpvfkaenfdrratdDkffllieatdpkfdeeel 156
                                   +Lf a+a ++  ++  ++++++ p +k++ f+r   + +++ lie ++ +fd++++
  gi|15668877|ref|NP_247680.1|   4 ILFIAIAFLINSFISYKITNMQ-PKIKSRIFKR--VKMHYLNLIEGKKAEFDKKAM 56 
                                   9*****************7776.999*****99..666777788888888888765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 7.9e-05
                                   -SS-HHHHHHHHTHHHHHHHHHHHHHTTTTTT-S-----TTTT-TTGGG.TTTS---EE--S-S CS
                       DUF3341  85 PlfslpafipitFEltvLfaalatvlgllllnglprlyhpvfkaenfdrratdDkffllieatd 148
                                    + s++a i+i+  + ++  a+   + ++l+     + +++++++n+++   dD f++l+ +++
  gi|15668877|ref|NP_247680.1|  83 SITSIIAEILIIISMIIIWKAFNKEISVYLCDDGIYYSNKFISWKNIENVKKDDGFIVLFGKKK 146
                                   47899***************************999**************889999999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1260  (0.0702772); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1292.42
//
Query:       gi|15668878|ref|NP_247681.1|  [L=230]
Description: fibrillarin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.2e-101  337.7   0.6   2.4e-101  337.6   0.6    1.0  1  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
       0.02   14.5   0.0      0.042   13.4   0.0    1.7  1  MTS              Methyltransferase small domain
       0.18   12.6   0.0       0.53   11.0   0.0    1.8  2  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.6   0.6  4.1e-105  2.4e-101       2     225 ..       5     228 ..       4     229 .. 0.99

  Alignments for each domain:
  == domain 1  score: 337.6 bits;  conditional E-value: 4.1e-105
                                   EEECSSTTEEEEE.TTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTTT CS
                   Fibrillarin   2 eeheklegvyivk.ekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaas 81 
                                   + +e +e++y+v+ ++g +r+atk++v+g+kvY+Ek+ik+++eEyR+Wnp++sKlaaai+kglk +pik++sk+LYlGa++
  gi|15668878|ref|NP_247681.1|   5 KIKEIFENIYEVDlGDGLKRIATKSIVKGKKVYDEKIIKIGDEEYRIWNPNKSKLAAAIIKGLKVMPIKRDSKILYLGASA 85 
                                   67899**************************************************************************** PP

                                   SHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHHHHHHH CS
                   Fibrillarin  82 GttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqarilaknak 162
                                   Gtt+sHv+Di + +g+vya+e++pr++rel++ + +R+ni+Pil+DA+kP++Y+++vekvDvi++Dvaqp+qa+il+knak
  gi|15668878|ref|NP_247681.1|  86 GTTPSHVADIAD-KGIVYAIEYAPRIMRELLDACAERENIIPILGDANKPQEYANIVEKVDVIYEDVAQPNQAEILIKNAK 165
                                   **********99.9******************************************************************* PP

                                   HHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEEEE CS
                   Fibrillarin 163 lflkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgkyk 225
                                   +flk+ggy +i+ikarsidvtk+p+e+fke++e l+  g+k++++v++ep+ekdh+++vg ++
  gi|15668878|ref|NP_247681.1| 166 WFLKKGGYGMIAIKARSIDVTKDPKEIFKEQKEILEAGGFKIVDEVDIEPFEKDHVMFVGIWE 228
                                   ***********************************************************9875 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     7e-06     0.042     111     168 ..     150     208 ..      60     209 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-06
                                   CHCHHHHHHHHHHHHHHHEEEEEE.EEEEEETTSCHHHHHHHHHS--EEEEEESSEEEE CS
                           MTS 111 katelavaeeliaeAkeaLkegGe.LliVanrklgyeslleelfgnvevvaktkkfkvl 168
                                     ++ + ae li++Ak +Lk+gG  ++ +  r +++ +  +e+f++ +++ + ++fk++
  gi|15668878|ref|NP_247681.1| 150 DVAQPNQAEILIKNAKWFLKKGGYgMIAIKARSIDVTKDPKEIFKEQKEILEAGGFKIV 208
                                   4457888999*************7377788899************************96 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.8e-05      0.53       1      97 []      78     172 ..      78     172 .. 0.82
   2 ?   -1.9   0.0      0.96   5.7e+03      80      97 .]     187     204 ..     177     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.8e-05
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSS...STTTEEEEEEESTGGGSS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpf...edgsfDlvvssgalhhls 78 
                                   +L lG+  G++  ++a+   k+ v++++++++ +++    ++e++ n+  + gda++ ++     +++D+++      + +
  gi|15668878|ref|NP_247681.1|  78 ILYLGASAGTTPSHVADIADKGIVYAIEYAPRIMRELLDACAERE-NIIPILGDANKPQEyanIVEKVDVIYE----DVAQ 153
                                   7899************99878***************999997765.9********776641115557777777....3456 PP

                                   HHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                   ++++e ++k+++  Lk+gG
  gi|15668878|ref|NP_247681.1| 154 PNQAEILIKNAKWFLKKGG 172
                                   77889999*********99 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.96
                                   HHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                   +d ++++ke +++L+ gG
  gi|15668878|ref|NP_247681.1| 187 KDPKEIFKEQKEILEAGG 204
                                   577899999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1582.58
//
Query:       gi|15668879|ref|NP_247682.1|  [L=197]
Description: imidazoleglycerol-phosphate dehydratase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-55  185.4   0.1    8.6e-55  185.0   0.1    1.1  1  IGPD      Imidazoleglycerol-phosphate dehydratase


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.0   0.1   4.8e-59   8.6e-55       1     144 []      36     176 ..      36     176 .. 0.99

  Alignments for each domain:
  == domain 1  score: 185.0 bits;  conditional E-value: 4.8e-59
                                   ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEEE--S CS
                          IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaevaldlsg 81 
                                   Tgi+f+dh+L ++akhg fdl vk++gdle+ddHhtvedvgi+lG al++   +kr+i Rfg+a++pmD+a a+va+dlsg
  gi|15668879|ref|NP_247682.1|  36 TGIPFFDHLLASFAKHGCFDLIVKARGDLEIDDHHTVEDVGICLGLALNQI--EKRNIFRFGWAIIPMDDARATVAIDLSG 114
                                   9************************************************98..59************************** PP

                                   S-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                          IGPD  82 rpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                   r+y+v + e kre +g+l+te++++ffes+a+   +++h +v+ g+n+hh++ealfKaf+ aL
  gi|15668879|ref|NP_247682.1| 115 RSYCVGNYEPKREFVGDLATENINHFFESVASYGMLNIHYEVI-GKNEHHKAEALFKAFGVAL 176
                                   *****9999**********************************.*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1419.88
//
Query:       gi|15668880|ref|NP_247683.1|  [L=380]
Description: chlorohydrolase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-53  181.9   0.0    2.4e-53  181.7   0.0    1.0  1  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
      0.037   13.5   0.0          2    7.8   0.0    2.4  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.7   0.0   2.7e-57   2.4e-53       1     339 [.      49     363 ..      49     371 .. 0.92

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 2.7e-57
                                   EEEE-EEEEEEECETTECSSS....GHHHHH.............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHH CS
                  Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl.............vppetaaealesgiktalksGtttvadmgattstgie 64 
                                   +v+P lI+aH+H+ ++ ++++    tl++++             ++++ +ae+++ g+  + ++G+ +++d++++ ++gi+
  gi|15668880|ref|NP_247683.1|  49 LVIPSLINAHTHIADNSIKDIginkTLDELVkppnglkhrylteCSDDLLAEGMKLGLGDMREHGIKYFCDFRENGVRGIS 129
                                   59**********************9999999************************************************** PP

                                   HHHHHHHT..SSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHH.... CS
                  Amidohydro_1  65 alleaaee..lplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealk.... 139
                                   +l +a+++  +     i++g      +  +++k+++e++++                +l+ ++a +f+d+elk ++k    
  gi|15668880|ref|NP_247683.1| 130 LLNKALKCydY--PKAIILG------RPIKVDKDEIEEVLKVS-------------NGLGLSGANEFKDDELKLIFKifkk 189
                                   ********543..2234444......99999********9998.............9********************9999 PP

                                   .HHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHH CS
                  Amidohydro_1 140 .eakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcp 219
                                    + k+ ++ +aiHa+e++g+ve++++++g     +t +e++ +l++  +    ++hg+hlt++++ellke+  ++ v+ c 
  gi|15668880|ref|NP_247683.1| 190 fKEKDDKKLFAIHAAEHRGAVEYSLNKYG-----MTEVERLIDLKIKPD---FIVHGTHLTDNDLELLKEN--NIPVVACV 260
                                   999999***********************.....99****999776555...5******************..******** PP

                                   HHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-T CS
                  Amidohydro_1 220 fsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalgld 300
                                   ++n++ + g+++l+++ d+ + vg+gtD + + ns+++++e+ + +kl++          +++k++lrmaTin+Ak+l+l+
  gi|15668880|ref|NP_247683.1| 261 RANLSFNVGMPKLNELNDN-LLVGIGTD-NFMANSPSIFKEMDFIYKLYH----------IEPKDILRMATINNAKILKLE 329
                                   ****************886.********.*****************6666..........********************5 PP

                                   TTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEE CS
                  Amidohydro_1 301 dkvGsievGkdADlvvvdldilaafvglkkdgnvkkviv 339
                                    +vG +++G++A ++++    +++ + l +++ +++v+ 
  gi|15668880|ref|NP_247683.1| 330 -NVGLVDEGFKAVFTFI----KPTNAILFSKNIIASVVT 363
                                   .****************....999999999999999987 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0    0.0074        66       8      22 ..      48      62 ..      43      70 .. 0.90
   2 ?    7.8   0.0   0.00023         2     411     443 ..     312     343 ..     307     361 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0074
                  Amidohydro_3  8 rlvlPGFvDsHtHla 22
                                  +lv+P ++ +HtH+a
  gi|15668880|ref|NP_247683.1| 48 GLVIPSLINAHTHIA 62
                                  58***********87 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00023
                  Amidohydro_3 411 eealalyTrgpAkalgledrkGtLevGadADlv 443
                                    ++l++ T + Ak+l+le   G + +G++A ++
  gi|15668880|ref|NP_247683.1| 312 KDILRMATINNAKILKLENV-GLVDEGFKAVFT 343
                                   579****************9.********9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2451.49
//
Query:       gi|15668881|ref|NP_247684.1|  [L=324]
Description: hypothetical protein MJ_0700 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-48  164.1   8.3    1.2e-47  162.1   8.3    1.9  1  MS_channel  Mechanosensitive ion channel
     0.0079   16.0   2.9     0.0079   16.0   2.9    2.2  2  DUF2976     Protein of unknown function (DUF2976)
  ------ inclusion threshold ------
      0.074   12.6   4.6       0.12   12.0   4.6    1.4  1  PMT_4TMC    C-terminal four TMM region of protein-O-mannosylt
        1.2    9.0   4.8        4.6    7.1   0.2    3.2  3  DUF3487     Protein of unknown function (DUF3487)


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   8.3   2.7e-51   1.2e-47       2     203 ..      82     302 ..      81     305 .. 0.97

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 2.7e-51
                                   .HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS........SEEE CS
                    MS_channel   2 kilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig........dieG 74 
                                    i+k+l++v+++l+++ ++++nvs+l++++G++g+a+++al+++i+n++++ii+l+++++kiGD++ i+        di++
  gi|15668881|ref|NP_247684.1|  82 YIFKYLVYVCVTLMIFGVIYQNVSSLVVSVGLIGAAVTYALQKPILNFAGWIIILYTRTIKIGDRIFIKnmgagdvfDIDT 162
                                   79******************************************************************************* PP

                                   EEEEE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-T... CS
                    MS_channel  75 tVediglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlk... 152
                                   +++ ++ +tt++ +++gr+++iPns+++t++ieNl+++s++ ++++++++t++s+++k+ek++ e ++++  + + +    
  gi|15668881|ref|NP_247684.1| 163 QHIYLSELTTDTFEPTGRVLIIPNSYIFTASIENLTKGSPYIWDNIVVHFTLNSNINKAEKIVFESADEVIGNLMRELyek 243
                                   **********************************************************************99999999999 PP

                                   .........TS-EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT CS
                    MS_channel 153 .........dkellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeeg 203
                                            +k  ++ + ++g+++ +f++++++    + e+ +++sein+ri +++++e+
  gi|15668881|ref|NP_247684.1| 244 wskrkylisRKLSDKPVVRVGITRSSFYIKALYLV-NVYEKAKIRSEINKRILEKVNKEN 302
                                   ********99***********************99.79*************999998875 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.62   2.8e+03      68      79 ..       8      19 ..       5      27 .. 0.58
   2 !   16.0   2.9   1.8e-06    0.0079      15      77 ..      30      97 ..      25     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.62
                       DUF2976 68 lvvGvvllvvvi 79
                                  lv+ vvll++ +
  gi|15668881|ref|NP_247684.1|  8 LVIKVVLLIFLL 19
                                  555566665543 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.8e-06
                       DUF2976 15 dllelikgylkdgvillgLvlaavaflaVakaalkkfneisegkae.wgk....fgltlvvGvvllvv 77
                                   +++++  y ++++i++ ++l+++ ++ +a++++kk++  +e+ka  +      f+ ++ v v l+++
  gi|15668881|ref|NP_247684.1| 30 TYIKILAKYQNQIMIIAIIILSGLIIVDIASEVFKKYARTREEKAGeYLTlnyiFKYLVYVCVTLMIF 97
                                  6899************************************9999842222111255566666666666 PP

>> PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.6   2.6e-05      0.12      63     162 ..      43     135 ..      10     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                      PMT_4TMC  63 stiallvfvllllalllrrqrgvkdleeeetrllnsglflllgwalhylPfflmgRvlf..lhhYlpAllfailllaalld 141
                                    +ia++++ +l+++++ ++  + ++  ++e+    +g +l l++++ yl ++ ++  +f  ++  + +l++++ l++a + 
  gi|15668881|ref|NP_247684.1|  43 MIIAIIILSGLIIVDIASEVFKKYAR-TREE---KAGEYLTLNYIFKYLVYVCVTLMIFgvIYQNVSSLVVSVGLIGAAVT 119
                                   45666666777777777777766655.3333...4688*********************77788899************** PP

                      PMT_4TMC 142 fllkslkkslkkkklvklivv 162
                                   + l++   +      +++i++
  gi|15668881|ref|NP_247684.1| 120 YALQKPILN-----FAGWIII 135
                                   *99444333.....3455554 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2     0.001       4.6      42      81 ..      33      72 ..       8      87 .. 0.74
   2 ?   -0.9   1.4      0.33   1.5e+03      51      64 ..     106     119 ..      78     149 .. 0.54
   3 ?    1.5   0.0     0.059   2.7e+02       5      28 ..     250     273 ..     246     281 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.001
                       DUF3487 42 llallvgslaliptialllvllvvlvggkllarlKRgkPd 81
                                   +++  ++ ++i++i++l+ l++v ++++++++  R + +
  gi|15668881|ref|NP_247684.1| 33 KILAKYQNQIMIIAIIILSGLIIVDIASEVFKKYARTREE 72
                                  3334456789************************999866 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.33
                       DUF3487  51 aliptialllvllv 64 
                                    l++ ++l++++++
  gi|15668881|ref|NP_247684.1| 106 SLVVSVGLIGAAVT 119
                                   23333333333333 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.059
                       DUF3487   5 flpdrLnrePvVfrGltadEllvl 28 
                                   ++ ++L  +PvV  G+t + + + 
  gi|15668881|ref|NP_247684.1| 250 LISRKLSDKPVVRVGITRSSFYIK 273
                                   57889************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1392  (0.0776396); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2054.69
//
Query:       gi|15668882|ref|NP_247685.1|  [L=414]
Description: hypothetical protein MJ_0701 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-32  112.7   0.7    3.4e-32  111.9   0.7    1.4  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
    0.00057   20.4   0.0    0.00057   20.4   0.0    3.2  4  Vac14_Fab1_bd    Vacuolar 14 Fab1-binding region
  ------ inclusion threshold ------
       0.02   14.7   6.3       0.16   11.7   0.5    3.0  3  SpoVIF           Stage VI sporulation protein F


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.7   5.6e-36   3.4e-32       3     265 ..     144     387 ..     142     403 .. 0.86

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 5.6e-36
                                   EEEEHHHHHHHTT.-G.......GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHHH CS
               DNA_primase_lrg   3 ykvpfedvldlvk.rr.......rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekleell 75 
                                    k+++++++++++ +r       r  l++G++ ++k + e + +e +r +l+k  e++k+++   ++++ke  +e+++ l+
  gi|15668882|ref|NP_247685.1| 144 NKISVWEFIKIASrSRindlhleRLDLENGFVDITKIK-EIFAKEIIRVELMKLGENIKKRKLPDDSVVKELLNEISDYLK 223
                                   69***********655999******************9.99999****************988877777777777777777 PP

                                   CT--.............TTSSTTGG.SHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHH................. CS
               DNA_primase_lrg  76 ealsesyvaedvqeeedskisakni.dklakesfPpCmrelleglkknghlkhegrlqltlFlk................. 138
                                   ++++         +e+ s+i+a n+ +++  e++PpC+r +l+++ ++g+++h++r++++++++                 
  gi|15668882|ref|NP_247685.1| 224 DKVK---------YEQISGIKALNYkGNIPLEWHPPCIRGILNDILSGGSPSHYARRSFVVYWFcakfnpnlrpldkngnl 295
                                   7777.........************9******************************************************* PP

                                   ......HCT--C......HHHHCCCHCHST..HHHHHH.HTHCHCHHHCC-STT--------.....HHHHHHS.....TT CS
               DNA_primase_lrg 139 ......diglsl......deilelwkeaftrteekFdk.eyrynirhnyGkegkrtnyspys.....Cekiltkppp.gkg 200
                                         di+ ++      de +e+  +    + e+Fd+ ++ry+i+hn+G       y++ +     Ce++++++++ gkg
  gi|15668882|ref|NP_247685.1| 296 vnvsatDIASEEeierfiDELIEMLFK----NVEDFDEkKTRYYIMHNIG-------YKVGHgrlthCEYCKNWQDDgGKG 365
                                   *99988776664444444555555444....69*****************.......5555555555************** PP

                                   ---S-HHHH.HHHHHHHHHHTT..HHHHHHHHHHHHTT.HHHHHHHHHHHHHS-TTT-SSCHHHC CS
               DNA_primase_lrg 201 dahgCpfrhdpdklktlLqeyglseediedilesvkegeyqvaCtkvFelthkcerdeikhPlqY 265
                                    +++C    +pd+l                                       c+++ i hPl+Y
  gi|15668882|ref|NP_247685.1| 366 LSYYC----KPDEL---------------------------------------CKKKFIIHPLDY 387
                                   *****....9***9.......................................555555555555 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.21   1.3e+03      53      83 ..      28      58 ..      18      70 .. 0.82
   2 ?   -3.1   0.1       2.1   1.2e+04      16      48 ..      99     132 ..      96     148 .. 0.59
   3 !   20.4   0.0   9.5e-08   0.00057       3      48 ..     291     337 ..     289     351 .. 0.89
   4 ?   -2.2   0.2       1.1   6.6e+03      52      67 ..     390     405 ..     387     406 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.21
                 Vac14_Fab1_bd 53 niakvakgevlkllneifdalvklvaDsdes 83
                                   + k++k+ ++  l++if   + +++   ++
  gi|15668882|ref|NP_247685.1| 28 DVLKMSKKFIIWRLKQIFGDSSTIFTNISSE 58
                                  5889999999999999998888888776655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.1
                 Vac14_Fab1_bd  16 alekk.ikeyleeivkpvlkcfsDkdsrvRyyac 48 
                                    ++k+ i++ l+ ++ ++l+     ++ vR ya 
  gi|15668882|ref|NP_247685.1|  99 EIKKEiITNLLDFLLIILLSHTPYFNAFVRKYAE 132
                                   5555555566666666666666666666666654 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 9.5e-08
                 Vac14_Fab1_bd   3 rkggligLaavaialekkikeyleeivkpvlkcfsDkd.srvRyyac 48 
                                   ++g l+ + a+ ia e++i+++++e++++++k ++D d +++Ryy +
  gi|15668882|ref|NP_247685.1| 291 KNGNLVNVSATDIASEEEIERFIDELIEMLFKNVEDFDeKKTRYYIM 337
                                   89**********************************872579***75 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.1
                 Vac14_Fab1_bd  52 yniakvakgevlklln 67 
                                   yni k +k+e +k+++
  gi|15668882|ref|NP_247685.1| 390 YNINKHLKKERFKKIK 405
                                   9******999888765 PP

>> SpoVIF  Stage VI sporulation protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2      0.49   2.9e+03      33      55 ..     123     145 ..      95     148 .. 0.50
   2 ?   11.7   0.5   2.7e-05      0.16      12      53 ..     190     231 ..     178     244 .. 0.89
   3 ?    4.9   0.0    0.0037        22      21      54 ..     297     330 ..     294     338 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.49
                        SpoVIF  33 lRqlikqvsklankpvskekedk 55 
                                      ++++ +++ + +v k+  +k
  gi|15668882|ref|NP_247685.1| 123 FNAFVRKYAEIKKIKVIKKLPNK 145
                                   44455555555555555555554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.7e-05
                        SpoVIF  12 kedilkLansvqkadlkdektlRqlikqvsklankpvskeke 53 
                                   + +++kL ++++k  l d+  +++l +++s+ ++ +v  e+ 
  gi|15668882|ref|NP_247685.1| 190 RVELMKLGENIKKRKLPDDSVVKELLNEISDYLKDKVKYEQI 231
                                   56899********************************99986 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0037
                        SpoVIF  21 svqkadlkdektlRqlikqvsklankpvskeked 54 
                                   +v+ +d+ +e+++ ++i+++ +++ k+v +  e+
  gi|15668882|ref|NP_247685.1| 297 NVSATDIASEEEIERFIDELIEMLFKNVEDFDEK 330
                                   6999***********************9987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1195  (0.0666518); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2497.71
//
Query:       gi|15668883|ref|NP_247686.1|  [L=594]
Description: DNA polymerase II small subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-10   39.5   0.0    8.1e-10   38.4   0.0    1.6  1  DNA_pol_E_B    DNA polymerase alpha/epsilon subunit B
    4.6e-10   40.4   0.6    4.6e-10   40.4   0.6    2.3  2  Metallophos    Calcineurin-like phosphoesterase
    6.7e-07   29.6   0.7    5.2e-05   23.5   0.0    2.7  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.091   13.0   0.2         31    4.9   0.2    3.3  3  DUF3135        Protein of unknown function (DUF3135)


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.8e-13   8.1e-10      69     193 ..     400     518 ..     326     527 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.8e-13
                                   HTHHHHTTS-TTSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EE CS
                   DNA_pol_E_B  69 lllsilesllekttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkres 149
                                   ++   l+++ e++++++ Pg  D++   + Pq+ lp+++++  +r   ++ +v NP+++ + + + +l+ +  ++dl  ++
  gi|15668883|ref|NP_247686.1| 400 EIAMYLDQIPEHISIIISPGNHDAVRP-AEPQPKLPEKITKLFNRD--NIYFVGNPCTLNIHGFDTLLYHGRSFDDLVGQI 477
                                   4556689999***************99.*****************7..7*******************9988888888877 PP

                                   ESHHHHHS-HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GG CS
                   DNA_pol_E_B 150 lkesntdverlrklvktildqrhlaPlaptlrpvswdkddalvl 193
                                      s    e+   ++k +++ r l+P++    p+  + +d lv+
  gi|15668883|ref|NP_247686.1| 478 RAASY---ENPVTIMKELIKRRLLCPTYGGRCPIAPEHKDYLVI 518
                                   77776...57789***************9888888888888876 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.6      0.04   1.8e+02      80     135 ..      36     112 ..      23     149 .. 0.61
   2 !   40.4   0.6     1e-13   4.6e-10       4     203 ..     326     532 ..     323     533 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.04
                                   HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE..EEEEEEESECEEE...................THHHHHHH CS
                   Metallophos  80 ellnkygylgifsepwrsdaevfnnlplaslgsgs..lkvlllhGgspel...................lvsldklg 135
                                   ++ ++ +y++ f  + +++ + f    l ++++ +  +++++++ g++e                     ++++ ++
  gi|15668883|ref|NP_247686.1|  36 KIREFKKYNNAFILLDEKFLDIFLQKDLDEIINEYkdFDFIFYYTGEEEKekpkevkkeikketeekieKEKIEFVK 112
                                   56677777788888888889999999999999999***********4444333334444443322222222222222 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 1e-13
                                   EEEESBTBTTCCTHHHHHHHHHHHH....HHH.......TTESEEEEESTSSSSS.........HHHHHHHHHHHHHHHH. CS
                   Metallophos   4 lvigDlHlalgggqlddllkllddl....lre.......ekpdlvllaGDlvdrg.........dlekellellaalvky. 63 
                                   ++++D+H+ + +  + +++k+++ l      +       ++  ++ +aGDlvd+           +e +++e++++  +y 
  gi|15668883|ref|NP_247686.1| 326 AFLSDIHVGSKEFLHKEFEKFIRFLngdvD-NeleekvvSRLKYICIAGDLVDGVgvypgqeedLYEVDIIEQYREIAMYl 405
                                   789****95566666666666655533331.1344334444599**********77********99999999999999999 PP

                                   .....TSEEEEEC-TTSCHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHH CS
                   Metallophos  64 .....pipvylllGNHegfee.ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgsln 138
                                        +i +++ +GNH++ +  e ++k ++  +  +++++d+ +f + p    + g +++ll+hG s ++   + +++  +
  gi|15668883|ref|NP_247686.1| 406 dqipeHISIIISPGNHDAVRPaEPQPKLPE--KITKLFNRDNIYFVGNPCTLNIHG-FDTLLYHGRSFDD--LVGQIRAAS 481
                                   999999999********3333344444333..227777777666666665554444.89*******3333..344444444 PP

                                   HSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                   Metallophos 139 leleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHv 203
                                   +e +++   +e++k+                p y g+ ++ ++e+ + l  + ++d+   GH+H 
  gi|15668883|ref|NP_247686.1| 482 YENPVTIM-KELIKR------------RLLCPTY-GGRCPIAPEHKDYLVIDRDIDILHTGHIHI 532
                                   44444444.666666............5678899.************99***************7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.018        81      70     119 ..      84     142 ..      62     145 .. 0.81
   2 !   23.5   0.0   1.1e-08   5.2e-05       4     151 ..     326     554 ..     324     569 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.018
                 Metallophos_2  70 vlreaaelgtdlpeeaelelagekvlliHgdpl.........gvkdalaellkeaeegs 119
                                     ++++e+++++++e e ++++ek+ +++++++          v+++l++l++++e+++
  gi|15668883|ref|NP_247686.1|  84 EKEKPKEVKKEIKKETEEKIEKEKIEFVKKEEKeqfikksdeDVEEKLKQLISKEEKKE 142
                                   46778888888888888888888888888887788888888899999999999977765 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.1e-08
                 Metallophos_2   4 aiiSDlH.................snldaleavlealkevgvdaiihaGD..........leeeep......evleellel 51 
                                   a++SD+H                  n+d  +++ e++ +  + +i+ aGD                      +++e+ +e+
  gi|15668883|ref|NP_247686.1| 326 AFLSDIHvgskeflhkefekfirfLNGDVDNELEEKVVSR-LKYICIAGDlvdgvgvypgQ----EedlyevDIIEQYREI 401
                                   7899999998888887777666666666666667777766.9********66665554440....1444555333333333 PP

                 Metallophos_2  52 a..........pvlaVrGNnD......eev.veedvlreaaelgtdlp.eeaelelagekvlliHgdpl............ 102
                                   a           +++ +GN+D      ++  + e++ + +++ + ++  +  +l++ g++ ll+Hg               
  gi|15668883|ref|NP_247686.1| 402 AmyldqipehiSIIISPGNHDavrpaePQPkLPEKITKLFNRDNIYFVgNPCTLNIHGFDTLLYHGRSFddlvgqiraasy 482
                                   3444555677789999*****88877522256777777777777777559999999**********977************ PP

                 Metallophos_2 103 .........................gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprd 151
                                                             ++++ ++l+ +   + d++  GH+H+ +    +gv++vn G  +e+ d
  gi|15668883|ref|NP_247686.1| 483 enpvtimkelikrrllcptyggrcpIAPEHKDYLVID--RDIDILHTGHIHINGYGIYRGVVMVNSGTFQEQTD 554
                                   *999999999999999999966554333333333333..5555*************************999855 PP

>> DUF3135  Protein of unknown function (DUF3135)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.007        31      17      47 ..     106     136 ..     102     141 .. 0.90
   2 ?   -1.0   0.0      0.49   2.2e+03      29      54 ..     153     178 ..     137     183 .. 0.79
   3 ?    3.8   0.0     0.016        70      25      66 ..     189     230 ..     187     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.007
                       DUF3135  17 ealealrqelieelIesapeemqrrLrglqf 47 
                                   e+ e +++e  e++I+++ e+  ++L++l +
  gi|15668883|ref|NP_247686.1| 106 EKIEFVKKEEKEQFIKKSDEDVEEKLKQLIS 136
                                   56788999********************987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.49
                       DUF3135  29 elIesapeemqrrLrglqfqiDmqls 54 
                                   e I++ +e+   r++ +  +iD +++
  gi|15668883|ref|NP_247686.1| 153 EHITKIKESVNSRIKWIAKDIDAVIE 178
                                   5799999**********999999987 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.016
                       DUF3135  25 elieelIesapeemqrrLrglqfqiDmqlsraknPvaacval 66 
                                   + +  +Ie+  + +++r ++l+  i+++ +r   P++   ++
  gi|15668883|ref|NP_247686.1| 189 STCTGTIEDFVKYFRDRFERLKVFIERKAQRKGYPLKDIKKM 230
                                   568889999999*******************99999876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2800  (0.156172); expected 358.6 (0.02)
Passed bias filter:                      783  (0.0436723); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.85u 0.29s 00:00:01.13 Elapsed: 00:00:00.48
# Mc/sec: 3739.10
//
Query:       gi|15668884|ref|NP_247687.1|  [L=226]
Description: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase HisA2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-31  108.2   4.7    1.8e-30  106.1   4.7    1.8  1  His_biosynth  Histidine biosynthesis protein
    2.2e-06   27.2   0.1    1.2e-05   24.8   0.1    1.9  2  ThiG          Thiazole biosynthesis protein ThiG
     0.0039   16.4   0.1       0.84    8.8   0.0    2.3  2  IGPS          Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
      0.052   12.6   0.1      0.097   11.8   0.1    1.3  1  Dus           Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   4.7   4.1e-34   1.8e-30       1     228 [.       2     215 ..       2     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 4.1e-34
                                   EEEEEEEEETTEEEEECTTCS......TCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSE CS
                  His_biosynth   1 riipalDlkdGkvVrlvkGdr......fqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfip 75 
                                   +iip++Dlkd  +V+ ++G+r      ++    + +p+e+ak+y+e ga+ ++++Dl+ +  g++ n d+++ei    fi+
  gi|15668884|ref|NP_247687.1|   2 KIIPVIDLKDKIAVHGKSGNRdeykplESVICKSSNPIEVAKAYKERGAKTIYIADLNFI-MGNGDNFDIIKEID---FIN 78 
                                   59*******************77777777777899**********************877.5**********996...568 PP

                                   EEEESSSSSHHHHHHHHHCT..-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHH CS
                  His_biosynth  76 vqvGGGIrsledveelleag..adkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelak 154
                                     v+ G++s ed+e++ +     d+ i++t+++k+ el+ke       + ivv++D+++g         +  ++++ e+++
  gi|15668884|ref|NP_247687.1|  79 KIVDIGVKSREDLETIKKVLnkDDRAIVATETLKDIELLKE-------KDIVVSLDFKNG---------NLLNYSLDEILS 143
                                   99******9988777665432268************99886.......58*********9.........334455555665 PP

                                   HHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                  His_biosynth 155 kleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegel 228
                                    + +     +++ di+++Gt+ G++ el+k + ++++ pv ++GG++ +edl+   + gvdav++++a+++g l
  gi|15668884|ref|NP_247687.1| 144 CVRD--DTPLIILDISSVGTQRGVNAELIKYVLDKTNNPVYVGGGIKGMEDLELCYNLGVDAVLIATAIHKGVL 215
                                   5544..4578999**********************************************************976 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.25   1.1e+03     204     221 ..      29      46 ..      28      53 .. 0.85
   2 !   24.8   0.1   2.7e-09   1.2e-05     153     209 ..     157     212 ..     149     214 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.25
                                   SHHHHTSSSHHHHHHHHH CS
                          ThiG 204 ntavaeakdpvamArafk 221
                                   ++ + ++++p+++A+a+k
  gi|15668884|ref|NP_247687.1|  29 ESVICKSSNPIEVAKAYK 46 
                                   5789999********987 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 2.7e-09
                                   SSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHT CS
                          ThiG 153 apiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavae 209
                                   + +G+ +G+ n+e +k ++++++ Pv v  Gi   +d     +lG+davl++ta+ +
  gi|15668884|ref|NP_247687.1| 157 SSVGTQRGV-NAELIKYVLDKTNNPVYVGGGIKGMEDLELCYNLGVDAVLIATAIHK 212
                                   789*****7.7899****************************************975 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00019      0.84      59     106 ..      27      73 ..      23      81 .. 0.86
   2 !    5.3   0.0    0.0021       9.4     201     243 ..     168     212 ..     155     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00019
                                   TTTEESBSS--HHHHHHHHTTT.-SEEEEE--CCCC---CCHHHHHHH CS
                          IGPS  59 PskgliredfdpaeiAkkyeeagAsaiSVLteekyFqGsledLrevrq 106
                                   P + +i++  +p e+Ak+y+e gA++i + ++ ++  G+ +++  +++
  gi|15668884|ref|NP_247687.1|  27 PLESVICKSSNPIEVAKAYKERGAKTIYI-ADLNFIMGNGDNFDIIKE 73 
                                   5667999********************76.799999998888777765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0021
                                   HHCHCC-..TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC CS
                          IGPS 201 eLaklvp..kdvllvaeSGiktredveklkeegvnafLvGeslmr 243
                                   eL+k+v   ++  +    Gik  ed+e + + gv+a+L+ +++ +
  gi|15668884|ref|NP_247687.1| 168 ELIKYVLdkTNNPVYVGGGIKGMEDLELCYNLGVDAVLIATAIHK 212
                                   555555532335566678*********************999865 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.2e-05     0.097     171     215 ..     166     209 ..     159     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.2e-05
                                   -CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCH CS
                           Dus 171 dweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrg 215
                                   + e Ik+v ++ + pv + G+Ik +ed++ + +  G+d+v+i+ +
  gi|15668884|ref|NP_247687.1| 166 NAELIKYVLDKTNNPVYVGGGIKGMEDLELCYNL-GVDAVLIATA 209
                                   6678****************************99.*******965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1460.27
//
Query:       gi|15668885|ref|NP_247688.1|  [L=102]
Description: hypothetical protein MJ_0703.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        2.9    6.1  11.1          3    6.0  11.1    1.0  1  DUF2070       Predicted membrane protein (DUF2070)
        3.6    7.5   7.3       0.94    9.4   2.3    2.1  2  Picorna_P3A   Picornaviridae P3A protein


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  11.1   0.00033         3       7      94 ..      10      93 ..       5     102 .] 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00033
                       DUF2070  7 yifrlPswk.vsllliillalligllaflssklfgillfglpalvaflltlpvlrilggrltykrslflalltelivviisll 88
                                  +i+++ +w  +   +i +++++i+++af++s     +l g+ +l+ fl++  + ++++++l  k   +  l+  +i +ii++ 
  gi|15668885|ref|NP_247688.1| 10 KIKSIKNWInFIKPIITIVGIVISAVAFTIS-----ILWGMLFLILFLILITFSKTIRKILSKKERSYQGLILSIIGSIIIIS 87
                                  6778888877777888999999999998776.....56677777777777777777777766666666666666666666666 PP

                       DUF2070 89 aillsa 94
                                   i++s+
  gi|15668885|ref|NP_247688.1| 88 IIVYSH 93
                                  666554 PP

>> Picorna_P3A  Picornaviridae P3A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.3    0.0001      0.94      52      86 ..       8      42 ..       5      73 .. 0.91
   2 ?    0.9   0.6     0.048   4.3e+02      61      86 ..      67      87 ..      51      95 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0001
                   Picorna_P3A 52 ddklksmlsfvernkkwlavvalvtsvlGilllvl 86
                                   dk+ks+ ++++  k  +++v +v+s++   +++l
  gi|15668885|ref|NP_247688.1|  8 RDKIKSIKNWINFIKPIITIVGIVISAVAFTISIL 42
                                  58999999999999999999999999999888876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.048
                   Picorna_P3A 61 fvernkkwlavvalvtsvlGilllvl 86
                                    er      +  l++s++G ++++ 
  gi|15668885|ref|NP_247688.1| 67 KKERS-----YQGLILSIIGSIIIIS 87
                                  43433.....3445555555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1691  (0.0943165); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 694.53
//
Query:       gi|15668886|ref|NP_247689.1|  [L=377]
Description: hypothetical protein MJ_0704 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
          2    8.8   9.1       0.14   12.5   2.8    2.4  3  Syntaxin_2  Syntaxin-like protein
        2.7    8.5  13.5        1.7    9.1   7.5    2.3  2  DUF2115     Uncharacterized protein conserved in archaea (DUF


Domain annotation for each model (and alignments):
>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.63   5.7e+03      70      86 ..     234     250 ..     212     256 .. 0.62
   2 ?   -2.0   0.1      0.54   4.8e+03      39      55 ..     296     312 ..     282     321 .. 0.57
   3 ?   12.5   2.8   1.6e-05      0.14      13      61 ..     327     376 ..     322     377 .] 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.63
                    Syntaxin_2  70 lqkekLkkdfkealqeF 86 
                                    ++ek  +df ++l+++
  gi|15668886|ref|NP_247689.1| 234 EKREKYLRDFLRILSKL 250
                                   36788888888887775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.54
                    Syntaxin_2  39 ieeinelikktnellkk 55 
                                   i++in+ +++t +++++
  gi|15668886|ref|NP_247689.1| 296 INSINKFLSETYNNISN 312
                                   44555555555555554 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 1.6e-05
                    Syntaxin_2  13 stleklvkqLgtkkdteelrekl.helieeinelikktnellkklsqldn 61 
                                     l++l+++ ++ k+  +l+e++ +el +e+ +li+k+n++l++l++  n
  gi|15668886|ref|NP_247689.1| 327 HHLKELLEKYEKEKNENKLDEEIfNELKDELEKLINKCNNKLRELESQNN 376
                                   67999****************************************98665 PP

>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.9   0.00088       7.9      21     114 ..     217     316 ..     198     319 .. 0.78
   2 ?    9.1   7.5   0.00019       1.7      12      96 ..     287     367 ..     275     376 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00088
                       DUF2115  21 lmkisarlekeikklpekyrkelseslteylfeaykelkn.krsgdkseykeevid....eeelkeflemleeqceeekee 96 
                                   l +i+++++k    ++++ r+++ +++ + l +   e ++ + + ++++y+++ ++    +e + +f +++ee++++++ +
  gi|15668886|ref|NP_247689.1| 217 LNMINKNFNKYWMFIKDEKREKYLRDFLRILSKLRVEYRKnCLNRKNKPYSKKGLEafkkTEFIVSFYKTIEEKIKTRDIN 297
                                   6789999********************999998777777767777777776654441000344566777788888877777 PP

                       DUF2115  97 k.eerlrklyylvslYliF 114
                                   + ++ l+  y+ +s Y +F
  gi|15668886|ref|NP_247689.1| 298 SiNKFLSETYNNISNYEMF 316
                                   7899999***********9 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00019
                       DUF2115  12 easkisieDlmkisarlekeikklpekyrkelseslteylfeaykelknkrsgdkseykeevideeelkeflemleeqcee 92 
                                     +ki+++D+ +i+++l+++ +++++ y     +++ e +++ +kel +k    ++e++e+++dee ++e+ ++le+ +++
  gi|15668886|ref|NP_247689.1| 287 IEEKIKTRDINSINKFLSETYNNISN-YEMFNDKTYLEIFVHHLKELLEK---YEKEKNENKLDEEIFNELKDELEKLINK 363
                                   457899*****************987.9999999**************93...3333333457888777777777777766 PP

                       DUF2115  93 ekee 96 
                                    +++
  gi|15668886|ref|NP_247689.1| 364 CNNK 367
                                   5543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2722  (0.151821); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2443.32
//
Query:       gi|15668887|ref|NP_247690.1|  [L=405]
Description: 3-hydroxy-3-methylglutaryl coenzyme A reductase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     9e-133  442.8   1.4     1e-132  442.6   1.4    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
  ------ inclusion threshold ------
      0.016   15.5   0.0       0.07   13.4   0.0    2.0  2  DUF2316      Uncharacterized protein conserved in bacteria (D


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.6   1.4  1.1e-136    1e-132       2     367 .]      31     405 .]      30     405 .] 0.98

  Alignments for each domain:
  == domain 1  score: 442.6 bits;  conditional E-value: 1.1e-136
                                   HHHHHHHHHHS-HHHHHHHTT----.HHHHHHHSSS---------EEEEEEEETTE....EEEEEE---STTHHHHHHHHH CS
                   HMG-CoA_red   2 veeRrklleelteeeleelkeesld.eevadkmiEnviGyvqlPlGvagpllingk....eylvPmAteEgslvAsasrga 77 
                                    e+Rrk++e++ + e++++ ++s+d e +++k+iEn+iG++q+PlG agpl+ing+    e+++P+At+Eg+lvAs++rg+
  gi|15668887|ref|NP_247690.1|  31 TEIRRKFIEKKVGIEFKHICNYSIDeEMAMKKNIENMIGAIQIPLGFAGPLKINGEyakgEFYIPLATTEGALVASVNRGC 111
                                   689**********************89999*************************************************** PP

                                   HHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHHHTHHHHHHHHHHCSHHCCT-EEEEEEE.EE-SSEEEEEEEEE CS
                   HMG-CoA_red  78 kainesgGvkttvlkdgmtraqvvllesvedaaelkkwiekkeeleelanaaestsrggglkdiev.vlagrlvvlrlkvd 157
                                   ++i+++gG++++v++d+mtra+++ ++sv da ++++wi  +e++e++++ aest+r+g+l +ie+  ++gr+++ r+ ++
  gi|15668887|ref|NP_247690.1| 112 SIITKCGGATVRVIDDKMTRAPCLKTKSVVDAIKVRDWI--RENFERIKEVAESTTRHGKLIKIEPiLIVGRNLYPRFVFK 190
                                   ***************************************..*************************9999*********** PP

                                   -TTC--HHHHHHHHHHHHHHHHHHHTS....EEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHHHHHHHHHH CS
                   HMG-CoA_red 158 tgDAmGaNmvnkateaaaelieeefge....eellsilsNlctdkkasainaiegrgksvvaeatigeevvekilkasaea 234
                                   tgDAmG+Nmv++ate+a+++ie e+++     +++++++N c dkk+s +n i+grgks+vae+ ++e+ v+k+lk++++a
  gi|15668887|ref|NP_247690.1| 191 TGDAMGMNMVTIATEKACNFIEGELKKegifVKTVAVSGNACVDKKPSGMNLINGRGKSIVAEVFLTEKEVNKYLKTTSQA 271
                                   **********************998876788899*********************************************** PP

                                   HH-HHHH....HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTTSEEETTTEEEEEEEEE.----SBSHHHHH CS
                   HMG-CoA_red 235 lvdlnra.n.igtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaaleevedgdlygsvtlPsleVGtvGGgtkl 313
                                   ++++nr  n ig+a + ++gfnah+aN+i A+flAtGqD a+++e+s +i++ e  +dg ly+svtlP +++GtvGGgt++
  gi|15668887|ref|NP_247690.1| 272 IAEVNRLkNyIGSAISNSMGFNAHYANIIGAIFLATGQDEAHIVEGSLGITMAEVEDDG-LYFSVTLPDVPIGTVGGGTRV 351
                                   **************************************************988887666.********************* PP

                                   -HHHHHHHHTT---HH...HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                   HMG-CoA_red 314 ppqaellkllgvkgaknakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                   ++q+e+l++lg++g ++a ++aei+ a++LA+els+l ALaa++l k+H++l+r
  gi|15668887|ref|NP_247690.1| 352 ETQKECLEMLGCYGDNKALKFAEIVGAAVLAGELSLLGALAAGHLGKAHQELGR 405
                                   ***************************************************987 PP

>> DUF2316  Uncharacterized protein conserved in bacteria (DUF2316)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.36   3.3e+03      46      66 ..     135     155 ..     122     164 .. 0.78
   2 ?   13.4   0.0   7.8e-06      0.07      27      70 ..     248     291 ..     240     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.36
                       DUF2316  46 lkasrledvWilrdyLeekik 66 
                                   lk++++ d+  +rd++ e+ +
  gi|15668887|ref|NP_247690.1| 135 LKTKSVVDAIKVRDWIRENFE 155
                                   677788899999999998765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.8e-06
                       DUF2316  27 eevaedLnlttekvekvLelkasrledvWilrdyLeekikeqgk 70 
                                   +++ ++  lt+++v+k L+ +++++++v +l++y+ ++i+++  
  gi|15668887|ref|NP_247690.1| 248 KSIVAEVFLTEKEVNKYLKTTSQAIAEVNRLKNYIGSAISNSMG 291
                                   567778889****************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2674.40
//
Query:       gi|15668888|ref|NP_247691.1|  [L=214]
Description: hypothetical protein MJ_0706 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-22   80.0  22.2    2.4e-22   79.7  22.2    1.1  1  SpoIIM    Stage II sporulation protein M
  ------ inclusion threshold ------
       0.02   15.2   1.6       0.02   15.2   1.6    3.2  3  Wzz       Chain length determinant protein


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7  22.2   2.7e-26   2.4e-22       3     155 ..      39     205 ..      34     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 2.7e-26
                        SpoIIM   3 llflvgillgallaa.............snfaeqis..seskensalslflaifanNlrvalllfllGllllgiptilvll 68 
                                   l+f+++++l ++l+              +nf+++++  +++ ++++l+++lai++nNl+v++l ++lG+     ++++v++
  gi|15668888|ref|NP_247691.1|  39 LVFILSLVLLYILVVnikyfsylgdiifQNFQKHVEnlKITLNEDNLHIILAIWKNNLTVCILNYILGI-----FSLFVIA 114
                                   67888888887777779999999999988888888899999999************************6.....899**** PP

                        SpoIIM  69 inGfvlGavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal........rsrrkalkeakrellklllllv 141
                                   +n+++l +v   +++fg    f+ l+lPhgi+e+pa+i++++ g+ + + l          +++    +++e+lkll+l++
  gi|15668888|ref|NP_247691.1| 115 VNSYILSYV---LYKFG-AESFIYLVLPHGIIEIPALILSASGGVLFNMGLvnflinikFGTKREVLYYIKESLKLLILSI 191
                                   *******99...66665.778**************************9999999998774455566669************ PP

                        SpoIIM 142 pllliAaliEafvt 155
                                   +l+++A+++E+ +t
  gi|15668888|ref|NP_247691.1| 192 ILFIVAGIVEGTIT 205
                                   ************98 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.6   2.2e-06      0.02       3      43 ..      18      59 ..      16      84 .. 0.80
   2 ?    2.2   1.3     0.025   2.2e+02       7      34 ..      86     113 ..      82     119 .. 0.87
   3 ?    3.5   0.5    0.0099        89      11      32 ..     179     200 ..     174     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-06
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXX-EEE CS
                           Wzz  3 iDLieLlsvLwkrkklIilvtllfallaviya.flatpkYta 43
                                  +DL+e+l+  +++kk+I++v l+f+l  v++  +++  kY +
  gi|15668888|ref|NP_247691.1| 18 FDLKEILKSPIRNKKVILFVSLVFILSLVLLYiLVVNIKYFS 59
                                  8***********************997665543777777755 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.025
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           Wzz   7 eLlsvLwkrkklIilvtllfallaviya 34 
                                   +++ ++wk+ +++ ++  +  ++++++ 
  gi|15668888|ref|NP_247691.1|  86 HIILAIWKNNLTVCILNYILGIFSLFVI 113
                                   68899************99999999875 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.0099
                                   XXXXXXXXXXXXXXXXXXXXXX CS
                           Wzz  11 vLwkrkklIilvtllfallavi 32 
                                    ++++ kl+il ++lf++++++
  gi|15668888|ref|NP_247691.1| 179 YIKESLKLLILSIILFIVAGIV 200
                                   6788999**********99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1590.07
//
Query:       gi|15668889|ref|NP_247692.1|  [L=47]
Description: 50S ribosomal protein L40e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-06   28.0   6.7    1.7e-06   27.8   6.7    1.1  1  Ribosomal_L40e  Ribosomal L40e family
     0.0037   17.2   0.7      0.004   17.1   0.7    1.2  1  DZR             Double zinc ribbon
     0.0042   16.8   1.6     0.0063   16.2   1.6    1.3  1  zinc_ribbon_2   zinc-ribbon domain
     0.0059   16.0   1.9     0.0078   15.6   1.9    1.2  1  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.019   14.6   4.8      0.019   14.6   4.8    1.8  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit


Domain annotation for each model (and alignments):
>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   6.7   4.9e-10   1.7e-06       9      48 ..       6      42 ..       5      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 4.9e-10
                Ribosomal_L40e  9 AqKyncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKK 48
                                  A K  + K+iC +C Ar p rAt+Cr  kCg  + lrpK 
  gi|15668889|ref|NP_247692.1|  6 AMKRLFMKKICMRCNARNPWRATKCR--KCGY-KGLRPKA 42
                                  5677889*******************..9**7.5677775 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.7   1.1e-06     0.004      31      49 .]      16      34 ..       4      44 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                           DZR 31 CpsCgekvdpearfCpeCG 49
                                  C++C++ ++ +a+ C +CG
  gi|15668889|ref|NP_247692.1| 16 CMRCNARNPWRATKCRKCG 34
                                  5555555555555555554 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.6   1.8e-06    0.0063       2      22 ..      16      36 ..      15      37 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-06
                 zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                  C +C a ++ +a+ C +CG++
  gi|15668889|ref|NP_247692.1| 16 CMRCNARNPWRATKCRKCGYK 36
                                  *******************97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.9   2.2e-06    0.0078       2      25 ..      13      36 ..      12      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.2e-06
                   zf-ribbon_3  2 tvrCPnCGa.plssddnvCpyCGtk 25
                                  ++ C +C+a +   ++++C +CG+k
  gi|15668889|ref|NP_247692.1| 13 KKICMRCNArN-PWRATKCRKCGYK 36
                                  67899******.***********97 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.5      0.93   3.3e+03      26      31 ..       9      14 ..       8      14 .. 0.85
   2 ?   14.6   4.8   5.4e-06     0.019       2      26 ..      15      36 ..      15      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.93
                                  ---B-- CS
                DNA_RNApol_7kD 26 RilYKk 31
                                  R+++Kk
  gi|15668889|ref|NP_247692.1|  9 RLFMKK 14
                                  899997 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.4e-06
                                  B-SSS--B----SSS----SSS--- CS
                DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCGhR 26
                                  iC++C+a++  +++   +C++CG++
  gi|15668889|ref|NP_247692.1| 15 ICMRCNARNPWRAT---KCRKCGYK 36
                                  8**********999...******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 321.81
//
Query:       gi|15668890|ref|NP_247693.1|  [L=172]
Description: hypothetical protein MJ_0708 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-48  161.7   0.3    8.4e-48  161.3   0.3    1.2  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
    8.1e-11   41.6   0.7    1.3e-10   40.9   0.7    1.4  1  RLI            Possible Fer4-like domain in RNase L inhibitor


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.3   0.3   9.3e-52   8.4e-48       1     127 []      45     170 ..      45     170 .. 0.98

  Alignments for each domain:
  == domain 1  score: 161.3 bits;  conditional E-value: 9.3e-52
                                   EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHHHHTT CS
                 Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaalyilg 81 
                                   ++l+p+a+k+lsp+D+eivek gi+++dcsW+++ e  fkk+k k++r+LP+LvA+Np+nYgkp++Ls++EA+ aalyi++
  gi|15668890|ref|NP_247693.1|  45 LILNPYAEKALSPEDKEIVEKFGITALDCSWKEA-ELMFKKFKFKNQRSLPFLVACNPINYGKPCMLSTLEAFIAALYITN 124
                                   69*******************************7.6778****************************************** PP

                                   -HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHHH CS
                 Ribo_biogen_C  82 lkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkeyl 127
                                   +k+ea +l s fkw+e+F+++n elle+Y+++k+s evve+q+++l
  gi|15668890|ref|NP_247693.1| 125 FKDEAWDLTSCFKWAETFIKVNYELLERYSNAKNSMEVVEIQQDFL 170
                                   *******************************************986 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.7   1.5e-14   1.3e-10       2      34 ..       6      38 ..       5      39 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.5e-14
                                  -EEEES---------TTHHHHHTTSEEEESS-- CS
                           RLI  2 rlAivdadqCdPKKCtgkkcarfcpvrlvrtgk 34
                                  +l+i++a+qC+PKKCt  k+a+++ + l++++ 
  gi|15668890|ref|NP_247693.1|  6 KLFIYHANQCNPKKCTSLKMAKMNKAILLKNPY 38
                                  79************************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 1291.80
//
Query:       gi|15668891|ref|NP_247694.1|  [L=450]
Description: hypothetical protein MJ_0709 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-73  245.3  40.4    4.6e-40  136.9   9.5    3.0  3  MatE             MatE
    9.2e-08   32.3  17.3    9.2e-08   32.3  17.3    4.5  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    3.6e-07   29.9  12.2    3.6e-07   29.9  12.2    2.7  3  Polysacc_synt    Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.9   9.5   7.7e-44   4.6e-40       1     161 []      21     181 ..      21     181 .. 0.99
   2 ?   -0.6   0.4      0.15   8.9e+02      75      89 ..     196     210 ..     191     219 .. 0.53
   3 !  118.5  16.8   3.4e-38   2.1e-34       1     161 []     243     408 ..     243     408 .. 0.98

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 7.7e-44
                          MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglillll 81 
                                   Pi+++ ++es++sl+d+++v++lg++alAav+++++il  ++++++gls+++++ +++++Gakn+++a +++++++il+l+
  gi|15668891|ref|NP_247694.1|  21 PIIVATFIESIYSLVDSIWVSGLGADALAAVGASFPILISIYAVSWGLSIGISSGIARRVGAKNKEEADKVANHAIILALI 101
                                   9******************************************************************************** PP

                          MatE  82 lsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplnyl 161
                                    +++ +++v+ + + ++sl+++  ++ +la +y +il+lg++++ ++ +l+gi+rg g+tk+++++s+i++l ni+l+++
  gi|15668891|ref|NP_247694.1| 102 AGILYIIAVYPNLDTLFSLMGTYGDCKSLAIKYSSILVLGTVIFTICDALYGIFRGEGNTKIVMIASVIGTLTNIILDPI 181
                                   *****************************************************************************986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.15
                          MatE  75 glilllllsliiall 89 
                                   ++++++++sl+i ++
  gi|15668891|ref|NP_247694.1| 196 ATLIAIIISLLILAY 210
                                   444555555554444 PP

  == domain 3  score: 118.5 bits;  conditional E-value: 3.4e-38
                          MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilll 80 
                                   P+al  +++ ++++i+t++++++ +s+ lA+++ al+i+++ f+++lgl++++t+++g  +Ga++f+++k+a+++++++++
  gi|15668891|ref|NP_247694.1| 243 PSALIEITVAVSFFIMTSIIMMVgDSRGLAVYTGALRITEFGFIPMLGLASGATSVIGATYGARSFEKLKTAYFYTIKIGV 323
                                   99*********************9999****************************************************** PP

                          MatE  81 llsliiallvllfseqilslftqdee...vlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnip 157
                                   l+ +ii++l++l+s+++++lft++++   + e   + lri+ l++++  + l++s++++g+gk + +l+is++++ +++i 
  gi|15668891|ref|NP_247694.1| 324 LMEIIIVALIMLLSPILAYLFTYTKTsmgIHEELVKALRIVPLYLLFTPFILTTSAMFQGIGKGEKSLIISIFRSlICHIS 404
                                   *****************************9999999999999999999999****************************** PP

                          MatE 158 lnyl 161
                                   ++yl
  gi|15668891|ref|NP_247694.1| 405 YAYL 408
                                   **97 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   2.6      0.15     9e+02     106     138 ..      62     110 ..      22     114 .. 0.60
   2 !   32.3  17.3   1.5e-11   9.2e-08       3     140 ..     136     280 ..     134     283 .. 0.70
   3 ?   -7.5  10.6         3   1.8e+04      76     104 ..     310     337 ..     249     357 .. 0.48
   4 !    7.4  10.2    0.0007       4.2       1      75 [.     360     437 ..     360     448 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.15
               Polysacc_synt_C 106 ylllllllglllla..................alalllavlvgalvYllll 138
                                   y  +++ l++  ++                  + a++la+ +++++Y++++
  gi|15668891|ref|NP_247694.1|  62 Y-AVSWGLSIGISSgiarrvgaknkeeadkvaNHAIILAL-IAGILYIIAV 110
                                   3.33344443333344555555666677765444666666.7778887765 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 1.5e-11
               Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli..plfgivGaaiatvlallvvavlnly..alrr 79 
                                   +il+l+++++++   l +i+ g g +ki+++a+vig l ++il  ++i    +gi Ga++at++a +++++++ y  ++++
  gi|15668891|ref|NP_247694.1| 136 SILVLGTVIFTICDALYGIFRGEGNTKIVMIASVIGTLTNIILDPIFIymLNLGISGASYATLIAIIISLLILAYelFIKK 216
                                   699*********************************************444669*******************87224566 PP

               Polysacc_synt_C  80 llgikl...ellrrllkpllaalvmgivvylllllllglllla..alalllavlvgalvYllllll 140
                                      + +   + ++  lk+++  + +gi   +l  +++ +++    +++++++   g +vY ++l +
  gi|15668891|ref|NP_247694.1| 217 SCYVTVklsK-FKPDLKIIADLIRVGIP-SALIEITVAVSFFImtSIIMMVGDSRGLAVYTGALRI 280
                                   5555555553.33333555444444444.2233333333333311223333434888888877766 PP

  == domain 3  score: -7.5 bits;  conditional E-value: 3
               Polysacc_synt_C  76 alrrllgiklellrrllkpllaalvmgiv 104
                                    l+  + + +  +  l+ ++++al+m + 
  gi|15668891|ref|NP_247694.1| 310 KLKTAYFYTI-KIGVLMEIIIVALIMLLS 337
                                   2222222223.244555666666666665 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0007
               Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvi.galvklilnllli..plfgivGaaiatvlallvvavlnly 75 
                                   +L+i+ l+++f+ ++ ++s+++qg+g+  + l+++++ ++++++   +l+     +g+ G+  + v++++++ ++ + 
  gi|15668891|ref|NP_247694.1| 360 ALRIVPLYLLFTPFILTTSAMFQGIGKGEKSLIISIFrSLICHISYAYLFAviLGLGMFGIYSGLVVGEFTAGIFAFL 437
                                   5889999********************999888888725556777777776336668899999999999988777654 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.15     9e+02     208     234 ..      16      43 ..      12      58 .. 0.75
   2 !   29.9  12.2     6e-11   3.6e-07      54     251 ..      70     281 ..      63     299 .. 0.83
   3 !    7.6  14.4   0.00037       2.2      81     187 ..     323     438 ..     305     448 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.15
                 Polysacc_synt 208 lsfsapltisslaillytyidsi.llgl 234
                                   + +s p+++ +++ ++y  +dsi + gl
  gi|15668891|ref|NP_247694.1|  16 IEVSKPIIVATFIESIYSLVDSIwVSGL 43 
                                   5677888899999999999999866665 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 6e-11
                 Polysacc_synt  54 lGlnaalvreiakyrekkelvslillnvllvllvlvllfllllliaa.........flgl.pelavlylilalmllllvgv 124
                                    G++  + r++   ++  e+  +  + ++++ l++ +l++++ +            ++g+ + la+ y  + + +++++++
  gi|15668891|ref|NP_247694.1|  70 IGISSGIARRVGAKNK--EEADKVANHAIILALIAGILYIIAVYP-NldtlfslmgTYGDcKSLAIKYSSILVLGTVIFTI 147
                                   5888888888888887..889999999999999999999988887.347888888766654789999999999999***** PP

                 Polysacc_synt 125 asfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfr.........prf 196
                                       +g+f+g  + k +++ +v+  l+ +il  i++++ +     + ga+ a+l+++i+sl++l  +++         +  
  gi|15668891|ref|NP_247694.1| 148 CDALYGIFRGEGNTKIVMIASVIGTLTNIILDPIFIYMLN---LGISGASYATLIAIIISLLILAYELFikkscyvtvKLS 225
                                   ****************************************...44455666677777777666664443456788999666 PP

                 Polysacc_synt 197 vils.lklvrellsfsapltisslaillytyidsillglllgaeavGiYnaayqll 251
                                   +++  lk + +l+++++p  + ++++ ++++i + ++    ++  ++ Y++a +++
  gi|15668891|ref|NP_247694.1| 226 KFKPdLKIIADLIRVGIPSALIEITVAVSFFIMTSIIMMVGDSRGLAVYTGALRIT 281
                                   66666***************************999998877777799999997775 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00037
                 Polysacc_synt  81 vllvllvlvllfllllliaa.......flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvi 154
                                   vl+ +++++l++ll++ +a+        +g +e  v  l +   +ll+++++++ + +fqg  + +  ++ ++ ++l+  i
  gi|15668891|ref|NP_247694.1| 323 VLMEIIIVALIMLLSPILAYlftytktSMGIHEELVKALRIVPLYLLFTPFILTTSAMFQGIGKGEKSLIISIFRSLICHI 403
                                   444556666666666666656666776888887666666666666679999999999********9999999999998776 PP

                 Polysacc_synt 155 ..lvliavflfldivaavlgavlaalvggivslav 187
                                     + l+av+l+l ++++  g+v++ +++gi+++++
  gi|15668891|ref|NP_247694.1| 404 syAYLFAVILGLGMFGIYSGLVVGEFTAGIFAFLF 438
                                   2345566666666*****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2814.04
//
Query:       gi|15668892|ref|NP_247695.1|  [L=351]
Description: hypothetical protein MJ_0710 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-31  107.0   0.0      7e-30  104.2   0.0    2.0  1  UPF0020          Putative RNA methylase family UPF0020
      3e-22   79.3   4.0      3e-22   79.3   4.0    1.9  2  THUMP            THUMP domain
    5.6e-12   45.9   0.0    4.3e-09   36.4   0.0    2.2  2  N6_N4_Mtase      DNA methylase
    1.3e-07   31.4   0.0      2e-07   30.8   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
    5.2e-07   29.2   0.0    1.3e-06   27.9   0.0    1.6  1  N6_Mtase         N-6 DNA Methylase
    6.4e-07   29.1   0.0    1.1e-06   28.3   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    1.8e-05   24.6   0.0    3.5e-05   23.6   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
     0.0022   17.6   0.0     0.0041   16.7   0.0    1.4  1  MTS              Methyltransferase small domain
      0.003   18.2   0.0     0.0063   17.2   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
     0.0077   15.8   0.0      0.016   14.7   0.0    1.5  1  Methyltransf_5   MraW methylase family
  ------ inclusion threshold ------
      0.025   14.0   0.1        2.5    7.5   0.0    2.3  2  AviRa            RRNA methyltransferase AviRa
        0.1   12.4   0.0        1.3    8.9   0.0    2.2  1  Methyltransf_23  Methyltransferase domain
        0.1   12.0   0.0       0.18   11.2   0.0    1.3  1  SBP_bac_3        Bacterial extracellular solute-binding prote


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.0   5.1e-33     7e-30       1     171 [.     178     324 ..     178     339 .. 0.87

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 5.1e-33
                                   -SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEE CS
                       UPF0020   1 RgyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklyg 81 
                                   ++ R++++p+ + ++LA+a+v+la++k+g+  lDP+CG+G++lIEa+l+ga+ +                          g
  gi|15668892|ref|NP_247695.1| 178 PHLRKYFHPGCMLPKLARAMVNLARVKEGDIVLDPFCGTGGFLIEAGLIGAKLI--------------------------G 232
                                   578*************************************************99..........................* PP

                                   EES-HHHHHHHHHHHHHTT-GGG.EEEEE--GGG--.....STTS---EEEE----------HHHHHHHHHHHHHHHHHH- CS
                       UPF0020  82 sDldrrvvqgareNaekagvgdl.iefsqadaakLr.....lkegevdvivtnpPYGerlgskkalekLYseflrelkrvl 156
                                    D+d+r+  g+  N+e++++ d+ i+++ +da+ ++     l+ ++vd+ivt+pPYG+++ +k+++ek+    l++l +v+
  gi|15668892|ref|NP_247695.1| 233 CDIDWRMASGTLINLEEYNLLDKvIKVKRLDAKYVKeflneLNIEKVDAIVTDPPYGISTAKKGEIEKI----LETLPEVI 309
                                   ******************98665289*******9999877545569********************976....55555556 PP

                                   TT..-EEEEEESSHH CS
                       UPF0020 157 rgggrlvlltsenka 171
                                   + +g  v++ +++ +
  gi|15668892|ref|NP_247695.1| 310 KDNGYFVFAYPKKIE 324
                                   666677777666655 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   4.0   2.2e-25     3e-22       1     142 [.      16     163 ..      16     165 .. 0.92
   2 ?   -0.0   0.2      0.62   8.5e+02      18      77 ..     261     311 ..     245     314 .. 0.54

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 2.2e-25
                                   HHHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTST..TECEEEEE.......EEEEESSHHHHHHHHH CS
                         THUMP   1 geieellkegkvnverveagkgrivvelkgekpeedeellkealekar..giqrvipv.......cevceadledileaak 72 
                                   ge+++ll+  ++n ++++ ++ +i+ ++  ++++++  +++e + +++         +         ++++ ++++++++ 
  gi|15668892|ref|NP_247695.1|  16 GELMALLEIFNYNGSVERLKRYVITEDSPAKDIVKRSGYIDEGHRIIFryN-----LEeksvdlvDKIVNDFINSFKDFVA 91 
                                   699*********************************************662.....334444455778899********** PP

                                   HHHHHHHHHCT-EEEEEEEESSSTS...SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEE CS
                         THUMP  73 eivkkkfeeeketFaVrvkrrgkhf...eftsreinrevGkaivektglkVdlenPdivvrveiikdkayisi 142
                                   +i+++ + e k ++aVrv + +k++   +++s +i++e+G++i+ kt++kV+l++Pdi+vrv i++++++is 
  gi|15668892|ref|NP_247695.1|  92 NIDYPDIDESK-SYAVRVLKLHKDEftkSIDSLRIEKEIGGIIKLKTNAKVNLTKPDILVRVVILENTFFISN 163
                                   ******98876.************99*********************************************96 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.62
                                   EEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHH CS
                         THUMP  18 eagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkk 77 
                                   +   + +  +l++ ++e+ ++++ ++ + +           ++  ++e+ile   e++k+
  gi|15668892|ref|NP_247695.1| 261 RLDAKYVKEFLNELNIEKVDAIVTDPPYGI---------STAKKGEIEKILETLPEVIKD 311
                                   333333333334344444444444333333.........477888889999988888887 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   3.1e-12   4.3e-09     149     225 ..     162     239 ..      47     246 .. 0.83
   2 !    7.6   0.0     0.002       2.7       1      39 [.     279     309 ..     279     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 3.1e-12
                                   BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHH.HHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHH CS
                   N6_N4_Mtase 149 ediWdlseiqsnekkskgdtkkkHpaqkPvallerlI.klstkkgdivlDpFaGSGtTavaakelgrkfiGieieeey 225
                                   +++ ++ ++ + +k++++  k  Hp ++  +l++ ++ ++  k+gdivlDpF+G+G  +++a   g k iG++i+++ 
  gi|15668892|ref|NP_247695.1| 162 SNVLEMRDREYFQKNRPHLRKYFHPGCMLPKLARAMVnLARVKEGDIVLDPFCGTGGFLIEAGLIGAKLIGCDIDWRM 239
                                   44456666666777777766899**************5566899******************************9876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.002
                                   EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHH CS
                   N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvl 39 
                                   vd ivtdpPY+++          ++ ++e+ le l +v+
  gi|15668892|ref|NP_247695.1| 279 VDAIVTDPPYGISTA--------KKGEIEKILETLPEVI 309
                                   799*********988........7777777777766666 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   1.4e-10     2e-07      41     168 ..     205     335 ..     194     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.4e-10
                                   CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T...TTEEEEES-HHHHCTS--SS-EEEEEE CS
                 Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee...etaelkedaleallklakkkeefdivf 118
                                   eg  vLD f+G+G+  +EA   ga k +  + d ++++    nlee +l +   +++ l  + ++++l++  + e++d + 
  gi|15668892|ref|NP_247695.1| 205 EGDIVLDPFCGTGGFLIEAGLIGA-KLIGCDIDWRMASGTLINLEEYNLLDkviKVKRLDAKYVKEFLNE-LNIEKVDAIV 283
                                   67789**************99996.567789999999988899999998886667777888888888888.577899**** PP

                                   E--SSSTTCH.....HHHHHHHHHTT-EEEEEEEEEEEECCSSS--.-TTEEEE CS
                 Cons_hypoth95 119 lDPPyakell....ieevlelleekkllkenalvvvetekekelpespenlelv 168
                                    DPPy  + +    ie++le+l   +++k+n+  v+ ++k+ el  ++e+l +v
  gi|15668892|ref|NP_247695.1| 284 TDPPYGISTAkkgeIEKILETLP--EVIKDNGYFVFAYPKKIELDMELEGLYKV 335
                                   *****877666667999999999..8****************999999988776 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   9.4e-10   1.3e-06      33     142 ..     192     295 ..     170     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 9.4e-10
                      N6_Mtase  33 evsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgd 113
                                   ++ + +v+l+  k+g  v+Dp cG+gg+l++a        +k     i       t ++L + Nll + i++k+++++   
  gi|15668892|ref|NP_247695.1| 192 KLARAMVNLARVKEGDIVLDPFCGTGGFLIEAGLI----GAKLIGCDIDWRMASGTLINLEEYNLLDKVIKVKRLDAKYVK 268
                                   578899*************************9874....5677777777777788889999************99999999 PP

                      N6_Mtase 114 tlekpkfekdkkfdvvvaNppfnqkewke 142
                                    + ++     +k+d++v+ pp++++  k+
  gi|15668892|ref|NP_247695.1| 269 EFLNELNI--EKVDAIVTDPPYGISTAKK 295
                                   99998887..9************994433 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   8.1e-10   1.1e-06       3      82 ..     208     289 ..     206     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 8.1e-10
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlv.lgdvfe...llaklklekikvdlvflSp 79 
                                   ++lD+f+G+GG  i+  l + k i+ +i+ +    +  N e Y+  dk+  v   d +     l++l+ ek+  d +++ p
  gi|15668892|ref|NP_247695.1| 208 IVLDPFCGTGGFLIEAGLIGAKLIGCDIDWRMASGTLINLEEYNLLDKVIKVkRLDAKYvkeFLNELNIEKV--DAIVTDP 286
                                   79*******************************************999765515565441115555555555..******* PP

               Methyltransf_15  80 PwG 82 
                                   P G
  gi|15668892|ref|NP_247695.1| 287 PYG 289
                                   *98 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.5e-08   3.5e-05       4     121 ..     206     322 ..     204     346 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.5e-08
               Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld..nveFeqgdieeleklled...ekfDlil 79 
                                   g  vlD+ CGtG +++e+  ++  +a+++G Di+ ++ +    n+++ +l    +++++ d+   ++ l++   ek+D i+
  gi|15668892|ref|NP_247695.1| 206 GDIVLDPFCGTGGFLIEAG-LI--GAKLIGCDIDWRMASGTLINLEEYNLLdkVIKVKRLDAKYVKEFLNElniEKVDAIV 283
                                   5669*************99.66..59********999999999888766644567777766666332223345689***** PP

               Methyltransf_31  80 snevl....naladpdkileeiervlkpggilliedprllaelpak 121
                                   ++ +     +   + +kile +++v+k++g+++ ++p+       k
  gi|15668892|ref|NP_247695.1| 284 TDPPYgistAKKGEIEKILETLPEVIKDNGYFVFAYPK-------K 322
                                   **8878888899999**********************9.......2 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     3e-06    0.0041      32     153 ..     206     333 ..     192     342 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3e-06
                                   CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHH.....HHHHHHHHHHTTGC....EEEEE-STTTTSTTS-EEEEEE CS
                           MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarA.....lesakenleankle....vevvasdvleeveekkfdlivs 103
                                    + vlD  cG+G   +++     +  +  +d+d+r      +++ + nl ++ ++       + ++ l+e++ +k+d+iv+
  gi|15668892|ref|NP_247695.1| 206 GDIVLDPFCGTGGFLIEAGLIGAK--LIGCDIDWRMasgtlINLEEYNLLDKVIKvkrlDAKYVKEFLNELNIEKVDAIVT 284
                                   445788888888666655554444..77777777651222244555555555555434322345678889999******** PP

                                   ---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHHHH CS
                           MTS 104 NPPfhagkatelavaeeliaeAkeaLkegGeLliVanrklgyeslleelf 153
                                    PP+  ++a ++  +e+++++ +e+ k++G +++ + +k++ +  le l+
  gi|15668892|ref|NP_247695.1| 285 DPPYGISTA-KKGEIEKILETLPEVIKDNGYFVFAYPKKIELDMELEGLY 333
                                   ******999.6667899***************999999999888887766 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.5e-06    0.0063       1      97 []     209     313 ..     209     313 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.5e-06
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCGBS.....SSTTTEEEEEE..E CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaedlp.....fedgsfDlvvs..s 71 
                                   vLd  cGtG +++++    g ak++g+Di+ +m   +  ++ee +l    +++ + da+ ++     ++ +++D++v    
  gi|15668892|ref|NP_247695.1| 209 VLDPFCGTGGFLIEAGLI-G-AKLIGCDIDWRMASGTLINLEEYNLldkVIKVKRLDAKYVKeflneLNIEKVDAIVTdpP 287
                                   89************9866.6.***************999999977788877777777755442222246679*****9554 PP

                                   STGGGSSHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  72 galhhlsdedlekalkeiarvLkpgG 97 
                                   ++++  ++ ++ek+l+ + +v+k++G
  gi|15668892|ref|NP_247695.1| 288 YGISTAKKGEIEKILETLPEVIKDNG 313
                                   55667788899999999999999998 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.016       6     105 ..     191     293 ..     187     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                   -TTTHHHHHHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....-..--.EEEEES-GGGHHH CS
                Methyltransf_5   6 pVLlqevvellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLkefe..kr.ltlvkgnfkelke 83 
                                   p L++++v+l ++ke+ + +D   G+gg    +   l   +lig+d+D ++   +  +L+e++  ++ +++ +   k +ke
  gi|15668892|ref|NP_247695.1| 191 PKLARAMVNLARVKEGDIVLDPFCGTGGF--LIEAGLIGAKLIGCDIDWRMASGTLINLEEYNllDKvIKVKRLDAKYVKE 269
                                   5688999*********************6..344556777********************998666734555555699*** PP

                                   HHHHTTTT-EEEEEEE..-S--HH CS
                Methyltransf_5  84 alaeanvtkvdgillD..LGvSsl 105
                                    l+e n++kvd+i+ D   G+S  
  gi|15668892|ref|NP_247695.1| 270 FLNELNIEKVDAIVTDppYGISTA 293
                                   ***************966688865 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.01        14      41     122 ..     195     267 ..     191     274 .. 0.64
   2 ?    7.5   0.0    0.0018       2.5     161     201 ..     273     309 ..     246     328 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.01
                         AviRa  41 ralellekkeegapltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLsLLtkeglakreeelrelaeey 121
                                   ra+  l   + +++  + Dp CG++ +l   gl+ +    k+++ D+d  + +     L  L +  l ++  ++++l ++y
  gi|15668892|ref|NP_247695.1| 195 RAMVNLA--RVKEGDIVLDPFCGTGGFLIEAGLIGA----KLIGCDIDWRMAS---GTLINLEEYNLLDKVIKVKRLDAKY 266
                                   4444443..334456789******9999999*9986....5778888876544...4444445555555555555555555 PP

                         AviRa 122 e 122
                                    
  gi|15668892|ref|NP_247695.1| 267 V 267
                                   5 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0018
                         AviRa 161 eeaekevdivitDlPYGelvswqgeseepvkqlleslaavl 201
                                   e + ++vd ++tD PYG  ++ +ge     +++le+l +v+
  gi|15668892|ref|NP_247695.1| 273 ELNIEKVDAIVTDPPYGISTAKKGEI----EKILETLPEVI 309
                                   334456***********988777664....46666666666 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00092       1.3      18     120 ..     201     320 ..     181     350 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00092
               Methyltransf_23  18 pklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...................kakkaqkdqfdeqeaaep 79 
                                   ++ ++g  vLd  cGtG +l ++   g++++g D++ ++ +                                        
  gi|15668892|ref|NP_247695.1| 201 ARVKEGDIVLDPFCGTGGFLIEAGLIGAKLIGCDIDWRMASGTLinleeynlldkvikvkrldA----------------- 264
                                   3457788999999*********************987766653355555555544333322220................. PP

               Methyltransf_23  80 qg............kfdlIvlr..evlehvp..dppellrqiatllkpgGylllsep 120
                                    +            k d Iv    +++ + +    ++ l ++ + +k++Gy+++ +p
  gi|15668892|ref|NP_247695.1| 265 -KyvkeflnelnieKVDAIVTDppYGISTAKkgEIEKILETLPEVIKDNGYFVFAYP 320
                                   .01111122222335555555322455555522355666666666666666666666 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.18     141     198 ..     267     325 ..     241     334 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                   HHHHHHHHHTTSSSEEEEEHHHHHHHHHHCCGCCEEEE.ECGGCECEEEEEEETTTHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                     SBP_bac_3 141 leealqaLkngrvdavvadspvlaylvkknpdkkvvlv.eeplsseeyaiavrkgdseL 198
                                     e l++L+ ++vda+v+d p     +kk + +k+ ++ +e++ +++y +++ +++ eL
  gi|15668892|ref|NP_247695.1| 267 VKEFLNELNIEKVDAIVTDPPYGISTAKKGEIEKILETlPEVIKDNGYFVFAYPKKIEL 325
                                   5678999******************************8888888888888877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 2362.76
//
Query:       gi|15668893|ref|NP_247696.1|  [L=322]
Description: hypothetical protein MJ_0711 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1141  (0.0636399); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2175.58
//
Query:       gi|15668894|ref|NP_247697.1|  [L=335]
Description: glycerol dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-57  195.1   0.1    4.5e-54  183.8   0.0    2.1  2  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    1.3e-20   73.6   0.5    9.5e-19   67.4   0.5    2.6  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    8.8e-09   34.9   3.8    4.2e-07   29.4   3.8    2.7  1  DHQ_synthase  3-dehydroquinate synthase
  ------ inclusion threshold ------
      0.013   14.9   0.1      0.057   12.7   0.1    2.0  1  PFK           Phosphofructokinase


Domain annotation for each model (and alignments):
>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00017      0.77       2      33 ..      11      42 ..      10      45 .. 0.94
   2 !  183.8   0.0     1e-57   4.5e-54      72     250 .]      65     252 ..      47     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00017
                      Fe-ADH_2  2 igegaleklgellkelelkkvllvadentkka 33
                                  i+ ga++k++e+lk+l+lk+ l+++++ntkk 
  gi|15668894|ref|NP_247697.1| 11 IEDGAINKIEEILKKLNLKNPLVITGKNTKKY 42
                                  899**************************985 PP

  == domain 2  score: 183.8 bits;  conditional E-value: 1e-57
                      Fe-ADH_2  72 reketdlvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrr 152
                                   + + +d+v+++GgG+ iD++ky+++kl++p++svpT+aS+DG+asp +s+++      +    aP+a+iaD+++++++Prr
  gi|15668894|ref|NP_247697.1|  65 KYTAYDCVIGIGGGRSIDTGKYLAYKLGIPFISVPTTASNDGIASPIVSIRQPS----F-MVDAPIAIIADTEIIKKSPRR 140
                                   34789*********************************************9885....5.4678***************** PP

                      Fe-ADH_2 153 llasGvGDllgkytaladwklan.evseplaklsaamvqeaaeklve...dkketealeellealalsgigi.....srpa 224
                                   ll +G+GD+++++ta+ dwkla  e  e+++++sa   ++ a++l++   + +  e  ++l++al+ sgi+i     srpa
  gi|15668894|ref|NP_247697.1| 141 LLSAGMGDIVSNITAVLDWKLAYkEKGEKYSESSAIFSKTIAKELISyvlNSDLSEYHNKLVKALVGSGIAIaiansSRPA 221
                                   ********************9986445555555555555555555443335666777788888876666666666669*** PP

                      Fe-ADH_2 225 SGsEHliSHaldmlal.....kqalHGeqVG 250
                                   SGsEHl+SHald+l++      + lHGeq+G
  gi|15668894|ref|NP_247697.1| 222 SGSEHLFSHALDKLKEeynlnINSLHGEQCG 252
                                   **************87555656799*****9 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.5   2.1e-22   9.5e-19       1     345 [.       6     308 ..       6     325 .. 0.73

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 2.1e-22
                                   -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT. CS
                        Fe-ADH   1 Ptrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareeg 81 
                                   P+ +++++ga+++++e lkkl++k++l++t+k++    ++  ++         +++ +d++  n ++e       l + + 
  gi|15668894|ref|NP_247697.1|   6 PRYTIIEDGAINKIEEILKKLNLKNPLVITGKNTK---KY-CRFF-------YDIVYYDEILNNLEIE-------LKKYTA 68 
                                   5667899**************************55...22.3333.......3446899997776643.......334455 PP

                                   --EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS- CS
                        Fe-ADH  82 advviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpell 162
                                   +d+vi++GGG +iDt+K++a+ l+                  +p+i +PTta+++  ++p+  i +++      ++     
  gi|15668894|ref|NP_247697.1|  69 YDCVIGIGGGRSIDTGKYLAYKLG------------------IPFISVPTTASNDGIASPIVSIRQPSF-----MV---DA 123
                                   8***********************..................***********************3333.....33...47 PP

                                   -SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHH.....T---TTSSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        Fe-ADH 163 PdlaivDpeltltlPkrvtaatglDalahalEayvsk.....kanplsdalaleairliaknleravadgedleareqmll 238
                                   P ++i D+e++ + P+r++ a+++D+++     +  k     k + +s+       ++iak l   v + +  e   +++ 
  gi|15668894|ref|NP_247697.1| 124 PIAIIADTEIIKKSPRRLLSAGMGDIVSNITAVLDWKlaykeKGEKYSESS-AIFSKTIAKELISYVLNSDLSEYHNKLVK 203
                                   999***********************9988877544444445555566543.33457777778787878766688888888 PP

                                   HHHHHHHHHHSS---.....HHHHHHHHHHC....CGGG....GGS-HHHHHHHHH..........HHHHHHT.......T CS
                        Fe-ADH 239 astlaglafsnaglg.....avHalahalgal...fgip....hglanaillpavlrfnaeaaperlaqlaralggesdee 307
                                   a + +g+a++ a  +       H ++hal +l   +++     hg+ ++i    ++          +  l ++     +++
  gi|15668894|ref|NP_247697.1| 204 ALVGSGIAIAIANSSrpasgSEHLFSHALDKLkeeYNLNinslHGEQCGI--GTIM----------MSYLHEK-----ENK 267
                                   88888887766655555666889999988886555444411345555555..2222..........2223333.....668 PP

                                   --HHHHHHHHHHHHHTT---SHHHHT-TT-...HHHHHHHH CS
                        Fe-ADH 308 aaeeliealrellkelglptsLselgvdee...dldklaea 345
                                   +   l e+++  lk++++pt+ +elg+de+   ++ ++a++
  gi|15668894|ref|NP_247697.1| 268 KLSGLHEKIKMSLKKVDAPTTAKELGFDEDiiiEALTMAHK 308
                                   889999999999****************9743333555554 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   3.8   9.4e-11   4.2e-07      27     257 ..      65     305 ..      48     310 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 9.4e-11
                                   T--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEEE---SEEEEEGGGGGG CS
                  DHQ_synthase  27 kleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGafaqPkavlidlevLkt 107
                                   k++  +++i +GGG   D   + A  y+ G+ f+ vPtt  a  D      ++i  p    ++     P a+++d+e++k 
  gi|15668894|ref|NP_247697.1|  65 KYTAYDCVIGIGGGRSIDTGKYLA--YKLGIPFISVPTT--ASNDGIASPIVSIRQPS--FMV---DAPIAIIADTEIIKK 136
                                   5677799****************9..999*********9..56665444444444443..444...57************* PP

                                   S-HHHHHHHHHHHHH.HHHHT-HHHHHHHHHHHHHHHC...................TTTHHHHHHHHHHHHHHHHHHHHH CS
                  DHQ_synthase 108 LperelraGlaEviK.yalikdeelfelleenaeallk...................eeeeealeeliarsievkaevvee 168
                                    p+r l+aG+++++  ++++ d +l  + + ++ +  +                   +  +e  ++l+++ +     +   
  gi|15668894|ref|NP_247697.1| 137 SPRRLLSAGMGDIVSnITAVLDWKLAYKEKGEKYS--EssaifsktiakelisyvlnSDLSEYHNKLVKALVGSGIAI--- 212
                                   ************99625666776663322222222..12345665444444443333112222222222222222222... PP

                                   CCTTTTGGGGGGTTHHHHHHHHHHHTT....TTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT---STTTT CS
                  DHQ_synthase 169 DekekglralLnlGHtigHaiEallgy....ekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpvslkel 245
                                       ++ r +    H ++Ha+++l +      + lHGe   iG ++  +l ek +   +   e+++  lkk++ p++ kel
  gi|15668894|ref|NP_247697.1| 213 -AIANSSRPASGSEHLFSHALDKLKEEynlnINSLHGEQCGIGTIMMSYLHEKENKKLSGLHEKIKMSLKKVDAPTTAKEL 292
                                   .2335566666777999999988776534445789****************999998889999**************9998 PP

                                   ..-HHHHHHHHTT CS
                  DHQ_synthase 246 .leveellealkk 257
                                    ++ + ++eal++
  gi|15668894|ref|NP_247697.1| 293 gFDEDIIIEALTM 305
                                   6666667777665 PP

>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.3e-05     0.057      91     133 ..      68     105 ..       1     112 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                                   T--EEEEEESHHHHHHHHHHHHT..T....--EEEEEEETT-- CS
                           PFK  91 gidaLvviGGdgslkganklseerkglleelkivgiPkTidND 133
                                     d+++ iGG  s+++ + l+ +  g    ++++ +P T +ND
  gi|15668894|ref|NP_247697.1|  68 AYDCVIGIGGGRSIDTGKYLAYKL-G----IPFISVPTTASND 105
                                   458999999999999999999887.9....************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2472.59
//
Query:       gi|15668895|ref|NP_247698.1|  [L=766]
Description: hydrogenase expression regulatory protein HypF [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-38  132.1   0.0    2.3e-38  131.5   0.0    1.3  1  Sua5_yciO_yrdC   Telomere recombination
    1.1e-33  114.6  14.1    1.1e-17   63.5   2.9    2.5  2  zf-HYPF          HypF finger
    9.5e-28   96.9   0.0    1.9e-27   95.9   0.0    1.5  1  HypF_C           HypF Kae1-like domain
    8.6e-27   93.4   0.1    2.1e-26   92.1   0.1    1.7  1  Acylphosphatase  Acylphosphatase
    0.00024   20.9   0.8     0.0052   16.5   0.8    2.3  1  Carbam_trans_N   Carbamoyltransferase N-terminus
     0.0099   15.6   0.0      0.055   13.2   0.0    2.0  2  Peptidase_M22    Glycoprotease family
  ------ inclusion threshold ------
       0.16   11.6   0.1        9.9    5.9   0.0    2.5  2  CopK             Copper resistance protein K
        0.9    8.9   6.9        9.3    5.6   0.5    2.7  2  NMD3             NMD3 family
        2.1    8.8   3.9        2.3    8.7   2.4    1.9  1  DUF4379          Probable Zinc-ribbon domain
        5.3    7.0   7.9        3.8    7.4   2.5    2.6  2  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
        5.4    7.1  10.5        1.9    8.5   3.8    2.9  2  zf-RING_5        zinc-RING finger domain
        9.6    7.0   8.0        9.2    7.1   4.2    2.5  2  zinc_ribbon_15   zinc-ribbon family


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.5   0.0   1.5e-41   2.3e-38       2     178 ..     218     390 ..     217     391 .. 0.95

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 1.5e-41
                                   HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-.TC--HHHHHHHHCT-SSSCEEE CS
                Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklae.seveeealkllerfwPGpitll 81 
                                   +l++G+i+ai+++++ +Lac++ ++++v +lr++ grp ++p+av+ +++e  + +ae +e e++al +l+r    pi++l
  gi|15668895|ref|NP_247698.1| 218 LLEEGHILAIKGIGGTHLACKVGEDDVVLELRKRLGRP-TQPFAVM-SKIEYTELFAEfDEDEKNALLSLRR----PIVVL 292
                                   799***********************************.******8.5799*********************....***** PP

                                   EE..E-T.S-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS-.--SSS CS
                Sua5_yciO_yrdC  82 lkrskek.lpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildgg.eiavg 160
                                   +k ++ +   ++  ++l+t+Gv+ P++ l++lL+++ +   v+TSanl+g p+++d++e+ ++l++i+d++l ++ +i ++
  gi|15668895|ref|NP_247698.1| 293 KKSQDYDkYFSKYVSNLDTIGVMFPYSGLHYLLFDK-EIAYVMTSANLPGLPMVKDNDEILKKLNGIADYFLLHNrRIVNR 372
                                   **8777787777789********************9.667***********************************9***** PP

                                   ---EEEETTSSTSSECEX CS
                Sua5_yciO_yrdC 161 vdstVvdltegkpkilRr 178
                                   +d++Vv+ + +++ +lRr
  gi|15668895|ref|NP_247698.1| 373 CDDSVVKKVADRLVFLRR 390
                                   *******9999******8 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   2.9   7.1e-21   1.1e-17       1      34 []     116     149 ..     116     149 .. 0.98
   2 !   56.4   3.5   1.2e-18   1.8e-15       1      33 [.     166     198 ..     166     199 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 7.1e-21
                                   --HHHHHHHC-TTSTTTT-TT---TTTS--EEEE CS
                       zf-HYPF   1 lCedClrEykdpldRRfhaqfisCtnCGPrlsli 34 
                                   +C+dCl+E+ d++dRR++++fi+CtnCGPr++++
  gi|15668895|ref|NP_247698.1| 116 ICDDCLKEMLDKNDRRYRYPFIACTNCGPRFTIV 149
                                   7*******************************96 PP

  == domain 2  score: 56.4 bits;  conditional E-value: 1.2e-18
                                   --HHHHHHHC-TTSTTTT-TT---TTTS--EEE CS
                       zf-HYPF   1 lCedClrEykdpldRRfhaqfisCtnCGPrlsl 33 
                                   lCe+Cl+Eyk+pldRRfhaq ++C+ CGP++ l
  gi|15668895|ref|NP_247698.1| 166 LCEKCLEEYKNPLDRRFHAQATCCPICGPKVFL 198
                                   7****************************9876 PP

>> HypF_C  HypF Kae1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.0   1.3e-30   1.9e-27       2     101 ..     405     505 ..     404     506 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 1.3e-30
                        HypF_C   2 aekevLAlGaelkntfalakggqallsqhlGdlenletleayeealeelekllei.kpevivcDlhpdylstklaeelaek 81 
                                   ++k++L++Gael++t +++k+++++l+q++G+ +++et+  +++a++++ +l+++ k+++ivcDlhp+++stklaeel+ek
  gi|15668895|ref|NP_247698.1| 405 NNKNILCVGAELNSTACIVKRDKFYLTQYIGNTSKYETFCYLRDAINNILRLTNTnKIDAIVCDLHPQFNSTKLAEELSEK 485
                                   6899*************************************************97479*********************** PP

                        HypF_C  82 eklelievqHHhAHllavla 101
                                    ++e+++vqHH AH++++l 
  gi|15668895|ref|NP_247698.1| 486 FGAEIFRVQHHFAHAYSLLG 505
                                   *****************986 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.1   1.4e-29   2.1e-26       1      85 []      12      96 ..      12      96 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 1.4e-29
               Acylphosphatase  1 vrllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppk.arvdeveveeleeeeefkd 82
                                  vr+ v+G+VQgvgFR+fv+r+Ak+ +lkGyv+N+ +  Vei++eg++e+++ f+++lk+++p+ +r+d++++ee++  eef+d
  gi|15668895|ref|NP_247698.1| 12 VRIKVKGIVQGVGFRPFVYRIAKKNNLKGYVKNMGNY-VEILIEGKKEDIRNFINDLKNKKPPlSRIDKLDIEEIKGIEEFDD 93
                                  5899*********************************.*********************77777******************* PP

               Acylphosphatase 83 Fei 85
                                  F i
  gi|15668895|ref|NP_247698.1| 94 FYI 96
                                  *76 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.8   3.5e-06    0.0052     117     331 ..     480     750 ..     423     756 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.5e-06
                Carbam_trans_N 117 e...kvdrkdvslyeHhlsHaaSaystSpFakkeklvlcldgdG.....diaprllavek.etelkikslvsfse...... 182
                                   e   +++  ++  ++Hh +Ha S      +  +++ +l ldg+G     +i+     ++k ++  ++  l +  +      
  gi|15668895|ref|NP_247698.1| 480 EelsEKFGAEIFRVQHHFAHAYSLLGDNNY-FDDAIILSLDGVGygldgNIWGGEVLLFKdGKMERVGHLEE--Qyqlggd 557
                                   24447888999999*********9999988.588999****9752222256655544554044445544443..1457999 PP

                Carbam_trans_N 183 ................siGhlYaaateylGfkknsde..............gKlmalaayGkpkeriveelyellk..... 228
                                                    iG         + f k  +                Kl   + + +    +++++  ll      
  gi|15668895|ref|NP_247698.1| 558 latkyplrmllsilykAIGEEA------FDFIKRYNFfsekelrllkfqleKKLNCPITTSTGR--VLDAVSALLGicfek 630
                                   9999999995555444444333......333333222333456788888878888766543332..444444444444445 PP

                Carbam_trans_N 229 ..............kagyrinlennieiskkkvhdffeasalrlkearek.....dedlaAsiqvflErlvvevlnivyek 290
                                                 + +++     +i+i  k  +++++++ l  k +        +e +a   + ++ + ++e  +++++k
  gi|15668895|ref|NP_247698.1| 631 tydgepsirlepvaN-RFK----GDINIEPKIKNNILNTTELIYKSYEMLlnnenKEKIAHFAHIYIADGLFEIAKKISNK 706
                                   555666666655321.444....3444444444444444444444433222222234799999****************** PP

                Carbam_trans_N 291 lkirnLclaGGvalNiklNsallesgl...FedvwvqPaanDsG 331
                                   ++i+ + ++GGv+ N ++  +++++++   F+ ++ q ++n +G
  gi|15668895|ref|NP_247698.1| 707 FGINTIGITGGVSYNKIITERIMNNAKregFNFIYHQRVPNGDG 750
                                   *****************999999876544488888888877666 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.54   8.1e+02      72     102 ..     478     508 ..     475     521 .. 0.76
   2 !   13.2   0.0   3.7e-05     0.055     138     256 ..     614     741 ..     603     744 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.54
                                   HHHHHHHHCT--EEEEEHHHHHHHCCHCTSE CS
                 Peptidase_M22  72 fAkglalalnkPlvgVnhleahalaarleek 102
                                    A+ l+ +++ ++  V+h  aha++   +++
  gi|15668895|ref|NP_247698.1| 478 LAEELSEKFGAEIFRVQHHFAHAYSLLGDNN 508
                                   69999*******************9865543 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.7e-05
                                   HHHHHHHHHHHT..S....SCCH..HHHHHHCTC.S.......EETTEEE.CHHHHHHHHHH..STT.HHHHHHHHHHHHH CS
                 Peptidase_M22 138 gealdkvarllglpy....pggp..kieklakeg.kkiefprplkgldfsfsGlktavlkel..eke.vedlaasfqeavv 208
                                   g  ld+v+ llg+ +    +g+p   +e +a++   +i++  p++++++    +  +   e+  ++e +e++a      ++
  gi|15668895|ref|NP_247698.1| 614 GRVLDAVSALLGICFektyDGEPsiRLEPVANRFkGDINIE-PKIKNNILNTTELIYKSYEMllNNEnKEKIAHFAHIYIA 693
                                   55666666666665544443333335555565444344422.33333344443333333333333325999999999999* PP

                                   HHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCHCCHHHHTTSEEEX CS
                 Peptidase_M22 209 dhlvekteralklpkakelvilGGvaankrLrealeeeaeelglklii 256
                                   d l e+++++ ++ +++++ i GGv+ nk + e++ + a++ g+++i+
  gi|15668895|ref|NP_247698.1| 694 DGLFEIAKKISNKFGINTIGITGGVSYNKIITERIMNNAKREGFNFIY 741
                                   *********************************998777667788876 PP

>> CopK  Copper resistance protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.052        77      46      61 ..     199     214 ..     192     224 .. 0.76
   2 ?    5.9   0.0    0.0066       9.9      14      26 ..     531     543 ..     530     558 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.052
                                   TTS-EEEEETTEEEEE CS
                          CopK  46 kDgqkiimkgdEvaRL 61 
                                   +Dg++ii ++dE +R 
  gi|15668895|ref|NP_247698.1| 199 SDGKEIIAEKDEAIRE 214
                                   7***********9995 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0066
                                   SEEEEEETTS-EE CS
                          CopK  14 GstlyifkDGKma 26 
                                   G+ + +fkDGKm 
  gi|15668895|ref|NP_247698.1| 531 GGEVLLFKDGKME 543
                                   78999*******5 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.5    0.0062       9.3      14      43 ..     113     144 ..      98     158 .. 0.83
   2 ?    5.3   4.7    0.0077        11       1      45 [.     139     196 ..     139     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0062
                          NMD3  14 g..lCedCllkevditegiekievevCkeCgr 43 
                                   +  +C+dCl++  d  +   ++ +  C +Cg 
  gi|15668895|ref|NP_247698.1| 113 DvaICDDCLKEMLDKNDRRYRYPFIACTNCGP 144
                                   1459**********9999999*********95 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0077
                          NMD3   1 CcrCGkei...........eeling......lCedCllkevditegiekievevCkeCgryl 45 
                                   C +CG +            +    +      lCe+Cl + ++ ++   +++ ++C+ Cg   
  gi|15668895|ref|NP_247698.1| 139 CTNCGPRFtiveklpydreN----TsmrdfpLCEKCLEEYKNPLDRRFHAQATCCPICGPKV 196
                                   89999998667666654331....2566788**************9999*********9644 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.4    0.0015       2.3      32      56 .]     167     192 ..     166     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                       DUF4379  32 CakCgheWeasvsnrtkgssk.CpkC 56 
                                   C+kC +e++  ++ r + + + Cp C
  gi|15668895|ref|NP_247698.1| 167 CEKCLEEYKNPLDRRFHAQATcCPIC 192
                                   ****************666668**** PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3      0.17   2.6e+02      24      37 ..     115     128 ..     111     146 .. 0.78
   2 ?    7.4   2.5    0.0026       3.8      25      44 ..     166     193 ..     163     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.17
                                   EE-HHHHHHHHHTT CS
                    zf-C3HC4_3  24 vlCeeCaekllkrk 37 
                                   ++C +C++++l+++
  gi|15668895|ref|NP_247698.1| 115 AICDDCLKEMLDKN 128
                                   69******998733 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0026
                                   E-HHHHHHHHH........TT-B-TTT- CS
                    zf-C3HC4_3  25 lCeeCaekllk........rkkkCpiCr 44 
                                   lCe+C+e++++        + + CpiC 
  gi|15668895|ref|NP_247698.1| 166 LCEKCLEEYKNpldrrfhaQATCCPICG 193
                                   7********999******9********7 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.5      0.24   3.6e+02      24      33 ..     116     125 ..     115     146 .. 0.64
   2 ?    8.5   3.8    0.0013       1.9      24      43 ..     166     193 ..     165     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.24
                     zf-RING_5  24 fCekClkkll 33 
                                   +C++Clk+ l
  gi|15668895|ref|NP_247698.1| 116 ICDDCLKEML 125
                                   6888888776 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0013
                     zf-RING_5  24 fCekClkkll........ekeavCpiCr 43 
                                   +CekCl +++        ++  +CpiC+
  gi|15668895|ref|NP_247698.1| 166 LCEKCLEEYKnpldrrfhAQATCCPICG 193
                                   6**************************6 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.64   9.5e+02      55      78 ..     104     127 ..      92     132 .. 0.60
   2 ?    7.1   4.2    0.0062       9.2      35      77 ..     134     176 ..     128     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.64
                zinc_ribbon_15  55 keiekkesse....kkeCknCgkeveee 78 
                                   +e e     +    + +C++C ke+ ++
  gi|15668895|ref|NP_247698.1| 104 DEEEG----TipadVAICDDCLKEMLDK 127
                                   22222....13445999****9987654 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0062
                zinc_ribbon_15  35 kpylacskCkslleaskelgkeiekkessekkeCknCgkevee 77 
                                    p++ac++C+ ++++ ++l  + e+++ ++   C++C +e ++
  gi|15668895|ref|NP_247698.1| 134 YPFIACTNCGPRFTIVEKLPYDRENTSMRDFPLCEKCLEEYKN 176
                                   589**************9999999999999*******776543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (766 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.73u 0.27s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 4827.48
//
Query:       gi|15668896|ref|NP_247699.1|  [L=118]
Description: hypothetical protein MJ_0714 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-24   85.2   0.8    2.4e-24   84.9   0.8    1.1  1  Robl_LC7    Roadblock/LC7 domain
  ------ inclusion threshold ------
      0.017   14.9   0.0       0.02   14.7   0.0    1.1  1  MAPKK1_Int  Mitogen-activated protein kinase kinase 1 interac
      0.072   13.0   0.2      0.094   12.6   0.2    1.4  1  LAMTOR5     Ragulator complex protein LAMTOR5


Domain annotation for each model (and alignments):
>> Robl_LC7  Roadblock/LC7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.8     4e-28   2.4e-24       1      91 []       5      94 ..       5      94 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 4e-28
                                  HHHHHHHHCCHHCTECEEEEEETTS-EEEECCSSSS-HHHHHHHHHHHHHHHHHHHHHCTSSSECEEEEEETTEEEEEEECTT CS
                      Robl_LC7  1 lveelleelqsvpgvrgalvvskdGlviatstldnddadqlAalasgllsaakaaarelgegelkelliegkkgelyltpage 83
                                  +++ +l el++++gv+g++vv kdGlvia++ ++n da+ ++a+as++++aa++ ++e+g  +l++++ieg++g+ +++ age
  gi|15668896|ref|NP_247699.1|  5 MIDRVLLELNRTDGVKGSMVVGKDGLVIASQLPGNVDAELVGAMASAAFGAAERTSSEIGLSGLEQTMIEGEHGKTLMVDAGE 87
                                  57899****************************************************************************** PP

                                  TEEEEEEE CS
                      Robl_LC7 84 galLvvla 91
                                    +Lvvl+
  gi|15668896|ref|NP_247699.1| 88 -GILVVLT 94
                                  .9999985 PP

>> MAPKK1_Int  Mitogen-activated protein kinase kinase 1 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.3e-06      0.02      11     101 ..      13     103 ..       4     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-06
                    MAPKK1_Int  11 lsevdgllaiivtDrDGvvllkvgddssadsalrpslistfvlatdQasKLdlgknksiislyedyqvvqfnklplilsvi 91 
                                   l++ dg+++ +v  +DG v+++    + + + +     ++f  a   +s ++l+  ++++   e+     +++ + il v+
  gi|15668896|ref|NP_247699.1|  13 LNRTDGVKGSMVVGKDGLVIASQLPGNVDAELVGAMASAAFGAAERTSSEIGLSGLEQTMIEGEHGKTLMVDAGEGILVVL 93 
                                   67889*****************99999999999999999****************9999999999999999********** PP

                    MAPKK1_Int  92 astecNiGli 101
                                   ++ + N Gli
  gi|15668896|ref|NP_247699.1|  94 TDAKVNLGLI 103
                                   ********99 PP

>> LAMTOR5  Ragulator complex protein LAMTOR5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.6e-05     0.094       2      47 ..       3      50 ..       2      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                       LAMTOR5  2 ekqleevldevmskegvvGvlcaDeqGLclgsr..Gtlsnksagiita 47
                                  e++++ vl e+  + gv+G +++ ++GL ++s+  G+++ +  g++++
  gi|15668896|ref|NP_247699.1|  3 ESMIDRVLLELNRTDGVKGSMVVGKDGLVIASQlpGNVDAELVGAMAS 50
                                  778899999999******************998667776666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 987.73
//
Query:       gi|15668897|ref|NP_247700.1|  [L=338]
Description: H(2)-dependent methylenetetrahydromethanopterin dehydrogenase-like protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-38  129.2   5.3    5.2e-38  129.2   2.2    2.4  3  HMD            H2-forming N5,N10-methylene-tetrahydromethanop
  ------ inclusion threshold ------
      0.013   15.7   0.2      0.022   15.0   0.2    1.4  1  VPS9           Vacuolar sorting protein 9 (VPS9) domain
      0.014   15.3   0.1       0.36   10.7   0.0    2.6  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.088   13.0   0.1       0.24   11.6   0.0    1.7  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd


Domain annotation for each model (and alignments):
>> HMD  H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.3   1.4e+03      24      53 ..     155     184 ..     153     187 .. 0.84
   2 !  129.2   2.2   1.2e-41   5.2e-38       1      96 [.     194     289 ..     194     290 .. 0.99
   3 ?   -3.4   0.0       2.6   1.2e+04      50      64 ..     315     329 ..     306     334 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.3
                                   HHHHHHHHTT---HHHHHHHHHHHHHHHHH CS
                           HMD  24 dyydvvtkilkapkemvekqilesLqtias 53 
                                   +yy+++ k l+ ++  +e qi++ ++ ++s
  gi|15668897|ref|NP_247700.1| 155 KYYTIAGKALEGKEYATEDQINKLVELVKS 184
                                   699999999999999999999987776665 PP

  == domain 2  score: 129.2 bits;  conditional E-value: 1.2e-41
                                   HHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-HHHHHHCHHCC-S CS
                           HMD   1 AdlvsaVaDmgslvTAvtlagildyydvvtkilkapkemvekqilesLqtiaslveksGieglekalnpelllksaksmnl 81 
                                   Ad+v+aVaDmg+lvTAv+l+g+ldyy+v+t+i++apk+m+ekqil sLqtias++e+sG+egl+k++n+++ll+sak+m +
  gi|15668897|ref|NP_247700.1| 194 ADVVPAVADMGALVTAVALVGVLDYYRVGTQIINAPKDMIEKQILISLQTIASIIETSGMEGLMKVFNKDALLSSAKNMLI 274
                                   89******************************************************************************* PP

                                   CCCTCHHHHHHHHHH CS
                           HMD  82 geeqeeLpaalkvle 96 
                                   +e+qe+L+ alk++e
  gi|15668897|ref|NP_247700.1| 275 DERQEDLNLALKIIE 289
                                   *************98 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.6
                                   HHHHHHHHHHHHHHH CS
                           HMD  50 tiaslveksGiegle 64 
                                      sl+ ks +eg++
  gi|15668897|ref|NP_247700.1| 315 EAVSLIGKSAVEGMI 329
                                   344666666666665 PP

>> VPS9  Vacuolar sorting protein 9 (VPS9) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   4.9e-06     0.022      20      79 ..     236     295 ..     224     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.9e-06
                          VPS9  20 KlkcllrtieeiteavskseegeslgaDdlLPiliyviikssppnlysnvqfikrFrskt 79 
                                    + + l+ti +i+e+  ++   + ++ D lL++   ++i  + ++l + ++ i++F ++t
  gi|15668897|ref|NP_247700.1| 236 QILISLQTIASIIETSGMEGLMKVFNKDALLSSAKNMLIDERQEDLNLALKIIEEFDKST 295
                                   46678999999999999***************************************4333 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     8e-05      0.36      11      90 ..      32     110 ..      31     118 .. 0.68
   2 ?    1.5   0.0     0.052   2.3e+02     155     177 ..     170     192 ..     164     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8e-05
                                   HHHHHHHHHHTT-EEEEE-S-HHHHHHHH.HHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SEEEE-S-SSH CS
                       3HCDH_N  11 GagiaavfasagleVvlvdiseealekal.ekieksleklvekgklkeeeveaalarisfttdleeavdadlviEavvEnl 90 
                                   Gag+a  fa+ag++Vvl + +++ + + l +k+e+   k+  +  +++++  ++    ++   +     a+ +iE v+En 
  gi|15668897|ref|NP_247700.1|  32 GAGMAIEFAKAGHDVVLSEPNRDVMSDDLwKKVEDAGVKV-VSDDIEAAKHGEIHVLFTPFGRITL-NIANTIIEHVPENA 110
                                   99******************99988765415555544444.4455555555555555554444432.26778888888875 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.052
                                   --HHHHHHHHHHHHHTT-EEEEE CS
                       3HCDH_N 155 Tseetvatvvelakkigktpvvv 177
                                     e+ ++++vel+k++gk p v+
  gi|15668897|ref|NP_247700.1| 170 ATEDQINKLVELVKSVGKIPYVT 192
                                   56778999**********99776 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.4e-05      0.24      11      92 ..      32     118 ..      31     132 .. 0.85
   2 ?   -2.3   0.1      0.98   4.4e+03      56      87 ..     194     226 ..     167     247 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.4e-05
                                   HHHHHHHHHHTT-EEEEE-SSHHHH.....HHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EE CS
                 NAD_binding_2  11 Gsnmalnllkagykvavynrtkekv.....eelvaegakaaesieelvasldvvitmvkagkavdeviegllealkkgdil 86 
                                   G+ ma +++kag++v++ + +++ +     +++ ++g+k++++  e++++ ++ +++ + g+ + ++ + ++e++ +++i+
  gi|15668897|ref|NP_247700.1|  32 GAGMAIEFAKAGHDVVLSEPNRDVMsddlwKKVEDAGVKVVSDDIEAAKHGEIHVLFTPFGRITLNIANTIIEHVPENAII 112
                                   899***************988765521111445555699999999************************************ PP

                                   EE-S-- CS
                 NAD_binding_2  87 idgsts 92 
                                    ++ t+
  gi|15668897|ref|NP_247700.1| 113 CNTCTI 118
                                   999887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.98
                                   CSEEEE-SSSHHHHHHHHHS.HCCC--TT-EEE CS
                 NAD_binding_2  56 ldvvitmvkagkavdevieg.llealkkgdili 87 
                                   +dvv  +   g+ v +v    +l++++ g+ +i
  gi|15668897|ref|NP_247700.1| 194 ADVVPAVADMGALVTAVALVgVLDYYRVGTQII 226
                                   355555555555555555444666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2304.00
//
Query:       gi|15668898|ref|NP_247702.1|  [L=119]
Description: molybdopterin converting factor subunit 2 MoaE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-20   73.1   0.0    2.4e-20   72.9   0.0    1.1  1  MoaE           MoaE protein
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.015   14.6   0.0    1.2  1  BsuBI_PstI_RE  BsuBI/PstI restriction endonuclease domain
      0.038   14.0   0.0      0.069   13.2   0.0    1.5  1  YolD           YolD-like protein
       0.78   10.6   4.3        1.1   10.1   0.1    2.6  3  KMP11          Kinetoplastid membrane protein 11


Domain annotation for each model (and alignments):
>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   5.3e-24   2.4e-20      10     112 ..      15     117 ..       5     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 5.3e-24
                                   HHHHHH--TT--EEEEEEEE------...TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEEETTSEEE CS
                          MoaE  10 eiealvaspkaGAvvlFvGtvRdsfd...gkkvteLeyeayepmaektleeiaeearerwelervavvHrlGelevgeasv 87 
                                   e+ +   + k G++v+F G+vR+  d   g+kv +  ++   +  +++l+ ++eea++++++ +++ +H +G l++ge + 
  gi|15668898|ref|NP_247702.1|  15 ECIEK-YKGKFGCIVTFNGFVRE-YDlkdGEKVPSKGMKID-EDILEKLKLVIEEAKNKFDVIDILFYHNTGFLSIGERIA 92 
                                   43333.25679***********5.45577999999999988.999************************************ PP

                                   EEEEEESSHHHHHHHHHHHHHHHHH CS
                          MoaE  88 vvavssahRkeafeaceylidelKk 112
                                    +av ++hRke fea ey+i+e+Kk
  gi|15668898|ref|NP_247702.1|  93 SIAVFARHRKEGFEALEYIINEMKK 117
                                   ************************7 PP

>> BsuBI_PstI_RE  BsuBI/PstI restriction endonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.3e-06     0.015      47     106 ..      47     108 ..      33     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-06
                 BsuBI_PstI_RE  47 dkvlvldeellkelgleidshkklPDiv..lydeeknlLvliEavtsdGpinekRkeelkel 106
                                   +k + +de+ l++l+l i++ k+  D++  l++++  +L + E ++s   + ++Rke +++l
  gi|15668898|ref|NP_247702.1|  47 SKGMKIDEDILEKLKLVIEEAKNKFDVIdiLFYHNTGFLSIGERIASIAVFARHRKEGFEAL 108
                                   477899*********************5449999**********************988766 PP

>> YolD  YolD-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.5e-05     0.069      21      67 ..      48      95 ..      34     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                          YolD 21 kp.eLDeqqleeineklqealeeeqpvtityyedgeleevtgyiekid 67
                                  k  ++De+ le+++ +++ea ++ + + i +y++  + ++  +i +i 
  gi|15668898|ref|NP_247702.1| 48 KGmKIDEDILEKLKLVIEEAKNKFDVIDILFYHNTGFLSIGERIASIA 95
                                  4458******************************99999988888876 PP

>> KMP11  Kinetoplastid membrane protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00025       1.1      54      80 ..       1      27 [.       1      33 [. 0.87
   2 ?    1.0   0.1      0.17   7.6e+02      47      63 ..      56      72 ..      32      78 .. 0.69
   3 ?   -0.7   0.1      0.58   2.6e+03      42      58 ..      99     115 ..      92     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                         KMP11 54 mikehtekfnkkmrehsehfkakfael 80
                                  mi +  e f kkm e  e++k kf  +
  gi|15668898|ref|NP_247702.1|  1 MIFNEYEEFCKKMDECIEKYKGKFGCI 27
                                  67778899***************9765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.17
                         KMP11 47 hyekfekmikehtekfn 63
                                    ek++ +i+e  +kf+
  gi|15668898|ref|NP_247702.1| 56 ILEKLKLVIEEAKNKFD 72
                                  35777777888888885 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.58
                         KMP11  42 pemkehyekfekmikeh 58 
                                      ke +e +e +i+e 
  gi|15668898|ref|NP_247702.1|  99 RHRKEGFEALEYIINEM 115
                                   56789999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 780.73
//
Query:       gi|15668899|ref|NP_247703.1|  [L=402]
Description: chromate resistance protein ChrA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-66  223.8  41.6    1.9e-33  115.8  16.4    2.1  2  Chromate_transp  Chromate transporter


Domain annotation for each model (and alignments):
>> Chromate_transp  Chromate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1  17.3   3.5e-37   6.4e-33       1     156 [.      24     186 ..      24     187 .. 0.94
   2 !  115.8  16.4   1.1e-37   1.9e-33       3     156 ..     238     398 ..     236     399 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 3.5e-37
               Chromate_transp   1 lelflfflkiGllifGGgyavipllreevverkgwlteeefldglalaqalPGPiavnlatfvGylilgvlGaliatlgff 81 
                                   l++f +flk+G+++fGG+ ++i+++re vv++k+w++e+ f +g+alaq++PG+ ++++a++vG+ ++g++Ga++a+++  
  gi|15668899|ref|NP_247703.1|  24 LNIFMSFLKLGMVAFGGP-TAIAYVREMVVDEKKWMDEKSFNNGVALAQIIPGASVMQVAAYVGFYLRGIVGAFAAFMAYA 103
                                   579*************95.559*********999********************************55************* PP

               Chromate_transp  82 lPsfllilllaplleklrknplvkaaleglnaavvglilaaalslakk........iallaflllllfkvspilvillaal 154
                                   lP+fl++l+l+ ++ ++++ p   +++e+l+ +vv l ++ +l++ kk        ++ll+ +ll+++k+sp++vi+++++
  gi|15668899|ref|NP_247703.1| 104 LPAFLIMLFLTIIYMHVKSLPKTVSIFEALRIIVVSLAANGTLNFSKKnirtigdvFLLLISALLFILKFSPFIVIFVSIF 184
                                   *****************9988899*******************9888899999999778889999999************9 PP

               Chromate_transp 155 lg 156
                                   +g
  gi|15668899|ref|NP_247703.1| 185 IG 186
                                   98 PP

  == domain 2  score: 115.8 bits;  conditional E-value: 1.1e-37
               Chromate_transp   3 lflfflkiGllifGGgyavipllreevverkgwlteeefldglalaqalPGPiavnlatfvGylil.gvlGaliatlgffl 82 
                                   l+  ++k+ +++fGGgy+ +p++ +evv++++ +++++f+dg+al+q++PGPi+  +atfvGy  + g++G++i+t+++f+
  gi|15668899|ref|NP_247703.1| 238 LSTLMMKVDVFAFGGGYGSVPFMLHEVVDKYNLMDAKTFMDGIALGQITPGPIV-ITATFVGYI-VgGFIGSIISTISVFT 316
                                   667789999********************************************5.99******9.55************** PP

               Chromate_transp  83 Psfllilllaplleklrknplvkaaleglnaavvglilaaalslakk.........iallaflllllfkvspilvillaal 154
                                   Psf+++l  +p++++l++n+++k++l+ +    vgl++a+++++a           i+++  +lll+ k++++lv+ll+++
  gi|15668899|ref|NP_247703.1| 317 PSFIILLSSIPIFDSLKHNTIFKNILHMILVSFVGLLVAVTIRFALLvdwsiqaliIFIV-SFLLLYKKYNMLLVVLLSLV 396
                                   ****************99************************554335558888844444.44555677999999999999 PP

               Chromate_transp 155 lg 156
                                   lg
  gi|15668899|ref|NP_247703.1| 397 LG 398
                                   98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1246  (0.0694963); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 2808.38
//
Query:       gi|15668900|ref|NP_247704.1|  [L=600]
Description: putative ATPase RIL [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-45  154.3   0.0    1.8e-22   80.3   0.0    2.4  2  ABC_tran      ABC transporter
    2.5e-14   53.8   7.8     0.0059   16.5   0.7    4.2  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    6.2e-14   51.5   4.9    1.4e-13   50.4   4.9    1.7  1  RLI           Possible Fer4-like domain in RNase L inhibitor,
    1.1e-13   51.2   3.1    9.5e-07   28.5   0.0    3.2  3  SMC_N         RecF/RecN/SMC N terminal domain
    5.3e-06   26.3  10.9     0.0015   18.5   2.5    2.4  2  Fer4_6        4Fe-4S binding domain
    5.8e-06   25.9   2.7    5.8e-06   25.9   2.7    3.0  3  Fer4          4Fe-4S binding domain
    2.8e-05   24.5   0.1       0.34   11.3   0.0    2.5  2  AAA_16        AAA ATPase domain
    2.9e-05   24.7   7.2      0.039   14.4   2.5    2.7  2  AAA_23        AAA domain
    7.6e-05   22.5   0.5      0.059   13.1   0.0    2.6  2  AAA_24        AAA domain
    0.00014   21.8   0.3       0.42   10.5   0.0    2.6  2  RsgA_GTPase   RsgA GTPase
    0.00015   21.8  10.4      0.005   16.9   0.9    2.3  2  Fer4_10       4Fe-4S dicluster domain
    0.00016   22.0   0.0       0.61   10.4   0.0    2.6  2  AAA_22        AAA domain
    0.00038   21.0   2.1        2.6    8.6   0.0    3.7  3  AAA_18        AAA domain
    0.00045   20.3   8.2    0.00073   19.6   8.2    1.3  1  Fer4_21       4Fe-4S dicluster domain
    0.00046   20.6   0.0       0.78   10.2   0.0    2.8  2  AAA           ATPase family associated with various cellular 
    0.00046   19.9   0.9       0.23   11.3   0.0    2.4  2  AAA_29        P-loop containing region of AAA domain
    0.00047   20.3   0.0        0.2   11.8   0.0    2.8  2  AAA_33        AAA domain
    0.00049   20.5   0.1        1.6    9.2   0.0    2.5  2  RNA_helicase  RNA helicase
    0.00077   19.4   0.8       0.77    9.7   0.1    2.4  2  NACHT         NACHT domain
     0.0018   18.2   0.0        2.6    7.9   0.0    2.5  2  Rad17         Rad17 P-loop domain
     0.0024   18.4   8.6     0.0063   17.1   8.7    1.7  1  Fer4_7        4Fe-4S dicluster domain
     0.0032   17.6   0.0       0.27   11.4   0.0    2.4  2  Lactococcin   Lactococcin-like family
     0.0045   17.1   0.4        1.2    9.2   0.0    2.9  2  MMR_HSR1      50S ribosome-binding GTPase
     0.0045   17.1   9.3     0.0087   16.2   9.3    1.5  1  Fer4_9        4Fe-4S dicluster domain
     0.0058   16.2   2.6        1.5    8.3   0.0    3.1  4  AAA_25        AAA domain
     0.0086   16.1   4.3        1.7    8.7   0.1    3.4  3  AAA_14        AAA domain
  ------ inclusion threshold ------
      0.012   15.7   2.2        5.2    7.1   0.0    3.5  3  DUF87         Helicase HerA, central domain
      0.018   14.3   0.0       0.47    9.6   0.0    2.1  2  KAP_NTPase    KAP family P-loop domain
      0.025   14.5   1.6        1.3    9.0   0.2    2.9  2  NTPase_1      NTPase
      0.027   14.7   0.1        7.5    6.8   0.1    2.6  2  AAA_28        AAA domain
      0.027   14.5   0.6        4.1    7.4   0.0    3.1  2  AAA_5         AAA domain (dynein-related subfamily)
      0.033   15.1   6.3      0.042   14.8   0.3    2.5  2  Fer4_16       4Fe-4S double cluster binding domain
       0.07   12.8  11.4       0.54    9.9   0.2    3.7  4  AAA_15        AAA ATPase domain
      0.077   12.7   0.0        6.1    6.5   0.0    2.3  2  PRK           Phosphoribulokinase / Uridine kinase family
      0.085   12.6   0.8        7.9    6.2   0.2    2.6  2  AAA_30        AAA domain
        0.1   12.2   1.1        1.2    8.7   0.1    2.3  2  SRP54         SRP54-type protein, GTPase domain
       0.17   11.9   0.2        3.2    7.7   0.1    2.4  2  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.21   10.7   2.1         12    4.9   0.0    2.4  2  NB-ARC        NB-ARC domain
       0.26   10.2   2.7        2.7    6.9   0.1    2.3  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.67   10.2  10.4        0.1   12.7   2.1    2.4  2  Fer4_2        4Fe-4S binding domain
       0.82    8.4   4.1        2.5    6.8   0.1    2.4  2  ABC_ATPase    Predicted ATPase of the ABC class
          8    7.7  16.3       0.75   10.9   4.2    2.3  2  Fer4_3        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0     2e-22   8.4e-20       8     136 ..     107     251 ..     101     252 .. 0.79
   2 !   80.3   0.0   4.3e-25   1.8e-22       7     137 .]     369     491 ..     363     491 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 2e-22
                                   EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSB CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                      ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGei...........lldgkdlkeqeleslrkeigvlpqe..pqlfpelt 75 
                                   + ++ +v+i+G+nG GKSt+l++lag+l p+ G+             ++g++l+e  ++  +k ++ +++     + p++ 
  gi|15668900|ref|NP_247704.1| 107 IPRDGVVGIIGQNGIGKSTVLRILAGELIPNLGKHdkepnyddvikYFRGTELQEYFEKLKNKGVKAIHKVqyVDILPKV- 186
                                   667889************************99999666666666655557777764444445555554444334444444. PP

                                   HHHH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  76 vren........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   v+ +        +++ +++++++kl+lk++ d+ +    s+LSgG+ qrva+a+a l++ +++++DEp+
  gi|15668900|ref|NP_247704.1| 187 VKGKvgdllkkvDEKGKFDEVVEKLELKNILDREL----SQLSGGELQRVAIAAAYLRNGDIYFFDEPS 251
                                   44337888997777778******************....*****************************7 PP

  == domain 2  score: 80.3 bits;  conditional E-value: 4.3e-25
                                   EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.......H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......x RF
                      ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.......e 80 
                                   ++++ge+++i+G+nG GK+t++kllag  kp+eGe+           +++ + ++++ pq  + +++ tv++        +
  gi|15668900|ref|NP_247704.1| 369 TIYKGEVIGILGPNGIGKTTFVKLLAGVIKPDEGEV-----------IKEGDIKVSYKPQYITPDYDGTVEDLlssitniH 438
                                   799*********************************...........6778888999999988889988888888877776 PP

                                   HHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  81 sdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    +   +++++ l+l++l d+ v    ++LSgG+ qrva+a++l ++++++llDEp+a
  gi|15668900|ref|NP_247704.1| 439 TSYYKSEIINPLQLEKLLDREV----RELSGGELQRVAIAACLSRDADIYLLDEPSA 491
                                   6667889999999999999999....*****************************75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.7   1.4e-05    0.0059       2      50 ..     113     155 ..     112     169 .. 0.70
   2 !   15.0   0.1   3.9e-05     0.016     163     286 ..     140     270 ..     133     283 .. 0.75
   3 !   14.6   0.1     5e-05     0.022       2      68 ..     376     435 ..     375     446 .. 0.66
   4 !   10.5   0.0   0.00089      0.38     232     279 ..     458     509 ..     442     518 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-05
                        AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslld 50 
                                    ++iG Ng GKS++L++l      ++++++   + ++  ++++++++++
  gi|15668900|ref|NP_247704.1| 113 VGIIGQNGIGKSTVLRIL------AGELIPNLGKHDKEPNYDDVIKYFR 155
                                   68****************......5555555555555555555555555 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.9e-05
                        AAA_21 163 ke.rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer.........gvvflengdgqelp 233
                                   k+ + ++++++++yf + ++++++++l ++  ++  +++  ++ ++  +    +l+ +          v  le ++  ++ 
  gi|15668900|ref|NP_247704.1| 140 KHdKEPNYDDVIKYFRGTELQEYFEKLKNKGVKAIHKVQYVDILPKVVKGKVGDLLKKvdekgkfdeVVEKLELKNILDRE 220
                                   44566677777777777777777777777777776666666666655555555555557888999999999999******* PP

                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkels 286
                                   +++lS G ++  a+++a+lr     +++++DEp + L+ +     ++l++el+
  gi|15668900|ref|NP_247704.1| 221 LSQLSGGELQRVAIAAAYLRNG---DIYFFDEPSSWLDIRQRFNAARLIRELN 270
                                   ***********9*******988...9*********999977766666665554 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 5e-05
                        AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsq 68 
                                    ++ GpNg GK+++ ++l ++   ++  eg+ +++    g +k+++++  + p+++++ e+ +  ++
  gi|15668900|ref|NP_247704.1| 376 IGILGPNGIGKTTFVKLLAGV---IKPDEGEVIKE----GDIKVSYKPQYITPDYDGTVEDLLSSIT 435
                                   689***************777...44444444444....5555666666666666666665555555 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.00089
                        AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHP.......kllrrll 279
                                   + +relS G ++  a+++ l r++   +++l+DEp ++L+        k++rr++
  gi|15668900|ref|NP_247704.1| 458 REVRELSGGELQRVAIAACLSRDA---DIYLLDEPSAFLDVeqrlrvsKVIRRIA 509
                                   568999***999967777777766...9************976644444444443 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   4.9   3.4e-16   1.4e-13       1      35 []      13      44 ..      13      44 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 3.4e-16
                                  --EEEES---------TTHHHHHTTSEEEESS--S CS
                           RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrtgkk 35
                                  mrlAi+d+d+C+PKKC+  +c+++cp   vr+g k
  gi|15668900|ref|NP_247704.1| 13 MRLAIIDYDRCQPKKCSM-ECMKYCPG--VRMGEK 44
                                  9*****************.********..****76 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   2.2e-09   9.5e-07      24     188 ..     110     271 ..      93     292 .. 0.79
   2 ?    4.1   0.2     0.063        27      26      42 ..     375     391 ..     367     412 .. 0.85
   3 !   17.5   0.1   5.1e-06    0.0022     135     196 ..     461     520 ..     400     526 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.2e-09
                                   SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEE...EETTEESSSSSSCEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
                         SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitf...dnedkklkiekeevsisr 101
                                   +++  i+G+NG GKs +l  +   L  +  k+ ++ +++d+i++          e++ +f   +n++ k+  + + v i  
  gi|15668900|ref|NP_247704.1| 110 DGVVGIIGQNGIGKSTVLRILAGELIPNLGKHDKEPNYDDVIKY------FRGTELQEYFeklKNKGVKAIHKVQYVDILP 184
                                   56889**************99999999999999**********9......3334444444222666666666777788888 PP

                                   EEETTSE.EEEEETTEEE-HHHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                   xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 102 rvkrkge.seykingkevtkkevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                   +v++++     k  +++ ++ ev e le ++i   + ++LSgGe + va+a        +   +y++De  + LD +++ +
  gi|15668900|ref|NP_247704.1| 185 KVVKGKVgDLLKKVDEKGKFDEVVEKLELKNIldrELSQLSGGELQRVAIA----AAYLRNGDIYFFDEPSSWLDIRQRFN 261
                                   88887763334445677899********9999333356899***9888775....55788899****************** PP

                                   HHHHHHHHCT CS
                                   xxxxxxxxxx RF
                         SMC_N 179 vaellkeksk 188
                                    a+l++e +k
  gi|15668900|ref|NP_247704.1| 262 AARLIRELNK 271
                                   ******9985 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.063
                                   EEEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                         SMC_N  26 ftaivGpNGSGKsnlld 42 
                                   +  i+GpNG GK+ ++ 
  gi|15668900|ref|NP_247704.1| 375 VIGILGPNGIGKTTFVK 391
                                   6789*********9886 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 5.1e-06
                                   TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                         SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivis 196
                                    +LSgGe + va+a  +     + a +yllDe  a LD +++ +v+++++  +++k+a ++v+ 
  gi|15668900|ref|NP_247704.1| 461 RELSGGELQRVAIAACL----SRDADIYLLDEPSAFLDVEQRLRVSKVIRriADEKEAGMFVVD 520
                                   38******999998776....47899***********************954456667777775 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   1.3   0.00029      0.13       3      20 ..      17      37 ..      15      44 .. 0.90
   2 !   18.5   2.5   3.5e-06    0.0015       1      24 []      54      77 ..      54      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00029
                        Fer4_6  3 eidpdkCi..gC.gdCvrvCP 20
                                   id+d+C    C ++C++ CP
  gi|15668900|ref|NP_247704.1| 17 IIDYDRCQpkKCsMECMKYCP 37
                                  59*****9888*********9 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 3.5e-06
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  +++i + +C gCg Cv+ CP++ai
  gi|15668900|ref|NP_247704.1| 54 KPVISEVLCSGCGICVKRCPFKAI 77
                                  68999****************998 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       2.1   9.1e+02       2       8 ..      17      23 ..      16      24 .. 0.88
   2 ?    1.1   0.4      0.92   3.9e+02      13      19 ..      31      37 ..      30      38 .. 0.89
   3 !   25.9   2.7   1.4e-08   5.8e-06       1      24 []      55      78 ..      55      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.1
                                  EEETTTS CS
                          Fer4  2 videekC 8 
                                  +id+++C
  gi|15668900|ref|NP_247704.1| 17 IIDYDRC 23
                                  79***** PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.92
                                  HHHHHST CS
                          Fer4 13 aCvevCP 19
                                  +C++ CP
  gi|15668900|ref|NP_247704.1| 31 ECMKYCP 37
                                  7****** PP

  == domain 3  score: 25.9 bits;  conditional E-value: 1.4e-08
                                  EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                  +vi e +C gCG+Cv+ CP+ AI+
  gi|15668900|ref|NP_247704.1| 55 PVISEVLCSGCGICVKRCPFKAIS 78
                                  588999****************96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0    0.0008      0.34      25      76 ..     111     154 ..     102     263 .. 0.77
   2 !   10.8   0.0    0.0011      0.49      25      59 ..     374     408 ..     361     500 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0008
                        AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqal 76 
                                   ++v ++G+ G+GKs+++r l+ +l  +      gk d+      y+ +++++
  gi|15668900|ref|NP_247704.1| 111 GVVGIIGQNGIGKSTVLRILAGELIPN-----LGKHDKE---PNYDDVIKYF 154
                                   57789*************999988888.....6666666...4454454444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0011
                        AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgk 59 
                                   e++ + G+ G+GK++ v+ l+  ++ d+g ++++ 
  gi|15668900|ref|NP_247704.1| 374 EVIGILGPNGIGKTTFVKLLAGVIKPDEGEVIKEG 408
                                   77889***************998888877665554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   2.5   9.2e-05     0.039      17      78 ..     102     167 ..      92     233 .. 0.52
   2 !   11.4   0.2    0.0008      0.34      20      39 ..     374     393 ..     349     420 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.2e-05
                        AAA_23  17 F......skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese.gkvkay.velt 78 
                                   +       +g++ I+G+NG GK+T+l+ +   L     +l++ ++   + +dv   ++ ++ ++y  +l+
  gi|15668900|ref|NP_247704.1| 102 LfglvipRDGVVGIIGQNGIGKSTVLRILAGELIP---NLGKHDK-EPNYDDVIKYFRgTELQEYfEKLK 167
                                   445566688*****************988766664...4444433.333444443333244455533333 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0008
                        AAA_23  20 gltlItGpNGaGKTTildAi 39 
                                    +  I GpNG GKTT++  +
  gi|15668900|ref|NP_247704.1| 374 EVIGILGPNGIGKTTFVKLL 393
                                   4789***********98765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0081       3.5       5      22 ..     113     130 ..     110     207 .. 0.87
   2 !   13.1   0.0   0.00014     0.059       4      22 ..     375     393 ..     372     465 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0081
                        AAA_24   5 iliyGpsgiGKTtlakel 22 
                                   + i+G++giGK+t+++ l
  gi|15668900|ref|NP_247704.1| 113 VGIIGQNGIGKSTVLRIL 130
                                   679**********99876 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00014
                        AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                    i i Gp+giGKTt++k l
  gi|15668900|ref|NP_247704.1| 375 VIGILGPNGIGKTTFVKLL 393
                                   689*************988 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00099      0.42     100     123 ..     111     134 ..     105     150 .. 0.85
   2 !    8.4   0.1    0.0043       1.8      98     130 ..     372     404 ..     365     410 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00099
                                   SEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpel 123
                                    ++ ++Gq G+GKSt++  l++el
  gi|15668900|ref|NP_247704.1| 111 GVVGIIGQNGIGKSTVLRILAGEL 134
                                   56779**************99986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0043
                                   TTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgev 130
                                   k++++ ++G+ G+GK+t+++ l++  +   gev
  gi|15668900|ref|NP_247704.1| 372 KGEVIGILGPNGIGKTTFVKLLAGVIKPDEGEV 404
                                   6788899***************99776666665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1  12.7   4.4e-05     0.019       2      56 .]      16      73 ..      15      73 .. 0.84
   2 !   16.9   0.9   1.2e-05     0.005       2      26 ..      55      79 ..      54     101 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.4e-05
                       Fer4_10  2 vvidddtC..irCg.kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  ++id d+C   +C  +C+k CP    + ++++++++ ++  +    C gcg Cv+ CP
  gi|15668900|ref|NP_247704.1| 16 AIIDYDRCqpKKCSmECMKYCPGVRMGEKTIEIDENTGKPVISEVLCSGCGICVKRCP 73
                                  689*****7769999********77777777777777777777778***********9 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.2e-05
                       Fer4_10  2 vvidddtCirCgkCvkaCPadltsv 26
                                  +vi +  C +Cg Cvk CP+++ s 
  gi|15668900|ref|NP_247704.1| 55 PVISEVLCSGCGICVKRCPFKAISI 79
                                  6788899*************66333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0039       1.6       6      29 ..     111     134 ..     108     171 .. 0.82
   2 !   10.4   0.0    0.0014      0.61       8      86 ..     376     464 ..     371     519 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0039
                        AAA_22   6 gilvvtGesGtGKTtllrrlleql 29 
                                   g++ ++G+ G+GK+t+lr l+ +l
  gi|15668900|ref|NP_247704.1| 111 GVVGIIGQNGIGKSTVLRILAGEL 134
                                   66779*************988665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0014
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.....erpevv.....fvtlpsstsskdllrellralglelka...erlss 75 
                                   + + G+ G+GKTt ++ l+       k++e     e++  v     ++t+  +++ +dll+ + ++ ++  k+   ++l++
  gi|15668900|ref|NP_247704.1| 376 IGILGPNGIGKTTFVKLLAGVI----KPDEgevikEGDIKVsykpqYITPDYDGTVEDLLSSITNIHTSYYKSeiiNPLQL 452
                                   6689*************99865....3333446664555554668888888888999999999988887666688866666 PP

                        AAA_22  76 eell.ealeqal 86 
                                   e ll + +++ +
  gi|15668900|ref|NP_247704.1| 453 EKLLdREVRELS 464
                                   666645544443 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0062       2.6       1      47 [.     113     167 ..     113     219 .. 0.63
   2 ?    2.5   0.0      0.46     2e+02      24      82 ..     224     285 ..     206     293 .. 0.69
   3 ?    7.5   0.0     0.014       5.8       1      20 [.     376     395 ..     376     463 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0062
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.........gvnlrdvakenglllevdpeald 47 
                                   +++ G  G GK+t+ + L+ +l  +          + ++++++  +l +++++   +
  gi|15668900|ref|NP_247704.1| 113 VGIIGQNGIGKSTVLRILAGELiPNlgkhdkepnYDDVIKYFRGTELQEYFEKL--K 167
                                   689999************888755568888888844444444444444444444..2 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.46
                        AAA_18  24 f.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenss.aleegknlvidgh 82 
                                   +      ++ +  a+ ++  +++++e   +s  ld+ ++ ++ ++++e ++    e++ +v+d +
  gi|15668900|ref|NP_247704.1| 224 LsggelQRVAIAAAYLRNGDIYFFDE---PSSWLDIRQRFNAARLIRELNKvVVVEHDLIVLDYL 285
                                   24444444444555555566666666...788999999999999999998887889999999875 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.014
                        AAA_18   1 IlltGtpGvGKttlakeLsk 20 
                                   I++ G+ G GKtt+ k L+ 
  gi|15668900|ref|NP_247704.1| 376 IGILGPNGIGKTTFVKLLAG 395
                                   89***************964 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   8.2   1.7e-06   0.00073       1      57 [.      16      77 ..      16      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.7e-06
                       Fer4_21  1 AridedkCi..gCg.kCliaCe..dtshqaieidaktvlkvved.eCvGCnlCssvCPvedci 57
                                  A+id d+C   +C  +C++ C+    + + ieid++t  +v+++  C GC +C++ CP  ++i
  gi|15668900|ref|NP_247704.1| 16 AIIDYDRCQpkKCSmECMKYCPgvRMGEKTIEIDENTGKPVISEvLCSGCGICVKRCPF-KAI 77
                                  678888985336753688888833357899***********95549************7.776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0098       4.2       3      35 ..     115     151 ..     113     274 .. 0.78
   2 !   10.2   0.0    0.0018      0.78       3      22 ..     378     397 ..     376     460 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0098
                                   EESSTTSSHHHHHHHHHHHH....THEEEEEETTTCS CS
                           AAA   3 lyGppGtGKTllakavakel....gvefleisgsell 35 
                                   ++G  G+GK+++ + +a el    g +  e +  +++
  gi|15668900|ref|NP_247704.1| 115 IIGQNGIGKSTVLRILAGELipnlGKHDKEPNYDDVI 151
                                   68*****************755443333333333333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0018
                                   EESSTTSSHHHHHHHHHHHH CS
                           AAA   3 lyGppGtGKTllakavakel 22 
                                   + Gp G+GKT+++k +a  +
  gi|15668900|ref|NP_247704.1| 378 ILGPNGIGKTTFVKLLAGVI 397
                                   57**************9865 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00053      0.23      20      39 ..     108     127 ..      99     137 .. 0.85
   2 ?    6.6   0.2     0.015       6.3      24      39 ..     375     390 ..     367     403 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00053
                        AAA_29  20 dlkgatlltGpsGsGKSTll 39 
                                    ++g++ ++G++G GKST+l
  gi|15668900|ref|NP_247704.1| 108 PRDGVVGIIGQNGIGKSTVL 127
                                   4567899***********97 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                        AAA_29  24 atlltGpsGsGKSTll 39 
                                   ++ + Gp+G GK+T++
  gi|15668900|ref|NP_247704.1| 375 VIGILGPNGIGKTTFV 390
                                   66699*********98 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.034        15       1      23 [.     112     134 ..     112     279 .. 0.85
   2 !   11.8   0.0   0.00047       0.2       4     109 ..     378     522 ..     375     528 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.034
                        AAA_33   1 lvllvGlpGsGKstlaerllkkl 23 
                                   +v ++G +G GKst+++ l+ +l
  gi|15668900|ref|NP_247704.1| 112 VVGIIGQNGIGKSTVLRILAGEL 134
                                   56789***********9998776 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00047
                        AAA_33   4 lvGlpGsGKstlaerllkklg...avllssdt...........................lrrrlfgtdqqsktdytrvldr 54 
                                   + G++G GK+t+++ l+   +   ++++ + +                           +++ +++++  ++ ++ ++ldr
  gi|15668900|ref|NP_247704.1| 378 ILGPNGIGKTTFVKLLAGVIKpdeGEVIKEGDikvsykpqyitpdydgtvedllssitnIHTSYYKSEIINPLQLEKLLDR 458
                                   67************9954444445999999887888888888888788777777777775555555444444444444444 PP

                        AAA_33  55 .....lyqilne.larkalsagrn.vildat..nlsrrerarflklarrlgvpvrivvvetdee 109
                                          + l++  ++ +ls+ ++ ++ld +  +l+ ++r r+ k+ rr+  + ++  + +d +
  gi|15668900|ref|NP_247704.1| 459 evrelSGGELQRvAIAACLSRDADiYLLDEPsaFLDVEQRLRVSKVIRRIADEKEAGMFVVDHD 522
                                   2222222233330445677888887888888889999999999999988877777777766665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0037       1.6       3      32 ..     115     144 ..     113     175 .. 0.74
   2 !    8.8   0.0    0.0049       2.1       3      23 ..     378     398 ..     376     426 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0037
                  RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkkd 32 
                                   + G++g+GKSt+ + La +l  +l+++ k+
  gi|15668900|ref|NP_247704.1| 115 IIGQNGIGKSTVLRILAGELIPNLGKHDKE 144
                                   78*************999999777443333 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0049
                  RNA_helicase   3 lyGpsgeGKStlakeLakall 23 
                                   + Gp+g+GK+t++k La  + 
  gi|15668900|ref|NP_247704.1| 378 ILGPNGIGKTTFVKLLAGVIK 398
                                   78*************886665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0063       2.7       3      23 ..     113     133 ..     111     145 .. 0.86
   2 !    9.7   0.1    0.0018      0.77       2      21 ..     375     394 ..     374     403 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0063
                                   EEEEC-TTTCHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                   v + G++G+GK+t l+ la +
  gi|15668900|ref|NP_247704.1| 113 VGIIGQNGIGKSTVLRILAGE 133
                                   6799***********988865 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0018
                                   CEEEEC-TTTCHHHHHHHHH CS
                         NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                   ++ + G++G+GKTt+++ la
  gi|15668900|ref|NP_247704.1| 375 VIGILGPNGIGKTTFVKLLA 394
                                   56799***********9887 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0     0.006       2.6      48      74 ..     113     139 ..     105     182 .. 0.87
   2 !    7.7   0.0    0.0072       3.1      47      71 ..     375     399 ..     361     439 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.006
                         Rad17  48 LLisGPsGCgkstvvkvLskelgiklr 74 
                                   + i G  G gkstv+++L+ el ++l 
  gi|15668900|ref|NP_247704.1| 113 VGIIGQNGIGKSTVLRILAGELIPNLG 139
                                   558899***************998875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0072
                         Rad17  47 iLLisGPsGCgkstvvkvLskelgi 71 
                                   ++ i GP G gk+t vk L+    +
  gi|15668900|ref|NP_247704.1| 375 VIGILGPNGIGKTTFVKLLAGVIKP 399
                                   66799**************976655 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   8.7   1.5e-05    0.0063       4      52 .]      27      76 ..      21      76 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-05
                        Fer4_7  4 gCg.aCvaaCpvkaieldeeenek.gtekveidpekClgCgaCvavCPtga 52
                                  +C   C+++Cp ++++ ++  + +  t k++i++  C+gCg Cv++CP++a
  gi|15668900|ref|NP_247704.1| 27 KCSmECMKYCP-GVRMGEKTIEIDeNTGKPVISEVLCSGCGICVKRCPFKA 76
                                  56448*****9.444444433333146899******************986 PP

>> Lactococcin  Lactococcin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00064      0.27       4      32 ..     210     238 ..     208     242 .. 0.85
   2 ?    3.4   0.0      0.19        83      11      30 ..     456     475 ..     448     479 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00064
                   Lactococcin   4 qlNFnIvSDeELsevnGGkLtyvqskgal 32 
                                   +l  + + D ELs+ +GG+L+ v  ++a+
  gi|15668900|ref|NP_247704.1| 210 KLELKNILDRELSQLSGGELQRVAIAAAY 238
                                   55666677**************9999887 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.19
                   Lactococcin  11 SDeELsevnGGkLtyvqskg 30 
                                    D E  e +GG+L+ v  ++
  gi|15668900|ref|NP_247704.1| 456 LDREVRELSGGELQRVAIAA 475
                                   599***********998776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0028       1.2       2      22 ..     113     133 ..     112     203 .. 0.87
   2 ?    5.0   0.1     0.058        25       2      22 ..     376     401 ..     375     535 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0028
                                   EEEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                   v+i+G+   GKSt+++ l ge
  gi|15668900|ref|NP_247704.1| 113 VGIIGQNGIGKSTVLRILAGE 133
                                   89****************997 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.058
                                   EEEEESTTSSHHHHHHHHHT.....S CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg.....e 22 
                                   ++i+G    GK+t+++ l g     e
  gi|15668900|ref|NP_247704.1| 376 IGILGPNGIGKTTFVKLLAGvikpdE 401
                                   899*************9997554441 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   9.3     2e-05    0.0087       4      51 .]      27      77 ..      22      77 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2e-05
                        Fer4_9  4 gCg.aCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkgai 51
                                  +C  +C++ Cp   + e+  e   +  +         C gCg Cv++Cp +ai
  gi|15668900|ref|NP_247704.1| 27 KCSmECMKYCPGVRMGEKTIEIDENTGK--PviseVLCSGCGICVKRCPFKAI 77
                                  4752599999888877777766666544..1357789************9887 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0036       1.5      24      54 ..     101     131 ..      87     142 .. 0.86
   2 ?   -1.8   0.1       4.5   1.9e+03     127     153 ..     263     287 ..     230     291 .. 0.62
   3 ?    6.3   0.1     0.015       6.6      28      54 ..     368     394 ..     364     403 .. 0.87
   4 ?   -2.5   0.1       7.4   3.2e+03      86     149 ..     468     520 ..     462     521 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0036
                        AAA_25  24 wlvkgllpagelallaGapgtGKttlaldla 54 
                                   +l++ ++p+++++ ++G+ g GK+t++  la
  gi|15668900|ref|NP_247704.1| 101 KLFGLVIPRDGVVGIIGQNGIGKSTVLRILA 131
                                   677889*******************986555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.5
                        AAA_25 127 tadvdaleaaieevegvrlvviDplsr 153
                                   ++ +++l +++   e  +l+v+D ls 
  gi|15668900|ref|NP_247704.1| 263 ARLIRELNKVVVV-E-HDLIVLDYLSD 287
                                   3445555555444.3.79999999886 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.015
                        AAA_25  28 gllpagelallaGapgtGKttlaldla 54 
                                   g + +ge++ + G+ g GKtt++  la
  gi|15668900|ref|NP_247704.1| 368 GTIYKGEVIGILGPNGIGKTTFVKLLA 394
                                   78899****************986665 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 7.4
                        AAA_25  86 lrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviD 149
                                   l+r + a++  +  da+ ++ld ++       ++d ++ l    v +++++i + +++++ v+D
  gi|15668900|ref|NP_247704.1| 468 LQRVAIAACLSR--DADIYLLDEPSA------FLDVEQRL---RVSKVIRRIADEKEAGMFVVD 520
                                   555555555554..566666664332......22222222...123334444443556666666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1     0.004       1.7       3      84 ..     111     188 ..     109     202 .. 0.65
   2 ?    7.1   0.1     0.013       5.4       2      23 ..     373     394 ..     372     413 .. 0.87
   3 ?   -0.7   0.0       3.1   1.3e+03      31      95 ..     445     517 ..     431     520 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.004
                        AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe..kllelileklkeekktylflDEiqevpewek 81 
                                    ++ i G   +GK+t+l+ l+ el+    +    + + + d+ ++ ++  +l e++ ++ k  +k +  +  +q+v+ + k
  gi|15668900|ref|NP_247704.1| 111 GVVGIIGQNGIGKSTVLRILAGELI---PNLGKHDKEPNYDDVIKYFRgtELQEYFEKL-K--NKGVKAIHKVQYVDILPK 185
                                   5789*****************9999...4444444444333333322222455555554.3..455667777777776666 PP

                        AAA_14  82 alk 84 
                                   ++k
  gi|15668900|ref|NP_247704.1| 186 VVK 188
                                   666 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.013
                        AAA_14   2 rkilvitGaRrvGKTtllkqli 23 
                                   ++++ i G+  +GKTt++k l+
  gi|15668900|ref|NP_247704.1| 373 GEVIGILGPNGIGKTTFVKLLA 394
                                   57899************99886 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 3.1
                        AAA_14  31 esilyinldderdkkladpe..kllelilek.lkeekktylflDEiqev......pewekalkslvdegknldv 95 
                                   e i  ++l++  d++ ++ +  +l ++  +  l++ +  + +lDE +         +++k+++++ de++ + +
  gi|15668900|ref|NP_247704.1| 445 EIINPLQLEKLLDREVRELSggELQRVAIAAcLSR-DADIYLLDEPSAFldveqrLRVSKVIRRIADEKEAGMF 517
                                   44555666666666655544455555555543444.66677888877774444445566777777777755555 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.012       5.2      26      48 ..     113     135 ..     112     151 .. 0.88
   2 ?    0.4   0.1       1.3   5.7e+02      40      68 ..     262     292 ..     260     351 .. 0.79
   3 ?    5.5   0.1     0.037        16      26      44 ..     376     394 ..     374     405 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.012
                         DUF87  26 lAilgsTGsGKSntvavLleell 48 
                                   ++i+g+ G GKS+  ++L  el+
  gi|15668900|ref|NP_247704.1| 113 VGIIGQNGIGKSTVLRILAGELI 135
                                   69*****************9998 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.3
                         DUF87  40 vavLleelle..kkgatililDpHGEYgkal 68 
                                   +a L++el +       +++lD  ++Y ++ 
  gi|15668900|ref|NP_247704.1| 262 AARLIRELNKvvVVEHDLIVLDYLSDYIHIM 292
                                   788999999655444599*********9987 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.037
                         DUF87  26 lAilgsTGsGKSntvavLl 44 
                                   ++ilg  G GK+++v++L 
  gi|15668900|ref|NP_247704.1| 376 IGILGPNGIGKTTFVKLLA 394
                                   69**************996 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.16        67      22      44 ..     112     134 ..     107     253 .. 0.93
   2 ?    9.6   0.0    0.0011      0.47      20     101 ..     373     458 ..     354     520 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.16
                    KAP_NTPase  22 vvgLygkWGsGKssllnkledel 44 
                                   vvg+ g+ G GKs++l  l  el
  gi|15668900|ref|NP_247704.1| 112 VVGIIGQNGIGKSTVLRILAGEL 134
                                   89**************9998776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
                    KAP_NTPase  20 pivvgLygkWGsGKssllnkledelkefa....kpvrflfaefnawsfkggddavaellaaLadaleeeygqlatkllrak 96 
                                   + v+g+ g+ G GK++++++l   +k       k+ ++++ +     + ++d+ v++ll+++ +  ++ y+++ ++ l  +
  gi|15668900|ref|NP_247704.1| 373 GEVIGILGPNGIGKTTFVKLLAGVIKPDEgeviKEGDIKVSYKPQYITPDYDGTVEDLLSSITNIHTSYYKSEIINPLQLE 453
                                   5699******************99999988888899999999999999999***********9999999999988887777 PP

                    KAP_NTPase  97 klkal 101
                                   kl ++
  gi|15668900|ref|NP_247704.1| 454 KLLDR 458
                                   76655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.15        63       2      22 ..     113     133 ..     112     138 .. 0.83
   2 ?    9.0   0.2    0.0029       1.3       2      25 ..     376     399 ..     375     406 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.15
                                   EEEE--TTSSHHHHHHHHHHH CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlel 22 
                                   v i G+ G+GK+T+++ ++ +
  gi|15668900|ref|NP_247704.1| 113 VGIIGQNGIGKSTVLRILAGE 133
                                   6688**********9877665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0029
                                   EEEE--TTSSHHHHHHHHHHHH.. CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellks 25 
                                   + i Gp G+GKtT+vk ++ ++k 
  gi|15668900|ref|NP_247704.1| 376 IGILGPNGIGKTTFVKLLAGVIKP 399
                                   6688************99999875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.057        24       3      21 ..     114     132 ..     112     175 .. 0.86
   2 ?    6.8   0.1     0.017       7.5       2      20 ..     376     394 ..     375     408 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.057
                        AAA_28   3 vitGgestGKTtlleaLaa 21 
                                    i+G  + GK+t+l+ La 
  gi|15668900|ref|NP_247704.1| 114 GIIGQNGIGKSTVLRILAG 132
                                   599**************94 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.017
                        AAA_28   2 ivitGgestGKTtlleaLa 20 
                                   i i+G+ + GKTt ++ La
  gi|15668900|ref|NP_247704.1| 376 IGILGPNGIGKTTFVKLLA 394
                                   5699*************99 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.14        61       4      21 ..     115     132 ..     113     141 .. 0.87
   2 ?    7.4   0.0    0.0095       4.1       4      24 ..     378     399 ..     376     410 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.14
                                   EE--SSSSHHHHHHHGGG CS
                         AAA_5   4 LvGppGtgKselaerlaa 21 
                                   ++G+ G+gKs++ + la 
  gi|15668900|ref|NP_247704.1| 115 IIGQNGIGKSTVLRILAG 132
                                   79***********99985 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0095
                                   EE--SSSSHHHHHHHGGGGB.S CS
                         AAA_5   4 LvGppGtgKselaerlaaal.n 24 
                                   ++Gp G+gK+++++ la ++  
  gi|15668900|ref|NP_247704.1| 378 ILGPNGIGKTTFVKLLAGVIkP 399
                                   68**************998854 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.2      0.73   3.1e+02       4      26 ..      27      49 ..      22      59 .. 0.72
   2 ?   14.8   0.3   9.8e-05     0.042       2      18 ..      62      78 ..      61      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.73
                       Fer4_16  4 tCgk.CaevCPtnaikekkekeie 26
                                  +C   C++ CP   + ek   ei+
  gi|15668900|ref|NP_247704.1| 27 KCSMeCMKYCPGVRMGEK-TIEID 49
                                  676669999999988888.33333 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 9.8e-05
                       Fer4_16  2 CgtCgkCaevCPtnaik 18
                                  C +Cg C++ CP +ai+
  gi|15668900|ref|NP_247704.1| 62 CSGCGICVKRCPFKAIS 78
                                  99999999999999997 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2    0.0013      0.54      26      43 ..     113     130 ..     100     135 .. 0.88
   2 ?    0.1   0.7       1.2   5.2e+02      96     184 ..     140     228 ..     133     269 .. 0.82
   3 ?   -0.5   0.0       1.8   7.7e+02     112     165 ..     313     366 ..     308     373 .. 0.87
   4 ?    7.5   0.1    0.0067       2.9      25      50 ..     375     400 ..     356     448 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                        AAA_15  26 tvliGkNnsGKSsileal 43 
                                     +iG N++GKS++l++l
  gi|15668900|ref|NP_247704.1| 113 VGIIGQNGIGKSTVLRIL 130
                                   569************998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.2
                        AAA_15  96 lkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkl 176
                                   +++ke +++d++  +  ++l++++++ k k  k   +++ +++  k  k +  ++ ++  ek k +  ++k +lk+++++ 
  gi|15668900|ref|NP_247704.1| 140 KHDKEPNYDDVIKYFRGTELQEYFEKLKNKGVKAIHKVQYVDILPKVVKGKVGDLLKKVDEKGKFDEVVEKLELKNILDRE 220
                                   678888888888888888899999998888888888888888888888888888888888888888889999999999988 PP

                        AAA_15 177 eeslkkee 184
                                    ++l++ e
  gi|15668900|ref|NP_247704.1| 221 LSQLSGGE 228
                                   88877665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.8
                        AAA_15 112 esdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkid 165
                                   ++ l+  ++++++ + k+ ++ ek  v + k++ +l ++++ k+++ + +l++ 
  gi|15668900|ref|NP_247704.1| 313 NEYLYGELREENIRFRKEPIIFEKRAVIDFKNRPILLSYSSMKKTLGDFKLEVS 366
                                   6778889999999**************************999999999998876 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0067
                        AAA_15  25 ltvliGkNnsGKSsilealdlFlnnk 50 
                                   +  + G+N++GK++++++l   ++ +
  gi|15668900|ref|NP_247704.1| 375 VIGILGPNGIGKTTFVKLLAGVIKPD 400
                                   55688*************97666644 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.089        38       1      22 [.     112     133 ..     112     176 .. 0.74
   2 ?    6.5   0.0     0.014       6.1       1      25 [.     375     399 ..     375     424 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.089
                           PRK   1 vIgvagsSGaGkttvarkleki 22 
                                   v+g+ g+ G Gk+tv r l   
  gi|15668900|ref|NP_247704.1| 112 VVGIIGQNGIGKSTVLRILAGE 133
                                   79*************9987644 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                           PRK   1 vIgvagsSGaGkttvarklekifgr 25 
                                   vIg+ g+ G Gktt+ + l  +++ 
  gi|15668900|ref|NP_247704.1| 375 VIGILGPNGIGKTTFVKLLAGVIKP 399
                                   8****************99988873 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.086        37      18      39 ..     110     131 ..     104     141 .. 0.84
   2 ?    6.2   0.2     0.018       7.9      20      50 ..     375     405 ..     368     408 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.086
                        AAA_30  18 drvavltGpAGtGKttalkalr 39 
                                   d v+ + G  G GK+t+l+ l+
  gi|15668900|ref|NP_247704.1| 110 DGVVGIIGQNGIGKSTVLRILA 131
                                   568999************9885 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.018
                        AAA_30  20 vavltGpAGtGKttalkalreaweaaggrvi 50 
                                   v  + Gp G GKtt +k l+ +++ ++g+vi
  gi|15668900|ref|NP_247704.1| 375 VIGILGPNGIGKTTFVKLLAGVIKPDEGEVI 405
                                   77899***************99998877775 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.35   1.5e+02       4      23 ..     113     132 ..     111     141 .. 0.82
   2 ?    8.7   0.1    0.0028       1.2       3      28 ..     375     400 ..     373     406 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.35
                                   EEEEESTTSSHHHHHHHHHH CS
                         SRP54   4 illvGlqGaGKTttlaKLaa 23 
                                   + ++G +G+GK t l  La 
  gi|15668900|ref|NP_247704.1| 113 VGIIGQNGIGKSTVLRILAG 132
                                   5689*********9988885 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0028
                                   EEEEEESTTSSHHHHHHHHHHHHHHT CS
                         SRP54   3 villvGlqGaGKTttlaKLaallkke 28 
                                   vi ++G++G+GKTt +  La ++k +
  gi|15668900|ref|NP_247704.1| 375 VIGILGPNGIGKTTFVKLLAGVIKPD 400
                                   77899***********9999888765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.82   3.5e+02      21      43 ..     112     134 ..      89     158 .. 0.78
   2 ?    7.7   0.1    0.0076       3.2      19      41 ..     373     395 ..     352     404 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.82
                                   EEEEEESTTSSHHHHHHHHHHHT CS
                          TsaE  21 vilLeGdLGaGKTtlvrglakal 43 
                                   v+ + G+ G GK+t  r la +l
  gi|15668900|ref|NP_247704.1| 112 VVGIIGQNGIGKSTVLRILAGEL 134
                                   5788999**********999876 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0076
                                   TEEEEEEESTTSSHHHHHHHHHH CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglak 41 
                                   g+vi + G+ G GKTt+v+ la 
  gi|15668900|ref|NP_247704.1| 373 GEVIGILGPNGIGKTTFVKLLAG 395
                                   7789999************9875 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.029        12      22      38 ..     112     128 ..     105     151 .. 0.89
   2 ?    4.2   0.9     0.047        20      22      38 ..     375     391 ..     368     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.029
                                   EEEEEESTTSSHHHHHH CS
                        NB-ARC  22 vvalvGmgGvGKttlak 38 
                                   vv++ G  G+GK+t+++
  gi|15668900|ref|NP_247704.1| 112 VVGIIGQNGIGKSTVLR 128
                                   89************875 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.047
                                   EEEEEESTTSSHHHHHH CS
                        NB-ARC  22 vvalvGmgGvGKttlak 38 
                                   v+++ G  G+GKtt +k
  gi|15668900|ref|NP_247704.1| 375 VIGILGPNGIGKTTFVK 391
                                   89************875 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0064       2.7      29      54 ..     110     135 ..     101     141 .. 0.87
   2 ?    3.0   0.3     0.095        40      29      50 ..     373     394 ..     363     404 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0064
                                   SEEEEEEE-TTSSHHHHHHHHHHHHH CS
                          MeaB  29 aqvvGltGvPGaGkstlvealglelr 54 
                                     vvG+ G  G Gkst++  l+ el+
  gi|15668900|ref|NP_247704.1| 110 DGVVGIIGQNGIGKSTVLRILAGELI 135
                                   569***************99988876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.095
                                   SEEEEEEE-TTSSHHHHHHHHH CS
                          MeaB  29 aqvvGltGvPGaGkstlvealg 50 
                                    +v+G+ G  G Gk t+v+ l+
  gi|15668900|ref|NP_247704.1| 373 GEVIGILGPNGIGKTTFVKLLA 394
                                   679***************8775 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.4      0.73   3.1e+02       4      21 ..      17      37 ..      14      37 .. 0.74
   2 ?   12.7   2.1   0.00024       0.1       9      21 ..      61      73 ..      53      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.73
                        Fer4_2  4 vvdtdrC.i.gCg.aCvsaCP 21
                                   +d drC    C+  C + CP
  gi|15668900|ref|NP_247704.1| 17 IIDYDRCqPkKCSmECMKYCP 37
                                  688999953349779999999 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00024
                        Fer4_2  9 rCigCgaCvsaCP 21
                                   C gCg+Cv+ CP
  gi|15668900|ref|NP_247704.1| 61 LCSGCGICVKRCP 73
                                  7************ PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0058       2.5     234     264 ..      99     130 ..      69     135 .. 0.83
   2 ?    1.6   1.1      0.22        94     235     264 ..     363     393 ..     350     399 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0058
                                   TEEEEEEEE-SS.EEEEEE-TTSSHHHHHHHH CS
                    ABC_ATPase 234 gkkvsGmgipkG.vtlIvGggfhGKsTLLeAl 264
                                   + k+ G+ ip+  v+ I+G +  GKsT L+ l
  gi|15668900|ref|NP_247704.1|  99 RFKLFGLVIPRDgVVGIIGQNGIGKSTVLRIL 130
                                   457789***9855****************976 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.22
                                   EEEEEEEE-SS.EEEEEE-TTSSHHHHHHHH CS
                    ABC_ATPase 235 kkvsGmgipkG.vtlIvGggfhGKsTLLeAl 264
                                    +vsG  i kG v+ I G++  GK+T ++ l
  gi|15668900|ref|NP_247704.1| 363 LEVSGGTIYKGeVIGILGPNGIGKTTFVKLL 393
                                   5899**********************99866 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   4.2      0.95   4.1e+02       4      12 ..      28      37 ..      23      40 .. 0.77
   2 ?   10.9   4.2    0.0018      0.75       1      15 []      62      76 ..      62      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.95
                        Fer4_3  4 Cg.aCvevCP 12
                                  C+  C++ CP
  gi|15668900|ref|NP_247704.1| 28 CSmECMKYCP 37
                                  8559****** PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0018
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C gCg Cv+ CP +A
  gi|15668900|ref|NP_247704.1| 62 CSGCGICVKRCPFKA 76
                                  99**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        44  (0.00245412); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.47
# Mc/sec: 3866.74
//
Query:       gi|15668901|ref|NP_247705.1|  [L=333]
Description: multifunctional 3-isopropylmalate dehydrogenase/D-malate dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.5e-106  354.2   0.3   8.4e-106  354.0   0.3    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.0   0.3  4.7e-110  8.4e-106       1     348 []       3     326 ..       3     330 .. 0.95

  Alignments for each domain:
  == domain 1  score: 354.0 bits;  conditional E-value: 4.7e-110
                                   EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSSSSH CS
                        Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkekevrp 81 
                                   ki ++egdgiG+evv+a+++vl+a      l +ef ++++G +++++tg++lpeet+e + + d+vl+ga g         
  gi|15668901|ref|NP_247705.1|   3 KICVIEGDGIGKEVVPATIQVLEATG----LPFEFVYAEAGDEVYKRTGKALPEETIETALDCDAVLFGAAGETA------ 73 
                                   699********************998....679*************************************98877...... PP

                                   HHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEEEEEHHHH CS
                        Iso_dh  82 engLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtklyseeei 162
                                      +++Lr+ ld++an+rpvk ++     + l++    ++d vivRe+t+g+Y g+e e+++        + t +++e++ 
  gi|15668901|ref|NP_247705.1|  74 ADVIVKLRHILDTYANIRPVKAYK---GVKCLRP----DIDYVIVRENTEGLYKGIEAEIDEG-----ITIATRVITEKAC 142
                                   55699******************4...3445665....69**********************8.....69*********** PP

                                   HHHHHHHHHHHHHT....TTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE- CS
                        Iso_dh 163 eriaraafelAlkr....gkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamqlvkspkqfdVivtk 238
                                   eri r+af+lA++r    ++ kvt+ +Kanvlk ++ l++ki+++vae ey di+ e+ ++D++ m+++++p+ fdV+vt+
  gi|15668901|ref|NP_247705.1| 143 ERIFRFAFNLARERkkmgKEGKVTCAHKANVLKLTDgLFKKIFYKVAE-EYDDIKAEDYYIDAMNMYIITKPQVFDVVVTS 222
                                   *************97776778***************************.******************************** PP

                                   HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT-HHHHHHHHHHHH CS
                        Iso_dh 239 NlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLryslgleeaAdkiekAve 319
                                   NlfGDilSD aa  vG+lGl+pSa++g +++++fE+vHGsapdiagk++aNp+a+ilSa+lmLry lg+ eaAdk+ekA+e
  gi|15668901|ref|NP_247705.1| 223 NLFGDILSDGAAGTVGGLGLAPSANIG-DEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRY-LGEYEAADKVEKALE 301
                                   ***************************.79***********************************.*************** PP

                                   HHHHHTSCCHHHCTTSTCCCHHHHHHHHH CS
                        Iso_dh 320 kvleagivTkDlageaakevstsefgdav 348
                                   +vl+ g +T Dl+g+     +t e+ ++v
  gi|15668901|ref|NP_247705.1| 302 EVLALGLTTPDLGGNL----NTFEMAEEV 326
                                   **************99....777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2278.85
//
Query:       gi|15668902|ref|NP_247706.1|  [L=398]
Description: acetylornithine aminotransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.1e-128  428.5   0.0   2.6e-128  428.1   0.0    1.0  1  Aminotran_3      Aminotransferase class-III
    4.4e-08   32.7   0.0    1.7e-05   24.2   0.0    2.0  2  Aminotran_1_2    Aminotransferase class I and II
    7.2e-05   22.2   0.0    0.00021   20.7   0.0    1.6  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.024   14.0   0.1      0.038   13.3   0.1    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.1   0.0  5.8e-132  2.6e-128       9     405 ..      21     392 ..      16     393 .. 0.98

  Alignments for each domain:
  == domain 1  score: 428.1 bits;  conditional E-value: 5.8e-132
                                   SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SE CS
                   Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldk 89 
                                   l++v+ +++G+ ++d dgk+ylD++++i v+n+Gh+hPkvv+a+k+qa++l h+s +++ + p++kla+kl++l +   d+
  gi|15668902|ref|NP_247706.1|  21 LPVVLVEGKGMEVYDIDGKKYLDFLAGIGVNNVGHCHPKVVEAIKKQAETLIHTS-NIYYTIPQIKLAKKLVELSGL--DR 98 
                                   568999*************************************************.******************999..** PP

                                   EEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB- CS
                   Aminotran_3  90 vflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlke 170
                                    f++nsG+eA+e+A+K+arky  ++   e  +ii++ +afHGrtl++l++t + +ky+++f p++p++++++++d      
  gi|15668902|ref|NP_247706.1|  99 AFFCNSGAEANEGAIKFARKYVSKVLGREGGEIISMYNAFHGRTLTTLAATPK-PKYQDGFYPLPPGFKYVPFND------ 172
                                   ********************9999999999*********************99.********************9...... PP

                                   HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGGCT CS
                   Aminotran_3 171 neeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAlehag 251
                                              +eal+++++d++aA+++Ep+qgegG+ va++++l+++r+lc++++++li+DEvq+G+GrTG +fA eh+g
  gi|15668902|ref|NP_247706.1| 173 -----------IEALKEAITDKTAAIMIEPVQGEGGIHVADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRMFAFEHYG 242
                                   ...........9********************************************************************* PP

                                   S--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHC CS
                   Aminotran_3 252 vspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllenaqelgaalkegLeelq 332
                                   v+pD++tlaKal+gG p+ av+ ++e+++al+ g+hg+TfgGnplac++ala++e+iee    +++ e+g+++  +Le+l 
  gi|15668902|ref|NP_247706.1| 243 VEPDILTLAKALGGGVPIGAVVLKEEIAKALSYGDHGTTFGGNPLACSAALASVEVIEELIKDDKVIEKGKYFIRKLENLI 323
                                   ********************************************************************************* PP

                                   TT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHHHHHHHHHH CS
                   Aminotran_3 333 kkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitdeeidelleilkka 405
                                   +ky++ikevRg+Glmi++el+ +      +i+kk++ekG li  + d+v+r+lppli+++e+id+l+++l ++
  gi|15668902|ref|NP_247706.1| 324 EKYNFIKEVRGLGLMIGAELEFNGA----DIVKKMLEKGFLINCTSDTVLRFLPPLIVEKEHIDALINALDEV 392
                                   ***********************99....9**************************************99875 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0   0.00085       3.8      10      88 ..      50     117 ..      45     126 .. 0.82
   2 !   24.2   0.0   3.7e-09   1.7e-05     120     327 ..     168     357 ..     154     388 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00085
                                   STTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHH CS
                 Aminotran_1_2  10 eylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifll 88 
                                    +  +  +p + e++k+++e     +t n+y +i  + +l ++l ++ g         ++a  + sGa a+  a++f+ 
  gi|15668902|ref|NP_247706.1|  50 VNNVGHCHPKVVEAIKKQAE--TLIHTSNIYYTIP-QIKLAKKLVELSG--------LDRAFFCNSGAEANEGAIKFAR 117
                                   44444447777778888877..99***********.*************........77679999****9999999975 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 3.7e-09
                                   EEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--.B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSH CS
                 Aminotran_1_2 120 yplyseedfhldlealeealkeapegnkktkvilvesphNPtGt.vatleeleklldlakkynlllfvDeaYagfvfgsld 199
                                   +p        +d+eal+ea+++      kt  i +e ++   G  va+++ l+++ dl++ +n++l++De+  g+  +   
  gi|15668902|ref|NP_247706.1| 168 VP-------FNDIEALKEAITD------KTAAIMIEPVQGEGGIhVADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRM 235
                                   45.......68***********......9**************65899****************************99876 PP

                                   THHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 200 avatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemr 278
                                   ++  + +ve+++      +l+Ka+G  G  +G+++ +++++++l     + ++      + a++aal  ++ + +el    
  gi|15668902|ref|NP_247706.1| 236 FAFEHYGVEPDIL-----TLAKALG-GGVPIGAVVLKEEIAKALSYGDHGTTFggN---PLACSAALASVEVI-EELI-KD 305
                                   6656999999887.....******8.47789*************999988877642...34444444444433.2333.33 PP

                                   HHHHHHHHHHHHHHHHS..TEEEECCSCSSEEEEEETHH.CHHHHHHHHHHT CS
                 Aminotran_1_2 279 qrlqkrrkelrdeLael..glkvlasqsgmflltdlsae.takelskkLlee 327
                                   ++++++ k++  +L++l    +++++  g+ l+ + + e +  ++ kk+le+
  gi|15668902|ref|NP_247706.1| 306 DKVIEKGKYFIRKLENLieKYNFIKEVRGLGLMIGAELEfNGADIVKKMLEK 357
                                   5556666666666666665555555556666665555555555555555555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   4.8e-08   0.00021      36     233 ..      85     343 ..      82     360 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.8e-08
                                   HHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT.-HHHHSSTTHHHHCC--EEEEE-EBTT......... CS
               Beta_elim_lyase  36 rLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtep.ahihfdetgaiaelagvklrdlknkea......... 106
                                   +L++++ el g + a+f+ +G  An+ ++k    ++ +++++++ + i+          +  + r+l++ +a         
  gi|15668902|ref|NP_247706.1|  85 KLAKKLVELSGLDRAFFCNSGAEANEGAIKFAR-KYVSKVLGREgGEIISMY-------NAFHGRTLTTLAAtpkpkyqdg 157
                                   6889999*********************97655.333333333323332222.......2222222222222222344456 PP

                                   ........TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHT CS
               Beta_elim_lyase 107 ........GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslg 179
                                            ++ ++++ea+ ++  +  +k+++i+++      g  v   ++l++v++++++++i l++D   +    +   
  gi|15668902|ref|NP_247706.1| 158 fyplppgfKYVPFNDIEALKEA--I-TDKTAAIMIEPVQGEGGIHVADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRM 235
                                   6777777778888888876666..3.579********9997555788999*******************988877777777 PP

                                   S-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH............................................... CS
               Beta_elim_lyase 180 eivkemfsyvDsvtmslkKdllanvGgvlafrddel............................................. 215
                                      + +    D++t+    ++++++G+v++ ++                                                
  gi|15668902|ref|NP_247706.1| 236 FAFEHYGVEPDILTLAKALGGGVPIGAVVLKEEIAKalsygdhgttfggnplacsaalasvevieelikddkviekgkyfi 316
                                   777777788899999999999999999887666533667777777777777777777777777766666666666666666 PP

                                   ...........HHHHHHHHHHHHT--- CS
               Beta_elim_lyase 216 .........edylaerveqrkylgggl 233
                                             ++++e + +  ++g +l
  gi|15668902|ref|NP_247706.1| 317 rklenliekYNFIKEVRGLGLMIGAEL 343
                                   666666666666666666655555555 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   8.4e-06     0.038     100     145 ..     172     224 ..      62     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.4e-06
                                   -GGGCGGG--TTEEEEEEB-GGG....B---...HHHHHHHHHHCT-EEEEE- CS
               DegT_DnrJ_EryC1 100 dpaaieaaitertkaIlpVhlyG....qvad...mdalkaiaakhglkvieDa 145
                                   d +a+++ait +t+aI++  + G    +vad   ++a++++++++++++i D 
  gi|15668902|ref|NP_247706.1| 172 DIEALKEAITDKTAAIMIEPVQGeggiHVADkdyLKAVRDLCDDKNIVLIFDE 224
                                   8899*************76666522444565556899*************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2572.12
//
Query:       gi|15668903|ref|NP_247707.1|  [L=77]
Description: ferredoxin FdxA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-15   55.5  14.0    5.7e-09   35.4   4.9    2.2  2  Fer4      4Fe-4S binding domain
    1.7e-10   41.3   9.8    2.8e-10   40.6   9.8    1.4  1  Fer4_7    4Fe-4S dicluster domain
    2.9e-10   40.2  20.6      3e-07   30.5  10.9    1.8  2  Fer4_9    4Fe-4S dicluster domain
    5.9e-10   39.1   6.2    8.1e-10   38.7   6.2    1.2  1  Fer4_21   4Fe-4S dicluster domain
    1.5e-09   37.5  14.1    2.4e-08   33.7   3.1    2.2  2  Fer4_6    4Fe-4S binding domain
    4.9e-09   36.2  11.9      1e-05   25.6   2.1    2.1  2  Fer4_10   4Fe-4S dicluster domain
    1.6e-08   35.4   9.6    0.00098   20.0   0.6    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    2.9e-08   33.3  12.7    5.4e-07   29.3   2.5    2.2  2  Fer4_2    4Fe-4S binding domain
      3e-06   27.3  12.5    5.9e-06   26.4   1.3    2.2  2  Fer4_4    4Fe-4S binding domain
    5.4e-06   26.8  12.4    0.00061   20.2  12.7    2.1  2  Fer4_8    4Fe-4S dicluster domain
    5.2e-05   24.0   7.2     0.0011   19.8   1.7    2.1  2  Fer4_22   4Fe-4S dicluster domain
    0.00011   22.6  12.0     0.0029   18.1  12.0    2.5  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    0.00015   22.2  12.6      0.038   14.5   3.0    2.2  3  Fer4_17   4Fe-4S dicluster domain
    0.00025   21.7  10.8      0.024   15.4  10.8    2.3  1  Fer4_15   4Fe-4S single cluster domain
     0.0027   18.5   4.7     0.0027   18.5   4.7    2.2  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.017   15.3   0.0    1.1  1  Tau95_N   Tau95 Triple barrel domain
      0.066   13.4   8.8          3    8.1   0.7    2.1  1  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   4.9   5.4e-12   5.7e-09       1      21 [.       5      25 ..       5      28 .. 0.91
   2 !   25.8   1.7   5.8e-09   6.1e-06       3      23 ..      40      60 ..      38      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 5.4e-12
                                  EEEETTTSSS-THHHHHSTTT CS
                          Fer4  1 vvideekCigCGaCvevCPvg 21
                                  +++d ekCigCG+C++vCP g
  gi|15668903|ref|NP_247707.1|  5 IIVDREKCIGCGRCYDVCPKG 25
                                  689****************98 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 5.8e-09
                                  EETTTSSS-THHHHHSTTTEE CS
                          Fer4  3 ideekCigCGaCvevCPvgAI 23
                                  +d e C +C+ C+  CP++AI
  gi|15668903|ref|NP_247707.1| 40 YDVEYCHNCKFCAGRCPTNAI 60
                                  799*****************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   9.8   2.7e-13   2.8e-10       1      52 []      11      59 ..       7      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.7e-13
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  +CigCg+C ++Cp + + ++++en  g +++++d e+C +C+ C+ +CPt+a
  gi|15668903|ref|NP_247707.1| 11 KCIGCGRCYDVCPKGPLIWTKDEN--G-KYYAYDVEYCHNCKFCAGRCPTNA 59
                                  7******************99854..4.6799******************97 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   2.1   3.1e-07   0.00033      34      49 ..      10      25 ..       2      27 .. 0.80
   2 !   30.5  10.9   2.9e-10     3e-07       1      51 []      11      60 ..      11      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.1e-07
                        Fer4_9 34 eaCigCgaCveaCpkg 49
                                  e+CigCg+C+++Cpkg
  gi|15668903|ref|NP_247707.1| 10 EKCIGCGRCYDVCPKG 25
                                  589**********997 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 2.9e-10
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  kC+gCg+C ++Cp+g  +  + e+   +   + e C+ C+ C+ +Cp++ai
  gi|15668903|ref|NP_247707.1| 11 KCIGCGRCYDVCPKGPLIWTKDENGKYYAY-DVEYCHNCKFCAGRCPTNAI 60
                                  7************99776665555554433.3347*************997 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   6.2   7.7e-13   8.1e-10       3      57 ..       7      60 ..       5      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 7.7e-13
                       Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                  +d++kCigCg+C+ +C+++     + ++ +++++  + C  C+ C+  CP+ ++i
  gi|15668903|ref|NP_247707.1|  7 VDREKCIGCGRCYDVCPKGPLIWTKDENGKYYAYDVEYCHNCKFCAGRCPT-NAI 60
                                  89***************876666677777899999***************7.776 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   3.1   2.3e-11   2.4e-08       2      21 ..       5      24 ..       4      28 .. 0.91
   2 !    9.6   3.3   0.00094      0.99       4      24 .]      40      60 ..      39      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.3e-11
                        Fer4_6  2 veidpdkCigCgdCvrvCPe 21
                                  + +d++kCigCg+C++vCP 
  gi|15668903|ref|NP_247707.1|  5 IIVDREKCIGCGRCYDVCPK 24
                                  569****************6 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00094
                        Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                  +d + C  C  C+  CP++ai
  gi|15668903|ref|NP_247707.1| 40 YDVEYCHNCKFCAGRCPTNAI 60
                                  68899***************8 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   2.1   9.6e-09     1e-05       2      21 ..       5      24 ..       4      41 .. 0.80
   2 !   17.1   2.1   4.1e-06    0.0043       4      35 ..      40      73 ..      37      77 .] 0.67

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 9.6e-09
                       Fer4_10  2 vvidddtCirCgkCvkaCPa 21
                                  +++d+++Ci+Cg+C ++CP 
  gi|15668903|ref|NP_247707.1|  5 IIVDREKCIGCGRCYDVCPK 24
                                  6899***************8 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.1e-06
                       Fer4_10  4 idddtCirCgkCvkaCPadl..tsvgakgeasee 35
                                  +d + C +C+ C   CP+++   +v++ ++++e+
  gi|15668903|ref|NP_247707.1| 40 YDVEYCHNCKFCAGRCPTNAilIKVVKPKKKDEN 73
                                  7899**************8865333333333333 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.6   9.3e-07   0.00098       1      17 [.      11      27 ..      10      40 .. 0.82
   2 !   19.8   2.9   1.1e-06    0.0011       2      32 ..      45      72 ..      44      77 .] 0.72

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.3e-07
                       Fer4_16  1 rCgtCgkCaevCPtnai 17
                                  +C++Cg+C +vCP + +
  gi|15668903|ref|NP_247707.1| 11 KCIGCGRCYDVCPKGPL 27
                                  599**********9765 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.1e-06
                       Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecis 32
                                  C++C+ Ca  CPtnai  k   +++++++ +
  gi|15668903|ref|NP_247707.1| 45 CHNCKFCAGRCPTNAILIK---VVKPKKKDE 72
                                  ****************988...444444333 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   2.5   5.1e-10   5.4e-07       3      21 ..       5      23 ..       2      24 .. 0.93
   2 !    9.7   2.7   0.00093      0.98       2      22 .]      37      57 ..      36      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.1e-10
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  + vd+++CigCg C+++CP
  gi|15668903|ref|NP_247707.1|  5 IIVDREKCIGCGRCYDVCP 23
                                  689***************9 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00093
                        Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                  ++++d + C +C+ C   CP+
  gi|15668903|ref|NP_247707.1| 37 YYAYDVEYCHNCKFCAGRCPT 57
                                  5899***********999**7 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   1.3   5.6e-09   5.9e-06       2      16 ..      10      24 ..       9      37 .. 0.92
   2 ?    6.2   4.0     0.016        17       2      17 .]      43      58 ..      42      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 5.6e-09
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  e+CigCg+C+++CP 
  gi|15668903|ref|NP_247707.1| 10 EKCIGCGRCYDVCPK 24
                                  89************6 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.016
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  e C +C+ C   CP++
  gi|15668903|ref|NP_247707.1| 43 EYCHNCKFCAGRCPTN 58
                                  67***********985 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2  12.7   5.8e-07   0.00061       3      64 ..      10      58 ..       8      59 .. 0.70
   2 !   13.1   3.3   9.2e-05     0.097       2      17 ..      42      59 ..      41      77 .] 0.56

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.8e-07
                        Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                  ekCi+Cg+C + Cp       + +d +g+        +       +++C++c+ C+ +Cp++
  gi|15668903|ref|NP_247707.1| 10 EKCIGCGRCYDVCPKGPL--IWTKDENGK----YYAYD-------VEYCHNCKFCAGRCPTN 58
                                  79***********92222..233333333....33344.......59*************97 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.2e-05
                        Fer4_8  2 lekCieCgaCqsaCp..v 17
                                  +e+C++C +C   Cp  +
  gi|15668903|ref|NP_247707.1| 42 VEYCHNCKFCAGRCPtnA 59
                                  566777777777776440 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.7     1e-06    0.0011      78      94 ..       8      24 ..       2      26 .. 0.87
   2 !    7.9   0.3    0.0053       5.6       2      17 ..      45      60 ..      36      77 .] 0.69

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-06
                       Fer4_22 78 gesgCvGCgRCieacpv 94
                                  ++++C+GCgRC ++cp+
  gi|15668903|ref|NP_247707.1|  8 DREKCIGCGRCYDVCPK 24
                                  7899***********97 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0053
                       Fer4_22  2 ClsCgaCtlvCptCsC 17
                                  C +C  C+  Cpt   
  gi|15668903|ref|NP_247707.1| 45 CHNCKFCAGRCPTNAI 60
                                  8889999999998654 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1  12.0   2.8e-06    0.0029       1      56 [.       7      60 ..       7      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.8e-06
                       Fer4_13  1 VDrdtCiacgaCvelaPd...vFeeddeggasvvaeqptseeekadaeeAadaCPvesI 56
                                  VDr++Ci+cg C++++P+   +   d++ g+++ ++     e  ++++  a  CP+++I
  gi|15668903|ref|NP_247707.1|  7 VDREKCIGCGRCYDVCPKgplIWTKDEN-GKYYAYD----VEYCHNCKFCAGRCPTNAI 60
                                  9***************987768888887.6666555....3567799999999999999 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   3.0   3.6e-05     0.038      44      59 ..      10      25 ..       8      26 .. 0.80
   2 !   12.3   2.4   0.00018      0.19      42      59 ..      41      58 ..      26      60 .. 0.74
   3 !   10.6   3.1   0.00061      0.64       2      17 ..      45      60 ..      44      76 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                       Fer4_17 44 slCieCgeCerkCPqg 59
                                  ++Ci+Cg+C  +CP+g
  gi|15668903|ref|NP_247707.1| 10 EKCIGCGRCYDVCPKG 25
                                  5788888888888875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00018
                       Fer4_17 42 kaslCieCgeCerkCPqg 59
                                   ++ C++C+ C+ +CP +
  gi|15668903|ref|NP_247707.1| 41 DVEYCHNCKFCAGRCPTN 58
                                  567899999999999875 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00061
                       Fer4_17  2 CiqCgyClpeCpsyea 17
                                  C++C++C+  Cp++++
  gi|15668903|ref|NP_247707.1| 45 CHNCKFCAGRCPTNAI 60
                                  7788888888877655 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4  10.8   2.3e-05     0.024       1      64 [.       5      60 ..       5      62 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-05
                       Fer4_15  1 VvvDrdaCigcglCvaea...pevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAI 64
                                  + vDr++Cigcg+C++++   p + ++de+g+ +             + +   + ++ a  CP+ AI
  gi|15668903|ref|NP_247707.1|  5 IIVDREKCIGCGRCYDVCpkgPLIWTKDENGKYYAY-----------DVEYCHNCKFCAGRCPTNAI 60
                                  68****************555557777777776444...........34455566666666666666 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   4.7   2.6e-06    0.0027       1      14 [.      12      25 ..      12      25 .. 0.97
   2 ?    5.4   5.6     0.041        43       1      15 []      45      59 ..      45      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.6e-06
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C+gCg+C +vCP+g
  gi|15668903|ref|NP_247707.1| 12 CIGCGRCYDVCPKG 25
                                  ************98 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.041
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C++C  C   CP++A
  gi|15668903|ref|NP_247707.1| 45 CHNCKFCAGRCPTNA 59
                                  ****88*******98 PP

>> Tau95_N  Tau95 Triple barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.6e-05     0.017      52      77 ..      50      76 ..      31      77 .] 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                                  EE-EEE----EEEEE........ETTT CS
                       Tau95_N 52 ilgeraptnnlllkvtvpkr.tgkkrk 77
                                   ++ r ptn +l+kv++pk+  ++k+k
  gi|15668903|ref|NP_247707.1| 50 FCAGRCPTNAILIKVVKPKKkDENKNK 76
                                  477889************883344443 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.7    0.0029         3      56      74 ..      40      58 ..      26      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0029
                       Fer4_18 56 kgagdcidcescvkvcPtg 74
                                   ++  c +c++c   cPt+
  gi|15668903|ref|NP_247707.1| 40 YDVEYCHNCKFCAGRCPTN 58
                                  45677************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 589.94
//
Query:       gi|15668904|ref|NP_247708.1|  [L=156]
Description: AsnC family transcriptional regulator [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-16   60.0   0.3      2e-16   59.5   0.3    1.2  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.6e-16   59.6   0.9    2.5e-16   59.0   0.9    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.4e-13   50.6   0.0    2.5e-13   49.8   0.0    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    4.2e-07   30.0   0.0    6.3e-07   29.4   0.0    1.3  1  HTH_28          Helix-turn-helix domain
    2.5e-06   27.3   0.2    3.9e-06   26.7   0.2    1.4  1  HTH_11          HTH domain
    4.3e-06   26.7   0.0    6.4e-06   26.1   0.0    1.3  1  HTH_20          Helix-turn-helix domain
      1e-05   25.3   0.1    1.7e-05   24.6   0.1    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
    1.3e-05   25.1   0.0    2.3e-05   24.3   0.0    1.5  1  HTH_Mga         M protein trans-acting positive regulator (MG
    1.5e-05   24.6   0.1    2.3e-05   24.0   0.1    1.3  1  HTH_23          Homeodomain-like domain
    2.5e-05   24.1   0.0    3.9e-05   23.5   0.0    1.2  1  MarR_2          MarR family
    5.8e-05   22.8   0.3    0.00011   21.9   0.3    1.4  1  HTH_38          Helix-turn-helix domain
    0.00014   22.2   0.1    0.00028   21.3   0.1    1.4  1  HTH_27          Winged helix DNA-binding domain
    0.00015   21.7   0.0     0.0005   20.0   0.0    1.7  2  MarR            MarR family
    0.00017   21.3   0.0    0.00025   20.8   0.0    1.2  1  HTH_IclR        IclR helix-turn-helix domain
    0.00043   19.9   0.1    0.00071   19.2   0.1    1.3  1  Sigma70_r4_2    Sigma-70, region 4
    0.00065   19.7   0.0      0.001   19.0   0.0    1.2  1  HTH_29          Winged helix-turn helix
    0.00066   19.6   0.0    0.00096   19.1   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00069   19.4   0.1      0.001   18.9   0.1    1.3  1  TFIIE_alpha     TFIIE alpha subunit
    0.00073   19.4   0.1     0.0011   18.8   0.1    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00091   19.0   0.0     0.0014   18.5   0.0    1.4  1  HxlR            HxlR-like helix-turn-helix
     0.0015   18.2   0.1     0.0024   17.6   0.1    1.3  1  HTH_DeoR        DeoR-like helix-turn-helix domain
     0.0016   18.6   0.0     0.0027   17.8   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0028   17.6   0.0      0.006   16.5   0.0    1.5  1  HTH_36          Helix-turn-helix domain
      0.004   17.3   0.0     0.0081   16.3   0.0    1.5  1  HTH_34          Winged helix DNA-binding domain
      0.006   16.5   0.0       0.01   15.8   0.0    1.3  1  HTH_1           Bacterial regulatory helix-turn-helix protein
     0.0097   15.9   0.0      0.016   15.2   0.0    1.3  1  HTH_6           Helix-turn-helix domain, rpiR family
  ------ inclusion threshold ------
      0.012   15.1   0.1      0.019   14.5   0.1    1.3  1  Sigma70_r4      Sigma-70, region 4
      0.014   15.4   0.0      0.023   14.8   0.0    1.3  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
      0.015   14.7   0.0      0.023   14.1   0.0    1.2  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.019   15.3   0.0      0.032   14.6   0.0    1.4  1  Rrf2            Transcriptional regulator
      0.027   14.0   0.0      0.045   13.3   0.0    1.4  1  HTH_47          winged helix-turn-helix
      0.054   14.1   0.0       0.09   13.4   0.0    1.3  1  Mga             Mga helix-turn-helix domain
      0.065   13.4   0.0       0.11   12.6   0.0    1.4  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.12   12.5   0.0        0.2   11.8   0.0    1.3  1  DUF2250         Uncharacterized protein conserved in archaea 
       0.14   11.8   0.0       0.22   11.1   0.0    1.3  1  HTH_50          Helix-turn-helix domain
       0.17   11.7   0.0       0.31   10.9   0.0    1.4  1  HTH_30          PucR C-terminal helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.3   4.1e-19     2e-16       1      42 []      17      58 ..      17      58 .. 0.99

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 4.1e-19
                 HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                  +De D+kI+e+L++d+R sy+++A+++G Ses +++Rv++Le
  gi|15668904|ref|NP_247708.1| 17 MDEKDLKIIEILMRDGRKSYTDIARELGTSESSIRKRVKKLE 58
                                  9****************************************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.9     5e-19   2.5e-16       1      48 []      17      64 ..      17      64 .. 0.99

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 5e-19
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +de+d+kI+e+L++++r s++++A++lg S s +++r+k+LeeeG+Ik
  gi|15668904|ref|NP_247708.1| 17 MDEKDLKIIEILMRDGRKSYTDIARELGTSESSIRKRVKKLEEEGVIK 64
                                  8**********************************************8 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0     5e-16   2.5e-13       5      75 .]      87     154 ..      83     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 5e-16
                                   E-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                AsnC_trans_reg   5 lepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                   +ep++   + +++++l+++peV+ +++ tGd+ ++ +++++d +++++++ +k+++++g++++   i+le+
  gi|15668904|ref|NP_247708.1|  87 TEPDK---FLNVAKELCKFPEVKKVFTSTGDHMIMTEIWAKDGKEFSDLIFNKIGKIEGIKKICPAIILEQ 154
                                   45555...999*********************************************************996 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.3e-09   6.3e-07       4      41 ..      23      62 ..      22      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.3e-09
                        HTH_28  4 eii.kllaaGh.svreaArelgisrrtvyrWikryeegGi 41
                                  +ii  l+ +G+ s++++Arelg+s++++++ +k++ee+G+
  gi|15668904|ref|NP_247708.1| 23 KIIeILMRDGRkSYTDIARELGTSESSIRKRVKKLEEEGV 62
                                  666456779*9****************************5 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.2   7.8e-09   3.9e-06       3      44 ..      22      66 ..      20      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 7.8e-09
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....v 44
                                  l+i+e+L   +g  s  ++A+eL+ S++ +r+++k+Lee g    +
  gi|15668904|ref|NP_247708.1| 22 LKIIEIL-MRDGRKSYTDIARELGTSESSIRKRVKKLEEEGvikgY 66
                                  699****.555568***************************55552 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.3e-08   6.4e-06      13      56 ..      22      65 ..      16      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.3e-08
                                  HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                  ++i   L+r++  + +++a++l++s +++++++++Lee g +++
  gi|15668904|ref|NP_247708.1| 22 LKIIEILMRDGRKSYTDIARELGTSESSIRKRVKKLEEEGVIKG 65
                                  78999***********************************9986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   3.5e-08   1.7e-05       1      45 [.      18      63 ..      18      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.5e-08
                                  SHHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  1 dptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                  d++ lkI+ +L++ g ++ +++a+elg s+s ++   kkL+e+G++
  gi|15668904|ref|NP_247708.1| 18 DEKDLKIIEILMRdGRKSYTDIARELGTSESSIRKRVKKLEEEGVI 63
                                  56679********9******************************98 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   4.6e-08   2.3e-05       5      56 ..      19      70 ..      17      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4.6e-08
                       HTH_Mga  5 krklkLlelLteneksltldelakeLglseltlqsdiseLnel.Fpeelsivi 56
                                  + +lk++e+L   +++ +++++a eLg+se+++++++ +L e+ +++ ++ +i
  gi|15668904|ref|NP_247708.1| 19 EKDLKIIEILMR-DGRKSYTDIARELGTSESSIRKRVKKLEEEgVIKGYTAII 70
                                  5689********.***************************9887777666555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   4.7e-08   2.3e-05      12      46 ..      28      62 ..      22      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.7e-08
                        HTH_23 12 lllaeGlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                  l+ + ++s+++IAreLg s++ +++ +k+ +eeG+
  gi|15668904|ref|NP_247708.1| 28 LMRDGRKSYTDIARELGTSESSIRKRVKKLEEEGV 62
                                  445559******************99999999*95 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   7.8e-08   3.9e-05      13      52 ..      26      64 ..      24      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 7.8e-08
                                  HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                        MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                  ++  r+gr+ + +++ar+lg s s++ +++k+L++ G + 
  gi|15668904|ref|NP_247708.1| 26 EILMRDGRK-SYTDIARELGTSESSIRKRVKKLEEEGVIK 64
                                  788899988.9**************************985 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.3   2.1e-07   0.00011      12      42 ..      24      55 ..      18      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.1e-07
                        HTH_38 12 eIerllaeG.lslreIArrLgrspsTIsRElk 42
                                   Ie+l   G +s+ +IAr+Lg s s+I + +k
  gi|15668904|ref|NP_247708.1| 24 IIEILMRDGrKSYTDIARELGTSESSIRKRVK 55
                                  599**99999*****************99887 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   5.6e-07   0.00028      13      48 ..      26      63 ..      19      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 5.6e-07
                        HTH_27 13 r..hrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                  +  +r++rk+ +d+++ l ++ s+i + +kkL+e G++
  gi|15668904|ref|NP_247708.1| 26 EilMRDGRKSYTDIARELGTSESSIRKRVKKLEEEGVI 63
                                  3447********************************99 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     1e-06    0.0005       6      47 ..      22      63 ..      18      66 .. 0.93
   2 ?   -1.5   0.0         5   2.5e+03       6      23 ..     115     132 ..     111     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1e-06
                                  HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                  ++i++il + g  s +++a+ lg+s s++ + +++Le++G i
  gi|15668904|ref|NP_247708.1| 22 LKIIEILMRDGRKSYTDIARELGTSESSIRKRVKKLEEEGVI 63
                                  78999999********************************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5
                                   HHHHHHHHHSTTEEHHHH CS
                          MarR   6 fviLrilyeqgplsvseL 23 
                                   ++i++ ++ +++   s+L
  gi|15668904|ref|NP_247708.1| 115 HMIMTEIWAKDGKEFSDL 132
                                   679999999998888877 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     5e-07   0.00025       6      49 ..      22      64 ..      19      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5e-07
                                  HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                  l i+++l + ++  + +++Ar++g + S+ +  ++ L+e+G ++
  gi|15668904|ref|NP_247708.1| 22 LKIIEILMRDGRK-SYTDIARELGTSESSIRKRVKKLEEEGVIK 64
                                  89**********9.9**************************875 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.4e-06   0.00071      25      49 ..      32      56 ..      25      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-06
                                  S---HHHHHHHHT--HHHHHHHHHH CS
                  Sigma70_r4_2 25 eglsykEIAellgisegtVksrlsR 49
                                    +sy +IA++lg+se+++++r+++
  gi|15668904|ref|NP_247708.1| 32 GRKSYTDIARELGTSESSIRKRVKK 56
                                  678******************9875 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.1e-06     0.001       6      41 ..      27      62 ..      25      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.1e-06
                        HTH_29  6 lllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                  +l+++G ++  +iA+ lg s++++++ +k  ee+G+
  gi|15668904|ref|NP_247708.1| 27 ILMRDGRKSYTDIARELGTSESSIRKRVKKLEEEGV 62
                                  68999******************************5 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.9e-06   0.00096      23      60 ..      35      70 ..      18      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.9e-06
                                  HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES CS
                     HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisrgrriril 60
                                  + +++A+ lG++ +++ +  ++L++eg+i+      i 
  gi|15668904|ref|NP_247708.1| 35 SYTDIARELGTSESSIRKRVKKLEEEGVIKGY--TAII 70
                                  678**************************943..3444 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1     2e-06     0.001       9      58 ..      15      64 ..      12      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-06
                                  HCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                   TFIIE_alpha  9 kfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                   +++e+  +++++L+++g  +  d+a+el+     +rk + +L e++++k
  gi|15668904|ref|NP_247708.1| 15 DIMDEKDLKIIEILMRDGRKSYTDIARELGTSESSIRKRVKKLEEEGVIK 64
                                  56788999****************************************98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   2.3e-06    0.0011       8      53 ..      19      64 ..      17      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.3e-06
                                  HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                          TrmB  8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                  e + k+   L++ g+++ ++ia+elg ++s++ + +++Le+ G+++
  gi|15668904|ref|NP_247708.1| 19 EKDLKIIEILMRDGRKSYTDIARELGTSESSIRKRVKKLEEEGVIK 64
                                  56778888999********************************986 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.7e-06    0.0014       9      65 ..      24      79 ..      16     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.7e-06
                                  HHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE CS
                          HxlR  9 lilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsl 65
                                  +i + + +g+k +++++r+l + s++ + +r ++Le++g+i+  +    P k+ Y++
  gi|15668904|ref|NP_247708.1| 24 IIEILMRDGRKSYTDIAREL-GTSESSIRKRVKKLEEEGVIKGYTAIIDPSKIGYNV 79
                                  44445667************.88*******************************986 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   4.9e-06    0.0024       4      45 ..      23      64 ..      21      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.9e-06
                      HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                  +i+e l ++g  s ++++ +lg+Se  iR+  ++Lee+g+++
  gi|15668904|ref|NP_247708.1| 23 KIIEILMRDGRKSYTDIARELGTSESSIRKRVKKLEEEGVIK 64
                                  79*************************************964 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.5e-06    0.0027      25      52 ..      36      63 ..      27      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.5e-06
                                  HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                Fe_dep_repress 25 tkdlaerLnvspssVsemlkkLekdGyv 52
                                   +d+a++L+ s ss+ + +kkLe++G +
  gi|15668904|ref|NP_247708.1| 36 YTDIARELGTSESSIRKRVKKLEEEGVI 63
                                  689**********************965 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.2e-05     0.006      27      55 .]      35      63 ..      31      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-05
                        HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                  s+ ++a+ lg s++++++ +k+Le+ G i
  gi|15668904|ref|NP_247708.1| 35 SYTDIARELGTSESSIRKRVKKLEEEGVI 63
                                  99**********************98865 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.6e-05    0.0081       3      45 ..      22      64 ..      21      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-05
                        HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                  l+++ +L+ + + +++++  +l+++++ + + +kkLe+ g i+
  gi|15668904|ref|NP_247708.1| 22 LKIIEILMRDGRKSYTDIARELGTSESSIRKRVKKLEEEGVIK 64
                                  89*************************************9887 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     2e-05      0.01       4      40 ..      22      60 ..      20      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-05
                                  HHHHHHHHHHS..SHHHHHHHHTS-HHHHHHHHHHHHHH CS
                         HTH_1  4 lrlfvavaeeg..sftrAAeeLglsqpavsrqikrLEee 40
                                  l++ + +++ g  s t  A+eLg+s +++ +++k+LEee
  gi|15668904|ref|NP_247708.1| 22 LKIIEILMRDGrkSYTDIARELGTSESSIRKRVKKLEEE 60
                                  566666666666688999*******************96 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.1e-05     0.016      13      62 ..      16      61 ..       2      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-05
                                  ---HHHHHHHHHHHH-S---TT--HHHHHHHTT--HHHHHHHH---S-SS CS
                         HTH_6 13 kltksekkiaeyilaspdkaielsikalAkaaavSeativrfakkLGfkG 62
                                   + + + ki+e++ ++  k    s  ++A +++ Se++i +  kkL  +G
  gi|15668904|ref|NP_247708.1| 16 IMDEKDLKIIEILMRDGRK----SYTDIARELGTSESSIRKRVKKLEEEG 61
                                  3788999999999999865....678*******************98665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.9e-05     0.019      14      43 ..      28      56 ..      15      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-05
                                  HHHHTTT--HHHHHHHHTS-HHHHHHHHHH CS
                    Sigma70_r4 14 elrfgeglTleEIgerlgiSrerVrqiekr 43
                                   +r g++ ++ +I+++lg S++ +r + k+
  gi|15668904|ref|NP_247708.1| 28 LMRDGRK-SYTDIARELGTSESSIRKRVKK 56
                                  3555666.******************9986 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.7e-05     0.023      17      46 ..      23      52 ..      13      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-05
                                  HHHHHHHHHSSBEHHHHHHHHSSTHHHHHH CS
                         HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkk 46
                                  k++e L+r gr++ ++++++++ s ++++k
  gi|15668904|ref|NP_247708.1| 23 KIIEILMRDGRKSYTDIARELGTSESSIRK 52
                                  89**************************98 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.7e-05     0.023      23      49 ..      28      55 ..      24      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.7e-05
                  HTH_Tnp_ISL3 23 llles.rsvkavArqlgvSwtTVwrild 49
                                  l++++ +s +++Ar+lg+S+++++ +++
  gi|15668904|ref|NP_247708.1| 28 LMRDGrKSYTDIARELGTSESSIRKRVK 55
                                  5566778****************98876 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   6.4e-05     0.032      21      56 ..      31      64 ..      22      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.4e-05
                                  STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                  +++   s ++ia++ ++s+s ++k ++kL+++g++k
  gi|15668904|ref|NP_247708.1| 31 DGR--KSYTDIARELGTSESSIRKRVKKLEEEGVIK 64
                                  444..4899*************************98 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     9e-05     0.045      38      77 ..      26      64 ..       7      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9e-05
                                  HHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                        HTH_47 38 wvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                  ++L + DG++s  diA ++g +   + + +++L+e+g+++
  gi|15668904|ref|NP_247708.1| 26 EIL-MRDGRKSYTDIARELGTSESSIRKRVKKLEEEGVIK 64
                                  444.78********************************96 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00018      0.09      16      56 ..      19      59 ..       8      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00018
                                  SHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
                           Mga 16 slkyqllkflfeeeevsieelaqelyiSestlkrkikelnk 56
                                    ++++++ l+ + ++s +++a+el  Ses++ + +k+l++
  gi|15668904|ref|NP_247708.1| 19 EKDLKIIEILMRDGRKSYTDIARELGTSESSIRKRVKKLEE 59
                                  56899*********************************986 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00022      0.11      23      54 ..      38      69 ..      35     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00022
                B-block_TFIIIC 23 dLakeskqdprslfyrlksLekkgLIvkqsii 54
                                  d+a+e++ + +s+ +r+k+Le+ g I++ ++i
  gi|15668904|ref|NP_247708.1| 38 DIARELGTSESSIRKRVKKLEEEGVIKGYTAI 69
                                  8999***********************98886 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00041       0.2       7      57 ..      18      68 ..      14      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00041
                       DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerveg 57
                                  de++lk++++l + +      ia+el  + + +r+ +kkLee G ++ +++
  gi|15668904|ref|NP_247708.1| 18 DEKDLKIIEILMRDGRKSYTDIARELGTSESSIRKRVKKLEEEGVIKGYTA 68
                                  778899999999988888889*************************99886 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00044      0.22      24      46 ..      34      56 ..      12      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00044
                        HTH_50 24 pStRklAkrLGvShtaianklrk 46
                                  +S   +A+ LG+S + i ++++k
  gi|15668904|ref|NP_247708.1| 34 KSYTDIARELGTSESSIRKRVKK 56
                                  677789***************98 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00063      0.31      13      38 ..      34      59 ..      23      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00063
                                  T-HHHHHHHHTS-HHHHHHHHHHHHH CS
                        HTH_30 13 gnisatAkaLhvHrnTlryRLrriee 38
                                   ++++ A++L+ +  ++r+R++++ee
  gi|15668904|ref|NP_247708.1| 34 KSYTDIARELGTSESSIRKRVKKLEE 59
                                  58999*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1124.06
//
Query:       gi|15668905|ref|NP_247709.1|  [L=207]
Description: N-glycosylase/DNA lyase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0037   17.0   3.1      0.032   13.9   0.2    2.2  2  GrpE      GrpE
  ------ inclusion threshold ------
      0.029   14.8   0.0      0.061   13.8   0.0    1.7  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
      0.096   13.2   0.3        6.6    7.3   0.0    2.4  2  MRFAP1    MORF4 family-associated protein1


Domain annotation for each model (and alignments):
>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.4   0.2    0.0092        55      20      52 ..       6      36 ..       2      45 .. 0.79
   2 !   13.9   0.2   5.4e-06     0.032      22      69 ..      72     119 ..      56     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0092
                                  CTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHH CS
                          GrpE 20 eleelekevkelkekllrllaefenlrkrteke 52
                                  ++eel++   e+k+ +++  +ef+ ++++ ++e
  gi|15668905|ref|NP_247709.1|  6 KIEELKN--SEIKDIIDKRIQEFKSFKNKSNEE 36
                                  5566555..899999999999999999998887 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.4e-06
                                   TCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          GrpE  22 eelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLL 69 
                                   eele+++k+l  ++ r++ae+  l +r+++ k+ +++f++ek+a+++L
  gi|15668905|ref|NP_247709.1|  72 EELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFL 119
                                   789*******************************************98 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     1e-05     0.061      38      94 ..      75     165 ..      44     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1e-05
                                   HHHHHHHHTTSTTHHHHHHHHHHHHHHHH......................................S-SSS--TTSHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................xxxxxxxxxxxxxx RF
                       HhH-GPD  38 eekLrelirelGfyrrKakyikelArilv......................................gkpdvlivvDvhvr 80 
                                   eekL++l  +++fyr++a+yi  lAr +                                       g+ dv+i+ D h+ 
  gi|15668905|ref|NP_247709.1|  75 EEKLKNL--GHRFYRKRAEYIV-LARRFKnikdivesfenekvareflvrnikgigykeashflrnvGYDDVAII-DRHIL 151
                                   7888888..8**********97.8888888999999999999999999999999999999999999999886666.99998 PP

                                   HHHHHHTTSSSSTT CS
                                   xxxxxxxxxxxxxx RF
                       HhH-GPD  81 rilkrlrsikekkt 94 
                                   r l   + i+e ++
  gi|15668905|ref|NP_247709.1| 152 RELYENNYIDEIPK 165
                                   88777777776644 PP

>> MRFAP1  MORF4 family-associated protein1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.013        77      76     115 ..      69     108 ..      60     116 .. 0.79
   2 ?    7.3   0.0    0.0011       6.6      45      64 ..     168     187 ..     136     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.013
                        MRFAP1  76 sPgaeaeervaklcakaerkakeaarmgkrlvelvrrier 115
                                    P++e ee+   l+ +  rk +e   +++r  +++  +e+
  gi|15668905|ref|NP_247709.1|  69 LPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVES 108
                                   5899999999999999999999988888887776665555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0011
                        MRFAP1  45 arrklleidslldeikseve 64 
                                   +rrk lei+++l +i  ev+
  gi|15668905|ref|NP_247709.1| 168 SRRKYLEIENILRDIGEEVN 187
                                   69*************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1316  (0.0734006); expected 358.6 (0.02)
Passed bias filter:                      783  (0.0436723); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1315.53
//
Query:       gi|15668906|ref|NP_247710.1|  [L=261]
Description: coenzyme F420-reducing hydrogenase subunit beta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-36  123.2   0.7    1.2e-35  122.6   0.7    1.3  1  FrhB_FdhB_C    Coenzyme F420 hydrogenase/dehydrogenase, beta 
    1.2e-20   73.4   0.1    4.8e-20   71.5   0.0    1.9  2  FrhB_FdhB_N    Coenzyme F420 hydrogenase/dehydrogenase, beta 
  ------ inclusion threshold ------
      0.068   13.5   0.8       0.68   10.3   0.0    2.8  3  ATP-synt_ab_C  ATP synthase alpha/beta chain, C terminal doma
      0.084   12.9   0.2       0.17   11.9   0.2    1.5  1  HTH_Crp_2      Crp-like helix-turn-helix domain
       0.88    9.6   3.9        1.9    8.5   3.9    1.5  1  TnpV           Transposon-encoded protein TnpV


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6   0.7   3.4e-39   1.2e-35       2     153 ..      82     229 ..      81     231 .. 0.97

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 3.4e-39
                   FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqkkklkekilltiglfCggnfspealrk.lleelgvdpedvkklefrgkgkfrvelkd..... 76 
                                   +kv++vG+PC+i +  ++         +l +glfC++nf+++ +++ ++e+ gv+ ++v k+++ +kgkf+ve+ +     
  gi|15668906|ref|NP_247710.1|  82 DKVGLVGLPCHILGGLQFDL-------TLKVGLFCTKNFYYDTIKSiIKERFGVNIDEVAKMNI-TKGKFVVETLKkkgfa 154
                                   69*************99999.......8******************99****************.9******998889*** PP

                   FrhB_FdhB_C  77 .....ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveageleleel 152
                                        ++ei++ke+e+ ++ +C+vC+d+ a+ AD+svG+v      g +++g++tv+vr+++ e+++++++e+g +e++e+
  gi|15668906|ref|NP_247710.1| 155 gtekvVYEIPIKEIEKLCNLGCRVCTDFSAKYADVSVGSV------G-SEDGWNTVIVRNKMVEDIINEMAEKGLIEVKET 228
                                   *****99*********************************......8.******************************997 PP

                   FrhB_FdhB_C 153 d 153
                                    
  gi|15668906|ref|NP_247710.1| 229 V 229
                                   5 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   1.3e-23   4.8e-20      13      77 ..      12      74 ..       3      75 .. 0.91
   2 ?   -0.9   0.0      0.52   1.9e+03      20      36 ..     209     225 ..     194     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1.3e-23
                   FrhB_FdhB_N 13 kkaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYtlspnlklL 77
                                    aq+GG +t+ll y+Le+gi d+v+vv  +  +w+p++++att+ ell++ +skY++spn klL
  gi|15668906|ref|NP_247710.1| 12 IDAQDGGFTTTLLSYCLENGILDAVVVVGDK--NWKPVAYLATTPTELLKSTKSKYSISPNNKLL 74
                                  579**************************77..6*****************************99 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.52
                   FrhB_FdhB_N  20 ivtallkylLeegiidg 36 
                                   +v  ++ ++ e+g+i+ 
  gi|15668906|ref|NP_247710.1| 209 MVEDIINEMAEKGLIEV 225
                                   56677888888888875 PP

>> ATP-synt_ab_C  ATP synthase alpha/beta chain, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.47   1.7e+03      68     114 ..      26      70 ..      21      83 .. 0.63
   2 ?   10.3   0.0   0.00019      0.68      27      56 ..     125     154 ..     123     186 .. 0.92
   3 ?   -1.5   0.4      0.81   2.9e+03      87     110 ..     219     242 ..     202     251 .. 0.43

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.47
                 ATP-synt_ab_C  68 yaatngllddipvekvkefekelleyleeekkeileeieekkklsde 114
                                   y+++ng+ld + v  v + + + ++yl ++ +e+l++ ++k ++s +
  gi|15668906|ref|NP_247710.1|  26 YCLENGILDAVVV--VGDKNWKPVAYLATTPTELLKSTKSKYSISPN 70 
                                   5666777776655..45555556677777777777777777666655 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
                 ATP-synt_ab_C  27 qFgsdLDeatkkqLerGerlvelLkQkqys 56 
                                   +Fg ++De  k ++++G+ +ve Lk k ++
  gi|15668906|ref|NP_247710.1| 125 RFGVNIDEVAKMNITKGKFVVETLKKKGFA 154
                                   7************************98765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.81
                 ATP-synt_ab_C  87 ekelleyleeekkeileeieekkk 110
                                   ek l+e+ e+   + +e++e+ kk
  gi|15668906|ref|NP_247710.1| 219 EKGLIEVKETVDIKAIEKLENIKK 242
                                   233333333333333333333333 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   4.7e-05      0.17      38      68 .]     210     240 ..     204     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
                                   HHHHHHHHHHTTSEE.ETEEEEES-HHHHHHH CS
                     HTH_Crp_2  38 vsrilseLkreglis.rgrririldleaLral 68 
                                   v  i++e+ ++gli+ +++ + i+ +e+L+++
  gi|15668906|ref|NP_247710.1| 210 VEDIINEMAEKGLIEvKET-VDIKAIEKLENI 240
                                   6779***********6566.*********986 PP

>> TnpV  Transposon-encoded protein TnpV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.9   0.00054       1.9      64     106 ..     207     247 ..     204     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00054
                          TnpV  64 eerlerlvkqlaekegvteelkakdqmewvqrmnnirnraeEi 106
                                   ++++e++++++aek  +  e+k++  ++ +++ +ni+++ eEi
  gi|15668906|ref|NP_247710.1| 207 NKMVEDIINEMAEKGLI--EVKETVDIKAIEKLENIKKKNEEI 247
                                   79************666..59*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1160  (0.0646996); expected 358.6 (0.02)
Passed bias filter:                      713  (0.039768); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1719.77
//
Query:       gi|15668907|ref|NP_247711.1|  [L=216]
Description: coenzyme F420-reducing hydrogenase subunit gamma [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-20   72.0   0.2      4e-20   72.0   0.2    1.7  2  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
      1e-08   34.6  27.1    2.5e-07   30.2   3.1    4.5  4  Fer4         4Fe-4S binding domain
    3.6e-07   30.2  11.8    3.6e-07   30.2  11.8    3.4  4  Fer4_10      4Fe-4S dicluster domain
    3.7e-07   30.2  11.4    3.7e-07   30.2  11.4    3.0  3  Fer4_9       4Fe-4S dicluster domain
      2e-06   27.6  26.4    0.00025   21.0   3.0    4.1  4  Fer4_6       4Fe-4S binding domain
      8e-05   23.2  13.2      8e-05   23.2  13.2    3.5  3  Fer4_7       4Fe-4S dicluster domain
     0.0015   18.7  20.1       0.18   11.9   2.0    3.9  3  Fer4_21      4Fe-4S dicluster domain
     0.0015   19.4   9.2     0.0015   19.4   9.2    3.6  4  Fer4_16      4Fe-4S double cluster binding domain
     0.0019   18.1  29.0     0.0044   17.0   5.4    4.4  4  Fer4_2       4Fe-4S binding domain
  ------ inclusion threshold ------
      0.019   15.4   3.6      0.019   15.4   3.6    4.6  4  Fer4_4       4Fe-4S binding domain
      0.047   13.9   9.5       0.14   12.4   9.5    1.9  1  Fer4_18      4Fe-4S dicluster domain
      0.071   13.7   2.8      0.071   13.7   2.8    3.5  4  Fer4_17      4Fe-4S dicluster domain
        1.1    9.8  23.5       0.16   12.5   1.7    3.3  3  Fer4_8       4Fe-4S dicluster domain
        2.3    9.1  19.6        3.8    8.4   6.2    4.0  3  Fer4_22      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.2   3.1e-23     4e-20      41     130 ..      20     111 ..       7     112 .. 0.89
   2 ?   -3.0   0.8       4.7     6e+03       1      13 [.     169     181 ..     169     199 .. 0.63

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 3.1e-23
                                   THTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-..HHHHHHHC.S-E.EEE-SSS- CS
                   Oxidored_q6  41 akekeadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvg..eevgellevvpvdinipGCPp 119
                                   ++ ke+d+++v Gav+ +++e+++++ e+++++k++iavG+CA++GG++++    + g  +++ ++ +vv+vd+ i GCPp
  gi|15668907|ref|NP_247711.1|  20 NQLKEKDIVLVGGAVNLDDEEEVKKIMEIRKNSKVLIAVGSCAVSGGFQRMLIGLENGfpQRFVRIGDVVKVDYAIIGCPP 100
                                   45579********************************************9988777766799999**************** PP

                                   -HHHHHHHHHH CS
                   Oxidored_q6 120 hpeailetlla 130
                                   ++e++ ++++a
  gi|15668907|ref|NP_247711.1| 101 DEEEVERIVKA 111
                                   ****9988876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.7
                                   -SHHHHHHT-TTT CS
                   Oxidored_q6   1 CtGcsisllalee 13 
                                   CtGc   ++++  
  gi|15668907|ref|NP_247711.1| 169 CTGCGTCVAKCPA 181
                                   7777665554444 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.4      0.19   2.5e+02       9      14 ..       2       7 ..       2      10 .. 0.84
   2 ?    2.7   0.1     0.099   1.3e+02       4      11 ..     152     159 ..     149     160 .. 0.87
   3 !   30.2   3.1     2e-10   2.5e-07       2      24 .]     163     185 ..     162     185 .. 0.94
   4 !   14.0   2.9   2.6e-05     0.033       2      18 ..     191     207 ..     190     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.19
                                  SS-THH CS
                          Fer4  9 igCGaC 14
                                  +gCG C
  gi|15668907|ref|NP_247711.1|  2 TGCGSC 7 
                                  69**** PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.099
                                   ETTTSSS- CS
                          Fer4   4 deekCigC 11 
                                   ++e+C gC
  gi|15668907|ref|NP_247711.1| 152 NKELCLGC 159
                                   89****** PP

  == domain 3  score: 30.2 bits;  conditional E-value: 2e-10
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                    i+ e C+gCG+Cv  CP +A+t
  gi|15668907|ref|NP_247711.1| 163 PINDEFCTGCGTCVAKCPANALT 185
                                   5999*****************86 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 2.6e-05
                                   EEETTTSSS-THHHHHS CS
                          Fer4   2 videekCigCGaCvevC 18 
                                   +++ +kCi+CG+C   C
  gi|15668907|ref|NP_247711.1| 191 KVNISKCIKCGTCFFNC 207
                                   7899*********8877 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.0      0.92   1.2e+03      12      17 ..       4       9 ..       2      65 .. 0.48
   2 ?   -3.0   0.0       6.3   8.1e+03      19      31 ..      98     110 ..      96     120 .. 0.50
   3 ?   -0.6   0.1       1.2   1.5e+03       4      13 ..     151     160 ..     148     161 .. 0.78
   4 !   30.2  11.8   2.8e-10   3.6e-07       4      55 ..     164     207 ..     162     208 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.92
                       Fer4_10 12 CgkCvk 17
                                  Cg C k
  gi|15668907|ref|NP_247711.1|  4 CGSCGK 9 
                                  444433 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.3
                       Fer4_10  19 CPadltsvgakge 31 
                                   CP d ++v+ + +
  gi|15668907|ref|NP_247711.1|  98 CPPDEEEVERIVK 110
                                   7774433333333 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.2
                       Fer4_10   4 idddtCirCg 13 
                                    +++ C++C 
  gi|15668907|ref|NP_247711.1| 151 SNKELCLGCD 160
                                   6788999996 PP

  == domain 4  score: 30.2 bits;  conditional E-value: 2.8e-10
                       Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                   i+d+ C++Cg+Cv+ CPa        ++ +++e+ +++++kC++cg C   C
  gi|15668907|ref|NP_247711.1| 164 INDEFCTGCGTCVAKCPA--------NALTIDEKPKVNISKCIKCGTCFFNC 207
                                   7999**************........9*********************8777 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       1.2   1.5e+03      38      42 ..       3       7 ..       2      12 .. 0.60
   2 ?    0.6   0.0      0.49   6.3e+02      33      40 ..     146     160 ..      98     161 .. 0.72
   3 !   30.2  11.4   2.9e-10   3.7e-07       2      46 ..     169     207 ..     168     211 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                        Fer4_9 38 gCgaC 42
                                  gCg+C
  gi|15668907|ref|NP_247711.1|  3 GCGSC 7 
                                  45555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.49
                        Fer4_9  33 e.......eaCigCg 40 
                                   +       e C+gC 
  gi|15668907|ref|NP_247711.1| 146 DvlltsnkELCLGCD 160
                                   134444457899996 PP

  == domain 3  score: 30.2 bits;  conditional E-value: 2.9e-10
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaC 46 
                                   CtgCg+Cv++Cpa++ + d++++ +        +Ci+Cg+C+  C
  gi|15668907|ref|NP_247711.1| 169 CTGCGTCVAKCPANALTIDEKPKVNIS------KCIKCGTCFFNC 207
                                   ************************997......7********999 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.9       2.7   3.5e+03      11      15 ..       3       7 ..       2       9 .. 0.77
   2 ?    4.7   0.2     0.028        36       5      14 ..     152     161 ..     149     161 .. 0.85
   3 !   21.0   3.0     2e-07   0.00025       4      24 .]     164     184 ..     164     184 .. 0.92
   4 !   16.9   2.8   3.9e-06     0.005       1      19 [.     189     207 ..     189     213 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.7
                        Fer4_6 11 gCgdC 15
                                  gCg C
  gi|15668907|ref|NP_247711.1|  3 GCGSC 7 
                                  78888 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.028
                        Fer4_6   5 dpdkCigCgd 14 
                                   ++++C+gC+d
  gi|15668907|ref|NP_247711.1| 152 NKELCLGCDD 161
                                   899*****85 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 2e-07
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   i+++ C+gCg Cv+ CP++a+
  gi|15668907|ref|NP_247711.1| 164 INDEFCTGCGTCVAKCPANAL 184
                                   68889**************97 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 3.9e-06
                        Fer4_6   1 vveidpdkCigCgdCvrvC 19 
                                   ++ ++ +kCi Cg C+ +C
  gi|15668907|ref|NP_247711.1| 189 KPKVNISKCIKCGTCFFNC 207
                                   6899*************** PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.8       1.1   1.5e+03       4       9 ..       3       8 ..       2      63 .. 0.79
   2 ?    0.7   0.0      0.66   8.5e+02      32      42 ..     150     160 ..      95     161 .. 0.69
   3 !   23.2  13.2   6.2e-08     8e-05       2      48 ..     169     207 ..     168     209 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                        Fer4_7 4 gCgaCv 9
                                 gCg C 
  gi|15668907|ref|NP_247711.1| 3 GCGSCG 8
                                 677775 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.66
                        Fer4_7  32 eidpekClgCg 42 
                                   + + e ClgC+
  gi|15668907|ref|NP_247711.1| 150 TSNKELCLGCD 160
                                   55678899996 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 6.2e-08
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavC 48 
                                   C+gCg Cva Cp++a+++de+        ++++ +kC+ Cg C   C
  gi|15668907|ref|NP_247711.1| 169 CTGCGTCVAKCPANALTIDEK--------PKVNISKCIKCGTCFFNC 207
                                   ******************997........688999********9888 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       2.6   3.3e+03      43      48 ..       3       8 ..       2      23 .. 0.69
   2 !   11.3   7.0   0.00023      0.29      35      57 ..     163     184 ..     133     186 .. 0.84
   3 !   11.9   2.0   0.00014      0.18       3      19 ..     192     208 ..     190     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.6
                       Fer4_21 43 GCnlCs 48
                                  GC  C 
  gi|15668907|ref|NP_247711.1|  3 GCGSCG 8 
                                  444443 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00023
                       Fer4_21  35 kvvedeCvGCnlCssvCPvedci 57 
                                   ++ ++ C+GC  C++ CP  +++
  gi|15668907|ref|NP_247711.1| 163 PINDEFCTGCGTCVAKCPA-NAL 184
                                   677899************5.665 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00014
                       Fer4_21   3 idedkCigCgkCliaCe 19 
                                   ++ +kCi+Cg C+  C 
  gi|15668907|ref|NP_247711.1| 192 VNISKCIKCGTCFFNCI 208
                                   6778************5 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.5       3.2   4.1e+03      56      61 ..       3       8 ..       1      62 [. 0.78
   2 ?   -2.3   0.0         7   8.9e+03      51      58 ..     153     160 ..     126     161 .. 0.67
   3 !   19.4   9.2   1.2e-06    0.0015       1      32 [.     168     199 ..     168     200 .. 0.96
   4 ?    2.9   3.7      0.16   2.1e+02       1      12 [.     196     207 ..     196     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.2
                       Fer4_16 56 gCdiCq 61
                                  gC+ C 
  gi|15668907|ref|NP_247711.1|  3 GCGSCG 8 
                                  454443 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7
                       Fer4_16  51 qeaitgCd 58 
                                   +e + gCd
  gi|15668907|ref|NP_247711.1| 153 KELCLGCD 160
                                   34477776 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 1.2e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecis 32 
                                   +C++Cg C+  CP+na++ ++++++++ +ci+
  gi|15668907|ref|NP_247711.1| 168 FCTGCGTCVAKCPANALTIDEKPKVNISKCIK 199
                                   6*****************************97 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.16
                       Fer4_16   1 rCgtCgkCaevC 12 
                                   +C++Cg C   C
  gi|15668907|ref|NP_247711.1| 196 KCIKCGTCFFNC 207
                                   5********999 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.4      0.52   6.7e+02      11      16 ..       2       7 ..       2       9 .. 0.85
   2 ?    1.7   0.3      0.25   3.3e+02       6      13 ..     152     159 ..     150     163 .. 0.86
   3 !   17.0   5.4   3.4e-06    0.0044       5      22 .]     164     181 ..     161     181 .. 0.92
   4 !   13.2   1.6   5.8e-05     0.075       2      20 ..     189     207 ..     188     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.52
                        Fer4_2 11 igCgaC 16
                                  +gCg+C
  gi|15668907|ref|NP_247711.1|  2 TGCGSC 7 
                                  689999 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.25
                        Fer4_2   6 dtdrCigC 13 
                                   + + C+gC
  gi|15668907|ref|NP_247711.1| 152 NKELCLGC 159
                                   6799**** PP

  == domain 3  score: 17.0 bits;  conditional E-value: 3.4e-06
                        Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                   ++ + C+gCg+Cv  CPa
  gi|15668907|ref|NP_247711.1| 164 INDEFCTGCGTCVAKCPA 181
                                   68899*******999**8 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 5.8e-05
                        Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                   +++v+  +Ci Cg+C  +C
  gi|15668907|ref|NP_247711.1| 189 KPKVNISKCIKCGTCFFNC 207
                                   789999*********9999 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.1      0.45   5.7e+02       5      10 ..       2       7 ..       2       7 .. 0.91
   2 ?    2.2   0.3      0.26   3.4e+02       1       8 [.     153     160 ..     153     161 .. 0.86
   3 ?   15.4   3.6   1.5e-05     0.019       4      16 ..     169     181 ..     165     182 .. 0.92
   4 ?    3.7   3.5     0.087   1.1e+02       3      10 ..     196     203 ..     194     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.45
                        Fer4_4  5 igCgsC 10
                                  +gCgsC
  gi|15668907|ref|NP_247711.1|  2 TGCGSC 7 
                                  69**** PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.26
                        Fer4_4   1 qerCigCg 8  
                                   +e C+gC+
  gi|15668907|ref|NP_247711.1| 153 KELCLGCD 160
                                   588****7 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.5e-05
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   C+gCg Cva CP 
  gi|15668907|ref|NP_247711.1| 169 CTGCGTCVAKCPA 181
                                   ************7 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.087
                        Fer4_4   3 rCigCgsC 10 
                                   +Ci Cg C
  gi|15668907|ref|NP_247711.1| 196 KCIKCGTC 203
                                   8******9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   9.5   0.00011      0.14      59     101 ..     167     213 ..     121     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                       Fer4_18  59 gdcidcescvkvcPtg...idirkGlql.eciscllcidacdkvmek 101
                                     c+ c++cv+ cP +   id +  + + +ci+c+ c   c +v e+
  gi|15668907|ref|NP_247711.1| 167 EFCTGCGTCVAKCPANaltIDEKPKVNIsKCIKCGTCFFNCIRVKEA 213
                                   45************7433388887777647***********998776 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.5       2.4   3.1e+03       5       9 ..       4       8 ..       2      54 .. 0.73
   2 ?   10.1   6.6   0.00074      0.95      45      59 ..     168     182 ..     133     184 .. 0.85
   3 ?   13.7   2.8   5.6e-05     0.071       2      16 ..     169     183 ..     168     193 .. 0.62
   4 ?    8.6   2.2    0.0021       2.7      41      56 ..     192     207 ..     183     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.4
                       Fer4_17 5 CgyCl 9
                                 Cg C 
  gi|15668907|ref|NP_247711.1| 4 CGSCG 8
                                 44443 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00074
                       Fer4_17  45 lCieCgeCerkCPqg 59 
                                    C++Cg C++kCP++
  gi|15668907|ref|NP_247711.1| 168 FCTGCGTCVAKCPAN 182
                                   588899999999875 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 5.6e-05
                       Fer4_17   2 CiqCgyClpeCpsye 16 
                                   C++Cg C+++Cp ++
  gi|15668907|ref|NP_247711.1| 169 CTGCGTCVAKCPANA 183
                                   666666666666655 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0021
                       Fer4_17  41 ekaslCieCgeCerkC 56 
                                    ++s+Ci+Cg C   C
  gi|15668907|ref|NP_247711.1| 192 VNISKCIKCGTCFFNC 207
                                   3899999999999999 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.6       2.1   2.7e+03       8      11 ..       4       7 ..       2      63 .. 0.74
   2 ?   10.3   4.2   0.00057      0.72      51      63 ..     169     181 ..     165     189 .. 0.67
   3 ?   12.5   1.7   0.00012      0.16       2      17 ..     194     209 ..     193     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.1
                        Fer4_8  8 CgaC 11
                                  Cg C
  gi|15668907|ref|NP_247711.1|  4 CGSC 7 
                                  4444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00057
                        Fer4_8  51 CttcgaCtevCpv 63 
                                   Ct+cg C+ +Cp 
  gi|15668907|ref|NP_247711.1| 169 CTGCGTCVAKCPA 181
                                   5555555555554 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00012
                        Fer4_8   2 lekCieCgaCqsaCpv 17 
                                   ++kCi+Cg C+ +C  
  gi|15668907|ref|NP_247711.1| 194 ISKCIKCGTCFFNCIR 209
                                   589***********64 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       1.9   2.5e+03      83      90 ..       2       9 ..       1      17 [. 0.71
   2 ?    8.4   6.2     0.003       3.8      77      95 ..     164     182 ..     137     183 .. 0.89
   3 ?    6.0   1.2     0.016        21       1      12 [.     196     207 ..     187     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.9
                       Fer4_22 83 vGCgRCie 90
                                  +GCg C +
  gi|15668907|ref|NP_247711.1|  2 TGCGSCGK 9 
                                  57777765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.003
                       Fer4_22  77 fgesgCvGCgRCieacpvk 95 
                                   ++ + C+GCg C+++cp++
  gi|15668907|ref|NP_247711.1| 164 INDEFCTGCGTCVAKCPAN 182
                                   57889***********986 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.016
                       Fer4_22   1 rClsCgaCtlvC 12 
                                   +C++Cg+C + C
  gi|15668907|ref|NP_247711.1| 196 KCIKCGTCFFNC 207
                                   466777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1359.22
//
Query:       gi|15668908|ref|NP_247712.1|  [L=298]
Description: coenzyme F420-reducing hydrogenase subunit alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-09   36.1   0.0    4.1e-08   32.6   0.0    2.3  2  NiFeSe_Hases  Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   2.3e-12   4.1e-08       1      59 [.       4      62 ..       4      80 .. 0.93
   2 !    1.2   0.0    0.0073   1.3e+02     181     337 ..     101     183 ..      66     219 .. 0.51

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.3e-12
                                  --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHH CS
                  NiFeSe_Hases  1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaa 59
                                  RG+E  + g+d       + R C     +Hala+v+ave+A++i++p++++++r++   
  gi|15668908|ref|NP_247712.1|  4 RGFESSMMGKDIDFIPPAMTRLCCLNEISHALAGVMAVEKAYNITVPNEGQYLREIARL 62
                                  9******************************************************9765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.0073
                                   BTTBESSGBGS........BSHHHHHHHHH.HHHHHHHHHHHTHHHHHHHHHHHTGGGGCS--GGGGT-EEEEEEEESSTT CS
                  NiFeSe_Hases 181 vvGGvtcaidl........lnaerlaevks.likevkefveevylpDvlaiakaYkdwakigkglgkknflsvgefpeeks 252
                                   +vGGv  +i+         l +e l+ v++ ++k v e   ++ lpDv +i ++  d+ k++++   k             
  gi|15668908|ref|NP_247712.1| 101 AVGGVLENISDkrkeklinLAKEGLNLVDKdFVKLVDERKAKIPLPDVELIDAYNFDANKVETNGLPK------------- 168
                                   46666666555333333333333333332212233333333444455544444333333333322223............. PP

                                   -STTGGEEEEEEEESTTETTSEBEE-TTTEEEE-TTSSBSTS-B-GGG---EB---EEE--TTSB-BSS-EEEETTB--BE CS
                  NiFeSe_Hases 253 eelkeslllpsGvilngdlskveevdeekitEevkhswYkekslhplegetepkytleeldeegkYswikaPrykgkamev 333
                                                                                                         +  y+gk++  
  gi|15668908|ref|NP_247712.1| 169 ----------------------------------------------------------------------TALYDGKVVYS 179
                                   ......................................................................33333333333 PP

                                   SHHH CS
                  NiFeSe_Hases 334 Gpla 337
                                   G+la
  gi|15668908|ref|NP_247712.1| 180 GSLA 183
                                   3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1735.34
//
Query:       gi|15668909|ref|NP_247713.1|  [L=624]
Description: carbon monoxide dehydrogenase catalytic subunit CooS [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   9.9e-146  486.4   1.7   1.1e-145  486.2   1.7    1.0  1  Prismane  Prismane/CO dehydrogenase family


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  486.2   1.7  6.3e-150  1.1e-145       2     510 ..      45     604 ..      44     605 .. 0.98

  Alignments for each domain:
  == domain 1  score: 486.2 bits;  conditional E-value: 6.3e-150
                                   EE-SSTCT-ECSC.S.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCHTSTTTB-SHHHHHHHHHHH CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane   2 fCrqCengpCrit.knkrGvCGkdadtavardlliavlkgaaahaahareladtliakalfktltnvnfddekklkrlaea 81 
                                   +C +C ngpCrit k++ GvCG++ad++var+l++av++g++++++ a+++a++l  +++++   ++++++ekklk+la++
  gi|15668909|ref|NP_247713.1|  45 YCILCANGPCRITeKTPYGVCGATADVIVARNLCRAVAAGTSCYVHCAENAARALLSAGKGEG--SYEIRNEKKLKFLAKK 123
                                   8*************************************************************9..**************** PP

                                   HCHHHCCSSHHHHHHHHCCHHHCGGGS-SSHHHHHHHCCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHCCCCTTSTHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane  82 lgieeelkdieelaakvaevaledlskeenedirslkellpkglkglyaehaivlgyadeevveflaktlaglesdpldll 162
                                   lg+++++ d ++la +vae+ l+d++k++ e+ +++ +l+p+++ +++++++i++g+a+ e+v++l+kt+++l+s+p+dll
  gi|15668909|ref|NP_247713.1| 124 LGFDANK-DAKQLAVEVAEFILDDMYKPRWEKSELVPKLCPEKRLEVFEKLDILPGGAKGEIVDALTKTSTNLNSNPMDLL 203
                                   ****999.************************************************************************* PP

                                   HHHHHHHHHH.HHHHHHHHHHHHHHH-----EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCCCCCC.....G CS
                                   xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x RF
                      Prismane 163 skalrlGlld.lkgmelldeantslfGtPeppltevnlgvldkdkvnIlvsGHdladleelleqtegkglnvyth.....g 237
                                    ++lrlGl   ++g+ ++  +n++lfG+P+++++e ++  +++++vnI+++GH++a+++ l+e++ +++l ++++      
  gi|15668909|ref|NP_247713.1| 204 VHCLRLGLHAgFTGLLMTCWLNDILFGSPKITVVENGFSSVKPNNVNIMITGHQHALIQPLCEAAMEEDLIKMAKeagadE 284
                                   *********99********************************************************************9* PP

                                   CCCCCCHHHHHHHHHCC......EEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-.TTSE CS
                                   xxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                      Prismane 238 emLpghcctalklkyrh......lvgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktrlittsevak.pgak 311
                                   ++++g +c +++++ r       +vg ++n++++e  ++tg++da+v ++nC+++ l+ vaek+kt+li+++++a+ +ga+
  gi|15668909|ref|NP_247713.1| 285 IKIIGATCNGQDMETRIahlpesFVGYIANNFTTEPLVATGLIDAVVSEFNCTFHGLKFVAEKTKTKLICIDDMAYvEGAE 365
                                   ************5554455************************************************************** PP

                                   EE-.-CTTCHHHHHHHHHHHHCCHCCTTCGG.-............................HHHHHTTSS-EEEEE-B--- CS
                                   xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................xxxxxxxxxxxxxxxxxxxx RF
                      Prismane 312 hie.eeekadkdaseiiekAielakareekkve............................idaiksGtIkgvvlvvGCdn 363
                                   +i+ e+e+a+++a+eii+kAie++k+r+  + +                            i++i+sG+Ikgvv+vvGC+n
  gi|15668909|ref|NP_247713.1| 366 YIPwEPENAKEKAREIIKKAIEAFKERKGMQKDyydekvksvvgvgeeslveflggsvkplIELIASGKIKGVVGVVGCSN 446
                                   ***99**********************7744446789999***************************************** PP

                                   TTCGCC..HHHHHHHHCHHTTEEEEEECHHHHHCCCTTTTECGHHHHSTHC.........EESEEEEESCCCHHHHHHHHH CS
                                   xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxx RF
                      Prismane 364 akkgrd..yytelakelikrdvlvltaGCakyalnklglgtieaaelageg.........iPrvLdvGsCvdnyrivvial 433
                                    ++g++   +++l+kelikrd+lvl+ GC +  l+++gl +++ aelage+         iP+vL++G C++++ri ++a+
  gi|15668909|ref|NP_247713.1| 447 LASGGHdnIIVTLTKELIKRDILVLAGGCVNSPLKHAGLFDPASAELAGENlkevckslgIPPVLNFGACLSIARIEQVAV 527
                                   ***9998899***************************************99****************************** PP

                                   HHHHHTTSSGGGSSEEEEECC--SHHHHHHHHHHHHTT-CEEECSS-TTTT-HHHHHHHHCHHHHHHCEEEECHCHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Prismane 434 klaealgvdindLplaalalewyeqKAvailltllalGinihlgptlpafgspnvlkvlvedfedriggivtveedp 510
                                   ++ae+lgvdi+dLp+aa+a++w+e++A+a++++++ +G ++h++p++ ++gs+ v+kvl+e +e+ +gg++++e++p
  gi|15668909|ref|NP_247713.1| 528 AIAEELGVDIPDLPVAASAPQWLEEQALADATYAVDMGFTVHVSPVPFVTGSELVTKVLTEAVEGLTGGKLIPEPNP 604
                                   **************************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 3685.96
//
Query:       gi|15668910|ref|NP_247714.1|  [L=124]
Description: hypothetical protein MJ_0729 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-15   57.5   1.1    3.1e-08   33.9   0.0    2.2  2  CBS           CBS domain
  ------ inclusion threshold ------
      0.023   15.0   1.9      0.047   14.0   0.8    1.8  2  DUF1462       Protein of unknown function (DUF1462)
      0.028   14.5   0.0        8.3    6.5   0.0    2.1  2  sCache_3_2    Single cache domain 3
       0.63    9.9   5.2       0.17   11.7   1.2    2.1  2  partial_CstF  Partial cleavage stimulation factor domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0     7e-12   3.1e-08       1      52 [.       6      56 ..       6      58 .. 0.91
   2 !   22.1   0.6   3.4e-08   0.00015      19      55 ..      85     121 ..      63     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 7e-12
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52
                                  V+++m++d++ ++p++  +e+++++ +++ +  PV+ edgklvG +t  Dll
  gi|15668910|ref|NP_247714.1|  6 VKEVMNKDFIKISPNDIGGEVVQTLYKEKKNYAPVI-EDGKLVGWITALDLL 56
                                  89**********************865445889***.9************98 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 3.4e-08
                                   HHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS  19 eealelmrekg.vsrlPVVdedgklvGivtlrDllral 55 
                                    e+++++++++ + ++PV+++ +++vG ++  Dll++ 
  gi|15668910|ref|NP_247714.1|  85 DELIDEIIKNEdI-AYPVINDRDEVVGTLSVFDLLKYY 121
                                   688888665556*.*****9999*************96 PP

>> DUF1462  Protein of unknown function (DUF1462)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       0.3   1.4e+03      50      78 ..      19      47 ..       6      54 .. 0.69
   2 ?   14.0   0.8   1.1e-05     0.047      32      79 ..      63     110 ..      49     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.3
                       DUF1462 50 eeeekkefaekiledelfyPlvviedevv 78
                                   ++   e+++++ +++  y  v+ ++++v
  gi|15668910|ref|NP_247714.1| 19 PNDIGGEVVQTLYKEKKNYAPVIEDGKLV 47
                                  45556677777777777777777777766 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.1e-05
                       DUF1462  32 kypeqkleleyvDieeekeeeekkefaekiledelfyPlvviedevva 79 
                                   k ++ +l ++ + i +e++e +++ + e i+++++ yP++   devv+
  gi|15668910|ref|NP_247714.1|  63 KIEDLMLLIDEIKILKENDEVTDELIDEIIKNEDIAYPVINDRDEVVG 110
                                   55666777788888888877777777778899*************997 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0024        11     106     123 ..      35      51 ..      17      68 .. 0.72
   2 ?    6.5   0.0    0.0019       8.3      84     124 ..      74     114 ..      67     114 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0024
                    sCache_3_2 106 rvklPvfdadgrviGivs 123
                                   + ++Pv++ dg+++G++ 
  gi|15668910|ref|NP_247714.1|  35 KNYAPVIE-DGKLVGWIT 51 
                                   669*****.9******96 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0019
                    sCache_3_2  84 aaalkagrayvgtvtgtlgpslrvklPvfdadgrviGivsv 124
                                   +++lk++ +++++    + +  +++ Pv+ ++++v+G++sv
  gi|15668910|ref|NP_247714.1|  74 IKILKENDEVTDELIDEIIKNEDIAYPVINDRDEVVGTLSV 114
                                   56677777777777666677777777777777777777765 PP

>> partial_CstF  Partial cleavage stimulation factor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.43   1.9e+03      18      24 ..       6      12 ..       5      15 .. 0.83
   2 ?   11.7   1.2   3.9e-05      0.17       8      27 ..      78      97 ..      70     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.43
                  partial_CstF 18 VdeVikn 24
                                  V+eV+++
  gi|15668910|ref|NP_247714.1|  6 VKEVMNK 12
                                  89***97 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.9e-05
                  partial_CstF  8 sgvepaeeaLVdeViknkdi 27
                                  ++ ++  ++L+de+ikn+di
  gi|15668910|ref|NP_247714.1| 78 KENDEVTDELIDEIIKNEDI 97
                                  55567789***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 752.38
//
Query:       gi|15668911|ref|NP_247715.1|  [L=186]
Description: DNA/pantothenate metabolism flavoprotein-like protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-23   82.9   0.0      7e-22   77.9   0.0    2.0  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.0   3.9e-26     7e-22       2     107 ..       3     125 ..       2     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 3.9e-26
                                   EEEEEE-SSCGGGCH.HHHHHHHHH.TTEEEEEEESCHHHHCCHHGGS....TCSSHHHHHHCT..............TES CS
                  Flavoprotein   2 killgiTGsvaaika.lellekLkk.egievqvvltkaAkkfiskeklklaaredpilhielrr..............wad 66 
                                   ki++giTG+ + + + +e+++kLk+  + +v+++l+k+Ak +++     ++  ed+  +  ++               ++d
  gi|15668911|ref|NP_247715.1|   3 KIAWGITGCGDKLPEvVEIMKKLKNkYNLDVDIYLSKNAKIVVKWY-KLWQVLEDEFYDLRVEVnanapflvgklqtgKYD 82 
                                   8**********99988*********66*****************33.3333434444443333366778888888889*** PP

                                   EEEEEEEEHHHHHHHHTT--SSHHHHHH.HT.HCCTTEEEEE. CS
                  Flavoprotein  67 llviaPasantlakianGiadnlltlil.ra.takkpiliaPa 107
                                   l+++aPa+ant akia+Giad+l+t+ +  a +ak+p++i+P 
  gi|15668911|ref|NP_247715.1|  83 LFLVAPATANTTAKIAYGIADTLITNSVaQAmKAKVPVYIFPP 125
                                   ************************8877422566666666662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1166.64
//
Query:       gi|15668912|ref|NP_247716.1|  [L=198]
Description: iron-sulfur flavoprotein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.9e-37  126.1   0.0    1.2e-36  125.8   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    1.2e-08   34.9   0.0    1.5e-08   34.6   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
     0.0011   19.3   0.0     0.0017   18.6   0.0    1.3  1  Flavodoxin_5  Flavodoxin domain


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.8   0.0     2e-40   1.2e-36       1     151 [.       1     156 [.       1     160 [. 0.94

  Alignments for each domain:
  == domain 1  score: 125.8 bits;  conditional E-value: 2e-40
                                   -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH-SCEE CS
                       FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaaadali 77 
                                   mk+ +isGS+r ++ t  ++++a++ lke+gaev ++ ++ + i  c   ++c k++ + + ++dd++e++e + +ad++i
  gi|15668912|ref|NP_247716.1|   1 MKVFGISGSPRLQG-THFAVNYALNYLKEKGAEVRYFSVSRKkINFClhcDYCIKKK-EGCIHKDDMEEVYENLIWADGVI 79 
                                   9**********999.9999********************999999998877777666.45********************* PP

                                   EEEEECTTCE-HHHHHHHHCHT-...SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEECSEEEET CS
                       FMN_red  78 ivtPeYngsysgllKnalDrlsr..trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpraavavg 151
                                   i+tP+Y+g+++g+lK+++Dr+++   +++k lrg++++++avgg+r+gg++++    + +  ++++i+v+++ + ++
  gi|15668912|ref|NP_247716.1|  80 IGTPVYQGNVTGQLKTLMDRCRAilAKNPKVLRGRVGMAIAVGGDRNGGQEIALRTIHDFFiINEMIPVGGGSFGAN 156
                                   *********************99**************************************88*******9998765 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   2.6e-12   1.5e-08       1     103 [.       1     100 [.       1     141 [. 0.78

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.6e-12
                                   -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----C.CCCHCCHHHHTTC.HHHHHHH.HHHHHCS CS
                  Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvltt.rdlaaklayeekp.adveseq.iekllaa 78 
                                   mk+  i ++pr     ++ + + +++ l+++g +ev+++ + +  + ++ + ++       +e++ ++ ++e+  e+l +a
  gi|15668912|ref|NP_247716.1|   1 MKVFGISGSPRL--QGTHFAVNYALNYLKEKG-AEVRYFSVSRKKINFCLHcDYC---IKKKEGCiHKDDMEEvYENLIWA 75 
                                   89999*******..45577778889*******.9*********843333331333...35666666777777778****** PP

                                   SEEEEEEE-BTTB--HHHHHHHHHH CS
                  Flavodoxin_2  79 daivlqfPlwwfgvPailKgwiDrv 103
                                   d +++++P++  +v  +lK  +Dr 
  gi|15668912|ref|NP_247716.1|  76 DGVIIGTPVYQGNVTGQLKTLMDRC 100
                                   ***********************94 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.9e-07    0.0017      26      78 ..      60     109 ..      49     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.9e-07
                  Flavodoxin_5  26 gelvdvedvekesedlesydavvigasvyygkllpelakFvekhreaLstkpv 78 
                                   ++  d+e+v    e+l ++d v+ig++vy+g++ ++l+ + ++ r+ L++ p 
  gi|15668912|ref|NP_247716.1|  60 IHKDDMEEV---YENLIWADGVIIGTPVYQGNVTGQLKTLMDRCRAILAKNPK 109
                                   566667776...599****************************9999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1200.64
//
Query:       gi|15668913|ref|NP_247717.1|  [L=393]
Description: flavoprotein FprA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-15   55.8   0.0    8.4e-15   55.2   0.0    1.3  1  Flavodoxin_1   Flavodoxin
    4.8e-11   43.0   0.0    9.8e-11   42.0   0.0    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
    8.9e-05   22.2   0.0    0.00018   21.2   0.0    1.4  1  PGM_PMM_I      Phosphoglucomutase/phosphomannomutase, alpha/b
    0.00029   21.1   0.0    0.00048   20.4   0.0    1.4  1  Flavodoxin_5   Flavodoxin domain
     0.0006   19.4   0.0     0.0012   18.4   0.0    1.6  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0052   16.5   0.1     0.0086   15.7   0.1    1.3  1  UPF0160        Uncharacterised protein family (UPF0160)


Domain annotation for each model (and alignments):
>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   2.8e-18   8.4e-15       1     142 [.     252     384 ..     252     385 .. 0.87

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 2.8e-18
                                   EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSCGGGGGTHSEEEEEEEEETTTBEEGGGH.HHHHHHHHHHCHHG CS
                  Flavodoxin_1   1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydeslseieeealllvvtsTfgnGdppenge.sffqdllelkgdel 80 
                                   i+Y++++ +t+k+A+++ae+l+e+g++++++++ + +  ls i++e+l +++++   +G+p+ n +  +++  +  ++d  
  gi|15668913|ref|NP_247717.1| 252 IVYDTMYNSTKKMAHAIAEGLMEKGVEVKIYRVCETS--LSRIMTEILDAKYVL---VGSPTVNRNlYPEVGKFLAYMDCI 327
                                   89*********************99877777777777..889999999999888...888888888888899999998766 PP

                                   CCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEES.SSEEEETTST.HGHHHHHHH CS
                  Flavodoxin_1  81 edgdlsgvrfavfglGdsayenFcaagkkldekleelGaerll.kllegdednq.egqeeafrk 142
                                   +      +    +++G++++ +  +a  k++e++++lG++++  + l++  +++ e ++++++ 
  gi|15668913|ref|NP_247717.1| 328 R-----PLDKIGVAFGSYGWME--CATEKIKEIFKNLGFKIVDdECLTVRFAPKeEHLKKCYEF 384
                                   6.....45566679********..******************9888999999999999998875 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   3.3e-14   9.8e-11       6     171 ..      36     223 ..      32     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 3.3e-14
                                   SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHH CS
                   Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmee 86 
                                    nsyli  d++++LiDt  +  ++ + +   ++ ++pkd+d++i+ H   DH G +++lve  ++ ++ +++ +++l   +
  gi|15668913|ref|NP_247717.1|  36 YNSYLI-KDKKNVLIDTAKDYMFNELIY-GISKFIDPKDLDYIIVNHVEKDHSGCVDKLVEISNATIITNEKGKEHLSLYY 114
                                   59****.8**********9999999987.77899*********************************************** PP

                                   HHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC..... CS
                   Lactamase_B  87 addaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl..... 162
                                     +++ +             ++++ ++++n g+r +  +    +h ++ +  +++++k+lf+ Da+ ++   + ++     
  gi|15668913|ref|NP_247717.1| 115 DTKDWDF-------------IIVDTGDEINIGDRTLKFIRTPMLHWPDNMLTYCKEEKILFSNDAFGQHIASSERFdyeig 182
                                   *555555.............58888899999999999999999***********************966555555555777 PP

                                   .................................TTCEEE-S CS
                   Lactamase_B 163 ................................tlrgaevrd 171
                                                                    +   ++ +
  gi|15668913|ref|NP_247717.1| 183 egifehakdyfanilmpykmlipdaikavknlDIELICPSH 223
                                   77777755555544444444444444444444444444444 PP

>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   6.2e-08   0.00018      20      93 ..     228     301 ..     222     312 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.2e-08
                                   CCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTH.HHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHHHHHCCECE CS
                     PGM_PMM_I  20 pelveklgqaiaeylkaeakkkkvvvGrDtRvss.relaealaaglaanGvevillgllptPavsfairklkada 93 
                                   +e++ ++++ + e+  ++ +k+k v+ +Dt + s +++a+a+a+gl+++Gvev ++ ++ t   + +++ l+a+ 
  gi|15668913|ref|NP_247717.1| 228 KEYINEIIEKYNEWAMNK-TKNKAVIVYDTMYNStKKMAHAIAEGLMEKGVEVKIYRVCETSLSRIMTEILDAKY 301
                                   577888888888888885.99999999***99883579***********************99999999888775 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.6e-07   0.00048       2      68 ..     252     323 ..     251     376 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.6e-07
                  Flavodoxin_5   2 ilYsSrdGqTkkiaeriaeelreegelvdvedvekese.....dlesydavvigasvyygkllpelakFvek 68 
                                   i+Y + +++Tkk a +iae l e+g +v++  v + s      ++ +++ v++g++  +++l pe+ kF+  
  gi|15668913|ref|NP_247717.1| 252 IVYDTMYNSTKKMAHAIAEGLMEKGVEVKIYRVCETSLsrimtEILDAKYVLVGSPTVNRNLYPEVGKFLAY 323
                                   9***********************77777766532222222338889999*******************874 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.9e-07    0.0012       2     116 ..      46     150 ..      45     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.9e-07
                                   EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT CS
                 Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee 82 
                                   ++LiD+  d + +   +    ++  +++++d +++ h + DH   ++ l e+++  ++++ +++  ++l+    y+ ++  
  gi|15668913|ref|NP_247717.1|  46 NVLIDTAKDYMFN--ELIYGISKFIDPKDLDYIIVNHVEKDHSGCVDKLVEISN--ATIITNEKGKEHLSLY--YDTKDW- 119
                                   8999999995544..2222334777999***************99******877..799**********999..444444. PP

                                   TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C CS
                 Lactamase_B_2  83 pavnvheldwgesfelgdggleitatparhksgr 116
                                      ++  +d+g+++ +gd  l++  tp  h+  +
  gi|15668913|ref|NP_247717.1| 120 ---DFIIVDTGDEINIGDRTLKFIRTPMLHWPDN 150
                                   ...488************9999999999999777 PP

>> UPF0160  Uncharacterised protein family (UPF0160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.9e-06    0.0086      80     148 ..     221     292 ..     184     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.9e-06
                       UPF0160  80 SSaGLvYkhfgkeiikkllkle..ldeeevellyeklyeefveaiDaiDnGisvyeevekkykikt.slssr 148
                                    S G ++k++ +eii+k+ +    +++++  ++y+ +y++  +   ai  G        k y++ + sls++
  gi|15668913|ref|NP_247717.1| 221 PSHGVIWKEYINEIIEKYNEWAmnKTKNKAVIVYDTMYNSTKKMAHAIAEGLMEKGVEVKIYRVCEtSLSRI 292
                                   589***************87777788899999****************999986654445555544366555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2425.32
//
Query:       gi|15668914|ref|NP_247718.1|  [L=121]
Description: hypothetical protein MJ_0733 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-07   30.1   0.0    5.5e-07   30.0   0.0    1.1  1  DrsE            DsrE/DsrF-like family
  ------ inclusion threshold ------
      0.049   13.6   0.1      0.084   12.8   0.1    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
      0.053   13.3   0.3       0.28   10.9   0.1    2.1  2  zinc_ribbon_5   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   9.1e-11   5.5e-07       1     115 [.       6     119 ..       6     121 .] 0.83

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 9.1e-11
                                   -EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT.....-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEE CS
                          DrsE   1 kkvfilvtggpygseaarealelalaaaalg.....hevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyv 76 
                                   +kv++l+ +  ++++    + ++ +++ a++      ev++++ g++vl+++       ++  +l+  ++++k+    ++v
  gi|15668914|ref|NP_247718.1|   6 MKVAFLIFSYFHKNQ-PNMPVMMHTLLFANElkekgDEVKIILEGEAVLWAKD----LLSENHPLKSHFEKVKDD---FVV 78 
                                   678888887777777.88888888877777788888*****************....55666699*****99999...9** PP

                                   EHHHHHHTT--GGG...E-T--EEEE-HHHHHHHHHH-SEEE CS
                          DrsE  77 Cgqaakargldede...dlgvgvevsglgelaelqnegdrvi 115
                                   C+++a  ++++e e   +l+++  + g  +l ++++ g+r+i
  gi|15668914|ref|NP_247718.1|  79 CEACASMFNVKE-EikgKLKLENDLFGHVSLKKYLDGGYRII 119
                                   ***********6.445544559999***************99 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.4e-05     0.084      15      39 ..      30      56 ..      28      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                                  CHHHCCEEC.TCEEEEEECTT.CCCCC CS
                MazE_antitoxin 15 vrfelgire.Gdevelevdgd.kiilr 39
                                  + f+++++e Gdev ++ +g+  ++ +
  gi|15668914|ref|NP_247718.1| 30 LLFANELKEkGDEVKIILEGEaVLWAK 56
                                  67999***************9888866 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.15   8.9e+02      17      27 ..      34      44 ..      31      45 .. 0.84
   2 ?   10.9   0.1   4.8e-05      0.28       4      16 ..      78      90 ..      76      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.15
                 zinc_ribbon_5 17 sklKksgkkVr 27
                                   +lK+ g  V+
  gi|15668914|ref|NP_247718.1| 34 NELKEKGDEVK 44
                                  799****9997 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.8e-05
                 zinc_ribbon_5  4 rCpdCdtkFklvd 16
                                   C++C ++F + +
  gi|15668914|ref|NP_247718.1| 78 VCEACASMFNVKE 90
                                  5********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 851.33
//
Query:       gi|15668915|ref|NP_247719.1|  [L=204]
Description: rubrerythrin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-38  130.5   8.5    6.4e-38  130.3   8.5    1.1  1  Rubrerythrin   Rubrerythrin
    2.5e-09   37.2   4.4    3.3e-09   36.8   4.4    1.1  1  Ferritin       Ferritin-like domain
    0.00024   21.1   5.3       0.02   14.9   0.9    2.1  2  DUF892         Domain of unknown function (DUF892)
     0.0027   17.7   0.4      0.017   15.1   0.1    2.0  2  HypA           Hydrogenase/urease nickel incorporation, metal
  ------ inclusion threshold ------
      0.017   14.8   0.1       0.28   10.8   0.0    2.0  2  DUF3394        Domain of unknown function (DUF3394)
      0.043   13.8   0.4      0.079   13.0   0.4    1.4  1  zf-C2HC5       Putative zinc finger motif, C2HC5-type
      0.043   13.8   2.4          1    9.5   0.0    2.4  2  Rubredoxin     Rubredoxin
        3.2    7.5   6.2        1.9    8.3   0.1    2.3  2  Rubredoxin_2   Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   8.5   2.8e-41   6.4e-38       1     137 []      15     152 ..      15     152 .. 0.99

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 2.8e-41
                                   HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGG CS
                  Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflt 80 
                                   ++L+kA++gEs ar++Y+++a+ ak egy+qiae+F+ +Ae+EreHak+l+ l+ +l+++++++ k+ +++ +e+++    
  gi|15668915|ref|NP_247719.1|  15 KNLTKAYIGESLARNRYTCYAKIAKqEGYEQIAEIFLLTAENEREHAKWLYYLITELKKKYNIDDKAIKVDGVEVPIVLGN 95 
                                   69******************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin  81 taknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkll 137
                                   ta+nL++ ieg++ e++emy++++++aekeg +e++++++++  aEk+Heer++kll
  gi|15668915|ref|NP_247719.1|  96 TAENLKASIEGEHFEHTEMYPKFADIAEKEGLKEIADRLRAIGIAEKHHEERFKKLL 152
                                   *******************************************************95 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   4.4   1.5e-12   3.3e-09       2     139 ..      15     155 ..      14     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.5e-12
                                   HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH..C-SSSSCSS CS
                      Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee..ieapkefgs 80 
                                   k L ++   e  a + y  +a  +k++g+e++ae f   ae ereha+ l+  i +l  + +++++ ++   +e p   g+
  gi|15668915|ref|NP_247719.1|  15 KNLTKAYIGESLARNRYTCYAKIAKQEGYEQIAEIFLLTAENEREHAKWLYYLITELKKKYNIDDKAIKVdgVEVPIVLGN 95 
                                   5677777789999*************************************************9999777755545555889 PP

                                   HHHHHHHHHHHHH.HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Ferritin  81 veevleaalehek.kvteslrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                   + e l+a +e e  + te++ + +++ae+eg    ad l  +   + +he+ +++ll+++
  gi|15668915|ref|NP_247719.1|  96 TAENLKASIEGEHfEHTEMYPKFADIAEKEGLKEIADRLRAIGIAEKHHEERFKKLLKEV 155
                                   999999999988658*****************************************9876 PP

>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.9   8.9e-06      0.02      90     156 ..      11      74 ..       6      76 .. 0.89
   2 !    8.3   0.2   0.00096       2.2     102     152 ..     106     154 ..      93     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.9e-06
                                   THHHHHHH...HHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DUF892  90 deslkdaaliaaaqavehyEiAsYgtLialAeqlgekeaaklLeqtleeekatdekltelaeslvnq 156
                                   +e+lk++     a+  e +   +Y++ +++A+q g++++a+++  t e+e++ +++l  l+++l ++
  gi|15668915|ref|NP_247719.1|  11 KETLKNLT---KAYIGESLARNRYTCYAKIAKQEGYEQIAEIFLLTAENEREHAKWLYYLITELKKK 74 
                                   56677777...88999999999***********************************9999887665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00096
                                   HHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DUF892 102 aqavehyEiAsYgtLialAeqlgekeaaklLeqtleeekatdekltelaes 152
                                   + ++eh E+  Y   + +Ae+ g ke+a+ L+++   ek  +e+ ++l+++
  gi|15668915|ref|NP_247719.1| 106 GEHFEHTEM--YPKFADIAEKEGLKEIADRLRAIGIAEKHHEERFKKLLKE 154
                                   445666664..*********************************9999976 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.23   5.1e+02      11      69 ..      31      89 ..      24     101 .. 0.80
   2 !   15.1   0.1   7.8e-06     0.017      32      95 ..     136     193 ..     112     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.23
                                  HHHHHHHHCCTT..EEEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE-- CS
                          HypA 11 vevveeeakeaaarkvtkvkvevGelsgvepeaLefafellaegtvlegaeLeieevpv 69
                                  ++   + ak+++ +++ ++ +   e +  + + L +  + l+++  ++++ ++++ v+v
  gi|15668915|ref|NP_247719.1| 31 YTCYAKIAKQEGYEQIAEIFLLTAENEREHAKWLYYLITELKKKYNIDDKAIKVDGVEV 89
                                  55566777888899999999999999999999999999999999888888888877665 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7.8e-06
                                   EEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                          HypA  32 evGelsgvepeaLefafellaegtvlegaeLeieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                                    +G  ++ ++e ++  ++ ++egtv++      +++pv+  Cr+Cg     +e  ++Cp+C++ 
  gi|15668915|ref|NP_247719.1| 136 AIGIAEKHHEERFKKLLKEVEEGTVFK------KDKPVEWVCRKCGFVHLGKEPPEKCPSCSHP 193
                                   567777777888888888888888887......899**********65554443678****976 PP

>> DUF3394  Domain of unknown function (DUF3394)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.072   1.6e+02     133     162 ..      37      66 ..      30      69 .. 0.88
   2 ?   10.8   0.0   0.00013      0.28      73     137 ..      96     164 ..      76     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.072
                       DUF3394 133 paekagldfdfeivevevpadrppkelvyi 162
                                    a+++g ++  ei  + ++++r + +++y 
  gi|15668915|ref|NP_247719.1|  37 IAKQEGYEQIAEIFLLTAENEREHAKWLYY 66 
                                   68899999999*********9999999985 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
                       DUF3394  73 kgselrlkvegenlegeeie.ktvalplge.eatgeerLeaaGltlleedg..kvlvdevefgspaeka 137
                                     ++l+ ++ege +e  e+  k + +  +e  ++ ++rL+a+G+   ++++  k l++eve g+  +k 
  gi|15668915|ref|NP_247719.1|  96 TAENLKASIEGEHFEHTEMYpKFADIAEKEgLKEIADRLRAIGIAEKHHEErfKKLLKEVEEGTVFKKD 164
                                   5789***********99998788888888877999*********7777766346679999999988775 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   3.5e-05     0.079      19      43 ..     170     193 ..     165     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.5e-05
                      zf-C2HC5  19 nClnCGkiiCakeglskpCsfCgsp 43 
                                    C +CG +   ke + ++C++C++p
  gi|15668915|ref|NP_247719.1| 170 VCRKCGFVHLGKEPP-EKCPSCSHP 193
                                   7**************.******986 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00045         1      21      41 ..     154     175 ..     151     180 .. 0.86
   2 ?    3.1   1.1     0.045     1e+02      36      47 .]     186     197 ..     184     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00045
                                   TB-TT--GG.GS-TT-BBTTTB CS
                    Rubredoxin  21 giapgTkFe.dlPddWvCPdCg 41 
                                   +++ gT F+ d P +WvC +Cg
  gi|15668915|ref|NP_247719.1| 154 EVEEGTVFKkDKPVEWVCRKCG 175
                                   688999995489*********8 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.045
                                   BBTTTB-BGGGE CS
                    Rubredoxin  36 vCPdCgvekeqF 47 
                                   +CP+C+ +++ F
  gi|15668915|ref|NP_247719.1| 186 KCPSCSHPRKYF 197
                                   6******99988 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00086       1.9       1      10 [.     169     178 ..     169     180 .. 0.89
   2 ?    1.1   1.8      0.15   3.3e+02      16      21 ..     186     191 ..     186     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00086
                  Rubredoxin_2   1 YvCsqCGfes 10 
                                   +vC++CGf++
  gi|15668915|ref|NP_247719.1| 169 WVCRKCGFVH 178
                                   89******87 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.15
                  Rubredoxin_2  16 rCpsCg 21 
                                   +CpsC 
  gi|15668915|ref|NP_247719.1| 186 KCPSCS 191
                                   7****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1289  (0.0718947); expected 358.6 (0.02)
Passed bias filter:                      801  (0.0446762); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1216.85
//
Query:       gi|15668916|ref|NP_247720.1|  [L=80]
Description: rubredoxin 1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-23   82.2   4.9    2.8e-23   81.7   4.9    1.2  1  Rubredoxin      Rubredoxin
     0.0012   18.9   0.7      0.014   15.5   0.7    2.4  1  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.075   12.8   3.3          3    7.7   0.1    2.4  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.16   12.9   2.1        5.9    8.0   0.2    2.5  2  zf-C2H2_4       C2H2-type zinc finger
       0.17   11.8   1.9        0.4   10.5   0.4    2.0  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO
       0.22   11.5   2.4        1.9    8.5   0.8    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.55   10.1   4.7       0.63    9.9   0.4    2.1  2  Cys_rich_CPCC   Cysteine-rich CPCC
       0.67    9.7   4.3         10    5.9   0.0    2.2  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal


Domain annotation for each model (and alignments):
>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   4.9   1.3e-26   2.8e-23       1      47 []      21      69 ..      21      69 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 1.3e-26
                                  EEEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTT..B-BGGGE CS
                    Rubredoxin  1 kyeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdC..gvekeqF 47
                                  ky+CkvCg+vYdp kGdp+++i+p+T+Fe+lPd+W+CP+C  +v+ke+F
  gi|15668916|ref|NP_247720.1| 21 KYKCKVCGWVYDPLKGDPSQNIPPKTPFEELPDTWICPVCrgKVGKESF 69
                                  7***************************************877889998 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.7   6.3e-06     0.014       5      37 ..      21      65 ..      17      67 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.3e-06
                   Zn-ribbon_8  5 eYrCeeCghefe...........vlqsisdaplta.CPeCgsevr 37
                                   Y+C+ Cg +++           +  ++ + p+t  CP C ++v 
  gi|15668916|ref|NP_247720.1| 21 KYKCKVCGWVYDplkgdpsqnipPKTPFEELPDTWiCPVCRGKVG 65
                                  4***********777775555554444445559*9*****99875 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0013         3       1      10 [.      22      31 ..      22      34 .. 0.90
   2 ?    5.4   0.6    0.0069        15      15      21 ..      55      61 ..      54      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0013
                  Rubredoxin_2  1 YvCsqCGfes 10
                                  Y C+ CG+++
  gi|15668916|ref|NP_247720.1| 22 YKCKVCGWVY 31
                                  99*****986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0069
                  Rubredoxin_2 15 GrCpsCg 21
                                  + Cp C+
  gi|15668916|ref|NP_247720.1| 55 WICPVCR 61
                                  9*****7 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0026       5.9       1      10 [.      22      31 ..      22      35 .. 0.88
   2 ?    4.3   0.1     0.042        95       2       8 ..      56      62 ..      55      69 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0026
                     zf-C2H2_4  1 fkCpiCgksF 10
                                  +kC++Cg ++
  gi|15668916|ref|NP_247720.1| 22 YKCKVCGWVY 31
                                  8*****9998 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.042
                     zf-C2H2_4  2 kCpiCgk 8 
                                  +Cp+C++
  gi|15668916|ref|NP_247720.1| 56 ICPVCRG 62
                                  7****54 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00018       0.4      10      25 ..      18      33 ..      13      37 .. 0.79
   2 ?    0.0   0.0      0.34   7.7e+02      16      19 ..      57      60 ..      47      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00018
                     zf-C2H2_3 10 sfgasqCkeCgMvYnp 25
                                   +++ +Ck+Cg vY p
  gi|15668916|ref|NP_247720.1| 18 RYRKYKCKVCGWVYDP 33
                                  566788********87 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.34
                     zf-C2H2_3 16 CkeC 19
                                  C++C
  gi|15668916|ref|NP_247720.1| 57 CPVC 60
                                  **** PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.8   0.00086       1.9      31      57 ..       8      32 ..       6      33 .. 0.78
   2 ?    2.7   0.0     0.052   1.2e+02      45      54 ..      53      62 ..      45      71 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00086
                OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfead 57
                                  C   gs  k+    r++kC+ Cg ++d
  gi|15668916|ref|NP_247720.1|  8 CKLDGSCEKP--RYRKYKCKVCGWVYD 32
                                  5555666666..99*********9987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.052
                OrfB_Zn_ribbon 45 rtfkCpnCgf 54
                                  +t+ Cp C  
  gi|15668916|ref|NP_247720.1| 53 DTWICPVCRG 62
                                  5677777754 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4   0.00028      0.63      19      32 ..      22      35 ..       7      47 .. 0.74
   2 ?    2.5   0.4     0.056   1.3e+02      19      24 ..      55      60 ..      45      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00028
                 Cys_rich_CPCC 19 diCpvCfWedDlvq 32
                                    C+vC W +D ++
  gi|15668916|ref|NP_247720.1| 22 YKCKVCGWVYDPLK 35
                                  46*********886 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.056
                 Cys_rich_CPCC 19 diCpvC 24
                                   iCpvC
  gi|15668916|ref|NP_247720.1| 55 WICPVC 60
                                  499999 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   2.5      0.02        46      37      51 ..      14      28 ..       7      31 .. 0.85
   2 ?    5.9   0.0    0.0047        10      44      51 ..      54      61 ..      41      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.02
                zinc_ribbon_10 37 keeleevkyrCpkCg 51
                                  +e++++ ky+C  Cg
  gi|15668916|ref|NP_247720.1| 14 CEKPRYRKYKCKVCG 28
                                  5789999*******9 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0047
                zinc_ribbon_10 44 kyrCpkCg 51
                                  +++Cp C+
  gi|15668916|ref|NP_247720.1| 54 TWICPVCR 61
                                  79999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 522.36
//
Query:       gi|15668917|ref|NP_247721.1|  [L=222]
Description: peroxiredoxin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-32  112.1   0.0    2.6e-32  111.3   0.0    1.4  2  AhpC-TSA    AhpC/TSA family
    6.8e-13   48.6   0.0    9.9e-13   48.0   0.0    1.1  1  Redoxin     Redoxin
    1.8e-12   46.9   0.1    3.5e-12   45.9   0.1    1.5  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
  ------ inclusion threshold ------
       0.09   12.9   0.0       0.11   12.6   0.0    1.3  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   5.8e-36   2.6e-32       1     123 [.       9     140 ..       9     141 .. 0.97
   2 ?   -3.6   0.0       2.2   9.9e+03      91     111 ..     155     174 ..     152     176 .. 0.59

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 5.8e-36
                                   TTSB----EEESTTCEEEECHHH...TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHH CS
                      AhpC-TSA   1 vgdkapdfelknadgetvslsdy...kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfie 78 
                                   +g+k+p++e+k+++ + ++l dy   kgk+ vlf +p+d++pvCtte   ++k+y+ef++++ e+ig+s+d+++sh k++e
  gi|15668917|ref|NP_247721.1|   9 IGEKFPEVEVKTTH-GAIKLPDYyveKGKWFVLFSHPADFTPVCTTEFVGFQKRYDEFRKLNTELIGLSIDQVFSHLKWVE 88 
                                   89*********999.99********999***************************************************** PP

                                   H-H.......SSEEEE-TTSHHHHHTT-EETT.TTECSCEEEEE-TTSBEEE CS
                      AhpC-TSA  79 kes......lnfpllsDeegkvakaygvlkee.kglalratfvidkegkiry 123
                                    ++      ++fp+++D  g++a+++g++ +   + ++ra+fv+d++g+ir+
  gi|15668917|ref|NP_247721.1|  89 WIKeklnveIEFPIIADDRGELAEKLGMISPYkGNNTVRAVFVVDNKGIIRA 140
                                   *****************************87778899*************97 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.2
                                   TSHHHHHTT-EETTTTECSCE CS
                      AhpC-TSA  91 egkvakaygvlkeekglalra 111
                                      ++ka++v +e+ g+a++a
  gi|15668917|ref|NP_247721.1| 155 IVRLVKALQVSDEK-GVAMPA 174
                                   45566677777554.666665 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   2.2e-16   9.9e-13       3     138 ..      10     149 ..       9     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 2.2e-16
                                   TSBB---ECCEETTCEEEEEHHH...HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH...HH CS
                       Redoxin   3 gdkaPdftlplaatdgnsvslse...fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf...vk 77 
                                   g+k+P+++    +t   +++l +    kgk  v+++ p+ f+P+C++e + ++k ++++++ + + +++++d+        
  gi|15668917|ref|NP_247721.1|  10 GEKFPEVEV---KTTHGAIKLPDyyvEKGKWFVLFSHPADFTPVCTTEFVGFQKRYDEFRKLNTELIGLSIDQVFShlkWV 87 
                                   789999884...4566667777765579999*******************999998999************9988866655 PP

                                   HHHHH...TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT CS
                       Redoxin  78 efwgk...eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet 138
                                   e++++    ++ fp+++D  ++++++lG+  +  ++++   ++++v+d +g ++++++ p +++
  gi|15668917|ref|NP_247721.1|  88 EWIKEklnVEIEFPIIADDRGELAEKLGMI-SPYKGNN-TVRAVFVVDNKGIIRAIIYYPQEVG 149
                                   55555798777*****************55.5555555.9****************99988764 PP

>> 1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.1   7.9e-16   3.5e-12       1      36 [.     161     200 ..     161     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 7.9e-16
                                   HHHHHHHHT-BB-TTT.T.....BT-EEE---SSHHHHHHH CS
                    1-cysPrx_C   1 ALQladkhgvatPAnWkp.....GdkvivpPpateedavkr 36 
                                   ALQ++d++gva PAnW p     Gdkvi+pP+++ e++++r
  gi|15668917|ref|NP_247721.1| 161 ALQVSDEKGVAMPANW-PendliGDKVIIPPASSVEEIKQR 200
                                   9***************.88******************9887 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.5e-05      0.11       3      54 ..      59     117 ..      57     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
                    AhpC-TSA_2   3 srdkpeldaagvklvaigigdp.sakkFvkl......tgfpfelyvDpsaklyqalglk 54 
                                   +++ +e+++ +++l++ +i+++ s  k+v+       +++ f++++D  ++l ++lg+ 
  gi|15668917|ref|NP_247721.1|  59 QKRYDEFRKLNTELIGLSIDQVfSHLKWVEWikeklnVEIEFPIIADDRGELAEKLGMI 117
                                   77889*****************995555543444888999*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1606.18
//
Query:       gi|15668918|ref|NP_247722.1|  [L=61]
Description: rubredoxin-like non-heme iron protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0031   17.6   6.3     0.0031   17.6   6.3    2.0  2  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.011   15.6   0.1    2.5  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.02   14.9   3.8       0.02   14.9   3.8    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.021   14.7   8.6      0.089   12.7   0.2    2.5  2  HalOD2          Halobacterial output domain 2
      0.021   14.8  10.1      0.037   14.1  10.1    1.4  1  DZR             Double zinc ribbon
      0.039   13.5   9.9        0.9    9.1   0.0    2.7  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.043   13.2  13.3        1.7    8.1   0.2    2.7  2  zf-ribbon_3     zinc-ribbon domain
      0.045   13.9   0.6      0.045   13.9   0.6    3.0  2  UPF0547         Uncharacterised protein family UPF0547
        0.1   12.4  10.4       0.33   10.7   0.5    3.0  3  Rubredoxin_2    Rubredoxin metal binding domain
        0.1   12.5   8.3        1.4    8.9   7.0    2.3  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.18   12.0   7.9        1.7    8.9   4.6    2.6  2  Fer4_2          4Fe-4S binding domain
       0.42   11.0  10.8        3.1    8.2   9.9    2.5  2  DUF4379         Probable Zinc-ribbon domain
        0.5    9.1   5.9       0.53    9.0   5.9    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.75   10.5   8.7       0.93   10.2   2.6    2.5  3  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
       0.79    9.5  16.3        1.8    8.4   3.6    3.2  3  zinc_ribbon_2   zinc-ribbon domain
       0.86    9.4   0.1       0.86    9.4   0.1    2.6  3  zinc_ribbon_5   zinc-ribbon domain
        1.3    9.0   7.5       0.66   10.0   5.0    1.9  2  ADK_lid         Adenylate kinase, active site lid
        1.5    8.8   9.4        0.8    9.6   0.5    2.2  2  C1_1            Phorbol esters/diacylglycerol binding domain 
        1.6    9.3   0.1        1.6    9.3   0.1    2.7  2  zf-H2C2_2       Zinc-finger double domain
        3.2    7.4  10.0         21    4.8   0.1    2.3  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
        3.2    7.7  12.2       0.75    9.8   0.4    2.8  3  zinc_ribbon_4   zinc-ribbon domain
        4.7    7.7   7.3        3.1    8.3   2.2    2.1  2  DUF983          Protein of unknown function (DUF983)
        5.3    7.1  11.9         30    4.7   3.1    3.2  3  Ogr_Delta       Ogr/Delta-like zinc finger
        6.2    7.1   8.0        8.9    6.6   8.0    1.5  1  DUF2072         Zn-ribbon containing protein
        8.9    6.3  10.3         13    5.8   2.1    2.8  3  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
        9.1    6.4  12.3        6.5    6.8   4.7    2.4  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   6.3   4.5e-06    0.0031       7      35 ..       5      28 ..       4      30 .. 0.81
   2 ?   -0.9   0.3       2.7   1.9e+03      30      33 ..      39      42 ..      31      45 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.5e-06
                   Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgse 35
                                  +C +Cg +fe+      +p++ CP+Cg++
  gi|15668918|ref|NP_247722.1|  5 KCSNCGYVFEAE-----KPPERCPNCGEK 28
                                  8*********54.....45677*****86 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.7
                   Zn-ribbon_8 30 PeCg 33
                                  PeCg
  gi|15668918|ref|NP_247722.1| 39 PECG 42
                                  4554 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1   1.5e-05     0.011      23      35 ..       5      17 ..       3      18 .. 0.86
   2 ?    0.4   1.5      0.87     6e+02       4       8 ..      22      26 ..      21      27 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                                  EESSSS-EEESSC CS
                RNA_POL_M_15KD 23 eCrqCgYeepadq 35
                                   C++CgY+++a++
  gi|15668918|ref|NP_247722.1|  5 KCSNCGYVFEAEK 17
                                  4**********96 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.87
                                  ESTTT CS
                RNA_POL_M_15KD  4 CpkCg 8 
                                  Cp Cg
  gi|15668918|ref|NP_247722.1| 22 CPNCG 26
                                  99998 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   3.8   2.9e-05      0.02      71      95 ..       4      28 ..       2      35 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-05
                                  EEETTTS-EEECHHHHHS-TTTSSS CS
                          HypA 71 vrCreCgkefeleekalrCpkCgsa 95
                                   +C++Cg+ fe e+  +rCp+Cg++
  gi|15668918|ref|NP_247722.1|  4 WKCSNCGYVFEAEKPPERCPNCGEK 28
                                  58*********9875679*****86 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   0.00013     0.089      32      46 ..       4      18 ..       2      20 .. 0.86
   2 ?    5.3   3.7     0.027        19       2      13 ..      19      30 ..      18      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                        HalOD2 32 WkCtrCGevqaaAdp 46
                                  WkC++CG v  a +p
  gi|15668918|ref|NP_247722.1|  4 WKCSNCGYVFEAEKP 18
                                  ********9988665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.027
                        HalOD2  2 PekCseCsldWt 13
                                  Pe+C++C+ + t
  gi|15668918|ref|NP_247722.1| 19 PERCPNCGEKCT 30
                                  99*****98765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1  10.1   5.3e-05     0.037      15      49 .]       6      42 ..       4      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.3e-05
                           DZR 15 CseCgtklkavaaedrCpsCgekvdpearfC..peCG 49
                                  Cs+Cg   +a++ ++rCp+Cgek++  +  C  peCG
  gi|15668918|ref|NP_247722.1|  6 CSNCGYVFEAEKPPERCPNCGEKCTFYDVSCytPECG 42
                                  *********9999***********9999888556776 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0013       0.9      22      32 ..       6      16 ..       5      21 .. 0.86
   2 ?    5.2   7.0     0.021        15       2      14 ..      21      33 ..      20      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                                  ESSSSBEEEEC CS
                  TF_Zn_Ribbon 22 CtdCGlVledn 32
                                  C++CG+V e +
  gi|15668918|ref|NP_247722.1|  6 CSNCGYVFEAE 16
                                  *******9976 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.021
                                  EETTTTCEECHEE CS
                  TF_Zn_Ribbon  2 kCPnCgstnlveD 14
                                  +CPnCg + + +D
  gi|15668918|ref|NP_247722.1| 21 RCPNCGEKCTFYD 33
                                  6******998888 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.2    0.0025       1.7      18      25 ..       5      12 ..       3      13 .. 0.75
   2 ?    7.3   8.0    0.0045       3.1       4      24 ..      21      43 ..      20      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0025
                   zf-ribbon_3 18 vCpyCGtk 25
                                  +C +CG++
  gi|15668918|ref|NP_247722.1|  5 KCSNCGYV 12
                                  58888886 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0045
                   zf-ribbon_3  4 rCPnCGaplssddnvC..pyCGt 24
                                  rCPnCG++ +  d+ C  p CG 
  gi|15668918|ref|NP_247722.1| 21 RCPNCGEKCTFYDVSCytPECGF 43
                                  8******7799999996666775 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   6.5e-05     0.045      16      26 .]       5      15 ..       4      15 .. 0.92
   2 ?    1.0  10.0      0.67   4.6e+02       2      22 ..      21      43 ..      20      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-05
                       UPF0547 16 fCphCGyvFqa 26
                                  +C+ CGyvF+a
  gi|15668918|ref|NP_247722.1|  5 KCSNCGYVFEA 15
                                  7********96 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.67
                       UPF0547  2 vCPeCeakvPvaaqfC..phCGy 22
                                  +CP C +k     ++C  p+CG+
  gi|15668918|ref|NP_247722.1| 21 RCPNCGEKCTFYDVSCytPECGF 43
                                  699999999999999*******9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5   0.00047      0.33       1      10 [.       4      13 ..       3      15 .. 0.80
   2 ?    5.8   1.4     0.016        11      16      22 ..      21      27 ..      21      27 .. 0.86
   3 ?    0.4   0.0      0.83   5.7e+02       5       9 ..      40      44 ..      39      47 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00047
                  Rubredoxin_2  1 YvCsqCGfes 10
                                  + Cs+CG+++
  gi|15668918|ref|NP_247722.1|  4 WKCSNCGYVF 13
                                  6799999975 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.016
                  Rubredoxin_2 16 rCpsCgs 22
                                  rCp+Cg+
  gi|15668918|ref|NP_247722.1| 21 RCPNCGE 27
                                  8999996 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.83
                  Rubredoxin_2  5 qCGfe 9 
                                  +CGf+
  gi|15668918|ref|NP_247722.1| 40 ECGFK 44
                                  69986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   7.0     0.002       1.4      30      56 ..       5      29 ..       4      37 .. 0.91
   2 ?    2.2   0.0      0.24   1.7e+02      28      41 ..      35      49 ..      30      58 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfea 56
                                  +Cs+Cg++ +   ++   +CpnCg ++
  gi|15668918|ref|NP_247722.1|  5 KCSNCGYVFEA--EKPPERCPNCGEKC 29
                                  7**********..999999*****985 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.24
                OrfB_Zn_ribbon 28 SktCseCgsknke.a 41
                                  S   +eCg k+++ +
  gi|15668918|ref|NP_247722.1| 35 SCYTPECGFKGYDpK 49
                                  555688998887743 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.088        61       9      14 ..       5      10 ..       2      12 .. 0.87
   2 ?    8.9   4.6    0.0025       1.7       6      18 ..      18      31 ..      13      41 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.088
                        Fer4_2  9 rCigCg 14
                                  +C +Cg
  gi|15668918|ref|NP_247722.1|  5 KCSNCG 10
                                  799998 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0025
                        Fer4_2  6 dtdrCigCg.aCvs 18
                                   ++rC +Cg +C+ 
  gi|15668918|ref|NP_247722.1| 18 PPERCPNCGeKCTF 31
                                  689*****99**83 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   9.9    0.0045       3.1      29      56 .]       3      25 ..       1      30 [. 0.74
   2 ?    0.8   2.1      0.97   6.7e+02      31      37 ..      21      27 ..      21      60 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0045
                       DUF4379 29 wWkCakCgheWeasvsnrtkgsskCpkC 56
                                  wWkC++Cg+ +ea+          Cp C
  gi|15668918|ref|NP_247722.1|  3 WWKCSNCGYVFEAEKPPER-----CPNC 25
                                  ***********99644333.....4444 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.97
                       DUF4379 31 kCakCgh 37
                                  +C++Cg+
  gi|15668918|ref|NP_247722.1| 21 RCPNCGE 27
                                  5777775 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.9   0.00077      0.53     509     533 ..       5      31 ..       2      46 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00077
                                   EETT.--..EESS..SB-TTT--BE.EEE CS
                          NRDD 509 vCnecgy..kgei..ekCpkCgseeevev 533
                                    C +cgy  + e+  e+Cp+Cg  e+++ 
  gi|15668918|ref|NP_247722.1|   5 KCSNCGYvfEAEKppERCPNCG--EKCTF 31 
                                   5******6555559999*****..44443 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.14        94       3       9 ..       4      10 ..       2      15 .. 0.77
   2 ?   10.2   2.6    0.0013      0.93       2      15 ..      19      33 ..      18      38 .. 0.83
   3 ?   -2.0   0.0       8.5   5.9e+03       6      10 ..      39      43 ..      39      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.14
                       zf-ISL3  3 hrCPnCg 9 
                                  ++C nCg
  gi|15668918|ref|NP_247722.1|  4 WKCSNCG 10
                                  5688887 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0013
                       zf-ISL3  2 phrCPnCgsk.tvvk 15
                                  p rCPnCg+k t ++
  gi|15668918|ref|NP_247722.1| 19 PERCPNCGEKcTFYD 33
                                  789******977665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 8.5
                       zf-ISL3  6 PnCgs 10
                                  P+Cg 
  gi|15668918|ref|NP_247722.1| 39 PECGF 43
                                  88985 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.8     0.005       3.4       1       7 [.       5      11 ..       5      12 .. 0.70
   2 ?    8.4   3.6    0.0026       1.8       1       8 [.      21      28 ..      21      31 .. 0.82
   3 ?    1.4   0.2      0.41   2.8e+02      17      22 ..      39      44 ..      39      45 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.005
                 zinc_ribbon_2  1 fCpnCGa 7 
                                  +C+nCG+
  gi|15668918|ref|NP_247722.1|  5 KCSNCGY 11
                                  6888874 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0026
                 zinc_ribbon_2  1 fCpnCGae 8 
                                  +CpnCG++
  gi|15668918|ref|NP_247722.1| 21 RCPNCGEK 28
                                  69999987 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.41
                 zinc_ribbon_2 17 pyCGtp 22
                                  p+CG++
  gi|15668918|ref|NP_247722.1| 39 PECGFK 44
                                  567765 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0012      0.86      25      37 .]       3      15 ..       2      15 .. 0.91
   2 ?    3.3   1.2       0.1        69       4      10 ..      21      27 ..      20      32 .. 0.82
   3 ?   -2.3   0.1       5.7   3.9e+03       6       9 ..      39      42 ..      34      44 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0012
                 zinc_ribbon_5 25 kVrCakCaevFda 37
                                  + +C  C+ vF a
  gi|15668918|ref|NP_247722.1|  3 WWKCSNCGYVFEA 15
                                  78*********87 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.1
                 zinc_ribbon_5  4 rCpdCdt 10
                                  rCp+C+ 
  gi|15668918|ref|NP_247722.1| 21 RCPNCGE 27
                                  7999985 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.7
                 zinc_ribbon_5  6 pdCd 9 
                                  p+C+
  gi|15668918|ref|NP_247722.1| 39 PECG 42
                                  6675 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.0   0.00095      0.66       2      30 ..       4      28 ..       4      31 .. 0.85
   2 ?   -1.9   0.0       4.9   3.4e+03       7       8 ..      41      42 ..      36      58 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00095
                                  EE-TTT--EEETTTB--SSTTB-TTT--. CS
                       ADK_lid  2 rvCpkCGrsYhvvfnpPkveglCDkCGep 30
                                  + C++CG ++  + +p   +  C +CGe+
  gi|15668918|ref|NP_247722.1|  4 WKCSNCGYVFE-AEKP---PERCPNCGEK 28
                                  77*********.6645...589*****96 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.9
                                  T- CS
                       ADK_lid  7 CG 8 
                                  CG
  gi|15668918|ref|NP_247722.1| 41 CG 42
                                  54 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.5    0.0012       0.8      27      38 ..       2      13 ..       1      16 [. 0.87
   2 ?    4.2   2.4     0.056        39      10      26 ..      18      31 ..      13      45 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                                  -EEEETTT--EE CS
                          C1_1 27 qglkCswCkllv 38
                                  +++kCs+C++++
  gi|15668918|ref|NP_247722.1|  2 PWWKCSNCGYVF 13
                                  79*******987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.056
                                  S--B-TTT-SB--SSSS CS
                          C1_1 10 qptfCkhCgeflwgkek 26
                                   p +C  Cge +    +
  gi|15668918|ref|NP_247722.1| 18 PPERCPNCGEKC---TF 31
                                  688999999999...33 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0023       1.6      15      24 ..       4      13 ..       1      15 [. 0.87
   2 ?    2.5   2.1      0.34   2.3e+02      16      23 ..      21      28 ..      16      31 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0023
                     zf-H2C2_2 15 yeCplCdkaF 24
                                  ++C+ C+++F
  gi|15668918|ref|NP_247722.1|  4 WKCSNCGYVF 13
                                  79*******9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.34
                     zf-H2C2_2 16 eCplCdka 23
                                   Cp C+ +
  gi|15668918|ref|NP_247722.1| 21 RCPNCGEK 28
                                  6****976 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.031        21      12      17 ..       5      10 ..       4      17 .. 0.77
   2 ?    4.6   5.8     0.037        26      12      33 ..      21      42 ..      20      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.031
                       zf-tcix 12 kCpkCG 17
                                  kC++CG
  gi|15668918|ref|NP_247722.1|  5 KCSNCG 10
                                  788888 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.037
                       zf-tcix 12 kCpkCGtyNGtRglsCkNkaCd 33
                                  +Cp+CG  +     sC  ++C 
  gi|15668918|ref|NP_247722.1| 21 RCPNCGEKCTFYDVSCYTPECG 42
                                  6********9999999998886 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4    0.0011      0.75      27      35 ..       5      13 ..       3      14 .. 0.90
   2 ?    4.3   2.3     0.054        38      27      33 ..      21      27 ..      21      31 .. 0.64
   3 ?   -1.3   0.1       3.1   2.2e+03       6      11 ..      39      44 ..      33      45 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                 zinc_ribbon_4 27 rCskCghvF 35
                                  +Cs+Cg vF
  gi|15668918|ref|NP_247722.1|  5 KCSNCGYVF 13
                                  8*******9 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.054
                 zinc_ribbon_4 27 rCskCgh 33
                                  rC++Cg+
  gi|15668918|ref|NP_247722.1| 21 RCPNCGE 27
                                  5666664 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.1
                 zinc_ribbon_4  6 psCkak 11
                                  p+C++k
  gi|15668918|ref|NP_247722.1| 39 PECGFK 44
                                  677765 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2      0.19   1.3e+02      10      21 ..       5      16 ..       3      19 .. 0.84
   2 ?    8.3   2.2    0.0044       3.1       6      24 ..      17      35 ..      16      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.19
                        DUF983 10 aCeaCgldlsha 21
                                  +C++Cg  ++++
  gi|15668918|ref|NP_247722.1|  5 KCSNCGYVFEAE 16
                                  7*****999876 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0044
                        DUF983  6 kvadaCeaCgldlsharad 24
                                  k  ++C++Cg++ ++++  
  gi|15668918|ref|NP_247722.1| 17 KPPERCPNCGEKCTFYDVS 35
                                  5679**********99875 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.086        59      28      39 ..       6      15 ..       4      17 .. 0.72
   2 ?    4.7   3.1     0.044        30       1       8 [.      21      28 ..      21      32 .. 0.87
   3 ?    3.4   0.7      0.11        75      26      36 ..      34      44 ..      28      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.086
                     Ogr_Delta 28 CsnfeCgatfva 39
                                  Csn  Cg+ f a
  gi|15668918|ref|NP_247722.1|  6 CSN--CGYVFEA 15
                                  777..8888765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.044
                     Ogr_Delta  1 rCPhCgap 8 
                                  rCP+Cg++
  gi|15668918|ref|NP_247722.1| 21 RCPNCGEK 28
                                  7*****97 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.11
                     Ogr_Delta 26 yqCsnfeCgat 36
                                   +C  +eCg++
  gi|15668918|ref|NP_247722.1| 34 VSCYTPECGFK 44
                                  799*****986 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   8.0     0.013       8.9       3      32 ..       5      32 ..       3      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
                       DUF2072  3 kCtkCekvfedgskeilkGCpsCGgkkFly 32
                                  kC +C+ vfe  +    + Cp+CG k   y
  gi|15668918|ref|NP_247722.1|  5 KCSNCGYVFEAEKP--PERCPNCGEKCTFY 32
                                  8*********9988..899*****986554 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.025        17      13      21 ..       5      13 ..       5      16 .. 0.87
   2 ?    5.8   2.1     0.019        13      26      33 ..      20      27 ..      18      31 .. 0.68
   3 ?   -1.3   0.2       3.1   2.1e+03      28      32 ..      36      42 ..      34      43 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.025
                       DUF35_N 13 rCpdCGtvq 21
                                  +C++CG v+
  gi|15668918|ref|NP_247722.1|  5 KCSNCGYVF 13
                                  7*****885 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.019
                       DUF35_N 26 avCphCgs 33
                                    Cp+Cg 
  gi|15668918|ref|NP_247722.1| 20 ERCPNCGE 27
                                  56888875 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.1
                       DUF35_N 28 C..phCg 32
                                  C  p Cg
  gi|15668918|ref|NP_247722.1| 36 CytPECG 42
                                  7778886 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.9     0.063        43      38      45 ..       4      11 ..       3      12 .. 0.85
   2 ?    6.8   4.7    0.0094       6.5      20      33 ..      21      35 ..      13      44 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.063
                 Zn_Tnp_IS1595 38 fqCkeCrk 45
                                  ++C+ C++
  gi|15668918|ref|NP_247722.1|  4 WKCSNCGY 11
                                  99999987 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0094
                 Zn_Tnp_IS1595 20 vCPhCgsr.kayrik 33
                                  +CP+Cg + ++y ++
  gi|15668918|ref|NP_247722.1| 21 RCPNCGEKcTFYDVS 35
                                  6*****999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 421.98
//
Query:       gi|15668919|ref|NP_247723.1|  [L=90]
Description: hypothetical protein MJ_0738 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-20   72.5   0.3    2.3e-20   72.1   0.3    1.2  1  MTH865    MTH865-like family


Domain annotation for each model (and alignments):
>> MTH865  MTH865-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.3   1.3e-24   2.3e-20       1      69 [.      18      83 ..      18      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 1.3e-24
                                  HHHHHHHHHHTTSS.STTBHHHHHHHH-TTSS-----BTTB---TTTTGGGS-GGGSB-SHHHHHHHHHH CS
                        MTH865  1 elkeqivealegad.FPikspeeLlaalPkGaettceagdvevtagelgkklkdsdFPyksaedladdiv 69
                                  e+k ++ve+++++d FPik++ eL++alP+G +  c     e++a el+k+l+d+dFP+k++edla +++
  gi|15668919|ref|NP_247723.1| 18 EFKLRLVEYFKDKDvFPIKNKVELAEALPCGISLPC----GEIEAAELVKLLTDNDFPIKDPEDLAMKLA 83
                                  68999*******************************....9*************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 631.54
//
Query:       gi|15668920|ref|NP_247724.1|  [L=151]
Description: hypothetical protein MJ_0739 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-18   65.5   1.4    4.4e-18   65.0   1.4    1.2  1  V4R            V4R domain
    9.3e-10   38.5   0.1    1.2e-09   38.2   0.1    1.1  1  DUF2507        Protein of unknown function (DUF2507)
      0.001   18.3   0.0     0.0015   17.7   0.0    1.3  1  MAAL_C         Methylaspartate ammonia-lyase C-terminus
      0.009   16.3   0.1      0.014   15.6   0.1    1.3  1  MSV199         MSV199 domain
  ------ inclusion threshold ------
       0.06   14.1   2.2       0.14   12.9   2.2    1.8  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola
      0.097   12.5   0.1       0.23   11.3   0.0    1.7  2  TusA           Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   1.4   1.5e-21   4.4e-18       2      62 .]      89     148 ..      88     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 1.5e-21
                                   -EEEEEES-S-TT---SS---HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEEEEE CS
                           V4R   2 elsieespelaglpgkeePvCyleaGllagalsellgkrveveEveCaaeGhdhCeFevep 62 
                                   e+++++++++++  ++eeP+C +eaGl+ag+l+ + +k++ v+E+ C+a+G+d+C+F+++p
  gi|15668920|ref|NP_247724.1|  89 EIKVKDCIFCRT-QKSEEPMCDFEAGLIAGFLESIKNKKYFVKEMYCQAQGYDACVFIAKP 148
                                   899*********.8********************************************986 PP

>> DUF2507  Protein of unknown function (DUF2507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.1   3.9e-13   1.2e-09      18     109 ..      43     131 ..      32     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 3.9e-13
                       DUF2507  18 edeeeilYwaGkelArkfplesledlieffekagwGtLellkekkkelefeLsgeiveerlkekeekefqLEaGflAeqie 98 
                                   +d  + lY +G e+ r ++ +s+ed+ +ffe  + G +e++++ + e+e + +  i+  r++++ee+   +EaG++A  +e
  gi|15668920|ref|NP_247724.1|  43 SD--TTLYEIGYEVGRLVSPKSYEDIKKFFEANNIGYIEIKEKDNGEVEIKVKDCIFC-RTQKSEEPMCDFEAGLIAGFLE 120
                                   44..679********************************************9877666.78889*************9999 PP

                       DUF2507  99 qqkevvaeake 109
                                   + k++ +  ke
  gi|15668920|ref|NP_247724.1| 121 SIKNKKYFVKE 131
                                   99887766554 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.1e-07    0.0015     150     189 ..      62     101 ..      35     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.1e-07
                        MAAL_C 150 tledirefvdaeaadlvqiktPDlGginntieavlyckek 189
                                   ++edi++f +a+   ++ ik  D+G ++  ++ +++c+++
  gi|15668920|ref|NP_247724.1|  62 SYEDIKKFFEANNIGYIEIKEKDNGEVEIKVKDCIFCRTQ 101
                                   68***********************************976 PP

>> MSV199  MSV199 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.7e-06     0.014      22      74 ..      31      86 ..      11      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.7e-06
                        MSV199 22 wqplvdkkdvlitneiLeflgy.eGeykkqk..kkfkklLkrnnieykelkykdee 74
                                   + +++k + l ++++L+ +gy  G++ + k  +++kk+ + nni y+e+k+kd+ 
  gi|15668920|ref|NP_247724.1| 31 IYAYMQKVKDLGSDTTLYEIGYeVGRLVSPKsyEDIKKFFEANNIGYIEIKEKDNG 86
                                  567788888888999999****7797665442289****************99985 PP

>> ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.2   4.7e-05      0.14      53     102 ..      62     104 ..      19     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-05
                 ATC_hydrolase  53 dkadvekflalyseifekenalkf.evleedkdeleidvtrCpyceawkke 102
                                   + +d++       ++fe+ n+++  e++e+d++e+ei+v+ C +c++ k e
  gi|15668920|ref|NP_247724.1|  62 SYEDIK-------KFFEA-NNIGYiEIKEKDNGEVEIKVKDCIFCRTQKSE 104
                                   334444.......44444.4444449*******************987765 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.6e-05      0.23      36      69 ..      59      93 ..      54      94 .. 0.88
   2 ?   -2.7   0.0       1.9   5.6e+03      46      53 ..     133     140 ..     131     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.6e-05
                                  SCHHHHHHHHHHHHHTEEEEEEE-.GCC-EEEEEE CS
                          TusA 36 dpaatediprfakklghelvevee.edgeyrivir 69
                                   p + edi++f + ++  ++e++e ++ge++i ++
  gi|15668920|ref|NP_247724.1| 59 SPKSYEDIKKFFEANNIGYIEIKEkDNGEVEIKVK 93
                                  5899*************999999955599999886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.9
                                   HHHHHTEE CS
                          TusA  46 fakklghe 53 
                                   +++ +g++
  gi|15668920|ref|NP_247724.1| 133 YCQAQGYD 140
                                   89999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1155.15
//
Query:       gi|15668921|ref|NP_247725.1|  [L=55]
Description: rubredoxin 2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-23   81.5   3.7    3.4e-23   81.4   3.7    1.0  1  Rubredoxin      Rubredoxin
  ------ inclusion threshold ------
        0.3   11.0   1.9        2.5    8.1   0.1    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   3.7   3.8e-27   3.4e-23       1      47 []       6      51 ..       6      51 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 3.8e-27
                                  EEEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                    Rubredoxin  1 kyeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47
                                  +y+C +Cg+vYd++kG+p+++i+pgTkFedlPd+++CP+Cg++k++F
  gi|15668921|ref|NP_247725.1|  6 RYQC-MCGWVYDEDKGEPSQNIPPGTKFEDLPDTFRCPQCGLGKNAF 51
                                  79**.9***************************************99 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2    0.0093        83      45      59 ..       5      18 ..       2      26 .. 0.87
   2 ?    8.1   0.1   0.00028       2.5      43      57 ..      35      49 ..      21      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0093
                OrfB_Zn_ribbon 45 rtfkCpnCgfeadrD 59
                                   +++C  Cg ++d D
  gi|15668921|ref|NP_247725.1|  5 ARYQCM-CGWVYDED 18
                                  5799*9.****9988 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00028
                OrfB_Zn_ribbon 43 sgrtfkCpnCgfead 57
                                   ++tf+Cp+Cg+  +
  gi|15668921|ref|NP_247725.1| 35 LPDTFRCPQCGLGKN 49
                                  5789******98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 376.42
//
Query:       gi|15668922|ref|NP_247726.1|  [L=116]
Description: desulfoferrodoxin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-31  108.9   0.2    1.7e-31  108.6   0.2    1.1  1  Desulfoferrodox  Desulfoferrodoxin


Domain annotation for each model (and alignments):
>> Desulfoferrodox  Desulfoferrodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.6   0.2   9.7e-36   1.7e-31       2      95 ..      13     109 ..      12     110 .. 0.95

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 9.7e-36
                                   SHTTTHTTSEEEEEESEEEETTEEEEEEEESSSS--BSSSS-EEEEEEEEEETTSSEEEE-TBSESEEEEEEEESSS.... CS
               Desulfoferrodox   2 adekeekHvPvieadevvkagelfevkvkvgkipHpneeeHyIewielyleeegekrvelsaedepevtftvklkke.... 78 
                                    ++ e+kH+P+ie+++ vka+++fevk+++g ipHp+e++H+I+wiely+++   +rv++++  +pev+++vk+ ++    
  gi|15668922|ref|NP_247726.1|  13 GTDFEKKHTPFIECKDRVKANDYFEVKISTG-IPHPMEDNHFIHWIELYMGDLYLARVDFTQFMKPEVKLMVKAPSKehek 92 
                                   57899**************************.****************************************998877887 PP

                                   EEEEEEEEETTTEEEEE CS
               Desulfoferrodox  79 kklvalsyCnlHGlWes 95 
                                     l+al+ CnlHG+We+
  gi|15668922|ref|NP_247726.1|  93 FILRALMRCNLHGVWEY 109
                                   89*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 756.57
//
Query:       gi|15668923|ref|NP_247727.1|  [L=104]
Description: hypothetical protein MJ_0742 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-12   47.6   0.0    1.4e-12   47.4   0.0    1.0  1  CMD       Carboxymuconolactone decarboxylase family
    0.00049   20.0   0.8     0.0011   19.0   0.8    1.7  1  NAC       NAC domain
  ------ inclusion threshold ------
      0.075   12.8   0.1       0.16   11.8   0.1    1.5  1  WIYLD     Ubiquitin-binding WIYLD domain
      0.088   12.8   0.0       0.11   12.5   0.0    1.2  1  DUF2095   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   3.2e-16   1.4e-12       1      84 [.      19     102 ..      19     103 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 3.2e-16
                                   HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHH.HTT--HHHHHHHHHHHHHHHSHHHHHHHH CS
                           CMD   1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAl.eaGvteeeiaevlaqaaayagwpaaraAl 80 
                                   p+l++ +++l++ ++  +  Ld k++ Lia+++ a++  e  +   ++ A+ e G t+eeia+vl++   ++g+pa+++A+
  gi|15668923|ref|NP_247727.1|  19 PDLYDIIVKLNDTVFT-GKTLDYKTQKLIAIGIVASRCDEVAIEKQMKSAMkELGITKEEIADVLRVVLLTSGMPAFTKAM 98 
                                   899************9.999*************9999999988999999999***************************** PP

                                   HHHH CS
                           CMD  81 aaae 84 
                                   +++e
  gi|15668923|ref|NP_247727.1|  99 KILE 102
                                   *997 PP

>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.8   2.4e-07    0.0011       1      28 [.      61      90 ..      61     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.4e-07
                           NAC  1 ekKlrkalkklgl..keipgieeVtirksd 28
                                  ek+++ a+k lg+  +ei+++ +V++ +s+
  gi|15668923|ref|NP_247727.1| 61 EKQMKSAMKELGItkEEIADVLRVVLLTSG 90
                                  8************************98875 PP

>> WIYLD  Ubiquitin-binding WIYLD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.6e-05      0.16      14      33 ..      67      86 ..      61      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                         WIYLD 14 amkelGfskeqvrpvlkkLL 33
                                  amkelG++ke++  vl+ +L
  gi|15668923|ref|NP_247727.1| 67 AMKELGITKEEIADVLRVVL 86
                                  8***************9877 PP

>> DUF2095  Uncharacterized protein conserved in archaea (DUF2095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.4e-05      0.11      73     115 ..      53      95 ..      28     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                       DUF2095  73 rrcetdeealeiinwmeergeithemakelrvvlvkkgvrafg 115
                                    rc+      ++   m+e g   +e+a  lrvvl   g+ af 
  gi|15668923|ref|NP_247727.1|  53 SRCDEVAIEKQMKSAMKELGITKEEIADVLRVVLLTSGMPAFT 95 
                                   567665555567899*****999*****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1064  (0.0593452); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 689.65
//
Query:       gi|15668924|ref|NP_247728.1|  [L=294]
Description: heterodisulfide reductase subunit HdrB1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-39  133.5   6.6    4.6e-21   74.8   0.7    2.7  3  CCG       Cysteine-rich domain
     0.0049   16.7   0.1      0.042   13.7   0.1    2.2  2  DUF2024   Domain of unknown function (DUF2024)
  ------ inclusion threshold ------
       0.21    9.8   0.0        0.3    9.2   0.0    1.1  1  FPP       Filament-like plant protein, long coiled-coil


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.1   1.3e-20   7.8e-17       2      84 ..       4      85 ..       3      86 .. 0.95
   2 ?   -1.0   0.1      0.36   2.1e+03      14      33 ..      95     114 ..      88     118 .. 0.81
   3 !   74.8   0.7   7.7e-25   4.6e-21       1      85 []     147     239 ..     147     239 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.3e-20
                           CCG  2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelae.alakrnvetaeetgadaivtacpgCllq 83
                                  ++f gC ++ ++yp  +ka+   +e+lg++l+++ek+sCC+a+g++ +++ +++ +la+rn+++aee+++d i+t+c+gC+++
  gi|15668924|ref|NP_247728.1|  4 VFFLGC-IAPNRYPGIEKATYITMEKLGIKLHPFEKASCCPAPGVFGSFDLKTWlTLAARNLCMAEEVEMD-ILTICNGCYGS 84
                                  69****.********************************************5555**************99.********998 PP

                           CCG 84 l 84
                                  l
  gi|15668924|ref|NP_247728.1| 85 L 85
                                  7 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.36
                           CCG  14 ypevrkalkkllealgvele 33 
                                   +++ rk + ++l++ g+e++
  gi|15668924|ref|NP_247728.1|  95 NEKARKMVNEILSKYGLEYK 114
                                   78899999999999999986 PP

  == domain 3  score: 74.8 bits;  conditional E-value: 7.7e-25
                           CCG   1 vayfdgChllraa......ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadai 73 
                                   va+++gCh+l++       ++e ++++ +l+ealg+  + + +k++CCGaggg++ ++  +a++++k ++e+++e++ad+i
  gi|15668924|ref|NP_247728.1| 147 VAVHYGCHYLKPTdikkleSSERPRSFDELVEALGAVSVNYkDKNMCCGAGGGVRARNLdVALKMTKTKLENIKEAKADCI 227
                                   89********9999***********************99999***************999********************* PP

                           CCG  74 vtacpgCllqlk 85 
                                      cp+C+lq++
  gi|15668924|ref|NP_247728.1| 228 TEVCPFCHLQFD 239
                                   **********96 PP

>> DUF2024  Domain of unknown function (DUF2024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.16   9.7e+02      27      47 ..     143     163 ..     133     173 .. 0.78
   2 !   13.7   0.1   7.1e-06     0.042      27      68 ..     203     244 ..     200     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.16
                                   --HHHHHHHHHHHHHHHT--- CS
                       DUF2024  27 kdeekaleyakeyLkskgeee 47 
                                    + + a++y+ +yLk + +++
  gi|15668924|ref|NP_247728.1| 143 LNVNVAVHYGCHYLKPTDIKK 163
                                   56778999******9877665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.1e-06
                                   --HHHHHHHHHHHHHHHT---S---TTTEEEEEEEE--HHHH CS
                       DUF2024  27 kdeekaleyakeyLkskgeeeakvtskeCkfCHseeaeeeve 68 
                                   ++ + al+++k  L+++ e +a+  ++ C fCH +  + +ve
  gi|15668924|ref|NP_247728.1| 203 RNLDVALKMTKTKLENIKEAKADCITEVCPFCHLQFDRGQVE 244
                                   677789999************************997666654 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0     5e-05       0.3      46      96 ..     201     251 ..     197     255 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 5e-05
                           FPP  46 raahlDgALkeCmrQlrsvkeeqeqklhdvvlkktkelekikaelEeklve 96 
                                   ra +lD ALk     l ++ke +   +++v      ++++ + e+ ek  e
  gi|15668924|ref|NP_247728.1| 201 RARNLDVALKMTKTKLENIKEAKADCITEVCPFCHLQFDRGQVEIKEKFGE 251
                                   899******************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1877.60
//
Query:       gi|15668925|ref|NP_247729.1|  [L=194]
Description: heterodisulfide reductase subunit HdrC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-10   40.9   7.9    4.8e-10   39.8   7.9    1.6  1  Fer4_17   4Fe-4S dicluster domain
    6.3e-10   39.1   7.5    1.5e-09   37.9   7.5    1.6  1  Fer4_9    4Fe-4S dicluster domain
    1.7e-09   38.0   6.3    1.7e-09   38.0   6.3    1.8  2  Fer4_8    4Fe-4S dicluster domain
    4.5e-09   36.3   7.6    1.3e-08   34.9   6.0    2.2  2  Fer4_10   4Fe-4S dicluster domain
    3.8e-07   30.6   7.6    8.1e-07   29.5   7.6    1.6  1  Fer4_7    4Fe-4S dicluster domain
    9.2e-05   23.3   9.9     0.0008   20.3   9.7    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
     0.0021   18.2   6.0     0.0065   16.6   6.0    1.8  1  Fer4_21   4Fe-4S dicluster domain
     0.0081   16.6  10.5       0.11   13.1   2.7    2.5  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.011   15.5  12.6       0.32   10.9   2.0    2.5  2  Fer4      4Fe-4S binding domain
       0.39   10.9  16.6       0.37   11.0   4.1    2.7  3  Fer4_2    4Fe-4S binding domain
       0.47   11.5  16.8        1.6    9.9   3.3    2.6  2  Fer4_3    4Fe-4S binding domain
       0.52   10.5   7.1        2.1    8.5   0.7    2.5  2  Fer4_18   4Fe-4S dicluster domain
        1.9    8.7  13.3        6.2    7.1   2.8    2.4  2  Fer4_6    4Fe-4S binding domain
          2    9.0   8.5        2.1    8.9   0.2    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        2.5    7.9   8.7       0.41   10.4   0.9    2.3  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
        5.7    7.9  12.4        6.7    7.6   0.8    2.4  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   7.9   4.3e-13   4.8e-10       1      60 [.      34      93 ..      34      94 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 4.3e-13
                       Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60
                                  +C qCg C+ +Cps++++ ++ +kl+r a++g++ +++++e    C++C eC ++CP  +
  gi|15668925|ref|NP_247729.1| 34 ACYQCGTCTGSCPSGRITAFRTRKLIRYAQFGMKSAIIDSEDLWMCTTCYECYERCPRTV 93
                                  5********************************************************865 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   7.5   1.3e-12   1.5e-09       1      49 [.      34      92 ..      34      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.3e-12
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase..........eaCigCgaCveaCpkg 49
                                  +C++Cg+C+ +Cp+g ++  + ++ +r+ ++++          + C++C +C+e+Cp++
  gi|15668925|ref|NP_247729.1| 34 ACYQCGTCTGSCPSGRITAFRTRKLIRYAQFGMksaiidsedlWMCTTCYECYERCPRT 92
                                  6***************************99999************************96 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   6.3   1.5e-12   1.7e-09       2      64 ..      32      92 ..      31      93 .. 0.83
   2 ?   -1.2   0.0       2.6   2.9e+03      47      58 ..     168     179 ..     106     182 .. 0.62

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.5e-12
                        Fer4_8  2 lekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                  +++C +Cg C+ +Cp+ r t+ + ++  r+ + + + +     + e lw Cttc +C e+Cp  
  gi|15668925|ref|NP_247729.1| 32 FKACYQCGTCTGSCPSGRITAfRTRKLIRYAQFG-MKSAI--IDSEDLWMCTTCYECYERCPRT 92
                                  689************9999999898999988777.33332..24677***************75 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.6
                        Fer4_8  47 alwsCttcgaCt 58 
                                    l  C + g Ct
  gi|15668925|ref|NP_247729.1| 168 DLRFCDMVGICT 179
                                   344455555555 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   6.0   1.1e-11   1.3e-08       6      56 .]      32      90 ..      28      90 .. 0.85
   2 ?    0.2   0.0      0.73   8.1e+02      39      53 ..     166     180 ..     150     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.1e-11
                       Fer4_10  6 ddtCirCgkCvkaCPadl.......tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                   + C +Cg+C+ +CP+         +  ++ ++ ++++ ++  +++ Ct+c +C+e CP
  gi|15668925|ref|NP_247729.1| 32 FKACYQCGTCTGSCPSGRitafrtrKLIRYAQFGMKSAIIDSeDLWMCTTCYECYERCP 90
                                  578*************88*****886677777777776666669**************9 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.73
                       Fer4_10  39 rkkvekCtgcgaCve 53 
                                    k++  C+++g C+e
  gi|15668925|ref|NP_247729.1| 166 MKDLRFCDMVGICTE 180
                                   467889999999987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   7.6   7.2e-10   8.1e-07       1      51 [.      34      92 ..      34      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 7.2e-10
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek.......gtekveidpe...kClgCgaCvavCPtg 51
                                  +C +Cg C+  Cp++ i+       k       g++++ id+e   +C++C++C ++CP  
  gi|15668925|ref|NP_247729.1| 34 ACYQCGTCTGSCPSGRITAFRTR--KliryaqfGMKSAIIDSEdlwMCTTCYECYERCPRT 92
                                  5**************99987542..2233444566777665442238************75 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   9.7   7.1e-07    0.0008       2      65 ..      35      90 ..      34      92 .. 0.91
   2 !    8.9   3.8    0.0025       2.8       2      16 ..      79      93 ..      78     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.1e-07
                       Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                  C +Cg C+ +CP++ i++      ++r+ i y++ + k++++d+e     + +t C  C + CP
  gi|15668925|ref|NP_247729.1| 35 CYQCGTCTGSCPSGRITAF-----RTRKLIRYAQFGMKSAIIDSED---LWMCTTCYECYERCP 90
                                  *****************99.....7889999*99999999999873...489***********9 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0025
                       Fer4_16  2 CgtCgkCaevCPtna 16
                                  C+tC +C e CP  +
  gi|15668925|ref|NP_247729.1| 79 CTTCYECYERCPRTV 93
                                  ************876 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   6.0   5.8e-06    0.0065       7      53 ..      34      91 ..      29     100 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.8e-06
                       Fer4_21  7 kCigCgkCliaCedtshqai......eidaktvl......kvv..ed..eCvGCnlCssvCPv 53
                                   C +Cg C+ +C+ + ++a       ++     +      +++  ed   C+ C  C++ CP 
  gi|15668925|ref|NP_247729.1| 34 ACYQCGTCTGSCPSGRITAFrtrkliRY-----AqfgmksAIIdsEDlwMCTTCYECYERCPR 91
                                  7*************99999955544322.....12233332332233446************5 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   2.7   9.8e-05      0.11       2      17 .]      33      48 ..      32      53 .. 0.91
   2 !    7.7   1.0    0.0051       5.7       4      15 ..      79      90 ..      74     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.8e-05
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  + C +Cg C+ +CP+g
  gi|15668925|ref|NP_247729.1| 33 KACYQCGTCTGSCPSG 48
                                  5799**********75 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0051
                        Fer4_4  4 CigCgsCvaaCP 15
                                  C+ C  C+  CP
  gi|15668925|ref|NP_247729.1| 79 CTTCYECYERCP 90
                                  *********999 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.0   0.00029      0.32       7      21 ..      34      48 ..      30      48 .. 0.89
   2 ?    9.4   3.2   0.00085      0.95       7      19 ..      78      90 ..      78      92 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                                  TSSS-THHHHHSTTT CS
                          Fer4  7 kCigCGaCvevCPvg 21
                                   C  CG+C   CP g
  gi|15668925|ref|NP_247729.1| 34 ACYQCGTCTGSCPSG 48
                                  699**********76 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00085
                                  TSSS-THHHHHST CS
                          Fer4  7 kCigCGaCvevCP 19
                                  +C+ C +C+e CP
  gi|15668925|ref|NP_247729.1| 78 MCTTCYECYERCP 90
                                  5************ PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.1   0.00033      0.37       9      21 ..      34      46 ..      31      47 .. 0.91
   2 ?    8.3   1.3    0.0024       2.6       8      21 ..      74      90 ..      68      91 .. 0.80
   3 ?   -2.7   0.1       7.7   8.6e+03      14      17 ..     176     179 ..     168     180 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                        Fer4_2  9 rCigCgaCvsaCP 21
                                  +C +Cg+C+ +CP
  gi|15668925|ref|NP_247729.1| 34 ACYQCGTCTGSCP 46
                                  6************ PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0024
                        Fer4_2  8 d...rCigCgaCvsaCP 21
                                  +   +C+ C  C+  CP
  gi|15668925|ref|NP_247729.1| 74 EdlwMCTTCYECYERCP 90
                                  33449********99*9 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 7.7
                        Fer4_2  14 gaCv 17 
                                   g+C+
  gi|15668925|ref|NP_247729.1| 176 GICT 179
                                   5665 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.6     0.013        15       1      14 [.      35      48 ..      35      48 .. 0.95
   2 ?    9.9   3.3    0.0014       1.6       1      12 [.      79      90 ..      79      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C +Cg+C  +CP+g
  gi|15668925|ref|NP_247729.1| 35 CYQCGTCTGSCPSG 48
                                  99**********97 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0014
                        Fer4_3  1 CtgCgaCvevCP 12
                                  Ct C+ C e CP
  gi|15668925|ref|NP_247729.1| 79 CTTCYECYERCP 90
                                  ************ PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.8     0.024        27      54      74 ..      28      48 ..       9      52 .. 0.82
   2 ?    8.5   0.7    0.0019       2.1      56      81 ..      74      99 ..      51     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.024
                       Fer4_18 54 kekgagdcidcescvkvcPtg 74
                                  + ++   c +c++c   cP g
  gi|15668925|ref|NP_247729.1| 28 HVSSFKACYQCGTCTGSCPSG 48
                                  5567788***********986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0019
                       Fer4_18 56 kgagdcidcescvkvcPtgidirkGl 81
                                  ++   c++c  c + cP  + i + +
  gi|15668925|ref|NP_247729.1| 74 EDLWMCTTCYECYERCPRTVKITDII 99
                                  55567**************9998754 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.8    0.0062       6.9       8      24 .]      34      50 ..      33      50 .. 0.88
   2 ?    7.1   2.8    0.0056       6.2       9      20 ..      79      90 ..      78      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0062
                        Fer4_6  8 kCigCgdCvrvCPegai 24
                                  +C +Cg C+  CP g i
  gi|15668925|ref|NP_247729.1| 34 ACYQCGTCTGSCPSGRI 50
                                  5889*********9976 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0056
                        Fer4_6  9 CigCgdCvrvCP 20
                                  C+ C++C+  CP
  gi|15668925|ref|NP_247729.1| 79 CTTCYECYERCP 90
                                  9**********9 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   3.1      0.16   1.8e+02       5      17 ..      34      46 ..      33      48 .. 0.90
   2 ?    8.9   0.2    0.0019       2.1       6      24 ..      79      97 ..      75     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.16
                       Fer4_13  5 tCiacgaCvelaP 17
                                   C  cg+C   +P
  gi|15668925|ref|NP_247729.1| 34 ACYQCGTCTGSCP 46
                                  6*********999 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0019
                       Fer4_13  6 CiacgaCvelaPdvFeedd 24
                                  C+ c  C+e +P + ++ d
  gi|15668925|ref|NP_247729.1| 79 CTTCYECYERCPRTVKITD 97
                                  ************9877766 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.5       0.2   2.2e+02      23      39 ..      34      48 ..      22      71 .. 0.77
   2 ?   10.4   0.9   0.00037      0.41      24      56 ..      79     109 ..      60     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.2
                                  T----TT-HHHHCSTT- CS
                       Fer4_20 23 RClqCkkapcvkgCPve 39
                                   C+qC   +c+ +CP  
  gi|15668925|ref|NP_247729.1| 34 ACYQC--GTCTGSCPSG 48
                                  58888..6788888854 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00037
                                   ----TT-HHHHCSTT---HHHHHHHHHTT-HHH CS
                       Fer4_20  24 ClqCkkapcvkgCPveidipefikkiaegnlee 56 
                                   C +C   +c + CP +++i + ik +++   +e
  gi|15668925|ref|NP_247729.1|  79 CTTC--YECYERCPRTVKITDIIKVLRNIAARE 109
                                   7777..67*************999877654443 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.3     0.023        26       2      16 ..      35      49 ..      34      69 .. 0.80
   2 ?    7.6   0.8     0.006       6.7      71      95 ..      68      92 ..      48      95 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.023
                       Fer4_22  2 ClsCgaCtlvCptCs 16
                                  C +Cg+Ct  Cp+  
  gi|15668925|ref|NP_247729.1| 35 CYQCGTCTGSCPSGR 49
                                  9**********9865 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.006
                       Fer4_22 71 sefkekfgesgCvGCgRCieacpvk 95
                                  s + ++ +  +C+ C  C e+cp +
  gi|15668925|ref|NP_247729.1| 68 SAIIDSEDLWMCTTCYECYERCPRT 92
                                  4567778999************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1263.80
//
Query:       gi|15668926|ref|NP_247730.1|  [L=181]
Description: hypothetical protein MJ_0745 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-20   72.9   1.9    2.2e-20   72.4   1.9    1.2  1  V4R       V4R domain
    0.00024   21.0   0.0    0.00055   19.9   0.0    1.6  2  DUF2507   Protein of unknown function (DUF2507)


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   1.9   2.4e-24   2.2e-20       2      61 ..     120     178 ..     119     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 2.4e-24
                                   -EEEEEES-S-TT---SS---HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEEEE CS
                           V4R   2 elsieespelaglpgkeePvCyleaGllagalsellgkrveveEveCaaeGhdhCeFeve 61 
                                   +l++e++ ++++l ++eeP+Cy+ aGl+aga++++l+k+v v+E++C+a+G+d+C F+ve
  gi|15668926|ref|NP_247730.1| 120 VLKVENCSFCEDL-SFEEPICYFDAGLIAGAYECILKKPVVVDEIKCMARGDDACYFKVE 178
                                   799*********7.*******************************************997 PP

>> DUF2507  Protein of unknown function (DUF2507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.39   3.5e+03      33      52 ..       6      25 ..       2      47 .. 0.71
   2 !   19.9   0.0   6.1e-08   0.00055      17     100 ..      73     153 ..      60     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.39
                       DUF2507 33 rkfplesledlieffekagw 52
                                   +++++++++ ++ f++ ++
  gi|15668926|ref|NP_247730.1|  6 VELKTKDMKEFYKIFSESEF 25
                                  45566666666666666555 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 6.1e-08
                       DUF2507  17 gedeeeilYwaGkelArkfplesledlieffekagwGtLellkekkkelefeLsgeiveerlkekeekefqLEaGflAeqi 97 
                                     d+e  lY +G e  ++++ + ++dl +ff++ + GtL++ +   k l+ + +   + e+l+ +e  ++ ++aG++A ++
  gi|15668926|ref|NP_247730.1|  73 ELDSEITLYDIGYEFGKHLNPKRYSDLKKFFKENNLGTLKVDSR--KPLVLKVENCSFCEDLSFEEPICY-FDAGLIAGAY 150
                                   55777789*******************************99765..567777778888888885555554.7999999988 PP

                       DUF2507  98 eqq 100
                                   e  
  gi|15668926|ref|NP_247730.1| 151 ECI 153
                                   865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1121.17
//
Query:       gi|15668927|ref|NP_247731.1|  [L=141]
Description: hypothetical protein MJ_0746 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-14   54.6   5.7      1e-12   48.6   5.2    2.0  1  Rubrerythrin     Rubrerythrin
    7.5e-07   29.2   2.9    6.9e-05   22.8   2.9    2.1  1  Ferritin         Ferritin-like domain
     0.0038   17.4   0.3       0.62   10.3   0.1    2.2  2  Ferritin_2       Ferritin-like domain
  ------ inclusion threshold ------
      0.018   14.8   0.2      0.027   14.3   0.2    1.2  1  Mob_Pre          Plasmid recombination enzyme
      0.047   12.5   1.4        0.4    9.5   0.3    2.0  2  FA_desaturase_2  Fatty acid desaturase


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   5.2   2.8e-16     1e-12       5     134 ..      25     133 ..      21     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 2.8e-16
                                   HHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHH CS
                  Rubrerythrin   5 kAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttakn 84 
                                   +++ gE+++  lY ++a++a+ eg+p++ae++ ++A eE++Ha+ ++++ + + ++l+                     +n
  gi|15668927|ref|NP_247731.1|  25 ANFEGECKEVGLYLAMARQAQrEGLPEVAEVLIRIAMEEAQHAAHFAEMNGLISENLK---------------------EN 84 
                                   6899************************************************999999.....................9* PP

                                   HHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin  85 LeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlr 134
                                   +e++++g+  +++e  +  +  a++ g ++a+++f++ +++E +H+++l+
  gi|15668927|ref|NP_247731.1|  85 IEMMLKGECMANKEK-KAAATKAKELGIDPAHDFFDESSRDEARHAKMLK 133
                                   **************9.56666666677777******************98 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   2.9   1.9e-08   6.9e-05      17     138 ..      36     138 ..      25     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.9e-08
                                   HHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCSSHHHHHHHHHHHHHHHHH CS
                      Ferritin  17 qylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkefgsveevleaalehekkvte 97 
                                   +ylama+ ++ +gl+++ae +   a ee +ha  +ae   + G         l         ++++e +e +l+ e  +++
  gi|15668927|ref|NP_247731.1|  36 LYLAMARQAQREGLPEVAEVLIRIAMEEAQHAAHFAE---MNG---------LIS-------ENLKENIEMMLKGECMANK 97 
                                   6*******************************99998...334.........344.......3999*************** PP

                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Ferritin  98 slrelielaeeegDpatadfledfleeqeeheweleallek 138
                                   + + ++  a+e g +  +df+++  +++ +h+++l+ +l++
  gi|15668927|ref|NP_247731.1|  98 EKKAAATKAKELGIDPAHDFFDESSRDEARHAKMLKGILDR 138
                                   *************************************9985 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00017      0.62     100     134 ..      37      74 ..      26      76 .. 0.78
   2 !    5.5   0.0     0.005        18      36      61 ..     111     136 ..      87     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00017
                    Ferritin_2 100 Ylgaaplls...nkelltaaasIlsvEArHaavirtll 134
                                   Yl  a++ +    +e++++ ++I+  EA+Haa ++++ 
  gi|15668927|ref|NP_247731.1|  37 YLAMARQAQregLPEVAEVLIRIAMEEAQHAAHFAEMN 74 
                                   555555555333578999***************99875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.005
                    Ferritin_2  36 daevrevaeeiakheeaHveflkaal 61 
                                    +  ++++ e   +e+ H+++lk+ l
  gi|15668927|ref|NP_247731.1| 111 IDPAHDFFDESSRDEARHAKMLKGIL 136
                                   3456899***************9987 PP

>> Mob_Pre  Plasmid recombination enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   7.5e-06     0.027      52     102 ..      78     128 ..      58     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.5e-06
                                   TS-HHHHHHHHHHHH-SSSS---TT---EEEEEEEE-HHHHHTS-HHHHHH CS
                       Mob_Pre  52 kkrykekikeyikenqvskrklRkdavlvieilitaskeffekltkeeake 102
                                   ++++ke+i+ ++k     ++++++ a+++ e+ i+   +ff++ +++ea++
  gi|15668927|ref|NP_247731.1|  78 SENLKENIEMMLKGECMANKEKKAAATKAKELGIDPAHDFFDESSRDEARH 128
                                   5799************9*************************999999986 PP

>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3   0.00011       0.4     172     207 ..      40      75 ..      37      97 .. 0.83
   2 ?    2.3   0.1     0.017        62     172     210 ..     102     140 ..      92     141 .] 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00011
               FA_desaturase_2 172 taklakeagdellakicgaiaadEkrHeaaYtrvve 207
                                   +a++a+++g + +a+++ +ia +E++H+a ++++  
  gi|15668927|ref|NP_247731.1|  40 MARQAQREGLPEVAEVLIRIAMEEAQHAAHFAEMNG 75 
                                   79**************************99988654 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.017
               FA_desaturase_2 172 taklakeagdellakicgaiaadEkrHeaaYtrvvekll 210
                                    a+ ake g + ++      + dE+rH+++ + ++++ +
  gi|15668927|ref|NP_247731.1| 102 AATKAKELGIDPAHDFFDESSRDEARHAKMLKGILDRYF 140
                                   5667777777778888888899*******9999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1030.56
//
Query:       gi|15668928|ref|NP_247732.1|  [L=169]
Description: hemerythrin sipunculid [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-14   54.5   0.4    2.1e-14   54.3   0.4    1.1  1  Hemerythrin  Hemerythrin HHE cation binding domain
  ------ inclusion threshold ------
      0.031   13.8   0.4      0.045   13.3   0.4    1.2  1  4HB_MCP_1    Four helix bundle sensory module for signal tran


Domain annotation for each model (and alignments):
>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.4   2.3e-18   2.1e-14       2     127 ..      37     150 ..      36     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 2.3e-18
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCHHHHHH.HHHHHHHHHHHHHHHHC....HHHHH.CCC.HHHHHHHH CS
                   Hemerythrin   2 ivealdeeHralrallerlraladaaaevhgalrklaelld.elvdeleaHhaaEEell....fPlledrpggravldvle 77 
                                   +++a+d+eH+ l++ l+++  l+++ +     +++++ell+ ++v++ ++H+++EEe++    +P le          +++
  gi|15668928|ref|NP_247732.1|  37 GIKAFDDEHKILVKTLNDIYNLLNEGK-----RDEAKELLKrRVVNYAAKHFKHEEEVMekygYPDLE----------RHR 102
                                   7899***************99999966.....99*************************999999999..........*** PP

                                   HHHHHHHHHHHHHHHHCHTCGGSTCHHHHHHHHHHHHHHHHHHHHHHHTH CS
                   Hemerythrin  78 reHdeirelleelrellkgleepsaaafaelleeladllreHiakEesil 127
                                   + H+ + + +  +++ll ++ee+s+++f+ +l  l  +l  Hiak ++++
  gi|15668928|ref|NP_247732.1| 103 KTHEIFVKTV--IEKLLPKIEEGSENDFRSALSFLVGWLTMHIAKPDKKY 150
                                   *******887..88999999999**********************99876 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   5.1e-06     0.045     111     163 ..      38      90 ..      31      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-06
                     4HB_MCP_1 111 leefkeqlnaYrevrkkvlelakegkkdeAyqlyetegrparekliealeelv 163
                                   +++f+++++   +  +++ +l +egk deA++l++  + ++++k ++  ee++
  gi|15668928|ref|NP_247732.1|  38 IKAFDDEHKILVKTLNDIYNLLNEGKRDEAKELLKRRVVNYAAKHFKHEEEVM 90 
                                   5789*******************************999988888777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1113.96
//
Query:       gi|15668929|ref|NP_247733.1|  [L=416]
Description: flavoprotein FpaA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-11   42.5   0.1    1.7e-10   41.3   0.0    1.7  2  Lactamase_B    Metallo-beta-lactamase superfamily
      9e-11   42.2   0.0      2e-10   41.0   0.0    1.6  2  Flavodoxin_1   Flavodoxin
    0.00023   20.7   0.0    0.00044   19.8   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0014   18.3   0.0     0.0039   16.9   0.0    1.7  2  PGM_PMM_I      Phosphoglucomutase/phosphomannomutase, alpha/b


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   3.7e-14   1.7e-10       5     160 ..      37     184 ..      33     245 .. 0.87
   2 ?   -1.8   0.0      0.58   2.6e+03      15      50 ..     265     298 ..     262     345 .. 0.67

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 3.7e-14
                                   SSEEEEEEETTCEEEES--SCHHHHHHHH...HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                   Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraal...elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                     n+yl+ gd++v LiD  +++  a+++    + + ++    ++d ++  H   DH G+l+++ ++++ +++++ e+a ++
  gi|15668929|ref|NP_247733.1|  37 TYNAYLVFGDEKVALIDNTYPGTSAQMWGrikDAFEKEGREFKIDVIVQNHVEKDHSGALPEIHKKFPDAPIYCTEVAVEG 117
                                   569**************999999999988999************************************************* PP

                                   HCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCC CS
                   Lactamase_B  83 fmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgri 160
                                   ++ +      +++            v+  ++++++gg  ++      +h ++++  +y +g++lf+ Da+ ++     
  gi|15668929|ref|NP_247733.1| 118 LKKHYPSLKDAQF-----------KVVHTGDTVDLGGKTLTFLEAPLLHWPDSMFTFYNEGGILFSNDAFGQHLCFPA 184
                                   *****66555554...........57777777777888888888888999*******************987766555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.58
                                   TCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE- CS
                   Lactamase_B  15 ggviLiDtGtsteaaraalelaalglkpkdvdavil 50 
                                   + vi++Dt   + +++ a+  +a+gl  + +d v +
  gi|15668929|ref|NP_247733.1| 265 KAVIVYDTMHYSTQKM-AH-AFAEGLMSEGIDVVMY 298
                                   5666666643333333.33.5666666666666654 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         3   1.4e+04       8      30 ..      58      77 ..      54      91 .. 0.66
   2 !   41.0   0.0   4.5e-14     2e-10       1     127 [.     268     386 ..     268     409 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3
                                  SHHHHHHHHHHHHHHHTTTEEEE CS
                  Flavodoxin_1  8 GnteklAkqlaeelgehgfnadv 30
                                  G++ ++  ++++ ++++g   ++
  gi|15668929|ref|NP_247733.1| 58 GTSAQMWGRIKDAFEKEG---RE 77
                                  788888888888888754...23 PP

  == domain 2  score: 41.0 bits;  conditional E-value: 4.5e-14
                                   EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSC...GGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHHHHHCH CS
                  Flavodoxin_1   1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydes...lseieeealllvvtsTfgnGdppengesffqdllelkgd 78 
                                   i+Y+++  +t+k+A++ ae+l+++g++  v+ + +yde    +++i + + +l++++T +++  p      +  ++  +  
  gi|15668929|ref|NP_247733.1| 268 IVYDTMHYSTQKMAHAFAEGLMSEGID-VVMYFLHYDERseiVKDILDAKAVLFGIPTIYDEPYP------SIGDIIYYLR 341
                                   89************************7.6666888888779999999999999999999976555......6777888877 PP

                                   HGCCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEESSSEE CS
                  Flavodoxin_1  79 eledgdlsgvrfavfglGdsayenFcaagkkldekleelGaerllklle 127
                                    l++ + +g +   + +G++++e+   a+ k+ e l + G+e++ +  e
  gi|15668929|ref|NP_247733.1| 342 GLKF-NRTGFKRLAVTFGSMGGEG--GAVAKIAEDLAKCGFEVINQ-YE 386
                                   7787.66778888899********..****************9986.44 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   9.7e-08   0.00044      25     116 ..      76     157 ..      51     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.7e-08
                                   S--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEE CS
                 Lactamase_B_2  25 rdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdgglei 105
                                   r+   +id+++  h + DH   l+ + +  p ++p+y+++   + l+++ +   l+ +   +++ +++g++++lg+   ++
  gi|15668929|ref|NP_247733.1|  76 REF--KIDVIVQNHVEKDHSGALPEIHKKFP-DAPIYCTEVAVEGLKKHYP--SLKDA---QFKVVHTGDTVDLGGK--TL 146
                                   344..8**********************444.69***************55..44444...789**********965..56 PP

                                   EEEEE-EE--C CS
                 Lactamase_B_2 106 tatparhksgr 116
                                   t+ +a+  + +
  gi|15668929|ref|NP_247733.1| 147 TFLEAPLLHWP 157
                                   66666555544 PP

>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.6e-07    0.0039      26      73 ..     249     297 ..     243     302 .. 0.82
   2 ?   -3.1   0.0       1.3   5.9e+03      59      79 ..     369     392 ..     366     393 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.6e-07
                                   HHHHHHHHCHHCSTS-EEEEEE-S.-TTHHHHHHHHHHHHHCCT-CEEE CS
                     PGM_PMM_I  26 lgqaiaeylkaeakkkkvvvGrDt.RvssrelaealaaglaanGvevil 73 
                                   +++a+ +  + +a+k k v+ +Dt ++s +++a+a+a+gl+++G++v++
  gi|15668929|ref|NP_247733.1| 249 VIKAYQDFATGKAAKDKAVIVYDTmHYSTQKMAHAFAEGLMSEGIDVVM 297
                                   5666666666677889999999974777789***************986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
                                   HHHHHHHCCT-CEEEEE...EB-H CS
                     PGM_PMM_I  59 alaaglaanGvevillg...llpt 79 
                                   ++a+ la+ G+evi+     ++pt
  gi|15668929|ref|NP_247733.1| 369 KIAEDLAKCGFEVINQYelyYVPT 392
                                   677889999999998766666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2828.39
//
Query:       gi|15668930|ref|NP_247734.1|  [L=246]
Description: hypothetical protein MJ_0749 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-16   60.6  22.8    2.7e-12   46.4   5.2    3.1  3  Fer4_5    4Fe-4S binding domain
    2.9e-10   39.5  14.3    2.5e-05   23.9   1.4    4.2  4  Fer4      4Fe-4S binding domain
      4e-08   33.7  10.3    0.00022   21.7   1.9    3.0  3  Fer4_7    4Fe-4S dicluster domain
    8.3e-08   32.3  13.1    0.00066   19.8   4.9    3.0  2  Fer4_21   4Fe-4S dicluster domain
    3.3e-06   26.9  16.8    0.00012   22.0   2.6    3.1  3  Fer4_6    4Fe-4S binding domain
      7e-05   22.9  26.8    0.00037   20.6  14.3    2.5  2  Fer4_9    4Fe-4S dicluster domain
    8.1e-05   22.8  10.6    8.1e-05   22.8  10.6    2.9  3  Fer4_18   4Fe-4S dicluster domain
    0.00029   21.2  13.0      0.099   13.1   1.4    3.3  3  Fer4_8    4Fe-4S dicluster domain
    0.00037   20.6  19.2    0.00045   20.3  14.8    2.9  4  Fer4_10   4Fe-4S dicluster domain
    0.00048   20.1  16.2     0.0015   18.5   0.8    3.4  3  Fer4_2    4Fe-4S binding domain
    0.00066   20.2  14.4     0.0013   19.2   1.6    3.2  4  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   16.4   0.8      0.012   16.4   0.8    2.7  2  Fer4_22   4Fe-4S dicluster domain
      0.013   16.0  21.2      0.019   15.4   4.4    3.4  3  Fer4_4    4Fe-4S binding domain
        0.2   12.7  27.1       0.53   11.4   3.3    3.9  4  Fer4_3    4Fe-4S binding domain
       0.33   11.9  19.3       0.68   10.9   1.3    3.5  5  Fer4_16   4Fe-4S double cluster binding domain
       0.83   10.4  11.4        3.8    8.3   1.5    2.4  2  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   5.2   2.4e-15   2.7e-12       4      47 ..      63     106 ..      61     107 .. 0.91
   2 ?   -3.0   0.3       6.8   7.6e+03      10      16 ..     128     134 ..     125     138 .. 0.41
   3 !   24.5   3.8   1.7e-08   1.9e-05       5      47 ..     147     189 ..     143     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.4e-15
                        Fer4_5   4 lllilflaivlvtllfGRafCgWiCPfGalqellakllrrklgk 47 
                                   + +i  +++++++++ GR+fCgW+CPfG+l+ l++ l+ + +++
  gi|15668930|ref|NP_247734.1|  63 ATIITKIIAIVLAFIAGRVFCGWMCPFGFLFNLVYELRVKLFKL 106
                                   56788899****************************99999987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.8
                        Fer4_5  10 laivlvt 16 
                                   l++v+++
  gi|15668930|ref|NP_247734.1| 128 LILVVLA 134
                                   3333333 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 1.7e-08
                        Fer4_5   5 llilflaivlvtllfGRafCgWiCPfGalqellakllrrklgk 47 
                                   +++l+++++++ ++   +fC ++CP+G+l  ++a+++ +kl++
  gi|15668930|ref|NP_247734.1| 147 AYLLLALFLVLGFIYPMFFCRYVCPVGSLLSIFARFSIFKLKL 189
                                   45556666666666999******************88888875 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.13   1.4e+02      14      23 ..      83      92 ..      82      93 .. 0.83
   2 ?    4.2   0.1     0.037        42      14      21 ..     166     173 ..     165     175 .. 0.86
   3 !   23.9   1.4   2.3e-08   2.5e-05       2      20 ..     188     206 ..     187     208 .. 0.90
   4 !   15.5   1.0   9.8e-06     0.011       2      23 ..     213     234 ..     212     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.13
                                  HHHHSTTTEE CS
                          Fer4 14 CvevCPvgAI 23
                                  C  +CP+g +
  gi|15668930|ref|NP_247734.1| 83 CGWMCPFGFL 92
                                  8899***975 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.037
                                   HHHHSTTT CS
                          Fer4  14 CvevCPvg 21 
                                   C  vCPvg
  gi|15668930|ref|NP_247734.1| 166 CRYVCPVG 173
                                   999****9 PP

  == domain 3  score: 23.9 bits;  conditional E-value: 2.3e-08
                                   EEETTTSSS-THHHHHSTT CS
                          Fer4   2 videekCigCGaCvevCPv 20 
                                   + de+kC+gC +C+  CP 
  gi|15668930|ref|NP_247734.1| 188 KLDENKCVGCRLCERKCPM 206
                                   579***************6 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 9.8e-06
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                   +id+  Ci+C +C++vC  gA+
  gi|15668930|ref|NP_247734.1| 213 KIDQMECIRCFECMSVCKKGAL 234
                                   69******************98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0         3   3.4e+03       8      15 ..      83      90 ..      81     101 .. 0.75
   2 !   21.7   1.9     2e-07   0.00022       7      51 ..     165     207 ..     164     208 .. 0.81
   3 !   16.1   0.6   1.2e-05     0.013      33      52 .]     214     233 ..     209     245 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3
                        Fer4_7  8 CvaaCpvk 15
                                  C  +Cp +
  gi|15668930|ref|NP_247734.1| 83 CGWMCPFG 90
                                  66677765 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2e-07
                        Fer4_7   7 aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                   +C  +Cpv+ +    +     + k+++d++kC+gC+ C++ CP +
  gi|15668930|ref|NP_247734.1| 165 FCRYVCPVGSLLSIFA--RFSIFKLKLDENKCVGCRLCERKCPMQ 207
                                   6999***887765443..2356899******************87 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.2e-05
                        Fer4_7  33 idpekClgCgaCvavCPtga 52 
                                   id+++C+ C +C++vC +ga
  gi|15668930|ref|NP_247734.1| 214 IDQMECIRCFECMSVCKKGA 233
                                   67777777777777777765 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   4.9   5.9e-07   0.00066      14      54 ..     166     207 ..     164     211 .. 0.77
   2 !   15.9   1.2   9.4e-06     0.011       2      24 ..     213     235 ..     212     246 .] 0.80

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.9e-07
                       Fer4_21  14 CliaCedtshqaieid.aktvlkvvedeCvGCnlCssvCPve 54 
                                   C  +C+ +s   i    +  +lk+ e++CvGC lC   CP++
  gi|15668930|ref|NP_247734.1| 166 CRYVCPVGSLLSIFARfSIFKLKLDENKCVGCRLCERKCPMQ 207
                                   8889999888888544134466889***************85 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 9.4e-06
                       Fer4_21   2 ridedkCigCgkCliaCedtshq 24 
                                   +id+ +Ci C +C+ +C++++  
  gi|15668930|ref|NP_247734.1| 213 KIDQMECIRCFECMSVCKKGALS 235
                                   69****************87754 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2       2.4   2.7e+03      18      22 ..     169     173 ..     166     175 .. 0.78
   2 !   22.0   2.6   1.1e-07   0.00012       5      23 ..     190     208 ..     189     208 .. 0.95
   3 !   13.2   1.9   6.4e-05     0.072       9      24 .]     219     234 ..     214     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.4
                        Fer4_6  18 vCPeg 22 
                                   vCP g
  gi|15668930|ref|NP_247734.1| 169 VCPVG 173
                                   8**87 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.1e-07
                        Fer4_6   5 dpdkCigCgdCvrvCPega 23 
                                   d++kC+gC+ C+r CP+++
  gi|15668930|ref|NP_247734.1| 190 DENKCVGCRLCERKCPMQI 208
                                   89**************985 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 6.4e-05
                        Fer4_6   9 CigCgdCvrvCPegai 24 
                                   Ci C +C++vC  ga+
  gi|15668930|ref|NP_247734.1| 219 CIRCFECMSVCKKGAL 234
                                   ***********99996 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   4.5   1.5e-05     0.016       8      49 ..     166     207 ..     164     209 .. 0.65
   2 !   20.6  14.3   3.3e-07   0.00037       1      50 [.     193     233 ..     193     234 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                        Fer4_9   8 CveaCpagvv.vedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   C ++Cp g   +  a   + +l+  +e++C+gC+ C+ +Cp +
  gi|15668930|ref|NP_247734.1| 166 CRYVCPVGSLlSIFARFSIFKLKL-DENKCVGCRLCERKCPMQ 207
                                   777777766524444444444443.446999999999999987 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.3e-07
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   kC+gC+ C+++Cp+++ + ++  ++         +Ci C +C+ +C+kga
  gi|15668930|ref|NP_247734.1| 193 KCVGCRLCERKCPMQIKITEKIDQM---------ECIRCFECMSVCKKGA 233
                                   7**************9998887776.........5************997 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.56   6.2e+02       5      21 ..      82      98 ..      80     108 .. 0.82
   2 ?    1.6   0.2      0.27   3.1e+02       5      18 ..     165     178 ..     163     184 .. 0.84
   3 !   22.8  10.6   7.2e-08   8.1e-05      57      97 ..     190     231 ..     184     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.56
                       Fer4_18  5 vcvyvcPyarvqsvlyd 21
                                  +c  +cP++ +   +y+
  gi|15668930|ref|NP_247734.1| 82 FCGWMCPFGFLFNLVYE 98
                                  799*****988877776 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.27
                       Fer4_18   5 vcvyvcPyarvqsv 18 
                                   +c yvcP + + s+
  gi|15668930|ref|NP_247734.1| 165 FCRYVCPVGSLLSI 178
                                   799****9988776 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 7.2e-08
                       Fer4_18  57 gagdcidcescvkvcPtgidirkGl.qleciscllcidacdk 97 
                                   ++++c+ c+ c + cP++i i + + q+eci c +c+  c+k
  gi|15668930|ref|NP_247734.1| 190 DENKCVGCRLCERKCPMQIKITEKIdQMECIRCFECMSVCKK 231
                                   5789*****************987659*************86 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       0.5   5.6e+02      57      64 ..     166     173 ..     164     183 .. 0.70
   2 !   13.1   1.4   8.9e-05     0.099       3      17 ..     192     206 ..     189     214 .. 0.69
   3 !   12.8   1.4   0.00011      0.12       3      16 ..     217     230 ..     215     246 .] 0.67

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.5
                        Fer4_8  57 CtevCpvg 64 
                                   C+ vCpvg
  gi|15668930|ref|NP_247734.1| 166 CRYVCPVG 173
                                   55556554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.9e-05
                        Fer4_8   3 ekCieCgaCqsaCpv 17 
                                   +kC++C +C+ +Cp+
  gi|15668930|ref|NP_247734.1| 192 NKCVGCRLCERKCPM 206
                                   467777777777764 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00011
                        Fer4_8   3 ekCieCgaCqsaCp 16 
                                   ++Ci+C+ C+s C 
  gi|15668930|ref|NP_247734.1| 217 MECIRCFECMSVCK 230
                                   68***********5 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.9   8.9e+03      16      21 ..      84      89 ..      83     114 .. 0.74
   2 ?   -0.4   0.1       1.1   1.3e+03      15      21 ..     166     172 ..     165     177 .. 0.83
   3 !   20.3  14.8     4e-07   0.00045       2      55 ..     187     229 ..     186     230 .. 0.82
   4 !   10.9   3.9   0.00035      0.39       3      19 ..     213     229 ..     211     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.9
                       Fer4_10 16 vkaCPa 21
                                    +CP+
  gi|15668930|ref|NP_247734.1| 84 GWMCPF 89
                                  557887 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                       Fer4_10  15 CvkaCPa 21 
                                   C+ +CP+
  gi|15668930|ref|NP_247734.1| 166 CRYVCPV 172
                                   8888987 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 4e-07
                       Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                   +++d+++C++C+ C + CP+         +  ++ +++++  +C++c++C+++C
  gi|15668930|ref|NP_247734.1| 187 LKLDENKCVGCRLCERKCPM---------Q--IKITEKIDQMECIRCFECMSVC 229
                                   5789****************.........4..4444444558************ PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00035
                       Fer4_10   3 vidddtCirCgkCvkaC 19 
                                   +id+  CirC +C+++C
  gi|15668930|ref|NP_247734.1| 213 KIDQMECIRCFECMSVC 229
                                   58889999999999999 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.8      0.14   1.6e+02      16      21 ..     166     171 ..     165     172 .. 0.89
   2 !   18.5   0.8   1.3e-06    0.0015       4      21 ..     188     205 ..     185     206 .. 0.91
   3 !    7.7   1.7    0.0038       4.2       6      20 ..     215     229 ..     213     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.14
                        Fer4_2  16 CvsaCP 21 
                                   C+ +CP
  gi|15668930|ref|NP_247734.1| 166 CRYVCP 171
                                   ****** PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.3e-06
                        Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                                   + d+++C+gC+ C   CP
  gi|15668930|ref|NP_247734.1| 188 KLDENKCVGCRLCERKCP 205
                                   789**************9 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0038
                        Fer4_2   6 dtdrCigCgaCvsaC 20 
                                   d   Ci+C  C s+C
  gi|15668930|ref|NP_247734.1| 215 DQMECIRCFECMSVC 229
                                   5556****99***** PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       9.9   1.1e+04       8      14 ..      83      89 ..      82     100 .. 0.66
   2 ?   -1.1   0.1       2.5   2.8e+03      52      57 ..     166     171 ..     164     177 .. 0.69
   3 !   19.2   1.6   1.2e-06    0.0013      44      60 ..     192     208 ..     183     209 .. 0.91
   4 !    8.8   0.9    0.0021       2.3       1      14 [.     218     231 ..     211     245 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.9
                       Fer4_17  8 ClpeCps 14
                                  C  +Cp+
  gi|15668930|ref|NP_247734.1| 83 CGWMCPF 89
                                  4455654 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.5
                       Fer4_17  52 CerkCP 57 
                                   C+++CP
  gi|15668930|ref|NP_247734.1| 166 CRYVCP 171
                                   666666 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 1.2e-06
                       Fer4_17  44 slCieCgeCerkCPqgl 60 
                                   ++C++C++CerkCP+++
  gi|15668930|ref|NP_247734.1| 192 NKCVGCRLCERKCPMQI 208
                                   79*************97 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0021
                       Fer4_17   1 rCiqCgyClpeCps 14 
                                   +Ci+C  C+ +C  
  gi|15668930|ref|NP_247734.1| 218 ECIRCFECMSVCKK 231
                                   36666666666654 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.4   0.8   1.1e-05     0.012      67      96 .]     179     208 ..     175     208 .. 0.90
   2 ?    5.3   1.4     0.032        36      75      94 ..     212     231 ..     209     234 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                       Fer4_22  67 lhklsefkekfgesgCvGCgRCieacpvki 96 
                                   + ++s fk k +e++CvGC  C+++cp++i
  gi|15668930|ref|NP_247734.1| 179 FARFSIFKLKLDENKCVGCRLCERKCPMQI 208
                                   6788999999*****************987 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.032
                       Fer4_22  75 ekfgesgCvGCgRCieacpv 94 
                                   ek++++ C+ C  C+++c++
  gi|15668930|ref|NP_247734.1| 212 EKIDQMECIRCFECMSVCKK 231
                                   56677777777777777765 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.4      0.17   1.9e+02      10      17 .]     166     173 ..     165     173 .. 0.88
   2 ?   15.4   4.4   1.7e-05     0.019       2      17 .]     192     207 ..     191     207 .. 0.92
   3 ?    6.9   2.7    0.0089        10       3      15 ..     218     230 ..     216     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.17
                        Fer4_4  10 CvaaCPqg 17 
                                   C+++CP+g
  gi|15668930|ref|NP_247734.1| 166 CRYVCPVG 173
                                   ******86 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.7e-05
                        Fer4_4   2 erCigCgsCvaaCPqg 17 
                                   ++C+gC+ C++ CP++
  gi|15668930|ref|NP_247734.1| 192 NKCVGCRLCERKCPMQ 207
                                   79************86 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0089
                        Fer4_4   3 rCigCgsCvaaCP 15 
                                    Ci+C  C+++C+
  gi|15668930|ref|NP_247734.1| 218 ECIRCFECMSVCK 230
                                   5999999999997 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       3.1   3.5e+03       7      14 ..      83      90 ..      82      90 .. 0.74
   2 ?    6.0   0.3     0.025        28       7      14 ..     166     173 ..     164     174 .. 0.92
   3 ?    9.0   4.4    0.0027       3.1       1      12 [.     194     205 ..     194     208 .. 0.95
   4 ?   11.4   3.3   0.00047      0.53       1      15 []     219     233 ..     219     233 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.1
                        Fer4_3  7 CvevCPvg 14
                                  C   CP g
  gi|15668930|ref|NP_247734.1| 83 CGWMCPFG 90
                                  66789976 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.025
                        Fer4_3   7 CvevCPvg 14 
                                   C  vCPvg
  gi|15668930|ref|NP_247734.1| 166 CRYVCPVG 173
                                   99****98 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0027
                        Fer4_3   1 CtgCgaCvevCP 12 
                                   C+gC++C++ CP
  gi|15668930|ref|NP_247734.1| 194 CVGCRLCERKCP 205
                                   ************ PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00047
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ C  C+ vC +gA
  gi|15668930|ref|NP_247734.1| 219 CIRCFECMSVCKKGA 233
                                   *************98 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       8.5   9.5e+03      60      66 ..      83      89 ..      79      90 .. 0.80
   2 ?    1.8   0.0      0.42   4.7e+02       8      17 ..     166     175 ..     165     192 .. 0.80
   3 ?    9.1   3.0    0.0022       2.5      51      66 ..     191     206 ..     180     207 .. 0.74
   4 ?    8.6   3.3    0.0031       3.5       1      16 [.     193     208 ..     193     217 .. 0.76
   5 ?   10.9   1.3   0.00061      0.68       2      20 ..     219     237 ..     218     246 .] 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.5
                       Fer4_16 60 CqdvCPa 66
                                  C  +CP+
  gi|15668930|ref|NP_247734.1| 83 CGWMCPF 89
                                  7888998 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.42
                       Fer4_16   8 CaevCPtnai 17 
                                   C  vCP++ +
  gi|15668930|ref|NP_247734.1| 166 CRYVCPVGSL 175
                                   7777777665 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0022
                       Fer4_16  51 qeaitgCdiCqdvCPa 66 
                                   ++++ gC+ C++ CP+
  gi|15668930|ref|NP_247734.1| 191 ENKCVGCRLCERKCPM 206
                                   5678888888888886 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0031
                       Fer4_16   1 rCgtCgkCaevCPtna 16 
                                   +C++C+ C   CP + 
  gi|15668930|ref|NP_247734.1| 193 KCVGCRLCERKCPMQI 208
                                   5999999999999876 PP

  == domain 5  score: 10.9 bits;  conditional E-value: 0.00061
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C++C +C++vC  +a++  
  gi|15668930|ref|NP_247734.1| 219 CIRCFECMSVCKKGALSFS 237
                                   ***************9977 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.5    0.0034       3.8       2      23 ..     188     209 ..     187     213 .. 0.85
   2 ?    6.9   2.7    0.0091        10       2      20 ..     213     231 ..     213     235 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0034
                       Fer4_15   2 vvDrdaCigcglCvaeapevfe 23 
                                   ++D+++C gc lC + +p  ++
  gi|15668930|ref|NP_247734.1| 188 KLDENKCVGCRLCERKCPMQIK 209
                                   68*************9997665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0091
                       Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                   ++D+ +Ci c+ C+ ++++
  gi|15668930|ref|NP_247734.1| 213 KIDQMECIRCFECMSVCKK 231
                                   59*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1283  (0.07156); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1491.78
//
Query:       gi|15668931|ref|NP_247735.1|  [L=238]
Description: ferredoxin-type protein NapH [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-17   63.5  42.0    3.9e-14   52.3   4.7    4.1  4  Fer4_5    4Fe-4S binding domain
      5e-05   23.5   8.8      5e-05   23.5   8.8    2.9  3  Fer4_18   4Fe-4S dicluster domain
    0.00075   19.2  14.4      0.067   13.0   2.1    4.7  5  Fer4      4Fe-4S binding domain
     0.0018   18.4  16.5      0.013   15.6   1.0    3.2  4  Fer4_21   4Fe-4S dicluster domain
     0.0034   17.5  24.9      0.015   15.5   2.5    2.7  3  Fer4_9    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   16.2   3.9      0.012   16.2   3.9    3.4  3  Fer4_17   4Fe-4S dicluster domain
      0.032   14.4   1.1      0.032   14.4   1.1    2.2  2  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
       0.16   12.6  18.2       0.28   11.8   0.9    3.5  5  Fer4_7    4Fe-4S dicluster domain
       0.33   11.1  14.9      0.095   12.8   2.2    2.7  2  Fer4_6    4Fe-4S binding domain
       0.82   10.2  20.2        0.3   11.6   1.2    3.1  4  Fer4_8    4Fe-4S dicluster domain
        3.9    8.5  18.1        1.4    9.9   3.0    3.6  4  Fer4_16   4Fe-4S double cluster binding domain
        7.9    7.3  25.2        5.1    7.9   3.8    4.0  4  Fer4_4    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   3.9       5.8   8.7e+03      12      32 ..      14      32 ..      12      48 .. 0.68
   2 !   52.3   4.7   2.6e-17   3.9e-14       9      44 ..      49      84 ..      42      91 .. 0.84
   3 !   11.9   1.7   0.00011      0.17       6      38 ..     106     138 ..     101     142 .. 0.80
   4 !   20.8   8.5   1.8e-07   0.00027       4      37 ..     141     174 ..     139     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.8
                        Fer4_5 12 ivlvtllfGRafCgWiCPfGa 32
                                  +++++++f   fC   C fG+
  gi|15668931|ref|NP_247735.1| 14 LFFIYFVFLTSFCL--CFFGI 32
                                  56666666666663..55555 PP

  == domain 2  score: 52.3 bits;  conditional E-value: 2.6e-17
                        Fer4_5  9 flaivlvtllfGRafCgWiCPfGalqellakllrrk 44
                                  +++iv++tl++GR+fCgW+CP+G+l+el++kl+ + 
  gi|15668931|ref|NP_247735.1| 49 LVVIVVLTLILGRVFCGWMCPLGFLFELMYKLRMKL 84
                                  579****************************44444 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00011
                        Fer4_5   6 lilflaivlvtllfGR.afCgWiCPfGalqella 38 
                                   ++ +++ +++t ++   afC  +CP+G+l+ l++
  gi|15668931|ref|NP_247735.1| 106 YVVLILSLVLTYYLSIyAFCQ-VCPIGFLTNLYG 138
                                   56677777777777777****.********9987 PP

  == domain 4  score: 20.8 bits;  conditional E-value: 1.8e-07
                        Fer4_5   4 lllilflaivlvtllfGRafCgWiCPfGalqell 37 
                                    +li++++++ +++++  afC ++CP+Ga+  ++
  gi|15668931|ref|NP_247735.1| 141 ISLIILIFFLSLSFFVPMAFCRYFCPLGAFLSIF 174
                                   579**************************98665 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.2   1.7e+03       5      21 ..      63      79 ..      61      90 .. 0.82
   2 ?    1.5   0.1      0.21   3.2e+02       5      19 ..     160     174 ..     157     179 .. 0.86
   3 !   23.5   8.8   3.3e-08     5e-05      55      97 ..     182     225 ..     175     233 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                       Fer4_18  5 vcvyvcPyarvqsvlyd 21
                                  +c  +cP + +   +y 
  gi|15668931|ref|NP_247735.1| 63 FCGWMCPLGFLFELMYK 79
                                  79999**9988888876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                       Fer4_18   5 vcvyvcPyarvqsvl 19 
                                   +c y cP + + s++
  gi|15668931|ref|NP_247735.1| 160 FCRYFCPLGAFLSIF 174
                                   8*******9998875 PP

  == domain 3  score: 23.5 bits;  conditional E-value: 3.3e-08
                       Fer4_18  55 ekgagdcidcescvkvcPtgidirkGl.qleciscllcidacdk 97 
                                    k++++c++c+ c   cP++i i + l q eci c +c  +c+k
  gi|15668931|ref|NP_247735.1| 182 LKTNNNCVKCKLCEFKCPMQIKITEKLdQKECIRCFECKSSCKK 225
                                   57889******************9988689************86 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.75   1.1e+03      14      22 ..      64      72 ..      63      74 .. 0.78
   2 ?    0.5   0.0       0.4     6e+02      16      23 ..     126     133 ..     126     134 .. 0.79
   3 ?    0.5   0.0       0.4     6e+02      14      22 ..     161     169 ..     160     170 .. 0.85
   4 !   13.0   2.1   4.5e-05     0.067       6      20 ..     186     200 ..     184     202 .. 0.89
   5 !    9.1   0.4   0.00078       1.2       3      23 ..     208     228 ..     206     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.75
                                  HHHHSTTTE CS
                          Fer4 14 CvevCPvgA 22
                                  C  +CP g 
  gi|15668931|ref|NP_247735.1| 64 CGWMCPLGF 72
                                  8899**775 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.4
                                   HHSTTTEE CS
                          Fer4  16 evCPvgAI 23 
                                   +vCP g +
  gi|15668931|ref|NP_247735.1| 126 QVCPIGFL 133
                                   59**9976 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.4
                                   HHHHSTTTE CS
                          Fer4  14 CvevCPvgA 22 
                                   C   CP gA
  gi|15668931|ref|NP_247735.1| 161 CRYFCPLGA 169
                                   8889**998 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 4.5e-05
                                   TTSSS-THHHHHSTT CS
                          Fer4   6 ekCigCGaCvevCPv 20 
                                   + C++C++C+  CP 
  gi|15668931|ref|NP_247735.1| 186 NNCVKCKLCEFKCPM 200
                                   57************6 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.00078
                                   EETTTSSS-THHHHHSTTTEE CS
                          Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                    d+  Ci+C +C + C  +A+
  gi|15668931|ref|NP_247735.1| 208 LDQKECIRCFECKSSCKKDAL 228
                                   68999************9998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1         7     1e+04      46      53 ..      63      70 ..      59      71 .. 0.76
   2 ?   -1.8   0.2       2.4   3.6e+03      49      53 ..     126     130 ..     124     134 .. 0.74
   3 !   15.6   1.0     9e-06     0.013      14      54 ..     161     201 ..     158     205 .. 0.69
   4 !   13.3   1.0   4.6e-05     0.069       3      22 ..     208     227 ..     206     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7
                       Fer4_21 46 lCssvCPv 53
                                   C  +CP+
  gi|15668931|ref|NP_247735.1| 63 FCGWMCPL 70
                                  58888995 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.4
                       Fer4_21  49 svCPv 53 
                                   +vCP+
  gi|15668931|ref|NP_247735.1| 126 QVCPI 130
                                   69997 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 9e-06
                       Fer4_21  14 CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPve 54 
                                   C   C+ ++   i   +      ++++Cv C+lC   CP++
  gi|15668931|ref|NP_247735.1| 161 CRYFCPLGAFLSIFSIKPFFQLKTNNNCVKCKLCEFKCPMQ 201
                                   677777777666644333333445899************85 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 4.6e-05
                       Fer4_21   3 idedkCigCgkCliaCedts 22 
                                   +d+++Ci C +C  +C++ +
  gi|15668931|ref|NP_247735.1| 208 LDQKECIRCFECKSSCKKDA 227
                                   799*************9744 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       8.6   1.3e+04      40      46 ..     126     128 ..     124     132 .. 0.49
   2 !   15.5   2.5   9.9e-06     0.015       8      49 ..     161     201 ..     159     203 .. 0.82
   3 !   14.8  14.8   1.6e-05     0.024       1      50 [.     187     227 ..     187     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8.6
                        Fer4_9  40 gaCveaC 46 
                                   +    +C
  gi|15668931|ref|NP_247735.1| 126 Q----VC 128
                                   2....23 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 9.9e-06
                        Fer4_9   8 CveaCpagvv.vedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   C + Cp g++ +  + + + +l+  +  +C++C+ C+ +Cp +
  gi|15668931|ref|NP_247735.1| 161 CRYFCPLGAFlSIFSIKPFFQLKTNN--NCVKCKLCEFKCPMQ 201
                                   88999999987777888888877664..6************98 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 1.6e-05
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   +C++C+ C+ +Cp+++ + ++  +k         +Ci C +C   C+k+a
  gi|15668931|ref|NP_247735.1| 187 NCVKCKLCEFKCPMQIKITEKLDQK---------ECIRCFECKSSCKKDA 227
                                   6****************99999888.........5************997 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.2   4.8e+03       8      16 ..      64      72 ..      62     100 .. 0.55
   2 ?   16.2   3.9   7.8e-06     0.012      42      60 ..     184     202 ..     175     203 .. 0.88
   3 ?    7.5   2.6    0.0039       5.9      44      58 ..     211     225 ..     204     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.2
                       Fer4_17  8 ClpeCpsye 16
                                  C  +Cp + 
  gi|15668931|ref|NP_247735.1| 64 CGWMCPLGF 72
                                  555666533 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 7.8e-06
                       Fer4_17  42 kaslCieCgeCerkCPqgl 60 
                                   + ++C++C++Ce kCP+++
  gi|15668931|ref|NP_247735.1| 184 TNNNCVKCKLCEFKCPMQI 202
                                   5799*************97 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0039
                       Fer4_17  44 slCieCgeCerkCPq 58 
                                   ++Ci C eC+++C +
  gi|15668931|ref|NP_247735.1| 211 KECIRCFECKSSCKK 225
                                   689*******99976 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.1   2.1e-05     0.032      47      88 ..     162     201 ..     156     208 .. 0.76
   2 ?   -0.4   1.2      0.86   1.3e+03      70      84 ..     208     222 ..     202     232 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                                   HHH-TTS-EEEEETTTTSSEEEEE-C.CC--S--HHHHH-TT- CS
                        ETF_QO  47 qryCPagvyeivedeeakekklqina.qnCvhCktCdikdpsq 88 
                                   + +CP g +  + +    ++ +q+ + +nCv Ck C+ k p q
  gi|15668931|ref|NP_247735.1| 162 RYFCPLGAFLSIFSI---KPFFQLKTnNNCVKCKLCEFKCPMQ 201
                                   568888888777555...56777754168***********998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.86
                                   E-CCC--S--HHHHH CS
                        ETF_QO  70 inaqnCvhCktCdik 84 
                                   ++ ++C+ C  C   
  gi|15668931|ref|NP_247735.1| 208 LDQKECIRCFECKSS 222
                                   677899999999755 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.5   5.2e+03       7      15 ..      63      71 ..      62      98 .. 0.76
   2 ?   -2.6   0.1       5.8   8.6e+03      46      50 ..     126     130 ..     123     133 .. 0.65
   3 ?    7.8   5.6    0.0034       5.1      35      51 ..     185     201 ..     159     202 .. 0.59
   4 ?    5.6  13.1     0.016        24       2      52 .]     188     227 ..     187     227 .. 0.83
   5 ?   11.8   0.9   0.00019      0.28       2      25 ..     213     236 ..     212     238 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.5
                        Fer4_7  7 aCvaaCpvk 15
                                  +C  +Cp +
  gi|15668931|ref|NP_247735.1| 63 FCGWMCPLG 71
                                  577778754 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.8
                        Fer4_7  46 avCPt 50 
                                   +vCP 
  gi|15668931|ref|NP_247735.1| 126 QVCPI 130
                                   46664 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0034
                        Fer4_7  35 pekClgCgaCvavCPtg 51 
                                    ++C+ C+ C+  CP +
  gi|15668931|ref|NP_247735.1| 185 NNNCVKCKLCEFKCPMQ 201
                                   46788888888888865 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.016
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   C++C+ C+  Cp++ i+++e+          +d+ +C+ C +C + C ++a
  gi|15668931|ref|NP_247735.1| 188 CVKCKLCEFKCPMQ-IKITEK----------LDQKECIRCFECKSSCKKDA 227
                                   ************65.555554..........78889***********9886 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 0.00019
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeene 25 
                                   Ci C  C + C+ +a+++ ++ ++
  gi|15668931|ref|NP_247735.1| 213 CIRCFECKSSCKKDALSFSYAFKK 236
                                   *****************9987655 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.2   6.4e-05     0.095       7      23 ..     186     202 ..     184     202 .. 0.92
   2 ?    6.9   1.3    0.0046       6.9       9      24 .]     213     228 ..     209     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.4e-05
                        Fer4_6   7 dkCigCgdCvrvCPega 23 
                                   ++C+ C  C+  CP+++
  gi|15668931|ref|NP_247735.1| 186 NNCVKCKLCEFKCPMQI 202
                                   89************985 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0046
                        Fer4_6   9 CigCgdCvrvCPegai 24 
                                   Ci C +C + C  +a+
  gi|15668931|ref|NP_247735.1| 213 CIRCFECKSSCKKDAL 228
                                   ***********98875 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         4     6e+03      11      19 ..      64      72 ..      63     101 .. 0.61
   2 ?   -3.1   0.0       7.6   1.1e+04      57      63 ..     161     167 ..     159     169 .. 0.65
   3 ?   11.3   2.4   0.00025      0.37      49      64 ..     186     201 ..     181     207 .. 0.63
   4 ?   11.6   1.2    0.0002       0.3       3      16 ..     211     224 ..     209     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4
                        Fer4_8 11 CqsaCpvlr 19
                                  C  +Cp+  
  gi|15668931|ref|NP_247735.1| 64 CGWMCPLGF 72
                                  666888433 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.6
                        Fer4_8  57 CtevCpv 63 
                                   C+  Cp 
  gi|15668931|ref|NP_247735.1| 161 CRYFCPL 167
                                   6666775 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00025
                        Fer4_8  49 wsCttcgaCtevCpvg 64 
                                   ++C+ c+ C+ +Cp++
  gi|15668931|ref|NP_247735.1| 186 NNCVKCKLCEFKCPMQ 201
                                   4455555555555554 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.0002
                        Fer4_8   3 ekCieCgaCqsaCp 16 
                                   ++Ci+C+ C+s+C 
  gi|15668931|ref|NP_247735.1| 211 KECIRCFECKSSCK 224
                                   78***********5 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       5.9   8.8e+03      62      65 ..     126     129 ..     122     134 .. 0.61
   2 ?   -0.6   0.0       1.8   2.8e+03       8      17 ..     161     170 ..     159     178 .. 0.76
   3 ?    9.9   3.0   0.00096       1.4       1      19 [.     187     206 ..     187     212 .. 0.79
   4 ?    7.4   1.3    0.0057       8.5       2      20 ..     213     231 ..     212     238 .] 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.9
                       Fer4_16  62 dvCP 65 
                                   +vCP
  gi|15668931|ref|NP_247735.1| 126 QVCP 129
                                   2444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.8
                       Fer4_16   8 CaevCPtnai 17 
                                   C   CP +a+
  gi|15668931|ref|NP_247735.1| 161 CRYFCPLGAF 170
                                   7778887776 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00096
                       Fer4_16   1 rCgtCgkCaevCPtna.ike 19 
                                   +C++C+ C   CP +  i+e
  gi|15668931|ref|NP_247735.1| 187 NCVKCKLCEFKCPMQIkITE 206
                                   6************9864554 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0057
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C++C +C ++C  +a++  
  gi|15668931|ref|NP_247735.1| 213 CIRCFECKSSCKKDALSFS 231
                                   ***************9876 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.5       9.7   1.5e+04       7      10 ..     125     128 ..     123     129 .. 0.67
   2 ?    4.3   0.1     0.046        69      10      16 ..     161     167 ..     158     172 .. 0.88
   3 ?    7.7   3.6    0.0039       5.8       2      17 .]     186     201 ..     185     201 .. 0.90
   4 ?    7.9   3.8    0.0034       5.1       1      15 [.     210     224 ..     210     229 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.7
                        Fer4_4   7 CgsC 10 
                                   C +C
  gi|15668931|ref|NP_247735.1| 125 CQVC 128
                                   5555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.046
                        Fer4_4  10 CvaaCPq 16 
                                   C+++CP 
  gi|15668931|ref|NP_247735.1| 161 CRYFCPL 167
                                   ******6 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0039
                        Fer4_4   2 erCigCgsCvaaCPqg 17 
                                   ++C+ C+ C+  CP++
  gi|15668931|ref|NP_247735.1| 186 NNCVKCKLCEFKCPMQ 201
                                   79********999985 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0034
                        Fer4_4   1 qerCigCgsCvaaCP 15 
                                   q+ Ci+C  C ++C+
  gi|15668931|ref|NP_247735.1| 210 QKECIRCFECKSSCK 224
                                   688***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1407  (0.0784762); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1525.28
//
Query:       gi|15668932|ref|NP_247736.1|  [L=278]
Description: hypothetical protein MJ_0751 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-24   85.6   1.4    2.4e-24   85.0   0.1    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00012   22.3   3.2    0.00012   22.3   3.2    1.5  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.041   14.2   0.9      0.073   13.4   0.9    1.4  1  C1_2            C1 domain
       0.49   10.0   8.9       0.43   10.2   0.5    2.4  2  RGI1            Respiratory growth induced protein 1
        3.9    7.9   5.7          9    6.7   0.5    3.1  4  DUF4160         Domain of unknown function (DUF4160)
        7.9    6.7   8.5        5.5    7.2   0.1    3.5  4  Sep15_SelM      Sep15/SelM redox domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.97   2.9e+03       1      28 [.     109     136 ..     109     138 .. 0.79
   2 !   85.0   0.1   8.1e-28   2.4e-24       1      69 []     192     259 ..     192     259 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.97
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTS 28 
                                   f+k +e+++ k  ++ +k+++  + y+ 
  gi|15668932|ref|NP_247736.1| 109 FSKKREKIQKKLSNKPMKLKTLMEKYSG 136
                                   6677889999999999999988888876 PP

  == domain 2  score: 85.0 bits;  conditional E-value: 8.1e-28
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                   f+kl+ ++eykak+ G  ve+vnp+ TSk C+ Cg+k+++ + +r++kC+nC++++drDv+A +N++k+
  gi|15668932|ref|NP_247736.1| 192 FSKLQFFIEYKAKWDGLDVEYVNPSRTSKLCPICGCKLDP-NGQRLLKCNNCNLVFDRDVVATFNLFKK 259
                                   89**************************************.*************************996 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   3.2     4e-08   0.00012      45     109 ..     101     163 ..      63     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4e-08
                    OrfB_IS605  45 rlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhllhklathliktlkevgve 109
                                   +lk+  ++++k++ ++q+kl+ +    k ++ + +++ + +r++ ++lhk+++ li +  + +v+
  gi|15668932|ref|NP_247736.1| 101 KLKRIHENFSKKREKIQKKLSNKP--MKLKTLMEKYSGREKRKVEDYLHKISKFLISEALKYNVK 163
                                   6899999**************999..9*****************************999998886 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   2.4e-05     0.073      11      43 ..     212     247 ..     194     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                          C1_2  11 kgedssesfnCsaCgrkidgff...YsCseCdfslh 43 
                                   + ++s  s+ C +Cg k d++     +C+ C+ +++
  gi|15668932|ref|NP_247736.1| 212 YVNPSRTSKLCPICGCKLDPNGqrlLKCNNCNLVFD 247
                                   66789999*********6555555********9988 PP

>> RGI1  Respiratory growth induced protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   2.9     0.019        56      77     124 ..     106     156 ..      58     161 .. 0.84
   2 ?   10.2   0.5   0.00014      0.43      88     115 ..     162     189 ..     157     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.019
                          RGI1  77 harlkyyppfilkevhdnlekikptvnknskkfkrnlq...hhvkkhlikd 124
                                   h +++   + i k+  ++  k+k+ ++k s + kr+++   h++ k li +
  gi|15668932|ref|NP_247736.1| 106 HENFSKKREKIQKKLSNKPMKLKTLMEKYSGREKRKVEdylHKISKFLISE 156
                                   55555556678899999999********99999998875557788888876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00014
                          RGI1  88 lkevhdnlekikptvnknskkfkrnlqh 115
                                   +k   ++l  i+ +vnk+sk f+r l+ 
  gi|15668932|ref|NP_247736.1| 162 VKILMEDLTNIREAVNKKSKNFRRRLNR 189
                                   5777899*****************9975 PP

>> DUF4160  Domain of unknown function (DUF4160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.091   2.7e+02      45      65 ..      17      37 ..       4      38 .. 0.83
   2 ?    6.7   0.5     0.003         9      12      63 ..      64     118 ..      54     119 .. 0.82
   3 ?   -1.5   0.0       1.1   3.4e+03      41      62 ..     133     154 ..     127     156 .. 0.79
   4 ?   -1.3   0.1      0.92   2.8e+03      35      61 ..     157     183 ..     142     190 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.091
                       DUF4160 45 kelklieewveehqeellekW 65
                                  ++   i  +v ++q++++e+W
  gi|15668932|ref|NP_247736.1| 17 RKFITINLVVSDYQKKFIEEW 37
                                  56666778899********** PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.003
                       DUF4160  12 dheppHvHv.kyggdeakiwl..edvellegsglpkkelklieewveehqeelle 63 
                                   + +  H+     +++++ +++  +d+++++  +l   +lk+i e   +++e++ +
  gi|15668932|ref|NP_247736.1|  64 PKNFEHIMTiDINEKNITYSIfdKDGNVIKTTRLDVYKLKRIHENFSKKREKIQK 118
                                   5566677775558889999**************************9999999865 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.1
                       DUF4160  41 glpkkelklieewveehqeell 62 
                                   +++ +e +++e+++++ ++ l+
  gi|15668932|ref|NP_247736.1| 133 KYSGREKRKVEDYLHKISKFLI 154
                                   5788999999999988777776 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.92
                       DUF4160  35 ellegsglpkkelklieewveehqeel 61 
                                    l+++ ++   +l +i+e v ++++++
  gi|15668932|ref|NP_247736.1| 157 ALKYNVKILMEDLTNIREAVNKKSKNF 183
                                   555555666778888888888877765 PP

>> Sep15_SelM  Sep15/SelM redox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0018       5.5      46      74 ..      84     112 ..      63     114 .. 0.90
   2 ?    2.9   0.0      0.04   1.2e+02      14      38 ..     192     214 ..     184     218 .. 0.78
   3 ?   -4.1   0.4         6   1.8e+04       6      11 ..     224     229 ..     222     230 .. 0.86
   4 ?   -0.6   0.1       0.5   1.5e+03       2      13 ..     235     246 ..     234     254 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0018
                                   EE-SSS---EEEE-SSS-HHHHHHHHHHH CS
                    Sep15_SelM  46 lldedgeeverislekwdrdeieelleek 74 
                                   ++d+dg+++++ +l+ ++ + i+e +++k
  gi|15668932|ref|NP_247736.1|  84 IFDKDGNVIKTTRLDVYKLKRIHENFSKK 112
                                   79**********************99887 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.04
                                   THHHHHHTTTHH.HHBTTEEEEEES CS
                    Sep15_SelM  14 lpevkaFvkedaaakfpnlevkyvr 38 
                                   + +++ F++ +a  k++ l+v+yv+
  gi|15668932|ref|NP_247736.1| 192 FSKLQFFIEYKA--KWDGLDVEYVN 214
                                   567888999988..*********98 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 6
                                   ETT--- CS
                    Sep15_SelM   6 vcgckl 11 
                                   +cgckl
  gi|15668932|ref|NP_247736.1| 224 ICGCKL 229
                                   79***8 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.5
                                   EEEEETT---ST CS
                    Sep15_SelM   2 avlevcgcklnr 13 
                                   ++l++++c+l +
  gi|15668932|ref|NP_247736.1| 235 RLLKCNNCNLVF 246
                                   6899****9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1719  (0.0958782); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1786.49
//
Query:       gi|15668933|ref|NP_247737.1|  [L=76]
Description: hypothetical protein MJ_0752 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.1   0.1      0.019   14.9   0.1    1.1  1  FERM_F1   FERM F1 ubiquitin-like domain
       0.12   12.3   0.1       0.22   11.5   0.1    1.5  1  Rho_N     Rho termination factor, N-terminal domain
       0.26   11.8   3.5       0.32   11.5   3.5    1.2  1  DUF1322   Protein of unknown function (DUF1322)


Domain annotation for each model (and alignments):
>> FERM_F1  FERM F1 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   3.3e-06     0.019      28      67 ..      28      67 ..      10      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-06
                       FERM_F1 28 elcieaakkvgitpvylslFalasekekvWypPnhvfevd 67
                                  + ci+ a ++git       a+++e ++ Wyp  h+  ++
  gi|15668933|ref|NP_247737.1| 28 NFCIDKAMELGITSYAKLRKAIYNEWKEKWYPKYHTHYCH 67
                                  68***********9999999************99987655 PP

>> Rho_N  Rho termination factor, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.7e-05      0.22      12      27 ..      32      47 ..      31      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                                  HHHHHTT-TTGGGS-H CS
                         Rho_N 12 aiAkelgienysrlRK 27
                                  + A elgi+ y++lRK
  gi|15668933|ref|NP_247737.1| 32 DKAMELGITSYAKLRK 47
                                  5799************ PP

>> DUF1322  Protein of unknown function (DUF1322)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.5   5.3e-05      0.32      27      69 ..       9      52 ..       1      56 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.3e-05
                       DUF1322 27 d.kYyfPvlmeiCsyndvkklkYdeLlevnkiaelkLekeiYek 69
                                  + kYy  v+  i  ++++ ++  d  +e+   +  kL+k iY+ 
  gi|15668933|ref|NP_247737.1|  9 EfKYYSDVVELIYDFKEMVNFCIDKAMELGITSYAKLRKAIYNE 52
                                  36****************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 534.26
//
Query:       gi|15668934|ref|NP_247738.1|  [L=210]
Description: hypothetical protein MJ_0753 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   14.8   2.9       0.25   11.1   0.0    3.1  4  DnaB_2    Replication initiation and membrane attachment


Domain annotation for each model (and alignments):
>> DnaB_2  Replication initiation and membrane attachment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       0.7   1.3e+04      48      55 ..       3      10 ..       2      11 .. 0.71
   2 ?    1.4   0.1     0.015   2.7e+02      14      41 ..      69      96 ..      66     108 .. 0.72
   3 ?    1.4   0.0     0.015   2.7e+02      19      35 ..     104     120 ..      88     129 .. 0.78
   4 ?   11.1   0.0   1.4e-05      0.25      22      55 ..     135     169 ..     125     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 0.7
                                  SHHHHHHH CS
                        DnaB_2 48 nlrYieki 55
                                  n++ i+ki
  gi|15668934|ref|NP_247738.1|  3 NMKIINKI 10
                                  77888887 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.015
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DnaB_2 14 pseletilywlddlglspevilllleya 41
                                   +e e+  + ++ l+l++e+i++ + ++
  gi|15668934|ref|NP_247738.1| 69 NNEEEIKTSNVSSLELTEELINEYVGIS 96
                                  5666666677788999999999877665 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.015
                                   HHHHHHHHHHHHHHHHH CS
                        DnaB_2  19 tilywlddlglspevil 35 
                                   ti++ +d++g+sp  ++
  gi|15668934|ref|NP_247738.1| 104 TIKQVCDKYGISPKCLK 120
                                   7999*******997665 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHHHHHHHHHHHHHHH.HHT--SHHHHHHH CS
                        DnaB_2  22 ywlddlglspevilllleyav.ekgkrnlrYieki 55 
                                   ++ + +g++p vi+ ++ ++  e+gk +l+  ++i
  gi|15668934|ref|NP_247738.1| 135 EIKEVYGIPPSVIKKAIVECMiEEGKIKLNTTNTI 169
                                   556779**************9888**999998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1362.91
//
Query:       gi|15668935|ref|NP_247739.1|  [L=185]
Description: hypothetical protein MJ_0754 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-79  265.8   4.6    1.4e-79  265.6   4.6    1.0  1  DUF2202         Uncharacterized protein domain (DUF2202)
    0.00011   22.6   0.7    0.00082   19.8   0.5    2.1  2  Rubrerythrin    Rubrerythrin
     0.0017   18.5   0.9     0.0054   16.8   0.2    1.9  2  HAD_2           Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.017   15.3   0.0        0.4   10.9   0.0    2.1  2  Ferritin_2      Ferritin-like domain
       0.03   14.4   0.4      0.094   12.8   0.1    1.9  2  Ribosomal_L19e  Ribosomal protein L19e
      0.034   14.7   0.0      0.073   13.6   0.0    1.6  1  TPPII_N         Tripeptidyl peptidase II N terminal
      0.083   13.2   0.5         10    6.5   0.0    2.2  2  Pneumo_M2       Pneumovirus M2 protein
      0.085   13.0   2.0       0.13   12.4   0.7    1.8  2  Imm40           Immunity protein 40


Domain annotation for each model (and alignments):
>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.6   4.6   6.4e-83   1.4e-79       1     161 [.      17     177 ..      17     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 265.6 bits;  conditional E-value: 6.4e-83
                       DUF2202   1 ekdsllymreeeklarDvYlelYdrwklqiflniakseqthtdavksllekYeledpvkederGkfedeelqelYnkLvek 81 
                                   ek++l++mreeeklarDvYl+lY++wklqif+nia+seqth+davk+llekY+++dpvk+d+ G+f++++++elY+kLvek
  gi|15668935|ref|NP_247739.1|  17 EKEGLIEMREEEKLARDVYLTLYNKWKLQIFKNIAESEQTHMDAVKYLLEKYNIPDPVKNDSIGVFSNPKFEELYKKLVEK 97 
                                   789****************************************************************************** PP

                       DUF2202  82 gsksledaLkvgatiedldiaDlekalketdnkdikevYenllkGsrnhlRsfvrkleergkeYepqyiseeefdeivss 161
                                   g+ks +daLkvgatiedldiaDlek++++tdn+dik vYenl+kGsrnh+R+fvr+l+++g +Y+pqyis+ee++ei+ss
  gi|15668935|ref|NP_247739.1|  98 GDKSEVDALKVGATIEDLDIADLEKWINKTDNEDIKFVYENLMKGSRNHMRAFVRMLNNYGSNYTPQYISKEEYEEIISS 177
                                   ******************************************************************************98 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.5   3.7e-07   0.00082      10     136 ..      28     153 ..      24     154 .. 0.87
   2 ?    5.1   0.0     0.012        28      26      67 ..     127     169 ..     104     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.7e-07
                                   HHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHH.... CS
                  Rubrerythrin  10 EssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLe.... 86 
                                   E  ar +Y  l+ k k       ++F+ +Ae E+ H + ++ llek++      vk++ ++++  ++ +++++k +e    
  gi|15668935|ref|NP_247739.1|  28 EKLARDVYLTLYNKWK------LQIFKNIAESEQTHMDAVKYLLEKYNIPDP--VKNDSIGVFSNPKFEELYKKLVEkgdk 100
                                   7889999999999999......67**********************999888..777888877777777788888888999 PP

                                   ...HHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin  87 ...eaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                      +a++ + + e   +  +e+  +k+ ne++k + ++l++  + H + + ++
  gi|15668935|ref|NP_247739.1| 101 sevDALKVGATIEDLDIADLEKWINKTDNEDIKFVYENLMKGSRNHMRAFVRM 153
                                   98889999999999999999999999999999999999999999999888665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.012
                                   TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SSB CS
                  Rubrerythrin  26 egypqiaelFeelAeeEreHakilnklleklepele.levkek 67 
                                     +++i+ ++e l +  r H + + ++l+++  ++   +++++
  gi|15668935|ref|NP_247739.1| 127 TDNEDIKFVYENLMKGSRNHMRAFVRMLNNYGSNYTpQYISKE 169
                                   44899999**********************9999985554444 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   2.4e-06    0.0054       9      78 ..      50     132 ..      48     142 .. 0.87
   2 ?   -0.2   0.0      0.42   9.5e+02      15      45 ..     149     179 ..     139     184 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.4e-06
                         HAD_2   9 lldteeliiqafnelleeygls.elseeelrkliglslrellrklgeseeeee.............kieellrkyneekkk 75 
                                   ++ +e+++++a+++lle+y+++  ++++ +  + +++ +el++kl e+ +++e             +i++l +++n+  ++
  gi|15668935|ref|NP_247739.1|  50 IAESEQTHMDAVKYLLEKYNIPdPVKNDSIGVFSNPKFEELYKKLVEKGDKSEvdalkvgatiedlDIADLEKWINKTDNE 130
                                   8899******************999***********************999999999999999999888886666666665 PP

                         HAD_2  76 kev 78 
                                     +
  gi|15668935|ref|NP_247739.1| 131 -DI 132
                                   .33 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.42
                         HAD_2  15 liiqafnelleeyglselseeelrkliglsl 45 
                                   + + ++n+   +y ++ +s+ee++++i  s+
  gi|15668935|ref|NP_247739.1| 149 AFVRMLNNYGSNYTPQYISKEEYEEIISSST 179
                                   4455555555666777888888888887776 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00018       0.4      33      71 ..      37      74 ..      16     114 .. 0.78
   2 ?    2.9   0.0     0.052   1.2e+02       4      68 ..     104     163 ..      88     173 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                    Ferritin_2 33 alldaevrevaeeiakheeaHveflkaaleGaaavakpt 71
                                  +l++++ ++++++ia+ e++H+++ k  le +  +++p 
  gi|15668935|ref|NP_247739.1| 37 TLYNKWKLQIFKNIAESEQTHMDAVKYLLE-KYNIPDPV 74
                                  6778999*******************9996.66666664 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.052
                    Ferritin_2   4 diLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaale..Gaaava 68 
                                   d L++  + E l +a  ++ ++       ++ +++++ v+e+++k  ++H++++ ++l+  G+++ +
  gi|15668935|ref|NP_247739.1| 104 DALKVGATIEDLDIADLEKWIN-------KTDNEDIKFVYENLMKGSRNHMRAFVRMLNnyGSNYTP 163
                                   4444444444444444444444.......44455556666666777777777777777666766654 PP

>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.2e-05     0.094     103     135 ..      20      52 ..      16      60 .. 0.89
   2 ?   -1.6   0.0       1.1   2.5e+03      95     121 ..     145     174 ..     141     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                                   HHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHH CS
                Ribosomal_L19e 103 lLkelrekkkidkktYrelYrkakGgefknkav 135
                                    L e+re++k+ +  Y +lY+k k   fkn a+
  gi|15668935|ref|NP_247739.1|  20 GLIEMREEEKLARDVYLTLYNKWKLQIFKNIAE 52 
                                   5889*************************9875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHT...TSS-HHHHHHH CS
                Ribosomal_L19e  95 kriRalRrlLkelrek...kkidkktYrel 121
                                   + +Ra  r+L+++ ++   + i+k++Y+e+
  gi|15668935|ref|NP_247739.1| 145 NHMRAFVRMLNNYGSNytpQYISKEEYEEI 174
                                   567888888888866522245888888765 PP

>> TPPII_N  Tripeptidyl peptidase II N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.3e-05     0.073      86     123 ..     123     160 ..      70     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                                   HHTTS-HHHHHHHHHHHHHH-TT-THHHHHHHHHHHHH CS
                       TPPII_N  86 qiakldlenAekiYnevvaahPkHLaAhLlliqniess 123
                                    i+k+d e  + +Y+++++   +H+ A + +++n  s+
  gi|15668935|ref|NP_247739.1| 123 WINKTDNEDIKFVYENLMKGSRNHMRAFVRMLNNYGSN 160
                                   599*******************************9886 PP

>> Pneumo_M2  Pneumovirus M2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0046        10      52      82 ..      44      74 ..      24      81 .. 0.85
   2 ?    5.0   0.1     0.013        30      30      54 ..     133     157 ..     124     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0046
                     Pneumo_M2 52 nnifdeihwtpknlldatqqflqhlnipedi 82
                                   +if +i  + +  +da + +l++ nip+ +
  gi|15668935|ref|NP_247739.1| 44 LQIFKNIAESEQTHMDAVKYLLEKYNIPDPV 74
                                  479999*99*******************876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.013
                     Pneumo_M2  30 tfnhknilqfnhnhldnhqrllnni 54 
                                    f + n+++   nh+    r+lnn 
  gi|15668935|ref|NP_247739.1| 133 KFVYENLMKGSRNHMRAFVRMLNNY 157
                                   58899******************96 PP

>> Imm40  Immunity protein 40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.1   2.5e+03      50      52 ..      41      43 ..      18      79 .. 0.60
   2 ?   12.4   0.7   5.6e-05      0.13      16      86 ..     104     172 ..      97     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                         Imm40 50 sws 52
                                  +w 
  gi|15668935|ref|NP_247739.1| 41 KWK 43
                                  332 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.6e-05
                         Imm40  16 dikeiiviledlkigilGGdvykielenikisyeswsinkdpgesleeyvrksklralryiedyekqaekl 86 
                                   d+ ++   +edl i+ l   + k ++e+ik+ ye+        + +  +vr    +  +y  +y  ++e +
  gi|15668935|ref|NP_247739.1| 104 DALKVGATIEDLDIADLEKWINKTDNEDIKFVYENLMK--GSRNHMRAFVRMLNNYGSNYTPQYISKEEYE 172
                                   555666789*************************9754..44589999******99999999998777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1190.99
//
Query:       gi|15668936|ref|NP_247740.1|  [L=342]
Description: N-acetylmuramoyl-L-alanine amidase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-05   25.8   0.1      0.015   15.9   0.0    2.6  2  CW_binding_2  Putative cell wall binding repeat 2


Domain annotation for each model (and alignments):
>> CW_binding_2  Putative cell wall binding repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.3   0.00051       9.1      19      67 ..      32      87 ..      15      91 .. 0.64
   2 !   15.9   0.0   8.3e-07     0.015       1      43 [.     103     163 ..     103     184 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00051
                                  EET.THHHHHHHHHHHHHT--EEEE-.TS.SS.-HHHHHHH.......EEEES-TTTS- CS
                  CW_binding_2 19 atg.faDALsaaalaakknaPiLLtd.kl.dtalkalksat.......vyilGGegvvs 67
                                  ++   aD  +a  +a ++na ++ t+ +  +++l    +++       v+i+GG  +v 
  gi|15668936|ref|NP_247740.1| 32 VSDnCADQCTALEVADALNATVITTEwGIyNESL---IDEIlalnpdkVIIIGGPLAVV 87
                                  3334588889999999999******974332232...2223444566799****87775 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 8.3e-07
                                   EE--SSHHHHHHHHHH.H...............EEETTHH.HHHHHHHHHHHT.--EEEE- CS
                  CW_binding_2   1 RiaGaDRyeTaaaiak.a...............latgfaD.ALsaaalaakkn.aPiLLtd 43 
                                   Ri+G++RyeT+a++   +               +  gf D AL  +    k++   +LLt+
  gi|15668936|ref|NP_247740.1| 103 RIGGSNRYETNANVTLrFqnqfryafgnnttvcVCHGFDDiALNETMGLIKNGtCLVLLTN 163
                                   9*************98558888877777666554667877666333222233424666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1245  (0.0694406); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2084.53
//
Query:       gi|15668937|ref|NP_247741.1|  [L=136]
Description: hypothetical protein MJ_0756 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 909.37
//
Query:       gi|15668938|ref|NP_247742.1|  [L=260]
Description: hypothetical protein MJ_0757 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-79  267.2   1.4    1.1e-79  267.0   1.4    1.0  1  DUF166          Domain of unknown function
     0.0048   16.9   0.2      0.015   15.3   0.2    1.9  1  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
  ------ inclusion threshold ------
       0.18   11.9   4.6         14    5.9   0.1    3.6  3  Fe_hyd_SSU      Iron hydrogenase small subunit
        2.3    8.5   5.6         22    5.3   0.3    2.8  3  Phage_DsbA      Transcriptional regulator DsbA


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.0   1.4   2.5e-83   1.1e-79       3     219 ..      22     259 ..      20     260 .] 0.96

  Alignments for each domain:
  == domain 1  score: 267.0 bits;  conditional E-value: 2.5e-83
                        DUF166   3 lts..geyGervvenilnepdfersl..............ivavvevpeeldefiedpeelLpelkeaDiviaytlhpDll 67 
                                   +++  ++++e++++n+lnepdf+r++               v+ + ++e  +ef+++p ++Lpel+e Di+ia +lh+Dll
  gi|15668938|ref|NP_247742.1|  22 IYHknNQRMEKFYKNLLNEPDFCRICddcyncrgnwtfknNVKNIVIEEVYEEFVDNPYDYLPELPEGDICIA-QLHEDLL 101
                                   5554599*********************************677777777777*********************.******* PP

                        DUF166  68 lelaekakekkvkalivpaeapk...aglrkelkekleelgievavpkpfCslee.egkpkideFlee..fGkPelevevk 142
                                   +el+  +kek++kalivp+e+p+    +lr++lk+ +++++ie+++pkpfCsle+ eg+++i++F+++  +GkPele+ev+
  gi|15668938|ref|NP_247742.1| 102 YELPLLLKEKGYKALIVPSETPHdlsLALRRDLKRVCSNYNIEFENPKPFCSLEKkEGNEYINKFIDYfkIGKPELEIEVE 182
                                   *************************99***************************999***********99*********** PP

                        DUF166 143 dgkikkVeVlrsapCGstwyvakklkGkeveeaeekageahqsYpClAsmerdfelketklhkAgyihkeavekAlk 219
                                   +g ik+V+V+ sapCG+t+y+ak+lkGk++++ +e++++ah++YpClAsme+d+el++t+lhkAgyi+ e vekAlk
  gi|15668938|ref|NP_247742.1| 183 NGLIKDVKVKISAPCGETYYIAKRLKGKAIDDLKEEIANAHHNYPCLASMEMDKELGDTILHKAGYIAFEVVEKALK 259
                                   ***************************************************************************98 PP

>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   3.3e-06     0.015       7      56 ..     165     213 ..     160     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.3e-06
                                   EEEEEETTEEEEEEEEEETTEEEEEEEEESBSSSSHCHHHHHHHTTSBSS CS
                Lip_prot_lig_C   7 kkkkrfdwGtvevrldvekgiIkdikiyGDffgpkdieeleekLigvkye 56 
                                   k   +f++G+ e++++ve+g+Ikd+k+       +++  ++++L+g+ ++
  gi|15668938|ref|NP_247742.1| 165 KFIDYFKIGKPELEIEVENGLIKDVKVKISA-PCGETYYIAKRLKGKAID 213
                                   55678*******************9986543.456666677777776655 PP

>> Fe_hyd_SSU  Iron hydrogenase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3     0.017        75      25      40 ..      26      41 ..      24      42 .. 0.91
   2 ?    5.9   0.1    0.0031        14      24      41 ..      63      80 ..      49      84 .. 0.83
   3 ?    1.8   0.0     0.058   2.6e+02       3      26 ..     202     225 ..     200     229 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.017
                                  G-HHHHHHHHCTTSST CS
                    Fe_hyd_SSU 25 eNpevkklYkeflgep 40
                                  +N+ + k+Yk+ l+ep
  gi|15668938|ref|NP_247742.1| 26 NNQRMEKFYKNLLNEP 41
                                  7999*********998 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0031
                                  GG-HHHHHHHHCTTSSTT CS
                    Fe_hyd_SSU 24 heNpevkklYkeflgepl 41
                                   +N  + ++Y+ef + p+
  gi|15668938|ref|NP_247742.1| 63 VKNIVIEEVYEEFVDNPY 80
                                  6899**********9996 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.058
                                   HHHHHHHCCCHHHHHCCC-SGGG- CS
                    Fe_hyd_SSU   3 vrkkRakalykiDkkkklrkSheN 26 
                                   +++kR k+   +D k+++  +h N
  gi|15668938|ref|NP_247742.1| 202 YIAKRLKGKAIDDLKEEIANAHHN 225
                                   7999****999999********99 PP

>> Phage_DsbA  Transcriptional regulator DsbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3    0.0049        22      35      51 ..      15      31 ..      12      39 .. 0.85
   2 ?   -3.1   0.2       2.2   9.8e+03      51      63 ..      69      81 ..      62      83 .. 0.58
   3 ?    5.0   0.0    0.0065        29       8      24 ..     176     192 ..     173     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0049
                    Phage_DsbA 35 dFnkllklYhkdnRdve 51
                                  +F + + +Yhk+n   e
  gi|15668938|ref|NP_247742.1| 15 EFMRAVFIYHKNNQRME 31
                                  68999********8766 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.2
                    Phage_DsbA 51 eeaktekvveLYe 63
                                  ee   e v++ Y+
  gi|15668938|ref|NP_247742.1| 69 EEVYEEFVDNPYD 81
                                  3444455666666 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0065
                    Phage_DsbA   8 kLkidsereLikDiaiR 24 
                                    L i+ e+ LikD++++
  gi|15668938|ref|NP_247742.1| 176 ELEIEVENGLIKDVKVK 192
                                   589**********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1677.34
//
Query:       gi|15668939|ref|NP_247743.1|  [L=159]
Description: hypothetical protein MJ_0758 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1152.51
//
Query:       gi|15668940|ref|NP_247744.1|  [L=118]
Description: hypothetical protein MJ_0759 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-45  152.6  12.3      4e-45  152.4  12.3    1.0  1  DUF5400   Family of unknown function (DUF5400)
  ------ inclusion threshold ------
        6.7    6.6   8.8       0.55   10.1   3.2    2.0  2  DUF3487   Protein of unknown function (DUF3487)


Domain annotation for each model (and alignments):
>> DUF5400  Family of unknown function (DUF5400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4  12.3   4.4e-49     4e-45       1     100 []      15     114 ..      15     114 .. 0.99

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 4.4e-49
                       DUF5400   1 vislaillssllsGfitfrllGmrlaphfavlilaliltlaalltkntivvylaillqvlaaltaytqilnilktsfqtsp 81 
                                   ++sl+++++++lsGf+tfrl+Gmrl+phfa+l++a+iltla+l+++n+i+ ylai++qv+++lt++++i+nilkt+fq+++
  gi|15668940|ref|NP_247744.1|  15 LVSLSVIFGAMLSGFATFRLTGMRLMPHFASLMIAFILTLASLFISNNIIGYLAIAFQVITPLTVCPTICNILKTQFQNTG 95 
                                   699****************************************************************************** PP

                       DUF5400  82 iyaahlalmtlllvlaias 100
                                   iy+ahlalm+++++la+++
  gi|15668940|ref|NP_247744.1|  96 IYSAHLALMGMMFILALGN 114
                                   ****************997 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.2   6.1e-05      0.55      15      72 ..       2      59 ..       1      67 [. 0.86
   2 ?   -0.4   0.3      0.11     1e+03      29      37 ..     102     110 ..      67     118 .] 0.57

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.1e-05
                       DUF3487 15 vVfrGltadEllvlaglglvvglvlglllallvgslaliptialllvllvvlvggkll 72
                                  v+ +G  ++E++ l++l++++g++l+ ++++ +  + l+p +a l++++++ +++ ++
  gi|15668940|ref|NP_247744.1|  2 VIKKGEIMNEIISLVSLSVIFGAMLSGFATFRLTGMRLMPHFASLMIAFILTLASLFI 59
                                  6779999******************99999988889999*999999888887776655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.11
                       DUF3487  29 aglglvvgl 37 
                                   a++g+++ l
  gi|15668940|ref|NP_247744.1| 102 ALMGMMFIL 110
                                   222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 884.56
//
Query:       gi|15668941|ref|NP_247745.1|  [L=275]
Description: hypothetical protein MJ_0760 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-19   70.2   0.0    4.3e-19   69.0   0.0    1.6  2  DrsE        DsrE/DsrF-like family
    6.8e-17   61.1   0.3    1.1e-13   50.7   0.0    2.3  2  TusA        Sulfurtransferase TusA
    3.1e-11   43.4   0.3    2.3e-06   27.6   0.0    2.7  3  DrsE_2      DsrE/DsrF/DrsH-like family
  ------ inclusion threshold ------
      0.026   14.7   1.6       0.12   12.6   0.3    2.2  2  UPF0180     Uncharacterised protein family (UPF0180)
      0.067   13.0   0.1       0.21   11.4   0.1    1.9  1  STN         Secretin and TonB N terminus short domain
       0.25   11.7   2.7        0.6   10.4   0.6    2.4  3  Phage_CI_C  Bacteriophage CI repressor C-terminal domain


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.2   1.2e+04      56      69 ..      41      54 ..      29      64 .. 0.55
   2 !   69.0   0.0   1.4e-22   4.3e-19       3     109 ..     159     266 ..     157     269 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.2
                                  TS---GGGGGGCGG CS
                          DrsE 56 deknlaellkalke 69
                                  + k++ +llk++  
  gi|15668941|ref|NP_247745.1| 41 QIKDIEKLLKKYNL 54
                                  44555555555544 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 1.4e-22
                                   EEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS..---TGGGTS---GGGGGGCGGGT-EEEEEHHHH CS
                          DrsE   3 vfilvtggpygseaarealelalaaaalghevsvffygdGvllllk..gqtanpadeknlaellkalkeygvklyvCgqaa 81 
                                   +fi++t+g  + e+a++ +++a +a++++++  +f+++dG+ l+lk   +  ++ +++ l +l++    +gvk+yvC+ +a
  gi|15668941|ref|NP_247745.1| 159 LFIINTTGTGNAEKAYATFMMADVALKMNLKPTIFLMMDGASLALKgeCDRVKHPAFPKLGDLVRDILSKGVKIYVCELSA 239
                                   79********************************************997888899************************** PP

                                   HHTT--GGGE-T--EEEE-HHHHHHHHH CS
                          DrsE  82 kargldededlgvgvevsglgelaelqn 109
                                   + rg+ e+ +l+ g+e++g++++ ++++
  gi|15668941|ref|NP_247745.1| 240 EFRGINEK-NLEEGFEIAGAPTFLNYLS 266
                                   ******76.7757**********99987 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00058       1.7      22      68 ..      25      67 ..      15      69 .. 0.82
   2 !   50.7   0.0   3.8e-17   1.1e-13       1      70 []      74     143 ..      74     143 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00058
                                  CCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEE CS
                          TusA 22 ekleegevlevladdpaatediprfakklghelveveeedgeyrivi 68
                                  +  eeg +l v +d ++ ++di++++kk +++  ev  ++++++i++
  gi|15668941|ref|NP_247745.1| 25 NDTEEG-ILVVETDGEEQIKDIEKLLKKYNLK-YEV--DGNVVKIYV 67
                                  555555.999*********************9.788..788888877 PP

  == domain 2  score: 50.7 bits;  conditional E-value: 3.8e-17
                                   EEEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-.GCC-EEEEEEE CS
                          TusA   1 ielDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelvevee.edgeyrivirk 70 
                                   +++++ G  CP+P++++   l k++ ge+le+++    +  d+ + +k +g+e+++ve+  dg+yri+++k
  gi|15668941|ref|NP_247745.1|  74 KTINVVGATCPGPIMMVSDMLSKMKNGEILEIICGKN-SLTDLTEGLKGMGNEIIKVEDkGDGTYRILVKK 143
                                   69********************************988.678****************99888*******98 PP

>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.2   3.6e+03      72      81 ..      93     102 ..      74     152 .. 0.67
   2 !   13.9   0.2   1.2e-05     0.036       5      54 ..     159     210 ..     155     217 .. 0.74
   3 !   27.6   0.0   7.7e-10   2.3e-06      90     150 ..     210     270 ..     195     271 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.2
                                   --SSS-GGGH CS
                        DrsE_2  72 klskmnmagi 81 
                                    lskm+ ++i
  gi|15668941|ref|NP_247745.1|  93 MLSKMKNGEI 102
                                   3444443333 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.2e-05
                                   EEEEE----H...HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GGG--- CS
                        DrsE_2   5 laiifskgtld..kalaalilAsgAaalglevtiFftFwGLnilrkeekkkv 54 
                                   l ii + gt +  ka+a++++A++A +++l+ tiF    G  +  k e ++v
  gi|15668941|ref|NP_247745.1| 159 LFIINTTGTGNaeKAYATFMMADVALKMNLKPTIFLMMDGASLALKGECDRV 210
                                   5666666554333**********************98777666666555555 PP

  == domain 3  score: 27.6 bits;  conditional E-value: 7.7e-10
                                   HHHCT---HHHHHHHHHHTT-EEEEEHHHHHHHT--GGGB-TT-EEE-HHHHHHHHHC-SE CS
                        DrsE_2  90 mkekgvasleeLleaakeagvklvaCqmtmdlmglkkeelidgveiagaatylkeaeeadv 150
                                   +k+   ++l +L+     +gvk++ C+++ +  g+++++l +g eiaga t+l+++++ +v
  gi|15668941|ref|NP_247745.1| 210 VKHPAFPKLGDLVRDILSKGVKIYVCELSAEFRGINEKNLEEGFEIAGAPTFLNYLSKPNV 270
                                   566678899**********************************************998776 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.23     7e+02      50      75 ..      24      50 ..      18      52 .. 0.74
   2 ?   12.6   0.3   3.9e-05      0.12       7      65 ..     110     167 ..     105     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.23
                       UPF0180 50 iedtetkapvInAsgk.taeeIlqeve 75
                                   +dte++++v++ +g   +++I++ ++
  gi|15668941|ref|NP_247745.1| 24 LNDTEEGILVVETDGEeQIKDIEKLLK 50
                                  578999999999999624577776665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.9e-05
                       UPF0180   7 egLsnvkeaLrekGYeVvdleteedaqsvdaiVvtGqdtnvmgiedtetkapvInAsgk 65 
                                   ++L+++ e L+  G e++++e+ + +  + ++V +G++++  +  ++  + ++In +g 
  gi|15668941|ref|NP_247745.1| 110 NSLTDLTEGLKGMGNEIIKVED-KGDGTYRILVKKGEKKEEKAAVTKIDELFIINTTGT 167
                                   79*******************5.88999********99999999999999*****9996 PP

>> STN  Secretin and TonB N terminus short domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   6.9e-05      0.21      30      50 ..      46      66 ..      45      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.9e-05
                           STN 30 deLLkgtgLqykitgntiris 50
                                  ++LLk ++L y+++gn+++i+
  gi|15668941|ref|NP_247745.1| 46 EKLLKKYNLKYEVDGNVVKIY 66
                                  68****************996 PP

>> Phage_CI_C  Bacteriophage CI repressor C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6    0.0002       0.6      43      75 ..      18      50 ..      14      80 .. 0.78
   2 ?   -0.0   0.0      0.36   1.1e+03      43      71 ..      88     116 ..      70     118 .. 0.85
   3 ?   -2.9   0.0       2.9   8.6e+03      30      47 ..     147     164 ..     126     167 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                    Phage_CI_C 43 ylvdkkeadvsdGkwLvdieGrlsirelariPv 75
                                   l+d   +d ++G   v+ +G+ +i+++ ++  
  gi|15668941|ref|NP_247745.1| 18 LLIDMILNDTEEGILVVETDGEEQIKDIEKLLK 50
                                  689999***********************9853 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.36
                    Phage_CI_C  43 ylvdkkeadvsdGkwLvdieGrlsirela 71 
                                   ++v    +++++G+ L  i G++s+ +l+
  gi|15668941|ref|NP_247745.1|  88 MMVSDMLSKMKNGEILEIICGKNSLTDLT 116
                                   667777789999*9999999999999986 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.9
                    Phage_CI_C  30 lkeplvieeekklylvdk 47 
                                    +e++++++ ++l+++++
  gi|15668941|ref|NP_247745.1| 147 KEEKAAVTKIDELFIINT 164
                                   233366666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1861.31
//
Query:       gi|15668942|ref|NP_247746.1|  [L=251]
Description: hypothetical protein MJ_0761 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-18   67.3   0.1      2e-18   66.7   0.1    1.3  1  TatD_DNase     TatD related DNase
    0.00035   19.9   0.3     0.0008   18.7   0.2    1.6  1  BsuBI_PstI_RE  BsuBI/PstI restriction endonuclease domain
     0.0028   17.0   1.1      0.022   14.1   1.1    2.3  1  Amidohydro_1   Amidohydrolase family
  ------ inclusion threshold ------
      0.013   15.6   0.1      0.029   14.4   0.1    1.6  1  Hpr_kinase_N   HPr Serine kinase N terminus
      0.093   13.2   0.4       0.13   12.8   0.4    1.2  1  P16-Arc        ARP2/3 complex 16 kDa subunit (p16-Arc)


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.1   5.5e-22     2e-18       1     178 [.       2     182 ..       2     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 5.5e-22
                                   EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSG..........GGHHHHHHHHTT.....TTTEEEEE---GGGGG CS
                    TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtss..........kdskavlelakk....ypnkvyavlGiHPnevd 67 
                                   iDaH+Hld ++f     e le+++ +g+++++++  ++           +++++++l  k    +  +v +++G+HP    
  gi|15668942|ref|NP_247746.1|   2 IDAHTHLDVRSF-----EDLEKMALSGIETIITCAHDPykmstpevylDHWDRLINLEVKrgemAGVEVKVAVGVHPMGYP 77 
                                   8********776.....778999999999999888888888888888778887777776666889999*********9999 PP

                                   CC.CCHHHHHHHHHHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES..-HHHHHHHHHHCG CS
                    TatD_DNase  68 easedlleelkelanvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrk..aeedlleilkeaa 146
                                   ++ e l+++l e+  +++++vvaiGe+GL y        e  + +++eql lAk+++ p++iH+ +   +e l+eilk ++
  gi|15668942|ref|NP_247746.1|  78 KNWEVLIKKLPEF--LDNENVVAIGETGLHY------LTEDEKNLLREQLYLAKDYNMPIIIHTPEknKKEALIEILKILD 150
                                   8778888999999..****************......4567899*********************9776666677776666 PP

                                   GCCS....EEEETT--S-HHHHHHHHHTTEEEEE-G CS
                    TatD_DNase 147 eaka....kvvlHsfsgsaeeakkflklgyyislsg 178
                                   e+k+     ++ H      +e   ++++++y++l+ 
  gi|15668942|ref|NP_247746.1| 151 EVKIkdslVMIDHI----NKETVDLIDRDVYVGLTV 182
                                   66664432333344....444445566667777665 PP

>> BsuBI_PstI_RE  BsuBI/PstI restriction endonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   2.2e-07    0.0008      25      89 ..      82     146 ..      62     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-07
                 BsuBI_PstI_RE  25 vieefaprFlkeaevlyvgdtedkvlvldeellkelgleidshkklPDivlydeeknlLvliEav 89 
                                   v+ + +p+Fl +++v+++g+t+ ++l+ de+ l + +l + +++++P i+   e+++   liE  
  gi|15668942|ref|NP_247746.1|  82 VLIKKLPEFLDNENVVAIGETGLHYLTEDEKNLLREQLYLAKDYNMPIIIHTPEKNKKEALIEIL 146
                                   5556689****************************************999998888888888866 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.1   6.1e-06     0.022      89     159 ..      71     140 ..       1     241 [. 0.62

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-06
                                   GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE.TSSCHHH CS
                  Amidohydro_1  89 gsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHa.letkgev 159
                                     +   ++++e l++   e++   ++ vv   +++ h  ++ ++++l+e l +ak++++p+ iH+    ++  
  gi|15668942|ref|NP_247746.1|  71 VHPMGYPKNWEVLIKKLPEFLD--NENVVAiGETGLHYLTEDEKNLLREQLYLAKDYNMPIIIHTpE-KNKKE 140
                                   4445566777777777766665..77888889*********************************52.33332 PP

>> Hpr_kinase_N  HPr Serine kinase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1     8e-06     0.029      44     101 ..      90     147 ..      87     171 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8e-06
                                   S-.--EEEEE-HHHHHHHHT-HHHHH..HHHHHHTT--S-EEEETTT---HHHHHHHH CS
                  Hpr_kinase_N  44 yfdperiqilGktElsYleklseeerkerleklfskkipciiltrgleppeellelae 101
                                   + d+e+++ +G+t l+Yl++ +++  +e+l    ++++p+ii t + + +e l+e+ +
  gi|15668942|ref|NP_247746.1|  90 FLDNENVVAIGETGLHYLTEDEKNLLREQLYLAKDYNMPIIIHTPEKNKKEALIEILK 147
                                   5689********************************************9****99865 PP

>> P16-Arc  ARP2/3 complex 16 kDa subunit (p16-Arc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   3.6e-05      0.13      57     114 ..     126     183 ..     103     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-05
                                   SS---S-S-HHHHHHHHHHHHHHHHTS-GGGHHHHHHHS-HHHHHHHHHHHHHHTT-- CS
                       P16-Arc  57 knppygakeqaakeralqlvlevLssikasdiekavksldkeeldvLmkYiYkgmesp 114
                                   + p + ++ ++ k++al  +l++L ++k +d   ++++ +ke++d++ + +Y g++ +
  gi|15668942|ref|NP_247746.1| 126 NMPIIIHTPEKNKKEALIEILKILDEVKIKDSLVMIDHINKETVDLIDRDVYVGLTVQ 183
                                   556677778999****************************************999543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1850.65
//
Query:       gi|15668943|ref|NP_247747.1|  [L=342]
Description: C4-dicarboxylate transporter [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-71  239.9  54.3    4.4e-71  239.8  54.3    1.0  1  SLAC1     Voltage-dependent anion channel
  ------ inclusion threshold ------
      0.021   14.8   4.7      0.021   14.8   4.7    2.7  3  WCOR413   Cold acclimation protein WCOR413


Domain annotation for each model (and alignments):
>> SLAC1  Voltage-dependent anion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.8  54.3     5e-75   4.4e-71       1     324 []       7     328 ..       7     328 .. 0.89

  Alignments for each domain:
  == domain 1  score: 239.8 bits;  conditional E-value: 5e-75
                         SLAC1   1 hftpawFaivMGtgilalllkalp.a..rglriislilfllalvlfllllvlyllrfilypeavrkelrhpveslflgtfp 78 
                                   +f+ +wFa+vMGtg+la+    +  +  + l+ is +lf+++++lf+++l+l++lr++ yp+++ +el+hpv s f +t++
  gi|15668943|ref|NP_247747.1|   7 NFESSWFAAVMGTGVLAVTS-LFYsEylPILKDISFLLFYFNILLFFVFLMLWILRWVKYPKNMIAELKHPVLSSFSPTVA 86 
                                   6999*************877.433223578999************************************************ PP

                         SLAC1  79 mglltilnglllvl.pgewlatlalvllW.igvllslltavvvvfllftek.eekleeitpawllpvvgllvvallgalla 156
                                   +++l++   + ++l +  + + l  + +W +g++ ++l++++v+f++f+++   kl++++p w++p+vgl+v++++g+l++
  gi|15668943|ref|NP_247747.1|  87 VAMLVLG--IDFILiK--NNLFLGKI-FWvFGAIGMFLFSLIVPFYMFKSEsI-KLDHVNPGWYIPPVGLIVIPIAGSLIM 161
                                   **75554..3333322..44556666.9*78*****************99745.5************************** PP

                         SLAC1 157 esqnpslqllgilvvslllwglGlllalvlfvlylyrlithklppaelrptlfiplGplgqgalallllgkaapk..aaev 235
                                   ++ +  ++ l ++++ ++ wg G++l+l+l+++++yr+i+h+++p++++pt++i+lGp+g g++al+++ +++p   ++e 
  gi|15668943|ref|NP_247747.1| 162 PHLTGVWHEL-TVLINYFGWGAGFFLYLALLAVVIYRFILHHPLPSAMAPTVWINLGPIGAGIVALINMVNNSPFitIKEP 241
                                   **77776778.9*****************************999*****************************99777777 PP

                         SLAC1 236 lkvlalllalflwglglfwllvavlsvls......lpvrlkfslswWaftFPlgalalatielgkaleseafkvlgtillv 310
                                   +++++++    +wg+gl+w l+a++++l       l     + +swWaf+FPlg++ ++t+ ++k ++ e + ++g++l++
  gi|15668943|ref|NP_247747.1| 242 FYIFSFI----FWGFGLWWSLMAIIMTLYyvkklkL----PYAMSWWAFIFPLGVYIASTHLVYKIFGFEIVDYIGFGLYW 314
                                   7777777....******************6665544....6**********************999*99************ PP

                         SLAC1 311 llvlvwllvlvgtl 324
                                   ll+++w+++l+ t+
  gi|15668943|ref|NP_247747.1| 315 LLFFFWIVTLIKTI 328
                                   ***********996 PP

>> WCOR413  Cold acclimation protein WCOR413
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.57   5.1e+03      68      83 ..     119     134 ..     116     152 .. 0.78
   2 ?   -1.7   1.3      0.26   2.3e+03      82     108 ..     172     200 ..     152     214 .. 0.62
   3 ?   14.8   4.7   2.3e-06     0.021      74     116 ..     234     272 ..     227     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.57
                       WCOR413  68 ltsllvPyialslPsv 83 
                                   l sl+vP+ +++  s+
  gi|15668943|ref|NP_247747.1| 119 LFSLIVPFYMFKSESI 134
                                   5689999999886655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.26
                       WCOR413  82 svifsllrgevG..kWiafiavvlrLFfp 108
                                   +v+++++    G   ++a++avv+  F+ 
  gi|15668943|ref|NP_247747.1| 172 TVLINYFGWGAGffLYLALLAVVIYRFIL 200
                                   56667766555522467999998866653 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 2.3e-06
                       WCOR413  74 PyialslPsvifsllrgevGkWiafiavvlrLFfpkefpdele 116
                                   P+i ++ P  ifs++   +G W +++a+++ L++ k++     
  gi|15668943|ref|NP_247747.1| 234 PFITIKEPFYIFSFIFWGFGLWWSLMAIIMTLYYVKKL----K 272
                                   9*********************************7765....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2303.90
//
Query:       gi|15668944|ref|NP_247748.1|  [L=121]
Description: hypothetical protein MJ_0763 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.088   13.1   0.0       0.19   12.1   0.0    1.5  1  FCH       Fes/CIP4, and EFC/F-BAR homology domain


Domain annotation for each model (and alignments):
>> FCH  Fes/CIP4, and EFC/F-BAR homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     1e-05      0.19       9      37 ..      63      91 ..      60      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           FCH  9 leqgialledlqeflkeRaeiEkeYakkL 37
                                  ++ +++++ d++e lke  e+Ek  akkL
  gi|15668944|ref|NP_247748.1| 63 IKAEVDTNADVIEILKETIELEKFLAKKL 91
                                  7899************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 816.11
//
Query:       gi|15668945|ref|NP_247749.1|  [L=116]
Description: hypothetical protein MJ_0764 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-06   27.0   0.1    3.9e-06   26.5   0.1    1.1  1  Cupin_1          Cupin
    8.2e-06   25.4   0.0    1.1e-05   25.1   0.0    1.2  1  Cupin_2          Cupin domain
    3.3e-05   23.3   0.0      4e-05   23.0   0.0    1.1  1  KduI             KduI/IolB family
    0.00068   19.3   0.0     0.0009   18.9   0.0    1.3  1  Cupin_3          Protein of unknown function (DUF861)
     0.0085   16.0   0.8      0.011   15.7   0.8    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.019   14.6   0.0    1.2  1  AraC_N           AraC-type transcriptional regulator N-termin
      0.015   15.2   0.0      0.018   14.9   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
      0.057   13.6   0.2      0.072   13.3   0.2    1.2  1  CENP-C_C         Mif2/CENP-C like


Domain annotation for each model (and alignments):
>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   1.8e-09   3.9e-06      27     120 ..      20     105 ..      12     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.8e-09
                                   TTHSSTEEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSE CS
                       Cupin_1  27 glntlgisaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepa 107
                                     nt+++ +  ++l +g +++ hy+ n+   +++++Ge++  ++ ++     +  +++eG +++vP ++ + ++n++ ++ 
  gi|15668945|ref|NP_247749.1|  20 LVNTEHVQINHIVLPRGEQMPKHYS-NSYVHLIIIKGEMT--LTLED----QEPHNYKEGNIVYVPFNVKMLIQNIN-SDI 92 
                                   4799*********************.**************..44444....356779*******************7.*** PP

                                   EEEEEEESSSTT- CS
                       Cupin_1 108 vaivvfdtnnpgn 120
                                   ++++v++  +p++
  gi|15668945|ref|NP_247749.1|  93 LEFFVVKAPHPKK 105
                                   ******9988865 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   4.7e-09   1.1e-05       3      70 ..      31      98 ..      29      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.7e-09
                                  EEEETTEEEEEECSSSEEEEEEEEESEEEEE.ECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                       Cupin_2  3 velppGesapshrHpgedeffyVleGegelt.vdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70
                                  ++lp Ge+ p h+       +++++Ge++lt  d e++ +++G +vy+p ++   + N  ++ ++++vv
  gi|15668945|ref|NP_247749.1| 31 IVLPRGEQMPKHYSNSY-VHLIIIKGEMTLTlEDQEPHNYKEGNIVYVPFNVKMLIQNINSDILEFFVV 98
                                  578889999****6666.899**********88999*************99998888888888888776 PP

>> KduI  KduI/IolB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.8e-08     4e-05      14     114 ..      13     107 ..       2     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.8e-08
                                   EEECTCCCCCCCCBECCCEEEECHHCHHCHGCSEEEEEEEECCEEEECCTT.EEEEE-TTSSGGGS..EEEEE-TT--EEE CS
                          KduI  14 vvdvtpesagweyvgfsvlkLaagesleletedrEvcvvllaGkvtvevageefeelgeRksvFegkpdavYvpkgakvti 94 
                                    ++v ++ ++ e+v+++ + L +ge++  + +++ v +++++G++t + +++e ++ +e         ++vYvp + k+ i
  gi|15668945|ref|NP_247749.1|  13 KTKVVEKLVNTEHVQINHIVLPRGEQMPKHYSNSYVHLIIIKGEMTLTLEDQEPHNYKEG--------NIVYVPFNVKMLI 85 
                                   5788899999***************************************77666666555........9************ PP

                                   EE.SST.EEEEEEEEE-SS--- CS
                          KduI  95 ta.etd.aevavasapaeeelp 114
                                   +  ++d +e++v++ap  ++l+
  gi|15668945|ref|NP_247749.1|  86 QNiNSDiLEFFVVKAPHPKKLN 107
                                   *964447*********998875 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     4e-07    0.0009      30      60 ..      51      81 ..      36     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4e-07
                                  EEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                       Cupin_3 30 yileGevkvtpeggetvelraGDlvvlpkgl 60
                                   i++Ge+++t e+ e++ +++G +v++p + 
  gi|15668945|ref|NP_247749.1| 51 IIIKGEMTLTLEDQEPHNYKEGNIVYVPFNV 81
                                  69*************************9665 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.8   4.8e-06     0.011      57     135 ..      20      98 ..      12     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.8e-06
               MannoseP_isomer  57 ldegeryqvkritvkPgeklslqkhhhra.ehWvvvkGtakvtvddev.lllkenestyiplgaihrlenpGkipleliev 135
                                   l ++e+ q+ +i++  ge++   kh+  +  h +++kG   +t +d++   +ke + +y+p ++   ++n     le+  v
  gi|15668945|ref|NP_247749.1|  20 LVNTEHVQINHIVLPRGEQM--PKHYSNSyVHLIIIKGEMTLTLEDQEpHNYKEGNIVYVPFNVKMLIQNINSDILEFFVV 98 
                                   55678889999988778775..577776636***********9988763789************99999998888887665 PP

>> AraC_N  AraC-type transcriptional regulator N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   8.4e-06     0.019      15      62 ..      39      87 ..      28      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.4e-06
                        AraC_N 15 evalvvyepslcivlqGkKrvhlgde.afeydpgeylvvsvdlpveiev 62
                                   +++  ++ +  i+++G+ +++l+d+  ++y++g+ + v+ ++++ i+ 
  gi|15668945|ref|NP_247749.1| 39 MPKHYSNSYVHLIIIKGEMTLTLEDQePHNYKEGNIVYVPFNVKMLIQN 87
                                  488899999999*************99******************9986 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     8e-06     0.018      13      77 ..      36     101 ..      30     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8e-06
                                   T-SEEEETT-SEEEEEEEEE-EEEEETTEE.EEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE- CS
                  AraC_binding  13 dhsfpphvhdeyvihyvteGtgrlrlngrt.ydlgpGdlfLlppgepHdyesdsedgweyrwlyfe 77 
                                   ++ +p+h  + yv  ++++G+ +l+l++++ ++ ++G ++ +p ++   ++  ++d +e+++++ +
  gi|15668945|ref|NP_247749.1|  36 GEQMPKHYSNSYVHLIIIKGEMTLTLEDQEpHNYKEGNIVYVPFNVKMLIQNINSDILEFFVVKAP 101
                                   567899******************9999888************99999999988888888877655 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.2e-05     0.072      18      84 ..      32      97 ..      16      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                  EE-TCCCEEEEE--SEEEEEEEEESEEEEEETTE.EEEEETT-EEEE-TT-EEEEEE-SSS-EEEEEE CS
                      CENP-C_C 18 kLppgaeKkkknskkatlvFyViqGrvevtvskt.sfvigkgsvFqvPagneysieNklnkeaklfFv 84
                                   Lp  +e  +k+  + ++   +i+G++  t++++  +   +g++ +vP   +  i+N  n++   fFv
  gi|15668945|ref|NP_247749.1| 32 VLP-RGEQMPKHYSNSYVHLIIIKGEMTLTLEDQePHNYKEGNIVYVPFNVKMLIQN-INSDILEFFV 97
                                  454.456678888999999************9862689999*******999999999.5666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 819.41
//
Query:       gi|298575370|ref|NP_247750.3|  [L=548]
Description: hydroxylamine reductase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.3e-176  586.9   0.1   3.7e-176  586.8   0.1    1.0  1  Prismane  Prismane/CO dehydrogenase family
  ------ inclusion threshold ------
      0.019   14.9   1.8      0.024   14.6   0.1    2.0  3  Ovate     Transcriptional repressor, ovate
      0.051   13.2   0.5        2.2    7.9   0.2    2.4  2  DUF3231   Protein of unknown function (DUF3231)


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  586.8   0.1  6.2e-180  3.7e-176       1     511 []      10     544 ..      10     544 .. 0.97

  Alignments for each domain:
  == domain 1  score: 586.8 bits;  conditional E-value: 6.2e-180
                                    -EE-SST....CT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHC...HHHHHHHHHCHTSTTTB-SHHH CS
                                    xxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane   1 mfCrqCe....ngpCritknkrGvCGkdadtavardlliavlkgaaahaaharel...adtliakalfktltnvnfddek 73 
                                    mfC+qC+    n++C+i+    GvCGkd  +a+++dlli+++kg++ ++++++ l   + ++i kalf t+tnvnfdd++
  gi|298575370|ref|NP_247750.3|  10 MFCFQCQeaakNEGCTIK----GVCGKDDVVANLQDLLIYTIKGLCYVCDKGNYLddeVMDYIPKALFVTITNVNFDDKD 85 
                                    9*****************....*******************************9999999******************** PP

                                    HHHHHHHHHCHHHCC...................SSHHHHHHHHCCHHHCGGGS-SSHHHHHHHCCCHHHHHHH..HHHH CS
                                    xxxxxxxxxxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                       Prismane  74 klkrlaealgieeel...................kdieelaakvaevaledlskeenedirslkellpkglkgl..yaeh 132
                                    +++++++ ++++e++                   +++e+l++ +++  ++ l+++ nedirslkel+++g+kg+  y +h
  gi|298575370|ref|NP_247750.3|  86 VINWIKKGVALREKIieknnlnkeelpycatwayETDEDLINLANTKEVSVLAED-NEDIRSLKELITYGIKGIgaYLSH 164
                                    *****************************************************88.8*********************** PP

                                    CHHTT-HHHHHHHHHHHCCCCTTS.THHH.HHHHHHHHHHHHHHHHHHHHHHHHHHH-----EEEEECGCG-.SSSEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane 133 aivlgyadeevveflaktlagles.dpld.llskalrlGlldlkgmelldeantslfGtPeppltevnlgvldkdkvnIl 210
                                    a+ lgy++e++++f+ k+ +++ + ++ d l ++a+++G++ +++++lld+ant+++G+Pe+  tevnlgv+    ++Il
  gi|298575370|ref|NP_247750.3| 165 AMHLGYNNEDIHKFIIKAFTKIVDsKDADeLFNLAMETGKYAVETLALLDKANTETYGHPEI--TEVNLGVR-D-RPGIL 240
                                    *********************955245557********************************..********.4.49*** PP

                                    EESS-HHHHHHHHHHHCTTCCCCCCCGCCCCCCHHHHHHHHHCCEEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane 211 vsGHdladleelleqtegkglnvythgemLpghcctalklkyrhlvgnvGnawqqekaeftgavdaivvdtnCivpplas 290
                                    +sGHdl+dle+lleq ++ g++ yth+emLp+h+++ +k ky+h+vgn+G +w  +++ef++++++iv++tnC+vpp++s
  gi|298575370|ref|NP_247750.3| 241 ISGHDLKDLEQLLEQSKDAGVDIYTHCEMLPAHYYPFFK-KYEHFVGNYGGSWPFQREEFEKFNGPIVMTTNCLVPPKDS 319
                                    ***************************************.*************************************777 PP

                                    HHHCHCCEEEEECTTB-TTSEEE--CTTCHHHHHHHHHHHHCCHCCTTCGG.-.................HHHHHTTSS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxx RF
                       Prismane 291 vaekyktrlittsevakpgakhieeeekadkdaseiiekAielakareekkve.................idaiksGtIk 353
                                        yk+r++ t+ev++pg+k+i+ +e+  kd+se+ie+A+++++++  ++ +                 i+a+ksG+I+
  gi|298575370|ref|NP_247750.3| 320 ----YKDRVYVTNEVGYPGLKRIPVKEDGTKDFSEVIEHAKKCKPPTPLENGKivggfahnqvlaladkvIEAVKSGKIR 395
                                    ....********************999999*****************765555779************************ PP

                                    EEEEE-B---TTCGCCHHHHHHHHCHHTTEEEEEECHHHHHCCCTTTTECGHHHHSTHCEESEEEEESCCCHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane 354 gvvlvvGCdnakkgrdyytelakelikrdvlvltaGCakyalnklglgtieaaelagegiPrvLdvGsCvdnyrivvial 433
                                    ++v+++GCd+++k+r+yyte+ak+l ++d+++lt GCaky++ kl+lg+i       +giPrvLd+G+C+d+y++v+ial
  gi|298575370|ref|NP_247750.3| 396 KFVVMAGCDGRHKTREYYTEFAKKL-PKDTVILTCGCAKYRFIKLDLGDI-------DGIPRVLDAGQCNDSYSLVKIAL 467
                                    *************************.************************.......59********************* PP

                                    HHHHHTTS.SGGGSSEEEEECC--SHHHHHHHHHHHHTT-.CEEECSS-TTTT-HHHHHHHHCHHHHHHCEEEECHCHHH CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane 434 klaealgv.dindLplaalalewyeqKAvailltllalGi.nihlgptlpafgspnvlkvlvedfedriggivtveedpe 511
                                    +l++a+g+ d+n+Lp+ a++++wyeqKAv +ll+ll+lG+ ni+lgptlpaf+spnv+kvlve+f  +i  i+tv+ed++
  gi|298575370|ref|NP_247750.3| 468 ALKDAFGLnDVNELPI-AYNISWYEQKAVTVLLALLYLGVkNIVLGPTLPAFLSPNVTKVLVEKF--GISTISTVDEDIK 544
                                    *******99*******.************************************************..***********86 PP

>> Ovate  Transcriptional repressor, ovate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.4   1.4e+04      21      31 ..     141     151 ..     136     155 .. 0.69
   2 ?   14.6   0.1     4e-06     0.024      33      54 ..     166     187 ..     159     189 .. 0.90
   3 ?   -2.9   0.1       1.1   6.9e+03      22      32 ..     244     254 ..     242     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.4
                          Ovate  21 ikdweeLeeLL 31 
                                     +d ++L+eL+
  gi|298575370|ref|NP_247750.3| 141 NEDIRSLKELI 151
                                    56778888886 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4e-06
                          Ovate  33 cYLslNskehhklIvaaFadll 54 
                                    ++L +N++++hk+I++aF++++
  gi|298575370|ref|NP_247750.3| 166 MHLGYNNEDIHKFIIKAFTKIV 187
                                    67899**************987 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.1
                          Ovate  22 kdweeLeeLLa 32 
                                    +d ++Le+LL+
  gi|298575370|ref|NP_247750.3| 244 HDLKDLEQLLE 254
                                    57899****97 PP

>> DUF3231  Protein of unknown function (DUF3231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0    0.0098        58      41      83 ..      80     121 ..      62     167 .. 0.76
   2 ?    7.9   0.2   0.00036       2.2      24      66 ..     169     211 ..     163     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0098
                        DUF3231  41 vaedkeikelleralelsnkhikelkelLkeenlpiPsgfs.es 83 
                                    + +dk++ + ++++ +l +k i++  + L++e+lp  +++  e+
  gi|298575370|ref|NP_247750.3|  80 NFDDKDVINWIKKGVALREKIIEK--NNLNKEELPYCATWAyET 121
                                    579******************996..779******999995433 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00036
                        DUF3231  24 syianslgialitgFlqvaedkeikelleralelsnkhikelk 66 
                                     y+++ + + +i++F + +++k+  el++ a+e ++  +++l+
  gi|298575370|ref|NP_247750.3| 169 GYNNEDIHKFIIKAFTKIVDSKDADELFNLAMETGKYAVETLA 211
                                    589999***************************9999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3555.94
//
Query:       gi|15668947|ref|NP_247751.1|  [L=66]
Description: hypothetical protein MJ_0766 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-14   52.0   1.0    6.9e-14   51.9   1.0    1.0  1  CGGC           CGGC domain
     0.0026   17.7   0.1        1.3    9.0   0.0    2.1  2  PTCB-BRCT      twin BRCT domain
  ------ inclusion threshold ------
      0.025   13.8   0.0      0.026   13.7   0.0    1.0  1  Melibiase_2    Alpha galactosidase A
      0.026   14.9   0.2        3.7    8.0   0.0    2.1  2  BRCT_2         BRCT domain, a BRCA1 C-terminus domain
      0.038   14.3   1.0       0.22   11.9   1.0    1.9  1  Ribosomal_L12  Ribosomal protein L7/L12 C-terminal domain


Domain annotation for each model (and alignments):
>> CGGC  CGGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   1.0   1.9e-17   6.9e-14      40     106 .]       1      65 [.       1      65 [. 0.94

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.9e-17
                          CGGC  40 vgfvtCggCpgkkvveklkelk.kegvdvihlssCiktkkakkeCpeieeikeaieeklgievvegth 106
                                   ++++tCggCpg+  ++++k+l+ k+g++v+h+++C++    k++C ++e++ke ie+  g +vv+ +h
  gi|15668947|ref|NP_247751.1|   1 MSVITCGGCPGRLGLNQIKQLIgKNGAEVVHFATCMT--AFKPKCRYAEKMKEEIEKM-GAKVVMSSH 65 
                                   5799*****************999***********93..5899*************98.*****9998 PP

>> PTCB-BRCT  twin BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0012       4.4       2      28 ..       3      30 ..       2      34 .. 0.85
   2 !    9.0   0.0   0.00037       1.3       3      28 ..      34      61 ..      32      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0012
                                  EEEEECB-TTC.HHHHHHHHHHTT-EEE CS
                     PTCB-BRCT  2 vicvtgysgdd.rkslqklieamGaeys 28
                                  vi+  g+ g   ++++++li ++Gae++
  gi|15668947|ref|NP_247751.1|  3 VITCGGCPGRLgLNQIKQLIGKNGAEVV 30
                                  57777888888899***********986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00037
                                  EEEECB-TTC..HHHHHHHHHHTT-EEE CS
                     PTCB-BRCT  3 icvtgysgdd..rkslqklieamGaeys 28
                                  +c+t ++++    +++++ ie+mGa+++
  gi|15668947|ref|NP_247751.1| 34 TCMTAFKPKCryAEKMKEEIEKMGAKVV 61
                                  699999999988899**********985 PP

>> Melibiase_2  Alpha galactosidase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.2e-06     0.026     101     163 ..       3      64 ..       1      66 [] 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.2e-06
                                   SB-TTSSB--TTTHHHHHHHHHHHT--EEEEE-TSSSHHHHHHHHHHHHHHHHHTTS--EEEE CS
                   Melibiase_2 101 tktcagypgslkyleidaktfadwgvdllkldgcysnleelaegykelslalnktgrsivysc 163
                                   + tc+g pg l   +i  + + + g +++++  c++  +   +  ++++  ++k g ++v s 
  gi|15668947|ref|NP_247751.1|   3 VITCGGCPGRLGLNQI-KQLIGKNGAEVVHFATCMTAFKPKCRYAEKMKEEIEKMGAKVVMSS 64 
                                   67********997666.6899********************9999**************9996 PP

>> BRCT_2  BRCT domain, a BRCA1 C-terminus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0     0.001       3.7      22      39 ..      16      33 ..      10      45 .. 0.84
   2 ?    5.6   0.0    0.0058        21      21      38 ..      46      63 ..      39      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.001
                        BRCT_2 22 eklkklIeknGGevveti 39
                                  +++k+lI knG evv+  
  gi|15668947|ref|NP_247751.1| 16 NQIKQLIGKNGAEVVHFA 33
                                  689***********9876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0058
                        BRCT_2 21 reklkklIeknGGevvet 38
                                   ek+k+ Iek G +vv++
  gi|15668947|ref|NP_247751.1| 46 AEKMKEEIEKMGAKVVMS 63
                                  689************987 PP

>> Ribosomal_L12  Ribosomal protein L7/L12 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.0   6.1e-05      0.22      47      65 ..      43      61 ..       9      63 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.1e-05
                                  HHHHHHHHHHHHCTT-EEE CS
                 Ribosomal_L12 47 keeAeeikkkLeeaGAeve 65
                                     Ae++k+++e++GA+v 
  gi|15668947|ref|NP_247751.1| 43 CRYAEKMKEEIEKMGAKVV 61
                                  3569*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 519.96
//
Query:       gi|15668948|ref|NP_247752.1|  [L=135]
Description: hypothetical protein MJ_0767 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-09   35.0   0.1    2.3e-08   33.7   0.1    1.7  2  RHH_1            Ribbon-helix-helix protein, copG family
    2.1e-06   27.8   0.0    3.6e-06   27.1   0.0    1.4  1  NikR_C           NikR C terminal nickel binding domain
    1.9e-05   24.7   0.3    8.7e-05   22.6   0.0    1.9  2  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
    6.2e-05   23.2   0.1    0.00012   22.3   0.0    1.4  1  RHH_8            Ribbon-Helix-Helix transcriptional regulator
     0.0015   18.8   0.1     0.0036   17.6   0.0    1.6  2  DUF4375          Domain of unknown function (DUF4375)


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.1   6.4e-12   2.3e-08       1      37 [.       6      43 ..       6      45 .. 0.97
   2 ?   -2.2   0.0       1.3   4.7e+03      10      17 ..      66      73 ..      62      75 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 6.4e-12
                                  EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                         RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                  r+si+ ++ ll+++de +++ g +SrSelIR+A+r y+
  gi|15668948|ref|NP_247752.1|  6 RISISFPKFLLKEIDEVVKKKGySSRSELIRDAVRKYV 43
                                  89***********************************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                                  HHHHHHHH CS
                         RHH_1 10 llerLdel 17
                                  ++e+L+++
  gi|15668948|ref|NP_247752.1| 66 TKEALEKM 73
                                  67888887 PP

>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   9.9e-10   3.6e-06       2      68 ..      57     126 ..      56     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 9.9e-10
                                   EEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEES....SSEEEEEEEEEE-HHHHHHHHHHHHTSTT CS
                        NikR_C   2 Gvitivydhhqrelserltdiqheyhdliisslhvhld....hdncLevivlkGeaeeikelaeklralkg 68 
                                   G+i++vy+  ++e  e+++++  e++++i+s  + +++    ++  +e++v++G++++i+++ e++ +++g
  gi|15668948|ref|NP_247752.1|  57 GIIIVVYNP-TKEALEKMSKLYFEHNKVIKSLNQAYVTtscgKNAKVEIFVVEGNSKDISKFYEEIEKING 126
                                   99*******.788889***************999998733335788********************99987 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.4e-08   8.7e-05      88     121 ..       3      37 ..       1      39 [. 0.90
   2 ?    0.3   0.1       0.2   7.2e+02      39      93 ..      68     125 ..      54     133 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.4e-08
               HicB_lk_antitox  88 kaeriNitlpervlkriDaavkaag.esRSgflak 121
                                   ++eri i++p+ +lk+iD++vk++g +sRS ++ +
  gi|15668948|ref|NP_247752.1|   3 NVERISISFPKFLLKEIDEVVKKKGySSRSELIRD 37 
                                   689**********************679**99875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.2
               HicB_lk_antitox  39 eaielhlegliedgeeipepssi...eellanpeyaggiwalvdvdlskldgkaeriN 93 
                                   ea+e   +   e+++ i++ ++    +++ +n+ ++ +++   + d+sk+ ++ e+iN
  gi|15668948|ref|NP_247752.1|  68 EALEKMSKLYFEHNKVIKSLNQAyvtTSCGKNAKVEIFVVEGNSKDISKFYEEIEKIN 125
                                   5555554555555555444333200022334444444444445567888888888887 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   3.2e-08   0.00012       3      74 ..       4      74 ..       2      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.2e-08
                         RHH_8  3 tekvtinlgvvDLgqiDlLveeGfYsnRtDlirtairaqLakhddalkqavkrkslvlGvtklsraeleevq 74
                                   e+++i +    L +iD +v++  Ys+R++lir a+r+ +  +++ l++  + + + + v + +++ le++ 
  gi|15668948|ref|NP_247752.1|  4 VERISISFPKFLLKEIDEVVKKKGYSSRSELIRDAVRKYVL-ENNPLNKNETVSGIIIVVYNPTKEALEKMS 74
                                  689999999999*************************8765.566788888888888888888888888875 PP

>> DUF4375  Domain of unknown function (DUF4375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   9.9e-07    0.0036      38     115 ..      15      94 ..       7      98 .. 0.85
   2 ?   -1.9   0.0         1   3.8e+03      97     109 ..     116     128 ..     111     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.9e-07
                                   H.CCHHHHHHCTT--HHHHHHHHHHHHHHHHHHHHHHHHHTT.-HHHHHHH.-GGGHHHHHHHHHHHHHHHHHHHHHHHC CS
                       DUF4375  38 i.nealkalrliGaeelakllekakklykkgkeelereerde.elealyeeeeeefdelDdefyeyeeeltellaeYvde 115
                                     +e+ + +++ G ++ ++l+++a + y  ++++l+++e+    +  +y+ ++e+++++ + ++e+++ +++l  +Yv  
  gi|15668948|ref|NP_247752.1|  15 LlKEIDEVVKKKGYSSRSELIRDAVRKYVLENNPLNKNETVSgIIIVVYNPTKEALEKMSKLYFEHNKVIKSLNQAYVTT 94 
                                   4588999999****************88888888899888883555556655*************************976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1
                                   HHHHHHHHHHHHH CS
                       DUF4375  97 efyeyeeeltell 109
                                   +fye+ e+++ ++
  gi|15668948|ref|NP_247752.1| 116 KFYEEIEKINGKI 128
                                   7888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 868.86
//
Query:       gi|15668949|ref|NP_247753.1|  [L=249]
Description: F420-0--gamma-glutamyl ligase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-61  206.6   1.1      4e-61  206.5   1.1    1.0  1  F420_ligase  F420-0:Gamma-glutamyl ligase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.5   1.1   2.2e-65     4e-61      20     244 .]      28     225 ..      12     225 .. 0.94

  Alignments for each domain:
  == domain 1  score: 206.5 bits;  conditional E-value: 2.2e-65
                                   CS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H..................HHHHHHHHTE CS
                   F420_ligase  20 svkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfsliLkalakatrkvevvlsep 100
                                   ++  a++ +edgDi+v++e++++k eg +++ ++i ps++A+e+a+k+ ++dp                  + v+v+l+e+
  gi|15668949|ref|NP_247753.1|  28 ELI-AQYPIEDGDIIVIAETLISKLEGGVIDRDKIIPSKEAIELAKKT-GKDP------------------KVVQVILDEA 88 
                                   333.35789***************************************.****..................********** PP

                                   EEEEE-...S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHHHHHHHHHHHHHS---EEEE..EEEEEE CS
                   F420_ligase 101 sdevgn...qlidekytdevlvklGllgsnagidesnveegllkllPedpdksaeeikkklkertgkdveVliygkDpegr 178
                                   +++v+    ++i+e+       k+G++++n g+desn+ +g +k+lP++pd+sae+i+k++++ tgk+v+V+i  +D++gr
  gi|15668949|ref|NP_247753.1|  89 KEIVKVgknFIITET-------KHGFVCANSGVDESNIYKG-IKILPKNPDESAEKIRKEIEKLTGKRVGVII--SDSVGR 159
                                   ****97777******.......****************665.9******************************..****** PP

                                   TTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC-SSSS---EEEEES CS
                   F420_ligase 179 iweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladLvsGsadegtPvvlvrg 244
                                   +++ + +++aig+sg+ al+d +g+kdl+g+el+tt+ a++del+s+a++v+G+adeg+Pvv++rg
  gi|15668949|ref|NP_247753.1| 160 PFRKGAVGIAIGVSGILALWDRKGEKDLFGRELKTTEVAIADELASMANVVMGEADEGIPVVIIRG 225
                                   *****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1561.42
//
Query:       gi|15668950|ref|NP_247754.1|  [L=169]
Description: hypothetical protein MJ_0769 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-06   26.8   0.1    2.3e-05   24.4   0.1    2.2  2  HTH_7         Helix-turn-helix domain of resolvase
    0.00047   20.6   0.0     0.0011   19.3   0.0    1.7  1  HTH_40        Helix-turn-helix domain
    0.00054   19.7   0.2     0.0017   18.1   0.0    1.9  2  HTH_38        Helix-turn-helix domain
     0.0021   17.6   0.0     0.0055   16.2   0.0    1.8  1  HTH_24        Winged helix-turn-helix DNA-binding
     0.0027   17.5   0.0     0.0053   16.5   0.0    1.5  1  HTH_23        Homeodomain-like domain
     0.0028   17.6   0.0     0.0038   17.1   0.0    1.2  1  Sigma70_ECF   ECF sigma factor
     0.0099   16.1   0.5        0.1   12.8   0.0    2.5  2  HTH_17        Helix-turn-helix domain
  ------ inclusion threshold ------
       0.02   14.4   0.0      0.048   13.2   0.0    1.8  1  Sigma70_r4    Sigma-70, region 4
      0.024   14.2   0.0      0.045   13.3   0.0    1.4  1  GerE          Bacterial regulatory proteins, luxR family
       0.03   13.7   0.0      0.054   12.9   0.0    1.5  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
      0.066   13.8   0.0       0.15   12.7   0.0    1.6  1  HTH_32        Homeodomain-like domain
      0.072   12.8   0.0        0.5   10.1   0.0    2.2  2  Sigma70_r4_2  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.9   1.3e+03      10      19 ..      14      23 ..       5      24 .. 0.76
   2 !   24.4   0.1   1.5e-08   2.3e-05       1      38 [.      63     100 ..      63     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.9
                                  HHGGGGSSTT CS
                         HTH_7 10 dinrvvkLle 19
                                  +in +vkL+e
  gi|15668950|ref|NP_247754.1| 14 EINKIVKLRE 23
                                  5888999887 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1.5e-08
                                   S---SS-HHHHGGGGSSTTTT--STTTSSSS---SSSS CS
                         HTH_7   1 GRpsklskndinrvvkLleeGisiskIAkevnisRsTv 38 
                                   GR++k+++++   + +L+ eG+s+++I  +++i++sTv
  gi|15668950|ref|NP_247754.1|  63 GRKRKVDDETVKKIHELIIEGYSVREIGNILGIGKSTV 100
                                   9************************************9 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   7.6e-07    0.0011       6      83 ..      77     151 ..      72     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.6e-07
                        HTH_40   6 lelleeglsieeIAkerglkesTIegHLaelieegeeidlerl..vseeeekeIeeaiekvgseklkpikealpeevsyd 83 
                                    el+ eg+s+ eI ++ g+ +sT++++  ++i+e   ++ler+  +  e ++ +++  +   s +l+ ++ +l+ +v+yd
  gi|15668950|ref|NP_247754.1|  77 HELIIEGYSVREIGNILGIGKSTVWDYAKDCIKE---LKLERFkkLVWEYREYLINKGKY--SPSLQVLFLELEATVDYD 151
                                   68999*****************************...66766622233444444433333..345999999999999997 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.9   5.8e+03       8      20 ..      13      25 ..      12      26 .. 0.77
   2 !   18.1   0.0   1.1e-06    0.0017      11      37 ..      74     100 ..      65     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.9
                        HTH_38  8 eeReeIerllaeG 20
                                  +e ++I +l++++
  gi|15668950|ref|NP_247754.1| 13 DEINKIVKLREKD 25
                                  7889999998875 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.1e-06
                        HTH_38  11 eeIerllaeGlslreIArrLgrspsTI 37 
                                    +I  l+ eG+s+reI+ +Lg  +sT+
  gi|15668950|ref|NP_247754.1|  74 KKIHELIIEGYSVREIGNILGIGKSTV 100
                                   6799**********************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.7e-06    0.0055       2      44 ..      70     110 ..      69     110 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.7e-06
                        HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeee 44 
                                   det +kI el+ +  + s re+   lg+ +stv+ + k +++e
  gi|15668950|ref|NP_247754.1|  70 DETVKKIHELIIE--GYSVREIGNILGIGKSTVWDYAKDCIKE 110
                                   89999*******9..***********************99986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.6e-06    0.0053      15      40 ..      81     106 ..      72     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.6e-06
                        HTH_23  15 aeGlsvreIAreLgvsrrTvyrwlkr 40 
                                    eG+svreI  +Lg+ ++Tv+ + k 
  gi|15668950|ref|NP_247754.1|  81 IEGYSVREIGNILGIGKSTVWDYAKD 106
                                   36*******************98775 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.6e-06    0.0038     135     168 ..      67     100 ..      37     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.6e-06
                   Sigma70_ECF 135 sldpeqarlvelrkleGlsveEiAeklgvskrtv 168
                                   ++d+e  +++    +eG+sv Ei++ lg++k+tv
  gi|15668950|ref|NP_247754.1|  67 KVDDETVKKIHELIIEGYSVREIGNILGIGKSTV 100
                                   499******************************9 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.36   5.4e+02      23      39 ..      50      69 ..      38      75 .. 0.69
   2 !   12.8   0.0   6.8e-05       0.1       2      23 ..      84     105 ..      84     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.36
                        HTH_17 23 rrgelpaa...kiGrrwrip 39
                                  ++g ++ +   k+Gr+++++
  gi|15668950|ref|NP_247754.1| 50 KKGIFIEVenaKRGRKRKVD 69
                                  35555555877899999886 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.8e-05
                        HTH_17   2 ltveEaAelLgvsrstvyrlir 23 
                                   ++v E+ ++Lg+++stv ++++
  gi|15668950|ref|NP_247754.1|  84 YSVREIGNILGIGKSTVWDYAK 105
                                   89*****************996 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.2e-05     0.048      18      48 ..      81     111 ..      64     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-05
                                   TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                    Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                    eg++  EIg++lgi +++V    k++++ L
  gi|15668950|ref|NP_247754.1|  81 IEGYSVREIGNILGIGKSTVWDYAKDCIKEL 111
                                   699****************976666666666 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     3e-05     0.045      12      40 ..      78     106 ..      74     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                                   HHHCTTS-HHHHHHHHTS-HHHHHHHHHH CS
                          GerE  12 rllaeGksnkeIAeelniSekTVkvhksn 40 
                                   +l++eG+s+ eI+ +l+i + TV  + + 
  gi|15668950|ref|NP_247754.1|  78 ELIIEGYSVREIGNILGIGKSTVWDYAKD 106
                                   799********************766665 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.6e-05     0.054      22      51 ..      78     107 ..      68     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.6e-05
                  HTH_Tnp_ISL3  22 elllesrsvkavArqlgvSwtTVwrildry 51 
                                   el +e+ sv+++ ++lg++ +TVw++ +++
  gi|15668950|ref|NP_247754.1|  78 ELIIEGYSVREIGNILGIGKSTVWDYAKDC 107
                                   56667779******************9986 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.8e-05      0.15      21      70 ..      60     101 ..      42     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.8e-05
                        HTH_32  21 prrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvy 70 
                                   ++rgr+rk++de++++i +l+ e   +s r++   l       + +stv+
  gi|15668950|ref|NP_247754.1|  60 AKRGRKRKVDDETVKKIHELIIE--GYSVREIGNIL------GIGKSTVW 101
                                   5789*****************76..58999998888......67777776 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00034       0.5      24      44 ..      81     101 ..      70     105 .. 0.86
   2 ?   -0.3   0.0      0.58   8.7e+02      40      53 ..     145     158 ..     145     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00034
                                   TS---HHHHHHHHT--HHHHH CS
                  Sigma70_r4_2  24 leglsykEIAellgisegtVk 44 
                                   +eg+s +EI  +lgi  +tV 
  gi|15668950|ref|NP_247754.1|  81 IEGYSVREIGNILGIGKSTVW 101
                                   89*****************96 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.58
                                   HHHHHHHHHHHHHH CS
                  Sigma70_r4_2  40 egtVksrlsRArkk 53 
                                   e+tV++ l +A+k 
  gi|15668950|ref|NP_247754.1| 145 EATVDYDLEKAKKI 158
                                   689*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1253.61
//
Query:       gi|15668951|ref|NP_247755.1|  [L=223]
Description: hypothetical protein MJ_0770 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-08   32.6   0.7    1.5e-07   31.4   0.7    1.6  1  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.7   8.2e-12   1.5e-07      20     169 ..      55     208 ..      37     210 .. 0.63

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 8.2e-12
                                   HHHHHHHHHHHHHHT--HHHHT......T-BGGGEECTTT.EEEEEEEECSSSSE...EEEECT....HHHHHHHHHHHHH CS
               Phage_integrase  20 kirdklllellyetGlRisEll......sLrvkdldleng.vilvheregKgske...ravpls....eealellkellsk 86 
                                    i   + + + ++ G Ri E++      ++++++l+++++ +++v   ++ ++k+   r++ ++    +e  e+++++  +
  gi|15668951|ref|NP_247755.1|  55 RIAYLITFLFQLRNGCRIWEAIagminiAINIDNLNWNERiTVKV---RTQKRKDwefRELIIPkcikKEDIEMVRDVFLD 132
                                   555555577777777777777522222257777787776623445...333333335555555544556666777766666 PP

                                   HCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHHHHH CS
               Phage_integrase  87 aleeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHssisttqiYt 167
                                     +++ +++l + +k    + ++++ k+f ++ ++   ++ +++H+lR ++ t L e+g++ +v++k+  H++i+ +++Yt
  gi|15668951|ref|NP_247755.1| 133 I-KKEIDEKLTMDEK---LKAKKKIVKRFGAWLYK---NYGINTHSLRYAYVTYLGEHGIPAQVLAKITKHKNINYIETYT 206
                                   6.4444444555555...33333444444444443...34566************************************** PP

                                   CC CS
               Phage_integrase 168 hv 169
                                   ++
  gi|15668951|ref|NP_247755.1| 207 QS 208
                                   97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1428.89
//
Query:       gi|15668952|ref|NP_247756.1|  [L=230]
Description: cobalamin biosynthesis precorrin-2 methyltransferase CbiL [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-46  159.6   0.0    1.1e-46  159.4   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.073   13.3   0.0      0.089   13.1   0.0    1.3  1  Hydrolase     haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.4   0.0   1.3e-50   1.1e-46       1     212 [.       7     211 ..       7     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 159.4 bits;  conditional E-value: 1.3e-50
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsr......aleilldllaeel..eleapmgkekepleeayeeiaeala 73 
                                   k+y+VGvG Gd +llT++Al++lk++d ++ + s+      a+ei++d+++ +   el +pm k+ke+l + +e++ e++ 
  gi|15668952|ref|NP_247756.1|   7 KVYGVGVGVGDKKLLTLKALEVLKKVDKIFVPVSKkgkksiAYEIIKDYVDGKNieELLFPMIKDKERLKKYWENALEKVL 87 
                                   79***************************655533344568*********9888********************6666665 PP

                  TP_methylase  74 ealragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerel 154
                                   +   ++ +V+++++GDP++y+t+s++ + l++  +g+eve++ G+ss+ a aa+l+ipl+eg+e+l++l p+ +     +l
  gi|15668952|ref|NP_247756.1|  88 K---EDGEVAIITIGDPTLYSTFSYVWKLLKE--RGVEVEIVNGISSIFASAAALNIPLVEGDEKLCIL-PQGK-----DL 157
                                   4...4445*******************99999..9**********************************.7755.....99 PP

                  TP_methylase 155 eallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                   e+ ++++dt++++k+  +l+e + ++k +   d++ + +v+ra+ ede+vv g+l e+
  gi|15668952|ref|NP_247756.1| 158 EKYIDEFDTIIIMKTK-NLNEKLSVIKNR---DDYIIGLVKRATFEDEKVVIGKLDEI 211
                                   999**********555.5********999...578********************987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.9e-06     0.089      99     155 ..      84     139 ..      13     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.9e-06
                                   HHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  99 tvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanql 155
                                   + +l+++ ++a++ti dp +++     + + Lk++g+ev ++ g ++ +a +aa ++
  gi|15668952|ref|NP_247756.1|  84 EKVLKEDGEVAIITIGDP-TLYSTFSYVWKLLKERGVEVEIVNGISSIFASAAALNI 139
                                   3444478999********.********************************666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1740.65
//
Query:       gi|15668953|ref|NP_247757.1|  [L=353]
Description: hypothetical protein MJ_0772 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0045   16.8   0.6      0.011   15.6   0.6    1.6  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.013   16.2   0.2      0.013   16.2   0.2    2.6  3  RTP       Replication terminator protein
      0.014   15.9   1.4       0.48   10.9   0.0    2.8  3  HTH_40    Helix-turn-helix domain
       0.02   15.0   1.8      0.031   14.4   0.2    2.2  2  FUR       Ferric uptake regulator family
      0.021   14.8   0.5      0.099   12.6   0.1    2.4  2  HTH_36    Helix-turn-helix domain
      0.051   13.4   0.0        0.1   12.4   0.0    1.4  1  HTH_IclR  IclR helix-turn-helix domain
       0.11   12.4   1.2         11    6.1   0.1    2.4  2  PadR      Transcriptional regulator PadR-like family
       0.14   12.0   0.0       0.36   10.7   0.0    1.8  1  HTH_5     Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6     5e-06     0.011      17      59 ..     262     305 ..     254     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5e-06
                                   HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.T CS
                          TrmB  17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.p 59 
                                   +++l + ++++i  +++   s++Y++L +L++ G+ +++k + +
  gi|15668953|ref|NP_247757.1| 262 IIELRKFKVEDITYKVNYKLSTIYRYLDELVELGILTKIKHKgK 305
                                   3488999******************************9997743 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2       1.2   2.6e+03      11      35 ..      65      88 ..      43     113 .. 0.57
   2 ?   -1.3   0.0       1.5   3.4e+03      52      84 ..     177     206 ..     152     231 .. 0.74
   3 ?   16.2   0.2   5.6e-06     0.013      32      68 ..     266     304 ..     246     327 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                                  HHHHHHHHHTT-EBCTCHHHHHHHH CS
                           RTP 11 klylitlvekkklyglklldelkke 35
                                  k yl +  +k + +  +ll+ + ++
  gi|15668953|ref|NP_247757.1| 65 KYYLFKNHKKAN-WLKNLLEYMNNK 88
                                  333333332222.334444444443 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                                   HHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS. CS
                           RTP  52 lhelvedgilkrrkelkekaklqevviYsltde 84 
                                   ++e+  +gil+ + +++    + +v  Y+++d 
  gi|15668953|ref|NP_247757.1| 177 IREIFPEGILNTKATIR---YFAKVHGYYISDR 206
                                   56777788888877777...5556666777664 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 5.6e-06
                                   HHHHHTTTT----..HHHHHHHHHHHHHTTSEEEEEEEB CS
                           RTP  32 lkkeFkelgykPn..hseiyralhelvedgilkrrkelk 68 
                                    k +  +++yk n   s+iyr l+elve gil+++k++ 
  gi|15668953|ref|NP_247757.1| 266 RKFKVEDITYKVNykLSTIYRYLDELVELGILTKIKHKG 304
                                   34455667777652269*******************985 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.067   1.5e+02      50      84 ..      48      93 ..      24      96 .. 0.70
   2 ?   -3.2   0.0       5.5   1.2e+04      23      73 ..     160     178 ..     139     185 .. 0.50
   3 ?   10.9   0.0   0.00021      0.48      12      40 ..     267     295 ..     262     328 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.067
                        HTH_40 50 seeeekeIeeaiekvgsek...........lkpikealpeevsyde 84
                                  +++ +k+I++++ +++++            lk++ e++++++++d+
  gi|15668953|ref|NP_247757.1| 48 TPNLKKAIAKIVYQIKDKYylfknhkkanwLKNLLEYMNNKIEFDK 93
                                  446666677666664433344444457899*************997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.5
                        HTH_40  23 glkesTIegHLaelieegeeidlerlvseeeekeIeeaiekvgseklkpik 73 
                                   + + s ++++ ++                                   +i+
  gi|15668953|ref|NP_247757.1| 160 KNSISVVIRYPID--------------------------------CHEEIR 178
                                   2223333333233................................333333 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00021
                        HTH_40  12 glsieeIAkerglkesTIegHLaelieeg 40 
                                   + ++e+I  + + k sTI+++L el+e g
  gi|15668953|ref|NP_247757.1| 267 KFKVEDITYKVNYKLSTIYRYLDELVELG 295
                                   5689**********************998 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       4.3   9.7e+03      14      49 ..     192     226 ..     189     232 .. 0.57
   2 ?   14.4   0.2   1.4e-05     0.031      40      73 ..     279     311 ..     254     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.3
                                   HHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHH CS
                           FUR  14 levlekseehlsaeevykelkeedpeislaTVYrtL 49 
                                   +++++k + ++  + v + l +   +  l T+Y +L
  gi|15668953|ref|NP_247757.1| 192 IRYFAKVHGYYISDRVAEYLLK-ITNGNLETIYLIL 226
                                   5566666665555555555443.4445566666655 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.4e-05
                                   --HHHHHHHHHHHHHTTSEEEEEETTSEEEEEES CS
                           FUR  40 islaTVYrtLklleeaglvkelefedgesryela 73 
                                     l+T+Yr L+ l e+g++++++ + g+ r++++
  gi|15668953|ref|NP_247757.1| 279 YKLSTIYRYLDELVELGILTKIKHK-GKVRFKIR 311
                                   4599*******************99.88888876 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.4e-05     0.099      28      55 .]     270     297 ..     222     297 .. 0.90
   2 ?   -1.4   0.1         1   2.3e+03      10      27 ..     316     333 ..     313     336 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                        HTH_36  28 qetlakrlglsknTvsraikeLeqlGyi 55 
                                   +e++  + + + +T++r+++eL++lG++
  gi|15668953|ref|NP_247757.1| 270 VEDITYKVNYKLSTIYRYLDELVELGIL 297
                                   678888899999**************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1
                        HTH_36  10 llgslasfankngg.cfps 27 
                                   +l++l++ + kn++  ++s
  gi|15668953|ref|NP_247757.1| 316 ILLTLLKKS-KNNYlHWFS 333
                                   788899999.999989987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.5e-05       0.1      21      49 ..     270     298 ..     260     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.5e-05
                                   HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  21 lselArrtglpkStvhRlLqtLvelGyve 49 
                                   + ++  +     St +R+L  LvelG+++
  gi|15668953|ref|NP_247757.1| 270 VEDITYKVNYKLSTIYRYLDELVELGILT 298
                                   566777777889**************997 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.013        29       9      39 ..     197     227 ..     192     232 .. 0.80
   2 ?    6.1   0.1    0.0047        11      29      53 ..     279     303 ..     264     311 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.013
                                   -EEHHHHHHHHHCCSTT-CCTTHHHHHHHHH CS
                          PadR   9 psyGyeiikeleelsegllelseGslYpaLk 39 
                                   + +Gy i ++++e++  +++ +  ++Y +L+
  gi|15668953|ref|NP_247757.1| 197 KVHGYYISDRVAEYLLKITNGNLETIYLILR 227
                                   68************77666666667777775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0047
                                   TTHHHHHHHHHHHHHTTSEEEEEE- CS
                          PadR  29 lseGslYpaLkrLekeglvesewee 53 
                                    + +++Y+ L++L + g++++ + +
  gi|15668953|ref|NP_247757.1| 279 YKLSTIYRYLDELVELGILTKIKHK 303
                                   55689**************998765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.36       7      47 .]     258     299 ..     252     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                                   HHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5   7 ILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                   ++    e ++ +v +++ +++   st+ ++L  L e+G+++k
  gi|15668953|ref|NP_247757.1| 258 LVEVIIElRKFKVEDITYKVNYKLSTIYRYLDELVELGILTK 299
                                   5555566677799**************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2508.13
//
Query:       gi|15668954|ref|NP_247758.1|  [L=175]
Description: hypothetical protein MJ_0773 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1153.26
//
Query:       gi|15668955|ref|NP_247759.1|  [L=409]
Description: hypothetical protein MJ_0774 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-13   49.2   0.0    1.1e-12   47.6   0.0    2.0  1  HTH_5            Bacterial regulatory protein, arsR family
    1.5e-08   35.2   0.0    3.7e-08   33.9   0.0    1.6  1  AAA_16           AAA ATPase domain
    2.9e-08   33.9   0.0    1.5e-07   31.6   0.0    2.0  1  ATPase_2         ATPase domain predominantly from Archaea
    1.6e-05   25.2   0.0    4.4e-05   23.8   0.0    1.7  1  AAA_22           AAA domain
    2.5e-05   24.7   0.0    0.00011   22.7   0.0    2.1  1  AAA              ATPase family associated with various cellul
    3.9e-05   22.7   0.0     0.0027   16.6   0.1    2.3  2  DUF2791          P-loop Domain of unknown function (DUF2791)
    0.00031   20.0   0.1      0.027   13.7   0.0    2.2  2  NB-ARC           NB-ARC domain
    0.00039   20.3   0.0    0.00083   19.2   0.0    1.6  1  MarR_2           MarR family
    0.00082   19.9   0.2      0.003   18.1   0.1    2.0  2  ABC_tran         ABC transporter
     0.0012   19.2   0.0     0.0033   17.8   0.0    1.8  1  Penicillinase_R  Penicillinase repressor
     0.0046   16.9   0.0      0.011   15.7   0.0    1.6  1  MarR             MarR family
     0.0047   16.6   0.0      0.019   14.6   0.0    2.1  1  Sigma70_r4_2     Sigma-70, region 4
     0.0054   15.9   0.4      0.011   14.9   0.1    1.6  2  DUF815           Protein of unknown function (DUF815)
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.067   13.0   0.0    2.2  2  HTH_38           Helix-turn-helix domain
      0.016   15.4   0.0      0.053   13.7   0.0    1.8  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.021   15.0   0.0      0.055   13.7   0.0    1.8  1  PaaX             PaaX-like protein
      0.031   14.2   0.1      0.067   13.1   0.1    1.6  1  TrmB             Sugar-specific transcriptional regulator Trm
       0.04   14.3   0.2        1.5    9.3   0.0    2.5  2  Rrf2             Transcriptional regulator
      0.042   14.4   0.0       0.11   13.0   0.0    1.8  1  HTH_27           Winged helix DNA-binding domain
      0.064   13.1   0.0       0.14   11.9   0.0    1.7  1  HTH_IclR         IclR helix-turn-helix domain
      0.067   12.7   0.0        1.1    8.8   0.0    2.6  2  Sigma70_r4       Sigma-70, region 4
      0.079   12.9   0.1       0.18   11.7   0.0    1.8  2  RsgA_GTPase      RsgA GTPase
      0.082   12.9   0.0       0.24   11.4   0.0    1.8  1  HTH_11           HTH domain
      0.094   12.7   0.1        0.7    9.9   0.1    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
       0.13   12.2   1.4       0.33   10.9   0.2    2.0  2  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   1.6e-15   1.1e-12       2      47 .]     334     381 ..     333     381 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.6e-15
                                   HHHHHHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5   2 ptRlkILklLae..gelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                   p++++I++++ae  g+++v++lae+l++s+st+  HL+  +e+G+++k
  gi|15668955|ref|NP_247759.1| 334 PAQSEIVRAMAElgGSATVTQLAEYLKKSPSTIGTHLSDIYEMGYIYK 381
                                   899******************************************986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   5.1e-11   3.7e-08       2     151 ..      40     192 ..      40     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 5.1e-11
                        AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareell 82 
                                   +vGR  el+++ ++l+++  g+  +  ++G +G+GKss+++ ++ a +k+g ++++ ++ q    +p++ l+q+l +  l 
  gi|15668955|ref|NP_247759.1|  40 FVGRVSELREIGEILGSALHGSVANAAIVGTKGIGKSSMLNIIYYATKKQGHWVVEMTASQV---TPRQFLIQLLYN-ILT 116
                                   89******************************************777777777799999999...888668888855.777 PP

                        AAA_16  83 rqllde..aesaeleawrekleealaavpelagaea.....srllellkrllallsrderplvlvlDdlqwadeas 151
                                   + + ++  + +++  +++ ++++ ++  ++  ++ +     +r+ + l  l++  +++++  ++++D+++++   s
  gi|15668955|ref|NP_247759.1| 117 ENIITMsgTIKSDYMEHSSRILDMYRKLNNYGDKVPihyprERIERDLEYLINEVKSPDKLCIILIDEADQFAKKS 192
                                   777777553333444555666666664444444444777789**********777777888*********987755 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   2.1e-10   1.5e-07       1     232 [.      40     291 ..      40     292 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.1e-10
                      ATPase_2   1 FfdRekelkeleeiler...epneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie........ 70 
                                   F+ R+ el+e+ eil +   ++     i G +g+GK+++l+ i+   ++++  v+ ++a +    + l + +         
  gi|15668955|ref|NP_247759.1|  40 FVGRVSELREIGEILGSalhGSVANAAIVGTKGIGKSSMLNIIYYATKKQGHWVVEMTASQVTPRQFLIQLLYniltenii 120
                                   889999999999998762225556678****************99999888844444443333333332222233333443 PP

                      ATPase_2  71 .........eeeekkklekal................giavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDe 126
                                                       +                g++vp        +  ++ +++ +e+l++++k   k  ii+iDe
  gi|15668955|ref|NP_247759.1| 121 tmsgtiksdY----------MehssrildmyrklnnyGDKVPI-------HYPRERIERDLEYLINEVKSPDKLCIILIDE 184
                                   3333332331..........03333444433343332222222.......3568999************************ PP

                      ATPase_2 127 lqklidlglngaellvkeLlnliesltkekhlcvviclsSeglfiervyneselegrhky.ilvddldketalnflkegfk 206
                                   + +      +  ++   +Ll+++ s +  ++ ++ +++ S +l+ ++   + + ++r    i++ +l k+++ +++++  +
  gi|15668955|ref|NP_247759.1| 185 ADQFA----K--KS-CLSLLQFFHSFL-YEEGILTFMAGSPTLMDDLTKISPPIKDRIPKiINMPPLSKDESYDLIRRRLE 257
                                   ***99....3..22.335556666633.3678999***********999999*****9888****************9777 PP

                      ATPase_2 207 el..eel.......skedfeeiyryvGGkPkalve 232
                                   +             ++e + +i++  +G+P+++++
  gi|15668955|ref|NP_247759.1| 258 DAhiD-GaeefepfTEEAIHKIVEECDGIPRKIIM 291
                                   76631.23446777999***************985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   6.1e-08   4.4e-05       8     132 ..      65     218 ..      61     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.1e-08
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.................. 70 
                                    +++G +G+GK+  l+ + +  +++      +  vv++t+++ t ++++l +ll ++  e+                    
  gi|15668955|ref|NP_247759.1|  65 AAIVGTKGIGKSSMLNIIYYATKKQ------GHWVVEMTASQVT-PRQFLIQLLYNILTENIItmsgtiksdymehssril 138
                                   589*************999998643......5666666666666.8888666665555444445***************** PP

                        AAA_22  71 .................erlsseellealeqalraravielliiDEaqhlr..s.eealeeLrsllnlsrkgvqliLvGtp 131
                                                    +r + e+ le+l + +++ ++  +++iDEa+ +   s   +l++++s+l   + g+  +++G p
  gi|15668955|ref|NP_247759.1| 139 dmyrklnnygdkvpihyPRERIERDLEYLINEVKSPDKLCIILIDEADQFAkkScLSLLQFFHSFLY--EEGILTFMAGSP 217
                                   **************************************9**********974335666666666666..777777777777 PP

                        AAA_22 132 e 132
                                    
  gi|15668955|ref|NP_247759.1| 218 T 218
                                   5 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.5e-07   0.00011       3     130 ..      67     240 ..      65     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.5e-07
                                   EESSTTSSHHHHHHHHHHHHTHE...EEEEETTTCSSS........................................... CS
                           AAA   3 lyGppGtGKTllakavakelgve...fleisgsellsk........................................... 37 
                                   ++G++G+GK+++ + +   ++ +   ++e+ +s+++                                             
  gi|15668955|ref|NP_247759.1|  67 IVGTKGIGKSSMLNIIYYATKKQghwVVEMTASQVTPRqfliqllynilteniitmsgtiksdymehssrildmyrklnny 147
                                   68**************9998633344999999999955699**************************************** PP

                                   ........STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEES CS
                           AAA  38 ........yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatn 110
                                             +  e++++ l++e+k+  k +i++iDE+d++ak++              Ll+++  +  +e+ +++++ + 
  gi|15668955|ref|NP_247759.1| 148 gdkvpihyPRERIERDLEYLINEVKSPDKLCIILIDEADQFAKKS-----------CLSLLQFFHSFLYEEGILTFMAGSP 217
                                   *******555566999********999977*************99...........8888888888888766444444333 PP

                                   S....GGGSTHHHHSTTSSEEEET CS
                           AAA 111 r....pdkldpallrgRfdrkiei 130
                                   +      k++p++  +R+ ++i++
  gi|15668955|ref|NP_247759.1| 218 TlmddLTKISPPIK-DRIPKIINM 240
                                   36444445666666.777777765 PP

>> DUF2791  P-loop Domain of unknown function (DUF2791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   3.7e-06    0.0027      19     111 ..      32     121 ..      31     128 .. 0.87
   2 ?    3.5   0.0     0.035        25     312     374 ..     221     284 ..     179     310 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.7e-06
                       DUF2791  19 PriGleliaVGrereiealledlervaeggaafrfirGeYGsGKtFllqllreralergfvvaeadlsperrLhgtkgqle 99 
                                   P +G   + VGr +e +++ e l +  +g+ a  +i+G  G GK+ +l+++    +++g  v+e+  s+ ++ +     ++
  gi|15668955|ref|NP_247759.1|  32 PIRGNTKFFVGRVSELREIGEILGSALHGSVANAAIVGTKGIGKSSMLNIIYYATKKQGHWVVEMTASQVTPRQ---FLIQ 109
                                   7789999********************************************************99999555444...3467 PP

                       DUF2791 100 alYrelvenlst 111
                                    lY+ l+en+ t
  gi|15668955|ref|NP_247759.1| 110 LLYNILTENIIT 121
                                   777777777766 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.035
                       DUF2791 312 edrfakeaglkdlrapvirLkplteeellvlle.klrdiyaegyeeevlvsdeelkafleevtg 374
                                   +d  + ++ +kd    +i+++pl+++e + l++ +l+d + +g+ee    ++e++++++ee+ g
  gi|15668955|ref|NP_247759.1| 221 DDLTKISPPIKDRIPKIINMPPLSKDESYDLIRrRLEDAHIDGAEEFEPFTEEAIHKIVEECDG 284
                                   55555556778888899************998637********99999**********999976 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.029        21      24      51 ..      66      92 ..      49     147 .. 0.71
   2 !   13.7   0.0   3.8e-05     0.027     152     204 ..     236     292 ..     224     320 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.029
                                  EEEESTTSSHHHHHHHHCCSHCCCCCCB CS
                        NB-ARC 24 alvGmgGvGKttlakqilnksdevegrF 51
                                  a+vG  G+GK+ +++ i+    + +g++
  gi|15668955|ref|NP_247759.1| 66 AIVGTKGIGKSSMLNIIYYA-TKKQGHW 92
                                  79************999998.6666655 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.8e-05
                                   EEEEESS--HHHHHHHHHHCCTS-GGCHH......CHHHHHHHHHHCTT-HHHHHHH CS
                        NB-ARC 152 ekievelLekdeawellenkvfekkleekes....leevakeivekckGlPlalkvl 204
                                   + i++  L+kde+++l+     +++ +  e+     ee  ++ive+c G P  +++ 
  gi|15668955|ref|NP_247759.1| 236 KIINMPPLSKDESYDLIRRRLEDAHIDGAEEfepfTEEAIHKIVEECDGIPRKIIMT 292
                                   56677789***********99999998888788889999************988775 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06   0.00083       3      55 ..     332     383 ..     330     387 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                   --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                   ltpaq  +  a +  +g   tv++la++l+ s+s++  +l +  + G++ +++
  gi|15668955|ref|NP_247759.1| 332 LTPAQSEIVRAMAELGGS-ATVTQLAEYLKKSPSTIGTHLSDIYEMGYIYKER 383
                                   799999999999999986.6*****************************8886 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   4.2e-06     0.003      14      80 ..      65     132 ..      60     176 .. 0.72
   2 ?   -1.7   0.0       5.2   3.7e+03      87      87 ..     298     298 ..     214     361 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.2e-06
                                   EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH..H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                      ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren..e 80 
                                    aivG  G GKS++l++++  +k ++G+  ++++ ++ +++++l + +  +  e+ +    t+++   e
  gi|15668955|ref|NP_247759.1|  65 AAIVGTKGIGKSSMLNIIYYATK-KQGHWVVEMTASQVTPRQFLIQLLYNILTENIITMSGTIKSDymE 132
                                   79******************998.688888999999987777766555544444444444445555454 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.2
                                   H CS
                                   x RF
                      ABC_tran  87 k 87 
                                    
  gi|15668955|ref|NP_247759.1| 298 S 298
                                   1 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.5e-06    0.0033       1      63 [.     332     391 ..     332     400 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.5e-06
                                   ---S-SHHHHHHHHHS-.EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE CS
               Penicillinase_R   1 lgelEaevmeilwekge.atvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYs 63 
                                   l+++++e+ +++ e+g  atv+++ e l++     +sT+ t l+  ++ g++ +e+eg+   Y 
  gi|15668955|ref|NP_247759.1| 332 LTPAQSEIVRAMAELGGsATVTQLAEYLKKS----PSTIGTHLSDIYEMGYIYKEREGNNVYYK 391
                                   68999**********999*********9999....************************99885 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.5e-05     0.011       1      52 [.     332     384 ..     332     387 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                                   --HHHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                          MarR   1 ltltqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRsks 52 
                                   lt++q +i+r  +e g+ ++v++La+ l+ s+st+ + l   ++ G+i++++ 
  gi|15668955|ref|NP_247759.1| 332 LTPAQSEIVRAMAELGGsATVTQLAEYLKKSPSTIGTHLSDIYEMGYIYKERE 384
                                   799999999999999999*******************************9985 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.7e-05     0.019       6      48 ..     327     371 ..     326     374 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                                   HHHTTS-HHHHHHHHHHHTS---..HHHHHHHHT--HHHHHHHHH CS
                  Sigma70_r4_2   6 ealaeLperqreifllrylegls..ykEIAellgisegtVksrls 48 
                                   + l++L++ q+ei+   ++ g s    + Ae+l+ s++t+ ++ls
  gi|15668955|ref|NP_247759.1| 327 QILNHLTPAQSEIVRAMAELGGSatVTQLAEYLKKSPSTIGTHLS 371
                                   789************999999763378****************97 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.6e-05     0.011      49     110 ..      59     119 ..      45     124 .. 0.83
   2 ?   -3.2   0.0       5.1   3.7e+03      93     115 ..     162     184 ..     152     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                        DUF815  49 eglpannvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklvellrerperfi 110
                                   +g  an + ++G++G GKSs++  +  +++++g  ++e++ ++++  + l++ll +  ++ i
  gi|15668955|ref|NP_247759.1|  59 HGSVAN-AAIVGTKGIGKSSMLNIIYYATKKQGHWVVEMTASQVTPRQFLIQLLYNILTENI 119
                                   555555.5679******************************999988888888776655555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.1
                        DUF815  93 kelpklvellrerperfilfvDD 115
                                   ++l+ l++++++ ++ +i+++D 
  gi|15668955|ref|NP_247759.1| 162 RDLEYLINEVKSPDKLCIILIDE 184
                                   47999999999999999999995 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       7.4   5.3e+03      23      31 ..      47      55 ..      47      56 .. 0.88
   2 ?   13.0   0.0   9.3e-05     0.067       4      40 ..     331     369 ..     330     371 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.4
                        HTH_38 23 lreIArrLg 31
                                  lreI+ +Lg
  gi|15668955|ref|NP_247759.1| 47 LREIGEILG 55
                                  699**9998 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.3e-05
                        HTH_38   4 hLsleeReeIerllaeG..lslreIArrLgrspsTIsRE 40 
                                   hL++++ e   ++ + G   ++ + A +L++spsTI  +
  gi|15668955|ref|NP_247759.1| 331 HLTPAQSEIVRAMAELGgsATVTQLAEYLKKSPSTIGTH 369
                                   89999999999999877578888*************765 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.3e-05     0.053      20      53 ..     347     380 ..     339     385 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.3e-05
                                   HSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress  20 kkvvktkdlaerLnvspssVsemlkkLekdGyve 53 
                                   ++ +++++lae L+ sps++   l+   ++Gy+ 
  gi|15668955|ref|NP_247759.1| 347 GGSATVTQLAEYLKKSPSTIGTHLSDIYEMGYIY 380
                                   57799***************************74 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.7e-05     0.055      31      69 ..     357     395 ..     338     396 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.7e-05
                          PaaX  31 aelGiseslvRaalsRlakaGwlvrekegrrsfYrLsdk 69 
                                   + l  s s++ + ls + + G + +e+eg++++Y+Ls +
  gi|15668955|ref|NP_247759.1| 357 EYLKKSPSTIGTHLSDIYEMGYIYKEREGNNVYYKLSKE 395
                                   4444577888999999999******************86 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.4e-05     0.067      21      64 ..     348     391 ..     332     395 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.4e-05
                                   CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                          TrmB  21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64 
                                   g+at++++ae l+ + s++   L+   ++G++++e++  ++Y  
  gi|15668955|ref|NP_247759.1| 348 GSATVTQLAEYLKKSPSTIGTHLSDIYEMGYIYKEREGNNVYYK 391
                                   789*********************************98887754 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.28     2e+02      18      56 ..      85     121 ..      75     124 .. 0.75
   2 ?    9.3   0.0     0.002       1.5      23      77 ..     347     402 ..     331     403 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.28
                                   HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2  18 akeeeeepvsseeiaerqnispsylekilakLrkaglvk 56 
                                   a+++++    + e+ ++q +++++l ++l +   +++++
  gi|15668955|ref|NP_247759.1|  85 ATKKQG--HWVVEMTASQVTPRQFLIQLLYNILTENIIT 121
                                   333333..4688999**************9988888775 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.002
                                   CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE.EEETTT-TCEEESSHCCCSBHH CS
                          Rrf2  23 eepvsseeiaerqnispsylekilakLrkaglv.ksvrGkgGGyrLakppeeItll 77 
                                   +++++++++ae  + sps +   l+   + g++ k ++G++  y+L+k+++++ ++
  gi|15668955|ref|NP_247759.1| 347 GGSATVTQLAEYLKKSPSTIGTHLSDIYEMGYIyKEREGNNVYYKLSKELRDVLIG 402
                                   34589****************************44567************999776 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00015      0.11       1      64 [.     332     392 ..     332     395 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                        HTH_27   1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrl 64 
                                   lt+ q+ +++ +++ ++ ++ ++l+++l+ + s+i   l+   e+G++    +e+++ ++ ++l
  gi|15668955|ref|NP_247759.1| 332 LTPAQSEIVRAMAELGGSATVTQLAEYLKKSPSTIGTHLSDIYEMGYI---YKEREGNNVYYKL 392
                                   7999*********99999999***************************...5556666677766 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.14       8      50 ..     339     381 ..     321     383 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                   HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                   i +a ae ++  t+++lA+ +  ++St   +L+   e+Gy+ +
  gi|15668955|ref|NP_247759.1| 339 IVRAMAELGGSATVTQLAEYLKKSPSTIGTHLSDIYEMGYIYK 381
                                   56666777777*****************999999999999876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.66   4.7e+02      22      31 ..      46      55 ..      39      56 .. 0.85
   2 ?    8.8   0.0    0.0015       1.1       2      37 ..     329     366 ..     328     374 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.66
                                  -HHHHHHHHT CS
                    Sigma70_r4 22 TleEIgerlg 31
                                   l EIge+lg
  gi|15668955|ref|NP_247759.1| 46 ELREIGEILG 55
                                  589*****98 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0015
                                   HHHS-HHHHHHHHHHH..TTT--HHHHHHHHTS-HHHH CS
                    Sigma70_r4   2 LasLpererevlelrf..geglTleEIgerlgiSrerV 37 
                                   L++L++ + e+++     g   T  +++e l  S +++
  gi|15668955|ref|NP_247759.1| 329 LNHLTPAQSEIVRAMAelGGSATVTQLAEYLKKSPSTI 366
                                   89********************************9998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00025      0.18     101     123 ..      64      86 ..      25     150 .. 0.86
   2 ?   -3.0   0.0       8.2   5.9e+03      90     121 ..     305     334 ..     283     355 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                                   EEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase 101 tsvlvGqSGvGKStLinallpel 123
                                    +++vG  G+GKS+++n +   +
  gi|15668955|ref|NP_247759.1|  64 NAAIVGTKGIGKSSMLNIIYYAT 86 
                                   4689*************997654 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.2
                                   HHHHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  90 leelkellkdktsvlvGqSGvGKStLinallp 121
                                   l+++ e++ ++ +  +G S vG   ++n+l+p
  gi|15668955|ref|NP_247759.1| 305 LTKIDEKVVKEAMHSLGIS-VGH-QILNHLTP 334
                                   3333333333333333333.332.24455555 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00034      0.24      14      50 ..     348     383 ..     336     388 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                        HTH_11  14 gpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesep 50 
                                   g  +  +LAe+L+ S +t+  ++ ++ e+g  I++e+
  gi|15668955|ref|NP_247759.1| 348 GSATVTQLAEYLKKSPSTIGTHLSDIYEMG-YIYKER 383
                                   557999************************.888777 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00098       0.7       4      47 ..      67     112 ..      64     202 .. 0.85
   2 ?   -1.9   0.0       4.2     3e+03     113     137 ..     203     233 ..     180     234 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00098
                                   EE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH--B-- CS
                         AAA_5   4 LvGppGtgKselaerlaaal..nreveyvqltrdtteedlkgrrei 47 
                                   +vG +G+gKs++   +  a+  +  +++ +  ++ t+++++ ++ +
  gi|15668955|ref|NP_247759.1|  67 IVGTKGIGKSSMLNIIYYATkkQGHWVVEMTASQVTPRQFLIQLLY 112
                                   79******************97777777777778888888877766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.2
                                   .......-EEEEEESS--.-TT-TTHHHHTT CS
                         AAA_5 113 r......frviatanpldrslnelspalrsR 137
                                          ++++a + +l+ +l ++sp++++R
  gi|15668955|ref|NP_247759.1| 203 FlyeegiLTFMAGSPTLMDDLTKISPPIKDR 233
                                   0444556677778888888888888888888 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00046      0.33      83     145 ..      65     124 ..      45     127 .. 0.81
   2 ?   -0.5   0.1       1.4     1e+03      63      86 ..     293     316 ..     273     346 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00046
               Methyltransf_18  83 vdtvviaGmGgelileILeeakeklkkikklilqpnseaeelRkylvengfkiedEelvkeeg 145
                                   + +v   G+G + +l+I+  a    kk  +++++   ++ + R++l++  ++i  E++++ +g
  gi|15668955|ref|NP_247759.1|  65 AAIVGTKGIGKSSMLNIIYYAT---KKQGHWVVEMTASQVTPRQFLIQLLYNILTENIITMSG 124
                                   55666789***********994...44568****************************98766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.4
               Methyltransf_18  63 ledkievrlsdGleklkeeevdtv 86 
                                   ++++i++ + +Gl+k++e+ v+ +
  gi|15668955|ref|NP_247759.1| 293 CSESISIAIRKGLTKIDEKVVKEA 316
                                   456667777777777765433332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2376.24
//
Query:       gi|15668956|ref|NP_247760.1|  [L=316]
Description: GTP cyclohydrolase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-78  262.5   2.2      5e-78  262.2   2.2    1.0  1  GCHY-1    Type I GTP cyclohydrolase folE2
  ------ inclusion threshold ------
       0.01   15.1   1.3      0.018   14.3   0.2    1.8  2  LYTB      LytB protein
      0.035   14.7   0.3       0.18   12.5   0.0    2.2  2  FRP       Photoprotection regulator fluorescence recovery pro
      0.051   12.2   1.5       0.12   11.0   0.2    1.8  2  PFL-like  Pyruvate formate lyase-like


Domain annotation for each model (and alignments):
>> GCHY-1  Type I GTP cyclohydrolase folE2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.2   2.2   1.1e-81     5e-78       3     259 .]       9     299 ..       8     299 .. 0.93

  Alignments for each domain:
  == domain 1  score: 262.2 bits;  conditional E-value: 1.1e-81
                                   XXXXXXXXX----SEEEEEEEEEEEEE--TTTS-EEEEEEEEEEEES-SS--GGGGGHHHHHHH.HS-SSEEG..GGHHH. CS
                        GCHY-1   3 DvqsekderkipldrVGvkgvklpvkvkdkekkaqtlvaevdlfvdLpaekkGihmSRlvevle.eaeeelee..kslee. 79 
                                   Dvq+ ++++ki+l+rVGv+++k++v++k+ +k+++ l +++++fv+Lp+++kGihmSR+ ev+e   +e+le   +++e+ 
  gi|15668956|ref|NP_247760.1|   9 DVQNFEPDVKISLTRVGVTNLKKLVRLKRTNKRPIILLSTFEVFVNLPSSQKGIHMSRNPEVIEgIIDEALELesYEMETi 89 
                                   9***************************************************************87777777534444445 PP

                                   ...HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE....TT.EEEEEEEEEEEEEEE-HHHHHHS CS
                        GCHY-1  80 ...ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaeler..ke.evkltvgvevpvttlCPCskeis 154
                                      i+++l+ek+eya++aev + +++++++k+p+sgk ++e  +++  a+  +  +e e++++vg+ev+++t+CPC+++++
  gi|15668956|ref|NP_247760.1|  90 ceeIVKRLFEKHEYATEAEVFMVSDFMTKEKSPISGKYSQEIHKIMGGAKGIKkdDEiELTKIVGAEVVGITACPCAQNLI 170
                                   567*********************************99********9999877433355********************** PP

                                   .........................SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE--S---HHHHHHHHHH CS
                        GCHY-1 155 rell.....................eagaHnQRsvvtvkvelaeeekeveiedlielvessassevyellKReDEkavtek 214
                                   +e+                       +++HnQR++ ++ +e+ ++  ++ei d+ie++++s+s+e++ +lKR+DE++v+e+
  gi|15668956|ref|NP_247760.1| 171 KEICiknlkekgfsdedidkildsvIFATHNQRGIGRIILEV-PTGYDIEIMDIIEIIKKSMSAEIHGILKRADEAYVVEQ 250
                                   9999*********************9***************5.6899********************************** PP

                                   HHTS---HHHHHHHHHHHHHS-TTEEEE.........EEEEEEE-TTTSSEEEE CS
                        GCHY-1 215 ayenpkFvEDvvRevaaaleeeerveef.........sveveneESiHnHnavA 259
                                   +++npkFvED+vRe+a+++     ve+f          +++ n+ESiH+H+a+A
  gi|15668956|ref|NP_247760.1| 251 SHKNPKFVEDCVREMAKRV-----VEKFkhlpdetkvLIRQINMESIHRHDAFA 299
                                   *******************.....55555558888889***************8 PP

>> LYTB  LytB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2     4e-06     0.018     153     259 ..      63     173 ..      27     179 .. 0.82
   2 ?   -0.8   0.1      0.16   7.4e+02     116     155 ..     232     256 ..     219     299 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4e-06
                                   -HHHHHHHHHHHHHHSTCEEE..C-S--CHHHHHHHHHHHHHGHSSEEEE...ES-TT-HHHHHHHHHHHHCSCTEEEESS CS
                          LYTB 153 sveefeeivealkkklkelev..kdtiCkatqeRqeavkelakevdlviv...vGgknSsNtkkLveiakeknkktylies 228
                                   ++++  e++e + ++  ele   ++tiC++  +R  + +e a+e+++++v    + ++S  + k  + +++    +  i++
  gi|15668956|ref|NP_247760.1|  63 HMSRNPEVIEGIIDEALELESyeMETICEEIVKRLFEKHEYATEAEVFMVsdfMTKEKSPISGKYSQEIHKIMGGAKGIKK 143
                                   555555666666666666666669********************9999975658999***999999999999999****** PP

                                   GGG--HHHHTT-SEEEEEE-TTS-HHHHHHH CS
                          LYTB 229 aeeldeewlegvkkvgitaGaStpeelieev 259
                                    +e++ +++ g++ vgita   +  +li+e+
  gi|15668956|ref|NP_247760.1| 144 DDEIELTKIVGAEVVGITACPCAQ-NLIKEI 173
                                   ******************986555.455554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.16
                                   -HHHHHHHCCT--TEEEESSCHHHHHGCEEEEE-TTS-HH CS
                          LYTB 116 HpEvegilgqaeekvvvveeseeveklkvalvsQTTlsve 155
                                    +E+ gil  a+e ++vve+s                + +
  gi|15668956|ref|NP_247760.1| 232 SAEIHGILKRADE-AYVVEQS--------------HKNPK 256
                                   4566666666544.4444332..............22222 PP

>> FRP  Photoprotection regulator fluorescence recovery protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     4e-05      0.18      22      86 ..      91     154 ..      72     161 .. 0.73
   2 ?   -2.0   0.1       1.2   5.6e+03      72      95 ..     168     191 ..     166     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                           FRP  22 ealiaevkekaeslsdlddlWqlhdfLsakRydidgkydfreskllfvlarlvkeklleleeLeG 86 
                                   e +++++ ek e ++   +++ + df+++++  i gky ++ +k++     + k++ +el  + G
  gi|15668956|ref|NP_247760.1|  91 EEIVKRLFEKHEYAT-EAEVFMVSDFMTKEKSPISGKYSQEIHKIMGGAKGIKKDDEIELTKIVG 154
                                   556666666665555.568**********************999997766666777777666665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                           FRP  72 rlvkeklleleeLeGLeaeklakv 95 
                                   +l+ke  ++    +G ++e + k+
  gi|15668956|ref|NP_247760.1| 168 NLIKEICIKNLKEKGFSDEDIDKI 191
                                   689999999988899999998887 PP

>> PFL-like  Pyruvate formate lyase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1     0.056   2.5e+02     117     183 ..      81     150 ..      50     157 .. 0.75
   2 ?   11.0   0.2   2.6e-05      0.12     131     240 ..     184     293 ..     166     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.056
                                   HHHHTTTSHHHHHHHHCHHTTHHHHTSTSEE--CHGGSSCEEEE--HHHHHTC...HHHHHHHHHHHHHH CS
                      PFL-like 117 fpyWkgktvnegvfdayteetkaaresgiitvglpdasgrGhiipdyervlky...Gldglieeikekla 183
                                    + ++ +t+ e + + + e+++ a e+++++v+  ++++++ i ++y + + +   G +g++++ + +l 
  gi|15668956|ref|NP_247760.1|  81 LESYEMETICEEIVKRLFEKHEYATEAEVFMVSDFMTKEKSPISGKYSQEIHKimgGAKGIKKDDEIELT 150
                                   45567777777788888899999999*****999999999999999988764434477777777666665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.6e-05
                                   HHCHHTTHHHHTSTSEE--CHGGSSCEEEE--HHHHHTCHHHHHHHHHHHHHHHHCC....TTTCCHHHHHHHHHHHHHHH CS
                      PFL-like 131 dayteetkaaresgiitvglpdasgrGhiipdyervlkyGldglieeikeklakldl....ddpeaiekaefykaviisle 207
                                   +   e++ ++++s i+    + ++g G+ii+  ++ ++  + ++ie ik+ +++       +++ea+  ++ +k  + + +
  gi|15668956|ref|NP_247760.1| 184 SD--EDIDKILDSVIFA--THNQRGIGRIILEVPTGYDIEIMDIIEIIKKSMSAEIHgilkRADEAYVVEQSHKNPKFVED 260
                                   22..4459999999999..788***********************99998886533235669999**************** PP

                                   HHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHH CS
                      PFL-like 208 avieyaeryarlaeelaeqetdpkrkaeLleia 240
                                   +v+e+a+r++++ + l ++++   r+ +++ i 
  gi|15668956|ref|NP_247760.1| 261 CVREMAKRVVEKFKHLPDETKVLIRQINMESIH 293
                                   ****************99988899999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2070.29
//
Query:       gi|15668957|ref|NP_247761.1|  [L=383]
Description: hypothetical protein MJ_0776 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-42  143.4   0.2    1.2e-41  142.4   0.2    1.5  1  ATP-grasp_3     ATP-grasp domain
    1.9e-07   30.6   1.0    4.1e-07   29.5   0.3    1.8  2  ATPgrasp_YheCD  YheC/D like ATP-grasp
    7.4e-06   25.7   0.0     0.0001   22.0   0.0    2.3  2  ATPgrasp_Ter    ATP-grasp in the biosynthetic pathway with Te
    1.7e-05   24.2   1.1     0.0056   16.0   0.3    2.5  2  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
    2.6e-05   23.7   0.0    8.8e-05   22.0   0.0    1.9  1  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
    2.6e-05   23.9   0.2    0.00021   20.9   0.2    2.2  1  RimK            RimK-like ATP-grasp domain
  ------ inclusion threshold ------
      0.046   13.3   0.8      0.067   12.7   0.8    1.1  1  Drc1-Sld2       DNA replication and checkpoint protein


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.4   0.2   4.8e-45   1.2e-41       1     161 []     124     282 ..     124     282 .. 0.98

  Alignments for each domain:
  == domain 1  score: 142.4 bits;  conditional E-value: 4.8e-45
                                   HTSHHHHHHHHTTT.S---..........-EESS--SSSEEEEESS-------B--SS--TTE..........EEEE---S CS
                   ATP-grasp_3   1 asdKlktykkLkeagvkvP......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve...lvqefieG 72 
                                   +s+K+ktykkLk+ g+++P      +k++ +++ ee k++++Kp++G+gg s++++e ++ ++++i+e++   ++qe+i+G
  gi|15668957|ref|NP_247761.1| 124 ISNKYKTYKKLKNLGFNIPetkkinNKTQLYKFLEEFKTCILKPIYGSGG-SILKIELNNFDDEIINEIKfpiIAQEYIRG 203
                                   69**********************999***********************.9***************************** PP

                                   EEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEE CS
                   ATP-grasp_3  73 kplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkdeepyviE 153
                                   k++S+++++++    ++++n+q+i k     +yaGn+tp+  +l +++ve++ ev+e++ +l+G+ G+D+++kd++py+++
  gi|15668957|ref|NP_247761.1| 204 KSFSANFIGNT----FITFNKQIIIK----GMYAGNLTPYI-NLPNKFVEIFGEVIESF-ELKGMSGIDFLIKDNGPYIVD 274
                                   *********77....*********98....9*********9.9****************.********************* PP

                                   EESS--GG CS
                   ATP-grasp_3 154 vNPRltts 161
                                   +NPR+ ++
  gi|15668957|ref|NP_247761.1| 275 INPRILGT 282
                                   *****986 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.3   1.6e-10   4.1e-07       8      69 ..     123     180 ..     119     206 .. 0.89
   2 ?   -1.6   0.0      0.52   1.3e+03     205     228 ..     257     279 ..     242     306 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.6e-10
                ATPgrasp_YheCD   8 kffnKwevyelLskdpelrpyLPetellesledleemlekyksvylKpanGskGkgilriek 69 
                                   ++ nK+++y+ L++   l   +Pet++++++ +l ++le++k+++lKp++Gs+G  il+ie 
  gi|15668957|ref|NP_247761.1| 123 EISNKYKTYKKLKN---LGFNIPETKKINNKTQLYKFLEEFKTCILKPIYGSGG-SILKIEL 180
                                   4789******9998...5688*******************************99.5888886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.52
                ATPgrasp_YheCD 205 gElGlDlgidkegkvWllEvNskp 228
                                   g  G+D+ i ++g  ++ ++N + 
  gi|15668957|ref|NP_247761.1| 257 GMSGIDFLIKDNG-PYIVDINPRI 279
                                   55599*9998877.6888999875 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.14   3.7e+02      38      65 ..      68      95 ..      63      98 .. 0.82
   2 !   22.0   0.0     4e-08    0.0001      42     107 ..     235     301 ..     194     320 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.14
                  ATPgrasp_Ter 38 gglqelekdeelielaerlaeefgldgl 65
                                  g+l+e  ++++lie+a++la+e+ + ++
  gi|15668957|ref|NP_247761.1| 68 GRLKENYDENKLIEIANKLADEVDCIFI 95
                                  66677778999**********9988665 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 4e-08
                  ATPgrasp_Ter  42 elekdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgys.alaGvnlpylalkl 107
                                   +++  ++ +e+  +++e+f+l+g+ ++ +  +++gp++ +iNpR+ G+ +   + a  nl+ + l+ 
  gi|15668957|ref|NP_247761.1| 235 YINLPNKFVEIFGEVIESFELKGMSGIDFLIKDNGPYIVDINPRILGTYETIeMSASQNLAMVLLNN 301
                                   666778899**************************************86543033345555444443 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   2.2e-06    0.0056      13     102 ..     118     202 ..     113     222 .. 0.82
   2 !    6.4   0.0    0.0018       4.5     227     273 ..     241     288 ..     234     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-06
                   ATPgrasp_ST  13 raefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqdylkssgk 93 
                                    +++  + +K k+++ +++ g+++p+     k+ ++ ++l +f++e+++  ++Kp++gsgG+ + +  ++ d++++++ + 
  gi|15668957|ref|NP_247761.1| 118 PKKINEISNKYKTYKKLKNLGFNIPE----TKKINNKTQLYKFLEEFKT-CILKPIYGSGGSILKIELNNFDDEIINEIKF 193
                                   56677899***999999*********....4444566678888889966.99**********9999999999999888888 PP

                   ATPgrasp_ST  94 salldeler 102
                                    + ++e+ r
  gi|15668957|ref|NP_247761.1| 194 PIIAQEYIR 202
                                   888887776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0018
                   ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNar..pglaivqi 273
                                   +++e+  ++ e +   g+ G+D+ + +++ p+++ +N r    ++ +++
  gi|15668957|ref|NP_247761.1| 241 KFVEIFGEVIESFELKGMSGIDFLIKDNG-PYIVDINPRilGTYETIEM 288
                                   66777788888888999************.*******986334444455 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.4e-08   8.8e-05      11      79 ..     140     202 ..     132     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.4e-08
                                   CS--EEEES-HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTTTS-EEEEE--G CS
                     GSH-S_ATP  11 lipktlvskdkeeirafleeqgdvilKPldgkgGegvfrvkksdpnlksilellteegkepviaqrylp 79 
                                    ip+t   ++k+++ +flee ++ ilKP++g+gG ++++++      +   + +++e k p+iaq+y+ 
  gi|15668957|ref|NP_247761.1| 140 NIPETKKINNKTQLYKFLEEFKTCILKPIYGSGG-SILKIEL-----NNFDDEIINEIKFPIIAQEYIR 202
                                   489999999***********************99.5887765.....5555677777888999999986 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2   8.2e-08   0.00021       2     184 ..     125     298 ..     124     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 8.2e-08
                                   H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--EEEEE- CS
                          RimK   2 rdKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlealkeailvqeyi 82 
                                   ++K+k+ k L   + ++p+t+ ++++ ++ k++e++k     ++K ++gs G  ++  + ++   ++++ +k  i+ qeyi
  gi|15668957|ref|NP_247761.1| 125 SNKYKTYKKLKNLGFNIPETKKINNKTQLYKFLEEFK---TCILKPIYGSGGS-ILKIELNNFDDEIINEIKFPIIAQEYI 201
                                   69**********************************7...89*******9885.5556666677789999*********** PP

                                   -SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-S.EEEEEEEEETTEEEEEE CS
                          RimK  83 eeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelv.vaGvDllrakrgllvlE 162
                                     +         +++  ++  +++         ++ G+ +  ++l ++  e+  ++ +  el  + G+D l +++g+++++
  gi|15668957|ref|NP_247761.1| 202 RGKSFS---ANFIGNTFITFNKQIII-----KGMYAGNLTPYINLPNKFVEIFGEVIESFELKgMSGIDFLIKDNGPYIVD 274
                                   977654...45689999888777744.....46899999********************9997588*************** PP

                                   EESS-..-SHHHHHHHT--HHHHH CS
                          RimK 163 vnssp..glekiektlgidiakkl 184
                                   +n       e ie+    ++a+ l
  gi|15668957|ref|NP_247761.1| 275 INPRIlgTYETIEMSASQNLAMVL 298
                                   **8753245778888888877766 PP

>> Drc1-Sld2  DNA replication and checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.8   2.6e-05     0.067      29      48 ..     119     138 ..     100     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                     Drc1-Sld2  29 KknpeIaakYkeYskLkake 48 
                                   Kk +eI++kYk+Y+kLk+  
  gi|15668957|ref|NP_247761.1| 119 KKINEISNKYKTYKKLKNLG 138
                                   899**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2603.60
//
Query:       gi|15668958|ref|NP_247762.1|  [L=191]
Description: transcription initiation factor E subunit alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-40  136.2   5.0    3.2e-40  136.2   5.0    1.7  2  TFIIE_alpha     TFIIE alpha subunit
      1e-08   34.6   1.8      2e-08   33.6   1.8    1.6  1  TF_Zn_Ribbon    TFIIB zinc-binding
    0.00014   21.9   1.4    0.00022   21.2   0.0    2.0  1  Sigma70_r3      Sigma-70 region 3
    0.00037   20.5   0.1    0.00049   20.1   0.1    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
    0.00053   20.0   0.0      0.001   19.1   0.0    1.4  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
     0.0037   17.6   0.0     0.0072   16.7   0.0    1.4  1  Rrf2            Transcriptional regulator
     0.0042   16.9   2.1     0.0084   16.0   0.6    2.3  3  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.011   15.6   0.4      0.011   15.6   0.4    3.4  3  Rad50_zn_hook   Rad50 zinc hook motif
      0.011   15.3   0.1      0.059   12.9   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.017   14.8   0.2      0.064   12.9   0.0    2.0  2  GntR            Bacterial regulatory proteins, gntR family
      0.019   15.0   0.8      0.038   14.0   0.3    1.8  1  DUF2095         Uncharacterized protein conserved in archaea 
      0.024   14.8   0.3      0.074   13.3   0.0    2.0  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.031   14.1   0.1      0.084   12.7   0.0    1.7  1  HTH_5           Bacterial regulatory protein, arsR family
      0.033   14.2   0.0      0.066   13.3   0.0    1.4  1  HTH_20          Helix-turn-helix domain
      0.046   13.7   0.0      0.072   13.1   0.0    1.3  1  Dimerisation2   Dimerisation domain
       0.06   13.2   0.0        0.1   12.4   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
      0.063   13.0   0.0       0.13   12.0   0.0    1.5  1  Sigma70_r4_2    Sigma-70, region 4
      0.079   12.9   2.5       0.21   11.5   0.4    2.2  2  zinc_ribbon_4   zinc-ribbon domain
        0.1   12.9   0.1        6.5    7.1   0.0    2.3  2  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
       0.13   12.1   2.8      0.063   13.1   0.6    1.6  2  DUF2202         Uncharacterized protein domain (DUF2202)
       0.15   11.5   1.8        9.9    5.7   0.1    2.3  2  zf-ribbon_3     zinc-ribbon domain
       0.15   12.3   0.5       0.26   11.6   0.5    1.4  1  zf-LITAF-like   LITAF-like zinc ribbon domain
       0.18   11.8   0.1       0.18   11.8   0.1    3.0  3  Prefoldin_2     Prefoldin subunit
       0.45   10.6   2.4        1.1    9.4   0.9    2.0  2  DUF2752         Protein of unknown function (DUF2752)
       0.51    9.9   1.6        5.2    6.7   0.0    2.3  2  zf_C2H2_10      C2H2 type zinc-finger
        2.5    8.1   4.0         33    4.6   0.3    2.5  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        2.6    8.0   8.8        7.9    6.4   0.2    3.4  3  IF2_N           Translation initiation factor IF-2, N-termina
        8.5    6.3   8.2        1.9    8.3   1.9    2.9  3  DUF4187         Domain of unknown function (DUF4187)


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.2   5.0     5e-43   3.2e-40       2     105 .]      24     129 ..      23     129 .. 0.98
   2 ?   -1.7   0.1       4.2   2.7e+03      91     102 ..     168     179 ..     162     186 .. 0.68

  Alignments for each domain:
  == domain 1  score: 136.2 bits;  conditional E-value: 5e-43
                                   HHHHHHHHCS-..HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCC CS
                   TFIIE_alpha   2 llkevvrkfyg..eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyek 80 
                                   l++ev++++++  e+ ++v+dvLlekge+tee++akel+++ln++rklL++Ly+arlv+ykr++de+++wy+y+w+++ ek
  gi|15668958|ref|NP_247762.1|  24 LVQEVLFNIFEgdEKGFEVIDVLLEKGETTEEEIAKELGVKLNVVRKLLYKLYDARLVDYKRWKDEDTNWYSYTWLPTLEK 104
                                   99********988999***************************************************************** PP

                                   HCCCHHHHHHHHHHHHHHHHCCCTS CS
                   TFIIE_alpha  81 lvdvvkrkleevvkkLeeklekeen 105
                                   l++vvk+k++e++k+Le+kle+e+n
  gi|15668958|ref|NP_247762.1| 105 LPYVVKKKINELIKDLEKKLEFEKN 129
                                   ***********************98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.2
                                   HHHHHHHHHHCC CS
                   TFIIE_alpha  91 evvkkLeeklek 102
                                   e++k+Lee++++
  gi|15668958|ref|NP_247762.1| 168 ELIKDLEEQIKF 179
                                   666777776655 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   1.8   3.2e-11     2e-08       1      38 [.     133     170 ..     133     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3.2e-11
                                   EEETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCC CS
                  TF_Zn_Ribbon   1 ykCPnCgstnlveDpergelvCtdCGlVlednsidegp 38 
                                   + CPnC+ +++ e+++   + C+ CG++l++++++e +
  gi|15668958|ref|NP_247762.1| 133 FFCPNCNVRFTFEEAMDYGFSCPGCGNMLQEFDNSELI 170
                                   57*******************************99876 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.5e-07   0.00022      20      60 ..      51      91 ..      41      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.5e-07
                                  XXXHHHHHHHHTXXHHHHHHHHHHHXXXEETTXBSSSSTTX CS
                    Sigma70_r3 20 ePtpeEiAeeLglseekVrevleaarepvSldlpvgeeedt 60
                                  e t+eEiA+eLg+ ++ Vr++l    +++++d++ +++edt
  gi|15668958|ref|NP_247762.1| 51 ETTEEEIAKELGVKLNVVRKLLYKLYDARLVDYKRWKDEDT 91
                                  679*************************************8 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   7.7e-07   0.00049      59      98 ..     121     163 ..      41     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.7e-07
                                   T-EEEEEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS-EE CS
                          HypA  59 gaeLeieevpvkvrCreCgkefelee..k.alrCpkCgsadve 98 
                                   +++Le+e+ ++ + C +C+ +f+ ee  +  ++Cp Cg+   e
  gi|15668958|ref|NP_247762.1| 121 EKKLEFEKNNMFFFCPNCNVRFTFEEamDyGFSCPGCGNMLQE 163
                                   489********************766444677******97554 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.6e-06     0.001      18      59 ..      42      83 ..      38      85 .. 0.97

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-06
                                  HHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEEE CS
                         HTH_9 18 VvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVqy 59
                                  V+++Ll+kg  t  e++k++++ l+ V+k L+ L   rlV+y
  gi|15668958|ref|NP_247762.1| 42 VIDVLLEKGETTEEEIAKELGVKLNVVRKLLYKLYDARLVDY 83
                                  99**************************************99 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-05    0.0072      24      59 ..      50      85 ..      42      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                                  C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksvr 59
                                  +  + eeia++ +++ ++++k+l kL  a lv  +r
  gi|15668958|ref|NP_247762.1| 50 GETTEEEIAKELGVKLNVVRKLLYKLYDARLVDYKR 85
                                  33789**************************98665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         6   3.8e+03      37      44 ..      14      21 ..       7      23 .. 0.67
   2 !   16.0   0.6   1.3e-05    0.0084      16      55 ..      45      84 ..      37     108 .. 0.88
   3 ?   -1.6   0.0       4.1   2.6e+03      36      49 ..     110     123 ..     101     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6
                                  HCHHHHHH CS
                          TrmB 37 skvYevLr 44
                                   ++Ye+L+
  gi|15668958|ref|NP_247762.1| 14 ERIYEMLN 21
                                  46777775 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.3e-05
                                  HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                          TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                  +Ll++g+ t +eia+elgv  + v + L +L d+ lV+ +
  gi|15668958|ref|NP_247762.1| 45 VLLEKGETTEEEIAKELGVKLNVVRKLLYKLYDARLVDYK 84
                                  79******************************99999765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.1
                                   CHCHHHHHHHHHHC CS
                          TrmB  36 rskvYevLrsLedk 49 
                                   + k++e ++ Le+k
  gi|15668958|ref|NP_247762.1| 110 KKKINELIKDLEKK 123
                                   67999999999986 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.1   7.1e+02      33      46 ..      52      66 ..      49      71 .. 0.75
   2 ?    1.6   1.5      0.38   2.5e+02      33      46 ..     112     125 ..     110     129 .. 0.81
   3 ?   15.6   0.4   1.7e-05     0.011      21      52 .]     153     184 ..     145     184 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.1
                                  H.HHHHHHHHHHHHH CS
                 Rad50_zn_hook 33 h.rseLikelqskle 46
                                     +e++kel  kl+
  gi|15668958|ref|NP_247762.1| 52 TtEEEIAKELGVKLN 66
                                  448999999999987 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.38
                                   HHHHHHHHHHHHHH CS
                 Rad50_zn_hook  33 hrseLikelqskle 46 
                                   + +eLik+l++kle
  gi|15668958|ref|NP_247762.1| 112 KINELIKDLEKKLE 125
                                   58899999999986 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.7e-05
                                   E-TTT--EE-HHHHHHHHHHHHHHHHHHH... CS
                 Rad50_zn_hook  21 cCPlCgReldeehrseLikelqsklerlpeel 52 
                                   +CP Cg  l e + seLik+l+++++ l+eel
  gi|15668958|ref|NP_247762.1| 153 SCPGCGNMLQEFDNSELIKDLEEQIKFLKEEL 184
                                   8*************************999986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.2e-05     0.059       2      37 ..      36      71 ..      35      81 .. 0.89
   2 ?   -0.9   0.1         2   1.3e+03      33      44 ..     112     123 ..     110     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.2e-05
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrr 37
                                  de+ ++++ +L +++ ++  e+A++lg+ ++ v++ 
  gi|15668958|ref|NP_247762.1| 36 DEKGFEVIDVLLEKGETTEEEIAKELGVKLNVVRKL 71
                                  778899**********************99999875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                        HTH_24  33 tvnrrlkrLeee 44 
                                    +n+ +k Le++
  gi|15668958|ref|NP_247762.1| 112 KINELIKDLEKK 123
                                   578899999986 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         4   2.6e+03       2      16 ..      13      27 ..      12      29 .. 0.76
   2 ?   12.9   0.0    0.0001     0.064      26      55 ..      53      82 ..      43      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4
                                  HHHHHHHHHHHHHTT CS
                          GntR  2 yeqvyerLredIlsg 16
                                   e++ye+L + +++ 
  gi|15668958|ref|NP_247762.1| 13 IERIYEMLNDPLVQE 27
                                  589999999887765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.0001
                                  -HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          GntR 26 sereLaaefgVsrttvReALrrLeaeglve 55
                                  +e+e+a+e+gV+ ++vR+ L +L  + lv 
  gi|15668958|ref|NP_247762.1| 53 TEEEIAKELGVKLNVVRKLLYKLYDARLVD 82
                                  69******************9999999986 PP

>> DUF2095  Uncharacterized protein conserved in archaea (DUF2095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   5.9e-05     0.038      74     106 ..      32      65 ..       3      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-05
                       DUF2095  74 rcetdeealeiinwmeergeith.emakelrvvl 106
                                     e de+ +e+i+ + e+ge t+ e+akel v l
  gi|15668958|ref|NP_247762.1|  32 IFEGDEKGFEVIDVLLEKGETTEeEIAKELGVKL 65 
                                   4689*****************96369****9876 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00012     0.074      19      56 ..      48      85 ..      37      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                                  HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                  ek+  +  ++a++L+v+   V + l kL ++ +v+y+ 
  gi|15668958|ref|NP_247762.1| 48 EKGETTEEEIAKELGVKLNVVRKLLYKLYDARLVDYKR 85
                                  56667789****************************96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013     0.084      10      47 .]      46      83 ..      37      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                                  HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5 10 lLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  lL++ge++  e+a+elg+    v+  L kL++a+LV++
  gi|15668958|ref|NP_247762.1| 46 LLEKGETTEEEIAKELGVKLNVVRKLLYKLYDARLVDY 83
                                  5666********************************86 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0    0.0001     0.066      15      55 ..      42      82 ..      36      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                                  HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                  + + L ++++ t +e+a++l+++ n +++ L +L +a Lv+
  gi|15668958|ref|NP_247762.1| 42 VIDVLLEKGETTEEEIAKELGVKLNVVRKLLYKLYDARLVD 82
                                  566777999******************************97 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.072      22      77 ..      41      97 ..      25     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                 Dimerisation2 22 gvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLere.kkeekkalYsnt 77
                                  +v d+L e+++++ ee+a+elg++++ ++ Ll  +   +L   +  k+e+++ Ys t
  gi|15668958|ref|NP_247762.1| 41 EVIDVLLEKGETTEEEIAKELGVKLNVVRKLLYKLYDARLVDYKrWKDEDTNWYSYT 97
                                  789*****************************9999999998774455567888877 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016       0.1       3      49 ..      37      82 ..      37      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                                  HHHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  3 dRalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                  +++++++d l e ++  t  e+A+++g+    v+ lL  L   ++v 
  gi|15668958|ref|NP_247762.1| 37 EKGFEVIDVLLEKGET-TEEEIAKELGVKLNVVRKLLYKLYDARLVD 82
                                  69*************8.***********************9999886 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.13      27      49 ..      52      74 ..      46      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                  --HHHHHHHHT--HHHHHHHHHH CS
                  Sigma70_r4_2 27 lsykEIAellgisegtVksrlsR 49
                                   + +EIA++lg++ + V++ l++
  gi|15668958|ref|NP_247762.1| 52 TTEEEIAKELGVKLNVVRKLLYK 74
                                  5789***************9986 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00033      0.21       1      17 [.     131     147 ..     131     149 .. 0.91
   2 ?    0.7   0.1       0.8   5.1e+02       4       9 ..     153     158 ..     151     160 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                 zinc_ribbon_4   1 MkitCpsCkakyeidde 17 
                                   M + Cp+C+ +++++++
  gi|15668958|ref|NP_247762.1| 131 MFFFCPNCNVRFTFEEA 147
                                   8899*********9986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.8
                 zinc_ribbon_4   4 tCpsCk 9  
                                   +Cp C+
  gi|15668958|ref|NP_247762.1| 153 SCPGCG 158
                                   677775 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.12        78       3      15 ..     133     145 ..     113     149 .. 0.85
   2 ?    7.1   0.0      0.01       6.5       3      24 ..     152     176 ..     150     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                       zf-Di19   3 ftCPyCgkeltvk 15 
                                   f CP C+  +t +
  gi|15668958|ref|NP_247762.1| 133 FFCPNCNVRFTFE 145
                                   8899999877754 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.01
                       zf-Di19   3 ftCPyCgk...eltvkeLveHvede 24 
                                   f CP Cg+   e++ +eL++ +e++
  gi|15668958|ref|NP_247762.1| 152 FSCPGCGNmlqEFDNSELIKDLEEQ 176
                                   99*****744359999999988875 PP

>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   9.9e-05     0.063       4      68 ..       3      66 ..       1      88 [. 0.83
   2 ?   -2.8   0.1       7.9   5.1e+03      95     113 ..     112     129 ..     107     131 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.9e-05
                       DUF2202  4 sllymreeeklarDvYlelYdrwklqiflniakseqthtdavksllekYeledpvkederGkfed 68
                                  s+  mr+e k+ r +Y+ l d   +++  ni + +++  + +  llek e ++    +e G+  +
  gi|15668958|ref|NP_247762.1|  3 SVQSMRKEKKIER-IYEMLNDPLVQEVLFNIFEGDEKGFEVIDVLLEKGETTEEEIAKELGVKLN 66
                                  6778***999987.9*********************************99998888887887544 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.9
                       DUF2202  95 tiedldiaDlekalketdn 113
                                   +i++l i+Dlek l+ ++n
  gi|15668958|ref|NP_247762.1| 112 KINEL-IKDLEKKLEFEKN 129
                                   55565.7888877776655 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.023        14       4       9 ..     134     139 ..     131     142 .. 0.77
   2 ?    5.7   0.1     0.015       9.9       4      14 ..     153     163 ..     151     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.023
                   zf-ribbon_3   4 rCPnCG 9  
                                   +CPnC+
  gi|15668958|ref|NP_247762.1| 134 FCPNCN 139
                                   788885 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.015
                   zf-ribbon_3   4 rCPnCGaplss 14 
                                   +CP CG+ l++
  gi|15668958|ref|NP_247762.1| 153 SCPGCGNMLQE 163
                                   7*****94465 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   0.00041      0.26      36      68 ..     132     163 ..     129     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00041
                 zf-LITAF-like  36 lfgcllccliPfcvdslkdvehyCpnCgallgt 68 
                                   +f+ +  c + f +++ +d   +Cp Cg++l  
  gi|15668958|ref|NP_247762.1| 132 FFF-CPNCNVRFTFEEAMDYGFSCPGCGNMLQE 163
                                   333.4678899******************9975 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       3.5   2.3e+03      68      79 ..      47      58 ..      38      76 .. 0.57
   2 ?    2.3   0.5      0.25   1.6e+02      56      73 ..     109     126 ..     103     131 .. 0.64
   3 ?   11.8   0.1   0.00028      0.18      51      79 ..     157     185 ..     155     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.5
                                  HHHHHHHHHHHH CS
                   Prefoldin_2 68 eerketlekeik 79
                                   e+ et e+ei+
  gi|15668958|ref|NP_247762.1| 47 LEKGETTEEEIA 58
                                  333444444432 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.25
                                   EEE-HHHHHHHHHHHHHH CS
                   Prefoldin_2  56 vkqdkeevkeeLeerket 73 
                                   vk++ +e++++Le+++e+
  gi|15668958|ref|NP_247762.1| 109 VKKKINELIKDLEKKLEF 126
                                   555666666666666665 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00028
                                   ETTEEEEE-HHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  51 vGdvlvkqdkeevkeeLeerketlekeik 79 
                                   +G++l ++d  e++++Lee++++l++e+k
  gi|15668958|ref|NP_247762.1| 157 CGNMLQEFDNSELIKDLEEQIKFLKEELK 185
                                   7**************************98 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       1.4     9e+02       8      15 ..     132     139 ..     128     141 .. 0.77
   2 ?    9.4   0.9    0.0017       1.1       8      16 ..     151     159 ..     147     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.4
                       DUF2752   8 GipCPGCG 15 
                                    + CP C 
  gi|15668958|ref|NP_247762.1| 132 FFFCPNCN 139
                                   578****6 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0017
                       DUF2752   8 GipCPGCGl 16 
                                   G++CPGCG 
  gi|15668958|ref|NP_247762.1| 151 GFSCPGCGN 159
                                   9*******5 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.5      0.25   1.6e+02       3       9 ..     133     139 ..     132     142 .. 0.85
   2 ?    6.7   0.0    0.0081       5.2       3      13 ..     152     162 ..     151     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.25
                    zf_C2H2_10   3 fsCPKCq 9  
                                   f CP C+
  gi|15668958|ref|NP_247762.1| 133 FFCPNCN 139
                                   77****8 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0081
                    zf_C2H2_10   3 fsCPKCqeklP 13 
                                   fsCP C+  l 
  gi|15668958|ref|NP_247762.1| 152 FSCPGCGNMLQ 162
                                   9*****99875 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2      0.06        39      19      27 ..     133     141 ..     126     150 .. 0.77
   2 ?    4.6   0.3     0.051        33      18      27 ..     151     160 ..     147     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.06
                 Zn_Tnp_IS1595  19 fvCPhCgsr 27 
                                   f CP+C +r
  gi|15668958|ref|NP_247762.1| 133 FFCPNCNVR 141
                                   66****987 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.051
                 Zn_Tnp_IS1595  18 gfvCPhCgsr 27 
                                   gf CP Cg++
  gi|15668958|ref|NP_247762.1| 151 GFSCPGCGNM 160
                                   799*****97 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2     0.012       7.9       8      24 ..      56      72 ..      49      76 .. 0.83
   2 ?    4.6   0.7     0.045        29      14      36 ..     110     131 ..     108     132 .. 0.87
   3 ?   -0.1   0.1       1.3   8.5e+02      16      26 ..     165     175 ..     162     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.012
                         IF2_N  8 eLAkeLgvkskevikkL 24
                                  e+AkeLgvk + v k L
  gi|15668958|ref|NP_247762.1| 56 EIAKELGVKLNVVRKLL 72
                                  9********98876666 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.045
                         IF2_N  14 gvkskevikkLfkelGievkshs 36 
                                   ++k +e+ik L+k+l +e k+ +
  gi|15668958|ref|NP_247762.1| 110 KKKINELIKDLEKKLEFE-KNNM 131
                                   68899********99999.8765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.3
                         IF2_N  16 kskevikkLfk 26 
                                   ++ e+ik L++
  gi|15668958|ref|NP_247762.1| 165 DNSELIKDLEE 175
                                   799****9954 PP

>> DUF4187  Domain of unknown function (DUF4187)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.2   2.1e+03       6      22 ..       4      20 ..       2      22 .. 0.81
   2 ?    8.3   1.9    0.0029       1.9      25      48 ..     131     156 ..     109     160 .. 0.84
   3 ?    0.1   0.1       1.1   7.1e+02       3      25 ..     161     183 ..     159     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.2
                       DUF4187  6 feeleaeerLeklleyL 22
                                  ++++ +e+++e++ e+L
  gi|15668958|ref|NP_247762.1|  4 VQSMRKEKKIERIYEML 20
                                  57889999999999887 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0029
                       DUF4187  25 eylYCfwCgtkYedeedLee..nCPG 48 
                                    +++C  C ++++ ee ++   +CPG
  gi|15668958|ref|NP_247762.1| 131 MFFFCPNCNVRFTFEEAMDYgfSCPG 156
                                   589**************998778**9 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.1
                       DUF4187   3 leefeeleaeerLeklleyLRee 25 
                                   l+ef++ e+ ++Le+ +++L ee
  gi|15668958|ref|NP_247762.1| 161 LQEFDNSELIKDLEEQIKFLKEE 183
                                   57899999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1607  (0.0896313); expected 358.6 (0.02)
Passed bias filter:                      990  (0.0552178); expected 358.6 (0.02)
Passed Vit filter:                       149  (0.00831056); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1259.53
//
Query:       gi|15668959|ref|NP_247763.1|  [L=169]
Description: hypothetical protein MJ_0778 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-19   70.1   1.0    1.9e-19   70.1   1.0    1.4  2  HD        HD domain
    3.2e-05   23.8   0.3    0.00011   22.0   0.1    2.0  2  HD_2      HD containing hydrolase-like enzyme
    3.2e-05   23.5   0.0     0.0012   18.3   0.0    2.1  2  HDOD      HDOD domain
  ------ inclusion threshold ------
      0.085   12.5   0.0       0.12   12.0   0.0    1.3  1  ApbA      Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   1.0   4.2e-23   1.9e-19       2     119 ..      19     127 ..      18     130 .. 0.91
   2 ?   -3.1   0.0       1.9   8.5e+03      66      82 ..     139     155 ..     134     162 .. 0.61

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 4.2e-23
                                   HHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHHH CS
                            HD   2 leHsleVaklarrlaedlge...eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldle 79 
                                    eH+l+V ++a +la  ++    e d+el++l++LlHDiG  +++              +H +vgaeilre++ ++     
  gi|15668959|ref|NP_247763.1|  19 VEHCLAVSEYAYELALAIKNkgyEVDVELVRLGGLLHDIGRSRTHG------------IEHGVVGAEILRELGFDE----- 82 
                                   79*****************9***********************774............56****************..... PP

                                   HHHHHHHTTCCHHHHHHHH...H..HHHCCTSCHHHHHHHHHHHH CS
                            HD  80 dvaklirehheswegkkrp...r..glaerqlslearivklaDrl 119
                                    +a ++++h +   +k++        +++ +++le++iv+ aD+l
  gi|15668959|ref|NP_247763.1|  83 KLALIAERHIGAGITKEEAielGlpPKDYLPITLEEKIVAHADNL 127
                                   7799999999999877776866166******************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.9
                                   HHHHHHHHHHHHHHHHH CS
                            HD  66 ilrevekrlgldledva 82 
                                   +++++ekrlg++   + 
  gi|15668959|ref|NP_247763.1| 139 VIKKFEKRLGKNHPSIK 155
                                   67788888777633333 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   2.6e-08   0.00011      17      66 ..       9      57 ..       1      67 [. 0.88
   2 ?   -0.6   0.0      0.21   9.5e+02     127     143 ..     119     135 ..     110     169 .] 0.49

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.6e-08
                          HD_2 17 lmrntreenvaeHslevaliahalal.ienkkfggkldaerlallalyHDa 66
                                    +n  +env eH+l v+ +a+ lal i+nk    ++d+e + l +l+HD+
  gi|15668959|ref|NP_247763.1|  9 ILKNLCSENVVEHCLAVSEYAYELALaIKNKG--YEVDVELVRLGGLLHDI 57
                                  5678899******************9788866..59**************7 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.21
                          HD_2 127 klvkaaDklsalikcle 143
                                   k+v  aD+l    k +e
  gi|15668959|ref|NP_247763.1| 119 KIVAHADNLIFGTKRVE 135
                                   55555555544444332 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.8e-07    0.0012      90     132 ..      13      59 ..       3      62 .. 0.83
   2 !    3.5   0.0    0.0099        44     163     193 ..      61      91 ..      59      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.8e-07
                                   S-HHHHHHHHHHHHHHHHHHHHHTT-S-H....HHHHHHHHTTTHHH CS
                          HDOD  90 adlkklwehslavAlvarelaeelgledp....eeaflaGLLhdiGk 132
                                   +  ++++eh+lav+ +a ela +++ +      e + l+GLLhdiG+
  gi|15668959|ref|NP_247763.1|  13 LCSENVVEHCLAVSEYAYELALAIKNKGYevdvELVRLGGLLHDIGR 59 
                                   5678899**************999655522446*************6 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0099
                                   HHHSS-HHHHHHHHHHHTT--HHHHHHHHHT CS
                          HDOD 163 ellgtdhaevGaallekWnlPeelveaiayh 193
                                   +  g++h  vGa++l++  ++e+l  +++ h
  gi|15668959|ref|NP_247763.1|  61 RTHGIEHGVVGAEILRELGFDEKLALIAERH 91 
                                   56799****************9998777766 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.7e-05      0.12      59      96 ..     113     151 ..      74     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.7e-05
                                   CCH.SCCCCS-ESEEEE-SSGGGHHHHHHHHGGGECTCE CS
                          ApbA  59 sae.ekselepidlvivtvKayqteealeeikplldpnt 96 
                                   + + e++  +++d++i+ +K    ++++++++++l++n 
  gi|15668959|ref|NP_247763.1| 113 PITlEEKIVAHADNLIFGTKRVEIDDVIKKFEKRLGKNH 151
                                   333666799***************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1240.82
//
Query:       gi|15668960|ref|NP_247764.1|  [L=299]
Description: hypothetical protein MJ_0779 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-13   50.5   1.8    1.9e-13   50.5   1.8    2.6  4  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3      0.13   2.4e+03     107     121 ..      34      47 ..      29      51 .. 0.46
   2 ?   -3.5   1.7      0.53   9.4e+03     105     117 ..      59      71 ..      52      76 .. 0.49
   3 !   50.5   1.8     1e-17   1.9e-13       4     124 ..      93     217 ..      90     218 .. 0.94
   4 ?   -4.9   1.2         1   1.8e+04     108     121 ..     253     266 ..     251     267 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.13
                                   XXXXXXXXXXXXXXX CS
                         T2SSF 107 lllvvallvllilla 121
                                   lll+++++++l+ ++
  gi|15668960|ref|NP_247764.1|  34 LLLIIIAAIPLL-IS 47 
                                   334444444443.33 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.53
                                   TXXXXXXXXXXXX CS
                         T2SSF 105 pllllvvallvll 117
                                     ++++v++++++
  gi|15668960|ref|NP_247764.1|  59 IFVVIYVGAALFI 71 
                                   3344444444444 PP

  == domain 3  score: 50.5 bits;  conditional E-value: 1e-17
                                   HHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-HHH CS
                         T2SSF   4 qlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageeggnLae 79 
                                    + ++l++G +++eaL  + ++   +++++++++++  +++ + s++e++      + s+++++l++ +i+  ++gg+L++
  gi|15668960|ref|NP_247764.1|  93 IMILALESGRSINEALLEVVKSN-IKEVSDIFRKVLYLMENQKlSFEESMTivsnLYDSKVLRMLARIMIENRKYGGDLSD 172
                                   68999******************.*******************9********9965555677******************* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                         T2SSF  80 vLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                    L+ la++le+  + +r+ll+ +++ l++ +++l+ +++ +a ll
  gi|15668960|ref|NP_247764.1| 173 SLKILAKTLEDFKMYKRQLLSVTASGLAIGFIILCGVIPAVAALL 217
                                   **************************************9999876 PP

  == domain 4  score: -4.9 bits;  conditional E-value: 1
                                   XXXXXXXXXXXXXX CS
                         T2SSF 108 llvvallvllilla 121
                                   ++++++l+++++++
  gi|15668960|ref|NP_247764.1| 253 TAIIGALFAIPIFG 266
                                   56777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2168.69
//
Query:       gi|15668961|ref|NP_247765.1|  [L=335]
Description: hypothetical protein MJ_0780 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-16   61.0   0.3      1e-16   61.0   0.3    2.6  3  T2SSF     Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
          3    6.5   8.4       0.24   10.1   1.6    1.9  2  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4      0.33     3e+03     108     120 ..     108     120 ..      98     124 .. 0.47
   2 !   61.0   0.3   1.2e-20     1e-16       3     124 ..     170     295 ..     168     296 .. 0.95
   3 ?   -1.1   0.1      0.19   1.7e+03      96     115 ..     311     330 ..     308     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.33
                                   XXXXXXXXXXXXX CS
                         T2SSF 108 llvvallvllill 120
                                   ++++++ +l++l+
  gi|15668961|ref|NP_247765.1| 108 VIYMIITFLALLF 120
                                   3333333333333 PP

  == domain 2  score: 61.0 bits;  conditional E-value: 1.2e-20
                                   HHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-HH CS
                         T2SSF   3 rqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageeggnLa 78 
                                    ++ + l+aG++l e+Le+++++ e+g++a e k+i+r+++ Gg +l eale    rt  + +++l++q+i +g   gnL+
  gi|15668961|ref|NP_247765.1| 170 IYMISILRAGASLPEVLESISKSREYGVVAFEAKSIIRDVNIGGyNLVEALErakmRTRIPILKKLYDQMI-VGYNKGNLP 249
                                   5899****************************************9889999988876655688********.********* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                         T2SSF  79 evLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                     L +l e++ +e + + ++ + +++ l  l++++ ++l++ +++l
  gi|15668961|ref|NP_247765.1| 250 LLLGKLYEDIVRESMVKLDSSKFMIQNLGNLAFGVGLILPFTGMIL 295
                                   ********************************************97 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.19
                                   HHHHHHHHTTXXXXXXXXXX CS
                         T2SSF  96 rkllaallepllllvvallv 115
                                   ++ll+ +++pll+l+++++v
  gi|15668961|ref|NP_247765.1| 311 INLLLLKIGPLLTLIFGIFV 330
                                   567788999******99997 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.6   2.7e-05      0.24     316     433 ..      35     153 ..       6     166 .. 0.68
   2 ?    0.4   0.7     0.024   2.1e+02     384     433 ..     280     329 ..     206     333 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 2.7e-05
                       DUF2207 316 dpyEkalldlLfdkseegkslkeikkyakkskkkakkfkkalkkwksavkk......kergyfdkkgkkklkklsalglgl 390
                                   ++ E+++l++   ++e + ++ +i+ky      +++ + k+ +++ +  k       +e +y+  k   + +++  + +  
  gi|15668961|ref|NP_247765.1|  35 SRKEREVLEFYDVYMEPE-EFVDIEKYEFILY-EGDIVGKTAESLSKIFKGnlfpsrNELRYMGVK--DEVAYFKKVVIYM 111
                                   788999999998555333.2555666666655.899999999999998888888777777777777..4444555555555 PP

                       DUF2207 391 iilglilillallllvlllvfllilllillliaiivlllfsrl 433
                                   ii +l+l++++ll  +l l +++  l++ ++i+++ l++++++
  gi|15668961|ref|NP_247765.1| 112 IITFLALLFMGLLDNNL-LQGFVNGLIGAGIILVLSLFYPKIR 153
                                   55555555566666666.8999999999999999999988765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.024
                       DUF2207 384 salglgliilglilillallllvlllvfllilllillliaiivlllfsrl 433
                                    a+g+gli+ ++ +il ++++ ++++ +l+ + l+ll i+ +++l+f ++
  gi|15668961|ref|NP_247765.1| 280 LAFGVGLILPFTGMILSTMIGNQGFSGILSTINLLLLKIGPLLTLIFGIF 329
                                   34444444444444455555555555555555555555555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2342.64
//
Query:       gi|15668962|ref|NP_247766.1|  [L=721]
Description: type II secretion system protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-55  188.4   0.0    2.1e-52  177.9   0.0    2.2  2  T2SSE            Type II/IV secretion system protein
    1.6e-20   73.4   5.2      4e-20   72.1   5.2    1.8  1  Intein_splicing  Intein splicing domain
    1.1e-05   25.0   0.1      2e-05   24.2   0.1    1.3  1  Hint             Hint module
    1.8e-05   25.0   0.9    4.6e-05   23.7   0.9    1.7  1  PT-HINT          Pretoxin HINT domain
    0.00036   20.0   0.1    0.00084   18.8   0.0    1.6  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
     0.0006   20.3   0.1     0.0019   18.7   0.0    1.9  2  ABC_tran         ABC transporter
     0.0028   17.4   1.2      0.011   15.5   0.7    2.3  2  AAA_29           P-loop containing region of AAA domain
     0.0074   15.6   0.0      0.017   14.4   0.0    1.5  1  Zeta_toxin       Zeta toxin
     0.0088   16.6   0.3     0.0088   16.6   0.3    2.7  2  AAA_23           AAA domain
  ------ inclusion threshold ------
      0.048   13.2   0.1       0.11   12.0   0.1    1.5  1  E1-E2_ATPase     E1-E2 ATPase
       0.18   12.4   0.1       0.42   11.2   0.1    1.5  1  OAD_gamma        Oxaloacetate decarboxylase, gamma chain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.9   0.0   1.3e-55   2.1e-52       4     229 ..     171     407 ..     168     408 .. 0.93
   2 !    8.3   0.0   0.00066       1.1     229     256 ..     575     602 ..     560     617 .. 0.72

  Alignments for each domain:
  == domain 1  score: 177.9 bits;  conditional E-value: 1.3e-55
                         T2SSE   4 lleallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvv 83 
                                   lle  l+d++  +++v+ ++  v+v +   + + ++   l+++++ r+i+ ia l+++ i+++ p++da lp +g r+++ 
  gi|15668962|ref|NP_247766.1| 171 LLEVPLNDDRLEEVMVNGYNVpVFV-FHRKHQMCETNIVLDRNEVDRIIESIANLVNRPIDSRVPMLDAFLP-DGSRVNAT 249
                                   5677789******************.6666669999999*********************************.******** PP

                         T2SSE  84 llPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrer.....glilvsGgTgsGKttllyallkeinksde 158
                                   ++ ++ +  +l+iRk s++ lt+ dl+  ++l+ + a++l +av+ +      + l++GgTgsGKttll++l + +  ++e
  gi|15668962|ref|NP_247766.1| 250 TADITMNgATLTIRKFSKNPLTVIDLINFGTLDIDTAAFLWQAVEGYfgakpANTLIAGGTGSGKTTLLNVL-SLFSMYNE 329
                                   **99988799**********************************8552222279****************76.5666777* PP

                         T2SSE 159 rivtvEDpvEiqleganqvqlnak.......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgsls 229
                                   ri+t+ED+ E+q+ ++++++++++       + +vt+ dl+++aLR+rPDri+vGE+R+ke+ ++l A+nTGH+g+l+
  gi|15668962|ref|NP_247766.1| 330 RIITIEDTPELQIPHKHVIKMVTRparpgmpEYEVTMDDLIKNALRMRPDRIFVGEVRGKEAHSLLVAMNTGHDGALA 407
                                   ***************************************************************************875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00066
                         T2SSE 229 sTlHansaagalerLeqlgaeveaaelk 256
                                   +TlHansa +a+ rL    ++v++ +l+
  gi|15668962|ref|NP_247766.1| 575 GTLHANSADEAILRLTSPPMNVPKIMLT 602
                                   7**************9877555554444 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   5.2   2.5e-23     4e-20       3     128 ..     414     564 ..     412     572 .. 0.86

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 2.5e-23
                                   ECTTCEEEEHHHHCC..........ECTTEEEE.EETTTTEEEEEE............EEEEEEEEEE.EEEEEEETTS-E CS
                                   xxxxxxxxxxxxxxx..........xxxxxxxx.xxxxxxxxxxxx............xxxxxxxxxx.xxxxxxxxxxxx RF
               Intein_splicing   3 ledgeekvkieelve..........kegeevls.lnledlklevks............vkkliklklk.elyeiklesgrk 59 
                                   l dg++  +i+e+v+          k++++  + +++ +++++ ks            + +++++k++ +l++i++++ r+
  gi|15668962|ref|NP_247766.1| 414 LSDGNII-NIGEFVDkffkkyknsiKKEDNGFGwIDIGNENIYIKSfnklsliiedkrILRVWRKKYSgKLIKITTKNRRE 493
                                   6676666.89999999999999999444444322788888888888888888888888*********************** PP

                                   EEEETT-EEEECCTTEEEEEECCC--TT-EEEEEHSC.EEEEEEEEEEEEECEEEEEEEEETTT-EEEE.C CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
               Intein_splicing  60 ikaTpeHkllvvrdegivEkradeLkegdliavpdad.vvwdkvksievedeeeyVYdltvednhNFva.n 128
                                   i +T +H++ + + ++++E +a+ +k+gd+i +p+++ + +d+v ++e+ d+++ +Ydltvednh ++a +
  gi|15668962|ref|NP_247766.1| 494 ITLTHDHPVYISKTGEVLEINAEMVKVGDYIYIPKNNtINLDEVIKVETVDYNGHIYDLTVEDNHTYIAgK 564
                                   ************88*********************99899****************************952 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   1.2e-08     2e-05      63     140 ..     480     550 ..     470     557 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.2e-08
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXX CS
                          Hint  63 raefveietengekltlTpaHLvfvsenekssseeeeavfaskvregdyvlvedtaskelrpskvvsvsteektGvyA 140
                                   + + ++i+t+n++++tlT+ H v++s++ +  +     + a+ v+ gdy+++   ++++++  +v +v+t+  +G   
  gi|15668962|ref|NP_247766.1| 480 SGKLIKITTKNRREITLTHDHPVYISKTGEVLE-----INAEMVKVGDYIYI--PKNNTINLDEVIKVETVDYNGHIY 550
                                   557899********************9886655.....89************..88899**********999888655 PP

>> PT-HINT  Pretoxin HINT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.9   2.8e-08   4.6e-05      33     135 ..     469     571 ..     455     573 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.8e-08
                       PT-HINT  33 kpvlarygneyqelvylkisdgignsevlisnkihPfysk..gkf..ieakelkvGdklldesGkvlvvee.iklk..deP 106
                                   k +l  + ++y   + +ki+    n + +  ++ hP y    g+   i+a+ +kvGd ++  + ++  ++e ik++  d  
  gi|15668962|ref|NP_247766.1| 469 KRILRVWRKKYSGKL-IKITT--KNRREITLTHDHPVYISktGEVleINAEMVKVGDYIYIPKNNTINLDEvIKVEtvDYN 546
                                   555555555555443.56665..68899999*******75554432389*************9999988763678887889 PP

                       PT-HINT 107 lkaynlkvadfhtyfvkgnraeteGvlvh 135
                                     +y+l+v+d hty  +    ++eG  v 
  gi|15668962|ref|NP_247766.1| 547 GHIYDLTVEDNHTYIAG----KNEGFAVS 571
                                   99************999....56666665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   5.2e-07   0.00084      39      59 ..     301     321 ..     283     329 .. 0.84
   2 ?   -4.1   0.0       5.1   8.3e+03     110     141 ..     675     709 ..     668     714 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.2e-07
                                   -.SEEEE--TTSSHHHHHHHH CS
                  FtsK_SpoIIIE  39 ashllvaGatgsGKStalntL 59 
                                   ++++l+aG+tgsGK+t ln+L
  gi|15668962|ref|NP_247766.1| 301 PANTLIAGGTGSGKTTLLNVL 321
                                   46*****************87 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 5.1
                                   HHHHHHHHHHHHHHH...HTT-SSHHHHHHHHHHH CS
                  FtsK_SpoIIIE 110 eeLvkemeeryalfr...eagvrsiaaydgeiaed 141
                                   eeL+  +e+r+++++   + ++r+++++ + i ++
  gi|15668962|ref|NP_247766.1| 675 EELLRDRENRKKVLSylyKNNIRKLENVSDYIMRY 709
                                   68888999999666511144555555566666555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.3   8.6e+03      57      72 ..      39      54 ..      25     129 .. 0.50
   2 !   18.7   0.0   1.2e-06    0.0019      14      56 ..     304     346 ..     299     404 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.3
                                  CCHCEEEE-SS--S-T CS
                                  xxxxxxxxxxxxxxxx RF
                      ABC_tran 57 lrkeigvlpqepqlfp 72
                                   +k+  v+p +++l+p
  gi|15668962|ref|NP_247766.1| 39 EKKSETVIPSDTKLKP 54
                                  4444444444433322 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.2e-06
                                   EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeles 56 
                                   + i G +G+GK+tLl++l+  +  +e  i++++++  ++++++
  gi|15668962|ref|NP_247766.1| 304 TLIAGGTGSGKTTLLNVLSLFSMYNERIITIEDTPELQIPHKH 346
                                   6799*******************99999999988766655554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.7   6.5e-06     0.011      20      40 ..     300     319 ..     270     329 .. 0.79
   2 ?   -2.3   0.0       2.3   3.7e+03      12      31 ..     545     565 ..     542     566 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.5e-06
                        AAA_29  20 dlkgatlltGpsGsGKSTllD 40 
                                   +++ +tl++G +GsGK+Tll 
  gi|15668962|ref|NP_247766.1| 300 KPA-NTLIAGGTGSGKTTLLN 319
                                   344.5**************94 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.3
                        AAA_29  12 fdghtieidlkg.atlltGps 31 
                                   ++gh +++++++  t ++G++
  gi|15668962|ref|NP_247766.1| 545 YNGHIYDLTVEDnHTYIAGKN 565
                                   7889999999998999**998 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     1e-05     0.017      14      50 ..     299     335 ..     294     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                    Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                    +P+  l++G++G+GK++l++ l      ++++++++
  gi|15668962|ref|NP_247766.1| 299 AKPANTLIAGGTGSGKTTLLNVLSLFSMYNERIITIE 335
                                   68999****************9987665666666664 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3   5.4e-06    0.0088      19      41 ..     301     323 ..     273     332 .. 0.80
   2 ?   -2.3   0.1       3.3   5.4e+03     103     123 ..     438     458 ..     408     519 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.4e-06
                        AAA_23  19 kgltlItGpNGaGKTTildAikl 41 
                                   +  tlI G +G+GKTT+l+ + l
  gi|15668962|ref|NP_247766.1| 301 PANTLIAGGTGSGKTTLLNVLSL 323
                                   5569**************98875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.3
                        AAA_23 103 ttkkaklelleideleqfise 123
                                   ++ ++ + +++i + + +i++
  gi|15668962|ref|NP_247766.1| 438 KKEDNGFGWIDIGNENIYIKS 458
                                   333333333333222222222 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   6.8e-05      0.11       9      43 ..     504     538 ..     496     546 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.8e-05
                                   EE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEE CS
                  E1-E2_ATPase   9 virdgteeeidakelvpGDivllkagdrvpaDgri 43 
                                   + + g++ ei+a+ +++GD++ +++++++ +D +i
  gi|15668962|ref|NP_247766.1| 504 ISKTGEVLEINAEMVKVGDYIYIPKNNTINLDEVI 538
                                   4488999*************************887 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00026      0.42      16      53 ..      14      51 ..      12      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                     OAD_gamma 16 vvLilLslvislfskiikkkakkkkkkakaaaaaaaaa 53
                                  v+Li+ ++v+ ++ ki kk +k +k+k++++  ++ ++
  gi|15668962|ref|NP_247766.1| 14 VILIIWWFVMGILDKIQKKSEKIEKEKKSETVIPSDTK 51
                                  89************************999988777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 4491.00
//
Query:       gi|15668963|ref|NP_247767.1|  [L=673]
Description: transcription initiation factor IIB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-41  140.2   0.9      2e-20   72.6   0.0    2.5  2  TFIIB            Transcription factor TFIIB repeat
      8e-23   80.9   7.4      8e-23   80.9   7.4    1.8  2  Intein_splicing  Intein splicing domain
    6.8e-16   57.5   2.4    1.6e-15   56.3   2.4    1.7  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0036   17.6   2.6      0.012   16.0   1.6    2.2  2  Lar_restr_allev  Restriction alleviation protein Lar
     0.0038   17.0   0.2      0.023   14.5   0.2    2.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0069   15.9   0.8      0.063   12.8   0.2    2.7  2  Sigma70_r4       Sigma-70, region 4
  ------ inclusion threshold ------
      0.029   13.8   1.7       0.59    9.6   0.0    2.3  2  zf-ribbon_3      zinc-ribbon domain
      0.057   13.7   4.9        3.8    7.9   0.4    2.9  2  LAGLIDADG_3      LAGLIDADG-like domain
      0.059   13.2   2.2       0.13   12.1   0.2    2.5  2  TMIE             TMIE protein
       0.24   10.8   1.1       0.53    9.7   0.2    2.1  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
        0.9    9.3   3.7        2.3    8.0   3.7    1.6  1  Ribosomal_S27e   Ribosomal protein S27
        1.2    9.2   4.0       0.54   10.3   1.4    1.7  2  DZR              Double zinc ribbon
        1.8    8.7   4.7        1.2    9.3   0.1    2.5  2  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.2   1.9e-21   2.6e-18       2      71 .]     493     562 ..     492     562 .. 0.97
   2 !   72.6   0.0   1.5e-23     2e-20       1      71 []     586     656 ..     586     656 .. 0.99

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 1.9e-21
                                   HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                         TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                    r+ ++l+Lp  V+++A  +++ a+e++++ Grs +g++AA++y Acr+++v rt+ ei++ ++V  k+i
  gi|15668963|ref|NP_247767.1| 493 DRITSKLGLPRHVRENAAIIYRGAVEKGLIRGRSIEGVVAAAIYAACRRCRVPRTLDEIAEASRVDRKEI 562
                                   58899*************************************************************9997 PP

  == domain 2  score: 72.6 bits;  conditional E-value: 1.5e-23
                                   HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                         TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                   ++rfa++l+Lp +V+++A +++++a+e+++++Gr p+g+aAA++yiA+ + + +rtq+e+++v+ V+e+ti
  gi|15668963|ref|NP_247767.1| 586 VPRFASELGLPGEVESKAIQILQQAAEKGLTSGRGPTGVAAAAIYIASVLLGCRRTQREVAEVAGVTEVTI 656
                                   689******************************************************************98 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.2       6.9   9.5e+03      70      89 ..      23      40 ..      10      51 .. 0.52
   2 !   80.9   7.4   5.8e-26     8e-23       1     134 []     108     434 ..     108     434 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.9
                                  ECCTTEEEEEECCC--TT-E CS
                                  xxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing 70 vvrdegivEkradeLkegdl 89
                                  +   e+  Ek+ ++++e+++
  gi|15668963|ref|NP_247767.1| 23 TK-VEKS-EKKEENVREEEI 40
                                  22.1222.455555555554 PP

  == domain 2  score: 80.9 bits;  conditional E-value: 5.8e-26
                                   EEECTTCEE.EEHHHHCC...................ECTTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEE CS
                                   xxxxxxxxx.xxxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing   1 iiledgeek.vkieelve...................kegeevlslnledlklevksvkkliklklkelyeiklesgrkik 61 
                                   ii e+ge+k vki+el++                    +g ev++ n +++k +   v+++ ++ ++e++ei +e ++k++
  gi|15668963|ref|NP_247767.1| 108 IIKENGEIKvVKIGELIDkiiensenirregileiakCKGIEVIAFN-SNYKFKFMPVSEVSRHPVSEMFEIVVEGNKKVR 187
                                   6889**************99888888888888888877788888887.777777777************************ PP

                                   EETT-EEEECCTTEEEEEECCC--TT-EEEEE................................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................. RF
               Intein_splicing  62 aTpeHkllvvrdegivEkradeLkegdliavp................................................. 93 
                                   +T+ H+++++rd+++v  r+deLk+gd+++++                                                 
  gi|15668963|ref|NP_247767.1| 188 VTRSHSVFTIRDNEVVPIRVDELKVGDILVLAkelpnieedieidkkfskilgyiiaegyyddkkivlsydynekefinet 268
                                   *******************************9************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15668963|ref|NP_247767.1| 269 idyfkslnsditiyskdlniqievknkkiinllkklrvknkripsiifkspyeikksfidgifngkdakvfvskelaedvi 349
                                   ********************************************************************************* PP

                                   .........................................HSCEEEEEEEEEEEEEC.EEEEEEEEETTT-EEEE..CTT CS
                                   .........................................xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx..xxx RF
               Intein_splicing  94 .........................................dadvvwdkvksievede.eeyVYdltvednhNFva..ngi 130
                                                                            ++d ++ k+k+i++ +   +y Ydltv++ +NFva   g+
  gi|15668963|ref|NP_247767.1| 350 flllqikenatinkksindievyevrritniytnrklekliNSDFIFLKIKEINKVEPtSGYAYDLTVPNAENFVAgfGGF 430
                                   *****************************************************8655449****************98889 PP

                                   EEE- CS
                                   xxxx RF
               Intein_splicing 131 ivHN 134
                                   ++HN
  gi|15668963|ref|NP_247767.1| 431 VLHN 434
                                   9**9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   2.4   1.2e-18   1.6e-15       2      43 .]      41      82 ..      40      82 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.2e-18
                                  EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                  +CP+Cgs+++v D+er+e+vC +CG+V+ +   d gpewr+f
  gi|15668963|ref|NP_247767.1| 41 VCPICGSKEVVKDYERAEIVCAKCGCVIKEKLFDIGPEWRAF 82
                                  8***************************************98 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.6   8.8e-06     0.012       6      37 ..      42      69 ..      37      87 .. 0.79
   2 ?   -0.7   0.0       1.4   1.9e+03      27      39 ..     529     547 ..     504     562 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.8e-06
               Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCga..s 37
                                  CP Cg+++v++  +r        + Ca+Cg+   
  gi|15668963|ref|NP_247767.1| 42 CPICGSKEVVKDYERA------EIVCAKCGCviK 69
                                  **********999887......59******9543 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
               Lar_restr_allev  27 q......cvyCadCgastp 39 
                                          + +C  C +  +
  gi|15668963|ref|NP_247767.1| 529 GvvaaaiYAACRRCRVPRT 547
                                   1444555899999*99333 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   1.7e-05     0.023      16      41 ..     638     663 ..     636     664 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                 HTH_AsnC-type  16 aRisyaeLAervGlSestvlrRvrrL 41 
                                   +R++ +e+Ae  G++e t+++R++ L
  gi|15668963|ref|NP_247767.1| 638 CRRTQREVAEVAGVTEVTIRNRYKEL 663
                                   79*********************988 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.53   7.3e+02      20      29 ..     545     554 ..     539     562 .. 0.85
   2 !   12.8   0.2   4.6e-05     0.063      18      45 ..     637     664 ..     629     667 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.53
                                   T--HHHHHHH CS
                    Sigma70_r4  20 glTleEIger 29 
                                   ++Tl EI+e 
  gi|15668963|ref|NP_247767.1| 545 PRTLDEIAEA 554
                                   79******95 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.6e-05
                                   TTT--HHHHHHHHTS-HHHHHHHHHHHH CS
                    Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAl 45 
                                   g  +T+ E++e+ g+++ ++r + k+  
  gi|15668963|ref|NP_247767.1| 637 GCRRTQREVAEVAGVTEVTIRNRYKELT 664
                                   5679*******************99765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00042      0.59      11      25 ..      34      48 ..      31      48 .. 0.82
   2 ?    3.1   0.4      0.05        68      17      24 ..      59      66 ..      55      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00042
                   zf-ribbon_3 11 plssddnvCpyCGtk 25
                                  +++++ +vCp CG+k
  gi|15668963|ref|NP_247767.1| 34 NVREEEIVCPICGSK 48
                                  789999999999986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.05
                   zf-ribbon_3 17 nvCpyCGt 24
                                  +vC++CG 
  gi|15668963|ref|NP_247767.1| 59 IVCAKCGC 66
                                  79****95 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.4    0.0057       7.9       3      56 ..     234     284 ..     232     311 .. 0.81
   2 ?    7.9   0.4    0.0027       3.8      33      79 ..     341     387 ..     321     391 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0057
                                   HHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEE CS
                   LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyek 56 
                                   k   + G++ a+G+ + +k     +s+  ++ke++++   + + l+   tiy k
  gi|15668963|ref|NP_247767.1| 234 KFSKILGYIIAEGYYDDKKIV---LSYDYNEKEFINETIDYFKSLNSDITIYSK 284
                                   566789*************77...9999*********99999999888888877 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0027
                                   -HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGGG CS
                   LAGLIDADG_3  33 skelledvqrlLlrlGIestiyekkkakgrgvyrlliisgenlkrFl 79 
                                   skel+edv  lLl++  ++ti +k +++  ++  ++i++    +++ 
  gi|15668963|ref|NP_247767.1| 341 SKELAEDVIFLLLQIKENATINKKSINDIEVYEVRRITNIYTNRKLE 387
                                   89**********************77777776655555544444444 PP

>> TMIE  TMIE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.5   2.1e+03      49      70 ..     373     395 ..     363     407 .. 0.53
   2 ?   12.1   0.2   9.6e-05      0.13      26      58 ..     534     567 ..     526     584 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
                          TMIE  49 arkklakkfr.ekLelisnseld 70 
                                     +++++ ++  kLe++ ns++ 
  gi|15668963|ref|NP_247767.1| 373 EVRRITNIYTnRKLEKLINSDFI 395
                                   44445554431456666666554 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 9.6e-05
                          TMIE  26 villCCvirfRiPRTkqeI.ea.dyarkklakkfr 58 
                                    i +  + r+R+PRT  eI ea +  rk + +++r
  gi|15668963|ref|NP_247767.1| 534 AIYA-ACRRCRVPRTLDEIaEAsRVDRKEIGRTYR 567
                                   4444.468***********5442566777777765 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.7   3.7e+03      17      36 ..     535     554 ..     532     566 .. 0.63
   2 ?    9.7   0.2   0.00038      0.53      19      51 ..     630     663 ..     625     664 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.7
                  HTH_Tnp_ISL3  17 eayilelllesrsvkavArq 36 
                                    +++ ++++  r+  ++A+ 
  gi|15668963|ref|NP_247767.1| 535 IYAACRRCRVPRTLDEIAEA 554
                                   45555566655777777765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00038
                  HTH_Tnp_ISL3  19 yilellles.rsvkavArqlgvSwtTVwrildry 51 
                                   yi+  ll + r+ ++vA+  gv++ T++++++++
  gi|15668963|ref|NP_247767.1| 630 YIASVLLGCrRTQREVAEVAGVTEVTIRNRYKEL 663
                                   8888899999********************9976 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.7    0.0017       2.3       8      36 ..      40      68 ..      38      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0017
                                  EE-TTTS-EEEEESS-SS-EEESSSTCEE CS
                Ribosomal_S27e  8 vkCpdCenetvvFshaatvvkCisCgkvL 36
                                  + Cp C+ + vv +     + C +Cg v+
  gi|15668963|ref|NP_247767.1| 40 IVCPICGSKEVVKDYERAEIVCAKCGCVI 68
                                  78************************887 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.4   0.00039      0.54       7      38 ..      34      68 ..      31      72 .. 0.81
   2 ?   -2.9   0.1       5.1     7e+03      15      19 ..     539     543 ..     532     550 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
                           DZR  7 elppdarfCseCgtk..lkavaa.edrCpsCgekv 38
                                  +++++ ++C+ Cg+k  +k +++ e++C +Cg  +
  gi|15668963|ref|NP_247767.1| 34 NVREEEIVCPICGSKevVKDYERaEIVCAKCGCVI 68
                                  5677889*******9887777768*******9765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.1
                           DZR  15 CseCg 19 
                                   C +C+
  gi|15668963|ref|NP_247767.1| 539 CRRCR 543
                                   44443 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00088       1.2      23      38 ..      36      52 ..      26      54 .. 0.78
   2 ?    1.8   4.1      0.19   2.6e+02       8      33 ..      42      65 ..      42      73 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00088
                   Zn-ribbon_8 23 dapltaCPeCgs.evrr 38
                                  ++++++CP Cgs ev +
  gi|15668963|ref|NP_247767.1| 36 REEEIVCPICGSkEVVK 52
                                  456888******99988 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.19
                   Zn-ribbon_8  8 CeeCghefevlqsis.dapltaCPeCg 33
                                  C  Cg   ev+   + ++++++C +Cg
  gi|15668963|ref|NP_247767.1| 42 CPICG-SKEVVK--DyERAEIVCAKCG 65
                                  77777.666664..3367777888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (673 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1792  (0.0999498); expected 358.6 (0.02)
Passed bias filter:                      860  (0.047967); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 4361.92
//
Query:       gi|15668964|ref|NP_247768.1|  [L=81]
Description: H/ACA RNA-protein complex component Gar1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-06   26.4   0.5    5.7e-06   26.2   0.5    1.1  1  Gar1      Gar1/Naf1 RNA binding region
  ------ inclusion threshold ------
      0.012   15.6   1.2       0.02   14.9   0.4    1.6  2  TRAM      TRAM domain


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.5   6.4e-10   5.7e-06      45      94 ..      20      69 ..      12      80 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6.4e-10
                                  B--BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GG.HHHHHHHTTTT CS
                          Gar1 45 kvldfnsilflenktqiGkVdEifGpvnepyysVklnss.eeikaksfkvg 94
                                  + ++++s++ ++nk +iGkV +ifGpv +py  + + ++  e++ + + ++
  gi|15668964|ref|NP_247768.1| 20 REIKIGSVVIFKNK-KIGKVVDIFGPVAKPYIKILPINKdIEVSGTAYIKN 69
                                  56789999999998.7***************99987533244444444444 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.4   2.3e-06      0.02       9      47 ..       2      41 ..       1      41 [. 0.90
   2 ?   -1.2   0.0      0.24   2.1e+03      19      30 ..      60      71 ..      50      79 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-06
                                  EEEEEEE-.TTSEEEEEET.....TEEEEETT--T..TEEEEE CS
                          TRAM  9 eVlveglsksegegiGrtdn....gkvvfvpgdlpgIGdfVeV 47
                                   V++  ++ ++g +i+r ++    g vv++++ ++ IG++V++
  gi|15668964|ref|NP_247768.1|  2 KVEILHKT-PKGFLIARGKReikiGSVVIFKN-KK-IGKVVDI 41
                                  58899999.***********************.44.8****97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.24
                                  TSEEEEEET.TE CS
                          TRAM 19 egegiGrtdngk 30
                                  e  g+++++n+k
  gi|15668964|ref|NP_247768.1| 60 EVSGTAYIKNDK 71
                                  445666666643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 537.34
//
Query:       gi|15668965|ref|NP_247769.1|  [L=186]
Description: hypothetical protein MJ_0783 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-09   38.4   0.0    1.1e-08   35.4   0.0    1.9  1  Cyclase   Putative cyclase


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   6.1e-13   1.1e-08       2     134 ..       5     131 ..       4     132 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 6.1e-13
                       Cyclase   2 dLshplsedtpvwpdp................islsehtGTHlDapgHfaektide.lpleelvgpavvldvsakaaaedy 65 
                                   dL+++l + +p+ +dp                i +++h  TH+D p H+   ++++ +p    + ++ ++        ++y
  gi|15668965|ref|NP_247769.1|   5 DLTQTLIN-FPYPGDPelriiekkidgfivseIIMGSHLCTHIDYPKHV---GLENrIP----FKDG-IIKG------KGY 70 
                                   78888844.333334456666677788888889***************6...3332133....4455.4444......478 PP

                       Cyclase  66 eiitaedleaalakqgveikpgdivlirTgwskrledkekyrnpglseeaaewlaekgvkavGvDtlsv 134
                                     i+ +d+e+       ++++ di+li+Tg+sk+ +++++y +  ++  +++ +++ ++k+vG+D+  +
  gi|15668965|ref|NP_247769.1|  71 -CISLDDFERN------KLPACDILLIYTGFSKY-WGRDEYFEKIPEIPFLDDIIKSNIKCVGIDACTI 131
                                   .6699999764......799************99.778999889999******************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1245.72
//
Query:       gi|15668966|ref|NP_247770.1|  [L=358]
Description: H(2)-dependent methylenetetrahydromethanopterin dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-41  138.7   0.4    9.5e-41  137.9   0.4    1.4  1  HMD              H2-forming N5,N10-methylene-tetrahydromethan
     0.0032   17.7   0.0      0.007   16.5   0.0    1.6  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0065   15.4   0.0      0.012   14.6   0.0    1.4  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
  ------ inclusion threshold ------
      0.044   13.8   0.1       0.11   12.5   0.1    1.7  1  FliH             Flagellar assembly protein FliH
      0.092   13.0   0.6       0.95    9.7   0.0    2.4  3  IlvC             Acetohydroxy acid isomeroreductase, catalyti


Domain annotation for each model (and alignments):
>> HMD  H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.9   0.4   2.7e-44   9.5e-41       1      97 []     243     339 ..     243     339 .. 0.99

  Alignments for each domain:
  == domain 1  score: 137.9 bits;  conditional E-value: 2.7e-44
                                   HHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-HHHHHHCHHCC-S CS
                           HMD   1 AdlvsaVaDmgslvTAvtlagildyydvvtkilkapkemvekqilesLqtiaslveksGieglekalnpelllksaksmnl 81 
                                   A+l+++V+Dm+s+vTA+++ag+l+y+d+vtkil+ap++++++++ e+L++i++l++++Gi+++e+al+p++ll++a+sm++
  gi|15668966|ref|NP_247770.1| 243 ANLIGPVCDMCSAVTATVYAGLLAYRDAVTKILGAPADFAQMMADEALTQIHNLMKEKGIANMEEALDPAALLGTADSMCF 323
                                   89******************************************************************************* PP

                                   CCCTCHHHHHHHHHHC CS
                           HMD  82 geeqeeLpaalkvlek 97 
                                   g+ +e+Lp+alkvlek
  gi|15668966|ref|NP_247770.1| 324 GPLAEILPTALKVLEK 339
                                   **************97 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     2e-06     0.007      42     109 ..     128     195 ..      99     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2e-06
                                   TEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HHHHHHHHHHHHHTT- CS
                 NAD_binding_2  42 gakaaesieelvasldvvitmvkagkavdeviegllealkkgdilidgstsspedtrelakelkekgl 109
                                   g+k++++ +e+v+++d+vit +++g++  ++i++ ++a+ +g+i+    t+  ++  ++ k+l +++l
  gi|15668966|ref|NP_247770.1| 128 GLKVTSDDREAVEGADIVITWLPKGNKQPDIIKKFADAIPEGAIVTHACTIPTTKFAKIFKDLGREDL 195
                                   48999999*******************************************99999999888877665 PP

>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.3e-06     0.012     164     204 ..     112     152 ..      94     178 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-06
                                   HHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----S CS
               OCD_Mu_crystall 164 eeaaekfaenlqefefevsackseeeavegadivvtvTaak 204
                                   ++  +++++ ++  ++  ++ ++ +eavegadiv+t  ++ 
  gi|15668966|ref|NP_247770.1| 112 PKPPKACIHLVHPEDVGLKVTSDDREAVEGADIVITWLPKG 152
                                   45567888888889**********************87764 PP

>> FliH  Flagellar assembly protein FliH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   3.1e-05      0.11      38      80 ..      82     128 ..      81     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                                   HHHHHHS--S-HHHHHHHHHHHHTTSCHH...HS-EEEE.E-HHHHH CS
                          FliH  38 rkvikkelsvdpekilalvrealaklpvd...ekkitlr.vnpdDle 80 
                                   ++v++++ls +pe i++ +re++++++      +k+ ++ v+p+D+ 
  gi|15668966|ref|NP_247770.1|  82 KEVMEAHLSGNPESIMPKIREVVKAKAKElpkPPKACIHlVHPEDVG 128
                                   79********************9766554000444555536888886 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.4   1.2e+04      30      49 ..      13      32 ..      10      38 .. 0.49
   2 ?    0.6   0.1      0.18   6.4e+02      29      47 ..     211     229 ..     207     236 .. 0.83
   3 ?    9.7   0.0   0.00026      0.95      35      77 ..     276     318 ..     243     323 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.4
                                  HHHHTT--HHHHHHHHTHHH CS
                          IlvC 30 tlveaGyspelAyfeclhel 49
                                  t  +aG+++ +   e+ +e+
  gi|15668966|ref|NP_247770.1| 13 THAAAGITNFMRACEVAKEV 32
                                  44445554444444444444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.18
                                   HHHHHTT--HHHHHHHHTH CS
                          IlvC  29 etlveaGyspelAyfeclh 47 
                                   ++++++Gy  e+A++++++
  gi|15668966|ref|NP_247770.1| 211 QVYIAEGYASEEAVNKLYE 229
                                   68999*********99875 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00026
                                   T--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHH CS
                          IlvC  35 GyspelAyfeclhelklivdliyegGiakmresiSdtaeygdl 77 
                                   G +   A +   + l  i +l++e+Gia+m e+++  a  g  
  gi|15668966|ref|NP_247770.1| 276 GAPADFAQMMADEALTQIHNLMKEKGIANMEEALDPAALLGTA 318
                                   555555655555777******************9998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 2244.39
//
Query:       gi|15668967|ref|NP_247771.1|  [L=375]
Description: biotin synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-15   56.4   0.9    4.6e-15   56.4   0.9    2.1  2  Radical_SAM    Radical SAM superfamily
    2.9e-10   40.1   0.0    1.5e-09   37.8   0.0    2.2  2  BATS           Biotin and Thiamin Synthesis associated domain
     0.0076   15.3   0.0      0.014   14.4   0.0    1.4  1  IMPDH          IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.064   13.7   1.5        2.3    8.7   0.0    3.2  3  ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.56   2.5e+03     115     139 ..      48      71 ..      17      83 .. 0.75
   2 !   56.4   0.9     1e-18   4.6e-15       3     166 ..      88     249 ..      86     250 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.56
                                   HHHHHHHTCTSHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 115 ekvlklmnrghtfeevlealeklre 139
                                   ++ lkl+ + +++ ++l++++++ +
  gi|15668967|ref|NP_247771.1|  48 DEALKLF-KIDNWRDYLKLFDIASR 71 
                                   3367777.66788888888877765 PP

  == domain 2  score: 56.4 bits;  conditional E-value: 1e-18
                                   EESEESS-..-TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                   xxxxxxxx..xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlr..CsfCarpet..vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                   +t+ C+ +  C +C +     ++ ++ +  l+ eei++ + ++ +e g+k v  ++ +    ++ +++l+  +k    +++
  gi|15668967|ref|NP_247771.1|  88 ITNICHVNpkCLYCGFAAGtsKEGYYEPFRLTDEEIKKSAIAI-EESGIKRVSCSSAHGYQGKEVIRALKIVKKY--TNLE 165
                                   7999999999*******99999999999999999******999.9************888877777777777776..5666 PP

                                   EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeel 160
                                   + v + + l  ee +++l+++g+d++  +le++++    k++++g+++e++++++++ ++++i+  +++++++ Ge+ e++
  gi|15668967|ref|NP_247771.1| 166 VLVNAGADLT-EESIKELKKYGIDTICCNLETINEN-LFKKVKPGEELEDRIRVCKLVNKYDIE-LSTGLLIGIGESYEDR 243
                                   6666666665.*************************.777777*********************.**************** PP

                                   HHHHHH CS
                                   xxxxxx RF
                   Radical_SAM 161 eellel 166
                                   +e+l +
  gi|15668967|ref|NP_247771.1| 244 VEHLFY 249
                                   999865 PP

>> BATS  Biotin and Thiamin Synthesis associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.46   2.1e+03      15      49 ..     150     187 ..     114     205 .. 0.57
   2 !   37.8   0.0   3.5e-13   1.5e-09       1      86 []     260     358 ..     260     358 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.46
                                   HHHHHHHHHSTTSE...CCCTCHH-HHHHHHHHHCCT- CS
                          BATS  15 kiiaalRlllPkag...illsgResaefrdqlllklGa 49 
                                    +i al+++  +++   ++ +g    e++ + l k+G+
  gi|15668967|ref|NP_247771.1| 150 EVIRALKIVKKYTNlevLVNAGADLTEESIKELKKYGI 187
                                   34444444444444444333444333333333334444 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 3.5e-13
                                   E--B----TCCCC...........HHHHHHHHHHSTTSECCCTCHH-HHHHHHHHHCCT--EEE-C---TTTGGGSES... CS
                          BATS   1 siprlrpikdtpl...........lkiiaalRlllPkagillsgResaefrdqlllklGansisagsktevggyaflt... 67 
                                   +i+ ++p+k+tp+           +k+ia++Rl++P+++i++ + +  ++  q++l  Ga+++ +     +  + + +   
  gi|15668967|ref|NP_247771.1| 260 PIMGFNPYKGTPMenhpkcsaleqAKTIAITRLIFPNIRITSPTPTIGAELVQFALFGGASNVATVI---PKNHPMNVkgv 337
                                   8999*************************************************999*******9955...45555444111 PP

                                   STT-T..CCCCHHHHHHTT-E CS
                          BATS  68 tdgrs..leedvkmleelGle 86 
                                   ++ ++  lee+vkm+++lGl+
  gi|15668967|ref|NP_247771.1| 338 GNPKTgnLEEVVKMIMDLGLK 358
                                   2333345************85 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.1e-06     0.014     103     171 ..     121     191 ..      92     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-06
                                   TTHHHHHHHHHHTT-SEEEEE-STSSS.HHHHHHHHHHHHHTTT.SEEEEEEE-SHHHHHHHHHTT-SEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 103 edalervkalveagvdvlvvdsahghs.ekvleavkeikkkvee.veviaGnvataegakaLieagadavk 171
                                   e+ ++ + a+ e+g+  +   sahg++ ++v++a+k +kk ++  v v aG   t+e +k+L + g+d++ 
  gi|15668967|ref|NP_247771.1| 121 EEIKKSAIAIEESGIKRVSCSSAHGYQgKEVIRALKIVKKYTNLeVLVNAGADLTEESIKELKKYGIDTIC 191
                                   566777889999*************874679999999997775335555*******************985 PP

>> ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00051       2.3      18      38 ..      78      98 ..      68     113 .. 0.88
   2 ?   -0.0   0.1      0.27   1.2e+03      40      59 ..     203     219 ..     191     224 .. 0.62
   3 ?    1.4   0.1     0.097   4.4e+02      28      44 ..     319     334 ..     318     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00051
                 ribosomal_L24 18 giiekEapIhvSnVmlvdpkc 38
                                  + ie+   Ih+ n+ +v+pkc
  gi|15668967|ref|NP_247771.1| 78 KKIEITSTIHITNICHVNPKC 98
                                  6799****************8 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.27
                 ribosomal_L24  40 kptrvgfrlkedgkkvRvsk 59 
                                   k+++ g +l   + ++Rv+k
  gi|15668967|ref|NP_247771.1| 203 KKVKPGEEL---EDRIRVCK 219
                                   444444433...2489***9 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.097
                 ribosomal_L24  28 vSnVmlvdpkcgkptrv 44 
                                   +SnV+ v pk + p  v
  gi|15668967|ref|NP_247771.1| 319 ASNVATVIPK-NHPMNV 334
                                   7********9.677666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2350.65
//
Query:       gi|15668968|ref|NP_247772.1|  [L=189]
Description: hypothetical protein MJ_0785.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1242.41
//
Query:       gi|15668969|ref|NP_247773.1|  [L=186]
Description: hypothetical protein MJ_0786 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.033   14.1   2.2      0.054   13.4   0.9    1.9  2  Prefoldin  Prefoldin subunit
       0.68   10.6   6.4        1.5    9.5   6.4    1.7  1  BLI1       BLOC-1 interactor 1


Domain annotation for each model (and alignments):
>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.11   9.7e+02      20      35 ..      66      81 ..      47      88 .. 0.56
   2 ?   13.4   0.9   6.1e-06     0.054      72     109 ..      86     123 ..      79     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.11
                                  HHHHHHHHHHHHHTT. CS
                     Prefoldin 20 eelektletlktlkke 35
                                   ++ ++++ l++lkk 
  gi|15668969|ref|NP_247773.1| 66 ATFMDLIKSLEELKKL 81
                                  4555566666666662 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.1e-06
                                   EEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  72 eksleeAiellkkkleelekqlekleeeleklkdqitt 109
                                   e +++++ie+lk+k++e++k +++l+ +++ +++ i +
  gi|15668969|ref|NP_247773.1|  86 EGKIDKSIEFLKNKEKEIKKLVKDLNVKVNPKTEFIRK 123
                                   5679************************9999988876 PP

>> BLI1  BLOC-1 interactor 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.4   0.00017       1.5      35     103 ..      44     115 ..      12     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00017
                          BLI1  35 skkteenekWleeikekyklkde...delkalkalkkkklkkleelekkveyyeklldeleefqdelevktk 103
                                   sk  +e  k l+  +e +++k     d +k+l++lkk  + k ++++k +e+  +  +e++ ++++l+vk  
  gi|15668969|ref|NP_247773.1|  44 SKGYKERVKKLNPESEIFEVKSAtfmDLIKSLEELKKLGIGKEGKIDKSIEFLKNKEKEIKKLVKDLNVKVN 115
                                   5555566666666677777776522255689999***********************************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1057.42
//
Query:       gi|15668970|ref|NP_247774.1|  [L=504]
Description: hypothetical protein MJ_0787 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   9.7e-247  819.5   1.9   1.1e-246  819.2   1.9    1.0  1  Fibrillarin_2  Fibrillarin-like archaeal protein
  ------ inclusion threshold ------
       0.15   12.5   0.7       0.56   10.6   0.0    2.1  2  DUF1041        Domain of Unknown Function (DUF1041)


Domain annotation for each model (and alignments):
>> Fibrillarin_2  Fibrillarin-like archaeal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  819.2   1.9  1.3e-250  1.1e-246       1     497 [.       1     498 [.       1     501 [. 0.99

  Alignments for each domain:
  == domain 1  score: 819.2 bits;  conditional E-value: 1.3e-250
                 Fibrillarin_2   1 mkdlikeavndldaalelkkl...........ekdveevvdavselsleeliklGknlkkfPlGcdlveilvGtcasdlek 70 
                                   m++likeavn+ld+alel+kl           e+d++e+vdav++lslee++klG+nl++fP+Gcdlvei+vG+c+s+l++
  gi|15668970|ref|NP_247774.1|   1 MRELIKEAVNSLDSALELRKLiikklnekklkESDIIEIVDAVDDLSLEEIQKLGSNLRTFPMGCDLVEIAVGPCSSSLTL 81 
                                   99*****************************99************************************************ PP

                 Fibrillarin_2  71 kdllgnciladalGasihvcayaladiaekeglrgiellkkvrelvevPldldhfGkyGpmrfPkeivgceGecyneGppf 151
                                   +++++ncil+d++G++ih+c+ya+adiaekegl++ie+lk+v e+v+vP+d+dhfG+yGpmrfPkei++c+G+cy++Gppf
  gi|15668970|ref|NP_247774.1|  82 IQFIENCILTDYMGFPIHICSYAVADIAEKEGLKPIEVLKMVLENVDVPIDIDHFGMYGPMRFPKEITHCYGDCYFKGPPF 162
                                   ********************************************************************************* PP

                 Fibrillarin_2 152 kecPrdrihkrlldkekeeledkeeWvklsssvavnltsvqgaeehaapleeakevaelakkygkgleailfvgdGyddli 232
                                   k+cPr+rihkrl++keke+++++e+W+kl+s++++n++++qg+eehaaplee+k vae+akkygkgle+i+++gdGyddli
  gi|15668970|ref|NP_247774.1| 163 KGCPRNRIHKRLIEKEKEHADEFEDWIKLASTLCINVVEEQGGEEHAAPLEEMKIVAETAKKYGKGLEGIFHIGDGYDDLI 243
                                   ********************************************************************************* PP

                 Fibrillarin_2 233 kgleaaielgvdvfvveGgPfnrakdrleafakavaaarilvpGkvvatnGayedecrvGlrsGlnaiitGfpknhhGymc 313
                                   +g++a+i+l+vdvfvveG+Pfnrak+rl+afaka+a++rilv+G+vvatnGayedecrvGlrsGln+i+tGfp nhhGymc
  gi|15668970|ref|NP_247774.1| 244 TGIKACIDLDVDVFVVEGAPFNRAKNRLKAFAKAIAVSRILVKGGVVATNGAYEDECRVGLRSGLNTILTGFPLNHHGYMC 324
                                   ********************************************************************************* PP

                 Fibrillarin_2 314 GysPgtakrgkfGlprvlkiikeeve.ekltkvpiqkeelealakavkvvgkeniyPkkigalavGdahWaalkesklakk 393
                                   GysP+takrg+fGl+rv++iikee++  ++++++i+k++++a+a +++++ k niyP +ig +++GdahWaa+kes+l+kk
  gi|15668970|ref|NP_247774.1| 325 GYSPKTAKRGNFGLRRVMRIIKEEIRaGNVNATFIDKDMVKAIALGNRFL-KGNIYPYSIGGFYLGDAHWAAIKESNLCKK 404
                                   *************************96788999*****************.89**************************** PP

                 Fibrillarin_2 394 lkvkktvediakeveadkvallGgrfvsWviakeldkkvdeilisdadpwvekvtvenlreeldaeiiagdgddkkaveea 474
                                   lk++kt++di+    a+kv+l+Ggr++sW+ia++    ++e++isd+d+wvek+t+++l+e+  +++++++gddkk+ e a
  gi|15668970|ref|NP_247774.1| 405 LKINKTIDDIS----AEKVGLIGGRYISWAIAEK----AEEVYISDTDSWVEKATIKILNEA-GINAYPCNGDDKKVLE-A 475
                                   **********9....69***************98....67*********************9.*************997.* PP

                 Fibrillarin_2 475 dksiitstiPeiaekikkklrda 497
                                   dk++it++iP+ia ki +klrd+
  gi|15668970|ref|NP_247774.1| 476 DKAYITTFIPNIALKILNKLRDS 498
                                   *******************9875 PP

>> DUF1041  Domain of Unknown Function (DUF1041)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3      0.27   2.4e+03      45      74 ..       9      38 ..       4      54 .. 0.76
   2 ?   10.6   0.0   6.2e-05      0.56      39      71 ..     176     210 ..     158     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.27
                       DUF1041 45 kkkleeltkLaeLvievlqqdkehyaevle 74
                                   ++l+  + L +L+i+ l++ k   ++++e
  gi|15668970|ref|NP_247774.1|  9 VNSLDSALELRKLIIKKLNEKKLKESDIIE 38
                                  67899999999****999998766665555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 6.2e-05
                       DUF1041  39 eeegtskkkleeltkLa.eLvievlqqd.kehyae 71 
                                   e+e+++++++e+++kLa +L+i+v+++   e +a+
  gi|15668970|ref|NP_247774.1| 176 EKEKEHADEFEDWIKLAsTLCINVVEEQgGEEHAA 210
                                   3556899*********856******9752455654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 3051.98
//
Query:       gi|15668971|ref|NP_247775.1|  [L=79]
Description: hypothetical protein MJ_0788 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0011   19.3   0.2     0.0014   19.0   0.2    1.1  1  DUF2969   Protein of unknown function (DUF2969)


Domain annotation for each model (and alignments):
>> DUF2969  Protein of unknown function (DUF2969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   7.8e-08    0.0014       3      42 ..      23      65 ..      22      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.8e-08
                       DUF2969  3 kknKkieveieetkv...neqpvtelligkktIGeieeedekf 42
                                  kk K +e++ie +++   ne++ +e+l+++k +G  +++d+kf
  gi|15668971|ref|NP_247775.1| 23 KKTKHFEIRIELREDnipNEEELFEILTKNKPVGILKQKDDKF 65
                                  899999999998888889************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 528.86
//
Query:       gi|15668972|ref|NP_247776.1|  [L=116]
Description: hypothetical protein MJ_0789 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-13   48.8   4.2      6e-13   48.8   4.2    1.8  2  DUF2283   Protein of unknown function (DUF2283)
  ------ inclusion threshold ------
      0.048   13.8   1.2       0.07   13.3   0.8    1.5  1  CHASE9    Periplasmic sensor domain, extracellular


Domain annotation for each model (and alignments):
>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   4.2   6.7e-17     6e-13       1      49 []       4      51 ..       4      51 .. 0.98
   2 ?   -1.5   0.0      0.34     3e+03      12      24 ..      86      99 ..      85     115 .. 0.50

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 6.7e-17
                       DUF2283  1 kitYDpeaDalYIylsegpveeseevdddiilDfDedGrlvGIEiLnAS 49
                                  ki+YD+e+D l +y + ++++++ +  ddi++DfDe+G +vGIEiLnAS
  gi|15668972|ref|NP_247776.1|  4 KIDYDYENDNLLVYKEGAKSKKTLD-LDDILIDFDENGDVVGIEILNAS 51
                                  89*************99999*****.9*********************8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.34
                       DUF2283 12 YIyl.segpveese 24
                                  Y+   +++ ++es 
  gi|15668972|ref|NP_247776.1| 86 YLLRrKKEIIKESV 99
                                  55443555565554 PP

>> CHASE9  Periplasmic sensor domain, extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.8   7.8e-06      0.07      14      54 ..      60     101 ..      48     110 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.8e-06
                        CHASE9  14 elieknlgnf..fskiekeadalkdalyllkdeeeikravllk 54 
                                    l+++ ++ f    ki k+  +l   lyll++++ei++  + k
  gi|15668972|ref|NP_247776.1|  60 DLLKNLIK-FeaVGKITKDLITLNIKLYLLRRKKEIIKESVVK 101
                                   55554444.423679********************97754433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 804.69
//
Query:       gi|15668973|ref|NP_247777.1|  [L=229]
Description: NADH dehydrogenase subunit 1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-20   73.5   1.7    5.9e-20   71.3   1.7    2.1  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   1.7   3.3e-24   5.9e-20       1     137 [.       1     211 [.       1     229 [] 0.81

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 3.3e-24
                          YdjM   1 MdgltHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklg.llskklak.................. 62 
                                   M  + H +lG++ gl + +          +++a++gAl PD+Dh       k g l+s+ +                    
  gi|15668973|ref|NP_247777.1|   1 MNWKGHTILGIIFGLPFISSPE------QIFLALAGALYPDLDHDVKEDIVKRGlLISGGI-Vfinillyffdkhlfnvdl 74 
                                   88999*********99999875......5899***********543322222220333322.257788889999******* PP

                          YdjM  63 ...............lvgHRgftHSllflallalvlllllrlfgrsa.................................. 94 
                                                  +  HRg+tH+++ l++++ +l +l+ ++  +                                   
  gi|15668973|ref|NP_247777.1|  75 filgvlilliylipyFSDHRGLTHTFWSLLFVSSILGYLAYKLSFISsvfaglisllmvtnevllgrvmifavfawavldi 155
                                   ****************************************99999889********************************* PP

                          YdjM  95 ..........lrlglllllgvlsHlllDlltkyGvpllwPfsk...kkvrlsllfi 137
                                             l + l++++g+lsHl++D++t++Gv+ ++P+s+   +k+  ++l+ 
  gi|15668973|ref|NP_247777.1| 156 lnpninvngaLYYILPVVFGYLSHLVGDTMTPAGVRAFYPLSNyklRKKEGYILVA 211
                                   *******997667777*************************983333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1560.20
//
Query:       gi|15668974|ref|NP_247778.1|  [L=484]
Description: argininosuccinate lyase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-63  212.5   0.1    1.6e-62  211.7   0.1    1.4  1  Lyase_1         Lyase
    7.6e-21   74.7   0.0    6.4e-20   71.7   0.0    2.4  2  ASL_C2          Argininosuccinate lyase C-terminal
  ------ inclusion threshold ------
      0.075   12.6   2.6       0.12   11.9   0.4    2.2  2  DUF1002         Protein of unknown function (DUF1002)
       0.62   10.6   3.3        2.2    8.9   0.4    3.0  3  Inhibitor_G39P  Loader and inhibitor of phage G40P
       0.92   10.0   0.0       0.92   10.0   0.0    4.5  6  DUF1048         Protein of unknown function (DUF1048)
        1.1    9.2   9.5      0.046   13.7   1.1    2.6  2  DUF2150         Uncharacterized protein conserved in archaea 
        8.7    6.6   8.7         17    5.7   0.5    3.1  3  SRI             SRI (Set2 Rpb1 interacting) domain


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.7   0.1   6.4e-66   1.6e-62      11     310 ..      17     299 ..       7     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: 211.7 bits;  conditional E-value: 6.4e-66
                                   HHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHHH CS
                       Lyase_1  11 mgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnevi 91 
                                   ++++t+++++++++ e+di   +a    + + +++ ke a++ii++l+e+ ++g +  ++ l+++  +++  ++ +l + +
  gi|15668974|ref|NP_247778.1|  17 VAKYTTSLSFDKEIFEADILCDIAHVIMLYEQGIIKKEDAKKIIEGLKEIYKKGME--NLNLDPSLDDIHMVIESELIKKL 95 
                                   67899**************99999999999**********************5555..5****************888888 PP

                                   HHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHH CS
                       Lyase_1  92 gellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqel 172
                                   g       ++++  htg+S+nD v+T+lr+al++++   + + l ++ + + e a+++k+++ +G+Thlq+A+Pvt+++ l
  gi|15668974|ref|NP_247778.1|  96 G------EDVAGRMHTGRSRNDEVATDLRIALREKVLI-IAKSLIKMLKDILELAEKHKETLIVGYTHLQHAQPVTFAHHL 169
                                   8......69***************************55.****************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHHHHHH CS
                       Lyase_1 173 sayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglpvkapnsfeavsdrDavvellgalk 253
                                    +y+ a+erd+ rl +++kr++ ++lg+g+++ tg+++++e   +  + l+ ++      +ns++ vs+rD+++e+++ l+
  gi|15668974|ref|NP_247778.1| 170 LSYVSAIERDILRLLDAYKRINISPLGCGAMATTGFKINRE---RTKELLG-FDA---LIENSMDGVSARDFILETMADLA 243
                                   *****************************************...6666666.999...9********************** PP

                                   HHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHH CS
                       Lyase_1 254 llatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagrv 310
                                   +l t+Lsk++e+l+l+s+ e+g +e+     +  SSiMP+K+NP+ +E  + ++++ 
  gi|15668974|ref|NP_247778.1| 244 ILGTNLSKICEELILFSTYEFGTIEIANEFCS-TSSIMPQKKNPDVAEIARAKLSKL 299
                                   **************************999988.8***************99998775 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.77     2e+03      45      68 ..     319     342 ..     299     343 .. 0.82
   2 !   71.7   0.0   2.5e-23   6.4e-20       1      68 [.     364     433 ..     364     434 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.77
                                   HHHHHH-TT--GGGGGGSSHHHHT CS
                        ASL_C2  45 eelkeisplleedveeaLdpeasV 68 
                                    +l+eisp+l + v++ +d  ++V
  gi|15668974|ref|NP_247778.1| 319 RDLQEISPHLWDSVYTTIDTIKMV 342
                                   6899999**999999999988777 PP

  == domain 2  score: 71.7 bits;  conditional E-value: 2.5e-23
                                   STTHHHHHHHHHHC.TS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-TT--.GGGGGGSSHHHHT CS
                        ASL_C2   1 FstATdlADyLvrk.GlpFReAHeivgravrlaeekgkeleeltleelkeisplle.edveeaLdpeasV 68 
                                   +stAT+lAD Lvr+ G+pFR+AH ivg++vr+++e++k++ e+ +e l++++  ++ e++++aLdp + V
  gi|15668974|ref|NP_247778.1| 364 YSTATELADTLVREtGIPFRTAHGIVGEVVRRSIEEKKDMIEVIYEVLEKYNLKVDeEKIKKALDPYENV 433
                                   89***********************************************888779999********9988 PP

>> DUF1002  Protein of unknown function (DUF1002)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.29   7.5e+02     157     217 ..      11      79 ..       7      83 .. 0.63
   2 ?   11.9   0.4   4.5e-05      0.12     156     205 ..     385     434 ..     342     440 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.29
                       DUF1002 157 aevkeevak.......eklkteeeikkiveevanelnin.lsdeqiqqivnllkkiqkldldlkelkkq 217
                                   +++ke+vak       +k+  e++i   +  v+  ++   +++e++++i++ lk+i k  +++ +l  +
  gi|15668974|ref|NP_247778.1|  11 NSIKEDVAKyttslsfDKEIFEADILCDIAHVIMLYEQGiIKKEDAKKIIEGLKEIYKKGMENLNLDPS 79 
                                   678888888775444444444444444455555555555788899999999988888887766666555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.5e-05
                       DUF1002 156 vaevkeevakeklkteeeikkiveevanelninlsdeqiqqivnllkkiq 205
                                      +  ev+++++++++++ +++ ev++++n+++++e+i++  +  ++++
  gi|15668974|ref|NP_247778.1| 385 AHGIVGEVVRRSIEEKKDMIEVIYEVLEKYNLKVDEEKIKKALDPYENVK 434
                                   345777888889999************************99988777766 PP

>> Inhibitor_G39P  Loader and inhibitor of phage G40P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.83   2.1e+03       3      25 ..      53      75 ..      48      88 .. 0.68
   2 ?   -0.6   0.0      0.76     2e+03      13      41 ..     309     334 ..     302     355 .. 0.57
   3 ?    8.9   0.4   0.00086       2.2      24      54 ..     395     425 ..     391     431 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.83
                Inhibitor_G39P  3 reetikiLavlkaaYPrfyngrs 25
                                  +e+  ki+  lk +Y + +++++
  gi|15668974|ref|NP_247778.1| 53 KEDAKKIIEGLKEIYKKGMENLN 75
                                  45556777777777776666655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.76
                Inhibitor_G39P  13 lkaaYPrfyngrskkenkmvvevWadllk 41 
                                   +  a P+  ++r+ +e     ++W ++  
  gi|15668974|ref|NP_247778.1| 309 ILKALPNT-YNRDLQE--ISPHLWDSVYT 334
                                   34455666.6666666..44456665555 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00086
                Inhibitor_G39P  24 rskkenkmvvevWadllkdydyklvskalka 54 
                                   rs +e+k ++ev +++l++y++k+ ++++k+
  gi|15668974|ref|NP_247778.1| 395 RSIEEKKDMIEVIYEVLEKYNLKVDEEKIKK 425
                                   7899******************998888887 PP

>> DUF1048  Protein of unknown function (DUF1048)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.56   1.4e+03      50      71 ..      39      60 ..      13      71 .. 0.74
   2 ?   -0.3   0.0      0.58   1.5e+03      45      59 ..     131     145 ..     124     153 .. 0.86
   3 ?   -1.8   0.0       1.7   4.3e+03      69      84 ..     243     258 ..     238     265 .. 0.84
   4 ?   10.0   0.0   0.00036      0.92      17      58 ..     310     350 ..     304     386 .. 0.70
   5 ?   -1.5   0.0       1.4   3.5e+03      39      58 ..     396     415 ..     382     428 .. 0.70
   6 ?   -3.2   0.2       4.7   1.2e+04       8      32 ..     449     473 ..     444     475 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.56
                                  HHHHHHHHHHHHHTT--HHHHH CS
                       DUF1048 50 lkevldLfEeaaadgkevkevv 71
                                  + +v+ L+E++ ++ ++ k+++
  gi|15668974|ref|NP_247778.1| 39 IAHVIMLYEQGIIKKEDAKKII 60
                                  4567888899888888777765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.58
                                   HHHHHHHHHHHHHHH CS
                       DUF1048  45 dlleilkevldLfEe 59 
                                    l+++lk++l+L E+
  gi|15668974|ref|NP_247778.1| 131 SLIKMLKDILELAEK 145
                                   6789********997 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.7
                                   HHH-S-HHHHHHHCCT CS
                       DUF1048  69 evvGedvaaFadelvk 84 
                                    ++G+++ + ++el+ 
  gi|15668974|ref|NP_247778.1| 243 AILGTNLSKICEELIL 258
                                   699*********9985 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00036
                                   HHHS-HHHHHHHHHHHHHHCCCTB-SHHHHHHHHHHHHHHHH CS
                       DUF1048  17 vkaLPedYqtvykeiqkylwkvgategadlleilkevldLfE 58 
                                   +kaLP+ Y+ + +ei+  lw +  t+  d++++++++l    
  gi|15668974|ref|NP_247778.1| 310 LKALPNTYNRDLQEISPHLWDSVYTTI-DTIKMVHGMLKTIK 350
                                   69*******************987766.66677777665544 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 1.4
                                   TB-SHHHHHHHHHHHHHHHH CS
                       DUF1048  39 gategadlleilkevldLfE 58 
                                   +  e +d++e+++evl+ + 
  gi|15668974|ref|NP_247778.1| 396 SIEEKKDMIEVIYEVLEKYN 415
                                   55567788888888887654 PP

  == domain 6  score: -3.2 bits;  conditional E-value: 4.7
                                   HHHHHHHHHHHHS-HHHHHHHHHHH CS
                       DUF1048   8 keykefeaRvkaLPedYqtvykeiq 32 
                                   k  k f++R++   ++  +  ++i+
  gi|15668974|ref|NP_247778.1| 449 KRIKVFRERLDRYEKEVDEKLQKIN 473
                                   5556666666666666666666655 PP

>> DUF2150  Uncharacterized protein conserved in archaea (DUF2150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.1   1.8e-05     0.046      37      79 ..      31      73 ..      12      94 .. 0.83
   2 ?   -1.0   0.1      0.56   1.4e+03      54      75 ..     460     481 ..     451     483 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                       DUF2150 37 lqdDvilavlkiikaveeeelskeeAleeleevreivleevee 79
                                  ++ D+   ++++i  +e++ ++ke+A + +e  +ei  + +e 
  gi|15668974|ref|NP_247778.1| 31 FEADILCDIAHVIMLYEQGIIKKEDAKKIIEGLKEIYKKGMEN 73
                                  789*********************************9887765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.56
                       DUF2150  54 eeelskeeAleeleevreivle 75 
                                   + e + +e l+++++v+ei+l+
  gi|15668974|ref|NP_247778.1| 460 RYEKEVDEKLQKINKVKEILLS 481
                                   4555667889999999999875 PP

>> SRI  SRI (Set2 Rpb1 interacting) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1    0.0088        22       5      39 ..      28      63 ..      26     100 .. 0.85
   2 ?    5.7   0.5    0.0066        17       9      34 ..     400     425 ..     396     428 .. 0.93
   3 ?   -3.1   0.3       3.5     9e+03      20      26 ..     458     464 ..     445     476 .. 0.47

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0088
                           SRI  5 ekkfkkelakvVvnvlnkYrkk.lkkedfKklakel 39
                                  +++f+  +   +++v+  Y++  +kked Kk+   l
  gi|15668974|ref|NP_247778.1| 28 KEIFEADILCDIAHVIMLYEQGiIKKEDAKKIIEGL 63
                                  67899999999*******************987554 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0066
                           SRI   9 kkelakvVvnvlnkYrkklkkedfKk 34 
                                   kk + +v+ +vl+kY  k+++e++Kk
  gi|15668974|ref|NP_247778.1| 400 KKDMIEVIYEVLEKYNLKVDEEKIKK 425
                                   68899********************8 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.5
                           SRI  20 lnkYrkk 26 
                                   l++Y+k+
  gi|15668974|ref|NP_247778.1| 458 LDRYEKE 464
                                   3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1287  (0.0717831); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 3145.68
//
Query:       gi|15668975|ref|NP_247779.1|  [L=89]
Description: hypothetical protein MJ_0792 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 603.56
//
Query:       gi|15668976|ref|NP_247780.1|  [L=162]
Description: hypothetical protein MJ_0792.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.041   12.6  15.7       0.05   12.3  15.7    1.1  1  EMP70            Endomembrane protein 70
       0.58   10.3  10.3        0.1   12.8   6.1    1.7  2  DUF2178          Predicted membrane protein (DUF2178)
        7.5    5.8  25.4         40    3.4  25.4    2.0  1  Glucos_trans_II  Glucosyl transferase GtrII


Domain annotation for each model (and alignments):
>> EMP70  Endomembrane protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  15.7   8.4e-06      0.05     274     393 ..      21     152 ..      10     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.4e-06
                         EMP70 274 lllmalvtlllallgflspsnrgslltvalllyvllgliaGYv.sarlyktf...ggekwkkn........tlltalllpg 342
                                   +l+m ++++l+    f+ ++ + +++   ++  ++l+++aG++ s  ly+ +   + e+ k+         t++    + +
  gi|15668976|ref|NP_247780.1|  21 CLVMPFMLILVLDTTFTFNKFNLNFVYRQIVELIVLSIFAGFItSFALYNKIcriSTEELKRDilennglkTIFKIAQYEV 101
                                   466777777777777888889999999999999999999999725567777655433455554666678889999999*** PP

                         EMP70 343 llflvffllnlilwakessgalpfgtlvlllllwflisvPlvliGsllgfk 393
                                   ++ +++ ll li+++++    + f+ ++ +++ ++ i vPl ++Gsl++++
  gi|15668976|ref|NP_247780.1| 102 MVSIFYSLLLLIILLNKQLLYYGFTAIFQIFFTFCAIFVPLFIFGSLVCRT 152
                                   **********************************************99875 PP

>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.52   3.1e+03      89     103 ..      16      30 ..      10      33 .. 0.55
   2 ?   12.8   6.1   1.7e-05       0.1      22     104 ..      51     140 ..      31     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.52
                       DUF2178  89 trvgfllafsallll 103
                                     + ++l++ ++l+l
  gi|15668976|ref|NP_247780.1|  16 LALVLCLVMPFMLIL 30 
                                   444455555555444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.7e-05
                       DUF2178  22 vllaviavaaGvllaillkkkveevveDERlariaekAsrktl.qi....llfliallgvvliv.lksdfpey.trvgfll 95 
                                   v+l v++++aG +++  l +k+  + + E ++ i e+  +kt+ +i    ++++i  + ++li+ l+++  +y   + f +
  gi|15668976|ref|NP_247780.1|  51 VELIVLSIFAGFITSFALYNKICRISTEELKRDILENNGLKTIfKIaqyeVMVSIFYSLLLLIIlLNKQLLYYgFTAIFQI 131
                                   7899**************************************845578884444444333333335666667778999999 PP

                       DUF2178  96 afsalllli 104
                                   +f+++++ +
  gi|15668976|ref|NP_247780.1| 132 FFTFCAIFV 140
                                   999988765 PP

>> Glucos_trans_II  Glucosyl transferase GtrII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4  25.4    0.0066        40     140     273 ..      13     144 ..       4     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0066
               Glucos_trans_II 140 giYQaylnvyia.lllilllrdl.ldekkklkeilkkllllllv.liisfvlylllykiilklfglelsy.isel.lqnlk 215
                                   ++Y a++   ++ + lil+l+   + +k +l+ + + ++ l+++  +++f+ ++ ly  i++++ +el++ i  l  + lk
  gi|15668976|ref|NP_247780.1|  13 FTYLALVLCLVMpFMLILVLDTTfTFNKFNLNFVYRQIVELIVLsIFAGFITSFALYNKICRISTEELKRdI--LeNNGLK 91 
                                   678888888888777777777777667777776677776666655999**********************75..44899** PP

               Glucos_trans_II 216 ryysisnygvkpkklllililliliilllalllkkkkkkkksllllllllllllpfal 273
                                   ++++i+ y v++  ++ +l+l+il+   l++     + +     +++ +++++ p+++
  gi|15668976|ref|NP_247780.1|  92 TIFKIAQYEVMVSIFYSLLLLIILLNKQLLYYGFTAIFQ-----IFFTFCAIFVPLFI 144
                                   ****99999999999888888888776666655555555.....44444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1212  (0.0676); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1071.33
//
Query:       gi|15668977|ref|NP_247781.1|  [L=178]
Description: hypothetical protein MJ_0793 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-33  114.9  13.2    4.1e-33  114.6  13.2    1.0  1  SpoIIM    Stage II sporulation protein M
  ------ inclusion threshold ------
       0.19   11.8   2.1       0.62   10.1   0.1    2.1  2  Jagunal   Jagunal, ER re-organisation during oogenesis
       0.19   12.1   0.1       0.19   12.1   0.1    1.9  2  DUF4396   Domain of unknown function (DUF4396)


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6  13.2   6.8e-37   4.1e-33       2     156 .]       9     170 ..       8     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 6.8e-37
                        SpoIIM   2 lllflvgillgallaasnfaeqis....seskensalslflaifanNlrvalllfllGllllgiptilvllinGfvlG.av 77 
                                   l+lf +g+++g+++ ++   ++i+    s+++ n  + +f +i++nNl+v++l++++ + ++g+ t++ l++nGf++G ++
  gi|15668977|ref|NP_247781.1|   9 LMLFSLGFIFGFISINN--LSKINdkdlSNYIPNI-QFNFPSILTNNLKVIFLMLAGSI-TFGLSTFINLIFNGFNVGvLI 85 
                                   689*************3..2344555654444443.479************99999997.******************655 PP

                        SpoIIM  78 aalvaefgglllflllilPhgilelpaiiiagaaglrlgkal......rsrrkalkeakrellklllllvpllliAaliEa 152
                                   +++  ++  l l+ +lilPhgi+e++a++i+++ag+++ +++      ++++  ++e ++++lkl l++++l++iAa+iE+
  gi|15668977|ref|NP_247781.1|  86 GSISLTNEPLKLITALILPHGIFEISAMLISAVAGFKIPYKVtlylldKKEKPLTEEDIKDFLKLSLISIILIVIAAFIEV 166
                                   999999999*********************************999998777777888************************ PP

                        SpoIIM 153 fvtp 156
                                   ++tp
  gi|15668977|ref|NP_247781.1| 167 YITP 170
                                   ***8 PP

>> Jagunal  Jagunal, ER re-organisation during oogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2     0.074   4.4e+02      96     125 ..      45      74 ..      37      81 .. 0.79
   2 ?   10.1   0.1    0.0001      0.62      92     170 ..      83     166 ..      75     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.074
                       Jagunal  96 llalkknkikllklyligtlvlgllpllyg 125
                                   + ++  n+ k + l+l g++ +gl + +  
  gi|15668977|ref|NP_247781.1|  45 FPSILTNNLKVIFLMLAGSITFGLSTFINL 74 
                                   567888999999999999999999887755 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0001
                       Jagunal  92 sllgllalkknkikllklyligtlvlgllpllygaveylk...evleylkskease....eitllqgfplvvlwyifvlia 165
                                   +l+g  +l+    kl+   ++   ++ + ++l++av  +k   +v  yl +k+++     +i+ + +++l+ ++  +++ia
  gi|15668977|ref|NP_247781.1|  83 VLIGSISLTNEPLKLITALILPHGIFEISAMLISAVAGFKipyKVTLYLLDKKEKPlteeDIKDFLKLSLISII--LIVIA 161
                                   799*****************************999887762225555666666554765567777777775555..55566 PP

                       Jagunal 166 lqvhl 170
                                     + +
  gi|15668977|ref|NP_247781.1| 162 AFIEV 166
                                   55544 PP

>> DUF4396  Domain of unknown function (DUF4396)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.4       2.9   1.7e+04      46      54 ..      12      20 ..       5      22 .. 0.53
   2 ?   12.1   0.1   3.2e-05      0.19      37      99 ..     108     170 ..      80     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.9
                       DUF4396 46 vvlalllgl 54
                                  + l++++g+
  gi|15668977|ref|NP_247781.1| 12 FSLGFIFGF 20
                                  445555554 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.2e-05
                       DUF4396  37 pmaatmilsvvlalllgllletalllrekglslaealktAlkadtlSmlamevgmnlvmllll 99 
                                     ++ m++s v+++ + + ++++ll ++++  + e +k+ lk +++S++ + ++ ++ +++ +
  gi|15668977|ref|NP_247781.1| 108 FEISAMLISAVAGFKIPYKVTLYLLDKKEKPLTEEDIKDFLKLSLISIILIVIAAFIEVYITP 170
                                   447889*********************98899999*****************99999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1155.25
//
Query:       gi|15668978|ref|NP_247782.1|  [L=141]
Description: hypothetical protein MJ_0794 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-27   95.9   7.7    2.5e-27   95.7   7.7    1.0  1  Yip1         Yip1 domain
    1.5e-12   47.7   6.0    1.8e-12   47.4   6.0    1.0  1  DUF1282      Protein of unknown function (DUF1282)
     0.0012   18.5   7.4     0.0016   18.1   7.4    1.2  1  MatE         MatE
      0.007   16.5  11.2     0.0095   16.0  11.2    1.2  1  ECF_trnsprt  ECF transporter, substrate-specific component
  ------ inclusion threshold ------
      0.015   14.9   7.0      0.015   14.9   7.0    2.0  2  DUF1189      Protein of unknown function (DUF1189)
      0.035   14.1   6.7      0.051   13.6   6.7    1.3  1  Colicin_V    Colicin V production protein
      0.037   13.5   4.6      0.041   13.3   4.6    1.1  1  DUF373       Domain of unknown function (DUF373)
        0.2   12.1  11.4       0.54   10.8   4.1    2.2  2  FtsX         FtsX-like permease family


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   7.7   1.1e-30   2.5e-27       2     124 ..      10     130 ..       9     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 1.1e-30
                          Yip1   2 lldPrevfrrlkkeppilrapdlallllalltlllgllaslnlgqtlasgeevqgltlssllgaiiggylglllgllllal 82 
                                   l++P+ +f++l +++ +l++p l++l++ +l ++++++++++++++++++   q+   ++ + a+i++++g+++++l++a+
  gi|15668978|ref|NP_247782.1|  10 LTNPDTFFKKLSQKEISLKEPFLIVLIFSILIAISAYISTSIIYKIFPPQ--YQQVLAFTKIIALISTFIGGIVAWLIIAG 88 
                                   89************************************************..778888888889999999999******** PP

                          Yip1  83 llhliakllggkgsfkqtlsvvgyallPlilgaliailllll 124
                                   ++hli+++++g+gsfk+tls++gy++lP+i+gali+i+++++
  gi|15668978|ref|NP_247782.1|  89 FMHLISMIFKGEGSFKKTLSFTGYGFLPNIVGALITIPIAYY 130
                                   **************************************9987 PP

>> DUF1282  Protein of unknown function (DUF1282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   6.0   7.9e-16   1.8e-12       2     121 ..      10     129 ..       9     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 7.9e-16
                       DUF1282   2 ltsPaeefeeikkreetgkvlyivlillllliglvvfiystfqvlseiltkq...ankltlassliisvvfylalgvlvla 79 
                                   lt P+  f++++++e + k +++++++   li ++++++st+ +  +i+ +q   +  +t + +li+  ++++++ +l++a
  gi|15668978|ref|NP_247782.1|  10 LTNPDTFFKKLSQKEISLKEPFLIVLIFSILI-AISAYISTS-IIYKIFPPQyqqVLAFTKIIALISTFIGGIVA-WLIIA 87 
                                   689******************88777766666.999999999.899*****976655677777888888888888.***** PP

                       DUF1282  80 yliklmgrtydsqhsyskifafaayalvplflgglalglsll 121
                                   ++++l+++++ ++ s++k++ f++y + p + g+l+++ +++
  gi|15668978|ref|NP_247782.1|  88 GFMHLISMIFKGEGSFKKTLSFTGYGFLPNIVGALITIPIAY 129
                                   ************************************987776 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   7.4     7e-07    0.0016      75     160 ..      30     122 ..      18     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7e-07
                          MatE  75 glilllllsliiallvllfseqilslftqdee.......vlelakrylrililgipalalqlvlsgilrgagktkvplyis 148
                                    ++++l++s++ia+ +++ + +i ++f    +       +++l+++++  ++  +++ ++ +++s i++g g +k +l ++
  gi|15668978|ref|NP_247782.1|  30 PFLIVLIFSILIAISAYISTSIIYKIFPPQYQqvlaftkIIALISTFIGGIVAWLIIAGFMHLISMIFKGEGSFKKTLSFT 110
                                   567777777777777777777777777655556777777****************************************** PP

                          MatE 149 lislllniplny 160
                                     ++l ni+ + 
  gi|15668978|ref|NP_247782.1| 111 GYGFLPNIVGAL 122
                                   *******99875 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  11.2   4.3e-06    0.0095       4      96 ..      35     137 ..      20     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.3e-06
                                   HHHHHHHHHHHHHHH...H.HEEE.STSEEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHH....... CS
                   ECF_trnsprt   4 vitglliAisivlsl...l.gyiplpnikitiihipvllggllfGpikGailgiitsvlkailtggtgalssfv....... 73 
                                    i ++liAis+ +s       ++p     + +  i++l++ ++ G ++ +i++++ +++++i+ +g g++  ++       
  gi|15668978|ref|NP_247782.1|  35 LIFSILIAISAYISTsiiYkIFPPQYQQVLAFTKIIALISTFIGGIVAWLIIAGFMHLISMIF-KGEGSFKKTLsftgygf 114
                                   467788888887776654345555554479999999999999999999999999999999999.77777766667778999 PP

                                   HHHHHHHHCHHHHHHHHHHCCCH CS
                   ECF_trnsprt  74 piaflsriligliagllykkgkk 96 
                                   + +++ +++++ ia+++++++++
  gi|15668978|ref|NP_247782.1| 115 LPNIVGALITIPIAYYMREISQQ 137
                                   99999999999999999888765 PP

>> DUF1189  Protein of unknown function (DUF1189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   3.2      0.55   1.2e+03      30      47 ..      31      48 ..      26      55 .. 0.55
   2 ?   14.9   7.0   6.5e-06     0.015     149     220 ..      55     125 ..      47     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.55
                       DUF1189 30 llLslilalpisiiifye 47
                                  +l++li++++i+i+ +++
  gi|15668978|ref|NP_247782.1| 31 FLIVLIFSILIAISAYIS 48
                                  455555555555554442 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.5e-06
                       DUF1189 149 svksilkiilvlilivlflvsllltlidalilaliglilarilkiklsYkqlfkisvyalTlPtilnailei 220
                                    + + ++ +l+++ i++++ ++++ ++  li+a++  ++++i+k + s+k+ ++++ y++ lP i+ a+++i
  gi|15668978|ref|NP_247782.1|  55 IFPPQYQQVLAFTKIIALISTFIGGIVAWLIIAGFMHLISMIFKGEGSFKKTLSFTGYGF-LPNIVGALITI 125
                                   45788999**************************************************98.88888887765 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   6.7   2.3e-05     0.051      22     100 ..      33     109 ..      32     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                     Colicin_V  22 vrevlsllgwvvafvvasllypslaellaelilspalaaiiaflllfllvllivsllgallsklv.sktglglldrllGa 100
                                   +  ++s+l  + a++ +s  y+ + ++++++    a+ +iia + +f+++++++ +++ +++ +   ++g g + ++l +
  gi|15668978|ref|NP_247782.1|  33 IVLIFSILIAISAYISTSIIYKIFPPQYQQV---LAFTKIIALISTFIGGIVAWLIIAGFMHLISmIFKGEGSFKKTLSF 109
                                   6678999***********************7...7888888888888888888888888887755455666666666654 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   4.6   1.8e-05     0.041     220     317 ..      31     131 ..       3     140 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                        DUF373 220 tfvtyvvallllligiisgyislesvss.asvssglltlilafiygavewlalailtaslgkiideylkre..ekdiarll 297
                                    +++ + ++l+++ + is+ i   ++   + ++   +t+i+a+i++++  +++ +++a + ++i++++k+e   k++ ++ 
  gi|15668978|ref|NP_247782.1|  31 FLIVLIFSILIAISAYISTSII-YKIFPpQYQQVLAFTKIIALISTFIGGIVAWLIIAGFMHLISMIFKGEgsFKKTLSFT 110
                                   3344444455544444444333.2222244444444445555555555555555555555555555555552233333334 PP

                        DUF373 298 llpflvlaiglvl.ygasayl 317
                                    + fl  ++g+++ + +++y+
  gi|15668978|ref|NP_247782.1| 111 GYGFLPNIVGALItIPIAYYM 131
                                   344444444444425555555 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.7     0.007        16      68      94 ..      30      55 ..      13      57 .. 0.68
   2 ?   10.8   4.1   0.00024      0.54      26      94 ..      68     137 ..      60     139 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.007
                          FtsX 68 tvliiivlllllallagllsiskilkk 94
                                  ++li++++++l+a+ a ++s+s i k+
  gi|15668978|ref|NP_247782.1| 30 PFLIVLIFSILIAISA-YISTSIIYKI 55
                                  4555555555555555.8888888775 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00024
                          FtsX  26 llitlvalviGlglgllaaqllsdvllssvfs.selkisidlitvliiivlllllallagllsiskilkk 94 
                                    +i+l++++iG ++++l++  ++++++ ++ + ++ k ++++  + ++  ++  l+++ +++ ++ i+ +
  gi|15668978|ref|NP_247782.1|  68 KIIALISTFIGGIVAWLIIAGFMHLISMIFKGeGSFKKTLSFTGYGFLPNIVGALITIPIAYYMREISQQ 137
                                   589***********************99999784444444444444444444444444444777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 918.37
//
Query:       gi|15668979|ref|NP_247783.1|  [L=504]
Description: hypothetical protein MJ_0795 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.8   1.2      0.033   14.5   0.2    2.2  2  Orf78     Orf78 (ac78)
       0.08   12.8   0.8       0.45   10.4   0.1    2.4  2  SmpB      SmpB protein


Domain annotation for each model (and alignments):
>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.75   6.7e+03      25      25 ..     222     222 ..     195     260 .. 0.44
   2 ?   14.5   0.2   3.7e-06     0.033      11      84 ..     434     497 ..     430     503 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.75
                         Orf78  25 d 25 
                                   +
  gi|15668979|ref|NP_247783.1| 222 N 222
                                   2 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.7e-06
                         Orf78  11 kekvdyIPLKLAlndldnddndkaenkkekksaaeknditekesnaaekaqalnillisllavvcvlvllyviy 84 
                                   + +v+ IPLK+ ++d   +dn+   +  ++  ++ ++++ + ++n   +++  n l++++  ++cv v+ y+iy
  gi|15668979|ref|NP_247783.1| 434 NGNVNEIPLKISYRD---EDNNL-ITIYKT--VKISKEVVSLKTN---NNGGINYLVVGIAILFCVGVV-YLIY 497
                                   5689**********9...33333.232322..2333333333333...467788999999999998764.6666 PP

>> SmpB  SmpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.12     1e+03      90     111 ..     192     213 ..     184     222 .. 0.79
   2 ?   10.4   0.1     5e-05      0.45      72     111 ..     311     352 ..     280     364 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.12
                                   HHHHT-EEEEEEEEE.ESSEEE CS
                          SmpB  90 veekgltlvplklyfkkkglvK 111
                                   + +k  t +pl+++ kk+g+  
  gi|15668979|ref|NP_247783.1| 192 LGSKTSTYIPLTIFAKKEGVYS 213
                                   5578899********9988755 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 5e-05
                                   --EEBB--HHHHHHHHH..HHHHHT-EEEEEEEEE.ESSEEE CS
                          SmpB  72 rkrkLLlhkkeikklag..kveekgltlvplklyfkkkglvK 111
                                    ++ + ++k e k+l+   kv+++g+t +p+ +yf+++++ K
  gi|15668979|ref|NP_247783.1| 311 NQKSIFIKKGETKNLTFqiKVDKEGVTSIPIVIYFDNNQIEK 352
                                   46788999999999865116789************7765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3240.48
//
Query:       gi|15668980|ref|NP_247784.1|  [L=170]
Description: hypothetical protein MJ_0795.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.082   13.3   0.4       0.15   12.5   0.4    1.4  1  FERM_C           FERM C-terminal PH-like domain
        1.7    7.8  11.6       0.81    8.8   1.0    2.1  2  Glyco_transf_22  Alg9-like mannosyltransferase family
        7.3    6.3   5.7        3.6    7.4   3.4    1.5  2  FA_desaturase    Fatty acid desaturase


Domain annotation for each model (and alignments):
>> FERM_C  FERM C-terminal PH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   2.5e-05      0.15      16      48 ..     122     154 ..     119     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                                   EEEEBTTBSSS-SEEEEGGGEEEEEEETTEEEE CS
                        FERM_C  16 ilvyekqnkitpklafpWreieklsfkdkkfsi 48 
                                   i +yek+  i+    ++W+eiek + kdk+ +i
  gi|15668980|ref|NP_247784.1| 122 IRIYEKGILIEGIAFYSWEEIEKTTNKDKNQTI 154
                                   789**************************9887 PP

>> Glyco_transf_22  Alg9-like mannosyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   3.9    0.0042        25     257     302 ..       3      49 ..       2      58 .. 0.78
   2 ?    8.8   1.0   0.00014      0.81      99     155 ..      63     119 ..      55     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0042
               Glyco_transf_22 257 GvhPwyfYllqnlpnilgvlllavllgllvllsrkvsr.llllllti 302
                                   G +P+yfY+  +l +  +v++l++   +l  ++ ++ + +  +l++i
  gi|15668980|ref|NP_247784.1|   3 GINPFYFYIGMALILASIVSILLITKSILLFILLAFGSlVGITLILI 49 
                                   899*******************9998888887666666344444444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00014
               Glyco_transf_22  99 lfravcrkygseiakialllslsswglfvfstrtfsnslemlltsialyllsellsr 155
                                   l + v+r +g+++ ki+ l++++ +  f++ + tf ns  + +++i+   +se  ++
  gi|15668980|ref|NP_247784.1|  63 LKKEVKRIFGNRVYKILRLMLVLGYAGFIYFSGTFYNSAVLFFIFIVAFTISEFYKT 119
                                   55789999******************************9999999999888875544 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.6      0.13   8.1e+02     141     170 ..      14      36 ..       3      56 .. 0.36
   2 ?    7.4   3.4    0.0006       3.6     117     176 ..      56     113 ..      26     125 .. 0.48

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.13
                 FA_desaturase 141 lllllawlglwlalllllglalllwlvpll 170
                                   +l+l++++ ++l +    +    + l+ ll
  gi|15668980|ref|NP_247784.1|  14 ALILASIVSILLIT---KS----ILLFILL 36 
                                   33333221111111...11....1111111 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0006
                 FA_desaturase 117 wlrrlarrrapsksrrrkwrllawlllllawlglwlalllllglall.lwlvplllllfll 176
                                   ++ + +r ++ +k++  ++++  ++l+l   +++++++++++g + + ++l+++++++f++
  gi|15668980|ref|NP_247784.1|  56 LKIDKGRLKKEVKRIFGNRVYKILRLML---VLGYAGFIYFSGTFYNsAVLFFIFIVAFTI 113
                                   3444444444444444445555555555...567777777777644443333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1106  (0.0616878); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1070.49
//
Query:       gi|15668981|ref|NP_247785.1|  [L=235]
Description: ABC transporter ATP-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-37  128.7   0.0    3.1e-37  128.1   0.0    1.3  1  ABC_tran     ABC transporter
    8.6e-09   35.2   0.8      1e-06   28.3   0.8    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    8.1e-07   29.1   0.0     0.0029   17.5   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00027   20.6   0.0     0.0005   19.8   0.0    1.3  1  AAA_29       P-loop containing region of AAA domain
    0.00029   21.3   0.0    0.00085   19.7   0.0    1.7  1  AAA_16       AAA ATPase domain
    0.00067   19.6   0.0     0.0029   17.6   0.0    1.9  1  ATPase_2     ATPase domain predominantly from Archaea
    0.00089   19.1   0.0     0.0042   16.9   0.0    1.7  2  AAA_15       AAA ATPase domain
     0.0013   18.6   0.0     0.0027   17.6   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
     0.0014   19.2   0.1      0.025   15.1   0.0    2.2  2  AAA_18       AAA domain
  ------ inclusion threshold ------
      0.016   14.9   0.0        1.8    8.3   0.0    2.2  2  IstB_IS21    IstB-like ATP binding protein
       0.03   14.0   0.0       0.44   10.2   0.0    2.2  2  AAA_30       AAA domain
      0.038   14.3   0.1       0.33   11.2   0.0    2.0  2  AAA_22       AAA domain
       0.04   13.9   0.0      0.057   13.3   0.0    1.4  1  Rad17        Rad17 P-loop domain
      0.042   13.6   0.0       0.46   10.2   0.0    2.0  2  AAA_24       AAA domain
      0.067   12.8   0.0       0.53    9.8   0.0    2.0  2  AAA_25       AAA domain
      0.074   13.5   0.2      0.074   13.5   0.2    2.2  2  AAA_23       AAA domain
       0.11   11.6   0.0        0.2   10.7   0.0    1.5  1  T2SSE        Type II/IV secretion system protein
       0.11   12.5   0.0       0.78    9.8   0.0    2.1  2  MMR_HSR1     50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.1   0.0   3.1e-40   3.1e-37       1     136 [.      21     173 ..      21     174 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 3.1e-40
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvr 77 
                                   lknv+l++kege v i+G++G+GKSt+l+++  l kpteGe+ +d+ ++++    + +++ r +ig+++q+ +l p lt+ 
  gi|15668981|ref|NP_247785.1|  21 LKNVNLNIKEGEFVSIMGPSGSGKSTMLNIIGCLDKPTEGEVYIDNIKTNDldddELTKIRRDKIGFVFQQFNLIPLLTAL 101
                                   79****************************************999988888888777889999****************** PP

                                   HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   en               +e+ ++al+ l++ el+++ ++++p++LSgGq+qrva+aral+++p+++l+DEpt
  gi|15668981|ref|NP_247785.1| 102 ENvelplifkyrgamSGEERRKRALECLKMAELEERFANHKPNQLSGGQQQRVAIARALANNPPIILADEPT 173
                                   *************98888889**************************************************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.8     1e-09     1e-06      16     209 ..      22     216 ..      18     225 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1e-09
                                   EEEEEETTS.SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--....BTTCSSTTEEEEEEEEEETTEE.. CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx.. RF
                         SMC_N  16 ktvilpfsk.sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk....skekasvkkaeveitfdnedkk.. 89 
                                   k+v l++++ +f +i+Gp GSGKs +l+ i  +L + +  ++  ++++          +e  ++ + ++  +f++ +    
  gi|15668981|ref|NP_247785.1|  22 KNVNLNIKEgEFVSIMGPSGSGKSTMLNII-GCLDKPTEGEVYIDNIK----TndldDDELTKIRRDKIGFVFQQFNLIpl 97 
                                   5566666542699**************999.78887666554444433....22332578888899999999998888774 PP

                                   .SSSSSSC..EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTT CS
                                   .xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  90 .lkiekee..vsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDei 167
                                    +  e+ e  +  + r   +ge + k   +  + +e++e ++++  ++++LSgG+++ va+a  +A    +  p+ l De 
  gi|15668981|ref|NP_247785.1|  98 lTALENVElpLIFKYRGAMSGEERRKRALECLKMAELEERFANH--KPNQLSGGQQQRVAIARALA----NNPPIILADEP 172
                                   42333333223333444444554555555555667777777665..588**********9998877....668******** PP

                                   TTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEE CS
                                   xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 168 daaLDeknvkkvaellkekskn..aQfivislreemlekadklv 209
                                     aLD k  +k+ +llk+ +++    ++v++++ ++ +  ++++
  gi|15668981|ref|NP_247785.1| 173 TGALDSKTGEKIMQLLKKLNEEdgKTVVVVTHDINVARFGERII 216
                                   *****************887765588999999999888877776 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00071       0.7       4      49 ..      36      64 ..      33      92 .. 0.63
   2 !   17.5   0.0   2.9e-06    0.0029     234     299 ..     143     206 ..     103     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00071
                        AAA_21  4 liGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsll 49
                                  + Gp gsGKS+ L ++ +l   d              ++++ + ++
  gi|15668981|ref|NP_247785.1| 36 IMGPSGSGKSTMLNIIGCL---D--------------KPTEGEVYI 64
                                  78**************999...3..............333333333 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.9e-06
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                   +++lS G+++  a++ al+  +   +++l DEp   L+ k  +++++llk+l++  g  v+++TH+ 
  gi|15668981|ref|NP_247785.1| 143 PNQLSGGQQQRVAIARALANNP---PIILADEPTGALDSKTGEKIMQLLKKLNEeDGKTVVVVTHDI 206
                                   5788999999988888888888...************************66666599999*****95 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     5e-07    0.0005      14      39 ..      23      48 ..      19      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5e-07
                        AAA_29 14 ghtieidlkgatlltGpsGsGKSTll 39
                                  +  ++i++ +++ ++GpsGsGKST+l
  gi|15668981|ref|NP_247785.1| 23 NVNLNIKEGEFVSIMGPSGSGKSTML 48
                                  456778766699************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   8.6e-07   0.00085      20     148 ..      27     210 ..      14     219 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.6e-07
                        AAA_16  20 rsgrpelvllsGesGvGKsslv...rellralekdggiflrgkcdqlesa....ipysalaqalareellrqllde..... 88 
                                   +  ++e v + G+sG+GKs+++    +l ++ e++ ++  + k+ +l+ +    i+++ +  ++ +  l+  l +      
  gi|15668981|ref|NP_247785.1|  27 NIKEGEFVSIMGPSGSGKSTMLniiGCLDKPTEGE-VYIDNIKTNDLDDDeltkIRRDKIGFVFQQFNLIPLLTALenvel 106
                                   3445589**************96666777766666.777666666663334555333333333333333333333333333 PP

                        AAA_16  89 ......aesaeleawrekleeala.........................................avpelagaeasrllel 122
                                           + + e+ r++ +e l+                                         ++++l+    s   e+
  gi|15668981|ref|NP_247785.1| 107 plifkyRGAMSGEERRKRALECLKmaeleerfanhkpnqlsggqqqrvaiaralannppiiladePTGALD----SKTGEK 183
                                   33333355555556666666666667777777788777777777777777777777777553333333333....444455 PP

                        AAA_16 123 lkrll.allsrderplvlvlDdlqwad 148
                                   + +ll +l ++d++++v+v  d+  a+
  gi|15668981|ref|NP_247785.1| 184 IMQLLkKLNEEDGKTVVVVTHDINVAR 210
                                   555554444777777777777766665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.9e-06    0.0029      19     150 ..      30     189 ..      16     219 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.9e-06
                      ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal................. 82 
                                   + e++ i Gp gsGK+++l+ ii  l++  +  +y++++++ +++  + +   +  ++k+  ++                 
  gi|15668981|ref|NP_247785.1|  30 EGEFVSIMGPSGSGKSTMLN-IIGCLDKPTEGEVYIDNIKTNDLDDDELT---KIRRDKIGFVFqqfnliplltalenvel 106
                                   468899***********886.8889989999*********9999887776...2222222222255578888888888888 PP

                      ATPase_2  83 ...................giavpkaeleeilkeksklvfkaielllekikkkgkk..iiiiiDelqklidlglngaellv 142
                                                      ++ ++ aelee + +++ +  +  ++   +i +      +ii++De   + d +    e+  
  gi|15668981|ref|NP_247785.1| 107 plifkyrgamsgeerrkraLECLKMAELEERFANHKPNQLSGGQQQRVAIARALANnpPIILADEPTGALDSKTG--EK-- 183
                                   888888888888888888777777788888777555555555555566666665556788888888887754443..33.. PP

                      ATPase_2 143 keLlnlie 150
                                     +++l++
  gi|15668981|ref|NP_247785.1| 184 --IMQLLK 189
                                   ..333333 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.2e-06    0.0042      14      84 ..      21     115 ..      20     153 .. 0.70
   2 ?   -0.0   0.0      0.56   5.6e+02     324     365 ..     164     205 ..     144     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.2e-06
                        AAA_15  14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenisesk..dikIdvef........ 83 
                                   lk+v ++++e  +  + G+ +sGKS+ l+++  + + +    + +++i++ ++++ ++++  k  + kI + f        
  gi|15668981|ref|NP_247785.1|  21 LKNVNLNIKEGeFVSIMGPSGSGKSTMLNIIGCLDKPT----EGEVYIDNIKTNDLDDDELTKirRDKIGFVFqqfnlipl 97 
                                   899999999999**********************9999....788899999988887766554115566666666666666 PP

                        AAA_15  84 .................a 84 
                                                    a
  gi|15668981|ref|NP_247785.1|  98 ltalenvelplifkyrgA 115
                                   666666666665544441 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.56
                        AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                   + i+l +EP   L  +  + +++llk+l +++ + v++ TH 
  gi|15668981|ref|NP_247785.1| 164 PPIILADEPTGALDSKTGEKIMQLLKKLNEEDGKTVVVVTHD 205
                                   556677777777777777888999999999999899999996 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.7e-06    0.0027      90     120 ..      21      52 ..       4      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.7e-06
                                   HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                   RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinall 120
                                   l++++ ++k+ +++ ++G+SG GKSt++n + 
  gi|15668981|ref|NP_247785.1|  21 LKNVNLNIKEgEFVSIMGPSGSGKSTMLNIIG 52 
                                   56666677777999***************875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.5e-05     0.025       3      65 ..      36     102 ..      34     145 .. 0.63
   2 ?    2.3   0.0      0.22   2.2e+02      49      86 ..     173     208 ..     132     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                        AAA_18   3 ltGtpGvGKttlakeLskrlgf......gvnlrdvakenglllevdpealdesk...rldedkldklldale 65 
                                   ++G++G+GK+t+ + +     +      g++++d++k n+l +++  + +++ k   ++++ +l  ll+ale
  gi|15668981|ref|NP_247785.1|  36 IMGPSGSGKSTMLNIIG----CldkpteGEVYIDNIKTNDLDDDELTK-IRRDKigfVFQQFNLIPLLTALE 102
                                   89**************3....333345799999999999999988887.33333111333334444444444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.22
                        AAA_18  49 skrldedkldklldaleenssaleegknlvidghlael 86 
                                   +  ld +  +k++++l++ ++  e+gk++v+  h  + 
  gi|15668981|ref|NP_247785.1| 173 TGALDSKTGEKIMQLLKKLNE--EDGKTVVVVTHDINV 208
                                   556666666778888888875..889999998887665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0018       1.8      34      67 ..      17      51 ..       5      84 .. 0.79
   2 ?    4.7   0.0     0.022        22     104     158 ..     158     215 ..     130     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                     IstB_IS21 34 kvkeLatlsf.iekkenivllGpsGvGKshlaial 67
                                  ++ +L + +  i++ e + ++GpsG GKs +   +
  gi|15668981|ref|NP_247785.1| 17 IIYALKNVNLnIKEGEFVSIMGPSGSGKSTMLNII 51
                                  555565544328899999**********9876555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.022
                     IstB_IS21 104 krllkvdllilDdlgllpldqaeaellfeviekrye...rrsiiitsnlpfaewdevl 158
                                   ++l++   +il d  +  ld++  e+++++++k  e   ++ +++t ++++a+++e +
  gi|15668981|ref|NP_247785.1| 158 RALANNPPIILADEPTGALDSKTGEKIMQLLKKLNEedgKTVVVVTHDINVARFGERI 215
                                   44555555777777788888888888888887766522278899********998865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00044      0.44      19      38 ..      32      51 ..      23      83 .. 0.85
   2 ?    1.5   0.0      0.22   2.2e+02       5      59 ..     151     209 ..     147     212 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00044
                        AAA_30 19 rvavltGpAGtGKttalkal 38
                                   ++ + Gp G+GK+t+l+ +
  gi|15668981|ref|NP_247785.1| 32 EFVSIMGPSGSGKSTMLNII 51
                                  478899***********987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.22
                        AAA_30   5 eQaaavealltsgdrvavltGpAGt..GKt..talkalreaweaaggrviglAptgkaA 59 
                                   +Q+ a++++l+++  + ++  p G+   Kt   +++ l+++ e++g++v+++++  ++A
  gi|15668981|ref|NP_247785.1| 151 QQRVAIARALANNPPIILADEPTGAldSKTgeKIMQLLKKLNEEDGKTVVVVTHDINVA 209
                                   56666666666666666666666664445544478888888888899999988776665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00033      0.33       4      23 ..      30      49 ..      26      56 .. 0.87
   2 ?    0.7   0.0      0.59   5.9e+02      89     132 ..     158     205 ..     113     209 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                        AAA_22  4 tagilvvtGesGtGKTtllr 23
                                  +  ++ ++G+sG+GK+t l+
  gi|15668981|ref|NP_247785.1| 30 EGEFVSIMGPSGSGKSTMLN 49
                                  567899***********986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.59
                        AAA_22  89 rav...ielliiDEaqh.lr..s.eealeeLrsllnlsrkgvqliLvGtpe 132
                                   ra    +++++ DE    l+  + e++++ L++l n  + + + ++v t++
  gi|15668981|ref|NP_247785.1| 158 RALannPPIILADEPTGaLDskTgEKIMQLLKKL-N--EEDGKTVVVVTHD 205
                                   2224466788888877777654234444444444.4..5555555665555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.7e-05     0.057      29      66 ..      15      52 ..       7     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.7e-05
                         Rad17 29 eevkewlkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                  ee+  +lk   L+ ++ + + i GPsG gkst+++++ 
  gi|15668981|ref|NP_247785.1| 15 EEIIYALKNVNLNIKEGEFVSIMGPSGSGKSTMLNIIG 52
                                  56777899999999999999*************99864 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00047      0.46       6      47 ..      35      81 ..      32     121 .. 0.75
   2 ?    1.2   0.0      0.27   2.7e+02     107     130 ..     180     204 ..     171     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00047
                        AAA_24  6 liyGpsgiGKTtlakel......gpkplfidtekGlksldadkfpdie 47
                                   i+Gpsg+GK+t+++ +      ++  ++id  k +++ld+d++ +i+
  gi|15668981|ref|NP_247785.1| 35 SIMGPSGSGKSTMLNIIgcldkpTEGEVYIDNIK-TNDLDDDELTKIR 81
                                  59***********998888664433334444444.6666666666665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.27
                        AAA_24 107 laeefrrllkklqelrk.nvifiah 130
                                    +e++++llkkl+e ++ +v+++ h
  gi|15668981|ref|NP_247785.1| 180 TGEKIMQLLKKLNEEDGkTVVVVTH 204
                                   6789999999999998889999998 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00053      0.53      30      50 ..      28      48 ..      22      52 .. 0.90
   2 ?    0.5   0.0      0.38   3.8e+02     166     188 ..     182     204 ..     119     205 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00053
                        AAA_25 30 lpagelallaGapgtGKttla 50
                                  + +ge++ ++G++g+GK+t++
  gi|15668981|ref|NP_247785.1| 28 IKEGEFVSIMGPSGSGKSTML 48
                                  679****************86 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.38
                        AAA_25 166 galvealeriarrtgaavllvhH 188
                                   +++++ l+++ ++ g +v++v H
  gi|15668981|ref|NP_247785.1| 182 EKIMQLLKKLNEEDGKTVVVVTH 204
                                   55556666666666666666666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   7.5e-05     0.074      11      39 ..      22      51 ..       2      54 .. 0.79
   2 ?    0.9   0.5      0.54   5.4e+02     108     143 ..      68     135 ..      55     199 .. 0.44

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.5e-05
                        AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildAi 39
                                  ++++++  +  ++ I Gp G+GK+T l+ i
  gi|15668981|ref|NP_247785.1| 22 KNVNLNIkEGEFVSIMGPSGSGKSTMLNII 51
                                  56666664446778*************987 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.54
                        AAA_23 108 klelleideleqfisellgskkiilnlilflgqer................................f 143
                                   k++ l++del+++ ++++g  ++++nli +l + +                                +
  gi|15668981|ref|NP_247785.1|  68 KTNDLDDDELTKIRRDKIGFVFQQFNLIPLLTALEnvelplifkyrgamsgeerrkraleclkmaelE 135
                                   44455555555555555554445555554433333344444433333333333333333332222222 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0002       0.2     123     149 ..      25      51 ..       2      91 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                         T2SSE 123 rkavrerglilvsGgTgsGKttllyal 149
                                   +  ++e   + + G+ gsGK+t+l+++
  gi|15668981|ref|NP_247785.1|  25 NLNIKEGEFVSIMGPSGSGKSTMLNII 51 
                                   3456677778899***********975 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00078      0.78       2      19 ..      34      51 ..      33     103 .. 0.86
   2 ?    0.5   0.0       0.6     6e+02      45      84 ..     163     205 ..     132     229 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00078
                                  EEEEESTTSSHHHHHHHH CS
                      MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                  v i+G + +GKSt++n +
  gi|15668981|ref|NP_247785.1| 34 VSIMGPSGSGKSTMLNII 51
                                  78**************76 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.6
                                   TEEEEEEECG.GCSSHHHHHHHHHHHHHHHHC...TSEEEEEEE CS
                      MMR_HSR1  45 gkeielvDtp.Gliegaseekglgkaflalee...adlillvvd 84 
                                   +++i+l+D p G ++ +++++++ + +++l+e     ++++  d
  gi|15668981|ref|NP_247785.1| 163 NPPIILADEPtGALD-SKTGEKIMQLLKKLNEedgKTVVVVTHD 205
                                   466777777623333.3333322222222222111233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 1554.15
//
Query:       gi|15668982|ref|NP_247786.1|  [L=137]
Description: hypothetical protein MJ_0796.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.21   11.5   0.8        2.7    7.9   0.0    2.4  2  Importin_rep_2   Importin 13 repeat
          3    7.8  11.9        8.5    6.4  12.3    1.6  2  MARVEL           Membrane-associating domain


Domain annotation for each model (and alignments):
>> Importin_rep_2  Importin 13 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0003       2.7       8      17 ..      57      66 ..      55      80 .. 0.87
   2 ?    1.6   0.2     0.029   2.6e+02      13      22 ..     124     133 ..     122     137 .] 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0003
                Importin_rep_2  8 iqiLGlLlsl 17
                                  i+i G+Llsl
  gi|15668982|ref|NP_247786.1| 57 IHIIGFLLSL 66
                                  9*******98 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.029
                Importin_rep_2  13 lLlslltvld 22 
                                   +Ll+l++ ld
  gi|15668982|ref|NP_247786.1| 124 FLLNLFKKLD 133
                                   9*****9887 PP

>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  12.3   0.00095       8.5      12     103 ..      21     112 ..      11     129 .. 0.83
   2 ?   -1.6   0.1      0.28   2.5e+03      56      66 ..     120     130 ..     112     136 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00095
                        MARVEL  12 lqlvfaiiilgliasliakldqllgspssalnfavfvavfsflyalfllvlylfk.nsaftsilwplidlivdalaallwl 91 
                                   l ++  +++ g+i+sli+k+ ++  + + +++f+ f+ +++fl++l +    +++ +   +++++  i +++++++ +  +
  gi|15668982|ref|NP_247786.1|  21 LYIFIILVVDGSISSLIGKYITYPSDEYHIIEFYDFIHIIGFLLSLSISTY-FSSkDIIKDFAKFFTIFFGITFILGITLF 100
                                   4455667888********9999999999***************99876655.55569999********************* PP

                        MARVEL  92 vafialaaglrd 103
                                    + +++ +++ +
  gi|15668982|ref|NP_247786.1| 101 LGLTFFENHIPS 112
                                   **9998776665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.28
                        MARVEL  56 alfllvlylfk 66 
                                   +lf+++l+lfk
  gi|15668982|ref|NP_247786.1| 120 MLFFFLLNLFK 130
                                   56666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 934.92
//
Query:       gi|15668983|ref|NP_247787.1|  [L=367]
Description: hypothetical protein MJ_0797 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-15   56.6   0.0    4.4e-15   56.6   0.0    2.3  3  MacB_PCD         MacB-like periplasmic core domain
    1.6e-12   47.7   9.7    1.6e-12   47.7   9.7    2.9  3  FtsX             FtsX-like permease family
  ------ inclusion threshold ------
       0.22   11.8   6.1       0.11   12.7   3.6    2.0  1  EI24             Etoposide-induced protein 2.4 (EI24)
       0.55    9.5   8.9        1.3    8.3   0.1    2.5  3  DUF4191          Domain of unknown function (DUF4191)


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   9.7e-19   4.4e-15       1     194 [.      17     211 ..      17     212 .. 0.73
   2 ?   -2.6   1.8       1.3   5.9e+03       3      23 ..     249     269 ..     244     292 .. 0.59
   3 ?   -4.3   1.6         4   1.8e+04       4      13 ..     333     342 ..     331     348 .. 0.75

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 9.7e-19
                      MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgk.gsgeslsdpdvealrrevpve..avapvvtvrgg 78 
                                   s+l++LGi+iGvaa++++++lg gl++ + +++ + +n ++v+p++ +  +s++ +d+e l    +v   +v pv    ++
  gi|15668983|ref|NP_247787.1|  17 SILALLGIIIGVAAISSLGILGGGLKQGIMENLGSISNYIIVFPNYqNGYTSFDKRDIEKL----RVLncKVIPV----YA 89 
                                   79********************************99*988888876322223555677544....3333468888....33 PP

                      MacB_PCD  79 gsgeeevtvvg.vdpdyfkvfglklaeGrffteadlr.ggpnvvvigeelaerlf.......pvGdtirl..kpftVvGvl 148
                                   +s+   v + g    +y+ +fg+        +++d++  + +v v + ++a + f        vG ++++  +++++ G++
  gi|15668983|ref|NP_247787.1|  90 TSDF--VYIKGkNRKAYANIFGI--------DKNDIKyLNLKVKVSDTSVAVDTFfsnvndvNVGNQLEIknISLRICGIY 160
                                   3223..56777444577777766........33445533666777777787775558777777*****************9 PP

                      MacB_PCD 149 edppgsgsalgddavylplttlqrrs.........itvrlkdgadleaaaaelek 194
                                       +s++ + d++++l ++t++r +         i++ +k+  d++++++e +k
  gi|15668983|ref|NP_247787.1| 161 ----NSTFLFPDNSLILTAKTYRRFYgennynysrIILYVKNINDIDKIKNETDK 211
                                   ....33466779******88874333455556677**************999776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                      MacB_PCD   3 ltvLGiaiGvaaviaivslge 23 
                                   +++L   iG++ v+++ ++ +
  gi|15668983|ref|NP_247787.1| 249 ISLLVAGIGIGNVMLMSVVER 269
                                   344444555555555555444 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 4
                      MacB_PCD   4 tvLGiaiGva 13 
                                   +++Gi++G+ 
  gi|15668983|ref|NP_247787.1| 333 MIIGIIFGIL 342
                                   6889999985 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.3     0.064   2.9e+02      21      53 ..      18      51 ..      10      70 .. 0.50
   2 ?   -1.8   1.7      0.97   4.4e+03      25      41 ..     246     260 ..     222     267 .. 0.56
   3 !   47.7   9.7   3.5e-16   1.6e-12       2      96 .]     271     360 ..     270     360 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.064
                          FtsX 21 llteillitlvalviGlgl.gllaaqllsdvlls 53
                                  +l  + +i+ va++++lg+ g  + q ++  l+s
  gi|15668983|ref|NP_247787.1| 18 ILALLGIIIGVAAISSLGIlGGGLKQGIMENLGS 51
                                  3333333333333333222244444444444444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.97
                          FtsX  25 illitlvalviGlglgl 41 
                                   i +i+l+ +   +g+g+
  gi|15668983|ref|NP_247787.1| 246 IGAISLLVAG--IGIGN 260
                                   3333333333..33333 PP

  == domain 3  score: 47.7 bits;  conditional E-value: 3.5e-16
                          FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllall 82 
                                    eig++r++G++kk+++ l+l+e+l++++++++iG  l+l++ +l+ ++ll+    s   + i ++++ ii+++l+ l+++
  gi|15668983|ref|NP_247787.1| 271 TEIGVMRSIGASKKDIIILFLYEALILGVIGSLIGAFLSLFFGYLIVHYLLKT---SLSYYAIFYMIIGIIFGILTSLISA 348
                                   69**************************************************9...5566666665555555555555555 PP

                          FtsX  83 agllsiskilkkep 96 
                                     l++++k++k +p
  gi|15668983|ref|NP_247787.1| 349 --LYPAYKASKLDP 360
                                   ..5*******9987 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.6   2.6e-05      0.11      42     130 ..     229     321 ..       3     332 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHHHHHHHHHHH.HHHHHHHHHH.....HHHHHHHHHH.HH..CCTTSHHHHHHHHHHHHHHHHHHHHHHHTTHH CS
                          EI24  42 lasllvllllllplwlfp.lvalllaapf.....ygllaekvekrhl..glvkslaeslkslllllllllvllplliPvvg 114
                                   l+++ ++++ + ++++   +++ll+a++      +  ++e++       g+++s++ s k +++l+l+ +++l ++  ++g
  gi|15668983|ref|NP_247787.1| 229 LEAINGVITKVSYFLMGIgAISLLVAGIGignvmLMSVVERT----TeiGVMRSIGASKKDIIILFLYEALILGVIGSLIG 305
                                   344444444444444444788888888877544444444444....23499*****99999999998888777774499** PP

                                   H....HHHHHHHHHHH CS
                          EI24 115 lilsplllswltayfy 130
                                    +ls+++++++ +y++
  gi|15668983|ref|NP_247787.1| 306 AFLSLFFGYLIVHYLL 321
                                   *********9999965 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.4   6.2e+03      31      63 ..      19      29 ..       3      39 .. 0.52
   2 ?    8.3   0.1   0.00028       1.3      16      81 ..     211     279 ..     198     283 .. 0.78
   3 ?    4.1   3.3    0.0056        25      28      67 ..     306     346 ..     295     354 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.4
                       DUF4191 31 aaflvvvvvfvvlglllgslilllilgillgll 63
                                  +                       +lgi++g+ 
  gi|15668983|ref|NP_247787.1| 19 L----------------------ALLGIIIGVA 29
                                  2......................3333333333 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00028
                       DUF4191  16 kltrkedkkllwlllaaflvvv..vvfvvlglllg.slilllilgillgllvalivltrraekaayaqi 81 
                                   k+ ++++kk++ + l  +l ++  v++ v  +l+g + i ll+ gi +g ++ + v +r +e  ++++i
  gi|15668983|ref|NP_247787.1| 211 KILNRKEKKCIIISLNSILEAIngVITKVSYFLMGiGAISLLVAGIGIGNVMLMSVVERTTEIGVMRSI 279
                                   5667788888888887777554225666667777646**********************9988777665 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0056
                       DUF4191  28 lllaaflvvvvvfvvlglllgs.lilllilgillgllvali 67 
                                   ++l +f + ++v  +l   l+   i+++i+gi++g+l+ li
  gi|15668983|ref|NP_247787.1| 306 AFLSLFFGYLIVHYLLKTSLSYyAIFYMIIGIIFGILTSLI 346
                                   456667777777777777776459*************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1180  (0.0658152); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 2871.43
//
Query:       gi|15668984|ref|NP_247788.1|  [L=334]
Description: hypothetical protein MJ_0798 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.1e-35  117.4  48.7    1.5e-08   34.1   0.4    7.7  7  TPR_1        Tetratricopeptide repeat
      3e-33  111.2  41.0    1.6e-07   30.9   0.2    7.6  7  TPR_2        Tetratricopeptide repeat
    8.1e-30  100.5  41.9    5.1e-06   26.3   0.2    8.1  8  TPR_8        Tetratricopeptide repeat
    6.2e-19   66.6  10.4     0.0021   18.0   0.1    6.8  6  TPR_7        Tetratricopeptide repeat
    8.2e-19   67.0  28.0     0.0004   20.0   0.1    6.6  6  TPR_11       TPR repeat
    2.6e-18   66.1  10.8    2.7e-06   27.6   0.1    5.7  5  TPR_12       Tetratricopeptide repeat
    6.2e-18   64.2  10.0     0.0012   19.4   0.0    6.7  6  TPR_6        Tetratricopeptide repeat
    1.9e-15   56.2   0.0       0.01   16.6   0.0    6.8  7  TPR_14       Tetratricopeptide repeat
    1.1e-14   54.7   2.7    7.7e-06   26.3   0.1    5.6  5  TPR_19       Tetratricopeptide repeat
    4.1e-11   43.3   0.0      0.003   18.2   0.0    4.2  4  TPR_16       Tetratricopeptide repeat
    2.3e-10   40.1  26.4    0.00023   21.3   0.2    8.6  9  TPR_17       Tetratricopeptide repeat
      4e-09   36.5   0.0    1.8e-05   24.8   0.0    4.1  4  TPR_9        Tetratricopeptide repeat
    1.2e-07   31.3   0.8    6.9e-07   28.8   0.8    1.9  1  TPR_15       Tetratricopeptide repeat
    6.1e-07   29.6  25.5      9e-07   29.0   3.1    4.3  4  ANAPC3       Anaphase-promoting complex, cyclosome, subunit 3
    2.9e-06   27.0   0.7       0.49   10.3   0.0    6.0  6  TPR_10       Tetratricopeptide repeat
    0.00013   21.1   1.0      0.043   12.8   0.1    2.4  3  ChAPs        ChAPs (Chs5p-Arf1p-binding proteins)
     0.0013   18.6   7.3      0.012   15.4   0.2    3.4  3  DUF2989      Protein of unknown function (DUF2989)
     0.0019   18.5   0.0       0.68   10.3   0.0    3.2  3  TPR_20       Tetratricopeptide repeat
     0.0086   16.1  16.5       0.81    9.8   0.1    6.3  6  MIT          MIT (microtubule interacting and transport) doma
  ------ inclusion threshold ------
      0.011   15.4   0.1      0.024   14.2   0.1    1.5  1  CAMP_factor  CAMP factor (Cfa)
      0.015   15.4   0.4      0.015   15.4   0.4    3.9  3  Fis1_TPR_C   Fis1 C-terminal tetratricopeptide repeat
      0.019   15.7  20.9        2.5    8.9   0.3    6.9  7  Sel1         Sel1 repeat
      0.037   14.4   2.7      0.095   13.0   2.7    2.0  1  SusD-like_3  Starch-binding associating with outer membrane
       0.16   12.0   0.1          2    8.5   0.0    2.7  2  UPF0154      Uncharacterised protein family (UPF0154)
       0.19   12.0  10.1        9.1    6.8   0.2    5.1  4  PPR          PPR repeat
        0.4   11.6   1.7         30    5.6   0.1    2.6  2  Pup          Pup-like protein
        6.8    7.2  17.8         27    5.3   0.1    4.3  3  NBD94        Nucleotide-Binding Domain 94 of RH
        9.6    6.1  13.3         15    5.5   0.4    4.2  3  Prefoldin    Prefoldin subunit


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   5.1   4.9e-08   3.1e-05       2      33 ..     103     134 ..     102     135 .. 0.96
   2 !   13.0   2.2   0.00011     0.068       3      34 .]     137     168 ..     135     168 .. 0.93
   3 !   31.1   0.2     2e-10   1.3e-07       2      34 .]     170     202 ..     169     202 .. 0.97
   4 !   16.1   1.9   1.1e-05    0.0071      18      34 .]     219     235 ..     203     235 .. 0.89
   5 !   34.1   0.4   2.4e-11   1.5e-08       9      33 ..     244     268 ..     242     269 .. 0.94
   6 !   16.6   0.2   8.1e-06    0.0052       5      31 ..     277     303 ..     274     303 .. 0.86
   7 !   10.6   0.5    0.0006      0.39       7      26 ..     313     332 ..     307     333 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.9e-08
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                   k ++nlG   +  + y eAl +y+kALeln n
  gi|15668984|ref|NP_247788.1| 103 KLWKNLGDKAYLWKAYYEALFCYNKALELNQN 134
                                   78****************************87 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                    l+ +G+a++kl k d A++y+ekA e + nn
  gi|15668984|ref|NP_247788.1| 137 LLCKKGYALLKLYKRDLAIKYFEKASEKDRNN 168
                                   7899*********************9999997 PP

  == domain 3  score: 31.1 bits;  conditional E-value: 2e-10
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   kal++lG  y+ + + +  ++y+ek+LelnPn+
  gi|15668984|ref|NP_247788.1| 170 KALFGLGKSYYLMSDNKNSIKYFEKVLELNPND 202
                                   8******************************97 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHHHHHHSTTH CS
                         TPR_1  18 deAleyyekALelnPnn 34 
                                   ++A+ y++kALel P++
  gi|15668984|ref|NP_247788.1| 219 EKAINYFKKALELKPDD 235
                                   8**************96 PP

  == domain 5  score: 34.1 bits;  conditional E-value: 2.4e-11
                                   HHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   9 nayfklgkydeAleyyekALelnPn 33 
                                    +yfkl+ky+ Al+y+ekAL+lnPn
  gi|15668984|ref|NP_247788.1| 244 FTYFKLKKYKHALKYFEKALKLNPN 268
                                   68**********************9 PP

  == domain 6  score: 16.6 bits;  conditional E-value: 8.1e-06
                                   HHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                         TPR_1   5 ynlGnayfklgkydeAleyyekALeln 31 
                                     +G +y +lg+ ++A+e++ek  e+n
  gi|15668984|ref|NP_247788.1| 277 ESMGRIYIYLGEDEKAIECFEKLKEIN 303
                                   5799*****************976665 PP

  == domain 7  score: 10.6 bits;  conditional E-value: 0.0006
                                   HHHHHHHTT-HHHHHHHHHH CS
                         TPR_1   7 lGnayfklgkydeAleyyek 26 
                                   ++++y + g+ ++A e+y+k
  gi|15668984|ref|NP_247788.1| 313 IALTYEEVGNIEKAKEFYKK 332
                                   899***************98 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   3.7   0.00019      0.12       2      33 ..     103     134 ..     102     135 .. 0.91
   2 !   16.1   1.3   1.3e-05    0.0085       2      34 .]     136     168 ..     135     168 .. 0.94
   3 !   26.3   0.1   7.3e-09   4.7e-06       2      34 .]     170     202 ..     169     202 .. 0.97
   4 !   16.6   2.5   9.6e-06    0.0061       2      34 .]     204     235 ..     203     235 .. 0.91
   5 !   30.9   0.2   2.4e-10   1.6e-07       8      33 ..     243     268 ..     238     269 .. 0.94
   6 !   20.0   0.2   7.7e-07   0.00049       4      31 ..     276     303 ..     274     305 .. 0.90
   7 !   11.5   0.1    0.0004      0.26       2      27 ..     308     333 ..     307     334 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                   +++ nlG+ +y  + y eAl +++kAlel+ n
  gi|15668984|ref|NP_247788.1| 103 KLWKNLGDKAYLWKAYYEALFCYNKALELNQN 134
                                   689999999999999**************976 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.3e-05
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   e+l+  G+a++kl + + A+++fekA e d nn
  gi|15668984|ref|NP_247788.1| 136 ELLCKKGYALLKLYKRDLAIKYFEKASEKDRNN 168
                                   67999***********************99987 PP

  == domain 3  score: 26.3 bits;  conditional E-value: 7.3e-09
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +al+ lG++yy + d +  +++fek+lel+Pn+
  gi|15668984|ref|NP_247788.1| 170 KALFGLGKSYYLMSDNKNSIKYFEKVLELNPND 202
                                   79*****************************97 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 9.6e-06
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   eal +lG++yy   d e+A+++f+kAlel P++
  gi|15668984|ref|NP_247788.1| 204 EALEYLGELYY-EEDCEKAINYFKKALELKPDD 235
                                   78999999999.8888***************97 PP

  == domain 5  score: 30.9 bits;  conditional E-value: 2.4e-10
                         TPR_2   8 GlayyklgdyeeAleafekAleldPn 33 
                                   +  y+kl++y+ Al++fekAl+l+Pn
  gi|15668984|ref|NP_247788.1| 243 AFTYFKLKKYKHALKYFEKALKLNPN 268
                                   789**********************8 PP

  == domain 6  score: 20.0 bits;  conditional E-value: 7.7e-07
                         TPR_2   4 lynlGlayyklgdyeeAleafekAleld 31 
                                   +  +G++y++lg+ e+A+e+fek  e++
  gi|15668984|ref|NP_247788.1| 276 YESMGRIYIYLGEDEKAIECFEKLKEIN 303
                                   6679*******************98886 PP

  == domain 7  score: 11.5 bits;  conditional E-value: 0.0004
                         TPR_2   2 ealynlGlayyklgdyeeAleafekA 27 
                                   e++  ++l y++ g+ e+A+e+++k 
  gi|15668984|ref|NP_247788.1| 308 EIYEIIALTYEEVGNIEKAKEFYKKL 333
                                   6777899*****************96 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       5.2   3.3e+03       3      16 ..      70      83 ..      70      91 .. 0.80
   2 !    8.8   0.4    0.0032       2.1      17      33 ..     118     134 ..     105     135 .. 0.87
   3 !   14.6   1.9   4.3e-05     0.028       2      32 ..     136     166 ..     135     168 .. 0.89
   4 !   23.9   0.2   4.5e-08   2.9e-05       2      34 .]     170     202 ..     169     202 .. 0.95
   5 !   14.7   0.6   4.2e-05     0.027      18      34 .]     219     235 ..     211     235 .. 0.91
   6 !   26.3   0.2     8e-09   5.1e-06       7      33 ..     242     268 ..     236     269 .. 0.90
   7 !   21.4   0.6     3e-07   0.00019       2      31 ..     274     303 ..     273     306 .. 0.92
   8 !   17.5   0.5   5.3e-06    0.0034       2      27 ..     308     333 ..     307     334 .] 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.2
                                  HHHHHHHHHHHTT- CS
                         TPR_8  3 ayynlgsiylklgd 16
                                  +y++l+ +y++  +
  gi|15668984|ref|NP_247788.1| 70 IYNKLSTLYEDIDK 83
                                  58999999988665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0032
                                   HHHHHHHHHHHHHHHHH CS
                         TPR_8  17 yeeAkeyyekaleldpd 33 
                                   y eA  +y+kalel+++
  gi|15668984|ref|NP_247788.1| 118 YYEALFCYNKALELNQN 134
                                   789***********987 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 4.3e-05
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                   e+++++g+++lkl + + A++y+eka e d+
  gi|15668984|ref|NP_247788.1| 136 ELLCKKGYALLKLYKRDLAIKYFEKASEKDR 166
                                   6899**********************98555 PP

  == domain 4  score: 23.9 bits;  conditional E-value: 4.5e-08
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   +a++ lg+ y  + d +++++y+ek+lel+p++
  gi|15668984|ref|NP_247788.1| 170 KALFGLGKSYYLMSDNKNSIKYFEKVLELNPND 202
                                   799****************************96 PP

  == domain 5  score: 14.7 bits;  conditional E-value: 4.2e-05
                                   HHHHHHHHHHHHHHHH. CS
                         TPR_8  18 eeAkeyyekaleldpdn 34 
                                   e+A+ y++kalel+pd+
  gi|15668984|ref|NP_247788.1| 219 EKAINYFKKALELKPDD 235
                                   89*************96 PP

  == domain 6  score: 26.3 bits;  conditional E-value: 8e-09
                                   HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                                    + +y+kl++y+ A +y+ekal+l+p+
  gi|15668984|ref|NP_247788.1| 242 VAFTYFKLKKYKHALKYFEKALKLNPN 268
                                   6779**********************7 PP

  == domain 7  score: 21.4 bits;  conditional E-value: 3e-07
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                   ++y  +g+iy+ lg+ e+A+e++ek  e++
  gi|15668984|ref|NP_247788.1| 274 QIYESMGRIYIYLGEDEKAIECFEKLKEIN 303
                                   578899*******************99997 PP

  == domain 8  score: 17.5 bits;  conditional E-value: 5.3e-06
                                   CHHHHHHHHHHHTT-HHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyeka 27 
                                   e+y  ++++y++ g++e+Ake+y+k 
  gi|15668984|ref|NP_247788.1| 308 EIYEIIALTYEEVGNIEKAKEFYKKL 333
                                   78999*******************97 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.021        14      11      34 ..     147     168 ..     137     170 .. 0.77
   2 !   10.8   0.0   0.00061      0.39       1      34 [.     171     202 ..     171     204 .. 0.86
   3 !   14.3   0.1   4.9e-05     0.032       1      31 [.     205     234 ..     205     237 .. 0.84
   4 !    9.8   0.0    0.0013      0.85       8      31 ..     245     266 ..     243     273 .. 0.82
   5 !   18.0   0.1   3.2e-06    0.0021       3      24 ..     277     298 ..     275     305 .. 0.89
   6 !    8.9   0.0    0.0026       1.7       5      24 ..     313     332 ..     309     334 .] 0.92

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.021
                         TPR_7  11 rlGdyeeAielyeqsLaltkdped 34 
                                   +l +++ Ai+++e+  a +kd ++
  gi|15668984|ref|NP_247788.1| 147 KLYKRDLAIKYFEK--ASEKDRNN 168
                                   5557899*******..99999875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00061
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                   aL+ L+  y  + d ++ i+++e+  +l+  p+d
  gi|15668984|ref|NP_247788.1| 171 ALFGLGKSYYLMSDNKNSIKYFEK--VLELNPND 202
                                   7899********************..77777666 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 4.9e-05
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                   aL +L++ly +  d e+Ai +++++L+l  d
  gi|15668984|ref|NP_247788.1| 205 ALEYLGELYYE-EDCEKAINYFKKALELKPD 234
                                   68899999999.9***********7777655 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0013
                         TPR_7   8 lysrlGdyeeAielyeqsLaltkd 31 
                                   +y++l +y+ A++++e++L l   
  gi|15668984|ref|NP_247788.1| 245 TYFKLKKYKHALKYFEKALKL--N 266
                                   7999*************5554..4 PP

  == domain 5  score: 18.0 bits;  conditional E-value: 3.2e-06
                         TPR_7   3 lnLarlysrlGdyeeAielyeq 24 
                                     ++r+y  lG+ e+Aie++e+
  gi|15668984|ref|NP_247788.1| 277 ESMGRIYIYLGEDEKAIECFEK 298
                                   579******************9 PP

  == domain 6  score: 8.9 bits;  conditional E-value: 0.0026
                         TPR_7   5 LarlysrlGdyeeAielyeq 24 
                                   +a +y+++G+ e+A e+y++
  gi|15668984|ref|NP_247788.1| 313 IALTYEEVGNIEKAKEFYKK 332
                                   799***************98 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   1.5   0.00037      0.24      10      40 ..     118     147 ..     109     149 .. 0.83
   2 !   14.0   1.0   4.8e-05     0.031      11      41 ..     152     182 ..     142     183 .. 0.86
   3 !   19.7   1.6   7.6e-07   0.00049       4      40 ..     179     215 ..     179     217 .. 0.93
   4 !   20.0   0.1   6.2e-07    0.0004      10      41 ..     218     249 ..     215     250 .. 0.94
   5 !   14.0   0.1   4.8e-05     0.031       4      26 ..     246     268 ..     245     272 .. 0.93
   6 !   10.7   0.4    0.0005      0.32       1      24 [.     280     303 ..     280     321 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                        TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                   y eA+ +Y+kAl+l+++  e++++ G+a++k
  gi|15668984|ref|NP_247788.1| 118 YYEALFCYNKALELNQN-TELLCKKGYALLK 147
                                   779***********975.5788888888877 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.8e-05
                        TPR_11  11 eeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                   + Ai+ ++kA + d +n  a+++LG+ yy +
  gi|15668984|ref|NP_247788.1| 152 DLAIKYFEKASEKDRNNYKALFGLGKSYYLM 182
                                   779**************************75 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 7.6e-07
                        TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                   yy   +++++i+ ++k l+l+P+++ea+  LG++yy+
  gi|15668984|ref|NP_247788.1| 179 YYLMSDNKNSIKYFEKVLELNPNDVEALEYLGELYYE 215
                                   777788999***************************7 PP

  == domain 4  score: 20.0 bits;  conditional E-value: 6.2e-07
                        TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                    e+Ai+ +kkAl+l+Pd+ ++ ++ +++y+k+
  gi|15668984|ref|NP_247788.1| 218 CEKAINYFKKALELKPDDIDLILKVAFTYFKL 249
                                   59****************************97 PP

  == domain 5  score: 14.0 bits;  conditional E-value: 4.8e-05
                        TPR_11   4 yyeqGkyeeAieaYkkAlkldPd 26 
                                   y+++ ky+ A++ ++kAlkl+P+
  gi|15668984|ref|NP_247788.1| 246 YFKLKKYKHALKYFEKALKLNPN 268
                                   9*********************8 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.0005
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkld 24 
                                   G++y  +G+ e+Aie+++k  +++
  gi|15668984|ref|NP_247788.1| 280 GRIYIYLGEDEKAIECFEKLKEIN 303
                                   99***************9976666 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.052        33      49      76 ..     106     133 ..     103     134 .. 0.84
   2 !   13.4   0.0   0.00011     0.071      10      74 ..     142     198 ..     134     201 .. 0.78
   3 !   27.6   0.1   4.3e-09   2.7e-06       6      75 ..     172     232 ..     169     234 .. 0.91
   4 !   27.5   0.0   4.3e-09   2.7e-06       5      71 ..     239     299 ..     235     304 .. 0.92
   5 !   17.3   0.1   6.7e-06    0.0043       3      70 ..     273     332 ..     271     334 .] 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.052
                        TPR_12  49 rnLgrlyralgryeeAlelleealaiae 76 
                                    nLg+  ++++ y eAl  +++al++ +
  gi|15668984|ref|NP_247788.1| 106 KNLGDKAYLWKAYYEALFCYNKALELNQ 133
                                   6899999999999999999999999865 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00011
                        TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   + +l++l + d A++++eka e        ++     +l++Lg  y+++ + +  ++++e++l++
  gi|15668984|ref|NP_247788.1| 142 GYALLKLYKRDLAIKYFEKASEKD-----RNN---YKALFGLGKSYYLMSDNKNSIKYFEKVLEL 198
                                   556666666789999999994444.....222...259*************************98 PP

  == domain 3  score: 27.6 bits;  conditional E-value: 4.3e-09
                        TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                   l  l+  ++ + +   +++++ek+le+      p+    +++l  Lg+ly++  + e+A++++++al+++
  gi|15668984|ref|NP_247788.1| 172 LFGLGKSYYLMSDNKNSIKYFEKVLELN-----PND---VEALEYLGELYYEE-DCEKAINYFKKALELK 232
                                   55799***********************.....875...99*********888.**************97 PP

  == domain 4  score: 27.5 bits;  conditional E-value: 4.3e-09
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                   +l ++a ++++l++y  Al+++ekal +      p+  ++ +++  +gr+y +lg+ e+A+e +e+ 
  gi|15668984|ref|NP_247788.1| 239 IL-KVAFTYFKLKKYKHALKYFEKALKLN-----PNVFELEQIYESMGRIYIYLGEDEKAIECFEKL 299
                                   45.89************************.....9999999***********************985 PP

  == domain 5  score: 17.3 bits;  conditional E-value: 6.7e-06
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlellee 70 
                                    +++  ++ ++ +lg+ ++A+e++ek  ei       +h++   ++  ++ +y++ g+ e+A e++++
  gi|15668984|ref|NP_247788.1| 273 EQIYESMGRIYIYLGEDEKAIECFEKLKEIN-----LYHYE---IYEIIALTYEEVGNIEKAKEFYKK 332
                                   568888*********************9999.....57755...8*********************97 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.35   2.3e+02       7      28 ..     142     163 ..     139     167 .. 0.84
   2 !   19.4   0.0   1.8e-06    0.0012       2      32 ..     171     201 ..     170     202 .. 0.96
   3 !   12.9   0.2   0.00021      0.14       1      31 [.     204     233 ..     204     235 .. 0.90
   4 !    9.6   0.1    0.0023       1.5       4      32 ..     240     268 ..     237     268 .. 0.93
   5 !   10.7   0.0    0.0011      0.68       6      28 ..     279     301 ..     278     303 .. 0.93
   6 !    9.3   0.0     0.003       1.9       6      27 ..     313     334 .]     310     334 .] 0.91

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.35
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                   +++++kl + d A++++e+  +
  gi|15668984|ref|NP_247788.1| 142 GYALLKLYKRDLAIKYFEKASE 163
                                   8899997799********9765 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.8e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                   Al+ l++sy+ + d  ++++++e++++  P+
  gi|15668984|ref|NP_247788.1| 171 ALFGLGKSYYLMSDNKNSIKYFEKVLELNPN 201
                                   9**********99****************98 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00021
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                         TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                   +Al +l+++y++  d +kA+ ++++ ++  P
  gi|15668984|ref|NP_247788.1| 204 EALEYLGELYYEE-DCEKAINYFKKALELKP 233
                                   6999*********.***********998655 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0023
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                                   +k a  y+kl+++  Al+++e+ +k  P+
  gi|15668984|ref|NP_247788.1| 240 LKVAFTYFKLKKYKHALKYFEKALKLNPN 268
                                   89999****99**************9997 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                   +++ y+ lg+ +kA+e +e+l +
  gi|15668984|ref|NP_247788.1| 279 MGRIYIYLGEDEKAIECFEKLKE 301
                                   79*****99***********976 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.003
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   6 lalsyrklgdtdkAlealerli 27 
                                   +al y++ g+ +kA+e +++l+
  gi|15668984|ref|NP_247788.1| 313 IALTYEEVGNIEKAKEFYKKLV 334
                                   89*****66***********96 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       6.2     4e+03      17      33 ..     118     134 ..     116     146 .. 0.78
   2 !    8.0   0.0    0.0093         6       8      43 ..     142     177 ..     135     178 .. 0.88
   3 !   16.6   0.0   1.6e-05      0.01       3      44 .]     171     212 ..     170     212 .. 0.90
   4 !    8.1   0.0    0.0082       5.2      18      38 ..     219     239 ..     214     245 .. 0.84
   5 !   11.4   0.0   0.00073      0.47       5      34 ..     240     269 ..     236     276 .. 0.86
   6 ?    4.7   0.0       0.1        66       7      27 ..     279     299 ..     273     316 .. 0.86
   7 ?    1.0   0.0       1.6     1e+03       7      27 ..     313     333 ..     308     334 .] 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 6.2
                        TPR_14  17 pdeAiallrralalaPd 33 
                                   + eA+ ++++al+l+ +
  gi|15668984|ref|NP_247788.1| 118 YYEALFCYNKALELNQN 134
                                   56899999999998755 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0093
                        TPR_14   8 aeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                   + all l + d Ai+++++a +++ ++  a++ l++
  gi|15668984|ref|NP_247788.1| 142 GYALLKLYKRDLAIKYFEKASEKDRNNYKALFGLGK 177
                                   67888899999*****************99999986 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 1.6e-05
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaql 44 
                                   al  l++ ++   d + +i++++++l+l+P+d ea+ +l++l
  gi|15668984|ref|NP_247788.1| 171 ALFGLGKSYYLMSDNKNSIKYFEKVLELNPNDVEALEYLGEL 212
                                   56678888899999999**********************986 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0082
                        TPR_14  18 deAiallrralalaPddaeaw 38 
                                   ++Ai+++++al+l Pdd ++ 
  gi|15668984|ref|NP_247788.1| 219 EKAINYFKKALELKPDDIDLI 239
                                   79**************98765 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 0.00073
                        TPR_14   5 lalaeallalGdpdeAiallrralalaPdd 34 
                                   l+ a  ++ l +++ A++++++al+l+P+ 
  gi|15668984|ref|NP_247788.1| 240 LKVAFTYFKLKKYKHALKYFEKALKLNPNV 269
                                   666778999*******************86 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.1
                        TPR_14   7 laeallalGdpdeAiallrra 27 
                                   +++++  lG+ ++Ai++++++
  gi|15668984|ref|NP_247788.1| 279 MGRIYIYLGEDEKAIECFEKL 299
                                   7999**************986 PP

  == domain 7  score: 1.0 bits;  conditional E-value: 1.6
                        TPR_14   7 laeallalGdpdeAiallrra 27 
                                   +a  +++ G+ ++A + ++++
  gi|15668984|ref|NP_247788.1| 313 IALTYEEVGNIEKAKEFYKKL 333
                                   57889***********99875 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0043       2.8       8      37 ..     152     181 ..     145     187 .. 0.87
   2 !   11.2   0.1   0.00063       0.4       7      37 ..     185     215 ..     179     217 .. 0.88
   3 !   26.3   0.1   1.2e-08   7.7e-06       1      57 [.     212     268 ..     212     271 .. 0.96
   4 !   14.9   0.0   4.6e-05     0.029       6      53 ..     251     301 ..     250     305 .. 0.84
   5 ?    1.2   0.0      0.83   5.3e+02      34      51 ..     316     333 ..     306     334 .] 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0043
                        TPR_19   8 aeAlalleqalqedpknaearllLAealla 37 
                                   + A++++e+a ++d +n  a+ +L + ++ 
  gi|15668984|ref|NP_247788.1| 152 DLAIKYFEKASEKDRNNYKALFGLGKSYYL 181
                                   569*********************998875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00063
                        TPR_19   7 yaeAlalleqalqedpknaearllLAealla 37 
                                     + ++++e++l+ +p++ ea+ +L e++++
  gi|15668984|ref|NP_247788.1| 185 NKNSIKYFEKVLELNPNDVEALEYLGELYYE 215
                                   566799***********************87 PP

  == domain 3  score: 26.3 bits;  conditional E-value: 1.2e-08
                        TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                   l++e+d + A++++++al+ +p++ ++ l  A  +++l+ ++ A +  +++++ +p+
  gi|15668984|ref|NP_247788.1| 212 LYYEEDCEKAINYFKKALELKPDDIDLILKVAFTYFKLKKYKHALKYFEKALKLNPN 268
                                   6789999*********************************************99998 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 4.6e-05
                        TPR_19   6 dyaeAlalleqalqedpknaearl...lLAeallalgqldeAealLdalpe 53 
                                   +y  Al+++e+al+ +p+  e+      + ++++ lg+ ++A+++ ++l e
  gi|15668984|ref|NP_247788.1| 251 KYKHALKYFEKALKLNPNVFELEQiyeSMGRIYIYLGEDEKAIECFEKLKE 301
                                   7999**************55555523477****************999876 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.83
                        TPR_19  34 allalgqldeAealLdal 51 
                                    + + g++++A++  ++l
  gi|15668984|ref|NP_247788.1| 316 TYEEVGNIEKAKEFYKKL 333
                                   688899******988765 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.7e-06     0.003       2      67 ..     140     202 ..     139     203 .. 0.95
   2 !   18.0   0.0   5.3e-06    0.0034      16      67 ..     188     235 ..     182     236 .. 0.94
   3 ?    7.2   0.0     0.012       7.9       7      31 ..     246     267 ..     240     271 .. 0.86
   4 ?    1.5   0.0      0.74   4.7e+02       3      59 ..     279     332 ..     278     334 .] 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.7e-06
                        TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                   ++++a+l++ + d A++++e a ++d     ++ Al++lg +++  ++ +  + ++++ l+  p++
  gi|15668984|ref|NP_247788.1| 140 KKGYALLKLYKRDLAIKYFEKASEKD---RNNYKALFGLGKSYYLMSDNKNSIKYFEKVLELNPND 202
                                   689999********************...99999***************************99987 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 5.3e-06
                        TPR_16  16 AaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                    ++++e +l+++   P ++eAl +lg+++++  + ++A+ ++++al+  pd+
  gi|15668984|ref|NP_247788.1| 188 SIKYFEKVLELN---PNDVEALEYLGELYYEE-DCEKAINYFKKALELKPDD 235
                                   5799********...*****************.*****************98 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.012
                        TPR_16   7 alragdyddAaaaleaalkrdpssP 31 
                                   ++++++y  A++++e alk++   P
  gi|15668984|ref|NP_247788.1| 246 YFKLKKYKHALKYFEKALKLN---P 267
                                   889999999999999999999...5 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.74
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyra 59 
                                   ++r+++++g+ ++A++ +e + + +     ++e +   ++ + + g+ ++A ++y++
  gi|15668984|ref|NP_247788.1| 279 MGRIYIYLGEDEKAIECFEKLKEIN---LYHYEIYEIIALTYEEVGNIEKAKEFYKK 332
                                   5788888888888998888888888...66888999999999999999998777765 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       2.9   1.9e+03       7      16 ..      56      65 ..      52      68 .. 0.80
   2 ?   -1.4   0.0       6.4   4.1e+03      15      28 ..      70      83 ..      69      89 .. 0.79
   3 ?   -1.6   0.1       7.2   4.6e+03      11      20 ..     100     109 ..      94     117 .. 0.75
   4 ?    2.7   0.7      0.31     2e+02       1      25 [.     124     147 ..     124     156 .. 0.71
   5 !   11.0   0.2   0.00072      0.46       1      28 [.     157     184 ..     157     190 .. 0.82
   6 !   21.3   0.2   3.6e-07   0.00023       1      25 [.     191     215 ..     191     221 .. 0.92
   7 !    9.9   0.1    0.0016       1.1       1      30 [.     224     253 ..     224     257 .. 0.91
   8 ?    6.3   0.1     0.022        14       1      33 [.     258     293 ..     258     294 .. 0.74
   9 ?    1.1   0.0         1   6.4e+02      13      34 .]     307     328 ..     290     328 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.9
                        TPR_17  7 eldPnnaday 16
                                  ++ Pnn+ +y
  gi|15668984|ref|NP_247788.1| 56 KNSPNNSSLY 65
                                  678***9988 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.4
                        TPR_17 15 aynnLAelllknGd 28
                                   yn L +l++ + +
  gi|15668984|ref|NP_247788.1| 70 IYNKLSTLYEDIDK 83
                                  6999***9987654 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 7.2
                        TPR_17  11 nnadaynnLA 20 
                                   +n++++ nL+
  gi|15668984|ref|NP_247788.1| 100 KNWKLWKNLG 109
                                   6788888887 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.31
                        TPR_17   1 lylkaleldPnnadaynnLAelllk 25 
                                   +y kalel+  n ++++ ++++llk
  gi|15668984|ref|NP_247788.1| 124 CYNKALELNQ-NTELLCKKGYALLK 147
                                   7999999985.56666777766665 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 0.00072
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGd 28 
                                   +++ka e+d nn +a++ L++ ++   d
  gi|15668984|ref|NP_247788.1| 157 YFEKASEKDRNNYKALFGLGKSYYLMSD 184
                                   59*******************9984433 PP

  == domain 6  score: 21.3 bits;  conditional E-value: 3.6e-07
                        TPR_17   1 lylkaleldPnnadaynnLAelllk 25 
                                   +++k+lel+Pn+++a+ +L+el+++
  gi|15668984|ref|NP_247788.1| 191 YFEKVLELNPNDVEALEYLGELYYE 215
                                   59********************984 PP

  == domain 7  score: 9.9 bits;  conditional E-value: 0.0016
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlm 30 
                                   +++kalel P++ d+    A ++ k+++++
  gi|15668984|ref|NP_247788.1| 224 YFKKALELKPDDIDLILKVAFTYFKLKKYK 253
                                   599********************9999986 PP

  == domain 8  score: 6.3 bits;  conditional E-value: 0.022
                        TPR_17   1 lylkaleldPnn...adaynnLAelllknGdlmtAr 33 
                                   +++kal+l+Pn       y  +++++  +G+ ++A+
  gi|15668984|ref|NP_247788.1| 258 YFEKALKLNPNVfelEQIYESMGRIYIYLGEDEKAI 293
                                   59*********7566667777777777777777766 PP

  == domain 9  score: 1.1 bits;  conditional E-value: 1
                        TPR_17  13 adaynnLAelllknGdlmtArq 34 
                                    + y   A ++++ G+ ++A++
  gi|15668984|ref|NP_247788.1| 307 YEIYEIIALTYEEVGNIEKAKE 328
                                   5666667889999999998875 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.52   3.3e+02       9      59 ..      79     132 ..      76     138 .. 0.79
   2 ?    5.3   0.0     0.034        22      11      44 ..     185     218 ..     178     218 .. 0.87
   3 !   24.8   0.0   2.8e-08   1.8e-05       8      61 ..     215     268 ..     214     279 .. 0.92
   4 ?    0.7   0.0      0.92   5.9e+02       8      48 ..     286     326 ..     280     328 .. 0.50

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.52
                         TPR_9   9 edweralavverllll...aPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                   ed +++l  +e +l l   + + + ++   G   + + ++ +Al++ + +l+l+
  gi|15668984|ref|NP_247788.1|  79 EDIDKLLGEIECILSLsnkDIKNWKLWKNLGDKAYLWKAYYEALFCYNKALELN 132
                                   688888888999999955555667888899999999999999999998888875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.034
                         TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGc 44 
                                   +   +++ e +l l+P+d+e +   G l+++ +c
  gi|15668984|ref|NP_247788.1| 185 NKNSIKYFEKVLELNPNDVEALEYLGELYYEEDC 218
                                   56668999********************998776 PP

  == domain 3  score: 24.8 bits;  conditional E-value: 2.8e-08
                         TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                   eed e+a+ +    l l+Pdd+++++  ++ +++l  ++ Al+ +e +l l+p+
  gi|15668984|ref|NP_247788.1| 215 EEDCEKAINYFKKALELKPDDIDLILKVAFTYFKLKKYKHALKYFEKALKLNPN 268
                                   7999***********************************************996 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.92
                         TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaA 48 
                                     + e+a+++ e l  ++  + e +   +l ++++G++++A
  gi|15668984|ref|NP_247788.1| 286 LGEDEKAIECFEKLKEINLYHYEIYEIIALTYEEVGNIEKA 326
                                   33445555555555555555544444456666666666665 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.8   1.1e-09   6.9e-07      41     248 ..      99     307 ..      91     333 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.1e-09
                        TPR_15  41 skdteyWrtladLAwalqqedearkAyrqLlasgkaraedyerliellydaepkeaarlaekgwrrfrsprlLssalelle 121
                                   +k+ + W++l+d A   + + ea   y++ l+ ++ ++   ++ ++ll+  +++ a+++ ek+ +++r+   +++ + l++
  gi|15668984|ref|NP_247788.1|  99 IKNWKLWKNLGDKAYLWKAYYEALFCYNKALELNQNTELLCKKGYALLKLYKRDLAIKYFEKASEKDRNN--YKALFGLGK 177
                                   567789********************************99999999999999999********9999875..677777777 PP

                        TPR_15 122 rakdydriaellksleeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrrae.Lr 200
                                       ++  ++ +k+ e+  +++ ++   l +++ely +e+  ++A++ +++Al+l+pd+ +l+ +  +++  l++++  L+
  gi|15668984|ref|NP_247788.1| 178 SYYLMSDNKNSIKYFEKVLELNpNDVEALEYLGELYYEED-CEKAINYFKKALELKPDDIDLILKVAFTYFKLKKYKHaLK 257
                                   77777777788888887666666889999*******9875.679******************************9998666 PP

                        TPR_15 201 ellkawkara..esdasLwgplaaAlllLgrpkkALeylrkqakenrkdp 248
                                   +  ka+k +    + +++++ ++  + +Lg+ +kA e ++k  + n   +
  gi|15668984|ref|NP_247788.1| 258 YFEKALKLNPnvFELEQIYESMGRIYIYLGEDEKAIECFEKLKEINLYHY 307
                                   6666666655889***************************9988776555 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       7.2   4.6e+03       5      30 ..      44      66 ..      41      75 .. 0.63
   2 !    9.5   9.2    0.0018       1.1       8      63 ..     154     210 ..     114     214 .. 0.78
   3 !   29.0   3.1   1.4e-09     9e-07       5      82 .]     185     262 ..     181     262 .. 0.95
   4 ?    3.0   0.4      0.18   1.2e+02      36      78 ..     286     329 ..     268     333 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 7.2
                                  HHHHHHHHHHHH.HHH--HHHHHHHH CS
                        ANAPC3  5 yknAiflaerllaaetespedayllA 30
                                  +++A  ++e +    ++sp+++ l+ 
  gi|15668984|ref|NP_247788.1| 44 IETANEISEEIS---KNSPNNSSLYD 66
                                  556666666666...66666666654 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0018
                                   HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHH CS
                        ANAPC3   8 AiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfA 63 
                                   Ai ++e++ +++++++++++ l++++yl+++ k  +++++k  +ln+++ +++  ++
  gi|15668984|ref|NP_247788.1| 154 AIKYFEKASEKDRNNYKALFGLGKSYYLMSDNKNSIKYFEKVlELNPNDVEALEYLG 210
                                   778888888888888888888888888888888888888888888888887776655 PP

  == domain 3  score: 29.0 bits;  conditional E-value: 1.4e-09
                                   HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
                        ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLekl 82 
                                    kn i ++e++l+ ++++ e++ +l++ +y+ ++ ++A+++++ka +l++ ++   +  A +++kLkky+ A++ +ek+
  gi|15668984|ref|NP_247788.1| 185 NKNSIKYFEKVLELNPNDVEALEYLGELYYE-EDCEKAINYFKKAlELKPDDIDLILKVAFTYFKLKKYKHALKYFEKA 262
                                   5899*************************97.69*****************************************9985 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.18
                                   TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                        ANAPC3  36 ngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                   +g+ ++A+e ++k+ ++n  + ++  ++A ++ + +++e+A   
  gi|15668984|ref|NP_247788.1| 286 LGEDEKAIECFEKLkEINLYHYEIYEIIALTYEEVGNIEKAKEF 329
                                   55556666666666666666666666666666666666666444 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.34   2.2e+02       9      28 ..     142     161 ..     141     164 .. 0.91
   2 ?    0.1   0.0       1.3     8e+02       8      31 ..     175     198 ..     174     199 .. 0.87
   3 ?    1.4   0.1      0.51   3.3e+02      17      30 ..     217     230 ..     204     235 .. 0.72
   4 !   10.3   0.0   0.00077      0.49       9      30 ..     243     264 ..     241     266 .. 0.92
   5 ?    2.8   0.0      0.17   1.1e+02       5      27 ..     276     298 ..     274     302 .. 0.87
   6 ?    0.6   0.0      0.91   5.8e+02       8      27 ..     313     332 ..     310     334 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.34
                        TPR_10   9 analrqrgrydeAealleea 28 
                                   + al +++++d A +++e+a
  gi|15668984|ref|NP_247788.1| 142 GYALLKLYKRDLAIKYFEKA 161
                                   678999************98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                        TPR_10   8 LanalrqrgrydeAealleealai 31 
                                   L+  ++ + + + + +++e++l++
  gi|15668984|ref|NP_247788.1| 175 LGKSYYLMSDNKNSIKYFEKVLEL 198
                                   778899999999999******985 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.51
                        TPR_10  17 rydeAealleeala 30 
                                   + ++A +++++al+
  gi|15668984|ref|NP_247788.1| 217 DCEKAINYFKKALE 230
                                   45667777777776 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00077
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   a +++++++y+ A++++e+al 
  gi|15668984|ref|NP_247788.1| 243 AFTYFKLKKYKHALKYFEKALK 264
                                   789*****************97 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.17
                        TPR_10   5 lnNLanalrqrgrydeAeallee 27 
                                   +  +++++  +g+ ++A + +e+
  gi|15668984|ref|NP_247788.1| 276 YESMGRIYIYLGEDEKAIECFEK 298
                                   66789************999997 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 0.91
                        TPR_10   8 LanalrqrgrydeAeallee 27 
                                   +a ++ ++g+ ++A +++++
  gi|15668984|ref|NP_247788.1| 313 IALTYEEVGNIEKAKEFYKK 332
                                   58899999*****9999876 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.7   2.4e+03     250     270 ..      42      64 ..      18      88 .. 0.60
   2 !    6.5   0.1    0.0056       3.6     224     288 ..     126     189 ..     117     195 .. 0.89
   3 !   12.8   0.1   6.7e-05     0.043     194     288 ..     197     293 ..     188     300 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.7
                                   -..HHHHHHHHHHHHH-TT-HHH CS
                         ChAPs 250 e..elAlevakravksaPsefkt 270
                                   +  e A e++++  k +P++++ 
  gi|15668984|ref|NP_247788.1|  42 KliETANEISEEISKNSPNNSSL 64 
                                   33344555555555555555443 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0056
                                   HHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                         ChAPs 224 neeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienAL 288
                                   n++l e ++++elL+ +   ll+  k +lA++  ++a +   +++k  + L k+Y  + d +n +
  gi|15668984|ref|NP_247788.1| 126 NKAL-ELNQNTELLCKKGYALLKLYKRDLAIKYFEKASEKDRNNYKALFGLGKSYYLMSDNKNSI 189
                                   5555.667889**************************************************9976 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 6.7e-05
                                   HHHTT-GGGHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHH...H CS
                         ChAPs 194 kLkeeepevvillarvllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefkt...W 271
                                   +L+ +++e+   l +++   d E +a++  +++le +++d +l+l  a    + kk++ Al+  ++a k+ P+ f+    +
  gi|15668984|ref|NP_247788.1| 197 ELNPNDVEALEYLGELYYEEDCE-KAINYFKKALELKPDDIDLILKVAFTYFKLKKYKHALKYFEKALKLNPNVFELeqiY 276
                                   45666677778888899888888.9****************9875444445677888****************99742237 PP

                                   HHHHHHHHHTT-HHHHH CS
                         ChAPs 272 alLvkvYikledienAL 288
                                     + ++Yi l++ e+A+
  gi|15668984|ref|NP_247788.1| 277 ESMGRIYIYLGEDEKAI 293
                                   88999***999999987 PP

>> DUF2989  Protein of unknown function (DUF2989)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.2    0.0078         5     125     172 ..     155     202 ..     147     208 .. 0.72
   2 !   15.4   0.2   1.9e-05     0.012     138     196 ..     201     255 ..     200     260 .. 0.92
   3 ?   -1.2   0.0       2.2   1.4e+03     121     164 ..     289     332 ..     271     334 .] 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0078
                       DUF2989 125 lkkflalekqgeleeaelqlalAtyylkrdaekakklllkaLelskkd 172
                                    k f ++ ++ + +   l     +yyl +d+++++k+++k+Lel+ +d
  gi|15668984|ref|NP_247788.1| 155 IKYFEKASEKDRNNYKALFGLGKSYYLMSDNKNSIKYFEKVLELNPND 202
                                   5556555555554444444444489*******************9877 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.9e-05
                       DUF2989 138 eeaelqlalAtyylkrdaekakklllkaLelskkddkvdpeillsLasiyqkqknleka 196
                                   +++e +  l+  y++ d eka+++++kaLel  +d    ++++l++a +y k+k++++a
  gi|15668984|ref|NP_247788.1| 201 NDVEALEYLGELYYEEDCEKAINYFKKALELKPDD----IDLILKVAFTYFKLKKYKHA 255
                                   57888999***********************9988....999*************9998 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.2
                       DUF2989 121 dqeAlkkflalekqgeleeaelqlalAtyylkr.daekakklllk 164
                                   d++A + f +l+ + +l + e+   +A  y +  + ekak+ ++k
  gi|15668984|ref|NP_247788.1| 289 DEKAIECFEKLK-EINLYHYEIYEIIALTYEEVgNIEKAKEFYKK 332
                                   677777776664.56677888888888888776355777777766 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.17   1.1e+02       7      49 ..     154     196 ..     149     202 .. 0.83
   2 ?    3.8   0.0      0.12        74       5      42 ..     186     222 ..     182     227 .. 0.80
   3 !   10.3   0.0    0.0011      0.68       8      54 ..     222     268 ..     215     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.17
                        TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleil 49 
                                    ++ +e+a +++ ++++a + l + ++  ++++ +++ + ++l
  gi|15668984|ref|NP_247788.1| 154 AIKYFEKASEKDRNNYKALFGLGKSYYLMSDNKNSIKYFEKVL 196
                                   567789999*********************9999987766665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.12
                        TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAl 42 
                                   + +++ +e+ l+ np+d++a   l ++++++ + e+A+
  gi|15668984|ref|NP_247788.1| 186 KNSIKYFEKVLELNPNDVEALEYLGELYYEE-DCEKAI 222
                                   5678889999***********9999999864.556665 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0011
                        TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                   +  +++al+ +pdd+d+ l++A  +++ ++y+ Al+ + + lk + +
  gi|15668984|ref|NP_247788.1| 222 INYFKKALELKPDDIDLILKVAFTYFKLKKYKHALKYFEKALKLNPN 268
                                   6668899****************************988888877665 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.5     0.076        48      19      33 ..     117     131 ..     115     134 .. 0.90
   2 ?    1.3   0.1      0.58   3.7e+02       4      19 ..     154     168 ..     147     172 .. 0.76
   3 ?   -0.0   0.0       1.5   9.5e+02      28      49 ..     186     206 ..     186     216 .. 0.72
   4 ?    3.6   0.1      0.11        70      21      33 ..     219     231 ..     211     248 .. 0.67
   5 !    9.8   0.1    0.0013      0.81      24      41 ..     249     267 ..     249     280 .. 0.80
   6 ?    3.0   0.1      0.17   1.1e+02      11      29 ..     314     332 ..     313     332 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.076
                           MIT  19 nyeeAlelYkealel 33 
                                    y eAl +Y +alel
  gi|15668984|ref|NP_247788.1| 117 AYYEALFCYNKALEL 131
                                   799**********97 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.58
                           MIT   4 AlelvkkAveeDnagn 19 
                                   A+++++kA e+D++ n
  gi|15668984|ref|NP_247788.1| 154 AIKYFEKASEKDRN-N 168
                                   88888888888874.3 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.5
                           MIT  28 kealelLlqalkekneerrell 49 
                                   k++++++ ++l   n+++ e+l
  gi|15668984|ref|NP_247788.1| 186 KNSIKYFEKVLE-LNPNDVEAL 206
                                   689999999997.455555554 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.11
                           MIT  21 eeAlelYkealel 33 
                                   e+A++++k+alel
  gi|15668984|ref|NP_247788.1| 219 EKAINYFKKALEL 231
                                   5555555555543 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.0013
                           MIT  24 lelYkealelLlqalk.ek 41 
                                   l++Yk+al+++ +alk + 
  gi|15668984|ref|NP_247788.1| 249 LKKYKHALKYFEKALKlNP 267
                                   689************9443 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.17
                           MIT  11 AveeDnagnyeeAlelYke 29 
                                   A  +++ gn+e+A e Yk+
  gi|15668984|ref|NP_247788.1| 314 ALTYEEVGNIEKAKEFYKK 332
                                   7889*************96 PP

>> CAMP_factor  CAMP factor (Cfa)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   3.8e-05     0.024      35      79 ..      36      80 ..       8      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-05
                   CAMP_factor 35 yekeiekllktakelkealeaiakgkvtlydlksIlaRvellvdi 79
                                  + +ei+kl++ta+e++e++++ + ++ +lydl  I  +   l + 
  gi|15668984|ref|NP_247788.1| 36 LIDEIDKLIETANEISEEISKNSPNNSSLYDLRLIYNKLSTLYED 80
                                  579********************************9988777665 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.26   1.7e+02      11      38 ..     179     206 ..     169     209 .. 0.81
   2 ?   -0.9   0.0       2.8   1.8e+03      18      33 ..     219     234 ..     216     238 .. 0.87
   3 ?   15.4   0.4   2.3e-05     0.015       7      33 ..     242     268 ..     236     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.26
                                   HHHHT-HHHHHHHHHHHHHHTTS-HHHH CS
                    Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPenrQaq 38 
                                   +y + + +++ +y + +Le+ P+   a+
  gi|15668984|ref|NP_247788.1| 179 YYLMSDNKNSIKYFEKVLELNPNDVEAL 206
                                   7778888999************987775 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.8
                                   HHHHHHHHHHHHHTTS CS
                    Fis1_TPR_C  18 seArryvdalLeiEPe 33 
                                   ++A +y +  Le+ P+
  gi|15668984|ref|NP_247788.1| 219 EKAINYFKKALELKPD 234
                                   68999*******9998 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHHT-HHHHHHHHHHHHHHTTS CS
                    Fis1_TPR_C   7 lAlGhyklgeYseArryvdalLeiEPe 33 
                                   +A+ ++kl++Y+ A++y +  L++ P+
  gi|15668984|ref|NP_247788.1| 242 VAFTYFKLKKYKHALKYFEKALKLNPN 268
                                   58889*******************997 PP

>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       3.9   2.5e+03      25      36 ..     120     131 ..     117     132 .. 0.85
   2 ?    8.3   0.2    0.0062       3.9      24      36 ..     152     164 ..     141     165 .. 0.87
   3 ?    0.2   0.1       2.2   1.4e+03      22      32 ..     184     194 ..     170     209 .. 0.61
   4 ?    8.9   0.3    0.0039       2.5      16      36 ..     210     231 ..     203     232 .. 0.78
   5 ?    6.0   0.1     0.033        21      23      36 ..     252     265 ..     247     267 .. 0.84
   6 ?    0.6   0.0       1.6     1e+03      24      32 ..     290     298 ..     279     299 .. 0.88
   7 ?    0.1   0.0       2.3   1.5e+03      22      32 ..     322     332 ..     316     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.9
                          Sel1  25 kAiewyekAAeq 36 
                                   +A+ +y kA e+
  gi|15668984|ref|NP_247788.1| 120 EALFCYNKALEL 131
                                   7999*****987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0062
                          Sel1  24 ekAiewyekAAeq 36 
                                   ++Ai+++ekA e+
  gi|15668984|ref|NP_247788.1| 152 DLAIKYFEKASEK 164
                                   68********997 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 2.2
                          Sel1  22 DpekAiewyek 32 
                                   D +  i+++ek
  gi|15668984|ref|NP_247788.1| 184 DNKNSIKYFEK 194
                                   44555666665 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0039
                          Sel1  16 Glg.vpkDpekAiewyekAAeq 36 
                                   G    + D ekAi +++kA e+
  gi|15668984|ref|NP_247788.1| 210 GELyYEEDCEKAINYFKKALEL 231
                                   443377899**********886 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.033
                          Sel1  23 pekAiewyekAAeq 36 
                                   ++ A++++ekA ++
  gi|15668984|ref|NP_247788.1| 252 YKHALKYFEKALKL 265
                                   567********987 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 1.6
                          Sel1  24 ekAiewyek 32 
                                   ekAie++ek
  gi|15668984|ref|NP_247788.1| 290 EKAIECFEK 298
                                   799**9998 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 2.3
                          Sel1  22 DpekAiewyek 32 
                                   ++ekA e+y+k
  gi|15668984|ref|NP_247788.1| 322 NIEKAKEFYKK 332
                                   89*******98 PP

>> SusD-like_3  Starch-binding associating with outer membrane
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.7   0.00015     0.095      55     112 ..      93     145 ..      32     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                   SusD-like_3  55 qslyseqeawedvtstaatktnlWsnlYkvIfdaNivLeelekekaeeelkqvkGeAl 112
                                   + ++++++ w+ +++   +k +lW+++Y+++f+ N +Le     + ++el   kG+Al
  gi|15668984|ref|NP_247788.1|  93 SLSNKDIKNWKLWKN-LGDKAYLWKAYYEALFCYNKALELN---Q-NTELLCKKGYAL 145
                                   445666666666666.4889999****************92...2.234555555555 PP

>> UPF0154  Uncharacterised protein family (UPF0154)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.9   1.2e+03      17      28 ..     189     200 ..     187     206 .. 0.86
   2 ?    8.5   0.0    0.0032         2      16      44 ..     255     281 ..     252     282 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.9
                       UPF0154  17 rkymkkqlkenP 28 
                                    ky++k l+ nP
  gi|15668984|ref|NP_247788.1| 189 IKYFEKVLELNP 200
                                   59******9998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0032
                       UPF0154  16 arkymkkqlkenPpinekmirammkqmGr 44 
                                   a ky++k lk nP + e  + +++++mGr
  gi|15668984|ref|NP_247788.1| 255 ALKYFEKALKLNPNVFE--LEQIYESMGR 281
                                   679*********97766..9999*****8 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       2.1   1.4e+03      15      27 ..     217     229 ..     215     232 .. 0.78
   2 ?    3.9   0.1      0.11        73      10      27 ..     246     263 ..     245     266 .. 0.87
   3 ?    6.8   0.2     0.014       9.1       3      30 ..     276     303 ..     275     304 .. 0.84
   4 ?    3.2   0.1       0.2   1.3e+02      13      26 ..     320     333 ..     317     334 .] 0.85

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 2.1
                           PPR  15 kleeAlelfkeMk 27 
                                   ++e+A+ +fk+ +
  gi|15668984|ref|NP_247788.1| 217 DCEKAINYFKKAL 229
                                   7899999999855 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.11
                           PPR  10 ycknGkleeAlelfkeMk 27 
                                   y k  k++ Al++f++ +
  gi|15668984|ref|NP_247788.1| 246 YFKLKKYKHALKYFEKAL 263
                                   8999**********9865 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.014
                           PPR   3 ynslIsgycknGkleeAlelfkeMkekG 30 
                                   y s+ + y   G+ e+A+e+f+++ke +
  gi|15668984|ref|NP_247788.1| 276 YESMGRIYIYLGEDEKAIECFEKLKEIN 303
                                   55777888889999**********9976 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.2
                           PPR  13 nGkleeAlelfkeM 26 
                                    G++e+A+e++k++
  gi|15668984|ref|NP_247788.1| 320 VGNIEKAKEFYKKL 333
                                   69*********986 PP

>> Pup  Pup-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3     0.091        58      40      55 ..      33      48 ..      18      58 .. 0.77
   2 ?    5.6   0.1     0.047        30      34      51 ..      75      92 ..      60      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.091
                           Pup 40 vDdlLDeIDevLEeNA 55
                                  +  l+DeID+++E+  
  gi|15668984|ref|NP_247788.1| 33 TEMLIDEIDKLIETAN 48
                                  5678999999999754 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.047
                           Pup 34 eelsedvDdlLDeIDevL 51
                                    l ed+D lL eI  +L
  gi|15668984|ref|NP_247788.1| 75 STLYEDIDKLLGEIECIL 92
                                  5688**********9888 PP

>> NBD94  Nucleotide-Binding Domain 94 of RH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   2.9      0.18   1.1e+02      56      89 ..      22      55 ..       4      61 .. 0.58
   2 ?    5.3   0.1     0.042        27      12      32 ..      72      92 ..      66     106 .. 0.77
   3 ?    3.8   3.2      0.12        75       3      48 ..     261     306 ..     259     333 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.18
                         NBD94 56 lvqkIdeekkkaenlieeiekyienideikkkls 89
                                  l +++   k+ +e+li+ei+k ie  +ei +++s
  gi|15668984|ref|NP_247788.1| 22 LKNRLKIGKELTEMLIDEIDKLIETANEISEEIS 55
                                  3334444455555666666666665555555444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.042
                         NBD94 12 dkkkkiyeniekllnEleeie 32
                                  +k+ ++ye+i+kll E+e i 
  gi|15668984|ref|NP_247788.1| 72 NKLSTLYEDIDKLLGEIECIL 92
                                  788899**********99874 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.12
                         NBD94   3 KtknivtkidkkkkiyeniekllnEleeiekektsleevknielsY 48 
                                   K  +++ ++ ++++iye +  ++  l e ek     e++k+i+l  
  gi|15668984|ref|NP_247788.1| 261 KALKLNPNVFELEQIYESMGRIYIYLGEDEKAIECFEKLKEINLYH 306
                                   5666777778899999999999999999999999999999999854 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.4     0.023        15      81     117 ..      21      57 ..      19      60 .. 0.90
   2 ?    4.1   0.1     0.063        40      59      88 ..     169     198 ..     153     208 .. 0.83
   3 ?    3.7   0.2     0.085        54      69      87 ..     212     230 ..     209     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.023
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  81 llkkkleelekqlekleeeleklkdqittleanlaql 117
                                   +lk++l+  ++  e l +e++kl ++++++ ++++++
  gi|15668984|ref|NP_247788.1|  21 VLKNRLKIGKELTEMLIDEIDKLIETANEISEEISKN 57 
                                   6899999999999******************999876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.063
                                   TEEEEEEETTEEEEEEHHHHHHHHHHHHHH CS
                     Prefoldin  59 dkvlvdlGagyyveksleeAiellkkklee 88 
                                    k+l  lG++yy+  + +++i++++k le 
  gi|15668984|ref|NP_247788.1| 169 YKALFGLGKSYYLMSDNKNSIKYFEKVLEL 198
                                   468999******************998775 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.085
                                   EEEEEEHHHHHHHHHHHHH CS
                     Prefoldin  69 yyveksleeAiellkkkle 87 
                                    y e ++e+Ai ++kk le
  gi|15668984|ref|NP_247788.1| 212 LYYEEDCEKAINYFKKALE 230
                                   699************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1381  (0.077026); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.64u 0.24s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2217.57
//
Query:       gi|15668985|ref|NP_247789.1|  [L=296]
Description: phosphoribosylformylglycinamidine cyclo-ligase PurM [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-10   40.8   0.1    4.2e-10   40.1   0.1    1.3  1  AIRS      AIR synthase related protein, N-terminal domain
    3.4e-10   40.2   0.0    1.9e-09   37.8   0.0    2.2  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.1   4.7e-14   4.2e-10      24      93 ..      66     140 ..      44     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 4.7e-14
                                   HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC...HHHHHHHHHHHHHHHTT-EEEEEEEEEESS..EEEEEEEEEE CS
                          AIRS  24 iGakavavnlsDlaamGArPlalllslalp...wleevvrglaeaaeelgvplvgGdtsfsne..ptisvtavGl 93 
                                    +++a+ +++ D++amGA+P ++l+++  +   +++ +v+gl++    l++p++gG+t+  +e    isv+++G+
  gi|15668985|ref|NP_247789.1|  66 GAKTALIHTACDVVAMGAEPKFALNAIQAKnedEIKLAVDGLRKQSIGLNIPIIGGNTQTVEElkSCISVAVFGE 140
                                   5899*****************99*************************************999888899999996 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   2.2e-13   1.9e-09      45     152 ..     178     273 ..     148     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.2e-13
                                   HHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHH CS
                        AIRS_C  45 ptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdelesplemllsensGrllvavppeead 125
                                   +++ + ++++ +++ +++a++D ++GG lg+l em+ +++ gaei +   p             + + G +++avp+ee +
  gi|15668985|ref|NP_247789.1| 178 KKKFDTYLEILENGIKINACKDASRGGWLGNLLEMLIKAKKGAEIKSL--PYPRA---------TRYLGTYIIAVPEEEYE 247
                                   555555555555599*********************************..55554.........4689************* PP

                                   HHHHHHHHTTCCCEEEEEEEEESSSEE CS
                        AIRS_C 126 avlaileeeglpeaavIGevtakeels 152
                                   +v++i+ +  +p +   G++ +k++l 
  gi|15668985|ref|NP_247789.1| 248 KVVDIALKNKCP-VVLFGRILEKPKLI 273
                                   ***********7.99******999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 2191.19
//
Query:       gi|15668986|ref|NP_247790.1|  [L=415]
Description: (R)-2-hydroxyglutaryl-CoA dehydratase activator [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-65  221.9   7.2    1.4e-65  221.5   7.2    1.2  1  BcrAD_BadFG    BadF/BadG/BcrA/BcrD ATPase family
     0.0027   17.4   0.0       0.42   10.3   0.0    2.4  2  Peptidase_M22  Glycoprotease family
  ------ inclusion threshold ------
       0.01   16.2   2.0       0.23   11.9   2.0    2.6  1  FtsA           Cell division protein FtsA
      0.096   12.2   0.3        6.6    6.2   0.0    2.3  2  FGGY_N         FGGY family of carbohydrate kinases, N-termina
       0.86    9.3   8.5       0.14   11.9   1.6    2.6  3  Hydant_A_N     Hydantoinase/oxoprolinase N-terminal region


Domain annotation for each model (and alignments):
>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.5   7.2   3.8e-69   1.4e-65       1     266 [.     151     404 ..     151     405 .. 0.99

  Alignments for each domain:
  == domain 1  score: 221.5 bits;  conditional E-value: 3.8e-69
                                   EEEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCTCTTB CS
                   BcrAD_BadFG   1 vGiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratlpekf 81 
                                   +GiD+GsTttkav+m +++   + +i + + +es++         ea+++al++ag + +++e++  ++tgyGr t++e f
  gi|15668986|ref|NP_247790.1| 151 LGIDSGSTTTKAVVMIDDEVAGTGWIYTKDVIESAK---------EAVNNALKEAGISLDQVETI--GTTGYGRYTVGEYF 220
                                   8*****************9999***********887.........9*****************99..************** PP

                                   SEEE-..HHHHHHHHHHHH-TT--...EEEEEETTEEEEEEEETTEEEEEEEESS--TTSHHHHHHHHHHHT--TTTHHHH CS
                   BcrAD_BadFG  82 ekeiirseilvhgdGavalypgtr...tvldigGqdskgiqidkgkvenfqmndrcaageGrylgiiadelnmglreldgl 159
                                   +++ i++e++v+++Ga +l+++++   tv+digG+d+k+i + + +++ f+m++ ca+ +Gr+++i+a++l+++l+el++l
  gi|15668986|ref|NP_247790.1| 221 KADLIQEELTVNSKGAAYLADKQEgeaTVIDIGGMDNKAISLYDAIPDGFTMGGICAGASGRFFEITARRLGVSLQELGEL 301
                                   ********************************************************************************* PP

                                   HTT--.S-------SHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG-HHHHHHH... CS
                   BcrAD_BadFG 160 aekat.kkarinstcavfaeaelrdalsggekaedIlaglhraialrvialisrsggvtdevtltGGvakneaavkelrkl 239
                                   a+k++ +k+++ns+c vf  ++l++al++g+kaed+ a +++++a++v +++ ++ +v+d v+l+GG +  +++v ++   
  gi|15668986|ref|NP_247790.1| 302 AAKGDwRKIKMNSYCIVFGIQDLVTALAEGAKAEDVAAAAAHSVAEQVFEQQLQEVDVRDPVILVGGSSLLKGLVIAM--- 379
                                   *****999**********************************************************************... PP

                                   ..HHHH-S-EE--GGGGGHHHHHHHHH CS
                   BcrAD_BadFG 240 vkenygevkininpdsiytgalGAalf 266
                                     e++++ ki ++++s+  ga+GAal+
  gi|15668986|ref|NP_247790.1| 380 --EEVLGRKIIVPRYSQLIGAVGAALL 404
                                   ..999999*****************97 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0061        22      31      57 ..     183     209 ..     177     211 .. 0.88
   2 !   10.3   0.0   0.00012      0.42     143     263 ..     286     394 ..     268     402 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0061
                                   HHHHHHHHHHHHHHTSTGGGEEEEEEE CS
                 Peptidase_M22  31 erllplieealaeaglsledldaIavt 57 
                                   e   +++++al+eag+sl++++ I  t
  gi|15668986|ref|NP_247790.1| 183 ESAKEAVNNALKEAGISLDQVETIGTT 209
                                   667889****************99876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00012
                                   HHHHHHT..SSCCHHHHHHHCTC..S.......EETTEEE.CHHHHHHHHHHST.THHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Peptidase_M22 143 kvarllglpypggpkieklakeg..kkiefprplkgldfsfsGlktavlkelek.evedlaasfqeavvdhlvekteralk 220
                                    +ar lg++ +   ++ +la +g  +ki+     ++  ++  G++  v+ ++e  ++ed+aa+  ++v+++   + e+ l+
  gi|15668986|ref|NP_247790.1| 286 ITARRLGVSLQ---ELGELAAKGdwRKIK-----MNSYCIVFGIQDLVTALAEGaKAEDVAAAAAHSVAEQ---VFEQQLQ 355
                                   56666655553...456788888677777.....44446777888778777744469*********98887...5666678 PP

                                   HCTBSEEEEESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHS CS
                 Peptidase_M22 221 lpkakelvilGGvaankrLrealeeeaeelglkliiPplkyct 263
                                   + ++++ vil  v++ ++L+  + +++e lg k+i+P+  y +
  gi|15668986|ref|NP_247790.1| 356 EVDVRDPVIL--VGGSSLLKGLVIAMEEVLGRKIIVPR--YSQ 394
                                   8999999999..88888888777766666999999999..765 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.0   6.4e-05      0.23       2      99 ..     152     393 ..     151     399 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-05
                                   EEEE-SSSEEEEEEETTEEEEEEEES--HHHHHHHHHHHHT--HHHHHHHHHHH--S--...................EEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................xxx RF
                          FtsA   2 lvDiGagktdvavaedgalvhlrvigvggngitkdiakalrtaveeAerikikyGsala...................eke 63 
                                   ++D G+++t+++v+ d++++ +  i       tkd+ ++ ++av++A + +   G  l                    +  
  gi|15668986|ref|NP_247790.1| 152 GIDSGSTTTKAVVMIDDEVAGTGWI------YTKDVIESAKEAVNNALKEA---GISLDqvetigttgygrytvgeyfK-- 221
                                   79**************877776555......45555555555555555555...3322233333333333333355551.. PP

                                   EEHHHHH.......................................................................... CS
                                   xxxxxxx.......................................................................... RF
                          FtsA  64 igrkels.......................................................................... 70 
                                         +                                                                          
  gi|15668986|ref|NP_247790.1| 222 ------Adliqeeltvnskgaayladkqegeatvidiggmdnkaislydaipdgftmggicagasgrffeitarrlgvslq 296
                                   ......033334444666666677777777777778889999999999999999999999999999999999999999999 PP

                                   .......................................................................GGGGSTTHHH CS
                                   .......................................................................xxxxxxxxxx RF
                          FtsA  71 .......................................................................ggsalpnlee 80 
                                                                                                          g+s l++l+ 
  gi|15668986|ref|NP_247790.1| 297 elgelaakgdwrkikmnsycivfgiqdlvtalaegakaedvaaaaahsvaeqvfeqqlqevdvrdpvilvgGSSLLKGLVI 377
                                   999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                   HHHHHH.T-..HHHT-GGGH CS
                                   xxxxxx.xxxxxxxxxxxxx RF
                          FtsA  81 laeral.spkleevsdpeya 99 
                                   ++e++l +    ++  p+y+
  gi|15668986|ref|NP_247790.1| 378 AMEEVLgR----KIIVPRYS 393
                                   99999731....24445555 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2      0.01        37       2      17 ..     150     165 ..     149     173 .. 0.87
   2 ?    6.2   0.0    0.0019       6.6      47      82 ..     180     215 ..     176     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.01
                                   EEEEEEESSEEEEEEE CS
                        FGGY_N   2 ilglDcGttstkaivl 17 
                                    lg+D G t tka+v+
  gi|15668986|ref|NP_247790.1| 150 SLGIDSGSTTTKAVVM 165
                                   59************97 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0019
                                   HHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS-E CS
                        FGGY_N  47 eiwqalaeairkvleqagisekqikaIgisgqregl 82 
                                    ++++  ea++++l++agis +q++ Ig +g +  +
  gi|15668986|ref|NP_247790.1| 180 DVIESAKEAVNNALKEAGISLDQVETIGTTGYGRYT 215
                                   57889999**********************988655 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.97   3.5e+03     138     168 ..      94     124 ..      76     134 .. 0.66
   2 ?   11.9   1.6   3.8e-05      0.14       2      65 ..     151     209 ..     150     211 .. 0.83
   3 ?    0.6   0.2      0.11   3.9e+02     147     172 ..     331     356 ..     320     359 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.97
                    Hydant_A_N 138 vrealkalkaagvesiavvllhSylnpehEl 168
                                   vr+++++l +++ +  +v++ +  +  ++El
  gi|15668986|ref|NP_247790.1|  94 VRNEVRKLIQQNTNLPVVMYSFTERTKASEL 124
                                   4555555555555555555555555555554 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.8e-05
                    Hydant_A_N   2 igIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTT 65 
                                   +gID G+T T av++ ++ e+  +  + ++  +v+e  +ea++++l+e++++ ++++++  GTT
  gi|15668986|ref|NP_247790.1| 151 LGIDSGSTTTKAVVMIDD-EVAGTGWIYTK--DVIESAKEAVNNALKEAGISLDQVETI--GTT 209
                                   79**************66.65555555555..****************99999988875..665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.11
                    Hydant_A_N 147 aagvesiavvllhSylnpehElrvae 172
                                    a++e +a + +hS++    E++ +e
  gi|15668986|ref|NP_247790.1| 331 GAKAEDVAAAAAHSVAEQVFEQQLQE 356
                                   344566899999*******9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      712  (0.0397122); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2556.11
//
Query:       gi|15668987|ref|NP_247791.1|  [L=379]
Description: hypothetical protein MJ_0801 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-91  303.8   7.5    9.6e-91  303.8   7.5    1.6  2  ATPase_2  ATPase domain predominantly from Archaea
    2.2e-10   40.7   6.2    5.1e-05   23.3   0.2    3.0  3  AAA_14    AAA domain
    2.9e-09   37.5   0.0    5.8e-09   36.6   0.0    1.6  2  AAA_16    AAA ATPase domain
    9.7e-05   21.4   0.1      0.032   13.1   0.0    2.7  2  AAA_35    AAA-like domain
    0.00016   22.1   0.1       0.02   15.3   0.0    2.9  2  AAA       ATPase family associated with various cellular acti
     0.0036   17.6   0.0       0.03   14.6   0.0    2.5  1  AAA_22    AAA domain
     0.0083   15.7   0.0      0.017   14.7   0.0    1.5  1  AAA_7     P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.019   14.6   0.0      0.047   13.3   0.0    1.7  2  cobW      CobW/HypB/UreG, nucleotide-binding domain
      0.051   13.6   0.0      0.099   12.6   0.0    1.5  1  TsaE      Threonylcarbamoyl adenosine biosynthesis protein Ts
       0.06   13.2   0.1       0.16   11.8   0.0    1.9  2  TK        Thymidine kinase


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.8   7.5   5.4e-94   9.6e-91       1     233 []       3     271 ..       3     271 .. 0.98
   2 ?   -1.7   0.3       1.3   2.3e+03      87     112 ..     308     333 ..     273     344 .. 0.42

  Alignments for each domain:
  == domain 1  score: 303.8 bits;  conditional E-value: 5.4e-94
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...eeeekkkl 78 
                                   FfdRe+e++e+++il+rep++iyfiYGp +sGKtaL+k+iien+++ d+y+++yi++r++ is+++efie   ++++++++
  gi|15668987|ref|NP_247791.1|   3 FFDREREINEILHILNREPDDIYFIYGPLNSGKTALIKHIIENKLS-DDYKVFYINFRTYLISEKREFIEaifTTKKDDFF 82 
                                   9*******************************************77.668***********************99999999 PP

                      ATPase_2  79 ekal.................giavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlgln...... 136
                                   ek +                 gi++p++e++++++ek++++f+++++ll ++kk+gkk+i+i+Delq+++d+ ln      
  gi|15668987|ref|NP_247791.1|  83 EKIKdkdevlnlitkgvriltGIPIPEVEFDKLFEEKINDAFQYLNSLLLEVKKSGKKPILIFDELQMIKDVVLNtenqrf 163
                                   9999***************************************************************************** PP

                      ATPase_2 137 ..........gaellvkeLlnliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfke 207
                                             g+++l+keL+++++sltke+hlc+v+clsS++lfie+vy+++elegr+ky+lvdd+dketal+f+++++ e
  gi|15668987|ref|NP_247791.1| 164 safpslrfgnGQKYLLKELFQFLVSLTKEQHLCHVFCLSSDSLFIEYVYSTGELEGRAKYLLVDDFDKETALKFMDFLAVE 244
                                   ********************************************************************************* PP

                      ATPase_2 208 l.eelskedfeeiyryvGGkPkalvel 233
                                   + ++l++ed+e+iy+yvGGkPk+++++
  gi|15668987|ref|NP_247791.1| 245 NnINLTNEDKELIYSYVGGKPKDIKYV 271
                                   *9**********************986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                      ATPase_2  87 pkaeleeilkeksklvfkaielllek 112
                                   + + ++e+++ k+ +v +a++l++++
  gi|15668987|ref|NP_247791.1| 308 KVDVGDEVIEIKKDNVIEALKLFKDE 333
                                   22223344444444444444444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.2   2.8e-08   5.1e-05       3      59 ..      23      77 ..      21      97 .. 0.77
   2 !   19.4   0.1   4.5e-07    0.0008      35     120 ..     109     224 ..      94     235 .. 0.83
   3 ?   -0.4   0.2      0.63   1.1e+03      55      79 ..     286     298 ..     236     338 .. 0.54

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.8e-08
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek 59
                                   i++i G+  +GKT l+k++i+++l ++ +++yin+ +   ++++++  ++ ++  k
  gi|15668987|ref|NP_247791.1| 23 DIYFIYGPLNSGKTALIKHIIENKLSDDYKVFYINFRTYLISEKREF--IEAIFTTK 77
                                  5899*********************9************999888866..33333332 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 4.5e-07
                        AAA_14  35 yinldderdkklad.pekllelileklkeekktylflDEiqev............................pewekalksl 86 
                                   ++++d+  ++k++d ++ l++l+le  k+ kk +l++DE q++                            +e++++l sl
  gi|15668987|ref|NP_247791.1| 109 EVEFDKLFEEKINDaFQYLNSLLLEVKKSGKKPILIFDELQMIkdvvlntenqrfsafpslrfgngqkyllKELFQFLVSL 189
                                   6777777676666425556677777534469999*********************************************** PP

                        AAA_14  87 vdegknldvivtGSnskllskeiat.slagrvaei 120
                                    +e++ ++v++  S s+++    +t +l gr++++
  gi|15668987|ref|NP_247791.1| 190 TKEQHLCHVFCLSSDSLFIEYVYSTgELEGRAKYL 224
                                   ****99***********998855543788888766 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.63
                        AAA_14  55 lileklkeekktylflDEiqevpew 79 
                                   +            ++ D +q+++ +
  gi|15668987|ref|NP_247791.1| 286 F------------MLKDAVQKLDMF 298
                                   1............222222222222 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   3.2e-12   5.8e-09       1     152 [.       2     156 ..       2     198 .. 0.81
   2 ?   -3.1   0.0       5.1   9.1e+03     138     146 ..     223     231 ..     206     245 .. 0.74

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 3.2e-12
                        AAA_16   1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellr.alekdg.giflrgkcdqlesaipysalaqalare 79 
                                   +++ Re+e++++l++l+r  +    + +++G+  +GK++l++++ +  l++d+ +++++ ++   +++++++  + + +++
  gi|15668987|ref|NP_247791.1|   2 KFFDREREINEILHILNREPD---DIYFIYGPLNSGKTALIKHIIEnKLSDDYkVFYINFRTYLISEKREFIEAIFTTKKD 79 
                                   5899************95444...69***************9999746777753555777777779999998877777799 PP

                        AAA_16  80 ellrqlldeaesaeleawrekleealaavpelagaea.....srllellkrllallsrderplvlvlDdlqwadeasl 152
                                   +++++++d++e  +l     ++++ +  +pe++ ++      ++ ++ l++ll   ++ +++ +l++D+lq +++  l
  gi|15668987|ref|NP_247791.1|  80 DFFEKIKDKDEVLNLITKGVRILTGIP-IPEVEFDKLfeekiNDAFQYLNSLLLEVKKSGKKPILIFDELQMIKDVVL 156
                                   999999999888888888888888887.7888888878877799999999999666666888*********7776444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.1
                        AAA_16 138 vlvlDdlqw 146
                                   +l++Dd+++
  gi|15668987|ref|NP_247791.1| 223 YLLVDDFDK 231
                                   789999994 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   1.8e-05     0.032      35      69 ..      26      60 ..       4     161 .. 0.82
   2 !    5.3   0.0    0.0041       7.3     209     273 ..     241     307 ..     229     333 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                        AAA_35 35 rikapkkmGKtSLlarilakakqqgyktvsldlql 69
                                   i +p + GKt L+++i++++ + +yk++++++++
  gi|15668987|ref|NP_247791.1| 26 FIYGPLNSGKTALIKHIIENKLSDDYKVFYINFRT 60
                                  68899****************************86 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0041
                        AAA_35 209 LaqryglelsekqleqLmslvgGhPylvrlalyhlaqeelt..leelleeaateegiYsdhLrrllv 273
                                   La + +++l++++ e ++s vgG+P  ++  +++ + ++l   le +l++a ++ +++ d L+    
  gi|15668987|ref|NP_247791.1| 241 LAVENNINLTNEDKELIYSYVGGKPKDIKYVVEESKFKDLReiLEFMLKDAVQKLDMFLDMLNYSKP 307
                                   788899999*********************999988886655599999****999999999987655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05      0.02       3      70 ..      27     151 ..      25     165 .. 0.60
   2 ?   -1.8   0.0       2.2     4e+03      33      56 ..     255     278 ..     241     294 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                   EESSTTSSHHHHHHHHHHH.H..THEEEEEETTTCS.SS.......................................... CS
                           AAA   3 lyGppGtGKTllakavake.l..gvefleisgsell.sk.......................................... 37 
                                   +yGp   GKT+l+k ++++ l  + +++ i+  + l s+                                          
  gi|15668987|ref|NP_247791.1|  27 IYGPLNSGKTALIKHIIENkLsdDYKVFYINFRTYLiSEkrefieaifttkkddffekikdkdevlnlitkgvriltgipi 107
                                   8****************9953332444444444443222233444444444444444577777777777777777777777 PP

                                   ....STTHHHHHHHHHHHHHHHTS.......TSEEEEEETGGGH CS
                           AAA  38 ....yvgesekkirelfkeakeka.......kpsilfiDEidal 70 
                                       + +  e+ki++ f+ + +         k+ il++DE+  +
  gi|15668987|ref|NP_247791.1| 108 peveFDKLFEEKINDAFQYLNSLLlevkksgKKPILIFDELQMI 151
                                   77775555555555555555333333334446789999988765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                                   TCSSSSTTHHHHHHHHHHHHHHHT CS
                           AAA  33 ellskyvgesekkirelfkeakek 56 
                                   el+ +yvg ++k+i+ +++e k k
  gi|15668987|ref|NP_247791.1| 255 ELIYSYVGGKPKDIKYVVEESKFK 278
                                   555679999999999999887655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.7e-05      0.03       5     111 ..      22     158 ..      18     206 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka............. 70 
                                   + i +++G+  +GKT l++ + e++  +      + +v++++       + +++ ++++   +++  +             
  gi|15668987|ref|NP_247791.1|  22 DDIYFIYGPLNSGKTALIKHIIENKLSD------DYKVFYINFRTYLisEKREFIEAIFTTKKDDFFEkikdkdevlnlit 96 
                                   67899******************99655......33444444333333344444444444444333334555555555567 PP

                        AAA_22  71 ......................erlsseell.ealeqalrarav...ielliiDEaqhlrseealee 111
                                                         + ++  ++l ++l +      +   +++li DE q + ++ +l++
  gi|15668987|ref|NP_247791.1|  97 kgvriltgipipevefdklfeeKINDAFQYLnSLLLEVK----KsgkKPILIFDELQMI-KDVVLNT 158
                                   888999999998888888866644444445523333333....24446*********99.7666654 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   9.4e-06     0.017      37      94 ..      26      82 ..      10      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.4e-06
                         AAA_7 37 llvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvy 94
                                  +++Gp  +GKt++ik+++++  +++y++  inf  +  +++ +++ie+ +  ++ + +
  gi|15668987|ref|NP_247791.1| 26 FIYGPLNSGKTALIKHIIENKLSDDYKVFYINFRTYLISEK-REFIEAIFTTKKDDFF 82
                                  578*************7766666***********9988776.5677776666666655 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.6e-05     0.047       3      31 ..      25      53 ..      23      75 .. 0.81
   2 ?   -4.0   0.1       5.3   9.5e+03      32      46 ..     243     257 ..     239     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-05
                                  EEEEESTTCCHHHHHHHHHCT--SS-EEE CS
                          cobW  3 tvltGflGsGKTtLlnhllenraglklav 31
                                  + + G+l sGKT+L++h++en+ + ++ v
  gi|15668987|ref|NP_247791.1| 25 YFIYGPLNSGKTALIKHIIENKLSDDYKV 53
                                  6799***************8876666555 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.3
                                   EESS-SSCHCCCCCC CS
                          cobW  32 ivNefgevsiDaell 46 
                                   ++N++  +++D+el+
  gi|15668987|ref|NP_247791.1| 243 VENNINLTNEDKELI 257
                                   789999999999987 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.5e-05     0.099       5      43 ..       8      46 ..       4      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.5e-05
                                  HHHHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHT CS
                          TsaE  5 eetealgkklakalgdvilLeGdLGaGKTtlvrglakal 43
                                  +e++++ + l ++  d+ +++G+L +GKT+l+++++++ 
  gi|15668987|ref|NP_247791.1|  8 REINEILHILNREPDDIYFIYGPLNSGKTALIKHIIENK 46
                                  566666666666668899*****************9864 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.2e-05      0.16       3      36 ..      24      57 ..      22     134 .. 0.75
   2 ?   -3.0   0.0       3.1   5.6e+03      75      94 ..     137     155 ..     112     160 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.2e-05
                            TK  3 ielilgpmfaGKsteLlrrvkryqlaekkvvvik 36
                                  i++i+gp+++GK++ + + +++    ++kv  i 
  gi|15668987|ref|NP_247791.1| 24 IYFIYGPLNSGKTALIKHIIENKLSDDYKVFYIN 57
                                  99**********9877777777777788887664 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
                            TK  75 eedvdvvlvDEaqFfeqdiv 94 
                                   + +  +++ DE q ++ d+v
  gi|15668987|ref|NP_247791.1| 137 SGKKPILIFDELQMIK-DVV 155
                                   2233566779999888.665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2341.45
//
Query:       gi|15668988|ref|NP_247792.1|  [L=188]
Description: hypothetical protein MJ_0802 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-52  178.0   4.1    1.3e-52  177.8   4.1    1.0  1  DUF2113   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
      0.029   14.6   1.7      0.075   13.3   0.2    2.3  2  DUF4889   Domain of unknown function (DUF4889)


Domain annotation for each model (and alignments):
>> DUF2113  Uncharacterized protein conserved in archaea (DUF2113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.8   4.1   1.5e-56   1.3e-52       1     184 [.       4     179 ..       4     180 .. 0.97

  Alignments for each domain:
  == domain 1  score: 177.8 bits;  conditional E-value: 1.5e-56
                       DUF2113   1 fevectdeegaeaYeeiirdilqDlnllrsierlkvyidpeeplFiiavllrktsspiklgdvaeveedk.eegkv..kik 78 
                                   ++v+c+d++g+e+Y+++i+++l+Dl l++si r++++ +++ep+Fi+ vl+++t+++ikl+d+ae+ e+k e gk+  k+k
  gi|15668988|ref|NP_247792.1|   4 IVVHCEDKAGKEIYTKVIQTALEDLLLGKSIIRVEFIAKEKEPYFILGVLPKHTRRAIKLRDFAEIVEQKkEGGKIiyKLK 84 
                                   68****************************************************************9998677777889** PP

                       DUF2113  79 iedEtylpelLkkLwekygrenveqpdRfeiiiesdedleeleelvVaDpkeelkkkvidaliriaPEGfrvrkealedns 159
                                   i+dEtylp+lLkk+      + ++qp+Rfe++++sd dl    ++ V+D+ +++ +kv+d++ r++PEG+r+++ ++ d+ 
  gi|15668988|ref|NP_247792.1|  85 ITDETYLPHLLKKI------HVIDQPSRFEVVTDSDIDL----DMEVYDAGKDFIDKVMDFMGRVFPEGMRIKN-TYIDKA 154
                                   **************......9****************99....*****************************98.89999* PP

                       DUF2113 160 fvfvAseetlkeewieeakelkeel 184
                                   +v++Ase++lk+e ieea +lk++l
  gi|15668988|ref|NP_247792.1| 155 IVCIASERPLKDEEIEEALKLKDKL 179
                                   *********************9998 PP

>> DUF4889  Domain of unknown function (DUF4889)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   8.4e-06     0.075      29      69 ..      58      99 ..      51     101 .. 0.83
   2 ?   -0.8   0.1       0.2   1.8e+03      14      25 ..     165     176 ..     146     182 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.4e-06
                       DUF4889 29 dvkvkkgDFvklv..kkddskkivkkkkvkhDDvPhGLmmkih 69
                                     +k  DF  +v  kk+ +k i+k k+ +    Ph L+ kih
  gi|15668988|ref|NP_247792.1| 58 RRAIKLRDFAEIVeqKKEGGKIIYKLKITDETYLPH-LLKKIH 99
                                  5567889****9987788889999************.889**9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.2
                       DUF4889  14 kdekveknvklp 25 
                                   kde++e+ +kl+
  gi|15668988|ref|NP_247792.1| 165 KDEEIEEALKLK 176
                                   788888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1342.39
//
Query:       gi|15668989|ref|NP_247793.1|  [L=172]
Description: hypothetical protein MJ_0803 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.28   11.0   4.2       0.33   10.7   2.2    1.8  2  DUF2157   Predicted membrane protein (DUF2157)
       0.72    9.9   9.6      0.029   14.5   3.3    1.8  2  DUF986    Protein of unknown function (DUF986)


Domain annotation for each model (and alignments):
>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3    0.0095        85      73     114 ..      18      73 ..       9      75 .. 0.64
   2 ?   10.7   2.2   3.7e-05      0.33      35      84 ..      57     106 ..      44     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0095
                       DUF2157  73 llllslllgavlwrdr..............rvpprlgeallllaalllgaaialvg 114
                                   +l++ l+ g++l  ++              ++++++g+  +l+ +l++g  i+ +g
  gi|15668989|ref|NP_247793.1|  18 ALAGILCYGIYLAIKSeknlikdalfvykdNNFNVFGKKYALMIFLAFGFPIFFIG 73 
                                   33333333322222222467778888888888999999999999999998888876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3.7e-05
                       DUF2157  35 leallvlGalllglGlilfvAanWqglsrlvkfllllvllllslllgavl 84 
                                   + ++++l+  +  + + +f + +W++l++  +f l +++++++l++  +l
  gi|15668989|ref|NP_247793.1|  57 YALMIFLAFGFPIFFIGSFLYLFWEKLPEGFRFSLTFAITFFVLFIFGLL 106
                                   4555666666666667789999**************99988887766333 PP

>> DUF986  Protein of unknown function (DUF986)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.4       0.2   1.8e+03      75     100 ..      23      47 ..       8      62 .. 0.67
   2 ?   14.5   3.3   3.2e-06     0.029      47     144 ..      71     167 ..      67     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.2
                        DUF986  75 illaiYlafiRspklllKeeGffyan 100
                                   +   iYla i+s k l+K+  f y+ 
  gi|15668989|ref|NP_247793.1|  23 LCYGIYLA-IKSEKNLIKDALFVYKD 47 
                                   33345544.67788888888777764 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.2e-06
                        DUF986  47 livliviliyqnvteegesltlyLLavlillaiYlafiRspklllKeeGffyanifieYkkikainlsedgilvidlekrr 127
                                   +i+  + l+++++  eg ++ l++ +++ +l+i+   + + k+ + ++G++ +  fi++k  +  ++ +++i++i  +   
  gi|15668989|ref|NP_247793.1|  71 FIGSFLYLFWEKLP-EGFRFSLTFAITFFVLFIFGLLFVKYKIRVCKNGIYVGFRFITWKGFEGYKIENNKIILIGKKGVT 150
                                   55555556666666.455566666677778888877777778888999****************************999** PP

                        DUF986 128 llikvkklddlekivkf 144
                                     +++k  ++le i+k 
  gi|15668989|ref|NP_247793.1| 151 YPVHLKYSKELEDIIKN 167
                                   *************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1250.01
//
Query:       gi|15668990|ref|NP_247794.1|  [L=286]
Description: pyruvate formate-lyase activating enzyme [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-22   80.0   4.9    8.4e-21   75.1   3.1    2.8  2  Radical_SAM  Radical SAM superfamily
     0.0022   17.0   0.1     0.0035   16.3   0.1    1.2  1  Rota_NS53    Rotavirus RNA-binding Protein 53 (NS53)
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.032   14.3   0.0    1.5  1  Hydrolase_6  Haloacid dehalogenase-like hydrolase
      0.021   14.6   3.0       0.22   11.2   0.0    2.2  2  DUF1848      Domain of unknown function (DUF1848)
          1    9.5   8.0         17    5.5   3.6    3.6  2  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   3.1   2.3e-24   8.4e-21       2     166 ..      45     190 ..      44     191 .. 0.87
   2 ?   -0.9   0.0       0.5   1.8e+03      76     121 ..     239     281 ..     196     285 .. 0.67

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 2.3e-24
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                   + t+ Cnl+C++C+ + +  + +rg +  +ee +               i+  gepll+ + v+++ + +k    g+r+ +
  gi|15668990|ref|NP_247794.1|  45 ELTQKCNLNCIYCYSRLK--TVKRGIYGNLEEAETV------------TISQYGEPLLDLEGVKKAIEFCKD--LGLRVDL 109
                                   78999***********63..4444444333333333............34457*******************..7****** PP

                                   EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleel 163
                                    tngtl++ee++++l++lg+d + ++l +++ ek++ l+ +++ f +vl++++++ ++ ++ +++r + +pG+nd el +l
  gi|15668990|ref|NP_247794.1| 110 QTNGTLLNEEIIKELKDLGLDLIMISLSSFSREKYKLLT-GKDYFNRVLNNIKIASKY-LH-TIVRSIYIPGFNDNELLNL 187
                                   *********************************888888.99****************.**.****************999 PP

                                   HHH CS
                                   xxx RF
                   Radical_SAM 164 lel 166
                                   +++
  gi|15668990|ref|NP_247794.1| 188 AKE 190
                                   986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.5
                                   CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklm 121
                                   +  +i v++ g l+   +l++++   ++ ++ ++ +  ++ +++ +
  gi|15668990|ref|NP_247794.1| 239 NAPKINVTIKGCLL--VQLKEMDGFILNNITYDVFSEVPD-IKREH 281
                                   34445555555553..678888888888888888888887.77766 PP

>> Rota_NS53  Rotavirus RNA-binding Protein 53 (NS53)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   9.7e-07    0.0035     211     348 ..     135     273 ..     129     281 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.7e-07
                     Rota_NS53 211 sksrlisekkkqlkksdfsknllenkkaktkk.lqvlrnvseesveWneeielvkdkkkylevlktsetekysvsdrnklf 290
                                   s s +  ek k l+ +d+ +++l+n k+ +k   +++r++    ++ ne ++l k+ ++y + ++  +  +y+ +++ +  
  gi|15668990|ref|NP_247794.1| 135 SLSSFSREKYKLLTGKDYFNRVLNNIKIASKYlHTIVRSIYIPGFNDNELLNLAKELNNYADEIMVHQLISYKENENLLKN 215
                                   67999999*****************998877516799*****9************************************** PP

                     Rota_NS53 291 vkaklkelsklikPnyvasnheqlasevknC.kwCsiknafkvledfrlkkiynevlef 348
                                      +l+ l++      ++ + +++a +++   k C +  ++k ++ f l++i  +v++ 
  gi|15668990|ref|NP_247794.1| 216 AGIDLNNLGRIRDLLLIVDEMQKNAPKINVTiKGC-LLVQLKEMDGFILNNITYDVFSE 273
                                   ************9***************9761556.5567899*9******99988875 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.9e-06     0.032      16      59 ..      90     142 ..      85     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.9e-06
                                   -TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT---..........- CS
                   Hydrolase_6  16 ipgaaealnalraagkpvvllTNnsskseeeyakkleklgvdi..........t 59 
                                   ++g+++a++++++ g +v l TN++  + ee++k+l++lg+d+          +
  gi|15668990|ref|NP_247794.1|  90 LEGVKKAIEFCKDLGLRVDLQTNGTLLN-EEIIKELKDLGLDLimislssfsrE 142
                                   79*********************88776.9***********9755555555551 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.5     0.026        93     254     264 ..      48      58 ..      43      59 .. 0.87
   2 ?   11.2   0.0   6.2e-05      0.22     122     201 ..     170     251 ..     149     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.026
                       DUF1848 254 ntClhgCvYCY 264
                                   + C+ +C+YCY
  gi|15668990|ref|NP_247794.1|  48 QKCNLNCIYCY 58 
                                   57********* PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.2e-05
                       DUF1848 122 lltekltvelhlekfeklaeelkgytekvviSfvdlykkvkrnlkkk.lelrelseeek.eelaeelaeiakklglelatC 200
                                   ++ + +   ++ +++ +la+el++y +++++  +  yk+ ++ lk++ ++l++l + +    +++e+++ a k +++++ C
  gi|15668990|ref|NP_247794.1| 170 IVRSIYIPGFNDNELLNLAKELNNYADEIMVHQLISYKENENLLKNAgIDLNNLGRIRDlLLIVDEMQKNAPKINVTIKGC 250
                                   5566666677778999*************************999875688888877555268899**************** PP

                       DUF1848 201 a 201
                                    
  gi|15668990|ref|NP_247794.1| 251 L 251
                                   7 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   3.6    0.0049        17       6      91 ..      48     115 ..      45     142 .. 0.59
   2 ?    0.1   0.1      0.24   8.7e+02      65      86 ..     227     248 ..     186     262 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0049
                       Fer4_14   6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeeypekkiwl 85 
                                    +Cnl+C  C+ + +   + g + + e+              ++ ++++  GePL   + + + k ++  k+ +  +++ l
  gi|15668990|ref|NP_247794.1|  48 QKCNLNCIYCYSRLKTV-KRGIYGNLEE--------------AETVTISQyGEPL--LDLEGVKKAIEFCKDLG--LRVDL 109
                                   67888888888665222.2222222222..............2223343337777..55666666666666666..77777 PP

                       Fer4_14  86 etngtl 91 
                                   +tngtl
  gi|15668990|ref|NP_247794.1| 110 QTNGTL 115
                                   777766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.24
                       Fer4_14  65 kellklvkrlkeeypekkiwle 86 
                                   ++ll +v++++++ p+++++++
  gi|15668990|ref|NP_247794.1| 227 RDLLLIVDEMQKNAPKINVTIK 248
                                   4566677778888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1984.84
//
Query:       gi|15668991|ref|NP_247795.1|  [L=221]
Description: hypothetical protein MJ_0805 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-72  241.7   6.0    4.3e-72  241.4   6.0    1.1  1  DUF366    Domain of unknown function (DUF366)


Domain annotation for each model (and alignments):
>> DUF366  Domain of unknown function (DUF366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.4   6.0   2.4e-76   4.3e-72       1     182 [.      32     217 ..      32     218 .. 0.98

  Alignments for each domain:
  == domain 1  score: 241.4 bits;  conditional E-value: 2.4e-76
                        DUF366   1 mkvlvleekikYdGsqlsslwaykefgiqgdsivafrGecevkleelvDleDvke....eeeIksedmlhfivehFdstdl 77 
                                   m++++++++++Y+G+++++lwa+k+f+iq+dsiv+frG++ev++e+++Dl+D+k+    +++Iksed+++f+vehFd+ dl
  gi|15668991|ref|NP_247795.1|  32 MSIIFVKDRLDYTGKEIEPLWAFKTFDIQKDSIVVFRGRMEVTTENMKDLKDIKRekdiKTPIKSEDAINFVVEHFDVIDL 112
                                   7899*************************************************9977777899****************** PP

                        DUF366  78 klavlrQrllvaivkevleekgvklkreGdDlyvndkKLsvsiataslvsvkiHlglNvesegtp.vetigLkdlgieedi 157
                                   k+++lrQrllv+i+kev+e++++klkr+GdDly++dkKLsv+ia++++vs+kiHlg+Nv+s+g+  v++igL+dlgi +di
  gi|15668991|ref|NP_247795.1| 113 KTIYLRQRLLVFIAKEVIESYNIKLKRDGDDLYFEDKKLSVCIACKGTVSAKIHLGINVKSKGAEhVKIIGLEDLGI-KDI 192
                                   ****************************************************************99***********.*** PP

                        DUF366 158 eelaeevakkyaeeiediekdirKv 182
                                   +++++e+a +ya+ei++ie+d+rK+
  gi|15668991|ref|NP_247795.1| 193 DKVMREIAINYAKEIDKIERDLRKT 217
                                   ************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1503.20
//
Query:       gi|15668992|ref|NP_247796.1|  [L=347]
Description: X-pro aminopeptidase PepQ [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-57  194.1   0.0    2.9e-57  193.7   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24
      1e-05   26.2   0.0    2.2e-05   25.1   0.0    1.7  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.7   0.0   3.2e-61   2.9e-57       2     208 ..     130     332 ..     129     333 .. 0.93

  Alignments for each domain:
  == domain 1  score: 193.7 bits;  conditional E-value: 3.2e-61
                                   HHHHHHHHHHHHHHHHHHHHH..TTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEEEE CS
                 Peptidase_M24   2 lirkaariasaaleavleaik..pgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvlid 80 
                                   li+kaa+i+++a++ vl+++   +  te+el aeie+  +k+hg+ ++af+ iv sg++++++h+ p+++++   d++l+d
  gi|15668992|ref|NP_247796.1| 130 LIKKAAEISDKAINWVLNNLDevKNLTEYELVAEIEYI-MKKHGSIKPAFDSIVVSGKKTSFPHALPTKDKIA--DILLVD 207
                                   79**************98877334789*********77.9****************************99995..6***** PP

                                   EEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESSSS CS
                 Peptidase_M24  81 agaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGlev 161
                                   +ga+y+gy+sDitrT+l+ k+++e++++y++v ea + a + +k+G+++++id+++re++ +  +++ f h+lGHgvGlev
  gi|15668992|ref|NP_247796.1| 208 IGAVYEGYCSDITRTFLL-KDDEEMKKIYNLVYEAKKVAEEHLKEGISAKQIDNIVREFFND--YKELFIHSLGHGVGLEV 285
                                   ****************99.58899*************************************9..5778************* PP

                                   SEEEEEESS..STTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                 Peptidase_M24 162 hdegpsvsr..esndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                   h+e p++s+  + +++  l+eGmv+tiEpg+y  ++++gvried++lv+
  gi|15668992|ref|NP_247796.1| 286 HEE-PRLSNklKDDEDIILKEGMVVTIEPGLY-LKDKFGVRIEDLYLVK 332
                                   **9.**987655558999**************.78899*********98 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   2.5e-09   2.2e-05       1      83 [.      12      88 ..      12     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.5e-09
                                  HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH.TTSEEEEESTHSSHHHH CS
                  Creatinase_N  1 RlerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadgalllvdalryteaaeesatveevveyddpvealad 83
                                  R+er+ + me +g+  +++ ++en++Y+ G     + ++ +l v +++ +l+v +l+   a e+   + e++e+++ +e++++
  gi|15668992|ref|NP_247796.1| 12 RIERFLKYMESEGIKKAVILKKENINYFLGK---YFMSFSVL-VFEEQPYLYVGKLDKDYAEEHF-NFLEIREFKS-WEEIFK 88
                                  9******************************...88888888.777888*****99999999999.9999999998.888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2596.54
//
Query:       gi|15668993|ref|NP_247797.1|  [L=184]
Description: hypothetical protein MJ_0807 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.4e-21   75.1   0.4    1.8e-16   60.4   0.1    2.1  2  DUF98       p-hydroxybenzoic acid synthase
  ------ inclusion threshold ------
      0.032   14.3   0.2       0.27   11.3   0.1    2.2  2  DUF3848     Protein of unknown function (DUF3848)
       0.16   11.6   0.0       0.25   11.0   0.0    1.6  1  Chor_lyase  Chorismate lyase


Domain annotation for each model (and alignments):
>> DUF98  p-hydroxybenzoic acid synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.3e-06      0.02       1      30 [.      34      63 ..      33      66 .. 0.90
   2 !   60.4   0.1     3e-20   1.8e-16      43     143 ..      61     172 ..      59     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-06
                                  HH--S-HHHHHHHHHSS-EEEEEEEEEEEE CS
                         DUF98  1 LlgDGsvTrhlelltqekveveliemeaee 30
                                  L +DGsvT +le+l + + +ve+i++++++
  gi|15668993|ref|NP_247797.1| 34 LGTDGSVTNILEILFEGECRVETINQKIVA 63
                                  568**********************99876 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 3e-20
                                   TT-EEEEEEEEEEETTEEEEEEEEEEEGGGS-.HHHHH........SSS-HHHHHHHTT--BEEEEEEEEEEE--.HHHHH CS
                         DUF98  43 lkkpllrRqVwlrangqklayAeSwwneeele.kylke........kdqpiwksLtkerlelfReirglalgead.eLeea 113
                                   + ++ ++R+V l+ n+ +l+yA+S ++ +++e ++l+e        +d+pi+k+++k++le++Rei+ + + e d  L++ 
  gi|15668993|ref|NP_247797.1|  61 IVANTNYREVILKVNNIPLVYAVSKTPFKNIEeENLREeikrdllsADIPIGKIIRKHNLETRREIKYIGIAEIDdYLKSL 141
                                   667899******************9999888624677788889999*************************9988799999 PP

                                   HT.SS-EEEEEEEEEEETTEEEEEEEEEEEG CS
                         DUF98 114 fg.ekgpfwsRhYrlfhkgkpltvirEvFsp 143
                                   ++ + +++  R+Y++++k+k+l+ i+E+F +
  gi|15668993|ref|NP_247797.1| 142 LKtNYSRLPKRTYNIIYKNKVLMEITEIFAV 172
                                   9956799**********************86 PP

>> DUF3848  Protein of unknown function (DUF3848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.11   6.5e+02      44      70 ..      90     116 ..      80     129 .. 0.81
   2 ?   11.3   0.1   4.6e-05      0.27      11      47 ..     132     168 ..     123     172 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.11
                       DUF3848  44 sleeeelsdeqakaLlksenpLddvye 70 
                                    +eee+l +e  + Ll+ + p+ ++ +
  gi|15668993|ref|NP_247797.1|  90 NIEEENLREEIKRDLLSADIPIGKIIR 116
                                   578999999999999999999888765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.6e-05
                       DUF3848  11 aEqdefrdelkskppeeilesaYeltvkedilmslee 47 
                                   aE d +++ l++ +   + +++Y++++k+ +lm ++e
  gi|15668993|ref|NP_247797.1| 132 AEIDDYLKSLLKTNYSRLPKRTYNIIYKNKVLMEITE 168
                                   89******************************98765 PP

>> Chor_lyase  Chorismate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.2e-05      0.25      62      96 ..      58      92 ..      33     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.2e-05
                    Chor_lyase 62 aseealsgwvRevilkgddrPlvfartliprssle 96
                                  + +  +++  Revilk +++Plv+a +  p   +e
  gi|15668993|ref|NP_247797.1| 58 NQKIVANTNYREVILKVNNIPLVYAVSKTPFKNIE 92
                                  3444456678***************9988766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1297.81
//
Query:       gi|15668994|ref|NP_247798.1|  [L=333]
Description: pyruvate-formate-lyase-activating enzyme [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-21   76.4   0.3    1.7e-20   74.0   0.2    2.1  2  Radical_SAM    Radical SAM superfamily
    9.8e-05   22.6   0.0    0.00018   21.8   0.0    1.4  1  Fer4_12        4Fe-4S single cluster domain
    0.00044   19.6   0.9       0.06   12.8   0.1    2.9  2  zf-ribbon_3    zinc-ribbon domain
  ------ inclusion threshold ------
      0.036   14.2   2.6        1.4    9.1   0.0    3.6  4  Zn-ribbon_8    Zinc ribbon domain
      0.095   12.7   0.1      0.095   12.7   0.1    2.9  4  DZR            Double zinc ribbon
       0.39   10.3   0.0       0.39   10.3   0.0    3.0  3  TF_Zn_Ribbon   TFIIB zinc-binding
        1.4    8.5   5.1       0.24   11.0   0.2    2.1  3  DpnI           Dam-replacing family
        6.8    6.8   7.8        3.4    7.7   0.3    3.4  4  YhfH           YhfH-like protein
        8.4    6.3  13.9       0.26   11.0   0.3    3.6  4  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.2   8.8e-24   1.7e-20       5     163 ..      80     226 ..      77     230 .. 0.94
   2 ?   -1.0   0.0         1     2e+03     132     156 ..     263     292 ..     245     293 .. 0.72

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 8.8e-24
                                   SEESS--TTTSCCTT...HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   5 rgCnlrCsfCarpet...vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                    gCn+rC +C++++      +e ++r++++eei+e + ++     + ++  +  ep++y++f  ++  +a++  +g+ +++
  gi|15668994|ref|NP_247798.1|  80 GGCNFRCLHCQNWTIsqfPPDEIPYREMTPEEIVEVAIRYN----CPGISYTYTEPTVYYEFMYDTSVIARE--NGMFNVM 154
                                   69***********99*************************8....***************************..8****** PP

                                   EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleel 163
                                   +tng+       e l+ l+vd ++++++   d+ ++k +  + t+e vle++++++++gi  v ++ +++p++nd  +++l
  gi|15668994|ref|NP_247798.1| 155 ITNGYIE----KEPLKALPVDAMNIDIKGNADF-YKKVC--KATLEPVLETCKLAKKLGIW-VEVTNLIVPNYNDN-IDDL 226
                                   ******7....59999999**************.*****..49******************.99999999999997.5665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1
                                   HHHHHHHHTTSET.....EEEEEEEBTTTS CS
                                   xxxxxxxxxxxxx.....xxxxxxxxxxxx RF
                   Radical_SAM 132 ealeklreagikr.....vvdrivglpGen 156
                                   e+le++r++ i++      + +++g++Gen
  gi|15668994|ref|NP_247798.1| 263 ETLEMARNLAIEEglkyvYIGNVPGHEGEN 292
                                   556666666655555568888999999998 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   9.2e-08   0.00018       8     100 ..      75     165 ..      70     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9.2e-08
                       Fer4_12   8 lslfvsgCnlsCkgCfnketwsfk.sgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekd 87 
                                   +sl ++gCn++C  C n  + +f   + ++ + + eei+e +  ++ +g++++  EP ++++    ++++   +e+++  +
  gi|15668994|ref|NP_247798.1|  75 VSLAIGGCNFRCLHCQNWTISQFPpDEIPYREMTPEEIVEVAIRYNCPGISYTYTEPTVYYEFMYDTSVI--ARENGM-FN 152
                                   68889************98877652778999****************************55555444444..455555.57 PP

                       Fer4_12  88 iwlytgytleels 100
                                   +++++gy+ +e +
  gi|15668994|ref|NP_247798.1| 153 VMITNGYIEKEPL 165
                                   99****9987765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1     3e-05      0.06       2      12 ..     292     303 ..     291     305 .. 0.78
   2 ?    4.2   0.1     0.015        29       2      12 ..     319     329 ..     318     331 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
                   zf-ribbon_3   2 tvrCPnCGa.pl 12 
                                    ++CPnCGa ++
  gi|15668994|ref|NP_247798.1| 292 NTYCPNCGAlLI 303
                                   689******555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.015
                   zf-ribbon_3   2 tvrCPnCGapl 12 
                                   t+rC  CG+++
  gi|15668994|ref|NP_247798.1| 319 TKRCKICGEKI 329
                                   78888888855 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       5.1     1e+04      27      32 ..      15      20 ..       9      22 .. 0.58
   2 ?    0.0   0.0      0.48   9.5e+02       6      13 ..      84      91 ..      83      99 .. 0.85
   3 ?    9.1   0.0   0.00071       1.4      22      38 ..     288     305 ..     284     307 .. 0.77
   4 ?    2.2   0.0       0.1     2e+02      27      34 ..     319     327 ..     310     332 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.1
                   Zn-ribbon_8 27 taCPeC 32
                                  + C  C
  gi|15668994|ref|NP_247798.1| 15 VRCHIC 20
                                  336555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.48
                   Zn-ribbon_8  6 YrCeeCgh 13
                                  +rC  C++
  gi|15668994|ref|NP_247798.1| 84 FRCLHCQN 91
                                  89999984 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00071
                   Zn-ribbon_8  22 sdapltaCPeCgs.evrr 38 
                                   ++ ++t CP+Cg+   +r
  gi|15668994|ref|NP_247798.1| 288 HEGENTYCPNCGAlLIER 305
                                   4677788*****988777 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.1
                   Zn-ribbon_8  27 ta.CPeCgs 34 
                                   t+ C+ Cg+
  gi|15668994|ref|NP_247798.1| 319 TKrCKICGE 327
                                   455777775 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.5       1.7   3.4e+03      29      37 ..      15      23 ..       8      36 .. 0.54
   2 ?   -1.0   0.1      0.96   1.9e+03      30      36 ..      85      91 ..      52      97 .. 0.77
   3 ?   -3.5   0.1       5.6   1.1e+04      18      24 ..     188     194 ..     186     200 .. 0.42
   4 ?   12.7   0.1   4.8e-05     0.095      11      39 ..     291     330 ..     286     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.7
                           DZR 29 drCpsCgek 37
                                   rC  C + 
  gi|15668994|ref|NP_247798.1| 15 VRCHICPRH 23
                                  344444444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.96
                           DZR 30 rCpsCge 36
                                  rC +C+ 
  gi|15668994|ref|NP_247798.1| 85 RCLHCQN 91
                                  6777764 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.6
                           DZR  18 Cgtklka 24 
                                   C+++l++
  gi|15668994|ref|NP_247798.1| 188 CKATLEP 194
                                   4444432 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 4.8e-05
                           DZR  11 darfCseCgtklkavaa...........edrCpsCgekvd 39 
                                   ++ +C++Cg+ l +               +rC  Cgek+d
  gi|15668994|ref|NP_247798.1| 291 ENTYCPNCGALLIERYIfnakiinldveTKRCKICGEKID 330
                                   5779*******9854449999******999*****99875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.4       3.7   7.3e+03       3      11 ..      17      25 ..      16      32 .. 0.57
   2 ?   10.3   0.0    0.0002      0.39      17      36 ..     290     309 ..     287     313 .. 0.81
   3 ?    1.3   0.1      0.13   2.5e+02       3      28 ..     322     328 ..     318     332 .. 0.60

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.7
                                  ETTTTCEEC CS
                  TF_Zn_Ribbon  3 CPnCgstnl 11
                                  C +C    +
  gi|15668994|ref|NP_247798.1| 17 CHICPRHCI 25
                                  666665555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0002
                                   TTCEEESSSSBEEEECCCCC CS
                  TF_Zn_Ribbon  17 rgelvCtdCGlVlednside 36 
                                     +++C++CG++l +++i +
  gi|15668994|ref|NP_247798.1| 290 GENTYCPNCGALLIERYIFN 309
                                   4678*******999999876 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.13
                                   ETTTTCEECHEETSTTCEEESSSSBE CS
                  TF_Zn_Ribbon   3 CPnCgstnlveDpergelvCtdCGlV 28 
                                   C++Cg                   + 
  gi|15668994|ref|NP_247798.1| 322 CKICG-------------------EK 328
                                   55555...................44 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2         1     2e+03      31      46 ..      83      98 ..      80     101 .. 0.85
   2 ?   -3.9   0.0       4.5   9.1e+03      52      62 ..     181     191 ..     178     201 .. 0.80
   3 ?   11.0   0.2   0.00012      0.24      30      54 ..     291     315 ..     288     331 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                                  H---TTT--SS-EE-- CS
                          DpnI 31 nlyCpkCgskklsefe 46
                                  n+ C +C++ ++s+f 
  gi|15668994|ref|NP_247798.1| 83 NFRCLHCQNWTISQFP 98
                                  7889999999999996 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.5
                                   -EEE-TTT--E CS
                          DpnI  52 aDfyCesckee 62 
                                   aDfy + ck  
  gi|15668994|ref|NP_247798.1| 181 ADFYKKVCKAT 191
                                   89999999865 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00012
                                   HH---TTT--SS-EE--------EE CS
                          DpnI  30 knlyCpkCgskklsefennkpvaDf 54 
                                   +n+yCp+Cg+  ++++  n ++ ++
  gi|15668994|ref|NP_247798.1| 291 ENTYCPNCGALLIERYIFNAKIINL 315
                                   79**************999988654 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       1.2   2.4e+03       4      13 ..       3      12 ..       1      24 [. 0.70
   2 ?   -3.4   0.0       5.1     1e+04       6      34 ..     182     188 ..     177     189 .. 0.49
   3 ?    1.9   0.0      0.12   2.3e+02      15      25 ..     294     304 ..     291     306 .. 0.80
   4 ?    7.7   0.3    0.0017       3.4      12      24 ..     318     330 ..     314     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.2
                          YhfH  4 iveFfrnLPk 13
                                   ++F+++L +
  gi|15668994|ref|NP_247798.1|  3 EAMFYEKLDD 12
                                  5789999975 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.1
                          YhfH   6 eFfrnLPkKkCteCGkeieEqaecYgneC 34 
                                   +F++                      + C
  gi|15668994|ref|NP_247798.1| 182 DFYK----------------------KVC 188
                                   4444......................444 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.12
                          YhfH  15 kCteCGkeieE 25 
                                    C++CG  + E
  gi|15668994|ref|NP_247798.1| 294 YCPNCGALLIE 304
                                   6*****87665 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0017
                          YhfH  12 PkKkCteCGkeie 24 
                                   ++K C  CG++i+
  gi|15668994|ref|NP_247798.1| 318 ETKRCKICGEKID 330
                                   68*********97 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.67   1.3e+03       8      19 ..       9      20 ..       8      22 .. 0.83
   2 ?   -2.5   0.4       2.4   4.7e+03       1       6 [.      85      90 ..      85      91 .. 0.71
   3 ?   11.0   0.3   0.00013      0.26      13      21 ..     292     300 ..     288     302 .. 0.76
   4 ?    3.4   0.2     0.034        68       1      10 [.     321     330 ..     321     331 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.67
                 zinc_ribbon_2  8 elqdnakFCpyC 19
                                  +l+dn + C  C
  gi|15668994|ref|NP_247798.1|  9 KLDDNKVRCHIC 20
                                  899999999877 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                 zinc_ribbon_2  1 fCpnCG 6 
                                  +C +C 
  gi|15668994|ref|NP_247798.1| 85 RCLHCQ 90
                                  588995 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00013
                 zinc_ribbon_2  13 akFCpyCGt 21 
                                   +++Cp+CG+
  gi|15668994|ref|NP_247798.1| 292 NTYCPNCGA 300
                                   788888887 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.034
                 zinc_ribbon_2   1 fCpnCGaelq 10 
                                   +C+ CG++++
  gi|15668994|ref|NP_247798.1| 321 RCKICGEKID 330
                                   6999***996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2163.01
//
Query:       gi|15668995|ref|NP_247799.1|  [L=138]
Description: hypothetical protein MJ_0808.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00021   21.2  17.2    0.00021   21.2  17.2    2.4  2  FlxA           FlxA-like protein
     0.0045   16.8   4.3     0.0045   16.8   4.3    3.2  3  CdvA           CdvA-like coiled-coil domain
     0.0075   15.2   1.5     0.0075   15.2   1.5    1.4  2  DUF3375        Protein of unknown function (DUF3375)
  ------ inclusion threshold ------
      0.021   14.8   5.8      0.056   13.5   2.7    2.2  2  DUF1043        Protein of unknown function (DUF1043)
      0.057   13.9   0.0       0.11   13.0   0.0    1.5  1  DUF1091        Protein of unknown function (DUF1091)
       0.11   12.6  12.8      0.043   13.9   5.4    2.2  2  DUF1664        Protein of unknown function (DUF1664)
       0.12   12.1   4.0      0.094   12.4   1.6    1.8  2  DSHCT          DSHCT (NUC185) domain
       0.14   12.1   2.5       0.17   11.8   0.6    1.9  2  DUF2461        Conserved hypothetical protein (DUF2461)
       0.19   11.3   6.7        0.2   11.2   6.7    1.1  1  Exonuc_VII_L   Exonuclease VII, large subunit
       0.19   11.8   7.9        4.2    7.5   0.6    2.8  3  GvpK           Gas vesicle protein K
       0.21   11.7   8.1        1.4    9.0   3.5    2.1  2  COG2           COG (conserved oligomeric Golgi) complex compo
       0.24   12.0   1.1       0.62   10.6   1.1    2.0  1  YtxH           YtxH-like protein
       0.31   11.6   8.9       0.39   11.3   4.2    2.6  2  Syntaxin-6_N   Syntaxin 6, N-terminal
       0.37   10.5   9.0          2    8.1   3.3    2.2  2  DUF1845        Domain of unknown function (DUF1845)
       0.44    9.8  11.9        1.3    8.3   0.5    2.1  2  MIS13          Mis12-Mtw1 protein family
        0.5   10.4   5.5        3.6    7.6   0.4    2.6  2  DUF1515        Protein of unknown function (DUF1515)
        0.5   10.8   6.3         12    6.5   2.3    2.9  3  DUF4140        N-terminal domain of unknown function (DUF4140
       0.85    9.1  14.8         17    4.8  14.8    2.0  1  Leu_zip        Leucine zipper
          1    9.0   7.9       0.75    9.4   3.2    2.1  2  DUF4988        Domain of unknown function
        1.5    8.2  12.1      0.087   12.2   4.7    1.9  2  HBM            Helical bimodular sensor domain
        1.7    8.8   9.7        1.8    8.8   4.4    2.1  2  PIN_2          PIN domain
        3.7    6.7  13.7        7.7    5.7  13.7    1.7  1  TMPIT          TMPIT-like protein
        4.2    8.0  16.0       0.12   13.0   7.1    2.1  2  DUF4665        Domain of unknown function (DUF4665)
        4.3    6.6  16.3       0.18   11.1   9.6    1.8  2  DUF3450        Protein of unknown function (DUF3450)
        5.1    7.5  15.9       0.38   11.2   3.8    3.4  3  V-SNARE        Vesicle transport v-SNARE protein N-terminus
        5.3    7.8   7.3        2.9    8.6   4.0    1.9  2  DUF2203        Uncharacterized conserved protein (DUF2203)
        5.4    7.4  20.9        1.3    9.4   5.7    3.3  4  BLOC1_2        Biogenesis of lysosome-related organelles comp
        5.6    7.3   7.6        5.4    7.3   4.2    2.4  2  DUF948         Bacterial protein of unknown function (DUF948)
        6.3    7.9   5.6         24    6.1   0.1    2.4  2  DUF5320        Family of unknown function (DUF5320)
          7    7.5  13.0       0.44   11.4   3.4    2.8  3  FliT           Flagellar protein FliT
        7.2    7.3  15.3        1.5    9.5   6.4    2.3  2  YabA           Initiation control protein YabA
        8.6    6.0  17.6        2.3    7.9   8.3    2.6  3  DUF3251        Protein of unknown function (DUF3251)
        9.3    6.7  17.5         17    5.8   0.6    3.1  3  Csm1_N         Csm1 N-terminal domain


Domain annotation for each model (and alignments):
>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2  17.2   3.9e-07   0.00021      13      72 ..      14      71 ..       2      82 .. 0.82
   2 ?    2.7   4.4      0.23   1.3e+02      46      70 ..     110     134 ..      99     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.9e-07
                          FlxA 13 sgsasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqq 72
                                  ++++++i++L++Qi++++kq++ + ++ +l+++ +++ +q i+ QI +++  I ++++  
  gi|15668995|ref|NP_247799.1| 14 EKMTQKIQELNQQITQIKKQIQIIEQN-NLSDQ-QNQTIQKIKRQIYSIEFDILRVESNR 71
                                  578899999999999999999999888.78777.67888999999999999998887765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.23
                          FlxA  46 ekkkqqqliqaQIqqlqaQIaqlqq 70 
                                   + +kq  +++ QI +++++I+ +++
  gi|15668995|ref|NP_247799.1| 110 QLMKQLVMMEDQIIKIKQEIRMIEK 134
                                   5678888888888888888887776 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   4.3   8.3e-06    0.0045      31      63 ..       2      34 ..       1      39 [. 0.92
   2 ?    4.0   2.2     0.079        43      32      64 ..      40      72 ..      37     115 .. 0.84
   3 ?    0.4   2.7      0.98   5.3e+02      37      61 ..     111     134 ..      71     137 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.3e-06
                          CdvA 31 lkklkekakelkeklkkrlkeledqikslekal 63
                                  lk++k++ ++++ek++++++el++qi++++k +
  gi|15668995|ref|NP_247799.1|  2 LKEIKNDYDKIREKMTQKIQELNQQITQIKKQI 34
                                  799**************************9865 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.079
                          CdvA 32 kklkekakelkeklkkrlkeledqikslekala 64
                                  + l +++++ ++k+k+++ ++e  i ++e+   
  gi|15668995|ref|NP_247799.1| 40 NNLSDQQNQTIQKIKRQIYSIEFDILRVESNRS 72
                                  567888888888888888888888888877655 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.98
                          CdvA  37 kakelkeklkkrlkeledqikslek 61 
                                    +k+l  +++ ++ +++++i+ +ek
  gi|15668995|ref|NP_247799.1| 111 LMKQL-VMMEDQIIKIKQEIRMIEK 134
                                   22222.2445555555555555544 PP

>> DUF3375  Protein of unknown function (DUF3375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.5   1.4e-05    0.0075     130     195 ..       3      71 ..       1      84 [. 0.75
   2 ?   -2.4   0.2       3.2   1.7e+03     139     158 ..     114     133 ..      92     136 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                       DUF3375 130 eetepDpeeRlaeLeaeiaeidaeidrlra..geveeld.deqvlerireilnlareLpaDFrrVeeef 195
                                   +e+++D ++++++++++i+e++++i ++++  + +e+   ++q+   i++i  ++ ++  D+ rVe + 
  gi|15668995|ref|NP_247799.1|   3 KEIKNDYDKIREKMTQKIQELNQQITQIKKqiQIIEQNNlSDQQNQTIQKIKRQIYSIEFDILRVESNR 71 
                                   56778888888888888888888888888753333332213566778999***************9985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.2
                       DUF3375 139 RlaeLeaeiaeidaeidrlr 158
                                    l ++e +i +i++ei  ++
  gi|15668995|ref|NP_247799.1| 114 QLVMMEDQIIKIKQEIRMIE 133
                                   44555666666666666554 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.7    0.0001     0.056      57     100 ..       1      48 [.       1      75 [. 0.70
   2 ?    2.5   0.1      0.25   1.4e+02      11      47 ..      93     129 ..      91     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0001
                       DUF1043  57 lLetlaedyqkLyqhlaksseeL....lpeleeqelfqqkkleekkae 100
                                   +L+++++dy+k+ ++++++ +eL    +  +++ ++  q++l+ ++++
  gi|15668995|ref|NP_247799.1|   1 MLKEIKNDYDKIREKMTQKIQELnqqiTQIKKQIQIIEQNNLSDQQNQ 48 
                                   79*********************6553113333334444444444332 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.25
                       DUF1043  11 iGalilrltnsklkkqkklekelekakaeleeqkqel 47 
                                   iG + +  + ++++k+ +l k+l   ++++ + kqe+
  gi|15668995|ref|NP_247799.1|  93 IGRIFAESFMREIEKNIQLMKQLVMMEDQIIKIKQEI 129
                                   7778888888999999********9999999999997 PP

>> DUF1091  Protein of unknown function (DUF1091)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00021      0.11       2      47 ..      61     105 ..      60     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00021
                       DUF1091   2 nlsifkrsngykpflynit.ldfCkflknpnnnplfkifykslkkys 47 
                                   +++i +  ++   ++y+ t  d+C++l++  ++ + +if +s+++  
  gi|15668995|ref|NP_247799.1|  61 EFDILRVESNRSNMIYSKTfEDMCEYLDS--HSGIGRIFAESFMREI 105
                                   677888887788899****99******88..456*********9876 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   5.4   7.9e-05     0.043      44     108 ..       3      69 ..       1      87 [. 0.81
   2 ?    3.6   0.7      0.12        63      75     103 ..     109     136 ..      96     138 .] 0.56

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.9e-05
                       DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkld..eqkeiskeikeevtevredlseigedvesvke 108
                                   +++ ++ +++ e++++  ++L+++i ++ k+++  eq+++s + ++ ++++++++ +i+ d+  v++
  gi|15668995|ref|NP_247799.1|   3 KEIKNDYDKIREKMTQKIQELNQQITQIKKQIQiiEQNNLSDQQNQTIQKIKRQIYSIEFDILRVES 69 
                                   5677778888899999999999999999888765578888999999999999999999998887765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                       DUF1664  75 ldeqkeiskeikeevtevredlseigedv 103
                                   ++ +k+    +++++ +++++++ i++d+
  gi|15668995|ref|NP_247799.1| 109 IQLMKQ-LVMMEDQIIKIKQEIRMIEKDL 136
                                   332222.2346666777777776666665 PP

>> DSHCT  DSHCT (NUC185) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.6   0.00017     0.094     124     161 ..      20      57 ..      15      59 .. 0.86
   2 ?   -0.5   0.0       1.6   8.5e+02     123     137 ..     104     118 ..      74     136 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                         DSHCT 124 lrrleellrqlakaakvigneeLkkkaeeaielikRdi 161
                                   ++ l++ + q++k  ++i++++L+++ ++ i++ikR+i
  gi|15668995|ref|NP_247799.1|  20 IQELNQQITQIKKQIQIIEQNNLSDQQNQTIQKIKRQI 57 
                                   56677778888888889*******************98 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                         DSHCT 123 llrrleellrqlaka 137
                                    + + ++l++ql  +
  gi|15668995|ref|NP_247799.1| 104 EIEKNIQLMKQLVMM 118
                                   444444444444333 PP

>> DUF2461  Conserved hypothetical protein (DUF2461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6   0.00032      0.17      19      57 ..       3      41 ..       1      59 [. 0.79
   2 ?   -0.1   0.0       1.4   7.5e+02      36      67 ..      98     130 ..      85     136 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
                       DUF2461 19 kahkaeYerakkpfealveelteelaevdpeipelpakd 57
                                  k+ k++Y+++++++ + ++el++++++++++i+ ++ ++
  gi|15668995|ref|NP_247799.1|  3 KEIKNDYDKIREKMTQKIQELNQQITQIKKQIQIIEQNN 41
                                  67799**************************99865543 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.4
                       DUF2461  36 veelteelaevdpeipelpa.kdvvfRiyRDvR 67 
                                   +e++  e+++  + +++l + +d + +i+  +R
  gi|15668995|ref|NP_247799.1|  98 AESFMREIEKNIQLMKQLVMmEDQIIKIKQEIR 130
                                   444444444444444443333666666666666 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   6.7   0.00036       0.2     147     223 ..       3     100 ..       1     138 [] 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00036
                  Exonuc_VII_L 147 eqleelerrlekaikrlleekkqrleklasrlk..speellerkrqrldeleerleralkkqlkkkrerleelkerl.k.. 222
                                   +++++  ++++++++++++e +q++++++++++  ++++l ++++q ++++++++ +     l+ +++r + + +++ +  
  gi|15668995|ref|NP_247799.1|   3 KEIKNDYDKIREKMTQKIQELNQQITQIKKQIQiiEQNNLSDQQNQTIQKIKRQIYSIEFDILRVESNRSNMIYSKTfEdm 83 
                                   677888899999999999999999999999996546777888889999999999999666666666666666654443444 PP

                  Exonuc_VII_L 223 ................e 223
                                                   +
  gi|15668995|ref|NP_247799.1|  84 ceyldshsgigrifaeS 100
                                   43333333333333321 PP

>> GvpK  Gas vesicle protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.0    0.0087       4.8      46      72 ..      13      39 ..       5      47 .. 0.83
   2 ?    1.7   0.1       0.5   2.7e+02      36      62 ..      37      59 ..      33      70 .. 0.76
   3 ?    7.5   0.6    0.0078       4.2      48      76 ..     110     138 .]      99     138 .] 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0087
                          GvpK 46 ierlgetLmkleeeleelkesfgleee 72
                                   e++ +++++l+++++++k++ ++ e+
  gi|15668995|ref|NP_247799.1| 13 REKMTQKIQELNQQITQIKKQIQIIEQ 39
                                  58999***************9998665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.5
                          GvpK 36 meagdlsdeeierlgetLmkleeelee 62
                                  +e+++lsd++     +t++k+++++  
  gi|15668995|ref|NP_247799.1| 37 IEQNNLSDQQN----QTIQKIKRQIYS 59
                                  79999999998....777777777755 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0078
                          GvpK  48 rlgetLmkleeeleelkesfgleeedLnl 76 
                                   +l ++L  +e+++ ++k++ ++ e+dL++
  gi|15668995|ref|NP_247799.1| 110 QLMKQLVMMEDQIIKIKQEIRMIEKDLKI 138
                                   7889***********************86 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.5    0.0026       1.4      71     131 ..       2      62 ..       1      64 [. 0.88
   2 ?    5.3   0.1     0.036        19      27      85 ..      79     136 ..      67     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0026
                          COG2  71 leevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkldevveklea 131
                                   l+e++ +  ++r+k+++ +++l++++++++++++  ++ +   +  + ++k+++ ++++e 
  gi|15668995|ref|NP_247799.1|   2 LKEIKNDYDKIREKMTQKIQELNQQITQIKKQIQIIEQNNLSDQQNQTIQKIKRQIYSIEF 62 
                                   789999999***********************99999888888888888888888888875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.036
                          COG2  27 pLeslrrdLeaylkllekellelvnedyadFvslSghLvglqeeleevesplaaarkkv 85 
                                   ++e++++ L++++  + +  +e+  ++++  ++l ++Lv +++++ ++++++  + k++
  gi|15668995|ref|NP_247799.1|  79 TFEDMCEYLDSHS-GIGRIFAESFMREIEKNIQLMKQLVMMEDQIIKIKQEIRMIEKDL 136
                                   5667777776654.466777777777888888999999999999999999998888765 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.1    0.0011      0.62      28      67 ..       3      57 ..       1     131 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                          YtxH 28 kdlkekaddlkekakelleeakeka...............kekaedlkekvkeka 67
                                  k++k+ +d+++ek+++ ++e++++                +++ ++  +k+k ++
  gi|15668995|ref|NP_247799.1|  3 KEIKNDYDKIREKMTQKIQELNQQItqikkqiqiieqnnlSDQQNQTIQKIKRQI 57
                                  6789999999999999999997777777777777777666666666666666554 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.2   0.00072      0.39      36      87 ..       6      56 ..       2      68 .. 0.74
   2 ?    2.1   0.1      0.53   2.9e+02      45      69 ..     110     134 ..      77     137 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00072
                  Syntaxin-6_N 36 seeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrraf 87
                                  ++++d+ r+++ ++++++++++ ++++ ++i+e+n+     +++++++ ++ 
  gi|15668995|ref|NP_247799.1|  6 KNDYDKIREKMTQKIQELNQQITQIKKQIQIIEQNN-LSDQQNQTIQKIKRQ 56
                                  6789999***************************84.233334444433333 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.53
                  Syntaxin-6_N  45 eLrkalrsiewdledLeetvrivek 69 
                                   +L k+l  +e ++  +++ +r++ek
  gi|15668995|ref|NP_247799.1| 110 QLMKQLVMMEDQIIKIKQEIRMIEK 134
                                   3445555555555555555555555 PP

>> DUF1845  Domain of unknown function (DUF1845)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.3    0.0037         2      64     103 ..       2      41 ..       1      51 [. 0.87
   2 ?    6.0   0.2     0.016       8.8      32      96 ..      71     136 ..      65     138 .] 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0037
                       DUF1845  64 Llkleekleeareelqklleelealleelpkglslselas 103
                                   L ++++   ++re+++++++el++++++++k++++ e ++
  gi|15668995|ref|NP_247799.1|   2 LKEIKNDYDKIREKMTQKIQELNQQITQIKKQIQIIEQNN 41 
                                   6678888899***********************9977665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.016
                       DUF1845  32 rkpaIiglprfasrlrqiwrdasaddPYAdaaLlkleekleeare..elqklleelealleelpkgl 96 
                                   r ++I   + f ++ + ++ ++     +A+ ++ ++e++++ +++   +++++ ++++ ++ ++k l
  gi|15668995|ref|NP_247799.1|  71 RSNMIY-SKTFEDMCEYLDSHSGIGRIFAESFMREIEKNIQLMKQlvMMEDQIIKIKQEIRMIEKDL 136
                                   444444.478999999************************999884456777777777777766665 PP

>> MIS13  Mis12-Mtw1 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.0     0.015       8.3     223     272 ..       5      59 ..       1      79 [. 0.68
   2 ?    8.3   0.5    0.0023       1.3     154     182 ..     103     131 ..      68     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHCTSTTTSS CS
                         MIS13 223 ilsdnanveskletkvDeLqdsvhkLdsa.....skalnelstqklqklsrllak 272
                                   i++d  ++ +k+ +k+ eL++++ +++++     ++ l++ ++q +qk++r++++
  gi|15668995|ref|NP_247799.1|   5 IKNDYDKIREKMTQKIQELNQQITQIKKQiqiieQNNLSDQQNQTIQKIKRQIYS 59 
                                   5566667777777777777777766665311111367888888888899888875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0023
                                   .XXSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MIS13 154 lpnaknieneenlailkekikalknEike 182
                                    + +kni++ ++l +++ +i ++k+Ei  
  gi|15668995|ref|NP_247799.1| 103 REIEKNIQLMKQLVMMEDQIIKIKQEIRM 131
                                   6678**********************975 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.4    0.0067       3.6      31      60 ..       9      38 ..       1      47 [. 0.68
   2 ?    4.8   0.8     0.053        29       7      68 ..      47     114 ..      42     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0067
                       DUF1515 31 sdasrakmyrkmdelvervtalegsvvklk 60
                                   d +r km++k+ el +++t ++  +  ++
  gi|15668995|ref|NP_247799.1|  9 YDKIREKMTQKIQELNQQITQIKKQIQIIE 38
                                  566788888888888888777776665554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.053
                       DUF1515   7 lqqlgtllaevkelredlkrse.drsdasrakmyrkmdelvervtal.....egsvvklkaditsvke 68 
                                    q+++++++++  +  d+ r e +rs+++ +k ++ m e ++  + +     e+ + +++++i  +k+
  gi|15668995|ref|NP_247799.1|  47 NQTIQKIKRQIYSIEFDILRVEsNRSNMIYSKTFEDMCEYLDSHSGIgrifaESFMREIEKNIQLMKQ 114
                                   58899999999999999988774689999999988888877654332111226667777777777776 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.3     0.021        12      67      93 ..      13      39 ..       2      46 .. 0.68
   2 ?    2.6   0.1      0.33   1.8e+02      58      90 ..      41      73 ..      37      81 .. 0.76
   3 ?    3.4   0.0       0.2   1.1e+02      61      96 ..     104     137 ..      88     138 .] 0.67

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.021
                       DUF4140 67 lkalraeleeledelaaledelaaaea 93
                                   ++++++++el++++++++++++ +e+
  gi|15668995|ref|NP_247799.1| 13 REKMTQKIQELNQQITQIKKQIQIIEQ 39
                                  455667777777777777777776665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.33
                       DUF4140 58 pnreaeeeelkalraeleeledelaaledelaa 90
                                    ++++++ ++++++++ ++e ++ ++e+ +++
  gi|15668995|ref|NP_247799.1| 41 NLSDQQNQTIQKIKRQIYSIEFDILRVESNRSN 73
                                  455566656999999999999999999988765 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.2
                       DUF4140  61 eaeeeelkalraeleeledelaaledelaaaearla 96 
                                   e+e++   +l ++l   ed++ ++++e++ +e+ l+
  gi|15668995|ref|NP_247799.1| 104 EIEKN--IQLMKQLVMMEDQIIKIKQEIRMIEKDLK 137
                                   44443..56667777777777777777777776665 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  14.8     0.031        17     131     244 ..      16     137 ..       2     138 .] 0.68

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.031
                       Leu_zip 131 LkkeierLkeenekLkerlkelEkqatsaleek..sklekalkelqkelgekkdekenskeiskleeklae......lkld 203
                                   + ++i++L+++ +++k++++ +E++  s  +++  +k+++++ +++ ++   +++++n  + ++ e+  +       +   
  gi|15668995|ref|NP_247799.1|  16 MTQKIQELNQQITQIKKQIQIIEQNNLSDQQNQtiQKIKRQIYSIEFDILRVESNRSNMIYSKTFEDMCEYldshsgIGRI 96 
                                   567899999999999999999998766544443225777777777666555554444444333344333330000003444 PP

                       Leu_zip 204 lektleektasaksleedlastkhelLkvqeqLelaekeLe 244
                                   + ++  ++ +++ +l+++l+ +  +++k+++++ + ek+L+
  gi|15668995|ref|NP_247799.1|  97 FAESFMREIEKNIQLMKQLVMMEDQIIKIKQEIRMIEKDLK 137
                                   66677888889999************************995 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.2    0.0014      0.75       6      45 ..      14      56 ..       8      73 .. 0.82
   2 ?    2.2   0.2      0.23   1.3e+02      18      44 ..     101     127 ..      94     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                       DUF4988  6 ndlkdrvaaleeqvkelndniealkk..ll.eegkviteveen 45
                                  +++ ++++ l++q+ +++++i+ +++  l  +++++i +++++
  gi|15668995|ref|NP_247799.1| 14 EKMTQKIQELNQQITQIKKQIQIIEQnnLSdQQNQTIQKIKRQ 56
                                  568899999***********9999752255899*****99984 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.23
                       DUF4988  18 qvkelndniealkklleegkvitevee 44 
                                    ++e+++ni+ +k+l+  +  i+++++
  gi|15668995|ref|NP_247799.1| 101 FMREIEKNIQLMKQLVMMEDQIIKIKQ 127
                                   567788888888888766666666655 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   4.7   0.00016     0.087      41     104 ..      10      74 ..       2      83 .. 0.67
   2 ?    0.8   0.8      0.51   2.8e+02     209     242 ..      99     132 ..      95     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                   HHHHH.HHHHHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           HBM  41 ataaa.vqkkldelkaqlqklkakfkspenvrlLqeqlalvqeyrksfnelraayesrnaaRqel 104
                                   ++  +  ++k++el++q +++k++ +  e+  l ++q +++q+++++   ++  + + +  R+++
  gi|15668995|ref|NP_247799.1|  10 DKIREkMTQKIQELNQQITQIKKQIQIIEQNNLSDQQNQTIQKIKRQIYSIEFDILRVESNRSNM 74 
                                   44444477777777777777777777777777777777777777777766666666666666666 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.51
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           HBM 209 eqfkaavaaieqarkemteqgdeivkisdeLyqi 242
                                   e+f +++++ +q+ k++  + d+i+ki +e+  i
  gi|15668995|ref|NP_247799.1|  99 ESFMREIEKNIQLMKQLVMMEDQIIKIKQEIRMI 132
                                   6788889999999999999999999999998765 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.4    0.0032       1.8      36      88 ..       2      54 ..       1      67 [. 0.89
   2 ?    3.5   0.2      0.15        79      26      84 ..      92     126 ..      60     137 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0032
                         PIN_2 36 veeiekhkealvkksklseeeleellelletkikiveeslyeskikeAkeria 88
                                  ++ei++  +++ +k  ++ +el++ +  ++++i+i+e++ ++++ ++  + i+
  gi|15668995|ref|NP_247799.1|  2 LKEIKNDYDKIREKMTQKIQELNQQITQIKKQIQIIEQNNLSDQQNQTIQKIK 54
                                  689**************************************988777666555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.15
                         PIN_2  26 aleliapeeaveeiekhkealvkksklseeeleellelletkikiveeslye.skikeAk 84 
                                    +  i +e  + eiek  +                         ++++ ++  ++i + k
  gi|15668995|ref|NP_247799.1|  92 GIGRIFAESFMREIEKNIQ-------------------------LMKQLVMMeDQIIKIK 126
                                   3334445555555555555.........................4444444333333333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  13.7     0.014       7.7      23      88 ..       4      70 ..       1     137 [. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.014
                         TMPIT 23 qkleelsklqskcskeikkqkkrlkelksslkklkks.vkeeeeeeveelkeelkerkkvlkevesl 88
                                  +  +++ k  +k++++i++ +++++++k++++ ++++ ++++++++++++k+++ +++  + +ves 
  gi|15668995|ref|NP_247799.1|  4 EIKNDYDKIREKMTQKIQELNQQITQIKKQIQIIEQNnLSDQQNQTIQKIKRQIYSIEFDILRVESN 70
                                  4456677778888888888888888888888888776355777778888888888777776666654 PP

>> DUF4665  Domain of unknown function (DUF4665)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   7.1   0.00023      0.12      30      80 ..       3      52 ..       2      70 .. 0.76
   2 ?    0.4   1.5       1.8   9.9e+02      45      68 ..     113     136 ..     102     138 .] 0.51

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00023
                       DUF4665 30 kpVttnLKkinavkkekvenldkalvdiqkdlkslskklkletkkkekvkk 80
                                  k ++ +  ki  +  +k+++l++++++i+k+++ + ++  +++ ++++++k
  gi|15668995|ref|NP_247799.1|  3 KEIKNDYDKIREKMTQKIQELNQQITQIKKQIQIIEQNNLSDQ-QNQTIQK 52
                                  567777889999*********************9988554444.4444543 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.8
                       DUF4665  45 ekvenldkalvdiqkdlkslskkl 68 
                                   ++   ++ ++++i+++++ + k+l
  gi|15668995|ref|NP_247799.1| 113 KQLVMMEDQIIKIKQEIRMIEKDL 136
                                   334445555555555555554443 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   9.6   0.00033      0.18      39      92 ..       6      61 ..       2      67 .. 0.89
   2 ?   -1.0   0.5       1.6   8.8e+02      67      92 ..     108     133 ..      99     136 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                       DUF3450 39 idklddekqellaeyralkeeleslevyne..qlerlvasqeqeiasleeqieeie 92
                                  ++++d+ ++++ +++++l++++ +++++ +  ++++l ++q+q+i+++++qi +ie
  gi|15668995|ref|NP_247799.1|  6 KNDYDKIREKMTQKIQELNQQITQIKKQIQiiEQNNLSDQQNQTIQKIKRQIYSIE 61
                                  6899999******************9887633778899**************9987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                       DUF3450  67 neqlerlvasqeqeiasleeqieeie 92 
                                   n ql +++  +e +i +++++i  ie
  gi|15668995|ref|NP_247799.1| 108 NIQLMKQLVMMEDQIIKIKQEIRMIE 133
                                   45566666666666666666666555 PP

>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.6    0.0081       4.4      53      78 ..      10      35 ..       1      36 [. 0.82
   2 ?   11.2   3.8    0.0007      0.38       3      37 ..      25      60 ..      23      66 .. 0.88
   3 ?    0.9   0.4       1.1   5.9e+02      58      78 ..     117     137 ..      98     138 .] 0.60

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0081
                       V-SNARE 53 sserasykaklreykselkklkkelk 78
                                  ++ r ++++k++e ++++ ++kk+++
  gi|15668995|ref|NP_247799.1| 10 DKIREKMTQKIQELNQQITQIKKQIQ 35
                                  4899*******************987 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0007
                       V-SNARE  3 ellaeiksklarlsslag.eerkaalreiekkldea 37
                                  + +++ik++++ + +++  +++++++++i++++ ++
  gi|15668995|ref|NP_247799.1| 25 QQITQIKKQIQIIEQNNLsDQQNQTIQKIKRQIYSI 60
                                  6789**********999779***********99765 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.1
                       V-SNARE  58 sykaklreykselkklkkelk 78 
                                   ++  ++  +k+e+  ++k+lk
  gi|15668995|ref|NP_247799.1| 117 MMEDQIIKIKQEIRMIEKDLK 137
                                   455555666666666666665 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.0    0.0054       2.9      12      69 ..       2      60 ..       1      72 [. 0.65
   2 ?    0.3   0.1         2   1.1e+03      13      28 ..     113     128 ..      85     137 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0054
                       DUF2203 12 Lpllkelleelr.alrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveei 69
                                  L ++k+ ++++r +++++++el ++++++k++ +  e+++l  + ++  ++i++ +  i
  gi|15668995|ref|NP_247799.1|  2 LKEIKNDYDKIReKMTQKIQELNQQITQIKKQIQIIEQNNLSDQQNQTIQKIKRQIYSI 60
                                  66666666666633456677777777777777666667777777777777776666655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2
                       DUF2203  13 pllkelleelralrke 28 
                                    +l  + +++++ ++e
  gi|15668995|ref|NP_247799.1| 113 KQLVMMEDQIIKIKQE 128
                                   1111112222222222 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.7    0.0023       1.3      43      79 ..       2      39 ..       1      42 [. 0.84
   2 ?    5.8  10.7     0.032        17      29      78 ..      13      61 ..      10      74 .. 0.86
   3 ?   -2.0   0.0       8.7   4.7e+03       3      13 ..      79      89 ..      77      93 .. 0.55
   4 ?    4.7   1.3     0.069        37      43      79 ..      98     134 ..      95     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0023
                       BLOC1_2 43 aaslekkleklnekye.elqpylqqidqiekqvteLee 79
                                  +++++++ +k++ek   ++q++ qqi qi+kq++ +e+
  gi|15668995|ref|NP_247799.1|  2 LKEIKNDYDKIREKMTqKIQELNQQITQIKKQIQIIEQ 39
                                  67788888888888776999999999999999998887 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.032
                       BLOC1_2 29 NeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78
                                   e++++k+++l++++ +++k+++ +++ ++  +++ q i++i++q+ ++e
  gi|15668995|ref|NP_247799.1| 13 REKMTQKIQELNQQITQIKKQIQIIEQ-NNLSDQQNQTIQKIKRQIYSIE 61
                                  578999999999999999999999988.8888999999999999998887 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 8.7
                       BLOC1_2  3 mfekvskylea 13
                                  +fe++ +yl++
  gi|15668995|ref|NP_247799.1| 79 TFEDMCEYLDS 89
                                  45555555554 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.069
                       BLOC1_2  43 aaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                   a+s+ +++ek  ++ ++l  + +qi +i+++++ +e+
  gi|15668995|ref|NP_247799.1|  98 AESFMREIEKNIQLMKQLVMMEDQIIKIKQEIRMIEK 134
                                   5667777777778888888888888888888887775 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.2    0.0099       5.4      23      66 ..      15      56 ..       1      61 [. 0.50
   2 ?   -0.2   0.1       2.3   1.2e+03      34      48 ..     114     128 ..      97     137 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0099
                        DUF948 23 klkktldeaaatieelekqvdpilkevedllakvnelledvnek 66
                                  k+++ ++e++++i++++kq++ i  e ++l ++ n++ + ++++
  gi|15668995|ref|NP_247799.1| 15 KMTQKIQELNQQITQIKKQIQII--EQNNLSDQQNQTIQKIKRQ 56
                                  33444555555555555555433..3334444444444444444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.3
                        DUF948  34 tieelekqvdpilke 48 
                                   ++  +e+q+ +i +e
  gi|15668995|ref|NP_247799.1| 114 QLVMMEDQIIKIKQE 128
                                   222233444444444 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.9      0.29   1.6e+02      76      97 ..      14      35 ..       4      42 .. 0.76
   2 ?    6.1   0.1     0.044        24      45      97 ..      92     137 ..      70     138 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.29
                       DUF5320 76 elLeeqaeaLeeeleaikkrlk 97
                                  e ++++++ L++++ +ikk+++
  gi|15668995|ref|NP_247799.1| 14 EKMTQKIQELNQQITQIKKQIQ 35
                                  5567888888888888888875 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.044
                       DUF5320  45 glgrgfgrrrraggarlaaaetaeaskeeekelLeeqaeaLeeeleaikkrlk 97 
                                   g+gr f  ++++          ++ +  ++  ++e+q+  +++e+  i+k lk
  gi|15668995|ref|NP_247799.1|  92 GIGRIFAESFMREI-------EKNIQLMKQLVMMEDQIIKIKQEIRMIEKDLK 137
                                   55555555333333.......44557778888899999999999999998886 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.4   0.00081      0.44      46      81 ..       1      36 [.       1      39 [. 0.92
   2 ?    2.4   0.5      0.52   2.8e+02      28      54 ..      38      61 ..      33      67 .. 0.76
   3 ?   -0.3   0.2       3.7     2e+03      48      58 ..     118     130 ..      96     136 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00081
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHCHTHHHHHH CS
                          FliT 46 llrrilandaeirallqprldelqkllgalrrqrka 81
                                  +l++i  + ++ir+ + ++ +el ++++++++q + 
  gi|15668995|ref|NP_247799.1|  1 MLKEIKNDYDKIREKMTQKIQELNQQITQIKKQIQI 36
                                  6899****************************9875 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.52
                                  HCS--ST--HHHHHHHHHHHHHHHHHH CS
                          FliT 28 reldaaplspaereekrellrriland 54
                                  +   + +ls+++ + +++++r+i  ++
  gi|15668995|ref|NP_247799.1| 38 E---QNNLSDQQNQTIQKIKRQIYSIE 61
                                  3...44699************997765 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 3.7
                                   H..HHHHHHHHHH CS
                          FliT  48 r..rilandaeir 58 
                                   +  +i+++ +eir
  gi|15668995|ref|NP_247799.1| 118 MedQIIKIKQEIR 130
                                   1234444444444 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.4    0.0027       1.5      11      52 ..      14      54 ..       4     102 .. 0.70
   2 ?    3.3   1.5      0.24   1.3e+02       5      29 ..     110     134 ..     101     138 .] 0.57

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0027
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA 11 eeleeqleelleeleelkeelaelleenaeLeleneklrerl 52
                                  e+++++++el+++++++k++++ ++e+n+    +n+++++  
  gi|15668995|ref|NP_247799.1| 14 EKMTQKIQELNQQITQIKKQIQ-IIEQNNLSDQQNQTIQKIK 54
                                  57999*************9996.6777777777787777654 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.24
                                   HHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA   5 elfdkleeleeqleelleeleelke 29 
                                   +l+++l  +e+q+ ++++e++ +++
  gi|15668995|ref|NP_247799.1| 110 QLMKQLVMMEDQIIKIKQEIRMIEK 134
                                   3555555555555555555555554 PP

>> DUF3251  Protein of unknown function (DUF3251)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   8.3    0.0042       2.3       9      39 ..      15      44 ..       9      53 .. 0.81
   2 ?    0.4   0.1       0.8   4.3e+02      16      44 ..      45      72 ..      43      96 .. 0.73
   3 ?    2.6   1.7      0.17        94       6      34 ..     101     128 ..      96     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0042
                                  ---S-------------HHHHHHHHHHHHHH CS
                       DUF3251  9 qlkqsvsklnqelktleqetvkieqqnaLna 39
                                  +++q++ +lnq+++++++++  ieq+n L  
  gi|15668995|ref|NP_247799.1| 15 KMTQKIQELNQQITQIKKQIQIIEQNN-LSD 44
                                  8*****************998888875.444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.8
                                  ----------HHHHHHHHHHHHHHH-SSS CS
                       DUF3251 16 klnqelktleqetvkieqqnaLnakskkg 44
                                  + nq +++++ ++  ie    L ++s+++
  gi|15668995|ref|NP_247799.1| 45 QQNQTIQKIKRQIYSIEFD-ILRVESNRS 72
                                  5688888888888888876.777777654 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.17
                                   ------S-------------HHHHHHHHH CS
                       DUF3251   6 elrqlkqsvsklnqelktleqetvkieqq 34 
                                    +r++++++ +l ++l  +e++++ki+q+
  gi|15668995|ref|NP_247799.1| 101 FMREIEKNI-QLMKQLVMMEDQIIKIKQE 128
                                   577777777.6888999999999999997 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   5.3     0.042        23      38      64 ..      15      41 ..       9      46 .. 0.74
   2 ?    5.8   0.6     0.032        17      36      64 ..      43      71 ..      37      74 .. 0.82
   3 ?    3.4   1.3      0.17        95      26      58 ..     105     137 ..     102     138 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.042
                        Csm1_N 38 tkdqeiesLkeqlaeleekvkeleerr 64
                                  + +q+i++L +q+ +++++++ +e+++
  gi|15668995|ref|NP_247799.1| 15 KMTQKIQELNQQITQIKKQIQIIEQNN 41
                                  557888888888888888888777665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.032
                        Csm1_N 36 letkdqeiesLkeqlaeleekvkeleerr 64
                                   ++++q i+++k+q+ ++e ++ + e++r
  gi|15668995|ref|NP_247799.1| 43 SDQQNQTIQKIKRQIYSIEFDILRVESNR 71
                                  58999************999887777665 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.17
                        Csm1_N  26 vhENsvLsqkletkdqeiesLkeqlaeleekvk 58 
                                   ++ N  L+++l   +++i ++k+++  +e+++k
  gi|15668995|ref|NP_247799.1| 105 IEKNIQLMKQLVMMEDQIIKIKQEIRMIEKDLK 137
                                   567999999****************99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3787  (0.211222); expected 358.6 (0.02)
Passed bias filter:                      854  (0.0476323); expected 358.6 (0.02)
Passed Vit filter:                       146  (0.00814323); expected 17.9 (0.001)
Passed Fwd filter:                        51  (0.00284455); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 965.75
//
Query:       gi|15668996|ref|NP_247800.1|  [L=167]
Description: hypothetical protein MJ_0809 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-14   53.6   0.2    6.6e-14   52.1   0.0    1.7  2  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
        0.1   13.2   1.7        3.9    8.1   0.3    2.4  2  DUF3994          Domain of unknown function (DUF3994)
        2.1    8.2   8.5       0.16   11.8   1.5    2.3  3  SUB1_ProdP9      SUB1 protease Prodomain ProdP9


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   1.1e-17   6.6e-14       1      78 [.       9      90 ..       9      96 .. 0.82
   2 ?   -1.4   0.0      0.53   3.2e+03      55      76 ..     123     145 ..     111     152 .. 0.66

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.1e-17
               Acylphosphatase  1 vrllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaeg.eeek...vekfleelksgppkarvdeveveeleeee 78
                                  ++l ++G+VQ vgFR  + ++ k lg++G + N +dg+V+i+a   +ee+   ++k++e+l+++ + ++++++e + l++  
  gi|15668996|ref|NP_247800.1|  9 YELKIYGKVQHVGFRDRIENIGKGLGINGIIYNYKDGTVRILANFdDEEDkelFKKYIERLEKKDKLIEIEKIEEKRLNTYI 90
                                  5789****************************************95444433355555666666666*******99887655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.53
               Acylphosphatase  55 eelksgppk.arvdeveveelee 76 
                                   +el++ ++   +++++ v+++e 
  gi|15668996|ref|NP_247800.1| 123 AELEEHKKVlLEIKDMHVKTVEI 145
                                   55666444457788877777664 PP

>> DUF3994  Domain of unknown function (DUF3994)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0098        58      50      65 ..      32      47 ..      19      80 .. 0.85
   2 ?    8.1   0.3   0.00066       3.9       8      62 ..     107     165 ..     101     166 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0098
                       DUF3994 50 GikienvinnvkdGte 65
                                  G+ i+ +i n+kdGt 
  gi|15668996|ref|NP_247800.1| 32 GLGINGIIYNYKDGTV 47
                                  788999********95 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00066
                       DUF3994   8 ankklkeakriwkkafkklkaeikiG....dGtvssddlksldkkaGikienvinnvkd 62 
                                    nkkl+e+ ++ k +f +l+++ k+     d  v + ++ s + +   +i++ ++++kd
  gi|15668996|ref|NP_247800.1| 107 LNKKLDEGVKYIKLIFAELEEHKKVLleikDMHVKTVEILSEHTRILNEIKDTLKDIKD 165
                                   599*****************998876554444444445544444444477777777776 PP

>> SUB1_ProdP9  SUB1 protease Prodomain ProdP9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.5   2.6e-05      0.16      35      76 ..      39      81 ..      31      84 .. 0.80
   2 ?   -0.4   0.3      0.17     1e+03      55      64 ..     112     121 ..      99     142 .. 0.60
   3 ?   -0.4   0.3      0.18   1.1e+03      36      65 ..     123     154 ..     114     166 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                   SUB1_ProdP9 35 lanlknlksiiielkedttdeeli.eyikileekGaliesdkl 76
                                  + n k+    i+   +d  d+el  +yi+ le+k  lie +k+
  gi|15668996|ref|NP_247800.1| 39 IYNYKDGTVRILANFDDEEDKELFkKYIERLEKKDKLIEIEKI 81
                                  55666666667777799999999637*************9996 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.17
                   SUB1_ProdP9  55 eelieyikil 64 
                                   +e ++yik++
  gi|15668996|ref|NP_247800.1| 112 DEGVKYIKLI 121
                                   5667777764 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.18
                   SUB1_ProdP9  36 anlknlksiiielked..ttdeelieyikile 65 
                                   a+l + k +++e+k+    t e l e+ +il+
  gi|15668996|ref|NP_247800.1| 123 AELEEHKKVLLEIKDMhvKTVEILSEHTRILN 154
                                   55666666666666641135555666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1783  (0.0994478); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1325.04
//
Query:       gi|15668997|ref|NP_247801.1|  [L=225]
Description: hypothetical protein MJ_0810 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-55  186.1   0.0    4.2e-55  185.9   0.0    1.0  1  AMMECR1   AMMECR1


Domain annotation for each model (and alignments):
>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.9   0.0   2.4e-59   4.2e-55       1     166 []      37     210 ..      37     210 .. 0.95

  Alignments for each domain:
  == domain 1  score: 185.9 bits;  conditional E-value: 2.4e-59
                                   HHHHHHHHHHHTTSS-S-HH---HHHHSEEEEEEEEE.EE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS----HH CS
                       AMMECR1   1 lklareaieealkeekkleeeakeelkekaglFVtlk.ekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRFspvtae 80 
                                   +++ar++ie++l  +k + e+++e ++ek+g+F tl+   ++eLRGCiG  ep +pL e++ e+A++aA++DpRF+pvt e
  gi|15668997|ref|NP_247801.1|  37 VRYARAVIENYLAGKKIVIESYPEVFNEKRGCFCTLHtYPDKELRGCIGIPEPIMPLIEALEEAAISAATKDPRFPPVTLE 117
                                   689*************999******************98889*************************************** PP

                                   HHTTEEEEEEEE---EE-...-....GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS-TTCCCST CS
                       AMMECR1  81 ElpeleveVsvLtepepi...v....ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKaglrpdewkds 154
                                   E++++ veVs+Lt+pe i   +    le++++g++Gliie+g ++++lLPqv+ve+gwd+ee+la+l+ Kagl+pd w  +
  gi|15668997|ref|NP_247801.1| 118 EMDSIVVEVSILTPPELIkvnHpkeyLEKIKIGRDGLIIEYGFYRGLLLPQVPVEYGWDVEEYLAHLCLKAGLPPDMWLAE 198
                                   ******************66514556999**********************************************9999** PP

                                   TSEEEEE-EEEE CS
                       AMMECR1 155 eikltryevekf 166
                                    +k++r+e+++f
  gi|15668997|ref|NP_247801.1| 199 GVKIYRFEAQIF 210
                                   *********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1451.92
//
Query:       gi|15668998|ref|NP_247802.1|  [L=439]
Description: hypothetical protein MJ_0811 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-06   27.5   0.0    2.2e-05   25.1   0.0    2.2  2  VWA_2       von Willebrand factor type A domain
     0.0023   17.3   0.0     0.0045   16.4   0.0    1.4  1  VWA_CoxE    VWA domain containing CoxE-like protein
     0.0081   15.8   0.2      0.033   13.9   0.2    2.0  1  TUDOR_5     Histone methyltransferase Tudor domain 1
  ------ inclusion threshold ------
      0.013   15.5   0.6      0.043   13.8   0.1    2.2  2  DUF4446     Protein of unknown function (DUF4446)
      0.028   14.6   0.0      0.076   13.2   0.0    1.7  1  DUF2201     VWA-like domain (DUF2201)
       0.11   12.2   0.0       0.19   11.5   0.0    1.3  1  LnmK_N_HDF  LnmK N-terminal Hot Dog Fold domain


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.4   4.1e+03      43      80 ..      55      88 ..      49     100 .. 0.64
   2 !   25.1   0.0   7.3e-09   2.2e-05       1     106 [.     274     377 ..     274     378 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.4
                         VWA_2 43 vtfsdgpevlipltkdkakilnalrnleakgggtnlaa 80
                                  v f++ +e +++ +k  a ++ a++n+e++  ++ l +
  gi|15668998|ref|NP_247802.1| 55 VEFNEYVEEKFKINK--AILEGAIKNIEYE--KSKLLT 88
                                  666666666666555..7788888888864..444444 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 7.3e-09
                         VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallk..slpgdrvglvtfsdgp..evlipltkdkakilnalrnleak.gggt 76 
                                   ++++lD SgSm ++     r    k+ + ++++  ++ +  +  ++f+dg+  e++i++++   +++++++    + gggt
  gi|15668998|ref|NP_247802.1| 274 IIILLDHSGSMYGD-----REIWGKAVALSIIEiaKRENRDIYYIAFDDGVrfEKKINPKT--ITFDEIIEIASLYfGGGT 347
                                   689********998.....5666666777777754666779********983356666654..444554444443348*** PP

                         VWA_2  77 nlaaaLqlarkalkkrrkgekrvivlitDg 106
                                   n+   L+ a++++k+  + +++ i+litDg
  gi|15668998|ref|NP_247802.1| 348 NFIMPLNRAMSIIKEHETFKNADILLITDG 377
                                   *************99999***********9 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.5e-06    0.0045      54     162 ..     268     379 ..     253     389 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                      VWA_CoxE  54 erkprelvllvDvSgSma.....aysaiflallhAllqqlprtevfaFdtrlvdlTralrerDpaeaLarvsaaved.lgG 128
                                   e+++ ++++l+D SgSm      +  a+ l++++ + ++ +++  +aFd+ + +  ++++    +  ++++ +++    gG
  gi|15668998|ref|NP_247802.1| 268 EKQKGPIIILLDHSGSMYgdreiWGKAVALSIIEIAKRENRDIYYIAFDDGV-RFEKKIN--PKTITFDEIIEIASLyFGG 345
                                   455669***********722222224667888888888888********986.7888888..7889999998888888*** PP

                      VWA_CoxE 129 gTrigaalaeflelvtrpaLsrravvvlvsDgle 162
                                   gT+    l+ +++ ++     + a ++l++Dg+ 
  gi|15668998|ref|NP_247802.1| 346 GTNFIMPLNRAMSIIKEHETFKNADILLITDGYA 379
                                   ****************99999***********96 PP

>> TUDOR_5  Histone methyltransferase Tudor domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.2   1.1e-05     0.033      25      45 ..     299     319 ..     296     321 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                       TUDOR_5  25 iAEppkktNryRYlifFDDGy 45 
                                   i E+ k++Nr  Y i FDDG 
  gi|15668998|ref|NP_247802.1| 299 IIEIAKRENRDIYYIAFDDGV 319
                                   67999***************5 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.7     5e+03      52      59 ..      33      40 ..       9      82 .. 0.54
   2 ?   13.8   0.1   1.4e-05     0.043      10      71 ..      98     160 ..      92     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                       DUF4446 52 eeveelke 59
                                  ++++ ++e
  gi|15668998|ref|NP_247802.1| 33 SQYHPIHE 40
                                  33333333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.4e-05
                       DUF4446  10 vvillillivllvklkklkkkykklmkgkdgksleellkeklee.veelkeeseelekeieel 71 
                                   + i+++  ++ ++kl kl+k++kk+ ++ +g+ le++lke  ++ ++++ ee++e+ + ++++
  gi|15668998|ref|NP_247802.1|  98 ATIMFCEKFFENLKLAKLNKELKKFASEGKGEGLEDKLKEIAKNtMKDIAEEVSEVIQGFNAV 160
                                   67888899999***************************9987642788888888877766665 PP

>> DUF2201  VWA-like domain (DUF2201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.5e-05     0.076       1      76 [.     274     357 ..     274     366 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                       DUF2201   1 lvlavDtSgSikdk.el..arfaaeiadilrrleaevhvvavdeevqsvqrlep.....aeklaelqltggGGTdlvpvlE 73 
                                   +++ +D SgS+  + e+  +  a  i +i +r + ++  +a+d+ v+ +++++p     +e ++  +l  gGGT+++ +l 
  gi|15668998|ref|NP_247802.1| 274 IIILLDHSGSMYGDrEIwgKAVALSIIEIAKRENRDIYYIAFDDGVRFEKKINPktitfDEIIEIASLYFGGGTNFIMPLN 354
                                   578899999996541543345666888999999********************985554454555678889*****99998 PP

                       DUF2201  74 ava 76 
                                   ++ 
  gi|15668998|ref|NP_247802.1| 355 RAM 357
                                   875 PP

>> LnmK_N_HDF  LnmK N-terminal Hot Dog Fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.2e-05      0.19      49      95 ..     312     357 ..     295     391 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.2e-05
                    LnmK_N_HDF  49 ylsfayfrvrgseelsprgltfGdrldvtskvfdlGsesvltlhrva 95 
                                   y++f    vr +++++p+++tf + ++++s  f+ G++ ++ l r +
  gi|15668998|ref|NP_247802.1| 312 YIAFDD-GVRFEKKINPKTITFDEIIEIASLYFGGGTNFIMPLNRAM 357
                                   556554.69********************************998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1060  (0.0591221); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 2908.77
//
Query:       gi|15668999|ref|NP_247803.1|  [L=373]
Description: hypothetical protein MJ_0812 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-27   94.0   0.0    2.2e-26   92.5   0.0    1.8  2  AAA_5            AAA domain (dynein-related subfamily)
      7e-16   57.9   0.2    2.6e-15   56.1   0.2    2.0  1  AAA_lid_8        AAA lid domain
     0.0004   20.8   0.1     0.0012   19.3   0.0    1.9  1  AAA              ATPase family associated with various cellul
    0.00061   19.0   0.0     0.0064   15.6   0.0    2.1  2  MCM              MCM P-loop domain
     0.0013   18.6   0.0     0.0022   17.8   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
     0.0028   17.6   0.0       0.01   15.7   0.0    1.9  2  RsgA_GTPase      RsgA GTPase
     0.0087   15.8   0.0      0.014   15.2   0.0    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.017   14.9   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
      0.015   15.7   0.0      0.038   14.4   0.0    1.9  1  AAA_16           AAA ATPase domain
       0.11   12.0   0.0       0.22   11.0   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
       0.57   10.4   4.6       0.28   11.4   1.1    2.3  2  DUF2097          Uncharacterized protein conserved in archaea


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.0   1.4e-29   2.2e-26       2     138 .]      33     160 ..      32     160 .. 0.89
   2 ?   -2.2   0.0       2.3   3.8e+03      93      93 ..     219     219 ..     181     263 .. 0.46

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.4e-29
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------....G-SEEEEESGGG CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraar....egeilvlDEver 76 
                                    + +G+pG++Ks+l++ +a+ +n++++++++tr+tte++l+g+++ik  +++ ++v      +      ++ei++lDEv++
  gi|15668999|ref|NP_247803.1|  33 TVFLGNPGVAKSQLIRAIASHINANYFEKLITRFTTEDELFGPLSIKelKDNDRFVR-----KTSgylpTAEIAFLDEVFK 108
                                   6789******************************************66633333333.....3334445************ PP

                                   --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                         AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                   a+s++ln+Lls+++er ++  +g++ +k++       +++++++n+l+ ++ne   a+++Rf
  gi|15668999|ref|NP_247803.1| 109 ANSSILNALLSIINERIYH--NGDRIEKVPL------ISLFGASNELP-EENE-LLAFYDRF 160
                                   *******************..*********9......***********.9999.899****9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.3
                                   E CS
                         AAA_5  93 r 93 
                                   +
  gi|15668999|ref|NP_247803.1| 219 K 219
                                   2 PP

>> AAA_lid_8  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.2   1.6e-18   2.6e-15       4      68 ..     213     275 ..     208     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1.6e-18
                     AAA_lid_8   4 elileiknkleeeeeaiyvSDRRwkkivkllkasAylngrdevnlsDllllkhclWnepeqkekv 68 
                                   + +++ik +l  e e+i +SDRR+kk+vk  k  Aylng+++ ++ Dl +l+h++Wnep++  kv
  gi|15668999|ref|NP_247803.1| 213 DDLIKIKLSL--ESEGIRISDRRFKKSVKAVKCFAYLNGKEKADENDLDILRHIYWNEPDEFYKV 275
                                   5677888888..89*********************************************998777 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   7.1e-07    0.0012       2     124 ..      34     160 ..      33     167 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.1e-07
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.......STTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHH CS
                           AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk.......yvgesekkirelfkeakeka....kpsilfiDEidala 71 
                                   ++ G+pG+ K+ l++a+a++++++++e   ++++ +        +    k++++  + +++ +    +  i f+DE+ + +
  gi|15668999|ref|NP_247803.1|  34 VFLGNPGVAKSQLIRAIASHINANYFEKLITRFTTEdelfgplSI----KELKDNDRFVRKTSgylpTAEIAFLDEVFKAN 110
                                   589*******************************55587665422....222222222333334555669******99987 PP

                                   HHHTTCCCHHHHHHHHHHHHHHHHTTTS.......SSTEEEEEEESSGGGSTHHHHS.TTS CS
                           AAA  72 ksrsgseseeeervvnqLlteldgvkkk.......eskvivigatnrpdkldpallr.gRf 124
                                   +s            +n+Ll+ +++   +          + + ga+n+  + ++ l   +Rf
  gi|15668999|ref|NP_247803.1| 111 SSI-----------LNALLSIINERIYHngdriekVPLISLFGASNELPEENELLAFyDRF 160
                                   777...........88998888877666566655433355566777655555555555555 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.9e-06    0.0064      53     140 ..      26     116 ..      13     124 .. 0.66
   2 ?    2.5   0.0     0.041        66       9      47 ..     108     147 ..      99     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.9e-06
                                   BBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEE..SSSSSSSHS.SSEEEEESSSSS.EEEE.ETHHHHTTTSEEEEE CS
                           MCM  53 klrgdinvllvgdpgtaKsqlLkyveklapravyts..gkgssaagL.taavvrdeetge.fvle.aGalvladkGvcciD 128
                                   ++ ++ + +++g+pg+aKsql++++++ ++ + + +   + +++ +L  +   ++ + ++ fv + +G l   +  ++ +D
  gi|15668999|ref|NP_247803.1|  26 SILANEHTVFLGNPGVAKSQLIRAIASHINANYFEKliTRFTTEDELfGPLSIKELKDNDrFVRKtSGYLP--TAEIAFLD 104
                                   56678899******************999988876422566777777534444444444413333133333..33466777 PP

                                   SGGGSTCHHHHH CS
                           MCM 129 efdkmkeedrsa 140
                                   e+ k +++  +a
  gi|15668999|ref|NP_247803.1| 105 EVFKANSSILNA 116
                                   776666655555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.041
                                   HTSSTHHHHHHHHSSTTSSS-HH.HHHHHHHHHH---EBB CS
                           MCM   9 akekdiieklvksiapsiyghed.vkkaillqlfggvkkk 47 
                                   +++++i++ l+++i ++iy + d + k  l++lfg++++ 
  gi|15668999|ref|NP_247803.1| 108 KANSSILNALLSIINERIYHNGDrIEKVPLISLFGASNEL 147
                                   5677899999********9987669999999999998854 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.4e-06    0.0022       1      94 [.      32     129 ..      32     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.4e-06
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfe...ekekefefkkGpv.fanllladeinrappk 77 
                                   h ++ g PG+ak +l++a+a+++++++    +t      ++ G   ++   ++++ ++ ++G +  a++ + de+ +a++ 
  gi|15668999|ref|NP_247803.1|  32 HTVFLGNPGVAKSQLIRAIASHINANYFEKLITRFTTEDELFGPLSIKelkDNDRFVRKTSGYLpTAEIAFLDEVFKANSS 112
                                   778889*******************987766666666677777543330103445556667777357999*********** PP

                         AAA_3  78 tqsalleameerqvtve 94 
                                   +  all +++er    +
  gi|15668999|ref|NP_247803.1| 113 ILNALLSIINERIYHNG 129
                                   **********9865554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.3e-06      0.01      91     124 ..      21      55 ..       3      70 .. 0.83
   2 ?   -2.0   0.1       1.8     3e+03      36      81 ..     158     205 ..     149     226 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.3e-06
                                   H.HHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-- CS
                   RsgA_GTPase  91 e.elkellkdktsvlvGqSGvGKStLinallpele 124
                                   + +l++ l+++ +v++G+ Gv KS Li a++++ +
  gi|15668999|ref|NP_247803.1|  21 DiALTSILANEHTVFLGNPGVAKSQLIRAIASHIN 55 
                                   337999************************99865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                                   HHHHHHHHHTT-EEEEEEE-.GGG--HHH.....HHHHHHHHHHHTTSEEEE CS
                   RsgA_GTPase  36 drfLvlaeekgiepvivlnK.iDlleeee.....eleelkeelealgyevll 81 
                                   drfL+    +gi+    l+K iDl ee +     +     e++++++ e l+
  gi|15668999|ref|NP_247803.1| 158 DRFLFRKVVRGIRSYENLSKlIDLEEEYKpktiiD----VEDVKKMQNEALK 205
                                   77777777777777777777446666555432221....2333333333333 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   8.3e-06     0.014       2      87 ..      34     122 ..      33     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.3e-06
               Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegk...........pklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                   v  G pG  KS+lir ++++      n + +e l  ++            k+ +++ r v++ ++  +++  ++i +lDE 
  gi|15668999|ref|NP_247803.1|  34 VFLGNPGVAKSQLIRAIASHI-----NANYFEKLITRFttedelfgplsIKELKDNDRFVRK-TSGYLPT--AEIAFLDEV 106
                                   67799*************994.....333333333333344556666856666666666665.5666665..9******** PP

               Viral_helicase1  72 lllhaGyilllaalsk 87 
                                   +++++ ++++l+ + +
  gi|15668999|ref|NP_247803.1| 107 FKANSSILNALLSIIN 122
                                   ********99887766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     1e-05     0.017      42     138 ..      25     125 ..      10     132 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                     IstB_IS21  42 sfiekkenivllGpsGvGKshlaialgveavr...aglsvlfvrvedLveelkra..rrdgklaralkrllkv.dllilDd 116
                                     i ++e  v+lG +Gv Ks l  a++ +  +   + l ++f++ ++L+  l+++  ++++++ r+ + +l + ++  lD+
  gi|15668999|ref|NP_247803.1|  25 TSILANEHTVFLGNPGVAKSQLIRAIASHINAnyfEKLITRFTTEDELFGPLSIKelKDNDRFVRKTSGYLPTaEIAFLDE 105
                                   456678999*****************987555233566789********98876622567888888877665438999999 PP

                     IstB_IS21 117 lgllpldqaeaellfeviekry 138
                                   +   + ++   + l+ +i++r 
  gi|15668999|ref|NP_247803.1| 106 VF--KANSSILNALLSIINERI 125
                                   74..556666777888887775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.3e-05     0.038       3      55 ..      14      59 ..      12     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                        AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                    R+ee+     al ++ ++  e +++ G++Gv Ks l+r+++ +++++  +f
  gi|15668999|ref|NP_247803.1| 14 LERREEI---DIALTSILAN--EHTVFLGNPGVAKSQLIRAIASHINAN--YF 59
                                  5666776...6677777777..6899********************999..33 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013      0.22      30      70 ..      27      67 ..      19      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                         AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldkekylsltinfs 70
                                  + ++ ++++ G+ G++K+ +i+ + ++++ + +  l+  f+
  gi|15668999|ref|NP_247803.1| 27 ILANEHTVFLGNPGVAKSQLIRAIASHINANYFEKLITRFT 67
                                  456788999********************888888887776 PP

>> DUF2097  Uncharacterized protein conserved in archaea (DUF2097)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.1   0.00017      0.28      42      77 ..     183     220 ..     169     229 .. 0.81
   2 ?   -1.2   0.1       1.5   2.4e+03      50      74 ..     323     345 ..     290     354 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                       DUF2097  42 k..keslrltlkldgelinqlvevdleeikddliElrH 77 
                                   +  k+++ + ++   ++ n+ ++vd+ +ikddli ++ 
  gi|15668999|ref|NP_247803.1| 183 EeyKPKTIIDVEDVKKMQNEALKVDISNIKDDLIKIKL 220
                                   3457778888888899******************9875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                       DUF2097  50 lkldgelinqlvevdleeikddliE 74 
                                   l++ g+l +  + + l+++k++ iE
  gi|15668999|ref|NP_247803.1| 323 LEILGKLNS--MSITLKDVKNKAIE 345
                                   333344333..56666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2590.97
//
Query:       gi|15669000|ref|NP_247804.1|  [L=249]
Description: cobalamin biosynthesis precorrin-3 methylase CbiH [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-35  120.6   0.0      1e-34  120.4   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
       0.13   12.5   0.1       0.93    9.8   0.1    2.0  2  GRASP55_65    GRASP55/65 PDZ-like domain
       0.14   12.2   1.9        1.4    9.0   0.0    2.8  3  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.0   1.7e-38     1e-34       1     212 [.       1     206 [.       1     207 [. 0.89

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 1.7e-38
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleea.yeeiaeal.aealrag 79 
                                   +ly+VG+G G+  + T +A ++l+++d++++++ ++ + +++l +                +++  +ei +   a + +++
  gi|15669000|ref|NP_247804.1|   1 MLYVVGIGSGNERHFTKEAEEILNKVDLIVCYK-NYKKFVERLNK-------------PIYTTGmTREIDRVDyALKEAKD 67 
                                   79*******************************.99999988763.............33444423444444466777777 PP

                  TP_methylase  80 kdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeereleall 158
                                   kdV+l++sGD ++yg +s  +e+ + ++ +++++v+PG+++ ++a a lg pl+++++v s++  l++l+++ +r + al 
  gi|15669000|ref|NP_247804.1|  68 KDVALVSSGDATIYGLASLAYEINAVKGYNVDIKVVPGITACSLASAILGSPLNHDFVVISFSdlLTPLETILKRFRCALE 148
                                   88************999999999999889999*********************************9***********9987 PP

                  TP_methylase 159 angdtlvllkapr.k.....laelaelLkealyddttpvavveragtedervvrgtleel 212
                                      d+++ +++p  k     + +++e+L+e+ +d+++ + +v++ag+++e+vv ++ ++l
  gi|15669000|ref|NP_247804.1| 149 G--DFVICIYNPLsKrrkepFLKAMEILAEFAKDKDYIIGIVKNAGRNKEEVVITNFKDL 206
                                   7..*********974689*************9999******************9998876 PP

>> GRASP55_65  GRASP55/65 PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.15   8.7e+02      63     105 ..     120     162 ..      59     174 .. 0.58
   2 ?    9.8   0.1   0.00015      0.93      59     114 ..     175     241 ..     170     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.15
                                   TTTEEEEEEE.SSSSSTSCSHHHHTTTSSS-EEEEEEETTTTE CS
                    GRASP55_65  63 pksDYiiGldkgllkgeedlselveaheekelkLlvYnsesde 105
                                    ++D+++   + ll+  e++ ++ +   e + ++ +Yn  s+ 
  gi|15669000|ref|NP_247804.1| 120 LNHDFVVISFSDLLTPLETILKRFRCALEGDFVICIYNPLSKR 162
                                   3678888777788888888888888888888888888876655 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00015
                                   HT--TTTEEEEEEE.........SSSSSTSCSHHHHTTTSSS...-EEEEEEETTTTEEEEEEE--- CS
                    GRASP55_65  59 agLvpksDYiiGldk........gllkgeedlselveaheek...elkLlvYnsesdevrevtvkps 114
                                   a++ + +DYiiG+ k         ++++ +dl++ +e++ e    +  L++ ns+++++   +++p+
  gi|15669000|ref|NP_247804.1| 175 AEFAKDKDYIIGIVKnagrnkeeVVITNFKDLYKNLEKYLEFidmNTILIIGNSSTKIINGKMITPR 241
                                   677889*******998888888888889999999998886545558889999999999988888775 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.071   4.2e+02      52      77 ..      16      39 ..       8      51 .. 0.61
   2 ?    9.0   0.0   0.00024       1.4      27      69 ..      62     103 ..      56     118 .. 0.86
   3 ?   -0.8   0.1      0.27   1.6e+03      42      42 ..     192     192 ..     150     238 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.071
                                  HHHHHHH.SSSEEEEEETTTS-HHHH CS
                       Polbeta 52 aaelediklgkkvDlvdlneapplll 77
                                   +e e+i   +kvDl+++ ++ + + 
  gi|15669000|ref|NP_247804.1| 16 TKEAEEI--LNKVDLIVCYKNYKKFV 39
                                  5556666..36677766554444443 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00024
                                   -----EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEET CS
                       Polbeta  27 areeSDiDlavllkekldleeelelaaelediklgkkvDlvdl 69 
                                   ++e  D D+a++ + + +++  ++la e++ + +g++vD+ ++
  gi|15669000|ref|NP_247804.1|  62 LKEAKDKDVALVSSGDATIYGLASLAYEINAV-KGYNVDIKVV 103
                                   67889***************************.99****9876 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.27
                                   - CS
                       Polbeta  42 k 42 
                                    
  gi|15669000|ref|NP_247804.1| 192 G 192
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1626.37
//
Query:       gi|15669001|ref|NP_247805.1|  [L=370]
Description: putative deoxyhypusine synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     5e-115  383.7   0.0   5.7e-115  383.5   0.0    1.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.5   0.0  3.2e-119  5.7e-115       5     286 ..      71     366 ..      66     368 .. 0.95

  Alignments for each domain:
  == domain 1  score: 383.5 bits;  conditional E-value: 3.2e-119
                            DS   5 syekigfqatslgeaidilnkm....rkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgkk 81 
                                    y kigfqa+++g+ai+i++++    +k +++t+f+g+tsn++ssGlreiia+lvk+k +d+ivtTagg+eeD+ik+l++ 
  gi|15669001|ref|NP_247805.1|  71 YYLKIGFQASHIGKAIKIWKHIeekrKKGDEITVFFGYTSNIVSSGLREIIAYLVKHKKIDIIVTTAGGVEEDFIKCLKP- 150
                                   57899***************99887777889*************************************************. PP

                            DS  82 tylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqk....vwspselikelGkein.......deeS 151
                                   ++lgd+e+d+++LrekginRign++vpn++y +fe++++e+++++++ q+    +++ se++++lG+ ++       +e+S
  gi|15669001|ref|NP_247805.1| 151 FILGDWEVDGKMLREKGINRIGNIFVPNDRYIAFEEYMMEFFEEILNLQRetgkIITASEFCYKLGEFMDkklkskeKEKS 231
                                   ***********************************************997566455**********8888777798889** PP

                            DS 152 ilywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanlmrn 232
                                   ilywAykn+ip+fcpa+tDgs+Gd l +f++++++++lk+d+++Di +lndia+++k+t++i+lGG++pKh i+nanl+r+
  gi|15669001|ref|NP_247805.1| 232 ILYWAYKNNIPIFCPAITDGSIGDMLYFFKKYNKDEELKIDVANDIVKLNDIAINSKETACIVLGGSLPKHSIINANLFRE 312
                                   ************************6666667889999******************************************** PP

                            DS 233 gadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlva 286
                                   g+dya+y+tta ++dGslsga ++E+vSwgki a+a+ v++++DaTi++PLlv 
  gi|15669001|ref|NP_247805.1| 313 GTDYAIYVTTALPWDGSLSGAPPEEGVSWGKIGAKADYVEIWGDATIIFPLLVY 366
                                   ****************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2373.87
//
Query:       gi|15669002|ref|NP_247806.1|  [L=308]
Description: hypothetical protein MJ_0815 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-41  142.5   0.6    1.8e-41  141.9   0.6    1.3  1  ATP-grasp_3      ATP-grasp domain
    8.7e-12   45.1   0.0    1.5e-11   44.4   0.0    1.4  1  preATP-grasp_3   pre ATP-grasp 3 domain
    0.00018   21.2   0.0    0.00035   20.3   0.0    1.5  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    0.00077   19.1   0.4     0.0021   17.7   0.4    1.8  1  RimK             RimK-like ATP-grasp domain
     0.0019   17.8   0.1     0.0069   16.0   0.1    1.9  1  ATP-grasp_4      ATP-grasp domain
     0.0028   17.2   1.7      0.011   15.3   0.2    2.4  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
     0.0091   15.5   0.1      0.015   14.8   0.1    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
  ------ inclusion threshold ------
      0.016   15.3   4.3          9    6.5   0.0    3.5  3  Ribosomal_L38e   Ribosomal L38e protein family
       0.05   12.8   2.0      0.069   12.4   0.1    2.1  3  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
      0.078   13.4   1.0          1    9.8   1.2    2.1  2  DUF4059          Protein of unknown function (DUF4059)


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.9   0.6     1e-44   1.8e-41       1     161 []     136     272 ..     136     272 .. 0.98

  Alignments for each domain:
  == domain 1  score: 141.9 bits;  conditional E-value: 1e-44
                                   HTSHHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEEEEEEE CS
                   ATP-grasp_3   1 asdKlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplSvslls 81 
                                   a +K+ ty ++k+a vk+P        ++ +kk+vvK++d++gg+++++ e++           l+qefi+G++lSvsl++
  gi|15669002|ref|NP_247806.1| 136 AGNKYLTYLAIKDA-VKTP-------KTFPPKKYVVKKIDSCGGKFNLFDENF-----------LIQEFIDGENLSVSLIV 197
                                   579***********.****.......99***********************99...........***************** PP

                                   .SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS--GG CS
                   ATP-grasp_3  82 dgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPRltts 161
                                    g+k+++l++nrq+i+k      ++G+ ++i+++lk++++++a ++v++++gl+GyvGvD++++++++y+iE+NPR+tt+
  gi|15669002|ref|NP_247806.1| 198 -GKKIHPLSLNRQYIDK----RGFVGGEVNINHKLKDKIFNEAIKAVKCINGLNGYVGVDVIVNNDGIYIIEINPRITTT 272
                                   .89************98....99*******************************************************97 PP

>> preATP-grasp_3  pre ATP-grasp 3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   8.5e-15   1.5e-11      18      77 .]      72     133 ..      56     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 8.5e-15
                preATP-grasp_3  18 avevlvvdseedvdetfrrl..aaeaDaVlvIAPEtdgiLarltrlveaagkrlLGssskAi 77 
                                   ++e++ +++e++  + ++ l   ++ D+ lv+APE ++iL++lt+++e+   ++LG+ss+Ai
  gi|15669002|ref|NP_247806.1|  72 NLEIVKIKKENEIENKLKSLlkSENIDYALVVAPEDEDILYNLTKIIESYPVKNLGCSSEAI 133
                                   48999***************77789************************************9 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     2e-07   0.00035       3     111 ..     178     293 ..     176     306 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2e-07
                  ATPgrasp_Ter   3 pallvmeyLegpEySvDvlaekgevlaavpRrKe......kgglq.elekdeelielaerlae.efgldglvnvQvreded 75 
                                   +++l++e+++g+  Sv  + +k      + R+         g+++ + + ++++++ a + ++   gl+g+v+v v  ++d
  gi|15669002|ref|NP_247806.1| 178 ENFLIQEFIDGENLSVSLIVGKKIHPLSLNRQYIdkrgfvGGEVNiNHKLKDKIFNEAIKAVKcINGLNGYVGVDVIVNND 258
                                   579999**********999987555566677543221343444445444455666655555551568************** PP

                  ATPgrasp_Ter  76 gpkLLEiNpRasGGlgysalaGvnlpylalklllgl 111
                                   g +++EiNpR+  +++    ++  l++l +k + ++
  gi|15669002|ref|NP_247806.1| 259 GIYIIEINPRITTTIY-GLKTNPSLAELLIKNANNE 293
                                   ***********98885.5677888888888877764 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.4   1.2e-06    0.0021      73     173 ..     177     275 ..     160     289 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                                   GG--EEEEE--SS-SEEEEEEEETTEEE.EEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-S..EEEEE CS
                          RimK  73 keailvqeyieeaenediRvlvvddevv.aalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelv..vaGvD 150
                                   +e+ l+qe+i+  en  + ++ v++++   +l+r+  +   +     G v  + +l+++  + Aika k ++    ++GvD
  gi|15669002|ref|NP_247806.1| 177 DENFLIQEFIDG-ENLSVSLI-VGKKIHpLSLNRQYID---KRGFVGGEVNINHKLKDKIFNEAIKAVKCINGLngYVGVD 252
                                   577899999985.45556544.4555431466666555...3344556666677777777788*****999753349**** PP

                                   EEEETTEEEEEEEESS--SHHHH CS
                          RimK 151 llrakrgllvlEvnsspglekie 173
                                   ++ +++g++++E+n    ++ + 
  gi|15669002|ref|NP_247806.1| 253 VIVNNDGIYIIEINPRITTTIYG 275
                                   **************988877664 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   3.9e-06    0.0069      50     151 ..     175     268 ..     159     275 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.9e-06
                   ATP-grasp_4  50 veeesflvEeyieGeEfavdayfdeeGepvilnilkkefaseedvsdrlyvtsakvieetl..ealeellkevnallglkn 128
                                   + +e+fl+ e+i+Ge  +v + +   G+++     +   ++ +++ +r +v ++  i+++l  + ++e++k+v+   gl n
  gi|15669002|ref|NP_247806.1| 175 LFDENFLIQEFIDGENLSVSLIV---GKKI-----HPLSLNRQYIDKRGFVGGEVNINHKLkdKIFNEAIKAVKCINGL-N 246
                                   55899*****************9...6553.....34456666777777776654444433113468888888855555.7 PP

                   ATP-grasp_4 129 fpvHiElrvsedgkiipiEvnpl 151
                                   + v + + v++dg i+ iE+np+
  gi|15669002|ref|NP_247806.1| 247 GYVGVDVIVNNDG-IYIIEINPR 268
                                   8899*******98.999*****6 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       1.2   2.1e+03     112     141 ..      62      91 ..      49     103 .. 0.61
   2 !   15.3   0.2   6.1e-06     0.011     113     174 ..     206     267 ..     172     289 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                                   -HHHHHC.TT-EEESS----HHHHHHHHHH CS
               Dala_Dala_lig_C 112 dyeakysddkaqlevpaklekeveekiqel 141
                                   d+   y+d k    v++k e+e+e+k++ l
  gi|15669002|ref|NP_247806.1|  62 DFVDNYIDFKNLEIVKIKKENEIENKLKSL 91 
                                   455555553333345555666666655544 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 6.1e-06
                                   HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT.--SEEEEEEEEETTTEEEEEEEES CS
               Dala_Dala_lig_C 113 yeakysddkaqlevpaklekeveekiqelalkaykald.lrGlaRvDfflteegeivlnEvNt 174
                                    + +y+d++  +  +++++++ ++ki + a+ka k ++ l+G + vD++++ ++ i++ E+N+
  gi|15669002|ref|NP_247806.1| 206 LNRQYIDKRGFVGGEVNINHKLKDKIFNEAIKAVKCINgLNGYVGVDVIVN-NDGIYIIEINP 267
                                   5778999999999999*********************7379*********9.778*******6 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   8.5e-06     0.015     133     205 ..     223     292 ..     220     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.5e-06
                                   --HHHHHHHHHHHHHHHHHH.T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT CS
                   CPSase_L_D2 133 Ltdeerqalreaavkvvrev.gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialg 205
                                   ++++  +++ ++a+k+v+++ g+ g   v+ +++  ++ +y+iE+N+R+    ++    T   l++  +k a++
  gi|15669002|ref|NP_247806.1| 223 INHKLKDKIFNEAIKAVKCInGLNGYVGVDVIVN--NDGIYIIEINPRITT--TIYGLKTNPSLAELLIKNANN 292
                                   56778899***********944778889*****9..599*********974..455555555555555555555 PP

>> Ribosomal_L38e  Ribosomal L38e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4     0.049        87      16      48 ..      70     104 ..      59     125 .. 0.77
   2 ?    5.1   0.1     0.014        25      34      55 ..     133     154 ..     119     164 .. 0.87
   3 ?    6.5   0.0     0.005         9      22      41 ..     285     304 ..     276     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.049
                Ribosomal_L38e  16 rkDaksvkikknk..kdntKfKvRcsryLYTLvvk 48 
                                    k+ + vkikk++  +++ K  ++ +   Y Lvv+
  gi|15669002|ref|NP_247806.1|  70 FKNLEIVKIKKENeiENKLKSLLKSENIDYALVVA 104
                                   56677899999986777777779999999999986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.014
                Ribosomal_L38e  34 fKvRcsryLYTLvvkdkekaek 55 
                                   +K+ +++yL  L +kd+ k  k
  gi|15669002|ref|NP_247806.1| 133 IKIAGNKYLTYLAIKDAVKTPK 154
                                   79**************999876 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.005
                Ribosomal_L38e  22 vkikknkkdntKfKvRcsry 41 
                                     ik+ ++++ KfKv+++++
  gi|15669002|ref|NP_247806.1| 285 LLIKNANNEELKFKVKGEKF 304
                                   56888888*********997 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.64   1.1e+03      19      46 ..      29      62 ..      20      94 .. 0.67
   2 ?   -3.3   0.0       2.3   4.2e+03      58      74 ..     155     172 ..     134     175 .. 0.67
   3 ?   12.4   0.1   3.9e-05     0.069     235     281 ..     238     284 ..     227     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.64
                   ATPgrasp_ST 19 vddKl.......kfkelalraglkvpkllgvikeq 46
                                  ++dK+        f +l l+++l+++k++  +++ 
  gi|15669002|ref|NP_247806.1| 29 FEDKNilkegkmMFDTL-LKQFLEIDKVISLLYKD 62
                                  66666565555466666.88899999988777766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.3
                   ATPgrasp_ST  58 eleeg.vviKpakgsgGk 74 
                                    +++  +v+K +++ gGk
  gi|15669002|ref|NP_247806.1| 155 TFPPKkYVVKKIDSCGGK 172
                                   444445777777777776 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 3.9e-05
                   ATPgrasp_ST 235 aaeklpgl.gylGwDivldeekgplllElNarpglaivqiangegllp 281
                                   a + + gl gy+G+D+ + +++ ++++E+N r   +i  +  + +l +
  gi|15669002|ref|NP_247806.1| 238 AVKCINGLnGYVGVDVIVNNDG-IYIIEINPRITTTIYGLKTNPSLAE 284
                                   4444445448******999999.*********9999988877777765 PP

>> DUF4059  Protein of unknown function (DUF4059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.2   0.00057         1       8      58 ..       2      52 ..       1      57 [. 0.92
   2 ?    0.8   0.0      0.37   6.7e+02       4      41 ..     116     154 ..     113     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00057
                       DUF4059  8 lYlqgLllsillvllvsliwillralrkkdKtakerqavLydillidilti 58
                                  l lq++l++ ++v+ + l++    a    dK   +  ++++d ll + l i
  gi|15669002|ref|NP_247806.1|  2 LLLQSILITKIMVIQLILFFEYALASGFEDKNILKEGKMMFDTLLKQFLEI 52
                                  679******************99*********************9877765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.37
                       DUF4059   4 eilslY.lqgLllsillvllvsliwillralrkkdKtak 41 
                                   +i++ Y ++ L  s+ ++ +++  ++ + a+++  Kt k
  gi|15669002|ref|NP_247806.1| 116 KIIESYpVKNLGCSSEAIKIAGNKYLTYLAIKDAVKTPK 154
                                   56655557899999999****************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2238.31
//
Query:       gi|15669003|ref|NP_247807.1|  [L=297]
Description: hypothetical protein MJ_0816 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.25   11.3   7.0       0.95    9.5   4.2    3.1  2  KH_7      KH domain
       0.35   10.7   5.9        0.1   12.5   2.1    2.2  2  KH_2      KH domain
        4.4    7.6   8.7        1.1    9.5   0.2    3.2  4  BEN       BEN domain


Domain annotation for each model (and alignments):
>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.2   0.00016      0.95      18      39 ..      34      55 ..       3      85 .. 0.78
   2 ?   -3.1   0.0       1.4   8.2e+03      44      55 ..     267     278 ..     264     281 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00016
                          KH_7 18 evkitdveFEGPelViYtknpk 39
                                  e  i d+e EG  l+iYtkn  
  gi|15669003|ref|NP_247807.1| 34 EFDIVDIEIEGKVLIIYTKNRT 55
                                  56799**************975 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                          KH_7  44 ngdlirklAkel 55 
                                   ++++i+k++ke+
  gi|15669003|ref|NP_247807.1| 267 KEKFIKKVVKEV 278
                                   455666666655 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.1   1.7e-05       0.1      14      61 ..      34      82 ..      12      98 .. 0.85
   2 ?   -3.1   0.1       1.2   7.4e+03      18      28 ..     261     271 ..     258     281 .. 0.45

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                                  T..EEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHH CS
                          KH_2 14 g..vskveIertanrviiviresqpgivIGkgGsnikkigkelrkdiekl 61
                                  +  + ++eIe  +  +i++     +  +IG gG  + k+++e ++++e++
  gi|15669003|ref|NP_247807.1| 34 EfdIVDIEIEG-KVLIIYTKNRTDKSTIIGPGGWVVGKLREEMKNRFEII 82
                                  34478899988.458889999999***********************976 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                                   EEEECCSCEEE CS
                          KH_2  18 veIertanrvi 28 
                                   ++I++++++ i
  gi|15669003|ref|NP_247807.1| 261 CKIDKNKEKFI 271
                                   55555333222 PP

>> BEN  BEN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.1   1.2e+04      39      52 ..      11      24 ..       8      34 .. 0.67
   2 ?    2.8   0.2     0.023   1.4e+02      37      55 ..     104     122 ..      86     136 .. 0.80
   3 ?   -3.7   0.1       2.5   1.5e+04      65      77 ..     164     176 ..     162     177 .. 0.76
   4 ?    9.5   0.2   0.00019       1.1      36      71 ..     262     297 .]     247     297 .] 0.95

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.1
                                  HHHHHHHHHHHHHH CS
                           BEN 39 pnklsaIrnyveer 52
                                  + ++++I++ v + 
  gi|15669003|ref|NP_247807.1| 11 EQIINDIKKRVLKI 24
                                  56677777777654 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.023
                                   --HHHHHHHHHHHHHHH-- CS
                           BEN  37 LDpnklsaIrnyveeryps 55 
                                    D   +++I+ny+ +r   
  gi|15669003|ref|NP_247807.1| 104 FDDEVIQDICNYFLYRKIP 122
                                   68999*******9988555 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.5
                                   .-HHHHHHHHHHH CS
                           BEN  65 ecldqInkilrrk 77 
                                   +++++I ++l++k
  gi|15669003|ref|NP_247807.1| 164 KTKKKIANFLNNK 176
                                   5678888999888 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00019
                                   E--HHHHHHHHHHHHHHH--..........-HHHHH CS
                           BEN  36 aLDpnklsaIrnyveerypsekededwwrecldqIn 71 
                                   ++D nk ++I+++v+e+y   ke++d  +e+l++I+
  gi|15669003|ref|NP_247807.1| 262 KIDKNKEKFIKKVVKEVYKGFKEPTDASEEILSMIK 297
                                   79******************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2193.77
//
Query:       gi|15669004|ref|NP_247808.1|  [L=206]
Description: phosphatidylserine decarboxylase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-39  134.8   0.1    3.3e-39  134.5   0.1    1.1  1  PS_Dcarbxylase  Phosphatidylserine decarboxylase
    2.6e-05   24.3   1.2        3.2    8.0   0.1    3.5  3  Peptidase_M23   Peptidase family M23
     0.0011   18.8   1.2        1.2    9.0   0.1    3.3  4  Biotin_lipoyl   Biotin-requiring enzyme
     0.0067   16.4   0.4        4.5    7.3   0.1    3.3  4  RnfC_N          RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.014   15.2   0.1       0.49   10.2   0.0    2.6  3  PTS_EIIA_1      phosphoenolpyruvate-dependent sugar phosphotr


Domain annotation for each model (and alignments):
>> PS_Dcarbxylase  Phosphatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.5   0.1   9.1e-43   3.3e-39       3     199 ..      17     199 ..      15     200 .. 0.93

  Alignments for each domain:
  == domain 1  score: 134.5 bits;  conditional E-value: 9.1e-43
                PS_Dcarbxylase   3 effvrklkdgaRpidddpgaivsPaDgrilqigeieegsviqvKgityslrdLlgeasessadsfkngyfvviyLspgdyH 83 
                                    f v++++d++R i ++++ i+sPaDg++ +i+  e+g+ +  K  +  + +    + +      +++y+v i++sp d+H
  gi|15669004|ref|NP_247808.1|  17 LFTVYFYRDPDRVITKGNNIILSPADGTVEYIKFYENGNPEVFKDGNCYVLNV-SRYFP------NGCYVVGIFMSPLDVH 90 
                                   5999*********************************9999999999555553.33444......589999********** PP

                PS_Dcarbxylase  84 ryhaPvsgkveerrhipGellsvnpsalkelrglftlneRvvlviewkG..kvavvpvGatnvgsivlnvlkgdelkkGee 162
                                   +++aP+ g+++ ++hi+G ++++   +++++      neR++++i++ G  +v vv++++++++++ l++++g+ ++ G++
  gi|15669004|ref|NP_247808.1|  91 VNRAPIGGRIVYIKHIDGSFYPAFLEGVEKI------NERNIVIIKN-GseYVGVVQIAGFVARRCWLSIKEGECINMGQK 164
                                   *******************************......*********7.6436***************************** PP

                PS_Dcarbxylase 163 lGyFqfGStvvlvfeagkfieslvekgqkvkmGeklg 199
                                   +G++++GS++ ++++a+  ++ +v++g++v++G++++
  gi|15669004|ref|NP_247808.1| 165 IGMIKLGSQTAVIIPAN--YNITVKVGERVYAGQTII 199
                                   ****************9..****************97 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0028        10      11      35 ..      32      55 ..      27      77 .. 0.74
   2 !    8.0   0.1    0.0009       3.2      18      73 ..      94     169 ..      88     176 .. 0.66
   3 !    7.7   0.1    0.0011         4      43      75 ..     172     204 ..     167     206 .] 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0028
                                  TTT-EEEESSSEEEEEEEEETTTEE CS
                 Peptidase_M23 11 pkgtpVlAaadGtVvfagkkegyGn 35
                                  + ++ +l++adGtV +++ + + Gn
  gi|15669004|ref|NP_247808.1| 32 KGNNIILSPADGTVEYIKFY-ENGN 55
                                  456789********999876.3344 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0009
                                   ESSSEEEEEEEE.ET.............TTEEEEEEEECTCEEEEEEEESEES......S-TTEEE-TTCEEEEEB CS
                 Peptidase_M23  18 AaadGtVvfagk.ke.............gyGnvviidhgdgystlyahlskis......vkegqkVkaGqvIGtvg 73 
                                   A+  G++v+++  ++             +  n+vii+ g++y+ +      ++      +keg+ ++ Gq+IG + 
  gi|15669004|ref|NP_247808.1|  94 APIGGRIVYIKHiDGsfypaflegvekiNERNIVIIKNGSEYVGVVQIAGFVArrcwlsIKEGECINMGQKIGMIK 169
                                   556666666665322455566666665555899999999887666554333222334459*************875 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0011
                                   TCEEEEEEEESEESS-TTEEE-TTCEEEEEBST CS
                 Peptidase_M23  43 dgystlyahlskisvkegqkVkaGqvIGtvgst 75 
                                   +++  ++  + +i+vk+g++V aGq+I  v  t
  gi|15669004|ref|NP_247808.1| 172 SQTAVIIPANYNITVKVGERVYAGQTIIAVKRT 204
                                   55555566667899************9777665 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0024       8.4      40      58 ..      32      50 ..      30      58 .. 0.84
   2 ?   -2.9   0.0       1.8   6.3e+03      47      61 ..      94     108 ..      93     109 .. 0.79
   3 ?   -0.6   0.0      0.34   1.2e+03      58      71 ..     153     166 ..     149     168 .. 0.58
   4 !    9.0   0.1   0.00034       1.2      17      36 ..     182     201 ..     168     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0024
                                  TEEEEEEBSSSEEEEEESS CS
                 Biotin_lipoyl 40 KmemeieapkaGvvkeilv 58
                                  K ++ i +p++G+v++i+ 
  gi|15669004|ref|NP_247808.1| 32 KGNNIILSPADGTVEYIKF 50
                                  77899************85 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.8
                                   BSSSEEEEEESSTTT CS
                 Biotin_lipoyl  47 apkaGvvkeilvkeG 61 
                                   ap  G++++i++ +G
  gi|15669004|ref|NP_247808.1|  94 APIGGRIVYIKHIDG 108
                                   667799999998777 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.34
                                   STTTEEE-TTCEEE CS
                 Biotin_lipoyl  58 vkeGdtvevgdlla 71 
                                   +keG+ ++ g+ + 
  gi|15669004|ref|NP_247808.1| 153 IKEGECINMGQKIG 166
                                   55666666666554 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.00034
                                   CSESSSTTCEE-TTSEEEEE CS
                 Biotin_lipoyl  17 vevlvkvGdkVkagqvlaev 36 
                                    +++vkvG+ V agq+++ v
  gi|15669004|ref|NP_247808.1| 182 YNITVKVGERVYAGQTIIAV 201
                                   5689*************988 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.39   1.4e+03      69      87 ..      37      55 ..      28      68 .. 0.74
   2 ?   -2.3   0.0       1.2   4.4e+03      71      83 ..      94     106 ..      87     109 .. 0.80
   3 !    5.4   0.0     0.005        18      33      62 ..     140     169 ..     116     181 .. 0.73
   4 !    7.3   0.1    0.0013       4.5      40      59 ..     180     199 ..     172     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.39
                        RnfC_N 69 vhasvsGtVkaiekrlvah 87
                                  + ++  GtV  i+ +++ +
  gi|15669004|ref|NP_247808.1| 37 ILSPADGTVEYIKFYENGN 55
                                  889999**99998777655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                        RnfC_N  71 asvsGtVkaiekr 83 
                                   a++ G+++ i+++
  gi|15669004|ref|NP_247808.1|  94 APIGGRIVYIKHI 106
                                   8999999999875 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.005
                        RnfC_N  33 plsqhiGapakplvkvgdkVlkGqkiaeae 62 
                                    ++  +  ++ + +k+g+ +++Gqki+  +
  gi|15669004|ref|NP_247808.1| 140 QIAGFVARRCWLSIKEGECINMGQKIGMIK 169
                                   44455566778889************9765 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0013
                        RnfC_N  40 apakplvkvgdkVlkGqkia 59 
                                   a+ ++ vkvg++V  Gq i 
  gi|15669004|ref|NP_247808.1| 180 ANYNITVKVGERVYAGQTII 199
                                   667899***********985 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.042   1.5e+02      35      51 ..      32      48 ..      28      55 .. 0.77
   2 ?   -3.0   0.0       1.6   5.6e+03      42      50 ..      94     102 ..      76     110 .. 0.58
   3 ?   10.2   0.0   0.00014      0.49      69     104 ..     167     202 ..     151     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.042
                                  E-SSEEEES--EEEEE- CS
                    PTS_EIIA_1 35 psegkvvapvdGkvekv 51
                                    ++ +++p+dG+ve +
  gi|15669004|ref|NP_247808.1| 32 KGNNIILSPADGTVEYI 48
                                  4467899******9876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.6
                                   ES--EEEEE CS
                    PTS_EIIA_1  42 apvdGkvek 50 
                                   ap+ G+++ 
  gi|15669004|ref|NP_247808.1|  94 APIGGRIVY 102
                                   444444433 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00014
                                   EEE-SSSTTTTTTTTEEES----SEE-SEEEEEEE- CS
                    PTS_EIIA_1  69 lihiGidtvklkgegFellvkegdkVkagdklvevd 104
                                   +i++G  t  +    +++ vk g++V ag++++ v+
  gi|15669004|ref|NP_247808.1| 167 MIKLGSQTAVIIPANYNITVKVGERVYAGQTIIAVK 202
                                   899*****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1374.64
//
Query:       gi|15669005|ref|NP_247809.1|  [L=203]
Description: hypothetical protein MJ_0818 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-14   53.9   0.5    1.8e-10   40.6   0.2    2.3  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
    0.00053   20.0   0.0     0.0009   19.2   0.0    1.5  1  Ada_Zn_binding   Metal binding domain of Ada
     0.0016   18.1   0.0     0.0024   17.5   0.0    1.2  1  DUF4131          Domain of unknown function (DUF4131)
     0.0024   17.7   0.2       0.77    9.6   0.0    2.2  2  RMI2             RecQ-mediated genome instability protein 2
     0.0036   17.5   0.1       0.18   12.0   0.0    2.1  2  tRNA_anti_2      OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.043   13.8   0.3        3.4    7.7   0.1    2.7  3  Peptidase_S24    Peptidase S24-like


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0     7e-05      0.21      36      60 ..      28      53 ..      10      66 .. 0.82
   2 !   40.6   0.2     6e-14   1.8e-10      18      75 ..      67     130 ..      56     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7e-05
                                  T.HHHHHHHTTS-TTSEEEEEEEEEE CS
               tRNA_anti-codon 36 r.eeatklaenlkeGdvvrvtGrvkr 60
                                  + + ++k   ++keGd+v ++G++++
  gi|15669005|ref|NP_247809.1| 28 PiQPKEKHIAEIKEGDYVVIKGYIQE 53
                                  3667899999*************997 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 6e-14
                                   EEEEEEEETTEEEEEEEET.......HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEE CS
               tRNA_anti-codon  18 vifidlrDgtgriqvvlfr.......eeatklaenlkeGdvvrvtGrvkrrpggelelkveeiel 75 
                                   ++ i+++Dgtg++ vv+f        +   +++  +keGd+++v+Grv+ ++g+ +e++ ++i++
  gi|15669005|ref|NP_247809.1|  67 ISRIVINDGTGNLDVVAFGktreellTYILSYNPMIKEGDYIEVKGRVTLYKGK-YEIILNNIKD 130
                                   67899******************999999*************************.*******986 PP

>> Ada_Zn_binding  Metal binding domain of Ada
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0     3e-07    0.0009      36      63 ..     172     199 ..     135     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3e-07
                                   -S-SCCEEEESSHHHHHHTT-EEETTTT CS
                Ada_Zn_binding  36 lPkrenveFfdtaaeAeaagfrpCkrcr 63 
                                   + k+en+ +f + ++A+a g+  Ck c+
  gi|15669005|ref|NP_247809.1| 172 RLKEENIIYFYSEDDAKALGYEKCKWCE 199
                                   4469***********************7 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   8.1e-07    0.0024      32     133 ..       9     115 ..       3     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.1e-07
                       DUF4131  32 vllllllllllallgfalrapqpnandlsqllesgqeviveGvvaslpeltgsgtrfvleverv........lsagktkpv 104
                                   +l++l+ + ++ + +++l   qp +++++ + e g +v+++G+++ +  +++++ r v +++r+        l+  +  ++
  gi|15669005|ref|NP_247809.1|   9 TLFALTCFVIISTTWLFLNPIQPKEKHIAEIKE-GDYVVIKGYIQ-EMYVKRDKYRHVINISRIvindgtgnLDVVAFGKT 87 
                                   678889999999999999999999999999999.**********5.56677777788999999999995544334444444 PP

                       DUF4131 105 sgrvlvtvpkspaeglrpGdrlrltgrlk 133
                                   ++ +l ++ +  + +++ Gd++ ++gr+ 
  gi|15669005|ref|NP_247809.1|  88 REELLTYILSYNP-MIKEGDYIEVKGRVT 115
                                   4444444433333.6**********9986 PP

>> RMI2  RecQ-mediated genome instability protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0013       3.9      79     103 ..      34      65 ..      14      71 .. 0.73
   2 !    9.6   0.0   0.00026      0.77      57      99 ..      69     119 ..      55     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0013
                          RMI2  79 k..kclkeGkYVmVvGvvqssspe.....pvl 103
                                   k   ++keG+YV + G++q++  +     +v+
  gi|15669005|ref|NP_247809.1|  34 KhiAEIKEGDYVVIKGYIQEMYVKrdkyrHVI 65 
                                   244789************98765545455555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00026
                          RMI2  57 sllldDgtgvfvveglnelpktk........kclkeGkYVmVvGvvqsssp 99 
                                   +++++Dgtg++ v +  +  ++         + +keG+Y+ V G v+  + 
  gi|15669005|ref|NP_247809.1|  69 RIVINDGTGNLDVVAFGKTREELltyilsynPMIKEGDYIEVKGRVTLYKG 119
                                   799*******888777776666688889999*************9965544 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.036   1.1e+02      64      91 ..      37      65 ..      15      68 .. 0.76
   2 !   12.0   0.0     6e-05      0.18      44      94 ..      73     128 ..      69     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.036
                   tRNA_anti_2 64 ftledGmkVlvkgrls.vYeprGsyqliv 91
                                  +++++G+ V++kg ++ +Y +r +y  ++
  gi|15669005|ref|NP_247809.1| 37 AEIKEGDYVVIKGYIQeMYVKRDKYRHVI 65
                                  4589*********9954888888777655 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6e-05
                   tRNA_anti_2  44 kDekakisavifrsraaklk.....ft..ledGmkVlvkgrlsvYeprGsyqlivedi 94 
                                    D + ++++v f +++++l       +  +++G+ + vkgr+++Y+  G+y++i ++i
  gi|15669005|ref|NP_247809.1|  73 NDGTGNLDVVAFGKTREELLtyilsYNpmIKEGDYIEVKGRVTLYK--GKYEIILNNI 128
                                   688889999999988877764554322667***************6..6777777665 PP

>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0011       3.4      23      45 ..      34      58 ..      17      67 .. 0.82
   2 ?    3.3   0.0     0.027        82       8      30 ..      99     121 ..      97     145 .. 0.83
   3 ?   -3.1   0.0       2.7   8.1e+03      26      37 ..     174     185 ..     161     188 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                                  S...---TTSEEEEEETTCE-EEEEE CS
                 Peptidase_S24 23 s...epkrGdivvfrlpgeeeayiKr 45
                                      e+k Gd+vv++   +e  y+Kr
  gi|15669005|ref|NP_247809.1| 34 KhiaEIKEGDYVVIKGYIQE-MYVKR 58
                                  044599**********9998.9**99 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.027
                                   CCTXXTTXEEEEECTS---TTSE CS
                 Peptidase_S24   8 eptlldGdlilVdkfsepkrGdi 30 
                                   +p +++Gd+i V+  +++ +G +
  gi|15669005|ref|NP_247809.1|  99 NPMIKEGDYIEVKGRVTLYKGKY 121
                                   699*******9998888887764 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.7
                                   -TTSEEEEEETT CS
                 Peptidase_S24  26 krGdivvfrlpg 37 
                                   k   i++f  ++
  gi|15669005|ref|NP_247809.1| 174 KEENIIYFYSED 185
                                   444566665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1375.61
//
Query:       gi|15669006|ref|NP_247810.1|  [L=109]
Description: hypothetical protein MJ_0819 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0012   19.5   0.8     0.0035   18.0   0.4    1.8  2  Pre-PUA   Pre-PUA-like domain
  ------ inclusion threshold ------
      0.018   14.8   0.2      0.022   14.5   0.2    1.1  1  FTCD_C    Formiminotransferase-cyclodeaminase


Domain annotation for each model (and alignments):
>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.13   1.1e+03      28      46 ..      16      33 ..      14      52 .. 0.73
   2 !   18.0   0.4   3.9e-07    0.0035      36      85 ..      55     103 ..      32     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.13
                       Pre-PUA 28 qfpslseeqleellpkkee 46
                                  ++++l +e+l+e++  +++
  gi|15669006|ref|NP_247810.1| 16 RYENL-KEILDEMFRDEVQ 33
                                  58888.8999998876543 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.9e-07
                       Pre-PUA  36 qleellpkkeevkvvklqgehvelyvvdgeplffqdregellPtlytlwk 85 
                                   +  +l++++ e++ +k+  +++ +++v++++lf+++++g l P  y++w+
  gi|15669006|ref|NP_247810.1|  55 DALKLFKENYEIEDIKIP-KKIRVFLVKNNILFLNPQKGSLKPQSYLVWN 103
                                   333566667799999999.******************************7 PP

>> FTCD_C  Formiminotransferase-cyclodeaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   2.4e-06     0.022      40      93 ..      11      65 ..       2      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-06
                                  TTT-TT-GGGHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHTTTT....... CS
                        FTCD_C 40 tlgkkkyedveeemeell.ekleelrkellelideDaeaFnevmeayklpketee 93
                                   ++  +ye+++e ++e++ +++++l+  l ++ +eD+e +n++++a+kl ke+ e
  gi|15669006|ref|NP_247810.1| 11 VIDSLRYENLKEILDEMFrDEVQKLKYFLEDVKEEDEELYNKIVDALKLFKENYE 65
                                  556667888888887665167799999999999****************998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1382  (0.0770818); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 693.15
//
Query:       gi|15669007|ref|NP_247811.1|  [L=47]
Description: hypothetical protein MJ_0820 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.8e-12   45.4   0.2      1e-11   45.2   0.2    1.0  1  ATPase_2    ATPase domain predominantly from Archaea
     0.0068   16.2   0.3     0.0085   15.9   0.3    1.1  1  SGTA_dimer  Homodimerisation domain of SGTA


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.2   1.1e-15     1e-11     189     228 ..       1      42 [.       1      43 [. 0.93

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.1e-15
                      ATPase_2 189 vddldketalnflkegfkel..eelskedfeeiyryvGGkPk 228
                                   +dd+dketa +f++++++e+  ++ls++++e+iy+yvGGkP+
  gi|15669007|ref|NP_247811.1|   1 MDDFDKETAIKFMDFLAEEIlnKKLSEDEKELIYSYVGGKPI 42 
                                   59******************87777****************7 PP

>> SGTA_dimer  Homodimerisation domain of SGTA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   9.4e-07    0.0085       3      29 ..       6      32 ..       5      34 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.4e-07
                    SGTA_dimer  3 krlalaIidFLstslkdgtvseDdaES 29
                                  k+ a  + dFL + + ++++seD++E 
  gi|15669007|ref|NP_247811.1|  6 KETAIKFMDFLAEEILNKKLSEDEKEL 32
                                  899**********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 288.18
//
Query:       gi|15669008|ref|NP_247812.1|  [L=56]
Description: hypothetical protein MJ_0821 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-13   49.2   0.3    6.6e-13   49.1   0.3    1.1  1  ATPase_2  ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.3   3.7e-17   6.6e-13       1      38 [.       3      40 ..       3      47 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 3.7e-17
                      ATPase_2  1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlk 38
                                  Ff+Reke++++++i+e epn iyfiYG+ +sGK  L  
  gi|15669008|ref|NP_247812.1|  3 FFNREKEINKILSIIEGEPNLIYFIYGSLNSGKFNLTE 40
                                  9********************************88866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 368.53
//
Query:       gi|15669009|ref|NP_247813.1|  [L=558]
Description: S-layer protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   6.6e-107  357.6  20.4   6.6e-107  357.6  20.4    2.2  2  S_layer_N  S-layer like family, N-terminal region
    6.4e-82  274.8  15.9    6.4e-82  274.8  15.9    2.9  3  S_layer_C  S-layer like family, C-terminal region


Domain annotation for each model (and alignments):
>> S_layer_N  S-layer like family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.6  20.4  7.4e-111  6.6e-107       1     284 []       6     282 ..       6     282 .. 0.99
   2 ?   -1.8   6.2      0.25   2.2e+03     118     206 ..     357     464 ..     319     507 .. 0.59

  Alignments for each domain:
  == domain 1  score: 357.6 bits;  conditional E-value: 7.4e-111
                     S_layer_N   1 KKigalavGaamvaaalatgvfAseki.G..dveefkdkvvkdGepnvkiVvGsna.aalDVvSAadiaakiGsllyteed 77 
                                   KKiga+avG+amva+ala+gv+A+ ++ G  d++e+kd +vkdG+pn+++VvG++a +++DVvSAadiaakiGsl+y+e++
  gi|15669009|ref|NP_247813.1|   6 KKIGAIAVGGAMVATALASGVAAEVTTsGfsDYKELKDILVKDGQPNCYVVVGADApSTMDVVSAADIAAKIGSLCYKEGT 86 
                                   9************************998788*************************99*********************** PP

                     S_layer_N  78 vedgsakvvvkasaesddadlltdkllsaltdkayllveaakd.dytaklkdsswddglvdkavlgdadkvgkvaskdlaa 157
                                   vedgsa+++v+a+a+sdd+dl++d+++sa+ ++ay+l+ aa+d dy++k+++++ +++++d++vlgdadk        +++
  gi|15669009|ref|NP_247813.1|  87 VEDGSADITVHAEANSDDFDLKKDWNNSAMPANAYALFVAASDgDYSEKFENDTGKPSFMDNGVLGDADK--------INK 159
                                   *************************************9999888**************************........699 PP

                     S_layer_N 158 avslgklstLkevkdvdpsdifeddddavelvvaevvanvsekkgddlkvkedelvyaslaykddkeafkdyqdlieGvei 238
                                   +v+lg+++t+++v+dvdpsd++++ddda e+v++e+++++s    d ++v++++++y++l+ykdd+e+f++++++ eG++i
  gi|15669009|ref|NP_247813.1| 160 TVDLGDIATMMKVDDVDPSDWYDSDDDAGEIVMVELKNDTS----DGFTVYKKNMLYETLVYKDDEENFANTTKMEEGMRI 236
                                   *****************************************....99********************************** PP

                     S_layer_N 239 pllgkeykivkidkDddiiylGkevyegvikegetyslGdGytvkv 284
                                   p+lgke+++v+idkDdd+iylG+ vy+g+ikegety+lG+Gy+vk+
  gi|15669009|ref|NP_247813.1| 237 PFLGKEMVVVDIDKDDDAIYLGTPVYDGIIKEGETYDLGNGYQVKI 282
                                   *********************************************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.25
                     S_layer_N 118 akddytaklkdss..wddglvdkavlgdadkvgkvaskdlaaavslgklstLkevkdvdpsdi..fed............. 181
                                   ++++y+++ k  +   d+g ++ ++  + ++v+kv +  +a   + +kl+ L++ ++vd  d+  f+              
  gi|15669009|ref|NP_247813.1| 357 LDEEYVTDWKAYAvlNDNGTMKLEDDLNDNNVDKVVG--IALRYDGDKLDDLDSGDEVDILDYvkFKLddedsndklkvyf 435
                                   4446666555433113455555555555666666555..555666666666666666666666443322233222222233 PP

                     S_layer_N 182 ....dddavelvvaevvanvsekkgddlk 206
                                       d da+  + ++v+a ++e+k++d+k
  gi|15669009|ref|NP_247813.1| 436 smdkDVDATLNIGEKVKALNAEVKLKDIK 464
                                   33334444444444455544455555544 PP

>> S_layer_C  S-layer like family, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   2.2      0.58   5.2e+03      82      93 ..     194     207 ..     111     259 .. 0.58
   2 ?   -0.1   1.2     0.085   7.6e+02      20      63 ..     266     324 ..     251     333 .. 0.60
   3 !  274.8  15.9   7.2e-86   6.4e-82       1     220 []     335     558 .]     335     558 .] 0.99

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.58
                     S_layer_C  82 klkfdD..klsvyf 93 
                                   +lk+d     +vy+
  gi|15669009|ref|NP_247813.1| 194 ELKNDTsdGFTVYK 207
                                   22222122222222 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.085
                     S_layer_C  20 lelGeeyvldweakvvidsgitleykde...............ekledkvvglalkykg 63 
                                   +++Ge y l++ ++v+i+   +   +++               +  + ++++l l yk 
  gi|15669009|ref|NP_247813.1| 266 IKEGETYDLGNGYQVKIKAILKTTVNNTdvykvdvqilkdgkvVAEKYDKAPLELEYKD 324
                                   58899999999999988888555555553355555444444432222234444444444 PP

  == domain 3  score: 274.8 bits;  conditional E-value: 7.2e-86
                     S_layer_C   1 tkiggeygya.lkvvkdikelelGeeyvldweakvvidsgitleykde..ekledkvvglalkykgdkladikdkdkvdia 78 
                                   +++gg+ygya l+++kd+k+lel+eeyv+dw+a++v+++++t++++d+  +++ dkvvg+al+y+gdkl+d++++d+vdi 
  gi|15669009|ref|NP_247813.1| 335 ENVGGDYGYAeLVISKDLKKLELDEEYVTDWKAYAVLNDNGTMKLEDDlnDNNVDKVVGIALRYDGDKLDDLDSGDEVDIL 415
                                   589********************************************98889999************************** PP

                     S_layer_C  79 nyaklkfdD.....klsvyfkideekevelivgekvkvlsadvkaekikakaeqvvkltaPivvLDtEveldsvdknLiLv 154
                                   +y+k+k dD     kl+vyf++d++ +++l++gekvk+l+a+vk+++ika+a+++v+ltaPi++LDtEv+ld++dknL+Lv
  gi|15669009|ref|NP_247813.1| 416 DYVKFKLDDedsndKLKVYFSMDKDVDATLNIGEKVKALNAEVKLKDIKANAVEPVSLTAPIAKLDTEVSLDTADKNLVLV 496
                                   ********************************************************************************* PP

                     S_layer_C 155 GGPvvNkvtkeLedklkvaityeednksaatiavienaangndvlvvAGsDRegTkaAalaliekl 220
                                   GGPv+Nk+tkeL+d++k+a+    dn+s+atia+i +aang+dv+vvAG+DRe+T++Aal+li++l
  gi|15669009|ref|NP_247813.1| 497 GGPVANKLTKELVDAGKLAL----DNNSPATIALIPDAANGHDVIVVAGGDREKTREAALELIKNL 558
                                   ********************....***************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 3212.96
//
Query:       gi|15669010|ref|NP_247814.1|  [L=257]
Description: CODH nickel-insertion accessory protein CooC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-27   96.6   0.2    1.3e-27   96.4   0.2    1.1  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    7.4e-12   45.3   0.7    5.4e-05   22.8   0.0    2.2  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
    1.4e-09   37.8   0.7    0.00087   18.8   0.0    2.6  2  ParA             NUBPL iron-transfer P-loop NTPase
      2e-08   34.4   0.0    9.4e-08   32.2   0.0    2.0  1  AAA_31           AAA domain
    6.1e-08   32.2   2.6    2.3e-05   23.7   0.0    2.4  3  ArsA_ATPase      Anion-transporting ATPase
    4.2e-07   30.0   1.4    0.00017   21.5   0.2    2.3  2  AAA_26           AAA domain
      1e-06   28.5   0.0     0.0022   17.5   0.0    2.1  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
    6.4e-05   22.9   2.4    0.00082   19.3   0.0    2.3  2  NTPase_1         NTPase
     0.0002   21.1   0.6      0.047   13.4   0.0    3.0  3  AAA_24           AAA domain
    0.00026   21.4   0.0    0.00043   20.7   0.0    1.5  1  AAA_16           AAA ATPase domain
     0.0027   18.4   0.1        1.8    9.3   0.0    2.7  2  PTS_IIB          PTS system, Lactose/Cellobiose specific IIB 
  ------ inclusion threshold ------
      0.022   14.5   0.0      0.046   13.4   0.0    1.5  1  AAA_30           AAA domain
      0.022   14.5   0.1      0.061   13.0   0.0    1.7  2  Sigma54_activat  Sigma-54 interaction domain
      0.045   14.0   0.2       0.17   12.2   0.0    1.9  2  AAA_22           AAA domain
      0.098   11.6   0.1       0.18   10.7   0.0    1.6  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
        0.1   13.1   0.0       0.25   11.9   0.0    1.7  1  AAA_18           AAA domain
       0.13   11.1   0.1        0.9    8.4   0.0    1.9  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.14   12.4   0.0       0.29   11.4   0.0    1.5  1  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.16   12.1   3.6          1    9.4   0.3    2.5  2  DUF87            Helicase HerA, central domain
       0.25   10.5   1.7       0.63    9.2   0.4    2.0  2  NB-ARC           NB-ARC domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.2   1.4e-30   1.3e-27       3     128 .]       4     233 ..       2     233 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 1.4e-30
                                   EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
                          CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................. 54 
                                   ++ +kGGvGKT++a +L+r++ ++g++V+ vD+Dp  + la+++g+e++i p                             
  gi|15669010|ref|NP_247814.1|   4 AITGKGGVGKTFIASTLMRLFEKNGFKVIGVDCDPN-PTLALAFGVEEEIVPlskrhdiieertgakpgtygnifkinpkv 83 
                                   6789********************************.66677*************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|15669010|ref|NP_247814.1|  84 ddlidkvgykignitllvmgtieeggegcvcpasvllrrllrhlilkrdevvildmeagiehfgrktidtvdlmliviept 164
                                   ********************************************************************************* PP

                                   .....CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS-H CS
                                   .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 .....dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargepv 128
                                        ++kr+++l+++lg+k       +gv++n+v++e+ ++llk+ ++e++   g++vlg++p+de+v++++  g+p+
  gi|15669010|ref|NP_247814.1| 165 kksliTAKRMKKLANDLGIK------NLGVIVNKVRNED-KELLKDIIKEEL---GLEVLGFVPYDEEVIKSEFLGKPI 233
                                   ******************76......7*********994.788888888887...****************99888876 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   6.1e-08   5.4e-05       1      40 [.       1      40 [.       1      66 [. 0.84
   2 !   21.0   0.2   2.1e-07   0.00019     162     225 ..     171     234 ..     148     256 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.1e-08
                     Fer4_NifH  1 rkiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPka 40
                                  +kiai GkGG+Gk++ ++ l+  + ++g kv+ v CDP  
  gi|15669010|ref|NP_247814.1|  1 MKIAITGKGGVGKTFIASTLMRLFEKNGFKVIGVDCDPNP 40
                                  69************************************74 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.1e-07
                     Fer4_NifH 162 akgiekyaksggvrlgGliinsrkvddereliekfa.eelgtkvlevvPrdeivrkaelrkktvi 225
                                   ak ++k a+  g++  G+i+n +  ++++el+++++ eelg++vl +vP de+v k+e+  k ++
  gi|15669010|ref|NP_247814.1| 171 AKRMKKLANDLGIKNLGVIVN-KVRNEDKELLKDIIkEELGLEVLGFVPYDEEVIKSEFLGKPIN 234
                                   5678999**************.54566677777765268*****************998877554 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   9.7e-07   0.00087       9      55 ..       5      50 ..       1      71 [. 0.82
   2 !   16.4   0.2   5.1e-06    0.0046     103     241 ..     123     250 ..     111     253 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.7e-07
                          ParA  9 lSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee 55
                                  + gKGGVGK+ +a++l   ++k+g+kv  +D D   p ++  +gvee
  gi|15669010|ref|NP_247814.1|  5 ITGKGGVGKTFIASTLMRLFEKNGFKVIGVDCDP-NPTLALAFGVEE 50
                                  57*************************9999994.366666666665 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 5.1e-06
                          ParA 103 llkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcg 183
                                   ll++   +  +++i+D+  G        ++  +++ ++iV  p + +l+ +k+  ++++++ +k lGv+ N          
  gi|15669010|ref|NP_247814.1| 123 LLRHLILKRDEVVILDMEAGIEHFGRKTID--TVDLMLIVIEPTKKSLITAKRMKKLANDLGIKNLGVIVNKVRN------ 195
                                   555555555556666665555444333344..456789*******************************985433...... PP

                          ParA 184 ekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepe.seaakaleei 241
                                   e +e+++    + + eelg+++lg +p d+e+ ++   gkp+ l+++  +e++k+++ i
  gi|15669010|ref|NP_247814.1| 196 EDKELLK----DIIKEELGLEVLGFVPYDEEVIKSEFLGKPINLDSKAaKEIEKIFNYI 250
                                   3334443....3567899**********************9887654324444444444 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0     1e-10   9.4e-08       8     164 ..       6     178 ..       2     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1e-10
                        AAA_31   8 nqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne....iektlyevli.eeknikeaiiktkvenldl 83 
                                     KGGvGKT  +  l   + k+g kv+ vD+Dp   ++ ++g+e++     + ++++e  +  +  +   i k + +  dl
  gi|15669010|ref|NP_247814.1|   6 TGKGGVGKTFIASTLMRLFEKNGFKVIGVDCDPNPTLALAFGVEEEIvplsKRHDIIEERTgAKPGTYGNIFKINPKVDDL 86 
                                   56****************************************988775544344444444422222333333333333367 PP

                        AAA_31  84 ip.ssidLaeaeielvelekk.........eeilkellekvkdeYD.yiiiDcpPsLglltenaLvasdsviipvqaeaya 153
                                   i     ++ ++   ++++ ++            l++ll+++  + D ++i+D+   ++ + ++ + + d ++i++++++ +
  gi|15669010|ref|NP_247814.1|  87 IDkVGYKIGNITLLVMGTIEEggegcvcpaSVLLRRLLRHLILKRDeVVILDMEAGIEHFGRKTIDTVDLMLIVIEPTKKS 167
                                   641456677777777777777777777775555799998876555538999***************************999 PP

                        AAA_31 154 leGleqllkti 164
                                   l +++++ k  
  gi|15669010|ref|NP_247814.1| 168 LITAKRMKKLA 178
                                   99988887655 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.6e-08   2.3e-05       4      51 ..       3      50 ..       1      62 [. 0.90
   2 !    8.4   0.2    0.0012       1.1     209     250 ..     157     198 ..     129     208 .. 0.85
   3 ?   -3.1   0.0         4   3.5e+03     250     277 ..     223     249 ..     219     254 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.6e-08
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS-- CS
                   ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqkl 51
                                  i ++GKGGVGKt +++++     ++g kv+ +  DP + l+ +f  + 
  gi|15669010|ref|NP_247814.1|  3 IAITGKGGVGKTFIASTLMRLFEKNGFKVIGVDCDPNPTLALAFGVEE 50
                                  789***********99998889999****************9999865 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0012
                                   EEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE-TTCS CS
                   ArsA_ATPase 209 frlVvipEklslkEteRaikeLkkygikvdavivNkllpeee 250
                                   + +V+ p k sl   +R+ k  + +gik   vivNk+ +e++
  gi|15669010|ref|NP_247814.1| 157 MLIVIEPTKKSLITAKRMKKLANDLGIKNLGVIVNKVRNEDK 198
                                   67899************999999*************988876 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4
                                   SSSTSHHHHHHHHHHHHHHHHHHHHTTT CS
                   ArsA_ATPase 250 eqenCeflearkkiqkkylkeieelfed 277
                                   + +  efl +  ++++k  keie+ f+ 
  gi|15669010|ref|NP_247814.1| 223 VIK-SEFLGKPINLDSKAAKEIEKIFNY 249
                                   443.577888888888888888888864 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0036       3.2      10      32 ..       9      31 ..       2      32 .. 0.88
   2 !   21.5   0.2   1.9e-07   0.00017     131     195 ..     157     224 ..     149     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0036
                        AAA_26 10 tgvGKTvvslgLvralkrkgvkv 32
                                   gvGKT+++  L+r ++++g+kv
  gi|15669010|ref|NP_247814.1|  9 GGVGKTFIASTLMRLFEKNGFKV 31
                                  48***************999997 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.9e-07
                        AAA_26 131 vilVargglgtinqllltiealrqknvrvlGvilNkvrnpe...nvetlekksgipvlGvvPylpdle 195
                                   +++V+ ++++++  +  + +++ + +++ lGvi+Nkvrn++     + +++  g++vlG vPy+++++
  gi|15669010|ref|NP_247814.1| 157 MLIVIEPTKKSLITAKRMKKLANDLGIKNLGVIVNKVRNEDkelLKDIIKEELGLEVLGFVPYDEEVI 224
                                   5778888888888888888888999***************755566899999************9986 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.4e-06    0.0022       4      51 ..       3      49 ..       1      55 [. 0.92
   2 !    9.0   0.0   0.00098      0.87     102     158 ..     117     174 ..      93     204 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-06
                      CBP_BcsQ  4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvd 51
                                  +a++G +GGvG+t ++++L + +++ g +v+ +D  p+  L+l F v+
  gi|15669010|ref|NP_247814.1|  3 IAITG-KGGVGKTFIASTLMRLFEKNGFKVIGVDCDPNPTLALAFGVE 49
                                  56666.8**************************************987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00098
                      CBP_BcsQ 102 aeallaalkelk.eqyrwillDlpagasaltrellaladlvllvvepdanchvrLhqq 158
                                   +  l + l++l  ++++ ++lD+ ag ++  r+++ + dl+l v+ep   + +  ++ 
  gi|15669010|ref|NP_247814.1| 117 SVLLRRLLRHLIlKRDEVVILDMEAGIEHFGRKTIDTVDLMLIVIEPTKKSLITAKRM 174
                                   5555666666666999*******************************99887765554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   9.2e-07   0.00082       1      35 [.       2      36 ..       2      66 .. 0.95
   2 ?    3.1   0.6     0.089        80      94     162 ..     130     200 ..     113     207 .. 0.53

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.2e-07
                                  EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEE CS
                      NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyt 35
                                  k++iTG+ GvGKt + + +++l +++g+kv G+ +
  gi|15669010|ref|NP_247814.1|  2 KIAITGKGGVGKTFIASTLMRLFEKNGFKVIGVDC 36
                                  689*****************************987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.089
                                   HHH-EEEE---STTGGG-HHHHHHHHHHH...TTTSEEEEE--SS--SHHHHHHHT-TT-EEEE.--TTTTTT CS
                      NTPase_1  94 seadviviDEiGkmElkskkfkeaveevL...ksekpvlavihrrkdlalveeirerkdvkvfe.vteenrda 162
                                   ++ +v+++D    +E + +k +++v+ +L   ++ k  l++ +r k+  l +++  ++ +++++ v +e+++ 
  gi|15669010|ref|NP_247814.1| 130 KRDEVVILDMEAGIEHFGRKTIDTVDLMLiviEPTKKSLITAKRMKK--LANDLGIKNLGVIVNkVRNEDKEL 200
                                   44457777744446777777766666544222566777777777743..444444333344443255555543 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   5.2e-05     0.047       4      43 ..       2      37 ..       1      77 [. 0.79
   2 ?    1.2   0.0      0.29   2.6e+02      24      47 ..     132     155 ..     122     205 .. 0.73
   3 ?    3.5   0.0     0.056        50     144     171 ..     227     254 ..     218     257 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-05
                        AAA_24  4 kiliyGpsgiGKTtlakelgpkplfidtek.Glksldadkf 43
                                  ki+i+G+ g+GKT +a++l     +  +ek G+k + +d  
  gi|15669010|ref|NP_247814.1|  2 KIAITGKGGVGKTFIASTL-----MRLFEKnGFKVIGVDCD 37
                                  9*****************9.....33444445555555544 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.29
                        AAA_24  24 pkplfidtekGlksldadkfpdie 47 
                                   ++++++d+e+G  +   + ++++ 
  gi|15669010|ref|NP_247814.1| 132 DEVVILDMEAGIEHFGRKTIDTVD 155
                                   78999******9999999888776 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.056
                        AAA_24 144 kytrlepklgkktanelkeevDlvlran 171
                                   ++ + +++l++k+a+e+++++ +++ ++
  gi|15669010|ref|NP_247814.1| 227 EFLGKPINLDSKAAKEIEKIFNYIIKLK 254
                                   56667899****************9987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   4.7e-07   0.00043      28      88 ..       4      59 ..       2     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.7e-07
                        AAA_16 28 llsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88
                                   ++G  GvGK+ ++ +l+r +ek+g+ ++  +cd +    p +ala    +ee++   +++
  gi|15669010|ref|NP_247814.1|  4 AITGKGGVGKTFIASTLMRLFEKNGFKVIGVDCDPN----PTLALAFGV-EEEIVPLSKRH 59
                                  79**********************************....555555555.33555554444 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0     0.002       1.8       1      37 [.       2      37 ..       2      70 .. 0.89
   2 ?    6.3   0.1     0.018        16      13      37 ..     167     191 ..     164     211 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.002
                                  EEEEEESSSHHHHHHHHHHHHHHHHHCTEEEEETTEE CS
                       PTS_IIB  1 killaCgaGmatSlmaaeklekaakelgieaegeagv 37
                                  ki +    G++ +++a ++l + ++++g++++g+ ++
  gi|15669010|ref|NP_247814.1|  2 KIAITGKGGVGKTFIA-STLMRLFEKNGFKVIGVDCD 37
                                  57777889********.**************999987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.018
                                   HHHHHHHHHHHHHHCTEEEEETTEE CS
                       PTS_IIB  13 Slmaaeklekaakelgieaegeagv 37 
                                   Sl+ a++++k a++lgi+  g+   
  gi|15669010|ref|NP_247814.1| 167 SLITAKRMKKLANDLGIKNLGVIVN 191
                                   8999************876443333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.1e-05     0.046      22      52 ..       4      34 ..       2      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-05
                        AAA_30 22 vltGpAGtGKttalkalreaweaaggrvigl 52
                                  ++tG  G GKt++ ++l +++e++g++vig+
  gi|15669010|ref|NP_247814.1|  4 AITGKGGVGKTFIASTLMRLFEKNGFKVIGV 34
                                  689**************************96 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.8e-05     0.061      24      61 ..       2      39 ..       1      50 [. 0.87
   2 ?   -2.0   0.0       2.8   2.5e+03     122     158 ..     143     181 ..     135     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.8e-05
                                  -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
               Sigma54_activat 24 svlitGesGtGKellaraiheaskrkekpfvavncaai 61
                                  ++ itG+ G+GK+++a+++ +  +++  +++ v+c   
  gi|15669010|ref|NP_247814.1|  2 KIAITGKGGVGKTFIASTLMRLFEKNGFKVIGVDCDPN 39
                                  688*******************************9654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                                   EESBTSSSEEE--EEE..EEEESS-HHHHHHTTSS-HHH CS
               Sigma54_activat 122 vervGsskeikvdvri..iaatnedleeaveegkfredL 158
                                   +e+ G ++  +vd+++  i  t+++l +a + +k+ +dL
  gi|15669010|ref|NP_247814.1| 143 IEHFGRKTIDTVDLMLivIEPTKKSLITAKRMKKLANDL 181
                                   677788777777766511456888887777777777776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.17       8      49 ..       3      38 ..       2      52 .. 0.86
   2 ?   -1.6   0.0       3.4   3.1e+03      78      98 ..     119     138 ..     114     146 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                        AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49
                                  +++tG  G+GKT+ + +l++ +++       + +v+ v++  
  gi|15669010|ref|NP_247814.1|  3 IAITGKGGVGKTFIASTLMRLFEKN------GFKVIGVDCDP 38
                                  68*******************9754......88888888865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.4
                        AAA_22  78 llealeqalraravielliiD 98 
                                   ll++l ++l  +++ e++i+D
  gi|15669010|ref|NP_247814.1| 119 LLRRLLRHLILKRD-EVVILD 138
                                   55666666666666.688887 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0002      0.18      31      69 ..       2      40 ..       1      94 [. 0.91
   2 ?   -3.3   0.0       3.9   3.5e+03     233     258 ..     184     209 ..     181     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                                  EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                          MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                  ++ +tG  G+Gk  + + l+  + ++G +v  +  DP  
  gi|15669010|ref|NP_247814.1|  2 KIAITGKGGVGKTFIASTLMRLFEKNGFKVIGVDCDPNP 40
                                  689***************************999999975 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.9
                                   HHTTHHHHHHHHHHHHHHHHHHHHHH CS
                          MeaB 233 kktGllekrrrerakeelrelvedel 258
                                   k+ G + ++ r+ +ke l+ ++++el
  gi|15669010|ref|NP_247814.1| 184 KNLGVIVNKVRNEDKELLKDIIKEEL 209
                                   55677777788888888888877766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00028      0.25       1      27 [.       3      30 ..       3      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                        AAA_18  1 IlltGtpGvGKttlakeLskrl.gfgvn 27
                                  I++tG+ GvGKt +a  L ++  ++g++
  gi|15669010|ref|NP_247814.1|  3 IAITGKGGVGKTFIASTLMRLFeKNGFK 30
                                  89****************9997555444 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0     0.001       0.9      17      51 ..       2      36 ..       1      53 [. 0.89
   2 ?    0.5   0.0      0.25   2.2e+02      30      65 ..     118     152 ..     107     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.001
                 TrwB_AAD_bind 17 hilivGttGsGKtqalekllrairargdraivlDl 51
                                  +i+i+G  G GKt  ++ l+r  ++ g ++i +D 
  gi|15669010|ref|NP_247814.1|  2 KIAITGKGGVGKTFIASTLMRLFEKNGFKVIGVDC 36
                                  689************************99998775 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.25
                 TrwB_AAD_bind  30 qalekllrairargdraivlDltGafvsrfydegkd 65 
                                   + l+ llr++  + d +++lD++   +++f +++ d
  gi|15669010|ref|NP_247814.1| 118 VLLRRLLRHLILKRDEVVILDMEAG-IEHFGRKTID 152
                                   67899****************9965.5777776555 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00032      0.29       1      36 [.       2      36 ..       2      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                                  EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEE CS
                           Roc  1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdf 36
                                  K+ + G++gvGKt +++ ++ + f+++  + igvd 
  gi|15669010|ref|NP_247814.1|  2 KIAITGKGGVGKTFIASTLM-RLFEKNGFKVIGVDC 36
                                  899**************999.788899899999986 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.3    0.0011         1      25      57 ..       2      33 ..       1      37 [. 0.84
   2 ?    2.7   0.2      0.13   1.1e+02      41      61 ..     117     140 ..     115     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                         DUF87 25 HlAilgsTGsGKSntvavLleellekkgatili 57
                                   +Ai g+ G+GK++ ++ L++    k+g +++ 
  gi|15669010|ref|NP_247814.1|  2 KIAITGKGGVGKTFIASTLMRLFE-KNGFKVIG 33
                                  58*****************98666.88888885 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.13
                         DUF87  41 avLleelle...kkgatililDpH 61 
                                   +vLl++ll+    k+ +++ilD+ 
  gi|15669010|ref|NP_247814.1| 117 SVLLRRLLRhliLKRDEVVILDME 140
                                   4566666655559999******96 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4    0.0007      0.63      23      42 ..       3      22 ..       1      30 [. 0.85
   2 ?    0.1   0.0       0.4   3.6e+02     199     240 ..     156     199 ..     120     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0007
                                  EEEEESTTSSHHHHHHHHCC CS
                        NB-ARC 23 valvGmgGvGKttlakqiln 42
                                  +a+ G+gGvGKt +a+  ++
  gi|15669010|ref|NP_247814.1|  3 IAITGKGGVGKTFIASTLMR 22
                                  79*************98876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.4
                                   HHHHHHHHHHC-TCSCCHHHHHHHHHHCTGCC..TS--SSSSSS CS
                        NB-ARC 199 lalkvlggllstkktveewkkvleklesklle..vekstsksle 240
                                   l l+v+  ++++  t +++kk+++ l  k+l+  v+k  +++ e
  gi|15669010|ref|NP_247814.1| 156 LMLIVIEPTKKSLITAKRMKKLANDLGIKNLGviVNKVRNEDKE 199
                                   66777777777778999999999999999988544444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 1479.79
//
Query:       gi|15669011|ref|NP_247815.1|  [L=298]
Description: molybdenum cofactor biosynthesis protein A [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-28   99.5   0.2    3.9e-28   98.9   0.2    1.3  1  Radical_SAM  Radical SAM superfamily
    2.4e-19   69.6   0.1    1.2e-18   67.2   0.0    2.0  2  Mob_synth_C  Molybdenum Cofactor Synthesis C
    2.2e-11   44.2   0.2    4.3e-11   43.2   0.2    1.6  1  Fer4_12      4Fe-4S single cluster domain
    1.1e-10   41.7   0.3    2.3e-10   40.7   0.3    1.5  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.096   13.1   0.0       0.31   11.5   0.0    1.9  1  EF-hand_7    EF-hand domain pair


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.2   1.1e-31   3.9e-28       1     152 [.      14     158 ..      14     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 1.1e-31
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgirit 81 
                                   +++t+ Cnl+C +C+r  +  +    r++++eei  ++k    + gvk + ++ggepll++d  e++e+++ +  +   i+
  gi|15669011|ref|NP_247815.1|  14 ISITNKCNLQCFYCHREGH--DSNNDRYMTPEEIGIIAKTS-TKFGVKKIKISGGEPLLRKDVCEIIENIKDE--RIKDIS 89 
                                   689**************97..********************.8999***************************..7***** PP

                                   EEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  82 vetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                   ++tng+l+ e  +e+l+++g++rv+++l+++++e ++k++ + +++e+v+++++k+ ++ + + +++ + +
  gi|15669011|ref|NP_247815.1|  90 LTTNGILL-ENLAEKLKDAGLNRVNVSLDTLNPELYKKIT-KFGDVERVINGIKKAIDVSLTPLKVNFLAM 158
                                   ********.*************************888888.55***************9998855555544 PP

>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.28     1e+03      50      71 ..      37      55 ..       9      57 .. 0.71
   2 !   67.2   0.0   3.5e-22   1.2e-18       3     127 ..     179     296 ..     177     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.28
                                  EEEEETTT--EEEEE-TTTS-- CS
                   Mob_synth_C 50 krykikdgkgeiglIapvsepF 71
                                  +ry       eig+Ia  s +F
  gi|15669011|ref|NP_247815.1| 37 DRYMT---PEEIGIIAKTSTKF 55
                                  34433...34799999999998 PP

  == domain 2  score: 67.2 bits;  conditional E-value: 3.5e-22
                                   EEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE--SS...T-SSEEEEETTT--EEEEE-TTTS-.-GGG--EEE CS
                   Mob_synth_C   3 lrfIElmpvgegeewrekkvvsadeilerieerlalleakket...kgpakrykikdgkgeiglIapvsep.FCasCnRlR 79 
                                   l++IE+ p++e           +   +  ie++++++++k  t   ++++k+y +++ +  i++++p++++ FC +C+R+R
  gi|15669011|ref|NP_247815.1| 179 LQIIEFIPLKEEL-------KGYYYNISPIENEIKEKADKVITrnfMQNRKKYIVDGLE--IEFVRPMDNSeFCMHCTRIR 250
                                   7888888888553.......334444555555555555553323369********8888..*********99********* PP

                                   E-TTSEEESSSS-SS-.EEHHHHHHTT--HHHHHHHHHHHHHT----HH CS
                   Mob_synth_C  80 ltadGklktCLfaeee.idlrdllregaseeeLkelikealarkkekhk 127
                                   lt dG lk+CL ++++ +d+ + lr+g+   +L+  + e ++r+++++k
  gi|15669011|ref|NP_247815.1| 251 LTYDGYLKPCLLRDDNlVDVLTPLRKGE---NLEPYFIECINRREPYFK 296
                                   ***************************6...599999999999998875 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.2   1.2e-14   4.3e-11      12     116 ..      17     117 ..       6     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 1.2e-14
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlyt 92 
                                   ++ Cnl+C +C+ +e ++ ++ + +t e +  i +   k  ++++ ++GGEPll   ++++ e+++++k e ++   + ++
  gi|15669011|ref|NP_247815.1|  17 TNKCNLQCFYCH-REGHDSNNDRYMTPEEIGIIAKTSTKFGVKKIKISGGEPLL---RKDVCEIIENIKDERIKDISLTTN 93 
                                   578*********.89999999999998888777777777888************...9***************88889999 PP

                       Fer4_12  93 gytleelskkekeellkeidvlvd 116
                                   g  le+l +k k+  l+ ++v +d
  gi|15669011|ref|NP_247815.1|  94 GILLENLAEKLKDAGLNRVNVSLD 117
                                   *******99988888999999887 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.3   6.3e-14   2.3e-10       5      96 ..      17     101 ..      14     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 6.3e-14
                       Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwl 85 
                                   +++Cnl+C  C ++   +s+   + t e++  i+  ++ +++  +++ ++GGePL+    k+++++++++k+e   k+i l
  gi|15669011|ref|NP_247815.1|  17 TNKCNLQCFYCHREG-HDSNNDRYMTPEEI-GII-AKTSTKFGVKKIKISGGEPLLR---KDVCEIIENIKDER-IKDISL 90 
                                   79**********988.78888888888888.666.47777888899*********55...99*********998.89**** PP

                       Fer4_14  86 etngtleiele 96 
                                    tng l  +l 
  gi|15669011|ref|NP_247815.1|  91 TTNGILLENLA 101
                                   ****9986665 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.7e-05      0.31      11      53 ..      32      80 ..      22      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.7e-05
                     EF-hand_7 11 lDtdgdgyldkeellrllrkifqga.......gegsklsdeelellfkef 53
                                  +D+++d y+++ee+  ++ k ++++       + g++l ++ + ++++++
  gi|15669011|ref|NP_247815.1| 32 HDSNNDRYMTPEEIG-IIAKTSTKFgvkkikiSGGEPLLRKDVCEIIENI 80
                                  9**************.9999999999999999999999998888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1907.87
//
Query:       gi|15669012|ref|NP_247816.1|  [L=231]
Description: peptidyl-prolyl cis-trans isomerase SlyD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-26   91.7   3.6    5.6e-26   90.4   3.6    1.7  1  FKBP26_C  FKBP26_C-terminal
    2.6e-15   56.5   0.0    4.5e-15   55.8   0.0    1.5  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase


Domain annotation for each model (and alignments):
>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   3.6   6.3e-30   5.6e-26       1      72 []     152     221 ..     152     221 .. 0.99

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 6.3e-30
                                   HHHHHHHHHHHH-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEEEE CS
                      FKBP26_C   1 dkekikelIkryiPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvdefe 72 
                                   +k+++ke++k+y+P+++  ++k++i+++tv+Ielpe a Fi niq+ak++IA++ilkr+e++ekV+Fv++fe
  gi|15669012|ref|NP_247816.1| 152 KKNIVKEIVKMYVPRLS--DVKVTIRNGTVKIELPEFAPFIPNIQTAKMAIANEILKRLEDAEKVSFVETFE 221
                                   699**************..****************************************************7 PP

>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0     5e-19   4.5e-15       6      79 ..       3      88 ..       1     146 [. 0.87

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 5e-19
                                  -TTCEEEEEEEEEETTSSEEEEH..........CC...HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTTTTT CS
                        FKBP_C  6 kegdtVtvhykgkledgkvfdss..........rs...rakplefkvGsgqvikGfeealegmkvGekrtltippelaYgekg 75
                                  ++g+ V++ y+g++ dgk+fd++          ++    + p+ +  G+gqv++G++ea+ +m vGe+r++  ppe a+g+++
  gi|15669012|ref|NP_247816.1|  3 EKGKMVKISYDGYV-DGKLFDTTneelakkegiYNpamIYGPVAIFAGEGQVLPGLDEAILEMDVGEEREVVLPPEKAFGKRD 84
                                  79************.********999999999944566*******************************************87 PP

                                  BCTT CS
                        FKBP_C 76 lagg 79
                                    + 
  gi|15669012|ref|NP_247816.1| 85 PSKI 88
                                  6553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1355.65
//
Query:       gi|15669013|ref|NP_247817.1|  [L=138]
Description: hypothetical protein MJ_0826 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-17   63.1   2.9    4.2e-17   62.3   2.9    1.3  1  NfeD      NfeD-like C-terminal, partner-binding


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   2.9   2.3e-21   4.2e-17       2      84 .]      51     134 ..      49     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.3e-21
                                   XXXXXXXXXXXXXXXS---SSS--S..S---GGTTSEEEEEE-B...S-EEEEETTEEEEEE-.SSB-TT-EEEEEEE-SS CS
                          NfeD   2 favvsvlllvllrplllkklkkkek.ktnaealiGkegvvledi...gtGrvkvdGeeWsarsegeiekgerVrVveveGl 78 
                                   +++++vl++++l +++     k  + k +ae+ +G++g+++ed+   g Gr+k+++++W a+s+++i+ g++V++v+veG+
  gi|15669013|ref|NP_247817.1|  51 AIIAGVLTIIILHKFVYGVG-K--EiKVGAERFVGMIGIAIEDFeenGYGRIKIENQIWLAKSKDKIKNGDKVEIVGVEGV 128
                                   57778888899999988865.3..2349999*************98558******************************** PP

                                   SEEEEE CS
                          NfeD  79 tliVep 84 
                                    liV++
  gi|15669013|ref|NP_247817.1| 129 SLIVKK 134
                                   ****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 841.06
//
Query:       gi|15669014|ref|NP_247818.1|  [L=199]
Description: membrane protein regulator of cation conductance [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-37  129.2   2.6    1.8e-37  129.1   2.6    1.0  1  Band_7    SPFH domain / Band 7 family
      0.003   17.3   0.3      0.004   16.9   0.3    1.3  1  Band_7_1  SPFH domain-Band 7 family
  ------ inclusion threshold ------
      0.063   13.8   1.0      0.088   13.3   1.0    1.2  1  FlgN      FlgN protein


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.1   2.6     3e-41   1.8e-37       2     178 .]      27     197 ..      26     197 .. 0.99

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 3e-41
                        Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaav 82 
                                   i+++ e g+++r G++ + l+pG+ +i+Pf+++ ++v++r++++d++  ++++tkD+ +v++d++v+yrv  d+ k++++v
  gi|15669014|ref|NP_247818.1|  27 IVNQYEGGLIFRLGRVIGKLKPGINIIIPFLDVPVKVDMRTRVTDIPP-QEMITKDNAVVKVDAVVYYRV-IDVEKAILEV 105
                                   899*********************************************.*********************.********** PP

                        Band_7  83 eresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakqaa 163
                                       ++++  i ++++ +lr++i++m+l+e+l++re ++++l + l  + + +Gv ++ v +++idpp+++++a+a+ ++a
  gi|15669014|ref|NP_247818.1| 106 ----EDYEYAIINLAQTTLRAIIGSMELDEVLNKREYINSKLLEILDRETDAWGVRIEKVEVKEIDPPEDIKNAMAQQMKA 182
                                   ....***************************************************************************** PP

                        Band_7 164 eaeaqaeiaraeaea 178
                                   e+ ++a+i +ae+e+
  gi|15669014|ref|NP_247818.1| 183 ERLKRAAILEAEGEK 197
                                   ************996 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   6.7e-07     0.004     157     209 ..     130     182 ..      81     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.7e-07
                      Band_7_1 157 ldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                    ++  k e + +kl e l+ e ++ G+ +ek+e+++i+ pe++++a+ ++ ++
  gi|15669014|ref|NP_247818.1| 130 DEVLNKREYINSKLLEILDRETDAWGVRIEKVEVKEIDPPEDIKNAMAQQMKA 182
                                   344567788999***********************************998765 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.0   1.5e-05     0.088       6      71 ..     128     197 ..     126     199 .] 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH....HHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-- CS
                          FlgN   6 eLielleeelelleeLlelleeEtea....LkagdieaLeelleekqellekleqleqkrakllaelgls 71 
                                   eL e l+++  + ++Lle+l++Et+a    + + +++++++  + k++ +++++++  kra++l++ g++
  gi|15669014|ref|NP_247818.1| 128 ELDEVLNKREYINSKLLEILDRETDAwgvrIEKVEVKEIDPPEDIKNAMAQQMKAERLKRAAILEAEGEK 197
                                   78899999999999***********855557777******************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1377.09
//
Query:       gi|15669015|ref|NP_247819.1|  [L=66]
Description: hypothetical protein MJ_0828, partial [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00028   21.1   1.7    0.00029   21.0   1.7    1.1  1  Flot      Flotillin


Domain annotation for each model (and alignments):
>> Flot  Flotillin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.7   1.6e-08   0.00029       1      42 [.       4      45 ..       4      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.6e-08
                          Flot  1 eAeaeAeaakleAeAkrakaeaeAegiralnEAenalseeqi 42
                                  eAe +A+a+++ AeA+r+ ++ eA+  +al  A+n+l++++ 
  gi|15669015|ref|NP_247819.1|  4 EAEGQAKAIQIVAEAARQYFKDEAQLYKALEVANNVLKDNAK 45
                                  8************************************99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 436.25
//
Query:       gi|15669016|ref|NP_247820.1|  [L=425]
Description: peptide chain release factor 1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-46  157.2   0.0    7.8e-46  155.7   0.0    1.8  1  eRF1_2          eRF1 domain 2
    8.4e-34  116.4   2.0    2.7e-33  114.8   2.0    1.9  1  eRF1_3          eRF1 domain 3
    2.6e-14   53.3   0.0    5.3e-14   52.3   0.0    1.6  1  eRF1_1          eRF1 domain 1
    3.5e-14   53.2   0.0    1.4e-13   51.3   0.0    1.9  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    4.5e-12   46.4   0.0    6.3e-11   42.7   0.0    2.2  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
  ------ inclusion threshold ------
      0.012   15.6   0.3      0.026   14.6   0.3    1.6  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.017   15.2   3.1      0.078   13.1   0.2    2.6  2  Zn-ribbon_8     Zinc ribbon domain
        0.1   12.7   0.1       0.19   11.8   0.1    1.4  1  Flagellin_N     Bacterial flagellin N-terminal helical region
       0.13   12.3   0.3         16    5.5   0.1    2.4  2  zinc_ribbon_4   zinc-ribbon domain
       0.13   13.0   0.8       0.26   12.1   0.8    1.4  1  zinc_ribbon_15  zinc-ribbon family
       0.18   11.6   1.0        2.4    8.0   0.0    2.9  3  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
       0.72    9.8   4.7       0.84    9.6   0.2    2.6  3  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.7   0.0   5.2e-49   7.8e-46       2     133 .]     146     278 ..     145     278 .. 0.99

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 5.2e-49
                                   EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHH.HCHTTTESEEE CS
                        eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafl.lvdkdklkgii 81 
                                   +g+i++d++eAti+l+kg+++++lkk+++ vP+K k+Ggqsarr+eRl++ +++efl++v+++an++fl l++++kl+gi+
  gi|15669016|ref|NP_247820.1| 146 YGVILVDRNEATIALVKGRNINILKKLTSGVPGKFKAGGQSARRLERLIDLAAHEFLQRVGQKANEQFLpLLQEKKLRGIL 226
                                   8******************************************************************************** PP

                                   EEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHCC CS
                        eRF1_2  82 lagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlkd 133
                                   ++gpg++k+ef+++d+l++elkk v++++d++y++e g++e+lekaa  lkd
  gi|15669016|ref|NP_247820.1| 227 VGGPGHTKNEFVEGDYLHHELKKIVLDTFDLCYTEEFGIRELLEKAAPLLKD 278
                                   ***********************************************99987 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8   2.0   1.8e-36   2.7e-33       1     113 []     281     423 ..     281     423 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 1.8e-36
                                   HHHHHHHHHHHHHHHHC.TCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSH.HHHHS..................... CS
                        eRF1_3   1 liqekklleefleelak.dtgkavYGveevlkalemgAvetLLvseelersrdt.lkekv..................... 58 
                                   l++e++++++fl+el k d+g+a+YG++evl+al+mgAv+tL+vseele+++++ +++++                     
  gi|15669016|ref|NP_247820.1| 281 LMKEREAVQRFLKELIKeDGGLACYGEKEVLEALMMGAVDTLIVSEELEKYKVKiACNNCdyleektvnklelikleeelk 361
                                   589***********998899*********************************9888888********************* PP

                                   ....-HHH-HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                        eRF1_3  59 ....ketgeelelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                       +++g  l++ve   +ie l e +e+sgak++ +sse+eeG+++++af+GiaaiLRyk+
  gi|15669016|ref|NP_247820.1| 362 naqcPKCGGALSIVEekdYIEYLSELCEQSGAKLVTVSSETEEGAMILNAFKGIAAILRYKI 423
                                   ************************************************************97 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.0   3.6e-17   5.3e-14       1     128 [.      17     139 ..      17     140 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 3.6e-17
                                   HEEEEE..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT.. CS
                        eRF1_1   1 mkllkr..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd.. 77 
                                   +k+lk+  + +++g+++++L+++    ++++ + ++++ s+++++++k +r         ++v+++++   +++++ k+  
  gi|15669016|ref|NP_247820.1|  17 KKMLKElkSKKGKGTELISLYIPAGRRISDVAQHLREEMSQASNIKSKSTR---------KNVQSAIEAILQRLKLLKEpl 88 
                                   688888877889*************************************99.........9******************99 PP

                                   .SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                        eRF1_1  78 .agvlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                    +gv+ + G v  + +   ++++ t+ +e+++p++++ ++ +++f+le+L+e 
  gi|15669016|ref|NP_247820.1|  89 eKGVVIFAGMVPRSGP--GTEKMETYVIEPPEPIKTYIYRcDSEFYLEPLEEF 139
                                   99**************..6*******************999*********996 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   9.2e-17   1.4e-13       2     136 ..     132     273 ..     132     277 .. 0.91
   2 ?   -1.6   0.0         2   2.9e+03      77     108 ..     381     412 ..     378     414 .. 0.81

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 9.2e-17
                baeRF_family10   2 ylapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellak 82 
                                   yl+pL e l++ + ygv+lvdr++a ++ v ++ +   +++++ vpg+ k+gg+ s +r +r  +  a+++l++v++ +++
  gi|15669016|ref|NP_247820.1| 132 YLEPLEEFLEDKDAYGVILVDRNEATIALVKGRNINILKKLTSGVPGKFKAGGQ-SARRLERLIDLAAHEFLQRVGQKANE 211
                                   799***************************************************.************************99 PP

                baeRF_family10  83 ....lleergverlvlgGdeeetaall..drlpkalrarvvgtlplpvda..saaaVlekae 136
                                       ll+e++++ +++gG+ + +++++  d l+ +l++ v +t++l  ++    +++leka+
  gi|15669016|ref|NP_247820.1| 212 qflpLLQEKKLRGILVGGPGHTKNEFVegDYLHHELKKIVLDTFDLCYTEefGIRELLEKAA 273
                                   5555678999*********88888886346899****9999999998855588889888887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                baeRF_family10  77 AellaklleergverlvlgGdeeetaalldrl 108
                                    e l +l+e++g++ + ++  +ee a++l+++
  gi|15669016|ref|NP_247820.1| 381 IEYLSELCEQSGAKLVTVSSETEEGAMILNAF 412
                                   5778999999**99999999999988887766 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   4.2e-14   6.3e-11       2      97 ..     145     245 ..     144     282 .. 0.85
   2 ?    1.3   0.0      0.26   3.8e+02      64      93 ..     286     318 ..     265     334 .. 0.73

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 4.2e-14
                       acVLRF1   2 rlgvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae.....v 77 
                                    +gv+lv r   ++++v+g+++   k+ t+ v g+ +aGG+S +R +R ++  a + l++v ++a++ + +  +e     +
  gi|15669016|ref|NP_247820.1| 145 AYGVILVDRNEATIALVKGRNINILKKLTSGVPGKFKAGGQSARRLERLIDLAAHEFLQRVGQKANEQFLPLLQEkklrgI 225
                                   578999999999*********************************************************77777777789* PP

                       acVLRF1  78 vlgGdrslvaevledarlap 97 
                                   ++gG+  + +e+ e   l++
  gi|15669016|ref|NP_247820.1| 226 LVGGPGHTKNEFVEGDYLHH 245
                                   ********999999865333 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.26
                       acVLRF1  64 eaaarllaeesae...vvlgGdrslvaevleda 93 
                                   ea++r l+e  +e   +++ G+++++++++  a
  gi|15669016|ref|NP_247820.1| 286 EAVQRFLKELIKEdggLACYGEKEVLEALMMGA 318
                                   5555555444444555**********9999775 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3   1.7e-05     0.026      63     101 ..     327     376 ..     279     386 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
                                   EEEEE--EEEETTTS-EEECHHHHH............S-TTTSSS-EEEEE CS
                          HypA  63 eieevpvkvrCreCgkefeleekal............rCpkCgsadveivs 101
                                   e+e+ +vk+ C++C++  e++ ++l            +CpkCg+a ++iv+
  gi|15669016|ref|NP_247820.1| 327 ELEKYKVKIACNNCDYLEEKTVNKLelikleeelknaQCPKCGGA-LSIVE 376
                                   478999*********87775543335589999***********95.55555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3      0.18   2.7e+02       3      14 ..     122     132 ..     122     145 .. 0.69
   2 ?   13.1   0.2   5.2e-05     0.078       8      36 ..     337     372 ..     330     375 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.18
                   Zn-ribbon_8   3 iYeYrCeeCghe 14 
                                   +Y YrC++    
  gi|15669016|ref|NP_247820.1| 122 TYIYRCDS-EFY 132
                                   7*****98.444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.2e-05
                   Zn-ribbon_8   8 CeeCghefe......vlqsisdaplta.CPeCgsev 36 
                                   C++C+   e      +l +  ++ + a CP+Cg+++
  gi|15669016|ref|NP_247820.1| 337 CNNCDYLEEktvnklELIKLEEELKNAqCPKCGGAL 372
                                   *****66669999665555553334455*****976 PP

>> Flagellin_N  Bacterial flagellin N-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00013      0.19      56     120 ..      19      82 ..       9      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TTTS-SHHHHHHHHHHHHHHHHH CS
                   Flagellin_N  56 glsqlvrnnslgisrlqtaqgalselsdilqrlkelavaasndsnsdedrqslqaelqqLtdeln 120
                                    l+ l+++++ g+++++    a   +sd++q l+e + +asn + +++ r+ +q+++++  + l 
  gi|15669016|ref|NP_247820.1|  19 MLKELKSKKGKGTELISLYIPAGRRISDVAQHLREEMSQASNIKSKST-RKNVQSAIEAILQRLK 82 
                                   5788999999*******************************9998776.9999999999998887 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.027        40      17      32 ..     326     341 ..     323     343 .. 0.80
   2 ?    5.5   0.1     0.011        16      18      32 ..     355     369 ..     348     371 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.027
                 zinc_ribbon_4  17 eklpakgvkvrCskCg 32 
                                   e l + +vk+ C +C 
  gi|15669016|ref|NP_247820.1| 326 EELEKYKVKIACNNCD 341
                                   6788889999999997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                 zinc_ribbon_4  18 klpakgvkvrCskCg 32 
                                   kl ++ ++++C+kCg
  gi|15669016|ref|NP_247820.1| 355 KLEEELKNAQCPKCG 369
                                   6677778999****8 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   0.00017      0.26      31      74 ..     328     371 ..     322     380 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                zinc_ribbon_15  31 wkkkkpylacskCkslleaskelgkeiekkessekkeCknCgke 74 
                                   ++k+k  +ac++C +l e+  ++ + i+ +e+ ++ +C++Cg +
  gi|15669016|ref|NP_247820.1| 328 LEKYKVKIACNNCDYLEEKTVNKLELIKLEEELKNAQCPKCGGA 371
                                   56778899*********************************965 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.59   8.9e+02      22      34 ..     335     344 ..     328     347 .. 0.76
   2 ?    8.0   0.0    0.0016       2.4       3      15 ..     364     376 ..     362     384 .. 0.81
   3 ?   -0.7   0.0      0.86   1.3e+03       2      16 ..     386     400 ..     385     403 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.59
                                   EEESST.T----E CS
                zf-C4_Topoisom  22 vGCsnYPeCkftk 34 
                                   ++C+n   C++ +
  gi|15669016|ref|NP_247820.1| 335 IACNN---CDYLE 344
                                   89999...99976 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0016
                                   E-SSS--EEEEEE CS
                zf-C4_Topoisom   3 kCPkCggdLvlkr 15 
                                   +CPkCgg L + +
  gi|15669016|ref|NP_247820.1| 364 QCPKCGGALSIVE 376
                                   7******997765 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.86
                                   EE-SSS--EEEEEE- CS
                zf-C4_Topoisom   2 ekCPkCggdLvlkrg 16 
                                   e C++ g++Lv  ++
  gi|15669016|ref|NP_247820.1| 386 ELCEQSGAKLVTVSS 400
                                   68********98776 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       4.3   6.4e+03      21      35 ..     123     138 ..     120     139 .. 0.66
   2 ?    9.6   0.2   0.00056      0.84      20      34 ..     332     347 ..     321     349 .. 0.74
   3 ?    1.3   0.1      0.21   3.2e+02       4      10 ..     365     371 ..     364     379 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.3
                                   E.EEESSSS-EEESSC CS
                RNA_POL_M_15KD  21 n.feCrqCgYeepadq 35 
                                   + + C++  Y ep ++
  gi|15669016|ref|NP_247820.1| 123 YiYRCDSEFYLEPLEE 138
                                   5577887777777776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00056
                                   CE.EEESSSS-EEESS CS
                RNA_POL_M_15KD  20 kn.feCrqCgYeepad 34 
                                   k+  +C +C+Y e+++
  gi|15669016|ref|NP_247820.1| 332 KVkIACNNCDYLEEKT 347
                                   3368*********986 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.21
                                   ESTTTSB CS
                RNA_POL_M_15KD   4 CpkCgNl 10 
                                   CpkCg  
  gi|15669016|ref|NP_247820.1| 365 CPKCGGA 371
                                   ****965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1470  (0.0819901); expected 358.6 (0.02)
Passed bias filter:                     1078  (0.0601261); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 2660.24
//
Query:       gi|15669017|ref|NP_247821.1|  [L=252]
Description: hypothetical protein MJ_0830 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00024   20.3   0.0    0.00058   19.0   0.0    1.7  2  NAD_synthase  NAD synthase
    0.00032   20.5   0.1      0.002   17.9   0.1    2.2  2  ATP_bind_3    PP-loop family
     0.0016   18.5   0.1      0.014   15.5   0.0    2.2  2  PAPS_reduct   Phosphoadenosine phosphosulfate reductase famil
  ------ inclusion threshold ------
      0.052   13.1   3.7       0.62    9.6   0.1    3.1  3  ThiI          Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.3e-07   0.00058       9      90 ..      10      89 ..       3     108 .. 0.85
   2 ?   -3.3   0.0      0.85   3.8e+03       2      14 ..     188     200 ..     187     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-07
                                  HHHHHHHC.TTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHH CS
                  NAD_synthase  9 lkeyvkka.gakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpivrafeq 90
                                  lk+++k++ + k++++  SGG+DS l + l  ++    + l + + + + se ++++a+  a++++++ k+i+i++i++ + +
  gi|15669017|ref|NP_247821.1| 10 LKNNLKEKfKNKKIIIAYSGGIDSLLLSILLSEIT---ETLCIFIKTPYISEWSLNNAIINAKKYNLNLKVIKIDKIIKNVPE 89
                                  555665441569******************99998...7899999999*****************************998766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.85
                                   HHHHHHHHHHHHH CS
                  NAD_synthase   2 ieelvdflkeyvk 14 
                                   ieel++fl++yvk
  gi|15669017|ref|NP_247821.1| 188 IEELEEFLRNYVK 200
                                   78999******97 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   4.5e-07     0.002       1     111 [.      22     125 ..      22     128 .. 0.70
   2 ?   -2.4   0.0      0.78   3.5e+03     146     164 ..     146     164 ..     129     178 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.5e-07
                                   EEEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--HHHCTTSTCCC... CS
                    ATP_bind_3   1 kvlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdvakkkgknlee... 78 
                                   k+++A+SgG+DS++L  ll +  +       +i +     +e   ++++++  +kk+n++l++ k+d      kn+ e   
  gi|15669017|ref|NP_247821.1|  22 KIIIAYSGGIDSLLLSILLSEITE-----TLCIFIKTPYISEWSLNNAIIN--AKKYNLNLKVIKIDK---IIKNVPErcy 92 
                                   589****************99966.....3444455444455555555554..466666677777773...3344444111 PP

                                   HHHHHHHHHHHHCHHCCT.CEEE---BHHHHHH CS
                    ATP_bind_3  79 aARelRYevlkealkkegievlllAhhadDqaE 111
                                      ++ +e+l++  +k++++v++ + + dD +E
  gi|15669017|ref|NP_247821.1|  93 LCKKMFFEILTKEKEKYNYDVVVDGTNYDDLFE 125
                                   578899999999999999999999999999988 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.78
                                   T--HHHHHHHHHHTT---B CS
                    ATP_bind_3 146 kvskeeleeylkekkikwv 164
                                   k+ k+++ e++ke +i+  
  gi|15669017|ref|NP_247821.1| 146 KIGKKDILEIAKELNINIP 164
                                   5679999999999888755 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.1e-06     0.014       2      63 ..      23      83 ..      22     134 .. 0.82
   2 ?    1.0   0.0     0.088   3.9e+02      81     102 ..     181     202 ..     152     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-06
                                  EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCH CS
                   PAPS_reduct  2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeee 63
                                  +++++sgG+dsl l +L++++ +    +f++t +  +  ++     +++y+l+lkv + ++ 
  gi|15669017|ref|NP_247821.1| 23 IIIAYSGGIDSLLLSILLSEITET-LCIFIKTPYISEWSLNNAIINAKKYNLNLKVIKIDKI 83
                                  799***************999988.7***************************999887765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.088
                                   HHHHHHTHHHHHHHHHCTTECE CS
                   PAPS_reduct  81 aaeriaKveplkkaLekldeda 102
                                    +e++ K+e+l++ L+++ + a
  gi|15669017|ref|NP_247821.1| 181 SIEDLKKIEELEEFLRNYVKGA 202
                                   6788999999999999886554 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00014      0.62      40     117 ..      55     119 ..      18     124 .. 0.61
   2 ?    2.4   0.1     0.022     1e+02     148     192 ..     148     189 ..     131     195 .. 0.67
   3 ?    1.0   0.1     0.062   2.8e+02      41      76 ..     180     212 ..     170     242 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00014
                          ThiI  40 gtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvkekltivllkrkmlriAekvaeeegakalvtGes 117
                                   + se   +     a    +y    +++l v++ ++++k+    v+   ++ l+k++++ i  k  e+++++ +v+G +
  gi|15669017|ref|NP_247821.1|  55 YISEWSLNNAIINA---KKY----NLNLKVIKIDKIIKN----VP--ERCYLCKKMFFEILTKEKEKYNYDVVVDGTN 119
                                   44444433322111...122....244555555444444....43..4799*************************86 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.022
                          ThiI 148 dKeeiiklAkeigtyeisiekedkCsvlakhPttkakleevekae 192
                                    K++i ++Ake+   +i i ++++C +   + + +  +e+++k+e
  gi|15669017|ref|NP_247821.1| 148 GKKDILEIAKEL---NINIPPKETCLLTRFEFNREISIEDLKKIE 189
                                   577888888876...466777777766555555555555555555 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.062
                          ThiI  41 tseeaiekveklaellaeyqtslevklvvvdfkevl 76 
                                    s e  +k+e+l e l +y    +  ++v d+k++ 
  gi|15669017|ref|NP_247821.1| 180 ISIEDLKKIEELEEFLRNYV---KGAIRVRDYKNLA 212
                                   56678899999999999996...3444444554431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1364  (0.0760779); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1751.58
//
Query:       gi|15669018|ref|NP_247822.1|  [L=432]
Description: hypothetical protein MJ_0831 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-17   63.3   2.0    3.1e-17   63.3   2.0    2.1  2  DHHA1     DHHA1 domain
  ------ inclusion threshold ------
       0.13   12.5   0.1       0.29   11.4   0.1    1.5  1  DHH       DHH family
       0.16   11.9   4.3       0.37   10.7   0.2    3.0  3  Cauli_AT  Aphid transmission protein


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.32   1.9e+03       6      25 ..       3      20 ..       1      82 [. 0.67
   2 !   63.3   2.0   5.2e-21   3.1e-17      24     138 .]     314     426 ..     306     426 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.32
                                  HHHHHHHHHHHCHHHHHHHH CS
                         DHHA1  6 eerkelekeleelkealakl 25
                                  e++ke+ek  +  ke+  +l
  gi|15669018|ref|NP_247822.1|  3 EKLKEIEKVTKAIKEK--IL 20
                                  5666666666333333..23 PP

  == domain 2  score: 63.3 bits;  conditional E-value: 5.2e-21
                                   HHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSH....SS-HHHHH CS
                         DHHA1  24 klkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvakeegdkvkvsarskkd....gvdagela 100
                                   +  +++l+++++ vk +k+   ++  e ++g++gi+a+ l +  +kpvi   ++ +   +k+sar ++d    g++++ ++
  gi|15669018|ref|NP_247822.1| 314 WEYKKNLINELKSVKLKKLNNIYY-FEGKKGMIGIIASILVD--DKPVIGYHIEGD--IAKFSARGNRDlvnrGLNLSVAM 389
                                   455677888888885333333444.78999************..999999999765..*******************9999 PP

                                   HHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHHH CS
                         DHHA1 101 keaaaklgggGGGHdlAaGagipaekleealealeeai 138
                                      a+++gg+GGGHd A+Ga ++++k++e+l++++e+i
  gi|15669018|ref|NP_247822.1| 390 AV-AKEFGGNGGGHDVASGAVVSKDKVQEFLKRVDEII 426
                                   88.********************************987 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   4.8e-05      0.29       6      55 ..      28     110 ..      25     144 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.8e-05
                                   -ECSSSHHHHHHHHHHHH....................................CECS--TCGGCGCCHHCCCSEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxx....................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH   6 ghknpDtDsigSaialan....................................llvDhneksqavegeakeeaedviiiD 50 
                                    + + DtD++ S   la+                                    +  D+++ + +++   ++++ + ii+D
  gi|15669018|ref|NP_247822.1|  28 VITHHDTDGLSSGGILAKmlmrtnklfhltvvehlskevieklakenevnkplfIFADMGSGQIEEI---IKHNFNAIILD 105
                                   378899******5555554677777777776666666666666666666666666888888877775...79********* PP

                                   -S--- CS
                                   xxxxx RF
                           DHH  51 HHrlg 55 
                                   HH + 
  gi|15669018|ref|NP_247822.1| 106 HHPPV 110
                                   **885 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.31   1.9e+03     118     135 ..       3      20 ..       1      29 [. 0.76
   2 ?    0.9   0.0     0.065   3.9e+02      23      53 ..      73     102 ..      48     108 .. 0.75
   3 ?   10.7   0.2   6.1e-05      0.37      11      45 ..     316     350 ..     312     361 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.31
                      Cauli_AT 118 nrikkleeetkklaekiv 135
                                   ++ k++e+ tk ++eki 
  gi|15669018|ref|NP_247822.1|   3 EKLKEIEKVTKAIKEKIL 20 
                                   577888888888888875 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.065
                      Cauli_AT  23 elssndrkyvfss.kkssiksiiahcnnlnei 53 
                                   e + n+  ++f+    ++i+ ii+h  n+n i
  gi|15669018|ref|NP_247822.1|  73 ENEVNKPLFIFADmGSGQIEEIIKH--NFNAI 102
                                   345577789999967899*****99..55555 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 6.1e-05
                      Cauli_AT  11 YkkdkivrLkpLelssndrkyvfsskkssiksiia 45 
                                   Ykk+ i  Lk+++l++ +  y+f  kk+ i  i++
  gi|15669018|ref|NP_247822.1| 316 YKKNLINELKSVKLKKLNNIYYFEGKKGMIGIIAS 350
                                   9****************************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2923.42
//
Query:       gi|15669019|ref|NP_247823.1|  [L=1750]
Description: anaerobic ribonucleoside-triphosphate reductase NrdD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.7e-157  523.3  11.6      7e-64  216.6   0.5    3.6  3  NRDD             Anaerobic ribonucleoside-triphosphate reduct
    3.1e-60  202.0   0.0    3.5e-39  133.8   0.0    3.4  2  Intein_splicing  Intein splicing domain
    5.4e-30  103.5  10.4    6.1e-11   42.5   0.3    6.2  5  LAGLIDADG_3      LAGLIDADG-like domain
    3.5e-17   62.8  13.0    3.3e-09   37.2   0.6    4.0  4  ATP-cone         ATP cone domain
    6.5e-12   45.6   0.3    0.00016   21.8   0.0    3.8  3  Hom_end          Homing endonuclease
    1.3e-05   25.2   0.7      0.056   13.5   0.0    4.7  4  LAGLIDADG_WhiA   WhiA LAGLIDADG-like domain
     0.0067   16.0   0.0      0.026   14.1   0.0    1.9  2  Hint             Hint module
  ------ inclusion threshold ------
       0.07   13.4   0.0       0.23   11.7   0.0    1.9  1  TAT_ubiq         Aminotransferase ubiquitination site
       0.28   11.8   5.5        4.4    8.0   0.1    3.8  3  QIL1             MICOS complex subunit MIC13, QIL1
        1.1    8.8   9.1       0.78    9.3   0.5    3.5  4  LepB_N           LepB N-terminal domain


Domain annotation for each model (and alignments):
>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.7   0.2   2.6e-49   4.7e-46       1     158 [.     186     338 ..     186     339 .. 0.97
   2 !  216.6   0.5   3.9e-67     7e-64     157     413 ..     790    1058 ..     775    1083 .. 0.90
   3 !  154.6   0.7   2.3e-48   4.2e-45     413     559 ..    1591    1746 ..    1587    1747 .. 0.96

  Alignments for each domain:
  == domain 1  score: 157.7 bits;  conditional E-value: 2.6e-49
                                   .XHTTHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHHHTTSEEETTGGGTTT.S--EEE--SHHHHHH-CTT-SSS... CS
                          NRDD   1 enanvdskslsglrlklasevskeyalkkllpkevaeaheegdiHiHDldylallttyClgidlkdlleeGlktgngv... 78 
                                   enan+  ++++ +++ +a+e++k+yal  ++pk++a+ah +gdiH+HDl+y+a+  + Cl++dl++++++Glk+ +g+   
  gi|15669019|ref|NP_247823.1| 186 ENANL-MYNPESIHKWVADETMKQYALLAIFPKHIADAHIKGDIHLHDLEYAAT-RPVCLQHDLRPFFKYGLKV-DGTglh 263
                                   8****.*********************************************998.78***************98.667799 PP

                                   ...-B---SHHHHHHHHHHHHHHHHTSSSS-EEETTHHHHHHHHHHHHHHTTSS-GHHHHHHHHHHHHHHHTTS-S..SSS CS
                          NRDD  79 ...srppkhietalalavnilqtlqneqaGgqaissfdtylapfvrkdyekklkkltkkeikqamqefvynlntlpsrrGa 156
                                      s+p+kh e+a+++a+++++++q++++Ggq+i++f+++lap+vr        +l++++ikq mq+f+y+ln+++++rG+
  gi|15669019|ref|NP_247823.1| 264 tsvSKPAKHPEVAIQHAAKVMMAAQTNMSGGQSIDEFNVWLAPYVR--------GLSYEKIKQLMQMFIYELNQMYVARGG 336
                                   9*9******************************************4........67************************* PP

                                   S- CS
                          NRDD 157 Qv 158
                                   Q+
  gi|15669019|ref|NP_247823.1| 337 QS 338
                                   *7 PP

  == domain 2  score: 216.6 bits;  conditional E-value: 3.9e-67
                                    S---EEEEEE.-HH...............................HHHHHTTTTS-HCH----SEEEEEEEEETETTH. CS
                          NRDD  157 QvpFtninlgldtp................tegrfee..kliikallevmleGdgnkgtpftFPilifklkedfnleee 217 
                                    +++F++inl+l+ p                t+g++ee  kli +al++vm+eGd+  g+pf FP+ i+kl+e+   +e 
  gi|15669019|ref|NP_247823.1|  790 NTIFSSINLELEIPeflkdkpaviagttrgTYGDYEEeaKLILEALVDVMMEGDAM-GKPFLFPNFIIKLRENAFKDE- 866 
                                    799*********************************99******************.****************86555. PP

                                    ....HHHHHHHHHHTTT--EEE.......EEES--GGGTT-------.-.......S---EEEEEEEEEEHHHHHH..H CS
                          NRDD  218 dpnydlfklalevtakrgfpyffnlledlepedekevasmgCRlrld.eg..e...rlggrgslgvvtiNlprlaleak 290 
                                      n++l+ ++++++ak g+pyf n+l+d+   + +++++mgCR+rl+ ++  +    +  +g+++  ++Nlpr+a+ea+
  gi|15669019|ref|NP_247823.1|  867 --NKELMYKIHQLSAKFGIPYFINMLPDW---QVTNTNAMGCRTRLSgNWtgDaeiDTLRTGNMQWYSLNLPRIAYEAN 940 
                                    ..99*********************9743...345589*********5222213355555******************* PP

                                    H-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT..-HHH.....HTTSS-GE.............EEEEEEE-HHHH CS
                          NRDD  291 gdeekffelLdellelakealeerrkilekllakg..lpflm....gkgylksrkkkdeveevlkngtltiGfiGlaEa 363 
                                    gd++k+fe+L+e+le+ keal++++++ ++ l  +  +pfl+    g+ y++           ++n t t+Gf+Gl+E+
  gi|15669019|ref|NP_247823.1|  941 GDDTKLFEILHERLEILKEALLIKHEVTKERLYVDnlMPFLTqefdGESYYR-----------YENTTKTFGFVGLNEM 1008
                                    ****************************998766669***985555555554...........7999************ PP

                                    HHHTTEEEE..-HHHHHHHHHHHHHHHHHHHHHHHHHSS-EEEEE---TT CS
                          NRDD  364 lkaltgkkigeseeakefalkvlkhmrekadelkeetglnfsleatPaEs 413 
                                    lk++ g++++es++a +f+ kv++++re+ad+lkeetgl++++ +tPaEs
  gi|15669019|ref|NP_247823.1| 1009 LKYHLGEELHESKDAVKFGEKVIEYIREYADKLKEETGLRWTVTQTPAES 1058
                                    *************************************************8 PP

  == domain 3  score: 154.6 bits;  conditional E-value: 2.3e-48
                                    THHHHHHHHH..HH...................HHG-SSSS-TTSSB-HHHHHHHHHHHTGGGTT-S-EEEEBSS--SS CS
                          NRDD  413 slsgrfakldkkkf.........geipgvdkepyYtNsfhvpvdekislfekikleaefqklttGGailyieldeekkn 482 
                                    +++grfa+ld k +         g++++vd   yYtNs+hv vd++i+l ek+++e++f++l++GG+i++i+  e+  +
  gi|15669019|ref|NP_247823.1| 1591 NTAGRFARLDYKYYkeetisvvrGDLNDVDSL-YYTNSSHVRVDAPITLGEKVRIEEKFHPLCNGGHIMHIWNIESAAD 1668
                                    69************888888888888888888.********************************************** PP

                                    HHHHHHHHHHHHHTT--EEEEE--EEEETT.--..EESSSB-TTT--BE.EEEEEESSSSEEEHHHHHHHHHHHSGG-- CS
                          NRDD  483 pealeklvkiakktgigYfsinpkidvCnecgy..kgeiekCpkCgseeevevirRitGYlrpvsswnkgkkaElkdRv 559 
                                    pe+l++++k ++kt+ig+++++++++vCn+cg    g++++C +Cgse+ v  ++RitGYl+++s+wn++k++El+dR+
  gi|15669019|ref|NP_247823.1| 1669 PEVLMDITKKITKTHIGFWTYTKNLSVCNRCGIsmGGLRDRCINCGSED-VAKFSRITGYLQNISNWNRAKQKELEDRK 1746
                                    *********88999*******************988899*******888.****************************8 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0     6e-21   1.1e-17      19     134 .]     388     790 ..     356     790 .. 0.95
   2 !  133.8   0.0   1.9e-42   3.5e-39       2     134 .]    1068    1591 ..    1067    1591 .. 1.00

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 6e-21
                                   CTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCT.TEEEEEECCC--TT-EEEEE.... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.... RF
               Intein_splicing  19 egeevlslnledlklevksvkkliklklk.elyeiklesgrkikaTpeHkllvvrd.egivEkradeLkegdliavp.... 93 
                                    +   +s+n+++ k e k+v ++ ++k + ++y++  + g++i++T +H+l+ +++ +++  ++++  + + +i       
  gi|15669019|ref|NP_247823.1| 388 AEVYTISVNVKTGKAEFKRVYAISRHKPRgKVYKVIGKDGTSIIVTEDHSLFNYDEnGNL--VCVKPRQMKHIIRNFnnpy 466
                                   5566789***********************************************997777..66666666666665599** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669019|ref|NP_247823.1| 467 dveyrigdyietnyqrtdskynsrqndipeklkitkelcqflglfvaegsyitngisittkdddiakfierfvkeqineni 547
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669019|ref|NP_247823.1| 548 avkryedsvrfvnkgfyrflkehingkainknspefilkgdkemklaflgglisgdgyvskdgrvqiyttseqllgqlhll 628
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669019|ref|NP_247823.1| 629 lsdlgmiysitkikeegekieikrneivrnyklyvieiaknctedlkpyvipkykkerikpanydqlpydyriikehlrki 709
                                   ********************************************************************************* PP

                                   ........................................HSCEEEEEEEEEEEEECEEEEEEEEETTT-EEEE.CTTEEE CS
                                   ........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
               Intein_splicing  94 ........................................dadvvwdkvksievedeeeyVYdltvednhNFva.ngiivH 133
                                                                           + ++ + ++k+i++ d+++yVYdl+vedn+NF+   gi+ H
  gi|15669019|ref|NP_247823.1| 710 tdkkpyndyawksnnrklklntlekieqlnphlreeinkfKLNIPF-EIKEIKEIDYNGYVYDLSVEDNENFITaTGILCH 789
                                   ************************************9988888766.7*************************999***** PP

                                   - CS
                                   x RF
               Intein_splicing 134 N 134
                                   N
  gi|15669019|ref|NP_247823.1| 790 N 790
                                   9 PP

  == domain 2  score: 133.8 bits;  conditional E-value: 1.9e-42
                                    EECTTCEE.EEHHHHCC...........ECTTEEEEEETTTTEEEEEE...........EEEEEEEEEEEEEEEEETTS CS
                                    xxxxxxxx.xxxxxxxx...........xxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing    2 iledgeek.vkieelve...........kegeevlslnledlklevks...........vkkliklklkelyeiklesg 57  
                                    i+e++e+k vki+e+ve           ++g+++++++++d++++++s           ++++i+++ ke+yei+lesg
  gi|15669019|ref|NP_247823.1| 1068 IFENNEYKlVKIGEFVEkylnrykdraiTYGDNNIEVYIKDENIYAPSfdkdgkivlkpITHAIRHRGKEIYEIELESG 1146
                                    89***************************************************************************** PP

                                    -EEEEETT-EEEECCT.TEEEEEECCC--TT-EEEEE.......................................... CS
                                    xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.......................................... RF
               Intein_splicing   58 rkikaTpeHkllvvrd.egivEkradeLkegdliavp.......................................... 93  
                                    +k+++T++H++++++d  ++vE++a++Lk+gd+i++p                                          
  gi|15669019|ref|NP_247823.1| 1147 KKVRVTGDHSVFTINDnLDVVEVKASDLKVGDFIITPkiipsiskdkiylseivknkdkyyvkikdhikfieeheeilk 1225
                                    ***************9*************************************************************** PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669019|ref|NP_247823.1| 1226 esykeyktkwkdlkpvlkkknafrldliedlvdkekiekisyghanyinnkikldekfgyligaflseghwndkcveis 1304
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669019|ref|NP_247823.1| 1305 stnkefienlveiieeilgkdayyitvkgdkrrykdlyviglnktvamifeslglnklssnkeipsillsnetflkgli 1383
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669019|ref|NP_247823.1| 1384 kgyidgdgsiyvdeskrdysirlyttsetlrdtlclalkilginyrlsidkkskvnenwrdcyvikitgkenieklldv 1462
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669019|ref|NP_247823.1| 1463 eiknnggkdvipkiaekfkeiinqysqrewkerfgidvnnlhiwedlkkgymsryrakkvlnimknvkeieekygrlld 1541
                                    ******************************************************************************* PP

                                    ......HSCEEEEEEEEEEEEEC.EEEEEEEEETTT-EEEE.CTTE.EE- CS
                                    ......xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxx.xxx RF
               Intein_splicing   94 ......dadvvwdkvksievede.eeyVYdltvednhNFva.ngii.vHN 134 
                                          d+d++++++ksi+v de +eyVYd++ve+++NF++ +g+i +HN
  gi|15669019|ref|NP_247823.1| 1542 kigqliDNDLLFERIKSIRVLDEiPEYVYDISVEGTENFIGgEGFIcLHN 1591
                                    *************************************************9 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00048      0.85       8      56 ..     508     550 ..     503     575 .. 0.80
   2 !   39.9   0.2   2.2e-13   3.9e-10       1      65 [.     590     650 ..     590     670 .. 0.86
   3 ?    0.4   0.0      0.46   8.2e+02      29      50 ..     863     884 ..     857     888 .. 0.88
   4 !   11.5   0.0   0.00016      0.29       2      56 ..    1281    1331 ..    1280    1355 .. 0.77
   5 !   42.5   0.3   3.4e-14   6.1e-11       3      79 ..    1379    1460 ..    1377    1462 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00048
                                   HHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEE CS
                   LAGLIDADG_3   8 rGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyek 56 
                                    Glf a+Gs  +++     is+t+++ ++++ + r  ++  I+ +i  k
  gi|15669019|ref|NP_247823.1| 508 LGLFVAEGSYITNG-----ISITTKDDDIAKFIERFVKEQ-INENIAVK 550
                                   69************.....**************9998765.66666666 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 2.2e-13
                                   HHHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCC CS
                   LAGLIDADG_3   1 evkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvy 65 
                                   e k+afL Gl+++DG+vsk+++    + ++++s++ll ++  lL+ lG++ +i++ k+++ +   
  gi|15669019|ref|NP_247823.1| 590 EMKLAFLGGLISGDGYVSKDGR----VQIYTTSEQLLGQLHLLLSDLGMIYSITKIKEEGEKIEI 650
                                   5789*****************7....******************************777766554 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.46
                                   EEES-HHHHHHHHHHHHHCT.H CS
                   LAGLIDADG_3  29 ltssskelledvqrlLlrlGIe 50 
                                   ++  +kel++++ +l +++GI 
  gi|15669019|ref|NP_247823.1| 863 FKDENKELMYKIHQLSAKFGIP 884
                                   56789***************96 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00016
                                    HHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHH.HCT.HSCEEEE CS
                   LAGLIDADG_3    2 vkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLl.rlGIestiyek 56  
                                    +k ++L G f ++G+ + +      ++++s++ke++e + ++ +  lG  ++  + 
  gi|15669019|ref|NP_247823.1| 1281 EKFGYLIGAFLSEGHWNDKC-----VEISSTNKEFIENLVEIIEeILGKDAYYITV 1331
                                    6889****************.....*************999999555555544444 PP

  == domain 5  score: 42.5 bits;  conditional E-value: 3.4e-14
                                    HHHHHHHHHHHCCECCECSTTTTS.EEEEES-HHHHHHHHHHHHHCT.HSCEEEE....EEE-SCCCCECCCHCHCTTC CS
                   LAGLIDADG_3    3 kaafLrGlfdaDGsvskskkkgvs.isltssskelledvqrlLlrlGIestiyek....kkakgrgvyrlliisgenlk 76  
                                     +++++G++d+DGs+ +++ k+ + i+l+++s+ l + +   L+ lGI+ ++  +     ++++r++y + i+++en++
  gi|15669019|ref|NP_247823.1| 1379 LKGLIKGYIDGDGSIYVDESKRDYsIRLYTTSETLRDTLCLALKILGINYRLSIDkkskVNENWRDCYVIKITGKENIE 1457
                                    57899*****************99****************************9998788888999999*********** PP

                                    GGG CS
                   LAGLIDADG_3   77 rFl 79  
                                    ++l
  gi|15669019|ref|NP_247823.1| 1458 KLL 1460
                                    987 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.6   1.9e-12   3.3e-09       2      77 ..      15      84 ..      14      86 .. 0.85
   2 !   31.6   1.3     1e-10   1.8e-07       2      71 ..      91     160 ..      90     167 .. 0.93
   3 ?   -3.2   0.1       7.2   1.3e+04      33      55 ..     528     550 ..     520     556 .. 0.77
   4 ?   -1.7   0.0       2.5   4.5e+03      49      71 ..    1071    1093 ..    1061    1096 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.9e-12
                                  EEE-TTS-EEE--HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS-HHHHHHH CS
                      ATP-cone  2 kViKRdGtvepfdvekIkraiekAcegseeeideiaeeveaevrkrlrdgisteeIqdlvektliehpdyavaaay 77
                                  +ViKRd+++e f+v+k+++++ ++  +   ++d i+    +ev+ + ++gi+t+e+ d+v ++l++  d +va+ y
  gi|15669019|ref|NP_247823.1| 15 YVIKRDKRKEKFNVNKLAKSLINSGVN-YGDLDTII----SEVCAKVYNGITTDELKDIVYNVLKK-IDKDVAENY 84
                                  8***********************777.55666665....5559999*****************85.556788776 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1e-10
                                   EEE-TTS-EEE--HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS-H CS
                      ATP-cone   2 kViKRdGtvepfdvekIkraiekAcegseeeideiaeeveaevrkrlrdgisteeIqdlvektliehpdy 71 
                                   kV+   ++ e+fd+ekI++a+ +   ++ee++++ia+eve e++k +++  +   I+++v  +lie++  
  gi|15669019|ref|NP_247823.1|  91 KVRTSEKEFESFDKEKIAKALIRETGADEETARKIADEVERELKKLKVKYLTAPMIREIVNYKLIEYGFE 160
                                   688889999***************999**************************************87765 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 7.2
                                   HHHHHHHHHHHHHHHHIIT-BHH CS
                      ATP-cone  33 ideiaeeveaevrkrlrdgiste 55 
                                    d+ia+ +e  v+++++++i ++
  gi|15669019|ref|NP_247823.1| 528 DDDIAKFIERFVKEQINENIAVK 550
                                   57788888888888888888776 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 2.5
                                    IIT-BHHHHHHHHHHHHHHSS-H CS
                      ATP-cone   49 rdgisteeIqdlvektliehpdy 71  
                                    +++ +  +I+++vek+l ++ d 
  gi|15669019|ref|NP_247823.1| 1071 NNEYKLVKIGEFVEKYLNRYKDR 1093
                                    56677789*********877665 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     9e-08   0.00016       1      75 [.     579     651 ..     579     673 .. 0.78
   2 ?    2.4   0.0     0.097   1.7e+02      17      57 ..    1285    1323 ..    1274    1347 .. 0.85
   3 !   16.6   0.0   3.7e-06    0.0066       9      94 ..    1375    1460 ..    1367    1469 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9e-08
                       Hom_end   1 kipsflaseaievREaFlaGLvdsdgyvkkekedsatvktedksvmegivklarsLGikasvkt...keekidakgvk 75 
                                   ++p+f+   + e++ aFl GL+ +dgyv+k+  + + + t++++++ ++  l   LG+  s+++   +    ++ + k
  gi|15669019|ref|NP_247823.1| 579 NSPEFILKGDKEMKLAFLGGLISGDGYVSKD--GRVQIYTTSEQLLGQLHLLLSDLGMIYSITKikeE---GEKIEIK 651
                                   579999999999999****************..89****************************96442...2332222 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.097
                       Hom_end   17 FlaGLvdsdgyvkkekedsatvktedksvmegivklar.sLG 57  
                                    +l G   s+g+ +++   ++ +++++k+ +e++v++++ +LG
  gi|15669019|ref|NP_247823.1| 1285 YLIGAFLSEGHWNDK---CVEISSTNKEFIENLVEIIEeILG 1323
                                    789999999**9999...*****************9852565 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 3.7e-06
                       Hom_end    9 eaievREaFlaGLv....dsdg..yvkkeked.satvktedksvmegivklarsLGikasvktkeekidakgvkhqfcy 80  
                                    +     E+Fl GL+    d+dg  yv++ k d s+ + t+++++ + +    ++LGi+   +  ++++   + + + cy
  gi|15669019|ref|NP_247823.1| 1375 N-----ETFLKGLIkgyiDGDGsiYVDESKRDySIRLYTTSETLRDTLCLALKILGINYRLSIDKKSKV--NENWRDCY 1446
                                    4.....55555553333388884456666666999999************************9655544..4444558* PP

                       Hom_end   81 aitlsggdalksvl 94  
                                     i+++g++  +++l
  gi|15669019|ref|NP_247823.1| 1447 VIKITGKENIEKLL 1460
                                    *****998777665 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.7     1e+04       7      37 ..     509     535 ..     507     558 .. 0.61
   2 ?    2.6   0.1     0.079   1.4e+02       3      67 ..     594     656 ..     592     671 .. 0.83
   3 !   13.5   0.0   3.1e-05     0.056       3      55 ..    1284    1338 ..    1282    1365 .. 0.75
   4 ?    3.2   0.0     0.052        94       3      57 ..    1381    1437 ..    1379    1462 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.7
                LAGLIDADG_WhiA   7 GaflasGsindpekkyhLEivspdeelaeql 37 
                                   G+f+a+Gs           i ++d ++a+ +
  gi|15669019|ref|NP_247823.1| 509 GLFVAEGSYITNGI----SITTKDDDIAKFI 535
                                   88999998544222....2555555555555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.079
                LAGLIDADG_WhiA   3 aflrGaflasGsindpekkyhLEivspdeelaeqlqkllnefeleakilerrk.kyvvylKkaeqI 67 
                                   afl G++ + G +++  +     i++++e+l+ ql  ll+ +++ ++i++ ++ + ++ +K+ e +
  gi|15669019|ref|NP_247823.1| 594 AFLGGLISGDGYVSKDGR---VQIYTTSEQLLGQLHLLLSDLGMIYSITKIKEeGEKIEIKRNEIV 656
                                   799999999****99544...58************************9998861466777776655 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 3.1e-05
                LAGLIDADG_WhiA    3 aflrGaflasGsindpekkyhLEivspdeelaeqlqklln......efeleakilerrk 55  
                                     +l Gafl++G  nd       Ei+s+++e++e+l ++++       + ++ k  +rr 
  gi|15669019|ref|NP_247823.1| 1284 GYLIGAFLSEGHWND----KCVEISSTNKEFIENLVEIIEeilgkdAYYITVKGDKRRY 1338
                                    599************....368*****************93333333344444444444 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.052
                LAGLIDADG_WhiA    3 aflrGaflasGsindp.ekk.yhLEivspdeelaeqlqkllnefeleakilerrkky 57  
                                     +++G + + Gsi    +k+ y + +++++e l ++l+ +l+ ++++++++  +k+ 
  gi|15669019|ref|NP_247823.1| 1381 GLIKGYIDGDGSIYVDeSKRdYSIRLYTTSETLRDTLCLALKILGINYRLSIDKKSK 1437
                                    5678999999**986635558*********************999999887666554 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.2   2.1e+03      63      91 ..     416     444 ..     393     489 .. 0.71
   2 !   14.1   0.0   1.4e-05     0.026      41     114 ..    1116    1182 ..    1109    1205 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Hint  63 raefveietengekltlTpaHLvfvsene 91 
                                   r + +++  ++g+++ +T+ H +f  +++
  gi|15669019|ref|NP_247823.1| 416 RGKVYKVIGKDGTSIIVTEDHSLFNYDEN 444
                                   33445555677899999999999977765 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.4e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Hint   41 vdesgevvfsevllfldrdseqraefveietengekltlTpaHLvfvsenekssseeeeavfaskvregdyvlv 114 
                                    +d++g++v +++    ++ +++ +e +eie+e+g+k+++T  H vf+ + + +       v as+ + gd++++
  gi|15669019|ref|NP_247823.1| 1116 FDKDGKIVLKPI---THAIRHRGKEIYEIELESGKKVRVTGDHSVFTINDNLDVV----EVKASDLKVGDFIIT 1182
                                    678888888776...5778889999*********************998875555....799**********99 PP

>> TAT_ubiq  Aminotransferase ubiquitination site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.23       2      28 ..    1444    1470 ..    1443    1481 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                      TAT_ubiq    2 dsYliQmnGngslpsVLDvhVnvhGks 28  
                                    d Y+i+++G+ ++ ++LDv ++ +G  
  gi|15669019|ref|NP_247823.1| 1444 DCYVIKITGKENIEKLLDVEIKNNGGK 1470
                                    78*******************888744 PP

>> QIL1  MICOS complex subunit MIC13, QIL1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       7.5   1.3e+04      17      34 ..     667     685 ..     664     696 .. 0.68
   2 ?    8.0   0.1    0.0025       4.4       9      49 ..    1019    1061 ..    1017    1065 .. 0.83
   3 ?    4.1   0.2     0.041        73      17      53 ..    1477    1514 ..    1474    1532 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.5
                          QIL1  17 ykkakeyipPyvd.evkkk 34 
                                    k+  e ++Pyv  ++kk+
  gi|15669019|ref|NP_247823.1| 667 AKNCTEDLKPYVIpKYKKE 685
                                   5777889999999446655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0025
                          QIL1    9 sseeteelykkakeyipPyvdevkkkl..clevpklpsveevk 49  
                                    +s++  ++ +k+ eyi++y+d++k++    + v++ p+ +++ 
  gi|15669019|ref|NP_247823.1| 1019 ESKDAVKFGEKVIEYIREYADKLKEETglRWTVTQTPAESSLP 1061
                                    578888999******************5555599999988765 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.041
                          QIL1   17 ykkakeyipPyvd.evkkklclevpklpsveevkfslv 53  
                                     +k+ke i  y + e+k++++++v++l  +e++k+   
  gi|15669019|ref|NP_247823.1| 1477 AEKFKEIINQYSQrEWKERFGIDVNNLHIWEDLKKGYM 1514
                                    6899*********66****************9998444 PP

>> LepB_N  LepB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.5   0.00044      0.78      99     167 ..      45     112 ..      16     138 .. 0.74
   2 ?   -2.6   0.0         2   3.6e+03     117     154 ..     123     161 ..     108     168 .. 0.76
   3 ?   -3.9   0.3       4.9   8.8e+03      83     103 ..    1225    1245 ..    1207    1281 .. 0.59
   4 ?    3.4   0.1     0.029        52      82     135 ..    1506    1570 ..    1498    1578 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00044
                        LepB_N  99 lfpaiaekakklkekldekllkdivskalkkipadlldketkkelakylgidsfkevsfgeegnyqefa 167
                                   l + i e  +k+ + +++++lkdiv ++lkki +d+  ++ ++ +  ++  ++++ +sf +e+  ++++
  gi|15669019|ref|NP_247823.1|  45 LDTIISEVCAKVYNGITTDELKDIVYNVLKKIDKDV-AENYRNGIILKVRTSEKEFESFDKEKIAKALI 112
                                   55556677788899999******************9.67777777777776666666666666655554 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                        LepB_N 117 kllkdivskalkkipadlldketkkelakylgid.sfke 154
                                   ++++d v+  lkk+  ++l    ++e+ +y  i+  f+e
  gi|15669019|ref|NP_247823.1| 123 RKIADEVERELKKLKVKYLTAPMIREIVNYKLIEyGFEE 161
                                   568888999999999999999999999998776524555 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 4.9
                        LepB_N   83 kkftkgYilnykkikglfpai 103 
                                    k+ +k+Y  ++k +k+++++ 
  gi|15669019|ref|NP_247823.1| 1225 KESYKEYKTKWKDLKPVLKKK 1245
                                    445555555555555544332 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.029
                        LepB_N   82 lkkftkgYilnykk.....ikglfpaiaekakklkeklde....kllkdivsk..alkkipadll 135 
                                    ++ + kgY++ y+      i   +++i ek   l +k+ +    +ll + +++  +l++ip+++ 
  gi|15669019|ref|NP_247823.1| 1506 WEDLKKGYMSRYRAkkvlnIMKNVKEIEEKYGRLLDKIGQlidnDLLFERIKSirVLDEIPEYVY 1570
                                    67789*******97444345555667777777777777768888888888885337999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1750 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.99u 0.33s 00:00:01.32 Elapsed: 00:00:00.49
# Mc/sec: 10745.32
//
Query:       gi|15669020|ref|NP_247824.1|  [L=142]
Description: hypothetical protein MJ_0832.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-10   40.3   0.8      4e-10   39.3   0.8    1.5  1  Class_IIIsignal  Class III signal peptide
  ------ inclusion threshold ------
      0.031   14.5   0.4       0.08   13.2   0.2    1.8  2  DUF3333          Domain of unknown function (DUF3333)
      0.035   13.5   0.0      0.042   13.3   0.0    1.1  1  Rib_hydrolayse   ADP-ribosyl cyclase


Domain annotation for each model (and alignments):
>> Class_IIIsignal  Class III signal peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.8   6.6e-14     4e-10       1      25 [.       6      30 ..       6      32 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 6.6e-14
               Class_IIIsignal  1 kKGQiSlEyiLLilavlviaiiaiy 25
                                  k+GQiSlE++LL+l+vl++++ia  
  gi|15669020|ref|NP_247824.1|  6 KRGQISLEFSLLFLGVLLAIVIAVG 30
                                  8*********************975 PP

>> DUF3333  Domain of unknown function (DUF3333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.3e-05      0.08      14      46 ..       4      36 ..       2      68 .. 0.83
   2 ?   -1.4   0.0      0.39   2.3e+03     128     151 ..      98     121 ..      95     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                       DUF3333 14 FrlyGiaAialallfLviLlvsIvskGltAFtq 46
                                  Fr  G +++ ++llfL +Ll+ +++ G+++ + 
  gi|15669020|ref|NP_247824.1|  4 FRKRGQISLEFSLLFLGVLLAIVIAVGYPGMFG 36
                                  9999************************98754 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.39
                       DUF3333 128 vtvwllasddvDsllkGeidrslp 151
                                   ++++++a+ d++ +l G+ + s+p
  gi|15669020|ref|NP_247824.1|  98 IKFNITAKCDINIILNGNKTVSTP 121
                                   789999999999999999887766 PP

>> Rib_hydrolayse  ADP-ribosyl cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     7e-06     0.042     108     158 ..      67     117 ..      40     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7e-06
                                   BTTBSS--SS-B---SSS---HHHHHHHHHHHHHHHH--EEEEEEEESSSS CS
                Rib_hydrolayse 108 qeessglnyqsCpkwedcennavssfWkraSkkfaeaasGvvtvlLngsee 158
                                   +e++ ++ y +Cp  +   nn+   f++    kf  +a+ +++++Lng+++
  gi|15669020|ref|NP_247824.1|  67 DEGTMKIVYIKCPPGTWGANNNILYFYRDGNIKFNITAKCDINIILNGNKT 117
                                   366778999***************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 964.73
//
Query:       gi|15669021|ref|NP_247825.1|  [L=277]
Description: hypothetical protein MJ_0833 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1942.66
//
Query:       gi|15669022|ref|NP_247826.1|  [L=238]
Description: hypothetical protein MJ_0834 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1571.70
//
Query:       gi|15669023|ref|NP_247827.1|  [L=377]
Description: hypothetical protein MJ_0835 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     1e-141  472.4  40.0     5e-106  354.8  30.8    2.1  2  DUF515           Protein of unknown function (DUF515)
    0.00094   19.4   1.0     0.0025   18.0   0.3    2.1  1  Chordopox_A13L   Chordopoxvirus A13L protein
     0.0018   18.5   3.2     0.0018   18.5   3.2    2.1  2  GA               GA module
     0.0089   16.5   6.3       0.26   11.9   1.6    2.8  2  EF-G-binding_N   Elongation factor G-binding protein, N-termi
  ------ inclusion threshold ------
      0.014   15.2   0.2       0.02   14.7   0.2    1.3  1  HGD-D            2-hydroxyglutaryl-CoA dehydratase, D-compone
      0.022   15.2   2.0       0.15   12.6   0.2    3.1  3  Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; D
      0.034   13.0   0.2      0.048   12.5   0.2    1.1  1  EcsB             Bacterial ABC transporter protein EcsB
        0.1   13.3   0.1        1.3    9.6   0.0    2.2  2  DUF3528          Protein of unknown function (DUF3528)
       0.12   12.3   2.1        0.3   11.1   2.1    1.6  1  TNFR_16_TM       Tumor necrosis factor receptor member 16 tra
       0.23   11.8   1.6        0.5   10.7   1.6    1.5  1  DUF3365          Protein of unknown function (DUF3365)
       0.38   10.4   4.3       0.11   12.2   1.4    1.6  2  Baculo_VP91_N    Viral capsid protein 91 N-terminal
       0.52   11.2   2.5        9.4    7.1   0.2    3.1  3  Histone_HNS      H-NS histone family
        1.3    9.0   7.1        3.4    7.7   0.3    3.9  4  GA-like          GA-like domain
        4.2    6.8   7.2          3    7.3   4.0    2.1  2  Z1               Z1 domain


Domain annotation for each model (and alignments):
>> DUF515  Protein of unknown function (DUF515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.8  30.8  3.9e-109    5e-106       1     334 [.       1     294 [.       1     294 [. 0.99
   2 !  130.2   2.8   5.2e-41   6.7e-38     359     448 ..     287     374 ..     286     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 354.8 bits;  conditional E-value: 3.9e-109
                        DUF515   1 keetpklkplKkksrrssrisslrekerrkrliiGasvlvvivillvfaiYsyienkelee...LENakaakieeinklFa 78 
                                   +++t+k+k+lK+ksrr++     ++++++++lii   ++vviv+ll+f++Y++i+n +++e   LEN+k+a+ie+in++Fa
  gi|15669023|ref|NP_247827.1|   1 MVDTSKIKALKEKSRRTV-----KSGSLKFILII---LVVVIVGLLAFIAYNEISNLQFQEkitLENQKKAAIESINQMFA 73 
                                   579*************99.....99*********...******************************************** PP

                        DUF515  79 seyaNdpqKlllinKiqaansiEelekidvrtifeqakkeleeeiieleqakkekelkqlKqeainqikaafgellslsl. 158
                                    +y+NdpqKl++inKiq+an+iEe++++                   le+akk++++k++K+eainqik+++ge++slsl 
  gi|15669023|ref|NP_247827.1|  74 -KYPNDPQKLIYINKIQMANNIEEINEV-------------------LEEAKKYISFKNYKIEAINQIKSMYGEYYSLSLs 134
                                   .***************************...................********************************** PP

                        DUF515 159 adelkkKi.....vaeleeLlkqvdsaktieevleikvdkyllsldkkyYllkldkiptsdvilekngekslitkdevkki 234
                                   a+el++Ki     ++e+e+Llk+vd++k+i++++e+++d++l+s+dk+yY             +e+ng+++++t+de++k+
  gi|15669023|ref|NP_247827.1| 135 AQELVHKIslaqsTEEIENLLKSVDIEKDIRSIIEKQIDYVLASGDKYYY-------------VEINGKSMFMTRDEILKY 202
                                   **************************************************.............****************** PP

                        DUF515 235 iksvgslseLkeykvtpVelvevvlvlvrekqvGkliapGDevkvYaKdeatiayeivdssYvillllsveagsisvSEsq 315
                                   +k+++ lseLk++k+tpV+++++v++++++kq+Gkl+++GD++++Y+Kd+++i+y+i+dssYvil       +sis+SEs+
  gi|15669023|ref|NP_247827.1| 203 KKFWT-LSELKSLKITPVSQLNKVAIEISAKQCGKLPHKGDIISIYSKDGSFITYGIIDSSYVIL-------SSISYSESK 275
                                   *****.***********************************************************.......********* PP

                        DUF515 316 sqsssvseesstsssesss 334
                                   s+ss+++e ++++ss+sss
  gi|15669023|ref|NP_247827.1| 276 STSSNINELGESYSSSSSS 294
                                   **************99965 PP

  == domain 2  score: 130.2 bits;  conditional E-value: 5.2e-41
                        DUF515 359 stseslsssisYsv.NLaeiLkAiaadkldasdevkaqlgnYGkellelEdntqllaldEnvkllvivevPsekvpdilev 438
                                   s s s+sssisYs+ NL++iL+A+++d+ld+ d++k+++g+YGk+l+e+Ed+tq+  +dEnv++++i+++P++k+pdi+++
  gi|15669023|ref|NP_247827.1| 287 SYSSSSSSSISYSLnNLPGILHATVIDRLDY-DKIKKMFGEYGKKLNEIEDDTQI--FDENVNYFLIISIPDDKIPDIIQI 364
                                   5689***************************.***********************..************************ PP

                        DUF515 439 edeivvikva 448
                                   +++++vi+++
  gi|15669023|ref|NP_247827.1| 365 DPKDIVIVIK 374
                                   ********97 PP

>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3     2e-06    0.0025       5      42 ..      25      62 ..      23      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                Chordopox_A13L  5 lllliiCvaivglivYgiYnrkketqttnpstveeyee 42
                                  ++l+i+ v+ivgl+ +  Yn +++ q++++ t e+ ++
  gi|15669023|ref|NP_247827.1| 25 FILIILVVVIVGLLAFIAYNEISNLQFQEKITLENQKK 62
                                  89******************************776665 PP

>> GA  GA module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   3.2   1.4e-06    0.0018      14      60 .]      57     105 ..      48     105 .. 0.94
   2 ?   -3.4   0.0       9.5   1.2e+04      39      55 ..     138     154 ..     136     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                            GA  14 LaqaKqnAkqaInnL..tnLNnaQkqalkdqinqattraeVaqikqkAk 60 
                                   L++ K+ A++ In++  ++ N++Qk  ++++i+ a++++e+++++++Ak
  gi|15669023|ref|NP_247827.1|  57 LENQKKAAIESINQMfaKYPNDPQKLIYINKIQMANNIEEINEVLEEAK 105
                                   899**********9755899***************************97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.5
                            GA  39 lkdqinqattraeVaqi 55 
                                   l ++i+ a++ +e+++ 
  gi|15669023|ref|NP_247827.1| 138 LVHKISLAQSTEEIENL 154
                                   56778888888888765 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   1.6    0.0002      0.26      27      79 ..      54     108 ..      48     111 .. 0.81
   2 ?    6.3   0.2     0.011        14      34      74 ..     114     157 ..     109     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                EF-G-binding_N  27 kkvveavkalaaekIlelfpelseeqkel..LeqiddiktkekaeklLeeLkeyV 79 
                                   k ++e  k  a+e I+++f +  ++ ++l  +++i+  ++ e+++++Lee k+y+
  gi|15669023|ref|NP_247827.1|  54 KITLENQKKAAIESINQMFAKYPNDPQKLiyINKIQMANNIEEINEVLEEAKKYI 108
                                   5689999************997777766612678888888999999999999886 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                EF-G-binding_N  34 kalaaekIlel...fpelseeqkelLeqiddiktkekaeklLee 74 
                                   k +a+++I+ +     +ls  ++el+++i+  +++e++e+lL++
  gi|15669023|ref|NP_247827.1| 114 KIEAINQIKSMygeYYSLSLSAQELVHKISLAQSTEEIENLLKS 157
                                   5566667777766555688889*******************986 PP

>> HGD-D  2-hydroxyglutaryl-CoA dehydratase, D-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   1.5e-05      0.02     108     201 ..      42     139 ..      33     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                   HT----HHHHHHHHHHHHHHHHHHHHHHHHT.TSSS-SS-HHHHHHHHHHTT.S-HHHHHHHHHHHHHHHHHH.T..S..T CS
                         HGD-D 108 tgkrideesleaaikeanetrellkelytll.pqspapihgfdllllakvvf.lgkeeatealeelleeleer.sk.s..e 182
                                     ++i+  ++++ i + n+++ +++++ +++ ++   p   ++l+++ k+++  + ee++e lee  + +  +  k +  +
  gi|15669023|ref|NP_247827.1|  42 AYNEISNLQFQEKITLENQKKAAIESINQMFaKY---PNDPQKLIYINKIQMaNNIEEINEVLEEAKKYISFKnYKiEaiN 119
                                   5578999999*********************555...88888999*******66999999999955544444423433578 PP

                                   S-EEE.EEES---TT--HHH CS
                         HGD-D 183 riRll.ltGipvellaaklm 201
                                   +i+ +  + + + l a++l 
  gi|15669023|ref|NP_247827.1| 120 QIKSMyGEYYSLSLSAQELV 139
                                   88888667777777766664 PP

>> Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.87   1.1e+03      41      61 ..      81     101 ..      46     112 .. 0.65
   2 ?   12.6   0.2   0.00012      0.15      28      81 ..     113     167 ..     109     168 .. 0.84
   3 ?   -1.9   0.0       3.8   4.8e+03       4      19 ..     173     188 ..     172     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.87
                                   HHHHSSSS-HHHHHHHHHHHT CS
               Acetyltransf_11  41 rllyrsglsleealeeleeea 61 
                                   +l+y ++ ++++ +ee++e +
  gi|15669023|ref|NP_247827.1|  81 KLIYINKIQMANNIEEINEVL 101
                                   456666666777777775333 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00012
                                   --HHHHHHHHHHHHHHHSSSS-HHHHHHHHHHHTTTSCCHHHHHHHHHH-S..S-B CS
               Acetyltransf_11  28 fseeeikalkkayrllyrsglsleealeeleeeaeespevqelldFieask..RGi 81 
                                   ++ e+i+++k +y   y+ +ls +e + ++   a++++e+++ll++++ +k  R i
  gi|15669023|ref|NP_247827.1| 113 YKIEAINQIKSMYGEYYSLSLSAQELVHKIS-LAQSTEEIENLLKSVDIEKdiRSI 167
                                   56689*************************5.889999*******99844334655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.8
                                   TTEEEETTTTEEEEE- CS
               Acetyltransf_11   4 PfvlvagnparlrglN 19 
                                    +vl++g++  ++ +N
  gi|15669023|ref|NP_247827.1| 173 DYVLASGDKYYYVEIN 188
                                   599****999999999 PP

>> EcsB  Bacterial ABC transporter protein EcsB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   3.8e-05     0.048     187     243 ..      24      80 ..      17      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.8e-05
                          EcsB 187 lalllilllllvlllllkrkkkkklldWeklieeEqkrrmrfyrflnlFtDvpelkk 243
                                    ++l+il++++v ll ++ +++   l++++ i +E+++++ + ++ ++F+  p+ ++
  gi|15669023|ref|NP_247827.1|  24 KFILIILVVVIVGLLAFIAYNEISNLQFQEKITLENQKKAAIESINQMFAKYPNDPQ 80 
                                   5667779******************************************99998665 PP

>> DUF3528  Protein of unknown function (DUF3528)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0     0.001       1.3      34      85 ..     107     160 ..      88     183 .. 0.76
   2 ?    1.2   0.0      0.42   5.4e+02      31      62 ..     221     251 ..     211     311 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                       DUF3528  34 evafrdyaldasgKWh..hrgnlascyssedlvhrdllsastargemlvKnesv 85 
                                    ++f++y ++a ++ +  +   ++ + s+++lvh+  l++st+  e l K+  +
  gi|15669023|ref|NP_247827.1| 107 YISFKNYKIEAINQIKsmYGEYYSLSLSAQELVHKISLAQSTEEIENLLKSVDI 160
                                   479****9999864431044555666677*************999999998654 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.42
                       DUF3528  31 pvRevafrdyaldasgKWhhrgnlascyssed 62 
                                   ++  va +  +  + gK +h+g + s ys++ 
  gi|15669023|ref|NP_247827.1| 221 QLNKVAIE-ISAKQCGKLPHKGDIISIYSKDG 251
                                   55555555.56678899999999999999854 PP

>> TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.1   0.00024       0.3      13      27 ..      29      43 ..      27      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                    TNFR_16_TM 13 ILaaVvvgLlaYvif 27
                                  IL +V+vgLla++++
  gi|15669023|ref|NP_247827.1| 29 ILVVVIVGLLAFIAY 43
                                  8999**********9 PP

>> DUF3365  Protein of unknown function (DUF3365)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.6   0.00039       0.5       2      83 ..      31     120 ..      29     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00039
                                   .XXXXXXXXXXXXXXX...XXX--HHHHHHHHHHHHHHHHHHHHHHTTS-S.......--GGGGS--SHHHHHHHHT-EEE CS
                       DUF3365   2 lvvllglllalslrsq...krqaeeealekarllaeqleavreyvakslkp.....tivpayaareiaeefsekrkgysyk 74 
                                   +vv++gll+++ +++    + q +  ++++ ++++e ++++ + +++  ++     +i  a  + ei e+++e +k +s+k
  gi|15669023|ref|NP_247827.1|  31 VVVIVGLLAFIAYNEIsnlQFQEKITLENQKKAAIESINQMFAKYPNDPQKliyinKIQMANNIEEINEVLEEAKKYISFK 111
                                   56677777777766667555558888899999999999999888888877544333345566667777777777799**** PP

                                   EE-SS-SSG CS
                       DUF3365  75 etslnprnp 83 
                                   +++ +++n+
  gi|15669023|ref|NP_247827.1| 112 NYKIEAINQ 120
                                   ****99997 PP

>> Baculo_VP91_N  Viral capsid protein 91 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.4   8.3e-05      0.11       2      67 ..      26      93 ..      25     142 .. 0.87
   2 ?   -3.5   0.1       5.3   6.8e+03      81     107 ..     312     339 ..     308     348 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                 Baculo_VP91_N  2 llvvfllilvvllflaivfefdntafterl..kqrrrlvleeylksvgadestfdvlsyvskvldane 67
                                  +l+++++++v ll +  + e+ n +f e++  ++++++ +e+  +   + +  ++ l y+ k+ +an+
  gi|15669023|ref|NP_247827.1| 26 ILIILVVVIVGLLAFIAYNEISNLQFQEKItlENQKKAAIESINQMFAKYPNDPQKLIYINKIQMANN 93
                                  7899999999999999999*********973346778899999999999999***********66665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.3
                 Baculo_VP91_N  81 vsrsvfdeseekFdFltqtfeevd.vse 107
                                   + r  +d+ ++ F  + ++++e++  ++
  gi|15669023|ref|NP_247827.1| 312 IDRLDYDKIKKMFGEYGKKLNEIEdDTQ 339
                                   5666677888888888888888773333 PP

>> Histone_HNS  H-NS histone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2    0.0074       9.4       5      42 ..      45      82 ..      43      93 .. 0.89
   2 ?    1.7   0.1      0.36   4.7e+02       7      44 ..      98     140 ..      89     153 .. 0.51
   3 ?   -0.6   0.0         2   2.5e+03      26      44 ..     318     336 ..     316     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0074
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX----SS CS
                   Histone_HNS  5 lieelekqeealeaeerkealaeirelaaeyGltleel 42
                                  +i++l+ qe+   ++++k+a++ i+++ a+y  ++++l
  gi|15669023|ref|NP_247827.1| 45 EISNLQFQEKITLENQKKAAIESINQMFAKYPNDPQKL 82
                                  788999999999******************97776665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.36
                                   XXXXXXXXX..XXXXXXXXXXXXXXXXXXXXX...----SSS- CS
                   Histone_HNS   7 eelekqeea..leaeerkealaeirelaaeyG...ltleelaa 44 
                                   +e+ +++++    ++ + ea+++i+++  ey    l+++el +
  gi|15669023|ref|NP_247827.1|  98 NEVLEEAKKyiSFKNYKIEAINQIKSMYGEYYslsLSAQELVH 140
                                   2222333332223444455555555555554365566666655 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2
                                   XXXXXXXXXXX----SSS- CS
                   Histone_HNS  26 aeirelaaeyGltleelaa 44 
                                   ++i+++  eyG +l+e+++
  gi|15669023|ref|NP_247827.1| 318 DKIKKMFGEYGKKLNEIED 336
                                   689************9976 PP

>> GA-like  GA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.42   5.4e+02       4      19 ..      53      68 ..      51      71 .. 0.82
   2 ?    7.7   0.3    0.0026       3.4      29      47 ..      84     102 ..      81     104 .. 0.88
   3 ?    0.8   0.0      0.38   4.8e+02       2      20 ..     104     122 ..     103     124 .. 0.85
   4 ?   -0.1   0.0       0.7     9e+02      29      46 ..     138     155 ..     135     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.42
                       GA-like  4 kkeaLkeAKeaAkaeL 19
                                  +k  L+  K+aA++  
  gi|15669023|ref|NP_247827.1| 53 EKITLENQKKAAIESI 68
                                  677899*******976 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0026
                       GA-like  29 yiekIdkAkTvEgVkaLKe 47 
                                   yi+kI  A+ +E+ +++ e
  gi|15669023|ref|NP_247827.1|  84 YINKIQMANNIEEINEVLE 102
                                   9*************98755 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.38
                       GA-like   2 akkkeaLkeAKeaAkaeLk 20 
                                   akk+ ++k +K +A+++ k
  gi|15669023|ref|NP_247827.1| 104 AKKYISFKNYKIEAINQIK 122
                                   6889999********9877 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.7
                       GA-like  29 yiekIdkAkTvEgVkaLK 46 
                                    + kI  A++ E+ + L 
  gi|15669023|ref|NP_247827.1| 138 LVHKISLAQSTEEIENLL 155
                                   678**********99985 PP

>> Z1  Z1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.0    0.0024         3      38     139 ..      89     191 ..      82     193 .. 0.81
   2 ?   -0.5   0.0      0.57   7.3e+02      56     106 ..     268     338 ..     252     347 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0024
                            Z1  38 eqekvaelieelleelkkelkesaeekkeellkeleklweke.kts...tkseeeelsfeevkeelkealekievvvvNss 114
                                   + ++  e+i+e+lee kk ++ +  + k e+++++++++ +  +     +++  +++s+ + +ee+++ l+++++  +  s
  gi|15669023|ref|NP_247827.1|  89 QMANNIEEINEVLEEAKKYISFK--NYKIEAINQIKSMYGEYyS-LslsAQELVHKISLAQSTEEIENLLKSVDIEKDIRS 166
                                   44556678888999988888888..899999********99952.24668889999*****************99988888 PP

                            Z1 115 kkkerldYeeeeeeglsvIavGGnk 139
                                     ++++dY   + ++   + + G++
  gi|15669023|ref|NP_247827.1| 167 IIEKQIDYVLASGDKYYYVEINGKS 191
                                   8889999988888778888888776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.57
                            Z1  56 elkesaeekkeellkeleklwekekts....................tkseeeelsfeevkeelkealeki 106
                                   ++++s+++++++ ++el + + ++++s                     + ++ +  f e  ++l+e+ +++
  gi|15669023|ref|NP_247827.1| 268 SISYSESKSTSSNINELGESYSSSSSSsisyslnnlpgilhatvidrLDYDKIKKMFGEYGKKLNEIEDDT 338
                                   45555666666777777777776632245555555555554444433333333444555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1965  (0.109599); expected 358.6 (0.02)
Passed bias filter:                      775  (0.0432261); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 2354.28
//
Query:       gi|15669024|ref|NP_247828.1|  [L=130]
Description: hypothetical protein MJ_0835.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-10   40.4   0.4    4.1e-10   39.3   0.4    1.6  1  Class_IIIsignal  Class III signal peptide


Domain annotation for each model (and alignments):
>> Class_IIIsignal  Class III signal peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.4   2.3e-14   4.1e-10       1      27 []      12      38 ..      12      38 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 2.3e-14
               Class_IIIsignal  1 kKGQiSlEyiLLilavlviaiiaiyyy 27
                                  kK+Q+SlE+++L+la+l+++ii+i ++
  gi|15669024|ref|NP_247828.1| 12 KKAQVSLEFSFLFLAILLASIITISHF 38
                                  8***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1089  (0.0607396); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 864.63
//
Query:       gi|15669025|ref|NP_247829.1|  [L=339]
Description: hypothetical protein MJ_0835.2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-34  117.6  11.2    2.8e-34  117.6  11.2    1.7  2  Arc_PepC       Archaeal Peptidase A24 C-terminal Domain
    3.6e-11   43.4  11.4    3.6e-11   43.4  11.4    3.0  4  Peptidase_A24  Type IV leader peptidase family
     0.0047   17.4   0.6     0.0047   17.4   0.6    2.4  2  Arc_PepC_II    Archaeal Peptidase A24 C-terminus Type II


Domain annotation for each model (and alignments):
>> Arc_PepC  Archaeal Peptidase A24 C-terminal Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       1.1   6.3e+03       5      27 ..       9      31 ..       5      35 .. 0.50
   2 !  117.6  11.2   4.6e-38   2.8e-34       2     112 .]     208     313 ..     207     313 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.1
                      Arc_PepC  5 sitelkliskvikaltkeelsdk 27
                                  +i+ + l++  i+ ++ + + +k
  gi|15669025|ref|NP_247829.1|  9 IINFILLLLAAITDIKERIIPHK 31
                                  33344455555666666555555 PP

  == domain 2  score: 117.6 bits;  conditional E-value: 4.6e-38
                      Arc_PepC   2 llvsitelkliskvikaltkeelsdkkkveeLkEGdiladiilekeddevtvddksllkrlkealktgdvskietkgkvlv 82 
                                   ++++++e+ lis+vi+alt+ e+sdkk++eeLkEGdil+d+i++++d+ v+v++ +++kr+k++l+ ++++++e  +++++
  gi|15669025|ref|NP_247829.1| 208 SIIYLCEIILISIVIYALTGVETSDKKHIEELKEGDILRDVIIIDKDG-VEVKNLNIMKRIKFLLE-HEIKENE--KEIIL 284
                                   68*******************************************665.*****************.*******..99999 PP

                      Arc_PepC  83 sdlaeGLtkediellkkLvsegKiedefrv 112
                                   +d +eGL++edi+++kkL++egKi+d+++v
  gi|15669025|ref|NP_247829.1| 285 TD-GEGLSNEDIRKIKKLYMEGKIPDKLNV 313
                                   99.*************************97 PP

>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4  11.4   5.9e-15   3.6e-11       2     106 ..      10     114 ..       9     115 .. 0.85
   2 ?   -7.2   8.5         3   1.8e+04      41      61 ..     146     166 ..     124     224 .. 0.56
   3 ?   -1.3   1.2       0.5     3e+03       6      35 ..     187     216 ..     182     239 .. 0.59
   4 ?   -3.1   0.1       1.7     1e+04      50      55 ..     324     329 ..     307     337 .. 0.50

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 5.9e-15
                 Peptidase_A24   2 vlltillvlsviDldtrtlpdeltlpllllgvlfaqllllglpnlaqavlgalvgalvlllislvdeqamGgGDvklaavl 82 
                                   + +++ll+++++D++ r++p++ t++++++ ++++  ++    n   a+++ l+++l+l +       +mGgGDvkl+++l
  gi|15669025|ref|NP_247829.1|  10 INFILLLLAAITDIKERIIPHKYTIAMIIINLVVG--YYYFGFNAIIAFFSTLILCLILSI-------GMGGGDVKLFTAL 81 
                                   6799******************************9..667777777777788877777777.......************* PP

                 Peptidase_A24  83 gaflgwerl.........llavlvaillgavlg 106
                                   + ++  ++          l+++ ++++++av++
  gi|15669025|ref|NP_247829.1|  82 APIFAYPNSfvfyipkyiLYLIAISMFIAAVFP 114
                                   *****6666666667766888888899999885 PP

  == domain 2  score: -7.2 bits;  conditional E-value: 3
                 Peptidase_A24  41 lglpnlaqavlgalvgalvll 61 
                                   ++   +a+ ++ a +++ +++
  gi|15669025|ref|NP_247829.1| 146 IYEIPYASIIIWAYIVLSIFV 166
                                   344444444444444444333 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.5
                 Peptidase_A24   6 illvlsviDldtrtlpdeltlpllllgvlf 35 
                                    ll+l +iD  + + ++ l  +++ l+ ++
  gi|15669025|ref|NP_247829.1| 187 YLLFLYIIDTTYFIKYNVLLTSIIYLCEII 216
                                   566666666666666666555554444333 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 1.7
                 Peptidase_A24  50 vlgalv 55 
                                   v+g ++
  gi|15669025|ref|NP_247829.1| 324 VIGYVI 329
                                   222222 PP

>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.2   7.4e+03      71      88 ..     147     164 ..     146     181 .. 0.73
   2 !   17.4   0.6   7.9e-07    0.0047      16      88 ..     262     332 ..     254     333 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                   Arc_PepC_II  71 ygvPflipitaGfiialv 88 
                                   y +P+   i+  +i+  +
  gi|15669025|ref|NP_247829.1| 147 YEIPYASIIIWAYIVLSI 164
                                   667777777777776544 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 7.9e-07
                   Arc_PepC_II  16 ellkkflfllee.feekdgkikrkfisvekeldeelrkelkkykkkglieetvWvtygvPflipitaGfiialv 88 
                                   ++ k+  flle+ ++e++++    +++ ++ l++e ++++kk+  +g+i ++  v    Pf++++++G++i l+
  gi|15669025|ref|NP_247829.1| 262 NIMKRIKFLLEHeIKENEKE---IILTDGEGLSNEDIRKIKKLYMEGKIPDKLNVIKTYPFVPFVVIGYVIVLM 332
                                   33455555555313443333...333445578899999********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1406  (0.0784204); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 2082.68
//
Query:       gi|15669026|ref|NP_247830.1|  [L=119]
Description: hypothetical protein MJ_0836 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-29  100.4   8.6    5.7e-29   99.9   8.6    1.2  1  zf-like   Cysteine-rich small domain
  ------ inclusion threshold ------
      0.058   13.5   0.8       0.51   10.4   0.2    2.1  2  CRF       Corticotropin-releasing factor family
      0.082   12.9   0.1       0.12   12.4   0.1    1.2  1  DUF2025   Protein of unknown function (DUF2025)


Domain annotation for each model (and alignments):
>> zf-like  Cysteine-rich small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   8.6   9.5e-33   5.7e-29       4      74 ..      16      86 ..      13      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 9.5e-33
                       zf-like  4 ffsnkeCeyyPCHktedenClfCyCPlYaledeelGefveteng.kvkdCskCllvHkkevadellkklkei 74
                                  + +n++CeyyPCH+ +++ Cl+CyCP+Y++edeelGe+ve+++g k+++C+kC +vH+++va+e+l+++ + 
  gi|15669026|ref|NP_247830.1| 16 CGANRNCEYYPCHF-DGQVCLWCYCPFYPCEDEELGEYVEKKDGtKIWSCMKCFWVHREDVATEILREILNL 86
                                  7899**********.99************************************************9765443 PP

>> CRF  Corticotropin-releasing factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.049   2.9e+02      15      22 ..       1       8 [.       1      21 [. 0.81
   2 ?   10.4   0.2   8.6e-05      0.51       6      36 ..      74     106 ..      74     108 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.049
                                  HHHHHHHH CS
                           CRF 15 lleiARak 22
                                  ++e+A+++
  gi|15669026|ref|NP_247830.1|  1 MIELAKNH 8 
                                  9*****98 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 8.6e-05
                                   HHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHH CS
                           CRF   6 DlpfhvLRqlleiARaks..qreqaaaNrqiLd 36 
                                   D+ +++LR+ l++ + k+   + +   N++++ 
  gi|15669026|ref|NP_247830.1|  74 DVATEILREILNLTKDKDidEALKLLDNHELML 106
                                   899****************999********995 PP

>> DUF2025  Protein of unknown function (DUF2025)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.9e-05      0.12      46      95 ..      61     110 ..      47     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                                   -EEHHHHTEEESSSSEEEE-TTHHHHHHHHT-HHHHT--HHHHHHTT--S CS
                       DUF2025  46 itpasefvwaveeaqlmtlkrerlellleqniddrlnlseplrvylrrsd 95 
                                   i  +++  w+ +e+ + ++ re l+l  +++id+ l+l +     l+ +d
  gi|15669026|ref|NP_247830.1|  61 IWSCMKCFWVHREDVATEILREILNLTKDKDIDEALKLLDNHELMLKIKD 110
                                   77788999******************************998888777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 765.79
//
Query:       gi|15669027|ref|NP_247831.1|  [L=249]
Description: cmp-binding-factor 1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-15   57.1   2.0    4.4e-15   56.0   2.0    1.6  1  HD        HD domain
    5.1e-06   25.7   0.2    3.9e-05   22.8   0.1    2.3  2  TraI_2    Putative helicase
     0.0011   18.8   0.1     0.0027   17.5   0.1    1.6  1  HD_2      HD containing hydrolase-like enzyme


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   2.0   7.4e-19   4.4e-15       2     118 ..      59     168 ..      58     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 7.4e-19
                                   HHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHTTTTHHHHTS..HHH....HHH...CTCCHHHHHHHHHHHHHHH CS
                            HD   2 leHsleVaklarrlaedlge....eedrellllaaLlHDiGkgpfgdafekk....eee...fekflaHekvgaeilreve 71 
                                   +eH++ V k+a ++a+ l+e    e +r+ + ++aLlHDi k++++     k    +++   f+  l+H + ++  l ++ 
  gi|15669027|ref|NP_247831.1|  59 IEHTISVTKIALKMADVLEEvygvEVNRDYIIAGALLHDIMKPYNYIR---KedgtFDHydmFN--LDHLTLAVAELYKRD 134
                                   79******************************************8863...3344744444333..589999999999999 PP

                                   HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHH CS
                            HD  72 krlgldledvaklirehheswegkkrprglaerqlslearivklaDr 118
                                    +      +v+k++++hh+++         ++r++s+ea iv  aD 
  gi|15669027|ref|NP_247831.1| 135 FPI-----EVIKIVASHHGDHS--------PTRPNSIEAYIVHYADE 168
                                   999.....9************9........77**************7 PP

>> TraI_2  Putative helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   6.6e-09   3.9e-05      50     119 ..      41     101 ..      30     120 .. 0.77
   2 ?   -2.2   0.0      0.25   1.5e+03     143     163 ..     152     172 ..     146     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.6e-09
                        TraI_2  50 vqllPAseshhhskaGGLLdhglevaaaalklrqghilpaneepeeraaqeerWrvaailaaLlhdlgki 119
                                   v++ PAs + hh + GGL++h++ v  +alk+++  +l+   ++e ++          i++aLlhd+ k+
  gi|15669027|ref|NP_247831.1|  41 VEEAPASINWHHRYEGGLIEHTISVTKIALKMAD--VLEEVYGVEVNRD-------YIIAGALLHDIMKP 101
                                   8899***************************987..4444444443332.......24556666666666 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.25
                        TraI_2 143 warrrraerYflrwkskrkgr 163
                                   + r + +e Y+++++++++ +
  gi|15669027|ref|NP_247831.1| 152 PTRPNSIEAYIVHYADEADSK 172
                                   677788999999999997776 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   4.5e-07    0.0027      25      66 ..      57      98 ..      49     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.5e-07
                          HD_2 25 nvaeHslevaliahalalienkkfggkldaerlallalyHDa 66
                                   + eH+++v+ ia  +a + ++ +g +++ + +++ al+HD+
  gi|15669027|ref|NP_247831.1| 57 GLIEHTISVTKIALKMADVLEEVYGVEVNRDYIIAGALLHDI 98
                                  578**************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1682.22
//
Query:       gi|15669028|ref|NP_247832.1|  [L=223]
Description: hypothetical protein MJ_0838 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-64  215.8   0.2    5.8e-64  215.6   0.2    1.0  1  DUF166           Domain of unknown function
  ------ inclusion threshold ------
      0.071   12.8   1.0        9.2    6.0   0.0    3.5  4  PC4              Transcriptional Coactivator p15 (PC4)
          1    9.7   8.2        2.4    8.6   0.9    2.8  3  Phage_int_SAM_5  Phage integrase SAM-like domain


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.6   0.2   9.7e-68   5.8e-64       2     214 ..       5     217 ..       4     222 .. 0.98

  Alignments for each domain:
  == domain 1  score: 215.6 bits;  conditional E-value: 9.7e-68
                        DUF166   2 vltsgeyGervvenilnepdferslivavvevpeeldefiedpeelLpelkeaDiviaytlhpDlllelaekake.kkvka 81 
                                   +lt+g yG+r++++i++++ ++    +++v++++++de i+++e+++++lk++D++i+ytl+pDl++el++k+ke ++  +
  gi|15669028|ref|NP_247832.1|   5 ILTDGVYGDRAYNTIKSKFPCD----FITVKYYGDFDE-ITISENTIEKLKDYDLFITYTLNPDLTYELVRKIKElNNKAF 80 
                                   89********************....99**********.************************************999*** PP

                        DUF166  82 livpaeapkaglrkelkekleelgievavpkpfCslee..........egkpkideFleefGkPelevevkdgkikkVeVl 152
                                   ++v+a++++     ++k+++e++g ++++p  +C+++e          +++p+++eFl++fGkP++++++k++ki+k++Vl
  gi|15669028|ref|NP_247832.1|  81 VLVGAWKGE-----GFKKQIESFG-NAFCPYLMCDIDEdelkdykdylDNYPHLKEFLKYFGKPKVKLYIKNNKIEKIDVL 155
                                   *********.....**********.******************************************************** PP

                        DUF166 153 rsapCGstwyvakklkGkeveeaeeka.geahqsYpClAsmerdfelketklhkAgyihkeav 214
                                   r+apCGst ++ k+++G e++++++++ g+++q++ C+A+++r f +ke+k++kAg+i+++ +
  gi|15669028|ref|NP_247832.1| 156 REAPCGSTSETLKEFVGREFNDKTLIDiGLRVQHF-CRAGKIRLFVEKEGKKTKAGKILVSGI 217
                                   *************************999*******.***********************9988 PP

>> PC4  Transcriptional Coactivator p15 (PC4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.37   2.2e+03      39      51 ..      39      51 ..      39      52 .. 0.91
   2 ?   -0.5   0.0      0.17     1e+03       2      17 ..      74      89 ..      73      91 .. 0.87
   3 ?    6.0   0.0    0.0015       9.2       8      22 ..     169     183 ..     163     185 .. 0.81
   4 ?    2.5   0.0      0.02   1.2e+02      22      36 ..     196     211 ..     195     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.37
                                  EEEEHHHHHHHHH CS
                           PC4 39 IsLtleqweaLkk 51
                                  I++++ ++e+Lk+
  gi|15669028|ref|NP_247832.1| 39 ITISENTIEKLKD 51
                                  899********97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.17
                                  CTTCCEEEEEEEETTE CS
                           PC4  2 elskkrrvtvrefkGk 17
                                  el +k +v v  +kG+
  gi|15669028|ref|NP_247832.1| 74 ELNNKAFVLVGAWKGE 89
                                  7899999*******96 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0015
                                   EEEEEEETTEEEEEE CS
                           PC4   8 rvtvrefkGktlvdI 22 
                                   ++  ref++ktl+dI
  gi|15669028|ref|NP_247832.1| 169 EFVGREFNDKTLIDI 183
                                   44559*********9 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.02
                                   EEEEEEC.TTEEEEEE CS
                           PC4  22 IReyyek.dgelkPgk 36 
                                   IR ++ek  +++k gk
  gi|15669028|ref|NP_247832.1| 196 IRLFVEKeGKKTKAGK 211
                                   9******557788776 PP

>> Phage_int_SAM_5  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.8    0.0065        39      30      84 ..      31      80 ..      15      82 .. 0.86
   2 ?    8.6   0.9    0.0004       2.4      40      63 ..     104     126 ..      89     152 .. 0.74
   3 ?   -3.7   0.0       2.7   1.6e+04      28      36 ..     163     171 ..     160     182 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0065
                                  HHTTTS-..S---TTT--HHHHHHHHHHHHHTS---HHHHHHHHHHHHHHHHHHH CS
               Phage_int_SAM_5 30 khlkkFlkkkditfeeidkefleeFedYLkkkkglsentiskyfkklkavlnkAi 84
                                  k+  +F    +it++e + e l++++ ++   ++l++   +  ++k+k + nkA+
  gi|15669028|ref|NP_247832.1| 31 KYYGDFD---EITISENTIEKLKDYDLFI--TYTLNPDLTYELVRKIKELNNKAF 80
                                  4444555...8999999************..899999999999999999999997 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0004
                                   ---TTT--HHHHHHHHHHHHHTS- CS
               Phage_int_SAM_5  40 ditfeeidkefleeFedYLkkkkg 63 
                                      + +id++ l++++dYL ++++
  gi|15669028|ref|NP_247832.1| 104 PYLMCDIDEDELKDYKDYL-DNYP 126
                                   36699**************.4443 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.7
                                   HHHHTTTS- CS
               Phage_int_SAM_5  28 tlkhlkkFl 36 
                                   t + lk+F 
  gi|15669028|ref|NP_247832.1| 163 TSETLKEFV 171
                                   566778887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1615.91
//
Query:       gi|15669029|ref|NP_247833.1|  [L=350]
Description: DNA primase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-13   50.7   0.8    4.8e-13   49.5   0.8    1.6  1  DNA_primase_S  DNA primase small subunit
  ------ inclusion threshold ------
      0.022   15.0   0.7      0.022   15.0   0.7    2.1  2  D5_N           D5 N terminal like
       0.06   13.3   0.8       0.06   13.3   0.8    2.3  2  DUF4428        Domain of unknown function (DUF4428)


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.8     8e-17   4.8e-13       1     175 [.      96     279 ..      96     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 8e-17
                                   EEEEEETTT-...TT--HHHHHHH.HHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE..--TTEE...ES-HHHH CS
                 DNA_primase_S   1 FDiDmddydd..cseatvcekcwk.fvsvavkvldellredfgfk..dilwvfsgrrGfHcwv..sdkdar...pltdeer 71 
                                   FDiD+ ++ +   +++ +c+ c++   ++a+ +++e+l+ dfg +  d+++vfsg+rG+H+++  +d+++r   ++ ++e 
  gi|15669029|ref|NP_247833.1|  96 FDIDVHKTKKckHEDDWICKHCLEeAKNQAIYLIEEFLIPDFGLNeeDLKIVFSGNRGYHIYIkpRDEKIRdiiESYSKED 176
                                   9*********66566779**999626789********************************99555888884443333343 PP

                                   HHHHHH..........................................HCHHHHCT--------................. CS
                 DNA_primase_S  72 aaivnylnlyrplhpflsrs..mlkivkpvveeiileeqdpf......eikkllrllpdkslrekkkw...........ea 133
                                   + +           +++ ++   l++v              +      +ik+ ++++++k+l ++k+w           ++
  gi|15669029|ref|NP_247833.1| 177 RRFLM---------DYILGKnlNLNSVGS-----------GWrrrlikAIKERDKRISTKKLENEKNWkkvienlksknKI 237
                                   43333.........333333133333322...........334555669****************************9654 PP

                                   ............-----------------....--------- CS
                 DNA_primase_S 134 kedivlvllyprldeqvtkgikhllkapfcihgktgnvcvpl 175
                                    + i +++  ++lde+v  + ++ll+   ++hg tg+ + pl
  gi|15669029|ref|NP_247833.1| 238 YNIIEETKNKIELDEKVMDDDIRLLRVINSLHGYTGFIVKPL 279
                                   5555566779***************************99997 PP

>> D5_N  D5 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.6      0.48   2.9e+03     117     135 ..      51      70 ..       5     120 .. 0.62
   2 ?   15.0   0.7   3.6e-06     0.022      38     106 ..     200     266 ..     151     268 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.48
                          D5_N 117 rd.hepedyltkitpvdydp 135
                                    +  e +d++ k++p+++ +
  gi|15669029|ref|NP_247833.1|  51 KNeREYKDWVLKNAPMHFYK 70 
                                   33244467777777777644 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.6e-06
                          D5_N  38 reladkvaeaiaeeaeeaksalkalkkfakssrskkkvdnvlreaaelprldleideldadplllafaN 106
                                   r+l+++++e+ ++  ++  +  k++kk+ +   sk+k+ n+++e ++   ++l+ + +d+d +ll + N
  gi|15669029|ref|NP_247833.1| 200 RRLIKAIKERDKRISTKKLENEKNWKKVIENLKSKNKIYNIIEETKNK--IELDEKVMDDDIRLLRVIN 266
                                   33333333333333355578889***********************99..***********99998866 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.8     1e-05      0.06      12      31 ..     103     122 ..      99     132 .. 0.83
   2 ?   -1.3   0.3      0.36   2.2e+03       4       9 ..     318     323 ..     317     331 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                       DUF4428  12 lkrlkleDgyvCkdClkKls 31 
                                    k+ k eD+++Ck Cl++++
  gi|15669029|ref|NP_247833.1| 103 TKKCKHEDDWICKHCLEEAK 122
                                   466889**********9984 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.36
                       DUF4428   4 iCgkKi 9  
                                   iCgkK 
  gi|15669029|ref|NP_247833.1| 318 ICGKKY 323
                                   899995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1382  (0.0770818); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2257.58
//
Query:       gi|15669030|ref|NP_247834.1|  [L=330]
Description: hypothetical protein MJ_0840 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-48  166.1   0.0    7.3e-48  163.3   0.0    1.9  2  Hydantoinase_A  Hydantoinase/oxoprolinase
     0.0091   14.6   0.0       0.41    9.2   0.0    2.1  2  MutL            MutL protein
  ------ inclusion threshold ------
      0.023   14.4   3.9        1.8    8.3   0.1    3.7  4  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
       0.16   11.2   2.0         14    4.8   0.3    2.8  3  StbA            StbA protein
       0.41   11.1   1.3        6.2    7.3   0.0    2.7  2  FtsA            Cell division protein FtsA


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.074   2.6e+02      81     104 ..       5      28 ..       2      32 .. 0.84
   2 !  163.3   0.0     2e-51   7.3e-48       2     290 ..      54     326 ..      53     327 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.074
                Hydantoinase_A  81 vItfDmGGTstDvslikdgevevs 104
                                   ++++D+GG  t++  i+  ++++ 
  gi|15669030|ref|NP_247834.1|   5 ILGIDIGGANTKITEIEGDNYKIH 28 
                                   6789************98888765 PP

  == domain 2  score: 163.3 bits;  conditional E-value: 2e-51
                Hydantoinase_A   2 tetavvnAylspilreylesvekslekrgak..arlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekk 80 
                                   ++++v++A+l+++++++ e+ve++++k++++  ++++v++ +G++++ +ea+k+++++ +S+++a++ ++a+   ++++  
  gi|15669030|ref|NP_247834.1|  54 YVALVMTAELADCYKTKKEGVEDIIDKVEKAfnCPVYVFDVNGNFLTSEEAKKNYLDVSASNWNATAKFVAE--FIKDS-- 130
                                   6789**********************9998777***************************************..66666.. PP

                Hydantoinase_A  81 vItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsil.vvdeggklrvgpesagadpgpacyrkGg 160
                                   +I++DmG+T+tD+++ikd+ev         + k++l++l+++++++ G++++ v++ ++k++++++ ++ ++++       
  gi|15669030|ref|NP_247834.1| 131 CILVDMGSTTTDIIPIKDKEV--------LAEKTDLDRLMNNQLVYVGTLRTpVSFLANKIEFRGKLTNLSSEY------- 196
                                   *****************9999........799******************************************....... PP

                Hydantoinase_A 161 teltvTDanlvLGrlqpedfls.gpdgdqkldvelarraf.eelakelnlk...veevAegilsvavenmanavrklsver 236
                                    +++++D++l+L+++++ed+++ +pdg++k+ +++++r +   +a++ ++k   + ++A+++++++ e + ++v+++    
  gi|15669030|ref|NP_247834.1| 197 -FAITADISLILNKITEEDYTCdTPDGAGKDFESCLTRLVrVLCADREMVKddeLIDFANKLYNKLLELIRENVDTI---- 272
                                   .9**************************************999*****9999999**********************.... PP

                Hydantoinase_A 237 gldpkeltlvvfGGaGaqhaaalaeelgvkkvivppya.gvlsalGmalAdvree 290
                                    +++ +l+ vv++G G+ + + + +e+++ ++ +++++  +l+++++a+A++ ++
  gi|15669030|ref|NP_247834.1| 273 -AKRYNLNDVVITGLGEEILKDALDEYNIISIKETYGKdVSLATPSFAVAKLLQK 326
                                   .99999999*******99999999**************8889********99876 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.3   0.0    0.0072        26     249     268 ..       5      23 ..       3      42 .. 0.75
   2 !    9.2   0.0   0.00011      0.41     236     274 ..     121     156 ..     100     168 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0072
                          MutL 249 llvvDvGGaTTdvhsvaegs 268
                                   +l++D+GGa T +  + eg+
  gi|15669030|ref|NP_247834.1|   5 ILGIDIGGANTKITEI-EGD 23 
                                   5889999999999888.443 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00011
                          MutL 236 ellaeeeekglgdllvvDvGGaTTdvhsvaegspekekv 274
                                   +++ae  +   + +++vD+G++TTd++ + +++   ek+
  gi|15669030|ref|NP_247834.1| 121 KFVAEFIK---DSCILVDMGSTTTDIIPIKDKEVLAEKT 156
                                   44555222...3789***********9996665555554 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.015        54       2      24 ..       6      28 ..       5      47 .. 0.82
   2 ?   -0.3   0.0      0.21   7.7e+02      77     117 ..      53      92 ..      44     107 .. 0.75
   3 ?    8.3   0.1    0.0005       1.8       2      22 ..     132     151 ..     131     172 .. 0.84
   4 ?    0.4   0.0      0.13   4.7e+02     105     144 ..     256     297 ..     241     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.015
                    Hydant_A_N  2 igIDvGGTfTDavaldekeeeva 24
                                  +gID+GG +T +  +++++ +++
  gi|15669030|ref|NP_247834.1|  6 LGIDIGGANTKITEIEGDNYKIH 28
                                  69********9999998875555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.21
                    Hydant_A_N  77 ervaLittkgfrdlleigrqnrpdlfelrikkplvlyeevv 117
                                   + vaL++t    d ++++++  +d+ + +++k  ++   v+
  gi|15669030|ref|NP_247834.1|  53 DYVALVMTAELADCYKTKKEGVEDIID-KVEKAFNCPVYVF 92 
                                   668999999999999999999888855.5556655555555 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0005
                    Hydant_A_N   2 igIDvGGTfTDavaldekeee 22 
                                   i +D+G+T TD++ +++k e+
  gi|15669030|ref|NP_247834.1| 132 ILVDMGSTTTDIIPIKDK-EV 151
                                   789**********99976.43 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.13
                    Hydant_A_N 105 rik..kplvlyeevvevderveadgevlkpldeeevrealka 144
                                   +++    ++++e+v ++ +r++++  v++ l ee ++ al +
  gi|15669030|ref|NP_247834.1| 256 KLYnkLLELIRENVDTIAKRYNLNDVVITGLGEEILKDALDE 297
                                   3332245788999999*******9999999999999998876 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.32   1.2e+03     166     190 ..       6      30 ..       4      38 .. 0.82
   2 ?    4.8   0.3    0.0038        14     159     182 ..     123     148 ..      49     158 .. 0.65
   3 ?    4.6   0.0    0.0046        16     242     299 ..     248     305 ..     234     324 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.32
                          StbA 166 LiiDlGGttLDvakvrgklegiskv 190
                                   L iD+GG+   +++++g   +i ++
  gi|15669030|ref|NP_247834.1|   6 LGIDIGGANTKITEIEGDNYKIHHI 30 
                                   5699999999999999987777665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0038
                          StbA 159 ldel..eslLiiDlGGttLDvakvrg 182
                                   ++e+  +s +++D+G tt D+  ++ 
  gi|15669030|ref|NP_247834.1| 123 VAEFikDSCILVDMGSTTTDIIPIKD 148
                                   555434899***********988875 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0046
                          StbA 242 dkresvlevinekvkkLkerviravsefsgythvmvvGGGaeliaeaikkatevsdek 299
                                   d+     + + +k  +L ++ ++++++  + + v+++G G e++++a+ ++  +s ++
  gi|15669030|ref|NP_247834.1| 248 DELIDFANKLYNKLLELIRENVDTIAKRYNLNDVVITGLGEEILKDALDEYNIISIKE 305
                                   333333334444444445555566677777889**************99987665554 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.3     0.077   2.8e+02       2      18 ..       7      23 ..       6     107 .. 0.86
   2 ?    7.3   0.0    0.0017       6.2       1      19 [.     132     150 ..     132     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.077
                                  EEEE-SSSEEEEEEETT CS
                                  xxxxxxxxxxxxxxxxx RF
                          FtsA  2 lvDiGagktdvavaedg 18
                                  ++DiG+  t+++ +e++
  gi|15669030|ref|NP_247834.1|  7 GIDIGGANTKITEIEGD 23
                                  79*****9999877765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0017
                                   EEEEE-SSSEEEEEEETTE CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          FtsA   1 alvDiGagktdvavaedga 19 
                                   +lvD+G+++td++ ++d++
  gi|15669030|ref|NP_247834.1| 132 ILVDMGSTTTDIIPIKDKE 150
                                   58**********9888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      698  (0.0389313); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2060.88
//
Query:       gi|15669031|ref|NP_247835.1|  [L=415]
Description: hypothetical protein MJ_0841 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.8e-17   62.2  16.2    2.1e-13   51.0  12.8    3.8  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.017   14.4   0.1       0.18   11.1   0.0    2.5  2  DUF512       Protein of unknown function (DUF512)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0  12.8   2.3e-17   2.1e-13       6     165 ..      17     198 ..      13     200 .. 0.90
   2 !    5.8   0.1    0.0018        16      30      81 ..     236     344 ..     230     380 .. 0.48

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.3e-17
                                   EESS--TTTSCCTT........................HHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGST CS
                                   xxxxxxxxxxxxxx........................xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   6 gCnlrCsfCarpet........................vrregrgrslsveeileevkelk.aekgvkevilgggepllyp 61 
                                    Cn+ C+fC++++                         + re  g ++++   l e+++   +++  k+ +  gg+++ yp
  gi|15669031|ref|NP_247835.1|  17 NCNGFCKFCYFRKVnknnpqpfgcrycqftvgcdycmySVREINGDFIPLPFALMELQSSLlFKRYSKVNLTAGGDVSCYP 97 
                                   59999999999988999999999999999999******999****************9999777769999999******** PP

                                   THHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  62 dfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagi 142
                                    ++el +++  +   +i++ +++  + ++ e+++ l+++gvd v++++ +++++  +k  +  ++ e  l++l+++ e+ +
  gi|15669031|ref|NP_247835.1|  98 QLEELCKAINNIG-LKIHLGYTSGKGFDNVEIAKNLVDYGVDEVTFSVFSTNPK-LRKEWMNDKNAETALKCLRYFCEN-C 175
                                   ************5.999999999999988*************************.66655578****************.* PP

                                   ETEEEEEEEBTTTSH.HHHHHHHH CS
                                   xxxxxxxxxxxxxxx.xxxxxxxx RF
                   Radical_SAM 143 krvvdrivglpGend.eeleelle 165
                                   + v   i+++pG+nd eel+++++
  gi|15669031|ref|NP_247835.1| 176 E-VHCAIIVIPGVNDgEELKKTVS 198
                                   *.9************888888776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0018
                                   HHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....................TTHHHHHHHHHHTC............... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxx............... RF
                   Radical_SAM  30 sveeileevkelkaekgvkevilgggeplly.....................pdfvellerlakla............... 74 
                                   svee +++v+e++ +  ++++ ++g  pl +                     +            +               
  gi|15669031|ref|NP_247835.1| 236 SVEEFKNIVDEIH-NEFGDYIRVTGT-PLHDpvagtpfalakeenshilerlK------------Dkingeatiitgnvay 302
                                   899*********5.555888888855.55553333333334422222222220............2333333333333333 PP

                                   ...................................CCTEEEE CS
                                   ...................................xxxxxxx RF
                   Radical_SAM  75 ...................................vpgirit 81 
                                                                      ++  +++
  gi|15669031|ref|NP_247835.1| 303 pflkkifdetsvnvvkvnkdiadlitakdlekldlKDVKETV 344
                                   333333333333333333333333333333344443344444 PP

>> DUF512  Protein of unknown function (DUF512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.15   1.3e+03     120     143 ..     237     259 ..     227     260 .. 0.75
   2 ?   11.1   0.0     2e-05      0.18      89     171 ..     281     352 ..     271     362 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.15
                        DUF512 120 vkglkievvaikndfFGetitVaG 143
                                   v+++k  v +i+n+ FG+ i V+G
  gi|15669031|ref|NP_247835.1| 237 VEEFKNIVDEIHNE-FGDYIRVTG 259
                                   55666667788888.699999999 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 2e-05
                        DUF512  89 aleel....krkvtivtGklaaellkelaekleekvkglkievvaikndfFGetitVaGLltgqDlieqlkekelgeelll 165
                                    le+l    + ++ti+tG++a+++lk++++++       +++vv+++        ++a L+t++Dl e+l+ k+++e++++
  gi|15669031|ref|NP_247835.1| 281 ILERLkdkiNGEATIITGNVAYPFLKKIFDET-------SVNVVKVNK-------DIADLITAKDL-EKLDLKDVKETVFI 346
                                   444445556889***************99998.......567888865.......47889999997.55777778888888 PP

                        DUF512 166 psvmlr 171
                                   p   + 
  gi|15669031|ref|NP_247835.1| 347 PPKAFV 352
                                   877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2650.69
//
Query:       gi|15669032|ref|NP_247836.1|  [L=447]
Description: methyl coenzyme M reductase I subunit McrB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     3e-143  475.8   5.0   4.2e-143  475.3   5.0    1.2  1  MCR_beta    Methyl-coenzyme M reductase beta subunit, C-termi
    5.5e-83  277.1   1.4    5.5e-83  277.1   1.4    1.7  2  MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-termi


Domain annotation for each model (and alignments):
>> MCR_beta  Methyl-coenzyme M reductase beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.3   5.0  4.7e-147  4.2e-143       1     249 []     192     440 ..     192     440 .. 1.00

  Alignments for each domain:
  == domain 1  score: 475.3 bits;  conditional E-value: 4.7e-147
                      MCR_beta   1 GyalrnikanhvvaitkknalnaaalssileqtavfemGdavGaferahllglayqGlnannlvydlvkengkegtvGtvv 81 
                                   Gyalrni+anh+va+tkkn++na+a+++i+eqta+femGdavG fer hllglayqGlna+nlv+dlvk+ngk+gtvGtvv
  gi|15669032|ref|NP_247836.1| 192 GYALRNIMANHFVACTKKNVMNAVAFAAIMEQTAMFEMGDAVGLFERLHLLGLAYQGLNADNLVIDLVKANGKNGTVGTVV 272
                                   9******************************************************************************** PP

                      MCR_beta  82 eslveraiedkvikvekklpsgyklyetkdvalwnayaaaGllaavivnvgaaraaqavsstllyyndlleketglpGvdf 162
                                   +s+vera+ed+vik++k+lpsg+kly++ dva+wnayaaaGl+aa+ivn+gaaraaq+++st+lyynd+le+etglpGvdf
  gi|15669032|ref|NP_247836.1| 273 ASVVERALEDGVIKEDKTLPSGFKLYKPVDVAKWNAYAAAGLVAAAIVNCGAARAAQNIASTILYYNDILEYETGLPGVDF 353
                                   ********************************************************************************* PP

                      MCR_beta 163 GrveGtavGfsffshsiyGGGGpGifnGnhvvtrhskGfaipcvaaavaldaGtqlfspeatsglvgevfgeidefreplk 243
                                   Gr+eGtavGfsffshsiyGGGGpGifnGnh+vtrhskGfaip+vaaa++ldaGtq+fspe+ts+lvg+vf++idefreplk
  gi|15669032|ref|NP_247836.1| 354 GRAEGTAVGFSFFSHSIYGGGGPGIFNGNHIVTRHSKGFAIPPVAAAMCLDAGTQMFSPERTSALVGTVFSAIDEFREPLK 434
                                   ********************************************************************************* PP

                      MCR_beta 244 avaeaa 249
                                   +v+++a
  gi|15669032|ref|NP_247836.1| 435 YVIKGA 440
                                   **9986 PP

>> MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.1   1.4   6.1e-87   5.5e-83       1     182 []       9     190 ..       9     190 .. 1.00
   2 ?   -3.4   0.0      0.69   6.2e+03      53      78 ..     264     289 ..     257     296 .. 0.75

  Alignments for each domain:
  == domain 1  score: 277.1 bits;  conditional E-value: 6.1e-87
                    MCR_beta_N   1 DkidlyddkGkllesdvpleaisPlknpaikkivkdvkrtvavnlagiekalktgkvggkaskilGreldldivenadaia 81 
                                   D+i+lyd+kGkl+e++vpleaisPl+np+i+k+vkdvkrtvavnlagie+al+tg+vggk+++i+Greldl+ivena++ia
  gi|15669032|ref|NP_247836.1|   9 DTINLYDEKGKLVEENVPLEAISPLHNPTIQKLVKDVKRTVAVNLAGIENALRTGQVGGKGCMIKGRELDLPIVENAETIA 89 
                                   89******************************************************************************* PP

                    MCR_beta_N  82 ekikelvqveedddtkvkllngGkqllvqvPskRleaaaeysvallataaavveaiidefdvdmfdasvvkaavlGryPqt 162
                                   e ++++v+v+edddt++kl+n+Gkq+ vq+PskRl++aaeysv++l+ta+a++eaii +fdvd+fda++v+aavlG yP++
  gi|15669032|ref|NP_247836.1|  90 EYVEKVVRVSEDDDTSIKLINDGKQMAVQIPSKRLDVAAEYSVSVLVTAQALKEAIIRTFDVDIFDAPMVHAAVLGGYPHE 170
                                   ********************************************************************************* PP

                    MCR_beta_N 163 vdlaggnvasilsipqkneG 182
                                   v ++g+n+a++l+ p ++eG
  gi|15669032|ref|NP_247836.1| 171 VTMKGSNIAALLGSPLSLEG 190
                                   *****************998 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.69
                    MCR_beta_N  53 ktgkvggkaskilGreldldivenad 78 
                                   k+g+vg+   ++  r l+  ++++ +
  gi|15669032|ref|NP_247836.1| 264 KNGTVGTVVASVVERALEDGVIKEDK 289
                                   67888888888888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2952.23
//
Query:       gi|15669033|ref|NP_247837.1|  [L=164]
Description: methyl coenzyme M reductase I protein McrD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-59  199.1   0.0    3.1e-59  198.9   0.0    1.0  1  MCR_D     Methyl-coenzyme M reductase operon protein D


Domain annotation for each model (and alignments):
>> MCR_D  Methyl-coenzyme M reductase operon protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.9   0.0   1.7e-63   3.1e-59       1     142 [.       5     152 ..       5     153 .. 0.99

  Alignments for each domain:
  == domain 1  score: 198.9 bits;  conditional E-value: 1.7e-63
                         MCR_D   1 dveifpeRlLkpetteklLnelvelegikrvvihGprLPkkvpygpakGkevehkerkvievkgeeveLkvkvGrillele 81 
                                   +veifp+R+Lk++ttek+Ln++++l++++rvvihG+ LPk ++ygpa+G +v+h+erk+i+vkg  veL+v++Gr++++l+
  gi|15669033|ref|NP_247837.1|   5 EVEIFPHRYLKASTTEKFLNKIYDLKTVERVVIHGQPLPKVITYGPARGLPVNHTERKIIHVKGVPVELTVMAGRFWITLS 85 
                                   69******************************************************************************* PP

                         MCR_D  82 deeviekieeiceevlpfsyeikegkfirkkktvsDyakyGee......eadkrllGlvDpksklee 142
                                   d++ ++k++eic+e++pf+y++++gkf+++++tv+Dy+kyGe+      e+d+rl+G+vDp+s++++
  gi|15669033|ref|NP_247837.1|  86 DDSELDKLDEICKEMFPFGYNLRVGKFLKDRPTVTDYIKYGEDgvflinEMDRRLIGMVDPRSRMAN 152
                                   ****************************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1063.54
//
Query:       gi|15669034|ref|NP_247838.1|  [L=200]
Description: methyl coenzyme M reductase I protein McrC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-09   36.9   0.7    3.9e-09   36.0   0.7    1.4  1  MCR_C     Methyl-coenzyme M reductase operon protein C


Domain annotation for each model (and alignments):
>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.7   2.2e-13   3.9e-09      71     172 ..      37     147 ..      27     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.2e-13
                         MCR_C  71 eiavvsptLarhhlPhsaCDvaeylrraGaktnmiGlarGvg..........kriaqikeeekrlinehDlavfvlGnfkd 141
                                   ++ vv+++  r+h+  ++C+++  +r+aG +t ++ l  G g           ++  ik ee + in h l+v  +Gn  +
  gi|15669034|ref|NP_247838.1|  37 DVVVVAMSPGRRHITKPVCEITYGIREAGIQTSVLVLNAGSGiphdaprgalGSTFGIKPEEAEQINRHKLCVVHFGNVIS 117
                                   789********************************9988877333322111134567999********************* PP

                         MCR_C 142 CikkkkeklfedievPvvvtggPeelkleev 172
                                    i  k   l++ +e+P ++++    +++e++
  gi|15669034|ref|NP_247838.1| 118 HIVYKAGLLLKYVEIPTIIVCQA-PVDMEDL 147
                                   ****************8887754.4666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1372.03
//
Query:       gi|15669035|ref|NP_247839.1|  [L=260]
Description: methyl coenzyme M reductase I subunit McrG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   6.6e-132  438.2   0.4   7.5e-132  438.0   0.4    1.0  1  MCR_gamma  Methyl-coenzyme M reductase gamma subunit


Domain annotation for each model (and alignments):
>> MCR_gamma  Methyl-coenzyme M reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.0   0.4  4.2e-136  7.5e-132       1     245 [.       5     250 ..       5     251 .. 0.99

  Alignments for each domain:
  == domain 1  score: 438.0 bits;  conditional E-value: 4.2e-136
                     MCR_gamma   1 aqyyPGeskvaenrrkfmdpeaeleklreisdedvvkilghraPGeeyksvhPPleemdepedpirelvePieGakaGdrv 81 
                                   +q+yPG++k+a+nrr +m+p+++leklr+i+d+dvvki+ghr+PGe+yk+vhPPleemd ped +r+lveP++Gak+G+r+
  gi|15669035|ref|NP_247839.1|   5 PQFYPGQTKIAQNRRDHMNPDVQLEKLRDIPDDDVVKIMGHRQPGEDYKTVHPPLEEMDLPEDYVRDLVEPLNGAKEGHRI 85 
                                   7******************************************************************************** PP

                     MCR_gamma  82 ryiqfadsmyfaPaqPyqrarlellryrgvdtGtlsGrqiievrerdlekiske.lletelfdpartgirGatvhGhslrl 161
                                   ryiqf+dsmyfaPaqPy+rar++++r+rgvdtGtlsGrq+ie+re dle +sk+ l++t +fdpar+girGatvhGhslrl
  gi|15669035|ref|NP_247839.1|  86 RYIQFTDSMYFAPAQPYDRARTYMWRFRGVDTGTLSGRQVIEMRESDLEALSKNfLIDTAFFDPARIGIRGATVHGHSLRL 166
                                   *****************************************************8468************************ PP

                     MCR_gamma 162 denGlmfdalqrlvldeedgevkyvkdqvgvpldkkvdvGkpldedelkkkttiyrldgvalrddkevvevvkrihelrtk 242
                                   denGlmfdalqr+v+de++g+v yvkdqvg+pld++vdvG+pl e++lk++ttiyr+dgv +r+d+e++ vvkrih++rt 
  gi|15669035|ref|NP_247839.1| 167 DENGLMFDALQRYVYDEKTGHVLYVKDQVGRPLDEPVDVGEPLPEEKLKEITTIYRIDGVPMREDEELLTVVKRIHRARTL 247
                                   ********************************************************************************* PP

                     MCR_gamma 243 lgf 245
                                   +gf
  gi|15669035|ref|NP_247839.1| 248 GGF 250
                                   *99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1941.79
//
Query:       gi|15669036|ref|NP_247840.1|  [L=553]
Description: methyl coenzyme M reductase I subunit McrA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.3e-153  510.0   0.0   1.7e-153  509.6   0.0    1.1  1  MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-ter
    1.4e-70  235.6   4.2    3.1e-70  234.5   4.2    1.6  1  MCR_alpha    Methyl-coenzyme M reductase alpha subunit, C-ter


Domain annotation for each model (and alignments):
>> MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  509.6   0.0  1.9e-157  1.7e-153       2     270 .]       6     271 ..       5     271 .. 0.99

  Alignments for each domain:
  == domain 1  score: 509.6 bits;  conditional E-value: 1.9e-157
                                   X--HHHHHHH-S.S-TT--B---S-S-GGGG-HHHHHHHHHHHHHHHHH.-S----TTS...S--S-SS---EEEBTTS-- CS
                   MCR_alpha_N   2 klflkalkkkfkkedpeekktkfykfeGlkqserkrefveaakkiakkr.gislynpdilhlGvplGqrklmpykvsgtdv 81 
                                   +lflkalk+kf+ edp+ek+tkfy f+G++qs+rkrefveaa+k+ +kr gi++ynpdi   GvplGqrklmpykvs+td+
  gi|15669036|ref|NP_247840.1|   6 RLFLKALKEKFE-EDPREKYTKFYVFGGWRQSARKREFVEAAQKLIEKRgGIPFYNPDI---GVPLGQRKLMPYKVSNTDA 82 
                                   79**********.9********************************99977******99...******************* PP

                                   EEEGGGSSGGG-HHHHHHHHHHHTEEEEE-HHHHHHHHHTT-----HHHHHHHHHHHHHHTTT--SS-TT-----TTT-TT CS
                   MCR_alpha_N  82 lvegddlhfvnnaalqqlwddirrtvivgldtahevlekrlGkevtPetineylevlnhalPGgavvqehmvethPalved 162
                                   +vegddlhf+nnaa+qq+wddirrtvivg+dtah+vlekrlG+evtPetiney+e++nhalPGgavvqehmve+hPalv+d
  gi|15669036|ref|NP_247840.1|  83 IVEGDDLHFMNNAAMQQFWDDIRRTVIVGMDTAHAVLEKRLGVEVTPETINEYMETINHALPGGAVVQEHMVEVHPALVWD 163
                                   ********************************************************************************* PP

                                   -EEEEEES-HHHHTTS-GGGB--HHHHS-HHHHHHHHHHH-S-EEEEEE--HHHHHHS-HHHHHHHHHHHHHHHHHHHHT- CS
                   MCR_alpha_N 163 cyvkvftGddeladeidkqflidinkefpeeqaeqlkkaiGkklyqvvriPtivsrtcdGgttsrwsamqigmsfisaykl 243
                                   cy+k+ftGddeladeidk+flidink+fpeeqaeq+kkaiGk++yqv+r+Pt+v+r+cdGgt++rwsamqigmsfi+aykl
  gi|15669036|ref|NP_247840.1| 164 CYAKIFTGDDELADEIDKRFLIDINKLFPEEQAEQIKKAIGKRTYQVSRVPTLVGRVCDGGTIARWSAMQIGMSFITAYKL 244
                                   ********************************************************************************* PP

                                   -SS-TTHHHHHHHHHTTSEEES---B- CS
                   MCR_alpha_N 244 caGeaavadlayaakhaeviemgellP 270
                                   caGeaa+ad++yaakha+vi+m+++lP
  gi|15669036|ref|NP_247840.1| 245 CAGEAAIADFSYAAKHADVIQMASFLP 271
                                   **************************9 PP

>> MCR_alpha  Methyl-coenzyme M reductase alpha subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.5   4.2   3.5e-74   3.1e-70       1     127 []     318     444 ..     318     444 .. 1.00

  Alignments for each domain:
  == domain 1  score: 234.5 bits;  conditional E-value: 3.5e-74
                     MCR_alpha   1 dqiwlGsymsGGvGftqyataaytdnilddfvyygvdyvkdkygglakvkatlevvkdiatevtlyaleqyekyptlledh 81 
                                   dqiwlG+ymsGGvGftqyata+ytd+ilddf+yyg+dy+++kygg+++vk+t++vv+diatevtly+leqy+++p+lledh
  gi|15669036|ref|NP_247840.1| 318 DQIWLGGYMSGGVGFTQYATATYTDDILDDFSYYGYDYITKKYGGCNSVKPTMDVVEDIATEVTLYGLEQYDTFPALLEDH 398
                                   9******************************************************************************** PP

                     MCR_alpha  82 fGGsqraavlaaaagistalatgnsnaGlngwylsmllhkeahsrl 127
                                   fGGsqra+v+aaaagi+talatgnsnaG+ngwyls++lhke hsrl
  gi|15669036|ref|NP_247840.1| 399 FGGSQRAGVTAAAAGITTALATGNSNAGVNGWYLSQILHKEYHSRL 444
                                   *********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3740.19
//
Query:       gi|15669037|ref|NP_247841.1|  [L=303]
Description: tetrahydromethanopterin S-methyltransferase subunit E [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.7e-131  435.3  13.4   8.8e-131  435.1  13.4    1.0  1  MtrE      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrE  Tetrahydromethanopterin S-methyltransferase, subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.1  13.4  4.9e-135  8.8e-131       1     271 []       8     287 ..       8     287 .. 0.99

  Alignments for each domain:
  == domain 1  score: 435.1 bits;  conditional E-value: 4.9e-135
                          MtrE   1 lGvlalmgalatiagaaedlesdvgsqsnpnsqvqLapqmgylhrifnkaisGePvaygllaavagavalvllsalklnvv 81 
                                   lG+lal galat+ag+aedlesdvgsqsnpnsqvqLapqmg++hr+fnkaisGePv+ygl++avag+va++++ +++ln++
  gi|15669037|ref|NP_247841.1|   8 LGALALSGALATVAGCAEDLESDVGSQSNPNSQVQLAPQMGNIHRYFNKAISGEPVSYGLYVAVAGTVAYAIM-QMGLNPI 87 
                                   79***********************************************************************.99***** PP

                          MtrE  82 laivlgalvaalvhgvyavtaylGriasqak.fkqpvyldvlkshlgaivahafiavfaivvlsylmtlvlkhpfplplla 161
                                   la++lga vaa+vhg+ya++aylGri++q+k f+qpvy+dv++shlg+iv+h+fiavf++v ++yl++++l++pfplpl+a
  gi|15669037|ref|NP_247841.1|  88 LALILGAGVAAFVHGAYAISAYLGRIVGQSKnFGQPVYWDVVMSHLGPIVGHGFIAVFCMVLMAYLANTILGNPFPLPLIA 168
                                   *****************************988************************************************* PP

                          MtrE 162 liwGitvGaiGsstGdvhyGaereyqkkefGaGvpvaasGdivrkaeaGlrnsidnalfcakfggpltGlafglivflelW 242
                                   li+GitvGaiGsstGdvhyGaereyqk++fG+Gvpva++Gdi  kae+Glrn++d+++fc+++gg ltGl+fglivfl+ W
  gi|15669037|ref|NP_247841.1| 169 LIFGITVGAIGSSTGDVHYGAEREYQKYPFGGGVPVANHGDIDIKAEYGLRNGMDSSYFCSRLGGVLTGLCFGLIVFLDGW 249
                                   ********************************************************************************* PP

                          MtrE 243 rtivfekv.........tagwlavivgliivllliiln 271
                                   r ++++++         ta+++++++gliiv++l+i+n
  gi|15669037|ref|NP_247841.1| 250 RGVLGDILkggqggsviTASIISIVIGLIIVAILAIIN 287
                                   ******99999999999999***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1920.21
//
Query:       gi|15669038|ref|NP_247842.1|  [L=230]
Description: tetrahydromethanopterin S-methyltransferase subunit D [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-93  311.3  27.7    4.4e-93  311.0  27.7    1.1  1  MtrD      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrD  Tetrahydromethanopterin S-methyltransferase, subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.0  27.7   2.4e-97   4.4e-93       2     218 .]       7     218 ..       6     218 .. 0.98

  Alignments for each domain:
  == domain 1  score: 311.0 bits;  conditional E-value: 2.4e-97
                          MtrD   2 illliliviggvligvgvhfvPvGGapaamaqatGvgtGtaqlaaGagltGlltaaalaektd....slllillsGavgam 78 
                                   i+ li+++i+g++i+++vhf+PvGGapaama++tGvgtGt+qlaaGag+tGl++aa++a++ +     ++li++sGav++m
  gi|15669038|ref|NP_247842.1|   7 IVPLIEMTIAGAIINASVHFIPVGGAPAAMATSTGVGTGTTQLAAGAGFTGLMGAAVMASNVGlspiGMALIMISGAVSSM 87 
                                   789*********************************************************998888899************ PP

                          MtrD  79 lmlaitmlvgnliyvygvGvvaasakvekdpitgdkqekyvsqGteGhgiPtvsfvsGviGgllgGiGGalvyyallellk 159
                                   +ml++tml+g+liyv+gvGvv+a++k+e dpit+d q+ yv++Gt+Ghg+Ptv+fvsG+iG++lgGiGGal+y+al +l  
  gi|15669038|ref|NP_247842.1|  88 IMLGVTMLIGQLIYVFGVGVVPAADKCEIDPITKDPQKPYVTPGTTGHGVPTVCFVSGLIGAALGGIGGALAYIALRKLGL 168
                                   *****************************************************************************8877 PP

                          MtrD 160 aalklaaaaavalaailavglflvnavlasynigGtieGfhdpkfkrlpkavvaslvas 218
                                              ++a++lavg+f++navlasynigGtieGfhdpkfk++p++v+as+vas
  gi|15669038|ref|NP_247842.1| 169 ---------DPGVAGMLAVGFFFINAVLASYNIGGTIEGFHDPKFKKMPNGVIASTVAS 218
                                   .........79**********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1535.09
//
Query:       gi|15669039|ref|NP_247843.1|  [L=265]
Description: tetrahydromethanopterin S-methyltransferase subunit C [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     5e-101  337.3  22.1   5.7e-101  337.1  22.1    1.0  1  MtrC             Tetrahydromethanopterin S-methyltransferase,
  ------ inclusion threshold ------
       0.42   10.5   1.1        2.7    7.8   0.1    2.1  2  Myc_target_1     Myc target protein 1
        2.9    8.0  12.6          1    9.5   2.4    2.8  3  DUF2456          Protein of unknown function (DUF2456)
        3.6    7.7   4.5          8    6.6   0.3    2.9  2  DUF3042          Protein of unknown function (DUF3042)
        6.4    7.3  11.5        0.2   12.1   1.2    3.1  3  Phage_holin_3_1  Phage holin family (Lysis protein S)


Domain annotation for each model (and alignments):
>> MtrC  Tetrahydromethanopterin S-methyltransferase, subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.1  22.1  1.6e-104  5.7e-101       1     268 []       1     264 [.       1     264 [. 0.98

  Alignments for each domain:
  == domain 1  score: 337.1 bits;  conditional E-value: 1.6e-104
                          MtrC   1 msaggggkeaeeaipekkllalgivggligiylasvlepa.lgsllaalgaicaivwGadavrrvasYglGTGVPSigmla 80 
                                   ms+gggg++ae  +pe++++a+gi ++l+g+yla++l+p  lg+l+++l+a +a+v+Ga++vr+va+YglGTGVPSigm++
  gi|15669039|ref|NP_247843.1|   1 MSHGGGGHAAE-LYPEEQIFAVGIALSLVGCYLANFLSPYgLGMLIGGLLASAACVAGANTVRKVAAYGLGTGVPSIGMVS 80 
                                   9******9998.*************************775489************************************** PP

                          MtrC  81 lgmGivaalaglavgsalkl..lagpiialvvaliiglvvgvlakkvikmkipileksttelaaagalsiiglsvaiagsf 159
                                   lgmG++aa+ag+ ++++++l  l++pii+l+v+++ig++vg l+ ++++mkipi+++s+t l++aga++++g++va++gs+
  gi|15669039|ref|NP_247843.1|  81 LGMGTLAAVAGVLIPDYFNLpyLVAPIITLIVSAVIGYIVGRLTVNPVGMKIPIMVRSMTFLSIAGAMALLGFTVAYVGSL 161
                                   ******************9999*********************************************************** PP

                          MtrC 160 eikailskviatGliallfilaglailhPfNaclGPdEkqdRTLklalekgalaliivgivsletesaaalvviivgliiW 240
                                   e ++++++++++G++al+fi+ag+ailhPfNaclGP+E+++RTL+la+++g+++++++++v+l+      +v+iiv++i+W
  gi|15669039|ref|NP_247843.1| 162 EPQKYIDYALNNGMMALAFIAAGMAILHPFNACLGPNESHKRTLTLAVACGFITWFVFSVVKLD------IVSIIVSIILW 236
                                   ****************************************************************......9********** PP

                          MtrC 241 lisfkkfvklvkrdaakvkgtgllPkee 268
                                   +i+++kfvk++++da++v +++++Pk+e
  gi|15669039|ref|NP_247843.1| 237 AIVYVKFVKMSFKDACAVLHVPEIPKKE 264
                                   **************************97 PP

>> Myc_target_1  Myc target protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2     0.091   3.3e+02      22      38 ..     107     123 ..      97     126 .. 0.88
   2 ?    7.8   0.1   0.00076       2.7      26      56 ..     226     256 ..     219     265 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.091
                  Myc_target_1  22 ilaFcvSmvvGLllgal 38 
                                   i++  vS v+G ++g l
  gi|15669039|ref|NP_247843.1| 107 IITLIVSAVIGYIVGRL 123
                                   88999*********987 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00076
                  Myc_target_1  26 cvSmvvGLllgaliyvlltwlsrrrasarit 56 
                                    vS++v ++l a++yv ++ +s + a a + 
  gi|15669039|ref|NP_247843.1| 226 IVSIIVSIILWAIVYVKFVKMSFKDACAVLH 256
                                   59********************999988664 PP

>> DUF2456  Protein of unknown function (DUF2456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.3     0.012        44      47      86 ..      81     120 ..      61     133 .. 0.85
   2 ?   -1.5   0.0      0.77   2.8e+03      35      69 ..     141     175 ..     125     191 .. 0.67
   3 ?    9.5   2.4   0.00028         1      20      48 ..     211     239 ..     199     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.012
                       DUF2456  47 vtigilagigkklgsdyyfnntwapqviKlvygvvlglit 86 
                                   + +g la++   l  dy    + ++ +i l+ ++v+g+i+
  gi|15669039|ref|NP_247843.1|  81 LGMGTLAAVAGVLIPDYFNLPYLVAPIITLIVSAVIGYIV 120
                                   56899999966666699888999**************996 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.77
                       DUF2456  35 llsviiflvlWpvtigilagigkklgsdyyfnntw 69 
                                   +ls++  ++l   t++ +++++ + + dy +nn +
  gi|15669039|ref|NP_247843.1| 141 FLSIAGAMALLGFTVAYVGSLEPQKYIDYALNNGM 175
                                   45555556666666666666655545577777654 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00028
                       DUF2456  20 vnfiewlvskairglllsviiflvlWpvt 48 
                                   + fi+w+v+++++  ++s+i+ ++lW + 
  gi|15669039|ref|NP_247843.1| 211 CGFITWFVFSVVKLDIVSIIVSIILWAIV 239
                                   579***********************985 PP

>> DUF3042  Protein of unknown function (DUF3042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3    0.0022         8       4      28 ..      39      63 ..      37      65 .. 0.75
   2 ?    1.1   0.4      0.11     4e+02      13      23 ..      83      93 ..      77      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0022
                       DUF3042  4 FlkGflvGvlatiaavagavfvfKk 28
                                  ++ G+l+G l+  aa ++ + +++k
  gi|15669039|ref|NP_247843.1| 39 YGLGMLIGGLLASAACVAGANTVRK 63
                                  899****988777776666666666 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                       DUF3042 13 latiaavagav 23
                                  ++t+aavag++
  gi|15669039|ref|NP_247843.1| 83 MGTLAAVAGVL 93
                                  579******97 PP

>> Phage_holin_3_1  Phage holin family (Lysis protein S)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.1       0.3   1.1e+03      64      83 ..      96     119 ..      17     132 .. 0.76
   2 ?    0.4   0.6      0.25   8.9e+02      23      58 ..     141     179 ..     128     188 .. 0.61
   3 ?   12.1   1.2   5.6e-05       0.2      21      73 ..     180     234 ..     170     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.3
               Phage_holin_3_1  64 ellglp....aslavviggliGfl 83 
                                   ++++lp      ++ +++++iG++
  gi|15669039|ref|NP_247843.1|  96 DYFNLPylvaPIITLIVSAVIGYI 119
                                   555555333345556677777775 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.25
               Phage_holin_3_1  23 aavlAlviall..rviYdgk.swkkvlleallCgllala 58 
                                     ++A ++all   v+Y g+ + +k +  al  g++ala
  gi|15669039|ref|NP_247843.1| 141 FLSIAGAMALLgfTVAYVGSlEPQKYIDYALNNGMMALA 179
                                   445566666542256676665555555556666666655 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 5.6e-05
               Phage_holin_3_1  21 iiaavlAlviallrviYdgkswkkvlleallCgllalavrslle..llglpasla 73 
                                   +iaa +A++  +   +  ++s k++l  a+ Cg+++++v s+++  ++++  s++
  gi|15669039|ref|NP_247843.1| 180 FIAAGMAILHPFNACLGPNESHKRTLTLAVACGFITWFVFSVVKldIVSIIVSII 234
                                   455666666666666666779******************9986511445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1097  (0.0611858); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1683.30
//
Query:       gi|15669040|ref|NP_247844.1|  [L=103]
Description: tetrahydromethanopterin S-methyltransferase subunit B [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-30  105.9   0.0    1.3e-30  105.7   0.0    1.0  1  MtrB      Tetrahydromethanopterin S-methyltransferase subunit


Domain annotation for each model (and alignments):
>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.0   7.1e-35   1.3e-30       1      94 []       4      97 ..       4      97 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 7.1e-35
                          MtrB  1 lvkvlpelnlvldpetgvvaearedvvllsldpvleeidkLekiaddlvnsLdpetallesypgRektlviaGlltnlfyGfi 83
                                  +v + +++ lv+ +etgv+++  +d+++++++p++e+i+kLe+++d++++sLdp+ ++l+s+p+R+++++i+G+++++f+Gf+
  gi|15669040|ref|NP_247844.1|  4 YVFIDQNIPLVYTVETGVITKGFGDLLFVDVSPIEEQIKKLETLVDAYEHSLDPRYPPLNSFPNRDGVYAISGYFKSAFFGFW 86
                                  799******************************************************************************** PP

                          MtrB 84 vglviaallal 94
                                  +gl i+alla+
  gi|15669040|ref|NP_247844.1| 87 IGLGIMALLAI 97
                                  ********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 712.20
//
Query:       gi|15669041|ref|NP_247845.1|  [L=245]
Description: tetrahydromethanopterin S-methyltransferase subunit A [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-84  282.1   0.8    1.7e-84  281.7   0.8    1.1  1  MtrA      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrA  Tetrahydromethanopterin S-methyltransferase, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.7   0.8   9.5e-89   1.7e-84       1     170 [.       8     178 ..       8     183 .. 0.98

  Alignments for each domain:
  == domain 1  score: 281.7 bits;  conditional E-value: 9.5e-89
                                   -----TTSS-S--S-EE--TT-SEEEE-TT-SS-HHHHHHCT-SEEE----TTHHHHHHHHHHHT-TT--EEEEEE---TT CS
                          MtrA   1 kkepaegWPvvkGdyevGdaespvavvtlgshleeeavleaGaaiaGplktenlGiekvvanvisnpnirflivtGaevkG 81 
                                   k+epa gWP+v+G+y vG++es+v vvtlgsh  e+a+++aGaaiaGp++tenlGiekvvan+isnpnirf+i++G+ev+G
  gi|15669041|ref|NP_247845.1|   8 KREPAPGWPIVSGEYVVGNPESCVGVVTLGSHGLEQACIDAGAAIAGPCHTENLGIEKVVANYISNPNIRFMILCGSEVQG 88 
                                   89******************************************************************************* PP

                                   T-HHHHHHHHHHH-B-TTSBBTT--SSS-B-SSS-HHHHHHHHHH-.EEEEEET---HHHHHHHHHHHHHT-----SS--- CS
                          MtrA  82 hitGqalkalhenGvdkekkivgakGaiPfienlteeaverfqeqv.elvdlidtedvgaikakikelvakdpgafeeepl 161
                                   hitGq++kal+enG+ +++ i+gakGaiPf+en+++eaverf++q+ e+vdlid+ed+g+i+++ike+++kdpga++e+p+
  gi|15669041|ref|NP_247845.1|  89 HITGQCFKALWENGIGDDGGIIGAKGAIPFLENVNKEAVERFRRQIvEVVDLIDCEDIGKITQAIKECLSKDPGAIDEDPF 169
                                   *********************************************88********************************** PP

                                   ----XXXXX CS
                          MtrA 162 vievkeeee 170
                                   +ie++ +++
  gi|15669041|ref|NP_247845.1| 170 IIELEGGKG 178
                                   ****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1683.33
//
Query:       gi|15669042|ref|NP_247846.1|  [L=68]
Description: tetrahydromethanopterin S-methyltransferase subunit F [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-24   84.2   0.1    3.4e-24   84.0   0.1    1.0  1  MtrF      Tetrahydromethanopterin S-methyltransferase, F subu


Domain annotation for each model (and alignments):
>> MtrF  Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.1   1.9e-28   3.4e-24       1      62 []       2      63 ..       2      63 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 1.9e-28
                          MtrF  1 gvptvnkpnmkaiksvvedirYraqLiaReqkLdSGvsatgivGfaiGfvlAllLvvlPvll 62
                                  gv+++nkpn+++i+s+ved++Y+++Li+R+++L+SG +++g++G++iG+v A++L+++P++l
  gi|15669042|ref|NP_247846.1|  2 GVEVSNKPNVSSIQSYVEDLEYKVGLITRNRGLESGTESAGTKGLIIGVVSAIVLMGIPLAL 63
                                  79*********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 464.96
//
Query:       gi|15669043|ref|NP_247847.1|  [L=84]
Description: tetrahydromethanopterin S-methyltransferase subunit G [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-29  100.2   0.1    4.9e-29  100.0   0.1    1.1  1  MtrG           Tetrahydromethanopterin S-methyltransferase, s
  ------ inclusion threshold ------
      0.034   14.1   0.3      0.047   13.7   0.3    1.3  1  Ribosomal_L29  Ribosomal L29 protein
      0.058   13.7   0.2      0.079   13.3   0.2    1.3  1  HalX           HalX domain
      0.092   12.7   0.0       0.12   12.3   0.0    1.2  1  DUF2605        Protein of unknown function (DUF2605)
      0.098   12.2   0.1       0.16   11.6   0.1    1.3  1  Trimer_CC      Trimerisation motif
        0.1   11.4   0.0        0.1   11.3   0.0    1.0  1  DUF2207        Predicted membrane protein (DUF2207)
       0.15   11.4   0.1       0.21   11.0   0.1    1.2  1  TraE           TraE protein


Domain annotation for each model (and alignments):
>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   0.1   1.9e-32   4.9e-29       2      63 ..       7      68 ..       6      69 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 1.9e-32
                          MtrG  2 iPsvvvdpddfnevkkrLdeieekvefvnsEiaqriGkkvGRdiGilYGlviGliillvyil 63
                                  +P+v++dp+d++++kkrLde+e+kve++n+E++q +GkkvGRdiGilYGlviG+i+ +++ +
  gi|15669043|ref|NP_247847.1|  7 LPQVIMDPADYEALKKRLDELEKKVENTNAELFQLAGKKVGRDIGILYGLVIGIILSYILPA 68
                                  8*********************************************************9876 PP

>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   1.9e-05     0.047       5      31 ..      21      47 ..      17      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                  HS-HHHHHHHHHHHHHHHHHHHHHHHH CS
                 Ribosomal_L29  5 elsdeeLkeklkelkkeLfnLrfqkat 31
                                  ++  +eL++k+++  +eLf+L  +k+ 
  gi|15669043|ref|NP_247847.1| 21 KKRLDELEKKVENTNAELFQLAGKKVG 47
                                  67789****************988875 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.1e-05     0.079      25      57 ..       5      37 ..       3      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                          HalX 25 ekseaeLadseeYqeLearleelraqldetlde 57
                                  ek +    d   Y++L+ rl+el+ +++ t +e
  gi|15669043|ref|NP_247847.1|  5 EKLPQVIMDPADYEALKKRLDELEKKVENTNAE 37
                                  566666678899*****************9887 PP

>> DUF2605  Protein of unknown function (DUF2605)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.8e-05      0.12      33      77 ..       8      53 ..       2      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.8e-05
                       DUF2605 33 elsflseeeqadllarvkeaqqeveaaka.Lfkatdgqvgvevevl 77
                                  +  ++++++ ++l +r++e +++ve ++a Lf+ ++++vg ++ +l
  gi|15669043|ref|NP_247847.1|  8 PQVIMDPADYEALKKRLDELEKKVENTNAeLFQLAGKKVGRDIGIL 53
                                  45789*******************877644**********988776 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   6.2e-05      0.16      38      50 ..      20      32 ..      17      34 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.2e-05
                                  HHHHHHHHHHHHH CS
                     Trimer_CC 38 lQkRLDrLEetvq 50
                                  l kRLD+LE +v+
  gi|15669043|ref|NP_247847.1| 20 LKKRLDELEKKVE 32
                                  78*********97 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.1e-05       0.1     349     404 ..      16      71 ..       2      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.1e-05
                       DUF2207 349 kakkfkkalkkwksavkkkergyfdkkgkkklkklsalglgliilglilillalll 404
                                   +++ +kk l++++++v++++ ++f+ +gkk    +++l+ ++i ++l  il al+ 
  gi|15669043|ref|NP_247847.1|  16 DYEALKKRLDELEKKVENTNAELFQLAGKKVGRDIGILYGLVIGIILSYILPALIK 71 
                                   7899***********************99998888877777776666666666654 PP

>> TraE  TraE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   8.1e-05      0.21      99     124 ..      11      36 ..       5      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.1e-05
                          TraE  99 lvapeaygelkkqlaeeaerikksnv 124
                                   +++p++y++lkk+l+e++++++++n+
  gi|15669043|ref|NP_247847.1|  11 IMDPADYEALKKRLDELEKKVENTNA 36 
                                   79*******************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1339  (0.0746835); expected 358.6 (0.02)
Passed bias filter:                      948  (0.0528752); expected 358.6 (0.02)
Passed Vit filter:                       128  (0.00713927); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 542.96
//
Query:       gi|161579524|ref|NP_247848.2|  [L=319]
Description: tetrahydromethanopterin S-methyltransferase subunit H [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.5e-160  531.1   1.0   7.3e-160  530.9   1.0    1.0  1  MtrH      Tetrahydromethanopterin S-methyltransferase MtrH su
  ------ inclusion threshold ------
      0.072   12.4   0.0       0.34   10.2   0.0    1.8  2  DUF2092   Predicted periplasmic protein (DUF2092)


Domain annotation for each model (and alignments):
>> MtrH  Tetrahydromethanopterin S-methyltransferase MtrH subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.9   1.0  8.2e-164  7.3e-160       1     299 []       6     310 ..       6     310 .. 0.99

  Alignments for each domain:
  == domain 1  score: 530.9 bits;  conditional E-value: 8.2e-164
                           MtrH   1 keqkvleiaGvkiGGqpGeyPtvlvgtifyakhkivedekkGifdkeaaealikkqeelsdktGnPalvqvvGeteeaiv 80 
                                    +eq+v+eiaG+kiGGqpGeyPt+l+gtifya+hkivede+kGifdk+aae+li+kq+e++d+tGnPalvqv+G t+ea+v
  gi|161579524|ref|NP_247848.2|   6 REQMVVEIAGRKIGGQPGEYPTALAGTIFYARHKIVEDERKGIFDKAAAEDLINKQAEMEDITGNPALVQVFGGTPEALV 85 
                                    79****************************************************************************** PP

                           MtrH  81 kyidfvadvtdaPllidstsaevklaaakyatevGladrviynsinasiedaeiealkesdveaaivlafnpmdptvegk 160
                                    +yidfva+v+d+P+l+dsts+e+++aaak+ate+G+a+++iynsin+si+++e+++l+esd+ea+ivl+f+pmdptvegk
  gi|161579524|ref|NP_247848.2|  86 NYIDFVAEVWDGPMLLDSTSGEARMAAAKRATEAGYAKQCIYNSINVSIDEQEYQVLVESDLEASIVLCFDPMDPTVEGK 165
                                    ******************************************************************************** PP

                           MtrH 161 lkileegegtaekgllelaeeaGiekplidvavtplgsgagaavkaslavkaklGlPvGsgihnvpsaWdwlrefkkkek 240
                                    +++l++g++ta+kg+lelae+aGi+ plid+avtplg+gagaav+as+avka +G+PvGsgihn+psaWdwlref+k+++
  gi|161579524|ref|NP_247848.2| 166 INVLTNGGKTADKGMLELAEKAGIKYPLIDTAVTPLGNGAGAAVRASFAVKALFGYPVGSGIHNIPSAWDWLREFRKQLR 245
                                    ******************************************************************************** PP

                           MtrH 241 ekaae......yevadvganlvqvilgsdfvlyGPienakkvfPavamvdilikeaakelgvelv 299
                                    e++++      ++v+dvganlvqv++++dfvlyGPi+na+++fPavamvd++i+eaakelg+e++
  gi|161579524|ref|NP_247848.2| 246 EAGERekakdiHHVCDVGANLVQVMASGDFVLYGPIDNAYMTFPAVAMVDAIIAEAAKELGIEPI 310
                                    *9999999999****************************************************85 PP

>> DUF2092  Predicted periplasmic protein (DUF2092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0     0.088   7.9e+02      89     115 ..     174     200 ..     169     217 .. 0.79
   2 ?   10.2   0.0   3.8e-05      0.34      71     105 ..     274     308 ..     265     310 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.088
                        DUF2092  89 gtidelldklqekygielPladlllsd 115
                                    +t+d+ + +l ek+gi+ Pl+d  ++ 
  gi|161579524|ref|NP_247848.2| 174 KTADKGMLELAEKAGIKYPLIDTAVTP 200
                                    6778888899**********9987765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 3.8e-05
                        DUF2092  71 tftlydkaenvYaqapapgtidelldklqekygie 105
                                     f+ly++ +n Y++ pa + +d+++ ++ +++gie
  gi|161579524|ref|NP_247848.2| 274 DFVLYGPIDNAYMTFPAVAMVDAIIAEAAKELGIE 308
                                    699*****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2283.96
//
Query:       gi|15669045|ref|NP_247849.1|  [L=228]
Description: hypothetical protein MJ_0855 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-12   45.5   1.6      1e-11   44.6   1.6    1.5  1  V4R       V4R domain
    4.3e-08   33.1   0.0      8e-08   32.3   0.0    1.4  1  DUF2507   Protein of unknown function (DUF2507)


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   1.6   1.2e-15     1e-11       3      61 ..     163     222 ..     161     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.2e-15
                                   EEEEEES-S-TT---SS---HHHHHHHHHHHHHHHSSE..EEEEEEE-GGGT-SSEEEEEE CS
                           V4R   3 lsieespelaglpgkeePvCyleaGllagalsellgkr..veveEveCaaeGhdhCeFeve 61 
                                   + ++++ e++ + ++ eP+Cyl aG++ag+l++ ++k   vev E +C+a+G+ +C F+++
  gi|15669045|ref|NP_247849.1| 163 VVVKDNKECKNC-KASEPICYLTAGFIAGCLENMTNKTyiVEVTEEKCQAVGDPYCTFVAK 222
                                   568999*****7.899*********************933466799************987 PP

>> DUF2507  Protein of unknown function (DUF2507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   8.9e-12     8e-08       8     113 ..     107     208 ..     102     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 8.9e-12
                       DUF2507   8 RdallpelLgedeeeilYwaGkelArkfplesledlieffekagwGtLellkekkkelefeLsgeiveerlkekeekefqL 88 
                                   +++l +  Lg++ ++i Y +Gk+ A k+ +++++d+i+f +   +G++ + k++  +++ + + e+ +   k  +e+   L
  gi|15669045|ref|NP_247849.1| 107 KEYLRKYYLGNNVKRIFYDIGKDYAIKLGINTYDDMITFMK-KDFGEVVIEKSEPLTVVVKDNKECKNC--K-ASEPICYL 183
                                   566667789****************************9875.59***9999988888888777766654..4.45666679 PP

                       DUF2507  89 EaGflAeqieqqkevvaeakeekkk 113
                                    aGf+A ++e+++++++  + +++k
  gi|15669045|ref|NP_247849.1| 184 TAGFIAGCLENMTNKTYIVEVTEEK 208
                                   ***********99988766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1085  (0.0605165); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1341.47
//
Query:       gi|15669046|ref|NP_247850.1|  [L=181]
Description: hypothetical protein MJ_0856 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-60  204.0   2.8    1.8e-60  203.9   2.8    1.0  1  DUF2096        Uncharacterized protein conserved in archaea (
  ------ inclusion threshold ------
      0.084   13.3   0.4       0.21   12.0   0.2    1.7  1  Ribosomal_S13  Ribosomal protein S13/S18


Domain annotation for each model (and alignments):
>> DUF2096  Uncharacterized protein conserved in archaea (DUF2096)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.9   2.8     2e-64   1.8e-60       1     169 []      13     179 ..      13     179 .. 0.99

  Alignments for each domain:
  == domain 1  score: 203.9 bits;  conditional E-value: 2e-64
                       DUF2096   1 lekqWvvlnellsdLkkrgkevpkevlenlrlaktiinfYkldphapdlikelkkaekelneiqeaLldlaekvdeeyakk 81 
                                   l+kqWvvl+el+++L +rg++vp+ v+e+lrla++++++Y+ldpha+  i+ l+++e+eln++q++L++l+   d+e+++k
  gi|15669046|ref|NP_247850.1|  13 LDKQWVVLSELSAELVNRGIKVPEIVFEKLRLANALLSYYILDPHAS--INILANVERELNYVQSQLFSLC---DTELTEK 88 
                                   69*********************************************..**********************...******* PP

                       DUF2096  82 wldklkkasrgekvleepkkkskFivevpr..gfetirvklkkpleeerlqeiaEyegvIiefeeddv.vvvyGdkedikk 159
                                   +ld++ ka+rge+++++p +ks++++ev++  ++e+irvkl+k++++erl+++ E++gvI+e++++++ v+++G+ +++k+
  gi|15669046|ref|NP_247850.1|  89 YLDRMIKAIRGEINAKFPVSKSNYNREVKKrgKVEAIRVKLQKEMQIERLSDLGEWHGVIFEYSDEKDkVIIEGNIDRVKR 169
                                   *****************************9999*******************************99988************ PP

                       DUF2096 160 aLkelselfk 169
                                   aLk+++ ++k
  gi|15669046|ref|NP_247850.1| 170 ALKDFAFMWK 179
                                   *********7 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   2.4e-05      0.21      44     109 ..      83     147 ..      79     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                 Ribosomal_S13  44 gelteeeiekieeivenkaqykipnwi.nrqkdikdGkdshvvendlrrklredieRlkkirsyrGl 109
                                    elte+ ++++ + +  +++ k p    n ++++k+  +   +  +l++  +++ieRl +++ + G+
  gi|15669046|ref|NP_247850.1|  83 TELTEKYLDRMIKAIRGEINAKFPVSKsNYNREVKKRGKVEAIRVKLQK--EMQIERLSDLGEWHGV 147
                                   599*********************9988999999988888888877766..568***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1205.81
//
Query:       gi|15669047|ref|NP_247851.1|  [L=109]
Description: hypothetical protein MJ_0856.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-26   89.9   0.1    8.6e-26   89.7   0.1    1.1  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0035   17.3   0.6      0.005   16.8   0.6    1.3  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.5   0.4      0.072   12.8   0.0    2.3  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.013   14.9   1.6      0.061   12.7   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain
      0.031   14.3   1.1       0.57   10.2   1.0    2.1  1  DZR             Double zinc ribbon
       0.05   13.8   0.3      0.068   13.4   0.3    1.2  1  Yippee-Mis18    Yippee zinc-binding/DNA-binding /Mis18, centr
      0.063   12.8   0.8       0.15   11.6   0.0    1.9  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.068   13.0   1.7       0.14   11.9   0.1    2.0  2  zf-HYPF         HypF finger
       0.09   12.1   1.4       0.22   10.9   1.4    1.6  1  zf-TFIIB        Transcription factor zinc-finger
       0.36   10.6   5.7       0.48   10.2   0.2    2.4  2  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.1   4.8e-29   8.6e-26       2      69 .]       7      82 ..       6      82 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 4.8e-29
                OrfB_Zn_ribbon  2 rklkeqleykakeyGikveevnpayTSktCseCgsknke........alsgrtfkCpnCgfeadrDvnAaiNilkr 69
                                  +k+  +l++k+ e+G+kv+e npayTS +C++Cgs++++        al +r+++C++Cgf+adrD++A++N++kr
  gi|15669047|ref|NP_247851.1|  7 KKFLGYLKNKCLEFGVKVIEGNPAYTSIKCPNCGSRLSQlykladerALPSRLMYCFDCGFYADRDTVAVFNLIKR 82
                                  79************************************************************************97 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.6   2.8e-06     0.005      19      44 ..      34      66 ..      15      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.8e-06
                 Zn_Tnp_IS1595 19 fvCPhCgsr..kayrikt.....rglfqCkeCr 44
                                    CP+Cgsr  ++y++++      +l  C +C+
  gi|15669047|ref|NP_247851.1| 34 IKCPNCGSRlsQLYKLADeralpSRLMYCFDCG 66
                                  57****************999998999999997 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     4e-05     0.072      17      30 ..      33      48 ..      28      49 .. 0.82
   2 ?   -0.1   0.1      0.43   7.7e+02      20      25 ..      62      67 ..      57      68 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-05
                                  ----SSS----..-B- CS
                DNA_RNApol_7kD 17 piRCkeCGhRi..lYK 30
                                  +i+C +CG+R+  lYK
  gi|15669047|ref|NP_247851.1| 33 SIKCPNCGSRLsqLYK 48
                                  79********755665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.43
                                  -SSS-- CS
                DNA_RNApol_7kD 20 CkeCGh 25
                                  C +CG+
  gi|15669047|ref|NP_247851.1| 62 CFDCGF 67
                                  777876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   3.4e-05     0.061      17      26 .]      34      43 ..      27      44 .. 0.71
   2 ?    1.0   0.1      0.17     3e+02      19      23 ..      62      66 ..      55      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                   zf-ribbon_3 17 nvCpyCGtkl 26
                                  ++Cp+CG++l
  gi|15669047|ref|NP_247851.1| 34 IKCPNCGSRL 43
                                  6777777765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.17
                   zf-ribbon_3 19 CpyCG 23
                                  C  CG
  gi|15669047|ref|NP_247851.1| 62 CFDCG 66
                                  99**9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.0   0.00032      0.57       1      19 [.      36      66 ..      36      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00032
                           DZR  1 CpqCgee............lppdarfCseCg 19
                                  Cp+Cg+             lp++  +C++Cg
  gi|15669047|ref|NP_247851.1| 36 CPNCGSRlsqlykladeraLPSRLMYCFDCG 66
                                  8888888888888888888888888888887 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   3.8e-05     0.068      49      86 ..      27      64 ..      14      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-05
                                  TTEEEEEEEETTT--EEEEEEEECSCCCCCCCTCEEEE CS
                  Yippee-Mis18 49 gkctystlsCkgCnsvlGwkYksteeelkykrglfile 86
                                  g+ +y++++C +C+s l   Yk + e   + r +++++
  gi|15669047|ref|NP_247851.1| 27 GNPAYTSIKCPNCGSRLSQLYKLADERALPSRLMYCFD 64
                                  45789**********************999999**997 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.4e-05      0.15       2      10 ..      35      43 ..      34      54 .. 0.80
   2 ?   -1.4   0.2      0.97   1.7e+03      21      26 ..      61      66 ..      59      68 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                                  EETTTTCEE CS
                  TF_Zn_Ribbon  2 kCPnCgstn 10
                                  kCPnCgs+ 
  gi|15669047|ref|NP_247851.1| 35 KCPNCGSRL 43
                                  9******85 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.97
                                  EESSSS CS
                  TF_Zn_Ribbon 21 vCtdCG 26
                                  +C dCG
  gi|15669047|ref|NP_247851.1| 61 YCFDCG 66
                                  677787 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.9e-05      0.14      19      32 ..      31      44 ..      30      46 .. 0.87
   2 ?   -0.3   0.1      0.52   9.3e+02      24      28 ..      62      66 ..      59      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.9e-05
                                  -TT---TTTS--EE CS
                       zf-HYPF 19 aqfisCtnCGPrls 32
                                  +  i C+nCG rls
  gi|15669047|ref|NP_247851.1| 31 YTSIKCPNCGSRLS 44
                                  66799*******98 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.52
                                  -TTTS CS
                       zf-HYPF 24 CtnCG 28
                                  C +CG
  gi|15669047|ref|NP_247851.1| 62 CFDCG 66
                                  99999 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.4   0.00012      0.22       1      26 [.      35      66 ..      35      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                      zf-TFIIB  1 kCPkCqdeleeser......ggveidyCpqCr 26
                                  kCP+C++ l ++ +          + yC++C+
  gi|15669047|ref|NP_247851.1| 35 KCPNCGSRLSQLYKladeraLPSRLMYCFDCG 66
                                  8*********7776676663448999***997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00027      0.48       1       9 [.      35      43 ..      34      45 .. 0.75
   2 ?    2.2   1.1     0.091   1.6e+02      15      20 ..      61      66 ..      60      68 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00027
                 zinc_ribbon_2  1 fCpnCGael 9 
                                  +CpnCG  l
  gi|15669047|ref|NP_247851.1| 35 KCPNCGSRL 43
                                  688888765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.091
                 zinc_ribbon_2 15 FCpyCG 20
                                  +C  CG
  gi|15669047|ref|NP_247851.1| 61 YCFDCG 66
                                  666676 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 804.83
//
Query:       gi|15669048|ref|NP_247852.1|  [L=274]
Description: hypothetical protein MJ_0857 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2079.52
//
Query:       gi|15669049|ref|NP_247853.1|  [L=113]
Description: hypothetical protein MJ_0858 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-36  122.9   5.9      5e-36  122.7   5.9    1.1  1  DUF749    Domain of unknown function (DUF749)
  ------ inclusion threshold ------
      0.025   14.8   2.7      0.032   14.4   2.7    1.3  1  DUF3213   Protein of unknown function (DUF3213)
       0.05   14.2   2.7       0.77   10.4   0.2    2.2  2  LtuB      Late transcription unit B
      0.082   13.3   0.2       0.17   12.3   0.1    1.6  2  YfcL      YfcL protein


Domain annotation for each model (and alignments):
>> DUF749  Domain of unknown function (DUF749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   5.9   1.1e-39     5e-36       1      87 []       8      95 ..       8      95 .. 0.99

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 1.1e-39
                                  ----EEEEEESTT.-STTTS-STHHHHCTTT---SS--EEEEEE-TTTT-EEEEE-S---S-HHHHHHHHHHHHSSS-SSSHH CS
                        DUF749  1 Fvatllgifkvke.LpeelekfvklkaalekkelkdddeiaIlniegTtsyhvlFldsyesieeikkeLkeadaklnhdskki 82
                                  Fvatl++i++vke L++e+e+fvk++aa++k+elkddd++aI+ni++Ttsy+v+F+d++++iee+k+e+k++++++n+ds+++
  gi|15669049|ref|NP_247853.1|  8 FVATLISILTVKEaLNSEMENFVKVRAAIDKRELKDDDKVAIFNINSTTSYQVFFIDKDTNIEELKEEFKKMNVRINYDSEQV 90
                                  9********************************************************************************** PP

                                  HHHH- CS
                        DUF749 83 lkgyl 87
                                  lk+y+
  gi|15669049|ref|NP_247853.1| 91 LKRYI 95
                                  ***97 PP

>> DUF3213  Protein of unknown function (DUF3213)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.7   7.2e-06     0.032       8      75 ..      30      96 ..      16     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.2e-06
                                  TTTTTHHHHHTTTTTTTB------TTSS--EEE--B-S-SHHHHHHHT...TT-SS-------SS--X CS
                       DUF3213  8 tpekakikqyelekdervyrvflngyakvaevvideekvnieelkkkleelkgevveekeltlqelie 75
                                     +a i + el+ d++v    +n+ +   +v + ++  nieelk++++++   +  + e  l+  ie
  gi|15669049|ref|NP_247853.1| 30 VKVRAAIDKRELKDDDKVAIFNINSTTS-YQVFFIDKDTNIEELKEEFKKMNVRINYDSEQVLKRYIE 96
                                  556899***********98877888665.5667777789********988887777777777777766 PP

>> LtuB  Late transcription unit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00017      0.77      24      61 ..      17      53 ..       2      69 .. 0.74
   2 ?    4.6   0.3     0.011        50       6      33 ..      68      94 ..      61      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                          LtuB 24 kekeslrkrakefdvlvrslldkqvsqdadqvliftyq 61
                                    ke l    ++f v vr+ +dk+  +d d+v if+  
  gi|15669049|ref|NP_247853.1| 17 TVKEALNSEMENF-VKVRAAIDKRELKDDDKVAIFNIN 53
                                  5688888888887.889******************843 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                          LtuB  6 klkgekkkkfkhhysliskekeslrkra 33
                                  +++ e k++fk+    i  + e++ kr 
  gi|15669049|ref|NP_247853.1| 68 NIE-ELKEEFKKMNVRINYDSEQVLKRY 94
                                  577.99*****************99985 PP

>> YfcL  YfcL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   3.7e-05      0.17      49      79 ..      20      52 ..      11      56 .. 0.84
   2 ?   -2.5   0.0       1.5   6.6e+03      49      56 ..      70      77 ..      64      96 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
                          YfcL 49 ealkekvee..slekAikkgELspaDqalVkel 79
                                  eal++++e+  ++++Ai k EL+++D++ + ++
  gi|15669049|ref|NP_247853.1| 20 EALNSEMENfvKVRAAIDKRELKDDDKVAIFNI 52
                                  789999998335689*************99875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                          YfcL 49 ealkekve 56
                                  e+lke+ +
  gi|15669049|ref|NP_247853.1| 70 EELKEEFK 77
                                  44444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1465  (0.0817112); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 730.35
//
Query:       gi|15669050|ref|NP_247854.1|  [L=164]
Description: hypothetical protein MJ_0859 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-57  193.8   3.4    1.6e-57  193.7   3.4    1.0  1  DUF2118   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.7   3.4   9.2e-62   1.6e-57       1     151 []       4     156 ..       4     156 .. 0.99

  Alignments for each domain:
  == domain 1  score: 193.7 bits;  conditional E-value: 9.2e-62
                       DUF2118   1 yklPrlYvEgkeseeevevileeeeevekfadkveekklkgkvvYeelldeivd.vleekvtrdviivlp..derklillk 78 
                                   +++PrlYvE++e++e+++v++e++++v+kf+dk+ee++ +gkv+Y++++d++++ vl+ +vt+d+ii+++  ++r+++++k
  gi|15669050|ref|NP_247854.1|   4 MRIPRLYVENAEKHEGRKVVIENGGKVIKFLDKDEEYEGDGKVLYQVIYDDFDNyVLMGTVTKDMIIEYEvgGVRQITYIK 84 
                                   89****************************************************9***************999******** PP

                       DUF2118  79 kGdklklipvegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvVvfikeepagkrpnyiyyilpe 151
                                   kG+kl +ip+eg+kv++ivd+G+r+ +g+++aa+++rkg++r++++pv+g+V+f+ke+pa kr+ny++yilpe
  gi|15669050|ref|NP_247854.1|  85 KGTKLLEIPAEGYKVYPIVDFGCRILGGHRIAALQSRKGDIRFVNTPVNGIVLFLKEVPA-KRENYVFYILPE 156
                                   ************************************************************.***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 1262.91
//
Query:       gi|15669051|ref|NP_247855.1|  [L=327]
Description: bifunctional short chain isoprenyl diphosphate synthase IdsA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-79  266.4   1.2    2.5e-79  266.0   1.2    1.2  1  polyprenyl_synt  Polyprenyl synthetase
    0.00015   21.4   0.1    0.00027   20.5   0.1    1.5  1  SQS_PSY          Squalene/phytoene synthase
    0.00052   19.4   0.6      0.002   17.5   0.0    2.1  3  Terpene_synth_C  Terpene synthase family, metal binding domai
  ------ inclusion threshold ------
       0.22   11.7   2.6       0.79   10.0   0.7    2.3  2  SMBP             Small metal-binding protein
          1   10.0   5.5          6    7.6   0.1    2.5  2  Cytochrom_B562   Cytochrome b562


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.0   1.2   6.9e-83   2.5e-79       3     255 ..      34     281 ..      32     282 .. 0.95

  Alignments for each domain:
  == domain 1  score: 266.0 bits;  conditional E-value: 6.9e-83
                                   HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHH CS
               polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklA 83 
                                    l++a+++l+ agGKr+Rp l++ ++ + k   +++e+++ +a++vel+h+++L+hDDimD+++ RRG+p++h ++G+++A
  gi|15669051|ref|NP_247855.1|  34 KLYNASKHLLFAGGKRIRPYLTVVTYMLKK---DDIEEVLPAAAAVELIHNYTLIHDDIMDNDDERRGKPTVHVVYGEPMA 111
                                   6899999**99**************99988...479********************************************* PP

                                   HHHHHHHHHHHHHHHHHHH..STTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHH CS
               polyprenyl_synt  84 indgdfllarafellaklf..ekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvala 162
                                   i++gd+l+a+afe ++++   +k  e+l+++s+++++++eGq++d+e e   ++  +++eeyl+++++KT++l++++v ++
  gi|15669051|ref|NP_247855.1| 112 ILAGDLLYAKAFEAVSRIKdnKKAHEVLKILSKACVEVCEGQAMDMEFE---NYY-PTMEEYLDMIRKKTGALLEASVGIG 188
                                   ******************9854449*********************766...344.67*********************** PP

                                   HHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHHHHHHTTSSH CS
               polyprenyl_synt 163 allagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqrkvlkeilgkka 243
                                   a++a++++ee ealk++++++Gl FQiqDD+lDl gd+++lgKp+g+Di+egk t+++++al++ +++++k+l eilg+k+
  gi|15669051|ref|NP_247855.1| 189 AVMADCNEEEREALKEYAKRIGLTFQIQDDVLDLIGDQKKLGKPVGSDIREGKKTIIVIHALKTLDEDKKKRLLEILGNKN 269
                                   ******99**********************************************************************999 PP

                                   HHHHHHHHHHHH CS
               polyprenyl_synt 244 ekeedvkealel 255
                                    k+e++kea+e+
  gi|15669051|ref|NP_247855.1| 270 VKDEEIKEAIEI 281
                                   9********997 PP

>> SQS_PSY  Squalene/phytoene synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   7.5e-08   0.00027      79     154 ..     134     215 ..      36     227 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.5e-08
                                   HHHHHHT...--HHHHHHHHHHTS--SS-..--.SHHHHHHHHHHHHHHHHHHHHHHH-S......S-HHHHHHHHHHHHH CS
                       SQS_PSY  79 qlirtyk...lpkellleliegmeadleftrye.tlddLeeYcyrvagvVgelclrllgar.....rsdralaeaarrlGk 150
                                   ++    +   + ++ + e++eg ++d+ef+ y  t++++ +  ++  g++ e +  +  +      ++++al e+a+r+G+
  gi|15669051|ref|NP_247855.1| 134 KAH---EvlkILSKACVEVCEGQAMDMEFENYYpTMEEYLDMIRKKTGALLEASVGIGAVMadcneEEREALKEYAKRIGL 211
                                   233...25559999999************88766**********************998877788755579********** PP

                                   HHHH CS
                       SQS_PSY 151 alQl 154
                                    +Q+
  gi|15669051|ref|NP_247855.1| 212 TFQI 215
                                   ***8 PP

>> Terpene_synth_C  Terpene synthase family, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       0.8   2.9e+03     196     228 ..      62      94 ..      18     103 .. 0.65
   2 !   17.5   0.0   5.7e-07     0.002     118     218 ..     123     214 ..     115     240 .. 0.68
   3 ?   -1.0   0.1      0.26   9.2e+02     153     171 ..     286     304 ..     245     323 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.8
               Terpene_synth_C 196 tkeafewvasypklvkalstilRLlnDiasyer 228
                                   +k+ +e v+     v+++   + + +Di +  +
  gi|15669051|ref|NP_247855.1|  62 KKDDIEEVLPAAAAVELIHNYTLIHDDIMDNDD 94 
                                   344444555555555555555555555555554 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.7e-07
               Terpene_synth_C 118 lntfneledelekeeksdrvskylkeawkelvkaylkeakWreekyvPsfeEylenslvssglpllllaa.lvgmgdevtk 197
                                   ++ ++ +    ++++k ++v k+l++a+ e+++     ++   e+y P++eEyl++   ++g+ l + +   ++m d +++
  gi|15669051|ref|NP_247855.1| 123 FEAVSRI----KDNKKAHEVLKILSKACVEVCEGQAMDMEF--ENYYPTMEEYLDMIRKKTGALLEASVGiGAVMAD-CNE 196
                                   4444444....44445556999***********98888887..89***********877776655444442334444.888 PP

               Terpene_synth_C 198 eafewvasypklvkalstilR 218
                                   e+ e +++y k    +  ++ 
  gi|15669051|ref|NP_247855.1| 197 EEREALKEYAKR---IGLTFQ 214
                                   878887777654...444444 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.26
               Terpene_synth_C 153 lkeakWreekyvPsfeEyl 171
                                   ++ ak   ++++++ +Eyl
  gi|15669051|ref|NP_247855.1| 286 IEYAKELMKQKTEEAKEYL 304
                                   2222222222222222222 PP

>> SMBP  Small metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.15   5.5e+02      59      91 ..     119     151 ..     115     156 .. 0.80
   2 ?   10.0   0.7   0.00022      0.79      43      91 ..     239     291 ..     234     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.15
                                   HHHHH...-------HHHHHHHHHHHHHHHHHC CS
                          SMBP  59 hakaaaekakeeekehldegikhLeeAIkhgka 91 
                                   +aka +++++ +++++ +e +k L +A  +  +
  gi|15669051|ref|NP_247855.1| 119 YAKAFEAVSRIKDNKKAHEVLKILSKACVEVCE 151
                                   6788788999999**********9999766555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00022
                                   TT-HHHHHHHHHHHHHHHHHH.......-------HHHHHHHHHHHHHHHHHC CS
                          SMBP  43 aghakalveHaeealkhakaa....aekakeeekehldegikhLeeAIkhgka 91 
                                   +g+ + +v Ha + l + k+     +  +k+ ++e ++e+i+ L+ +I+ +k+
  gi|15669051|ref|NP_247855.1| 239 EGKKTIIVIHALKTLDEDKKKrlleILGNKNVKDEEIKEAIEILKPSIEYAKE 291
                                   5778999*********9999999977777888999***************997 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0017         6      11      71 ..     121     176 ..     119     205 .. 0.90
   2 ?    3.7   1.5     0.028     1e+02      47      95 ..     265     312 ..     241     321 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0017
                Cytochrom_B562  11 kalkqvakaddaeelkkalkelraaaedakeatpsklekdseeqkdYqeGldklidqldka 71 
                                   ka+++v++++d +++++ lk l +a  +  e+++      + e+++Y   +++ +d + k 
  gi|15669051|ref|NP_247855.1| 121 KAFEAVSRIKDNKKAHEVLKILSKACVEVCEGQA-----MDMEFENYYPTMEEYLDMIRKK 176
                                   7899******************************.....8899999999999999999775 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.028
                Cytochrom_B562  47 lekdseeqkdYqeGldklidqldkaealakagkleeakaalkelkdlrk 95 
                                   l +++ + ++ +e ++ l   ++ a++l+k +k eeak+ lk +++ r+
  gi|15669051|ref|NP_247855.1| 265 LGNKNVKDEEIKEAIEILKPSIEYAKELMK-QKTEEAKEYLKIFNKDRR 312
                                   444555555555666666666666666555.466666666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1733  (0.096659); expected 358.6 (0.02)
Passed bias filter:                      866  (0.0483016); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2037.88
//
Query:       gi|15669052|ref|NP_247856.1|  [L=448]
Description: hypothetical protein MJ_0861 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-10   40.6   3.0    3.1e-10   39.8   0.1    2.8  3  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.2e-08   35.2   1.4    1.2e-08   35.2   1.4    1.9  2  Lactamase_B    Metallo-beta-lactamase superfamily
    1.8e-08   34.1   0.0    3.6e-08   33.2   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0056   15.8   0.1     0.0086   15.2   0.1    1.2  1  PDEase_II      cAMP phosphodiesterases class-II


Domain annotation for each model (and alignments):
>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.33   1.5e+03      34      50 ..      77      93 ..      72     126 .. 0.72
   2 ?   -2.9   0.0       1.5   6.7e+03      22      43 ..     304     325 ..     304     335 .. 0.76
   3 !   39.8   0.1   6.9e-14   3.1e-10      12      60 ..     383     434 ..     376     436 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.33
                         RMMBL 34 vilvHGeeeatsalarl 50
                                  ++l HG+ +++ a  +l
  gi|15669052|ref|NP_247856.1| 77 IVLSHGHLDHIGAVPKL 93
                                  88999988887765554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.5
                         RMMBL  22 llelirklkprnvilvHGeeea 43 
                                   l+++++  k +++i+  G++ +
  gi|15669052|ref|NP_247856.1| 304 LKNIVKEGKEKYLIIATGHQGE 325
                                   5778888899999988887765 PP

  == domain 3  score: 39.8 bits;  conditional E-value: 6.9e-14
                         RMMBL  12 dfSgHadknellelirklkprnvilvHGeeeatsalarllkeeeg....idvf 60 
                                   ++SgHa k+++++++r l+p+++i+ HG+ + t+++ +l+ eeeg    +dv+
  gi|15669052|ref|NP_247856.1| 383 HVSGHAAKEDHRDMLRWLNPEHIIPSHGDFNLTAEYTKLA-EEEGyrlgEDVH 434
                                   39**************************************.999855555555 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   1.4   2.7e-12   1.2e-08      44      98 ..      73     131 ..      12     173 .. 0.76
   2 ?   -3.8   0.1       2.5   1.1e+04     169     197 .]     384     409 ..     369     411 .. 0.55

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 2.7e-12
                                   GEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH....T CS
                   Lactamase_B  44 dvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgll....l 98 
                                   +v+a++l+H+HlDHiG++++l++++++p++  + + +  ++e +        ++     
  gi|15669052|ref|NP_247856.1|  73 EVKAIVLSHGHLDHIGAVPKLAHRYNAPIIGTPYTIELVKREILSEKKFDVRNPlivlN 131
                                   79****************************99999999988888554433333343332 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.5
                                   E-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                   Lactamase_B 169 vrdpsdaekyldsllklaglkaevlvpgH 197
                                   v  ++ +e+ +d l   + l++e ++p+H
  gi|15669052|ref|NP_247856.1| 384 VSGHAAKEDHRDML---RWLNPEHIIPSH 409
                                   44444444444322...244444444444 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   8.1e-12   3.6e-08      30     116 ..      73     155 ..      64     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 8.1e-12
                                   SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE CS
                 Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatpa 110
                                   +++a++l+h+H DH+  ++ l+++++  +p+++++ +++ +++++  + +    + ++  l++ges++l+ ++++++++ +
  gi|15669052|ref|NP_247856.1|  73 EVKAIVLSHGHLDHIGAVPKLAHRYN--APIIGTPYTIELVKREILSEKKFDV-RNPLIVLNAGESIDLT-PNITLEFIRI 149
                                   699********************665..8***************887777777.999************9.699******* PP

                                   -EE--C CS
                 Lactamase_B_2 111 rhksgr 116
                                    h+ + 
  gi|15669052|ref|NP_247856.1| 150 THSIPD 155
                                   **9887 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.9e-06    0.0086      74     129 ..      67     116 ..      49     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-06
                                   HHHHHHTEEEEE-S---GGGTHHHHHHGGGGGS-S.--EEEEE-HHHHHHHHHHTB CS
                     PDEase_II  74 tyeiknniksylItHsHLDHvsglvinSaefykaqlkkktivGlpytInalqkhlF 129
                                   + +i+ ++k   ++H HLDH+++ v   a+ y+a      i+G pytI+ +++++ 
  gi|15669052|ref|NP_247856.1|  67 MKNIEGEVKAIVLSHGHLDHIGA-VPKLAHRYNA-----PIIGTPYTIELVKREIL 116
                                   5689999*************975.5555555554.....799*******9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2753.34
//
Query:       gi|15669053|ref|NP_247857.1|  [L=359]
Description: isopentenyl pyrophosphate isomerase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-22   80.1   0.0    3.1e-15   56.1   0.0    2.1  2  FMN_dh        FMN-dependent dehydrogenase
    4.5e-05   22.7   0.3     0.0033   16.6   0.1    2.5  2  Glu_synthase  Conserved region in glutamate synthase
    5.3e-05   22.4   7.3      0.047   12.7   1.8    3.2  3  IMPDH         IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.3e-08   7.7e-05      27      97 ..      29     101 ..      22     109 .. 0.81
   2 !   56.1   0.0   5.2e-19   3.1e-15     214     344 ..     191     342 ..     150     346 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.3e-08
                                   HHGGGGEEE---SSSS-..SS-B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT- CS
                        FMN_dh  27 raaferirlrprvlrdv..skvdlsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvlstva 97 
                                   ++ +e+i+l ++   ++  ++++++++l+G+kls+P++++ +      +++ + ++a+a +++g+ ++++++ 
  gi|15669053|ref|NP_247857.1|  29 TTLLEDIELIHKGTCGInfNDIETEIELFGKKLSAPIIVSGMTGGHSKAKEINKNIAKAVEELGLGMGVGSQR 101
                                   5566777777776665511566888999**************888888899****************999875 PP

  == domain 2  score: 56.1 bits;  conditional E-value: 5.2e-19
                                   HHSSEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG.....................TSSTT---HHHCHHHHHHHH.. CS
                        FMN_dh 214 qtklplvvKGv...ltaedakraveaGvdgivvSNHGG.....................RqldgapatidvLpeiveavgg 270
                                     ++p++ K v    ++eda  + ++G d+i v   GG                     +  +  ++t   + e+    + 
  gi|15669053|ref|NP_247857.1| 191 YKNIPFIAKQVgegFSKEDALILKDIGFDAIDVQGSGGtswakveiyrvkeeeikrlaeKFANWGIPTAASIFEVKSVYD- 270
                                   33489999*9999999****************************999999999986665555556666666666655554. PP

                                   SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHHCG CS
                        FMN_dh 271 rievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvksvaeldrs 344
                                      v+ +gGir G D++k +a+G d++ ++ p+l + +++G e v +vle   +el+ +m l+G+++++el+++
  gi|15669053|ref|NP_247857.1| 271 -GIVIGSGGIRGGLDIAKCIAIGCDCCSVALPILKA-SLKGWEEVVKVLESYIKELKIAMFLVGAENIEELKKT 342
                                   .68999***************************988.89********************************987 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.0    0.0052        31      62     100 ..      59      98 ..      18     108 .. 0.80
   2 !   16.6   0.1   5.6e-07    0.0033     170     304 ..     160     300 ..     154     306 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0052
                                   HHHHTTEE---B-TT.TS-HHHHHHHHHHHHHHT-B-EET CS
                  Glu_synthase  62 lkikkriltsamSyG.alseeahealakamnrlgtksntG 100
                                   +k++ +i++s+m  G + ++e ++ +aka+++lg  +  G
  gi|15669053|ref|NP_247857.1|  59 KKLSAPIIVSGMTGGhSKAKEINKNIAKAVEELGLGMGVG 98 
                                   478999******999667889999**********998877 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5.6e-07
                                   -TT--EE--SS-TT-SSHHHHHHHHHHHHHH-TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHHH... CS
                  Glu_synthase 170 kpgvdliSPaphhdiysiedlaqliedLkevnkeakvsvKlvaeagvetiaagvakanadiilidGleGGTGAspkss... 247
                                   +p +++i P    ++++   l++ i++ k+  k+ +   K v e   +  a+ + + + d+i ++G+ GGT  ++ ++   
  gi|15669053|ref|NP_247857.1| 160 NPLQEIIQPEGDLNFKNLYKLKEIISNYKKSYKNIPFIAKQVGEGFSKEDALILKDIGFDAIDVQGS-GGTSWAKVEIyrv 239
                                   56778999999999****************************999999999999999*********7.5665554433111 PP

                                   .....HHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SH CS
                  Glu_synthase 248 .....ikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigt 304
                                           a      +++ +      + + d ++ i +Gg++ g d++k++a+G d  +++ 
  gi|15669053|ref|NP_247857.1| 240 keeeiKRLAEKFANWGIPTAASIFEVKSVYDGIV-IGSGGIRGGLDIAKCIAIGCDCCSVAL 300
                                   1111033344556678888888887777888775.579******************988875 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.31   1.8e+03     154     177 ..      72      98 ..      48     102 .. 0.48
   2 !   12.7   1.8   7.9e-06     0.047     185     233 ..     251     296 ..     176     300 .. 0.72
   3 !   10.7   0.0   3.2e-05      0.19     298     335 ..     312     349 ..     303     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.31
                                   -SHHHHHHH...HHTT-SEEEE-SS-S CS
                                   xxxxxxxxx...xxxxxxxxxxxxxxx RF
                         IMPDH 154 ataegakaL...ieagadavkvGiGpG 177
                                     ++ ak++   i+  ++ +  G+G G
  gi|15669053|ref|NP_247857.1|  72 GGHSKAKEInknIAKAVEELGLGMGVG 98 
                                   222223322000223333344555555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.9e-06
                                   HCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 185 vagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadav 233
                                    a  G+p + +++ev ++   ++  vi  GGi+   di+k +a+G d++
  gi|15669053|ref|NP_247857.1| 251 FANWGIPTAASIFEVKSV---YDGIVIGSGGIRGGLDIAKCIAIGCDCC 296
                                   467799999999988776...55679********************997 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 3.2e-05
                                   -HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 298 svkevveqlvgglrsgmgylGaktieelkekakfvrit 335
                                   +v +v+e  +++l+ +m  +Ga++ieelk+++ +v+ t
  gi|15669053|ref|NP_247857.1| 312 EVVKVLESYIKELKIAMFLVGAENIEELKKTSYIVKGT 349
                                   68899************************999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2265.08
//
Query:       gi|15669054|ref|NP_247858.1|  [L=295]
Description: heterodisulfide reductase subunit HdrB2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-42  143.0   2.9    2.1e-20   72.7   0.1    2.5  3  CCG       Cysteine-rich domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.1   5.3e-24   9.6e-20       1      84 [.       3      85 ..       3      86 .. 0.95
   2 ?   -3.4   0.0      0.68   1.2e+04      52      67 ..      96     111 ..      90     116 .. 0.69
   3 !   72.7   0.1   1.2e-24   2.1e-20       1      85 []     148     240 ..     148     240 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 5.3e-24
                           CCG  1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelae.alakrnvetaeetgadaivtacpgCll 82
                                  +a+f gC ++ ++yp v+ka+k ++e+lgvele++ ++sCC+a+g++ +++++++ +la+rn++ aee+g d ivt c+gC++
  gi|15669054|ref|NP_247858.1|  3 YAFFLGC-IMPHRYPGVEKATKIVMEELGVELEYMPGASCCPAPGVFGSFDQKTWlTLAARNLCIAEEMGLD-IVTVCNGCYG 83
                                  79*****.******************************************995555*************999.********98 PP

                           CCG 83 ql 84
                                  +l
  gi|15669054|ref|NP_247858.1| 84 SL 85
                                  86 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.68
                           CCG  52 elaealakrnvetaee 67 
                                   ++a+++++++++ + +
  gi|15669054|ref|NP_247858.1|  96 KEALDFVNEKLDKIGK 111
                                   3677888888877765 PP

  == domain 3  score: 72.7 bits;  conditional E-value: 1.2e-24
                           CCG   1 vayfdgChllraa......ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadai 73 
                                   va+++gCh+l+++      +pe +k+l+++++a+g++ + + +  +CCGaggg++ +   +a++++k++++++ e+gad+ 
  gi|15669054|ref|NP_247858.1| 148 VAIHYGCHFLKPSdvkhldSPERPKLLEEIVAATGAKPVMYrDYLMCCGAGGGVRARFLpTALDMTKEKIRNMLEAGADCT 228
                                   89***************************************9999**********99999********************* PP

                           CCG  74 vtacpgCllqlk 85 
                                   v+ cp+C+lq++
  gi|15669054|ref|NP_247858.1| 229 VNVCPFCHLQFD 240
                                   **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 2017.08
//
Query:       gi|15669055|ref|NP_247859.1|  [L=186]
Description: heterodisulfide reductase subunit HdrC2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   41.5   5.8    2.4e-10   40.7   5.8    1.4  1  Fer4_8    4Fe-4S dicluster domain
    3.4e-09   37.1   5.6    5.7e-09   36.4   5.6    1.4  1  Fer4_17   4Fe-4S dicluster domain
    8.1e-09   35.5  17.8    8.3e-08   32.3   8.0    1.6  2  Fer4_9    4Fe-4S dicluster domain
    1.4e-07   31.5   8.4    3.8e-07   30.1   8.4    1.7  1  Fer4_10   4Fe-4S dicluster domain
    7.2e-06   26.5   8.6    2.6e-05   24.7   9.0    1.7  2  Fer4_7    4Fe-4S dicluster domain
    2.9e-05   24.9   3.8      0.092   13.7   0.2    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
     0.0025   17.6  12.2      0.089   12.6   2.0    2.3  2  Fer4      4Fe-4S binding domain
     0.0046   17.0   6.5      0.013   15.7   6.5    1.6  1  Fer4_21   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.013   15.6  11.0      0.094   12.9   2.4    2.3  2  Fer4_2    4Fe-4S binding domain
      0.015   15.8  11.5        0.2   12.2   3.5    2.2  2  Fer4_4    4Fe-4S binding domain
      0.065   13.0   6.5      0.096   12.5   0.5    2.2  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
       0.24   12.4  16.6       0.56   11.3   3.2    2.2  2  Fer4_3    4Fe-4S binding domain
        2.5    9.0  10.2        7.2    7.5   0.2    2.4  2  Fer4_22   4Fe-4S dicluster domain
        3.5    7.8   8.6        3.6    7.8   0.9    2.3  2  Fer4_18   4Fe-4S dicluster domain
        4.6    7.5  12.1        8.6    6.6   2.1    2.3  2  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   5.8     2e-13   2.4e-10       2      65 .]      33      93 ..      32      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 2e-13
                        Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae...dvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                  +++C +Cg C+ +Cp+ rrt+ +  +   ++     dv +++       +w+Cttc  C e+Cp ++
  gi|15669055|ref|NP_247859.1| 33 IKACYQCGTCTGSCPSGRRTAYRTRKVLRKVLLgldDVLDSD------DIWYCTTCYTCYERCPRDV 93
                                  579*****************9665655555555454455555......5***************875 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   5.6   4.8e-12   5.7e-09       1      60 [.      35      93 ..      35      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 4.8e-12
                       Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60
                                  +C qCg C+ +Cps++++  + +k+lr++ lg l+++ +++ +  C++C  C ++CP ++
  gi|15669055|ref|NP_247859.1| 35 ACYQCGTCTGSCPSGRRTAYRTRKVLRKVLLG-LDDVLDSDDIWYCTTCYTCYERCPRDV 93
                                  5******************************8.77888999****************987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.2   1.2e-05     0.014      33      49 ..      30      49 ..       7      50 .. 0.72
   2 !   32.3   8.0     7e-11   8.3e-08       1      49 [.      35      92 ..      35      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                        Fer4_9 33 e...eaCigCgaCveaCpkg 49
                                      +aC++Cg+C+  Cp+g
  gi|15669055|ref|NP_247859.1| 30 VksiKACYQCGTCTGSCPSG 49
                                  04446799999999999986 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 7e-11
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.........eaCigCgaCveaCpkg 49
                                  +C++Cg+C+ +Cp+g  +  + ++  r    +          + C++C +C+e+Cp++
  gi|15669055|ref|NP_247859.1| 35 ACYQCGTCTGSCPSGRRTAYRTRKVLRKVLLGLddvldsddiWYCTTCYTCYERCPRD 92
                                  6**************999999999999888877999********************98 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   8.4   3.2e-10   3.8e-07       4      56 .]      31      90 ..      28      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.2e-10
                       Fer4_10  4 idddtCirCgkCvkaCPadl.......tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  +  + C +Cg+C+ +CP+         +  ++     ++  ++++++ Ct+c  C+e CP
  gi|15669055|ref|NP_247859.1| 31 KSIKACYQCGTCTGSCPSGRrtayrtrKVLRKVLLGLDDVLDSDDIWYCTTCYTCYERCP 90
                                  56689*************88****974333333444455555669**************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   2.1   0.00011      0.14      29      51 ..      27      49 ..       2      50 .. 0.68
   2 !   24.7   9.0   2.2e-08   2.6e-05       1      52 []      35      93 ..      35      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                        Fer4_7 29 ekveidpekClgCgaCvavCPtg 51
                                  e+++ +   C++Cg C   CP+g
  gi|15669055|ref|NP_247859.1| 27 EDIVKSIKACYQCGTCTGSCPSG 49
                                  55677788999999999999987 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2.2e-08
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekv.........eidpekClgCgaCvavCPtga 52
                                  +C +Cg C+  Cp++ ++     ++   +kv           d ++C++C+ C ++CP ++
  gi|15669055|ref|NP_247859.1| 35 ACYQCGTCTGSCPSGRRTAYRT-RKVL-RKVllglddvldSDDIWYCTTCYTCYERCPRDV 93
                                  5************999998654.3332.233345554343345789************875 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   7.7e-05     0.092       2      14 ..      36      48 ..       5      59 .. 0.71
   2 !   12.1   0.4   0.00024      0.28       2      17 ..      79      95 ..      78     126 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.7e-05
                       Fer4_16  2 CgtCgkCaevCPt 14
                                  C +Cg C+ +CP+
  gi|15669055|ref|NP_247859.1| 36 CYQCGTCTGSCPS 48
                                  5555555555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00024
                       Fer4_16  2 CgtCgkCaevCPtna.i 17
                                  C+tC  C e CP ++ i
  gi|15669055|ref|NP_247859.1| 79 CTTCYTCYERCPRDVkI 95
                                  ************98733 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   2.8   0.00045      0.54       7      21 ..      35      49 ..      29      49 .. 0.87
   2 !   12.6   2.0   7.4e-05     0.089       8      22 ..      79      93 ..      78      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00045
                                  TSSS-THHHHHSTTT CS
                          Fer4  7 kCigCGaCvevCPvg 21
                                   C  CG+C   CP g
  gi|15669055|ref|NP_247859.1| 35 ACYQCGTCTGSCPSG 49
                                  699**********76 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.4e-05
                                  SSS-THHHHHSTTTE CS
                          Fer4  8 CigCGaCvevCPvgA 22
                                  C+ C +C+e CP ++
  gi|15669055|ref|NP_247859.1| 79 CTTCYTCYERCPRDV 93
                                  ************985 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   6.5   1.1e-05     0.013       7      54 ..      35      92 ..      31      97 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                       Fer4_21  7 kCigCgkCliaCedtshqaieidaktvl......kvv.ed...eCvGCnlCssvCPve 54
                                   C +Cg C+ +C+ +  +a ++ +  +        v+ +d    C+ C  C++ CP +
  gi|15669055|ref|NP_247859.1| 35 ACYQCGTCTGSCPSGRRTAYRTRKVLRKvllgldDVLdSDdiwYCTTCYTCYERCPRD 92
                                  7************9999998665443223456664542332446************54 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.4   7.8e-05     0.094       9      21 ..      35      47 ..      27      48 .. 0.91
   2 ?    7.7   1.5    0.0035       4.2      10      21 ..      79      90 ..      70      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.8e-05
                        Fer4_2  9 rCigCgaCvsaCP 21
                                  +C +Cg+C+ +CP
  gi|15669055|ref|NP_247859.1| 35 ACYQCGTCTGSCP 47
                                  7************ PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0035
                        Fer4_2 10 CigCgaCvsaCP 21
                                  C+ C +C+  CP
  gi|15669055|ref|NP_247859.1| 79 CTTCYTCYERCP 90
                                  ********99*9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.5   0.00017       0.2       2      17 .]      34      49 ..      33      53 .. 0.90
   2 ?    8.2   1.1    0.0032       3.9       4      16 ..      79      91 ..      73     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  + C +Cg C+ +CP+g
  gi|15669055|ref|NP_247859.1| 34 KACYQCGTCTGSCPSG 49
                                  5799**********75 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0032
                        Fer4_4  4 CigCgsCvaaCPq 16
                                  C+ C  C+  CP 
  gi|15669055|ref|NP_247859.1| 79 CTTCYTCYERCPR 91
                                  ***********94 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.9     0.036        43      15      39 ..      27      49 ..      11      63 .. 0.77
   2 ?   12.5   0.5     8e-05     0.096      24      60 ..      79     113 ..      55     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.036
                                  HHHHHHHTT----TT-HHHHCSTT- CS
                       Fer4_20 15 eealeeAsRClqCkkapcvkgCPve 39
                                  e++++  + C+qC   +c+ +CP  
  gi|15669055|ref|NP_247859.1| 27 EDIVKSIKACYQC--GTCTGSCPSG 49
                                  5667777889999..7899999975 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8e-05
                                   ----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHH CS
                       Fer4_20  24 ClqCkkapcvkgCPveidipefikkiaegnleeaaki 60 
                                   C +C   +c + CP +++i e ik++++   ++    
  gi|15669055|ref|NP_247859.1|  79 CTTC--YTCYERCPRDVKITEIIKTLRNIAAQKGNMA 113
                                   8888..78****************9988766655444 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.6     0.012        14       1      14 [.      36      49 ..      36      49 .. 0.95
   2 ?   11.3   3.2   0.00047      0.56       1      14 [.      79      92 ..      79      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C +Cg+C  +CP+g
  gi|15669055|ref|NP_247859.1| 36 CYQCGTCTGSCPSG 49
                                  99**********97 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00047
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  Ct C++C e CP +
  gi|15669055|ref|NP_247859.1| 79 CTTCYTCYERCPRD 92
                                  ************76 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   5.6      0.08        96       2      14 ..      36      48 ..      35      63 .. 0.84
   2 ?    7.5   0.2     0.006       7.2      60      95 ..      57      92 ..      49      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.08
                       Fer4_22  2 ClsCgaCtlvCpt 14
                                  C +Cg+Ct  Cp+
  gi|15669055|ref|NP_247859.1| 36 CYQCGTCTGSCPS 48
                                  99*********97 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.006
                       Fer4_22 60 erlrqrllhklsefkekfgesgCvGCgRCieacpvk 95
                                  +++ +++l  l ++ ++ +   C+ C  C e+cp +
  gi|15669055|ref|NP_247859.1| 57 RKVLRKVLLGLDDVLDSDDIWYCTTCYTCYERCPRD 92
                                  4455566667778888889999***********976 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.5     0.039        46      55      74 ..      30      49 ..      10      52 .. 0.82
   2 ?    7.8   0.9     0.003       3.6      56      79 ..      74      97 ..      50     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.039
                       Fer4_18 55 ekgagdcidcescvkvcPtg 74
                                   k+   c +c++c   cP g
  gi|15669055|ref|NP_247859.1| 30 VKSIKACYQCGTCTGSCPSG 49
                                  56677899999999999976 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.003
                       Fer4_18 56 kgagdcidcescvkvcPtgidirk 79
                                  ++   c++c +c + cP ++ i +
  gi|15669055|ref|NP_247859.1| 74 DDIWYCTTCYTCYERCPRDVKITE 97
                                  55567**************99976 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.1    0.0072       8.6       8      22 ..      35      49 ..      32      53 .. 0.88
   2 ?    6.0   2.6     0.011        13       9      20 ..      79      90 ..      78      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0072
                        Fer4_6  8 kCigCgdCvrvCPeg 22
                                  +C +Cg C+  CP g
  gi|15669055|ref|NP_247859.1| 35 ACYQCGTCTGSCPSG 49
                                  6889*********86 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
                        Fer4_6  9 CigCgdCvrvCP 20
                                  C+ C+ C+  CP
  gi|15669055|ref|NP_247859.1| 79 CTTCYTCYERCP 90
                                  999********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1182.06
//
Query:       gi|15669056|ref|NP_247860.1|  [L=449]
Description: hypothetical protein MJ_0865 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.6e-28   97.8   0.8    2.8e-27   96.1   0.1    2.1  3  Radical_SAM  Radical SAM superfamily
      3e-10   40.2   0.1      6e-09   36.0   0.0    2.6  2  B12-binding  B12 binding domain
  ------ inclusion threshold ------
      0.035   14.1   0.0        0.1   12.7   0.0    1.8  2  UPF0004      Uncharacterized protein family UPF0004
       0.13   12.1   0.1       0.44   10.4   0.1    1.9  1  DUF1450      Protein of unknown function (DUF1450)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.2   5.6e+03     125     144 ..      68      87 ..      60      97 .. 0.72
   2 ?   -0.9   0.1      0.41   1.8e+03      45      64 ..     104     123 ..      68     161 .. 0.59
   3 !   96.1   0.1   6.2e-31   2.8e-27       2     166 ..     172     340 ..     171     341 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                                   SHHHHHHHHHHHHHHTTSET CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 125 htfeevlealeklreagikr 144
                                   +++ e ++ ++k r++  k+
  gi|15669056|ref|NP_247860.1|  68 KNIREAIDFIKKVRKNKTKV 87 
                                   46677788888888887774 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.41
                                   TTSEEEEEESSTGGGSTTHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  45 kgvkevilgggepllypdfv 64 
                                    +v++vi+g ge +  + ++
  gi|15669056|ref|NP_247860.1| 104 LNVDGVIVGEGEITTPKIIE 123
                                   23566666666666654444 PP

  == domain 3  score: 96.1 bits;  conditional E-value: 6.2e-31
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS........TTHHHHHHHHHHTC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly........pdfvellerlakla 74 
                                   ++ rgC ++C+fC++p+    +++ rs++ve+++eevk++ ++ g+k + ++gg+ +ly        ++f elle+ ++  
  gi|15669056|ref|NP_247860.1| 172 ETHRGCLGNCTFCQVPKF--FGKTIRSRDVEDVVEEVKAF-KRAGAKRIAISGGTGSLYafkksinrDKFFELLEKVSEV- 248
                                   6789*************8..********************.7**********************9988888888888886. PP

                                   CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                   xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  75 vpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                       ++ ++++ +++d   ee+le+++++ + +v  g+e+++d+ +lk m++g ++e+ l+a++++++ g+k+  ++iv  
  gi|15669056|ref|NP_247860.1| 249 --IGKNNLSVPDMRVDyvdEEILEAIKNYTIGWVFYGIESGSDK-ILKDMKKGTNREKNLDAIKLAKDCGVKVAGSFIVAY 326
                                   ..******************************************.************************************ PP

                                   TTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxx RF
                   Radical_SAM 153 pGendeeleellel 166
                                   p e++ ++  + ++
  gi|15669056|ref|NP_247860.1| 327 PTETEMDYLLTKDF 340
                                   *****998877776 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   1.3e-12     6e-09       4     120 ..      11     121 ..       8     122 .. 0.80
   2 ?    1.0   0.0     0.094   4.2e+02      40      74 ..     199     235 ..     180     249 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.3e-12
                   B12-binding   4 llatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel....lkrirp 80 
                                    ++ +  +++++G++++ ++l+++g++V+l+       + +++   +k dv+ +S+++t ++   k++ e+    +k +++
  gi|15669056|ref|NP_247860.1|  11 RITIYSPEVYTYGAMLIGGILKHKGYNVHLV-------RKIDKTLFLKSDVIIFSLYSTLHI-LDKNIREAidfiKKVRKN 83 
                                   566677899*******************998.......4566788899********655554.444444445556555566 PP

                   B12-binding  81 rvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                   ++kv v G  +s++pe +l++ l +d v+vgege + + +
  gi|15669056|ref|NP_247860.1|  84 KTKVYVAG-CVSTYPEIILNE-LNVDGVIVGEGEITTPKI 121
                                   9*******.58********99.************998876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.094
                   B12-binding  40 nedivaairae.kpdv..vglSalltsqleavkelvel 74 
                                   +ed+v++++a+ ++ +  +++S   t +l a+k+ +++
  gi|15669056|ref|NP_247860.1| 199 VEDVVEEVKAFkRAGAkrIAISG-GTGSLYAFKKSINR 235
                                   39999999999666668899998.88888888877776 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.3e-05       0.1      36      92 ..      51     106 ..      21     112 .. 0.64
   2 ?   -3.0   0.0       1.7   7.8e+03      47      76 ..     194     221 ..     193     228 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                                   --SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHHHS-HHHHHHH-TT CS
                       UPF0004  36 eAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCmaqrekeellkeepe 92 
                                   ++dv+++   +  +  +k++++a+  +k+ +k+++kv+v+GC++  ++e +l+e ++
  gi|15669056|ref|NP_247860.1|  51 KSDVIIFSLYSTLHILDKNIREAIDFIKKVRKNKTKVYVAGCVST-YPEIILNELNV 106
                                   56666655444444555666666666666666679*******975.66666666664 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                                   SSSSHHHHTHHHHHHHHTTST.--EEEEEE CS
                       UPF0004  47 vrekaekkviqalrelkalkkpekkvvvlG 76 
                                   +r++  ++v+++++++k++    k++++ G
  gi|15669056|ref|NP_247860.1| 194 IRSRDVEDVVEEVKAFKRAG--AKRIAISG 221
                                   55666778888888888877..46666666 PP

>> DUF1450  Protein of unknown function (DUF1450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   9.8e-05      0.44      34      70 ..     175     208 ..     159     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.8e-05
                       DUF1450  34 ygClsnCglCakspfAlVnGeivaaetpeellekiyk 70 
                                    gCl+nC+ C+  +f    G+++++++ e+++e++++
  gi|15669056|ref|NP_247860.1| 175 RGCLGNCTFCQVPKFF---GKTIRSRDVEDVVEEVKA 208
                                   59**********9995...9**********9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2762.19
//
Query:       gi|15669057|ref|NP_247861.1|  [L=129]
Description: HIT family protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-33  113.2   0.1    8.9e-33  112.9   0.1    1.1  1  HIT       HIT domain
    8.4e-17   61.7   0.1      1e-16   61.4   0.1    1.1  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   0.1   9.9e-37   8.9e-33       2      97 ..      10     104 ..       9     105 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 9.9e-37
                                   GCC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT CS
                           HIT   2 keipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahag 82 
                                   +eip++vvyed++vlafldi+p+ +gh+Lv+pkkh++++++++++el+++++ vkk +++l+k +  +g+++v nng+ ag
  gi|15669057|ref|NP_247861.1|  10 GEIPAKVVYEDEHVLAFLDINPRNKGHTLVVPKKHYERFDEMPDDELCNFIKGVKKTVEVLKK-LGFDGYNIVNNNGRVAG 89 
                                   79************************************************************8.999************** PP

                                   -SSSS-EEEEEEC-T CS
                           HIT  83 qsvahlHiHviprre 97 
                                   q+v+h+H+H+ipr+e
  gi|15669057|ref|NP_247861.1|  90 QEVNHVHFHIIPRYE 104
                                   *************97 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.1   1.1e-20     1e-16       2     104 ..       2     103 ..       1     112 [. 0.90

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 1.1e-20
                                   -HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEEEE CS
                        DcpS_C   2 wvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdaeel 82 
                                   ++f+++++g++p++vvyede+++++ Di+p++k h lv+pk++ +   ++ +++l    + ++k  +v+++    ++    
  gi|15669057|ref|NP_247861.1|   2 CIFCKIINGEIPAKVVYEDEHVLAFLDINPRNKGHTLVVPKKHYERFDEMPDDELCNFIKGVKKTVEVLKKLGFDGYNIVN 82 
                                   9*************************************************877777777777888889999888999999* PP

                                   --SCCCT--S-S--EEEEE... CS
                        DcpS_C  83 rvgvhyqPsvyhlHlHvisldf 104
                                   + g  + + v+h+H+H+i  ++
  gi|15669057|ref|NP_247861.1|  83 NNGRVAGQEVNHVHFHIIP-RY 103
                                   *****************96.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 822.64
//
Query:       gi|15669058|ref|NP_247862.1|  [L=427]
Description: hypothetical protein MJ_0867 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-24   85.5   1.6    7.2e-24   85.0   0.5    1.8  2  Radical_SAM      Radical SAM superfamily
    4.8e-22   77.8   0.6    1.2e-21   76.6   0.3    1.8  2  UPF0004          Uncharacterized protein family UPF0004
    2.2e-07   30.7   1.2      5e-07   29.6   1.2    1.7  1  TRAM             TRAM domain
     0.0025   17.9   0.2      0.027   14.6   0.2    2.5  1  TRAM_2           TRAM domain
  ------ inclusion threshold ------
      0.059   13.6   0.3       0.26   11.5   0.1    2.2  2  UPF0180          Uncharacterised protein family (UPF0180)
      0.078   11.6   0.0       0.11   11.0   0.0    1.1  1  Pectate_lyase_2  Periplasmic pectate lyase
      0.081   13.0   0.1       0.33   11.0   0.1    2.1  1  Phg_2220_C       Conserved phage C-terminus (Phg_2220_C)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.4   3.6e+03      27      27 ..      60      60 ..      22     130 .. 0.63
   2 !   85.0   0.5   2.8e-27   7.2e-24       3     166 ..     151     320 ..     149     321 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                                  H CS
                                  x RF
                   Radical_SAM 27 r 27
                                  r
  gi|15669058|ref|NP_247862.1| 60 R 60
                                  1 PP

  == domain 2  score: 85.0 bits;  conditional E-value: 2.8e-27
                                   EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....TTHHHHHHHHHHTCCCTE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.....pdfvellerlaklavpgi 78 
                                   + +gC ++Cs+C+++     +g   s + e+i++++kel  +kg+k ++++ ++   y     ++++ ll +l +++  ++
  gi|15669058|ref|NP_247862.1| 151 ICEGCIGNCSYCIVKI---ARGGLISYPREKIVNKAKEL-INKGAKCLLITAQDTACYgfdigDNLANLLNELTQIK-GEF 226
                                   678************8...8*******************.8****************99999988888888888886.444 PP

                                   EEEEEECSSCHG....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET...EEEEEEE CS
                                   xxxxxxxxxxxx....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                   Radical_SAM  79 ritvetngtlpd....eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr...vvdrivg 151
                                    ++v   + +      +e +e   +      ++l+l+++dde +lk+m+rg+t++e+++ +  +r++ ik+   ++d+ivg
  gi|15669058|ref|NP_247862.1| 227 IMRVGMMHAKNAelilDELIEVYQNEKvGKFLHLPLQSGDDE-ILKRMKRGYTVDEFKDIVNEFRRK-IKNlcfTTDIIVG 305
                                   444444444433555599999999988***************.************************.************* PP

                                   BTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxx RF
                   Radical_SAM 152 lpGendeeleellel 166
                                   +pGe++e+++++le 
  gi|15669058|ref|NP_247862.1| 306 FPGETEEQFQNTLEV 320
                                   ************985 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.3   4.6e-25   1.2e-21       1      87 [.      13      96 ..      13     101 .. 0.96
   2 ?   -3.5   0.0       4.4   1.1e+04      59      89 ..     216     244 ..     211     248 .. 0.65

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 4.6e-25
                                  XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHHHS-H CS
                       UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCmaqrek 83
                                  +v++e +GC  N++d+e++ ++Lkk+g+e+v++ eeAd+ ++nTC vr ++e+++i +++elk+l    k+vvv+GC++++ k
  gi|15669058|ref|NP_247862.1| 13 RVYVEGYGCVLNTADTEIIKNSLKKHGFEVVNNLEEADIAIINTCVVRLETENRMIYRINELKNLG---KEVVVAGCLPKALK 92
                                  79**************************************************************99...89*********999 PP

                                  HHHH CS
                       UPF0004 84 eell 87
                                  ++++
  gi|15669058|ref|NP_247862.1| 93 NKVK 96
                                  8875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.4
                                   HHHHHTTST.--EEEEEEHHHHS-HHHHHHH CS
                       UPF0004  59 lrelkalkkpekkvvvlGCmaqrekeellke 89 
                                   l+el + k  ++ ++ +G m  ++ e +l+e
  gi|15669058|ref|NP_247862.1| 216 LNELTQIK--GEFIMRVGMMHAKNAELILDE 244
                                   55666666..567778887777777766665 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   1.2     2e-10     5e-07       1      62 []     373     426 ..     373     426 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2e-10
                                   XXXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                          TRAM   1 rsyvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                   ++y+G+ + Vlv +++ +     G+tdn kvv ++g++   G+f +VkIt++k + L+Gel+
  gi|15669058|ref|NP_247862.1| 373 KKYIGKAMKVLVLDEG-K-----GYTDNFKVVKFEGGEV--GEFRKVKITDAKTFGLKGELI 426
                                   689999********99.6.....*************999..******************985 PP

>> TRAM_2  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   1.1e-05     0.027      33      64 .]     399     426 ..     376     426 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                   EEES---T....T-EEEEEEEEEETTEEEEEE- CS
                        TRAM_2  33 yvtgaeklsk.vGdfvkvkItdadeyDLiGevv 64 
                                    ++g     + vG+f kvkItda+ + L Ge++
  gi|15669058|ref|NP_247862.1| 399 KFEG-----GeVGEFRKVKITDAKTFGLKGELI 426
                                   3332.....137*******************98 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0001      0.26      12      53 ..      31      75 ..      27      90 .. 0.76
   2 ?   -3.1   0.0       3.5     9e+03      18      27 ..     274     283 ..     273     289 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                       UPF0180 12 vkeaLrekGYeVvdleteedaqsvdaiVv..tGqdtnvmgied.t 53
                                  +k+ L++ G+eVv+  +e+d   ++ +Vv  + +++ +  i++ +
  gi|15669058|ref|NP_247862.1| 31 IKNSLKKHGFEVVNNLEEADIAIINTCVVrlETENRMIYRINElK 75
                                  89***********98889999999999995544555555666544 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.5
                       UPF0180  18 ekGYeVvdle 27 
                                   ++GY+V +++
  gi|15669058|ref|NP_247862.1| 274 KRGYTVDEFK 283
                                   5777776655 PP

>> Pectate_lyase_2  Periplasmic pectate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.4e-05      0.11     414     481 ..     213     281 ..     194     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.4e-05
               Pectate_lyase_2 414 aqglgelgsapgkdv.kvdlatknndpyalfalldlyqaskvkdylslaekvgdnmistrykngffmae 481
                                   a+ l el    g+ + +v +   +n    l  l+++yq  kv  +l l  + gd+ i  r k g+ + e
  gi|15669058|ref|NP_247862.1| 213 ANLLNELTQIKGEFImRVGMMHAKNAELILDELIEVYQNEKVGKFLHLPLQSGDDEILKRMKRGYTVDE 281
                                   55677777777775427888888999999***********************************98876 PP

>> Phg_2220_C  Conserved phage C-terminus (Phg_2220_C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00013      0.33       6      43 ..     251     288 ..     246     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                    Phg_2220_C   6 NekagkkfkaeskktkklIkarlkegytvedlkkVidl 43 
                                   Nek gk  +   ++  + I +r+k+gytv+++k++++ 
  gi|15669058|ref|NP_247862.1| 251 NEKVGKFLHLPLQSGDDEILKRMKRGYTVDEFKDIVNE 288
                                   777777777778888999*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1243  (0.069329); expected 358.6 (0.02)
Passed bias filter:                      824  (0.0459591); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 2675.08
//
Query:       gi|15669059|ref|NP_247863.1|  [L=127]
Description: inosine-5'-monophosphate dehydrogenase GuaB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-27   95.0   3.1    1.6e-14   54.1   0.0    2.1  2  CBS              CBS domain
     0.0095   15.5   0.1      0.012   15.2   0.1    1.2  1  CobU             Cobinamide kinase / cobinamide phosphate gua
  ------ inclusion threshold ------
      0.081   13.2   0.1         17    5.8   0.0    2.2  2  SMC_hinge        SMC proteins Flexible Hinge Domain
       0.09   12.2   0.0      0.094   12.1   0.0    1.2  1  Put_Phosphatase  Putative Phosphatase
      0.093   12.8   0.0       0.17   12.0   0.0    1.4  1  UPF0270          Uncharacterised protein family (UPF0270)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.9   4.1e-14   1.5e-10       1      54 [.       7      59 ..       7      62 .. 0.91
   2 !   54.1   0.0   4.4e-18   1.6e-14       2      55 ..      68     122 ..      67     124 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 4.1e-14
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTB.EEEEEEHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgk.lvGivtlrDllra 54
                                  V+d+m + vv v+ dt l++++++m+++++s++ VV +dg+ + Gi+t++D+l+ 
  gi|15669059|ref|NP_247863.1|  7 VRDVMKKGVVEVTLDTKLSDVIKTMAKYDISSV-VV-SDGEtFWGIITDTDVLKH 59
                                  89***********************9999****.99.5554399*********86 PP

  == domain 2  score: 54.1 bits;  conditional E-value: 4.4e-18
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEE.EETTTBEEEEEEHHHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPV.VdedgklvGivtlrDllral 55 
                                   ++imt++++tv+p+++le+a+e+m+ekg+++l+V  + ++k+vG+++ +D++++ 
  gi|15669059|ref|NP_247863.1|  68 EEIMTTNPITVSPEAPLEKAVEIMAEKGIHHLYVkSPCEDKIVGVLSSKDIIKLF 122
                                   79******************************9977****************976 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   3.4e-06     0.012      86     147 ..       3      67 ..       1      79 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.4e-06
                          CobU  86 tnllleeeaek..veekleeeveellealkelkatvvlVsn.EvglgvvpenalgrlfrdllGrl 147
                                   +++l+++  +k  ve +l+++++++++++++ + + v+Vs+ E+ +g++ ++ + +++ dl  ++
  gi|15669059|ref|NP_247863.1|   3 SKYLVRDVMKKgvVEVTLDTKLSDVIKTMAKYDISSVVVSDgETFWGIITDTDVLKHYNDLDKTA 67 
                                   55555555444668899**********************987*****************986555 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0047        17      13      45 ..      19      51 ..      15      69 .. 0.86
   2 ?    5.7   0.0    0.0049        17      13      38 ..      79     104 ..      76     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0047
                     SMC_hinge 13 evdegyekAveaalgnrlqalvvedeetakkii 45
                                  ++d +    + + +  +++++vv+d et + ii
  gi|15669059|ref|NP_247863.1| 19 TLDTKLSDVIKTMAKYDISSVVVSDGETFWGII 51
                                  5678888999******************99998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0049
                     SMC_hinge  13 evdegyekAveaalgnrlqalvvede 38 
                                   +++   ekAve+ +++ +++l v+++
  gi|15669059|ref|NP_247863.1|  79 SPEAPLEKAVEIMAEKGIHHLYVKSP 104
                                   5666789****************997 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.6e-05     0.094      62     127 ..      10      79 ..       3     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
               Put_Phosphatase  62 dikkvlrsiplspglvelikslakkkleldliiiSDaNsff..i..eeileaag.ledlFse.iftNPaavd 127
                                    +kk + +++l+ +l ++ik++ak++  +  +++SD  +f   i    +l++++ l +  +e + tNP +v 
  gi|15669059|ref|NP_247863.1|  10 VMKKGVVEVTLDTKLSDVIKTMAKYD--ISSVVVSDGETFWgiItdTDVLKHYNdLDKTAEEiMTTNPITVS 79 
                                   47888999**************8855..8899******9954333235788876256666663457998775 PP

>> UPF0270  Uncharacterised protein family (UPF0270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.6e-05      0.17      16      49 ..       1      34 [.       1      47 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.6e-05
                                  HHHHHHH--------.---HHHHHHHHHHHHHTT CS
                       UPF0270 16 lieefvlregtDyGeqelsleekveqvkqqLksg 49
                                  +i ++++r++   G  e++l++k ++v + +++ 
  gi|15669059|ref|NP_247863.1|  1 MISKYLVRDVMKKGVVEVTLDTKLSDVIKTMAKY 34
                                  799************************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 797.72
//
Query:       gi|15669060|ref|NP_247864.1|  [L=352]
Description: DNA repair and recombination protein RadA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-83  279.6   0.0    2.6e-83  279.2   0.0    1.1  1  Rad51            Rad51
    3.3e-15   56.4   0.4    8.5e-15   55.1   0.4    1.7  1  HHH_5            Helix-hairpin-helix domain
    2.1e-11   43.8   0.5    1.8e-10   40.7   0.5    2.0  1  RecA             recA bacterial DNA recombination protein
    1.3e-09   37.7   0.4    2.7e-08   33.5   0.4    2.3  1  ATPase           KaiC
    3.8e-09   36.0   0.8     0.0002   21.1   0.0    2.5  2  HHH              Helix-hairpin-helix motif
      3e-07   30.2   0.0      1e-06   28.5   0.0    1.8  2  AAA_25           AAA domain
      1e-05   25.5   0.1    3.3e-05   23.9   0.0    1.9  2  HHH_2            Helix-hairpin-helix motif
    3.5e-05   24.0   0.1      0.063   13.5   0.0    2.4  2  HHH_3            Helix-hairpin-helix motif
     0.0005   20.4   0.2       0.31   11.4   0.0    2.9  3  HHH_8            Helix-hairpin-helix domain
      0.002   17.9   0.0      0.025   14.4   0.0    2.5  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0025   18.0   0.0      0.015   15.5   0.0    2.2  2  Cdd1             Pathogenicity locus
     0.0099   15.6   0.0       0.02   14.6   0.0    1.5  1  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.018   15.2   0.0    1.5  1  AAA_33           AAA domain
      0.013   15.8   0.2       0.15   12.5   0.0    2.8  3  IMS_HHH          IMS family HHH motif
      0.015   15.8   0.1       0.41   11.1   0.0    3.0  3  BAF              Barrier to autointegration factor
      0.052   13.1   0.0       0.51    9.9   0.0    2.4  2  CobU             Cobinamide kinase / cobinamide phosphate gua
       0.06   12.5   0.2       0.21   10.7   0.1    1.7  2  PAXNEB           PAXNEB protein
       0.15   12.7   0.3         13    6.5   0.0    2.7  3  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.2   0.0   2.6e-86   2.6e-83       1     254 [.      93     352 .]      93     352 .] 0.93

  Alignments for each domain:
  == domain 1  score: 279.2 bits;  conditional E-value: 2.6e-86
                                   -S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS-.........-SS CS
                         Rad51   1 lgfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgG.........geg 72 
                                   lgf s++e+l++r+++ +l+tGsk+lDe+LgGG+e++s+te  G f+sGktq++h+ cv  q p  +            e 
  gi|15669060|ref|NP_247864.1|  93 LGFKSGTEVLSQRKNIWKLSTGSKNLDEILGGGLESQSVTEFAGMFGSGKTQIAHQACVNLQCPERIVAddaikdeilNEP 173
                                   599************************************************************976543112222222578 PP

                                   EEEEEESSS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHH.S-EEEEEEETTTGGGCH----- CS
                         Rad51  73 kavyidtegtfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaallae.dkfallivDsvtalyRtdfsgr 152
                                   kavyidtegtfrper+v++ae  +ld++evl+n+ +aRay+++ q+   +++ +l+ e ++++l+ivDs+t+++Rt++ gr
  gi|15669060|ref|NP_247864.1| 174 KAVYIDTEGTFRPERIVQMAEALGLDGNEVLNNIFVARAYNSDMQMLYAENVENLIREgHNIKLVIVDSLTSTFRTEYIGR 254
                                   9*********************************************9999999999873689******************* PP

                                   --THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEE CS
                         Rad51 153 gelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvv 233
                                   g+la+Rqqklg+++ tL+klad ++  v++tnqv a++d+      + +++ igG++++ha+t R+ lrk kg++R++k++
  gi|15669060|ref|NP_247864.1| 255 GKLAERQQKLGRHMATLNKLADIYNCVVIVTNQVAARPDA----LFGPSEQAIGGHIVGHAATFRIFLRKAKGDKRVAKLY 331
                                   ****************************************....55677889***************************** PP

                                   S-SSS-S-EEEEEEETTEEE- CS
                         Rad51 234 dsPnlpeleavfaigeeGied 254
                                   dsP+lp++ea+f i+e+Gi+d
  gi|15669060|ref|NP_247864.1| 332 DSPHLPDAEAMFRITEKGIHD 352
                                   *******************87 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.4   8.6e-18   8.5e-15       2      57 .]      34      89 ..      33      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 8.6e-18
                                  HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                         HHH_5  2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                  ++L++++G+Gp tA +l +aG++ + ++a a++ eL++i Gi++k A rii+++++
  gi|15669060|ref|NP_247864.1| 34 DDLTQLPGVGPTTAEKLKEAGYTDFMKIATASIGELTEIDGISEKAAARIIEAARE 89
                                  69****************************************************96 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.5   1.8e-13   1.8e-10      27     224 ..     104     323 ..      84     332 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.8e-13
                                   .-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH...........H....TT--EEEEESS-- CS
                          RecA  27 eklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq...........k....kggvaafidaeha 92 
                                   +++++  +s+Gs  ld  lG GGl    ++e  G   sGkt +a +a ++ q           k    +   a++id+e +
  gi|15669060|ref|NP_247864.1| 104 QRKNIWKLSTGSKNLDEILG-GGLESQSVTEFAGMFGSGKTQIAHQACVNLQcperivaddaiKdeilNEPKAVYIDTEGT 183
                                   4578999*************.***********************998887772222222111111111234578******* PP

                                   --H....HHHHHTT--....GGG-EEE--SSHH.HHH..HHHHHHHTTT.--SEEEEE-TTT---STT-.----------H CS
                          RecA  93 ldp....kyakklGvd....idellvsqpdtGe.qal..eiadalvrsg.aidlivvdsvaalvpkaei.eGemgdskvgl 160
                                   + p    + a++lG+d    +++++v++  + + q l  e ++ l+r g  i l++vds+++      i  G++++ +  l
  gi|15669060|ref|NP_247864.1| 184 FRPerivQMAEALGLDgnevLNNIFVARAYNSDmQMLyaENVENLIREGhNIKLVIVDSLTSTFRTEYIgRGKLAERQQKL 264
                                   *9843335799****955545677899887665244444778999998747********9986655555235555555443 PP

                                   HHHHHHHHHHHHHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES- CS
                          RecA 161 qarlmsqalrkltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrriee 224
                                     r m+ +l kl    +  n+vvi  nq+  +   +fg  e + GG+ +   a+ r+ +r+++ 
  gi|15669060|ref|NP_247864.1| 265 -GRHMA-TLNKL---ADIYNCVVIVTNQVAARPDALFGPSEQAIGGHIVGHAATFRIFLRKAKG 323
                                   .34443.35555...56679****************************************9875 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.4   2.7e-11   2.7e-08       2     205 ..     112     330 ..     111     351 .. 0.66

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.7e-11
                        ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlik...............gaekygepgvfvtveepa..edlre 65 
                                   +tg + lDeil gG+ +++v+  +G  G+GKt +a q  ++                + + + + v++ +e +   e + +
  gi|15669060|ref|NP_247864.1| 112 STGSKNLDEILGGGLESQSVTEFAGMFGSGKTQIAHQACVNlqcperivaddaikdEILN-EPKAVYIDTEGTFrpERIVQ 191
                                   7999*****************************999977763111111111111111222.34566666666534466777 PP

                        ATPase  66 nakslGwdlekleeegklaiidasesaeesaeekdkedleel.ieelaeaike.ikakrvviDsitgl.aye........e 135
                                    a++lG d +++ ++  +++  a++s+ +            l +e++++ i+e  ++k v++Ds+t+   +e        e
  gi|15669060|ref|NP_247864.1| 192 MAEALGLDGNEVLNN--IFVARAYNSDMQ-----------MLyAENVENLIREgHNIKLVIVDSLTSTfRTEyigrgklaE 259
                                   777777777776666..666555555544...........33145566666662455888888888764322222222226 PP

                        ATPase 136 keavaReilrqlvrvlkklgvTailvsekss........seeaaggygveefivdgvivLdlkeieeelvRtleivkm 205
                                   +++++ + + +l +    ++++ i ++++          se+a+gg+ v + +++  i L++ + ++++       k+
  gi|15669060|ref|NP_247864.1| 260 RQQKLGRHMATLNKLADIYNCVVIVTNQVAArpdalfgpSEQAIGGHIVGH-AATFRIFLRKAKGDKRV------AKL 330
                                   788889999999999999**********99999******99**********.99999999977766643......444 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0     2e-07    0.0002      11      28 ..      34      51 ..      33      53 .. 0.89
   2 !   13.1   0.2   6.9e-05     0.068       5      29 ..      61      85 ..      58      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2e-07
                                  HHHHTSTT-SHHHHHHHH CS
                           HHH 11 eeLlalPGVGpktAeaIl 28
                                  ++L++lPGVGp tAe+  
  gi|15669060|ref|NP_247864.1| 34 DDLTQLPGVGPTTAEKLK 51
                                  9**************976 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.9e-05
                                  HHTSSHHHHHTSTT-SHHHHHHHHH CS
                           HHH  5 lipasreeLlalPGVGpktAeaIls 29
                                  + +as+ eL+++ G+ +k A +I++
  gi|15669060|ref|NP_247864.1| 61 IATASIGELTEIDGISEKAAARIIE 85
                                  789********************87 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.1   2.1e+03     158     176 ..      73      91 ..      66      94 .. 0.79
   2 !   28.5   0.0     1e-09     1e-06      21     189 ..     117     288 ..     103     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.1
                        AAA_25 158 densnsdvgalvealeria 176
                                   d  s++++++++ea+++++
  gi|15669060|ref|NP_247864.1|  73 DGISEKAAARIIEAARELC 91 
                                   55578899999**999998 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 1e-09
                        AAA_25  21 prrwlvkgllpagelallaGapgtGKttlaldlalava.....tGkpwlg.......pvapeqgkVlyvsaEdsedelrrR 89 
                                    ++ +++g l  ++++ +aG  g+GKt +a + ++ +                    ++     k +y+++E++    ++R
  gi|15669060|ref|NP_247864.1| 117 NLDEILGGGLESQSVTEFAGMFGSGKTQIAHQACVNLQcperiV-----AddaikdeIL--NEPKAVYIDTEGTF--RPER 188
                                   5677888888999**********************998643331.....2366545433..899**********8..799* PP

                        AAA_25  90 lravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg.....densnsd. 164
                                   + ++ eal +d+++ + ++  +   +  +  ++++ l    +++e+ i+e ++++lv++D+l+++++      ++ ++++ 
  gi|15669060|ref|NP_247864.1| 189 IVQMAEALGLDGNEVLNNI--F-VARA-Y-NSDMQMLY--AENVENLIREGHNIKLVIVDSLTSTFRTeyigrGKLAERQq 262
                                   ********88888877764..1.1111.2.23334432..3567888888899***********99986665544444443 PP

                        AAA_25 165 .vgalvealeriarrtgaavllvhHv 189
                                     g+ ++ l+++a+ +++ v+++ +v
  gi|15669060|ref|NP_247864.1| 263 kLGRHMATLNKLADIYNCVVIVTNQV 288
                                   36*******************99876 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.3e-08   3.3e-05       9      54 ..      40      86 ..      35      92 .. 0.93
   2 ?   -2.8   0.0       7.2   7.2e+03      26      38 ..     217     229 ..     209     250 .. 0.55

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.3e-08
                         HHH_2  9 rhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsivef 54
                                  + VG +tA++L ++ + ++ ++++as+ eL+e+d+i e+ A+ i+e 
  gi|15669060|ref|NP_247864.1| 40 PGVGPTTAEKLKEAgYTDFMKIATASIGELTEIDGISEKAAARIIEA 86
                                  89*********9866*****************************985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.2
                         HHH_2  26 ldaLkkasleeLl 38 
                                   ++ L + ++e+L+
  gi|15669060|ref|NP_247864.1| 217 MQMLYAENVENLI 229
                                   5555555555554 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0038       3.8      14      30 ..      34      50 ..      30      53 .. 0.74
   2 !   13.5   0.0   6.4e-05     0.063       8      33 ..      61      86 ..      58     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0038
                         HHH_3 14 eeLqklpGlgpklAknI 30
                                  ++L++lpG+gp++A+++
  gi|15669060|ref|NP_247864.1| 34 DDLTQLPGVGPTTAEKL 50
                                  67888888888888875 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6.4e-05
                         HHH_3  8 iNtAsaeeLqklpGlgpklAknIvay 33
                                  i tAs  eL+ + G+++k A +I+++
  gi|15669060|ref|NP_247864.1| 61 IATASIGELTEIDGISEKAAARIIEA 86
                                  67*********************985 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00031      0.31      46      65 ..      34      52 ..      19      53 .. 0.77
   2 ?    5.5   0.1     0.022        22      44      66 ..      63      86 ..      57      88 .. 0.78
   3 ?   -2.5   0.0         7     7e+03      11      29 ..     192     214 ..     188     215 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                                  TTHCTTSTT--HHHHHHHHH CS
                         HHH_8 46 eeeltklpgiGkkiaakiee 65
                                  ++ lt+lpg+G+ +a+k++e
  gi|15669060|ref|NP_247864.1| 34 DD-LTQLPGVGPTTAEKLKE 52
                                  44.**************998 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.022
                                  HH.TTHCTTSTT--HHHHHHHHHH CS
                         HHH_8 44 sl.eeeltklpgiGkkiaakieei 66
                                  ++  +elt+++gi +k aa+i e 
  gi|15669060|ref|NP_247864.1| 63 TAsIGELTEIDGISEKAAARIIEA 86
                                  433335***************996 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 7
                                   HHHHHHHCT....--CCCHHHHH CS
                         HHH_8  11 ladllelkg....edpfrvraYr 29 
                                   +a+ l l g    ++ f +raY 
  gi|15669060|ref|NP_247864.1| 192 MAEALGLDGnevlNNIFVARAYN 214
                                   55555555555558889999995 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.5e-05     0.025       3      30 ..      36      63 ..      35      81 .. 0.84
   2 ?    0.2   0.0      0.67   6.7e+02      13      30 ..      86     103 ..      83     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
               DNA_pol_lambd_f  3 FtkvyGVGpktAkkwyakGirtledlra 30
                                  +t+  GVGp+tA+k+ ++G++++  + +
  gi|15669060|ref|NP_247864.1| 36 LTQLPGVGPTTAEKLKEAGYTDFMKIAT 63
                                  56778*****************998877 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.67
               DNA_pol_lambd_f  13 tAkkwyakGirtledlra 30 
                                   +A+++ + G+++  +++ 
  gi|15669060|ref|NP_247864.1|  86 AARELCNLGFKSGTEVLS 103
                                   79*********9888877 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.5e-05     0.015       5      39 ..      33      67 ..      31      81 .. 0.87
   2 ?   -0.8   0.0       1.9   1.9e+03      18      33 ..      86     101 ..      64     107 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                          Cdd1  5 lkelqdiPniGkalaedlvelGirsveelkgedpe 39
                                  +++l+++P++G+ +ae+l e G++++ +++  +  
  gi|15669060|ref|NP_247864.1| 33 MDDLTQLPGVGPTTAEKLKEAGYTDFMKIATASIG 67
                                  579*********************99998877655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.9
                          Cdd1  18 laedlvelGirsveel 33 
                                    a++l +lG++s +e+
  gi|15669060|ref|NP_247864.1|  86 AARELCNLGFKSGTEV 101
                                   5778888888887665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.1e-05      0.02       9      91 ..     136     258 ..     134     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                        AAA_24   9 GpsgiGKTtlakel......................gpkplfidtekGlksldadkfpdie.................... 47 
                                   G  g+GKT +a ++                      +pk+++idte+      + +++++                     
  gi|15669060|ref|NP_247864.1| 136 GMFGSGKTQIAHQAcvnlqcperivaddaikdeilnEPKAVYIDTEG---TFRPERIVQMAealgldgnevlnnifvaray 213
                                   77899*******999999*99999999999999999***********...55888888888899***99999999999999 PP

                        AAA_24  48 ..swedfldevvel.aaeladyktlviDtideleelclaevirqnek 91 
                                      +++++ e ve+  +e +++k +++D+++ + +  ++++ r + +
  gi|15669060|ref|NP_247864.1| 214 nsDMQMLYAENVENlIREGHNIKLVIVDSLTSTFR--TEYIGRGKLA 258
                                   999999998888888****************9976..6777666655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.8e-05     0.018       1      63 [.     131     193 ..     131     267 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                        AAA_33   1 lvllvGlpGsGKstlaerllkklg.avllssdtlrr.rlfgtdqqsktdytrvldrlyqilnela 63 
                                   ++++ G+ GsGK++ a++ + +l+  +++  d++++  +  ++++     t+ ++r  +i+ ++a
  gi|15669060|ref|NP_247864.1| 131 VTEFAGMFGSGKTQIAHQACVNLQcPERIVADDAIKdEIL-NEPKAVYIDTEGTFRPERIV-QMA 193
                                   67899*******************9999988888773444.44444444455555555554.444 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015      0.15      12      31 ..      35      54 ..      33      55 .. 0.91
   2 ?   -1.1   0.0         3     3e+03      12      28 ..      68      85 ..      64      87 .. 0.81
   3 ?   -1.9   0.2       5.4   5.4e+03      21      31 ..     255     265 ..     255     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                       IMS_HHH 12 pitkipGiGgklgekLeklG 31
                                  ++t +pG+G+ ++ekL+  G
  gi|15669060|ref|NP_247864.1| 35 DLTQLPGVGPTTAEKLKEAG 54
                                  6899*************988 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3
                       IMS_HHH 12 pitkipGiGgklgek.Le 28
                                  ++t+i Gi  k +++ +e
  gi|15669060|ref|NP_247864.1| 68 ELTEIDGISEKAAARiIE 85
                                  588999*****9999665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.4
                       IMS_HHH  21 gklgekLeklG 31 
                                   gkl+e+ +klG
  gi|15669060|ref|NP_247864.1| 255 GKLAERQQKLG 265
                                   799***99998 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00041      0.41      19      41 ..      35      57 ..      23      64 .. 0.85
   2 ?    0.6   0.0      0.76   7.5e+02      20      36 ..      69      85 ..      65     105 .. 0.60
   3 ?   -2.2   0.0       5.9   5.9e+03       7      23 ..     314     330 ..     311     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00041
                           BAF 19 evtalaGigevlgkkLeekGfdk 41
                                  + t+l+G+g++ ++kL+e+G+  
  gi|15669060|ref|NP_247864.1| 35 DLTQLPGVGPTTAEKLKEAGYTD 57
                                  6799****************975 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.76
                           BAF 20 vtalaGigevlgkkLee 36
                                   t+++Gi+e+ ++++ e
  gi|15669060|ref|NP_247864.1| 69 LTEIDGISEKAAARIIE 85
                                  57788888877665443 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.9
                           BAF   7 hrnFvsepmgdKevtal 23 
                                   +r F+++  gdK v +l
  gi|15669060|ref|NP_247864.1| 314 FRIFLRKAKGDKRVAKL 330
                                   578999999****9987 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.6     6e+02       5      36 ..     136     167 ..     133     172 .. 0.75
   2 ?    9.9   0.0   0.00051      0.51      61     127 ..     223     289 ..     210     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.6
                          CobU   5 GgarSGKSefAeklaeeskekvvYiATaealD 36 
                                   G   SGK ++A + + + + +   +A    +D
  gi|15669060|ref|NP_247864.1| 136 GMFGSGKTQIAHQACVNLQCPERIVADDAIKD 167
                                   6677*********9988777766666655555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00051
                          CobU  61 ldlaealkeeekkevvLvDcltlwl.tnllleeeaekveekleeeveellealkelkatvvlVsnEvg 127
                                   ++++++++e ++ + v+vD+lt    t+++ + + ++ ++kl ++++  l++l++  + vv+V+n v 
  gi|15669060|ref|NP_247864.1| 223 ENVENLIREGHNIKLVIVDSLTSTFrTEYIGRGKLAERQQKLGRHMA-TLNKLADIYNCVVIVTNQVA 289
                                   57888898877789*******97651556666555556666666665.56777888889******996 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00022      0.21      17      34 ..     109     126 ..      98     132 .. 0.84
   2 ?   -1.0   0.0      0.73   7.2e+02     205     255 ..     230     285 ..     188     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                        PAXNEB  17 lltStGtpsLDklLgGGL 34 
                                   +  StG+++LD++LgGGL
  gi|15669060|ref|NP_247864.1| 109 WKLSTGSKNLDEILGGGL 126
                                   568**************9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.73
                        PAXNEB 205 k..knvlRivipsLlspllyd...yppeeskpedllkFLhsLrallrssnlvalit 255
                                      +n+  +++ sL s+  ++     + ++++++l + + +L  l+   n+v+++t
  gi|15669060|ref|NP_247864.1| 230 RegHNIKLVIVDSLTSTFRTEyigRGKLAERQQKLGRHMATLNKLADIYNCVVIVT 285
                                   23356888999999999987766656789999999999999999999999999888 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.095        94      17      34 ..      33      50 ..      27      64 .. 0.86
   2 ?    6.5   0.0     0.013        13       7      44 ..      56      93 ..      51     120 .. 0.80
   3 ?   -2.8   0.0        10   9.9e+03      60      77 ..     257     272 ..     224     284 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.095
                    5_3_exonuc 17 sDnipGvpgiGektAakL 34
                                   D++   pg+G+ tA kL
  gi|15669060|ref|NP_247864.1| 33 MDDLTQLPGVGPTTAEKL 50
                                  5889999********998 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                    5_3_exonuc  7 idlkaLvGDssDnipGvpgiGektAakLlkeygsleei 44
                                  +d++ ++  s  ++  + gi+ek+Aa++++   +l ++
  gi|15669060|ref|NP_247864.1| 56 TDFMKIATASIGELTEIDGISEKAAARIIEAARELCNL 93
                                  6777777777788899**************99988776 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 10
                    5_3_exonuc  60 LeenkeearlskkLatik 77 
                                   L+e   + +l +++at++
  gi|15669060|ref|NP_247864.1| 257 LAER--QQKLGRHMATLN 272
                                   3332..223444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2144.07
//
Query:       gi|15669061|ref|NP_247865.1|  [L=620]
Description: coenzyme F420-reducing hydrogenase subunit beta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-37  128.4   0.2    5.6e-37  127.0   0.2    1.8  1  FrhB_FdhB_C   Coenzyme F420 hydrogenase/dehydrogenase, beta s
    2.1e-36  124.9   0.9    4.3e-36  123.8   0.5    1.8  2  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    1.2e-18   67.0   0.0    2.7e-18   65.9   0.0    1.6  1  FrhB_FdhB_N   Coenzyme F420 hydrogenase/dehydrogenase, beta s
    8.4e-13   48.7  28.3    0.00068   20.2   0.5    4.8  4  Fer4_7        4Fe-4S dicluster domain
    4.2e-12   45.3  57.0    1.6e-07   30.8   5.1    6.2  6  Fer4          4Fe-4S binding domain
    3.8e-11   42.4  37.5    0.00017   21.5   2.7    5.7  5  Fer4_2        4Fe-4S binding domain
    5.2e-11   42.2   0.0    2.2e-10   40.2   0.0    2.2  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
    3.7e-09   36.6  35.2    9.6e-05   22.4  15.0    4.5  5  Fer4_10       4Fe-4S dicluster domain
    1.4e-08   34.4  40.8    2.3e-05   24.3   3.2    5.4  5  Fer4_6        4Fe-4S binding domain
    3.2e-08   34.4  28.6      0.028   15.3   1.3    5.8  4  Fer4_16       4Fe-4S double cluster binding domain
    3.4e-08   33.5  34.0    3.3e-06   27.1  13.1    4.4  4  Fer4_9        4Fe-4S dicluster domain
    7.9e-08   32.6  21.3      0.093   13.2   0.0    5.4  5  Fer4_8        4Fe-4S dicluster domain
    8.3e-08   32.2  34.2     0.0015   18.6   5.7    4.4  4  Fer4_21       4Fe-4S dicluster domain
    2.2e-05   25.2  29.5      0.025   15.4   1.7    5.4  4  Fer4_22       4Fe-4S dicluster domain
     0.0012   19.0  18.6     0.0053   16.9   4.7    3.0  2  Fer4_18       4Fe-4S dicluster domain
     0.0013   19.1  43.3      0.047   14.2   2.1    5.6  5  Fer4_4        4Fe-4S binding domain
      0.006   17.1  35.1        0.2   12.2   2.4    5.5  5  Fer4_17       4Fe-4S dicluster domain
  ------ inclusion threshold ------
        2.9    7.8   5.2         10    6.1   5.2    1.9  1  EGL-1         Programmed cell death activator EGL-1
        3.1    8.4  31.3       0.83   10.2   0.1    5.9  6  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
          9    5.3  13.1       0.88    8.6   0.2    2.7  3  GcpE          GcpE protein


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.0   0.2   6.2e-40   5.6e-37       2     153 ..     151     309 ..     150     310 .. 0.95

  Alignments for each domain:
  == domain 1  score: 127.0 bits;  conditional E-value: 6.2e-40
                   FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqk................kklkekilltiglfCggnfspealrklleelgvdpedvkklefrg 66 
                                   +kvavvG+PCqi++lrklq                 +    ki ++iglfC++ f +++++++l ++g+d e+v+k+++ +
  gi|15669061|ref|NP_247865.1| 151 EKVAVVGLPCQINGLRKLQYfpyhakhdlelgrngkPVKLPKIEYLIGLFCTEKFRYDNMKEVLSKHGIDIEKVEKFDI-K 230
                                   79*****************88899999999*****97778899************************************.7 PP

                   FrhB_FdhB_C  67 kgkfrvelkd.ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveage 146
                                   kgk+ v+++  +ke++lke+e  i ++Ck+C+d+ ae+AD+svG v      g +++g+st+++rtekgee+ ++++ ++ 
  gi|15669061|ref|NP_247865.1| 231 KGKLLVYVNGeKKEFDLKEFE--ICSGCKMCRDFDAEMADVSVGCV------G-SPDGYSTIIIRTEKGEEIKNAVELKEG 302
                                   9*****999999999999999..89*********************......9.*********************999999 PP

                   FrhB_FdhB_C 147 leleeld 153
                                   ++lee++
  gi|15669061|ref|NP_247865.1| 303 VNLEEIE 309
                                   9999987 PP

>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         3   2.7e+03      96     114 ..     351     373 ..     255     379 .. 0.65
   2 !  123.8   0.5   4.8e-39   4.3e-36       2     158 ..     419     618 ..     418     619 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3
                                   TCEEEEE.....EEEEGGGHHHHH CS
                                   xxxxxxx.....xxxxxxxxxxxx RF
                       NIR_SIR  96 kktsarl.....gfvpeeevlevv 114
                                   + +++ +     g+ ++ee++e++
  gi|15669061|ref|NP_247865.1| 351 TYFIR-VrakpgGWYKPEEIKEIL 373
                                   22222.235666777777666665 PP

  == domain 2  score: 123.8 bits;  conditional E-value: 4.8e-39
                                   SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei... 79 
                                   g  +r++ +cpg g c   l+Dttela+ ie    ++++e+  P+KfKia+sgcpn cv+ +++Dig+ gvk ++ ++   
  gi|15669061|ref|NP_247865.1| 419 GPLVRATLACPGGGNCSSGLVDTTELARIIE----DNFKERPAPYKFKIAISGCPNGCVRPQVHDIGIAGVKYPKVNEekc 495
                                   6679***************************....****************************************999*** PP

                                   .................................................EEEEEE--B-SSSTC-TCEEEEEEEEEGGGHH CS
                                   .................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR  80 .................................................gfnilvGGglgrthgakktsarlgfvpeeevl 111
                                                                                    g+ ++vGG++gr+  ++ +++    +  +e++
  gi|15669061|ref|NP_247865.1| 496 ngcgrcaevckveaidirgetsytnynvcvgcgkcikncpnearevkeeGYLVYVGGKTGREVVEGVKMKL---MSVDEII 573
                                   **********************************************************************4...77778** PP

                                   HHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHHHHCCTCG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR 112 evveaivevyrdhgdrknrkkeRlkylverlGvekFrekveeelgkk 158
                                   +++++++ vy    ++++ ++eRl+ +++r+G+ kF+e+v+e ++k+
  gi|15669061|ref|NP_247865.1| 574 NFIDKVLVVYG--KYAEKPQRERLAAVMKRVGYGKFLEEVKELMKKE 618
                                   ***********..99*************************9999875 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0     3e-21   2.7e-18      14      74 ..      82     140 ..      74     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 3e-21
                   FrhB_FdhB_N  14 kaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYtlspnl 74 
                                   ++q+GG+vta lkylLe+g+idg+ivv  +   w+p+  +++++e+ll++a+skY++s + 
  gi|15669061|ref|NP_247865.1|  82 EGQDGGVVTAFLKYLLENGKIDGAIVVGDE--CWKPVSLVVQNAEDLLKTAKSKYAISTLD 140
                                   49**************************55..8***********************99864 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   5.5   9.2e-06    0.0083       2      49 ..      15      55 ..      14      58 .. 0.84
   2 ?    2.7   0.0      0.21   1.9e+02      35      44 ..     250     259 ..     215     262 .. 0.72
   3 !   19.7   5.1     1e-06   0.00092      11      52 .]     467     509 ..     465     509 .. 0.85
   4 !   20.2   0.5   7.5e-07   0.00068       2      22 ..     524     544 ..     523     568 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.2e-06
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga..CvavCP 49
                                  C  Cg C+ +Cp++ +++de+  +          ++Cl  g+  C +vCP
  gi|15669061|ref|NP_247865.1| 15 CARCGTCTIVCPNGILTFDER--P-------KLIDECLRKGHgmCFEVCP 55
                                  99****************998..2.......3589999655444*****9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.21
                        Fer4_7  35 pekClgCgaC 44 
                                    e C+gC++C
  gi|15669061|ref|NP_247865.1| 250 FEICSGCKMC 259
                                   5668888887 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 1e-06
                        Fer4_7  11 aCpvkaieldee.enekgtekveidpekClgCgaCvavCPtga 52 
                                    Cp+++++ + +    +g++++++++ekC gCg+C++vC ++a
  gi|15669061|ref|NP_247865.1| 467 GCPNGCVRPQVHdIGIAGVKYPKVNEEKCNGCGRCAEVCKVEA 509
                                   69***9998754255679999******************9976 PP

  == domain 4  score: 20.2 bits;  conditional E-value: 7.5e-07
                        Fer4_7   2 CigCgaCvaaCpvkaieldee 22 
                                   C+gCg+C ++Cp++a+e++ee
  gi|15669061|ref|NP_247865.1| 524 CVGCGKCIKNCPNEAREVKEE 544
                                   *****************9975 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   3.8   1.9e-06    0.0017       2      24 .]       9      31 ..       8      31 .. 0.91
   2 ?    4.2   0.7     0.045        40      12      19 ..      48      55 ..      48      57 .. 0.91
   3 ?    3.8   1.1      0.06        54       6      15 ..     251     260 ..     248     262 .. 0.84
   4 ?   -1.9   0.2       3.8   3.5e+03      18      23 ..     468     473 ..     466     474 .. 0.84
   5 !   30.8   5.1   1.8e-10   1.6e-07       1      23 [.     488     510 ..     488     511 .. 0.94
   6 !   22.5   3.7   7.8e-08   6.9e-05       4      23 ..     520     539 ..     518     540 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.9e-06
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  ++d   C +CG+C  vCP+g +t
  gi|15669061|ref|NP_247865.1|  9 IVDSGVCARCGTCTIVCPNGILT 31
                                  68999**************9875 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.045
                                  THHHHHST CS
                          Fer4 12 GaCvevCP 19
                                  G C evCP
  gi|15669061|ref|NP_247865.1| 48 GMCFEVCP 55
                                  89****** PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.06
                                   TTSSS-THHH CS
                          Fer4   6 ekCigCGaCv 15 
                                   e C gC+ C 
  gi|15669061|ref|NP_247865.1| 251 EICSGCKMCR 260
                                   88*******6 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 3.8
                                   STTTEE CS
                          Fer4  18 CPvgAI 23 
                                   CP+g+ 
  gi|15669061|ref|NP_247865.1| 468 CPNGCV 473
                                   ***986 PP

  == domain 5  score: 30.8 bits;  conditional E-value: 1.8e-10
                                   EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                   ++++eekC gCG+C+evC v+AI
  gi|15669061|ref|NP_247865.1| 488 PKVNEEKCNGCGRCAEVCKVEAI 510
                                   589*******************9 PP

  == domain 6  score: 22.5 bits;  conditional E-value: 7.8e-08
                                   ETTTSSS-THHHHHSTTTEE CS
                          Fer4   4 deekCigCGaCvevCPvgAI 23 
                                   +++ C+gCG+C++ CP++A 
  gi|15669061|ref|NP_247865.1| 520 NYNVCVGCGKCIKNCPNEAR 539
                                   8899**************96 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   4.9   4.3e-05     0.038       5      22 .]      10      27 ..       9      27 .. 0.91
   2 ?    1.4   0.1      0.45     4e+02      13      21 ..      47      55 ..      37      56 .. 0.77
   3 ?    6.4   0.3     0.012        11       7      18 ..     250     261 ..     246     263 .. 0.86
   4 !   21.5   2.7   1.9e-07   0.00017       2      21 ..     487     506 ..     486     507 .. 0.92
   5 !   16.9   3.6   5.3e-06    0.0047       6      22 .]     520     536 ..     518     536 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-05
                        Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                  vd+  C +Cg+C+ +CP+
  gi|15669061|ref|NP_247865.1| 10 VDSGVCARCGTCTIVCPN 27
                                  78999************5 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.45
                        Fer4_2 13 CgaCvsaCP 21
                                   g C  +CP
  gi|15669061|ref|NP_247865.1| 47 HGMCFEVCP 55
                                  589*****9 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.012
                        Fer4_2   7 tdrCigCgaCvs 18 
                                    ++C gC+ C++
  gi|15669061|ref|NP_247865.1| 250 FEICSGCKMCRD 261
                                   589*******96 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 1.9e-07
                        Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                   +++v++++C+gCg C  +C 
  gi|15669061|ref|NP_247865.1| 487 YPKVNEEKCNGCGRCAEVCK 506
                                   689****************5 PP

  == domain 5  score: 16.9 bits;  conditional E-value: 5.3e-06
                        Fer4_2   6 dtdrCigCgaCvsaCPa 22 
                                   + + C+gCg+C+++CP+
  gi|15669061|ref|NP_247865.1| 520 NYNVCVGCGKCIKNCPN 536
                                   7899************5 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   2.4e-13   2.2e-10       4      68 ..     348     410 ..     344     411 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.4e-13
                  NIR_SIR_ferr   4 kdgkgyymvrlrvp.nGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLae 68 
                                    dg+  y++r+r + +G++ +e+ +++ diae+y    i++T r + +lhg++  d+e+i  +L+e
  gi|15669061|ref|NP_247865.1| 348 ADGT--YFIRVRAKpGGWYKPEEIKEILDIAEEYN-AKIKVTDRAGYELHGISGFDVEDIVLRLRE 410
                                   4544..7******999*******************.************************999987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   4.2   3.4e-07   0.00031       4      56 .]      10      55 ..       7      64 .. 0.82
   2 ?    3.1   0.2      0.12   1.1e+02       5      18 ..     249     262 ..     242     298 .. 0.82
   3 ?   -2.8   0.1       8.2   7.4e+03      44      51 ..     427     434 ..     420     436 .. 0.60
   4 !   22.4  15.0   1.1e-07   9.6e-05       3      56 .]     489     535 ..     487     535 .. 0.93
   5 !   17.1   2.7   5.1e-06    0.0045       5      27 ..     520     542 ..     517     561 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.4e-07
                       Fer4_10  4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg..cgaCveaCP 56
                                  +d+  C rCg+C+ +CP         g+ + +e   k +++C +  +g+C e+CP
  gi|15669061|ref|NP_247865.1| 10 VDSGVCARCGTCTIVCPN--------GILTFDE-RPKLIDECLRkgHGMCFEVCP 55
                                  68889*************........4444444.45568999885568******9 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.12
                       Fer4_10   5 dddtCirCgkCvka 18 
                                   + + C +C+ C+++
  gi|15669061|ref|NP_247865.1| 249 EFEICSGCKMCRDF 262
                                   55789999999875 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 8.2
                       Fer4_10  44 kCtgcgaC 51 
                                   +C+g g+C
  gi|15669061|ref|NP_247865.1| 427 ACPGGGNC 434
                                   45555555 PP

  == domain 4  score: 22.4 bits;  conditional E-value: 1.1e-07
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   ++++++C +Cg+C ++C       ++++++ ++e+  +++  C gcg+C++ CP
  gi|15669061|ref|NP_247865.1| 489 KVNEEKCNGCGRCAEVC-------KVEAIDIRGETSYTNYNVCVGCGKCIKNCP 535
                                   5789*************.......78999999999999***************9 PP

  == domain 5  score: 17.1 bits;  conditional E-value: 5.1e-06
                       Fer4_10   5 dddtCirCgkCvkaCPadltsvg 27 
                                   + + C++CgkC k CP  +++v+
  gi|15669061|ref|NP_247865.1| 520 NYNVCVGCGKCIKNCPNEAREVK 542
                                   7789************9553333 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   3.1    0.0002      0.18       5      23 ..      11      29 ..       9      30 .. 0.84
   2 ?    2.9   0.3      0.15   1.3e+02      13      20 ..      48      55 ..      42      63 .. 0.87
   3 ?   -1.8   2.8       4.3   3.9e+03       8      15 ..     252     259 ..     251     260 .. 0.89
   4 !   24.3   3.2   2.5e-08   2.3e-05       2      24 .]     488     510 ..     487     510 .. 0.93
   5 !   17.9   2.8   2.6e-06    0.0023       5      21 ..     520     536 ..     517     539 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                        Fer4_6  5 dpdkCigCgdCvrvCPega 23
                                  d   C  Cg C++vCP g+
  gi|15669061|ref|NP_247865.1| 11 DSGVCARCGTCTIVCPNGI 29
                                  6667************886 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.15
                        Fer4_6 13 gdCvrvCP 20
                                  g C+ vCP
  gi|15669061|ref|NP_247865.1| 48 GMCFEVCP 55
                                  67****** PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.3
                        Fer4_6   8 kCigCgdC 15 
                                    C gC  C
  gi|15669061|ref|NP_247865.1| 252 ICSGCKMC 259
                                   7****999 PP

  == domain 4  score: 24.3 bits;  conditional E-value: 2.5e-08
                        Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                   + ++++kC+gCg+C+ vC   ai
  gi|15669061|ref|NP_247865.1| 488 PKVNEEKCNGCGRCAEVCKVEAI 510
                                   689***************99997 PP

  == domain 5  score: 17.9 bits;  conditional E-value: 2.6e-06
                        Fer4_6   5 dpdkCigCgdCvrvCPe 21 
                                   +++ C+gCg+C+++CP 
  gi|15669061|ref|NP_247865.1| 520 NYNVCVGCGKCIKNCPN 536
                                   5678************5 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   7.5    0.0024       2.2       2      25 ..      15      38 ..      14      79 .. 0.81
   2 ?    3.2   0.1      0.19   1.7e+02      45      62 ..     244     261 ..     217     262 .. 0.69
   3 !   15.3   1.3   3.1e-05     0.028       1      20 [.     494     513 ..     494     522 .. 0.83
   4 !   15.1   1.2   3.7e-05     0.033       2      20 ..     524     542 ..     523     550 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0024
                       Fer4_16  2 CgtCgkCaevCPtnaikekkekei 25
                                  C +Cg C+ vCP + ++ ++++++
  gi|15669061|ref|NP_247865.1| 15 CARCGTCTIVCPNGILTFDERPKL 38
                                  *****************9977664 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.19
                       Fer4_16  45 eekckkqeaitgCdiCqd 62 
                                   e+  k+ e + gC++C d
  gi|15669061|ref|NP_247865.1| 244 EFDLKEFEICSGCKMCRD 261
                                   333444567899999976 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 3.1e-05
                       Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                   +C +Cg+CaevC ++ai+ +
  gi|15669061|ref|NP_247865.1| 494 KCNGCGRCAEVCKVEAIDIR 513
                                   5***************9866 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 3.7e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C++CgkC++ CP +a + k
  gi|15669061|ref|NP_247865.1| 524 CVGCGKCIKNCPNEAREVK 542
                                   *************996665 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   2.2   0.00011       0.1      35      50 ..      14      29 ..       5      30 .. 0.81
   2 !   11.3   7.2   0.00032      0.29       2      48 ..      15      56 ..      14      59 .. 0.81
   3 ?    2.6   0.1      0.18   1.6e+02       2       8 ..     253     259 ..     227     263 .. 0.71
   4 !   27.1  13.1   3.7e-09   3.3e-06       1      49 [.     494     537 ..     494     539 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                        Fer4_9 35 aCigCgaCveaCpkga 50
                                   C  Cg+C+ +Cp+g+
  gi|15669061|ref|NP_247865.1| 14 VCARCGTCTIVCPNGI 29
                                  49***********984 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00032
                        Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga..CveaCpk 48
                                  C++Cg+C+ +Cp+g+ + d+ ++ +         C+  g   C+e+Cp+
  gi|15669061|ref|NP_247865.1| 15 CARCGTCTIVCPNGILTFDERPKLIDE-------CLRKGHgmCFEVCPR 56
                                  999************999999999885.......754333449999997 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.18
                        Fer4_9   2 CtgCgaC 8  
                                   C gC+ C
  gi|15669061|ref|NP_247865.1| 253 CSGCKMC 259
                                   5555555 PP

  == domain 4  score: 27.1 bits;  conditional E-value: 3.7e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   kC+gCg+C e+C+ +++  +  + + +++      C+gCg+C++ Cp++
  gi|15669061|ref|NP_247865.1| 494 KCNGCGRCAEVCKVEAIDIRGETSYTNYNV-----CVGCGKCIKNCPNE 537
                                   7****************9999999999865.....************97 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   1.7   0.00063      0.57      51      65 .]      15      29 ..       5      29 .. 0.89
   2 ?    2.9   0.0      0.16   1.5e+02       9      22 ..      48      61 ..      37      92 .. 0.70
   3 ?    3.4   0.1      0.12     1e+02      45      58 ..     247     260 ..     205     276 .. 0.75
   4 !   10.7   3.4    0.0006      0.54      49      63 ..     493     507 ..     466     510 .. 0.82
   5 !   13.2   0.0    0.0001     0.093       4      17 ..     523     536 ..     513     594 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00063
                        Fer4_8 51 CttcgaCtevCpvgi 65
                                  C  cg Ct vCp+gi
  gi|15669061|ref|NP_247865.1| 15 CARCGTCTIVCPNGI 29
                                  9***********987 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                        Fer4_8  9 gaCqsaCpvlrrtk 22
                                  g+C++ Cp +++ k
  gi|15669061|ref|NP_247865.1| 48 GMCFEVCPRVSSAK 61
                                  57888888666654 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.12
                        Fer4_8  45 eealwsCttcgaCt 58 
                                    + ++ C++c++C+
  gi|15669061|ref|NP_247865.1| 247 LKEFEICSGCKMCR 260
                                   45567788888886 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.0006
                        Fer4_8  49 wsCttcgaCtevCpv 63 
                                   ++C++cg+C+evC+v
  gi|15669061|ref|NP_247865.1| 493 EKCNGCGRCAEVCKV 507
                                   568888888888876 PP

  == domain 5  score: 13.2 bits;  conditional E-value: 0.0001
                        Fer4_8   4 kCieCgaCqsaCpv 17 
                                    C++Cg C ++Cp 
  gi|15669061|ref|NP_247865.1| 523 VCVGCGKCIKNCPN 536
                                   58888888888882 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   5.2    0.0002      0.18       3      52 ..      10      55 ..       8      60 .. 0.75
   2 ?    3.1   0.2      0.12   1.1e+02      39      48 ..     251     260 ..     236     262 .. 0.74
   3 !   18.6   5.7   1.7e-06    0.0015      14      58 ..     468     511 ..     463     512 .. 0.88
   4 !   12.0   3.0   0.00019      0.17       6      22 ..     522     538 ..     517     545 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                       Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeC..vGCnlCssvCP 52
                                  +d+  C  Cg C+i+C++     +++d++   + + deC   G  +C +vCP
  gi|15669061|ref|NP_247865.1| 10 VDSGVCARCGTCTIVCPN---GILTFDER---PKLIDEClrKGHGMCFEVCP 55
                                  78889************5...44455533...335567733699******** PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.12
                       Fer4_21  39 deCvGCnlCs 48 
                                   + C GC++C 
  gi|15669061|ref|NP_247865.1| 251 EICSGCKMCR 260
                                   78*******6 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.7e-06
                       Fer4_21  14 CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                   C   C    +  i i++ ++ kv e++C GC  C++vC v ++i+
  gi|15669061|ref|NP_247865.1| 468 CPNGCVRPQVHDIGIAGVKYPKVNEEKCNGCGRCAEVCKV-EAID 511
                                   777888888899999************************9.7775 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00019
                       Fer4_21   6 dkCigCgkCliaCedts 22 
                                   + C+gCgkC++ C++++
  gi|15669061|ref|NP_247865.1| 522 NVCVGCGKCIKNCPNEA 538
                                   67888888888888766 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   7.8      0.13   1.1e+02       2      51 ..      15      53 ..      14      88 .. 0.56
   2 ?    1.2   0.0      0.78     7e+02      78      90 ..     249     261 ..     209     266 .. 0.77
   3 !   14.2   2.1   6.8e-05     0.061      76      95 ..     489     508 ..     481     509 .. 0.87
   4 !   15.4   1.7   2.8e-05     0.025      77      95 ..     519     537 ..     512     538 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                       Fer4_22  2 ClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvagg 51
                                  C +Cg+Ct+vCp  +   +           er + +d Cl +++ +  + 
  gi|15669061|ref|NP_247865.1| 15 CARCGTCTIVCPNGIL--TF---------DERPKLIDECLRKGHGMCFEV 53
                                  99**********7542..11.........234455555555555555444 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.78
                       Fer4_22  78 gesgCvGCgRCie 90 
                                   + + C GC  C +
  gi|15669061|ref|NP_247865.1| 249 EFEICSGCKMCRD 261
                                   6689****99986 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 6.8e-05
                       Fer4_22  76 kfgesgCvGCgRCieacpvk 95 
                                   k++e++C GCgRC e+c+v+
  gi|15669061|ref|NP_247865.1| 489 KVNEEKCNGCGRCAEVCKVE 508
                                   67899************975 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 2.8e-05
                       Fer4_22  77 fgesgCvGCgRCieacpvk 95 
                                   ++ ++CvGCg+Ci++cp++
  gi|15669061|ref|NP_247865.1| 519 TNYNVCVGCGKCIKNCPNE 537
                                   57889***********975 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   2.7   0.00099      0.89      57      99 ..      11      58 ..       3      67 .. 0.79
   2 !   16.9   4.7   5.9e-06    0.0053      57     105 ..     491     544 ..     480     551 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00099
                       Fer4_18 57 gagdcidcescvkvcPtgi...dirkGlqlecisc..llcidacdkvm 99
                                  ++g c  c++c  vcP gi   d r  l  ec+    + c + c +v 
  gi|15669061|ref|NP_247865.1| 11 DSGVCARCGTCTIVCPNGIltfDERPKLIDECLRKghGMCFEVCPRVS 58
                                  6788*************9866688999999999752257888888775 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 5.9e-06
                       Fer4_18  57 gagdcidcescvkvcPt.gidirkGlqle....ciscllcidacdkvmeklgkp 105
                                   ++ +c  c+ c +vc +  idir    +     c+ c++ci  c +   +++ +
  gi|15669061|ref|NP_247865.1| 491 NEEKCNGCGRCAEVCKVeAIDIRGETSYTnynvCVGCGKCIKNCPNEAREVKEE 544
                                   5678***********9835****8876644445***********8877777666 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.2   5.4e-05     0.049       4      16 ..      15      27 ..       7      32 .. 0.91
   2 ?   -0.4   0.3       2.5   2.3e+03       2      15 ..      40      55 ..      39      63 .. 0.76
   3 ?    5.4   1.2     0.034        31       4      13 ..     253     262 ..     249     262 .. 0.88
   4 !   10.6   5.0   0.00077      0.69       2      16 ..     493     507 ..     492     508 .. 0.90
   5 !   14.2   2.1   5.2e-05     0.047       2      15 ..     522     535 ..     521     546 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-05
                        Fer4_4  4 CigCgsCvaaCPq 16
                                  C +Cg C+++CP 
  gi|15669061|ref|NP_247865.1| 15 CARCGTCTIVCPN 27
                                  ************5 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.5
                        Fer4_4  2 erCigCg..sCvaaCP 15
                                  + C++ g   C  +CP
  gi|15669061|ref|NP_247865.1| 40 DECLRKGhgMCFEVCP 55
                                  5677666557999999 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.034
                        Fer4_4   4 CigCgsCvaa 13 
                                   C gC+ C+++
  gi|15669061|ref|NP_247865.1| 253 CSGCKMCRDF 262
                                   *******997 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00077
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   e+C+gCg+C  +C++
  gi|15669061|ref|NP_247865.1| 493 EKCNGCGRCAEVCKV 507
                                   89***********86 PP

  == domain 5  score: 14.2 bits;  conditional E-value: 5.2e-05
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   + C+gCg+C+  CP
  gi|15669061|ref|NP_247865.1| 522 NVCVGCGKCIKNCP 535
                                   78************ PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   2.1    0.0018       1.6      46      60 ..      15      29 ..       6      30 .. 0.87
   2 ?    1.9   0.4      0.38   3.4e+02       6      19 ..      48      61 ..      41      87 .. 0.63
   3 ?    4.8   0.1     0.045        40      41      53 ..     248     260 ..     223     266 .. 0.75
   4 ?    6.3   4.6     0.016        14      44      57 ..     493     506 ..     476     511 .. 0.79
   5 !   12.2   2.4   0.00023       0.2      38      59 ..     516     537 ..     507     539 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                       Fer4_17 46 CieCgeCerkCPqgl 60
                                  C+ Cg C+ +CP+g+
  gi|15669061|ref|NP_247865.1| 15 CARCGTCTIVCPNGI 29
                                  999999999999986 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.38
                       Fer4_17  6 gyClpeCpsyeayd 19
                                  g+C ++Cp+    +
  gi|15669061|ref|NP_247865.1| 48 GMCFEVCPRVSSAK 61
                                  68******976633 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.045
                       Fer4_17  41 ekaslCieCgeCe 53 
                                   ++++ C++C++C+
  gi|15669061|ref|NP_247865.1| 248 KEFEICSGCKMCR 260
                                   5667777777775 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.016
                       Fer4_17  44 slCieCgeCerkCP 57 
                                   ++C++Cg+C+++C 
  gi|15669061|ref|NP_247865.1| 493 EKCNGCGRCAEVCK 506
                                   56788888877774 PP

  == domain 5  score: 12.2 bits;  conditional E-value: 0.00023
                       Fer4_17  38 ekeekaslCieCgeCerkCPqg 59 
                                      ++ + C++Cg+C + CP++
  gi|15669061|ref|NP_247865.1| 516 TSYTNYNVCVGCGKCIKNCPNE 537
                                   44578899************86 PP

>> EGL-1  Programmed cell death activator EGL-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.2     0.011        10       9      18 ..     257     266 ..     256     266 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
                                   HHHHHHHHHH CS
                         EGL-1   9 aMCDdFDaem 18 
                                   +MC dFDaem
  gi|15669061|ref|NP_247865.1| 257 KMCRDFDAEM 266
                                   8********9 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.3     0.011       9.5       1      18 [.      10      27 ..      10      41 .. 0.83
   2 ?    0.1   0.2       1.4   1.2e+03       8      19 ..      46      57 ..      39      59 .. 0.82
   3 ?    0.8   0.5      0.81   7.2e+02       6      15 ..     253     262 ..     249     266 .. 0.84
   4 ?   -1.3   0.0       3.8   3.4e+03      45      56 ..     462     473 ..     445     474 .. 0.83
   5 ?    6.1   3.1     0.018        16       1      16 [.     490     505 ..     490     507 .. 0.94
   6 ?   10.2   0.1   0.00092      0.83       5      38 ..     523     556 ..     520     566 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                       Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                  VD   C  cg+C  ++P+
  gi|15669061|ref|NP_247865.1| 10 VDSGVCARCGTCTIVCPN 27
                                  89999************8 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.4
                       Fer4_13  8 acgaCvelaPdv 19
                                  ++g C e++P v
  gi|15669061|ref|NP_247865.1| 46 GHGMCFEVCPRV 57
                                  6899******87 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.81
                       Fer4_13   6 CiacgaCvel 15 
                                   C++c+ C+++
  gi|15669061|ref|NP_247865.1| 253 CSGCKMCRDF 262
                                   *******986 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.8
                       Fer4_13  45 eeAadaCPvesI 56 
                                   + A+ +CP  ++
  gi|15669061|ref|NP_247865.1| 462 KIAISGCPNGCV 473
                                   67999***9886 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.018
                       Fer4_13   1 VDrdtCiacgaCvela 16 
                                   V++++C +cg C+e++
  gi|15669061|ref|NP_247865.1| 490 VNEEKCNGCGRCAEVC 505
                                   899***********99 PP

  == domain 6  score: 10.2 bits;  conditional E-value: 0.00092
                       Fer4_13   5 tCiacgaCvelaPdvFeeddeggasvvaeqptse 38 
                                    C++cg+C + +P+  +e +e+g+ v + ++t+ 
  gi|15669061|ref|NP_247865.1| 523 VCVGCGKCIKNCPNEAREVKEEGYLVYVGGKTGR 556
                                   6************988888888888877777665 PP

>> GcpE  GcpE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.7   2.4e+03      98     132 ..     355     385 ..     346     390 .. 0.85
   2 ?    8.6   0.2   0.00098      0.88     265     321 ..     426     486 ..     421     492 .. 0.79
   3 ?   -0.3   6.9      0.49   4.4e+02     266     317 ..     494     546 ..     485     578 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.7
                                   EEEE-TTTSSSTTHHHHHHHHHHHHHHHHT-EEEE CS
                          GcpE  98 kvRiNPGnigdgkkkeekvkelveaakekgtaiRi 132
                                   +vR  PG   +     e++ke++++a+e++  i++
  gi|15669061|ref|NP_247865.1| 355 RVRAKPGGWYK----PEEIKEILDIAEEYNAKIKV 385
                                   68899999998....999*********99999987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00098
                                   EE---...-TTS-CHHHHHHHHHHHHCCCH..HCG-EEEEESSTCCHHHHCCCSSEEEEEBT CS
                          GcpE 265 isCPs...CgRtlfdlqelveeveealehl..kkglkiavmGCiVNGpgEaadAdlGivggk 321
                                    +CP+   C+  l+d +el++ +e+++++     ++kia+ GC  NG    +  d+Gi+g k
  gi|15669061|ref|NP_247865.1| 426 LACPGggnCSSGLVDTTELARIIEDNFKERpaPYKFKIAISGCP-NGCVRPQVHDIGIAGVK 486
                                   79**73336666678888889999999776334789*******7.*************9987 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.49
                                   E----TTS-CHHHHHHHHHHHHCCCHHCG-EEEEESSTCCHHHHCCCSS.EEE CS
                          GcpE 266 sCPsCgRtlfdlqelveeveealehlkkglkiavmGCiVNGpgEaadAd.lGi 317
                                    C +CgR+    +  + +++ +++ ++ ++ ++   Ci N p Ea++    G+
  gi|15669061|ref|NP_247865.1| 494 KCNGCGRCAEVCKVEAIDIRGETSYTNYNVCVGCGKCIKNCPNEAREVKeEGY 546
                                   599******99999999*********99*****************98632343 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (620 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 3916.11
//
Query:       gi|15669062|ref|NP_247866.1|  [L=317]
Description: hypothetical protein MJ_0871 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-11   44.3  16.4    9.2e-06   25.9   4.0    2.7  2  Gate          Nucleoside recognition
  ------ inclusion threshold ------
      0.097   11.9   8.4      0.046   12.9   6.0    1.7  1  Bac_export_2  FlhB HrpN YscU SpaS Family
        1.3    8.5   3.3        8.2    5.9   0.6    2.1  2  TMCO5         TMCO5 family


Domain annotation for each model (and alignments):
>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   3.5   4.1e-09   2.4e-05       4     108 ..      24     123 ..      21     136 .. 0.85
   2 !   25.9   4.0   1.5e-09   9.2e-06       2      94 ..     185     268 ..     184     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.1e-09
                          Gate   4 agpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtpks 84 
                                   +  i+l  +++++++ s++++++++++l+p++++l+   +  ++ s l+ f++ +v++++l++         ++++ ++++
  gi|15669062|ref|NP_247866.1|  24 ISIIVLTTVFIVNYIMSTGIMKKLSNMLSPILRRLK--VNPLSISSTLACFFSPTVGYSILAEGL-------KENKVNERE 95 
                                   566888899999************************..88888888888899999******9996.......99999**** PP

                          Gate  85 alafllfvllytpcvat....lavivre 108
                                   ++ + l +++ ++   t    ++v+v +
  gi|15669062|ref|NP_247866.1|  96 VIGASLANSFPSVLSHTftffIPVVVPI 123
                                   **99999999997777744445555555 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.5e-09
                          Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtp 82 
                                   ++++pi++++++l+ +ls+ ++++++ k+++p+ + l   l+ ++ +  lt +++  +++ ++g +         +g+ + 
  gi|15669062|ref|NP_247866.1| 185 KRLIPIMFFMMTLVLYLSKIGFFDYVEKFVQPITNLLN--LNPNVGILALTEIMNVQAAIVMAGGFL-------NEGILSS 256
                                   89************************************..888888888888886666666666664.......7788888 PP

                          Gate  83 ksalafllfvll 94 
                                   k++l+ l+++  
  gi|15669062|ref|NP_247866.1| 257 KEVLIGLIIGNV 268
                                   887777766655 PP

>> Bac_export_2  FlhB HrpN YscU SpaS Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   6.0   7.6e-06     0.046      29     164 ..      25     227 ..      22     255 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.6e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX................................................ CS
                  Bac_export_2  29 salvllaglllllllgpslveelaellrevlsa................................................ 61 
                                   s++vl++++++ ++++  ++++l+++l+ +l++                                                
  gi|15669062|ref|NP_247866.1|  25 SIIVLTTVFIVNYIMSTGIMKKLSNMLSPILRRlkvnplsisstlacffsptvgysilaeglkenkvnerevigaslansf 105
                                   678999999999*******************99***********************************9999999986666 PP

                                   XXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  Bac_export_2  62 lelllelllallllllpl......llvlllaallanllqvgflf......stkalkpklsklnplkglkrifslrslvell 130
                                    ++l+++++ ++ +++p+      l vl+ ++++     +gfl         +  +p+++kln  +++k+ f  +s ++++
  gi|15669062|ref|NP_247866.1| 106 PSVLSHTFTFFIPVVVPIlghtgvLYVLIRLGVALAKTIIGFLYlsiiseDYSFEMPEINKLNKKENAKKSF--KSTIRFA 184
                                   444455555555555554444433222222222222222244333232222233357788888888888877..899**** PP

                                   XXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXX CS
                  Bac_export_2 131 ksllkvvlvgavaylvlks.........eleellalaeldlea 164
                                   k l+ +++++++++l+l++          ++ +++l++l+++ 
  gi|15669062|ref|NP_247866.1| 185 KRLIPIMFFMMTLVLYLSKigffdyvekFVQPITNLLNLNPNV 227
                                   ***********99999988765553322223333444444443 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.01        60     246     266 ..      35      55 ..      13      63 .. 0.78
   2 ?    5.9   0.6    0.0014       8.2     189     237 ..     165     210 ..     151     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.01
                         TMCO5 246 LPkilsrrtlwkLReilaPfL 266
                                      i+s ++++kL ++l+P L
  gi|15669062|ref|NP_247866.1|  35 VNYIMSTGIMKKLSNMLSPIL 55 
                                   3469***************99 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0014
                         TMCO5 189 vetiqknaektiikkkkrvfwkralrflffmvlifirLlgyvlfhlqyi 237
                                   ++ ++k++ k+++k + r+  kr++ ++ffm+ ++  L+   +f  +y+
  gi|15669062|ref|NP_247866.1| 165 NKLNKKENAKKSFKSTIRF-AKRLIPIMFFMMTLVLYLSKIGFF--DYV 210
                                   3455555666666666555.9*******************9999..665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1949.67
//
Query:       gi|15669063|ref|NP_247867.1|  [L=405]
Description: hypothetical protein MJ_0872 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-17   62.9   0.2    4.9e-17   62.3   0.2    1.3  1  Peripla_BP_2    Periplasmic binding protein
  ------ inclusion threshold ------
       0.02   15.2   0.0      0.034   14.4   0.0    1.3  1  Cytomega_UL20A  Cytomegalovirus UL20A protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.2   5.5e-21   4.9e-17      26     237 ..     146     367 ..     129     368 .. 0.83

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 5.5e-21
                                   GGG--GGGGGGT.......TS-BSBES.SSB-HHHHHHH--SEEEE-GGG.....GGGHHHHHHHS-EEE----TTSHHHH CS
                  Peripla_BP_2  26 tttsdpldadklee.....aivevgad.geidvEklaalkPDlvilskgl..gltdedeellksgiptvivessntgeslk 98 
                                   ++++   +++kl+e     ++v++g++ + +++E +++l PD+v+l      ++++e  ++l + +  +   + +t  ++ 
  gi|15669063|ref|NP_247867.1| 146 KYAVE--KSPKLKElfdegKVVDIGSPsKGVNYELIVNLTPDIVFLGDWKseDVVEEKLKELGVTVSRFYTYQEPTYMGRV 224
                                   44433..334444455777889988862569***************9777777888888888888776655666677**** PP

                                   HHHHHHHHHTT-H..HHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE...EEEE-TTSTTTHHHHTS--EESTTT CS
                  Peripla_BP_2  99 eqiralgellgle..deaeklvaeidsklaaaksaidse.kpkpvlvfggade.ggyvvagsnsyigdlldalgieniaae 175
                                   e+i+  +   g++  ++a+k+++ + +  +++ +++++  ++++v++f+++    ++ + g++sy ++++ + +++n++++
  gi|15669063|ref|NP_247867.1| 225 EWIKFAAAFWGSNayKKADKWFENVVKVRENILKKVQNVtNEPTVVIFSWSKTkNMPGIYGNDSYYSKMIAEFKGKNVFDD 305
                                   *************999***********************555555555555558899999********************* PP

                                   --STT-EEE-HHHHHH..H--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-HH CS
                  Peripla_BP_2 176 skkseyeeisaEqila..sdpdvifvsgraeadnktgleflkenpllaelpAvkngrVyaldss 237
                                   + + +y+ ++ E++++  +++dv++  +    d kt+ + lk np +ae++A+k+gr+y  +++
  gi|15669063|ref|NP_247867.1| 306 Y-NRGYQYVDKETFYEraMNADVVILIWF-YGDVKTKEDLLKINPNFAEFKAFKTGRFYVSHPD 367
                                   *.***************************.*****************************98876 PP

>> Cytomega_UL20A  Cytomegalovirus UL20A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.8e-06     0.034       2      53 ..      15      66 ..      14      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-06
                Cytomega_UL20A  2 arrlwilsllavtltvalaapsqkskrsvtveqpststnsdgnttpsknvtl 53
                                   r+l++ls+l + + va+a   + sk +  ++q + s     +t p   v +
  gi|15669063|ref|NP_247867.1| 15 MRKLFLLSILMIGVIVAFAGCVEESKTTTQLQQTTQSESQKAETQPKLGVNV 66
                                  699****************************999999999999999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2376.24
//
Query:       gi|15669064|ref|NP_247868.1|  [L=290]
Description: ferric enterobactin transport ATP-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-29  102.0   0.0    5.3e-29  101.5   0.0    1.3  1  ABC_tran      ABC transporter
    8.4e-11   42.2   2.7     0.0001   22.3   0.2    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    5.5e-08   32.9   0.5    2.8e-05   24.2   0.0    2.6  2  AAA_14        AAA domain
    1.1e-06   29.1   0.6    1.1e-05   25.8   0.6    2.0  1  AAA_16        AAA ATPase domain
    1.3e-06   28.4   0.0      2e-06   27.8   0.0    1.3  1  AAA_15        AAA ATPase domain
    2.1e-06   27.4   0.7      4e-05   23.2   0.7    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    3.5e-06   26.7   0.0    7.2e-06   25.7   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
    3.9e-06   27.2   0.9    4.2e-05   23.8   0.9    2.3  1  AAA_22        AAA domain
    7.3e-05   22.8   2.4    0.00018   21.5   2.2    1.8  1  ATPase_2      ATPase domain predominantly from Archaea
    0.00026   21.4   3.4     0.0039   17.6   3.4    2.4  1  AAA           ATPase family associated with various cellular 
    0.00049   20.1   1.3      0.013   15.4   0.1    2.8  3  Rad17         Rad17 P-loop domain
    0.00059   20.4   2.5    0.00059   20.4   2.5    1.8  1  AAA_23        AAA domain
    0.00086   18.6   0.0     0.0082   15.4   0.0    2.2  2  Zeta_toxin    Zeta toxin
     0.0026   17.7   0.5      0.011   15.6   0.0    2.0  2  NACHT         NACHT domain
     0.0038   17.2   0.0      0.029   14.3   0.0    2.2  2  AAA_5         AAA domain (dynein-related subfamily)
     0.0071   16.0   0.0     0.0088   15.7   0.0    1.4  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
     0.0082   16.1   1.7      0.016   15.1   0.1    2.1  2  RsgA_GTPase   RsgA GTPase
     0.0082   15.9   0.0      0.014   15.1   0.0    1.5  1  AAA_24        AAA domain
  ------ inclusion threshold ------
      0.011   15.4   0.1      0.027   14.2   0.1    1.7  1  AAA_30        AAA domain
      0.017   14.7   0.0      0.029   13.9   0.0    1.3  1  AAA_27        AAA domain
       0.02   15.3   0.1      0.054   13.9   0.1    1.7  1  RNA_helicase  RNA helicase
      0.021   14.3   0.8       0.96    8.8   0.2    2.3  2  TniB          Bacterial TniB protein
      0.031   14.4   0.0      0.059   13.5   0.0    1.7  1  AAA_33        AAA domain
      0.032   13.1   1.4       0.12   11.2   0.1    2.3  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.033   13.1   0.1      0.088   11.7   0.0    1.7  2  AAA_10        AAA-like domain
      0.035   14.7   0.9       0.55   10.8   0.9    2.6  1  AAA_18        AAA domain
      0.045   14.0   0.4       0.28   11.4   0.1    2.1  2  AAA_28        AAA domain
      0.068   13.1   2.4       0.94    9.4   2.4    2.6  1  NTPase_1      NTPase
      0.069   13.5   1.2       0.58   10.5   0.9    2.6  2  AAA_19        AAA domain
      0.073   12.8   0.4       0.57    9.9   0.0    2.2  2  IstB_IS21     IstB-like ATP binding protein
      0.075   11.7   0.6        3.4    6.2   0.0    2.0  2  AAA_13        AAA domain
       0.12   11.8   0.0       0.24   10.8   0.0    1.5  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.13   11.9   0.1       0.25   11.0   0.1    1.5  1  SRP54         SRP54-type protein, GTPase domain
       0.14   11.3   1.0          1    8.5   0.1    2.2  2  NB-ARC        NB-ARC domain
       0.17   11.9   0.3        1.2    9.1   0.1    2.1  2  MutS_V        MutS domain V
        0.2   11.7   0.8       0.49   10.5   0.8    2.0  1  MMR_HSR1      50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.5   0.0   1.1e-31   5.3e-29       2     137 .]      18     166 ..      17     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 1.1e-31
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   + ++l++++ge++ i+G+nGaGKStLlk++a  lkp++G + l+gk++++ + + l ke++v+  e     ++t  +    
  gi|15669064|ref|NP_247868.1|  18 EGINLEINRGEILCIIGPNGAGKSTLLKTIATYLKPKKGVVYLNGKKIHDLKPKDLAKEMAVVLTERVNPGNMTGFDVvai 98 
                                   679************************************************************999666677777777999 PP

                                   ..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                  +++ i + ++ ++ ++l +++      ++S G++q++++aral+++pk+l+lDEpt+
  gi|15669064|ref|NP_247868.1|  99 grhpytdlfgrlteRDKKIIIESARAVNAEYLLEKNF----FEMSDGERQKIMIARALAQEPKVLILDEPTS 166
                                   **********987433333777777777777777777....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2     2e-07    0.0001       2      21 ..      30      49 ..      29      89 .. 0.78
   2 !   20.4   0.2   7.7e-07   0.00038     231     298 ..     132     197 ..     100     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2e-07
                        AAA_21  2 nvliGpNgsGKSnLLdaldl 21
                                   ++iGpNg+GKS+LL+++  
  gi|15669064|ref|NP_247868.1| 30 LCIIGPNGAGKSTLLKTIAT 49
                                  58****************43 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 7.7e-07
                        AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                   e +++e+SdG ++   +++  l++ +  ++l++DEp ++L+ k   +l  ll++l++ ++  +++t H+
  gi|15669064|ref|NP_247868.1| 132 EKNFFEMSDGERQK-IMIARALAQEP--KVLILDEPTSFLDAKHKIELTLLLRKLADeKNLAIVVTLHD 197
                                   5589**********.88888888777..8************9777777777755444477777777666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   5.6e-08   2.8e-05       2      58 ..      27      82 ..      26      96 .. 0.79
   2 ?    6.3   0.2     0.019       9.3      32      98 ..     129     194 ..     110     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5.6e-08
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelile 58
                                  ++il+i G+  +GK+tllk+++  l  +k+ ++y+n ++ +d k +d +k + ++l 
  gi|15669064|ref|NP_247868.1| 27 GEILCIIGPNGAGKSTLLKTIATYLK-PKKGVVYLNGKKIHDLKPKDLAKEMAVVLT 82
                                  5799*****************97777.**************9887776544444433 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.019
                        AAA_14  32 silyinldderdkkladpekllelileklkeekktylflDEiqev......pewekalkslvdegknldvivt 98 
                                     l+ n+ + +d ++++      +i + l  ++ ++l+lDE           e+   l++l de+ nl ++vt
  gi|15669064|ref|NP_247868.1| 129 YLLEKNFFEMSDGERQKI-----MIARALA-QEPKVLILDEPTSFldakhkIELTLLLRKLADEK-NLAIVVT 194
                                   444444444444333322.....2222233.47899*****999988888888999999999999.9999988 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.6   2.3e-08   1.1e-05      22     170 .]      25     192 ..      21     193 .. 0.58

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.3e-08
                        AAA_16  22 grpelvllsGesGvGKsslvrellralekdggif.lrgkcdql..esa..................ipysa.laqalaree 80 
                                   +r+e++ ++G+ G GKs+l+++++++l+ ++g++ l+gk  +   +++                  +      + a+  ++
  gi|15669064|ref|NP_247868.1|  25 NRGEILCIIGPNGAGKSTLLKTIATYLKPKKGVVyLNGKKIHDlkPKDlakemavvltervnpgnmT---GfDVVAI-GRH 101
                                   56799*************************7555599888888552223333334443333222221...2122222.223 PP

                        AAA_16  81 llrqlldeaesaeleawrekleealaavpelagaea...srllellkrll.allsrderplvlvlDdlqwadeaslql.la 156
                                    +++l  +    + e++++ + e+++av++    e+   +    + ++++ a++   ++p vl+lD+   + +a +++ l 
  gi|15669064|ref|NP_247868.1| 102 PYTDLFGR----LTERDKKIIIESARAVNAEYLLEKnffEMSDGERQKIMiARALA-QEPKVLILDEPTSFLDAKHKIeLT 177
                                   33333333....34444444444444333333333366533344444444444445.567899999999999999999999 PP

                        AAA_16 157 aLlrllesk.pllvv 170
                                   +Llr l +  +l++v
  gi|15669064|ref|NP_247868.1| 178 LLLRKLADEkNLAIV 192
                                   999988885588765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   4.1e-09     2e-06      18     136 ..      23     221 ..      13     263 .. 0.62

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 4.1e-09
                        AAA_15  18 eidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef............... 83 
                                   ei+  e + ++iG+N++GKS++l+ +   l+ k    k v++++ +++++ + ++  k++ + +++               
  gi|15669064|ref|NP_247868.1|  23 EINRGE-ILCIIGPNGAGKSTLLKTIATYLKPK----KGVVYLNGKKIHDLKPKDLAKEMAVVLTErvnpgnmtgfdvvai 98 
                                   344344.9***********************99....89999999999999999999999999988888888888888888 PP

                        AAA_15  84 ................................................................................. 83 
                                                                                                                    
  gi|15669064|ref|NP_247868.1|  99 grhpytdlfgrlterdkkiiiesaravnaeylleknffemsdgerqkimiaralaqepkvlildeptsfldakhkieltll 179
                                   888888888888877777777777777777777777777777777777777777766666666555544322221111111 PP

                        AAA_15  84 .aekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdeki 136
                                    +            k  ++k   + ++  + +l  +i dk+  +k+ +++   +
  gi|15669064|ref|NP_247868.1| 180 lR------------KLADEKNLAIVVTLHDIELALRIADKMALIKNHKVIAYGY 221
                                   10............1112222223344444444444555544444444444443 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.7     8e-08     4e-05      26     199 ..      29     197 ..      18     217 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8e-08
                                   EEEEEESTTSSHHHHHHHHHHHCTT..TTTTTTCHCCCCCC--BTTCSSTTEEEEEEE.EEETTEESSSSSSCEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  26 ftaivGpNGSGKsnlldAilFvLGer.sakklrseklsdlihkskekasvkkaeveit.fdnedkklkiekeevsisrrvk 104
                                   + +i+GpNG+GKs ll  i  +L  +     l  +k++dl  k    + +k+  v +t   n+++   +  + v i r+ +
  gi|15669064|ref|NP_247868.1|  29 ILCIIGPNGAGKSTLLKTIATYLKPKkGVVYLNGKKIHDLKPK----DLAKEMAVVLTeRVNPGN--MTGFDVVAIGRHPY 103
                                   679****************999985514456777887777555....333333333330334444..46667777777766 PP

                                   TTSE.......EEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                   xxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 105 rkge.......seykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                   ++          ++ i+    +  + + lle+  +   ++S Ge++ +++a  +A    +p+ + +lDe  + LD+k+  +
  gi|15669064|ref|NP_247868.1| 104 TDLFgrlterdKKIIIESA--RAVNAEYLLEKNFF---EMSDGERQKIMIARALAQ---EPK-VLILDEPTSFLDAKHKIE 175
                                   6543111110134444443..33444446666666...59******9999988773...344.679*************** PP

                                   HHHHHHHHCTT.SEEEEE-SSH CS
                                   xxxxxxxxxxx.xxxxxxxxxx RF
                         SMC_N 179 vaellkekskn.aQfivislre 199
                                   +  ll++  ++    iv++l++
  gi|15669064|ref|NP_247868.1| 176 LTLLLRKLADEkNLAIVVTLHD 197
                                   ******8876635568888765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.4e-08   7.2e-06      15      52 ..      20      57 ..      11      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.4e-08
                        AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpakkv 52
                                    +ei++ ++  ++Gp+G+GKSTll  i++ L p+k v
  gi|15669064|ref|NP_247868.1| 20 INLEINRGEILCIIGPNGAGKSTLLKTIATYLKPKKGV 57
                                  56788877799**********************99854 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.9   8.5e-08   4.2e-05       5     129 ..      27     195 ..      23     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 8.5e-08
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka............. 70 
                                     il+++G+ G+GK+tll++++  l+       ++++vv+ + ++    ++kdl++e++  l+++ +              
  gi|15669064|ref|NP_247868.1|  27 GEILCIIGPNGAGKSTLLKTIATYLK-------PKKGVVYLNGKKIHdlKPKDLAKEMAVVLTERVNPgnmtgfdvvaigr 100
                                   679********************995.......477777777777668999999999999999888889999999999999 PP

                        AAA_22  71 ....................................erlsseellealeqalraravielliiDEaqh.lr...seealee 111
                                                                       e  + e+   ++++al +   +++li+DE    l+   + e+   
  gi|15669064|ref|NP_247868.1| 101 hpytdlfgrlterdkkiiiesaravnaeylleknffEMSDGERQKIMIARALAQE--PKVLILDEPTSfLDakhKIELTLL 179
                                   9999999999999999999999888888775555544444444444444444444..56******9997768533666666 PP

                        AAA_22 112 LrsllnlsrkgvqliLvG 129
                                   Lr+l++  +k++++++  
  gi|15669064|ref|NP_247868.1| 180 LRKLAD--EKNLAIVVTL 195
                                   699999..9999999865 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   2.2   3.6e-07   0.00018      16     220 ..      23     246 ..      19     258 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.6e-07
                      ATPase_2  16 erepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal.............. 82 
                                   e ++ ei+ i Gp g GK++Llk i++ l+  +k v+y++  + ++++ +d     +e +  l++ +              
  gi|15669064|ref|NP_247868.1|  23 EINRGEILCIIGPNGAGKSTLLKTIATYLKP-KKGVVYLNGKKIHDLKPKDLA---KEMAVVLTERVnpgnmtgfdvvaig 99 
                                   567789**********************966.668999877777777766666...4444445555577777888888888 PP

                      ATPase_2  83 ................giavpkaeleeilkeksklvfkaielllekikkkgkk............iiiiiDelqklidlgl 135
                                                   +i +++         +  +++  +e+ + ++++  ++             ++i+De     d + 
  gi|15669064|ref|NP_247868.1| 100 rhpytdlfgrlterdkKIIIES--------ARAVNAEYLLEKNFFEMSDGERQkimiaralaqepKVLILDEPTSFLDAKH 172
                                   8888888866555555333333........333444444444444444433332111111122444666666666664444 PP

                      ATPase_2 136 ngaellvkeLlnliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkeleelskedf 216
                                   +       eL  l+ +l  ek+l++v+ l    l ++ + ++  l++ hk i            + +e  +el++l++ + 
  gi|15669064|ref|NP_247868.1| 173 K------IELTLLLRKLADEKNLAIVVTLHDIELALR-IADKMALIKNHKVIAYGYP----ENVMKREIVNELYDLKNANY 242
                                   4......467777777788888888888888888888.7777777777777554444....24455566666676666666 PP

                      ATPase_2 217 eeiy 220
                                    e+ 
  gi|15669064|ref|NP_247868.1| 243 SEVI 246
                                   6665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   3.4   7.7e-06    0.0039       1      98 [.      30     188 ..      30     286 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.7e-06
                                   EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS.......................................... CS
                           AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellsk.......................................... 37 
                                   ++++Gp G GK++l k +a+ l+    ++ ++g+++ +                                           
  gi|15669064|ref|NP_247868.1|  30 LCIIGPNGAGKSTLLKTIATYLKpkKGVVYLNGKKIHDLkpkdlakemavvltervnpgnmtgfdvvaigrhpytdlfgrl 110
                                   5899******************74355777777777733467777778888888888888888888888888888888888 PP

                                   .........................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
                           AAA  38 .........................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlte 92 
                                                            +     ++ + +++  ++ a +p++l++DE  ++  ++       ++  +  Ll++
  gi|15669064|ref|NP_247868.1| 111 terdkkiiiesaravnaeylleknfFEMSDGERQKIMIA--RALAqEPKVLILDEPTSFLDAK-------HKIELTLLLRK 182
                                   888888888888888888888887433333334444444..4444459999999988888877.......45556666677 PP

                                   HHHTTT CS
                           AAA  93 ldgvkk 98 
                                   l ++k+
  gi|15669064|ref|NP_247868.1| 183 LADEKN 188
                                   766666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.6e-05     0.013      40      81 ..      22      64 ..      16     119 .. 0.82
   2 ?    3.3   0.1      0.14        70      65     176 ..      73     199 ..      68     207 .. 0.51
   3 ?   -2.6   0.0       8.7   4.3e+03      41      52 ..     255     266 ..     230     280 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.6e-05
                         Rad17 40 LesrkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvs 81
                                  Le ++ +iL i GP G gkst +k ++  l +k    +ln+ +
  gi|15669064|ref|NP_247868.1| 22 LEINRGEILCIIGPNGAGKSTLLKTIATYLKPKKgVVYLNGKK 64
                                  6777788*******************99888764145566655 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                         Rad17  65 Lskelgiklrewlnpvslkepdn......qksdfkgltekesrf...lsqiesfkeleL.......kdakylklqklGddl 129
                                   L+ke+++ l e +np ++   d         +d+ g +   ++     s  ++  e++L        d + +k+      l
  gi|15669064|ref|NP_247868.1|  73 LAKEMAVVLTERVNPGNMTGFDVvaigrhPYTDLFGRLTERDKKiiiESARAVNAEYLLeknffemSDGERQKIM-IARAL 152
                                   666666666666666665554443333222334333333333223444444444444220000000333333333.33444 PP

                         Rad17 130 rtdkklilvedlPnkfyrdsdalr.evirkylrssealplilviteie 176
                                     + k++++ d P  f    ++++  ++++ l  ++ l++++ + +ie
  gi|15669064|ref|NP_247868.1| 153 AQEPKVLIL-DEPTSFLDAKHKIElTLLLRKLADEKNLAIVVTLHDIE 199
                                   444454444.44888888887775367778888888888888888776 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 8.7
                         Rad17  41 esrkkriLLisG 52 
                                   + ++k+i +i+G
  gi|15669064|ref|NP_247868.1| 255 PIKNKKIFVICG 266
                                   445567888887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   2.5   1.2e-06   0.00059      15      41 ..      22      49 ..      10     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.2e-06
                        AAA_23 15 idFsk.gltlItGpNGaGKTTildAikl 41
                                  ++ ++  + +I+GpNGaGK+T+l  i  
  gi|15669064|ref|NP_247868.1| 22 LEINRgEILCIIGPNGAGKSTLLKTIAT 49
                                  444442588**************98875 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.7e-05    0.0082      20      60 ..      31      71 ..      21      85 .. 0.88
   2 ?    0.3   0.0       0.7   3.5e+02      71     100 ..     257     286 ..     241     287 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                    Zeta_toxin 20 llgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                   + G  GAGKs+l++ ++++l+++++vv l++ ++  l P+
  gi|15669064|ref|NP_247868.1| 31 CIIGPNGAGKSTLLKTIATYLKPKKGVVYLNGKKIHDLKPK 71
                                  566889*************************9999988886 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.7
                    Zeta_toxin  71 kaseltqkdaselvekllqeaiengyniiv 100
                                   k+ + +    +  ++++l ++++n+y+++v
  gi|15669064|ref|NP_247868.1| 257 KNKKIFVICGGGTGANVLRYLVKNRYDVVV 286
                                   444444444444556677777777777775 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.2e-05     0.011       2      26 ..      29      53 ..      28      59 .. 0.88
   2 ?   -0.2   0.1       1.7   8.5e+02      66     115 ..     139     186 ..     115     199 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.2e-05
                                  CEEEEC-TTTCHHHHHHHHHHHHCT CS
                         NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                  ++++ G++G GK+tLl+ +a+ ++ 
  gi|15669064|ref|NP_247868.1| 29 ILCIIGPNGAGKSTLLKTIATYLKP 53
                                  589*****************98875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.7
                                   -SSS-C.CHHHHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCT CS
                         NACHT  66 aapvse.vwavllelperlLlilDglDelvtdlgqkekqpvrtlLselirk 115
                                   ++  ++ +++ ++  +e  +lilD    +   l++k+k ++  lL++l  +
  gi|15669064|ref|NP_247868.1| 139 SDGERQkIMIARALAQEPKVLILDEPTSF---LDAKHKIELTLLLRKLADE 186
                                   44444435566666666667777644433...3444456666666666555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   5.9e-05     0.029       2      42 ..      30      74 ..      29      94 .. 0.74
   2 ?    0.1   0.0       1.4   7.2e+02      48      73 ..     137     163 ..      98     181 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.9e-05
                                  EEEE--SSSSHHHHHHHGGGGB..S--EEEEE--T..T--HHHHH CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal..nreveyvqltr..dtteedlk 42
                                  ++++Gp G gKs+l + +a  l  ++ v+y ++++  d++++dl 
  gi|15669064|ref|NP_247868.1| 30 LCIIGPNGAGKSTLLKTIATYLkpKKGVVYLNGKKihDLKPKDLA 74
                                  79********************86666666665543355555555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.4
                                   .........--------.G-SEEEEES CS
                         AAA_5  48 kngttslvdsplvraar.egeilvlDE 73 
                                   ++++ ++++  + ra   e+++l+lDE
  gi|15669064|ref|NP_247868.1| 137 EMSDGERQKIMIARALAqEPKVLILDE 163
                                   445555555555555435999999998 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.8e-05    0.0088      11      50 ..      24      62 ..      19     280 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                                  EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEES CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 11 ivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiG 50
                                  i +G+ ++i+g +g Gk++++++++ + + ++ ++y   G
  gi|15669064|ref|NP_247868.1| 24 INRGEILCIIGPNGAGKSTLLKTIATYLKPKKGVVYLN-G 62
                                  67999**********************98886666654.3 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.3e-05     0.016      98     123 ..      26      51 ..       6      64 .. 0.82
   2 ?   -0.2   0.2       1.6   8.2e+02      14      41 ..     184     211 ..     156     287 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-05
                                   TTSEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpel 123
                                   ++++ +++G+ G+GKStL+++++  l
  gi|15669064|ref|NP_247868.1|  26 RGEILCIIGPNGAGKSTLLKTIATYL 51 
                                   45999***************998765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
                                   ES--EEEEEEESTTTT--HHHHHHHHHH CS
                   RsgA_GTPase  14 aNvdqllivvslkepelslnlldrfLvl 41 
                                   a   +l ivv+l++ el l++ d++ ++
  gi|15669064|ref|NP_247868.1| 184 ADEKNLAIVVTLHDIELALRIADKMALI 211
                                   3334444555555555555555544333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.9e-05     0.014       5      47 ..      30      69 ..      26     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.9e-05
                        AAA_24  5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie 47
                                  ++i+Gp+g+GK+tl+k++   + ++   kG+  l+++k+ d++
  gi|15669064|ref|NP_247868.1| 30 LCIIGPNGAGKSTLLKTI---ATYLKPKKGVVYLNGKKIHDLK 69
                                  79****************...6666666666666666666654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   5.3e-05     0.027      19      46 ..      28      56 ..      21     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.3e-05
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g 46
                                   + ++ Gp G+GK+t+lk+++  ++ + g
  gi|15669064|ref|NP_247868.1| 28 EILCIIGPNGAGKSTLLKTIATYLKPKkG 56
                                  47899***************999887733 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.9e-05     0.029      20      48 ..      21      49 ..       9      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-05
                        AAA_27 20 dfsaeeadlhliyGpNEAGKstalrAisd 48
                                  +++ ++ ++  i+GpN AGKst+l+ i  
  gi|15669064|ref|NP_247868.1| 21 NLEINRGEILCIIGPNGAGKSTLLKTIAT 49
                                  4444567788899***********99976 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   0.00011     0.054       1      38 [.      30      62 ..      30      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00011
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrn 38
                                  +++ Gp+g GKStl k++a+ l      +kk+ vy ++
  gi|15669064|ref|NP_247868.1| 30 LCIIGPNGAGKSTLLKTIATYLK-----PKKGVVYLNG 62
                                  5899*************888877.....6777777644 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.078        39      34      56 ..      26      48 ..      21      61 .. 0.82
   2 ?    8.8   0.2    0.0019      0.96     116     159 ..     152     193 ..     128     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.078
                          TniB 34 rmpnlllvGdsnnGKtmivekFa 56
                                  r + l ++G+   GK+++++  a
  gi|15669064|ref|NP_247868.1| 26 RGEILCIIGPNGAGKSTLLKTIA 48
                                  556789************99766 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0019
                          TniB 116 relkvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                    + +++vLi+DE  ++l   a+++ e++ +l++L +e +++iv+
  gi|15669064|ref|NP_247868.1| 152 LAQEPKVLILDEPTSFL--DAKHKIELTLLLRKLADEKNLAIVV 193
                                   35689************..77788899999*******9999996 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00012     0.059       3      32 ..      31      64 ..      29     210 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                        AAA_33  3 llvGlpGsGKstlaerllkklg....avllssdt 32
                                   ++G++G+GKstl++ ++  l+    +v l+  +
  gi|15669064|ref|NP_247868.1| 31 CIIGPNGAGKSTLLKTIATYLKpkkgVVYLNGKK 64
                                  689************9976665555555566665 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00023      0.12     240     265 ..      22      48 ..       8      53 .. 0.87
   2 ?    0.2   0.1      0.52   2.6e+02     376     416 ..     176     216 ..     142     246 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                   EEE-SS.EEEEEE-TTSSHHHHHHHHH CS
                    ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAle 265
                                   + i +G +  I+G++  GKsTLL+ ++
  gi|15669064|ref|NP_247868.1|  22 LEINRGeILCIIGPNGAGKSTLLKTIA 48 
                                   4588999*****************996 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.52
                                   HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEETTEE CS
                    ABC_ATPase 376 lvdrvrelykklgvstilvvggsgdyldvAdtvilmeeykp 416
                                   l+ ++r+l ++ ++ +++    ++  l++Ad++ l++++k+
  gi|15669064|ref|NP_247868.1| 176 LTLLLRKLADEKNLAIVVTLHDIELALRIADKMALIKNHKV 216
                                   33455666666777766666777777777777777777776 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00018     0.088      25      55 ..      31      60 ..      17      89 .. 0.79
   2 ?   -3.0   0.0       5.2   2.6e+03     238     257 ..     153     172 ..     146     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                        AAA_10 25 liiGdlGnGKSvlakllvlyisllggkalii 55
                                   iiG+ G+GKS l k++  y+   +g ++++
  gi|15669064|ref|NP_247868.1| 31 CIIGPNGAGKSTLLKTIATYLKPKKG-VVYL 60
                                  79******************986655.4455 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.2
                        AAA_10 238 kkefkvvifDEawiftssae 257
                                   ++e kv i+DE  +f + + 
  gi|15669064|ref|NP_247868.1| 153 AQEPKVLILDEPTSFLDAKH 172
                                   57788889999888877654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.9    0.0011      0.55       2      42 ..      31      84 ..      30     216 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0011
                        AAA_18  2 lltGtpGvGKttlakeLskrlgf.............gvnlrdvakenglllevd 42
                                  ++ G+ G+GK+tl k ++  l+                + +d+ake   +l++ 
  gi|15669064|ref|NP_247868.1| 31 CIIGPNGAGKSTLLKTIATYLKPkkgvvylngkkihDLKPKDLAKEMAVVLTER 84
                                  899*********999885443223333556655555444455555544444444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00056      0.28       3      22 ..      31      50 ..      29      62 .. 0.83
   2 ?    0.0   0.0       1.8   8.9e+02      19     129 ..     110     145 ..     103     169 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00056
                        AAA_28  3 vitGgestGKTtlleaLaar 22
                                  +i+G+ ++GK+tll+ +a  
  gi|15669064|ref|NP_247868.1| 31 CIIGPNGAGKSTLLKTIATY 50
                                  8**************99954 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.8
                        AAA_28  19 LaargypvvpEaareileekl.akgedalpwvedllafaervleeqleeeaaaaankvlfcDrglldtlaYarayggeaea 98 
                                   L++r+ +++ E+ar +  e l +                                                          
  gi|15669064|ref|NP_247868.1| 110 LTERDKKIIIESARAVNAEYLlE---------------------------------------------------------- 132
                                   55555555555555554443332.......................................................... PP

                        AAA_28  99 eleaaarekrydlvfllppapeidddgeRre 129
                                                    ++ +e+ +dgeR++
  gi|15669064|ref|NP_247868.1| 133 -----------------KNFFEM-SDGERQK 145
                                   .................222233.3333332 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.4    0.0019      0.94       3      26 ..      31      54 ..      29     235 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0019
                                  EEE--TTSSHHHHHHHHHHHH... CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvlellkss 26
                                  +i Gp G GK+Tl+k ++  lk +
  gi|15669064|ref|NP_247868.1| 31 CIIGPNGAGKSTLLKTIATYLKPK 54
                                  688*****************9865 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.9    0.0012      0.58      10      40 ..      27      57 ..      19     197 .. 0.78
   2 ?   -0.0   0.0         2   9.9e+02       8      22 ..     256     270 ..     252     284 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0012
                        AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelggv 40
                                   ++l+++++ G GK+++lk+i ++l+  +gv
  gi|15669064|ref|NP_247868.1| 27 GEILCIIGPNGAGKSTLLKTIATYLKPKKGV 57
                                  57899*****************999988876 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2
                        AAA_19   8 lkekvllvtaGpGtG 22 
                                   +k+k ++v+ G GtG
  gi|15669064|ref|NP_247868.1| 256 IKNKKIFVICGGGTG 270
                                   5789999*******9 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0012      0.57      44      69 ..      24      49 ..      21      79 .. 0.84
   2 ?    0.6   0.1      0.82   4.1e+02      99     141 ..     148     187 ..     123     211 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                     IstB_IS21 44 iekkenivllGpsGvGKshlaialgv 69
                                  i++ e ++++Gp G+GKs l  ++++
  gi|15669064|ref|NP_247868.1| 24 INRGEILCIIGPNGAGKSTLLKTIAT 49
                                  678899************99888775 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.82
                     IstB_IS21  99 laralkrllkvdllilDdlgllpldqaeaellfeviekryerr 141
                                   +aral   +++++lilD+     ld +++ +l  ++ k  + +
  gi|15669064|ref|NP_247868.1| 148 IARAL--AQEPKVLILDEPT-SFLDAKHKIELTLLLRKLADEK 187
                                   33333..346799***9964.4455555555555555555554 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0067       3.4      21      39 ..      32      50 ..      22      72 .. 0.85
   2 ?    3.9   0.1     0.033        16     525     616 ..     154     258 ..     135     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0067
                        AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                  i G NGaGK+tL + ++  
  gi|15669064|ref|NP_247868.1| 32 IIGPNGAGKSTLLKTIATY 50
                                  78**********9999875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.033
                        AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkntkr............krkkke.... 589
                                   ++ k+ ++D P S LD+++      l+++ + ++k+   + +  H +e+   + +++              +    +    
  gi|15669064|ref|NP_247868.1| 154 QEPKVLILDEPTSFLDAKHKIELTLLLRKLA-DEKNL-AIVVTLHDIELALRIADKMALiknhkviaygypE----Nvmkr 228
                                   5789************************998.44444.4666669999999998876633223344433331....13334 PP

                        AAA_13 590 ...esfyllkksqksskikelkrllneies 616
                                      +++y lk+++ s  i + + ++n+i++
  gi|15669064|ref|NP_247868.1| 229 eivNELYDLKNANYSEVIGYFELKNNPIKN 258
                                   556888888887666677776666788876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00048      0.24      25      67 ..      30      72 ..      12      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00048
                  Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvagkk 67
                                  l ++Gp G+GK+ l k +++ l p +    l+ +ki+ ++ k+
  gi|15669064|ref|NP_247868.1| 30 LCIIGPNGAGKSTLLKTIATYLKPKKGVVYLNGKKIHDLKPKD 72
                                  7899******************999999999999998877644 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00049      0.25       3      33 ..      29      59 ..      27      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00049
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                         SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvl 33
                                  ++ ++G++GaGK t l  +a +lk ++  v 
  gi|15669064|ref|NP_247868.1| 29 ILCIIGPNGAGKSTLLKTIATYLKPKKGVVY 59
                                  6789*******************98876555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1     0.002         1      21      42 ..      28      49 ..      19      59 .. 0.84
   2 ?    1.3   0.2      0.33   1.6e+02      81     111 ..     133     163 ..     111     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.002
                                  EEEEEEESTTSSHHHHHHHHCC CS
                        NB-ARC 21 lvvalvGmgGvGKttlakqiln 42
                                   ++ + G  G GK+tl+k i  
  gi|15669064|ref|NP_247868.1| 28 EILCIIGPNGAGKSTLLKTIAT 49
                                  4899**************9976 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.33
                                   TTSSSS-STTSHHHHHHHHCCCTTEEEEEEE CS
                        NB-ARC  81 ddleekeeveslkrklvrlLltkrfllvlDD 111
                                   ++  e++++e  k ++ r+L +   +l+lD 
  gi|15669064|ref|NP_247868.1| 133 KNFFEMSDGERQKIMIARALAQEPKVLILDE 163
                                   4555677788799999999999999999995 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0025       1.2       2      20 ..      31      49 ..      30      52 .. 0.88
   2 ?    0.5   0.0         1   5.2e+02     112     149 ..     165     202 ..     141     233 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0025
                                  EEE-STTSSHHHHHHHHHH CS
                        MutS_V  2 litGpnmaGkstylrqval 20
                                   i Gpn aGkst+l+ +a 
  gi|15669064|ref|NP_247868.1| 31 CIIGPNGAGKSTLLKTIAT 49
                                  589************9985 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1
                                   -EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEE CS
                        MutS_V 112 aktlfatHyheltklaekleevknlhlavkeeeedivf 149
                                   +  l a H  elt l +kl++ knl + v+ ++ ++++
  gi|15669064|ref|NP_247868.1| 165 TSFLDAKHKIELTLLLRKLADEKNLAIVVTLHDIELAL 202
                                   55667889999999999999988888888766544443 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.8   0.00098      0.49       3      21 ..      31      49 ..      29     219 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00098
                                  EEEESTTSSHHHHHHHHHT CS
                      MMR_HSR1  3 aivGrpNvGKStLinaltg 21
                                  +i+G   +GKStL++++  
  gi|15669064|ref|NP_247868.1| 31 CIIGPNGAGKSTLLKTIAT 49
                                  89*************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 1654.29
//
Query:       gi|15669065|ref|NP_247869.1|  [L=93]
Description: hypothetical protein MJ_0874 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.051   12.7   0.1      0.051   12.7   0.1    1.1  1  Plant_NMP1  Plant nuclear matrix protein 1 (NMP1)


Domain annotation for each model (and alignments):
>> Plant_NMP1  Plant nuclear matrix protein 1 (NMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.8e-06     0.051     140     181 ..      36      78 ..       5      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.8e-06
                    Plant_NMP1 140 aqifseeck.lfpadvqiqsiyplpdiaelekklseyskklss 181
                                    + f e  k l  +dv + + +p+ ++ el++kl e++k+l +
  gi|15669065|ref|NP_247869.1|  36 KETFEEALKeLKNSDVVVYTDFPIGEMNELNLKLIEEAKNLKK 78 
                                   45677777646789*************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1315  (0.0733449); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 652.14
//
Query:       gi|15669066|ref|NP_247870.1|  [L=748]
Description: hypothetical protein MJ_0875 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-10   39.5   6.7    9.4e-05   22.6   0.2    5.6  5  TPR_12          Tetratricopeptide repeat
    1.1e-06   28.3   4.2        1.9    8.7   0.0    6.7  7  TPR_7           Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.13   12.6   0.0       0.13   12.6   0.0    3.3  3  HEPN_Swt1       Swt1-like HEPN
       0.16   12.2  42.2       0.61   10.3   0.9    8.0  9  TPR_2           Tetratricopeptide repeat
       0.33   12.0   6.9        1.5    9.9   0.1    3.7  3  SpoIIAA-like    SpoIIAA-like
        1.9    8.5  40.1       0.22   11.4   0.9    8.1  9  TPR_1           Tetratricopeptide repeat
          6    7.4  11.4         58    4.3   0.3    5.9  6  PPR             PPR repeat


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.2   3.7e-08   9.4e-05      15      75 ..      27      89 ..      25      91 .. 0.83
   2 !    7.6   0.0    0.0018       4.6      16      41 ..     171     196 ..     165     199 .. 0.88
   3 ?    1.8   0.1      0.12     3e+02      48      71 ..     212     235 ..     210     238 .. 0.84
   4 ?    5.2   0.0      0.01        27      57      71 ..     347     361 ..     343     367 .. 0.66
   5 ?   -0.2   0.0       0.5   1.3e+03      58      74 ..     395     411 ..     392     419 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.7e-08
                        TPR_12 15 rlgrydeAlellekaleiarrl.lGpdhpl.tattlrnLgrlyralgryeeAlelleealaia 75
                                  + g+y ++ el+ ka ei++++  ++++ + +a+++  ++  y+ ++++++A+e++++a +++
  gi|15669066|ref|NP_247870.1| 27 QNGNYKKSAELFLKASEIYNKIrDEKNKKWtLANYYSIMAKEYSFSNEFDKAREFYKKAEELF 89
                                  78********************44444455256677778999*****************9987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0018
                        TPR_12  16 lgrydeAlellekaleiarrllGpdh 41 
                                    g++d+A+el ek++ +a++++++ +
  gi|15669066|ref|NP_247870.1| 171 EGNLDKAIELTEKCYKLAEESYNKFN 196
                                   79*****************9998765 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.12
                        TPR_12  48 lrnLgrlyralgryeeAlelleea 71 
                                   ++ +++ ++   +++eA e+++++
  gi|15669066|ref|NP_247870.1| 212 YNLMAQKFESERKFKEAAEYYKKS 235
                                   77888888777899*******986 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.01
                        TPR_12  57 algryeeAlelleea 71 
                                   + g+ye+Al++l++a
  gi|15669066|ref|NP_247870.1| 347 LNGNYEKALNFLQKA 361
                                   457777777777766 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.5
                        TPR_12  58 lgryeeAlelleealai 74 
                                   +g++++ +ell e l+i
  gi|15669066|ref|NP_247870.1| 395 QGEFKKSVELLDEYLEI 411
                                   45555555555555555 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.11   2.8e+02      12      28 ..      28      44 ..      26      53 .. 0.78
   2 ?    4.8   0.0     0.013        33       9      24 ..      69      84 ..      62      96 .. 0.84
   3 ?    2.3   0.0     0.084   2.2e+02      10      31 ..     168     190 ..     164     194 .. 0.78
   4 !    8.7   0.0   0.00072       1.9       2      24 ..     212     234 ..     212     246 .. 0.85
   5 ?    2.8   0.0     0.058   1.5e+02      13      24 ..     349     360 ..     346     368 .. 0.87
   6 ?    1.3   0.0      0.17   4.3e+02      11      24 ..     394     407 ..     388     418 .. 0.78
   7 ?   -4.2   0.0         7   1.8e+04      13      23 ..     605     615 ..     605     618 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.11
                         TPR_7 12 lGdyeeAielyeqsLal 28
                                   G+y++ +el+ ++ ++
  gi|15669066|ref|NP_247870.1| 28 NGNYKKSAELFLKASEI 44
                                  59*********996555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.013
                         TPR_7  9 ysrlGdyeeAielyeq 24
                                  ys  +++++A e+y++
  gi|15669066|ref|NP_247870.1| 69 YSFSNEFDKAREFYKK 84
                                  66689**********9 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.084
                         TPR_7  10 sr.lGdyeeAielyeqsLaltkd 31 
                                   ++ +G+ ++Aiel e++  l+++
  gi|15669066|ref|NP_247870.1| 168 RKfEGNLDKAIELTEKCYKLAEE 190
                                   55689********9998877766 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.00072
                         TPR_7   2 LlnLarlysrlGdyeeAielyeq 24 
                                   ++ +a+ ++++++++eA+e+y++
  gi|15669066|ref|NP_247870.1| 212 YNLMAQKFESERKFKEAAEYYKK 234
                                   5678888999************9 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.058
                         TPR_7  13 GdyeeAielyeq 24 
                                   G+ye+A+ ++++
  gi|15669066|ref|NP_247870.1| 349 GNYEKALNFLQK 360
                                   9*********99 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.17
                         TPR_7  11 rlGdyeeAielyeq 24 
                                   ++G++++ +el+ +
  gi|15669066|ref|NP_247870.1| 394 SQGEFKKSVELLDE 407
                                   59*********987 PP

  == domain 7  score: -4.2 bits;  conditional E-value: 7
                         TPR_7  13 GdyeeAielye 23 
                                   Gd+++ ++l++
  gi|15669066|ref|NP_247870.1| 605 GDFAQSLRLLK 615
                                   78888888776 PP

>> HEPN_Swt1  Swt1-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.9      0.33   8.4e+02      22      77 ..      27      80 ..      14      89 .. 0.73
   2 ?   -2.2   0.1         2   5.1e+03       4      39 ..     100     134 ..      98     178 .. 0.52
   3 ?   12.6   0.0     5e-05      0.13       4      93 ..     562     646 ..     560     665 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.33
                     HEPN_Swt1 22 ygedwweeveaslekdeeekkesekeiskldvqdllrvitenWkevFkkklsraer 77
                                   + ++ + +e  l+++e  +k ++++ +k+++++  +++ +++ + F++++ +a +
  gi|15669066|ref|NP_247870.1| 27 QNGNYKKSAELFLKASEIYNKIRDEKNKKWTLANYYSIMAKEY-S-FSNEFDKARE 80
                                  3334666666677777777778999999*************98.5.9999988775 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                     HEPN_Swt1   4 dlLeegLrpfverelskaygedwweeveaslekdee 39 
                                   +++   L++++ +e +k  ++d  + +e  l+k+  
  gi|15669066|ref|NP_247870.1| 100 YCFYYYLKTYIYEEKEKVEKKDNDKYLEL-LNKYII 134
                                   55556666666665555444443333332.222222 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 5e-05
                     HEPN_Swt1   4 dlLeegLrpfverelskaygedwweeveaslekdeeekkesekeiskldvqdllrvitenWkevFkkklsraerslaseLr 84 
                                   +lLe+ L+  ve    + +g++w + +e+    + +++k++ +     d++++lr+++++  e + k++  +   l ++  
  gi|15669066|ref|NP_247870.1| 562 RLLENYLKIIVEFNAMALWGDTWKQILEE----KISNRKKPFEIFTFGDFAQSLRLLKNEGCE-YCKNIDDEIFDLLDKHV 637
                                   58999999999999999999999999997....45555568899999****************.99*************** PP

                     HEPN_Swt1  85 evRNkwaHq 93 
                                   ++RN+++H 
  gi|15669066|ref|NP_247870.1| 638 KIRNNLSHD 646
                                   ********5 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.6     0.003       7.7      13      31 ..      27      45 ..      18      48 .. 0.87
   2 ?   10.3   0.9   0.00024      0.61       2      30 ..      60      88 ..      59      91 .. 0.89
   3 ?    6.8   0.1    0.0031         8      15      32 ..     172     189 ..     170     191 .. 0.91
   4 ?   -4.0   0.1         7   1.8e+04      13      20 ..     196     203 ..     195     204 .. 0.75
   5 ?    5.8   1.8    0.0069        18       3      26 ..     211     234 ..     209     235 .. 0.91
   6 ?   -2.9   0.4       4.3   1.1e+04       4      12 ..     290     298 ..     288     300 .. 0.74
   7 ?    7.8   0.8    0.0016         4      13      28 ..     347     362 ..     338     367 .. 0.89
   8 ?    0.8   0.0      0.26   6.8e+02      12      30 ..     393     411 ..     390     413 .. 0.87
   9 ?   -3.6   0.0       6.7   1.7e+04      16      29 ..     537     550 ..     536     553 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.003
                         TPR_2 13 klgdyeeAleafekAleld 31
                                  ++g+y++ +e+f kA e++
  gi|15669066|ref|NP_247870.1| 27 QNGNYKKSAELFLKASEIY 45
                                  89*************9987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00024
                         TPR_2  2 ealynlGlayyklgdyeeAleafekAlel 30
                                   ++  +++ y  ++++++A+e+++kA el
  gi|15669066|ref|NP_247870.1| 60 NYYSIMAKEYSFSNEFDKAREFYKKAEEL 88
                                  6788899999999*************988 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0031
                         TPR_2  15 gdyeeAleafekAleldP 32 
                                   g++++A+e+ ek+ +l++
  gi|15669066|ref|NP_247870.1| 172 GNLDKAIELTEKCYKLAE 189
                                   9**************987 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 7
                         TPR_2  13 klgdyeeA 20 
                                   + ++y++A
  gi|15669066|ref|NP_247870.1| 196 NDKNYKKA 203
                                   56899999 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.0069
                         TPR_2   3 alynlGlayyklgdyeeAleafek 26 
                                   +++ +++  +   +++eA+e+++k
  gi|15669066|ref|NP_247870.1| 211 YYNLMAQKFESERKFKEAAEYYKK 234
                                   7999999999************98 PP

  == domain 6  score: -2.9 bits;  conditional E-value: 4.3
                         TPR_2   4 lynlGlayy 12 
                                   +y+lGl y 
  gi|15669066|ref|NP_247870.1| 290 YYYLGLKYD 298
                                   899998875 PP

  == domain 7  score: 7.8 bits;  conditional E-value: 0.0016
                         TPR_2  13 klgdyeeAleafekAl 28 
                                    +g+ye+Al++++kA 
  gi|15669066|ref|NP_247870.1| 347 LNGNYEKALNFLQKAK 362
                                   58************96 PP

  == domain 8  score: 0.8 bits;  conditional E-value: 0.26
                         TPR_2  12 yklgdyeeAleafekAlel 30 
                                   + +g++++ +e++++ le+
  gi|15669066|ref|NP_247870.1| 393 ISQGEFKKSVELLDEYLEI 411
                                   579***********99987 PP

  == domain 9  score: -3.6 bits;  conditional E-value: 6.7
                         TPR_2  16 dyeeAleafekAle 29 
                                   +++ ++ ++e++l 
  gi|15669066|ref|NP_247870.1| 537 NFDNCIYFLEEVLD 550
                                   89999999999986 PP

>> SpoIIAA-like  SpoIIAA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.4     0.083   2.1e+02       9      65 ..     116     190 ..     110     230 .. 0.61
   2 ?    0.1   0.1      0.69   1.8e+03       5      39 ..     259     305 ..     256     359 .. 0.49
   3 ?    9.9   0.1   0.00059       1.5       3      83 ..     495     604 ..     494     612 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.083
                                   EE-HHHHHH.HHHHHHHHC.C..........SSSEEEEEEE.....HHHHHHH.CCCGGECEEEEE-SS..CCCCC CS
                  SpoIIAA-like   9 kitaedykevliellekal.a..........hgkirllvdl.....ediklgl.ahlsrfrrvAvvtdk..kwika 65 
                                   k++++d ++ + ell+k + +             i++++d+     +++++++ ++ + ++++  +t+k  k+++ 
  gi|15669066|ref|NP_247870.1| 116 KVEKKDNDK-YLELLNKYIiEaeqflekykeFSDIWMYFDIkiyyyKKLSIKHrKFEGNLDKAIELTEKcyKLAEE 190
                                   677777777.777774444444444445555788999999966666444333333355555555555544444444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.69
                                   EEEEEE-HHHHHH.HHHHH...HHHCC.SSSEEEEEEE...........H CS
                  SpoIIAA-like   5 eisgkitaedykevliell...ekala.hgkirllvdl...........e 39 
                                    i+ k ++e ++e++++++   e   + ++k++ ++ l           +
  gi|15669066|ref|NP_247870.1| 259 AIENKYNKEKFEEYINKAIefsE---KrGDKLQEYYYLglkydhlvrfaN 305
                                   57778888889998888883331...135555555555333332222221 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00059
                                   EEEEEEEE-HHHHHH.HHHHHHHHCCSSSEEEEEEE...................HHHH.HHHCC.............CGG CS
                  SpoIIAA-like   3 aveisgkitaedykevliellekalahgkirllvdl...................edik.lglah.............lsr 50 
                                    ++i ++it+ed+ + l++ ++ ++a ++ ++l+ l                   +++k +   +             + +
  gi|15669066|ref|NP_247870.1| 495 KLKIIKQITTEDVSKDLENRIKIQMAIERNDWLLRLppalvenfdnciyfleevlDEFKhAA--YrefyrllenylkiIVE 573
                                   678999*********9****97666799*************999988888876663333222..1224555566778899* PP

                                   ECEEEEE-SSCCCCCC.CCHHCCH.-CCEEEEE CS
                  SpoIIAA-like  51 frrvAvvtdkkwikalvallasalflslevkvF 83 
                                   f+++A+++d+ w + l +++++  ++ +e+ +F
  gi|15669066|ref|NP_247870.1| 574 FNAMALWGDT-WKQILEEKISNRKKP-FEIFTF 604
                                   *********9.888887888776544.565555 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4     0.082   2.1e+02      13      30 ..      27      44 ..      25      47 .. 0.89
   2 ?   11.4   0.9   8.8e-05      0.22       2      30 ..      60      88 ..      59      89 .. 0.88
   3 ?    3.6   0.3     0.026        67      15      32 ..     172     189 ..     170     194 .. 0.84
   4 ?    7.3   2.2    0.0017       4.5       4      26 ..     212     234 ..     210     235 .. 0.93
   5 ?   -2.2   0.1       1.7   4.4e+03      22      30 ..     271     279 ..     270     282 .. 0.77
   6 ?   -1.7   0.3       1.2   3.1e+03       4      14 ..     290     300 ..     288     304 .. 0.80
   7 ?    7.8   0.3    0.0011       2.9      13      27 ..     347     361 ..     345     363 .. 0.89
   8 ?   -0.8   0.0      0.61   1.6e+03      13      30 ..     394     411 ..     393     412 .. 0.88
   9 ?   -3.8   0.0       5.4   1.4e+04      16      28 ..     537     549 ..     536     550 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.082
                                  HTT-HHHHHHHHHHHHHH CS
                         TPR_1 13 klgkydeAleyyekALel 30
                                  ++g+y++  e + kA e+
  gi|15669066|ref|NP_247870.1| 27 QNGNYKKSAELFLKASEI 44
                                  79************9877 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8.8e-05
                                  HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1  2 kalynlGnayfklgkydeAleyyekALel 30
                                  + +  ++  y   +++d+A e+y+kA el
  gi|15669066|ref|NP_247870.1| 60 NYYSIMAKEYSFSNEFDKAREFYKKAEEL 88
                                  668889999*****************876 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.026
                                   T-HHHHHHHHHHHHHHST CS
                         TPR_1  15 gkydeAleyyekALelnP 32 
                                   g++d+A+e  ek+ +l +
  gi|15669066|ref|NP_247870.1| 172 GNLDKAIELTEKCYKLAE 189
                                   899999999999988765 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0017
                                   HHHHHHHHHHTT-HHHHHHHHHH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyek 26 
                                   ++ +++ + +  k++eA eyy+k
  gi|15669066|ref|NP_247870.1| 212 YNLMAQKFESERKFKEAAEYYKK 234
                                   899999****************9 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 1.7
                                   HHHHHHHHH CS
                         TPR_1  22 eyyekALel 30 
                                   ey +kA+e 
  gi|15669066|ref|NP_247870.1| 271 EYINKAIEF 279
                                   788999986 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHT CS
                         TPR_1   4 lynlGnayfkl 14 
                                   +y lG+ y +l
  gi|15669066|ref|NP_247870.1| 290 YYYLGLKYDHL 300
                                   999**999776 PP

  == domain 7  score: 7.8 bits;  conditional E-value: 0.0011
                                   HTT-HHHHHHHHHHH CS
                         TPR_1  13 klgkydeAleyyekA 27 
                                    +g+y++Al + +kA
  gi|15669066|ref|NP_247870.1| 347 LNGNYEKALNFLQKA 361
                                   58************9 PP

  == domain 8  score: -0.8 bits;  conditional E-value: 0.61
                                   HTT-HHHHHHHHHHHHHH CS
                         TPR_1  13 klgkydeAleyyekALel 30 
                                   ++g++++ +e  ++ Le+
  gi|15669066|ref|NP_247870.1| 394 SQGEFKKSVELLDEYLEI 411
                                   69********99999987 PP

  == domain 9  score: -3.8 bits;  conditional E-value: 5.4
                                   -HHHHHHHHHHHH CS
                         TPR_1  16 kydeAleyyekAL 28 
                                   ++d ++ + e++L
  gi|15669066|ref|NP_247870.1| 537 NFDNCIYFLEEVL 549
                                   8999999999988 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.86   2.2e+03      12      25 ..      27      40 ..      26      51 .. 0.71
   2 ?    4.3   0.3     0.023        58       3      27 ..      62      86 ..      61      91 .. 0.90
   3 ?   -0.9   0.0      0.97   2.5e+03      13      23 ..     171     181 ..     171     184 .. 0.84
   4 ?    2.7   0.2     0.073   1.9e+02       3      25 ..     212     234 ..     210     235 .. 0.93
   5 ?    1.8   0.0      0.14   3.7e+02      13      28 ..     348     363 ..     347     364 .. 0.87
   6 ?   -1.6   0.0       1.7   4.4e+03      13      25 ..     395     407 ..     394     411 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.86
                           PPR 12 knGkleeAlelfke 25
                                  +nG++++  elf +
  gi|15669066|ref|NP_247870.1| 27 QNGNYKKSAELFLK 40
                                  57777777777754 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.023
                           PPR  3 ynslIsgycknGkleeAlelfkeMk 27
                                  y+++ + y+ ++++++A e++k+ +
  gi|15669066|ref|NP_247870.1| 62 YSIMAKEYSFSNEFDKAREFYKKAE 86
                                  8999999**************9855 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.97
                           PPR  13 nGkleeAlelf 23 
                                   +G+l++A+el 
  gi|15669066|ref|NP_247870.1| 171 EGNLDKAIELT 181
                                   59*******95 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.073
                           PPR   3 ynslIsgycknGkleeAlelfke 25 
                                   yn + + + +++k++eA e++k+
  gi|15669066|ref|NP_247870.1| 212 YNLMAQKFESERKFKEAAEYYKK 234
                                   9******************9986 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.14
                           PPR  13 nGkleeAlelfkeMke 28 
                                   nG++e+Al ++++ k+
  gi|15669066|ref|NP_247870.1| 348 NGNYEKALNFLQKAKK 363
                                   8*********998776 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 1.7
                           PPR  13 nGkleeAlelfke 25 
                                    G++++ +el++e
  gi|15669066|ref|NP_247870.1| 395 QGEFKKSVELLDE 407
                                   6999*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (748 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1796  (0.100173); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.77u 0.29s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 4499.97
//
Query:       gi|15669067|ref|NP_247871.1|  [L=351]
Description: iron(III dicitrate transport system permease [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-58  197.7  34.6    3.5e-58  197.0  34.6    1.3  1  FecCD     FecCD transport family
    4.9e-06   26.2  15.9    4.9e-06   26.2  15.9    2.9  4  ABC-3     ABC 3 transport family
  ------ inclusion threshold ------
      0.023   13.0  29.6      0.017   13.5  16.2    2.0  2  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.0  34.6   5.9e-62   3.5e-58       5     312 .]      10     343 ..       6     343 .. 0.91

  Alignments for each domain:
  == domain 1  score: 197.0 bits;  conditional E-value: 5.9e-62
                         FecCD   5 llllsl........llgav.kispsevfeallgka..dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadP 74 
                                   l++lsl        l+g++  i++++++++ll+++  +++++ i+ ++rlp ++ a+l+G  ++vaG++lQt++rN La+P
  gi|15669067|ref|NP_247871.1|  10 LFILSLilpftalyLAGDThLITVKDIINFLLKGTtgNEFKDIIIKDVRLPPIIGAVLIGLTISVAGLMLQTLFRNLLASP 90 
                                   55555444444445666666999********99889999****************************************** PP

                         FecCD  75 silGissgaalgavlallll.....lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsl 150
                                   ++ Gissg  ++++l++++      ++ +++ ++++a   g++++++l++++a   +  +   +i++ + +s+++ +l ++
  gi|15669067|ref|NP_247871.1|  91 YTTGISSGVLMVVALVIFIDslshlFEIFGEKSILVAGWCGGIFSMILLIIIA--LRVREANGVIIVALLLSYFFMGLRAY 169
                                   ********8887777776559999999999***********************..88888899****************** PP

                         FecCD 151 lllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvall 231
                                   l+++++e +++++   ++Gsls++++ +v+ + + ++++++ +++l++ l++l +g++ Aks+G++++++rll+l++++++
  gi|15669067|ref|NP_247871.1| 170 LIANAEELKIQEYWGFTIGSLSKITLGDVIPMTICSIIFIIGVMFLIKSLNALLFGEQYAKSFGLDIKKTRLLVLFFASFI 250
                                   ********************************************************************************* PP

                         FecCD 232 tavavalvGpigFvGLivPhiarllvg.adhrkllplsallGallllladllarlllsptel...........pvgivtal 300
                                   t++++ +vG i+F+G+i+P +ar l++ +dhr+l+p++++lG++l++ + +l+  ++ p+             p+g+v+ +
  gi|15669067|ref|NP_247871.1| 251 TGAIIPYVGLIAFIGIIAPYLARPLIKtSDHRYLVPATMFLGVILMVSCHILSLKYYLPIHYlyginrpasplPIGAVLDI 331
                                   ****************************************************988776665445666666666******** PP

                         FecCD 301 iGapffiylllr 312
                                   +G+++ +yl+++
  gi|15669067|ref|NP_247871.1| 332 LGGMLVVYLVYK 343
                                   ********9976 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2      0.41   2.5e+03     186     207 ..       3      25 ..       1      46 [. 0.53
   2 ?    0.8   2.3     0.047   2.8e+02      56     101 ..      61     108 ..      57     120 .. 0.62
   3 ?   -1.4   9.0      0.23   1.4e+03     187     254 ..      97     165 ..      72     169 .. 0.77
   4 !   26.2  15.9   8.2e-10   4.9e-06      73     235 ..     141     306 ..     121     310 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.41
                         ABC-3 186 avGviLviall..iiPaatArrlt 207
                                    vG++L+  +l  i+P  tA++l+
  gi|15669067|ref|NP_247871.1|   3 KVGILLILFILslILP-FTALYLA 25 
                                   5677666655411333.3444444 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.047
                         ABC-3  56 lllgailvgliaavalellkrktk..lkedtaigivlsvflalglvlv 101
                                   +++ga+l+gl ++va  +l++  +  l++   +gi   v + ++lv++
  gi|15669067|ref|NP_247871.1|  61 PIIGAVLIGLTISVAGLMLQTLFRnlLASPYTTGISSGVLMVVALVIF 108
                                   666666666666666666666555224555666666666666666654 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.23
                         ABC-3 187 vGviLvialliiPaatArrltrslesllivAill.glvsvvaGlllSyyldlatGavivlvatllflla 254
                                    Gv++v+al+i   ++  ++    e+ ++vA  + g++s+++ +++   +  a G +iv+++ + f++ 
  gi|15669067|ref|NP_247871.1|  97 SGVLMVVALVIFIDSLSHLFEIFGEKSILVAGWCgGIFSMILLIIIALRVREANGVIIVALLLSYFFMG 165
                                   4999*****999999999998877777777766615667777888899999999999999988888775 PP

  == domain 4  score: 26.2 bits;  conditional E-value: 8.2e-10
                         ABC-3  73 llkrktklkedtai.givls.vflalglvlvslikk.skvdldsyLfGniltisqedliliaiieavvllllllfwkelll 150
                                   +++ + + ++ ++i +++ls +f++l   l+  +++   ++ + +  G++  i+  d+i ++i +++ ++ ++++ k+l +
  gi|15669067|ref|NP_247871.1| 141 IIALRVREANGVIIvALLLSyFFMGLRAYLIANAEElKIQEYWGFTIGSLSKITLGDVIPMTICSIIFIIGVMFLIKSLNA 221
                                   4444444444444414444413445555666666665567788899*********************************** PP

                         ABC-3 151 itfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltr..slesllivAillglvsvvaGl 229
                                   + f e++Ak+ gl +k  +ll l   +    ++++ vG+i  i + i+P  +Ar l +  + + l+   + lg++ +v+  
  gi|15669067|ref|NP_247871.1| 222 LLFGEQYAKSFGLDIKKTRLLVLFFASFITGAIIPYVGLIAFIGI-IAP-YLARPLIKtsDHRYLVPATMFLGVILMVSCH 300
                                   ***************************************999986.556.4555554400445566667778999999888 PP

                         ABC-3 230 llSyyl 235
                                   +lS  +
  gi|15669067|ref|NP_247871.1| 301 ILSLKY 306
                                   888766 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5  16.2   2.8e-06     0.017      35     176 ..      28     220 ..       4     224 .. 0.76
   2 ?    5.5   5.6   0.00074       4.4       4     119 ..     227     342 ..     224     349 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-06
                       DUF2070  35 ssk...............................lfgillfglpalvaflltlpvlrilggrltykrslflalltelivvi 84 
                                    +                                ++g +l+gl++ va+l+++ + r l   l +   + ++   +++v++
  gi|15669067|ref|NP_247871.1|  28 THLitvkdiinfllkgttgnefkdiiikdvrlppIIGAVLIGLTISVAGLMLQTLFRNL---LASPYTTGISSGVLMVVAL 105
                                   33366666666666668888888899999999999*******************99988...6666666666666666666 PP

                       DUF2070  85 isllaillsallqalvllalvls..lalvfalrllvlvavsdesllkavlpaliqpllailllvly............... 148
                                   ++++ +l   l++ +   +++++  +  +f++ ll+++a+  ++   ++++al+ +++++ l  ++               
  gi|15669067|ref|NP_247871.1| 106 VIFIDSLSH-LFEIFGEKSILVAgwCGGIFSMILLIIIALRVREANGVIIVALLLSYFFMGLRAYLianaeelkiqeywgf 185
                                   566666654.3434444555555557799999999999999999999999999999998888777789************* PP

                       DUF2070 149 .......fspesfllllllslifalavylfivvvd 176
                                          ++  +++++ + s+if+++v+++i+ ++
  gi|15669067|ref|NP_247871.1| 186 tigslskITLGDVIPMTICSIIFIIGVMFLIKSLN 220
                                   *******9***********************9877 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.00074
                       DUF2070   4 lskyifrlPswkvsllliillalligllaflssklfgillfglpalvaflltlpvlrilggrltykrslflalltelivvi 84 
                                    + + f l+  k+ ll++++ ++++g++   ++ l++++      ++a  l  p+++++ +r+ +   +fl ++ ++ + i
  gi|15669067|ref|NP_247871.1| 227 QYAKSFGLDIKKTRLLVLFFASFITGAIIPYVG-LIAFI-----GIIAPYLARPLIKTSDHRYLVPATMFLGVILMVSCHI 301
                                   567778888888999999999999888875444.44444.....456666666666666666668999************* PP

                       DUF2070  85 isllaillsall......qalvllalvlslalvfalrllvl 119
                                   +sl  +l  ++l      ++ ++   vl++   + +++lv+
  gi|15669067|ref|NP_247871.1| 302 LSLKYYLPIHYLyginrpASPLPIGAVLDILGGMLVVYLVY 342
                                   99999998888877666666666666666666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2249.80
//
Query:       gi|15669068|ref|NP_247873.1|  [L=414]
Description: hypothetical protein MJ_0878 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-23   81.8   0.0    9.4e-23   81.0   0.0    1.3  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.0   5.2e-27   9.4e-23      33     233 ..     157     361 ..     143     366 .. 0.87

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 5.2e-27
                                   GGGGT......TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHHHS-EEE----TTS..HHHHHHHHHHHHH CS
                  Peripla_BP_2  33 dadklee....aivevgadgeidvEklaalkPDlvilskglgltdedeellksgiptvivessntg..eslkeqiralgel 107
                                   ++d +++    +i++vg++++++++k+++  P ++++ +g++  + + +  ++gi +v++ +  +    +++e++++++  
  gi|15669068|ref|NP_247873.1| 157 FKDINKSlaegKIIDVGSSSNPNWDKIIEINPQVIFVYPGYDGDKIIAKCKELGITYVADAEYLENdpLGRCEWVKMFAAF 237
                                   444444444589*****************************88888889999******9988766677************* PP

                                   TT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TTSTTT.HHHHTS--EESTTT--STT-EEE-HH CS
                  Peripla_BP_2 108 lgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsnsyig.dlldalgieniaaeskkseyeeisaE 187
                                   +++e ea+ +++++++   ++ +++++  + +v++ +++++ g +v+ +nsy+  +++   ++++i+++ ++ ++++i+ E
  gi|15669068|ref|NP_247873.1| 238 YNKEPEAKRYFEKVEDNCLKVINKTKNCPKVTVAWGYNSQW-GCYVPENNSYVAkEIMFYCNGDYIFKDLNGTGSAKINYE 317
                                   ****************************8888888888888.888888888886156666********************* PP

                                   HHHH..H--SEEEEEEHHHHT-S--HHHHT-S.HHHHTSHHHHTT-EEE CS
                  Peripla_BP_2 188 qila..sdpdvifvsgraeadnktgleflken.pllaelpAvkngrVya 233
                                   ++++   d+dv++v ++     ++ l+ +ke+ p+++ ++AvkngrV++
  gi|15669068|ref|NP_247873.1| 318 TFAEraKDADVWVVPSS-----TAWLSTFKEDnPGYETFKAVKNGRVFC 361
                                   *****************.....77888887777**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2696.01
//
Query:       gi|15669069|ref|NP_247874.1|  [L=279]
Description: nitrogenase reductase-like protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     2e-121  404.6   4.1   2.2e-121  404.4   4.1    1.0  1  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
    2.4e-12   47.2   1.1    5.5e-11   42.7   0.1    2.5  3  AAA_31           AAA domain
    6.8e-12   45.6   0.0    1.7e-11   44.3   0.0    1.6  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    1.4e-11   44.4   1.1    1.8e-06   27.6   0.2    2.5  2  ParA             NUBPL iron-transfer P-loop NTPase
    5.5e-08   32.3   0.3      1e-07   31.5   0.3    1.4  1  ArsA_ATPase      Anion-transporting ATPase
    2.2e-05   23.6   0.1      4e-05   22.7   0.1    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    4.8e-05   23.2   0.2    9.5e-05   22.2   0.0    1.6  2  AAA_24           AAA domain
    0.00049   19.5   0.1      0.001   18.4   0.1    1.5  1  MipZ             ATPase MipZ
    0.00081   19.1   0.3     0.0024   17.5   0.2    1.8  2  SRP54            SRP54-type protein, GTPase domain
    0.00083   19.7   0.0     0.0028   18.0   0.0    1.9  2  RNA_helicase     RNA helicase
     0.0029   17.7   0.0     0.0052   16.9   0.0    1.5  1  DUF87            Helicase HerA, central domain
     0.0047   16.7   0.9      0.031   14.0   0.2    2.1  2  ATP_bind_1       Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.013   15.9   0.0      0.038   14.4   0.0    1.7  2  AAA_16           AAA ATPase domain
      0.018   14.6   0.0      0.033   13.8   0.0    1.3  1  AAA_25           AAA domain
      0.023   14.2   0.0       0.27   10.7   0.0    2.1  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
      0.027   14.4   0.2      0.054   13.4   0.2    1.5  1  NTPase_1         NTPase
      0.034   13.9   0.0       0.11   12.2   0.0    1.8  2  AAA_30           AAA domain
       0.06   13.2   0.2       0.32   10.8   0.0    2.1  2  AAA_26           AAA domain
      0.082   12.8   0.0       0.14   12.1   0.0    1.3  1  NACHT            NACHT domain
      0.086   12.1   0.1       0.15   11.3   0.1    1.3  1  VirC1            VirC1 protein
        0.1   12.6   0.0       0.19   11.7   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
        0.1   12.4   0.3       0.23   11.2   0.1    1.7  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
       0.15   11.7   0.7       0.93    9.1   0.0    2.3  3  Thymidylate_kin  Thymidylate kinase
       0.18   12.1   0.1       0.41   10.9   0.0    1.6  1  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.4   4.1    3e-124  2.2e-121       1     269 [.       2     270 ..       2     272 .. 0.97

  Alignments for each domain:
  == domain 1  score: 404.4 bits;  conditional E-value: 3e-124
                     Fer4_NifH   1 rkiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkGyggv 81 
                                   rk+++yGkGGiGkstt++n++aalae+gkkvl+vGCDPkaD+tr l+ g++++tvld++r+kga e++k+ed+v++G+ggv
  gi|15669069|ref|NP_247874.1|   2 RKFCVYGKGGIGKSTTVSNIAAALAEDGKKVLVVGCDPKADTTRNLV-GRKIPTVLDVFRKKGA-ENMKLEDIVFEGFGGV 80 
                                   799****************************************9866.56678**********7.**************** PP

                     Fer4_NifH  82 kcvesGGPepGvGCaGrgvitaielleelgaydd..lDfvlyDvLGDvvCGGfalPiredkaqevyivtsgelmalyaann 160
                                   +cvesGGPepGvGCaGrgvita+++l++lga+++   D+v+yD+LGDvvCGGfa+P++++ a++vyivt+++ ma+yaann
  gi|15669069|ref|NP_247874.1|  81 YCVESGGPEPGVGCAGRGVITAVDMLNRLGAFEElkPDVVIYDILGDVVCGGFAMPLQKHLADDVYIVTTCDPMAIYAANN 161
                                   *********************************6569******************************************** PP

                     Fer4_NifH 161 iakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrela 241
                                   i+kgi++ya +g+++lgG+i+n+r+v d  e++++fa+++gt+v+ ++P+++i+++ae+ kktvieyap+se+a+++re+a
  gi|15669069|ref|NP_247874.1| 162 ICKGIKRYASRGKIALGGIIYNGRSVIDAPEIVKDFAKKIGTQVIGKIPMSNIITRAEIYKKTVIEYAPDSEIANTFREIA 242
                                   ********************************************************************************* PP

                     Fer4_NifH 242 rkilenkklviPkplsedeLeelleefe 269
                                   ++i+en++ viP+plse+eL+e++e+++
  gi|15669069|ref|NP_247874.1| 243 KAIYENENRVIPNPLSEEELDEITEKID 270
                                   ***********************99876 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.1   7.3e-14   5.5e-11       9      49 ..       8      48 ..       4      76 .. 0.79
   2 ?    2.4   0.0      0.18   1.3e+02     140     169 ..     142     171 ..     136     177 .. 0.89
   3 ?   -2.3   0.0       4.8   3.6e+03      69      69 ..     241     241 ..     195     273 .. 0.49

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 7.3e-14
                        AAA_31  9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglg 49
                                   KGG+GK+Tt+ n+aaala+ gkkvL+v +Dp a +t +l 
  gi|15669069|ref|NP_247874.1|  8 GKGGIGKSTTVSNIAAALAEDGKKVLVVGCDPKADTTRNLV 48
                                  5************************************9764 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.18
                        AAA_31 140 sdsviipvqaeayaleGleqllktieevkk 169
                                   +d v i++ ++++a++ +++++k i++  +
  gi|15669069|ref|NP_247874.1| 142 ADDVYIVTTCDPMAIYAANNICKGIKRYAS 171
                                   899********************9998765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.8
                        AAA_31  69 i 69 
                                   i
  gi|15669069|ref|NP_247874.1| 241 I 241
                                   1 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   2.3e-14   1.7e-11       4     126 ..       6     223 ..       4     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 2.3e-14
                                   EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.............................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
                          CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.............................. 54 
                                   + +kGG GK+t++ n+a+ala++g++Vl+v +Dp a  ++    l++++ p                              
  gi|15669069|ref|NP_247874.1|   6 VYGKGGIGKSTTVSNIAAALAEDGKKVLVVGCDPKADTTR---NLVGRKIPtvldvfrkkgaenmkledivfegfggvycv 83 
                                   579********************************99999...4444444456699999999999**************** PP

                                   ..............................................................................CCH CS
                                   ..............................................................................xxx RF
                          CbiA  55 ..............................................................................dlk 57 
                                                                                                                  +k
  gi|15669069|ref|NP_247874.1|  84 esggpepgvgcagrgvitavdmlnrlgafeelkpdvviydilgdvvcggfamplqkhladdvyivttcdpmaiyaannICK 164
                                   ************************************************************999999999996665554333 PP

                                   CCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  58 rllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparge 126
                                    +++ +++ +      + + g++ n     ++ +  k++ +++    g +v+g+ip +  +++a+  ++
  gi|15669069|ref|NP_247874.1| 165 GIKRYASRGK------IALGGIIYNGRSVIDAPEIVKDFAKKI----GTQVIGKIPMSNIITRAEIYKK 223
                                   3333333333......668899999766666666666666555....9999999999999988877665 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.2   2.4e-09   1.8e-06      10      56 ..       7      61 ..       3      83 .. 0.80
   2 !   15.2   0.1   1.4e-05     0.011     193     245 ..     193     245 ..     130     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.4e-09
                          ParA 10 SgKGGVGKStvavnlAlaLakkglkvgllDaD........iyGpsiprllgveee 56
                                   gKGG+GKSt+ +n+A+aLa+ g+kv ++  D        ++G  ip++l+v ++
  gi|15669069|ref|NP_247874.1|  7 YGKGGIGKSTTVSNIAAALAEDGKKVLVVGCDpkadttrnLVGRKIPTVLDVFRK 61
                                  59**************************987755555555677788877777665 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.4e-05
                          ParA 193 ggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                                    ++++a+++g++++g+ip+++ i++a   +k++++ +p+se+a++++eia+++
  gi|15669069|ref|NP_247874.1| 193 IVKDFAKKIGTQVIGKIPMSNIITRAEIYKKTVIEYAPDSEIANTFREIAKAI 245
                                   57899**********************9**********************987 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.3   1.4e-10     1e-07       1      40 [.       1      40 [.       1      55 [. 0.92

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.4e-10
                                  -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT CS
                   ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDPA 40
                                  ++ + v GKGG+GK+t  + +a+ l+e gkkvl++  DP 
  gi|15669069|ref|NP_247874.1|  1 MRKFCVYGKGGIGKSTTVSNIAAALAEDGKKVLVVGCDPK 40
                                  5778899********************************4 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   5.3e-08     4e-05      34      72 ..       6      44 ..       2      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.3e-08
                                  EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------- CS
                          MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavlavDPsspft 72
                                  + G  G Gkst+v+++++ l++ Gk+v v+  DP +  t
  gi|15669069|ref|NP_247874.1|  6 VYGKGGIGKSTTVSNIAAALAEDGKKVLVVGCDPKADTT 44
                                  67999*****************************98765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.3e-07   9.5e-05       4      53 ..       3      60 ..       1     129 [. 0.80
   2 ?   -1.9   0.0       3.1   2.3e+03     147     168 ..     252     273 ..     210     278 .. 0.53

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.3e-07
                        AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtek...Glksldadkfpdieswedfl 53
                                  k+++yG+ giGK+t+++++       g+k+l++ ++     +++l ++k+p++  ++ f+
  gi|15669069|ref|NP_247874.1|  3 KFCVYGKGGIGKSTTVSNIaaalaedGKKVLVVGCDPkadTTRNLVGRKIPTV--LDVFR 60
                                  89*******************************99972223444444554433..44444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.1
                        AAA_24 147 rlepklgkktanelkeevDlvl 168
                                    ++  l++   +e++e+ D++l
  gi|15669069|ref|NP_247874.1| 252 VIPNPLSEEELDEITEKIDVLL 273
                                   3333355555667777777766 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.4e-06     0.001       9      49 ..       9      49 ..       4      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                                  STTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHH CS
                          MipZ  9 kGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryle 49
                                  kGG Gkstt   +a aL++ G++v ++  d +  t    ++
  gi|15669069|ref|NP_247874.1|  9 KGGIGKSTTVSNIAAALAEDGKKVLVVGCDPKADTTRNLVG 49
                                  9***************************9999888766655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   3.2e-06    0.0024       6      38 ..       6      38 ..       2      45 .. 0.92
   2 ?   -3.3   0.0       7.8   5.8e+03      35      49 ..     101     116 ..      98     124 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.2e-06
                                  EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  + G  G+GK tt++ +aa l ++gkkvl+v +D
  gi|15669069|ref|NP_247874.1|  6 VYGKGGIGKSTTVSNIAAALAEDGKKVLVVGCD 38
                                  77999**************************99 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.8
                                   EEESTS.STTHHHHHH CS
                         SRP54  35 vaaDtf.RaaAveQLk 49 
                                    a+D+  R +A+e Lk
  gi|15669069|ref|NP_247874.1| 101 TAVDMLnRLGAFEELK 116
                                   5566433777777765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.8e-06    0.0028       2      68 ..       5      68 ..       4      75 .. 0.83
   2 ?   -1.9   0.0       5.9   4.4e+03      39      40 ..     230     231 ..     192     268 .. 0.53

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.8e-06
                  RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenps 68
                                  ++yG+ g+GKSt++ ++a+al+   ++ kk  v+   p+ d   +  g ++  + D+ ++k  en +
  gi|15669069|ref|NP_247874.1|  5 CVYGKGGIGKSTTVSNIAAALA---EDGKKVLVVGCDPKADTTRNLVGRKIPTVLDVFRKKGAENMK 68
                                  79********************...555766777799999999999999999999999998553444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.9
                  RNA_helicase  39 pe 40 
                                   p+
  gi|15669069|ref|NP_247874.1| 230 PD 231
                                   33 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     7e-06    0.0052      24      58 ..       2      35 ..       1      72 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7e-06
                         DUF87 24 rHlAilgsTGsGKSntvavLleellekkgatilil 58
                                  r +++ g+ G GKS+tv+ + + l+ ++g ++l++
  gi|15669069|ref|NP_247874.1|  2 RKFCVYGKGGIGKSTTVSNIAAALA-EDGKKVLVV 35
                                  789**********************.888888885 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2   4.2e-05     0.031       1      38 [.       6      43 ..       6      52 .. 0.94
   2 ?    1.0   0.0      0.41   3.1e+02     156     217 ..     208     266 ..     188     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-05
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaee 38
                                  v G  G GK+t v++++  l + g++v vv  DP a++
  gi|15669069|ref|NP_247874.1|  6 VYGKGGIGKSTTVSNIAAALAEDGKKVLVVGCDPKADT 43
                                  78999*****************************9986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.41
                    ATP_bind_1 156 elPhvvvlnkfDllkeklekeleffedvealslllekeeekykklaeaiaelleefalvlrf 217
                                   ++P+ ++++++++ k   +  +e+ +d e  ++  e  +  y++ ++ i + l+e +l   +
  gi|15669069|ref|NP_247874.1| 208 KIPMSNIITRAEIYK---KTVIEYAPDSEIANTFREIAKAIYENENRVIPNPLSEEELDEIT 266
                                   789999999999988...88899999998888888888888888887777777776665444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.1e-05     0.038      29      62 ..       6      39 ..       3      71 .. 0.77
   2 ?   -1.8   0.0       4.6   3.4e+03      72      89 ..     234     249 ..     194     276 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-05
                        AAA_16 29 lsGesGvGKsslvrellralekdggiflrgkcdq 62
                                  ++G  G+GKs+ v  ++ al +dg  +l   cd 
  gi|15669069|ref|NP_247874.1|  6 VYGKGGIGKSTTVSNIAAALAEDGKKVLVVGCDP 39
                                  9********************9965555555554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.6
                        AAA_16  72 laqalareellrqlldea 89 
                                   +a+++ r e+ +++ +++
  gi|15669069|ref|NP_247874.1| 234 IANTF-R-EIAKAIYENE 249
                                   33333.2.3333333332 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.4e-05     0.033      38      87 ..       6      45 ..       3      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-05
                        AAA_25 38 laGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelr 87
                                  ++G +g GK+t ++++a+a+a  Gk           kVl+v ++ ++d++r
  gi|15669069|ref|NP_247874.1|  6 VYGKGGIGKSTTVSNIAAALAeDGK-----------KVLVVGCDPKADTTR 45
                                  79*******************5555...........677777666665555 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00037      0.27      10      40 ..       9      39 ..       1      45 [. 0.87
   2 ?    1.2   0.0      0.29   2.2e+02     206     231 ..     218     243 ..     208     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00037
                      CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDlsp 40
                                  +GG+G+++ ++ +a al e g++vlv+   p
  gi|15669069|ref|NP_247874.1|  9 KGGIGKSTTVSNIAAALAEDGKKVLVVGCDP 39
                                  7*************************97665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.29
                      CBP_BcsQ 206 alaakqPlgeyrpdslaaeevktLan 231
                                   a ++k+ + ey+pds  a++ + +a+
  gi|15669069|ref|NP_247874.1| 218 AEIYKKTVIEYAPDSEIANTFREIAK 243
                                   6678999***********99998886 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   7.2e-05     0.054       2      35 ..       4      37 ..       3      68 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.2e-05
                                  EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyt 35
                                  +++ G+ G+GK+T v++++ +l+++g kv  + +
  gi|15669069|ref|NP_247874.1|  4 FCVYGKGGIGKSTTVSNIAAALAEDGKKVLVVGC 37
                                  67889*********************99866655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.11      22      54 ..       5      37 ..       2      61 .. 0.83
   2 ?   -1.7   0.0       2.6     2e+03      43      64 ..     219     240 ..     209     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                        AAA_30 22 vltGpAGtGKttalkalreaweaaggrviglAp 54
                                  ++ G  G GK+t+++ +++a++++g++v+++  
  gi|15669069|ref|NP_247874.1|  5 CVYGKGGIGKSTTVSNIAAALAEDGKKVLVVGC 37
                                  577999*******************99887654 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
                        AAA_30  43 eaaggrviglAptgkaAkvLae 64 
                                   e  +++vi +Ap ++ A++ +e
  gi|15669069|ref|NP_247874.1| 219 EIYKKTVIEYAPDSEIANTFRE 240
                                   4446899999999999988775 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.2   9.1e+02      84     110 ..      14      40 ..       8      58 .. 0.68
   2 ?   10.8   0.0   0.00043      0.32     142     195 ..     159     216 ..     136     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.2
                        AAA_26  84 edidlekivkelekdadivvVEGaggl 110
                                   ++ ++++i  +l++d + v+V G ++ 
  gi|15669069|ref|NP_247874.1|  14 KSTTVSNIAAALAEDGKKVLVVGCDPK 40 
                                   344455555666666677777776665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00043
                        AAA_26 142 inqllltiealrqk.nvrvlGvilNk...vrnpenvetlekksgipvlGvvPylpdle 195
                                    n++   i+ + ++ ++ + G+i N+   + +pe v+ + kk+g++v+G +P++  ++
  gi|15669069|ref|NP_247874.1| 159 ANNICKGIKRYASRgKIALGGIIYNGrsvIDAPEIVKDFAKKIGTQVIGKIPMSNIIT 216
                                   45555555666554278999******776677799*****************998776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00018      0.14       3      28 ..       4      29 ..       2      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                  EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                         NACHT  3 vilqGeaGsGKTtLlqklalawaegk 28
                                   ++ G+ G+GK+t +  +a a+ae+ 
  gi|15669069|ref|NP_247874.1|  4 FCVYGKGGIGKSTTVSNIAAALAEDG 29
                                  689********************986 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0002      0.15       9      39 ..       8      38 ..       2      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                         VirC1  9 lkGGaGkttalmglcsalasdgkrvalfead 39
                                   kGG Gk+t++  + +ala dgk+v +  +d
  gi|15669069|ref|NP_247874.1|  8 GKGGIGKSTTVSNIAAALAEDGKKVLVVGCD 38
                                  49**********************9887666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00025      0.19       2      36 ..       4      41 ..       3      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                                  EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT- CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal...nreveyvqltrdt 36
                                  +++ G+ G+gKs+ +  +aaal   +++v++v +  + 
  gi|15669069|ref|NP_247874.1|  4 FCVYGKGGIGKSTTVSNIAAALaedGKKVLVVGCDPKA 41
                                  7999********************99999999886443 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00031      0.23       1      33 [.       8      40 ..       8      44 .. 0.91
   2 ?   -2.1   0.0       3.8   2.9e+03     104     136 ..     184     216 ..     178     243 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                  G+   GKST + +++  +++ g+k+++v +D+ 
  gi|15669069|ref|NP_247874.1|  8 GKGGIGKSTTVSNIAAALAEDGKKVLVVGCDPK 40
                                  56678**************************95 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.8
                        CLP1_P 104 sgliIntpGwvkglgaellleliealepdvvvv 136
                                   ++ +I+ p +vk++++++ +++i  + +++++ 
  gi|15669069|ref|NP_247874.1| 184 GRSVIDAPEIVKDFAKKIGTQVIGKIPMSNIIT 216
                                   567899999999999988888887777776665 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0012      0.93       5      47 ..      10      57 ..       6      74 .. 0.71
   2 ?   -3.1   0.0       7.2   5.3e+03     116     124 ..     115     123 ..     102     125 .. 0.70
   3 ?    0.1   0.1      0.73   5.4e+02      36      72 ..     232     268 ..     211     277 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                                  TTSSHHHHHHHHHHHHHHTTE...EEEESSSTTSH...HHHHHHHHHH CS
               Thymidylate_kin  5 DGaGKttqaellkerlkeegik..vvltrepggte...iGekirelll 47
                                   G GK+t + +++++l e g+k  vv   ++ +t+   +G+ki  +l 
  gi|15669069|ref|NP_247874.1| 10 GGIGKSTTVSNIAAALAEDGKKvlVVGCDPKADTTrnlVGRKIPTVLD 57
                                  699******************974444555555533336666666665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.2
                                   SE-SEEEEE CS
               Thymidylate_kin 116 lkPdltfll 124
                                   lkPd++++ 
  gi|15669069|ref|NP_247874.1| 115 LKPDVVIYD 123
                                   399999995 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.73
                                   SHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHH CS
               Thymidylate_kin  36 teiGekirelllkeeeleeqteallfaadriehleek 72 
                                   +ei++++re+ +  +e e+  + + ++ +  ++++ek
  gi|15669069|ref|NP_247874.1| 232 SEIANTFREIAKAIYENENRVIPNPLSEEELDEITEK 268
                                   5555555555554444444444444444444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00055      0.41       9      60 ..       5      52 ..       3      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00055
                        AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrel 60
                                  +v+G  G+GK+t++ +++  l e     + +++ vv ++++++t++  + r++
  gi|15669069|ref|NP_247874.1|  5 CVYGKGGIGKSTTVSNIAAALAE-----DgKKVLVVGCDPKADTTRNLVGRKI 52
                                  699*****************954.....2357777788888887776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1504.83
//
Query:       gi|15669070|ref|NP_247875.1|  [L=308]
Description: hypothetical protein MJ_0880 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-17   62.7  19.1    7.6e-11   42.3   5.3    2.7  3  Gate      Nucleoside recognition


Domain annotation for each model (and alignments):
>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   1.3   2.3e-11   4.2e-07       5     100 ..       8      97 ..       4     112 .. 0.90
   2 ?   -3.3   0.1      0.59   1.1e+04      11      20 ..     122     131 ..     113     144 .. 0.51
   3 !   42.3   5.3   4.2e-15   7.6e-11       1      98 [.     175     263 ..     175     281 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.3e-11
                          Gate   5 gpiillasiliwflss...ssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtp 82 
                                    +iill si i ++s    ++l+++i k+ +p+       l+ +++vsll +f++ +v+ ++l+ +y       ++++ ++
  gi|15669070|ref|NP_247875.1|   8 TKIILLSSIGITIASIiveTNLISKIKKITKPICLISN--LPEECVVSLLGNFINPTVGKSMLSGFY-------KENKVNE 79 
                                   6889999999988888888**************99966..***************************.......******* PP

                          Gate  83 ksalafllfvllytpcva 100
                                   k+++++ +++ l t+ + 
  gi|15669070|ref|NP_247875.1|  80 KEVIVTTIISPLPTILGE 97 
                                   ************997665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.59
                          Gate  11 asiliwflss 20 
                                   + ++ +fl++
  gi|15669070|ref|NP_247875.1| 122 LNVISGFLQA 131
                                   3344444433 PP

  == domain 3  score: 42.3 bits;  conditional E-value: 4.2e-15
                          Gate   1 llkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdt 81 
                                   l+k++p+i+++++li+fl + +l++ +  l++p+f+ l+  l+++a++ l++++a   +++ t+  l        ++g  +
  gi|15669070|ref|NP_247875.1| 175 LKKVIPMIVIFTLLINFLIKLGLMDVVKGLFSPIFRILD--LPGEAITVLIANLAHFSAGYTTVDILI-------KNGVLN 246
                                   79*************************************..***********************9996.......9***** PP

                          Gate  82 pksalafllfvllytpc 98 
                                   +k+al++ll++ + ++ 
  gi|15669070|ref|NP_247875.1| 247 EKQALIVLLIGNIISVT 263
                                   ***99888888776532 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1855.96
//
Query:       gi|15669071|ref|NP_247876.1|  [L=305]
Description: ornithine carbamoyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-58  194.7   0.0    1.6e-57  194.0   0.0    1.3  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    5.5e-50  169.2   0.0    7.6e-50  168.8   0.0    1.2  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.0   0.0   1.8e-61   1.6e-57       1     155 [.     145     299 ..     145     301 .. 0.98

  Alignments for each domain:
  == domain 1  score: 194.0 bits;  conditional E-value: 1.8e-61
                                   CC.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT.-EEEEESSCHHHHTT-SEEEE--S CS
                        OTCace   1 kglkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksg.gsititedleeavkgaDvvytdvw 80 
                                   kglkia++Gd+ nnv+nsli + a +gmd ++ +Pkg+ep+ +v+ +ak++++++g gs+t+t+d+ ea+++aDv+ytdvw
  gi|15669071|ref|NP_247876.1| 145 KGLKIAYLGDG-NNVCNSLILGSALVGMDTYVGTPKGYEPNAKVVLKAKEIINNYGeGSLTLTNDPIEAAEDADVLYTDVW 224
                                   79*********.*******************************************77************************ PP

                                   SETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
                        OTCace  81 vsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                                   +smg++k++ee lk + ++q++++ll+ ak+d+iv+HcLPa+rg+E+td+V+d+++svv+++aeNrlh++k ++ 
  gi|15669071|ref|NP_247876.1| 225 ISMGDDKDKEEVLKIFPPFQINSKLLEYAKDDVIVMHCLPANRGYEITDDVIDGEHSVVYDEAENRLHVQKGVFK 299
                                   ************************************************************************986 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.8   0.0   8.4e-54   7.6e-50       2     148 .]       2     139 ..       1     139 [. 0.97

  Alignments for each domain:
  == domain 1  score: 168.8 bits;  conditional E-value: 8.4e-54
                                   -BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTTG CS
                      OTCace_N   2 hllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlssv 82 
                                   hll+l+ ls+e++ ++++    +k++++  k+ek+l+gk++a+lFe+pStRTr+Sf++A+++lGg++l ++ +++i+l+  
  gi|15669071|ref|NP_247876.1|   2 HLLDLDVLSREDVLKIIEYGIYFKKNRR--KHEKILEGKSVAILFEKPSTRTRMSFDIAVYELGGHPLIMN-QNEIHLG-- 77 
                                   9***********************9976..9****************************************.889***9.. PP

                                   GSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                      OTCace_N  83 skgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                      +kEs++Dta+v++ryvd+iv+R++++++lee+aky+svpviNa+ +d  HP+Q+LaDl+ti+e
  gi|15669071|ref|NP_247876.1|  78 ---KKESIKDTAKVMGRYVDTIVARVYKHRHLEEMAKYSSVPVINAL-SDLAHPCQILADLMTIKE 139
                                   ...77******************************************.****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2035.46
//
Query:       gi|15669072|ref|NP_247877.1|  [L=197]
Description: hypothetical protein MJ_0882 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-52  177.5   0.1    1.8e-52  177.3   0.1    1.0  1  MTS              Methyltransferase small domain
      9e-14   51.5   0.1    1.2e-13   51.2   0.1    1.2  1  Methyltransf_31  Methyltransferase domain
    1.5e-12   47.5   1.4    1.8e-12   47.3   1.4    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.7e-10   40.8   0.0    4.2e-10   40.2   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    1.9e-09   37.6   1.0    2.9e-09   37.0   1.0    1.2  1  Methyltransf_18  Methyltransferase domain
    4.6e-09   35.7   0.0    5.9e-09   35.4   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
    4.1e-07   30.0   0.4      6e-07   29.4   0.3    1.3  1  Met_10           Met-10+ like-protein
    9.5e-07   28.6   0.0    1.2e-06   28.3   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    1.4e-06   28.1   0.2      2e-06   27.6   0.2    1.3  1  Methyltransf_16  Lysine methyltransferase
    3.1e-06   27.7   0.0    8.8e-06   26.3   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
      1e-05   25.5   0.0    1.4e-05   25.0   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.7e-05   25.4   0.1    2.8e-05   24.8   0.1    1.3  1  Methyltransf_12  Methyltransferase domain
      3e-05   23.7   0.0    5.9e-05   22.7   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    5.2e-05   22.7   0.3    6.3e-05   22.4   0.3    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00014   21.4   1.9    0.00027   20.4   1.1    1.8  2  TehB             Tellurite resistance protein TehB
    0.00015   21.2   1.6    0.00019   20.8   1.6    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00029   20.0   0.1    0.00036   19.7   0.1    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00034   20.0   0.2    0.00043   19.6   0.2    1.1  1  GidB             rRNA small subunit methyltransferase G
    0.00058   19.5   0.0      0.001   18.7   0.0    1.4  1  NodS             Nodulation protein S (NodS)
     0.0011   18.2   0.2     0.0015   17.8   0.2    1.2  1  DUF43            Branched-chain polyamine synthase A C-termin
     0.0014   17.9   0.1     0.0022   17.3   0.1    1.3  1  N6_Mtase         N-6 DNA Methylase
     0.0015   18.3   0.2      0.002   17.9   0.2    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0044   16.3   0.2      0.005   16.0   0.2    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
     0.0052   16.0   0.2     0.0061   15.8   0.2    1.1  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
     0.0076   16.0   1.1      0.087   12.5   0.1    2.1  2  N6_N4_Mtase      DNA methylase
  ------ inclusion threshold ------
      0.013   14.9   0.1      0.017   14.5   0.1    1.2  1  SPOUT_MTase_2    AF2226-like SPOUT RNA Methylase fused to THU
      0.015   15.0   0.4      0.027   14.1   0.2    1.6  1  UPF0020          Putative RNA methylase family UPF0020
      0.031   13.7   0.1      0.053   13.0   0.1    1.6  1  Methyltransf_4   Putative methyltransferase
       0.12   11.9   0.2       0.37   10.2   0.1    1.6  2  AviRa            RRNA methyltransferase AviRa


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.3   0.1     3e-55   1.8e-52       2     169 .]      26     193 ..      25     193 .. 0.98

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 3e-55
                                   EEEEEETTSTTTTS--HHHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC. CS
                           MTS   2 ltlktlpgvFskdklDkGsklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle. 81 
                                   l++kt++gvFs++k+DkG+k+L+e++  ++++++lDlGcG+Gv+g+ala+e ++   t+ d++ rA+++aken++ n+l+ 
  gi|15669072|ref|NP_247877.1|  26 LKFKTDSGVFSYGKVDKGTKILVENVVVDKDDDILDLGCGYGVIGIALADEVKS--TTMADINRRAIKLAKENIKLNNLDn 104
                                   79************************************************9998..8***********************9 PP

                                   ..EEEEE-STTTTSTTS-EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHH...HHHHHS--E CS
                           MTS  82 ..vevvasdvleeveekkfdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLliVanrklgyesl...leelfgnve 157
                                     ++vv+sd++e+v+++k++ i++NPP++agk+    v +++i+e ke Lk++Ge+++V+++k+g++sl   ++++fgnve
  gi|15669072|ref|NP_247877.1| 105 ydIRVVHSDLYENVKDRKYNKIITNPPIRAGKE----VLHRIIEEGKELLKDNGEIWVVIQTKQGAKSLakyMKDVFGNVE 181
                                   99*******************************....*******************************9999********* PP

                                   EEEEESSEEEEE CS
                           MTS 158 vvaktkkfkvlk 169
                                   +v+ +++++vlk
  gi|15669072|ref|NP_247877.1| 182 TVTIKGGYRVLK 193
                                   **********96 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.1   1.9e-16   1.2e-13       2     110 ..      54     159 ..      53     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.9e-16
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                   dk+  +lDlGCG G ++++la+e+ +    +  Di+ +ai+lA+en + ++ldn+  ++      e+ ++d+k++ i++n 
  gi|15669072|ref|NP_247877.1|  54 DKDDDILDLGCGYGVIGIALADEVKS---TTMADINRRAIKLAKENIKLNNLDNYDIRVVHSDLYEN-VKDRKYNKIITNP 130
                                   67889*****************9866...7889********************99999988777665.89**********9 PP

               Methyltransf_31  83 vl.naladpdkileeiervlkpggillie 110
                                   ++ +    +  i+ee +++lk++g++ + 
  gi|15669072|ref|NP_247877.1| 131 PIrAGKEVLHRIIEEGKELLKDNGEIWVV 159
                                   9988888899**************98543 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   1.4   2.8e-15   1.8e-12     158     282 ..      52     182 ..       7     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.8e-15
                          PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseell...keekadvivaN. 233
                                   +v +++ +lD+G+G G++ ia a  + k+ +  Di+  A+k akeN++lN++++  ++v ++++l    k++k++ i+ N 
  gi|15669072|ref|NP_247877.1|  52 VVDKDDDILDLGCGYGVIGIALAD-EVKSTTMADINRRAIKLAKENIKLNNLDNyDIRV-VHSDLYenvKDRKYNKIITNp 130
                                   477889**************9887.77888888*********************98888.444444222579********8 PP

                          PrmA 234 .ILa..evlielaedikklvkeggllilSGilkekaeevaealeqgfeleev 282
                                    I a  evl +++e+ k+l+k++g + +    k+ a+++a+ +++ f  +e+
  gi|15669072|ref|NP_247877.1| 131 pIRAgkEVLHRIIEEGKELLKDNGEIWVVIQTKQGAKSLAKYMKDVFGNVET 182
                                   87776689****************9987433333456666666776644433 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   6.7e-13   4.2e-10       1      97 []      59     154 ..      59     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 6.7e-13
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCGBSSSTTTEEEEEEEST.GGGS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaedlpfedgsfDlvvssga.lhhl 77 
                                   +LdlGcG G + +ala+++  ++ t+ Di+ ++++ a+e+++ ++l   ++++v+ d+ +   +d++++ ++ +   +   
  gi|15669072|ref|NP_247877.1|  59 ILDLGCGYGVIGIALADEV--KSTTMADINRRAIKLAKENIKLNNLdnyDIRVVHSDLYEN-VKDRKYNKIITN-PpIRA- 134
                                   8*****************9..9*******************998888889999****9664.46889******5.64776. PP

                                   SHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                    +e l+++++e +++Lk++G
  gi|15669072|ref|NP_247877.1| 135 GKEVLHRIIEEGKELLKDNG 154
                                   67899************998 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   1.0   4.8e-12   2.9e-09      11     129 ..      52     174 ..      46     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 4.8e-12
               Methyltransf_18  11 lvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagled.kievrlsdGleklkeeevdtvvi.. 88 
                                   +v+k++ ++D G+  g++ i+l+  + +k+ +++Din+ +++ akeni+ ++l++ +i+v+ sd  e++k+++++ ++   
  gi|15669072|ref|NP_247877.1|  52 VVDKDDDILDLGCGYGVIGIALA--DEVKSTTMADINRRAIKLAKENIKLNNLDNyDIRVVHSDLYENVKDRKYNKIITnp 130
                                   578899****************9..5788899*********************7658*************99988887622 PP

               Methyltransf_18  89 .aGmGgelileILeeakeklkkikk..lilqpnseaeelRkylv 129
                                       G e+  +I+ee+ke lk+  +  +++q ++ a++l ky+ 
  gi|15669072|ref|NP_247877.1| 131 pIRAGKEVLHRIIEEGKELLKDNGEiwVVIQTKQGAKSLAKYMK 174
                                   23479*************99987776799********9999986 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   9.6e-12   5.9e-09     166     265 ..      22     118 ..       9     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 9.6e-12
               tRNA_U5-meth_tr 166 adrelvyrqvensftqPnaavnekmleWalevtqeskgdllelycGnGnfslalarnfekvlateiakssveaaqyniaan 246
                                    +++l ++   + f     +  +k+l  + +v+ ++++d+l+l cG+G   +ala +++    ++i + +++ a+ ni+ n
  gi|15669072|ref|NP_247877.1|  22 RGKKLKFKTDSGVFSYGKVDKGTKIL--VENVVVDKDDDILDLGCGYGVIGIALADEVKSTTMADINRRAIKLAKENIKLN 100
                                   56777777777777666655566665..66788999********************************************* PP

               tRNA_U5-meth_tr 247 kidnvqiirlsaeelteal 265
                                   ++dn +i r+   +l e +
  gi|15669072|ref|NP_247877.1| 101 NLDNYDI-RVVHSDLYENV 118
                                   ****996.55555555554 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.3   9.6e-10     6e-07      88     190 ..      42     145 ..      12     159 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 9.6e-10
                                   HHHHHHHHTT.--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTC.EEEEES-GGG---T CS
                        Met_10  88 eaErerlakl.veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekv.vkpileDgrevire 166
                                   +  +  + ++ v++++ ++d+  G G   i++a   + k     d+n +++k+ keniklN+++++ ++++ +D  e +++
  gi|15669072|ref|NP_247877.1|  42 KGTKILVENVvVDKDDDILDLGCGYGVIGIALAD--EVKSTTMADINRRAIKLAKENIKLNNLDNYdIRVVHSDLYENVKD 120
                                   33333333445889999****9999999999998..55666888*******************99779************* PP

                                   T-EEEEEE--TTTG.GGGHHHHHHH CS
                        Met_10 167 qladrvvmnlpksa.ieFldkvlaa 190
                                    + ++++ n p +a  e l+ +++ 
  gi|15669072|ref|NP_247877.1| 121 RKYNKIITNPPIRAgKEVLHRIIEE 145
                                   *********9988735677777765 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.9e-09   1.2e-06      42     158 ..      56     166 ..      14     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.9e-09
                                   C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T.TTEEEEES-HHHHCTS--SS-EEEEEEE-- CS
                 Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee.etaelkedaleallklakkkeefdivflDP 121
                                   +  +LDl +G G++g+ Al  ++k+ ++ + +++a+k+ ken++  +l++  ++++  d +e+++      ++++ +  +P
  gi|15669072|ref|NP_247877.1|  56 DDDILDLGCGYGVIGI-ALADEVKSTTMADINRRAIKLAKENIKLNNLDNyDIRVVHSDLYENVKD-----RKYNKIITNP 130
                                   4579************.****************************999996666666666666644.....57899***** PP

                                   SSSTTCH.HHHHHHHHH.TT-EEEEEEEEEEEECCSSS CS
                 Cons_hypoth95 122 Pyakellieevlellee.kkllkenalvvvetekekel 158
                                   P ++++  e + + +ee k+llk+n+ + v  ++++  
  gi|15669072|ref|NP_247877.1| 131 PIRAGK--EVLHRIIEEgKELLKDNGEIWVVIQTKQGA 166
                                   ***996..344444444257999988776665555433 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.2   3.3e-09     2e-06      46     152 ..      55     155 ..      36     178 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.3e-09
               Methyltransf_16  46 sklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvkvevLdWgeeleedllekeevDlil 125
                                   ++  +l+LG G G++G+a+a      + +++D++  +++l k+ni+ln+ + + +++v       +l+e++ +++ ++ i+
  gi|15669072|ref|NP_247877.1|  55 KDDDILDLGCGYGVIGIALADE--VKSTTMADINRrAIKLAKENIKLNN-LDNYDIRVVHS----DLYENVKDRK-YNKII 127
                                   56789****************9..77889****9889**********77.55555555443....3444443333.33333 PP

               Methyltransf_16 126 aa.DcvYledslelLvkvLkellkkesk 152
                                       +   ++ l  +++  kellk +++
  gi|15669072|ref|NP_247877.1| 128 TNpPIRAGKEVLHRIIEEGKELLKDNGE 155
                                   3303334455555666666666666666 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.4e-08   8.8e-06       1      94 [.      60     156 ..      60     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.4e-08
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-...EEEETTEECCCTSS-TT-EEEEEEES-CCC-.CCH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl...kvefvvadaeklpfednsfDlvvssevlhhv.edp 77 
                                   Ld+GcG G +  ala+ +++++  D++ +++klake+++ ++l    +++v++d+ + +++d ++  ++ +  +    e +
  gi|15669072|ref|NP_247877.1|  60 LDLGCGYGVIGIALADEVKSTTMADINRRAIKLAKENIKLNNLdnyDIRVVHSDLYE-NVKDRKYNKIITNPPIRAGkEVL 139
                                   8****************************************999999999****998.89999999998888888776778 PP

                                   HHHHHHHHHHEEEEEEE CS
               Methyltransf_11  78 ekalkeiaRvLkpgGll 94 
                                   +++++e + +Lk +G +
  gi|15669072|ref|NP_247877.1| 140 HRIIEEGKELLKDNGEI 156
                                   88888888888888876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   2.2e-08   1.4e-05      21     123 ..      54     164 ..      36     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.2e-08
               Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...........kakkaqkdqfdeqeaaepqgkfdlIvlre 90 
                                   +++  +Ld+GcG+G     l+++++s t+ D++++a+++a+            ++  ++d +    + ++++k++ I+ + 
  gi|15669072|ref|NP_247877.1|  54 DKDDDILDLGCGYGVIGIALADEVKSTTMADINRRAIKLAKeniklnnldnyDIRVVHSDLY----ENVKDRKYNKIITNP 130
                                   567799*********9999*********************9855555444443333333333....666999999999999 PP

               Methyltransf_23  91 vlehvpd.ppellrqiatllkpgGylllseplas 123
                                    +   +  +++ +   ++llk++G + +  +++ 
  gi|15669072|ref|NP_247877.1| 131 PIRAGKEvLHRIIEEGKELLKDNGEIWVVIQTKQ 164
                                   9999986589999999999999999988877654 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   4.4e-08   2.8e-05       1      98 [.      60     155 ..      60     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.4e-08
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl.k 80 
                                   L++GcG G +  al+++   ++ t  Di+++ai + +++  k +n++n  +++ + dl +  +  ++  ++ +  + +  +
  gi|15669072|ref|NP_247877.1|  60 LDLGCGYGVIGIALADE--VKSTTMADINRRAI-KLAKENIKLNNLDNYDIRVVHSDLYENVKDRKYNKIITNPPIRAGkE 137
                                   8****************..99999*********.6667777777789999999999988888889*****99999999867 PP

               Methyltransf_12  81 direvldnirklLkpgGr 98 
                                    +++++++ ++lLk++G 
  gi|15669072|ref|NP_247877.1| 138 VLHRIIEEGKELLKDNGE 155
                                   777999999999999996 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   9.5e-08   5.9e-05       4      70 ..      59     126 ..      57     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 9.5e-08
               Methyltransf_15   4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgv.sdkitlvlgdvfellaklkleki 70 
                                   ilDl +G G   i++a + +++   +in++ +++a++N ++ +  +  i +v+ d+ e ++  k +ki
  gi|15669072|ref|NP_247877.1|  59 ILDLGCGYGVIGIALADEVKSTTMADINRRAIKLAKENIKLNNLdNYDIRVVHSDLYENVKDRKYNKI 126
                                   89*****************************************95668**************999998 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.3     1e-07   6.3e-05      51     171 ..      44     165 ..      28     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1e-07
                                   HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEE.ES-HHHHHHHHHHHH..TS-SSS-EEEEES-GGG---.- CS
                          CMAS  51 ldlileklelkpGmtlLdiGcGWGslvrraverydvkvvgl.TlSkeqaklakkrvd..eldlerkvevklldyedlde.k 127
                                   +++++e + +++ + +Ld+GcG+G + +  +++  vk   +  + +   klak++++  +ld+ + + v+   ye++++ k
  gi|15669072|ref|NP_247877.1|  44 TKILVENVVVDKDDDILDLGCGYGVIGIALADE--VKSTTMaDINRRAIKLAKENIKlnNLDNYDIRVVHSDLYENVKDrK 122
                                   4677899999***************99999998..55444314777778888887642277778888888889****9999 PP

                                   -SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE-- CS
                          CMAS 128 vdrvvsvgafehvgkenydtffkklkkllkedGllllhtitslh 171
                                   ++++++   +   gke +++ +++ k+llk++G + +   t++ 
  gi|15669072|ref|NP_247877.1| 123 YNKIITNPPIR-AGKEVLHRIIEEGKELLKDNGEIWVVIQTKQG 165
                                   *****988886.59999999999999999999988765555444 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   1.1   4.3e-07   0.00027      23     102 ..      48     129 ..      36     167 .. 0.81
   2 ?   -0.9   0.0       1.4   8.9e+02     112     132 ..     172     192 ..     167     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.3e-07
                                   HHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE-..-GGG----S-EEEEEE CS
                          TehB  23 veavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistaly..dineaklderydfils 101
                                   ve v + k   +ldlgcg g   + l+      t  d n  +i+  +e ++ +nl+n + +++  d+ e   d++y+ i++
  gi|15669072|ref|NP_247877.1|  48 VENVVVDKDDDILDLGCGYGVIGIALADEVKSTTMADINRRAIKLAKENIKLNNLDNYDIRVVhsDLYENVKDRKYNKIIT 128
                                   566777788899********************************************97666643389999999***99986 PP

                                   E CS
                          TehB 102 t 102
                                    
  gi|15669072|ref|NP_247877.1| 129 N 129
                                   5 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                                   GHHHHHHHHHHTEEEEEEEEE CS
                          TehB 112 ripsiienmqectkvggynli 132
                                    + ++  n+++ t  ggy ++
  gi|15669072|ref|NP_247877.1| 172 YMKDVFGNVETVTIKGGYRVL 192
                                   567889999*********875 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   1.6   3.1e-07   0.00019       9     109 ..      17     116 ..       9     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.1e-07
                                   XXXXXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHH CS
               Ubie_methyltran   9 vkevfesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvge 89 
                                   v+++      k+ +   v+s+g  ++  k + + v v +  ++lD+ +G g + ++l+d+v+++   +++Din   +k ++
  gi|15669072|ref|NP_247877.1|  17 VEDILRGKKLKFKTDSGVFSYGKVDKGTKILVENVVVDKDDDILDLGCGYGVIGIALADEVKST---TMADINRRAIKLAK 94 
                                   677777777777788889999999999997777788888899*******************987...589**********9 PP

                                   HHHH..HHTSSTEEEEE--TTT CS
               Ubie_methyltran  90 kklk..eegkinieflqanaee 109
                                   + +k  +   ++i+ ++++  e
  gi|15669072|ref|NP_247877.1|  95 ENIKlnNLDNYDIRVVHSDLYE 116
                                   9766115556699999987654 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   5.9e-07   0.00036      23     126 ..      48     146 ..      25     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.9e-07
                                   HHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT....TCCCEEEE-S-CCGHHHHHHHCTTTC CS
                        RrnaAD  23 ldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls....kdeklkvvhqDflkfetpeevtekds 99 
                                   ++++ + +++ +l++g G G+    La+ +k+ ++  + +r +kl +++++    ++  + vvh D ++           +
  gi|15669072|ref|NP_247877.1|  48 VENVVVDKDDDILDLGCGYGVIGIALADEVKSTTMADINRRAIKLAKENIKlnnlDNYDIRVVHSDLYEN---------VK 119
                                   555666799************************************9997666566666666676666643.........33 PP

                                   CCCEEEEEEE--TTTHHHHHHHHHHGG CS
                        RrnaAD 100 ihqeflvvanlPyeistqlvkqllees 126
                                   + +  +++ n P  ++++   +++ee+
  gi|15669072|ref|NP_247877.1| 120 DRKYNKIITNPPIRAGKEVLHRIIEEG 146
                                   344456777777777777777777743 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2     7e-07   0.00043      44     158 ..      52     171 ..      44     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7e-07
                                   CS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SS..EEEEES-CCCTTTTT-EEEEE.. CS
                          GidB  44 llkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklen..veivearaeekqeeekydvvt.. 120
                                   ++++++  ++D+G G G+ Gi L  a++ ++ t+ + + + i+  +e ++  +l+n  +++v++++ e  +  ky+ ++  
  gi|15669072|ref|NP_247877.1|  52 VVDKDD-DILDLGCGYGVIGIAL--ADEVKSTTMADINRRAIKLAKENIKLNNLDNydIRVVHSDLYENVKDRKYNKIItn 129
                                   344444.7*********988765..566667778888888888777777666666633789****9886666666655536 PP

                                   ..EC-SSS.HHHHHHHHCCCEEEEEEE.EEEESS--HHHHHC CS
                          GidB 121 ..sRAlas.lnelteillkllkeggli.lalKGksaedelee 158
                                     +RA  + l++++e  ++llk++g+i ++++ k+ ++ l++
  gi|15669072|ref|NP_247877.1| 130 ppIRAGKEvLHRIIEEGKELLKDNGEIwVVIQTKQGAKSLAK 171
                                   6679987735789999999**999975266777776666655 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.7e-06     0.001      45     112 ..      57     128 ..      39     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                          NodS  45 adalevGcaaGalterlapyckrltvvdvveeaiararervk....esshiswivsdvqqfstdekfdlivv 112
                                    d+l++Gc  G +   la   k+ t+ d+  +ai+ a+e +k    +  +i  + sd+ +  +d+k++ i+ 
  gi|15669072|ref|NP_247877.1|  57 DDILDLGCGYGVIGIALADEVKSTTMADINRRAIKLAKENIKlnnlDNYDIRVVHSDLYENVKDRKYNKIIT 128
                                   589********************************999988743333569999***************9996 PP

>> DUF43  Branched-chain polyamine synthase A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   2.5e-06    0.0015      58     153 ..      68     165 ..      40     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                                   HHHHHHHT--SEEEEE-S-HHHHHHHHHHHHHHT--...EEEE---TTS---TTTSS-BSEEEE---..SSHHHHHHHHHH CS
                         DUF43  58 slalaLtglpkkvvvvDiDeRlikfiervakelglk...ieaivyDlrkplpeelkekFdvfitDPp..etvealkaFlgR 133
                                    + +aL++  k   + Di+ R ik+ ++ +k  +l+   i+++  Dl + + +   +k++ +it+Pp   + e l+  +  
  gi|15669072|ref|NP_247877.1|  68 VIGIALADEVKSTTMADINRRAIKLAKENIKLNNLDnydIRVVHSDLYENVKD---RKYNKIITNPPirAGKEVLHRIIEE 145
                                   3678999*******************988776655433388888888776665...79999*****943467899999999 PP

                                   HHHTB-STT-EEEEEE-TTT CS
                         DUF43 134 GiaaLkgegcagYlgltrre 153
                                   G + Lk++g +  +  t++ 
  gi|15669072|ref|NP_247877.1| 146 GKELLKDNGEIWVVIQTKQG 165
                                   9999**99977655555544 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   3.5e-06    0.0022      37     135 ..      46     132 ..      41     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.5e-06
                      N6_Mtase  37 livellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlek 117
                                   ++ve +   ++  ++D  cG g + +  ++ +k++            ++n+ +++Lak N+ l + ++ ++++ ++d +e+
  gi|15669072|ref|NP_247877.1|  46 ILVENVVVDKDDDILDLGCGYGVIGIALADEVKST---------TMADINRRAIKLAKENIKLNNLDNYDIRVVHSDLYEN 117
                                   55555544444458888888888888888877522.........225899***************************9987 PP

                      N6_Mtase 118 pkfekdkkfdvvvaNppf 135
                                    k    +k + +++Npp 
  gi|15669072|ref|NP_247877.1| 118 VKD---RKYNKIITNPPI 132
                                   665...59*********6 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   3.3e-06     0.002      66     188 ..      48     176 ..      42     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.3e-06
                                   HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHH..HHCTTCSEEEEES-GGGTTGGG-SEE CS
                          PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnl..kkldlenvivvvgDGrkGyeekaPYd 144
                                   +e + ++k + +L++G+G G     la  v++++ +  i+r +  ++ ak+n+  ++ld  ++ vv++D ++ ++++  Y+
  gi|15669072|ref|NP_247877.1|  48 VENVVVDKDDDILDLGCGYGVIGIALADEVKSTT-MADINRRA--IKLAKENIklNNLDNYDIRVVHSDLYENVKDR-KYN 124
                                   56777999***********************998.66777665..455555550056666699*******9999987.599 PP

                                   EEEES...SBBSS--HHHHHT....EEEEEEEEEEESB.SSSEEEEEEEEET CS
                          PCMT 145 aihvg...aaapeiPealidQ....LkeGGrlvvPvge.eeeQvlklvdkka 188
                                   +i++     a +e+ + +i+     Lk+ G + v +++ ++ + l ++ k+ 
  gi|15669072|ref|NP_247877.1| 125 KIITNppiRAGKEVLHRIIEEgkelLKDNGEIWVVIQTkQGAKSLAKYMKDV 176
                                   9998733347788888887644444888888888888656666666666654 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   8.1e-06     0.005      53     106 ..      59     111 ..      14     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.1e-06
                                   EEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--..GGEEEE CS
                           TRM  53 vldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneve..eivvin 106
                                   +ld   + G+ +i  a E   vk+  + Di+ +A++l keN+kln+ +  +i v++
  gi|15669072|ref|NP_247877.1|  59 ILDLGCGYGVIGIALADE---VKSTTMADINRRAIKLAKENIKLNNLDnyDIRVVH 111
                                   666667778888888888...7888999******************9943333333 PP

>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   9.8e-06    0.0061     112     238 ..      41     160 ..       9     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.8e-06
               Methyltrans_SAM 112 rlgrdwvqenakdknvlnlfaytcgfsvaaia..ggaskvvnvdmargslnkgrdnhrlnghdlrrvsflgydifkswgki 190
                                    +g + + en    +  +++   cg+ v  ia     +     d+ r +++  ++n +ln+ d   +  +  d++      
  gi|15669072|ref|NP_247877.1|  41 DKGTKILVENVVVDKDDDILDLGCGYGVIGIAlaDEVKSTTMADINRRAIKLAKENIKLNNLDNYDIRVVHSDLYENV--- 118
                                   55666666666666666777889*****876511556677788999****************************9864... PP

               Methyltrans_SAM 191 kksgpydlviidppsfqkgsfaltkdykkilrrlpellveggevlacv 238
                                    k  +y+ +i +pp ++ g  +l    ++i+    ell + ge+   +
  gi|15669072|ref|NP_247877.1| 119 -KDRKYNKIITNPP-IRAGKEVL----HRIIEEGKELLKDNGEIWVVI 160
                                   .66789*9999999.46676666....567777888888888776666 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.23   1.4e+02     189     231 .]      53      95 ..      44      95 .. 0.91
   2 !   12.5   0.1   0.00014     0.087      33      76 ..     137     179 ..     107     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.23
                                   S-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                   N6_N4_Mtase 189 tkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelaek 231
                                    +k+d +lD  +G G +++a + + +     +i++++++la++
  gi|15669072|ref|NP_247877.1|  53 VDKDDDILDLGCGYGVIGIALADEVKSTTMADINRRAIKLAKE 95 
                                   578999******************999999*****99999986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHHHHHTT-E CS
                   N6_N4_Mtase  33 eflekvlkevrrvLkddgsifiniddseikkelkaladeifggf 76 
                                   e l+++++e +++Lkd+g i++ i+ +  +k l + ++++fg +
  gi|15669072|ref|NP_247877.1| 137 EVLHRIIEEGKELLKDNGEIWVVIQTKQGAKSLAKYMKDVFG-N 179
                                   67899*********************9999999999999999.4 PP

>> SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.8e-05     0.017      75     134 ..     105     166 ..      70     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.8e-05
                 SPOUT_MTase_2  75 rkvpvlvqdlyqlvrkrrkkellivtdP..eGeei.sevkeelaealrkakevvvlvGsReGi 134
                                     ++v+  dly+ v++r+  + +i   P   G+e+ +++ ee +e l+ + e+ v++ +++G 
  gi|15669072|ref|NP_247877.1| 105 YDIRVVHSDLYENVKDRKY-NKIITNPPirAGKEVlHRIIEEGKELLKDNGEIWVVIQTKQGA 166
                                   56889999********999.666666555557765278999999*************999985 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   4.4e-05     0.027      79     181 ..      80     175 ..      66     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.4e-05
                                   EEEEES-HHHHHHHHHHHHHTT-GG.GEEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHHHHHHHH-TT CS
                       UPF0020  79 lygsDldrrvvqgareNaekagvgd.liefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYseflrelkrvlrg 158
                                      +D++rr+++ a+eN +  ++++  i ++  d  +   k+ +++ i+tnpP  +r       ++  + + +e k+ l+ 
  gi|15669072|ref|NP_247877.1|  80 TTMADINRRAIKLAKENIKLNNLDNyDIRVVHSDLYENV-KDRKYNKIITNPP--IRA-----GKEVLHRIIEEGKELLKD 152
                                   5668*************9988887524666666654333.4558*********..444.....444556677888888888 PP

                                   ..-EEEEEESSHHHHHCC---ES CS
                       UPF0020 159 ggrlvlltsenkalekaleeral 181
                                   +g + +++++++  +++++ ++ 
  gi|15669072|ref|NP_247877.1| 153 NGEIWVVIQTKQGAKSLAKYMKD 175
                                   88888888888777777766654 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   8.6e-05     0.053       5      76 ..      59     126 ..      55     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.6e-05
                                   EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEE CS
                Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgsleki 76 
                                   +l++GcG+G + +alA +  ++++  i+ r   +ak + k ++l+   +r++++d      e ++d++ +ki
  gi|15669072|ref|NP_247877.1|  59 ILDLGCGYGVIGIALADEVKSTTMADINRRAIKLAKENIKLNNLDNYDIRVVHSDL----YENVKDRKYNKI 126
                                   79**********************99999999999988888888888899999994....555566666665 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0006      0.37      69     102 ..      67     100 ..      52     125 .. 0.82
   2 ?   -2.3   0.0       3.8   2.4e+03      28      46 ..     128     146 ..     121     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0006
                         AviRa  69 tvlgllhgkkikkvlasDvdeevlelakkNLsLL 102
                                    v+g+  ++++k+ + +D+++ +++lak+N++L 
  gi|15669072|ref|NP_247877.1|  67 GVIGIALADEVKSTTMADINRRAIKLAKENIKLN 100
                                   4899999************************995 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.8
                         AviRa  28 paFPvRlasEilqralell 46 
                                   +  P+R ++E+l+r +e  
  gi|15669072|ref|NP_247877.1| 128 TNPPIRAGKEVLHRIIEEG 146
                                   5569999999999987755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1256.22
//
Query:       gi|15669073|ref|NP_247878.1|  [L=336]
Description: hypothetical protein MJ_0883 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-74  249.8   0.9    2.7e-74  249.3   0.9    1.2  1  Met_10           Met-10+ like-protein
      4e-19   68.2   2.0      4e-19   68.2   2.0    3.2  3  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    7.8e-08   32.1   0.2    1.8e-07   30.9   0.2    1.5  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    4.8e-07   29.5   0.1    8.7e-07   28.7   0.1    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    2.2e-06   27.3   0.0    4.1e-06   26.5   0.0    1.4  1  MTS              Methyltransferase small domain
    6.2e-05   22.7   0.0    0.00013   21.6   0.0    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00015   21.3   0.4    0.00048   19.6   0.0    1.8  2  DNA_methylase    C-5 cytosine-specific DNA methylase
    0.00021   20.6   2.3    0.00028   20.2   2.3    1.3  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    0.00053   19.7   0.1    0.00081   19.1   0.1    1.4  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
    0.00072   19.5   0.3     0.0033   17.4   0.0    2.2  2  Methyltransf_18  Methyltransferase domain
     0.0019   18.9   0.0     0.0041   17.8   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
     0.0029   17.5   0.0     0.0053   16.6   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
     0.0065   16.1   0.0      0.062   12.9   0.0    2.2  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0085   16.7   0.1       0.04   14.5   0.1    2.1  2  ING              Inhibitor of growth proteins N-terminal hist
     0.0086   15.9   0.1      0.015   15.1   0.1    1.4  1  PRMT5            PRMT5 arginine-N-methyltransferase
     0.0093   15.7   0.0      0.024   14.4   0.0    1.7  1  N6_N4_Mtase      DNA methylase
  ------ inclusion threshold ------
       0.02   14.7   0.1       0.06   13.1   0.0    2.0  2  Methyltransf_31  Methyltransferase domain
      0.075   13.7   0.0       0.19   12.4   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
        0.1   13.3   0.0        0.3   11.8   0.0    1.8  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.3   0.9   2.8e-77   2.7e-74       2     199 .]      96     289 ..      95     289 .. 0.98

  Alignments for each domain:
  == domain 1  score: 249.3 bits;  conditional E-value: 2.8e-77
                                   EEEEETTEEEEEB-TTSSH.HHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS CS
                        Met_10   2 kfeiiGdvvilnlreelke.ykkvigevildktkvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskv 81 
                                   +++++Gd+vil++++e++e ++k+ige++++  ++k+v+r++sev+gefR++ele+laG+++t tihkEng+r+++D++kv
  gi|15669073|ref|NP_247878.1|  96 SYDVVGDLVILQISDEVDEkIRKEIGELAYKLIPCKGVFRRKSEVKGEFRVRELEHLAGENRTLTIHKENGYRLWVDIAKV 176
                                   79***************988************************************************************* PP

                                   ---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG CS
                        Met_10  82 yfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgre 162
                                   yfs++l  Er+r++k+v+ ++vVvd+fAG+Gpf+i+++    ak+++aid+nP+++++lk+niklNk+e+++ pil+D+re
  gi|15669073|ref|NP_247878.1| 177 YFSPRLGGERARIMKKVSLNDVVVDMFAGVGPFSIACKN---AKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVRE 254
                                   *************************************95...999************************************ PP

                                   ---TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                        Met_10 163 vireqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                   v  + + +rv+mnlpk a++F+dk+l+++++ggvihy
  gi|15669073|ref|NP_247878.1| 255 V--DVKGNRVIMNLPKFAHKFIDKALDIVEEGGVIHY 289
                                   *..699******************************9 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   2.0   4.3e-22     4e-19       1      45 [.       4      48 ..       4      51 .. 0.96
   2 ?   -1.1   0.3       1.9   1.8e+03      21      43 ..     231     252 ..     228     256 .. 0.62
   3 ?   -2.3   0.0       4.5   4.2e+03      19      35 ..     271     287 ..     269     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 4.3e-22
                                  EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S--HH CS
                        Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkeepeg 45
                                  c+k++kk gE++R++L+e++lL+++yKI+s+++yly+P+k+  e+
  gi|15669073|ref|NP_247878.1|  4 CLKINKKHGEQTRRILIENNLLNKDYKITSEGNYLYLPIKDVDED 48
                                  9***************************************98876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                                   -B-TTS--EEETTEEEEEB-S-- CS
                        Trm5_N  21 lLdrnyKIksdddylyIPvkeep 43 
                                   lL +n K+ + +   +IP+ +++
  gi|15669073|ref|NP_247878.1| 231 LLKKNIKLNKLEHK-IIPILSDV 252
                                   66666666665554.47888777 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.5
                                   TT-B-TTS--EEETTEE CS
                        Trm5_N  19 kglLdrnyKIksdddyl 35 
                                   ++ +d+ + I  +++ +
  gi|15669073|ref|NP_247878.1| 271 HKFIDKALDIVEEGGVI 287
                                   67899999999999876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.2   1.9e-10   1.8e-07     162     256 ..     196     287 ..     185     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.9e-10
                          PrmA 162 geevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk.eekadvivaNILaevlie 241
                                   ++ v+D+ +G G  +ia +  +akk++a+Di++ A++  k+N++lNk+e+k+ + + +++ + + k + ++ N L +   +
  gi|15669073|ref|NP_247878.1| 196 NDVVVDMFAGVGPFSIACK--NAKKIYAIDINPHAIELLKKNIKLNKLEHKI-IPILSDVREvDVKGNRVIMN-LPKFAHK 272
                                   56799***********998..7****************************88.55556666545788999999.7999999 PP

                          PrmA 242 laedikklvkeggll 256
                                   +++++  +v+egg++
  gi|15669073|ref|NP_247878.1| 273 FIDKALDIVEEGGVI 287
                                   *********999987 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   9.3e-10   8.7e-07       3      61 ..     198     263 ..     196     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 9.3e-10
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe........l 61 
                                   v++D+f+G G  +i+ ++  +k++ai+in++ +++ ++N ++   ++ki ++l dv e        +
  gi|15669073|ref|NP_247878.1| 198 VVVDMFAGVGPFSIACKN-AKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREvdvkgnrvI 263
                                   79***************9.56***********************************99666666662 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   4.3e-09   4.1e-06      31     121 ..     195     273 ..     187     308 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.3e-09
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE..-STTTTSTTS-EEEEEE---STT CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevva..sdvleeveekkfdlivsNPPfha 109
                                   l++ v+D+ +G+G+ ++a++++    ++ ++d++ +A+e+ k+n++ nkle +++   sdv e v + k + +++N P   
  gi|15669073|ref|NP_247878.1| 195 LNDVVVDMFAGVGPFSIACKNA---KKIYAIDINPHAIELLKKNIKLNKLEHKIIPilSDVRE-V-DVKGNRVIMNLPK-- 268
                                   67789************99874...358***********************666541155544.3.3688999999773.. PP

                                   TCHCHHHHHHHH CS
                           MTS 110 gkatelavaeel 121
                                           a+++
  gi|15669073|ref|NP_247878.1| 269 -------FAHKF 273
                                   .......33334 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.4e-07   0.00013      42     141 ..     196     286 ..     187     315 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.4e-07
                                   C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--S CS
                 Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDPP 122
                                   +  v+D+faG G  ++  ++ +akk+++++ +++a+++lk+n++  kle+++  +  d  ++++ +++      ++   P 
  gi|15669073|ref|NP_247878.1| 196 NDVVVDMFAGVGPFSI--ACKNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDV-REVDVKGN-----RVIMNLPK 268
                                   4569********9998..79***************************998655555444.33444421.....25555666 PP

                                   SSTTCH.HHHHHHHHHTT- CS
                 Cons_hypoth95 123 yakellieevlelleekkl 141
                                   +a++ +i ++l+ +ee ++
  gi|15669073|ref|NP_247878.1| 269 FAHK-FIDKALDIVEEGGV 286
                                   6666.35777766666655 PP

>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.67   6.3e+02     188     234 ..      40      81 ..       7     166 .. 0.48
   2 !   19.6   0.0   5.1e-07   0.00048       3      56 ..     199     258 ..     198     274 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.67
                                   .TSGGGTTS-EE.BTTTB--GGGSSSTT-EE--.......S---HHHT CS
                 DNA_methylase 188 ktlrdlleekse.ldeektalsdklvekeekikkttkaseegypkels 234
                                     ++d++e+  + + + + +l dk +e+++ i      ++ ++++ +s
  gi|15669073|ref|NP_247878.1|  40 LPIKDVDEDILKsILNIEFELVDKELEEKKII------KKPSFREIIS 81 
                                   44444444422222222222222222222222......2222221111 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 5.1e-07
                                   EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.........-SEEEES-TTTS- CS
                 DNA_methylase   3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk........kvsigDitkidkk 56 
                                   ++d+faG+G f+++ ++a+   ++a++i+++a++++++n+k         +++ D++++d k
  gi|15669073|ref|NP_247878.1| 199 VVDMFAGVGPFSIACKNAK--KIYAIDINPHAIELLKKNIKlnklehkiIPILSDVREVDVK 258
                                   69***************99..99*****************8876654444455566666655 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   2.3   2.9e-07   0.00028      53     143 ..     199     281 ..      16     290 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-07
                                   EEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--G CS
                           TRM  53 vldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDPfGspa 133
                                   v+d +++ G     f+   +++k+++a Di+++A+el+k+N+kln+ e+ + +  +d + +  + ++   ++ l  f  + 
  gi|15669073|ref|NP_247878.1| 199 VVDMFAGVGP----FSIACKNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDVKGNR--VIMNLPKF--AH 271
                                   5556665554....45556799**************************9777776676655422222..23344444..44 PP

                                   GGHHHHHHHE CS
                           TRM 134 pfldsavqsv 143
                                   +f+d+a+  v
  gi|15669073|ref|NP_247878.1| 272 KFIDKALDIV 281
                                   5555555555 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   8.6e-07   0.00081      19      64 ..     193     238 ..     187     309 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.6e-07
                                   ..--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCH CS
               MethyltransfD12  19 d.kgktfvepFaGggaVffeakkqgkkvlinDinedlinlykalikn 64 
                                      ++++v+ FaG g +++++k + kk+++ Din++ i l k+ ik 
  gi|15669073|ref|NP_247878.1| 193 VsLNDVVVDMFAGVGPFSIACK-NAKKIYAIDINPHAIELLKKNIKL 238
                                   346789***************6.6*****************988876 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.8   1.7e+03     120     148 ..      11      39 ..       7      42 .. 0.74
   2 !   17.4   0.0   3.5e-06    0.0033      31      74 ..     209     252 ..     179     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.8
               Methyltransf_18 120 eaeelRkylvengfkiedEelvkeegkiY 148
                                   + e+ R+ l+en+   +d ++  e++ +Y
  gi|15669073|ref|NP_247878.1|  11 HGEQTRRILIENNLLNKDYKITSEGNYLY 39 
                                   55777888888888888888877777777 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.5e-06
               Methyltransf_18  31 ylvkegkakkviasDinegplekakeniekagledkievrlsdG 74 
                                   + +  ++akk++a+Din++++e  k+ni+ ++le+ki  +lsd 
  gi|15669073|ref|NP_247878.1| 209 FSIACKNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDV 252
                                   3445678999*******************************997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.3e-06    0.0041       1      63 [.     199     260 ..     199     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.3e-06
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTT CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedg 63 
                                   v+d+ +G G +++a+ ++   +k++++Di++ ++e  +++++ ++l  ++  +  d+++++ + +
  gi|15669073|ref|NP_247878.1| 199 VVDMFAGVGPFSIACKNA---KKIYAIDINPHAIELLKKNIKLNKLehKIIPILSDVREVDVKGN 260
                                   78999*********9977...8*******************999887788889999999887764 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.6e-06    0.0053      10     149 ..     183     323 ..     174     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.6e-06
               Methyltransf_23  10 sdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlre 90 
                                     +++r+++k   +  v+d+ +G+G ++  + +n ++++++D++p+a+e+++k +k +k  +  + +  + +  d+   + 
  gi|15669073|ref|NP_247878.1| 183 GGERARIMKKVSLNDVVVDMFAGVGPFSIAC-KNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDV-KGNR 261
                                   5567788887888899************988.6779***************9999999999988888888889996.6666 PP

               Methyltransf_23  91 vlehvpd.ppellrqiatllkpgGylllseplasl.kedrllldw.lylvpagrhisffsar 149
                                   v+ ++p   ++ ++++ +++++gG++   +++++  k+ +l+++   ++v + r ++ +  r
  gi|15669073|ref|NP_247878.1| 262 VIMNLPKfAHKFIDKALDIVEEGGVIHYYTIGKDFdKAIKLFEKKcDCEVLEKRIVKSYAPR 323
                                   7777775489********************99988458888888667888887777666555 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   6.6e-05     0.062      30     100 ..     213     279 ..     192     283 .. 0.74
   2 ?    3.5   0.0      0.05        47     107     139 ..     260     292 ..     253     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-05
                                   TTTTSEEEEEESSCCCHHHHHHHHHHTT--S.EEEEES-CTCCHHHHCC..EEEEEEEE--CCGGGTTT-TC CS
               Methyltr_RsmB-F  30 mknkgtvvAvdankeRlkrvaenlkrLgvtn.tivleaDarkidkvlggelfDriLlDaPCsgtgvirrdpd 100
                                    kn+++++A+d+n + ++ +++n+k   +++ +i +  D+r++d v g     r+++  P  +   i++  d
  gi|15669073|ref|NP_247878.1| 213 CKNAKKIYAIDINPHAIELLKKNIKLNKLEHkIIPILSDVREVD-VKG----NRVIMNLPKFAHKFIDKALD 279
                                   5899*******************986666640555889***994.444....48888888777777777665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.05
                                   HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES CS
               Methyltr_RsmB-F 107 ekdiaqlaklqkellsaaidllkkgGvlvYsTC 139
                                   ++ i++l k  ++ ++ a+d + +gGv+ Y T 
  gi|15669073|ref|NP_247878.1| 260 NRVIMNLPKFAHKFIDKALDIVEEGGVIHYYTI 292
                                   566899999999******************996 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.5   5.2e+03      35      46 ..     110     136 ..     102     157 .. 0.55
   2 !   14.5   0.1   4.2e-05      0.04       9      78 ..     238     308 ..     235     316 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.5
                                   HHHHHHHHHHH...............T CS
                           ING  35 keidskiekfl...............k 46 
                                   +e+d+ki+k +               +
  gi|15669073|ref|NP_247878.1| 110 DEVDEKIRKEIgelayklipckgvfrR 136
                                   455555555554444444455455444 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.2e-05
                                   GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.TS..S-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           ING   9 venLPlelqrnltelreiDakvqellkeidskiekfl.kngslqknekeeelsriqeelkeaqelldeKiq 78 
                                   + +L +++   l+ +re+D+k + ++ ++ + ++kf+ k+ ++ ++    ++++i +++++a++l ++K+ 
  gi|15669073|ref|NP_247878.1| 238 LNKLEHKIIPILSDVREVDVKGNRVIMNLPKFAHKFIdKALDIVEEGGVIHYYTIGKDFDKAIKLFEKKCD 308
                                   56788899999**************************8888899999999999****************85 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.6e-05     0.015      92     135 ..     215     258 ..     195     275 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                                   CEEEEEEEES-HHHHHHHHHHHHHHTTCCGCEEEES-CCCCCHC CS
                         PRMT5  92 tkvkivavEKnpnavvtLqkkvneekWeekveviksdmrelkae 135
                                   +  ki+a++ np+a+ +L+k+++ +k e+k+  i sd+re++ +
  gi|15669073|ref|NP_247878.1| 215 NAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDVK 258
                                   4569***************************99******99876 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.5e-05     0.024     192     231 .]     196     234 ..     187     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                                   T-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                   N6_N4_Mtase 192 gdivlDpFaGSGtTavaakelgrkfiGieieeeyvelaek 231
                                   +d+v+D FaG G   +a+k+ + k + i+i+++++el +k
  gi|15669073|ref|NP_247878.1| 196 NDVVVDMFAGVGPFSIACKNAK-KIYAIDINPHAIELLKK 234
                                   9*******************99.8999********99875 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         4   3.8e+03      55      80 ..      55      81 ..      50     128 .. 0.71
   2 ?   13.1   0.0   6.4e-05      0.06       5      54 ..     197     242 ..     194     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4
               Methyltransf_31 55 nveFeqgdieelekl.ledekfDlils 80
                                  n+eFe  d e  ek+ +++ +f  i+s
  gi|15669073|ref|NP_247878.1| 55 NIEFELVDKELEEKKiIKKPSFREIIS 81
                                  777777777776666666555544444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.4e-05
               Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld 54 
                                    +v+D  +G G ++++   +    ++++ iDi+++aiel ++n + ++l+
  gi|15669073|ref|NP_247878.1| 197 DVVVDMFAGVGPFSIACK-N---AKKIYAIDINPHAIELLKKNIKLNKLE 242
                                   578899999999888888.2...456*****************9988886 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0002      0.19       7      80 ..     206     299 ..     200     305 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                                   TSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.........EEEE.........TTEECCCT..SS-TT-EEEEEE CS
               Methyltransf_11   7 tGrlaealakrgarvvgvDlskemlklakekaseegl.........kvef.........vvadaekl..pfednsfDlvvs 67 
                                    G ++ a++ ++++++++D+++ +++l k++++ ++l            +         v +++ k+  +f d+  D+v  
  gi|15669073|ref|NP_247878.1| 206 VGPFSIACK-NAKKIYAIDINPHAIELLKKNIKLNKLehkiipilsD--VrevdvkgnrVIMNLPKFahKFIDKALDIVEE 283
                                   444444444.558*********************9987655544330..23333344444444444222466666666666 PP

                                   ES-CCC-...CCHHHH CS
               Methyltransf_11  68 sevlhhv...edpeka 80 
                                     v+h+    +d +ka
  gi|15669073|ref|NP_247878.1| 284 GGVIHYYtigKDFDKA 299
                                   6666666555555555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00032       0.3       5      86 ..     204     300 ..     200     307 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
               Methyltransf_12   5 cGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..................... 64 
                                   +G+G ++ a+ ++   ++++++Di+p+ai    e l+k++++n  + ++  +   ++  +                     
  gi|15669073|ref|NP_247878.1| 204 AGVGPFSIACKNA---KKIYAIDINPHAI----ELLKKNIKLNKLEHKIIPIL--SDVREvdvkgnrvimnlpkfahkfid 275
                                   7999999999999...*************....55555554443333333332..22222235556888888889999999 PP

               Methyltransf_12  65 ssfDlvvasnvlhhl...kdirevl 86 
                                   ++ D+v   +v+h+    kd ++++
  gi|15669073|ref|NP_247878.1| 276 KALDIVEEGGVIHYYtigKDFDKAI 300
                                   8999999999999887777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2084.39
//
Query:       gi|15669074|ref|NP_247879.1|  [L=516]
Description: replication factor C large subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-15   58.0   2.1    1.4e-15   57.8   0.0    2.2  1  AAA              ATPase family associated with various cellul
    1.5e-12   47.8   0.1    1.5e-12   47.8   0.1    2.4  2  Rad17            Rad17 P-loop domain
    2.2e-10   40.5   0.0    4.6e-10   39.5   0.0    1.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.2e-07   31.2   1.7    1.3e-07   31.0   0.0    2.1  2  DUF815           Protein of unknown function (DUF815)
    1.9e-06   27.9   2.6    3.1e-06   27.2   0.0    2.7  2  AAA_14           AAA domain
    3.3e-06   27.0   0.0      9e-06   25.5   0.0    1.7  1  IstB_IS21        IstB-like ATP binding protein
    1.3e-05   25.5   1.2     0.0013   19.0   0.0    3.7  4  AAA_22           AAA domain
    3.8e-05   23.7   0.0       0.08   12.9   0.0    2.5  2  NACHT            NACHT domain
    5.2e-05   22.6   0.0    0.00016   21.0   0.0    1.9  2  Zeta_toxin       Zeta toxin
    7.2e-05   22.8   0.0     0.0003   20.8   0.0    2.1  1  AAA_5            AAA domain (dynein-related subfamily)
    7.4e-05   23.2   0.4    0.00051   20.5   0.0    2.6  2  AAA_16           AAA ATPase domain
    0.00016   22.0   0.1    0.00073   19.8   0.0    2.2  1  AAA_28           AAA domain
    0.00017   21.8   0.0    0.00051   20.2   0.0    1.9  1  AAA_33           AAA domain
    0.00044   20.5   0.1    0.00044   20.5   0.1    2.6  1  AAA_assoc_2      AAA C-terminal domain
    0.00093   19.6   0.0    0.00093   19.6   0.0    3.4  1  AAA_17           AAA domain
     0.0011   19.3   0.2     0.0046   17.3   0.0    2.2  1  RNA_helicase     RNA helicase
     0.0019   18.7   0.1     0.0019   18.7   0.1    2.9  1  AAA_18           AAA domain
     0.0023   17.6   0.0     0.0064   16.1   0.0    1.7  1  AAA_25           AAA domain
     0.0035   16.7   0.0     0.0073   15.7   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.004   16.7   0.0      0.008   15.7   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
     0.0091   15.1   0.0      0.057   12.5   0.0    2.2  2  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
       0.01   16.0   3.1       0.72    9.9   0.0    3.4  3  tRNA_lig_kinase  tRNA ligase kinase domain
      0.026   14.5   0.0       0.16   12.0   0.0    2.2  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.029   14.9   0.0      0.029   14.9   0.0    2.9  2  ABC_tran         ABC transporter
      0.048   13.4   0.0       0.12   12.1   0.0    1.7  1  AAA_30           AAA domain
       0.88    9.3   0.0       0.88    9.3   0.0    3.4  2  AAA_11           AAA domain
       0.95    9.6   0.0       0.95    9.6   0.0    3.0  1  MMR_HSR1         50S ribosome-binding GTPase
        1.6    9.1   4.8        1.5    9.1   0.2    3.0  4  AAA_19           AAA domain
        2.6    8.5   0.0        2.6    8.5   0.0    3.5  2  AAA_23           AAA domain
        3.5    7.8   0.0        3.5    7.8   0.0    2.4  1  Hydin_ADK        Hydin Adenylate kinase-like domain
        5.4    5.7  15.4        8.3    5.1  15.4    1.2  1  ALMT             Aluminium activated malate transporter
        5.7    5.6  14.9        7.4    5.2  14.9    1.1  1  Presenilin       Presenilin
        5.9    7.0  23.9         15    5.7  23.9    1.6  1  TP53IP5          Cellular tumour antigen p53-inducible 5
        6.6    7.1  35.8         13    6.1  35.8    1.5  1  DUF4604          Domain of unknown function (DUF4604)


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.0   2.7e-18   1.4e-15       1     111 [.      42     138 ..      42     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 2.7e-18
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHHTTC CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka....kpsilfiDEidalaksrsgs 77 
                                   +ll+GppG+GKT+la a+a++ g+e++e+++s+ +      +++ i++++ +a +++    k+  +++DE+d + +++   
  gi|15669074|ref|NP_247879.1|  42 ILLVGPPGCGKTTLAYALANDYGFEVIELNASDKR------NSSAIKKVVGHAATSSsifgKKFLIVLDEVDGISGKE--- 113
                                   69*********************************......8899999999987777899878***********9999... PP

                                   CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                           AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnr 111
                                       +   v++L++++++ k+      +i+++n+
  gi|15669074|ref|NP_247879.1| 114 ----DAGGVSELIKVIKKAKN-----PIILTAND 138
                                   ....8889***********99.....58888887 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.1   2.9e-15   1.5e-12       8      81 ..       3      74 ..       1     104 [. 0.84
   2 ?   -0.6   0.0         2   1.1e+03     146     181 ..      75     112 ..      68     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 2.9e-15
                         Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvs 81
                                   W+eky+P+ ++++a h k  e++k+w+++    + +k iLL  GP+GCgk+t    L+  +g++++e  n+  
  gi|15669074|ref|NP_247879.1|  3 SWVEKYRPKSLKDVAGHEKVKEKLKTWIESYLKGETPKPILL-VGPPGCGKTTLAYALANDYGFEVIEL-NASD 74
                                  6*****************999********9998899888876.5**********************995.4444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2
                         Rad17 146 yrdsdalrevirkylrsseal..plilviteieslegd 181
                                   +r+s a+++v+ ++ +ss  +   +++v+ e++ ++g+
  gi|15669074|ref|NP_247879.1|  75 KRNSSAIKKVVGHAATSSSIFgkKFLIVLDEVDGISGK 112
                                   577899999*********99998899999999998886 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   8.7e-13   4.6e-10       2      62 ..       9      68 ..       8     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 8.7e-13
                        RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklk 62
                                  rPksl++  g ekvkeklk  ie+   ++e+   +ll+GpPG Gkttla  +a++ g ++ 
  gi|15669074|ref|NP_247879.1|  9 RPKSLKDVAGHEKVKEKLKTWIESY-LKGETPKPILLVGPPGCGKTTLAYALANDYGFEVI 68
                                  9*********************976.6789999*********************9987653 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   2.6e-10   1.3e-07      17     115 ..       3     105 ..       1     128 [. 0.86
   2 ?   -3.7   0.4       9.9   5.2e+03     163     180 ..     454     471 ..     446     472 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.6e-10
                        DUF815  17 epveevdevklddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpk 97 
                                   + ve++++ +l+d+ g +k ke+l++ +e +l+g++ + +LL+G  G+GK +l  al n+y  e + l   +k++ + ++k
  gi|15669074|ref|NP_247879.1|   3 SWVEKYRPKSLKDVAGHEKVKEKLKTWIESYLKGETPKPILLVGPPGCGKTTLAYALANDYGFEVIELNASDKRNSSAIKK 83 
                                   668999999***************************************************998888888888888888888 PP

                        DUF815  98 lvellrerp....erfilfvDD 115
                                   +v + ++++    ++f++++D 
  gi|15669074|ref|NP_247879.1|  84 VVGHAATSSsifgKKFLIVLDE 105
                                   8887775542233677887775 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.9
                        DUF815 163 eeleeeeihaseaveekl 180
                                   +e+++ e++++e v+ek+
  gi|15669074|ref|NP_247879.1| 454 KEEVKAEVEKKEEVKEKI 471
                                   335679999999999997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0     6e-09   3.1e-06       3      80 ..      40     113 ..      38     174 .. 0.79
   2 ?   -2.2   0.0       7.3   3.8e+03     102     123 ..     208     229 ..     206     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6e-09
                        AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqevpewe 80 
                                   k+++++G+  +GKTtl++ l++++     +++++n  d+r++++ ++  + ++  ++ + + kk +++lDE+  +++ e
  gi|15669074|ref|NP_247879.1|  40 KPILLVGPPGCGKTTLAYALANDYG---FEVIELNASDKRNSSAIKK-VVGHAATSSsIFG-KKFLIVLDEVDGISGKE 113
                                   899******************9999...999****999999764433.2334444444666.999*******9885443 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.3
                        AAA_14 102 skllskeiatslagrvaeiely 123
                                   s++ls e+a++l +r  e +++
  gi|15669074|ref|NP_247879.1| 208 SGDLSYEAAQKLPDRKREANIF 229
                                   78999**********9988775 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.7e-08     9e-06      48     150 ..      40     139 ..      19     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.7e-08
                     IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdl.gllpldqae. 126
                                   + i+l+Gp+G GK+ la al+ +    g++v+ + ++d  ++ ++++  g++a+  + + k  l++lD++ g+   ++a  
  gi|15669074|ref|NP_247879.1|  40 KPILLVGPPGCGKTTLAYALAND---YGFEVIELNASDKRNSSAIKKVVGHAATSSSIFGKKFLIVLDEVdGISGKEDAGg 117
                                   5699****************875...7******************************************955555544432 PP

                     IstB_IS21 127 aellfeviekryerrsiiitsnlp 150
                                    ++l +vi+k+  +++ii+t+n  
  gi|15669074|ref|NP_247879.1| 118 VSELIKVIKKA--KNPIILTANDA 139
                                   57899999986..899****9975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.5e-06    0.0013       5      58 ..      39      83 ..      35      98 .. 0.84
   2 ?   -0.7   0.0       2.9   1.5e+03      94     106 ..     100     115 ..      87     140 .. 0.69
   3 ?   -1.6   0.0       5.6   2.9e+03      42      83 ..     153     200 ..     134     254 .. 0.60
   4 ?    1.9   0.1      0.47   2.5e+02      43      85 ..     332     373 ..     306     400 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.5e-06
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllr 58
                                   + ++++G++G+GKTtl+  l++ +         + ev++ +++ + +s+ + +
  gi|15669074|ref|NP_247879.1| 39 PKPILLVGPPGCGKTTLAYALANDY---------GFEVIELNASDKRNSSAIKK 83
                                  67799*******************9.........99999999999887777655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.9
                        AAA_22  94 lliiDEaqhlrs....e 106
                                   l+++DE++ + s    +
  gi|15669074|ref|NP_247879.1| 100 LIVLDEVDGI-SgkedA 115
                                   89******99.433343 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5.6
                        AAA_22  42 vvfvtlpsstsskdllrellralglelka......erlsseelleale 83 
                                   v+  ++ + +s  ++l++++++ gl+ ++      + +s  +l++a++
  gi|15669074|ref|NP_247879.1| 153 VIQLNPVHTNSVYKVLKKIAEKEGLDVDDktlkmiAQHSAGDLRSAIN 200
                                   555555555566666666666666555554454544444444444443 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.47
                        AAA_22  43 vfvtlpsstsskdllrellralglelkaerlsseell.ealeqa 85 
                                   +f  l++ +  +++l+++l+++g+++++   s+++ +  ++ + 
  gi|15669074|ref|NP_247879.1| 332 IFRLLTKTKAEREILNKILKKIGEKTHT--SSKRARFdLQMLKL 373
                                   5556677778899**********99999..33333333444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00015      0.08       2      22 ..      41      61 ..      40      68 .. 0.89
   2 !    8.2   0.0     0.004       2.1      81     163 ..      97     172 ..      89     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                                  CEEEEC-TTTCHHHHHHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLlqklal 22
                                  +++l G++G+GKTtL+  la 
  gi|15669074|ref|NP_247879.1| 41 PILLVGPPGCGKTTLAYALAN 61
                                  689*************99986 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.004
                                   CCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE--TCCHHHHHHHH CS
                         NACHT  81 erlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqleeaivlevegfsesrrkqlvrk 161
                                   ++ L++lD +D ++ + ++     v +l+ + i+k    +++++lt+     + ++++l   +v+++++   +++ +++ k
  gi|15669074|ref|NP_247879.1|  97 KKFLIVLDEVDGISGKEDA---GGVSELI-KVIKK---AKNPIILTANDAYAPSIRSLLPYVEVIQLNPVHTNSVYKVLKK 170
                                   57899********996666...7788877.89999...9*******************************99999999887 PP

                                   CT CS
                         NACHT 162 yf 163
                                     
  gi|15669074|ref|NP_247879.1| 171 IA 172
                                   65 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.1e-07   0.00016       8      55 ..      30      76 ..      23      94 .. 0.87
   2 ?   -3.3   0.0       8.5   4.5e+03     137     171 ..     216     252 ..     213     256 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.1e-07
                    Zeta_toxin  8 kk.ypsqerPklillgGqpGAGKselaellkdelerqgnvvrldpDdlR 55
                                  ++ y ++e+Pk ill+G pG+GK++la +l+++   + +v++l++ d R
  gi|15669074|ref|NP_247879.1| 30 IEsYLKGETPKPILLVGPPGCGKTTLAYALANDY--GFEVIELNASDKR 76
                                  4558899************************998..8899999887766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.5
                    Zeta_toxin 137 rlgvldRyeee..vaegRlvpkeehdeafeglresve 171
                                   ++++ dR +e    ++ R++ k++h  + + +  +v+
  gi|15669074|ref|NP_247879.1| 216 AQKLPDRKREAniFDALRVILKTTHYGIATTALMNVD 252
                                   5566677777653445699999999888887777766 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   5.8e-07    0.0003       2      75 ..      42     107 ..      41     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.8e-07
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGG CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEve 75 
                                   +lLvGppG+gK++la  la  ++ ev + + +++ +++ +k  +      ++ + s++     ++ ++vlDEv+
  gi|15669074|ref|NP_247879.1|  42 ILLVGPPGCGKTTLAYALANDYGFEVIELNASDKRNSSAIKKVVGH----AATSSSIF----GKKFLIVLDEVD 107
                                   89************************99999999999999876662....33333333....367777777776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   9.6e-07   0.00051      10      51 ..      24      66 ..      16     139 .. 0.73
   2 ?   -1.5   0.2       5.3   2.8e+03      88     106 ..     352     375 ..     306     447 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 9.6e-07
                        AAA_16 10 eqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd 51
                                  e+L++ +e+  +g++   +ll+G++G+GK++l+ +l++ +  +
  gi|15669074|ref|NP_247879.1| 24 EKLKTWIESYLKGETpKPILLVGPPGCGKTTLAYALANDYGFE 66
                                  67777888888888889****************9998765544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.3
                        AAA_16  88 e.....aesaeleawrekleeala 106
                                   +     ++s+++++++ + ++ la
  gi|15669074|ref|NP_247879.1| 352 KigektHTSSKRARFDLQMLKLLA 375
                                   233333333333333333333333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.4e-06   0.00073       2      28 ..      42      69 ..      41      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.4e-06
                        AAA_28  2 ivitGgestGKTtlleaLaar.gypvvp 28
                                  i ++G++++GKTtl+ aLa++ g++v++
  gi|15669074|ref|NP_247879.1| 42 ILLVGPPGCGKTTLAYALANDyGFEVIE 69
                                  789****************987999985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   9.7e-07   0.00051       2      44 ..      42      91 ..      42     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.7e-07
                        AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdt.......lrrrlfgtdqqs 44
                                  +llvG+pG+GK+tla  l++  g+++++ ++       ++++++g   +s
  gi|15669074|ref|NP_247879.1| 42 ILLVGPPGCGKTTLAYALANDYGFEVIELNAsdkrnssAIKKVVGHAATS 91
                                  689********************999998876667777666666655544 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   8.3e-07   0.00044       3      38 ..     175     210 ..     173     247 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.3e-07
                                   X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaae 38 
                                   + l+++d++l+++a+ + GD R+a+n LE++a + +
  gi|15669074|ref|NP_247879.1| 175 EGLDVDDKTLKMIAQHSAGDLRSAINDLEALALSGD 210
                                   5689*************************8887654 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.8e-06   0.00093       1      25 [.      45      69 ..      45      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.8e-06
                                  EE-TTSSHHHHHHHHHHHHTEEEEE CS
                        AAA_17  1 lGgPGsGKgtqceklvekygfthls 25
                                  +G+PG+GK+t++  l+ +ygf++++
  gi|15669074|ref|NP_247879.1| 45 VGPPGCGKTTLAYALANDYGFEVIE 69
                                  7*********************985 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   8.7e-06    0.0046       1      27 [.      42      73 ..      42     138 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.7e-06
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl.....k 27
                                  i+l+Gp+g+GK+tla+ La++   ++      
  gi|15669074|ref|NP_247879.1| 42 ILLVGPPGCGKTTLAYALANDYGFEVielnaS 73
                                  689****************9988444454442 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   3.6e-06    0.0019       1      25 [.      42      69 ..      42     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.6e-06
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgf...g 25
                                  Ill G+pG+GKttla +L++  gf    
  gi|15669074|ref|NP_247879.1| 42 ILLVGPPGCGKTTLAYALANDYGFeviE 69
                                  99****************9886555441 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.2e-05    0.0064      34      54 ..      40      60 ..       8      64 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
                        AAA_25 34 elallaGapgtGKttlaldla 54
                                  + +ll+G+pg+GKttla+ la
  gi|15669074|ref|NP_247879.1| 40 KPILLVGPPGCGKTTLAYALA 60
                                  469***************998 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.4e-05    0.0073       2      44 ..      13      61 ..      12     100 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                  Mg_chelatase  2 lkdvkGqeeakraleiaa....aGg..HnlllvGppGsGKtmlakrlps 44
                                  lkdv+G+e+ k+ l+  +     G+    +llvGppG+GKt la +l++
  gi|15669074|ref|NP_247879.1| 13 LKDVAGHEKVKEKLKTWIesylKGEtpKPILLVGPPGCGKTTLAYALAN 61
                                  677777777777665433111145422569**************99875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.5e-05     0.008      32      82 ..      38      85 ..      22     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                         AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82
                                    kp+llvGp G+GKt+++  l + +    + ++ +n s + +++ +++++
  gi|15669074|ref|NP_247879.1| 38 TPKPILLVGPPGCGKTTLAYALANDYG---FEVIELNASDKRNSSAIKKVV 85
                                  4589****************9999888...999999999988888887765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00011     0.057     104     150 ..      12      60 ..       6      67 .. 0.80
   2 ?   -1.0   0.0       1.4   7.3e+02     230     245 ..     158     173 ..     152     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                         T2SSE 104 tlddlgaeealkekiaevlrkavr..erglilvsGgTgsGKttllyall 150
                                   +l+d++ +e++kek++  +++ ++  + + il+ G+ g GKttl+yal 
  gi|15669074|ref|NP_247879.1|  12 SLKDVAGHEKVKEKLKTWIESYLKgeTPKPILLVGPPGCGKTTLAYALA 60 
                                   577888888888888888888776225578****************986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                         T2SSE 230 TlHansaagalerLeq 245
                                    +H+ns+ ++l+++++
  gi|15669074|ref|NP_247879.1| 158 PVHTNSVYKVLKKIAE 173
                                   6899999999998865 PP

>> tRNA_lig_kinase  tRNA ligase kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0014      0.72       9      47 ..      49      85 ..      42      93 .. 0.78
   2 ?    2.3   0.0      0.29   1.6e+02      20      88 ..      92     162 ..      84     181 .. 0.67
   3 ?   -0.6   3.0       2.3   1.2e+03      27      83 ..     389     445 ..     380     493 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0014
                                  TSSHHHHHHHHHHH-TTSEEEEGGGS-TT-SS-HHHHHH CS
               tRNA_lig_kinase  9 GCGkttvaltlenlfgeWghvqnDnitgkdkkklvkeal 47
                                  GCGktt a +l n +g ++ v + n ++k+++  +k+++
  gi|15669074|ref|NP_247879.1| 49 GCGKTTLAYALANDYG-FE-VIELNASDKRNSSAIKKVV 85
                                  9***************.55.5566778887777777765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.29
                                   HHH-TT.SEEE..EGGGS-TT-SS-HHHHHHHTTSSTT--EEEEES---SHHHHHHHHHHHHHHHHHH--TT CS
               tRNA_lig_kinase  20 enlfge.Wghv..qnDnitgkdkkklvkealellkkdeskvvlvDrnnhqkreRkqlfeeidelkeeylsyd 88 
                                   +++fg+ +  v    D i+gk++   v+e+++++kk ++ ++ +  n++ +   + l+  ++ ++ ++++++
  gi|15669074|ref|NP_247879.1|  92 SSIFGKkFLIVldEVDGISGKEDAGGVSELIKVIKKAKNPII-LTANDAYAPSIRSLLPYVEVIQLNPVHTN 162
                                   56777743333112367899999999********66666555.55566665555566666666666666555 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.3
                                   EEEEGGGS-TT-SS-HHHHHHHTTSSTT--EEEEES---SHHHHHHHH.HHHHHHHHH CS
               tRNA_lig_kinase  27 ghvqnDnitgkdkkklvkealellkkdeskvvlvDrnnhqkreRkqlf.eeidelkee 83 
                                     +++D+++     kl++e+l++l k+++k+    +  ++k e+++   e+ +e++++
  gi|15669074|ref|NP_247879.1| 389 FEIKEDELKVLVGDKLASEILKIL-KEKKKLERKKKKEKEKLEKEKKKeEKAKEKQSN 445
                                   46899999999999**********.555555444444444444443330333333343 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0003      0.16      12      46 ..      24      66 ..      13      72 .. 0.68
   2 ?   -0.9   0.0         3   1.6e+03      69     102 ..     229     264 ..     191     286 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0003
                                  HHHHHCH.....TEE...EEEEESTTSSHHHHHHHHHHHTT-- CS
                          TsaE 12 kklakal.....gdv...ilLeGdLGaGKTtlvrglakalgve 46
                                  +kl++ +     g++   ilL G+ G+GKTtl+ +la+ +g+e
  gi|15669074|ref|NP_247879.1| 24 EKLKTWIesylkGETpkpILLVGPPGCGKTTLAYALANDYGFE 66
                                  333333322224222566*******************999876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3
                                   EE-TT-SSTHHHHHCTTCCCCS.TS.CEEEEETGGG CS
                          TsaE  69 fDlYRledeeeleelgleeyle.ee.avvlvEWpek 102
                                   fD+ R+  ++  + +  + +++ +e   v++EW  +
  gi|15669074|ref|NP_247879.1| 229 FDALRVILKTTHYGIATTALMNvDEtPDVVIEWIAE 264
                                   566666555555555555555544423688999765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   5.6e-05     0.029      14      36 ..      42      64 ..      34     295 .. 0.93
   2 ?   -1.8   4.3       7.6     4e+03      27      97 ..     408     480 ..     388     506 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.6e-05
                                  EEEEESTTSSHHHHHHHHTTSS- CS
                                  xxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 14 vaivGenGaGKStLlkllagllk 36
                                  + +vG+ G+GK+tL+ +la+ + 
  gi|15669074|ref|NP_247879.1| 42 ILLVGPPGCGKTTLAYALANDYG 64
                                  679***************98875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.6
                                   HHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS--S-TTSBHHHHHHHTCHHHHHHHSTTGGT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  27 LlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqepqlfpeltvrenesdeeiekalsklglkel 97 
                                   +lk+l ++ k +  + + ++++l++   +e++  +k++  + q +++++e++++ ++++e  ek+++k + +e+
  gi|15669074|ref|NP_247879.1| 408 ILKILKEKKKLERKK-KKEKEKLEKekkKEEKAKEKQSNLIIQPKEIKEEVKAEVEKKEEVKEKIVEKPKAEEV 480
                                   555555554443333.2233333334445677777777888887777777754444333334444444433332 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00023      0.12      22     131 ..      43     144 ..      33     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                        AAA_30  22 vltGpAGtGKttalkalreaweaaggrvi.glAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEagmv. 100
                                   +l+Gp+G GKtt+  al++   + g++vi + A+ ++ + ++++ +g +a+t  ++     g     ++ l++ DE+  + 
  gi|15669074|ref|NP_247879.1|  43 LLVGPPGCGKTTLAYALAN---DYGFEVIeLNASDKRNSSAIKKVVG-HAATSSSIF----G-----KKFLIVLDEVDGIs 110
                                   799*********9777654...5578887466888888888888877.555666666....3.....45788888875554 PP

                        AAA_30 101 ...dtkqlaallkaaekagakvilvGDerQlasV 131
                                      d+  + +l+k ++ka+  +il   ++  +s+
  gi|15669074|ref|NP_247879.1| 111 gkeDAGGVSELIKVIKKAKNPIILTANDAYAPSI 144
                                   4447777788888888887777777666666655 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0017      0.88       7      41 ..      27      63 ..      21      93 .. 0.74
   2 ?   -3.0   0.0       9.2   4.9e+03     186     222 ..     222     259 ..     165     259 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                        AAA_11  7 reaiksalsese..itliqGPPGtgKTktivellsql 41
                                  +++i+s l+ +     l+ GPPG+gKT+   +l +  
  gi|15669074|ref|NP_247879.1| 27 KTWIESYLKGETpkPILLVGPPGCGKTTLAYALANDY 63
                                  5566666665555566999*********999888765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.2
                        AAA_11 186 esleeevldeaeivl.tTlsgagsklleklakkfdvvi 222
                                   ++ e+++ d  +++l tT  g++  +l ++++  dvvi
  gi|15669074|ref|NP_247879.1| 222 RKREANIFDALRVILkTTHYGIATTALMNVDETPDVVI 259
                                   33346777777777745555677777777777777766 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0018      0.95       2      22 ..      42      62 ..      41     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0018
                                  EEEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                  +++vG p  GK+tL  al ++
  gi|15669074|ref|NP_247879.1| 42 ILLVGPPGCGKTTLAYALAND 62
                                  789***************985 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2    0.0029       1.5      10      27 ..      39      56 ..      33      90 .. 0.89
   2 ?   -1.6   0.0         6   3.2e+03      95     115 ..      90     110 ..      58     135 .. 0.63
   3 ?   -1.3   0.0       4.9   2.6e+03      89     114 ..     230     257 ..     161     274 .. 0.56
   4 ?   -0.4   0.1       2.4   1.3e+03      47      78 ..     335     412 ..     304     449 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0029
                        AAA_19 10 ekvllvtaGpGtGKTrvl 27
                                   k++l++++pG+GKT++ 
  gi|15669074|ref|NP_247879.1| 39 PKPILLVGPPGCGKTTLA 56
                                  5899***********975 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6
                        AAA_19  95 eeekklqeeellivDEfqdvd 115
                                   ++++ + +++l++ DE+  ++
  gi|15669074|ref|NP_247879.1|  90 TSSSIFGKKFLIVLDEVDGIS 110
                                   333444444599999998876 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.9
                        AAA_19  89 elle..eaeeekklqeeellivDEfqdv 114
                                    +l+   ++++  +  ++l+ vDE+ dv
  gi|15669074|ref|NP_247879.1| 230 DALRviLKTTHYGIATTALMNVDETPDV 257
                                   2333432234445544557777777776 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.4
                        AAA_19  47 lvaftgrAakelrerlaalgaeatTiHrlal..............................................l 78 
                                   l++ t+   + l++ l+++g++++T  + a                                               l
  gi|15669074|ref|NP_247879.1| 335 LLTKTKAEREILNKILKKIGEKTHTSSKRARfdlqmlkllakenpsvaadlvdyfeikedelkvlvgdklaseilkiL 412
                                   555555555556777777777777777775545455555555555555555444444444444433333333333330 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0049       2.6      22      39 ..      42      59 ..      31      61 .. 0.90
   2 ?    1.8  22.5      0.55   2.9e+02      96     192 ..     320     446 ..     227     454 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0049
                        AAA_23 22 tlItGpNGaGKTTildAi 39
                                   l++Gp G+GKTT+  A+
  gi|15669074|ref|NP_247879.1| 42 ILLVGPPGCGKTTLAYAL 59
                                  599***********9887 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.55
                        AAA_23  96 lskkkgkttkkaklellei.deleqfisellgskki...........ilnlilflgqer.............feefel... 148
                                   +++k + + + ++++ll++ ++ +++++++l++  +            l+++ +l++e+             +   e+   
  gi|15669074|ref|NP_247879.1| 320 KYRKWTPYSYPKIFRLLTKtKAEREILNKILKKIGEkthtsskrarfDLQMLKLLAKENpsvaadlvdyfeiK---EDelk 397
                                   4444444444444444433244444444443333333344444477777888888888888888887764331...22223 PP

                        AAA_23 149 .....kdkkerleelekeleeledekkllekleqekekekeleeleeel 192
                                        k  +e l+ l+++++ + ++kk+ ekle+ek+ke++ +e++++l
  gi|15669074|ref|NP_247879.1| 398 vlvgdKLASEILKILKEKKKLERKKKKEKEKLEKEKKKEEKAKEKQSNL 446
                                   4444433333666666666666677777777777777777777777766 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0067       3.5       2      28 ..      42      68 ..      41      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0067
                     Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAll 28
                                  i++ G+P  GKt+ a +La  Y+  ++
  gi|15669074|ref|NP_247879.1| 42 ILLVGPPGCGKTTLAYALANDYGFEVI 68
                                  6778******************97655 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  15.4     0.016       8.3     253     430 ..     280     497 ..     269     515 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.016
                          ALMT 253 frhpwkqyvkvggvlrqcaytveal...........................hgcilseiqapeelrkkfkeelqrvsles 306
                                   f++  k    +g v+r+ +y+   +                              +l++++a +e+ +k+ +++ + +  s
  gi|15669074|ref|NP_247879.1| 280 FEYLSKADRYLGRVMRRQNYSFWKYattlmtagvalskdekyrkwtpysypkIFRLLTKTKAEREILNKILKKIGEKTHTS 360
                                   566666666666666666666666666666666666666666666665554333458899999999999999999999999 PP

                          ALMT 307 akvlrelaesvkkmkklsk..veellkevkvaaeeLqskl..dskskLlvnsekweaakkkekaeeveekkeeekeseskk 383
                                   +k  r   +++k   k+++  + +l++  +   +eL+  +  +  s++l + +++++ ++k+k+e+++ +ke++ke+++k+
  gi|15669074|ref|NP_247879.1| 361 SKRARFDLQMLKLLAKENPsvAADLVDYFEIKEDELKVLVgdKLASEILKILKEKKKLERKKKKEKEKLEKEKKKEEKAKE 441
                                   999887777777655555543789999999999999998853334444433333333333333333333333333333333 PP

                          ALMT 384 eea.........eaveeaeseseksllkeskrslklskkesapaeesleekqlske 430
                                   +++         +++ +ae+e++++++++  ++ k ++ ++ +++e++e k+ +k+
  gi|15669074|ref|NP_247879.1| 442 KQSnliiqpkeiKEEVKAEVEKKEEVKEKIVEKPKAEEVKEKSKTEEKETKKDKKK 497
                                   33346676554422223333333333333333333332222222222222222233 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  14.9     0.014       7.4     230     326 ..     418     511 ..     385     515 .. 0.42

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.014
                    Presenilin 230 aevaeseeeeeaekkkeeasesskeeeseeesseksaqsseseeeseeesseaessaeesseekeseessesseeeeeeee 310
                                       e+++++e+ek ++e+++++k++e++++   + ++ +e+ + + e+++e++++  e+ + +e +e+s+++e+e+++++
  gi|15669074|ref|NP_247879.1| 418 L---ERKKKKEKEKLEKEKKKEEKAKEKQSNLIIQPKEIKEEVKAEVEKKEEVKEKIVEKPKAEEVKEKSKTEEKETKKDK 495
                                   1...11222222222222222222222222222222222222233333333333333333333333444444444444444 PP

                    Presenilin 311 eeeeseseergvkLGL 326
                                   ++ ++++e++g +L L
  gi|15669074|ref|NP_247879.1| 496 KKGKKKKEDKGKQLTL 511
                                   5555555666666655 PP

>> TP53IP5  Cellular tumour antigen p53-inducible 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  23.9     0.028        15      51     149 ..     407     504 ..     399     514 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.028
                       TP53IP5  51 kilrissgenevlekvkqnneelqearalekkleskklestkepkelkskewkeeskvrnkakgspaavpkkeeqaeaevp 131
                                   +il+i   +++  +k k+++e+l++ + +e+k + k+ + + +pke+k+ e+k e++ ++++k++++ +pk ee +e+ + 
  gi|15669074|ref|NP_247879.1| 407 EILKILKEKKKLERKKKKEKEKLEKEKKKEEKAKEKQSNLIIQPKEIKE-EVKAEVEKKEEVKEKIVEKPKAEEVKEKSKT 486
                                   6999999999999**********************************77.8888888888888888888876655554444 PP

                       TP53IP5 132 ktsrgeglntkaqkkqla 149
                                     +++++ ++k++kk+  
  gi|15669074|ref|NP_247879.1| 487 EEKETKKDKKKGKKKKED 504
                                   444444444444444433 PP

>> DUF4604  Domain of unknown function (DUF4604)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  35.8     0.026        13      49     167 ..     394     509 ..     346     512 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.026
                       DUF4604  49 eaPqVVvlkeGkhlsaeevevekdaakgke.keeeeeeeeegeeaeediefkkpkkasi.keka..sslaaksskkkkkgk 125
                                   ++  V+v   G+ l a+e+ +  +++k+ e k+++e+e+ e+e+++e +++k+++++ i + k+  ++ +a+ +kk  +++
  gi|15669074|ref|NP_247879.1| 394 DELKVLV---GDKL-ASEILKILKEKKKLErKKKKEKEKLEKEKKKE-EKAKEKQSNLIiQPKEikEEVKAEVEKKEEVKE 469
                                   4445555...8889.88888888877777732222222222222222.222222222223333343333333333333333 PP

                       DUF4604 126 vvgeedeeeedkskakkkekekkkakkkkkkkkkkkkkkklL 167
                                    + e+ ++e  + k+k+k++ek+++k+kkk kkkk  k+k+L
  gi|15669074|ref|NP_247879.1| 470 KIVEKPKAE--EVKEKSKTEEKETKKDKKKGKKKKEDKGKQL 509
                                   333333233..3444444455555555555566666777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4122  (0.229907); expected 358.6 (0.02)
Passed bias filter:                     1078  (0.0601261); expected 358.6 (0.02)
Passed Vit filter:                       378  (0.0210832); expected 17.9 (0.001)
Passed Fwd filter:                        76  (0.00423894); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 1.17u 0.41s 00:00:01.57 Elapsed: 00:00:00.58
# Mc/sec: 2688.24
//
Query:       gi|15669075|ref|NP_247880.1|  [L=1634]
Description: DNA polymerase B1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-65  221.1   9.4    1.7e-42  145.7   4.5    3.5  3  DNA_pol_B        DNA polymerase family B
    6.4e-46  157.0  11.3    2.8e-45  154.9  11.3    2.2  1  DNA_pol_B_exo1   DNA polymerase family B, exonuclease domain
    1.9e-42  144.4   0.0    1.2e-31  109.4   0.0    5.1  6  Intein_splicing  Intein splicing domain
    1.1e-10   41.2   4.1    1.1e-10   41.2   4.1    2.8  2  PI-TkoII_IV      DNA polymerase II intein Domain IV
    1.2e-09   38.4   0.5    7.7e-09   35.7   0.5    2.5  1  RNase_H_2        RNase_H superfamily
    1.4e-08   34.9   0.6    1.4e-08   34.9   0.6    6.3  6  LAGLIDADG_3      LAGLIDADG-like domain
    2.1e-06   27.6   0.3    5.4e-06   26.2   0.3    1.7  1  DNA_pol_B_exo2   Predicted 3'-5' exonuclease related to the e
     0.0019   18.0   0.0     0.0084   15.9   0.0    2.1  1  Vint             Hint-domain
  ------ inclusion threshold ------
        0.3   11.0   1.4       0.83    9.6   0.0    2.6  3  Hom_end_hint     Hom_end-associated Hint
        9.3    6.3   7.7        9.2    6.3   0.3    3.7  4  RST              RCD1-SRO-TAF4 (RST) plant domain


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.6e-08   0.00012      13      66 ..     369     424 ..     361     426 .. 0.82
   2 !   54.9   0.1   3.2e-18   5.8e-15      64     166 ..     791     884 ..     778     885 .. 0.85
   3 !  145.7   4.5   9.4e-46   1.7e-42     164     458 ..    1358    1612 ..    1354    1613 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.6e-08
                                   HHHHHHHHHHHHHTTBE-B-----.--SS.....-S----BE----EEESS-EEEEEE CS
                     DNA_pol_B  13 irveslLlrlakeegfilpdrtekkgkeee....gYqGatVlePkkglydkpvlvlDF 66 
                                   + ve+lL++ a +e++i+p+++++++ + +    +Y+G+ V eP+kg++++  + +DF
  gi|15669075|ref|NP_247880.1| 369 QMVEYLLMKRAFKENMIVPNKPDEEEYR-RrvltTYEGGYVKEPEKGMFEDI-ISMDF 424
                                   5799***************988774444.347757**************985.56888 PP

  == domain 2  score: 54.9 bits;  conditional E-value: 3.2e-18
                                   EEETTHHHHHHHHTT-STTTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS- CS
                     DNA_pol_B  64 lDFaSLYPsiiqahNlcyttlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeek 144
                                   l  +SLYPsii+ +N+++ tl+++  +  ++++           + +  ++ +++egl+pk L++l+++R +ik+++k+  
  gi|15669075|ref|NP_247880.1| 791 LTHNSLYPSIIISYNISPDTLDCECCK--DVSE-----------KILGHWFCKKKEGLIPKTLRNLIERRINIKRRMKKMA 858
                                   668*******************98766..3344...........4466789999************************655 PP

                                   -H....HHHHHHHHHHHHHHHHHHHH CS
                     DNA_pol_B 145 de....fekalldkqQlalKvtaNsv 166
                                   +     +e  lld  Q+ lK++aNs+
  gi|15669075|ref|NP_247880.1| 859 EIgeinEEYNLLDYEQKSLKILANSI 884
                                   5433445899**************96 PP

  == domain 3  score: 145.7 bits;  conditional E-value: 9.4e-46
                                    HHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-.SS CS
                     DNA_pol_B  164 NsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkv.kd 241 
                                    NsvYG++ +   r+++ + A+ vT+ GR+ +++t +  ek                  ++kv Y DTD  +   k   +
  gi|15669075|ref|NP_247880.1| 1358 NSVYGYLAFPRARFYSRECAEIVTYLGRKYILETVKEAEKF-----------------GFKVLYIDTDGFYAIWKEkIS 1419
                                    **********************************9999977.................9************99988789 PP

                                    HHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEETTEEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHH CS
                     DNA_pol_B  242 veellkigkelaeevseklfkkplklefekvykkllLisKKkYaglkvektskanklliKGvdlvRrdncklvkevikk 320 
                                     eel+k + e+ e++++ +++  ++lefe  +k+ ++++KK+Ya +  +     +++ +KG++ vRrd+++++k + ++
  gi|15669075|ref|NP_247880.1| 1420 KEELIKKAMEFVEYINS-KLPGTMELEFEGYFKRGIFVTKKRYALIDEN-----GRVTVKGLEFVRRDWSNIAKITQRR 1492
                                    9****************.88888********************988877.....99*********************** PP

                                    HHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS--- CS
                     DNA_pol_B  321 vlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksknlphlevakrlkkrneeape 399 
                                    vle ll +     s+e++ +++++++    ++l+e+k++ e++++ ++l+k+p++yk+++ ph+e+ak+l+++ +++++
  gi|15669075|ref|NP_247880.1| 1493 VLEALLVE----GSIEKAKKIIQDVI----KDLREKKIKKEDLIIYTQLTKDPKEYKTTA-PHVEIAKKLMRE-GKRIK 1561
                                    ********....88887777777777....99*************************999.********9988.89*** PP

                                    TTCEEEEEEBETSS.....SS-GGGTEEEHHHHHHCCSEB-HHHHHH.TTHHHHHHHHTT CS
                     DNA_pol_B  400 vgdrisYvivekkkevkkknllaseraedpeyvleknlpidieyYls.qllkevarllea 458 
                                    vgd i Y+iv+ +k       ++sera+ pe v  +   id++yY++ q+l++v r++ea
  gi|15669075|ref|NP_247880.1| 1562 VGDIIGYIIVKGTK-------SISERAKLPEEVDID--DIDVNYYIDnQILPPVLRIMEA 1612
                                    ************76.......89*****99887665..58999**************986 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.9  11.3   1.6e-48   2.8e-45      10     337 .]      36     298 ..      32     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 154.9 bits;  conditional E-value: 1.6e-48
                                   EEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHHHHHHHHHH CS
                DNA_pol_B_exo1  10 vnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnelkkirkels 90 
                                    +  +fkpyfY+e  ++k ++e +e +ke+  + +  ++ ++++e v+kk ++  ek+   ++k+  ++p++++k+rk+++
  gi|15669075|ref|NP_247880.1|  36 LKDRDFKPYFYVELHKEKVENEDIEKIKEFLLKND-LLKFVENIE-VVKKIILRKEKE---VIKIIATHPQKVPKLRKIKE 111
                                   45689**********88888899999999884443.344456666.999999999999...******************96 PP

                                   HCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCEETTTCCS-EEEEEEEEEETEE CS
                DNA_pol_B_exo1  91 pleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddliakpkesepplrvlsFDIecksk 171
                                     e + ++ye+d+++  r+lidn i ++ + + +          ++++v+i++             p+l+  +FD+e++ +
  gi|15669075|ref|NP_247880.1| 112 -CEIVKEIYEHDIPFAKRYLIDNEIIPMTYWDFE----------NKKPVSIEI-------------PKLKSVAFDMEVYNR 168
                                   .778999***********************9999..........999999999.............9************** PP

                                   TTSEETTTT..--EEEEEEEECCTC.SS.SEEEEEEECCCTSS----EE--SSTCSTTEEEEEESSHHHHHHHHHHHHHHH CS
                DNA_pol_B_exo1 172 kgkfpdaensedpiiqIscvldglgekepearklftlrecaseeeedfeltpkpeypgvkvlefdsEkelLqaflefikqy 252
                                   +   p++e+  dpi + s++ ++ g       k++t++e++                 +++  +++Ekel+++++e++k+y
  gi|15669075|ref|NP_247880.1| 169 DT-EPNPER--DPILMASFWDENGG-------KVITYKEFN----------------HPNIEVVKNEKELIKKIIETLKEY 223
                                   *9.9*****..**************.......*********................246888****************** PP

                                   --SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTCEECCCCESEEEEEECEEEETTSEEEEHHHHHHHHSSSSG-S CS
                DNA_pol_B_exo1 253 dPdvitgYNidnFDlpYilnRakelykvklsklgrlnkggrskvseigfskqarekvkisgrihlDlyrvvkrklklpsYk 333
                                     dvi++YN+dnFD+pY+++Rak +y +++  lg+  +g + k+++ g         +i+gr+h+Dly++ +r lkl++Y+
  gi|15669075|ref|NP_247880.1| 224 --DVIYTYNGDNFDFPYLKARAK-IYGIDIN-LGK--DGEELKIKRGGME----YRSYIPGRVHIDLYPISRRLLKLTKYT 294
                                   ..*********************.8877743.354..7888999998888....8899*********************** PP

                                   HHHH CS
                DNA_pol_B_exo1 334 Lnav 337
                                   L+ v
  gi|15669075|ref|NP_247880.1| 295 LEDV 298
                                   *987 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   2.2       4.6   8.3e+03       9      52 ..      60     106 ..      47     123 .. 0.48
   2 ?   -2.1   0.0       1.9   3.5e+03      70      96 ..     205     232 ..     188     338 .. 0.81
   3 !   26.4   0.0     3e-09   5.5e-06      35     134 .]     458     794 ..     427     794 .. 0.93
   4 ?   -2.3   0.0       2.2   3.9e+03      10      38 ..     858     884 ..     850     912 .. 0.69
   5 !  109.4   0.0   6.9e-35   1.2e-31       7     134 .]     917    1358 ..     891    1358 .. 0.98
   6 ?    0.0   0.6      0.43   7.7e+02      31      91 ..    1507    1567 ..    1478    1602 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.6
                                   EEEHHHHCCECTTEEEEEETTTTEEEEEE....EEEEEEEEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx RF
               Intein_splicing   9 kvkieelvekegeevlslnledlklevks....vkkliklklkelyei 52 
                                   + ki+e++ k++  + + n+e +k +  +    v k+i ++ +++ ++
  gi|15669075|ref|NP_247880.1|  60 E-KIKEFLLKNDLLKFVENIEVVKKIILRkekeVIKIIATHPQKVPKL 106
                                   3.4444444444444433444333322222333555555555544444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                                   ECCT.TEEEEEECCC--TT-EEEEEHSC CS
                                   xxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  70 vvrd.egivEkradeLkegdliavpdad 96 
                                   vv++ ++++ k  ++Lke d+i + ++d
  gi|15669075|ref|NP_247880.1| 205 VVKNeKELIKKIIETLKEYDVIYTYNGD 232
                                   3445577777888888888888766544 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 3e-09
                                   EEEEEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEE..................... CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
               Intein_splicing  35 vksvkkliklklk.elyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdliavp..................... 93 
                                   +++vkk++k++++ el++++      +k+Tp+Hk+      +i   + ++++++d+++                       
  gi|15669075|ref|NP_247880.1| 458 WQKVKKVWKYEYEgELINVN-----GLKCTPNHKIPLR--YKI---KHKKINKNDYLVRDiyakslltkfkgegklilckd 528
                                   566*********99999888.....8*********988..566...99**********99********************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669075|ref|NP_247880.1| 529 fetignyekyindmdedfilkseligillaeghllrrdieyfdssrgkkrishqyrveitvnedekdfiekikyifkklfn 609
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669075|ref|NP_247880.1| 610 yelyvrrkkgtkaitlgcakkdiylkieeilknkekylpnailrgffegdgyvntvrravvvnqgtnnydkikfiaslldr 690
                                   ********************************************************************************* PP

                                   .............................................................HSCEEEEEEEE..EEEEECE CS
                                   .............................................................xxxxxxxxxxx..xxxxxxx RF
               Intein_splicing  94 .............................................................dadvvwdkvks..ievedee 111
                                                                                                 +d  + ++ +  +  e+++
  gi|15669075|ref|NP_247880.1| 691 lgikysfytysyeergkklkryvieifskgdlikfsilisfisrrknnllneiirqktlykIGDYGFYDLDDvcVSLESYK 771
                                   ************************************************************966666666665115667889 PP

                                   EEEEEEEETTT-EEEECTTEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing 112 eyVYdltvednhNFvangiivHN 134
                                   ++VYdlt e+   ++angi+ HN
  gi|15669075|ref|NP_247880.1| 772 GEVYDLTLEGRPYYFANGILTHN 794
                                   **********************9 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 2.2
                                   EEHHHHCCECTTEEEEEETTTTEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  10 vkieelvekegeevlslnledlklevksv 38 
                                    +i+e+  +e+++ l ++ ++lk+ ++s+
  gi|15669075|ref|NP_247880.1| 858 AEIGEI--NEEYNLLDYEQKSLKILANSI 884
                                   355555..778888888888888877774 PP

  == domain 5  score: 109.4 bits;  conditional E-value: 6.9e-35
                                    CEE.EEHHHHCCECTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC CS
                                    xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing    7 eek.vkieelvekegeevlslnledlklevksvkkliklklk.elyeiklesgrkikaTpeHkllvvrdegivEkrade 83  
                                    ++k   i+e++e+++ +  s +  + k e k+vk+li++ +  + y+ikl+sgr+ik+T++H+l+ +++++ivE+++d+
  gi|15669075|ref|NP_247880.1|  917 KIKfSGISEILETKNLKTFSFDKITKKCEIKKVKALIRHPYFgKAYKIKLRSGRTIKVTRGHSLFKYENGKIVEVKGDD 995 
                                    444456888888*****************************99************************99********** PP

                                    --TT-EEEEE..................................................................... CS
                                    xxxxxxxxxx..................................................................... RF
               Intein_splicing   84 Lkegdliavp..................................................................... 93  
                                    ++ gdli+vp                                                                     
  gi|15669075|ref|NP_247880.1|  996 VRFGDLIVVPkkltcvdkevvinipkrlinadeeeikdlvitkhkdkaffvklkktlediennklkvifddcilylkel 1074
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669075|ref|NP_247880.1| 1075 glidyniikkinkvdikildeekfkaykkyfdtviehgnfkkgrcniqyikikdyianipdkefedceigaysgkinal 1153
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669075|ref|NP_247880.1| 1154 lkldeklakflgffvtrgrlkkqklkgetvyeisvykslpeyqkeiaetfkevfgagsmvkdkvtmdnkivylvlkyif 1232
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669075|ref|NP_247880.1| 1233 kcgdkdkkhipeelflasesviksfldgflkakknshkgtstfmakdekylnqlmilfnlvgiptrftpvknkgykltl 1311
                                    ******************************************************************************* PP

                                    ......HSCEEEEEEEEEEEEECEEEEEEEEETTT-EEEECTTEEE- CS
                                    ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing   94 ......dadvvwdkvksievedeeeyVYdltvednhNFvangiivHN 134 
                                           +d+++d+vk+ie  ++ +yVYdl+vedn+NF++n+i +HN
  gi|15669075|ref|NP_247880.1| 1312 npkygtVKDLMLDEVKEIEAFEYSGYVYDLSVEDNENFLVNNIYAHN 1358
                                    ******9***************************************9 PP

  == domain 6  score: 0.0 bits;  conditional E-value: 0.43
                                    TEEEEEEEEEEEEEEEE....EEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEE CS
                                    xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing   31 lklevksvkkliklklk....elyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdlia 91  
                                     k++++ +k l ++k+k     +y+  ++  ++ k+T+ H  ++    +++ ++++ +k+gd+i 
  gi|15669075|ref|NP_247880.1| 1507 KKIIQDVIKDLREKKIKkedlIIYTQLTKDPKEYKTTAPHVEIAK---KLM-REGKRIKVGDIIG 1567
                                    444555577777777777666677777899999999999987776...553.8999999999986 PP

>> PI-TkoII_IV  DNA polymerase II intein Domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   4.1     6e-14   1.1e-10       1     142 [.    1006    1148 ..    1006    1154 .. 0.82
   2 ?   -2.8   0.1       2.1   3.8e+03      85     120 ..    1498    1533 ..    1466    1552 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 6e-14
                                    S---------EEEHHHHHHTS-GGGCTTEEEEEESTT-TTHHHHHHHHHHHHTTSS---TTHHHHHHHHHHCTSE.... CS
                   PI-TkoII_IV    1 krlklpereevlnlvelllklpeeetadivltipvkGrknffkGmlrtlrwifgeekrirtarrylkhleklGyv.... 75  
                                    k+l   ++e v+n+++ l++  eee +d+v+t   +  k ff  + +tl  i +++     ++  + +l++lG++    
  gi|15669075|ref|NP_247880.1| 1006 KKLTCVDKEVVINIPKRLINADEEEIKDLVIT--KHKDKAFFVKLKKTLEDIENNK-LKVIFDDCILYLKELGLIdyni 1081
                                    57778899********************9987..566799**********996555.4456666666777777653333 PP

                                    ..EE-SSSEEES-HHHHHHHHHHHHHHHHH-EEETTTTEEEEEGGGGCCCHCCS-HHHHTT-EEEETTS CS
                   PI-TkoII_IV   76 ..klkkrGyevldweglkkykklyeklvekvkynGnkreylvefndlrdviellpeeelkewkiGtlnG 142 
                                      k++k+ +++ld+e +k ykk +++++e+ ++   k+   +++ +++d i  +p +e+++  iG   G
  gi|15669075|ref|NP_247880.1| 1082 ikKINKVDIKILDEEKFKAYKKYFDTVIEHGNF--KKGRCNIQYIKIKDYIANIPDKEFEDCEIGAYSG 1148
                                    445677889********************8765..5777889***********************9988 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.1
                                    S-HHHHHHHHHHHHHHHHH-EEETTTTEEEEEGGGG CS
                   PI-TkoII_IV   85 ldweglkkykklyeklvekvkynGnkreylvefndl 120 
                                    l + +++k kk+ + ++++++    k+e l+ + +l
  gi|15669075|ref|NP_247880.1| 1498 LVEGSIEKAKKIIQDVIKDLREKKIKKEDLIIYTQL 1533
                                    345567888888888888888888888888877766 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.5   4.3e-12   7.7e-09       4     133 ..     169     320 ..     159     342 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 4.3e-12
                     RNase_H_2   4 DiEttGlspkknliyliGvldvdekeiekltqllaeepeeekailelf...lellekkkalvtfngksFDvpflkrlfkky 81 
                                   D+E +   p+++ i + +++d ++ ++++++++++++ e  k+ +el+    e+l++++ ++t+ng +FD+p+lk ++k y
  gi|15669075|ref|NP_247880.1| 169 DTEPN---PERDPILMASFWDENGGKVITYKEFNHPNIEVVKNEKELIkkiIETLKEYDVIYTYNGDNFDFPYLKARAKIY 246
                                   44444...89999***********999999999998865444433333333699************************778 PP

                     RNase_H_2  82 klde......................eefrhiDLlkelrk.kklesysLksveke.lgierreedlsGsqavklyq 133
                                    +d                       + + hiDL+ + r+  kl+ y L++v    +gie    +++  ++v ++ 
  gi|15669075|ref|NP_247880.1| 247 GIDInlgkdgeelkikrggmeyrsyiPGRVHIDLYPISRRlLKLTKYTLEDVVYNlFGIEKL--KIPHTKIVDYWA 320
                                   88877888999999999999988888888*******99885666999**9987764666655..677777777775 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.77   1.4e+03      22      52 ..     198     228 ..     189     241 .. 0.80
   2 ?    3.5   0.5     0.051        91      19      64 ..     579     623 ..     568     643 .. 0.72
   3 !   34.9   0.6   7.8e-12   1.4e-08       4      78 ..     649     725 ..     647     729 .. 0.87
   4 ?   -1.5   0.5       1.8   3.2e+03      41      82 ..     841     884 ..     836     884 .. 0.85
   5 ?    0.6   0.1       0.4   7.2e+02       3      66 ..    1159    1230 ..    1157    1259 .. 0.78
   6 ?    2.7   0.1     0.085   1.5e+02      20      62 ..    1265    1308 ..    1252    1350 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.77
                                   TTTTSEEEEES-HHHHHHHHHHHHHCT.HSC CS
                   LAGLIDADG_3  22 kkgvsisltssskelledvqrlLlrlGIest 52 
                                    ++++i++  ++kel++++ + L++  ++ t
  gi|15669075|ref|NP_247880.1| 198 FNHPNIEVVKNEKELIKKIIETLKEYDVIYT 228
                                   344559*****************99998876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.051
                                   ECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCC CS
                   LAGLIDADG_3  19 kskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgv 64 
                                    s +++v+i++   +k+++e+++++ ++l  +  +y ++k++ + +
  gi|15669075|ref|NP_247880.1| 579 ISHQYRVEITVNEDEKDFIEKIKYIFKKL-FNYELYVRRKKGTKAI 623
                                   444555668888889************98.8888888866666554 PP

  == domain 3  score: 34.9 bits;  conditional E-value: 7.8e-12
                                   HHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEE...EEE-SCCCCECCCHCHCTTCGG CS
                   LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyek...kkakgrgvyrlliisgenlkrF 78 
                                    a LrG+f++DG+v++ ++  v ++ ++++++ ++ ++ lL rlGI+ + y+     ++k+   y + i s+ +l +F
  gi|15669075|ref|NP_247880.1| 649 NAILRGFFEGDGYVNTVRRAVV-VNQGTNNYDKIKFIASLLDRLGIKYSFYTYsyeERGKKLKRYVIEIFSKGDLIKF 725
                                   689***************8766.*******************************766666666678888888888888 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.8
                                   HHHHH.HCT.HSCEEEE.EEE-SCCCCECCCHCHCTTCGGGTTT CS
                   LAGLIDADG_3  41 qrlLl.rlGIestiyek.kkakgrgvyrlliisgenlkrFleki 82 
                                   ++l + r++I+ + ++   +++ +  y ll + +++lk +++ i
  gi|15669075|ref|NP_247880.1| 841 RNLIErRINIKRRMKKMaEIGEINEEYNLLDYEQKSLKILANSI 884
                                   55666689999999999999999999*********999988766 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.4
                                    HHHHHHHHHHHCCECCECSTTTTS...EEEEES-HHHHHHHHHHHH.HCT.HSCEEEEEEE-SCCCC....E CS
                   LAGLIDADG_3    3 kaafLrGlfdaDGsvskskkkgvs...isltssskelledvqrlLl.rlGIestiyekkkakgrgvy....r 66  
                                    k+a   G+f + G   k+k kg     is++ s  e+ +++++  +  +G  s+++ k   +++ vy    +
  gi|15669075|ref|NP_247880.1| 1159 KLAKFLGFFVTRGRLKKQKLKGETvyeISVYKSLPEYQKEIAETFKeVFGAGSMVKDKVTMDNKIVYlvlkY 1230
                                    667777999999998888877777779999999999999999999988999999999988889988844442 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.085
                                    CSTTTTS.EEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SC CS
                   LAGLIDADG_3   20 skkkgvs.isltssskelledvqrlLlrlGIestiyekkkakgr 62  
                                    +k+ +++  ++  +++++l++++ l +  GI ++ +  k+++ +
  gi|15669075|ref|NP_247880.1| 1265 KKNSHKGtSTFMAKDEKYLNQLMILFNLVGIPTRFTPVKNKGYK 1308
                                    34333334888999*******************99998555544 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.3     3e-09   5.4e-06      34     168 ..     206     339 ..     179     357 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3e-09
                DNA_pol_B_exo2  34 essekelikkffegvekkkpqlVsfngrgfDlpvleyralkhgvsapkyfdegdedrekkwnnylsrystr.hlDLmdlls 113
                                    ++ekelikk +e+++++   + ++ng +fD+p l+ ra ++g+ ++   d ++ + +    +y+s    r h+DL+ +  
  gi|15669075|ref|NP_247880.1| 206 VKNEKELIKKIIETLKEYD-VIYTYNGDNFDFPYLKARAKIYGIDINLGKDGEELKIKRGGMEYRSYIPGRvHIDLYPISR 285
                                   357***************9.899**********************986666555443433447888888888****99988 PP

                DNA_pol_B_exo2 114 eygaranakLdela.kllglPGKlgvdGskVaelyqegklkeireYcetDvlnTYl 168
                                   +  + ++  L+++  +l+g+  Kl +   k+++++++++  ++ eY   D+  TY 
  gi|15669075|ref|NP_247880.1| 286 RLLKLTKYTLEDVVyNLFGI-EKLKIPHTKIVDYWANNDK-TLIEYSLQDAKYTYK 339
                                   88888888898775144454.5999999999999988775.555799888888885 PP

>> Vint  Hint-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.7e-06    0.0084       2      65 ..     426     488 ..     425     503 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.7e-06
                          Vint   2 CfagesrvklaegktvkiselrkgmkvqtpkgarkvaavlktkveeeelcrlgellvTpwHPvr 65 
                                   C    ++v ++ + +v+i+++++g  v   +g +kv+ v k + e  el+++++l  Tp H + 
  gi|15669075|ref|NP_247880.1| 426 CHPKGTKVVVKGKGIVNIEDVKEGNYVLGIDGWQKVKKVWKYEYEG-ELINVNGLKCTPNHKIP 488
                                   788889************************************9986.699***********664 PP

>> Hom_end_hint  Hom_end-associated Hint
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       2.3   4.1e+03      87     126 ..      82     121 ..      47     170 .. 0.58
   2 ?    9.6   0.0   0.00046      0.83       1      34 [.     426     459 ..     426     515 .. 0.91
   3 ?   -2.4   0.0       2.1   3.8e+03     182     209 ..    1386    1413 ..    1149    1427 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.3
                                   EEEESTEEEEEEEEEEEEEEE-TTS-EEEEEEEEEEEEE. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hom_end_hint  87 erklrgkkytsVtyfalekektedgrvieivkevtksfeh 126
                                   ++ +  k+ + ++  a++ +k+ + r+i+ ++ v++ +eh
  gi|15669075|ref|NP_247880.1|  82 KKIILRKEKEVIKIIATHPQKVPKLRKIKECEIVKEIYEH 121
                                   4444444444444444444444444444444444444444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00046
                                   CEETT-EEEBTTS-EEEGGG--TT-EEEBTTSSE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hom_end_hint   1 cFakgTevlmadGsdksiedievgekvmGkdGkp 34 
                                   c  kgT+v++    + +ied++ g++v+G dG  
  gi|15669075|ref|NP_247880.1| 426 CHPKGTKVVVKGKGIVNIEDVKEGNYVLGIDGWQ 459
                                   889********99*******************64 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.1
                                    -HHHHHHH--EEE-EEEEEEEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hom_end_hint  182 eklaevleeavpfkFelekkeedeyyGi 209 
                                    + + e+++ea +f F++   ++d +y i
  gi|15669075|ref|NP_247880.1| 1386 KYILETVKEAEKFGFKVLYIDTDGFYAI 1413
                                    2333444488888888888888888876 PP

>> RST  RCD1-SRO-TAF4 (RST) plant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.2   5.7e+03       6      18 ..     722     734 ..     719     737 .. 0.86
   2 ?   -3.2   0.2       4.6   8.3e+03      33      52 ..     933     952 ..     929     953 .. 0.80
   3 ?    2.4   0.0     0.084   1.5e+02      37      49 ..    1415    1427 ..    1408    1431 .. 0.82
   4 ?    6.3   0.3    0.0051       9.2      24      46 ..    1506    1528 ..    1498    1531 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.2
                           RST   6 wvpFpmLlaalsk 18 
                                    ++F+ L++ +s+
  gi|15669075|ref|NP_247880.1| 722 LIKFSILISFISR 734
                                   689*******997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.6
                           RST  33 edlkkkkIsreefvrklRsi 52 
                                   + +   kI+++  ++k++ +
  gi|15669075|ref|NP_247880.1| 933 KTFSFDKITKKCEIKKVKAL 952
                                   678889*****999999865 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.084
                           RST   37 kkkIsreefvrkl 49  
                                    k+kIs+ee+++k 
  gi|15669075|ref|NP_247880.1| 1415 KEKISKEELIKKA 1427
                                    78*********85 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0051
                           RST   24 kmdllqkhYedlkkkkIsreefv 46  
                                      +++q   +dl++kkI++e+++
  gi|15669075|ref|NP_247880.1| 1506 AKKIIQDVIKDLREKKIKKEDLI 1528
                                    567899999************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1250  (0.0697194); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 1.09u 0.31s 00:00:01.40 Elapsed: 00:00:00.52
# Mc/sec: 9465.05
//
Query:       gi|15669076|ref|NP_247881.1|  [L=620]
Description: putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-60  201.9   0.0    9.6e-60  201.0   0.0    1.4  1  PBP_like       PBP superfamily domain
    1.5e-46  158.0   0.1    2.3e-46  157.4   0.1    1.3  1  MoeA_N         MoeA N-terminal region (domain I and II)
    2.8e-27   95.1   0.0    5.4e-27   94.2   0.0    1.4  1  MoCF_biosynth  Probable molybdopterin binding domain
    1.5e-17   63.5   0.0    3.8e-17   62.2   0.0    1.8  1  MoeA_C         MoeA C-terminal region (domain IV)
  ------ inclusion threshold ------
      0.045   13.3   0.0      0.072   12.6   0.0    1.3  1  OpuAC          Substrate binding domain of ABC-type glycine b
      0.087   11.9   0.1       0.38    9.8   0.0    1.9  2  T2SSE          Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.0   0.0   3.2e-63   9.6e-60      10     193 .]     420     601 ..     416     601 .. 0.96

  Alignments for each domain:
  == domain 1  score: 201.0 bits;  conditional E-value: 3.2e-63
                                   TCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BGGGC- CS
                      PBP_like  10 gvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkkitnwkdla 90 
                                   ++ ++++nvGs+gG+ ++++geadiag+hlld++t++yn+p+l+k+ ++ ++vlv++++reqg++++k+  ++ ++++++ 
  gi|15669076|ref|NP_247881.1| 420 KLLAKTINVGSLGGVLSIKRGEADIAGIHLLDEKTNTYNIPFLEKYKVK-DAVLVRGYIREQGFMFRKE--LGFKSIEEII 497
                                   566899****************************************999.69*****************..99*******5 PP

                                   S..-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCCETTCCECCCGG-HCCCCCCECTTCE-E CS
                      PBP_like  91 d..aplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVaagradvgvgieavaeelkgldfvplaee 169
                                   +   +l ++nR++GSGtr+lfd+ lk+ +i++++ikgy+ ea++h+ava+a+a  +ad+g+gi++vae+ ++l f+pla e
  gi|15669076|ref|NP_247881.1| 498 EhiYKLEFINRNKGSGTRILFDKFLKDYNINPKEIKGYNIEAKTHSAVATAIAMKKADIGLGIRTVAEQ-YNLAFIPLANE 577
                                   5459***************************************************************98.7********** PP

                                   EEEEEEECTCCCSHHHHHHHHHHC CS
                      PBP_like 170 rydlvvrkealddpevqafleflk 193
                                   +yd+++rke+++d+ vq f+++lk
  gi|15669076|ref|NP_247881.1| 578 HYDFLIRKERFNDEDVQNFIKALK 601
                                   *********************985 PP

>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.4   0.1   7.8e-50   2.3e-46       2     157 .]       9     174 ..       8     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 157.4 bits;  conditional E-value: 7.8e-50
                                   -HHHHHHHHHHH-.HH..-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--............... CS
                        MoeA_N   2 sveealaiilaal.el..eeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........sa 70 
                                   s+eea +ii ++l +l  e  e v+l  +a+grvlaedv +++d+Pp+d++ mDGYAv+ae++ +a+e++p         +
  gi|15669076|ref|NP_247881.1|   9 SIEEAKSIINESLkKLknEV-EeVDL-FNAIGRVLAEDVFSNIDIPPYDRAKMDGYAVKAEDTYEADEDNPvelkvigsLK 87 
                                   799**********7778544.45***.99**************************************************88 PP

                                   ....-S---TT-.EEEE-TTSB--TT--EEEEGGGE..E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB--CC CS
                        MoeA_N  71 ageeperllpgg.avrimTGaplPegadaVvpvEdte.eeeaketvev.kavkpgenvrraGedikaGevllragtrltpa 148
                                   age ++ ++++g +v+i+TGa +P+ga+aVv+vE+te +   ++ v++ +av p en++  G+di aGe++lr++t+ltp+
  gi|15669076|ref|NP_247881.1|  88 AGEIKDLEINNGeCVEIATGAIIPKGANAVVMVEYTErD--NDR-VKIyRAVPPMENIQFTGSDIMAGELVLRKNTKLTPR 165
                                   8999999988888***********************632..233.444699****************************** PP

                                   CHHHHHHCT CS
                        MoeA_N 149 eigllasvG 157
                                   +ig+la++G
  gi|15669076|ref|NP_247881.1| 166 DIGVLAAIG 174
                                   *******98 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.2   0.0   1.8e-30   5.4e-27       1     138 [.     187     318 ..     187     323 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 1.8e-30
                                   EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--H CS
                 MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvt 74 
                                   ++i++G+e++        gki+D n+++l++++k lg++ +  ++ +Dd+ee+ke++++a  + d+i+++GGt+++  D+t
  gi|15669076|ref|NP_247881.1| 187 GIISTGNEIIspneqleFGKIYDINSYTLVSYIKTLGYDFEFFGIAKDDKEELKEKIKKA-LKCDIILLSGGTSAGVGDLT 266
                                   69**************99***************************************888.677***************** PP

                                   HHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHH CS
                 MoCF_biosynth  75 pealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeil 138
                                     a+++l++k      +++++++ kpgkp++++++   ++   k i+gLPG+p ++ ++++++ 
  gi|15669076|ref|NP_247881.1| 267 ETAIKELGGK------ILVHGIKIKPGKPTIIGKI---DN---KLIVGLPGYPTSCLTIFDVLF 318
                                   *********9......***************9999...54...4799*************9875 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0   1.3e-20   3.8e-17       1      72 []     326     395 ..     326     395 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.3e-20
                                   EEEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                        MoeA_C   1 karlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                   ka+   ++ s++gr e+l+vil ++++++ a+p+ ++gSg+++sl+eA+g+i+i+e++e + + e+Vev+l+
  gi|15669076|ref|NP_247881.1| 326 KAKFPVRYISAKGRVEYLPVILVKHKNGFSAYPI-TKGSGAITSLSEADGYIIIDENKE-ILENEDVEVHLF 395
                                   6889999****************99999******.************************.99*******986 PP

>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.4e-05     0.072      73     179 ..     464     562 ..     412     582 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                                   HHEEEEEE.EESEEECEEEEEEHHHHHHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHHHHHHHHHT-TTCEEEG CS
                         OpuAC  73 kkglevlg.plgagnteglavpkyvaekygiksisDLkkpaedlelgakgeflgrpdgwgcekvtegllkaYgldkvelve 152
                                   k++++ +    g+   +g++ +k++    g ksi+++  +        k ef++r+ g+g++ + +++lk+Y++ + ++++
  gi|15669076|ref|NP_247881.1| 464 KYKVKDAVlVRGYIREQGFMFRKEL----GFKSIEEIIEH------IYKLEFINRNKGSGTRILFDKFLKDYNI-NPKEIK 533
                                   4433322225556667788888777....99999999444......569*************************.455553 PP

                                   SCEEEEHH..HHHHHHHTTCSSEEEEETT CS
                         OpuAC 153 gseaamda..elyaaykrgepvvvyawtP 179
                                   g      +  ++++a++ ++++++ +  +
  gi|15669076|ref|NP_247881.1| 534 GYNIEAKThsAVATAIAMKKADIGLGIRT 562
                                   33222222469999999999998877665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00013      0.38     108     153 ..     229     273 ..     217     279 .. 0.84
   2 ?   -1.5   0.0      0.34     1e+03      54     108 ..     537     596 ..     530     604 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00013
                         T2SSE 108 lgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkei 153
                                   +g+++++ke+++e ++ka  +  +il+sGgT+ G   l+ +++ke+
  gi|15669076|ref|NP_247881.1| 229 FGIAKDDKEELKEKIKKA-LKCDIILLSGGTSAGVGDLTETAIKEL 273
                                   677888999999999999.66789**********999999988887 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.34
                         T2SSE  54 iaalakldiseerplqdarlp....ekgvrlrvvllPvvag.ealviRkksakeltlddl 108
                                   i a +++ +++   +  a +     + +++ +++++P++++   + iRk++ ++ +++++
  gi|15669076|ref|NP_247881.1| 537 IEAKTHSAVATAIAMKKADIGlgirTVAEQYNLAFIPLANEhYDFLIRKERFNDEDVQNF 596
                                   666666666666677777766666677888999999999998889999887777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (620 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 3639.03
//
Query:       gi|15669077|ref|NP_247882.1|  [L=224]
Description: hypothetical protein MJ_0887 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   3.8e-110  366.2   4.4   4.2e-110  366.0   4.4    1.0  1  CofC          Guanylyl transferase CofC like
    6.3e-08   33.1   0.0      1e-07   32.4   0.0    1.3  2  NTP_transf_3  MobA-like NTP transferase domain
    4.7e-06   26.4   0.0    7.9e-06   25.7   0.0    1.4  1  DUF2064       Uncharacterized protein conserved in bacteria (
  ------ inclusion threshold ------
       0.02   15.4   0.2      0.093   13.2   0.2    1.9  2  YflT          Heat induced stress protein YflT
       0.12   12.4   2.5        1.7    8.7   0.2    2.2  2  PHD_like      Antitoxin of toxin-antitoxin, RelE / RelB, TA s
       0.19   11.9   3.8        2.5    8.3   0.4    3.1  4  Imm40         Immunity protein 40


Domain annotation for each model (and alignments):
>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.0   4.4  1.4e-113  4.2e-110       1     217 []       7     224 .]       7     224 .] 1.00

  Alignments for each domain:
  == domain 1  score: 366.0 bits;  conditional E-value: 1.4e-113
                          CofC   1 mkviiPvsainsaktrlseilseeerkellkamlldvidalkrldvlvvsedeevleyaldelgvevvkekekdlntavek 81 
                                   mkviiPvs+ins+ktrlse+ls+eerk+ll++ml+d+i+al++ld+++vs+dee+l++a++el++e++kek+k+ln+a+++
  gi|15669077|ref|NP_247882.1|   7 MKVIIPVSPINSLKTRLSEFLSGEERKNLLLNMLKDIIKALDGLDIVIVSRDEEILDFAKNELKAETIKEKYKGLNNAIKQ 87 
                                   89******************************************************************************* PP

                          CofC  82 afeeieekeviiipsdiPlikkedvkdllelekradvviaPargGGtnllllr.ksalevkyedfsflkhleearkrglkv 161
                                   afeeie+keviiip+diPlikk++++d+l+l+k++d++iaP+rgGGtnll+l+ k+++e+kye+fsflkhleea+kr+l++
  gi|15669077|ref|NP_247882.1|  88 AFEEIEDKEVIIIPADIPLIKKKHIEDILKLSKNYDLIIAPSRGGGTNLLYLKsKDLIEIKYEGFSFLKHLEEAKKRNLRY 168
                                   ********************************************************************************* PP

                          CofC 162 kiydsfylsvdinteedlgeillhGegtkakeylrklgfsvepeessalrlevkrr 217
                                   +iydsf++svdint+edlgei++hG++t++k+yl++lg++vep++ssa+r++vkrr
  gi|15669077|ref|NP_247882.1| 169 YIYDSFLISVDINTPEDLGEIFIHGNDTYTKNYLKSLGIDVEPKHSSAGRFVVKRR 224
                                   *****************************************************996 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   3.5e-11     1e-07      26     138 ..      39     144 ..      26     171 .. 0.77
   2 ?   -3.9   0.0       5.4   1.6e+04      40      62 ..     187     209 ..     180     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 3.5e-11
                                   HHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHH CS
                  NTP_transf_3  26 llervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltpelver 106
                                   +l+ +++al  +   ++v+v +dee+l+ +a+ +++  + ++++kg   +++ a +++ +++ v+++++D+Pl++++++e 
  gi|15669077|ref|NP_247882.1|  39 MLKDIIKALDGL---DIVIVSRDEEILD-FAKNELKAETIKEKYKGLNNAIKQAFEEI-EDKEVIIIPADIPLIKKKHIED 114
                                   677777777777...8**********97.555555555555569**************.8********************* PP

                                   HHHCHHHHTSSEEEEESSSEEEECCEEEGGGH CS
                  NTP_transf_3 107 llaaaaasgadvvvptyegerghpllfrarll 138
                                   +l+  +  ++d +++ ++g+  + l+++++ l
  gi|15669077|ref|NP_247882.1| 115 ILKLSK--NYDLIIAPSRGGGTNLLYLKSKDL 144
                                   ***965..777777777777767776644443 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.4
                                   CEEEEECSHCHHHHHHTTCTS-E CS
                  NTP_transf_3  40 devvvvggdeevlaalarlgvrv 62 
                                   +e+++ g+d   +++l++lg++v
  gi|15669077|ref|NP_247882.1| 187 GEIFIHGNDTYTKNYLKSLGIDV 209
                                   68888999988888888888765 PP

>> DUF2064  Uncharacterized protein conserved in bacteria (DUF2064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   2.6e-09   7.9e-06      42     107 ..      78     140 ..      39     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.6e-09
                                   SSSHHHHHHHHHHHHHHTT-S.EEEEE-SS-TT--HHHHHHHHHHTTT-SEEEEEBTTSSEEEEEEE CS
                       DUF2064  42 ggdlgeRlarafdrafeagee.pvlliGsDcpqltaalleqAfeaLeeadaVlgpaeDGGYyllGlk 107
                                    + l + +++af+++    e+ +v++i +D+p ++++++e+ ++  +++d+++ p+  GG  ll lk
  gi|15669077|ref|NP_247882.1|  78 YKGLNNAIKQAFEEI----EDkEVIIIPADIPLIKKKHIEDILKLSKNYDLIIAPSRGGGTNLLYLK 140
                                   555555555555555....666**************************************9998777 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   3.1e-05     0.093      26      70 ..      51      95 ..      44      98 .. 0.90
   2 ?   -1.2   0.0      0.97   2.9e+03      59      81 ..     185     208 ..     180     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                          YflT 26 diyvvakdkdrlerlaentdaetettseeglwdsiknlfrskgde 70
                                  di++v+ d++ l+  +++ +aet++++++gl ++ik++f+  +d+
  gi|15669077|ref|NP_247882.1| 51 DIVIVSRDEEILDFAKNELKAETIKEKYKGLNNAIKQAFEEIEDK 95
                                  9*********999999***********************986664 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.97
                          YflT  59 siknlfrskgdelre.kleslGlt 81 
                                   ++ ++f +++d +++  l+slG+ 
  gi|15669077|ref|NP_247882.1| 185 DLGEIFIHGNDTYTKnYLKSLGID 208
                                   677889998888885589999986 PP

>> PHD_like  Antitoxin of toxin-antitoxin, RelE / RelB, TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.016        48       5      57 ..      69     124 ..      66     140 .. 0.59
   2 ?    8.7   0.2   0.00057       1.7      43     108 ..     141     205 ..     124     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.016
                                   EEHHHHHHTHHHH...HHHHHHT.--EEEEETT...EEEEEEEHHHHHHHT.....TT- CS
                      PHD_like   5 lsitearkefsal...idqvvkeykpvlvkrnrkk.ekvsiistdllkell..drgykl 57 
                                   l++  ++++++ l   i+q+++e +++ v        ++ +i+ ++++++l   ++y+l
  gi|15669077|ref|NP_247882.1|  69 LKAETIKEKYKGLnnaIKQAFEEIEDKEVII---IpADIPLIKKKHIEDILklSKNYDL 124
                                   5556666666555111556665543322222...247899**********944445544 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00057
                                   EHHHHHHHT...TT--EEEEEEEETTEEEEEECCGTEEEEESSHHHHHHHHHHHHHHHHHHHHHTH CS
                      PHD_like  43 stdllkelldrgyklepeieeekdgevytltldelevyvegstkeeaaedLvedlldYaqdYlnrl 108
                                   s dl++    +g+++  + ee k  ++     d + + v+ +t e+  e +++    Y+++Yl+ l
  gi|15669077|ref|NP_247882.1| 141 SKDLIEIK-YEGFSFLKHLEEAKKRNLRYYIYDSFLISVDINTPEDLGEIFIHGNDTYTKNYLKSL 205
                                   44555544.499**********9999988999*******************************975 PP

>> Imm40  Immunity protein 40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.2   6.6e+03      18      35 ..      41      58 ..      37      69 .. 0.76
   2 ?    8.3   0.4   0.00083       2.5      14      45 ..      82     113 ..      68     122 .. 0.86
   3 ?    3.0   0.0     0.036   1.1e+02      36      60 ..     137     161 ..     124     173 .. 0.80
   4 ?   -1.2   0.0      0.76   2.3e+03      60      77 ..     186     203 ..     169     211 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.2
                         Imm40 18 keiiviledlkigilGGd 35
                                  k+ii+ l+ l i i+  d
  gi|15669077|ref|NP_247882.1| 41 KDIIKALDGLDIVIVSRD 58
                                  778888888888887655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00083
                         Imm40  14 kddikeiiviledlkigilGGdvykielenik 45 
                                   ++ ik++++++ed+++ i+  d+ +i++  i+
  gi|15669077|ref|NP_247882.1|  82 NNAIKQAFEEIEDKEVIIIPADIPLIKKKHIE 113
                                   6789*******************999988886 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.036
                         Imm40  36 vykielenikisyeswsinkdpges 60 
                                   +y+++++ i+i ye +s+ k+  e+
  gi|15669077|ref|NP_247882.1| 137 LYLKSKDLIEIKYEGFSFLKHLEEA 161
                                   699*************998885544 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.76
                         Imm40  60 sleeyvrksklralryie 77 
                                     e +++    ++++y++
  gi|15669077|ref|NP_247882.1| 186 LGEIFIHGNDTYTKNYLK 203
                                   445566666777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1397.54
//
Query:       gi|15669078|ref|NP_247883.1|  [L=206]
Description: hypothetical protein MJ_0888 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-27   95.7   0.0    3.9e-27   95.5   0.0    1.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    3.3e-06   26.8   0.0      4e-06   26.5   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00017   21.5   0.0    0.00024   21.0   0.0    1.2  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0054   16.2   0.0     0.0083   15.6   0.0    1.2  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.0   8.8e-31   3.9e-27       4     197 .]      10     190 ..       7     190 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 8.8e-31
                                   CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHC CS
                   Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfm 84 
                                    ++nsyli  ++++iLiD+Gts+ ++ +++   +++ ++kd+d +i+TH H+DH+++   + e +++p++++ +e ++l++
  gi|15669078|ref|NP_247883.1|  10 YSSNSYLI-IGKKNILIDPGTSGTFNILME--ELERNGIKDIDLIINTHCHFDHTSADYLIEEYFNCPTIIEDKEVKHLKN 87 
                                   679*****.9*******************5..99999******************************************** PP

                                   HHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TT CS
                   Lactamase_B  85 eeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridltlr 165
                                     + + +s +      + + +p   + +l +++ + ++++   + ++gh+ g++++  ++ l+tGD+++a   gr+dl   
  gi|15669078|ref|NP_247883.1|  88 GDEVTVSSLF------GAKLNPPKEIIPLSEIEEELKSYGLEIIRTPGHTYGSISIIYENSLITGDTIFAYGVGRWDL--- 159
                                   ********97......6799999*******************************************************... PP

                                   CEEE-SHCHHHHHHHHHHHHH.HHCHSEEEESS CS
                   Lactamase_B 166 gaevrdpsdaekyldsllkla.glkaevlvpgH 197
                                     +++d  + +++++ l+++a + ++++l+pgH
  gi|15669078|ref|NP_247883.1| 160 --PTGDVIQLRNSINLLERIAnERNIDKLYPGH 190
                                   ..5555555555555555555146677788888 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0     9e-10     4e-06       2      52 ..      22      68 ..      21     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 9e-10
                                  EEEES--TT....HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC CS
                 Lactamase_B_2  2 riLiDagpd....lrqqalralqPvelrdelppidaVllthaHyDHlaglltlre 52
                                  +iLiD+g++    +   ++  l     r+ +++id+++ th+H+DH+  ++ l e
  gi|15669078|ref|NP_247883.1| 22 NILIDPGTSgtfnI---LMEEL----ERNGIKDIDLIINTHCHFDHTS-ADYLIE 68
                                  9********64321...23333....478899***************3.555555 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   5.4e-08   0.00024       7      76 ..      12      96 ..       5     119 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.4e-08
                 Lactamase_B_3  7 hnsflletagarilvDPfka.nlgyeppa......eeaDlvlisqaledHahletlkql.........aenvkvleegeslev 73
                                  +ns+l+ ++ ++il+DP++  + +   ++      +++Dl++ ++ + dH  ++ l +          +++vk+l++g++++v
  gi|15669078|ref|NP_247883.1| 12 SNSYLI-IGKKNILIDPGTSgTFNILMEElerngiKDIDLIINTHCHFDHTSADYLIEEyfncptiieDKEVKHLKNGDEVTV 93
                                  456655.4569*******76544444444668888******************998877788888888888888888888888 PP

                 Lactamase_B_3 74 ggl 76
                                   +l
  gi|15669078|ref|NP_247883.1| 94 SSL 96
                                  765 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.9e-06    0.0083       6      55 ..      20      67 ..      16      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-06
                 Lactamase_B_6  6 nvkiLlDvGwdeskvslesalkelekv.iptvdliLLshatlehlGayall 55
                                  + +iL+D+G++++ +++   ++ele+  i+++dli+ +h   +h +a  l+
  gi|15669078|ref|NP_247883.1| 20 KKNILIDPGTSGT-FNI--LMEELERNgIKDIDLIINTHCHFDHTSADYLI 67
                                  568*********8.444..788888755******************94433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1404.18
//
Query:       gi|15669079|ref|NP_247884.1|  [L=469]
Description: hypothetical protein MJ_0889 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.12   12.5   2.8       0.33   11.0   2.8    1.7  1  NAD_binding_6  Ferric reductase NAD binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.8   1.9e-05      0.33      22     101 ..     309     399 ..     306     456 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.9e-05
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                 NAD_binding_6  22 dllkkskkealktkkikliwvvressslewfkdvLneleeeksegnieihiYlTseyeaedasdqlissiegenseslk.. 100
                                   d++++s+  +++t ki++i v++e +s ++  + ++++++ +s +n+++++ +T+++++++ +  l + + ge s+++k  
  gi|15669079|ref|NP_247884.1| 309 DIVNNSS-YQVNTSKISIITVNNENKSTNISLNPIQTVKTVSSLNNLDLNNTITKSKNKDSLKI-LVKFQVGEISKDIKkl 387
                                   7888997.99**********************************************99987765.4444444544444445 PP

                                   ...........x RF
                 NAD_binding_6 101 ...........q 101
                                               
  gi|15669079|ref|NP_247884.1| 388 pisimfpeqgyY 399
                                   555555555551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1222  (0.0681577); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3028.39
//
Query:       gi|15669080|ref|NP_247885.1|  [L=137]
Description: hypothetical protein MJ_0890 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-14   52.3   3.1      7e-14   51.7   3.1    1.3  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
  ------ inclusion threshold ------
       0.34   10.5   4.1       0.15   11.6   1.0    2.1  2  RecR           RecR protein


Domain annotation for each model (and alignments):
>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   3.1   7.8e-18     7e-14       2      40 .]      25      61 ..      24      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 7.8e-18
                 Auto_anti-p27  2 kmgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaCd 40
                                   +++ LlkG++ML+++C++Cg+PL++  k+gk+yC++C+
  gi|15669080|ref|NP_247885.1| 25 VLSNELLKGAKMLSTHCSKCGCPLFE--KDGKIYCPICE 61
                                  68999*********************..689*******5 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1      0.96   8.7e+03      22      27 ..      10      15 ..       9      16 .. 0.77
   2 ?   11.6   1.0   1.7e-05      0.15      10      35 ..      32      61 ..      25      64 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.96
                                  T--EES CS
                          RecR 22 Cgnlte 27
                                  C+n+ e
  gi|15669080|ref|NP_247885.1| 10 CYNFGE 15
                                  999876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.7e-05
                                  HHHHHH-EE-TTT--E...ESSS.S-CCCC CS
                          RecR 10 qeakekvrhCsrCgnl...teed.lCaICs 35
                                  + ak   +hCs+Cg+     +    C+IC 
  gi|15669080|ref|NP_247885.1| 32 KGAKMLSTHCSKCGCPlfeKDGKiYCPICE 61
                                  55666678*******8755444445****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1933  (0.107814); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 962.15
//
Query:       gi|15669081|ref|NP_247886.1|  [L=217]
Description: flagellin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-52  175.9   5.1    8.8e-52  175.6   5.1    1.1  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.6   5.1   4.9e-56   8.8e-52       1     164 []      12     203 ..      12     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 175.6 bits;  conditional E-value: 4.9e-56
                                   X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE.EEE-SSSSSEEEEEEE--TTS- CS
                Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg.dsatngtineitiyvklnaGss 80 
                                   G++gigtlI+fIAmVlVAAvaa vlint+gflqqka++tg+esteqv+sgl ++g++g +++t g i++++iy+++naGs 
  gi|15669081|ref|NP_247886.1|  12 GAMGIGTLIIFIAMVLVAAVAAAVLINTSGFLQQKAMATGKESTEQVASGLMCIGVTGhYDKTLGGIDKLAIYITPNAGSA 92 
                                   89********************************************************88899999*************** PP

                                   -EEGGG-EEEEEESS--EE--E.............................................T-EE-TT-EEEEEE CS
                Arch_flagellin  81 pidlnkttisvtddgqetlltad...........................efgivvisdtdgsltngdevlekgekvelev 134
                                   pidl++ ++++++dg++++l+++                           ++ + vi+d+dgsl+ng  v++kg+++ l v
  gi|15669081|ref|NP_247886.1|  93 PIDLKNAKLFLIYDGESHVLNYStvttatlgaddifnssaitdwsladssSYVVGVIQDADGSLSNG--VINKGDIAVLLV 171
                                   ************************************************88888899***********..************ PP

                                   E--..TTT---TT-EEEEEEE-SSS--EEEEE CS
                Arch_flagellin 135 nvn..eddgitagdevsvevvpenGasttief 164
                                   n+n   ++ i++++evs++++pe+Ga+++i+f
  gi|15669081|ref|NP_247886.1| 172 NANavFNKAIPTRSEVSGQFQPEFGAPAVIQF 203
                                   ****96777*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1421.56
//
Query:       gi|15669082|ref|NP_247887.1|  [L=217]
Description: flagellin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-55  188.0   8.0    1.6e-55  187.8   8.0    1.0  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.8   8.0   8.8e-60   1.6e-55       1     164 []      12     201 ..      12     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 187.8 bits;  conditional E-value: 8.8e-60
                                   X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS-- CS
                Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGssp 81 
                                   G++gigtlI+fIAmVlVAAvaa vlint+gflqqka++tg+esteqv+sgl++++++g +++n++in+++iy+++naGs +
  gi|15669082|ref|NP_247887.1|  12 GAMGIGTLIIFIAMVLVAAVAAAVLINTSGFLQQKAMATGKESTEQVASGLSTLQVIG-IHDNKAINYLAIYITPNAGSAA 91 
                                   89********************************************************.9********************* PP

                                   EEGGG-EEEEEESS--EE--E............................................T-EE-TT-EEEEEEE- CS
                Arch_flagellin  82 idlnkttisvtddgqetlltad..........................efgivvisdtdgsltngdevlekgekvelevnv 136
                                   idln+t+i +td +++++l ++                          efgi+v++d+dgs++++++v++kg++v+l++n+
  gi|15669082|ref|NP_247887.1|  92 IDLNQTKILITDGEKKAVLRYNsnayadlttggevtntslaawnlsggEFGIIVLQDADGSCKSTTPVINKGDIVALTINA 172
                                   ************99999999999*********************************************************9 PP

                                   -.TTT---TT-EEEEEEE-SSS--EEEEE CS
                Arch_flagellin 137 n.eddgitagdevsvevvpenGasttief 164
                                   + +  ++ ++++v++ v+pe+Ga+++ief
  gi|15669082|ref|NP_247887.1| 173 SaVGLNLVPRTTVTGSVIPEFGAPAVIEF 201
                                   997778*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1623.54
//
Query:       gi|15669083|ref|NP_247888.1|  [L=223]
Description: flagellin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-42  143.0   7.4    1.1e-41  142.7   7.4    1.1  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.7   7.4   6.3e-46   1.1e-41       1     164 []      18     209 ..      18     209 .. 0.97

  Alignments for each domain:
  == domain 1  score: 142.7 bits;  conditional E-value: 6.3e-46
                                   X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS-- CS
                Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGssp 81 
                                   G++gigtlI+fIA+VlVAAvaa v+inta  lq+ka  +geest qv+sg++++ ++g+  ++++i++++i v +n G++ 
  gi|15669083|ref|NP_247888.1|  18 GAIGIGTLIIFIALVLVAAVAAAVIINTAANLQHKAARVGEESTRQVASGIQVLKITGYAVNTKNITKLAILVSPNVGDE- 97 
                                   899***************************************************************************66. PP

                                   EEGGG-EEEEEESS--EE--E..............................................T-EE-TT-EEEEEE CS
                Arch_flagellin  82 idlnkttisvtddgqetlltad...........................efgivvisdtdgsltng.devlekgekvelev 134
                                   idl++t++++++ + +++l +                            efg++v++d+dgs+ n+ +++++ g+k+ +++
  gi|15669083|ref|NP_247888.1|  98 IDLSSTIVTISNGDYKASLVYGgqityvntngtrdifneswpnianpttEFGVIVLQDADGSMNNTeHPTMNFGDKAIIAI 178
                                   **************777777777*******************************************9************** PP

                                   E--.TTT---TT-EEEEEEE-SSS--EEEEE CS
                Arch_flagellin 135 nvn.eddgitagdevsvevvpenGasttief 164
                                   nv  ++ gi++++++ +ev+pe+Gas++ief
  gi|15669083|ref|NP_247888.1| 179 NVGdVFGGIMPRERIYGEVIPEFGASGIIEF 209
                                   **999************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1407.19
//
Query:       gi|15669084|ref|NP_247889.1|  [L=141]
Description: flagella-like protein C [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-21   74.5  14.7      5e-20   71.6   6.2    2.5  2  FlaC_arch        Flagella accessory protein C (FlaC)
      4e-05   22.2   5.8    4.4e-05   22.1   5.8    1.0  1  MAD              Mitotic checkpoint protein
    0.00051   19.9   3.2      0.004   17.1   0.2    2.1  2  Sec34            Sec34-like family
    0.00081   19.4  10.1     0.0015   18.6   1.9    2.2  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
     0.0014   18.5   3.1     0.0021   18.0   3.1    1.3  1  DASH_Spc19       Spc19
     0.0015   18.6   0.8       0.42   10.7   0.2    2.3  2  TolA_bind_tri    TolA binding protein trimerisation
     0.0026   17.7   3.5       0.18   11.7   0.4    2.4  2  Prefoldin        Prefoldin subunit
     0.0036   16.0   6.0     0.0043   15.7   6.0    1.1  1  FapA             Flagellar Assembly Protein A
     0.0055   16.7   7.1       0.32   11.0   1.0    2.5  2  Prefoldin_2      Prefoldin subunit
     0.0081   16.4  10.7      0.081   13.2   2.2    2.6  2  HALZ             Homeobox associated leucine zipper
     0.0082   14.2   4.3     0.0092   14.0   4.3    1.0  1  Prominin         Prominin
     0.0092   16.3   0.6      0.055   13.7   0.1    1.9  2  DUF2431          Domain of unknown function (DUF2431)
  ------ inclusion threshold ------
       0.01   15.4   4.3      0.014   15.0   3.3    1.6  2  TBK1_CCD1        TANK-binding kinase 1 coiled-coil domain 1
       0.01   16.3   1.2      0.013   15.9   1.2    1.3  1  Fez1             Fez1
      0.012   15.7   2.8       0.64   10.1   0.3    2.2  2  ADIP             Afadin- and alpha -actinin-Binding
      0.012   15.9   6.9       0.13   12.6   1.6    2.3  2  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.013   15.2   8.4      0.021   14.5   4.9    1.8  2  SHE3             SWI5-dependent HO expression protein 3
      0.017   15.2   8.8       0.12   12.5   1.8    2.4  2  bZIP_1           bZIP transcription factor
      0.018   14.7   5.2       0.36   10.5   0.7    2.2  2  Lebercilin       Ciliary protein causing Leber congenital ama
       0.02   14.9   3.7        1.6    8.8   0.5    2.2  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.021   14.6   4.2        1.1    9.1   0.6    2.5  2  DivIC            Septum formation initiator
      0.022   14.8   4.5        2.6    8.2   0.8    2.4  2  BRE1             BRE1 E3 ubiquitin ligase
      0.023   15.3   3.4        1.1    9.9   0.6    2.4  2  Syntaxin-6_N     Syntaxin 6, N-terminal
      0.023   14.9  11.9      0.017   15.3   8.5    2.0  2  Tropomyosin_1    Tropomyosin like
      0.023   13.9   0.1      0.025   13.8   0.1    1.1  1  Glutaminase      Glutaminase
      0.031   14.8   2.5       0.17   12.3   2.5    2.1  1  Spectrin         Spectrin repeat
      0.031   14.2   1.2      0.045   13.7   1.2    1.2  1  STAT_alpha       STAT protein, all-alpha domain
      0.033   14.5   1.2        2.4    8.5   0.0    2.3  2  KxDL             Uncharacterized conserved protein
      0.038   14.5   7.9       0.34   11.4   0.4    2.3  2  APG6_N           Apg6 coiled-coil region
      0.038   14.1   3.0       0.88    9.7   0.7    2.3  2  Med9             RNA polymerase II transcription mediator com
      0.039   14.0   4.8       0.09   12.8   4.8    1.6  1  Cep57_CLD        Centrosome localisation domain of Cep57
       0.04   14.4   4.8        1.4    9.4   0.8    2.3  2  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
      0.049   14.0   5.6       0.48   10.8   0.7    2.5  2  CLZ              C-terminal leucine zipper domain of cyclic n
       0.05   13.6   4.3       0.18   11.8   0.3    2.2  2  DUF1640          Protein of unknown function (DUF1640)
      0.058   12.6   1.1      0.065   12.5   1.1    1.1  1  TMPIT            TMPIT-like protein
      0.062   13.4   0.4      0.079   13.1   0.4    1.3  1  Cob_adeno_trans  Cobalamin adenosyltransferase
      0.066   13.1   3.3        1.6    8.6   0.4    2.2  2  Wtap             WTAP/Mum2p family
      0.067   13.5   8.0      0.086   13.1   8.0    1.2  1  zf-C4H2          Zinc finger-containing protein
      0.071   13.2   3.2       0.19   11.8   2.2    2.1  2  DUF1664          Protein of unknown function (DUF1664)
      0.073   13.6   4.3       0.12   12.9   0.6    2.2  2  DUF16            Protein of unknown function DUF16
      0.076   11.1   2.6      0.079   11.0   2.6    1.1  1  HCR              Alpha helical coiled-coil rod protein (HCR)
      0.084   13.3   4.9       0.44   11.0   4.1    2.2  2  Snapin_Pallidin  Snapin/Pallidin
       0.11   12.6   0.6       0.11   12.6   0.6    2.8  2  DMPK_coil        DMPK coiled coil domain like
       0.12   12.6   9.7      0.068   13.4   6.3    2.2  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
       0.12   13.1   3.1        4.2    8.1   0.2    2.2  3  Occludin_ELL     Occludin homology domain
       0.13   12.4   5.4        0.1   12.7   0.7    2.3  2  DUF2730          Protein of unknown function (DUF2730)
       0.15   10.9   7.8        1.1    8.1   4.6    1.8  2  Spc7             Spc7 kinetochore protein
       0.16   12.5  13.1       0.54   10.7   2.5    2.4  2  ZapB             Cell division protein ZapB
       0.16   12.0   5.1       0.12   12.5   1.3    2.3  2  COG2             COG (conserved oligomeric Golgi) complex com
       0.17   12.1   9.9       0.13   12.5   1.8    2.4  2  Spc24            Spc24 subunit of Ndc80
       0.17   11.8   4.6        1.2    9.1   0.6    2.2  2  DUF4446          Protein of unknown function (DUF4446)
       0.19   11.6   0.1       0.19   11.6   0.1    2.8  3  HSBP1            Heat shock factor binding protein 1
        0.2   11.9  10.0      0.076   13.2   6.8    1.9  1  Cnn_1N           Centrosomin N-terminal motif 1
        0.2   11.7   8.7       0.24   11.4   1.9    2.2  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.29   11.4  12.6        0.9    9.8   3.5    2.5  2  XhlA             Haemolysin XhlA
        0.3   11.7  10.1        9.1    7.0  10.1    2.3  1  YabA             Initiation control protein YabA
       0.33   11.0   5.6        1.1    9.3   5.4    1.9  1  Laminin_II       Laminin Domain II
       0.39   10.9   4.8        1.2    9.4   4.0    1.8  1  Fib_alpha        Fibrinogen alpha/beta chain family
       0.47   10.0   5.0        1.9    8.1   0.3    2.7  2  YvrJ             YvrJ protein family
       0.53   10.8   6.7         19    5.8   6.7    2.5  1  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.74    9.9   9.0        1.5    9.0   0.8    2.6  3  bZIP_2           Basic region leucine zipper
       0.98    9.2   5.4        2.3    8.1   0.8    2.3  2  CCDC92           Coiled-coil domain of unknown function
          1   10.0   6.4          4    8.1   1.4    2.5  2  SlyX             SlyX
        1.2    9.5   6.0       0.81   10.0   0.8    2.1  2  DUF4806          Domain of unknown function (DUF4806)
        1.3   10.2   2.8        3.1    8.9   0.6    2.1  2  DUF5320          Family of unknown function (DUF5320)
        1.3    8.9   6.2        2.9    7.8   1.0    2.8  2  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
        1.9    8.6   5.0        2.4    8.3   0.2    2.8  3  YojJ             Bacterial membrane-spanning protein N-termin
        2.1    8.6   7.3       0.84    9.9   0.6    2.6  2  Med21            Subunit 21 of Mediator complex
        3.3    7.8  14.7       0.78    9.8   2.6    3.1  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        6.5    6.9  10.3        2.4    8.3   0.2    3.2  3  DUF5595          Domain of unknown function (DUF5595)
        6.8    7.2   9.6        1.6    9.2   3.3    2.6  2  DUF2497          Protein of unknown function (DUF2497)


Domain annotation for each model (and alignments):
>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   6.2     2e-22     5e-20       1      55 []      10      64 ..      10      64 .. 0.99
   2 ?    8.0   1.3     0.015       3.8      14      41 ..      74     102 ..      66     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 2e-22
                     FlaC_arch  1 ridelEnklsklsteletvkkeneelsksveelkenVkdllsLYEvVsnqvNPFv 55
                                  +++++E+kl+kl++++++++kene l+ ++++++en +d+++LYEvVsnq+NPF+
  gi|15669084|ref|NP_247889.1| 10 KVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQINPFI 64
                                  89****************************************************7 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.015
                     FlaC_arch  14 t.eletvkkeneelsksveelkenVkdll 41 
                                     +le +++e + l+k+veel  +   l 
  gi|15669084|ref|NP_247889.1|  74 LeKLERLETEYKRLKKTVEELTNDLIILG 102
                                   35778888888888888888877665555 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   5.8   1.7e-07   4.4e-05     442     545 ..      10     115 ..       2     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.7e-07
                           MAD 442 evdslkkkleeLelerqrLreqkeelElele..rreLqgdydlkktkVlhlseNPaakakqqkk...eqlekLqaEierlk 517
                                    v+ +  kl +Le   ++Lr+++e+l +el   +++Lq    ++ + V+  + NP     ++++   e+le+L+ E +rlk
  gi|15669084|ref|NP_247889.1|  10 KVNDIESKLPKLESSINNLRKENEMLRVELNkiNENLQDI--MALYEVVSNQINPFIGVSKITAtslEKLERLETEYKRLK 88 
                                   5889999***********************9778899988..78899********86666665511167777899****** PP

                           MAD 518 ellkkleedkekkvaslpessltlafke 545
                                   + +++l +d    + sl  + l+++  e
  gi|15669084|ref|NP_247889.1|  89 KTVEELTNDLI-ILGSLYLHQLDINLDE 115
                                   ****9998866.5666666666666555 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   1.6e-05     0.004      10      78 ..       2      70 ..       1      72 [. 0.94
   2 ?    5.1   0.2     0.076        19      39      68 ..      69      98 ..      63     120 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.6e-05
                         Sec34 10 eecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpit 78
                                  e+++ ll+++++++++L +le++ ++  ++ + l+ + +++ e+ ++++ l+e ++++++ F  + +it
  gi|15669084|ref|NP_247889.1|  2 ETTEGLLAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQINPFIGVSKIT 70
                                  57889*********************************************************9988887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.076
                         Sec34 39 ktsslheaceqlleeqkrleelaeeieekL 68
                                   t +  e+ e+l +e krl++++ee++++L
  gi|15669084|ref|NP_247889.1| 69 ITATSLEKLERLETEYKRLKKTVEELTNDL 98
                                  444445566777777777777777777666 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.9   5.9e-06    0.0015      53     110 ..       3      60 ..       1      62 [. 0.91
   2 ?    5.9   1.4     0.048        12      51      77 ..      74     100 ..      67     132 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.9e-06
                CENP-F_leu_zip  53 evetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenll 110
                                   + e+l ++++ ++++l +le+ +++lr+e+e L  el+k +e  ++  +l + ++n++
  gi|15669084|ref|NP_247889.1|   3 TTEGLLAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQI 60 
                                   678999*************************************999988888877776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.048
                CENP-F_leu_zip  51 kaevetlkeeieelaeelreleldLva 77 
                                    +++e l++e ++l+++ +el+ dL  
  gi|15669084|ref|NP_247889.1|  74 LEKLERLETEYKRLKKTVEELTNDLII 100
                                   344444444444444444444444433 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   3.1   8.3e-06    0.0021      68     157 .]      10      94 ..       2      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.3e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXXX......XXXXXXXXXXX CS
                    DASH_Spc19  68 llekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskkk......ltkeelerlkk 142
                                   +++ +e++l kle+  ++L+++ e++++ l++ +++ ++  +  e  +++ +                   t+  le+l++
  gi|15669084|ref|NP_247889.1|  10 KVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQIN-----------PfigvskITATSLEKLER 79 
                                   567899**************************65555555555544442221...........12223348999******* PP

                                   XXXXXXXXXXXXXXX CS
                    DASH_Spc19 143 LkqkKerLkytlerL 157
                                   L  + +rLk+t+e+L
  gi|15669084|ref|NP_247889.1|  80 LETEYKRLKKTVEEL 94 
                                   *************87 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.2    0.0017      0.42      22      63 ..      13      54 ..       5      62 .. 0.82
   2 ?    6.3   0.0     0.041        10      25      48 ..      75      98 ..      68     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0017
                 TolA_bind_tri 22 elqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlD 63
                                  ++ ++l +l++ ++ LR ++E l+ +l++++e  +d+    +
  gi|15669084|ref|NP_247889.1| 13 DIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYE 54
                                  56678889999999****************999999876555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.041
                 TolA_bind_tri 25 qqlealqqelreLRGqiEelqyql 48
                                  ++le+l++e ++L+  +Eel+++l
  gi|15669084|ref|NP_247889.1| 75 EKLERLETEYKRLKKTVEELTNDL 98
                                  679*****************9987 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.4   0.00071      0.18      82     116 ..      14      48 ..       2      57 .. 0.86
   2 ?    6.9   0.2     0.023       5.7      12      34 ..      74      96 ..      70     114 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00071
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanlaq 116
                                   ++ kl +le+++ +l +e e+l+ +++++++nl+ 
  gi|15669084|ref|NP_247889.1|  14 IESKLPKLESSINNLRKENEMLRVELNKINENLQD 48 
                                   56788899999999999999999999999999986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.023
                                  HHHHHHHHHHHHHHHHHHHHHTT CS
                     Prefoldin 12 laqlkeaieelektletlktlkk 34
                                  l++l+   +e++++++t+++l +
  gi|15669084|ref|NP_247889.1| 74 LEKLERLETEYKRLKKTVEELTN 96
                                  56666666666666666666655 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   6.0   1.7e-05    0.0043     331     438 ..      17     120 ..       7     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
                          FapA 331 depelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk 411
                                   + p+l +++++l++e e l+ el+k++++++ + +    +++ s++ + +  + +      e+le le+e+k+lk+ +e+ 
  gi|15669084|ref|NP_247889.1|  17 KLPKLESSINNLRKENEMLRVELNKINENLQDIMA---LYEVVSNQINPFIGVSKITATSLEKLERLETEYKRLKKTVEEL 94 
                                   56899999999***99999*********9777766...7888899999999999999999999999999999999999999 PP

                          FapA 412 keeakikvnkeiypgvkikigkkklii 438
                                     +  i+ ++      +i++++  +++
  gi|15669084|ref|NP_247889.1|  95 -TNDLIILGSLYLHQLDINLDEIIEEV 120
                                   .55577766666666666666655555 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   1.0    0.0013      0.32      66      98 ..      13      45 ..       1      61 [. 0.57
   2 !    8.8   0.6    0.0058       1.5      73      99 ..      72      98 ..      66     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0013
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2 66 eLeerketlekeiktlekqleklekeleelkee 98
                                  + e ++ +le  i++l k+ e l+ el+++ e+
  gi|15669084|ref|NP_247889.1| 13 DIESKLPKLESSINNLRKENEMLRVELNKINEN 45
                                  334444444444555555555555555555444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0058
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2 73 tlekeiktlekqleklekeleelkeel 99
                                  t  +++++le ++++l+k++eel + l
  gi|15669084|ref|NP_247889.1| 72 TSLEKLERLETEYKRLKKTVEELTNDL 98
                                  556778888888888888888887776 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   2.2   0.00032     0.081      16      43 .]      20      47 ..      16      47 .. 0.93
   2 ?    7.8   1.1     0.015       3.7       3      40 ..      80      96 ..      74      99 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00032
                          HALZ 16 aLksdydsLkkenekLkaelqeLkeklq 43
                                  +L s+ ++L+kene L+ el++ +e lq
  gi|15669084|ref|NP_247889.1| 20 KLESSINNLRKENEMLRVELNKINENLQ 47
                                  6999******************999886 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.015
                          HALZ  3 LErDYdvLKasYdaLksdydsLkkenekLkaelqeLke 40
                                  LE +Y+ LK+  + L+                     +
  gi|15669084|ref|NP_247889.1| 80 LETEYKRLKKTVEELT---------------------N 96
                                  6666666666666666.....................3 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   4.3   3.7e-05    0.0092     241     369 ..       4     130 ..       1     138 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                      Prominin 241 lerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsn.lCqseeCskilssleiekldtskcldqlpnv 320
                                    e ll ++++++ +L +++++ ++Lrk+ + Lr  l+++ ++l+++++  +  s++ + +   ++i    t ++l++l+ +
  gi|15669084|ref|NP_247889.1|   4 TEGLLAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALyEVVSNQINPFIGVSKI----TATSLEKLERL 80 
                                   5779999**************************************999977777777888777777....7778899**** PP

                      Prominin 321 devlealeevletnlssivkeglarlneipekvknqtaevvp.dlkkala 369
                                   +++ ++l++ +e+ ++ ++  g  +l+++   + + ++ev++ +++k+++
  gi|15669084|ref|NP_247889.1|  81 ETEYKRLKKTVEELTNDLIILGSLYLHQLDINLDEIIEEVLEeEIIKSMS 130
                                   *****************************999999999998855666654 PP

>> DUF2431  Domain of unknown function (DUF2431)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       2.2   5.5e+02      31      53 ..      11      33 ..       2      55 .. 0.69
   2 !   13.7   0.1   0.00022     0.055      20      60 ..      66     110 ..      51     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2.2
                       DUF2431 31 eeellekypqaeenieeLeeegv 53
                                   +++++k p+ e+ i++L++e+ 
  gi|15669084|ref|NP_247889.1| 11 VNDIESKLPKLESSINNLRKENE 33
                                  45677788888888888887744 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00022
                       DUF2431  20 cenlvaTsydseeellekypqaeenieeLeee....gvkvlfgVD 60 
                                    ++++aTs+++ e l+++y+  ++++eeL++     g  +l++ D
  gi|15669084|ref|NP_247889.1|  66 VSKITATSLEKLERLETEYKRLKKTVEELTNDliilGSLYLHQLD 110
                                   568**************************9986666666666666 PP

>> TBK1_CCD1  TANK-binding kinase 1 coiled-coil domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.4     0.087        22      81     123 ..       6      49 ..       2      52 .. 0.71
   2 ?   15.0   3.3   5.6e-05     0.014      54     133 ..      24     104 ..      18     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.087
                     TBK1_CCD1  81 kllevlmqanlepsElde.iselhkkllrlssslerieeslqei 123
                                    ll ++  ++++ + l+  i +l+k+   l+ +l++i+e+lq+i
  gi|15669084|ref|NP_247889.1|   6 GLLAKVNDIESKLPKLESsINNLRKENEMLRVELNKINENLQDI 49 
                                   55666666666666665558888888888888999999988887 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.6e-05
                     TBK1_CCD1  54 dvnkllhkktevelkceiceetlekaekllevlmqanlepsEldeiselh.kkllrlssslerieeslqeiknklipeell 133
                                    +n+l + +  + ++++  +e+l+    l+ev+++       +++i+  + +kl rl+++ +r++++++e+ n li  ++l
  gi|15669084|ref|NP_247889.1|  24 SINNLRKENEMLRVELNKINENLQDIMALYEVVSNQINPFIGVSKITATSlEKLERLETEYKRLKKTVEELTNDLIILGSL 104
                                   566666777888999******************98777777999998665389*********************9974444 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   1.2   5.3e-05     0.013      37     107 ..       8      95 ..       3     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.3e-05
                          Fez1  37 kaqlrelrakleekeeeikeleesleektlelevcenelqrk..................kseaellrekvekleeelkel 99 
                                    a++ ++++kl + e++i++l+++ e    el++++++lq                    k +a+   ek+e+le+e k+l
  gi|15669084|ref|NP_247889.1|   8 LAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDImalyevvsnqinpfigvsKITAT-SLEKLERLETEYKRL 87 
                                   57888999999999999999999999999999999999999999999999999999999554444.556799999999999 PP

                          Fez1 100 reelsels 107
                                   +++++el+
  gi|15669084|ref|NP_247889.1|  88 KKTVEELT 95 
                                   99888755 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3    0.0025      0.64      89     130 ..      10      51 ..       1      59 [. 0.63
   2 ?    6.0   0.1     0.045        11      59      82 ..      74      97 ..      67     105 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0025
                          ADIP  89 elalvqakerqlekklktleqklknekeelqrlknalqqikt 130
                                   ++   ++k+ +le ++ +l + +  ++ el++ + +lq+i +
  gi|15669084|ref|NP_247889.1|  10 KVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMA 51 
                                   455556666667777777777777777777777777776655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.045
                          ADIP 59 netirkleaeierlqskierlktq 82
                                   e++++le+e++rl++++e l++ 
  gi|15669084|ref|NP_247889.1| 74 LEKLERLETEYKRLKKTVEELTND 97
                                  566667777777777777776654 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.6    0.0005      0.13      34      82 ..       9      57 ..       3      61 .. 0.91
   2 ?    6.3   0.5     0.047        12      63      84 ..      73      94 ..      54     120 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0005
                       BLOC1_2 34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavs 82
                                  +k++++++++ +le+++++l++++e l+  l++i++  +++  L e+vs
  gi|15669084|ref|NP_247889.1|  9 AKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVS 57
                                  6899999999************************999999999999986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.047
                       BLOC1_2 63 ylqqidqiekqvteLeeavseL 84
                                   l++++++e++ ++L+++v+eL
  gi|15669084|ref|NP_247889.1| 73 SLEKLERLETEYKRLKKTVEEL 94
                                  3444444444444444444444 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   4.9   8.5e-05     0.021      26     104 ..       4      82 ..       1      86 [. 0.83
   2 ?    2.9   0.5       0.3        77      67      88 ..      76      97 ..      73     119 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.5e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH CS
                          SHE3  26 sqeLleklelaqkkeskflenlaslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenssaset 104
                                    + Ll k +  ++k  k+  ++++l++EN++L   L++ +  l+d+   ++  +++++      k   + le+++  et
  gi|15669084|ref|NP_247889.1|   4 TEGLLAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQINPFIGVSKITATSLEKLERLET 82 
                                   5789999999999999999999999999999999999999999999999999999998877777777777777666665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.3
                                  HHHHHHHHHHHHHHHHHHHHHH CS
                          SHE3 67 rlkdlekelselkesveelkle 88
                                  +l  le+e++ lk+ veel+ +
  gi|15669084|ref|NP_247889.1| 76 KLERLETEYKRLKKTVEELTND 97
                                  4556666777777776666543 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.8   0.00049      0.12      30      57 ..      20      47 ..       5      51 .. 0.90
   2 ?    6.7   0.8     0.031       7.8      34      54 ..      76      96 ..      72     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00049
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1 30 eLerrvkaLekeNksLkseleelkkeve 57
                                  +Le+    L keN++L+ el++++++ +
  gi|15669084|ref|NP_247889.1| 20 KLESSINNLRKENEMLRVELNKINENLQ 47
                                  799999****************999877 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.031
                                  HHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1 34 rvkaLekeNksLkseleelkk 54
                                  + + Le+e k Lk+++eel++
  gi|15669084|ref|NP_247889.1| 76 KLERLETEYKRLKKTVEELTN 96
                                  677788888888888888876 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.7    0.0014      0.36      11      38 ..       9      36 ..       6      53 .. 0.89
   2 ?    6.5   0.3     0.023       5.9       5      44 ..      69     108 ..      66     116 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0014
                    Lebercilin 11 lkikeLqnelaelqskleelrkEnklLk 38
                                   k+++ +++l +l+s +++lrkEn++L+
  gi|15669084|ref|NP_247889.1|  9 AKVNDIESKLPKLESSINNLRKENEMLR 36
                                  6999***********************8 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.023
                    Lebercilin   5 vlsarllkikeLqnelaelqskleelrkEnklLkrlqkrq 44 
                                   +   +l+k+++L+ e + l++ +eel++++ +L  l   q
  gi|15669084|ref|NP_247889.1|  69 ITATSLEKLERLETEYKRLKKTVEELTNDLIILGSLYLHQ 108
                                   6666778888888888888888888888877777666555 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.5    0.0063       1.6      86     125 ..      20      59 ..       2      62 .. 0.51
   2 ?    7.1   0.1     0.021       5.4      53      79 ..      71      97 ..      68     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0063
                    TPR_MLP1_2  86 eleeseesweeqkeelekelselekriedlneqNklLhdQ 125
                                   +le s +++ ++ e+l+ el+++++ ++d+ +  ++  +Q
  gi|15669084|ref|NP_247889.1|  20 KLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQ 59 
                                   3333334444455566666666666666665555555555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.021
                    TPR_MLP1_2 53 aedvkelqalreelnelkaeiaelkae 79
                                  a+ +++l++l +e+++lk++++el+++
  gi|15669084|ref|NP_247889.1| 71 ATSLEKLERLETEYKRLKKTVEELTND 97
                                  667788888888888888888888765 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.6    0.0044       1.1      16      50 ..       8      42 ..       3      51 .. 0.86
   2 ?    6.8   0.0     0.022       5.6      31      53 ..      75      97 ..      56     102 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0044
                                  XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                         DivIC 16 llaykqlkqeiaalqaelaklkaeneeLeaevkdL 50
                                  l ++ ++++++ +l+  +++l++ene L  e+++ 
  gi|15669084|ref|NP_247889.1|  8 LAKVNDIESKLPKLESSINNLRKENEMLRVELNKI 42
                                  667889999999****************9999987 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.022
                                  HHHHHHHHHHHHHHHHHCC-XXX CS
                         DivIC 31 aelaklkaeneeLeaevkdLksd 53
                                  ++l++l  e ++L++ v++L++d
  gi|15669084|ref|NP_247889.1| 75 EKLERLETEYKRLKKTVEELTND 97
                                  56666777777777777777544 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.8      0.01       2.6      44      77 ..      15      48 ..       2      61 .. 0.69
   2 ?    8.0   0.2     0.012         3       4      29 ..      76     101 ..      73     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.01
                          BRE1 44 dqkyfaamrskdalenelkkLnkllsKsselieq 77
                                  + k   ++ s+++l++e+ +L+  l+K +e  ++
  gi|15669084|ref|NP_247889.1| 15 ESKLPKLESSINNLRKENEMLRVELNKINENLQD 48
                                  4555566777777777777777777777776655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.012
                          BRE1   4 ELvklekafeelseqlskkvkeltil 29 
                                    L++le++++ l++++++++++l il
  gi|15669084|ref|NP_247889.1|  76 KLERLETEYKRLKKTVEELTNDLIIL 101
                                   5999*****************99988 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.6    0.0044       1.1      41      91 ..       2      52 ..       1      59 [. 0.72
   2 ?    6.3   0.3     0.056        14       2      60 ..      62      94 ..      42     126 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0044
                  Syntaxin-6_N 41 etrteLrkalrsiewdledLeetvriveknpskfkidekelsrrrafveev 91
                                  et++ L +++++ie +l  Le +++ ++k+++  +++ +++++  + + ++
  gi|15669084|ref|NP_247889.1|  2 ETTEGLLAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMAL 52
                                  577778888888888888888888888888888888888777765555554 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.056
                  Syntaxin-6_N  2 PFfevkeeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledL 60
                                  PF+ v +    sl+k+e l ++++rl+++ ++                          L
  gi|15669084|ref|NP_247889.1| 62 PFIGVSKITATSLEKLERLETEYKRLKKTVEE--------------------------L 94
                                  55555555566666666666666655444333..........................2 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   8.5   6.8e-05     0.017      16     104 ..       4      95 ..       1      98 [. 0.84
   2 ?    2.1   3.8      0.76   1.9e+02      12      58 ..      73     120 ..      67     140 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.8e-05
                 Tropomyosin_1  16 aeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrk.iqlLE..eeleesd 93 
                                    e l +kv + e++  + e+ i++L k n++l  e++k++e+l++ ++  e  +++      +++     LE  e le   
  gi|15669084|ref|NP_247889.1|   4 TEGLLAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQINPFIGVSKItATSLEklERLETEY 84 
                                   677789999****************************************99988887776666654134566556788899 PP

                 Tropomyosin_1  94 kkLkettekLr 104
                                   k+Lk+t+e L+
  gi|15669084|ref|NP_247889.1|  85 KRLKKTVEELT 95 
                                   99999999996 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.76
                 Tropomyosin_1  12 aqekaeeleekvKeleqenlekeqeiksLtk.knqqleeevekleekl 58 
                                   ++ek e le ++K+l ++ +e  +++  L    ++ql+ +++++ e++
  gi|15669084|ref|NP_247889.1|  73 SLEKLERLETEYKRLKKTVEELTNDLIILGSlYLHQLDINLDEIIEEV 120
                                   567778888888888877777777777664425677777777754443 PP

>> Glutaminase  Glutaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1    0.0001     0.025      48     126 ..      19      97 ..      14     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHH-HHHHHCCC-S---SS-TT-HHHHHCTTT--C-TTSHHHHHHHHHHSSSSSHHHHHHHHHHHHHHHHST CS
                   Glutaminase  48 ftlalaleelgeeevlervgvepsgeafnsivqleeekgkprNpminaGAivvasllkgesaeerferileflrklagr 126
                                     l   +++l +e+ + rv+ +  +e+ ++i++l e  ++  Np+i    i+++sl k e+ e++++r+ + +++l+++
  gi|15669084|ref|NP_247889.1|  19 PKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQINPFIGVSKITATSLEKLERLETEYKRLKKTVEELTND 97 
                                   5556667777788888899*************************************77799**************9987 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.5   0.00069      0.17      26     101 ..      15      96 ..       1      99 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00069
                                   CSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT......HTTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Spectrin  26 sedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeg......hsaseeieerleelnerWeeLkelaaerk 100
                                   +  l+k  +++ +l k+ + l+ el+   e+++++++l e + +         + ++   e+le l++ ++ Lk++++e  
  gi|15669084|ref|NP_247889.1|  15 ESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQInpfigvSKITATSLEKLERLETEYKRLKKTVEELT 95 
                                   3345899999**************************99999944443666544445888899*************999865 PP

                                   H CS
                      Spectrin 101 q 101
                                   +
  gi|15669084|ref|NP_247889.1|  96 N 96 
                                   5 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.2   0.00018     0.045       6      71 ..       9     101 ..       5     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00018
                    STAT_alpha   6 qrleelrskvqeteqdirkLedeqeeFdfqyqelqkl...........................eqeraesekkelkkqke 59 
                                   +++++++sk +++e++i++L +e e + ++ ++++++                           + e+ e+ ++e+k+ k+
  gi|15669084|ref|NP_247889.1|   9 AKVNDIESKLPKLESSINNLRKENEMLRVELNKINENlqdimalyevvsnqinpfigvskitatSLEKLERLETEYKRLKK 89 
                                   6899*****************************999999********************9998877777788888888888 PP

                    STAT_alpha  60 llqqmlnaLdqk 71 
                                   +++++ n L+  
  gi|15669084|ref|NP_247889.1|  90 TVEELTNDLIIL 101
                                   888888775543 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3      0.15        37      45      74 ..      20      49 ..       2      61 .. 0.47
   2 ?    8.5   0.0    0.0094       2.4      34      64 ..      68      98 ..      65     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.15
                          KxDL 45 klrarfkqgtkllkevkkdLesifkkirsl 74
                                  kl++ +++  k    ++ +L++i+++++ +
  gi|15669084|ref|NP_247889.1| 20 KLESSINNLRKENEMLRVELNKINENLQDI 49
                                  333333333333333333333333333333 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0094
                          KxDL 34 elnalsqerlaklrarfkqgtkllkevkkdL 64
                                  ++ a s e+l++l++++k+ +k++ e+ +dL
  gi|15669084|ref|NP_247889.1| 68 KITATSLEKLERLETEYKRLKKTVEELTNDL 98
                                  66788999**********************9 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4    0.0014      0.34      52      94 ..       7      49 ..       1      62 [. 0.56
   2 ?    7.0   1.5     0.032         8      64      90 ..      71      97 ..      65     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0014
                        APG6_N 52 leeeleklekeeeelleeLkelekereeleaelaaleeeleal 94
                                  l  ++ ++e++  +l++ +++l ke+e l+ el+++ e l+++
  gi|15669084|ref|NP_247889.1|  7 LLAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDI 49
                                  4445555555555566666666666666666666655555543 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.032
                        APG6_N 64 eelleeLkelekereeleaelaaleee 90
                                  ++ le+L++le+e ++l++ +++l++ 
  gi|15669084|ref|NP_247889.1| 71 ATSLEKLERLETEYKRLKKTVEELTND 97
                                  678999999999999999999999875 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.7    0.0035      0.88      41      78 ..       7      44 ..       4      50 .. 0.91
   2 ?    4.4   0.1      0.16        39      46      78 ..      64      96 ..      53      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0035
                          Med9 41 lirelpgidrsveeqeaeieeleeqlakKrelLkkykn 78
                                  l++++ +i+      e  i++l++++++ r  L+k+++
  gi|15669084|ref|NP_247889.1|  7 LLAKVNDIESKLPKLESSINNLRKENEMLRVELNKINE 44
                                  57899999999*******************99999876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.16
                          Med9 46 pgidrsveeqeaeieeleeqlakKrelLkkykn 78
                                   g+++ +++ ++++e le + ++ ++  +++ n
  gi|15669084|ref|NP_247889.1| 64 IGVSKITATSLEKLERLETEYKRLKKTVEELTN 96
                                  578888889999**********99999988876 PP

>> Cep57_CLD  Centrosome localisation domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   4.8   0.00036      0.09      62     136 ..       7      91 ..       1     101 [. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00036
                     Cep57_CLD  62 lesqLaaaesrcslLEkqLeymrk...mvesaekerkavle......kqaslekek...kqesselqaklekLekLEkeyl 130
                                   l ++++  es+  +LE  ++++rk   m++   +  ++ l+      +   ++++       s+ + + lekLe+LE+ey 
  gi|15669084|ref|NP_247889.1|   7 LLAKVNDIESKLPKLESSINNLRKeneMLRVELNKINENLQdimalyE--VVSNQInpfIGVSKITATSLEKLERLETEYK 85 
                                   556666667777777777777776333444443333444443332322..2222223455567777899************ PP

                     Cep57_CLD 131 rLtatq 136
                                   rL++t 
  gi|15669084|ref|NP_247889.1|  86 RLKKTV 91 
                                   **9985 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.8    0.0057       1.4      25      62 ..      11      47 ..       9      54 .. 0.76
   2 ?    6.5   0.2     0.045        11      38      61 ..      75      98 ..      69     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0057
                   Fungal_TACC 25 VkllkkgyeakyqkkldklelenkslkqeieqLkkqle 62
                                  V+ +  +   k ++++++l++en+ l+ e+++++++l+
  gi|15669084|ref|NP_247889.1| 11 VNDIESKL-PKLESSINNLRKENEMLRVELNKINENLQ 47
                                  55555555.67888999999999999999999998886 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.045
                   Fungal_TACC 38 kkldklelenkslkqeieqLkkql 61
                                  +kl++le+e k+lk+ +e+L++ l
  gi|15669084|ref|NP_247889.1| 75 EKLERLETEYKRLKKTVEELTNDL 98
                                  799*****************9987 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7    0.0019      0.48      25      62 ..      10      47 ..       2      54 .. 0.85
   2 ?    5.0   0.4      0.12        31      32      51 ..      76      95 ..      68     101 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0019
                           CLZ 25 eqkeleekverLessLeaLqtrlarLlaeyessqrkLk 62
                                  + +++e+k+ +Less+++L +  + L  e+++ ++ L+
  gi|15669084|ref|NP_247889.1| 10 KVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQ 47
                                  667999**************999999999999998887 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.12
                           CLZ 32 kverLessLeaLqtrlarLl 51
                                  k+erLe++ + L++ ++ L 
  gi|15669084|ref|NP_247889.1| 76 KLERLETEYKRLKKTVEELT 95
                                  33444444333333333333 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00072      0.18      71      97 ..      22      48 ..       4      61 .. 0.86
   2 ?    3.7   0.4      0.23        58      73      95 ..      76      98 ..      66     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00072
                       DUF1640 71 rsefaalrseteklqreleklkqkLre 97
                                  +s +++lr+e+e l++el+k++++L++
  gi|15669084|ref|NP_247889.1| 22 ESSINNLRKENEMLRVELNKINENLQD 48
                                  67899********************97 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.23
                       DUF1640 73 efaalrseteklqreleklkqkL 95
                                  + + l++e+++l++ +e+l+++L
  gi|15669084|ref|NP_247889.1| 76 KLERLETEYKRLKKTVEELTNDL 98
                                  45677788888888888888877 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.1   0.00026     0.065      19      97 ..      12     106 ..       1     120 [. 0.45

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00026
                         TMPIT  19 keykqkleelsklqskcskeikkqkkrlkelksslkklkksvk................eeeeeeveelkeelkerkkvlk 83 
                                   + +++kl +l++++++++ke +  + +l++++++l+++ +  +                + + e++e+l++e k+ kk+++
  gi|15669084|ref|NP_247889.1|  12 NDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEvvsnqinpfigvskitATSLEKLERLETEYKRLKKTVE 92 
                                   222223333333333333333333333333333333332222244444445555555555555555566666666666666 PP

                         TMPIT  84 evesllpkknglyl 97 
                                   e+ + l    +lyl
  gi|15669084|ref|NP_247889.1|  93 ELTNDLIILGSLYL 106
                                   65555555555555 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   0.00031     0.079      34     112 ..      20     101 ..       6     127 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00031
                                   HHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT..........-BTCCG-S--HHHHHHHHHHHHHHHHHS--E CS
               Cob_adeno_trans  34 elnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatp.........ekkkekkkiteeeveelekeideleaelppl 105
                                   +l+s i  +r    +e+e l+ +L++i ++L d++a   +             ++ ++ + e++e+le+e ++l++++++l
  gi|15669084|ref|NP_247889.1|  20 KLESSINNLR----KENEMLRVELNKINENLQDIMALYEVVsnqinpfigV--SKITATSLEKLERLETEYKRLKKTVEEL 94 
                                   4555555555....2367888999999999999998765434467556432..2333344445899999999999999998 PP

                                   ESEEES- CS
               Cob_adeno_trans 106 ksfilpg 112
                                   ++ ++  
  gi|15669084|ref|NP_247889.1|  95 TNDLIIL 101
                                   8755544 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.4    0.0065       1.6     111     156 .]      15      60 ..       6      60 .. 0.85
   2 ?    5.4   0.1     0.063        16     112     135 ..      75      98 ..      68     120 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0065
                          Wtap 111 egrvakLeselalqkkfveelkkaleeleelleeleeevevlqstl 156
                                   e ++ kLes ++ ++k +e l+ +l++++e l+++ +  ev+++++
  gi|15669084|ref|NP_247889.1|  15 ESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQI 60 
                                   5688899999999999999999999999999999999999999886 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.063
                          Wtap 112 grvakLeselalqkkfveelkkal 135
                                   +++++Le+e + +kk+veel + l
  gi|15669084|ref|NP_247889.1|  75 EKLERLETEYKRLKKTVEELTNDL 98 
                                   455666666666666666665544 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   8.0   0.00034     0.086      17     120 ..       9     118 ..       1     140 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00034
                       zf-C4H2  17 nklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvike...aeeekekslekakklyeeykklke 94 
                                   +k+ +  + l k e+ +++ +ke e+L  E ++  e+L+ I a  + + + i+      + +  slek ++l +eyk+lk+
  gi|15669084|ref|NP_247889.1|   9 AKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQINPfigVSKITATSLEKLERLETEYKRLKK 89 
                                   5555556667788999*************************9988888887764222455667899*************** PP

                       zf-C4H2  95 evnelrse.lglekl..edleeeeeellk 120
                                   +v+el ++ ++l +l  ++l+ + +e+++
  gi|15669084|ref|NP_247889.1|  90 TVEELTNDlIILGSLylHQLDINLDEIIE 118
                                   ********544444311333333333332 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.2   0.00074      0.19      35     115 ..       3      96 ..       1     104 [. 0.63
   2 ?    2.8   0.2      0.45   1.1e+02      94     117 ..      75      98 ..      68     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00074
                       DUF1664  35 Tkrslsdavesvskqleqvseslaatkrh...Lssridrvdkkldeqkeiskeikeevt...evr.......edlseiged 102
                                   T  +l   v+++ ++l ++ +s+++ +++   L  ++++++++l++ +++ + ++++++    v+       e+l++++++
  gi|15669084|ref|NP_247889.1|   3 TTEGLLAKVNDIESKLPKLESSINNLRKEnemLRVELNKINENLQDIMALYEVVSNQINpfiGVSkitatslEKLERLETE 83 
                                   566777778888888777776666555433339999999999999999999999988762222221111112455566666 PP

                       DUF1664 103 vesvkeavegles 115
                                    + +k++ve+l +
  gi|15669084|ref|NP_247889.1|  84 YKRLKKTVEELTN 96 
                                   6666666666655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.45
                       DUF1664  94 edlseigedvesvkeavegleskl 117
                                   e+l++++++ + +k++ve+l + l
  gi|15669084|ref|NP_247889.1|  75 EKLERLETEYKRLKKTVEELTNDL 98 
                                   566666777777777777776655 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   0.00048      0.12      48      93 ..       9      54 ..       2      65 .. 0.85
   2 ?    2.5   0.2      0.82   2.1e+02      62      82 ..      75      95 ..      55     125 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00048
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHH CS
                         DUF16 48 eqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLq 93
                                   ++n +e k  k++  i++l++e +  + elnk++e l+ i+   +
  gi|15669084|ref|NP_247889.1|  9 AKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYE 54
                                  68999999999*************************9999886555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.82
                                  HHHHHHHHHHHHHHH...... CS
                         DUF16 62 ekikelkveqkaqgeelnkvd 82
                                  ek+++l+ e k  ++ ++++ 
  gi|15669084|ref|NP_247889.1| 75 EKLERLETEYKRLKKTVEELT 95
                                  233333333333333222222 PP

>> HCR  Alpha helical coiled-coil rod protein (HCR)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.6   0.00031     0.079     171     261 ..       4     101 ..       1     138 [. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                           HCR 171 aeglekslnsletkrageakqlavaqkeaellrkqlsktqeeleaqvtlveslrk....yvgeqvpp..evhs.qeweler 244
                                   +egl   +n +e k       +   +ke e+lr +l k +e+l+  ++l e +      ++g    +   +++ +  e e 
  gi|15669084|ref|NP_247889.1|   4 TEGLLAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNqinpFIGVSKITatSLEKlERLETEY 84 
                                   689999999999999999999999********************9999988655411114553322200222213456677 PP

                           HCR 245 kelldtlkhlkedradl 261
                                   k+l +t++ l +d   l
  gi|15669084|ref|NP_247889.1|  85 KRLKKTVEELTNDLIIL 101
                                   77777777777765444 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.1    0.0018      0.44      11      84 ..      14      89 ..       4      95 .. 0.73
   2 ?    2.1   0.2       1.1   2.7e+02      21      41 ..      76      96 ..      68     105 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0018
               Snapin_Pallidin 11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeya..kKLvnik.krmsslnerlqklkk 84
                                  +e+kl +l++++++lr++ e L+ +l++ ne+L+++  + e  v +++++ +   K+++    ++++l++  ++lkk
  gi|15669084|ref|NP_247889.1| 14 IESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYE-VVSNQINPFIgvSKITATSlEKLERLETEYKRLKK 89
                                  689999*****************************999888.55556665543355554432455566666666555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 1.1
               Snapin_Pallidin 21 klkelrqsQeeLleqldrlne 41
                                  kl+ l+++ + L++++++l++
  gi|15669084|ref|NP_247889.1| 76 KLERLETEYKRLKKTVEELTN 96
                                  344444444444444444444 PP

>> DMPK_coil  DMPK coiled coil domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   0.00045      0.11      33      60 ..      10      37 ..       5      38 .. 0.92
   2 ?    4.2   0.3      0.19        47      42      59 ..      78      95 ..      68      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00045
                     DMPK_coil 33 kLkeaEkknreLeeeleqLkkemEelra 60
                                  k  + E+k   Le+ +++L+ke E+lr 
  gi|15669084|ref|NP_247889.1| 10 KVNDIESKLPKLESSINNLRKENEMLRV 37
                                  77899*********************96 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.19
                     DMPK_coil 42 reLeeeleqLkkemEelr 59
                                    Le e ++Lkk +Eel 
  gi|15669084|ref|NP_247889.1| 78 ERLETEYKRLKKTVEELT 95
                                  56999**********985 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   6.3   0.00027     0.068      14     111 ..      11     108 ..       3     112 .. 0.92
   2 ?    0.1   0.1       3.6   9.2e+02      42      61 ..     118     137 ..     105     141 .] 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00027
                   TMF_TATA_bd  14 verlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEev 94 
                                   v+ ++s++ +lE+ +++l++e+e l  e ++++e + ++m+  e ++++ +    ++k  +   e++e l + ++  +  v
  gi|15669084|ref|NP_247889.1|  11 VNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQINPFIGVSKITATSLEKLERLETEYKRLKKTV 91 
                                   78899*****************************************************99999999999999999999*** PP

                   TMF_TATA_bd  95 eELraDvaDlKemykeq 111
                                   eEL +D+  l  +y  q
  gi|15669084|ref|NP_247889.1|  92 EELTNDLIILGSLYLHQ 108
                                   ******98888887776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 3.6
                   TMF_TATA_bd  42 rdeareeivklmkeneelke 61 
                                    + ++eei+k m+  ++ ++
  gi|15669084|ref|NP_247889.1| 118 EEVLEEEIIKSMSGEDTHDT 137
                                   45678889998877666555 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.2     0.017       4.2      27      69 ..       7      49 ..       5      61 .. 0.78
   2 ?    6.9   0.4     0.042        11      30      90 ..      38      99 ..      35     104 .. 0.67
   3 ?    4.5   0.3      0.22        56      22      43 ..      82     103 ..      75     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.017
                  Occludin_ELL 27 lhaeleevskkfseLerelkelkegskeykkieeeilqeykkl 69
                                  l a+++++++k+ +Le+ +++l+++++  +   ++i ++++++
  gi|15669084|ref|NP_247889.1|  7 LLAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDI 49
                                  668999****************999996666666666666655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.042
                  Occludin_ELL 30 eleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekkkrceyLkekLs 90
                                  el++++++++++ +  +  +++ + +  + +    +++kl++ ++ey++ kk +e+L + L 
  gi|15669084|ref|NP_247889.1| 38 ELNKINENLQDIMALYEVVSNQINPFIGVSKITATSLEKLERlETEYKRLKKTVEELTNDLI 99
                                  56666666666666666666666644444444455677777779999999999999999886 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.22
                  Occludin_ELL  22 keYkelhaeleevskkfseLer 43 
                                   +eYk+l++ +ee+++++  L +
  gi|15669084|ref|NP_247889.1|  82 TEYKRLKKTVEELTNDLIILGS 103
                                   4788888888888887777765 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7    0.0004       0.1      36      85 ..       5      52 ..       2      65 .. 0.76
   2 ?    1.7   0.3         1   2.6e+02      73      89 ..      78      94 ..      66     122 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0004
                       DUF2730 36 eklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleae 85
                                  e l  kv++++++l +le++++nL  ++++  L+++l++++ +l+++ a 
  gi|15669084|ref|NP_247889.1|  5 EGLLAKVNDIESKLPKLESSINNLRKENEM--LRVELNKINENLQDIMAL 52
                                  678899******************877766..667777777777766554 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1
                       DUF2730 73 adlrgelkaleaevrql 89
                                  + l+ e k l+++v++l
  gi|15669084|ref|NP_247889.1| 78 ERLETEYKRLKKTVEEL 94
                                  22333333333333332 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.6    0.0043       1.1     200     280 ..      10      89 ..       3      91 .. 0.70
   2 ?    5.4   1.0     0.028         7     168     216 ..      69     121 ..      65     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0043
                          Spc7 200 eLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkalee 280
                                   +++ + ++l +l++ i++++ke + l+ +l++++e+++++ + ++ + ++i+    v + +   s + ++rl++e+k+l++
  gi|15669084|ref|NP_247889.1|  10 KVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQINPFIGVSKIT-ATSLEKLERLETEYKRLKK 89 
                                   5677777888888888888888888888888888888888888888888887665555543.3445556666666666655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.028
                          Spc7 168 llpeleeekaeleeeleklqeaaeeles....idkeeLeelreelaelkaeie 216
                                   +     e+ ++le e+++l++ +eel++    + + +L++l  +l+e+ +e+ 
  gi|15669084|ref|NP_247889.1|  69 ITATSLEKLERLETEYKRLKKTVEELTNdliiLGSLYLHQLDINLDEIIEEVL 121
                                   55556677888888888888888888887776667888888888877777765 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.5    0.0021      0.54      18      66 ..       2      50 ..       1      54 [. 0.85
   2 ?    7.3   3.0     0.026       6.6       2      25 ..      73      96 ..      68     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0021
                          ZapB 18 dtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLL 66
                                  +t + L  ++ + + +  +l++ +++l++ene l+ e ++++e l+ ++
  gi|15669084|ref|NP_247889.1|  2 ETTEGLLAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIM 50
                                  5777788889999999999999999999999999999999999998765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.026
                          ZapB  2 slelLeqLEskiqkaidtitlLqm 25
                                  sle Le+LE+ ++ +  t+++L +
  gi|15669084|ref|NP_247889.1| 73 SLEKLERLETEYKRLKKTVEELTN 96
                                  456666666666666666666654 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3     0.045        11      66     101 ..      13      48 ..       5      51 .. 0.52
   2 ?   12.5   1.3   0.00047      0.12      29      91 ..      33      97 ..      23     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.045
                          COG2  66 glqeeleevesplaaarkkvesvreklsereeeves 101
                                   +++++l ++es+++++rk+ e +r +l++  e++++
  gi|15669084|ref|NP_247889.1|  13 DIESKLPKLESSINNLRKENEMLRVELNKINENLQD 48 
                                   444555555555555555555555555554444443 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00047
                          COG2 29 eslrrdLeaylkllekell..elvnedyadFvslSghLvglqeeleevesplaaarkkvesvrek 91
                                  e lr +L+++ + l++ ++  e+v + ++ F+ +S+      e+le++e++ ++++k ve++++ 
  gi|15669084|ref|NP_247889.1| 33 EMLRVELNKINENLQDIMAlyEVVSNQINPFIGVSKITATSLEKLERLETEYKRLKKTVEELTND 97
                                  67999**********98754499*************************************99876 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.8   0.00052      0.13       8      43 ..      13      48 ..       7      70 .. 0.84
   2 ?    4.5   1.3      0.16        39      19      39 ..      76      96 ..      64     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00052
                         Spc24  8 riakelsdleselesleselaelkeeleeleeesee 43
                                  +i  +l +les++++l++e + l+ el++++e+ ++
  gi|15669084|ref|NP_247889.1| 13 DIESKLPKLESSINNLRKENEMLRVELNKINENLQD 48
                                  6788899999*****************999999887 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.16
                         Spc24 19 elesleselaelkeeleelee 39
                                  +le+le+e ++lk+++eel +
  gi|15669084|ref|NP_247889.1| 76 KLERLETEYKRLKKTVEELTN 96
                                  445555555555555555543 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.6    0.0046       1.2      40      85 ..      11      56 ..       4      59 .. 0.89
   2 ?    4.2   0.3      0.15        38      45      75 ..      68      98 ..      57     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0046
                       DUF4446 40 gksleellkekleeveelkeeseelekeieeleeklkkslqkvglv 85
                                   +++e++l +  +++++l++e+e l+ e+++++e+l+  +  +++v
  gi|15669084|ref|NP_247889.1| 11 VNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVV 56
                                  5799********************************9988776665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.15
                       DUF4446 45 ellkekleeveelkeeseelekeieeleekl 75
                                  ++ ++ le++e+l++e ++l+k++eel+++l
  gi|15669084|ref|NP_247889.1| 68 KITATSLEKLERLETEYKRLKKTVEELTNDL 98
                                  5667789999999999999999999998765 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00077      0.19      22      50 ..       4      32 ..       1      33 [. 0.88
   2 ?   -1.5   0.1       9.3   2.4e+03      40      47 ..      43      50 ..      38      61 .. 0.62
   3 ?   -1.4   0.0       8.6   2.2e+03      29      46 ..      77      94 ..      67      98 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00077
                         HSBP1 22 sdqilsriDdMssriDdLEksiadlmtqa 50
                                  ++ +l +++d++s++  LE si++l +++
  gi|15669084|ref|NP_247889.1|  4 TEGLLAKVNDIESKLPKLESSINNLRKEN 32
                                  567899******************98775 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 9.3
                         HSBP1 40 Eksiadlm 47
                                   ++++d+m
  gi|15669084|ref|NP_247889.1| 43 NENLQDIM 50
                                  45555555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 8.6
                         HSBP1 29 iDdMssriDdLEksiadl 46
                                  ++ +++    L k++++l
  gi|15669084|ref|NP_247889.1| 77 LERLETEYKRLKKTVEEL 94
                                  444444333444444444 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   6.8    0.0003     0.076       5      58 ..      21      97 ..      18     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0003
                        Cnn_1N  5 qeeqidkLkKENFdLKLriyfLeerleklse.......................eqkeellkenielkveveslqke 58
                                  +e++i++L+KEN  L+ +++  +e+l+ +                         e+ e l+ e   lk +ve+l+++
  gi|15669084|ref|NP_247889.1| 21 LESSINNLRKENEMLRVELNKINENLQDIMAlyevvsnqinpfigvskitatslEKLERLETEYKRLKKTVEELTND 97
                                  6899*********************************9999999998666555555555555555555555555554 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.9   0.00095      0.24      63      99 ..      12      51 ..       2      65 .. 0.64
   2 ?    4.6   1.0      0.12        31      38      78 ..      75     119 ..      49     134 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00095
                  Baculo_PEP_C 63 trldtlltnLtdalnalq...dtlrneLtnlnsiltnLls 99
                                  +++++ l +L++++n+l    + lr eL+ +n +l ++++
  gi|15669084|ref|NP_247889.1| 12 NDIESKLPKLESSINNLRkenEMLRVELNKINENLQDIMA 51
                                  3566666677777777776667777777777777776654 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.12
                  Baculo_PEP_C  38 tlldaietqLnalsedlksllaeldt....rldtlltnLtdalna 78 
                                   + l+ +et+ + l++ +++l ++l       l++l  nL++ + +
  gi|15669084|ref|NP_247889.1|  75 EKLERLETEYKRLKKTVEELTNDLIIlgslYLHQLDINLDEIIEE 119
                                   223333333333333333333333224444555555555555554 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.5    0.0036       0.9       4      44 ..       9      49 ..       7      52 .. 0.89
   2 ?    6.8   1.5     0.031       7.8       3      26 ..      74      97 ..      73     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0036
                          XhlA  4 erlerietkldnleervdkleekaaeaeekiknleedlkkl 44
                                   +++ ie+kl +le+ ++ l + ++  + ++  ++e+l ++
  gi|15669084|ref|NP_247889.1|  9 AKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDI 49
                                  68999999999999999999999999999999999999988 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.031
                          XhlA  3 kerlerietkldnleervdkleek 26
                                  +e+ler+et+ + l+++v++l ++
  gi|15669084|ref|NP_247889.1| 74 LEKLERLETEYKRLKKTVEELTND 97
                                  599*************99999765 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  10.1     0.036       9.1      12      53 ..       6      67 ..       1     140 [. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.036
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....................X CS
                          YabA 12 eleeqleelleeleelkeelaelleenaeLeleneklrerl....................e 53
                                   l  +++++ ++l +l++++++l +en+ L++e +k+ e+l                    +
  gi|15669084|ref|NP_247889.1|  6 GLLAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLqdimalyevvsnqinpfigvS 67
                                  56678899999999*******************66666666444477777766666666662 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.4    0.0043       1.1       9      95 ..       8      94 ..       1     118 [. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0043
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHH CS
                    Laminin_II  9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdn 91
                                  + +++ ++++l +l+  ++n++++ + ++ +++++ne+++d +   + +++++     +       l++l+ le + + l++ 
  gi|15669084|ref|NP_247889.1|  8 LAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQINPFIGVSKITATSLEKLERLETEYKRLKKT 90
                                  45677788888888888888888888899999999999999999999888888876655555555666666666665558888 PP

                                  HHHH CS
                    Laminin_II 92 isei 95
                                  ++e+
  gi|15669084|ref|NP_247889.1| 91 VEEL 94
                                  8876 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.0    0.0046       1.2      51     129 ..      11      88 ..       2      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0046
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  51 tkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqke 129
                                    +++e+   ++++s+++  k+++     ++k++++l+ +i+ l e +++q++      ++  +  +k+++Le++ + ++
  gi|15669084|ref|NP_247889.1|  11 VNDIESKLPKLESSINNLRKENEMLRVELNKINENLQ-DIMALYEVVSNQINPFIGVSKITATSLEKLERLETEYKRLK 88 
                                   566777777778888777777777789999999***9.9************9999999999999999999999887765 PP

>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.3    0.0075       1.9      19      35 ..      14      30 ..      14      31 .. 0.93
   2 ?    3.1   0.6      0.28        70      18      35 ..      79      96 ..      77      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0075
                          YvrJ 19 iEkkLdeLtksIeeLse 35
                                  iE kL +L  sI++L++
  gi|15669084|ref|NP_247889.1| 14 IESKLPKLESSINNLRK 30
                                  8**************87 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.28
                          YvrJ 18 RiEkkLdeLtksIeeLse 35
                                  R+E+  ++L+k++eeL++
  gi|15669084|ref|NP_247889.1| 79 RLETEYKRLKKTVEELTN 96
                                  9999999*********97 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   6.7     0.075        19      10      57 ..       8      52 ..       5     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.075
                       NPV_P10 10 radikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletk 57
                                  +a ++++++k+  l++++++++++ +    l  +L++++++L+++ + 
  gi|15669084|ref|NP_247889.1|  8 LAKVNDIESKLPKLESSINNLRKENEM---LRVELNKINENLQDIMAL 52
                                  677899999999999999999987665...667777777777776652 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.8    0.0058       1.5      26      53 ..      10      37 ..       8      38 .. 0.75
   2 ?    8.4   1.3    0.0087       2.2      30      50 ..      21      41 ..      19      54 .. 0.90
   3 ?    4.9   0.8      0.11        27      32      53 ..      75      96 ..      70      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0058
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_2 26 keeeleervkeLeeeNaqLrqkveqLek 53
                                  k +++e+++ +Le+ ++ Lr+++e+L+ 
  gi|15669084|ref|NP_247889.1| 10 KVNDIESKLPKLESSINNLRKENEMLRV 37
                                  6678888888888888888888888865 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0087
                                  HHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_2 30 leervkeLeeeNaqLrqkveq 50
                                  le+ +++L++eN+ Lr ++ +
  gi|15669084|ref|NP_247889.1| 21 LESSINNLRKENEMLRVELNK 41
                                  8999***********998865 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.11
                                  HHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_2 32 ervkeLeeeNaqLrqkveqLek 53
                                  e++++Le+e  +L++ ve+L++
  gi|15669084|ref|NP_247889.1| 75 EKLERLETEYKRLKKTVEELTN 96
                                  6889999999999999999986 PP

>> CCDC92  Coiled-coil domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3      0.33        83      24      43 ..      20      39 ..      15      48 .. 0.74
   2 ?    8.1   0.8     0.009       2.3      22      45 ..      77     100 ..      74     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.33
                        CCDC92 24 gLHkEIekLqkenkdLtfkl 43
                                  +L + I++L+ken  L  +l
  gi|15669084|ref|NP_247889.1| 20 KLESSINNLRKENEMLRVEL 39
                                  55566899999999887776 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.009
                        CCDC92  22 LkgLHkEIekLqkenkdLtfklim 45 
                                   L+ L  E ++L+k++ +Lt +li+
  gi|15669084|ref|NP_247889.1|  77 LERLETEYKRLKKTVEELTNDLII 100
                                   7888899**************997 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2      0.25        63      12      48 ..      18      47 ..       7      59 .. 0.51
   2 ?    8.1   1.4     0.016         4       3      47 ..      75     120 ..      73     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.25
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-X CS
                          SlyX 12 lafqedtieeLndvvaeqqqqidrlqrqlrllaerlk 48
                                  l  +e         + + +++ + l+ +l++++e+l+
  gi|15669084|ref|NP_247889.1| 18 LPKLESS-------INNLRKENEMLRVELNKINENLQ 47
                                  3333333.......33444444444444444444444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHT- CS
                          SlyX   3 erleeLEiklafqedtieeL.ndvvaeqqqqidrlqrqlrllaerl 47 
                                   e+le+LE+++  + +t+eeL nd ++     + +l   l+++ e++
  gi|15669084|ref|NP_247889.1|  75 EKLERLETEYKRLKKTVEELtNDLIILGSLYLHQLDINLDEIIEEV 120
                                   789****************966666666666666666666666666 PP

>> DUF4806  Domain of unknown function (DUF4806)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.4      0.74   1.9e+02      13      48 ..      16      51 ..      11      69 .. 0.69
   2 ?   10.0   0.8    0.0032      0.81      10      71 ..      72     138 ..      70     141 .] 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.74
                       DUF4806 13 eelerLEaavrtdekirqqyvnyLrkikgkkadlkk 48
                                   +l +LE ++++ +k  + +  +L+ki  + +d++ 
  gi|15669084|ref|NP_247889.1| 16 SKLPKLESSINNLRKENEMLRVELNKINENLQDIMA 51
                                  678899999996666666666688888864444433 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0032
                       DUF4806  10 sseeelerLEaavrtdekirqqyvnyLrkikgk.....kadlkkvfdklftdealvnynwtGksrks 71 
                                   +s+e+lerLE++ ++ +k+ ++++n L   ++      + +l +++ +++++e++++++    + ++
  gi|15669084|ref|NP_247889.1|  72 TSLEKLERLETEYKRLKKTVEELTNDLIILGSLylhqlDINLDEIIEEVLEEEIIKSMSGEDTHDTK 138
                                   6899***********************8887768876667888999999999999998877666655 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.6     0.012       3.1      69      98 ..      19      48 ..       4      49 .. 0.86
   2 ?    1.2   0.1       3.1   7.7e+02      73      93 ..      75      95 ..      59      99 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.012
                       DUF5320 69 askeeekelLeeqaeaLeeeleaikkrlke 98
                                  ++ e++++ L+++ e+L+ el++i+++l++
  gi|15669084|ref|NP_247889.1| 19 PKLESSINNLRKENEMLRVELNKINENLQD 48
                                  677899999******************986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 3.1
                       DUF5320 73 eekelLeeqaeaLeeeleaik 93
                                  e+ e Le + + L++ +e++ 
  gi|15669084|ref|NP_247889.1| 75 EKLERLETEYKRLKKTVEELT 95
                                  555666666666666666665 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.0     0.011       2.9     112     147 ..      10      45 ..       3      59 .. 0.74
   2 ?    2.8   0.4      0.38        96     110     135 ..      74      99 ..      56     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.011
                   EMP24_GP25L 112 kletleselkkleekldsikreqkylrereerlrdt 147
                                   k++++es+l kle++++++++e ++lr   ++  + 
  gi|15669084|ref|NP_247889.1|  10 KVNDIESKLPKLESSINNLRKENEMLRVELNKINEN 45 
                                   788888888888888888888888888765554444 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.38
                   EMP24_GP25L 110 kekletleselkkleekldsikreqk 135
                                    ekle le+e k+l++ ++++ ++++
  gi|15669084|ref|NP_247889.1|  74 LEKLERLETEYKRLKKTVEELTNDLI 99 
                                   47788888888888888777776655 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0095       2.4      24      54 ..      20      50 ..       2      54 .. 0.78
   2 ?   -1.3   0.1       9.3   2.3e+03      48      52 ..      82      86 ..      68      99 .. 0.50
   3 ?    1.6   0.1       1.2     3e+02      13      36 ..     108     133 ..     100     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0095
                          YojJ 24 eleevlkaldeedeClLcelesirekfaele 54
                                  +le ++++l +e+e l  el++i e+++++ 
  gi|15669084|ref|NP_247889.1| 20 KLESSINNLRKENEMLRVELNKINENLQDIM 50
                                  5788999999999999999999999999875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 9.3
                          YojJ 48 ekfae 52
                                  ++ ++
  gi|15669084|ref|NP_247889.1| 82 TEYKR 86
                                  22222 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 1.2
                          YojJ  13 klkeeLeqiekel..eevlkaldeed 36 
                                   +l  +L +i++e+  ee++k++  ed
  gi|15669084|ref|NP_247889.1| 108 QLDINLDEIIEEVleEEIIKSMSGED 133
                                   56667888877775678999999887 PP

>> Med21  Subunit 21 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.6    0.0033      0.84      86     139 ..      14      64 ..       2      68 .. 0.85
   2 ?    2.3   0.1      0.75   1.9e+02     101     123 ..      71      93 ..      62      99 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0033
                         Med21  86 IeyLIssLPgigsseeeqeerikeLeeelreveeereekvkekeellkkveell 139
                                   Ie   s+LP+++ss ++  ++ + L  el++++e++++ +   e + ++++  +
  gi|15669084|ref|NP_247889.1|  14 IE---SKLPKLESSINNLRKENEMLRVELNKINENLQDIMALYEVVSNQINPFI 64 
                                   44...79*******************************9999999999988666 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.75
                         Med21 101 eeqeerikeLeeelreveeeree 123
                                   ++ +e++++Le+e ++ ++  ee
  gi|15669084|ref|NP_247889.1|  71 ATSLEKLERLETEYKRLKKTVEE 93 
                                   55667777888887777776655 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.6    0.0031      0.78      16      57 ..       6      47 ..       2      55 .. 0.82
   2 ?    5.2   0.5     0.083        21      30      47 ..      79      96 ..      67     102 .. 0.51
   3 ?    0.3   0.3       2.9   7.3e+02      11      20 ..     114     123 ..     113     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0031
                    TMF_DNA_bd 16 qLmeEGekLskkelklnntikkLrkknkelekeikelkkkle 57
                                   L++   + ++k  kl+ +i +Lrk+n++l  e+++ ++ l+
  gi|15669084|ref|NP_247889.1|  6 GLLAKVNDIESKLPKLESSINNLRKENEMLRVELNKINENLQ 47
                                  577777788889999999999999999999999999887776 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.083
                    TMF_DNA_bd 30 klnntikkLrkknkelek 47
                                  +l++  k+L+k+++el++
  gi|15669084|ref|NP_247889.1| 79 RLETEYKRLKKTVEELTN 96
                                  333334444444444443 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.9
                    TMF_DNA_bd  11 DeqIaqLmeE 20 
                                   De+I++++eE
  gi|15669084|ref|NP_247889.1| 114 DEIIEEVLEE 123
                                   7888888887 PP

>> DUF5595  Domain of unknown function (DUF5595)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.8       0.2        51      47      71 ..      19      43 ..       2      45 .. 0.77
   2 ?    8.3   0.2    0.0095       2.4      51      70 ..      75      94 ..      64      97 .. 0.85
   3 ?   -1.0   0.1       7.4   1.9e+03      25      36 ..     129     140 ..     126     141 .] 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.2
                       DUF5595 47 nvdeaqlesleeeekrLeeEierle 71
                                     e+ +++l +e+++L  E+++++
  gi|15669084|ref|NP_247889.1| 19 PKLESSINNLRKENEMLRVELNKIN 43
                                  4457889999999999999998875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0095
                       DUF5595 51 aqlesleeeekrLeeEierl 70
                                  ++le+le e+krL++ +e+l
  gi|15669084|ref|NP_247889.1| 75 EKLERLETEYKRLKKTVEEL 94
                                  689**************998 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 7.4
                       DUF5595  25 mqgeDtFeeeda 36 
                                   m geDt +  d+
  gi|15669084|ref|NP_247889.1| 129 MSGEDTHDTKDN 140
                                   99****998886 PP

>> DUF2497  Protein of unknown function (DUF2497)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4       2.1   5.3e+02      43      61 ..      32      49 ..       9      62 .. 0.71
   2 ?    9.2   3.3    0.0065       1.6      15      72 ..      73     127 ..      66     130 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 2.1
                       DUF2497 43 remLrpmLkeWLDenLpsl 61
                                  +emLr  L + ++enL+++
  gi|15669084|ref|NP_247889.1| 32 NEMLRVELNK-INENLQDI 49
                                  4677777776.67777666 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0065
                       DUF2497  15 afakLakavaakesressssgrtledlvrem..LrpmLkeWLDenLpslVerlVrkEIeR 72 
                                   +++kL++  ++ +     + ++t+e+l++++  L  +    LD nL +++e++ ++EI +
  gi|15669084|ref|NP_247889.1|  73 SLEKLERLETEYK-----RLKKTVEELTNDLiiLGSLYLHQLDINLDEIIEEVLEEEIIK 127
                                   4444544444443.....56899999999963367777778****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1657  (0.0924201); expected 358.6 (0.02)
Passed bias filter:                      752  (0.0419432); expected 358.6 (0.02)
Passed Vit filter:                       171  (0.00953762); expected 17.9 (0.001)
Passed Fwd filter:                        71  (0.00396006); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              71  [number of targets reported over threshold]
# CPU time: 0.75u 0.37s 00:00:01.12 Elapsed: 00:00:00.54
# Mc/sec: 792.08
//
Query:       gi|15669085|ref|NP_247890.1|  [L=342]
Description: flagella-like protein D [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-28   98.8   0.0    4.6e-28   96.9   0.0    2.0  1  Arch_fla_DE  Archaeal flagella protein
     0.0044   16.6   1.1     0.0058   16.2   1.1    1.1  1  UCH          Ubiquitin carboxyl-terminal hydrolase
  ------ inclusion threshold ------
      0.011   15.5   0.3      0.021   14.6   0.3    1.4  1  DUF3636      Protein of unknown function (DUF3636)
      0.012   15.9  10.2        1.3    9.4   0.0    4.2  5  TFIIE_beta   TFIIE beta subunit core domain


Domain annotation for each model (and alignments):
>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.0     1e-31   4.6e-28       2      95 .]     221     314 ..     220     314 .. 0.94

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 1e-31
                   Arch_fla_DE   2 ekpyLeelpedyaaelvvleWlefLvervgvenaaealdyYeeigWiseevreeLlkylkgikledeekeelk.kseltve 81 
                                   ++++L+++ped++++++v++WlefL++r+g++ + ++ldyY++igWis++v  +Ll+++k++k+ + ++eel+ +++l+++
  gi|15669085|ref|NP_247890.1| 221 KEYRLNDIPEDAVSMTLVFKWLEFLISRGGMTYLPDILDYYNKIGWISNRVILKLLRFAKNMKI-TFDEEELRpRDKLSPS 300
                                   6789***********************************************************9.4455678889****** PP

                   Arch_fla_DE  82 dHvkSllyieklag 95 
                                   dH++Sllyieklag
  gi|15669085|ref|NP_247890.1| 301 DHIVSLLYIEKLAG 314
                                   ************96 PP

>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.1   1.3e-06    0.0058      69     168 ..      45     283 ..       8     315 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-06
                                   H..SH-CCEE--HHHHHHHHHHSGGGTSSSTCEHHHHHHHHHHHHHHHHCC..HCCCHHHHHHCCCTTSHHHHHH-EEEEE CS
                                   x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           UCH  69 l..kskskavsPkklkktlsklaksfsgykqqDaqEflaflLdqlhedlnr..evaeekwkkhlkrndslitdlfegqlks 145
                                   l  + + k v+ k+l k+++++ + +s++++ D +E l+  L++l+++l++  +   ++   +++++ + i+++ + ++++
  gi|15669085|ref|NP_247890.1|  45 LknNLRGKRVTKKQLDKIVERITEVLSKGRRDDKTEELNKKLQTLEQKLDAimKLTTMAVSTKTSEEIEKIKTNEKIEIEN 125
                                   2665578899*****************************************773344444555555666666666666666 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                           UCH 146 ................................................................................. 145
                                                                                                                    
  gi|15669085|ref|NP_247890.1| 126 apikikseekpekpveievskkketmdtgkkteteekvkeievpkpvekthekveetktkgeikkevkkevklkkyelpke 206
                                   666666677788888888888888888888888888888888888888888888888888888889999999999999999 PP

                                   .........................................EEEEEEB-SEE.............EEEEESEEETEE CS
                                   .........................................xxxxxxxxxxx.............xxxxxxxxxxxx RF
                           UCH 146 .........................................klklkrlPeiL.............iihlkRfsynss 168
                                                                            +  ++ lP+iL             i++l Rf  n +
  gi|15669085|ref|NP_247890.1| 207 spmggsfmtpieeekeyrlndipedavsmtlvfkwleflisRGGMTYLPDILdyynkigwisnrvILKLLRFAKNMK 283
                                   99999999999999999999999999999999999999999999999999998888888888888888888887655 PP

>> DUF3636  Protein of unknown function (DUF3636)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3   4.8e-06     0.021      74     131 ..      55     112 ..      39     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.8e-06
                                   HHHHHHHHHHHHHHHHHS--T....TS-TTSHHHHHHHHHHHHHHHHHHHSHHHHHHH CS
                       DUF3636  74 qkavekaiidrvsnlLteepradegeakvteaeilelrleaLrvLtafarspfgslal 131
                                   +k++ + i++r++ +L+   r+d++e+  ++ ++le +l a++ Lt++a s+  s+++
  gi|15669085|ref|NP_247890.1|  55 TKKQLDKIVERITEVLSKGRRDDKTEELNKKLQTLEQKLDAIMKLTTMAVSTKTSEEI 112
                                   6788899********************************************9888776 PP

>> TFIIE_beta  TFIIE beta subunit core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2     0.046     2e+02      17      48 ..      19      48 ..      16      57 .. 0.70
   2 ?   -1.0   0.2       0.5   2.2e+03      22      48 ..      64      89 ..      40      95 .. 0.60
   3 ?    7.3   1.3    0.0013       5.7      18      55 ..      90     125 ..      78     133 .. 0.84
   4 ?    9.4   0.0   0.00028       1.3       2      56 ..     235     289 ..     234     298 .. 0.85
   5 ?   -2.3   0.0       1.2   5.5e+03      22      40 ..     319     336 ..     308     338 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.046
                    TFIIE_beta 17 gplsleeIlsylslqldlsdknwllleaLknn 48
                                  + l+ +eI++yl+  l+ +     ++ +Lknn
  gi|15669085|ref|NP_247890.1| 19 EILTEDEIEEYLD-NLKSK-LPSFVIILLKNN 48
                                  568899******9.45543.223666666666 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.5
                    TFIIE_beta 22 eeIlsylslqldlsdknwllleaLknn 48
                                  e I + ls +   +dk ++l++ L++ 
  gi|15669085|ref|NP_247890.1| 64 ERITEVLS-KGRRDDKTEELNKKLQTL 89
                                  33444444.333336666777666654 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0013
                    TFIIE_beta  18 plsleeIlsylslqldlsdknwllleaLknnpkieyDp 55 
                                     +l+ I++ + +   +s+k  + +e  k+n+kie++ 
  gi|15669085|ref|NP_247890.1|  90 EQKLDAIMKLTTM--AVSTKTSEEIEKIKTNEKIEIEN 125
                                   5678889999999..899999**************964 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.00028
                    TFIIE_beta   2 ftqLakiveylKkkdgplsleeIlsylslqldls.dknwllleaLk..nnpkieyDpk 56 
                                   +t + k  e+l +++g   l +Il+y +   +++   n+ +l++L+  +n ki++D++
  gi|15669085|ref|NP_247890.1| 235 MTLVFKWLEFLISRGGMTYLPDILDYYN---KIGwISNRVILKLLRfaKNMKITFDEE 289
                                   8999999*********************...46667789999999866899****974 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 1.2
                    TFIIE_beta  22 eeIlsylslqldls.dknwl 40 
                                   +eIl+ l +  +++  k+w+
  gi|15669085|ref|NP_247890.1| 319 SEILEMLEI--EIRrIKKWA 336
                                   589999998..666566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2511  (0.140052); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 1984.11
//
Query:       gi|15669086|ref|NP_247891.1|  [L=140]
Description: flagella-like protein E [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.3e-27   92.9   0.0    1.1e-26   92.5   0.0    1.2  1  Arch_fla_DE  Archaeal flagella protein


Domain annotation for each model (and alignments):
>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.0   6.3e-31   1.1e-26       2      95 .]      19     112 ..      18     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 6.3e-31
                   Arch_fla_DE   2 ekpyLeelp.edyaaelvvleWlefLvervgvenaaealdyYeeigWiseevreeLlkylkgikledeekeelk.kseltv 80 
                                   + ++Le++p ed++a +++l+Wle+L+er+gven++++ld+Y+ +gW+++++ ++Llk+lkgik+ dee + ++ + +l++
  gi|15669086|ref|NP_247891.1|  19 KPAKLEDIPdEDPIAIILALKWLEYLCERAGVENVSDILDFYYMLGWLGDKALAKLLKFLKGIKV-DEE-NVVEgSGKLNI 97 
                                   5789****96689***************************************************9.554.3555589**** PP

                   Arch_fla_DE  81 edHvkSllyieklag 95 
                                   +dH+ Sll+ie+l+g
  gi|15669086|ref|NP_247891.1|  98 TDHIISLLFIERLNG 112
                                   *************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.51
# Mc/sec: 833.31
//
Query:       gi|15669087|ref|NP_247892.1|  [L=139]
Description: hypothetical protein MJ_0897 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0099   15.5   0.3      0.013   15.2   0.3    1.3  1  Spherulin4      Spherulation-specific family 4
  ------ inclusion threshold ------
      0.014   15.6   0.3      0.018   15.3   0.3    1.2  1  Arch_flagellin  Archaebacterial flagellin
       0.49   10.6   3.7        2.3    8.4   0.4    2.2  2  DUF3378         Domain of unknown function (DUF3378)


Domain annotation for each model (and alignments):
>> Spherulin4  Spherulation-specific family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   2.2e-06     0.013     108     170 ..      35     105 ..      21     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-06
                                   -HHHHHHHHHHHHHHHHSTT.......STTT-EEEEE-SS-..--GGGG.GGSSEEEEEEEEHHHHHHT... CS
                    Spherulin4 108 dakyldylqritdlvkssaa.......ttkeaivihNPGtv..sedaffsrlaDyvvvfEnslaayedsgdk 170
                                   d++y +y++++++   ++         t++++i+i+N G+v    d+f   l D +vv E++ + y + +++
  gi|15669087|ref|NP_247892.1|  35 DEAYTTYYSHVHAKLNEKLVitdvkssTSQTNITIYNNGSVvvEPDKFT-ILFDGTVVPEENISYYPKLKKY 105
                                   555666666666665555557777777889*********9974444576.9**********99999887655 PP

>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3     3e-06     0.018       3     136 ..       4     118 ..       2     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-06
                                   -H.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS--E CS
                Arch_flagellin   3 vg.igtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGsspi 82 
                                   ++ +g+ +++IA+++  A ++ ++      + +++++ ++   ++++++l it +   +++       +i++  n Gs  +
  gi|15669087|ref|NP_247892.1|   4 SSvVGATVMIIALLVCGAYLYVTMDSYYENVDEAYTTYYSHVHAKLNEKLVITDVKSSTSQ------TNITIY-NNGS--V 75 
                                   5549**********************************************99987762222......468888.9995..5 PP

                                   EGGG-EEEEEESS--EE--E..................T-EE-TT-EEEEEEE- CS
                Arch_flagellin  83 dlnkttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnv 136
                                    ++ ++ +++ dg           +vv++++ ++  + +++l + + ++++vn 
  gi|15669087|ref|NP_247892.1|  76 VVEPDKFTILFDG-----------TVVPEENISYYPKLKKYLVPLDSITIVVNW 118
                                   7778888888888...........444444444444445778888888877776 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3     0.019   1.2e+02      13      42 ..      26      56 ..      22      61 .. 0.86
   2 ?    8.4   0.4   0.00038       2.3      36      51 ..      62      77 ..      58      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.019
                       DUF3378 13 kmkeyyksklrskkppyavfaakkndt.tIt 42
                                  +m +yy++  ++ +  y +  ak n+  +It
  gi|15669087|ref|NP_247892.1| 26 TMDSYYENVDEAYTTYYSHVHAKLNEKlVIT 56
                                  699*******************987654776 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00038
                       DUF3378 36 kndttItaYtSgKVlF 51
                                  +++t+It+Y++g V++
  gi|15669087|ref|NP_247892.1| 62 TSQTNITIYNNGSVVV 77
                                  689***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 908.91
//
Query:       gi|15669088|ref|NP_247893.1|  [L=154]
Description: flagella-like protein G [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-31  107.9   4.8    6.3e-31  107.8   4.8    1.0  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.018   15.1   0.1       0.44   10.6   0.1    2.3  1  DUF1573         Protein of unknown function (DUF1573)


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.8   4.8   7.1e-35   6.3e-31       1     162 [.       5     149 ..       5     151 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 7.1e-35
                                   X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS-- CS
                Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGssp 81 
                                   +++ ++++++f+A++l+AA +ag+l++++++++ +++++g+   +++s+++ei++d+gd+ +n++  +i++y+k n+G++p
  gi|15669088|ref|NP_247893.1|   5 ASSAMSEIVMFVAVLLIAAFVAGILTTSTYKISLNINKKGDALATKLSQDFEIINDPGDIVRNSSAGTIALYIK-NTGKDP 84 
                                   57789*********************************************************************.****** PP

                                   EEGGG-EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS--EEE CS
                Arch_flagellin  82 idlnkttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvpenGastti 162
                                   i +++++ +v++dg          +iv+i++t++ ++ g+++l++g+++e++vn      ++++++++++v++e G s++i
  gi|15669088|ref|NP_247893.1|  85 IIFTNDSFTVIIDG----------SIVEINTTNQLTSPGSNILSPGDVGEIVVN------YNETGYHRIKVISECGISRII 149
                                   **************..........******************************......69***************9988 PP

>> DUF1573  Protein of unknown function (DUF1573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1     5e-05      0.44      10      70 ..      61     133 ..      54     144 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5e-05
                       DUF1573  10 fgki.eegekvtatFeftNtgkaplvitn..vktsCgCttpey.........pkepiapGesgkikvtfnakg 70 
                                    g+i ++++  t+   ++Ntgk+p++ tn   +   +   +e+           + + pG+ g+i v++n +g
  gi|15669088|ref|NP_247893.1|  61 PGDIvRNSSAGTIALYIKNTGKDPIIFTNdsFTVIIDGSIVEInttnqltspGSNILSPGDVGEIVVNYNETG 133
                                   5666677777888899999999999987633222223333333334444443345689999999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1049.17
//
Query:       gi|15669089|ref|NP_247894.1|  [L=233]
Description: flagellar accessory protein FlaH [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.3e-14   51.7   0.2    9.9e-14   51.2   0.2    1.2  1  ATPase      KaiC
    1.2e-05   25.0   0.0      7e-05   22.5   0.0    1.9  1  AAA_25      AAA domain
    2.1e-05   23.9   0.2    4.9e-05   22.7   0.2    1.7  1  Rad51       Rad51
    9.2e-05   21.9   0.0    0.00012   21.5   0.0    1.4  1  DnaB_C      DnaB-like helicase C terminal domain
     0.0031   18.0   0.4     0.0075   16.7   0.4    1.6  1  AAA         ATPase family associated with various cellular ac
     0.0031   17.0   0.1        0.1   12.1   0.0    2.1  2  RecA        recA bacterial DNA recombination protein
     0.0049   15.8   0.0     0.0063   15.4   0.0    1.2  1  AAA_35      AAA-like domain
     0.0088   16.1   1.3      0.081   13.0   1.3    2.1  1  AAA_14      AAA domain
     0.0095   16.2   0.1      0.015   15.6   0.1    1.4  1  AAA_22      AAA domain
  ------ inclusion threshold ------
      0.013   14.7   0.0      0.024   13.8   0.0    1.4  1  PAXNEB      PAXNEB protein
      0.017   14.3   0.1       0.11   11.7   0.0    2.0  2  DAP3        Mitochondrial ribosomal death-associated protein 
      0.041   13.6   0.0       0.09   12.5   0.0    1.5  2  IstB_IS21   IstB-like ATP binding protein
      0.057   13.3   0.0       0.18   11.7   0.0    2.0  1  NACHT       NACHT domain
      0.093   12.2   0.3       0.13   11.7   0.3    1.3  1  Elong_Iki1  Elongator subunit Iki1
        0.1   12.0   0.0       0.18   11.3   0.0    1.3  1  KTI12       Chromatin associated protein KTI12
       0.19   12.0   0.0       0.34   11.2   0.0    1.4  1  AAA_28      AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.2   8.8e-17   9.9e-14       7     211 ..      15     210 ..      13     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 8.8e-17
                        ATPase   7 glDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiid 87 
                                    lD+ + gGip+g+ + i Ge  tGK++++++ ++  +++  + + +v++  +  +++++++sl   ++k   +g l +i 
  gi|15669089|ref|NP_247894.1|  15 DLDKRIGGGIPHGSLIIIEGEESTGKSVLCQRLAYGFLQN-RYSVTYVSTQLTTLEFIKQMNSLNYSINKKLLSGALLYIP 94 
                                   599*****************************99988777.**************************************** PP

                        ATPase  88 asesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklgvTailvsekssse 168
                                   ++   ++      +++ + ++++++e  + ++   ++ Dsi++l  ++ ++v  + l+ +++++  l+   i + +   +e
  gi|15669089|ref|NP_247894.1|  95 VYPLIAD------NKKKDGFLKKVMETRAFYEKDVIIFDSISALIANDASEVNVDDLMAFFKRITALKKIIICTVN--PKE 167
                                   ***9987......7788899999999999***************88888888888888888888877755444444..444 PP

                        ATPase 169 eaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhs 211
                                      +   +   +++  i+ +l +  ++l+   +i+k+ +++ s
  gi|15669089|ref|NP_247894.1| 168 LPESVLTIIRTSATMLIRTELFTFGGDLKNLAKILKYNMAPGS 210
                                   4444444444466666666666666666666666666666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   6.2e-08     7e-05      15     183 ..       9     163 ..       4     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.2e-08
                        AAA_25  15 laapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravge 95 
                                   ++ +   +++ ++g +p g+l+++ G + tGK++l+  la+  ++ +            V yvs+  +  e+ + +  +  
  gi|15669089|ref|NP_247894.1|   9 IDLSRDDLDKRIGGGIPHGSLIIIEGEESTGKSVLCQRLAYGFLQNR----------YSVTYVSTQLTTLEFIKQMNSLNY 79 
                                   555667788999********************************977..........49*****99999999999998888 PP

                        AAA_25  96 alrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg..densnsdvgalvealer 174
                                    ++ ++   +l++a    +p++ +++++++ ++++++++++ ++ ++ +++++D++s++ ++  +e + +d  a+++++  
  gi|15669089|ref|NP_247894.1|  80 SIN-KK---LLSGAL-LYIPVYPLIADNKKKDGFLKKVMET-RAFYEKDVIIFDSISALIANdaSEVNVDDLMAFFKRITA 154
                                   873.22...233222.2467777777888889999999887.555889**********99997666667778888888888 PP

                        AAA_25 175 iarrtgaav 183
                                   +++   ++v
  gi|15669089|ref|NP_247894.1| 155 LKKIIICTV 163
                                   877776766 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2   4.3e-08   4.9e-05      16      59 ..       6      49 ..       3     161 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.3e-08
                                  S-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHH CS
                         Rad51 16 llqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcv 59
                                  l ++     +lD+ +gGGi+ gs+  i Ge  +Gk+ lc+ l+ 
  gi|15669089|ref|NP_247894.1|  6 LARIDLSRDDLDKRIGGGIPHGSLIIIEGEESTGKSVLCQRLAY 49
                                  5667777889******************************9985 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.1e-07   0.00012       7      82 ..      14      88 ..       9     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.1e-07
                                  HHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHT CS
                                  xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  7 kdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtg 82
                                  +dLDk + +G+ +g liii +  s+Gk++l+  +a    + ++ +v+++s   ++ + ++++ s + +i++k l +g
  gi|15669089|ref|NP_247894.1| 14 DDLDKRIgGGIPHGSLIIIEGEESTGKSVLCQRLAYGFLQ-NRYSVTYVSTQLTTLEFIKQMNSLNYSINKKLL-SG 88
                                  6899766267999***********************9885.6779*******************9999976655.34 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.4   6.7e-06    0.0075       2     121 ..      31     174 ..      30     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.7e-06
                                   EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCS.SS........................STTHHHHHHHHHHHH CS
                           AAA   2 llyGppGtGKTllakavakel.....gvefleisgsell.sk........................yvgesekkirelfke 52 
                                   ++ G   tGK+ l++ +a  +     +v+++++++++l   k                         + + +kk  +++k+
  gi|15669089|ref|NP_247894.1|  31 IIEGEESTGKSVLCQRLAYGFlqnrySVTYVSTQLTTLEfIKqmnslnysinkkllsgallyipvyPLIADNKKKDGFLKK 111
                                   677899999999999999995444444666665555555333577788888889999999999998444555555666666 PP

                                   HHHTS...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS CS
                           AAA  53 akeka...kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr 121
                                   + e +   ++ ++++D i al+ ++       +e  v+ L++++++ +  ++  i+i++ n p++l++ +l 
  gi|15669089|ref|NP_247894.1| 112 VMETRafyEKDVIIFDSISALIAND------ASEVNVDDLMAFFKRITALKK--IIICTVN-PKELPESVLT 174
                                   5444448778***********9999......8889999*********99866..6666555.5566655554 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   9.1e-05       0.1      40      71 ..      15      45 ..       4      85 .. 0.87
   2 ?    3.3   0.0     0.044        49     133     156 ..     122     145 ..     108     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.1e-05
                                  HHHHHTSSSSEETTSEEEEEESTTSSHHHHHH CS
                          RecA 40 aldialGiGGlpkGriieiyGpessGkttlal 71
                                   ld  +G GG+p+G +i i G es+Gk+ l+ 
  gi|15669089|ref|NP_247894.1| 15 DLDKRIG-GGIPHGSLIIIEGEESTGKSVLCQ 45
                                  5788899.*******************99875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.044
                                   SEEEEE-TTT---STT-------- CS
                          RecA 133 dlivvdsvaalvpkaeieGemgds 156
                                   d+i+ ds++al+ ++  e +++d 
  gi|15669089|ref|NP_247894.1| 122 DVIIFDSISALIANDASEVNVDDL 145
                                   9***********998877777653 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.6e-06    0.0063      30      85 ..      26      81 ..       9     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.6e-06
                        AAA_35 30 pGalirikapkkmGKtSLlarilakakqqgyktvsldlqladkeilsdldkflrwf 85
                                  +G+li i++ + +GK+ L +r+     q++y++ +++ ql+  e++++++++   +
  gi|15669089|ref|NP_247894.1| 26 HGSLIIIEGEESTGKSVLCQRLAYGFLQNRYSVTYVSTQLTTLEFIKQMNSLNYSI 81
                                  69*********************************************999876555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.3   7.2e-05     0.081       4      60 ..      29      86 ..      26     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                        AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.l 60
                                  +++i+G   +GK++l+++l++  l ++ s+ y++ +  +++ +++ ++l+  i +k l
  gi|15669089|ref|NP_247894.1| 29 LIIIEGEESTGKSVLCQRLAYGFLQNRYSVTYVSTQLTTLEFIKQMNSLNYSINKKlL 86
                                  789*****************99999999999999888777544444434444444422 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.4e-05     0.015       5      45 ..      27      61 ..      25     163 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfv 45
                                   +++++ Ge  tGK++l++rl++ + +       r +v +v
  gi|15669089|ref|NP_247894.1| 27 GSLIIIEGEESTGKSVLCQRLAYGFLQN------RYSVTYV 61
                                  6899*******************99764......2222222 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.1e-05     0.024      24      84 ..      14      73 ..      13      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                        PAXNEB 24 psLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkh.evlvlsldddpeewlre 84
                                  ++LDk +gGG+p Gs+++ie +++t  ++vL++  lA G +q++ +v+++s + ++ e++++
  gi|15669089|ref|NP_247894.1| 14 DDLDKRIGGGIPHGSLIIIEGEEST-GKSVLCQR-LAYGFLQNRySVTYVSTQLTTLEFIKQ 73
                                  58*****************977554.46677665.788888887678888876666666665 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.4e-05      0.11      26      51 ..      30      54 ..      26      87 .. 0.84
   2 ?    0.6   0.0      0.22   2.5e+02     161     188 ..     140     168 ..     104     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.4e-05
                                  EEEE-SSSSSTTTTHHHHHHHGGGS- CS
                          DAP3 26 lvltGekgsGKSvlLlqalayAlekg 51
                                  ++++Ge+ +GKSv L+q lay++ ++
  gi|15669089|ref|NP_247894.1| 30 IIIEGEESTGKSV-LCQRLAYGFLQN 54
                                  69**********8.8********996 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.22
                                   EEEE-GGGGSS-.BS---TTS--B-GGGB CS
                          DAP3 161 vtvDglnallkn.tkyksadkkpihahdL 188
                                   v vD+l a++k+ t++k+     +++++L
  gi|15669089|ref|NP_247894.1| 140 VNVDDLMAFFKRiTALKKIIICTVNPKEL 168
                                   67999999999999999988888887775 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.1e-05      0.09      49     145 ..      29     126 ..      24     147 .. 0.79
   2 ?    0.1   0.0      0.52   5.8e+02      95     126 ..     105     138 ..      89     162 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.1e-05
                     IstB_IS21  49 nivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaral.krllkvdllilDdlgllpldqaeae 128
                                    i++ G   +GKs l   l++   ++ +sv++v+++  +++l+  ++ ++l+  + k+ll  +ll +  + l   ++++  
  gi|15669089|ref|NP_247894.1|  29 LIIIEGEESTGKSVLCQRLAYGFLQNRYSVTYVSTQ--LTTLEFIKQMNSLNYSInKKLLSGALLYIPVYPLIADNKKKDG 107
                                   57899****************************987..5678888888888766514566668888888888877777777 PP

                     IstB_IS21 129 llfeviekr..yerrsiii 145
                                    l +v+e r  ye+  ii 
  gi|15669089|ref|NP_247894.1| 108 FLKKVMETRafYEKDVIIF 126
                                   7778887766677777765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.52
                     IstB_IS21  95 rdgklar..alkrllkvdllilDdlgllpldqae 126
                                   +dg l++  + +++ + d++i D ++ l  ++a+
  gi|15669089|ref|NP_247894.1| 105 KDGFLKKvmETRAFYEKDVIIFDSISALIANDAS 138
                                   4444444004556778899999998877666655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.18       2     134 ..      29     170 ..      28     196 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC..-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCSC CS
                         NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqga..fklvFflslrelsrsgnarsladllfsqlpepaapvsevwavllelp 80 
                                   l+i++Ge   GK++L q+la    ++++   +   +      l +l+ ++++ sl + + ++l+  a    +v  +++ ++
  gi|15669089|ref|NP_247894.1|  29 LIIIEGEESTGKSVLCQRLAYGFLQNRYSVTYvsTQ------LTTLEFIKQMNSLNYSINKKLLSGALLYIPVYPLIADNK 103
                                   79*******************999999655433322......233333333334444444444333333333232332222 PP

                                   CC..EE..............EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHH CS
                         NACHT  81 er..lL..............lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrd 134
                                   ++   L              +i+D++  l + +    + +v++l+   +++    +  ++ tv p+ l++
  gi|15669089|ref|NP_247894.1| 104 KKdgFLkkvmetrafyekdvIIFDSISALIANDAS--EVNVDDLM-AFFKRITALKKIIICTVNPKELPE 170
                                   22111133333333333444888888888875544..66677766.555554444555555555555544 PP

>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00012      0.13      90     151 ..     112     182 ..      36     204 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                    Elong_Iki1  90 k.......kkalviiDslnplas....likeeslaaflssllsspsvslvavYHtdveyapspltlLkylAtt 151
                                           +k ++i+Ds+++l++      + ++l+af++++++ +++ +++v  +++    s lt+++  At 
  gi|15669089|ref|NP_247894.1| 112 VmetrafyEKDVIIFDSISALIAndasEVNVDDLMAFFKRITALKKIIICTVNPKEL--PESVLTIIRTSATM 182
                                   03333466999********9988899877899**********988998888766666..33445555555555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016      0.18       3      41 ..      29      67 ..      28      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                  EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                         KTI12  3 LvvltGlPssGKstrakeLakaleeekrsvvviddeslg 41
                                  L+++ G  s+GKs + ++La  + ++ +sv++++++   
  gi|15669089|ref|NP_247894.1| 29 LIIIEGEESTGKSVLCQRLAYGFLQNRYSVTYVSTQLTT 67
                                  9*********************************98766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0003      0.34       2      21 ..      30      53 ..      29      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                        AAA_28  2 ivitGgestGKTtlleaLa....a 21
                                  i+i G estGK+ l+++La    +
  gi|15669089|ref|NP_247894.1| 30 IIIEGEESTGKSVLCQRLAygflQ 53
                                  89****************965553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1707.37
//
Query:       gi|15669090|ref|NP_247895.1|  [L=551]
Description: type II secretion system protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-45  155.6   0.0      2e-45  155.0   0.0    1.2  1  T2SSE         Type II/IV secretion system protein
    0.00059   19.5   0.0     0.0016   18.2   0.0    1.7  1  AAA_29        P-loop containing region of AAA domain
     0.0083   16.2   0.0      0.021   14.9   0.0    1.6  1  YaiA          YaiA protein
  ------ inclusion threshold ------
      0.015   15.0   0.2       0.03   14.1   0.2    1.4  1  DUF4303       Domain of unknown function (DUF4303)
      0.018   15.3   0.0      0.057   13.7   0.0    1.9  1  AAA_22        AAA domain
      0.019   14.7   0.1        0.1   12.3   0.0    2.0  2  AAA_15        AAA ATPase domain
      0.027   15.0   0.0      0.055   14.0   0.0    1.5  1  ABC_tran      ABC transporter
      0.041   13.8   0.0      0.093   12.7   0.0    1.7  1  Microtub_bd   Microtubule binding
       0.17   11.6   0.1        2.7    7.7   0.0    2.4  2  DEAD          DEAD/DEAH box helicase
       0.21   10.9   0.0       0.54    9.6   0.0    1.6  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
       0.22   11.9   0.0          1    9.7   0.0    2.0  2  AAA_16        AAA ATPase domain
        0.3   11.5   3.6       0.18   12.3   1.2    1.8  2  AAA_23        AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.0   0.0   1.3e-48     2e-45      10     244 ..     178     416 ..     170     440 .. 0.93

  Alignments for each domain:
  == domain 1  score: 155.0 bits;  conditional E-value: 1.3e-48
                         T2SSE  10 ddekvsdihvekpervkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllPvvag 90 
                                   +d+   dihv  p ++ v  ++ g+   ++   ++ +l+  ++++   +++ +s+ +p++d++lp +g r++++    v  
  gi|15669090|ref|NP_247895.1| 178 RDPYLEDIHVIGPKNCHVVHKIFGMLPTNITWEDEIELADYLKNLGERMGRPVSDANPIVDGTLP-DGSRINIIYSTDVSP 257
                                   567789*********7777888888999*************************************.999999987654443 PP

                         T2SSE  91 ..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEi 169
                                     ++++iRk +   +++ +l+  ++++ ++a+ l   ++  ++i + G T sGKtt+l+a+l +i+ +  +i   ED+ E+
  gi|15669090|ref|NP_247895.1| 258 kgPSFTIRKFTDVPISVTQLISWGTFSTEVAAYLWLCLEYGMSIFICGETASGKTTTLNAILPFIKPN-SKIFSCEDTPEV 337
                                   379**********************************999**************************99.************ PP

                         T2SSE 170 qleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagalerLe 244
                                   ++ ++   ql+++     + +vt+ dllraaLR rP  i+vGEiR  e++ + +A++TGH++ lsT Ha ++ + ++rL+
  gi|15669090|ref|NP_247895.1| 338 KPPHPVWQQLVTRergpeESRVTLFDLLRAALRSRPNYIIVGEIRSVEAAVAFQAMQTGHPV-LSTFHAANVRKMIQRLN 416
                                   *************9***99*******************************************.***************97 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     1e-06    0.0016       4      51 ..     275     327 ..     272     330 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1e-06
                        AAA_29   4 lqlvNWgtfdghtie....idlkg.atlltGpsGsGKSTllDAiqalLvpakk 51 
                                    ql+ Wgtf+ +++       + g ++++ G++ sGK+T l Ai   + p++k
  gi|15669090|ref|NP_247895.1| 275 TQLISWGTFSTEVAAylwlCLEYGmSIFICGETASGKTTTLNAILPFIKPNSK 327
                                   699*******97654111133467899*****************998888875 PP

>> YaiA  YaiA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.4e-05     0.021       4      42 ..     338     378 ..     336     390 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                          YaiA   4 kPPYPReakivtvekGtagktvtwYeL.RaD.hPkPdtLis 42 
                                   kPP+P   ++vt e+G+ +  vt+++L Ra    +P+ +i 
  gi|15669090|ref|NP_247895.1| 338 KPPHPVWQQLVTRERGPEESRVTLFDLlRAAlRSRPNYIIV 378
                                   9************************9647752578887775 PP

>> DUF4303  Domain of unknown function (DUF4303)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2     2e-05      0.03      88     126 ..     105     142 ..      84     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                       DUF4303  88 dnefeleekefeafrdklleamvkAlkeldkeglfgkgq 126
                                    ++ +++e efe++  +l++a+ k+ +++ +eg+f++  
  gi|15669090|ref|NP_247895.1| 105 EETPKSVE-EFEEVLTRLFNACTKVTEAVGEEGFFQRIF 142
                                   33444444.**************************9975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.8e-05     0.057       5     100 ..     298     381 ..     295     429 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseellealeq 84 
                                     +++++Ge+ +GKTt+l+ +l   +       +++++++++ + +   +  ++++l+     +    + s+  l+++l+ 
  gi|15669090|ref|NP_247895.1| 298 GMSIFICGETASGKTTTLNAILPFIK-------PNSKIFSCEDTPEVkPPHPVWQQLVTRERGP----EESRVTLFDLLRA 367
                                   5689****************999984.......2444444444444445666666666555433....3357888888888 PP

                        AAA_22  85 alraravielliiDEa 100
                                   alr+r     +i+ E+
  gi|15669090|ref|NP_247895.1| 368 ALRSRPN--YIIVGEI 381
                                   8888877..7777776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.56   8.4e+02     234     283 ..      93     156 ..      61     174 .. 0.53
   2 ?   12.3   0.0   6.9e-05       0.1      27      54 ..     302     329 ..     295     377 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.56
                        AAA_15 234 l.............eeelteklkeiqeklkeidkklaeelk....kilkkkidkikkfnykgkknee 283
                                   +             + ++ e+++e+++ l ++  k++   +    + +++ i+ + + ++k+ ++e 
  gi|15669090|ref|NP_247895.1|  93 MilnkilelapyeeTPKSVEEFEEVLTRLFNACTKVT---EavgeEGFFQRIFRFADNKIKITPEER 156
                                   0222223334433333333444444444444444433...133366666666666666666666665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6.9e-05
                        AAA_15  27 vliGkNnsGKSsilealdlFlnnkekkn 54 
                                   +++G+ +sGK++ l+a+  F++ ++k +
  gi|15669090|ref|NP_247895.1| 302 FICGETASGKTTTLNAILPFIKPNSKIF 329
                                   89********************997766 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.6e-05     0.055       6      45 ..     293     332 ..     290     364 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-05
                                   EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilld 45 
                                   l l+ g  + i Ge+ +GK+t l++++   kp++    ++
  gi|15669090|ref|NP_247895.1| 293 LCLEYGMSIFICGETASGKTTTLNAILPFIKPNSKIFSCE 332
                                   6789999********************9999976655555 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.2e-05     0.093      67     102 ..     283     317 ..     235     330 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.2e-05
                                   CCCCCHHHHHHHHTT--EEEEEEES........... CS
                   Microtub_bd  67 vfeeisqlvqsaldgynvcifaygqTGsGKtyTmeg 102
                                   +  e+++++  +l +y ++if +g+T sGKt T+++
  gi|15669090|ref|NP_247895.1| 283 FSTEVAAYLWLCL-EYGMSIFICGETASGKTTTLNA 317
                                   5678888888888.599****************976 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       0.2     3e+02      44      65 ..      69      90 ..      54     129 .. 0.83
   2 ?    7.7   0.0    0.0018       2.7      10      33 ..     294     319 ..     285     338 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.2
                                  TSTS-EEEEEESSHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 44 gktgpkalivePtreLaeqtln 65
                                   +t++k +++ePt e ae+ l+
  gi|15669090|ref|NP_247895.1| 69 PETKTKYIVIEPTLETAEEKLK 90
                                  578889*********9998775 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0018
                                   HHHTTCEEEEEESTTSSHHHH..HHH CS
                                   xxxxxxxxxxxxxxxxxxxxx..xxx RF
                          DEAD  10 lilgggdvlvaaeTGsGKTla..fli 33 
                                   ++  g ++++++eT+sGKT+   +++
  gi|15669090|ref|NP_247895.1| 294 CLEYGMSIFICGETASGKTTTlnAIL 319
                                   4457889************8733444 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00036      0.54      42      60 ..     301     319 ..     292     320 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00036
                                   EEEE--TTSSHHHHHHHHH CS
                  FtsK_SpoIIIE  42 llvaGatgsGKStalntLi 60 
                                   + ++G t sGK+t+ln+++
  gi|15669090|ref|NP_247895.1| 301 IFICGETASGKTTTLNAIL 319
                                   68**************985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.7   4.1e+03      62     119 ..      84     141 ..      70     164 .. 0.59
   2 ?    9.7   0.0   0.00067         1      26      88 ..     300     359 ..     294     414 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.7
                        AAA_16  62 qlesaipysalaqalareellrqlldeaesaeleawrekleealaavpelagaea..srl 119
                                     e+++ y ++++ +   el   ++++++  e+e+  ++l  a + v e+ g+e   +r+
  gi|15669090|ref|NP_247895.1|  84 TAEEKLKYKMILNKI-L-ELAPYEETPKSVEEFEEVLTRLFNACTKVTEAVGEEGffQRI 141
                                   445556677766666.4.677777777666666666666666666666666665555444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00067
                        AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                   ++++ Ge ++GK++ ++++l  ++ +  if  +++ +     p  +++q+l ++e   ++ + 
  gi|15669090|ref|NP_247895.1| 300 SIFICGETASGKTTTLNAILPFIKPNSKIFSCEDTPEV---KPPHPVWQQLVTRERGPEESRV 359
                                   799*****************777777444433333333...5556766666555554444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.3   6.4e+03     167     173 ..      94     100 ..      38     156 .. 0.62
   2 ?   12.3   1.2   0.00012      0.18      23      39 ..     302     318 ..     298     319 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.3
                        AAA_23 167 dekklle 173
                                     +k le
  gi|15669090|ref|NP_247895.1|  94 ILNKILE 100
                                   2222222 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00012
                        AAA_23  23 lItGpNGaGKTTildAi 39 
                                    I+G++ +GKTT l+Ai
  gi|15669090|ref|NP_247895.1| 302 FICGETASGKTTTLNAI 318
                                   7***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3611.39
//
Query:       gi|15669091|ref|NP_247896.1|  [L=562]
Description: flagellar assembly protein J [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-20   71.8   0.0    2.9e-12   46.6   0.1    4.0  4  T2SSF     Type II secretion system (T2SS), protein F
     0.0071   16.6  10.0     0.0071   16.6  10.0    3.8  2  EI24      Etoposide-induced protein 2.4 (EI24)


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.2   7.1         2   1.8e+04     103     121 ..      29      47 ..      20      62 .. 0.60
   2 !   46.6   0.1   3.2e-16   2.9e-12       1     122 [.      83     210 ..      83     213 .. 0.97
   3 ?   -2.4   0.5      0.48   4.3e+03     106     117 ..     273     284 ..     267     288 .. 0.48
   4 !   31.3   0.0   1.8e-11   1.6e-07       1     119 [.     338     460 ..     338     466 .. 0.75

  Alignments for each domain:
  == domain 1  score: -7.2 bits;  conditional E-value: 2
                                   HTTXXXXXXXXXXXXXXXX CS
                         T2SSF 103 lepllllvvallvllilla 121
                                   +  ++l+++++++++ +++
  gi|15669091|ref|NP_247896.1|  29 ITSIVLILLGFMLFSGIIL 47 
                                   4444444444444444444 PP

  == domain 2  score: 46.6 bits;  conditional E-value: 3.2e-16
                                   HHHHHHHHHHTT--HHHHHHHHHHHHS.SHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT CS
                         T2SSF   1 flrqlatllsaGvplveaLellaeeae.ngplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageegg 75 
                                   f++ ++tl+ + ++  + L++l+ee e  g+la+e ++++   + +g sl+ea +    rtpssef++++++l  a ++g 
  gi|15669091|ref|NP_247896.1|  83 FITKFGTLSITDLNRKDLLKILSEEREeLGELAKESEKLYVLTDKWGrSLAEACRflaqRTPSSEFADFLDRLAYALDSGE 163
                                   7889999999*********************************9988899******************************* PP

                                   -HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXX CS
                         T2SSF  76 nLaevLerlaeyleeerelrrkllaallepllllvvallvllillai 122
                                    L e+L + ++ ++++++  +k+++ +l    +l+v ++ ++++++ 
  gi|15669091|ref|NP_247896.1| 164 ELKEFLIKEQDIVMDDYAAFYKRMLYSLDMYKELYVSAMTSIAFFLA 210
                                   ******************************************99975 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.48
                                   XXXXXXXXXXXX CS
                         T2SSF 106 llllvvallvll 117
                                   ++++++++++l+
  gi|15669091|ref|NP_247896.1| 273 IISVILVVILLP 284
                                   233333333333 PP

  == domain 4  score: 31.3 bits;  conditional E-value: 1.8e-11
                                   HHHHHHHHHH.TT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC.......T-TT.TS-HHHHHHHHHHHH CS
                         T2SSF   1 flrqlatlls.aGvplveaLellaeeaengplaeelkriarrlraGgslseale.......rtpssefpelvvqliragee 73 
                                   flr+l+  +s  G ++v +Le+l++++ +gpl+  +kr+++rl+ G++ +++++       ++    +  + + ++r +  
  gi|15669091|ref|NP_247896.1| 338 FLRSLGDSVSaKGGGMVSSLEYLSNHD-FGPLTHDIKRLYKRLALGIDSNKSWRlfgfdscSY---LIQLFSDIFSRCIYF 414
                                   7888888888689**************.**************************998864433...447777777777777 PP

                                   HT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXX CS
                         T2SSF  74 ggnLaevLerlaeyleeerelrrkllaallepllllvvallvllil 119
                                   gg+   + e +++++++  +lr+ +  ++ + + +++ ++  l++ 
  gi|15669091|ref|NP_247896.1| 415 GGDPKTAAEIISKNFRKIVQLRKSKYQNIQQFVGVVYGLGGGLALA 460
                                   7777777777777777777777666666666666665544444433 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6  10.0   7.9e-07    0.0071      13     136 ..      17     245 ..      11     263 .. 0.62
   2 ?  -14.2  20.0         2   1.8e+04      15      64 ..     268     315 ..     255     561 .. 0.50

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.9e-07
                                   TTTHHHHHHHHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH................ CS
                          EI24  13 pkllallllplllnlllfllllvlllwvllasllvllllllplwlfplvalllaapfygllaekv................ 77 
                                   + +l  ++lp l+++++++ll           + ++++++l+++l+  + +l++a+ y+ +a                   
  gi|15669091|ref|NP_247896.1|  17 RDYLLRIVLPALITSIVLILL----------GFMLFSGIILYIYLLLPIIILVSAIGYPYIALDSqknkinerlhifitkf 87 
                                   6678999************88..........89999999999999999999999999999998885555554444444444 PP

                                   ..................HH.H..................................H........................ CS
                          EI24  78 ..................ekrh..................................l........................ 82 
                                                     e  +                                  +                        
  gi|15669091|ref|NP_247896.1|  88 gtlsitdlnrkdllkilsE--EreelgelakeseklyvltdkwgrslaeacrflaqRtpssefadfldrlayaldsgeelk 166
                                   4444444444444444441..044555555555555555555555555554444440444444444455555555555566 PP

                                   .........................CCTTSHH.HHHHHHHHHHHHHHHHHHHHHTTHHH....HHHHHHHHHHHHHHHHH CS
                          EI24  83 .........................glvksla.eslkslllllllllvllplliPvvglilsplllswltayfycfeyld 136
                                                            ++ k+l  ++++s++++l + + l p+l+P+  +++++++l+ ++a ++ + ++ 
  gi|15669091|ref|NP_247896.1| 167 eflikeqdivmddyaafykrmlyslDMYKELYvSAMTSIAFFLAFSI-LVPFLLPYNFVFMATIALFAFFAVELLIVVVI 245
                                   66666676667777766664444455555555344444444443333.33334499999999999999998877766655 PP

  == domain 2  score: -14.2 bits;  conditional E-value: 2
                                   THHHHHHHHHHHHHHHHHHHHHHH......-....TTHHHHHHHHHHHHHHHHHH.HHHHH CS
                          EI24  15 llallllplllnlllfllllvlll......w....vllasllvllllllplwlfp.lvall 64 
                                   l+++l+++++l ++l+ +ll++ +      +    +             ++++   ++ l+
  gi|15669091|ref|NP_247896.1| 268 LRKWLIISVILVVILLPFLLWAKYivglspFsqmpY-------------MILVALgFTPLA 315
                                   555555555555555553433333322222022221.............111111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 3505.80
//
Query:       gi|15669092|ref|NP_247897.1|  [L=238]
Description: hypothetical protein MJ_0902 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-16   59.7  11.8    6.5e-16   58.7  11.3    1.8  1  Peptidase_A24    Type IV leader peptidase family
    4.7e-07   30.2   1.1    4.7e-07   30.2   1.1    4.2  4  Arc_PepC_II      Archaeal Peptidase A24 C-terminus Type II


Domain annotation for each model (and alignments):
>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7  11.3   7.2e-20   6.5e-16       1     105 [.       9     132 ..       9     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 7.2e-20
                 Peptidase_A24   1 lvlltillvlsviDldtrtlpdeltlpllllgvlfaqllllglpnlaqavlgalvgalvllli.slvdeqamGgGDvklaa 80 
                                   +v ++ ll++s+ Dl++r+++d+++++++++g++++  +l+ + + + +v++ +vg++v++++ +++ + ++GgGD kl++
  gi|15669092|ref|NP_247897.1|   9 IVGAIGLLIASIYDLKSREIEDYVWVSMVIFGLIYN-GYLSFISHDMLYVIQSIVGFIVCFFLgFFMFLLGVGGGDGKLIM 88 
                                   578999*****************************9.678899999999999999999999964444555*********** PP

                 Peptidase_A24  81 vlgaflgwerl...................llavlvaillgavl 105
                                   +lga+++ +++                   +++v++a+++ + l
  gi|15669092|ref|NP_247897.1|  89 GLGALIPKYNMpihtplgailnylylpsfpIMVVINAMFFSITL 132
                                   **********9999999999999999999888888888888776 PP

>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2     0.072   6.5e+02      57      73 ..      23      38 ..      16      50 .. 0.73
   2 ?    0.6   0.9     0.093   8.4e+02      69      90 ..      50      71 ..      40      78 .. 0.72
   3 ?   -4.0   1.6         2   1.8e+04      76      84 ..     120     128 ..     115     138 .. 0.48
   4 !   30.2   1.1   5.3e-11   4.7e-07      55      91 ..     194     226 ..     151     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.072
                   Arc_PepC_II 57 ykkkglieetvWvtygv 73
                                  +k+++ ie+ vWv+  +
  gi|15669092|ref|NP_247897.1| 23 LKSRE-IEDYVWVSMVI 38
                                  45555.9999***9755 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.093
                   Arc_PepC_II 69 vtygvPflipitaGfiialvlG 90
                                  +++ + ++i  ++Gfi+ ++lG
  gi|15669092|ref|NP_247897.1| 50 ISHDMLYVIQSIVGFIVCFFLG 71
                                  6666667777777777777776 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 2
                   Arc_PepC_II  76 lipitaGfi 84 
                                   ++ i a f 
  gi|15669092|ref|NP_247897.1| 120 MVVINAMFF 128
                                   555544433 PP

  == domain 4  score: 30.2 bits;  conditional E-value: 5.3e-11
                   Arc_PepC_II  55 kkykkkglieetvWvtygvPflipitaGfiialvlGD 91 
                                   +k+ k++    ++Wvt+++Pf++pi+++++++ ++GD
  gi|15669092|ref|NP_247897.1| 194 SKFDKNE----EIWVTPAIPFVVPIFLSYLLTSIIGD 226
                                   5555555....8************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1528.49
//
Query:       gi|15669093|ref|NP_247898.1|  [L=643]
Description: hypothetical protein MJ_0903 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.7   0.3        3.6    7.8   0.2    2.7  2  DUF4115   Domain of unknown function (DUF4115)


Domain annotation for each model (and alignments):
>> DUF4115  Domain of unknown function (DUF4115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.016   2.8e+02       7      18 ..     171     182 ..     169     215 .. 0.73
   2 ?    7.8   0.2    0.0002       3.6       5      20 ..     572     587 ..     568     593 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.016
                       DUF4115   7 adsWveVrdadG 18 
                                   a++W++V+d d+
  gi|15669093|ref|NP_247898.1| 171 AKVWINVKDGDN 182
                                   579*****8886 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0002
                       DUF4115   5 atadsWveVrdadGkv 20 
                                   ++ d+W+eV d+dGkv
  gi|15669093|ref|NP_247898.1| 572 VDCDVWIEVIDKDGKV 587
                                   5669***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3998.84
//
Query:       gi|15669094|ref|NP_247899.1|  [L=195]
Description: hypothetical protein MJ_0904 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2339  (0.130459); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1232.64
//
Query:       gi|15669095|ref|NP_247900.1|  [L=111]
Description: hypothetical protein MJ_0905 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-36  121.5   0.5    1.1e-35  121.3   0.5    1.0  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
  ------ inclusion threshold ------
      0.068   12.9   0.0      0.068   12.9   0.0    1.5  2  DUF4364   Domain of unknown function (DUF4364)
        0.1   10.9   0.0       0.13   10.6   0.0    1.1  1  DUF505    Protein of unknown function (DUF505)


Domain annotation for each model (and alignments):
>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.3   0.5   1.8e-39   1.1e-35       1      90 []      10      98 ..      10      98 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 1.8e-39
                       DUF1495  1 ilrslnkSkvRkkvllyLysiypeksnlqeisrrvrskpsnvkGaleGmgkrynsessLielGLveeeeeseglklYklteeG 83
                                  i+rslnkSk+Rkk+l+ Ly++yp+  +l+eisrrvrs+psnv G+l+Gm+ ryn++ sLielGLv e+ e+ g+k+Yklt++G
  gi|15669095|ref|NP_247900.1| 10 IIRSLNKSKLRKKILYLLYKMYPHGIYLSEISRRVRSDPSNVLGCLKGMNGRYNGHFSLIELGLV-ECVERGGVKIYKLTDYG 91
                                  89***************************************************************.69*************** PP

                       DUF1495 84 ieivevl 90
                                  ++ivevl
  gi|15669095|ref|NP_247900.1| 92 KKIVEVL 98
                                  ****986 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.8       2.1   1.3e+04       5      12 ..      23      30 ..      22      31 .. 0.86
   2 ?   12.9   0.0   1.1e-05     0.068      42      76 ..      67     101 ..      65     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 2.1
                       DUF4364  5 ilYllkkv 12
                                  ilYll+k+
  gi|15669095|ref|NP_247900.1| 23 ILYLLYKM 30
                                  89999987 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.1e-05
                       DUF4364  42 eLvesglieeeekenktlykiTekGketlelfenr 76 
                                    L+e gl+e+ e+ + ++yk+T+ Gk+++e ++++
  gi|15669095|ref|NP_247900.1|  67 SLIELGLVECVERGGVKIYKLTDYGKKIVEVLKDQ 101
                                   59999*************************99986 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   2.2e-05      0.13     382     406 ..      72     100 ..      61     109 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.2e-05
                        DUF505 382 ev....eekgkevyvlTeyGekvledqek 406
                                    +    e+ g ++y lT+yG+k++e ++ 
  gi|15669095|ref|NP_247900.1|  72 GLvecvERGGVKIYKLTDYGKKIVEVLKD 100
                                   33333366788888888888888776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 787.77
//
Query:       gi|15669096|ref|NP_247901.1|  [L=366]
Description: hypothetical protein MJ_0906 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-17   62.6   0.2      3e-16   59.6   0.0    2.1  2  Methyltransf_31  Methyltransferase domain
      2e-09   38.0   0.0    4.6e-09   36.9   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    6.8e-09   36.4   0.0    4.2e-08   33.8   0.0    2.3  2  Methyltransf_12  Methyltransferase domain
      4e-08   33.8   0.0    2.1e-07   31.5   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
    2.1e-07   30.9   0.0    3.4e-07   30.3   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    4.3e-06   26.6   0.0    6.3e-06   26.1   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    8.6e-06   25.3   0.2    3.3e-05   23.3   0.0    2.0  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.001   18.4   0.0     0.0017   17.7   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0086   15.6   0.0      0.015   14.8   0.0    1.4  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.029   13.8   0.0      0.062   12.7   0.0    1.5  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.22     4e+02      63      85 ..     127     149 ..      97     166 .. 0.67
   2 !   59.6   0.0   1.7e-19     3e-16       1     142 [.     200     338 ..     200     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.22
               Methyltransf_31  63 ieeleklledekfDlilsnevl..n 85 
                                    +el+  ++  kfD i+s+ v+  n
  gi|15669096|ref|NP_247901.1| 127 DFELN--IKMPKFDKIISDYVMkyN 149
                                   22333..45579******9988542 PP

  == domain 2  score: 59.6 bits;  conditional E-value: 1.7e-19
               Methyltransf_31   1 ldkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlils 80 
                                   +dkg ++lD+GCG+ +  + + + ++p+++++G+Dis+  ++ A+ + ++l  d +e++  d+++ ++k    ek+D+i++
  gi|15669096|ref|NP_247901.1| 200 IDKGDYILDVGCGS-RSPKYFIDMIYPEGHYMGVDISKGLLQIAECRIKRLYCDSYELKNIDFTKiIPK----EKYDYIIC 275
                                   58999*********.5555555599****************************************9994....89****** PP

               Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedprllaelpakveeeskayevvegakigt.qkd 142
                                     ++ + ++++++l+++ + +++gg + i++  +l+++  + +e  ++y+ +++   g+  ++
  gi|15669096|ref|NP_247901.1| 276 SHTMIYAPSLKQFLNKMMSSIHSGGKIFISEEFILDKNENICKEVFEFYNRLNKRFRGYySEK 338
                                   ****************************99999899999888888887755555444545444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   2.6e-12   4.6e-09       1      97 []     206     300 ..     206     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.6e-12
                                   EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                   +Ld+GcG+ r  +++ + + ++++++gvDis+++l++a+ r+++  + + e+ + d++++  +++++D++++s+++ +   
  gi|15669096|ref|NP_247901.1| 206 ILDVGCGS-RSPKYFIDMIyPEGHYMGVDISKGLLQIAECRIKRLYCdSYELKNIDFTKII-PKEKYDYIICSHTMIYA-- 282
                                   8******9.5666666666589********************9888899**********86.5679******9777774.. PP

                                   HHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                   + l+++l+++ + +  gG
  gi|15669096|ref|NP_247901.1| 283 PSLKQFLNKMMSSIHSGG 300
                                   6899*******9999998 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.8   3.3e+03      37      77 ..     111     147 ..      95     158 .. 0.59
   2 !   33.8   0.0   2.4e-11   4.2e-08       1      99 []     207     302 ..     207     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.8
               Methyltransf_12  37 keklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                   k ++ k+e+++ + +e ++l++       +fD +++  v+ 
  gi|15669096|ref|NP_247901.1| 111 KLEILKYEDEKIKINEDFELNIKM----PKFDKIISDYVMK 147
                                   455555555555555555555433....3777777666554 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 2.4e-11
               Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                   L++GcG+ +  +++ + + p+ +y gvDis+  ++ a+ ++++     ++ +el+++d  +  +++++D++++s+++ + +
  gi|15669096|ref|NP_247901.1| 207 LDVGCGS-RSPKYFIDMIyPEGHYMGVDISKGLLQIAECRIKRLY---CDSYELKNIDFTKIIPKEKYDYIICSHTMIYAP 283
                                   8*****5.55555555556***************88888877777...678888888888888889*************** PP

               Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                    ++++l+++ + +  gG++
  gi|15669096|ref|NP_247901.1| 284 SLKQFLNKMMSSIHSGGKI 302
                                   **************99985 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.2   2.1e+03      24      72 ..     103     147 ..      92     159 .. 0.66
   2 !   31.5   0.0   1.2e-10   2.1e-07       1      96 []     207     304 ..     207     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                                   EES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CC CS
               Methyltransf_11  24 vDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlh 72 
                                   +D+ k++lkl   k+++e++k   + +d+e l+++  +fD ++s  v+ 
  gi|15669096|ref|NP_247901.1| 103 LDYIKTALKLEILKYEDEKIK---INEDFE-LNIKMPKFDKIISDYVMK 147
                                   677777777777777777755...677777.566666677777766544 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 1.2e-10
                                   EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhvedpe 78 
                                   LdvGcG+ +    +   +  ++++gvD+sk +l++a+ ++++ +  + e+   d++k+ ++++++D +++s+++ + + ++
  gi|15669096|ref|NP_247901.1| 207 LDVGCGSRSPKYFIDMIYpeGHYMGVDISKGLLQIAECRIKRLYCdSYELKNIDFTKI-IPKEKYDYIICSHTMIYAPSLK 286
                                   8****9766555555445889*********************9988888899999996.8899****************** PP

                                   HHHHHHHHHEEEEEEEEE CS
               Methyltransf_11  79 kalkeiaRvLkpgGllvi 96 
                                   ++l++++     gG+++i
  gi|15669096|ref|NP_247901.1| 287 QFLNKMMSSIHSGGKIFI 304
                                   **************9986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.9e-10   3.4e-07      20     161 ..     200     350 ..     185     354 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.9e-10
               Methyltransf_23  20 lraggrvLdiGcGtGi...llevlrengfsvtgvDlspeaveiae...........kakkaqkdqfdeqeaaepqgkfdlI 86 
                                    ++g  +Ld+GcG+ +   + + + ++g ++ gvD+s  + +iae           + k+  +++        p++k+d+I
  gi|15669096|ref|NP_247901.1| 200 IDKGDYILDVGCGSRSpkyFIDMIYPEG-HYMGVDISKGLLQIAEcrikrlycdsyELKNIDFTKI------IPKEKYDYI 273
                                   578889********95455666666665.699******9999997777655555544444444444......4999***** PP

               Methyltransf_23  87 vlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldw..lylvpagrhisffsarslkelleeaGle 161
                                   ++++++   p++   l+++ + +  gG +++se    +k+++  +++   y + + r + ++s++++ ++le  G++
  gi|15669096|ref|NP_247901.1| 274 ICSHTMIYAPSLKQFLNKMMSSIHSGGKIFISEEFILDKNENICKEVfeFYNRLNKRFRGYYSEKDIVDILESLGYD 350
                                   *********************************77778899998887656889999999************999985 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   3.5e-09   6.3e-06      63     151 ..     192     278 ..     138     311 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.5e-09
                                   HHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SE CS
                          PCMT  63 alalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPY 143
                                    +a ++l+++kg+ +L+vG+Gs      +  ++ ++g+ ++++ +k l + a+ ++k+l  ++  ++  D +k  +++  Y
  gi|15669096|ref|NP_247901.1| 192 EIASDYLKIDKGDYILDVGCGSR-SPKYFIDMIYPEGHYMGVDISKGLLQIAECRIKRLYCDSYELKNIDFTKIIPKE-KY 270
                                   46789*****************6.5678999****************************9999998888877766554.57 PP

                                   EEEEESSB CS
                          PCMT 144 daihvgaa 151
                                   d i+ + +
  gi|15669096|ref|NP_247901.1| 271 DYIICSHT 278
                                   77766544 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.51   9.2e+02     162     193 ..     124     153 ..     106     157 .. 0.74
   2 !   23.3   0.0   1.8e-08   3.3e-05      17     153 ..     172     306 ..     164     361 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.51
                                   HHHHHHHHHH.HHHHHHHHHHS-HHHHHHHHH CS
               Ubie_methyltran 162 lsqayelyskevlPvlGkllakdldsyryLve 193
                                   +++ +el  k  +P++ k++++ + +y+++++
  gi|15669096|ref|NP_247901.1| 124 INEDFELNIK--MPKFDKIISDYVMKYNFITH 153
                                   4456666666..9*******999999999875 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 1.8e-08
                                   HHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTS CS
               Ubie_methyltran  17 askyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegk 97 
                                    ++ D  + +ls   + l ++   +     +g  +lDv +G+      + d++  +g+ +++Di++ +L+++e ++k+   
  gi|15669096|ref|NP_247901.1| 172 KKDPDIWDMILSSPYYSLCREIASDYLKIDKGDYILDVGCGSRSP-KYFIDMIYPEGHYMGVDISKGLLQIAECRIKRLYC 251
                                   5667888889999999999**99******************9875.56889**************************9877 PP

                                   STEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
               Ubie_methyltran  98 inieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                    + e+ + +  ++   ++ +D++  s+ +   +  ++ L++++  +  GG++++ e
  gi|15669096|ref|NP_247901.1| 252 DSYELKNIDFTKI-IPKEKYDYIICSHTMIYAPSLKQFLNKMMSSIHSGGKIFISE 306
                                   7666655555554.56789********************************99876 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   9.3e-07    0.0017      53     176 ..     193     316 ..     183     330 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.3e-07
                                   HHHTTTT--TT-EEEEES-TTSH..HHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-..----S CS
                          CMAS  53 lileklelkpGmtlLdiGcGWGs..lvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedl..dekvd 129
                                   ++ + l++++G+++Ld+GcG  s   ++ ++   + + +g+ +Sk   + a+ r+++l   ++ e+k  d+  +  +ek+d
  gi|15669096|ref|NP_247901.1| 193 IASDYLKIDKGDYILDVGCGSRSpkYFIDMIYP-EGHYMGVDISKGLLQIAECRIKRLY-CDSYELKNIDFTKIipKEKYD 271
                                   67789***************8761145556655.89*******************9997.78999******9985456*** PP

                                   EEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHH CS
                          CMAS 130 rvvsvgafehvgkenydtffkklkkllkedGllllhtitslhkkela 176
                                    ++       +   ++++f +k+ + ++++G + +   ++l+k+e+ 
  gi|15669096|ref|NP_247901.1| 272 YIICSHT--MIYAPSLKQFLNKMMSSIHSGGKIFISEEFILDKNENI 316
                                   9875443..366789999*************9999887777777665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   8.6e-06     0.015      27     143 ..     198     310 ..     191     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.6e-06
                                   CHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE--- CS
                           MTS  27 lpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsNPP 106
                                   l+ ++ + +lD+GcG       +   +pe +   vd+++  l++a+  +++  ++  e+ + d ++ ++++k+d+i++   
  gi|15669096|ref|NP_247901.1| 198 LKIDKGDYILDVGCGSRSPKYFIDMIYPEGHYMGVDISKGLLQIAECRIKRLYCDsYELKNIDFTKIIPKEKYDYIICS-- 276
                                   66667788***********************************************9*********************95.. PP

                                   STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTS CS
                           MTS 107 fhagkatelavaeeliaeAkeaLkegGeLliVanrkl 143
                                      ++ +     ++++++  +  ++gG+++i  +  l
  gi|15669096|ref|NP_247901.1| 277 ---HTMIYAPSLKQFLNKMMSSIHSGGKIFISEEFIL 310
                                   ...2233344566777777777777777776555555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.5e-05     0.062     159     272 ..     200     319 ..     187     330 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                          PrmA 159 vkegeevlDvGtGSGiLaiaaakLg.akkvvavDiDevAvkvakeNaelNkvea.klevalseellkeekadvivaN...I 234
                                   + +g+ +lDvG+GS        ++    + ++vDi +  +++a+  +++  +++ +l+ +   +++ +ek+d i++    I
  gi|15669096|ref|NP_247901.1| 200 IDKGDYILDVGCGSRSPKYFIDMIYpEGHYMGVDISKGLLQIAECRIKRLYCDSyELKNIDFTKIIPKEKYDYIICShtmI 280
                                   3466799*******88776666654156889******************99999766554444444459******966669 PP

                          PrmA 235 LaevlielaedikklvkeggllilSG.ilkekaeevaea 272
                                    a  l ++++++++ +++gg + +S   + +k+e+++++
  gi|15669096|ref|NP_247901.1| 281 YAPSLKQFLNKMMSSIHSGGKIFISEeFILDKNENICKE 319
                                   ********************9988843667777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2396.70
//
Query:       gi|15669097|ref|NP_247902.1|  [L=286]
Description: chondro-6-sulfatase regulatory protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-19   69.9   0.2    1.9e-17   64.1   0.2    2.1  2  Radical_SAM     Radical SAM superfamily
    1.5e-12   48.0   0.4    2.3e-12   47.4   0.4    1.3  1  Fer4_12         4Fe-4S single cluster domain
      7e-10   39.1   1.5    1.5e-09   38.0   1.5    1.5  1  Fer4_14         4Fe-4S single cluster domain
     0.0074   16.3   0.3       0.02   14.9   0.3    1.8  1  DUF4980         Domain of unknown function (DUF4980)
  ------ inclusion threshold ------
      0.025   14.2   0.4      0.065   12.9   0.4    1.7  1  PUF             Pumilio-family RNA binding repeat
      0.077   12.9   0.1       0.11   12.4   0.1    1.2  1  CTP_transf_3    Cytidylyltransferase
       0.32   11.5   3.9        0.4   11.3   0.8    2.6  3  EF-G-binding_N  Elongation factor G-binding protein, N-termin


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.2   7.5e-21   1.9e-17       2     166 ..      11     170 ..      10     171 .. 0.89
   2 !    8.8   0.0   0.00078         2      80     139 ..     153     210 ..     150     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 7.5e-21
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC..CCTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla..vpgiri 80 
                                    vt+ Cnl+C++C+ + +  ++++  +++  + ++ +  l  +     + ++ggepll+ +++e++  ++     + +i  
  gi|15669097|ref|NP_247902.1|  11 KVTNRCNLNCIYCYANNK--NNKDMDFKTAKNAIDYLLNL-DN--QIKIQFTGGEPLLNFNLIEKIVDYCNDNysNCNIQY 86 
                                   589*************63..66666666666666666666.34..899***********************99******** PP

                                   EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeel 160
                                   ++ tn+tl++e+++e+++el    v ++++ +   ++l++ + ++++  ++l+++ +l++++i+  + +++++ + n   l
  gi|15669097|ref|NP_247902.1|  87 AIQTNATLINEKIAEKIKELD-IKVGISIDGLEINDILRPYKnGKPSTLDTLKGMYILKSYNIP--FGITTVVTNKNLPYL 164
                                   *********************.***********999****************************..888888888888888 PP

                                   HHHHHH CS
                                   xxxxxx RF
                   Radical_SAM 161 eellel 166
                                   ee++++
  gi|15669097|ref|NP_247902.1| 165 EEFVKY 170
                                   888776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00078
                                   EEEEECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  80 itvetngtlpd.eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklre 139
                                   +tv+tn  lp+ ee+++ l   gv  +s++l  + ++++l lm   +++ee+ ++l kl +
  gi|15669097|ref|NP_247902.1| 153 TTVVTNKNLPYlEEFVKYLIAFGVKSISFDLLKPKKKEHLTLM---PNIEEFNKLLNKLGR 210
                                   7999*****99**************************999999...799999888888765 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.4     9e-16   2.3e-12      11     117 ..      12     116 ..       2     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 9e-16
                       Fer4_12  11 fvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk.esiegltllGGEPllpenaeallelvkevkeekpekdiwl 90 
                                    +++Cnl+C +C++++    k++k++++++++++i+ l + ++++++ ++GGEPll  n + + ++v+++  ++++   + 
  gi|15669097|ref|NP_247902.1|  12 VTNRCNLNCIYCYANN----KNNKDMDFKTAKNAIDYLLNlDNQIKIQFTGGEPLL--NFNLIEKIVDYCNDNYSN-CNIQ 85 
                                   4789*********665....5566666666666666655548889***********..*****************6.7999 PP

                       Fer4_12  91 ytgytleelskkekeellkeid....vlvdG 117
                                   y   t+ +l +++  e +ke+d    + +dG
  gi|15669097|ref|NP_247902.1|  86 YAIQTNATLINEKIAEKIKELDikvgISIDG 116
                                   *********9999999999999444445566 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   1.5   5.9e-13   1.5e-09       5     116 ..      13     115 ..      10     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 5.9e-13
                       Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw. 84 
                                   +++Cnl+C  C+ +++ ++++  + +++ ++  l    +++ikiq   +tGGePL   n + + k+v++  ++y + +i+ 
  gi|15669097|ref|NP_247902.1|  13 TNRCNLNCIYCYANNKNNKDMDFKTAKNAIDYLL--NLDNQIKIQ---FTGGEPL--LNFNLIEKIVDYCNDNYSNCNIQy 86 
                                   79**********8888888888888889998888..566666556...*******..889999999999999998877752 PP

                       Fer4_14  85 .letngtleielektpdlkekleals.kidllvd 116
                                    ++tn+tl  +    ++  ek++ l+ k+ +++d
  gi|15669097|ref|NP_247902.1|  87 aIQTNATLI-N----EKIAEKIKELDiKVGISID 115
                                   278999887.2....2345555666655555555 PP

>> DUF4980  Domain of unknown function (DUF4980)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.3   7.6e-06      0.02      13      57 ..       5      49 ..       2     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.6e-06
                       DUF4980 13 kkylLLPvqesaeeakvkviknnkavkelnvrLavdkvdYyvPld 57
                                   k l+L v ++ +   +   +nnk +k+++ + a++ +dY + ld
  gi|15669097|ref|NP_247902.1|  5 MKHLILKVTNRCNLNCIYCYANNKNNKDMDFKTAKNAIDYLLNLD 49
                                  58899***********************************98775 PP

>> PUF  Pumilio-family RNA binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   2.6e-05     0.065       3      30 ..      68      96 ..      67      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                                  GGGHHHHHTSTTHHHHHHHHHHH.SCHHH CS
                           PUF  3 kgnlvqLstdqyGnyvvQklleh.ateeq 30
                                  ++++v++++d y n+ +Q+ +++ at+ +
  gi|15669097|ref|NP_247902.1| 68 IEKIVDYCNDNYSNCNIQYAIQTnATLIN 96
                                  789*******************9888766 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.1e-05      0.11      63     134 ..      23      90 ..      11     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.1e-05
                                   EEE--TTCSSHHHHHHHHHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTTSSEEEEEEETTSHH CS
                  CTP_transf_3  63 vlvtrsslesdterflevvkaflmseneeiivnlqGdnPllqeevikkaietlkenqedylstlvkkvgkee 134
                                   ++   ++ ++ +  +++   ++l + +++i ++ +G +Pll+  +i+k++++ ++n     s+++ ++  ++
  gi|15669097|ref|NP_247902.1|  23 CYANNKNNKDMDFKTAKNAIDYLLNLDNQIKIQFTGGEPLLNFNLIEKIVDYCNDNY----SNCNIQYAIQT 90 
                                   55555555555556666677788888999**************************93....44444444333 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.8   1.5e+04      61      76 ..      34      49 ..      33      52 .. 0.71
   2 ?   11.3   0.8   0.00015       0.4       6      51 ..      64     109 ..      63     151 .. 0.80
   3 ?   -0.2   0.0      0.59   1.5e+03      48      78 ..     184     211 ..     161     214 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.8
                EF-G-binding_N 61 diktkekaeklLeeLk 76
                                  d kt ++a  +L +L 
  gi|15669097|ref|NP_247902.1| 34 DFKTAKNAIDYLLNLD 49
                                  6677788888887775 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00015
                EF-G-binding_N   6 qYnfIkkqveqllnayrsvnDkkvveavkalaaekIlelfpelsee 51 
                                   ++n+I+k v+  +  y+++n +  +++   l++ekI e  +el  +
  gi|15669097|ref|NP_247902.1|  64 NFNLIEKIVDYCNDNYSNCNIQYAIQTNATLINEKIAEKIKELDIK 109
                                   69************************************99998765 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.59
                EF-G-binding_N  48 lseeqkelLeqiddik.tkekaeklLeeLkey 78 
                                   l++++ke L    +   + e+++klL++L  y
  gi|15669097|ref|NP_247902.1| 184 LKPKKKEHL----TLMpNIEEFNKLLNKLGRY 211
                                   455555555....2333667888888888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1828.32
//
Query:       gi|15669098|ref|NP_247903.1|  [L=1232]
Description: cobalamin biosynthesis protein CobN [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
          0 1337.1   0.0          0 1336.9   0.0    1.0  1  CobN-Mg_chel   CobN/Magnesium Chelatase
    0.00072   19.3   0.0     0.0022   17.7   0.0    1.8  1  LexA_DNA_bind  LexA DNA binding domain
  ------ inclusion threshold ------
       0.08   13.0   0.0       0.41   10.7   0.0    2.3  1  DUF3921        Protein of unknown function (DUF3921)
        0.1   12.8   3.1         11    6.3   0.0    3.8  4  PI_PP_I        Phosphoinositide phosphatase insertion domain
       0.11   12.5   0.0       0.25   11.3   0.0    1.5  1  HTH_Crp_2      Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1336.9   0.0         0         0       2    1088 ..     117    1213 ..     116    1214 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1336.9 bits;  conditional E-value: 0
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel    2 aYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewyk.kakkekaptvgilfyra 79  
                                    +Yl ++gv N+knll yla+++ +  + e+e+p+++p++giy   + ++fe+l++yl+++k    + ++p +g+lfyr+
  gi|15669098|ref|NP_247903.1|  117 KYLGYEGVYNYKNLLLYLANRFGN-LNVEYEEPRPMPWQGIYY--KGKYFETLDDYLNYLKeLGRDLDKPIIGVLFYRN 192 
                                    7*********************97.66699************8..789***********997778899*********** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel   80 hllagntavidaliraleerglnvlpvfvssl..d...seaqealeelftkegeekvdalinttsfalvkgpaeeeeee 153 
                                     ++a+n++++++li+ +e++g+ +++vf+s+l  +     + e+++++f+k+g++ v alintt+f+l++g ++e  ++
  gi|15669098|ref|NP_247903.1|  193 WFVANNIDYVNDLIDIIENKGAIPIAVFSSHLknElgsIGTLETFKRFFYKDGKPIVHALINTTMFTLSMGVKAELLKD 271 
                                    ********************************8625558889999999**********************998776654 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx.xxxxxxxxxxxxx RF
                  CobN-Mg_chel  154 aeeealkelnvPvlqailssqsreeWeessqGlspldlamsvalpEldGriepvvisfke..eee.eetevekyepipe 229 
                                    +  e lkelnvP+lq+i+s++ +e+W++s +Gl+p dl + +a+pE+dG+i++++i++ke  ++      + ky++i++
  gi|15669098|ref|NP_247903.1|  272 E-PEFLKELNVPILQGIISTGFIEDWKKSVSGLNPIDLIIGMAMPEFDGAIIHFPIGGKEkiKDGeVGVPIIKYRAIRD 349 
                                    4.3347*****************************************************9763334777889******* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  230 rvervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeGYdveelpesgdeLiell 308 
                                    r+e+++dla r+a+L+ k+n++kk+aii++nypp+++++++a gLd+p+S+vn+Lk++k++G+ v+e+p++g+eLi+++
  gi|15669098|ref|NP_247903.1|  350 RAEKIVDLALRYANLKLKSNKDKKIAIIFHNYPPRNDKIASAFGLDSPESVVNILKEMKKRGFIVDEIPKNGTELIKKM 428 
                                    *****************************************************************999*********** PP

                                    xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  309 leggtndpew...eelkvgaaallpaeeYeewfeeLpeelreeveerWgeppgemveeeksgekklvipglqlGnvfvg 384 
                                    l+ +tnd++    e++k +a+ ++++e+Ye+wf++L+e++++e++++Wg+ pg    + ++ +++l+ipg+  Gnvf+ 
  gi|15669098|ref|NP_247903.1|  429 LNYATNDKRFlteEMIK-KAVGKVKKEDYEKWFNSLSEKVKQELIKNWGAIPG----DVMNFDGELIIPGIINGNVFIS 502 
                                    *********99955556.***********************************....677789**************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  385 vQPargyeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwlPGKqvglseecyPdillgdlPhlYp 463 
                                    vQP+rg++e+ps++yh+pdlpPth Y+AfY+W++++f+ada++H+GkHG+lEwlPGK vgls+ecyPdi++ +lP++Yp
  gi|15669098|ref|NP_247903.1|  503 VQPPRGFGENPSAIYHSPDLPPTHYYIAFYKWIKDVFKADAIMHIGKHGNLEWLPGKCVGLSNECYPDICM-ELPNIYP 580 
                                    *********************************************************************96.8****** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  464 YivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeaesldperlkalreqilelveelnldkdlg 542 
                                    +ivnnpgEGtqAKRRsyA+ii+Hl+Ppmt ++lyg+l eLe+ id+Y+e+e++  e+++ l+++il++++el+ld+dl 
  gi|15669098|ref|NP_247903.1|  581 FIVNNPGEGTQAKRRSYATIISHLIPPMTISDLYGDLVELEKSIDDYYETENK--EKKEFLKKEILKKIKELKLDEDLL 657 
                                    *************************************************8766..78999******************7 PP

                                    ..xxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  543 ..leea..keeeeeefeellekldgyleelkeaqirdglhilGeapegeqlvdlvvailrleneegesltealaealgl 617 
                                      +     +e ++e+fe+ll+k+++yle lk++qi+dglhi+G + eg++lv+++  i+r++     ++ e lae l +
  gi|15669098|ref|NP_247903.1|  658 dgK--VidEEINDENFEKLLNKIHDYLETLKNRQINDGLHIMGVPLEGDKLVNMLFMIIRYQ----FNYLEILAEILDY 730 
                                    442..23367889**********************************************885....6677777777766 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxx RF
                  CobN-Mg_chel  618 dldeleeksekelrtagdalealeeeaeelveelleeeaeeeeaeaeeleeeeeeeee.............eteeEita 683 
                                    +++el+e++     +++++l++++e   +l++e+++ +++e+++++ ++ + +++ ++             + +eEi +
  gi|15669098|ref|NP_247903.1|  731 SWEELNENK----GKYHKILDEINEIGLNLLKEYMQYNFDENKIDELKTVKINSKLRDvlktvstiyknlmKVDEEIIN 805 
                                    676655444....456899*********************9999988888888877779***********9999***** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  684 llraLdGeyippgpsGdptrgraevLPTGrNfysvDpraiPteaAwevGkklaeellerylqehgeyPekvglslwgte 762 
                                     ++aL+G yipp  +G+pt++ + +LPTGrNfys++p++iPt++A+e+Gkklae+l+++yl+e+g+yPe +g+++wg+ 
  gi|15669098|ref|NP_247903.1|  806 AVNALEGFYIPPRVAGAPTKDIN-CLPTGRNFYSCNPQEIPTKSAYEMGKKLAEDLINKYLKEEGKYPEYIGVIVWGSP 883 
                                    ********************965.******************************************************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  763 tmrteGediAqiLallGvrPvwdaagrvvdlelipleeLgRPRiDVtvriSGffRDafpnlielldkavelvaeldEpe 841 
                                    tmrt+G+di++iL+llGv+Pvw+++grvv+le+ipleeLgRPRiDVt+riSG+fRD+fpn++el+d+a+++va+ldEp+
  gi|15669098|ref|NP_247903.1|  884 TMRTKGDDIGEILYLLGVKPVWNKMGRVVGLEVIPLEELGRPRIDVTLRISGLFRDTFPNVVELIDEAIKMVANLDEPD 962 
                                    ******************************************************************************* PP

                                    xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  842 edNfvrkhvleeeaeleeke....eaeeratyRvFgskpGaYgagvqeliessnWedeedLaeaYlnwssyaYgkgaeg 916 
                                    e+N+v+kh++ee +e  +k+    +a+e++ yR+F++kpG Ygagv++li+++nWe+ ed+a++Y++w++yaYgkg +g
  gi|15669098|ref|NP_247903.1|  963 EMNYVKKHYREEVEEKIKKGidekTAKETSLYRIFSDKPGCYGAGVSHLIDEKNWESIEDFAKVYVEWGGYAYGKGYYG 1041
                                    ***************999555423556**************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  917 eeaeeafearLkrvdvvvqnqdsrehdlldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvrtlkeeiarel 995 
                                    +ea+e f +rL++++++v+n+ds+e+d+++ dd+ +++GGl+a+v+ +sgkkp +y+gd+snp+++++++lkee +  +
  gi|15669098|ref|NP_247903.1| 1042 VEAKEEFINRLSKIELTVKNEDSQEWDIFEGDDFNSYHGGLIASVTYYSGKKPVSYVGDTSNPNDIRTKHLKEEGKEIF 1120
                                    ******************************************************************************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  996 rsrvlNPkWiegmmrhGykGafelaatvdnlfgwdatadvvddwvyeevaetYvlDeevrefleekNpwAlreiaerLl 1074
                                    r++++NPkWiegm+rhGykGa ++++ vd++f+wdat++++ddw+ye++ae+Yv+D++++ef++e+Np+Al +i+erLl
  gi|15669098|ref|NP_247903.1| 1121 RTKIMNPKWIEGMKRHGYKGAADFSKYVDHMFAWDATSGIIDDWMYEKIAEKYVFDKDMEEFFKENNPYALLNITERLL 1199
                                    ******************************************************************************* PP

                                    xxxxxxxxxxxxxx RF
                  CobN-Mg_chel 1075 EaarrglWeaseet 1088
                                    Ea++rg+W+a+ee+
  gi|15669098|ref|NP_247903.1| 1200 EAIERGMWKADEEM 1213
                                    ***********985 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   6.1e-07    0.0022      22      56 ..     379     413 ..     373     419 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.1e-07
                                   HSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSE CS
                 LexA_DNA_bind  22 tgypPsireiaralglkSpsaveehLkaLerKGyi 56 
                                   + ypP    ia a+gl Sp++v + Lk ++++G+i
  gi|15669098|ref|NP_247903.1| 379 HNYPPRNDKIASAFGLDSPESVVNILKEMKKRGFI 413
                                   68*******************************98 PP

>> DUF3921  Protein of unknown function (DUF3921)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.41      20      56 ..     403     439 ..     400     441 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                       DUF3921  20 lGkeldlqGvvvdeiqkaqeeyLsaLsyetlidkryL 56 
                                   + ke++ +G +vdei k   e +  +   +  dkr+L
  gi|15669098|ref|NP_247903.1| 403 ILKEMKKRGFIVDEIPKNGTELIKKMLNYATNDKRFL 439
                                   669****************9999865555557***98 PP

>> PI_PP_I  Phosphoinositide phosphatase insertion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.6   5.8e+03      13      65 ..     160     216 ..     157     226 .. 0.64
   2 ?    6.3   0.0    0.0031        11      56      92 ..     450     485 ..     404     490 .. 0.73
   3 ?    4.4   0.2     0.012        42       8      56 ..     757     805 ..     753     813 .. 0.90
   4 ?   -2.0   0.0       1.2   4.2e+03      49      74 ..    1111    1136 ..    1105    1139 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.6
                                   HHHHHC--TT--SHHHHHHHHHH......HHHHHHHHHHH-SSHHHHHHHHHCT-SS-- CS
                       PI_PP_I  13 qaYflnleskeaslkklkqdlnq......fllkWeeikktslsLeedLnkiannktplP 65 
                                     Yf +l+   + lk+l +dl +      f  +W     ++++  +dL +i +nk  +P
  gi|15669098|ref|NP_247903.1| 160 GKYFETLDDYLNYLKELGRDLDKpiigvlFYRNWF--VANNIDYVNDLIDIIENKGAIP 216
                                   56777777777777777777766333333444443..3556677788888887776666 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0031
                                   HHHCT-SS--HHHHTS-HH.HHHHHHHHT.T..SCCCH CS
                       PI_PP_I  56 kiannktplPsWfnelska.qqellrvlaeaklsveei 92 
                                   k+++  +++ +Wfn+ls++ +qel++       +v ++
  gi|15669098|ref|NP_247903.1| 450 KVKK--EDYEKWFNSLSEKvKQELIKNWGAIPGDVMNF 485
                                   4444..56********9653789999876555555555 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.012
                                   S-HHHHHHHHC--TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHH CS
                       PI_PP_I   8 LeeyqqaYflnleskeaslkklkqdlnqfllkWeeikktslsLeedLnk 56 
                                   L+ey+q  f + +++e ++ k++++l + l++ ++i k+ +++ e++ +
  gi|15669098|ref|NP_247903.1| 757 LKEYMQYNFDENKIDELKTVKINSKLRDVLKTVSTIYKNLMKVDEEIIN 805
                                   89***********************************999999998765 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.2
                                    SHHHHHHHHHCT-SS--HHHHTS-HH CS
                       PI_PP_I   49 sLeedLnkiannktplPsWfnelska 74  
                                    +L+e+ ++i   k   P+W + ++++
  gi|15669098|ref|NP_247903.1| 1111 HLKEEGKEIFRTKIMNPKWIEGMKRH 1136
                                    6889999999999999***9999876 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     7e-05      0.25      20      52 ..     381     414 ..     354     426 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7e-05
                                   EEHHHHHHHHHTT.SSHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2  20 lpltqeelAsmlG.ltretvsrilseLkreglis 52 
                                    p  ++ +As  G  ++e+v  il+e+k++g i 
  gi|15669098|ref|NP_247903.1| 381 YPPRNDKIASAFGlDSPESVVNILKEMKKRGFIV 414
                                   4788999******669***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1332  (0.074293); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 1.01u 0.36s 00:00:01.37 Elapsed: 00:00:00.53
# Mc/sec: 7028.43
//
Query:       gi|15669099|ref|NP_247904.1|  [L=91]
Description: hypothetical protein MJ_0909 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-13   50.0   0.3    3.7e-13   49.9   0.3    1.0  1  ParE_toxin  ParE toxin of type II toxin-antitoxin system, par


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.3   2.1e-17   3.7e-13       2      90 .]       7      87 ..       6      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 2.1e-17
                                  EEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTCCTTEEEEEECTEEEEEEEETSTTEEEEEEEE CS
                    ParE_toxin  2 rltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrprrelglkglrririgdyriiYriddeelvvvilrvl 84
                                   l++++ kdlk++ ++i      ++++++ + e + +  ++p++    + +g + ++rir+gdyri ++++ ++++v + rvl
  gi|15669099|ref|NP_247904.1|  7 LLKKSFIKDLKELPKNI------QEKIKKLVFEEIPNKNNPPEIPNVKKLKGADSYYRIRVGDYRIGFKYE-NGKIV-FYRVL 81
                                  6899*************......**********************998888899***************97.66899.***** PP

                                  EHHHHC CS
                    ParE_toxin 85 hrsedy 90
                                  hr+++y
  gi|15669099|ref|NP_247904.1| 82 HRKQIY 87
                                  ***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 627.13
//
Query:       gi|15669100|ref|NP_247905.1|  [L=174]
Description: magnesium chelatase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-07   30.6   0.0    8.5e-07   29.6   0.0    1.5  2  VWA_2     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   4.7e-11   8.5e-07      19     106 ..       5      97 ..       1      98 [. 0.86
   2 ?   -2.9   0.0      0.59   1.1e+04      34      50 ..     117     133 ..     104     143 .. 0.56

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.7e-11
                         VWA_2  19 trleaakdaveallk.slp.gdrvglvtfsd.gpevlipltkdkakilnalrnleakgggtnlaaaLqlarkalkkrr... 93 
                                   +r+eaak a+++ll  +++ ++++g ++f++ ++e+++p+t++ +  ++ l++l + gg+t la+a+ +  ++++++    
  gi|15669100|ref|NP_247905.1|   5 RRMEAAKGAIISLLLdAYQkRNKIGMIAFRKdKAELILPFTSSVELGEKLLKDLPT-GGKTPLADAFIKSYEVFDREIrkn 84 
                                   589*****99987774555499********978**********************7.7****************8776566 PP

                         VWA_2  94 kgekrvivlitDg 106
                                    +   ++++i+D 
  gi|15669100|ref|NP_247905.1|  85 PNIIPIMIVISDF 97 
                                   7888899999996 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.59
                         VWA_2  34 slpgdrvglvtfsdgpe 50 
                                   ++++  ++++  +++p+
  gi|15669100|ref|NP_247905.1| 117 KIAEKGINVILIDTEPQ 133
                                   44555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1079.46
//
Query:       gi|15669101|ref|NP_247906.1|  [L=365]
Description: magnesium-chelatase subunit ChlI [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-24   85.9   0.0    2.4e-24   84.9   0.0    1.5  1  AAA_lid_2        AAA lid domain
      2e-11   43.7   0.1    1.3e-06   28.0   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.8e-10   39.9   0.2    5.1e-06   26.5   0.0    2.8  3  AAA_5            AAA domain (dynein-related subfamily)
    7.5e-05   21.9   0.2      0.019   14.1   0.0    3.1  2  MCM              MCM P-loop domain
     0.0041   17.5   0.2      0.025   15.0   0.0    2.3  2  AAA_16           AAA ATPase domain
     0.0043   17.2   0.8      0.011   15.8   0.8    1.8  1  TIP49_C          TIP49 AAA-lid domain
     0.0056   16.6   0.5      0.012   15.5   0.4    1.7  1  HSDR_N           Type I restriction enzyme R protein N termin
     0.0093   15.7   0.0        2.9    7.6   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
       0.01   16.1   0.3      0.048   13.9   0.0    2.2  2  AAA_22           AAA domain
      0.038   13.8   0.0        2.4    8.0   0.0    2.4  2  AAA_3            ATPase family associated with various cellul
      0.056   13.9   0.5       0.59   10.6   0.1    2.9  2  AAA              ATPase family associated with various cellul
       0.13   12.7   1.6       0.27   11.7   0.0    2.2  2  MCM_lid          MCM AAA-lid domain


Domain annotation for each model (and alignments):
>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.0   1.6e-27   2.4e-24       3      72 ..     266     335 ..     264     336 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 1.6e-27
                     AAA_lid_2   3 trahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegetteeivee 72 
                                    +++ +ielg+++ Rad++++r+A+AlAa++gr+yVt +Dvkea +l+L+HR+rr+p+++++ ++e++e+
  gi|15669101|ref|NP_247906.1| 266 FISKVCIELGIQTNRADITVVRTAKALAAYNGRTYVTIDDVKEAMELALPHRMRRKPFEPPQLNKEKLEQ 335
                                   57899********************************************************999999876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   3.6e-05     0.054       2      51 ..      10      61 ..       9      68 .. 0.87
   2 !   28.0   0.0   8.5e-10   1.3e-06      93     158 ..     122     187 ..     115     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.6e-05
                  Mg_chelatase  2 lkdvkGqeeakraleiaaaGgH..nlllvGppGsGKtmlakrlpsllpplse 51
                                  ++ ++Gqe+ k+al + a+      +l+ G  G+ K+   ++l+ llp+++ 
  gi|15669101|ref|NP_247906.1| 10 FTAIVGQEKMKKALILNAINPKigGVLIRGEKGTAKSTAVRALADLLPEIEI 61
                                  5789************9987542279**********************9875 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 8.5e-10
                  Mg_chelatase  93 ggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                   g +  +pG ++ a++ +L++DE+  ++ ++++vL +    g   i+r   k+++p+rf lv +mNp
  gi|15669101|ref|NP_247906.1| 122 GIKALEPGILAEANRNILYIDEVNLLDDHIIDVLLDAAAMGWNIIEREGVKIKHPSRFILVGTMNP 187
                                   667889***********************************************************9 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00033       0.5       2      23 ..      35      56 ..      34      65 .. 0.89
   2 !   26.5   0.0   3.4e-09   5.1e-06      23     138 .]      91     200 ..      87     200 .. 0.87
   3 ?   -2.6   0.0       3.4   5.1e+03      59      77 ..     285     309 ..     272     321 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                                  EEEE--SSSSHHHHHHHGGGGB CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                  vl+ G++Gt+Ks+ ++ la +l
  gi|15669101|ref|NP_247906.1| 35 VLIRGEKGTAKSTAVRALADLL 56
                                  899****************998 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 3.4e-09
                                   BS--EEEEE--TT--HHHHH--B--.............--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-S CS
                         AAA_5  23 lnreveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllleeg 99 
                                   +++++ +v+l+ + te+ ++g ++i+    +g ++l++++l +a r   il++DEv+ ++++++++Ll         +e  
  gi|15669101|ref|NP_247906.1|  91 TKKKMKVVNLPIGATEDRVIGTLDIEkaikEGIKALEPGILAEANR--NILYIDEVNLLDDHIIDVLLDAAAMGWNIIERE 169
                                   5788999999*******************9************7765..7******************88888777777777 PP

                                   SSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                         AAA_5 100 gelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                   g  +k+++      f +++t+np +    el p++++Rf
  gi|15669101|ref|NP_247906.1| 170 GVKIKHPSR-----FILVGTMNPEE---GELRPQILDRF 200
                                   777777764.....*********99...67788999998 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.4
                                   ------.....G-SE.EEEESGGG- CS
                         AAA_5  59 lvraar.....egei.lvlDEvera 77 
                                   +vr a+     +g++ + +D+v++a
  gi|15669101|ref|NP_247906.1| 285 VVRTAKalaayNGRTyVTIDDVKEA 309
                                   4444444444444331346666555 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.013        19      25      83 ..      12      58 ..       2      66 .. 0.69
   2 !   14.1   0.0   1.3e-05     0.019      98     178 ..     112     192 ..      82     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.013
                                  TSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSS CS
                           MCM 25 siyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapr 83
                                  +i+g+e++kka++l  + +                vl+ g+ gtaKs+ ++++++l+p+
  gi|15669101|ref|NP_247906.1| 12 AIVGQEKMKKALILNAINPKI---G---------GVLIRGEKGTAKSTAVRALADLLPE 58
                                  577777777777776665433...1.........3888899999999988888888776 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.3e-05
                                   SSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSC CS
                           MCM  98 taavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagry 178
                                   t  + +  ++g  +le G l  a++ +++iDe++  +++  ++l++a       i + G++++ ++r  ++  +np++g+ 
  gi|15669101|ref|NP_247906.1| 112 TLDIEKAIKEGIKALEPGILAEANRNILYIDEVNLLDDHIIDVLLDAAAMGWNIIEREGVKIKHPSRFILVGTMNPEEGEL 192
                                   66666777777789*********************************9999999**********************99975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.7e-05     0.025      22      63 ..      30      72 ..      13     166 .. 0.57
   2 ?   -0.4   0.0      0.88   1.3e+03     115     147 ..     277     309 ..     214     319 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                        AAA_16 22 grpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                  +  + vl++Ge+G+ Ks+ vr+l++ l + +++     +cd +
  gi|15669101|ref|NP_247906.1| 30 PKIGGVLIRGEKGTAKSTAVRALADLLPEIEIVEgCPFNCDPN 72
                                  33478*******************6555443222455555555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.88
                        AAA_16 115 easrllellkrll.allsrderplvlvlDdlqwa 147
                                   + +r   ++ r + al++ ++r +++++Dd+  a
  gi|15669101|ref|NP_247906.1| 277 QTNRADITVVRTAkALAAYNGR-TYVTIDDVKEA 309
                                   3377777777777677777666.99999998655 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.8   7.4e-06     0.011       1      63 [.     247     312 ..     247     314 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.4e-06
                       TIP49_C   1 IlkiRakeEgvkldeeAldlLakigtetSL...RYaiqLltpasilakkrkkkevevedveeveeL 63 
                                   I+k R    +v+++++ l++++k+ +e +    R  i  +  a+ la  ++++ v+++dv+e+ eL
  gi|15669101|ref|NP_247906.1| 247 IIKARELLNKVEISDDLLEFISKVCIELGIqtnRADITVVRTAKALAAYNGRTYVTIDDVKEAMEL 312
                                   899********************9999766555999***************************998 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   8.2e-06     0.012      12     135 ..     152     292 ..     145     355 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.2e-06
                                   HHHHH..HHTT-EE................----SHHHHHHHHHHHHHHHH...............-HHHHHHHH...... CS
                        HSDR_N  12 idell..relGyqvlskkdveiegrrpe.vrkskaevaleknlreqlgaln...............ikkltkrla...... 68 
                                   id ll   ++G+++ + ++v+i+      +++    ++ e +lr q+  +                +              
  gi|15669101|ref|NP_247906.1| 152 IDVLLdaAAMGWNIIEREGVKIKHPSRFiLVGT--MNPEEGELRPQILDRFglmvdveglndvkdrV-------Evikrve 223
                                   555554456899999999999888555563333..34445555555554446777999955555544.......4444445 PP

                                   .TT--HHHHHHHHHTS-EEEETS-EEEEESS-SSSGGGS-EEEEE----S.SSS---EEEEEEETTEEE CS
                        HSDR_N  69 .lsdgnkefyellkegkvkfkegrkknikLiDkknlenNrfqvvnQvtvt.gnqkrrpDivlfvnglpl 135
                                     +++ ++fy++ +e++ k++e  +k  +L++k +++    ++++ v ++ g q++r+Di++    + l
  gi|15669101|ref|NP_247906.1| 224 eFNENPEAFYKKFEEEQNKLRERIIKARELLNKVEISDDLLEFISKVCIElGIQTNRADITVVRTAKAL 292
                                   599999**********989889999999*********************************98765555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0064       9.6      20      44 ..      30      54 ..      13      70 .. 0.75
   2 !    7.6   0.0    0.0019       2.9      80     116 ..     122     158 ..      89     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0064
                                  TSSS-EEEECSTTSSHHHHHHHHHH CS
               Sigma54_activat 20 ktdlsvlitGesGtGKellaraihe 44
                                  ++   vli+Ge+Gt K++  ra+ +
  gi|15669101|ref|NP_247906.1| 30 PKIGGVLIRGEKGTAKSTAVRALAD 54
                                  444679***********99998765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0019
                                   TTSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHH CS
               Sigma54_activat  80 GAekekkGlfekadgGtlfLDeigelplelQekLlrv 116
                                   G ++ + G + +a+  +l++De++ l+ ++   Ll +
  gi|15669101|ref|NP_247906.1| 122 GIKALEPGILAEANRNILYIDEVNLLDDHIIDVLLDA 158
                                   5566678*****************9999988888864 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.2e-05     0.048       9     130 ..      36     184 ..      33     189 .. 0.81
   2 ?   -1.1   0.1       1.4   2.1e+03      54      99 ..     264     305 ..     217     348 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
                        AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsstsskdllrellralglelka................ 70 
                                   ++ Ge+Gt K+t +r l++ l+        + e+v    +++   +++ d+++e  +  +l++ +                
  gi|15669101|ref|NP_247906.1|  36 LIRGEKGTAKSTAVRALADLLP--------EIEIVegcPFNCDPNGNLCDICKEKKKRGELKTTKkkmkvvnlpigatedr 108
                                   788******************8........777777778888888888888888877777766667789999999999999 PP

                        AAA_22  71 ......erlsseellealeqalraravielliiDEaqhlr.s..eealeeLrsllnl.......srkgvqliLvGt 130
                                          ++  +e ++ale  + a a + +l iDE+  l+ +  + +l    + +n+        +++ ++iLvGt
  gi|15669101|ref|NP_247906.1| 109 vigtldIEKAIKEGIKALEPGILAEANRNILYIDEVNLLDdHiiDVLLDAAAMGWNIieregvkIKHPSRFILVGT 184
                                   999999999999999999999999999************7636566666666667778777778888888899987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                        AAA_22  54 kdllrellralglelkaerlsseellealeqalraravielliiDE 99 
                                    ++ ++++ +lg ++++     +  + + ++al a+  +  + iD+
  gi|15669101|ref|NP_247906.1| 264 LEFISKVCIELGIQTNR----ADITVVRTAKALAAYNGRTYVTIDD 305
                                   44444444444443333....3333334444444443334444444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.043        64       2      23 ..      35      56 ..      34      61 .. 0.91
   2 ?    8.0   0.0    0.0016       2.4      63     115 ..     136     190 ..     107     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.043
                         AAA_3  2 vllegvPGlaktllvkalakal 23
                                  vl++g  G+ak ++v+ala+ l
  gi|15669101|ref|NP_247906.1| 35 VLIRGEKGTAKSTAVRALADLL 56
                                  899****************976 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0016
                         AAA_3  63 anllladeinrappktqsallea..meerqvtvegethklpepflvlatqnPieq 115
                                    n+l  de+n    ++   ll+a  m  + +  eg + k p+ f+++ t nP e 
  gi|15669101|ref|NP_247906.1| 136 RNILYIDEVNLLDDHIIDVLLDAaaMGWNIIEREGVKIKHPSRFILVGTMNPEEG 190
                                   58999****************853377888999999999999**********875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0004      0.59       1     126 [.      35     202 ..      35     207 .. 0.53
   2 ?   -2.9   0.0       5.7   8.5e+03      37      57 ..     234     254 ..     226     272 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0004
                                   EEEESSTTSSHHHHHHHHHHHH..........THE...................EEEEETTTCSSS...........STTH CS
                           AAA   1 vllyGppGtGKTllakavakel..........gve...................fleisgsellsk...........yvge 41 
                                   vl+ G +Gt K+++++a+a  l            +                   +          k            +g+
  gi|15669101|ref|NP_247906.1|  35 VLIRGEKGTAKSTAVRALADLLpeieivegcpF-NcdpngnlcdickekkkrgeL----------KttkkkmkvvnlPIGA 104
                                   6889****************9864444443330.133333333333333333331..........0333444444444444 PP

                                   HHHHHHHHHHHHHHTS..............TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS...SSTEEE CS
                           AAA  42 sekkirelfkeakeka..............kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk...eskviv 105
                                   +e+++ ++++  k+ +              +  il iDE+  l  +  +   + +    n + +e      k    s++i+
  gi|15669101|ref|NP_247906.1| 105 TEDRVIGTLDIEKAIKegikalepgilaeaNRNILYIDEVNLLDDHIIDVLLDAAAMGWNIIEREGV----KikhPSRFIL 181
                                   4444444443322222333444444577755699999999988555533333333333333333333....2445677888 PP

                                   EEEESS.GGGSTHHHHSTTSSE CS
                           AAA 106 igatnr.pdkldpallrgRfdr 126
                                   +g+ n  + +l p++l +Rf  
  gi|15669101|ref|NP_247906.1| 182 VGTMNPeEGELRPQIL-DRFGL 202
                                   8888877888888888.88865 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.7
                                   SSTTHHHHHHHHHHHHHHHTS CS
                           AAA  37 kyvgesekkirelfkeakeka 57 
                                   k ++e ++k+re + +a+e  
  gi|15669101|ref|NP_247906.1| 234 KKFEEEQNKLRERIIKARELL 254
                                   455666666776666666654 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00018      0.27      49      83 ..     279     313 ..     273     315 .. 0.89
   2 ?   -1.8   0.1       2.8   4.2e+03      16      38 ..     326     348 ..     320     356 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                   HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHHHH CS
                       MCM_lid  49 vRqLesliRLseAlAklrlsevvteedveeairll 83 
                                    R+  +++R ++AlA  + +++vt +dv+ea++l 
  gi|15669101|ref|NP_247906.1| 279 NRADITVVRTAKALAAYNGRTYVTIDDVKEAMELA 313
                                   5666689*************************985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.8
                                   -BETCHHHHHHHHHHHHHHHHHT CS
                       MCM_lid  16 PklseeakeklseaYvelRkeee 38 
                                   P+l++e+ e++ + +++  ++++
  gi|15669101|ref|NP_247906.1| 326 PQLNKEKLEQMINEFKQQNNKDN 348
                                   67888888888888877766663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2093  (0.116738); expected 358.6 (0.02)
Passed bias filter:                      772  (0.0430587); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 2535.95
//
Query:       gi|15669102|ref|NP_247907.1|  [L=243]
Description: hypothetical protein MJ_0912 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-29  100.8   0.0    1.5e-28  100.1   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    5.7e-14   53.1   3.4    8.4e-13   49.3   3.4    2.0  1  Metallophos    Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.012   14.0   0.2      0.017   13.4   0.2    1.3  1  FBPase_2       Firmicute fructose-1,6-bisphosphatase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1   0.0   2.5e-32   1.5e-28       3     163 ..       6     206 ..       5     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 2.5e-32
                 Metallophos_2   3 laiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepevleellelapvlaVrGNnD.................ee 64 
                                   +a+iSD+Hsnl+al+avl+++k+ g+ +i+++GD+  ++++p+ + el++ +  l V GN+D                   
  gi|15669102|ref|NP_247907.1|   6 IAVISDIHSNLEALNAVLNDIKNRGIKKIFCLGDIvgYGANPNECVELIRDLNCLSVVGNHDygvlgkesldyfnkygaI- 85 
                                   89*****************************************999999999***************9999888888641. PP

                 Metallophos_2  65 v...veedvlreaaelgtdlpeeaelelagekvlliHgdpl...gvkdalaellkeaeegsdvvvcGHtHvpevekeg... 136
                                   +    ++ + +e+ ++ ++lp   e +++g+kv + H  p+    +++ + + +++  +  d++++GH+H+p v  e+   
  gi|15669102|ref|NP_247907.1|  86 AilwTKKVIKNENLKFLDSLPLIIEENIKGKKVIFSHANPKhpeIWEYLFPDYVDDVFNYGDLIFVGHSHIPFVNSEEgnl 166
                                   2456666777778888888899999999**********988888555556666666555688**********888774334 PP

                 Metallophos_2 137 ............gvlvvnPGsvgeprdgdpe.tyaildtd 163
                                               + +++nPGsvg+prdg ++ +y+i+d +
  gi|15669102|ref|NP_247907.1| 167 llhegkiyldedKKYLINPGSVGQPRDGINKaSYCIFDEK 206
                                   44444444444466***********************976 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   3.4   1.4e-16   8.4e-13       3     202 ..       6     155 ..       4     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 1.4e-16
                                   EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS....CHHH CS
                   Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe....gfee 79 
                                   i+vi+D+H      +l++l+++l+d++++ ++  ++++GD+v  g  ++e++el++ l         + GNH+    g e 
  gi|15669102|ref|NP_247907.1|   6 IAVISDIH-----SNLEALNAVLNDIKNR-GIKKIFCLGDIVGYGANPNECVELIRDLNC-----LSVVGNHDygvlGKES 75 
                                   89******.....*************999.***************99999****999999.....********98887677 PP

                                   .HHHHHHHHHHHH...HHHHEHHHCEEETSEEEEEETTE.EEEEEEESE..CEEETHHHHHHHHHHHSCHHHHCCHHHHHH CS
                   Metallophos  80 .ellnkygylgif...sepwrsdaevfnnlplaslgsgs.lkvlllhGg..spellvsldklgslnleleapepgdewlkd 153
                                    +++nkyg ++i    + +++ + ++++ lpl+   + +  kv++ h++                                
  gi|15669102|ref|NP_247907.1|  76 lDYFNKYGAIAILwtkKVIKNENLKFLDSLPLIIEENIKgKKVIFSHANpkH----------------------------- 127
                                   7888888888888887666666688888888888444445688888888222............................. PP

                                   HHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSS CS
                   Metallophos 154 lekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtH 202
                                                    ++   +ylf+d + +   ++yg dl++ GH+H
  gi|15669102|ref|NP_247907.1| 128 ---------------PEIW---EYLFPDYVDD--VFNYG-DLIFVGHSH 155
                                   ...............2222...3333333334..44455.566666666 PP

>> FBPase_2  Firmicute fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   2.9e-06     0.017     156     226 ..       3      72 ..       1     103 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-06
                      FBPase_2 156 eeiietiielgraeefiialaeliqrlavdklhivGDiyDRGpeadkildeLmkyhsvdiqWGNHDilWmG 226
                                   +++i  i +++++ e + a+ + i++  + k+  +GDi   G +++  ++ + + + + +  GNHD   +G
  gi|15669102|ref|NP_247907.1|   3 KSMIAVISDIHSNLEALNAVLNDIKNRGIKKIFCLGDIVGYGANPNECVELIRDLNCLSV-VGNHDYGVLG 72 
                                   67899999999999*****************************************99998.5****87666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1531.82
//
Query:       gi|15669103|ref|NP_247908.1|  [L=403]
Description: pantothenate metabolism flavoprotein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-49  167.7   0.0    8.6e-49  165.9   0.0    1.9  2  DFP           DNA / pantothenate metabolism flavoprotein
    1.2e-34  119.3   1.1    1.2e-34  119.3   1.1    2.2  3  Flavoprotein  Flavoprotein
  ------ inclusion threshold ------
       0.53   10.4   4.5        5.8    7.1   0.4    3.8  5  KHA           KHA, dimerisation domain of potassium ion chann


Domain annotation for each model (and alignments):
>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.32   1.9e+03      35      52 ..      41      58 ..      13      88 .. 0.67
   2 !  165.9   0.0   1.4e-52   8.6e-49       2     186 .]     194     374 ..     193     374 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.32
                                  HHHHHHHTT-EEEEEE-S CS
                           DFP 35 lAeaaaarGaeVtlvsgp 52
                                  l +++++ GaeV  +  +
  gi|15669103|ref|NP_247908.1| 41 LMRELIRHGAEVYCIITE 58
                                  445666667777766655 PP

  == domain 2  score: 165.9 bits;  conditional E-value: 1.4e-52
                                   TT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHTT CS
                           DFP   2 egkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveealke 82 
                                   eg++vl+  G+T+E iD+VR+isN SSGkmG+alAea++++G  V+++++   le p  ++ +kv +a+eml+++ e +k+
  gi|15669103|ref|NP_247908.1| 194 EGNRVLILNGGTVEFIDKVRVISNLSSGKMGVALAEAFCKEGFYVEVITAM-GLEPPYYIKNHKVLTAKEMLNKAIELAKD 273
                                   689**********************************************99.7999999********************** PP

                                   -SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-SS....-HHHHHHHHHHHT CS
                           DFP  83 adivimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaete....ellenareklerk 159
                                    di+i++AA++D+++++  e+K++    eeel l+l++np++l+el+ +  k+++++GF+ae +    el+++a+e+l++ 
  gi|15669103|ref|NP_247908.1| 274 FDIIISSAAISDFTVES-FEGKLSS---EEELILKLKRNPKVLEELR-RIYKDKVIIGFKAEYNldekELINRAKERLNKY 349
                                   ***************85.899**96...568***************5.556778********755678************* PP

                                   T-SEEEEEEGGGTTGGG-SS-EEEEE. CS
                           DFP 160 gldlivaNdvskeeagfgsdenevtll 186
                                   +l++i+aNd+sk+   fg+d  ev+++
  gi|15669103|ref|NP_247908.1| 350 NLNMIIANDLSKH--YFGDDYIEVYII 374
                                   ***********87..9****9999886 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.3   1.1     2e-38   1.2e-34       1     157 [.      23     186 ..      23     187 .. 0.93
   2 ?   -3.9   0.0       1.7     1e+04       3      26 ..     198     221 ..     197     228 .. 0.76
   3 ?   -0.6   0.0      0.16   9.6e+02      14      45 ..     258     289 ..     255     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 2e-38
                                   EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHHCTTESEEEEEEEE CS
                  Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhielrrwadllviaPas 74 
                                   kkil+++T s+aai++++l+++L+++g+ev +++t++ kk+i ke lk+         ++++i+hi l ++ d+l+i+Pa+
  gi|15669103|ref|NP_247908.1|  23 KKILVAVTSSIAAIETPKLMRELIRHGAEVYCIITEETKKIIGKEALKFGCgnevyeeITGDIEHILLYNECDCLLIYPAT 103
                                   79*******************************************77775588999999********************** PP

                                   HHHHHHHHTT--SSHHHHHHHT.HCCTTEEEEE.--HHCCTCSTCHHHHHHH.H.T................GHHHHHHHH CS
                  Flavoprotein  75 antlakianGiadnlltlilra.takkpiliaPamnpamyenpqtlknlekl.e.egvtvikPsegdigkgkmaeieeivg 152
                                   an+++ki +Giadn + +++++   +kpi+i+Pam+ +m++    +++++kl e +++ +i+P+  ++gk+k+a+ie++v+
  gi|15669103|ref|NP_247908.1| 104 ANIISKINLGIADNIVNTTALMfFGNKPIFIVPAMHENMFNA--IKRHIDKLkEkDKIYIISPK-FEEGKAKVANIEDVVK 181
                                   ****************6666444888**************96..5799****977*********.8999***********9 PP

                                   HHCHH CS
                  Flavoprotein 153 kildk 157
                                    +++k
  gi|15669103|ref|NP_247908.1| 182 AVIEK 186
                                   99886 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.7
                                   EEEEE-SSCGGGCHHHHHHHHHHT CS
                  Flavoprotein   3 illgiTGsvaaikalellekLkke 26 
                                   +l+   G+v  i  ++++++L + 
  gi|15669103|ref|NP_247908.1| 198 VLILNGGTVEFIDKVRVISNLSSG 221
                                   777788999999999999988764 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.16
                                   GCHHHHHHHHHHTTEEEEEEESCHHHHCCHHG CS
                  Flavoprotein  14 ikalellekLkkegievqvvltkaAkkfiske 45 
                                   + a+e+l+k ++   +++++++ aA   ++ e
  gi|15669103|ref|NP_247908.1| 258 LTAKEMLNKAIELAKDFDIIISSAAISDFTVE 289
                                   56778888888888888888888887766655 PP

>> KHA  KHA, dimerisation domain of potassium ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.1   6.3e+03      24      37 ..      39      52 ..      31      64 .. 0.72
   2 ?    2.0   0.0     0.036   2.2e+02      33      67 .]      64      99 ..      57      99 .. 0.89
   3 ?    7.1   0.4   0.00096       5.8      15      60 ..     168     213 ..     150     217 .. 0.86
   4 ?   -3.3   0.0       1.7     1e+04      24      37 ..     309     322 ..     303     329 .. 0.79
   5 ?   -0.8   0.0      0.27   1.6e+03      28      49 ..     336     358 ..     334     361 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.1
                           KHA 24 pdsleeLlkiasek 37
                                  p+ ++eL++ ++e 
  gi|15669103|ref|NP_247908.1| 39 PKLMRELIRHGAEV 52
                                  66677888777665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.036
                           KHA 33 iasekfgi.aatrvltedgAeiddidvirDgDhLyl 67
                                  i++e +++  ++ v+ e  + i+ i + ++ D L++
  gi|15669103|ref|NP_247908.1| 64 IGKEALKFgCGNEVYEEITGDIEHILLYNECDCLLI 99
                                  788999999****************99999998875 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.00096
                           KHA  15 rseGklvllpdsleeLlkiasekfgiaatrvltedgAeiddidvir 60 
                                   + + k+ ++ d ++  ++ +++ ++++++rvl  +g+ ++ id +r
  gi|15669103|ref|NP_247908.1| 168 EGKAKVANIEDVVKAVIEKIGNNLKKEGNRVLILNGGTVEFIDKVR 213
                                   4678999999****************************99988776 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 1.7
                           KHA  24 pdsleeLlkiasek 37 
                                   p+ leeL +i ++k
  gi|15669103|ref|NP_247908.1| 309 PKVLEELRRIYKDK 322
                                   67789999988777 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 0.27
                           KHA  28 eeLlkiasekfgi.aatrvlted 49 
                                   +eL++ a+e++++ + ++++ +d
  gi|15669103|ref|NP_247908.1| 336 KELINRAKERLNKyNLNMIIAND 358
                                   59**********99999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1146  (0.0639188); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 2934.64
//
Query:       gi|15669104|ref|NP_247909.1|  [L=136]
Description: hypothetical protein MJ_0914 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-09   37.8   0.6    4.1e-09   37.0   0.6    1.4  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.071   13.4   0.1        0.1   12.8   0.1    1.4  1  PIN_2     PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.6   4.6e-13   4.1e-09       1     119 [.      18     126 ..      18     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 4.6e-13
                                   EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHH CS
                           PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeea 81 
                                   i++DTsvli++++        +++leel+  ++s++++ E++++++         +++  l++ ++ ++i+ id+ei    
  gi|15669104|ref|NP_247909.1|  18 ILVDTSVLIDYFK--------KRRLEELGGEAISIITAVEFIRGISE-------HKQEQVLNIFKELFEIVYIDEEIIIPF 83 
                                   79*******9994........45566678889***************.......7777777888***************** PP

                                   HHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTH.HHHH CS
                           PIN  82 aeialkyg.....llpnDaliaAtAkehgikliatfDed.frrv 119
                                   ++i+++++     ++ +D++ia tA+  + +l  t++++ f+r+
  gi|15669104|ref|NP_247909.1|  84 SKIYRQLKkrgmlIDDADLYIACTAIIKNYPLW-TKNKKhFERL 126
                                   ******************************988.9998867776 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.2e-05       0.1      51     116 ..      56     123 ..      11     133 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                         PIN_2  51 klseeeleellelletkikiveeslye..skikeAkeriarvDpdDtpfvAlaLlleapiWTeDkdli 116
                                   + ++e++ ++++ l++ + i ee ++   +  ++ k+r   +D  D  +  +a+  + p+WT+ k+ +
  gi|15669104|ref|NP_247909.1|  56 EHKQEQVLNIFKELFEIVYIDEEIIIPfsKIYRQLKKRGMLIDDADLYIACTAIIKNYPLWTKNKKHF 123
                                   23334555555566665555555555553556788888889999***9999************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 836.13
//
Query:       gi|15669105|ref|NP_247910.1|  [L=267]
Description: L-aspartate dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-29  101.8   0.6    2.2e-28   99.3   0.3    2.1  2  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
    1.5e-25   89.4   1.2    2.4e-25   88.7   1.2    1.3  1  DUF108         Domain of unknown function DUF108
    3.6e-07   31.0   0.2    1.3e-06   29.2   0.0    1.9  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
    1.4e-06   28.8   1.2    1.4e-06   28.8   1.2    2.3  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
    9.9e-05   22.5   1.1    0.00014   22.0   0.3    1.6  2  DapB_N         Dihydrodipicolinate reductase, N-terminus
     0.0014   18.8   0.1     0.0026   18.0   0.1    1.5  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
  ------ inclusion threshold ------
      0.062   13.8   0.0       0.27   11.7   0.0    2.1  1  RuvA_C         RuvA, C-terminal domain
       0.17   12.3   0.3       0.39   11.1   0.3    1.7  1  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 


Domain annotation for each model (and alignments):
>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.3   9.8e-32   2.2e-28       1     117 []       8     121 ..       8     121 .. 0.98
   2 ?    0.2   0.0       0.5   1.1e+03      18      37 ..     199     218 ..     177     258 .. 0.76

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 9.8e-32
                                   --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHHH CS
                 NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvlkaLk 81 
                                   G+GaiG+ +++++++++ + +++++av+dr+   +++++++++ +++++++ddl++ +d d+vVE+as +av+e+++k L 
  gi|15669105|ref|NP_247910.1|   8 GCGAIGNFITKKVLDGTIK-NAKISAVYDRN-FDKAKTLSERTGAKICSSIDDLVK-EDLDLVVEAASIKAVEEIAEKSLI 85 
                                   9*****************8.***********.99999*******************.77********************** PP

                                   TTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                 NAD_binding_3  82 agkdvvtankgaladealyeeLreaaeangakiyve 117
                                   ++kdv+++++galad++l+ +Lr++a++ g+kiy++
  gi|15669105|ref|NP_247910.1|  86 NNKDVLIMSVGALADKKLFLKLRDLAKTVGRKIYLP 121
                                   **********************************86 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.5
                                   -SSEEEEEEEEESSEEE-TT CS
                 NAD_binding_3  18 seielelvavadrdsllskd 37 
                                   +e+++++v+vad + +l+k+
  gi|15669105|ref|NP_247910.1| 199 AEFPAKVVIVADPNAKLNKH 218
                                   45899999999999444443 PP

>> DUF108  Domain of unknown function DUF108
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   1.2   1.1e-28   2.4e-25       2      89 .]     168     253 ..     167     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 1.1e-28
                                   SS-EEEEEEEHHHHHHHSTTS-CHHHHHHHHHH.CCGEEEEEEEETT-SSEEEEEEEEETTEEEEEEEEE-EETTEEEEEH CS
                        DUF108   2 teptvlFeGsareaikkfPknvNvaaalaLaalgfdrvkvelvadpnldkniheieveGsfgefslevenkpspenPktsa 82 
                                   ++p+++FeG + +aik+fP+n+Nv+++l++aa     +kv +vadpn++ n he+ v++s g++++ +en+p +enP+tsa
  gi|15669105|ref|NP_247910.1| 168 KNPVIVFEGDVFKAIKEFPANINVSVTLSIAA--EFPAKVVIVADPNAKLNKHELFVKSSIGTLRVCIENVPFEENPRTSA 246
                                   7899****************************..56799****************************************** PP

                                   HHHHHHH CS
                        DUF108  83 laalsvi 89 
                                   laa+s++
  gi|15669105|ref|NP_247910.1| 247 LAAYSAV 253
                                   *****85 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   5.7e-10   1.3e-06       1      91 [.       2      92 ..       2      92 .. 0.90
   2 ?   -1.4   0.0       1.8   4.1e+03      58      76 ..     201     219 ..     179     229 .. 0.59

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.7e-10
                                  EEEEEETTSHHHHHHHHHHHHTT.TTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHH CS
                  GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesq.rleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelakaa 82
                                  l+++i+G+G ig    +++ + + +++++ a++d++  +a++++e++g++ +s++++l++ ++ d+v+ a   +  ee+a++ 
  gi|15669105|ref|NP_247910.1|  2 LKIGIVGCGAIGNFITKKVLDGTiKNAKISAVYDRNFDKAKTLSERTGAKICSSIDDLVK-EDLDLVVEAASIKAVEEIAEKS 83
                                  689************999988762556*********************************.7799999888889999999999 PP

                                  HHTT-EEEE CS
                  GFO_IDH_MocA 83 leagkhvll 91
                                  l ++k+vl+
  gi|15669105|ref|NP_247910.1| 84 LINNKDVLI 92
                                  999999885 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                                   HTCTTESEEEE-S-G...GGHH CS
                  GFO_IDH_MocA  58 ladpeidavivatpn...gthe 76 
                                   +    +++viva pn   ++he
  gi|15669105|ref|NP_247910.1| 201 FP---AKVVIVADPNaklNKHE 219
                                   33...56788888884333344 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   1.2   6.1e-10   1.4e-06       1      95 [.       3      96 ..       3      98 .. 0.90
   2 ?   -0.1   0.2      0.63   1.4e+03      37      37 ..     180     180 ..     122     218 .. 0.55

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 6.1e-10
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH.H-SEEEE-S-HHHHHHHHHHCG CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae.eadvvvlavkpedveevlsela 82
                                  kigi+G+G +g  +++++l    ++ +i  + +rn +ka+ l e+ g+k+++ +  ++++ + d vv a   ++vee++++  
  gi|15669105|ref|NP_247910.1|  3 KIGIVGCGAIGNFITKKVLDGTIKNAKISAVYDRNFDKAKTLSERTGAKICS-SIDDLVKeDLDLVVEAASIKAVEEIAEKS- 83
                                  7***************9998877*****************************.8888888689****************998. PP

                                  HHHHTTSEEEEES CS
                 F420_oxidored 83 kdalkgklvisvl 95
                                    + k+ l+ sv 
  gi|15669105|ref|NP_247910.1| 84 LINNKDVLIMSVG 96
                                  4557787777775 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.63
                                   C CS
                 F420_oxidored  37 e 37 
                                   +
  gi|15669105|ref|NP_247910.1| 180 K 180
                                   1 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.3   6.1e-08   0.00014       2     114 ..       3     112 ..       2     119 .. 0.81
   2 ?   -2.9   0.0       3.1     7e+03      62      69 ..     196     204 ..     173     225 .. 0.53

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.1e-08
                                   EEEEETTTSHHHHHHHHHHHH..STTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH.-SEEEE-S-HHH CS
                        DapB_N   2 kvavvGasGrmGkevvkavee..aedlelvaavdrkeselegkdagellglgklgvavtddleevlek.advliDFTtpea 79 
                                   k+++vG+ G +G+ ++k v +   ++++++a++dr+       +a +   ++++g ++ +++++++++  d +++  + +a
  gi|15669105|ref|NP_247910.1|   3 KIGIVGC-GAIGNFITKKVLDgtIKNAKISAVYDRNFD-----KAKT--LSERTGAKICSSIDDLVKEdLDLVVEAASIKA 75 
                                   9******.***********984459**********872.....2222..224899**********9999************ PP

                                   HHHHHHHHHHTT-EEEE--SS-..-HHHHHHHHHHTT CS
                        DapB_N  80 vlenlklalekgvklViGTTGl..seeelaeleelak 114
                                   v e ++  l +++++ i + G   +++   +l++lak
  gi|15669105|ref|NP_247910.1|  76 VEEIAEKSLINNKDVLIMSVGAlaDKKLFLKLRDLAK 112
                                   ************9999988887434444455556665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.1
                                   HHHHHH.-S CS
                        DapB_N  62 eevlek.ad 69 
                                   + ++e  a 
  gi|15669105|ref|NP_247910.1| 196 SIAAEFpAK 204
                                   222222222 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.1e-06    0.0026       1      75 [.       3      82 ..       3     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                                  EEEEE--SHHHHHHHHHH....HHTT-EEEEE-SSHHHHHHHHHT.TEEE-SSHHHHHHHC.SEEEE-SSSHHHHHHHHHS CS
                 NAD_binding_2  1 kigfiGlGvMGsnmalnl....lkagykvavynrtkekveelvae.gakaaesieelvasl.dvvitmvkagkavdevieg 75
                                  kig++G G +G+ + +++    +k+    avy+r+ +k+++l ++ gak+++si +lv++  d+v+    + kav+e+ e+
  gi|15669105|ref|NP_247910.1|  3 KIGIVGCGAIGNFITKKVldgtIKNAKISAVYDRNFDKAKTLSERtGAKICSSIDDLVKEDlDLVVE-AASIKAVEEIAEK 82
                                  79***************95554444445689***********99845***********986366543.3455666666666 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.27       7      21 ..     154     168 ..     151     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                   HHHHHHCTS-HHHHH CS
                        RuvA_C   7 veALlaLGYkekeae 21 
                                   + AL++LGYk+++++
  gi|15669105|ref|NP_247910.1| 154 EDALKNLGYKPEDIK 168
                                   67**********997 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00017      0.39       2      77 ..       3      80 ..       2     101 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                                  EEEEESTSHHHHHHHHHHH..HHTTCEEEEEE-.TS-HHHHHHHHHEETTTEC-SS-EEEETTEEEETTEEEEEE--SS CS
                       Gp_dh_N  2 kvainGfGRIGrlvlrall..eekelevvaind.ltdletlayllkyDsvhgrfkgeveaeeealvvngkkikvlaekd 77
                                  k++i G G IG  + +++l  + k+ ++ a+ d   d ++  +      +  +++  v+ e+ +lvv+  +ik ++e +
  gi|15669105|ref|NP_247910.1|  3 KIGIVGCGAIGNFITKKVLdgTIKNAKISAVYDrNFDKAKTLSERTGAKICSSIDDLVK-EDLDLVVEAASIKAVEEIA 80
                                  8******************7655688899988843443333333333333444444443.5667888888887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1597.14
//
Query:       gi|15669106|ref|NP_247911.1|  [L=89]
Description: hypothetical protein MJ_0916 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-16   60.1   0.5    1.8e-16   60.0   0.5    1.0  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.5   9.9e-21   1.8e-16       4      77 ..       3      81 ..       1      83 [. 0.95

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 9.9e-21
                                  CCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT...........-EEEEEGG.CEECCCTEEEETTS-G CS
                           PRC  4 frasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi......gekevliPfdlavkigkdriivdapke 77
                                  +r+sd+ +k++yt++  ++GkV+Dv++d + g + +l+vs+     +       +k+v++Pf+  + +++++i+v++p++
  gi|15669106|ref|NP_247911.1|  3 IRVSDILDKPIYTTTAIYVGKVYDVMLDLNKGVISGLIVSDIQNGCLkdyvtdPSKKVVLPFN-LITAIGNIILVKPPAD 81
                                  899***************************************99555****************.*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 638.46
//
Query:       gi|15669107|ref|NP_247912.1|  [L=574]
Description: inorganic polyphosphate/ATP-NAD kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-79  264.9   1.9    3.3e-77  259.6   0.8    2.6  2  NAD_kinase       ATP-NAD kinase
      3e-23   82.7   0.1    1.1e-13   51.4   0.0    2.1  2  Inositol_P       Inositol monophosphatase family
     0.0061   16.1   0.1      0.012   15.1   0.1    1.5  1  FBPase           Fructose-1-6-bisphosphatase, N-terminal doma
  ------ inclusion threshold ------
      0.078   12.8   0.0        0.2   11.4   0.0    1.6  1  Methyltransf_31  Methyltransferase domain
      0.098   12.3   0.2       0.55    9.8   0.0    2.1  2  DAGK_cat         Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.51   1.8e+03      78      99 ..      29      50 ..      27      58 .. 0.75
   2 !  259.6   0.8   9.2e-81   3.3e-77       1     291 [.     303     559 ..     303     560 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.51
                                  SSSEEEEEE-HHHHHHHHHHHH CS
                    NAD_kinase 78 gvdliivvGGDGTaldvarllq 99
                                  ++d ++ +G DGT ++   +++
  gi|15669107|ref|NP_247912.1| 29 KADEVVKIGADGTPTKRIDVIA 50
                                  78899999****9877666655 PP

  == domain 2  score: 259.6 bits;  conditional E-value: 9.2e-81
                                   .EEEEESSCGGTCSHHHHHHHHHHHCT-..EEEEECCGGCCSSSTT--HHHHTTTT--.......EEECCC-TTTTTSSSE CS
                    NAD_kinase   1 kvgivvnpikkeaieraeevarwLldalsrvlevtveeklgeslaeaaefrsevisvlkkvkttddtrkaleafadagvdl 81 
                                   k+givv+++k+eai++a e++++L+d+   ++ ++ve+ l+                         +r   ++f  + + +
  gi|15669107|ref|NP_247912.1| 303 KFGIVVREDKEEAINLAIEICKYLKDK---NIPFCVEDFLR-------------------------ERVGGDKFDISAISH 355
                                   789************************...9*********5.........................5577899******** PP

                                   EEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE......EEE CS
                    NAD_kinase  82 iivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavimrskgeediadivi 162
                                   ii++GGDGT+l+++rl++ ++iP+++vn+G++gfl+ef+ ++++e+++k++ ge+++ekr++l+++i ++++      +++
  gi|15669107|ref|NP_247912.1| 356 IIAIGGDGTILRASRLVNGETIPIIAVNMGKVGFLAEFCKDEVFEIIDKVIYGEYEIEKRSKLSCKIIKDNR------VIK 430
                                   ************************************************************************......9** PP

                                   EEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEESESSS----EE CS
                    NAD_kinase 163 ensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivpicPhslssrpiV 243
                                   ++s+lne+v+i++++++++e+++yv+++l+e++++dg+ivstPtGstayslsaGgp+++P+v++++i+picP++lssrp+V
  gi|15669107|ref|NP_247912.1| 431 TPSALNEMVVITKNPAKILEFDVYVNDTLVENVRADGIIVSTPTGSTAYSLSAGGPIVEPNVDCFIISPICPFKLSSRPLV 511
                                   ********************************************************************************* PP

                                   E-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
                    NAD_kinase 244 vssssklrirvasrseallaldGseelelspgdevrvtasdkkfklir 291
                                   +s s++++++++ ++ all++dGs e+e++++de+ + +sd+ +++++
  gi|15669107|ref|NP_247912.1| 512 ISASNRIKLKLKLEKPALLVIDGSVEYEINKDDELIFEKSDSYAYFVK 559
                                   *********************************************997 PP

>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.1     2e-10   7.2e-07      42     114 ..      41     110 ..       5     117 .. 0.72
   2 !   51.4   0.0     3e-17   1.1e-13     120     267 ..     144     293 ..     138     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2e-10
                                   HHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEE CS
                    Inositol_P  42 lvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwivDPiDGTknFvrgipqvaVsigllv 114
                                   + t+   ++ e++  ++ ekf++  +++ee + k     ++e ++++i+DPiDGT+n ++ ip++ +si++++
  gi|15669107|ref|NP_247912.1|  41 TPTKRIDVIAENMAINILEKFSGGILISEEIGLKVV---GDELEYIFILDPIDGTYNALKSIPIYSTSIAVAK 110
                                   434444455556666678999999999999998888...8888999*************************97 PP

  == domain 2  score: 51.4 bits;  conditional E-value: 3e-17
                                   EEEEEETTTTEEECEETTTEEEETC..EEEEECTTS..EGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCHEEEBESSH CS
                    Inositol_P 120 lGviaqPllgqlysaakgkGaflng..eklplsrap..piseallvtlfavssrkdtseasllekvesavsaegvrsvgss 196
                                   +G++ + ++g ly a kg+G+fl+   ek+++++++  +++ea +v+lf +   +d  e      +e+ v++  vr +gs 
  gi|15669107|ref|NP_247912.1| 144 VGIVKNLATGDLYYAIKGEGSFLEKdgEKIKIETKNikDLKEA-SVGLFVYGLSNDLLE----FLKERKVRR--VRLFGSM 217
                                   89*********************887899*9999998555555.556666655555555....233334444..5899*** PP

                                   HHHHHHHHHTSTSEEEEEC..EBHHHHHHHHHHHHHTTEEEEESSSC....SSSTTSS.EEEEESCHHHHHHHHHHH CS
                    Inositol_P 197 alklaavaeGkadaylefg.rekkWDhAAGeaileeaGGvvtdakge....grlllar.giiaanqkelaellaaav 267
                                   al++++v++G +day++   +    D+A++ +i++e  ++vt+ +g+    ++ l++r ++i++n k l+++l+a++
  gi|15669107|ref|NP_247912.1| 218 ALEMCYVVSGALDAYINVNeNSRLCDIAGAYVICREGNAIVTNKNGKplnmKLHLMERtSLIVSN-KYLHKKLIALF 293
                                   ******************9866667**********************999877776662666666.******99986 PP

>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.4e-06     0.012      56     116 ..      38      94 ..       2     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-06
                        FBPase  56 vtGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSn 116
                                    +G   k++Dv+a+++ i+ l++     +l+SEE   l+v+    e +y+ ++DP+DG  n
  gi|15669107|ref|NP_247912.1|  38 ADGTPTKRIDVIAENMAINILEKF-SGGILISEEI-GLKVV--GDELEYIFILDPIDGTYN 94 
                                   468889***************986.7889999997.68999..78899**********877 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.7e-05       0.2      37      77 ..     312     350 ..     310     381 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.7e-05
               Methyltransf_31  37 seeaielArenaqklgldnveFeqgdieeleklledekfDl 77 
                                   +eeai+lA e+++ l+ +n+ F+++d+      +  +kfD+
  gi|15669107|ref|NP_247912.1| 312 KEEAINLAIEICKYLKDKNIPFCVEDFLRER--VGGDKFDI 350
                                   69***************************88..999****9 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.3   1.1e+03      54      77 ..      28      51 ..       9      59 .. 0.75
   2 ?    9.8   0.0   0.00015      0.55      54      85 ..     351     379 ..     306     392 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.3
                                  CC-SEEEEEESHHHHHHHHHHHCT CS
                      DAGK_cat 54 egvdlivvaGGDGtvsevlnglle 77
                                  e++d +v +G DGt  + +++++e
  gi|15669107|ref|NP_247912.1| 28 EKADEVVKIGADGTPTKRIDVIAE 51
                                  377999********9988888887 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00015
                                   CC-SEEEEEESHHHHHHHHHHHCTHHCTTSEE CS
                      DAGK_cat  54 egvdlivvaGGDGtvsevlnglleelatkppl 85 
                                   + ++ i+++GGDGt+  +   + +   +++p+
  gi|15669107|ref|NP_247912.1| 351 SAISHIIAIGGDGTILRASRLVNG---ETIPI 379
                                   46789*********9887766666...44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3582.50
//
Query:       gi|15669108|ref|NP_247913.1|  [L=266]
Description: indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase TrpC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.3e-70  235.3   4.6    7.1e-70  235.1   4.6    1.0  1  IGPS       Indole-3-glycerol phosphate synthase
     0.0028   17.5   2.5     0.0052   16.6   0.1    2.1  2  QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal
  ------ inclusion threshold ------
       0.57   10.6   3.1        3.4    8.1   0.1    2.5  2  PDZ        PDZ domain


Domain annotation for each model (and alignments):
>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.1   4.6   1.2e-73   7.1e-70       1     253 [.       4     262 ..       4     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 235.1 bits;  conditional E-value: 1.2e-73
                                   HHHCHHHHHHHHHHHHCCS-GGCCCCG........-SS-SS-HHHHCHCH.TTS-EEEEEE-SEETTTEESBS..S--HHH CS
                          IGPS   1 lekivaekkeevaeakkrqsladleaav......klakpkrsfaeaLres.ekklaliaEvKkaSPskglire..dfdpae 72 
                                   l++iva++k+ v+ +k++  +++l++ +       ++k k  + +a++++ e k  +i+E+K  SPskg ire    d+++
  gi|15669108|ref|NP_247913.1|   4 LDEIVANRKKMVEIEKRKDIIKNLRSFIdeldidVEKKRKLRLSKAIKKAkEIKNPIITEIKPSSPSKGSIREinLEDVKN 84 
                                   789999999999888777666555554443354446777788999**999778899***************9732348999 PP

                                   HHHHHTTT.-SEEEEE--CCCC---CCHHHHHHHH-SS-EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHH CS
                          IGPS  73 iAkkyeeagAsaiSVLteekyFqGsledLrevrqavslpvlrKdFiideyqieearalgadaiLLivkvledeeleelaea 153
                                   iA+++ e+gA+a+S+Lte+kyF+Gs+++L  v+++ ++p+l+KdFi+d yqi+ a  +ga+a+LLiv+ l+++   e+ ++
  gi|15669108|ref|NP_247913.1|  85 IANEMVEGGATALSILTEPKYFNGSYKNLI-VAREFDIPILMKDFIVDFYQIDVASEIGANAVLLIVSSLKEDI-GEFLDY 163
                                   *****************************7.55679**********************************9876.9999** PP

                                   HCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SE CS
                          IGPS 154 akslglevLvEvhdeeeleralklgakiiGvNnRnLktlevdlntteeLaklvpkdvllvaeSGiktredveklkeegvna 234
                                   ak+ +le LvE+h+e+e+++al++gakiiG+NnR+Lktl++dl tte+La+l+pk+ + v eSGi+t+e+++ + +   +a
  gi|15669108|ref|NP_247913.1| 164 AKENDLECLVETHSEDEIDIALDAGAKIIGINNRDLKTLKIDLSTTEKLAPLIPKNKIKVGESGIYTKEQLNYVLKF-TDA 243
                                   ****************************************************************************9.9** PP

                                   EEESHHHHC-TTHHHHHHH CS
                          IGPS 235 fLvGeslmrqedvekaire 253
                                    L+G+s+m++e+ ++++re
  gi|15669108|ref|NP_247913.1| 244 ALIGSSIMESENIREKVRE 262
                                   ****************998 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3     0.061   3.7e+02      85     128 ..      15      60 ..       1      99 [. 0.50
   2 !   16.6   0.1   8.7e-07    0.0052      62     156 ..     149     248 ..     141     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.061
                                   EEESSHHHHHHHHHHT-SEEEEES--H..HHHHHHHHHHHHHSTTS CS
                     QRPTase_C  85 vevesleeleevleaeadiimLDnfsv..eelkkaveelkeknkrv 128
                                   ve+e+ +++ + l    d   +D  +     l ka+++ ke+++ +
  gi|15669108|ref|NP_247913.1|  15 VEIEKRKDIIKNLRSFIDELDIDVEKKrkLRLSKAIKKAKEIKNPI 60 
                                   4444444444444444444444443331123334555444444444 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 8.7e-07
                                   HHSSHHHHHHHHHHHH.TTTSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT.....SEEEEESS- CS
                     QRPTase_C  62 aagsiveavksvreav.dkevkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkr.....vlievSGgv 136
                                   +++s++e + ++ +++ ++ +++ ve++s++e++ +l a+a ii + n + ++lk  + ++++ ++      +++  SG  
  gi|15669108|ref|NP_247913.1| 149 IVSSLKEDIGEFLDYAkENDLECLVETHSEDEIDIALDAGAKIIGINNRDLKTLKIDLSTTEKLAPLipknkIKVGESGIY 229
                                   5667777777777777244566***************************99999988887777666556666888889998 PP

                                   -TTTHHHHHCTT-SEEEECH CS
                     QRPTase_C 137 tlenveeyaksgvdvisvga 156
                                   t+e+++ + k   d+  +g+
  gi|15669108|ref|NP_247913.1| 230 TKEQLNYVLKFT-DAALIGS 248
                                   888888777666.5555554 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.5     0.037   2.2e+02      24      65 ..      55      89 ..      35      93 .. 0.75
   2 ?    8.1   0.1   0.00057       3.4      44      61 ..     185     202 ..     172     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.037
                                  SSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHH CS
                           PDZ 24 gdkgifvsevlpggaaeadglkvGDkIlsvNgvdvenvshee 65
                                  + k+ +++e+ p ++ + +       I ++N +dv+n+++e 
  gi|15669108|ref|NP_247913.1| 55 EIKNPIITEIKPSSPSKGS-------IREINLEDVKNIANEM 89
                                  6677888888888888888.......8888888888887775 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00057
                                   SSTTEEEEEETTEETTTS CS
                           PDZ  44 lkvGDkIlsvNgvdvenv 61 
                                   l +G kI+++N++d++++
  gi|15669108|ref|NP_247913.1| 185 LDAGAKIIGINNRDLKTL 202
                                   899***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1197  (0.0667633); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1900.59
//
Query:       gi|15669109|ref|NP_247914.1|  [L=149]
Description: hypothetical protein MJ_0919 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-07   30.5   0.6    4.9e-07   29.9   0.6    1.3  1  SepF      Cell division protein SepF
  ------ inclusion threshold ------
      0.032   14.1   0.1      0.051   13.4   0.1    1.3  1  KNTase_C  KNTase C-terminal domain
       0.09   13.0   0.6        2.6    8.3   0.6    2.2  1  ApbA_C    Ketopantoate reductase PanE/ApbA C terminal


Domain annotation for each model (and alignments):
>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.6   8.2e-11   4.9e-07       1      72 []      46     120 ..      46     120 .. 0.98

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 8.2e-11
                                   EEEEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTC...HHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-TT-EE CS
                          SepF   1 vvvveprsfedaqeiadalkegkiVilnledldk...eeakrivdflsgvvyaldGdiqkvgkkvflitPknvdi 72 
                                   ++v+ +++ +da +++   ++g+iVi +  +l+k   +e+  i+ +++  v + +G +  +g++ +litP+nv i
  gi|15669109|ref|NP_247914.1|  46 IKVCSIEDEKDAVNAIVMAEAGYIVIAKTPNLEKeidDEFIEIIRKMRNEVAKFGGMLLALGDEHLLITPRNVVI 120
                                   89**********************************************************************976 PP

>> KNTase_C  KNTase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   8.5e-06     0.051      15      84 ..      50     123 ..      40     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.5e-06
                      KNTase_C  15 eeeefvkaieealvgel.yEfigKlrnvrkegdetal...atlalqlAqyaallvgLsnrklysssatvlkEal 84 
                                     e+  +a++ ++++e  y +i+K  n++ke d +++   +++  ++A+++ +l +L + +l  + + v+ E l
  gi|15669109|ref|NP_247914.1|  50 SIEDEKDAVNAIVMAEAgYIVIAKTPNLEKEIDDEFIeiiRKMRNEVAKFGGMLLALGDEHLLITPRNVVIEKL 123
                                   557788899999999976999********99888776111566789*******************999998876 PP

>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.6   0.00043       2.6      88     124 ..      91     127 ..      43     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00043
                        ApbA_C  88 grktEidyinGavvklAeklgvetPvnellyellkal 124
                                   + + E+  + G +++l++++ + tP+n ++  l+k++
  gi|15669109|ref|NP_247914.1|  91 KMRNEVAKFGGMLLALGDEHLLITPRNVVIEKLIKEK 127
                                   4456788888888888888888888888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1258  (0.0701657); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1140.42
//
Query:       gi|15669110|ref|NP_247915.1|  [L=185]
Description: GTP-binding protein YphC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-19   69.6   0.0    3.1e-19   69.2   0.0    1.2  1  MMR_HSR1      50S ribosome-binding GTPase
    1.2e-11   44.4   0.0    1.7e-11   43.9   0.0    1.2  1  FeoB_N        Ferrous iron transport protein B
      2e-09   37.7   0.6    0.00013   22.1   0.1    2.3  2  Dynamin_N     Dynamin family
    3.3e-09   36.5   0.0    3.9e-07   29.8   0.0    2.4  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    4.4e-07   29.5   0.0      6e-07   29.1   0.0    1.2  1  Gtr1_RagA     Gtr1/RagA G protein conserved region
    1.6e-06   27.7   0.1      0.028   13.9   0.0    2.2  2  Arf           ADP-ribosylation factor family
    3.3e-06   27.1   0.1      0.015   15.2   0.0    2.1  2  RsgA_GTPase   RsgA GTPase
    6.3e-05   22.6   0.0    0.00013   21.6   0.0    1.5  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
    0.00015   21.7   0.4     0.0003   20.8   0.4    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    0.00046   19.6   0.4       0.45    9.8   0.0    2.1  2  Septin        Septin
    0.00047   20.4   0.1       0.16   12.2   0.0    2.3  2  Roc           Ras of Complex, Roc, domain of DAPkinase
     0.0092   15.7   0.0       0.54   10.0   0.0    2.2  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
  ------ inclusion threshold ------
      0.011   16.2   0.0      0.011   16.2   0.0    1.3  1  ABC_tran      ABC transporter
      0.016   14.8   0.1        1.9    8.1   0.0    2.2  2  Ras           Ras family
      0.019   15.2   0.1      0.036   14.3   0.1    1.4  1  AAA_28        AAA domain
      0.023   15.2   0.0      0.037   14.5   0.0    1.4  1  AAA_23        AAA domain
       0.03   14.0   0.7      0.048   13.4   0.7    1.7  1  AAA_15        AAA ATPase domain
      0.032   14.0   0.1       0.22   11.3   0.0    2.1  2  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.057   12.6   0.5        4.4    6.3   0.4    2.2  2  G-alpha       G-protein alpha subunit
      0.071   12.9   0.7       0.23   11.3   0.2    2.1  2  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
      0.097   12.4   0.9       0.61    9.8   0.1    2.3  3  AAA_24        AAA domain
       0.14   11.9   0.0       0.24   11.2   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
       0.22   10.1   0.0       0.26    9.8   0.0    1.1  1  MutL          MutL protein


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.0   3.9e-22   3.1e-19       1     114 []       7     137 ..       7     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 3.9e-22
                                   EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE..........ETT.EEEEEEECGGCSS..HHHHHH... CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk..........lkg.keielvDtpGlie..gaseek... 64 
                                   ++ai+G  N+GKS+++nal+g+ ++ vs+  gtT+ ++++ +             +  ++++vD+ Gl+   ++++     
  gi|15669110|ref|NP_247915.1|   7 KIAIIGPENAGKSSIMNALFGKyVSLVSEVGGTTKMPIKRYWGklkigrikeeP-EfVNLVFVDLGGLYTttDKQSPImtp 86 
                                   69********************999************99988755555543322.23559*******98533222222344 PP

                                   .HHHHHHHHHHCTSEEEEEEETT...TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  65 .glgkaflaleeadlillvvdas...eeklkpldeeleelleeakkplilvlnk 114
                                     l+k+f++++++d+i++v+d s    +++++l ++l +++   +kp+i+v+nk
  gi|15669110|ref|NP_247915.1|  87 kVLEKTFEEINDSDMIIHVIDGSvglLRSFERL-HHLLKFR--YQKPIIVVINK 137
                                   4799*****************774442233333.5555554..79********8 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   2.2e-14   1.7e-11       2     154 ..       7     177 ..       6     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 2.2e-14
                                   EEEEEESTTSSHHHHHHHHHTTSEE.EEESTTSS...SEEEEEEEEE.......TTEEEEEEE----SSS....SSSSHHH CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqk.vgNwpGvt...vekkegklkl.......kgkeveivDlPGiYsl....sayseee 67 
                                   ++a++G  n+Gk++++nal g++ + v+   G+t   +++  gklk+       +  ++ +vDl G Y+     s++ + +
  gi|15669110|ref|NP_247915.1|   7 KIAIIGPENAGKSSIMNALFGKYVSlVSEVGGTTkmpIKRYWGKLKIgrikeepEFVNLVFVDLGGLYTTtdkqSPIMTPK 87 
                                   79*******************98532555555553337777777776544433222567889*******954433334444 PP

                                   HHHHHHHHCTSSSEEEEEEEGG.GHHHHHHHHHHHHHTT..SSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTT CS
                        FeoB_N  68 kvardflleeepdvvvnvvdat.nlernLyLtlqllelg..vpvvlalnmideaekkgieidlkkLsekLgvpvvktsakk 145
                                    + ++f   ++ d++++v+d +  l r++  +  ll ++  +p+++++n++d ++++  e  ++ ++++++   + +sak+
  gi|15669110|ref|NP_247915.1|  88 VLEKTFEEINDSDMIIHVIDGSvGLLRSFERLHHLLKFRyqKPIIVVINKCDLLNDSDKEHLKNYVERRIKNTPIFVSAKT 168
                                   444445556889********6527******9999998754499************************************** PP

                                   TBTHHHHHH CS
                        FeoB_N 146 kegieellk 154
                                    egi ell+
  gi|15669110|ref|NP_247915.1| 169 FEGIPELLD 177
                                   ******987 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   1.7e-07   0.00013       1      36 [.       8      44 ..       8      47 .. 0.84
   2 !   13.8   0.0   5.7e-05     0.045     100     167 ..      62     137 ..      50     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.7e-07
                                  EEEEEBTTTTHHHHHHHHHTS--S-.--SSS---S-E CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilp.rgpnptTrrpl 36
                                  ia++G  ++GKSS++naL g+ +   ++ + tT  p+
  gi|15669110|ref|NP_247915.1|  8 IAIIGPENAGKSSIMNALFGKYVSLvSEVGGTTKMPI 44
                                  89********************977255567777776 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.7e-05
                                   S-SEEEEE---B-SSSGTTS........HHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTT.EEEEEE- CS
                     Dynamin_N 100 vkgltlvDlPGldsvnkrdq........elvkeyikkadiilavtsanhdlsnsealflarevdpkgkr.tivvltk 167
                                     +l++vDl Gl  + +++         e ++e i+++d+i++v + ++ l +s  ++l+++++ + ++ +ivv++k
  gi|15669110|ref|NP_247915.1|  62 FVNLVFVDLGGLYTTTDKQSpimtpkvlEKTFEEINDSDMIIHVIDGSVGLLRS-FERLHHLLKFRYQKpIIVVINK 137
                                   5699**********999999********99*******************99955.6666666666555547888877 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.028        22       5      24 ..       7      26 ..       3      42 .. 0.88
   2 !   29.8   0.0     5e-10   3.9e-07      91     193 ..      96     184 ..      89     185 .] 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.028
                                  EEEEEESTTSSHHHHHHHHH CS
                      GTP_EFTU  5 nigiighvDhGKtTLtdrLl 24
                                  +i+iig  ++GK++++ +L 
  gi|15669110|ref|NP_247915.1|  7 KIAIIGPENAGKSSIMNALF 26
                                  699*************9996 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 5e-10
                                   HHT-SEEEEEEETTTBSTHHHHHHHHHH.HHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEE CS
                      GTP_EFTU  91 lrvlDgavlvvdaveGvepqteevlrla.lkegvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevp 169
                                   ++  D+ + v+d + G     e++ +l+  +++ piiv+iNK+D l +++ +++++ v++++            k+    +
  gi|15669110|ref|NP_247915.1|  96 INDSDMIIHVIDGSVGLLRSFERLHHLLkFRYQKPIIVVINKCDLLnDSDKEHLKNYVERRI------------KN----T 160
                                   56789***********9888887666551578888***********5555555555566555............33....5 PP

                                   EEEEBTTTTBTHHHHHHHHHHHSH CS
                      GTP_EFTU 170 vvfgSalkgegvktllealvellp 193
                                    +f+Sa++ eg+ +ll+ ++++l+
  gi|15669110|ref|NP_247915.1| 161 PIFVSAKTFEGIPELLDIIIKYLK 184
                                   79*******************986 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   7.7e-10     6e-07       1     142 [.       7     159 ..       7     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 7.7e-10
                     Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgati.........dveksevrfl.gnltlnlwDcgGqeafvee....yls 67 
                                   k+ ++G++++GK+s+ + +F +y+   + ++g t+         +++  +++   ++++l  +D+gG  +  ++    +  
  gi|15669110|ref|NP_247915.1|   7 KIAIIGPENAGKSSIMNALFGKYVSL-VSEVGGTTkmpikrywgKLKIGRIKEEpEFVNLVFVDLGGLYTTTDKqspiMTP 86 
                                   67789******************987.66676666699999999777777775437899*********9999995554334 PP

                     Gtr1_RagA  68 sqkeeifrnvg...vliyVfDvesreleedletlkeilealrqyspeakvfvlihKmDliqedereeifeerkeeire 142
                                   +  e+ f++++    +i+V+D +   l +++e+l    ++l ++  +  + v i+K+Dl++++ +e++ +  +++i++
  gi|15669110|ref|NP_247915.1|  87 KVLEKTFEEINdsdMIIHVIDGS-VGLLRSFERL----HHLLKFRYQKPIIVVINKCDLLNDSDKEHLKNYVERRIKN 159
                                   556788888877779******99.4455555555....5556666677899*************99999999888876 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00014      0.11      11      37 ..       2      28 ..       1      53 [. 0.85
   2 !   13.9   0.0   3.6e-05     0.028      81     174 ..      98     182 ..      89     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                  .TTEEEEEEEESTTSSHHHHHHHHHHS CS
                           Arf 11 kkkelrilllGLDnaGKtTilkklkle 37
                                  ++ke++i ++G +naGK+ i++ l  +
  gi|15669110|ref|NP_247915.1|  2 QDKEFKIAIIGPENAGKSSIMNALFGK 28
                                  489******************998655 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.6e-05
                                   TESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTT CS
                           Arf  81 ktdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkg 161
                                   + d +i+v+D +    l  + e L++ll+ +     +++v+ NK Dl ++ ++e+l++ ++ +++k ++++ +   sa + 
  gi|15669110|ref|NP_247915.1|  98 DSDMIIHVIDGSV--GLLRSFERLHHLLKFRYQ--KPIIVVINKCDLLNDSDKEHLKNYVE-RRIK-NTPIFV---SAKTF 169
                                   5688999999765..477788999999988764..5889999**********999998765.6788.677665...67777 PP

                                   BTHHHHHHHHHHH CS
                           Arf 162 eglkeglewlses 174
                                   eg+ e l+ ++++
  gi|15669110|ref|NP_247915.1| 170 EGIPELLDIIIKY 182
                                   8888888877765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00077       0.6     102     131 ..       8      37 ..       3      44 .. 0.84
   2 !   15.2   0.0     2e-05     0.015      47      95 ..     129     177 ..     101     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00077
                                   EEEECSTTSSHHHHHHHHCTT-----S--- CS
                   RsgA_GTPase 102 svlvGqSGvGKStLinallpelelktgevs 131
                                   ++++G+  +GKS+++nal ++    ++ev 
  gi|15669110|ref|NP_247915.1|   8 IAIIGPENAGKSSIMNALFGKYVSLVSEVG 37 
                                   5789****************9888888775 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2e-05
                                   -EEEEEEE-GGG--HHHHHHHHHH.HHHHTTSEEEE--TTTHTTHHHHHH CS
                   RsgA_GTPase  47 iepvivlnKiDlleeeeeleelke.elealgyevllvsaktkegleelke 95 
                                    ++++v+nK+Dll++++  e+lk+   +++  ++++vsakt eg+ el +
  gi|15669110|ref|NP_247915.1| 129 KPIIVVINKCDLLNDSD-KEHLKNyVERRIKNTPIFVSAKTFEGIPELLD 177
                                   467899***********.444444145689999**********9999876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.7   2.9e+03       5      21 ..      10      26 ..       7      32 .. 0.79
   2 !   21.6   0.0   1.7e-07   0.00013      73     171 ..      53     158 ..      46     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.7
                                  EEESTTCCHHHHHHHHH CS
                          cobW  5 ltGflGsGKTtLlnhll 21
                                  + G+  +GK++++n+l 
  gi|15669110|ref|NP_247915.1| 10 IIGPENAGKSSIMNALF 26
                                  66777899*99999875 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.7e-07
                                   HHHHHHHHTT-SEEEEEECTTTTHHHH...HTT....SHHHHHCCCECEEEEEEETTTH..CCHCCHHHHHHHHHHTSSEE CS
                          cobW  73 lealeereerldviliEttGlaePapv...aft....eeelksdltldavvavvDaknl.eaeeekieekaedqlaaadll 145
                                   + +++e++e ++++++  +Gl + +     ++t    e+++++    d+++ v+D++    ++ e+ +++++   ++  ++
  gi|15669110|ref|NP_247915.1|  53 IGRIKEEPEFVNLVFVDLGGLYTTTDKqspIMTpkvlEKTFEEINDSDMIIHVIDGSVGlLRSFERLHHLLKFRYQKPIIV 133
                                   567788888889999999997666544446444567799999999***********654788999**************** PP

                                   EEE-HHHHCHC..HHHHHHHHHHHHT CS
                          cobW 146 vlnKtDlldeeallekleerlrqlnp 171
                                   v+nK+Dll+++++ e+l++++++  +
  gi|15669110|ref|NP_247915.1| 134 VINKCDLLNDSDK-EHLKNYVERRIK 158
                                   ***********76.999999876544 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.4   3.8e-07    0.0003      55     105 ..     128     184 ..      90     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.8e-07
                  MMR_HSR1_Xtn  55 YipclyvlNKiDlisleeldelare......pnsvviSaekelnldeLkekiweeLn 105
                                    +p ++v+NK+Dl+++++ ++l++       +  +++Sa++  ++ eL++ i ++L+
  gi|15669110|ref|NP_247915.1| 128 QKPIIVVINKCDLLNDSDKEHLKNYverrikNTPIFVSAKTFEGIPELLDIIIKYLK 184
                                   47899********88887777777334566568899****************99985 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00058      0.45       3      33 ..       4      34 ..       2      99 .. 0.73
   2 !    8.3   0.1    0.0016       1.3     142     176 ..     129     163 ..     113     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00058
                                  EEEEEEEEEBTTSSCCCCCCTTSSSS----- CS
                        Septin  3 ieftlmvvGesglGkttlintlfetdlieee 33
                                   ef + ++G +  Gk++++n+lf + +   +
  gi|15669110|ref|NP_247915.1|  4 KEFKIAIIGPENAGKSSIMNALFGKYVSLVS 34
                                  5899*******************98766554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0016
                                   S-EEEEESSGGGS-HHHHHHHHHHHHHHHHHTT-- CS
                        Septin 142 vnliPviaKaDtltkeElkefKkkireeleeeeik 176
                                     +i vi K D l +++ +++K+ + ++++++ i 
  gi|15669110|ref|NP_247915.1| 129 KPIIVVINKCDLLNDSDKEHLKNYVERRIKNTPIF 163
                                   56999************************998775 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00021      0.16       1      24 [.       7      30 ..       7      81 .. 0.85
   2 ?    6.5   0.0     0.012       9.3      79     120 .]      98     140 ..      84     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                                  EEEEESSTTSSHHHHHHCHCT-CC CS
                           Roc  1 KvvlvGdsgvGKtsllkrfvedkf 24
                                  K+ ++G +++GK+s+++ +  + +
  gi|15669110|ref|NP_247915.1|  7 KIAIIGPENAGKSSIMNALFGKYV 30
                                  99***************9987655 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.012
                                   TSCEEEEEEEGHHH.HCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                           Roc  79 eaalailvydsrss.enlkeWlkelkkvagkspvilvgnkiDl 120
                                   +++++i v+d +    +  e l++l k + ++p+i+v+nk+Dl
  gi|15669110|ref|NP_247915.1|  98 DSDMIIHVIDGSVGlLRSFERLHHLLKFRYQKPIIVVINKCDL 140
                                   6677777777443313344556778888999**********95 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.062        49       3      24 ..       7      28 ..       5      34 .. 0.88
   2 !   10.0   0.0   0.00069      0.54      88     141 ..     127     179 ..      97     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.062
                     PduV-EutP  3 killiGkvgsGKttLtqalkge 24
                                  ki +iG+ ++GK ++++al g+
  gi|15669110|ref|NP_247915.1|  7 KIAIIGPENAGKSSIMNALFGK 28
                                  7999************999876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00069
                     PduV-EutP  88 fnkeviGiitkidlaedeenieaveelLksaGaekifevsavekegieellkyl 141
                                    +k++i +i k dl +d ++ e  +++++    ++ + vsa + egi ell+ +
  gi|15669110|ref|NP_247915.1| 127 YQKPIIVVINKCDLLND-SDKEHLKNYVERRIKNTPIFVSAKTFEGIPELLDII 179
                                   68*************55.55577788888888888899***********99876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.2   0.0   1.5e-05     0.011      13      67 ..       7      59 ..       3     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-05
                                  EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                      ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe 67
                                  k+ai+G+  aGKS+++++l g++     e+   g  +k+ +++ + + +ig +++e
  gi|15669110|ref|NP_247915.1|  7 KIAIIGPENAGKSSIMNALFGKYVSLVSEV---GGTTKMpIKRYWGKLKIGRIKEE 59
                                  79*******************998766666...33333324444555555555555 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.021        17       1      19 [.       7      25 ..       7      36 .. 0.87
   2 ?    8.1   0.0    0.0025       1.9     102     159 ..     127     182 ..      90     185 .] 0.71

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.021
                                  EEEEEESTTSSHHHHHHHH CS
                           Ras  1 KlvlvGdsavGKtslllrf 19
                                  K+ ++G ++ GK+s+++  
  gi|15669110|ref|NP_247915.1|  7 KIAIIGPENAGKSSIMNAL 25
                                  899************9865 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0025
                                   TTTSEEEEEEETTTGGGG-SS-HHHHH.HHHHHHTSEEEEEBTTTTCTHHHHHHHHHHH CS
                           Ras 102 eenvpivLvGnKvDleekravsteege.elakelglkfletSAktnenveeafeellre 159
                                     + pi++v nK+Dl ++    +e+ +  + ++++ + + +SAkt e++ e+++ +++ 
  gi|15669110|ref|NP_247915.1| 127 Y-QKPIIVVINKCDLLNDSD--KEHLKnYVERRIKNTPIFVSAKTFEGIPELLDIIIKY 182
                                   2.4699*********98443..3333304556677777888999999998888877765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   4.6e-05     0.036       1      32 [.       7      38 ..       7      40 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-05
                        AAA_28  1 kivitGgestGKTtlleaLaargypvvpEaar 32
                                  ki+i+G+e +GK+++++aL  + ++ v E++ 
  gi|15669110|ref|NP_247915.1|  7 KIAIIGPENAGKSSIMNALFGKYVSLVSEVGG 38
                                  79*************************99985 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.8e-05     0.037      23     114 ..       9      98 ..       7     172 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.8e-05
                        AAA_23  23 lItGpNGaGKTTildAik...laLygetprlsrks.grgfeksdveiesegkvkayveltfenkdgrytrsiererelskk 99 
                                   +I+Gp  aGK++i++A+      L  e++++ +   +r + k +  i+  ++ +++v l f + +g y    + + + s  
  gi|15669110|ref|NP_247915.1|   9 AIIGPENAGKSSIMNALFgkyVSLVSEVGGTTKMPiKRYWGKLK--IGRIKEEPEFVNLVFVDLGGLY----TTTDKQSPI 83 
                                   79*************98733223444443333322344444444..4455678888999988888854....334444444 PP

                        AAA_23 100 kgkttkkaklellei 114
                                   ++ ++ ++++e++++
  gi|15669110|ref|NP_247915.1|  84 MTPKVLEKTFEEIND 98 
                                   444444444444444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7   6.2e-05     0.048      25      43 ..       7      25 ..       2     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.2e-05
                        AAA_15 25 ltvliGkNnsGKSsileal 43
                                     +iG+ n+GKSsi++al
  gi|15669110|ref|NP_247915.1|  7 KIAIIGPENAGKSSIMNAL 25
                                  568***************9 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.45   3.5e+02       1      16 [.      10      25 ..      10      34 .. 0.89
   2 ?   11.3   0.0   0.00028      0.22     152     182 ..     124     154 ..      85     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.45
                    ATP_bind_1  1 vvGpaGsGKttfvgal 16
                                  ++Gp  +GK+++++al
  gi|15669110|ref|NP_247915.1| 10 IIGPENAGKSSIMNAL 25
                                  79***********987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00028
                    ATP_bind_1 152 mlrlelPhvvvlnkfDllkeklekeleffed 182
                                    +r++ P +vv+nk+Dll+++++++l+ + +
  gi|15669110|ref|NP_247915.1| 124 KFRYQKPIIVVINKCDLLNDSDKEHLKNYVE 154
                                   568899*************989999988765 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.021        17      22      42 ..       4      24 ..       1      31 [. 0.88
   2 ?    6.3   0.4    0.0057       4.4     268     295 ..     127     153 ..      93     185 .] 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.021
                                  .EEEEEEEESTTSSHHHHHHH CS
                       G-alpha 22 revkllllGqseSGKsTilkq 42
                                  +e+k+ ++G +  GKs+i++ 
  gi|15669110|ref|NP_247915.1|  4 KEFKIAIIGPENAGKSSIMNA 24
                                  589***************986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0057
                                   TTSEEEEEEE-HHHHHHHCCCS-GGGCC CS
                       G-alpha 268 kntpiiLflnKlDileeKlkkgklskyf 295
                                    ++pii++ nK+D+l+   +k++l++y+
  gi|15669110|ref|NP_247915.1| 127 YQKPIIVVINKCDLLNDS-DKEHLKNYV 153
                                   5899***********975.355666665 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00029      0.23      39      58 .]     121     139 ..      99     139 .. 0.75
   2 ?   -1.5   0.0       2.8   2.2e+03      36      52 ..     148     164 ..     145     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                          NOG1  39 eeikelfankpvivvlnKiD 58 
                                   + +k + + kp+ivv+nK+D
  gi|15669110|ref|NP_247915.1| 121 HLLKFRYQ-KPIIVVINKCD 139
                                   44455555.9*********9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.8
                          NOG1  36 sLleeikelfankpviv 52 
                                   +L + ++ +++n p++v
  gi|15669110|ref|NP_247915.1| 148 HLKNYVERRIKNTPIFV 164
                                   67788999999999876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00078      0.61       3      22 ..       6      25 ..       4      48 .. 0.80
   2 ?   -2.9   0.0       5.8   4.6e+03     143     161 ..      79      97 ..      73     105 .. 0.68
   3 ?    0.7   0.0      0.47   3.7e+02     118     168 ..     122     180 ..     114     184 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00078
                        AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                   ki+i+Gp+ +GK+++++ l
  gi|15669110|ref|NP_247915.1|  6 FKIAIIGPENAGKSSIMNAL 25
                                  69**************9988 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.8
                        AAA_24 143 akytrlepklgkktanelk 161
                                   ++   ++pk+ +kt++e++
  gi|15669110|ref|NP_247915.1|  79 KQSPIMTPKVLEKTFEEIN 97 
                                   3456788888888888886 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.47
                        AAA_24 118 lqelrk...nvifiahektrkdedpege.....akytrlepklgkktanelkeevDlvl 168
                                   l ++r+    +++i +++  +d d+e+        +   ++ ++ kt++ ++e +D+++
  gi|15669110|ref|NP_247915.1| 122 LLKFRYqkpIIVVINKCDLLNDSDKEHLknyveRRIKNTPIFVSAKTFEGIPELLDIII 180
                                   55555565556666666666666665554444445556667788999999999999997 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00031      0.24      24      42 ..       7      25 ..       1      27 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                        AAA_29 24 atlltGpsGsGKSTllDAi 42
                                   + ++Gp  +GKS+++ A+
  gi|15669110|ref|NP_247915.1|  7 KIAIIGPENAGKSSIMNAL 25
                                  578*************996 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00034      0.26     242     332 ..      58     162 ..      47     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00034
                          MutL 242 eekglgdllvvDvGG..aTTdvhsvaegspekekvllk.lpeprakrtVegdLGmrvsaknvleeageeelare..l.... 313
                                   ee ++ +l+ vD+GG  +TTd  s +   +  ek++ + ++++++   + g +G+  s + + + ++ +  +    +    
  gi|15669110|ref|NP_247915.1|  58 EEPEFVNLVFVDLGGlyTTTDKQSPIMTPKVLEKTFEEiNDSDMIIHVIDGSVGLLRSFERLHHLLKFRYQKPIivVinkc 138
                                   4566889********6669*****999999999999999999****************99998887665544444313444 PP

                          MutL 314 .....iseeelrerlenlmerpkt 332
                                         ++e+l++++e++ +++ +
  gi|15669110|ref|NP_247915.1| 139 dllndSDKEHLKNYVERRIKNTPI 162
                                   556777788888888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1199.78
//
Query:       gi|15669111|ref|NP_247916.1|  [L=300]
Description: hypothetical protein MJ_0921 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-11   44.1   2.4      3e-08   33.7   0.1    3.9  3  DUF1743   Domain of unknown function (DUF1743)


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.13   2.4e+03      51      75 ..       5      45 ..       2      65 .. 0.66
   2 !   33.7   0.1   1.7e-12     3e-08       1     113 [.     145     235 ..     145     238 .. 0.88
   3 !    2.4   0.1    0.0085   1.5e+02       3      13 ..     274     284 ..     272     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.13
                                  TTCECTSEBTTTTCECCS-STTSS................E CS
                       DUF1743 51 ypetfdnvDlshklvvlvPhtpdp................v 75
                                  y++++  vD + +lv +v + p+p                +
  gi|15669111|ref|NP_247916.1|  5 YKSVIAMVDDALNLVEIVEEHPCPngsewviyqyqrtsplI 45
                                  67777788888888888888888888888444444444444 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 1.7e-12
                                   TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSS....... CS
                       DUF1743   1 grgiiGAtaalganialedstyEllaYreperwgerevdeesvieadektypetfdnvDlshklvvlvPhtpdp....... 74 
                                   +++++GAt++l+++i le +  E l Y                                l+h++v+l+P +p++       
  gi|15669111|ref|NP_247916.1| 145 DTKEEGATWVLAHEIGLE-VEKEGLGY-------------------------------YLDHTIVQLYPGNPNKtqncvsi 193
                                   79999********99986.44444443...............................389******************** PP

                                   .EEEEEEES-HHHHHHHHHCSEE..S-EEC..EEEEEESTTS CS
                       DUF1743  75 .vlfGirgedpeallkaakeilskeeesee..mavfrtnqgt 113
                                    + f++++e++++l k++k++l++++ s+e  mav+ ++ ++
  gi|15669111|ref|NP_247916.1| 194 aLSFAVYPEYKYKLDKFIKKLLKERSLSDEtaMAVYYGLFPS 235
                                   ************************************988666 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.0085
                                   HHHHHHHHHH- CS
                       DUF1743   3 giiGAtaalga 13 
                                   giiGA+aalg+
  gi|15669111|ref|NP_247916.1| 274 GIIGAVAALGL 284
                                   89*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2076.84
//
Query:       gi|15669112|ref|NP_247917.1|  [L=138]
Description: hypothetical protein MJ_0922 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-33  115.4   7.6    1.1e-17   64.2   1.0    2.1  2  CBS            CBS domain
  ------ inclusion threshold ------
      0.025   14.7   0.0          7    6.8   0.0    2.2  2  sCache_3_2     Single cache domain 3
      0.029   14.2   0.1        1.2    9.0   0.0    2.5  3  CAAD           CAAD domains of cyanobacterial aminoacyl-tRNA 
       0.12   12.5   2.5       0.13   12.3   0.3    2.0  2  Thioredoxin_3  Thioredoxin domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.8   1.6e-18     7e-15       1      51 [.      10      60 ..      10      60 .. 0.98
   2 !   64.2   1.0   2.5e-21   1.1e-17       1      56 [.      75     135 ..      75     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.6e-18
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51
                                  V+d+mt++v+t++  + + ea+e+m ++++s+lPV+d+++k++Givt +D+
  gi|15669112|ref|NP_247917.1| 10 VKDVMTKNVITAKRHEGVVEAFEKMLKYKISSLPVIDDENKVIGIVTTTDI 60
                                  89************************************************8 PP

  == domain 2  score: 64.2 bits;  conditional E-value: 2.5e-21
                                   HHHHSBSSCEEEETTSBHHHHHHHHH...HHT..SSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 Vgdimtrdvvtvppdttleealelmr...ekg..vsrlPVVdedgklvGivtlrDllrall 56 
                                   +gd+mt+dv+t+++d+++ ea+++m    +k+  +++lPVVd+++klvGi+++ D++r ++
  gi|15669112|ref|NP_247917.1|  75 IGDVMTKDVITIHEDASILEAIKKMDisgKKEeiINQLPVVDKNNKLVGIISDGDIIRTIS 135
                                   69***********************655544479***********************9876 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0016         7     108     123 ..      41      56 ..      20      65 .. 0.88
   2 ?    6.0   0.0    0.0027        12     108     125 ..     111     128 ..      99     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0016
                    sCache_3_2 108 klPvfdadgrviGivs 123
                                    lPv+d++++viGiv 
  gi|15669112|ref|NP_247917.1|  41 SLPVIDDENKVIGIVT 56 
                                   79************95 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0027
                    sCache_3_2 108 klPvfdadgrviGivsvG 125
                                   +lPv+d++++++Gi+s G
  gi|15669112|ref|NP_247917.1| 111 QLPVVDKNNKLVGIISDG 128
                                   79*************855 PP

>> CAAD  CAAD domains of cyanobacterial aminoacyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         1   4.5e+03      61      79 ..      16      34 ..      14      38 .. 0.74
   2 ?    3.1   0.0     0.019        86      37      60 ..      39      62 ..      27      81 .. 0.83
   3 ?    9.0   0.0   0.00026       1.2      28      53 ..     100     125 ..      73     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1
                          CAAD 61 ryLlkaekRqellekiksl 79
                                  +++++a+  + ++e ++++
  gi|15669112|ref|NP_247917.1| 16 KNVITAKRHEGVVEAFEKM 34
                                  6788888888888888776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.019
                          CAAD 37 iddiPllpplleLvGlgytgwFvy 60
                                  i ++P++    +++G++ t+   y
  gi|15669112|ref|NP_247917.1| 39 ISSLPVIDDENKVIGIVTTTDIGY 62
                                  899*************99876555 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00026
                          CAAD  28 klalavldaiddiPllpplleLvGlg 53 
                                    ++ +  + i+++P++ +  +LvG++
  gi|15669112|ref|NP_247917.1| 100 DISGKKEEIINQLPVVDKNNKLVGII 125
                                   555666689***************97 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3     3e-05      0.13      20      69 ..      10      58 ..       5      65 .. 0.78
   2 ?   -0.5   0.1      0.29   1.3e+03      54      63 ..     114     123 ..      89     135 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                                  HHHHCHCCTCECEEEC.C.TTHHHHHHCT-SSSSEEECTTCEEEESS---CC CS
                 Thioredoxin_3 20 vkeaaaekgikaevek.v.tdfeeiekygVmsvPalvidgkvvvsGkvpsee 69
                                  vk +++++ i+a+ ++ v + fe++ ky++ s P  vid++ +v G + ++ 
  gi|15669112|ref|NP_247917.1| 10 VKDVMTKNVITAKRHEgVvEAFEKMLKYKISSLP--VIDDENKVIG-IVTTT 58
                                  566777777888544424699*************..8*********.55444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.29
                                   ECTTCEEEES CS
                 Thioredoxin_3  54 vidgkvvvsG 63 
                                   v+d + + +G
  gi|15669112|ref|NP_247917.1| 114 VVDKNNKLVG 123
                                   4455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1042.54
//
Query:       gi|15669113|ref|NP_247918.1|  [L=297]
Description: hypothetical protein MJ_0923 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0012   19.1   1.0     0.0027   18.0   1.0    1.6  1  Methylase_S  Type I restriction modification DNA specificity 


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.0   1.5e-07    0.0027     115     150 ..     243     284 ..     209     293 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-07
                                   H......CCSSTTT---HHHHCC-EEEE--HHHHHHHHHHHH CS
                   Methylase_S 115 l......svgstqpkltkenlkkikIplPpleeQkkIakiLs 150
                                   +      ++  ++ +++ e lkk+++++P+ eeQk+I+k+L 
  gi|15669113|ref|NP_247918.1| 243 YidkeikINCKNMLNVDEELLKKYNVKIPSEEEQKEILKTLV 284
                                   233334456788899************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1278  (0.0712812); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1868.82
//
Query:       gi|15669114|ref|NP_247919.1|  [L=263]
Description: capsular polysaccharide biosynthesis protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.1e-18   65.3   1.8    6.1e-18   65.3   1.8    2.1  2  AAA_31       AAA domain
      6e-16   58.7   1.0    7.2e-16   58.4   0.1    1.6  2  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
      7e-09   35.5   3.6      1e-08   35.0   1.2    2.5  3  ParA         NUBPL iron-transfer P-loop NTPase
    1.7e-08   34.2   6.3    3.5e-06   26.7   0.6    2.3  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
      2e-06   27.3   0.0    3.1e-06   26.7   0.0    1.3  1  MipZ         ATPase MipZ
    3.9e-06   26.5   0.0    9.6e-06   25.2   0.0    1.7  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    9.3e-05   21.8   2.4    9.3e-05   21.8   2.4    2.6  2  ArsA_ATPase  Anion-transporting ATPase
    0.00012   21.5   0.3    0.00021   20.7   0.3    1.4  1  VirC1        VirC1 protein
     0.0054   16.2   1.1     0.0076   15.7   0.3    1.6  2  PhoH         PhoH-like protein
      0.009   15.6   0.1      0.022   14.4   0.1    1.7  1  AAA_25       AAA domain
  ------ inclusion threshold ------
       0.01   16.2   0.5      0.028   14.8   0.5    1.7  2  CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, olig
      0.023   14.7   0.8      0.079   13.0   0.0    2.0  2  ResIII       Type III restriction enzyme, res subunit
       0.14   12.0   0.0       0.19   11.6   0.0    1.3  1  APS_kinase   Adenylylsulphate kinase


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   1.8   4.5e-21   6.1e-18       1     153 [.       8     151 ..       8     171 .. 0.77
   2 ?   -1.9   0.2         2   2.7e+03      82     100 ..     220     238 ..     180     260 .. 0.51

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 4.5e-21
                        AAA_31   1 gkvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkvenl 81 
                                   +kvI+++  KGG GKT  + n aaalak+gkk+Ll+D D  + + ++l   k++    l +++ ee  ik+ai++t +en+
  gi|15669114|ref|NP_247919.1|   8 MKVITFSIAKGGTGKTIITANAAAALAKKGKKILLIDGDVGSKSLSHLLNVKSN--IFLADIIEEERPIKDAIVNTPIENI 86 
                                   79*************************************976655544333333..478888889*********9999999 PP

                        AAA_31  82 dlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpP.sLglltenaLvasdsviipvqaeaya 153
                                   +l+    +La++ +         +ilk+ ++++  +YDy++iD+p  s g+ t  aL  sd++i +++ +a+ 
  gi|15669114|ref|NP_247919.1|  87 ELLAVGKSLADYLKFD------INILKR-FKEL-GDYDYVFIDAPStSSGVETYLALGLSDYFIPVLDYTAFG 151
                                   9999888888774332......233333.3443.57********97256788999********9888887763 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                        AAA_31  82 dlipssidLaeaeielvel 100
                                   +l  s+ +++e  +++v++
  gi|15669114|ref|NP_247919.1| 220 YLTSSDKKFVEEIDKIVDA 238
                                   3334444433333333333 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.1   5.2e-19   7.2e-16       6     126 ..      16     217 ..      11     219 .. 0.87
   2 ?   -3.0   0.0       5.3   7.3e+03      57      71 ..     233     247 ..     226     259 .. 0.52

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 5.2e-19
                                   SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.......HTTEB-HHHH......................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxx......................... RF
                          CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.......leglendiep......................... 54 
                                    kGG+GKT ++an a+ala++g+++ll+D D+ +++l++       +                                  
  gi|15669114|ref|NP_247919.1|  16 AKGGTGKTIITANAAAALAKKGKKILLIDGDVGSKSLSHllnvksnI-------FLadiieeerpikdaivntpieniell 89 
                                   69************************************855444442.......33556666689**************** PP

                                   ...............................................................CCHCCCHHHHHHCHCHHH CS
                                   ...............................................................xxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ...............................................................dlkrllellealgkkkal 72 
                                                                                                  +l+     +++++++k+ 
  gi|15669114|ref|NP_247919.1|  90 avgksladylkfdinilkrfkelgdydyvfidapstssgvetylalglsdyfipvldytafgpSLQG---AINTIVIGKNY 167
                                   **********************************************************998665555...55556666666 PP

                                   H...EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                   x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  73 l.lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparge 126
                                   l  ++ag+++n+ +     ++ ++++++++   g++++ +i++++ v +++a++e
  gi|15669114|ref|NP_247919.1| 168 LeSTPAGFIINKAEDL--PESVINDIKKIL---GLECISIIHKNSLVEQSYAKKE 217
                                   679*********8765..999999999999...************9999888765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.3
                                   HCCCHHHHHHCHCHH CS
                                   xxxxxxxxxxxxxxx RF
                          CbiA  57 krllellealgkkka 71 
                                   ++++  le+l+++k+
  gi|15669114|ref|NP_247919.1| 233 DKIVDALEKLKEVKE 247
                                   444444444444433 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   1.2   7.3e-12     1e-08       4      56 ..       9      69 ..       6     134 .. 0.75
   2 ?   -1.1   0.0      0.76     1e+03      20      49 ..     129     156 ..     124     170 .. 0.76
   3 ?   -2.5   0.0         2   2.8e+03     203     244 ..     197     238 ..     183     240 .. 0.61

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 7.3e-12
                          ParA  4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee........e 56
                                  kvi+ + +KGG GK+ +++n A+aLakkg+k+ l+D D+   s+ +ll+v++        e
  gi|15669114|ref|NP_247919.1|  9 KVITFSIAKGGTGKTIITANAAAALAKKGKKILLIDGDVGSKSLSHLLNVKSnifladiiE 69
                                  56777789******************************************99444433321 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.76
                          ParA  20 vavnlAlaLakkglkvgllDaDiyGpsipr 49 
                                   v + lAl L  +++ + +lD   +Gps+  
  gi|15669114|ref|NP_247919.1| 129 VETYLALGL--SDYFIPVLDYTAFGPSLQG 156
                                   445555555..789999*********9865 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2
                          ParA 203 vpllgeipldpeireasdegkplvlkepeseaakaleeiaek 244
                                   +++++ i  ++ + ++  +++ ++l++++++  +++++i+++
  gi|15669114|ref|NP_247919.1| 197 LECISIIHKNSLVEQSYAKKEIVYLTSSDKKFVEEIDKIVDA 238
                                   444444444455555555566666677777777777777765 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.6   2.6e-09   3.5e-06       7      66 ..      16      75 ..       9     123 .. 0.87
   2 !   10.6   0.7    0.0002      0.28     177     257 ..     173     255 ..     157     263 .] 0.80

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.6e-09
                     Fer4_NifH  7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgave 66
                                   kGG Gk++ ++n +aala++gkk+l++  D  + s + ll+ k +  + d+++e+    
  gi|15669114|ref|NP_247919.1| 16 AKGGTGKTIITANAAAALAKKGKKILLIDGDVGSKSLSHLLNVKSNIFLADIIEEERPIK 75
                                  69******************************************9999999988877653 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0002
                     Fer4_NifH 177 gGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelar...kilenkklviPk 254
                                   +G iin +  d  + +i+++ + lg++ + ++ ++  v+++ ++k++v   +++++  +e  ++ +   k++e k+  iPk
  gi|15669114|ref|NP_247919.1| 173 AGFIIN-KAEDLPESVINDIKKILGLECISIIHKNSLVEQSYAKKEIVYLTSSDKKFVEEIDKIVDaleKLKEVKERDIPK 252
                                   89****.767888889999999**************************999999997777777765111455666666777 PP

                     Fer4_NifH 255 pls 257
                                    ++
  gi|15669114|ref|NP_247919.1| 253 VIE 255
                                   665 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   2.3e-09   3.1e-06       2     123 ..      10     139 ..       9     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.3e-09
                                   EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT------EEE-SSS-HHHHTT... CS
                          MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkglsLplpealalseaeeaeve... 79 
                                   vi ++  kGG+Gk+ ++   a aL+kkG+++  id d+  ++l++ l+ ++++     ++ + p   a+ ++  +++e   
  gi|15669114|ref|NP_247919.1|  10 VITFSIAKGGTGKTIITANAAAALAKKGKKILLIDGDVGSKSLSHLLNVKSNIFLADIIEEERPIKDAIVNTPIENIElla 90 
                                   7889999*******************************************9998888888777776666555444443111 PP

                                   .S-HHHHHHHHH.HHHHHHHH..H-SEEEEE--SS--HH.HHHHHHT-S CS
                          MipZ  80 .eeeeaevaele.elvadlea..eldfividtPGsdsal.srlahslad 123
                                    +++ a+  +++ ++++++++  ++d++ id+P + s + + la  l+d
  gi|15669114|ref|NP_247919.1|  91 vGKSLADYLKFDiNILKRFKElgDYDYVFIDAPSTSSGVeTYLALGLSD 139
                                   1333344455542345555543368999999998877551344555555 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   6.9e-09   9.6e-06       1     131 [.       8     130 ..       8     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.9e-09
                      CBP_BcsQ   1 mkvlalqGvRGGvGttsllaaLawalhelgesvlviDlsp.dnlLrlhFnvdieqregwaraeldgapwrqaaley.apgl 79 
                                   mkv++++  +GG+G+t ++a  a al + g+++l+iD  + +  L    nv+  ++  +a    +++p+++a+++  ++++
  gi|15669114|ref|NP_247919.1|   8 MKVITFSIAKGGTGKTIITANAAAALAKKGKKILLIDGDVgSKSLSHLLNVK--SNIFLADIIEEERPIKDAIVNTpIENI 86 
                                   99***********************************866144555555555..7778899999999****9998647899 PP

                      CBP_BcsQ  80 dllPfGelnveekenlqqlaekaeallaalkelkeqyrwillDlpagasalt 131
                                   +ll  G+  +        + + + ++l+++kel ++y+++++D p+  s + 
  gi|15669114|ref|NP_247919.1|  87 ELLAVGKSLA-------DYLKFDINILKRFKEL-GDYDYVFIDAPSTSSGVE 130
                                   9999997543.......3445567788888888.589999999998776654 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   2.4   6.7e-08   9.3e-05       1      50 [.       8      59 ..       8     130 .. 0.85
   2 ?   -0.3   0.1      0.34   4.7e+02     171     191 ..     227     246 ..     183     261 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.7e-08
                                  -EEEEEE.ESTTSSHHHHHHHHHHHHHHTTS-EEEEE-ST.TTHHHHHHTS- CS
                   ArsA_ATPase  1 lkvilvg.GKGGVGKttvsaatavklsekgkkvllistDP.AhslsDsfdqk 50
                                  +kvi+++  KGG GKt + a  a+ l++kgkk+lli  D    sls  ++ k
  gi|15669114|ref|NP_247919.1|  8 MKVITFSiAKGGTGKTIITANAAAALAKKGKKILLIDGDVgSKSLSHLLNVK 59
                                  788888768****************************995267888888874 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.34
                                   CCSHCHHHHHHHHHHHHHHHH CS
                   ArsA_ATPase 171 kllglggvsieealeeleetk 191
                                   k ++ +++ ++ ale+l+e+k
  gi|15669114|ref|NP_247919.1| 227 KFVEEIDKIVD-ALEKLKEVK 246
                                   22222222222.333333333 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.3   1.5e-07   0.00021       1      39 [.       8      46 ..       8      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-07
                         VirC1  1 mklitfcslkGGaGkttalmglcsalasdgkrvalfead 39
                                  mk+itf+  kGG+Gkt     + +ala +gk++ l ++d
  gi|15669114|ref|NP_247919.1|  8 MKVITFSIAKGGTGKTIITANAAAALAKKGKKILLIDGD 46
                                  99***********************************99 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   5.5e-06    0.0076      15      48 ..       5      38 ..       2      55 .. 0.84
   2 ?   -2.8   0.0       2.7   3.7e+03      73      90 ..     225     242 ..     201     256 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.5e-06
                                  HHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS CS
                          PhoH 15 alkkndivfaiGpaGtGKtylavalavealkkkk 48
                                   ++ + i+f i++ GtGKt ++  +a+++ kk+k
  gi|15669114|ref|NP_247919.1|  5 WIQMKVITFSIAKGGTGKTIITANAAAALAKKGK 38
                                  577888****************999999887764 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                                   -----TTTHHHHHHHTTT CS
                          PhoH  73 eekvdpylrplydaLkdl 90 
                                   ++k+   +  ++daL++l
  gi|15669114|ref|NP_247919.1| 225 DKKFVEEIDKIVDALEKL 242
                                   334444444444444443 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.6e-05     0.022      28      63 ..       4      40 ..       1      54 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                        AAA_25 28 gllpagelallaGapgtGKttlaldlalava.tGkpw 63
                                  +++ ++ ++  ++ +gtGKt ++ + a+a+a +Gk+ 
  gi|15669114|ref|NP_247919.1|  4 RWIQMKVITFSIAKGGTGKTIITANAAAALAkKGKKI 40
                                  689999999**********************888865 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         5   6.9e+03      50      73 ..      94     116 ..      86     132 .. 0.67
   2 ?   14.8   0.5     2e-05     0.028      18      68 ..     209     259 ..     200     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5
                   CPSase_L_D3  50 elkkkkkeldeellreakklGfsD 73 
                                   +l+++  ++d ++l++ k+lG  D
  gi|15669114|ref|NP_247919.1|  94 SLADYL-KFDINILKRFKELGDYD 116
                                   444443.56677777777777555 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2e-05
                   CPSase_L_D3  18 lrrglsveeiheltkidpwFLekleelvelekelkkkkkeldeellreakk 68 
                                   +++ +  +ei  lt+ d+ F+e++ ++v++ ++lk+ k++  +++++++k+
  gi|15669114|ref|NP_247919.1| 209 VEQSYAKKEIVYLTSSDKKFVEEIDKIVDALEKLKEVKERDIPKVIEKIKE 259
                                   4788999******************************99777777888876 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.7e-05     0.079      33      60 ..      18      43 ..       9      89 .. 0.85
   2 ?   -0.1   0.2       0.6   8.3e+02      58      96 ..     200     243 ..     177     260 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-05
                                  TTSTHHHHHHHHHHHH-S.....-EEEE CS
                        ResIII 33 TGtGKTlvaaklierllkkgkeekflfl 60
                                   GtGKT++ a+++++l+kkgk  k+l++
  gi|15669114|ref|NP_247919.1| 18 GGTGKTIITANAAAALAKKGK--KILLI 43
                                  59****************988..77765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.6
                                   EEEESSHHHHHHHH..HHGGGGTGG.......GEEEESSS-B-- CS
                        ResIII  58 lflvprkslleqtl..eefkkflseayke...igkkvsgdkkka 96 
                                   + +++++sl+eq +  +e+  ++s+++k+   i k+v+  +k +
  gi|15669114|ref|NP_247919.1| 200 ISIIHKNSLVEQSYakKEIVYLTSSDKKFveeIDKIVDALEKLK 243
                                   56778888888877444444444444444555444455444444 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.19      11      49 ..      18      56 ..       8     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                  TTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                    APS_kinase 11 sgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49
                                   g+GK+ i+ + + +L +kg+++ l+dGd+  + L++ L
  gi|15669114|ref|NP_247919.1| 18 GGTGKTIITANAAAALAKKGKKILLIDGDVGSKSLSHLL 56
                                  589**************************9877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1294  (0.0721736); expected 358.6 (0.02)
Passed bias filter:                      846  (0.0471861); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 1652.19
//
Query:       gi|15669115|ref|NP_247920.1|  [L=106]
Description: hypothetical protein MJ_0925 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.1e-11   41.5   0.3    2.3e-10   40.2   0.3    1.6  1  HxlR       HxlR-like helix-turn-helix
    1.4e-09   37.8   1.0    2.1e-09   37.2   1.0    1.3  1  HTH_45     Winged helix-turn-helix
     0.0007   19.4   0.2    0.00099   18.9   0.2    1.4  1  DUF4364    Domain of unknown function (DUF4364)
      0.002   18.1   0.2     0.0028   17.6   0.2    1.2  1  HTH_12     Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
      0.018   14.6   0.0      0.033   13.8   0.0    1.5  1  HTH_24     Winged helix-turn-helix DNA-binding
      0.036   14.1   0.5      0.047   13.7   0.5    1.3  1  DUF61      Protein of unknown function DUF61
      0.058   13.5   0.0      0.086   12.9   0.0    1.3  1  HemN_C     HemN C-terminal domain
      0.092   12.7   0.0       0.15   12.1   0.0    1.3  1  HTH_Crp_2  Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.3     1e-13   2.3e-10       1      89 [.       6      91 ..       6      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1e-13
                                  HHHSTTHHHHHHHHTTS-EEHHHHHHHS....TTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHH CS
                          HxlR  1 liggkWkllilvellkgkkRfselkral....pkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqel 79
                                  ++g+k ++ il+++ +g + f+ +k+al     ++s+++La+rL eLe ++li+++         +Y lt+kG++  ++++++
  gi|15669115|ref|NP_247920.1|  6 VLGKKGTIEILYKIKEGVNSFTSIKNALdmegCGVSTRTLAERLNELEDENLIQKDGS-------KYYLTKKGQEALEIIENV 81
                                  6899*********************998333347*******************98753.......6***************** PP

                                  HHHHHHHHHC CS
                          HxlR 80 kkwgeeylee 89
                                  +kw +++ e+
  gi|15669115|ref|NP_247920.1| 82 MKWEAKWKEA 91
                                  *******986 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   1.0   9.4e-13   2.1e-09       9      74 ..      13      83 ..       9      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 9.4e-13
                        HTH_45  9 adILeaisegeakkTki.....mykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkelee 74
                                  ++IL +i+eg ++ T+i     m     s ++l + L+ L +++li+k+++kY+lT+kG+e le ++++ +
  gi|15669115|ref|NP_247920.1| 13 IEILYKIKEGVNSFTSIknaldMEGCGVSTRTLAERLNELEDENLIQKDGSKYYLTKKGQEALEIIENVMK 83
                                  578888888888888884444555666799************************************99876 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   4.4e-07   0.00099      35      77 ..      44      82 ..      15      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.4e-07
                       DUF4364 35 dlqqalseLvesglieeeekenktlykiTekGketlelfenri 77
                                  +l + l+eL++++li++    + + y +T+kG+e+le++en +
  gi|15669115|ref|NP_247920.1| 44 TLAERLNELEDENLIQK----DGSKYYLTKKGQEALEIIENVM 82
                                  68899***********6....778899***********99965 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   1.2e-06    0.0028       2      66 .]      14      75 ..      13      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-06
                        HTH_12  2 eILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGleeL 66
                                  eIL  ++e  +  +   i + L   g  +++r++  rL  le+++l+++ g     lt kG e L
  gi|15669115|ref|NP_247920.1| 14 EILYKIKEGVN--SFTSIKNALDMEGCGVSTRTLAERLNELEDENLIQKDGSK-YYLTKKGQEAL 75
                                  55555555555..667899999999*************************987.99*****9876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.5e-05     0.033      25      48 .]      36      59 ..      35      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                        HTH_24 25 erlglSpstvnrrlkrLeeeGlIk 48
                                  e +g+S  t+ +rl++Le+e lI+
  gi|15669115|ref|NP_247920.1| 36 EGCGVSTRTLAERLNELEDENLIQ 59
                                  679*******************95 PP

>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   2.1e-05     0.047      18      68 ..      41      97 ..      29     106 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                                  S-EEHHHHHHT.--EEEB.TTS-EEE--HHH...HHHHHTTS-.GGGGGT-EES.EE CS
                         DUF61 18 erktLkelLee.ekptivtkdgsehrfdkee...leklkeilp.eelwdklkLP.Il 68
                                  +++tL+e L+e e++ ++ kdgs++++ k+    le ++++++ e +w+  k+P I+
  gi|15669115|ref|NP_247920.1| 41 STRTLAERLNElEDENLIQKDGSKYYLTKKGqeaLEIIENVMKwEAKWKEAKIPkII 97
                                  689******9878888999********997522255555555423456788888444 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.8e-05     0.086      38      65 ..      45      72 ..      38      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.8e-05
                        HemN_C 38 laaaleklqeqGLLeldggrlrltprGr 65
                                  la  l +l++++L++ dg+++ lt++G 
  gi|15669115|ref|NP_247920.1| 45 LAERLNELEDENLIQKDGSKYYLTKKGQ 72
                                  567799********************95 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.6e-05      0.15      31      54 ..      38      62 ..      36      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.6e-05
                                  TTSSHHHHHHHHHHHHHTTSEEE.T CS
                     HTH_Crp_2 31 lGltretvsrilseLkreglisr.g 54
                                  +G++  t+   l+eL++e+li++ g
  gi|15669115|ref|NP_247920.1| 38 CGVSTRTLAERLNELEDENLIQKdG 62
                                  79********************525 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 769.23
//
Query:       gi|15669116|ref|NP_247921.1|  [L=87]
Description: hypothetical protein MJ_0926 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.068   13.5   0.8      0.099   13.0   0.8    1.2  1  SPARC_Ca_bdg  Secreted protein acidic and rich in cysteine Ca


Domain annotation for each model (and alignments):
>> SPARC_Ca_bdg  Secreted protein acidic and rich in cysteine Ca binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.8   5.5e-06     0.099      61      99 ..       7      45 ..       6      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.5e-06
                  SPARC_Ca_bdg 61 sklDtnsdkvlsksELaplraplvklehCikpflescDa 99
                                  ++lD+n   +l+ ++L + +a  vk+e+C ++++ +cD+
  gi|15669116|ref|NP_247921.1|  7 NELDKNILSILKDQDLIEDYALKVKIERCNNKYICTCDV 45
                                  689*************9999999***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 581.57
//
Query:       gi|15669117|ref|NP_247922.1|  [L=249]
Description: hypothetical protein MJ_0927 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-57  193.5   0.1    5.5e-57  193.2   0.1    1.0  1  NIF3      NIF3 (NGG1p interacting factor 3)


Domain annotation for each model (and alignments):
>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.2   0.1   3.1e-61   5.5e-57       1     242 [.      10     240 ..      10     243 .. 0.95

  Alignments for each domain:
  == domain 1  score: 193.2 bits;  conditional E-value: 3.1e-61
                          NIF3   1 eivevleelaplelaeswDnvGlqvg.dpekevkkvllaldlteevleeAiekgadliithHPlifkplkrlteddykkrl 80 
                                   ei+e++e +ap++la + Dn+Glqvg + +ke+kk+ +ald++ +v+++A ++g+d+++thHPl+  p+++ t+   +++ 
  gi|15669117|ref|NP_247922.1|  10 EIIEFIETFAPKDLAIEGDNIGLQVGdNLDKEIKKLGIALDPSLSVIKKAEKEGVDFLFTHHPLLKDPIRNFTGV--IYKK 88 
                                   69************************77888********************************************..9*** PP

                          NIF3  81 lkkliknnislysaHtnlDaapgGvndwlakalglekieplepskeekkeeeeglgrigeleepvsleelakklkkklgle 161
                                   lk l++n+i lysaHtnlD++++G+nd la++ +le+ +pl          ++glgr+g ++   s+ee+++  kk ++ +
  gi|15669117|ref|NP_247922.1|  89 LKILMENDIILYSAHTNLDICKNGLNDALAELYNLENPKPLY---------DNGLGRVGIFKG--SFEEFLEITKKYIHKN 158
                                   ************************************999987.........579********7..*************998 PP

                          NIF3 162 kvrvagdldkkvkkvaicaGsGaslie.eakakgaDlliTGelkhhealdakekgiavidvgHyatErvflealaelLkek 241
                                    + v +++     k a+++G G s  + +  a++aD++++G+l+hh  + a+e g+ v+d+ Hy+tE ++l++++e L+++
  gi|15669117|ref|NP_247922.1| 159 PIVVKSKEVDDNFKLAVLSGYGLSQSSiKYVAEKADVYLSGDLTHHSKILAEELGLVVVDATHYSTEVFGLKKFKEFLSSN 239
                                   88888888888889*******996666589999*********************************************998 PP

                          NIF3 242 l 242
                                   l
  gi|15669117|ref|NP_247922.1| 240 L 240
                                   7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1459.39
//
Query:       gi|15669118|ref|NP_247923.1|  [L=197]
Description: protoporphyrinogen oxidase HemK [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-22   78.9   0.0    1.1e-20   73.8   0.0    2.0  1  MTS              Methyltransferase small domain
    1.4e-16   60.8   0.5    2.2e-16   60.1   0.5    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    6.2e-15   55.3   0.0    7.8e-15   55.0   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.2e-12   48.4   0.0    2.1e-12   47.6   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.4e-08   35.3   0.0    3.5e-08   34.0   0.0    1.8  1  Methyltransf_11  Methyltransferase domain
    1.5e-08   34.7   0.1    1.9e-08   34.3   0.1    1.3  1  Met_10           Met-10+ like-protein
    3.6e-08   33.4   0.0    5.6e-08   32.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.7e-07   30.7   0.0    2.4e-07   30.2   0.0    1.1  1  DUF43            Branched-chain polyamine synthase A C-termin
    6.5e-07   30.0   0.0    1.2e-06   29.2   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    2.3e-06   27.4   0.0    3.4e-06   26.8   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
      6e-06   25.6   0.1    9.2e-06   25.0   0.1    1.2  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
    5.4e-05   22.6   0.0    6.6e-05   22.3   0.0    1.1  1  N6_Mtase         N-6 DNA Methylase
    8.6e-05   21.9   0.0    0.00061   19.1   0.0    1.9  2  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
     0.0001   22.1   0.1    0.00014   21.7   0.1    1.2  1  Methyltransf_16  Lysine methyltransferase
    0.00012   21.8   0.0    0.00017   21.3   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
    0.00028   20.6   0.4        0.3   10.7   0.0    2.1  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
      0.001   19.0   0.0     0.0017   18.3   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
     0.0013   18.2   0.2     0.0074   15.8   0.1    1.9  2  Methyltransf_4   Putative methyltransferase
     0.0024   17.1   0.1     0.0042   16.3   0.1    1.4  1  Methyltransf_3   O-methyltransferase
     0.0065   16.1   0.1      0.008   15.8   0.1    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
      0.021   13.8   0.0      0.034   13.1   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.029   14.3   0.0      0.058   13.4   0.0    1.5  1  ADH_zinc_N       Zinc-binding dehydrogenase
      0.041   12.9   0.2      0.057   12.4   0.2    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.043   13.9   0.0      0.047   13.8   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
      0.045   13.6   0.0       0.06   13.2   0.0    1.3  1  N6-adenineMlase  Probable N6-adenine methyltransferase
      0.052   13.3   0.0      0.076   12.8   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.057   12.5   0.0      0.066   12.3   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.061   12.7   0.2      0.099   12.0   0.2    1.5  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.065   14.3   0.0      0.093   13.8   0.0    1.2  1  Methyltransf_24  Methyltransferase domain
       0.14   12.6   0.1       0.29   11.7   0.0    1.7  1  Eco57I           Eco57I restriction-modification methylase
       0.16   11.9   0.0       0.38   10.7   0.0    1.6  2  rRNA_methylase   Putative rRNA methylase
        0.2   11.7   0.0       0.25   11.3   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.21   10.8   0.0       0.67    9.2   0.0    1.8  1  CMAS             Mycolic acid cyclopropane synthetase


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   2.1e-23   1.1e-20      20     111 ..      23     112 ..       8     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 2.1e-23
                                   HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEE CS
                           MTS  20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdl 100
                                   s lLl++l + ++++vl +G G+G++++a+ak+  + +++ vd++ +A+++aken++ n++++++++sd++e+v+ +kfd+
  gi|15669118|ref|NP_247923.1|  23 SILLLKNLVDVKNKDVLEIGVGTGLISIACAKKGAK-KIVGVDINPYAVKLAKENAKLNNVNISFFESDLFENVT-GKFDV 101
                                   779*****************************9988.8*************************************.***** PP

                                   EEE---STTTC CS
                           MTS 101 ivsNPPfhagk 111
                                   i+ NPP+   +
  gi|15669118|ref|NP_247923.1| 102 ILFNPPYLPTS 112
                                   ******85444 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.5     4e-19   2.2e-16     154     233 ..      26     105 ..      20     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 4e-19
                          PrmA 154 aleklvk.egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk..eekadviv 231
                                   +l +lv  +++ vl +G G+G+++ia ak gakk+v+vDi++ Avk akeNa+lN+v+ ++    +++l++  ++k+dvi+
  gi|15669118|ref|NP_247923.1|  26 LLKNLVDvKNKDVLEIGVGTGLISIACAKKGAKKIVGVDINPYAVKLAKENAKLNNVNISF---FESDLFEnvTGKFDVIL 103
                                   566665515579**********************************************988...455555444689****8 PP

                          PrmA 232 aN 233
                                    N
  gi|15669118|ref|NP_247923.1| 104 FN 105
                                   77 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   1.4e-17   7.8e-15       3     113 ..      34     158 ..      32     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.4e-17
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsn. 81 
                                   k++ vl++G GtG ++++ a++ g  +++vG+Di++ a++lA+ena+ +++ n++F ++d +e         kfD+il n 
  gi|15669118|ref|NP_247923.1|  34 KNKDVLEIGVGTGLISIACAKK-G-AKKIVGVDINPYAVKLAKENAKLNNV-NISFFESDLFEnVT-----GKFDVILFNp 106
                                   899*****************44.4.578*****************998888.9**********555.....89*******8 PP

               Methyltransf_31  82 ............evl....naladpdkile....eiervlkpggilliedpr 113
                                               + l    +  +d  +il     e++++lk+gg++ i + +
  gi|15669118|ref|NP_247923.1| 107 pylptsedekidSYLnfafDGGKDGREILDrfiyELPNYLKKGGVVQILQSS 158
                                   7777777766652225566666666666667777***********9888777 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   3.9e-15   2.1e-12       1      79 [.      38     114 ..      38     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 3.9e-15
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC.CGBSSSTTTEEEEEEEST.GGGSSH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgda.edlpfedgsfDlvvssga.lhhlsd 79 
                                   vL++G GtG +++a+ak+ g++k++gvDi++ +++ a+e+a+ +++n++f + d+ e++    g+fD+++ +   l   +d
  gi|15669118|ref|NP_247923.1|  38 VLEIGVGTGLISIACAKK-GAKKIVGVDINPYAVKLAKENAKLNNVNISFFESDLfENV---TGKFDVILFNPPyLPTSED 114
                                   9*****************.69*********************************94444...589****996544444444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   6.4e-11   3.5e-08       1      67 [.      39     104 ..      39     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 6.4e-11
                                   EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEE CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvs 67 
                                   L++G+GtG+++ a+ak+g +++vgvD++++++klake+a+ ++++++f ++d+ +     ++fD+++ 
  gi|15669118|ref|NP_247923.1|  39 LEIGVGTGLISIACAKKGaKKIVGVDINPYAVKLAKENAKLNNVNISFFESDLFE--NVTGKFDVILF 104
                                   89****************************************999***9999997..44568999876 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   3.5e-11   1.9e-08     100     170 ..      34     100 ..      26     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 3.5e-11
                                   TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EE CS
                        Met_10 100 egevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqlad 170
                                   +++ V+++  G G  +i++ak   ak+++++d+nP++vk+ ken klN+v+   + +++D  e + + ++d
  gi|15669118|ref|NP_247923.1|  34 KNKDVLEIGVGTGLISIACAK-KGAKKIVGVDINPYAVKLAKENAKLNNVNI--SFFESDLFENV-TGKFD 100
                                   5677999999***********.556779**********************84..44777765544.45555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0     1e-10   5.6e-08      20      88 ..      32     104 ..      15     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1e-10
               Methyltransf_23  20 lraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae........kakkaqkdqfdeqeaaepqgkfdlIvl 88 
                                   + +++ vL+iG GtG  +  ++++g+ +++gvD++p av++a+        ++++ ++d f     ++  gkfd+I  
  gi|15669118|ref|NP_247923.1|  32 DVKNKDVLEIGVGTGLISIACAKKGAkKIVGVDINPYAVKLAKenaklnnvNISFFESDLF-----ENVTGKFDVILF 104
                                   67999**********999999***9989**************9996555444444444444.....66788****986 PP

>> DUF43  Branched-chain polyamine synthase A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   4.4e-10   2.4e-07      34     122 ..      24     108 ..      16     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4.4e-10
                                   HHHHHHTT-STT-EEEEES.-TT-HHHHHHHHT--SEEEEE-S-HHHHHHHHHHHHHHT--EEEE---TTS---TTTSS-B CS
                         DUF43  34 vallyerGDLegkeilvlG.dDDLtslalaLtglpkkvvvvDiDeRlikfiervakelglkieaivyDlrkplpeelkekF 113
                                   ++ll++  D+++k++l +G    L+s+a a    +kk+v vDi++  +k+ ++ ak  +++i  +  Dl     e+++ kF
  gi|15669118|ref|NP_247923.1|  24 ILLLKNLVDVKNKDVLEIGvGTGLISIACAKK-GAKKIVGVDINPYAVKLAKENAKLNNVNISFFESDLF----ENVTGKF 99 
                                   7899999************8899*****9965.599******************************9985....67889** PP

                                   SEEEE---S CS
                         DUF43 114 dvfitDPpe 122
                                   dv++ +Pp+
  gi|15669118|ref|NP_247923.1| 100 DVILFNPPY 108
                                   *******98 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   2.2e-09   1.2e-06       1      72 [.      39     104 ..      39     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.2e-09
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvva 72 
                                   LeiG GtG ++ a+++k   ++++gvDi+p a+    +  +++ ++nn n+ +++ dl++   g +fD+++ 
  gi|15669118|ref|NP_247923.1|  39 LEIGVGTGLISIACAKK-GAKKIVGVDINPYAV----KLAKENAKLNNVNISFFESDLFENVTG-KFDVILF 104
                                   8****************.999************....444444445567888888887766665.****985 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   6.2e-09   3.4e-06      40     124 ..      33     109 ..      23     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 6.2e-09
                                   HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE- CS
                 Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflD 120
                                   ++++ vL++  G+G +++ ++  gakk+v v+ ++ avk+ ken +  +++  ++ +  d +e++       ++fd++ ++
  gi|15669118|ref|NP_247923.1|  33 VKNKDVLEIGVGTGLISIACAKKGAKKIVGVDINPYAVKLAKENAKLNNVN--ISFFESDLFENVT------GKFDVILFN 105
                                   88999***************************************9877744..6777776666664......45******* PP

                                   -SSS CS
                 Cons_hypoth95 121 PPya 124
                                   PPy 
  gi|15669118|ref|NP_247923.1| 106 PPYL 109
                                   ***6 PP

>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   1.7e-08   9.2e-06     122     270 ..      33     187 ..      28     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.7e-08
               Methyltrans_SAM 122 akdknvlnlfaytcgfsvaaiaggaskvvnvdmargslnkgrdnhrlnghdlrrvsflgydifkswgkikksgpydlviid 202
                                    k+k+vl++   t  +s+a+   ga+k+v vd+   +++  ++n +ln+ +   +sf+  d+f        +g++d+++ +
  gi|15669118|ref|NP_247923.1|  33 VKNKDVLEIGVGTGLISIACAKKGAKKIVGVDINPYAVKLAKENAKLNNVN---ISFFESDLFEN-----VTGKFDVILFN 105
                                   6899********************************************987...58*******96.....47999999999 PP

               Methyltrans_SAM 203 pp...........sfqkgsfaltkdykkilrr....lpellveggevlacvnspavspdflieemaeeapslefverldnp 268
                                   pp           s+ + +f   kd + il r    lp+ l +gg  +  ++s   + +  i++++    ++e+  rl+ p
  gi|15669118|ref|NP_247923.1| 106 PPylptsedekidSYLNFAFDGGKDGREILDRfiyeLPNYLKKGGV-VQILQSSLTGEKETINKLKPLGFKVEISARLKVP 185
                                   9944333333333344455666899999998755557999999885.4566666666777777777777777777777777 PP

               Methyltrans_SAM 269 pe 270
                                    e
  gi|15669118|ref|NP_247923.1| 186 FE 187
                                   55 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.2e-07   6.6e-05      27     143 ..      15     114 ..       8     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.2e-07
                      N6_Mtase  27 effTPrevsklivell.epksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykk 106
                                   e++ P e s l+ + l + k++  v+   +G+g + +  +k        + +++i G+++n+ +++Lak N  l +++ + 
  gi|15669118|ref|NP_247923.1|  15 EVYEPAEDSILLLKNLvDVKNK-DVLEIGVGTGLISIACAK--------KGAKKIVGVDINPYAVKLAKENAKLNNVNIS- 85 
                                   6777777665555544155555.588888888855555444........67899***********************999. PP

                      N6_Mtase 107 vkirlgdtlekpkfekdkkfdvvvaNppfnqkewkek 143
                                        +d +e+     + kfdv++ Npp+  +  +e+
  gi|15669118|ref|NP_247923.1|  86 --FFESDLFEN----VTGKFDVILFNPPYLPT--SED 114
                                   ..444444443....4568**********877..333 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.1e-06   0.00061      52     124 ..      37     102 ..      17     109 .. 0.76
   2 ?    0.6   0.0      0.46   2.5e+02     318     354 ..     142     178 ..     131     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                                   EEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEE CS
                           TRM  52 kvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdvi 124
                                    vl+   ++Gl +i  a+   g+k+++  Di++ Av+l keN+kln+v+    + e   + l+++++ +fdvi
  gi|15669118|ref|NP_247923.1|  37 DVLEIGVGTGLISIACAKK--GAKKIVGVDINPYAVKLAKENAKLNNVNI--SFFE---SDLFENVTGKFDVI 102
                                   577777899*****99998..9*************************983..2222...12344555555555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.46
                                   -SS-EEHHHHHHHHT-SS---HHHHHHH....TT-EE CS
                           TRM 318 aplyydlsqlasvlklsvpplkkvvsalkelgfevsr 354
                                    p y +   + ++l++s    k+ +++lk lgf+v  
  gi|15669118|ref|NP_247923.1| 142 LPNYLKKGGVVQILQSSLTGEKETINKLKPLGFKVEI 178
                                   56677777888999999999**************975 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   2.5e-07   0.00014      44      93 ..      32      81 ..      16     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.5e-07
               Methyltransf_16 44 elsklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnk 93
                                  +++++ vlE+G GtGl+ +a a++ +  k++  D++  +++l k+n +ln+
  gi|15669118|ref|NP_247923.1| 32 DVKNKDVLEIGVGTGLISIACAKK-GAKKIVGVDINPyAVKLAKENAKLNN 81
                                  67899*******************.777777788887699********987 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   3.2e-07   0.00017      76     135 ..      57     112 ..      34     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.2e-07
                                   H--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE-------- CS
                       UPF0020  76 elklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerl 135
                                     k++g+D+++ +v+ a+eNa+  +v+ +  f++  + +++   g++dvi+ npPY    
  gi|15669118|ref|NP_247923.1|  57 AKKIVGVDINPYAVKLAKENAKLNNVNIS-FFESDLFENVT---GKFDVILFNPPYLPTS 112
                                   446*******************9998744.45555777777...88**********8655 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00054       0.3      13      59 ..      28      74 ..       7      78 .. 0.84
   2 !   10.2   0.1   0.00081      0.44     150     215 ..      72     134 ..      71     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00054
                                  HCCS-..--SEEEETT-TTSCCHHCS....SSCEEEEES-HHHHHHHH CS
               MethyltransfD12 13 kelipkdkgktfvepFaGggaVffeakk.qgkkvlinDinedlinlyk 59
                                  k+l++  k+k + e  +G+g +++++ k   kk++  Din++ + l+k
  gi|15669118|ref|NP_247923.1| 28 KNLVDV-KNKDVLEIGVGTGLISIACAKkGAKKIVGVDINPYAVKLAK 74
                                  445554.889999*************9967899999*********998 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00081
                                   HHHHHHHHHHCCEEEC-CHHHHTT--TTE.EEEE--S-T.S...TS--GGGG.CS-HHHHHHHHHH CS
               MethyltransfD12 150 lklrseklknakiecgdfdavllkakieddivYlDPPYnprqytanytlyetlafsdedevrlaev 215
                                   l + + kl+n+ i+ +  d +++    + d++ + PPY p+++  +  +y +  f  +  ++++e+
  gi|15669118|ref|NP_247923.1|  72 LAKENAKLNNVNISFFESDLFENVT-GKFDVILFNPPYLPTSEDEKIDSYLN--FAFDGGKDGREI 134
                                   55678999*************9999.6666**********777766666655..444444445555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.1e-06    0.0017      14      86 ..      34     102 ..      24     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.1e-06
               Methyltransf_18  14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtv 86 
                                   k++ v+ iG   g+++i+ +k+g akk++ +Din+ +++ aken++ +++  +i++  sd +e+++ +++d++
  gi|15669118|ref|NP_247923.1|  34 KNKDVLEIGVGTGLISIACAKKG-AKKIVGVDINPYAVKLAKENAKLNNV--NISFFESDLFENVT-GKFDVI 102
                                   456999************99755.78*********************998..79999999999986.556665 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.4e-05    0.0074       2      62 ..      35      93 ..      34     105 .. 0.76
   2 ?    0.2   0.0       0.8   4.3e+02      97     115 ..     136     154 ..     130     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                                  -EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCC CS
                Methyltransf_4  2 apvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalk 62
                                  ++ vleiG+G G + +a Akk ++ +++G++i+   v+ +  + ++l+  N+  +++d ++
  gi|15669118|ref|NP_247923.1| 35 NKDVLEIGVGTGLISIACAKKGAK-KIVGVDINPYAVKLAK-ENAKLNNVNISFFESDLFE 93
                                  6789***************99875.699****988886554.4455555677777777554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.8
                                   HHHHHHHHHHEEEEEEEEE CS
                Methyltransf_4  97 pellkelarvLkkgGvlel 115
                                   + ++ el + LkkgGv+++
  gi|15669118|ref|NP_247923.1| 136 DRFIYELPNYLKKGGVVQI 154
                                   67999999*******9975 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   7.7e-06    0.0042      38      97 ..      26      82 ..       8     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.7e-06
                                  HHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT- CS
                Methyltransf_3 38 fLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagv 97
                                  +L+ Lv++ n k vleiGv tG    ++a a     ki+ +di++ a+++a++  +   v
  gi|15669118|ref|NP_247923.1| 26 LLKNLVDVKN-KDVLEIGVGTGLI--SIACAKKGAKKIVGVDINPYAVKLAKENAKLNNV 82
                                  5677787765.99******99965..5555566778****************97766555 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.5e-05     0.008       4      80 ..      38     107 ..      35     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
               Methyltransf_15   4 ilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpP 80 
                                   +l +  G+G  +i+ a++  +k+++++in+  +++a++Na++   + +i +   d+fe +        k+d+++  pP
  gi|15669118|ref|NP_247923.1|  38 VLEIGVGTGLISIACAKKgAKKIVGVDINPYAVKLAKENAKLN--NVNISFFESDLFENVTG------KFDVILFNPP 107
                                   5666678888888888885689*********************..6689********97766......3355555555 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.3e-05     0.034     108     147 ..      27      66 ..      24      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.3e-05
                                   GGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE--- CS
                Methyltransf_9 108 lphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPs 147
                                   l+ l d+k++ +l++G g+G      + +gak +vG+d +
  gi|15669118|ref|NP_247923.1|  27 LKNLVDVKNKDVLEIGVGTGLISIACAKKGAKKIVGVDIN 66 
                                   68899*******************************9854 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00011     0.058       1      41 [.      42      84 ..      42     107 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                                  HHHHHHHHHHH.HTT-.EEEEEESSHHHHHHHHHTTESEEEET CS
                    ADH_zinc_N  1 gvGlaavqlAk.alGa.eviavdsseeklelakklGadeviny 41
                                  gvG+ ++ +A    Ga ++++vd+++  ++lak++     +n 
  gi|15669118|ref|NP_247923.1| 42 GVGTGLISIACaKKGAkKIVGVDINPYAVKLAKENAKLNNVNI 84
                                  78888888777356779****************9865555555 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2    0.0001     0.057     198     249 ..      31      83 ..      22      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
               tRNA_U5-meth_tr 198 tqeskgdllelycGnGnfslalarn.fekvlateiakssveaaqyniaankid 249
                                   ++ +++d+le+  G G  s+a a++  +k++  +i   +v+ a+ n + n+++
  gi|15669118|ref|NP_247923.1|  31 VDVKNKDVLEIGVGTGLISIACAKKgAKKIVGVDINPYAVKLAKENAKLNNVN 83 
                                   556789*****************874689********************9984 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.7e-05     0.047      20      70 ..      32      84 ..      20     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.7e-05
                                  -.TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS........HHHTTEEEECS-C CS
                          FtsJ 20 k.pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm........aplpgvttiqgdi 70
                                  + ++k v+++g ++G  s  ++++ ga +k+v+vD++p+        a     ++ + +i
  gi|15669118|ref|NP_247923.1| 32 DvKNKDVLEIGVGTGLISIACAKK-GA-KKIVGVDINPYavklakenA-----KLNNVNI 84
                                  447788*********999999999.88.9**********765544332.....3333333 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00011      0.06      81     151 ..      91     185 ..      51     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
               N6-adenineMlase  81 lpeelkgkfdviviDPPFlseeclkklaktaklllk..........................klilctgevmeelekllgv 135
                                   l e+++gkfdvi++ PP+l     +k+   +++                             +++ ++    e+ e+  ++
  gi|15669118|ref|NP_247923.1|  91 LFENVTGKFDVILFNPPYLPTSEDEKIDSYLNFAFDggkdgreildrfiyelpnylkkggvvQILQSS-LTGEK-ETINKL 169
                                   337789************99988888777777666577777777776666666666656554333333.11222.222256 PP

               N6-adenineMlase 136 kktkfepehenklsne 151
                                   k+  f++e++ +l+  
  gi|15669118|ref|NP_247923.1| 170 KPLGFKVEISARLKVP 185
                                   7777777777776655 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014     0.076      73     132 ..      34      90 ..      22     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                                   TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                          PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                   k + vLe+G G+G  +   a+      ++v+++  +  v+ ak+n k  +  n+++ ++D
  gi|15669118|ref|NP_247923.1|  34 KNKDVLEIGVGTGLISIACAKK--GAKKIVGVDINPYAVKLAKENAKL-NNVNISFFESD 90 
                                   4568*********987666653..34468**************99764.44466666665 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012     0.066      27      97 ..      29     113 ..      13     170 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                   -GG..TTSEEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-CCGHHHHHHHCT....... CS
                        RrnaAD  27 nle..ekltvleigpGkGilTeeLakra.kqvvvlElderLakllqkkls.kdeklkvvhqDflkfetpeevte....... 96 
                                   nl   +++ vleig G+G+ +   ak   k+ v + + +  +kl +++ + ++ ++   + D  +  t ++          
  gi|15669118|ref|NP_247923.1|  29 NLVdvKNKDVLEIGVGTGLISIACAKKGaKKIVGVDINPYAVKLAKENAKlNNVNISFFESDLFENVTGKFDVIlfnppyl 109
                                   444668899***************77666**************99997766667777777777766666643326666666 PP

                                   ...T CS
                        RrnaAD  97 ...k 97 
                                      +
  gi|15669118|ref|NP_247923.1| 110 ptsE 113
                                   6662 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00018     0.099      46     105 ..      33      89 ..      24     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                   --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE- CS
               Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqa 105
                                    + ++vl++  Gtg ++++ +++     k+v++Din+  +k +++ +k +  +ni f  +
  gi|15669118|ref|NP_247923.1|  33 VKNKDVLEIGVGTGLISIACAKKG--AKKIVGVDINPYAVKLAKENAKLNN-VNISFFES 89 
                                   567899********9999988764..458***************9998654.46777655 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   0.00017     0.093       1     101 [.      39     152 ..      39     154 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00017
               Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare.aglddr.vrlikadsee.alasla............ 66 
                                   +EiG   G   + +++a  + ga ++v vd +p    a +la+e a+l+++ + + ++d++e + ++++            
  gi|15669118|ref|NP_247923.1|  39 LEIG--VGTGLISIACA--KKGAKKIVGVDINP---YAVKLAKEnAKLNNVnISFFESDLFEnVTGKFDvilfnppylpts 112
                                   79**..55555555544..344458********...888899987777774588899998552444555666666666666 PP

               Methyltransf_24  67 .agsiD...llfiDgghaaeavledl.eallprlapggvv 101
                                    +++iD    + +Dgg ++++ l+ +   l ++l++ggvv
  gi|15669118|ref|NP_247923.1| 113 eDEKIDsylNFAFDGGKDGREILDRFiYELPNYLKKGGVV 152
                                   6888886655668999999888887624444588888887 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00053      0.29       2      22 ..      98     118 ..      97     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00053
                        Eco57I   2 kfdviiGNPPYqeseakkelk 22 
                                   kfdvi+ NPPY  ++++++ +
  gi|15669118|ref|NP_247923.1|  98 KFDVILFNPPYLPTSEDEKID 118
                                   9**********9888655554 PP

>> rRNA_methylase  Putative rRNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0007      0.38       1      61 [.      60     115 ..      60     122 .. 0.81
   2 ?   -2.4   0.0       7.6   4.1e+03      76      88 ..     142     154 ..     126     165 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0007
                                   EEEEES-HHHHHHHHHHHHHTT-GGSEEEEES-GGGGGGT--S-EEEEEEEESB-CTS-TT CS
                rRNA_methylase   1 vyafDiQeeAleatkerleeekleervelildsHekleeyvkekvkavifNLGYLPggdks 61 
                                   ++++Di   A++ +ke+ + ++++  +++++   ++l e v++k+++++fN  YLP ++ +
  gi|15669118|ref|NP_247923.1|  60 IVGVDINPYAVKLAKENAKLNNVN--ISFFE---SDLFENVTGKFDVILFNPPYLPTSEDE 115
                                   578999999999999999888776..55554...57888899**************98654 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.6
                                   HHHHEEEEEEEEE CS
                rRNA_methylase  76 alelLkkgGliti 88 
                                   + + LkkgG++ i
  gi|15669118|ref|NP_247923.1| 142 LPNYLKKGGVVQI 154
                                   4456677777665 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00047      0.25      22      74 ..      31      79 ..      11      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00047
               Methyltransf_32 22 kesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraekl 74
                                   + ++++v+++G G g  s + a    +   k+vg+d++   v+ a++ a+ l
  gi|15669118|ref|NP_247923.1| 31 VDVKNKDVLEIGVGTGLISIACAK---KGAKKIVGVDINPYAVKLAKENAK-L 79
                                  3456899*************9999...7788**********9998887665.3 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0012      0.67      64     131 ..      36     102 ..      22     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                                   -EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEE CS
                          CMAS  64 mtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrv 131
                                   + +L+iG G G + +  +++   k+vg+ +     klak++ +  +  +    +   +e++ +k+d +
  gi|15669118|ref|NP_247923.1|  36 KDVLEIGVGTGLISIACAKKGAKKIVGVDINPYAVKLAKENAKLNN-VNISFFESDLFENVTGKFDVI 102
                                   679*****************8889*****99999999988765444.344445555567777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1237.91
//
Query:       gi|15669119|ref|NP_247924.1|  [L=462]
Description: adenylosuccinate lyase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-63  214.6   0.8    3.4e-63  213.9   0.8    1.3  1  Lyase_1      Lyase
    9.7e-26   90.1   5.7    1.5e-25   89.5   0.2    3.4  4  ADSL_C       Adenylosuccinate lyase C-terminus
    5.4e-08   32.9   1.3    5.4e-08   32.9   1.3    2.2  2  ASL_C        Adenylosuccinate lyase C-terminal
     0.0016   18.8   0.2     0.0016   18.8   0.2    2.7  3  FumaraseC_C  Fumarase C C-terminus
     0.0029   18.3   0.2      0.013   16.3   0.0    2.2  2  ASL_C2       Argininosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.9   0.8   9.5e-67   3.4e-63       6     309 ..      23     308 ..      19     310 .. 0.91

  Alignments for each domain:
  == domain 1  score: 213.9 bits;  conditional E-value: 9.5e-67
                                   ETCHHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHH CS
                       Lyase_1   6 kadklmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmn 86 
                                    ++++++++ e+++++++l+     ++aal+ka a++++++ke+a++i k ++     +kl++  ++++ ++++ +a+ ++
  gi|15669119|ref|NP_247924.1|  23 GTPEMRKVWEEENKLEKMLK-----VEAALAKAQAELGLIPKEAAEEINKKASTKY--VKLERVKEIEKQTKHDVVAMIRA 96 
                                   5899****************.....99*********************99887654..599999***************** PP

                                   HHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEE CS
                       Lyase_1  87 lnevigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvt 167
                                   l ev         ++ +++h+g++snD+v+Ta +l++k+++ e ++++l+qL+d+l +ka+e+k++v +GrTh+q+A P+t
  gi|15669119|ref|NP_247924.1|  97 LAEVCE------GNAGEYIHFGATSNDIVDTANSLLIKESI-EIIEDKLKQLRDILLDKAEEHKYTVCVGRTHGQHAIPTT 170
                                   ****99......59***************************.88************************************* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCC.THHHHHHHHHHHHHCST.EESSSHHHHHHC-HHHH CS
                       Lyase_1 168 lgqelsayaealerdrerlkellkrllvellgggtavgtglnadp.efaelvakelakvtglp.vkapnsfeavsdrDavv 246
                                    g+ ++ +a++++r++erlke++kr+ v+ + g++++ ++++ +  e++++va+ l+    l+ v   n+   v +rD+++
  gi|15669119|ref|NP_247924.1| 171 YGMRFALWAAEIDRHLERLKEAKKRICVSMITGAVGTMAAMGEKGlEVHKRVAEILG----LEpVLISNQ---VIQRDRHA 244
                                   *********************************999999999988677777777777....333666555...59****** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHTSTTTSSE.EEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHH CS
                       Lyase_1 247 ellgalkllatsLskfaeDlrllssgeaglv.elslaesepGSSiMPgKvNPvqlElltgvagr 309
                                   e+++ l+l+a  L k++  +r ++ +e+g+  e+ +++++ GSS+MP+K+NP+++E + g ++ 
  gi|15669119|ref|NP_247924.1| 245 EFVFLLALIAQTLNKIGVTVRSMQRTEIGELeEEFDPTKQTGSSTMPHKRNPITFEQICGLSRV 308
                                   ***************************77651678999999****************9988765 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.9       1.1   3.8e+03      31      51 ..      29      52 ..      25      87 .. 0.65
   2 ?   -2.7   0.0       2.5   8.9e+03       9      26 ..      75      92 ..      68      96 .. 0.79
   3 ?    1.2   0.0      0.15   5.5e+02      51      66 ..     273     288 ..     237     290 .. 0.82
   4 !   89.5   0.2   4.1e-29   1.5e-25       1      73 []     375     453 ..     375     453 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                                  HHHHC...HHHHHHT-HHHHCHHC CS
                        ADSL_C 31 kawee...llelLaadpevkksee 51
                                  k+wee   l   L+ +++++k+++
  gi|15669119|ref|NP_247924.1| 29 KVWEEenkLEKMLKVEAALAKAQA 52
                                  667777775555554444443222 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                                  HHHHHHTH-HHHHHHHHH CS
                        ADSL_C  9 llaLvkglgReeAyelVq 26
                                   l+ vk +++++ +++V+
  gi|15669119|ref|NP_247924.1| 75 KLERVKEIEKQTKHDVVA 92
                                  566788899999999986 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.15
                                   CHHHHHT-GGGCCTTH CS
                        ADSL_C  51 eeldalfdpayylgsa 66 
                                    el++ fdp++ +gs+
  gi|15669119|ref|NP_247924.1| 273 GELEEEFDPTKQTGSS 288
                                   389*********9987 PP

  == domain 4  score: 89.5 bits;  conditional E-value: 4.1e-29
                                   TGGGHHHHHHHHHH.TH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHH.C.HHCHHHHHT-GGGCCTTHHHHHHHH CS
                        ADSL_C   1 GlifservllaLvk.glgReeAyelVqeaamkawee...llelLaadpevk.k.seeeldalfdpayylgsadeivdrv 73 
                                   Gli++er++++L+k g+gR++A+e+V+++amka ee   l++ L++++ev+ + ++eel++l++p++y+g a++ivd+v
  gi|15669119|ref|NP_247924.1| 375 GLIMAERIMIELAKrGMGRQTAHEIVRQCAMKAYEEkrhLKDILLENEEVMkYiTKEELEELMNPKTYIGLAPQIVDEV 453
                                   9************66************************************55*999********************97 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2      0.61   2.2e+03      71      88 ..      72      89 ..      27     103 .. 0.56
   2 !   32.9   1.3   1.5e-11   5.4e-08       5     115 .]     326     443 ..     324     443 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.61
                                  HHHHHHHHHTTS---HHH CS
                         ASL_C 71 pYeklkeltrgkkitkes 88
                                   Y kl ++   +k+tk++
  gi|15669119|ref|NP_247924.1| 72 KYVKLERVKEIEKQTKHD 89
                                  233333333333333333 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 1.5e-11
                                   --TCHHHHHTTCHHHHHHHHHH.HHHHHHHHCCEEE-HHHHHHHHHT-.GGGGHHHHHHHHHHT..T-TTHHHHHHHHHTT CS
                         ASL_C   5 RDLtdStvlRnlgvalahslia.lksllkglsklevneealaedLden.wevlaEaiqtvlrre..giekpYeklkeltrg 81 
                                   RDLt+S+  R + + ++  +   l+ ++kg++kl+vn+e+++++L+ +   ++aE i + l +   g + ++e +++   +
  gi|15669119|ref|NP_247924.1| 326 RDLTNSSAERCIFAEVCVLTDHiLTLAIKGVKKLKVNKENVERNLELTkGLIMAERIMIELAKRgmGRQTAHEIVRQCAMK 406
                                   **********998877766544145678******************8725689****9999765126689*********** PP

                                   S---HHHHHHHHHCS-..S-HHHHHHHHC-.-CCC-- CS
                         ASL_C  82 kkitkeslkefiesle..vseeakeeLkal.tpatYi 115
                                   +  +k++lk+++ ++e  ++  +keeL++l +p+tYi
  gi|15669119|ref|NP_247924.1| 407 AYEEKRHLKDILLENEevMKYITKEELEELmNPKTYI 443
                                   *********9876664435556789999863799997 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.81   2.9e+03      28      46 ..      47      65 ..      37      78 .. 0.67
   2 ?   -2.4   0.0       1.9     7e+03      16      31 ..     252     267 ..     251     280 .. 0.75
   3 !   18.8   0.2   4.4e-07    0.0016      16      51 ..     402     441 ..     397     444 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.81
                                  HHHHHHHTT-.-HHHHHHH CS
                   FumaraseC_C 28 lreavlelgllteeeldel 46
                                  l  a  elgl+ +e  +e+
  gi|15669119|ref|NP_247924.1| 47 LAKAQAELGLIPKEAAEEI 65
                                  4555556666666666655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.9
                                   HHHHHHHHHT--HHHH CS
                   FumaraseC_C  16 kIAkeAlkegktlrea 31 
                                    IA++  k g t+r +
  gi|15669119|ref|NP_247924.1| 252 LIAQTLNKIGVTVRSM 267
                                   5899999999999875 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 4.4e-07
                                   HHHHHHHHHT--HHHHHHH....TT-.-HHHHHHHT-HHH CS
                   FumaraseC_C  16 kIAkeAlkegktlreavle....lgllteeeldelldpek 51 
                                   + A +A++e++ l+++ le    ++++t+eel+el++p++
  gi|15669119|ref|NP_247924.1| 402 QCAMKAYEEKRHLKDILLEneevMKYITKEELEELMNPKT 441
                                   6799***************9999999************86 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.9     1e+04      34      59 ..      66      91 ..      57      99 .. 0.60
   2 !   16.3   0.0   3.5e-06     0.013      11      67 ..     386     442 ..     384     444 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.9
                                  HTT--GGG--HHHHHHH-TT--GGGG CS
                        ASL_C2 34 ekgkeleeltleelkeisplleedve 59
                                  +k+ + + ++le +kei++  + dv 
  gi|15669119|ref|NP_247924.1| 66 NKKASTKYVKLERVKEIEKQTKHDVV 91
                                  44555566777777777665555554 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.5e-06
                                   HHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-TT--.GGGGGGSSHHHH CS
                        ASL_C2  11 LvrkGlpFReAHeivgravrlaeekgkeleeltleelkeisplle.edveeaLdpeas 67 
                                   L+++G+   +AHeiv +++ +a e++++l+++ le  + + + ++ e++ee ++p++ 
  gi|15669119|ref|NP_247924.1| 386 LAKRGMGRQTAHEIVRQCAMKAYEEKRHLKDILLENEE-VMKYITkEELEELMNPKTY 442
                                   789999999***********************999988.6667888999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1114  (0.062134); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3036.26
//
Query:       gi|15669120|ref|NP_247925.1|  [L=210]
Description: precorrin-8X methylmutase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-68  228.5   1.7    6.3e-68  228.3   1.7    1.0  1  CbiC      Precorrin-8X methylmutase


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.3   1.7   3.5e-72   6.3e-68       2     195 ..      11     203 ..      10     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 228.3 bits;  conditional E-value: 3.5e-72
                                   HHHHHHHHHHCHC-TT.......S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-H CS
                          CbiC   2 IeaeSfaiideelgeee......lseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitk 76 
                                   I+++S +i++++++e        ++e+e+ +++Rv+hatad+e+a+ll+f+++ +e+g++a+k+++pi++Dv+m+kaGi  
  gi|15669120|ref|NP_247925.1|  11 IANKSREIVRNKIKEVLgdrineFNEKEMGIIERVVHATADPEYAKLLVFKNNPIEEGIKAIKEEKPIIVDVNMIKAGI-- 89 
                                   899********997653556677********************************************************.. PP

                                   HHHHTTC-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE----SC CS
                          CbiC  77 krleklgnevlclladpevaelakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPvGFv 157
                                       +  n+v+c++++p+v e ak++gitr++a+m++a++  +++ivviGn+PtAL+e+++l++e+++kp+l++gvPvGFv
  gi|15669120|ref|NP_247925.1|  90 ----R-YNKVHCFINHPDVYEVAKKEGITRAVASMRLAKDLIDDGIVVIGNSPTALFEVIRLVKEENIKPKLIVGVPVGFV 165
                                   ....3.478************************************************************************ PP

                                   CHHHHHHHHHCSSS-EEEESSS---HHHHHHHHHHHHH CS
                          CbiC 158 gaaesKealaesevpyitveGrkGGsavAaaivnaLle 195
                                   +a+esKeal+e +vp+i + G kGG++vA+ai+n +++
  gi|15669120|ref|NP_247925.1| 166 QASESKEALREVNVPSISTIGPKGGTPVAVAIINGIIA 203
                                   **********************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1369.16
//
Query:       gi|15669121|ref|NP_247926.1|  [L=381]
Description: hypothetical protein MJ_0931 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-87  291.7   0.8    2.2e-87  291.7   0.8    1.8  3  ThiI           Thiamine biosynthesis protein (ThiI)
    4.3e-33  114.4   7.1    4.3e-33  114.4   7.1    2.5  2  THUMP          THUMP domain
    4.4e-06   26.3   0.2    5.3e-05   22.8   0.2    2.6  1  QueC           Queuosine biosynthesis protein QueC
    9.3e-05   21.4   0.7    0.00051   18.9   0.3    2.5  2  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
      0.018   15.4   0.2        0.5   10.7   0.0    2.4  2  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
       0.05   13.2   0.3       0.18   11.4   0.2    2.0  1  PrpR_N         Propionate catabolism activator
      0.056   13.1   0.1       0.15   11.8   0.1    1.7  1  BRCA2          BRCA2 repeat


Domain annotation for each model (and alignments):
>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.1   2.7e+03      49      80 ..      34      62 ..      18     105 .. 0.59
   2 ?   -2.1   0.1      0.97   2.5e+03     147     176 ..      91     120 ..      70     138 .. 0.72
   3 !  291.7   0.8   8.6e-91   2.2e-87       1     197 []     186     380 ..     186     380 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                          ThiI 49 veklaellaeyqtslevklvvvdfkevlkeil 80
                                  ++++ +ll +y+   evk+    ++++l +i 
  gi|15669121|ref|NP_247926.1| 34 RKNIIKLLRKYEIDAEVKIL---HRKLLVKIN 62
                                  45555566666554444432...222233333 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.97
                          ThiI 147 ldKeeiiklAkeigtyeisiekedkCsvla 176
                                   ld +ei+ +A +i   ++ + +++k ++ +
  gi|15669121|ref|NP_247926.1|  91 LDINEIVSFAVQIMKKKLKTLNKEKVTFAV 120
                                   577788888888877777777776666655 PP

  == domain 3  score: 291.7 bits;  conditional E-value: 8.6e-91
                          ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeile 81 
                                   g+qgkvl+L+S+GiDSpVaa+++++RGcr+vl+hlk    +seea +kv+k++e+l++y+t  e+++vv+d+k+ +++i+e
  gi|15669121|ref|NP_247926.1| 186 GSQGKVLCLISDGIDSPVAAFMMIRRGCRAVLLHLK----MSEEALNKVRKIVEVLSDYDT--ELEFVVYDYKKDIEDIVE 260
                                   79*********************************7....9*******************9..****************** PP

                          ThiI  82 kv....kekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiiklAke 158
                                   k+    ke++t++++krkml++Aek+a++ +++a+vtG++LgqVaSqtl+Nlrvis+++n++ilrPLigldK++i+k+Ake
  gi|15669121|ref|NP_247926.1| 261 KLksikKENYTCIFCKRKMLKVAEKYAKYLDCDAIVTGDNLGQVASQTLKNLRVISENINYPILRPLIGLDKNDIVKIAKE 341
                                   9988889************************************************************************** PP

                          ThiI 159 igtyeisiekedkCsvlakhPttkakleevekaeeklkl 197
                                   igtyeis+eke kC++l+khP+t+ak+eev+k++ek+kl
  gi|15669121|ref|NP_247926.1| 342 IGTYEISTEKEIKCPYLPKHPKTIAKPEEVKKIKEKVKL 380
                                   ************************************986 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4   7.1   1.7e-36   4.3e-33       1     143 [.      35     175 ..      35     176 .. 0.97
   2 ?    2.5   0.2     0.054   1.4e+02      55      78 ..     246     269 ..     209     288 .. 0.72

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 1.7e-36
                                   HHHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                         THUMP   1 geieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfee 81 
                                   ++i +ll ++++++e+++ + ++++v++++++   +e l+ ++l+k++gi++ +pv ++c+ d+++i  +a++i kkk++ 
  gi|15669121|ref|NP_247926.1|  35 KNIIKLLRKYEIDAEVKILH-RKLLVKINTKD---KEDLALKLLKKVAGIVSYSPV-YECPLDINEIVSFAVQIMKKKLKT 110
                                   68999**************6.89999999997...99999999*************.************************ PP

                                   CT-...EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                         THUMP  82 eke...tFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisid 143
                                    ++   tFaV++kr +k+f fts+e+n++vG+aivek+gl+VdlenPdiv+ +ei++d ayi+++
  gi|15669121|ref|NP_247926.1| 111 LNKekvTFAVKTKRSYKKFPFTSVEVNKKVGEAIVEKLGLEVDLENPDIVLGIEILNDGAYIFTE 175
                                   **9***********************************************************986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.054
                                   EEEEEEESSHHHHHHHHHHHHHHH CS
                         THUMP  55 pvcevceadledileaakeivkkk 78 
                                   +v+++  +d+edi e+ k+i+k++
  gi|15669121|ref|NP_247926.1| 246 FVVYDYKKDIEDIVEKLKSIKKEN 269
                                   336777888888888888888876 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.2   2.1e-08   5.3e-05       1     183 [.     190     355 ..     190     365 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.1e-08
                                   EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG--------- CS
                          QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeeievpk 81 
                                   k+++l+S G+DS ++++++ ++g +  +l+++  + + + +++  ++ ++++  e + +  d+ k++ +  ++++ ++++k
  gi|15669121|ref|NP_247926.1| 190 KVLCLISDGIDSPVAAFMMIRRGCRAVLLHLKMSEEALNKVRKIVEVLSDYDT-ELEFVVYDYKKDIED--IVEKLKSIKK 267
                                   5799***************************9888777777777777777777.666666665555543..3344333444 PP

                                   --...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHHHTS--EEE-TTTT-- CS
                          QueC  82 eeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlgedkkieieaPlidls 162
                                        e+    f   R   +l +a  ya+ l+++ai++G n  +++      ++++k+l +   ++e+ +  i  Pli l+
  gi|15669121|ref|NP_247926.1| 268 -----ENYTCIFC-KR--KMLKVAEKYAKYLDCDAIVTGDNLGQVA------SQTLKNLRV---ISENINYPILRPLIGLD 331
                                   .....44444444.44..489******************8887743......455555554...55666799********* PP

                                   HHHHHHHHHHTT...HHHHH-B-S CS
                          QueC 163 Kaeivklgkelg...vpleetlsC 183
                                   K++ivk++ke+g   + +e+ + C
  gi|15669121|ref|NP_247926.1| 332 KNDIVKIAKEIGtyeISTEKEIKC 355
                                   ***********9766666666666 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.41     1e+03     295     336 ..      41      80 ..      15      82 .. 0.69
   2 !   18.9   0.3     2e-07   0.00051       2     124 ..     190     299 ..     189     353 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.41
                 tRNA_Me_trans 295 kekealelevkvrhkqelvkakvelkedetvevkldekvrav 336
                                    +k ++++evk+ h++ lvk  +++k++e++ +kl +kv ++
  gi|15669121|ref|NP_247926.1|  41 LRKYEIDAEVKILHRKLLVK--INTKDKEDLALKLLKKVAGI 80 
                                   44456677777777766655..55555555888888888776 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2e-07
                 tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfeef 82 
                                   kv++++S G+DS vaa+++ ++g   + ++lk++ee+ +         +++++ +v +  + +le v    +yk++ +e++
  gi|15669121|ref|NP_247926.1| 190 KVLCLISDGIDSPVAAFMMIRRGCRAVLLHLKMSEEALN---------KVRKIVEVLSDYDTELEFVV--YDYKKD-IEDI 258
                                   89*********************9999999998877222.........22333333333333333332..234444.3455 PP

                 tRNA_Me_trans  83 leeyeeGrTPn.PdvlCNkeiKfgallekakeelgadalatGH 124
                                   +e++++ +  n  ++ C +++   +++ek  + l++da++tG 
  gi|15669121|ref|NP_247926.1| 259 VEKLKSIKKENyTCIFCKRKM--LKVAEKYAKYLDCDAIVTGD 299
                                   555555444442488888865..33444444458888888885 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.11   2.7e+02      49      79 ..     207     237 ..     196     244 .. 0.72
   2 ?   10.7   0.0   0.00019       0.5      14      74 ..     245     312 ..     244     318 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.11
                                   HHHHTT-SEE.EESSSCHHHHHHHCTTTSEEE CS
                 Nitro_FeMo-Co  49 llaeegvdvv.ivgkiGpralakleaagievy 79 
                                   ++  +g+++v +  k+ ++al+k+++  +ev+
  gi|15669121|ref|NP_247926.1| 207 MMIRRGCRAVlLHLKMSEEALNKVRKI-VEVL 237
                                   455599965515679*******99986.6665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00019
                                   EEEEEEESSSCEEEEEEE....E.GCCCTSS....CSSTHHHHHHHH.TT-SEEEES.SSCHHHHHHHCTT CS
                 Nitro_FeMo-Co  14 yFaiyeveegevkivenr....veeaadaeg....ggggklaqllae.egvdvvivg.kiGpralakleaa 74 
                                   +F++y+++++ + ive+      e+++   +    ++  k+a+  a+  ++d++++g + G+ a + l++ 
  gi|15669121|ref|NP_247926.1| 245 EFVVYDYKKDIEDIVEKLksikKENYT---CifckRKMLKVAEKYAKyLDCDAIVTGdNLGQVASQTLKNL 312
                                   6********9999****9865522222...24446999*****************9856799999888875 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   6.9e-05      0.18      84     136 ..     228     286 ..     221     300 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.9e-05
                        PrpR_N  84 kglktlsell...dldieiytinseeeaeaavkel...kaegvevvvGdgvvadlAeka 136
                                   ++++++ e+l   d+++e+  ++  +++e++v++l   k+e+++++ +   + ++Aek+
  gi|15669121|ref|NP_247926.1| 228 NKVRKIVEVLsdyDTELEFVVYDYKKDIEDIVEKLksiKKENYTCIFCKRKMLKVAEKY 286
                                   5555555554422666777777777777766666633378*********9999999986 PP

>> BRCA2  BRCA2 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   5.7e-05      0.15      16      28 ..     221     233 ..     219     235 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.7e-05
                         BRCA2  16 rVSkesLqKAkkl 28 
                                   ++S+e+L+K++k+
  gi|15669121|ref|NP_247926.1| 221 KMSEEALNKVRKI 233
                                   8***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1365  (0.0761336); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2715.22
//
Query:       gi|15669122|ref|NP_247927.1|  [L=67]
Description: histone A2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.5e-21   74.2   3.2    8.2e-21   74.1   3.2    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    9.2e-13   48.7   1.2      1e-12   48.6   1.2    1.1  1  Histone        Core histone H2A/H2B/H3/H4
      1e-07   32.0   0.9    1.1e-07   31.9   0.9    1.1  1  TAF            TATA box binding protein associated factor (TA
    1.7e-06   28.3   0.2    1.9e-06   28.2   0.2    1.1  1  CENP-S         CENP-S protein
    1.8e-05   25.1   0.3    2.1e-05   24.9   0.3    1.2  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 
    1.9e-05   24.7   0.1    2.1e-05   24.6   0.1    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
    2.8e-05   24.0   0.0    3.4e-05   23.8   0.0    1.0  1  Bromo_TP       Bromodomain associated
    3.4e-05   23.9   0.1    3.7e-05   23.8   0.1    1.0  1  CENP-T_C       Centromere kinetochore component CENP-T histon
    0.00067   19.6   0.1    0.00074   19.5   0.1    1.1  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu
     0.0022   18.1   1.1     0.0024   18.0   1.1    1.0  1  DUF1931        Domain of unknown function (DUF1931)


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   3.2   4.6e-24   8.2e-21       1      65 []       2      65 ..       2      65 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 4.6e-24
                                  XXXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                 CBFD_NFYB_HMF  1 aeLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                  aeLP+a+ ++I+k++ +a++++++A e++ae+vee + e+a+eA+e++k++krKt+k e+iklA+
  gi|15669122|ref|NP_247927.1|  2 AELPVAPFERILKKA-GAERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLAL 65
                                  69*************.***********************************************97 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   1.2   5.6e-16     1e-12      63     129 ..       5      66 ..       1      67 [] 0.93

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 5.6e-16
                                   XHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                       Histone  63 qklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                   + +pf+R++++         r+s+ a ++l+ea+E +  e+++eA  lakhaKR+T+  +Di+lA++
  gi|15669122|ref|NP_247927.1|   5 PVAPFERILKKAGA-----ERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALK 66 
                                   5689***9998876.....9*********************************************87 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.9   6.1e-11   1.1e-07      16      66 .]      16      66 ..       2      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 6.1e-11
                                  TT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH- CS
                           TAF 16 lGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsALr 66
                                   G + +s  aa+ Lae ve+   ei++ea+   +h+kR++  v+D+  AL+
  gi|15669122|ref|NP_247927.1| 16 AGAERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALK 66
                                  688889999****************************************98 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.2     1e-09   1.9e-06      24      71 ..      19      66 ..       9      67 .] 0.87

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1e-09
                        CENP-S 24 veatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLlaR 71
                                   ++++ + + l+e v + + ++ak     akHAkR+t++++D++L ++
  gi|15669122|ref|NP_247927.1| 19 ERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALK 66
                                  468888899999***99999*************************876 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.3   1.2e-08   2.1e-05      21      63 ..      24      66 ..      11      67 .] 0.89

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.2e-08
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH CS
                   TFIID_20kDa 21 dvedlLleiaddFvesvtkfacklakhRksdklevrDiqlhle 63
                                     + L+e +++   ++ k a++lakh k +++ v Di+l l+
  gi|15669122|ref|NP_247927.1| 24 AAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALK 66
                                  567889999999999**************************98 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   1.2e-08   2.1e-05      12      68 ..      10      66 ..       5      67 .] 0.95

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.2e-08
                   TFIID-31kDa 12 hliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiq 68
                                  + iL++ g + ++    + L + +     ++ ++A  la+hak+k+v+++d++lA++
  gi|15669122|ref|NP_247927.1| 10 ERILKKAGAERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALK 66
                                  679****************************************************87 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.9e-08   3.4e-05      15      69 ..      12      66 ..      10      67 .] 0.97

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.9e-08
                                  HHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHH CS
                      Bromo_TP 15 ileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvltLq 69
                                  il++aG +++  +a E L e +++  +e++++a + a ha R +++++D+ l+L+
  gi|15669122|ref|NP_247927.1| 12 ILKKAGAERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALK 66
                                  89**************************************************997 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1     2e-08   3.7e-05      24      75 ..      15      66 ..       2      67 .] 0.87

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2e-08
                      CENP-T_C 24 sgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmk 75
                                  ++  ++++++a + l +a ++    ++++    akHa+RKt++ +D+ l +k
  gi|15669122|ref|NP_247927.1| 15 KAGAERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALK 66
                                  356789*****************************************99887 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   4.1e-07   0.00074      23      65 ..      24      66 ..      14      67 .] 0.90

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.1e-07
                                  HHHHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXXX CS
                   TFIID-18kDa 23 etvqlledlvrgyliellqqaakvaklrgsrkitlEDllfliR 65
                                  ++++ l + v++   e+ ++a+++ak+ +++ +++ED++ +++
  gi|15669122|ref|NP_247927.1| 24 AAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKLALK 66
                                  677889999*****************************99886 PP

>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.1   1.4e-06    0.0024       1      55 [.       9      63 ..       9      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
                                  HHHHHHHHHS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-- CS
                       DUF1931  1 lerlfreaagLdvdkedlkrisdfVekklydLllvaeenAkangrdviepaDLPi 55
                                  +er++++a    v +  ++ + + Ve++  +++  a e Ak  +r++++++D+ +
  gi|15669122|ref|NP_247927.1|  9 FERILKKAGAERVSRAAAEYLAEAVEEIALEIAKEAVELAKHAKRKTVKVEDIKL 63
                                  89**************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1091  (0.0608511); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 478.77
//
Query:       gi|15669123|ref|NP_247928.1|  [L=238]
Description: hypothetical protein MJ_0933 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-52  177.1  11.9    7.9e-52  176.0  11.9    1.5  1  DUF92            Integral membrane protein DUF92
  ------ inclusion threshold ------
      0.034   14.2   0.8      0.034   14.2   0.8    3.6  3  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        0.5    9.8   1.1       0.98    8.8   1.1    1.5  1  Mucin15          Cell-membrane associated Mucin15
        7.9    6.3  12.4        2.8    7.7   0.5    4.0  4  PRD1_DD          PRD1 phage membrane DNA delivery
        8.5    5.6   5.4        2.8    7.2   2.1    1.7  2  DUF3810          Protein of unknown function (DUF3810)


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.0  11.9   2.2e-55   7.9e-52       2     235 ..      18     227 ..      17     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 176.0 bits;  conditional E-value: 2.2e-55
                         DUF92   2 ltlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKakleeekegaRdavqVlans 82 
                                   ++++lal+  +++ L+ +G++ + ++g+++++   g+++++lll Ff+lg l+++v+ ++K+  +   e  R+ ++Vlan+
  gi|15669123|ref|NP_247928.1|  18 IICVLALMIKKSRCLDNEGVIGSSIMGFILLYF-CGFKYLILLLSFFILGVLVSRVGLEKKKAKK-MDETCRSLKNVLANG 96 
                                   67899999999*****************99998.8889*******************99998544.44678********** PP

                         DUF92  83 lvalllally.lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnGgVsllGllasllGalliall 162
                                   l+++l+a+l+ ++ ++ l+g+++s+Aa+++DT++SElG ils++kprlitt++ v++Gt+G+++++G+la++lGa+li+l+
  gi|15669123|ref|NP_247928.1|  97 LIPILFAILAiFGFNWALIGYISSIAAATSDTFSSELG-ILSNEKPRLITTFEVVEKGTDGAITIFGTLAGVLGAFLIGLF 176
                                   *********95337899*********************.99999***********************************99 PP

                         DUF92 163 .avlllllellillltlaGllGsllDSlLGatlqasvvdkrtgkvvegeggekvvsGldlLdNnaVNllsallt 235
                                    ++l+  + +++l++t+ G++G+l+DSl+Ga+++++                       +L+N++VNl++++++
  gi|15669123|ref|NP_247928.1| 177 gYLLFGDI-KIVLCGTAGGIAGNLADSLVGALFERK----------------------GILNNEHVNLIATIVG 227
                                   55455433.3899999********************......................7899999999988875 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.8   9.5e-06     0.034      59     107 ..      38      91 ..       8      95 .. 0.67
   2 ?   -1.2   1.4      0.56     2e+03      55      62 ..     101     110 ..      92     131 .. 0.43
   3 ?   -4.4  10.0         5   1.8e+04      42      68 ..     164     200 ..     146     237 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.5e-06
               Phage_holin_3_6  59 a......lalaa..lwlaalivaavllvlagvlalvglkklkkakplpertieelke 107
                                   +      ++l +    + +li+ + +++l++++ +vgl k k+  +++++t ++lk+
  gi|15669123|ref|NP_247928.1|  38 IgssimgFIL-LyfCGFKYLILLLSFFILGVLVSRVGLEKKKA--KKMDETCRSLKN 91 
                                   0444333111.123568999*******************7777..459*******97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.56
               Phage_holin_3_6  55 lval..alal 62 
                                   l+a+  ++++
  gi|15669123|ref|NP_247928.1| 101 LFAIlaIFGF 110
                                   2222111111 PP

  == domain 3  score: -4.4 bits;  conditional E-value: 5
               Phage_holin_3_6  42 aagvlallalllllvala...........lalaalwla 68 
                                   +agvl+++ ++l+  +l+            ++ a  la
  gi|15669123|ref|NP_247928.1| 164 LAGVLGAFLIGLFGYLLFgdikivlcgtaGGI-AGNLA 200
                                   33444444333333333222233333322222.12223 PP

>> Mucin15  Cell-membrane associated Mucin15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.1   0.00027      0.98     219     246 ..     159     185 ..     144     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00027
                       Mucin15 219 vvfGaiLGaiLGasLLsLvGYllCGkrk 246
                                    +fG++ G +LGa L+ L GYll G  k
  gi|15669123|ref|NP_247928.1| 159 TIFGTLAG-VLGAFLIGLFGYLLFGDIK 185
                                   58998666.8*************99765 PP

>> PRD1_DD  PRD1 phage membrane DNA delivery
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0069        25       6      42 ..       7      45 ..       3      49 .. 0.81
   2 ?   -0.9   0.0      0.37   1.3e+03      20      27 ..      64      71 ..      59      73 .. 0.86
   3 ?   -1.6   0.5      0.63   2.2e+03      20      20 ..     114     114 ..      91     135 .. 0.55
   4 ?    7.7   0.5   0.00077       2.8       2      21 ..     216     235 ..     215     238 .] 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0069
                       PRD1_DD  6 ktlvtvltAiiGvAilAvlv..srrsntAGvikaassGF 42
                                  +tl+ +   i+ + +lA ++  sr     Gvi ++  GF
  gi|15669123|ref|NP_247928.1|  7 ETLIRLFVSILIICVLALMIkkSRCLDNEGVIGSSIMGF 45
                                  68888888898899999887556777899***9999999 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.37
                       PRD1_DD 20 ilAvlvsr 27
                                  il vlvsr
  gi|15669123|ref|NP_247928.1| 64 ILGVLVSR 71
                                  999****8 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.63
                       PRD1_DD  20 i 20 
                                   +
  gi|15669123|ref|NP_247928.1| 114 L 114
                                   1 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.00077
                       PRD1_DD   2 neFvktlvtvltAiiGvAil 21 
                                   ne v+ + t++  iiGv i 
  gi|15669123|ref|NP_247928.1| 216 NEHVNLIATIVGGIIGVLIY 235
                                   789999***********985 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.6      0.15   5.2e+02      27      77 ..       8      50 ..       5      56 .. 0.36
   2 ?    7.2   2.1   0.00078       2.8      20      88 ..      48     122 ..      37     133 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                       DUF3810 27 llivlli.llvilylvlaiklkkrkkkkkrllkvllrvllvllvvyflftll 77
                                   li l++ +l+i++l+l+i    +k++      v+++     +++ f+ + +
  gi|15669123|ref|NP_247928.1|  8 TLIRLFVsILIICVLALMI----KKSRCLDNEGVIGS-----SIMGFILLYF 50
                                  4554444044444555555....22222222222222.....2233333333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00078
                       DUF3810  20 fpFSvgellivllillvilylvlai.....klkkrkkkkkrllkvllr.vllvllvvyflftllwglnYyrepls 88 
                                   + F     li+ll ++++ +lv  +     k kk  +  ++l++vl + ++ +l +++++f ++w+l  y ++++
  gi|15669123|ref|NP_247928.1|  48 LYFCGFKYLILLLSFFILGVLVSRVglekkKAKKMDETCRSLKNVLANgLIPILFAILAIFGFNWALIGYISSIA 122
                                   556667778888888888888888886544333333344444444444256678888888888888876665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1507.90
//
Query:       gi|15669124|ref|NP_247929.1|  [L=209]
Description: polyferredoxin MvhB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-33  112.8  58.2    4.5e-09   35.7   3.9    6.2  6  Fer4      4Fe-4S binding domain
    1.1e-20   72.8  57.1    5.5e-05   23.1   4.9    6.2  6  Fer4_6    4Fe-4S binding domain
    2.1e-18   66.7  46.7    1.4e-06   28.8  12.6    5.3  5  Fer4_7    4Fe-4S dicluster domain
    2.8e-18   65.8  41.8      7e-07   29.3  10.3    4.5  4  Fer4_9    4Fe-4S dicluster domain
    8.6e-18   64.2  50.0    2.3e-07   30.8   9.7    4.6  4  Fer4_10   4Fe-4S dicluster domain
      3e-17   61.6  51.1    0.00015   21.7   2.3    6.2  6  Fer4_2    4Fe-4S binding domain
    4.7e-15   55.5  51.4    4.6e-05   23.5   9.6    4.3  4  Fer4_21   4Fe-4S dicluster domain
      2e-14   54.3  47.5    4.1e-05   24.4   0.6    5.9  6  Fer4_16   4Fe-4S double cluster binding domain
    9.9e-12   44.4  53.8    0.00041   20.6   2.1    6.3  6  Fer4_4    4Fe-4S binding domain
    1.1e-07   32.2  48.7      0.014   15.9   1.9    6.1  6  Fer4_8    4Fe-4S dicluster domain
    2.1e-07   31.4  50.0     0.0031   18.0   0.2    6.1  7  Fer4_17   4Fe-4S dicluster domain
    1.6e-05   25.5  67.3    0.00024   21.8   5.2    6.3  6  Fer4_3    4Fe-4S binding domain
      2e-05   24.7   8.9      2e-05   24.7   8.9    4.4  5  Fer4_18   4Fe-4S dicluster domain
    0.00097   19.8  45.0       0.13   13.1   1.0    6.3  6  Fer4_15   4Fe-4S single cluster domain
     0.0017   18.9  54.2      0.055   14.0   1.7    6.2  6  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.039   14.8   0.9      0.039   14.8   0.9    5.8  5  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   3.9     4e-12   4.5e-09       6      24 .]      45      63 ..      41      63 .. 0.90
   2 !   27.0   2.6   2.3e-09   2.6e-06       5      23 ..      69      87 ..      65      88 .. 0.89
   3 !   26.0   3.9   4.8e-09   5.3e-06       2      23 ..      93     114 ..      92     115 .. 0.89
   4 !   10.2   3.3   0.00047      0.53       1      15 [.     124     138 ..     124     140 .. 0.90
   5 !   25.1   1.2   9.4e-09   1.1e-05       2      23 ..     148     169 ..     147     170 .. 0.95
   6 !   19.6   4.9     5e-07   0.00056       1      19 [.     181     199 ..     181     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 4e-12
                                  TTSSS-THHHHHSTTTEEE CS
                          Fer4  6 ekCigCGaCvevCPvgAIt 24
                                    CigCG+Cv+vCP++AI+
  gi|15669124|ref|NP_247929.1| 45 TECIGCGLCVDVCPTNAIK 63
                                  68****************6 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 2.3e-09
                                  TTTSSS-THHHHHSTTTEE CS
                          Fer4  5 eekCigCGaCvevCPvgAI 23
                                  e  C  CG+Cv+vCP++AI
  gi|15669124|ref|NP_247929.1| 69 ETICSVCGTCVDVCPNNAI 87
                                  678***************9 PP

  == domain 3  score: 26.0 bits;  conditional E-value: 4.8e-09
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                   +id +kC++CG Cv  CP   I
  gi|15669124|ref|NP_247929.1|  93 TIDADKCTKCGVCVLFCPIPII 114
                                   79****************8666 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00047
                                   EEEETTTSSS-THHH CS
                          Fer4   1 vvideekCigCGaCv 15 
                                   +vi +++C  CG+C+
  gi|15669124|ref|NP_247929.1| 124 PVILKDRCNSCGLCE 138
                                   57899*********7 PP

  == domain 5  score: 25.1 bits;  conditional E-value: 9.4e-09
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                   +i++ekC  C  C+e CP  AI
  gi|15669124|ref|NP_247929.1| 148 EINPEKCKLCLSCIEKCPLQAI 169
                                   69****************9999 PP

  == domain 6  score: 19.6 bits;  conditional E-value: 5e-07
                                   EEEETTTSSS-THHHHHST CS
                          Fer4   1 vvideekCigCGaCvevCP 19 
                                   v++d + Ci+C +C+e+CP
  gi|15669124|ref|NP_247929.1| 181 VKVDIDSCIFCRECEEICP 199
                                   5899*************** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   4.9   4.9e-08   5.5e-05       9      24 .]      47      62 ..      45      62 .. 0.98
   2 !   18.9   2.7     1e-06    0.0011       4      24 .]      67      87 ..      64      87 .. 0.88
   3 !   19.7   3.2   5.6e-07   0.00063       3      20 ..      93     110 ..      91     114 .. 0.93
   4 !    9.5   2.5   0.00092         1       2      16 ..     124     138 ..     123     142 .. 0.88
   5 !   14.5   1.5   2.5e-05     0.029       3      24 .]     148     169 ..     147     169 .. 0.92
   6 !   17.7   3.7   2.4e-06    0.0027       1      20 [.     180     199 ..     180     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.9e-08
                        Fer4_6  9 CigCgdCvrvCPegai 24
                                  CigCg Cv+vCP++ai
  gi|15669124|ref|NP_247929.1| 47 CIGCGLCVDVCPTNAI 62
                                  ***************8 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1e-06
                        Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                  + +  C  Cg Cv+vCP +ai
  gi|15669124|ref|NP_247929.1| 67 FRETICSVCGTCVDVCPNNAI 87
                                  67889************9998 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 5.6e-07
                        Fer4_6   3 eidpdkCigCgdCvrvCP 20 
                                   +id+dkC+ Cg Cv  CP
  gi|15669124|ref|NP_247929.1|  93 TIDADKCTKCGVCVLFCP 110
                                   8****************9 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00092
                        Fer4_6   2 veidpdkCigCgdCv 16 
                                   ++i +d+C++Cg C+
  gi|15669124|ref|NP_247929.1| 124 PVILKDRCNSCGLCE 138
                                   78889********96 PP

  == domain 5  score: 14.5 bits;  conditional E-value: 2.5e-05
                        Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                   ei+p+kC  C  C+  CP +ai
  gi|15669124|ref|NP_247929.1| 148 EINPEKCKLCLSCIEKCPLQAI 169
                                   79****************7776 PP

  == domain 6  score: 17.7 bits;  conditional E-value: 2.4e-06
                        Fer4_6   1 vveidpdkCigCgdCvrvCP 20 
                                   +v +d d+Ci C++C+ +CP
  gi|15669124|ref|NP_247929.1| 180 IVKVDIDSCIFCRECEEICP 199
                                   689***************** PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8  12.6   1.3e-09   1.4e-06       2      52 .]      47      86 ..      46      86 .. 0.92
   2 !   24.6  12.5   2.5e-08   2.8e-05       2      49 ..      72     110 ..      71     113 .. 0.93
   3 !   15.1  11.0   2.4e-05     0.027       1      45 [.      98     138 ..      98     141 .. 0.85
   4 !   12.9   1.7   0.00011      0.13      32      52 .]     148     168 ..     143     168 .. 0.90
   5 !   23.8   9.6   4.6e-08   5.2e-05       1      49 [.     153     199 ..     153     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.3e-09
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  CigCg Cv++Cp++ai++  +           +++ C+ Cg Cv+vCP +a
  gi|15669124|ref|NP_247929.1| 47 CIGCGLCVDVCPTNAIKIFSF-----------RETICSVCGTCVDVCPNNA 86
                                  ******************776...........5789************987 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 2.5e-08
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                   C  Cg Cv++Cp++ai  d +         +id++kC+ Cg+Cv  CP
  gi|15669124|ref|NP_247929.1|  72 CSVCGTCVDVCPNNAIIKDRF---------TIDADKCTKCGVCVLFCP 110
                                   999*************98765.........9****************9 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2.4e-05
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCv 45 
                                   +C++Cg Cv  Cp   i+ +      + ++++i  ++C +Cg C+
  gi|15669124|ref|NP_247929.1|  98 KCTKCGVCVLFCPIPIIKKEIP----KPKTPVILKDRCNSCGLCE 138
                                   7************888887554....3367899**********97 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 0.00011
                        Fer4_7  32 eidpekClgCgaCvavCPtga 52 
                                   ei+pekC  C +C++ CP +a
  gi|15669124|ref|NP_247929.1| 148 EINPEKCKLCLSCIEKCPLQA 168
                                   689***************875 PP

  == domain 5  score: 23.8 bits;  conditional E-value: 4.6e-08
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                   +C  C  C + Cp +ai +++e  ++    v++d ++C++C++C++ CP
  gi|15669124|ref|NP_247929.1| 153 KCKLCLSCIEKCPLQAILTPDEYINS--LIVKVDIDSCIFCRECEEICP 199
                                   79***********9999998874443..58999**************** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.3     4e-08   4.5e-05      27      51 .]      38      62 ..      22      62 .. 0.71
   2 !   29.3  10.3   6.2e-10     7e-07       2      47 ..      72     110 ..      71     114 .. 0.94
   3 !   13.6  20.3   5.1e-05     0.057       1      51 []      98     169 ..      98     169 .. 0.89
   4 !   23.3   9.2   4.6e-08   5.2e-05       1      47 [.     153     199 ..     153     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4e-08
                        Fer4_9 27 rlraaseeaCigCgaCveaCpkgai 51
                                  + +  + ++CigCg Cv++Cp++ai
  gi|15669124|ref|NP_247929.1| 38 KTKPIQLTECIGCGLCVDVCPTNAI 62
                                  333333378*************987 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 6.2e-10
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCp 47 
                                   C  Cg+Cv++Cp++++++d+++  a        +C++Cg Cv  Cp
  gi|15669124|ref|NP_247929.1|  72 CSVCGTCVDVCPNNAIIKDRFTIDAD-------KCTKCGVCVLFCP 110
                                   99**********************99.......5***********9 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 5.1e-05
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.....................eaCigCgaCveaCpkgai 51 
                                   kCt+Cg Cv  Cp  +++++  + k  +  ++                      e+C  C +C+e+Cp +ai
  gi|15669124|ref|NP_247929.1|  98 KCTKCGVCVLFCPIPIIKKEIPKPKTPVILKDRcnscglceceaidiinkeinpEKCKLCLSCIEKCPLQAI 169
                                   7************999988887777777555557899*******************************9987 PP

  == domain 4  score: 23.3 bits;  conditional E-value: 4.6e-08
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCp 47 
                                   kC  C +C+e+Cp +++   +      + + + ++Ci+C++C+e+Cp
  gi|15669124|ref|NP_247929.1| 153 KCKLCLSCIEKCPLQAILTPDEYINSLIVKVDIDSCIFCRECEEICP 199
                                   7**************99766666666666666679***********9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6  13.7   1.4e-06    0.0015       4      56 .]      42      83 ..      39      83 .. 0.78
   2 !   22.1  13.3   1.1e-07   0.00012       6      56 .]      69     110 ..      64     110 .. 0.88
   3 !   18.4  11.3   1.6e-06    0.0018       3      52 ..      93     138 ..      91     142 .. 0.89
   4 !   30.8   9.7     2e-10   2.3e-07       3      56 .]     148     199 ..     146     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                       Fer4_10  4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  i+   Ci+Cg Cv++CP+       ++++  + ++      C  cg Cv++CP
  gi|15669124|ref|NP_247929.1| 42 IQLTECIGCGLCVDVCPT-------NAIKIFSFRET----ICSVCGTCVDVCP 83
                                  66789*************.......44444444444....4999********9 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.1e-07
                       Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +  C  Cg+Cv++CP           a ++++  ++ +kCt+cg Cv  CP
  gi|15669124|ref|NP_247929.1|  69 ETICSVCGTCVDVCPN---------NAIIKDRFTIDADKCTKCGVCVLFCP 110
                                   678*************.........777777778888*************9 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.6e-06
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCv 52 
                                    id+d+C++Cg Cv +CP        k+e+ + ++  +  ++C  cg C 
  gi|15669124|ref|NP_247929.1|  93 TIDADKCTKCGVCVLFCPI----PIIKKEIPKPKTPVILKDRCNSCGLCE 138
                                   69*****************....88889999999999999*******774 PP

  == domain 4  score: 30.8 bits;  conditional E-value: 2e-10
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +i++++C  C  C + CP   ++  + +e+ ++  v++++++C++c +C e+CP
  gi|15669124|ref|NP_247929.1| 148 EINPEKCKLCLSCIEKCPL--QAILTPDEYINSLIVKVDIDSCIFCRECEEICP 199
                                   699****************..77788888888888888***************9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   2.9   2.6e-07   0.00029       7      22 .]      45      59 ..      40      59 .. 0.86
   2 !   15.2   2.7   1.5e-05     0.016       9      22 .]      71      84 ..      64      84 .. 0.87
   3 !   21.7   2.3   1.3e-07   0.00015       2      21 ..      91     110 ..      90     111 .. 0.93
   4 !   11.0   2.2   0.00033      0.37       3      16 ..     124     137 ..     121     141 .. 0.87
   5 !   14.0   1.3   3.7e-05     0.042       5      21 ..     149     165 ..     147     166 .. 0.94
   6 !    8.6   2.0    0.0018       2.1       3      21 ..     181     199 ..     179     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.6e-07
                        Fer4_2  7 tdrCigCgaCvsaCPa 22
                                  t+ CigCg Cv++CP+
  gi|15669124|ref|NP_247929.1| 45 TE-CIGCGLCVDVCPT 59
                                  55.************7 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.5e-05
                        Fer4_2  9 rCigCgaCvsaCPa 22
                                  +C  Cg+Cv++CP+
  gi|15669124|ref|NP_247929.1| 71 ICSVCGTCVDVCPN 84
                                  7999*********5 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 1.3e-07
                        Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                   ++ +d+d+C+ Cg Cv  CP
  gi|15669124|ref|NP_247929.1|  91 RFTIDADKCTKCGVCVLFCP 110
                                   5789***************9 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00033
                        Fer4_2   3 vvvdtdrCigCgaC 16 
                                   +v+  drC++Cg C
  gi|15669124|ref|NP_247929.1| 124 PVILKDRCNSCGLC 137
                                   78899********* PP

  == domain 5  score: 14.0 bits;  conditional E-value: 3.7e-05
                        Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                   +++++C  C +C+  CP
  gi|15669124|ref|NP_247929.1| 149 INPEKCKLCLSCIEKCP 165
                                   8***************9 PP

  == domain 6  score: 8.6 bits;  conditional E-value: 0.0018
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   v+vd d+Ci C+ C   CP
  gi|15669124|ref|NP_247929.1| 181 VKVDIDSCIFCRECEEICP 199
                                   78999*************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   3.4   6.8e-08   7.6e-05      32      58 ..      38      63 ..      28      64 .. 0.83
   2 !    9.2   4.7    0.0012       1.3      36      57 ..      67      87 ..      63      90 .. 0.78
   3 !   18.9  10.0   1.1e-06    0.0012       2      48 ..      93     138 ..      92     146 .. 0.84
   4 !   23.5   9.6   4.1e-08   4.6e-05       2      55 ..     148     202 ..     147     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.8e-08
                       Fer4_21 32 tvlkvvedeCvGCnlCssvCPvedcie 58
                                  ++ +++  eC+GC lC++vCP+ ++i+
  gi|15669124|ref|NP_247929.1| 38 KTKPIQLTECIGCGLCVDVCPT-NAIK 63
                                  556777889************7.9987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0012
                       Fer4_21 36 vvedeCvGCnlCssvCPvedci 57
                                   +e  C  C  C++vCP  ++i
  gi|15669124|ref|NP_247929.1| 67 FRETICSVCGTCVDVCPN-NAI 87
                                  56788************5.555 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 1.1e-06
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieid.aktvlkvv.edeCvGCnlCs 48 
                                   +id dkC +Cg C++ C+   +  i+++ +k +++v+ +d+C  C lC 
  gi|15669124|ref|NP_247929.1|  93 TIDADKCTKCGVCVLFCP---IPIIKKEiPKPKTPVIlKDRCNSCGLCE 138
                                   59****************...78896554677777765**********5 PP

  == domain 4  score: 23.5 bits;  conditional E-value: 4.1e-08
                       Fer4_21   2 ridedkCigCgkCliaCedtshqai....eidaktvlkvvedeCvGCnlCssvCPved 55 
                                    i+++kC  C +C+  C+    qai    e+ ++ ++kv  d+C+ C  C ++CP+ +
  gi|15669124|ref|NP_247929.1| 148 EINPEKCKLCLSCIEKCP---LQAIltpdEYINSLIVKVDIDSCIFCRECEEICPIRG 202
                                   599***************...8***666656666778999***************975 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.6   3.7e-08   4.1e-05       2      18 ..      47      63 ..      30      70 .. 0.91
   2 !   23.5   3.4   7.1e-08     8e-05       2      31 ..      72     100 ..      71     101 .. 0.93
   3 !    7.9   8.4    0.0053       5.9       1      20 [.      98     117 ..      98     134 .. 0.73
   4 ?   -1.7   3.2       5.3   5.9e+03       1       8 [.     130     137 ..     130     148 .. 0.87
   5 !   15.6   1.2   2.1e-05     0.024       1      22 [.     153     174 ..     153     180 .. 0.87
   6 !    9.4   2.1    0.0018         2      52      66 ..     186     200 ..     175     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.7e-08
                       Fer4_16  2 CgtCgkCaevCPtnaik 18
                                  C++Cg C++vCPtnaik
  gi|15669124|ref|NP_247929.1| 47 CIGCGLCVDVCPTNAIK 63
                                  99*************98 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 7.1e-08
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeieareci 31 
                                   C  Cg C++vCP nai ++ +++i+a++c+
  gi|15669124|ref|NP_247929.1|  72 CSVCGTCVDVCPNNAIIKD-RFTIDADKCT 100
                                   99*****************.89*****997 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0053
                       Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                   +C++Cg C+  CP   ik++
  gi|15669124|ref|NP_247929.1|  98 KCTKCGVCVLFCPIPIIKKE 117
                                   5*************999977 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 5.3
                       Fer4_16   1 rCgtCgkC 8  
                                   rC +Cg C
  gi|15669124|ref|NP_247929.1| 130 RCNSCGLC 137
                                   59999999 PP

  == domain 5  score: 15.6 bits;  conditional E-value: 2.1e-05
                       Fer4_16   1 rCgtCgkCaevCPtnaikekke 22 
                                   +C+ C  C+e CP +ai ++ e
  gi|15669124|ref|NP_247929.1| 153 KCKLCLSCIEKCPLQAILTPDE 174
                                   5****************99943 PP

  == domain 6  score: 9.4 bits;  conditional E-value: 0.0018
                       Fer4_16  52 eaitgCdiCqdvCPa 66 
                                     +++C+ C+++CP+
  gi|15669124|ref|NP_247929.1| 186 DSCIFCRECEEICPI 200
                                   567888888888885 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   2.1   3.6e-07   0.00041       3      17 .]      46      60 ..      44      60 .. 0.91
   2 !   10.7   2.9   0.00058      0.64       4      16 ..      72      84 ..      69      87 .. 0.87
   3 !   18.9   2.2   1.3e-06    0.0014       2      15 ..      97     110 ..      96     117 .. 0.94
   4 ?    6.6   4.2     0.011        13       1      11 [.     128     138 ..     128     142 .. 0.85
   5 ?    6.6   1.6     0.012        13       1      16 [.     151     166 ..     151     170 .. 0.91
   6 !   10.6   2.6   0.00058      0.65       2      15 ..     186     199 ..     185     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.6e-07
                        Fer4_4  3 rCigCgsCvaaCPqg 17
                                   CigCg Cv++CP++
  gi|15669124|ref|NP_247929.1| 46 ECIGCGLCVDVCPTN 60
                                  6************86 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00058
                        Fer4_4  4 CigCgsCvaaCPq 16
                                  C  Cg Cv++CP 
  gi|15669124|ref|NP_247929.1| 72 CSVCGTCVDVCPN 84
                                  666*********5 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 1.3e-06
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   ++C+ Cg+Cv +CP
  gi|15669124|ref|NP_247929.1|  97 DKCTKCGVCVLFCP 110
                                   89***********9 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.011
                        Fer4_4   1 qerCigCgsCv 11 
                                   ++rC+ Cg C+
  gi|15669124|ref|NP_247929.1| 128 KDRCNSCGLCE 138
                                   69******985 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.012
                        Fer4_4   1 qerCigCgsCvaaCPq 16 
                                   +e+C  C sC+  CP 
  gi|15669124|ref|NP_247929.1| 151 PEKCKLCLSCIEKCPL 166
                                   699************6 PP

  == domain 6  score: 10.6 bits;  conditional E-value: 0.00058
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   ++Ci C+ C+ +CP
  gi|15669124|ref|NP_247929.1| 186 DSCIFCRECEEICP 199
                                   79***********9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.9   1.2e-05     0.014       2      17 ..      44      59 ..      43      70 .. 0.76
   2 !    8.5   3.9    0.0024       2.7      51      64 ..      72      85 ..      67      86 .. 0.89
   3 !   12.8   0.4   0.00011      0.13       2      17 ..      96     111 ..      94     124 .. 0.70
   4 ?    2.0   4.5      0.26   2.9e+02       3      12 ..     129     138 ..     127     152 .. 0.84
   5 ?    5.4   5.0     0.023        25      48      63 ..     151     166 ..     139     169 .. 0.82
   6 !   12.4   0.2   0.00014      0.16      48      63 ..     185     200 ..     170     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                        Fer4_8  2 lekCieCgaCqsaCpv 17
                                  l +Ci+Cg+C + Cp+
  gi|15669124|ref|NP_247929.1| 44 LTECIGCGLCVDVCPT 59
                                  5679999999999984 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0024
                        Fer4_8 51 CttcgaCtevCpvg 64
                                  C+ cg C++vCp++
  gi|15669124|ref|NP_247929.1| 72 CSVCGTCVDVCPNN 85
                                  999********986 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00011
                        Fer4_8   2 lekCieCgaCqsaCpv 17 
                                   ++kC++Cg C   Cp+
  gi|15669124|ref|NP_247929.1|  96 ADKCTKCGVCVLFCPI 111
                                   5677777777777764 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.26
                        Fer4_8   3 ekCieCgaCq 12 
                                   ++C+ Cg+C+
  gi|15669124|ref|NP_247929.1| 129 DRCNSCGLCE 138
                                   5799999996 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.023
                        Fer4_8  48 lwsCttcgaCtevCpv 63 
                                    ++C  c +C e+Cp 
  gi|15669124|ref|NP_247929.1| 151 PEKCKLCLSCIEKCPL 166
                                   5789999999999995 PP

  == domain 6  score: 12.4 bits;  conditional E-value: 0.00014
                        Fer4_8  48 lwsCttcgaCtevCpv 63 
                                   ++sC  c++C+e Cp+
  gi|15669124|ref|NP_247929.1| 185 IDSCIFCRECEEICPI 200
                                   6788888888888885 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   2.8e-06    0.0031      42      59 ..      43      60 ..      18      63 .. 0.70
   2 !   10.4   2.3   0.00064      0.72       2      16 ..      72      86 ..      71      91 .. 0.62
   3 !   10.9   1.2   0.00046      0.51      42      57 ..      95     110 ..      85     114 .. 0.79
   4 !    9.9   1.5   0.00098       1.1       1      20 [.      98     117 ..      98     128 .. 0.74
   5 ?    2.2   4.6      0.23   2.6e+02      44      53 ..     129     138 ..     117     142 .. 0.83
   6 ?    5.9   3.5     0.017        19      40      57 ..     148     165 ..     140     169 .. 0.75
   7 ?    4.2  13.6     0.058        65       1      57 [.     153     199 ..     153     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.8e-06
                       Fer4_17 42 kaslCieCgeCerkCPqg 59
                                  +  +Ci+Cg+C+ +CP +
  gi|15669124|ref|NP_247929.1| 43 QLTECIGCGLCVDVCPTN 60
                                  677888888888888865 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00064
                       Fer4_17  2 CiqCgyClpeCpsye 16
                                  C+ Cg C+++Cp ++
  gi|15669124|ref|NP_247929.1| 72 CSVCGTCVDVCPNNA 86
                                  666666666666655 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00046
                       Fer4_17  42 kaslCieCgeCerkCP 57 
                                    a++C++Cg C+  CP
  gi|15669124|ref|NP_247929.1|  95 DADKCTKCGVCVLFCP 110
                                   5788999999998888 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00098
                       Fer4_17   1 rCiqCgyClpeCpsyeaydn 20 
                                   +C++Cg C+  Cp  ++ ++
  gi|15669124|ref|NP_247929.1|  98 KCTKCGVCVLFCPIPIIKKE 117
                                   59999999999998666555 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.23
                       Fer4_17  44 slCieCgeCe 53 
                                   ++C++Cg+Ce
  gi|15669124|ref|NP_247929.1| 129 DRCNSCGLCE 138
                                   6899999998 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.017
                       Fer4_17  40 eekaslCieCgeCerkCP 57 
                                   e + ++C  C  C +kCP
  gi|15669124|ref|NP_247929.1| 148 EINPEKCKLCLSCIEKCP 165
                                   456788999999999998 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.058
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57 
                                   +C  C  C+++Cp  ++    p+++++ + +        +  +++Ci C+eCe+ CP
  gi|15669124|ref|NP_247929.1| 153 KCKLCLSCIEKCPLQAIL--TPDEYINSLIV--------KVDIDSCIFCRECEEICP 199
                                   699999999999988773..35667776333........34799************9 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   5.2   2.2e-07   0.00024       1      15 []      47      61 ..      47      61 .. 0.98
   2 !   11.4   6.1   0.00045       0.5       4      15 .]      75      86 ..      72      86 .. 0.91
   3 !    8.1   5.5    0.0053       5.9       1      12 [.      99     110 ..      99     112 .. 0.96
   4 ?   -2.0   6.5       8.5   9.5e+03       1       8 [.     131     138 ..     131     140 .. 0.90
   5 ?    4.1   2.9     0.099   1.1e+02       1      12 [.     154     165 ..     154     168 .. 0.86
   6 !   13.1   1.9   0.00013      0.14       1      13 [.     188     200 ..     188     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.2e-07
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gCg+Cv+vCP++A
  gi|15669124|ref|NP_247929.1| 47 CIGCGLCVDVCPTNA 61
                                  *************98 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00045
                        Fer4_3  4 CgaCvevCPvgA 15
                                  Cg+Cv+vCP++A
  gi|15669124|ref|NP_247929.1| 75 CGTCVDVCPNNA 86
                                  9*********98 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0053
                        Fer4_3   1 CtgCgaCvevCP 12 
                                   Ct Cg Cv  CP
  gi|15669124|ref|NP_247929.1|  99 CTKCGVCVLFCP 110
                                   ************ PP

  == domain 4  score: -2.0 bits;  conditional E-value: 8.5
                        Fer4_3   1 CtgCgaCv 8  
                                   C+ Cg+C+
  gi|15669124|ref|NP_247929.1| 131 CNSCGLCE 138
                                   999**995 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.099
                        Fer4_3   1 CtgCgaCvevCP 12 
                                   C  C  C e CP
  gi|15669124|ref|NP_247929.1| 154 CKLCLSCIEKCP 165
                                   999*88****** PP

  == domain 6  score: 13.1 bits;  conditional E-value: 0.00013
                        Fer4_3   1 CtgCgaCvevCPv 13 
                                   C+ C+ C+e CP 
  gi|15669124|ref|NP_247929.1| 188 CIFCRECEEICPI 200
                                   ************6 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   8.9   1.8e-08     2e-05      47      96 ..      33      83 ..      22      92 .. 0.83
   2 !   10.5  11.1   0.00047      0.53      60      95 ..      71     109 ..      67     110 .. 0.82
   3 ?    3.0  10.7     0.099   1.1e+02      57      92 ..      95     138 ..      87     152 .. 0.64
   4 ?    2.9   1.4      0.11   1.2e+02      59      73 ..     152     166 ..     146     171 .. 0.79
   5 ?    5.2   2.0     0.021        23      58      73 ..     185     200 ..     173     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.8e-08
                       Fer4_18 47 lkekeerkekgagdcidcescvkvcPtg.idirkGlqleciscllcidacd 96
                                   ++  ++k  + ++ci c+ cv+vcPt+ i i       c  c+ c+d c 
  gi|15669124|ref|NP_247929.1| 33 FSKPSKTKPIQLTECIGCGLCVDVCPTNaIKIFSFRETICSVCGTCVDVCP 83
                                  4455566677889*************96599*******************5 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00047
                       Fer4_18  60 dcidcescvkvcPtgidirkGlqle...ciscllcidac 95 
                                    c  c++cv+vcP +  i++ + ++   c +c+ c+  c
  gi|15669124|ref|NP_247929.1|  71 ICSVCGTCVDVCPNNAIIKDRFTIDadkCTKCGVCVLFC 109
                                   5999******************99633478888887665 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.099
                       Fer4_18  57 gagdcidcescvkvcPtgi...dirkG.....lqleciscllci 92 
                                   +a +c++c++cv  cP+ i   +i k      l+  c sc+lc 
  gi|15669124|ref|NP_247929.1|  95 DADKCTKCGVCVLFCPIPIikkEIPKPktpviLKDRCNSCGLCE 138
                                   5678************9882333333222322555788888883 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.11
                       Fer4_18  59 gdcidcescvkvcPt 73 
                                    +c  c sc++ cP 
  gi|15669124|ref|NP_247929.1| 152 EKCKLCLSCIEKCPL 166
                                   579999999999997 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.021
                       Fer4_18  58 agdcidcescvkvcPt 73 
                                      ci c+ c ++cP+
  gi|15669124|ref|NP_247929.1| 185 IDSCIFCRECEEICPI 200
                                   578************7 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   1.3   0.00013      0.14       6      20 ..      45      59 ..      42      64 .. 0.88
   2 !    7.2   1.0    0.0078       8.8       6      20 ..      70      84 ..      66      91 .. 0.85
   3 !   13.1   1.0   0.00011      0.13       2      19 ..      93     110 ..      92     117 .. 0.91
   4 ?    3.0   2.9      0.15   1.7e+02       5      19 ..     128     142 ..     125     149 .. 0.78
   5 ?    3.1   1.4      0.15   1.6e+02       3      19 ..     149     165 ..     148     171 .. 0.85
   6 !    8.0   1.5    0.0042       4.7       1      19 [.     181     199 ..     181     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                       Fer4_15  6 daCigcglCvaeape 20
                                  ++CigcglCv+++p+
  gi|15669124|ref|NP_247929.1| 45 TECIGCGLCVDVCPT 59
                                  78***********96 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0078
                       Fer4_15  6 daCigcglCvaeape 20
                                  + C  cg Cv+++p+
  gi|15669124|ref|NP_247929.1| 70 TICSVCGTCVDVCPN 84
                                  78***********97 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00011
                       Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                   ++D d+C+ cg+Cv  +p
  gi|15669124|ref|NP_247929.1|  93 TIDADKCTKCGVCVLFCP 110
                                   79************9997 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.15
                       Fer4_15   5 rdaCigcglCvaeap 19 
                                   +d+C +cglC  ea 
  gi|15669124|ref|NP_247929.1| 128 KDRCNSCGLCECEAI 142
                                   79********76665 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.15
                       Fer4_15   3 vDrdaCigcglCvaeap 19 
                                   ++ ++C  c  C++ +p
  gi|15669124|ref|NP_247929.1| 149 INPEKCKLCLSCIEKCP 165
                                   67789999999999997 PP

  == domain 6  score: 8.0 bits;  conditional E-value: 0.0042
                       Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                   V+vD d Ci c  C + +p
  gi|15669124|ref|NP_247929.1| 181 VKVDIDSCIFCRECEEICP 199
                                   89************99998 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   1.7   4.9e-05     0.055       4      18 ..      45      59 ..      42      64 .. 0.91
   2 ?    6.5   3.5     0.011        12       6      18 ..      72      84 ..      69      85 .. 0.91
   3 !   13.0   2.8   9.9e-05      0.11       1      17 [.      94     110 ..      94     111 .. 0.96
   4 ?    0.3   3.7      0.91     1e+03       3      14 ..     128     139 ..     126     144 .. 0.81
   5 ?    2.4   4.8      0.21   2.4e+02      35      56 ..     148     169 ..     138     171 .. 0.66
   6 !   10.2   2.1   0.00075      0.84       1      17 [.     183     199 ..     183     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.9e-05
                       Fer4_13  4 dtCiacgaCvelaPd 18
                                   +Ci+cg+Cv+++P 
  gi|15669124|ref|NP_247929.1| 45 TECIGCGLCVDVCPT 59
                                  68************6 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                       Fer4_13  6 CiacgaCvelaPd 18
                                  C+ cg+Cv+++P+
  gi|15669124|ref|NP_247929.1| 72 CSVCGTCVDVCPN 84
                                  9***********7 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 9.9e-05
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   +D d+C+ cg+Cv ++P
  gi|15669124|ref|NP_247929.1|  94 IDADKCTKCGVCVLFCP 110
                                   899*************9 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.91
                       Fer4_13   3 rdtCiacgaCve 14 
                                   +d+C +cg+C  
  gi|15669124|ref|NP_247929.1| 128 KDRCNSCGLCEC 139
                                   689*******65 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.21
                       Fer4_13  35 ptseeekadaeeAadaCPvesI 56 
                                   + ++e+ +++ + ++ CP ++I
  gi|15669124|ref|NP_247929.1| 148 EINPEKCKLCLSCIEKCPLQAI 169
                                   5566666777777777777776 PP

  == domain 6  score: 10.2 bits;  conditional E-value: 0.00075
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   VD d+Ci c  C e++P
  gi|15669124|ref|NP_247929.1| 183 VDIDSCIFCRECEEICP 199
                                   8999************9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.9   3.5e-05     0.039      75      95 ..      40      60 ..       4      61 .. 0.74
   2 ?    6.0   3.1      0.02        22      77      95 ..      67      85 ..      61      87 .. 0.81
   3 ?    4.1   3.5     0.077        86       1      14 [.      98     111 ..      98     117 .. 0.87
   4 ?    1.6   2.2      0.46   5.1e+02      73      94 ..     145     166 ..     139     168 .. 0.79
   5 ?    6.2   0.3     0.016        18      78      93 ..     184     199 ..     174     205 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.5e-05
                       Fer4_22 75 ekfgesgCvGCgRCieacpvk 95
                                  + ++ + C+GCg C+++cp++
  gi|15669124|ref|NP_247929.1| 40 KPIQLTECIGCGLCVDVCPTN 60
                                  3347889***********975 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                       Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                  f e+ C  Cg C+++cp++
  gi|15669124|ref|NP_247929.1| 67 FRETICSVCGTCVDVCPNN 85
                                  5678899999999999875 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.077
                       Fer4_22   1 rClsCgaCtlvCpt 14 
                                   +C +Cg C l Cp 
  gi|15669124|ref|NP_247929.1|  98 KCTKCGVCVLFCPI 111
                                   69999999999995 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.46
                       Fer4_22  73 fkekfgesgCvGCgRCieacpv 94 
                                   ++++++ ++C  C  Cie+cp 
  gi|15669124|ref|NP_247929.1| 145 INKEINPEKCKLCLSCIEKCPL 166
                                   5677788899999999999986 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.016
                       Fer4_22  78 gesgCvGCgRCieacp 93 
                                   +  +C+ C  C+e cp
  gi|15669124|ref|NP_247929.1| 184 DIDSCIFCRECEEICP 199
                                   5556666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1577.62
//
Query:       gi|15669125|ref|NP_247930.1|  [L=208]
Description: hypothetical protein MJ_0935 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-42  142.6   2.1    1.3e-41  142.2   2.1    1.2  1  DUF5616   Domain of unknown function (DUF5616)
    2.3e-21   75.2   0.7    4.2e-21   74.4   0.7    1.4  1  DUF434    Protein of unknown function (DUF434)


Domain annotation for each model (and alignments):
>> DUF5616  Domain of unknown function (DUF5616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.2   2.1   1.5e-45   1.3e-41       2     139 ..      62     199 ..      61     200 .. 0.94

  Alignments for each domain:
  == domain 1  score: 142.2 bits;  conditional E-value: 1.5e-45
                       DUF5616   2 eelkgkelliDGfNvlitlesalsgevlllcdDgviRDlagvrgkyklveeteealelilellkelkvkkvifllDkpvSn 82 
                                   +++kgk+++iDGfNvli le++++g+ ++lcdD+++RD ++v+gkyk++e  ++a++l+le+lk++++k v ++lD++vS+
  gi|15669125|ref|NP_247930.1|  62 KDFKGKTIYIDGFNVLISLEALIKGNKIVLCDDNIYRDFENVYGKYKINEYSDKAISLLLEILKHYNIKAV-IYLDAQVSK 141
                                   7899****************************************************************865.79******* PP

                       DUF5616  83 SgelaklireileeaglegevelvknvDkeLkeseeivatsDsvild..kvksvldlaa 139
                                   Sg lak+ire++++ ++egev  vkn D eLk++e  vatsDsvi++  +vk v+dl a
  gi|15669125|ref|NP_247930.1| 142 SGILAKKIREKMKAFSIEGEVFCVKNCDYELKNKEV-VATSDSVIIKseNVKYVVDLIA 199
                                   ********************************8887.*********7336788999875 PP

>> DUF434  Protein of unknown function (DUF434)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.7   4.7e-25   4.2e-21       2      56 .]       3      57 ..       2      57 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 4.7e-25
                        DUF434  2 LkeAaeDlryLLnRGYpkksalelVgnhYqLskrqRlaLaRcvssdeeiearksK 56
                                  +++A eD++yL+nRGY+k+ al++V+nhY+Lsk++Rl + R+++sd+ei+ +k+K
  gi|15669125|ref|NP_247930.1|  3 IEKAKEDFKYLINRGYKKDVALNFVANHYKLSKEDRLKIIRTTHSDKEIKLTKRK 57
                                  689**************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1382  (0.0770818); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1364.94
//
Query:       gi|15669126|ref|NP_247931.1|  [L=166]
Description: hypothetical protein MJ_0936 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-31  107.3   0.4      1e-30  107.1   0.4    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    4.8e-08   33.7   8.5    1.3e-07   32.3   2.7    2.1  1  Metallophos    Calcineurin-like phosphoesterase
     0.0004   19.8   0.4     0.0049   16.2   0.1    2.2  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
  ------ inclusion threshold ------
       0.49   10.4   2.9       0.35   10.9   0.3    2.1  3  Tfb5           Transcription factor TFIIH complex subunit Tfb


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   0.4   2.2e-34     1e-30       1     165 []       1     158 [.       1     158 [. 0.84

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 2.2e-34
                 Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela.pvlaVrGNnDeevveedvlreaaelgtd 80 
                                   Mk++i+SD+H++l  +++++e++++++v+++ih+GD+  +++ v++e+++l+  ++a +GNnD+e        + +e+ +d
  gi|15669126|ref|NP_247931.1|   1 MKIGIMSDTHDHLPNIRKAIEIFNDENVETVIHCGDF--VSLFVIKEFENLNaNIIATYGNNDGER------CKLKEWLKD 73 
                                   *************************************..9999********************444......233334444 PP

                 Metallophos_2  81 l......peeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe 155
                                   +       +   +e+++ k++++Hg+    ++++ e++ + +   dvv++GHtH++  e+ ++vlv+nPG+ ++  +g p 
  gi|15669126|ref|NP_247931.1|  74 IneeniiDDFISVEIDDLKFFITHGH----HQSVLEMAIK-SGLYDVVIYGHTHERVFEEVDDVLVINPGECCGYLTGIP- 148
                                   422222256678888***********....5555555555.24455*********************************9. PP

                 Metallophos_2 156 tyaildtdek 165
                                   t+ ildt++k
  gi|15669126|ref|NP_247931.1| 149 TIGILDTEKK 158
                                   ******9975 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   2.7   2.9e-11   1.3e-07       1     123 [.       1      99 [.       1     113 [. 0.75

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 2.9e-11
                                   EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHHHH CS
                   Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfeeel 81 
                                   ++i +++D+H      +l++++k+++ +++e ++  v+++GD+v        +++ ++ l +   +++++ GN +  e  +
  gi|15669126|ref|NP_247931.1|   1 MKIGIMSDTH-----DHLPNIRKAIEIFNDE-NVETVIHCGDFVSLF-----VIKEFENLNA---NIIATYGNND-GE-RC 65 
                                   89********.....**********999999.************998.....7888899999...99********.22.22 PP

                                   HHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEEEEESE CS
                   Metallophos  82 lnkygylgifsepwrsdaevfnnlplaslgsgs.lkvlllhGg 123
                                   + k          w +d +  n++  +  ++   lk+++ hG+
  gi|15669126|ref|NP_247931.1|  66 KLK---------EWLKDINEENIIDDFISVEIDdLKFFITHGH 99 
                                   222.........3333333334333333333335699999999 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.026   1.2e+02      11      44 ..       6      39 ..       1      71 [. 0.82
   2 !   16.2   0.1   1.1e-06    0.0049     197     236 ..      99     139 ..      66     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.026
                                  EE--TT-GGGHHHHHHHHHHH--SEEEEES---- CS
                 Metallophos_3 11 isdlkgevellerlveviedkdpDllvlvGdlvk 44
                                  +sd +++   + + +e+ +d +++ ++  Gd v+
  gi|15669126|ref|NP_247931.1|  6 MSDTHDHLPNIRKAIEIFNDENVETVIHCGDFVS 39
                                  566777777777888888999*********9976 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.1e-06
                                   -S-HHHHHHHHHH--SEEEE-SS--EE.EEETTEEEEE--B CS
                 Metallophos_3 197 kgsevvaelvktlnPevvvvghavkeh.eelgktlvvnPGa 236
                                   + + v+   +k+   +vv+ gh++ +  ee+++ lv+nPG+
  gi|15669126|ref|NP_247931.1|  99 HHQSVLEMAIKSGLYDVVIYGHTHERVfEEVDDVLVINPGE 139
                                   445688889**************99889************8 PP

>> Tfb5  Transcription factor TFIIH complex subunit Tfb5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.74   3.3e+03      47      64 ..      11      28 ..       9      31 .. 0.78
   2 ?   10.9   0.3   7.9e-05      0.35      16      52 ..      67     103 ..      65     113 .. 0.87
   3 ?   -3.6   0.1       2.6   1.2e+04      31      41 ..     123     132 ..     120     137 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.74
                          Tfb5 47 evveelkkeleelleknt 64
                                  + +  ++k++e + ++n 
  gi|15669126|ref|NP_247931.1| 11 DHLPNIRKAIEIFNDENV 28
                                  567789999999999885 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.9e-05
                          Tfb5  16 ikqlilkldeqepsqkfiiedLDethlfvkeevveel 52 
                                    k+ + +++e++   +fi  ++D+   f++   ++++
  gi|15669126|ref|NP_247931.1|  67 LKEWLKDINEENIIDDFISVEIDDLKFFITHGHHQSV 103
                                   689999*****9999**************98777765 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.6
                          Tfb5  31 kfiiedLDeth 41 
                                   + + e+ D+  
  gi|15669126|ref|NP_247931.1| 123 ERVFEEVDD-V 132
                                   456677776.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1065.70
//
Query:       gi|15669127|ref|NP_247932.1|  [L=444]
Description: phosphoribosylamine--glycine ligase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-66  224.3   1.8    1.1e-66  224.3   1.8    1.8  2  GARS_A         Phosphoribosylglycinamide synthetase, ATP-gras
    2.4e-25   89.1   1.8    3.3e-24   85.5   0.4    2.3  2  GARS_N         Phosphoribosylglycinamide synthetase, N domain
    2.2e-16   59.9   0.7    8.8e-16   58.0   0.4    2.1  2  GARS_C         Phosphoribosylglycinamide synthetase, C domain
    9.2e-07   29.0   0.0    3.5e-06   27.1   0.0    2.1  1  ATP-grasp_3    ATP-grasp domain
    0.00035   20.2   0.1     0.0028   17.3   0.0    2.2  2  ATP-grasp_4    ATP-grasp domain
     0.0078   17.0   0.0      0.026   15.4   0.0    1.9  1  DUF3887        Protein of unknown function (DUF3887)
     0.0089   16.1   0.0      0.038   14.1   0.0    2.2  1  DpaA_N         Dipicolinate synthase subunit A N-terminal dom
  ------ inclusion threshold ------
      0.015   15.6   2.3       0.02   15.2   0.3    2.2  3  IlvC           Acetohydroxy acid isomeroreductase, catalytic 
      0.044   13.3   0.2       0.14   11.6   0.1    1.9  2  CPSase_L_D2    Carbamoyl-phosphate synthase L chain, ATP bind
       0.12   12.3   0.1        1.6    8.6   0.0    2.5  2  Dak2           DAK2 domain
       0.17   11.5   0.1       0.82    9.3   0.0    2.0  2  SpoIISA_toxin  Toxin SpoIISA, type II toxin-antitoxin system


Domain annotation for each model (and alignments):
>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.3   1.8   6.8e-70   1.1e-66       1     194 []     103     304 ..     103     304 .. 0.96
   2 ?   -3.5   0.1       4.7   7.6e+03      54      71 ..     396     413 ..     387     420 .. 0.69

  Alignments for each domain:
  == domain 1  score: 224.3 bits;  conditional E-value: 6.8e-70
                                   HBHHHHHHHHHHTT--B-.-EEEESS.HHHHHHHHHHHSSSE..EEEEESC-GGGT-EEEE....SSHHHHHHHHHHHCTS CS
                        GARS_A   1 asKsfakdllkkagipta.eyeaftd.peeakeyieeataka..lVvKadglaagKgviva....kseeealkavkeilek 73 
                                   ++K+f+++l+kk++i+++ +y+af++  ee++++i+e+t+k+  +VvK++gl++gKgv+v+    k++eea k++kei+e+
  gi|15669127|ref|NP_247932.1| 103 TNKEFMRNLFKKYNIKGSlMYKAFEEyGEELESFIDELTEKGikAVVKPVGLTGGKGVKVVgeqlKDNEEAKKYAKEIFET 183
                                   68****************9******96799**********98778****************99999*************95 PP

                                   -TTCCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEE....S-TTS-HHHHHHHHHHT CS
                        GARS_A  74 kkfGeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGays....papvvteellekikeei 150
                                     +   g kv+iEe+leG E++l+ +vdg+t+k +p++qdh+++legD+g++TGGmG+ys    ++p++tee+++ +ke i
  gi|15669127|ref|NP_247932.1| 184 GLG---GGKVLIEEKLEGVEFTLHGFVDGDTIKFTPFVQDHPHALEGDEGSITGGMGSYScpdhKLPFMTEEDVKLAKE-I 260
                                   555...59****************************************************99999**********9999.* PP

                                   HHHHHHHHHCTT---EEEEEEEEEEETTEEEEEEEESS--TTCH CS
                        GARS_A 151 leptveglkkegipfkGvLyaglmlvedgpkvlefnvRfgDpet 194
                                   +e+tv++lk+e   +kG+Ly+++ml+++gpk++e+n+RfgDpe+
  gi|15669127|ref|NP_247932.1| 261 MEETVKALKEEVGGYKGILYGQFMLTKEGPKIIEYNARFGDPEA 304
                                   ******************************************97 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.7
                                   EEEESSHHHHHHHHHHHC CS
                        GARS_A  54 vivakseeealkavkeil 71 
                                   v va++ eea ++++e  
  gi|15669127|ref|NP_247932.1| 396 VGVADTIEEAERIAEEAT 413
                                   456688888888887765 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   0.4   2.1e-27   3.3e-24       1      90 []       1     102 [.       1     102 [. 0.93
   2 ?    2.6   0.0      0.14   2.3e+02      44      75 ..     375     406 ..     318     412 .. 0.67

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 2.1e-27
                                   EEEEEEESSHHHHHHHHHHTTSTTESEEEEEE..--CGG............TTHHHHHHHHHHCTESEEEE-SHHHHHTTH CS
                        GARS_N   1 mkvLvvGsGGRehalawklaqspkvekvyvap..gNagt............edlealvefakeekidlvvvGpeapLvaGv 67 
                                   mk+L++G+G+Re a+a++l+++++v+ +y+++  +N+g+            +dl+a+ efa++ k dl+v+GpeapL +Gv
  gi|15669127|ref|NP_247932.1|   1 MKILLIGGGARESAIAHALKKNEEVK-LYTLMknKNPGIarlseeiklakeTDLDAVKEFAEKVKPDLAVIGPEAPLGEGV 80 
                                   9***********************99.666664688999****9999998888899************************* PP

                                   HHHHHHHHT-EEES--CCCCHHH CS
                        GARS_N  68 adaleeekgikvfGpskeaAqlE 90 
                                   +d lee  gi+++Gp+k aAq+E
  gi|15669127|ref|NP_247932.1|  81 VDLLEEM-GISAVGPKKLAAQIE 102
                                   ****777.**************9 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                                   HHHHHHCTESEEEE-SHHHHHTTHHHHHHHHH CS
                        GARS_N  44 vefakeekidlvvvGpeapLvaGvadaleeek 75 
                                    + ++e + +l + G  a  v Gvad++ee++
  gi|15669127|ref|NP_247932.1| 375 YASVNEDNGSLYMTGSRAVAVVGVADTIEEAE 406
                                   3345677889*****************97765 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.5   2.4e+03      35      61 ..     152     179 ..     116     185 .. 0.68
   2 !   58.0   0.4   5.4e-19   8.8e-16       1      80 []     339     429 ..     339     429 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.5
                                   EEE-SSEEEEEEEE.ESSHHHHHHHHHH CS
                        GARS_C  35 lvtsGGRvlavvav.getleeArakaye 61 
                                   +  +GG+ + vv+   ++ eeA++ a e
  gi|15669127|ref|NP_247932.1| 152 VGLTGGKGVKVVGEqLKDNEEAKKYAKE 179
                                   5678999888888634677788777765 PP

  == domain 2  score: 58.0 bits;  conditional E-value: 5.4e-19
                                   EEEEEEEETTTTSS--ST-EEBS.......TTEEEEESSEE.....EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-T CS
                        GARS_C   1 avgvvlaskGYPgsyekgkeitg.......egvkvfhagtk.....lvtsGGRvlavvavgetleeArakayeavkkikfe 69 
                                   +v+ ++++kGYP+++  g++it        +g+ + +a+++     l+++G+R +avv+v++t+eeA++ a+ea k ik  
  gi|15669127|ref|NP_247932.1| 339 TVCKYVVPKGYPDNPVRGEPITVdeeaikkTGAILHYASVNedngsLYMTGSRAVAVVGVADTIEEAERIAEEATKYIKG- 418
                                   69*******************8888888764454555555589999********************************76. PP

                                   TEE--STTTHH CS
                        GARS_C  70 glfyRkDIGar 80 
                                   ++++R+DIG++
  gi|15669127|ref|NP_247932.1| 419 EVYHRSDIGKK 429
                                   7********85 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   2.2e-09   3.5e-06      25     159 ..     138     300 ..     114     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.2e-09
                                   EESS--SSSEEEEESS-------B--SS--TTE....................EEEE---SEEEEEEEEE.SSSEEEEEEE CS
                   ATP-grasp_3  25 eeleeeekklvvKprdGaggesvrvveekeeaeaaieeve.............lvqefieGkplSvsllsdgekvlvlavn 92 
                                   +el+e+  k vvKp+   gg++v vv e+ ++++  ++ +             l+ e +eG ++++   +dg ++++  + 
  gi|15669127|ref|NP_247932.1| 138 DELTEKGIKAVVKPVGLTGGKGVKVVGEQLKDNEEAKKYAkeifetglgggkvLIEEKLEGVEFTLHGFVDGDTIKFTPFV 218
                                   68899999*****************999988887777666799*************************9999877776665 PP

                                   EEEEET...............TEEEEEEES----H.HHHHHHHHHHHHTTST.T--EEEEE...EEEESS.SEEEEEEESS CS
                   ATP-grasp_3  93 rqliekaeke...........fvyaGnvtpietel.keevvelaeevvekle.glaGyvGv...DlvlkdeepyviEvNPR 157
                                   + + +  e +           ++      p+ te+  + + e++ee+v++l+ ++ Gy G+    ++l++e+p +iE N+R
  gi|15669127|ref|NP_247932.1| 219 QDHPHALE-GdegsitggmgsYSCPDHKLPFMTEEdVKLAKEIMEETVKALKeEVGGYKGIlygQFMLTKEGPKIIEYNAR 298
                                   55543322.2355666666333333345677777745667788999*****99999****98888**************** PP

                                   -- CS
                   ATP-grasp_3 158 lt 159
                                   + 
  gi|15669127|ref|NP_247932.1| 299 FG 300
                                   95 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.7e-06    0.0028       5      75 ..     147     210 ..     144     229 .. 0.76
   2 ?   -0.3   0.0      0.45   7.3e+02     109     155 ..     257     301 ..     244     304 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
                   ATP-grasp_4   5 vviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGeEfavdayfdee 75 
                                    v+KP+  ++  GV ++ ++  +k+     +ee+++ ++e  e+ + ++++l+Ee +eG Ef + +++d +
  gi|15669127|ref|NP_247932.1| 147 AVVKPVGLTGGKGVKVVGEQ--LKD-----NEEAKKYAKEIFETGLGGGKVLIEEKLEGVEFTLHGFVDGD 210
                                   699***********999754..333.....22333444455567899*********************866 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.45
                   ATP-grasp_4 109 tlealeellkevnallglknfpvHiElrvsedgkiipiEvnplrfag 155
                                    +e +ee++k++++++g  ++ +   + ++++g+ i iE n+ rf++
  gi|15669127|ref|NP_247932.1| 257 AKEIMEETVKALKEEVGGYKGILYGQFMLTKEGPKI-IEYNA-RFGD 301
                                   456678899999999999999999999999999766.79998.7775 PP

>> DUF3887  Protein of unknown function (DUF3887)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.6e-05     0.026      20      74 ..     248     302 ..     245     314 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                       DUF3887  20 fsedlkealseetleeawkalkeelGefesieeyeveetseeyavvtveakfekg 74 
                                   f+ +   +l +e +ee+ kalkee+G +++i + +++ t+e  ++++++a f + 
  gi|15669127|ref|NP_247932.1| 248 FMTEEDVKLAKEIMEETVKALKEEVGGYKGILYGQFMLTKEGPKIIEYNARFGDP 302
                                   566666778999*****************************999*****999875 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.3e-05     0.038       1      46 [.       2      46 ..       2      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                                  EEEEESB-HHHHHHHHHHHHTT-EEEEES-TSSS-BTTEEE.E-GGG CS
                        DpaA_N  1 kiaviGGDaRqlylarkLaekgakvslygleleekiegvek.aesle 46
                                  ki++iGG aR+ ++a+ L++++ +v+ly l +++k+ g+++ +e+++
  gi|15669127|ref|NP_247932.1|  2 KILLIGGGARESAIAHALKKNE-EVKLYTL-MKNKNPGIARlSEEIK 46
                                  699****************996.9****99.4444444443033333 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.5     9e+03      60      89 ..      37      64 ..       8      70 .. 0.55
   2 ?   15.2   0.3   1.2e-05      0.02      22      96 ..     106     181 ..     102     186 .. 0.89
   3 ?   -3.4   0.0       6.6   1.1e+04      79      97 ..     256     276 ..     251     285 .. 0.53

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.5
                                  HHHHHHHHS-HHHHHHHHHHHHHHS-HHHH CS
                          IlvC 60 GiakmresiSdtaeygdltagprviteevk 89
                                  Gia++ e+i   a+  dl+a +++  e+vk
  gi|15669127|ref|NP_247932.1| 37 GIARLSEEIK-LAKETDLDAVKEF-AEKVK 64
                                  5555555554.4555666666666.45555 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHS.-HHHHHHHHHHH CS
                          IlvC  22 elveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdltagprvi.teevkeemkeil 96 
                                   e ++++F+++  +G     A+ e  +el++ +d + e+Gi+++ + +  t  +g  ++g+++  +ee+k+  kei+
  gi|15669127|ref|NP_247932.1| 106 EFMRNLFKKYNIKGSLMYKAFEEYGEELESFIDELTEKGIKAVVKPVGLTGGKGVKVVGEQLKdNEEAKKYAKEIF 181
                                   67999********************************************************953456666666665 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6.6
                                   HHHHHS-HHHHHHHHHH..HH CS
                          IlvC  79 agprviteevkeemkei..le 97 
                                    ++++++e vk+  +e+  ++
  gi|15669127|ref|NP_247932.1| 256 LAKEIMEETVKALKEEVggYK 276
                                   455555555555555554455 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   8.9e-05      0.14      17      91 ..     123     198 ..     104     202 .. 0.76
   2 ?   -2.2   0.0       1.5   2.4e+03     140     180 ..     259     299 ..     251     304 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.9e-05
                                   SSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSH.HHHHHHHHHHHHHHHHHHSTS-EEEEE--SS CS
                   CPSase_L_D2  17 vpssaapvetleealaiakeigyPviikaafglGGkGmrvarne.eelaelvkkalaeakaafgnkqvlvekslkg 91 
                                    ++++  +e+le  ++   e g   ++k+    GGkG +v+ ++ ++ +e+ k a +  ++ +g  +vl+e+ l+g
  gi|15669127|ref|NP_247932.1| 123 YKAFEEYGEELESFIDELTEKGIKAVVKPVGLTGGKGVKVVGEQlKDNEEAKKYAKEIFETGLGGGKVLIEEKLEG 198
                                   456666778888899999999999****************97652444555555666667789********99987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHH.H.T-EEEEEEEEEEETTTTEEEEEEEESS- CS
                   CPSase_L_D2 140 alreaavkvvre.v.gvvgagtveflldpkskeyyviEvNtRl 180
                                   ++ e++vk+++e v g++g    +f+l +  +   +iE N+R 
  gi|15669127|ref|NP_247932.1| 259 EIMEETVKALKEeVgGYKGILYGQFMLTK--EGPKIIEYNARF 299
                                   45555555554323256666677888885..666789999885 PP

>> Dak2  DAK2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.34   5.6e+02      61     111 ..      16      64 ..      13     108 .. 0.63
   2 ?    8.6   0.0   0.00099       1.6      30      58 ..     257     285 ..     248     288 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.34
                                   HHHC.....TT---HHHHHHHHHHHHHHHH---TTSSSTHHHHHHHHHHHH CS
                          Dak2  61 akalkekeeldaedlaaalkaaleaiqavgkarpgdkTmlDvlrpaveale 111
                                   a+alk++ee++  +l +  + +++ +++    +  + T lD++++++e+++
  gi|15669127|ref|NP_247932.1|  16 AHALKKNEEVKLYTLMKNKNPGIARLSEE--IKLAKETDLDAVKEFAEKVK 64 
                                   55565555555555555555555555555..56666666666666666554 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00099
                                   HHHHHHHHHHHHHHH--STHHHHHHHHHH CS
                          Dak2  30 laevlkalakallsgagGtsGvlysqflr 58 
                                   ++e++++  kal +++gG  G+ly+qf++
  gi|15669127|ref|NP_247932.1| 257 AKEIMEETVKALKEEVGGYKGILYGQFML 285
                                   678999********************986 PP

>> SpoIISA_toxin  Toxin SpoIISA, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0005      0.82     113     165 ..     104     155 ..      93     206 .. 0.74
   2 ?   -1.2   0.0      0.83   1.4e+03     161     186 ..     247     272 ..     245     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0005
                                   HHHHHHHHHHHS-EEEE..ESSHHHHHHHHHHHHHHHHHTTTSEEEEEE-SSH CS
                 SpoIISA_toxin 113 rvetftellqnesihvyeeygskeayieglkkllksyadkfeisvsivpfevk 165
                                     e + +l +  +i+    y+  e+y e+l+ +++++++k +i++ + p   +
  gi|15669127|ref|NP_247932.1| 104 NKEFMRNLFKKYNIKGSLMYKAFEEYGEELESFIDELTEK-GIKAVVKPVGLT 155
                                   3455667889999999999*********************.9**999887666 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.83
                                   E-SSHHHHHHHHTTSS-HHH.....H CS
                 SpoIISA_toxin 161 pfevkeekdelleaieqqlstikeev 186
                                   pf+++e++  ++e +e++++ +keev
  gi|15669127|ref|NP_247932.1| 247 PFMTEEDVKLAKEIMEETVKALKEEV 272
                                   89*****************9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2800.29
//
Query:       gi|15669128|ref|NP_247933.1|  [L=250]
Description: hypothetical protein MJ_0938 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-65  219.4  27.3    5.2e-65  219.2  27.3    1.0  1  UPF0014   Uncharacterised protein family (UPF0014)


Domain annotation for each model (and alignments):
>> UPF0014  Uncharacterised protein family (UPF0014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.2  27.3   2.9e-69   5.2e-65       2     241 ..      11     247 ..      10     248 .. 0.93

  Alignments for each domain:
  == domain 1  score: 219.2 bits;  conditional E-value: 2.9e-69
                       UPF0014   2 lqlalalllvlialllslvlklglekelliaavrmvvQLllvGyvLklifalnslllvllillvmllvAaieaakrvkkkl 82 
                                   ++l++a+++v+ia+l+++++klg+ek++l+ ++ +++QL+++G+vL +if+   ++ ++l++ vm+++A++ +++ ++ k 
  gi|15669128|ref|NP_247933.1|  11 IELTYAFIFVIIAVLIAYREKLGIEKKILYVSILALIQLFILGFVLLYIFSF-GMVGAFLMIGVMITLASYLIMREINLKN 90 
                                   7899***********************************************9.99**********************9988 PP

                       UPF0014  83 kklll.ivllsllvstlltlllllllviqpepwyepqylIPlaGmilGnamnaialalerllselksereeiealLalGat 162
                                   k  l   +++++l++t++ l++l+   i + +++ep y+IPl+Gm++Gn+mn+i+lal+++++ +kser+ ++ +LalGat
  gi|15669128|ref|NP_247933.1|  91 KTKLFiCLFITFLTTTIVSLAVLT---IPKVVKFEPIYVIPLMGMVIGNTMNTIHLALDKIIDMVKSERDILWGYLALGAT 168
                                   876651445555555555544444...57779************************************************* PP

                       UPF0014 163 pkeAvkeivreairaaliPtinsmatvGlVsLPGmmtGqiLaGaspleAvkyqilimfmilastalstvlvvlllyrrl 241
                                   + eA+++++++a+++a+iP++n++++vG++++PG+m+G++L+Ga+p++A+++qi+im+mil+s+++s +l+++l+y+++
  gi|15669128|ref|NP_247933.1| 169 EIEALRPFIKNAVKSAVIPQMNRTKSVGVIFIPGAMVGMLLSGANPIYAAEIQIIIMWMILSSAVISGILICYLMYKEI 247
                                   ****************************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1381  (0.077026); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 1554.09
//
Query:       gi|15669129|ref|NP_247934.1|  [L=276]
Description: hypothetical protein MJ_0939 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-12   46.3   7.9    5.3e-12   46.3   7.9    1.8  2  CxxCxxCC  Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
      0.092   12.6   1.8       0.38   10.6   0.2    2.5  3  Arc_C     Arc C-lobe


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   7.9   5.9e-16   5.3e-12       1      84 [.      16     112 ..      16     113 .. 0.92
   2 ?   -2.4   0.0      0.87   7.8e+03      15      29 ..     197     211 ..     186     231 .. 0.58

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 5.9e-16
                      CxxCxxCC   1 eCkeCgaCCk..elkvklteedlerlkaaevaeeeeeskkiak...adgrCvfldeetklCki.....YeeRpkicrlfpa 71 
                                   eC +C+ CC+   ++++l++ d+ +lk++e+a e +e + +++   +++ Cv+l+++  lC+i     Ye +p++c++fp+
  gi|15669129|ref|NP_247934.1|  16 ECINCAYCCSckGWRIYLNYFDRLKLKDYEYAIEPCEGEFKYRlkvNEKGCVLLNNN--LCRIhlekgYEFKPLMCMIFPF 94 
                                   6*******99889**************************99999999**********..9***777777777********* PP

                      CxxCxxCC  72 s.....ekeellaraetC 84 
                                   s     + + ll+++++C
  gi|15669129|ref|NP_247934.1|  95 ScmikwDGTPLLIIKHYC 112
                                   *99999999999999999 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.87
                      CxxCxxCC  15 klteedlerlkaaev 29 
                                   kl+ e+++++k    
  gi|15669129|ref|NP_247934.1| 197 KLNLEEIDEIKNNLQ 211
                                   555566666654333 PP

>> Arc_C  Arc C-lobe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.33     3e+03      30      42 ..     130     142 ..     116     149 .. 0.64
   2 ?   -0.1   0.0     0.098   8.8e+02      28      50 ..     153     176 ..     150     198 .. 0.76
   3 ?   10.6   0.2   4.2e-05      0.38      32      76 ..     210     252 ..     194     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.33
                         Arc_C  30 dlyqtlyvdaeee 42 
                                   +l + ly d  ee
  gi|15669129|ref|NP_247934.1| 130 ELIKELYFDMFEE 142
                                   5666777776554 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.098
                         Arc_C  28 krdlyqtlyvdaee.eeiiqyvvg 50 
                                   k ++++++ vd ee e++ +y+ +
  gi|15669129|ref|NP_247934.1| 153 KTEIFENFRVDWEErEDFGRYIFS 176
                                   667888888998873557788876 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 4.2e-05
                         Arc_C  32 yqtlyvdaeeeeiiqyvvgtlrpklkrflkpplpktleqliqkGk 76 
                                    q+  +  +eeei++y++   r +   f k p+ + +++li+ G+
  gi|15669129|ref|NP_247934.1| 210 LQRYNTKENEEEILRYLLELNRRE--HFRKLPFYREVNKLINIGN 252
                                   47888999*********9877655..68899**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1115  (0.0621897); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2002.45
//
Query:       gi|15669130|ref|NP_247935.1|  [L=318]
Description: transformation sensitive protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-41  138.7  37.6    1.1e-09   37.6   1.5    9.1  9  TPR_1            Tetratricopeptide repeat
    2.1e-37  124.2  27.9    6.1e-09   35.3   1.0    9.2  9  TPR_2            Tetratricopeptide repeat
      7e-37  122.6  35.0    6.2e-07   29.1   0.8    9.5  9  TPR_8            Tetratricopeptide repeat
    1.5e-27   93.9   1.0     0.0053   17.5   0.0    8.9  9  TPR_14           Tetratricopeptide repeat
    1.4e-24   86.2  18.8     0.0013   19.0   0.2    7.8  8  TPR_12           Tetratricopeptide repeat
    4.6e-24   83.8  20.3    0.00018   21.1   0.1    8.5  8  TPR_11           TPR repeat
    9.9e-23   80.1   0.9    1.2e-07   31.7   0.0    6.4  7  TPR_9            Tetratricopeptide repeat
    1.3e-22   80.1   5.5    3.4e-07   30.7   0.2    5.5  5  TPR_19           Tetratricopeptide repeat
    1.6e-22   77.8  14.3    3.8e-06   26.6   0.4    7.8  7  TPR_7            Tetratricopeptide repeat
    3.1e-18   66.1   1.3    2.3e-06   28.1   0.0    5.2  5  TPR_16           Tetratricopeptide repeat
    3.7e-18   65.5  20.6    2.9e-07   30.6   1.7    4.1  4  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    2.4e-17   62.0  12.1      0.011   16.1   0.2    7.7  7  TPR_17           Tetratricopeptide repeat
    2.6e-14   53.0   3.1    3.5e-05   22.9   0.4    4.4  4  NARP1            NMDA receptor-regulated protein 1
    3.5e-11   43.0  13.4       0.25   12.1   0.1    6.8  6  TPR_6            Tetratricopeptide repeat
    8.3e-10   38.2  15.3       0.27   11.1   0.1    6.7  7  TPR_10           Tetratricopeptide repeat
    1.2e-09   38.4   1.0       0.16   12.1   0.0    4.4  3  DUF3856          Domain of Unknown Function (DUF3856)
    4.9e-08   32.9  12.4       0.01   15.9   0.2    6.7  7  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    5.4e-08   32.4   0.3      0.038   13.2   0.0    4.2  3  TPR_15           Tetratricopeptide repeat
    3.6e-07   30.1  10.7      0.015   15.0   0.3    5.1  5  RPN7             26S proteasome subunit RPN7
    5.5e-07   29.3   0.0       0.56    9.9   0.0    3.3  3  HrpB1_HrpK       Bacterial type III secretion protein (HrpB1_
    1.2e-06   28.5  14.9       0.03   14.4   0.7    5.5  5  MIT              MIT (microtubule interacting and transport) 
    1.2e-05   25.4   0.0        2.6    8.9   0.0    3.8  3  TPR_4            Tetratricopeptide repeat
    1.5e-05   25.5   0.2       0.19   12.2   0.1    3.1  3  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    2.8e-05   24.1  10.5     0.0041   17.1   0.7    4.2  4  SRP_TPR_like     Putative TPR-like repeat
    0.00016   21.2   0.3       0.04   13.3   0.2    3.7  2  TPR_MalT         MalT-like TPR region
    0.00046   20.2  12.7         19    5.8   0.0    7.3  7  PPR              PPR repeat
    0.00052   19.8   8.4        1.1    9.1   0.2    5.0  6  DUF5113          Domain of unknown function (DUF5113)
     0.0011   18.7   0.0     0.0037   17.1   0.0    1.8  1  Nuc_rec_co-act   Nuclear receptor coactivator
     0.0016   18.7   0.1       0.22   11.7   0.0    3.3  3  TPR_5            Tetratrico peptide repeat
     0.0018   18.0   7.7      0.092   12.5   0.4    3.5  3  DUF2225          Uncharacterized protein conserved in bacteri
     0.0034   17.6   0.1      0.022   14.9   0.0    2.0  2  Kinesin_assoc    Kinesin-associated
     0.0042   17.3   2.3        2.4    8.4   0.0    4.3  5  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
     0.0048   17.5  10.5       0.18   12.6   0.7    5.4  5  Sel1             Sel1 repeat
      0.006   17.0   1.8       0.33   11.4   0.0    2.6  2  BTAD             Bacterial transcriptional activator domain
     0.0069   16.1   0.2       0.61    9.8   0.1    3.1  3  TPR_21           Tetratricopeptide repeat-like domain
  ------ inclusion threshold ------
      0.014   14.2   0.7        2.2    6.9   0.2    3.9  5  DUF3808          Protein of unknown function (DUF3808)
      0.054   14.2   0.6      0.054   14.2   0.6    3.6  4  BLI1             BLOC-1 interactor 1
      0.073   12.1   0.4       0.41    9.6   0.3    1.9  2  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
        0.1   12.1   1.6         11    5.5   0.0    3.8  4  SHNi-TPR         SHNi-TPR
       0.16   11.2   2.0        2.2    7.4   1.8    2.6  2  FAT              FAT domain
        2.2    7.9  21.8        7.7    6.2   0.4    6.9  6  HTH_Bact         Helix-turn-helix bacterial domain


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.6     4e-05     0.017      10      34 .]      26      50 ..      25      50 .. 0.94
   2 ?    3.7   0.0      0.14        62       5      25 ..      55      75 ..      52      76 .. 0.87
   3 !   31.6   0.4   2.1e-10   9.3e-08       2      33 ..      85     116 ..      84     117 .. 0.92
   4 ?    3.3   0.0      0.18        80      10      34 .]     127     151 ..     126     151 .. 0.88
   5 !   27.6   0.2     4e-09   1.7e-06       3      34 .]     154     185 ..     152     185 .. 0.94
   6 !   10.0   0.6    0.0014      0.59       3      26 ..     188     211 ..     186     214 .. 0.91
   7 !   10.2   0.1    0.0012      0.51      15      34 .]     235     254 ..     232     254 .. 0.93
   8 !   37.6   1.5   2.6e-12   1.1e-09       1      34 []     255     288 ..     255     288 .. 0.94
   9 !   21.4   0.1   3.5e-07   0.00015       2      29 ..     290     317 ..     289     318 .] 0.93

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-05
                                  HHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1 10 ayfklgkydeAleyyekALelnPnn 34
                                   y+  g++ e l y +kALelnP++
  gi|15669130|ref|NP_247935.1| 26 EYRDRGNLLESLYYLDKALELNPDF 50
                                  5999*******************97 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.14
                                  HHHHHHHHHTT-HHHHHHHHH CS
                         TPR_1  5 ynlGnayfklgkydeAleyye 25
                                  + ++  +  lg+ ++ +e+ e
  gi|15669130|ref|NP_247935.1| 55 FLKAISLAILGDINKSIECLE 75
                                  568899999**********86 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 2.1e-10
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                    a+  lG++y  lg++d Ale+yek L ++++
  gi|15669130|ref|NP_247935.1|  85 VAYALLGQLYELLGNFDNALECYEKSLGIEEK 116
                                   699************************88876 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.18
                                   HHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1  10 ayfklgkydeAleyyekALelnPnn 34 
                                   ++   gkyde l+++++ ++  Pn+
  gi|15669130|ref|NP_247935.1| 127 CLGLSGKYDELLKCCDRLISFAPNF 151
                                   77788999999********999997 PP

  == domain 5  score: 27.6 bits;  conditional E-value: 4e-09
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                   a+  ++n+++klg+y+eAl++ +k+Lel +n+
  gi|15669130|ref|NP_247935.1| 154 AYIIKANMLRKLGRYEEALACVNKVLELKEND 185
                                   89999***********************9996 PP

  == domain 6  score: 10.0 bits;  conditional E-value: 0.0014
                                   HHHHHHHHHHHTT-HHHHHHHHHH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyek 26 
                                   a y +++++ + g+ deAl+yyek
  gi|15669130|ref|NP_247935.1| 188 AIYLKALILNRIGNCDEALKYYEK 211
                                   66999******************9 PP

  == domain 7  score: 10.2 bits;  conditional E-value: 0.0012
                                   T-HHHHHHHHHHHHHHSTTH CS
                         TPR_1  15 gkydeAleyyekALelnPnn 34 
                                   +k+d+A++y e  L+l+P++
  gi|15669130|ref|NP_247935.1| 235 NKLDKAEKYIEMGLKLRPDD 254
                                   799***************96 PP

  == domain 8  score: 37.6 bits;  conditional E-value: 2.6e-12
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   a  +y +G +y k++k++eAl+yy+kA++l P++
  gi|15669130|ref|NP_247935.1| 255 ASLWYFKGKLYEKQNKFEEALKYYNKAIQLMPHH 288
                                   568***************************9985 PP

  == domain 9  score: 21.4 bits;  conditional E-value: 3.5e-07
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALe 29 
                                   kal  ++ ++ klg+ +e +e+y+kAL 
  gi|15669130|ref|NP_247935.1| 290 KALLAKARVLEKLGRIEESIECYNKALD 317
                                   6889999*******************96 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   2.3e-05      0.01       8      33 ..      24      49 ..      18      50 .. 0.90
   2 ?    4.4   0.0      0.11        49       4      25 ..      54      75 ..      52      79 .. 0.89
   3 !   24.1   0.2   5.6e-08   2.5e-05       3      28 ..      86     111 ..      84     117 .. 0.90
   4 ?    1.0   0.0       1.3   5.8e+02      14      33 ..     131     150 ..     126     151 .. 0.84
   5 !   23.0   0.1   1.2e-07   5.2e-05       3      34 .]     154     185 ..     153     185 .. 0.92
   6 ?    6.9   0.2     0.018       7.9      13      28 ..     198     213 ..     187     216 .. 0.73
   7 ?    6.2   0.0      0.03        13      15      34 .]     235     254 ..     229     254 .. 0.91
   8 !   35.3   1.0   1.4e-11   6.1e-09       1      34 []     255     288 ..     255     288 .. 0.95
   9 !   20.2   0.1     1e-06   0.00044       2      29 ..     290     317 ..     289     318 .] 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.3e-05
                         TPR_2  8 GlayyklgdyeeAleafekAleldPn 33
                                   + y+ +g++ e l +++kAlel+P+
  gi|15669130|ref|NP_247935.1| 24 SYEYRDRGNLLESLYYLDKALELNPD 49
                                  6789*********************8 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.11
                         TPR_2  4 lynlGlayyklgdyeeAleafe 25
                                   +  + +++ lgd ++ +e++e
  gi|15669130|ref|NP_247935.1| 54 KFLKAISLAILGDINKSIECLE 75
                                  578899**************98 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 5.6e-08
                         TPR_2   3 alynlGlayyklgdyeeAleafekAl 28 
                                   a+  lG++y+ lg+++ Ale++ek+l
  gi|15669130|ref|NP_247935.1|  86 AYALLGQLYELLGNFDNALECYEKSL 111
                                   8999********************98 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 1.3
                         TPR_2  14 lgdyeeAleafekAleldPn 33 
                                   +g+y+e l+++++ ++ +Pn
  gi|15669130|ref|NP_247935.1| 131 SGKYDELLKCCDRLISFAPN 150
                                   688999899******99998 PP

  == domain 5  score: 23.0 bits;  conditional E-value: 1.2e-07
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                   a+   ++ ++klg+yeeAl++ +k+lel +n+
  gi|15669130|ref|NP_247935.1| 154 AYIIKANMLRKLGRYEEALACVNKVLELKEND 185
                                   677889**********************9886 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.018
                         TPR_2  13 klgdyeeAleafekAl 28 
                                   + g+ +eAl+++ek +
  gi|15669130|ref|NP_247935.1| 198 RIGNCDEALKYYEKLI 213
                                   5566699*****9987 PP

  == domain 7  score: 6.2 bits;  conditional E-value: 0.03
                         TPR_2  15 gdyeeAleafekAleldPnn 34 
                                   +++++A+++ e  l+l P++
  gi|15669130|ref|NP_247935.1| 235 NKLDKAEKYIEMGLKLRPDD 254
                                   689***************96 PP

  == domain 8  score: 35.3 bits;  conditional E-value: 1.4e-11
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   a ++y  G++y+k++++eeAl++++kA++l P++
  gi|15669130|ref|NP_247935.1| 255 ASLWYFKGKLYEKQNKFEEALKYYNKAIQLMPHH 288
                                   568*****************************86 PP

  == domain 9  score: 20.2 bits;  conditional E-value: 1e-06
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                   +al + +++++klg+ ee +e+++kAl 
  gi|15669130|ref|NP_247935.1| 290 KALLAKARVLEKLGRIEESIECYNKALD 317
                                   689999********************96 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.4   0.00082      0.36       4      33 ..      20      49 ..      18      50 .. 0.94
   2 ?    5.8   0.0     0.041        18       5      28 ..      55      78 ..      53      83 .. 0.80
   3 !   28.7   0.4     2e-09   8.8e-07       3      33 ..      86     116 ..      85     117 .. 0.95
   4 ?    3.3   0.0      0.28   1.2e+02       2      33 ..     119     150 ..     118     151 .. 0.88
   5 !   23.5   0.1   9.2e-08     4e-05       2      34 .]     153     185 ..     152     185 .. 0.95
   6 !   12.4   0.5   0.00032      0.14       3      28 ..     188     213 ..     186     214 .. 0.93
   7 ?    5.2   0.1     0.069        30      15      34 .]     235     254 ..     229     254 .. 0.91
   8 !   29.1   0.8   1.4e-09   6.2e-07       1      32 [.     255     286 ..     255     288 .. 0.92
   9 !   22.9   0.2   1.4e-07   6.3e-05       2      29 ..     290     317 ..     289     318 .] 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00082
                                  HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8  4 yynlgsiylklgdyeeAkeyyekaleldpd 33
                                  y+ +++ y++ g++ e+  y+ kalel+pd
  gi|15669130|ref|NP_247935.1| 20 YLIKSYEYRDRGNLLESLYYLDKALELNPD 49
                                  88899************************8 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.041
                                  HHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_8  5 ynlgsiylklgdyeeAkeyyekal 28
                                  ++++  +  lgd+++++e++e  +
  gi|15669130|ref|NP_247935.1| 55 FLKAISLAILGDINKSIECLEDIT 78
                                  567777889***********9765 PP

  == domain 3  score: 28.7 bits;  conditional E-value: 2e-09
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   ay +lg++y+ lg++++A e+yek l ++++
  gi|15669130|ref|NP_247935.1|  86 AYALLGQLYELLGNFDNALECYEKSLGIEEK 116
                                   79*************************9986 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.28
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                    a +++ +++   g+y+e  +++ + ++ +p+
  gi|15669130|ref|NP_247935.1| 119 TAFFLKVLCLGLSGKYDELLKCCDRLISFAPN 150
                                   5778888888999****************998 PP

  == domain 5  score: 23.5 bits;  conditional E-value: 9.2e-08
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   +ay  +++ ++klg+yeeA ++ +k+lel++++
  gi|15669130|ref|NP_247935.1| 153 PAYIIKANMLRKLGRYEEALACVNKVLELKEND 185
                                   79****************************985 PP

  == domain 6  score: 12.4 bits;  conditional E-value: 0.00032
                                   HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekal 28 
                                   a y++++i+   g+ +eA +yyek +
  gi|15669130|ref|NP_247935.1| 188 AIYLKALILNRIGNCDEALKYYEKLI 213
                                   779*********************98 PP

  == domain 7  score: 5.2 bits;  conditional E-value: 0.069
                                   T-HHHHHHHHHHHHHHHHH. CS
                         TPR_8  15 gdyeeAkeyyekaleldpdn 34 
                                   +++++A++y+e  l+l+pd+
  gi|15669130|ref|NP_247935.1| 235 NKLDKAEKYIEMGLKLRPDD 254
                                   689***************96 PP

  == domain 8  score: 29.1 bits;  conditional E-value: 1.4e-09
                                   CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                         TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                   a+++y +g++y+k++++eeA +yy+ka++l p
  gi|15669130|ref|NP_247935.1| 255 ASLWYFKGKLYEKQNKFEEALKYYNKAIQLMP 286
                                   679*************************9855 PP

  == domain 9  score: 22.9 bits;  conditional E-value: 1.4e-07
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                   +a++ ++++++klg++ee++e+y+kal+
  gi|15669130|ref|NP_247935.1| 290 KALLAKARVLEKLGRIEESIECYNKALD 317
                                   68999*********************96 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.033        15      11      41 ..      27      57 ..      18      60 .. 0.82
   2 !    8.5   0.0    0.0092         4       8      44 .]      58      93 ..      52      93 .. 0.89
   3 !   17.5   0.0   1.2e-05    0.0053       2      40 ..      85     123 ..      84     127 .. 0.89
   4 ?    5.9   0.0     0.065        28      14      39 ..     131     156 ..     126     161 .. 0.88
   5 !    9.1   0.0    0.0058       2.5       8      40 ..     159     191 ..     153     195 .. 0.81
   6 ?    7.3   0.0     0.023       9.9       3      29 ..     188     214 ..     186     227 .. 0.88
   7 !   14.7   0.0   9.6e-05     0.042      16      44 .]     236     264 ..     225     264 .. 0.90
   8 !   17.2   0.1   1.4e-05    0.0063       3      43 ..     257     297 ..     257     297 .. 0.94
   9 !   13.6   0.1   0.00022     0.094       2      29 ..     290     317 ..     289     318 .] 0.94

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.033
                        TPR_14 11 llalGdpdeAiallrralalaPddaeawlll 41
                                  ++ +G++ e++ +l++al+l+Pd+  a +l 
  gi|15669130|ref|NP_247935.1| 27 YRDRGNLLESLYYLDKALELNPDFKFAKFLK 57
                                  78899999***************87776665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0092
                        TPR_14  8 aeallalGdpdeAiallrralalaPddaeawlllaql 44
                                  a  l+ lGd  ++i++l+++ + + +d++a+ ll+ql
  gi|15669130|ref|NP_247935.1| 58 AISLAILGDINKSIECLEDITS-NSNDPVAYALLGQL 93
                                  778999**************99.7788*******997 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 1.2e-05
                        TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawll 40 
                                    a+++l+++++ lG++d A++++++ l    ++a+a +l
  gi|15669130|ref|NP_247935.1|  85 VAYALLGQLYELLGNFDNALECYEKSLGIEEKFATAFFL 123
                                   5899***********************999999888765 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.065
                        TPR_14  14 lGdpdeAiallrralalaPddaeawl 39 
                                   +G++de +++++r+++ aP++  a++
  gi|15669130|ref|NP_247935.1| 131 SGKYDELLKCCDRLISFAPNFIPAYI 156
                                   699****************9988876 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.0058
                        TPR_14   8 aeallalGdpdeAiallrralalaPddaeawll 40 
                                   a  l+ lG+++eA+a+ +++l+l  +d  a +l
  gi|15669130|ref|NP_247935.1| 159 ANMLRKLGRYEEALACVNKVLELKENDTNAIYL 191
                                   788999****************98887766555 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.023
                        TPR_14   3 allalaeallalGdpdeAiallrrala 29 
                                   a ++ a +l + G+ deA+++++++++
  gi|15669130|ref|NP_247935.1| 188 AIYLKALILNRIGNCDEALKYYEKLID 214
                                   6678899999*************9986 PP

  == domain 7  score: 14.7 bits;  conditional E-value: 9.6e-05
                        TPR_14  16 dpdeAiallrralalaPddaeawlllaql 44 
                                   ++d+A+++ +  l+l Pdda +w++ ++l
  gi|15669130|ref|NP_247935.1| 236 KLDKAEKYIEMGLKLRPDDASLWYFKGKL 264
                                   69*********************999875 PP

  == domain 8  score: 17.2 bits;  conditional E-value: 1.4e-05
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                   +++  +++++ + +++eA++++++a++l P +  a+l+ a+
  gi|15669130|ref|NP_247935.1| 257 LWYFKGKLYEKQNKFEEALKYYNKAIQLMPHHTKALLAKAR 297
                                   5888899****************************999986 PP

  == domain 9  score: 13.6 bits;  conditional E-value: 0.00022
                        TPR_14   2 eallalaeallalGdpdeAiallrrala 29 
                                   +alla a++l+ lG+ +e+i+++++al+
  gi|15669130|ref|NP_247935.1| 290 KALLAKARVLEKLGRIEESIECYNKALD 317
                                   5899**********************97 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.024        11      13      32 ..      27      46 ..      16      68 .. 0.88
   2 !   19.0   0.2   2.9e-06    0.0013      46      73 ..      85     112 ..      53     116 .. 0.76
   3 ?    0.2   0.0       2.1   9.1e+02      10      30 ..     125     145 ..     116     149 .. 0.79
   4 !   18.3   0.1   4.8e-06    0.0021       9      34 ..     158     183 ..     152     189 .. 0.86
   5 !   15.0   0.1     5e-05     0.022       3      30 ..     187     213 ..     185     216 .. 0.87
   6 ?    0.9   0.0       1.3   5.7e+02      57      76 ..     233     252 ..     225     253 .. 0.79
   7 !   17.7   0.1   7.6e-06    0.0033      42      75 ..     252     285 ..     235     287 .. 0.79
   8 !   14.6   0.1   6.7e-05     0.029       5      31 ..     291     317 ..     287     318 .] 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.024
                        TPR_12 13 lrrlgrydeAlellekalei 32
                                  +r +g++ e+l +l+kale+
  gi|15669130|ref|NP_247935.1| 27 YRDRGNLLESLYYLDKALEL 46
                                  67899999999999999997 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 2.9e-06
                        TPR_12  46 ttlrnLgrlyralgryeeAlelleeala 73 
                                    ++  Lg+ly++lg+++ Ale +e++l 
  gi|15669130|ref|NP_247935.1|  85 VAYALLGQLYELLGNFDNALECYEKSLG 112
                                   4677788888888888888888888774 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 2.1
                        TPR_12  10 aavlrrlgrydeAlellekal 30 
                                    ++l   g+yde l+++++ +
  gi|15669130|ref|NP_247935.1| 125 VLCLGLSGKYDELLKCCDRLI 145
                                   56778899******9999876 PP

  == domain 4  score: 18.3 bits;  conditional E-value: 4.8e-06
                        TPR_12   9 laavlrrlgrydeAlellekaleiar 34 
                                    a++lr+lgry+eAl++ +k+le+ +
  gi|15669130|ref|NP_247935.1| 158 KANMLRKLGRYEEALACVNKVLELKE 183
                                   69999***************999975 PP

  == domain 5  score: 15.0 bits;  conditional E-value: 5e-05
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekal 30 
                                    +++   a++l+r g++deAl+++ek +
  gi|15669130|ref|NP_247935.1| 187 NAIY-LKALILNRIGNCDEALKYYEKLI 213
                                   4566.99******************976 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 1.3
                        TPR_12  57 algryeeAlelleealaiae 76 
                                   +++++++A+++ e  l++++
  gi|15669130|ref|NP_247935.1| 233 LFNKLDKAEKYIEMGLKLRP 252
                                   67999******999998875 PP

  == domain 7  score: 17.7 bits;  conditional E-value: 7.6e-06
                        TPR_12  42 pltattlrnLgrlyralgryeeAlelleealaia 75 
                                   p+ a+  +  g ly++++++eeAl+++++a++++
  gi|15669130|ref|NP_247935.1| 252 PDDASLWYFKGKLYEKQNKFEEALKYYNKAIQLM 285
                                   4457777888999999999999999999999875 PP

  == domain 8  score: 14.6 bits;  conditional E-value: 6.7e-05
                        TPR_12   5 alnnlaavlrrlgrydeAlellekale 31 
                                   al   a vl +lgr +e++e+++kal+
  gi|15669130|ref|NP_247935.1| 291 ALLAKARVLEKLGRIEESIECYNKALD 317
                                   455789999999999999999999997 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.3   0.00026      0.12       3      26 ..      26      49 ..      25      50 .. 0.95
   2 !    7.3   0.1    0.0085       3.7       7      42 .]      64      98 ..      60      98 .. 0.80
   3 !   14.2   0.0   6.1e-05     0.027       1      32 [.      91     122 ..      91     124 .. 0.91
   4 !   21.1   0.1   4.2e-07   0.00018       2      38 ..     160     196 ..     159     200 .. 0.89
   5 ?    1.4   0.1      0.61   2.7e+02       6      21 ..     198     213 ..     193     214 .. 0.81
   6 !   11.4   0.0   0.00045       0.2      21      41 ..     248     268 ..     245     269 .. 0.94
   7 !   20.9   0.5   4.8e-07   0.00021       1      42 []     262     303 ..     262     303 .. 0.87
   8 !   14.6   0.0   4.3e-05     0.019       6      22 ..     301     317 ..     296     317 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00026
                        TPR_11  3 ayyeqGkyeeAieaYkkAlkldPd 26
                                  +y+++G++ e++  + kAl+l+Pd
  gi|15669130|ref|NP_247935.1| 26 EYRDRGNLLESLYYLDKALELNPD 49
                                  7**********************9 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0085
                        TPR_11  7 qGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                  +G+++++ie+++  +  +++++ ay  LG++y  +G
  gi|15669130|ref|NP_247935.1| 64 LGDINKSIECLED-ITSNSNDPVAYALLGQLYELLG 98
                                  5666666766665.77799*************9987 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 6.1e-05
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayy 32 
                                   G++y  +G++++A+e+Y+k l + +++a+a++
  gi|15669130|ref|NP_247935.1|  91 GQLYELLGNFDNALECYEKSLGIEEKFATAFF 122
                                   6777789**********************987 PP

  == domain 4  score: 21.1 bits;  conditional E-value: 4.2e-07
                        TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                   ++++++G+yeeA+++ +k l+l++++ +a y  +l++
  gi|15669130|ref|NP_247935.1| 160 NMLRKLGRYEEALACVNKVLELKENDTNAIYLKALIL 196
                                   99*************************9999887776 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.61
                        TPR_11   6 eqGkyeeAieaYkkAl 21 
                                     G+ +eA++ Y+k +
  gi|15669130|ref|NP_247935.1| 198 RIGNCDEALKYYEKLI 213
                                   56999*******9987 PP

  == domain 6  score: 11.4 bits;  conditional E-value: 0.00045
                        TPR_11  21 lkldPdnaeayynLGlayykq 41 
                                   lkl+Pd+a+++y  G++y kq
  gi|15669130|ref|NP_247935.1| 248 LKLRPDDASLWYFKGKLYEKQ 268
                                   89*****************99 PP

  == domain 7  score: 20.9 bits;  conditional E-value: 4.8e-07
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   G++y +q+k+eeA++ Y+kA++l P    a+++ + ++ k+G
  gi|15669130|ref|NP_247935.1| 262 GKLYEKQNKFEEALKYYNKAIQLMPHHTKALLAKARVLEKLG 303
                                   78899******************9988888888777777776 PP

  == domain 8  score: 14.6 bits;  conditional E-value: 4.3e-05
                        TPR_11   6 eqGkyeeAieaYkkAlk 22 
                                   ++G++ee+ie+Y+kAl+
  gi|15669130|ref|NP_247935.1| 301 KLGRIEESIECYNKALD 317
                                   79*************95 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.13        56      30      49 ..      25      44 ..      22      49 .. 0.83
   2 ?    0.3   0.0       1.8   7.9e+02      34      59 ..      56      81 ..      36      89 .. 0.68
   3 ?    7.2   0.0     0.012       5.4      25      56 ..      80     111 ..      51     124 .. 0.84
   4 !    9.5   0.0    0.0025       1.1      10      48 ..     133     171 ..     130     171 .. 0.92
   5 !   18.9   0.0   2.9e-06    0.0012       9      57 ..     166     214 ..     157     218 .. 0.90
   6 !   31.7   0.0   2.8e-10   1.2e-07      10      71 ..     236     297 ..     234     298 .. 0.96
   7 !   24.0   0.0   7.2e-08   3.2e-05       4      57 ..     264     317 ..     262     318 .] 0.95

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.13
                         TPR_9 30 eerrdRGlllaqlGclsaAl 49
                                  +e+rdRG ll+ l  l +Al
  gi|15669130|ref|NP_247935.1| 25 YEYRDRGNLLESLYYLDKAL 44
                                  899***99999987777776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.8
                         TPR_9 34 dRGlllaqlGclsaAladLeaylala 59
                                    ++ la lG++++ +++Le   +++
  gi|15669130|ref|NP_247935.1| 56 LKAISLAILGDINKSIECLEDITSNS 81
                                  56777888999999999999877665 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.012
                         TPR_9  25 aPddpeerrdRGlllaqlGclsaAladLeayl 56 
                                   +++dp  +   G+l++ lG++  Al++ e  l
  gi|15669130|ref|NP_247935.1|  80 NSNDPVAYALLGQLYELLGNFDNALECYEKSL 111
                                   57888899999***************999765 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0025
                         TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaA 48 
                                   +++++l++++rl+ +aP+ +  +   + +l +lG++++A
  gi|15669130|ref|NP_247935.1| 133 KYDELLKCCDRLISFAPNFIPAYIIKANMLRKLGRYEEA 171
                                   6899***************99999999999999999987 PP

  == domain 5  score: 18.9 bits;  conditional E-value: 2.9e-06
                         TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57 
                                    ++e+ala+v+ +l l+ +d   ++  +l+l + G+  +Al+  e  ++
  gi|15669130|ref|NP_247935.1| 166 GRYEEALACVNKVLELKENDTNAIYLKALILNRIGNCDEALKYYEKLID 214
                                   689**************************************99997665 PP

  == domain 6  score: 31.7 bits;  conditional E-value: 2.8e-10
                         TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaq 71 
                                   + ++a +++e+ l l Pdd+++++  G l+++++ +++Al+  + +++l p+   a +++a+
  gi|15669130|ref|NP_247935.1| 236 KLDKAEKYIEMGLKLRPDDASLWYFKGKLYEKQNKFEEALKYYNKAIQLMPHHTKALLAKAR 297
                                   6799*****************************************************99998 PP

  == domain 7  score: 24.0 bits;  conditional E-value: 7.2e-08
                         TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57 
                                   ++  ++++e+al++++  ++l P++   ++  +++l++lG++++ +++ + +l+
  gi|15669130|ref|NP_247935.1| 264 LYEKQNKFEEALKYYNKAIQLMPHHTKALLAKARVLEKLGRIEESIECYNKALD 317
                                   68999*******************************************999886 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1     6e-06    0.0026       3      68 .]      29      93 ..      27      93 .. 0.95
   2 ?    7.0   0.0     0.019       8.1       5      57 ..      98     150 ..      96     156 .. 0.88
   3 !   15.6   0.1     4e-05     0.018      22      67 ..     149     194 ..     141     195 .. 0.85
   4 ?    7.5   0.0     0.013       5.7       7      68 .]     202     264 ..     196     264 .. 0.81
   5 !   30.7   0.2   7.8e-10   3.4e-07       3      53 ..     267     317 ..     265     318 .] 0.95

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6e-06
                        TPR_19  3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAkl 68
                                  ++g++ e l +l +al+ +p+   a+ l A+ l  lg++++ +++L+++     d + + +Ll++l
  gi|15669130|ref|NP_247935.1| 29 DRGNLLESLYYLDKALELNPDFKFAKFLKAISLAILGDINKSIECLEDITSNSND-PVAYALLGQL 93
                                  6899999999*********************************************.99999*9997 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.019
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                   g++++Al+ +e+ l  + k a a  l + +l  +g +de  +++d+l   +p+
  gi|15669130|ref|NP_247935.1|  98 GNFDNALECYEKSLGIEEKFATAFFLKVLCLGLSGKYDELLKCCDRLISFAPN 150
                                   89***********************999999999****999999988877777 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 4e-05
                        TPR_19  22 pknaearllLAeallalgqldeAealLdalpeedpddaryasLlAk 67 
                                   p+   a +  A+ l +lg+++eA a++++++e + +d ++  L+A 
  gi|15669130|ref|NP_247935.1| 149 PNFIPAYIIKANMLRKLGRYEEALACVNKVLELKENDTNAIYLKAL 194
                                   6666677777999***********************9998888886 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.013
                        TPR_19   7 yaeAlalleqalqe.dpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAkl 68 
                                    +eAl+++e++++e +    e+    + + +  + ld+Ae+ ++  ++  pdda ++  ++kl
  gi|15669130|ref|NP_247935.1| 202 CDEALKYYEKLIDElNVTWIEVIREAIYLSFLFNKLDKAEKYIEMGLKLRPDDASLWYFKGKL 264
                                   5788888888765536667777778888888889*******************9999888886 PP

  == domain 5  score: 30.7 bits;  conditional E-value: 7.8e-10
                        TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                   ++++++eAl+++ +a+q  p++  a+l+ A++l +lg+++e +++ +++++
  gi|15669130|ref|NP_247935.1| 267 KQNKFEEALKYYNKAIQLMPHHTKALLAKARVLEKLGRIEESIECYNKALD 317
                                   5899****************************************9998875 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.4   8.6e-09   3.8e-06       1      30 [.      86     115 ..      86     118 .. 0.93
   2 ?    1.9   0.0      0.64   2.8e+02      12      25 ..     131     144 ..     123     150 .. 0.84
   3 !   12.1   0.0   0.00035      0.16       6      34 ..     159     187 ..     154     189 .. 0.86
   4 !    9.7   0.1    0.0021       0.9       6      27 ..     193     215 ..     188     219 .. 0.79
   5 ?    2.6   0.0      0.37   1.6e+02      13      35 ..     235     255 ..     227     256 .. 0.83
   6 !   14.5   0.0   5.9e-05     0.026       4      27 ..     260     283 ..     257     287 .. 0.84
   7 !   13.0   0.1   0.00019     0.083       1      29 [.     291     317 ..     291     318 .] 0.91

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 8.6e-09
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                                   a+  L++ly+ lG++++A+e+ye+sL++++
  gi|15669130|ref|NP_247935.1|  86 AYALLGQLYELLGNFDNALECYEKSLGIEE 115
                                   7899**********************9875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.64
                         TPR_7  12 lGdyeeAielyeqs 25 
                                    G+y+e+++++ ++
  gi|15669130|ref|NP_247935.1| 131 SGKYDELLKCCDRL 144
                                   69********9994 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00035
                         TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                   a++ ++lG+yeeA+ +  ++L+l + +++
  gi|15669130|ref|NP_247935.1| 159 ANMLRKLGRYEEALACVNKVLELKENDTN 187
                                   8999***************9999887765 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0021
                         TPR_7   6 arlysrlGdyeeAielyeqsL.a 27 
                                   a +  r G+ +eA+++ye+++ +
  gi|15669130|ref|NP_247935.1| 193 ALILNRIGNCDEALKYYEKLIdE 215
                                   7778899************6655 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.37
                         TPR_7  13 GdyeeAielyeqsLaltkdpeda 35 
                                   ++ ++A+++ e   +l  +p+da
  gi|15669130|ref|NP_247935.1| 235 NKLDKAEKYIEM--GLKLRPDDA 255
                                   6789********..999998886 PP

  == domain 6  score: 14.5 bits;  conditional E-value: 5.9e-05
                         TPR_7   4 nLarlysrlGdyeeAielyeqsLa 27 
                                     + ly++++++eeA+++y ++++
  gi|15669130|ref|NP_247935.1| 260 FKGKLYEKQNKFEEALKYYNKAIQ 283
                                   5699***************99654 PP

  == domain 7  score: 13.0 bits;  conditional E-value: 0.00019
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                   aLl+ ar+ ++lG+ ee ie+y +  al+
  gi|15669130|ref|NP_247935.1| 291 ALLAKARVLEKLGRIEESIECYNK--ALD 317
                                   7999******************99..655 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.11        50       6      50 ..      26      67 ..      23      77 .. 0.85
   2 !    8.1   0.0    0.0094       4.1      27      61 ..      80     111 ..      64     116 .. 0.81
   3 !   14.3   0.0   0.00011     0.048       7      62 ..     162     214 ..     158     217 .. 0.92
   4 !   24.5   0.0     7e-08   3.1e-05      11      62 ..     235     283 ..     234     288 .. 0.93
   5 !   28.1   0.0   5.2e-09   2.3e-06       4      62 ..     262     317 ..     261     318 .] 0.96

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.11
                        TPR_16  6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrl 50
                                  +++++g+  + + +l+ al+++   Pd   A +l++ +++ +g+ 
  gi|15669130|ref|NP_247935.1| 26 EYRDRGNLLESLYYLDKALELN---PDFKFAKFLKAISLAILGDI 67
                                  789999999999999*******...66666999999999999986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0094
                        TPR_16  27 dpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                   ++ +P+   A+ llg+++  +g+++ A++ y++ l
  gi|15669130|ref|NP_247935.1|  80 NSNDPV---AYALLGQLYELLGNFDNALECYEKSL 111
                                   447788...******************99888766 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 0.00011
                        TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                   ++++g+y++A+a  + +l++      +  A +l+++++ r g+ +eA+ +y+++++
  gi|15669130|ref|NP_247935.1| 162 LRKLGRYEEALACVNKVLELK---ENDTNAIYLKALILNRIGNCDEALKYYEKLID 214
                                   7899*****************...99999**********************99876 PP

  == domain 4  score: 24.5 bits;  conditional E-value: 7e-08
                        TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                   ++ d+A+++ e  lk++   Pd+a  ++++g ++ +q+ ++eA+ +y++a++
  gi|15669130|ref|NP_247935.1| 235 NKLDKAEKYIEMGLKLR---PDDASLWYFKGKLYEKQNKFEEALKYYNKAIQ 283
                                   57899************...*****************************985 PP

  == domain 5  score: 28.1 bits;  conditional E-value: 5.2e-09
                        TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                   ++++ +++++++A+++++ a+ +    P +  All++++++ ++gr +e ++ y++al+
  gi|15669130|ref|NP_247935.1| 262 GKLYEKQNKFEEALKYYNKAIQLM---PHHTKALLAKARVLEKLGRIEESIECYNKALD 317
                                   789*********************...****************************9986 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.048        21      29      81 ..      23      76 ..       7      77 .. 0.89
   2 !   16.0   0.1   2.4e-05     0.011       7      74 ..      69     136 ..      65     137 .. 0.79
   3 !   30.6   1.7   6.5e-10   2.9e-07       3      81 ..     132     211 ..     130     212 .. 0.94
   4 !   30.4   2.0   7.7e-10   3.4e-07       4      81 ..     236     314 ..     235     315 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.048
                                  HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3 29 lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                  +++ +  +g+  + +++l+ka +ln+  + + +l+A +l  L+ +++ i +Le 
  gi|15669130|ref|NP_247935.1| 23 KSYEYRDRGNLLESLYYLDKAlELNPDFKFAKFLKAISLAILGDINKSIECLED 76
                                  47779999999999***********************************99986 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.4e-05
                                   HHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHT.T-HHH CS
                        ANAPC3   7 nAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkL.kkyee 74 
                                   + i ++e +  +++++p +  ll++ + l+g+++ A+e ++k+ ++ ++  + ++ +   +l L +ky+e
  gi|15669130|ref|NP_247935.1|  69 KSIECLEDIT-SNSNDPVAYALLGQLYELLGNFDNALECYEKSlGI-EEKFATAFFLKVLCLGLsGKYDE 136
                                   5667778888.89999999999*********************555.55556666666667766699998 PP

  == domain 3  score: 30.6 bits;  conditional E-value: 6.5e-10
                                   T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   ++y++ + +++rl +  ++   +   +A  l ++g+y++A+  ++k  +l++++ ++ yl+A  l  +++ +eA++ +ek
  gi|15669130|ref|NP_247935.1| 132 GKYDELLKCCDRLISFAPNFIPAYIIKANMLRKLGRYEEALACVNKVlELKENDTNAIYLKALILNRIGNCDEALKYYEK 211
                                   57999*********8888888888889*************************************************9997 PP

  == domain 4  score: 30.4 bits;  conditional E-value: 7.7e-10
                                   -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   ++++A+ ++e  l+  +++++  y++++ + +++++++A+++++ka +l +++ ++++ +A++l kL+++ee i ++ k
  gi|15669130|ref|NP_247935.1| 236 KLDKAEKYIEMGLKLRPDDASLWYFKGKLYEKQNKFEEALKYYNKAiQLMPHHTKALLAKARVLEKLGRIEESIECYNK 314
                                   56788888888887888888888889************************************************99877 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.027        12       2      31 ..      40      69 ..      39      75 .. 0.86
   2 !   16.1   0.2   2.4e-05     0.011       6      34 .]      77     105 ..      67     105 .. 0.83
   3 ?    2.5   0.0      0.55   2.4e+02       1      31 [.     106     136 ..     106     139 .. 0.92
   4 !   13.8   0.0   0.00014     0.059       1      33 [.     140     172 ..     140     173 .. 0.95
   5 ?    5.8   0.2     0.048        21       3      32 ..     176     205 ..     174     207 .. 0.87
   6 !   11.8   0.0   0.00058      0.26       6      33 ..     248     275 ..     243     276 .. 0.91
   7 ?    7.3   0.0     0.016         7       1      33 [.     277     309 ..     277     310 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.027
                        TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmt 31
                                  + kalel+P+   a +++A  l+ +Gd  +
  gi|15669130|ref|NP_247935.1| 40 LDKALELNPDFKFAKFLKAISLAILGDINK 69
                                  679********9999999999999998655 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.4e-05
                        TPR_17   6 leldPnnadaynnLAelllknGdlmtArq 34 
                                   +  + n+++ay +L++l++ +G+++ A++
  gi|15669130|ref|NP_247935.1|  77 ITSNSNDPVAYALLGQLYELLGNFDNALE 105
                                   44599*******************99975 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.55
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                   +y+k+l ++ + a a++++  +l   G++++
  gi|15669130|ref|NP_247935.1| 106 CYEKSLGIEEKFATAFFLKVLCLGLSGKYDE 136
                                   8*****************9999999999987 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 0.00014
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   ++ + +   Pn  +ay  +A+ l+k+G++++A+
  gi|15669130|ref|NP_247935.1| 140 CCDRLISFAPNFIPAYIIKANMLRKLGRYEEAL 172
                                   7899***************************97 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.048
                        TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtA 32 
                                    k+lel  n+ +a +++A +l ++G+ ++A
  gi|15669130|ref|NP_247935.1| 176 NKVLELKENDTNAIYLKALILNRIGNCDEA 205
                                   599******************999986655 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 0.00058
                        TPR_17   6 leldPnnadaynnLAelllknGdlmtAr 33 
                                   l+l P++a +++ +++l++k++++++A+
  gi|15669130|ref|NP_247935.1| 248 LKLRPDDASLWYFKGKLYEKQNKFEEAL 275
                                   8999**********************97 PP

  == domain 7  score: 7.3 bits;  conditional E-value: 0.016
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   +y ka++l P + +a+  +A++l+k+G+ ++ +
  gi|15669130|ref|NP_247935.1| 277 YYNKAIQLMPHHTKALLAKARVLEKLGRIEESI 309
                                   69*************************988765 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00042      0.18     181     251 ..       5      76 ..       1      83 [. 0.78
   2 !   13.1   0.0   7.6e-05     0.033     205     259 ..     131     185 ..      75     186 .. 0.91
   3 !   14.6   0.1   2.7e-05     0.012     199     250 ..     159     210 ..     151     217 .. 0.85
   4 !   22.9   0.4   7.9e-08   3.5e-05     186     252 ..     251     315 ..     221     318 .] 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00042
                                   GSS----SSHHHHHHHHHHHHHHHHT-SH..HHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                         NARP1 181 edsekepesallwvlyflAqhydklgsre..kAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmee 251
                                   +++ ke+  + l  l++l + y++  + +  ++l y+dka+e +p +      Ka  l   Gd++k +e++e 
  gi|15669130|ref|NP_247935.1|   5 NKKLKETSDV-LLSLTYLIKSYEYRDRGNllESLYYLDKALELNPDFKFAKFLKAISLAILGDINKSIECLED 76 
                                   3445566666.55566666666665555555************************************999875 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.6e-05
                                   HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                         NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                    g++++ l++ d+ i+  p+++  y++Ka++l++ G  ++A +++++  +l ++D
  gi|15669130|ref|NP_247935.1| 131 SGKYDELLKCCDRLISFAPNFIPAYIIKANMLRKLGRYEEALACVNKVLELKEND 185
                                   56789999**************************************999998877 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 2.7e-05
                                   HHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                         NARP1 199 AqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevme 250
                                   A    klg++e+Al +++k +e + + ++  + Ka il + G+ ++A +  e
  gi|15669130|ref|NP_247935.1| 159 ANMLRKLGRYEEALACVNKVLELKENDTNAIYLKALILNRIGNCDEALKYYE 210
                                   6666789999999999999999999999999999999999999999998766 PP

  == domain 4  score: 22.9 bits;  conditional E-value: 7.9e-08
                                   --SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                         NARP1 186 epesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                   +p  a lw  yf  + y+k ++ e+Al+y +kai+  p  +   l+Kar+l++ G +++ +e+ ++a
  gi|15669130|ref|NP_247935.1| 251 RPDDASLW--YFKGKLYEKQNKFEEALKYYNKAIQLMPHHTKALLAKARVLEKLGRIEESIECYNKA 315
                                   55666666..9999***********************************************999987 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       4.9   2.2e+03      13      28 ..      64      79 ..      53      81 .. 0.78
   2 !   11.5   0.1   0.00088      0.39       2      25 ..      86     109 ..      85     111 .. 0.92
   3 ?    2.1   0.0      0.85   3.7e+02       7      26 ..     159     178 ..     154     181 .. 0.76
   4 !   12.1   0.1   0.00057      0.25       2      29 ..     188     215 ..     187     215 .. 0.92
   5 !   11.8   0.0   0.00068       0.3       7      28 ..     262     283 ..     257     288 .. 0.89
   6 !    8.3   0.1    0.0092         4       2      29 ..     291     318 .]     290     318 .] 0.93

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 4.9
                                  HHHHHHHHHHHHHHHH CS
                         TPR_6 13 lgdtdkAlealerlik 28
                                  lgd  k++e le++ +
  gi|15669130|ref|NP_247935.1| 64 LGDINKSIECLEDITS 79
                                  58999******99876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00088
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealer 25 
                                   A+ +l+++y+ lg+ d+Ale +e+
  gi|15669130|ref|NP_247935.1|  86 AYALLGQLYELLGNFDNALECYEK 109
                                   7789*******99*********97 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.85
                                   HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrklgdtdkAlealerl 26 
                                   a  +rklg++++Al+  +++
  gi|15669130|ref|NP_247935.1| 159 ANMLRKLGRYEEALACVNKV 178
                                   55678899*****9876655 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00057
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlike 29 
                                   A y+ al + + g+ d+Al+++e+li+e
  gi|15669130|ref|NP_247935.1| 188 AIYLKALILNRIGNCDEALKYYEKLIDE 215
                                   7899999999988*************86 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 0.00068
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                   +++y+k+++ ++Al+++++ i+
  gi|15669130|ref|NP_247935.1| 262 GKLYEKQNKFEEALKYYNKAIQ 283
                                   899****************998 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0092
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlike 29 
                                   Al+  a+ ++klg+ ++++e +++ +++
  gi|15669130|ref|NP_247935.1| 291 ALLAKARVLEKLGRIEESIECYNKALDR 318
                                   89999******9************9986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.089        39      12      31 ..      27      46 ..      24      47 .. 0.93
   2 !   10.3   0.1    0.0011      0.49       5      32 ..      87     114 ..      85     116 .. 0.87
   3 !   11.1   0.1   0.00062      0.27       9      32 ..     159     182 ..     158     184 .. 0.89
   4 ?    6.3   0.0     0.021         9       9      29 ..     193     213 ..     192     214 .. 0.87
   5 ?   -1.8   0.0       7.4   3.2e+03      16      26 ..     235     245 ..     229     251 .. 0.81
   6 !    9.4   0.1    0.0023      0.99      11      31 ..     264     284 ..     262     285 .. 0.89
   7 ?    2.1   0.1      0.44   1.9e+02       9      30 ..     296     317 ..     291     318 .] 0.74

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.089
                        TPR_10 12 lrqrgrydeAealleealai 31
                                  +r+rg++ e++ +l++al++
  gi|15669130|ref|NP_247935.1| 27 YRDRGNLLESLYYLDKALEL 46
                                  9*****************86 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0011
                        TPR_10   5 lnNLanalrqrgrydeAealleealair 32 
                                   +  L+ ++  +g++d A++ +e++l i 
  gi|15669130|ref|NP_247935.1|  87 YALLGQLYELLGNFDNALECYEKSLGIE 114
                                   6679********************9875 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00062
                        TPR_10   9 analrqrgrydeAealleealair 32 
                                   an+lr++gry+eA+a   ++l++ 
  gi|15669130|ref|NP_247935.1| 159 ANMLRKLGRYEEALACVNKVLELK 182
                                   89*************998888875 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.021
                        TPR_10   9 analrqrgrydeAealleeal 29 
                                   a +l + g+ deA++++e+ +
  gi|15669130|ref|NP_247935.1| 193 ALILNRIGNCDEALKYYEKLI 213
                                   6788899***********965 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 7.4
                        TPR_10  16 grydeAealle 26 
                                   +++d+Ae++ e
  gi|15669130|ref|NP_247935.1| 235 NKLDKAEKYIE 245
                                   7899***9977 PP

  == domain 6  score: 9.4 bits;  conditional E-value: 0.0023
                        TPR_10  11 alrqrgrydeAealleealai 31 
                                   ++ ++++++eA++++ +a+++
  gi|15669130|ref|NP_247935.1| 264 LYEKQNKFEEALKYYNKAIQL 284
                                   6889**************986 PP

  == domain 7  score: 2.1 bits;  conditional E-value: 0.44
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   a++l ++gr +e+ + + +al+
  gi|15669130|ref|NP_247935.1| 296 ARVLEKLGRIEESIECYNKALD 317
                                   6677777888888887777775 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0031       1.4      37      82 ..      66     111 ..      38     117 .. 0.89
   2 !   12.1   0.0   0.00035      0.16      62     126 ..     159     212 ..     152     219 .. 0.81
   3 !   11.8   0.1   0.00042      0.18      76     127 ..     269     316 ..     235     318 .] 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0031
                                   HHHTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                       DUF3856  37 evsrtipaeeafdheGfdalchaglsealaklgrydealesadkal 82 
                                   ++ ++i   e    +  d +++a l + +  lg++d+ale+ +k+l
  gi|15669130|ref|NP_247935.1|  66 DINKSIECLEDITSNSNDPVAYALLGQLYELLGNFDNALECYEKSL 111
                                   7889999999999999************************999987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00035
                                   HHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                       DUF3856  62 sealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                   ++ l klgry+eal +++k l       el++++     +a++ +a  l+ +G+ dealk++++ 
  gi|15669130|ref|NP_247935.1| 159 ANMLRKLGRYEEALACVNKVL-------ELKENDT----NAIYLKALILNRIGNCDEALKYYEKL 212
                                   667889999999998887777.......7888875....699*******************9875 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00042
                                   HHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                       DUF3856  76 esadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                   +  ++al+y+n+  +l     k    a++ +a+ le+lGr +e+++ +++a 
  gi|15669130|ref|NP_247935.1| 269 NKFEEALKYYNKAIQLMPHHTK----ALLAKARVLEKLGRIEESIECYNKAL 316
                                   56789***********998776....7889******************9985 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.016       6.9      15      42 ..      31      58 ..      29      61 .. 0.89
   2 ?    4.2   0.0       0.1        45      14      43 ..      97     126 ..      95     128 .. 0.90
   3 ?    3.0   0.0      0.24   1.1e+02      15      34 ..     132     151 ..     131     154 .. 0.90
   4 !   15.9   0.2   2.3e-05      0.01      13      48 ..     164     199 ..     162     201 .. 0.95
   5 ?    3.3   0.1       0.2        89       3      28 ..     188     213 ..     187     215 .. 0.87
   6 ?    1.3   0.0      0.85   3.7e+02      17      34 ..     237     254 ..     234     257 .. 0.87
   7 ?    2.8   0.4      0.29   1.3e+02      13      37 ..     267     291 ..     265     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.016
                                  T-HHHHHHHHHHHHHHTTS-HHHHHHHH CS
                    Fis1_TPR_C 15 geYseArryvdalLeiEPenrQaqsLke 42
                                  g+  e++ y+d  Le+ P+++ a+ Lk+
  gi|15669130|ref|NP_247935.1| 31 GNLLESLYYLDKALELNPDFKFAKFLKA 58
                                  56678999****************9996 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.1
                                   HT-HHHHHHHHHHHHHHTTS-HHHHHHHHH CS
                    Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaqsLkel 43 
                                   lg++++A+++ +  L iE ++  a  Lk l
  gi|15669130|ref|NP_247935.1|  97 LGNFDNALECYEKSLGIEEKFATAFFLKVL 126
                                   79****************999988888865 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.24
                                   T-HHHHHHHHHHHHHHTTS- CS
                    Fis1_TPR_C  15 geYseArryvdalLeiEPen 34 
                                   g+Y+e ++++d+l++  P++
  gi|15669130|ref|NP_247935.1| 132 GKYDELLKCCDRLISFAPNF 151
                                   79************999986 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 2.3e-05
                                   HHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHH CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQaqsLkeliedki 48 
                                   klg+Y+eA+ +v+ +Le+  +  +a  Lk+li ++i
  gi|15669130|ref|NP_247935.1| 164 KLGRYEEALACVNKVLELKENDTNAIYLKALILNRI 199
                                   9******************************98877 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.2
                                   HHHHHHHHHHHHT-HHHHHHHHHHHH CS
                    Fis1_TPR_C   3 clYylAlGhyklgeYseArryvdalL 28 
                                    +Y+ Al   ++g+ +eA++y + l+
  gi|15669130|ref|NP_247935.1| 188 AIYLKALILNRIGNCDEALKYYEKLI 213
                                   5788888899***********99986 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.85
                                   HHHHHHHHHHHHHHTTS- CS
                    Fis1_TPR_C  17 YseArryvdalLeiEPen 34 
                                    ++A +y+++ L++ P+ 
  gi|15669130|ref|NP_247935.1| 237 LDKAEKYIEMGLKLRPDD 254
                                   689***********9986 PP

  == domain 7  score: 2.8 bits;  conditional E-value: 0.29
                                   HHT-HHHHHHHHHHHHHHTTS-HHH CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQa 37 
                                   k+ +++eA++y +  +++ P    a
  gi|15669130|ref|NP_247935.1| 267 KQNKFEEALKYYNKAIQLMPHHTKA 291
                                   8899**********99998876655 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   8.6e-05     0.038     129     278 ..      67     216 ..       8     218 .. 0.79
   2 !   11.9   0.1   0.00021     0.092     126     181 ..     237     290 ..     219     294 .. 0.76
   3 ?    1.9   0.0      0.24   1.1e+02     148     175 ..     291     318 .]     288     318 .] 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.6e-05
                        TPR_15 129 iaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkar 209
                                   i++ ++ le     ++++  ++++++ly+  g+ d+Al++y++ l  + + +++    +  l  +g+++e   llk   + 
  gi|15669130|ref|NP_247935.1|  67 INKSIECLEDITSNSNDPVAYALLGQLYELLGNFDNALECYEKSLGIEEKFATAFFLKVLCLGLSGKYDE---LLKCCDRL 144
                                   555555555555567999999**********************999887755544444444444788887...55555555 PP

                        TPR_15 210 aesdasLwgpl...aaAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAwrlRrqvwrel 278
                                    +  ++  +++   a  l +Lgr+++AL+ ++k ++ +++d       A +l++ g+ deA ++  ++ +el
  gi|15669130|ref|NP_247935.1| 145 ISFAPNFIPAYiikANMLRKLGRYEEALACVNKVLELKENDTNAIYLKALILNRIGNCDEALKYYEKLIDEL 216
                                   555666666663224455579************99999999999999999**********999888777766 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00021
                        TPR_15 126 ydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsse 181
                                   +d+ ++ ++    ++   ++a  ++  ++ly+++++ ++Al+ y +A++l p  ++
  gi|15669130|ref|NP_247935.1| 237 LDKAEKYIEM--GLKLRPDDASLWYFKGKLYEKQNKFEEALKYYNKAIQLMPHHTK 290
                                   4444444444..34444499*******************************99876 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.24
                        TPR_15 148 fllaraelyrqegqtdaAlrdyreAlal 175
                                    lla a++ ++ g+ ++++++y +Al++
  gi|15669130|ref|NP_247935.1| 291 ALLAKARVLEKLGRIEESIECYNKALDR 318
                                   58999********************985 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.022       9.6      39      61 ..      87     109 ..      64     119 .. 0.88
   2 ?    0.1   0.0       1.3   5.7e+02      42      64 ..     158     180 ..     154     189 .. 0.82
   3 !   15.0   0.3   3.5e-05     0.015      38      97 ..     188     245 ..     180     249 .. 0.87
   4 ?    5.8   0.2     0.023       9.9      40      64 ..     259     283 ..     253     289 .. 0.87
   5 ?    6.0   0.0      0.02       8.6      37      64 ..     290     317 ..     285     318 .] 0.92

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.022
                                   HHHHHHHHHHCT-HHHHHHHHHT CS
                          RPN7  39 kldlaehYlkigdleeAlkaysr 61 
                                   +  l++ Y   g++++Al++y++
  gi|15669130|ref|NP_247935.1|  87 YALLGQLYELLGNFDNALECYEK 109
                                   56699****************98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                                   HHHHHHHCT-HHHHHHHHHTCCC CS
                          RPN7  42 laehYlkigdleeAlkaysrire 64 
                                   +a+   k g +eeAl+++++++e
  gi|15669130|ref|NP_247935.1| 158 KANMLRKLGRYEEALACVNKVLE 180
                                   56666789999******999876 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 3.5e-05
                                   HHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                          RPN7  38 akldlaehYlkigdleeAlkaysrireyctslkhkidmllnlirvaiffndwdlvskyle 97 
                                   a + +a    +ig+++eAlk+y+++++++      i+++ + i +++ fn  d+++ky+e
  gi|15669130|ref|NP_247935.1| 188 AIYLKALILNRIGNCDEALKYYEKLIDELNV--TWIEVIREAIYLSFLFNKLDKAEKYIE 245
                                   55667778889*************9999987..68***********************97 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.023
                                   HHHHHHHHHCT-HHHHHHHHHTCCC CS
                          RPN7  40 ldlaehYlkigdleeAlkaysrire 64 
                                   + +++ Y k  ++eeAlk+y+++++
  gi|15669130|ref|NP_247935.1| 259 YFKGKLYEKQNKFEEALKYYNKAIQ 283
                                   5689*****************9865 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.02
                                   HHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                          RPN7  37 rakldlaehYlkigdleeAlkaysrire 64 
                                   +a l++a+   k g +ee++++y+++++
  gi|15669130|ref|NP_247935.1| 290 KALLAKARVLEKLGRIEESIECYNKALD 317
                                   68899********************987 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0021       0.9      58     120 ..      30      93 ..      27      97 .. 0.83
   2 !    9.9   0.0    0.0013      0.56      25      93 ..     132     200 ..     118     216 .. 0.85
   3 ?    6.4   0.0     0.015       6.4      26      86 ..     236     294 ..     208     303 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                    HrpB1_HrpK  58 rgrweeAlrlLreveaeasgtpyakaLlAlcLaalrDeeWr.ayAeevlesdadpdalaLvkaL 120
                                   rg++ e l +L +  + ++ +++ak L A+ La+l+D +      e + ++++dp a aL+ +L
  gi|15669130|ref|NP_247935.1|  30 RGNLLESLYYLDKALELNPDFKFAKFLKAISLAILGDINKSiECLEDITSNSNDPVAYALLGQL 93 
                                   8999999******************************664414567777778888888877776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0013
                    HrpB1_HrpK  25 edtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyakaLlAlcLaalr 93 
                                   ++ +++ +  d l  + P++  + ++ +++l + gr+eeAl   ++v + +++   a  L Al L+  +
  gi|15669130|ref|NP_247935.1| 132 GKYDELLKCCDRLISFAPNFIPAYIIKANMLRKLGRYEEALACVNKVLELKENDTNAIYLKALILNRIG 200
                                   55566666677788899*******************************999999999999999998765 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.015
                    HrpB1_HrpK  26 dtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyakaLlA 86 
                                   + + ae+ ++    LrP  a l  + g l+ +++++eeAl++ ++  +  ++    kaLlA
  gi|15669130|ref|NP_247935.1| 236 KLDKAEKYIEMGLKLRPDDASLWYFKGKLYEKQNKFEEALKYYNKAIQLMPHH--TKALLA 294
                                   556666666666679***************************99988665554..455554 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.019       8.1      14      32 ..      94     112 ..      86     114 .. 0.87
   2 ?   -0.2   0.0       2.4   1.1e+03      26      39 ..     167     180 ..     163     200 .. 0.66
   3 ?    4.4   0.2     0.092        40      15      34 ..     197     216 ..     188     227 .. 0.83
   4 !   14.4   0.7   6.9e-05      0.03      14      35 ..     265     286 ..     261     291 .. 0.87
   5 !    9.2   0.1    0.0029       1.3       6      32 ..     291     317 ..     288     318 .] 0.92

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.019
                           MIT  14 eDnagnyeeAlelYkeale 32 
                                   ++  gn++ Ale+Y+++l+
  gi|15669130|ref|NP_247935.1|  94 YELLGNFDNALECYEKSLG 112
                                   56779***********986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.4
                           MIT  26 lYkealelLlqalk 39 
                                    Y+eal   +++l 
  gi|15669130|ref|NP_247935.1| 167 RYEEALACVNKVLE 180
                                   57777777777776 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.092
                           MIT  15 DnagnyeeAlelYkealelL 34 
                                    + gn +eAl++Y++ ++ L
  gi|15669130|ref|NP_247935.1| 197 NRIGNCDEALKYYEKLIDEL 216
                                   56699*********988877 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 6.9e-05
                           MIT  14 eDnagnyeeAlelYkealelLl 35 
                                   +++++++eeAl++Y +a++l+ 
  gi|15669130|ref|NP_247935.1| 265 YEKQNKFEEALKYYNKAIQLMP 286
                                   899****************975 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0029
                           MIT   6 elvkkAveeDnagnyeeAlelYkeale 32 
                                   +l+ kA  +++ g +ee +e+Y +al+
  gi|15669130|ref|NP_247935.1| 291 ALLAKARVLEKLGRIEESIECYNKALD 317
                                   5788999******************98 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0061       2.6       1      25 [.      84     108 ..      84     109 .. 0.91
   2 ?    7.9   0.0     0.013       5.5       4      23 ..     155     174 ..     153     176 .. 0.85
   3 ?    3.7   0.0      0.29   1.2e+02       3      19 ..     291     307 ..     290     310 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0061
                         TPR_4   1 arallaLArallalGdldeAralle 25 
                                   ++a+++L++++ +lG++d A++  e
  gi|15669130|ref|NP_247935.1|  84 PVAYALLGQLYELLGNFDNALECYE 108
                                   6899****************99876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.013
                         TPR_4   4 llaLArallalGdldeAral 23 
                                   ++  A  l  lG+++eA+a 
  gi|15669130|ref|NP_247935.1| 155 YIIKANMLRKLGRYEEALAC 174
                                   66779999**********96 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.29
                         TPR_4   3 allaLArallalGdlde 19 
                                   alla Ar+l  lG+ +e
  gi|15669130|ref|NP_247935.1| 291 ALLAKARVLEKLGRIEE 307
                                   78999*********998 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       1.3   5.5e+02      78     122 ..      26      70 ..      18      74 .. 0.84
   2 !    8.3   0.0    0.0066       2.9      75     122 ..     158     205 ..     153     215 .. 0.89
   3 !   12.2   0.1   0.00044      0.19      77     124 ..     263     310 ..     234     316 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.3
                                   HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
               Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                   e++++g++  ++  l+++++ +p+ + ak lka +l  lg  ++s
  gi|15669130|ref|NP_247935.1|  26 EYRDRGNLLESLYYLDKALELNPDFKFAKFLKAISLAILGDINKS 70 
                                   567888888899999999999************999999877665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0066
                                   HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
               Alkyl_sulf_dimr  75 kakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                   ka+  +k g y+ a+  +n++++ ++++++a  lka +l+++g+  e+
  gi|15669130|ref|NP_247935.1| 158 KANMLRKLGRYEEALACVNKVLELKENDTNAIYLKALILNRIGNCDEA 205
                                   5666778899*******************************9987765 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00044
                                   HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHH CS
               Alkyl_sulf_dimr  77 kealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesat 124
                                   k + k+++++ a++  n++++  p++++a  +ka++le+lg+ +es  
  gi|15669130|ref|NP_247935.1| 263 KLYEKQNKFEEALKYYNKAIQLMPHHTKALLAKARVLEKLGRIEESIE 310
                                   44558899************************************9976 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.07        31      32      97 ..      35     106 ..      21     110 .. 0.79
   2 !   17.1   0.7   9.3e-06    0.0041       3      98 ..     105     209 ..     103     216 .. 0.75
   3 !   11.6   1.3   0.00048      0.21      21      74 ..     159     215 ..     150     250 .. 0.78
   4 ?    6.1   0.8     0.024        11      26      68 ..     267     312 ..     250     317 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.07
                  SRP_TPR_like  32 eaLkllkkgsalsedvrfE...kaYvlYklkkykkalkilkkveaee...kvkvlksqvlYrlgsyekAYkl 97 
                                   e+L +l+k+ +l+ d +f    ka  l  l   +k+ + l+ +++++    +  l+ q++  lg++++A ++
  gi|15669130|ref|NP_247935.1|  35 ESLYYLDKALELNPDFKFAkflKAISLAILGDINKSIECLEDITSNSndpVAYALLGQLYELLGNFDNALEC 106
                                   678888888888888765422268888899999********9998764344678999**********99766 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 9.3e-06
                  SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsalsedvr...fEkaYvlYklkkykkalkilkkv....eae 74 
                                   e+yek l +e+k  + f  kv++l   +ky+e Lk ++   + + + +     ka +l kl +y++al  ++kv    e++
  gi|15669130|ref|NP_247935.1| 105 ECYEKSLGIEEKFATAFflKVLCLGLSGKYDELLKCCDRLISFAPNFIpayIIKANMLRKLGRYEEALACVNKVlelkEND 185
                                   7899999999999999999******************9988555443211145666789********97666542221444 PP

                  SRP_TPR_like  75 ekvkvlksqvlYrlgsyekAYklL 98 
                                    ++  lk+ +l r+g+ ++A k+ 
  gi|15669130|ref|NP_247935.1| 186 TNAIYLKALILNRIGNCDEALKYY 209
                                   477889999999999999996554 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00048
                  SRP_TPR_like  21 vvaliklekyeeaLkllkkgsalse...dvrfEkaYvlYklkkykkalkilkkveae 74 
                                   +  l kl++yeeaL  ++k  +l e   + ++ ka +l ++ +  +alk  +k+ +e
  gi|15669130|ref|NP_247935.1| 159 ANMLRKLGRYEEALACVNKVLELKEndtNAIYLKALILNRIGNCDEALKYYEKLIDE 215
                                   55677999*******999988555421268999**************9998887665 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.024
                  SRP_TPR_like  26 klekyeeaLkllkkgsals...edvrfEkaYvlYklkkykkalkil 68 
                                   k +k+eeaLk+ +k+ +l     +    ka vl kl + +++ +  
  gi|15669130|ref|NP_247935.1| 267 KQNKFEEALKYYNKAIQLMphhTKALLAKARVLEKLGRIEESIECY 312
                                   679*********9998554111345578999999999999887665 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.49   2.1e+02      42      64 ..      86     108 ..      72     119 .. 0.65
   2 !   13.3   0.2   9.1e-05      0.04      80     183 ..     221     311 ..     155     317 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.49
                      TPR_MalT  42 atavlGeasllqGdleaAlqalq 64 
                                   a+a+lG  + l G++++Al+ ++
  gi|15669130|ref|NP_247935.1|  86 AYALLGQLYELLGNFDNALECYE 108
                                   45555555555555555555444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 9.1e-05
                      TPR_MalT  80 llallqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlepeaa 160
                                   +  ++  + + +  ++L++A++  e++l+l ++       ++ ++    ++l+  +n++eeA ++ +++i+l  ++     
  gi|15669130|ref|NP_247935.1| 221 IEVIREAIYLSFLFNKLDKAEKYIEMGLKLRPDD------ASLWY--FKGKLYEKQNKFEEALKYYNKAIQLMPHH----- 288
                                   5555555566666677777777777777754443......33344..33788888888888888888888888777..... PP

                      TPR_MalT 161 ldayvllarialaqGdleeAetl 183
                                   ++a+++ ar+    G++ee+ + 
  gi|15669130|ref|NP_247935.1| 289 TKALLAKARVLEKLGRIEESIEC 311
                                   66666666777777777666555 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       9.1     4e+03      10      27 ..      61      78 ..      60      81 .. 0.80
   2 ?    2.2   0.1      0.58   2.5e+02       9      25 ..      93     109 ..      85     112 .. 0.80
   3 ?   -0.4   0.1         4   1.8e+03      10      27 ..     128     145 ..     126     147 .. 0.82
   4 ?    4.5   0.1      0.11        49      10      27 ..     162     179 ..     160     182 .. 0.81
   5 ?    5.8   0.0     0.043        19      12      28 ..     198     214 ..     195     215 .. 0.86
   6 ?    5.8   0.1     0.044        19      10      25 ..     265     280 ..     263     284 .. 0.87
   7 ?    3.0   0.0      0.34   1.5e+02      10      25 ..     299     314 ..     297     318 .] 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 9.1
                           PPR 10 ycknGkleeAlelfkeMk 27
                                  ++  G++ + +e+++++ 
  gi|15669130|ref|NP_247935.1| 61 LAILGDINKSIECLEDIT 78
                                  566899999999999876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.58
                           PPR   9 gycknGkleeAlelfke 25 
                                    y   G+++ Ale++++
  gi|15669130|ref|NP_247935.1|  93 LYELLGNFDNALECYEK 109
                                   67778*********986 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 4
                           PPR  10 ycknGkleeAlelfkeMk 27 
                                   ++ +Gk++e l++ ++++
  gi|15669130|ref|NP_247935.1| 128 LGLSGKYDELLKCCDRLI 145
                                   6789*****999988876 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.11
                           PPR  10 ycknGkleeAlelfkeMk 27 
                                   + k G++eeAl + ++ +
  gi|15669130|ref|NP_247935.1| 162 LRKLGRYEEALACVNKVL 179
                                   6699*******9988866 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.043
                           PPR  12 knGkleeAlelfkeMke 28 
                                   + G+++eAl++++++++
  gi|15669130|ref|NP_247935.1| 198 RIGNCDEALKYYEKLID 214
                                   679**********9875 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.044
                           PPR  10 ycknGkleeAlelfke 25 
                                   y k +k+eeAl+++++
  gi|15669130|ref|NP_247935.1| 265 YEKQNKFEEALKYYNK 280
                                   8899**********97 PP

  == domain 7  score: 3.0 bits;  conditional E-value: 0.34
                           PPR  10 ycknGkleeAlelfke 25 
                                   + k G++ee +e++++
  gi|15669130|ref|NP_247935.1| 299 LEKLGRIEESIECYNK 314
                                   6699*********997 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.9   8.4e+02      10      36 ..      19      45 ..      14      56 .. 0.84
   2 ?    1.4   0.0      0.58   2.5e+02      10      37 ..      86     113 ..      81     124 .. 0.84
   3 ?   -0.3   0.0       1.9   8.2e+02       8      49 ..     118     159 ..     107     165 .. 0.74
   4 ?    5.3   0.1     0.035        15      10      37 ..     154     181 ..     141     193 .. 0.84
   5 ?    4.6   0.1     0.061        26      15      69 ..     193     246 ..     184     248 .. 0.83
   6 !    9.1   0.2    0.0025       1.1      15      56 ..     262     302 ..     253     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.9
                       DUF5113 10 dYanlayylnvegeyeeALeyldsale 36
                                  +Y    y++  +g+  e+L yld+ale
  gi|15669130|ref|NP_247935.1| 19 TYLIKSYEYRDRGNLLESLYYLDKALE 45
                                  57777888899999999********97 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.58
                       DUF5113  10 dYanlayylnvegeyeeALeyldsaley 37 
                                   +Ya l++ +   g++++ALe+ ++ l +
  gi|15669130|ref|NP_247935.1|  86 AYALLGQLYELLGNFDNALECYEKSLGI 113
                                   6999999999999999999999998865 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.9
                       DUF5113   8 andYanlayylnvegeyeeALeyldsaleylNahyekYakkk 49 
                                   a ++   + +l  +g+y+e L++ d  +++  ++   Y  k+
  gi|15669130|ref|NP_247935.1| 118 ATAFFLKVLCLGLSGKYDELLKCCDRLISFAPNFIPAYIIKA 159
                                   45555668888999*********9999988777777776655 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.035
                       DUF5113  10 dYanlayylnvegeyeeALeyldsaley 37 
                                   +Y   a++l   g+yeeAL++++++le+
  gi|15669130|ref|NP_247935.1| 154 AYIIKANMLRKLGRYEEALACVNKVLEL 181
                                   677888899999*************985 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.061
                       DUF5113  15 ayylnvegeyeeALeyldsaleylNahyekYakkkadtldklkmllegegeaael 69 
                                   a  ln  g+ +eAL+y ++ ++ lN  + +  +++   l+ l  +l+++++++e+
  gi|15669130|ref|NP_247935.1| 193 ALILNRIGNCDEALKYYEKLIDELNVTWIEVIREAI-YLSFLFNKLDKAEKYIEM 246
                                   5678999******************99999888885.787887777777777776 PP

  == domain 6  score: 9.1 bits;  conditional E-value: 0.0025
                       DUF5113  15 ayylnvegeyeeALeyldsaleylNahyekYakkkadtldkl 56 
                                   ++ +  ++++eeAL+y ++a++++ +h +    k+   l+kl
  gi|15669130|ref|NP_247935.1| 262 GKLYEKQNKFEEALKYYNKAIQLMPHHTKALLAKA-RVLEKL 302
                                   66778899****************99988777776.366555 PP

>> Nuc_rec_co-act  Nuclear receptor coactivator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   8.5e-06    0.0037       8      36 ..      88     115 ..      83     117 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.5e-06
                Nuc_rec_co-act   8 ALLdQLvslLkntDeigLeEiDraLGIpe 36 
                                   ALL QL+ lL n+D  +Le   + LGI e
  gi|15669130|ref|NP_247935.1|  88 ALLGQLYELLGNFD-NALECYEKSLGIEE 115
                                   9*************.9***********86 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.7   7.4e+02      45      78 ..      58      91 ..      40     112 .. 0.79
   2 !   11.7   0.0   0.00051      0.22      42      95 ..     156     207 ..     153     217 .. 0.84
   3 ?    2.1   0.0      0.51   2.2e+02       3      29 ..     291     317 ..     260     318 .] 0.79

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.7
                         TPR_5 45 assLRnlGeaeealaLLraeleapsdelddalaa 78
                                  a sL  lG+++++++ L++ +++++d +  al +
  gi|15669130|ref|NP_247935.1| 58 AISLAILGDINKSIECLEDITSNSNDPVAYALLG 91
                                  6788999999999999999888888887777755 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00051
                         TPR_5  42 iqLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgrereavs 95 
                                   i  a  LR lG+ eeala +++ le ++++  +a+  + aL+L   g   ea++
  gi|15669130|ref|NP_247935.1| 156 IIKANMLRKLGRYEEALACVNKVLELKENDT-NAI-YLKALILNRIGNCDEALK 207
                                   556889*****************99987775.455.589*********999997 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.51
                         TPR_5   3 aaFeragarDstGhedkavplYrraLa 29 
                                   a+ ++a + +  G+ +++++ Y++aL+
  gi|15669130|ref|NP_247935.1| 291 ALLAKARVLEKLGRIEESIECYNKALD 317
                                   566677777777777788888887776 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.43   1.9e+02     108     147 ..       7      46 ..       1     117 [. 0.59
   2 !   12.5   0.4   0.00021     0.092     145     198 ..     165     219 ..      71     230 .. 0.88
   3 ?    6.8   0.3     0.011       4.8     163     209 ..     253     298 ..     231     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.43
                       DUF2225 108 elkkekkskkAklalrlAWlyrdkedeekeklflkkAlel 147
                                   +lk+ ++     ++l  ++ yrd ++  +++++l kAlel
  gi|15669130|ref|NP_247935.1|   7 KLKETSDVLLSLTYLIKSYEYRDRGNLLESLYYLDKALEL 46 
                                   4555555555666666677788888888888888888875 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00021
                       DUF2225 145 lelykeayekesfpve.gideatvlYLiaeLerrlgnkeealrwlskvigskkas 198
                                   l  y+ea+ + ++  e + ++++ +YL a    r+gn +eal++++k+i++ ++ 
  gi|15669130|ref|NP_247935.1| 165 LGRYEEALACVNKVLElKENDTNAIYLKALILNRIGNCDEALKYYEKLIDELNVT 219
                                   56799999999998885666777**************************987765 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.011
                       DUF2225 163 deatvlYLiaeLerrlgnkeealrwlskvigskkaskpskikdkare 209
                                   d+a++ Y  ++L  +  + eeal++++k i+    +  ++++ kar 
  gi|15669130|ref|NP_247935.1| 253 DDASLWYFKGKLYEKQNKFEEALKYYNKAIQLMPHHT-KALLAKARV 298
                                   5677889999999999999999999999998776666.677777776 PP

>> Kinesin_assoc  Kinesin-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.3     1e+03      97     130 ..     159     192 ..     145     201 .. 0.84
   2 !   14.9   0.0     5e-05     0.022     101     153 ..     204     261 ..     197     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.3
                 Kinesin_assoc  97 eeaierlketekiiaelnetWeeklrkteairle 130
                                    +++ +l   e  +a +n+  e k   t+ai l+
  gi|15669130|ref|NP_247935.1| 159 ANMLRKLGRYEEALACVNKVLELKENDTNAIYLK 192
                                   5678899999999****************99885 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 5e-05
                 Kinesin_assoc 101 erlketekiiaelnetWeeklrkteai.....rlereallaelGvairedGGtlGvfs 153
                                   e lk  ek+i eln tW e +r++  +     +l++ +   e+G+ +r d  +l  f 
  gi|15669130|ref|NP_247935.1| 204 EALKYYEKLIDELNVTWIEVIREAIYLsflfnKLDKAEKYIEMGLKLRPDDASLWYFK 261
                                   679999****************87654444447899999999**99999988887765 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       8.5   3.7e+03      22      34 ..      98     110 ..      95     114 .. 0.87
   2 ?   -1.2   0.0       5.5   2.4e+03      21      32 ..     131     142 ..     126     147 .. 0.82
   3 !    8.4   0.0    0.0056       2.4      14      35 ..     158     179 ..     150     191 .. 0.86
   4 ?    0.4   0.1       1.8   7.9e+02      22      38 ..     269     285 ..     264     297 .. 0.81
   5 ?    3.9   0.1      0.14        62      15      34 ..     296     315 ..     288     318 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 8.5
                     NRBF2_MIT  22 Gkyeeaischkka 34 
                                   G +++a+ c++k+
  gi|15669130|ref|NP_247935.1|  98 GNFDNALECYEKS 110
                                   899******9996 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.5
                     NRBF2_MIT  21 aGkyeeaischk 32 
                                   +Gky+e + c  
  gi|15669130|ref|NP_247935.1| 131 SGKYDELLKCCD 142
                                   79****999965 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0056
                     NRBF2_MIT  14 kadrllaaGkyeeaischkkaa 35 
                                   ka+ l   G+yeea++c +k  
  gi|15669130|ref|NP_247935.1| 158 KANMLRKLGRYEEALACVNKVL 179
                                   78899999*********99975 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.8
                     NRBF2_MIT  22 Gkyeeaischkkaaayl 38 
                                    k+eea+  ++ka + +
  gi|15669130|ref|NP_247935.1| 269 NKFEEALKYYNKAIQLM 285
                                   599****9999998766 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.14
                     NRBF2_MIT  15 adrllaaGkyeeaischkka 34 
                                   a  l   G+ ee+i c++ka
  gi|15669130|ref|NP_247935.1| 296 ARVLEKLGRIEESIECYNKA 315
                                   55566789***********9 PP

>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       1.6   6.8e+02      20      37 ..      30      47 ..      22      48 .. 0.78
   2 ?    1.9   0.4      0.89   3.9e+02       2      32 ..      85     109 ..      84     111 .. 0.71
   3 ?    3.3   0.0      0.34   1.5e+02      22      32 ..     201     211 ..     189     215 .. 0.84
   4 !   12.6   0.7    0.0004      0.18      11      35 ..     257     283 ..     255     284 .. 0.81
   5 ?   -1.0   0.0       7.3   3.2e+03      24      35 ..     306     317 ..     304     318 .] 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.6
                          Sel1 20 pkDpekAiewyekAAeqG 37
                                    +  + ++++ kA e++
  gi|15669130|ref|NP_247935.1| 30 RGNLLESLYYLDKALELN 47
                                  4488899*******9875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.89
                          Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyek 32 
                                    A++ LG  +  l+ l    + + A+e+yek
  gi|15669130|ref|NP_247935.1|  85 VAYALLG--Q--LYEL--LGNFDNALECYEK 109
                                   5777788..7..5554..6788888888888 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.34
                          Sel1  22 DpekAiewyek 32 
                                   + ++A+++yek
  gi|15669130|ref|NP_247935.1| 201 NCDEALKYYEK 211
                                   7789******9 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.0004
                          Sel1  11 ylylnGlg.vpkD.pekAiewyekAAe 35 
                                   ++y++G+  ++++  e+A+++y kA +
  gi|15669130|ref|NP_247935.1| 257 LWYFKGKLyEKQNkFEEALKYYNKAIQ 283
                                   467****7688896777********75 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 7.3
                          Sel1  24 ekAiewyekAAe 35 
                                   e+ ie+y kA +
  gi|15669130|ref|NP_247935.1| 306 EESIECYNKALD 317
                                   7899*****976 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00075      0.33      69     126 ..     159     216 ..     142     219 .. 0.89
   2 ?    4.3   0.1      0.11        49      77     122 ..     270     315 ..     261     318 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00075
                                   HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          BTAD  69 aeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlL 126
                                   a+++ +lGr+eeala  ++ ++++  + ++  +  + l r G+  eAL++Ye+l + L
  gi|15669130|ref|NP_247935.1| 159 ANMLRKLGRYEEALACVNKVLELKENDTNAIYLKALILNRIGNCDEALKYYEKLIDEL 216
                                   566779**********************************************998766 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.11
                                   -HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          BTAD  77 raeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                   + eeal+++++++++ P++ ++  +  r l ++Gr +e +e Y+++
  gi|15669130|ref|NP_247935.1| 270 KFEEALKYYNKAIQLMPHHTKALLAKARVLEKLGRIEESIECYNKA 315
                                   66899999999************9*****************99986 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.29   1.3e+02     127     173 ..      65     111 ..      14     125 .. 0.74
   2 ?    0.1   0.0       1.3   5.6e+02     122     176 ..     161     216 ..     157     230 .. 0.68
   3 !    9.8   0.1    0.0014      0.61     151     184 ..     260     293 ..     234     317 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.29
                        TPR_21 127 kkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAl 173
                                   +++++ ++ Le+ ++++ +  +  l G ++   g++d+A + Y+++l
  gi|15669130|ref|NP_247935.1|  65 GDINKSIECLEDITSNSNDPVAYALLGQLYELLGNFDNALECYEKSL 111
                                   55566666677777777777777777777777777777777777766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                        TPR_21 122 vllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                   +l + + y+eAl+ ++++ e ++ +  +  l+  il + g+ deA + Y++ +++l
  gi|15669130|ref|NP_247935.1| 161 MLRKLGRYEEALACVNKVLElKENDTNAIYLKALILNRIGNCDEALKYYEKLIDEL 216
                                   56667778888888877644245555555666667777777777777777766655 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0014
                        TPR_21 151 lrGDilvaqgkldeAraaYqaAlaaleekarell 184
                                    +G ++ +q+k++eA + Y++A++ + +++++ll
  gi|15669130|ref|NP_247935.1| 260 FKGKLYEKQNKFEEALKYYNKAIQLMPHHTKALL 293
                                   69**********************9999975554 PP

>> DUF3808  Protein of unknown function (DUF3808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.2   1.8e+03     258     300 ..      40      81 ..      27      85 .. 0.78
   2 ?   -1.6   0.0         2   8.6e+02     276     296 ..      91     111 ..      88     146 .. 0.78
   3 ?   -0.6   0.0      0.95   4.2e+02     275     302 ..     158     185 ..     154     216 .. 0.58
   4 ?    0.1   0.0      0.59   2.6e+02     276     307 ..     193     224 ..     188     233 .. 0.82
   5 ?    6.9   0.2    0.0051       2.2     256     301 ..     242     287 ..     230     318 .] 0.65

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.2
                       DUF3808 258 LlksrkrfPksalwllfearieslkgnldeAlelleeiieesq 300
                                   L k++++ P+ +   + +a  +++ g++++++e le+i+ +++
  gi|15669130|ref|NP_247935.1|  40 LDKALELNPDFKFAKFLKAISLAILGDINKSIECLEDIT-SNS 81 
                                   667777778888888899999999999999999999887.444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                       DUF3808 276 arieslkgnldeAlelleeii 296
                                   +++++l gn+d+Ale +e+++
  gi|15669130|ref|NP_247935.1|  91 GQLYELLGNFDNALECYEKSL 111
                                   6888999*********99987 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.95
                       DUF3808 275 earieslkgnldeAlelleeiieesqse 302
                                   +a +++  g+ +eAl+ +++++e ++++
  gi|15669130|ref|NP_247935.1| 158 KANMLRKLGRYEEALACVNKVLELKEND 185
                                   6777888888888888887776433333 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.59
                       DUF3808 276 arieslkgnldeAlelleeiieesqselkqvk 307
                                   a i+   gn deAl+++e++i+e ++ + +v 
  gi|15669130|ref|NP_247935.1| 193 ALILNRIGNCDEALKYYEKLIDELNVTWIEVI 224
                                   556677799************99999987775 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0051
                       DUF3808 256 elLlksrkrfPksalwllfearieslkgnldeAlelleeiieesqs 301
                                   + ++  +k+ P+ a +  f++++++ + +++eAl++++++i+   +
  gi|15669130|ref|NP_247935.1| 242 KYIEMGLKLRPDDASLWYFKGKLYEKQNKFEEALKYYNKAIQLMPH 287
                                   5555555555655555556777777777777777777777644433 PP

>> BLI1  BLOC-1 interactor 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       2.7   1.2e+03      59      89 ..      49      79 ..       6      84 .. 0.79
   2 ?   14.2   0.6   0.00012     0.054      39      92 ..     166     217 ..     136     228 .. 0.80
   3 ?    0.6   0.4       2.1     9e+02      63     103 ..     257     297 ..     223     303 .. 0.73
   4 ?    2.4   0.7      0.54   2.4e+02      65      89 ..     293     317 ..     255     318 .] 0.65

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.7
                          BLI1 59 elkalkalkkkklkkleelekkveyyeklld 89
                                  ++k  k lk  +l  l++++k +e  e++  
  gi|15669130|ref|NP_247935.1| 49 DFKFAKFLKAISLAILGDINKSIECLEDITS 79
                                  4555677999999999999999999998765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00012
                          BLI1  39 eenekWleeikekyklkdedelkalkalkkkklkkleelekkveyyeklldele 92 
                                      e+ l+ +++  +lk++d+  +   lk   l+++++ ++ ++yyekl+del+
  gi|15669130|ref|NP_247935.1| 166 GRYEEALACVNKVLELKENDT--NAIYLKALILNRIGNCDEALKYYEKLIDELN 217
                                   556667777778888888876..3457999***********************8 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 2.1
                          BLI1  63 lkalkkkklkkleelekkveyyeklldeleefqdelevktk 103
                                   l  +k k  +k +++e+ ++yy+k ++ +   ++ l  k++
  gi|15669130|ref|NP_247935.1| 257 LWYFKGKLYEKQNKFEEALKYYNKAIQLMPHHTKALLAKAR 297
                                   55677788889999999999999988877777666666655 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.54
                          BLI1  65 alkkkklkkleelekkveyyeklld 89 
                                     k + l+kl+++e+ +e y+k ld
  gi|15669130|ref|NP_247935.1| 293 LAKARVLEKLGRIEESIECYNKALD 317
                                   3467788999999999999988665 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.18        79     186     293 ..      68     177 ..      50     190 .. 0.72
   2 ?    9.6   0.3   0.00095      0.41     179     293 ..     162     280 ..     136     301 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHHTT-..GGGHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH- CS
                         ChAPs 186 dralellekLkeee..pevvillarvllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksa 264
                                   ++++e le +++++  p + +ll +++ l  +  +a++  +++l  eek a    l++  l    k++  l++ +r +++a
  gi|15669130|ref|NP_247935.1|  68 NKSIECLEDITSNSndPVAYALLGQLYELLGNFDNALECYEKSLGIEEKFATAFFLKVLCLGLSGKYDELLKCCDRLISFA 148
                                   555666666654432366677777777666666677777777776666666666666666666677777789999999999 PP

                                   TT-HHHHHHHHHHHHHTT-HHHHHHHHHT CS
                         ChAPs 265 PsefktWalLvkvYikledienALltLNs 293
                                   P+    +++ +++  kl+ +e+AL  +N 
  gi|15669130|ref|NP_247935.1| 149 PNFIPAYIIKANMLRKLGRYEEALACVNK 177
                                   99888888889999999999999998886 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00095
                                   HHHHT-HHHHHHHHHH...HHTT-GGGHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-H.HHHH..HHHHHHHHHSS--HHH CS
                         ChAPs 179 vrltkrydralellek...LkeeepevvillarvllladeEvdavkllneeleeeekd.aelL..llqaefllskkkeelA 253
                                   +r   ry++al  ++k   Lke++ +++ l a +l    +  +a+k  ++ ++e + +  e++   +   fl +k   + A
  gi|15669130|ref|NP_247935.1| 162 LRKLGRYEEALACVNKvleLKENDTNAIYLKALILNRIGNCDEALKYYEKLIDELNVTwIEVIreAIYLSFLFNKL--DKA 240
                                   4445555554444443111455555554444444433334444555544444444433233331134445555544..568 PP

                                   HHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHT CS
                         ChAPs 254 levakravksaPsefktWalLvkvYikledienALltLNs 293
                                    +  + + k+ P + + W+   k Y k++ +e+AL   N 
  gi|15669130|ref|NP_247935.1| 241 EKYIEMGLKLRPDDASLWYFKGKLYEKQNKFEEALKYYNK 280
                                   9999999****************************98884 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.17        77      15      32 ..      98     115 ..      87     119 .. 0.86
   2 ?   -2.2   0.0       6.9     3e+03      16      32 ..     167     183 ..     166     184 .. 0.68
   3 ?   -2.0   0.0       5.7   2.5e+03      26      34 ..     204     212 ..     202     214 .. 0.86
   4 ?    5.5   0.0     0.026        11      14      30 ..     268     284 ..     267     286 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.17
                      SHNi-TPR  15 enFpqAveDlrkaLeLre 32 
                                   +nF+ A+e ++k+L + e
  gi|15669130|ref|NP_247935.1|  98 GNFDNALECYEKSLGIEE 115
                                   69***********97755 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.9
                      SHNi-TPR  16 nFpqAveDlrkaLeLre 32 
                                   ++++A+   +k LeL+e
  gi|15669130|ref|NP_247935.1| 167 RYEEALACVNKVLELKE 183
                                   78888776666677776 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.7
                      SHNi-TPR  26 kaLeLreql 34 
                                   +aL+++e+l
  gi|15669130|ref|NP_247935.1| 204 EALKYYEKL 212
                                   89***9997 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.026
                      SHNi-TPR  14 nenFpqAveDlrkaLeL 30 
                                   +++F++A++ ++ka++L
  gi|15669130|ref|NP_247935.1| 268 QNKFEEALKYYNKAIQL 284
                                   689***********998 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.53   2.3e+02      25      55 ..     108     144 ..      54     148 .. 0.68
   2 ?    7.4   1.8     0.005       2.2     154     290 ..     159     293 ..     154     310 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.53
                                   ......TSSSS--CCCHCCCCHH.--CCHCHHCCCHC CS
                           FAT  25 k.....kdspdkaffeailalhr.nqfdeakelieka 55 
                                   +     ++++  aff  +l+l    ++de+ +++++ 
  gi|15669130|ref|NP_247935.1| 108 EkslgiEEKFATAFFLKVLCLGLsGKYDELLKCCDRL 144
                                   2333456666677777777766657777777777765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.005
                                   CCCHCHHHHCCSTTHHCCCCCHCTT.....TT.TSSCCCHHHHHHHCCHHHHHSSCCHHHHCCTSSCCC.SS-SS---... CS
                           FAT 154 anlarksgrlslAekaLkelleedpeewlprappevvyaylKylwssgeqkealqkLreftsellekke.elqsgleaq.. 231
                                   an  rk gr++ A    +++le ++++       + +y ++ +l   g+++eal+  ++ ++el       ++++++ +  
  gi|15669130|ref|NP_247935.1| 159 ANMLRKLGRYEEALACVNKVLELKEND------TNAIYLKALILNRIGNCDEALKYYEKLIDELNVTWIeVIREAIYLSfl 233
                                   777888888888888888887777733......345777777777777788888777777775533322323333333333 PP

                                   ...................HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTC CS
                           FAT 232 ........keptnleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykawh 290
                                           k  +   +++   a +  +kG+  e+ +k       +ee+l++y +a ++ p+ +ka  
  gi|15669130|ref|NP_247935.1| 234 fnkldkaeKYIEMGLKLRPDDASLWYFKGKLYEKQNK-------FEEALKYYNKAIQLMPHHTKALL 293
                                   3333322112222223333335555555555555555.......99**********99999999865 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.2   5.4e+02       4      14 ..      35      45 ..      30      47 .. 0.85
   2 ?    1.8   1.7      0.43   1.9e+02      23      29 ..      88      94 ..      67     116 .. 0.84
   3 ?    6.2   0.4     0.018       7.7       1      48 [.     167     215 ..     167     216 .. 0.87
   4 ?    0.9   0.2      0.81   3.5e+02      28      39 ..     257     268 ..     256     271 .. 0.89
   5 ?    4.5   0.1      0.06        26       2      14 ..     271     283 ..     270     288 .. 0.90
   6 ?    2.7   0.1      0.21        93      32      47 ..     295     310 ..     292     312 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.2
                                  HHHHHHHHHHH CS
                      HTH_Bact  4 eaLeqvnkAie 14
                                  e+L++ +kA+e
  gi|15669130|ref|NP_247935.1| 35 ESLYYLDKALE 45
                                  79999999988 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.43
                                  TTHHHHH CS
                      HTH_Bact 23 sLlGQLy 29
                                  +LlGQLy
  gi|15669130|ref|NP_247935.1| 88 ALLGQLY 94
                                  89****9 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.018
                                   -HHHHHHHHHHHHHHHHHTTB-TTHHHHHHHH.HHHHHHTT--HHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAieiSirinsMsLlGQLyYqk.gecleklgfseeeIke 48 
                                   rYeeaL  vnk +e+  +  + + l  L   + g+c e l++ e+ I e
  gi|15669130|ref|NP_247935.1| 167 RYEEALACVNKVLELKENDTNAIYLKALILNRiGNCDEALKYYEKLIDE 215
                                   7*************99999999999988888878999999998887766 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.81
                                   HHHHHHHHHHHT CS
                      HTH_Bact  28 LyYqkgeclekl 39 
                                   L+Y kg++ ek 
  gi|15669130|ref|NP_247935.1| 257 LWYFKGKLYEKQ 268
                                   89********95 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.06
                                   HHHHHHHHHHHHH CS
                      HTH_Bact   2 YeeaLeqvnkAie 14 
                                   +eeaL++ nkAi+
  gi|15669130|ref|NP_247935.1| 271 FEEALKYYNKAIQ 283
                                   79**********8 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.21
                                   HHHHHHHTT--HHHHH CS
                      HTH_Bact  32 kgecleklgfseeeIk 47 
                                   k+  leklg  ee+I+
  gi|15669130|ref|NP_247935.1| 295 KARVLEKLGRIEESIE 310
                                   8999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              41  [number of targets reported over threshold]
# CPU time: 0.79u 0.35s 00:00:01.14 Elapsed: 00:00:00.58
# Mc/sec: 1649.81
//
Query:       gi|15669131|ref|NP_247936.1|  [L=338]
Description: hypothetical protein MJ_0941 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-43  145.3  28.4    5.5e-10   38.6   0.4    8.8  9  TPR_1         Tetratricopeptide repeat
    1.5e-40  134.0  27.7    1.4e-08   34.2   0.4    9.1  9  TPR_2         Tetratricopeptide repeat
      8e-39  128.6  23.2    4.6e-08   32.7   0.2    8.7  9  TPR_8         Tetratricopeptide repeat
    2.4e-30  103.9  13.6    1.2e-07   31.3   0.1    8.7  9  TPR_11        TPR repeat
    1.5e-28   97.0   5.7    3.4e-05   24.3   0.1    9.0  9  TPR_14        Tetratricopeptide repeat
    1.1e-27   94.0   5.5     0.0012   18.8   0.1    7.6  7  TPR_7         Tetratricopeptide repeat
    7.5e-27   93.4  15.4    4.1e-10   39.8   0.4    6.8  6  TPR_12        Tetratricopeptide repeat
    2.4e-25   88.9   2.4    1.5e-08   35.2   0.0    5.7  5  TPR_16        Tetratricopeptide repeat
    3.2e-24   83.5   1.5     0.0022   18.3   0.0    6.6  6  TPR_17        Tetratricopeptide repeat
    9.4e-23   80.5   7.5    1.9e-05   25.1   0.2    5.7  6  TPR_19        Tetratricopeptide repeat
      6e-22   77.6   2.1    4.1e-06   26.8   0.1    5.6  6  TPR_9         Tetratricopeptide repeat
    6.2e-19   67.3   9.7     0.0078   16.8   0.0    7.1  7  TPR_6         Tetratricopeptide repeat
    6.1e-18   65.0   0.1      6e-08   32.0   0.2    4.5  5  NARP1         NMDA receptor-regulated protein 1
    4.5e-17   62.1  12.8    1.5e-06   28.3   0.3    4.4  4  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    2.8e-11   43.2   0.0      0.052   12.8   0.0    4.4  4  TPR_15        Tetratricopeptide repeat
    2.5e-09   37.4   4.7       0.28   11.2   0.0    6.2  6  DUF3856       Domain of Unknown Function (DUF3856)
    9.5e-09   35.2  12.1     0.0019   18.2   0.3    5.9  7  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
    3.2e-08   33.3  13.9          2    8.9   0.2    7.2  6  PPR           PPR repeat
    6.4e-08   32.2  11.8       0.34   10.8   0.1    7.0  7  TPR_10        Tetratricopeptide repeat
      8e-08   32.2  10.3      0.064   13.0   0.2    5.7  6  RPN7          26S proteasome subunit RPN7
      9e-08   32.7   0.8       0.13   12.7   0.0    3.2  3  BTAD          Bacterial transcriptional activator domain
      2e-07   30.7   0.0       0.11   11.8   0.0    3.9  4  TPR_MalT      MalT-like TPR region
    1.2e-05   25.1   2.8       0.16   11.7   0.1    3.9  3  DUF2225       Uncharacterized protein conserved in bacteria (
    2.3e-05   23.4   0.3       0.78    8.4   0.0    4.5  3  DUF3808       Protein of unknown function (DUF3808)
    5.9e-05   23.3   0.0         38    5.3   0.0    5.9  6  TPR_4         Tetratricopeptide repeat
    7.2e-05   22.8  19.4     0.0068   16.5   0.6    6.3  7  MIT           MIT (microtubule interacting and transport) dom
    7.3e-05   22.4   0.3        1.5    8.5   0.1    4.3  4  HrpB1_HrpK    Bacterial type III secretion protein (HrpB1_Hrp
    0.00012   21.3   0.3        0.1   11.6   0.0    2.1  2  ChAPs         ChAPs (Chs5p-Arf1p-binding proteins)
    0.00016   21.7   3.1    0.00081   19.4   0.2    2.7  2  SRP_TPR_like  Putative TPR-like repeat
    0.00039   19.7   0.6     0.0021   17.4   0.2    2.4  2  FAT           FAT domain
    0.00058   19.4   6.1         12    5.6   0.0    5.9  6  HTH_Bact      Helix-turn-helix bacterial domain
     0.0015   18.2   2.8         16    5.1   0.1    4.6  5  TPR_21        Tetratricopeptide repeat-like domain
     0.0032   16.9   0.3        1.3    8.4   0.0    3.1  4  Coatomer_E    Coatomer epsilon subunit
     0.0073   15.8   3.2        1.3    8.4   0.4    4.1  5  SNAP          Soluble NSF attachment protein, SNAP
     0.0075   16.5   1.0        2.2    8.6   0.0    4.4  5  TPR_5         Tetratrico peptide repeat
  ------ inclusion threshold ------
      0.021   15.1   3.6         28    5.0   0.0    4.7  4  NRBF2_MIT     MIT domain of nuclear receptor-binding factor 2
      0.028   12.9   1.0       0.98    7.8   0.0    2.8  3  Cohesin_load  Cohesin loading factor
      0.031   15.0  10.6         11    6.9   0.1    5.8  5  Sel1          Sel1 repeat
       0.11   10.8   0.0        2.5    6.4   0.0    2.3  2  SMG1          Serine/threonine-protein kinase smg-1
       0.16   11.8   6.1       0.65    9.9   2.3    3.5  3  Clathrin      Region in Clathrin and VPS


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1    0.0014      0.64      15      34 .]      43      62 ..      40      62 .. 0.92
   2 !   11.4   0.1   0.00049      0.22       3      29 ..      65      91 ..      63      96 .. 0.87
   3 !   15.9   0.0   1.8e-05    0.0082       7      30 ..     103     126 ..      97     129 .. 0.86
   4 ?    5.8   0.1     0.028        13      10      34 .]     140     164 ..     139     164 .. 0.87
   5 !   29.1   0.0   1.3e-09   5.7e-07       4      34 .]     168     198 ..     165     198 .. 0.93
   6 !   23.2   0.2   9.5e-08   4.2e-05       3      26 ..     201     224 ..     200     227 .. 0.94
   7 ?   -0.6   0.1         3   1.3e+03      14      33 ..     247     266 ..     245     267 .. 0.77
   8 !   38.6   0.4   1.2e-12   5.5e-10       3      34 .]     270     301 ..     268     301 .. 0.95
   9 !   25.9   0.7   1.3e-08   5.8e-06       2      29 ..     303     330 ..     302     335 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0014
                                  T-HHHHHHHHHHHHHHSTTH CS
                         TPR_1 15 gkydeAleyyekALelnPnn 34
                                  g++ +Al y +kALel+P++
  gi|15669131|ref|NP_247936.1| 43 GNLIKALYYVDKALELEPDF 62
                                  8888**************97 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00049
                                  HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_1  3 alynlGnayfklgkydeAleyyekALe 29
                                  al+ +G+a+  +g+ +eA+  +e+ L+
  gi|15669131|ref|NP_247936.1| 65 ALFLKGLALSAKGEIKEAITTFEELLS 91
                                  899******************998665 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1   7 lGnayfklgkydeAleyyekALel 30 
                                    G++y   g+ deAl++y+kAL +
  gi|15669131|ref|NP_247936.1| 103 VGQLYGMSGNCDEALKCYNKALGI 126
                                   5999*****************965 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.028
                                   HHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1  10 ayfklgkydeAleyyekALelnPnn 34 
                                   ++  lg+yde l++y+++L+  Pn+
  gi|15669131|ref|NP_247936.1| 140 CLEFLGEYDELLKCYNEVLTYTPNF 164
                                   77789**************987775 PP

  == domain 5  score: 29.1 bits;  conditional E-value: 1.3e-09
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                   +  ++ +++klg+y++Al + ++ALel P++
  gi|15669131|ref|NP_247936.1| 168 WVKKAEILRKLGRYEDALLCLNRALELKPHD 198
                                   77899************************86 PP

  == domain 6  score: 23.2 bits;  conditional E-value: 9.5e-08
                                   HHHHHHHHHHHTT-HHHHHHHHHH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyek 26 
                                   aly +G+++ ++gk+ eAle+++k
  gi|15669131|ref|NP_247936.1| 201 ALYLKGVLLKRMGKFREALECFKK 224
                                   9**********************9 PP

  == domain 7  score: -0.6 bits;  conditional E-value: 3
                                   TT-HHHHHHHHHHHHHHSTT CS
                         TPR_1  14 lgkydeAleyyekALelnPn 33 
                                   l ++++A+ y +  Le++ +
  gi|15669131|ref|NP_247936.1| 247 LDDLKDAERYINIGLEIRKD 266
                                   77889999998888888765 PP

  == domain 8  score: 38.6 bits;  conditional E-value: 1.2e-12
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                    +y +G +y +lgk+deAl++yek++el+P++
  gi|15669131|ref|NP_247936.1| 270 LWYFKGELYERLGKLDEALKCYEKVIELQPHY 301
                                   7*****************************97 PP

  == domain 9  score: 25.9 bits;  conditional E-value: 1.3e-08
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALe 29 
                                   kal  ++ +y ++g+ + A+eyy+kA+e
  gi|15669131|ref|NP_247936.1| 303 KALLSKARIYERQGNIEAAIEYYNKAVE 330
                                   8999**********************98 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.3   0.00055      0.25       6      33 ..      34      61 ..      29      62 .. 0.84
   2 !   15.0   0.1   4.5e-05      0.02       2      33 ..      64      95 ..      63      96 .. 0.91
   3 !   13.6   0.0   0.00013     0.056       3      28 ..      99     124 ..      97     129 .. 0.90
   4 ?    5.5   0.0     0.048        22      10      33 ..     140     163 ..     139     164 .. 0.88
   5 !   25.8   0.1   1.5e-08   6.8e-06       4      34 .]     168     198 ..     167     198 .. 0.94
   6 !   19.6   0.2   1.5e-06   0.00068       3      29 ..     201     227 ..     200     229 .. 0.94
   7 ?    0.8   0.0       1.6     7e+02      12      33 ..     245     266 ..     243     267 .. 0.82
   8 !   34.2   0.4   3.2e-11   1.4e-08       2      33 ..     269     300 ..     268     301 .. 0.95
   9 !   21.4   0.4     4e-07   0.00018       2      29 ..     303     330 ..     302     332 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00055
                         TPR_2  6 nlGlayyklgdyeeAleafekAleldPn 33
                                   +++  +  g++ +Al + +kAlel+P+
  gi|15669131|ref|NP_247936.1| 34 LRAYRELFEGNLIKALYYVDKALELEPD 61
                                  566777778******************8 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.5e-05
                         TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPn 33
                                   al+  Gla+ ++g+ +eA+  fe+ l+++ +
  gi|15669131|ref|NP_247936.1| 64 LALFLKGLALSAKGEIKEAITTFEELLSYESK 95
                                  589************************98765 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00013
                         TPR_2   3 alynlGlayyklgdyeeAleafekAl 28 
                                    +   G++y  +g+ +eAl++++kAl
  gi|15669131|ref|NP_247936.1|  99 TWVFVGQLYGMSGNCDEALKCYNKAL 124
                                   67888********************9 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.048
                         TPR_2  10 ayyklgdyeeAleafekAleldPn 33 
                                   +++ lg+y+e l++++++l + Pn
  gi|15669131|ref|NP_247936.1| 140 CLEFLGEYDELLKCYNEVLTYTPN 163
                                   56679999999***********98 PP

  == domain 5  score: 25.8 bits;  conditional E-value: 1.5e-08
                         TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +   +++++klg+ye+Al ++++Alel P++
  gi|15669131|ref|NP_247936.1| 168 WVKKAEILRKLGRYEDALLCLNRALELKPHD 198
                                   67789************************86 PP

  == domain 6  score: 19.6 bits;  conditional E-value: 1.5e-06
                         TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                                   aly  G ++ ++g++ eAle+f+k + 
  gi|15669131|ref|NP_247936.1| 201 ALYLKGVLLKRMGKFREALECFKKLID 227
                                   89**********************985 PP

  == domain 7  score: 0.8 bits;  conditional E-value: 1.6
                         TPR_2  12 yklgdyeeAleafekAleldPn 33 
                                   ++l+d+++A+++ +  le+  +
  gi|15669131|ref|NP_247936.1| 245 LALDDLKDAERYINIGLEIRKD 266
                                   6899********9988888765 PP

  == domain 8  score: 34.2 bits;  conditional E-value: 3.2e-11
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                    ++y  G++y++lg+++eAl+++ek++el P+
  gi|15669131|ref|NP_247936.1| 269 ALWYFKGELYERLGKLDEALKCYEKVIELQPH 300
                                   58*****************************8 PP

  == domain 9  score: 21.4 bits;  conditional E-value: 4e-07
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                   +al   +++y+++g+ e A+e+++kA+e
  gi|15669131|ref|NP_247936.1| 303 KALLSKARIYERQGNIEAAIEYYNKAVE 330
                                   577889********************97 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.48   2.2e+02      14      33 ..      42      61 ..      29      62 .. 0.83
   2 !   16.6   0.3   1.4e-05    0.0064       3      33 ..      65      95 ..      63      96 .. 0.93
   3 !   11.9   0.0   0.00046      0.21       4      31 ..     100     127 ..      99     130 .. 0.90
   4 ?    7.0   0.0     0.018         8      11      33 ..     141     163 ..     139     164 .. 0.91
   5 !   24.6   0.0   4.1e-08   1.8e-05       2      33 ..     166     197 ..     165     198 .. 0.95
   6 !   16.7   0.1   1.3e-05     0.006       3      28 ..     201     226 ..     200     227 .. 0.94
   7 ?   -1.4   0.0       8.5   3.8e+03      14      32 ..     247     265 ..     238     267 .. 0.66
   8 !   32.7   0.2     1e-10   4.6e-08       3      33 ..     270     300 ..     268     301 .. 0.94
   9 !   25.9   0.8   1.5e-08   6.7e-06       2      29 ..     303     330 ..     302     331 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.48
                                  TT-HHHHHHHHHHHHHHHHH CS
                         TPR_8 14 lgdyeeAkeyyekaleldpd 33
                                   g++ +A  y  kalel+pd
  gi|15669131|ref|NP_247936.1| 42 EGNLIKALYYVDKALELEPD 61
                                  577778888999*******8 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.4e-05
                                  HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpd 33
                                  a++++g++++ +g+++eA+ ++e+ l+++ +
  gi|15669131|ref|NP_247936.1| 65 ALFLKGLALSAKGEIKEAITTFEELLSYESK 95
                                  799************************9877 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00046
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                         TPR_8   4 yynlgsiylklgdyeeAkeyyekaleld 31 
                                   ++  g++y   g+ +eA ++y+kal ++
  gi|15669131|ref|NP_247936.1| 100 WVFVGQLYGMSGNCDEALKCYNKALGIE 127
                                   788899*******************997 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.018
                                   HHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8  11 ylklgdyeeAkeyyekaleldpd 33 
                                   ++ lg+y+e  ++y+++l++ p+
  gi|15669131|ref|NP_247936.1| 141 LEFLGEYDELLKCYNEVLTYTPN 163
                                   678****************9997 PP

  == domain 5  score: 24.6 bits;  conditional E-value: 4.1e-08
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   +++++++ i++klg+ye A  ++++alel+p 
  gi|15669131|ref|NP_247936.1| 166 PMWVKKAEILRKLGRYEDALLCLNRALELKPH 197
                                   79****************************96 PP

  == domain 6  score: 16.7 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekal 28 
                                   a+y++g +++ +g++ eA e+++k +
  gi|15669131|ref|NP_247936.1| 201 ALYLKGVLLKRMGKFREALECFKKLI 226
                                   89**********************98 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 8.5
                                   TT-HHHHHHHHHHHHHHHH CS
                         TPR_8  14 lgdyeeAkeyyekaleldp 32 
                                   l d++ A+ y++  le+++
  gi|15669131|ref|NP_247936.1| 247 LDDLKDAERYINIGLEIRK 265
                                   6666777776666666655 PP

  == domain 8  score: 32.7 bits;  conditional E-value: 1e-10
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   ++y +g +y+ lg+++eA ++yek++el+p 
  gi|15669131|ref|NP_247936.1| 270 LWYFKGELYERLGKLDEALKCYEKVIELQPH 300
                                   7****************************96 PP

  == domain 9  score: 25.9 bits;  conditional E-value: 1.5e-08
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                   +a++ +++iy+ +g++e+A+eyy+ka+e
  gi|15669131|ref|NP_247936.1| 303 KALLSKARIYERQGNIEAAIEYYNKAVE 330
                                   78999*********************97 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0065       2.9      18      42 .]      53      77 ..      42      77 .. 0.89
   2 !   14.0   0.0   6.8e-05      0.03       1      41 [.      70     110 ..      70     111 .. 0.89
   3 !   12.0   0.1   0.00028      0.13       6      25 ..     109     128 ..     104     136 .. 0.78
   4 !    8.1   0.0    0.0047       2.1       7      27 ..     144     164 ..     144     168 .. 0.93
   5 !   31.3   0.1   2.7e-10   1.2e-07       3      42 .]     174     213 ..     172     213 .. 0.96
   6 ?    3.3   0.0      0.14        64       7      21 ..     212     226 ..     209     227 .. 0.88
   7 ?    4.3   0.0     0.071        32      21      42 .]     261     282 ..     259     282 .. 0.95
   8 !   28.0   0.3   2.8e-09   1.3e-06       1      42 []     275     316 ..     275     316 .. 0.93
   9 !   10.5   2.0    0.0008      0.36       2      22 ..     310     330 ..     309     330 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0065
                        TPR_11 18 kkAlkldPdnaeayynLGlayykqG 42
                                   kAl+l Pd+  a++  Gla+ ++G
  gi|15669131|ref|NP_247936.1| 53 DKALELEPDFYLALFLKGLALSAKG 77
                                  59******************98887 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6.8e-05
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                   G a+ ++G+++eAi+ +++ l + ++n+  +   G++y + 
  gi|15669131|ref|NP_247936.1|  70 GLALSAKGEIKEAITTFEELLSYESKNPITWVFVGQLYGMS 110
                                   778889**********************9998888888765 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00028
                        TPR_11   6 eqGkyeeAieaYkkAlkldP 25 
                                     G+ +eA+++Y+kAl + +
  gi|15669131|ref|NP_247936.1| 109 MSGNCDEALKCYNKALGIEN 128
                                   57999**********97766 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0047
                        TPR_11   7 qGkyeeAieaYkkAlkldPdn 27 
                                   +G+y+e +++Y++ l ++P++
  gi|15669131|ref|NP_247936.1| 144 LGEYDELLKCYNEVLTYTPNF 164
                                   69*****************97 PP

  == domain 5  score: 31.3 bits;  conditional E-value: 2.7e-10
                        TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   +++++G+ye+A+ ++++Al+l+P + +a+y  G+++ ++G
  gi|15669131|ref|NP_247936.1| 174 ILRKLGRYEDALLCLNRALELKPHDKNALYLKGVLLKRMG 213
                                   89***********************************998 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.14
                        TPR_11   7 qGkyeeAieaYkkAl 21 
                                    Gk+ eA+e++kk +
  gi|15669131|ref|NP_247936.1| 212 MGKFREALECFKKLI 226
                                   69**********987 PP

  == domain 7  score: 4.3 bits;  conditional E-value: 0.071
                        TPR_11  21 lkldPdnaeayynLGlayykqG 42 
                                   l+++ d++ ++y  G++y ++G
  gi|15669131|ref|NP_247936.1| 261 LEIRKDDVALWYFKGELYERLG 282
                                   89******************98 PP

  == domain 8  score: 28.0 bits;  conditional E-value: 2.8e-09
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   G +y  +Gk++eA+++Y+k ++l P +  a++  + +y +qG
  gi|15669131|ref|NP_247936.1| 275 GELYERLGKLDEALKCYEKVIELQPHYIKALLSKARIYERQG 316
                                   5567779**********************************9 PP

  == domain 9  score: 10.5 bits;  conditional E-value: 0.0008
                        TPR_11   2 dayyeqGkyeeAieaYkkAlk 22 
                                   ++y  qG++e+Aie Y+kA++
  gi|15669131|ref|NP_247936.1| 310 RIYERQGNIEAAIEYYNKAVE 330
                                   57778**************86 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2     0.023        11       9      42 ..      35      70 ..      27      72 .. 0.78
   2 !    8.6   0.0    0.0083       3.7       6      42 ..      68     104 ..      65     106 .. 0.80
   3 ?    4.1   0.0      0.23     1e+02       8      31 ..     104     127 ..      97     140 .. 0.78
   4 ?    5.8   0.0     0.065        29      11      42 ..     141     172 ..     131     173 .. 0.85
   5 !   17.6   0.1   1.1e-05    0.0049       3      42 ..     167     206 ..     165     208 .. 0.90
   6 ?    7.6   0.0     0.017       7.6       3      29 ..     201     227 ..     199     231 .. 0.89
   7 !   14.9   0.1     8e-05     0.036       3      44 .]     236     277 ..     234     277 .. 0.90
   8 !   24.3   0.1   7.5e-08   3.4e-05       2      43 ..     269     310 ..     268     311 .. 0.93
   9 !   16.2   0.0   3.1e-05     0.014       3      29 ..     304     330 ..     302     338 .] 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.023
                        TPR_14  9 eallal..GdpdeAiallrralalaPddaeawllla 42
                                  +a+++l  G++ +A+ + ++al+l Pd+  a++l +
  gi|15669131|ref|NP_247936.1| 35 RAYRELfeGNLIKALYYVDKALELEPDFYLALFLKG 70
                                  444443339*******************99998765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0083
                        TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawllla 42 
                                   + + al a G+ +eAi+ ++++l+   +++ +w + +
  gi|15669131|ref|NP_247936.1|  68 LKGLALSAKGEIKEAITTFEELLSYESKNPITWVFVG 104
                                   557899*****************97777777776655 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.23
                        TPR_14   8 aeallalGdpdeAiallrralala 31 
                                   ++++  +G+ deA++++++al   
  gi|15669131|ref|NP_247936.1| 104 GQLYGMSGNCDEALKCYNKALGIE 127
                                   5666678999**********9665 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.065
                        TPR_14  11 llalGdpdeAiallrralalaPddaeawllla 42 
                                   l+ lG++de +++++++l   P++   w   a
  gi|15669131|ref|NP_247936.1| 141 LEFLGEYDELLKCYNEVLTYTPNFVPMWVKKA 172
                                   5669**************99999998888766 PP

  == domain 5  score: 17.6 bits;  conditional E-value: 1.1e-05
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                   ++ + ae+l+ lG++++A+ +l+ral+l P d  a++l +
  gi|15669131|ref|NP_247936.1| 167 MWVKKAEILRKLGRYEDALLCLNRALELKPHDKNALYLKG 206
                                   58889***************************99988776 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.017
                        TPR_14   3 allalaeallalGdpdeAiallrrala 29 
                                   al++ + +l + G+++eA+++++++++
  gi|15669131|ref|NP_247936.1| 201 ALYLKGVLLKRMGKFREALECFKKLID 227
                                   78888999***************9886 PP

  == domain 7  score: 14.9 bits;  conditional E-value: 8e-05
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaql 44 
                                   a + +++++lal+d+++A+++ +  l+   dd ++w++ ++l
  gi|15669131|ref|NP_247936.1| 236 AIRHAVSLMLALDDLKDAERYINIGLEIRKDDVALWYFKGEL 277
                                   556778999***************************999875 PP

  == domain 8  score: 24.3 bits;  conditional E-value: 7.5e-08
                        TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                   ++++  +e++++lG++deA+++++++++l+P    a+l  a+
  gi|15669131|ref|NP_247936.1| 269 ALWYFKGELYERLGKLDEALKCYEKVIELQPHYIKALLSKAR 310
                                   78999***************************9999988877 PP

  == domain 9  score: 16.2 bits;  conditional E-value: 3.1e-05
                        TPR_14   3 allalaeallalGdpdeAiallrrala 29 
                                   all  a++++++G+ ++Ai+++++a++
  gi|15669131|ref|NP_247936.1| 304 ALLSKARIYERQGNIEAAIEYYNKAVE 330
                                   78889********************98 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0085       3.8       1      26 [.      65      90 ..      65      97 .. 0.84
   2 ?    7.4   0.0     0.011       4.8       6      31 ..     104     129 ..      99     133 .. 0.82
   3 !    9.4   0.0    0.0025       1.1       9      33 ..     140     163 ..     134     165 .. 0.84
   4 !   13.3   0.0   0.00014     0.063       6      34 ..     172     198 ..     168     200 .. 0.83
   5 !   14.1   0.1   8.1e-05     0.036       1      27 [.     201     228 ..     201     256 .. 0.83
   6 !   18.3   0.1   3.7e-06    0.0017       3      30 ..     272     297 ..     269     300 .. 0.83
   7 !   18.8   0.1   2.6e-06    0.0012       1      28 [.     304     329 ..     304     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0085
                         TPR_7  1 aLlnLarlysrlGdyeeAielyeqsL 26
                                  aL+  + + s+ G+ +eAi+ +e++L
  gi|15669131|ref|NP_247936.1| 65 ALFLKGLALSAKGEIKEAITTFEELL 90
                                  677889999***************55 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                         TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                   ++ly   G+ +eA+++y ++L+++++
  gi|15669131|ref|NP_247936.1| 104 GQLYGMSGNCDEALKCYNKALGIENR 129
                                   7777778************9999876 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0025
                         TPR_7   9 ysr.lGdyeeAielyeqsLaltkdpe 33 
                                   + + lG+y+e++++y +  +lt+ p+
  gi|15669131|ref|NP_247936.1| 140 CLEfLGEYDELLKCYNE--VLTYTPN 163
                                   55559************..9999886 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00014
                         TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                   a++ ++lG+ye+A+ ++ +  al+  p+d
  gi|15669131|ref|NP_247936.1| 172 AEILRKLGRYEDALLCLNR--ALELKPHD 198
                                   899****************..66666655 PP

  == domain 5  score: 14.1 bits;  conditional E-value: 8.1e-05
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsL.a 27 
                                   aL+  ++l  r+G+++eA+e++++++ +
  gi|15669131|ref|NP_247936.1| 201 ALYLKGVLLKRMGKFREALECFKKLIdE 228
                                   688899******************5544 PP

  == domain 6  score: 18.3 bits;  conditional E-value: 3.7e-06
                         TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltk 30 
                                   +  ++ly+rlG+ +eA+++ye+  +++ 
  gi|15669131|ref|NP_247936.1| 272 YFKGELYERLGKLDEALKCYEK--VIEL 297
                                   56699*****************..5554 PP

  == domain 7  score: 18.8 bits;  conditional E-value: 2.6e-06
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                   aLl  ar+y+r+G+ e Aie+y +  a+
  gi|15669131|ref|NP_247936.1| 304 ALLSKARIYERQGNIEAAIEYYNK--AV 329
                                   78999*****************99..54 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.4     0.011       4.7      14      72 ..      40      90 ..      27      92 .. 0.76
   2 !   13.7   0.0   0.00013      0.06       8      32 ..     102     126 ..      96     139 .. 0.65
   3 ?    4.6   0.0     0.086        38      12      30 ..     140     158 ..     130     161 .. 0.88
   4 !   31.5   0.1   3.6e-10   1.6e-07       5      71 ..     167     225 ..     165     227 .. 0.93
   5 ?   -0.7   0.0       3.9   1.7e+03      56      75 ..     245     264 ..     234     266 .. 0.64
   6 !   39.8   0.4   9.2e-13   4.1e-10       5      73 ..     270     330 ..     267     332 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.011
                        TPR_12 14 rrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72
                                  +  g++ +Al + +kale+      pd  ++  +l+  g +++a g+ +eA+  +ee l
  gi|15669131|ref|NP_247936.1| 40 LFEGNLIKALYYVDKALELE-----PDF-YL--ALFLKGLALSAKGEIKEAITTFEELL 90
                                  56799999999999999998.....654.34..57777777778999999999999876 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00013
                        TPR_12   8 nlaavlrrlgrydeAlellekalei 32 
                                    +++++   g++deAl++++kal i
  gi|15669131|ref|NP_247936.1| 102 FVGQLYGMSGNCDEALKCYNKALGI 126
                                   4566666666666666666666655 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.086
                        TPR_12  12 vlrrlgrydeAlellekal 30 
                                   +l  lg+yde l++++++l
  gi|15669131|ref|NP_247936.1| 140 CLEFLGEYDELLKCYNEVL 158
                                   7889************998 PP

  == domain 4  score: 31.5 bits;  conditional E-value: 3.6e-10
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                   ++++ a++lr+lgry++Al +l++ale+      p h    ++l+  g l+ ++g+++eAle +++ 
  gi|15669131|ref|NP_247936.1| 167 MWVKKAEILRKLGRYEDALLCLNRALELK-----P-H--DKNALYLKGVLLKRMGKFREALECFKKL 225
                                   67889************************.....8.5..689**********************986 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 3.9
                        TPR_12  56 ralgryeeAlelleealaia 75 
                                   +al+++++A+++ +  l+i+
  gi|15669131|ref|NP_247936.1| 245 LALDDLKDAERYINIGLEIR 264
                                   46777777777766666655 PP

  == domain 6  score: 39.8 bits;  conditional E-value: 9.2e-13
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                   +++  ++++ rlg++deAl+++ek++e++     p h  ++ +l   +r+y+++g+ e+A+e++++a++
  gi|15669131|ref|NP_247936.1| 270 LWYFKGELYERLGKLDEALKCYEKVIELQ-----P-H--YIKALLSKARIYERQGNIEAAIEYYNKAVE 330
                                   34489************************.....9.6..8***************************97 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   9.3e-06    0.0042      16      61 ..      48      90 ..      33      96 .. 0.85
   2 ?    3.0   0.0      0.36   1.6e+02       7      24 ..     107     124 ..     103     133 .. 0.85
   3 !   25.6   0.0   3.2e-08   1.4e-05       2      61 ..     170     226 ..     169     229 .. 0.92
   4 !   18.0   0.0   7.3e-06    0.0033      12      65 ..     249     299 ..     245     300 .. 0.89
   5 !   35.2   0.0   3.3e-11   1.5e-08       4      63 ..     275     331 ..     274     335 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.3e-06
                        TPR_16 16 AaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61
                                  A+ + + al++    Pd + Al+l+g+a+ ++g+ +eA+  ++++l
  gi|15669131|ref|NP_247936.1| 48 ALYYVDKALELE---PDFYLALFLKGLALSAKGEIKEAITTFEELL 90
                                  55566899****...************************9998876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.36
                        TPR_16   7 alragdyddAaaaleaal 24 
                                   +  +g+ d+A++ ++ al
  gi|15669131|ref|NP_247936.1| 107 YGMSGNCDEALKCYNKAL 124
                                   55589*********9998 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 3.2e-08
                        TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                   ++a +++++g+y+dA+  l++al++    P +  Al+l+g+++ r g + eA++ +++++
  gi|15669131|ref|NP_247936.1| 170 KKAEILRKLGRYEDALLCLNRALELK---PHDKNALYLKGVLLKRMGKFREALECFKKLI 226
                                   57999*********************...********************99998777765 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 7.3e-06
                        TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                   d  dA+++ ++ l+ +    d+++ ++++g+++ r+g l+eA+  y++ ++  p
  gi|15669131|ref|NP_247936.1| 249 DLKDAERYINIGLEIR---KDDVALWYFKGELYERLGKLDEALKCYEKVIELQP 299
                                   77899***********...99**********************99888877665 PP

  == domain 5  score: 35.2 bits;  conditional E-value: 3.3e-11
                        TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                   + ++ r+g+ d+A++ +e +++++   P    All +++++ rqg+ ++A+++y++a+++
  gi|15669131|ref|NP_247936.1| 275 GELYERLGKLDEALKCYEKVIELQ---PHYIKALLSKARIYERQGNIEAAIEYYNKAVEN 331
                                   77899*******************...*****************************9865 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   6.3e-05     0.028       3      33 ..      53      83 ..      51      84 .. 0.95
   2 ?   -0.4   0.0       4.6     2e+03       2      28 ..      86     112 ..      85     118 .. 0.75
   3 !   17.7   0.0   7.5e-06    0.0034       1      32 [.     153     184 ..     153     185 .. 0.97
   4 !   16.4   0.1   1.9e-05    0.0086       1      34 []     187     220 ..     187     220 .. 0.95
   5 !    8.5   0.0    0.0063       2.8       6      33 ..     261     288 ..     260     289 .. 0.93
   6 !   18.3   0.0   4.9e-06    0.0022       1      34 []     290     323 ..     290     323 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.3e-05
                        TPR_17  3 lkaleldPnnadaynnLAelllknGdlmtAr 33
                                   kalel+P+   a+++++ +l+ +G+ ++A+
  gi|15669131|ref|NP_247936.1| 53 DKALELEPDFYLALFLKGLALSAKGEIKEAI 83
                                  59************************99996 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 4.6
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGd 28 
                                   +++ l ++ +n+  +   ++l+ + G+
  gi|15669131|ref|NP_247936.1|  86 FEELLSYESKNPITWVFVGQLYGMSGN 112
                                   899999999999999766666666665 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 7.5e-06
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtA 32 
                                   +y ++l + Pn ++ +  +Ae+l+k+G++++A
  gi|15669131|ref|NP_247936.1| 153 CYNEVLTYTPNFVPMWVKKAEILRKLGRYEDA 184
                                   8*****************************99 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 1.9e-05
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   ++ +alel P + +a++++++ll++ G++++A++
  gi|15669131|ref|NP_247936.1| 187 CLNRALELKPHDKNALYLKGVLLKRMGKFREALE 220
                                   678****************************985 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0063
                        TPR_17   6 leldPnnadaynnLAelllknGdlmtAr 33 
                                   le+ ++++ +++ ++el++++G+l++A+
  gi|15669131|ref|NP_247936.1| 261 LEIRKDDVALWYFKGELYERLGKLDEAL 288
                                   788999*********************7 PP

  == domain 6  score: 18.3 bits;  conditional E-value: 4.9e-06
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   +y+k++el P + +a+  +A++++++G+ + A++
  gi|15669131|ref|NP_247936.1| 290 CYEKVIELQPHYIKALLSKARIYERQGNIEAAIE 323
                                   8****************************99986 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.4e-05    0.0065       4      55 ..      42      93 ..      40      98 .. 0.91
   2 !   10.0   0.0    0.0022      0.99       4      57 ..     110     163 ..     109     174 .. 0.87
   3 !   19.4   0.0   2.4e-06    0.0011      14      64 ..     154     204 ..     151     208 .. 0.89
   4 !   25.1   0.2   4.3e-08   1.9e-05       3      54 ..     177     228 ..     175     232 .. 0.94
   5 !    7.9   0.1    0.0098       4.4       4      60 ..     212     269 ..     209     277 .. 0.85
   6 !   24.9   0.2   4.7e-08   2.1e-05       5      54 ..     282     331 ..     278     336 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.4e-05
                        TPR_19  4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55
                                  eg++  Al +  +al+ +p+   a+ l   al a g+++eA+ + ++l+  +
  gi|15669131|ref|NP_247936.1| 42 EGNLIKALYYVDKALELEPDFYLALFLKGLALSAKGEIKEAITTFEELLSYE 93
                                  688889**************9999999******************9998765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0022
                        TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                   +g+ +eAl+ + +al  ++  + a ll  ++l  lg++de  ++ ++++  +p+
  gi|15669131|ref|NP_247936.1| 110 SGNCDEALKCYNKALGIENRFLSAFLLKTICLEFLGEYDELLKCYNEVLTYTPN 163
                                   58889**********************************977777777666665 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 2.4e-06
                        TPR_19  14 leqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL 64 
                                   + ++l++ p+    +   Ae+l +lg++++A  +L++++e +p d ++  L
  gi|15669131|ref|NP_247936.1| 154 YNEVLTYTPNFVPMWVKKAEILRKLGRYEDALLCLNRALELKPHDKNALYL 204
                                   77899999***********************************99776655 PP

  == domain 4  score: 25.1 bits;  conditional E-value: 4.3e-08
                        TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpee 54 
                                   + g+y++Al  l +al+ +p++ +a++l   +l  +g + eA ++ ++l +e
  gi|15669131|ref|NP_247936.1| 177 KLGRYEDALLCLNRALELKPHDKNALYLKGVLLKRMGKFREALECFKKLIDE 228
                                   669********************************************99886 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0098
                        TPR_19   4 egdyaeAlalleqalqe.dpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                   +g++ eAl+ ++++++e + k  +a    + ++lal +l++Ae+ ++  +e  +dd +
  gi|15669131|ref|NP_247936.1| 212 MGKFREALECFKKLIDElNVKWIDAIRHAVSLMLALDDLKDAERYINIGLEIRKDDVA 269
                                   899**********876659999999999***************999998888888733 PP

  == domain 6  score: 24.9 bits;  conditional E-value: 4.7e-08
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpee 54 
                                   g+++eAl+ +e++++  p++  a+l  A+++  +g++++A++  +++ e 
  gi|15669131|ref|NP_247936.1| 282 GKLDEALKCYEKVIELQPHYIKALLSKARIYERQGNIEAAIEYYNKAVEN 331
                                   89***************************************998887765 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.013         6      13      56 ..      47      90 ..      42      99 .. 0.89
   2 ?    3.6   0.0      0.16        72       7      56 ..      75     124 ..      68     129 .. 0.85
   3 !   21.5   0.0   4.1e-07   0.00019      11      66 ..     147     202 ..     144     205 .. 0.94
   4 !   26.8   0.1   9.2e-09   4.1e-06       6      72 ..     176     245 ..     172     246 .. 0.86
   5 !   23.7   0.1   8.9e-08     4e-05       5      61 ..     244     300 ..     240     304 .. 0.93
   6 !   22.5   0.0   2.1e-07   9.5e-05      11      57 ..     284     330 ..     283     336 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                         TPR_9 13 ralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl 56
                                  +al +v+  l l Pd    ++  Gl+l   G +++A+  +e  l
  gi|15669131|ref|NP_247936.1| 47 KALYYVDKALELEPDFYLALFLKGLALSAKGEIKEAITTFEELL 90
                                  79**********************************99998766 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.16
                         TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl 56 
                                    + +  +a+ + e ll   ++ p  +   G+l+  +G+  +Al++ + +l
  gi|15669131|ref|NP_247936.1|  75 AKGEIKEAITTFEELLSYESKNPITWVFVGQLYGMSGNCDEALKCYNKAL 124
                                   556678899999*******************************9998877 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 4.1e-07
                         TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                                   ++++l++++ +l   P+ +  +   + +l +lG+++ Al +L+++l+l p++  a 
  gi|15669131|ref|NP_247936.1| 147 YDELLKCYNEVLTYTPNFVPMWVKKAEILRKLGRYEDALLCLNRALELKPHDKNAL 202
                                   7899***********************************************99886 PP

  == domain 4  score: 26.8 bits;  conditional E-value: 9.2e-09
                         TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap...dapdaeairaqL 72 
                                       ++e al +++r l l+P+d   ++  G+ll ++G +++Al+++   ++       ++ ++a+  +L
  gi|15669131|ref|NP_247936.1| 176 RKLGRYEDALLCLNRALELKPHDKNALYLKGVLLKRMGKFREALECFKKLIDELNvkwIDAIRHAVSLML 245
                                   556799*****************************************99997766666777777776666 PP

  == domain 5  score: 23.7 bits;  conditional E-value: 8.9e-08
                         TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                   ++  +d   a ++++  l +  dd+ +++  G l+++lG l +Al++ e  ++l+p+
  gi|15669131|ref|NP_247936.1| 244 MLALDDLKDAERYINIGLEIRKDDVALWYFKGELYERLGKLDEALKCYEKVIELQPH 300
                                   56779999**********************************************996 PP

  == domain 6  score: 22.5 bits;  conditional E-value: 2.1e-07
                         TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57 
                                    ++al+++e ++ l+P+ +  ++  +++++++G+++aA++  + +++
  gi|15669131|ref|NP_247936.1| 284 LDEALKCYEKVIELQPHYIKALLSKARIYERQGNIEAAIEYYNKAVE 330
                                   589*************************************9999886 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1    0.0014      0.61       2      28 ..      65      91 ..      64      95 .. 0.93
   2 ?    1.6   0.0       1.2   5.6e+02       7      26 ..     104     123 ..     103     125 .. 0.82
   3 ?   -1.1   0.0       8.7   3.9e+03       9      28 ..     140     159 ..     133     163 .. 0.77
   4 ?    5.4   0.0     0.074        33       5      28 ..     170     193 ..     168     197 .. 0.88
   5 !   16.1   0.1   2.9e-05     0.013       2      29 ..     201     228 ..     200     228 .. 0.96
   6 !   16.8   0.0   1.7e-05    0.0078       6      31 ..     274     299 ..     269     301 .. 0.89
   7 !   15.5   0.1   4.3e-05     0.019       2      29 ..     304     331 ..     303     333 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0014
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6  2 AlyklalsyrklgdtdkAlealerlik 28
                                  Al++ +l++ + g+  +A++++e+l++
  gi|15669131|ref|NP_247936.1| 65 ALFLKGLALSAKGEIKEAITTFEELLS 91
                                  9**********89************86 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrklgdtdkAlealerl 26 
                                   +++y + g+ d+Al+ +++ 
  gi|15669131|ref|NP_247936.1| 104 GQLYGMSGNCDEALKCYNKA 123
                                   6778876799*******986 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 8.7
                                   HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   9 syrklgdtdkAlealerlik 28 
                                   +++ lg++d+ l+ ++++++
  gi|15669131|ref|NP_247936.1| 140 CLEFLGEYDELLKCYNEVLT 159
                                   56668899999999999987 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.074
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                   k a+ +rklg++++Al  l+r ++
  gi|15669131|ref|NP_247936.1| 170 KKAEILRKLGRYEDALLCLNRALE 193
                                   67999***99********999886 PP

  == domain 5  score: 16.1 bits;  conditional E-value: 2.9e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlike 29 
                                   Aly+ + +++++g+ ++Ale +++li+e
  gi|15669131|ref|NP_247936.1| 201 ALYLKGVLLKRMGKFREALECFKKLIDE 228
                                   9*************************86 PP

  == domain 6  score: 16.8 bits;  conditional E-value: 1.7e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                         TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                    +++y++lg+ d+Al+ +e++i+  P
  gi|15669131|ref|NP_247936.1| 274 KGELYERLGKLDEALKCYEKVIELQP 299
                                   5999***9***************998 PP

  == domain 7  score: 15.5 bits;  conditional E-value: 4.3e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlike 29 
                                   Al+  a+ y+++g+ ++A+e++++ +++
  gi|15669131|ref|NP_247936.1| 304 ALLSKARIYERQGNIEAAIEYYNKAVEN 331
                                   89999*******************9986 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0012      0.54     207     251 ..      44      88 ..      15      96 .. 0.86
   2 ?    4.7   0.0     0.026        12     194     247 ..      99     152 ..      90     158 .. 0.87
   3 !   13.5   0.0   5.6e-05     0.025     203     259 ..     142     198 ..     126     200 .. 0.89
   4 !   13.1   0.0   7.5e-05     0.034     201     250 ..     174     223 ..     152     259 .. 0.73
   5 !   32.0   0.2   1.3e-10     6e-08     192     253 ..     270     329 ..     253     336 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                                   -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                         NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmee 251
                                   +  kAl y+dka+e +p +      K+  l  +G++k+A+++ ee
  gi|15669131|ref|NP_247936.1|  44 NLIKALYYVDKALELEPDFYLALFLKGLALSAKGEIKEAITTFEE 88 
                                   3449************************************99887 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.026
                                   HHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHH CS
                         NARP1 194 vlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAae 247
                                   +  f+ q y   g+ ++Al++ +ka+  +  ++  +l K   l+  G+ ++  +
  gi|15669131|ref|NP_247936.1|  99 TWVFVGQLYGMSGNCDEALKCYNKALGIENRFLSAFLLKTICLEFLGEYDELLK 152
                                   456999**************************************9999887655 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 5.6e-05
                                   HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                         NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                   + lg++++ l++ ++ +  tp++v +++ Ka+il++ G  ++A  ++++a +l  +D
  gi|15669131|ref|NP_247936.1| 142 EFLGEYDELLKCYNEVLTYTPNFVPMWVKKAEILRKLGRYEDALLCLNRALELKPHD 198
                                   6689999*****************************************999987766 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 7.5e-05
                                   HHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                         NARP1 201 hydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevme 250
                                      klg++e Al ++++a+e +p   +  + K+ +lk++G +++A e+ +
  gi|15669131|ref|NP_247936.1| 174 ILRKLGRYEDALLCLNRALELKPHDKNALYLKGVLLKRMGKFREALECFK 223
                                   33457888999999999999999999999999999999999999988765 PP

  == domain 5  score: 32.0 bits;  conditional E-value: 1.3e-10
                                   HHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                         NARP1 192 lwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeear 253
                                   lw  yf    y++lg+ ++Al++ +k ie +p  +   l Kari++++G++++A+e  ++a 
  gi|15669131|ref|NP_247936.1| 270 LW--YFKGELYERLGKLDEALKCYEKVIELQPHYIKALLSKARIYERQGNIEAAIEYYNKAV 329
                                   44..899999**********************************************999985 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00028      0.13       6      49 ..      46      89 ..      42     101 .. 0.87
   2 !   21.9   0.2   3.5e-07   0.00016       2      79 ..      76     154 ..      75     157 .. 0.90
   3 !   28.3   0.3   3.4e-09   1.5e-06       3      78 ..     179     256 ..     177     259 .. 0.83
   4 !   15.4   0.2   3.5e-05     0.016       4      51 ..     283     331 ..     261     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00028
                                  HHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                        ANAPC3  6 knAiflaerllaaetespedayllAlclylngqykrAyellrka 49
                                   +A+ + +++l+ e++ + +++l++l+l   g+ k+A++ ++++
  gi|15669131|ref|NP_247936.1| 46 IKALYYVDKALELEPDFYLALFLKGLALSAKGEIKEAITTFEEL 89
                                  5799***********************************99988 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 3.5e-07
                                   TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                        ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                   ++ +k+Ai  +e ll++e+++p    + ++ +  +g+ ++A++ ++ka +++++ l + +l+  cl  L++y+e ++++
  gi|15669131|ref|NP_247936.1|  76 KGEIKEAITTFEELLSYESKNPITWVFVGQLYGMSGNCDEALKCYNKAlGIENRFLSAFLLKTICLEFLGEYDELLKCY 154
                                   56799**********9999999999999********************9999999988888889999*******77766 PP

  == domain 3  score: 28.3 bits;  conditional E-value: 3.4e-09
                                   T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHH.HHTT-HHHHHHH CS
                        ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcl.lkLkkyeeAiaa 78 
                                   ++y++A+++++r+l+ ++++ +++yl++  l ++g++ +A+e ++k+ ++ +     ++ +A +l l+L+ +++A++ 
  gi|15669131|ref|NP_247936.1| 179 GRYEDALLCLNRALELKPHDKNALYLKGVLLKRMGKFREALECFKKLiDELNVKWIDAIRHAVSLmLALDDLKDAERY 256
                                   68*********************************************7554444455566666664688888888765 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 3.5e-05
                                   -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SH CS
                        ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.kl 51 
                                   ++++A+ ++e++ + +++  ++++ +A  + ++g+ + A+e+++ka + 
  gi|15669131|ref|NP_247936.1| 283 KLDEALKCYEKVIELQPHYIKALLSKARIYERQGNIEAAIEYYNKAvEN 331
                                   5789999999999999999999999999999999999999999998444 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00012     0.052     112     175 ..      62     126 ..      57     133 .. 0.86
   2 !   10.5   0.0   0.00055      0.25     148     182 ..     167     201 ..     164     233 .. 0.92
   3 !   11.4   0.0    0.0003      0.13     142     178 ..     264     300 ..     233     306 .. 0.78
   4 ?    2.5   0.0      0.16        71     149     176 ..     305     332 ..     302     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                        TPR_15 112 lLssalellerakdydriaellksleeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlal 175
                                   ++ + +  + ++ +  +i+e +++ ee+  +e +++  ++ +++ly   g+ d+Al++y +Al  
  gi|15669131|ref|NP_247936.1|  62 FYLALFLKGLALSAKGEIKEAITTFEELLSYEsKNPITWVFVGQLYGMSGNCDEALKCYNKALGI 126
                                   55555556667888899*********999988799***************************976 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00055
                        TPR_15 148 fllaraelyrqegqtdaAlrdyreAlalapdssel 182
                                   +++  ae+ r+ g+ ++Al ++ +Al+l+p ++++
  gi|15669131|ref|NP_247936.1| 167 MWVKKAEILRKLGRYEDALLCLNRALELKPHDKNA 201
                                   89****************************99865 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.0003
                        TPR_15 142 aeqsaafllaraelyrqegqtdaAlrdyreAlalapd 178
                                    +++ a ++  +ely++ g+ d+Al++y+++++l+p 
  gi|15669131|ref|NP_247936.1| 264 RKDDVALWYFKGELYERLGKLDEALKCYEKVIELQPH 300
                                   358999***************************9996 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.16
                        TPR_15 149 llaraelyrqegqtdaAlrdyreAlala 176
                                   ll  a++y+++g+ +aA++ y +A++  
  gi|15669131|ref|NP_247936.1| 305 LLSKARIYERQGNIEAAIEYYNKAVENI 332
                                   677899******************9865 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.057        25      68     124 ..      34      87 ..      25      96 .. 0.79
   2 ?    2.2   0.0      0.39   1.7e+02      99     124 ..     130     155 ..      87     163 .. 0.67
   3 ?    5.3   0.0     0.042        19     105     128 ..     170     193 ..     131     200 .. 0.72
   4 ?    6.1   0.0     0.024        11      62      91 ..     172     194 ..     164     233 .. 0.56
   5 !    8.4   0.0    0.0048       2.1      74     129 ..     246     297 ..     232     300 .. 0.88
   6 !   11.2   0.0   0.00063      0.28      99     136 ..     301     338 .]     298     338 .] 0.95

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.057
                                   TT-HHHHHHH.HHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                       DUF3856  68 lgrydeales.adkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafr 124
                                   l+ y e +e    kal+y ++  ele d    +  a+f ++ al+  G  +ea+ +f+
  gi|15669131|ref|NP_247936.1|  34 LRAYRELFEGnLIKALYYVDKALELEPD----FYLALFLKGLALSAKGEIKEAITTFE 87 
                                   6667776664145899999999999887....5668999***************9997 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.39
                                   HHHHHHHHHHHHHHTT-HHHHHHHHH CS
                       DUF3856  99 WiaavfsravaleelGrkdealkafr 124
                                   +++a + ++ +le lG +de lk ++
  gi|15669131|ref|NP_247936.1| 130 FLSAFLLKTICLEFLGEYDELLKCYN 155
                                   45555555566666666666666555 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.042
                                   HHHHHHHHTT-HHHHHHHHHHHHH CS
                       DUF3856 105 sravaleelGrkdealkafrmage 128
                                   ++a  l +lGr+++al  ++ a e
  gi|15669131|ref|NP_247936.1| 170 KKAEILRKLGRYEDALLCLNRALE 193
                                   455555555555555555555444 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.024
                                   HHHHHHTT-HHHHHHHHHHHHHHHHHH--T CS
                       DUF3856  62 sealaklgrydealesadkalryfnrrGel 91 
                                   +e l klgry++al + ++al       el
  gi|15669131|ref|NP_247936.1| 172 AEILRKLGRYEDALLCLNRAL-------EL 194
                                   444555666665555544444.......33 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0048
                                   HHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                       DUF3856  74 alesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                   al   + a ry n   e+++d+  lW    + ++  +e lG+ dealk ++++ e+
  gi|15669131|ref|NP_247936.1| 246 ALDDLKDAERYINIGLEIRKDDVALW----YFKGELYERLGKLDEALKCYEKVIEL 297
                                   6777788999***999******9999....679******************99986 PP

  == domain 6  score: 11.2 bits;  conditional E-value: 0.00063
                                   HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH--S- CS
                       DUF3856  99 WiaavfsravaleelGrkdealkafrmagemiaerkGe 136
                                   +i+a++s+a+ +e  G+ + a++++++a+e i+  +Ge
  gi|15669131|ref|NP_247936.1| 301 YIKALLSKARIYERQGNIEAAIEYYNKAVENIHKDHGE 338
                                   89******************************999887 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00039      0.18      15      43 ..      43      71 ..      42      75 .. 0.91
   2 ?    2.9   0.0      0.26   1.2e+02      15      43 ..     111     139 ..     110     142 .. 0.86
   3 ?   -1.4   0.1       5.5   2.5e+03      14      33 ..     144     163 ..     144     164 .. 0.84
   4 !   18.2   0.3   4.3e-06    0.0019      13      49 ..     177     213 ..     175     219 .. 0.93
   5 ?    0.2   0.0       1.8     8e+02      13      28 ..     211     226 ..     209     227 .. 0.89
   6 ?   -2.0   0.0       8.6   3.9e+03      15      30 ..     248     263 ..     247     266 .. 0.82
   7 ?    5.0   0.1     0.056        25      13      34 ..     280     301 ..     275     311 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00039
                                  T-HHHHHHHHHHHHHHTTS-HHHHHHHHH CS
                    Fis1_TPR_C 15 geYseArryvdalLeiEPenrQaqsLkel 43
                                  g+  +A+ yvd  Le+EP++  a+ Lk l
  gi|15669131|ref|NP_247936.1| 43 GNLIKALYYVDKALELEPDFYLALFLKGL 71
                                  7889****************999999865 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.26
                                   T-HHHHHHHHHHHHHHTTS-HHHHHHHHH CS
                    Fis1_TPR_C  15 geYseArryvdalLeiEPenrQaqsLkel 43 
                                   g+ +eA+++ +  L iE ++  a  Lk++
  gi|15669131|ref|NP_247936.1| 111 GNCDEALKCYNKALGIENRFLSAFLLKTI 139
                                   56689**************9999999875 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 5.5
                                   HT-HHHHHHHHHHHHHHTTS CS
                    Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                   lgeY+e +++ + +L   P+
  gi|15669131|ref|NP_247936.1| 144 LGEYDELLKCYNEVLTYTPN 163
                                   799**999999999988776 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 4.3e-06
                                   HHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHH CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQaqsLkeliedkik 49 
                                   klg+Y++A+ ++++ Le+ P  ++a+ Lk ++ +++ 
  gi|15669131|ref|NP_247936.1| 177 KLGRYEDALLCLNRALELKPHDKNALYLKGVLLKRMG 213
                                   9****************************99988886 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 1.8
                                   HHT-HHHHHHHHHHHH CS
                    Fis1_TPR_C  13 klgeYseArryvdalL 28 
                                   ++g+++eA+++ + l+
  gi|15669131|ref|NP_247936.1| 211 RMGKFREALECFKKLI 226
                                   89********999885 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 8.6
                                   T-HHHHHHHHHHHHHH CS
                    Fis1_TPR_C  15 geYseArryvdalLei 30 
                                    + ++A ry++  Lei
  gi|15669131|ref|NP_247936.1| 248 DDLKDAERYINIGLEI 263
                                   57889*****998887 PP

  == domain 7  score: 5.0 bits;  conditional E-value: 0.056
                                   HHT-HHHHHHHHHHHHHHTTS- CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPen 34 
                                   +lg+ +eA+++ + ++e++P  
  gi|15669131|ref|NP_247936.1| 280 RLGKLDEALKCYEKVIELQPHY 301
                                   9*******************86 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.15        66       9      28 ..      72      91 ..      72      93 .. 0.87
   2 !    8.5   0.1     0.006       2.7       5      25 ..     102     122 ..      98     125 .. 0.82
   3 ?    1.6   0.0       0.9     4e+02      12      25 ..     177     190 ..     174     195 .. 0.83
   4 !    8.7   0.4    0.0049       2.2      12      28 ..     211     227 ..     208     228 .. 0.87
   5 !    8.9   0.2    0.0044         2      10      28 ..     278     296 ..     276     298 .. 0.88
   6 ?    4.1   0.0      0.14        64       9      28 ..     311     330 ..     310     331 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.15
                           PPR  9 gycknGkleeAlelfkeMke 28
                                  +++ +G+++eA+  f+e+++
  gi|15669131|ref|NP_247936.1| 72 ALSAKGEIKEAITTFEELLS 91
                                  57889************875 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.006
                           PPR   5 slIsgycknGkleeAlelfke 25 
                                    + + y+ +G+++eAl+++++
  gi|15669131|ref|NP_247936.1| 102 FVGQLYGMSGNCDEALKCYNK 122
                                   55578*************987 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.9
                           PPR  12 knGkleeAlelfke 25 
                                   k G++e+Al ++++
  gi|15669131|ref|NP_247936.1| 177 KLGRYEDALLCLNR 190
                                   89*******99987 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0049
                           PPR  12 knGkleeAlelfkeMke 28 
                                   + Gk++eAle+fk++++
  gi|15669131|ref|NP_247936.1| 211 RMGKFREALECFKKLID 227
                                   89***********9875 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0044
                           PPR  10 ycknGkleeAlelfkeMke 28 
                                   y + Gkl+eAl+++++ +e
  gi|15669131|ref|NP_247936.1| 278 YERLGKLDEALKCYEKVIE 296
                                   889************9876 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.14
                           PPR   9 gycknGkleeAlelfkeMke 28 
                                    y + G++e A+e++++ +e
  gi|15669131|ref|NP_247936.1| 311 IYERQGNIEAAIEYYNKAVE 330
                                   5889***********98665 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         8   3.6e+03      16      30 ..      43      57 ..      35      58 .. 0.73
   2 ?   -0.7   0.0       3.1   1.4e+03       9      27 ..      70      88 ..      70      93 .. 0.68
   3 ?    4.4   0.0      0.08        36      11      30 ..     106     125 ..     103     129 .. 0.67
   4 ?    6.4   0.2     0.019       8.4       9      31 ..     172     194 ..     172     195 .. 0.90
   5 ?    4.5   0.0     0.072        32       9      27 ..     206     224 ..     202     227 .. 0.88
   6 !   10.8   0.1   0.00077      0.34      10      31 ..     276     297 ..     275     298 .. 0.89
   7 ?    6.6   0.3     0.016       7.3       9      30 ..     309     330 ..     303     330 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 8
                        TPR_10 16 grydeAealleeala 30
                                  g++ +A+ + ++al+
  gi|15669131|ref|NP_247936.1| 43 GNLIKALYYVDKALE 57
                                  677778888888876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.1
                        TPR_10  9 analrqrgrydeAeallee 27
                                  + al++ g+ +eA   +ee
  gi|15669131|ref|NP_247936.1| 70 GLALSAKGEIKEAITTFEE 88
                                  5678888888888665555 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.08
                        TPR_10  11 alrqrgrydeAealleeala 30 
                                   ++   g+ deA++ + +al 
  gi|15669131|ref|NP_247936.1| 106 LYGMSGNCDEALKCYNKALG 125
                                   66667777777777777764 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.019
                        TPR_10   9 analrqrgrydeAealleealai 31 
                                   a +lr++gry++A+  l +al++
  gi|15669131|ref|NP_247936.1| 172 AEILRKLGRYEDALLCLNRALEL 194
                                   6789**********999999985 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.072
                        TPR_10   9 analrqrgrydeAeallee 27 
                                   +++l ++g++ eA++ +++
  gi|15669131|ref|NP_247936.1| 206 GVLLKRMGKFREALECFKK 224
                                   78899*********99887 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.00077
                        TPR_10  10 nalrqrgrydeAealleealai 31 
                                    ++ ++g++deA++ +e+++++
  gi|15669131|ref|NP_247936.1| 276 ELYERLGKLDEALKCYEKVIEL 297
                                   67999***************97 PP

  == domain 7  score: 6.6 bits;  conditional E-value: 0.016
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   a+++ ++g+ ++A +++ +a++
  gi|15669131|ref|NP_247936.1| 309 ARIYERQGNIEAAIEYYNKAVE 330
                                   899***************9986 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         4   1.8e+03      50      66 ..      77      93 ..      72     102 .. 0.79
   2 !    7.1   0.0    0.0089         4      43      63 ..     104     124 ..      99     128 .. 0.90
   3 ?    0.2   0.0       1.2   5.2e+02      40      64 ..     169     193 ..     146     200 .. 0.88
   4 ?    4.3   0.1     0.064        29      42      97 ..     205     258 ..     197     267 .. 0.74
   5 !   13.0   0.2   0.00014     0.064      37      64 ..     269     296 ..     230     299 .. 0.64
   6 !    9.5   0.3    0.0016      0.73      38      65 ..     304     331 ..     300     335 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4
                                  T-HHHHHHHHHTCCCC- CS
                          RPN7 50 gdleeAlkaysrireyc 66
                                  g+++eA+ ++++++ y 
  gi|15669131|ref|NP_247936.1| 77 GEIKEAITTFEELLSYE 93
                                  77888888888877765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0089
                                   HHHHHHCT-HHHHHHHHHTCC CS
                          RPN7  43 aehYlkigdleeAlkaysrir 63 
                                   ++ Y + g+++eAlk+y++++
  gi|15669131|ref|NP_247936.1| 104 GQLYGMSGNCDEALKCYNKAL 124
                                   78999*************985 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.2
                                   HHHHHHHHHCT-HHHHHHHHHTCCC CS
                          RPN7  40 ldlaehYlkigdleeAlkaysrire 64 
                                    ++ae   k g +e Al +++r++e
  gi|15669131|ref|NP_247936.1| 169 VKKAEILRKLGRYEDALLCLNRALE 193
                                   6889999999999999999999886 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.064
                                   HHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                          RPN7  42 laehYlkigdleeAlkaysrireyctslkhkidmllnlirvaiffndwdlvskyle 97 
                                   ++    ++g+++eAl++++++++++      id + + + + +++ d + +++y++
  gi|15669131|ref|NP_247936.1| 205 KGVLLKRMGKFREALECFKKLIDELNV--KWIDAIRHAVSLMLALDDLKDAERYIN 258
                                   555556789999999999998888765..567777777777777777777777765 PP

  == domain 5  score: 13.0 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                          RPN7  37 rakldlaehYlkigdleeAlkaysrire 64 
                                   ++++ ++e Y + g+l+eAlk+y++++e
  gi|15669131|ref|NP_247936.1| 269 ALWYFKGELYERLGKLDEALKCYEKVIE 296
                                   4566689*****************9876 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.0016
                                   HHHHHHHHHHHCT-HHHHHHHHHTCCCC CS
                          RPN7  38 akldlaehYlkigdleeAlkaysrirey 65 
                                   a l +a+ Y + g++e A+++y++++e 
  gi|15669131|ref|NP_247936.1| 304 ALLSKARIYERQGNIEAAIEYYNKAVEN 331
                                   7889********************9986 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0014      0.62      18     122 ..      23     123 ..      13     127 .. 0.86
   2 !   12.7   0.0   0.00028      0.13      60     126 ..     163     229 ..     142     242 .. 0.86
   3 ?    6.6   0.1     0.021       9.6      68     124 ..     274     330 ..     243     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0014
                                   HTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHH CS
                          BTAD  18 aagdpeeaaelleaAlalwrGpaladleagewleaererleelrlealealaeaelrlGraeealaelealvaehPlrErl 98 
                                   + +  e+ a+ l+a ++l++G + +         +++ +le ++  al     a+++ G+++ea+++ e+l++ +  +  +
  gi|15669131|ref|NP_247936.1|  23 RVDTLEAVANVLRAYRELFEGNLIKA----LYYVDKALELEPDFYLALFLKGLALSAKGEIKEAITTFEELLSYESKNPIT 99 
                                   44556666677777777777777777....556999999****************************************** PP

                                   HHHHHHHHHHTT-HHHHHHHHHHH CS
                          BTAD  99 hrqlmrAlarsGrqaeALevYerl 122
                                   +  + + +  sG+  eAL+ Y+++
  gi|15669131|ref|NP_247936.1| 100 WVFVGQLYGMSGNCDEALKCYNKA 123
                                   *********************975 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00028
                                   HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          BTAD  60 lrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrlL 126
                                    ++ +  + ae + +lGr+e+al  l+++++++P++ ++  +    l r+G+  eALe +++l + L
  gi|15669131|ref|NP_247936.1| 163 NFVPMWVKKAEILRKLGRYEDALLCLNRALELKPHDKNALYLKGVLLKRMGKFREALECFKKLIDEL 229
                                   56666677899999**********************************************9987766 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.021
                                   HHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          BTAD  68 laeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                     e+  rlG+ +eal+ +e+ ++++P+  ++     r + r+G+ ++A+e+Y+++++
  gi|15669131|ref|NP_247936.1| 274 KGELYERLGKLDEALKCYEKVIELQPHYIKALLSKARIYERQGNIEAAIEYYNKAVE 330
                                   5566679999*****************99999999999**************99876 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0023         1       4     107 ..      32     124 ..      29     130 .. 0.85
   2 ?    4.8   0.0     0.034        15      81     184 ..     166     257 ..     155     265 .. 0.68
   3 ?    4.9   0.0     0.031        14      87     111 ..     275     299 ..     259     302 .. 0.85
   4 !   11.8   0.0   0.00025      0.11     129     194 ..     275     335 ..     268     338 .] 0.52

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0023
                      TPR_MalT   4 aalrAllaiasgdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallall 84 
                                   ++lrA+  +++g+  +al +  +AL+l p+       +a+++ G a   +G+ ++A  +++e+ +      s +   + ++
  gi|15669131|ref|NP_247936.1|  32 NVLRAYRELFEGNLIKALYYVDKALELEPDFY-----LALFLKGLALSAKGEIKEAITTFEELLSYE----SKNPITWVFV 103
                                   799***********************999876.....89999******************9987654....3333346666 PP

                      TPR_MalT  85 qqaeilvaqGrLheAletyeqal 107
                                     ++++ + G  +eAl+ y++al
  gi|15669131|ref|NP_247936.1| 104 --GQLYGMSGNCDEALKCYNKAL 124
                                   ..899999999999999999998 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.034
                      TPR_MalT  81 lallqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlepeaal 161
                                   +  ++ aeil++ Gr ++Al   ++al+l ++ + + l        l + ll  +++++eA ++ ++ i+   +l +  ++
  gi|15669131|ref|NP_247936.1| 166 PMWVKKAEILRKLGRYEDALLCLNRALELKPHDKNA-L-------YLKGVLLKRMGKFREALECFKKLID---EL-NVKWI 234
                                   556778899999999999999999999976665554.2.......2336667777778888888776544...33.33345 PP

                      TPR_MalT 162 dayvllarialaqGdleeAetll 184
                                   da    + + la +dl++Ae+++
  gi|15669131|ref|NP_247936.1| 235 DAIRHAVSLMLALDDLKDAERYI 257
                                   56666666677777777777765 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.031
                      TPR_MalT  87 aeilvaqGrLheAletyeqalqlat 111
                                   +e++   G+L+eAl+ ye+ ++l +
  gi|15669131|ref|NP_247936.1| 275 GELYERLGKLDEALKCYEKVIELQP 299
                                   8999*****************9976 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00025
                      TPR_MalT 129 adllyEwndLeeAeqhlqeGielleqlepeaaldayvllarialaqGdleeAetllekaeelares 194
                                   ++l+   ++L+eA ++ ++ iel  ++     ++a++  ari+  qG++e+A ++ +ka e  +++
  gi|15669131|ref|NP_247936.1| 275 GELYERLGKLDEALKCYEKVIELQPHY-----IKALLSKARIYERQGNIEAAIEYYNKAVENIHKD 335
                                   444444455555555555555554444.....5555556666666666666666666555555544 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00073      0.33     147     209 ..     180     239 ..      62     244 .. 0.87
   2 !   11.7   0.1   0.00036      0.16     161     208 ..     264     310 ..     243     314 .. 0.78
   3 ?    0.9   0.1      0.71   3.2e+02     123     147 ..     307     331 ..     298     335 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00073
                       DUF2225 147 lykeayekesfpve.gideatvlYLiaeLerrlgnkeealrwlskvigskkaskpskikdkare 209
                                    y++a+ + ++  e +  +++ lYL + L +r+g+ +eal+ ++k+i++ +++     +d++r+
  gi|15669131|ref|NP_247936.1| 180 RYEDALLCLNRALElKPHDKNALYLKGVLLKRMGKFREALECFKKLIDELNVKW----IDAIRH 239
                                   4666666666666634445669*************************9888776....555555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00036
                       DUF2225 161 gideatvlYLiaeLerrlgnkeealrwlskvigskkaskpskikdkar 208
                                     d+  + Y  +eL  rlg+ +eal+ ++kvi+ +     ++++ kar
  gi|15669131|ref|NP_247936.1| 264 RKDDVALWYFKGELYERLGKLDEALKCYEKVIELQPHYI-KALLSKAR 310
                                   45677799************************9876554.55666655 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.71
                       DUF2225 123 rlAWlyrdkedeekeklflkkAlel 147
                                     A +y+ +++ e   ++++kA+e 
  gi|15669131|ref|NP_247936.1| 307 SKARIYERQGNIEAAIEYYNKAVEN 331
                                   5567788888888888888888764 PP

>> DUF3808  Protein of unknown function (DUF3808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0081       3.6     268     296 ..      62      90 ..      31     147 .. 0.73
   2 ?    0.1   0.0      0.58   2.6e+02     271     336 ..     167     227 ..     148     232 .. 0.69
   3 !    8.4   0.0    0.0018      0.78     259     297 ..     292     330 ..     266     336 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0081
                       DUF3808 268 salwllfearieslkgnldeAlelleeii 296
                                     l l+ ++ ++s+kg+++eA++++ee++
  gi|15669131|ref|NP_247936.1|  62 FYLALFLKGLALSAKGEIKEAITTFEELL 90 
                                   55666777777777777777777776655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.58
                       DUF3808 271 wllfearieslkgnldeAlelleeiieesqselkqvkhlclfelaltlvylheykeaaesfleLlk 336
                                   + +++a i++  g+ ++Al  l+ ++     elk   +  l+ +++ l  + +++ea+e f++L++
  gi|15669131|ref|NP_247936.1| 167 MWVKKAEILRKLGRYEDALLCLNRAL-----ELKPHDKNALYLKGVLLKRMGKFREALECFKKLID 227
                                   55677888888888888888777766.....45555555666666777777777777777777766 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0018
                       DUF3808 259 lksrkrfPksalwllfearieslkgnldeAlelleeiie 297
                                   +k+ ++ P+    ll +ari++ +gn++ A+e++++++e
  gi|15669131|ref|NP_247936.1| 292 EKVIELQPHYIKALLSKARIYERQGNIEAAIEYYNKAVE 330
                                   5555555666667999******************99873 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       3.7   1.7e+03       3      26 .]      65      88 ..      64      88 .. 0.84
   2 ?    2.9   0.0       0.5   2.2e+02       8      21 ..     172     185 ..     170     188 .. 0.92
   3 ?    0.9   0.0       2.3     1e+03       3      23 ..     201     221 ..     200     223 .. 0.88
   4 ?   -1.1   0.0       9.9   4.4e+03      11      22 ..     244     255 ..     242     255 .. 0.86
   5 ?    5.3   0.0     0.084        38       4      21 ..     271     288 ..     268     293 .. 0.85
   6 ?    4.3   0.0      0.18        81       3      20 ..     304     321 ..     303     323 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 3.7
                         TPR_4  3 allaLArallalGdldeAraller 26
                                  al + + al a G+  eA +++e+
  gi|15669131|ref|NP_247936.1| 65 ALFLKGLALSAKGEIKEAITTFEE 88
                                  677789999999******888875 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.5
                         TPR_4   8 ArallalGdldeAr 21 
                                   A+ l  lG++++A+
  gi|15669131|ref|NP_247936.1| 172 AEILRKLGRYEDAL 185
                                   89999*******97 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 2.3
                         TPR_4   3 allaLArallalGdldeAral 23 
                                   al++ + +l + G + eA++ 
  gi|15669131|ref|NP_247936.1| 201 ALYLKGVLLKRMGKFREALEC 221
                                   7888999999********985 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 9.9
                         TPR_4  11 llalGdldeAra 22 
                                   +lal dl +A++
  gi|15669131|ref|NP_247936.1| 244 MLALDDLKDAER 255
                                   68999****997 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.084
                         TPR_4   4 llaLArallalGdldeAr 21 
                                    ++ ++++ +lG ldeA+
  gi|15669131|ref|NP_247936.1| 271 WYFKGELYERLGKLDEAL 288
                                   67889************8 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.18
                         TPR_4   3 allaLArallalGdldeA 20 
                                   all  Ar + ++G+ ++A
  gi|15669131|ref|NP_247936.1| 304 ALLSKARIYERQGNIEAA 321
                                   67889***********99 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       7.1   3.2e+03      21      33 ..      80      85 ..      64      97 .. 0.55
   2 ?    6.4   0.0     0.021       9.6      17      32 ..     110     125 ..     108     133 .. 0.90
   3 ?   -0.1   0.0       2.3     1e+03       9      32 ..     170     193 ..     168     196 .. 0.65
   4 ?    0.2   0.0       1.7   7.8e+02      26      48 ..     180     201 ..     177     209 .. 0.68
   5 ?    2.3   0.0       0.4   1.8e+02      18      34 ..     213     229 ..     201     246 .. 0.66
   6 ?    6.1   0.1     0.027        12      13      33 ..     277     297 ..     274     304 .. 0.84
   7 !   16.5   0.6   1.5e-05    0.0068       6      35 ..     304     333 ..     303     334 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.1
                           MIT 21 eeAlelYkealel 33
                                  +e       a+  
  gi|15669131|ref|NP_247936.1| 80 KE-------AITT 85
                                  33.......3333 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.021
                           MIT  17 agnyeeAlelYkeale 32 
                                   +gn +eAl++Y +al+
  gi|15669131|ref|NP_247936.1| 110 SGNCDEALKCYNKALG 125
                                   5899**********97 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.3
                           MIT   9 kkAveeDnagnyeeAlelYkeale 32 
                                   kkA  + + g ye+Al +   ale
  gi|15669131|ref|NP_247936.1| 170 KKAEILRKLGRYEDALLCLNRALE 193
                                   666666667777777766666665 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.7
                           MIT  26 lYkealelLlqalkekneerrel 48 
                                    Y++al  L+ al   ++ ++++
  gi|15669131|ref|NP_247936.1| 180 RYEDALLCLNRALE-LKPHDKNA 201
                                   58888888888886.23344554 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.4
                           MIT  18 gnyeeAlelYkealelL 34 
                                   g++ eAle++k+ ++ L
  gi|15669131|ref|NP_247936.1| 213 GKFREALECFKKLIDEL 229
                                   55556666555544444 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.027
                           MIT  13 eeDnagnyeeAlelYkealel 33 
                                    +++ g+ +eAl++Y++ +el
  gi|15669131|ref|NP_247936.1| 277 LYERLGKLDEALKCYEKVIEL 297
                                   57899***********98876 PP

  == domain 7  score: 16.5 bits;  conditional E-value: 1.5e-05
                           MIT   6 elvkkAveeDnagnyeeAlelYkealelLl 35 
                                   +l++kA  ++++gn+e+A+e+Y +a+e ++
  gi|15669131|ref|NP_247936.1| 304 ALLSKARIYERQGNIEAAIEYYNKAVENIH 333
                                   58899999******************9875 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0       0.1        45      40      79 ..      58      97 ..      25     101 .. 0.86
   2 ?    1.1   0.0      0.64   2.9e+02      52      94 ..     104     146 ..      99     160 .. 0.88
   3 !    8.5   0.1    0.0033       1.5      24      73 ..     178     227 ..     165     249 .. 0.88
   4 ?    3.7   0.0     0.098        44      21      86 ..     244     307 ..     226     334 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.1
                    HrpB1_HrpK 40 LrPevaeldllegvlliergrweeAlrlLreveaeasgtp 79
                                  L P +  + +l g+ l ++g+++eA+ +++e+   +s+ p
  gi|15669131|ref|NP_247936.1| 58 LEPDFYLALFLKGLALSAKGEIKEAITTFEELLSYESKNP 97
                                  8899999999999999***************997776655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.64
                    HrpB1_HrpK  52 gvlliergrweeAlrlLreveaeasgtpyakaLlAlcLaalrD 94 
                                   g+l+   g+ +eAl+  ++  + ++++  a  L  +cL++l++
  gi|15669131|ref|NP_247936.1| 104 GQLYGMSGNCDEALKCYNKALGIENRFLSAFLLKTICLEFLGE 146
                                   5666678999****************************99875 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0033
                    HrpB1_HrpK  24 sedtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLrevea 73 
                                    ++ eda l L+    L+P+ +++  l gvll + g++ eAl  ++++ +
  gi|15669131|ref|NP_247936.1| 178 LGRYEDALLCLNRALELKPHDKNALYLKGVLLKRMGKFREALECFKKLID 227
                                   6778999999999999****************************999875 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.098
                    HrpB1_HrpK  21 alasedtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyakaLlA 86 
                                    la +d +dae+ ++    +r   ++l  + g l+ + g+++eAl+  ++v + +++  y kaLl+
  gi|15669131|ref|NP_247936.1| 244 MLALDDLKDAERYINIGLEIRKDDVALWYFKGELYERLGKLDEALKCYEKVIELQPH--YIKALLS 307
                                   555555555555555555555555566666666666666666666666666644443..5555554 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00023       0.1     183     294 ..      77     191 ..      12     205 .. 0.74
   2 !    8.4   0.1    0.0021      0.93     170     292 ..     203     326 ..     193     336 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                   T-HHHHHHHHHHH...HTT-GGGHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHH CS
                         ChAPs 183 krydralellekL...keeepevvillarvllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakra 260
                                    ++++a++ +e+L   ++++p   + + +++ +  +  +a+k  n++l  e++  +  ll++  l    +++  l++ ++ 
  gi|15669131|ref|NP_247936.1|  77 GEIKEAITTFEELlsyESKNPITWVFVGQLYGMSGNCDEALKCYNKALGIENRFLSAFLLKTICLEFLGEYDELLKCYNEV 157
                                   4577788888887332356688888999999999999999999999996555554433344444444455666799***** PP

                                   HHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHT- CS
                         ChAPs 261 vksaPsefktWalLvkvYikledienALltLNsc 294
                                    + +P+    W++ +++  kl+ +e+ALl LN  
  gi|15669131|ref|NP_247936.1| 158 LTYTPNFVPMWVKKAEILRKLGRYEDALLCLNRA 191
                                   ********************************75 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0021
                                   HHHHHHHHHHHHHT-.HHHHHHHHHHHHTT-GGGHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS- CS
                         ChAPs 170 yLvetllklvrltkr.ydralellekLkeeepevvillarvllladeEvdavkllneeleeeekdaelLllqaefllskkk 249
                                   yL   llk +   ++ ++   +l+++L+ +  +++   + ++l+ d+  da + +n  le +++d++l   + e      k
  gi|15669131|ref|NP_247936.1| 203 YLKGVLLKRMGKFREaLECFKKLIDELNVKWIDAIRHAVSLMLALDDLKDAERYINIGLEIRKDDVALWYFKGELYERLGK 283
                                   5555566655444440444467888888889999999999999********************************999999 PP

                                   -HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                         ChAPs 250 eelAlevakravksaPsefktWalLvkvYikledienALltLN 292
                                    + Al++ ++ +++ P   k     +++Y ++++ie A+   N
  gi|15669131|ref|NP_247936.1| 284 LDEALKCYEKVIELQPHYIKALLSKARIYERQGNIEAAIEYYN 326
                                   9*************************************97777 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   1.8e-06   0.00081       3     101 ..     118     225 ..     116     259 .. 0.84
   2 ?    3.7   1.6      0.13        60      20      71 ..     205     294 ..     192     336 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.8e-06
                  SRP_TPR_like   3 eeyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsalsed...vrfEkaYvlYklkkykkalkilkkv...eaee 75 
                                   ++y+k l +e+  l+ f  k ++l  l+ y+e Lk  ++  + + +   + + ka +l kl +y++al  l+++   + ++
  gi|15669131|ref|NP_247936.1| 118 KCYNKALGIENRFLSAFllKTICLEFLGEYDELLKCYNEVLTYTPNfvpMWVKKAEILRKLGRYEDALLCLNRAlelKPHD 198
                                   68999*******************************9999866554223789******************99862224445 PP

                  SRP_TPR_like  76 .kvkvlksqvlYrlgsyekAYklLske 101
                                    ++  lk  +l r+g++++A ++  k 
  gi|15669131|ref|NP_247936.1| 199 kNALYLKGVLLKRMGKFREALECFKKL 225
                                   466789999999********8877554 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.13
                  SRP_TPR_like  20 kvvaliklekyeeaLkllkkgs......................................alsedvrfEkaYvlYklkkyk 62 
                                   k v l +++k++eaL+  kk                                        + +  + + k   + +l k+ 
  gi|15669131|ref|NP_247936.1| 205 KGVLLKRMGKFREALECFKKLIdelnvkwidairhavslmlalddlkdaeryinigleirKDDVALWYFKGELYERLGKLD 285
                                   556666777888888777775444444444444444444444444444444444444433333334455555555666666 PP

                  SRP_TPR_like  63 kalkilkkv 71 
                                   +alk  +kv
  gi|15669131|ref|NP_247936.1| 286 EALKCYEKV 294
                                   666665555 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.1   1.8e+03      26      58 ..      19      58 ..      13      66 .. 0.66
   2 !   17.4   0.2   4.6e-06    0.0021     148     294 ..     166     310 ..     150     331 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.1
                                  TSSSS--CCCHCCC...CHH....--CCHCHHCCCHCCCC CS
                           FAT 26 kdspdkaffeaila...lhr....nqfdeakeliekarql 58
                                  k +p+  ++ea+ +    +r     ++ +a ++++ka +l
  gi|15669131|ref|NP_247936.1| 19 KRTPRVDTLEAVANvlrAYRelfeGNLIKALYYVDKALEL 58
                                  5566666666666643322244448899999999999876 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 4.6e-06
                                   TCCCCCCCCHCHHHHCCSTTHHCCCCCHCTT.....TT.TSSCCCHHHHHHHCCHHHHHSSCCHHHHCCTSSCCC...... CS
                           FAT 148 emwlkfanlarksgrlslAekaLkelleedpeewlprappevvyaylKylwssgeqkealqkLreftsellekke...... 222
                                    mw+k a++ rk gr++ A   L+++le +p +       + +y +  +l   g+ +eal++ ++ ++el  k        
  gi|15669131|ref|NP_247936.1| 166 PMWVKKAEILRKLGRYEDALLCLNRALELKPHD------KNALYLKGVLLKRMGKFREALECFKKLIDELNVKWIdairha 240
                                   59*****************************33......334555555666667777777777777776555543544544 PP

                                   .....SS-SS---...................HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                           FAT 223 .....elqsgleaq.......keptnleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykawht 291
                                        +               +  +   e++k    +  +kGe  e+l+k        +e+l++y +  e++p+ +ka  +
  gi|15669131|ref|NP_247936.1| 241 vslmlA-------LddlkdaeRYINIGLEIRKDDVALWYFKGELYERLGK-------LDEALKCYEKVIELQPHYIKALLS 307
                                   444432.......1333333322233334555554666678999999999.......89***************9999766 PP

                                   CCH CS
                           FAT 292 wal 294
                                    a+
  gi|15669131|ref|NP_247936.1| 308 KAR 310
                                   555 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.36   1.6e+02       4      14 ..      47      57 ..      46      59 .. 0.89
   2 ?    5.6   0.0     0.027        12      24      41 ..     102     119 ..      94     127 .. 0.87
   3 ?   -2.2   0.0       7.2   3.2e+03      31      40 ..     170     179 ..     168     179 .. 0.87
   4 ?    2.9   0.0      0.18        79       1      15 [.     180     194 ..     180     224 .. 0.87
   5 ?    5.4   0.4      0.03        13      28      42 ..     270     284 ..     269     296 .. 0.87
   6 ?   -0.8   0.1       2.5   1.1e+03       3      14 ..     319     330 ..     318     333 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.36
                                  HHHHHHHHHHH CS
                      HTH_Bact  4 eaLeqvnkAie 14
                                  +aL++v+kA+e
  gi|15669131|ref|NP_247936.1| 47 KALYYVDKALE 57
                                  79*******98 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.027
                                   THHHHHHHHHHHHHHTT- CS
                      HTH_Bact  24 LlGQLyYqkgecleklgf 41 
                                   ++GQLy   g+c e l+ 
  gi|15669131|ref|NP_247936.1| 102 FVGQLYGMSGNCDEALKC 119
                                   89**********999985 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.2
                                   HHHHHHHHTT CS
                      HTH_Bact  31 qkgecleklg 40 
                                    k+e l+klg
  gi|15669131|ref|NP_247936.1| 170 KKAEILRKLG 179
                                   59******96 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.18
                                   -HHHHHHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                   rYe aL   n+A+e+
  gi|15669131|ref|NP_247936.1| 180 RYEDALLCLNRALEL 194
                                   7***********997 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.03
                                   HHHHHHHHHHHTT-- CS
                      HTH_Bact  28 LyYqkgecleklgfs 42 
                                   L+Y kge+ e+lg  
  gi|15669131|ref|NP_247936.1| 270 LWYFKGELYERLGKL 284
                                   89**********865 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 2.5
                                   HHHHHHHHHHHH CS
                      HTH_Bact   3 eeaLeqvnkAie 14 
                                   e a+e+ nkA+e
  gi|15669131|ref|NP_247936.1| 319 EAAIEYYNKAVE 330
                                   679999999997 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.61   2.7e+02     151     173 ..      68      90 ..      25     101 .. 0.79
   2 ?   -0.2   0.0       1.6   7.1e+02     153     173 ..     104     124 ..     102     129 .. 0.88
   3 ?    5.1   0.1     0.037        16     120     181 ..     172     238 ..     169     252 .. 0.79
   4 ?    4.0   0.0     0.079        35     152     175 ..     274     297 ..     269     309 .. 0.86
   5 ?    3.3   0.1      0.13        58     155     179 ..     311     335 ..     304     338 .] 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.61
                        TPR_21 151 lrGDilvaqgkldeAraaYqaAl 173
                                   l+G +l+a+g+++eA + +++ l
  gi|15669131|ref|NP_247936.1|  68 LKGLALSAKGEIKEAITTFEELL 90 
                                   7999999********99998865 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
                        TPR_21 153 GDilvaqgkldeAraaYqaAl 173
                                   G ++   g+ deA + Y++Al
  gi|15669131|ref|NP_247936.1| 104 GQLYGMSGNCDEALKCYNKAL 124
                                   7889999************98 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.037
                        TPR_21 120 arvllaekkydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAlaaleeka....r 181
                                   a++l + + y++Al  L+++ + +  +  +  l+G +l ++gk+ eA + +++ +++l+ k     r
  gi|15669131|ref|NP_247936.1| 172 AEILRKLGRYEDALLCLNRAlELKPHDKNALYLKGVLLKRMGKFREALECFKKLIDELNVKWidaiR 238
                                   788899999********876255789999999********************999998877666664 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.079
                        TPR_21 152 rGDilvaqgkldeAraaYqaAlaa 175
                                   +G+++ + gkldeA + Y++ ++ 
  gi|15669131|ref|NP_247936.1| 274 KGELYERLGKLDEALKCYEKVIEL 297
                                   9******************98875 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.13
                        TPR_21 155 ilvaqgkldeAraaYqaAlaaleek 179
                                   i+ +qg+++ A + Y++A+++++++
  gi|15669131|ref|NP_247936.1| 311 IYERQGNIEAAIEYYNKAVENIHKD 335
                                   7889999999999999999998775 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         6   2.7e+03     188     227 ..       9      48 ..       8      54 .. 0.74
   2 ?    4.9   0.0     0.034        15      81     139 ..      78     134 ..      65     139 .. 0.81
   3 !    8.4   0.0    0.0029       1.3     207     255 ..     171     219 ..     146     242 .. 0.83
   4 ?    0.0   0.0         1   4.6e+02     179     233 ..     280     334 ..     206     337 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6
                                   HHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                    Coatomer_E 188 yifqelsekykstplllngkAvvslllgryeeAeslLkea 227
                                   y + ++    k+tp + + +Av+++l    e  e  L +a
  gi|15669131|ref|NP_247936.1|   9 YFYGDMRMNRKRTPRVDTLEAVANVLRAYRELFEGNLIKA 48 
                                   7888888888999999999999988766555555555555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.034
                                   THHHHHHHHHHHHHS----S-HHHHHHHHHHHHHTT-HHHHHHHHTT--SHHHHHHHHH CS
                    Coatomer_E  81 rkeeilaelkeeladseiesnevlrllaaivflkegdfddalkllkksenLeavAlkvq 139
                                   + +e++   +e l+ +++  n +  +  + ++   g+ d+alk  +k  ++e + l+ +
  gi|15669131|ref|NP_247936.1|  78 EIKEAITTFEELLSYESK--NPITWVFVGQLYGMSGNCDEALKCYNKALGIENRFLSAF 134
                                   567788888888887765..999***********************9999998777665 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0029
                                   HHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHH CS
                    Coatomer_E 207 kAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevs 255
                                   kA +  +lgrye+A   L+ aL+ +++d+++L    v+ + +gk  e+ 
  gi|15669131|ref|NP_247936.1| 171 KAEILRKLGRYEDALLCLNRALELKPHDKNALYLKGVLLKRMGKFREAL 219
                                   556666799***********************99999999999977664 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 1
                                   -TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT CS
                    Coatomer_E 179 ggekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdak 233
                                     +k+ +A+  ++ + e  ++    l  kA +   +g+ e+A +  ++a +  +k
  gi|15669131|ref|NP_247936.1| 280 RLGKLDEALKCYEKVIELQPHYIKALLSKARIYERQGNIEAAIEYYNKAVENIHK 334
                                   3356666666666666666666666666666666666666666666666665555 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       5.1   2.3e+03     168     191 ..      76      99 ..      71     114 .. 0.76
   2 ?    0.1   0.0      0.98   4.4e+02     121     142 ..     104     124 ..      99     129 .. 0.75
   3 ?    0.1   0.0      0.99   4.4e+02     121     181 ..     172     225 ..     165     232 .. 0.47
   4 ?    3.5   0.0     0.091        41     121     143 ..     275     296 ..     210     305 .. 0.55
   5 !    8.4   0.4    0.0029       1.3     120     148 ..     308     335 ..     302     338 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.1
                                   TT-HHHHHHHHHHHHHTTSS-TTT CS
                          SNAP 168 lekyekAieiyekvakkslennll 191
                                   +++ ++Ai+ +e++ +   +n ++
  gi|15669131|ref|NP_247936.1|  76 KGEIKEAITTFEELLSYESKNPIT 99 
                                   567889999999998888888776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.98
                                   HHHHHHTT--HHHHHHHHHHHH CS
                          SNAP 121 aelyekelgdlekAieaYekAa 142
                                   ++ly    g+ ++A+++Y+kA 
  gi|15669131|ref|NP_247936.1| 104 GQLYGMS-GNCDEALKCYNKAL 124
                                   6777777.78888888888875 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.99
                                   HHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          SNAP 121 aelyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiyekv 181
                                   ae++ k  g++e+A+ + ++A el  ++      n ++lk   l  +++k+ +A+e ++k+
  gi|15669131|ref|NP_247936.1| 172 AEILRKL-GRYEDALLCLNRALELKPHD-----KNALYLKG-VLLKRMGKFREALECFKKL 225
                                   4444443.55555555555555443222.....23333332.2223455555555555555 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.091
                                   HHHHHHTT--HHHHHHHHHHHHH CS
                          SNAP 121 aelyekelgdlekAieaYekAae 143
                                   +elye   g+l++A+++Yek  e
  gi|15669131|ref|NP_247936.1| 275 GELYERL-GKLDEALKCYEKVIE 296
                                   3444433.667777777776554 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0029
                                   HHHHHHHTT--HHHHHHHHHHHHHHHHHT CS
                          SNAP 120 iaelyekelgdlekAieaYekAaelyeqe 148
                                    a +ye + g++e+Aie+Y+kA e  +++
  gi|15669131|ref|NP_247936.1| 308 KARIYERQ-GNIEAAIEYYNKAVENIHKD 335
                                   589*****.*************9976666 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       9.4   4.2e+03      81      96 ..      70      85 ..      62      92 .. 0.64
   2 ?   -0.6   0.0       3.2   1.5e+03      14      28 ..     110     124 ..     105     164 .. 0.77
   3 !    8.6   0.0    0.0048       2.2      43      95 ..     170     220 ..     143     230 .. 0.83
   4 ?    3.9   0.0      0.14        61      48      86 ..     209     247 ..     206     262 .. 0.84
   5 ?    0.7   0.0       1.3   5.8e+02       3      30 ..     304     331 ..     302     336 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.4
                         TPR_5 81 aLvLsdlgrereavsi 96
                                   L+Ls++g  +ea+++
  gi|15669131|ref|NP_247936.1| 70 GLALSAKGEIKEAITT 85
                                  4666666666666654 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.2
                         TPR_5  14 tGhedkavplYrraL 28 
                                    G+ d+a + Y++aL
  gi|15669131|ref|NP_247936.1| 110 SGNCDEALKCYNKAL 124
                                   688899999999998 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0048
                         TPR_5  43 qLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgrereavs 95 
                                   + a  LR lG+ e+al  L+  le ++++  +al  +  + L  +g+ rea+ 
  gi|15669131|ref|NP_247936.1| 170 KKAEILRKLGRYEDALLCLNRALELKPHDK-NALY-LKGVLLKRMGKFREALE 220
                                   56788**************99999987764.4554.56777999999999986 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.14
                         TPR_5  48 LRnlGeaeealaLLraeleapsdelddalaaflaLvLsd 86 
                                   L+ +G+  eal+  ++++++ + +  da++  ++L+L+ 
  gi|15669131|ref|NP_247936.1| 209 LKRMGKFREALECFKKLIDELNVKWIDAIRHAVSLMLAL 247
                                   7889****************9999999999999999863 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 1.3
                         TPR_5   3 aaFeragarDstGhedkavplYrraLae 30 
                                   a+  +a + +  G+ ++a++ Y++a+++
  gi|15669131|ref|NP_247936.1| 304 ALLSKARIYERQGNIEAAIEYYNKAVEN 331
                                   566788888999*************987 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       2.6   1.2e+03      21      34 ..     110     123 ..     107     131 .. 0.87
   2 ?    5.0   0.0     0.063        28      13      36 ..     170     193 ..     162     206 .. 0.88
   3 ?    4.6   0.0     0.085        38      20      37 ..     211     228 ..     204     249 .. 0.82
   4 ?    1.7   0.0      0.67     3e+02      22      36 ..     282     296 ..     274     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.6
                     NRBF2_MIT  21 aGkyeeaischkka 34 
                                   +G  +ea+ c++ka
  gi|15669131|ref|NP_247936.1| 110 SGNCDEALKCYNKA 123
                                   58899*******99 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.063
                     NRBF2_MIT  13 rkadrllaaGkyeeaischkkaaa 36 
                                   +ka+ l   G+ye+a+ c ++a +
  gi|15669131|ref|NP_247936.1| 170 KKAEILRKLGRYEDALLCLNRALE 193
                                   7999999***********998865 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.085
                     NRBF2_MIT  20 aaGkyeeaischkkaaay 37 
                                     Gk+ ea+ c kk  + 
  gi|15669131|ref|NP_247936.1| 211 RMGKFREALECFKKLIDE 228
                                   57***********97665 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.67
                     NRBF2_MIT  22 Gkyeeaischkkaaa 36 
                                   Gk +ea+ c++k  +
  gi|15669131|ref|NP_247936.1| 282 GKLDEALKCYEKVIE 296
                                   9*********99876 PP

>> Cohesin_load  Cohesin loading factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.12        52     404     437 ..      64      97 ..      41     105 .. 0.85
   2 ?    7.8   0.0    0.0022      0.98     368     429 ..     160     225 ..     100     263 .. 0.72
   3 ?    0.1   0.1      0.47   2.1e+02     405     432 ..     299     331 ..     270     336 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.12
                  Cohesin_load 404 lllyLeglyaqskgdlkaAlaqyketaarksker 437
                                   l l+L+gl   +kg++k+A +++ e+++ +sk+ 
  gi|15669131|ref|NP_247936.1|  64 LALFLKGLALSAKGEIKEAITTFEELLSYESKNP 97 
                                   6789*******************98877777665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0022
                  Cohesin_load 368 liafvlknwkkankeleeletasnklesk....llkelaplllyLeglyaqskgdlkaAlaqyket 429
                                   ++   +  w+k  + l +l  +  +l +     +lk ++ + lyL+g+   ++g++ +Al+ +k++
  gi|15669131|ref|NP_247936.1| 160 YTPNFVPMWVKKAEILRKLGRYEDALLCLnralELKPHDKNALYLKGVLLKRMGKFREALECFKKL 225
                                   4444455555555566666666655555455678999**************************833 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.47
                  Cohesin_load 405 llyLeglyaqsk.....gdlkaAlaqyketaar 432
                                    +y ++l + ++     g ++aA ++y +++ +
  gi|15669131|ref|NP_247936.1| 299 PHYIKALLSKARiyerqGNIEAAIEYYNKAVEN 331
                                   356666655555555558888888888655444 PP

>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2       1.3   5.8e+02      22      35 ..      44      57 ..       7      59 .. 0.73
   2 ?    3.2   0.0      0.35   1.5e+02      11      33 ..     105     123 ..     100     124 .. 0.79
   3 ?    0.3   0.0       2.9   1.3e+03      13      32 ..     203     224 ..     201     227 .. 0.81
   4 ?    4.4   0.2      0.15        66       8      32 ..     269     293 ..     267     297 .. 0.84
   5 ?    6.9   0.1     0.024        11      21      36 ..     315     331 ..     308     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1.3
                          Sel1 22 DpekAiewyekAAe 35
                                  + +kA+++  kA e
  gi|15669131|ref|NP_247936.1| 44 NLIKALYYVDKALE 57
                                  67788888777765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.35
                          Sel1  11 ylylnGlgvpkDpekAiewyekA 33 
                                   +  l+G     + ++A+++y kA
  gi|15669131|ref|NP_247936.1| 105 Q--LYG--MSGNCDEALKCYNKA 123
                                   3..444..79999*********9 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.9
                          Sel1  13 ylnGlgvpk..DpekAiewyek 32 
                                   yl+G  +++    ++A+e+++k
  gi|15669131|ref|NP_247936.1| 203 YLKGVLLKRmgKFREALECFKK 224
                                   688887888877899*****98 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.15
                          Sel1   8 GmfylylnGlgvpk..DpekAiewyek 32 
                                   +  ++y++G   ++    ++A+++yek
  gi|15669131|ref|NP_247936.1| 269 A--LWYFKGELYERlgKLDEALKCYEK 293
                                   7..566****8888777*********8 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.024
                          Sel1  21 k.DpekAiewyekAAeq 36 
                                   + ++e Aie+y kA e+
  gi|15669131|ref|NP_247936.1| 315 QgNIEAAIEYYNKAVEN 331
                                   359999********887 PP

>> SMG1  Serine/threonine-protein kinase smg-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0056       2.5     455     533 ..      17      99 ..      10     191 .. 0.69
   2 ?    1.9   0.0      0.13        57     496     528 ..     198     230 ..     182     252 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0056
                          SMG1 455 knsktqgaefeqaivllaeAlvelkeadalrGlyvwskekss.ksl...qwlkavaeqAaGkfekAaeeykelLkektevs 531
                                   + ++t+  +   a+  + +A+ el e++ ++ ly   k+      +    +lk +a  A+G   +A+  ++elL+ + +  
  gi|15669131|ref|NP_247936.1|  17 NRKRTPRVDTLEAVANVLRAYRELFEGNLIKALYYVDKALELePDFylaLFLKGLALSAKGEIKEAITTFEELLSYESKNP 97 
                                   456778888889999999***************988776432233322369***********************9977664 PP

                          SMG1 532 el 533
                                     
  gi|15669131|ref|NP_247936.1|  98 IT 99 
                                   33 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.13
                          SMG1 496 skslqwlkavaeqAaGkfekAaeeykelLkekt 528
                                   +k+  +lk v  +  Gkf +A+e +k+l++e +
  gi|15669131|ref|NP_247936.1| 198 DKNALYLKGVLLKRMGKFREALECFKKLIDELN 230
                                   68999**********************999854 PP

>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.9   1.7e+03      92     109 ..     106     123 ..      88     139 .. 0.79
   2 ?    1.9   0.1       0.4   1.8e+02      99      99 ..     200     200 ..     166     242 .. 0.51
   3 ?    9.9   2.3    0.0014      0.65      20     128 ..     212     321 ..     207     335 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.9
                                   HHHTTXTHSSHSSXSSSS CS
                      Clathrin  92 lykkinefkkaisllkkl 109
                                   ly   ++ ++a+++++k 
  gi|15669131|ref|NP_247936.1| 106 LYGMSGNCDEALKCYNKA 123
                                   899999999999998875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.4
                                   H CS
                      Clathrin  99 f 99 
                                   +
  gi|15669131|ref|NP_247936.1| 200 N 200
                                   1 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0014
                                   TT-HHHHCHHHCCHHHCHTS.--HHHHHHHHHHHHHTT-HHHHHHTTSS---S-TTHHHHHHHT-SSHHHHHHHHHTTXTH CS
                      Clathrin  20 aglleelleyLekvlkedsk.enpalqtallelyakyddpqeleeflkknnnydlekvaklcekadlyeeavilykkinef 99 
                                    g+++e+le+ +k+++e +     a+  a+  ++a +d ++++e++++   ++ ++ va +  k +lye++  l  +++++
  gi|15669131|ref|NP_247936.1| 212 MGKFREALECFKKLIDELNVkWIDAIRHAVSLMLALDD-LKDAERYINIGLEIRKDDVALWYFKGELYERLGKLDEALKCY 291
                                   67777777777777765544434566666666666666.8***************************************** PP

                                   SSHSSX.SSSSHCSCHHHHTTTTTXXSHHH CS
                      Clathrin 100 kkaisl.lkklkdfddaieyaakvsnpelw 128
                                   +k+i+l  ++ k++  ++++++++ n e++
  gi|15669131|ref|NP_247936.1| 292 EKVIELqPHYIKALLSKARIYERQGNIEAA 321
                                   *************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.87u 0.28s 00:00:01.14 Elapsed: 00:00:00.52
# Mc/sec: 1959.20
//
Query:       gi|15669132|ref|NP_247937.1|  [L=651]
Description: ATP-dependent DNA helicase DinG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-28   97.9   0.2    2.1e-27   96.4   0.0    2.0  2  Helicase_C_2    Helicase C-terminal domain
    1.6e-10   41.3   0.0    7.4e-10   39.1   0.0    2.0  1  ResIII          Type III restriction enzyme, res subunit
    5.4e-09   36.1   0.0    4.9e-06   26.4   0.0    2.8  3  DEAD            DEAD/DEAH box helicase
    6.9e-07   29.6   4.4     0.0002   21.7   0.2    4.2  3  Helicase_C      Helicase conserved C-terminal domain
     0.0055   17.0   0.9      0.014   15.6   0.9    1.7  1  FliS            Flagellar protein FliS
  ------ inclusion threshold ------
      0.019   14.7   1.4      0.019   14.7   1.4    1.9  2  DNA_pol3_delta  DNA polymerase III, delta subunit
      0.029   14.7   0.0        9.4    6.5   0.0    2.7  2  AAA_22          AAA domain
      0.032   12.9   0.4       0.42    9.3   0.0    2.2  2  SNF2_N          SNF2 family N-terminal domain
      0.053   12.8   0.4       0.13   11.5   0.0    1.7  2  DUF2075         Uncharacterized conserved protein (DUF2075)
        0.8    9.3   7.7        1.7    8.2   7.7    1.6  1  DEAD_2          DEAD_2


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       6.4   1.1e+04      92     110 ..      10      28 ..       7      36 .. 0.74
   2 !   96.4   0.0   1.2e-30   2.1e-27       1     157 [.     450     614 ..     450     623 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.4
                  Helicase_C_2  92 glPfpnpkdpeveakreyl 110
                                   + P+p++ +p+ ++  + +
  gi|15669132|ref|NP_247937.1|  10 KFPYPKVREPQKRMMLKIY 28 
                                   6799999999877666655 PP

  == domain 2  score: 96.4 bits;  conditional E-value: 1.2e-30
                  Helicase_C_2   1 llellevvpggvlvffpSyklleevverlkeel.....eskkieifvee.keesrekvleeykekkkkgaillavcrGkls 75 
                                   ll++le+++g+ lv+f+S++ l++++++lk+e      ++k+i+++++  + ++ +++ e++++    g illa+   ++ 
  gi|15669132|ref|NP_247937.1| 450 LLKILEAINGNSLVLFKSFEDLDSFYKYLKREItktniKNKNIHVYEQGmDGKEAKELKERFEK---IGGILLATG--RFA 525
                                   6899**************************9764555577777999987777788888888988...9******96..*** PP

                  Helicase_C_2  76 EGidfsddllraviivglPfpnpkdpeveakreyldekgk........knsgkewylpealravnQaiGRliRhkdDygai 148
                                   EG+d+++++l  v+i  lPfp p  p +   ++ l+e++k         +++     +++ r++ Q iGRliR+++Dyg++
  gi|15669132|ref|NP_247937.1| 526 EGVDIPGEALVGVVIDSLPFPVP-TPLILREQKILEERFKirgvrdahWRAFLMTSFDRMARTLVQMIGRLIRTENDYGVV 605
                                   ***********************.5888888899******999987665666677778899******************** PP

                  Helicase_C_2 149 vllDeRfak 157
                                   v+ D+Rfa+
  gi|15669132|ref|NP_247937.1| 606 VIQDKRFAD 614
                                   *******85 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   4.1e-13   7.4e-10       3     147 ..      15     203 ..      14     226 .. 0.70

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 4.1e-13
                                   EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG... CS
                        ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayk 83 
                                   ++re Q++++ ++ e +k  ++++++++++TG+GKTl ++  + ++++ +  +++l+l  +++   + +e+++++ ++ + 
  gi|15669132|ref|NP_247937.1|  15 KVREPQKRMMLKIYECIK--NKRNLIVEAPTGVGKTLGYLIPALYFAERR--KRVLILTETIDQQVRIYEDLSSLRHNLKV 91 
                                   689**************5..999999**********99988888887765..5**********999999999666666544 PP

                                   .........GEEEESSS-B--.....................................................-SEEEEE CS
                        ResIII  84 e........igkkvsgdkkka..............................................kekdstnkkilvtt 110
                                   +        i+k++ g+ ++                                                +++s  ++i+v++
  gi|15669132|ref|NP_247937.1|  92 AflmgksnfICKSKGGKANRLycqlnkkclyrpnkrpicycgtkkqpvnlgdkviyycpyctceyqkAKIESILADIVVMN 172
                                   455555444444433333333555555555555555666666666678887778888888885554444455555666666 PP

                                   HHHHHHTH........HHHTTT-SEEEEETGGGTTS. CS
                        ResIII 111 iqsldadseeeeeeseellrdrfdviiiDEaHrlgak 147
                                    ++++ ++     e+ e  +  +d+ii+DEaH+l ++
  gi|15669132|ref|NP_247937.1| 173 NSMFYYAK-----EDIE-AKRDIDIIICDEAHKLESS 203
                                   66666666.....3333.444577*********9984 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.8e-09   4.9e-06       7      83 ..      27      96 ..      19     116 .. 0.81
   2 !    6.3   0.0    0.0042       7.5      90     136 ..     157     203 ..     147     216 .. 0.76
   3 ?   -2.7   0.0       2.4   4.3e+03     160     170 ..     387     397 ..     376     401 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.8e-09
                                  HHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  7 aiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig 83
                                  ++++i ++++++v+a+TG GKTl +lip+l        ++++++li++ t      ++++l+++ ++  l+v  ++g
  gi|15669132|ref|NP_247937.1| 27 IYECIKNKRNLIVEAPTGVGKTLGYLIPALYFA-----ERRKRVLILTETIDQQVRIYEDLSSLRHN--LKVAFLMG 96
                                  56778899**********************444.....68889999999988888888888888775..45554444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0042
                                   HHHHHHTT.CSEEEEEHHHHHHHHHCTSSH.CTTEEEEEEETHHHHHHT CS
                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                          DEAD  90 qlskldng.vdivvgtpgrlddllstgkln.lsqvrflVlDEadrlldq 136
                                   q++k+++  +divv++ +++    +   ++  +++ +++ DEa++l ++
  gi|15669132|ref|NP_247937.1| 157 QKAKIESIlADIVVMNNSMFYYAKE--DIEaKRDIDIIICDEAHKLESS 203
                                   5566643369999999999998553..33326799***********987 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.4
                                   SEEEEEESSBS CS
                                   xxxxxxxxxxx RF
                          DEAD 160 rqvivlSATlp 170
                                     vi +SAT+ 
  gi|15669132|ref|NP_247937.1| 387 AVVIHCSATIG 397
                                   33999****85 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.015        27       8      49 ..      54      97 ..      47     117 .. 0.76
   2 ?    1.2   0.1      0.25   4.5e+02      74      94 ..     251     271 ..     135     294 .. 0.73
   3 !   21.7   0.2   1.1e-07    0.0002       5     109 ..     449     597 ..     444     599 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.015
                                  HHHHHTTTTSEEEEEESSHH...HHHH.HHHHHHHTTSTEEEESTT CS
                    Helicase_C  8 ellkleeeggkilifvntid...rlek.vklllekkgikvavlhge 49
                                    l + e+++++li ++tid   r+++ ++ l  ++++kva l g+
  gi|15669132|ref|NP_247937.1| 54 PALYFAERRKRVLILTETIDqqvRIYEdLSSL--RHNLKVAFLMGK 97
                                  4446789*************755554344555..667888887775 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.25
                                   GGGTSSSTSTTESEEEESSSS CS
                    Helicase_C  74 dvaerGidipkvnlVinfdlp 94 
                                      +rGi+i+ ++  i+fd  
  gi|15669132|ref|NP_247937.1| 251 YLTSRGINIDICKETIIFDGE 271
                                   347899999999999999865 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 1.1e-07
                                   HHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT......TSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESGGGT CS
                    Helicase_C   5 allellkleeeggkilifvntidrlek.vklllekk......gikvavlhgelpqnereeileqfnkgesd.vLiatdvae 77 
                                    ll++l  e+++g++l+  ++ ++l++  k+l+++       + ++ v+   +  +e +e  e+f   ++  +L+at   +
  gi|15669132|ref|NP_247937.1| 449 NLLKIL--EAINGNSLVLFKSFEDLDSfYKYLKREItktnikNKNIHVYEQGMDGKEAKELKERFE--KIGgILLATGRFA 525
                                   455555..899************9988878883322555577899999999**************3..4555********* PP

                                   SSSTSTTESEE..EESSSSSSH......................................HHHHHHHTTSSS CS
                    Helicase_C  78 rGidipkvnlV..infdlprnv......................................tsyiqriGRtgR 109
                                   +G+dip+  lV  ++ +lp+ v                                      ++++q+iGR +R
  gi|15669132|ref|NP_247937.1| 526 EGVDIPGEALVgvVIDSLPFPVptplilreqkileerfkirgvrdahwraflmtsfdrmaRTLVQMIGRLIR 597
                                   ******855431144455544445677777777888888888888888888888888888888888888877 PP

>> FliS  Flagellar protein FliS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.9     8e-06     0.014      35      94 ..     437     491 ..     426     508 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8e-06
                                   HHHTTTHHHHHHHHHHHHHHHHHHHHTCCTTTSCHHHHHHHHHHHHHHHHHHHHHHCT-H CS
                          FliS  35 aieekdiekkgeaiskaqdIiseLrasLdlekggeiaknLaalYdyiirrlleanlkkda 94 
                                     e+kd ek+++++ k  + i++ +  L ++      ++L+++Y+y+ r++++ n+k++ 
  gi|15669132|ref|NP_247937.1| 437 KYERKDREKANKNLLKILEAINGNSLVL-FK----SFEDLDSFYKYLKREITKTNIKNKN 491
                                   56899*****************976666.43....489*******************986 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1         5   8.9e+03      57      87 ..     321     350 ..     310     363 .. 0.60
   2 ?   14.7   1.4   1.1e-05     0.019      57     130 ..     424     503 ..     416     515 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5
                                   SEEEEEEE--.....TT-S-TTHHHHHHHHT CS
                DNA_pol3_delta  57 dkrivvlknpklltkesklnekllkeLeeyl 87 
                                   d++ +++  + ++ k++ l++  l e+ e +
  gi|15669132|ref|NP_247937.1| 321 DNKALIAIELDFIHKKK-LSDLYLLEFIENI 350
                                   55555555555664444.4444444444444 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.1e-05
                                   SEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHH.....HHHH.HTTTEEEEEE----TTT CS
                DNA_pol3_delta  57 dkrivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkk.....lvkl.Lkkkatvveaktlkeee 130
                                    k+i+ lk+  +++ e+k+ ek +k+L ++l+ ++ ++l ++ + ++ld+  k     ++k+ +k+k + v ++ ++++e
  gi|15669132|ref|NP_247937.1| 424 RKKIIALKDGVDMKYERKDREKANKNLLKILEAINGNSLVLFKSFEDLDSFYKylkreITKTnIKNKNIHVYEQGMDGKE 503
                                   589*********9999**********************9999999****9888766666665355566666666665444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.014        25       4      20 ..      33      49 ..      29      91 .. 0.90
   2 ?    6.5   0.0    0.0052       9.4      78     105 ..     175     203 ..     141     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.014
                        AAA_22  4 tagilvvtGesGtGKTt 20
                                  +++ l+v +++G+GKT+
  gi|15669132|ref|NP_247937.1| 33 NKRNLIVEAPTGVGKTL 49
                                  78999***********8 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0052
                        AAA_22  78 llealeqalraravielliiDEaqhlr.s 105
                                   ++ +  + ++a+++i ++i DEa++l  s
  gi|15669132|ref|NP_247937.1| 175 MFYYAKEDIEAKRDIDIIICDEAHKLEsS 203
                                   454555566666667***********533 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00024      0.42     174     198 ..     185     209 ..     153     216 .. 0.75
   2 ?    1.2   0.1     0.065   1.2e+02     243     310 ..     432     505 ..     414     516 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00024
                                   -S-S-SEEEES-GGGT--TTSHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 174 kqvewkrvvlDEghtlknstskaae 198
                                    +++++ +++DE+h+l++s +++++
  gi|15669132|ref|NP_247937.1| 185 AKRDIDIIICDEAHKLESSIRNTST 209
                                   466799************9555544 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.065
                                   HHTHHHHH.HHHHHHHHHHHTT-S.....TTEE---GGGT--S---EEEEEEEEE--HHHHHHHH......... CS
                                   xxxxxxxx.xxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 243 kllqrpie.aqaekgrsrLlqllq.....rlmlrrakkdveknlPpkteeiiflklskverksYnrllevlrkk 310
                                   ++++ ++e + +ek  ++Ll++l+     +l+l+++++d++      + ei+  ++++++ ++Y++ ++ +  k
  gi|15669132|ref|NP_247937.1| 432 DGVDMKYErKDREKANKNLLKILEaingnSLVLFKSFEDLDSFYKYLKREITKTNIKNKNIHVYEQGMDGKEAK 505
                                   56666777455667778999999966666699********888888899999999*********9777665554 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.1e-05      0.13      72     102 ..     171     202 ..     153     216 .. 0.76
   2 ?   -3.3   0.1       2.3   4.1e+03     202     223 ..     465     486 ..     444     513 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.1e-05
                       DUF2075  72 nnlsef.kkaeekkeepkedvvivDEAhrllt 102
                                   +n s f + +e+ ++++++d++i+DEAh+l +
  gi|15669132|ref|NP_247937.1| 171 MNNSMFyYAKEDIEAKRDIDIIICDEAHKLES 202
                                   34444546667778999************987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.3
                       DUF2075 202 irvfddleelkkalkeknkesg 223
                                   ++ f+dl++++k+lk++ ++++
  gi|15669132|ref|NP_247937.1| 465 FKSFEDLDSFYKYLKREITKTN 486
                                   4555555555555555433333 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   7.7   0.00094       1.7      59     171 ..     102     212 ..      71     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00094
                                   HHHHHCCHHCCH...TTTTTT-SCCCCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCC CS
                        DEAD_2  59 Ckelkkkkaeek...eekCsffenleelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldek 136
                                   Ck++  k ++ +   ++kC +  n++ +      +++++v++ d v +     +C Y  ++     adi+++  +++  +k
  gi|15669132|ref|NP_247937.1| 102 CKSKGGKANRLYcqlNKKCLYRPNKRPICY--CGTKKQPVNLGDKVIYYCPYCTCEYQKAKIESILADIVVMNNSMFYYAK 180
                                   555555544433444555555555533332..3445555666555555555667888888999999999999998887666 PP

                                   CHHHHHT..GCGCEEEECTCCCHHHHHHHCC-EEE CS
                        DEAD_2 137 ireslkgislknsivilDEAhNiedvceeaasvei 171
                                      ++   +    i+i DEAh +e+ ++++  + i
  gi|15669132|ref|NP_247937.1| 181 EDIEA---KRDIDIIICDEAHKLESSIRNTSTIII 212
                                   44444...47779**************99877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 4212.76
//
Query:       gi|15669133|ref|NP_247938.1|  [L=417]
Description: hypothetical protein MJ_0943 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.012   14.6   2.1      0.019   13.9   2.1    1.2  1  PA26            PA26 p53-induced protein (sestrin)
      0.043   14.4   0.0       0.15   12.6   0.0    1.9  2  LEA_2           Late embryogenesis abundant protein
      0.095   12.9   1.3       0.17   12.1   1.3    1.3  1  Shisa           Wnt and FGF inhibitory regulator
       0.45    9.2   5.4       0.71    8.6   5.4    1.3  1  Presenilin      Presenilin
       0.72    8.2   4.8        0.3    9.5   1.4    1.8  2  SID-1_RNA_chan  dsRNA-gated channel SID-1


Domain annotation for each model (and alignments):
>> PA26  PA26 p53-induced protein (sestrin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.1   5.2e-06     0.019     162     277 ..      13     130 ..       6     144 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-06
                          PA26 162 hfhslasfvfgcglepeldlesskklksasas..anekedsseeeeeelerkaaaeaeaevealmermkklqeeedeeeea 240
                                    f  l+ +v++cg+ +  ++   +  +++ +   +++  ++++++ +++e+k+ ++++++++   ++  k qe++  ++++
  gi|15669133|ref|NP_247938.1|  13 CFSILSILVLACGCVNTPEKIDININSNTNNGenTEKPINQENQNVNNVENKKESQSTQNIQSYENKEIKNQENHPLQSNQ 93 
                                   455688899999988766655543333333221123455666666666666666666777766666666666666665666 PP

                          PA26 241 seeelserfekeeseslllaaadaeeaavasdlsryv 277
                                   + e++  +f++e++++++ + +++ + + ++ ++ y+
  gi|15669133|ref|NP_247938.1|  94 NYEQTNGNFNEENENAMTNVGESEVNYNNEPAYNYYI 130
                                   6677777787777776666655455555555555555 PP

>> LEA_2  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.57     2e+03       2      22 ..     286     306 ..     285     308 .. 0.88
   2 ?   12.6   0.0   4.2e-05      0.15       4      96 ..     307     390 ..     304     397 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.57
                                   EEEEESSSS-EEEEEEEEEEE CS
                         LEA_2   2 lrvrNPNsfgvrydgleldls 22 
                                   ++++N  ++ ++y ++++dl 
  gi|15669133|ref|NP_247938.1| 286 IEMENGEKINLKYVSMDVDLI 306
                                   7899**************996 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.2e-05
                                   EEESSSS-EEEEEEEEEEEE.SSSEEEEEEECE-EEESSSCEEEEEEEEEEEHHHHHHHHHHHH..HCCSEEEEEEEEEEE CS
                         LEA_2   4 vrNPNsfgvrydgleldlsy.ngqrlasgtspqgfsqpargtttlevpvsvsaddlarelrallagevgleleytlrgrlk 83 
                                   ++NPNs ++++d++ l     +g +l++g++++ +  p  +  t++v ++++     ++lr+l     g+e+  ++ g ++
  gi|15669133|ref|NP_247938.1| 307 IDNPNSESITIDKIILNMFDdEGHSLGRGEVSNIVITPGENPVTVKVNIPINKMG-YEILRKL----SGEEVFAEISGSAY 382
                                   89************999985378****9999999888888888777777777765.4444444....47777777777765 PP

                                   .EEETTTSCEEEE CS
                         LEA_2  84 vlgkpilgsvtvp 96 
                                          gs +vp
  gi|15669133|ref|NP_247938.1| 383 I-----EGSGEVP 390
                                   2.....2233444 PP

>> Shisa  Wnt and FGF inhibitory regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.3   4.7e-05      0.17      91     180 ..       9      96 ..       2     104 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.7e-05
                         Shisa  91 tifivfvivgvvvivcccgclk.kkqrekrpgrenlssalaevgpivtettsattvvhsrysepqqssssssypgatnqgy 170
                                    +++ f i+ ++  v  cgc+  + + +  + ++n++    + +pi +e+++ ++v + ++s+++q+  s ++++ +nq+ 
  gi|15669133|ref|NP_247938.1|   9 KALVCFSILSIL--VLACGCVNtPEKIDI-NINSNTNNGENTEKPINQENQNVNNVENKKESQSTQNIQSYENKEIKNQEN 86 
                                   567777666444..445556440444333.355555555555589999888888888788877777777777777779999 PP

                         Shisa 171 qpvpvqpgmp 180
                                   +p+ +++ ++
  gi|15669133|ref|NP_247938.1|  87 HPLQSNQNYE 96 
                                   9998876665 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.4    0.0002      0.71     215     305 ..      21     112 ..      14     148 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0002
                    Presenilin 215 iYsatvvvlaaeek.kaevaeseeeeeaekkkeeasesskeeeseeesseksaqsseseeeseeesseaessaeesseeke 294
                                   + +   v + ++ + + + ++++ e++++  ++e+++ ++ e+++e++s+++ qs e++e +++e+++ +s+++ ++++ +
  gi|15669133|ref|NP_247938.1|  21 VLACGCVNTPEKIDiNINSNTNNGENTEKPINQENQNVNNVENKKESQSTQNIQSYENKEIKNQENHPLQSNQNYEQTNGN 101
                                   555555555555555555555555555555666666666666666666666666666666666666666666665555555 PP

                    Presenilin 295 seessesseee 305
                                    +e++e++ ++
  gi|15669133|ref|NP_247938.1| 102 FNEENENAMTN 112
                                   44444433333 PP

>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.4   8.3e-05       0.3     127     247 ..      11     157 ..       2     160 .. 0.57
   2 ?   -0.7   0.1     0.099   3.5e+02      41      74 ..     225     259 ..     218     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 8.3e-05
                SID-1_RNA_chan 127 llvllsfllltllvvivekvre...................sseekrvkessssesaseslesvssavrsesessveeesd 188
                                   l+++ ++ +l+l+  +v++ ++                   ++e+++v   ++ e+++es+++ + +  +++e + +e++ 
  gi|15669133|ref|NP_247938.1|  11 LVCFSILSILVLACGCVNTPEKidininsntnngentekpiNQENQNV---NNVENKKESQSTQNIQSYENKEIKNQENHP 88 
                                   455555566666666665444477888888888887775532333332...222222222222222233444444457777 PP

                SID-1_RNA_chan 189 ydtleeiesdknvirtkkvlvvsdlsrkdkrvlekkykiylwniiti..........avfYalpviqlv 247
                                    ++ ++ e+ +  +++++   + ++ + + + +++   +y ++i+             + Y + vi ++
  gi|15669133|ref|NP_247938.1|  89 LQSNQNYEQTNGNFNEENENAMTNVGESEVNYNNEPAYNYYIEITYPdgtipdkieeQMLYYIKVIDPI 157
                                   788888888888888888888888887776666666555665554435555666666555666666655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.099
                SID-1_RNA_chan  41 yd.ldsnvefnglyqtmtkkaaitvqkkefesgkf 74 
                                   yd  d+n e+n l qt t++++i v  ++++ +++
  gi|15669133|ref|NP_247938.1| 225 YDeYDNNYESNDLQQTQTQFSEIEVYVDDIKPSNS 259
                                   78789999999************999999987754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2456  (0.136985); expected 358.6 (0.02)
Passed bias filter:                      765  (0.0426683); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 2516.62
//
Query:       gi|15669134|ref|NP_247939.1|  [L=120]
Description: hypothetical protein MJ_0944 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-07   31.4   0.7    3.5e-07   30.1   0.7    1.6  1  PadR             Transcriptional regulator PadR-like family
    1.5e-06   28.3   0.2    2.1e-06   27.8   0.2    1.2  1  HTH_34           Winged helix DNA-binding domain
    1.7e-05   24.6   1.3    2.4e-05   24.2   0.8    1.5  1  TFIIE_alpha      TFIIE alpha subunit
    2.3e-05   24.1   0.5    3.4e-05   23.6   0.4    1.4  1  HxlR             HxlR-like helix-turn-helix
    2.7e-05   24.0   0.1    4.3e-05   23.3   0.1    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
    3.6e-05   23.7   0.0      5e-05   23.3   0.0    1.2  1  HTH_20           Helix-turn-helix domain
    4.1e-05   23.4   0.2      7e-05   22.7   0.2    1.3  1  MarR             MarR family
    4.8e-05   23.2   0.0    6.8e-05   22.8   0.0    1.2  1  Dimerisation2    Dimerisation domain
    6.5e-05   23.1   0.0    7.2e-05   22.9   0.0    1.1  1  Replic_Relax     Replication-relaxation
    0.00033   20.4   0.0    0.00046   19.9   0.0    1.2  1  HTH_IclR         IclR helix-turn-helix domain
      0.001   19.0   0.6      0.001   19.0   0.6    1.7  1  HTH_45           Winged helix-turn-helix
     0.0039   17.8   0.7     0.0053   17.4   0.7    1.3  1  RTP              Replication terminator protein
     0.0072   16.2   0.0      0.014   15.3   0.0    1.4  1  MarR_2           MarR family
     0.0077   16.1   0.6      0.013   15.4   0.6    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.012   15.7   0.4      0.018   15.0   0.3    1.4  1  DUF1803          Domain of unknown function (DUF1803)
      0.016   15.7   0.0      0.029   14.9   0.0    1.4  1  HTH_27           Winged helix DNA-binding domain
       0.02   14.7   0.4      0.098   12.5   0.1    2.3  2  DUF1495          Winged helix DNA-binding domain (DUF1495)
      0.026   14.5   0.8      0.035   14.1   0.0    1.7  2  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.029   14.7   0.1      0.048   14.0   0.0    1.4  1  Penicillinase_R  Penicillinase repressor
      0.043   13.9   0.1        1.6    8.9   0.1    2.4  2  Mrr_N            Mrr N-terminal domain
      0.068   13.3   1.4        1.5    9.0   1.4    2.3  1  DUF2250          Uncharacterized protein conserved in archaea
      0.072   13.3   0.1       0.11   12.7   0.1    1.3  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
       0.11   12.9   0.8       0.36   11.2   0.1    2.1  2  Rrf2             Transcriptional regulator


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.7   4.5e-10   3.5e-07       1      73 [.      14      79 ..      10      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.5e-10
                                  HHHHHCC.S-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                          PadR  1 iLallee.qpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                  iL+ll+e ++++  +i ke+ ++        ++sl ++L++L k gl+++++e++++  p+ yY+lT+ G+++l
  gi|15669134|ref|NP_247939.1| 14 ILELLNEkGELHFSQIHKEIPTH--------MSSLNRTLNELVKLGLISKRKEDNKQALPKTYYKLTPLGKKAL 79
                                  67777555777777777777777........67899***********************************987 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.2   2.7e-09   2.1e-06       4      70 ..      13      80 ..      12      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.7e-09
                        HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkef.kgkkprtllriTpeGreafk 70
                                  ++l +L+++ e  f+++ +++ +  + L   l+ L k g i+ +ke  k+  p+t +++Tp G++a  
  gi|15669134|ref|NP_247939.1| 13 EILELLNEKGELHFSQIHKEIPTHMSSLNRTLNELVKLGLISKRKEDnKQALPKTYYKLTPLGKKALL 80
                                  58999************************************99997615668************9975 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.8     3e-08   2.4e-05      13      94 ..       9      89 ..       1      97 [. 0.85

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3e-08
                                  HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHHH CS
                   TFIIE_alpha 13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevvk 94
                                  + ++++l+ L ekge+   ++ ke+      l + Ln+L + +l++ kr+ d+++   k y+++++      + +++e+++ 
  gi|15669134|ref|NP_247939.1|  9 KYVKEILELLNEKGELHFSQIHKEIPTHMSSLNRTLNELVKLGLIS-KRKEDNKQALPKTYYKLTPLGKKALLLYEVEKIIE 89
                                  55789****************************************8.56678888899999999987777777777777765 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.4   4.3e-08   3.4e-05       2      71 ..       6      77 ..       5      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.3e-08
                                  HHSTTHHHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE..ESSSS-EEEEEE-TCGGG CS
                          HxlR  2 iggkWkllilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierev..ypevPpkveYsltekGrs 71
                                  +++k+   il  l + g+  fs++++++p+   + L ++L eL + gli+++    ++  pk  Y+lt+ G++
  gi|15669134|ref|NP_247939.1|  6 LSKKYVKEILELLNEkGELHFSQIHKEIPTH-MSSLNRTLNELVKLGLISKRKedNKQALPKTYYKLTPLGKK 77
                                  7788888899888878************975.5679*************865511467779**********97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   5.5e-08   4.3e-05      16      64 ..      16      71 ..       6      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.5e-08
                                  HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....TT.EEEE CS
                          TrmB 16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.....pk.lYra 64
                                   Ll ++g++  ++i++e+    s+ +++L++L++ Gl+ ++k+      pk +Y+ 
  gi|15669134|ref|NP_247939.1| 16 ELLnEKGELHFSQIHKEIPTHMSSLNRTLNELVKLGLISKRKEDnkqalPKtYYKL 71
                                  56779*************************************98899996625554 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   6.5e-08     5e-05      13      59 ..      12      58 ..       2      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.5e-08
                                  HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                        HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                   +il +L+++++l +s++++++ +++++l++ L++L++ gL+  ++e
  gi|15669134|ref|NP_247939.1| 12 KEILELLNEKGELHFSQIHKEIPTHMSSLNRTLNELVKLGLISKRKE 58
                                  68*****************************************9997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2     9e-08     7e-05       8      52 ..      14      58 ..      13      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 9e-08
                                  HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                          MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                  iL++l e+g+l  s++ k + ++ s++ r+l +L+k Gli+++k 
  gi|15669134|ref|NP_247939.1| 14 ILELLNEKGELHFSQIHKEIPTHMSSLNRTLNELVKLGLISKRKE 58
                                  9****************************************9986 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   8.7e-08   6.8e-05      23      84 ..      14      79 ..      11      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8.7e-08
                 Dimerisation2 23 vFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeek....kalYsntelastyL 84
                                  + +lL+e+++l+ +++ +e+ + +++++r l+ +v LgL +++k+++k    k+ Y+ t+l ++ L
  gi|15669134|ref|NP_247939.1| 14 ILELLNEKGELHFSQIHKEIPTHMSSLNRTLNELVKLGLISKRKEDNKqalpKTYYKLTPLGKKAL 79
                                  7799*************************************9988875122235688888777665 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   9.2e-08   7.2e-05       1      69 [.      15      79 ..      15     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 9.2e-08
                  Replic_Relax  1 LrlLaehrvlTtrqiarllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarll 69
                                  L+lL+e++ l  +qi++ + ++h ++++r L++L +lgl+s+ rk++ ++++   ++ Y Ltp+G+++l
  gi|15669134|ref|NP_247939.1| 15 LELLNEKGELHFSQIHKEI-PTHMSSLNRTLNELVKLGLISK-RKED-NKQA-LPKTYYKLTPLGKKAL 79
                                  6788888888899999985.555555****************.4442.3444.46899*********99 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   5.9e-07   0.00046       7      50 ..      13      55 ..      12      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.9e-07
                                  HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  +iL++l+e ++ l +s++++++  + S+  R L+ Lv+lG++ +
  gi|15669134|ref|NP_247939.1| 13 EILELLNEKGE-LHFSQIHKEIPTHMSSLNRTLNELVKLGLISK 55
                                  59*******99.9****************************976 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.6   1.3e-06     0.001       9      69 ..      12      82 ..       7      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-06
                        HTH_45  9 adILeais.egeakkTkimykanLsykllnkYLdmLvekgli.......kk..skekYvlTekGlellekl 69
                                   +ILe ++ +ge + ++i ++     + ln+ L+ Lv+ gli       k+   k+ Y+lT  G++ l  +
  gi|15669134|ref|NP_247939.1| 12 KEILELLNeKGELHFSQIHKEIPTHMSSLNRTLNELVKLGLIskrkednKQalPKTYYKLTPLGKKALLLY 82
                                  68999999789999****************************9998876333467889******9987544 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.7   6.8e-06    0.0053      22      99 ..       8      89 ..       2     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.8e-06
                                  -EBCTCHHHHHHHH....HTTTT.----H.HHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHHHHHHHHHHHH CS
                           RTP 22 klyglklldelkke....Fkelg.ykPnh.seiyralhelvedgilkrrkelkekaklqevviYsltdeGkekaklykkqvki 98
                                  k+y  ++l+ l ++    F ++    P+h s + r+l+elv+ g++++rke +++a      +Y+lt  Gk ++ ly  +  i
  gi|15669134|ref|NP_247939.1|  8 KKYVKEILELLNEKgelhFSQIHkEIPTHmSSLNRTLNELVKLGLISKRKEDNKQAL--PKTYYKLTPLGKKALLLYEVEKII 88
                                  5577777777766433336666633365548999***************99884444..4479**********9999765444 PP

                                  H CS
                           RTP 99 d 99
                                  +
  gi|15669134|ref|NP_247939.1| 89 E 89
                                  4 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.8e-05     0.014      12      59 ..      16      59 ..      12      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                                  HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSS CS
                        MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeD 59
                                    L   ++  l  +++ ++     s+++r+l++Lv+ GL+ +r+   D
  gi|15669134|ref|NP_247939.1| 16 ELLNEKGE--LHFSQIHKEIPTHMSSLNRTLNELVKLGLISKRKE--D 59
                                  34444444..99999999999999****************99965..3 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.6   1.6e-05     0.013       6      47 .]      13      55 ..      10      55 .. 0.97

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                                  HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  +IL lL+e gel ++++ +e+    s + + L+ L ++GL++k
  gi|15669134|ref|NP_247939.1| 13 EILELLNEkGELHFSQIHKEIPTHMSSLNRTLNELVKLGLISK 55
                                  8****************************************97 PP

>> DUF1803  Domain of unknown function (DUF1803)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   2.3e-05     0.018      12      63 ..       9      61 ..       5      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                       DUF1803 12 plFkeLieyLaehddviLRelkkeFa.dqkkldrlldelidaglikRenkrYk 63
                                  +  ke++e L+e+ +    +++ke + + + l+r+l+el++ gli++     k
  gi|15669134|ref|NP_247939.1|  9 KYVKEILELLNEKGELHFSQIHKEIPtHMSSLNRTLNELVKLGLISKRKEDNK 61
                                  567899999***************9725689**************86544333 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.7e-05     0.029       8      68 .]      14      75 ..      12      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.7e-05
                        HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre...krvrlTdkG 68
                                  +L+l++ + ++ + +++++   +  s+    l++L++ GL+ ++++e ++ +   + ++lT+ G
  gi|15669134|ref|NP_247939.1| 14 ILELLN-EKGELHFSQIHKEIPTHMSSLNRTLNELVKLGLI-SKRKEDNKQAlpkTYYKLTPLG 75
                                  788899.9999999999999999999999************.666654555599999****977 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00013     0.098      58      85 ..      46      77 ..       5      82 .. 0.87
   2 ?   -1.2   0.0       2.4   1.9e+03      20      35 ..      86     101 ..      77     113 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                       DUF1495 58 sLielGLveeeeeseglk....lYklteeGie 85
                                   L++lGL+++++e++  +    +Yklt+ G++
  gi|15669134|ref|NP_247939.1| 46 ELVKLGLISKRKEDNKQAlpktYYKLTPLGKK 77
                                  59******999987665445569*******97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.4
                       DUF1495  20 siypeksnlqeisrrv 35 
                                   +i+++++n q+i+ ++
  gi|15669134|ref|NP_247939.1|  86 KIIENSKNNQNIIIQI 101
                                   4555555555554332 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.5e-05     0.035      33      55 ..      35      57 ..      12      63 .. 0.89
   2 ?   -3.0   0.2       9.3   7.3e+03      48      59 ..      85      99 ..      83     102 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.5e-05
                                  SSHHHHHHHHHHHHHTTSEEETE CS
                     HTH_Crp_2 33 ltretvsrilseLkreglisrgr 55
                                  ++ ++++r+l+eL + glis+++
  gi|15669134|ref|NP_247939.1| 35 THMSSLNRTLNELVKLGLISKRK 57
                                  67789***************653 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.3
                                  TTSEE..ETEE.EEE CS
                     HTH_Crp_2 48 eglis..rgrr.iri 59
                                  e++i+  ++++ i+i
  gi|15669134|ref|NP_247939.1| 85 EKIIEnsKNNQnIII 99
                                  678886434445766 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.2e-05     0.048       7      59 ..      13      61 ..       9      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.2e-05
                                  HHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTE CS
               Penicillinase_R  7 evmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegra 59
                                  e++e+l ekge+  +++++e++       s+   +l+ Lvk gl+s++ke ++
  gi|15669134|ref|NP_247939.1| 13 EILELLNEKGELHFSQIHKEIPTH----MSSLNRTLNELVKLGLISKRKEDNK 61
                                  9*********************99....8999999***********9999776 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1     0.002       1.6       3      40 ..       9      46 ..       8      61 .. 0.80
   2 ?    3.8   0.0      0.08        63      60      85 ..      46      79 ..      40      80 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                         Mrr_N  3 elmlplLealad.gsehrlkeirervaerfglseeerae 40
                                  ++++++Le l++ g++h  ++i++++  +++     ++e
  gi|15669134|ref|NP_247939.1|  9 KYVKEILELLNEkGELHF-SQIHKEIPTHMSSLNRTLNE 46
                                  6899********888887.*******9999554455555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.08
                         Mrr_N 60 yLkkagllespk........rgvwkiTekGrevl 85
                                  +L+k gl+++ k        + ++k+T+ G+++l
  gi|15669134|ref|NP_247939.1| 46 ELVKLGLISKRKednkqalpKTYYKLTPLGKKAL 79
                                  677777777766666666667899******9987 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.4    0.0019       1.5      11      57 ..      12      58 ..       4      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0019
                       DUF2250 11 lkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerveg 57
                                   ++l+ l++ +  +  +i ke+  +++  ++ l++L +lGL+ + ++
  gi|15669134|ref|NP_247939.1| 12 KEILELLNEKGELHFSQIHKEIPTHMSSLNRTLNELVKLGLISKRKE 58
                                  57899999999999999999999999999999*********988664 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00014      0.11       8      55 ..       9      56 ..       7      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                  HHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                Fe_dep_repress  8 dYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                  +Y + I++l +ek+    +++ +++  + ss   +l++L k G++   
  gi|15669134|ref|NP_247939.1|  9 KYVKEILELLNEKGELHFSQIHKEIPTHMSSLNRTLNELVKLGLISKR 56
                                  69*****************************************98765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00047      0.36      19      58 ..      17      56 ..       9      58 .. 0.85
   2 ?   -1.0   0.0       2.9   2.2e+03      27      47 ..      83     103 ..      73     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00047
                                  HSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2 19 keeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                  + +e++ +  ++i+++  ++ s l + l++L k gl+  +
  gi|15669134|ref|NP_247939.1| 17 LLNEKGELHFSQIHKEIPTHMSSLNRTLNELVKLGLISKR 56
                                  4445556999**************************9865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.9
                                   -HHHHHHHHTS-HHHHHHHHH CS
                          Rrf2  27 sseeiaerqnispsylekila 47 
                                   ++e+i e+ + +++++ +i++
  gi|15669134|ref|NP_247939.1|  83 EVEKIIENSKNNQNIIIQIIN 103
                                   567788888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1259  (0.0702214); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 844.20
//
Query:       gi|15669135|ref|NP_247940.1|  [L=224]
Description: hypothetical protein MJ_0945 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-07   32.1   0.4    1.4e-07   31.8   0.4    1.1  1  DUF1080   Domain of Unknown Function (DUF1080)


Domain annotation for each model (and alignments):
>> DUF1080  Domain of Unknown Function (DUF1080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.4   7.8e-12   1.4e-07      36     184 ..      85     220 ..      45     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 7.8e-12
                                   CGG.ESSS--EEESSEBSSEEEEEEEEEETTTEE.EEEEEESCTTTSSGGGTSCEEEEE-TTTHSTCCCSTTSBTTTBTTB CS
                       DUF1080  36 aessgkgggflitkkefgdfeLklefkiseggnS.GillrsqkeekgkdavagyevqildsekekganrstGslydeeskq 115
                                   +     ++g ++ +k+++df++ +++k  e+++S  i++r       ++a+agy ++i   +++    +  G+ +    ++
  gi|15669135|ref|NP_247940.1|  85 KVAVPINNGIIYIDKNYTDFKFIVDIKRLEESDSpKIYFRLI-----NNANAGYYIDIEGFDRGYVLYKFNGTKV----EK 156
                                   33344568999999************9877776637999999.....*************999988889999999....67 PP

                                   --SSS--S--TTSEEEEEEEEETTEEEEEETTEEEEEEETTSHHHHHHSSBEEEEECCCSTEEEEEEEE CS
                       DUF1080 116 vkpkakaakppgeWntyeiivkgdrvtvwlNGvlvldftdldaetekgkkgpIaLqdhgaeveFRniki 184
                                    + + +aa    ++ +ye+++k++++     G++ +++td+ +      kg I++    + +++ n+++
  gi|15669135|ref|NP_247940.1| 157 LAESYDAAPAGTDFYRYEVVAKDNKIIFLAGGQKYIEYTDNNTPI---LKGGIGIGG--GRAYYDNVRV 220
                                   7799**************************************987...999999974..4468888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1501.39
//
Query:       gi|15669136|ref|NP_247941.1|  [L=374]
Description: N(2),N(2)-dimethylguanosine tRNA methyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.4e-138  459.8   0.6   8.7e-138  459.6   0.6    1.0  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    4.7e-05   23.2   0.0      9e-05   22.3   0.0    1.6  1  Met_10           Met-10+ like-protein
     0.0023   17.8   0.1      0.025   14.4   0.0    2.1  2  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.019   14.5   0.0       0.27   10.8   0.0    2.7  1  HTH_24           Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.6   0.6  1.9e-141  8.7e-138       1     375 [.       6     367 ..       6     368 .. 0.97

  Alignments for each domain:
  == domain 1  score: 459.6 bits;  conditional E-value: 1.9e-141
                                   TTEEEEE----SS--TT--SS--GGGHHHHHHHHHH....HHHHHHHH-S-EEEEESS-TTSHHHHHHH..HH-S-EEEEE CS
                           TRM   1 GeakikvedkevtvskkeeVFYNPvqefnRDlsvlvir.qlellkkklgekikvldaLsasGlRaiRfa..lEvpgvkevl 78 
                                   Ge+ ++v+dk +tv+kk+eVFYNP+++++RD+s++vi+ +l+l++k+   k++++daL++sG+R++R+a  lE++g+ +v+
  gi|15669136|ref|NP_247941.1|   6 GEVVFEVPDK-LTVTKKDEVFYNPRMKTCRDISIAVIQaFLNLYHKR--DKFYIADALAGSGIRGLRYAkeLEFNGELKVF 83 
                                   88999****8.************************************..7*******************555678999*** PP

                                   EE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEE.EEEEEEE--HHH CS
                           TRM  79 aNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkek.glLlvTaTDtav 158
                                   +NDi++kA+e+i +N+klne+e+i v+ne dAn++l+++ + f+v+D+DPfGspap++++a++++ ++ glL++TaTDta+
  gi|15669136|ref|NP_247941.1|  84 LNDINPKAYEKIINNAKLNEIENIDVFNE-DANTFLSKHFRFFNVVDIDPFGSPAPYVEQAIRALVTRnGLLCLTATDTAA 163
                                   ***********************999999.*********************************965544************ PP

                                   HTTSSHHHHHHHHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEE CS
                           TRM 159 LaGaspekclrkYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglv 239
                                   L+G+s+++clrkY a++l  + cHE+alR+l+++v+r+a+kYe a++p++++++d+Yvrv++++++ga++++kv+e+lg+v
  gi|15669136|ref|NP_247941.1| 164 LCGRSKKSCLRKYLAYPLFGRDCHEFALRVLVGYVMRMATKYELALKPVFCHATDHYVRVYLVTDRGAKRADKVFEMLGYV 244
                                   ********************************************************************************* PP

                                   EEETTT--EEEE--GGG--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHH.S--S CS
                           TRM 240 lhCsgClseekvkglakfkaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeEl.ldap 319
                                   ++         v+g++    ++++ g+++ +aGPl++g+l+dk++vee l++aek   +e+++rv+k+L++ik E+ ++++
  gi|15669136|ref|NP_247941.1| 245 KD---------VNGIKI--IKKFEEGYEKGFAGPLYIGNLYDKALVEEALKIAEK---REFSERVLKILNAIKGESaINQV 311
                                   99.........899999..699*********************************...89***************99**** PP

                                   S-EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHH CS
                           TRM 320 lyydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvevl 375
                                   ++yd++q++++lk+svpp+++++++lke+gf++++tH++pk+ikT+a+l++v+e++
  gi|15669136|ref|NP_247941.1| 312 GCYDTHQIGKMLKISVPPMQDIINKLKEMGFNAVVTHYNPKGIKTDATLKNVIEAI 367
                                   ****************************************************9976 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0     2e-08     9e-05     106     168 ..      58     122 ..      44     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2e-08
                                   ETT-TTTCCHHHCCH...HTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT- CS
                        Met_10 106 dvfAGiGpfaipiak...yskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireql 168
                                   d +AG G   +  ak   +  + +v+ +d+nP++++ + +n klN++e+ + +++eD+++++ +++
  gi|15669136|ref|NP_247941.1|  58 DALAGSGIRGLRYAKeleFNGELKVFLNDINPKAYEKIINNAKLNEIEN-IDVFNEDANTFLSKHF 122
                                   6666666666666652223456789**********************98.579********98654 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.6e-06     0.025       6     112 ..      55     159 ..      50     199 .. 0.77
   2 ?    1.3   0.0     0.061   2.7e+02      36      77 ..     274     316 ..     251     370 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.6e-06
               Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkae..vvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnev 83 
                                   ++ D+ +G+G  +++ a+el +++e  v++ Di+++a e+  +na+ ++++n+ +  +d+++ l+k++    f++ ++   
  gi|15669136|ref|NP_247941.1|  55 YIADALAGSGIRGLRYAKELEFNGElkVFLNDINPKAYEKIINNAKLNEIENIDVFNEDANTfLSKHFR--FFNV-VD--- 129
                                   677888999999******666655555***********************************8887644..4666.44... PP

               Methyltransf_31  84 lnaladpdkileeiervl.kpggilliedp 112
                                   ++ + +p+ + e+++r+l + +g l+++  
  gi|15669136|ref|NP_247941.1| 130 IDPFGSPAPYVEQAIRALvTRNGLLCLTAT 159
                                   357788888777777765144555555444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.061
               Methyltransf_31  36 iseeaielArenaqklgldnveFeqgdieelekl.ledekfDl 77 
                                   +++  +e A ++a+k ++++  +++ ++ + e++  +  ++D 
  gi|15669136|ref|NP_247941.1| 274 YDKALVEEALKIAEKREFSERVLKILNAIKGESAiNQVGCYDT 316
                                   6788999999999999999888877777775545333366665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.1e-05      0.27      22      46 ..     318     342 ..     291     342 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.1e-05
                        HTH_24  22 eLAerlglSpstvnrrlkrLeeeGl 46 
                                   ++ ++l +S+++    +++L+e+G+
  gi|15669136|ref|NP_247941.1| 318 QIGKMLKISVPPMQDIINKLKEMGF 342
                                   899********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2885.10
//
Query:       gi|15669137|ref|NP_247942.1|  [L=1039]
Description: isoleucyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   9.3e-193  641.8  15.6   9.3e-193  641.8  15.6    1.5  2  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.6e-28   99.6   3.5      3e-10   39.4   0.1    4.4  3  tRNA-synt_1g   tRNA synthetases class I (M)
    6.4e-27   94.4   1.6    2.7e-26   92.4   1.6    2.2  1  Anticodon_1    Anticodon-binding domain of tRNA
    2.8e-08   33.5   0.1    2.3e-06   27.2   0.1    2.7  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
      1e-07   31.6   3.9    3.8e-07   29.8   0.4    2.6  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    7.3e-06   25.1   0.0    0.00049   19.1   0.0    2.6  2  tRNA-synt_1f   tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.061   12.9   0.5        3.5    7.3   0.1    2.8  2  zf_UBZ         Ubiquitin-Binding Zinc Finger
      0.075   12.8   0.0       0.26   11.1   0.0    1.9  1  DUF2922        Protein of unknown function (DUF2922)
       0.14   12.0   8.0      0.022   14.6   3.4    1.9  2  DUF445         Protein of unknown function (DUF445)


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  641.8  15.6  4.7e-196  9.3e-193       2     600 ..      16     638 ..      15     640 .. 0.95
   2 ?   -3.0   0.0      0.78   1.5e+03     406     423 ..     673     690 ..     663     692 .. 0.86

  Alignments for each domain:
  == domain 1  score: 641.8 bits;  conditional E-value: 4.7e-196
                   tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvek 82 
                                   + ++Wee+d+++k ++k++++kef +vdgPPy  G++H+G a++k++kd+  r+krm+G++vl + GwD++Gl+ie kve+
  gi|15669137|ref|NP_247942.1|  16 IKKFWEENDIYQKVKKKNERNKEFYFVDGPPYCSGAIHLGTAWNKIIKDTYLRFKRMQGYNVLDKAGWDMHGLPIEVKVEN 96 
                                   6689**********999999************************************************************* PP

                   tRNA-synt_1  83 klgakekke.rkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkkl 162
                                   ++g+k+kke  +k+g+++f+ek++e++ + +e ++kq+k+lGv++D+++ y+ + ke++e  +++++  ++kgl+ r  ++
  gi|15669137|ref|NP_247942.1|  97 EFGIKNKKEiETKIGVKQFIEKCKEFALKHKEIMEKQFKNLGVWLDWENAYMPITKEYMEIGWWTLKVAHEKGLLTRDLRV 177
                                   ***9998872579******************************************************************** PP

                   tRNA-synt_1 163 vnwstklktalselEv..eykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv.......itkekli 234
                                   v+w+++++tal+e Ev  eyk++ d++++v+f la++e++++vi+TTtP+Tl++++av+v+p+ dy+        +ke +i
  gi|15669137|ref|NP_247942.1| 178 VYWCPRCETALAEHEVrgEYKEVYDPSVYVKFRLANEENTYIVIWTTTPWTLVANLAVTVHPDYDYAyvevefdDKKEVWI 258
                                   ******************************************************************999*999888999** PP

                   tRNA-synt_1 235 laeallkslvkke.sek.....kiledergkeLegkevelpl............vnrkipiiaddyvdkeaGtGvVkiaPa 297
                                   +ae+l++++++k  + +     ki ++++gkeLeg ++++pl             +++ ++i +++v+ e GtG+V++aP+
  gi|15669137|ref|NP_247942.1| 259 IAEKLVEEVINKAkKFHniknyKIIKKVKGKELEGIKYIHPLleenerqkefaeLENAHTVILGEHVTLEGGTGLVHTAPG 339
                                   *********98753211233459*****************************9999999********************** PP

                   tRNA-synt_1 298 hdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrate 378
                                   h+e+D+evgkkynl++ +++d++g++ e  ++++g+ v+da+  ++e+lk+kgll+ a ki+hs+p+c+r k+p+++rate
  gi|15669137|ref|NP_247942.1| 340 HGEEDFEVGKKYNLPIYSPIDDEGKYVE--GKWKGVFVKDADAEIIETLKNKGLLVYAGKIKHSYPHCWRCKTPLLFRATE 418
                                   **************************98..69************************************************* PP

                   tRNA-synt_1 379 qWfvrvkeladaalkavekvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagree.. 457
                                   qWf ++++++d+++++ + vq++p++ e+ry + ++ + dW+iSRqr+WG +ip++v ++ ++ +v+ +++el++++ +  
  gi|15669137|ref|NP_247942.1| 419 QWFLEISKIKDNIIEHAKTVQWIPHWVETRYINGVKFVGDWNISRQRYWGIPIPVWVCEKCGKYIVVGSVEELEEKMINkd 499
                                   ******************************************************************9*9999999876511 PP

                   tRNA-synt_1 458 eeaekkalekeakdkl...kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarli 535
                                   e +e+++l+k ++dk+    +  ge+++++dvlDvWF+Sg+ p++++g      +elk    ad+++eG D++  W+++  
  gi|15669137|ref|NP_247942.1| 500 EVGEINDLHKPTVDKIklrCECGGEMKRVPDVLDVWFDSGLAPYASIG-----VKELK---KADFITEGHDQVTKWFYSQH 572
                                   457999*********9773344689***********************.....46777...79****************** PP

                   tRNA-synt_1 536 llslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdin 600
                                    ls  ++++ P+k+ l+hg+++de+G KmSKslgNv++p+dv++kygad lR++l+  ++v +d++
  gi|15669137|ref|NP_247942.1| 573 ALSAIVFNDIPYKKCLMHGFTLDEHGDKMSKSLGNVVNPDDVVEKYGADLLRFYLLsANKVWEDLR 638
                                   ********************************************************6666666665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.78
                   tRNA-synt_1 406 ekryaswleniqdWciSR 423
                                   +++y+++l++   W +SR
  gi|15669137|ref|NP_247942.1| 673 DEKYFEYLKDEDRWIVSR 690
                                   4789*************9 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.1   1.5e-13     3e-10       8     138 ..      46     196 ..      40     276 .. 0.74
   2 !   20.6   0.1   7.8e-08   0.00016     167     245 ..     403     483 ..     375     486 .. 0.87
   3 !   36.8   0.1   9.5e-13   1.9e-09     316     372 ..     588     645 ..     572     664 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.5e-13
                                   B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT...........TS-HHHHHHHH....... CS
                  tRNA-synt_1g   8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke...........gvtpeelvekv....... 70 
                                   pY +g++HlG + + i+ D + R+kr++g++vl  +g D+hG pie+k e+e           ++ +++++ek        
  gi|15669137|ref|NP_247942.1|  46 PYCSGAIHLGTAWNKIIKDTYLRFKRMQGYNVLDKAGWDMHGLPIEVKVENEfgiknkkeietKIGVKQFIEKCkefalkh 126
                                   9**********************************************9875432222221222344455554431111111 PP

                                   HHHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE. CS
                  tRNA-synt_1g  71 heeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegt 138
                                   +e+++++fk+l++  d  + +   ++e  e+    +k  +ekgl+++    +++cp++e+ l++ +v+g+
  gi|15669137|ref|NP_247942.1| 127 KEIMEKQFKNLGVWLDweNAYMPITKEYMEIGWWTLKVAHEKGLLTRDLRVVYWCPRCETALAEHEVRGE 196
                                   4556666777776554222233334445555555666667777777777777778888888888777775 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 7.8e-08
                                   ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET....TECCE CS
                  tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP....gaekk 243
                                   p++  +++   ++ te++f+++sk+++++ e+  ++ +  ++ v++   + +k  + d++isr+  wGip+P    ++ +k
  gi|15669137|ref|NP_247942.1| 403 PHCWRCKTPLLFRATEQWFLEISKIKDNIIEHA-KTVQWIPHWVETRYINGVKF-VGDWNISRQRYWGIPIPvwvcEKCGK 481
                                   89******************************9.66666788888888888888.99***************887777777 PP

                                   EE CS
                  tRNA-synt_1g 244 vl 245
                                   ++
  gi|15669137|ref|NP_247942.1| 482 YI 483
                                   76 PP

  == domain 3  score: 36.8 bits;  conditional E-value: 9.5e-13
                                   EEE--.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHH CS
                  tRNA-synt_1g 316 vahey.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfv 372
                                     h++ l  +g+K+SkS g+vv +++++e++ adllR+yl+++++  +Dl f w+++ 
  gi|15669137|ref|NP_247942.1| 588 LMHGFtLDEHGDKMSKSLGNVVNPDDVVEKYGADLLRFYLLSANKVWEDLRFVWSEMD 645
                                   55666345679*******************************************9875 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   1.6   1.3e-29   2.7e-26       1     147 [.     684     829 ..     684     860 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 1.3e-29
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrllaPf 80 
                                   drwi+s++n+++k + e++e   f++    l +f++ndl++wy++l+++r ++e+++ ++  a+++l++vl +l  +laP+
  gi|15669137|ref|NP_247942.1| 684 DRWIVSRINSVAKIAIENLEVPYFHTYTWTLKDFILNDLSRWYIRLIRDRTWKEKDDADKLaAYQTLYYVLLKLATILAPV 764
                                   9****************************************************99877777799***************** PP

                   Anticodon_1  81 mPfitEelwqr..eeeelgkkesimlaewpekaeelekeleeeevellkeivkairklrselkikpsse 147
                                   +P+++E ++q+     e + +esi++++ + ++e+ ++el e+++++++++v ai + r ++k   + +
  gi|15669137|ref|NP_247942.1| 765 APHTAEAIYQNlkT--E-DMEESIFMNKIEVDEEFIDEEL-ERDMAIVRDVVDAIYRGRDRIKYTLRYP 829
                                   *********99632..3.579********97777778888.99************99887766655554 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.023        45      19      48 ..      48      77 ..      29      79 .. 0.80
   2 !   27.2   0.1   1.2e-09   2.3e-06     226     284 ..     572     631 ..     549     649 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.023
                                  TTS--BHHHHHHHHHHHHHHHHHHHTT-EE CS
                  tRNA-synt_1e 19 vydashlGhaRslvafDilrrilqalgYdv 48
                                     a+hlG a + ++ D   r+ +++gY+v
  gi|15669137|ref|NP_247942.1| 48 CSGAIHLGTAWNKIIKDTYLRFKRMQGYNV 77
                                  55789***********************98 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 1.2e-09
                                   HHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS- CS
                  tRNA-synt_1e 226 laqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsah 284
                                    a s  +f+  ++ k  +h   l  +g+kmsksL+n++   dv++k+ +  lR++llsa+
  gi|15669137|ref|NP_247942.1| 572 HALSAIVFNdIPYKKCLMHGFTLDEHGDKMSKSLGNVVNPDDVVEKYGADLLRFYLLSAN 631
                                   5666666655899999***************************************99864 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2     0.069   1.4e+02      52     100 ..     106     157 ..      92     168 .. 0.75
   2 !   29.8   0.4   1.9e-10   3.8e-07      11     146 ..     206     365 ..     203     394 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.069
                 tRNA-synt_1_2  52 aekkkelaafieevkkksesereletke..keGvftgl.kaihPitgekipi 100
                                    e+k  +++fie++k+   +++e+ +k+  + Gv  +  +a  Pit+e ++i
  gi|15669137|ref|NP_247942.1| 106 IETKIGVKQFIEKCKEFALKHKEIMEKQfkNLGVWLDWeNAYMPITKEYMEI 157
                                   5667789********9877766665554326799666527899999998877 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.9e-10
                 tRNA-synt_1_2  11 eiefkvees.eeklevfttrpdtlfGvtfvalapehplvekl..........aekkkelaafieevkkksesereletkek 80 
                                    ++f+++++ ++ + ++tt p tl+    v++ p+ + +                +k +++ i+++kk +++++ +  k+ 
  gi|15669137|ref|NP_247942.1| 206 YVKFRLANEeNTYIVIWTTTPWTLVANLAVTVHPDYDYAYVEvefddkkevwIIAEKLVEEVINKAKKFHNIKNYKIIKKV 286
                                   689999999667999**********99999999999887544455543222333456678888888888888887777888 PP

                 tRNA-synt_1_2  81 eGv.ftglkaihPitgek............ipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedee 146
                                   +G   +g+k ihP+ +e+              + + ++v  e gtg v + P+h ++Dfe  kkynlpi   i  e++ 
  gi|15669137|ref|NP_247942.1| 287 KGKeLEGIKYIHPLLEENerqkefaelenaHTVILGEHVTLEGGTGLVHTAPGHGEEDFEVGKKYNLPIYSPIDDEGKY 365
                                   998789********97777899****999989*************************************9999877654 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.02        41       9      44 ..      23      59 ..      18      80 .. 0.75
   2 !   19.1   0.0   2.5e-07   0.00049     269     312 ..     588     631 ..     557     663 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.02
                  tRNA-synt_1f  9 eklieerkkkka.ekdevvvesGispSGliHiGnlre 44
                                  +++ ++ kkk++ +k+ + v+     SG iH+G++ +
  gi|15669137|ref|NP_247942.1| 23 NDIYQKVKKKNErNKEFYFVDGPPYCSGAIHLGTAWN 59
                                  4566666666665788999999999********9865 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.5e-07
                  tRNA-synt_1f 269 vvYelillkggekmssSkGnvltledwlevaepevlrflilrrk 312
                                   ++  + l+++g+kms+S Gnv+ ++d++e +  ++lrf++l+++
  gi|15669137|ref|NP_247942.1| 588 LMHGFTLDEHGDKMSKSLGNVVNPDDVVEKYGADLLRFYLLSAN 631
                                   567788999999**************************998743 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.044        88       3      17 ..     179     193 ..     178     194 .. 0.85
   2 ?    7.3   0.1    0.0018       3.5       3      18 ..     474     489 ..     473     490 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.044
                        zf_UBZ   3 ylCerCgkeipesel 17 
                                   y C+rC + + e+e+
  gi|15669137|ref|NP_247942.1| 179 YWCPRCETALAEHEV 193
                                   66*****99999985 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0018
                        zf_UBZ   3 ylCerCgkeipeselq 18 
                                   ++Ce+Cgk+i + +++
  gi|15669137|ref|NP_247942.1| 474 WVCEKCGKYIVVGSVE 489
                                   79*******9876665 PP

>> DUF2922  Protein of unknown function (DUF2922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00013      0.26      10      44 ..     879     913 ..     877     920 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                       DUF2922  10 eegktvtlsipnpkedlteaeVkaaMdlIiakniF 44 
                                   e gk+++  +p++ e l++a++k++M+ + +  ++
  gi|15669137|ref|NP_247942.1| 879 ELGKRYRSEVPKVVEALNKADAKELMERLKEGAVI 913
                                   679************************99887665 PP

>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.3   2.5e+03     180     210 ..     260     290 ..     220     317 .. 0.51
   2 ?   14.6   3.4   1.1e-05     0.022     165     339 ..     791    1003 ..     750    1006 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                        DUF445 180 lesivsmflreltsilekvksdpdhllreee 210
                                    e++v+ ++++++++ +  + +  + ++ +e
  gi|15669137|ref|NP_247942.1| 260 AEKLVEEVINKAKKFHNIKNYKIIKKVKGKE 290
                                   3333333333333333333333333333333 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.1e-05
                        DUF445  165 elidelieeesgklv..lesivsmflreltsilekvksdpdhllreeedkkvreliadllndpelaakveklkkkklsd 241 
                                    e+++e+i ee ++ +   + +v+ ++r++++i   ++  p +++  +  ++v++ +++++    ++++  ++k+ k+ +
  gi|15669137|ref|NP_247942.1|  791 EVDEEFIDEELERDMaiVRDVVDAIYRGRDRIKYTLR-YPLKEITIAGGEEVKKAVERFEY---IIKEQGNVKNIKFGE 865 
                                    456666666666655679**********999999999.9**********************...9************** PP

                        DUF445  242 levqeyeea.lwealkdlllkdlneee.sllrerisklleklge................................... 283 
                                    +e ++y  + + ++l +  + ++ +    l +  +++l+e+l+e                                   
  gi|15669137|ref|NP_247942.1|  866 VEGSKYIIKpNYRELGKRYRSEVPKVVeALNKADAKELMERLKEgavildgyeikpeyveirleipehiagvefskgtv 944 
                                    ******9999999999999999988657899999*******************************************99 PP

                        DUF445  284 ....klaedpklreklnkflenaaakvlekyrldiskiveetvnafdaeeleelIelivg 339 
                                        +++ d+ ++e l +++ + ++++ ++  ldi++ ++ +v+  d +e +e+Ie  v+
  gi|15669137|ref|NP_247942.1|  945 fintEIT-DDLIKEGLMREVIRRIQAMRKDMDLDIEEKIKIKVEGIDLDEFKEIIEREVR 1003
                                    8874444.468999999***************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1039 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1167  (0.0650901); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.84u 0.32s 00:00:01.15 Elapsed: 00:00:00.53
# Mc/sec: 5927.26
//
Query:       gi|15669138|ref|NP_247943.1|  [L=191]
Description: hypothetical protein MJ_0948 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.031   14.6   0.6       0.11   12.8   0.0    2.0  2  DUF3510   Domain of unknown function (DUF3510)
       0.48   10.8   8.5       0.75   10.1   2.7    2.3  2  BLOC1_2   Biogenesis of lysosome-related organelles complex-1


Domain annotation for each model (and alignments):
>> DUF3510  Domain of unknown function (DUF3510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.17   1.6e+03      50      58 ..      61      69 ..      22     109 .. 0.58
   2 ?   12.8   0.0   1.3e-05      0.11       9      61 ..     135     185 ..     131     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.17
                       DUF3510 50 sekklseev 58
                                   e++l++ev
  gi|15669138|ref|NP_247943.1| 61 EESHLTSEV 69
                                  223344444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.3e-05
                       DUF3510   9 eaLkqvssiprlyRrtnkevptepSkyvseilkplktfkkesekklseevlee 61 
                                   + Lk+++++p  y +  ke p+ + ky s+i++ ++++ ke++++l+e v ++
  gi|15669138|ref|NP_247943.1| 135 NILKKIQNLPDDYPKETKEDPNLQNKYLSKIISRISRL-KEFKSNLDEIV-SD 185
                                   579**********************************9.67777665543.44 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.7   8.4e-05      0.75      20      92 ..       8      80 ..       4      82 .. 0.91
   2 ?    4.1   0.3    0.0065        58      62      91 ..     157     186 ..     112     191 .] 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.4e-05
                       BLOC1_2 20 edyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92
                                  ++y +L ++  +  e ++k + ++ +l++   klne+  +    l+ i q+e++ ++L++ v +LD  +k LE
  gi|15669138|ref|NP_247943.1|  8 TEYPTLVEIKDKKGEMIEKGEAKLRDLNNIRVKLNELRTSNPDDLDTIAQLEEEESHLTSEVLKLDLSIKILE 80
                                  67788888888888899999999999999999***********************************999998 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0065
                       BLOC1_2  62 pylqqidqiekqvteLeeavseLDeyskeL 91 
                                    + + + +i  ++++L+e  s LDe+++++
  gi|15669138|ref|NP_247943.1| 157 LQNKYLSKIISRISRLKEFKSNLDEIVSDI 186
                                   455678888889999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1190  (0.0663729); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1219.21
//
Query:       gi|15669139|ref|NP_247944.1|  [L=123]
Description: hypothetical protein MJ_0949 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-38  129.2   0.7    7.9e-38  129.0   0.7    1.1  1  DUF356    Protein of unknown function (DUF356)


Domain annotation for each model (and alignments):
>> DUF356  Protein of unknown function (DUF356)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   0.7   4.4e-42   7.9e-38       1     105 [.       3     107 ..       3     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 4.4e-42
                        DUF356   1 liliRadnkeKvlnalaDlerygklkiegkPriiepevadkilekvlkeelkkkvkvaalveveedatkaisklrkiHPPa 81 
                                   ++liR+d++eK++nalaD++r+++l+i gkP+ii pe+ad+il+++l+ e+kk +k+a+l+++ e+a kai+++rkiHPPa
  gi|15669139|ref|NP_247944.1|   3 ILLIRGDSYEKLKNALADVDRHAELTIIGKPKIIVPEAADEILSHILG-EVKKPCKTACLAKIAEKAPKAIDRIRKIHPPA 82 
                                   579*********************************************.9******************************* PP

                        DUF356  82 Hvvvvseeyde.yeellekleklke 105
                                   H+vv+se+y + y +ll+++ kl+ 
  gi|15669139|ref|NP_247944.1|  83 HIVVISERYGDiYYKLLDDFPKLPV 107
                                   *********877********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 966.75
//
Query:       gi|15669140|ref|NP_247945.1|  [L=233]
Description: hypothetical protein MJ_0950 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-91  304.0   0.1    4.5e-91  303.9   0.1    1.0  1  PIN_5     PINc domain ribonuclease
     0.0095   16.1   0.1          3    8.1   0.0    2.4  2  SRI       SRI (Set2 Rpb1 interacting) domain
  ------ inclusion threshold ------
       0.18   11.5   0.0       0.25   11.0   0.0    1.4  1  DUF4042   Domain of unknown function (DUF4042)


Domain annotation for each model (and alignments):
>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.9   0.1   7.6e-95   4.5e-91       1     206 []       9     223 ..       9     223 .. 0.98

  Alignments for each domain:
  == domain 1  score: 303.9 bits;  conditional E-value: 7.6e-95
                         PIN_5   1 rfvlDTsaltdpevreklgeeeleeavkklldliaearlklgiscyip.psvykElkeflkreeveeeviakldtwlvkks 80 
                                   rf+lDTsa+t+p+vr++lg+++++e ++k++dliaear+kl+isc+ip p+vy+El+ fl++e+++++vi+k+dtwlvkk+
  gi|15669140|ref|NP_247945.1|   9 RFCLDTSAFTEPSVRKALGVKTVTELTDKVMDLIAEARIKLNISCHIPyPTVYNELMGFLENENCPRDVIVKVDTWLVKKT 89 
                                   8******************************************************************************** PP

                         PIN_5  81 pdryevkipaeilyeyveevrerinkGlrvaEeavreaaeeseklekee........eeeevgelikklRekYrealRkGi 153
                                   p+rye+kip+ei+yeyv+++rerinkG+r++Ee++ +a++  ++l+k++         +++++++i+++R+kYr+alR G+
  gi|15669140|ref|NP_247945.1|  90 PNRYEIKIPSEIFYEYVKDLRERINKGMRIGEEHIIKATDMVYELSKKHpemgkneiINKVLSKTINTFRNKYRSALRVGT 170
                                   *******************************************9965556788888899********************** PP

                         PIN_5 154 lDsaeDldvllLAkELdaavvssDeGikkwaeklGlrlveakkfpkvlkeylk 206
                                   lDsa+DldvllLAkELdaavv+sD Gi+kwa++lGlr+v+a++fp +l+eylk
  gi|15669140|ref|NP_247945.1| 171 LDSAPDLDVLLLAKELDAAVVASDGGIEKWAQRLGLRFVDASDFPFMLEEYLK 223
                                   ***************************************************96 PP

>> SRI  SRI (Set2 Rpb1 interacting) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.2    0.0033        19      15      43 ..      85     113 ..      83     141 .. 0.77
   2 !    8.1   0.0   0.00051         3       5      47 ..     144     194 ..     140     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0033
                           SRI  15 vVvnvlnkYrkklkkedfKklakeltkkl 43 
                                   +V+++ n+Y+ k+++e f++++k+l + +
  gi|15669140|ref|NP_247945.1|  85 LVKKTPNRYEIKIPSEIFYEYVKDLRERI 113
                                   589999******************98876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00051
                           SRI   5 ekkfkkelakvVvnvlnkYrkklk........kedfKklakeltkklvekE 47 
                                    ++ +k l+k++  + nkYr++l         + d+  lakel   +v+++
  gi|15669140|ref|NP_247945.1| 144 NEIINKVLSKTINTFRNKYRSALRvgtldsapDLDVLLLAKELDAAVVASD 194
                                   567799****************8888*99999999999****999999886 PP

>> DUF4042  Domain of unknown function (DUF4042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.2e-05      0.25     101     182 .]      59     141 ..      17     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.2e-05
                       DUF4042 101 elhrglllaleaetslqvltqllkcLavlvsatP..ye.rLkkglltevvksvkkllkekdsnvkvsallvlgalvstkel 178
                                   ++++ l+  le+e++++ +  ++k+ + lv+ tP  ye +++ ++ +e vk++++++++     +++++ +  ++   ++ 
  gi|15669140|ref|NP_247945.1|  59 TVYNELMGFLENENCPRDV--IVKVDTWLVKKTPnrYEiKIPSEIFYEYVKDLRERINKGMRIGEEHIIKATDMVYELSKK 137
                                   6899*********999865..789**********666579******************98888888888888888877777 PP

                       DUF4042 179 lpev 182
                                    pe+
  gi|15669140|ref|NP_247945.1| 138 HPEM 141
                                   7775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1454.08
//
Query:       gi|15669141|ref|NP_247946.1|  [L=355]
Description: hypothetical protein MJ_0951 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-81  272.9   8.3    1.9e-81  272.9   8.3    1.4  2  HIGH_NTase1_ass  Cytidyltransferase-related C-terminal region
    3.3e-21   76.0   1.2    1.2e-14   54.4   0.0    2.3  2  HIGH_NTase1      HIGH Nucleotidyl Transferase
     0.0011   18.7   0.0      0.058   13.1   0.0    2.5  2  Citrate_ly_lig   Citrate lyase ligase C-terminal domain
     0.0012   19.1   0.5      0.064   13.5   0.0    3.0  2  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.018   14.5   0.0    1.3  1  DUF554           Protein of unknown function (DUF554)
      0.028   13.9   0.0       0.19   11.2   0.0    2.0  2  ATP-sulfurylase  ATP-sulfurylase
      0.078   13.1   3.5        0.1   12.7   0.6    2.2  2  CRISPR_Cas9_WED  CRISPR-Cas9 WED domain


Domain annotation for each model (and alignments):
>> HIGH_NTase1_ass  Cytidyltransferase-related C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       2.8   7.1e+03      20      31 ..      32      43 ..      10      57 .. 0.47
   2 !  272.9   8.3   7.4e-85   1.9e-81       1     203 [.     150     351 ..     150     352 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.8
               HIGH_NTase1_ass 20 kikPykivdlet 31
                                    k +k +  e 
  gi|15669141|ref|NP_247946.1| 32 SFKDFKKIVEEI 43
                                  222222222222 PP

  == domain 2  score: 272.9 bits;  conditional E-value: 7.4e-85
               HIGH_NTase1_ass   1 reeetfdkvlkrinkghhikikPykivdletkevlledkLeeDnyviaslskslkklk...fdfkdkfifverieGvsGtk 78 
                                   ++e+t++kv+++inkg hi++kPyki+++et+e+l+e kL++Dnyvias+s+ ++kl+    +f++kf+fv+r+eG+sGtk
  gi|15669141|ref|NP_247946.1| 150 IPEKTMEKVIDCINKGYHIQVKPYKIICIETGEILGE-KLNIDNYVIASMSQMIYKLNregLKFNPKFVFVKRLEGISGTK 229
                                   589**********************************.********************9999******************* PP

               HIGH_NTase1_ass  79 ireavvegnlekvkdmlPeetievlkeelendnpledi...rdeekiletvneldldelldlnlldeklankliekrpyes 156
                                   irea++ g++e++k+mlP++t+++lke  +n++ l+++   r+e++ilet+ne+dl e     +l+ ++a+ l++krp+++
  gi|15669141|ref|NP_247946.1| 230 IREAIFSGKFEDIKNMLPKTTLSILKELYDNGK-LNELilkRFEDRILETANEYDLYE-----YLPSNVAEILEKKRPFNN 304
                                   *******************************98.7777789*****************.....****************** PP

               HIGH_NTase1_ass 157 ieeikeaiprgfskhykerilsvLeakiekdviskyienyPakiriL 203
                                   ieeik+ +p+gfs+h++erils+Lea+i ++++skyi+nyPaki+iL
  gi|15669141|ref|NP_247946.1| 305 IEEIKNSLPYGFSRHFRERILSKLEARIPNETLSKYINNYPAKIKIL 351
                                   **********************************************9 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   4.6e-18   1.2e-14       8      80 ..      57     128 ..      51     145 .. 0.87
   2 !   20.1   0.4   1.2e-07    0.0003     183     337 ..     203     353 ..     192     355 .] 0.71

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 4.6e-18
                   HIGH_NTase1   8 aEYNPfHnGHlyhlekakeltgadvviavmSGnF..vqRGepAildKwtRaemALenGvDlViElPvvyavqsAe 80 
                                   +EYNP+H+GH+y lek ke+    + i v+ G      RG p +l+++ RaemA+++G+D+V+E P +  + s +
  gi|15669141|ref|NP_247946.1|  57 TEYNPLHKGHKYALEKGKEH---GIFISVLPGPLerSGRGIPYFLNRYIRAEMAIRAGADIVVEGPPMGIMGSGQ 128
                                   7*****************96...9********873356****************************887776655 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.2e-07
                   HIGH_NTase1 183 vtikRegagyhdeels.eeeeiaSAtaiRkalkeekkleelkklvPestleilkeelkkkaslsledlskllkyklltesk 262
                                   + ++Reg +++ + +  ++ e  S t+iR+a+ +  k e++k+++P++tl+ilke +++++   +e + k ++ ++l++  
  gi|15669141|ref|NP_247946.1| 203 YKLNREGLKFNPKFVFvKRLEGISGTKIREAIFSG-KFEDIKNMLPKTTLSILKELYDNGKL--NELILKRFEDRILETA- 279
                                   56677777777774333556789*********666.589***************99766554..4555555555555555. PP

                   HIGH_NTase1 263 eelkkildvsegLenrikkalkkaesleelleklktKrytytri..qRillhillnikkedlkklkkkkp.ylrvLGf 337
                                       + +d+ e L + + + l+k + ++++ e  ++  y  +r   +Ril ++   i +e+l+k+ ++ p  +++L++
  gi|15669141|ref|NP_247946.1| 280 ----NEYDLYEYLPSNVAEILEKKRPFNNIEEIKNSLPYGFSRHfrERILSKLEARIPNETLSKYINNYPaKIKILAV 353
                                   ....44666666666666666666666666666666677777753378999999999999999999888669999987 PP

>> Citrate_ly_lig  Citrate lyase ligase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.026        67       8      25 ..      59      76 ..      51      83 .. 0.83
   2 !   13.1   0.0   2.3e-05     0.058     151     181 ..     223     253 ..     191     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.026
                Citrate_ly_lig  8 anPftlGhryLvekaake 25
                                   nP  +Gh+y +ek  ++
  gi|15669141|ref|NP_247946.1| 59 YNPLHKGHKYALEKGKEH 76
                                  69***********98765 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.3e-05
                Citrate_ly_lig 151 elisaskvrkllkeknleklaelvPkttley 181
                                   e is +k+r+++ ++++e++++++Pkttl+ 
  gi|15669141|ref|NP_247946.1| 223 EGISGTKIREAIFSGKFEDIKNMLPKTTLSI 253
                                   569*************************985 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.6      0.11   2.9e+02      48      89 ..      15      54 ..      13      57 .. 0.88
   2 !   13.5   0.0   2.5e-05     0.064       6     143 .]      59     233 ..      56     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.11
                                  HHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTTTTEEEEEE CS
               CTP_transf_like 48 aeeRlemlelakevdevisvdpweltrevlkklkpdklylvi 89
                                  +e+R e ++ ak++de    d+ +++ e++++ + d   +v+
  gi|15669141|ref|NP_247946.1| 15 LEDREEIIRDAKRKDEKSFKDFKKIVEEIKERENKD--KIVC 54
                                  589999*****9999999999999999****99999..7776 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.5e-05
                                   -TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-.SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH.........HH CS
               CTP_transf_like   6 FDpiHlGHlrlleqakklleedlivgvpsdeppkkkk.kplasaeeRlemlelakevdevisvdpweltr.........ev 76 
                                   ++p+H+GH   le+ k+++   + v +p + +    + + + + + R em  +a   d v++  p  +           + 
  gi|15669141|ref|NP_247946.1|  59 YNPLHKGHKYALEKGKEHGIF-ISV-LPGPLERSGRGiPYFLNRYIRAEMAIRA-GADIVVEGPPMGIMGsgqymrcliKM 136
                                   9*****************987.333.3333333333459999999999999999.77777888888888899999988888 PP

                                   HHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEE..................................HTTCE CS
               CTP_transf_like  77 lkklkpdklylvigadvledfsewkeleeilgnvklvvvsrp..................................ekqan 123
                                     +l+++  ++ +g ++ +++  +k ++ i + +++ v+ ++                                    ++n
  gi|15669141|ref|NP_247946.1| 137 FYSLGAE--IIPRGYIPEKTM--EKVIDCINKGYHIQVKPYKiicietgeilgeklnidnyviasmsqmiyklnreGLKFN 213
                                   8888889..999999999999..9999999999999999888999999999999999999999999999999998855666 PP

                                   EEEEEECCTTTCSHHHHHHH CS
               CTP_transf_like 124 vllkaekrtngiSstkirer 143
                                    ++   kr +giS+tkire+
  gi|15669141|ref|NP_247946.1| 214 PKFVFVKRLEGISGTKIREA 233
                                   66777779999*****9985 PP

>> DUF554  Protein of unknown function (DUF554)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.9e-06     0.018      55     135 ..     172     253 ..     154     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.9e-06
                        DUF554  55 llvilslvlGaviGelldleerlerlgealkkkvkksk.rfaegfvtasllfcvGamailGslqeGltgdatlLltKslLD 134
                                   ++ i+++  G ++Ge l++++ + + ++ +  k+++++ +f  +fv +  l  ++++ i  ++ +G  +d + +l K++L 
  gi|15669141|ref|NP_247946.1| 172 PYKIICIETGEILGEKLNIDNYVIASMSQMIYKLNREGlKFNPKFVFVKRLEGISGTKIREAIFSGKFEDIKNMLPKTTLS 252
                                   56689999*************988887778888886666************************************999996 PP

                        DUF554 135 g 135
                                   +
  gi|15669141|ref|NP_247946.1| 253 I 253
                                   5 PP

>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.5e-05      0.19      12      59 ..      41      87 ..      33      98 .. 0.74
   2 ?    0.1   0.0      0.18   4.7e+02     177     194 ..     221     238 ..     193     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.5e-05
                                  HHHHHTT-S.S.EEEEEESS---HHHHHHHHHHHHHTSEEEEEEEB-SB- CS
               ATP-sulfurylase 12 eefkekgwd.k.VvAfqtrnplHraHeellkraleeeadglllhplvgpt 59
                                  ee+ke++ + k V  f   nplH++H++ l++  e   +g++++ l gp 
  gi|15669141|ref|NP_247946.1| 41 EEIKERENKdKiVCDFTEYNPLHKGHKYALEKGKE---HGIFISVLPGPL 87
                                  5555555542536667779*********9999988...359999888875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.18
                                   GEEE--HHHHHCCHHTT- CS
               ATP-sulfurylase 177 evesisgtelrkllrege 194
                                   + e isgt++r+ + +g+
  gi|15669141|ref|NP_247946.1| 221 RLEGISGTKIREAIFSGK 238
                                   56779*******998886 PP

>> CRISPR_Cas9_WED  CRISPR-Cas9 WED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6     4e-05       0.1      50      93 ..      26      73 ..       4      78 .. 0.81
   2 ?    0.3   0.1      0.26   6.8e+02      20      55 ..     250     283 ..     225     328 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4e-05
               CRISPR_Cas9_WED 50 akkdpktfeklkkilkeysdkkeksek.vkevdvnPfk...kYreenG 93
                                  ++kd+k+f++ kki++e ++ ++k++  +  ++ nP++   kY  e+G
  gi|15669141|ref|NP_247946.1| 26 KRKDEKSFKDFKKIVEEIKERENKDKIvCDFTEYNPLHkghKYALEKG 73
                                  689*******************99998667899****72225777766 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.26
               CRISPR_Cas9_WED  20 viekikniydkkeakkvkkllkkdkekflmakkdpk 55 
                                   ++  +k++yd+ + +++  +lk  +++ l   ++  
  gi|15669141|ref|NP_247946.1| 250 TLSILKELYDNGKLNEL--ILKRFEDRILETANEYD 283
                                   34445555555543221..12223333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2187.41
//
Query:       gi|15669142|ref|NP_247947.1|  [L=142]
Description: prefoldin subunit alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-24   83.8   7.4    1.3e-23   83.1   7.4    1.3  1  Prefoldin       Prefoldin subunit
    3.1e-07   30.3  12.5     0.0022   17.9   0.4    2.2  2  Prefoldin_2     Prefoldin subunit
     0.0012   19.0   4.3     0.0012   19.0   4.3    2.0  2  DUF848          Gammaherpesvirus protein of unknown function 
      0.004   17.7  15.2       0.11   13.0   7.6    2.0  2  APG6_N          Apg6 coiled-coil region
      0.009   16.6   3.6      0.009   16.6   3.6    2.2  2  BST2            Bone marrow stromal antigen 2
     0.0099   15.9   5.0       0.73    9.9   0.2    2.1  2  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
  ------ inclusion threshold ------
      0.015   15.1   0.5      0.015   15.1   0.5    2.6  2  CdvA            CdvA-like coiled-coil domain
      0.068   13.2  17.6       0.24   11.5   8.1    2.3  2  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
      0.088   12.1   0.1      0.093   12.0   0.1    1.1  1  Amidohydro_1    Amidohydrolase family
      0.095   12.4   7.3       0.13   12.0   1.0    2.0  2  Hormone_1       Somatotropin hormone family
       0.16   11.3  17.8       0.79    9.0   1.6    2.1  2  GAS             Growth-arrest specific micro-tubule binding
       0.27   10.8  15.0        0.3   10.6   4.2    2.0  2  Filament        Intermediate filament protein
       0.44   10.6  22.0       0.14   12.1   9.5    2.4  2  FlxA            FlxA-like protein
       0.66   10.1   4.9        1.2    9.3   0.9    2.1  2  DUF1993         Domain of unknown function (DUF1993)
          1    8.2  19.2        1.9    7.3   3.6    2.0  2  Spc7            Spc7 kinetochore protein
        1.7    7.8  13.0       0.26   10.5   6.3    2.0  2  Tho2            Transcription factor/nuclear export subunit p
        1.9    9.0   8.9        2.8    8.4   1.3    3.1  3  FlaC_arch       Flagella accessory protein C (FlaC)
        2.1    7.5  10.9        6.9    5.8   5.3    2.0  2  TMPIT           TMPIT-like protein
        3.6    7.8  12.5        6.2    7.0   2.9    2.3  2  Fib_alpha       Fibrinogen alpha/beta chain family
        3.9    7.9  14.6        2.1    8.8   1.0    2.1  2  CENP-H          Centromere protein H (CENP-H)
        4.5    7.8   9.0       0.32   11.5   1.6    2.3  2  Arm-DNA-bind_5  Arm DNA-binding domain
        5.7    6.5  10.2        7.2    6.1   2.5    2.0  2  HAUS6_N         HAUS augmin-like complex subunit 6 N-terminus
        6.9    6.9  12.9         14    5.9   0.5    2.8  3  bZIP_1          bZIP transcription factor
          7    7.3  13.6        2.1    9.0   4.7    2.4  2  YabA            Initiation control protein YabA
        7.5    7.5  17.1        7.5    7.5   1.4    2.3  2  Rho_Binding     Rho Binding


Domain annotation for each model (and alignments):
>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   7.4   1.9e-26   1.3e-23       1     119 [.      18     132 ..      18     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 1.9e-26
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHH CS
                     Prefoldin   1 lkeeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiel 81 
                                   ++++l+ +q+e++++++ ++e+ ++++t++++k+   ++e+l+p+g g+++ka++  +dk+l+ + +++yveks++e ie 
  gi|15669142|ref|NP_247947.1|  18 YNQQLQMIQSEITSIRALKSEIMNSIKTIENIKA---DEETLIPVGPGVFLKAKI-VDDKALIGVKSDIYVEKSFNEVIED 94 
                                   89********************************...99****************.5689********************* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                   lkk +e+l+k+ ++  +++e+l+++it l+++l++  q
  gi|15669142|ref|NP_247947.1|  95 LKKSVEDLDKAEKEGMKKAEELAKAITALRKELQTEIQ 132
                                   **********************************9877 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.4   3.1e-06    0.0022       3      53 ..      11      61 ..       9      75 .. 0.86
   2 !   16.5   6.2   8.3e-06     0.006      53     105 ..      81     133 ..      69     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.1e-06
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETT CS
                   Prefoldin_2  3 linkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGd 53
                                  +++ ++ ++qqlq+++++i+++++ ++e+   ++++e+++ d++    vG+
  gi|15669142|ref|NP_247947.1| 11 KAMALEIYNQQLQMIQSEITSIRALKSEIMNSIKTIENIKADEETLIPVGP 61
                                  56667779**********************************998888886 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 8.3e-06
                                   TEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS- CS
                   Prefoldin_2  53 dvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkklqq 105
                                   d+ v+++ +ev+e+L+++ e+l+k  k+  k+ e+l k ++ l++elq  +q+
  gi|15669142|ref|NP_247947.1|  81 DIYVEKSFNEVIEDLKKSVEDLDKAEKEGMKKAEELAKAITALRKELQTEIQK 133
                                   67899*******************************************99887 PP

>> DUF848  Gammaherpesvirus protein of unknown function (DUF848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3      0.34   2.4e+02      63     112 ..      16      47 ..       2      58 .. 0.44
   2 !   19.0   4.3   1.6e-06    0.0012      65     118 ..      88     141 ..      77     142 .] 0.93

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.34
                        DUF848  63 eavdteieakkkelslLkklnrkkvarveeLtdkvlelkeevsleldsle 112
                                   e ++++++  + e+ +                  +  lk e+   + ++e
  gi|15669142|ref|NP_247947.1|  16 EIYNQQLQMIQSEITS------------------IRALKSEIMNSIKTIE 47 
                                   3333333333333333..................3333333333333333 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.6e-06
                        DUF848  65 vdteieakkkelslLkklnrkkvarveeLtdkvlelkeevsleldsleeaqeey 118
                                    +++ie+ kk ++ L k +++ ++++eeL  ++  l++e++ e+++ ++aq+++
  gi|15669142|ref|NP_247947.1|  88 FNEVIEDLKKSVEDLDKAEKEGMKKAEELAKAITALRKELQTEIQKAQQAQDKK 141
                                   6889**********************************************9986 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.8    0.0015       1.1      11      67 ..       1      57 [.       1      58 [. 0.93
   2 !   13.0   7.6   0.00016      0.11      46      98 ..      89     141 ..      68     142 .] 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0015
                        APG6_N 11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeell 67
                                  +e++ + l+q     + Y++ l+ +++e ++ ++ ++e+ ++ + +e+++++ee+l+
  gi|15669142|ref|NP_247947.1|  1 MENMAEDLRQKAMALEIYNQQLQMIQSEITSIRALKSEIMNSIKTIENIKADEETLI 57
                                  58999999999999**************999999*******************9985 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00016
                        APG6_N  46 deeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeee 98 
                                   +e +e+l++++e+l+k+e+e +++ +el k+  +l++el++  +++++ ++++
  gi|15669142|ref|NP_247947.1|  89 NEVIEDLKKSVEDLDKAEKEGMKKAEELAKAITALRKELQTEIQKAQQAQDKK 141
                                   46799************************************999999988765 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.7       0.7     5e+02      65      77 ..      19      31 ..       1      55 [. 0.44
   2 !   16.6   3.6   1.2e-05     0.009      41      90 ..      86     135 ..      79     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.7
                                  HHHHHHHHHHHHH CS
                          BST2 65 qakvqelqgeikk 77
                                  ++++q +q ei++
  gi|15669142|ref|NP_247947.1| 19 NQQLQMIQSEITS 31
                                  2333333333322 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                          BST2  41 atcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90 
                                    + n+++++Lk+s e     +++  +k++el + i+ L ++Lq   ++ +
  gi|15669142|ref|NP_247947.1|  86 KSFNEVIEDLKKSVEDLDKAEKEGMKKAEELAKAITALRKELQTEIQKAQ 135
                                   589*************99999**********************9877766 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.8    0.0033       2.4      75     111 ..      11      49 ..       1      57 [. 0.56
   2 !    9.9   0.2     0.001      0.73      43      89 ..      84     133 ..      77     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0033
                  Baculo_PEP_C  75 alnalqdtlrneLtnlnsiltn...LlssvtNinstLnnl 111
                                   +  al+   +++L+ ++s++t+   L s++ N ++t++n+
  gi|15669142|ref|NP_247947.1|  11 KAMALE-IYNQQLQMIQSEITSiraLKSEIMNSIKTIENI 49 
                                   333333.555566666666554222677777777777776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.001
                  Baculo_PEP_C  43 ietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtn 89 
                                   +e+++n++ edlk+++++ld+   +  + +++L +a+ al ++l++e++ 
  gi|15669142|ref|NP_247947.1|  84 VEKSFNEVIEDLKKSVEDLDKaekEGMKKAEELAKAITALRKELQTEIQK 133
                                   67889999999999999999976655567788999999999888888876 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.5   2.1e-05     0.015      79     120 ..      17      58 ..       6      61 .. 0.93
   2 ?    2.3   5.5      0.19   1.4e+02      18      59 ..      90     134 ..      80     138 .. 0.46

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                          CdvA  79 aYksaieairellesaleekeeikklleklskleleeeevee 120
                                    Y+++ ++i+++++s+++ k+ei + ++++++++++ee+ ++
  gi|15669142|ref|NP_247947.1|  17 IYNQQLQMIQSEITSIRALKSEIMNSIKTIENIKADEETLIP 58 
                                   6***********************************998765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.19
                          CdvA  18 styeeikek...leealkklkekakelkeklkkrlkeledqiksl 59 
                                   ++ e++k+    l++a k+  +ka+el++ +++  kel+ +i++ 
  gi|15669142|ref|NP_247947.1|  90 EVIEDLKKSvedLDKAEKEGMKKAEELAKAITALRKELQTEIQKA 134
                                   344444433000333334444445555555555555555555554 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.9    0.0065       4.6      41      82 ..      14      55 ..       1      57 [. 0.80
   2 ?   11.5   8.1   0.00033      0.24      21      79 ..      85     140 ..      79     142 .] 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0065
                    TPR_MLP1_2 41 aqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaes 82
                                  a + Y ++l+   +++++++al++e+ +  ++i+++ka+ e+
  gi|15669142|ref|NP_247947.1| 14 ALEIYNQQLQMIQSEITSIRALKSEIMNSIKTIENIKADEET 55
                                  4456889********************999999999999887 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00033
                    TPR_MLP1_2  21 eaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                   e+ ++++ edl+k  e + +a++   + + k +e +k+++alr+el++  +++++++++
  gi|15669142|ref|NP_247947.1|  85 EKSFNEVIEDLKKSVEDLDKAEK---EGMKKAEELAKAITALRKELQTEIQKAQQAQDK 140
                                   56677888999999999999999...666677777899999999999999999998876 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00013     0.093      41     123 ..      21     118 ..       4     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                   HHHHHHTTEEEEEEEEHSSTHHHHHHHH.HHHT...SSSEEEEEEESSEGGS..........GCCCSHHHHHHHHHHHHHH CS
                  Amidohydro_1  41 iktalksGtttvadmgattstgiealle.aaee...lplglrilggkvsldr..........gsaetskasreklkagaae 107
                                     ++++s +t++++      ++i+ + +  a+e   +p+g++++++  ++d           ++++++ +++e lk+ +++
  gi|15669142|ref|NP_247947.1|  21 QLQMIQSEITSIRALKSEIMNSIKTIENiKADEetlIPVGPGVFLKAKIVDDkaligvksdiYVEKSFNEVIEDLKKSVED 101
                                   567899999999999985433333333332333579999*******999999***************************** PP

                                   HHHHCTTTCEE.EEEEE CS
                  Amidohydro_1 108 tikgkadgvvk.valap 123
                                   + k++++g+ k  +la 
  gi|15669142|ref|NP_247947.1| 102 LDKAEKEGMKKaEELAK 118
                                   *****999999666655 PP

>> Hormone_1  Somatotropin hormone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.7     0.035        25      95     135 ..       8      48 ..       1      57 [. 0.82
   2 ?   12.0   1.0   0.00018      0.13      96     157 ..      79     140 ..      66     142 .] 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.035
                                   HHHHHHHHHTTTTGGGGGG....GGGSSS------TTTGGG CS
                     Hormone_1  95 lklslllleswkePLkhlvtelssmkevsetilskakeiee 135
                                   l+  ++ le +++ L+ + +e++s+ ++  +i+ + k ie+
  gi|15669142|ref|NP_247947.1|   8 LRQKAMALEIYNQQLQMIQSEITSIRALKSEIMNSIKTIEN 48 
                                   67778889999999999999999999999999999998886 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00018
                                   HHHHHHHHTTTTGGGGGG....GGGSSS------TTTGGGHHHHHHHHHHHHHHHH------ CS
                     Hormone_1  96 klslllleswkePLkhlvtelssmkevsetilskakeieeklkeLlegierilskvevpver 157
                                   k+ +   +s++e +++l + ++++ ++ ++ ++ka+e+ + + +L+  +++ ++k ++   +
  gi|15669142|ref|NP_247947.1|  79 KSDIYVEKSFNEVIEDLKKSVEDLDKAEKEGMKKAEELAKAITALRKELQTEIQKAQQAQDK 140
                                   5667777899**********************************************974443 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.6    0.0011      0.79      57     111 ..       2      56 ..       1      57 [. 0.94
   2 ?    7.9   8.8    0.0025       1.8      26      75 ..      90     139 ..      87     142 .] 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                           GAS  57 krlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevl 111
                                   +++ e L++    +e  ++ql+  +++  s+++lk+++ ++ k ++++k + e l
  gi|15669142|ref|NP_247947.1|   2 ENMAEDLRQKAMALEIYNQQLQMIQSEITSIRALKSEIMNSIKTIENIKADEETL 56 
                                   5899*********************************************999876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0025
                           GAS  26 elIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrk 75 
                                   e+I+ lK+ +e+l+k e++  k+ +e+++    l+++L++  ++ ++ + 
  gi|15669142|ref|NP_247947.1|  90 EVIEDLKKSVEDLDKAEKEGMKKAEELAKAITALRKELQTEIQKAQQAQD 139
                                   6899**********************************998888877665 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.1    0.0081       5.8     207     254 ..       4      51 ..       1      57 [. 0.86
   2 ?   10.6   4.2   0.00042       0.3      48     102 ..      84     138 ..      65     142 .] 0.71

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0081
                                   XXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Filament 207 nsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerle 254
                                     e+lr+    ++ +++q+q  ++e+ s+++ k+ + ++++ +e+  +
  gi|15669142|ref|NP_247947.1|   4 MAEDLRQKAMALEIYNQQLQMIQSEITSIRALKSEIMNSIKTIENIKA 51 
                                   56889999999999*************************999998655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00042
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Filament  48 lkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevE 102
                                   +++ +++ +e+l+k +++l k+++      ++l++++  lrk +++e++k +++ 
  gi|15669142|ref|NP_247947.1|  84 VEKSFNEVIEDLKKSVEDLDKAEKEGMKKAEELAKAITALRKELQTEIQKAQQAQ 138
                                   5667777777777777777777777777777777777777777777777766654 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   4.5     0.056        40      38      63 ..      10      34 ..       1      55 [. 0.67
   2 ?   12.1   9.5    0.0002      0.14      22      81 ..      88     142 .]      79     142 .] 0.73

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.056
                          FlxA 38 esdeltkeekkkqqqliqaQIqqlqa 63
                                  + +++  e  ++q q+iq++I++++a
  gi|15669142|ref|NP_247947.1| 10 Q-KAMALEIYNQQLQMIQSEITSIRA 34
                                  2.355555555666666666666654 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0002
                          FlxA  22 LqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqqaekaqekqq 81 
                                    ++ i++l+k++++l +     ++e +k+++++ + I++l++++ q ++q+a++aq+k+q
  gi|15669142|ref|NP_247947.1|  88 FNEVIEDLKKSVEDLDKA----EKEGMKKAEELAKAITALRKEL-QTEIQKAQQAQDKKQ 142
                                   444455555555555444....44566**************999.578999999999876 PP

>> DUF1993  Domain of unknown function (DUF1993)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.16   1.2e+02      63     102 ..      13      52 ..       3      56 .. 0.77
   2 ?    9.3   0.9    0.0017       1.2      79     126 ..      85     132 ..      65     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.16
                                   HHCHHCT-GS----S.-SSHHHHHHHHHHHHHHHHCS-GG CS
                       DUF1993  63 avarlagkeppsledeektfadlrariaktialLesvdpe 102
                                   ++ ++ +++ + +++e +++  l++ i + i+ +e+++++
  gi|15669142|ref|NP_247947.1|  13 MALEIYNQQLQMIQSEITSIRALKSEIMNSIKTIENIKAD 52 
                                   444555566666688899*****************99887 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0017
                                   -SSHHHHHHHHHHHHHHHHCS-GGGHCCCCCEEEE.C.CCCCEEEEHH CS
                       DUF1993  79 ektfadlrariaktialLesvdpekldakeekevelklggkeleftge 126
                                   ek+f+++++ ++k ++ L+++++e ++++ee + ++++  kel+ + +
  gi|15669142|ref|NP_247947.1|  85 EKSFNEVIEDLKKSVEDLDKAEKEGMKKAEELAKAITALRKELQTEIQ 132
                                   89***************************9888888776666665544 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.6    0.0027       1.9     211     258 ..       4      51 ..       1      56 [. 0.89
   2 ?    7.1   7.8    0.0031       2.2     144     258 ..      88     139 ..      83     142 .] 0.52

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0027
                          Spc7 211 lkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervle 258
                                     +++++k   l+  ++ql+ ++++i+++++ kse+++ i+  e+++ 
  gi|15669142|ref|NP_247947.1|   4 MAEDLRQKAMALEIYNQQLQMIQSEITSIRALKSEIMNSIKTIENIKA 51 
                                   66889999999******************************9998876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0031
                          Spc7 144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelae 224
                                    +e +e+l++  e L+k e+e ++  +el +  ++l++el+++ ++a+                                 
  gi|15669142|ref|NP_247947.1|  88 FNEVIEDLKKSVEDLDKAEKEGMKKAEELAKAITALRKELQTEIQKAQ--------------------------------- 135
                                   455555555555555555555555555555555555555555555554................................. PP

                          Spc7 225 lqeqleeleekieelkeqkseleeeiaeaervle 258
                                                                 + ++
  gi|15669142|ref|NP_247947.1| 136 ------------------------------QAQD 139
                                   ..............................4444 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.5      0.19   1.3e+02      25      64 ..      16      51 ..       7      57 .. 0.64
   2 ?   10.5   6.3   0.00036      0.26      18      80 ..      80     138 ..      79     142 .] 0.71

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.19
                          Tho2 25 eqYekeieklkseieelakdrsderaaakkkkkekkrlke 64
                                  e Y+++++ ++sei++++      +++++++ k+++++k+
  gi|15669142|ref|NP_247947.1| 16 EIYNQQLQMIQSEITSIRAL----KSEIMNSIKTIENIKA 51
                                  67999999999999999322....3334444455555544 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00036
                          Tho2  18 yDiyvpkeqYekeieklkseieelakdrsderaaakkkkkekkrlkeliekLeeEkkeqiehv 80 
                                   +Diyv  +++++ ie lk+++e+l+k++   ++++kk ++ +k +++l+++L++E ++ ++++
  gi|15669142|ref|NP_247947.1|  80 SDIYVE-KSFNEVIEDLKKSVEDLDKAE---KEGMKKAEELAKAITALRKELQTEIQKAQQAQ 138
                                   588885.6899********999994433...34677777777777777777777776666655 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.3     0.004       2.8       7      34 ..      20      47 ..       2      52 .. 0.91
   2 ?    3.6   0.3      0.12        88      22      35 ..      91     104 ..      84     111 .. 0.74
   3 ?    2.5   0.8      0.27     2e+02      24      35 ..      93     104 ..      92     139 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.004
                     FlaC_arch  7 nklsklsteletvkkeneelsksveelk 34
                                  ++l+ +++e++++++  +e+ +s+++++
  gi|15669142|ref|NP_247947.1| 20 QQLQMIQSEITSIRALKSEIMNSIKTIE 47
                                  789999****************999997 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                     FlaC_arch  22 eneelsksveelke 35 
                                    +e+l+ksve+l++
  gi|15669142|ref|NP_247947.1|  91 VIEDLKKSVEDLDK 104
                                   46777888887775 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.27
                     FlaC_arch  24 eelsksveelke 35 
                                   e+l+ksve+l++
  gi|15669142|ref|NP_247947.1|  93 EDLKKSVEDLDK 104
                                   556666666654 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.3     0.012       8.9      35      98 ..       4      66 ..       1      73 [. 0.76
   2 ?    5.8   5.3    0.0096       6.9       3      51 ..      91     139 ..      84     142 .] 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.012
                         TMPIT 35 cskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesllpkknglylk 98
                                  ++++++++   l+  +++l+ +++++ ++ +   +e+ +++k+++++ ++ e l+p   g++lk
  gi|15669142|ref|NP_247947.1|  4 MAEDLRQKAMALEIYNQQLQMIQSEI-TSIRALKSEIMNSIKTIENIKADEETLIPVGPGVFLK 66
                                  55666667777777888888888886.4666777888888999998888999999999999987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0096
                         TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelks 51 
                                    +e+l+k++++l +++ke ++k eel+k +++++ke++++ +++++ ++
  gi|15669142|ref|NP_247947.1|  91 VIEDLKKSVEDLDKAEKEGMKKAEELAKAITALRKELQTEIQKAQQAQD 139
                                   4677888888888888888888888888888888888887777777654 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.2     0.015        11      93     124 ..      21      52 ..       1      58 [. 0.52
   2 ?    7.0   2.9    0.0086       6.2      30      76 ..      85     135 ..      82     142 .] 0.58

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                                   HHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  93 lketidaqesnirvLqnvlesneqkiqkLeqd 124
                                     + i++++++ir+L++ + +  + i++++ d
  gi|15669142|ref|NP_247947.1|  21 QLQMIQSEITSIRALKSEIMNSIKTIENIKAD 52 
                                   22345555566666666666666666666655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0086
                                   CCCCCHHHCCCCCCCCCCCCHHHH....HHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  30 ekdvkkdlekleneleeisnstke....aeelvkeikdslrekqkskkdnd 76 
                                   ek++++ +e+l++++e++ + +ke    aeel k+i+   +e q++ ++ +
  gi|15669142|ref|NP_247947.1|  85 EKSFNEVIEDLKKSVEDLDKAEKEgmkkAEELAKAITALRKELQTEIQKAQ 135
                                   677888888888888888777654111155555555555555555544433 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.0    0.0029       2.1      12      60 ..       5      54 ..       1      92 [. 0.79
   2 ?    4.8   6.7     0.052        38      43      83 ..      95     135 ..      82     142 .] 0.46

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0029
                        CENP-H 12 ssellklsqelrelqeeltevekenlrlkrknrelaael.lelakekese 60
                                  +++l + + +l+  +++l+ ++ e+ ++++ + e+++++ + ++ ++++e
  gi|15669142|ref|NP_247947.1|  5 AEDLRQKAMALEIYNQQLQMIQSEITSIRALKSEIMNSIkTIENIKADEE 54
                                  67788999999****************************55555555444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.052
                        CENP-H  43 nrelaaellelakekesekeklkeelekleaelkksrqrwr 83 
                                    ++ +++l + +ke +++ e+l++++ +l++el++++q+++
  gi|15669142|ref|NP_247947.1|  95 LKKSVEDLDKAEKEGMKKAEELAKAITALRKELQTEIQKAQ 135
                                   33333333333333333334555555555555555555543 PP

>> Arm-DNA-bind_5  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   1.0         1   7.4e+02      57      76 ..      25      44 ..       3      56 .. 0.51
   2 ?   11.5   1.6   0.00045      0.32      32      79 ..      96     138 ..      64     142 .] 0.73

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1
                Arm-DNA-bind_5 57 lnskirqerekledivrklr 76
                                  ++s+i ++r+   +i+++++
  gi|15669142|ref|NP_247947.1| 25 IQSEITSIRALKSEIMNSIK 44
                                  33333333333333333333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00045
                Arm-DNA-bind_5  32 glyitpepwdkkkgkvkerepntlelnskirqerekledivrklrqke 79 
                                   + ++ + ++ +k     e  ++++el+++i + r +l+ +++k +q++
  gi|15669142|ref|NP_247947.1|  96 KKSVEDLDKAEK-----EGMKKAEELAKAITALRKELQTEIQKAQQAQ 138
                                   444433322222.....44566***********************986 PP

>> HAUS6_N  HAUS augmin-like complex subunit 6 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.0     0.015        11     159     207 ..       4      52 ..       1      59 [. 0.74
   2 ?    6.1   2.5      0.01       7.2     159     207 ..      91     136 ..      64     142 .] 0.40

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                       HAUS6_N 159 flrekaaadrarqkyqenaqllekkerelraeleelqaelkaekeaakk 207
                                   + ++++++  a + y++++q ++ ++ ++ra ++e+ + +k  ++++++
  gi|15669142|ref|NP_247947.1|   4 MAEDLRQKAMALEIYNQQLQMIQSEITSIRALKSEIMNSIKTIENIKAD 52 
                                   5556666666789999999999999999999999999988855444433 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                       HAUS6_N 159 flrekaaadrarqkyqenaqllekkerelraeleelqaelkaekeaakk 207
                                   ++++++++    +++ +  ++  kk +el++ + +l +el+ e ++a++
  gi|15669142|ref|NP_247947.1|  91 VIEDLKKS---VEDLDKAEKEGMKKAEELAKAITALRKELQTEIQKAQQ 136
                                   22222222...23333333333333333333333333333322111111 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.5      0.02        14      28      63 ..       5      39 ..       2      40 .. 0.87
   2 ?    1.3   0.0      0.53   3.8e+02      44      61 ..      34      51 ..      31      54 .. 0.83
   3 ?    5.8   4.7     0.021        15      27      63 ..      91     127 ..      89     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1 28 ieeLerrvkaLekeNksLkseleelkkevekLkskv 63
                                   e L +++ aLe  N++L+   +e++  ++ Lks++
  gi|15669142|ref|NP_247947.1|  5 AEDLRQKAMALEIYNQQLQMIQSEITSIRA-LKSEI 39
                                  589****************99999998888.88886 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.53
                                  HHHHHHHHHHHHHHHHHH CS
                        bZIP_1 44 sLkseleelkkevekLks 61
                                  +Lkse+ +  k++e+ k 
  gi|15669142|ref|NP_247947.1| 34 ALKSEIMNSIKTIENIKA 51
                                  699999999999999886 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.021
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  27 eieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                    ie L++ v+ L+k  k+  +++eel+k +  L++++
  gi|15669142|ref|NP_247947.1|  91 VIEDLKKSVEDLDKAEKEGMKKAEELAKAITALRKEL 127
                                   5899*****************************9986 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.6      0.17   1.2e+02      17      41 ..      25      49 ..       1      59 [. 0.43
   2 ?    9.0   4.7    0.0029       2.1      11      64 ..      86     139 ..      79     142 .] 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.17
                                  HHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA 17 leelleeleelkeelaelleenaeL 41
                                  +++  +++++lk+e+ + ++  +++
  gi|15669142|ref|NP_247947.1| 25 IQSEITSIRALKSEIMNSIKTIENI 49
                                  2222233333444444444433333 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0029
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXX CS
                          YabA  11 eeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkk 64 
                                   ++++e +e+l++++e+l ++ +e +++ +eL    + lr++l++e +k+++ + 
  gi|15669142|ref|NP_247947.1|  86 KSFNEVIEDLKKSVEDLDKAEKEGMKKAEELAKAITALRKELQTEIQKAQQAQD 139
                                   5688999***********************************666555555443 PP

>> Rho_Binding  Rho Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.4      0.01       7.5       3      52 ..       6      55 ..       4      57 .. 0.78
   2 ?    5.3   8.4      0.05        36      14      57 ..      94     137 ..      83     141 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.01
                   Rho_Binding  3 kdvenlakekeelnkklkkleeelekak.eeeeeieklkasyekqLktErl 52
                                  +d+ ++a   e  n++l+ +++e+   +  ++e ++++k + e+    E++
  gi|15669142|ref|NP_247947.1|  6 EDLRQKAMALEIYNQQLQMIQSEITSIRaLKSEIMNSIK-TIENIKADEET 55
                                  5788899999999***************55888889998.55555555555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.05
                   Rho_Binding  14 elnkkl....kkleeelekakeeeeeieklkasyekqLktErlLKtqA 57 
                                   +l+k +    k  +e ++ka+e ++ i+ l+    k+L+tE  + +qA
  gi|15669142|ref|NP_247947.1|  94 DLKKSVedldKAEKEGMKKAEELAKAITALR----KELQTEIQKAQQA 137
                                   3333332222233344444445556666666....8888888887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2737  (0.152658); expected 358.6 (0.02)
Passed bias filter:                      800  (0.0446204); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 979.01
//
Query:       gi|15669143|ref|NP_247948.1|  [L=100]
Description: putative monovalent cation/H+ antiporter subunit E [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-15   56.7   0.1    2.2e-15   56.7   0.1    1.0  1  MNHE      Na+/H+ ion antiporter subunit


Domain annotation for each model (and alignments):
>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.1   1.2e-19   2.2e-15      44     126 ..       4      84 ..       1      98 [. 0.87

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 1.2e-19
                          MNHE  44 lrllayllvflweivkanldVakrvlrpklpirpgivkvplrlksdlaltllansitltPGTltvdvdedrrvlyvHvldv 124
                                   l+++ yl+v+++ i ++ +dV+kr ++   +i+p++++++  ++++++l+ll+ sit tPGTl++d+  ++r l v v+  
  gi|15669143|ref|NP_247948.1|   4 LGVIGYLAVLIKAICESWVDVVKRSIN--GEIHPQVIEIESIINNPTGLVLLSWSITATPGTLVIDLIPEERKLKVAVISP 82 
                                   5699**********************9..56*********************************************99954 PP

                          MNHE 125 ed 126
                                   ++
  gi|15669143|ref|NP_247948.1|  83 RS 84 
                                   33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 670.14
//
Query:       gi|15669144|ref|NP_247949.1|  [L=440]
Description: S-layer protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-53  181.8  14.0    1.8e-53  181.8  14.0    3.3  2  S_layer_C  S-layer like family, C-terminal region
  ------ inclusion threshold ------
        0.1   13.0   0.1       0.28   11.6   0.1    1.7  1  DUF2996    Protein of unknown function (DUF2996)


Domain annotation for each model (and alignments):
>> S_layer_C  S-layer like family, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   6.8      0.93   8.4e+03      40     108 ..     102     155 ..      55     188 .. 0.39
   2 !  181.8  14.0     2e-57   1.8e-53       1     220 []     212     421 ..     212     421 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.93
                     S_layer_C  40 itleykdeekledkvvglalkykgdkladikdkdkvd..ianyaklkfdDklsvyfkideekevelivgek 108
                                    +++ykd      + +   +++kg+++   ++   v+    ny+ lk  D             +e  ++e+
  gi|15669144|ref|NP_247949.1| 102 NKVKYKDI-----ECIEYLNLKKGEEISLFNKSYIVEdiTSNYVILKEKD------------GKEVLTNES 155
                                   22333333.....2222222222222222222222222112222222222............222222222 PP

  == domain 2  score: 181.8 bits;  conditional E-value: 2e-57
                     S_layer_C   1 tkiggeygyalkvvkdikelelGeeyvldweakvvidsg..itleykde................ekledkvvglalkykg 63 
                                   t+ig++y+++++v+++ik +e+Ge+y+ld+e+kv++ s+  i+leyk+                 ek+++++v +++++++
  gi|15669144|ref|NP_247949.1| 212 TRIGKGYRFTFRVYSTIK-IEEGEDYPLDKEFKVKEISTdkIKLEYKNIdslgneiylfnytiipEKCYKDYVLFKVIKRK 291
                                   689***************.******************999***************************************** PP

                     S_layer_C  64 dkladikdkdkvdianyaklkfdDklsvyfkideekevelivgekvkvlsadvkaekikakaeqvvkltaPivvLDtEvel 144
                                   +k++d+kd+++++++ ya +k +++++v++k++e k++e+i+ ++v+v+s+                            ++
  gi|15669144|ref|NP_247949.1| 292 EKTVDVKDVAYIGDGIYA-VKVNNTVHVFYKGKELKNHEKIYLGSVDVYSS----------------------------NP 343
                                   ******************.67767***************************............................99 PP

                     S_layer_C 145 dsvdknLiLvGGPvvNkvtkeLedk..lkvaityeednksaatiavienaangndvlvvAGsDRegTkaAalaliekl 220
                                   ++v+k++iL+GGP+vNk++keLedk  lkv+i+++++++++++i +i+n++n+n+++++AGsDR+gTkaA+l++++k+
  gi|15669144|ref|NP_247949.1| 344 LNVNKDIILIGGPKVNKIVKELEDKglLKVNISTNYPGNNRGIILKIKNPYNDNNIYILAGSDRWGTKAAILVFLTKY 421
                                   *************************999**********************************************9986 PP

>> DUF2996  Protein of unknown function (DUF2996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.1e-05      0.28      14     108 ..      76     170 ..      70     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.1e-05
                       DUF2996  14 dflPalkkalekkgiedlelefkkeklpvagleseecwqvvgelkegqrqFnlyfleedikgkkafslaesgskpstlEsF 94 
                                    ++P++ +   k+g ++l ++f ++   v+  + e +  +  +  e+   Fn ++  edi+++ ++   ++g++  t EsF
  gi|15669144|ref|NP_247949.1|  76 MYIPSIDELEIKNGDKNLIIKFDRDGNKVKYKDIECIEYLNLKKGEEISLFNKSYIVEDITSNYVILKEKDGKEVLTNESF 156
                                   59999999888999999*******99999986655556666666677789******************************* PP

                       DUF2996  95 liDErkvtLdllvl 108
                                     D  kv ++l+ +
  gi|15669144|ref|NP_247949.1| 157 EYDGYKVVVKLVSS 170
                                   *******9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3437.74
//
Query:       gi|15669145|ref|NP_247950.1|  [L=373]
Description: histidinol-phosphate aminotransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-62  210.6   0.0    4.3e-62  210.4   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.8e-09   36.9   0.2    7.7e-08   31.6   0.1    2.1  2  Alliinase_C      Allinase
    4.8e-09   35.7   0.2    2.1e-07   30.3   0.2    2.1  2  Aminotran_5      Aminotransferase class-V
    2.4e-07   29.6   0.9    3.4e-07   29.1   0.2    1.5  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.002   17.5   0.4      0.003   16.9   0.4    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.063   13.7   0.0        2.2    8.8   0.0    2.2  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.4   0.0   1.4e-65   4.3e-62       2     361 ..      39     366 ..      38     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: 210.4 bits;  conditional E-value: 1.4e-65
                                   EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHH CS
                 Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalie 82 
                                   d+i+Lgsne++ +    ++p+++++  +   +  ++++y+ +   p l ++l kfl+      ++ e  +v g Ga+++i+
  gi|15669145|ref|NP_247950.1|  39 DIIKLGSNENPWG----PSPKIKEKILD---EIDKIHQYPEPV-NPILMKELSKFLN------VDEENIIVGGDGADEIID 105
                                   89***********....******99988...************.*************......88886677788******* PP

                                   HHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                 Aminotran_1_2  83 alifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                   ++++ + ++ gde+++p pt+++y   + ++ +++ + ++++e+df+l++e++++ +++      ktkvi++++p+NPtG 
  gi|15669145|ref|NP_247950.1| 106 TIFRTF-VDDGDEVIIPIPTFTQYRVSATIHNAKIKYAKYDKEKDFKLNVESVLNNITD------KTKVIFLCTPNNPTGN 179
                                   ******.9***************************************************......**************** PP

                                   B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHH CS
                 Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlr 244
                                   ++   ++e +   +++  +l+++D aY + + ++ d      ++ e++n+++++++sK fGlaG RvGy ++n+++++++ 
  gi|15669145|ref|NP_247950.1| 180 IIENRDVERV---INETDALVVIDHAYIEYAKKEYDW---TQKAPEYDNVIVLRTFSKVFGLAGMRVGYGVANKKIIDYMM 254
                                   **********...********************7664...568999999******************************** PP

                                   HHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHHCHHHHHHHH CS
                 Aminotran_1_2 245 klsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsaetakelskkL 324
                                   +++  f  + l q  + +al+d +    ++e  ++  +k+r+ l+++L++  ++kv++s+++++l+ + + + ake++++L
  gi|15669145|ref|NP_247950.1| 255 RVKPIFSLTRLSQVCAITALRDRE----FFERCVRDGIKSREMLYNGLKKFkDIKVYPSEANYLLVELKTMK-AKEFCEEL 330
                                   **********************99....89******************888***************999998.******** PP

                                   HHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHH CS
                 Aminotran_1_2 325 leevgvyvtpgtsftv..pgrlRitvAglteeeleelve 361
                                   l++ gv+v+ +tsf     + +R+++  +t ee+e++++
  gi|15669145|ref|NP_247950.1| 331 LKR-GVIVRDCTSFDGlgDNYVRVSI--GTFEEVERFLK 366
                                   ***.**********999*********..******99986 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.1   2.6e-11   7.7e-08      72     217 ..      97     253 ..      85     276 .. 0.68
   2 ?    3.3   0.0      0.01        31     303     360 ..     312     369 ..     297     372 .. 0.61

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.6e-11
                                   ECHHHHHHHHHHHHHHHH..SSSSSEEEEE-SS--THHHHHTTTT-BT.TEEEEEESTT-........--S..S-EEEEEE CS
                   Alliinase_C  72 GtGstqLlqalvyalspeasseskpvkvvaavPyysvykeqtslldsk.lykweGdaaayv.......kkknpeefielvt 144
                                   G G+ ++++++  ++           +v+  +P ++ y+  +++ + k +y    + ++++       ++ + +  + +  
  gi|15669145|ref|NP_247950.1|  97 GDGADEIIDTIFRTFVDD------GDEVIIPIPTFTQYRVSATIHNAKiKYAKYDKEKDFKlnvesvlNNITDKTKVIFLC 171
                                   455555555555554444......567899999999999988887665234434455666666666655555555566778 PP

                                   SS-TTT----.....-----TT-EEEEEE-TT..-STT...TS---S-B--SEEEEEHHHHHS-GGG-EEEEEES-HHHHH CS
                   Alliinase_C 145 sPnnPdgllr.....eavvkgseakviyDlay..YWPh...ytpitskadedimLftlskltGhaGsrlGWalvkdkevak 215
                                    PnnP g++      e v+++++a v+ D+ay  Y  +   +t+   + d+ i+L t+sk+ G aG r+G+++   k++ +
  gi|15669145|ref|NP_247950.1| 172 TPNNPTGNIIenrdvERVINETDALVVIDHAYieYAKKeydWTQKAPEYDNVIVLRTFSKVFGLAGMRVGYGVAN-KKIID 251
                                   8******996222225799************9554433212566666678899******************9754.44444 PP

                                   HH CS
                   Alliinase_C 216 kl 217
                                    +
  gi|15669145|ref|NP_247950.1| 252 YM 253
                                   33 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.01
                                   SEEEEEESSSS..-.HHHHHHTTTEEEEEGGGG.TS-TTEEEEESSS-HHHHHHHHHHHH CS
                   Alliinase_C 303 ayaWlkcekeeded.caevlrekkiltrsGevf.eaesryvrlsllkrdddfdvllerlk 360
                                    y  ++ +  + ++ c+e+l++ +++ r+ + f + + +yvr+s+  + ++ + +l+ l+
  gi|15669145|ref|NP_247950.1| 312 NYLLVELKTMKAKEfCEELLKR-GVIVRDCTSFdGLGDNYVRVSI-GTFEEVERFLKILE 369
                                   5666666666655515555555.555666666626799******7.44444555555555 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.2     7e-11   2.1e-07      51     177 ..      81     202 ..      78     209 .. 0.81
   2 ?    3.2   0.0     0.011        34     278     360 ..     285     356 ..     258     364 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 7e-11
                                   HHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBE..G CS
                   Aminotran_5  51 kvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeld..l 129
                                   ++ +++n+++e+ i+   G+ e i ++ +++   +++gde+++        +   +     ++ak+k+++ d+e+  +  +
  gi|15669145|ref|NP_247950.1|  81 ELSKFLNVDEENIIVGGDGADEIIDTIFRTF---VDDGDEVIIPIPTFTQYR-VSAT---IHNAKIKYAKYDKEKDFKlnV 154
                                   6789999998555555667777888888888...99****999876655555.3333...457899999888777655449 PP

                                   GGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                   Aminotran_5 130 delekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                   + + +++++ktk+++++  +n tG+i +  ++ +++ + +alv++D a
  gi|15669145|ref|NP_247950.1| 155 ESVLNNITDKTKVIFLCTPNNPTGNIIENRDVERVINETDALVVIDHA 202
                                   9*********************************************87 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S.-EEEE CS
                   Aminotran_5 278 khekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlale.gtvRa 357
                                   +   + +e+l+++lk+ +++++y       +a+ + + +k+++a+++   L ++g+ vr    c+    ++ +l  + vR+
  gi|15669145|ref|NP_247950.1| 285 RDGIKSREMLYNGLKKFKDIKVYP-----SEANYLLVELKTMKAKEFCEELLKRGVIVRD---CT----SFDGLGdNYVRV 353
                                   55667889**************55.....688999999********************94...44....222333355666 PP

                                   E-- CS
                   Aminotran_5 358 Sly 360
                                   S++
  gi|15669145|ref|NP_247950.1| 354 SIG 356
                                   665 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.2   1.1e-10   3.4e-07      61     176 ..      82     203 ..      68     207 .. 0.78
   2 ?   -2.9   0.0      0.63   1.9e+03     355     371 ..     345     362 ..     342     369 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.1e-10
                                   HHHHHT-SEEEEESSHHHH...HHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....TSHHHHHHH CS
               Cys_Met_Meta_PP  61 iaaLeggeaalavssGmaA...iaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.....sdleeleka 133
                                   +++  ++++  ++  G +A   i++++++++  Gde+++    +  tq  ++ ++++ +i++  +d+      ++e++ + 
  gi|15669145|ref|NP_247950.1|  82 LSKFLNVDEENIIVGGDGAdeiIDTIFRTFVDDGDEVIIPIPTF--TQYRVSATIHNAKIKYAKYDKekdfkLNVESVLNN 160
                                   555555555555555555533346778999*********98877..78888999999999999988844444567888899 PP

                                   CCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTT CS
               Cys_Met_Meta_PP 134 ikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntf 176
                                   i+++tk+++l tp np+ +++  +++ +++ + ++lvv+D ++
  gi|15669145|ref|NP_247950.1| 161 ITDKTKVIFLCTPNNPTGNIIENRDVERVINETDALVVIDHAY 203
                                   999*************************************875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.63
                                   TS-TTEEEEE--S.S-HH CS
               Cys_Met_Meta_PP 355 gvtddliRlsvGi.Edvd 371
                                   g+ d+ +R+s+G  E+v+
  gi|15669145|ref|NP_247950.1| 345 GLGDNYVRVSIGTfEEVE 362
                                   788999*****9536665 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4     1e-06     0.003      60     145 ..     112     201 ..      97     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1e-06
                                   TTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-T.TTSSB-GGGCGGG--TTEEEEE...EB-GGGB---HHHHHHHHHH CS
               DegT_DnrJ_EryC1  60 vgpgdeVIvpsltFvatanavlelgakpvfvDvdp.dtynidpaaieaaitertkaIl...pVhlyGqvadmdalkaiaak 136
                                   v++gdeVI+p  tF+    +++  +ak  ++  d+ +++ ++++++ + it +tk I+   p +  G++ +   ++++ ++
  gi|15669145|ref|NP_247950.1| 112 VDDGDEVIIPIPTFTQYRVSATIHNAKIKYAKYDKeKDFKLNVESVLNNITDKTKVIFlctPNNPTGNIIENRDVERVINE 192
                                   779*****************************986268*******************722245677888888888888888 PP

                                   CT-EEEEE- CS
               DegT_DnrJ_EryC1 137 hglkvieDa 145
                                   ++  v+ D 
  gi|15669145|ref|NP_247950.1| 193 TDALVVIDH 201
                                   777777775 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00072       2.2      30      84 ..     130     182 ..     122     203 .. 0.75
   2 ?    2.4   0.0     0.066     2e+02      65      98 ..     309     342 ..     284     346 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00072
                                   EEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHH CS
                Semialdhyde_dh  30 llsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvskelap 84 
                                   ++++ ++a  k+a++ k  e+  +l+ve+v ++++++ +++fl++p++ + ++ +
  gi|15669145|ref|NP_247950.1| 130 VSATIHNAKIKYAKYDK--EKDFKLNVESVLNNITDKTKVIFLCTPNNPTGNIIE 182
                                   55555555566666644..8888999999999999************98888766 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.066
                                   TT-SEEEE-SCHHHHHHHHHHHHHTTSEEEESSS CS
                Semialdhyde_dh  65 kevdivflalpagvskelapklaeagvkviDlss 98 
                                   +e+++++  l    +ke+ ++l+++gv+v D +s
  gi|15669145|ref|NP_247950.1| 309 SEANYLLVELKTMKAKEFCEELLKRGVIVRDCTS 342
                                   67788888888999***************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.23s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2547.57
//
Query:       gi|15669146|ref|NP_247951.1|  [L=260]
Description: hypothetical protein MJ_0956 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.079   13.0   0.0       0.16   12.0   0.0    1.5  1  DUF4752   Domain of unknown function (DUF4752)


Domain annotation for each model (and alignments):
>> DUF4752  Domain of unknown function (DUF4752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.9e-06      0.16      16      59 ..     167     211 ..     156     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.9e-06
                       DUF4752  16 wlyimfksgrWlvsv.llKqwekrkkkekrqkAlnefydaFdlds 59 
                                   ++ i +k g+ l+ + ++ + +    +e+++ Alnefyda + ++
  gi|15669146|ref|NP_247951.1| 167 FCPILYKLGKSLIKSeIFYKKKILTDNERKEHALNEFYDAMKEQD 211
                                   5667777777666441445556677899************86554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1713.10
//
Query:       gi|15669147|ref|NP_247952.1|  [L=350]
Description: hypothetical protein MJ_0957 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.36   11.4   6.3       0.55   10.7   6.3    1.2  1  TonB_N    TonB polyproline region


Domain annotation for each model (and alignments):
>> TonB_N  TonB polyproline region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   6.3   3.1e-05      0.55      66      80 ..       8      22 ..       4      29 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.1e-05
                                  X..XXXXXXXXXXXX CS
                        TonB_N 66 kPePkPkPkPkpvkk 80
                                   P+PkPkPkPkp+ k
  gi|15669147|ref|NP_247952.1|  8 PPKPKPKPKPKPEYK 22
                                  378999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2304.92
//
Query:       gi|15669148|ref|NP_247953.1|  [L=426]
Description: hypothetical protein MJ_0958 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1196  (0.0667076); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2616.58
//
Query:       gi|15669149|ref|NP_247954.1|  [L=385]
Description: aspartate aminotransferase AspC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-44  152.0   0.0    2.4e-44  151.8   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    1.4e-06   27.1   0.2    2.4e-06   26.4   0.2    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    1.8e-05   24.1   0.0    3.4e-05   23.2   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
    0.00054   19.3   0.6     0.0029   16.9   0.8    1.8  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.065   12.6   0.1        0.3   10.4   0.0    1.8  2  FAD_oxidored     FAD dependent oxidoreductase
       0.11   12.1   0.0       0.22   11.0   0.0    1.5  1  DUF2982          Protein of unknown function (DUF2982)


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.8   0.0   8.1e-48   2.4e-44       3     359 ..      10     344 ..       8     356 .. 0.90

  Alignments for each domain:
  == domain 1  score: 151.8 bits;  conditional E-value: 8.1e-48
                                   EBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCC CS
                   Aminotran_5   3 ldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslar 83 
                                   l+ +++t++p+eVl+a++             ++h++k+ ++ +e++ ek+++++ +e+ ++ + t ++t a+ +++ ++  
  gi|15669149|ref|NP_247954.1|  10 LMIPGPTMVPPEVLNAMALP----------VIGHRTKDYSNLLEDTIEKLKKVFITEN-DTFLITGSGTAAMDMAISNI-- 77 
                                   899**************999..........69*************************7.99999999999*********.. PP

                                   C-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--..TTEEEEEEESBETTTTEB--HHHHH CS
                   Aminotran_5  84 slkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldeleklln..ektklvaithvsnvtGtiqpveeig 162
                                    +k+gd+++  +++  +++   +++ k+ + +   + ++++   +++++++ l+  +++k+v++ h++++tG  +p++eig
  gi|15669149|ref|NP_247954.1|  78 -IKRGDKVLNIVTGNFGER--FANIVKAYKGEAIRLDVEWGDMAEPEAVKEILDkyDDIKAVTVVHNETSTGARNPIKEIG 155
                                   .******************..555555555555599*****************8779************************ PP

                                   HHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..S.S.STTSEEEEET.TEEE CS
                   Aminotran_5 163 klakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkelleklepl.llggemveevsl.eett 240
                                   +++k+++al++vD ++++g   ++v+k+ +D+ + +++K l +P+G+ ++ v+++++e +++     g +++   + +++ 
  gi|15669149|ref|NP_247954.1| 156 EVVKDYDALYIVDTVSSLGGDYVNVDKFHIDICVTGSQKcLAAPPGLAAITVSEKAWEVIKKNdDKVGFYLDLLAYkKYYE 236
                                   ***************************************999******************665257899999999954443 PP

                                   .EHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEE.TTC CS
                   Aminotran_5 241 .faeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnf.kgv 319
                                     +++p+     Tp v+  ++l+ al+++ e g+e+  k++++la++++++l++++   +   ++  r+ +++s ++ +g+
  gi|15669149|ref|NP_247954.1| 237 eKKQTPY-----TPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELF-A-KERARSVTVTSAKYpEGI 310
                                   3566666.....9*****************************************988777.3.57788999999999999* PP

                                   SHHHHHHHHHHT.TEEEEEE-TTTHHHHHHTT.S-EEEEE.- CS
                   Aminotran_5 320 haedvatlLdee.gIavrsGhhcaqplmkrlalegtvRaS.l 359
                                   + ++++ +L ++ +I v +G++++          +++R++ +
  gi|15669149|ref|NP_247954.1| 311 EDSKFRGILSNKyNIVVAGGQKHL--------AGKIFRIGhM 344
                                   *********9999*********99........5556665544 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.2   7.9e-10   2.4e-06      55     198 ..      40     194 ..      33     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 7.9e-10
                                   HHHHHHHHHHHT-.....SEEEEESSHHHHHHHHHHTTS-TTEEEE..EESTSSHHHH.HHHHHTHHH.TTCEEEEESTTS CS
               Cys_Met_Meta_PP  55 svleeriaaLegg.....eaalavssGmaAiaaailallkaGdeiv..vsddlYggtq.rllkkvlkk.lgievkfvdtsd 126
                                   + le++i +L+++     +  l++ sG+aA+++ai +++k Gd+++  v+ + +g  + +++k +  + + ++v++ d+++
  gi|15669149|ref|NP_247954.1|  40 NLLEDTIEKLKKVfitenDTFLITGSGTAAMDMAISNIIKRGDKVLniVTGN-FGERFaNIVKAYKGEaIRLDVEWGDMAE 119
                                   568888888887766655778999********************86214444.5555505555554434888999****** PP

                                   HHHHHHHCCT.....TEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTT CS
               Cys_Met_Meta_PP 127 leelekaike.....ntklvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp.llqrplklgaDivvhSaTK 198
                                   +e++++ +++      + +v+ Et t        i++i +++k+ ++l +vD + + +  +++  k+ +Di v    K
  gi|15669149|ref|NP_247954.1| 120 PEAVKEILDKyddikAVTVVHNETSTGA---RNPIKEIGEVVKDYDALYIVDTVSSLGgDYVNVDKFHIDICVTGSQK 194
                                   *******998763434455555665554...56689999999**********98765548889899999999887766 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.2e-08   3.4e-05      57     346 ..      49     341 ..      32     347 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.2e-08
                                   HCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEE.EEESS-TH.HHHHHHHTTSEEEEEEBEETTTTEE-HHHH CS
                 Aminotran_1_2  57 lgrseklklkreaavvvgsGagaliealifllklnpgdeil.vpdptyas.yknilrlsggevvryplyseedfhldleal 135
                                   l+  ++  +++++ +++gsG+ a++ a+  ++k  +gd++l + + ++++ + ni+++++ge +r  ++   +     ea+
  gi|15669149|ref|NP_247954.1|  49 LK--KVFITENDTFLITGSGTAAMDMAISNIIK--RGDKVLnIVTGNFGErFANIVKAYKGEAIRLDVE--WGDMAEPEAV 123
                                   33..3445677779******************8..8888876889999754****************77..4445677888 PP

                                   HHHHTTHHCTTETEEEEEEESS-TT..T--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEE CS
                 Aminotran_1_2 136 eealkeapegnkktkvilvesphNP..tGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnll 214
                                   +e l++  ++++  k  +v+ +hN   tG+  + +e+ ++   +k y +l +vD + + +          ++nv++   ++
  gi|15669149|ref|NP_247954.1| 124 KEILDK--YDDI--K--AVTVVHNEtsTGARNPIKEIGEV---VKDYDALYIVDTVSSLGGD--------YVNVDKFHIDI 187
                                   888887..4444..4..44445554005655555555555...***********99554443........899*9976678 PP

                                   EEEESSSTTSSGGG-EEEEEEEH....................HHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 215 ivgslsKafGlaGeRvGyilgna....................avvsqlrklsrpfls.ssllqaavaaalsdallkqsel 274
                                   +v++  K ++++   +++i++++                    a++++ +  +++ +  s  l +a++ al+ +l++   +
  gi|15669149|ref|NP_247954.1| 188 CVTGSQKCLAAPP-GLAAITVSEkawevikknddkvgfyldllAYKKYYEEKKQTPYTpSVNLTYALNVALDLVLEE--GI 265
                                   8888889998865.2777777779***********************999999888886777888888888888876..9* PP

                                   HHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH.....CHHHHHHHHHHTCTEEEEEGGGGTSTTEEEE CS
                 Aminotran_1_2 275 eemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae.....takelskkLleevgvyvtpgtsftvpgrlRi 346
                                   e++++r+++++k  r++L++ g++ +a++ +  +  ++sa+     +++++   L ++++++v  g+   + + +Ri
  gi|15669149|ref|NP_247954.1| 266 ENRVKRHERLAKATRAGLEAMGIELFAKERARSVT-VTSAKypegiEDSKFRGILSNKYNIVVAGGQKHLAGKIFRI 341
                                   ******************999*******9776555.45555589*9999**************99887777777776 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.8   9.7e-07    0.0029      17     160 ..      25     161 ..      16     306 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.7e-07
                                   HHHCS----CCCT--HHHHHHHHHHHH..HTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC- CS
               Beta_elim_lyase  17 aqaaamlGdesYgedktvnrLedavae..lfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelag 95 
                                   a+a  ++G+     ++  ++  +++++  +++ +  l + +GtaA  ++++ +++rg++v+   ++++  + +  +++++g
  gi|15669149|ref|NP_247954.1|  25 AMALPVIGHRTKDYSNLLEDTIEKLKKvfITENDTFLITGSGTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKG 105
                                   5555555555555555444444555555556777777799*********************99999998888888888877 PP

                                   -EEEEE-EBTTTBE.-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHC CS
               Beta_elim_lyase  96 vklrdlknkeaGkm.dlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakky 160
                                     ++ l+ +  G+m ++e++++++++    +++ik++++   n+t+ G   +++e+ ev   +k+y
  gi|15669149|ref|NP_247954.1| 106 E-AIRLDVEW-GDMaEPEAVKEILDK----YDDIKAVTVV-HNETSTGARNPIKEIGEV---VKDY 161
                                   7.999****9.887469999999999....3557776553.355556887776666555...4555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0001       0.3      24     115 ..      51     149 ..      48     169 .. 0.75
   2 ?   -0.4   0.0      0.19   5.7e+02      72     130 ..     234     296 ..     205     307 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                  FAD_oxidored  24 kvlLveergvl.GGlltsglvatdignkaee....qvvtgiareflerlrq.rggarlkkrskw.ntfepevakavleeml 97 
                                   kv ++e++ +l  G  t+++ +++ +  +++    ++vtg ++e ++++ +  +g+ ++ + +w  + epe++k++l++  
  gi|15669149|ref|NP_247954.1|  51 KVFITENDTFLiTGSGTAAMDMAISNIIKRGdkvlNIVTGNFGERFANIVKaYKGEAIRLDVEWgDMAEPEAVKEILDKYD 131
                                   677777666643688888887777776655588898888877777777766444445678899988*************** PP

                  FAD_oxidored  98 aeagvtvllntrlvevek 115
                                   + + vtv++n++ ++++ 
  gi|15669149|ref|NP_247954.1| 132 DIKAVTVVHNETSTGARN 149
                                   99********99988765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.19
                  FAD_oxidored  72 garlkkrskwn....tfepevakavleemlaeagvt..vllntrlvevekegkriesvtveske.g 130
                                   ++++ k++  +    +++ + a +v+ +++ e+g++  v  ++rl ++++ g +  ++++  ke  
  gi|15669149|ref|NP_247954.1| 234 YYEE-KKQ--TpytpSVNLTYALNVALDLVLEEGIEnrVKRHERLAKATRAGLEAMGIELFAKErA 296
                                   2221.222..11234688888889999999777775337788899998888866666666665533 PP

>> DUF2982  Protein of unknown function (DUF2982)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.5e-05      0.22      36      81 ..      23      68 ..      18      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.5e-05
                       DUF2982 36 lelveLpyiGiklkdleefldkispRlatklLleQrpLlllaakek 81
                                  l+ + Lp+iG + kd++++l++   +l +  ++e    l+++  ++
  gi|15669149|ref|NP_247954.1| 23 LNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFLITGSGTA 68
                                  56789******************************99999987644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2337.69
//
Query:       gi|15669150|ref|NP_247955.1|  [L=217]
Description: putative translaldolase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-65  220.8   0.7    1.5e-64  218.1   0.7    2.0  1  TAL_FSA   Transaldolase/Fructose-6-phosphate aldolase


Domain annotation for each model (and alignments):
>> TAL_FSA  Transaldolase/Fructose-6-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.1   0.7   8.4e-69   1.5e-64       1     271 [.       3     200 ..       3     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 218.1 bits;  conditional E-value: 8.4e-69
                                   EEEE---HHHHHHHHHTT---EEE--HHHHHH..TTS.-HHHHHHHHHHH........................H-S-EEE CS
                       TAL_FSA   1 lvlDtadrelikklleekgiqgvTtNPsliekaikykalydeaieeikkegkkvkeaydkLavedilealdllgadgrvsl 81 
                                   ++lDta++e+ikk++e + ++gvTtNP+l++k  +++ ++ e+++ei+++                      +  +g+vs+
  gi|15669150|ref|NP_247955.1|   3 FFLDTANVEEIKKYAELGLVDGVTTNPTLVAK--EGR-DFYEVVKEICEI----------------------V--EGPVSA 56 
                                   69******************************..666.9999******88......................6..****** PP

                                   E-S-...-SHHHHHHHHHHHHTT-T..TEEEEEESSHHHHHHHHHHHHTT--EEEEEE-SHHHHHHHHHHT-SEEEEBHHH CS
                       TAL_FSA  82 EVdarlsddteatieeArrlialyerenvlIKiPateeGikAikeLkkeGinvnvTliFsleqalaaaeagasviSpFvgR 162
                                   EV +   +d+e++++eAr+l++l++  n++IKiP+t++G+kA+k L++eGi++nvTl+Fs+ qal aa+aga+++SpFvgR
  gi|15669150|ref|NP_247955.1|  57 EVIS---TDAEGMVKEARELAKLAD--NIVIKIPMTKDGMKAVKILSAEGIKTNVTLVFSPLQALVAAKAGATYVSPFVGR 132
                                   ****...******************..****************************************************** PP

                                   HHTTT............S-HHHHHHHHHHHHHHHT-S-EEEEBS--SHHHHH..HHHT-SEEEE-HHHHHHHT--HHH... CS
                       TAL_FSA 163 iddllkkleekdklkgkddgvalvkeiynyykklgysTkvmaasfrnveeve..elagcdtvTippkllealakhgktsek 241
                                   +dd++            + g++l+++++++yk+++++T+v+ as+r++ +v+  +++g+d+ T+pp+++++l +h++t   
  gi|15669150|ref|NP_247955.1| 133 LDDIG------------HVGMKLIEDVVKIYKNYDIKTEVIVASVRHPWHVLeaAKIGADIATMPPAVMDKLFNHPLT--- 198
                                   *****............9**********************************999**********************9... PP

                                   ............................HH CS
                       TAL_FSA 242 leeeeieklleklfrlginedavaeellde 271
                                                               d 
  gi|15669150|ref|NP_247955.1| 199 ----------------------------DI 200
                                   ............................33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1442.38
//
Query:       gi|15669151|ref|NP_247956.1|  [L=762]
Description: cell division control protein 54 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-75  252.1   0.0    5.4e-75  251.3   0.0    1.4  1  MCM           MCM P-loop domain
      1e-21   77.1   2.0    5.4e-20   71.6   0.1    3.5  3  MCM_lid       MCM AAA-lid domain
    1.3e-10   41.0   0.0    7.4e-07   28.7   0.0    2.4  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
    1.8e-07   31.3   0.0    4.1e-07   30.1   0.0    1.7  1  AAA_5         AAA domain (dynein-related subfamily)
    4.7e-06   26.5   0.6    3.1e-05   23.8   0.2    2.5  2  MCM_OB        MCM OB domain
    0.00083   19.8   0.0      0.002   18.6   0.0    1.6  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.017   15.8   0.0      0.043   14.5   0.0    1.6  1  RPA_C         Replication protein A C terminal
      0.019   15.3   0.0      0.049   13.9   0.0    1.7  1  AAA_22        AAA domain
      0.042   13.7   0.0        1.1    9.2   0.0    2.6  1  AAA_3         ATPase family associated with various cellular 
       0.11   12.6   0.1       0.56   10.4   0.0    2.3  3  Mrr_N         Mrr N-terminal domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.3   0.0     3e-78   5.4e-75       3     224 .]     323     545 ..     321     545 .. 0.97

  Alignments for each domain:
  == domain 1  score: 251.3 bits;  conditional E-value: 3e-78
                                   HHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSS CS
                           MCM   3 eeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapr 83 
                                   e+++el ++k+ii++l+++++ +i g+e vkkai lq+++g  k l+d+t lr d ++ll++dpg++Ks++L+++++l+p+
  gi|15669151|ref|NP_247956.1| 323 ETLNELGRKKNIIDILSNYLISQIKGYELVKKAIFLQQIKGAFKFLPDGTPLRRDSHILLITDPGIGKSTMLRRIARLFPQ 403
                                   7899***************************************************************************** PP

                                   EEEEESSSSSSSHSSSEEEEESSSSS..EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE CS
                           MCM  84 avytsgkgssaagLtaavvrdeetge..fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLn 162
                                   + y+s +++++ gLta v+r+ ++    +v++ G  v a++G +ciDe+   k+   ++++EamE+qti+++K+Gi+++L+
  gi|15669151|ref|NP_247956.1| 404 NAYASVTTATGGGLTAIVTREATEIGdgWVVKPGVFVRANEGTACIDELTVDKN-VMKYILEAMESQTIHVNKGGINVKLP 483
                                   ********************99876556*********************87666.99************************ PP

                                   --EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                           MCM 163 artsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                   ar++vlaA+npk gr+d++ +v+e+i+++a+lLsrFDlif l+Dk+++++Dee+aehi+++h
  gi|15669151|ref|NP_247956.1| 484 ARCAVLAACNPKRGRFDRNLTVIEQIDIPAPLLSRFDLIFPLMDKPNRKSDEEIAEHILNTH 545
                                   ***********************************************************987 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.23   4.2e+02      43      76 ..     287     321 ..     277     327 .. 0.74
   2 ?    0.7   0.2      0.39     7e+02       2      14 ..     570     581 ..     569     593 .. 0.80
   3 !   71.6   0.1     3e-23   5.4e-20      13      86 ..     600     671 ..     596     672 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.23
                                   SSST--HHHHHH.HHHHHHHHHHHHTSSSE-HHHH CS
                       MCM_lid  43 ksipitvRqLes.liRLseAlAklrlsevvteedv 76 
                                   ++ipi    ++s  i++se+  k++++++ ++e  
  gi|15669151|ref|NP_247956.1| 287 HNIPIYKIYIKSnYIKISESYNKIEVKDILRNEEL 321
                                   556666666666469************99988765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.39
                                   HHHHHHHHHHHTT CS
                       MCM_lid   2 llrkYiayareki 14 
                                   ll+ Yi yar  +
  gi|15669151|ref|NP_247956.1| 570 LLKYYIIYAR-SC 581
                                   799*******.44 PP

  == domain 3  score: 71.6 bits;  conditional E-value: 3e-23
                                   TT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHHHHHHH CS
                       MCM_lid  13 kikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeairllkes 86 
                                    i P l+++ak++++++Y+e+Rk  e   ++ ipit+RqLe++iR++e +Ak rls+ v++ d+e ai++++++
  gi|15669151|ref|NP_247956.1| 600 LIMPYLTDKAKKMIKKYYLEMRKLGE--GDNPIPITARQLEAIIRIAEMHAKARLSDKVEDVDAEVAISIIDDC 671
                                   588********************885..479***************************************9887 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00027      0.49      24      52 ..     379     407 ..     376     415 .. 0.87
   2 !   28.7   0.0   4.1e-10   7.4e-07      89     160 ..     426     496 ..     418     531 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00027
                  Mg_chelatase  24 nlllvGppGsGKtmlakrlpsllpplsee 52 
                                   ++ll+  pG GK+ + +r++ l+p+   +
  gi|15669151|ref|NP_247956.1| 379 HILLITDPGIGKSTMLRRIARLFPQNAYA 407
                                   799*********************97765 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 4.1e-10
                  Mg_chelatase  89 alvGggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcp 160
                                   + +G g  +kpG   +a++G   +DEl+  +++v++ + e +e++++++++   +v+ par+ ++aa Np +
  gi|15669151|ref|NP_247956.1| 426 TEIGDGWVVKPGVFVRANEGTACIDELT-VDKNVMKYILEAMESQTIHVNKGGINVKLPARCAVLAACNPKR 496
                                   55999*********************96.89***************************************76 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   2.3e-10   4.1e-07       1     125 [.     379     499 ..     379     519 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.3e-10
                                   EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--..........--------G-SEEEEESGGG--H CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreik.ngttslvdsplvraaregeilvlDEveraes 79 
                                   ++lL+ +pG+gKs++ +r+a+++ ++ +  v    +   + ++ r  ++ +++ + +++++vra +e  ++++DE++ +++
  gi|15669151|ref|NP_247956.1| 379 HILLITDPGIGKSTMLRRIARLFpQNAYASVTTATGGGLTAIVTREATEiGDGWVVKPGVFVRA-NE-GTACIDELT-VDK 456
                                   689999*****************76666666666666677777776666789999999999954.44.5789*****.*** PP

                                   HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--... CS
                         AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpld..r 125
                                   +v++  l  +e +++++++gg  vk ++        v+a++np +  +
  gi|15669151|ref|NP_247956.1| 457 NVMKYILEAMESQTIHVNKGGINVKLPAR-----CAVLAACNPKRgrF 499
                                   ************************99996.....9*******998542 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.2   1.7e-08   3.1e-05       4     104 ..     104     265 ..     101     280 .. 0.75
   2 ?   -2.9   0.0       3.2   5.8e+03      39      60 ..     470     493 ..     437     504 .. 0.59

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.7e-08
                                   G--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE......S---............................ CS
                        MCM_OB   4 dlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev......elee............................ 50 
                                   ++++e+i+klvk eG + +a +v+  lkkav++c+k  k ++       +                               
  gi|15669151|ref|NP_247956.1| 104 EISAEDINKLVKFEGNILQAGKVNALLKKAVYYCNKRIKDENGgflckyT--Ytpcdgrveieiddyfsegefikdmlspr 182
                                   7899******************************9877655533466432..25577777777888888888888999966 PP

                                   .....................-SB-...........TTT-HHH-EEE-GGGSEEEEEEEEEEE------------.-EEEE CS
                        MCM_OB  51 .....................PrkCe.........ekeCeskdpfkletekskfvdfqklklQEspeevpaGelP.rslev 100
                                                        Pr C          +++ + + +f l+   s +v+ q++++Q   + + + e P rs+ v
  gi|15669151|ref|NP_247956.1| 183 evkkilenkkvwdklvekgkiPR-CVdlkendevfKENLK-EIKFILDEYDSIYVNIQEMEIQQPIDLMKNPEEPaRSIRV 261
                                   66556655555555555555555.7678776555433333.569999999***************9999776665488888 PP

                                   EEEG CS
                        MCM_OB 101 iled 104
                                   +le+
  gi|15669151|ref|NP_247956.1| 262 FLEN 265
                                   8875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.2
                                   TT-.-EE.ES----SB-...TTT- CS
                        MCM_OB  39 kcgktve.veleePrkCe.ekeCe 60 
                                   + + +++ ++++ P +C    +C+
  gi|15669151|ref|NP_247956.1| 470 TIHVNKGgINVKLPARCAvLAACN 493
                                   222222233566699997545676 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06     0.002       9      55 ..     358     407 ..     350     431 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                        AAA_16   9 leqLlsalervrsgrp....elvllsGesGvGKsslvrellralekdggif 55 
                                   l+q++ a++ + +g+p    + +ll+ ++G+GKs+++r+++r + ++ +++
  gi|15669151|ref|NP_247956.1| 358 LQQIKGAFKFLPDGTPlrrdSHILLITDPGIGKSTMLRRIARLFPQN-AYA 407
                                   68999************************************877666.444 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.4e-05     0.043      45      98 ..     694     752 ..     674     754 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                                   .XSXHHHHHHHHHHHH..SXSTTTEEHH.HHHHHS...TSXHHHHHHHHHHHHHTTSEE CS
                         RPA_C  45 kgltalaqqvlnlikq.speseeGvhvd.eiaqkl...rlsvndvkqavdeLsneGiiY 98 
                                   k++ +  + vln+i++    +++G+  + ei +k    +ls++dv+ a+++L ++G iY
  gi|15669151|ref|NP_247956.1| 694 KSRRDKMDAVLNIIREiVSLRDDGLAPEeEIYEKAmaiGLSEKDVNDALEYLKKAGDIY 752
                                   567788899*******98899****9752676443367********************* PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.7e-05     0.049       4      35 ..     376     407 ..     374     432 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeaka 35 
                                   ++++++++  +G+GK+t lrr+++ +++ a+a
  gi|15669151|ref|NP_247956.1| 376 RDSHILLITDPGIGKSTMLRRIARLFPQNAYA 407
                                   6799**********************865544 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0006       1.1       1     112 [.     379     494 ..     379     502 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0006
                         AAA_3   1 hvllegvPGlaktllvkalakaldle.fkriqftpdllPsdilGtevfeekekefefkkGpvfan...llladeinrappk 77 
                                   h+ll   PG++k ++ + +a+ +  + +  +  ++    + i+  e   e    + +k+G  +         de+      
  gi|15669151|ref|NP_247956.1| 379 HILLITDPGIGKSTMLRRIARLFPQNaYASVTTATGGGLTAIVTREAT-EIGDGWVVKPGVFVRAnegTACIDELTV-DKN 457
                                   899999999999999999999886551444433322222223333332.2335667777754432122456677754.445 PP

                         AAA_3  78 tqsalleameerqvtve..gethklpepflvlatqnP 112
                                   +   +leame +++ v+  g + klp    vla+ nP
  gi|15669151|ref|NP_247956.1| 458 VMKYILEAMESQTIHVNkgGINVKLPARCAVLAACNP 494
                                   6778999999998776511567889999999999999 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.4   7.9e+03      20      43 ..     303     326 ..     293     345 .. 0.72
   2 ?   -4.1   0.0        10   1.8e+04       4      17 ..     458     471 ..     457     474 .. 0.78
   3 ?   10.4   0.0   0.00031      0.56      51      76 ..     735     760 ..     699     761 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.4
                         Mrr_N  20 lkeirervaerfglseeeraellp 43 
                                   ++e +++++ +  l  ee+ e+l+
  gi|15669151|ref|NP_247956.1| 303 ISESYNKIEVKDILRNEELIETLN 326
                                   577788888888888888888873 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 10
                         Mrr_N   4 lmlplLealadgse 17 
                                   +m+ +Lea++++ +
  gi|15669151|ref|NP_247956.1| 458 VMKYILEAMESQTI 471
                                   69999999987665 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00031
                         Mrr_N  51 knrvgWartyLkkagllespkrgvwk 76 
                                   ++ v+ a+ yLkkag + +p+ g+w 
  gi|15669151|ref|NP_247956.1| 735 EKDVNDALEYLKKAGDIYNPRYGFWG 760
                                   678999******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (762 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 4787.69
//
Query:       gi|15669152|ref|NP_247957.1|  [L=128]
Description: hypothetical protein MJ_0962 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-17   63.4   0.1    1.8e-17   63.4   0.1    1.5  2  Rpr2           RNAse P Rpr2/Rpp21/SNM1 subunit domain
    0.00068   19.6   1.5       0.73    9.9   0.4    2.3  2  ADK_lid        Adenylate kinase, active site lid
  ------ inclusion threshold ------
       0.01   15.5   0.7        1.5    8.6   0.1    2.2  2  A2L_zn_ribbon  A2L zinc ribbon domain
      0.055   13.4   2.1       0.56   10.2   0.1    2.4  2  zinc_ribbon_4  zinc-ribbon domain
      0.081   13.0   0.1       0.15   12.1   0.1    1.4  1  DZR            Double zinc ribbon
       0.12   11.9   0.1         12    5.5   0.0    2.2  2  TF_Zn_Ribbon   TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.1   6.1e-21   1.8e-17       1      90 []      16      96 ..      16      96 .. 0.93
   2 ?   -2.5   0.2       2.1   6.3e+03      73      77 ..     110     114 ..     101     124 .. 0.48

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 6.1e-21
                                  HHHHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EE CS
                          Rpr2  1 rlnfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlv 83
                                  r+++L+++a+ + ++ + + ++++++ +r++++k+++r p+++kr++CkkCg++l+ g +++vr+++k+ +        + +v
  gi|15669152|ref|NP_247957.1| 16 RIDILMSLAEEEAKKGNWDRAKRYVYLARRIAMKMRIRFPKKWKRRICKKCGTFLLYGRNARVRIKSKRYP--------H-VV 89
                                  8999*******99****************************************************875555........3.48 PP

                                  EEETTTT CS
                          Rpr2 84 vtClaCg 90
                                  +tCl+Cg
  gi|15669152|ref|NP_247957.1| 90 ITCLECG 96
                                  ******7 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.1
                                   ..... CS
                          Rpr2  73 kkkkk 77 
                                   k++kk
  gi|15669152|ref|NP_247957.1| 110 KRRKK 114
                                   22222 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.4   0.00024      0.73       1       9 [.      60      68 ..      60      74 .. 0.94
   2 !    8.7   0.0   0.00058       1.7       3      16 ..      91     104 ..      90     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00024
                                  EEE-TTT-- CS
                       ADK_lid  1 RrvCpkCGr 9 
                                  Rr+C+kCG+
  gi|15669152|ref|NP_247957.1| 60 RRICKKCGT 68
                                  9*******6 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00058
                                   E-TTT--EEETTTB CS
                       ADK_lid   3 vCpkCGrsYhvvfn 16 
                                   +C  CG++Y + ++
  gi|15669152|ref|NP_247957.1|  91 TCLECGAIYRIPMI 104
                                   8********84444 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0005       1.5       4      15 ..      61      72 ..      59      76 .. 0.82
   2 ?    5.4   0.1    0.0053        16      24      31 ..      92      99 ..      90     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0005
                 A2L_zn_ribbon  4 kvCsvCggngil 15
                                  ++C++Cg++ ++
  gi|15669152|ref|NP_247957.1| 61 RICKKCGTFLLY 72
                                  79999*999987 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0053
                 A2L_zn_ribbon 24 CieCgasf 31
                                  C eCga++
  gi|15669152|ref|NP_247957.1| 92 CLECGAIY 99
                                  ******98 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.046   1.4e+02      28      33 ..      63      68 ..      54      69 .. 0.82
   2 ?   10.2   0.1   0.00019      0.56       3      15 ..      90     102 ..      89     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.046
                 zinc_ribbon_4 28 CskCgh 33
                                  C+kCg+
  gi|15669152|ref|NP_247957.1| 63 CKKCGT 68
                                  888876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00019
                 zinc_ribbon_4   3 itCpsCkakyeid 15 
                                   itC +C+a y+i+
  gi|15669152|ref|NP_247957.1|  90 ITCLECGAIYRIP 102
                                   9***********9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.1e-05      0.15      12      37 ..      60      98 ..      54     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.1e-05
                           DZR 12 arfCseCgtklkavaa..............edrCpsCgek 37
                                   r C++Cgt l  + +               ++C +Cg+ 
  gi|15669152|ref|NP_247957.1| 60 RRICKKCGTFLL-YGRnarvrikskryphvVITCLECGAI 98
                                  689*******85.555689999999************985 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0086        26      21      27 ..      62      68 ..      60      79 .. 0.77
   2 ?    5.5   0.0     0.004        12      20      42 ..      90     112 ..      81     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0086
                                  EESSSSB CS
                  TF_Zn_Ribbon 21 vCtdCGl 27
                                  +C++CG+
  gi|15669152|ref|NP_247957.1| 62 ICKKCGT 68
                                  5777775 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.004
                                   EEESSSSBEEEECCCCCCCHHHH CS
                  TF_Zn_Ribbon  20 lvCtdCGlVlednsidegpewre 42 
                                   ++C +CG++     i e++e+r+
  gi|15669152|ref|NP_247957.1|  90 ITCLECGAIYRIPMIREKKEKRR 112
                                   58999**9999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1440  (0.0803168); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 901.44
//
Query:       gi|15669153|ref|NP_247958.1|  [L=563]
Description: hydantoin utilization protein HyuB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   3.2e-190  632.9   0.0   4.8e-190  632.4   0.0    1.3  2  Hydantoinase_B  Hydantoinase B/oxoprolinase
  ------ inclusion threshold ------
      0.038   14.1   0.1      0.067   13.3   0.1    1.3  1  Spore_III_AB    Stage III sporulation protein AB (spore_III_A


Domain annotation for each model (and alignments):
>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  632.4   0.0  5.3e-194  4.8e-190       1     516 []       2     513 ..       2     513 .. 0.97
   2 ?   -4.1   0.1      0.44   3.9e+03     243     263 ..     538     558 ..     519     559 .. 0.60

  Alignments for each domain:
  == domain 1  score: 632.4 bits;  conditional E-value: 5.3e-194
                Hydantoinase_B   1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfeg...el 78 
                                   D+it+ev++++ + iaeemg  l++ta+Spnik+rlDfsca+++++gel+aqa+hipvhlgsm+  vk++++++++   e+
  gi|15669153|ref|NP_247958.1|   2 DKITVEVIKSSTSYIAEEMGIILRNTAYSPNIKDRLDFSCAILSSNGELIAQAEHIPVHLGSMAIGVKNTVDYLKKesiEI 82 
                                   89*********************************************************************999443578* PP

                Hydantoinase_B  79 kpGDvlltNdPyaggtHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveegelee 159
                                   ++ Dv+++NdPy  gtHl+Dit+++P+f+++e++++va++aHh+D+GG +pGs++++ +e+++EGl+ipp klv +g+l++
  gi|15669153|ref|NP_247958.1|  83 EKDDVIIVNDPYIAGTHLNDITLLKPIFYNDEIIGYVANKAHHVDVGGYAPGSISSNVKELYHEGLIIPPSKLVINGKLNK 163
                                   ********************************************************************************* PP

                Hydantoinase_B 160 dvlelllanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelpdgtyeaedyl.. 238
                                   ++l+l+++nvR+p+ ++gDlkAqia++++g +r+ +lie+yG  +v++a+++ ld++e+ +++ +++++    ea dyl  
  gi|15669153|ref|NP_247958.1| 164 ELLNLITSNVRVPKSTIGDLKAQIASLNIGVERILKLIEKYGDREVTEAWNKSLDYSEEYLKSKIRDINCI-CEAVDYLey 243
                                   ********************************************************************996.899998844 PP

                Hydantoinase_B 239 .ddgipikvtvtidgdeatvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclrpievklpegsllnpsep 318
                                    d+ i+i+++++i++ +++vDftgt++q++ ++Na++ vt + + ++l++++d+d+p+N+G++r +++++pe++++np++p
  gi|15669153|ref|NP_247958.1| 244 kDKLININMKIEIKNGKIKVDFTGTHRQLDAPLNAVYGVTVASTSFALKAVIDPDLPMNHGIFRVLNIIAPEETIVNPKKP 324
                                   34459**************************************************************************** PP

                Hydantoinase_B 319 aavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyetiagGaGArpgkdGasavhvhmt 399
                                   a+v+ gnvetsqr+vdv++kal +  p+rv+Aas+g+mnn+++g      g+ +++yeti+gG G+r+gkdG+++vh++mt
  gi|15669153|ref|NP_247958.1| 325 APVSVGNVETSQRIVDVIFKALYHEFPDRVPAASNGSMNNVIIG------GRGWAFYETIGGGFGGRNGKDGVDGVHANMT 399
                                   ********************************************......6678*************************** PP

                Hydantoinase_B 400 ntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserrvfapwGlaGGepGargrvvlnl 480
                                   nt nt++E++E++yP+++ +++lr+dsgGaGkyrGG+G++r +++l++ + +si+++r +++pwG++ G++Ga+g+   ++
  gi|15669153|ref|NP_247958.1| 400 NTLNTPIEVIENEYPIMILEYSLREDSGGAGKYRGGLGIRRVYKMLSD-CMLSIIADRIKISPWGVNNGYSGACGE---HY 476
                                   ***********************************************7.***************************...77 PP

                Hydantoinase_B 481 lvr.geeenlggkatvelkagdvlvietpGGGGyGdp 516
                                   +++ g+++ l+gk+t+ l+ gd+++i+tpGGGGyG+p
  gi|15669153|ref|NP_247958.1| 477 VIKdGKKIPLSGKDTLYLSCGDIVEINTPGGGGYGSP 513
                                   77779******************************97 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.44
                Hydantoinase_B 243 pikvtvtidgdeatvDftgts 263
                                     kv++  ++d+++vD ++t+
  gi|15669153|ref|NP_247958.1| 538 DYKVKIIKKDDDFVVDMEETK 558
                                   357777446667999999886 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   7.5e-06     0.067      34     122 ..     163     246 ..     160     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.5e-06
                                   HHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHHHHHHHHHHH.STSS-HHHHHHHHHHHHGGGS---HHHHHHHHHHH CS
                  Spore_III_AB  34 kralellegeirygatpLpealeklaeksesplseffeevaerleekegesfeeaweeavekllkklaLkkedkeilkelg 114
                                   k++l+l+++ +r  ++++ ++ +++a +    l+  +e++ + +e+ + ++++eaw+++++ +++ l+ k  d++ ++e  
  gi|15669153|ref|NP_247958.1| 163 KELLNLITSNVRVPKSTIGDLKAQIA-S----LNIGVERILKLIEKYGDREVTEAWNKSLDYSEEYLKSKIRDINCICEAV 238
                                   57899999999999999999999999.3....333355555555556********************************** PP

                                   HHHT--SH CS
                  Spore_III_AB 115 eslgysdr 122
                                   + l y d+
  gi|15669153|ref|NP_247958.1| 239 DYLEYKDK 246
                                   ****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3649.32
//
Query:       gi|15669154|ref|NP_247959.1|  [L=680]
Description: hydantoin utilization protein HyuA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.9e-109  363.8   0.5   6.8e-108  360.3   0.1    2.1  2  Hydantoinase_A  Hydantoinase/oxoprolinase
      6e-55  185.7   0.0      6e-55  185.7   0.0    2.3  3  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
      0.006   16.7   0.1      0.012   15.8   0.1    1.4  1  MGDG_synth      Monogalactosyldiacylglycerol (MGDG) synthase
  ------ inclusion threshold ------
      0.063   12.8   0.0         14    5.1   0.0    2.6  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.033   1.5e+02      82     100 ..       7      25 ..       4      50 .. 0.77
   2 !  360.3   0.1  1.5e-111  6.8e-108       1     290 [.     204     501 ..     204     502 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.033
                Hydantoinase_A  82 ItfDmGGTstDvslikdge 100
                                   +++D+GGT tD+  +++ +
  gi|15669154|ref|NP_247959.1|   7 VGIDIGGTFTDLVYFDEYS 25 
                                   689*********9988433 PP

  == domain 2  score: 360.3 bits;  conditional E-value: 1.5e-111
                Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekkv 81 
                                   rt+t+v+nAyl+p++++yl+++ +sl+++g++ +++vmqs+Gg+ ++++a+++p+ +i+SGPaaG++++a++sk+ +++kv
  gi|15669154|ref|NP_247959.1| 204 RTSTTVINAYLKPLVSNYLKNFIDSLKNKGFNGKFYVMQSSGGISNIKYATERPAAFIESGPAAGAIAVAYFSKILNDNKV 284
                                   89******************************************************************************* PP

                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevsletei............agvkvrlpaldirtvgagGgsilvvdeggklrvgpesagad 150
                                   I+fDmGGT++++s+i+++++ v++e+e+            +g++vr+p++d+++v+agGg+i++vdeg++lrvgp sagad
  gi|15669154|ref|NP_247959.1| 285 IGFDMGGTTAKASTIINNSPLVTNEYEVggevhagrlikgSGYPVRFPFIDLAEVSAGGGTIAWVDEGNALRVGPISAGAD 365
                                   ********************************************************************************* PP

                Hydantoinase_A 151 pgpacyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegilsvavenmanavrk 231
                                   pgp+cy+kG +++t+TDanl+LGrl ++ ++   +g  kl+++la++a+++la++++++vee+A+gi+++a+++ma+a+r 
  gi|15669154|ref|NP_247959.1| 366 PGPVCYGKGNDKPTITDANLILGRLGEK-LS---GGLLKLRKDLAEKAISKLAEKIGESVEEIAYGIIRLANTTMAKALRI 442
                                   ***************************9.99...9********************************************** PP

                Hydantoinase_A 232 lsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvree 290
                                   ++verg+dp++++++vfGGaG++h  +laee++++++++pp++gv+salG++lAd+r +
  gi|15669154|ref|NP_247959.1| 443 VTVERGYDPRDFVMYVFGGAGPLHGVELAEEMEISSILIPPSCGVFSALGLLLADCRVD 501
                                   ********************************************************976 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.7   0.0   1.3e-58     6e-55       1     177 [.       6     183 ..       6     184 .. 0.97
   2 ?   -4.1   0.2       2.5   1.1e+04       2      10 ..     285     293 ..     284     302 .. 0.82
   3 ?   -1.3   0.1      0.34   1.5e+03     128     151 ..     508     531 ..     489     533 .. 0.71

  Alignments for each domain:
  == domain 1  score: 185.7 bits;  conditional E-value: 1.3e-58
                    Hydant_A_N   1 rigIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkg...er 78 
                                   r+gID+GGTfTD+v++de ++e++v+K+++tp+ +  g ++a+e+++ e     +ki+ ++++TT+ tN++l +++   ++
  gi|15669154|ref|NP_247959.1|   6 RVGIDIGGTFTDLVYFDEYSKEFHVVKVPTTPKSPDVGAINAIETAKIE----FDKINILIHATTLGTNMFLGQEHlnpPK 82 
                                   79*******************************************9544....9*************************** PP

                    Hydant_A_N  79 vaLittkgfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavvl 157
                                   +aLittkgf+d++eigrq+rp+l++l ++  kpl+ +++++ev+er++a+g++++pl+eee++++++ +k++++e +++++
  gi|15669154|ref|NP_247959.1|  83 IALITTKGFKDVIEIGRQRRPKLYDLFFEkpKPLIKRRDRYEVEERIDANGNIITPLNEEELQKIAEIIKKKDYEVVVISF 163
                                   *************************88888999************************************************ PP

                    Hydant_A_N 158 lhSylnpehElrvaeiarei 177
                                   lhSy+np hE++++ei++++
  gi|15669154|ref|NP_247959.1| 164 LHSYKNPIHEKKAREIIKNL 183
                                   *****************986 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 2.5
                    Hydant_A_N   2 igIDvGGTf 10 
                                   ig D+GGT 
  gi|15669154|ref|NP_247959.1| 285 IGFDMGGTT 293
                                   788999996 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.34
                    Hydant_A_N 128 evlkpldeeevrealkalkaagve 151
                                   + ++++deee++++  +l ++g +
  gi|15669154|ref|NP_247959.1| 508 KDIDEVDEEEIENIFIELIEEGLK 531
                                   345678899999999999888865 PP

>> MGDG_synth  Monogalactosyldiacylglycerol (MGDG) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   2.6e-06     0.012      63     148 ..     129     214 ..      90     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-06
                                   ---------------HHHHHHHHHHH--SEEEE-STTTTHHHHHHHHTTT-TTTSEE.EEE---SSS--GGG--TT-SEEE CS
                    MGDG_synth  63 kiqkksilaklatflakelaalleeeqPDiiisthplvaelplsvLkskellkrvlv.vtvvtDfellhktWlrkeidryy 142
                                    + + +i+  l++  ++++a++++++  ++++ ++    + p++  k++e +k++ + v v+t +e+ ++ + + e ++  
  gi|15669154|ref|NP_247959.1| 129 IDANGNIITPLNEEELQKIAEIIKKKDYEVVVISFLHSYKNPIHEKKAREIIKNLCSnVDVITSYEI-NPEYKEYERTSTT 208
                                   3448899999***************************9**************99875269*****86.***9998888888 PP

                                   ESSHHH CS
                    MGDG_synth 143 vaskev 148
                                   v + ++
  gi|15669154|ref|NP_247959.1| 209 VINAYL 214
                                   777765 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0031        14       1      19 [.       7      25 ..       7     104 .. 0.90
   2 ?    5.0   0.0    0.0033        15       1      64 [.     285     426 ..     285     481 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0031
                                  EEEEE-SSEEEEEEEETTT CS
                   BcrAD_BadFG  1 vGiDgGsTttkavlmdekg 19
                                  vGiD+G+T t  v +de +
  gi|15669154|ref|NP_247959.1|  7 VGIDIGGTFTDLVYFDEYS 25
                                  8************999854 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0033
                                   EEEEE-SSEEEEEEEETTTEEEEEEEE--.................................................... CS
                   BcrAD_BadFG   1 vGiDgGsTttkavlmdekgevlgrgitns.................................................... 29 
                                   +G D+G+Tt ka  + +++ ++++ + ++                                                    
  gi|15669154|ref|NP_247959.1| 285 IGFDMGGTTAKASTIINNSPLVTNEYEVGgevhagrlikgsgypvrfpfidlaevsagggtiawvdegnalrvgpisagad 365
                                   699*********888866665555555555777777777779999999999999999999999999999999999999999 PP

                                   ..........................TTS-HHH.........HHHHHHHHHHT--GGGECE CS
                   BcrAD_BadFG  30 ..........................anlesvrfeaaekvleealtealerageeeadiee 64 
                                                             ++l++   +   +  e+a++++ e+ ge+ ++i++
  gi|15669154|ref|NP_247959.1| 366 pgpvcygkgndkptitdanlilgrlgEKLSGGLLKLRKDLAEKAISKLAEKIGESVEEIAY 426
                                   9999999999999999999999999944444444444445555555555555555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (680 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 4560.60
//
Query:       gi|15669155|ref|NP_247960.1|  [L=253]
Description: uroporphyrin-III C-methyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-54  183.3   0.2    6.3e-54  183.1   0.2    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.083   12.3   0.0       0.11   11.9   0.0    1.2  1  Adeno_52K     Adenoviral protein L1 52/55-kDa
      0.096   13.1   0.3       0.21   11.9   0.2    1.6  1  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.1   0.2     1e-57   6.3e-54       1     212 [.      15     226 ..      15     227 .. 0.92

  Alignments for each domain:
  == domain 1  score: 183.1 bits;  conditional E-value: 1e-57
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeel.eleapmgkekepleeayeeiaealaealragk 80 
                                   k++lVG+GpGdpel+T+++l+a+k+advv++dd + ++ ll+++++++  ++  ++k    +  ++eei+++l+e++++gk
  gi|15669155|ref|NP_247960.1|  15 KVILVGAGPGDPELITIKGLKAIKEADVVVYDD-LISKELLNYAKKDAeLIYVGKRKG--KHSFKQEEINKILVEKAKEGK 92 
                                   79*******************************.***********9986555555555..67779**************** PP

                  TP_methylase  81 dVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.....lpglakeeerelea 156
                                    Vv+l++GDP+v+g+g+e++ +l++  ++i++eviPG++s+ a++  +gip+t++++++s++     +   +ke++ +l++
  gi|15669155|ref|NP_247960.1|  93 LVVRLKGGDPFVFGRGGEEILELKK--HNIPYEVIPGITSAIAVPEVAGIPVTHRKVATSFTvvtghEAEDKKEKQVDLSK 171
                                   ********************88888..*************************************99955556789999999 PP

                  TP_methylase 157 llangdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                   l a  dt+v+l++  +l++l+++L++   + ++tpva++ +++t+++rv++gtl+++
  gi|15669155|ref|NP_247960.1| 172 LNA--DTIVILMGITNLENLVKELLQNpKRSKETPVAIIMEGTTKNQRVIKGTLGDI 226
                                   877..***********************555677********************986 PP

>> Adeno_52K  Adenoviral protein L1 52/55-kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.9e-05      0.11     120     171 ..     179     230 ..     146     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                     Adeno_52K 120 vllglmyLwdfvqaylehpeskaltvqlllvaqhvedegvlreallsiseke 171
                                   +l+g++ L+++v+ +l++p++++ t+  + +   +++  v++  l +i ek 
  gi|15669155|ref|NP_247960.1| 179 ILMGITNLENLVKELLQNPKRSKETPVAIIMEGTTKNQRVIKGTLGDIVEKA 230
                                   689*****************88888777775555666667788888887765 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   3.5e-05      0.21      22      91 ..      68     164 ..      55     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC..........................CC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........................xx RF
                   Radical_SAM  22 regrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla..........................vp 76 
                                   +++  +s  +eei +++ e  a+ g+ +v l gg+p++  +  e++++l+k                            + 
  gi|15669155|ref|NP_247960.1|  68 KRKGKHSFKQEEINKILVEK-AKEGKLVVRLKGGDPFVFGRGGEEILELKKHNipyevipgitsaiavpevagipvthrKV 147
                                   56777888999****99999.7899**************************998888877777777777777766665555 PP

                                   TEEEEEEECSSCHG..H CS
                                   xxxxxxxxxxxxxx..x RF
                   Radical_SAM  77 giritvetngtlpd..e 91 
                                     ++tv+t +   d  e
  gi|15669155|ref|NP_247960.1| 148 ATSFTVVTGHEAEDkkE 164
                                   55555555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 1943.96
//
Query:       gi|15669156|ref|NP_247961.1|  [L=444]
Description: hypothetical protein MJ_0966 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-18   66.5   0.4    1.1e-17   64.9   0.1    2.0  3  Radical_SAM  Radical SAM superfamily
    6.3e-05   23.0   0.0     0.0037   17.3   0.0    2.9  3  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.89     8e+03     132     153 ..      69      91 ..      55      93 .. 0.63
   2 !   64.9   0.1   1.2e-21   1.1e-17       2     166 ..     173     329 ..     172     330 .. 0.85
   3 ?   -2.4   0.0       0.6   5.4e+03      61      79 ..     353     381 ..     331     393 .. 0.51

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.89
                                   HHHHHHHHTTSET.EEEEEEEBT CS
                                   xxxxxxxxxxxxx.xxxxxxxxx RF
                   Radical_SAM 132 ealeklreagikr.vvdrivglp 153
                                   +a++++++++ ++ + +++ g+p
  gi|15669156|ref|NP_247961.1|  69 NAIKIIKDLRKNNpNAIFVAGGP 91 
                                   45555555544444666666665 PP

  == domain 2  score: 64.9 bits;  conditional E-value: 1.2e-21
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgirit 81 
                                   +++rgC++rC+fC  +     ++++r++ +++++ +++e+  + + v+ v l    + +y+ +   +e +  l  +++ ++
  gi|15669156|ref|NP_247961.1| 173 EIGRGCPRRCRFCLARA---IYYPPRFRKLDDLMYLAEEGV-KVNkVNKVALIAPSVGDYKYI---VELCNFL--DDMGVH 244
                                   689*************8...6*******************6.555499999999877777755...5555555..467888 PP

                                   EEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTTTSHHH CS
                                   xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                   Radical_SAM  82 vetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglpGendee 159
                                   ++ + ++ d   + l r+l+  + ++++  ea++++  ++ +++     ++ +a++++++ g+++   +++vg+p e+de+
  gi|15669156|ref|NP_247961.1| 245 ISPSSLRADtlNDDLMRILK--PKTLTIAPEAGSER-LREFIKKDIRERDIANAIDLAKKFGVEKvKLYFMVGIPTETDED 322
                                   88888887778555555555..49************.******9999*****************9999************* PP

                                   HHHHHHH CS
                                   xxxxxxx RF
                   Radical_SAM 160 leellel 166
                                   +eel++l
  gi|15669156|ref|NP_247961.1| 323 IEELINL 329
                                   ****986 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.6
                                   TTHHHHHHHHHHTC..........CCTEE CS
                                   xxxxxxxxxxxxxx..........xxxxx RF
                   Radical_SAM  61 pdfvellerlakla..........vpgir 79 
                                    df+++ + l+ ++          ++gir
  gi|15669156|ref|NP_247961.1| 353 TDFEVEEFDLSSKKkikyiekalkKEGIR 381
                                   44444444444443333333333334444 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.1e-07    0.0037      29     114 ..      31     113 ..       7     119 .. 0.73
   2 ?    0.9   0.0     0.051   4.5e+02      55      83 ..     313     338 ..     286     340 .. 0.74
   3 ?    0.2   0.0     0.084   7.5e+02      17      37 ..     368     388 ..     366     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.1e-07
                   B12-binding  29 feVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvv 109
                                   +  ++ ++nv +  +++  r  ++d++ +++ +   + ++ ++++ l++++p+++ v+GG+   +++ ++  a + +d+ +
  gi|15669156|ref|NP_247961.1|  31 HLSKYRDLNVGVYFLENYDRIKNFDAIFITLQYENDYFNAIKIIKDLRKNNPNAIFVAGGPC--VMENFFPIA-EFFDVFI 108
                                   44556666666522223333347799999999****************************87..777776655.7778888 PP

                   B12-binding 110 vgege 114
                                   vge e
  gi|15669156|ref|NP_247961.1| 109 VGEIE 113
                                   88876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.051
                   B12-binding  55 vglSalltsqleavkelvellkrirprvk 83 
                                   v    ++t + e+++el++l k+++++++
  gi|15669156|ref|NP_247961.1| 313 V---GIPTETDEDIEELINLTKKVKKEIR 338
                                   3...34999***********888887775 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.084
                   B12-binding  17 lavlaaalrdagfeVqllgan 37 
                                   ++++  al+++g++V++ ++n
  gi|15669156|ref|NP_247961.1| 368 IKYIEKALKKEGIRVEYENFN 388
                                   789************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3032.99
//
Query:       gi|15669157|ref|NP_247962.1|  [L=205]
Description: intracellular protease Pfpi [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-51  174.5   0.3    1.7e-51  174.3   0.3    1.0  1  DJ-1_PfpI    DJ-1/PfpI family
  ------ inclusion threshold ------
      0.028   14.3   0.2      0.099   12.5   0.0    2.0  2  SUB1_ProdP9  SUB1 protease Prodomain ProdP9
       0.18   12.4   0.0       0.18   12.4   0.0    2.7  3  SlpA         Surface later protein A domain


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.3   0.3   2.9e-55   1.7e-51       2     164 ..      33     198 ..      32     199 .. 0.99

  Alignments for each domain:
  == domain 1  score: 174.3 bits;  conditional E-value: 2.9e-55
                                   EEEEEEE.TTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHHHHHTSH CS
                     DJ-1_PfpI   2 kvlvlla.dgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGragperlrene 81 
                                   kvl+++a ++++d El++p++v++++g+kvdvvs++k+e++g+ G k+tv++++ dv++++y a+v++GG  + e+l++n+
  gi|15669157|ref|NP_247962.1|  33 KVLMVIApKDFRDEELFEPMAVFESNGLKVDVVSTTKGECVGMLGNKITVEKTIYDVNPDDYVAIVIVGGIGSKEYLWNNT 113
                                   9*****99************************************************************************* PP

                                   HHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGH..HHHHHTTSEE-SSSEEEETTEEEESSGGGHHHHHH CS
                     DJ-1_PfpI  82 kvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavk..dklekagakyvdkrvvvdgnlvTsrgpgaaiefal 160
                                   k++elvkef++k+k+v aIC +p++La+ag+lkg+++T ypa +  ++l+kaga y+d+ vvvdgn++T+++p+ a  f+l
  gi|15669157|ref|NP_247962.1| 114 KLIELVKEFYNKNKVVSAICLSPVVLARAGILKGKKATVYPAPEaiEELKKAGAIYEDRGVVVDGNVITAKSPDYARLFGL 194
                                   ******************************************99999********************************** PP

                                   HHHH CS
                     DJ-1_PfpI 161 elle 164
                                   e+l+
  gi|15669157|ref|NP_247962.1| 195 EVLK 198
                                   **98 PP

>> SUB1_ProdP9  SUB1 protease Prodomain ProdP9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.7e-05     0.099      26      70 ..      17      61 ..      10      69 .. 0.89
   2 ?   -3.6   0.0       1.7     1e+04      57      69 ..     162     174 ..     158     179 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                   SUB1_ProdP9 26 lsfleskGklanlknlksiiielkedttdeelieyikileekGal 70
                                  +   +s  k  n+kn k +++   +d  deel e + ++e  G  
  gi|15669157|ref|NP_247962.1| 17 MCITNSNEKRENMKNAKVLMVIAPKDFRDEELFEPMAVFESNGLK 61
                                  6677899999*********9999*****************99865 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.7
                   SUB1_ProdP9  57 lieyikileekGa 69 
                                   l +   i e++G 
  gi|15669157|ref|NP_247962.1| 162 LKKAGAIYEDRGV 174
                                   3333344444444 PP

>> SlpA  Surface later protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       2.6   1.6e+04      10      19 ..      21      31 ..      21      35 .. 0.57
   2 ?   12.4   0.0     3e-05      0.18       8      53 ..      54      96 ..      53      98 .. 0.87
   3 ?   -0.5   0.2      0.32   1.9e+03      23      33 ..     145     155 ..     122     184 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.6
                          SlpA 10 dknGkrvk.kt 19
                                  ++n kr + k+
  gi|15669157|ref|NP_247962.1| 21 NSNEKRENmKN 31
                                  56777777433 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3e-05
                          SlpA  8 vYdknGkrvkktkklkkgssvktygkkvtIkNgkkYYkIgknqYik 53
                                  v+ +nG +v       kg+ v ++g+k+t+   k+ Y ++ + Y++
  gi|15669157|ref|NP_247962.1| 54 VFESNGLKVD-VVSTTKGECVGMLGNKITV--EKTIYDVNPDDYVA 96
                                  6778888888.45699**************..5***********97 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.32
                          SlpA  23 kkgssvktygk 33 
                                    kg++ ++y +
  gi|15669157|ref|NP_247962.1| 145 LKGKKATVYPA 155
                                   56666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1362.71
//
Query:       gi|15669158|ref|NP_247963.1|  [L=273]
Description: copper transporting P type ATPase CopA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-20   74.9   0.2    2.9e-20   73.4   0.2    1.7  1  Hydrolase    haloacid dehalogenase-like hydrolase
    3.8e-05   23.5   1.8      0.023   14.4   0.0    2.9  3  Hydrolase_3  haloacid dehalogenase-like hydrolase
     0.0002   21.5   0.3     0.0011   19.1   0.2    2.3  2  HAD_2        Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.011   16.1   0.0       0.05   14.0   0.0    1.9  1  HAD          haloacid dehalogenase-like hydrolase
      0.065   13.3   0.0       0.13   12.3   0.0    1.4  1  Macro        Macro domain


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.2   8.2e-24   2.9e-20       3     209 ..       4     221 ..       3     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 8.2e-24
                                   EEEEESBTTTBCHHHHHHHHHHHH...........CHHHHHHHHHHHHCHHHHHHHHHHHHH.HHHHHHHHHETTTE.... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.... RF
                     Hydrolase   3 tvvfDkdGTLttgepsvedvivsa...........alalaaaletgsehpigkalvaaakar.sgaltgfatfigrg.... 67 
                                   ++vfD  GTL++  ++++d+ +             +++ ++al +  e p+     +  +++ s  l++++     g    
  gi|15669158|ref|NP_247963.1|   4 AIVFDSAGTLVKIMRVIKDLKKNKficnsqtvdivDKKKGRALVIIKEDPLKVVDKENPEKLiSDLLKEVEI----Gisyc 80 
                                   79*********9999999977777777777788778888888888899999999988888886555566665....22244 PP

                                   ..........HHHHTHHHHHHHH....HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTT CS
                                   ..........xxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  68 ..........ayaigkpewltal....dippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaag 134
                                             +    ++  +++l    +i + ++ ++g   +   + +    ++   ++ a    +++e++e++++Lk+ g
  gi|15669158|ref|NP_247963.1|  81 nppinregifK---DRKTKVKELqeplNILKRYEVETGYGSALIIDTYAG--EVEYTIATAGC--LFKEVKETIKQLKDLG 154
                                   45554443442...222222333122355555555555555555555555..66666666666..**************** PP

                                   EEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES...STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 135 ievvlltgdnpetaeraanqlGddyfdaviasdiet...vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                   ++v++++gd + + +r+a+  G           +++    a++++e k+ +ir L+ ++  ++mVGDg+nD++a+ + 
  gi|15669158|ref|NP_247963.1| 155 VKVFIASGDRKGFIKRLAEITG-----------VDEryiMAEAHQELKRDLIRNLKKEGYFTIMVGDGANDVPAMIES 221
                                   **********************...........5555799****************99999*************9765 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.27   9.6e+02     113     151 ..      24      62 ..       5     108 .. 0.60
   2 !   14.4   0.0   6.4e-06     0.023      18      59 ..     141     182 ..     136     186 .. 0.88
   3 !    7.3   0.1     0.001       3.6     195     228 ..     194     227 ..     190     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.27
                                   THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEEEES-H CS
                   Hydrolase_3 113 ksekkkkeeektkkkkeeidseeeledeeiakililkdk 151
                                   k++k + + ++++  ++++     + +e++ k++  +++
  gi|15669158|ref|NP_247963.1|  24 KKNKFICNSQTVDIVDKKKGRALVIIKEDPLKVVDKENP 62 
                                   444444444445555555555555555555555522222 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.4e-06
                                   HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEE CS
                   Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgldlpvi 59 
                                   ++ ke+ik+lk+ g+kv+iA+G    ++++++e  g+d  +i
  gi|15669158|ref|NP_247963.1| 141 KEVKETIKQLKDLGVKVFIASGDRKGFIKRLAEITGVDERYI 182
                                   5789**************************999999885544 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.001
                                   HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEE CS
                   Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAm 228
                                   l+ +l+ +   +i +GDg ND++ +  ++l+v  
  gi|15669158|ref|NP_247963.1| 194 LIRNLKKEGYFTIMVGDGANDVPAMIESDLAVVT 227
                                   566667777779**********999888888753 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   3.1e-07    0.0011      51     174 ..     109     224 ..      79     228 .. 0.76
   2 ?   -1.2   0.0      0.51   1.8e+03      97     120 ..     222     245 ..     220     252 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.1e-07
                         HAD_2  51 klgeseeeee.....kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdviv 126
                                   ++++++   +     +i+++  +++    +   +++++vke++++Lk+ g+k+ i++  ++  +++  e +g+++ +    
  gi|15669158|ref|NP_247963.1| 109 RYEVET---GygsalIIDTYAGEVEYTIAT-AGCLFKEVKETIKQLKDLGVKVFIASGDRKGFIKRLAEITGVDERYIMAE 185
                                   333333...133466888888888888888.99**************************9999999999999877543333 PP

                         HAD_2 127 tsedvekkKPdpeviekaleklklkkeeviyvGDsptDieaakkagik 174
                                     ++         + + ++++lk +   +i+vGD  +D+ a  +  + 
  gi|15669158|ref|NP_247963.1| 186 AHQE---------LKRDLIRNLKKEGYFTIMVGDGANDVPAMIESDLA 224
                                   2222.........33668888888999999999999999887776655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.51
                         HAD_2  97 klgivTsksreaveekleqlgies 120
                                    l++vT ++ ++ ++ le  +i+ 
  gi|15669158|ref|NP_247963.1| 222 DLAVVTLQNGNVSRRALETADIKI 245
                                   599***********9999998875 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.4e-05      0.05      85     187 ..     139     218 ..     116     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                           HAD  85 lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaae 165
                                   l+  +++e +++ ++ G++v + Sg  + ++++l++  g    +++      r+ +         ++e k + +r  l++e
  gi|15669158|ref|NP_247963.1| 139 LF-KEVKETIKQLKDLGVKVFIASGDRKGFIKRLAEITG----VDE------RYIMA------EAHQELKRDLIRN-LKKE 201
                                   55.899******************************999....888......55555......5667667778888.5555 PP

                           HAD 166 gegidleevvayGDspsDlpll 187
                                   g+      ++ +GD+ +D+p++
  gi|15669158|ref|NP_247963.1| 202 GY-----FTIMVGDGANDVPAM 218
                                   53.....489**********97 PP

>> Macro  Macro domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.7e-05      0.13      24      77 ..      98     149 ..      93     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
                                   HHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHH CS
                         Macro  24 kalkeeckelekkqggcllGeavvtpaynlpakyvihtvgplftsskskeeeel 77 
                                   k+l+e  + l++++ +   G a+++++y  +++y i t+g+lf++   ke+ ++
  gi|15669158|ref|NP_247963.1|  98 KELQEPLNILKRYEVETGYGSALIIDTYAGEVEYTIATAGCLFKE--VKETIKQ 149
                                   688888999999999999*************************84..4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1748.81
//
Query:       gi|15669159|ref|NP_247964.1|  [L=270]
Description: hypothetical protein MJ_0969 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-07   30.2   0.3    8.7e-07   29.1   0.1    1.7  2  GHMP_kinases_N  GHMP kinases N terminal domain
    0.00073   19.9   0.3      0.028   14.8   0.0    2.7  3  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.1   9.7e-11   8.7e-07       1      63 [.      75     134 ..      75     137 .. 0.82
   2 ?   -2.8   0.0      0.89   7.9e+03      27      44 ..     191     210 ..     190     219 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 9.7e-11
                                   EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHH CS
                GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasv 63 
                                   di ++s++P+g+GLG S+ +a+ l++ l+++l+l+ + a++a  +e +     ++ gDv a +
  gi|15669159|ref|NP_247964.1|  75 DIIFSSDFPLGSGLGMSGGCALILAKKLNEMLNLNENYAEIAHISEVEC---GTGLGDVIAQY 134
                                   68899***************************75533378888888655...48999999877 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.89
                                   HHHHHTTEH.HHH.HHHHHH CS
                GHMP_kinases_N  27 Allallgls.lee.aklale 44 
                                   +l++ll ++ le+ ++l++e
  gi|15669159|ref|NP_247964.1| 191 CLNELLKNPtLENfVNLSYE 210
                                   78888877766666776655 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.028   2.5e+02      49      71 ..      84     104 ..      78     114 .. 0.82
   2 ?   -2.8   0.2      0.97   8.7e+03      54      63 ..     123     132 ..     123     132 .. 0.86
   3 !   14.8   0.0   3.1e-06     0.028       3      78 ..     194     259 ..     192     264 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.028
                GHMP_kinases_C  49 lgaklsGaGgGptvfalfkdkde 71 
                                   lg++l ++  G++  +l+k+ +e
  gi|15669159|ref|NP_247964.1|  84 LGSGLGMS--GGCALILAKKLNE 104
                                   68899999..******9977665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.97
                GHMP_kinases_C  54 sGaGgGptvf 63 
                                   +G+G+G+ ++
  gi|15669159|ref|NP_247964.1| 123 CGTGLGDVIA 132
                                   69*****985 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 3.1e-06
                GHMP_kinases_C   3 ealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvara 78 
                                   e+l++  le + +l ++++       +g +++ + +++e l     + ++ s++++G t+f++  +k+  e++++ 
  gi|15669159|ref|NP_247964.1| 194 ELLKNPTLENFVNLSYEFAV-----NTGLINEKILSICEDL----KFTVGASQSMLGNTLFCIS-KKETLEDALSI 259
                                   66777666666667777777.....6888888888888888....47799*************9.88887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1557.62
//
Query:       gi|15669160|ref|NP_247965.1|  [L=143]
Description: sirohydrochlorin cobaltochelatase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-37  125.9   2.7    1.2e-36  125.3   2.7    1.2  1  CbiX            CbiX
    4.5e-06   26.2   0.1    5.9e-06   25.8   0.1    1.2  1  CbiK            Cobalt chelatase (CbiK)
    0.00031   20.7   0.0     0.0004   20.3   0.0    1.2  1  NTPase_1        NTPase
    0.00049   19.3   0.0    0.00058   19.0   0.0    1.1  1  Ferrochelatase  Ferrochelatase
  ------ inclusion threshold ------
      0.076   13.8   3.6       0.16   12.7   3.6    1.5  1  PDGF_N          Platelet-derived growth factor, N terminal re
        2.9    7.2  18.8        4.1    6.7  18.8    1.2  1  SelP_N          Selenoprotein P, N terminal region


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.3   2.7   3.9e-40   1.2e-36       1     106 [.       9     137 ..       9     138 .. 0.99

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 3.9e-40
                                   -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--SS CS
                          CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeaee 81 
                                   HGSr+p+s+e + klae+++e++ f++ve+g +e++ep++++a+++++eqg+kri+vvP+fl++G+h+++DIp++l+++e+
  gi|15669160|ref|NP_247965.1|   9 HGSRLPYSKELLVKLAEKVKERNLFPIVEIGLMEFSEPTIPQAVKKAIEQGAKRIIVVPVFLAHGIHTTRDIPRLLGLIED 89 
                                   ********************************************************************************* PP

                                   SS-.......................TTEEEEE---CCCSCCHHHHHH CS
                          CbiX  82 ahp.......................kdveieytepLGthplvaevlk 106
                                   +h+                       +dvei+y+ep+G++++++++++
  gi|15669160|ref|NP_247965.1|  90 NHEhhhehshhhhhhhhhehekleipEDVEIIYREPIGADDRIVDIII 137
                                   **********************************************97 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1     2e-09   5.9e-06     142     217 ..       2      80 ..       1      98 [. 0.89

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2e-09
                                   EEEEEEE---SCH.HHHHHHHHHHHHHH.CT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHCCC CS
                          CbiK 142 ealvfvgHGtehe.snavyaeldkvlke.kdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlvAGdHaknDm 217
                                   ealv+vgHG++ + s++   +l + +ke + f  v +g +e + P++ + +++  ++g+k++ ++P++l  G H ++D+
  gi|15669160|ref|NP_247965.1|   2 EALVLVGHGSRLPySKELLVKLAEKVKErNLFPIVEIGLMEfSEPTIPQAVKKAIEQGAKRIIVVPVFLAHGIHTTRDI 80 
                                   79********987356677788766666488999******9899**********************************8 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.3e-07    0.0004      86     145 ..      21      75 ..      10      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                                   HHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHH CS
                      NTPase_1  86 lealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeir 145
                                   + +l ++++e +++ i EiG mE++ +++ +av+++++++   ++v+++       + i+
  gi|15669160|ref|NP_247965.1|  21 V-KLAEKVKERNLFPIVEIGLMEFSEPTIPQAVKKAIEQGAKRIIVVPVFL----AHGIH 75 
                                   3.455668999***************************9999999999984....44444 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.9e-07   0.00058      69     144 ..      14      90 ..       3     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.9e-07
                                   HHHHHHHHHHHHHHHHH---EEEEEE.ESSSSSBHHHHHHHHHCTT-SEEEEEES-SS--TTTHHHHHHHHHHHHHH CS
                Ferrochelatase  69 eitrkqaealekelaergidvkvyla.mrywePsiedaleelkadgvervvvlplyPqysasttgssleeleralkk 144
                                    +++++  +l+++++er+    v+++ m+++eP i +a+++  ++g +r++v+p +  ++  tt+ + + l    ++
  gi|15669160|ref|NP_247965.1|  14 PYSKELLVKLAEKVKERNLFPIVEIGlMEFSEPTIPQAVKKAIEQGAKRIIVVPVFLAHGIHTTRDIPRLLGLIEDN 90 
                                   57888999999999999966667777699**********************************99876655444433 PP

>> PDGF_N  Platelet-derived growth factor, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.6   5.4e-05      0.16      17      58 ..      73     112 ..      70     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-05
                        PDGF_N  17 eIrSisDLqRLLeidsvgeedeeseeskhrakkkhsaeslel 58 
                                    I+  +D+ RLL +  +++++e+++e++h+++++h++e+ +l
  gi|15669160|ref|NP_247965.1|  73 GIHTTRDIPRLLGL--IEDNHEHHHEHSHHHHHHHHHEHEKL 112
                                   699999*****987..55666666777777777777766444 PP

>> SelP_N  Selenoprotein P, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  18.8    0.0014       4.1     184     206 ..      89     111 ..      75     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0014
                        SelP_N 184 hehahshkqghkhhekhghhHke 206
                                   ++h+h+h+++h+hh++h+h+H++
  gi|15669160|ref|NP_247965.1|  89 DNHEHHHEHSHHHHHHHHHEHEK 111
                                   45556666677777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 923.50
//
Query:       gi|15669161|ref|NP_247966.1|  [L=365]
Description: hypothetical protein MJ_0971 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-24   84.8   0.3    5.5e-24   84.8   0.3    2.1  2  Peptidase_M50  Peptidase family M50
    2.8e-08   34.0   0.0    6.7e-08   32.7   0.0    1.6  2  PDZ_2          PDZ domain
    0.00027   20.7   0.0    0.00048   19.9   0.0    1.4  1  PDZ_6          PDZ domain
     0.0019   18.5   0.2     0.0064   16.8   0.0    1.9  3  PDZ            PDZ domain
      0.003   17.5   0.0     0.0077   16.2   0.0    1.7  1  PDZ_1          PDZ-like domain
  ------ inclusion threshold ------
       0.11   12.7   0.1       0.11   12.7   0.1    3.5  4  DUF3267        Putative zincin peptidase


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.5      0.32   9.6e+02     149     203 ..      11      68 ..       2      80 .. 0.69
   2 !   84.8   0.3   1.8e-27   5.5e-24       2     246 ..     112     336 ..     111     340 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.32
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 149 vvvltvkalgklitgklslktlggpisiaqla...seaaeaglssflqllalisvnLg 203
                                   +v +++  +   i  +++lkt gg  +i ++    +   + g  +++q + +is+ + 
  gi|15669161|ref|NP_247966.1|  11 IVAIIIWIILYSIRDSINLKTYGGIFGILRTKlglKTIEKLGKYKIWQKIGIISIPIC 68 
                                   4444555555556668888999999888877655555556677788888888888654 PP

  == domain 2  score: 84.8 bits;  conditional E-value: 1.8e-27
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkk 82 
                                    i++l+i + vHEl+H+++Ak +g+kv++ +i++               +  lpLG++V++ + e            f+ +
  gi|15669161|ref|NP_247966.1| 112 GIIALLIAISVHELAHGIFAKSFGIKVKSSGILL---------------LLGLPLGAFVELGD-E------------FKTA 164
                                   599*******************************...............999********976.4............6778 PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXX.......-EEECECTTTSCEE-SEEEC-.................XXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxx RF
                 Peptidase_M50  83 spwqrllivlAGplanfilailvfvv.......pkkskeseeekrgviGvspkp.................vkkeglleal 139
                                   +   r +i+ AGplan+i+ +  + +       p        ++ ++i v+ +                  +++ + ++ +
  gi|15669161|ref|NP_247966.1| 165 DKKIRGAIASAGPLANLIIFLTSIPLlsfsytlP--------TELKIIDVKEPAseflqkgdiiyeingkkINSLEDFKEF 237
                                   8899**************9999998855555551........555555555555555555555555553335566666666 PP

                                   XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 140 kegvektlkvvvltvkalgklitg.klslktlggpisiaqlaseaaeaglssflqllalisvnLgilNLlPipvLDGghll 219
                                   ++ +e   ++ + +++   k++t   +s ++ +  i++ + +++  +a ++++++++++ ++ L+++NLlP ++LDG+h++
  gi|15669161|ref|NP_247966.1| 238 AKTIEPKKEYEIKILRDN-KILTYkIVSSNEGKLGIMV-SPTKN--TALFINTIYWTYWFNFLLALFNLLPAMPLDGFHVW 314
                                   666666666666666654.5555514444433333333.33332..34788****************************** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 220 falleairrkplserkeevanlvglal 246
                                   +a+ e ++     erk++++++vg +l
  gi|15669161|ref|NP_247966.1| 315 NAFPELLK-----ERKNRFISKVGQIL 336
                                   ***99777.....77777777777665 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   2.3e-11   6.7e-08      19      80 ..     204     262 ..     191     263 .. 0.89
   2 ?   -3.1   0.0       3.5   1.1e+04       1      12 [.     268     279 ..     268     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.3e-11
                                   EEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEEEE CS
                         PDZ_2  19 vsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkktvev 80 
                                   ++   + Pa++  l++gD+i++++gkk++sled+++   + +p ++ ++++lRd+k +t+++
  gi|15669161|ref|NP_247966.1| 204 ID--VKEPASEF-LQKGDIIYEINGKKINSLEDFKEFAKTIEPKKEYEIKILRDNKILTYKI 262
                                   44..45688888.*******************************************999886 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.5
                                   ....XX------ CS
                         PDZ_2   1 pylGvsvsdeed 12 
                                   ++lG++vs+ ++
  gi|15669161|ref|NP_247966.1| 268 GKLGIMVSPTKN 279
                                   579***999987 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.6e-07   0.00048       9      43 ..     208     239 ..     202     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.6e-07
                         PDZ_6   9 sPAdrAGlrvGDiilsvNGqpveglsladvaallr 43 
                                    PA +  l+ GDii ++NG+ +   sl+d+++  +
  gi|15669161|ref|NP_247966.1| 208 EPASEF-LQKGDIIYEINGKKI--NSLEDFKEFAK 239
                                   588877.***************..*****998766 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         6   1.8e+04      29      46 ..     121     138 ..     120     139 .. 0.72
   2 !   16.8   0.0   2.1e-06    0.0064      42      75 ..     211     245 ..     204     252 .. 0.73
   3 ?   -3.5   0.0       4.6   1.4e+04       8      19 ..     266     277 ..     262     286 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 6
                                   EEEEECTTSHHHHHTSST CS
                           PDZ  29 fvsevlpggaaeadglkv 46 
                                    v e+ +g  a+  g+kv
  gi|15669161|ref|NP_247966.1| 121 SVHELAHGIFAKSFGIKV 138
                                   678888888888777765 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.1e-06
                                   HT.SSTTEEEEEETTEETTTSHHHHHHHHHHTTTS CS
                           PDZ  42 dg.lkvGDkIlsvNgvdvenvsheeavqaikgskg 75 
                                   +  l++GD+I ++Ng++++++++ +  +++ ++k+
  gi|15669161|ref|NP_247966.1| 211 SEfLQKGDIIYEINGKKINSLEDFKEFAKTIEPKK 245
                                   4449****************987665555554444 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.6
                                   TTSESSEEEEEE CS
                           PDZ   8 grgglGfslkgg 19 
                                   ++g+lG+ ++  
  gi|15669161|ref|NP_247966.1| 266 NEGKLGIMVSPT 277
                                   678889888764 PP

>> PDZ_1  PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.6e-06    0.0077      48      75 ..     214     241 ..     193     244 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.6e-06
                         PDZ_1  48 ekkgviitsinnqptpnLdefievvkki 75 
                                    +kg ii++in++++ +L++f+e++k+i
  gi|15669161|ref|NP_247966.1| 214 LQKGDIIYEINGKKINSLEDFKEFAKTI 241
                                   68999*********************99 PP

>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1         2   5.9e+03      63      73 ..      11      21 ..       7      41 .. 0.59
   2 ?   -2.0   2.1       1.4   4.2e+03      44      69 ..      54      78 ..      16      91 .. 0.73
   3 ?   12.7   0.1   3.8e-05      0.11       2      26 ..     117     141 ..     116     197 .. 0.81
   4 ?   -0.5   0.5      0.49   1.5e+03      78      93 ..     286     301 ..     270     309 .. 0.51

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2
                       DUF3267 63 illlllalllp 73
                                  i+ ++++++l 
  gi|15669161|ref|NP_247966.1| 11 IVAIIIWIILY 21
                                  44444444433 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                       DUF3267 44 llskkqfiiillaPfvllgillllla 69
                                  + + +q i i   P+ ++   ++ll 
  gi|15669161|ref|NP_247966.1| 54 Y-KIWQKIGIISIPICVILGFFMLLN 78
                                  4.788999999999888644444333 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 3.8e-05
                       DUF3267   2 lvlvilHEllHglffklfgkkpkkk 26 
                                   l+ + +HEl+Hg+f k fg k+k++
  gi|15669161|ref|NP_247966.1| 117 LIAISVHELAHGIFAKSFGIKVKSS 141
                                   67889*************8876654 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.49
                       DUF3267  78 llllllalnaagsagD 93 
                                   ++++  ++n++++   
  gi|15669161|ref|NP_247966.1| 286 TIYWTYWFNFLLALFN 301
                                   4444444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2186.68
//
Query:       gi|15669162|ref|NP_247967.1|  [L=228]
Description: hypothetical protein MJ_0972 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-76  253.7  12.4    1.1e-75  253.5  12.4    1.0  1  MarC      MarC family integral membrane protein
  ------ inclusion threshold ------
        1.8    8.4   9.2          3    7.7   0.0    2.4  2  DUF2721   Protein of unknown function (DUF2721)


Domain annotation for each model (and alignments):
>> MarC  MarC family integral membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.5  12.4   1.2e-79   1.1e-75       1     202 [.      20     221 ..      20     222 .. 0.99

  Alignments for each domain:
  == domain 1  score: 253.5 bits;  conditional E-value: 1.2e-79
                          MarC   1 lkaiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgillf 81 
                                   l+++i++fvsL+++i+p+g +p+++sl++ ++ke+r ri++ka+i+++++ll+f+lfG++i+ +fgi+ida+++aGgillf
  gi|15669162|ref|NP_247967.1|  20 LNFYIYGFVSLFITIDPIGLIPIVHSLTYPYPKEQRIRIIKKAIISSTVVLLLFALFGNYIFGYFGITIDAFRVAGGILLF 100
                                   589****************************************************************************** PP

                          MarC  82 liaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalitllill 162
                                   +ia+dml+a+ +k+k+k++e+ + e++d+i++vPLA+Pli+GPgaitt+++l+s+++si ek +vvl+il+a+l++ +il+
  gi|15669162|ref|NP_247967.1| 101 KIAWDMLHAEIPKTKHKPDERLDLEDIDSIVYVPLAIPLISGPGAITTTMILISKTQSILEKGVVVLSILSAMLVSGIILS 181
                                   ********************************************************************************* PP

                          MarC 163 lsslilrllgktginaleRlmGllLvalavqlivdGikei 202
                                   l+++i+r+++ +gina+ R+mGllLva++vq+i++Gi ++
  gi|15669162|ref|NP_247967.1| 182 LTDFIIRRVNIYGINAFVRIMGLLLVAISVQIIFTGIVGL 221
                                   *************************************986 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00034         3      58      86 ..      54      82 ..      52     117 .. 0.79
   2 ?    1.3   6.3     0.032   2.8e+02      66     116 ..     164     214 ..     145     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00034
                       DUF2721 58 rRarlirrailllvlsallvvlvvlllfl 86
                                  +R+r+i++ai++ ++ +ll++l    +f 
  gi|15669162|ref|NP_247967.1| 54 QRIRIIKKAIISSTVVLLLFALFGNYIFG 82
                                  7******************9998777766 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.032
                       DUF2721  66 ailllvlsallvvlvvlllflsallsldlsllaailfvlalllllvslllf 116
                                    ++l +lsa+lv+ ++l l    + ++++  + a++ +++lll+++s+ + 
  gi|15669162|ref|NP_247967.1| 164 VVVLSILSAMLVSGIILSLTDFIIRRVNIYGINAFVRIMGLLLVAISVQII 214
                                   578899999999999998877668899999999999999999999998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 1879.15
//
Query:       gi|15669163|ref|NP_247968.1|  [L=411]
Description: hypothetical protein MJ_0973 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-54  184.3   0.0    3.9e-54  183.3   0.0    1.5  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
      0.007   15.9   0.0      0.015   14.8   0.0    1.5  1  QueC         Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
       0.13   12.0   0.0        2.1    8.0   0.0    2.2  2  ATP_bind_3   PP-loop family


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.3   0.0   6.5e-58   3.9e-54       2     173 ..     181     350 ..     180     351 .. 0.97

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 6.5e-58
                                   EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHCHH CS
                   PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyeeaa 82 
                                   + +s+sgGkds+V   La k+ ++ +v+f+dtg ef++ti+fv++++++y+l+  v+ + ++++e +++e++++++y++ +
  gi|15669163|ref|NP_247968.1| 181 INTSFSGGKDSSVSTLLANKVIDDLEVIFIDTGLEFKDTIDFVKKFAKKYDLN-LVVLKGKNFWEYLEKEGIPTKDYRW-C 259
                                   5689*************************************************.566788999****************.* PP

                                   HHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT--B-CCCCTT- CS
                   PAPS_reduct  83 eriaKveplkkaLekldedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilrenipynpLydqgf 163
                                   ++++K+eplk+ L+k+++++++ G+Rr+es++r+kl + ++   +e+++++fP+l+W  +dvw++i+ +++ yn+Lyd+gf
  gi|15669163|ref|NP_247968.1| 260 NSVCKLEPLKEYLKKYKRVYTIDGSRRYESFTREKLTYERKSGFIENQINIFPILDWRGTDVWSWIYLNDVIYNELYDKGF 340
                                   ********************************************************************************* PP

                                   SS--BCTTB- CS
                   PAPS_reduct 164 rsiGcvpctg 173
                                   ++iGc++c++
  gi|15669163|ref|NP_247968.1| 341 ERIGCYMCPA 350
                                   ********97 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.5e-06     0.015       5      58 ..     184     236 ..     180     251 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-06
                                   E--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEE CS
                          QueC   5 llSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehki 58 
                                    +SGG DS++ ++la+k ++ +e++ +d g   k +++ +kk+ak++++ +  +
  gi|15669163|ref|NP_247968.1| 184 SFSGGKDSSVSTLLANKVIDDLEVIFIDTGLEFKDTIDFVKKFAKKYDL-NLVV 236
                                   59********************************************998.5544 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00036       2.1       5      66 ..     184     239 ..     180     257 .. 0.85
   2 ?    1.5   0.0     0.038   2.2e+02     151     178 ..     267     294 ..     261     297 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00036
                                   E--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE- CS
                    ATP_bind_3   5 AvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekv 66 
                                    +SgG DS + +ll++k  +    +l +i +d gl  e k+  ++vk+++kk++++l++ k 
  gi|15669163|ref|NP_247968.1| 184 SFSGGKDSSVSTLLANKVID----DLEVIFIDTGL--EFKDTIDFVKKFAKKYDLNLVVLKG 239
                                   69*******99999988866....899*****999..5678999*********999998775 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.038
                                   HHHHHHHHTT---B--CGGGCTTSHHHH CS
                    ATP_bind_3 151 eleeylkekkikwveDesNadekyeRnr 178
                                    l+eylk+ k  +  D s + e+++R +
  gi|15669163|ref|NP_247968.1| 267 PLKEYLKKYKRVYTIDGSRRYESFTREK 294
                                   589***********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1324  (0.0738468); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2725.29
//
Query:       gi|15669164|ref|NP_247969.1|  [L=149]
Description: hypothetical protein MJ_0974 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-28   97.7   0.6    7.4e-28   97.5   0.6    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   0.6   4.1e-32   7.4e-28       1     122 []      11     144 ..      11     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 4.1e-32
                                   EEE-HHHHHHHHTTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHS...........SCHCHHHHHHHHHHHHHHHTSE CS
                           PIN   1 ivlDTsvliallrgeekaeaarklleel.eelvtsalvlaEllyvlar...........rkskrekaaelvelllllsalk 69 
                                   i++D+++li++l g+++a+++ + +e+     +++++v++E+l+++ r           ++++++k+ +l  +++l s ++
  gi|15669164|ref|NP_247969.1|  11 IFFDSNILIYHLCGKVEAKKLIEKVENKeICGFINPIVISEVLFFYIRattnkrhydikKHPEILKSLDLDIVFELFSIFQ 91 
                                   79**************9955555555559999************************************************* PP

                                   EEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHHC CS
                           PIN  70 ilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvakl 122
                                   il++++ei+++ +ei++ky+llpnDali +t+k ++i++i++fD+df+rv++l
  gi|15669164|ref|NP_247969.1|  92 ILDLNSEIVKISREIIKKYCLLPNDALICSTCKFYKINKICSFDDDFKRVDFL 144
                                   **************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 988.54
//
Query:       gi|15669165|ref|NP_247970.1|  [L=68]
Description: hypothetical protein MJ_0975 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-17   62.7   7.8    3.9e-17   62.4   7.8    1.1  1  DUF104    Protein of unknown function DUF104
  ------ inclusion threshold ------
      0.053   13.8   0.1      0.075   13.3   0.1    1.2  1  DUF2757   Protein of unknown function (DUF2757)


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   7.8   4.4e-21   3.9e-17       1      59 []       5      61 ..       5      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 4.4e-21
                        DUF104  1 MskvIeavYEnGvLKPLekvdLkEGeevkikIeeakeilkklkgilkeadeeeleelle 59
                                  M+ v++a+YE+GvLK  + ++L+EG ev+ikI   k+i++k++gilk ++++e++e+le
  gi|15669165|ref|NP_247970.1|  5 MEIVVDAIYEKGVLKLKKSINLPEGCEVEIKIIP-KKISEKTFGILK-LSDKEIKEILE 61
                                  999*******************************.***********9.99******987 PP

>> DUF2757  Protein of unknown function (DUF2757)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   8.4e-06     0.075      10      47 ..      30      66 ..      27      68 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.4e-06
                                  T--BTT-SSTTT---SS---SSSSHHHHHHTSSS-TT- CS
                       DUF2757 10 CgkkigtlekkeieeealgfnkLteeerqdmieyeeng 47
                                  C+++i  + k +i+e++ g+ kL+++e ++++e  eng
  gi|15669165|ref|NP_247970.1| 30 CEVEIKIIPK-KISEKTFGILKLSDKEIKEILEEIENG 66
                                  99***99996.99*******************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 455.74
//
Query:       gi|15669166|ref|NP_247971.1|  [L=366]
Description: hypothetical protein MJ_0976 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.015   15.4   3.0      0.024   14.7   3.0    1.3  1  Duffy_binding  Duffy binding domain
      0.039   14.6   0.4      0.079   13.6   0.4    1.5  1  DUF573         Protein of unknown function, DUF573
      0.073   13.1   1.7       0.24   11.4   1.7    1.9  1  Cpta_toxin     Membrane-bound toxin component of toxin-antito
       0.14   12.6   0.2       0.33   11.4   0.2    1.7  1  L31            Mitochondrial ribosomal protein L31
       0.46   10.2   7.0       0.29   10.8   3.9    2.0  2  RPW8           Arabidopsis broad-spectrum mildew resistance p
       0.73   10.3   0.1       0.73   10.3   0.1    2.4  3  PhoR           Phosphate regulon sensor protein PhoR


Domain annotation for each model (and alignments):
>> Duffy_binding  Duffy binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   3.0   8.2e-06     0.024      69     132 ..     253     322 ..     240     364 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.2e-06
                 Duffy_binding  69 kipseflrqlaytfaDyrDilrg.kdllkgnkkkkeekkkeekleenlkkifkkieeklkk.....nsek 132
                                     ++ ++ +l +t  D+ Di++  k++  +++kk+e kkk +k+++ +++++k  + ++++     n e+
  gi|15669166|ref|NP_247971.1| 253 IENTIIMLSLERTVNDIDDIIKIlKNIRLDDTKKEELKKKLRKIKKLIENVIKLLGGTSENgtqnnNLEE 322
                                   344567789************8626888888888899999999999999999988888877765553333 PP

>> DUF573  Protein of unknown function, DUF573
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   2.6e-05     0.079      29      93 ..     266     334 ..     254     336 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                        DUF573  29 ksdldafyeavksslssdvsksqlseKlrrLkkkyrnavskik....kgkdpsfkkphdrklfelskki 93 
                                    +d+d++++ +k+   +d +k++l++Klr++kk  +n+ +       +g++++  ++  +k+ e ++ki
  gi|15669166|ref|NP_247971.1| 266 VNDIDDIIKILKNIRLDDTKKEELKKKLRKIKKLIENVIKLLGgtseNGTQNNNLEEAKSKITEACRKI 334
                                   379999999999999999999***************999876666667777777777778887777777 PP

>> Cpta_toxin  Membrane-bound toxin component of toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.7   8.1e-05      0.24      19      61 ..     210     254 ..     197     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.1e-05
                    Cpta_toxin  19 llvygllalliLlapw.Pedyallwllllllvvfecvrsqrk.ik 61 
                                   l+ y ++ ++ L++ + Pe++++  +++l++v+++++ +++k i+
  gi|15669166|ref|NP_247971.1| 210 LMNYFIYDIINLICSYiPESFIVAMIVILIFVIIDVYYNAKKhIE 254
                                   44566667777777777******************9988765154 PP

>> L31  Mitochondrial ribosomal protein L31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00011      0.33      12      60 ..     278     329 ..     271     359 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                           L31  12 pwrlsktqkarqrkRlkavDevieavkeslkkk...gvslkalekakaelpk 60 
                                   + rl  t+k +++k+l+++ + ie+v + l  +   g++ ++le+ak+++ +
  gi|15669166|ref|NP_247971.1| 278 NIRLDDTKKEELKKKLRKIKKLIENVIKLLGGTsenGTQNNNLEEAKSKITE 329
                                   579*********************9998775444448999999998887655 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.9   9.6e-05      0.29      15      85 ..     241     306 ..     232     308 .. 0.78
   2 ?   -0.7   0.1      0.36   1.1e+03      78      91 ..     327     340 ..     310     363 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.6e-05
                          RPW8  15 ellkaileakkksldfksilkrLestleritPvvkeieklnkeldrpreeieeLkklLekaekLVekcskl 85 
                                   +++++ ++akk   ++  i+ +Le+t+++i  ++k +++++  ld  +   eeLkk+L+k +kL+e   kl
  gi|15669166|ref|NP_247971.1| 241 VIIDVYYNAKKHIENT-IIMLSLERTVNDIDDIIKILKNIR--LDDTK--KEELKKKLRKIKKLIENVIKL 306
                                   4555555566655555.999**************9999998..75555..489*************99886 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.36
                          RPW8  78 LVekcsklkrynvl 91 
                                   + e+c k++  n++
  gi|15669166|ref|NP_247971.1| 327 ITEACRKISGNNIF 340
                                   44555555544443 PP

>> PhoR  Phosphate regulon sensor protein PhoR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3       2.6   7.7e+03      11      21 ..      75      85 ..      66     109 .. 0.55
   2 ?   10.3   0.1   0.00025      0.73      11      61 ..     144     195 ..     137     201 .. 0.84
   3 ?   -2.4   0.1       2.2   6.7e+03      27      40 ..     227     240 ..     214     249 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.6
                          PhoR 11 llllaallvgl 21
                                   +ll+++ + +
  gi|15669166|ref|NP_247971.1| 75 NILLSLIGIIV 85
                                  22233333333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00025
                          PhoR  11 llllaallvgllvgalaallllalllllawhlyqllrLsrWL.rkpkklepP 61 
                                   +++++++++g+l++  +  +l+++ ++++  + + l L +W+ r+ +++e+ 
  gi|15669166|ref|NP_247971.1| 144 IYMISVIALGYLANSCKTIILFGTGFFIIVVIIYFLDLLDWIyRRIDSNEYR 195
                                   67788889*********************************96666666655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.2
                          PhoR  27 aallllalllllaw 40 
                                   +   ++a++++l++
  gi|15669166|ref|NP_247971.1| 227 PESFIVAMIVILIF 240
                                   44444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2166  (0.12081); expected 358.6 (0.02)
Passed bias filter:                      718  (0.0400469); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.33s 00:00:01.07 Elapsed: 00:00:00.50
# Mc/sec: 2183.92
//
Query:       gi|15669167|ref|NP_247972.1|  [L=469]
Description: hypothetical protein MJ_0977 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-16   61.6   0.3    9.9e-16   58.4   0.0    2.3  2  DHHA1           DHHA1 domain
    1.9e-05   24.8   0.2    4.4e-05   23.7   0.1    1.6  2  DHH             DHH family
  ------ inclusion threshold ------
      0.035   14.0   0.1      0.083   12.8   0.1    1.6  1  Glyco_hydro_45  Glycosyl hydrolase family 45
      0.081   13.3   0.0       0.19   12.2   0.0    1.6  1  Rubrerythrin    Rubrerythrin


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.13     6e+02      23      74 ..       6      54 ..       1      60 [. 0.68
   2 !   58.4   0.0   2.2e-19   9.9e-16       6     135 ..     336     465 ..     332     468 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
                                  HHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEE CS
                         DHHA1 23 aklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkk.pvivf 74
                                  + +k +++l++++   + k+l++    ++d  + + +  kl ++l+  +  +f
  gi|15669167|ref|NP_247972.1|  6 ELKKGAKVLQNNK---NNKILIVTH-IDTDGLTSRAILQKLAERLNLdADFMF 54
                                  4556666666654...777777777.788888888888888888744366666 PP

  == domain 2  score: 58.4 bits;  conditional E-value: 2.2e-19
                                   HHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHG.BT.TCEEEEEEEECTEEE CS
                         DHHA1   6 eerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklkskl.kk.pvivfvakeegdkvk 84 
                                   + +++l+k+ ++l+eal+++k++  + +     ++ + + e  +++  +++gi+a++  s    + +  +f+++e+++ +k
  gi|15669167|ref|NP_247972.1| 336 KMLSNLRKHRNNLREALEHVKNDVEIIQ-----KDRFQYFET-DKIMSNIVGIVAGMSYSIEeVDwMKPIFAITEDENGYK 410
                                   5577888888889999999888777665.....666666666.667777888887777773358889999******99*** PP

                                   EEEEESSH.....SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHH CS
                         DHHA1  85 vsarskkd.....gvdagelakeaaaklgggGGGHdlAaGagipaekleealeale 135
                                   vsar+ k      +v++++++k a++k++g+GGGH++A+Ga ip +k  e+++ le
  gi|15669167|ref|NP_247972.1| 411 VSARCPKLlcfaeDVNLAKAIKYASEKVNGSGGGHKFACGAYIPDNK-REFIKYLE 465
                                   ******88***********************************8555.99999876 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   9.8e-09   4.4e-05       1      84 [.      21     147 ..      21     164 .. 0.72
   2 ?   -3.3   0.0       2.4   1.1e+04      48      61 ..     361     373 ..     337     401 .. 0.59

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 9.8e-09
                                   EEEEE-ECSSSHHHHHH.HHHHHH................................CECS--TCGGCGCCH......HCCC CS
                                   xxxxxxxxxxxxxxxxx.xxxxxx................................xxxxxxxxxxxxxxx......xxxx RF
                           DHH   1 kilivghknpDtDsigS.aialan................................llvDhneksqavege......akee 42 
                                   kili  + + DtD+++S ai+ +                                 +  D ++ + + ++e      + ++
  gi|15669167|ref|NP_247972.1|  21 KILI--VTHIDTDGLTSrAILQKLaerlnldadfmflkqitietindipfkdydliIFADLGSGQLKMIKEkldelnLSDK 99 
                                   6888..999********5555554777777777777777777777777777777766778887777777777788889*** PP

                                   SEEEEEEE-S---S.....S---SS--EEEE-SSS.-HHHHHHHHHHH CS
                                   xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                           DHH  43 aedviiiDHHrlge.....efetlapilflnepvg.staeivaellee 84 
                                    +++ii+DHH+++e     ++ +++p+++ ++ +  ++a++ + ++++
  gi|15669167|ref|NP_247972.1| 100 RDKIIILDHHQPEEikipkTIIHINPLTIAKSGAEiCGAGVSYLFAKA 147
                                   ************988888777777777766554432666666666554 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.4
                                   EEE-S---SS---S CS
                                   xxxxxxxxxxxxxx RF
                           DHH  48 iiDHHrlgeefetl 61 
                                   ii   r +  fet 
  gi|15669167|ref|NP_247972.1| 361 IIQKDRFQ-YFETD 373
                                   44444443.33333 PP

>> Glyco_hydro_45  Glycosyl hydrolase family 45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.9e-05     0.083      20      63 ..     410     454 ..     404     462 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                Glyco_hydro_45  20 kaavyapvdacdkddvtlidskkd.tsavsgceggskyacsnlsp 63 
                                   k +   p + c ++dv+l+++ k  ++ v+g  gg k+ac ++ p
  gi|15669167|ref|NP_247972.1| 410 KVSARCPKLLCFAEDVNLAKAIKYaSEKVNGSGGGHKFACGAYIP 454
                                   56677899**********998776156799************998 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.1e-05      0.19      12     114 ..     311     411 ..     306     425 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.1e-05
                                   HHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHHHHHHHH CS
                  Rubrerythrin  12 sarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLeeaiega 92 
                                    a+++Y  ++  ++  +++  ++++++  + r+H+++l+++le ++ + e +++++ ++y+e+++ + +    + + +   
  gi|15669167|ref|NP_247972.1| 311 NACSRYGDYETALNVLMGDRDKYYRKMLSNLRKHRNNLREALEHVKNDVE-IIQKDRFQYFETDKIM-SNIVGIVAGMSYS 389
                                   688999999999999999999*****************************.7777777777777655.4444444466666 PP

                                   HHHHHCHHHHHHHHHHHTTSHH CS
                  Rubrerythrin  93 yaeeeemyrfyeelaekegnee 114
                                   ++e   m + ++   +++g++ 
  gi|15669167|ref|NP_247972.1| 390 IEEVDWMKPIFAITEDENGYKV 411
                                   6666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      694  (0.0387082); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 3196.92
//
Query:       gi|15669168|ref|NP_247973.1|  [L=147]
Description: hypothetical protein MJ_0978 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-43  145.8   0.6    6.5e-43  145.5   0.6    1.1  1  Cas6b_C      Cas6b C-terminal domain
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.014   14.9   0.0    1.1  1  Mak10        Mak10 subunit, NatC N(alpha)-terminal acetyltran
      0.098   13.2   6.6        0.2   12.2   6.6    1.5  1  Cas_Cas6     CRISPR associated protein Cas6
       0.16   12.7   0.3       0.22   12.2   0.3    1.5  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
        2.8    7.9   5.2        4.8    7.2   5.2    1.4  1  RAMPs        RAMP superfamily


Domain annotation for each model (and alignments):
>> Cas6b_C  Cas6b C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5   0.6   1.8e-46   6.5e-43       2     113 ..      34     144 ..      33     145 .. 0.98

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 1.8e-46
                       Cas6b_C   2 lseelieYkfltpwlaLnqenykkykklkseeekkellekiLvgnilsmakglgvtveekievkiteveekkvklkeqkml 82 
                                   ++e++i+Ykf++pw+aLn++ny +yk+l +e+ kkellekiLvgnilsm+k+l++tveek+++ + e+e+  vk+k++k++
  gi|15669168|ref|NP_247973.1|  34 VAENMIKYKFISPWIALNEKNYLEYKEL-DEDGKKELLEKILVGNILSMSKYLDYTVEEKLKAGLLEYEDFVVKYKGNKFI 113
                                   7899************************.**************************************************** PP

                       Cas6b_C  83 afkgeFktnfliPdylGlGksvsrGfGtvkk 113
                                   +f geF +nf+iP+ylG+G++vs+GfG+v +
  gi|15669168|ref|NP_247973.1| 114 GFWGEFLVNFNIPNYLGIGRKVSKGFGSVIR 144
                                   ****************************987 PP

>> Mak10  Mak10 subunit, NatC N(alpha)-terminal acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     4e-06     0.014     103     152 ..      58     107 ..      37     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-06
                         Mak10 103 edeekektelelvdkvLrayvlalvkfcdlvleelskevlyeeEDfvtnk 152
                                    +e +e  ++el++k+L   +l++ k  d++ ee  k+ l e EDfv++ 
  gi|15669168|ref|NP_247973.1|  58 YKELDEDGKKELLEKILVGNILSMSKYLDYTVEEKLKAGLLEYEDFVVKY 107
                                   4455778899************************************9875 PP

>> Cas_Cas6  CRISPR associated protein Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   6.6   5.5e-05       0.2       8     144 ..      11     142 ..       5     143 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.5e-05
                                   EEETTEEEEEEEEEE.----S..--TCEE.EEESS-BBEEEEEEETTCCEEEEE-TTSTTHHHHHHHHHHHHHHHHHSS.. CS
                      Cas_Cas6   8 irlgnnefkveevel.lkepe..itssevvfktlSPivvrstkkengkkktyylspddeeFsellkenlkkkykalygee. 84 
                                   ++l+++  +v + ++ +k +e    +++++ k++SP ++ +   e++  ++++l  d++  +ell++ l   + ++ +   
  gi|15669168|ref|NP_247973.1|  11 LNLKGEVYRVVNGYAkVKFEEfgVAENMIKYKFISPWIALN---EKNYLEYKEL--DEDGKKELLEKILVGNILSMSKYLd 86 
                                   555544444444333123233556788999******99992...3344444444..7777777777777777544444335 PP

                                   ...SS---EEEEEEEEE......TEEEEEEEEEEEEEE-HHHHHHHHHC-SCS-CCCT-S-E CS
                      Cas_Cas6  85 ..keeklsikpdkkvkkivvkkketyirGylgrfelegdpellklaydaGlGeknsqGFGmv 144
                                      eekl+    +  +++vvk k+ ++ G+ g+f ++     +++  + G+G k s GFG v
  gi|15669168|ref|NP_247973.1|  87 ytVEEKLKAGLLE-YEDFVVKYKGNKFIGFWGEFLVN-----FNIPNYLGIGRKVSKGFGSV 142
                                   4456666555666.9999*****************76.....7888899***********75 PP

>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   6.1e-05      0.22      49      86 .]     114     142 ..      15     142 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.1e-05
                                   EEEEEEEE--HHHECCCHHHHHHHH-SSSTGGGTTT-E CS
                   CRISPR_Cas6  49 GfvGevkysgeleelekllrfaeylgvGkktafGlGkv 86 
                                   Gf Ge+            +++ +ylg+G+k + G+G v
  gi|15669168|ref|NP_247973.1| 114 GFWGEFLV---------NFNIPNYLGIGRKVSKGFGSV 142
                                   44444444.........66889**************86 PP

>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.2    0.0013       4.8     132     212 ..      39     142 ..       7     143 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0013
                                   EEEEEE--SSS-EEEEEE......-TT-EEEEEEEESS....................................HHHHHHH CS
                         RAMPs 132 dhsterrtrvaidrktktngk...kkgglftleaipae......................rikfsgrirlenlsdeelgal 187
                                   ++++ +++ +a+++k+  + k   + g++  le i  +                       ++ ++  ++ n++    g++
  gi|15669168|ref|NP_247973.1|  39 IKYKFISPWIALNEKNYLEYKeldEDGKKELLEKILVGnilsmskyldytveeklkagllEYEDFVVKYKGNKFIGFWGEF 119
                                   555555566666666666666665444555555555556666666666666666777666666666667777777777777 PP

                                   HHHHHHH.HHH---STTTTBTTT-E CS
                         RAMPs 188 lklLdlldlhflglGggkplGfGsv 212
                                   l  ++++  ++lg+G + + GfGsv
  gi|15669168|ref|NP_247973.1| 120 LVNFNIP--NYLGIGRKVSKGFGSV 142
                                   7777777..**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1010.31
//
Query:       gi|15669169|ref|NP_247974.1|  [L=197]
Description: hypothetical protein MJ_0979 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.051   13.9   0.9      0.051   13.9   0.9    3.4  3  DUF308         Short repeat of unknown function (DUF308)
       0.99    9.7   2.8        1.9    8.8   2.8    1.5  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.9   5.7e-06     0.051       4      26 ..      11      33 ..      11      43 .. 0.93
   2 ?    1.0   4.3      0.06   5.4e+02      31      72 ..      87     126 ..      83     127 .. 0.74
   3 ?    2.2   0.3     0.026   2.3e+02       5      18 ..     180     193 ..     174     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-06
                        DUF308  4 illivlGilalllPvaallalvl 26
                                  i liv+Gi+al+lP ++++a+++
  gi|15669169|ref|NP_247974.1| 11 IALIVVGIIALFLPWLTISASTI 33
                                  789*****************997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.06
                        DUF308  31 lllvsGivqiiaafaarkknrggrwlglllGilyliaGllll 72 
                                   +++++Gi+ ii ++ a  +  ++  + +  Gi  + ++ +++
  gi|15669169|ref|NP_247974.1|  87 FMMIFGIIPIILYI-ASIFVDKKA-VVVGAGIAGITCASIFV 126
                                   78999999999999.555566544.56678888888887775 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.026
                        DUF308   5 llivlGilalllPv 18 
                                   l +++G++++++P+
  gi|15669169|ref|NP_247974.1| 180 LTMIIGLALIAYPF 193
                                   56788888888887 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.8   0.00021       1.9       1      13 [.     111     123 ..     111     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00021
                                   EE--SHHHHHHHH CS
                 NAD_binding_8   1 IvGaGlsGlvaAy 13 
                                   +vGaG++G ++A+
  gi|15669169|ref|NP_247974.1| 111 VVGAGIAGITCAS 123
                                   8**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1070  (0.0596798); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1250.99
//
Query:       gi|15669170|ref|NP_247975.1|  [L=222]
Description: 30S ribosomal protein S3Ae [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-62  208.8   3.8    7.1e-62  208.6   3.8    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
     0.0005   20.1   0.1    0.00065   19.7   0.1    1.2  1  PSCyt2          Protein of unknown function (DUF1549)
  ------ inclusion threshold ------
      0.093   13.2   1.8        7.8    7.0   0.1    2.5  2  DUF3888         Protein of unknown function (DUF3888)
       0.11   12.7   1.7        4.9    7.3   0.3    3.1  3  Y1_Tnp          Transposase IS200 like


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.6   3.8   1.6e-65   7.1e-62       2     200 ..      12     199 ..      11     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 208.6 bits;  conditional E-value: 1.6e-65
                                   S----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCS.HTSSSEEEEEEEEEEESS CS
                Ribosomal_S3Ae   2 kkkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtnde.keqafrklklkieevqgk 81 
                                   k +kv+Dk+k+K Wy+++a   fg + iG+t++       ++++ + grv e+sl+DLt+d+ k+  + ++++ki  v+g+
  gi|15669170|ref|NP_247975.1|  12 KVRKVRDKWKEKVWYEIYATPEFGGVFIGYTPA-------NDPSLVLGRVAETSLRDLTGDPtKH--MHRVYFKIFGVTGN 83 
                                   5689*****************************.......*********************9666..9************* PP

                                   EEEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHHHHS-H CS
                Ribosomal_S3Ae  82 naltnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteeaseldl 162
                                   +a+ +++g+++tr++++s +r+++s+I+ai+dvkt+Dg+++r +++++T +r   a+++qk+ Irkkm+ei+++ a+e+++
  gi|15669170|ref|NP_247975.1|  84 KAIAQYYGHDTTREFMKSQIRRRRSRIDAILDVKTQDGHKIRTKAMVLTAYR---ANTKQKSDIRKKMEEIIKAMAKEKTF 161
                                   ****************************************************...************************** PP

                                   HHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE CS
                Ribosomal_S3Ae 163 kelvkklipeslgkeiekeakkIyplrnveirKvkvlk 200
                                    + v+++++ +++++i++e+kkI+p++nv i+K++vl+
  gi|15669170|ref|NP_247975.1| 162 PQYVQAMLFGEMAEKIKNECKKIFPIKNVIIYKSEVLS 199
                                   *********66*************************96 PP

>> PSCyt2  Protein of unknown function (DUF1549)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   1.5e-07   0.00065      22     143 ..      65     211 ..      49     222 .] 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-07
                        PSCyt2  22 drrtllRRvsldLtGlpPtpeeveaFladksad.......ayeklvdrlLaspa.ygerwarhwldlaryadskgyekdee 94 
                                   d+++ + Rv++++ G+    + ++ + +d++++        +   +d +L+ ++  g+++ ++ + l+ y+ ++++++d +
  gi|15669170|ref|NP_247975.1|  65 DPTKHMHRVYFKIFGVTGNKAIAQYYGHDTTREfmksqirRRRSRIDAILDVKTqDGHKIRTKAMVLTAYRANTKQKSDIR 145
                                   7788999************9999999999988778888888999******9776489999999999999999888776555 PP

                        PSCyt2  95 rkeawryrdwviralnedkPYdqfvreqlagdllpate......................aeqlvatgFlr 143
                                   + ++      +i+a++++k + q v+ +l g++ ++ +                      a+++  +gF++
  gi|15669170|ref|NP_247975.1| 146 K-KME----EIIKAMAKEKTFPQYVQAMLFGEMAEKIKneckkifpiknviiyksevlslAKKEENEGFVK 211
                                   5.444....48*********************777433335555555555555555444444444444444 PP

>> DUF3888  Protein of unknown function (DUF3888)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0017       7.8      14      59 ..      83     121 ..      81     148 .. 0.62
   2 ?    5.2   0.2    0.0066        30       7      45 ..     167     208 ..     163     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0017
                       DUF3888  14 qeaikkyYkkdlkeeleqakiLeikrvegvrefefeitlevkpyvg 59 
                                   ++ai +yY++d++ e+ + +i         r+++    l+vk+ +g
  gi|15669170|ref|NP_247975.1|  83 NKAIAQYYGHDTTREFMKSQI------RR-RRSRIDAILDVKTQDG 121
                                   689**********96663332......12.2223444444444444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0066
                       DUF3888   7 tlLtpyIqeaikkyYkkdlke...eleqakiLeikrvegvre 45 
                                    +L+ +  e+ik+ +kk+ +     + + ++L++ + e++++
  gi|15669170|ref|NP_247975.1| 167 AMLFGEMAEKIKNECKKIFPIknvIIYKSEVLSLAKKEENEG 208
                                   588888889999999998888444334788999999988776 PP

>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.075   3.4e+02      41      77 ..      24      60 ..       2      81 .. 0.57
   2 ?    7.3   0.3    0.0011       4.9       4      40 ..     124     161 ..     121     164 .. 0.88
   3 ?    2.0   0.1     0.048   2.2e+02      12      46 ..     162     196 ..     160     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.075
                        Y1_Tnp 41 kilelelmpDHvHllvelppklsiskivkalkgassr 77
                                   ++e+   p++  +++ ++p++++s +++++  +s r
  gi|15669170|ref|NP_247975.1| 24 VWYEIYATPEFGGVFIGYTPANDPSLVLGRVAETSLR 60
                                  2344555555556666666666666666666666555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0011
                        Y1_Tnp   4 lkyhivlvtkyRrkvltge.veerlkeiikeiaekkev 40 
                                   +  + ++ t yR +  +++ ++++++eiik +a++k +
  gi|15669170|ref|NP_247975.1| 124 IRTKAMVLTAYRANTKQKSdIRKKMEEIIKAMAKEKTF 161
                                   56677899*******99999**************9876 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.048
                        Y1_Tnp  12 tkyRrkvltgeveerlkeiikeiaekkevkilele 46 
                                   ++y + +l ge++e++k+ +k+i   k+v i++ e
  gi|15669170|ref|NP_247975.1| 162 PQYVQAMLFGEMAEKIKNECKKIFPIKNVIIYKSE 196
                                   6788999*****************99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1378  (0.0768587); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1398.79
//
Query:       gi|15669171|ref|NP_247976.1|  [L=204]
Description: hypothetical protein MJ_0981 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-05   22.4   0.3    0.00014   21.7   0.3    1.4  1  zf-DNL          DNL zinc finger
     0.0071   16.2   2.8        0.2   11.6   0.0    3.4  4  zinc_ribbon_4   zinc-ribbon domain
     0.0086   16.2   0.5        0.5   10.6   0.0    2.5  2  zf-RING_7       C4-type zinc ribbon domain
  ------ inclusion threshold ------
      0.011   15.8   1.2      0.035   14.2   1.3    1.8  1  Zn-ribbon_8     Zinc ribbon domain
      0.011   15.4   1.9        2.3    8.0   0.4    2.3  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.014   14.9   1.6      0.039   13.5   1.6    1.7  1  TF_Zn_Ribbon    TFIIB zinc-binding
      0.023   14.7   0.4      0.061   13.3   0.4    1.7  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.028   14.1   0.4        4.8    7.0   0.0    2.5  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.031   13.7   2.6       0.17   11.3   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain
       0.05   13.3   1.6        5.1    6.9   0.2    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.071   12.8   3.2        2.9    7.7   0.1    2.5  2  zinc_ribbon_2   zinc-ribbon domain
      0.081   12.9   0.2        9.2    6.3   0.0    2.4  2  Ogr_Delta       Ogr/Delta-like zinc finger
       0.13   11.8   2.3        6.1    6.5   0.1    2.2  2  Sgf11           Sgf11 (transcriptional regulation protein)
       0.29   11.0   5.6        1.1    9.2   0.5    3.0  3  DUF3797         Domain of unknown function (DUF3797)


Domain annotation for each model (and alignments):
>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.3   1.1e-07   0.00014       2      49 ..       7      55 ..       6      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.1e-07
                        zf-DNL  2 ltftCkaCetrsskeiskkaYekG.vVivqCpgCknrHliaDnLgwfed 49
                                  +  +C++C+  ++  + kk Y+k    +v+Cp+C +   i D++++ + 
  gi|15669171|ref|NP_247976.1|  7 IYLKCENCGFEEQEVLKKKIYNKSaYYLVRCPNCGSVREIVDKVKLSQA 55
                                  6779*****************9862579***************998865 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.094   1.2e+02      26      32 ..       9      15 ..       5      17 .. 0.67
   2 !   11.6   0.0   0.00016       0.2       3      18 ..      35      49 ..      34      57 .. 0.77
   3 ?   -1.4   0.0       1.8   2.3e+03      11      19 ..      61      69 ..      60      71 .. 0.87
   4 ?   -1.9   0.0       2.6   3.4e+03      10      17 ..     151     158 ..     150     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.094
                 zinc_ribbon_4 26 vrCskCg 32
                                  ++C +Cg
  gi|15669171|ref|NP_247976.1|  9 LKCENCG 15
                                  5666665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00016
                 zinc_ribbon_4  3 itCpsCkakyeiddek 18
                                  ++Cp+C++++ei d k
  gi|15669171|ref|NP_247976.1| 35 VRCPNCGSVREIVD-K 49
                                  89*******99988.4 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.8
                 zinc_ribbon_4 11 kyeiddekl 19
                                  +y i+++k+
  gi|15669171|ref|NP_247976.1| 61 RYDISESKV 69
                                  8******97 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 2.6
                 zinc_ribbon_4  10 akyeidde 17 
                                   ++y+i+d 
  gi|15669171|ref|NP_247976.1| 151 KVYRINDG 158
                                   79***985 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.064        82      24      30 ..       9      15 ..       3      15 .. 0.83
   2 !   10.6   0.0   0.00039       0.5      23      30 ..      34      41 ..      17      43 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.064
                                  EE-TTT- CS
                     zf-RING_7 24 vtCpeCG 30
                                   +C++CG
  gi|15669171|ref|NP_247976.1|  9 LKCENCG 15
                                  68****9 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00039
                                  -EE-TTT- CS
                     zf-RING_7 23 vvtCpeCG 30
                                  +v+Cp+CG
  gi|15669171|ref|NP_247976.1| 34 LVRCPNCG 41
                                  8******9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.3   2.7e-05     0.035       7      34 ..      10      42 ..       8      47 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                   Zn-ribbon_8  7 rCeeCghefe...vlqsis.dap...ltaCPeCgs 34
                                  +Ce+Cg  fe   vl +    ++   l+ CP+Cgs
  gi|15669171|ref|NP_247976.1| 10 KCENCG--FEeqeVLKKKIyNKSayyLVRCPNCGS 42
                                  8*****..555566666554444787999****99 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4    0.0018       2.3      13      32 ..       1      19 [.       1      19 [. 0.90
   2 ?    6.6   0.0    0.0049       6.3      13      31 ..      25      44 ..      23      46 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0018
                 A2L_zn_ribbon 13 gilnseqgylvCieCgasfp 32
                                  +++ +e+ yl C +Cg++++
  gi|15669171|ref|NP_247976.1|  1 MEM-TEKIYLKCENCGFEEQ 19
                                  788.9999*********986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0049
                 A2L_zn_ribbon 13 gilnseqgylv.CieCgasf 31
                                  +i+n+   ylv C++Cg++ 
  gi|15669171|ref|NP_247976.1| 25 KIYNKSAYYLVrCPNCGSVR 44
                                  677766667767*****986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.6     3e-05     0.039       2      33 ..      10      48 ..       9      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-05
                                  EETTTTCEEC......HEETSTTCE.EESSSSBEEEECC CS
                  TF_Zn_Ribbon  2 kCPnCgstnl......veDpergel.vCtdCGlVledns 33
                                  kC nCg +++      +++ +   l +C++CG+V e  +
  gi|15669171|ref|NP_247976.1| 10 KCENCGFEEQevlkkkIYNKSAYYLvRCPNCGSVREIVD 48
                                  899999999889999999999999999*******99665 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   4.8e-05     0.061      67      96 ..       5      44 ..       2      57 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-05
                                  E--EEEETTTS-EEECHHHHH...........S-TTTSSS- CS
                          HypA 67 vpvkvrCreCgkefeleekal...........rCpkCgsad 96
                                  +++ ++C++Cg e ++  k             rCp+Cgs +
  gi|15669171|ref|NP_247976.1|  5 EKIYLKCENCGFEEQEVLK-KkiynksayylvRCPNCGSVR 44
                                  67789******65552222.1246788999********975 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1      0.02        26      18      25 ..       9      16 ..       2      18 .. 0.85
   2 ?    7.0   0.0    0.0037       4.8      18      25 ..      35      42 ..      30      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.02
                                  ---SSS-- CS
                DNA_RNApol_7kD 18 iRCkeCGh 25
                                  ++C +CG+
  gi|15669171|ref|NP_247976.1|  9 LKCENCGF 16
                                  69*****8 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0037
                                  ---SSS-- CS
                DNA_RNApol_7kD 18 iRCkeCGh 25
                                  +RC +CG+
  gi|15669171|ref|NP_247976.1| 35 VRCPNCGS 42
                                  9******6 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2       0.1   1.3e+02      18      24 ..      10      16 ..       9      17 .. 0.76
   2 ?   11.3   0.2   0.00014      0.17       3      11 ..      35      43 ..      34      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.1
                   zf-ribbon_3 18 vCpyCGt 24
                                  +C +CG 
  gi|15669171|ref|NP_247976.1| 10 KCENCGF 16
                                  5889985 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00014
                   zf-ribbon_3  3 vrCPnCGap 11
                                  vrCPnCG++
  gi|15669171|ref|NP_247976.1| 35 VRCPNCGSV 43
                                  79*****86 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2     0.004       5.1       3      11 ..      11      19 ..      10      22 .. 0.82
   2 ?    5.6   0.1     0.011        13      16      22 ..      36      42 ..      30      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.004
                  Rubredoxin_2  3 CsqCGfesa 11
                                  C++CGfe +
  gi|15669171|ref|NP_247976.1| 11 CENCGFEEQ 19
                                  ******976 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                  Rubredoxin_2 16 rCpsCgs 22
                                  rCp+Cgs
  gi|15669171|ref|NP_247976.1| 36 RCPNCGS 42
                                  89***96 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.5     0.016        20       2       7 ..      11      16 ..       9      17 .. 0.57
   2 ?    7.7   0.1    0.0023       2.9       2       6 ..      37      41 ..      24      43 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.016
                 zinc_ribbon_2  2 CpnCGa 7 
                                  C nCG 
  gi|15669171|ref|NP_247976.1| 11 CENCGF 16
                                  666664 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
                 zinc_ribbon_2  2 CpnCG 6 
                                  CpnCG
  gi|15669171|ref|NP_247976.1| 37 CPNCG 41
                                  66665 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.028        36      20      35 ..       3      16 ..       1      18 [. 0.84
   2 ?    6.3   0.0    0.0072       9.2       1      10 [.      36      45 ..      36      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.028
                     Ogr_Delta 20 dvreryyqCsnfeCga 35
                                  ++ ++y  C n  Cg+
  gi|15669171|ref|NP_247976.1|  3 MTEKIYLKCEN--CGF 16
                                  5778*******..997 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0072
                     Ogr_Delta  1 rCPhCgapaa 10
                                  rCP+Cg+   
  gi|15669171|ref|NP_247976.1| 36 RCPNCGSVRE 45
                                  7*****9755 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.013        17       3      11 ..       7      15 ..       5      15 .. 0.86
   2 ?    6.5   0.1    0.0048       6.1       3      11 ..      33      41 ..      31      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                                  -EEE-TTTS CS
                         Sgf11  3 eyvtCpnCg 11
                                   y +C+nCg
  gi|15669171|ref|NP_247976.1|  7 IYLKCENCG 15
                                  699*****7 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0048
                                  -EEE-TTTS CS
                         Sgf11  3 eyvtCpnCg 11
                                   +v+CpnCg
  gi|15669171|ref|NP_247976.1| 33 YLVRCPNCG 41
                                  589*****8 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.0      0.09   1.2e+02       8      20 ..       2      15 ..       1      29 [. 0.86
   2 ?    9.2   0.5   0.00089       1.1      14      34 ..      35      60 ..      20      64 .. 0.74
   3 ?   -2.3   0.0       3.3   4.2e+03      27      38 ..      65      78 ..      61      80 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.09
                       DUF3797  8 kLdek.YvqCPeCg 20
                                  ++ ek Y +C +Cg
  gi|15669171|ref|NP_247976.1|  2 EMTEKiYLKCENCG 15
                                  567888*******9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00089
                       DUF3797 14 vqCPeCgN.....nkvlNsegkviie 34
                                  v CP+Cg      +kv  s++k+ii+
  gi|15669171|ref|NP_247976.1| 35 VRCPNCGSvreivDKVKLSQAKLIIS 60
                                  89*****7555557899999999997 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.3
                       DUF3797 27 segkv..iieddtf 38
                                  se+kv  i ed+t+
  gi|15669171|ref|NP_247976.1| 65 SESKVinIPEDETY 78
                                  67788645566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1062  (0.0592336); expected 358.6 (0.02)
Passed bias filter:                      759  (0.0423336); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1367.15
//
Query:       gi|15669172|ref|NP_247977.1|  [L=222]
Description: 30S ribosomal protein S2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-25   89.4   0.0    9.3e-14   51.2   0.0    2.1  2  Ribosomal_S2  Ribosomal protein S2


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   1.8e-13   3.2e-09       2      95 ..      14     104 ..      13     109 .. 0.92
   2 !   51.2   0.0   5.2e-18   9.3e-14     148     211 ..     112     175 ..     106     178 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.8e-13
                  Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIygern.gihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaakrang 81 
                                   L++g+h+G q++  +++m+++Iy +r+ g +++d++kt + lr a+k++ +   + + il v+ +  +   ++e  k ++ 
  gi|15669172|ref|NP_247977.1|  14 LASGIHIGTQQK--TKDMEKFIYRVRSdGLYVLDVRKTDERLRIAAKFLARY--EPEDILAVSRRIYTMGPLEEFGKYTGI 90 
                                   799*****6665..899******999549********************875..6789*********************** PP

                  Ribosomal_S2  82 yyvnerWlgGtLTN 95 
                                     v  r+++GtLTN
  gi|15669172|ref|NP_247977.1|  91 RTVAGRFVPGTLTN 104
                                   ************** PP

  == domain 2  score: 51.2 bits;  conditional E-value: 5.2e-18
                  Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvlada 211
                                    P++v++ dp+ ++ a+kEa++ g+p+++++Dt+  ++ +d +Ip N++  +++ li+ +l++ 
  gi|15669172|ref|NP_247977.1| 112 EPEVVFISDPRVDRQALKEATEIGVPIVGLCDTEHLTSFIDLVIPTNNKGKKAVALIYYLLTRE 175
                                   59********************************************************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1579.61
//
Query:       gi|15669173|ref|NP_247978.1|  [L=194]
Description: 50S ribosomal protein L15e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-90  301.3   4.8    2.8e-90  301.2   4.8    1.0  1  Ribosomal_L15e  Ribosomal L15
  ------ inclusion threshold ------
        1.1    9.3   2.5         11    6.1   0.1    2.2  2  DUF3889         Protein of unknown function (DUF3889)


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.2   4.8   3.1e-94   2.8e-90       1     191 []       2     189 ..       2     189 .. 0.99

  Alignments for each domain:
  == domain 1  score: 301.2 bits;  conditional E-value: 3.1e-94
                                   -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..---SS-- CS
                Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskgktgr 81 
                                   g+yky+re+wk+++++++r+ll+erl+++r+epavvr+erptrldrAr+LGYk kqGi+vvrvrvrrGg +k  ++ k+++
  gi|15669173|ref|NP_247978.1|   2 GIYKYIREAWKRPKESYVRQLLWERLQQWRREPAVVRIERPTRLDRARALGYKPKQGIIVVRVRVRRGGLRK--PRPKNSK 80 
                                   78**********************************************************************..******* PP

                                   -GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGGGTTGGGGT CS
                Ribosomal_L15e  82 kpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkvhkhRelrG 162
                                   kp++ gvnk+++ ks+q+iaeer++rk+pn++vLnSYwvgeDg++k+yEvilvDp h+ai+ d+++nw+c+ +h++R++rG
  gi|15669173|ref|NP_247978.1|  81 KPATLGVNKITMGKSIQRIAEERAARKYPNMEVLNSYWVGEDGKHKWYEVILVDPYHPAIKADPQLNWLCTGKHRGRAFRG 161
                                   ********************************************************************************* PP

                                   -SHHHHHHTT-S-SS.TT-TTTSS-TGGG CS
                Ribosomal_L15e 163 ltsagkksRGlrkkglkgaekirgsrran 191
                                   ltsagkk+RGlr+kg  gaek+r+s+ra+
  gi|15669173|ref|NP_247978.1| 162 LTSAGKKGRGLRNKG-IGAEKVRPSIRAH 189
                                   ***************.99********995 PP

>> DUF3889  Protein of unknown function (DUF3889)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.4     0.011        95      23      51 ..       5      33 ..       2      37 .. 0.91
   2 ?    6.1   0.1    0.0012        11      25      51 ..      97     123 ..      80     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.011
                                  SSTTHHHHHHHHT-TT-EE---EEEEEEE CS
                       DUF3889 23 kwerlAvketkkkYpgaevvdyqyvGrtk 51
                                  k+ r A+k  k++Y  + +   ++++r++
  gi|15669173|ref|NP_247978.1|  5 KYIREAWKRPKESYVRQLLWERLQQWRRE 33
                                  89999*********************986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0012
                                   TTHHHHHHHHT-TT-EE---EEEEEEE CS
                       DUF3889  25 erlAvketkkkYpgaevvdyqyvGrtk 51 
                                    r+A + ++ kYp+ ev+    vG+  
  gi|15669173|ref|NP_247978.1|  97 QRIAEERAARKYPNMEVLNSYWVGEDG 123
                                   599***************999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1302.97
//
Query:       gi|15669174|ref|NP_247979.1|  [L=222]
Description: type II R/M system restriction enzyme 1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-67  224.7   6.6    6.8e-67  224.4   6.6    1.1  1  RE_MjaI   MjaI restriction endonuclease
  ------ inclusion threshold ------
       0.05   13.6   0.1        3.8    7.5   0.0    2.7  2  TTRAP     Putative tranposon-transfer assisting protein


Domain annotation for each model (and alignments):
>> RE_MjaI  MjaI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.4   6.6   7.6e-71   6.8e-67       2     164 .]      40     209 ..      39     209 .. 0.98

  Alignments for each domain:
  == domain 1  score: 224.4 bits;  conditional E-value: 7.6e-71
                       RE_MjaI   2 qilNlannraqltrkkvVgqvselikefe...gktleeWkkwYleklpeaieeatkkiykkieelkeeieevdeedvrkwv 79 
                                   q++Nlan ++q+tr+kvVgq+selikef+   g+t+e+WkkwYl+k+p+ai+eat+ki+++++++ke++e+++++dvrkwv
  gi|15669174|ref|NP_247979.1|  40 QLINLANIFSQGTRPKVVGQMSELIKEFRktgGRTFEDWKKWYLQKYPNAIDEATEKIWNMLNNFKETLEQLERDDVRKWV 120
                                   89***************************777788********************************************** PP

                       RE_MjaI  80 edLvinktfeGlkvqeailkklakelnvkyrlatdeeeskgiDgyi....keigisiKpktykekekelseekdvkiityk 156
                                   edLv+ kt+eGl++q+ailkk+a+el+ +yr++t eeeskgiDg+i    kei++siK+kty+++ek+lsee + ++i+y+
  gi|15669174|ref|NP_247979.1| 121 EDLVLIKTYEGLMLQDAILKKVAEELGGNYRPSTIEEESKGIDGVIiiddKEIPVSIKSKTYVNQEKHLSEELKGHLIIYE 201
                                   ********************************************************************************* PP

                       RE_MjaI 157 kkksgikv 164
                                   kkk++i v
  gi|15669174|ref|NP_247979.1| 202 KKKNKIIV 209
                                   ****9976 PP

>> TTRAP  Putative tranposon-transfer assisting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00043       3.8       6      30 ..      42      66 ..      42      74 .. 0.91
   2 ?    2.8   0.1     0.013   1.2e+02      20      42 ..     100     122 ..      94     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00043
                                  HHHHHHH--SHHHHHHHHHHHSTTT CS
                         TTRAP  6 lnLiaiynegtRkelieelkaalky 30
                                  +nL  i+++gtR +++ ++++ +k 
  gi|15669174|ref|NP_247979.1| 42 INLANIFSQGTRPKVVGQMSELIKE 66
                                  69999**************999875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.013
                                   HHHHHHHSTTTS.-HHHHHHHHH CS
                         TTRAP  20 lieelkaalkyleddelreLaes 42 
                                   ++++ k++l++le d+ r+++e 
  gi|15669174|ref|NP_247979.1| 100 MLNNFKETLEQLERDDVRKWVED 122
                                   67899*******99999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1430.36
//
Query:       gi|15669175|ref|NP_247980.1|  [L=303]
Description: type II R/M system modification methyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-50  171.9   0.2      2e-50  171.7   0.2    1.1  1  N6_N4_Mtase      DNA methylase
  ------ inclusion threshold ------
      0.029   14.0   0.0        2.2    7.9   0.0    2.3  2  UPF0020          Putative RNA methylase family UPF0020
      0.039   14.7   0.0        1.3    9.8   0.0    2.8  3  Methyltransf_25  Methyltransferase domain
      0.081   12.2   0.2       0.27   10.5   0.3    1.8  2  N6_Mtase         N-6 DNA Methylase
        0.2   12.3   0.0        5.2    7.8   0.0    2.7  3  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.7   0.2   5.5e-54     2e-50       1     230 [.      28     281 ..      28     282 .. 0.91

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 5.5e-54
                                   EEEEEE--SSSSSCS.......................GCCGCCH.....HHHHHHHHHHHHHHHHHHEEEEEEEEEEE-C CS
                   N6_N4_Mtase   1 vdlivtdpPYntgkdy..................endeqyeeeds.....yeeyleflekvlkevrrvLkddgsifinidd 58 
                                   v+l+vt+pPY + + +                  en+e++e++++     y+ +++ l++v++ev+rvL ++g+++ini+d
  gi|15669175|ref|NP_247980.1|  28 VHLVVTSPPYPMIEMWdelfkmlnleinkrwmemENEEDEEKKEKlimqiYNLMHQTLYPVWEEVYRVLVPGGIACINIGD 108
                                   89***************************777654444444333388888******************************* PP

                                   CCHHT........HHHHHHHHHTT.-EEEEEEEEEEES.........SSTTTSTCCS-B--EEEEEEEESSTT-..---GG CS
                   N6_N4_Mtase  59 seikk........elkaladeifg.gffllnvivwkkp.........nsmpesnkdrltsthEyilvfsknkkyllkfnld 121
                                    + k         ++ ++++++ + gf+ l  i wkkp         +++  +n+ ++t + Eyil+f+k+k +       
  gi|15669175|ref|NP_247980.1| 109 ATRKIngvfrlfpNHSKIIENFEKiGFVTLPYILWKKPsnkpnaflgSGFLPPNA-YVTLDVEYILIFRKGKPR------- 181
                                   **999*********************************87777777444455554.******************....... PP

                                   GSSBSS-HHHHHHHHHHCHHHCC-B--BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS-TT-EEEETT-TT CS
                   N6_N4_Mtase 122 aikvpyeekdklekrgaytskkkgkkiediWdlseiqsnekkskgdtkkkHpaqkPvallerlIklstkkgdivlDpFaGS 202
                                       +++ kd l++ +ayt++++++++++iW  +++ +++ + k +  ++ +a++P+++++rlI++++  gd+vlDpF+G+
  gi|15669175|ref|NP_247980.1| 182 ----KFKPKDPLRYASAYTKEERDRWFSQIW--EIVGDKQTHPKIE--RR-TASFPEEIPRRLIRMFSIIGDTVLDPFLGT 253
                                   ....9999***********************..9999999998874..66.9***************************** PP

                                   THHHHHHHHTT-EEEEEESSHHHHHHHH CS
                   N6_N4_Mtase 203 GtTavaakelgrkfiGieieeeyvelae 230
                                   GtT++aa+el+r++iG+ei+++ + ++e
  gi|15669175|ref|NP_247980.1| 254 GTTVKAAIELKRNSIGYEIDKSLKPIIE 281
                                   *********************9999887 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.01        37     108     131 ..      13      37 ..       3      40 .. 0.75
   2 ?    7.9   0.0   0.00063       2.2      29      89 ..     243     300 ..     225     303 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.01
                                   EE--GGG--.STTS---EEEE---- CS
                       UPF0020 108 sqadaakLr.lkegevdvivtnpPY 131
                                      da+k+   ++++v ++vt pPY
  gi|15669175|ref|NP_247980.1|  13 IFGDARKMDeIEDESVHLVVTSPPY 37 
                                   446777777545569********** PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00063
                                   TS-EEETT-TTSHHHHHHHH.HHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHH CS
                       UPF0020  29 gepllDPmCGsGtilIEaal.lganiapgllrefvlelkaeaeeearaelklygsDldrrvv 89 
                                   g++ lDP+ G+Gt    aa+ l++n +     e    lk  +ee++  ++k +g+D++ + +
  gi|15669175|ref|NP_247980.1| 243 GDTVLDPFLGTGTTV-KAAIeLKRNSI---GYEIDKSLKPIIEEKIGIKQKRIGMDFNVEFI 300
                                   7899*********65.55551555555...22333447777777777888888888887776 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.15   5.4e+02      47      71 ..       9      34 ..       5      51 .. 0.74
   2 ?    9.8   0.0   0.00037       1.3      32      97 .]      38     100 ..      15     100 .. 0.79
   3 ?    0.9   0.0      0.22   7.8e+02       1      41 [.     246     284 ..     246     302 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.15
                                  TEEEEESBCCGBSS.STTTEEEEEEE CS
               Methyltransf_25 47 nvefvqgdaedlpf.edgsfDlvvss 71
                                  n +++ gda+++++ ed+s++lvv s
  gi|15669175|ref|NP_247980.1|  9 NHKIIFGDARKMDEiEDESVHLVVTS 34
                                  5677889****985499******985 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00037
                                   HHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  32 emleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                    m+e   e ++  +l+++ + +++e+ + e+++  l++ +++l+h   + l  + +e++rvL pgG
  gi|15669175|ref|NP_247980.1|  38 PMIEMWDELFKMLNLEINKRWMEMENEEDEEKKEKLIMQIYNLMH---QTLYPVWEEVYRVLVPGG 100
                                   688888888887777788888888898999999999999988777...45899************9 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.22
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaarera 41 
                                   vLd   GtG++++a+ +   k + +g +i++++  +++e++
  gi|15669175|ref|NP_247980.1| 246 VLDPFLGTGTTVKAAIEL--KRNSIGYEIDKSLKPIIEEKI 284
                                   788899999999998887..388888888777666655555 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   7.4e-05      0.27     101     159 ..       5      66 ..       1      84 [. 0.72
   2 ?   -1.8   0.0      0.41   1.5e+03      31      60 ..     228     256 ..     204     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.4e-05
                      N6_Mtase 101 gieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqke.w....kektlekderfrea.vapks 159
                                   +i ++  ki  gd+ + ++ e d++++ vv+ pp+   e w    k  +le ++r+ e+   +++
  gi|15669175|ref|NP_247980.1|   5 DITTN-HKIIFGDARKMDEIE-DESVHLVVTSPPYPMIEmWdelfKMLNLEINKRWMEMeN-EED 66 
                                   66666.68999********99.*************87652677777788999999998852.322 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.41
                      N6_Mtase  31 PrevsklivellepksgesvyDpacGsggl 60 
                                   P+e+ + ++++     ++ v+Dp  G+g  
  gi|15669175|ref|NP_247980.1| 228 PEEIPRRLIRMFSIIGDT-VLDPFLGTGTT 256
                                   778888888888887775.99999999975 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.21   7.6e+02      46      68 ..      11      34 ..       4      52 .. 0.76
   2 ?    7.8   0.0    0.0015       5.2      77      95 ..      85     103 ..      72     104 .. 0.81
   3 ?   -1.6   0.0       1.2   4.4e+03       5      42 ..     251     288 ..     247     300 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.21
                                  EETTEECCCT.SS-TT-EEEEEEE CS
               Methyltransf_11 46 efvvadaekl.pfednsfDlvvss 68
                                  +++ +da+k+  +ed+s+ lvv s
  gi|15669175|ref|NP_247980.1| 11 KIIFGDARKMdEIEDESVHLVVTS 34
                                  567799***988********9987 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0015
                                   HHHHHHHHHHHEEEEEEEE CS
               Methyltransf_11  77 pekalkeiaRvLkpgGllv 95 
                                   +  +++e++RvL pgG+ +
  gi|15669175|ref|NP_247980.1|  85 LYPVWEEVYRVLVPGGIAC 103
                                   667899**********986 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.2
                                   -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT CS
               Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseeg 42 
                                    GtG  ++a  +  ++ +g +++k +  + +ek+  ++
  gi|15669175|ref|NP_247980.1| 251 LGTGTTVKAAIELKRNSIGYEIDKSLKPIIEEKIGIKQ 288
                                   58888888888777888888888887777776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1882.78
//
Query:       gi|15669176|ref|NP_247981.1|  [L=76]
Description: hypothetical protein MJ_0986 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 530.48
//
Query:       gi|15669177|ref|NP_247982.1|  [L=116]
Description: erpK protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-29  101.7  26.4    2.1e-29  101.6  26.4    1.0  1  Prefoldin_2      Prefoldin subunit
    3.6e-05   24.1  18.3    0.00048   20.5   6.9    2.3  2  FlaC_arch        Flagella accessory protein C (FlaC)
    0.00021   20.3  13.8     0.0059   15.5   1.5    2.0  2  Spc7             Spc7 kinetochore protein
     0.0016   18.3  19.2        1.4    8.9  19.2    2.4  1  Prefoldin        Prefoldin subunit
     0.0021   18.1  24.6        0.1   12.7  10.2    2.0  2  DHR10            Designed helical repeat protein 10 domain
     0.0023   18.1   6.8     0.0023   18.1   6.8    2.2  2  XhlA             Haemolysin XhlA
     0.0025   18.1  17.7     0.0029   17.9   5.6    2.2  2  CLZ              C-terminal leucine zipper domain of cyclic n
     0.0029   17.8  14.5      0.005   17.0  14.5    1.5  1  Fib_alpha        Fibrinogen alpha/beta chain family
     0.0047   16.5   0.7     0.0047   16.5   0.7    1.9  2  BRI3BP           Negative regulator of p53/TP53
     0.0073   16.0  14.0      0.011   15.4  14.0    1.3  1  UBN_AB           Ubinuclein conserved middle domain
  ------ inclusion threshold ------
      0.011   15.8  22.4       0.32   11.0   9.1    2.1  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.011   13.7   8.7      0.013   13.5   8.7    1.1  1  Prominin         Prominin
      0.012   15.6  25.3      0.047   13.7   7.3    2.1  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.014   13.9   1.0      0.018   13.6   1.0    1.0  1  FUSC             Fusaric acid resistance protein family
      0.016   15.1   4.6      0.016   15.1   4.6    2.6  1  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
      0.017   15.0  22.2      0.042   13.7   7.5    2.0  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
      0.019   15.0  14.5       0.06   13.4  14.5    1.7  1  Laminin_II       Laminin Domain II
      0.027   15.0   8.2        1.2    9.7   1.8    2.2  2  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.03   14.1   3.4       0.03   14.1   3.4    2.4  2  DUF4201          Domain of unknown function (DUF4201)
      0.038   13.8   7.0      0.047   13.5   7.0    1.1  1  Baculo_p24       Baculovirus P24 capsid protein
       0.04   13.8  17.9       0.74    9.7   7.9    2.3  2  CdvA             CdvA-like coiled-coil domain
       0.05   13.8   3.9       0.11   12.7   0.4    2.0  2  ABC1             ABC1 family
       0.08   13.6  18.3        1.1    9.9   8.6    2.1  2  YabA             Initiation control protein YabA
      0.095   11.4  16.0       0.52    9.0   4.7    2.1  2  Tektin           Tektin family
       0.11   12.6   9.2        1.1    9.3   9.2    2.0  1  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.14   12.5  20.8        1.6    9.0   7.8    2.2  2  Spc24            Spc24 subunit of Ndc80
       0.14   12.7  23.3       0.91   10.1   8.9    2.1  2  APG6_N           Apg6 coiled-coil region
       0.16   11.6  21.8       0.25   10.9  21.8    1.3  1  DUF4795          Domain of unknown function (DUF4795)
       0.18   11.9  12.1       0.52   10.5  11.9    1.7  1  GCN5L1           GCN5-like protein 1 (GCN5L1)
       0.21   11.2   4.2        0.2   11.3   0.7    2.0  2  DUF4988          Domain of unknown function
       0.21   11.3   8.4       0.24   11.2   8.4    1.0  1  AAA_11           AAA domain
       0.24   11.6  17.6        1.3    9.3   4.7    2.0  2  ATG16            Autophagy protein 16 (ATG16)
       0.25   10.9  19.8       0.59    9.7   5.0    2.1  2  Filament         Intermediate filament protein
       0.28   11.6  10.0       0.73   10.2   9.9    1.6  1  PRP1_N           PRP1 splicing factor, N-terminal
       0.29   11.2  15.0      0.061   13.3   3.7    2.7  2  Bcr-Abl_Oligo    Bcr-Abl oncoprotein oligomerisation domain
       0.34   11.2  12.0        1.1    9.6   2.3    2.6  3  DUF4164          Domain of unknown function (DUF4164)
       0.35   11.0  17.6      0.072   13.2   4.4    2.1  2  YojJ             Bacterial membrane-spanning protein N-termin
       0.37   11.3  11.9       0.31   11.5   2.0    2.5  2  DUF4140          N-terminal domain of unknown function (DUF41
        0.4   11.1  20.7        1.9    8.9  20.7    1.9  1  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
       0.41   11.0  20.4        1.3    9.4   6.3    2.1  2  YlqD             YlqD protein
       0.53    9.5  21.3          6    6.1  21.3    1.9  1  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.56   10.7  11.7        1.8    9.1   1.6    2.6  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.58   10.1   5.4        6.9    6.6   1.2    2.1  2  LppA             Lipoprotein confined to pathogenic Mycobacte
       0.64    9.5   9.6       0.74    9.3   9.6    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
       0.66   10.0  14.2        1.2    9.1   4.5    2.1  2  DUF1664          Protein of unknown function (DUF1664)
       0.73   10.8   8.0       0.28   12.2   1.1    2.3  2  Rotamase         PPIC-type PPIASE domain
        0.8   10.0   9.2        4.6    7.5   0.2    2.6  2  WXG100           Proteins of 100 residues with WXG
       0.83   10.1   4.1        2.9    8.4   1.4    2.2  2  FAA_hydro_N_2    Fumarylacetoacetase N-terminal domain 2
        1.1    9.2  15.4       0.68    9.9   4.8    2.0  2  DUF4446          Protein of unknown function (DUF4446)
        1.2    8.5  10.0        1.7    7.9  10.0    1.3  1  DUF4407          Domain of unknown function (DUF4407)
        1.2    7.6  17.7       0.47    8.9   4.3    2.0  2  Herpes_UL6       Herpesvirus UL6 like
        1.3    9.1  16.6         24    5.0  16.6    2.1  1  Nup54            Nucleoporin complex subunit 54
        1.4    8.2  25.2       0.68    9.3  10.2    2.0  2  DUF4618          Domain of unknown function (DUF4618)
        1.6    9.4  16.4          1   10.1   2.9    2.2  2  DUF4404          Domain of unknown function (DUF4404)
        1.7    8.8  26.8        2.2    8.5  12.7    2.0  2  Tropomyosin_1    Tropomyosin like
          2    7.8  23.0        4.7    6.6  23.0    1.5  1  Golgin_A5        Golgin subfamily A member 5
        2.2    7.9  20.4         65    3.1  19.4    1.9  1  Laminin_I        Laminin Domain I
        2.3    8.5  19.4        1.3    9.2  14.0    2.2  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        2.4    8.8   8.2    3.7e+02    1.8   8.2    2.3  1  Ribosomal_S20p   Ribosomal protein S20
        2.4    7.9  10.5       0.33   10.7   2.6    2.0  2  DUF3287          Protein of unknown function (DUF3287)
        2.4    8.6  24.6       0.13   12.7   3.3    3.1  2  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
        2.6    8.4  17.4        2.1    8.7   5.5    2.2  2  BLOC1_2          Biogenesis of lysosome-related organelles co
        2.7    8.0   5.3       0.85    9.6   0.9    1.9  2  TIR-like         Predicted nucleotide-binding protein contain
        2.8    7.8   8.8        2.6    7.9   0.3    3.3  4  DASH_Dam1        DASH complex subunit Dam1
        3.1    7.6   9.6        7.6    6.3   1.5    2.1  2  SPACA9           Sperm acrosome-associated protein 9
        3.4    8.8  14.1        3.2    8.9   2.9    2.3  2  DUF5320          Family of unknown function (DUF5320)
        3.8    7.7  30.3       0.14   12.3  14.3    2.9  2  bZIP_1           bZIP transcription factor
        3.9    7.3  16.3        5.2    6.9   5.7    2.1  2  Nsp1_C           Nsp1-like C-terminal region
        3.9    7.7  24.1         18    5.6  24.1    2.1  1  DUF3958          Protein of unknown function (DUF3958)
          4    6.7  19.1        0.9    8.8   5.9    2.0  2  DUF3450          Protein of unknown function (DUF3450)
          4    7.5  16.7        4.9    7.3   6.4    2.2  2  DivIVA           DivIVA protein
        4.2    6.9  22.3       0.92    9.0   7.0    2.0  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
        4.2    8.0   8.7        2.6    8.7   4.0    2.2  2  YtxH             YtxH-like protein
        4.4    6.7  10.4       0.59    9.5   2.4    2.1  2  FliD_C           Flagellar hook-associated protein 2 C-termin
        4.5    5.1  13.8        6.7    4.5  13.8    1.3  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        5.6    7.2  24.4         11    6.2  24.4    1.5  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
        6.2    6.4  21.8        1.9    8.1   4.2    2.1  2  DUF2968          Protein of unknown function (DUF2968)
        6.2    5.3  17.7         11    4.4  17.7    1.4  1  FapA             Flagellar Assembly Protein A
        6.9    5.2  14.7         26    3.3  14.8    1.7  1  AAA_13           AAA domain
        7.8    6.6   7.5         19    5.3   7.5    1.6  1  Cob_adeno_trans  Cobalamin adenosyltransferase
        8.2    6.6  17.9       0.68   10.1   5.7    2.1  2  RasGAP_C         RasGAP C-terminus
          9    6.8  10.2        4.7    7.7   0.6    2.6  2  LPP              Lipoprotein leucine-zipper
        9.7    5.4  14.8         14    4.9  14.8    1.3  1  FAM76            FAM76 protein


Domain annotation for each model (and alignments):
>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6  26.4   9.9e-32   2.1e-29       1     103 [.      11     112 ..      11     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 9.9e-32
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktl 81 
                                   q++++++qqlqqqlq++ +q++++et+lke++++leele+  +d +vyklvG+++vk++ke+vk+eLee+ etle ++ktl
  gi|15669177|ref|NP_247982.1|  11 QAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSD-EVYKLVGGLFVKRKKEDVKKELEEKVETLELRVKTL 90 
                                   89******************************************.************************************ PP

                                   HHHHHHHHHHHHHHHHHHHCCT CS
                   Prefoldin_2  82 ekqleklekeleelkeelqkkl 103
                                   ekq+ekl+ +l+el+e++qk++
  gi|15669177|ref|NP_247982.1|  91 EKQEEKLQSRLKELQEKIQKMI 112
                                   ********************97 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   3.5    0.0067       1.4       3      36 ..      18      51 ..      16      60 .. 0.90
   2 !   20.5   6.9   2.2e-06   0.00048       3      41 ..      74     112 ..      73     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0067
                     FlaC_arch  3 delEnklsklsteletvkkeneelsksveelken 36
                                  ++l+++l+ + ++ ++v++e++e +k +eel+++
  gi|15669177|ref|NP_247982.1| 18 QQLQQQLQMILMQKQSVETELKECKKALEELEKS 51
                                  6899***************************986 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.2e-06
                     FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkdll 41 
                                   +elE+k++ l+ +++t++k+ e+l++ ++el+e++++++
  gi|15669177|ref|NP_247982.1|  74 KELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKMI 112
                                   69**********************************997 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.5   2.7e-05    0.0059     221     271 ..       9      59 ..       2      63 .. 0.84
   2 !   10.4   5.0     0.001      0.22     138     178 ..      70     110 ..      64     115 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-05
                          Spc7 221 elaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrl 271
                                   +++    ql++l+++++ +  qk+++e+e++e ++ lee +++s++ev +l
  gi|15669177|ref|NP_247982.1|   9 QIQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSDEVYKL 59 
                                   566666789999999999999999999999999999999999999999876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.001
                          Spc7 138 egLkegleenlegleedkelLekqeeeldellpeleeekae 178
                                   e++k++lee++e+le   ++Lekqee+l++ l+el+e+ ++
  gi|15669177|ref|NP_247982.1|  70 EDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQK 110
                                   56677777777777777777777777777777777776554 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9  19.2    0.0063       1.4       5     111 ..      17     112 ..       9     116 .] 0.50

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0063
                                   HHHHHHHHHHHHHHHH....HHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHH CS
                     Prefoldin   5 leslqaelaqlkeaie....elektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiel 81 
                                   l+ lq++l+ +  ++     el++++++l++l+k   +   +++l +gl+vk + +d             v+k+lee +e+
  gi|15669177|ref|NP_247982.1|  17 LQQLQQQLQMILMQKQsvetELKECKKALEELEK--SSSDEVYKLVGGLFVKRKKED-------------VKKELEEKVET 82 
                                   3444444444444433000033333333333333..444444445566666664444.............35566777777 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  82 lkkkleelekqlekleeeleklkdqittle 111
                                   l+ ++++lekq ekl+  l++l+++i+++ 
  gi|15669177|ref|NP_247982.1|  83 LELRVKTLEKQEEKLQSRLKELQEKIQKMI 112
                                   777777777777777777777777777665 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   6.5   0.00099      0.21       8      48 ..      11      51 ..       9      57 .. 0.84
   2 !   12.7  10.2   0.00047       0.1      56      98 ..      70     112 ..      65     116 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00099
                         DHR10  8 keelaelErkarelqakidalqvvekdlrsciklleeieae 48
                                  +++l +l++ +++lq+ +   q ve++l++c k+lee+e+ 
  gi|15669177|ref|NP_247982.1| 11 QAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKS 51
                                  68889999999999999999999999999999999999886 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00047
                         DHR10  56 kkklkelrdaleekeielrelerkeerlqrqlenaeeklerlr 98 
                                   ++  kel++++e++e +++ le++ee lq +l+  +ek++++ 
  gi|15669177|ref|NP_247982.1|  70 EDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKMI 112
                                   556789999******************************9975 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.3      0.31        67      14      46 ..      18      50 ..      10      53 .. 0.80
   2 !   18.1   6.8   1.1e-05    0.0023       7      44 ..      74     111 ..      68     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.31
                          XhlA 14 dnleervdkleekaaeaeekiknleedlkkles 46
                                    l+++++ + + +  +e+++k+  + l++le+
  gi|15669177|ref|NP_247982.1| 18 QQLQQQLQMILMQKQSVETELKECKKALEELEK 50
                                  566777788888888999999999999999986 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.1e-05
                          XhlA   7 erietkldnleervdkleekaaeaeekiknleedlkkl 44 
                                   +++e+k+++le rv++le+ +++ ++++k+l+e++ k+
  gi|15669177|ref|NP_247982.1|  74 KELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKM 111
                                   579********************************998 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   4.2     0.065        14      38      70 ..      15      47 ..       5      51 .. 0.82
   2 !   17.9   5.6   1.3e-05    0.0029      21      64 ..      68     111 ..      62     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.065
                           CLZ 38 ssLeaLqtrlarLlaeyessqrkLkqRitkLEk 70
                                   +L++Lq++l+ +l + +s++++Lk+  ++LE+
  gi|15669177|ref|NP_247982.1| 15 MQLQQLQQQLQMILMQKQSVETELKECKKALEE 47
                                  589********************9876555553 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.3e-05
                           CLZ  21 kagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLkqR 64 
                                   k+++ +keleekve Le ++++L+++ ++L + +++ q+k+++ 
  gi|15669177|ref|NP_247982.1|  68 KKEDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKM 111
                                   667889**********************************9975 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0  14.5   2.3e-05     0.005      35     121 ..      15     111 ..       5     115 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.3e-05
                                   HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH..........HHHHHHHHHHHHHHCCCHHHHHHHCCHHHHH CS
                     Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkd..........ndnvikksskeleeeilrlketidaqesnir 105
                                    +l++l+++l+ i  +++++e+  ke k+ l+e +ks++d           ++  ++++kelee++++l+ ++++ e++ +
  gi|15669177|ref|NP_247982.1|  15 MQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSDevyklvgglfVKRKKEDVKKELEEKVETLELRVKTLEKQEE 95 
                                   589***********************************9977777766544899999************************ PP

                                   HHHHHHHHHHHHHHHH CS
                     Fib_alpha 106 vLqnvlesneqkiqkL 121
                                   +Lq+ l+++++kiqk+
  gi|15669177|ref|NP_247982.1|  96 KLQSRLKELQEKIQKM 111
                                   **************96 PP

>> BRI3BP  Negative regulator of p53/TP53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.7   2.2e-05    0.0047     140     178 ..      56      93 ..      54      95 .. 0.87
   2 ?   -0.6   0.1       3.7   8.1e+02     157     175 ..      93     111 ..      91     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.2e-05
                        BRI3BP 140 vyvLlgslglyaksseesgasleakvrsLerqvrelnkr 178
                                   vy L g l +  +++e+ +++le+kv+ Le +v+ l+k+
  gi|15669177|ref|NP_247982.1|  56 VYKLVGGL-FVKRKKEDVKKELEEKVETLELRVKTLEKQ 93 
                                   78999999.666777799*******************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.7
                        BRI3BP 157 sgasleakvrsLerqvrel 175
                                   ++++l+ ++++L ++++++
  gi|15669177|ref|NP_247982.1|  93 QEEKLQSRLKELQEKIQKM 111
                                   5678888999999988875 PP

>> UBN_AB  Ubinuclein conserved middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4  14.0   5.2e-05     0.011       4     107 ..       5     115 ..       4     116 .] 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.2e-05
                        UBN_AB   4 gLpeeleesiekLkeaakseeaegkkkfFseelnnllldielqarelstsarsavyshLes.vlpcskdtLlkrlkk.... 79 
                                   +Lp+++++++ +L+++ ++ ++     + ++++++ l + +++ +el++s  ++vy+++   +++ +k+ + k l      
  gi|15669177|ref|NP_247982.1|   5 ELPPQIQAQLMQLQQLQQQLQMIL---MQKQSVETELKECKKALEELEKSSSDEVYKLVGGlFVKRKKEDVKKELEEkvet 82 
                                   79***************9999433...4589****************************8725567777888888778888 PP

                        UBN_AB  80 .....lrlkkeeerlkellekLkeaidevmpeq 107
                                          l+k+ee+l++ l++L+e i++++p +
  gi|15669177|ref|NP_247982.1|  83 lelrvKTLEKQEEKLQSRLKELQEKIQKMIPTA 115
                                   9966555679999******************86 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   5.4    0.0018      0.38      57      96 ..      15      54 ..       9      61 .. 0.64
   2 ?   11.0   9.1    0.0015      0.32      77     117 ..      66     106 ..      64     111 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0018
                    TPR_MLP1_2 57 kelqalreelnelkaeiaelkaeaesakaeleeseeswee 96
                                   +lq+l ++l+ +  + +++++e+++ k++lee e+s + 
  gi|15669177|ref|NP_247982.1| 15 MQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSD 54
                                  5666777777777777777777777777777776666554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0015
                    TPR_MLP1_2  77 kaeaesakaeleeseesweeqkeelekelselekriedlne 117
                                   k + e++k+elee+ e +e + ++lek+ ++l++r+++l+e
  gi|15669177|ref|NP_247982.1|  66 KRKKEDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQE 106
                                   45566677777777777777777777777777777777765 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   8.7   6.2e-05     0.013     604     698 ..      16     112 ..       3     116 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.2e-05
                      Prominin 604 glskihsslyleqlckkltkvnletlaekleelanelsngk..knlkqslkneaqdlraiqqelvlplessvkklkksvkk 682
                                   +l++++ +l +  ++k+ ++++l+++++ leel ++ s +    + +  +k++++d+++  +e+v++le  vk+l+k+ +k
  gi|15669177|ref|NP_247982.1|  16 QLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSDEVykLVGGLFVKRKKEDVKKELEEKVETLELRVKTLEKQEEK 96 
                                   566677777788899*******************99987765455666778888999999999999999999999999999 PP

                      Prominin 683 ldeensdlqesikkll 698
                                   l+++ ++lqe+i+k++
  gi|15669177|ref|NP_247982.1|  97 LQSRLKELQEKIQKMI 112
                                   9999999999998875 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   7.3   0.00022     0.047      54     105 ..       3      54 ..       1      60 [. 0.89
   2 ?    8.1  10.0     0.011       2.5      58      98 ..      70     110 ..      65     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00022
                CENP-F_leu_zip  54 vetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnss 105
                                   v +l  +i+    +l++l+++L+ +  +k+++e el++ ++  +eLe++ s+
  gi|15669177|ref|NP_247982.1|   3 VMELPPQIQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSD 54 
                                   56677788888889**********************************9987 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.011
                CENP-F_leu_zip  58 keeieelaeelreleldLvalrsekeeLekelqkkqervse 98 
                                   ++ ++el+e+ + lel +++l ++ e+L+  l++ qe+++ 
  gi|15669177|ref|NP_247982.1|  70 EDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQK 110
                                   45677888899999999999999999999999999999975 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.0   8.2e-05     0.018     212     307 ..       8     108 ..       4     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.2e-05
                          FUSC 212 prirararalrrllsrmlallallsslarllarlraeeaaavpe.laallaelaal....eaaaaaealeaalaalrarlr 287
                                   p+i+a+  +l++l+++++++l + +s++++l++ +++ ++ +++  +++ + +  l    ++++ +++le+++++l+ r++
  gi|15669177|ref|NP_247982.1|   8 PQIQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSsSDEVYKLVGGLfvkrKKEDVKKELEEKVETLELRVK 88 
                                   6788999999999999999999999999999999988888877666666666666688898889***************** PP

                          FUSC 288 alrraleadadtaalllarl 307
                                    l++++e+ +++  +l++  
  gi|15669177|ref|NP_247982.1|  89 TLEKQEEKLQSRLKELQEKI 108
                                   *******8888887777665 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   4.6   7.3e-05     0.016      20      56 ..      75     111 ..      72     114 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.3e-05
                        GIT_CC  20 elKkalaaseakiqqLlkvNtslsdelrlLQskvqkL 56 
                                   el +++ + e +++ L k  ++l+  l++LQ+k+qk+
  gi|15669177|ref|NP_247982.1|  75 ELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKM 111
                                   78899******************************98 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   6.7     0.015       3.2      39      82 ..       8      51 ..       2      59 .. 0.84
   2 ?   13.7   7.5   0.00019     0.042      76     114 ..      73     111 ..      64     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.015
                      KASH_CCD 39 akLteeieeLkkklkstQqalqkaklleeEleelkalvkeleEk 82
                                   ++ + + +L++  + +Q  l++++++e El e k+ ++ele +
  gi|15669177|ref|NP_247982.1|  8 PQIQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKS 51
                                  577788888988888999999****************9999865 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00019
                      KASH_CCD  76 vkeleEkrarlkaqnkqlekenqsLiakiesLqeenikl 114
                                    keleEk + l+ + k lek ++ L++++++Lqe+++k+
  gi|15669177|ref|NP_247982.1|  73 KKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKM 111
                                   4789********************************997 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4  14.5   0.00028      0.06       6     102 ..      18     115 ..       2     116 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00028
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH. CS
                    Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsv.eetnekvkdankairdArrsvkkLeklapqLldklkelkqleeas 85 
                                   ++ +++++ +l q++ ++++l++ k+ l+e+++s  +e+ ++v     + r  ++  k+Le++++ L+ ++k+l+++ee+ 
  gi|15669177|ref|NP_247982.1|  18 QQLQQQLQMILMQKQSVETELKECKKALEELEKSSsDEVYKLVG-GLFVKRKKEDVKKELEEKVETLELRVKTLEKQEEKL 97 
                                   55677888899999999999999999999998873133444443.33344555666789*********************9 PP

                                   ...HHHHHHHHHHHHHHH CS
                    Laminin_II  86 ss.lsdniseikelIaqA 102
                                   +s l++  ++i+++I  A
  gi|15669177|ref|NP_247982.1|  98 QSrLKELQEKIQKMIPTA 115
                                   999888888899999766 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.6    0.0071       1.5       9      48 ..       9      50 ..       4      61 .. 0.63
   2 ?    9.7   1.8    0.0057       1.2      51      85 ..      74     108 ..      64     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0071
                  Syntaxin-6_N  9 eVqkslnkaeslyrrwerlledtss..stseeldetrteLrk 48
                                  ++q +l ++++l ++ + +l +++s  ++ +e++++ +eL+k
  gi|15669177|ref|NP_247982.1|  9 QIQAQLMQLQQLQQQLQMILMQKQSveTELKECKKALEELEK 50
                                  688889999999999986665555423334444444444444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0057
                  Syntaxin-6_N  51 rsiewdledLeetvriveknpskfkidekelsrrr 85 
                                   +++e+++e Le  v+++ek+++k + + kel+++ 
  gi|15669177|ref|NP_247982.1|  74 KELEEKVETLELRVKTLEKQEEKLQSRLKELQEKI 108
                                   67899999999999999999999999999998864 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.4   0.00014      0.03      71     114 ..       9      52 ..       3      58 .. 0.90
   2 ?    2.1   9.6      0.64   1.4e+02     102     138 ..      68     104 ..      63     110 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00014
                       DUF4201  71 kttktvhalthlkeklhmleselselkkelkekeerlaklrkel 114
                                   +++ ++ +l++l++ l+m+ ++ +  ++elke+++ l++l+k+ 
  gi|15669177|ref|NP_247982.1|   9 QIQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSS 52 
                                   6778999*********************************9975 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.64
                       DUF4201 102 ekeerlaklrkelykvklerdklrkqneklkqqggll 138
                                   +ke+ +++l+++++ ++l+ + l+kq ekl++++ +l
  gi|15669177|ref|NP_247982.1|  68 KKEDVKKELEEKVETLELRVKTLEKQEEKLQSRLKEL 104
                                   5556666666666666666666666666666665554 PP

>> Baculo_p24  Baculovirus P24 capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   7.0   0.00022     0.047      86     172 ..      12     112 ..       3     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00022
                    Baculo_p24  86 peyyvlkqLvrDL.lvGaqse.avdplkdiktqlctlqecleesnvlvn............sttesssn.....enieslr 147
                                   ++++ l+qL + L ++  q++ +  +lk+ k+ l++l+++ +++ ++++            +     ++     e++e   
  gi|15669177|ref|NP_247982.1|  12 AQLMQLQQLQQQLqMILMQKQsVETELKECKKALEELEKSSSDEVYKLVgglfvkrkkedvK-----KEleekvETLELRV 87 
                                   45566666666663334555525568*************99999988889**9987543211.....21334558888888 PP

                    Baculo_p24 148 eilrseeasllsnlnsllesikslq 172
                                   ++l+++e++l s l++l e+i++++
  gi|15669177|ref|NP_247982.1|  88 KTLEKQEEKLQSRLKELQEKIQKMI 112
                                   9999999999999999999999875 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.4    0.0035      0.76      80     115 ..      20      55 ..       9      59 .. 0.89
   2 ?    9.7   7.9    0.0034      0.74      19      59 ..      68     111 ..      64     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0035
                          CdvA  80 Yksaieairellesaleekeeikklleklsklelee 115
                                    +++ ++i  +++s++ e++e kk+le+l+k +++e
  gi|15669177|ref|NP_247982.1|  20 LQQQLQMILMQKQSVETELKECKKALEELEKSSSDE 55 
                                   6899999**********************9987765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0034
                          CdvA  19 tyeeikekleealkklkekakelk...eklkkrlkeledqiksl 59 
                                   + e++k++lee++++l+ + k+l    ekl++rlkel+++i+++
  gi|15669177|ref|NP_247982.1|  68 KKEDVKKELEEKVETLELRVKTLEkqeEKLQSRLKELQEKIQKM 111
                                   56899************999999633379**********99875 PP

>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.63   1.4e+02      74     110 ..      15      51 ..       2      60 .. 0.61
   2 ?   12.7   0.4   0.00051      0.11      40      87 ..      65     112 ..      61     115 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.63
                          ABC1  74 ldleelvdefskslleEldferEAknaekfrenfakl 110
                                   ++l++l ++++  l++    e+E k+ +k+ e+++k 
  gi|15669177|ref|NP_247982.1|  15 MQLQQLQQQLQMILMQKQSVETELKECKKALEELEKS 51 
                                   3566666666777766666666666666666666655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00051
                          ABC1  40 vKvqrpgvkkriksDlellkllakllkkflkelrldleelvdefsksl 87 
                                   vK ++ +vkk++++ +e+l+l +k+l+k  ++l+++l+el ++++k +
  gi|15669177|ref|NP_247982.1|  65 VKRKKEDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKMI 112
                                   9***************************************99999877 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   8.6    0.0051       1.1       9      63 ..       2      56 ..       1      81 [. 0.85
   2 ?    7.1   4.8     0.037       8.1       3      40 ..      73     110 ..      71     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0051
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXX CS
                          YabA  9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekk 63
                                  +++el  q+++ l +l++l+++l+ +l + +++e+e ++ ++ lee ek+++++ 
  gi|15669177|ref|NP_247982.1|  2 TVMELPPQIQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSDEV 56
                                  5789999*************************************76666655544 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.037
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA   3 kkelfdkleeleeqleelleeleelkeelaelleenae 40 
                                   kkel +k+e+le ++++l ++ e+l+++l+el e+ ++
  gi|15669177|ref|NP_247982.1|  73 KKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQK 110
                                   67777888888888888888888888888887776555 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.4    0.0034      0.74     259     293 ..      16      50 ..       3      59 .. 0.63
   2 ?    9.0   4.7    0.0024      0.52     243     282 ..      70     109 ..      64     115 .. 0.42

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0034
                        Tektin 259 aknkleeqlkkvleeiaeleknieeLekairdkea 293
                                     ++l++ql+ +l + +++e++++e +ka+++ e+
  gi|15669177|ref|NP_247982.1|  16 QLQQLQQQLQMILMQKQSVETELKECKKALEELEK 50 
                                   45566666666666666666666666666665554 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0024
                        Tektin 243 eavnealrkrieetedaknkleeqlkkvleeiaeleknie 282
                                   e+v ++l++++e +e   + le+q +k++ +++el+++i+
  gi|15669177|ref|NP_247982.1|  70 EDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQ 109
                                   3333333333333333333333333333333333333333 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   9.2    0.0051       1.1      25     104 ..      10     111 ..       3     116 .] 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0051
                  Baculo_PEP_C  25 irlqnvqilaqlatlldaietqLnalsedlksllaeldt....................rldtlltnLtdalnalq...dt 82 
                                   i++q++q+  ql+++l+ i  q ++++++lk+  ++l++                    + +++ ++L++++ +l+   +t
  gi|15669177|ref|NP_247982.1|  10 IQAQLMQL-QQLQQQLQMILMQKQSVETELKECKKALEEleksssdevyklvgglfvkrKKEDVKKELEEKVETLElrvKT 89 
                                   77777777.777777777777777777777766666665666777788888888888886666777777777777777777 PP

                  Baculo_PEP_C  83 lrneLtnlnsiltnLlssvtNi 104
                                   l+++ + l+s l +L+ ++  +
  gi|15669177|ref|NP_247982.1|  90 LEKQEEKLQSRLKELQEKIQKM 111
                                   7777777777777777666555 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   7.1     0.016       3.5       5      43 ..      16      54 ..      12      75 .. 0.83
   2 ?    9.0   7.8    0.0075       1.6       3      43 ..      70     110 ..      68     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.016
                         Spc24  5 ekfriakelsdleselesleselaelkeeleeleeesee 43
                                  ++++++++l+ + ++ +s+e+el+e k+ leele++s++
  gi|15669177|ref|NP_247982.1| 16 QLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSD 54
                                  6789999****************************9988 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0075
                         Spc24   3 dnekfriakelsdleselesleselaelkeeleeleeesee 43 
                                   ++ k ++ ++++ le  ++ le++ ++l+++l+el+e+ ++
  gi|15669177|ref|NP_247982.1|  70 EDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQK 110
                                   5667789999***************************9886 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   6.4     0.011       2.3      57      97 ..      11      51 ..       3      59 .. 0.64
   2 ?   10.1   8.9    0.0042      0.91      37      77 ..      69     108 ..      63     113 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.011
                        APG6_N 57 eklekeeeelleeLkelekereeleaelaaleeelealeee 97
                                  ++   + ++l+++L+ +  +++++e el++ ++ le+le+ 
  gi|15669177|ref|NP_247982.1| 11 QAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKS 51
                                  44445556677777777777777777777777777777665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0042
                        APG6_N  37 kekkeeekqdeeleeleeeleklekeeeelleeLkeleker 77 
                                   ke++++e  +e++e le ++++lek+ee+l++ Lkel+++ 
  gi|15669177|ref|NP_247982.1|  69 KEDVKKE-LEEKVETLELRVKTLEKQEEKLQSRLKELQEKI 108
                                   3334433.466667777777777777777777777776553 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  21.8    0.0012      0.25       9     101 ..      17     112 ..       3     115 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0012
                       DUF4795   9 lkklqeaieklqeelekleekvkelekrledkekkl.ealkkqieelekvkadkeeveeelaekadkeaLatkvsrdq... 85 
                                   l++lq++++ +  +++++e + ke +k le++ek+  + ++k +  l  vk +ke+v++el+ek+ +  L+ k+ ++q   
  gi|15669177|ref|NP_247982.1|  17 LQQLQQQLQMILMQKQSVETELKECKKALEELEKSSsDEVYKLVGGL-FVKRKKEDVKKELEEKVETLELRVKTLEKQeek 96 
                                   44444444444444444444444444444444433212333333333.3679**********************8888999 PP

                       DUF4795  86 fDeakkeLekmleell 101
                                   +++++keL++++++++
  gi|15669177|ref|NP_247982.1|  97 LQSRLKELQEKIQKMI 112
                                   *************997 PP

>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  11.9    0.0024      0.52      10      88 ..      28     105 ..      16     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0024
                        GCN5L1  10 aerreeqekakkeaiesaaaltealvdklnsgvaeayanqkklekeakalqanvakfakqtdqWlalvesfnsalkeiG 88 
                                     ++++ e++ ke+ +++++l ++  d++ + v  ++++ kk e+  k+l+++v++++ +++   +  e+++s+lke+ 
  gi|15669177|ref|NP_247982.1|  28 LMQKQSVETELKECKKALEELEKSSSDEVYKLVGGLFVKRKK-EDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQ 105
                                   46789999*******************************999.666799999999999999999999999999999985 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2         1   2.2e+02      15      48 ..      13      44 ..       2      61 .. 0.54
   2 ?   11.3   0.7   0.00094       0.2       1      32 [.      76     107 ..      76     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1
                       DUF4988 15 leeqvkelndniealkklleegkviteveensdg 48
                                     q+++l+++++ +  l++++ v te++e ++ 
  gi|15669177|ref|NP_247982.1| 13 QLMQLQQLQQQLQMI--LMQKQSVETELKECKKA 44
                                  333444444444444..44555555666665555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00094
                       DUF4988   1 leddvndlkdrvaaleeqvkelndniealkkl 32 
                                   le++v+ l+ rv++le+q ++l++ ++ l++ 
  gi|15669177|ref|NP_247982.1|  76 LEEKVETLELRVKTLEKQEEKLQSRLKELQEK 107
                                   789**********************9999875 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   8.4    0.0011      0.24     113     192 ..      20     112 ..       5     116 .] 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0011
                        AAA_11 113 vekrlekeekaqlakeiskeleklakelrafeeeeek...............eklkkskekskskleqerrklkkerkels 178
                                   ++++l  ++  +++++++ el++ +k+l++ e+ +++               e +kk+ e++ ++le + ++l+k+ ++l+
  gi|15669177|ref|NP_247982.1|  20 LQQQL--QMILMQKQSVETELKECKKALEELEKSSSDevyklvgglfvkrkkEDVKKELEEKVETLELRVKTLEKQEEKLQ 98 
                                   22222..2235555666666666666666665555558889*********999999999999999**************** PP

                        AAA_11 179 keleeaeesleeev 192
                                   ++l+e +e++++ +
  gi|15669177|ref|NP_247982.1|  99 SRLKELQEKIQKMI 112
                                   *********97644 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.0      0.01       2.2      75     120 ..       9      54 ..       4      60 .. 0.89
   2 ?    9.3   4.7    0.0058       1.3      76     112 ..      73     109 ..      63     113 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.01
                         ATG16  75 kiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklke 120
                                   +iq++  +l+ql+++l+  + +++  ++ l+e +++l++le++++ 
  gi|15669177|ref|NP_247982.1|   9 QIQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSD 54 
                                   68889999********************************998765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0058
                         ATG16  76 iqsleqklaqlreelaelyksrgelaqrllelneelq 112
                                    ++le+k+ +l   +++l k+ ++l++rl+el+e++q
  gi|15669177|ref|NP_247982.1|  73 KKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQ 109
                                   3445555555555555555555555555555555544 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.0    0.0027      0.59     218     256 ..      10      48 ..       3      63 .. 0.66
   2 ?    7.6   6.7     0.011       2.5     213     257 ..      67     112 ..      62     116 .] 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0027
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Filament 218 itelrrqiqsleieleslkkqkasleaqlaeleerleae 256
                                   i+   +q+q+l+ +l+ +  qk+s+e++l+e ++ le+ 
  gi|15669177|ref|NP_247982.1|  10 IQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEEL 48 
                                   555556677777777777777777777777776665543 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.011
                                   X-HHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Filament 213 sakeei.telrrqiqsleieleslkkqkasleaqlaeleerleael 257
                                   + ke++ +el  ++++le  ++ l+kq+++l+++l+el+e++++ +
  gi|15669177|ref|NP_247982.1|  67 RKKEDVkKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKMI 112
                                   5556652478888888888888888888888888888888887655 PP

>> PRP1_N  PRP1 splicing factor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   9.9    0.0034      0.73      62     141 ..      34     114 ..      13     116 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0034
                                   ----.--------------------HHHHHHHHHHHHHHTT-------......-HHHHHHHHHHHHHTT--HHHHHS--- CS
                        PRP1_N  62 gese.glfakaeydedDeeAdriyeeiderlderrkkrreakekeelekvreekpkiqeqFadlkrkLaevseeeWeniPe 141
                                    e+e + ++ka ++ +    d++y+ +     +r+k++ +++ +e++e  + + +++++q + l+ +L+e++e+  ++iP 
  gi|15669177|ref|NP_247982.1|  34 VETElKECKKALEELEKSSSDEVYKLVGGLFVKRKKEDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKMIPT 114
                                   3334455667788899999*****************************999999999999999999999999988888876 PP

>> Bcr-Abl_Oligo  Bcr-Abl oncoprotein oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   3.7   0.00028     0.061      20      55 ..      25      60 ..       5      72 .. 0.89
   2 ?    2.5   4.3      0.66   1.4e+02      29      61 ..      76     108 ..      64     112 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00028
                 Bcr-Abl_Oligo 20 kmeLdsvedieqeLerCkaslrrLekelneekfkvi 55
                                  +m L   + +e eL++Ck+ l +Lek  + e +k++
  gi|15669177|ref|NP_247982.1| 25 QMILMQKQSVETELKECKKALEELEKSSSDEVYKLV 60
                                  6778888999**********************9986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.66
                 Bcr-Abl_Oligo  29 ieqeLerCkaslrrLekelneekfkviyLqtll 61 
                                   +e+ +e+    ++ Lek+ ++ + ++  Lq  +
  gi|15669177|ref|NP_247982.1|  76 LEEKVETLELRVKTLEKQEEKLQSRLKELQEKI 108
                                   444445555555555555544444444444433 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.2      0.07        15      36      70 ..       9      43 ..       5      51 .. 0.84
   2 ?    4.8   0.2      0.16        34       2      25 ..      30      53 ..      29      59 .. 0.86
   3 ?    9.6   2.3    0.0049       1.1       7      84 ..      70     109 ..      64     114 .. 0.49

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.07
                       DUF4164 36 eleaeiealgedrsRLaeeLdqaearaarleevnr 70
                                  +++a++ +l++ +++L + L+q++  +++l+e ++
  gi|15669177|ref|NP_247982.1|  9 QIQAQLMQLQQLQQQLQMILMQKQSVETELKECKK 43
                                  67899999999999999999999999999988765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.16
                       DUF4164  2 vtkeleaaltrLeaaldsLEkavd 25
                                  +++++e  l++ ++al++LEk++ 
  gi|15669177|ref|NP_247982.1| 30 QKQSVETELKECKKALEELEKSSS 53
                                  688999999***********9875 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0049
                       DUF4164   7 eaaltrLeaaldsLEkavdrrleaerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietir 84 
                                   e++ ++Le+++++LE +v+                                       le+  + +++rLk + e+i+
  gi|15669177|ref|NP_247982.1|  70 EDVKKELEEKVETLELRVKT--------------------------------------LEKQEEKLQSRLKELQEKIQ 109
                                   55555666666666655554......................................44444444444444444443 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   5.3      0.31        67      13      58 ..       9      53 ..       4      54 .. 0.79
   2 ?   13.2   4.4   0.00033     0.072      11      53 ..      69     111 ..      65     115 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.31
                          YojJ 13 klkeeLeqiekeleevlkaldeedeClLcelesirekfaeletlas 58
                                  +++ +L+q  ++l++ l+ +  + + + +el++ ++ ++ele+ +s
  gi|15669177|ref|NP_247982.1|  9 QIQAQLMQL-QQLQQQLQMILMQKQSVETELKECKKALEELEKSSS 53
                                  778888885.578888888888888899999999999999988766 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00033
                          YojJ  11 keklkeeLeqiekeleevlkaldeedeClLcelesirekfael 53 
                                   ke++k+eLe+  ++le  +k+l++++e l + l++++ek++++
  gi|15669177|ref|NP_247982.1|  69 KEDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKM 111
                                   99**************************************998 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   2.6      0.17        36      72      96 ..      15      39 ..       1      55 [. 0.53
   2 ?   11.5   2.0    0.0014      0.31      57      95 ..      70     108 ..      58     111 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.17
                       DUF4140 72 aeleeledelaaledelaaaearla 96
                                   +l++l+++l+ +  +++++e++l+
  gi|15669177|ref|NP_247982.1| 15 MQLQQLQQQLQMILMQKQSVETELK 39
                                  3444444444444444444444433 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0014
                       DUF4140  57 vpnreaeeeelkalraeleeledelaaledelaaaearl 95 
                                   +  +++ ee++++l+ ++++le++ ++l+++l+ +++++
  gi|15669177|ref|NP_247982.1|  70 EDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKI 108
                                   333333344588888888888888888888888777766 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  20.7    0.0087       1.9       3      73 ..      17     106 ..      15     115 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0087
                   Uso1_p115_C   3 aseleseaaslkdeneklkaelqslskalesleqk...................eakkaaesqakeleaenkklekelekl 64 
                                   +++l+++ +++  ++++ ++el++ +kale+le++                     kk+ e++ ++le ++k lek+ ekl
  gi|15669177|ref|NP_247982.1|  17 LQQLQQQLQMILMQKQSVETELKECKKALEELEKSssdevyklvgglfvkrkkeDVKKELEEKVETLELRVKTLEKQEEKL 97 
                                   6899*******************************9999977777775555444444444444445555555555555555 PP

                   Uso1_p115_C  65 raelkeeke 73 
                                   +++lke +e
  gi|15669177|ref|NP_247982.1|  98 QSRLKELQE 106
                                   555555555 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.1     0.018         4      24      64 ..      13      51 ..       4      61 .. 0.57
   2 ?    9.4   6.3    0.0059       1.3      16      56 ..      67     107 ..      63     116 .] 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.018
                          YlqD 24 qlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeq 64
                                  ql  q++ql+++lq + +q++ +++e+k+ + ++ ee++++
  gi|15669177|ref|NP_247982.1| 13 QL-MQLQQLQQQLQMILMQKQSVETELKECK-KALEELEKS 51
                                  22.3566677777777777777777775533.344444444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0059
                          YlqD  16 klKeelqqqlqaqieqldkelqqLefqakrlikeikkqsaq 56 
                                   + Ke+++++l++++e+l+  ++ Le q+++l + +k+ +++
  gi|15669177|ref|NP_247982.1|  67 RKKEDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEK 107
                                   78*****************************9999774433 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  21.3     0.028         6      20      99 ..      12     111 ..       2     116 .] 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.028
                          HemX  20 aglyylgqqqvqeltaev..aelqqqlaaleqqlaq..................veaekeqkqeleerlqqlaeklealek 80 
                                   a l++l+q+q+q +   +  ++++++l++ +++l++                   ++++  k+elee++++l+ ++++lek
  gi|15669177|ref|NP_247982.1|  12 AQLMQLQQLQQQLQMILMqkQSVETELKECKKALEEleksssdevyklvgglfvKRKKEDVKKELEEKVETLELRVKTLEK 92 
                                   5566666655543332223466666666666666667777888*********966666777999***************** PP

                          HemX  81 eleqlqkqleelqqqlskv 99 
                                   + e+lq++l+elq++++k+
  gi|15669177|ref|NP_247982.1|  93 QEEKLQSRLKELQEKIQKM 111
                                   *****************97 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.9     0.057        12      29      63 ..       9      43 ..       1      59 [. 0.59
   2 ?    9.1   1.6    0.0082       1.8      14      52 ..      74     109 ..      65     114 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.057
                       NPV_P10 29 dvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63
                                  ++q++l ++++l+++L+ +  q +++et++++ ++
  gi|15669177|ref|NP_247982.1|  9 QIQAQLMQLQQLQQQLQMILMQKQSVETELKECKK 43
                                  34555555555555555555555555555555444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0082
                       NPV_P10  14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLa 52 
                                   k++++kV+ l+ +v+ ++++ ++   l+++L +++++++
  gi|15669177|ref|NP_247982.1|  74 KELEEKVETLELRVKTLEKQEEK---LQSRLKELQEKIQ 109
                                   46788888888888888776665...5555555555554 PP

>> LppA  Lipoprotein confined to pathogenic Mycobacterium
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.7     0.052        11      14      51 ..      22      63 ..      11      81 .. 0.72
   2 ?    6.6   1.2     0.032       6.9      12      50 ..      75     114 ..      65     116 .] 0.74

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.052
                                  HHHHHHHGGG--HHHHHHHHHHHHHHH....HHHHHHHSTT- CS
                          LppA 14 aeaedelrqkPslEeaeeqleallari....adaisalvpgl 51
                                  ++++  l+qk s+E++ ++ +++l+++     d++ +lv+gl
  gi|15669177|ref|NP_247982.1| 22 QQLQMILMQKQSVETELKECKKALEELekssSDEVYKLVGGL 63
                                  6778899*******9988877777766111156777777776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.032
                                   HHHHHHHHHGGG.--HHHHHHHHHHHHHHHHHHHHHHSTT CS
                          LppA  12 evaeaedelrqk.PslEeaeeqleallariadaisalvpg 50 
                                   e++e  ++l+ +  +lE+ ee+l++ l+++ ++i++++p 
  gi|15669177|ref|NP_247982.1|  75 ELEEKVETLELRvKTLEKQEEKLQSRLKELQEKIQKMIPT 114
                                   4455555554442389*********************996 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   9.6    0.0034      0.74     166     259 ..      12     111 ..       2     116 .] 0.33

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0034
                  Exonuc_VII_L 166 ekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlk.............ekleekkerlk 233
                                    +  +l++l+++l+   ++ ++ + +               lk+ +++leel+++ +             +k e+ k++l+
  gi|15669177|ref|NP_247982.1|  12 AQLMQLQQLQQQLQMILMQKQSVETE---------------LKECKKALEELEKSSSdevyklvgglfvkRKKEDVKKELE 77 
                                   22233333333333222222222222...............3333344444333331234444444333311122222221 PP

                  Exonuc_VII_L 234 klkerle........lleekkerleeleekleal 259
                                   +  e le        + e+ ++rl+el+ek++++
  gi|15669177|ref|NP_247982.1|  78 EKVETLElrvktlekQEEKLQSRLKELQEKIQKM 111
                                   1111111222222222333444444455555544 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.7     0.054        12      67     101 ..      16      50 ..       3      69 .. 0.54
   2 ?    9.1   4.5    0.0057       1.2      79     120 ..      70     111 ..      65     114 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.054
                       DUF1664  67 ridrvdkkldeqkeiskeikeevtevredlseige 101
                                   ++++++++l+     +++++ e++e ++ l+e+++
  gi|15669177|ref|NP_247982.1|  16 QLQQLQQQLQMILMQKQSVETELKECKKALEELEK 50 
                                   34445555555555555555555555555555443 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0057
                       DUF1664  79 keiskeikeevtevredlseigedvesvkeavegleskleri 120
                                   ++++ke++e+v++++  +++++++ e++++  ++l++k++++
  gi|15669177|ref|NP_247982.1|  70 EDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKM 111
                                   445555666666666666666666666666666666666554 PP

>> Rotamase  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.1    0.0013      0.28      12      75 ..      21      83 ..       7      86 .. 0.86
   2 ?    2.8   0.9       1.1   2.3e+02       9      31 ..      88     110 ..      83     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0013
                                  ---HHHHHHHHHHHHCCTCCCHHHHHHHHCCC-.-CHHHCCTTEEECEETTTS-CCCHHHHCCS CS
                      Rotamase 12 ekeraeakakaeeileqlksgedtFeelArkySddknsakngGdlgwvekgqlppefekaafsl 75
                                  +++ + +  + +++  +lk+ ++++eel +  S d+  +  gG   + +k+++++e+e+++++l
  gi|15669177|ref|NP_247982.1| 21 QQQLQMILMQKQSVETELKECKKALEELEKSSS-DEVYKLVGGLFVKRKKEDVKKELEEKVETL 83
                                  5566666777889999999999******99999.9999*********************99887 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 1.1
                                   SE----HHHHHHHHHHHHCCTCC CS
                      Rotamase   9 kasekeraeakakaeeileqlks 31 
                                   k+ ek++++ + +++e++e++++
  gi|15669177|ref|NP_247982.1|  88 KTLEKQEEKLQSRLKELQEKIQK 110
                                   34789999999******999986 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   4.1      0.14        30       5      37 ..      16      48 ..       9      52 .. 0.59
   2 ?    7.5   0.2     0.021       4.6       7      37 ..      81     111 ..      70     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.14
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                        WXG100  5 dpeelrqaaarfqkqaeeledelqrlkaevdal 37
                                  + ++l+q  + +  q++++e+el+++k+ +++l
  gi|15669177|ref|NP_247982.1| 16 QLQQLQQQLQMILMQKQSVETELKECKKALEEL 48
                                  345555555555566777777777777666666 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.021
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                        WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdal 37 
                                   e l+   +++ kq+e+l+++l++l+ +++++
  gi|15669177|ref|NP_247982.1|  81 ETLELRVKTLEKQEEKLQSRLKELQEKIQKM 111
                                   5566667889999999999999999999987 PP

>> FAA_hydro_N_2  Fumarylacetoacetase N-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.4     0.013       2.9      23      62 ..      12      51 ..       9      59 .. 0.86
   2 ?    2.4   0.1      0.99   2.1e+02      30      57 ..      78     105 ..      61     114 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.013
                 FAA_hydro_N_2 23 kkavdaseiaptlqaaLdnWdevepaLeelyeaLnagtak 62
                                  ++ ++ +++ ++lq +L + ++ve++L+e  +aL++ +++
  gi|15669177|ref|NP_247982.1| 12 AQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKS 51
                                  577899999*************************987754 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.99
                 FAA_hydro_N_2  30 eiaptlqaaLdnWdevepaLeelyeaLn 57 
                                   e ++tl   +   ++ e++L+++ ++L+
  gi|15669177|ref|NP_247982.1|  78 EKVETLELRVKTLEKQEEKLQSRLKELQ 105
                                   3344444444444445555555555554 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.7      0.07        15      22      77 ..      15      54 ..       8      64 .. 0.56
   2 ?    9.9   4.8    0.0031      0.68      37      80 ..      70     113 ..      62     116 .] 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.07
                       DUF4446 22 vklkklkkkykklmkgkdgksleellkekleeveelkeeseelekeieeleeklkk 77
                                  ++l                ++l+++l+  l + +++++e +e++k +eele++ + 
  gi|15669177|ref|NP_247982.1| 15 MQL----------------QQLQQQLQMILMQKQSVETELKECKKALEELEKSSSD 54
                                  334................4555555555555555555555555555555555544 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0031
                       DUF4446  37 gkdgksleellkekleeveelkeeseelekeieeleeklkkslq 80 
                                   ++ +k+lee++++   +v++l++++e+l+++++el+ek++k++ 
  gi|15669177|ref|NP_247982.1|  70 EDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKMIP 113
                                   345788999999999999*********************99875 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  10.0    0.0078       1.7     129     225 ..      18     110 ..       4     116 .] 0.66

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0078
                       DUF4407 129 aaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakldat 209
                                   ++l+++l+ +  q ++ ++e+++ +++l++l++   +e+      g   ++ k+++ ke +++ ++++ ++++l+++   +
  gi|15669177|ref|NP_247982.1|  18 QQLQQQLQMILMQKQSVETELKECKKALEELEKSSSDEVYKL-VGGLFVKRKKEDVKKELEEKVETLELRVKTLEKQ---E 94 
                                   237777788888888888888888888888888888888854.4466667777777778888888888888888877...4 PP

                       DUF4407 210 arlaalraelaeleae 225
                                   ++l+++ +el+e  ++
  gi|15669177|ref|NP_247982.1|  95 EKLQSRLKELQEKIQK 110
                                   4444444444444333 PP

>> Herpes_UL6  Herpesvirus UL6 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.3    0.0022      0.47     370     417 ..       6      53 ..       2      60 .. 0.81
   2 ?    5.0   5.5     0.034       7.3     362     405 ..      68     111 ..      60     116 .] 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0022
                    Herpes_UL6 370 leeqineqfdtiekLkkenelllkklkelekeLerlreeakkeakare 417
                                   l  qi+ q+ ++++L+++ +++l + +++e+eL+++++  ++  k ++
  gi|15669177|ref|NP_247982.1|   6 LPPQIQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSS 53 
                                   5579********************************776665333333 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.034
                    Herpes_UL6 362 vsnsvikcleeqineqfdtiekLkkenelllkklkelekeLerl 405
                                    ++ v k lee+++++   +++L+k+ e+l+++lkel+++++++
  gi|15669177|ref|NP_247982.1|  68 KKEDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKM 111
                                   578999********************************999886 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  16.6      0.11        24      44     124 ..       9     109 ..       7     116 .] 0.70

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.11
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHTT-SS................. CS
                         Nup54  44 evaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelsh....Rllrllrkleilrsrgy................. 103
                                   +++++  +l++++++l+ +   +++++ ++l+++kk   el++     +++l+  l + r++                   
  gi|15669177|ref|NP_247982.1|   9 QIQAQLMQLQQLQQQLQMIL-MQKQSVETELKECKKALEELEKsssdEVYKLVGGLFVKRKKEDvkkeleekvetlelrvk 88 
                                   67888899999999999999.888899999999999888886611114444444444444443366666666666666666 PP

                                   ---SSHHHHHHHHHHHHHHHS CS
                         Nup54 104 aldaeEeelrarletleaqln 124
                                    l+++Ee+l++rl++l+++++
  gi|15669177|ref|NP_247982.1|  89 TLEKQEEKLQSRLKELQEKIQ 109
                                   888889999999988888887 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   8.4       0.1        22     118     169 ..      13      63 ..       9      70 .. 0.79
   2 ?    9.3  10.2    0.0032      0.68      65     105 ..      69     109 ..      63     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.1
                       DUF4618 118 kavqIanlvrqlqqlkdsqqdeldeleelikevleklskkiqkkkekllksl 169
                                   + +q+++l++qlq +  ++q    el+e +k+ le+l+k+   +  kl+  l
  gi|15669177|ref|NP_247982.1|  13 QLMQLQQLQQQLQMILMQKQSVETELKE-CKKALEELEKSSSDEVYKLVGGL 63 
                                   6799999999999999999999999998.56778999998888877777665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0032
                       DUF4618  65 leqakaeLqeweekeekklekLeqqleqlnakvqklqeeln 105
                                    e++k+eL+e+ e++e +++ Le+q e+l++++++lqe+++
  gi|15669177|ref|NP_247982.1|  69 KEDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQ 109
                                   4799**********************************987 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.9    0.0046         1      24      63 ..      15      51 ..       5      60 .. 0.67
   2 ?    5.3   5.8      0.14        31       1      37 [.      76     112 ..      68     116 .] 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0046
                       DUF4404 24 alLeslaedieellaeedaaaeeeelaerlneaverFeee 63
                                   +L++l+++++++l ++++ + e  l+ + ++a+e+ e++
  gi|15669177|ref|NP_247982.1| 15 MQLQQLQQQLQMILMQKQSVETE--LK-ECKKALEELEKS 51
                                  46777777777777777777666..33.366666666654 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.14
                       DUF4404   1 LkelLekLheeLeqnesldeetralLeslaedieell 37 
                                   L+e++e+L+  ++  e+ +e+ +++L++l+e+i++++
  gi|15669177|ref|NP_247982.1|  76 LEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKMI 112
                                   6788999999999999999999999999999999987 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   6.4     0.051        11      36      74 ..      16      54 ..       8      59 .. 0.89
   2 ?    8.5  12.7      0.01       2.2      24      66 ..      67     109 ..      64     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.051
                 Tropomyosin_1 36 eiksLtkknqqleeevekleeklkeakekaeesekkktn 74
                                  ++++L++++q++  +   +e++lke k+++ee ek +++
  gi|15669177|ref|NP_247982.1| 16 QLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSD 54
                                  7899***************************99998765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.01
                 Tropomyosin_1  24 KeleqenlekeqeiksLtkknqqleeevekleeklkeakekae 66 
                                   +++e+ ++e e++++ L+ ++++le++ ekl+++lke +ek +
  gi|15669177|ref|NP_247982.1|  67 RKKEDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQ 109
                                   6778888889999999999999999999999999999888865 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  23.0     0.022       4.7      47     151 ..      15     111 ..       4     114 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.022
                     Golgin_A5  47 aeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryle 127
                                   ++l++l+q+ +++  + q+++++++++++ l++le++         +++ +l   l   +++ke+v++ele++ e l+   
  gi|15669177|ref|NP_247982.1|  15 MQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSS-------SDEVYKLVGGLF-VKRKKEDVKKELEEKVETLELRV 87 
                                   33344444444444444444444444444444444433.......333444444444.35567778888888888888888 PP

                     Golgin_A5 128 eelvrskatlqsrikdrekeiekl 151
                                   + l ++ ++lqsr+k+ +++i+k+
  gi|15669177|ref|NP_247982.1|  88 KTLEKQEEKLQSRLKELQEKIQKM 111
                                   888888888888888888888875 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1  19.4       0.3        65      12     105 ..       8     108 ..       3     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.3
                     Laminin_I  12 eapykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatq...vlakaqkvnaese....rtlnnak 85 
                                   ++++  +++l++l+++Lq  l ++++ + +++  +k+le+L++     + k++    v +k ++v++e e    +   + k
  gi|15669177|ref|NP_247982.1|   8 PQIQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSDEVYKLVGglfVKRKKEDVKKELEekveTLELRVK 88 
                                   67888899*********************************9866555555554333567777777666511104555899 PP

                     Laminin_I  86 eLaekikkladnikeilekv 105
                                   +L+++ +kl+  +ke+ ek+
  gi|15669177|ref|NP_247982.1|  89 TLEKQEEKLQSRLKELQEKI 108
                                   ****************9997 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4       1.5   3.3e+02      81     102 ..       8      29 ..       2      31 .. 0.72
   2 ?    9.2  14.0    0.0062       1.3      34     104 ..      34     108 ..      30     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHHHHHHHHHC CS
                  Seryl_tRNA_N  81 eelkaleaelkeleaeleklll 102
                                    +++a   +l++l+++l+ +l+
  gi|15669177|ref|NP_247982.1|   8 PQIQAQLMQLQQLQQQLQMILM 29 
                                   5677777788888888888876 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0062
                                   HHHHHHHHHHHHHHH.HHHHHHHHHHCCCC..CCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                  Seryl_tRNA_N  34 ldekrrelqveleel.qaerNelskeIgka..kkkk.edaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                   ++++ +e++++leel ++ + e+ k +g +  k+kk + ++el ++v++l  ++k+le+++++l+++l++l  +i
  gi|15669177|ref|NP_247982.1|  34 VETELKECKKALEELeKSSSDEVYKLVGGLfvKRKKeDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKI 108
                                   68899**********4457899******973344455557789999***********************998877 PP

>> Ribosomal_S20p  Ribosomal protein S20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   8.2       1.7   3.7e+02      40      59 ..      82     111 ..       9     114 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 1.7
                                   C..........-HHHHHHHHHHHHHHHHHH CS
                Ribosomal_S20p  40 a..........dkekaqealkkaiskidka 59 
                                   +          ++ek+q  lk+++ ki+k+
  gi|15669177|ref|NP_247982.1|  82 TlelrvktlekQEEKLQSRLKELQEKIQKM 111
                                   122222222225566777777777777776 PP

>> DUF3287  Protein of unknown function (DUF3287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.0      0.53   1.1e+02      62      98 ..      15      51 ..       9      61 .. 0.69
   2 ?   10.7   2.6    0.0015      0.33      65     102 ..      67     104 ..      53     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.53
                       DUF3287 62 ekHrrlcderqklgkkrqtleaRiarveRklrelese 98
                                  ++ ++l ++ q ++ + q++e  + + ++ l ele  
  gi|15669177|ref|NP_247982.1| 15 MQLQQLQQQLQMILMQKQSVETELKECKKALEELEKS 51
                                  5666777777777777777777777777777777754 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0015
                       DUF3287  65 rrlcderqklgkkrqtleaRiarveRklreleseprdW 102
                                   r++ d +++l  k++tle R+  +e++  +l+s +++ 
  gi|15669177|ref|NP_247982.1|  67 RKKEDVKKELEEKVETLELRVKTLEKQEEKLQSRLKEL 104
                                   88999****************************98865 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   6.7       1.1   2.4e+02      29      66 ..      15      47 ..       3      60 .. 0.50
   2 ?   12.7   3.3   0.00061      0.13      12      43 ..      82     113 ..      81     116 .] 0.92

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 1.1
                   Cep57_MT_bd 29 lelqelaaqynaldpslgkrkRkdLaeeleelvkrlEa 66
                                  ++lq+l++q++         ++++++ el+e  k+lE+
  gi|15669177|ref|NP_247982.1| 15 MQLQQLQQQLQMI-----LMQKQSVETELKECKKALEE 47
                                  3334444444333.....34555555555555555444 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00061
                   Cep57_MT_bd  12 aLaevlkeLedEfehlklelqelaaqynaldp 43 
                                   +L+  +k+Le++ e+l+ +l+el+++++++ p
  gi|15669177|ref|NP_247982.1|  82 TLELRVKTLEKQEEKLQSRLKELQEKIQKMIP 113
                                   7999*************************976 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   4.0     0.089        19      45      89 ..       9      53 ..       2      56 .. 0.84
   2 ?    8.7   5.5    0.0096       2.1      61      95 ..      74     108 ..      64     112 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.089
                       BLOC1_2 45 slekkleklnekyeelqpylqqidqiekqvteLeeavseLDeysk 89
                                  +++++l +l++++++lq  l q + +e++++e ++a +eL++ s+
  gi|15669177|ref|NP_247982.1|  9 QIQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSS 53
                                  577888899999999999999999999999999999999988765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0096
                       BLOC1_2  61 qpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                   +++ ++++ +e +v++Le+  ++L +  keL++k+
  gi|15669177|ref|NP_247982.1|  74 KELEEKVETLELRVKTLEKQEEKLQSRLKELQEKI 108
                                   23334666666666666666666666666666665 PP

>> TIR-like  Predicted nucleotide-binding protein containing TIR-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2       2.4   5.1e+02      16      48 ..      20      52 ..       9      60 .. 0.54
   2 ?    9.6   0.9    0.0039      0.85       8      50 ..      68     110 ..      63     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 2.4
                      TIR-like 16 vkelLeklglepiileeqvnkgktiiekleeal 48
                                  +++ L+ + ++   +e++ ++ k  +e+le+++
  gi|15669177|ref|NP_247982.1| 20 LQQQLQMILMQKQSVETELKECKKALEELEKSS 52
                                  333333222333334445555566666666665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0039
                      TIR-like   8 edeeaaeevkelLeklglepiileeqvnkgktiiekleealks 50 
                                   ++e++++e++e +e+l+l++ +le+q +k+++ +++l+e++++
  gi|15669177|ref|NP_247982.1|  68 KKEDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQK 110
                                   6899**********************************99986 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.5      0.39        85      15      30 ..      10      25 ..       8      28 .. 0.86
   2 ?   -0.1   0.0       3.9   8.4e+02       5      17 ..      38      50 ..      32      55 .. 0.55
   3 ?    7.9   0.3     0.012       2.6       6      31 ..      74      99 ..      70     103 .. 0.90
   4 ?    0.8   0.1         2   4.3e+02       8      21 ..      97     110 ..      92     112 .. 0.52

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.39
                     DASH_Dam1 15 LdknledLqqihesLs 30
                                  ++++l++Lqq++++L+
  gi|15669177|ref|NP_247982.1| 10 IQAQLMQLQQLQQQLQ 25
                                  67899********996 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.9
                     DASH_Dam1  5 faeLaDsletLdk 17
                                  ++e +++le+L+k
  gi|15669177|ref|NP_247982.1| 38 LKECKKALEELEK 50
                                  4444445555544 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.012
                     DASH_Dam1  6 aeLaDsletLdknledLqqihesLsd 31
                                  +eL++++etL+ +++ L++ +e+L++
  gi|15669177|ref|NP_247982.1| 74 KELEEKVETLELRVKTLEKQEEKLQS 99
                                  69*****************9999986 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 2
                     DASH_Dam1   8 LaDsletLdknled 21 
                                   L+  l++L++++++
  gi|15669177|ref|NP_247982.1|  97 LQSRLKELQEKIQK 110
                                   44444444444444 PP

>> SPACA9  Sperm acrosome-associated protein 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.5     0.035       7.6      74     105 ..      16      47 ..      10      57 .. 0.77
   2 ?    6.2   1.4     0.036       7.8       2      38 ..      75     111 ..      74     116 .] 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.035
                        SPACA9  74 dLkklrkkleesnaerertaelLekcktLlkd 105
                                   +L++l+++l++   ++++ +  L++ck+ l++
  gi|15669177|ref|NP_247982.1|  16 QLQQLQQQLQMILMQKQSVETELKECKKALEE 47 
                                   68888888888888888888888888887765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.036
                        SPACA9   2 evkqqlkklelryklfkqqqktfisALeraresaldk 38 
                                   e+++++ +lelr k++++q   + s L++ +e+++++
  gi|15669177|ref|NP_247982.1|  75 ELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKM 111
                                   78999***********************999998544 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   3.5      0.15        32      66      99 .]      15      48 ..       2      48 .. 0.82
   2 ?    8.9   2.9     0.015       3.2      65      99 .]      70     104 ..      55     111 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.15
                       DUF5320 66 taeaskeeekelLeeqaeaLeeeleaikkrlkel 99
                                  ++ ++ +++ +++  q+++ e el++ kk l+el
  gi|15669177|ref|NP_247982.1| 15 MQLQQLQQQLQMILMQKQSVETELKECKKALEEL 48
                                  556677889999999999***********99997 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.015
                       DUF5320  65 etaeaskeeekelLeeqaeaLeeeleaikkrlkel 99 
                                   e  +++ ee+ e Le + ++Le++ e++++rlkel
  gi|15669177|ref|NP_247982.1|  70 EDVKKELEEKVETLELRVKTLEKQEEKLQSRLKEL 104
                                   44556667777777777777777777777777775 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   8.0       6.7   1.5e+03      26      62 ..      15      51 ..      11      53 .. 0.88
   2 ?   12.3  14.3   0.00064      0.14      25      59 ..      77     111 ..      65     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 6.7
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1 26 aeieeLerrvkaLekeNksLkseleelkkevekLksk 62
                                  ++ ++L+++ + +  + +s   el+e kk  e+L++ 
  gi|15669177|ref|NP_247982.1| 15 MQLQQLQQQLQMILMQKQSVETELKECKKALEELEKS 51
                                  667899999999999****************999875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00064
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  25 qaeieeLerrvkaLekeNksLkseleelkkevekL 59 
                                   ++++e Le rvk+Lek+ ++L+s+l+el+++++k+
  gi|15669177|ref|NP_247982.1|  77 EEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKM 111
                                   578999***************************98 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.7     0.024       5.2      73     107 ..      17      51 ..       3      59 .. 0.82
   2 ?    6.5   2.9     0.032       6.8      68     105 ..      75     112 ..      61     116 .] 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.024
                        Nsp1_C  73 qnkidqeLeyiesqqdeLeslLdnyEkeleellsk 107
                                    +++ q+L++i  q++  e+ L++  k leel ++
  gi|15669177|ref|NP_247982.1|  17 LQQLQQQLQMILMQKQSVETELKECKKALEELEKS 51 
                                   37899*******************99999999854 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.032
                        Nsp1_C  68 eaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleell 105
                                   e e++ + ++ + + +e+q + L+s L+++ ++++++ 
  gi|15669177|ref|NP_247982.1|  75 ELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKMI 112
                                   56777788889999999999999999999999999987 PP

>> DUF3958  Protein of unknown function (DUF3958)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  24.1     0.082        18       1     100 [.      15     111 ..      15     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.082
                       DUF3958   1 kkleelnqelrelaekqeenekelkkqeqlkeeyeehfnqskrlfdelletfrkdeeshlfeklrdevqrlsrklredLEe 81 
                                   ++l++l+q+l+ ++ +++++e elk+ ++  ee+e+    s ++++ ++  f k ++  + ++l++ v  l+  ++  LE+
  gi|15669177|ref|NP_247982.1|  15 MQLQQLQQQLQMILMQKQSVETELKECKKALEELEKS--SSDEVYKLVGGLFVKRKKEDVKKELEEKVETLELRVK-TLEK 92 
                                   589*******************************975..5789****************************99875.7*** PP

                       DUF3958  82 eeeeLkrekrqLedqeeel 100
                                   +ee+L+++ ++L+++++ +
  gi|15669177|ref|NP_247982.1|  93 QEEKLQSRLKELQEKIQKM 111
                                   ***************9976 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   5.3      0.11        23      47      86 ..      11      50 ..       3      59 .. 0.55
   2 ?    8.8   5.9    0.0042       0.9      51      91 ..      71     111 ..      65     116 .] 0.59

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.11
                       DUF3450 47 qellaeyralkeeleslevyneqlerlvasqeqeiaslee 86
                                  q  l ++++l+++l+ + ++++ +e  +++ ++ +++le+
  gi|15669177|ref|NP_247982.1| 11 QAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEK 50
                                  4444455555555555555555555555555555555554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0042
                       DUF3450  51 aeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                   +  ++l+e++e le+  + le++ +++++++++l+e+i+++
  gi|15669177|ref|NP_247982.1|  71 DVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKM 111
                                   44455666666666666666666666666666666666554 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.6     0.051        11      52      84 ..      11      43 ..       5      59 .. 0.75
   2 ?    7.3   6.4     0.023       4.9      41      83 ..      73     115 ..      66     116 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.051
                                  CCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        DivIVA 52 eeklkeykeleetLkktlvvaqetaeevkanak 84
                                  + +l++ ++l+++L+  l+  q+   e+k+  k
  gi|15669177|ref|NP_247982.1| 11 QAQLMQLQQLQQQLQMILMQKQSVETELKECKK 43
                                  678888888888888888888888888876444 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.023
                                   HHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        DivIVA  41 neelkekvkeleeklkeykeleetLkktlvvaqetaeevkana 83 
                                   ++el+ekv++le ++k  +++ee+L+  l   qe  +++  +a
  gi|15669177|ref|NP_247982.1|  73 KKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKMIPTA 115
                                   689***********************99988888877776666 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   7.0     0.091        20      89     141 ..       5      57 ..       2      63 .. 0.83
   2 ?    9.0   7.0    0.0043      0.92      70     108 ..      70     108 ..      54     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.091
                  HAUS-augmin3  89 eLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraena 141
                                   eL  + + +l +l++Lq q   +  +++++e+e ke kk l+e++++ + e  
  gi|15669177|ref|NP_247982.1|   5 ELPPQIQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSDEVY 57 
                                   66667788999999999999999999999999999999999999998877765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0043
                  HAUS-augmin3  70 evileeeeesleaLeqelqeLqkekalklkrlnkLqvqa 108
                                   e   +e+ee++e Le  +++L+k+++ +++rl++Lq  +
  gi|15669177|ref|NP_247982.1|  70 EDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKI 108
                                   4456788889*************************9766 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.8     0.036       7.8      33      71 ..      37      84 ..      14      88 .. 0.76
   2 ?    8.7   4.0     0.012       2.6      15      66 ..      61     111 ..      58     116 .] 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.036
                          YtxH 33 kaddlkekakelleeakeka.........kekaedlkekvkekadelk 71
                                  ++++ k+ ++el ++ ++ +         k+k ed+k++++ek++ l 
  gi|15669177|ref|NP_247982.1| 37 ELKECKKALEELEKSSSDEVyklvgglfvKRKKEDVKKELEEKVETLE 84
                                  455555555555555555558888999****************99875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.012
                          YtxH  15 glLlAPksGketRkdlkekaddlkekakelleeakekakekaedlkekvkek 66 
                                   g L+  ++ ++++k+l ek+++l  ++k l e+ +ek +++ ++l+ek+++ 
  gi|15669177|ref|NP_247982.1|  61 GGLFVKRKKEDVKKELEEKVETLELRVKTL-EKQEEKLQSRLKELQEKIQKM 111
                                   556667777999999999999999999665.888899999999999999986 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.2      0.52   1.1e+02     191     223 ..      19      51 ..       9      62 .. 0.63
   2 ?    9.5   2.4    0.0027      0.59     190     226 ..      74     110 ..      52     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.52
                                   HHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHH CS
                        FliD_C 191 tlqtasknltkqikdldkkiedldkrletleer 223
                                   +lq++ +++  q+++++++ ++ +k+le+le++
  gi|15669177|ref|NP_247982.1|  19 QLQQQLQMILMQKQSVETELKECKKALEELEKS 51 
                                   445555555566666666666666666666654 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0027
                                   SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHH CS
                        FliD_C 190 gtlqtasknltkqikdldkkiedldkrletleerlkk 226
                                   + l+++ ++l+ ++k+l+k+ e+l++rl++l+e+++k
  gi|15669177|ref|NP_247982.1|  74 KELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQK 110
                                   4566777788888888888888888888888887765 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  13.8     0.031       6.7      29     107 ..      14     109 ..       5     116 .] 0.68

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.031
                    V_ATPase_I  29 vrrcdemerklrfleeeieklekavikeeea.................eesleapeekeldeleeelekleeelkelnenl 92 
                                   + ++++++++l+++  + ++ e++  ++++a                     ++++e+  +elee++e+le ++k+l++++
  gi|15669177|ref|NP_247982.1|  14 LMQLQQLQQQLQMILMQKQSVETELKECKKAleeleksssdevyklvgGLFVKRKKEDVKKELEEKVETLELRVKTLEKQE 94 
                                   455555555555555555554555544444444444444444555666556666777777788****************** PP

                    V_ATPase_I  93 eklkkelnelvelka 107
                                   ekl+++l+el+e+ +
  gi|15669177|ref|NP_247982.1|  95 EKLQSRLKELQEKIQ 109
                                   **********99755 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  24.4     0.053        11      46     145 ..      11     113 ..       5     116 .] 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.053
                 Jnk-SapK_ap_N  46 eeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqe..kveqle.eenrelelkaknaadqlsrle 123
                                   +++  +l++l+++l+ +  +++    + k+ ++ lee+e++  +e  +l     v++ + + ++ele k++ ++ ++++le
  gi|15669177|ref|NP_247982.1|  11 QAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSDEVYKLVGglFVKRKKeDVKKELEEKVETLELRVKTLE 91 
                                   566678888888998888888888888888889999999999999999876223444441556789999999999999999 PP

                 Jnk-SapK_ap_N 124 ekeaelkkeysklheretellk 145
                                   ++e++l+++ ++l+e+ ++++ 
  gi|15669177|ref|NP_247982.1|  92 KQEEKLQSRLKELQEKIQKMIP 113
                                   9999999999999998888875 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   9.2     0.069        15     114     157 ..       9      52 ..       4      61 .. 0.80
   2 ?    8.1   4.2     0.009       1.9     138     174 ..      75     111 ..      52     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.069
                       DUF2968 114 qiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqr 157
                                   qi+a+  ++++Lq++l++   Q+q+v+++ k+ +k  + Le+  
  gi|15669177|ref|NP_247982.1|   9 QIQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSS 52 
                                   78888888999999999999999999999888888888888765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.009
                       DUF2968 138 avaerQkqarkeaaaLeaqreaaqaqlralqrqirqL 174
                                   +++e+ +++   +++Le+q e++q++l++lq++i+++
  gi|15669177|ref|NP_247982.1|  75 ELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKM 111
                                   455566666778899*******************975 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  17.7     0.053        11     330     411 ..      29     111 ..       4     115 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.053
                          FapA 330 ldepelkeklkeleeeleeleeeleklkkk........ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelk 402
                                   +++       + +e+el+e+++ le+l+k+        +  l  +++++++++e +e+++ l+   + l+++ e+l+ +lk
  gi|15669177|ref|NP_247982.1|  29 MQK-------QSVETELKECKKALEELEKSssdevyklVGGLFVKRKKEDVKKELEEKVETLELRVKTLEKQEEKLQSRLK 102
                                   222.......44444444444444444444544544444444333556667777777777777777777788888888888 PP

                          FapA 403 elkeelesk 411
                                   el+e+++++
  gi|15669177|ref|NP_247982.1| 103 ELQEKIQKM 111
                                   888777765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3  14.8      0.12        26     386     460 ..      32     115 ..       8     116 .] 0.64

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                        AAA_13 386 anleeekeeakkklelhlv...eeleseldeyk......kkykklekaieklekelkeeeaelkkleeeikeLekqlrdek 457
                                   +++e+e +e+kk+le  +     e+++ +  +       + +k+le+++e le ++k  e++ +kl+ + keL++++++  
  gi|15669177|ref|NP_247982.1|  32 QSVETELKECKKALEELEKsssDEVYKLVGGLFvkrkkeDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKMI 112
                                   344555555555555544411133333333222444444778999999999999999999999999999****99999888 PP

                        AAA_13 458 paa 460
                                   p+a
  gi|15669177|ref|NP_247982.1| 113 PTA 115
                                   777 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   7.5      0.09        19      49     106 ..      24     105 ..       2     113 .. 0.49

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.09
                                   T......THHHHHHHHHHHHHHHHHHHHHHT..................-BTCCG-S--.HHHH.......HHHHHHHHHH CS
               Cob_adeno_trans  49 e......eeelkeaLeeiqneLfdlgaelatp.................ekkkekkkit.eeev.......eelekeidel 98 
                                          +++++++L+e ++ L +l ++ + +                 +        + ee+v       ++lek+ ++l
  gi|15669177|ref|NP_247982.1|  24 LqmilmqKQSVETELKECKKALEELEKSSSDEvyklvgglfvkrkkedvK-------KElEEKVetlelrvKTLEKQEEKL 97 
                                   13334444555555555555555555555433555566677755333321.......333334511111115555555555 PP

                                   HHHS--EE CS
               Cob_adeno_trans  99 eaelpplk 106
                                   +++l++l+
  gi|15669177|ref|NP_247982.1|  98 QSRLKELQ 105
                                   55555555 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   5.8       1.3   2.8e+02      49      87 ..      14      52 ..       2      70 .. 0.61
   2 ?   10.1   5.7    0.0031      0.68      39      86 ..      67     114 ..      65     116 .] 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.3
                      RasGAP_C 49 keElesleetlktLseknnylesqlesYkayienvleql 87
                                    +l+ l++ l+ +  +++ +e++l++ k+ +e+  + +
  gi|15669177|ref|NP_247982.1| 14 LMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSS 52
                                  455666666666666666666666666666665544443 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0031
                      RasGAP_C  39 rnkgrlrekrkeElesleetlktLseknnylesqlesYkayienvleq 86 
                                   r+k++ +++ +e +e+le  +ktL++++++l+s+l+++++ i++++ +
  gi|15669177|ref|NP_247982.1|  67 RKKEDVKKELEEKVETLELRVKTLEKQEEKLQSRLKELQEKIQKMIPT 114
                                   57888999999999999999***********************98865 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   3.2      0.55   1.2e+02       8      34 ..      16      42 ..       9      50 .. 0.68
   2 ?    7.7   0.6     0.022       4.7       1      32 [.      79     110 ..      74     116 .] 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.55
                           LPP  8 qVsqLkskvdqlssdvnsakaaaqaak 34
                                  q++qL+++ +++  + +s+++++++ k
  gi|15669177|ref|NP_247982.1| 16 QLQQLQQQLQMILMQKQSVETELKECK 42
                                  667777777777666666666655544 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.022
                           LPP   1 kldeLssqVsqLkskvdqlssdvnsakaaaqa 32 
                                   k++ L   V++L+++ ++l+s ++++++ +q+
  gi|15669177|ref|NP_247982.1|  79 KVETLELRVKTLEKQEEKLQSRLKELQEKIQK 110
                                   67777778888888888888888888888876 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  14.8     0.064        14     212     297 ..       8      99 ..       2     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.064
                         FAM76 212 snssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekeke......lreklkelekeakekieklekkir 286
                                   ++ + +l++++qL+++++ +  q ++ ++el e +k + el     ++  +      +++k ++++ke +ek+e+le +++
  gi|15669177|ref|NP_247982.1|   8 PQIQAQLMQLQQLQQQLQMILMQKQSVETELKECKKALEELEKSSSDEVYKlvgglfVKRKKEDVKKELEEKVETLELRVK 88 
                                   67888999**********9999999999************987776665542223325889999***************** PP

                         FAM76 287 ellkevaelsk 297
                                   +l k+  +l+ 
  gi|15669177|ref|NP_247982.1|  89 TLEKQEEKLQS 99 
                                   *****988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3917  (0.218473); expected 358.6 (0.02)
Passed bias filter:                     1113  (0.0620782); expected 358.6 (0.02)
Passed Vit filter:                       241  (0.0134419); expected 17.9 (0.001)
Passed Fwd filter:                       126  (0.00702772); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              83  [number of targets reported over threshold]
# CPU time: 0.90u 0.34s 00:00:01.24 Elapsed: 00:00:00.53
# Mc/sec: 659.84
//
Query:       gi|15669178|ref|NP_247983.1|  [L=329]
Description: hypothetical protein MJ_0988 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-15   57.7   0.1    2.6e-15   56.5   0.0    1.6  2  DHH       DHH family
    1.8e-12   47.8   0.1    5.6e-12   46.2   0.1    1.9  2  DHHA1     DHHA1 domain


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   2.9e-19   2.6e-15       2     101 .]      12     155 ..      11     155 .. 0.82
   2 ?   -3.2   0.0       1.2     1e+04      68      78 ..     225     235 ..     209     253 .. 0.67

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.9e-19
                                   EEEE-ECSSSHHHHHHHHHHHH.............................................CECS--TCGGCGCC CS
                                   xxxxxxxxxxxxxxxxxxxxxx.............................................xxxxxxxxxxxxxx RF
                           DHH   2 ilivghknpDtDsigSaialan.............................................llvDhneksqaveg 37 
                                   +l ++h+n D D++gS++al++                                             ++vD+ + +q +++
  gi|15669178|ref|NP_247983.1|  12 VLFLCHHNADPDAVGSCVALKYlasqlnpngkfrisadsvsklsrnilneigervdieiypklpetvFIVDTASINQLKVN 92 
                                   67789*****************6666666666666666666666666666666666666666666666************9 PP

                                   HHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH  38 eakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                     + ++ +vi iDHH++  ++ ++ ++++++e++ st+ei+ae+++e ++ ++k++  +ll+gi
  gi|15669178|ref|NP_247983.1|  93 FDELKEREVILIDHHKKT-DLADICKYYIIKEDYPSTSEIIAEIFKELNIFPPKNVRIALLCGI 155
                                   55556678999******9.****************************99999***999999998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                                   E-SSS-HHHHH CS
                                   xxxxxxxxxxx RF
                           DHH  68 nepvgstaeiv 78 
                                   +++++++ +iv
  gi|15669178|ref|NP_247983.1| 225 SHEASCAKTIV 235
                                   34445554444 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.62   5.6e+03      52      90 ..      39      51 ..       5      65 .. 0.60
   2 !   46.2   0.1   6.3e-16   5.6e-12      61     124 ..     232     304 ..     161     318 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.62
                                  HH.HHHHHHHHHHHTHGBTTCEEEEEEEECTEEEEEEEES CS
                         DHHA1 52 da.galgiaadklksklkkpvivfvakeegdkvkvsarsk 90
                                  ++ g                           k ++sa s 
  gi|15669178|ref|NP_247983.1| 39 NPnG---------------------------KFRISADSV 51
                                  2222...........................444444444 PP

  == domain 2  score: 46.2 bits;  conditional E-value: 6.3e-16
                                   HHHHTHGBT.TCEEEEEEEECT.EEEEEEEESSH...SS-HHHHHHHHHHHTTCCEEEETCEEEEEEE......H CS
                         DHHA1  61 dklksklkk.pvivfvakeegd.kvkvsarskkd...gvdagelakeaaaklgggGGGHdlAaGagip......a 124
                                     + s ++  +  v+++ ++ + +++vsar++k     v++g+l++++ ++lgg+GGGH  A G++ p      +
  gi|15669178|ref|NP_247983.1| 232 KTIVS-IGAdVAFVVAVRKK-EkEIRVSARCRKHvskYVHLGNLMEKIGKELGGSGGGHSEAGGLNAPydksksK 304
                                   33334.23313333444444.36*********99*********************************94444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2103.08
//
Query:       gi|15669179|ref|NP_247984.1|  [L=114]
Description: hypothetical protein MJ_0989 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-29  101.1   0.0    5.1e-29  101.0   0.0    1.0  1  DrsE      DsrE/DsrF-like family
    4.2e-05   23.5   0.5      0.013   15.4   0.1    2.0  2  DrsE_2    DsrE/DsrF/DrsH-like family
     0.0038   17.3   0.0     0.0078   16.3   0.0    1.6  1  DsrH      DsrH like protein


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   8.6e-33   5.1e-29       1     117 []       1     114 []       1     114 [] 0.97

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 8.6e-33
                                   -EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHHHH CS
                          DrsE   1 kkvfilvtggpygseaarealelalaaaalghevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgqaa 81 
                                   +k+++++t++pyg+e+a++al++al a++ g ev++f+  +Gv++++k  ++np++ +n+ ellk ++e g+ + vCg + 
  gi|15669179|ref|NP_247984.1|   1 MKFTVIITEAPYGKERAYSALRFALTALLEGIEVNIFLLENGVYVAKK--EQNPSEVPNYLELLKNAIELGAVVKVCGPCC 79 
                                   89**********************************************..67999************************** PP

                                   HHTT--GGGE-T--EEEE-HHHHHHHHHH-SEEEE- CS
                          DrsE  82 kargldededlgvgvevsglgelaelqnegdrvitf 117
                                   kargl+e++++  g +++++ +l+ +++e+d v+tf
  gi|15669179|ref|NP_247984.1|  80 KARGLKEEDLI-EGAKLATMHDLIAFVKESDNVVTF 114
                                   ******88777.7**********************9 PP

>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0   0.00042       2.5      14      51 ..      14      51 ..       1      53 [. 0.78
   2 !   15.4   0.1   2.2e-06     0.013      91     149 ..      51     109 ..      42     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00042
                                  H.HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GGG CS
                        DrsE_2 14 ldkalaalilAsgAaalglevtiFftFwGLnilrkeek 51
                                   ++a+ al  A +A   g+ev+iF    G+ + +ke++
  gi|15669179|ref|NP_247984.1| 14 KERAYSALRFALTALLEGIEVNIFLLENGVYVAKKEQN 51
                                  348**********************9999999999876 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.2e-06
                                   HHCT---HHHHHHHHHHTT-EEEEEHHHHHHHT--GGGB-TT-EEE-HHHHHHHHHC-S CS
                        DrsE_2  91 kekgvasleeLleaakeagvklvaCqmtmdlmglkkeelidgveiagaatylkeaeead 149
                                   +  +v++  eLl++a e g  +  C       glk+e+li+g ++a+  +++  ++e+d
  gi|15669179|ref|NP_247984.1|  51 NPSEVPNYLELLKNAIELGAVVKVCGPCCKARGLKEEDLIEGAKLATMHDLIAFVKESD 109
                                   567888999************************************************98 PP

>> DsrH  DsrH like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.3e-06    0.0078      21      84 ..      35     108 ..      11     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-06
                                   EEEE-GGGGGGGBTTB......TTHHHHHTS...SSEEEEEHHHHHHTT-T.TSB-TTSEEE-HHHHHHHHHHS CS
                          DsrH  21 avlLieDgVyaalkgs......rllkalkea...svklyaLkeDleARGlt.eqlsegvkvidydgfVeltvkh 84 
                                   ++ L+e+gVy+a k++      ++l+ lk+a   ++ + +  +  +ARGl+ e+l+eg k+  ++++++ + + 
  gi|15669179|ref|NP_247984.1|  35 NIFLLENGVYVAKKEQnpsevpNYLELLKNAielGAVVKVCGPCCKARGLKeEDLIEGAKLATMHDLIAFVKES 108
                                   699*********665412222257778888899899999************888******99999988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 899.37
//
Query:       gi|15669180|ref|NP_247985.1|  [L=75]
Description: hypothetical protein MJ_0990 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-24   85.6   0.1    1.7e-24   85.4   0.1    1.0  1  TusA            Sulfurtransferase TusA
    0.00068   19.4   0.0     0.0012   18.7   0.0    1.4  1  DUF2249         Uncharacterized conserved protein (DUF2249)
  ------ inclusion threshold ------
       0.06   13.7   0.1      0.084   13.3   0.1    1.2  1  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.1   2.8e-28   1.7e-24       1      70 []       6      75 .]       6      75 .] 0.98

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 2.8e-28
                                  EEEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEEE CS
                          TusA  1 ielDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivirk 70
                                  ++lD++G +CP+P+lk+kkale+l+ege+lev+ d ++a e+i+rfa+++g+++v  ee++  +rivi+k
  gi|15669180|ref|NP_247985.1|  6 KKLDVTGDICPVPVLKTKKALEELNEGEELEVVGDYKPALENIKRFAENNGYTVVLAEETESRFRIVIKK 75
                                  58******************************************************************98 PP

>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.9e-07    0.0012       2      70 .]       8      75 .]       7      75 .] 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.9e-07
                       DUF2249  2 lDvRelppperhaaIfeafeaLapGetlelvndhdPkp.LlyqLearrpgffsweylergpgewrvlitk 70
                                  lDv +   p +  ++ +a+e+L +Ge+le+v d +P    +++++++  g+ ++   e+++ ++r+ i+k
  gi|15669180|ref|NP_247985.1|  8 LDVTGDICPVPVLKTKKALEELNEGEELEVVGDYKPALeNIKRFAEN-NGY-TVVLAEETESRFRIVIKK 75
                                  99**********************************86324444444.477.888888888888888875 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.4e-05     0.084      17      49 ..      26      57 ..      20      63 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                GHMP_kinases_C 17 lnlsqrselkavvgilppeleellealselGal 49
                                  l ++++ e+++vvg  +p+le+++++++++G +
  gi|15669180|ref|NP_247985.1| 26 LEELNEGEELEVVGDYKPALENIKRFAENNG-Y 57
                                  33333345699********************.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 515.40
//
Query:       gi|15669181|ref|NP_247986.1|  [L=144]
Description: hypothetical protein MJ_0991 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0047   17.4   0.1      0.011   16.3   0.1    1.6  1  NLE             NLE (NUC135) domain
  ------ inclusion threshold ------
      0.017   15.6   1.0      0.017   15.6   1.0    1.7  2  Ribosomal_L14e  Ribosomal protein L14
      0.057   14.2   0.0       0.12   13.2   0.0    1.4  1  DUF4037         Domain of unknown function (DUF4037)
       0.85    9.9   4.1          1    9.6   3.6    1.4  1  Ribosomal_L22   Ribosomal protein L22p/L17e
       0.87   10.0   5.4        0.5   10.7   1.3    2.3  2  DUF4160         Domain of unknown function (DUF4160)


Domain annotation for each model (and alignments):
>> NLE  NLE (NUC135) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     3e-06     0.011      20      63 ..      11      57 ..       6      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3e-06
                           NLE 20 plsvPasltrkqLselvnkLlkee...kpvpFdFlidgellrtsLee 63
                                  +l+vP+++++k+ +e ++kL  ee   k+  F +++++e l++ +++
  gi|15669181|ref|NP_247986.1| 11 TLKVPSNISKKKIEEAIKKLELEEkykKTENFKLFVKDEDLKMKIYK 57
                                  689*****************77445866577******999*999886 PP

>> Ribosomal_L14e  Ribosomal protein L14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   1.0   4.9e-06     0.017      15      51 ..      10      46 ..       4      72 .. 0.89
   2 ?   -3.1   0.1       3.2   1.1e+04      47      54 ..      95     102 ..      86     105 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.9e-06
                Ribosomal_L14e 15 ivlklprgartgavkkawekadveekwaksawakkla 51
                                  i+lk+p + +++ +++a++k ++eek++k++  k   
  gi|15669181|ref|NP_247986.1| 10 ITLKVPSNISKKKIEEAIKKLELEEKYKKTENFKLFV 46
                                  677***************************9887655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.2
                Ribosomal_L14e  47 akklaare 54 
                                    kkl++re
  gi|15669181|ref|NP_247986.1|  95 KKKLDKRE 102
                                   45555555 PP

>> DUF4037  Domain of unknown function (DUF4037)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.2e-05      0.12      33      85 ..      11      67 ..       6      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-05
                       DUF4037 33 ekayPedvrlkklaarlakiaqegqy....nleralkrgdelaarlalaefvrelms 85
                                  + ++P ++ +kk++++++k++ e++y    n++  +k +d  +  + +aefv+++++
  gi|15669181|ref|NP_247986.1| 11 TLKVPSNISKKKIEEAIKKLELEEKYkkteNFKLFVKDEDLKMKIYKIAEFVEDYLK 67
                                  5579**********************99999999999999999999*******9987 PP

>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.6   0.00029         1      16      60 ..      14      83 ..       7     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00029
                                  HHHHHTTSBHHHHHHHHHT..-SST.....................THHHHHHHHHHHHHHHH..HT....- CS
                 Ribosomal_L22 16 varlIrgmkveeAlkyLkf..skkk.....................aakfvlklLknaeanaelkgl....d 60
                                  v   I ++k+eeA+k L+   +                         a+fv++ Lk+  +  e +       
  gi|15669181|ref|NP_247986.1| 14 VPSNISKKKIEEAIKKLELeeK--YkktenfklfvkdedlkmkiykIAEFVEDYLKKKYSDEEFEIVldydG 83
                                  55689**************633..33699*****************99******998777766444355554 PP

>> DUF4160  Domain of unknown function (DUF4160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1       0.2   7.2e+02      33      56 ..       9      32 ..       2      39 .. 0.74
   2 ?   10.7   1.3   0.00014       0.5      34      65 ..      90     121 ..      66     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.2
                       DUF4160 33 dvellegsglpkkelklieewvee 56
                                  +++l+  s+++kk++ ++ + +e+
  gi|15669181|ref|NP_247986.1|  9 TITLKVPSNISKKKIEEAIKKLEL 32
                                  566666678999999988877665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                       DUF4160  34 vellegsglpkkelklieewveehqeellekW 65 
                                   ve++  ++l k+elk+i+ ++++ +e + ++W
  gi|15669181|ref|NP_247986.1|  90 VEIVFKKKLDKRELKDIKVIIRKLKEIIFDAW 121
                                   67777779************************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1805  (0.100675); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 998.17
//
Query:       gi|15669182|ref|NP_247987.1|  [L=177]
Description: hypothetical protein MJ_0992 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0041   17.2   0.7      0.014   15.5   0.5    2.0  1  HEPN      HEPN domain
  ------ inclusion threshold ------
        0.2   12.1   1.2        0.8   10.2   1.2    2.2  1  Latarcin  Latarcin precursor
        0.2   12.2   0.7       0.39   11.3   0.2    1.8  2  DUF1053   Domain of Unknown Function (DUF1053)


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.5   2.3e-06     0.014      11      96 ..      13     117 ..       4     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-06
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHC..CHHHT.............-HHHHHHH.. CS
                          HEPN  11 dleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLle..elkkelke..........seelreel.. 77 
                                   +l + + l +eg+y+ a+ ++++++++ l+ +  + +++  +  ++ eLl+  +++k l++                    
  gi|15669182|ref|NP_247987.1|  13 KLPTFKSLPNEGKYRTAIGRYYYCIFLKLREIVKEIEQD--REDGIYELLNsgKAHKALPAyfrtlsdkirV------Dnl 85 
                                   4667788889*****************999877666665..**********888888888795556555551......044 PP

                                   ...........HHHHCCCHHCCCTSS--S..- CS
                          HEPN  78 ...........eeLekayiesrYpdakee..y 96 
                                              e L+k++ + +Y+ + +    
  gi|15669182|ref|NP_247987.1|  86 kndlitlaealEDLRKLRNMCDYDVDVSIsfT 117
                                   55556666666999999999999998887532 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.2   0.00013       0.8      21      54 ..      71     106 ..       4     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                      Latarcin  21 ainrklmem..vnnlRkvqgRLeemvenlrkvedle 54 
                                   a++r+l +   v+nl+++   L+e++e+lrk+ ++ 
  gi|15669182|ref|NP_247987.1|  71 AYFRTLSDKirVDNLKNDLITLAEALEDLRKLRNMC 106
                                   6888888753389*******************9975 PP

>> DUF1053  Domain of Unknown Function (DUF1053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.82   4.9e+03      80      97 ..      11      28 ..       5      30 .. 0.77
   2 ?   11.3   0.2   6.6e-05      0.39      43      95 ..     111     166 ..      77     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.82
                       DUF1053 80 kkftliFkekslEkkYrq 97
                                   + +++Fk    E kYr+
  gi|15669182|ref|NP_247987.1| 11 AEKLPTFKSLPNEGKYRT 28
                                  555788999999999997 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.6e-05
                       DUF1053  43 ersasekarleeeld.erleqaIdglsskklwkrse..dlkkftliFkekslEkkY 95 
                                   + s s  +  e e+d e +eq+I  ls +k+ ++++   lk+ + +Fk+k+   +Y
  gi|15669182|ref|NP_247987.1| 111 DVSISFTKVIEAEIDiEIIEQTITNLSYQKPKSKTKivGLKNVLEYFKDKDNLPTY 166
                                   55556667889999856789***********877763247899999*999866555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1317.06
//
Query:       gi|15669183|ref|NP_247988.1|  [L=358]
Description: hydrogenase expression/formation protein HypD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.1e-147  489.9   1.1   4.6e-147  489.7   1.1    1.0  1  HypD      Hydrogenase formation hypA family


Domain annotation for each model (and alignments):
>> HypD  Hydrogenase formation hypA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  489.7   1.1  2.6e-151  4.6e-147       2     351 .]       9     356 ..       8     356 .. 0.99

  Alignments for each domain:
  == domain 1  score: 489.7 bits;  conditional E-value: 2.6e-151
                                   HHHHHHHHHHHHHHTSS-EEEEE--HHHHHHHHHTTHHHHS-TTEEEEE-S--TTTTS-HHHHHHHHHHHHH--EEEEE-C CS
                          HypD   2 lakkllekikkeakkerelkimevCGghthaivryglrslLpenielisGPGCpVCvtpeeeidkaielaekeevilatfg 82 
                                   l+kk ++ki+k+a+k ++lkim+vCG+h+h+i++yg+r++Lpeni+++ GPGCpVCvt+++eid+ai la++ +++++t+g
  gi|15669183|ref|NP_247988.1|   9 LIKKAIDKINKLAEKIDKLKIMHVCGSHEHTICKYGIRDVLPENITVVPGPGCPVCVTTQKEIDTAIYLADN-GYVITTLG 88 
                                   68999*****************************************************************99.******** PP

                                   CHHG---TT--HHHHHHTT-EEEE-SSHHHHHHHHHH-TTSEEEEEEEE-HHHHHHHHHHHHHHHHHT-SSEEEEEEEE-H CS
                          HypD  83 DmlrvpgskksLleakaegadvrivyspldalkiakenpdkevvflavGFEttapatalalleakkeglknfsvlsshklv 163
                                   Dm+rvpgs+ksL+e ++eg+dvrivys+ +a+k+ak+++dk++vf+a+GFEttap+t + l + k+++++nf++l +h+++
  gi|15669183|ref|NP_247988.1|  89 DMYRVPGSEKSLMEKQSEGCDVRIVYSISEAVKMAKKERDKKFVFVAIGFETTAPTTGAELISLKNKDVNNFFILNCHRQT 169
                                   ********************************************************************************* PP

                                   HHHHHHHHHTT.---SEEEEEHHHHHHHTTHHHHHHHHHH---EEEE-SSHHHHHHHHHHHHHHHHTT---EEETTTTT-- CS
                          HypD 164 ppalealleseelkidgfiapghvstviGlkayeelaeeykvpvvvaGFepldilqailmlvkqleegeaeveneYkrvvk 244
                                   pp++e+ll++  + +d+fi+pghvst++Glk+y  l+e+yk p+vvaGFep+d+l+ai+m++kq+ +gea+veneY r+vk
  gi|15669183|ref|NP_247988.1| 170 PPVMEFLLNEG-VYLDAFICPGHVSTITGLKPYYGLCEKYKAPMVVAGFEPIDVLMAIIMILKQVISGEAKVENEYIRAVK 249
                                   ********986.89******************************************************************* PP

                                   TT--HHHHHHHHHHEEEEEEEETTTEEEEEEEEEE-GGGGGGBGGGT----S---SS-TT--HHHHHTTS--GGGSTTBTT CS
                          HypD 245 eegnkkaqklieevfevrdaewRglgvipksglklreeyaefdaekkfelekeeekekkackcgevlkGkakPedCklFgk 325
                                   +egn+ aqk+i+evfe  d  wRg++v++++g+ lre+y++fd+ ++ ++++ +ek +k+c+c+++l+G++ P+dC+lFg+
  gi|15669183|ref|NP_247988.1| 250 PEGNVLAQKIINEVFESIDVPWRGFPVVKNGGFGLREKYKKFDIYEHEDIPEIKEKIPKGCICDKILRGEKLPTDCPLFGT 330
                                   ********************************************************************************* PP

                                   TB-SSS-SSHHHHSTT-HHHHHHHTT CS
                          HypD 326 aCtpenpvGacmvSsEGaCaayykyg 351
                                   +Ctp npvG+cmvS+EG+C+++yky+
  gi|15669183|ref|NP_247988.1| 331 VCTPLNPVGSCMVSDEGTCRIFYKYR 356
                                   ************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2278.49
//
Query:       gi|15669184|ref|NP_247989.1|  [L=240]
Description: uroporphyrinogen III synthase HemD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-43  146.6   0.0    8.2e-43  146.4   0.0    1.0  1  HEM4      Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.4   0.0   4.6e-47   8.2e-43       2     232 .]      14     232 ..      13     232 .. 0.91

  Alignments for each domain:
  == domain 1  score: 146.4 bits;  conditional E-value: 4.6e-47
                                   HHHHHHHHTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEESSHH CS
                          HEM4   2 elaealearGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealkreeedvkalaslkvaavGpa 82 
                                    +a +l+++G+ep+++P++ei+    +++l+  ld     +ydw++ftS+ +v  l++ l   e   +  +++k+a++G++
  gi|15669184|ref|NP_247989.1|  14 VFASLLKKEGFEPIIFPTLEIVY---NKDLDVNLD-----SYDWIAFTSPSGVIGLYNILT--ENERENVKNKKIAVIGEK 84 
                                   7899*******************...999999999.....9*******************9..88888999********** PP

                                   HHHHHHHT.T---SEE-..SSSHHHHGGGS-.---E.EEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHHHHHH CS
                          HEM4  83 TaraLeel.glrvdlvpseegtaegLaeelaeslag.krvlllrgeiarddlaegLeergaevdevevYetvpaeeepeel 161
                                   Ta+ ++++ g ++d++p+ e+tae+L+ e+++  ++ +++l++  + +rd l++ L     + d + vY+   +e+++e++
  gi|15669184|ref|NP_247989.1|  85 TAKTFKKYfGRDPDIMPN-EYTAESLLREIKKVSKEeEKFLIPTTPSTRDVLKNNL-----NADLLFVYKSAEPENLKEDI 159
                                   *******88********9.************97777799*****************.....6788999***6665544444 PP

                                   HHH..HHTT--SEEEESSHHHHHHHHHH-S-HH.HHHCTSEEEEESHHHHHHHHHTT---SEEETS--HHHHHH CS
                          HEM4 162 kea..lkagevdavvftSpstvrnllellkdeg.delkevkvaaiGptTaealkklglkvdvvaeeptaeglva 232
                                   k++  l a+++ +++ftS  t++n+++++ de  +  k+  ++aiGp+Ta+ ++k+g+k+ ++++ +t+eg+++
  gi|15669184|ref|NP_247989.1| 160 KKLkeLIAKDKFILTFTSGLTAKNFFKYVDDEFaEIIKDNYIVAIGPITAKVIEKFGFKP-LIPKVYTIEGMLE 232
                                   433002256779*******************9999*************************.***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1586.37
//
Query:       gi|15669185|ref|NP_247990.1|  [L=227]
Description: VAR1 protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.24   11.4   0.0    1.4  1  Pico_P2A  Picornavirus core protein 2A


Domain annotation for each model (and alignments):
>> Pico_P2A  Picornavirus core protein 2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.3e-05      0.24      35      91 ..     149     206 ..     124     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.3e-05
                      Pico_P2A  35 iarCnCttgvyycksrrkyypvs.vekptlieieeseyyparlqshvllgvGfaePGd 91 
                                   i r n t g+yy  + +k y +  ++kp+++ei++++  ++ lq++  + + + + Gd
  gi|15669185|ref|NP_247990.1| 149 IYRENYTIGIYYDLNSNKTYLIEvFRKPNNQEIDTEKLRNELLQKTNAVDCNVVDMGD 206
                                   66788999**************627999******999999999988888877777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1489.26
//
Query:       gi|15669186|ref|NP_247991.1|  [L=451]
Description: hypothetical protein MJ_0996 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-72  244.2   1.0    3.3e-72  243.7   0.9    1.3  2  PmbA_TldD  Putative modulator of DNA gyrase
  ------ inclusion threshold ------
       0.15   11.2   0.0       0.25   10.6   0.0    1.3  1  DUF3150    Protein of unknown function (DUF3150)


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.7   0.9   3.7e-76   3.3e-72       1     279 []      16     309 ..      16     309 .. 0.93
   2 ?   -3.8   0.0      0.99   8.9e+03     269     277 ..     387     395 ..     385     396 .. 0.84

  Alignments for each domain:
  == domain 1  score: 243.7 bits;  conditional E-value: 3.7e-76
                                   EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-...... CS
                     PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea...... 75 
                                   +a++r++ +es+++++ +g++e++ss   +g++vrv++++ +gf++++  s+e++e+++++a+++ak ++e  e+      
  gi|15669186|ref|NP_247991.1|  16 YADIRINFGESNTITLKDGKIEEISSGFGNGVAVRVLYKNGWGFVTSNIVSEEEIEKLINKAYKMAKISNEYSEKeiilkd 96 
                                   89*********************************99999****998988889**************99999999****** PP

                                   ................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEE CS
                     PmbA_TldD  76 ................eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtrv 140
                                                   ++v++eek+e++ ++ k     d+        +i+++s+s+s++ ++++++ SeG+++e + tr+
  gi|15669186|ref|NP_247991.1|  97 ykaiidnykmigkinpTDVDIEEKKEIIIDTYKN--MTDE--------KIKSISVSYSDVFGKRIFMISEGSRIEGEITRC 167
                                   **************************99999866..3455........99******************************* PP

                                   EEEEEEEE..STCS...ETEEEEEEEESSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGHHHHHT CS
                     PmbA_TldD 141 slslsvia.ddggs...gdgmgggsgyedleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllheavghal 217
                                    ++++++a ++ g+   g ++ gg+g+e +++ ++ ++a ea+++al++l+akp+p gk++V+l+pe +g+++heavgha 
  gi|15669186|ref|NP_247991.1| 168 IMYMNCVAkEN-GNlqyGAERTGGFGFEKIKD-NYLNLALEAKNRALRLLKAKPCPKGKFKVILDPELAGVFIHEAVGHAS 246
                                   ********444.33453336666777777777.9999******************************************** PP

                                   BHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                     PmbA_TldD 218 eadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                   ead vl++ S++kdklGe+v+se +t++dd+t+ g++gsy +DdEGv  ++tv+IenG+Lk+y
  gi|15669186|ref|NP_247991.1| 247 EADLVLQNDSVFKDKLGERVGSEYVTVIDDATIeGAFGSYKYDDEGVEGKKTVIIENGILKTY 309
                                   ************99************************************************9 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.99
                                   EEEETTEE- CS
                     PmbA_TldD 269 vlIenGvLk 277
                                   +lIenG L+
  gi|15669186|ref|NP_247991.1| 387 YLIENGELT 395
                                   89****997 PP

>> DUF3150  Protein of unknown function (DUF3150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   2.7e-05      0.25      61     115 ..      48     104 ..      45     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.7e-05
                       DUF3150  61 aerlllkvGvrflgGyavpedkaeevvk...eLekikqeFekekqeFLarydravedW 115
                                   a r+l k+G  f+   +v e+++e++++   +++ki +e++ ek+  L++y ++++++
  gi|15669186|ref|NP_247991.1|  48 AVRVLYKNGWGFVTSNIVSEEEIEKLINkayKMAKISNEYS-EKEIILKDYKAIIDNY 104
                                   889***********************8733469******96.7899********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2885.61
//
Query:       gi|15669187|ref|NP_247992.1|  [L=241]
Description: hypothetical protein MJ_0998 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0013   18.4   0.2      0.019   14.7   0.0    2.3  2  SHOCT     Short C-terminal domain
     0.0093   15.3   0.4      0.013   14.8   0.4    1.2  1  DUF1394   Protein of unknown function (DUF1394)
  ------ inclusion threshold ------
       0.15   12.6   3.9       0.22   12.1   3.9    1.3  1  PRESAN    Plasmodium RESA N-terminal


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.056   3.4e+02      12      21 ..     165     174 ..     163     176 .. 0.80
   2 !   14.7   0.0   3.2e-06     0.019       6      22 ..     200     216 ..     200     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.056
                         SHOCT  12 rGeIteEEFe 21 
                                   + eI +EEF 
  gi|15669187|ref|NP_247992.1| 165 SEEIAQEEFK 174
                                   56999****6 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.2e-06
                         SHOCT   6 LkeLyarGeIteEEFea 22 
                                   L++L+a+G+ ++EE++ 
  gi|15669187|ref|NP_247992.1| 200 LDDLLAKGVVSQEEYQN 216
                                   89*************95 PP

>> DUF1394  Protein of unknown function (DUF1394)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.4   2.1e-06     0.013      58     134 ..     165     240 ..     151     241 .] 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-06
                       DUF1394  58 aqekawkavlplvaklkefyefs..sklekvvpklleelcseklsakesLeqkqalakqfaeildfvlkFDelkmknpa 134
                                   ++e a +   +  ++  + + +s   + ++++pk l+ l     +   s e++q l+k +++il  +lk De kmk p+
  gi|15669187|ref|NP_247992.1| 165 SEEIAQEEFKKWYETEVKNFMYSlfITAKNAFPKFLDDLL---AKGVVSQEEYQNLIKLYSHILARILKNDEEKMKIPT 240
                                   3444444444444444444555511566899*********...45556679************************9986 PP

>> PRESAN  Plasmodium RESA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.9   3.7e-05      0.22      59     124 ..     170     235 ..     155     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                                   -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-SEEEHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        PRESAN  59 peeykkklwkeckneitkelkklekeynknfynllkkkklsidefkefinsyrklwkkllkklekk 124
                                    ee+kk +  e+kn + + + + ++ + k + +ll k+ +s +e++++i+ y +   ++lk+ e+k
  gi|15669187|ref|NP_247992.1| 170 QEEFKKWYETEVKNFMYSLFITAKNAFPKFLDDLLAKGVVSQEEYQNLIKLYSHILARILKNDEEK 235
                                   56666777789*******************************************999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1484  (0.0827709); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1465.15
//
Query:       gi|15669188|ref|NP_247993.1|  [L=542]
Description: thermosome [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   3.4e-188  626.2  26.1   3.9e-188  626.1  26.1    1.0  1  Cpn60_TCP1      TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.046   14.2   0.6      0.046   14.2   0.6    3.0  4  EF-G-binding_N  Elongation factor G-binding protein, N-termin


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  626.1  26.1  4.4e-192  3.9e-188       1     490 [.      34     523 ..      34     524 .. 0.98

  Alignments for each domain:
  == domain 1  score: 626.1 bits;  conditional E-value: 4.4e-192
                                   HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHH CS
                    Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekli 81 
                                   +a++v+ttlGPkGmdKmlv++ g++vvTnDG+tilke+ +ehPaak+l+e+a++q++evGDGTtt+v++ageLl++ae+l+
  gi|15669188|ref|NP_247993.1|  34 IAETVRTTLGPKGMDKMLVDELGDIVVTNDGVTILKEMSVEHPAAKMLIEVAKTQEKEVGDGTTTAVVIAGELLRKAEELL 114
                                   799****************************************************************************** PP

                                   HCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCCCSEECS CS
                    Cpn60_TCP1  82 aagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.klieenekeld 161
                                   ++++hp++ii+gye+a++ka+e+Lk+ia+e++   +d+e+L+k+a ts+++k  +k +e+l+++vv+Av  +++e+++++d
  gi|15669188|ref|NP_247993.1| 115 DQNIHPSVIINGYEMARNKAVEELKSIAKEVK--PEDTEMLKKIAMTSITGKGAEKAREQLAEIVVEAVrAVVDEETGKVD 193
                                   ***************************66666..669********************************88888888**** PP

                                   CCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHHH CS
                    Cpn60_TCP1 162 lgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekqle 242
                                    + ikv+k+eg  +e+++l++G+v+dk+ ++p+mpkk+enak++ll++++e ++tet+++++++d+++l ++ ++eek+++
  gi|15669188|ref|NP_247993.1| 194 KDLIKVEKKEGAPIEETKLIRGVVIDKERVNPQMPKKVENAKIALLNCPIEVKETETDAEIRITDPAKLMEFIEQEEKMIK 274
                                   ********************************************************************************* PP

                                   HHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEECCETTC CS
                    Cpn60_TCP1 243 ellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveeekigse 323
                                   +++eki+++g+nvv+cqkgiddla+h+lak+gila+rrvkk+d+e+lakatGa++v++++dltpe+lG+a+ vee+k+  +
  gi|15669188|ref|NP_247993.1| 275 DMVEKIAATGANVVFCQKGIDDLAQHYLAKKGILAVRRVKKSDMEKLAKATGARIVTKIDDLTPEDLGEAGLVEERKVAGD 355
                                   ********************************************************************************* PP

                                   CEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHHHHH CS
                    Cpn60_TCP1 324 kttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgeeqlaiea 404
                                    ++++e++k++k++til rg+t++v++e+ rai+dA+ vvk+a+e++k+v+GGGate+elak+l+++a+sv g+eqla++a
  gi|15669188|ref|NP_247993.1| 356 AMIFVEQCKHPKAVTILARGSTEHVVEEVARAIDDAIGVVKCALEEGKIVAGGGATEIELAKRLRKFAESVAGREQLAVKA 436
                                   ********************************************************************************* PP

                                   HHHHHTHHHHHHHHHCTSXHHHHHHHHHHHH..HTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCE CS
                    Cpn60_TCP1 405 fakALevipktLaeNaGldpievlaklraah..nkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLri 483
                                   fa+ALevip+tLaeN+Gldpi++l klraah  + ge  +g+dv +ge++d++e+gvv+plkvk+qa++sAtea  ++Lri
  gi|15669188|ref|NP_247993.1| 437 FADALEVIPRTLAENSGLDPIDMLVKLRAAHekEGGE-VYGLDVFEGEVVDMLEKGVVEPLKVKTQAIDSATEASVMLLRI 516
                                   ******************************9534455.9****************************************** PP

                                   EEEEXXX CS
                    Cpn60_TCP1 484 deiikak 490
                                   d++i a+
  gi|15669188|ref|NP_247993.1| 517 DDVIAAE 523
                                   ****986 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.4   1.2e+04      45      66 ..      68      91 ..      65      94 .. 0.60
   2 ?   14.2   0.6   5.1e-06     0.046      32      79 ..     129     177 ..     118     181 .. 0.92
   3 ?   -2.5   0.2      0.88   7.9e+03      39      60 ..     260     281 ..     243     286 .. 0.70
   4 ?   -2.7   0.0         1   9.1e+03      29      47 ..     321     339 ..     313     344 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.4
                EF-G-binding_N 45 fpelseeq..kelLeqiddiktke 66
                                  ++e+s e+  +++L +++++++ke
  gi|15669188|ref|NP_247993.1| 68 LKEMSVEHpaAKMLIEVAKTQEKE 91
                                  455555555545554888887665 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.1e-06
                EF-G-binding_N  32 avkalaaekIlelfpelseeqkelLeqiddik.tkekaeklLeeLkeyV 79 
                                     +  a e+++ + +e ++e++e+L++i+ ++ t + aek+ e+L e+V
  gi|15669188|ref|NP_247993.1| 129 MARNKAVEELKSIAKEVKPEDTEMLKKIAMTSiTGKGAEKAREQLAEIV 177
                                   5678899999*************************************99 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.88
                EF-G-binding_N  39 ekIlelfpelseeqkelLeqid 60 
                                   +k++e+ +++++  k+++e+i+
  gi|15669188|ref|NP_247993.1| 260 AKLMEFIEQEEKMIKDMVEKIA 281
                                   4666666666666677777776 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1
                EF-G-binding_N  29 vveavkalaaekIlelfpe 47 
                                     +a+ a + +kI +l pe
  gi|15669188|ref|NP_247993.1| 321 LAKATGARIVTKIDDLTPE 339
                                   5577778888999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3408.36
//
Query:       gi|15669189|ref|NP_247994.1|  [L=416]
Description: histidyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-73  247.3   0.0    2.8e-73  246.9   0.0    1.1  1  tRNA-synt_His   Histidyl-tRNA synthetase
    3.2e-14   53.3   0.0    7.8e-14   52.0   0.0    1.8  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    6.4e-13   48.7   0.9    6.4e-13   48.7   0.9    2.0  2  HGTP_anticodon  Anticodon binding domain
    1.8e-06   27.3   3.0     0.0013   17.9   1.7    2.9  2  tRNA-synt_2     tRNA synthetases class II (D, K and N)
      2e-05   24.2   0.1    7.8e-05   22.3   0.0    2.0  2  tRNA-synt_2d    tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
      0.081   13.3   0.0       0.16   12.3   0.0    1.4  1  HMw1_D2         HMW1 domain 2


Domain annotation for each model (and alignments):
>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.9   0.0   9.2e-77   2.8e-73       1     309 [.      10     314 ..      10     315 .. 0.97

  Alignments for each domain:
  == domain 1  score: 246.9 bits;  conditional E-value: 9.2e-77
                                   T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH.HS-EEE-TTSSEEEE-SSSHHHHHHHHH CS
                 tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld.qtfklvDqsgrllglRaDiTpqvaRiaa 80 
                                   g+rd+lpee++k++ ++++l ++fe++GY+++ +P++E  + + +++ge+ + q++ ++D+ gr ++lR+++T  v+R++ 
  gi|15669189|ref|NP_247994.1|  10 GTRDFLPEEMKKRRFVENKLREVFERYGYKEILTPTFESFELIAKKTGEEIRkQLYVFKDHGGREMALRPEMTSPVVRFYL 90 
                                   78************************************************8879*************************** PP

                                   HHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEEETCHHHHH CS
                 tRNA-synt_His  81 hrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlghvglvral 160
                                   + l+  ++plRl+Y+++++r ++ ++gr re+ Q+G+EliG++++ ad+Evl+l+++ l   +g+ ++ + +gh g+++ +
  gi|15669189|ref|NP_247994.1|  91 NELKnLQKPLRLYYFANCFRYERPQAGRFREFWQMGCELIGCKEPLADAEVLNLAMDGLI-NIGL-DFDVHIGHLGVLKGV 169
                                   *9988******************************************************6.****.9************** PP

                                   HHHTT--HHHHHHHHHHHHCT-HHHHHHHHHCCTTHHHCCHCC....HCCHCCCHHHHCHCCHCTHHHHHHHHHHHHHHHH CS
                 tRNA-synt_His 161 leaaglsesleeallaalarkdlaelkelaaeaglkealrellkal.elygdaevleealealaaapalqaaldeleelaa 240
                                   le++++se++e ++++++++ d+ +lk  + +  l e++ el+  + + +g++evl+e++e l + p+  +a+++lee+ +
  gi|15669189|ref|NP_247994.1| 170 LEKFNVSEEEEVKIRRLIDKEDYDNLKIYLTQ-ILGEEKKELIFEIlKFKGSREVLDELKEILKDFPKSMEAINNLEEILE 249
                                   ***************************99997.899******99999********************************** PP

                                   HHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-SS-SEEEEEECTTTGGG.T---EEEEEEEEHHH CS
                 tRNA-synt_His 241 llealakpevrvtlDlaelrgyeYytGlvFaayaegvgqaiarGGrYdelgaaf.grarpAtGfsldlea 309
                                    + +      ++t++l+  rg++YytG+vF++y ++  ++i +GGrYd+l++ f g++ pA+Gf+   ++
  gi|15669189|ref|NP_247994.1| 250 FVIH-----DKYTINLGIARGLDYYTGMVFEIYGKKGAKQICGGGRYDNLIETFgGEPTPAVGFAYGFDR 314
                                   *998.....58*******************************************99*********88776 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   2.6e-17   7.8e-14       1     148 [.      65     301 ..      65     385 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 2.6e-17
                                   EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslr 81 
                                   Y ++d  +re++L+P+ + ++v+ + +e l++ + Pl+ly++  ++R+E++ + G  R reF q +++ ++ ++  +  ++
  gi|15669189|ref|NP_247994.1|  65 YVFKDHGGREMALRPEMTSPVVRFYLNE-LKNLQKPLRLYYFANCFRYERP-QAG--RFREFWQMGCELIGCKE--PLADA 139
                                   899*************************.877556****************.99*..***************99..66778 PP

                                   HHHHHHHHHHHHTT.SCEEEEEEGTTSC..................................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................................... RF
                  tRNA-synt_2b  82 dlikaisriferlglefraiielmsaks..................................................... 109
                                   ++++++ + + ++gl f + i+  +  +                                                     
  gi|15669189|ref|NP_247994.1| 140 EVLNLAMDGLINIGLDFDVHIGHLGVLKgvlekfnvseeeevkirrlidkedydnlkiyltqilgeekkelifeilkfkgs 220
                                   999999999999**9998878876666667777778888999999999999999999999999999999999999988888 PP

                                   .............................................BTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHT CS
                                   .............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b 110 .............................................adykdkkefeavsesltkgieigtiqklgtrlserl 145
                                                                                +dy+   +fe++ ++  k+i   + ++++++l e++
  gi|15669189|ref|NP_247994.1| 221 revldelkeilkdfpksmeainnleeilefvihdkytinlgiargLDYYTGMVFEIYGKKGAKQI---CGGGRYDNLIETF 298
                                   88888888888888888888888888888888888888888888888888888888888655555...5566777777777 PP

                                   TEE CS
                                   xxx RF
                  tRNA-synt_2b 146 gat 148
                                   g++
  gi|15669189|ref|NP_247994.1| 299 GGE 301
                                   765 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.81   2.4e+03      44      66 ..     172     194 ..     167     213 .. 0.66
   2 !   48.7   0.9   2.2e-16   6.4e-13       2      89 ..     329     415 ..     328     416 .] 0.96

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.81
                                   HHHHHHHTT-SEEEEE-HHHHHH CS
                HGTP_anticodon  44 kireadllgipfavvvGekelek 66 
                                   k++ +++  + ++  ++++++++
  gi|15669189|ref|NP_247994.1| 172 KFNVSEEEEVKIRRLIDKEDYDN 194
                                   56666666666666666666655 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 2.2e-16
                                   EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEE CS
                HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqerv 82 
                                   +++ip+++ ++el +    +a++Lr+ag  vel   +++++k++ +a+  g+  +++vGekel++g+vtv+d+ t+eq  +
  gi|15669189|ref|NP_247994.1| 329 ILIIPVKK-DKELIKKSLIIADKLRKAGKIVELEIMGRKLRKALDYANSRGFKKVIIVGEKELNEGKVTVKDMITGEQKLI 408
                                   589****9.777****************99*************************************************** PP

                                   ETTHHHH CS
                HGTP_anticodon  83 sldelve 89 
                                    +del +
  gi|15669189|ref|NP_247994.1| 409 GIDELTN 415
                                   ****976 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.7   4.2e-07    0.0013      20     122 ..      17     129 ..       9     151 .. 0.72
   2 !    7.0   0.0   0.00092       2.7     270     298 ..     291     319 ..     275     329 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.2e-07
                                   HHHHHHHHHHHHHHHHHHHTT-EE----SEESS-.....-SSSS--EEEEETTT.T.EEE....-E-S-SHHHHHHHH.HC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxx.xxx....xxxxxxxxxxxxxx.xx RF
                   tRNA-synt_2  20 kvlrlrstvtkavrkyleengfieietPiLsksd.....teegarlFkvksrekek.eff....aLtqspqlylelli.va 89 
                                   + ++ r  v + +r+++e+ g+ ei tP++ + +     t+e+ r+ +   + + + e+     +      +yl  l    
  gi|15669189|ref|NP_247994.1|  17 EEMKKRRFVENKLREVFERYGYKEILTPTFESFEliakkTGEEIRKQLYVFKDHGGrEMAlrpeMTSPVVRFYLNELKnLQ 97 
                                   568899999********************8776644444555444333323444223444344322334578886654144 PP

                                   THSEEEEEEEEE--S--BTTB-S-CEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  90 gidrvfqiaraFRaEdsrtdrhlaEFtqieaem 122
                                   +  r + +a++FR E+ ++ r   EF+q+ +e+
  gi|15669189|ref|NP_247994.1|  98 KPLRLYYFANCFRYERPQAGRFR-EFWQMGCEL 129
                                   5789*****************99.*****9997 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00092
                                   GHHHHHHHHCT--SEEEEEEEHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 270 fswylealeyGapphgGlglGldRlvmll 298
                                   +++++e +     p  G+++G+dR++m +
  gi|15669189|ref|NP_247994.1| 291 YDNLIETFGGEPTPAVGFAYGFDRIMMNI 319
                                   7788999999999************9976 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.6e-08   7.8e-05      21     133 ..      24     131 ..      11     146 .. 0.79
   2 ?   -2.8   0.0       1.2   3.6e+03     200     224 ..     295     318 ..     284     323 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.6e-08
                                   HHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHH....TT CS
                  tRNA-synt_2d  21 kvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtl....ek 97 
                                    v ++++e+f ++g++e+  p        f+ +  +  + +R     +y+ k++    +++ LR  +t+  +r      ++
  gi|15669189|ref|NP_247994.1|  24 FVENKLREVFERYGYKEILTPTF----ESFELIAKKTGEEIR---KQLYVFKDHG--GREMALRPEMTSPVVRFYlnelKN 95 
                                   57789*************99986....557776655555555...4566656666..789*****9998888865577799 PP

                                   S-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEE CS
                  tRNA-synt_2d  98 kkppikiisigrvfRrdavDathlaeFhqveglvvd 133
                                    ++p+++  + ++fR +   a +  eF q+ + +++
  gi|15669189|ref|NP_247994.1|  96 LQKPLRLYYFANCFRYERPQAGRFREFWQMGCELIG 131
                                   99***************************9886665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                   HHHTT-.TTSEEEEEEEEHHHHHHH CS
                  tRNA-synt_2d 200 leavgideevsgfafGlGveRlaml 224
                                   +e +g  e +++++f  G++R+ m 
  gi|15669189|ref|NP_247994.1| 295 IETFGG-EPTPAVGFAYGFDRIMMN 318
                                   555555.455666666678999884 PP

>> HMw1_D2  HMW1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.5e-05      0.16      22      62 ..     216     256 ..     209     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-05
                       HMw1_D2  22 rfigteaafskraailqwlpeklaqlenldnlPsaishdvy 62 
                                   +f g+++  +  + il+ +p+ +++++nl+++ + ++hd y
  gi|15669189|ref|NP_247994.1| 216 KFKGSREVLDELKEILKDFPKSMEAINNLEEILEFVIHDKY 256
                                   67788888889999*************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 2601.17
//
Query:       gi|15669190|ref|NP_247995.1|  [L=290]
Description: 30S ribosomal protein S6 modification protein RimK [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-77  258.7   0.1    3.4e-77  258.3   0.1    1.1  1  RimK            RimK-like ATP-grasp domain
    1.6e-10   41.3   0.0    3.6e-10   40.1   0.0    1.6  1  ATP-grasp_3     ATP-grasp domain
    4.1e-09   36.1   0.0    5.9e-09   35.6   0.0    1.2  1  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
    8.6e-08   31.7   0.8    0.00018   20.9   0.0    3.0  2  ATPgrasp_YheCD  YheC/D like ATP-grasp
    1.1e-07   31.4   0.4     0.0093   15.2   0.1    2.1  2  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
    5.6e-05   22.7   0.0    0.00031   20.3   0.0    1.9  2  CPSase_L_D2     Carbamoyl-phosphate synthase L chain, ATP bin
     0.0024   17.4   0.0     0.0039   16.8   0.0    1.4  1  ATP-grasp       ATP-grasp domain
  ------ inclusion threshold ------
      0.034   13.7   0.0        3.2    7.2   0.0    2.3  2  Ins134_P3_kin   Inositol 1,3,4-trisphosphate 5/6-kinase ATP-g
      0.049   13.4   0.1      0.077   12.8   0.1    1.3  1  GARS_A          Phosphoribosylglycinamide synthetase, ATP-gra
      0.065   12.7   0.0       0.12   11.8   0.0    1.3  1  ATP-grasp_5     ATP-grasp domain


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.3   0.1   1.9e-80   3.4e-77       1     188 []      96     284 ..      96     284 .. 0.98

  Alignments for each domain:
  == domain 1  score: 258.3 bits;  conditional E-value: 1.9e-80
                                   HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--....E CS
                          RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlealkeai....l 77 
                                   ++dK+k++klLak+kik+p+tal+rd+eda+k+iek++lrfPvv+K++++++G+kv++a+++++lkq+   +k+ai    l
  gi|15669190|ref|NP_247995.1|  96 TSDKFKCIKLLAKNKIKTPKTALIRDYEDAVKFIEKYNLRFPVVIKNSFSKCGLKVFMARNYDELKQL---TKNAIwegkL 173
                                   68******************************************************************...888888888* PP

                                   EEEE--SS-S...EEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEEEEET CS
                          RimK  78 vqeyieeaen...ediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDllrak 155
                                   +qe+i+++en   +d+R+lvvd+evv+++rrvs++  FR+nl++G+v+ekl+++ee++elA+k+a+++e+v++GvD+l++k
  gi|15669190|ref|NP_247995.1| 174 IQEFIDFKENdlyRDMRILVVDGEVVGGYRRVSRD--FRTNLYLGNVVEKLNIDEELEELALKCADLSEAVILGVDILPTK 252
                                   ********************************999..******************************************** PP

                                   TEEEEEEEESS--SHHHHHHHT--HHHHHHHHH CS
                          RimK 156 rgllvlEvnsspglekiektlgidiakklieai 188
                                   ++++v+E+nsspg++++ +++gi+++kk++ea+
  gi|15669190|ref|NP_247995.1| 253 DNYYVIELNSSPGTKGF-RDIGINADKKIAEAL 284
                                   *****************.***********9975 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0     2e-13   3.6e-10       2     159 ..      97     265 ..      96     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2e-13
                                   TSHHHHHHHHTTT.S---.............-EESS--SSSEEEEESS-------B--SS--TTE...........EEEE- CS
                   ATP-grasp_3   2 sdKlktykkLkeagvkvP.........tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve....lvqef 69 
                                   sdK+k+ k L ++++k+P         + ++  e  +   ++v+K++ +  g +v+++++ +e+++  ++      l+qef
  gi|15669190|ref|NP_247995.1|  97 SDKFKCIKLLAKNKIKTPktalirdyeDAVKFIEKYNLRFPVVIKNSFSKCGLKVFMARNYDELKQLTKNAIwegkLIQEF 177
                                   8*****************87776544433444444444889********************999976666558899***** PP

                                   --SEEEEEEEEE.SSSEEEEEEEEEEEET..........TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEE CS
                   ATP-grasp_3  70 ieGkplSvsllsdgekvlvlavnrqliekaeke......fvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvl 144
                                   i+ k+  +       ++++l+v  ++++  ++       + y Gnv++   + +ee++ela + +++l + a ++GvD++ 
  gi|15669190|ref|NP_247995.1| 178 IDFKENDL---Y--RDMRILVVDGEVVGGYRRVsrdfrtNLYLGNVVEKL-NIDEELEELALK-CADL-SEAVILGVDILP 250
                                   **999754...3..57899999999997654447899999*******987.889999999987.7788.77889******* PP

                                   SS.SEEEEEEESS-- CS
                   ATP-grasp_3 145 kdeepyviEvNPRlt 159
                                   ++++ yviE N+ + 
  gi|15669190|ref|NP_247995.1| 251 TKDNYYVIELNSSPG 265
                                   ***********8665 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   3.3e-12   5.9e-09      12     153 ..     113     250 ..     103     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 3.3e-12
                                   S--EEEES-HHHHHHHHHHHSS...EEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTTTS-EEEEE--GGGGG...-EE CS
                     GSH-S_ATP  12 ipktlvskdkeeirafleeqgd...vilKPldgkgGegvfrvkksdpnlksilellteegkepviaqrylpeike...GDk 86 
                                   +pkt + +d e+  +f+e+++    v++K   +k G  vf+ ++   +lk++ +  + egk   ++q++++  ++    D 
  gi|15669190|ref|NP_247995.1| 113 TPKTALIRDYEDAVKFIEKYNLrfpVVIKNSFSKCGLKVFMARN-YDELKQLTKNAIWEGK---LIQEFIDFKENdlyRDM 189
                                   69999999999999***99986678***************8776.5689999999999999...8999998665522259* PP

                                   EEEEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEET CS
                     GSH-S_ATP  87 RillvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvig 153
                                   Ril+vdGe +g   +Rv+  +++R+nl  g  +e+ +++e+ +e+a + a+ L+e   ++ G+D++ 
  gi|15669190|ref|NP_247995.1| 190 RILVVDGEVVG-GYRRVS--RDFRTNLYLGNVVEKLNIDEELEELALKCAD-LSE--AVILGVDILP 250
                                   ***********.99**96..69***********************999875.444..3566888874 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.5    0.0028       5.1      11      69 ..      98     156 ..      90     197 .. 0.63
   2 !   20.9   0.0     1e-07   0.00018     180     254 ..     222     289 ..     200     290 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0028
                ATPgrasp_YheCD  11 nKwevyelLskdpelrpyLPetellesledleemlekyks...vylKpanGskGkgilriek 69 
                                   +K ++++lL+k++      P+t l++++ed  +++eky+    v++K + ++ G +++  ++
  gi|15669190|ref|NP_247995.1|  98 DKFKCIKLLAKNK---IKTPKTALIRDYEDAVKFIEKYNLrfpVVIKNSFSKCGLKVFMARN 156
                                   6666666666665...3457777777777777777777755557777777777777665554 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1e-07
                ATPgrasp_YheCD 180 ekileeleelalelaealeesfgrlgElGlDlgidkegkvWllEvNskpgrsifkeagdkeaarksvkrpleYak 254
                                    +i eeleelal+ a   e      + lG+D+   ++ +++++E Ns pg + f+++g  +a +k+++++++Yak
  gi|15669190|ref|NP_247995.1| 222 LNIDEELEELALKCADLSE-----AVILGVDIL-PTKDNYYVIELNSSPGTKGFRDIGI-NADKKIAEALVRYAK 289
                                   6788999999999988777.....488****95.667799******************9.9*************8 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   5.2e-06    0.0093       7      83 ..      84     158 ..      79     178 .. 0.86
   2 !   14.4   0.0   9.2e-06     0.017     227     270 ..     227     268 ..     216     280 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.2e-06
                   ATPgrasp_ST   7 irkyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvitere 83 
                                   +r +Np + + l  dK+k+ +l+ ++ +k+pk+ ++ ++++ ++ +e++  ++ + vviK   +  G  + ++ + +
  gi|15669190|ref|NP_247995.1|  84 CRFINPIKTLYLTSDKFKCIKLLAKNKIKTPKTALIRDYEDAVKFIEKYNLRF-P-VVIKNSFSKCGLKVFMARNYD 158
                                   7899**********************************************999.7.9***99998888777665544 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 9.2e-06
                   ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNarpglai 270
                                   e+ ela k+a+ l +  +lG+Di  ++++  +++ElN  pg + 
  gi|15669190|ref|NP_247995.1| 227 ELEELALKCAD-LSEAVILGVDILPTKDN-YYVIELNSSPGTKG 268
                                   6779*******.***********999999.*********99875 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.7e-07   0.00031       1      73 [.      98     170 ..      98     182 .. 0.86
   2 ?   -0.1   0.0      0.31   5.5e+02     166     178 ..     250     262 ..     233     263 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.7e-07
                                   SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH..-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHH CS
                   CPSase_L_D2   1 Dkesakealkkinvpvvpssaapvetleealaiakei..gyPviikaafglGGkGmrvarneeelaelvkkalae 73 
                                   Dk +  ++l+k ++++ + +    ++ e+a+++ +++   +Pv+ik +f+  G+   +arn +el++l+k+a+ e
  gi|15669190|ref|NP_247995.1|  98 DKFKCIKLLAKNKIKTPKTALI--RDYEDAVKFIEKYnlRFPVVIKNSFSKCGLKVFMARNYDELKQLTKNAIWE 170
                                   6777778888888888887766..**********9862269****************************999866 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.31
                                   TTTTEEEEEEEES CS
                   CPSase_L_D2 166 pkskeyyviEvNt 178
                                   p++++yyviE+N+
  gi|15669190|ref|NP_247995.1| 250 PTKDNYYVIELNS 262
                                   57899******96 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.1e-06    0.0039       2      76 ..     107     182 ..     106     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.1e-06
                                   HTTT--B-EEEEECCHHHHHHHHHH..H-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE----SE CS
                     ATP-grasp   2 eklglpvprflaveskeeleeaaee..lglpvvvKarrlgydGkGqsvvrseedleqalealkeekvivEefvpfek 76 
                                   +k+++++p+ +++++ e++ +++e+  l++pvv+K +  +  G   ++ r+ ++l+q+++++  e  ++ ef++f+ 
  gi|15669190|ref|NP_247995.1| 107 AKNKIKTPKTALIRDYEDAVKFIEKynLRFPVVIK-NSFSKCGLKVFMARNYDELKQLTKNAIWEGKLIQEFIDFKE 182
                                   6899*************9999998633699*****.99999*********************999999999****85 PP

>> Ins134_P3_kin  Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0018       3.2       4      64 ..     108     164 ..     106     209 .. 0.71
   2 ?    4.0   0.0     0.017        30     170     187 ..     251     268 ..     224     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0018
                                   BTTEE---EEEE-S-GTTHHHHHHHTT--SSEEEEESB-SST.TTTEEEEE-SGGGGTT-- CS
                 Ins134_P3_kin   4 servgvPkqlvvtkdasslseavakagLklPliakplvadGtakshelslvydqeglkklk 64 
                                   ++++ +Pk   +  d ++  + ++k +L++P++ k   ++      +++++ + + lk+l+
  gi|15669190|ref|NP_247995.1| 108 KNKIKTPKTALIR-DYEDAVKFIEKYNLRFPVVIKNSFSKCG---LKVFMARNYDELKQLT 164
                                   5788899998888.9999999**************9877766...3455555545555444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.017
                                   T.--EEEEEEEES---TT CS
                 Ins134_P3_kin 170 tkdrylvidinyfPGyak 187
                                   tkd y+vi++n  PG ++
  gi|15669190|ref|NP_247995.1| 251 TKDNYYVIELNSSPGTKG 268
                                   6799**********9765 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.3e-05     0.077       8      71 ..     104     168 ..      96     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.3e-05
                                   HHHHHTT--B--EEEESSHHHHHHHHHHHSSSE.EEEEESC-GGGT-EEEESSHHHHHHHHHHHC CS
                        GARS_A   8 dllkkagiptaeyeaftdpeeakeyieeataka.lVvKadglaagKgvivakseeealkavkeil 71 
                                   +ll+k +i+t++ + + d+e+a ++ie+ + +  +V+K++    g  v +a++ +e  +  k+ +
  gi|15669190|ref|NP_247995.1| 104 KLLAKNKIKTPKTALIRDYEDAVKFIEKYNLRFpVVIKNSFSKCGLKVFMARNYDELKQLTKNAI 168
                                   799************************99887767999999999999999999999888777665 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.5e-05      0.12      15      57 ..     102     146 ..      94     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.5e-05
                   ATP-grasp_5  15 akelleaygipvvetrlassaeeaveaaeei..gypvvlKivspd 57 
                                     +ll+   i++++t l+++ e+av+ +e+    +pvv+K    +
  gi|15669190|ref|NP_247995.1| 102 CIKLLAKNKIKTPKTALIRDYEDAVKFIEKYnlRFPVVIKNSFSK 146
                                   56899************************9744799****76655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1824.29
//
Query:       gi|15669191|ref|NP_247996.1|  [L=309]
Description: hypothetical protein MJ_1002 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-23   80.6   2.4    1.1e-22   79.8   0.2    2.4  3  DisA_N          DisA bacterial checkpoint controller nucleoti
    3.1e-09   37.1   3.0    1.8e-08   34.6   0.2    3.1  3  PK_C            Pyruvate kinase, alpha/beta domain
  ------ inclusion threshold ------
       0.06   13.7   0.9       0.36   11.2   0.0    2.5  2  DUF4467         Domain of unknown function with cystatin-like
      0.094   12.6   0.4          8    6.3   0.2    2.3  2  eIF2A           Eukaryotic translation initiation factor eIF2
       0.11   12.1   0.2       0.23   11.1   0.2    1.4  1  MEIOC           Meiosis-specific coiled-coil domain-containin
       0.12   12.0   0.0       0.19   11.4   0.0    1.2  1  Glyco_hydro_18  Glycosyl hydrolases family 18
       0.15   12.2   0.4        3.9    7.6   0.0    2.5  2  SAM_Exu         Exuperantia SAM-like domain
       0.16   12.8   1.2        1.7    9.6   0.1    2.7  2  DUF5611         Domain of unknown function (DUF5611)


Domain annotation for each model (and alignments):
>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.31   6.9e+02      61      97 ..      99     114 ..      37     150 .. 0.65
   2 ?   -1.7   0.0      0.92   2.1e+03      31      47 ..     135     151 ..     112     166 .. 0.60
   3 !   79.8   0.2   5.1e-26   1.1e-22       3     119 .]     173     295 ..     171     295 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.31
                                   ETTEEEEEEEEE--TT-TTSST-SHHHHHHHHHHHHS CS
                        DisA_N  61 rdgrivaagviLplsenkelkelGtRHraAlgiseet 97 
                                   ++g ++a                       ++i +e 
  gi|15669191|ref|NP_247996.1|  99 SSGIVHA---------------------LKMKILKEN 114
                                   3333333.....................333333333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.92
                                   SEEEEEE--HHHHHHHT CS
                        DisA_N  31 gvkldaevskellkeif 47 
                                    v+++++v++ +l+e+f
  gi|15669191|ref|NP_247996.1| 135 VVNVKEHVKTITLYELF 151
                                   34444444444444444 PP

  == domain 3  score: 79.8 bits;  conditional E-value: 5.1e-26
                                   HHHHHHHHT--EEEEEESSSC.........CCTTCCTSEEEEEE--HHHHHHHTSTTSTTCSSEEEE.ETTEEEEEEEEE- CS
                        DisA_N   3 aveelskkkiGaliviereee.........lkeiietgvkldaevskellkeifekksplhDGAvii.rdgrivaagviLp 73 
                                   + e+++++ +G+++v++++ +         l+ ++ +  ++ +e  k ++ke+     + +DGA+ii ++g++v+ag++L+
  gi|15669191|ref|NP_247996.1| 173 GREGREGEYVGTIFVMGDTLNvmsmskpliLNPFAGHNASIFDENVKGTIKEL-----SSIDGAFIItDEGKVVSAGRFLE 248
                                   6788999************9977777666556777777788888888888888.....99*******88************ PP

                                   -TT-TTS.ST-SHHHHHHHHHHHHSSSEEEEE-TTTS-EEEEETTEE CS
                        DisA_N  74 lsenkel.kelGtRHraAlgiseetdalvivVSeetgkislakdgkl 119
                                   ++ + ++ k+lG+RH aA++is++t+a++++VS++ g ++++kdgk+
  gi|15669191|ref|NP_247996.1| 249 IKGDVNIpKGLGARHLAAASISKNTNAIAVTVSQSGGIVRVFKDGKI 295
                                   *88778988************************************85 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.2   8.2e-12   1.8e-08       4     117 .]       7     136 ..       4     136 .. 0.89
   2 ?   -1.6   0.0       1.3     3e+03      73      89 ..     157     173 ..     140     193 .. 0.58
   3 ?   -1.5   0.1       1.3   2.8e+03       6      30 ..     265     288 ..     261     296 .. 0.65

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 8.2e-12
                                   HHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TS.................SEEEEEESHHHHHHHHH..HCTTEEHHH. CS
                          PK_C   4 akaaveaaeelgakaIvvltesGetArliskyrpk.................vpiiavtpneltarqla..lyrGvypvlv 65 
                                   +k   e+a++++a+a  ++te+G++  l+  + +k                 v+ii+ tpn+ t ++++     ++yp+ +
  gi|15669191|ref|NP_247996.1|   7 IKHGLELAYDIKADAFMIFTETGKSYELLKSFLKKdehsgiikildkishknVKIIVATPNQVTYKKISseNEENIYPIFI 87 
                                   5666799************************999999********************************866788****75 PP

                                   HHHHH...TTSHHHHHHHHHHHTTSS-STSEEEEEE-SSSS..SS--EEEEE CS
                          PK_C  66 ekaktaestdellreavkvakeaglvkkgdevvvtaGtpkgesgttNtlrVv 117
                                   +  + +++   ++  ++ +a++ +++k++ ++v++ G pk  +g+ +t+ Vv
  gi|15669191|ref|NP_247996.1|  88 K-HR-EDNRCMIISSGIVHALKMKILKENNKIVAVVGEPKT-PGKLDTIMVV 136
                                   4.33.35555578899***********************87.*******997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                                   .TTSHHHHHHHHHHHTT CS
                          PK_C  73 stdellreavkvakeag 89 
                                   + + +l+e++k a+e g
  gi|15669191|ref|NP_247996.1| 157 KQKRTLKEIIKLAMEIG 173
                                   23334555555555533 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.3
                                   HHHHHHHHHT-SEEEEE-SSSHHHH CS
                          PK_C   6 aaveaaeelgakaIvvltesGetAr 30 
                                   aa++++++ +a a v++++sG  +r
  gi|15669191|ref|NP_247996.1| 265 AAASISKNTNAIA-VTVSQSGGIVR 288
                                   4555555555444.56788877665 PP

>> DUF4467  Domain of unknown function with cystatin-like fold (DUF4467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.6      0.87   1.9e+03      18      59 ..      74     117 ..      55     143 .. 0.63
   2 ?   11.2   0.0   0.00016      0.36      18      46 ..     268     296 ..     255     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.87
                       DUF4467  18 klakkgndvevd.i.kkedanvyVyedgKlivlaykllknreev 59 
                                   + + +++++ +  i ++ed    +   g +  l++k+lk+++++
  gi|15669191|ref|NP_247996.1|  74 ISSENEENIYPIfIkHREDNRCMIISSGIVHALKMKILKENNKI 117
                                   33333333333334236677777778887778888888877765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00016
                       DUF4467  18 klakkgndvevdikkedanvyVyedgKli 46 
                                    ++k+ n + v + +   +v+V++dgK++
  gi|15669191|ref|NP_247996.1| 268 SISKNTNAIAVTVSQSGGIVRVFKDGKIV 296
                                   6899***********************87 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2    0.0036         8      17      78 ..      58     121 ..      49     150 .. 0.82
   2 ?    4.2   0.0     0.016        35      82     133 ..     208     259 ..     196     288 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0036
                                   TTEEEEEEE.E--TT-CEEEEEEEEEESSSTT--EEECCEESSS.EEEEEE-..TTSS-EEEEE CS
                         eIF2A  17 GtsllvlvstevdktnksyygetelyliklkkkksevvelkkegpihdvaWs..pkskefaviy 78 
                                      ++v +  +v+ ++ s   e+++y i +k+ ++++  +   g +h+++ +  +++++++ + 
  gi|15669191|ref|NP_247996.1|  58 NVKIIVATPNQVTYKKISSENEENIYPIFIKHREDNRCMIISSGIVHALKMKilKENNKIVAVV 121
                                   56789999999************************************98765223444555555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.016
                                   SCEEEEEECSCEEEEEEEEES--EEEE-TTSSEEEEE-TTSSS-EEEEEETT CS
                         eIF2A  82 pakvslfdlkvkviskleeqkrNtiffspkgklvllaGfgnlaGeleiwdvk 133
                                     ++s+fd +vk + k  ++   + +  ++gk+v  + f +++G+++i +  
  gi|15669191|ref|NP_247996.1| 208 GHNASIFDENVKGTIKELSSIDGAFIITDEGKVVSAGRFLEIKGDVNIPKGL 259
                                   56789999999988888888888889999******************95544 PP

>> MEIOC  Meiosis-specific coiled-coil domain-containing protein MEIOC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2    0.0001      0.23      41      98 ..     109     171 ..     103     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                         MEIOC  41 kvsssnnipip..rlpanpsrvdrLivdqlreharvitLlakmErLrgv...plhanisaale 98 
                                   k+  +nn+ ++    p+ p ++d ++v +++eh + itL +  E L +    +l++ i+ a+e
  gi|15669191|ref|NP_247996.1| 109 KILKENNKIVAvvGEPKTPGKLDTIMVVNVKEHVKTITLYELFETLDEKqkrTLKEIIKLAME 171
                                   566667766663356999************************999976411257777777766 PP

>> Glyco_hydro_18  Glycosyl hydrolases family 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.4e-05      0.19     129     200 ..     147     223 ..     127     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.4e-05
                                   HHHHHHHHH.HHHHHTSTTCEEEEEEESSHHHHHHHCHHHHHHHHTSEEEEETTTSSS...TTSSBE--SS-SSB...... CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx...... RF
                Glyco_hydro_18 129 lkelreald.kakategkkllLsaavpasasdlskgydlpkiakylDyvnvmtYDfhg...swdnvtghhaplyd...... 199
                                   l el e ld k+  ++  k ++ +a++ ++   ++g+++ +i  + D +nvm++   +     + ++gh+a+++d      
  gi|15669191|ref|NP_247996.1| 147 LYELFETLDeKQ--KRTLKEIIKLAMEIGREG-REGEYVGTIFVMGDTLNVMSM---SkplILNPFAGHNASIFDenvkgt 221
                                   567888888444..455568888888888888.6799*****************...32334455********99654432 PP

                                   .T CS
                                   .x RF
                Glyco_hydro_18 200 .a 200
                                    +
  gi|15669191|ref|NP_247996.1| 222 iK 223
                                   21 PP

>> SAM_Exu  Exuperantia SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0017       3.9      24      59 ..      24      58 ..      19      62 .. 0.89
   2 ?    1.9   0.1      0.11   2.4e+02      30      53 ..     145     168 ..     141     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0017
                       SAM_Exu 24 lLAEngidyesLkeiweekkkeGlekllkekitslk 59
                                  +  E g  ye Lk   +++++ G+ k+l +ki++++
  gi|15669191|ref|NP_247996.1| 24 IFTETGKSYELLKSFLKKDEHSGIIKIL-DKISHKN 58
                                  56799***********************.9998765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                       SAM_Exu  30 idyesLkeiweekkkeGlekllke 53 
                                   i++ +L e+  ek+k  l++++k 
  gi|15669191|ref|NP_247996.1| 145 ITLYELFETLDEKQKRTLKEIIKL 168
                                   788899999999999999999964 PP

>> DUF5611  Domain of unknown function (DUF5611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3      0.23   5.2e+02       3      68 ..       4      70 ..       2      83 .. 0.64
   2 ?    9.6   0.1   0.00074       1.7      19      75 ..      79     133 ..      70     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.23
                                  EE---SSS--SH.HHHHHHHHHHT.-EEEEETTEEEEE.....-TTBS-EEEEE..-SS-EEEEE--.B.. CS
                       DUF5611  3 eYkiKrGfkkeeeerlkelleeyfggeveeegdllvvs.....fgaikklevkisskkkklvvdteerdae 68
                                  +Y iK G ++    ++k+    +f +e  ++ +ll +        +i k+  kis+k+ k++v t ++  +
  gi|15669191|ref|NP_247996.1|  4 KYIIKHGLELAY--DIKADAFMIF-TETGKSYELLKSFlkkdeHSGIIKILDKISHKNVKIIVATPNQ-VT 70
                                  678888888777..7777777777.5555555555553345666666666668888999999998873.33 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00074
                                   HHHHHHHT.-EEEEETTEEEEE-TTBS-EEEEE..-SS-EEEEE--.B...-TTS-H CS
                       DUF5611  19 kelleeyfggeveeegdllvvsfgaikklevkisskkkklvvdteerdaeeeddeaa 75 
                                   +e +  +f  + +e++ ++++s g + +l++ki ++++k+v+ + e +++ ++ +++
  gi|15669191|ref|NP_247996.1|  79 EENIYPIF-IKHREDNRCMIISSGIVHALKMKILKENNKIVAVVGE-PKTPGKLDTI 133
                                   66677788.888899999999*************999999998888.4444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2012.36
//
Query:       gi|15669192|ref|NP_247997.1|  [L=420]
Description: 3-isopropylmalate dehydratase LeuC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   3.9e-102  342.6   4.7   3.7e-100  336.1   4.7    2.2  1  Aconitase  Aconitase family (aconitate hydratase)
  ------ inclusion threshold ------
      0.011   14.4   0.1      0.017   13.9   0.1    1.2  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.1   4.7  4.1e-104  3.7e-100       2     461 .]       6     413 ..       5     413 .. 0.89

  Alignments for each domain:
  == domain 1  score: 336.1 bits;  conditional E-value: 4.1e-104
                     Aconitase   2 kiwdahlvee....egiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeealeknled 78 
                                   ki+++++  e    ++i+  +d  +++d t + a + l+++ ++v+++++ +   dh+vp +     +v          + 
  gi|15669192|ref|NP_247997.1|   6 KILSKKVGYEvcagDSIEVEVDLAMTHDGTTPLAYKALKEMSDSVWNPDKIVVAFDHNVPPN-----TV---------KAA 72 
                                   666666553344323366668****************************************9.....44.........122 PP

                     Aconitase  79 efernkeryefLksaakafgirvvppg.qGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqp 158
                                   e+++    +e    + k+fgi+ +  g +GI+Hq+  E+ ++lp++ v g+DSHT+++g++G++a+G G ++++ + ++ +
  gi|15669192|ref|NP_247997.1|  73 EMQK--LALE----FVKRFGIKNFHKGgEGICHQILAEN-YVLPNMFVAGGDSHTCTHGAFGAFATGFGATDMAYIYATGE 146
                                   3333..4444....5779***7666665***********.***************************************** PP

                     Aconitase 159 lelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdek 239
                                   +++k+pk+++v + Gk +e v+akD+vl v+++++++g++  ++E+ Ge v+++ +++r+T++NMa+E+G +tg+++ de 
  gi|15669192|ref|NP_247997.1| 147 TWIKVPKTIRVDIVGK-NENVSAKDIVLRVCKEIGRRGATYMAIEYGGEVVKNMDMDGRLTLCNMAIEMGGKTGVIEADEI 226
                                   ***************9.789************************************************************* PP

                     Aconitase 240 tleYLkatgreeaavlveaydkaqalf.elaadedaeydkvleldlstlepsvagpkrPqdavplselvkkefkeelekea 319
                                   t++YLk ++r  +    e+++k ++   +++  ++a+y k++e+d+ ++e +va p++P+++ p+ ++v            
  gi|15669192|ref|NP_247997.1| 227 TYDYLK-KERGLSD---EDIAKLKKERiTVN-RDEANYYKEIEIDITDMEEQVAVPHHPDNVKPI-SDV------------ 289
                                   ******.7887777...56555555432444.55789****************************.333............ PP

                     Aconitase 320 aekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkayleaeGlleiL 400
                                                  + +++++++igSCTN++++d+r+aa+ l+     g++v+++vk++v P+S++v  ++ +eG+ +i+
  gi|15669192|ref|NP_247997.1| 290 ---------------EGTEINQVFIGSCTNGRLSDLREAAKYLK-----GREVHKDVKLIVIPASKKVFLQALKEGIIDIF 350
                                   ...............234589***********************.....******************************** PP

                     Aconitase 401 ekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqg.pntrayLaSPelvvaaAlaG 461
                                    kaG+ + ++gC++C+g  ++ l+ege ++s++NRNF+gR+g  n+  yLaSP++++ +A++G
  gi|15669192|ref|NP_247997.1| 351 VKAGAMICTPGCGPCLGaHQGVLAEGEICLSTTNRNFKGRMGhINSYIYLASPKIAAISAVKG 413
                                   *****************************************7366666************998 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.8e-06     0.017     285     357 ..     288     362 ..     241     375 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-06
                        DUF521 285 kakeekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvt.tsrevkeeaerlglveklekaGvkvlsdtC 357
                                   + + ++++ v++G c    l++lre a++lkg++++++v+l+v+ +s++v  +a ++g++++  kaG+ +++  C
  gi|15669192|ref|NP_247997.1| 288 DVEGTEINQVFIGsCTNGRLSDLREAAKYLKGREVHKDVKLIVIpASKKVFLQALKEGIIDIFVKAGAMICTPGC 362
                                   45667788888875778899********************998747888*********************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2861.26
//
Query:       gi|15669193|ref|NP_247998.1|  [L=214]
Description: hypothetical protein MJ_1004 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.2e-16   58.4   3.3    3.7e-09   36.9   0.1    2.4  2  CBS         CBS domain
     0.0022   18.2   0.2       0.19   11.8   0.1    2.3  2  sCache_3_2  Single cache domain 3
  ------ inclusion threshold ------
      0.087   12.9   1.0        1.3    9.2   0.0    2.8  3  TAFII28     hTAFII28-like protein conserved region
      0.099   13.2   0.0       0.21   12.2   0.0    1.5  1  Sar8_2      Sar8.2 family


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.1   8.3e-13   3.7e-09       1      52 [.       3      54 ..       3      58 .. 0.90
   2 !   21.5   1.0   5.4e-08   0.00024       2      55 ..      66     121 ..      65     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 8.3e-13
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHH CS
                           CBS  1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDll 52
                                  V+d+m +++  ++ d+t+e+a++l+++k+ + + P+Vd++++lvG vt   ll
  gi|15669193|ref|NP_247998.1|  3 VRDLMDKNFAKIYVDETVEDAINLLKKKKrF-SAPIVDKEDRLVGWVTTLELL 54
                                  89***********************855559.99*************976665 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 5.4e-08
                                   HHHSBS..SCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   2 gdimtr..dvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55 
                                   +++m++  +v+tv++d+  + ++ ++++++ v ++PV+  dg+++G+v   D+++ l
  gi|15669193|ref|NP_247998.1|  66 TEFMRPveEVITVYEDDEARNVVLKFVKYKvV-SIPVLTRDGRVIGMVRNCDVVKTL 121
                                   5777777799****************9***66.****999********877777766 PP

>> sCache_3_2  Single cache domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.0    0.0092        41     106     123 ..      32      49 ..      17      70 .. 0.84
   2 !   11.8   0.1   4.3e-05      0.19      95     123 ..      86     113 ..      62     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0092
                    sCache_3_2 106 rvklPvfdadgrviGivs 123
                                   r  +P++d+++r++G+v 
  gi|15669193|ref|NP_247998.1|  32 RFSAPIVDKEDRLVGWVT 49 
                                   6789************95 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4.3e-05
                    sCache_3_2  95 gtvtgtlgpslrvklPvfdadgrviGivs 123
                                     v++  +++  v  Pv+ +dgrviG+v+
  gi|15669193|ref|NP_247998.1|  86 N-VVLKFVKYKVVSIPVLTRDGRVIGMVR 113
                                   3.447789999****************96 PP

>> TAFII28  hTAFII28-like protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00029       1.3      50      75 ..      11      37 ..       6      44 .. 0.81
   2 ?   -0.8   0.0      0.37   1.7e+03      57      83 ..     147     172 ..     142     175 .. 0.70
   3 ?    0.3   0.1      0.16   7.3e+02      44      68 ..     182     210 ..     170     213 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00029
                       TAFII28 50 laKvFvgeiveeArevqeeweesg.pl 75
                                  +aK++v e ve A ++ ++++  + p+
  gi|15669193|ref|NP_247998.1| 11 FAKIYVDETVEDAINLLKKKKRFSaPI 37
                                  89*************999886655565 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.37
                       TAFII28  57 eiveeArevqeeweesgplqpehlrea 83 
                                   e++e+A  v +++   + ++p++ +e 
  gi|15669193|ref|NP_247998.1| 147 ELMEAAAVVTKRM-TGEDITPQEYEER 172
                                   7888888888776.3347777777765 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.16
                       TAFII28  44 aivvaglaKvFvg....eiveeArevqee 68 
                                   + +  gl K Fvg     +v  Ar++ ++
  gi|15669193|ref|NP_247998.1| 182 IWACGGLEKFFVGlieiGMVALARKLAKR 210
                                   56778999***994433347777776665 PP

>> Sar8_2  Sar8.2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.6e-05      0.21      28      68 ..     147     187 ..     141     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.6e-05
                        Sar8_2  28 emskaaapitqamnsnnisdqktGagiirklagkilkaakv 68 
                                   e+ +aaa +t+ m ++ i+ q     i ++  gk++ a+ +
  gi|15669193|ref|NP_247998.1| 147 ELMEAAAVVTKRMTGEDITPQEYEERIKKTTFGKAIWACGG 187
                                   7789*************************999**9988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1365.18
//
Query:       gi|15669194|ref|NP_247999.1|  [L=131]
Description: hypothetical protein MJ_1005 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.2e-14   51.3   0.0    1.3e-13   50.6   0.0    1.3  1  HTH_11        HTH domain
      4e-05   23.2   0.0    0.00017   21.2   0.0    1.9  2  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor


Domain annotation for each model (and alignments):
>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   1.5e-17   1.3e-13       3      55 .]      63     121 ..      61     121 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.5e-17
                        HTH_11   3 lqilel..Lleargp.isgeeLAeeLnv.SrrtvrrdIkaLeelgvpIesepgr..GYr 55 
                                   ++ile+  +++++++ isge+L++++++ Sr +v+++Ik+L++lg++Ies++g+  GY+
  gi|15669194|ref|NP_247999.1|  63 RKILERnkIFAKNSDfISGEFLKDYIDRkSRVAVHNRIKDLKTLGFKIESKSGPfgGYK 121
                                   7888888877888888***************************************9996 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.035   3.2e+02       8      37 ..      41      70 ..      38      76 .. 0.82
   2 !   21.2   0.0   1.9e-08   0.00017      15      64 ..      70     121 ..      59     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.035
                  HrcA_DNA-bdg  8 eilqaLielyrkkkravKgeeiAevlkrne 37
                                  +il  + +ly+k ++    ee  ++l+rn+
  gi|15669194|ref|NP_247999.1| 41 NILIGVNDLYHKLSEKFGEEEARKILERNK 70
                                  68888899***9999999999999999997 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.9e-08
                  HrcA_DNA-bdg  15 elyrkkkravKgeeiAevlkrne.GtvRNqlqsLkalgL.vegvpGPkGGYk 64 
                                   +++ k++  + ge + + ++r++   v N ++ Lk+lg  +e+++GP GGYk
  gi|15669194|ref|NP_247999.1|  70 KIFAKNSDFISGEFLKDYIDRKSrVAVHNRIKDLKTLGFkIESKSGPFGGYK 121
                                   67889999999999*****9986257************879**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 881.01
//
Query:       gi|15669195|ref|NP_248000.1|  [L=359]
Description: hypothetical protein MJ_1006 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-65  218.8   9.7      9e-65  218.8   9.7    2.0  2  ATPase_2  ATPase domain predominantly from Archaea
      3e-10   40.7   0.0    4.7e-10   40.1   0.0    1.3  1  AAA_16    AAA ATPase domain
    1.2e-07   32.1   0.0    2.8e-07   30.9   0.0    1.6  1  AAA_22    AAA domain
    1.6e-07   31.4   8.5    8.9e-05   22.5   0.0    3.4  3  AAA_14    AAA domain
      1e-06   29.2   0.3    4.6e-06   27.1   0.1    2.2  2  AAA       ATPase family associated with various cellular acti
     0.0013   18.2   0.0     0.0055   16.2   0.0    1.9  2  RecA      recA bacterial DNA recombination protein
  ------ inclusion threshold ------
      0.027   13.5   0.0      0.052   12.6   0.0    1.4  1  T2SSE     Type II/IV secretion system protein
      0.033   14.1   0.1       0.23   11.3   0.0    2.3  2  NACHT     NACHT domain
      0.033   13.8   0.0       0.94    9.1   0.0    2.4  2  Zot       Zonular occludens toxin (Zot)
      0.063   12.5   0.0      0.095   11.9   0.0    1.3  1  DUF2075   Uncharacterized conserved protein (DUF2075)
       0.19   11.5   0.0       0.43   10.3   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
        0.2   11.5   3.0       0.59   10.0   0.0    2.9  4  TK        Thymidine kinase


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.8   9.7     6e-68     9e-65       1     233 []      20     258 ..      20     258 .. 0.97
   2 ?    1.0   1.8      0.22   3.3e+02     101     157 ..     297     350 ..     264     355 .. 0.75

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 6e-68
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...eeeekkkl 78 
                                   F++Rekel++l+++++ epn+i+f+YGp++sGK++++ ++ie+l++kd+ v++y++lre+++ +++ef+e   e+ +kk+l
  gi|15669195|ref|NP_248000.1|  20 FYNREKELNYLKNYVQLEPNSILFVYGPKSSGKSTVMLRVIEELSKKDDLVFFYYDLREYATPTKEEFLEiffEKGDKKYL 100
                                   9******************************************************************************** PP

                      ATPase_2  79 ekal..giavpkaeleeilk...eksklvfkaielllekikkkgkkiiiiiDelqklidlgln....gaellvkeLlnlie 150
                                    + +  + ++ k+ +ee ++    k ++vf+++++ ++++ k+gkk+i+iiDelqkl+++++n    g+++l++eL+nl++
  gi|15669195|ref|NP_248000.1| 101 LNRFeiNLKIFKFGIEEKFDfdnIKLNDVFSKMKESINAVIKDGKKPILIIDELQKLKSIYFNgegkGDKSLLNELFNLFV 181
                                   *999667789999******9999999*************************************999899************ PP

                      ATPase_2 151 sltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkeleelskedfeeiyryvGGkPkalv 231
                                   +ltk +hlc+vicl+S++lfie++y++s+le++++y+l+d+l+ke+++n+lke     e++s+e+++++ +y+ + P+++ 
  gi|15669195|ref|NP_248000.1| 182 HLTKVRHLCHVICLTSDTLFIEEIYRNSTLENTSEYYLIDWLRKESIRNILKE-----EGFSEEEVDYCLKYL-SLPYEIS 256
                                   *****************************************************.....799************.9**9998 PP

                      ATPase_2 232 el 233
                                   +l
  gi|15669195|ref|NP_248000.1| 257 QL 258
                                   76 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.22
                      ATPase_2 101 lvfkaielllekikkkgkkii..iiiDelqklidlglngaellvkeLlnliesltkekh 157
                                   ++  a++l+ +kik + k+ii   ++De+  li     ++e l ++ +n i ++t+ k+
  gi|15669195|ref|NP_248000.1| 297 KLIDALKLFENKIKVDIKEIIrdNLMDEVKFLI-----KNEILFYDVMNGIIKPTSVKK 350
                                   345688999999999999988444888888888.....589999999999999998876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   3.2e-13   4.7e-10       1     150 [.      19     168 ..      19     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 3.2e-13
                        AAA_16   1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysa.laqalar 78 
                                   +++ Re+el+ L+++++   +  p ++++++G++ +GKs+++ ++ ++l+k++  +f++ + +++  a+p    +++++++
  gi|15669195|ref|NP_248000.1|  19 KFYNREKELNYLKNYVQ--LE--PnSILFVYGPKSSGKSTVMLRVIEELSKKDdLVFFYYDLREY--ATPTKEeFLEIFFE 93 
                                   6999*****88888887..33..338****************99999999997699999999999..9999888*****99 PP

                        AAA_16  79 eellrqlldeaesaeleawrekleealaavpelagaeasrllellkrll.allsrderplvlvlDdlqwade........a 150
                                   ++  + ll++ e  +l  ++  +ee +      +  + ++++ ++k+ + a ++  +++ +l++D+lq++++        +
  gi|15669195|ref|NP_248000.1|  94 KGDKKYLLNRFEI-NLKIFKFGIEEKFD----FDNIKLNDVFSKMKESInAVIKD-GKKPILIIDELQKLKSiyfngegkG 168
                                   9999999999555.99999999999999....5555569**********666676.777*********9987555555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   1.9e-10   2.8e-07       5     117 ..      39     185 ..      35     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.9e-10
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellralglelka............. 70 
                                    +il+v+G++ +GK+t++ r+ e+l +       ++++v  +++l +  ++++   e+l+++ +++++             
  gi|15669195|ref|NP_248000.1|  39 NSILFVYGPKSSGKSTVMLRVIEELSK-------KDDLVffYYDLREYATPTKE--EFLEIFFEKGDKkyllnrfeinlki 110
                                   689**********************75.......55555578999999866654..4444444444444579********* PP

                        AAA_22  71 ...............erlsseellealeqalraravielliiDEaqhlr....s......eealeeL....rslln 117
                                                   ++  + + e ++  +++ ++ ++liiDE q+l     +      + +l+eL    ++l +
  gi|15669195|ref|NP_248000.1| 111 fkfgieekfdfdnikLNDVFSKMKESINAVIKDGKK-PILIIDELQKLKsiyfNgegkgdKSLLNELfnlfVHLTK 185
                                   ***********6664444455555666666666666.***********7555515677775555555111144444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.9e-08   8.9e-05       2      68 ..      39     100 ..      38     102 .. 0.77
   2 !   10.3   0.5   0.00037      0.55      36      79 ..     119     160 ..     102     226 .. 0.67
   3 ?    1.9   0.7      0.14   2.1e+02      19      75 ..     268     327 ..     266     351 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.9e-08
                        AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktyl 68 
                                   + il++ G++ +GK+t++ ++i+el  kk++ +++  d  ++++ +++ ++le+++ek  + +k+yl
  gi|15669195|ref|NP_248000.1|  39 NSILFVYGPKSSGKSTVMLRVIEELS-KKDDLVFFYYDLREYATPTKE-EFLEIFFEK--G-DKKYL 100
                                   5799******************9999.888888888888777654443.588999887..3.34444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00037
                        AAA_14  36 inldderdkkladpekllelileklkeekktylflDEiqevpew 79 
                                   +++d+ ++ +   ++k+ e i + +k+ kk +l++DE q+++++
  gi|15669195|ref|NP_248000.1| 119 FDFDNIKLNDV--FSKMKESINAVIKDGKKPILIIDELQKLKSI 160
                                   44444444332..233555555555557999*********9543 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.14
                        AAA_14  19 lkqlikell.vkkesilyinldderdkkladpekllelileklkeekkty...lflDEiqe 75 
                                   ++q ik+ + +++++ily+   ++++++ +   + l+l+ +k+k + k++    ++DE++ 
  gi|15669195|ref|NP_248000.1| 268 VEQTIKQWInIERDKILYLISTQKEFEMGKLI-DALKLFENKIKVDIKEIirdNLMDEVKF 327
                                   67888888899999999999999888655544.4566666664332222212236677665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   3.1e-09   4.6e-06       2     112 ..      43     199 ..      42     215 .. 0.72
   2 ?   -2.9   0.0       5.5   8.3e+03      94     130 ..     276     311 ..     263     313 .. 0.59

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.1e-09
                                   EEESSTTSSHHHHHHHHHHHHTHE..............................EEEEETTTCSSS............... CS
                           AAA   2 llyGppGtGKTllakavakelgve..............................fleisgsellsk............... 37 
                                    +yGp+  GK++++  v++el+ +                                         k               
  gi|15669195|ref|NP_248000.1|  43 FVYGPKSSGKSTVMLRVIEELSKKddlvffyydlreyatptkeefleiffekgdK----------Kyllnrfeinlkifkf 113
                                   68******************96444555455555555555666655554444440..........1555555555555556 PP

                                   ...............STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTE CS
                           AAA  38 ...............yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskv 103
                                                  ++++++++i++++k+ k    + il+iDE+ +l +   ++e + +++++n+L++ +  ++k ++ +
  gi|15669195|ref|NP_248000.1| 114 gieekfdfdniklndVFSKMKESINAVIKDGK----KPILIIDELQKLKSIYFNGEGKGDKSLLNELFNLFVHLTKVRHLC 190
                                   56665666666666666778888888887754....48**********888899999********************9999 PP

                                   EEEEEESSG CS
                           AAA 104 ivigatnrp 112
                                    vi+ t + 
  gi|15669195|ref|NP_248000.1| 191 HVICLTSDT 199
                                   ***999874 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.5
                                   HHTTTSSSTEEEEEEESS...GGGSTHHHHSTTSSEEEET CS
                           AAA  94 dgvkkkeskvivigatnr...pdkldpallrgRfdrkiei 130
                                    + ++  +k++ ++ t++   + kl +al    f+ ki++
  gi|15669195|ref|NP_248000.1| 276 INIER--DKILYLISTQKefeMGKLIDALK--LFENKIKV 311
                                   44444..46777777777444555555555..67777765 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.7e-06    0.0055      55      86 ..      41      72 ..      36      84 .. 0.89
   2 ?   -1.1   0.1      0.69     1e+03     178     223 ..     268     317 ..     255     341 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.7e-06
                                  EEEEEESTTSSHHHHHHHHHHHHHHTT--EEE CS
                          RecA 55 iieiyGpessGkttlalhaiaeaqkkggvaaf 86
                                  i+ +yGp+ssGk+t+ l++i e  kk+ ++ f
  gi|15669195|ref|NP_248000.1| 41 ILFVYGPKSSGKSTVMLRVIEELSKKDDLVFF 72
                                  7789*********************9998776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.69
                                   TT--EEEEEEE----------.-------H..HHHHHH.-SEEEEEEEES CS
                          RecA 178 ksntvvifinqirekiGvmfg.npetttGG..ralkfy.asvrldvrrie 223
                                     +t+  +in  r+ki  +   + e   G    alk++   +++d+++i 
  gi|15669195|ref|NP_248000.1| 268 VEQTIKQWINIERDKILYLIStQKEFEMGKliDALKLFeNKIKVDIKEII 317
                                   45677778888888886655414444444322689977346888888764 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.5e-05     0.052     128     172 ..      38      82 ..       8      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                         T2SSE 128 erglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqle 172
                                    + ++ v G+ +sGK+t++  +++e+ k+d+ +    D +E+   
  gi|15669195|ref|NP_248000.1|  38 PNSILFVYGPKSSGKSTVMLRVIEELSKKDDLVFFYYDLREYATP 82 
                                   35678899*********************9999999999998765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016      0.23       2     113 ..      41     180 ..      40     240 .. 0.64
   2 ?   -2.7   0.0       3.3     5e+03     104     125 ..     308     329 ..     298     330 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C........... CS
                         NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse........... 71 
                                   ++++ G+  sGK+t + ++++++ +++       ++F+  lre  +++++  + ++ f++++++    +            
  gi|15669195|ref|NP_248000.1|  41 ILFVYGPKSSGKSTVMLRVIEELSKKD-----DLVFFYYDLREYATPTKE-EFLEIFFEKGDKKYLLNRFeinlkifkfgi 115
                                   57899*******************999.....4899**********9999.888888888877666655556666666666 PP

                                   ....................CHHHHCCSCCCEE.......EEEE-STT-SS-TCH............HHHHH CS
                         NACHT  72 ....................vwavllelperlL.......lilDglDelvtdlgq...kekqpvrtlLseli 113
                                                        ++ +               li+D l +l+++  +   k+ +++ + L +l+
  gi|15669195|ref|NP_248000.1| 116 eekfdfdniklndvfskmkeSINAV-------IkdgkkpiLIIDELQKLKSIYFNgegKGDKSLLNELFNLF 180
                                   6666666666666444444433333.......2555555599999999998776654544455544444444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.3
                                   .....HHHHHCTTTTT--EEEE CS
                         NACHT 104 pvrtlLselirkkllpeaslll 125
                                   ++++ ++e+ir +l+ e+++l+
  gi|15669195|ref|NP_248000.1| 308 KIKVDIKEIIRDNLMDEVKFLI 329
                                   4455789999999999998876 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.087   1.3e+02       1      27 [.      40      65 ..      40      82 .. 0.78
   2 ?    9.1   0.0   0.00063      0.94      59     124 ..     123     197 ..     101     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.087
                           Zot  1 aislvtGapGsgKtsgavkkdllpalk 27
                                  +i +v+G++ sgK+ + +   + + +k
  gi|15669195|ref|NP_248000.1| 40 SILFVYGPKSSGKSTVMLRV-IEELSK 65
                                  689***********988877.655554 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00063
                           Zot  59 ridnpegaetlkefakwatid.kgallviDEcqe...ifpvrakegrkd.....pevinaftehRhlgwDivllt 124
                                   +i+ ++ ++++ke+    + d k  +l+iDE q+   i+ +  ++g k       + +  +t+ Rhl + i+l+ 
  gi|15669195|ref|NP_248000.1| 123 NIKLNDVFSKMKESINAVIKDgKKPILIIDELQKlksIYFNGEGKGDKSllnelFNLFVHLTKVRHLCHVICLTS 197
                                   5667789999999999999899*********997333566666655555685555556777889****9999986 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.4e-05     0.095       2     103 ..      40     163 ..      39     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-05
                       DUF2075   2 avvlVtGvaGtGKtvvllnllaeledde.........................eertavylsvNhplvl.vlrealakke. 55 
                                   ++++V G   +GK+ v+l+++ el++++                         e+  ++yl+   + +l + +  +++k  
  gi|15669195|ref|NP_248000.1|  40 SILFVYGPKSSGKSTVMLRVIEELSKKDdlvffyydlreyatptkeefleiffEKGDKKYLLNRFEINLkIFKFGIEEKFd 120
                                   689*********************444467777788888888888888889987777777765544444266777777778 PP

                       DUF2075  56 .ekkkkkeafeklssfinnlsefkkaeekkeepkedvvivDEAhrllt...k 103
                                     + k +++f+k+++ in++          ++ k  ++i+DE ++l +   +
  gi|15669195|ref|NP_248000.1| 121 fDNIKLNDVFSKMKESINAVI---------KDGKKPILIIDELQKLKSiyfN 163
                                   888999***************.........899999*********9984442 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00029      0.43      17      39 ..      34      56 ..      28      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                        AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                  ++++++++ ++ Gp  sGKST++
  gi|15669195|ref|NP_248000.1| 34 VQLEPNSILFVYGPKSSGKSTVM 56
                                  67788889999**********86 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00039      0.59       2      33 ..      40      71 ..      39      79 .. 0.85
   2 ?   -0.5   0.1      0.66   9.9e+02      64      90 ..     132     158 ..      99     165 .. 0.66
   3 ?   -2.9   0.0       3.4   5.1e+03      29      52 ..     187     209 ..     174     245 .. 0.59
   4 ?   -0.5   0.1      0.66   9.9e+02      48      96 ..     287     335 ..     255     344 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00039
                            TK  2 sielilgpmfaGKsteLlrrvkryqlaekkvv 33
                                  si +++gp  +GKst +lr ++++++++  v 
  gi|15669195|ref|NP_248000.1| 40 SILFVYGPKSSGKSTVMLRVIEELSKKDDLVF 71
                                  689******************99988776555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.66
                            TK  64 ssleeikeeleeedvdvvlvDEaqFfe 90 
                                   +  e+i++++++ +  ++++DE q ++
  gi|15669195|ref|NP_248000.1| 132 KMKESINAVIKDGKKPILIIDELQKLK 158
                                   333455566666667899999998776 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.4
                            TK  29 ekkvvvikaakdnRysegkvvthd 52 
                                   +  + vi  + d+ + e +++  +
  gi|15669195|ref|NP_248000.1| 187 RHLCHVICLTSDTLFIE-EIYRNS 209
                                   44455555555555554.344444 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.66
                            TK  48 vvthdgisleakksktssleeikeeleeedvdvvlvDEaqFfeqdivel 96 
                                   ++t+++  + +  ++ + +e+ +++  +e +   l+DE++F+ ++ + +
  gi|15669195|ref|NP_248000.1| 287 ISTQKEFEMGKLIDALKLFENKIKVDIKEIIRDNLMDEVKFLIKNEILF 335
                                   4555555555555555555555555555555556899999998444445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2128.12
//
Query:       gi|15669196|ref|NP_248001.1|  [L=878]
Description: valyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.4e-156  522.2  10.7   1.9e-156  521.9   6.9    2.3  2  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
      9e-35  119.9   1.0    2.7e-34  118.3   1.0    1.8  1  Anticodon_1     Anticodon-binding domain of tRNA
    1.2e-25   90.1   9.3    2.2e-15   56.3   0.0    3.9  4  tRNA-synt_1g    tRNA synthetases class I (M)
    2.9e-06   26.9   0.0      0.014   14.8   0.0    2.4  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
    6.8e-05   22.5   0.2    0.00063   19.3   0.0    2.7  3  tRNA-synt_1_2   Leucyl-tRNA synthetase, Domain 2
    9.3e-05   21.5   0.1     0.0014   17.6   0.9    2.5  2  tRNA-synt_1f    tRNA synthetases class I (K)
     0.0053   16.8   1.0       0.26   11.3   0.1    3.1  3  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.069   13.1   3.2      0.093   12.7   0.4    2.6  2  Nudix_N_2       Nudix N-terminal
      0.084   12.2   0.0        2.3    7.5   0.0    2.4  2  tRNA-synt_1b    tRNA synthetases class I (W and Y)
       0.17   12.0   1.0        2.8    8.0   0.1    2.9  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.27   10.6   2.4        6.2    6.2   0.0    3.1  3  zf-TFIIB        Transcription factor zinc-finger
       0.29   11.2   4.6       0.21   11.6   2.2    2.0  2  ADK_lid         Adenylate kinase, active site lid
       0.43   10.5   1.4        2.6    8.0   1.6    2.3  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.52   10.6   5.1         12    6.2   0.4    3.3  3  IBR             IBR domain, a half RING-finger domain
        1.4    8.6   7.4         24    4.7   0.1    4.1  4  zf_UBZ          Ubiquitin-Binding Zinc Finger
        2.4    7.7  10.3        1.4    8.4   0.1    4.1  4  zf-ribbon_3     zinc-ribbon domain
        3.2    7.3   8.1        4.1    7.0   5.0    2.9  2  TF_Zn_Ribbon    TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.9   6.9  1.8e-159  1.9e-156       1     601 [.      14     565 ..      14     566 .. 0.96
   2 ?   -3.7   0.1       2.5   2.6e+03     214     278 ..     740     799 ..     738     802 .. 0.57

  Alignments for each domain:
  == domain 1  score: 521.9 bits;  conditional E-value: 1.8e-159
                   tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakve 81 
                                   ++++kWee++++k    +e +k+++i+  +PPy tG+lH+Ghal+ t +di+ rykrmkG++vl+  GwD++Gl++e kve
  gi|15669196|ref|NP_248001.1|  14 QIQKKWEESKIYKFD--EESNKPPYIIDTPPPYPTGRLHLGHALNWTYMDIIARYKRMKGFNVLFPQGWDCHGLPTEVKVE 92 
                                   5789*********98..78889*********************************************************** PP

                   tRNA-synt_1  82 kklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkkl 162
                                   +  g+++     ++ r++fre + e  +e +e++r+q+k lG+s+D+d+ey+T+ +e+ +  + +fvr++++gliyrgk +
  gi|15669196|ref|NP_248001.1|  93 EIHGITKS----DVDRHKFRELCIELTKENIEKMRRQIKSLGISIDWDKEYITMTPEYIKKSQTAFVRMYKDGLIYRGKFP 169
                                   *9988886....********************************************************************* PP

                   tRNA-synt_1 163 vnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitkeklilaeallksl 243
                                   vnw+++++ta++ +Eveyk+ ++ l +++fp+ad+e  +l iaTT+Pe + + +a+ v+pe                    
  gi|15669196|ref|NP_248001.1| 170 VNWCPRCQTAIAFAEVEYKERESKLNYIKFPAADGEG-HLLIATTRPELMAACVAILVHPE-------------------- 229
                                   *************************************.***********************.................... PP

                   tRNA-synt_1 244 vkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynlevinildedgtlt 324
                                              der+k+L+gke++ pl + k++++ad+ v+ke+GtG+V +    d+ D    ++++le+  ++de+g+lt
  gi|15669196|ref|NP_248001.1| 230 -----------DERYKHLIGKEFIVPLFGHKVKLLADEDVEKEFGTGAVMVCTFGDKTDVLWVNRHKLEIKKAIDEKGELT 299
                                   ...........9********************************************************************* PP

                   tRNA-synt_1 325 eeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpksk 405
                                   e a++++glk ++ar+k++e+lk++g l+k+e+i+ +v++c+r k+pi+  +teqWfv+v +l  ++ ++ ++++++p+  
  gi|15669196|ref|NP_248001.1| 300 EIAGKYKGLKTEEAREKIIEDLKKEGYLVKQEPIKQNVGVCWRCKTPIEIIVTEQWFVNVRKLIPKVREVADEIKWIPEHM 380
                                   ********************************************************************************* PP

                   tRNA-synt_1 406 ekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdklkkekgelekded 485
                                   + r  +w+e++  dW+iSRqr+  ++ip+++  + ++vvv         ++ee+   + + + ++ dk   ++++l  ++d
  gi|15669196|ref|NP_248001.1| 381 KIRLLNWIEDMDwDWVISRQRIFATPIPVWYCPKCGNVVV---------AKEEDLPIDPTKTGYVCDKC--GNKDLIPETD 450
                                   **********977*************************99.........23333333444444556655..89999***** PP

                   tRNA-synt_1 486 vlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSK 566
                                   vlD+W +S+ +p+ + ++ +   + ++k +p ++  +G Diir W    i+ s+altg++P+ e++++g+v  e+G+KmSK
  gi|15669196|ref|NP_248001.1| 451 VLDTWMDSSITPMVITKWLDD-DKFFEKHYPVQLRPQGHDIIRTWAFYTIVKSVALTGKKPWDEIVINGMVFGEDGHKMSK 530
                                   ******************998.899******************************************************** PP

                   tRNA-synt_1 567 slgNvidpldvikkygadalRltlilsdvgrdinl 601
                                   s gNv++p+++i kygadalRl+  +s vg d+++
  gi|15669196|ref|NP_248001.1| 531 SRGNVVEPDEIIAKYGADALRLWASNSVVGDDVQF 565
                                   *****************************999976 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.5
                   tRNA-synt_1 214 gdtavavnpeldyv...itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipii 278
                                   ++ ++a+n+ l+yv   +++e+          l+ +++ ++i+ + + +eL+  + ++ l+ + + ii
  gi|15669196|ref|NP_248001.1| 740 ANSGMALNAPLKYVeiyTEDEE--------TYLALNKTAEDIKGTLKIEELKIIKGKPALESKIVEII 799
                                   6888899999999866533333........33333334455666666666666666666655555555 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   1.0   2.5e-37   2.7e-34       1     151 [.     610     753 ..     610     754 .. 0.91

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 2.5e-37
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfm 81 
                                   d wils+l++l+++v++++e+yrfn+++ ++y+f+w+++cd+y+e+vk rly++++e k++a+++l++v+++++rll Pf+
  gi|15669196|ref|NP_248001.1| 610 DLWILSKLQRLIERVDKDLENYRFNTIV-EIYKFVWHEFCDNYIEMVKYRLYGDDEEAKKEARWTLYYVIDKVVRLLCPFA 689
                                   78************************55.89**********************99988866******************** PP

                   Anticodon_1  82 PfitEelwqreeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselkvv 151
                                   P++++++     e   k +  ++ ++pe ++ + ++e+ e+  e++k++v  ir+++++ +++ +++lk+v
  gi|15669196|ref|NP_248001.1| 690 PHFSDYIA----EI-YKIDN-LHFSFPEvDNRFINEEA-EKFGEIAKNTVISIRRFKANSGMALNAPLKYV 753
                                   ********....55.33344.5679***8888887777.89**************************9986 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0     2e-18   2.2e-15       2     132 ..      37     182 ..      36     192 .. 0.80
   2 !    7.4   0.1    0.0015       1.6     166     238 ..     337     408 ..     300     419 .. 0.84
   3 !   30.3   0.2   1.7e-10   1.8e-07     244     371 ..     451     570 ..     446     573 .. 0.75
   4 ?   -2.8   0.7       1.8   1.9e+03     246     276 ..     642     676 ..     638     685 .. 0.66

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 2e-18
                                   EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH.TTS-HH............HHHHH CS
                  tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek.egvtpe............elvek 69 
                                   ++ t+ pY++g+lHlGh+l+    Di+aRykr++g +vlf  g D hG p+e+k e+ +g+t +            el+++
  gi|15669196|ref|NP_248001.1|  37 IIDTPPPYPTGRLHLGHALNWTYMDIIARYKRMKGFNVLFPQGWDCHGLPTEVKVEEiHGITKSdvdrhkfrelciELTKE 117
                                   789999************************************************987567765422222222222234556 PP

                                   HHHHHHHHHHHTT--..-SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-G CS
                  tRNA-synt_1g  70 vheeikelfkklnis..fdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpd 132
                                   + e+++++ k+l+is  +dk + t + e  + +q  f ++++ gliy+++  + +cp++++ ++ 
  gi|15669196|ref|NP_248001.1| 118 NIEKMRRQIKSLGISidWDKEYITMTPEYIKKSQTAFVRMYKDGLIYRGKFPVNWCPRCQTAIAF 182
                                   667778889998877225666778999999999**************************987765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0015
                                   ...........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                  tRNA-synt_1g 166 npksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                     ++  +++  e+  te++f +++k+  k++e    e k  +e++k  +++w+++   d+ isr+  ++ p+P
  gi|15669196|ref|NP_248001.1| 337 VGVCWRCKTPIEIIVTEQWFVNVRKLIPKVREVA-DEIKWIPEHMKIRLLNWIEDMDWDWVISRQRIFATPIP 408
                                   457888999999999*****************99.5565789999999*******999***********9999 PP

  == domain 3  score: 30.3 bits;  conditional E-value: 1.7e-10
                                   EE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH.TT----S-EEEE--EEE CS
                  tRNA-synt_1g 244 vlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillg.aelklpkkvvaheyltv 323
                                   vl  W+d  i  + +tk l     +++ +++++            g dii+  + +      + ++ k  +++v ++++  
  gi|15669196|ref|NP_248001.1| 451 VLDTWMDSSITPMVITKWLD----DDKFFEKHYPV-----QLRPQGHDIIRTWAFYTIVKSVAlTGKKPWDEIVINGMVFG 522
                                   66679999999998888765....77899999933.....23446888887554443333334344456688999998875 PP

                                   .--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHH CS
                  tRNA-synt_1g 324 .egkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedf 371
                                    +g+K+SkSrg+vv ++e++ ++ ad+lR + a+++   +D++f w+++
  gi|15669196|ref|NP_248001.1| 523 eDGHKMSKSRGNVVEPDEIIAKYGADALRLW-ASNSVVGDDVQFLWKEV 570
                                   1689*************************76.6788999*******986 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1.8
                                   -HHHHHHHHHHHTTTTT-.......TTSGGGG.G- CS
                  tRNA-synt_1g 246 YVWldAligYisatkela....kkkgeeekwkeyW 276
                                   +VW +   +Yi ++k+      +++++e +w  y+
  gi|15669196|ref|NP_248001.1| 642 FVWHEFCDNYIEMVKYRLygddEEAKKEARWTLYY 676
                                   79************997733222223344666666 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00051      0.54      22      52 ..      48      78 ..      44     166 .. 0.87
   2 !   14.8   0.0   1.3e-05     0.014     226     280 ..     499     554 ..     480     571 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00051
                                  --BHHHHHHHHHHHHHHHHHHHTT-EEEEEE CS
                  tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdvqfvq 52
                                    hlGha +   +Di++r+ +++g++v f q
  gi|15669196|ref|NP_248001.1| 48 RLHLGHALNWTYMDIIARYKRMKGFNVLFPQ 78
                                  57*************************9966 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHSSS--EEEEEEE--EE.ETTBE--TTTT---BHHHHHTTS-HHHHHHHH CS
                  tRNA-synt_1e 226 laqseaafdkqlvkyflhnghlk.iegekmsksLknfitikdvlkkfdprqlRlll 280
                                   + +s a+++k+     + ng++   +g+kmsks +n++   +++ k+ + +lRl  
  gi|15669196|ref|NP_248001.1| 499 IVKSVALTGKKPWDEIVINGMVFgEDGHKMSKSRGNVVEPDEIIAKYGADALRLWA 554
                                   6788899997777777778888625799*************************975 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       3.7   3.9e+03     130     153 ..       5      28 ..       2      39 .. 0.74
   2 ?   -1.1   0.0       1.1   1.1e+03      12      46 ..     197     231 ..     192     240 .. 0.82
   3 !   19.3   0.0     6e-07   0.00063      86     150 ..     238     302 ..     228     322 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.7
                 tRNA-synt_1_2 130 kkynlpikqvikpedeekkleese 153
                                   k yn++i++ i+++ ee+k+ + +
  gi|15669196|ref|NP_248001.1|   5 KDYNIEIEKQIQKKWEESKIYKFD 28 
                                   789999999999988887666544 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                 tRNA-synt_1_2  12 iefkveeseeklevfttrpdtlfGvtfvalapehp 46 
                                   i+f+ ++ e +l + ttrp+ +     + + pe +
  gi|15669196|ref|NP_248001.1| 197 IKFPAADGEGHLLIATTRPELMAACVAILVHPEDE 231
                                   8999999999**********999888887777765 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 6e-07
                 tRNA-synt_1_2  86 glkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedeekkle 150
                                   g + i P+ g+k+ +   + v  e+gtgavm +   d+ D  + ++++l+ik+ i +++e ++++
  gi|15669196|ref|NP_248001.1| 238 GKEFIVPLFGHKVKLLADEDVEKEFGTGAVMVCTFGDKTDVLWVNRHKLEIKKAIDEKGELTEIA 302
                                   6677899************************************************9877655444 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         1   1.1e+03      21      62 ..      32      74 ..      17      81 .. 0.71
   2 !   17.6   0.9   1.3e-06    0.0014     175     308 ..     410     554 ..     282     570 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1
                  tRNA-synt_1f 21 ekdevvvesG.ispSGliHiGnlrevltadlvaralrkrgeev 62
                                  +k+ +++++    p G++H+G + +    d++ar  r +g +v
  gi|15669196|ref|NP_248001.1| 32 NKPPYIIDTPpPYPTGRLHLGHALNWTYMDIIARYKRMKGFNV 74
                                  456677776514599********99999999999888777765 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.3e-06
                  tRNA-synt_1f 175 pvcekcgrvdttevvevdaeeeeieYkceecGeee...evdiregn........gKLqWkvdwamrWaalgVdfEpaGkDh 244
                                    +c+kcg v  ++ +++  + ++  Y+c++cG++    e+d+ +++        +  +W  d     ++  V++ p G D+
  gi|15669196|ref|NP_248001.1| 410 WYCPKCGNVVVAKEEDLPIDPTKTGYVCDKCGNKDlipETDVLDTWmdssitpmVITKWLDDDKFFEKHYPVQLRPQGHDI 490
                                   48*******************************97334667777777877777666678888777778899********** PP

                  tRNA-synt_1f 245 aaaGgSvdvsskiaeilggeaP..ekvvYelillkggekmssSkGnvltledwlevaepevlrfli 308
                                   + + + +++ + +a  l g++P  e v+  ++  + g+kms+S+Gnv+ +++++  +  + lr+  
  gi|15669196|ref|NP_248001.1| 491 IRTWAFYTIVKSVA--LTGKKPwdEIVINGMVFGEDGHKMSKSRGNVVEPDEIIAKYGADALRLWA 554
                                   **777777777776..5666663366889999999999***************9999988888765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.51   5.3e+02      31      37 ..     173     179 ..     155     187 .. 0.75
   2 ?    0.4   0.0      0.66     7e+02      10      22 ..     335     347 ..     324     352 .. 0.62
   3 !   11.3   0.1   0.00025      0.26      14      41 ..     411     448 ..     405     451 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.51
                           DZR  31 CpsCgek 37 
                                   Cp+C+++
  gi|15669196|ref|NP_248001.1| 173 CPRCQTA 179
                                   4444443 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.66
                           DZR  10 pdarfCseCgtkl 22 
                                   ++  +C +C+t++
  gi|15669196|ref|NP_248001.1| 335 QNVGVCWRCKTPI 347
                                   4444455555544 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00025
                           DZR  14 fCseCgtklkavaa.........edrCpsCgek.vdpe 41 
                                   +C++Cg+ + a ++          ++C++Cg k + pe
  gi|15669196|ref|NP_248001.1| 411 YCPKCGNVVVAKEEdlpidptktGYVCDKCGNKdLIPE 448
                                   9*******98766699***9999********9866655 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.7   1.8e+03      24      30 ..     172     178 ..     171     183 .. 0.70
   2 ?   12.7   0.4   8.9e-05     0.093       2      29 ..     411     441 ..     410     442 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.7
                                   EETTTTE CS
                     Nudix_N_2  24 vCpaCgt 30 
                                   +Cp+C+t
  gi|15669196|ref|NP_248001.1| 172 WCPRCQT 178
                                   5777765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.9e-05
                                   B-TTT--B-E...EE--TT-SS-EEEETTTT CS
                     Nudix_N_2   2 FCsqCGtpve...lripdgDnreRlvCpaCg 29 
                                   +C++CG+ v      +p + +++ +vC++Cg
  gi|15669196|ref|NP_248001.1| 411 YCPKCGNVVVakeEDLPIDPTKTGYVCDKCG 441
                                   9*******8756688999************9 PP

>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.11   1.2e+02      14      24 ..      45      55 ..      44      76 .. 0.88
   2 ?    7.5   0.0    0.0022       2.3     183     209 ..     512     536 ..     498     547 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.11
                                  TSSS-BGGGHH CS
                  tRNA-synt_1b 14 PTgklHlGylv 24
                                  PTg+lHlG+ +
  gi|15669196|ref|NP_248001.1| 45 PTGRLHLGHAL 55
                                  9*******976 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0022
                                   -EEEEET-BBSTTSSSBTTCETTCGC- CS
                  tRNA-synt_1b 183 pegltvplltgldGekKmSKSagnsaI 209
                                    e++++ ++ g dG  KmSKS gn ++
  gi|15669196|ref|NP_248001.1| 512 DEIVINGMVFGEDGH-KMSKSRGN-VV 536
                                   467888899******.********.43 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.5   5.3e+02       2       9 ..     173     180 ..     173     188 .. 0.85
   2 ?    8.0   0.1    0.0027       2.8       2      15 ..     412     425 ..     411     434 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.5
                DNA_ligase_ZBD   2 CPvCGsav 9  
                                   CP C +a+
  gi|15669196|ref|NP_248001.1| 173 CPRCQTAI 180
                                   *****997 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0027
                DNA_ligase_ZBD   2 CPvCGsavvReege 15 
                                   CP CG  vv +e++
  gi|15669196|ref|NP_248001.1| 412 CPKCGNVVVAKEED 425
                                   *********77765 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.075        79       2       7 ..     173     178 ..     163     189 .. 0.73
   2 ?    6.2   0.0    0.0059       6.2      17      26 ..     407     416 ..     399     420 .. 0.85
   3 ?   -2.5   0.2       3.1   3.3e+03      20      26 ..     435     441 ..     432     441 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.075
                      zf-TFIIB   2 CPkCqd 7  
                                   CP+Cq+
  gi|15669196|ref|NP_248001.1| 173 CPRCQT 178
                                   666665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0059
                      zf-TFIIB  17 veidyCpqCr 26 
                                   ++++yCp+C+
  gi|15669196|ref|NP_248001.1| 407 IPVWYCPKCG 416
                                   8999999997 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.1
                      zf-TFIIB  20 dyCpqCr 26 
                                   ++C++C+
  gi|15669196|ref|NP_248001.1| 435 YVCDKCG 441
                                   6899997 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.6   9.1e+03      19      30 ..     335     346 ..     326     347 .. 0.71
   2 ?   11.6   2.2    0.0002      0.21       2      30 ..     410     443 ..     410     448 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.6
                                   SSTTB-TTT--. CS
                       ADK_lid  19 kveglCDkCGep 30 
                                   ++ g+C  C  p
  gi|15669196|ref|NP_248001.1| 335 QNVGVCWRCKTP 346
                                   477999999776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0002
                                   EE-TTT--EEETT....T.B--SSTTB-TTT--. CS
                       ADK_lid   2 rvCpkCGrsYhvv....f.npPkveglCDkCGep 30 
                                   + CpkCG +   +       p k+  +CDkCG +
  gi|15669196|ref|NP_248001.1| 410 WYCPKCGNVVVAKeedlPiDPTKTGYVCDKCGNK 443
                                   89*****986434777645888**********84 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.6    0.0024       2.6       3      28 ..     411     441 ..     409     444 .. 0.78
   2 ?    1.0   0.4      0.39   4.1e+02       4      17 ..     437     451 ..     436     454 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0024
                                   BESTTTSBEEEEECSC....CCE.EEESSSS CS
                RNA_POL_M_15KD   3 FCpkCgNlLlpkedke....gkn.feCrqCg 28 
                                    CpkCgN    ke ++    +k  + C++Cg
  gi|15669196|ref|NP_248001.1| 411 YCPKCGNVVVAKEEDLpidpTKTgYVCDKCG 441
                                   5***********9988443344489999997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.39
                                   ESTTTSB.EEEEECS CS
                RNA_POL_M_15KD   4 CpkCgNl.Llpkedk 17 
                                   C kCgN  L+p +d+
  gi|15669196|ref|NP_248001.1| 437 CDKCGNKdLIPETDV 451
                                   999999547777766 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.049        52      18      35 ..     170     185 ..     148     221 .. 0.82
   2 ?   -0.2   0.1       1.2   1.2e+03      48      55 ..     339     346 ..     334     348 .. 0.83
   3 ?    6.2   0.4     0.011        12      19      46 ..     410     442 ..     398     443 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.049
                           IBR  18 lkwCprpdCeaiiekseg 35 
                                   + wCp   C+++i   e 
  gi|15669196|ref|NP_248001.1| 170 VNWCP--RCQTAIAFAEV 185
                                   68***..9**99965544 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                           IBR  48 fCfnCkke 55 
                                    C++Ck +
  gi|15669196|ref|NP_248001.1| 339 VCWRCKTP 346
                                   6****987 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.011
                           IBR  19 kwCprpdCeaiiekseg......cks..vtCskCgf 46 
                                    +Cp  +C++++  +e+      + +    C kCg 
  gi|15669196|ref|NP_248001.1| 410 WYCP--KCGNVVVAKEEdlpidpT-KtgYVCDKCGN 442
                                   59**..***999777775666542.14567****86 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1       0.1   1.1e+02       5      16 ..     173     184 ..     172     186 .. 0.85
   2 ?   -0.4   0.1      0.85     9e+02       4      13 ..     339     348 ..     338     350 .. 0.87
   3 ?    2.4   0.1      0.12   1.2e+02       3      13 ..     410     420 ..     409     425 .. 0.78
   4 ?    4.7   0.1     0.022        24       2      11 ..     434     443 ..     433     451 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.1
                        zf_UBZ   5 CerCgkeipese 16 
                                   C+rC++ i  +e
  gi|15669196|ref|NP_248001.1| 173 CPRCQTAIAFAE 184
                                   ******998776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.85
                        zf_UBZ   4 lCerCgkeip 13 
                                   +C rC+++i+
  gi|15669196|ref|NP_248001.1| 339 VCWRCKTPIE 348
                                   799****997 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.12
                        zf_UBZ   3 ylCerCgkeip 13 
                                   + C++Cg  + 
  gi|15669196|ref|NP_248001.1| 410 WYCPKCGNVVV 420
                                   67*****9876 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.022
                        zf_UBZ   2 tylCerCgke 11 
                                    y+C++Cg +
  gi|15669196|ref|NP_248001.1| 434 GYVCDKCGNK 443
                                   69*****975 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       1.6   1.7e+03      19      23 ..     173     177 ..     170     180 .. 0.64
   2 ?    1.0   0.1      0.28     3e+02       5      13 ..     340     348 ..     339     349 .. 0.84
   3 ?    8.4   0.1    0.0014       1.4       4      13 ..     411     421 ..     410     425 .. 0.78
   4 ?    1.9   0.2      0.15   1.6e+02       4      10 ..     436     442 ..     434     446 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                   zf-ribbon_3  19 CpyCG 23 
                                   Cp C+
  gi|15669196|ref|NP_248001.1| 173 CPRCQ 177
                                   66665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.28
                   zf-ribbon_3   5 CPnCGapls 13 
                                   C++C++p++
  gi|15669196|ref|NP_248001.1| 340 CWRCKTPIE 348
                                   *****9875 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0014
                   zf-ribbon_3   4 rCPnCGa.pls 13 
                                   +CP+CG+ +++
  gi|15669196|ref|NP_248001.1| 411 YCPKCGNvVVA 421
                                   7******7755 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.15
                   zf-ribbon_3   4 rCPnCGa 10 
                                    C +CG+
  gi|15669196|ref|NP_248001.1| 436 VCDKCGN 442
                                   3555554 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       3.1   3.3e+03       3       8 ..     173     178 ..     173     185 .. 0.84
   2 ?    7.0   5.0    0.0039       4.1       3      27 ..     412     442 ..     410     455 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.1
                                   ETTTTC CS
                  TF_Zn_Ribbon   3 CPnCgs 8  
                                   CP C +
  gi|15669196|ref|NP_248001.1| 173 CPRCQT 178
                                   999986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0039
                                   ETTTTCEEC..HEE....TSTTCEEESSSSB CS
                  TF_Zn_Ribbon   3 CPnCgstnl..veD....pergelvCtdCGl 27 
                                   CP+Cg+  +  +eD    p  + +vC +CG+
  gi|15669196|ref|NP_248001.1| 412 CPKCGNVVVakEEDlpidPTKTGYVCDKCGN 442
                                   *****9865785555555************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (878 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.86u 0.33s 00:00:01.19 Elapsed: 00:00:00.57
# Mc/sec: 4609.01
//
Query:       gi|15669197|ref|NP_248002.1|  [L=288]
Description: branched-chain amino acid aminotransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-57  193.6   0.0    4.8e-57  193.4   0.0    1.0  1  Aminotran_4  Amino-transferase class IV


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.4   0.0   2.7e-61   4.8e-57       1     223 []      29     253 ..      29     253 .. 0.97

  Alignments for each domain:
  == domain 1  score: 193.4 bits;  conditional E-value: 2.7e-61
                   Aminotran_4   1 glfEtmrvyngeiffldeHleRLrksaellglelpfdeeelrkileelleannsengrlrllvsrgggglg.aatsepsva 80 
                                   g+fE++r+y+g +f l+eH++RL  sa+ l +++p+++ee+   + e+l+ nn + +++rl+v+rg g+lg ++ ++ +  
  gi|15669197|ref|NP_248002.1|  29 GVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDIPLTKEEMIDVVLETLRVNNLRDAYIRLVVTRGVGDLGlDPRKCGKPT 109
                                   8**************************9999*****************************************888888888 PP

                   Aminotran_4  81 vyvsalppgpeseke.lplvtssdvrrdapsplpgaKtlnyldnvlarreakergadevllvdedgnvtEgstsNvfivkg 160
                                   ++ +a+p++p    + ++++t s++r ++   +p +K+lnyl++vla+ +a+ +g+de+ l+d++g+v+Eg+  N+fivk+
  gi|15669197|ref|NP_248002.1| 110 IFCIAIPMPPLLGEDgIRAITVSVRRLPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEAFLLDDKGFVVEGTGDNIFIVKN 190
                                   88888888888888888**************************************************************** PP

                   Aminotran_4 161 gelitPplssgiLpGitrrallelakalgleveereitlkdleeadeafltntlrgvlpvrsi 223
                                   g l tPp+ ++iL+Gitr+++++lak++g+ev e+++tl dl  ade+f+t+t+++++pv +i
  gi|15669197|ref|NP_248002.1| 191 GVLKTPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADELFITGTAAEIVPVFEI 253
                                   ***********************************************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1845.39
//
Query:       gi|15669198|ref|NP_248003.1|  [L=236]
Description: phosphate transport system regulatory protein PhoU [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-36  122.1  18.3    3.1e-22   78.9   2.2    2.4  3  PhoU      PhoU domain
  ------ inclusion threshold ------
      0.011   16.3   0.3      0.011   16.3   0.3    3.0  4  DUF5344   Family of unknown function (DUF5344)
      0.093   12.8   1.4       0.57   10.2   0.1    2.3  2  BBS2_Mid  Ciliary BBSome complex subunit 2, middle region


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   2.2   5.1e-26   3.1e-22       1      88 [.      16     103 ..      16     104 .. 0.98
   2 !   54.9   2.1   1.5e-18   9.2e-15       3      88 ..     120     202 ..     118     203 .. 0.91
   3 ?   -3.9   0.5         3   1.8e+04      27      38 ..     217     228 ..     212     234 .. 0.44

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 5.1e-26
                                   HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81 
                                   l +mae++ e+ ++a++a+ e d+ela++v++rd  id +e++ie+++++a+a +qp++ dlrel+++++i++ lE +gD 
  gi|15669198|ref|NP_248003.1|  16 LIEMAELCAEQTENAVKAFIESDRELAKQVRKRDTTIDLMEMKIEEKCIKAIALYQPVSGDLRELMTAIKISSKLEKVGDN 96 
                                   679****************************************************************************** PP

                                   HHHHHHH CS
                          PhoU  82 avniaer 88 
                                   a +i+++
  gi|15669198|ref|NP_248003.1|  97 ASKICKI 103
                                   *****97 PP

  == domain 2  score: 54.9 bits;  conditional E-value: 1.5e-18
                                   HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   3 rmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhav 83 
                                    m+++  +ml++a+ a++++d+ lar+v+++d+++d+l+++++rs + ++  ++p+  +l   ++++ + ++lER g  ++
  gi|15669198|ref|NP_248003.1| 120 VMKDYLINMLKNAMIAFKTRDESLARDVYNMDKRLDDLYEQLYRSMISKII-ENPK--NLTLYTEIIFAGKYLERSGNIVA 197
                                   59*******************************************999994.5565..6788899**************99 PP

                                   HHHHH CS
                          PhoU  84 niaer 88 
                                   +i +r
  gi|15669198|ref|NP_248003.1| 198 SIGDR 202
                                   99877 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3
                                   HHHHHHHHHHHH CS
                          PhoU  27 arevierddeid 38 
                                   ++e ++++++i+
  gi|15669198|ref|NP_248003.1| 217 IEEELKKEKDIE 228
                                   333333333333 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   0.3   1.9e-06     0.011      47      87 .]       4      44 ..       2      44 .. 0.94
   2 ?   -2.5   0.0       1.4   8.2e+03      11      25 ..      86     100 ..      76     117 .. 0.63
   3 ?   -2.3   0.0       1.2   7.2e+03      68      86 ..     127     145 ..     125     146 .. 0.77
   4 ?   -0.4   0.3       0.3   1.8e+03      41      54 ..     220     233 ..     208     236 .] 0.46

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-06
                       DUF5344 47 eleeeleellkaYktlllknvedtesaVdslkeaDealass 87
                                  ++ee l+e+ +++ ++ +  +e+te+aV+ + e+D++la++
  gi|15669198|ref|NP_248003.1|  4 KFEEILKEVENDLIEMAELCAEQTENAVKAFIESDRELAKQ 44
                                  789999*********************************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                       DUF5344  11 VeqkLselktaaeel 25 
                                   + +kL+++ + a+++
  gi|15669198|ref|NP_248003.1|  86 ISSKLEKVGDNASKI 100
                                   445566665555555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.2
                       DUF5344  68 edtesaVdslkeaDealas 86 
                                   ++ ++a   +k  De+la+
  gi|15669198|ref|NP_248003.1| 127 NMLKNAMIAFKTRDESLAR 145
                                   5667777889999999987 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.3
                       DUF5344  41 vvekineleeelee 54 
                                    ++k +++e+++ +
  gi|15669198|ref|NP_248003.1| 220 ELKKEKDIEKNIDQ 233
                                   33444444444433 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2     0.073   4.4e+02      12      50 ..      19      59 ..       9      69 .. 0.77
   2 ?   10.2   0.1   9.5e-05      0.57       5      46 ..     107     148 ..     103     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.073
                      BBS2_Mid 12 eneLvvgsddfeirvfkee..elvaeitetekvvslarlek 50
                                  ++eL +  +++ ++ f e   el +++++++  + l++++ 
  gi|15669198|ref|NP_248003.1| 19 MAELCAEQTENAVKAFIESdrELAKQVRKRDTTIDLMEMKI 59
                                  57888888899999995543489999999999999999875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 9.5e-05
                      BBS2_Mid   5 advdgdgeneLvvgsddfeirvfkeeelvaeitetekvvsla 46 
                                   +dv+g+ +neL++  +d+ i ++k+  + ++++ ++    + 
  gi|15669198|ref|NP_248003.1| 107 SDVEGNRKNELLIVMKDYLINMLKNAMIAFKTRDESLARDVY 148
                                   7999************************99998877665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1487  (0.0829383); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1638.25
//
Query:       gi|15669199|ref|NP_248004.1|  [L=377]
Description: hypothetical protein MJ_1010 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-93  312.3  13.0    2.4e-93  312.3  13.0    2.1  2  ATPase_2       ATPase domain predominantly from Archaea
    1.1e-08   34.3   0.0     0.0016   17.2   0.0    2.2  2  RNA12          RNA12 protein
    1.2e-07   31.8  10.9     0.0017   18.4   0.3    3.6  3  AAA_14         AAA domain
    1.3e-07   32.1   0.0    3.4e-07   30.8   0.0    1.7  2  AAA_16         AAA ATPase domain
    1.4e-07   32.0   1.4     0.0013   19.2   0.1    3.2  2  AAA            ATPase family associated with various cellular
      7e-07   29.6   0.0    3.9e-06   27.2   0.0    2.2  2  AAA_22         AAA domain
  ------ inclusion threshold ------
      0.012   16.3   0.4        0.3   11.8   0.1    2.5  2  Pre-PUA        Pre-PUA-like domain
      0.013   15.3   0.7      0.034   13.9   0.7    1.7  1  SGTA_dimer     Homodimerisation domain of SGTA
      0.013   14.7   0.0      0.085   12.0   0.0    2.1  3  NB-ARC         NB-ARC domain
      0.018   14.9   0.4       0.18   11.7   0.0    2.7  3  TK             Thymidine kinase
      0.023   14.8   0.2      0.091   12.9   0.2    2.2  1  MMR_HSR1       50S ribosome-binding GTPase
      0.024   14.2   0.0       0.11   12.1   0.0    2.1  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.054   13.4   0.4        6.4    6.7   0.0    2.9  3  MobB           Molybdopterin guanine dinucleotide synthesis p
      0.061   12.8   0.0       0.27   10.7   0.0    2.0  2  AAA_7          P-loop containing dynein motor region
       0.46   10.9  10.4         12    6.3   0.2    3.2  3  AAA_23         AAA domain
       0.87    9.6   7.6       0.28   11.2   0.2    3.4  5  Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen r


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.3  13.0   2.2e-96   2.4e-93       1     233 []       6     269 ..       6     269 .. 0.94
   2 ?    1.2   0.7      0.27     3e+02     111     143 ..     271     304 ..     268     325 .. 0.78

  Alignments for each domain:
  == domain 1  score: 312.3 bits;  conditional E-value: 2.2e-96
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie........... 70 
                                   Ff+R++e+ke+++ile+epn iyfiYGp++sGKtaL++eii+n++dk+kyv++yi+lre++isk+def +           
  gi|15669199|ref|NP_248004.1|   6 FFNRVEEIKEILSILEEEPNLIYFIYGPINSGKTALINEIINNRLDKNKYVVFYIDLREIFISKYDEFEAklratktfgfr 86 
                                   9*******************************************************************5477777777777 PP

                      ATPase_2  71 .......eeeekkklekal..............giavpkaeleeilk.eksklvfkaielllekikkkgkkiiiiiDelqk 129
                                          ee+e++k    +              gi++pk++leeilk +++k+vfk+i+++l++ik++gk++iiiiDelqk
  gi|15669199|ref|NP_248004.1|  87 liievlfEEYEDDKKP--IeiirslikdapslcGIPTPKNTLEEILKkKTTKNVFKYITNILMDIKREGKQPIIIIDELQK 165
                                   7777777666666444..2559*************************9********************************* PP

                      ATPase_2 130 lidlglngaellvkeLlnliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkel.. 208
                                   ++d+++n  ++l++eL+n+++sltk+khlc+v+clsS++lfiervyne++l++r++yilvdd+dketal+f++++++e+  
  gi|15669199|ref|NP_248004.1| 166 IGDMKIN--GFLIYELFNYFVSLTKHKHLCHVFCLSSDSLFIERVYNEAMLKERVDYILVDDFDKETALKFIDFLSEEIln 244
                                   *******..**********************************************************************87 PP

                      ATPase_2 209 eelskedfeeiyryvGGkPkalvel 233
                                   ++ls+ed+e+iy+yvGGkP+ ++++
  gi|15669199|ref|NP_248004.1| 245 KKLSDEDKELIYSYVGGKPILIINV 269
                                   777*******************986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.27
                      ATPase_2 111 ekikkkgkk...iiiiiDelqklidlglngaellvk 143
                                    k+k k  k    i+++De+ kl+d+ +n   +++k
  gi|15669199|ref|NP_248004.1| 271 GKLKHKNLKdvlNILLMDEISKLKDFLSN--LDYIK 304
                                   56777777777789**********88777..66665 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.4e-06    0.0016       1      64 [.       9      76 ..       9      89 .. 0.84
   2 !   15.0   0.0   6.8e-06    0.0077     144     232 ..     150     241 ..     120     258 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                         RNA12  1 RkekiedlkewleEnvntFivvkGPrGSGkkeLvldrvlkdrkk.....vlvidCdelvkarndaelis 64
                                  R e+i+++ + leE++n    + GP  SGk+ L+ ++++++r +     v++id +e++ ++ d+   +
  gi|15669199|ref|NP_248004.1|  9 RVEEIKEILSILEEEPNLIYFIYGPINSGKTALI-NEIINNRLDknkyvVFYIDLREIFISKYDEFEAK 76
                                  889******************************9.8887776555677999********9999986555 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 6.8e-06
                         RNA12 144 ahpeakPvvvidnflakaek..ngvvykklaeWaasLvqsn.iahViflted.vsaskaLskaLpnqvfktislgDasees 220
                                   +++ ++P+++id+ ++  +   ng++  +l ++  sL++++ + hV  l++d   ++++ ++a+ ++    i + D ++e+
  gi|15669199|ref|NP_248004.1| 150 KREGKQPIIIIDELQKIGDMkiNGFLIYELFNYFVSLTKHKhLCHVFCLSSDsLFIERVYNEAMLKERVDYILVDDFDKET 230
                                   455678*********98876679**************986439********955678999********************* PP

                         RNA12 221 arkyVlsklkee 232
                                   a k++ + l+ee
  gi|15669199|ref|NP_248004.1| 231 ALKFI-DFLSEE 241
                                   ***97.445444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.3   1.5e-06    0.0017       3      52 ..      26      76 ..      24     116 .. 0.71
   2 !   14.0   0.7   3.4e-05     0.038      44     119 ..     132     220 ..     105     231 .. 0.73
   3 ?    4.7   1.0     0.027        30      63      86 ..     280     303 ..     209     311 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                        AAA_14  3 kilvitGaRrvGKTtllkqlikell.vkkesilyinldderdkkladpekl 52
                                   i++i G+  +GKT l++++i+++l  +k  ++yi+l +   +k++++e  
  gi|15669199|ref|NP_248004.1| 26 LIYFIYGPINSGKTALINEIINNRLdKNKYVVFYIDLREIFISKYDEFEAK 76
                                  6899*********************77777888999988888777776522 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.4e-05
                        AAA_14  44 kkladpekllelileklke....ekktylflDEiqev..........pewekalkslvdegknldvivtGSnskllskeia 110
                                   kk  +++++ ++i + l++     k+ ++++DE q++           e++++  sl ++++ ++v++  S s+++ +  +
  gi|15669199|ref|NP_248004.1| 132 KK--TTKNVFKYITNILMDikreGKQPIIIIDELQKIgdmkingfliYELFNYFVSLTKHKHLCHVFCLSSDSLFIERVYN 210
                                   22..222344455444323333468899*********999999999988888888999999899*********99988666 PP

                        AAA_14 111 ts.lagrvae 119
                                   +  l +rv++
  gi|15669199|ref|NP_248004.1| 211 EAmLKERVDY 220
                                   5414555555 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.027
                        AAA_14  63 ekktylflDEiqevpewekalksl 86 
                                   +  ++l++DEi++++++ + l ++
  gi|15669199|ref|NP_248004.1| 280 DVLNILLMDEISKLKDFLSNLDYI 303
                                   3456799**********9999887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0     3e-10   3.4e-07       1     150 [.       5     169 ..       5     190 .. 0.69
   2 ?   -2.7   0.0       5.9   6.6e+03     138     158 ..     220     238 ..     209     258 .. 0.67

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3e-10
                        AAA_16   1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellr.alekdggif........lrgkcdqlesaipysa 71 
                                   +++ R ee++++ls+le     +p  + +++G+  +GK++l++e+ + +l k++ ++        +  k+d++e++   + 
  gi|15669199|ref|NP_248004.1|   5 KFFNRVEEIKEILSILE----EEPnLIYFIYGPINSGKTALINEIINnRLDKNKYVVfyidlreiFISKYDEFEAK---LR 78 
                                   5888999*****99999....44459****************9999647777764441444333333444444333...33 PP

                        AAA_16  72 laqalareellrqllde..aesaeleawrekleeala......avpelagaea......srllellkrllallsrderplv 138
                                    ++++ ++ +++ l +e  ++++  e  r  +++a +      + + l+          + ++  ++++l+ ++r++++ +
  gi|15669199|ref|NP_248004.1|  79 ATKTFGFRLIIEVLFEEyeDDKKPIEIIRSLIKDAPSlcgiptPKNTLEE--IlkkkttKNVFKYITNILMDIKREGKQPI 157
                                   55555443333333333443344555555555555557777443333333..345888999**************9999** PP

                        AAA_16 139 lvlDdlqwadea 150
                                   +++D+lq++ ++
  gi|15669199|ref|NP_248004.1| 158 IIIDELQKIGDM 169
                                   *******98775 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.9
                        AAA_16 138 vlvlDdlqwadeaslqllaaL 158
                                   ++++Dd++  +e+ l+++++L
  gi|15669199|ref|NP_248004.1| 220 YILVDDFD--KETALKFIDFL 238
                                   57888888..33334444433 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.2e-06    0.0013       3      82 ..      30     172 ..      28     222 .. 0.81
   2 !    7.6   0.2    0.0042       4.7      24      70 ..     232     293 ..     220     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                   EESSTTSSHHHHHHHHHHHH....THEEEEEETTTCS.SS......................................... CS
                           AAA   3 lyGppGtGKTllakavakel....gvefleisgsell.sk......................................... 37 
                                   +yGp   GKT+l++ ++++     +  ++ i++ e++ sk                                         
  gi|15669199|ref|NP_248004.1|  30 IYGPINSGKTALINEIINNRldknKYVVFYIDLREIFiSKydefeaklratktfgfrliievlfeeyeddkkpieiirsli 110
                                   8*****************9445435668999999999888999999999999***************************** PP

                                   .......................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHH CS
                           AAA  38 .......................yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseee 82 
                                                          + ++  k i +++ ++k++ k+ i++iDE+ +++  +       +
  gi|15669199|ref|NP_248004.1| 111 kdapslcgiptpkntleeilkkkTTKNVFKYITNILMDIKREGKQPIIIIDELQKIGDMK------IN 172
                                   ****************99988888888888888888888888877**********98766......44 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0042
                                   HEEEEEETTTCSSS............STTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGH CS
                           AAA  24 vefleisgsellsk............yvgesekkirelfkeakeka...kpsilfiDEidal 70 
                                    +f+ +   e+l+k            yvg ++  i +++ ++k+k+      il++DEi +l
  gi|15669199|ref|NP_248004.1| 232 LKFIDFLSEEILNKklsdedkeliysYVGGKPILIINVIGKLKHKNlkdVLNILLMDEISKL 293
                                   55666666666665677777778888******************9998544********887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   3.4e-09   3.9e-06       6     128 ..      26     197 ..      21     205 .. 0.85
   2 ?   -0.8   0.1       1.5   1.7e+03      74      74 ..     261     261 ..     203     311 .. 0.54

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 3.4e-09
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee................erpevv.fvtlpsstsskdllrellralglelk 69 
                                    i +++G+  +GKT l++++ ++        +                 +     +  +++  + + + + l++++++++k
  gi|15669199|ref|NP_248004.1|  26 LIYFIYGPINSGKTALINEIINNRLDK----NkyvvfyidlreifiskYDEF-EaKLRATKTFGFRLIIEVLFEEYEDDKK 101
                                   6889****************9997422....135779999877777643333.3588888888**************9999 PP

                        AAA_22  70 a............................erlsseellealeqalrarav...ielliiDEaqhlr..s......eealee 111
                                                                + ++++ +++++++ l + ++   ++++iiDE q++   +       e++++
  gi|15669199|ref|NP_248004.1| 102 PieiirslikdapslcgiptpkntleeilKKKTTKNVFKYITNILMDIKRegkQPIIIIDELQKIGdmKingfliYELFNY 182
                                   9*******************************************999999999************6552667777888888 PP

                        AAA_22 112 LrsllnlsrkgvqliLv 128
                                   ++sl +  +k++ ++++
  gi|15669199|ref|NP_248004.1| 183 FVSLTK--HKHLCHVFC 197
                                   888888..888888876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                        AAA_22  74 s 74 
                                    
  gi|15669199|ref|NP_248004.1| 261 G 261
                                   1 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.34   3.8e+02      34      53 ..     123     142 ..     104     164 .. 0.75
   2 ?   11.8   0.1   0.00026       0.3      39      85 ..     326     371 ..     309     372 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.34
                       Pre-PUA  34 eeqleellpkkeevkvvklq 53 
                                   +++lee+l+kk+  +v+k+ 
  gi|15669199|ref|NP_248004.1| 123 KNTLEEILKKKTTKNVFKYI 142
                                   579*********99999987 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00026
                       Pre-PUA  39 ellpkkeevkvvklqgehvelyvvdgeplffqdregellPtlytlwk 85 
                                   +l++ k e++v k+  ++v +y+v++++lf+ ++ g+l P  +++w+
  gi|15669199|ref|NP_248004.1| 326 KLFKGKYEIEVDKIP-KAVYVYLVKKNILFLYPQRGTLKPQSFLVWN 371
                                   56778999*******.************************9999996 PP

>> SGTA_dimer  Homodimerisation domain of SGTA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.7     3e-05     0.034       3      28 ..     228     253 ..     227     255 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
                    SGTA_dimer   3 krlalaIidFLstslkdgtvseDdaE 28 
                                   k+ al +idFLs+ + ++++s++d+E
  gi|15669199|ref|NP_248004.1| 228 KETALKFIDFLSEEILNKKLSDEDKE 253
                                   899**********************9 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.6e-05     0.085       4      47 ..       9      50 ..       8      79 .. 0.78
   2 ?   -1.9   0.0       1.3   1.5e+03     190     225 ..     113     147 ..      80     155 .. 0.67
   3 ?   -2.0   0.0       1.5   1.6e+03     195     211 ..     260     276 ..     223     326 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-05
                                  HHHHHHHHHHC.TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCC CS
                        NB-ARC  4 svekviekLle.kdelqslvvalvGmgGvGKttlakqilnksdev 47
                                   ve+++e L+  ++e++ l+ +++G   +GKt l+++i+n+   +
  gi|15669199|ref|NP_248004.1|  9 RVEEIKEILSIlEEEPN-LIYFIYGPINSGKTALINEIINN-R-L 50
                                  58999999998567777.99******************998.3.3 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                                   HHHHCTT-HHHHHHHHHHHC-TCSCCHHHHHHHHHH CS
                        NB-ARC 190 ivekckGlPlalkvlggllstkktveewkkvlekle 225
                                     + c G P   ++l ++l++k+t + +k++ + l 
  gi|15669199|ref|NP_248004.1| 113 APSLC-GIPTPKNTLEEILKKKTTKNVFKYITNILM 147
                                   44444.777777888888888888888888777665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.5
                                   TT-H.HHHHHHHHHHC-T CS
                        NB-ARC 195 kGlP.lalkvlggllstk 211
                                   +G P l ++v+g+l+  k
  gi|15669199|ref|NP_248004.1| 260 GGKPiLIINVIGKLKH-K 276
                                   5555223344443333.2 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.18       3      35 ..      27      58 ..      25     106 .. 0.84
   2 ?   -0.3   0.0      0.73   8.2e+02      60      87 ..     140     164 ..     123     174 .. 0.68
   3 ?   -0.7   0.1      0.99   1.1e+03      79      88 ..     156     165 ..     137     218 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                            TK  3 ielilgpmfaGKsteLlrrvkryqlaekkvvvi 35
                                  i++i+gp+++GK+ +L++++ + +l + k vv+
  gi|15669199|ref|NP_248004.1| 27 IYFIYGPINSGKT-ALINEIINNRLDKNKYVVF 58
                                  89**********7.5888888888887777776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.73
                            TK  60 ksktssleeikeeleeedvdvvlvDEaq 87 
                                   k  t+ l +ik+e ++    ++++DE q
  gi|15669199|ref|NP_248004.1| 140 KYITNILMDIKREGKQ---PIIIIDELQ 164
                                   3445666666666666...7999**998 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.99
                            TK  79 dvvlvDEaqF 88 
                                    ++++DE q 
  gi|15669199|ref|NP_248004.1| 156 PIIIIDELQK 165
                                   4566666553 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   8.1e-05     0.091       4      28 ..      30      54 ..      28     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.1e-05
                                  EEESTTSSHHHHHHHHHTSTEEESS CS
                      MMR_HSR1  4 ivGrpNvGKStLinaltgekaivsd 28
                                  i+G  N+GK+ Lin +++++   ++
  gi|15669199|ref|NP_248004.1| 30 IYGPINSGKTALINEIINNRLDKNK 54
                                  89***************98765555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.4e-05      0.11       3      31 ..      28      56 ..      26      69 .. 0.81
   2 ?   -1.5   0.0       1.5   1.6e+03      23      49 ..     150     179 ..     141     225 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.4e-05
                                  EEEEESTTCCHHHHHHHHHCT--SS-EEE CS
                          cobW  3 tvltGflGsGKTtLlnhllenraglklav 31
                                  + + G++ sGKT+L+n++++nr +++  v
  gi|15669199|ref|NP_248004.1| 28 YFIYGPINSGKTALINEIINNRLDKNKYV 56
                                  6789***************8887765544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                   T--SS-EEEEESS-SS...CHCCCCCCHCC CS
                          cobW  23 nraglklavivNefge...vsiDaellret 49 
                                   +r+g++  +i+ e+++   ++i++ l+ e 
  gi|15669199|ref|NP_248004.1| 150 KREGKQPIIIIDELQKigdMKINGFLIYEL 179
                                   677778888887766422244555444444 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0057       6.4       3      29 ..      29      56 ..      27      62 .. 0.75
   2 ?    3.6   0.2      0.05        56      87     128 ..     213     255 ..     186     260 .. 0.76
   3 ?   -2.5   0.0       3.9   4.4e+03      11      29 ..     261     279 ..     257     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0057
                          MobB  3 givgksgsGKTtLleklipe.lkarglr 29
                                   i g  +sGKT+L++++i+  l ++++ 
  gi|15669199|ref|NP_248004.1| 29 FIYGPINSGKTALINEIINNrLDKNKYV 56
                                  577889***********97525555555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.05
                          MobB  87 rl.sevDlvlvEGfkkealpk.ievlraelgkeelllledekli 128
                                   +l ++vD +lv  f ke+  k i+ l +e+ +++l   ed++li
  gi|15669199|ref|NP_248004.1| 213 MLkERVDYILVDDFDKETALKfIDFLSEEILNKKLSD-EDKELI 255
                                   44356*********88877664888888887766644.566554 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.9
                          MobB  11 GKTtLleklipelkarglr 29 
                                   GK  L+ ++i +lk+++l+
  gi|15669199|ref|NP_248004.1| 261 GKPILIINVIGKLKHKNLK 279
                                   8999999999999998875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00024      0.27      37      69 ..      29      62 ..      16      70 .. 0.88
   2 ?   -2.3   0.0       2.4   2.6e+03     118     131 ..      98     111 ..      93     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                         AAA_7 37 llvGptGtGKtviikd.llkkldkekylsltinf 69
                                  +++Gp  +GKt++i++ + ++ldk+ky++  i +
  gi|15669199|ref|NP_248004.1| 29 FIYGPINSGKTALINEiINNRLDKNKYVVFYIDL 62
                                  578*************99999*******999876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                         AAA_7 118 gaqppiellRqlld 131
                                   ++++pie++R l+ 
  gi|15669199|ref|NP_248004.1|  98 DDKKPIEIIRSLIK 111
                                   4689******9985 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2     0.011        12      21      39 ..      27      45 ..      12      47 .. 0.90
   2 ?    5.7   0.0     0.017        19     126     199 ..      56     149 ..      43     150 .. 0.73
   3 ?    2.3   3.4      0.19   2.1e+02     115     197 ..     212     318 ..     198     333 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                        AAA_23 21 ltlItGpNGaGKTTildAi 39
                                  ++ I+Gp  +GKT++++ i
  gi|15669199|ref|NP_248004.1| 27 IYFIYGPINSGKTALINEI 45
                                  679************9865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.017
                        AAA_23 126 gskkiilnlilflgqerfeefelkdkke........rleelekeleeledekkllekl............eqekekekele 186
                                    +++i l+ i++ + ++fe +++++k            ee+e++++ +e +++l+++             ++e  k+k+ +
  gi|15669199|ref|NP_248004.1|  56 VVFYIDLREIFISKYDEFEAKLRATKTFgfrliievLFEEYEDDKKPIEIIRSLIKDApslcgiptpkntLEEILKKKTTK 136
                                   3344455566666666665555543333799988888999999999999999999999*********99988888999999 PP

                        AAA_23 187 eleeeleeilkel 199
                                   ++ + +++il+++
  gi|15669199|ref|NP_248004.1| 137 NVFKYITNILMDI 149
                                   9999999998887 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.19
                        AAA_23 115 deleqfisellgskki...ilnlilflgqerfeefelkdkke.......................rleelekel..eeled 167
                                   + l+++++ +l  +++    l++i+fl +e  ++++  ++ke                        l+++ + l  +e+++
  gi|15669199|ref|NP_248004.1| 212 AMLKERVDYILVDDFDketALKFIDFLSEEILNKKLSDEDKEliysyvggkpiliinvigklkhkNLKDVLNILlmDEISK 292
                                   556677777777666656677899999999876666666666788889999998888888885553333333321233333 PP

                        AAA_23 168 ekkllekleqekekekeleeleeeleeilk 197
                                    k++l +l    ++ k   ++eee+ ei k
  gi|15669199|ref|NP_248004.1| 293 LKDFLSNL----DYIKPKVNIEEEIIEIRK 318
                                   33333333....333333333333333332 PP

>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00025      0.28      43     106 ..       5      68 ..       2      69 .. 0.92
   2 ?    0.3   0.1      0.61   6.8e+02      45      86 ..      93     132 ..      91     152 .. 0.64
   3 ?   -3.5   0.0       9.6   1.1e+04      21      33 ..     166     178 ..     160     180 .. 0.78
   4 ?   -0.4   0.1         1   1.1e+03      68      88 ..     266     286 ..     234     297 .. 0.64
   5 ?   -1.0   0.1       1.5   1.7e+03      10      27 ..     274     291 ..     265     326 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                 Nit_Regul_Hom  43 kgflleedpesaikiikdlseeavlintvvdeekvekikeeleeklkderytiieipvekikvn 106
                                   k f+  e+++ +++i++++ +   +i   +++ k   i+e ++++l++++y +  i++++i ++
  gi|15669199|ref|NP_248004.1|   5 KFFNRVEEIKEILSILEEEPNLIYFIYGPINSGKTALINEIINNRLDKNKYVVFYIDLREIFIS 68 
                                   5678889**************999**********************************999875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.61
                 Nit_Regul_Hom  45 flleedpesaikiikdlseeavlintvvd.eekvekikeelee 86 
                                   f+  ed ++ i+ii+ l ++a  ++ +   ++++e+i +   +
  gi|15669199|ref|NP_248004.1|  93 FEEYEDDKKPIEIIRSLIKDAPSLCGIPTpKNTLEEILK---K 132
                                   556799999999999999998777776441444444433...3 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 9.6
                 Nit_Regul_Hom  21 lseagitGfylie 33 
                                   + ++ i Gf ++e
  gi|15669199|ref|NP_248004.1| 166 IGDMKINGFLIYE 178
                                   5678899999987 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1
                 Nit_Regul_Hom  68 intvvdeekvekikeeleekl 88 
                                   i  v+ + k +++k+ l+  l
  gi|15669199|ref|NP_248004.1| 266 IINVIGKLKHKNLKDVLNILL 286
                                   555555555555554444333 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 1.5
                 Nit_Regul_Hom  10 esenlgkvinalseagit 27 
                                    ++nl  v+n+l   +i+
  gi|15669199|ref|NP_248004.1| 274 KHKNLKDVLNILLMDEIS 291
                                   578888888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2318.29
//
Query:       gi|15669200|ref|NP_248005.1|  [L=130]
Description: peripheral membrane protein PhoU [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-05   24.9   0.4      2e-05   24.9   0.4    2.0  3  PhoU           PhoU domain
  ------ inclusion threshold ------
        2.1    8.2  10.3        1.6    8.6   1.8    2.5  2  Orthopox_B11R  Orthopoxvirus B11R protein


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.31   2.8e+03      34      45 ..       6      17 ..       4      24 .. 0.61
   2 !   24.9   0.4   2.3e-09     2e-05       3      86 ..      18     101 ..      16     103 .. 0.88
   3 ?   -1.2   0.0      0.33   2.9e+03       1      11 [.     118     128 ..     113     129 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.31
                                  HHHHHHHHHHHH CS
                          PhoU 34 ddeidrlekeie 45
                                  dd ++++ ++ie
  gi|15669200|ref|NP_248005.1|  6 DDIVNEMDRKIE 17
                                  566666666653 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 2.3e-09
                                   HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   3 rmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhav 83 
                                    ++e + + l++++e + ++ +++++ vi + + i +  + +e + ++al  + p+++dlr ll+++++++ lE i   av
  gi|15669200|ref|NP_248005.1|  18 LLGEEIIKNLNLSVEGYCTNKKDICNLVIYKNNNIIKNLESLEMYSVKALCLYRPVSKDLRKLLTIIKLCSMLEKIEECAV 98 
                                   68999********************888766555555557789999******************************99888 PP

                                   HHH CS
                          PhoU  84 nia 86 
                                   +i+
  gi|15669200|ref|NP_248005.1|  99 KIS 101
                                   885 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.33
                                   HHHHHHHHHHH CS
                          PhoU   1 lrrmaeiveem 11 
                                   ++rma+++ee+
  gi|15669200|ref|NP_248005.1| 118 IKRMASLTEEI 128
                                   35555555554 PP

>> Orthopox_B11R  Orthopoxvirus B11R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.8   0.00018       1.6       7      27 ..       5      29 ..       3      34 .. 0.75
   2 ?    4.3   1.5     0.004        36       5      26 ..      36      57 ..      32      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00018
                 Orthopox_B11R  7 vediineidrek....eeilknvei 27
                                   +di+ne+dr+     eei+kn+++
  gi|15669200|ref|NP_248005.1|  5 FDDIVNEMDRKIellgEEIIKNLNL 29
                                  58********852233699999865 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.004
                 Orthopox_B11R  5 tnvediineidrekeeilknve 26
                                  tn +di n +  + ++i+kn+e
  gi|15669200|ref|NP_248005.1| 36 TNKKDICNLVIYKNNNIIKNLE 57
                                  8889999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 875.30
//
Query:       gi|15669201|ref|NP_248006.1|  [L=252]
Description: phosphate ABC transporter ATP-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-32  111.7   0.0      5e-32  111.3   0.0    1.2  1  ABC_tran     ABC transporter
    1.1e-10   41.8   0.1    9.1e-05   22.4   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.2e-07   30.6   0.1      3e-05   23.6   0.1    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0002   21.9   0.3    0.00034   21.2   0.0    1.6  1  AAA_23       AAA domain
     0.0003   20.6   0.2     0.0012   18.7   0.0    1.8  2  AAA_15       AAA ATPase domain
     0.0008   19.4   0.0     0.0017   18.3   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
     0.0011   19.2   0.1     0.0024   18.2   0.1    1.8  1  AAA_22       AAA domain
      0.002   17.8   0.0     0.0037   17.0   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0021   18.0   0.0     0.0038   17.2   0.0    1.4  1  Rad17        Rad17 P-loop domain
     0.0034   17.8   0.0      0.007   16.8   0.0    1.7  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.026   15.0   0.0      0.083   13.4   0.0    1.8  2  AAA_18       AAA domain
      0.027   14.2   0.0      0.065   13.0   0.0    1.6  2  PRK          Phosphoribulokinase / Uridine kinase family
      0.064   13.4   0.0       0.11   12.6   0.0    1.5  1  AAA_33       AAA domain
      0.068   12.0   0.0        1.8    7.2   0.0    2.1  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.068   12.0   0.0       0.89    8.3   0.0    2.1  2  Adeno_IVa2   Adenovirus IVa2 protein
      0.085   12.6   0.0       0.35   10.6   0.0    1.9  2  AAA_24       AAA domain
      0.095   12.4   0.0        1.2    8.8   0.0    2.0  2  AAA_30       AAA domain
        0.1   11.7   0.0       0.33   10.1   0.0    1.7  1  G-alpha      G-protein alpha subunit
       0.15   12.4   0.0        1.6    9.2   0.0    2.1  2  AAA          ATPase family associated with various cellular a


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   5.3e-35     5e-32       3     137 .]      23     177 ..      21     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 5.3e-35
                                   EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSBH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqepqlfpeltv 76 
                                   +++l ++e++++a++G++G+GKSt+l++l +l +       eGe+lldgk++ +   +  +lrk++g+++q+p+ f  + +
  gi|15669201|ref|NP_248006.1|  23 DINLPIYENKITALIGPSGCGKSTFLRCLNRLNDLipnvrIEGEVLLDGKNIYDkdVDVYELRKRVGMVFQKPNPFAMS-I 102
                                   799*****************************99888999************9966677889***************99.9 PP

                                   HHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  77 ren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                   ++n              e d+ +e al+k  l +  ++ +++++ sLSgGq+qr+++ara++ kp++ll+DEpt+
  gi|15669201|ref|NP_248006.1| 103 YDNvafgprihgikdkkELDKIVEWALKKAALWDEVKDELHKNALSLSGGQQQRLCIARAIAVKPEVLLMDEPTS 177
                                   9999********9766555666***************************************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   9.7e-08   9.1e-05       1      32 [.      33      64 ..      33      92 .. 0.77
   2 !   17.6   0.0   2.8e-06    0.0027     235     298 ..     147     206 ..     104     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.7e-08
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegl 32
                                  +++liGp g+GKS++L++l  l +l+++v+ +
  gi|15669201|ref|NP_248006.1| 33 ITALIGPSGCGKSTFLRCLNRLNDLIPNVRIE 64
                                  79********************8884444433 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.8e-06
                        AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                    +lS G+++ l+++ a++  +    +ll DEp + L+P  + ++ el+ el++ +  ++++TH+
  gi|15669201|ref|NP_248006.1| 147 LSLSGGQQQRLCIARAIAVKP---EVLLMDEPTSALDPISTLKIEELMVELAK-DYTIVVVTHN 206
                                   567888888878888888766...9*************444444477777777.899******8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   3.1e-08     3e-05      23     206 ..      30     214 ..      23     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.1e-08
                                   TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCC....C--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdl....ihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                   ++++ta++Gp G+GKs +l  +   L +    ++r e    l    i+ ++      + +v ++f++++  +    ++v  
  gi|15669201|ref|NP_248006.1|  30 ENKITALIGPSGCGKSTFLRCL-NRLND-LIPNVRIEGEVLLdgknIYDKDVDVYELRKRVGMVFQKPNPFAMSIYDNVAF 108
                                   5789999999999999999999.55653.4445665533222111144455666667789999999999885555555544 PP

                                   EEEE..ETTSEEEEEETTEEE-H....HHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                   xxxx..xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 100 srrv..krkgeseykingkevtk....kevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                     r+  +++++   ki +   +k     ev++ l++  +   +LSgG+++ + +a  +A+   kp+   l+De  +aLD  
  gi|15669201|ref|NP_248006.1| 109 GPRIhgIKDKKELDKIVEWALKKaalwDEVKDELHKNAL---SLSGGQQQRLCIARAIAV---KPEV-LLMDEPTSALDPI 182
                                   433311444444444444333330003666666666666...59*****98888887775...6665.68*********** PP

                                   HHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 175 nvkkvaellkeksknaQfivislreemlekad 206
                                    + k+ el+ e  k+  ++v++++ ++ ++++
  gi|15669201|ref|NP_248006.1| 183 STLKIEELMVELAKDYTIVVVTHNMQQASRVS 214
                                   ***********************999887765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.6e-07   0.00034      13      39 ..      22      51 ..       5      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.6e-07
                        AAA_23 13 qeidF...skgltlItGpNGaGKTTildAi 39
                                  ++i++   ++++t+++Gp G+GK+T+l+++
  gi|15669201|ref|NP_248006.1| 22 FDINLpiyENKITALIGPSGCGKSTFLRCL 51
                                  457779999********************8 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.2e-06    0.0012      18      67 ..      25      76 ..      19     149 .. 0.64
   2 ?   -0.4   0.0      0.77   7.3e+02     320     365 ..     163     206 ..     147     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                        AAA_15 18 eidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn...kkvikiekedlei 67
                                   +++ e+ +t liG+ ++GKS++l+ l+ + +     n   + ++ ++ +++ +
  gi|15669201|ref|NP_248006.1| 25 NLPIYENkITALIGPSGCGKSTFLRCLNRLNDLIP--NvriEGEVLLDGKNIYD 76
                                  45555556*******************99988652..13353444444444444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.77
                        AAA_15 320 keeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                   +  k+ +ll++EP   L p     + +l+ ela+d    +++ TH+
  gi|15669201|ref|NP_248006.1| 163 IAVKPEVLLMDEPTSALDPISTLKIEELMVELAKDYT--IVVVTHN 206
                                   556788999999999999999999999999***9996..9999997 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.8e-06    0.0017      97     121 ..      29      53 ..       4      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.8e-06
                                   CTTSEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallp 121
                                    ++k+++l+G+SG GKSt++  l+ 
  gi|15669201|ref|NP_248006.1|  29 YENKITALIGPSGCGKSTFLRCLNR 53 
                                   567****************988865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.5e-06    0.0024       5      30 ..      31      56 ..      28     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.5e-06
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqld 30
                                   +i++++G+sG+GK+t lr l + +d
  gi|15669201|ref|NP_248006.1| 31 NKITALIGPSGCGKSTFLRCLNRLND 56
                                  6899***************9999876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     4e-06    0.0037      18      39 ..      27      48 ..      11      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4e-06
                        AAA_29 18 eidlkgatlltGpsGsGKSTll 39
                                  +i ++ +t l+GpsG GKST+l
  gi|15669201|ref|NP_248006.1| 27 PIYENKITALIGPSGCGKSTFL 48
                                  5555669*************98 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     4e-06    0.0038      35      67 ..      21      53 ..      17      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4e-06
                         Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                  l    L+  +++i  + GPsGCgkst ++ L +
  gi|15669201|ref|NP_248006.1| 21 LFDINLPIYENKITALIGPSGCGKSTFLRCLNR 53
                                  555567777889999**************9976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.4e-06     0.007      25      48 ..      32      54 ..      19     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.4e-06
                        AAA_16 25 elvllsGesGvGKsslvrellral 48
                                   ++ l+G+sG+GKs+ +r+l r l
  gi|15669201|ref|NP_248006.1| 32 KITALIGPSGCGKSTFLRCLNR-L 54
                                  6789***************996.3 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.8e-05     0.083       3      42 ..      36      78 ..      35     100 .. 0.73
   2 ?   -2.4   0.0       7.1   6.7e+03      26      35 ..     136     145 ..     111     174 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.8e-05
                        AAA_18  3 ltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevd 42
                                  l G++G+GK+t+ + L++++ +   +++ ++v+ ++   ++ d
  gi|15669201|ref|NP_248006.1| 36 LIGPSGCGKSTFLRCLNRLNDLipnVRIEGEVLLDGKNIYDKD 78
                                  89**************999755677555555555555555544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.1
                        AAA_18  26 vnlrdvaken 35 
                                   ++++d + +n
  gi|15669201|ref|NP_248006.1| 136 DEVKDELHKN 145
                                   2222222222 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.9e-05     0.065       3      47 ..      35      77 ..      33     104 .. 0.73
   2 ?   -2.4   0.0       3.6   3.4e+03      73     178 ..     230     237 ..     188     246 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-05
                           PRK  3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekd 47
                                  ++ g+SG+Gk+t+ r l+ + +   ++ + ieg ++l  ++++++
  gi|15669201|ref|NP_248006.1| 35 ALIGPSGCGKSTFLRCLNRL-N-DLIPNVRIEGEVLLDGKNIYDK 77
                                  788***********999765.4.4788899999998887666543 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.6
                           PRK  73 llyevlkelkegkkvdkpiYsheteeaapdkeeliegadvlviEGlhalydervaelldlkiyvdisidlelarklqRDia 153
                                   + ++ +                                                                           
  gi|15669201|ref|NP_248006.1| 230 ETEQIF--------------------------------------------------------------------------- 235
                                   444333........................................................................... PP

                           PRK 154 eRGrsleavldsilrrkpdyvnyik 178
                                                          ++
  gi|15669201|ref|NP_248006.1| 236 -----------------------LN 237
                                   .......................34 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012      0.11       3      28 ..      35      63 ..      33     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                        AAA_33  3 llvGlpGsGKstlaerllkklg...avll 28
                                   l+G++G+GKst+++ l + ++    v++
  gi|15669201|ref|NP_248006.1| 35 ALIGPSGCGKSTFLRCLNRLNDlipNVRI 63
                                  589***********987554445455555 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.049        46     244     265 ..      31      52 ..      26      55 .. 0.89
   2 ?    7.2   0.0    0.0019       1.8     324     396 ..     150     223 ..     137     231 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.049
                                   SSEEEEEE-TTSSHHHHHHHHH CS
                    ABC_ATPase 244 kGvtlIvGggfhGKsTLLeAle 265
                                   +++t+++G+   GKsT L+ l+
  gi|15669201|ref|NP_248006.1|  31 NKITALIGPSGCGKSTFLRCLN 52 
                                   579****************997 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0019
                                   -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HH...HH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEES CS
                    ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtN...lmirDermqelvskekepitplvdrvrelykklgvstilvvg 396
                                   SG   q   i++a+ ++ ++lL+DE tsA      +   e+m el   ++ +i  +++ +++  +  + + +  +g
  gi|15669201|ref|NP_248006.1| 150 SGGQQQRLCIARAIAVKPEVLLMDEPTSALDpisTLKIEELMVELA--KDYTIVVVTHNMQQASRVSDYTAFFLMG 223
                                   899999999********************76111233355555555..4446666666666666666666665555 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00094      0.89      89     108 ..      33      52 ..       3      63 .. 0.78
   2 ?    1.5   0.0      0.11     1e+02     234     251 ..     196     213 ..     171     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00094
                    Adeno_IVa2  89 iGviyGPtGsGksqllrnli 108
                                   i  + GP G+Gks +lr l 
  gi|15669201|ref|NP_248006.1|  33 ITALIGPSGCGKSTFLRCLN 52 
                                   66788************984 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
                    Adeno_IVa2 234 tgfsvlvvlhnlnPrsdi 251
                                     ++++vv hn++  s +
  gi|15669201|ref|NP_248006.1| 196 KDYTIVVVTHNMQQASRV 213
                                   579*********977665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00037      0.35       3      22 ..      32      51 ..      30      63 .. 0.85
   2 ?   -0.6   0.0      0.99   9.3e+02      38      60 ..     124     161 ..     110     209 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                        AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                  +  +++Gpsg GK+t+++ l
  gi|15669201|ref|NP_248006.1| 32 KITALIGPSGCGKSTFLRCL 51
                                  55789***********9987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.99
                        AAA_24  38 ldadkfpdieswedfldevvel...............a 60 
                                   +  + ++++  w++++de+ ++               +
  gi|15669201|ref|NP_248006.1| 124 IVEWALKKAALWDEVKDELHKNalslsggqqqrlciaR 161
                                   44455555555666666655554444444444444442 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0013       1.2      18      40 ..      31      53 ..      17      63 .. 0.88
   2 ?    1.5   0.0      0.23   2.1e+02      86     130 ..     163     211 ..     123     225 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                        AAA_30 18 drvavltGpAGtGKttalkalre 40
                                  +++++l Gp G GK+t l+ l++
  gi|15669201|ref|NP_248006.1| 31 NKITALIGPSGCGKSTFLRCLNR 53
                                  57999*************98876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.23
                        AAA_30  86 lepg.tllivDEagmv....dtkqlaallkaaekagakvilvGDerQlas 130
                                   ++ + ++l+ DE   +    +t ++++l+ +++k + ++++v  + Q as
  gi|15669201|ref|NP_248006.1| 163 IAVKpEVLLMDEPTSAldpiSTLKIEELMVELAK-DYTIVVVTHNMQQAS 211
                                   3444488999998777788899999999999988.666666666666544 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00035      0.33      28     163 ..      36     221 ..      29     247 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00035
                                   EEESTTSSHHHHHHHHHHHCS--........--HHHHHCCHHHHHHHHHHHHHHHHHHHHH.......TT........... CS
                       G-alpha  28 llGqseSGKsTilkqlkllykkg........fseeelatwraviqlnivrsiktileales.......leselsesf.... 89 
                                   l+G s++GKsT+l+ l +l +          +          +  +ni+++  ++ e  ++       +            
  gi|15669201|ref|NP_248006.1|  36 LIGPSGCGKSTFLRCLNRLNDLIpnvriegeV---------LLDGKNIYDKDVDVYELRKRvgmvfqkP-------Npfam 100
                                   89************999998544332222220.........2233444444444444444422222110.......11222 PP

                                   ............HHHC-SS-SCCCS-HCHHHH...........................................HHCCHH CS
                       G-alpha  90 ............elqelkerldplkkveasliaklssateee.................................qeiefn 125
                                               +  + k++ld++ +   +++a  +   ++e                                  ++ + 
  gi|15669201|ref|NP_248006.1| 101 siydnvafgpriHGIKDKKELDKIVEWALKKAALWD-EVKDElhknalslsggqqqrlciaraiavkpevllmdePTSALD 180
                                   334444444444555555555555555554433222.22222355555555555555666644444444444333222222 PP

                                   C..-HCHHHHHHHHCCSHHHHHHHCCG.CCTT--TTHHHHH CS
                       G-alpha 126 p..raevgedikaLwndpgiqelyerr.nkiklednaeyFl 163
                                   p  + ++ e +++L +d++i  +  +  + ++++d +++Fl
  gi|15669201|ref|NP_248006.1| 181 PisTLKIEELMVELAKDYTIVVVTHNMqQASRVSDYTAFFL 221
                                   25556666688888888877777664435666777777776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0016       1.6       3      35 ..      36      69 ..      34     104 .. 0.69
   2 ?    1.2   0.0      0.48   4.5e+02      45      66 ..     154     174 ..     117     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0016
                                  EESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCS CS
                           AAA  3 lyGppGtGKTllakavakelg.vefleisgsell 35
                                  l+Gp G+GK+++ + + +  + ++ ++i+g  ll
  gi|15669201|ref|NP_248006.1| 36 LIGPSGCGKSTFLRCLNRLNDlIPNVRIEGEVLL 69
                                  89*********99987554334555555555555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.48
                                   HHHHHHHHHHHTS.TSEEEEEET CS
                           AAA  45 kirelfkeakeka.kpsilfiDE 66 
                                   + r ++++a   a kp +l++DE
  gi|15669201|ref|NP_248006.1| 154 QQRLCIARA--IAvKPEVLLMDE 174
                                   444455444..445699999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1618.65
//
Query:       gi|15669202|ref|NP_248007.1|  [L=281]
Description: phosphate ABC transporter permease [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-14   54.6  16.9    1.1e-14   54.6  16.9    2.5  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.9     0.039   6.9e+02     153     182 ..      15      43 ..       4      46 .. 0.73
   2 !   54.6  16.9   6.2e-19   1.1e-14       1     171 [.      82     270 ..      82     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.039
                  BPD_transp_1 153 isnggvlalviavlllnlvadilqrlldpr 182
                                    + ++++++++ +l+++ ++ i+  ++++ 
  gi|15669202|ref|NP_248007.1|  15 KI-FLFIVGALTLLAILPLFHIIISIVEKG 43 
                                   44.778888888888888888888888775 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 6.2e-19
                  BPD_transp_1   1 gillGilaa....lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                   g++l++la+     ++n+++ ++   l +++l +P+++++ ++  ++v+    ++++l+++++l+l ++pyv + +++a+ 
  gi|15669202|ref|NP_248007.1|  82 GLPLAFLAGayayEFPNSFIGRATKMLLQIMLEFPTILVGTFVMGMLVV-PMGTFSALAGALALALILTPYVAVYTEEAMA 161
                                   5677777777777999999*************99999966665544322.344589999********************** PP

                  BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG............lgtllleail 146
                                   ++pk ++e  +alG++r q+++kv+ ++a+  i+tg+++ ++ + g+++ l+f++  +G            +g   l ++ 
  gi|15669202|ref|NP_248007.1| 162 EVPKIYKEGGYALGCTRAQVIFKVITKMAKKGILTGILIGMAKVAGETAPLLFTA--GGlyevyptnplepVGAIPLLIYT 240
                                   *******************************************************..447788888777775555555555 PP

                  BPD_transp_1 147 gydyseis.....nggvlalviavlllnlv 171
                                     + ++i      +g++l+++i++l++ + 
  gi|15669202|ref|NP_248007.1| 241 LVQSPSIEdhqmaWGAALVMLIIFLAIFVP 270
                                   555554447776668888888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1790.53
//
Query:       gi|15669203|ref|NP_248008.1|  [L=315]
Description: phosphate ABC transporter permease [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-13   50.0  14.8    2.8e-13   50.0  14.8    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        1.9    8.6   9.2        2.6    8.2   0.3    3.6  3  DUF4229       Protein of unknown function (DUF4229)
        7.4    6.4   7.7       0.79    9.6   0.9    2.3  2  Amastin       Amastin surface glycoprotein


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   9.8      0.53   3.2e+03      29      64 ..      20      95 ..       4     102 .. 0.58
   2 !   50.0  14.8   4.7e-17   2.8e-13       5     184 ..      98     310 ..      92     311 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.53
                  BPD_transp_1 29 slPsfvlaillvlvf........................................vilsilghlilpviillllsa 64
                                  +lP + ++++l++++                                         i+++++++ ++v+i+l ls+
  gi|15669203|ref|NP_248008.1| 20 TLPAIFVVFILFVLIlgfyffnalpaierygidlfitnvwkaaeepakevyglaaPIWGSIYTATIAVLIALPLSI 95
                                  3333333333222222336667777777777777777777777777777766666666666666666666555554 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 4.7e-17
                  BPD_transp_1   5 GilaalnrnkkldkllrpliivllslPsfv...laillvlvf...................vilsilghlilpviilllls 63 
                                   +i++  +  k+l++ l ++++++ +lP+++   ++ ++++ +                         g+  l++ ill ++
  gi|15669203|ref|NP_248008.1|  98 AIFVNDYAPKRLKYPLIVISDIMAGLPTIIygiWGAFILVPLlrdhimkflyehfsfiplfDYPPLSGYCYLSAGILLGIM 178
                                   56666667799999999*************77733333333368888888999999999986666789************* PP

                  BPD_transp_1  64 aapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtlllea 144
                                    +p++  i+r+a   +p+ ++e   alGa+r +   kv+++ + p ii+glilafg++lg++v+++++++++ ++++   +
  gi|15669203|ref|NP_248008.1| 179 VTPFAAAIIREAYAMIPSVYKEGLVALGATRYE-TTKVLIKYIRPAIISGLILAFGRALGETVAVSLVIGNS-FNLTYKLF 257
                                   *********************************.667********************************888.88888888 PP

                  BPD_transp_1 145 ilgydyseis.............nggvlalviavlllnlvadilqrlldprvr 184
                                     gy +s+ +               +++ ++++++++ lv++i+  +  +r r
  gi|15669203|ref|NP_248008.1| 258 APGYTISSLIanqfgnavlyeymTSVLYSAGLVLFVIGLVVNIIGIYYLKRWR 310
                                   8888888888899999999***99999999999999****9999877777765 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.4      0.73   4.4e+03      11      22 ..      25      36 ..      21      46 .. 0.49
   2 ?    8.2   0.3   0.00044       2.6      30      47 ..      78      95 ..      68      97 .. 0.80
   3 ?    4.1   0.0     0.008        48      29      58 ..     286     314 ..     270     315 .] 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.73
                       DUF4229 11 fvvltavillva 22
                                  fvv+ + +l ++
  gi|15669203|ref|NP_248008.1| 25 FVVFILFVLILG 36
                                  444333333332 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00044
                       DUF4229 30 pllvaallAlvvalplSm 47
                                  + ++ a++A+++alplS+
  gi|15669203|ref|NP_248008.1| 78 GSIYTATIAVLIALPLSI 95
                                  567899***********8 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.008
                       DUF4229  29 vpllvaallAlvvalplSmvllkklRdrat 58 
                                   +  lv+++++lvv  ++++  lk++R+ ++
  gi|15669203|ref|NP_248008.1| 286 SAGLVLFVIGLVVN-IIGIYYLKRWREHVS 314
                                   55688888888885.78999******9987 PP

>> Amastin  Amastin surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.9     0.085   5.1e+02      59      88 ..       7      36 ..       1     117 [. 0.59
   2 ?    9.6   0.9   0.00013      0.79     129     155 .]     280     306 ..     217     306 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.085
                       Amastin 59 rsrfraaqafsiisilvlaaalllsvllll 88
                                  ++ +r +  f ii++ + ++ ++l vl+l 
  gi|15669203|ref|NP_248008.1|  7 KKLLRKIDEFKIITLPAIFVVFILFVLILG 36
                                  566667777888887777777777666543 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00013
                       Amastin 129 sttakygaGFgLlvvawlldlinivvL 155
                                    t++ y+aG++L+v++ ++++i+i +L
  gi|15669203|ref|NP_248008.1| 280 MTSVLYSAGLVLFVIGLVVNIIGIYYL 306
                                   45568******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2037.35
//
Query:       gi|15669204|ref|NP_248009.1|  [L=389]
Description: periplasmic phosphate-binding protein PstS [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.1e-56  189.6   1.0    1.1e-55  189.3   1.0    1.0  1  PBP_like_2  PBP superfamily domain
    3.5e-27   96.2   7.7    4.5e-27   95.8   7.7    1.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    8.5e-07   28.3   0.0    8.5e-06   25.0   0.0    2.1  1  PBP_like    PBP superfamily domain


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.3   1.0   1.9e-59   1.1e-55       4     281 ..      48     358 ..      39     359 .. 0.89

  Alignments for each domain:
  == domain 1  score: 189.3 bits;  conditional E-value: 1.9e-59
                    PBP_like_2   4 aeatsvgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseia.agwaangag 83 
                                     +t    i+ +G+t+p+  ++k++++++k +p++k++y+++GSg g++a+++g +d++ +d p++es  + +++  +g  
  gi|15669204|ref|NP_248009.1|  48 KPSTII--IRTTGATFPKYQIQKWIEDYQKTHPNVKIEYEGGGSGYGQEAFAKGLTDIGRTDPPVKES--MwKKFLSTG-D 123
                                   444555..9***********************************************************..668888888.* PP

                    PBP_like_2  84 gliqvpvaigaialvvnkd....nplnlsreaLakIfsgkItnWnd.........vlglpadgpIkvvhrsdgsgttflfs 151
                                   ++ q+p  +ga+++ +n +    + l+lsr++La+If gkI  W+d         ++  ++ + I vvhrsd sgtt  f+
  gi|15669204|ref|NP_248009.1| 124 QPLQFPEIVGAVVVTYNIPeigdKTLKLSRDVLADIFLGKIEYWDDerikkinpeIADKLPHEKIIVVHRSDASGTTAIFT 204
                                   *****************7779777777****************************777777******************** PP

                    PBP_like_2 152 talaeq...............gpwt..asgigasgsegvasav.snngaigyvsvaywlavkgysladvtngagkfvlpta 214
                                   t+l+                 +p++   +g++ +g++gv+ +v s++++ +y++++y+ ++  +++a+++n++gkfv pt 
  gi|15669204|ref|NP_248009.1| 205 TYLSLIskewaekvgagktvnWPTDniGRGVAGKGNPGVVAIVkSTPYTVAYTELSYAIEQ-KLPVAALENKNGKFVKPTD 284
                                   ****889999999999999887776335555566699999999899*************99.******************* PP

                    PBP_like_2 215 ataasalkvakias....nplawslqpveeniadgayPlsrftyiivyqpyayh...gnnaalakaFldyllsd 281
                                   +t+++a++++k++     +  +++l+ + ++++d ayP+++ft+++v ++ +++   +++a+++k+Fl+++l++
  gi|15669204|ref|NP_248009.1| 285 ETIKAAVSAVKASIpnptEGYKEDLKQMLDAPGDNAYPIVAFTHLLVWENKNGKhysPEKAKAIKDFLTWVLTE 358
                                   *********888668799667777888999***************997766555457788***********985 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   7.7   7.5e-31   4.5e-27       9     314 ..      65     361 ..      55     362 .. 0.90

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 7.5e-31
                                   HHHHHHHHHHHHHHTTEEEEEEEECHHHHHH...HHHHHHHTTSSSCSEEEE.CGGHHHHHHHT..TSBECCHHHHHHTTE CS
                     SBP_bac_1   9 alqalvakafekehpgikVeiesvgsgslaq...kltlaiaaGdgpaDviav.dndwiarlaka..glllpldpyvkayla 83 
                                    +q+ + ++++k+hp++k+e+e +gsg +++   k+ ++i+ +d+p  v  + +  ++++  ++  ++++ ++++v+ y++
  gi|15669204|ref|NP_248009.1|  65 QIQKWI-EDYQKTHPNVKIEYEGGGSGYGQEafaKGLTDIGRTDPP--VKESmWKKFLST-GDQplQFPEIVGAVVVTYNI 141
                                   345555.669**********************************88..888866666664.66679*************** PP

                                   CTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCT...HCCHCCEEH CS
                     SBP_bac_1  84 pgvkdaadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkkp...iggarggsa 161
                                   p+  d ++kls +vl++i+             g+i                Wd+  ++  ++  ++k p   i+++++++a
  gi|15669204|ref|NP_248009.1| 142 PEIGDKTLKLSRDVLADIFL------------GKIE--------------YWDDERIKKINPEIADKLPhekIIVVHRSDA 196
                                   ********************............7888..............******************************* PP

                                   HHHHHHHHHHHHHHHTGGGEECCCT......................HHCSHHHHS..HHHHHHHHHHHHHHHHHHHTTEE CS
                     SBP_bac_1 162 sgtayyfalalakslggkvfdkdgg......................gldnpegvt..aatylvklyavanltkelkgkga 218
                                   sgt+++f+++l++ +   ++ +++g                      g+++ + +t  +++y + +ya++    +l+ +  
  gi|15669204|ref|NP_248009.1| 197 SGTTAIFTTYLSLISK--EWAEKVGagktvnwptdnigrgvagkgnpGVVAIVKSTpyTVAYTELSYAIEQ---KLPVAAL 272
                                   ****************..77777777****************88888888888888***********9998...******* PP

                                   ECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCST.. CS
                     SBP_bac_1 219 enkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgskn.. 297
                                   enk+g ++++  e+ +aa+   +  +a + +  ++ + + +++ +++++ ++++            +a ++ +++ +kn  
  gi|15669204|ref|NP_248009.1| 273 ENKNGKFVKPTDETIKAAV---SAVKASIPNPTEGYKEDLKQMLDAPGDNAYPI------------VAFTHLLVWENKNgk 338
                                   *************999999...56777889999*********************............*************99 PP

                                   ......HHHHHHHHHHHTSHHHH CS
                     SBP_bac_1 298 ......peaAkkFldfllspeaq 314
                                          +a+k+Fl+++l+++++
  gi|15669204|ref|NP_248009.1| 339 hyspekAKAIKDFLTWVLTEGQK 361
                                   9*9755555***********997 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.4e-09   8.5e-06       2     115 ..      71     209 ..      70     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.4e-09
                                   HHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS-...............................--CCCHHCCCC CS
                      PBP_like   2 eelaeknpgvrvavanvGsggGlkalrageadiagshll...............................dketeeynapa 51 
                                   e +++++p+v++++ + Gsg G +a+++g +di+ ++ +                               ++e ++  ++ 
  gi|15669204|ref|NP_248009.1|  71 EDYQKTHPNVKIEYEGGGSGYGQEAFAKGLTDIGRTDPPvkesmwkkflstgdqplqfpeivgavvvtynIPEIGDKTLKL 151
                                   679************************************777777777777777777777776666666655555556666 PP

                                   CEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BGGGC-S-B-EEEEE-TTSHHHHHHHHHHC- CS
                      PBP_like  52 lrkaldgievvlvnlarreqglvvakgnpkkitnwkdladaplrlvnRetGSGtrdlfdellkk 115
                                    r+ l++i +  ++ + +e    ++++       + +l+ +++ +v R   SGt   f++ l+ 
  gi|15669204|ref|NP_248009.1| 152 SRDVLADIFLGKIEYWDDERIKKINPE------IADKLPHEKIIVVHRSDASGTTAIFTTYLSL 209
                                   677777777777777777776666666......67899*********************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2689.14
//
Query:       gi|15669205|ref|NP_248010.1|  [L=294]
Description: hypothetical protein MJ_1016 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-06   27.1   0.0    3.9e-05   23.2   0.0    2.2  2  QueC            Queuosine biosynthesis protein QueC
    2.9e-05   24.2   0.0    0.00011   22.3   0.0    2.0  1  PAPS_reduct     Phosphoadenosine phosphosulfate reductase fam
    3.2e-05   23.6   0.1    0.00021   21.0   0.0    2.2  3  ThiI            Thiamine biosynthesis protein (ThiI)
     0.0055   16.5   0.0      0.011   15.5   0.0    1.5  1  ATP_bind_3      PP-loop family
  ------ inclusion threshold ------
       0.02   14.0   0.0      0.047   12.8   0.0    1.7  1  NAD_synthase    NAD synthase
      0.046   14.0   0.2       0.13   12.6   0.0    1.8  2  Init_tRNA_PT    Rit1 DUSP-like domain
      0.063   12.6   0.1      0.091   12.1   0.1    1.3  1  NAD_binding_5   Myo-inositol-1-phosphate synthase
        0.1   10.8   0.0       0.14   10.4   0.0    1.1  1  Exonuc_V_gamma  Exodeoxyribonuclease V, gamma subunit
       0.13   12.1   0.0        1.6    8.6   0.0    2.6  3  YycC            YycC-like protein


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     2e-08   3.9e-05       2      55 ..      37      90 ..      36     136 .. 0.83
   2 ?    1.6   0.0     0.084   1.7e+02     144     181 ..     175     212 ..     164     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2e-08
                                  EEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.- CS
                          QueC  2 avvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelgvee 55
                                  +vv+ SGG DS+t++alak+ g ++e l   Y++  +++  ++++k++k++++  
  gi|15669205|ref|NP_248010.1| 37 IVVMASGGKDSSTAIALAKDLGLNIEYLIHFYHRWsWDVSKKMVEKLSKKFDI-P 90
                                  599**********************9998889887799************998.3 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.084
                                   HHHHHTS--EEE-TTTT--HHHHHHHHHHTTHHHHH-B CS
                          QueC 144 lnlgedkkieieaPlidlsKaeivklgkelgvpleetl 181
                                   ++ g+dk++    Pli+l  ++++kl + +++++e ++
  gi|15669205|ref|NP_248010.1| 175 YSKGKDKEVLFFRPLIRLACEDVLKLMDYYNIEIERAH 212
                                   67789999999*****************9999888765 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   5.3e-08   0.00011       2     159 ..      37     212 ..      36     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.3e-08
                                   EEEE--SSCTCHHHHHHHHHHCTTHE.EEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHCH CS
                   PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvp.vvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyeea 81 
                                   +vv  sgGkds+  + La     +++ +++   ++  +   ++v++l++++++ +++y+  +e  +  + +k gss  +  
  gi|15669205|ref|NP_248010.1|  37 IVVMASGGKDSSTAIALAKDLGLNIEyLIHFYHRWSWDVSKKMVEKLSKKFDIPVIFYNITDELLKRTKGAK-GSSICRI- 115
                                   7999********************855************************************999999888.8999888. PP

                                   HHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S......................CEEE-CCCT-- CS
                   PAPS_reduct  82 aeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek......................slrvfPllnWt 140
                                   +++i+K +++    ++ +  +++tG  + e+ s a +++++      +                      +l + Pl+   
  gi|15669205|ref|NP_248010.1| 116 CKNIMKDKAVDI-SKEKGIRIIMTGDSALEKVSGAVMNYLRDVYG--EvvynkmeltpvpqkyskgkdkeVLFFRPLIRLA 193
                                   999999888777.45556677777777777776666666554333..1235566666666666667777555555888888 PP

                                   HHHHHHHHHHCT--B-CCC CS
                   PAPS_reduct 141 eedvwqyilrenipynpLy 159
                                    edv +++ + ni++   +
  gi|15669205|ref|NP_248010.1| 194 CEDVLKLMDYYNIEIERAH 212
                                   8888888888888876655 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     1e-07   0.00021       6     131 ..      37     156 ..      33     172 .. 0.80
   2 ?   -1.1   0.0      0.61   1.2e+03     137     155 ..     182     200 ..     176     213 .. 0.80
   3 ?   -2.5   0.0       1.6   3.1e+03      96     112 ..     247     263 ..     240     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1e-07
                          ThiI   6 vlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvkek 86 
                                   ++++ SgG DS  a  l+   G++++++  +          ++ +k++e+l++     ++ ++ ++ ++ l + ++ +k  
  gi|15669205|ref|NP_248010.1|  37 IVVMASGGKDSSTAIALAKDLGLNIEYLIHF----YHRWSWDVSKKMVEKLSKKF---DIPVIFYNITDELLKRTKGAKGS 110
                                   67889********************986543....33444555566666666533...47889999999999999999*** PP

                          ThiI  87 ltivllkrkmlriAekvaeeegakalvtGes.LgqVaSqtleNlrv 131
                                   + + ++k  m   A  + +e+g++ ++tG+s L +V+   ++ lr 
  gi|15669205|ref|NP_248010.1| 111 SICRICKNIMKDKAVDISKEKGIRIIMTGDSaLEKVSGAVMNYLRD 156
                                   *****************************95488898887777764 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.61
                          ThiI 137 nllilrPLigldKeeiikl 155
                                   ++l +rPLi l  e++ kl
  gi|15669205|ref|NP_248010.1| 182 EVLFFRPLIRLACEDVLKL 200
                                   56789*****999999876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.6
                          ThiI  96 mlriAekvaeeegakal 112
                                     +iA +va+++g +a 
  gi|15669205|ref|NP_248010.1| 247 YNKIATEVAKKHGFRAS 263
                                   46899999999998875 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.5e-06     0.011       2     161 ..      37     206 ..      36     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.5e-06
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H...HHCTTSTCCCH CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv...akkkgknleea 79 
                                   ++v  SgG DS + + l+++l  +      +  +++  r + +  +++v++l+kk++i+++  +++    +++kg +    
  gi|15669205|ref|NP_248010.1|  37 IVVMASGGKDSSTAIALAKDLGLN---IEYL--IHFYHRWSWDVSKKMVEKLSKKFDIPVIFYNITDellKRTKGAKGSSI 112
                                   57888********99999999442...2234..55555677888999*****************99988866677777777 PP

                                   HHHHHHHHHHH...CHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEE.........TTCCEE-CCCT-- CS
                    ATP_bind_3  80 ARelRYevlke...alkkegievlllAhhadDqaEtfllrlargsglaglagikeasei.........asirlvRPlLkvs 148
                                    R +   + ++   + k++gi++++++  a   +  ++++  r+   + ++   e +++         +++ + RPl+ + 
  gi|15669205|ref|NP_248010.1| 113 CRICKNIMKDKavdISKEKGIRIIMTGDSALEKVSGAVMNYLRDVYGEVVYNKMELTPVpqkyskgkdKEVLFFRPLIRLA 193
                                   777776655551115689999999999999999999999999988776666655555556667788766688899999998 PP

                                   HHHHHHHHHHTT- CS
                    ATP_bind_3 149 keeleeylkekki 161
                                    e++ ++++  +i
  gi|15669205|ref|NP_248010.1| 194 CEDVLKLMDYYNI 206
                                   8888888777666 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.3e-05     0.047       8      85 ..      22     100 ..      15     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHHCTT..SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHH CS
                  NAD_synthase   8 flkeyvkkaga..kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpiv 85 
                                    + e+ k+++a  +g+v+  SGG DSs++ ala+++ g +    + + +  s + +++   +l ++++i v  ++i++ +
  gi|15669205|ref|NP_248010.1|  22 DIIEQFKEKNAldEGIVVMASGGKDSSTAIALAKDL-GLNIEYLIHFYHRWSWDVSKKMVEKLSKKFDIPVIFYNITDEL 100
                                   44445555555579*******************986.4444444555588888888888999999999999888888765 PP

>> Init_tRNA_PT  Rit1 DUSP-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.5e-05      0.13       8      57 ..       7      54 ..       4      62 .. 0.90
   2 ?   -2.3   0.0       2.7   5.5e+03      23      46 ..      95     118 ..      69     130 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.5e-05
                  Init_tRNA_PT  8 gsgKkgsknLrtalpkivdfvrkrlsedkkkkilvacetGkdlsvgvaLa 57
                                  +++K + +nL++  ++i+++++++ + d+   i+v+   Gkd s ++aLa
  gi|15669205|ref|NP_248010.1|  7 TKNKRKLNNLEELKRDIIEQFKEKNALDE--GIVVMASGGKDSSTAIALA 54
                                  57899999999999999999999988877..9*****************8 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.7
                  Init_tRNA_PT  23 kivdfvrkrlsedkkkkilvacet 46 
                                   +i+d + kr +  k ++i+  c++
  gi|15669205|ref|NP_248010.1|  95 NITDELLKRTKGAKGSSICRICKN 118
                                   444444444444444666666655 PP

>> NAD_binding_5  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   4.6e-05     0.091     139     174 ..       7      43 ..       2      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.6e-05
                                   xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                 NAD_binding_5 139 lkgkskleqleqirkdi.reFkkknkldkvivlwtan 174
                                   +k+k+kl++le++++di ++Fk+kn ld+ iv+ ++ 
  gi|15669205|ref|NP_248010.1|   7 TKNKRKLNNLEELKRDIiEQFKEKNALDEGIVVMASG 43 
                                   5567899********96489*********99987665 PP

>> Exonuc_V_gamma  Exodeoxyribonuclease V, gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.8e-05      0.14      10      96 ..      13      97 ..      10     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.8e-05
                                  HHHHHHHHHHHHHHS--SSSS--EEEE-SSHHHHHHHHHHHHHTTS-BESEB---HHHHHHHHHHHHSSS--SS-TT-HHHHH CS
                Exonuc_V_gamma 10 levLaellakllreeplanpfepeiilvqskgmarwLklelAekkGiaanlefplpasflwqllkavlpevpeespfskealt 92
                                  l+ L el  +++++ +++n +++ i++  s g     +++lA++ G   ++   +  ++ w++ k+++++++  ++f+  ++ 
  gi|15669205|ref|NP_248010.1| 13 LNNLEELKRDIIEQFKEKNALDEGIVVMASGGKDSSTAIALAKDLGLNIEYLIHFYHRWSWDVSKKMVEKLS--KKFDIPVIF 93
                                  55566666666777778889***********************************************99864..566666666 PP

                                  HHHH CS
                Exonuc_V_gamma 93 Wrlm 96
                                  +++ 
  gi|15669205|ref|NP_248010.1| 94 YNIT 97
                                  6665 PP

>> YycC  YycC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00081       1.6       9      27 ..      48      66 ..      46      69 .. 0.93
   2 ?   -0.4   0.0      0.52     1e+03      11      22 ..      80      91 ..      74      91 .. 0.77
   3 ?   -3.2   0.0       3.9   7.7e+03      16      29 ..     262     275 ..     248     276 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00081
                          YycC  9 eTAvkLskkLnvPLEhlMH 27
                                   TA+ L+k L++ +E l H
  gi|15669205|ref|NP_248010.1| 48 STAIALAKDLGLNIEYLIH 66
                                  5*****************9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.52
                          YycC 11 AvkLskkLnvPL 22
                                    kLskk ++P+
  gi|15669205|ref|NP_248010.1| 80 VEKLSKKFDIPV 91
                                  569*****9995 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.9
                          YycC  16 kkLnvPLEhlMHmP 29 
                                     +++P  ++M +P
  gi|15669205|ref|NP_248010.1| 262 ASIKLPSKKIMVVP 275
                                   44566666777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1956.76
//
Query:       gi|15669206|ref|NP_248011.1|  [L=203]
Description: hypothetical protein MJ_1017 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.2    7.4   7.4        9.4    6.3   7.4    1.5  1  DUF4577   Domain of unknown function (DUF4577)


Domain annotation for each model (and alignments):
>> DUF4577  Domain of unknown function (DUF4577)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   7.4   0.00052       9.4      58      86 ..      10      38 ..       2      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00052
                       DUF4577 58 Gsrslffvgliivlivslalvsfviflii 86
                                  G +++f++ li++l++ la+v++ ifli+
  gi|15669206|ref|NP_248011.1| 10 GITGIFLIFLILLLLIILAIVALPIFLIL 38
                                  67899**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1616  (0.0901333); expected 358.6 (0.02)
Passed bias filter:                      868  (0.0484132); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 1416.91
//
Query:       gi|15669207|ref|NP_248012.1|  [L=524]
Description: D-3-phosphoglycerate dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-70  235.1   0.1    3.4e-69  231.8   0.0    2.4  3  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    2.3e-46  156.8   0.5    2.3e-46  156.8   0.5    1.9  3  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    1.4e-13   50.4   2.9    1.5e-12   47.0   0.0    3.3  3  ACT             ACT domain
    1.5e-09   38.2   1.7    3.6e-09   37.0   0.0    2.4  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00012   22.2   2.1      0.013   15.6   0.1    2.4  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
    0.00018   21.1   1.3     0.0068   16.0   0.0    2.9  3  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    0.00023   21.5   0.2     0.0037   17.7   0.0    2.4  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    0.00095   19.7   4.1      0.007   16.9   0.0    3.2  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0032   18.0   1.4      0.023   15.3   0.0    2.9  3  ACT_4           ACT domain
     0.0046   16.3   0.6      0.015   14.6   0.1    2.0  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.013   15.4   0.3       0.94    9.4   0.0    2.8  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.057   13.3   0.0        1.4    8.8   0.0    2.8  3  ACT_5           ACT domain
      0.081   13.1   0.2        3.3    7.8   0.0    2.6  2  DUF4442         Domain of unknown function (DUF4442)
        0.9   10.0   3.0        2.7    8.5   0.1    3.2  3  NAD_binding_7   Putative NAD(P)-binding
        1.4    9.0   4.7        4.5    7.4   0.3    3.0  2  DapB_N          Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.35   4.1e+02      77     112 ..      27      61 ..      14      84 .. 0.74
   2 !  231.8   0.0   2.8e-72   3.4e-69       1     178 []     105     280 ..     105     280 .. 0.97
   3 ?   -2.9   0.0       3.1   3.8e+03       4      43 ..     389     427 ..     388     428 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.35
                                   HHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHH CS
                  2-Hacid_dh_C  77 elgvelvsleellaesDivslhlpltpetrhlinae 112
                                   ++g+++++l e ++++D++++    t+ tr++i+++
  gi|15669207|ref|NP_248012.1|  27 ATGLTKEELLEKIKDADVLVVRS-GTKVTRDVIEKA 61 
                                   55777778888888888887764.477777777654 PP

  == domain 2  score: 231.8 bits;  conditional E-value: 2.8e-72
                                   HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCE CS
                  2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgve 81 
                                   ++l+la++r++++a +++++gew ++k+++g el+gkt+G+iGlGrIGq+v kr+kafgm++i+yd++  ke  +e++gve
  gi|15669207|ref|NP_248012.1| 105 MGLMLAAARNIPQATASLKRGEW-DRKRFKGIELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDPYIPKEV-AESMGVE 183
                                   689********************.9*******************************************99887.9999**8 PP

                                   EC.SHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSGT CS
                  2-Hacid_dh_C  82 lv.sleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeeplpe 161
                                   lv +++el++++D+++lh+pltp+trh+i++e++a+mkk+ai++N+aRGgl+de+aL+eaLk+gki++aalDvfeeep++ 
  gi|15669207|ref|NP_248012.1| 184 LVdDINELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEGKIRAAALDVFEEEPPK- 263
                                   777****************************************************************************9. PP

                                   CHHHHHSTTEEE-SS-T CS
                  2-Hacid_dh_C 162 dspllelpnviltPHia 178
                                   d+pll+l+nvi tPH +
  gi|15669207|ref|NP_248012.1| 264 DNPLLTLDNVIGTPHQG 280
                                   66*************86 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.1
                                   HHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES CS
                  2-Hacid_dh_C   4 llallrrlaeadeevregewksekallgkelsgktvGiiG 43 
                                   ++a +r+++ +++++ e+++  ++     e  +k+  i+G
  gi|15669207|ref|NP_248012.1| 389 IIAKNRNINVVESSTSEEKY-GNAIKITAESDKKKFSIVG 427
                                   56778999999999999999.5555555688888888888 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.8   0.5   1.9e-49   2.3e-46       1     134 []       4     312 ..       4     312 .. 0.99
   2 ?   -3.0   0.0       4.3   5.1e+03      73      89 ..     383     400 ..     379     405 .. 0.58
   3 ?   -3.7   0.0       7.5   8.9e+03      50      62 ..     501     513 ..     493     521 .. 0.60

  Alignments for each domain:
  == domain 1  score: 156.8 bits;  conditional E-value: 1.9e-49
                                   EEEEST.CHHHHHHHHHTTE.EEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHH CS
                                   xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh   1 vlileplreeelellkeegv.evevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaa 80 
                                   +l+++pl+e+++++l+e  v evev + l++eellek+kdad+l+vrs tkvt++v+e+++kLkvi+ragvGvDn+D++aa
  gi|15669207|ref|NP_248012.1|   4 ILVTDPLHEDAIKILEE--VgEVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVIEKAEKLKVIGRAGVGVDNIDVEAA 82 
                                   79***************..77************************************************************ PP

                                   HHTT-EEEE-TTTTHHHHHHHH........................................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxx........................................................... RF
                    2-Hacid_dh  81 kerGilVtnvpgystesvAElt........................................................... 102
                                   +e+Gi+V+n+p++s++svAElt                                                           
  gi|15669207|ref|NP_248012.1|  83 TEKGIIVVNAPDASSISVAELTmglmlaaarnipqataslkrgewdrkrfkgielygktlgviglgrigqqvvkrakafgm 163
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                    2-Hacid_dh 103 ................................................................................. 102
                                                                                                                    
  gi|15669207|ref|NP_248012.1| 164 niigydpyipkevaesmgvelvddinelckradfitlhvpltpktrhiigreqialmkknaiivncargglidekalyeal 244
                                   ********************************************************************************* PP

                                   ....................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBCS CS
                                   ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh 103 ....................................aaTeeaqeniaeeaaenlvaflkgespanavn 134
                                                                       a+Teeaq+++++++ae+++++l+ge ++n+vn
  gi|15669207|ref|NP_248012.1| 245 kegkiraaaldvfeeeppkdnplltldnvigtphqgASTEEAQKAAGTIVAEQIKKVLRGELAENVVN 312
                                   *******************************************************************8 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.3
                                   TTB-HH.HHHHTT-EEEE CS
                                   xxxxxx.xxxxxxxxxxx RF
                    2-Hacid_dh  73 DnvDld.aakerGilVtn 89 
                                   + v+ +  ak+r+i+V++
  gi|15669207|ref|NP_248012.1| 383 NLVNAPiIAKNRNINVVE 400
                                   444444136777777776 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 7.5
                                   -BSHHHHHHHTT- CS
                                   xxxxxxxxxxxxx RF
                    2-Hacid_dh  50 kvtaevlealpkL 62 
                                    v +ev+e+ +++
  gi|15669207|ref|NP_248012.1| 501 TVPEEVIEKIKEI 513
                                   5777777777443 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.3   1.5e+03      19      54 ..      65      97 ..      44     102 .. 0.76
   2 ?    1.6   0.1       0.2   2.4e+02      24      52 ..     394     420 ..     392     432 .. 0.66
   3 !   47.0   0.0   1.3e-15   1.5e-12       6      66 ..     456     514 ..     451     515 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                                  HHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHH CS
                           ACT 19 galadrgiNidsieqrssedkvagivfvvivvdeed 54
                                   +++++g+ +d+i +    +   + ++vv  +d+++
  gi|15669207|ref|NP_248012.1| 65 KVIGRAGVGVDNIDVEAATE---KGIIVVNAPDASS 97
                                  57788888888888888887...5666666666665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.2
                                   TTSEEEEEEEEEESTTECEEEEEEEEEEH CS
                           ACT  24 rgiNidsieqrssedkvagivfvvivvde 52 
                                   r+iN++  ++++ ++  ++ + ++ + d 
  gi|15669207|ref|NP_248012.1| 394 RNINVVESSTSEEKY--GNAIKITAESDK 420
                                   556665555555555..787777776665 PP

  == domain 3  score: 47.0 bits;  conditional E-value: 1.3e-15
                                   EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                           ACT   6 gvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66 
                                      DrPG+++rv+ +l+d+giNi+s+++++ e+  +g++++ +  d+ ++eev+e++k+++
  gi|15669207|ref|NP_248012.1| 456 KHIDRPGTIGRVCITLGDYGINIASMQVGRKEP--GGESVMLLNLDHTVPEEVIEKIKEIP 514
                                   566******************************..9**********************987 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       1.2   1.4e+03      75     107 ..      34      67 ..      10      96 .. 0.65
   2 !   37.0   0.0     3e-12   3.6e-09       2     110 ..     142     250 ..     141     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                                   SHCCC--TT-E.EEE-S---HHHHHHHHHHHHHT CS
                 NAD_binding_2  75 gllealkkgdi.lidgstsspedtrelakelkek 107
                                   +lle++k  d+ ++ ++t   +d +e a++lk  
  gi|15669207|ref|NP_248012.1|  34 ELLEKIKDADVlVVRSGTKVTRDVIEKAEKLKVI 67 
                                   2666665554414455555556666666665544 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 3e-12
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-.SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC- CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavyn.rtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.lleal 80 
                                   +g+iGlG +G++ +++ ++ g+++++y+   +++v e +  g++++++i+el++++d++ + v+ +++++++i +  ++ +
  gi|15669207|ref|NP_248012.1| 142 LGVIGLGRIGQQVVKRAKAFGMNIIGYDpYIPKEVAESM--GVELVDDINELCKRADFITLHVPLTPKTRHIIGReQIALM 220
                                   8***************************44455555544..8*******************************998999** PP

                                   -TT-EEEE-S---HHHHHHHHHHHHHTT-E CS
                 NAD_binding_2  81 kkgdilidgstsspedtrelakelkekglk 110
                                   kk++i+++++     d + l+++lke +++
  gi|15669207|ref|NP_248012.1| 221 KKNAIIVNCARGGLIDEKALYEALKEGKIR 250
                                   ************************998876 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3     0.012        14      66     153 ..      29     113 ..      19     121 .. 0.80
   2 !   15.6   0.1     1e-05     0.013      17     110 ..     133     230 ..     128     256 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
                                   T-EE--HHHCTTT-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EE CS
                 AdoHcyase_NAD  66 GfevvtleevvkkadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkki 146
                                   G+   +l e +k+ad++v  +G+k  +t++ ++k ++  +++  G    +idv+a +++++ +++  p+   + +++  + 
  gi|15669207|ref|NP_248012.1|  29 GLTKEELLEKIKDADVLVVRSGTK--VTRDVIEKAEKLKVIGRAGVGVDNIDVEAATEKGIIVVN-APDASSISVAELTMG 106
                                   55566778899***********98..8999************************99988877666.366666666666666 PP

                                   EEEGGGS CS
                 AdoHcyase_NAD 147 illaeGr 153
                                   ++la  r
  gi|15669207|ref|NP_248012.1| 107 LMLAAAR 113
                                   6666655 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1e-05
                                   H-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHH..HHHHCTT-EE--HHHCTTT-SEE...EE.-SSSSSS CS
                 AdoHcyase_NAD  17 tdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPica..lqaameGfevvtleevvkkadiv...vt.ttGnkdi 91 
                                     + l Gk+  v+G G +G+   +  k++G  +i    dP     +  +m    v  ++e+ k+ad++   v  t  ++ i
  gi|15669207|ref|NP_248012.1| 133 KGIELYGKTLGVIGLGRIGQQVVKRAKAFGMNII--GYDPYIPkeVAESMGVELVDDINELCKRADFItlhVPlTPKTRHI 211
                                   556688************************8765..678865411344454455778999*****986222332456899* PP

                                   B-HHHHCCS-TTEEEEE-S CS
                 AdoHcyase_NAD  92 itlehlkkmkddaivcniG 110
                                   i +e+++ mk++ai+ n  
  gi|15669207|ref|NP_248012.1| 212 IGREQIALMKKNAIIVNCA 230
                                   ***************9975 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.13   1.5e+02      75     113 ..      29      67 ..      23      78 .. 0.82
   2 !   16.0   0.0   5.7e-06    0.0068       2      96 ..     137     232 ..     136     243 .. 0.76
   3 ?   -3.5   0.0       5.6   6.7e+03      31      49 ..     273     291 ..     270     305 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.13
                                   HHHHHHTGGG--TT-EEEESSSHHHHTTSS---TTSEEE CS
                          IlvN  75 evyeeeiepnlkegkalafahGfnihfglikppkdvdvv 113
                                    + +ee+ +++k+ ++l+  +G ++  + i+  ++++v+
  gi|15669207|ref|NP_248012.1|  29 GLTKEELLEKIKDADVLVVRSGTKVTRDVIEKAEKLKVI 67 
                                   566788888999999999999999999999999888886 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 5.7e-06
                                   HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-E.EEEHHHHHHT-SEEEE-S-HH.HHHHHHHHH CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfe.vltvaeavkkadvvmiliPDe.lqkevyeee 80 
                                   l gk++ viG G  G+   +  +  g+++ +g        + A++ g+e v +++e++k+ad++++ +P +   ++++ +e
  gi|15669207|ref|NP_248012.1| 137 LYGKTLGVIGLGRIGQQVVKRAKAFGMNI-IGYDPYI-PKEVAESMGVElVDDINELCKRADFITLHVPLTpKTRHIIGRE 215
                                   679*************************7.6887776.7899*****995668**************99651334555444 PP

                                   TGGG--TT-.EEEESSS CS
                          IlvN  81 iepnlkegk.alafahG 96 
                                       +k+++ ++ +a G
  gi|15669207|ref|NP_248012.1| 216 QIALMKKNAiIVNCARG 232
                                   44455555514455555 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.6
                                   EEEE-TT-HHHHHHHHTT- CS
                          IlvN  31 vvglregsksvkkAkeegf 49 
                                   v+g  ++++s+++A++++ 
  gi|15669207|ref|NP_248012.1| 273 VIGTPHQGASTEEAQKAAG 291
                                   5566666666666665433 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.45   5.4e+02      34      77 ..       5      52 ..       1      77 [. 0.64
   2 !   17.7   0.0   3.1e-06    0.0037      22      96 ..     154     226 ..     152     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.45
                                  EEE-SSTHHCCCCHHGG.....BTCCEEES-CHHHHTT-SEEEE-S--G CS
                UDPG_MGDP_dh_C 34 kiyDPkvkeeaveaele.....ekgvevvdsleealkgadaiviltehd 77
                                   + DP  +++ +  e       ++g++  ++l e +k+ad++v+    +
  gi|15669207|ref|NP_248012.1|  5 LVTDPLHEDAIKILEEVgevevATGLT-KEELLEKIKDADVLVVRSGTK 52
                                  566666555554443335554433333.4578999******99976655 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3.1e-06
                                   HHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--.GGGGGS-HHHHHHCC.SS-EE CS
                UDPG_MGDP_dh_C  22 iieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaivilteh.defkeldlaklkelm.kpavv 96 
                                   ++++ ++ g+++  yDP++++e +e      gve+vd+++e +k ad i ++++  ++ +++   +  +lm k+a++
  gi|15669207|ref|NP_248012.1| 154 VVKRAKAFGMNIIGYDPYIPKEVAES----MGVELVDDINELCKRADFITLHVPLtPKTRHIIGREQIALMkKNAII 226
                                   78888999*************99987....79*****************9999753555665555555555455555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.15   1.8e+02      28      81 ..       4      61 ..       2      73 .. 0.77
   2 ?   -1.4   0.1         3   3.6e+03      37      70 ..      59      93 ..      53     108 .. 0.57
   3 !   16.9   0.0   5.9e-06     0.007       2      71 ..     142     204 ..     141     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.15
                                  EEEEEESSCCCHHHHHHHHC.....-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
                 F420_oxidored 28 ivvansrnpekaeelaeelg.....vkvtavdneeaaeeadvvvlavkpedveevlsel 81
                                  i+ ++++  e a ++ ee+g      ++t+ +  e +++adv+v+   ++++ +v++++
  gi|15669207|ref|NP_248012.1|  4 IL-VTDPLHEDAIKILEEVGevevaTGLTKEELLEKIKDADVLVVRSGTKVTRDVIEKA 61
                                  55.34777788888888888876665666667777788********9999999999987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3
                                  CCHHHHH..HHHC-EEECECHHHHHHH-SEEEE-S- CS
                 F420_oxidored 37 ekaeela..eelgvkvtavdneeaaeeadvvvlavk 70
                                  ekae+l+   ++gv+v      eaa+e  ++v+  +
  gi|15669207|ref|NP_248012.1| 59 EKAEKLKviGRAGVGVDNI-DVEAATEKGIIVVNAP 93
                                  5555555334445666663.3455555666665544 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 5.9e-06
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-H CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkp 71 
                                   +g+iG G++g+ +++++ a g    +i+ +   +p   +e ae++gv++   d +e++++ad++ l v+ 
  gi|15669207|ref|NP_248012.1| 142 LGVIGLGRIGQQVVKRAKAFG---MNII-G--YDPYIPKEVAESMGVELVD-DINELCKRADFITLHVPL 204
                                   89*******************...9999.6..78888899***********.**************9996 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       5.9   7.1e+03      25      47 ..      65      87 ..      64      92 .. 0.70
   2 ?   -0.5   0.2       1.6   1.9e+03      27      46 ..     390     410 ..     387     433 .. 0.73
   3 !   15.3   0.0   1.9e-05     0.023      11      78 ..     455     519 ..     452     520 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.9
                         ACT_4 25 qviseekanivsvnaktrkkdgl 47
                                  +vi  +++ + ++ +++  ++g+
  gi|15669207|ref|NP_248012.1| 65 KVIGRAGVGVDNIDVEAATEKGI 87
                                  68888888888888887655554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                         ACT_4  27 isee.kanivsvnaktrkkdg 46 
                                   i+++ ++n+v+ +++++k  +
  gi|15669207|ref|NP_248012.1| 390 IAKNrNINVVESSTSEEKYGN 410
                                   666668888888888876333 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.9e-05
                         ACT_4  11 veaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisV 78 
                                   ++ +dr+g +++++ ++ + ++ni s+++  ++  g   + +++   d+   ++vi+k+++ip++++V
  gi|15669207|ref|NP_248012.1| 455 IKHIDRPGTIGRVCITLGDYGINIASMQVGRKEPGGESVMLLNL---DHTVPEEVIEKIKEIPNIKDV 519
                                   6789***************************9888888888888...677889*************99 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.1   1.3e+03      80      96 ..      30      46 ..       6      75 .. 0.74
   2 !   14.6   0.1   1.3e-05     0.015      33     135 ..     144     235 ..     133     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                                  HHHHHHHHHHHH-SEEE CS
                   AlaDh_PNT_C 80 sqeellaeavkeadvvi 96
                                   ++e+l e++k+adv++
  gi|15669207|ref|NP_248012.1| 30 LTKEELLEKIKDADVLV 46
                                  45667778889999887 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.3e-05
                                   EESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTS.S---SC-H CS
                   AlaDh_PNT_C  33 viGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipGk.kaPkLvte 112
                                   viG G  G+q ++ ak++g ++  +D  +  +e  es+g +         + ++e +k+ad +  t ++p   k+ +++ +
  gi|15669207|ref|NP_248012.1| 144 VIGLGRIGQQVVKRAKAFGMNIIGYDPYIP-KEVAESMGVEL-------VDDINELCKRADFI--TLHVPLTpKTRHIIGR 214
                                   9*************************8775.57788899993.......35799*******98..667775415678**** PP

                                   HHHHTS-TTEEEEETTGGGT-SB CS
                   AlaDh_PNT_C 113 emvksMkpgsVivDvAidqGGnv 135
                                   e ++ Mk++++iv  A  +GG +
  gi|15669207|ref|NP_248012.1| 215 EQIALMKKNAIIVNCA--RGGLI 235
                                   ************9876..56665 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.081        97      60      92 ..      32      64 ..      21     103 .. 0.87
   2 ?    9.4   0.0   0.00078      0.94      54     106 ..     179     233 ..     169     255 .. 0.75
   3 ?   -2.9   0.0       4.9   5.9e+03      71      94 ..     492     515 ..     472     522 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.081
                                  ES-HHHHHTT--EEEE---HHHHHHHHHHHCCC CS
                NAD_Gly3P_dh_N 60 ttdlaealkgadiivlvvPsqalrevlkklkgl 92
                                  +++l e +k+ad++v+   ++++r+v++k+++l
  gi|15669207|ref|NP_248012.1| 32 KEELLEKIKDADVLVVRSGTKVTRDVIEKAEKL 64
                                  46788999******************9998875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00078
                                   -TTEEEES-HHHHHTT--EEEE---HH.HHHHHHHH.HCCC--TT-EEEE---SE CS
                NAD_Gly3P_dh_N  54 penlvattdlaealkgadiivlvvPsq.alrevlkk.lkgllkkkailvsliKGi 106
                                   +  ++ ++d++e +k+ad+i l vP    +r+++ +   +l+kk+ai+v++++G 
  gi|15669207|ref|NP_248012.1| 179 SMGVELVDDINELCKRADFITLHVPLTpKTRHIIGReQIALMKKNAIIVNCARGG 233
                                   4568999******************652566666540445669********9984 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.9
                                   -EEEE---HHHHHHHHHHHCCC-- CS
                NAD_Gly3P_dh_N  71 diivlvvPsqalrevlkklkgllk 94 
                                   ++++l++ + + +ev++k+k++ +
  gi|15669207|ref|NP_248012.1| 492 SVMLLNLDHTVPEEVIEKIKEIPN 515
                                   345555556666666666665554 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.33   3.9e+02      10      31 ..      64      85 ..      63      91 .. 0.83
   2 ?   -3.5   0.0         8   9.6e+03      28      44 ..     404     421 ..     396     427 .. 0.64
   3 ?    8.8   0.0    0.0012       1.4       1      34 [.     459     492 ..     459     519 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.33
                         ACT_5 10 lrvvrrrgFevkslnmsttedg 31
                                  l v+ r g+ v+++++++ +++
  gi|15669207|ref|NP_248012.1| 64 LKVIGRAGVGVDNIDVEAATEK 85
                                  6799*************95554 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8
                         ACT_5  28 tedggtvrieltVes.er 44 
                                   +e++    i++t es ++
  gi|15669207|ref|NP_248012.1| 404 SEEKYGNAIKITAESdKK 421
                                   455555568888888554 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0012
                         ACT_5   1 dapgvLeRvlrvvrrrgFevkslnmsttedggtv 34 
                                   d+pg++ Rv+ ++   g +++s+++ + e gg++
  gi|15669207|ref|NP_248012.1| 459 DRPGTIGRVCITLGDYGINIASMQVGRKEPGGES 492
                                   79***********************997766655 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.16     2e+02      53      68 ..      97     112 ..      95     126 .. 0.73
   2 ?    7.8   0.0    0.0028       3.3      41      71 ..     270     300 ..     267     307 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.16
                                   HHHHHHHHHHHHHHHH CS
                       DUF4442  53 icnlaElamGllaeat 68 
                                    +++aEl+mGl++ a+
  gi|15669207|ref|NP_248012.1|  97 SISVAELTMGLMLAAA 112
                                   5789********8763 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0028
                                   GB-TTSSB-HHHHHHHHHHHHHHHHHHHS-T CS
                       DUF4442  41 vrNhigtvHAiAicnlaElamGllaeatlpd 71 
                                   + N igt H +A +  a  a+G+++ +++++
  gi|15669207|ref|NP_248012.1| 270 LDNVIGTPHQGASTEEAQKAAGTIVAEQIKK 300
                                   57***********************999887 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       3.1   3.7e+03      52      76 ..      32      55 ..      11      84 .. 0.62
   2 ?    8.5   0.1    0.0022       2.7       4      92 ..     136     230 ..     134     292 .. 0.80
   3 ?   -1.0   0.0         2   2.4e+03      31      72 ..     394     433 ..     346     438 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.1
                 NAD_binding_7 52 eeelekdlegadlviaatddrelne 76
                                  +eel +++++ad++++    +++ +
  gi|15669207|ref|NP_248012.1| 32 KEELLEKIKDADVLVVRS-GTKVTR 55
                                  455555555555444443.233333 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0022
                 NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvkla.eeelekdlegadlviaatddrelneriae... 80 
                                   +l gk+  v+G G+++++ v++  ++g +++ ++p + +e+ e + ++  +++++ +++ad++   ++ +   ++i     
  gi|15669207|ref|NP_248012.1| 136 ELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDPYIPKEVAESMGVElVDDINELCKRADFITLHVPLTPKTRHIIGreq 216
                                   67799999***************************9877777666655456677778888877666555544444443233 PP

                 NAD_binding_7  81 ..aakarrilvnva 92 
                                     ++k++ i vn+a
  gi|15669207|ref|NP_248012.1| 217 iaLMKKNAIIVNCA 230
                                   22335566666655 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2
                 NAD_binding_7  31 akvtvvapevkeeleelvklaeeelekdlegadlviaatddr 72 
                                    ++ vv        e+  ++++ ++e+d +++ +v a+++++
  gi|15669207|ref|NP_248012.1| 394 RNINVVESS--TSEEKYGNAIKITAESDKKKFSIVGAIINNK 433
                                   344444444..1222333455555677777777777777775 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.6      0.18   2.1e+02      48     119 ..      19      90 ..       2      95 .. 0.59
   2 ?    7.4   0.3    0.0037       4.5       3      69 ..     142     196 ..     140     208 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.18
                                   SSSS--S-BEBSSHHHHHHH...-SEEEE-S-HHHHHHHHHHHHHTT-EEEE--SS--HHHHHHHHHHTTT.SEEE CS
                        DapB_N  48 lglgklgvavtddleevlek...advliDFTtpeavlenlklalekgvklViGTTGlseeelaeleelakk.igvv 119
                                    ++g+++va+  + ee+lek   advl+  +  +++ ++++ a   ++  ViG  G+  ++  ++e++++k i vv
  gi|15669207|ref|NP_248012.1|  19 EEVGEVEVATGLTKEELLEKikdADVLVVRSGTKVTRDVIEKA---EKLKVIGRAGVGVDN-IDVEAATEKgIIVV 90 
                                   3445777777666666666555599999777666666665544...556677877774443.34455454445555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0037
                                   EEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-S CS
                        DapB_N   3 vavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekad 69 
                                   ++v+G  Gr+G++vvk +++  ++++ +        ++ k++ e     ++gv++ dd++e+++ ad
  gi|15669207|ref|NP_248012.1| 142 LGVIGL-GRIGQQVVKRAKA-FGMNIIGYDP-----YIPKEVAE-----SMGVELVDDINELCKRAD 196
                                   6899*8.**********998.6666665522.....33344433.....667777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 3320.76
//
Query:       gi|15669208|ref|NP_248013.1|  [L=354]
Description: carbamoyl phosphate synthase small subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-50  170.5   0.0    5.1e-50  169.9   0.0    1.3  1  GATase           Glutamine amidotransferase class-I
    8.5e-45  151.7   0.0    1.4e-44  151.0   0.0    1.3  1  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    5.3e-09   36.1   0.3    1.5e-06   28.2   0.3    2.2  1  Peptidase_C26    Peptidase C26
  ------ inclusion threshold ------
      0.023   14.7   0.7      0.046   13.7   0.2    1.7  2  Inhibitor_I24    PinA peptidase inhibitor


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.9   0.0   1.1e-53   5.1e-50       1     189 [.     173     349 ..     173     350 .. 0.97

  Alignments for each domain:
  == domain 1  score: 169.9 bits;  conditional E-value: 1.1e-53
                                   EEEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEETHH CS
                        GATase   1 lliDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGICLG 80 
                                   +liD++  v+ n++++lv+++++v  vp++++ +eil  + +pd +l+s+Gpg+p+  ++ i++ik++++  +Pi GICLG
  gi|15669208|ref|NP_248013.1| 173 VLIDCG--VKLNIIRSLVQRNCEVIQVPYNTKYDEIL--EYKPDFVLISNGPGDPArLKEVIKNIKNLIG-VVPITGICLG 248
                                   589***..****************************6..699****************************.********** PP

                                   HHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEET CS
                        GATase  81 mQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekk 161
                                   +Qll ++fg++++k+k ++h+gg+++++d       ++++++i++++H+++v + e++p+++ev++ + +d ++++i++k+
  gi|15669208|ref|NP_248013.1| 249 NQLLSLAFGGETYKMK-FGHRGGNQPVKD------LKTQKVYITSQNHGFAVRK-ESLPDDVEVSFINLNDMTVEGIRHKD 321
                                   ****************.************......7778**************8.99************************ PP

                                   TTEEEESSBTTSTTSTTHHHHHHHHHHH CS
                        GATase 162 npfvgvQFHPEststpegpellfnflik 189
                                    p+++vQFHPE++++p+++ +lf+++ik
  gi|15669208|ref|NP_248013.1| 322 LPIFSVQFHPEARPGPHDTMFLFDEMIK 349
                                   *************************997 PP

>> CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CPSase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.0   0.0     3e-48   1.4e-44       2     127 ..       3     121 ..       2     122 .. 0.96

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 3e-48
               CPSase_sm_chain   2 avLvLedGtvfeGksfg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedvesekikvaglvvrel 81 
                                   avL+LedGt+++Gk+fg +ke++GE+vf+T mtGY e+ltDpsY+gqi+++typl GnyGv+++ +es+ ik++g+vvre+
  gi|15669208|ref|NP_248013.1|   3 AVLILEDGTILKGKGFGaEKEVFGELVFTTVMTGYVEVLTDPSYKGQIVMMTYPLEGNYGVKKDWFESDGIKAEGFVVREV 83 
                                   79***************77999**********************************************************9 PP

               CPSase_sm_chain  82 seepsnwraeesLsewlkeekipgisgvDTRaLtkklrekgamkgv 127
                                   ++        + L+++lke++ipgi+++DTR Lt+k+r+kg++k++
  gi|15669208|ref|NP_248013.1|  84 TS--------KALDDFLKEYDIPGIQDIDTRFLTRKIRDKGVVKSC 121
                                   84........58*****************************99876 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.3   3.3e-10   1.5e-06     105     216 .]     239     332 ..     216     332 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.3e-10
                 Peptidase_C26 105 gvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaike..lae 183
                                    vPi giC+G qll  a+GG++y+          hr  +     + v   k+   +++++     +   H +a+++  l +
  gi|15669208|ref|NP_248013.1| 239 VVPITGICLGNQLLSLAFGGETYKMKF------GHRGGN-----QPV---KDLKTQKVYI-----TSQNHGFAVRKesLPD 300
                                   58********************97544......354443.....222...3333344555.....44569999988779** PP

                 Peptidase_C26 184 elrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                   +++v+ +   D ++E i++++   ++++vQ+HPE
  gi|15669208|ref|NP_248013.1| 301 DVEVSFINLnDMTVEGIRHKD--LPIFSVQFHPE 332
                                   *****99977*********99..569*******9 PP

>> Inhibitor_I24  PinA peptidase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2     1e-05     0.046      27      91 ..      77     143 ..      59     153 .. 0.85
   2 ?   -2.7   0.0       1.2   5.4e+03      77      98 ..     180     201 ..     170     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                 Inhibitor_I24  27 vfkvrelvkeceddiepdtgiieielsdgkii..niydkpitywclwntesvengeieevvertnqv 91 
                                    f vre+  ++ dd   +  i  i+  d + +  +i dk +   cl  +e + + ei e++er ++ 
  gi|15669208|ref|NP_248013.1|  77 GFVVREVTSKALDDFLKEYDIPGIQDIDTRFLtrKIRDKGVVKSCLKVAEEISDDEISELLERVKRY 143
                                   589************999999999999999874469***************************8765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                 Inhibitor_I24  77 engeieevvertnqvvqkpkad 98 
                                   +   i  +v+r  +v+q p   
  gi|15669208|ref|NP_248013.1| 180 KLNIIRSLVQRNCEVIQVPYNT 201
                                   5556778899999999988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 2315.41
//
Query:       gi|15669209|ref|NP_248014.1|  [L=259]
Description: hypothetical protein MJ_1020 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-10   39.6   1.1    8.7e-10   38.9   1.1    1.4  1  HD        HD domain
  ------ inclusion threshold ------
       0.15   11.8   0.0       0.21   11.3   0.0    1.3  1  VCPO_N    Vanadium chloroperoxidase N-terminal domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   1.1   9.8e-14   8.7e-10       6     121 ..      63     172 ..      51     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 9.8e-14
                                   HHHHHHHHHHHHHHHH........HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH. CS
                            HD   6 leVaklarrlaedlge........eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld. 77 
                                   ++++k++ + +++  +        e+   ++ll+a+lHDiG+ +++d          +++ H+ + a  + e+ + + ++ 
  gi|15669209|ref|NP_248014.1|  63 IKMLKILYKKGIEPSFvkdckgsfEDSLVITLLGAYLHDIGNSVHRD----------IHHLHSAYLALDIVENILKKYYKe 133
                                   344455555555555599999999999999**************999..........555666655554444444443336 PP

                                   ......HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                            HD  78 ......ledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                         + +v+++i +h+e ++            l++ea ++++aD +++
  gi|15669209|ref|NP_248014.1| 134 ekayqmTTEVLHAIYSHSEGIM-----------GLTIEAGVIAVADGTDM 172
                                   6777*****************9...........89***********9876 PP

>> VCPO_N  Vanadium chloroperoxidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.4e-05      0.21      62     114 ..      26      79 ..      18     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.4e-05
                        VCPO_N  62 psadfttyltanaeeaeyrlPelvgaddarqavagaaitvleklytqp.spsis 114
                                    +++++t+l+ +   a  rl  +++ +   + va  ai++l+ ly+++ +ps  
  gi|15669209|ref|NP_248014.1|  26 KNKKVNTFLKMSNIMAVGRLGYNDHGKTHAKIVANNAIKMLKILYKKGiEPSFV 79 
                                   56889******9999999****99999999***************775256554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1802.86
//
Query:       gi|15669210|ref|NP_248015.1|  [L=163]
Description: hypothetical protein MJ_1021 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.034   14.0   0.8        6.9    6.5   0.0    2.2  2  GyrB_insert   DNA gyrase B subunit insert domain
      0.067   13.3   7.3       0.11   12.6   7.3    1.3  1  Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
      0.072   13.6   3.7       0.15   12.6   3.6    1.7  1  IZUMO         Izumo sperm-egg fusion, Ig domain-associated
        0.1   12.8   1.6       0.15   12.3   0.7    1.7  2  RRF_GI        Ribosome recycling factor
       0.14   10.0   4.6       0.23    9.4   4.6    1.4  1  Prominin      Prominin
       0.15   11.9   2.9        4.2    7.3   0.5    2.8  2  DASH_Dam1     DASH complex subunit Dam1
       0.16   12.5   3.3       0.13   12.8   1.2    1.9  2  DUF2115       Uncharacterized protein conserved in archaea (D
       0.21   12.0   1.9         13    6.2   0.1    2.4  2  DUF4094       Domain of unknown function (DUF4094)
       0.32   11.1   9.0       0.12   12.5   0.6    2.3  2  MetOD2        Metanogen output domain 2
       0.38   10.9   2.8        4.3    7.5   0.3    2.5  2  PspB          Phage shock protein B
       0.43   11.1   5.9         35    5.0   5.9    2.5  1  NPV_P10       Nucleopolyhedrovirus P10 protein
       0.53   10.2   9.4        2.3    8.2   4.5    2.8  2  Prefoldin     Prefoldin subunit
        1.2    8.7   9.0        3.5    7.2   8.9    2.0  1  DUF4795       Domain of unknown function (DUF4795)


Domain annotation for each model (and alignments):
>> GyrB_insert  DNA gyrase B subunit insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.005       6.9       1      36 [.       7      42 ..       7      47 .. 0.89
   2 ?    6.4   0.1    0.0055       7.6      16      76 ..      53     118 ..      50     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.005
                   GyrB_insert  1 AeLvvnedappisgeaLeeLvrqyrkaeaiIkRlsr 36
                                  AeL+  +d++  ++e L +L+r+y k+++ I+ l++
  gi|15669210|ref|NP_248015.1|  7 AELILLKDKNFKEKERLRDLLREYIKTKDEISYLEN 42
                                  8899999999999****************9998876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0055
                   GyrB_insert  16 aLeeLvrqyrkaeaiIkRlsrrydeevLealle....lpeldeedledea.aaeawakalearlnq 76 
                                   +L++L r+   +++i+ Rls+  +  v  ++++    ++++d+edle+   ++++ +++l+++l++
  gi|15669210|ref|NP_248015.1|  53 NLKHLKRDADIIKSILPRLSKFTNIPVFMKIVKmleaVEKIDTEDLESVRwNINKEIEELNDKLKT 118
                                   6889999999999***********999999988311234455555555332566667777777743 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   7.3   7.8e-05      0.11      27     143 ..      20     161 ..      10     163 .] 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.8e-05
                                   HHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHH......HCS-T..........THHHH...........HHHHHHHHH.S CS
                  Spore_III_AB  27 lkeleelkralellegeirygatpLpealekla......ekses..........plsef...........feevaerleek 80 
                                    ++l++l+r     + ei+y  + L++ +e+l       +              +ls+f           + e+ e+++++
  gi|15669210|ref|NP_248015.1|  20 KERLRDLLREYIKTKDEISYLENILED-FENLDvnlkhlK---RdadiiksilpRLSKFtnipvfmkivkMLEAVEKIDTE 96 
                                   567888888888889999999999877.666664443331...13333444444444445556656666666777777878 PP

                                   TSS-HHHHHHHHHHHHGGGS---HHH..HHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHH CS
                  Spore_III_AB  81 egesfeeaweeavekllkklaLkked..keilkelgeslgysdregqlkalelaleeleeeieea 143
                                   + es++  +++++e+l +kl+  +++    i+ e  +++g+s++e+  k le+++ e +++ eea
  gi|15669210|ref|NP_248015.1|  97 DLESVRWNINKEIEELNDKLKTLENElrVIIINEALSKIGTSNLEEFSKYLENLRYEEKNQKEEA 161
                                   99**************99988888883345678************************99999998 PP

>> IZUMO  Izumo sperm-egg fusion, Ig domain-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.6   0.00011      0.15       9     110 ..      43     153 ..      14     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHTHHHHHSGGHHHHHHHHHHHHHTTT.....---SGGGGGGSEEEHHHHHHHHHHHHHHHHHHHHS..---H CS
                         IZUMO   9 vvealksLeedllpselehreklleraealledls.....ekelaenkflgvvdeetlekvasslkkelkrltds..dlkg 82 
                                   ++e++++L  +l  ++l+++ ++++ +   l+++      +k ++  + ++++d+e le+v++++ ke+++l+d+  +l+ 
  gi|15669210|ref|NP_248015.1|  43 ILEDFENLDVNL--KHLKRDADIIKSILPRLSKFTnipvfMKIVKMLEAVEKIDTEDLESVRWNINKEIEELNDKlkTLEN 121
                                   556666665555..888888888888888888888777867777778999**********************985224444 PP

                                   HH...HHH.HHHHHHHHHHHHHHHHHHHHHHT CS
                         IZUMO  83 el...llk.eLlwllqkqkkklkealkefqke 110
                                   el   +++  L ++  ++ +++ ++l++ + e
  gi|15669210|ref|NP_248015.1| 122 ELrviIINeALSKIGTSNLEEFSKYLENLRYE 153
                                   43222444477777777778888887776655 PP

>> RRF_GI  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.5   2.1e+03      71      95 ..      32      57 ..      10      65 .. 0.56
   2 ?   12.3   0.7   0.00011      0.15      21      99 ..      55     130 ..      51     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.5
                        RRF_GI 71 ikkieta.llehadklepleekLarl 95
                                   +k e   l +  + +e l++ L++l
  gi|15669210|ref|NP_248015.1| 32 KTKDEISyLENILEDFENLDVNLKHL 57
                                  33333331223345555666666555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00011
                        RRF_GI  21 kkakalaleleCelkRvrRsRnWqlkgeaeklqslleelkakeeesleylikkietallehadklepleekLarlvkqn 99 
                                   k++k  a  ++  l R+ +  n  +  ++ k+ + +e++ +++ es+++ i+k   ++ e +dkl++le+ L  ++ ++
  gi|15669210|ref|NP_248015.1|  55 KHLKRDADIIKSILPRLSKFTNIPVFMKIVKMLEAVEKIDTEDLESVRWNINK---EIEELNDKLKTLENELRVIIINE 130
                                   55666666666777788888888888899999999999999999999998876...5667789*********9877654 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.6   0.00017      0.23     645     741 ..      55     153 ..       7     158 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00017
                      Prominin 645 knlkqslkneaqdlraiqqelvlplessvkklkksvkklde.....ensdlqesikkllaaveraenflkkngseiinnes 720
                                   k+lk+     ++ l ++ + +++p+  ++ k+ + v+k+d+        +++++i++l ++++ +en+l+     iin+  
  gi|15669210|ref|NP_248015.1|  55 KHLKRDADIIKSILPRLSKFTNIPVFMKIVKMLEAVEKIDTedlesVRWNINKEIEELNDKLKTLENELRV---IIINEAL 132
                                   34444444455555666777777788888888888888888777667788999999999999999998885...5788888 PP

                      Prominin 721 kklldrileqfeeYidwviee 741
                                   +k+ ++ le f++Y++  + e
  gi|15669210|ref|NP_248015.1| 133 SKIGTSNLEEFSKYLENLRYE 153
                                   999999999999999887765 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.032        45       5      24 ..      40      59 ..      34      74 .. 0.74
   2 ?    7.3   0.5     0.003       4.2       2      31 ..     106     134 ..     105     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.032
                     DASH_Dam1  5 faeLaDsletLdknledLqq 24
                                  ++++ +  e+Ld nl++L++
  gi|15669210|ref|NP_248015.1| 40 LENILEDFENLDVNLKHLKR 59
                                  45666777888888888875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.003
                     DASH_Dam1   2 epafaeLaDsletLdknledLqqihesLsd 31 
                                    ++++eL+D+l+tL++ l+ +  i+e+Ls+
  gi|15669210|ref|NP_248015.1| 106 NKEIEELNDKLKTLENELRVI-IINEALSK 134
                                   5789**********9998755.56666665 PP

>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.8   2.5e+03      29      29 ..      34      34 ..       5      74 .. 0.56
   2 ?   12.8   1.2   9.4e-05      0.13      11      74 ..      88     151 ..      80     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.8
                       DUF2115 29 e 29
                                  +
  gi|15669210|ref|NP_248015.1| 34 K 34
                                  1 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.4e-05
                       DUF2115  11 keaskisieDlmkisarlekeikklpekyrkelseslteylfeaykelknkrsgdkseykeevi 74 
                                   ++++ki +eDl++++++++kei++l++k ++  +e  +  + ea+ ++ +++ +++s+y e+  
  gi|15669210|ref|NP_248015.1|  88 EAVEKIDTEDLESVRWNINKEIEELNDKLKTLENELRVIIINEALSKIGTSNLEEFSKYLENLR 151
                                   6899***********************9988777777788888899998877777777765544 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0097        13      49      75 ..      18      44 ..       5      60 .. 0.78
   2 ?    5.3   0.2     0.019        26      65      83 ..     106     124 ..      83     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0097
                       DUF4094 49 daesrskdilgevskthkaiqtLdkti 75
                                  ++++r +d+l+e+ kt+++i+ L++ +
  gi|15669210|ref|NP_248015.1| 18 KEKERLRDLLREYIKTKDEISYLENIL 44
                                  4555678**************997655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                       DUF4094  65 hkaiqtLdktissLemeLa 83 
                                   +k+i+ L+ ++ +Le eL+
  gi|15669210|ref|NP_248015.1| 106 NKEIEELNDKLKTLENELR 124
                                   689**************97 PP

>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   2.1     0.077   1.1e+02      29      85 ..      14      69 ..       2      72 .. 0.86
   2 ?   12.5   0.6   8.8e-05      0.12      28      80 ..      73     126 ..      69     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.077
                        MetOD2 29 aksvevnkrllslLsqtydidddkaevseeieaalknlekkleaqeerlkqikkele 85
                                   k+ + + rl +lL++  +   d+    e+i +  +nl  +l+  +++   ik +l 
  gi|15669210|ref|NP_248015.1| 14 DKNFKEKERLRDLLREYIKTK-DEISYLENILEDFENLDVNLKHLKRDADIIKSILP 69
                                  578888899999999999998.55999999*************99999999999886 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8.8e-05
                        MetOD2  28 LaksvevnkrllslLsqtydidddkae.vseeieaalknlekkleaqeerlkqi 80 
                                   +++++ v  +++++L+++ +id++ +e v  +i++++++l++kl++ e++l+ i
  gi|15669210|ref|NP_248015.1|  73 KFTNIPVFMKIVKMLEAVEKIDTEDLEsVRWNINKEIEELNDKLKTLENELRVI 126
                                   678999999*************9876537889****************999876 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3    0.0031       4.3      38      66 ..      18      46 ..      12      49 .. 0.90
   2 ?    3.1   0.1     0.074     1e+02      33      62 ..      91     121 ..      77     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0031
                          PspB 38 edekrLeellekAekleeRietLEriLda 66
                                  ++++rL++ll++  k ++ i+ LE+iL+ 
  gi|15669210|ref|NP_248015.1| 18 KEKERLRDLLREYIKTKDEISYLENILED 46
                                  6999***********************85 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.074
                          PspB  33 kglsaedekrLe.ellekAekleeRietLEr 62 
                                   ++++ ed ++++ ++ ++ e+l++ ++tLE+
  gi|15669210|ref|NP_248015.1|  91 EKIDTEDLESVRwNINKEIEELNDKLKTLEN 121
                                   4455555555543466788999999999997 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   5.9     0.025        35      25      61 ..      88     126 ..      31     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.025
                       NPV_P10  25 qqvddvq.enlpdvt.elnekLdaqsaqLaeletkvenI 61 
                                   ++v++++ e+l+ v  ++n+++++++++L++le+++  I
  gi|15669210|ref|NP_248015.1|  88 EAVEKIDtEDLESVRwNINKEIEELNDKLKTLENELRVI 126
                                   455555313455554357777777777777777744332 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.5    0.0017       2.3      86     117 ..      95     126 ..      13     129 .. 0.85
   2 ?   -2.9   0.2       4.3     6e+03      19      31 ..     140     152 ..     137     160 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0017
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  86 leelekqlekleeeleklkdqittleanlaql 117
                                    e+le+ + ++++e+e+l d+++tle++l+ +
  gi|15669210|ref|NP_248015.1|  95 TEDLESVRWNINKEIEELNDKLKTLENELRVI 126
                                   589************************99865 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.3
                                   HHHHHHHHHHHHH CS
                     Prefoldin  19 ieelektletlkt 31 
                                   +ee+ k le+l+ 
  gi|15669210|ref|NP_248015.1| 140 LEEFSKYLENLRY 152
                                   3444444444443 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   8.9    0.0025       3.5      84     152 ..      48     119 ..      13     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0025
                       DUF4795  84 dqfDeakkeLekml...eellekleeqeealkkaldtLq.eelkekldrlelepLkeqleerlkelqkelqea 152
                                   +++D  +k L++ +   +++l +l++   ++  +++ ++  e  ek+d  +le+++ +++++++el+++l+  
  gi|15669210|ref|NP_248015.1|  48 ENLDVNLKHLKRDAdiiKSILPRLSKF-TNIPVFMKIVKmLEAVEKIDTEDLESVRWNINKEIEELNDKLKTL 119
                                   446666666666654444555555432.233334444434235689***********************9953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2193  (0.122316); expected 358.6 (0.02)
Passed bias filter:                      757  (0.0422221); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 979.37
//
Query:       gi|15669211|ref|NP_248016.1|  [L=569]
Description: queuine tRNA-ribosyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-46  157.3   1.5    3.3e-46  156.9   0.5    1.7  2  DUF5591          Domain of unknown function (DUF5591)
      3e-13   49.5   0.0    7.2e-13   48.3   0.0    1.6  1  PUA              PUA domain
    8.2e-05   22.7   0.0    0.00023   21.2   0.0    1.8  1  TGT_C2           Patch-forming domain C2 of tRNA-guanine tran
     0.0074   15.5   0.0       0.43    9.7   0.0    2.3  2  TGT              Queuine tRNA-ribosyltransferase
     0.0077   16.2   0.5      0.018   14.9   0.4    1.6  1  AAA_31           AAA domain
  ------ inclusion threshold ------
       0.11   12.7   0.1        1.5    9.1   0.0    2.6  2  Par3_HAL_N_term  N-terminal of Par3 and HAL proteins
       0.21   11.5   3.6       0.13   12.2   0.3    2.3  2  Tox-MPTase4      Metallopeptidase toxin 4


Domain annotation for each model (and alignments):
>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.4   3.6e+03     107     143 ..     197     233 ..     187     237 .. 0.71
   2 !  156.9   0.5   1.3e-49   3.3e-46       1     154 []     270     414 ..     270     414 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.4
                                   SEEEE---THHHHHHHHHHTT-SSEEEE--.SS-TTS CS
                       DUF5591 107 ekviahleeeyreiveevaeelgleiiytvvedkpts 143
                                   e+   + ++ y+ei+eev+ +++  +   vve++++s
  gi|15669211|ref|NP_248016.1| 197 EELYNNNKKVYEEILEEVRIAIKNGFLRNVVEETAVS 233
                                   5555566667899999998888888888887777766 PP

  == domain 2  score: 156.9 bits;  conditional E-value: 1.3e-49
                                   X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT----------- CS
                       DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqYdiav 81 
                                   vk++ er+ + Yep   ++++vLlPcs+kkPys s+sh+kf++aik++k  v+eviltsP+G+vPr+le++   ++Ydi+v
  gi|15669211|ref|NP_248016.1| 270 VKKYLERLDN-YEPY--SNIIVLLPCSSKKPYSISQSHQKFIKAIKSAKVVVEEVILTSPYGLVPRALERL---VNYDIPV 344
                                   89*******8.***9..7*****************************************************...******* PP

                                   -----HHHHHHHHHHHHHHHHHHT-....SEEEE---THHHHHHHHHHTT-SSEEEE--.SS-TTSHHHHHHHHHHH CS
                       DUF5591  82 tgewseeeiefvaellakylektky....ekviahleeeyreiveevaeelgleiiytvvedkptskeslknLkeaL 154
                                   tgews eeie+++++l+++l+k k+      viahl+e+y ei+e        +i++t+ +++pts+e+lknL+++L
  gi|15669211|ref|NP_248016.1| 345 TGEWSFEEIELINNCLKNFLKKVKEkfddYIVIAHLPEHYLEILELD------DIVITS-KGNPTSEEALKNLTDTL 414
                                   *********************9998666456*************995......699999.9************9987 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   2.8e-16   7.2e-13      15      73 ..     510     567 ..     503     568 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 2.8e-16
                                   TT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                           PUA  15 sgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                   ++ sL++pG v+++++++ +d+V+++   ++++++G+a++s+ e++k+k+g  v+i++v
  gi|15669211|ref|NP_248016.1| 510 KKGSLFPPGFVDCNENISYNDEVVLIKD-DTFLGIGRALMSGFEMKKAKHGALVNIRNV 567
                                   566********************99998.**************************9986 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0     9e-08   0.00023       3      66 ..     436     494 ..     434     496 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 9e-08
                        TGT_C2   3 lraiadYqFGagagdaLfpedvtitrsatgri.rqvlvdgerlatlraqdgrltLsleGarrlhe 66 
                                   ++++a++qFG     +++p+++ i    +g i  ++  +++++a++++++g+l+L+l G+++l +
  gi|15669211|ref|NP_248016.1| 436 IQQLAEFQFGI----NFIPNEIFIN--HKGQIfTKINNKNQQIASINPKNGLLILTLSGGELLWN 494
                                   8899*****65....7788877788..555542677779**********************9976 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00017      0.43     197     271 ..     122     193 ..     104     202 .. 0.79
   2 ?    3.6   0.0     0.012        30     317     348 ..     203     234 ..     197     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00017
                                   SSSSSSHHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTS CS
                           TGT 197 GlsvgeekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlkn 271
                                   G  + e  ++ l+++ +++e++  +  +y   v  P ++  +   GvD fd +++ ++a  g  +t++  +++ +
  gi|15669211|ref|NP_248016.1| 122 GRRLIE--RKELQIIPKIREKISPNSAIYSPAV-FPWEIPLLAYIGVDYFDDSLAKLYASMGYKFTKNRAVKVDS 193
                                   566666..4457999999999999888887765.6*******************************998887765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           TGT 317 NlhyylelfkriReaIkegtfeefveefarky 348
                                   N ++y e ++++R aIk+g + + vee a ++
  gi|15669211|ref|NP_248016.1| 203 NKKVYEEILEEVRIAIKNGFLRNVVEETAVSH 234
                                   8899*********************9988776 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.4   7.1e-06     0.018      65     171 ..     314     421 ..     285     427 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.1e-06
                        AAA_31  65 eeknikeaiiktkvenldlipssid.Laeaeielvelekkeei......lkellekvkdeY.DyiiiDcpPsLglltenaL 137
                                    ++ ++e+i    ++   l+p  ++ L++++i +++  + eei      lk++l+kvk+++ Dyi+i   P+  l     +
  gi|15669211|ref|NP_248016.1| 314 AKVVVEEVIL---TSPYGLVPRALErLVNYDIPVTGEWSFEEIelinncLKNFLKKVKEKFdDYIVIAHLPEHYL----EI 387
                                   4444445554...233478887766588888888887777555555555***********955********8543....34 PP

                        AAA_31 138 vasdsviipvqaeayaleGleqllktieevkkkl 171
                                   +  d ++i  + ++ + e l++l++t+++ k+ +
  gi|15669211|ref|NP_248016.1| 388 LELDDIVITSKGNPTSEEALKNLTDTLKKYKELT 421
                                   4568899999*****************9998754 PP

>> Par3_HAL_N_term  N-terminal of Par3 and HAL proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       0.4     1e+03       9      40 ..     285     313 ..     282     325 .. 0.70
   2 ?    9.1   0.0   0.00057       1.5      24      66 ..     353     395 ..     342     398 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.4
               Par3_HAL_N_term   9 evrvvvPCgdgellvrdLikqavqRykkatek 40 
                                   ++ v++PC++ +      i+q  q+++ka++ 
  gi|15669211|ref|NP_248016.1| 285 NIIVLLPCSSKK---PYSISQSHQKFIKAIKS 313
                                   677999999874...33577888888887765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00057
               Par3_HAL_N_term  24 rdLikqavqRykkatekdsdslvkvhsleskdggiLDpDDlla 66 
                                    +Li++ ++ + k ++++ d  + + +l ++   iL+ DD+++
  gi|15669211|ref|NP_248016.1| 353 IELINNCLKNFLKKVKEKFDDYIVIAHLPEHYLEILELDDIVI 395
                                   479********9999999999999****************985 PP

>> Tox-MPTase4  Metallopeptidase toxin 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2       1.1   2.9e+03      91     120 ..     183     211 ..     169     220 .. 0.67
   2 ?   12.2   0.3   5.1e-05      0.13       7      64 ..     422     484 ..     416     491 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                   Tox-MPTase4  91 Ylkqsvlereeyvyneimknkekfneaeil 120
                                   + k  +++ + + ++e+ +n++k+ e eil
  gi|15669211|ref|NP_248016.1| 183 FTKNRAVKVDSFSFEELYNNNKKVYE-EIL 211
                                   55666667778888888888877754.444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.1e-05
                   Tox-MPTase4   7 gqtkltknGerlmsvkdlkafkkelselgikvviDkkdkil.....penkaagfdpetgeivl 64 
                                     + ++k+G+r+ ++++l +f+  ++ +  ++ i++k++i+      +++ a+ +p++g ++l
  gi|15669211|ref|NP_248016.1| 422 KSKDINKKGQRIHNIQQLAEFQFGINFIPNEIFINHKGQIFtkinnKNQQIASINPKNGLLIL 484
                                   556899**********************************97776556677899999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3794.16
//
Query:       gi|15669212|ref|NP_248017.1|  [L=262]
Description: ABC transporter ATP-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-23   82.6   0.0    7.5e-23   81.6   0.0    1.6  1  ABC_tran     ABC transporter
    2.8e-11   43.8   0.9    1.3e-06   28.5   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00066   20.2   6.8     0.0013   19.3   6.8    1.6  1  AAA_23       AAA domain
      0.003   17.3   0.0     0.0047   16.7   0.0    1.3  1  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.021   14.3   0.9          4    6.8   0.0    2.7  3  SMC_N        RecF/RecN/SMC N terminal domain
      0.022   15.1   0.0      0.047   14.1   0.0    1.4  1  AAA_16       AAA ATPase domain
      0.059   13.3   0.2       0.27   11.1   0.0    2.1  3  RsgA_GTPase  RsgA GTPase
      0.094   13.0   0.0        0.3   11.3   0.0    1.9  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.11   11.1   2.9        2.4    6.7   0.2    2.2  2  AAA_13       AAA domain
       0.12   12.0   0.1       0.26   10.9   0.1    1.5  1  SRP54        SRP54-type protein, GTPase domain
       0.16   11.2   0.0       0.46    9.7   0.0    1.7  2  Zeta_toxin   Zeta toxin


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.0   4.6e-26   7.5e-23       1     136 [.      20     151 ..      20     152 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 4.6e-26
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+++s++++ege+ +++G+nGaGK+t l++lag  +   G +             +++ +ig+lp+e  l ++ +v +   
  gi|15669212|ref|NP_248017.1|  20 LDEISFEVYEGEIFGLLGHNGAGKTTTLRILAGIIEEYTGYV-------------EVNGKIGYLPEERGLYRDEKVVDVlk 87 
                                   789***************************************.............67899999999999999999999999 PP

                                   ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                              e  + i+ +l+kl++++ k +++    ++LS+G +q+v+   +++ +p++++lDEp+
  gi|15669212|ref|NP_248017.1|  88 ffgelagmkkeEIAKSIDYWLNKLKISNYKYSKI----KELSKGNQQKVQFIVSVIHNPDIVILDEPF 151
                                   99999997666666669999*****999999999....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   2.2e-05     0.036       2      23 ..      33      54 ..      32      91 .. 0.79
   2 !   28.5   0.0   7.8e-10   1.3e-06     234     299 ..     121     183 ..      96     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                        AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                   +l G Ng+GK++ L++l ++ 
  gi|15669212|ref|NP_248017.1| 33 FGLLGHNGAGKTTTLRILAGII 54
                                  6899**************8873 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 7.8e-10
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                                   + elS G ++   ++++++  +   +++++DEp +gL+   +r l +++ +++++ g  +il+TH+ 
  gi|15669212|ref|NP_248017.1| 121 IKELSKGNQQKVQFIVSVIHNP---DIVILDEPFSGLDVVNVRLLRDIIfELKEE-GKTIILSTHQL 183
                                   5689***************999...9*************9999999999566666.99*******85 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   6.8   7.7e-07    0.0013       1     130 [.       4     144 ..       4     248 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.7e-07
                        AAA_23   1 kLkienfrsf...rdq..eidF...skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvka 73 
                                   k+k+en+ ++   +++  ei F   +  ++ + G+NGaGKTT l+ +  +  + t+  + + + g+  ++  +  ++kv  
  gi|15669212|ref|NP_248017.1|   4 KIKVENLTKYfgdKKVldEISFevyEGEIFGLLGHNGAGKTTTLRILAGIIEEYTGYVEVNGKIGYLPEERGLYRDEKVVD 84 
                                   7999***99997533233599999999********************9999888888888777777777777777767777 PP

                        AAA_23  74 yveltfenkdgry...trsiererelskkkgkttkkaklelleideleqfisellgskki 130
                                   ++++  e  + ++    +si++  ++ k ++ +++k k+ + + +++ qfi + +++ +i
  gi|15669212|ref|NP_248017.1|  85 VLKFFGELAGMKKeeiAKSIDYWLNKLKISNYKYSKIKELSKGNQQKVQFIVSVIHNPDI 144
                                   777763332222223444565555555555555555555555556666666555544444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.9e-06    0.0047      21     132 ..      33     187 ..      26     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.9e-06
                        AAA_30  21 avltGpAGtGKttalkalreaweaa.g...........grviglAptgkaAkvLa...eelgi....eastiakllkrlk. 81 
                                     l G  G+GKtt+l+ l+ ++e+  g            +  gl   +k+ +vL+   e +g+     a++i+ +l++lk 
  gi|15669212|ref|NP_248017.1|  33 FGLLGHNGAGKTTTLRILAGIIEEYtGyvevngkigylPEERGLYRDEKVVDVLKffgELAGMkkeeIAKSIDYWLNKLKi 113
                                   568899*******************77999998888887778888999999999866545555333345666666666669 PP

                        AAA_30  82 ......................grarlepgtllivDE....agmvdtkqlaallkaaekagakvilvGDerQlasVe 132
                                                             +++ +++i DE      +v+ + l++++ +++++g ++il   ++Ql+ +e
  gi|15669212|ref|NP_248017.1| 114 snykyskikelskgnqqkvqfiV-SVIHNPDIVILDEpfsgLDVVNVRLLRDIIFELKEEGKTIILS--THQLEKIE 187
                                   99999999999999999888752.3456669999999543234567778888888888877777775..66666666 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.019        31      23      39 ..      29      45 ..       3      51 .. 0.65
   2 ?    0.0   0.1       0.3   4.8e+02     175     199 ..     117     141 ..     110     145 .. 0.79
   3 ?    6.8   0.0    0.0025         4     161     199 ..     144     182 ..     137     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.019
                                  TSSEEEEEESTTSSHHH CS
                                  xxxxxxxxxxxxxxxxx RF
                         SMC_N 23 sksftaivGpNGSGKsn 39
                                  + ++  ++G+NG+GK+ 
  gi|15669212|ref|NP_248017.1| 29 EGEIFGLLGHNGAGKTT 45
                                  44566799*******96 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.3
                                   HHHHHHHHHHHHCTTSEEEEE-SSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 175 nvkkvaellkeksknaQfivislre 199
                                   + +k+ el k +++++Qfiv  +++
  gi|15669212|ref|NP_248017.1| 117 KYSKIKELSKGNQQKVQFIVSVIHN 141
                                   567788888889999****987765 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0025
                                   EEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 161 lyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                   +++lDe  + LD  nv+ + +++ e +++   i+ s ++
  gi|15669212|ref|NP_248017.1| 144 IVILDEPFSGLDVVNVRLLRDIIFELKEEGKTIILSTHQ 182
                                   689************************998877766432 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.9e-05     0.047      25     102 ..      31     112 ..      24     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.9e-05
                        AAA_16  25 elvllsGesGvGKsslvrellralekdggif.lrgkcdql..esaipysa.laqalareellrqlldeaesaeleawrekl 101
                                   e+  l G+ G GK++ +r l+  +e+  g++ ++gk   l  e+++ ++  ++++l++ + l+ ++ e+ +++ ++w  kl
  gi|15669212|ref|NP_248017.1|  31 EIFGLLGHNGAGKTTTLRILAGIIEEYTGYVeVNGKIGYLpeERGLYRDEkVVDVLKFFGELAGMKKEEIAKSIDYWLNKL 111
                                   566699***************77777779999***9999976666777888999998888888888888888888888877 PP

                        AAA_16 102 e 102
                                   +
  gi|15669212|ref|NP_248017.1| 112 K 112
                                   6 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.27      86     131 ..      16      62 ..       3      69 .. 0.79
   2 ?   -2.1   0.0       1.9   3.1e+03      69      92 ..     108     134 ..      94     147 .. 0.44
   3 ?   -2.1   0.0       1.9   3.1e+03      21      46 ..     176     201 ..     172     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                                   THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                   RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                   +k+ l+e++ ++ + ++  l+G+ G+GK+t +  l++  e  tg v 
  gi|15669212|ref|NP_248017.1|  16 DKKVLDEISFEVYEgEIFGLLGHNGAGKTTTLRILAGIIEEYTGYVE 62 
                                   6677888887776659*******************998888887765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                                   HHHHHHTTSEEEE-...-TTTHTTHHH CS
                   RsgA_GTPase  69 keelealgyevllv...saktkeglee 92 
                                    ++l+  +y+  ++   s+ ++++++ 
  gi|15669212|ref|NP_248017.1| 108 LNKLKISNYKYSKIkelSKGNQQKVQF 134
                                   333333333333320003333333333 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.9
                                   EEEESTTTT--HHHHHHHHHHHHHTT CS
                   RsgA_GTPase  21 ivvslkepelslnlldrfLvlaeekg 46 
                                   i++s+++ e  ++l dr+L+l + k 
  gi|15669212|ref|NP_248017.1| 176 IILSTHQLEKIERLCDRVLILKKGKA 201
                                   78888888888889999998876655 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019       0.3      62      84 ..     140     162 ..     109     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                       SbcCD_C  62 palrlvfLDEAFsklDeesiatl 84 
                                   +++++v+LDE Fs+lD  +++ l
  gi|15669212|ref|NP_248017.1| 140 HNPDIVILDEPFSGLDVVNVRLL 162
                                   5699************9988765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0015       2.4      23      39 ..      37      53 ..      32      74 .. 0.84
   2 ?    4.5   0.1    0.0066        11     524     572 ..     139     184 ..     130     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0015
                        AAA_13 23 GwNGaGKTtLSrllrsl 39
                                  G NGaGKTt  r+l+ +
  gi|15669212|ref|NP_248017.1| 37 GHNGAGKTTTLRILAGI 53
                                  99**********99986 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0066
                        AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnle 572
                                   i +  iv++D P S LD   + +    i +    k++ k ++++TH le
  gi|15669212|ref|NP_248017.1| 139 IHNPDIVILDEPFSGLDVVNVRLLRDIIFEL---KEEGKTIILSTHQLE 184
                                   56789************87766666666555...5999********987 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00016      0.26       6      27 ..      35      56 ..      31      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                                  EEESTTSSHHHHHHHHHHHHHH CS
                         SRP54  6 lvGlqGaGKTttlaKLaallkk 27
                                  l+G +GaGKTttl  La ++++
  gi|15669212|ref|NP_248017.1| 35 LLGHNGAGKTTTLRILAGIIEE 56
                                  89***********999988765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00028      0.46      23      51 ..      37      65 ..      31      79 .. 0.93
   2 ?   -2.3   0.0       1.3   2.2e+03     170     194 ..     183     204 ..     173     207 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00028
                    Zeta_toxin 23 GqpGAGKselaellkdelerqgnvvrldp 51
                                  G  GAGK+++++ l+  +e++ ++v++++
  gi|15669212|ref|NP_248017.1| 37 GHNGAGKTTTLRILAGIIEEYTGYVEVNG 65
                                  899**********************9985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                    Zeta_toxin 170 vealeeekqldrvkikdrdgktvly 194
                                   +e++e+  ++drv i ++++ +v+y
  gi|15669212|ref|NP_248017.1| 183 LEKIER--LCDRVLILKKGK-AVHY 204
                                   444444..789999987777.8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1656.82
//
Query:       gi|15669213|ref|NP_248018.1|  [L=403]
Description: hypothetical protein MJ_1024 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-50  170.6  34.6    5.5e-50  170.4  34.6    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
    3.4e-10   39.7  24.9    6.2e-10   38.8  24.9    1.4  1  ABC2_membrane_2  ABC-2 family transporter protein
    0.00011   21.7  20.7    0.00011   21.7  20.7    2.8  3  ABC2_membrane    ABC-2 type transporter


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.4  34.6   9.2e-54   5.5e-50       1     344 [.      29     377 ..      29     378 .. 0.85

  Alignments for each domain:
  == domain 1  score: 170.4 bits;  conditional E-value: 9.2e-54
               ABC2_membrane_3   1 ksfliitlllPiilvlllglifsnsveddentpiavvdedn.sslsqqlvealeaspsvelvyevdseeeakkalkngdid 80 
                                   k fli t++ P+i+++l ++i s    d++++++++vde +     +++ +++ ++ ++   ++++++e+ k+++ n+ id
  gi|15669213|ref|NP_248018.1|  29 KQFLIATIIGPLIIIAL-AIIGSFMMFDIKEIKVGYVDEFGlGIPNKVVENNFGKNTTIY-FIKYENIEKGKEDVLNKSID 107
                                   679*************7.6666766779*************866668899*******998.******************** PP

               ABC2_membrane_3  81 gilvipkgfskdllkgesatvtvlinssnlnsskailnalns.llqqlnasalv..lqseatstsaninvestql..eeel 156
                                   +++vipk++++        + +++++s+  + +++i  +ln+ ll++ + + +v   + +  +++ n+++ s ++  +e++
  gi|15669213|ref|NP_248018.1| 108 ALIVIPKDYLD--------SGKIILYSTTKSPNPIITDTLNKfLLKK-LLKGKVdnKTYNRVINPMNLEIYSVSKkgFEKE 179
                                   *********96........7899*******************55555.544555677777777777777777777664433 PP

               ABC2_membrane_3 157 snvasflvg....liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafgl.. 231
                                     + s+l++    ++l+++i+  + +i++si+eEk++ri+el+l+   s+  ++++kilg+ +v+llq+ +++l+a+ +  
  gi|15669213|ref|NP_248018.1| 180 -TFLSQLLPigfvFLLYMAISSLSGIIVSSIIEEKQNRIMELLLCY-SSAENLMFGKILGISAVGLLQIGIWVLFALPIii 258
                                   .4444433334446666666666666888****************9.**************************97555555 PP

               ABC2_membrane_3 232 ....gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffggl.fpledlpsalkwifsiiPff 307
                                        ++ +  +++l++f+l++l y++l   lsslf+ +++a++li+++i++ ++ ++++  ++ ++++++++i+s++Pf+
  gi|15669213|ref|NP_248018.1| 259 tyavKVSLYLAIFALIYFVLGYLFYSSLLCGLSSLFSHPKDASQLISPIIIIQIIPIMFMnTIMVNPNHYMAKILSYVPFT 339
                                   553456666667777************************************888887777666889*************** PP

               ABC2_membrane_3 308 apglgllrlitgd.plweillsliilalfavvylllal 344
                                   ap  + lr + ++ pl+ei ls +i+++++v+ ++l++
  gi|15669213|ref|NP_248018.1| 340 APYAVVLRASVTQlPLIEIVLSTAIMIVSIVISFILSI 377
                                   *********98888**********************98 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8  24.9     1e-13   6.2e-10       2     284 ..      16     381 ..      15     382 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1e-13
               ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllpli................................dvalaylkdlgsslqseakaike 50 
                                   +i k+E+   ++ + fl+ t++ pli                                +v+   + ++ +    ++ +i +
  gi|15669213|ref|NP_248018.1|  16 TIGKREVLSNIKRKQFLIATIIGPLIiialaiigsfmmfdikeikvgyvdefglgipnKVVENNFGKNTTIYFIKYENIEK 96 
                                   78899*********************8888888888888888777777777777777766666666666666666666666 PP

               ABC2_membrane_2  51 atlaleyveaasasdeaedtdqdlkv....................................................... 76 
                                     + + + ++++   +++d+  ++k+                                                       
  gi|15669213|ref|NP_248018.1|  97 GKEDVLNKSIDALIVIPKDYLDSGKIilysttkspnpiitdtlnkfllkkllkgkvdnktynrvinpmnleiysvskkgfe 177
                                   666666666666666666666666669999*************************************************** PP

               ABC2_membrane_2  77 .............vstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvll 144
                                                v +++  +  + +++ +  +i +Ek ++ ++llL +  s   + +gK++g +a+   +++ +++ vl+
  gi|15669213|ref|NP_248018.1| 178 ketflsqllpigfVFLLYMAISSLSGIIVS--SIIEEKQNRIMELLLCYS-SAENLMFGKILGISAV---GLLQIGIWVLF 252
                                   ****99887777444444444444466655..799**************6.7799************...66666666666 PP

               ABC2_membrane_2 145 alaiilalgivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpav 225
                                   al ii  + + ++l   ++ ++ +vl  l  ++ +l  +lSs++   + a +l ++ +++ +i+ +++  +++ +++ +++
  gi|15669213|ref|NP_248018.1| 253 ALPIIITYAVKVSLYLAIFALIYFVLGYL--FYSSLLCGLSSLFSHPKDASQL-ISPIIIIQIIPIMFMNTIMVNPN-HYM 329
                                   56555555555555444444444443333..79************88877776.89999999*******88777777.666 PP

               ABC2_membrane_2 226 pqeindflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFk 284
                                         +ls+++ t++y ++l++  +  +   l+  + + +i+++ ++++++l++ lFk
  gi|15669213|ref|NP_248018.1| 330 ----AKILSYVPFTAPYAVVLRASVTQLP---LIEIVLSTAIMIVSIVISFILSIKLFK 381
                                   ....89************99999888887...8999*********************97 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.018   1.1e+02       4     110 ..      15      45 ..      12      68 .. 0.60
   2 !   21.7  20.7   1.8e-08   0.00011      52     197 ..     184     341 ..     138     353 .. 0.69
   3 ?   -1.4   1.0      0.21   1.3e+03     106     122 ..     359     375 ..     344     387 .. 0.46

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.018
                 ABC2_membrane   4 kallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnrpgllffsvlflafsaltsvapvferergvler 84 
                                   +++ kre+l+ +++++ + ++ +i pl+++                                                   
  gi|15669213|ref|NP_248018.1|  15 LTIGKREVLSNIKRKQFL-IATIIGPLIII--------------------------------------------------- 43 
                                   556666666666666444.55555554332................................................... PP

                 ABC2_membrane  85 elvsplyslsayvlakvlvelpvsll 110
                                                           +l
  gi|15669213|ref|NP_248018.1|  44 ------------------------AL 45 
                                   ........................22 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.8e-08
                 ABC2_membrane  52 r...pgllffsvlflafsaltsva.pvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv.gldl 127
                                       +g++f + + ++  +l++++ ++++ e+ +   el   ++s+   +++k+l+  +v+llq+ i++l++++++  + +
  gi|15669213|ref|NP_248018.1| 184 QllpIGFVFLLYMAIS--SLSGIIvSSIIEEKQNRIMELLLCYSSAENLMFGKILGISAVGLLQIGIWVLFALPIIiTYAV 262
                                   1454555555555555..444333044445555556677777779*****************************8664444 PP

                 ABC2_membrane 128 s.rf...flflllllltalaasslgllisalapsfedasqlaslvll....pllllsGffipidsm.pkwlqwiaylnP 197
                                   + +    +++l++++l +l+ ssl   +s+l+++ +dasql+s +++    p++++  ++++++    k l ++    P
  gi|15669213|ref|NP_248018.1| 263 KvSLylaIFALIYFVLGYLFYSSLLCGLSSLFSHPKDASQLISPIIIiqiiPIMFMNTIMVNPNHYmAKILSYVPFTAP 341
                                   44224468889999999*************************9987522226677777777766654345555444444 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.21
                 ABC2_membrane 106 pvsllqalifllivyfl 122
                                   ++s+++ ++ ++i+++l
  gi|15669213|ref|NP_248018.1| 359 VLSTAIMIVSIVISFIL 375
                                   22222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1212  (0.0676); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2605.31
//
Query:       gi|15669214|ref|NP_248019.1|  [L=388]
Description: hypothetical protein MJ_1025 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-26   93.8   0.0    1.8e-26   93.4   0.0    1.2  1  SDH_alpha  Serine dehydratase alpha chain


Domain annotation for each model (and alignments):
>> SDH_alpha  Serine dehydratase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4   0.0     1e-30   1.8e-26      22     259 ..     140     381 ..      86     382 .. 0.74

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 1e-30
                     SDH_alpha  22 s....................aeeidakleeiwevmdeaieeglsnkaiaeegllpgelkvkr.ayaalgkrlldklsaaA 81 
                                   s                     + i++  ee+ ++++e+ie   +nk++++ ++ p+++     +  ++ +++l    +++
  gi|15669214|ref|NP_248019.1| 140 SgkslsddlknayksltlkdfIDYIEDIPEEVIKIIKETIE---TNKNLSTPEV-PEDFISLDlK-DEILNHML--KKTVS 213
                                   04444444444444455545544444445777778888888...7888886666.5555544434.55555554..45778 PP

                     SDH_alpha  82 lavaemnaaggrvvtaptsGaaGi...lPavlvalleelkas.eellraLllaaligilikrnasisgAecGcqaevGvac 158
                                   +  ++m + + + ++ ++sG+ G+   lP++++   e  + + e+l++ ++l+al++i+ + ++s  +A+cGc+   G++ 
  gi|15669214|ref|NP_248019.1| 214 AVYNRMIGINKPAMAIAGSGNMGLtatLPIIAYD--EIKGHDeEKLTKSITLSALTTIYSAYHSSYISAMCGCVNRGGIG- 291
                                   899*********************9999999988..6445558*************************************. PP

                     SDH_alpha 159 amAAaglaallggspeqienAaeialehllGltCDpvaGlvkipCiernalgavkAvtaarlalagdggegivsldeviet 239
                                     A  gl +   g  ++ie+ ++   ++l G++CD+     ki+C+ ++a+g+ + + +    +    ++giv  +++ e+
  gi|15669214|ref|NP_248019.1| 292 --AVSGLSYYIFG-FDRIEESIKSFTANLPGIVCDG----GKIGCALKIASGVFAIYLSLFSKVPY--TNGIVG-KDFKEC 362
                                   ..*****998865.899*******************....***********998777666555555..58****.****** PP

                     SDH_alpha 240 mrntgkdmsekyketseggL 259
                                   ++n+gk+++  +k ++++++
  gi|15669214|ref|NP_248019.1| 363 IENIGKIGK-AMKPVDDEII 381
                                   *****9986.6888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2648.89
//
Query:       gi|161579523|ref|NP_248020.2|  [L=426]
Description: thiamine biosynthesis protein ThiC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.7e-197  655.6   1.7   3.1e-197  655.5   1.7    1.0  1  ThiC_Rad_SAM   Radical SAM ThiC family
  ------ inclusion threshold ------
      0.048   13.6   0.3          1    9.3   0.3    2.5  1  ADH_zinc_N     Zinc-binding dehydrogenase
      0.061   13.4   0.0        2.6    8.2   0.0    2.7  2  tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  655.5   1.7  5.1e-201  3.1e-197       1     417 [.       2     421 ..       2     422 .. 0.99

  Alignments for each domain:
  == domain 1  score: 655.5 bits;  conditional E-value: 5.1e-201
                   ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkekpvaiGkglrtkvnaniGtsadasdieeEveK 80 
                                    tq+++a++giiteem+ vaeke+++ e++r+ +a+G +vi++n+n++++pv+iG++lrtkvnaniGts d++die E++K
  gi|161579523|ref|NP_248020.2|   2 TQMDDAKNGIITEEMKIVAEKEKIDIEKLRKLIAKGYVVILKNVNRDTNPVGIGQSLRTKVNANIGTSPDCVDIELEIKK 81 
                                    8******************************************************************************* PP

                   ThiC_Rad_SAM  81 lkvalkagadtvmdLstggdideirekileespvpvgtvpiYqalee...kekkveelteeellevieeqaedGvdflti 157
                                    +k+a+k+gad+vmdLstgg+++eir++i++++++p+gtvpiY++ +    k+++v +++e+ +++vie+qa++Gvdf+t+
  gi|161579523|ref|NP_248020.2|  82 AKIAEKYGADAVMDLSTGGNLEEIRKAIMDAVKIPIGTVPIYEVGKLareKYGRVIDMNEDLMFKVIEKQAKEGVDFMTL 161
                                    *******************************************976555699**************************** PP

                   ThiC_Rad_SAM 158 HagvtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDatdeaql 237
                                    H+g+t++++e+lk+++R++g+vSrgG++l+a++l +++enply++fd+ll+ilke+dvt+Slgdg+RpG++aD+td+aq+
  gi|161579523|ref|NP_248020.2| 162 HCGITKQSVERLKRSGRIMGVVSRGGAFLTAYILYHNEENPLYKNFDYLLDILKEHDVTISLGDGMRPGCLADNTDRAQI 241
                                    ******************************************************************************** PP

                   ThiC_Rad_SAM 238 aelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsaiGaalaaaaGa 317
                                    +eli+lgelv+r+re+gvq+mveGPGH+p++ ie+n++lqk+lck+aPfyvlGp+vtDiapgYDhit+aiG+ala+++Ga
  gi|161579523|ref|NP_248020.2| 242 EELITLGELVERCREKGVQCMVEGPGHIPINYIETNIRLQKSLCKNAPFYVLGPIVTDIAPGYDHITAAIGGALAGYYGA 321
                                    ******************************************************************************** PP

                   ThiC_Rad_SAM 318 dllCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfelaldpekareireekl 397
                                    d+lCyvtp+EHl+lP+ edvkeGvia+kiaa+aad+akg+k a+e++++++ aRk+ dwekqfela+d+ekar++ree  
  gi|161579523|ref|NP_248020.2| 322 DFLCYVTPSEHLRLPTIEDVKEGVIATKIAAQAADVAKGNKLAWEKETEMAYARKNHDWEKQFELAIDKEKARKMREEIP 401
                                    ******************************************************************************** PP

                   ThiC_Rad_SAM 398 peeeeaCsmCgekCavkive 417
                                    ++ee+aCs+Cg++Ca+ +ve
  gi|161579523|ref|NP_248020.2| 402 SKEEKACSICGDYCALLMVE 421
                                    ***************98876 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.3   0.00018         1      25      88 ..      80     182 ..      71     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00018
                                    HHHHHHHHTTESEEEET...TTC.HHHHHHHHHT.........................................TTSSE CS
                     ADH_zinc_N  25 eklelakklGadeviny...kea.dlverikelt.........................................ggegv 59 
                                    +k+++a+k+Gad+v +     +  ++ ++i                                              +egv
  gi|161579523|ref|NP_248020.2|  80 KKAKIAEKYGADAVMDLstgGNLeEIRKAI---MdavkipigtvpiyevgklarekygrvidmnedlmfkviekqAKEGV 156
                                    689999999999999994442222344444...24448888888888888888888888888888888888888668899 PP

                                    EEEEESSCSHHHHHHHHHCEEEEEEEEEC CS
                     ADH_zinc_N  60 dvvfecvGsgatleaalkllkpgGrlvvv 88 
                                    d+   + G     +++++ lk+ Gr++ v
  gi|161579523|ref|NP_248020.2| 157 DFMTLHCG---ITKQSVERLKRSGRIMGV 182
                                    99999999...889999999999999876 PP

>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00043       2.6      17      82 ..     182     268 ..     172     273 .. 0.86
   2 ?    2.2   0.0     0.032   1.9e+02      24      35 ..     319     328 ..     316     393 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00043
                                    EEEECGGGTSSEEEE..TSCTTTSSCSEEEEEEETTSEE...................EHHHHHHHHHHHHHTTSEEEEE CS
                  tRNA_int_endo  17 vvrsGlkFGadFrvY..qrrpslehseylVvvvsedeel...................dwpdlsaavrlahsvkKklila 75 
                                    vv  G  F + +++Y  +++p  +  +yl+ +++e +                     ++++l+  ++l++  + k +++
  gi|161579523|ref|NP_248020.2| 182 VVSRGGAFLTAYILYhnEENPLYKNFDYLLDILKEHDVTislgdgmrpgcladntdraQIEELITLGELVERCREKGVQC 261
                                    5677889*********99****************9998889999999999999999998899999999999999998888 PP

                                    EETTTSC CS
                  tRNA_int_endo  76 ivdaegd 82 
                                    +v+ +g 
  gi|161579523|ref|NP_248020.2| 262 MVEGPGH 268
                                    8877776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.032
                                    GTSSEEEETSCT CS
                  tRNA_int_endo  24 FGadFrvYqrrp 35 
                                    +GadF+ Y    
  gi|161579523|ref|NP_248020.2| 319 YGADFLCY--VT 328
                                    9******9..22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2649.51
//
Query:       gi|15669216|ref|NP_248021.1|  [L=377]
Description: formate hydrogenlyase subunit 5 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-48  162.7   0.0    1.3e-36  126.1   0.0    2.1  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    1.7e-15   56.9   0.7    1.8e-14   53.5   0.2    2.2  2  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.1   0.0   1.4e-40   1.3e-36       2     162 ..     122     284 ..     122     300 .. 0.94
   2 !   34.7   0.0   1.1e-12   9.5e-09     208     271 .]     305     368 ..     287     368 .. 0.95

  Alignments for each domain:
  == domain 1  score: 126.1 bits;  conditional E-value: 1.4e-40
                                   TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBS..S---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHH CS
                Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGva..rDlpegllekikeflkelekkldeleklltknrifkkRt 80 
                                   lG  t+ + af  Re i+++l e+tG R ++s+ +iGG++   +++e+ +  + e l+++e++l++l +  ++++++++R+
  gi|15669216|ref|NP_248021.1| 122 LGFETMAFRAFMIREPIMQILGEITGGRAQYSCPIIGGIRprCNIKESKIPALLERLEKFEENLKKLLERTVNDPMIMSRI 202
                                   6889***********************************733689999********************************* PP

                                   SSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--. CS
                Complex1_49kDa  81 kgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpe 161
                                   k+vgvl+k++a +l + Gp++R+sG++ D+Rk     +Yd+++f+ +v ++gDv++R+ vr+ E+ +S+kIi+q l++lp+
  gi|15669216|ref|NP_248021.1| 203 KDVGVLDKKTAKKLHALGPTARGSGIHSDMRKMGQVPVYDNFEFEEIVFDDGDVFSRLAVRFYECFESVKIIRQGLKDLPN 283
                                   *******************************************************************************97 PP

                                   S CS
                Complex1_49kDa 162 g 162
                                    
  gi|15669216|ref|NP_248021.1| 284 L 284
                                   3 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 1.1e-12
                                   EEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                Complex1_49kDa 208 vEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                    Ea +G++ +    d++ +  ++kir+p+ +nl+ +e++l g+ ++D+  i++s+d+++ ++DR
  gi|15669216|ref|NP_248021.1| 305 NEAQRGQVYYSYGLDENGRVRQVKIRTPTATNLACMEAILPGHHVSDAELIIASCDPCFTCTDR 368
                                   699************************************************************9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.2     2e-18   1.8e-14       1      72 [.      46     117 ..      46     121 .. 0.98
   2 ?    1.6   0.0     0.011     1e+02     470     503 ..     339     366 ..     256     367 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 2e-18
                                   --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHH CS
                  NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhFYh 72 
                                   RG+Eli++g  p+   +l ++iCG+C ++H ++ v+  e+ ++i++p+ a++ir +++  + lh+h++ F h
  gi|15669216|ref|NP_248021.1|  46 RGIELIMEGLPPEKISILSEKICGICSHIHVWCNVTVTERGCDIEVPERAEYIRAIVEELERLHSHMLLFGH 117
                                   9*******************************************************************9965 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.011
                                   HHHHHHTT-B-SSTTS-HHHHHHHHHT--BHHHH CS
                  NiFeSe_Hases 470 ayEaaLigtpvadpekPleilrtihSfDPClACa 503
                                    +Ea L g++v+d+e       +i S DPC  C+
  gi|15669216|ref|NP_248021.1| 339 CMEAILPGHHVSDAE------LIIASCDPCFTCT 366
                                   566666666666655......37899*****995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2716.29
//
Query:       gi|15669217|ref|NP_248022.1|  [L=686]
Description: DNA topoisomerase VI subunit B [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-56  190.4   0.0    4.8e-56  189.0   0.0    1.7  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
      2e-12   47.6   0.2    4.8e-12   46.4   0.2    1.7  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    4.7e-09   36.2   0.0      1e-08   35.1   0.0    1.6  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
  ------ inclusion threshold ------
      0.026   14.8   0.5      0.056   13.7   0.5    1.6  1  Med29           Mediator complex subunit 29
      0.072   13.0   0.2       0.23   11.4   0.2    1.9  1  EMP24_GP25L     emp24/gp25L/p24 family/GOLD
        0.1   12.8   0.3       0.58   10.4   0.0    2.5  2  Costars         Costars
       0.12   12.6   8.0        5.1    7.4   0.3    3.9  4  DUF365          Domain of unknown function (DUF365)
        0.2   11.8   0.1        1.1    9.5   0.0    2.0  2  Cupin_5         Cupin superfamily (DUF985)
        1.3    9.1   4.3        1.9    8.6   0.9    2.8  3  Pox_A3L         Poxvirus A3L Protein
        1.6    8.5  13.4        1.6    8.4   9.6    2.6  2  DUF445          Protein of unknown function (DUF445)


Domain annotation for each model (and alignments):
>> Topo-VIb_trans  Topoisomerase VI B subunit, transducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.0   0.0   2.7e-59   4.8e-56       1     159 []     484     651 ..     484     651 .. 0.94

  Alignments for each domain:
  == domain 1  score: 189.0 bits;  conditional E-value: 2.7e-59
                Topo-VIb_trans   1 Pstdclspigeeliekglkkelkpefvaavtrkpkvyegh.pfivEvgiayGGele...keeka....eilRfaNrvPLly 73 
                                   P+t+ l+pig+e+iek+lk+ l+p+fv+a+tr+pk+y+g  pf vEv+iayGG++    +   +    ei+RfaN+vPLly
  gi|15669217|ref|NP_248022.1| 484 PPTTGLRPIGAENIEKSLKELLQPDFVKAITRNPKTYKGGiPFAVEVAIAYGGNAGrqgD---EgrrmEIMRFANHVPLLY 561
                                   8999**********************************988************9985542...33346************* PP

                Topo-VIb_trans  74 degadvitkavksinwkrYkleqpedpvvvlvhvastkvPfksegKeaia....dveeiekeiklalqevarkLkkylskk 150
                                   d++a+ +tkavksinwkrY+l+ ++ p++v+v+++st +P++s+gK+a+a    + eei++ei++al+ ++r+L+kyls+ 
  gi|15669217|ref|NP_248022.1| 562 DASACGLTKAVKSINWKRYGLRGEDAPITVFVNLISTFIPYTSAGKQAVAcsenENEEIYNEIRHALMICGRELEKYLSRI 642
                                   *************************************************99888899************************ PP

                Topo-VIb_trans 151 ekekeekek 159
                                   ++e+ee++k
  gi|15669217|ref|NP_248022.1| 643 RREAEEEKK 651
                                   ***999876 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.2   2.7e-15   4.8e-12       2     109 ..      60     175 ..      59     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.7e-15
                                   HHHHHHHHHHHHHHHHHHHHSTTT...EEEEEEEEEE...TEEEEEEEESSSSSTTHHHTGTCSTTCH...HCSTCHTSTS CS
                     HATPase_c   2 dekrLrqiisnlvdNavkfatkag...eieveikase...ddlvisveDnGiGipkedlkklfekfsq...ddstkrgggg 73 
                                   + + L+ ii +lv+N++++  +ag   +i+vei+  +   d++++ veDnG+Gip e ++k+f+k+          ++ g+
  gi|15669217|ref|NP_248022.1|  60 KIRSLTTIIHELVTNSLDACEEAGilpDIKVEIE--KlgaDHYKVAVEDNGPGIPLEFIPKVFGKMLAgskMHRFIQSRGQ 138
                                   67899*************95555555599*****..44579***********************77774553344445799 PP

                                   SSHHHHHHHHHHH.HTTTEEEEEEETTTEEEEEEEEE CS
                     HATPase_c  74 tGlGlsivkklve.lmgGeiwvesepgrGttftftlp 109
                                    G+G++ v  +++ + g  ++++++ g G  + ++++
  gi|15669217|ref|NP_248022.1| 139 QGIGAAGVLLFSQiTTGKPLKIITSTGDGNIYEVEVK 175
                                   9999999988888777888888888888877776665 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   5.6e-12     1e-08       5     119 ..      66     190 ..      61     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 5.6e-12
                   HATPase_c_3   5 kAlaelvdNsldAdaen.....vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiG... 76 
                                   + + elv NsldA  e      +k+e++k   ++ ++ +eD+G G++ e + +++ ++   sk  +r  +s+G+ GiG   
  gi|15669217|ref|NP_248022.1|  66 TIIHELVTNSLDACEEAgilpdIKVEIEKLGADHYKVAVEDNGPGIPLEFIPKVFgKMLAGSKM-HRFIQSRGQQGIGaag 145
                                   5689*********999999*9********99999*****************9977466666666.5667777777777333 PP

                   HATPase_c_3  77 .lklAslslgkkltvitk.kegesstltldvdkidkenekvleel 119
                                    l ++ +  gk l++it+  +g+ +++++++++ ++e+e v +++
  gi|15669217|ref|NP_248022.1| 146 vLLFSQITTGKPLKIITStGDGNIYEVEVKMNVEKNEGEIVSKKV 190
                                   336677778888888885166888899999998888888877765 PP

>> Med29  Mediator complex subunit 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   3.1e-05     0.056       4      59 ..     345     401 ..     343     453 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.1e-05
                         Med29   4 DpiskvkslvqkLkeSlvellktaaqllaqneevdsg.lkgddedkprfdkaleeFy 59 
                                   D+i+ v++l+++L eSl el + a +++  +   ++  +++ ++ k+ f+k  e+F 
  gi|15669217|ref|NP_248022.1| 345 DEIETVRMLIKNLPESLDELKRYALKYITMEYLFNKLsEEEINKLKNHFKKIPENFM 401
                                   99*****************************99999966699**********99996 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00013      0.23      88     150 ..     321     384 ..     309     392 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                   EMP24_GP25L  88 s.kkvsfdievgseasdykdsakkekletleselkkleekldsikreqkylrereerlrdtnes 150
                                   + ++++++i+++s  ++ kd  +++++et+   +k+l e+ld++kr+   + ++e  + +++e+
  gi|15669217|ref|NP_248022.1| 321 MvVSCYLNIDIESYLNKFKDYITDDEIETVRMLIKNLPESLDELKRYALKYITMEYLFNKLSEE 384
                                   1588999****999999**************************************999999986 PP

>> Costars  Costars
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.7   6.6e+03       4      29 ..     345     371 ..     343     396 .. 0.54
   2 ?   10.4   0.0   0.00032      0.58       4      44 ..     633     674 ..     630     686 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.7
                       Costars   4 keileLcevIkelGekndd.gkvvvtF 29 
                                   +ei+ +   Ik+l e+ d+ ++++ ++
  gi|15669217|ref|NP_248022.1| 345 DEIETVRMLIKNLPESLDElKRYALKY 371
                                   677777777777766444424443333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00032
                       Costars   4 keileLcevIkelGeknddgkvvvtFGeLf.ekytniseklv 44 
                                   +e ++ +  I++ +e+++++k+v+++ ++f e ++ni++k v
  gi|15669217|ref|NP_248022.1| 633 RELEKYLSRIRREAEEEKKRKYVMKYARIFaEALANILNKPV 674
                                   788899999*********************999****99654 PP

>> DUF365  Domain of unknown function (DUF365)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.1   1.9e+03      19      41 ..     296     318 ..     291     324 .. 0.81
   2 ?   -2.5   0.0       3.6   6.4e+03      26      48 ..     328     348 ..     320     366 .. 0.76
   3 ?    7.2   0.2    0.0035       6.2      22      67 ..     421     466 ..     410     478 .. 0.81
   4 ?    7.4   0.3    0.0029       5.1      27      68 ..     615     655 ..     602     663 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                                   EEEEEEEES-THHHHHHTSTTBS CS
                        DUF365  19 eikrvvlsedpleifekygdrvf 41 
                                   +ik+++ +   + i++k++d vf
  gi|15669217|ref|NP_248022.1| 296 RIKELINYMLRDLILKKFKDSVF 318
                                   67777777777889********9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.6
                                   ES-THHHHHHTSTTBSS-HHHHH CS
                        DUF365  26 sedpleifekygdrvfltkeelk 48 
                                   + d++++++k++d  ++t++e+ 
  gi|15669217|ref|NP_248022.1| 328 NIDIESYLNKFKD--YITDDEIE 348
                                   5567788888888..56888775 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0035
                                   EEEEES-THHHHHHTSTTBSS-HHHHHHHHHHHHHT----SS---E CS
                        DUF365  22 rvvlsedpleifekygdrvfltkeelkkyvkskerwrkgkkrkkaw 67 
                                     ++ ++p+e++ + +++ ++ +eelkk++ + +   +++ ++ +w
  gi|15669217|ref|NP_248022.1| 421 VKNIVKNPEEFIAEIKNKGLISDEELKKFEDEVKSILNKNPKELTW 466
                                   3457899**********************99877766666666666 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0029
                                   S-THHHHHHTSTTBSS-HHHHHHHHHHHHHT----SS---EE CS
                        DUF365  27 edpleifekygdrvfltkeelkkyvkskerwrkgkkrkkawl 68 
                                   ++ +ei+++ ++++++   el ky     r  ++ ++k++++
  gi|15669217|ref|NP_248022.1| 615 NENEEIYNEIRHALMICGRELEKYLSRIRREAEE-EKKRKYV 655
                                   45689*******************9766555554.4555554 PP

>> Cupin_5  Cupin superfamily (DUF985)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.96   1.7e+03      20      51 ..      46      74 ..      36      78 .. 0.71
   2 ?    9.5   0.0    0.0006       1.1      70     117 ..     154     203 ..     149     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.96
                                  EEEE.SSEEE.CSS.STC.CES-EEEEEEEET CS
                       Cupin_5 20 etdrseltvpsskledgkeRsasTaIyyllts 51
                                  e +r+++++      +gk Rs+ T I+ l+t+
  gi|15669217|ref|NP_248022.1| 46 EFFRKNKHMLG---YSGKIRSLTTIIHELVTN 74
                                  45554444443...45889********99985 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0006
                                   EES-EEEEEESTTSCEEEEEESS-TTT..TEBSEEEE-TTSEEEEEESSS CS
                       Cupin_5  70 aGrpLrlvllhadgrvetvvlGpdvaa..geklqlvVpagkwkaaellgd 117
                                   +G+pL++++++ dg++ +v +  +v++  ge ++  V +gkw +++++g+
  gi|15669217|ref|NP_248022.1| 154 TGKPLKIITSTGDGNIYEVEVKMNVEKneGEIVSKKVRKGKWRGTRVEGE 203
                                   7*********99*************9866889**************9985 PP

>> Pox_A3L  Poxvirus A3L Protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.9     0.001       1.9      18      65 ..     337     386 ..     333     389 .. 0.76
   2 ?   -1.9   0.1       1.9   3.4e+03      45      65 ..     429     446 ..     412     458 .. 0.69
   3 ?   -0.7   0.1      0.79   1.4e+03      23      41 ..     446     464 ..     443     466 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                       Pox_A3L  18 nlveylkeDr.etikmilesqpkklkilkeFLaavrnktlly.kiLDeEi 65 
                                    + +y+++D+ et++m++++ p+ l  lk++   + + ++l  k+  eEi
  gi|15669217|ref|NP_248022.1| 337 KFKDYITDDEiETVRMLIKNLPESLDELKRYALKYITMEYLFnKLSEEEI 386
                                   57789**99879******************96666666555404445555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.9
                       Pox_A3L  45 keFLaavrnktllykiLDeEi 65 
                                    eF+a ++nk l+    DeE+
  gi|15669217|ref|NP_248022.1| 429 EEFIAEIKNKGLIS---DEEL 446
                                   37999999998863...4444 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.79
                       Pox_A3L  23 lkeDretikmilesqpkkl 41 
                                   lk+ ++++k il+++pk l
  gi|15669217|ref|NP_248022.1| 446 LKKFEDEVKSILNKNPKEL 464
                                   56668999********976 PP

>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   9.6   0.00091       1.6      91     269 ..     275     456 ..     263     507 .. 0.60
   2 ?   -0.6   0.1       0.5   8.9e+02     199     243 ..     636     678 ..     590     685 .. 0.45

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00091
                        DUF445  91 ellkeiledlddesikellkknlk....kkleevipepllgkllellleeerhkkllddlldriknllkdeevkekikeli 167
                                   +  +++++++ +++++++  k++k    ++l+++i+++++++++ +++ + + +  +++ l++ k++++d+e +    +++
  gi|15669217|ref|NP_248022.1| 275 KTKSKKVSSMLVSELSRVTTKRIKelinYMLRDLILKKFKDSVFWNMVVSCYLNIDIESYLNKFKDYITDDEIE--TVRML 353
                                   44445555555555555544444444448999999999999999999999999999999999999999999999..55555 PP

                        DUF445 168 delieeesgklvlesivsmflreltsilekvksdpdhllreeedkkvreliadllndp....elaakveklkkkklsdlev 244
                                    ++++e   +  l++ + + ++  + + +k+ +++ + l++ ++k  +    ++++++    ++ ++++k  k  ++++e+
  gi|15669217|ref|NP_248022.1| 354 IKNLPESLDE--LKRYALKYITM-EYLFNKLSEEEINKLKNHFKKIPE-NFMEWAEKNylsaTVVDELNKKVKNIVKNPEE 430
                                   5555666555..45555554444.566666666666666666665433.33333333300003333333333334444444 PP

                        DUF445 245 qeyeealwealkdlllkdlneee.sl 269
                                    + e ++   ++d  lk++++e  s 
  gi|15669217|ref|NP_248022.1| 431 FIAEIKNKGLISDEELKKFEDEVkSI 456
                                   44444444444444444444422222 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.5
                        DUF445 199 ksdpdhllreeedkkvreliadllndpelaakveklkkkklsdle 243
                                   ++ + +  re+e++k r+++ + +    +a+ + ++++k ++++e
  gi|15669217|ref|NP_248022.1| 636 EKYLSRIRREAEEEKKRKYVMKYAR--IFAEALANILNKPVDEIE 678
                                   2222222222222222223333333..233333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1204  (0.0671538); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.53
# Mc/sec: 3921.79
//
Query:       gi|15669218|ref|NP_248023.1|  [L=275]
Description: dimethyladenosine transferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-57  192.5   3.4    8.4e-57  192.2   3.4    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    2.2e-06   28.2   0.0    1.1e-05   26.0   0.0    2.1  2  Methyltransf_25  Methyltransferase domain
    3.8e-05   24.2   0.0    0.00031   21.3   0.0    2.2  2  Methyltransf_11  Methyltransferase domain
    0.00039   20.3   0.0    0.00055   19.8   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
     0.0021   17.6   0.1     0.0041   16.7   0.0    1.6  2  MTS              Methyltransferase small domain
     0.0021   17.5   0.0     0.0041   16.6   0.0    1.5  1  Methyltransf_4   Putative methyltransferase
     0.0058   16.2   0.0      0.013   15.0   0.0    1.5  1  DOT1             Histone methylation protein DOT1
      0.006   16.4   0.4      0.012   15.4   0.4    1.8  1  Methyltransf_31  Methyltransferase domain
      0.008   15.8   0.0      0.013   15.1   0.0    1.2  1  NodS             Nodulation protein S (NodS)
  ------ inclusion threshold ------
      0.013   15.7   3.2      0.017   15.2   0.1    2.1  2  DUF4760          Domain of unknown function (DUF4760)
      0.019   14.9   0.3      0.045   13.8   0.0    1.7  2  Methyltransf_32  Methyltransferase domain
      0.035   13.2   0.0      0.072   12.2   0.0    1.5  1  DREV             DREV methyltransferase
      0.052   13.3   0.0      0.097   12.4   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.094   13.0   0.6          3    8.2   0.1    2.6  2  DUF5471          Family of unknown function (DUF5471)
       0.25   11.8  11.7       0.12   12.7   4.5    2.5  2  NBD94            Nucleotide-Binding Domain 94 of RH


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.2   3.4     7e-60   8.4e-57       2     258 ..       2     252 ..       1     257 [. 0.91

  Alignments for each domain:
  == domain 1  score: 192.2 bits;  conditional E-value: 7e-60
                                   GCCXXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE- CS
                        RrnaAD   2 nklrksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvh 82 
                                   +k +k++gq fl++k+ +n++++ +nl++++ vleig GkGilTeeLak ak+v v+E+d++L    +k  +++++++++ 
  gi|15669218|ref|NP_248023.1|   2 FKPKKKLGQCFLIDKNFVNKAVESANLTKDDVVLEIGLGKGILTEELAKNAKKVYVIEIDKSLEPYANKLKELYNNIEIIW 82 
                                   6889***********************************************************988888666********* PP

                                   S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHHHH CS
                        RrnaAD  83 qDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlrea 163
                                    D+lk ++ +         +  +vvanlPy+is+++ ++l++    g+  ++l+ q efa+r++a+ g k+++rlsv+++ 
  gi|15669218|ref|NP_248023.1|  83 GDALKVDLNKL--------DFNKVVANLPYQISSPITFKLIK---RGFDLAVLMYQYEFAKRMVAKEGTKDYGRLSVAVQS 152
                                   **********3........5569******************7...34679******************************* PP

                                   HEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHC.....CCTSTCHHHHHCTT CS
                        RrnaAD 164 ftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstsl.....ksllpggelqalss 239
                                    +dv++vakv++s+f P+pkv sa+v++++ + +   ++ + ++ ++r+++  ++k+++++l     + +++++e++++ +
  gi|15669218|ref|NP_248023.1| 153 RADVEIVAKVPPSAFYPKPKVYSAIVKIKPNKGKYHIENENFFDDFLRAIFQHRNKSVRKALidsskELNYNKDEMKKILE 233
                                   *********************************99*************************984433333577778888877 PP

                                   .T--TTTCCCCSGHHHHHH CS
                        RrnaAD 240 tgindnalvkklsaeqtld 258
                                    ++n n+++k+l  e++++
  gi|15669218|ref|NP_248023.1| 234 DFLNTNSEIKNLINEKVFK 252
                                   7999999999888777665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   9.1e-09   1.1e-05       1      73 [.      34     102 ..      34     121 .. 0.81
   2 ?   -0.8   0.0       2.2   2.7e+03      77      97 .]     253     273 ..     209     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 9.1e-09
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga 73 
                                   vL++G G+G lt++lak+   +kv+ ++i++++  +a++   e   n+e++ gda ++++++  f+ vv++  
  gi|15669218|ref|NP_248023.1|  34 VLEIGLGKGILTEELAKNA--KKVYVIEIDKSLEPYANKLK-ELYNNIEIIWGDALKVDLNKLDFNKVVAN-L 102
                                   9****************96..99999999987766666655.4445***************99*****995.3 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.2
                                   SSHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                   ls +d+ ++ +e++r L++ G
  gi|15669218|ref|NP_248023.1| 253 LSVKDIVNLSNEFYRFLQNRG 273
                                   567788888889999888776 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.6e-07   0.00031       1      68 [.      35     101 ..      35     107 .. 0.88
   2 ?   -0.0   0.0       1.2   1.4e+03      74      94 ..     255     275 .]     243     275 .] 0.80

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.6e-07
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEE CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvss 68 
                                   L++G G+G+l+e+lak++++v+ ++++k +  +a++ ++  + ++e++ +da k+ +++  f  vv++
  gi|15669218|ref|NP_248023.1|  35 LEIGLGKGILTEELAKNAKKVYVIEIDKSLEPYANKLKELYN-NIEIIWGDALKVDLNKLDFNKVVAN 101
                                   89*****************************99987777766.6999999999999888777777765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.2
                                   -CCHHHHHHHHHHHEEEEEEE CS
               Methyltransf_11  74 vedpekalkeiaRvLkpgGll 94 
                                   v+d   + +e++R L++ G+l
  gi|15669218|ref|NP_248023.1| 255 VKDIVNLSNEFYRFLQNRGRL 275
                                   488899999*******99986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.6e-07   0.00055      18      60 ..      26      68 ..      12     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.6e-07
               Methyltransf_23 18 pklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveia 60
                                  ++l ++  vL+iG G+Gil+e+l++n ++v++++++  + + a
  gi|15669218|ref|NP_248023.1| 26 ANLTKDDVVLEIGLGKGILTEELAKNAKKVYVIEIDKSLEPYA 68
                                  5578899****************************87665554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.5e-06    0.0041      31     119 ..      30     116 ..      17     152 .. 0.83
   2 ?   -3.0   0.0         4   4.8e+03     116     151 ..     209     244 ..     204     250 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.5e-06
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEEEE---STTT CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdlivsNPPfhag 110
                                   +++ vl +G G G+l+ +lak+ ++  v ++++d+ +le   + l++   ++e+++ d+l+ ++++ +f+ +v N P++ +
  gi|15669218|ref|NP_248023.1|  30 KDDVVLEIGLGKGILTEELAKNAKK--VYVIEIDK-SLEPYANKLKELYNNIEIIWGDALKvDLNKLDFNKVVANLPYQIS 107
                                   45679****************9888..77777774.688888888888888*******9874778899*********9988 PP

                                   CHCHHHHHH CS
                           MTS 111 katelavae 119
                                   + ++ ++++
  gi|15669218|ref|NP_248023.1| 108 SPITFKLIK 116
                                   776666655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4
                                   HHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHH CS
                           MTS 116 avaeeliaeAkeaLkegGeLliVanrklgyesllee 151
                                   +v ++li ++ke   ++ e+  + + +l+ +s +++
  gi|15669218|ref|NP_248023.1| 209 SVRKALIDSSKELNYNKDEMKKILEDFLNTNSEIKN 244
                                   555566666666555556666666666666655555 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.5e-06    0.0041       3      75 ..      32      97 ..      30     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.5e-06
                                  EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEE CS
                Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgslek 75
                                   vvleiG GkG ++ +lAk+  ++ ++ i+++ +  a+   k + + ++N++i+ gdalkv    l++  ++k
  gi|15669218|ref|NP_248023.1| 32 DVVLEIGLGKGILTEELAKNAKKVYVIEIDKSLEPYAN---KLK-ELYNNIEIIWGDALKV---DLNKLDFNK 97
                                  589***************99888877766655444433...333.4589*********655...444444455 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05     0.013      28     111 ..      16      96 ..      14     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTTB----EEEESS CS
                          DOT1  28 peflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlklfGkklakiefirk 108
                                    +f+++ ++  nl+k+dv +++G G G ++   a   + k+ + +Ei ++   +a+k ke +++   ++G    k+++ + 
  gi|15669218|ref|NP_248023.1|  16 KNFVNKAVESANLTKDDVVLEIGLGKGILTEELAK--NAKKVYVIEIDKSLEPYANKLKELYNNIEIIWGD-ALKVDLNKL 93 
                                   58999****************99888877776665..5677899**************************5.567888888 PP

                                   -ST CS
                          DOT1 109 sFv 111
                                   +F 
  gi|15669218|ref|NP_248023.1|  94 DFN 96 
                                   884 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4     1e-05     0.012       2      82 ..      29     111 ..      28     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn. 81 
                                   +k+ +vl++G G+G lt ela++    ++v+ i+i++    +A++   k  ++n+e   gd+ + +  l++  f+ +++n 
  gi|15669218|ref|NP_248023.1|  29 TKDDVVLEIGLGKGILTEELAKN---AKKVYVIEIDKSLEPYANKL--KELYNNIEIIWGDALKVD--LNKLDFNKVVANl 102
                                   68899****************55...46699999999998999998..67999***********99..77888****9995 PP

               Methyltransf_31  82 ........e 82 
                                            
  gi|15669218|ref|NP_248023.1| 103 pyqisspiT 111
                                   554444440 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.1e-05     0.013      47     119 ..      34     106 ..      20     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                          NodS  47 alevGcaaGalterlapyckrltvvdvveeaiararervke.sshiswivsdvqqfstdekfdlivvaevlyyi 119
                                   +le+G   G lte+la  +k++ v+++  ++++   +++ke  ++i  i  d  ++++++     vva++ y i
  gi|15669218|ref|NP_248023.1|  34 VLEIGLGKGILTEELAKNAKKVYVIEID-KSLEPYANKLKElYNNIEIIWGDALKVDLNKLDFNKVVANLPYQI 106
                                   8*************************84.455555555554245666666788888887764455667666665 PP

>> DUF4760  Domain of unknown function (DUF4760)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   1.4e-05     0.017      83     122 ..      38      77 ..      34      82 .. 0.91
   2 ?    0.4   0.7      0.56   6.7e+02      30      75 ..     203     247 ..     186     261 .. 0.49

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                       DUF4760  83 giesgildEdmikelsvttvikawdlleplikelredsnn 122
                                   g  +gil E++ k++  + vi+ ++ lep+ ++l+e  nn
  gi|15669218|ref|NP_248023.1|  38 GLGKGILTEELAKNAKKVYVIEIDKSLEPYANKLKELYNN 77 
                                   6779*******************************99887 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.56
                       DUF4760  30 fqealkqlrkvldsgkslakftlleekksekgeeeserekiltvlN 75 
                                   fq++ k +rk+l + ++  ++   +e+k+  ++  + +++i++++N
  gi|15669218|ref|NP_248023.1| 203 FQHRNKSVRKALIDSSKELNYN-KDEMKKILEDFLNTNSEIKNLIN 247
                                   3333444444333333333333.33333333444444444444444 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.7e-05     0.045      11      72 ..      17      73 ..       6      85 .. 0.81
   2 ?   -2.0   0.1       2.7   3.2e+03      51      81 ..     209     239 ..     198     256 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.7e-05
               Methyltransf_32 11 elvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekrae 72
                                  ++v+k++++ a+ +++  v+++G Gkg L+  la     +  kv+ i++ ++l   a+k++e
  gi|15669218|ref|NP_248023.1| 17 NFVNKAVES-ANLTKDDVVLEIGLGKGILTEELAK----NAKKVYVIEIDKSLEPYANKLKE 73
                                  699999999.58888999*****************....35677777777777777766655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
               Methyltransf_32  51 klkvvgidakeelvekaekraeklgkkfnkr 81 
                                   +++   id+++el+ +  ++++ l+  +n++
  gi|15669218|ref|NP_248023.1| 209 SVRKALIDSSKELNYNKDEMKKILEDFLNTN 239
                                   4455556777777777666666666444333 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     6e-05     0.072      76     141 ..      17      79 ..       6     103 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6e-05
                          DREV  76 eqfrkllaiekespasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkkk..ynvls 141
                                   +  +k +     + a   +d  +l++G G+G +t+ +a+  ++vy  e+ + +    +k+k  yn + 
  gi|15669218|ref|NP_248023.1|  17 NFVNKAV-----ESANLTKDDVVLEIGLGKGILTEELAKNAKKVYVIEIDKSLEPYANKLKelYNNIE 79 
                                   4444432.....2334468899**************************99887644433322255554 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.1e-05     0.097      62     112 ..      19      68 ..      11      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.1e-05
                                   HHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHH CS
                          PCMT  62 valalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelve 112
                                   v +a+e  +l+k + vLe+G G G+lt  la+  +++  v+ i+++ e ++
  gi|15669218|ref|NP_248023.1|  19 VNKAVESANLTKDDVVLEIGLGKGILTEELAKNAKKVY-VIEIDKSLEPYA 68 
                                   567788889*******************9999988877.777776654443 PP

>> DUF5471  Family of unknown function (DUF5471)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.17     2e+02       1      13 [.       1      13 [.       1      30 [. 0.81
   2 ?    8.2   0.1    0.0025         3       2      29 ..     112     141 ..     111     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.17
                       DUF5471  1 mfklikklGqllv 13
                                  mfk  kklGq ++
  gi|15669218|ref|NP_248023.1|  1 MFKPKKKLGQCFL 13
                                  9*********765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0025
                       DUF5471   2 fklikklGqllvrmynve.akrln.deark 29 
                                   fklik+   l v my  e akr+   e  k
  gi|15669218|ref|NP_248023.1| 112 FKLIKRGFDLAVLMYQYEfAKRMVaKEGTK 141
                                   9***************99889974134444 PP

>> NBD94  Nucleotide-Binding Domain 94 of RH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.7      0.11   1.4e+02      11      41 ..      68      98 ..      50     107 .. 0.65
   2 ?   12.7   4.5    0.0001      0.12       4      53 ..     218     270 ..     216     272 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                         NBD94 11 idkkkkiyeniekllnEleeiekektsleev 41
                                   +k+k++y+nie +  +  +++ +k   ++v
  gi|15669218|ref|NP_248023.1| 68 ANKLKELYNNIEIIWGDALKVDLNKLDFNKV 98
                                  4667777777777777777777777666665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0001
                         NBD94   4 tknivtkidkkkkiyeniekllnEleeiekekt...sleevknielsYgrsLi 53 
                                    k++++++d++kki e+  ++ +E++++ +ek+   s++++ n+  ++ r L+
  gi|15669218|ref|NP_248023.1| 218 SKELNYNKDEMKKILEDFLNTNSEIKNLINEKVfklSVKDIVNLSNEFYRFLQ 270
                                   589****************************8733366666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 1487.46
//
Query:       gi|15669219|ref|NP_248024.1|  [L=147]
Description: phosphopantetheine adenylyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-21   76.6   0.1    2.4e-21   76.4   0.1    1.0  1  CTP_transf_like  Cytidylyltransferase-like
      0.006   16.5   1.0      0.024   14.5   1.0    2.0  1  FAD_syn          FAD synthetase
     0.0089   15.5   0.3      0.011   15.2   0.3    1.1  1  ABC_transp_aux   ABC-type uncharacterized transport system
  ------ inclusion threshold ------
      0.011   15.2   2.3      0.013   15.0   2.3    1.1  1  Not3             Not1 N-terminal domain, CCR4-Not complex com
      0.034   14.0   0.9      0.041   13.8   0.9    1.1  1  Dynactin_p22     Dynactin subunit p22
      0.036   14.7   1.1       0.06   14.1   1.0    1.4  1  PTS_IIB          PTS system, Lactose/Cellobiose specific IIB 
       0.17   11.8   0.5       0.97    9.3   0.1    2.0  2  ProQ             ProQ/FINO family


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.1   9.3e-25   2.4e-21       1     142 [.       4     136 ..       4     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 9.3e-25
                                   EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-.SCSSTHHHHHHHHHHH....TTCTTEEEEEEESEHHHH CS
               CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk.kplasaeeRlemlela....kevdevisvdpweltrev 76 
                                   ++gGtFD++H GH +ll+ a +l+++   +g++sde +kk+k +++ ++++R+e+l+++    k + e+ ++++ + +  +
  gi|15669219|ref|NP_248024.1|   4 VVGGTFDILHRGHKELLKFASSLGKL--TIGITSDEFAKKYKtHKINDLKTRIENLKKFldsiKADYEIKVINDAYGD-AI 81 
                                   579*******************9996..99***********88****************5554444444444444444.46 PP

                                   HHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
               CTP_transf_like  77 lkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                   ++++  d  ++v+ +++l+++++ ++++e  g ++l +v ++        + +++ ++iS+t+ir+
  gi|15669219|ref|NP_248024.1|  82 TEDY--D--IIVVTQETLKNAEKINKIRESKGLKPLKIVIFK-------PILAEDGKPISTTRIRK 136
                                   6666..9..9*****************************998.......99999***********7 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.0   9.3e-06     0.024       9      33 ..       3      27 ..       1      61 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.3e-06
                       FAD_syn  9 vvtlGnFDGvHlGHqallkkaveaa 33
                                  vv+ G FD +H+GH++llk a ++ 
  gi|15669219|ref|NP_248024.1|  3 VVVGGTFDILHRGHKELLKFASSLG 27
                                  7888**************9987765 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   4.3e-06     0.011     149     203 ..      30      94 ..      17     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.3e-06
                ABC_transp_aux 149 kvgfltghgelslssp..........se.adfleeleenYnveevdldsedilpedidvlviakpt 203
                                   ++g+ ++    +++ +          ++ ++fl++++++Y+++ ++ +  d + ed+d++v+ + t
  gi|15669219|ref|NP_248024.1|  30 TIGITSDEFAKKYK-ThkindlktriENlKKFLDSIKADYEIKVINDAYGDAITEDYDIIVVTQET 94 
                                   78888866666665.2357889999977889*******************************9433 PP

>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   2.3   4.9e-06     0.013      38      99 ..      42     105 ..      11     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.9e-06
                          Not3  38 qkeKleadLKkeikKLqrlRdqiktwlssneikdk..kkLlenrkliEeamerFkavEkesKtK 99 
                                    k    +dLK+ i  L+++ d ik+  + + i+d   ++++e  + i    e+ k+ Ek +K++
  gi|15669219|ref|NP_248024.1|  42 YKTHKINDLKTRIENLKKFLDSIKADYEIKVINDAygDAITEDYDIIVVTQETLKNAEKINKIR 105
                                   3344449***************************9889*********************99986 PP

>> Dynactin_p22  Dynactin subunit p22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.9   1.6e-05     0.041      47     114 ..      43     111 ..      18     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                  Dynactin_p22  47 krekikellkkleelekyLdpeyedsee.lpdevKleliLaeedeLkktaalleqlqeLkpvldseeik 114
                                   k  ki++l +++e+l+k+Ld+  +d e  + +++  ++i +  d +  t++ l++ ++ +++ +s+ +k
  gi|15669219|ref|NP_248024.1|  43 KTHKINDLKTRIENLKKFLDSIKADYEIkVINDAYGDAITEDYDIIVVTQETLKNAEKINKIRESKGLK 111
                                   4568****************977776655999999*******************999999998888776 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.0   2.3e-05      0.06      18      85 ..      55     127 ..      51     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHHHCT..EEEEETTEEGGGHHHHHHT-SEEEEEESSGGCTHHHHTT.......SEEEEECTTHHHCCHCHH CS
                       PTS_IIB  18 eklekaakelg..ieaegeagveleaeeiaddaDlvllapqvrvkdlarfag.......kpvavinikdalgimdge 85 
                                   e+l+k+++      e+++ + +    ++i++d+D++++++++  k+ ++ ++       kp++++ +k++l  +dg+
  gi|15669219|ref|NP_248024.1|  55 ENLKKFLDSIKadYEIKVINDA--YGDAITEDYDIIVVTQETL-KNAEKINKireskglKPLKIVIFKPIL-AEDGK 127
                                   5677777777766444444444..6699************888.455555555557778899999999966.66665 PP

>> ProQ  ProQ/FINO family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.21   5.4e+02      28      48 ..      29      49 ..      22      70 .. 0.63
   2 ?    9.3   0.1   0.00038      0.97      24      53 ..     108     136 ..      92     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.21
                          ProQ 28 LkiGIfedllerladkeklsk 48
                                  L+iGI  d ++++ ++ k++ 
  gi|15669219|ref|NP_248024.1| 29 LTIGITSDEFAKKYKTHKIND 49
                                  677777777664444444433 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00038
                          ProQ  24 e.akPLkiGIfedllerladkeklskkklrk 53 
                                   +  kPLki If+ +l+  +d +++s +++rk
  gi|15669219|ref|NP_248024.1| 108 KgLKPLKIVIFKPILA--EDGKPISTTRIRK 136
                                   348************9..99999****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1244  (0.0693848); expected 358.6 (0.02)
Passed bias filter:                      722  (0.04027); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 792.65
//
Query:       gi|15669220|ref|NP_248025.1|  [L=308]
Description: hypothetical protein MJ_1031 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-46  155.9  26.7    2.3e-24   85.5   6.7    2.0  2  Mem_trans        Membrane transport protein
  ------ inclusion threshold ------
       0.17   12.5   0.0       0.25   12.0   0.0    1.2  1  G6PD_N           Glucose-6-phosphate dehydrogenase, NAD bindi


Domain annotation for each model (and alignments):
>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   6.7   2.6e-28   2.3e-24       5     135 ..       6     136 ..       2     152 .. 0.92
   2 !   76.6  12.0   1.3e-25   1.2e-21     241     386 ..     160     302 ..     154     303 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 2.6e-28
                     Mem_trans   5 avvplyvimllgYgsvkwvkiftpdqcsginrfVvlfavPllifhfisqnnpyemllrfiladvlvklivlillllgalls 85 
                                    v+ +++++l+gY+s+   +i+++++++++n++V+++a+P +if +is+n++   +l+f+ ++v+++l  l++ +l +ll 
  gi|15669220|ref|NP_248025.1|   6 VVLIVLILVLVGYFSKIF-GILKEEHAKILNNIVIYIAMPSTIFLTISKNVSSSQILEFLKLPVVIFLCCLFVGILAYLLG 85 
                                   58899999********99.*************************************************************9 PP

                     Mem_trans  86 k.ifkgslewtitlfslstlpNtlvlgipllkalygeygvslmvqvvvlqc 135
                                   k ifk++ e+   l+++s l+Nt++lg+p+  +++ge+g++ +++    ++
  gi|15669220|ref|NP_248025.1|  86 KhIFKLKDEKLGGLILVSMLGNTGFLGYPVALGMFGEEGLARAIFCDLGGV 136
                                   99*************************************999998876444 PP

  == domain 2  score: 76.6 bits;  conditional E-value: 1.3e-25
                     Mem_trans 241 rklirnPntyssllglilslvsfkwnvimpkiiqksisilgdaglpmalfslGlfLalqpkkiacgnsvatfalavRlilg 321
                                   +   + P+++  +l++il+  +fk n  +p++i ks++ l++a++p++++slGl+L+  pk ++ g+    +a++ R+i+ 
  gi|15669220|ref|NP_248025.1| 160 KDMAKFPPLITGILSIILVFFGFKLN-YIPSFILKSLNYLSSATVPLIMMSLGLSLS--PKALKFGVFWGIIASIFRFIVS 237
                                   455678********************.*****************************9..778******************* PP

                     Mem_trans 322 PlvmlvavlavgLrgslllvaivqaAlPqgivlfviAkeynvherelstllifgmlialpitlvy 386
                                   P+  + ++ ++ ++g  + v++v+ ++P++++  v+ ++y+++ ++ ++ +++++ ++l++++++
  gi|15669220|ref|NP_248025.1| 238 PATAFTLSELINIKGLEKNVLLVESSMPSAMMTLVLGTLYELDIKLIASSIFITTTFSLLVIALW 302
                                   **************************************************************999 PP

>> G6PD_N  Glucose-6-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.8e-05      0.25      88     126 ..      23      61 ..      16      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                        G6PD_N  88 yekLkekleeleanrlfYlavppslfeevaeklkkagla 126
                                   +  Lke+ ++  +n ++Y+a+p ++f +++++++++++ 
  gi|15669220|ref|NP_248025.1|  23 FGILKEEHAKILNNIVIYIAMPSTIFLTISKNVSSSQIL 61 
                                   5568888899899********************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1759.29
//
Query:       gi|15669221|ref|NP_248026.1|  [L=366]
Description: hypothetical protein MJ_1032 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-90  302.8  14.2    4.4e-90  302.5  14.2    1.0  1  DUF373           Domain of unknown function (DUF373)
  ------ inclusion threshold ------
        1.6    8.8   5.6        8.8    6.4   5.6    2.3  1  GWT1             GWT1
        1.9    8.1  12.4        1.9    8.1   0.9    2.8  2  DUF5058          Domain of unknown function (DUF5058)
        5.4    7.4  15.3       0.16   12.3   2.8    3.2  3  Phage_holin_5_2  Phage holin family Hol44, in holin superfami


Domain annotation for each model (and alignments):
>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.5  14.2   9.7e-94   4.4e-90       2     335 .]       9     338 ..       8     338 .. 0.95

  Alignments for each domain:
  == domain 1  score: 302.5 bits;  conditional E-value: 9.7e-94
                        DUF373   2 tLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvgvead 82 
                                   +Lvl+vD+DdD+grkag++tP++Gre++++a +kl+ladP DSDvNa++g++k+ydeLka+g+dve+a+++Gd +  ve++
  gi|15669221|ref|NP_248026.1|   9 YLVLVVDIDDDIGRKAGLNTPILGREENIKALIKLGLADPGDSDVNAILGGVKIYDELKASGKDVEIATISGDVD--VESE 87 
                                   7************************************************************************99..5666 PP

                        DUF373  83 r...kiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyll....kkalkdpelrkt 156
                                   +   +i+eq+d +l+ +++d +++VsDG+eDe++l++++s+  +++ krV+Vkqs+++Estyyl+    kk+++  e+  +
  gi|15669221|ref|NP_248026.1|  88 KcalRIKEQIDFLLYLYNPDFIYLVSDGKEDEMILKYLESKNIFVWKKRVIVKQSETLESTYYLIqefiKKTME--EYIPL 166
                                   5557*************************************************************777777777..9**** PP

                        DUF373 157 iLvplGlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvallllligiis 237
                                   iL+ +G+ l++ya+++     ++ ++i+++++Gly+l +G+g+++ll e ++  ke +  gr+  +++ +++++l+ig+i+
  gi|15669221|ref|NP_248026.1| 167 ILTFIGFSLILYAIFA-----DIGWRIVVGIIGLYILSEGVGVRKLLMEKIK-KKEEFDVGRVFPISASISIFILIIGLIY 241
                                   ***************9.....789*********************9988885.57889*********************** PP

                        DUF373 238 gyislesvssasvssglltlilafiygavewlalailtaslgkiideylkre...ekdiarllllpflvlaiglvlygasa 315
                                   +++s++++ss     +l++ i  f+ ++v+ l+l++l++++gk++d+++++e    + +++++++++++++ + ++++  +
  gi|15669221|ref|NP_248026.1| 242 SLSSINKTSS-----TLTEFIGEFLLHFVDSLTLSLLILMVGKFVDTIINSEkdlLEILKKYFFCLICIFISRELIISGGE 317
                                   *999777666.....88999999**************************99999999999********************* PP

                        DUF373 316 ylls.lsilalslvvgivval 335
                                   yll+ +s+++++++v+i++++
  gi|15669221|ref|NP_248026.1| 318 YLLKkISFIMFVMCVIIYISI 338
                                   **999************9986 PP

>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   5.6     0.002       8.8      34     117 ..     216     355 ..     109     365 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.002
                          GWT1  34 e.................................................eee...........kkkkkkkkesketlkll 54 
                                   e                                                   +           k  ++  +++k++l++l
  gi|15669221|ref|NP_248026.1| 216 EefdvgrvfpisasisifiliigliyslssinktsstltefigefllhfvD-SltlsllilmvgKFVDTIINSEKDLLEIL 295
                                   245555555555555555555555554444444444555555555544440.04455556666655566678899999999 PP

                          GWT1  55 ikllllsilllllllllelyvefvSRrlaNlpYvlwvvalnltllllfl.liellfvekeeeke 117
                                   +k +++ i++++   l+ +  e+  +++  + +v+ v+ +  ++++l++ l+ +    +++e++
  gi|15669221|ref|NP_248026.1| 296 KKYFFCLICIFISRELIISGGEYLLKKISFIMFVMCVIIYISIVIILSViLFTK----SSKEDK 355
                                   999999999999999999999998888888888888777777777666634444....222222 PP

>> DUF5058  Domain of unknown function (DUF5058)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.9   0.00042       1.9      22      70 ..     195     243 ..     174     249 .. 0.78
   2 ?    5.7   2.6    0.0024        11       2      32 ..     324     355 ..     323     365 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00042
                       DUF5058  22 lflrkalkaakelglskeklkkaikssaifsIgPslailivviaLiavl 70 
                                   l++ +      +l ++k k k+ + ++ +f I  s++i+i +i+Li +l
  gi|15669221|ref|NP_248026.1| 195 LYILSEGVGVRKLLMEKIKKKEEFDVGRVFPISASISIFILIIGLIYSL 243
                                   55555555566778999999*************************9886 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0024
                       DUF5058   2 spvlwllagiv.vlivlvqavlflrkalkaak 32 
                                   s +++++++i+ ++iv++++v+ + k+ k+ k
  gi|15669221|ref|NP_248026.1| 324 SFIMFVMCVIIyISIVIILSVILFTKSSKEDK 355
                                   56899888654399*******99999988766 PP

>> Phage_holin_5_2  Phage holin family Hol44, in holin superfamily V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.8   3.6e-05      0.16       6      48 ..     150     189 ..     147     204 .. 0.72
   2 ?   -1.0   0.1      0.51   2.3e+03      23      35 ..     230     242 ..     212     260 .. 0.69
   3 ?    1.6   1.9     0.079   3.5e+02      11      44 ..     319     352 ..     313     366 .] 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
               Phage_holin_5_2   6 yiiGeilKktekvkdkyIPlilgiiGiilgvvivftadfqaed 48 
                                   y+i e++Kkt    ++yIPlil++iG  l + ++f+++   + 
  gi|15669221|ref|NP_248026.1| 150 YLIQEFIKKTM---EEYIPLILTFIGFSLILYAIFADIGWRIV 189
                                   89999999995...9***********99985555555333333 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.51
               Phage_holin_5_2  23 IPlilgiiGiilg 35 
                                   I + ++iiG+i +
  gi|15669221|ref|NP_248026.1| 230 ISIFILIIGLIYS 242
                                   4445555555554 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.079
               Phage_holin_5_2  11 ilKktekvkdkyIPlilgiiGiilgvvivfta.df 44 
                                    lKk++ +   + ++i + i iil+ vi+ft+ + 
  gi|15669221|ref|NP_248026.1| 319 LLKKISFIMFVMCVIIYISIVIILS-VILFTKsSK 352
                                   6888888888888888888889999.666664233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1239  (0.0691059); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 1952.29
//
Query:       gi|15669222|ref|NP_248027.1|  [L=317]
Description: magnesium and cobalt transport protein CorA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-65  219.3   7.2    7.4e-65  219.1   7.2    1.0  1  CorA          CorA-like Mg2+ transporter protein
  ------ inclusion threshold ------
      0.086   12.9   0.7      0.086   12.9   0.7    1.9  2  Internalin_N  Bacterial adhesion/invasion protein N terminal
       0.73   10.3   6.5        1.5    9.2   6.5    1.5  1  DUF4212       Domain of unknown function (DUF4212)
        1.6    7.4   5.2        2.3    6.9   4.2    1.3  1  DUF2207       Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.1   7.2   1.7e-68   7.4e-65       4     292 .]      28     313 ..      25     313 .. 0.93

  Alignments for each domain:
  == domain 1  score: 219.1 bits;  conditional E-value: 1.7e-68
                          CorA   4 fvWldlsspteeeleeLaeelgldelaledlldseerprvedyddylllvlpsveldkseeeeeevplsillgdnflitvr 84 
                                   ++W+d+++p++eel +L+++ g+   +l+  ld++e prve +d+ ++l+++  +l +++  +  ++l+i++++n+l+t++
  gi|15669222|ref|NP_248027.1|  28 LIWIDCYDPKDEELYKLSKKIGISVSDLQIGLDEQEIPRVE-EDEDFYLIIYKAPLFEEDITT--TSLGIYIKNNLLLTIH 105
                                   79**********************9999999**********.566666666655555555553..4569************ PP

                          CorA  85 replealdevikrlk...deggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvk 162
                                   +++++a+  ++k ++   ++    +  g lly++l+ei+ ++ ++l +le+el+eled l    ++e +++++ lr++lv+
  gi|15669222|ref|NP_248027.1| 106 SDKIKAIGRLHKLIStkkPRIVFERGIGFLLYHILNEITRSYSRILMNLEDELEELEDKLLAGYDREVMEKILGLRKTLVY 186
                                   *******88888888655666778999****************************************************** PP

                          CorA 163 lrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtyssllserlNrvmkvLTvltai 243
                                   ++++l +nr+vl  ll+++  +  ++ed+e+++dl+ ++ +l++m+ ++re+l+s++d+  sl + ++N++mk+LT++t+i
  gi|15669222|ref|NP_248027.1| 187 FHKSLIANRDVL-VLLKRKYLPITTKEDRENFEDLYYDTLQLIDMSATYREVLTSMMDITLSLENIKMNQIMKILTMVTTI 266
                                   ************.99999*************************************************************** PP

                          CorA 244 f.lPlTlitGiyGmNfkglPelewsygypfvlllglmallailllfwfkr 292
                                   f +P + itGiyGmNf +lP ++++   +f+l+++lm+++ ++ ++ f+r
  gi|15669222|ref|NP_248027.1| 267 FaVP-MWITGIYGMNFSYLPLANNPQ--GFWLVMALMVVIIMIFVYIFRR 313
                                   ****.88*******************..88988***************98 PP

>> Internalin_N  Bacterial adhesion/invasion protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.7   1.9e-05     0.086       2      30 ..     252     280 ..     251     284 .. 0.91
   2 ?   -3.9   1.5       3.6   1.6e+04      13      19 ..     299     305 ..     294     311 .. 0.41

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                                   X.....XXXXXXXXXXXXXXXXXXXXXXX CS
                  Internalin_N   2 kknsvlKklltvtlvLllsllvltsnGek 30 
                                   k n+++K+l++vt+++++ ++++ + G++
  gi|15669222|ref|NP_248027.1| 252 KMNQIMKILTMVTTIFAVPMWITGIYGMN 280
                                   6799*******************999976 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.6
                                   XXXXXXX CS
                  Internalin_N  13 vtlvLll 19 
                                   +++v+++
  gi|15669222|ref|NP_248027.1| 299 LMVVIIM 305
                                   2333322 PP

>> DUF4212  Domain of unknown function (DUF4212)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   6.5   0.00034       1.5       7      69 ..     255     313 ..     252     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00034
                       DUF4212   7 enlrlililLviWfvvsfglgillaeelntirtflgfplgFwfaaqgsilvfvvlifvYalrm 69 
                                   + ++++ ++ +i++v ++++g ++  +++ +  +++ p gFw++   +++v++++ifvY+ r+
  gi|15669222|ref|NP_248027.1| 255 QIMKILTMVTTIFAVPMWITG-IYGMNFSYL-PLANNPQGFWLV--MALMVVIIMIFVYIFRR 313
                                   567788888899999999955.666777777.6**********7..6899999******9875 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.2   0.00051       2.3     375     431 ..     252     313 ..     193     315 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00051
                       DUF2207 375 kgkkklkklsalglgliilglilillallllvll.....lvfllilllillliaiivlllfs 431
                                   k ++++k+l ++ +++++ ++i +++++ + +l        f+l+++l++++i+i+v+++ +
  gi|15669222|ref|NP_248027.1| 252 KMNQIMKILTMVTTIFAVPMWITGIYGMNFSYLPlannpQGFWLVMALMVVIIMIFVYIFRR 313
                                   33567777777778888888877777754444448998899999999999999999999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1385  (0.0772491); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 1865.70
//
Query:       gi|15669223|ref|NP_248028.1|  [L=87]
Description: signal recognition particle subunit SRP19 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-23   83.2   0.5    2.2e-23   83.0   0.5    1.1  1  SRP19        SRP19 protein
  ------ inclusion threshold ------
      0.036   14.4   0.3       0.11   12.8   0.3    2.0  1  LAGLIDADG_3  LAGLIDADG-like domain
      0.069   13.1   0.0      0.079   12.9   0.0    1.0  1  JAKMIP_CC3   JAKMIP CC3 domain


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.5   3.7e-27   2.2e-23       1      92 [.       2      84 ..       2      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 3.7e-27
                                  EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSS.TTCCEEEEEC-..........SS-CHH CS
                         SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrd.wanpGrVrvklkedgkevnekiknkke 82
                                  +i+P Y+d+kk+r+eGR+vp+ela+e+P++++i +alk+lgle ++ ++k+yPr+ w   G+V v++k           nk +
  gi|15669223|ref|NP_248028.1|  2 IIWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQhWEICGCVEVDYK----------GNKLQ 74
                                  7******************************************************77777******94..........79999 PP

                                  HHHHHHHHHH CS
                         SRP19 83 llkkiaellk 92
                                  llk+i++ +k
  gi|15669223|ref|NP_248028.1| 75 LLKEICKIIK 84
                                  9999999997 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   1.9e-05      0.11      34      58 ..      28      52 ..       7      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                                  HHHHHHHHHHHHHCT.HSCEEEEEE CS
                   LAGLIDADG_3 34 kelledvqrlLlrlGIestiyekkk 58
                                  k  l+d+ + L++lG+e +iy++k+
  gi|15669223|ref|NP_248028.1| 28 KPSLKDIEKALKKLGLEPKIYRDKR 52
                                  56799******************32 PP

>> JAKMIP_CC3  JAKMIP CC3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.3e-05     0.079     102     172 ..       9      79 ..       5      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                    JAKMIP_CC3 102 daerelkareqleselrktkskikdLeeaLaqkGqdskwveekQalikrnqeLvekikk.leeeeskLkqei 172
                                   d  +  ++  ++ +el   k  +kd+e+aL++ G + k   +k  + +++ e+   ++   + ++ +L +ei
  gi|15669223|ref|NP_248028.1|   9 DKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKR-YPRQHWEICGCVEVdYKGNKLQLLKEI 79 
                                   66777788888999****************************99.999999988888742566777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 511.51
//
Query:       gi|15669224|ref|NP_248029.1|  [L=277]
Description: F420-dependent methylenetetrahydromethanopterin dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.6e-140  464.9   7.0   8.6e-140  464.8   7.0    1.0  1  MTD              methylene-5,6,7,8-tetrahydromethanopterin de
  ------ inclusion threshold ------
      0.011   15.9   0.4      0.035   14.3   0.1    1.9  2  Bac_DNA_binding  Bacterial DNA-binding protein


Domain annotation for each model (and alignments):
>> MTD  methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.8   7.0  9.6e-144  8.6e-140       1     274 []       3     277 .]       3     277 .] 0.99

  Alignments for each domain:
  == domain 1  score: 464.8 bits;  conditional E-value: 9.6e-144
                                   EEEEEEEES--HHHHHTTGGGSTTS--SSEEEEEEEEET--SHHHHHHHHHH.HHHH--SEEEEE-S-TTSHHHHHHHHHH CS
                           MTD   1 vkigiiklGnigtslvidlllDeradRedievrvvgsgaklkkeeveevvek.lkefdpdlvivisPnaaapgptkarell 80 
                                   vkigiik+Gnig+s+v+dl+lDeradR+di vrv+gsgak+++e+veev++k ++e++pd++i+i+Pn+aapgp+kare+l
  gi|15669224|ref|NP_248029.1|   3 VKIGIIKCGNIGMSPVVDLALDERADRKDIAVRVLGSGAKMDPESVEEVTKKmVEEVKPDFIIYIGPNPAAPGPKKAREIL 83 
                                   79************************************************994589************************* PP

                                   HHSSS-EEEEEEGGGGGGHHHHHHTT-EEEEETTS------TTT--HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH CS
                           MTD  81 sekdvpaivisDapgkkekdeleeeglGYiivkaDpliGarrefLDptemalfnadvlkvLaatGavRlvqeeldkviekv 161
                                   s++++pa++i+Dapg ++kde+e++glGYii+k+Dp+iGarrefLDp+emalfnadv++vLa tGa+R+vqe++dk+i++v
  gi|15669224|ref|NP_248029.1|  84 SQSGIPAVIIGDAPGLRVKDEMEQQGLGYIIIKCDPMIGARREFLDPVEMALFNADVIRVLAGTGALRIVQEAIDKMIDAV 164
                                   ********************************************************************************* PP

                                   TTT-GGGS-EEEESGGGGGGSS--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT---HHHHHHHHHHHHHHHHHHHHHHHHH CS
                           MTD 162 kagkeielPkividaekaveaaefsnPYakakalaayeiaekvadidvkaCfmekelekyilivasahellraaakLadea 242
                                   k+gkeielPkivi+++kavea+ef+nPYakaka+aa++iaekv+d+dvk+Cfm+ke+ekyi+ivasahe++r+aakL+dea
  gi|15669224|ref|NP_248029.1| 165 KEGKEIELPKIVITEQKAVEAMEFTNPYAKAKAMAAFTIAEKVGDVDVKGCFMTKEAEKYIPIVASAHEMIRYAAKLVDEA 245
                                   ********************************************************************************* PP

                                   HHHHHHTT---B--B-TTSSB--BSSTTS--- CS
                           MTD 243 ReieksndtvlRkphakdGkvlsktkllekPe 274
                                   Re+ek++d+v+Rkph+ +Gk lsk++l+ekPe
  gi|15669224|ref|NP_248029.1| 246 RELEKAMDAVSRKPHHPEGKRLSKKALMEKPE 277
                                   *******************************8 PP

>> Bac_DNA_binding  Bacterial DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.4   3.6e+03      14      32 ..      41      59 ..      28      62 .. 0.59
   2 ?   14.3   0.1   3.9e-06     0.035      21      67 ..     149     195 ..     143     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.4
                                  ----HHHHHHHHHHHHHHH CS
               Bac_DNA_binding 14 tgltkkdakrvveafldti 32
                                  +++  +++++v + +++++
  gi|15669224|ref|NP_248029.1| 41 AKMDPESVEEVTKKMVEEV 59
                                  3467777777777776665 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.9e-06
                                   HHHHHHHHHHHHHHHHHTT-EEEETTTEEEEEEEE--BS-B-TTT-- CS
               Bac_DNA_binding  21 akrvveafldtikeaLkkgekvelsgFGtfkvkerkartgrnpkTge 67 
                                   a r+v++ +d +++a+k+g+++el+++   + k+++a +  np  + 
  gi|15669224|ref|NP_248029.1| 149 ALRIVQEAIDKMIDAVKEGKEIELPKIVITEQKAVEAMEFTNPYAKA 195
                                   5689*********************************9999997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1681.83
//
Query:       gi|15669225|ref|NP_248030.1|  [L=233]
Description: hypothetical protein MJ_1036 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-22   78.7  21.8    5.9e-20   71.8   6.5    2.2  2  Zip       ZIP Zinc transporter
  ------ inclusion threshold ------
        0.8    9.4   7.7        1.8    8.3   7.7    1.6  1  PTPLA     Protein tyrosine phosphatase-like protein, PTPLA
        6.4    5.6  21.3        2.2    7.1   7.5    2.1  2  MFS_1     Major Facilitator Superfamily
        9.4    6.1   0.0        9.4    6.1   0.0    4.2  5  LapA_dom  Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   6.2   3.7e-06     0.017       5      99 ..      10      84 ..       6     103 .. 0.86
   2 !   71.8   6.5   1.3e-23   5.9e-20     184     333 .]     101     231 ..      91     231 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-06
                           Zip  5 ilaiiaililsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealealeesqleeehthplagllvllGfl 87
                                  ++ai++++++++  ll  + v++++k+        + a++ G ++g a l L+P+++               +  l+v+lG++
  gi|15669225|ref|NP_248030.1| 10 FIAILSFIVMCIGELLAYYSVSLKYKY-------EFEAISFGFIFGVATLILIPKSYS-------------NMFVLYVILGMI 72
                                  578888888888888888888888877.......789********************9.............899********* PP

                           Zip 88 llllveklltmi 99
                                  +++l+ek+l ++
  gi|15669225|ref|NP_248030.1| 73 TVYLIEKYLAYC 84
                                  *********997 PP

  == domain 2  score: 71.8 bits;  conditional E-value: 1.3e-23
                           Zip 184 vraiilllglilHsfidGLAlGvssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnllfaltaplGiliGi 264
                                    + +i+ +++++H fidGL ++vs  s+ g++l++A+l+H+lp+++ l+++L     +     +  ++++++++lG+++G+
  gi|15669225|ref|NP_248030.1| 101 RIKFIYPISFFIHTFIDGLIIAVSYISEIGLPLYLAILMHKLPAGFVLISPLKGVYKNPL---YPGVFVSFGTVLGTIVGL 178
                                   5678999*********************************************98876655...5569************** PP

                           Zip 265 lvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGfalmllla 333
                                   +       + ++++++illa+s+G+fl  a+  l p ++ ++k       + + +l++llG++l+ ++a
  gi|15669225|ref|NP_248030.1| 179 V-------TLKDVSTKILLAFSGGVFL-GAFLMLAP-HIYEHK-------EEKTFLYILLGYILVGIIA 231
                                   *.......9******************.89999999.666666.......7899*********999986 PP

>> PTPLA  Protein tyrosine phosphatase-like protein, PTPLA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   7.7    0.0004       1.8      54     154 ..      24     126 ..       8     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0004
                         PTPLA  54 lllaWsvtEviRYsfyalkl..slgkvpklltwlRYtlfivLYPlGvasElvliyaalpvlkeskklsielpnklnfsfsy 132
                                   ll  +sv+   +Y f a++   + g +  +l    Y+  +vLY +  +  + li + l + + skk+++e  n  +  +++
  gi|15669225|ref|NP_248030.1|  24 LLAYYSVSLKYKYEFEAISFgfIFGVATLILIPKSYSNMFVLYVILGMITVYLIEKYLAYCPLSKKYCVECDNLEENRIKF 104
                                   5677888889999****999864477777888889**********9999************************99999999 PP

                         PTPLA 133 kyflllllllyvpglyvlythm 154
                                    y + +++ +++ gl++ ++++
  gi|15669225|ref|NP_248030.1| 105 IYPISFFIHTFIDGLIIAVSYI 126
                                   9999999999999999999886 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   5.8    0.0029        13     244     312 ..       5      71 ..       1      83 [. 0.72
   2 ?    7.1   7.5   0.00049       2.2     222     312 ..     123     229 ..      98     232 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0029
                         MFS_1 244 llaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGf 312
                                   +++ +++a+l++++++++ l++++s  l+ +     + ++++++++ l+l++ + s++++l+  v++G+
  gi|15669225|ref|NP_248030.1|   5 VEVPIFIAILSFIVMCIGELLAYYSVSLKYKYEFEAISFGFIFGVATLILIPKSYSNMFVLY--VILGM 71 
                                   56778888888888888888888888888888888888888888888888888844444433..44444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00049
                         MFS_1 222 gfsglltllplylqevlgls...........glllaglllallalvgailallagrlsdr.lgrrrrlllallllllaalg 290
                                   + ++  + lplyl   ++             g++ + l+++++  +g +l+ ++g +  + ++    +lla+++++++ ++
  gi|15669225|ref|NP_248030.1| 123 VSYISEIGLPLYLAILMHKLpagfvlisplkGVYKNPLYPGVFVSFGTVLGTIVGLVTLKdVST--KILLAFSGGVFLGAF 201
                                   4444666777777666666667788999999999999999999999999999999999772444..555555555555555 PP

                         MFS_1 291 lallavt......ssavllllvlvliGf 312
                                   l+l++++      ++ + +ll+++l+G+
  gi|15669225|ref|NP_248030.1| 202 LMLAPHIyehkeeKTFLYILLGYILVGI 229
                                   5555555578874444444447777777 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.14   6.4e+02      20      36 ..      12      28 ..       3      37 .. 0.62
   2 ?   -2.6   0.2       1.1   4.9e+03      29      37 ..      43      51 ..      39      56 .. 0.50
   3 ?   -0.7   0.2      0.29   1.3e+03      13      25 ..     127     139 ..     120     149 .. 0.75
   4 ?   -2.3   0.9      0.94   4.2e+03      25      40 ..     164     179 ..     163     182 .. 0.74
   5 ?    6.1   0.0    0.0021       9.4      20      39 ..     185     204 ..     183     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.14
                      LapA_dom 20 sllllvafgiGallgwl 36
                                  ++l ++++ iG ll++ 
  gi|15669225|ref|NP_248030.1| 12 AILSFIVMCIGELLAYY 28
                                  34445777777777765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                      LapA_dom 29 iGallgwll 37
                                  +G+++g+ +
  gi|15669225|ref|NP_248030.1| 43 FGFIFGVAT 51
                                  444444433 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.29
                      LapA_dom  13 aqvelpLsllllv 25 
                                   +++ lpL+l +l+
  gi|15669225|ref|NP_248030.1| 127 SEIGLPLYLAILM 139
                                   4557899999885 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.94
                      LapA_dom  25 vafgiGallgwllslw 40 
                                   v++ +G +lg +++l+
  gi|15669225|ref|NP_248030.1| 164 VFVSFGTVLGTIVGLV 179
                                   5677888888888875 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.0021
                      LapA_dom  20 sllllvafgiGallgwllsl 39 
                                   s+ +l+af  G++lg +l+l
  gi|15669225|ref|NP_248030.1| 185 STKILLAFSGGVFLGAFLML 204
                                   6679**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1382.60
//
Query:       gi|15669226|ref|NP_248031.1|  [L=404]
Description: tryptophan synthase subunit beta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-50  172.5   0.3    1.8e-50  172.0   0.3    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.0   0.3     1e-54   1.8e-50       4     294 .]      64     387 ..      62     387 .. 0.81

  Alignments for each domain:
  == domain 1  score: 172.0 bits;  conditional E-value: 1e-54
                                   CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHH.HHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEE CS
                          PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgae.yllarlkegtgaktvveassGNhgralAaaaallGlkvti 83 
                                   + +pTPl  ++rls+elg++++lK+E+l ++g++K++ a   +l++ k g ++++++e+++G+hg+a+Aaa+a+lGl+++i
  gi|15669226|ref|NP_248031.1|  64 VGRPTPLYYAERLSEELGCKVYLKREDLAHLGAHKINNALgQALLAKKMG-KKRVIAETGAGQHGVATAAACAKLGLECII 143
                                   679*************************************6666666777.999999************************ PP

                                   EEETTS-...HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHH.....STTCEE--TTT..SHH...HHHHHHTHHHHHH CS
                          PALP  84 vvpadas...pekvallrllGaevvevggdydeavaaaaelaae.....gegaylvsqfd..npt...viegygtiglEil 151
                                   ++ a++    + +v +++l+Ga+v+ v g+ ++ ++a++e++++      + +yl+ +    +p+   v e +  ig E++
  gi|15669226|ref|NP_248031.1| 144 YMGAKDVerqKLNVFRMELMGAKVIPVFGGSQTLKDAVNEALRDwttnvRTTYYLLGSALgpHPYpmmVREFQRVIGKELK 224
                                   *******555599**************999999999999999998888755555555555464446645555********9 PP

                                   ....HHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEEC....TTCGGTTCC.........S..S.SS..B... CS
                          PALP 152 ....eqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepe....gsdalarsl.........ragrrvtvpvs.. 213
                                       e+ g+ pd++v++vGgG+++ G    + +   dv++++ve+     +    ++sl                   +  
  gi|15669226|ref|NP_248031.1| 225 eqilEKEGRLPDVIVACVGGGSNAIGAFYEFLD--DDVELYAVEAGgkgiETGMHGASLcagevgvlhG---------Aki 294
                                   54456666*************998887777775..6899****98855333333333334444455440.........355 PP

                                   .............SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHC CS
                          PALP 214 .............dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreage 281
                                                 +i  gl+ + ++++   l d+   ++v v+d+ealea +ll+r egi++   s +ala +  + a +
  gi|15669226|ref|NP_248031.1| 295 yvkedefgqieesYSISAGLDYPGVGPELSFLKDEGRIKAVCVTDDEALEAFQLLCRLEGILPALESSHALAYA-VKLADK 374
                                   55555566666559*********7777777788999999***********************************.****** PP

                                   CTTCEEEEEEE-B CS
                          PALP 282 lkegdrvvviltg 294
                                   l+++d +v+ l+g
  gi|15669226|ref|NP_248031.1| 375 LDKDDIMVINLSG 387
                                   ****888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.49
# Mc/sec: 2461.74
//
Query:       gi|15669227|ref|NP_248032.1|  [L=284]
Description: tryptophan synthase subunit alpha TrpA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-94  315.2   0.6    2.5e-94  315.0   0.6    1.0  1  Trp_syntA       Tryptophan synthase alpha chain
    2.4e-06   27.2   0.1    1.5e-05   24.6   0.1    2.0  2  His_biosynth    Histidine biosynthesis protein
    9.6e-05   21.9   2.0    0.00034   20.1   1.0    2.1  2  PcrB            PcrB family
    0.00025   20.6   0.1    0.00049   19.6   0.1    1.6  1  BtpA            BtpA family
  ------ inclusion threshold ------
      0.016   15.5   1.4        1.8    8.9   0.1    2.9  3  PIN_9           PIN like domain
      0.027   13.8   0.1      0.071   12.5   0.1    1.7  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
       0.48   11.1   4.3       0.61   10.8   2.2    2.2  2  PBECR1          phage-Barnase-EndoU-ColicinE5/D-RelE like nuc


Domain annotation for each model (and alignments):
>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.0   0.6   9.8e-98   2.5e-94       1     255 [.      12     271 ..      12     275 .. 0.94

  Alignments for each domain:
  == domain 1  score: 315.0 bits;  conditional E-value: 9.8e-98
                                   HHHHHCTTB-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHH CS
                     Trp_syntA   1 faklkaenraafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveev 81 
                                   f++lk+++++afv++ + gdp+le s ++l+ + k  ad++E+G+pfsdP+adG +Iq+a++raL++g+++ k++el +++
  gi|15669227|ref|NP_248032.1|  12 FEELKNKGEKAFVAFYVGGDPNLEISEKALEVICK-HADIVEIGIPFSDPVADGITIQKADVRALNSGMNPLKAFELAKKL 91 
                                   7899****************************999.9******************************************** PP

                                   HHHCSSS-EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH CS
                     Trp_syntA  82 rkkevevPivlltylnlvlsygeerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkevveq 162
                                   ++k ++vP v+lty+n+++++gee+f++++keagv g+ivpDlP eea++l +++kk+g++l+flvaptt+derlk+++e+
  gi|15669227|ref|NP_248032.1|  92 NEKAPNVPKVFLTYYNIIFKMGEEEFVKKCKEAGVSGIIVPDLPIEEADSLYNYCKKYGVDLIFLVAPTTPDERLKKILEK 172
                                   ********************************************************************************* PP

                                   --S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHHHHHHHC......TT CS
                     Trp_syntA 163 aegfvYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistkeqvkqvakvadGvivGSalvkkiee......ea 237
                                    +gfvYvvs++G+Tga+++va+e++el++r+kk+++ P+ vGFGis++e+v++++++adG+ivGSa+vk++e+      ++
  gi|15669227|ref|NP_248032.1| 173 CSGFVYVVSVTGITGAREKVAEETKELIKRVKKFSKIPACVGFGISKREHVEEITEIADGAIVGSAIVKIVEKhldengQI 253
                                   ************************************************************************955554445 PP

                                   TSHHHHHHHHHHHHHHHH CS
                     Trp_syntA 238 eekeqalekleelarelk 255
                                   +++e+ l++lee++++lk
  gi|15669227|ref|NP_248032.1| 254 KDEEKFLKELEEFVKNLK 271
                                   555555666666666665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.24     6e+02      87     120 ..     117     150 ..     111     157 .. 0.61
   2 !   24.6   0.1   5.9e-09   1.5e-05      48     108 ..     182     242 ..     160     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.24
                                   HHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHC CS
                  His_biosynth  87 dveelleagadkviigtaavknpelikelaekfg 120
                                    v++  eag++ +i+    +++ + + + ++k+g
  gi|15669227|ref|NP_248032.1| 117 FVKKCKEAGVSGIIVPDLPIEEADSLYNYCKKYG 150
                                   3455556666666666666666666666666666 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 5.9e-09
                                   EEEHHHHCTT.HHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH- CS
                  His_biosynth  48 vvDldaakeg.reanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavkn 108
                                   v  +++a+e+  e+ ++l++++ +  +ip +vG GI++ e+vee+ e+ ad  i+g+a vk 
  gi|15669227|ref|NP_248032.1| 182 VTGITGAREKvAEETKELIKRVKKFSKIPACVGFGISKREHVEEITEI-ADGAIVGSAIVKI 242
                                   45577777651456679******************************9.*********9985 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.2   5.1e+02     173     208 ..      14      54 ..       6      61 .. 0.59
   2 !   20.1   1.0   1.3e-07   0.00034     162     221 ..     186     249 ..     176     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.2
                                   HHHHHHSSSEE.EEESS...--SHHHHHHHHCC.SSEEEE- CS
                          PcrB 173 alkkklekarl.ivGGG...irsaEkAkevvea.ADvivvG 208
                                   +lk+k eka + ++ GG   ++ +EkA ev+ + AD++ +G
  gi|15669227|ref|NP_248032.1|  14 ELKNKGEKAFVaFYVGGdpnLEISEKALEVICKhADIVEIG 54 
                                   55555555533244444233555677777765558877665 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.3e-07
                                   TTSSS-H.HHHHHHHHHH...SSSEEEEESS--SHHHHHHHHCCSSEEEE-CHHHHHHHCHHHH CS
                          PcrB 162 sGaledv.eevialkkkl...ekarlivGGGirsaEkAkevveaADvivvGnvveekderkida 221
                                    Ga e+v ee+++l k++   +k+   vG Gi ++E+ +e+ e AD  +vG ++ +  e+++d+
  gi|15669227|ref|NP_248032.1| 186 TGAREKVaEETKELIKRVkkfSKIPACVGFGISKREHVEEITEIADGAIVGSAIVKIVEKHLDE 249
                                   578888888877776555111667788**************************98887777765 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   1.9e-07   0.00049     176     232 ..     180     241 ..     151     257 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.9e-07
                          BtpA 176 vilsGkatGgev....dleelklaketvkvkvlvgsGvse.enlekllsiadGvivgtsikk 232
                                   v ++G +   e       e +k++k+  k++  vg G+s+ e +e++ +iadG ivg+ i k
  gi|15669227|ref|NP_248032.1| 180 VSVTGITGAREKvaeeTKELIKRVKKFSKIPACVGFGISKrEHVEEITEIADGAIVGSAIVK 241
                                   55566554443301103456788999999********986378***************9865 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.5   3.9e+03      93     106 ..     160     173 ..     129     180 .. 0.69
   2 ?    8.9   0.1   0.00069       1.8      35      84 ..     190     238 ..     186     247 .. 0.92
   3 ?    4.1   0.4     0.022        56      36      60 ..     258     282 ..     239     283 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                         PIN_9  93 vTnDreLkkrllek 106
                                   +T D  Lkk l++ 
  gi|15669227|ref|NP_248032.1| 160 TTPDERLKKILEKC 173
                                   47788888877765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00069
                         PIN_9  35 kavleELerlakagkgkertaakvalsLaerceiveaeeekaDdailela 84 
                                   ++v eE ++l k+ k+ ++  a v+  +++r ++ e++ e aD ai+  a
  gi|15669227|ref|NP_248032.1| 190 EKVAEETKELIKRVKKFSKIPACVGFGISKREHVEEIT-EIADGAIVGSA 238
                                   689*********************************99.99**9998765 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.022
                         PIN_9  36 avleELerlakagkgkertaakval 60 
                                   + l+ELe+ +k+ k+ ++++akva 
  gi|15669227|ref|NP_248032.1| 258 KFLKELEEFVKNLKEGTKKKAKVAI 282
                                   6799*******************97 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3   3.3e+03      96     113 ..      10      27 ..       5      52 .. 0.66
   2 ?   12.5   0.1   2.8e-05     0.071      71     197 ..     116     239 ..     107     240 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                                   HHHHHHHHTTSEEEEEE- CS
                Ribul_P_3_epim  96 rtiqeikeaGakaglvln 113
                                   +  +e+k++G ka +++ 
  gi|15669227|ref|NP_248032.1|  10 EKFEELKNKGEKAFVAFY 27 
                                   556677888888887773 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.8e-05
                                   HCHHHHHHCT-SEEEEE-ST-TTHHHHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-S.EEEEESS-TT-SS----CCHH CS
                Ribul_P_3_epim  71 rivpefaeagasiisvHaEalehlkrtiqeikeaGakaglvlnpatplealeyllekld.lvllmsvePgfgGQkFipevl 150
                                   ++v++  eag s i v    +e+ + + +  k+ G+  +  + p+tp e l+++lek+  +v + sv     G +  ++v 
  gi|15669227|ref|NP_248032.1| 116 EFVKKCKEAGVSGIIVPDLPIEEADSLYNYCKKYGVDLIFLVAPTTPDERLKKILEKCSgFVYVVSVTG-ITGAR--EKVA 193
                                   5667777777777777767788888899999**************************963788999875.55543..3444 PP

                                   HHHHHHHHHHHHHT---EEEEESS--TTT.CHHHHHHT--EEEESHHH CS
                Ribul_P_3_epim 151 ekikkvrklidekeldlkievDGGvkldn.ieqiaeagadvlVagsav 197
                                   e+ k++ k++++   ++   v  G+++   +e+i+ + ad  ++gsa+
  gi|15669227|ref|NP_248032.1| 194 EETKELIKRVKK-FSKIPACVGFGISKREhVEEIT-EIADGAIVGSAI 239
                                   444444444443.3335666777776544044444.667777777776 PP

>> PBECR1  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.3   3.2e+03      29      61 ..     167     204 ..     163     227 .. 0.63
   2 ?   10.8   2.2   0.00024      0.61      28      67 ..     239     278 ..     228     284 .] 0.75

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                        PBECR1  29 ahilekhledfkefk......ekaeklinkleeiiekgk 61 
                                   ++ilek +  f  +          ek++++ +e i++ k
  gi|15669227|ref|NP_248032.1| 167 KKILEKCS-GFVYVVsvtgitGAREKVAEETKELIKRVK 204
                                   56666653.333222344552333777777777777665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00024
                        PBECR1  28 Lahilekhledfkefkekaeklinkleeiiekgk.vkeeee 67 
                                   + +i+ekhl++   + +++ek+ ++lee +++ k  ++++ 
  gi|15669227|ref|NP_248032.1| 239 IVKIVEKHLDEN-GQIKDEEKFLKELEEFVKNLKeGTKKKA 278
                                   789*****9555.66677899***********995333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1192  (0.0664845); expected 358.6 (0.02)
Passed bias filter:                      737  (0.0411066); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1761.92
//
Query:       gi|15669228|ref|NP_248033.1|  [L=78]
Description: DNA-directed RNA polymerase subunit H [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-31  107.7   2.1    2.2e-31  107.5   2.1    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
  ------ inclusion threshold ------
      0.072   13.0   0.1       0.09   12.7   0.1    1.1  1  MinC_N          Septum formation inhibitor MinC, N-terminal d


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   2.1   2.4e-35   2.2e-31       1      73 []       1      73 [.       1      73 [. 0.99

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 2.4e-35
                                  ..-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                RNA_pol_Rpb5_C  1 vnitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                  +++t+H lvPkhe++ +ee++e+lk+++ik +qLPki+++Dpv++++g+k+Gdvv+++rks+tag +++YRlV
  gi|15669228|ref|NP_248033.1|  1 MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQLPKIYEDDPVIQEIGAKEGDVVRVIRKSPTAGVSIAYRLV 73
                                  689*********************************************************************9 PP

>> MinC_N  Septum formation inhibitor MinC, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     1e-05      0.09      22      59 ..      17      54 ..      11      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
                        MinC_N 22 tsdlerikqkLsdkiaeaPklfknapvvldvskleekv 59
                                  ++++e+i +  + ki++ Pk++++ pv+ ++ + e++v
  gi|15669228|ref|NP_248033.1| 17 KEEVEEILKRYNIKIQQLPKIYEDDPVIQEIGAKEGDV 54
                                  568999**********************9998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 494.26
//
Query:       gi|15669229|ref|NP_248034.1|  [L=498]
Description: DNA-directed RNA polymerase subunit beta'' [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-56  189.3   0.0    6.6e-56  189.0   0.0    1.1  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    1.9e-26   92.9   0.0    2.9e-26   92.3   0.0    1.3  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    4.8e-26   90.7   0.0    8.9e-26   89.9   0.0    1.5  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.0   0.0   1.1e-59   6.6e-56       1     202 [.      16     392 ..      16     393 .. 0.99

  Alignments for each domain:
  == domain 1  score: 189.0 bits;  conditional E-value: 1.1e-59
                                   CTTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBXEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb2_1   1 gLvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltYsapl 81 
                                   gL+  q++S+n+fve++l+kii+e   ie+e         +++k+++i++gkPv++e+d+s r i+P+ear+r+ltYs pl
  gi|15669229|ref|NP_248034.1|  16 GLIDHQIESYNDFVENRLQKIIDEVGYIETEITG-----GYKVKLGKIKVGKPVIKEADGSIRPITPMEARIRDLTYSVPL 91 
                                   58899**********************9998885.....5***************************************** PP

                                   EEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE....... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                RNA_pol_Rpb2_1  82 yvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqek....... 155
                                   y++++ ++ e ++ +e +  evyiGelP+Ml sk c+l+++s eel++l+E+p+d+ GyFiinGtekv++ qe+       
  gi|15669229|ref|NP_248034.1|  92 YLEMTPIIGEGEDAREGETVEVYIGELPVMLGSKICHLYGKSREELIDLGEDPEDPFGYFIINGTEKVLITQEDlipnril 172
                                   *********999********************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                RNA_pol_Rpb2_1 156 ................................................................................. 155
                                                                                                                    
  gi|15669229|ref|NP_248034.1| 173 cekaersgkivdvakvfstrhgfralctverhpdgllyatfpgmpgqiplvilmkalgaetdkdiiesidderffmeivln 253
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                RNA_pol_Rpb2_1 156 ................................................................................. 155
                                                                                                                    
  gi|15669229|ref|NP_248034.1| 254 iqeireehninspedalefigkrvapgqakdyrlkraetvlcnyllphlgvtkedfpkkirflgimarnalelyfgyrged 334
                                   ********************************************************************************* PP

                                   ...........XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHH CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb2_1 156 ...........laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpit 202
                                              laG+L+++lfr ++ +l++d+k +l+++  ++++ + q++v+++ +t
  gi|15669229|ref|NP_248034.1| 335 dkdhyaykrakLAGDLMEDLFRYAFSQLVKDIKYQLERQTLRNKTPSIQAAVRSDILT 392
                                   ******************************************************9887 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.0   4.8e-30   2.9e-26       3     188 ..     169     343 ..     167     345 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 4.8e-30
                                   SCEEEEE-SSSSSE..SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSSTTHH CS
                RNA_pol_Rpb2_2   3 ngiyvekekdknki..satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericydsedsq 81 
                                   n+i++ek ++  ki  +a+v s+++  r++ ++++  ++ l++t +    +ip+vi++kAlg  +d++I e+i  d+  + 
  gi|15669229|ref|NP_248034.1| 169 NRILCEKAERSGKIvdVAKVFSTRHGFRALCTVERHPDGLLYATFPGMPGQIPLVILMKALGAETDKDIIESID-DERFFM 248
                                   99************999********************************************************9.677777 PP

                                   HHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH..HHHHHH CS
                RNA_pol_Rpb2_2  82 lleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenkrlkaqdil 162
                                    + +  +e  e+++i + e+al++igk+va ++ +  rl++a+ +l          ++ l+ hlg+ ++ + k  k ++++
  gi|15669229|ref|NP_248034.1| 249 EIVLNIQEIREEHNINSPEDALEFIGKRVAPGQAKDYRLKRAETVL---------CNYLLP-HLGVTKEDFPK--KIRFLG 317
                                   7888889999999********************************9.........589999.******98888..****** PP

                                   HHHHHHHHHHTTSSSS--TTSGGGEE CS
                RNA_pol_Rpb2_2 163 ymidrLlslklgrrevDDiDhlgnkR 188
                                   +m++  l+l +g r +DD+Dh++ kR
  gi|15669229|ref|NP_248034.1| 318 IMARNALELYFGYRGEDDKDHYAYKR 343
                                   ************************99 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.0   1.5e-29   8.9e-26       1      68 []     413     477 ..     413     477 .. 0.99

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 1.5e-29
                RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                   q+ldr+++l++ s+lrr+ s+   ls+++ ++e+R+lh +hwG iCp+eTPEG+ncGlvk++a++++v
  gi|15669229|ref|NP_248034.1| 413 QLLDRTSYLATNSQLRRIVSP---LSRSQPHFEARELHGTHWGKICPSETPEGPNCGLVKNFAIMCKV 477
                                   89*******************...******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3246.93
//
Query:       gi|15669230|ref|NP_248035.1|  [L=636]
Description: DNA-directed RNA polymerase subunit B' [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.6e-132  441.1   0.0   4.8e-132  440.7   0.0    1.2  1  RNA_pol_Rpb2_6   RNA polymerase Rpb2, domain 6
    7.4e-28   96.8   0.0    1.4e-27   95.9   0.0    1.5  1  RNA_pol_Rpb2_7   RNA polymerase Rpb2, domain 7
      4e-22   78.3   0.1    8.9e-22   77.2   0.1    1.6  1  RNA_pol_Rpb2_4   RNA polymerase Rpb2, domain 4
    1.8e-12   47.6   3.9    3.4e-12   46.7   2.6    2.3  2  RNA_pol_Rpb2_5   RNA polymerase Rpb2, domain 5
     0.0013   19.0   0.2      0.007   16.6   0.1    2.3  2  RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domai
  ------ inclusion threshold ------
      0.035   14.4   0.1       0.34   11.2   0.0    2.4  2  PAS_9            PAS domain
       0.54    9.9   2.8       0.66    9.6   0.0    2.1  1  RecR             RecR protein
        1.2    8.9   3.8        2.1    8.1   3.8    1.4  1  A2L_zn_ribbon    A2L zinc ribbon domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.7   0.0  2.2e-135  4.8e-132       2     390 .]     141     512 ..     140     512 .. 0.96

  Alignments for each domain:
  == domain 1  score: 440.7 bits;  conditional E-value: 2.2e-135
                                   HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SEEEEE CS
                RNA_pol_Rpb2_6   2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalGqnav 82 
                                   a +ap++eh+++pri++ aam+kq+lgi   n   r++++ + l+++q P+v+t+ + e+++        +++ ++Gqn+v
  gi|15669230|ref|NP_248035.1| 141 AGVAPYPEHNSAPRITMAAAMGKQSLGIPMSNIKWRLDTRGHYLHYPQVPIVRTK-HQEILG--------FDKRPAGQNFV 212
                                   7789***************************************************.999999........*********** PP

                                   BBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.....-SS-GGGS-TTSB--SS-EE CS
                RNA_pol_Rpb2_6  83 VAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.....seealkkLdedGivrvgaev 158
                                   VA+msyeGYn+EDai++n++++dr++ +s+++++y+   r++++g+ + ++ +++      see +++L+edGiv v+++v
  gi|15669230|ref|NP_248035.1| 213 VAIMSYEGYNMEDAIVFNKSAIDRGLGRSTFFRTYDACERRYPGGQMDRFEIPDKGvrgyrSEECYRYLEEDGIVAVESHV 293
                                   **********************************88888*******776766666589*********************** PP

                                   ETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT--EEEEEEEEEEE- CS
                RNA_pol_Rpb2_6 159 kegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvnklvkvyvaqkRk 239
                                   k gd++vgk+  ++ ++ +e    ++i+++ + + +d+s+ v++geeg++dkv++       ++++++n+lvkv+v++ R 
  gi|15669230|ref|NP_248035.1| 294 KGGDVIVGKT--SPPRFLEE----HEITIQVKPQRRDSSVVVRHGEEGYIDKVIL-------TETKEGNRLVKVKVRDLRI 361
                                   *********8..88888844....456677777889*******************.......89999************** PP

                                   --TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSSS--B--TT-...-HH CS
                RNA_pol_Rpb2_6 240 lqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaalegkkvdatvFdgakeee 320
                                   +++GDKfasrhGqKGv++l++pqeD+Pf+e+Giv+Di++NP+++PSRmt+gqllE+l gk++aleg+++d+t+F+g+ke +
  gi|15669230|ref|NP_248035.1| 362 PELGDKFASRHGQKGVMGLTVPQEDLPFTESGIVPDIIINPHAIPSRMTVGQLLEMLGGKVGALEGRRIDGTIFSGEKEWD 442
                                   ********************************************************************************* PP

                                   HHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT--B-SCGGG CS
                RNA_pol_Rpb2_6 321 ikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpyslltqQPlgGkaq 390
                                   ++++Le  g++++Gkev+ydG tG+k+e ei++G+ Yy+kL+hlv+ KihaRs+Gp+++lt+QP++G+a+
  gi|15669230|ref|NP_248035.1| 443 LRKALEALGFKHHGKEVMYDGKTGKKFEVEIYIGIAYYQKLHHLVAGKIHARSRGPVQVLTRQPTEGRAR 512
                                   ********************************************************************96 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.0   6.4e-31   1.4e-27       1      85 [.     514     610 ..     514     612 .. 0.88

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 6.4e-31
                                   BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTT......CSSSEEEEEEEHHHH CS
                RNA_pol_Rpb2_7   1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivk......seekiekveipeafk 69 
                                   GGlrfGEMErd+li++Gaa+lLkerl+++SD +++ +c++c+ +a+ +      +C+i+       s++ki  v+ip+afk
  gi|15669230|ref|NP_248035.1| 514 GGLRFGEMERDVLIGHGAAMLLKERLMDESDPYDICICSKCGDFAILDykrglkYCPICGeienlySSKKIPFVRIPYAFK 594
                                   9*********************************************999*****777776111121567778899****** PP

                                   HHHHHHHHTTBEEEEE CS
                RNA_pol_Rpb2_7  70 lLlqeLqslgialkll 85 
                                   lLl+eL+s++i ++++
  gi|15669230|ref|NP_248035.1| 595 LLLDELKSMCILPRIK 610
                                   ***********99986 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.1     4e-25   8.9e-22       1      62 []      11      72 ..      11      72 .. 0.99

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 4e-25
                                  EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE-S CS
                RNA_pol_Rpb2_4  1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiVe 62
                                  ++vNG+l+G+t++p++lv+ +Re RRkg++++ +++++ne+ + ++i+tD+GR++RPli+Ve
  gi|15669230|ref|NP_248035.1| 11 IYVNGKLVGTTDKPEELVNFIREKRRKGELPQYTTVAYNEESNDIHINTDAGRIVRPLIVVE 72
                                  7************************************************************7 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   2.6   1.5e-15   3.4e-12       1      58 []      93     133 ..      93     133 .. 0.95
   2 ?   -3.8   0.0         8   1.8e+04      17      33 ..     310     326 ..     310     336 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.5e-15
                                   HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEES-G CS
                RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcEIhP 58 
                                   ++dL++egv+EylDaeEEe+a+Ia+++e+l+++                 +TH+EI+P
  gi|15669230|ref|NP_248035.1|  93 FSDLVKEGVIEYLDAEEEENAYIALSEEELTEK-----------------HTHLEIDP 133
                                   89****************************776.................79999999 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8
                                   HHTT--EESSTTTCSST CS
                RNA_pol_Rpb2_5  17 EEetamIamtpedleks 33 
                                   EE+ + I ++p+  ++s
  gi|15669230|ref|NP_248035.1| 310 EEHEITIQVKPQRRDSS 326
                                   89999999999876665 PP

>> RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   3.1e-06     0.007      11      37 ..     101     127 ..      77     133 .. 0.88
   2 ?   -2.8   0.0       3.6   8.1e+03      37      55 ..     485     503 ..     480     505 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.1e-06
                                   EEEEEEHHHHTTSEEE-SSS-BETTSC CS
               RNA_pol_Rpb2_45  11 evvYLtAdeEekyviAqAnapldeegr 37 
                                    ++YL A+eEe+ +iA ++++l e+ +
  gi|15669230|ref|NP_248035.1| 101 VIEYLDAEEEENAYIALSEEELTEKHT 127
                                   58********************99865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.6
                                   CBSSSEEEEECSSCEEEEE CS
               RNA_pol_Rpb2_45  37 rfveerVlaRrkgevelve 55 
                                   ++v  +++aR +g v++ +
  gi|15669230|ref|NP_248035.1| 485 HLVAGKIHARSRGPVQVLT 503
                                   7788999***999888766 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.52   1.2e+03      42      82 ..      19      61 ..       9      73 .. 0.76
   2 ?   11.2   0.0   0.00015      0.34      19      82 ..     413     475 ..     412     483 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.52
                         PAS_9 42 tdpeanerlraaleqgrk..kerevevvlirkngetfwvllta 82
                                  +  +  e+l ++++++r+  +  ++++v ++++ + ++++  a
  gi|15669230|ref|NP_248035.1| 19 GTTDKPEELVNFIREKRRkgELPQYTTVAYNEESNDIHINTDA 61
                                  5567778888888888888878888888888888888876655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00015
                         PAS_9  19 aalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvllta 82 
                                   ++l++lG +  ++ g++i+ ++ ++ e + +lr+ale++  k + +ev +  k+g++f v++ +
  gi|15669230|ref|NP_248035.1| 413 QLLEMLGGKVGALEGRRIDGTI-FSGEKEWDLRKALEALGFKHHGKEVMYDGKTGKKFEVEIYI 475
                                   679*******************.*****************99*****************99876 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0003      0.66       8      25 ..     558     575 ..     557     578 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0003
                                   HHHHHHHH-EE-TTT--E CS
                          RecR   8 aLqeakekvrhCsrCgnl 25 
                                   a+ + k+++++C++Cg +
  gi|15669230|ref|NP_248035.1| 558 AILDYKRGLKYCPICGEI 575
                                   79999**********977 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.8   0.00095       2.1       4      30 ..     549     575 ..     547     578 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00095
                 A2L_zn_ribbon   4 kvCsvCggngilnseqgylvCieCgas 30 
                                    +Cs+Cg + il  ++g  +C+ Cg +
  gi|15669230|ref|NP_248035.1| 549 CICSKCGDFAILDYKRGLKYCPICGEI 575
                                   58**********************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.50
# Mc/sec: 3801.60
//
Query:       gi|15669231|ref|NP_248036.1|  [L=1341]
Description: DNA-directed RNA polymerase subunit alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.9e-108  361.2   0.0   1.4e-107  359.7   0.0    1.8  1  RNA_pol_Rpb1_1   RNA polymerase Rpb1, domain 1
    1.1e-65  220.9   0.6    6.1e-48  163.2   0.1    3.3  3  RNA_pol_Rpb1_2   RNA polymerase Rpb1, domain 2
    2.5e-36  125.0   0.5    5.3e-35  120.7   0.0    2.9  3  RNA_pol_Rpb1_3   RNA polymerase Rpb1, domain 3
    1.3e-32  111.9   0.0    3.7e-32  110.5   0.0    1.8  1  RNA_pol_Rpb1_4   RNA polymerase Rpb1, domain 4
    3.3e-26   92.3   0.0    3.3e-26   92.3   0.0    2.0  1  RNA_pol_Rpb1_5   RNA polymerase Rpb1, domain 5
    1.5e-15   57.3   2.8    1.5e-15   57.3   2.8    3.2  4  Intein_splicing  Intein splicing domain
    7.7e-05   22.9   2.5    0.00015   22.0   0.6    2.6  2  LAGLIDADG_3      LAGLIDADG-like domain
     0.0063   16.6   1.2        3.6    7.7   0.1    3.9  4  MqsA_antitoxin   Antitoxin component of bacterial toxin-antit
  ------ inclusion threshold ------
      0.026   14.8   0.3       0.12   12.7   0.0    2.3  2  KIX              KIX domain
      0.072   13.0   0.1         14    5.7   0.0    2.8  2  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial a
       0.15   11.5   1.7       0.36   10.2   1.7    1.6  1  DUF3552          Domain of unknown function (DUF3552)
       0.38   11.2   0.0       0.38   11.2   0.0    3.8  3  HMA              Heavy-metal-associated domain
       0.53   10.5   3.4         29    5.0   0.1    3.0  2  zf-RING_7        C4-type zinc ribbon domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.7   0.0    1e-110  1.4e-107       2     312 .]       8     316 ..       7     316 .. 0.94

  Alignments for each domain:
  == domain 1  score: 359.7 bits;  conditional E-value: 1e-110
                                   E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPvfh 82 
                                   k+i ei fg++sp+ ir++Sv+++ +++t++e+   P +gGl+D rlg+id  l C+tCg    eC+ghfGhieLakPv+h
  gi|15669231|ref|NP_248036.1|   8 KEIGEIMFGLLSPDYIRQMSVAKIVTPDTYDEDG-YPIDGGLMDTRLGVIDPGLVCKTCGGRIGECPGHFGHIELAKPVIH 87 
                                   8999****************************95.9********************************************* PP

                                   HHHHHHHHHHCTTCETTTTEBSS-TTSH.....HHHHHHCSSSCC.CCHHHHHHHHCCS-BE-SSSSB-EEEEEETTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1  83 igffklilkilecvckecskllldeekkkll.sklkkrekleelk.krlkaieelckkinlcekCgavqpkleeegeklka 161
                                   igf k+i+kil+ vc +c+++ ++e k+k + +k++k e+   +k + ++++ +  +k+++c +Cg ++  ++ e+ + + 
  gi|15669231|ref|NP_248036.1|  88 IGFAKTIYKILKAVCPHCGRVAISETKRKEIlEKMEKLERDGGNKwEVCEEVYKEASKVTICPHCGEIKYDIKFEKPTTYY 168
                                   ************************9987544044443333322224899*****************999888888888888 PP

                                   EESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1 162 alkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDlteklrdii 242
                                   +++ ++e   ++l++++v+++l++i+ded+ +lg++++ +rPew++ltvlPVpP+++RPs++l++g+rsedDlt+kl+dii
  gi|15669231|ref|NP_248036.1| 169 RIDGNEE---KTLTPSDVREILEKIPDEDCILLGLNPEVARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDII 246
                                   8888888...9********************************************************************** PP

                                   HHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1 243 krNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrfRgnL 312
                                   ++NnrL++++e gap+liie+ ++lLQ+hv+t+fdne +g++pa+++s+rplk+l qrLkGKeGrfR nL
  gi|15669231|ref|NP_248036.1| 247 RINNRLEENIEGGAPNLIIEDLWNLLQYHVNTYFDNEAPGIPPAKHRSGRPLKTLAQRLKGKEGRFRYNL 316
                                   *********************************************************************8 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.45   6.2e+02      40     119 ..     115     214 ..     106     226 .. 0.77
   2 !  163.2   0.1   4.4e-51   6.1e-48       1     134 [.     318     460 ..     318     465 .. 0.88
   3 !   52.9   0.1   3.5e-17   4.8e-14     133     166 .]     911     944 ..     904     944 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.45
                                   STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-S.CHHCCTTTTS...................EEEEE--TTSE CS
                RNA_pol_Rpb1_2  40 telnikklrklvengpevyPgasyvkredgsekklkakkr.klakelekgd...................iverhvkdgdv 100
                                    + + +k++kl + g +++  ++ v +e  +++   ++ + k + + ek +                    + +++ d+d 
  gi|15669231|ref|NP_248036.1| 115 RKEILEKMEKLERDGGNKWEVCEEVYKEASKVTICPHCGEiKYDIKFEKPTtyyridgneektltpsdvrEILEKIPDEDC 195
                                   566778899999999999999999988888888888776656666666655788888888888888888888899999999 PP

                                   EEEE-SSTTSGGGEEEEEE CS
                RNA_pol_Rpb1_2 101 vllNRqPsLhklsimahrv 119
                                   +ll  +P   +   m+ +v
  gi|15669231|ref|NP_248036.1| 196 ILLGLNPEVARPEWMVLTV 214
                                   9999999888887776655 PP

  == domain 2  score: 163.2 bits;  conditional E-value: 4.4e-51
                                   SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEEST......TSSEEETT CS
                RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkre......dgsekklk 75 
                                   Gkrv++s+R+vispdp l+++evgvP +vak ltvpe+vt++ni+++r+l +ng+e++Pg +yv+r+      +++e k+k
  gi|15669231|ref|NP_248036.1| 318 GKRVNFSSRTVISPDPCLSINEVGVPEVVAKELTVPEKVTKYNIERIRQLLRNGSEKHPGVNYVIRKmigrdgTEQEYKVK 398
                                   9**************************************************************966423332233444444 PP

                                   TT-SC...HHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGH CS
                RNA_pol_Rpb1_2  76 akkrk...lakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvt 134
                                    ++++    a+++++gdiverh++dgd+vl NRqPsLh++simahrv+vl+++t+r nl+v+
  gi|15669231|ref|NP_248036.1| 399 ITESNkdfWAENIREGDIVERHLMDGDIVLYNRQPSLHRMSIMAHRVRVLPYRTFRHNLCVC 460
                                   444323458999*************************************************9 PP

  == domain 3  score: 52.9 bits;  conditional E-value: 3.5e-17
                                   GHCCCT--SSS-EEEEE--SSHHHHHHHHHCSBT CS
                RNA_pol_Rpb1_2 133 vttayNaDFDGDemnlhlpqseearaEaeelllv 166
                                   ++ +yNaDFDGDemnlh+pqseearaEae+l+lv
  gi|15669231|ref|NP_248036.1| 911 NCPPYNADFDGDEMNLHVPQSEEARAEAEALMLV 944
                                   89*****************************986 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.9   2.7e+03      88     121 ..     562     595 ..     534     617 .. 0.71
   2 ?    0.7   0.2      0.34   4.6e+02      88     135 ..     851     904 ..     788     910 .. 0.77
   3 !  120.7   0.0   3.9e-38   5.3e-35       1     156 [.     947    1110 ..     947    1111 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.9
                                   S..STSEEECSSEEEES--SHHHHSSSSTTSHHHHH CS
                RNA_pol_Rpb1_3  88 k..dgkvlikngelikGvidkkvvgkksqgslihvl 121
                                      d++ +i ++e+ik vi  ++ g + ++++i++l
  gi|15669231|ref|NP_248036.1| 562 MfeDDNRVIVDEEKIKKVIN-NIGG-TYKNKIINEL 595
                                   13356666667777777776.4444.7777777766 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.34
                                   S........STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHH CS
                RNA_pol_Rpb1_3  88 k........dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfld 135
                                   k          + +ik++ l +G++++k+v    ++  ++++++   i et +f+ 
  gi|15669231|ref|NP_248036.1| 851 KlenntkfiTFDKFIKEKCLKNGFVKEKIVS--IEETKVDYVYDITTISETHNFIA 904
                                   144444556567899999999********98..55677899999999999988875 PP

  == domain 3  score: 120.7 bits;  conditional E-value: 3.9e-38
                                    CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESS.SEBEEHHHHHHCCCHCC CS
                RNA_pol_Rpb1_3    1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkp.kelwtgkqtfsrilpne 78  
                                    +ilsp+ g P+ig ++D+++G+yllT +  +++++ea  +l++g  +    ++++p+ + + ++l++gk +fs+ lp+ 
  gi|15669231|ref|NP_248036.1|  947 HILSPRFGGPIIGAIHDFISGAYLLTSN--YFTKDEATLILRSGGIK---DELWEPDKVENgVPLYSGKKIFSKALPKG 1020
                                    7***************************..9*************887...567999999999****************5 PP

                                    CCEEEE.....SSSS..........STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHH CS
                RNA_pol_Rpb1_3   79 inyerk.....neek..........dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgf 142 
                                    +n++ k     +             d +v+ik+gelikGvidk+ +g ++ g ++h+++ke+g+++ ++flds +++++
  gi|15669231|ref|NP_248036.1| 1021 LNLRYKakicrK--CdvckkeeceyDAYVVIKDGELIKGVIDKNGYG-AEAGLILHTIVKEFGPEAGRKFLDSATKMAI 1096
                                    555554433332..03355577888**********************.899**************************** PP

                                    HHHHHHCEB-TGGG CS
                RNA_pol_Rpb1_3  143 kyllqsgftigigD 156 
                                    + ++ +gft+gi+D
  gi|15669231|ref|NP_248036.1| 1097 RAVMLRGFTTGIDD 1110
                                    *************9 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   0.0   2.7e-35   3.7e-32       1     108 []    1136    1242 ..    1136    1242 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 2.7e-35
                                    HHHHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBT CS
                RNA_pol_Rpb1_4    1 ieeaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnve 79  
                                    ie++er g+le lpg +lee+ ea i+++l++ardkag ia+++l  +N+ +iM+ +Ga+G+i+n++q+a+clGqq+v+
  gi|15669231|ref|NP_248036.1| 1136 IEKYER-GELELLPGLNLEESREAYISNVLREARDKAGAIAERYLGLDNHAVIMAVTGARGNILNLTQMAACLGQQSVR 1213
                                    78999*.***************************************66******************************* PP

                                    TBSS--SSTSCSSTTSSSSESSTTTSSEE CS
                RNA_pol_Rpb1_4   80 gkripkgfsgrtlphfkkidespesrGFv 108 
                                    gkri++g++gr+lphf+k d +++s+GFv
  gi|15669231|ref|NP_248036.1| 1214 GKRIFRGYRGRVLPHFEKGDLGARSHGFV 1242
                                    ****************************8 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.0   2.4e-29   3.3e-26       1      73 [.    1249    1325 ..    1249    1332 .. 0.91

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 2.4e-29
                                    B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS....B--TT-B CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx RF
                RNA_pol_Rpb1_5    1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg....lvepGea 73  
                                    GL+++efffh+mggReGL+D Av+Ta+sGY+qRrl++al+d+  + d+tvr+s g ++qf+ygedg    l + G+a
  gi|15669231|ref|NP_248036.1| 1249 GLSPTEFFFHAMGGREGLVDQAVRTAQSGYMQRRLINALQDLKTEFDGTVRDSRGIMIQFKYGEDGidpmLADRGKA 1325
                                    9****************************************************************966655555555 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.77   1.1e+03      10      38 ..     120     155 ..     109     189 .. 0.64
   2 ?   -2.1   0.0       2.4   3.3e+03     103     103 ..     383     383 ..     330     428 .. 0.50
   3 !   57.3   2.8   1.1e-18   1.5e-15       5     132 ..     470     909 ..     466     911 .. 0.96
   4 ?   -2.2   0.1       2.7   3.8e+03       6      26 ..    1127    1146 ..    1123    1176 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.77
                                   EEHHHHCCECTTEEEEEETTTTEEEEEE........E CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx........x RF
               Intein_splicing  10 vkieelvekegeevlslnledlklevks........v 38 
                                    k+e+l e++g +++++ +e +k+  k         +
  gi|15669231|ref|NP_248036.1| 120 EKMEKL-ERDGGNKWEVCEEVYKEASKVticphcgeI 155
                                   466666.79******9998777766554433333333 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                                   E CS
                                   x RF
               Intein_splicing 103 k 103
                                   +
  gi|15669231|ref|NP_248036.1| 383 R 383
                                   1 PP

  == domain 3  score: 57.3 bits;  conditional E-value: 1.1e-18
                                   TTCEEEEHHHHCCECTTEEEEEETTTTEEEEEEEEEEEEEEEE....EEEEEEETTS-EEEEETT-EEEECCTTEEEEEEC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing   5 dgeekvkieelvekegeevlslnledlklevksvkkliklklk....elyeiklesgrkikaTpeHkllvvrdegivEkra 81 
                                   dg+   ki++l e++ + v +l  +dl+ +  s +k +kl+      ++y+ik+e gr+i+aT +H++ ++  +g   kr 
  gi|15669231|ref|NP_248036.1| 470 DGKL-IKIKDL-EDKWKDVKVLTSDDLNPKLTSLSKYWKLNADeygkKIYKIKTELGREIIATEDHPFYTT--NGR--KRC 544
                                   5444.489999.557778888999***************98766778************************..888..9** PP

                                   CC--TT-EEEEE..................................................................... CS
                                   xxxxxxxxxxxx..................................................................... RF
               Intein_splicing  82 deLkegdliavp..................................................................... 93 
                                    eLk+gd +++                                                                      
  gi|15669231|ref|NP_248036.1| 545 GELKVGDEVIIYpndfpmfeddnrvivdeekikkvinniggtyknkiinelkdrklipltyndqkasilarivghvmgdgs 625
                                   *******998878******************************************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669231|ref|NP_248036.1| 626 liinnknsrvvfrgdiedlktikedlkelgydgeeiklhegeteitdyngkkriikgkgysfevrkkslcillkalgcvgg 706
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669231|ref|NP_248036.1| 707 dktkkmygipnwiktapkyikkeflsayfgselttpkirnhgtsfkelsfkiakieeifdedrfikdikemlkefgielkv 787
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669231|ref|NP_248036.1| 788 rveegnlrkdgyktkvyvasiynhkeffgrigytyankketlaryayeylltkekylkdrnikklenntkfitfdkfikek 868
                                   ********************************************************************************* PP

                                   ..HSCEEEEEEEEEEEEECEEEEEEEE.ETTT-EEEECTTEE CS
                                   ..xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
               Intein_splicing  94 ..dadvvwdkvksievedeeeyVYdlt.vednhNFvangiiv 132
                                     ++  v +k++sie+++  +yVYd+t + ++hNF+ang++ 
  gi|15669231|ref|NP_248036.1| 869 clKNGFVKEKIVSIEETKV-DYVYDITtISETHNFIANGFLT 909
                                   *98889********98876.56***963789********986 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 2.7
                                    TCEEEEHHHHCCECTTEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing    6 geekvkieelvekegeevlsl 26  
                                    + e+ k++e++ek+++ +l+l
  gi|15669231|ref|NP_248036.1| 1127 EAEE-KVKEIIEKYERGELEL 1146
                                    3444.8999999888887765 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       8.7   1.2e+04       8      28 ..     617     636 ..     611     651 .. 0.69
   2 !   22.0   0.6   1.1e-07   0.00015       3      83 .]     727     819 ..     726     839 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 8.7
                                   HHHHHHCCECCECSTTTTSEE CS
                   LAGLIDADG_3   8 rGlfdaDGsvskskkkgvsis 28 
                                    G   +DGs   ++k+++ + 
  gi|15669231|ref|NP_248036.1| 617 VGHVMGDGSLIINNKNSR-VV 636
                                   556668888877776644.44 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.1e-07
                                   HHHHHHHHHHHCCECCECSTTTTS...EEEEES-.......HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCC..ECCCHC CS
                   LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvs...isltsss.......kelledvqrlLlrlGIestiyekkkakgrgvy..rlliis 71 
                                   k++fL+++f ++ +  k +++g+s   +s++ ++        ++++d++++L+++GIe +++ +  + +++ y  ++ + s
  gi|15669231|ref|NP_248036.1| 727 KKEFLSAYFGSELTTPKIRNHGTSfkeLSFKIAKieeifdeDRFIKDIKEMLKEFGIELKVRVEEGNLRKDGYktKVYVAS 807
                                   679********************9*99999999999****************************44444444444455555 PP

                                   HCTTCGGGTTTX CS
                   LAGLIDADG_3  72 genlkrFlekig 83 
                                     n k F+ +ig
  gi|15669231|ref|NP_248036.1| 808 IYNHKEFFGRIG 819
                                   566666666665 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0026       3.6      26      63 ..      91     128 ..      77     148 .. 0.85
   2 ?   -0.4   0.1      0.81   1.1e+03      31      47 ..     143     159 ..     133     171 .. 0.75
   3 ?   -1.9   0.0       2.3   3.2e+03      13      60 ..     596     643 ..     587     656 .. 0.69
   4 ?    4.2   0.0     0.033        45       7      91 ..    1050    1135 ..    1045    1145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0026
                MqsA_antitoxin  26 ktvikavtgdfCarCGegvldeeeedrlseellefrkk 63 
                                     +i ++    C++CG + ++e + +++ e++ ++++ 
  gi|15669231|ref|NP_248036.1|  91 AKTIYKILKAVCPHCGRVAISETKRKEILEKMEKLERD 128
                                   56788999999**********************99986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.81
                MqsA_antitoxin  31 avtgdfCarCGegvlde 47 
                                   a +   C++CGe  +d 
  gi|15669231|ref|NP_248036.1| 143 ASKVTICPHCGEIKYDI 159
                                   556678*****998876 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.3
                MqsA_antitoxin  13 rdtrdvpytykgektvikavtgdfCarCGegvldeeeedrlseellef 60 
                                   +d++ +p+ty+ +k+ i a    +    G  ++++++++ + +   e 
  gi|15669231|ref|NP_248036.1| 596 KDRKLIPLTYNDQKASILARIVGHVMGDGSLIINNKNSRVVFRGDIED 643
                                   56666899**99998887766667777787787777777776655555 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.033
                MqsA_antitoxin    7 gkaelvrdtrdvpytykgek.tvikavtgdfCarCGegvldeeeedrlseel.lefrkkvnaelvdpafiarvrkklel 83  
                                     ++el++++ d    y +e  ++++++  +f ++ G  +ld++ +  + + + + f   ++ e    + ++++ k l+ 
  gi|15669231|ref|NP_248036.1| 1050 KDGELIKGVIDKN-GYGAEAgLILHTIVKEFGPEAGRKFLDSATKMAIRAVMlRGFTTGIDDEDLPEEALKEIEKVLDE 1127
                                    5678888888865.666665278899*****************988887765267999999999999999999999988 PP

                MqsA_antitoxin   84 dqreaaei 91  
                                    + ++++ei
  gi|15669231|ref|NP_248036.1| 1128 AEEKVKEI 1135
                                    87777776 PP

>> KIX  KIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.6e-05      0.12      19      70 ..      94     145 ..      91     149 .. 0.95
   2 ?   -2.5   0.1       4.7   6.5e+03      69      79 ..     513     523 ..     499     524 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.6e-05
                           KIX  19 vdKlvkaifPapdqealnDkRmeelieyarkvEkeafekakdrdeYYhllae 70 
                                   + K+ ka+ P+    a+ + + +e+ e+++k+E++  +k + ++e Y+++++
  gi|15669231|ref|NP_248036.1|  94 IYKILKAVCPHCGRVAISETKRKEILEKMEKLERDGGNKWEVCEEVYKEASK 145
                                   88***********************************************987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
                           KIX  69 aekiyklqKel 79 
                                    +kiyk++ el
  gi|15669231|ref|NP_248036.1| 513 GKKIYKIKTEL 523
                                   579****9887 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0      0.01        14      19      39 ..     409     429 ..     405     434 .. 0.87
   2 ?    4.0   0.0     0.036        50      20      33 ..     546     559 ..     544     559 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.01
                                   CCEECTCEEEEEECTTCCCCC CS
                MazE_antitoxin  19 lgireGdevelevdgdkiilr 39 
                                    +ireGd ve + ++++i+l+
  gi|15669231|ref|NP_248036.1| 409 ENIREGDIVERHLMDGDIVLY 429
                                   59*************999987 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.036
                                   CEECTCEEEEEECT CS
                MazE_antitoxin  20 gireGdevelevdg 33 
                                   ++++Gdev++++++
  gi|15669231|ref|NP_248036.1| 546 ELKVGDEVIIYPND 559
                                   6899*******975 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.7   0.00026      0.36     112     168 ..    1115    1172 ..    1111    1178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00026
                       DUF3552  112 ekelkqkeqsleekeeeleelvee.qrqeLerisgLtkeeAkeilleeveeelkheaA 168 
                                    e+ lk+ e+ l+e ee+++e++e+ +r eLe + gL+ ee +e  +++v +e++  a+
  gi|15669231|ref|NP_248036.1| 1115 EEALKEIEKVLDEAEEKVKEIIEKyERGELELLPGLNLEESREAYISNVLREARDKAG 1172
                                    6788999999***********9884678***********************9987665 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       4.9   6.8e+03      46      60 ..     112     126 ..     108     128 .. 0.72
   2 ?   -0.6   0.0       1.4   1.9e+03      40      59 ..     170     190 ..     165     192 .. 0.83
   3 ?   11.2   0.0   0.00028      0.38      30      62 .]     627     657 ..     617     657 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.9
                           HMA  46 stklrkiieaiekag 60 
                                   +tk ++i+e++ek+ 
  gi|15669231|ref|NP_248036.1| 112 ETKRKEILEKMEKLE 126
                                   455577******986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                           HMA  40 Vegdaes.tklrkiieaieka 59 
                                   ++g++e+ +++++++e +ek+
  gi|15669231|ref|NP_248036.1| 170 IDGNEEKtLTPSDVREILEKI 190
                                   899999999998888888875 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00028
                           HMA  30 kvdlatktvtVegdaestklrkiieaiekagyk 62 
                                    +++++++v+++gd+e+  l++i+e ++++gy+
  gi|15669231|ref|NP_248036.1| 627 IINNKNSRVVFRGDIED--LKTIKEDLKELGYD 657
                                   589**************..599*********96 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.021        29      25      31 ..     101     107 ..      97     108 .. 0.88
   2 ?    4.9   0.6     0.022        30      18      30 ..     141     153 ..     134     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.021
                                   E-TTT-- CS
                     zf-RING_7  25 tCpeCGR 31 
                                    Cp+CGR
  gi|15669231|ref|NP_248036.1| 101 VCPHCGR 107
                                   5*****9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.022
                                   CCSTB-EE-TTT- CS
                     zf-RING_7  18 ragdevvtCpeCG 30 
                                   + + +v  Cp+CG
  gi|15669231|ref|NP_248036.1| 141 KEASKVTICPHCG 153
                                   455789******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1352  (0.0754086); expected 358.6 (0.02)
Passed bias filter:                      891  (0.049696); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 1.06u 0.33s 00:00:01.39 Elapsed: 00:00:00.51
# Mc/sec: 7980.04
//
Query:       gi|15669232|ref|NP_248037.1|  [L=859]
Description: DNA-directed RNA polymerase subunit A [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-49  168.7   7.1    1.4e-39  136.2   1.3    2.8  3  RNA_pol_Rpb1_5   RNA polymerase Rpb1, domain 5
    1.1e-23   83.3   3.9    1.9e-16   60.1   0.2    3.2  2  LAGLIDADG_3      LAGLIDADG-like domain
    2.4e-22   79.3   1.9    2.4e-22   79.3   1.9    2.0  2  Intein_splicing  Intein splicing domain
    9.1e-05   22.6   1.5       0.58   10.4   0.0    3.6  3  Hom_end          Homing endonuclease
    0.00073   19.6   0.7       0.73    9.9   0.1    3.3  2  LAGLIDADG_WhiA   WhiA LAGLIDADG-like domain
  ------ inclusion threshold ------
      0.043   13.1   0.0      0.079   12.3   0.0    1.3  1  LIX1             Limb expression 1
       0.05   11.3   0.1      0.071   10.8   0.1    1.1  1  ACR_tran         AcrB/AcrD/AcrF family
       0.13   12.1   0.1         16    5.4   0.0    3.1  2  RACo_linker      RACo linker region
        2.4    8.4   7.4        2.7    8.3   0.2    3.9  5  Bac_DNA_binding  Bacterial DNA-binding protein


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   5.3e-12   1.1e-08      66      91 ..      36      77 ..       3      78 .. 0.73
   2 ?   -2.0   0.2      0.94   1.9e+03     118     151 ..     382     460 ..     357     530 .. 0.46
   3 !  136.2   1.3   6.9e-43   1.4e-39      87     263 ..     544     795 ..     543     799 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 5.3e-12
                                  S................B--TT-BHHHHHHHHHHHHHHCCCS CS
                                  x................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5 66 g................lvepGeavGiiaaQSiGePgTQltl 91
                                  +                lvep eavGi+aaQSiGePgTQ+ l
  gi|15669232|ref|NP_248037.1| 36 EmvdeiidevvnayrkaLVEPYEAVGIVAAQSIGEPGTQMSL 77
                                  045555555555555569**********************87 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.94
                                   -SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSE..............................................C CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............................................x RF
                RNA_pol_Rpb1_5 118 skniksksltvllvdeeakelekakkvkkaiek..............................................g 151
                                   s + k+k+  vl+++++++++ +  +++ ++ek                                              +
  gi|15669232|ref|NP_248037.1| 382 SIKTKTKNQFVLIIPHRYAKKFH-EEINFSVEKkkselerlvsslnddktydsidmipsigdaltklgekvdypkvilkK 460
                                   55556666666666665333333.33333444412233334444444444444444444444444444333333333331 PP

  == domain 3  score: 136.2 bits;  conditional E-value: 6.9e-43
                                   HCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSE................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                RNA_pol_Rpb1_5  87 TQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakelekakkvkkaiek................. 150
                                   T  t++TFH+aGva+ nvtlG+pr+ ei+++ k+ +++ +t++l +e+++++eka +++k+ie+                 
  gi|15669232|ref|NP_248037.1| 544 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTIYLKEEYKDNREKAEEIAKEIESltlgsiaesisidlwtq 624
                                   6679***************************************************************************** PP

                                   .................................................................CBTTEEEEEEEEEEEE CS
                                   .................................................................xxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5 151 .................................................................gikkikrilvkeaekg 166
                                                                                                    gi++i+r+lvk     
  gi|15669232|ref|NP_248037.1| 625 sikveldenrladrgltiddvieaikkklkvkidvdgttlylkiktpsikalrkripkikniqlkGIPGIERVLVK----- 700
                                   ******************************************************8888888888888888888887..... PP

                                   EEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5 167 keeekelvletegvnlsevlkveevvdageilsndiaeileilgieaarkallkeiqevykvqgvsvndrHlelivdqmtk 247
                                   ke   e+vl t+g nl+ev+k+++ vd++++++n+i ei e+lgieaar+a+++e+++++++qg++v+ rHl+l++d+mt 
  gi|15669232|ref|NP_248037.1| 701 KEG-GEYVLYTQGSNLREVFKIDG-VDTTRTITNNIIEIQEVLGIEAARNAIINEMRNTLEQQGLEVDIRHLMLVADIMTA 779
                                   222.56799***************.******************************************************** PP

                                   TSS---SSTTCHCCSS CS
                                   xxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5 248 kgeivavnrsGinkae 263
                                    ge+++++r+G+  ++
  gi|15669232|ref|NP_248037.1| 780 DGEVKPIGRHGVAGEK 795
                                   ***********97665 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.4   3.7e-08   7.3e-05       2      83 .]     243     317 ..     242     317 .. 0.90
   2 !   60.1   0.2   9.6e-20   1.9e-16       1      83 []     335     408 ..     335     408 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.7e-08
                                   HHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGGGTTT CS
                   LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisgenlkrFleki 82 
                                   +  ++  G + a+Gsv+k       +s+++ ++ +l++++    +lG++   y +  ++g    + ++i ++ l  Fl++ 
  gi|15669232|ref|NP_248037.1| 243 YDFGYFIGIYLAEGSVTKYF-----VSISNVDELILNKIRAFADKLGLNYGEYDN--NNGFAESHDIRIYSSTLAEFLSNF 316
                                   667999**************.....******************************..555555579999999999999876 PP

                                   X CS
                   LAGLIDADG_3  83 g 83 
                                   g
  gi|15669232|ref|NP_248037.1| 317 G 317
                                   5 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 9.6e-20
                                   HHHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGGGTT CS
                   LAGLIDADG_3   1 evkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisgenlkrFlek 81 
                                   e++++++rG+fd+DG v+ ++k    i++ts+skel+++++ lL+r++I+s  +++     ++++ +lii ++ +k+F e+
  gi|15669232|ref|NP_248037.1| 335 EFVRGLIRGYFDGDGNVNADRKV---IRVTSNSKELIDGIAILLARFNIFSIKTKT-----KNQF-VLIIPHRYAKKFHEE 406
                                   689******************99...**************************9999.....8888.9************** PP

                                   TX CS
                   LAGLIDADG_3  82 ig 83 
                                   i+
  gi|15669232|ref|NP_248037.1| 407 IN 408
                                   96 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   1.9   1.2e-25   2.4e-22      23     134 .]     126     546 ..      83     546 .. 0.95
   2 ?   -2.1   0.1       1.7   3.4e+03      14      35 ..     644     666 ..     598     694 .. 0.56

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1.2e-25
                                   EEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEE......... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
               Intein_splicing  23 vlslnledlklevksvkkliklklk.elyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdliavp......... 93 
                                    lsl+ +d+k+++k++   i++k + +l++ik++sgr+i aTp H++ + +d++i+ ++++eLk gd i v+         
  gi|15669232|ref|NP_248037.1| 126 ALSLD-QDEKVHWKRIISCIRHKHNgKLIKIKTKSGREITATPYHSFVIRKDNKIIPVKGSELKIGDRIPVVkhipancve 205
                                   45555.788999999***********************************99******************99********* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669232|ref|NP_248037.1| 206 ainisdyvsgnyvvdninnkiapkingksipnnikldydfgyfigiylaegsvtkyfvsisnvdelilnkirafadklgln 286
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669232|ref|NP_248037.1| 287 ygeydnnngfaeshdiriysstlaeflsnfgtssntkkiaefvfgankefvrglirgyfdgdgnvnadrkvirvtsnskel 367
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669232|ref|NP_248037.1| 368 idgiaillarfnifsiktktknqfvliiphryakkfheeinfsvekkkselerlvsslnddktydsidmipsigdaltklg 448
                                   ********************************************************************************* PP

                                   .......................................................HSCEEEEEEEEEEEEEC.EEEEEEEE CS
                                   .......................................................xxxxxxxxxxxxxxxxx.xxxxxxxx RF
               Intein_splicing  94 .......................................................dadvvwdkvksievede.eeyVYdlt 118
                                                                                          ++dv+wd++++ie+ +  ++yVYd++
  gi|15669232|ref|NP_248037.1| 449 ekvdypkvilkkferkqkigratlqrhlrrieelavkkgvnilalkeywllkkavESDVIWDEIVKIEEISCdKKYVYDIS 529
                                   ********************************************************************9986599****** PP

                                   ETTT-EEEE.CTTEEE- CS
                                   xxxxxxxxx.xxxxxxx RF
               Intein_splicing 119 vednhNFva.ngiivHN 134
                                   ve+ + F   +g++ HN
  gi|15669232|ref|NP_248037.1| 530 VEGLETFTTfDGVLTHN 546
                                   *********999****9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.7
                                   HHCC.ECTTEEEEEETTTTEEEE CS
                                   xxxx.xxxxxxxxxxxxxxxxxx RF
               Intein_splicing  14 elve.kegeevlslnledlklev 35 
                                   +++e  + + +++++++   l+ 
  gi|15669232|ref|NP_248037.1| 644 DVIEaIKKKLKVKIDVDGTTLYL 666
                                   33332122222333333333333 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00029      0.58      17      62 ..     247     289 ..     246     329 .. 0.78
   2 !    6.1   0.1     0.006        12      16      54 ..     339     376 ..     324     408 .. 0.78
   3 ?    3.0   0.0     0.057   1.1e+02      43      64 ..     728     749 ..     709     773 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00029
                       Hom_end  17 FlaGLvdsdgyvkkekedsatvktedksvmegivklarsLGikasv 62 
                                   ++ G+  ++g+v+k     ++++ +d+ ++++i ++a++LG++   
  gi|15669232|ref|NP_248037.1| 247 YFIGIYLAEGSVTKY---FVSISNVDELILNKIRAFADKLGLNYGE 289
                                   788999*********...************************9754 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.006
                       Hom_end  16 aFlaGLvdsdgyvkkekedsatvktedksvmegivklar 54 
                                     + G  d+dg+v+ +  +++ v++++k++++gi  l  
  gi|15669232|ref|NP_248037.1| 339 GLIRGYFDGDGNVNAD-RKVIRVTSNSKELIDGIAILLA 376
                                   44567779*****999.66**************976544 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.057
                       Hom_end  43 ksvmegivklarsLGikasvkt 64 
                                   +++ ++i+++ + LGi+a  ++
  gi|15669232|ref|NP_248037.1| 728 RTITNNIIEIQEVLGIEAARNA 749
                                   5799*************99887 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1   0.00037      0.73       4      58 ..     247     297 ..     245     330 .. 0.79
   2 !    6.2   0.0    0.0053        11       3      61 ..     339     395 ..     337     402 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00037
                LAGLIDADG_WhiA   4 flrGaflasGsindpekkyhLEivspdeelaeqlqkllnefeleakilerrkkyv 58 
                                   ++ G+ la+Gs+++    y+  i+  de +++++   +++++l++   + ++++ 
  gi|15669232|ref|NP_248037.1| 247 YFIGIYLAEGSVTK----YFVSISNVDELILNKIRAFADKLGLNYGEYDNNNGFA 297
                                   899***********....**************************99998888764 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0053
                LAGLIDADG_WhiA   3 aflrGaflasGsindpekkyhLEivspdeelaeqlqkllnefeleakilerrkkyvvyl 61 
                                    ++rG f + G +n  +k   + + s+++el++ ++ ll +f++ +  ++ ++++v+ +
  gi|15669232|ref|NP_248037.1| 339 GLIRGYFDGDGNVNADRKV--IRVTSNSKELIDGIAILLARFNIFSIKTKTKNQFVLII 395
                                   679************6665..99*******************99888888888888765 PP

>> LIX1  Limb expression 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.9e-05     0.079      17      83 ..     485     550 ..     471     565 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.9e-05
                          LIX1  17 kdvnvvealqefWekkkargaklksealvvyesvpspsppyvcyvtLpggscfgsfknCptkaearr 83 
                                   k+   + al+e+W  kka  +++  +++v  e+++ + + yv  +++ g  +f +f    t++  r 
  gi|15669232|ref|NP_248037.1| 485 KKGVNILALKEYWLLKKAVESDVIWDEIVKIEEISCD-KKYVYDISVEGLETFTTFDGVLTHNTMRT 550
                                   444456799************************9886.579***************99999887764 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   3.6e-05     0.071     127     212 ..     573     654 ..     560     708 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.6e-05
                                   EEEEEECCECEEEEEEESSSSS-HHHHHHHHHHHTHHHHHTSTTEEEEEESS.-SEEEEEEE-HHHHHCTT--HHHHHHHH CS
                      ACR_tran 127 skiktssseilvlavtskdgsltktelrdlaetnikdqLsrveGVgdvqliGgsekavriwldpqklaklgltltdvvsal 207
                                      k++s++i+++ ++ +  + + ++ +++a++    +L ++    +++l     +++++ ld ++la  glt++dv++a+
  gi|15669232|ref|NP_248037.1| 573 DARKEPSTPIMTIYLKEE-YKDNREKAEEIAKEIESLTLGSIAESISIDLWT---QSIKVELDENRLADRGLTIDDVIEAI 649
                                   556777888888888877.455555556666666566777777777777765...89************************ PP

                                   HHHSS CS
                      ACR_tran 208 keqnv 212
                                   k++ +
  gi|15669232|ref|NP_248037.1| 650 KKKLK 654
                                   *9864 PP

>> RACo_linker  RACo linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.044        87      23      60 ..     410     446 ..     401     453 .. 0.74
   2 ?    5.4   0.0     0.008        16       3      48 ..     614     659 ..     612     680 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.044
                   RACo_linker  23 tledpsgDleRLkeaLekqwdleidlsvLrkLpevLrk 60 
                                   ++e++++ leRL  +L+++     ++ ++  + ++L k
  gi|15669232|ref|NP_248037.1| 410 SVEKKKSELERLVSSLNDDKT-YDSIDMIPSIGDALTK 446
                                   67999************9983.2235566666666655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.008
                   RACo_linker   3 erdieldPavkkvyveleePtledpsgDleRLkeaLekqwdleidl 48 
                                   +++i++d  ++ ++vel+e  l d    ++ ++ea++k+++++id+
  gi|15669232|ref|NP_248037.1| 614 AESISIDLWTQSIKVELDENRLADRGLTIDDVIEAIKKKLKVKIDV 659
                                   57899999********************************887775 PP

>> Bac_DNA_binding  Bacterial DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0013       2.7       3      37 ..      20      54 ..      19      64 .. 0.91
   2 ?    1.7   0.0      0.15     3e+02       5      77 ..      98     169 ..      96     178 .. 0.75
   3 ?   -3.5   0.0       6.4   1.3e+04      34      56 ..     365     387 ..     363     390 .. 0.75
   4 ?   -2.6   0.1       3.4   6.8e+03      30      44 ..     643     657 ..     640     662 .. 0.63
   5 ?   -3.1   0.0       4.8   9.5e+03      22      46 ..     744     769 ..     743     771 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0013
                                  HHHHHHHHHTT----HHHHHHHHHHHHHHHHHHHH CS
               Bac_DNA_binding  3 kkeLieeiaektgltkkdakrvveafldtikeaLk 37
                                  k eL e+++++ +lt++ + +++++++++  +aL 
  gi|15669232|ref|NP_248037.1| 20 KDELFEKLSKEKDLTEEMVDEIIDEVVNAYRKALV 54
                                  89***************************999995 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.15
                                   HHHHHHHTT----HHHHHHHHHHHHHHHHHHHHTT-EEEETTTEEEEEEEE--BS-B-TTT--B--B--EEEE CS
               Bac_DNA_binding   5 eLieeiaektgltkkdakrvveafldtikeaLkkgekvelsgFGtfkvkerkartgrnpkTgekvkiparkvv 77 
                                   +L++e+ e+ g++k   ++v +  +d+ + +L ++ekv  + + ++  ++ + +  + +kT+   +i a+   
  gi|15669232|ref|NP_248037.1|  98 KLVDEMIERFGFEKIGNSEVCDLPIDIYALSLDQDEKVHWKRIISCIRHKHNGK-LIKIKTKSGREITATPYH 169
                                   58999999999999999999999999****************999866666655.445555554444444444 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.4
                                   HHHHTT-EEEETTTEEEEEEEE- CS
               Bac_DNA_binding  34 eaLkkgekvelsgFGtfkvkerk 56 
                                   ++L  g  + l  F  f++k+++
  gi|15669232|ref|NP_248037.1| 365 KELIDGIAILLARFNIFSIKTKT 387
                                   56777788888889999988876 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 3.4
                                   HHHHHHHHTT-EEEE CS
               Bac_DNA_binding  30 dtikeaLkkgekvel 44 
                                   d ++ea+kk+ kv++
  gi|15669232|ref|NP_248037.1| 643 DDVIEAIKKKLKVKI 657
                                   556666666666665 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 4.8
                                   HHHHHHHHHHHHHHHHTT-.EEEETT CS
               Bac_DNA_binding  22 krvveafldtikeaLkkge.kvelsg 46 
                                   +++ +a+++++ ++L++++ +v +++
  gi|15669232|ref|NP_248037.1| 744 EAARNAIINEMRNTLEQQGlEVDIRH 769
                                   66778999999999965541577765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (859 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1200  (0.0669307); expected 358.6 (0.02)
Passed bias filter:                      753  (0.041999); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.82u 0.36s 00:00:01.18 Elapsed: 00:00:00.49
# Mc/sec: 5278.62
//
Query:       gi|15669233|ref|NP_248038.1|  [L=110]
Description: 50S ribosomal protein L30e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-22   78.1   0.1    3.5e-22   77.9   0.1    1.0  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.1     2e-26   3.5e-22       2      94 ..       8     100 ..       7     101 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 2e-26
                                   HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHH..HTTEEEEEESCHHHHHHHTTSSSEC CS
                Ribosomal_L7Ae   2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealck..ekevpyvkvkskkeLGelvgkkrpv 80 
                                   ++++++++a+++gk++lG k+++k +++ge klv+lA +++++  ++ +++++k  +++v+ +k++s  eLG+++gk++pv
  gi|15669233|ref|NP_248038.1|   8 DVNKAIRTAVDTGKVILGSKRTIKFVKHGEGKLVVLAGNIPKDLEED-VKYYAKlsNIPVYQHKITS-LELGAVCGKPFPV 86 
                                   689********************************************.******7777777788999.************* PP

                                   SEEEEEESTTTHHH CS
                Ribosomal_L7Ae  81 salaikdegdskdl 94 
                                   +al++ deg s+++
  gi|15669233|ref|NP_248038.1|  87 AALLVLDEGLSNIM 100
                                   *********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 762.39
//
Query:       gi|15669234|ref|NP_248039.1|  [L=183]
Description: transcription elongation factor NusA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-16   59.4   0.3    2.6e-16   59.4   0.3    2.2  2  KH_5      NusA-like KH domain
    1.3e-13   50.6   9.3    6.5e-13   48.3   0.5    2.4  2  KH_2      KH domain
    7.9e-05   22.4   2.4     0.0014   18.4   0.1    2.5  2  KH_1      KH domain


Domain annotation for each model (and alignments):
>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.3   4.4e-20   2.6e-16       2      67 ..      32      91 ..      31      93 .. 0.97
   2 ?   -0.1   0.6      0.17     1e+03      22      47 ..     114     143 ..     100     149 .. 0.61

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 4.4e-20
                          KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsV 67
                                  +er+ ++Vk+++     vGa++gk+G+++k+ ++++ g+k+d++e+s+D ++fi n+++P ++++V
  gi|15669234|ref|NP_248039.1| 32 DERVAFIVKEGD-----VGAAIGKGGENVKTAEEKF-GKKVDIIEYSDDWRKFIRNIFAPIQLDDV 91
                                  89**********.....*******************.*************************9998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.17
                          KH_5  22 ivgkkGsrikavsseLk....gekidvvew 47 
                                   ++g+kG++ +   + Lk     +ki+v+ +
  gi|15669234|ref|NP_248039.1| 114 VFGEKGKNLERALKILKrhtkITKIKVIVE 143
                                   566666665544444434433566666655 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.5   1.1e-16   6.5e-13       4      75 ..      14      95 ..      11     112 .. 0.91
   2 !    4.6   4.4    0.0047        28      37      76 ..     112     150 ..      98     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.1e-16
                                  HHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC............EEEEEEEET CS
                          KH_2  4 eslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk............VklnivkVk 74
                                  + ++++i++  + ++++++  +rv ++++e+  g +IGkgG+n+k+ +++++k+++++e+++            ++l+ v+Vk
  gi|15669234|ref|NP_248039.1| 14 IGFFEKIANVPILDCVLND--ERVAFIVKEGDVGAAIGKGGENVKTAEEKFGKKVDIIEYSDdwrkfirnifapIQLDDVWVK 94
                                  6789*************88..**********************************************9999999777777777 PP

                                  T CS
                          KH_2 75 k 75
                                  +
  gi|15669234|ref|NP_248039.1| 95 R 95
                                  6 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0047
                                   HHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETTT CS
                          KH_2  37 givIGkgGsnikkigkelrkdieklegkkVklnivkVkkp 76 
                                     v G +G+n+++  k l++ + k+ + kV ++  k+k++
  gi|15669234|ref|NP_248039.1| 112 RAVFGEKGKNLERALKILKRHT-KITKIKVIVENQKFKRK 150
                                   5688*****************9.69999999999999986 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   2.3e-07    0.0014       4      39 ..      37      73 ..      34      80 .. 0.87
   2 ?    3.4   0.4     0.011        66       3      24 ..     103     124 ..     101     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-07
                                  EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.ST CS
                          KH_1  4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpk.se 39
                                  ++v+   vg+ IGkgG+n+k  +e+ g k+++++ s+
  gi|15669234|ref|NP_248039.1| 37 FIVKEGDVGAAIGKGGENVKTAEEKFGKKVDIIEySD 73
                                  6788889*****************99******96554 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.011
                                   EEEEGGGHHHHHHTGGGHHHHH CS
                          KH_1   3 rilvPsslvgriIGkgGsnIke 24 
                                    i+++ +  +++ G +G+n+ +
  gi|15669234|ref|NP_248039.1| 103 FIKINPKVRRAVFGEKGKNLER 124
                                   589999999*********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1944  (0.108428); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1328.42
//
Query:       gi|15669235|ref|NP_248040.1|  [L=148]
Description: 30S ribosomal protein S12 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-47  158.9   1.0    3.6e-47  158.7   1.0    1.1  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.7   1.0     2e-51   3.6e-47       1     113 [.      32     146 ..      32     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: 158.7 bits;  conditional E-value: 2e-51
                                   --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--... CS
               Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrk. 80 
                                   r+ l++k+k d+legap++rG+v+ekv++eak+PnsA+Rk+vrv+Likng+ vtaf+pg++a+nf+dEhdev+++Gi+++ 
  gi|15669235|ref|NP_248040.1|  32 RRVLKLKEKYDPLEGAPMARGIVIEKVGLEAKQPNSAIRKCVRVQLIKNGRVVTAFCPGNHAINFIDEHDEVIIEGIGGPk 112
                                   678899************************************************************************988 PP

                                   ....BTTSTTEEEEBETS---TSSSTTTTT---- CS
               Ribosom_S12_S23  81 .gkavkDlpGvrykvvkvagvslkalskykkekp 113
                                     +a++D+pGv+ykv+ v + sl++l+++++ek 
  gi|15669235|ref|NP_248040.1| 113 gPRAKGDIPGVKYKVIMVGRNSLRELVRGRQEKI 146
                                   459*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1095.76
//
Query:       gi|15669236|ref|NP_248041.1|  [L=191]
Description: 30S ribosomal protein S7 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-40  136.6   6.2    5.7e-40  136.4   6.2    1.1  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.4   6.2   3.2e-44   5.7e-40      16     149 .]      48     191 .]      37     191 .] 0.95

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 3.2e-44
                                   SSTTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEEE- CS
                  Ribosomal_S7  16 pkynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpvevr 92 
                                   +k+++++ve+l+nk+m+    +Gkk +A kiv++a++iie++tk++p++vl++A+en+ Pr++++++ +GG+ y ++v+++
  gi|15669236|ref|NP_248041.1|  48 EKAKMNIVERLVNKVMRreenTGKKLKALKIVENAFEIIEKRTKQNPIQVLVDAIENAGPREDTTRISYGGIVYLQSVDCS 128
                                   458999*************************************************************************** PP

                                   HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-...SHHHHHHHHHHHHHHHTG CS
                  Ribosomal_S7  93 pkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege...gaavkkreethrmAeanr 149
                                   + Rr ++Alr+i+ +a   +++++k+++e+LaeE+i+Aa+g+   ++av+k+eet+r+A+++r
  gi|15669236|ref|NP_248041.1| 129 SLRRIDVALRNIALGAymaAHKSKKPIEEALAEEIIAAARGDmqkSYAVRKKEETERVAQSAR 191
                                   *************99999999999****************99999***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1288.57
//
Query:       gi|15669237|ref|NP_248042.1|  [L=726]
Description: elongation factor EF-2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-66  221.9   0.0    8.9e-66  221.1   0.0    1.4  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    4.8e-31  107.0   0.1    1.3e-30  105.7   0.1    1.8  1  EFG_IV       Elongation factor G, domain IV
    2.3e-27   94.8   0.1    7.7e-27   93.2   0.0    2.0  2  EFG_C        Elongation factor G C-terminus
    1.3e-23   82.9   0.4    3.7e-23   81.4   0.4    1.8  1  EFG_II       Elongation Factor G, domain II
      5e-17   62.1   0.1    3.2e-16   59.5   0.0    2.5  2  GTP_EFTU_D2  Elongation factor Tu domain 2
  ------ inclusion threshold ------
      0.026   14.6   0.0      0.062   13.4   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
       0.14   12.0   0.0        0.3   10.9   0.0    1.5  1  DUF4347      Domain of unknown function (DUF4347)


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.1   0.0   3.5e-69   8.9e-66       2     194 .]      20     258 ..      19     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: 221.1 bits;  conditional E-value: 3.5e-69
                                   CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEET..TCSSEEEEEEEESSS CS
                      GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaislek..etkkylinliDtPGH 80 
                                   rirnigi++h+DhGKtTL+d+Ll+ +g+isk  e a+e+ +lD+ +eE +rgiTi +a++s+ +  e+++ylinliDtPGH
  gi|15669237|ref|NP_248042.1|  20 RIRNIGICAHIDHGKTTLSDNLLAGAGMISK--ELAGEQLALDFDEEEAQRGITIFAANVSMVHtyEGNEYLINLIDTPGH 98 
                                   79*****************************..8899999***********************446*************** PP

                                   GGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH........ CS
                      GTP_EFTU  81 vdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk........ 153
                                   vdF  +v+r++r++Dga++vv+aveGv+pqte+vlr+al+e+v++++fiNK+Drl++elk ++ee+++++ +         
  gi|15669237|ref|NP_248042.1|  99 VDFGGDVTRAMRAIDGAIVVVCAVEGVMPQTETVLRQALRERVKPVLFINKVDRLINELKLTPEELQSRFIKIindinnli 179
                                   **********************************************************************88755655554 PP

                                   ..HHHHHHHHHTTT............TTEEEEEEBTTTTBTHH..................................HHHH CS
                      GTP_EFTU 154 ..eeklekygekge............kevpvvfgSalkgegvk..................................tlle 186
                                     +                       ++ +v+fgSa+++++++                                   +l+
  gi|15669237|ref|NP_248042.1| 180 rkM----------ApeefkdkwlvrvEDGSVAFGSAYNNWAISvpfmkksgitfkdiikyceedrqdelaekaplheVVLD 250
                                   440..........34444555666667889**********999999999999999999****************99889** PP

                                   HHHHHSHH CS
                      GTP_EFTU 187 alvellps 194
                                   +++++lps
  gi|15669237|ref|NP_248042.1| 251 MVIKHLPS 258
                                   *****996 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.1   4.9e-34   1.3e-30       6     121 .]     513     624 ..     508     624 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 4.9e-34
                                   CEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESE CS
                        EFG_IV   6 rEtirkpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdv 86 
                                    +t rk  ++++++l+k +g+d+++ak +++i++     gn+++++t+g+++++e++e++ +Gf+ea+++Gpla e++++v
  gi|15669237|ref|NP_248042.1| 513 VDTKRKLDDKIVQELIK-AGMDPEEAKRVMCIYE-----GNVLINMTRGIVHLDEVKELIIQGFKEAMRNGPLAAEKCQGV 587
                                   56778888889******.9***************.....9***************************************** PP

                                   EEEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC- CS
                        EFG_IV  87 kvtLldgslhe..vdsseaafkpaarralkeallkAs 121
                                   kv+L+d++lhe  +++++a+++paar+++++a+++A+
  gi|15669237|ref|NP_248042.1| 588 KVKLMDAVLHEdaIHRGPAQMIPAARFGIRDAMMQAN 624
                                   **********************************995 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.0         7   1.8e+04       3      15 ..     389     401 ..     388     402 .. 0.82
   2 !   93.2   0.0     3e-30   7.7e-27       1      88 [.     626     712 ..     626     713 .. 0.98

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 7
                                   EEEEEEEEEEEEC CS
                         EFG_C   3 lEPivkveievpe 15 
                                    EP+ +v ie+ +
  gi|15669237|ref|NP_248042.1| 389 SEPVITVAIEAKN 401
                                   69*****999865 PP

  == domain 2  score: 93.2 bits;  conditional E-value: 3e-30
                                   EEEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE- CS
                         EFG_C   1 vllEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYeev 81 
                                   vllEP++ v i++p++++g+++ ++s+rrG+i+dmeq+ ++++ii+a++P+ae++gfa ++r +T+G+  +s+ef+gYe+v
  gi|15669237|ref|NP_248042.1| 626 VLLEPMQFVYINTPQDFMGAAMREISNRRGQILDMEQE-GDMAIIKAKCPVAEMFGFAGAIRGATQGRCLWSIEFAGYEKV 705
                                   59************************************.****************************************** PP

                                   -HHHHHH CS
                         EFG_C  82 pgdklde 88 
                                   p d++++
  gi|15669237|ref|NP_248042.1| 706 PRDMQEQ 712
                                   ***9987 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.4   1.4e-26   3.7e-23       1      75 []     388     463 ..     388     463 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 1.4e-26
                        EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivve.rlkreykvevelgk 75 
                                   ++ePvi++aie+k+ +d  kl ++L+++++EDpt++ve +eeT+e +lsGmGelH+ei+++ +++r+ ++ ve+g+
  gi|15669237|ref|NP_248042.1| 388 ISEPVITVAIEAKNTKDLPKLIEVLRQVAREDPTVKVEINEETGEHLLSGMGELHIEIITKlKIERDAGIPVEVGQ 463
                                   689******************************************************998669*********9985 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.0   1.2e-19   3.2e-16       1      74 []     306     373 ..     306     373 .. 0.97
   2 ?   -1.6   0.0       1.4   3.7e+03      13      32 ..     459     479 ..     459     501 .. 0.78

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.2e-19
                                   EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                   G v+ +r++sG +k Gdev++  +  ++k    +i+++ +f+++e+++v+   aG+i+a++gl++a  +G+t++
  gi|15669237|ref|NP_248042.1| 306 GAVSVCRLFSGRIKQGDEVYM--VNNQQK---AKIQQVSVFMGPERIPVDSISAGNICALVGLKEA-SAGETIC 373
                                   889******************..777799...*********************************8.*****98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                                   EETTEEEEEEC.TCTTSEEEE CS
                   GTP_EFTU_D2  13 lkkGdevrilg.ndtskkeiv 32 
                                   +++G+ +++ +   t++++ v
  gi|15669237|ref|NP_248042.1| 459 VEVGQPIVVYReTVTGQSPVV 479
                                   579999***999999999733 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.4e-05     0.062       9     112 ..      31     147 ..      23     149 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                                   TSSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEE....ETTEEEEEEECGGCSSHHHHHHHHHHH CS
                      MMR_HSR1   9 NvGKStLinaltg................ekaivsdkpgtTrdinegrvk....lkgkeielvDtpGliegaseekglgka 69 
                                     GK+tL   l+                 +  + +++ g T+      +      ++  i+l+DtpG ++    + ++++a
  gi|15669237|ref|NP_248042.1|  31 DHGKTTLSDNLLAgagmiskelageqlalDFDEEEAQRGITIFAANVSMVhtyeGNEYLINLIDTPGHVD---FGGDVTRA 108
                                   568888888777433344444443333221234455556666553333322432223569*******665...22245555 PP

                                   HHHHHCTSEEEEEEETTTTCSHHHHHHHHHH.HHHTTSEEEEEE CS
                      MMR_HSR1  70 flaleeadlillvvdaseeklkpldeeleel.leeakkplilvl 112
                                   ++a    d +++vv a  e++ p+ e++ +  l+e+ kp+ l +
  gi|15669237|ref|NP_248042.1| 109 MRA---IDGAIVVVCAV-EGVMPQTETVLRQaLRERVKPV-LFI 147
                                   554...57777777656.5566666665544055555554.444 PP

>> DUF4347  Domain of unknown function (DUF4347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012       0.3      31     101 ..       5      78 ..       1      97 [. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                       DUF4347  31 rdgveqiteaLaqrsevdaihivshGsegalqLgntelnaenlekya...eelaqwgealsedadillYgCnvA 101
                                    + +++i+e +++++++++i i +h ++g+ +L ++ l  + + +++   e+la   ++ ++++ i ++++nv 
  gi|15669237|ref|NP_248042.1|   5 AKMIAKIKELMEKYDRIRNIGICAHIDHGKTTLSDNLLAGAGMISKElagEQLALDFDEEEAQRGITIFAANVS 78 
                                   56799*******************************99999888744222444433344447777888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (726 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 4481.75
//
Query:       gi|15669238|ref|NP_248043.1|  [L=161]
Description: hypothetical protein MJ_1049 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1005.76
//
Query:       gi|15669239|ref|NP_248044.1|  [L=177]
Description: putative kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-28   99.7   0.4    1.8e-28   99.7   0.4    1.5  1  AAA_18           AAA domain
    8.5e-10   39.2   4.0    8.6e-09   35.9   0.5    2.9  2  AAA_17           AAA domain
    6.8e-09   35.9   1.3    0.00067   19.6   0.1    2.3  2  dNK              Deoxynucleoside kinase
    2.1e-06   28.1   0.0    4.7e-06   26.9   0.0    1.5  2  AAA_28           AAA domain
    7.3e-06   26.2   0.0     0.0045   17.1   0.0    2.6  2  AAA_33           AAA domain
    1.1e-05   25.6   0.5      0.069   13.3   0.0    2.2  2  SKI              Shikimate kinase
      3e-05   23.8   5.3     0.0052   16.5   0.0    3.0  3  Thymidylate_kin  Thymidylate kinase
    3.1e-05   24.4   0.3    0.00016   22.1   0.1    2.0  2  AAA              ATPase family associated with various cellul
    5.6e-05   23.0   0.2      0.013   15.3   0.0    2.1  2  Cytidylate_kin   Cytidylate kinase
    0.00081   19.1   0.1     0.0018   18.0   0.0    1.7  1  CoaE             Dephospho-CoA kinase
     0.0013   18.7   0.0     0.0025   17.8   0.0    1.5  1  Rad17            Rad17 P-loop domain
     0.0016   18.6   0.2      0.004   17.3   0.2    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
     0.0019   17.9   0.0     0.0041   16.9   0.0    1.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0033   16.9   0.1      0.021   14.3   0.0    2.0  2  KTI12            Chromatin associated protein KTI12
     0.0039   17.1   9.8      0.017   15.0   1.7    3.2  3  NTPase_1         NTPase
     0.0055   16.5   0.1      0.013   15.2   0.0    1.6  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0058   16.9   0.1      0.016   15.5   0.1    1.7  2  AAA_22           AAA domain
     0.0097   16.0   0.8        1.7    8.8   0.8    2.4  1  ADK              Adenylate kinase
  ------ inclusion threshold ------
      0.012   16.0   2.6      0.017   15.4   1.1    2.0  2  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
      0.012   15.0   9.5       0.12   11.7   0.4    2.6  2  ATPase           KaiC
      0.013   15.6   5.3      0.065   13.3   5.3    2.0  1  AAA_14           AAA domain
      0.016   15.6   0.0      0.041   14.3   0.0    1.7  1  RNA_helicase     RNA helicase
      0.019   14.7   4.8      0.065   13.0   4.8    2.1  1  AAA_24           AAA domain
       0.02   14.6   0.2      0.069   12.9   0.2    2.0  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.045   13.7   0.3        0.1   12.5   0.1    1.7  2  RsgA_GTPase      RsgA GTPase
      0.058   12.7   0.2        0.2   10.9   0.1    2.0  1  Zeta_toxin       Zeta toxin
      0.067   13.4   6.6       0.33   11.2   0.7    3.0  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.069   13.2   2.4       0.21   11.7   2.4    2.1  1  MMR_HSR1         50S ribosome-binding GTPase
      0.072   14.0   4.2       0.72   10.7   0.3    2.5  2  DUF5611          Domain of unknown function (DUF5611)
      0.094   13.2   0.4       0.14   12.7   0.4    1.7  1  ABC_tran         ABC transporter
       0.11   11.5   0.6       0.17   10.8   0.1    1.6  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.13   12.7   0.1       0.28   11.5   0.1    1.6  1  AAA_16           AAA ATPase domain
       0.13   12.3   0.9       0.22   11.5   0.1    1.8  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.13   12.8   1.7       0.97   10.1   0.2    2.6  2  Fe-S_assembly    Iron-sulphur cluster assembly
       0.15   11.7   0.2       0.71    9.6   0.1    2.0  3  AAA_30           AAA domain
       0.26   11.3   1.5       0.65   10.0   0.3    2.3  2  AAA_5            AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.4   3.6e-31   1.8e-28       1     130 []       3     121 ..       3     121 .. 0.97

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 3.6e-31
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvid 80 
                                   I++tGtpGvGKtt++k L++rlg+ ++ +++ +k+  l++e d++   +s ++d +kl+k +d++ee       +k++++d
  gi|15669239|ref|NP_248044.1|   3 IAITGTPGVGKTTISKVLRDRLGIkVIDITEAVKKYKLYTEKDED--MDSYVIDFEKLEKFIDEIEEK------EKTIILD 75 
                                   89********************999********************..********************6......68***** PP

                        AAA_18  81 ghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeild 130
                                   gh+++l+ ++++    +vL+++pe+ +eRlekRgy+++k  en +aeild
  gi|15669239|ref|NP_248044.1|  76 GHVSHLLNPDYI----IVLRCNPEIIKERLEKRGYKPKKVLENIQAEILD 121
                                   *********999....*******************************986 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.5   1.7e-11   8.6e-09       1     122 [.       6     104 ..       6     117 .. 0.81
   2 ?    2.0   0.2       0.5   2.5e+02      49      75 ..     136     162 ..     124     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.7e-11
                                   EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-S CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeeakkkgvlvdghp 80 
                                   +G PG+GK+t+++ l +++g++++     + e +k+ +l  +++++m+  + +++ e +++ +++i+e+  +k++++dgh 
  gi|15669239|ref|NP_248044.1|   6 TGTPGVGKTTISKVLRDRLGIKVID----ITEAVKKYKLyTEKDEDMD--SYVIDFEKLEKFIDEIEEK--EKTIILDGHV 78 
                                   69***********************....7788888899666666674..446777778999999*995..899******9 PP

                                   EEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH CS
                        AAA_17  81 rikeqagfldglpkevleelkpdaiilleadpeeilerrlkd 122
                                   +                + l+pd ii+l ++pe i er+ k+
  gi|15669239|ref|NP_248044.1|  79 S----------------HLLNPDYIIVLRCNPEIIKERLEKR 104
                                   6................4589***********9777776665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.5
                                   SHHHHHHHHHHHHHHHHHHHHHSSEEE CS
                        AAA_17  49 lpleekkelqkeaaekiaeeakkkgvl 75 
                                     +++ + + +e++e+i++++++kgv+
  gi|15669239|ref|NP_248044.1| 136 TTNRDVENIVDEIIEAIKHKKERKGVV 162
                                   45677888999999****998777664 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   1.3e-06   0.00067       1      40 [.       3      56 ..       3      67 .. 0.73
   2 !   15.8   0.2     2e-05    0.0098     110     150 ..      71     114 ..      55     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-06
                                  EEEEESTTSSHHHHHHHHHCCSTCEE..EE-HHHHCCSSSS............H CS
                           dNK  1 ivveGnIgaGKstlvklLskklgvkv..feEpvdkwtnvqk............n 40
                                  i++ G+ g+GK+t+ k+L+++lg+kv  ++E v+k++   +            +
  gi|15669239|ref|NP_248044.1|  3 IAITGTPGVGKTTISKVLRDRLGIKVidITEAVKKYKLYTEkdedmdsyvidfE 56
                                  899********************8873358******665545544444444444 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2e-05
                                   HHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCT...T CS
                           dNK 110 kelldnlleelakpdlliYLkasletclerikkRgreeek...k 150
                                   + +ld  +++l +pd +i L++++e ++er++kRg + +k   +
  gi|15669239|ref|NP_248044.1|  71 TIILDGHVSHLLNPDYIIVLRCNPEIIKERLEKRGYKPKKvleN 114
                                   4556666778888**********************998774444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   9.5e-09   4.7e-06       1      76 [.       2      72 ..       2      82 .. 0.68
   2 ?   -2.2   0.0       8.7   4.3e+03      33      49 ..      95     111 ..      76     137 .. 0.60

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 9.5e-09
                        AAA_28  1 kivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvl 76
                                  +i+itG+++ GKTt+++ L +r g++v+  +Ea+ ++    ++k+ed ++++  +++f++  le+ + e ++  ++k++
  gi|15669239|ref|NP_248044.1|  2 RIAITGTPGVGKTTISKVLRDRlGIKVIdiTEAVKKYK-LYTEKDED-MDSY--VIDFEK--LEKFIDEIEE--KEKTI 72
                                  79******************999***99999*999986.23334443.3332..455555..3444443333..24445 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.7
                        AAA_28  33 eileeklakgedalpwv 49 
                                   ei++e+l+k++ + ++v
  gi|15669239|ref|NP_248044.1|  95 EIIKERLEKRGYKPKKV 111
                                   44444444444433333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   9.1e-06    0.0045       4     121 ..       5     107 ..       3     121 .. 0.70
   2 ?   -0.2   0.0       2.1     1e+03      53      93 ..     113     153 ..     106     163 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.1e-06
                        AAA_33   4 lvGlpGsGKstlaerllkklgavllssdtlrrrlfg.tdqqsktdytrvldrlyqilnelarkalsagrnvildatnlsrr 83 
                                   + G pG+GK+t ++ l  +lg  +++  ++ ++++  t+++ +   + v d     l++++++  ++++++ild       
  gi|15669239|ref|NP_248044.1|   5 ITGTPGVGKTTISKVLRDRLGIKVIDITEAVKKYKLyTEKDEDM-DSYVIDFE--KLEKFIDEIEEKEKTIILDG------ 76 
                                   679******************99999888888666533232222.22233332..46788888888999999986...... PP

                        AAA_33  84 erarflklarrlgvpvrivvvetdeetlkeRlakRaan 121
                                       + +l++    p+ i+v+++ +e +keRl+kR  +
  gi|15669239|ref|NP_248044.1|  77 ---HVSHLLN----PDYIIVLRCNPEIIKERLEKRGYK 107
                                   ...3445554....888888888888888888888775 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.1
                        AAA_33  53 drlyqilnelarkalsagrnvildatnlsr.rerarflklar 93 
                                   +++ + + +++  + s+g+ + +d tn++  +  ++++++ +
  gi|15669239|ref|NP_248044.1| 113 ENIQAEILDVC-LCESKGKVYEIDTTNRDVeNIVDEIIEAIK 153
                                   44444444444.456778888899999997344466665555 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00014     0.069       1      28 [.       9      36 ..       9      45 .. 0.90
   2 !   10.9   0.1   0.00077      0.38      80     157 ..      79     152 ..      55     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00014
                                  TTSSHHHHHHHHHHHHTSEEEEHHHHHH CS
                           SKI  1 mGaGKstvGkllAkklglefiDlDelie 28
                                  +G+GK+t+ k l ++lg+++iD+ e ++
  gi|15669239|ref|NP_248044.1|  9 PGVGKTTISKVLRDRLGIKVIDITEAVK 36
                                  69********************977665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00077
                                   HHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCCSSCEEEECTSSHHHHHHHHHHHHH CS
                           SKI  80 ellkekgiviyLdvsleellerlkadkeRPllqekskeeelleelaereplyeeaadvvvdeseeskeevaeeileal 157
                                   ++l +  ++i L++++e + erl+++  +P    ++     + e+   +   ++ + + +d+++++ e++++ei+ea+
  gi|15669239|ref|NP_248044.1|  79 SHLLNPDYIIVLRCNPEIIKERLEKRGYKPKKVLENI----QAEILDVCLCESKGKVYEIDTTNRDVENIVDEIIEAI 152
                                   344458999*******************775554444....33333466677888889999999999*******9988 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.013       6.6       3      20 ..       7      24 ..       5      29 .. 0.87
   2 ?    2.9   0.3      0.15        77     126     174 ..      29      76 ..      26      80 .. 0.83
   3 !   16.5   0.0     1e-05    0.0052     116     185 .]      82     148 ..      74     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.013
                                  ESTTSSHHHHHHHHHHHH CS
               Thymidylate_kin  3 GlDGaGKttqaellkerl 20
                                  G  G+GKtt+++ l++rl
  gi|15669239|ref|NP_248044.1|  7 GTPGVGKTTISKVLRDRL 24
                                  788************998 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.15
                                   SSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEET CS
               Thymidylate_kin 126 vdpevalkRlakrdeldeeeeeqldflrkvrerylelakederiliida 174
                                   +d  +a+k+ +   e+de++     +++k+++  +e+  e+e+++i+d 
  gi|15669239|ref|NP_248044.1|  29 IDITEAVKKYKLYTEKDEDMDSYVIDFEKLEKFIDEIE-EKEKTIILDG 76 
                                   68889999999999999999999999****99666655.6999999885 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1e-05
                                   SE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHH..TTSTEEEEETTS-.HHHHHHHH CS
               Thymidylate_kin 116 lkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelak..ederiliidasks.ieevheeI 185
                                   l Pd+++ l + pe+  +Rl+kr+       + +++l+++++  l++    ++++++ id+++  +e++++eI
  gi|15669239|ref|NP_248044.1|  82 LNPDYIIVLRCNPEIIKERLEKRGY------KPKKVLENIQAEILDVCLceSKGKVYEIDTTNRdVENIVDEI 148
                                   39**********************9......77778888888777765444799*******999999999988 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   3.2e-07   0.00016       3      69 ..       5      67 ..       3      83 .. 0.81
   2 ?    0.3   0.0       1.7   8.5e+02      96     120 ..     126     149 ..      95     162 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.2e-07
                                  EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGG CS
                           AAA  3 lyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEida 69
                                  ++G+pG+GKT++ k +   lg++++ i  +    k+  e+ +++  ++ + ++ +k    fiDEi++
  gi|15669239|ref|NP_248044.1|  5 ITGTPGVGKTTISKVLRDRLGIKVIDITEAVKKYKLYTEKDEDMDSYVIDFEKLEK----FIDEIEE 67
                                  78********************9999887777778888888888888888777663....8888875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.7
                                   TTTSSSTEEEEEEESS.GGGSTHHHH CS
                           AAA  96 vkkkeskvivigatnr.pdkldpall 120
                                   ++k  +kv  i +tnr ++++ ++++
  gi|15669239|ref|NP_248044.1| 126 ESK--GKVYEIDTTNRdVENIVDEII 149
                                   333..466667777776333333333 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.5e-05     0.013       1      62 [.       3      67 ..       3      90 .. 0.69
   2 ?    5.9   0.1     0.019       9.4     188     210 ..     131     153 ..     123     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-05
                                  EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHH...HHHHHHHHHHTT--TT-HHHHHHHHHT--E CS
                Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgal...YRalalaalrrkvdlldeaalvelakevel 62
                                  iai G  g GK ++++ l ++lg+k++d  +    Y+ ++    + +  ++d ++l++++ e+e 
  gi|15669239|ref|NP_248044.1|  3 IAITGTPGVGKTTISKVLRDRLGIKVIDITEAvkkYKLYTEKDEDMDSYVIDFEKLEKFIDEIEE 67
                                  89*************************95544122444444444445556788888888887765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.019
                                   -EEEETTTS-HHHHHHHHHHHHH CS
                Cytidylate_kin 188 aliidtskltieevvekilelik 210
                                   +  idt++  +e++v++i+e+ik
  gi|15669239|ref|NP_248044.1| 131 VYEIDTTNRDVENIVDEIIEAIK 153
                                   557*****************987 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.5e-06    0.0018       3      35 ..       3      36 ..       1      64 [. 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.5e-06
                                  EEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHH CS
                          CoaE  3 vgltGgiasGKstvanlfad.lgvpivDaDlvAr 35
                                  +++tG  + GK+t++++++d lg++++D   + +
  gi|15669239|ref|NP_248044.1|  3 IAITGTPGVGKTTISKVLRDrLGIKVIDITEAVK 36
                                  89**************************866554 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     5e-06    0.0025      50     106 ..       5      62 ..       2      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5e-06
                         Rad17  50 isGPsGCgkstvvkvLskelgiklrewlnpvs.lkepdnqksdfkgltekesrflsqi 106
                                   i+G +G gk+t+ kvL   lgik+++   +v+ +k    + +d+ + ++ ++++   i
  gi|15669239|ref|NP_248044.1|   5 ITGTPGVGKTTISKVLRDRLGIKVIDITEAVKkYKLYTEKDEDMDSYVIDFEKLEKFI 62 
                                   9**************************9999724444557777777666665443333 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   8.1e-06     0.004       2      66 ..       3      64 ..       2     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.1e-06
               Cytidylate_kin2  2 ITIsreyGsgGetigeaLAekLglpfydreiieevakelglseeeveevdersrlssflskllaa 66
                                  I+I+++ G g++ti + L ++Lg++++d    +e++k+ +l+ e+ e +d      + l+k++++
  gi|15669239|ref|NP_248044.1|  3 IAITGTPGVGKTTISKVLRDRLGIKVIDI---TEAVKKYKLYTEKDEDMDSYVIDFEKLEKFIDE 64
                                  9***************************5...999999999999999999844444555555544 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.2e-06    0.0041      37      95 ..       4      67 ..       2      74 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.2e-06
                        RuvB_N 37 llyGpPGlGkttlakiiakelgvkl.kitsgPv.....lekagdlaalltnleekdvlfideihr 95
                                   ++G PG+Gktt++k++ + lg+k+  it +        ek  d+ + + ++e+ +  fidei  
  gi|15669239|ref|NP_248044.1|  4 AITGTPGVGKTTISKVLRDRLGIKViDITEAVKkyklyTEKDEDMDSYVIDFEKLE-KFIDEIEE 67
                                  689*******************9862455443222222578889999999998887.58999875 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.2e-05     0.021       4      66 ..       3      80 ..       1      93 [. 0.68
   2 ?    0.7   0.0      0.57   2.8e+02     196     216 ..     138     158 ..     108     173 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-05
                                  EEEE--TTSSHHHHHHHHHHHHHH.........TT--EEEE-THHHH......TTSS.S--GGGHHHHHHHHHHHHHH CS
                         KTI12  4 vvltGlPssGKstrakeLakalee.........ekrsvvviddeslg.....iekds.ykdsakekalRsslrsavkr 66
                                  + +tG P +GK+t++k L++ l           +k++ +  +de +      +ek + + d+ +ek+    l  +v+ 
  gi|15669239|ref|NP_248044.1|  3 IAITGTPGVGKTTISKVLRDRLGIkviditeavKKYKLYTEKDEDMDsyvidFEKLEkFIDEIEEKEKTIILDGHVSH 80
                                  679******************988788888888777777777776665554433332366666666555555555555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.57
                                   HHHHHHHHHHHHH....HTT- CS
                         KTI12 196 dketseivkeileaqksavai 216
                                   ++ +++iv+ei+ea+k++++ 
  gi|15669239|ref|NP_248044.1| 138 NRDVENIVDEIIEAIKHKKER 158
                                   345566677777766665544 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.7   3.5e-05     0.017       1      23 [.       2      24 ..       2      28 .. 0.83
   2 ?    4.9   0.1     0.045        22      43      91 ..      22      67 ..      20      76 .. 0.71
   3 ?    3.1   0.1      0.16        78     137     164 ..     116     145 ..      93     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-05
                                  EEEEE--TTSSHHHHHHHHHHHH CS
                      NTPase_1  1 kvfiTGppGvGKtTlvkkvlell 23
                                  +++iTG pGvGKtT+ k + + l
  gi|15669239|ref|NP_248044.1|  2 RIAITGTPGVGKTTISKVLRDRL 24
                                  689***********988777766 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.045
                                  ---EEEEEET.T--EEEEEETT---SSEETTEEE-HHHHHHHHHHHHHH CS
                      NTPase_1 43 rrigFkivdlasgeegiLarveakreprvgkyvvdvesfeelalealrk 91
                                   r g k++d+++  +++   +e  +   +++yv+d e++e++ ++ +++
  gi|15669239|ref|NP_248044.1| 22 DRLGIKVIDITEAVKKYKLYTE--KDEDMDSYVIDFEKLEKF-IDEIEE 67
                                  5899999**9766666544444..7899**********9997.555554 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.16
                                   -SHHHHHHHT-TT-EEEE--TTTTT..THH CS
                      NTPase_1 137 dlalveeirerkdvkvfevteenrd..all 164
                                   + ++++   +++++kv+e++  nrd  +++
  gi|15669239|ref|NP_248044.1| 116 QAEILDVCLCESKGKVYEIDTTNRDveNIV 145
                                   45577777888999*********9944444 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.7e-05     0.013       2      69 ..       4      75 ..       3      79 .. 0.70
   2 ?   -1.5   0.0       3.5   1.8e+03      51      51 ..     116     116 ..      70     152 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-05
               Viral_helicase1  2 vvhGvpGcGKStlirkllrts.....liltvnrptaelltegk..pklpnlsvrtvdsflmalvkstkgkililD 69
                                   + G pG GK+t i k+lr++      ++t+ ++  +l+te    +++   + + +++f     ++   k++ilD
  gi|15669239|ref|NP_248044.1|  4 AITGTPGVGKTT-ISKVLRDRlgikvIDITEAVKKYKLYTEKDedMDSYVIDFEKLEKFIDEIEEK--EKTIILD 75
                                  699*********.*******9887776666666667777777655555555555555555555543..6777776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.5
               Viral_helicase1  51 d 51 
                                   +
  gi|15669239|ref|NP_248044.1| 116 Q 116
                                   2 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   3.3e-05     0.016       8      46 ..       3      32 ..       2      83 .. 0.69
   2 ?   -1.9   0.0       7.7   3.8e+03      44      66 ..     133     154 ..     100     162 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.3e-05
                        AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvt 46
                                  +++tG +G+GKTt  + l+++l         + +v+ +t
  gi|15669239|ref|NP_248044.1|  3 IAITGTPGVGKTTISKVLRDRL---------GIKVIDIT 32
                                  68*******************9.........44444333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.7
                        AAA_22  44 fvtlpsstsskdllrellralgl 66 
                                   +++ ++    +++  e+ +a+++
  gi|15669239|ref|NP_248044.1| 133 EIDTTNRD-VENIVDEIIEAIKH 154
                                   33333333.45555555555554 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.8    0.0033       1.7     100     134 ..      81     151 ..       5     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0033
                                   TSEESEEEEEE--HHHHHHHHHT....................................GSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx....................................xxxxxxxxxxxx RF
                           ADK 100 kvkldlvleldvpeevlveRltg....................................DneetvkkRlet 134
                                     + d+++ l+++ e+++eRl +                                    D e+ v + +e+
  gi|15669239|ref|NP_248044.1|  81 LLNPDYIIVLRCNPEIIKERLEKrgykpkkvleniqaeildvclceskgkvyeidttnrDVENIVDEIIEA 151
                                   35678888888888888888888777777777777777777777777777777776666555555555554 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.1   3.3e-05     0.017      15      93 ..      30     112 ..      18     115 .. 0.83
   2 ?    0.5   0.1       1.5   7.6e+02      54      84 ..     109     139 ..      95     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.3e-05
                                   T-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHH...HHHHHHHHHHHH..HSS--EEEEE-TT-S-------- CS
               AMP-binding_C_2  15 eieevepeYqivvtregelDelevkvEvkegfsdelkelea...lekkiakklksk..lgvsvkvelvepgtlprsegKak 90 
                                   +i e+ ++Y+++ ++++++D+  +  E  e+f de++e+e+   l+ ++++ l+    + ++++ e+++ + l++  +K k
  gi|15669239|ref|NP_248044.1|  30 DITEAVKKYKLYTEKDEDMDSYVIDFEKLEKFIDEIEEKEKtiiLDGHVSHLLNPDyiIVLRCNPEIIK-ERLEKRGYKPK 109
                                   6788899*****************************999987778899999998773344567777776.56777788888 PP

                                   -EE CS
               AMP-binding_C_2  91 rvi 93 
                                   +v+
  gi|15669239|ref|NP_248044.1| 110 KVL 112
                                   886 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHHHSS--EEEEE-TT-S-- CS
               AMP-binding_C_2  54 ealekkiakklksklgvsvkvelvepgtlpr 84 
                                   +++ ++i++++ +++ ++ k ++ e +t +r
  gi|15669239|ref|NP_248044.1| 109 KKVLENIQAEILDVCLCESKGKVYEIDTTNR 139
                                   5666777777777777777777777777666 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   3.4     0.012       6.1      22      79 ..       3      60 ..       1      80 [. 0.62
   2 ?   11.7   0.4   0.00024      0.12      59     131 ..      93     168 ..      83     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                        ATPase 22 vlitGepGtGKtifalqFlikgaekygepgvfvtveepa....edlrenakslGwdleklee 79
                                  + itG+pG GKt++++   ++   + g +++ +t   ++    ++  e++ s  +d+ekle+
  gi|15669239|ref|NP_248044.1|  3 IAITGTPGVGKTTISKV--LRD--RLGIKVIDITEAVKKyklyTEKDEDMDSYVIDFEKLEK 60
                                  78***********9983..333..44666666666666533443333445555555555554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00024
                        ATPase  59 paedlrenakslGwdlekleeegklaiidasesaeesaee...kdkedleelieelaeaikeikakrvviDsitgl 131
                                   ++e ++e+ ++ G   +k+ e+ +  i+d+   +++ +     +++ d+e++++e+ eaik++k+++ v+D  + +
  gi|15669239|ref|NP_248044.1|  93 NPEIIKERLEKRGYKPKKVLENIQAEILDVCLCESKGKVYeidTTNRDVENIVDEIIEAIKHKKERKGVVDWTEKY 168
                                   678899999999999999999999999998654433222236699**************************87766 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   5.3   0.00013     0.065       5      71 ..       3      75 ..       1     173 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                        AAA_14  5 lvitGaRrvGKTtllkqlikell.........vkkesilyinldderdkkladpekllelileklkeekktylflD 71
                                  ++itG   vGKTt+ k l +++l         + k+  ly + d++ d+   d+ekl+++i e  +e k++ ++lD
  gi|15669239|ref|NP_248044.1|  3 IAITGTPGVGKTTISKVL-RDRLgikviditeAVKKYKLYTEKDEDMDSYVIDFEKLEKFIDEI-EE-KEKTIILD 75
                                  689***********6555.666668887766655566666666666666666777777777774.44.66778888 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.2e-05     0.041       1      45 [.       3      49 ..       3      86 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.2e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl...............klkkkdsvysrnpeddfwd 45
                                  i ++G +g+GK+t++k L ++l  k+               k             d+ +d
  gi|15669239|ref|NP_248044.1|  3 IAITGTPGVGKTTISKVLRDRLGIKViditeavkkyklyteK-------------DEDMD 49
                                  5699*****************996666777444444444432.............22233 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   4.8   0.00013     0.065       4      72 ..       2      75 ..       1     171 [. 0.60

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                        AAA_24  4 kiliyGpsgiGKTtlakelgpkplfi..............dtekGlksldadkfpdie.......swedfldevvelaaelad 65
                                  +i+i+G +g+GKTt+ k l  + l i                          k +d+        ++e+f+de++e    +  
  gi|15669239|ref|NP_248044.1|  2 RIAITGTPGVGKTTISKVL-RDRLGIkviditeavkkyklY---------TEKDEDMDsyvidfeKLEKFIDEIEEK---E-- 69
                                  89*****************.444433333323322222221.........333333334333111334444444444...2.. PP

                        AAA_24 66 yktlviD 72
                                   kt+++D
  gi|15669239|ref|NP_248044.1| 70 -KTIILD 75
                                  .234433 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00014     0.069       2      44 ..       3      34 ..       2      89 .. 0.71
   2 ?   -2.2   0.0       5.7   2.8e+03     153     168 ..     102     117 ..      85     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                           PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldra 44
                                  I+++g  G Gktt+++ l++++g + +            +++a
  gi|15669239|ref|NP_248044.1|  3 IAITGTPGVGKTTISKVLRDRLGIKVID-----------ITEA 34
                                  9**********************44433...........2222 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.7
                           PRK 153 aeRGrsleavldsilr 168
                                   ++RG++ + vl++i++
  gi|15669239|ref|NP_248044.1| 102 EKRGYKPKKVLENIQA 117
                                   6899999999998875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00021       0.1     103     138 ..       4      39 ..       2      55 .. 0.86
   2 ?   -2.1   0.0       6.2   3.1e+03      46      46 ..     119     119 ..      86     158 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                                   EEECSTTSSHHHHHHHHCTT-----S---------- CS
                   RsgA_GTPase 103 vlvGqSGvGKStLinallpelelktgevseklgrGk 138
                                   ++ G  GvGK+t+ ++l+ +l +k+ ++ e+ ++ k
  gi|15669239|ref|NP_248044.1|   4 AITGTPGVGKTTISKVLRDRLGIKVIDITEAVKKYK 39 
                                   689*************************99988755 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.2
                                   T CS
                   RsgA_GTPase  46 g 46 
                                    
  gi|15669239|ref|NP_248044.1| 119 I 119
                                   1 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00041       0.2      20     103 ..       4      77 ..       2     112 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
                    Zeta_toxin  20 llgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdaselvekllqeaiengyniiv 100
                                    + G pG GK+++++ l+d+l  + +v+ + +  ++++   y e    +++++ +++ ++ +   ek ++e+ e+   ii+
  gi|15669239|ref|NP_248044.1|   4 AITGTPGVGKTTISKVLRDRL--GIKVIDITE-AVKKYK-LYTE----KDEDMDSYVIDFEK--LEKFIDEIEEKEKTIIL 74 
                                   688*****************9..666666643.334433.3444....55555555555432..46666777777777777 PP

                    Zeta_toxin 101 egt 103
                                   +g 
  gi|15669239|ref|NP_248044.1|  75 DGH 77 
                                   665 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.6      0.35   1.7e+02      65      92 ..      43      71 ..      29      75 .. 0.61
   2 ?   11.2   0.7   0.00066      0.33       6      33 ..      89     116 ..      81     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.35
                                  TT.S-TCCCCCCCHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N 65 kk.edaeeliaevkelkeelkaleaelke 92
                                  +k ed ++ + + ++l + ++++e+++k+
  gi|15669239|ref|NP_248044.1| 43 EKdEDMDSYVIDFEKLEKFIDEIEEKEKT 71
                                  22366666777777777777777777665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00066
                                   HHHH-HHHHHHHHCCCTCCCHHHHHHHH CS
                  Seryl_tRNA_N   6 lirenpeavkeklkkRgedkadvdelle 33 
                                    +r npe +ke+l+kRg  +++v e ++
  gi|15669239|ref|NP_248044.1|  89 VLRCNPEIIKERLEKRGYKPKKVLENIQ 116
                                   4788*************55555544444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.4   0.00043      0.21       1      55 [.       2      57 ..       2     166 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00043
                                  EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGG CS
                      MMR_HSR1  1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpG 55
                                  ++ai G p vGK+t+ + l ++   +v d+  + ++ + ++ k ++ + +++D   
  gi|15669239|ref|NP_248044.1|  2 RIAITGTPGVGKTTISKVLRDRlGIKVIDITEAVKKYKLYTEKDEDMDSYVIDFEK 57
                                  69***************999885456666666666655555554445566666555 PP

>> DUF5611  Domain of unknown function (DUF5611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3    0.0014      0.72      17      63 ..      30      77 ..      23      89 .. 0.85
   2 ?    4.1   0.4      0.17        86       7      41 ..     103     141 ..      98     171 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0014
                                  HHHHHHHHHT.-EEEEE.TTEEEEE-TTBS-EEEEE..-SS-EEEEE- CS
                       DUF5611 17 rlkelleeyfggeveee.gdllvvsfgaikklevkisskkkklvvdte 63
                                  +++e +++y   ++++e  d +v++f++++k+  +i++k+k++++d +
  gi|15669239|ref|NP_248044.1| 30 DITEAVKKYKLYTEKDEdMDSYVIDFEKLEKFIDEIEEKEKTIILDGH 77
                                  7899999999877777769*****************999999998865 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.17
                                   -SSS--SH..HHHHHHHHHHT.-EEEEETTEEEEE.....- CS
                       DUF5611   7 KrGfkkeee.erlkelleeyfggeveeegdllvvs.....f 41 
                                   KrG+k+++  e++++++ ++     e++g ++ ++      
  gi|15669239|ref|NP_248044.1| 103 KRGYKPKKVlENIQAEILDVC--LCESKGKVYEIDttnrdV 141
                                   778887777777777777776..456666666664344442 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   0.00027      0.14      13      35 ..       2      24 ..       1     161 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00027
                                  EEEEEESTTSSHHHHHHHHTTSS CS
                                  xxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 13 kvaivGenGaGKStLlkllagll 35
                                  ++ai+G  G GK+t+ k+l   l
  gi|15669239|ref|NP_248044.1|  2 RIAITGTPGVGKTTISKVLRDRL 24
                                  689***************98665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00034      0.17      31      50 ..       2      21 ..       1      35 [. 0.79
   2 ?   -2.6   0.0       4.4   2.2e+03     216     226 ..     143     153 ..     113     165 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                                  EEEEEE-TTSSHHHHHHHHH CS
                          MeaB 31 vvGltGvPGaGkstlvealg 50
                                  ++ +tG+PG+Gk t+ + l 
  gi|15669239|ref|NP_248044.1|  2 RIAITGTPGVGKTTISKVLR 21
                                  899*********99765554 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.4
                                   BSHHHHHHHHH CS
                          MeaB 216 eGidelvdaie 226
                                   + +de+++ai+
  gi|15669239|ref|NP_248044.1| 143 NIVDEIIEAIK 153
                                   23333444333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00056      0.28      27      51 ..       3      27 ..       2      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00056
                        AAA_16 27 vllsGesGvGKsslvrellralekd 51
                                  + ++G +GvGK+++ + l+++l  +
  gi|15669239|ref|NP_248044.1|  3 IAITGTPGVGKTTISKVLRDRLGIK 27
                                  579************9999988765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00044      0.22      22      63 ..       3      42 ..       1      80 [. 0.68
   2 ?   -1.8   0.0       5.8   2.9e+03      91     102 ..     156     167 ..     117     176 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00044
                                  EEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEEEE.. CS
                          TsaE 22 ilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeYelek 63
                                  i+++G  G+GKTt+++ l   lg++  +++      v++Y+l +
  gi|15669239|ref|NP_248044.1|  3 IAITGTPGVGKTTISKVLRDRLGIKviDIT----EAVKKYKLYT 42
                                  7899********************855554....3344444444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.8
                                   TSCEEEEETGGG CS
                          TsaE  91 eeavvlvEWpek 102
                                   +e   +v W ek
  gi|15669239|ref|NP_248044.1| 156 KERKGVVDWTEK 167
                                   224556777776 PP

>> Fe-S_assembly  Iron-sulphur cluster assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2     0.002      0.97      13      41 ..      40      69 ..      31      72 .. 0.84
   2 ?    0.7   0.0       1.6   8.2e+02      50      58 ..     110     118 ..     100     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.002
                 Fe-S_assembly 13 Lyeky.pdvdpltvrFtdLhewvleLpefd 41
                                  Ly+++ +d+d + + F++L++ + e++e +
  gi|15669239|ref|NP_248044.1| 40 LYTEKdEDMDSYVIDFEKLEKFIDEIEEKE 69
                                  5544449****************9999876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.6
                 Fe-S_assembly  50 kiLEaIqma 58 
                                   k+LE+Iq+ 
  gi|15669239|ref|NP_248044.1| 110 KVLENIQAE 118
                                   89*****85 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0014      0.71      22      40 ..       4      22 ..       2      44 .. 0.89
   2 ?   -1.1   0.0       2.6   1.3e+03     100     123 ..      53      76 ..      45      79 .. 0.86
   3 ?   -2.6   0.0       7.6   3.8e+03     143     174 ..     126     157 ..     116     167 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                        AAA_30 22 vltGpAGtGKttalkalre 40
                                  ++tG +G GKtt+ k+lr+
  gi|15669239|ref|NP_248044.1|  4 AITGTPGVGKTTISKVLRD 22
                                  69***********999986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.6
                        AAA_30 100 vdtkqlaallkaaekagakvilvG 123
                                   +d+++l+++++++e+++ ++il G
  gi|15669239|ref|NP_248044.1|  53 IDFEKLEKFIDEIEEKEKTIILDG 76 
                                   689999999999999999999877 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.6
                        AAA_30 143 aagigtaeLtevvRqkeseeraaalalregda 174
                                   +++ ++ e+++  R  e+   ++ +a+++ ++
  gi|15669239|ref|NP_248044.1| 126 ESKGKVYEIDTTNRDVENIVDEIIEAIKHKKE 157
                                   45556666666666655555555555555554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3    0.0013      0.65       4      25 ..       5      26 ..       2     102 .. 0.91
   2 ?   -0.3   0.1       1.9   9.5e+02      65      91 ..     128     154 ..      91     167 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0013
                                  EE--SSSSHHHHHHHGGGGBS- CS
                         AAA_5  4 LvGppGtgKselaerlaaalnr 25
                                  + G pG+gK+++++ l  +l+ 
  gi|15669239|ref|NP_248044.1|  5 ITGTPGVGKTTISKVLRDRLGI 26
                                  78**************999854 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.9
                                   G-SEEEEESGGG--HHHHHHHHHHHHS CS
                         AAA_5  65 egeilvlDEveraesevlnsLlsllee 91 
                                   +g+++ +D  +r   +++++ +  + +
  gi|15669239|ref|NP_248044.1| 128 KGKVYEIDTTNRDVENIVDEIIEAIKH 154
                                   555555555554444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1514  (0.0844442); expected 358.6 (0.02)
Passed bias filter:                      772  (0.0430587); expected 358.6 (0.02)
Passed Vit filter:                       138  (0.00769703); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 1087.06
//
Query:       gi|15669240|ref|NP_248045.1|  [L=513]
Description: nodulation protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-58  197.1   0.0    2.4e-58  196.4   0.0    1.3  1  Carbam_trans_C  Carbamoyltransferase C-terminus
    8.2e-36  124.3   0.2    2.5e-28   99.7   0.1    2.2  2  Carbam_trans_N  Carbamoyltransferase N-terminus
    1.5e-05   24.9   0.0    2.3e-05   24.2   0.0    1.2  1  Peptidase_M22   Glycoprotease family
  ------ inclusion threshold ------
       0.12   11.8   0.0       0.24   10.9   0.0    1.4  1  Sua5_yciO_yrdC  Telomere recombination


Domain annotation for each model (and alignments):
>> Carbam_trans_C  Carbamoyltransferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.4   0.0   5.5e-62   2.4e-58       3     170 .]     346     511 ..     344     511 .. 0.98

  Alignments for each domain:
  == domain 1  score: 196.4 bits;  conditional E-value: 5.5e-62
                Carbam_trans_C   3 llaegkvvgwfqgrmEfGpRALGnRSiladprkeemkeklnekikkResfrPfApsvleeeaeeyfeeekespymllvakv 83 
                                   l+ ++kvv++ +g+mEfGpRALGnRS++a p+ke+ kek+n+k+k R +f+PfAp++l + +++y+ + + sp+m+ ++kv
  gi|15669240|ref|NP_248045.1| 346 LILDNKVVCLSRGKMEFGPRALGNRSVIALPTKEN-KEKINKKLK-RSWFMPFAPTILYDFIDDYLINPRYSPFMTQIFKV 424
                                   7899***************************9988.9********.***********************9*********** PP

                Carbam_trans_C  84 keekreeipavtHvDgtaRvqtvkkeanpryhelleafekltgvpvllNTSfNvrgepivetpedalelflkteldalvlg 164
                                   ke+k +ei+ v+HvD+t+R+qt+kk++n++++ +++ + ++ g+pv+lNTSfN++gepiv++ +da+++flk ++dal+lg
  gi|15669240|ref|NP_248045.1| 425 KENKIKEIEGVIHVDKTTRPQTLKKDSNKTFYGIIRYIYDSIGIPVVLNTSFNLHGEPIVCNEKDAINSFLKADFDALLLG 505
                                   ********************************************************************************* PP

                Carbam_trans_C 165 dllvek 170
                                   ++l++k
  gi|15669240|ref|NP_248045.1| 506 NYLISK 511
                                   ***987 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.7e-08   7.7e-05       2      64 ..       2      58 ..       1      64 [. 0.91
   2 !   99.7   0.1   5.7e-32   2.5e-28     115     337 ..      77     290 ..      63     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.7e-08
                Carbam_trans_N  2 ilGikltlflHDgavalvddgklvaaveeErltrikrdqklpklkaidyaleeagvelsdiDq 64
                                  ilGi  +   H ++  l++  ++++a+ eEr+tr+k ++++p+ k++dy+l  + v++ +i +
  gi|15669240|ref|NP_248045.1|  2 ILGICDG---HNASSSLIKRDEILFAMSEERFTRKKNQRGFPE-KSVDYIL--NKVKPDEINY 58
                                  8999999...*********************************.*******..7788887766 PP

  == domain 2  score: 99.7 bits;  conditional E-value: 5.7e-32
                Carbam_trans_N 115 lvekvdrkdvslyeHhlsHaaSaystSpFakkeklvlcldgdGdiaprllaveketelkikslvsfsesiGhlYaaateyl 195
                                   + +++++k  ++  Hh+sH    +  S F  ke+lv+ +dg Gd  + l  + ++++l i +     +s+G  Ya +te l
  gi|15669240|ref|NP_248045.1|  77 FQNRINKK-FLYFYHHISHSY-LFKLSDF--KEALVISIDGGGDGLSFLASIANKNNLEIIAQSDLIDSVGDFYASITELL 153
                                   44455555.4555699***76.89*****..****************************977777777************* PP

                Carbam_trans_N 196 GfkknsdegKlmalaayGkpkeriveelyellkkagyrinl.ennieiskkkvhdffeasalrlkearekdedlaAsiqvf 275
                                   Gfk+ +degK+m+l +y   ++  +  +  +++  +++ +l   + e++k+ +++++ + + +l  +   +  ++   q+ 
  gi|15669240|ref|NP_248045.1| 154 GFKPMEDEGKVMSLSSYEGEDDINLTTIDYIKELKSFKNYLgVIGYEATKA-LKKLIVSDKSQLSFED--KVRISKFAQRT 231
                                   *****************7666555666666666669999987566666666.5566665553333222..23789999*** PP

                Carbam_trans_N 276 lErlvvevlnivyeklkirnLclaGGvalNiklNsallesglFedvwvqPaanDsGsAiGAA 337
                                   lE++v++  + ++++ +i n+   GGva N+klNs++ e+    +++v+P+++D+G  +GA 
  gi|15669240|ref|NP_248045.1| 232 LENIVLKAIDDLSNEYNIDNIVFVGGVAQNVKLNSKIAEK---YNLFVPPFMGDEGLCLGAS 290
                                   *************************************998...58****************7 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   5.1e-09   2.3e-05     107     266 ..     107     284 ..      75     288 .. 0.59

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5.1e-09
                                   EEEEESSSTEEEEEE...CT.TEEEEEEE.ESSSEHHHHHHHHHHHHT..S..SCCHHHHHHHC.TC.S.......EET.. CS
                 Peptidase_M22 107 vvllvsGghtqvylv...ke.gryeilge.tlddaagealdkvarllglpy..pggpkieklak.eg.kkiefprplkg.. 176
                                   +v+ ++Gg + + +     + ++ ei+++  l d +g+ + ++++llg++   ++g k+ +l + eg ++i+++    +  
  gi|15669240|ref|NP_248045.1| 107 LVISIDGGGDGLSFLasiANkNNLEIIAQsDLIDSVGDFYASITELLGFKPmeDEG-KVMSLSSyEGeDDINLTTI--Dyi 184
                                   6777777666544321112336677665515689***************9854444.4444666588866552222..122 PP

                                   ......TEEE.C.H.HHHHHHHHH..STT........HHHHHHHHHHHHHHHHHHHHHH.HHHHCTBSEEEEESGGGGXHH CS
                 Peptidase_M22 177 ......ldfsfs.G.lktavlkel..eke........vedlaasfqeavvdhlvekter.alklpkakelvilGGvaankr 238
                                         +++  + G ++t++lk+l  + +        +  +    q++ ++++v k+ +   ++++++++v +GGva+n +
  gi|15669240|ref|NP_248045.1| 185 kelksfKNYLGViGyEATKALKKLivS-DksqlsfedKVRISKFAQRT-LENIVLKAIDdLSNEYNIDNIVFVGGVAQNVK 263
                                   335446333332231334444444442.14678898855555555555.555555554404556***************** PP

                                   HHHCHCCHHHHTTSEEEXXXHHHHSSXC CS
                 Peptidase_M22 239 LrealeeeaeelglkliiPplkyctdna 266
                                   L+++++e     +++l++Pp  ++ d++
  gi|15669240|ref|NP_248045.1| 264 LNSKIAE-----KYNLFVPP--FMGDEG 284
                                   ***9973.....34789***..999986 PP

>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.3e-05      0.24     110     156 ..     459     507 ..     455     513 .] 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.3e-05
                                   HHHHHHHCTS-.EEEEES-STTS-S-SSHHHHHHH.C-TTSECB-SS-- CS
                Sua5_yciO_yrdC 110 arlLlealgep.lvaTSanlsgepsitdaeeveee.lgeivdlildgge 156
                                   +r + + +g p +  TS nl+gep++ +++++ +  l++ +d++l g+ 
  gi|15669240|ref|NP_248045.1| 459 IRYIYDSIGIPvVLNTSFNLHGEPIVCNEKDAINSfLKADFDALLLGNY 507
                                   566777778786778**********9999999988789******99984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 3057.06
//
Query:       gi|15669241|ref|NP_248046.1|  [L=100]
Description: hypothetical protein MJ_1052 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-29  102.2   0.4    1.2e-29  102.0   0.4    1.0  1  Thiamine_BP  Thiamine-binding protein
    0.00067   20.1   0.0    0.00079   19.9   0.0    1.1  1  Ykof         YKOF-related Family
  ------ inclusion threshold ------
      0.011   16.0   0.1      0.016   15.5   0.1    1.3  1  DUF5514      Family of unknown function (DUF5514)
      0.014   15.7   0.1      0.016   15.6   0.1    1.1  1  DUF3510      Domain of unknown function (DUF3510)
      0.045   14.2   0.3       0.89   10.1   0.0    2.4  2  RuvA_C       RuvA, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiamine_BP  Thiamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.4   3.4e-33   1.2e-29       1      90 [.       9      96 ..       9      98 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 3.4e-33
                                  EEEEEEECSSSSSGHHHHHHHHHHHHHTTSSEEEEETTEEEEEEEHHHHHHHHHHHHHHHHCTTSSEEEEEEEEEEESSS--- CS
                   Thiamine_BP  1 veisviPlgtegesvskyVakvvevlkesglkyeltpmgTtiegeldevmevvkkahealfeaGakRvstvikiddrrdkeqt 83
                                  +e+s+iPlg+ g+svskyV+k++ev k+ +lk e+++mgT++eg+lde++++ k+ah +++++ ++Rv++++kid+r+dke+t
  gi|15669241|ref|NP_248046.1|  9 AEVSIIPLGK-GASVSKYVKKAIEVFKKYDLKVETNAMGTVLEGDLDEILKAFKEAHSTVLND-VDRVVSSLKIDERKDKENT 89
                                  699******8.***************************************************9.******************* PP

                                  HHHHHHH CS
                   Thiamine_BP 84 leeKvks 90
                                  +e+K+k+
  gi|15669241|ref|NP_248046.1| 90 IERKLKA 96
                                  ****997 PP

>> Ykof  YKOF-related Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.2e-07   0.00079       4      69 ..       9      75 ..       6      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.2e-07
                                  EEEEEEETTSTTHHHH.HHHHHHHCHHTTSEEEEETTEEEEECBHHHHHHHHHHHHHHHHCCSSSEE CS
                          Ykof  4 aqfsLYpmgadDyvdv.IlgaldlldkskvrvetdhiatrlrGdveevFdalkavflkaaqsvkHvv 69
                                  a +s+ p+g++  v++ +++a+++ +k  ++vet+ + t+l+Gd +e+ +a k++   + + v+ vv
  gi|15669241|ref|NP_248046.1|  9 AEVSIIPLGKGASVSKyVKKAIEVFKKYDLKVETNAMGTVLEGDLDEILKAFKEAHSTVLNDVDRVV 75
                                  667888888888887647899**********************************999988888776 PP

>> DUF5514  Family of unknown function (DUF5514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   4.4e-06     0.016      73     123 ..      23      72 ..      13      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.4e-06
                       DUF5514  73 kkyritefelwkkhegdstydkgfgiviegsmdnpilkfkevysgslddwn 123
                                    ky    +e++kk++      +++g v+eg +d+ +  fke +s  l+d +
  gi|15669241|ref|NP_248046.1|  23 SKYVKKAIEVFKKYDLKV-ETNAMGTVLEGDLDEILKAFKEAHSTVLNDVD 72 
                                   578888899999998765.46789**********9999*********9976 PP

>> DUF3510  Domain of unknown function (DUF3510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1   4.4e-06     0.016      31     101 ..      21      87 ..       4      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.4e-06
                       DUF3510  31 epSkyvseilkplktfkkesekklseevleewlaevleevtsrYletisevlssvkkteesLkrlkkarkg 101
                                   + Skyv+++++ +k+       k++ +++  +l+  l+e+ +++ e+ s vl+ v +  +sLk   ++ k+
  gi|15669241|ref|NP_248046.1|  21 SVSKYVKKAIEVFKKY----DLKVETNAMGTVLEGDLDEILKAFKEAHSTVLNDVDRVVSSLKIDERKDKE 87 
                                   6799999999999985....34488899999*******************************976665554 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00025      0.89      21      43 ..       5      30 ..       4      31 .. 0.95
   2 ?    1.9   0.1     0.091   3.2e+02      19      40 ..      70      91 ..      68      98 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                                  HHHHHHHHC...-TTS-HHHHHHHHH CS
                        RuvA_C 21 ekAvakvla...npgasveelIraAL 43
                                  +k+va+v+    ++gasv+ ++++A+
  gi|15669241|ref|NP_248046.1|  5 RKVVAEVSIiplGKGASVSKYVKKAI 30
                                  69***********************8 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.091
                                  HHHHHHHHHHC-TTS-HHHHHH CS
                        RuvA_C 19 eaekAvakvlanpgasveelIr 40
                                  +++++v++++ ++  + e+ I 
  gi|15669241|ref|NP_248046.1| 70 DVDRVVSSLKIDERKDKENTIE 91
                                  7899*****9855555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1192  (0.0664845); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 701.67
//
Query:       gi|15669242|ref|NP_248047.1|  [L=163]
Description: hypothetical protein MJ_1053 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-07   28.4   1.4    4.6e-06   26.3   0.1    2.3  2  HTH_38           Helix-turn-helix domain
    1.3e-05   24.8   0.1    2.9e-05   23.7   0.1    1.6  1  HTH_23           Homeodomain-like domain
    0.00022   21.1   1.5     0.0017   18.3   0.0    2.5  2  HTH_11           HTH domain
     0.0004   20.0   0.6     0.0011   18.6   0.0    2.0  1  Sigma70_r4_2     Sigma-70, region 4
    0.00049   19.6   9.0    0.00057   19.4   9.0    1.1  1  Cluap1           Clusterin-associated protein-1
    0.00099   19.5  12.6      0.013   16.0  11.8    2.8  1  HTH_40           Helix-turn-helix domain
     0.0018   17.6   1.1     0.0023   17.2   1.1    1.0  1  HIGH_NTase1      HIGH Nucleotidyl Transferase
     0.0025   17.3   0.0     0.0025   17.3   0.0    2.4  2  HTH_24           Winged helix-turn-helix DNA-binding
     0.0027   17.7   0.0      0.006   16.6   0.0    1.6  1  HTH_29           Winged helix-turn helix
     0.0027   17.9   3.2     0.0066   16.7   3.2    1.7  1  Mto2_bdg         Micro-tubular organiser Mto1 C-term Mto2-bin
     0.0037   17.3   1.6     0.0037   17.3   1.6    1.7  1  TolA_bind_tri    TolA binding protein trimerisation
     0.0039   16.7   0.1      0.011   15.3   0.0    1.8  1  GerE             Bacterial regulatory proteins, luxR family
     0.0053   17.1   8.8     0.0053   17.1   8.8    2.8  2  FlaC_arch        Flagella accessory protein C (FlaC)
     0.0064   15.5   1.0      0.011   14.8   0.9    1.3  1  TnsD             Tn7-like transposition protein D
     0.0069   15.9   1.1      0.011   15.2   0.1    1.8  1  Sigma70_r4       Sigma-70, region 4
     0.0076   16.3   2.9      0.021   14.9   2.9    1.9  1  NYD-SP28_assoc   Sperm tail C-terminal domain
     0.0085   16.2   5.0      0.016   15.3   5.0    1.4  1  DUF148           Domain of unknown function DUF148
  ------ inclusion threshold ------
       0.01   15.8   0.6       0.01   15.8   0.6    2.4  2  HTH_19           Helix-turn-helix domain
      0.011   15.8   0.1      0.021   14.9   0.1    1.5  1  HTH_28           Helix-turn-helix domain
      0.011   16.0   8.8       0.27   11.5   6.2    2.4  2  DUF4164          Domain of unknown function (DUF4164)
      0.011   15.7   0.3      0.011   15.7   0.3    2.7  2  HTH_3            Helix-turn-helix
      0.012   16.0   0.1      0.025   14.9   0.1    1.7  1  HTH_31           Helix-turn-helix domain
      0.013   15.3   4.6      0.013   15.3   4.6    1.9  2  LXG              LXG domain of WXG superfamily
      0.017   15.0   1.4      0.029   14.3   0.0    2.1  1  Terminase_5      Putative ATPase subunit of terminase (gpP-li
       0.02   15.4  10.1      0.021   15.3  10.1    1.2  1  AAA_23           AAA domain
      0.021   14.6   2.9      0.046   13.5   2.9    1.6  1  CCDC92           Coiled-coil domain of unknown function
      0.025   14.6   0.0      0.057   13.5   0.0    1.7  1  HTH_20           Helix-turn-helix domain
      0.028   13.0   3.0      0.031   12.8   3.0    1.1  1  Herpes_UL6       Herpesvirus UL6 like
      0.031   14.0   1.2      0.061   13.1   0.1    2.1  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.037   13.4   2.1      0.046   13.1   2.1    1.1  1  FliD_C           Flagellar hook-associated protein 2 C-termin
      0.042   14.0   0.5       0.42   10.8   0.5    2.7  1  HTH_17           Helix-turn-helix domain
      0.042   14.1   7.4       0.19   12.0   7.7    1.9  1  HALZ             Homeobox associated leucine zipper
       0.06   13.6   3.3        7.2    6.9   0.0    2.8  3  DUF2316          Uncharacterized protein conserved in bacteri
      0.065   13.3   0.3       0.17   12.0   0.3    1.7  1  DUF3489          Protein of unknown function (DUF3489)
      0.074   13.0   0.1       0.13   12.2   0.1    1.4  1  MarR_2           MarR family
      0.086   12.4   5.3      0.092   12.3   5.3    1.2  1  Cas_DxTHG        CRISPR-associated (Cas) DxTHG family
      0.088   12.7   4.4       0.46   10.3   0.0    2.2  2  Sigma70_ECF      ECF sigma factor
      0.096   12.8   9.0       0.21   11.6   8.9    1.5  1  ADIP             Afadin- and alpha -actinin-Binding
       0.16   12.4  13.5       0.61   10.5   0.4    2.6  2  Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_
       0.16   12.4  14.6      0.074   13.5  11.5    2.0  2  ZapB             Cell division protein ZapB
       0.17   11.5   1.0       0.38   10.4   1.0    1.6  1  NAT              NAT, N-acetyltransferase, of N-acetylglutama
        0.2   11.8   8.5       0.27   11.4   8.5    1.2  1  Med30            Mediator complex subunit 30
       0.22    9.3  12.0       0.25    9.1  12.0    1.1  1  Nup88            Nuclear pore component
       0.23   10.6   7.2       0.26   10.4   7.2    1.2  1  Tho2             Transcription factor/nuclear export subunit 
       0.23   12.0   1.5        3.5    8.2   1.7    2.4  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.26   11.8  18.0       0.17   12.4  16.4    1.5  1  APG6_N           Apg6 coiled-coil region
       0.27   11.0  12.4      0.079   12.7   6.1    2.6  2  DivIC            Septum formation initiator
       0.39   10.8  14.8       0.73    9.9  14.8    1.5  1  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.42   10.7   4.8       0.57   10.3   3.2    2.1  1  YojJ             Bacterial membrane-spanning protein N-termin
        0.5    9.6   4.7       0.69    9.2   4.7    1.1  1  CorA             CorA-like Mg2+ transporter protein
        0.5    9.2  14.5       0.66    8.8  14.5    1.2  1  Spc7             Spc7 kinetochore protein
       0.53   10.7   5.3       0.43   11.0   3.6    1.7  1  Goodbye          fungal STAND N-terminal Goodbye domain
       0.65   10.3  10.8       0.41   11.0   8.5    1.7  2  Gp-FAR-1         Nematode fatty acid retinoid binding protein
       0.73   10.0  11.3        0.4   10.8   7.0    2.4  2  Swi5             Swi5
       0.97   10.0  12.2        2.3    8.8   8.8    2.1  2  DUF16            Protein of unknown function DUF16
          1    9.3   8.2        1.3    9.0   6.9    1.7  2  DUF4446          Protein of unknown function (DUF4446)
          1    9.4   6.9       0.17   11.9   2.9    1.9  1  MCC-bdg_PDZ      PDZ domain of MCC-2 bdg protein for Usher sy
        1.1    9.4  17.6       0.16   12.1  13.0    2.0  1  bZIP_1           bZIP transcription factor
        1.7    8.8   5.1        3.7    7.7   5.1    1.6  1  VGCC_beta4Aa_N   Voltage gated calcium channel subunit beta d
        1.8    8.5  15.0        0.5   10.3  10.9    1.6  2  Ax_dynein_light  Axonemal dynein light chain
        2.2    8.6  16.8        4.6    7.5  16.7    1.7  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        2.2    6.1   6.0        2.4    6.0   6.0    1.1  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        2.2    7.3   6.4        2.5    7.1   6.4    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        2.4    8.4   8.9        4.5    7.6   1.4    2.6  2  DUF948           Bacterial protein of unknown function (DUF94
        2.5    8.6   7.7        3.2    8.3   5.5    2.1  2  PhoU             PhoU domain
        2.5    8.1  15.5        3.4    7.7  15.5    1.3  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
        3.8    7.6   8.6        4.1    7.5   8.2    1.4  1  DUF4337          Domain of unknown function (DUF4337)
        4.5    7.9  10.1        5.1    7.8   3.4    2.5  2  DUF883           Bacterial protein of unknown function (DUF88
        5.2    7.2  12.5        3.9    7.6   0.0    3.0  2  Sigma70_r3       Sigma-70 region 3
        5.3    7.6   8.0         13    6.3   8.0    1.8  1  DUF4140          N-terminal domain of unknown function (DUF41
        5.9    7.3  10.5        7.3    7.0   8.9    1.9  1  DUF2175          Uncharacterized protein conserved in archaea
          6    7.1  18.8        2.9    8.1  11.4    2.4  2  Med21            Subunit 21 of Mediator complex
        6.4    5.9   8.8         14    4.8   8.7    1.6  1  TMPIT            TMPIT-like protein
        7.2    6.9  10.6        1.3    9.3   6.9    1.7  1  Spc24            Spc24 subunit of Ndc80
        7.3    6.5   9.1          6    6.7   5.0    2.1  2  DUF2570          Protein of unknown function (DUF2570)
        7.4    7.3  11.8        7.3    7.3   8.1    2.1  2  YabA             Initiation control protein YabA
        8.2    7.6   6.6         12    7.0   6.6    1.6  1  DUF5320          Family of unknown function (DUF5320)


Domain annotation for each model (and alignments):
>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1     2e-08   4.6e-06      18      42 ..      57      81 ..      41      82 .. 0.92
   2 ?    0.5   0.1       2.3   5.4e+02      11      22 ..     131     142 ..     130     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2e-08
                        HTH_38 18 aeGlslreIArrLgrspsTIsRElk 42
                                  ++G+++reIA +Lgr  +TI ++lk
  gi|15669242|ref|NP_248047.1| 57 KAGYTIREIADELGRTEQTIRKHLK 81
                                  69********************998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.3
                        HTH_38  11 eeIerllaeGls 22 
                                   eeIe+l +e++ 
  gi|15669242|ref|NP_248047.1| 131 EEIEKLKKENEE 142
                                   79*****99974 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   1.2e-07   2.9e-05      13      39 ..      53      81 ..      47      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.2e-07
                        HTH_23 13 llae..GlsvreIAreLgvsrrTvyrwlk 39
                                  l++e  G+++reIA+eLg++++T+++ lk
  gi|15669242|ref|NP_248047.1| 53 LAREkaGYTIREIADELGRTEQTIRKHLK 81
                                  344468******************98766 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   7.2e-06    0.0017      16      37 ..      60      81 ..      52      88 .. 0.87
   2 ?    1.0   0.2       1.8   4.2e+02      34      47 ..     124     137 ..     123     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.2e-06
                        HTH_11 16 isgeeLAeeLnvSrrtvrrdIk 37
                                   ++ e+A+eL+++++t+r+++k
  gi|15669242|ref|NP_248047.1| 60 YTIREIADELGRTEQTIRKHLK 81
                                  6999****************98 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.8
                        HTH_11  34 rdIkaLeelgvpIe 47 
                                    dIk+Lee   ++ 
  gi|15669242|ref|NP_248047.1| 124 TDIKKLEEEIEKLK 137
                                   599***99876655 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   4.7e-06    0.0011      26      47 ..      59      80 ..      53      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.7e-06
                                  ---HHHHHHHHT--HHHHHHHH CS
                  Sigma70_r4_2 26 glsykEIAellgisegtVksrl 47
                                  g++++EIA +lg +e+t++++l
  gi|15669242|ref|NP_248047.1| 59 GYTIREIADELGRTEQTIRKHL 80
                                  99*******************9 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   9.0   2.5e-06   0.00057     124     210 ..      61     155 ..      43     163 .] 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.5e-06
                        Cluap1 124 aarqlaseitekgasLydlLekeve....lreartkalsrqleleeiekalkeaikkvk....eelektkkalenlesdea 196
                                   + r++a e+ ++ +++ ++L+ e++    +re+ +++ + +l++ee+ek l++ ++k +    ++++k+++++e+l+++++
  gi|15669242|ref|NP_248047.1|  61 TIREIADELGRTEQTIRKHLKGETKagklVRETYEMMKRGELNIEEVEKFLEAVVRKEElekiTDIKKLEEEIEKLKKENE 141
                                   5799*********************99999*********************99998765333357999************* PP

                        Cluap1 197 nLeakiekkkqele 210
                                   +L+ak+ek k+ l 
  gi|15669242|ref|NP_248047.1| 142 ELAAKLEKVKEKLK 155
                                   ********998876 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  11.8   5.4e-05     0.013      10      77 ..      57     155 ..      51     162 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.4e-05
                        HTH_40  10 eeglsieeIAkerglkesTIegHLaelieeg.............eeidlerl.......vseeeekeIeeaiekvgsek.. 68 
                                   + g++i eIA+e g +e+TI +HL    ++g             e +++e++       v +ee ++I+++ +k+++e   
  gi|15669242|ref|NP_248047.1|  57 KAGYTIREIADELGRTEQTIRKHLKGETKAGklvretyemmkrgE-LNIEEVekfleavVRKEELEKITDI-KKLEEEIek 135
                                   689*********************999999766666665555532.4443333334443455555555433.332221122 PP

                        HTH_40  69 ...........lkpikealp 77 
                                              l ++ke+l+
  gi|15669242|ref|NP_248047.1| 136 lkkeneelaakLEKVKEKLK 155
                                   22223555666666666665 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.1     1e-05    0.0023     181     297 ..      49     155 ..      42     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1e-05
                   HIGH_NTase1 181 kpvtikRegagyhdeelseeeeiaSAtaiRkalkeekkleelkklvPestleilkeelkkkaslsledlskllkyklltes 261
                                      ++ Re+agy  +e+ + e     + iRk+lk e    + +  + ++t+e++k+      +l+ e+++k+l++ +++e+
  gi|15669242|ref|NP_248047.1|  49 AAGALAREKAGYTIREIAD-ELGRTEQTIRKHLKGE----TKAGKLVRETYEMMKRG-----ELNIEEVEKFLEAVVRKEE 119
                                   55678999*****999976.57788899*****766....44566667789999888.....5689*************** PP

                   HIGH_NTase1 262 keelkkildvsegLenrikkalkkaesleelleklk 297
                                    e++++i +++e++e+  k++ + a +le++ eklk
  gi|15669242|ref|NP_248047.1| 120 LEKITDIKKLEEEIEKLKKENEELAAKLEKVKEKLK 155
                                   999999999999999888888777778887777776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.1e-05    0.0025      13      39 ..      55      81 ..      52      81 .. 0.93
   2 ?   -1.8   0.1       9.8   2.3e+03      22      42 ..     142     162 ..     140     163 .] 0.55

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-05
                        HTH_24 13 qknprisqreLAerlglSpstvnrrlk 39
                                  +++++ ++re+A++lg + +t++++lk
  gi|15669242|ref|NP_248047.1| 55 REKAGYTIREIADELGRTEQTIRKHLK 81
                                  6899*********************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 9.8
                        HTH_24  22 eLAerlglSpstvnrrlkrLe 42 
                                   eLA +l   +  +++ l +Le
  gi|15669242|ref|NP_248047.1| 142 ELAAKLEKVKEKLKEVLSELE 162
                                   777776655555555555555 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.6e-05     0.006       5      34 ..      53      81 ..      48      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-05
                        HTH_29  5 llllaeGvstvsqiAkllglsrrtvyrwlk 34
                                  l+  + G  t+++iA  lg +++t++++lk
  gi|15669242|ref|NP_248047.1| 53 LAREKAGY-TIREIADELGRTEQTIRKHLK 81
                                  33334444.******************997 PP

>> Mto2_bdg  Micro-tubular organiser Mto1 C-term Mto2-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   3.2   2.8e-05    0.0066      27      50 ..     129     152 ..     115     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.8e-05
                      Mto2_bdg  27 arerLeelkaeNrlLkaeLerdrs 50 
                                     e++e+lk+eN++L+a+Le+ ++
  gi|15669242|ref|NP_248047.1| 129 LEEEIEKLKKENEELAAKLEKVKE 152
                                   679*****************9887 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.6   1.6e-05    0.0037      19      63 ..     118     162 ..     101     163 .] 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.6e-05
                 TolA_bind_tri  19 lllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlD 63 
                                     le  + +++l++e+ +L+ ++Eel+ +le+++e+ ++   +l+
  gi|15669242|ref|NP_248047.1| 118 EELEKITDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSELE 162
                                   4567778999*****************************998886 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.6e-05     0.011      16      39 ..      58      81 ..      53      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.6e-05
                                  TTS-HHHHHHHHTS-HHHHHHHHH CS
                          GerE 16 eGksnkeIAeelniSekTVkvhks 39
                                  +G++  eIA+el+  e+T++ h++
  gi|15669242|ref|NP_248047.1| 58 AGYTIREIADELGRTEQTIRKHLK 81
                                  799*****************9986 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.5       3.1   7.3e+02      27      27 ..      91      91 ..      58     125 .. 0.58
   2 !   17.1   8.8   2.3e-05    0.0053       3      42 ..     118     159 ..     116     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 3.1
                     FlaC_arch 27 s 27
                                  +
  gi|15669242|ref|NP_248047.1| 91 R 91
                                  1 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.3e-05
                     FlaC_arch   3 delEn..klsklsteletvkkeneelsksveelkenVkdlls 42 
                                   +elE+  +++kl+ e+e +kkeneel  ++e++ke+ k++ls
  gi|15669242|ref|NP_248047.1| 118 EELEKitDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLS 159
                                   5666444899******************************96 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.9   4.6e-05     0.011     175     279 ..      13     138 ..       5     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.6e-05
                          TnsD 175 yrisrikkfGivweerlkeLvee......................eglslkeiAkelgvdiktVlryakklgllkekkkqk 233
                                    ++++++ +G + + ++ eL+++                      +g +++eiA elg + +t+++++k +++  +     
  gi|15669242|ref|NP_248047.1|  13 DKLEHVLILGTLFRPEILELIKDpiekvtwvdslaiaagalarekAGYTIREIADELGRTEQTIRKHLKGETKAGKLVRET 93 
                                   5677888889999999999999999999999999999999999999***********************888777555555 PP

                          TnsD 234 kesrelsskdrekkrkewleliksypdlgktelrklnpalyawLyr 279
                                    e ++  + ++e+ +k + +++++    ++t ++kl+    ++L +
  gi|15669242|ref|NP_248047.1|  94 YEMMKRGELNIEEVEKFLEAVVRKEELEKITDIKKLEE-EIEKLKK 138
                                   55555555567777777777777777777777777743.3444444 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   4.7e-05     0.011      19      42 ..      58      81 ..      53      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-05
                                  TT--HHHHHHHHTS-HHHHHHHHH CS
                    Sigma70_r4 19 eglTleEIgerlgiSrerVrqiek 42
                                   g+T  EI+++lg ++ ++r ++k
  gi|15669242|ref|NP_248047.1| 58 AGYTIREIADELGRTEQTIRKHLK 81
                                  689*****************9875 PP

>> NYD-SP28_assoc  Sperm tail C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   2.9   9.2e-05     0.021      33      58 ..     124     149 ..     118     160 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.2e-05
                NYD-SP28_assoc  33 teRaklieetesLekqNeeLrnlLkq 58 
                                   t+ +kl ee+e+L+k+NeeL   L++
  gi|15669242|ref|NP_248047.1| 124 TDIKKLEEEIEKLKKENEELAAKLEK 149
                                   7899****************999975 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   5.0   6.7e-05     0.016       5      75 ..      92     160 ..      89     163 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.7e-05
                        DUF148   5 effaIlknenltiaeieeqleawaekygvtdeykefeakvkaqkeevkknvtavisnLssvqekleaIldn 75 
                                   e ++++k  +l+i+e+e+ lea + k ++++   +  +k++++ e++kk+ ++  ++L++v+ekl+++l++
  gi|15669242|ref|NP_248047.1|  92 ETYEMMKRGELNIEEVEKFLEAVVRKEELEKI--TDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSE 160
                                   678999*******************9988764..4578899999999999999999999999999999975 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.6   4.5e-05      0.01       7      40 ..      54      86 ..      52     114 .. 0.84
   2 ?   -0.1   3.4       4.2   9.7e+02      20      58 ..     109     156 ..      95     162 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.5e-05
                        HTH_19  7 aReelgltqeelaerlgisrskisaiEngkkdvp 40
                                  aRe++g+t++e+a++lg +   i++  +g++ ++
  gi|15669242|ref|NP_248047.1| 54 AREKAGYTIREIADELGRTEQTIRKHLKGET-KA 86
                                  8******************999999998865.43 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 4.2
                        HTH_19  20 e.........rlgisrskisaiEngkkdvps..aelllkiaealgidley 58 
                                   +         +l   ++ i ++E + +++++   e+l + +e+++  l++
  gi|15669242|ref|NP_248047.1| 109 KfleavvrkeELEK-ITDIKKLEEE-IEKLKkeNEELAAKLEKVKEKLKE 156
                                   55544444533333.6667777755.334444444444444444444443 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   9.1e-05     0.021       8      34 ..      52      81 ..      47      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.1e-05
                        HTH_28  8 llaa...GhsvreaArelgisrrtvyrWik 34
                                  +la+   G ++re+A elg +++t+++ +k
  gi|15669242|ref|NP_248047.1| 52 ALARekaGYTIREIADELGRTEQTIRKHLK 81
                                  555433489*****************9987 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.18        42      68      87 ..      61      80 ..      51      82 .. 0.84
   2 ?   11.5   6.2    0.0012      0.27      20      65 ..     111     157 ..      91     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.18
                       DUF4164 68 vnrEvsrrLkaaietiravL 87
                                  + rE++++L ++ +tir+ L
  gi|15669242|ref|NP_248047.1| 61 TIREIADELGRTEQTIRKHL 80
                                  679**************876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0012
                       DUF4164  20 LEkav.drrleaerkrdeleaeiealgedrsRLaeeLdqaearaarl 65 
                                   LE+ v ++ le+  + ++le+eie+l+++ + La++L +++ +++++
  gi|15669242|ref|NP_248047.1| 111 LEAVVrKEELEKITDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEV 157
                                   4444412345666666***********************99998875 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.3   4.9e-05     0.011       4      34 ..      54      84 ..      52      88 .. 0.90
   2 ?   -0.0   1.0       4.1   9.5e+02       2      19 ..     130     147 ..     129     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.9e-05
                                  HHHHTTHHHHHHHHHHTSSHHHHHHHHTTSS CS
                         HTH_3  4 lRkqlglsqeeLAeklGvsrstisriEnGer 34
                                  +R+++g++++e+A++lG + +ti++  +Ge+
  gi|15669242|ref|NP_248047.1| 54 AREKAGYTIREIADELGRTEQTIRKHLKGET 84
                                  8***********************9888877 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 4.1
                                   HHHHHHTTHHHHHHHHHH CS
                         HTH_3   2 kelRkqlglsqeeLAekl 19 
                                   +e  ++l+   eeLA+kl
  gi|15669242|ref|NP_248047.1| 130 EEEIEKLKKENEELAAKL 147
                                   67778899999****998 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   0.00011     0.025       9      39 ..      54      84 ..      52     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 0.00011
                        HTH_31  9 lReraGLsqeevAerlgvsestlsrlEqGrr 39
                                  +Re+aG + +e A+ lg +e t+++   G+ 
  gi|15669242|ref|NP_248047.1| 54 AREKAGYTIREIADELGRTEQTIRKHLKGET 84
                                  7***********************9988876 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1         3   6.9e+02      14      38 ..      92     116 ..      61     121 .. 0.71
   2 ?   15.3   4.6   5.4e-05     0.013       1      38 [.     122     160 ..     122     163 .] 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3
                           LXG  14 qlkseleelkeqleqlkkaiqklve 38 
                                   ++ +++++++ ++e+++k ++ +v 
  gi|15669242|ref|NP_248047.1|  92 ETYEMMKRGELNIEEVEKFLEAVVR 116
                                   4556666666677777776666665 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 5.4e-05
                           LXG   1 kvlDvaelieaieqlkseleelkeqleqlkkaiqk.lve 38 
                                   k+ D+++l+e+ie+lk+e+eel  +le++k+++++ l+e
  gi|15669242|ref|NP_248047.1| 122 KITDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEvLSE 160
                                   788********************************4555 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   0.00012     0.029      13      32 ..      59      78 ..      58      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00012
                   Terminase_5 13 GyrvaeIAeelglkeatVys 32
                                  Gy+++eIA elg+ e+t+  
  gi|15669242|ref|NP_248047.1| 59 GYTIREIADELGRTEQTIRK 78
                                  9****************976 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3  10.1   9.2e-05     0.021     115     200 .]      70     162 ..      13     162 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.2e-05
                        AAA_23 115 deleqfisellgskki....ilnlilflgqerfeefelkdkkerleel..ekeleeledekkllekleqekekek....el 185
                                     +eq+i+++l+ + +      + + +++ ++ + +e +   + le++  ++ele+++d+kkl e+ e++k++++    +l
  gi|15669242|ref|NP_248047.1|  70 GRTEQTIRKHLKGETKagklVRETYEMMKRGELNIEEVE---KFLEAVvrKEELEKITDIKKLEEEIEKLKKENEelaaKL 147
                                   334566666666554457555577777777776444443...444443334555555555555555544444444455699 PP

                        AAA_23 186 eeleeeleeilkele 200
                                   e+++e+l+e+l+ele
  gi|15669242|ref|NP_248047.1| 148 EKVKEKLKEVLSELE 162
                                   999999999999987 PP

>> CCDC92  Coiled-coil domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.9    0.0002     0.046      23      44 ..     127     148 ..     121     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0002
                        CCDC92  23 kgLHkEIekLqkenkdLtfkli 44 
                                   k+L +EIekL+ken +L  kl+
  gi|15669242|ref|NP_248047.1| 127 KKLEEEIEKLKKENEELAAKLE 148
                                   7899*************98885 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00025     0.057      20      46 ..      55      81 ..      26      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00025
                                  STCTTB-HHHHHHHHTS-HHHHHHHHH CS
                        HTH_20 20 araegltaselaerldlskntlsyHLr 46
                                  ++++g t  e+a++l+ + +t+++HL+
  gi|15669242|ref|NP_248047.1| 55 REKAGYTIREIADELGRTEQTIRKHLK 81
                                  6788999*******************8 PP

>> Herpes_UL6  Herpesvirus UL6 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.0   0.00013     0.031     348     407 ..      97     159 ..      60     163 .] 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                    Herpes_UL6 348 aqss....ekteqglkksvsnsvikcleeqineqfdtiekLkkenelllkklkelekeLerlre 407
                                   ++ +    e++e+ l+ +v+++  + +++ i+++ ++iekLkkene l++kl++++++L+++ +
  gi|15669242|ref|NP_248047.1|  97 MKRGelniEEVEKFLEAVVRKEELEKITD-IKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLS 159
                                   33335556677777777777777777765.99***************************99854 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00026     0.061      16      46 ..      61      91 ..      53      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00026
                      HTH_DeoR 16 sveelvellgvSeaTiRRDLneLeeqglltR 46
                                  ++ e++++lg +e+TiR+ L+  +++g+l+R
  gi|15669242|ref|NP_248047.1| 61 TIREIADELGRTEQTIRKHLKGETKAGKLVR 91
                                  899******************9999999988 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.1    0.0002     0.046     152     232 ..      75     162 ..      61     163 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0002
                                   HHHHHHTTTSS.......SXSHHHH.......HHHHHHHHHSTT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHH CS
                        FliD_C 152 sveelFsgstsqektvtsdsglatr.......lenllksyvkssngtlqtasknltkqikdldkkiedldkrletleerlk 225
                                    +++ + g+t++ k v ++ ++++r       +e++l+ +v+ ++    t++k+l+++i++l+k+ e+l+ +le+ +e+lk
  gi|15669242|ref|NP_248047.1|  75 TIRKHLKGETKAGKLVRETYEMMKRgelnieeVEKFLEAVVRKEELEKITDIKKLEEEIEKLKKENEELAAKLEKVKEKLK 155
                                   5667777777777888888888888888888899999999999988899******************************** PP

                                   HHHHHHH CS
                        FliD_C 226 kqfaale 232
                                   +  ++le
  gi|15669242|ref|NP_248047.1| 156 EVLSELE 162
                                   9988887 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5    0.0018      0.42       2      23 ..      60      81 ..      60     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0018
                        HTH_17  2 ltveEaAelLgvsrstvyrlir 23
                                  +t+ E+A+ Lg  ++t+++ ++
  gi|15669242|ref|NP_248047.1| 60 YTIREIADELGRTEQTIRKHLK 81
                                  8*****************9984 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   7.7   0.00082      0.19      16      42 ..     128     154 ..     126     155 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00082
                          HALZ  16 aLksdydsLkkenekLkaelqeLkekl 42 
                                   +L  + + Lkkene+L a+l++ kekl
  gi|15669242|ref|NP_248047.1| 128 KLEEEIEKLKKENEELAAKLEKVKEKL 154
                                   688899********************8 PP

>> DUF2316  Uncharacterized protein conserved in bacteria (DUF2316)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.031       7.2      19      45 ..      55      81 ..      52     119 .. 0.87
   2 ?    1.0   0.1       2.1   4.9e+02      18      48 ..      96     128 ..      87     136 .. 0.73
   3 ?    4.9   2.0      0.13        31      12      45 ..     126     159 ..     115     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.031
                       DUF2316 19 felsgltveevaedLnlttekvekvLe 45
                                   e++g+t+ e+a++L+ t++ + k L+
  gi|15669242|ref|NP_248047.1| 55 REKAGYTIREIADELGRTEQTIRKHLK 81
                                  5789*****************999886 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 2.1
                       DUF2316  18 nfelsgltveevaedLn..lttekvekvLelka 48 
                                    +++ +l++eev + L+  + +e++ek+ ++k+
  gi|15669242|ref|NP_248047.1|  96 MMKRGELNIEEVEKFLEavVRKEELEKITDIKK 128
                                   567778888888888874456788888888875 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.13
                       DUF2316  12 kkeLqanfelsgltveevaedLnlttekvekvLe 45 
                                    k+L+++ e+ + + ee+a++L+  +ek+++vL+
  gi|15669242|ref|NP_248047.1| 126 IKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLS 159
                                   47899999***********************996 PP

>> DUF3489  Protein of unknown function (DUF3489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   0.00073      0.17      15      49 ..      53      87 ..      50     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00073
                       DUF3489 15 lLrrpeGatiaeimeatgWqahtvRgalagalkkk 49
                                  l r+++G ti+ei+ ++g  + t+R  l g  k++
  gi|15669242|ref|NP_248047.1| 53 LAREKAGYTIREIADELGRTEQTIRKHLKGETKAG 87
                                  66899***********************9999987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00054      0.13      13      56 ..      52      94 ..      47     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00054
                                  HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                  aL+r+  +  t++e+a++lg + +++ ++lk   +aG ++r++ 
  gi|15669242|ref|NP_248047.1| 52 ALAREKAG-YTIREIADELGRTEQTIRKHLKGETKAGKLVRETY 94
                                  66677655.5*********************9999998877765 PP

>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.3    0.0004     0.092     188     281 ..      62     147 ..      16     163 .] 0.40

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0004
                     Cas_DxTHG 188 laellrekkekkkeklkklkklkeklkkeleefskalelirp.lellekaeklekeivek.....lk.eeleeiesleeee 261
                                   ++e++ e           l   ++ ++k l+   ka +l+r+ +e+++  e + +e vek     ++ eele+i      +
  gi|15669242|ref|NP_248047.1|  62 IREIADE-----------LGRTEQTIRKHLKGETKAGKLVREtYEMMKRGELNIEE-VEKfleavVRkEELEKI------T 124
                                   3333322...........22222222233333333333333323333111111111.22211112112333333......2 PP

                     Cas_DxTHG 262 sakplellldeikkklekf...l 281
                                    +k+le++++++kk+ e++   l
  gi|15669242|ref|NP_248047.1| 125 DIKKLEEEIEKLKKENEELaakL 147
                                   24444444444444444442221 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0     0.002      0.46     147     173 ..      55      81 ..      10      95 .. 0.84
   2 ?    3.1   1.9      0.33        77     110     145 ..     113     148 ..      91     155 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.002
                   Sigma70_ECF 147 rkleGlsveEiAeklgvskrtverrla 173
                                   r  +G+++ EiA++lg  ++t++++l+
  gi|15669242|ref|NP_248047.1|  55 REKAGYTIREIADELGRTEQTIRKHLK 81 
                                   5568*******************9985 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.33
                   Sigma70_ECF 110 eeedsvdsdspdelleLdealerllsldpeqarlve 145
                                    ++ + + ++  ++ +L+e +e+l ++++e a ++e
  gi|15669242|ref|NP_248047.1| 113 AVVRKEELEKITDIKKLEEEIEKLKKENEELAAKLE 148
                                   2222345588889999**********9999887776 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   8.9   0.00092      0.21      36     101 ..      88     158 ..      71     163 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00092
                          ADIP  36 aiinviysLlqardrdleqreslnetirkle.....aeierlqskierlktqleqlerelalvqakerqle 101
                                   +++   y+++++ + ++e+ e++ e + ++e     ++i++l+ +ie+lk+++e+l+ +l+ v++k+++  
  gi|15669242|ref|NP_248047.1|  88 KLVRETYEMMKRGELNIEEVEKFLEAVVRKEelekiTDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVL 158
                                   56666799*********999999998877763444469999999999999999999999999999988765 PP

>> Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_LLH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4    0.0026      0.61      51      97 ..      72     116 ..      61     117 .. 0.90
   2 ?    6.4   8.5      0.05        12      24      79 ..     107     161 ..     105     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0026
               Phage_holin_6_1  51 veqvakedakgeeKkeeAleklkellkekgisitddeleglIEaaVk 97 
                                   +eq++ ++ kge K  + +++  e++k   ++i  +e+e++ Ea V+
  gi|15669242|ref|NP_248047.1|  72 TEQTIRKHLKGETKAGKLVRETYEMMKRGELNI--EEVEKFLEAVVR 116
                                   69*****************************99..578899999886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.05
               Phage_holin_6_1  24 ikkllklkkqgekakkiaeiaknaVkaveqvakedakgeeKkeeAleklkellkek 79 
                                   + k l + + +e+++ki++i k+  +  e+++ke+++ ++K+e+++eklke l+e+
  gi|15669242|ref|NP_248047.1| 107 VEKFLEAVVRKEELEKITDI-KKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSEL 161
                                   567778888999********.99999***************************985 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1        10   2.3e+03      31      31 ..      97      97 ..      61     125 .. 0.59
   2 ?   13.5  11.5   0.00032     0.074      18      51 ..     124     157 ..     118     163 .] 0.50

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 10
                          ZapB 31 k 31
                                  +
  gi|15669242|ref|NP_248047.1| 97 M 97
                                  1 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00032
                          ZapB  18 dtitlLqmeieeLkeeneelkeenreleeeneql 51 
                                   + i++L +eie+Lk+eneel+ + ++++e++++ 
  gi|15669242|ref|NP_248047.1| 124 TDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEV 157
                                   4455555555555555555555555555544433 PP

>> NAT  NAT, N-acetyltransferase, of N-acetylglutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.0    0.0016      0.38       4      65 ..      78     157 ..      75     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0016
                                   HHHHSSSTSSEEEE---XEEEESSCCCS..................SXCCHHHHHHTTSTTTSSXHHHHHHHHHTSXEEE CS
                           NAT   4 kelftdsgagtlirrGlkvitvkslkel..................idlekLksliedsfkrkldvkdYldrlkgkiaki 65 
                                   k l  +++ag+l+r+ ++++++ +l+                    +d++kL++ ie+ +k++++++  l+++k+k+ ++
  gi|15669242|ref|NP_248047.1|  78 KHLKGETKAGKLVRETYEMMKRGELNIEevekfleavvrkeelekiTDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEV 157
                                   5566677788888888888777666544457778888888888888***************************9998776 PP

>> Med30  Mediator complex subunit 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   8.5    0.0011      0.27      50     134 ..      76     161 ..      61     163 .] 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0011
                         Med30  50 lqeqlrqlkvlfkkLrliYekckencqgleevp..iesLipyvdeekskreerkkseevkqlkeerkelleklkeknkqLk 128
                                   ++ +l+  +   k +r +Ye +k+   ++eev+  +e  +  ++e ++  + +k  ee+++lk+e++el  kl++++++Lk
  gi|15669242|ref|NP_248047.1|  76 IRKHLKGETKAGKLVRETYEMMKRGELNIEEVEkfLEAVVR-KEELEKITDIKKLEEEIEKLKKENEELAAKLEKVKEKLK 155
                                   55566666666788999*****9999889977764454444.444545555566678888888888888888888888888 PP

                         Med30 129 eimdql 134
                                   e+  +l
  gi|15669242|ref|NP_248047.1| 156 EVLSEL 161
                                   887766 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  12.0    0.0011      0.25     536     608 ..      85     160 ..      68     163 .] 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                         Nup88 536 ratqvlReey..lkkqelvreeiekrvkll.kkqkeqqleelqsleeerkslseraeklAekyeeikdkQeklvrr 608
                                   +a + +Re y  +k+ el  ee+ek  +++ +k+  ++ +++++leee ++l+ + e+lA k+e +k+k  +++  
  gi|15669242|ref|NP_248047.1|  85 KAGKLVRETYemMKRGELNIEEVEKFLEAVvRKEELEKITDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSE 160
                                   6667788866559999**********9976155566899*****************************98777665 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   7.2    0.0011      0.26      35      93 ..     101     160 ..      66     163 .] 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                          Tho2  35 kseieelakdrsde.raaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLkeekks 93 
                                   + +iee++k  ++  r+++ +k  ++k+l+e iekL++E++e  ++ ekvk++Lke++++
  gi|15669242|ref|NP_248047.1| 101 ELNIEEVEKFLEAVvRKEELEKITDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSE 160
                                   455666655556666888889999*******************************99875 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       2.2   5.1e+02       3      30 ..      27      53 ..      25      84 .. 0.64
   2 ?    8.2   1.7     0.015       3.5      28      60 ..     124     156 ..     103     163 .] 0.51

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 2.2
                       NPV_P10  3 qniLlvIradikavddkVdalqqqvddv 30
                                  + iL +I++ i++v + Vd+l  +   +
  gi|15669242|ref|NP_248047.1| 27 PEILELIKDPIEKV-TWVDSLAIAAGAL 53
                                  67888999988888.4566665555444 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.015
                       NPV_P10  28 ddvqenlpdvtelnekLdaqsaqLaeletkven 60 
                                   +d+++  +++++l+++ ++++a+L+++++k+++
  gi|15669242|ref|NP_248047.1| 124 TDIKKLEEEIEKLKKENEELAAKLEKVKEKLKE 156
                                   333333333333333333333333333333333 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4  16.4   0.00075      0.17      22      85 ..     101     162 ..      86     163 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00075
                        APG6_N  22 ekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaela 85 
                                   e  +++ e+fl+ + ++++ e+   +++++leee+ekl+ke eel ++L++++++ +e+ +el+
  gi|15669242|ref|NP_248047.1| 101 ELNIEEVEKFLEAVVRKEELEK--ITDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSELE 162
                                   5566778899999999977766..79***************************99999999987 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.4      0.95   2.2e+02      45      73 ..      74     102 ..      55     109 .. 0.75
   2 ?   12.7   6.1   0.00034     0.079      25      51 ..     125     151 ..     114     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.95
                                   HHHCC-XXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIC  45 aevkdLksdedyieerARselglvkpgEt 73 
                                   + +++  ++e    +  R+ + ++k gE 
  gi|15669242|ref|NP_248047.1|  74 QTIRKHLKGETKAGKLVRETYEMMKRGEL 102
                                   555544468888889999999***99996 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00034
                                   HHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                         DivIC  25 eiaalqaelaklkaeneeLeaevkdLk 51 
                                   +i++l++e++klk+eneeL+a++++ k
  gi|15669242|ref|NP_248047.1| 125 DIKKLEEEIEKLKKENEELAAKLEKVK 151
                                   688888888888888888888888875 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  14.8    0.0031      0.73      14     110 ..      63     163 .]      55     163 .] 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0031
                    TPR_MLP1_2  14 keekeeaeaklqklqedlekqaeiakeaqqkYerelvkhae.dvkelqa.....lreelnelkaeiaelkaeaesakaele 88 
                                   +e ++e+ +++q++++ l+ +++  k   + Y  e++k  e +++e+++     +r+e  e  ++i++l++e e++k+e+e
  gi|15669242|ref|NP_248047.1|  63 REIADELGRTEQTIRKHLKGETKAGKLVRETY--EMMKRGElNIEEVEKfleavVRKEELEKITDIKKLEEEIEKLKKENE 141
                                   56778888889999999999999999999977..46666653466666622222455557777899*************** PP

                    TPR_MLP1_2  89 eseesweeqkeelekelselek 110
                                   e  +++e+ ke+l++ lselek
  gi|15669242|ref|NP_248047.1| 142 ELAAKLEKVKEKLKEVLSELEK 163
                                   ****************999986 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.2    0.0024      0.57      15      53 ..     117     157 ..     102     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0024
                          YojJ  15 keeLeqie..keleevlkaldeedeClLcelesirekfael 53 
                                   keeLe+i+  k+lee +++l++e+e l  +le+++ek++e+
  gi|15669242|ref|NP_248047.1| 117 KEELEKITdiKKLEEEIEKLKKENEELAAKLEKVKEKLKEV 157
                                   677888854479*************************9986 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.7     0.003      0.69     126     228 ..      61     160 ..      54     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.003
                          CorA 126 llekleeeldeledel.....edstkkeilrelaqlrrr.lvklrralapnrevlkrllakaddkllddedkeylrdllde 200
                                   +++++ +el + e+++      + +  +++re++++ +r   +++++ + +++v+    +k++ ++++  d   ++ l++e
  gi|15669242|ref|NP_248047.1|  61 TIREIADELGRTEQTIrkhlkGETKAGKLVRETYEMMKRgELNIEEVEKFLEAVV----RKEELEKIT--D---IKKLEEE 132
                                   799*************877755555666777777766553555555555555555....333444444..4...7899999 PP

                          CorA 201 lerllemlealrerleslqdtyssllse 228
                                   +e+l ++ e l+ +le++++ +  +lse
  gi|15669242|ref|NP_248047.1| 133 IEKLKKENEELAAKLEKVKEKLKEVLSE 160
                                   9999999999999999999988877775 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  14.5    0.0028      0.66     160     251 ..      71     162 ..      56     163 .] 0.53

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0028
                          Spc7 160 kqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelk 240
                                   + e+ + + l+  ++  + ++e++e++++ + ++e+++k   + +r+e  e  ++i+++++e+++l+++ eel++k+e++k
  gi|15669242|ref|NP_248047.1|  71 RTEQTIRKHLKGETKAGKLVRETYEMMKRGELNIEEVEKFLEAVVRKEELEKITDIKKLEEEIEKLKKENEELAAKLEKVK 151
                                   334444444444444444455555555554444555443322223333333345677777777777777777777777777 PP

                          Spc7 241 eqkseleeeia 251
                                   e+ +e+ +e++
  gi|15669242|ref|NP_248047.1| 152 EKLKEVLSELE 162
                                   77777777765 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.6    0.0018      0.43      17      62 ..     116     161 ..     104     163 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0018
                       Goodbye  17 kdealkelssvedllkqieaekdkfeefrekkeklkealkkilspi 62 
                                   ++e+l++++ + +l+++ie+ k++ ee  +k ek+ke lk++ls +
  gi|15669242|ref|NP_248047.1| 116 RKEELEKITDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSEL 161
                                   566999************************************9876 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       7.9   1.8e+03      13      48 ..      64      99 ..      61     119 .. 0.66
   2 ?   11.0   8.5    0.0018      0.41      35      72 ..     122     162 ..     100     163 .] 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 7.9
                      Gp-FAR-1 13 ealknltdeekaqlkevvknykgyknedellaalKk 48
                                  e  ++l  +e+++ k +  + k  k + e  + +K+
  gi|15669242|ref|NP_248047.1| 64 EIADELGRTEQTIRKHLKGETKAGKLVRETYEMMKR 99
                                  556677777777777777777777777777777775 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0018
                      Gp-FAR-1  35 g...yknedellaalKkkspaLyekaeklqaklkekvdkLs 72 
                                   +    k  +e ++ lKk +++L++k+ek+++klke + +L+
  gi|15669242|ref|NP_248047.1| 122 KitdIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSELE 162
                                   14448999**************************9988885 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       2.3   5.4e+02      69      77 ..      63      71 ..      51     120 .. 0.68
   2 ?   10.8   7.0    0.0017       0.4       3      41 ..     124     159 ..     122     163 .] 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 2.3
                                  GGGHHHCT- CS
                          Swi5 69 kevfeefGv 77
                                  +e+ +e+G 
  gi|15669242|ref|NP_248047.1| 63 REIADELGR 71
                                  333333332 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0017
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHH CS
                          Swi5   3 aeikeleeqleelekelaelkeelkekkdpeetvkrhIk 41 
                                   ++ik+lee++e+l+ke +el ++l++ k   e +k+ ++
  gi|15669242|ref|NP_248047.1| 124 TDIKKLEEEIEKLKKENEELAAKLEKVK---EKLKEVLS 159
                                   689*********************9654...44444444 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.9      0.27        62      36      90 ..      62     116 ..      54     125 .. 0.80
   2 ?    8.8   8.8    0.0097       2.3      45      93 ..     115     162 ..     102     163 .] 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.27
                                   HHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHH CS
                         DUF16  36 Lkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetlelile 90 
                                   +++i +++   ++ i k  +  +k g+ ++e  + +k  + ++++v++ le +++
  gi|15669242|ref|NP_248047.1|  62 IREIADELGRTEQTIRKHLKGETKAGKLVRETYEMMKRGELNIEEVEKFLEAVVR 116
                                   5677788888889999999999999999999999999999999999999998874 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0097
                                   ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHH CS
                         DUF16  45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLq 93 
                                   +++e+++k+++ ++k++e+i++lk+e +   ++l+kv+e l+ +l  L+
  gi|15669242|ref|NP_248047.1| 115 VRKEELEKITD-IKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSELE 162
                                   45666777665.899**************************99999887 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3       1.3   3.1e+02      27      49 ..      90     113 ..      52     124 .. 0.54
   2 ?    9.0   6.9    0.0056       1.3      25      81 ..     105     160 ..      88     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.3
                       DUF4446  27 lkkkykklmkgk.dgksleellke 49 
                                   +++ y+++ +g+ + +++e+ l+ 
  gi|15669242|ref|NP_248047.1|  90 VRETYEMMKRGElNIEEVEKFLEA 113
                                   233333333333344444444433 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0056
                       DUF4446  25 kklkkkykklmkgkdgksleellkekleeveelkeeseelekeieeleeklkkslqk 81 
                                   ++++k +++++++++ +++   +k+  ee+e+lk+e+eel +++e+++eklk+ l++
  gi|15669242|ref|NP_248047.1| 105 EEVEKFLEAVVRKEELEKIT-DIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSE 160
                                   45555555555555555554.478999999999999999999999999999998765 PP

>> MCC-bdg_PDZ  PDZ domain of MCC-2 bdg protein for Usher syndrome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.9   0.00072      0.17       1      26 [.     128     153 ..     128     163 .] 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00072
                   MCC-bdg_PDZ   1 rLksrIeeLkaqnelLsltleerkqq 26 
                                   +L + Ie+Lk  ne L++ le  k++
  gi|15669242|ref|NP_248047.1| 128 KLEEEIEKLKKENEELAAKLEKVKEK 153
                                   799******************99986 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  13.0   0.00067      0.16      26      63 ..     124     161 ..     116     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00067
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                     i++Le++ ++L+keN++L+ +le+ k++ ++ +s++
  gi|15669242|ref|NP_248047.1| 124 TDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSEL 161
                                   679****************************9999886 PP

>> VGCC_beta4Aa_N  Voltage gated calcium channel subunit beta domain 4Aa N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.1     0.016       3.7      15      41 .]     128     153 ..     121     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.016
                VGCC_beta4Aa_N  15 sleedrEalRreaErqAllqLerArsK 41 
                                    lee+ E l +e E +A+ +Le+ ++K
  gi|15669242|ref|NP_248047.1| 128 KLEEEIEKLKKENEELAA-KLEKVKEK 153
                                   79**************95.8***9988 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  11.2    0.0033      0.77     111     186 ..      76     148 ..      52     149 .. 0.87
   2 ?   10.3  10.9    0.0022       0.5     113     164 ..     109     162 ..     106     163 .] 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0033
               Ax_dynein_light 111 mrkalqaeqgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekkheeeieflkksnqqlkeqle 186
                                   +rk l+ e +  +l ++     e  ++ e +++e+++ lea+ ++e+ ++ ++ kk eeeie+lkk+n++l ++le
  gi|15669242|ref|NP_248047.1|  76 IRKHLKGETKAGKLVRE---TYEMMKRGELNIEEVEKFLEAVVRKEELEKITDIKKLEEEIEKLKKENEELAAKLE 148
                                   68888888777777766...455566778899****************************************9998 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0022
               Ax_dynein_light 113 kalqaeqgkselekk..ikeLeeekeelekqvaelkaklealekrekerrqeee 164
                                   k l+a  +k+elek   ik+Leee e+l+k+++el akle+++++ ke ++e e
  gi|15669242|ref|NP_248047.1| 109 KFLEAVVRKEELEKItdIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSELE 162
                                   66666667777776555999***********************99999887766 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  16.7      0.02       4.6      13      98 ..      75     162 ..      60     163 .] 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.02
                                   HHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  13 avkeklkkRgedkadvdelleldekrrelqveleelqae..rNelskeIgkakkkkedaeeliaevkelkeelkaleaelk 91 
                                   +++++lk   ++ ++v e +e+ ++ +  + e+e++ +   r+e  ++I  +kk +e++e+l++e +el ++l++++++lk
  gi|15669242|ref|NP_248047.1|  75 TIRKHLKGETKAGKLVRETYEMMKRGELNIEEVEKFLEAvvRKEELEKITDIKKLEEEIEKLKKENEELAAKLEKVKEKLK 155
                                   667777777777777777777777777777777777664347778888888888888888888888888888888888888 PP

                                   HHHHHHH CS
                  Seryl_tRNA_N  92 eleaele 98 
                                   e+ +ele
  gi|15669242|ref|NP_248047.1| 156 EVLSELE 162
                                   8888887 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   6.0      0.01       2.4      59     103 ..      96     158 ..      56     163 .] 0.49

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.01
                    V_ATPase_I  59 a..................eesleapeekeldeleeelekleeelkelnenleklkkelnelv 103
                                   +                  ++++e ++ +++++leee+ekl++e +el ++lek+k++l+e++
  gi|15669242|ref|NP_248047.1|  96 MmkrgelnieevekfleavVRKEELEKITDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVL 158
                                   022222333333222333344444455555555555555555555555555555555554443 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   6.4     0.011       2.5      73     117 ..     116     160 ..      62     163 .] 0.70

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                         Atg14  73 ksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsd 117
                                   +++  ++   +++l++ +++lkke+ee  +kl+k ++klk+  s+
  gi|15669242|ref|NP_248047.1| 116 RKEELEKITDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSE 160
                                   445555556688888888888888888888888888888865555 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   1.4      0.18        42      20      77 ..      61     114 ..      45     124 .. 0.55
   2 ?    7.6   1.4     0.019       4.5      35      70 ..     126     157 ..     118     163 .] 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.18
                        DUF948  20 vllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteav 77 
                                   +   +++++de+ +t ++++k++++ + ++ +l++++ e+++  +  +e+v+++ eav
  gi|15669242|ref|NP_248047.1|  61 T---IREIADELGRTEQTIRKHLKGET-KAGKLVRETYEMMKRGELNIEEVEKFLEAV 114
                                   3...34444455555555554444433.345566666666666666666666666665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.019
                        DUF948  35 ieelekqvdpilkevedllakvnelledvneklekv 70 
                                   i++le++++++ ke e+l ak ++    v+ekl++v
  gi|15669242|ref|NP_248047.1| 126 IKKLEEEIEKLKKENEELAAKLEK----VKEKLKEV 157
                                   788899999999999999999988....55555554 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       5.6   1.3e+03      27      48 ..      58      80 ..      45      99 .. 0.64
   2 ?    8.3   5.5     0.014       3.2      12      54 ..     107     149 ..      86     162 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 5.6
                                  H.HHHHHHHHHHHHHHHHHHHHH CS
                          PhoU 27 a.revierddeidrlekeiersl 48
                                  a   ++e  de+ r e+ i+++l
  gi|15669242|ref|NP_248047.1| 58 AgYTIREIADELGRTEQTIRKHL 80
                                  44555566777777777776664 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.014
                                   HHHHHHHHHCT-H.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU  12 lddalealeekdt.elarevierddeidrlekeiersllealak 54 
                                   +++ lea+++k++ e + ++ ++++ei++l ke+e+    +l k
  gi|15669242|ref|NP_248047.1| 107 VEKFLEAVVRKEElEKITDIKKLEEEIEKLKKENEEL-AAKLEK 149
                                   66777886666444********************887.555544 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  15.5     0.014       3.4      82     141 ..      95     162 ..      46     163 .] 0.69

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.014
                       UPF0242  82 eglktkeealeelqeeeeeLkee........ldakeeelerlkeenqqLqekleaiaedfeelklele 141
                                   e +k  e ++ee+++  e   ++        +++ eee+e+lk+en++L  kle+++e  +e++ ele
  gi|15669242|ref|NP_248047.1|  95 EMMKRGELNIEEVEKFLEAVVRKeelekitdIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSELE 162
                                   33333333444444332222222224444459999***********************9999999987 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   8.2     0.017       4.1      56     111 ..     103     158 ..      86     163 .] 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.017
                       DUF4337  56 eleqlelllkak..aeelaaavdkkiakykkkiarykkekkeikkkAkeleaerdean 111
                                   + e++e  l+a   +eel++++d  i+k++++i++ kke +e+++k ++++++ +e  
  gi|15669242|ref|NP_248047.1| 103 NIEEVEKFLEAVvrKEELEKITD--IKKLEEEIEKLKKENEELAAKLEKVKEKLKEVL 158
                                   33444444444455777777665..9******************99999999888765 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.7      0.32        74      32      60 ..      54      82 ..      28     123 .. 0.72
   2 ?    7.8   3.4     0.022       5.1       5      43 ..     124     161 ..     118     163 .] 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.32
                        DUF883 32 lRerleerlerarerlrdaeeavaerake 60
                                  +Re++  ++++  ++l ++e++++++ k 
  gi|15669242|ref|NP_248047.1| 54 AREKAGYTIREIADELGRTEQTIRKHLKG 82
                                  67777777777777777777766666554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.022
                        DUF883   5 aeleslladleellkeaadeageeaeelRerleerlera 43 
                                    ++++l +++e+l ke ++  + ++e+++e+l+e l+++
  gi|15669242|ref|NP_248047.1| 124 TDIKKLEEEIEKLKKENEE-LAAKLEKVKEKLKEVLSEL 161
                                   699**********988876.56789*******9999875 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.017       3.9      22      42 ..      61      81 ..      61      86 .. 0.89
   2 ?    2.5   5.9      0.67   1.6e+02       6      42 ..     126     159 ..     121     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.017
                                  XHHHHHHHHTXXHHHHHHHHH CS
                    Sigma70_r3 22 tpeEiAeeLglseekVrevle 42
                                  t+ EiA+eLg +e+ +r+ l+
  gi|15669242|ref|NP_248047.1| 61 TIREIADELGRTEQTIRKHLK 81
                                  789*************99876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.67
                                   HHHHHHHHHHHHSSXXXHHHHHHHHTXXHHHHHHHHH CS
                    Sigma70_r3   6 ikraqreLeqelgrePtpeEiAeeLglseekVrevle 42 
                                   ik+  +e+e    +   +eE+A++L+   ek++evl 
  gi|15669242|ref|NP_248047.1| 126 IKKLEEEIEKLK-K--ENEELAAKLEKVKEKLKEVLS 159
                                   555555554333.2..47****************996 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.0     0.056        13      57      96 ..     118     155 ..      44     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.056
                       DUF4140  57 vpnreaeee....elkalraeleeledelaaledelaaaearla 96 
                                   ++           ++k+l++e+e+l++e ++l ++l+ ++++l+
  gi|15669242|ref|NP_248047.1| 118 EE------LekitDIKKLEEEIEKLKKENEELAAKLEKVKEKLK 155
                                   22......1245459**********************9999876 PP

>> DUF2175  Uncharacterized protein conserved in archaea (DUF2175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   8.9     0.031       7.3      47      95 ..     103     150 ..      88     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.031
                       DUF2175  47 aLleleevlneeivklkelervaedeevkkvleqkrkelEkaaakltkk 95 
                                    + e+e++l e +v+++ele++++ +++ + +e+ +ke E+ aakl k 
  gi|15669242|ref|NP_248047.1| 103 NIEEVEKFL-EAVVRKEELEKITDIKKLEEEIEKLKKENEELAAKLEKV 150
                                   566677766.579********************************9875 PP

>> Med21  Subunit 21 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3      0.33        78     106     140 ..      61      95 ..      53      99 .. 0.83
   2 ?    8.1  11.4     0.013       2.9      99     143 ..     118     162 ..     113     163 .] 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.33
                         Med21 106 rikeLeeelreveeereekvkekeellkkveellr 140
                                   +i+e+++el + e+  ++ +k   +  k v+e  +
  gi|15669242|ref|NP_248047.1|  61 TIREIADELGRTEQTIRKHLKGETKAGKLVRETYE 95 
                                   69999999999999999999999999999988766 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.013
                         Med21  99 seeeqeerikeLeeelreveeereekvkekeellkkveellrava 143
                                   +e e+ + ik+Leee+++ ++e ee   + e++ +k++e+l++++
  gi|15669242|ref|NP_248047.1| 118 EELEKITDIKKLEEEIEKLKKENEELAAKLEKVKEKLKEVLSELE 162
                                   56678889********************************99876 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   8.7     0.061        14       7      92 ..      65     150 ..      60     163 .] 0.56

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.061
                         TMPIT   7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeves 87 
                                   +++e+ + e+t ++  +   +  kl  ++ + +k+ + +++e+++ l+ + ++ + e+ + +++l+ee+++ kk  +e+++
  gi|15669242|ref|NP_248047.1|  65 IADELGRTEQTIRKHLKGETKAGKLVRETYEMMKRGELNIEEVEKFLEAVVRKEELEKITDIKKLEEEIEKLKKENEELAA 145
                                   555555555555555555556666666666666666666666666666666666655556666666666666665555555 PP

                         TMPIT  88 llpkk 92 
                                    l k 
  gi|15669242|ref|NP_248047.1| 146 KLEKV 150
                                   55443 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   6.9    0.0054       1.3       5      43 ..     118     156 ..     114     163 .] 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0054
                         Spc24   5 ekfriakelsdleselesleselaelkeeleeleeesee 43 
                                   e+++ + ++++le+e+e+l++e +el ++le+++e+ +e
  gi|15669242|ref|NP_248047.1| 118 EELEKITDIKKLEEEIEKLKKENEELAAKLEKVKEKLKE 156
                                   6667778899*************************9988 PP

>> DUF2570  Protein of unknown function (DUF2570)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2       0.9   2.1e+02      44      85 ..      71     111 ..      41     123 .. 0.71
   2 ?    6.7   5.0     0.026         6      54      86 ..     127     159 ..     113     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.9
                       DUF2570  44 kanqrLteqLeqerqavekqqkianelkakveeekeevktil 85 
                                   +++q + ++L+ e +a +  ++   e+ ++ e + eev + l
  gi|15669242|ref|NP_248047.1|  71 RTEQTIRKHLKGETKAGKLVRET-YEMMKRGELNIEEVEKFL 111
                                   56677888888888887766654.455555566666665544 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.026
                       DUF2570  54 eqerqavekqqkianelkakveeekeevktilk 86 
                                   ++    +ek +k ++el ak+e+ ke++k +l 
  gi|15669242|ref|NP_248047.1| 127 KKLEEEIEKLKKENEELAAKLEKVKEKLKEVLS 159
                                   44445699**********************996 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.7       1.8   4.3e+02       4      43 ..      63     104 ..      56     122 .. 0.52
   2 ?    7.3   8.1     0.031       7.3      20      54 ..     122     156 ..     103     163 .] 0.64

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.8
                                   HHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHH CS
                          YabA   4 kelfdkleeleeqleelle...eleelkeelaelleenaeLel 43 
                                   +e+ d+l + e+++++ l+   + ++l +e++e++++  eL++
  gi|15669242|ref|NP_248047.1|  63 REIADELGRTEQTIRKHLKgetKAGKLVRETYEMMKR-GELNI 104
                                   4666666666776666654111333444444444433.23333 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.031
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXX CS
                          YabA  20 lleeleelkeelaelleenaeLeleneklrerlee 54 
                                     +++++l+ee+++l +en+eL +  ek++e+l+e
  gi|15669242|ref|NP_248047.1| 122 KITDIKKLEEEIEKLKKENEELAAKLEKVKEKLKE 156
                                   34567777777777777777777777777777743 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   6.6     0.052        12      66      98 ..     124     156 ..      51     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.052
                       DUF5320  66 taeaskeeekelLeeqaeaLeeeleaikkrlke 98 
                                   t+ ++ eee+e L+++ e L ++le++k++lke
  gi|15669242|ref|NP_248047.1| 124 TDIKKLEEEIEKLKKENEELAAKLEKVKEKLKE 156
                                   56678899***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3476  (0.193876); expected 358.6 (0.02)
Passed bias filter:                     1468  (0.0818785); expected 358.6 (0.02)
Passed Vit filter:                       339  (0.0189079); expected 17.9 (0.001)
Passed Fwd filter:                        83  (0.00462937); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              77  [number of targets reported over threshold]
# CPU time: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 966.85
//
Query:       gi|15669243|ref|NP_248048.1|  [L=895]
Description: UDP-glucose dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-63  213.8   0.2    2.5e-63  213.1   0.2    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      5e-33  113.2   0.6    2.2e-26   91.9   0.0    3.3  3  UDPG_MGDP_dh     UDP-glucose/GDP-mannose dehydrogenase family
    8.2e-27   93.7   0.6    5.5e-26   91.0   0.1    2.6  2  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase family
    7.7e-21   74.2   7.7    8.4e-11   42.0   0.2    3.8  3  LAGLIDADG_3      LAGLIDADG-like domain
    2.4e-13   50.2   1.6    2.4e-13   50.2   1.6    2.2  2  Intein_splicing  Intein splicing domain
    0.00013   21.7   0.0    0.00035   20.2   0.0    1.8  1  ApbA             Ketopantoate reductase PanE/ApbA
    0.00037   20.7   0.0     0.0022   18.2   0.0    2.2  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0031   17.5   0.0        3.1    7.8   0.0    3.6  3  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
     0.0076   16.3   0.1       0.47   10.6   0.0    2.9  2  LAGLIDADG_WhiA   WhiA LAGLIDADG-like domain
     0.0094   15.8   0.0      0.021   14.7   0.0    1.6  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
  ------ inclusion threshold ------
      0.018   14.9   1.6      0.087   12.7   1.6    2.2  1  RsgI_N           Anti-sigma factor N-terminus
      0.022   14.9   0.0      0.051   13.7   0.0    1.6  1  Hom_end          Homing endonuclease
      0.025   14.6   3.9        2.3    8.2   0.1    3.3  2  LAGLIDADG_2      LAGLIDADG DNA endonuclease family
      0.042   14.4   0.2        6.6    7.4   0.0    4.1  5  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
       0.13   12.6   1.5         21    5.5   0.0    3.2  3  ATP-synt_F       ATP synthase (F/14-kDa) subunit


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.1   0.2   2.1e-66   2.5e-63       1     182 [.       1     177 [.       1     182 [. 0.94

  Alignments for each domain:
  == domain 1  score: 213.1 bits;  conditional E-value: 2.1e-66
                                   SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEE CS
                UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvif 81 
                                   m+isviG+GYvGl++a+ lae g++v+g+Dide+kv++ln+g++p+ye+gLe l+kk+v +++l+ftt+++  ++++dvif
  gi|15669243|ref|NP_248048.1|   1 MNISVIGTGYVGLIQAVGLAEFGFDVVGIDIDESKVKALNRGECPLYEEGLEGLLKKHV-NKNLTFTTSYKP-IKDSDVIF 79 
                                   89*********************************************************.8*********99.******** PP

                                   E-----B-TTTTCB-THHHHHHHHHHHHHHHC..EEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE------TTS CS
                UDPG_MGDP_dh_N  82 iaVgTPskkkgkaaDlkyvesaarsiaealkk..gkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvsnPEflregs 160
                                   ++VgTP++k + +aDl+++ sa+++i+e+++k  +kv+v+kSTvpvgt++  vk++l++      +++dvvsnPEflreg 
  gi|15669243|ref|NP_248048.1|  80 LCVGTPQDK-DGNADLRFLFSAVEKIKETIDKedYKVIVIKSTVPVGTNR-RVKELLKD------YNVDVVSNPEFLREGI 152
                                   *********.7777*****************9999**************9.88888874......568************* PP

                                   HHHHHHS-S-EEEEESSCHHH...H CS
                UDPG_MGDP_dh_N 161 avkdllnpdrvviGveekkae...a 182
                                   av+d++np+rv++G e+ +++   +
  gi|15669243|ref|NP_248048.1| 153 AVYDFFNPERVILGFENLNNKkpiE 177
                                   ****************988874444 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.0   1.9e-29   2.2e-26       1      76 [.     199     274 ..     199     286 .. 0.94
   2 ?   -1.0   0.1       1.7   2.1e+03      20      39 ..     503     522 ..     502     556 .. 0.74
   3 !   17.6   0.0   2.8e-06    0.0033      62      93 ..     714     745 ..     707     746 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 1.9e-29
                  UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalae 76 
                                   etAEliK+a+NaflatkIsfiNela+l +++ +d++ +  a+gldprig+kfl++g+G+GGsc+  D   ++++ +
  gi|15669243|ref|NP_248048.1| 199 ETAELIKYASNAFLATKISFINELAKLSDKVKADIKTISYAMGLDPRIGNKFLNAGIGYGGSCFHPDEVLFIDRGR 274
                                   69***************************************************************99888777665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                  UDPG_MGDP_dh  20 fiNelanlcealgidveeVi 39 
                                   +iN+++n+ ++lgi + e i
  gi|15669243|ref|NP_248048.1| 503 YINDVKNILNKLGIKYIEKI 522
                                   68999999999999865544 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 2.8e-06
                  UDPG_MGDP_dh  62 sclpkDvkaLvalaeelgleaelleavrevNe 93 
                                   +c+pkDvkaL+++ e++++e+ l++a++ vNe
  gi|15669243|ref|NP_248048.1| 714 NCFPKDVKALIKQFENNNIEPILIKATDIVNE 745
                                   6******************************8 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.3   1.6e+03      65      65 ..     150     150 ..      88     218 .. 0.51
   2 !   91.0   0.1   4.6e-29   5.5e-26       1     104 [.     768     879 ..     768     880 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.3
                                   T CS
                UDPG_MGDP_dh_C  65 k 65 
                                   +
  gi|15669243|ref|NP_248048.1| 150 E 150
                                   1 PP

  == domain 2  score: 91.0 bits;  conditional E-value: 4.6e-29
                                   EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-S..STHHCCCCHHGG.......BTCCEEES-CHHHHTT-SEEEE CS
                UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDP..kvkeeaveaele.......ekgvevvdsleealkgadaivi 72 
                                   a+lGlafK++tdDlReS+a+++i++Lle ga vk +D   k++e+ +++++         +++ v+d+l+e++k++d i+i
  gi|15669243|ref|NP_248048.1| 768 AVLGLAFKPNTDDLRESRAIKLIDMLLESGAIVKGFDYveKARENTINMYKLdkskgfyGYNLYVLDDLYETVKNVDGIII 848
                                   89***********************************9556667777665549******99******************** PP

                                   -S--GGGGGS-HHHHHHCCSS-EEEESSS-CC CS
                UDPG_MGDP_dh_C  73 ltehdefkeldlaklkelmkpavvfDgrnvld 104
                                   ++e d f++ d++k+ +l+k++vvfDgrn+ld
  gi|15669243|ref|NP_248048.1| 849 TVEYD-FNKEDWEKIGNLVKEKVVFDGRNILD 879
                                   ***95.6666********************98 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.5     7e-11   8.4e-08       3      80 ..     464     542 ..     462     545 .. 0.91
   2 !   42.0   0.2   7.1e-14   8.4e-11       3      78 ..     567     644 ..     565     649 .. 0.83
   3 ?    2.1   0.0      0.21   2.5e+02      67      82 ..     740     755 ..     716     756 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 7e-11
                                   HHHHHHHHHHHCCECCECSTTTTS......EEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTCG CS
                   LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvs......isltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisgenlkr 77 
                                     a L G++ ++G++sk+ ++++       ++++ +++e+++dv+++L++lGI+   + k     +g++ +li+s+  +  
  gi|15669243|ref|NP_248048.1| 464 DFARLIGYYLSEGWISKDYGRNGVvrkrigLCFGIHEEEYINDVKNILNKLGIKYIEKIK-----DGSHSILISSKILAYV 539
                                   6799***************99888999***************************999999.....8888889999999988 PP

                                   GGT CS
                   LAGLIDADG_3  78 Fle 80 
                                   F +
  gi|15669243|ref|NP_248048.1| 540 FEN 542
                                   876 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 7.1e-14
                                   HHHHHHHHHHHCCECCECSTTTTS.EEEEES-HHHHHHHHHHHHHCT.HSCEEEE.EEE-SCCCCECCCHCHCTTCGG CS
                   LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvs.isltssskelledvqrlLlrlGIestiyek.kkakgrgvyrlliisgenlkrF 78 
                                   k +fL+Glf +DG ++  +++++  i++++ sk+++  +  lL+ lGI++++++  ++++ +  y ++i + e++k+ 
  gi|15669243|ref|NP_248048.1| 567 KWEFLKGLFRGDGGIVRLNNNKNLnIEFATVSKKMAHSLLILLQLLGIVASVKKCyNNKSTTMAYIIRINGLEQVKKI 644
                                   568*************999998889******************************55555556666666666766665 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.21
                                   CCCHCHCTTCGGGTTT CS
                   LAGLIDADG_3  67 lliisgenlkrFleki 82 
                                     i+++e++k F+eki
  gi|15669243|ref|NP_248048.1| 740 TDIVNEEQIKWFFEKI 755
                                   579************9 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       2.1   2.5e+03       9      40 ..     102     132 ..      94     141 .. 0.71
   2 !   50.2   1.6     2e-16   2.4e-13      11     134 .]     280     714 ..     272     714 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.1
                                   EEEHHHHCCECTTEEEEEETTTTEEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing   9 kvkieelvekegeevlslnledlklevksvkk 40 
                                   + ki+e ++ke+++v++++       + +vk+
  gi|15669243|ref|NP_248048.1| 102 E-KIKETIDKEDYKVIVIKSTVPVGTNRRVKE 132
                                   3.789999999999998875554445555555 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 2e-16
                                   EHHHHCC.ECTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-E CS
                                   xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  11 kieelve.kegeevlslnledlklevksvkkliklklk.elyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdl 89 
                                   + +el+e ++ ++v  l+++ +kl  k+ k + k  ++  l++++ + gr+ik+T++H++ +++d+++  k  +++kegd 
  gi|15669243|ref|NP_248048.1| 280 TFKELFElEDKDNVKILSFDGEKLSLKKLKLASKRYYNdDLITLRFNLGREIKITKDHPVVILEDGELKIKLTSDVKEGDK 360
                                   67899997777888889***********99888888889************************99666559********** PP

                                   EEEE............................................................................. CS
                                   xxxx............................................................................. RF
               Intein_splicing  90 iavp............................................................................. 93 
                                   +++p                                                                             
  gi|15669243|ref|NP_248048.1| 361 VILPygnfgeereieidileelsktdliekvwihnkdlatnefniikpylsnkyphdvkrngtirakdilpikeildkygs 441
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669243|ref|NP_248048.1| 442 knrlftaksksttipykikidkdfarligyylsegwiskdygrngvvrkriglcfgiheeeyindvknilnklgikyieki 522
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669243|ref|NP_248048.1| 523 kdgshsilisskilayvfenilncgincynknippqmfnakeeikweflkglfrgdggivrlnnnknlniefatvskkmah 603
                                   ********************************************************************************* PP

                                   ......................................................................HSCEEEEEEEE CS
                                   ......................................................................xxxxxxxxxxx RF
               Intein_splicing  94 ......................................................................dadvvwdkvks 104
                                                                                                          ++ +  +vk+
  gi|15669243|ref|NP_248048.1| 604 sllillqllgivasvkkcynnksttmayiiringleqvkkigelfgkkwenykdiaesykrnieplgykkSDNFAILEVKE 684
                                   *********************************************************************666699****** PP

                                   EEEEECEEEEEEEEETTT-EEEE.CTTEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
               Intein_splicing 105 ievedeeeyVYdltvednhNFva.ngiivHN 134
                                   i +e++ +yVY++++e+    +   gi+ HN
  gi|15669243|ref|NP_248048.1| 685 IIKEHYSGYVYSVETENSLL-ITsYGILIHN 714
                                   **************995544.4459999998 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0     3e-07   0.00035       1      87 [.       3      93 ..       3     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3e-07
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT....CEEEEEECEEECCHSCCCCS-ESEEEE-SSG CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg....geeilrppealsaeekselepidlvivtvKa 78
                                  i ++G+G +G + a+ La+ g dv+ i+ ++ +++al++  + l++eg     ++++ ++ +++++  + +++ d+++++v +
  gi|15669243|ref|NP_248048.1|  3 ISVIGTGYVGLIQAVGLAEFGFDVVGIDIDEsKVKALNRGECPLYEEGleglLKKHVNKNLTFTTS-YKPIKDSDVIFLCVGT 84
                                  789*********************************************996634444444444444.799***********99 PP

                                  GGHHHHHHH CS
                          ApbA 79 yqteealee 87
                                   q+++  ++
  gi|15669243|ref|NP_248048.1| 85 PQDKDGNAD 93
                                  999886555 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.9e-06    0.0022       1     114 [.       2     144 ..       2     145 .. 0.80
   2 ?   -1.0   0.0       1.5   1.8e+03      18      66 ..     793     853 ..     788     877 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-06
                                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...................EEE-SSHHHHHHHCSEEEE- CS
                 NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...................akaaesieelvasldvvitm 62 
                                   +i +iG+G  G   a  l++ g++v++++ +++kv++l   +                   + ++++  + +++ dv++++
  gi|15669243|ref|NP_248048.1|   2 NISVIGTGYVGLIQAVGLAEFGFDVVGIDIDESKVKALNRGEcplyeeglegllkkhvnknL-TFTTSYKPIKDSDVIFLC 81 
                                   699**********************************9988899999999999976666533.333333455666****** PP

                                   SSSHHHHHHHHHS.........HCCC-..-TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEE CS
                 NAD_binding_2  63 vkagkavdevieg.........lleal..kkgdilidgstsspedtrelakelkekglkflda 114
                                   v   ++ d   +          ++e++  +  ++++  st+ + ++r++++ lk+ +++++  
  gi|15669243|ref|NP_248048.1|  82 VGTPQDKDGNADLrflfsavekIKETIdkEDYKVIVIKSTVPVGTNRRVKELLKDYNVDVVSN 144
                                   *9999988777666644444445555554455689999****************999998865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                                   HHHTT-EEEEE-SSHHHHHHHHHTT............EEE-SSHHHHHHHCSEEEE-SSSH CS
                 NAD_binding_2  18 llkagykvavynrtkekveelvaeg............akaaesieelvasldvvitmvkag 66 
                                   ll++g  v +++  +++ e+ ++              + +++++ e v+++d +i+ v+ +
  gi|15669243|ref|NP_248048.1| 793 LLESGAIVKGFDYVEKARENTINMYkldkskgfygynLYVLDDLYETVKNVDGIIITVEYD 853
                                   5666666777776666666666654555666666666889999999999999999999865 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0026       3.1       2     120 ..       3     136 ..       2     153 .. 0.73
   2 ?    2.5   0.0      0.11   1.3e+02      33     108 ..     171     244 ..     153     255 .. 0.80
   3 ?    2.3   0.0      0.12   1.4e+02      55      97 ..     828     870 ..     800     872 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0026
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHS.....SBTTTBTT----TTEEEES-HHHHHTT--EEEE-- CS
                NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineeh.....envkyLpgiklpenlvattdlaealkgadiivlvv 77 
                                   i+v+G+G  G   A  lae g +v+ +  +e  ++++n+ +     e  + L + ++++nl++tt  +  +k++d+i+l v
  gi|15669243|ref|NP_248048.1|   3 ISVIGTGYVGLIQAVGLAEFGFDVVGIDIDESKVKALNRGEcplyeEGLEGLLKKHVNKNLTFTTSYK-PIKDSDVIFLCV 82 
                                   99************************************976111114455566678999999999875.689999999998 PP

                                   -H..........HHHHHHHHHHCCC--TT-EEEE---SE.ET.TTEEHHHHHHH CS
                NAD_Gly3P_dh_N  78 Ps..........qalrevlkklkgllkkkailvsliKGi.eegtlkllseviee 120
                                    +           +l + ++k+k++++k+   v++iK     gt+++++e +++
  gi|15669243|ref|NP_248048.1|  83 GTpqdkdgnadlRFLFSAVEKIKETIDKEDYKVIVIKSTvPVGTNRRVKELLKD 136
                                   653333333333477788888888888888777788766466666666555543 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.11
                                   HHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SEET CS
                NAD_Gly3P_dh_N  33 elieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGiee 108
                                   +  + i+  +e  ky+++ ++p  +  + + ae +k a+  +l+   ++++e + kl++++k++ + +s + G+ +
  gi|15669243|ref|NP_248048.1| 171 NNKKPIEIMEEVYKYFKDKNIPFVI-TNWETAELIKYASNAFLATKISFINELA-KLSDKVKADIKTISYAMGLDP 244
                                   5556677778889999999999755.5678999****************99965.6888899*******9999954 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.12
                                   TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT- CS
                NAD_Gly3P_dh_N  55 enlvattdlaealkgadiivlvvPsqalrevlkklkgllkkka 97 
                                    nl + +dl e++k++d i++ v   + +e  +k+ +l+k+k+
  gi|15669243|ref|NP_248048.1| 828 YNLYVLDDLYETVKNVDGIIITVEYDFNKEDWEKIGNLVKEKV 870
                                   5888999********************9999999999998876 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.15   1.8e+02      24      48 ..     494     518 ..     467     533 .. 0.82
   2 !   10.6   0.0   0.00039      0.47       3      56 ..     569     624 ..     567     644 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.15
                LAGLIDADG_WhiA  24 LEivspdeelaeqlqkllnefelea 48 
                                   L + +++ee++++++++ln++++++
  gi|15669243|ref|NP_248048.1| 494 LCFGIHEEEYINDVKNILNKLGIKY 518
                                   5577899*************99875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00039
                LAGLIDADG_WhiA   3 aflrGaflasGsindp.ekk.yhLEivspdeelaeqlqkllnefeleakilerrkk 56 
                                    fl+G+f + G i +  ++k   +E+++ ++++a+ l  ll+ +++ a++++  ++
  gi|15669243|ref|NP_248048.1| 569 EFLKGLFRGDGGIVRLnNNKnLNIEFATVSKKMAHSLLILLQLLGIVASVKKCYNN 624
                                   59*******99998874333599*******************99998887765443 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.8e-05     0.021       1      82 [.       2      78 ..       2      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                                  EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SEE CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavdadlv 82
                                  ++ viG+G +G   a  +a+ g++Vv +di+e+++++ ++  e  l +   +g lk    +++ ++++ftt+++ ++d d++
  gi|15669243|ref|NP_248048.1|  2 NISVIGTGYVGLIQAVGLAEFGFDVVGIDIDESKVKALNRG-ECPLYEEGLEGLLK----KHVNKNLTFTTSYKPIKDSDVI 78
                                  589*****************************999765544.44455555666666....5667788888888888888876 PP

>> RsgI_N  Anti-sigma factor N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.6   7.3e-05     0.087       1      44 [.     331     373 ..     331     378 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-05
                        RsgI_N   1 leikkkkaivlTpdGeFikikrkggmkvGeEiefpekdiiekkr 44 
                                   ++i+k++ +v  +dGe +kik ++++k G+++ +p  ++ e+++
  gi|15669243|ref|NP_248048.1| 331 IKITKDHPVVILEDGE-LKIKLTSDVKEGDKVILPYGNFGEERE 373
                                   79**************.8*****************999988775 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.3e-05     0.051       1      86 [.     554     637 ..     554     645 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
                       Hom_end   1 kipsflaseaievREaFlaGLvdsdgyvkkeked...satvktedksvmegivklarsLGikasvktkeekidakgvkhqf 78 
                                   +ip ++   + e++  Fl GL  +dg   + +++    +   t++k+  + +  l + LGi asvk+       ++++  +
  gi|15669243|ref|NP_248048.1| 554 NIPPQMFNAKEEIKWEFLKGLFRGDGGIVRLNNNknlNIEFATVSKKMAHSLLILLQLLGIVASVKKC-----YNNKSTTM 629
                                   5777777777788888*********866555455566777789***********************94.....23344455 PP

                       Hom_end  79 cyaitlsg 86 
                                   +y i ++g
  gi|15669243|ref|NP_248048.1| 630 AYIIRING 637
                                   67777665 PP

>> LAGLIDADG_2  LAGLIDADG DNA endonuclease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0019       2.3       4      58 ..     468     525 ..     466     561 .. 0.78
   2 ?    6.0   0.3    0.0094        11       1     103 [.     568     669 ..     568     671 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                                   HHHHHHTT-EEE-SSTTS-B...EEEEEE..S-HHHHHHHHHHTGGG--S--EEEEEE CS
                   LAGLIDADG_2   4 liGlLLGDgslekrkkrknv...rfefkqskkhkeYllyvfellkeyllsnpkivkrk 58 
                                   liG  L+ g++ k  +r++v   r+ +  +++++eY++ v+++l+++++++ +  k+ 
  gi|15669243|ref|NP_248048.1| 468 LIGYYLSEGWISKDYGRNGVvrkRIGLCFGIHEEEYINDVKNILNKLGIKYIEKIKDG 525
                                   7999*******666666554333999999********************998876644 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0094
                                   HHHHHHHHHTT-EEE-SSTTS-BEEEEEE..S-HHHHHHHHHHTGGG--S--EEEEEE-TTSEEEEEEEE---BGGGHHHH CS
                   LAGLIDADG_2   1 reiliGlLLGDgslekrkkrknvrfefkqskkhkeYllyvfellkeyllsnpkivkrktrrksetklrfqtrslpcfnela 81 
                                   +e+l Gl  GDg + + +++kn ++ef   +k+ ++ l +  +l  +++s  k  ++k   ++  ++ ++   l++ +++ 
  gi|15669243|ref|NP_248048.1| 568 WEFLKGLFRGDGGIVRLNNNKNLNIEFATVSKKMAHSLLILLQLLGIVASVKKCYNNK---STTMAYIIRINGLEQVKKIG 645
                                   68899999********************955555555555555555666666654433...35666666666666666666 PP

                                   HHHBSS..SSB---TTHHHH--HH CS
                   LAGLIDADG_2  82 klfysk..gkkiipknilklLtpl 103
                                   +lf +k  + k i +++++ + pl
  gi|15669243|ref|NP_248048.1| 646 ELFGKKweNYKDIAESYKRNIEPL 669
                                   666666666777777777777776 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0055       6.6       2      72 ..       3      85 ..       2     109 .. 0.81
   2 ?   -2.3   0.0         6   7.1e+03      35      57 ..     126     146 ..      99     154 .. 0.64
   3 ?   -0.6   0.0       1.7     2e+03      50      81 ..     195     226 ..     158     239 .. 0.79
   4 ?   -2.2   0.0       5.5   6.6e+03      52      93 ..     699     738 ..     684     740 .. 0.73
   5 ?    0.5   0.0      0.79   9.5e+02      54      92 ..     835     872 ..     811     876 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0055
                                  EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.................-EEECECHHHHHHH-SEEEE CS
                 F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.................vkvtavdneeaaeeadvvvl 67
                                  i +iG+G +g   a gl++ g    ++v + + +++k+++l +  +                  ++t ++  + ++++dv++l
  gi|15669243|ref|NP_248048.1|  3 ISVIGTGYVGLIQAVGLAEFG---FDVV-GIDIDESKVKALNRG-EcplyeeglegllkkhvnKNLTFTTSYKPIKDSDVIFL 80
                                  889999999999999999999...8888.778888888887643.2357788888888888887777778999999******* PP

                                  -S-HH CS
                 F420_oxidored 68 avkpe 72
                                  +v + 
  gi|15669243|ref|NP_248048.1| 81 CVGTP 85
                                  *9765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6
                                   SCCCHHHHHHHHC-EEECECHHH CS
                 F420_oxidored  35 npekaeelaeelgvkvtavdnee 57 
                                   ++ +++el ++++v+v +  n e
  gi|15669243|ref|NP_248048.1| 126 TNRRVKELLKDYNVDVVS--NPE 146
                                   556777888888877766..555 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.7
                                   EECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
                 F420_oxidored  50 vtavdneeaaeeadvvvlavkpedveevlsel 81 
                                   +t  +++e+++ a   +la k + + e+++  
  gi|15669243|ref|NP_248048.1| 195 ITNWETAELIKYASNAFLATKISFINELAKLS 226
                                   56667889999999999****99999998766 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 5.5
                                   CECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEE CS
                 F420_oxidored  52 avdneeaaeeadvvvlavkpedveevlselakdalkgklvis 93 
                                   + +n+ ++++  +++  + p+dv++++++  +++  + ++i 
  gi|15669243|ref|NP_248048.1| 699 T-ENSLLITSYGILIHNCFPKDVKALIKQF-ENNNIEPILIK 738
                                   4.6777777777888888999999999999.77777777775 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.79
                                   CHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEE CS
                 F420_oxidored  54 dneeaaeeadvvvlavkpedveevlselakdalkgklvi 92 
                                   d  e++++ d ++++v +   +e ++++  ++ k+k+v 
  gi|15669243|ref|NP_248048.1| 835 DLYETVKNVDGIIITVEYDFNKEDWEKI-GNLVKEKVVF 872
                                   567999**************99999999.8999999885 PP

>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.018        21      29      61 ..     100     132 ..      73     143 .. 0.79
   2 ?    4.5   0.1     0.037        44      16      78 ..     165     227 ..     162     237 .. 0.85
   3 ?   -2.9   0.0       7.6   9.1e+03      45      71 ..     710     737 ..     709     741 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.018
                                   HHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHH CS
                    ATP-synt_F  29 ieealkelleredigiilitekiaeeirelide 61 
                                   + e++ke +++ed+++i+i+ ++    +++++e
  gi|15669243|ref|NP_248048.1| 100 AVEKIKETIDKEDYKVIVIKSTVPVGTNRRVKE 132
                                   77999**************99886666666655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.037
                                   TTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCSSSSEEEEESCSCC CS
                    ATP-synt_F  16 aGvgevevtdeeeieealkelleredigiilitekiaeeirelideykeealPaileIPskeg 78 
                                   +G+++ +++++ ei e + ++ ++++i  ++ + + ae i+   +++  +++ +i e+ + + 
  gi|15669243|ref|NP_248048.1| 165 LGFENLNNKKPIEIMEEVYKYFKDKNIPFVITNWETAELIKYASNAFLATKISFINELAKLSD 227
                                   7999*************************************9999988877777777655555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 7.6
                                   EEEEHHHHCCCHHHHHHCTCS.SSSEEE CS
                    ATP-synt_F  45 ilitekiaeeirelideykee.alPail 71 
                                   ili++ + ++++ li++++++   P+++
  gi|15669243|ref|NP_248048.1| 710 ILIHNCFPKDVKALIKQFENNnIEPILI 737
                                   6778888888889999998887777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (895 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.51
# Mc/sec: 5288.51
//
Query:       gi|15669244|ref|NP_248049.1|  [L=326]
Description: capsular polysaccharide biosynthesis protein I [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-60  202.0   0.1    1.6e-59  201.3   0.0    1.3  2  Epimerase        NAD dependent epimerase/dehydratase family
    1.3e-54  185.8   0.1    2.5e-54  184.9   0.1    1.4  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.1e-16   58.4   0.0    4.5e-15   55.5   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    7.6e-16   57.9   0.0    9.6e-16   57.6   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    7.9e-15   54.7   0.0      1e-14   54.3   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.6e-07   30.8   0.0    3.8e-05   23.0   0.0    2.2  2  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
      0.014   15.3   0.0       0.02   14.8   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
      0.039   13.4   0.0       0.06   12.8   0.0    1.3  1  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.3   0.0   6.9e-63   1.6e-59       1     241 []       6     249 ..       6     249 .. 0.97
   2 ?   -3.6   0.0       2.8   6.3e+03     189     212 ..     262     287 ..     260     289 .. 0.71

  Alignments for each domain:
  == domain 1  score: 201.3 bits;  conditional E-value: 6.9e-63
                                   EEEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC..........EEEE--TT-HHHHHHHHHHHT-SEEE CS
                     Epimerase   1 ilVtGatGfiGsalvkallekg..yevigldrlssasntarledl..........elveldltdrsalerlfkeeqpdavi 69 
                                   ilVtG +GfiG +l k+l+++    +vig+d+l++  n  ++e+           ++++ld+ d ++l + +k++++d ++
  gi|15669244|ref|NP_248049.1|   6 ILVTGSAGFIGFHLSKYLMDNYedLKVIGIDNLNNYYNPVLKEKRneilknyenyTFIKLDFSDWDDLVENLKDKEIDLIV 86 
                                   8********************96566************99999999*********************************** PP

                                   E--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS--.--SSHHHHHHHHH CS
                     Epimerase  70 hlAavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgpl.kpnspYaaaKlag 149
                                   hl+a++gv+ s ++p ++i++n +gtln++e ar+ ++++++++sSs+vYG + ++p +e+     + kp s Ya +K+  
  gi|15669244|ref|NP_248049.1|  87 HLGAQAGVRYSLQNPWAYIKSNEMGTLNIFEFARRFDIEKVVYASSSSVYGGNRKIPFSEDD---RVdKPISLYASTKRSN 164
                                   *********************************************************99999...788************* PP

                                   HHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHT CS
                     Epimerase 150 eklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvd 230
                                   e +++ y++ yg+++i lr f++yG++   g+++  +++++++il+gk e+ +++ g+  Rdf y++Dv+++il+++++  
  gi|15669244|ref|NP_248049.1| 165 ELMAHVYHHLYGIKMIGLRFFTVYGEY---GRPDMAYFKFAKNILLGK-EIEVYNYGNMERDFTYISDVVDGILRAIKK-- 239
                                   ***************************...99****************.******************************.. PP

                                   T-STTEEEEES CS
                     Epimerase 231 agdkgeiyniG 241
                                    + + ei+n+G
  gi|15669244|ref|NP_248049.1| 240 -DFDYEIFNLG 249
                                   .66799***98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.8
                                   HHHHHHTTS..SSEEEETTST-EEEE CS
                     Epimerase 189 lirkilegk..qevtllgdgtalRdf 212
                                   li+k l++k  ++++ + dg+ lR +
  gi|15669244|ref|NP_248049.1| 262 LIEKYLNKKakKKFLPMQDGDVLRTY 287
                                   56666665555688889999999987 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.9   0.1   1.1e-57   2.5e-54       1     331 [.       7     311 ..       7     312 .. 0.84

  Alignments for each domain:
  == domain 1  score: 184.9 bits;  conditional E-value: 1.1e-57
                                   EEETTTSHHHHHHHHHHHHC..T-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlek..gyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdev 79 
                                   L+TG aGfiG +l ++L+++  + +v+gi+++++ +n    e+  +++  ++ en++++k D +D + l + l++ ++d +
  gi|15669244|ref|NP_248049.1|   7 LVTGSAGFIGFHLSKYLMDNyeDLKVIGIDNLNNYYNPVLKEK--RNEILKNYENYTFIKLDFSDWDDLVENLKDKEIDLI 85 
                                   9*****************9833457888888888777444443..344455678*************************** PP

                                   EE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS--.---SHHHHHHHH CS
                 GDP_Man_Dehyd  80 ynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpf.yPrsPYaaaKly 159
                                   ++L+Aq  V++s+++P ++++ n +Gtl+++e +r+  +e   +++ aS+s vYG  +++p++E+ ++ +P s Ya +K +
  gi|15669244|ref|NP_248049.1|  86 VHLGAQAGVRYSLQNPWAYIKSNEMGTLNIFEFARRFDIE---KVVYASSSSVYGGNRKIPFSEDDRVdKPISLYASTKRS 163
                                   *************************************987...899******************999736*********** PP

                                   HHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS.-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC CS
                 GDP_Man_Dehyd 160 adwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgk.qevlylGnldakRdwghvkDyveamwlmlqq 239
                                    + +++ y++ yg+ ++  ++f  ++ +  ++       +++ +i+lgk  ev+++Gn++  Rd+++++D+v+++ +++++
  gi|15669244|ref|NP_248049.1| 164 NELMAHVYHHLYGIKMIGLRFFTVYGEYGRPD---MAYFKFAKNILLGKeIEVYNYGNME--RDFTYISDVVDGILRAIKK 239
                                   ****************************8666...5677888999999944778899995..***************9998 PP

                                   SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH--- CS
                 GDP_Man_Dehyd 240 dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWk 320
                                   d  +  +++ g++   + +  + f+el +++                 +++ + ++ ++++g+v ++++d sk ++ Lg+k
  gi|15669244|ref|NP_248049.1| 240 DF-DYEIFNLGNS---KPVKLMYFIELIEKYL----------------NKKAKKKFLPMQDGDVLRTYADLSKSEKLLGYK 300
                                   85.2223333333...3333455555554332................2345566778899******************** PP

                                   -SS-HHHHHHH CS
                 GDP_Man_Dehyd 321 pkvsfeelvre 331
                                   pkv++ee++++
  gi|15669244|ref|NP_248049.1| 301 PKVTIEEGLKR 311
                                   ********986 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0     2e-18   4.5e-15       1     252 [.       6     272 ..       6     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 2e-18
                                   EEEETTTSHHHHHHHHHHHHH.B-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SE CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkk.kpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdv 80 
                                   +lvtG++G iG +l + ++++ +  k+i +++  +    + ke+++e+ k+    +++ +  d  d + l + l++ ++d+
  gi|15669244|ref|NP_248049.1|   6 ILVTGSAGFIGFHLSKYLMDNyEDLKVIGIDNLNNYYNPVLKEKRNEILKNYE--NYTFIKLDFSDWDDLVENLKDKEIDL 84 
                                   89************999998755555665666555556666766666655333..3345668******************* PP

                                   EEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE...............GGGSS--SHHHHHHHHHH CS
               Polysacc_synt_2  81 vfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt...............DKAvnPtnvmGatKrlae 146
                                   ++h  A   V    +np+  ik N +gt n+ e a + +++kvv+ S+               D+  +P++++  tKr  e
  gi|15669244|ref|NP_248049.1|  85 IVHLGAQAGVRYSLQNPWAYIKSNEMGTLNIFEFARRFDIEKVVYASSssvyggnrkipfsedDRVDKPISLYASTKRSNE 165
                                   ********************************************998656666666666666678889************* PP

                                   HHHHHGGG--SSS--EEEEEEE-EETTGTTS...SHHHHHHHHHTTSSEEES-T.T-EEEEE-HHHHHHHHHHHHHH--SS CS
               Polysacc_synt_2 147 kllqalakeseekktkfvvvRfGNVlgSrGS...viplFkkqikeggpvtvTdp.emtRyfmtieeavqLvlqalalakgg 223
                                   +++  +++       k++  Rf  V g  G       +F k i  g+++ v +  +m R f  i++ v+ +l a+++  + 
  gi|15669244|ref|NP_248049.1| 166 LMAHVYHHLY---GIKMIGLRFFTVYGEYGRpdmAYFKFAKNILLGKEIEVYNYgNMERDFTYISDVVDGILRAIKKDFDY 243
                                   **99999988...899***********9996332456789***********88549************************* PP

                                   -EEEE--.-EEEHHHHHHHH......... CS
               Polysacc_synt_2 224 eifvldmGepvkivdlakalielsgleek 252
                                   eif l   +pvk++   + + ++ +++ k
  gi|15669244|ref|NP_248049.1| 244 EIFNLGNSKPVKLMYFIELIEKYLNKKAK 272
                                   ************99888877666655544 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   4.3e-19   9.6e-16       1     231 [.       7     239 ..       7     274 .. 0.78

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 4.3e-19
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD.......lrespelleelskvnvkkviegDvtdkdkleeale..gvdvvih 72 
                                   +vtG+aGF+G +l k L++  e  +v  +D        + +++  e l++ ++ ++i+ D  d d+l e l+  ++d+++h
  gi|15669244|ref|NP_248049.1|   7 LVTGSAGFIGFHLSKYLMDNYEDLKVIGIDnlnnyynPVLKEKRNEILKNYENYTFIKLDFSDWDDLVENLKdkEIDLIVH 87 
                                   69****************9987555555667777766444555557788888888***************97225789*** PP

                     3Beta_HSD  73 laslvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKal 152
                                   l +   v+   ++   + k n  GT n+ e +++ +++++vY Ss +v g+  ++ ++    E+  +  ++ + y+++K+ 
  gi|15669244|ref|NP_248049.1|  88 LGAQAGVRYsLQNPWAYIKSNEMGTLNIFEFARRFDIEKVVYASSSSVYGG-NRKIPFS---ED-DRVDKPISLYASTKRS 163
                                   *99888887366777899*********************************.4566676...44.45567899*******9 PP

                     3Beta_HSD 153 aEklvlkaNgrtlknggrlyTcaLRpagiyGegdk...llvpllkqlaklglalfkigdeevlsdrvYvgNvawahilAar 230
                                    E +        l ++     + LR  ++yGe+ +     ++++k+++ lg+++  +   ++  d++Y   v++ ++ A +
  gi|15669244|ref|NP_248049.1| 164 NELMAHVYHH--LYGI---KMIGLRFFTVYGEYGRpdmAYFKFAKNIL-LGKEIEVYNYGNMERDFTYISDVVDGILRAIK 238
                                   9976555444..4444...5578*********9661114455555544.444566666666777********999888876 PP

                     3Beta_HSD 231 a 231
                                   +
  gi|15669244|ref|NP_248049.1| 239 K 239
                                   5 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   4.6e-18     1e-14       2     228 ..       5     264 ..       4     285 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 4.6e-18
                                   EEEEESTTSHHHHHHHHHCTT..TSEEEEEE-TT.........................T--TTSHHHHHHHHHHH--SEE CS
                 RmlD_sub_bind   2 kilvtGanGqlGseLakqlae..eglevlaltre.........................eldltdaeavaellkeakpdvv 55 
                                   +ilvtG+ G +G +L k l    e+l+v+++++                          +ld++d + + e lk+++ d++
  gi|15669244|ref|NP_248049.1|   5 NILVTGSAGFIGFHLSKYLMDnyEDLKVIGIDNLnnyynpvlkekrneilknyenytfiKLDFSDWDDLVENLKDKEIDLI 85 
                                   69***************9987457888888866689********************************************* PP

                                   EE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS--.--SSHHHHHHHHHHH CS
                 RmlD_sub_bind  56 vnaAAytavDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddet.sPlnvYGrtKlaGEq 134
                                   v+++A   v    +++ a  + n+ ++ ++ e a++ ++ ++++ S+  V+ G++k p++edd++ +P+++Y+ tK   E 
  gi|15669244|ref|NP_248049.1|  86 VHLGAQAGVRYSLQNPWAYIKSNEMGTLNIFEFARRFDIeKVVYASSSSVYGGNRKIPFSEDDRVdKPISLYASTKRSNEL 166
                                   **************************************9469*********************9747*************8 PP

                                   HHHH....H-SSEEEEEE-SEESSSSS-..HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG- CS
                 RmlD_sub_bind 135 avla....agkkalivRtswvygekgkn..fvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekela 207
                                   +       +g k++ +R+  vyge+g+     +++ +     +e++v +     +  T+  d+ + +l +++k  +    +
  gi|15669244|ref|NP_248049.1| 167 MAHVyhhlYGIKMIGLRFFTVYGEYGRPdmAYFKFAKNILLGKEIEVYNYgnMERDFTYISDVVDGILRAIKKDFD----Y 243
                                   766533445668888*********9874114455666666777777766411345567777777777777777776....7 PP

                                   EEEE---BS-EEHHHHHHHHH CS
                 RmlD_sub_bind 208 gvyHlanegetswlefArail 228
                                   +++ l+n++ +  + f + i 
  gi|15669244|ref|NP_248049.1| 244 EIFNLGNSKPVKLMYFIELIE 264
                                   777777776666666655555 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0031       6.8       1      25 [.       8      32 ..       8      35 .. 0.91
   2 !   23.0   0.0   1.7e-08   3.8e-05      85     188 ..      79     169 ..      65     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0031
                                  EE-TTSHHHHHHHHHHHHHS-.TEE CS
                 NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevki 25
                                  +TG+ GF+G +L + L+++ +++k+
  gi|15669244|ref|NP_248049.1|  8 VTGSAGFIGFHLSKYLMDNYEDLKV 32
                                  7*****************9998877 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.7e-08
                                   HHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS-H......HH CS
                 NAD_binding_4  85 aeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekvyeegekeekl 161
                                    +e+d+i+h +A+  + +++++    ++ N +Gt +++e+a++      +++ S+ ++  g+r+  ++e            
  gi|15669244|ref|NP_248049.1|  79 DKEIDLIVHLGAQAGVRYSLQNpwaYIKSNEMGTLNIFEFARRFDIE-KVVYASSsSVYGGNRKIPFSE------------ 146
                                   479******************97777899***************999.555655538888877755533............ PP

                                   H--EEEETTTCCCHHHHHHHHHHHHHH CS
                 NAD_binding_4 162 dederaklkglpntYeqsKalaEklvr 188
                                        ++ ++    Y  +K   E + +
  gi|15669244|ref|NP_248049.1| 147 ----DDRVDKPISLYASTKRSNELMAH 169
                                   ....33333444444444444444444 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   8.8e-06      0.02      33     122 ..      51     159 ..      10     171 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.8e-06
                                   HHHHCT.TTCEEEE--TT-CCHHHHHHTT-SE.EEES---TCC..............HHHH..HHHHHHHHHHCT--EEEE CS
                NAD_binding_10  33 aeleae.eglevvegdvtdvedlaealkgada.Vvsalggggk..............deeg..aknivdaakeagvkRfvl 95 
                                   +e+ ++ e+ + +++d++d +dl e lk+ ++  ++ lg++++              +     + ni + a++ +++++v+
  gi|15669244|ref|NP_248049.1|  51 NEILKNyENYTFIKLDFSDWDDLVENLKDKEIdLIVHLGAQAGvryslqnpwayiksN--EmgTLNIFEFARRFDIEKVVY 129
                                   4443344899********************9888999988888667665555555433..057****************** PP

                                   EEETTTTS...GCGCHHHHHHHHCCHHHHH CS
                NAD_binding_10  96 vsaigvgd...evpgefgewnkellkayla 122
                                    s+  v+    ++p + ++ +++ ++ y+ 
  gi|15669244|ref|NP_248049.1| 130 ASSSSVYGgnrKIPFSEDDRVDKPISLYAS 159
                                   ****99852113333333444455555554 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.7e-05      0.06       1      68 [.       4      77 ..       4     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                                  SEEEEESTTSHHHHHHHHHHHH..TT-EEEEEESCHHHHHHHHHHHHHT....TSEEEEEE-TTTSHHHHHHHH CS
                     adh_short  1 kvvlvtGassGIGraiakelak..eGakvvvvdrseekleevakelkee....gakalaiqvDvtdreevealv 68
                                  k +lvtG ++ IG  ++k l+   e+ kv+ +d+ ++  + v+ke ++e     +++++i++D +d++++ + +
  gi|15669244|ref|NP_248049.1|  4 KNILVTGSAGFIGFHLSKYLMDnyEDLKVIGIDNLNNYYNPVLKEKRNEilknYENYTFIKLDFSDWDDLVENL 77
                                  789*****************97446999999********99999999988766677999****99888765444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2207.92
//
Query:       gi|15669245|ref|NP_248050.1|  [L=516]
Description: asparagine synthetase AsnB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-59  202.4   0.2    3.8e-55  188.0   0.1    2.1  2  Asn_synthase  Asparagine synthase
      2e-35  121.4   0.0    7.6e-35  119.5   0.0    2.0  1  GATase_7      Glutamine amidotransferase domain
    7.5e-32  110.3   0.0    1.4e-31  109.5   0.0    1.4  1  GATase_6      Glutamine amidotransferase domain
    2.6e-06   27.1   0.2    4.6e-06   26.3   0.2    1.3  1  DUF3700       Aluminium induced protein
  ------ inclusion threshold ------
      0.035   14.4   0.7       0.16   12.2   0.2    2.1  2  UPF0113       UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.0   0.1   1.1e-58   3.8e-55       3     142 ..     259     396 ..     257     407 .. 0.95
   2 !   14.7   0.0   4.9e-06     0.018     231     332 ..     391     501 ..     391     515 .. 0.82

  Alignments for each domain:
  == domain 1  score: 188.0 bits;  conditional E-value: 1.1e-58
                  Asn_synthase   3 relLedaVkrrlradvpvGalLSGGlDSSliaalaarqsk.splktFsigfeekgsdeakyakevaehlgtehtelvltee 82 
                                   ++lL daVk r+r+dvpvGa+LSGGlDSS+++ +++++++ s+l+tFsigf e ++de++y k v+++++t+h++++++e+
  gi|15669245|ref|NP_248050.1| 259 KKLLYDAVKIRMRSDVPVGAFLSGGLDSSTVVGVMREFTDlSKLHTFSIGF-EGKYDETPYIKIVVDYFKTQHHHYYFKER 338
                                   689************************************************.9**************************** PP

                  Asn_synthase  83 elldalpdviyhleepfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaa 142
                                   +++++++++ ++++epf+d s +p+y +s++a rk+v+vvLsG+G+DE+fgGY  ++   
  gi|15669245|ref|NP_248050.1| 339 DFEELIDKYSWIYDEPFGDYSGFPTYKVSEMA-RKFVTVVLSGDGGDEVFGGYM-THLNG 396
                                   ********************************.999*****************8.88765 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.9e-06
                  Asn_synthase 231 mahglEaRvPflDh..rlvevalr.lppelklrggieKyiLRealeg..ylPeeileRp.Kegfsapvgewklk.gelrel 304
                                   m h    R+ f+ +  ++++v+ + lp++  l+g  + y+L+ea++   + Pee+++   Ke++  p  ++k++ ++lr +
  gi|15669245|ref|NP_248050.1| 391 MTHLNGYRMDFIRKlpKFLRVVGSkLPVKKDLNGIANLYLLKEAFRLslINPEEFYAESiKEDAIRPEIYKKWTiEKLRYC 471
                                   66777789999999999****9988*********************98789****************99999999****** PP

                  Asn_synthase 305 aeellsds..rlakeglldreaveelleeh 332
                                   +++  ++    l+ + ll ++ ++++l + 
  gi|15669245|ref|NP_248050.1| 472 LNKGDNKLgeALRIFDLLFNTLCDNFLVKV 501
                                   999888875455555566666666666554 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.5   0.0   2.1e-38   7.6e-35       1     122 [.      51     181 ..      51     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 2.1e-38
                      GATase_7   1 hrrlsi.idseagaQPmvss.............edgrlvivfnGeiyNykelreeLeakghrfrtksDtevllalleaewg 67 
                                   h rl+i ++se+g+QPm  +             +  +++iv+nGeiyNy el+e+++   ++ +t +Dtev+l+l+++  g
  gi|15669245|ref|NP_248050.1|  51 HVRLAIlDLSEKGHQPMGYNvdedkiiyrddelDRADIIIVYNGEIYNYLELKEKFN---LETETGTDTEVILKLYNK-LG 127
                                   789***999********87567888999888777788******************95...5689*************8.** PP

                      GATase_7  68 eealerlnGmfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                    ++++++nGm+Af+i+d++++ +++ RDrlG+kP+yy++d g++++f+Selk +l
  gi|15669245|ref|NP_248050.1| 128 FDCVKEFNGMWAFCIFDKKKGLIFCSRDRLGVKPFYYYWD-GNEFIFSSELKGIL 181
                                   ****************************************.89*********987 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   0.0   3.9e-35   1.4e-31      12     134 .]      45     176 ..      32     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 3.9e-35
                      GATase_6  12 devalaHvRlaivglaeeegaqPf.psedgr.............lllvhNGeiynykelreelpalkglafrsrsDtevll 78 
                                    +++l+HvRlai +l+ e+g+qP+ ++ d+              +++v+NGeiyny el+e++      ++++ +Dtev+l
  gi|15669245|ref|NP_248050.1|  45 YSIGLGHVRLAILDLS-EKGHQPMgYNVDEDkiiyrddeldradIIIVYNGEIYNYLELKEKFNL----ETETGTDTEVIL 120
                                   369************9.*******967666678999999*************************9....44569******* PP

                      GATase_6  79 alleelGeevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                   +l+++lG +++++++Gm af+i dk+++ +++ rdrlgvkp yy  d++ ++f+se
  gi|15669245|ref|NP_248050.1| 121 KLYNKLGFDCVKEFNGMWAFCIFDKKKGLIFCSRDRLGVKPFYYYWDGNEFIFSSE 176
                                   *******************************************************8 PP

>> DUF3700  Aluminium induced protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.2   1.3e-09   4.6e-06      75     169 ..      86     174 ..      56     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.3e-09
                       DUF3700  75 ddifClfqGslenlasLkkqyGL.sktanevllvieayrtLrdrgPypadqvvkdleGkfafvlydskaktvfvaldadgs 154
                                    di  +++G++ n  +Lk+++ L + t ++  +++  y  L           vk+++G +af ++d+k++ +f ++d+ g 
  gi|15669245|ref|NP_248050.1|  86 ADIIIVYNGEIYNYLELKEKFNLeTETGTDTEVILKLYNKLG-------FDCVKEFNGMWAFCIFDKKKGLIFCSRDRLGV 159
                                   58999******************7778899999*****9994.......4679**************************** PP

                       DUF3700 155 vplyWGiaadgsvvi 169
                                    p+y+  +++  +  
  gi|15669245|ref|NP_248050.1| 160 KPFYYYWDGNEFIFS 174
                                   ***998877655444 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   4.5e-05      0.16      14      53 ..      11      54 ..       9      67 .. 0.81
   2 ?   -0.4   0.0       0.4   1.4e+03      15      41 ..      68      94 ..      56      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.5e-05
                       UPF0113 14 YGrdvlkesilkitesvk....enqvvvVlnengeplGiGkirk 53
                                  +G++v+ke+i k+++ +k    + ++++++n ++  +G+G++r 
  gi|15669245|ref|NP_248050.1| 11 FGKEVIKEEINKMNKAIKhrgpDDEGIFIYNFKNYSIGLGHVRL 54
                                  7*************888732234689**************9976 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.4
                       UPF0113 15 GrdvlkesilkitesvkenqvvvVlne 41
                                  G +v +++i++ ++++++ + ++V+n 
  gi|15669245|ref|NP_248050.1| 68 GYNVDEDKIIYRDDELDRADIIIVYNG 94
                                  6688899999999***********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3533.98
//
Query:       gi|15669246|ref|NP_248051.1|  [L=290]
Description: glycosyl transferase family protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-35  121.2   0.4    6.5e-35  120.4   0.4    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    4.9e-15   55.7   5.1    4.9e-15   55.7   5.1    1.7  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
    1.5e-12   47.9   0.0      3e-12   46.9   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0012   18.8   0.1     0.0029   17.6   0.1    1.6  1  Glyco_trans_2_3  Glycosyl transferase family group 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.4   1.4e-38   6.5e-35       1     169 [.      11     176 ..      11     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 1.4e-38
                                   EEEEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-.SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH-- CS
               Glycos_transf_2   1 svviptyNe.ektlletlesllaqdpypdfeiivvDDgS.tDetveileelakedprvrvirreenvGkagalnaglraat 79 
                                   svv+ tyNe ek+l+e++es+ +q + +df  i+v D+  + +++ei++e++++d+r+++i++e+n G ++++n+++  a+
  gi|15669246|ref|NP_248051.1|  11 SVVMATYNEpEKYLKESIESIXNQ-TXKDFXFIIVLDNPnNKKAEEIIKEYQQKDKRIIFIKNERNLGRGASRNKAVNIAR 90 
                                   8***********************.999999999988887***************************************** PP

                                   SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCE CS
               Glycos_transf_2  80 gdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaal 160
                                   g+yi++lDaDd+  p++lek  +++e++++   l +++++ +e+++i +     +++  y++++ ++++ + +  +++ ++
  gi|15669246|ref|NP_248051.1|  91 GKYIAILDADDIALPKRLEKQFKYMENNRDIDLLFSWVYFIDENGNILKE----FKPEKYKFKEIKKYFFKEHLTVHPSMM 167
                                   ***************************99999999999999999999987....789999999999999999999999999 PP

                                   EEEHHHHHC CS
               Glycos_transf_2 161 lrrealeel 169
                                   ++ ++l++l
  gi|15669246|ref|NP_248051.1| 168 VKSKILKKL 176
                                   999999875 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   5.1   1.1e-18   4.9e-15       1     203 [.      11     198 ..      11     219 .. 0.81
   2 ?   -1.1   0.1      0.23     1e+03     253     275 ..     213     235 ..     203     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.1e-18
               Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddg.Ssekfleevssiidlnllv.ylkdeddkayslaaarNrGask 79 
                                   svv++ +++ e+ y++e +  + ++  +++ +i+v d    +k  e ++   ++ +++ ++k+e  +  + +a+rN+ ++ 
  gi|15669246|ref|NP_248051.1|  11 SVVMATYNEPEK-YLKESIESIXNQTXKDFXFIIVLDNpNNKKAEEIIKEYQQKDKRIiFIKNE--RNLGRGASRNKAVNI 88 
                                   788888988887.******999999989999887655505556556679999999998666776..99************* PP

               Glyco_tranf_2_2  80 aesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledllaakstlvkf 160
                                   a + ++  lDaD+   + ++ek+ k      +++n d  + +++v++++e+ ++lk+ +    + +  ++ +       k 
  gi|15669246|ref|NP_248051.1|  89 ARGKYIAILDADDIALPKRLEKQFK-----YMENNRDIDLLFSWVYFIDENGNILKEFKPEKYKFKEIKKYFF------KE 158
                                   *************************.....9*************************99877776666656665......55 PP

               Glyco_tranf_2_2 161 fapssssilinrraflevGGyDErfrGhgaEDfdlllRlakai 203
                                    +    s++++ + + ++  yDE++    + D+d+ +R  +  
  gi|15669246|ref|NP_248051.1| 159 HLTVHPSMMVKSKILKKL-KYDEKL--IRSQDYDFWIRCIAND 198
                                   555566677777766666.6*****..7899****99965543 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.23
               Glyco_tranf_2_2 253 epksedylkkkdwkrellykafK 275
                                    p+ ++yl++  +++++ y ++K
  gi|15669246|ref|NP_248051.1| 213 IPNRDNYLSRIKKQKLYSYYTLK 235
                                   489999*************9998 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   6.7e-16     3e-12       4     200 ..      10     200 ..       8     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 6.7e-16
               Glyco_tranf_2_3   4 lavlVptfneed.vlgevlesllaqeyprvevvvvv.desdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                   ++v+ +t+ne++ +l e +es+ +q+  ++ +++v  +++ +++ e ++e +   +d r+  + n+rnlg +g+sr  n a
  gi|15669246|ref|NP_248051.1|  10 VSVVMATYNEPEkYLKESIESIXNQTXKDFXFIIVLdNPNNKKAEEIIKEYQ--QKDKRIIFIKNERNLG-RGASR--NKA 85 
                                   89********9978889*********9886655555499**********964..34558899********.69999..9** PP

               Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaarralgvltln 161
                                   ++++++++++++D+D++  P  l+++  ++ + ++++ +   v f +   + +      +++   ++  ++ + l+v +  
  gi|15669246|ref|NP_248051.1|  86 VNIARGKYIAILDADDIALPKRLEKQFKYMeNNRDIDLLFSWVyFIDENGNILKEFKPEKYKFKEIKKYFFKEHLTVHP-- 164
                                   *****************************98888998888555366767777776666666666667777777777765.. PP

               Glyco_tranf_2_3 162 GsgslirrevlkelegldplflltdDyelglrlrragfr 200
                                      +++  ++lk l + d++ +   Dy+ + r+ ++ ++
  gi|15669246|ref|NP_248051.1| 165 --SMMVKSKILKKL-KYDEKLIRSQDYDFWIRCIANDYK 200
                                   ..566778888888.677767777888888888776665 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   6.4e-07    0.0029       1     186 [.      93     268 ..      93     276 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.4e-07
               Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvlv.mnvanwleelaalffaedhgkdilvrealgrvvpsvGsgafl 79 
                                   +i++lDaD+   p  l++    ++ +++++++   v++ ++++n+l e++   ++   +k  ++    ++ ++++ s+++ 
  gi|15669246|ref|NP_248051.1|  93 YIAILDADDIALPKRLEKQFKYMEnNRDIDLLFSWVYFiDENGNILKEFKPEKYKFKEIKKYFF----KEHLTVHPSMMVK 169
                                   799*******9999**********5589999988888647999999999877665444555455....5566777777665 PP

               Glyco_trans_2_3  80 rrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspl.tlraalrQrkRwayGceleklillvrllgyl 159
                                   + + l+++ + +      s D+d+++r+ ++ y++  ++e l k   p+ + +  +  +++ +        + l  +++  
  gi|15669246|ref|NP_248051.1| 170 S-KILKKLKYDE--KLIRSQDYDFWIRCIANDYKFDIIEEFLLKYRIPNrDNYLSRIKKQKLYSY------YTLKTHWKNK 241
                                   5.99****9999..89***********************99776666663555555555553333......2234466666 PP

               Glyco_trans_2_3 160 gsllwsalplhlallllfsllalalvl 186
                                    +++ + +++ ++++ l  +l ++l++
  gi|15669246|ref|NP_248051.1| 242 KHFCNNVYFWKVFFYSLVVYLFIVLTP 268
                                   666666666655544444443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1181  (0.0658709); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1948.11
//
Query:       gi|15669247|ref|NP_248052.1|  [L=609]
Description: nodulation protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.1e-131  439.5   1.9   1.5e-131  439.1   1.9    1.2  1  Carbam_trans_N  Carbamoyltransferase N-terminus
    5.6e-65  218.0   0.0    9.7e-65  217.3   0.0    1.4  1  Carbam_trans_C  Carbamoyltransferase C-terminus
  ------ inclusion threshold ------
       0.12   12.1   0.0        0.2   11.3   0.0    1.3  1  Peptidase_M22   Glycoprotease family
       0.81    9.8   2.9        4.5    7.4   0.1    2.6  2  MetOD2          Metanogen output domain 2


Domain annotation for each model (and alignments):
>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.1   1.9  3.3e-135  1.5e-131       1     338 []       3     381 ..       3     381 .. 0.97

  Alignments for each domain:
  == domain 1  score: 439.1 bits;  conditional E-value: 3.3e-135
                Carbam_trans_N   1 kilGikltlflHDgavalvd.dgklvaaveeErltrikrdqk........lpklkaidyaleeagvelsdiDqivfdeidg 72 
                                   kilG+k  +flHD++v+++d ++k+++++ +Er+trik+d++        +pklk+idy++  +++e++++D+i+f++id+
  gi|15669247|ref|NP_248052.1|   3 KILGVK--YFLHDSGVFYIDtKNKEIFGILTERVTRIKHDGGtvipilneYPKLKNIDYVA--YPFEQTNLDFILFKHIDD 79 
                                   79****..*****************************************************..****************** PP

                Carbam_trans_N  73 eiesqlkekyveeaaerlkeliqgkslllleklylkkilekllve...........................kvdrkdvsl 126
                                   +i++++k+ky++e+a+++kel+q+k++++l+++y+++i+e+l+v+                           k++rkdvsl
  gi|15669247|ref|NP_248052.1|  80 YIKRTYKPKYIKEYAKYKKELSQNKTKFVLNNIYRPFIWEILAVYglrkllfkrfnniynklgnlaikrelkKIFRKDVSL 160
                                   ********************************************************************************* PP

                Carbam_trans_N 127 yeHhlsHaaSaystSpFakkeklvlcldgdGdiaprllaveketelkikslvsfse................siGhlYaaa 191
                                   yeHhl+HaaSay++SpF++ke+lv++ldg+Gd+++++l+++ke++++   lvs+s+                siGh+Y+++
  gi|15669247|ref|NP_248052.1| 161 YEHHLCHAASAYYFSPFFPKETLVFTLDGIGDWKYHSLWLFKEYDYR---LVSYSSfdiicyddvegifkgaSIGHIYSLF 238
                                   ***********************************************...9****99************************ PP

                Carbam_trans_N 192 teylGfkknsdegKlmalaayGkpkeriveelyellkkagyrinl.....ennieiskkkvhdffeasalrlkearek... 264
                                   te+lGf++nsdegK++alaayGkp+    +ely+llkk gy+in+     e++i+i+kk          l++k++++k   
  gi|15669247|ref|NP_248052.1| 239 TEILGFTPNSDEGKTEALAAYGKPN----GELYNLLKK-GYKINKeklrwEHDINILKK----------LHNKQYLQKwke 304
                                   *************************....*********.9****999999999999999..........555555555554 PP

                Carbam_trans_N 265 ...dedlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNiklNsallesglFedvwvqPaanDsGsAiGAAl 338
                                      de++aA+iq++lE++vve+lnivyek+ki++L++aGGv++N+++N++++e+++Fe+++++Pa++D+G+A+GAA+
  gi|15669247|ref|NP_248052.1| 305 kigDENFAATIQRWLEDTVVEYLNIVYEKFKIQRLAMAGGVVANVIMNLNIFERTPFEELYIFPAMGDDGVAAGAAI 381
                                   45599***********************************************************************7 PP

>> Carbam_trans_C  Carbamoyltransferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.3   0.0   2.2e-68   9.7e-65       1     170 []     438     607 ..     438     607 .. 0.99

  Alignments for each domain:
  == domain 1  score: 217.3 bits;  conditional E-value: 2.2e-68
                Carbam_trans_C   1 aellaegkvvgwfqgrmEfGpRALGnRSiladprkeemkeklnekikkResfrPfApsvleeeaeeyfeeekespymllva 81 
                                   ae++a+g++++++qg+mEfGpRALGnRSiladpr++++++k+n+++k+R +f+Pf+psvleee e++fe++ ++++m++++
  gi|15669247|ref|NP_248052.1| 438 AEMIAKGNIIAVYQGKMEFGPRALGNRSILADPRDPKTRDKINSTVKRRPWFQPFCPSVLEEERERLFEKSYKHKHMAIAF 518
                                   789********************************************************************9********* PP

                Carbam_trans_C  82 kvkeekreeipavtHvDgtaRvqtvkkeanpryhelleafekltgvpvllNTSfNvrgepivetpedalelflkteldalv 162
                                   ++k+e  +++p+++H+DgtaR+q v++++np+y++ll++f++ tg+ +++NTSfN++g+ iv+tpeda++ f + ++da++
  gi|15669247|ref|NP_248052.1| 519 RMKKEFWDKLPSAMHIDGTARPQFVEEKDNPNYYRLLKKFKEITGYGIVINTSFNLHGRTIVRTPEDAITDFIDCNIDAMF 599
                                   ********************************************************************************* PP

                Carbam_trans_C 163 lgdllvek 170
                                   ++ +lv++
  gi|15669247|ref|NP_248052.1| 600 IEGYLVKR 607
                                   ****9975 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.5e-05       0.2     180     239 ..     281     351 ..     227     370 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.5e-05
                                   E.CHHHHHHHHHHST.T..........HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHH CS
                 Peptidase_M22 180 sfsGlktavlkelek.e..........vedlaasfqeavvdhlvekteralklpkakelvilGGvaankrL 239
                                       ++ ++lk+l++ +           e++aa +q+   d++ve +  ++++ k+++l+++GGv an  +
  gi|15669247|ref|NP_248052.1| 281 LRWEHDINILKKLHNkQylqkwkekigDENFAATIQRWLEDTVVEYLNIVYEKFKIQRLAMAGGVVANVIM 351
                                   4444455555555332244556677889****************************************875 PP

>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4     0.065   2.9e+02      19      46 ..      87     113 ..      83     115 .. 0.80
   2 ?    7.4   0.1     0.001       4.5      36      69 ..     264     296 ..     255     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.065
                        MetOD2  19 keiidEYarLaksvevnkrllslLsqty 46 
                                   ++ i+EYa+  k+   nk +  +L+++y
  gi|15669247|ref|NP_248052.1|  87 PKYIKEYAKYKKELSQNKTKF-VLNNIY 113
                                   5789**********9999775.556655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.001
                        MetOD2  36 krllslLsqtydidddkaevseeieaalknlekk 69 
                                     l++lL++ y+i+++k++ +++i++ lk l +k
  gi|15669247|ref|NP_248052.1| 264 GELYNLLKKGYKINKEKLRWEHDINI-LKKLHNK 296
                                   579******************99974.5655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.24s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 4131.23
//
Query:       gi|15669248|ref|NP_248053.1|  [L=406]
Description: capsular polysaccharide biosynthsis protein M [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-30  104.9   1.3      7e-29  100.6   0.2    3.0  2  Glycos_transf_1  Glycosyl transferases group 1
    1.1e-21   77.6   0.0    2.3e-21   76.6   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    8.4e-06   25.9   2.0      2e-05   24.6   2.0    1.6  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    1.2e-05   25.4   0.0    2.1e-05   24.6   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
       0.24   12.0   0.0        2.2    8.9   0.0    2.4  3  PIG-L            GlcNAc-PI de-N-acetylase


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.26   9.2e+02      70      99 ..     107     138 ..     101     164 .. 0.74
   2 !  100.6   0.2     2e-32     7e-29       7     135 ..     194     320 ..     188     385 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.26
                                   CTTCGGGEEECCHSSSHHHHHHC..ESEEEEE CS
               Glycos_transf_1  70 elsdnviflgevsredleellkn..adifvlp 99 
                                   ++s+n++f+  v ++ +e++++   ++i++l 
  gi|15669248|ref|NP_248053.1| 107 KISNNTKFILWVRNNPIESYKEGlySKIIILA 138
                                   57888888888875555555555777777765 PP

  == domain 2  score: 100.6 bits;  conditional E-value: 2e-32
                                   HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHH CS
               Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredle 87 
                                   +  ++ ++  +++ +grl+++Kg+  li++f+++ ++  pn+kl+i G+ge +++l++l+ +l+l++nv +lg ++  +  
  gi|15669248|ref|NP_248053.1| 194 QYRNIFKDSFVFINIGRLTEQKGQWFLIRSFKRVTEK-YPNAKLIILGDGELKNKLQELINKLNLQNNVYLLGMQK--NPF 271
                                   556778999***************************9.**************************************..9** PP

                                   HHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTT CS
               Glycos_transf_1  88 ellknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdge 135
                                   ++lk++++fv++s +Eg++ +++EA++++lpvi+++   gp+e+++++ 
  gi|15669248|ref|NP_248053.1| 272 KFLKHSNCFVFSSLWEGLPNTVIEALSLNLPVISTDcKTGPREILCPEL 320
                                   ********************************************99876 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   6.4e-25   2.3e-21       3     109 ..     204     316 ..     202     327 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 6.4e-25
                                   EEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---THHHHHHHH-SEEEE CS
               Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfvedlaellaaadvfva 78 
                                   v++ +Grl+ ++kg+ +l++ ++++ +k + ++l+i Gdg+ + ++l+el++  +l+++v ++G  ++  ++l+++++fv+
  gi|15669248|ref|NP_248053.1| 204 VFINIGRLT-EQKGQWFLIRSFKRVTEKyPnAKLIILGDGElK-NKLQELINklNLQNNVYLLGMQKNPFKFLKHSNCFVF 282
                                   67889***5.66**************99736**********55.69**999779999*********99************* PP

                                   --..---SHHHHHHHHTT-EEEE-TGG.GTTT-- CS
               Glyco_trans_1_4  79 Ps..egfglkllEamaaglpvVatdvg.giaevv 109
                                    s  eg++++++Ea+++ lpv++td++ g++e++
  gi|15669248|ref|NP_248053.1| 283 SSlwEGLPNTVIEALSLNLPVISTDCKtGPREIL 316
                                   **************************87888865 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   2.0   5.6e-09     2e-05      56     138 ..      58     152 ..      40     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.6e-09
               Glyco_trans_4_2  56 g....pleylk.afklkklikkikPDvvhah......yakpygllgslaarlsgvipvvlsvwGldv..lkfpkksklkkl 123
                                        p++ lk   k+ k+i+++kPD+v++h       ++p++ll +++ ++s+  +++l v    +  +k++  sk+  l
  gi|15669248|ref|NP_248053.1|  58 NpllwPFKILKrTYKILKIIREFKPDLVITHhddanvSIIPVILLNKIF-KISNNTKFILWVRNNPIesYKEGLYSKIIIL 137
                                   33345889999667****************944443346*********9.88889*************9************ PP

               Glyco_trans_4_2 124 llklalkkatkvist 138
                                   ++k+ +k a+ +i++
  gi|15669248|ref|NP_248053.1| 138 AYKYFYKYADIIIVQ 152
                                   *************98 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   5.9e-09   2.1e-05      56     169 ..      65     181 ..      34     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.9e-09
                Glyco_transf_4  56 rslaflrrlrrllkrekpDvvHahspaalgaallalrr......rlgiplVltvHglyekrllkarlkplsrllralerrl 130
                                   ++l    ++ ++++++kpD+v +h+  a +     +++        + +++l v +     +  ++ +++s+++   ++++
  gi|15669248|ref|NP_248053.1|  65 KILKRTYKILKIIREFKPDLVITHHDDANVSIIPVILLnkifkiSNNTKFILWVRNNP---IESYKEGLYSKIIILAYKYF 142
                                   3455667899***********8887666554444444333677777777777776666...67889999************ PP

                Glyco_transf_4 131 lrradrviavSeatadelrerygvppekitVipnGvDle 169
                                   ++ ad +i+ +++ ++ ++++++  ++k  ++pn   ++
  gi|15669248|ref|NP_248053.1| 143 YKYADIIIVQTQENKKIIESHFKSLKNKTKIVPNVYEID 181
                                   ***********************8889*******77665 PP

>> PIG-L  GlcNAc-PI de-N-acetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00062       2.2      94     114 ..      72      92 ..      19      96 .. 0.84
   2 ?   -1.8   0.0       1.3   4.6e+03      70      98 ..     110     138 ..     102     170 .. 0.62
   3 ?   -0.8   0.0      0.64   2.3e+03      33      77 ..     239     265 ..     218     296 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00062
                                   HHHHHHHHH--SEEEEE-TTT CS
                         PIG-L  94 dlaklieryrPdvvltldpeg 114
                                   ++ k+i++++Pd+v+t++++ 
  gi|15669248|ref|NP_248053.1|  72 KILKIIREFKPDLVITHHDDA 92 
                                   5889*************9875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                                   .EEEEECCCBTT-STTS-CHHHHHHHHHH CS
                         PIG-L  70 dedvffldfpDgslesydedellddlakl 98 
                                   ++  f+l+++++  esy+e  +++ +  +
  gi|15669248|ref|NP_248053.1| 110 NNTKFILWVRNNPIESYKEGLYSKIIILA 138
                                   55668899999999996666555554333 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.64
                                   CE--TT---STTTTHH-HHHHHHHHHHHHHHHHCTE..EEEEECC CS
                         PIG-L  33 ltaGdagsplatleekeelaeiRekEaraaakhlgvadedvffld 77 
                                   l +G++++                  +++ ++ l++ +++v+ l+
  gi|15669248|ref|NP_248053.1| 239 LGDGELKN-----------------KLQELINKLNL-QNNVYLLG 265
                                   44444443.................33333444444.44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2562.98
//
Query:       gi|15669249|ref|NP_248054.1|  [L=537]
Description: hypothetical protein MJ_1060 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.047   13.7   0.0    1.8  2  Glyco_transf_4  Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.6e-06     0.047      43     163 ..     278     390 ..     266     392 .. 0.84
   2 ?   -3.5   0.0      0.49   8.7e+03      37      65 ..     421     463 ..     407     468 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-06
                Glyco_transf_4  43 vprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrr..rlgiplVltvHglyekrllkarlkplsr 121
                                   ++ ++++l+ +l++ l+f+++++  + + ++  +   s+  +++ l  + r  r++i++++  H             + ++
  gi|15669249|ref|NP_248054.1| 278 HTMFNIFLKHKLPFVLWFYLSIKDYISKTNIKCIVGDSERNFMFYLCNIYRlwRKNIKTIAFSHEVI----------NNNY 348
                                   556778899999**********************77776666554444444457*************..........7788 PP

                Glyco_transf_4 122 llralerrllrradrviavSeatadelrerygvppekitVip 163
                                   +   + ++     d+ ++  e +++ l+++y++p++k+ V p
  gi|15669249|ref|NP_248054.1| 349 IHLPISEKYSCIPDCKLVWNENIKKLLIDKYNFPKDKVIVFP 390
                                   888888888999**************************9988 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.49
                Glyco_transf_4  37 v..............elvvrvprvplpllkrllrslaflrrlr 65 
                                                  e+++++  +p+p+ + + +s++ l +l+
  gi|15669249|ref|NP_248054.1| 421 IfntfrdkklintliEHGYSFYFKPHPGEYLNDFSIRELEKLK 463
                                   4444444444444456666666677766666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1320  (0.0736237); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3227.16
//
Query:       gi|15669250|ref|NP_248055.1|  [L=333]
Description: capsular polysaccharide biosynthesis protein D [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.8e-116  387.0   0.4   5.5e-116  386.8   0.4    1.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.2e-25   90.0   0.2      2e-25   89.4   0.2    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.7e-22   78.3   0.0    4.8e-21   75.3   0.0    2.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    9.4e-18   64.7   0.0    1.4e-17   64.1   0.0    1.3  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.9e-12   45.9   0.0      1e-10   41.2   0.0    2.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.7e-11   43.8   2.1    9.4e-10   38.1   2.1    2.6  2  NAD_binding_4    Male sterility protein
    1.9e-11   44.2   0.0    2.9e-11   43.6   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    4.7e-09   36.0   0.1    7.6e-09   35.3   0.1    1.4  1  adh_short        short chain dehydrogenase
    1.4e-07   31.3   0.1    1.8e-07   31.0   0.1    1.3  1  NmrA             NmrA-like family
    2.6e-06   27.5   0.0    5.1e-06   26.5   0.0    1.4  1  KR               KR domain
    2.5e-05   24.5   0.2    7.1e-05   23.0   0.2    1.9  1  TrkA_N           TrkA-N domain
    4.8e-05   23.6   0.1    9.2e-05   22.7   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    7.1e-05   22.9   0.1    0.00014   21.9   0.1    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.021   15.5   0.0      0.059   14.1   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
       0.06   13.9   0.0       0.22   12.1   0.0    2.0  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.081   13.0   0.1       0.17   12.0   0.1    1.7  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
       0.14   12.3   0.0       0.37   10.9   0.0    1.7  1  Tautomerase_2    Tautomerase enzyme


Domain annotation for each model (and alignments):
>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.8   0.4  5.3e-119  5.5e-116       1     292 [.      14     295 ..      14     297 .. 0.97

  Alignments for each domain:
  == domain 1  score: 386.8 bits;  conditional E-value: 5.3e-119
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                   +lvtG++GsiG+e+v+++lk++pk+i++l+ +E++l+e+e+el    +++k++++    igdvrdk+rl++a+e  +vdvv
  gi|15669250|ref|NP_248055.1|  14 ILVTGGTGSIGKEIVKTLLKFNPKTIRVLDINETALFELEHEL----NSEKIRCF----IGDVRDKDRLKRAIE--EVDVV 84 
                                   89****************************************9....46788888....***************..***** PP

                                   EE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS--SHHHHHHHHHHHHHHHGGG--SSS--E CS
               Polysacc_synt_2  82 fhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAvnPtnvmGatKrlaekllqalakeseekktk 162
                                   fhaAAlKhVPl+e+np+ea+ktNv+gt+n+ie+a++ +v+k+++iStDKAvnP+nvmGatK+lae l+++++ +++++kt+
  gi|15669250|ref|NP_248055.1|  85 FHAAALKHVPLCEYNPFEAVKTNVIGTQNLIEVAMDEEVEKFITISTDKAVNPVNVMGATKLLAERLTISANLYKGKRKTA 165
                                   ********************************************************************************* PP

                                   EEEEEE-EETTGTTSSHHHHHHHHHTTSSEEES-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH CS
               Polysacc_synt_2 163 fvvvRfGNVlgSrGSviplFkkqikeggpvtvTdpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakal 243
                                   f+vvRfGNVl+SrGS++pl k+qik+ggpvt+T+p+mtR++m+i+eav+Lvl+a+ lakggeif+l+m ++v+i+dl + +
  gi|15669250|ref|NP_248055.1| 166 FSVVRFGNVLNSRGSILPLLKEQIKKGGPVTLTHPDMTRFIMSINEAVKLVLKACYLAKGGEIFILKM-PSVRIKDLIEVV 245
                                   ********************************************************************.************ PP

                                   ...........SSSS-EEE----TT--SS-EEE-GGGGGGEEE-SSEEEE CS
               Polysacc_synt_2 244 i.elsgleekkeedieikitGlRpGEklyEeLlieeesveetelekilra 292
                                   i el+ +   k edieiki+G RpGEklyEeL+ieee  + +ele+++++
  gi|15669250|ref|NP_248055.1| 246 IeELAPKYGYKPEDIEIKIIGKRPGEKLYEELIIEEEIYNLEELEDMFVV 295
                                   9667777777799********************************99987 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.2   1.9e-28     2e-25       1     122 [.      15     137 ..      15     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1.9e-28
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespel.leelskvnvkkviegDvtdkdkleealegvdvvihlaslvdva 80 
                                   +vtGg+G +G+++vk+L+++++ k++rvlD++e     le+  +++ + +  gDv+dkd+l++a+e+vdvv+h a+l  v 
  gi|15669250|ref|NP_248055.1|  15 LVTGGTGSIGKEIVKTLLKFNP-KTIRVLDINETALFeLEHELNSEKIRCFIGDVRDKDRLKRAIEEVDVVFHAAALKHVP 94 
                                   69*******************7.********998754145556666666******************************98 PP

                     3Beta_HSD  81 g.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgp 122
                                     +++  e  k nv GT+n++e +++ +v++++  S+ ++v p
  gi|15669250|ref|NP_248055.1|  95 LcEYNPFEAVKTNVIGTQNLIEVAMDEEVEKFITISTDKAVNP 137
                                   76899999******************************99998 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   4.5e-24   4.8e-21       1     204 [.      14     199 ..      14     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 4.5e-24
                                   EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE--S-- CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlAavg 75 
                                   ilVtG+tG iG+ +vk ll+ + + + +ld + ++  ++++++l     +   +d++d+++l+r+++  ++d+v+h+Aa +
  gi|15669250|ref|NP_248055.1|  14 ILVTGGTGSIGKEIVKTLLKFNPKtIRVLDIN-ETALFELEHELnsekiRCFIGDVRDKDRLKRAIE--EVDVVFHAAALK 91 
                                   8*******************996637777766.5555566666688889******************..89********** PP

                                   -HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHH CS
                     Epimerase  76 gvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveay 156
                                   +v+    +p + +++n++gt+nl+e+a + +v++++ +s++                   ++p +  +a+Kl++e+l+ ++
  gi|15669250|ref|NP_248055.1|  92 HVPLCEYNPFEAVKTNVIGTQNLIEVAMDEEVEKFITISTDKA-----------------VNPVNVMGATKLLAERLTISA 155
                                   ****************************************433.................356677777777777777777 PP

                                   HHHHT...-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEET CS
                     Epimerase 157 aaqyg...lnaiilrlfnlyGprngegevsrvipalirkilegkqevtllg 204
                                   +   g   + + ++r  n+   r       +++p l ++i++g  +vtl +
  gi|15669250|ref|NP_248055.1| 156 NLYKGkrkTAFSVVRFGNVLNSR------GSILPLLKEQIKKGG-PVTLTH 199
                                   66655455666777777776665......777777777777777.776654 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   1.3e-20   1.4e-17       1     131 [.      15     133 ..      15     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.3e-20
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   L+TG++G iG  +++ Ll+ + + + + + +++ ++ ++eh        ++e+++ + gD++D+++l+r+++ev  d v++
  gi|15669250|ref|NP_248055.1|  15 LVTGGTGSIGKEIVKTLLKFNPKTIRVLDINET-ALFELEHEL------NSEKIRCFIGDVRDKDRLKRAIEEV--DVVFH 86 
                                   9*******************9999988766554.444555533......346899******************9..9**** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGG CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsE 131
                                    AA +hV+    +P + +++nv+Gt++L+e++ + ++e   +f+ +St+ 
  gi|15669250|ref|NP_248055.1|  87 AAALKHVPLCEYNPFEAVKTNVIGTQNLIEVAMDEEVE---KFITISTDK 133
                                   ********************************998776...9******95 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   9.8e-14     1e-10       2     154 ..      13     177 ..      12     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 9.8e-14
                                   EEEEESTTSHHHHHHHHHCTT...TSEEEEEE-TT.................T--TTSHHHHHHHHHHH--SEEEE----- CS
                 RmlD_sub_bind   2 kilvtGanGqlGseLakqlae...eglevlaltre.................eldltdaeavaellkeakpdvvvnaAAyt 62 
                                   +ilvtG++G +G+e++k l +   + + vl ++++                   d++d+++++++++e   dvv +aAA +
  gi|15669250|ref|NP_248055.1|  13 TILVTGGTGSIGKEIVKTLLKfnpKTIRVLDINETalfelehelnsekircfIGDVRDKDRLKRAIEE--VDVVFHAAALK 91 
                                   69**************98876222556666665559**************9999*************9..899******** PP

                                   -HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH.... CS
                 RmlD_sub_bind  63 avDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla.... 138
                                    v  +E ++ +a + n+ ++++l e+a   ++ ++i +StD               +++P+nv G+tKl+ E+   +    
  gi|15669250|ref|NP_248055.1|  92 HVPLCEYNPFEAVKTNVIGTQNLIEVAMDEEVeKFITISTD--------------KAVNPVNVMGATKLLAERLTISanly 158
                                   ***************************99998469*****9..............36788888888888888876653444 PP

                                   ...H-SSEEEEEE-SEESS CS
                 RmlD_sub_bind 139 ...agkkalivRtswvyge 154
                                       +  + +vR++ v+ +
  gi|15669250|ref|NP_248055.1| 159 kgkRKTAFSVVRFGNVLNS 177
                                   3333344556666666655 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   2.1   8.9e-13   9.4e-10       1     142 [.      16     138 ..      16     164 .. 0.81
   2 ?   -0.6   0.0      0.56   5.9e+02     178     208 ..     143     176 ..     138     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 8.9e-13
                                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHH CS
                 NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedl 81 
                                   +TG+TG +Gk +++ LL+ +p+ +i +l    +       + +e + +el+++l+   +e+i++  GD+ +++      +l
  gi|15669250|ref|NP_248055.1|  16 VTGGTGSIGKEIVKTLLKFNPK-TIRVL----D-------I-NETALFELEHELN---SEKIRCFIGDVRDKD------RL 74 
                                   7********************7.55444....2.......2.3444566677776...9***********876......99 PP

                                   HHHHHH--EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS CS
                 NAD_binding_4  82 qelaeevdviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvST.ayvnge 142
                                   ++ +eevdv++h aA  ++     +  e++++Nv Gt++++e a   +    ++ +ST  +vn+ 
  gi|15669250|ref|NP_248055.1|  75 KRAIEEVDVVFHAAALKHVPLceyNPFEAVKTNVIGTQNLIEVAMDEEVE-KFITISTdKAVNPV 138
                                   9**************9997543115557*****************77666.9******9777654 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.56
                                   HHHHHHHHHHHHHHH...HH---EEEEEE-EEE- CS
                 NAD_binding_4 178 qsKalaEklvrearr...rsglpvvivRpsiitg 208
                                    +K laE+l  +a+    + +  +++vR ++++ 
  gi|15669250|ref|NP_248055.1| 143 ATKLLAERLTISANLykgKRKTAFSVVRFGNVLN 176
                                   6999999997776541112355579999999876 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   2.7e-14   2.9e-11       1     104 [.      18     137 ..      18     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.7e-14
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH...CTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC..... CS
                NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaele...aeeglevvegdvtdvedlaealkgadaVvsalggggk..... 73 
                                   G+tG++G+++vk ll+ +  ++++l  n+  l ele   ++e+++ + gdv d++ l++a++ +d+V+ a++ ++      
  gi|15669250|ref|NP_248055.1|  18 GGTGSIGKEIVKTLLKFNPKTIRVLDINETALFELEhelNSEKIRCFIGDVRDKDRLKRAIEEVDVVFHAAALKHVplcey 98 
                                   9****************9778888877888777777444568999**************************6555555554 PP

                                   ....HHHH......HHHHHHHHHHCT--EEEEEEETTTTSG CS
                NAD_binding_10  74 ....deeg......aknivdaakeagvkRfvlvsaigvgde 104
                                          +      ++n++++a  ++v++f+++s+ ++ + 
  gi|15669250|ref|NP_248055.1|  99 npfeA--VktnvigTQNLIEVAMDEEVEKFITISTDKAVNP 137
                                   44330..1344567********************9888763 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1   7.2e-12   7.6e-09       1      87 [.      12      90 ..      12     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 7.2e-12
                                  SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                     adh_short  1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLv 82
                                  k++lvtG+++ IG++i+k+l+k + k++  +d++e +l e+  el++  +k+ ++ +Dv+d++++++++e++       dv+ 
  gi|15669250|ref|NP_248055.1| 12 KTILVTGGTGSIGKEIVKTLLKFNPKTIRvLDINETALFELEHELNS--EKIRCFIGDVRDKDRLKRAIEEV-------DVVF 85
                                  79********************999988779*******999999997..58*****************9988.......6666 PP

                                  E---S CS
                     adh_short 83 nNAGi 87
                                  + A++
  gi|15669250|ref|NP_248055.1| 86 HAAAL 90
                                  66666 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1   1.7e-10   1.8e-07       1     106 [.      14     135 ..      14     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.7e-10
                                   EEESSTTSHHHHHHHHHHHH.HT-EEEEEES-S..-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG... CS
                          NmrA   1 IlviGaTGrqGksvvrallk.aghkvralvRdt..kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy... 75 
                                   Ilv+G+TG++Gk +v+ llk +  ++r+l  ++    el ++l+++      gd+ dk+ l++a+++vdvvf + +++   
  gi|15669250|ref|NP_248055.1|  14 ILVTGGTGSIGKEIVKTLLKfNPKTIRVLDINEtaLFELEHELNSEKIRCFIGDVRDKDRLKRAIEEVDVVFHAAALKhvp 94 
                                   9*******************655677888666645668889999*****************************99988888 PP

                                   ..........S-HHHHHHHHHHHHHHHS-SEEEEEE---GG CS
                          NmrA  76 ..........skeiedgkklvdAakeaGvkhfiySslgddn 106
                                             ++++   ++l+++a    v++fi  s  +++
  gi|15669250|ref|NP_248055.1|  95 lceynpfeavKTNVIGTQNLIEVAMDEEVEKFITISTDKAV 135
                                   88888988877777777889999999999999876666655 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   4.9e-09   5.1e-06       2     135 ..      13     130 ..      12     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.9e-09
                                   EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT..T-EEEE----TT-HHHHHHHHHHHHHHSS CS
                            KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal..gaevevvaaDvsdkdavealleeikaeep 80 
                                   t l+tGG+G++G+e++++l++   +++ +l  +       ++ + ele+     +++++  Dv dkd +++++ee++    
  gi|15669250|ref|NP_248055.1|  13 TILVTGGTGSIGKEIVKTLLKFNPKTIRVLDIN-------ETALFELEHElnSEKIRCFIGDVRDKDRLKRAIEEVD---- 82 
                                   679************************999888.......223444444322569*******************998.... PP

                                   ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEE CS
                            KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfS 135
                                       v+haA + +  +l  ++ + +e+ ++  v G++nL e+  de+++ f+++S
  gi|15669250|ref|NP_248055.1|  83 ---VVFHAAALKH-VPL--CEYNPFEA-VKTNVIGTQNLIEVAMDEEVEKFITIS 130
                                   ...6888887544.444..34444443.466899******************998 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.2   6.8e-08   7.1e-05       5      69 ..      19      87 ..      14     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.8e-08
                                  S-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT....SEEEES-TTSHHHHHHTTGGGESEEEE- CS
                        TrkA_N  5 GlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg....levvvgdatdeevLeeagiekadaviaa 69
                                  G G +G++++++L + + k + v d +e ++ el+ e     +++++gd+ d++ L++a ie++d+v  a
  gi|15669250|ref|NP_248055.1| 19 GTGSIGKEIVKTLLKfNPKTIRVLDINETALFELEHELnsekIRCFIGDVRDKDRLKRA-IEEVDVVFHA 87
                                  79*************87789********8866665444444499*************98.8888887655 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   8.7e-08   9.2e-05       1      77 [.      14      88 ..      14      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8.7e-08
                                  EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
               Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77
                                  +l+ G+ Gs+G+ +++ l++ ++   +i v d +++ l +l ++++++++ +   d+ +++  L+++++e d+v +++
  gi|15669250|ref|NP_248055.1| 14 ILVTGGtGSIGKEIVKTLLKFNPK--TIRVLDINETALFELEHELNSEKIRCFIGDVRDKDR-LKRAIEEVDVVFHAA 88
                                  6888888**************998..9***********************************.***********8876 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.3e-07   0.00014       9     118 ..       8     124 ..       2     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.3e-07
                                   ..TT-EEEEE.S-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-E.....EEEGCGHHHHHHT-SEEEE-S CS
                  Shikimate_DH   9 slkekkvlli.GaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeie.....alkleelkellaeadvvisat 83 
                                    +k+k++l+  G+G ++++++k Ll+ + k + v+  + +   el +el++e+i+     +++ + lk++++e+dvv+ a 
  gi|15669250|ref|NP_248055.1|   8 FYKDKTILVTgGTGSIGKEIVKTLLKFNPKTIRVLDINETALFELEHELNSEKIRcfigdVRDKDRLKRAIEEVDVVFHAA 88 
                                   4678888887459************************************99998633333678899*************99 PP

                                   SSSS.-SB-HHHHHCCHHH.S...EEEEE--SS-SB- CS
                  Shikimate_DH  84 asee.pilekeeveealkkrk.kplllvDiavPRdve 118
                                   a ++ p+ e + +e+++  +    + l+ +a+  +ve
  gi|15669250|ref|NP_248055.1|  89 ALKHvPLCEYNPFEAVK-TNViGTQNLIEVAMDEEVE 124
                                   98872444444455444.3333555666666655555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.6e-05     0.059       6      78 ..      18      94 ..      15     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.6e-05
                                  -TTSHHHHHHHCTS...TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG...BSSSTTTEEEEEEESTGGGSS CS
               Methyltransf_25  6 cGtGrltlalakrl...gkakvtgvDiseemleaareraeeeglnvefvqgdaed...lpfedgsfDlvvssgalhhls 78
                                   GtG + +++ k l   + +++  +Di+e++l + ++++++e  ++++  gd++d   l+ + +++D+v+ + al h++
  gi|15669250|ref|NP_248055.1| 18 GGTGSIGKEIVKTLlkfNPKTIRVLDINETALFELEHELNSE--KIRCFIGDVRDkdrLKRAIEEVDVVFHAAALKHVP 94
                                  59999999999887755689*******************766..79999999976555889999*******88899987 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00021      0.22       6      74 ..      19      93 ..      13      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                                  TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC..........-EEECECHHHHHHH-SEEEE-S-HHHH CS
                 F420_oxidored  6 GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg..........vkvtavdneeaaeeadvvvlavkpedv 74
                                  G+G++g+ +++ ll+ +  p+ i+v  + n+  + el+ el+          v+ +    + a+ee dvv+ a   ++v
  gi|15669250|ref|NP_248055.1| 19 GTGSIGKEIVKTLLKFN--PKTIRVL-DINETALFELEHELNsekircfigdVRDKD-RLKRAIEEVDVVFHAAALKHV 93
                                  9**************99..*****66.******************999997655555.7899*********99888877 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00016      0.17       3      98 ..      14     111 ..      12     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                   EEEETTTSHHHHHHHHHHHH.STTEEEEEEEETTC.STTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HHHHH CS
                        DapB_N   3 vavvGasGrmGkevvkavee.aedlelvaavdrke.selegkdagellglgklgvavtddleevlekadvliDFTtpeavl 81 
                                   ++v+G +G +Gke+vk++ + ++++  v  ++++   ele +  +e + ++  +v  +d+l++++e++dv+    + + v 
  gi|15669250|ref|NP_248055.1|  14 ILVTGGTGSIGKEIVKTLLKfNPKTIRVLDINETAlFELEHELNSEKIRCFIGDVRDKDRLKRAIEEVDVVFHAAALKHVP 94 
                                   89***************9995556555655555554555555566777777778888899999999999997666555554 PP

                                   HHHHHHHHTT-EEEE-- CS
                        DapB_N  82 enlklalekgvklViGT 98 
                                    +    +e+ +  ViGT
  gi|15669250|ref|NP_248055.1|  95 LCEYNPFEAVKTNVIGT 111
                                   44444455556666666 PP

>> Tautomerase_2  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00035      0.37      46      74 ..     239     267 ..     235     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                                   HHHHHHHHHHHHHHH---GGGEEEEEEEE CS
                 Tautomerase_2  46 kaLyralaerlaaklgirpeDvfivlven 74 
                                   k L++ ++e+la k g +peD++i ++ +
  gi|15669250|ref|NP_248055.1| 239 KDLIEVVIEELAPKYGYKPEDIEIKIIGK 267
                                   6899********************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2116.78
//
Query:       gi|15669251|ref|NP_248056.1|  [L=484]
Description: spore coat polysaccharide biosynthesis protein SpsG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-20   74.8   0.1    1.9e-20   74.0   0.1    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    1.6e-07   31.5   0.0    3.5e-07   30.3   0.0    1.5  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
    5.8e-06   25.9   0.0    1.4e-05   24.7   0.0    1.7  1  Glycos_transf_1  Glycosyl transferases group 1
    6.7e-06   26.3   0.0    1.9e-05   24.9   0.0    1.8  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    9.3e-06   24.9   0.6    9.3e-06   24.9   0.6    2.0  2  DUF354           Protein of unknown function (DUF354)
    3.2e-05   24.1   0.2    8.3e-05   22.8   0.2    1.7  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    5.4e-05   22.2   0.0    0.00012   21.1   0.0    1.5  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
      0.002   18.1   2.2     0.0029   17.5   0.9    2.0  2  Peroxin-22       Peroxisomal biogenesis protein family
  ------ inclusion threshold ------
      0.012   15.2   0.2      0.079   12.6   0.2    2.1  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
      0.031   14.2   0.0      0.066   13.2   0.0    1.6  1  FR47             FR47-like protein
       0.18   12.2   0.0       0.46   10.9   0.0    1.6  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.1   1.2e-23   1.9e-20       2     138 .]     334     468 ..     333     468 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 1.2e-23
                Acetyltransf_3   2 LlLrplteeDlealfelrsdpevmry...lpepltleeaeewlerawaeeseeegygwaivlkdtg..v.iGsvglrdlee 76 
                                   +++r++t+ Dle l ++rs+p + ++    +epl+ ee ++w  +  +e    + + w+i l++++    +Gsv++ +l+ 
  gi|15669251|ref|NP_248056.1| 334 IIIRQITDNDLELLMAWRSNPLIYKFfyiQKEPLKWEEHYSWWMS--RE----NRVDWIILLRENNtiRkVGSVNVSQLNT 408
                                   79************99*********7775555**********994..33....67889998877766755*********99 PP

                Acetyltransf_3  77 edeeaelgymlaps.fwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                   ++  +e+g+++++   wgk +++  v+ +l+++ ++ g+++  a+i ++N +Si+++e+lGf+
  gi|15669251|ref|NP_248056.1| 409 DN--PEIGILIGEFfLWGKHIGRHSVSLVLKWL-KNIGYKKAHARILENNIRSIKLFESLGFK 468
                                   97..*********999*****************.9999************************7 PP

>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   2.2e-10   3.5e-07       4      98 ..     175     268 ..     172     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.2e-10
                                   EEE-SSSHHHHHCCCTSHHHHHHHHHHHHCHHHCCT-E.EC---STT.-TTTT..CEEEEEESSSSHHHHHHHH-EEEECS CS
               Glyco_tran_28_C   4 VtGGSqgaeaLnelvlselkllelksrelqvlhqtGkr.eleevkik.veelt..lkvevfefidkmaeaikaadLvIsRA 80 
                                    +GGS +++ L   vl+el  +      +++    G++ ++e+  ++ +++++  +k+++++ id+mae++k+ dL+I+  
  gi|15669251|ref|NP_248056.1| 175 AFGGSDPSN-LTCKVLEELLSKDRD---FNINVVLGPKfQYEDELNNlLKRYSksDKIKIYKNIDNMAELMKDNDLIITSP 251
                                   589999999.777777776666655...9999999999988777777755555559************************9 PP

                                   -CHHHHHHHHTT--EEEE CS
               Glyco_tran_28_C  81 GagtiaEllalgkplIlv 98 
                                   G +t +E+l+lg p ++ 
  gi|15669251|ref|NP_248056.1| 252 G-MTMFEALFLGIPVVVL 268
                                   9.799*********9875 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   8.5e-09   1.4e-05      32     134 ..     184     281 ..     157     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 8.5e-09
                                   HHHHHHHCCCCCHCSCEEEEEES..STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHH CS
               Glycos_transf_1  32 llikafallkkqlnpnvklviaG.ngeeekelkklaeelelsdnviflgevsredleellknadifvlpsisEgfGivllE 111
                                   l  k++++l  + ++    v+ G + ++e+el +l + +  sd+++++++++  ++ el+k  d+++ +      G++  E
  gi|15669251|ref|NP_248056.1| 184 LTCKVLEELLSKDRDFNINVVLGpKFQYEDELNNLLKRYSKSDKIKIYKNID--NMAELMKDNDLIITS-----PGMTMFE 257
                                   5567888888888888999999*999**************************..************999.....8****** PP

                                   HHHTT--EEEET.TTTHCHHCHTT CS
               Glycos_transf_1 112 Amaaglpviasn.aggpaevvkdg 134
                                   A+ +g+pv++   ++  +e   d+
  gi|15669251|ref|NP_248056.1| 258 ALFLGIPVVVLYqNELQRECYDDY 281
                                   ********9976677777766666 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.1e-08   1.9e-05      17     117 .]     366     467 ..     350     467 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.1e-08
                                   HHHHHHHHHHHHHSTTC.EEEE.EEETTE..EEEEEEEEEEETTSTTEEEEEEEEESGGG.TTSSHHHHHHHHHHHHHHHT CS
                Acetyltransf_1  17 edaseeefeesfsleae.gllv.aeedge..liGfisllkipdekggvayieslaVspey.rgkGlGsaLlealeeraree 92 
                                   + ++ee + ++ s+e+   +++  +e+++   +G + +++ +    ++ +i ++ + + + +gk +G++ +  +++++++ 
  gi|15669251|ref|NP_248056.1| 366 PLKWEEHYSWWMSRENRvDWIIlLRENNTirKVGSVNVSQLNT---DNPEI-GILIGEFFlWGKHIGRHSVSLVLKWLKNI 442
                                   3334444889999999955555666666666788888888877...77777.999999999******************** PP

                                   TESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  93 gikkivlaveedndaairlYeklGF 117
                                   g+kk  + + e+n ++i+l+e lGF
  gi|15669251|ref|NP_248056.1| 443 GYKKAHARILENNIRSIKLFESLGF 467
                                   **999***************99**9 PP

>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.83   1.4e+03      18      41 ..      45      67 ..      25      84 .. 0.66
   2 !   24.9   0.6   5.7e-09   9.3e-06     126     283 ..     114     273 ..     107     295 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.83
                        DUF354 18 dlikkfekeGievlltardsGdla 41
                                  d+ikk+e++G +v+    d  d+ 
  gi|15669251|ref|NP_248056.1| 45 DVIKKIEENGFKVIK-CSDNNDIL 67
                                  677777777777653.33444444 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 5.7e-09
                        DUF354 126 adeiikpividendlkktGadpnrirryeGtsevinvqs.yeideeilkdlnlkledektilmrpepslasyldadchkdv 205
                                   ad ++  iv  e + +k+  + n+   + G   +i  ++ y++++e+l   +   ++ k il+    s  s l +    +v
  gi|15669251|ref|NP_248056.1| 114 ADIVVNAIVGSELKNRKYFDEENKTLYFYGPKYLILRNEfYKVKKEMLSRSK--NKETKNILIAFGGSDPSNLTC----KV 188
                                   6777777787777777777777888888888877766665899999998766..677788999999988998888....67 PP

                        DUF354 206 ltkiveklkd.ridilviprdeeqkei......yeevdnviviketvdal.sllkrsdlviGaGGtmnreaallGipvvsc 278
                                   l +++ k +d  i++++ p+++ + e+      y + d++ + k+ +d +  l+k  dl+i + G    ea +lGipvv  
  gi|15669251|ref|NP_248056.1| 189 LEELLSKDRDfNINVVLGPKFQYEDELnnllkrYSKSDKIKIYKN-IDNMaELMKDNDLIITSPGMTMFEALFLGIPVVVL 268
                                   77777777773589*******988886444444556676666665.666526***********999999************ PP

                        DUF354 279 ypqkl 283
                                   y ++l
  gi|15669251|ref|NP_248056.1| 269 YQNEL 273
                                   *9886 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.2   5.1e-08   8.3e-05       1     141 [.     336     474 ..     336     482 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.1e-08
                Acetyltransf_4   1 iraateeDakeilaiyaeyvvntaitfeyev.ssveefekflealdsekeyvflvae.sdrivGyaylgqfkkr.akdwka 78 
                                   ir +t +D++ + a+++++ + +++  + e  +  e +  ++++ +   ++++l ++   r vG   ++q++    + +  
  gi|15669251|ref|NP_248056.1| 336 IRQITDNDLELLMAWRSNPLIYKFFYIQKEPlKWEEHYSWWMSRENRVDWIILLRENnTIRKVGSVNVSQLNTDnPEIGIL 416
                                   899*************99999888876655514445555777776666688877777677789999999999955555555 PP

                Acetyltransf_4  79 elsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifk 141
                                   + +++l       + +gr  + ++ + lk+ ++++  a+i  +n+ si+++++lGF+++++ +
  gi|15669251|ref|NP_248056.1| 417 IGEFFLW-----GKHIGRHSVSLVLKWLKNIGYKKAHARILENNIRSIKLFESLGFKKTKKGR 474
                                   6666765.....4899*****************************************998765 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   7.5e-08   0.00012     203     286 ..     185     269 ..     175     285 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.5e-08
                                   HHHHHHHHHHH.H--EEEEE--..HHHHHHHHHHHHH-.T..TEEEE----HHHHHHHHHC-SEEEES-H.HHHHHHHHCT CS
                   Epimerase_2 203 ilealkalake.kdvevvvpvhnnprtrkrlleeleel.e..nvtlieplgyldflsllknaklvltdSg.GiqeEapslg 278
                                    +++l++l ++ +d+++ v++  + + +++l++ l+++ +  +++++++++  ++ +l+k+ +l++t  g ++  Ea +lg
  gi|15669251|ref|NP_248056.1| 185 TCKVLEELLSKdRDFNINVVLGPKFQYEDELNNLLKRYsKsdKIKIYKNID--NMAELMKDNDLIITSPGmTMF-EALFLG 262
                                   578899988888888888888877888999999999995488******997..79***************9999.****** PP

                                   --EEESSS CS
                   Epimerase_2 279 vpvvnlRe 286
                                   +pvv+l  
  gi|15669251|ref|NP_248056.1| 263 IPVVVL-Y 269
                                   *****9.3 PP

>> Peroxin-22  Peroxisomal biogenesis protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.9   1.8e-06    0.0029      52      98 ..      47      91 ..      17     101 .. 0.76
   2 ?   -2.7   0.0       3.3   5.4e+03      28      41 ..     236     249 ..     189     255 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                    Peroxin-22 52 eevsskneyKiilcdssdglsavvkqLkpsslivdedeleseeekte 98
                                   +  ++n +K+i+c+  + +++ +k++kp+ +i+  d+l++ee+  +
  gi|15669251|ref|NP_248056.1| 47 IKKIEENGFKVIKCSDNNDILKNIKNIKPDVVII--DDLGIEEDFAK 91
                                  35567889**********************9985..77877754444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.3
                    Peroxin-22  28 dlsellsedvvlil 41 
                                   ++ el++++  +i+
  gi|15669251|ref|NP_248056.1| 236 NMAELMKDNDLIIT 249
                                   23344444444555 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   4.8e-05     0.079       3     141 ..     341     471 ..     340     474 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.8e-05
                                   GGGHHHHHHHCTSCCCHHHH.-----HHHHHHHHHHHC.STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS---TT-EEE CS
                Acetyltransf_8   3 eaDlellhrWmnrprvaeww.eeagtleevrellakldadphsepliglldgepvgyfeiYwakedelaeyydaepgdrGi 82 
                                   ++Dlell +W ++p + ++   ++++l++++++   ++++++++ +i+l +++ +  + + ++++         +     i
  gi|15669251|ref|NP_248056.1| 341 DNDLELLMAWRSNPLIYKFFyIQKEPLKWEEHYSWWMSRENRVDWIILLRENNTIRKVGSVNVSQL--------NTDNPEI 413
                                   78************9876552777788**********96776666666666665555555544444........4455566 PP

                                   EEEESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                Acetyltransf_8  83 HlligeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                                    +lige    gk++++  ++ ++++l +  + ++  +    +N r+i+l+e++Gf+k k
  gi|15669251|ref|NP_248056.1| 414 GILIGEFFLWGKHIGRHSVSLVLKWLKNI-GYKKAHARILENNIRSIKLFESLGFKKTK 471
                                   67999999999999999999999988762.44444444457888999999999998877 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     4e-05     0.066      57      85 ..     447     478 ..     428     479 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4e-05
                                   EEEEEETT-HHHHHHHHHHT-EEE...EEEEE CS
                          FR47  57 vllvvvasNtpsirlyeklGfeki...eetew 85 
                                   + + + ++N +si+l+e+lGf+k    +e+ew
  gi|15669251|ref|NP_248056.1| 447 AHARILENNIRSIKLFESLGFKKTkkgRENEW 478
                                   5677889***************9966666777 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.46      32     100 ..     199     268 ..     179     281 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                                   EEEEEES---.....HHHHHHHT..T-T.TEEEE---THHHHHHHH-SEEEE-----SHHHHHHHHTT-EEEE- CS
               Glyco_trans_1_4  32 vrlvivGdgp...rpeeleelaa..gleerveftGfvedlaellaaadvfvaPsegfglkllEamaaglpvVat 100
                                   +++ +v  gp    ++el++l++    ++++++   ++++ael+++ d+ +      g+++ Ea+ +g+pvV+ 
  gi|15669251|ref|NP_248056.1| 199 FNINVVL-GPkfqYEDELNNLLKrySKSDKIKIYKNIDNMAELMKDNDLIITSP---GMTMFEALFLGIPVVVL 268
                                   5444433.2323433677766654533589*******99**********99866...8**************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2994.68
//
Query:       gi|15669252|ref|NP_248057.1|  [L=243]
Description: spore coat polysaccharide biosynthesis protein SpsF [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-55  187.0   0.4    5.1e-55  186.8   0.4    1.1  1  CTP_transf_3  Cytidylyltransferase
    0.00047   20.5   0.0     0.0007   20.0   0.0    1.2  1  NTP_transf_3  MobA-like NTP transferase domain
  ------ inclusion threshold ------
       0.18   11.5   0.0       0.29   10.9   0.0    1.4  1  IspD          2-C-methyl-D-erythritol 4-phosphate cytidylyltr


Domain annotation for each model (and alignments):
>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.8   0.4   8.5e-59   5.1e-55       1     220 [.       4     212 ..       4     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 186.8 bits;  conditional E-value: 8.5e-59
                                   EEEEEE-SSSSSSTTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTT..SEEEE--TTCSSHHHHHHH CS
                  CTP_transf_3   1 iaIipARsgSkRlpgKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefg..asvlvtrsslesdterfle 79 
                                   i Ii+AR+gSkRl++K+ll+lg++++++++le+++ksk+++++ivaT+ ++ +n+++e++   +v+v+r+s++++++rf++
  gi|15669252|ref|NP_248057.1|   4 IGIIQARTGSKRLKNKVLLKLGDRCILEILLERLKKSKKLDDIIVATTIKKEDNAIVELCnsLGVNVFRGSEKDVLDRFYN 84 
                                   78******************************************************************************* PP

                                   HHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTTSSEEEEEEETTSHHHHTSTTSTEEEETTTSBEEEEESSES CS
                  CTP_transf_3  80 vvkaflmseneeiivnlqGdnPllqeevikkaietlkenqedylstlvkkvgkeeevlnandlkvllddagkalyfeesvi 160
                                   + k ++ +    +iv+++GdnPl++ e+i+k++e+l++n+ dy+st++  +g ++ev+++++l++++++a k++y++e+v+
  gi|15669252|ref|NP_248057.1|  85 ASKFYSGD----VIVRITGDNPLTSIELIDKQVEYLLKNNFDYVSTKNIILGLSSEVFTFDALEKAWKNA-KEKYQREHVT 160
                                   ********....**********************************************************.********** PP

                                   SEEHHHHHCTSTTTSEEEEEEEEEEHHHHHHHHHHSHHHHHSHHHHHT-TTHHHHHTT-E CS
                  CTP_transf_3 161 pyireeplelsrrlylshagiytfrkeqplkelvidtptseilekiekleqlrvllegkk 220
                                   pyi+e+p+ ++  +++++   y +r+    ++l+idt ++  ++ + +l q+++ l + +
  gi|15669252|ref|NP_248057.1| 161 PYIYENPNLFK--VFYLEPPEYLKREG---IRLTIDTIKD--FKLYLEL-QKHFDLINVD 212
                                   **********9..*************6...**********..9999999.8887666654 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.2e-07    0.0007      13     109 ..      12     114 ..       6     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.2e-07
                                   TT....THHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSH....CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH. CS
                  NTP_transf_3  13 gg....dKallplggkpllervldalraa.gvdevvvvggd....eevlaalarlgvrvvededpgkgplaslaaalraaa 84 
                                   g+    +K ll+lg++ +le +l++l+++ ++d+++v++      +++ + +++lgv v++ +  +k  l  ++ a +   
  gi|15669252|ref|NP_248057.1|  12 GSkrlkNKVLLKLGDRCILEILLERLKKSkKLDDIIVATTIkkedNAIVELCNSLGVNVFRGS--EKDVLDRFYNASKFY- 89 
                                   4333449**********************559******85422225899999*********98..6999999***99998. PP

                                   SSSCEEEEETT-TT--HHHHHHHHH CS
                  NTP_transf_3  85 dadavlvlacDmPlltpelverlla 109
                                   + d ++ +++D Pl + el+++ ++
  gi|15669252|ref|NP_248057.1|  90 SGDVIVRITGDNPLTSIELIDKQVE 114
                                   89999999*****999999987666 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.8e-05      0.29      14      74 ..      16      74 ..       3     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.8e-05
                                  T-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-..GGGHHHHHHHHGGCCEEEEE-- CS
                          IspD 14 mkaglpKqflelkgqtllehtvdallaskavdkivvvvs..eddteefeqllldksiqlvaGG 74
                                  +   ++K +l+l ++ +le  ++ l +sk++d i+v+ +  ++d +++ +l  +  +++  G 
  gi|15669252|ref|NP_248057.1| 16 L---KNKVLLKLGDRCILEILLERLKKSKKLDDIIVATTikKED-NAIVELCNSLGVNVFRGS 74
                                  3...69******************************96510444.677777777667776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1879.62
//
Query:       gi|15669253|ref|NP_248058.1|  [L=214]
Description: galactoside acetyltransferase LacA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.8e-14   51.2  17.6      1e-10   40.9   3.4    3.9  4  Hexapep    Bacterial transferase hexapeptide (six repeats)
    5.4e-10   38.9  18.2    1.5e-07   31.0   2.3    3.1  3  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.36   3.2e+03      20      25 ..      81      86 ..      78      94 .. 0.71
   2 !    9.9   0.2   6.9e-05      0.62       3      16 ..     104     117 ..     103     120 .. 0.60
   3 !    9.0   0.4   0.00013       1.2       2      18 ..     123     139 ..     122     140 .. 0.76
   4 !   40.9   3.4   1.2e-14     1e-10       2      36 .]     160     194 ..     159     194 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.36
                                  EEE-TT CS
                       Hexapep 20 VkIGdn 25
                                  ++IG+n
  gi|15669253|ref|NP_248058.1| 81 IIIGEN 86
                                  556655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 6.9e-05
                                   EEETTEEE-TTEEE CS
                       Hexapep   3 vIGsnvlIgpfavi 16 
                                    IG+n+ Ig+f++i
  gi|15669253|ref|NP_248058.1| 104 EIGDNCGIGSFSII 117
                                   46666666666665 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00013
                                   EEEETTEEE-TTEEEET CS
                       Hexapep   2 tvIGsnvlIgpfavigg 18 
                                   ++IGsnvlI + ++i +
  gi|15669253|ref|NP_248058.1| 123 ITIGSNVLISSHVHIID 139
                                   57888888888888876 PP

  == domain 4  score: 40.9 bits;  conditional E-value: 1.2e-14
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                   + IG++v+Ig +++i+ +VkIG++++Igag+v+++
  gi|15669253|ref|NP_248058.1| 160 IEIGDDVWIGTGVKILKGVKIGEGAVIGAGSVVTR 194
                                   57*******************************85 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.4      0.27   2.4e+03       2       7 ..      81      86 ..      80      86 .. 0.76
   2 !   17.7   2.3   2.5e-07    0.0022       3      27 ..     104     132 ..     102     137 .. 0.86
   3 !   31.0   2.3   1.7e-11   1.5e-07       1      34 []     159     194 ..     159     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.27
                                  EEE-TT CS
                     Hexapep_2  2 viIGdn 7 
                                  +iIG+n
  gi|15669253|ref|NP_248058.1| 81 IIIGEN 86
                                  688887 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.5e-07
                                   EE-TT-EE-TT-EE....SEEE-TT-EE- CS
                     Hexapep_2   3 iIGdnCliGanagi....GvslGdncvvg 27 
                                    IGdnC iG++++i     +++G n+ ++
  gi|15669253|ref|NP_248058.1| 104 EIGDNCGIGSFSIInatkKITIGSNVLIS 132
                                   6************976555*******997 PP

  == domain 3  score: 31.0 bits;  conditional E-value: 1.7e-11
                                   .EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                     Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvgaGvvita 34 
                                   p+ IGd++ iG    i  Gv++G+++v+gaG+v+t+
  gi|15669253|ref|NP_248058.1| 159 PIEIGDDVWIGTGVKIlkGVKIGEGAVIGAGSVVTR 194
                                   789************99*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1379.14
//
Query:       gi|15669254|ref|NP_248059.1|  [L=337]
Description: spore coat polysaccharide biosynthesis protein E [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-95  317.6   0.0    6.8e-95  317.1   0.0    1.2  1  NeuB      NeuB family
    2.1e-07   31.4   0.0    1.4e-06   28.8   0.0    2.2  2  SAF       SAF domain
  ------ inclusion threshold ------
      0.019   15.1   0.0      0.037   14.2   0.0    1.5  1  Popeye    Popeye protein conserved region


Domain annotation for each model (and alignments):
>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.1   0.0   1.1e-98   6.8e-95       1     241 []      37     263 ..      37     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 317.1 bits;  conditional E-value: 1.1e-98
                                   HHHHHHHHT-SEEEEEE--HHHH--GGGGG--......TT-S-HHHHHHHH---HHHHHHHHHHHHHTT-EEEEEE-SHHH CS
                          NeuB   1 lieaAaeagadavKfQtfkaeelvskeakkaeyqkkekekeesqlellkklelseeehkelkeyceekgieflstpfdles 81 
                                   l+++A+++gada+KfQ++++e+++sk++              +++el+k+lelseee+ elkey+e++gi+f+stp dl+ 
  gi|15669254|ref|NP_248059.1|  37 LVKEAKKCGADAIKFQSYHTEDFISKKS--------------EYYELFKSLELSEEEFYELKEYAEKIGIMFISTPLDLKY 103
                                   799**********************943..............68************************************* PP

                                   HHHHHHHT-S-EEE-GGGTT-HHHHHHHHTT-S-EEEE-TT--HHHHHHHHHHH.HHHT--EEEEE----SS--GGG--TH CS
                          NeuB  82 vdlleslgveayKiaSgeltnlpllekiaktgkpvilStGmatleeieeavevlreagaeklvllhCtseYPapledvnLk 162
                                   vd+l++++v+a+KiaSg+lt +pllek+aktgkpvilStGm++++ei eav+vl+++g+++++llhC+s+YP+p+edvnL+
  gi|15669254|ref|NP_248059.1| 104 VDILNKMNVPAFKIASGDLTFYPLLEKVAKTGKPVILSTGMSDIGEIWEAVKVLENNGCRDIILLHCISSYPTPYEDVNLN 184
                                   ********************************************************************************* PP

                                   HHHHHHHH-TSEEEEE--SSSSHHHHHHHHHT--EEEEEB-S-TT--STTGGG-B-HHHHHHHHHHHHHHHHHSS--TT CS
                          NeuB 163 aietlkeafgvpvGySDHtlgiavaiaAvalGAkviEkHftldrnlegpDhkaSlepeelkelveairnvekalgegek 241
                                   ai+tlk+ f++pvGySDHtlgi +++++valGA+viEkHftld+n+egpDh++S +pee+ke+v++ir vek+lg+gek
  gi|15669254|ref|NP_248059.1| 185 AIKTLKSIFNIPVGYSDHTLGILAPVVSVALGADVIEKHFTLDKNMEGPDHALSADPEEFKEMVNNIRLVEKMLGSGEK 263
                                   ****************************************************************************986 PP

>> SAF  SAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.38   2.3e+03      23      42 ..     162     181 ..     158     182 .. 0.86
   2 !   28.8   0.0   2.3e-10   1.4e-06       2      62 ..     278     334 ..     277     335 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.38
                                   EECECGGCCTSCCCGGHHHH CS
                           SAF  23 lkrpiashkigllpiaygev 42 
                                   ++++i+ h+i  +p++y++v
  gi|15669254|ref|NP_248059.1| 162 CRDIILLHCISSYPTPYEDV 181
                                   6788888*********9876 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 2.3e-10
                                   EEEEESSTB-TT-BEBTTTEEEECECGGCCTSCCCGGHHHHTTEEESS-B-TT-B-BGGGE CS
                           SAF   2 nVvvAardikaGeviteddltlkrpiashkigllpiaygeviGkratrdikaGepvhahnl 62 
                                   +++vA+r+ik+Ge ++ d+++ krp+     g+ ++++  +++++ ++d ++++++ +++l
  gi|15669254|ref|NP_248059.1| 278 RSIVAKRNIKKGEYLSVDNISFKRPG----RGIETKYLSIILNRKIKNDKEEDDIIYWDDL 334
                                   799**********************8....*****************************98 PP

>> Popeye  Popeye protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.3e-06     0.037      88     139 ..      66     228 ..      53     229 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.3e-06
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx...................................................... RF
                        Popeye  88 YkklFqplkvsrkeFkklvseeeakil...................................................... 114
                                   Y +lF+ l++s++eF +l +  ++ki                                                       
  gi|15669254|ref|NP_248059.1|  66 YYELFKSLELSEEEFYELKE-YAEKIGimfistpldlkyvdilnkmnvpafkiasgdltfypllekvaktgkpvilstgms 145
                                   889***************88.77777789**************************************************** PP

                                   ..........................................................xxxxxxxxxxxxxxxxxxxxxxx RF
                        Popeye 115 ..........................................................eryLaavfsvligkDiteKlysl 137
                                                                                                La v sv++g+D++eK ++l
  gi|15669254|ref|NP_248059.1| 146 digeiweavkvlenngcrdiillhcissyptpyedvnlnaiktlksifnipvgysdhtLGILAPVVSVALGADVIEKHFTL 226
                                   *******************************************************987789****************9999 PP

                                   xx RF
                        Popeye 138 ne 139
                                   ++
  gi|15669254|ref|NP_248059.1| 227 DK 228
                                   76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2144.76
//
Query:       gi|15669255|ref|NP_248060.1|  [L=386]
Description: spore coat polysaccharide biosynthesis protein SpsC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.6e-147  490.9   0.0   2.9e-147  490.7   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.2e-06   27.1   0.1    3.6e-06   26.4   0.1    1.4  1  Aminotran_1_2    Aminotransferase class I and II
    2.1e-05   24.0   0.2    3.7e-05   23.2   0.2    1.4  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  490.7   0.0  4.8e-151  2.9e-147       2     360 ..      14     378 ..      13     379 .. 0.98

  Alignments for each domain:
  == domain 1  score: 490.7 bits;  conditional E-value: 4.8e-151
                                   HHHHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHH CS
               DegT_DnrJ_EryC1   2 ikeeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavle 82 
                                   i+eee+++v ++lks+w+t+gp++ +FE+ f++y+g+k+ai+++s+ta+lhl+L al+++++deVI++++tF+at n++++
  gi|15669255|ref|NP_248060.1|  14 IGEEEINEVIDTLKSDWITMGPKTLKFEELFRNYIGSKFAISLNSCTAGLHLSLVALNIKDKDEVITTPYTFAATGNVIVH 94 
                                   799****************************************************************************** PP

                                   TT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSS CS
               DegT_DnrJ_EryC1  83 lgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgd 163
                                     akpvfvD+d++tyni++++ie+aitertkaI+pVh++G++++md++ +ia++++l+vieDaAhAlGa+ykgkk+G++gd
  gi|15669255|ref|NP_248060.1|  95 QRAKPVFVDIDKETYNINVEEIENAITERTKAIIPVHYAGHPCEMDEILKIARDYDLYVIEDAAHALGAEYKGKKIGTIGD 175
                                   ********************************************************************************* PP

                                   EEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCS.......S---B-B-BHHHHHHHHHHHCTH CS
               DegT_DnrJ_EryC1 164 aavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgev.......elGynyrlteiqAAiglaqLerl 237
                                   +++fSFy+tKn+ttGeGG+v+t++ee+aek+++lr hG++r+a+kry +e        e+Gy+y++t+iqA+ig++qL++ 
  gi|15669255|ref|NP_248060.1| 176 TTSFSFYATKNITTGEGGMVTTDNEEIAEKIKILRLHGISRDAWKRYSSEGswyyeiiECGYKYNMTDIQASIGIHQLKKA 256
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHH.HCHHHHHHHHHHCCEE-B-SGSCHGGGSCC CS
               DegT_DnrJ_EryC1 238 delvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeae.vkrdelvealkeegigtrvhypnplhrqpv 317
                                   + +++rR+eia++y+ee+++leg +++t +k+ k hawhly++l++ ++  ++r++++e+lk+++igt+vh+ +plh++p+
  gi|15669255|ref|NP_248060.1| 257 EIMRKRREEIAKIYNEEFENLEGLITPTIKKHVK-HAWHLYPLLINIDRLkINRTKFIEELKKQNIGTSVHF-IPLHLHPF 335
                                   ***********************87777777776.*************999*********************.8******* PP

                                   HHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
               DegT_DnrJ_EryC1 318 yaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                                   y++++++++gd+pnae+++er +sLp+yp++t++dv +Vv+a+
  gi|15669255|ref|NP_248060.1| 336 YRKTFGYKKGDFPNAEWVYEREISLPIYPKMTDDDVIDVVNAV 378
                                   *****************************************98 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1     6e-10   3.6e-06      49     194 ..      40     163 ..      31     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 6e-10
                                   HHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTE CS
                 Aminotran_1_2  49 leealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfh 129
                                   +ee    ++g         + a+ + s++  l   l +l  +  +de++    t+a   n++ + +++ v + ++ +e+++
  gi|15669255|ref|NP_248060.1|  40 FEELFRNYIG--------SKFAISLNSCTAGLHLSLVALN-IKDKDEVITTPYTFAATGNVIVHQRAKPVFVDID-KETYN 110
                                   5666666666........5557888899999999999999.9*******************************66.99*** PP

                                   E-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCB CS
                 Aminotran_1_2 130 ldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfv 194
                                   +++e++e+a++e      +tk i+   p +  G  +  +e+ k+   a+ y l+++ D a+a ++
  gi|15669255|ref|NP_248060.1| 111 INVEEIENAITE------RTKAII---PVHYAGHPCEMDEILKI---ARDYDLYVIEDAAHALGA 163
                                   ************......888888...77777777899999999...**************9876 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.2   6.1e-09   3.7e-05      32     225 ..      35     208 ..      31     298 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.1e-09
                                   HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT.TBE- CS
               Beta_elim_lyase  32 ktvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknkea.Gkmd 110
                                   +++ ++e+ +++++g + a+ + + ta+ +++l +l  + ++evi t    + f  tg++ + + +k++ ++++++  +++
  gi|15669255|ref|NP_248060.1|  35 PKTLKFEELFRNYIGSKFAISLNSCTAGLHLSLVALNiKDKDEVITT---PYTFAATGNVIVHQRAKPVFVDIDKEtYNIN 112
                                   57889999***********************9977764888888655...478999*************9998776589** PP

                                   HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSE CS
               Beta_elim_lyase 111 lekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDs 191
                                   +e++e+ai+e+ +     ++i +       +G + ++   +e+ +ia++y++ ++ D+A  + a      + k++    D+
  gi|15669255|ref|NP_248060.1| 113 VEEIENAITERTK-----AIIPVHY-----AGHPCEM---DEILKIARDYDLYVIEDAAHALGAE----YKGKKIGTIGDT 176
                                   **********555.....4444433.....4777765...567899*************998886....555667777776 PP

                                   EEEE..SSSTT--SS-EEEEE-HH....HHHHHHHH CS
               Beta_elim_lyase 192 vtms..lkKdllanvGgvlafrddeledylaerveq 225
                                    ++s  ++K++++  Gg++ ++++e+    ae ++ 
  gi|15669255|ref|NP_248060.1| 177 TSFSfyATKNITTGEGGMVTTDNEEI----AEKIKI 208
                                   6555337***************9955....444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2843.57
//
Query:       gi|15669256|ref|NP_248061.1|  [L=507]
Description: polysaccharide biosynthesis protein CapF [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-70  237.2  37.7    2.1e-70  237.2  37.7    3.0  3  Polysacc_synt    Polysaccharide biosynthesis protein
    1.4e-26   93.3  22.0    1.4e-26   93.3  22.0    4.1  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    2.4e-09   37.1  29.1    3.3e-06   26.8  12.2    4.5  5  MatE             MatE
    9.5e-08   31.6  26.1    9.5e-08   31.6  26.1    2.5  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
     0.0014   17.3  45.9     0.0021   16.7  45.9    1.3  1  MurJ             Lipid II flippase MurJ


Domain annotation for each model (and alignments):
>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.2  37.7     6e-74   2.1e-70       2     274 .]       8     302 ..       7     302 .. 0.99
   2 ?   -4.3  11.4       2.6   9.2e+03     174     270 ..     317     420 ..     306     424 .. 0.71
   3 ?   -5.9  11.7         5   1.8e+04      95     177 ..     394     474 ..     383     503 .. 0.69

  Alignments for each domain:
  == domain 1  score: 237.2 bits;  conditional E-value: 6e-74
                 Polysacc_synt   2 lkgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek.......kelvs 75 
                                   +kgv+++lls+++++++a++++v++a+ +++ ++Gl++++l+++++lv+++ +Gl++al+r+i ky ++       +++v+
  gi|15669256|ref|NP_248061.1|   8 VKGVSWHLLSYFLAAPIAYLVRVLYANEIPKLDVGLFYAVLDFFSMLVVFRAFGLDQALIRYIPKYLAEnrldmlkSSIVF 88 
                                   79******************************************************************************* PP

                 Polysacc_synt  76 lillnvllvllvlvllfllllliaa........flglpelavlylilalmll.llvgvasfrrglfqglermkyaavsqvv 147
                                   +++l+++l+++v++l+++++++ia+        f+g+ +l++++li+++m++ +l ++++f++++++g++ ++ya++++vv
  gi|15669256|ref|NP_248061.1|  89 VGILQTILAFIVAFLVVIFAPYIAEfyinnqgqFTGRLDLVINILIIMAMGYyFLDSIVAFFSNILTGFQLQNYASSTRVV 169
                                   ********************************************************************************* PP

                 Polysacc_synt 148 eqlsrvilvliavflfld...ivaavlgavlaalvggivslavlrkkf.r..prfvilslklvrellsfsapltisslail 222
                                   + ls++i++li+++lf+    +v +v ++++a+++ +i++++v++k+f +  +++vi+s+kl+r+l+s++++++i+++++l
  gi|15669256|ref|NP_248061.1| 170 RILSVFIFSLIFIYLFNVhnaYVPSVSYLLMAVVMIIIYGYIVVKKIFpKfaKEKVIFSRKLIRNLFSYGMYVMIGYAGSL 250
                                   ************************************************8357***************************** PP

                 Polysacc_synt 223 lytyidsillglllgaeavGiYnaayqllvaisgllapivtaalfPvfselq 274
                                   ++ y+d i+l++++g +av++Y+++++++v+i +++a++v+a+lfP+ sel+
  gi|15669256|ref|NP_248061.1| 251 ILGYLDGICLTYFTGLNAVADYRNVAMPTVNILSYFAFSVGAVLFPMSSELW 302
                                   *************************************************986 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 2.6
                 Polysacc_synt 174 vlaalvggivslavlrkkf.r......prfvilslklvrellsfs.apltisslaillytyidsi.llglllgaeavGiYn 245
                                   v+ + + ++  la+l+ +f +      ++ + ls +   ++lsf+ + lt++s++ ++++ i +  + +++l  +  + +n
  gi|15669256|ref|NP_248061.1| 317 VFLYSLIIVTPLAILMAYFpTviinilFNPKYLSAAPAIQILSFGaMFLTFNSIGFNILNGIGRPnISTKIL--YIGASFN 395
                                   5555555566667777666535566775555555999999999983568999**999999999985666655..5668999 PP

                 Polysacc_synt 246 aayqllvaisgllapivtaalfPvf 270
                                   ++ ++l+++   ++ ++ +++f +f
  gi|15669256|ref|NP_248061.1| 396 LIFNILLIPKFGIIGAAITTVFGYF 420
                                   9999999999888877777887665 PP

  == domain 3  score: -5.9 bits;  conditional E-value: 5
                 Polysacc_synt  95 llliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavl 175
                                   + li+ +l  p + ++  +++ ++   +++ +f+ ++++ l   + +   +++  l+ + ++li v+ ++d+   v+ +++
  gi|15669256|ref|NP_248061.1| 394 FNLIFNILLIPKFGIIGAAITTVFG-YFIMWIFQIWFLNKLLEHQFLNKKWILVILVGI-FSLIPVMFIKDLIDNVILQLF 472
                                   5677788899999999888888888.677789999999999999999999999888877.888888888885444444443 PP

                 Polysacc_synt 176 aa 177
                                     
  gi|15669256|ref|NP_248061.1| 473 VC 474
                                   22 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   7.0       4.3   1.6e+04      92     109 ..      92     108 ..      41     143 .. 0.54
   2 ?    0.9  20.9      0.12   4.4e+02       4     118 ..     136     257 ..     132     297 .. 0.77
   3 ?   -5.6   6.7         5   1.8e+04      52     103 ..     240     294 ..     225     349 .. 0.55
   4 !   93.3  22.0   3.8e-30   1.4e-26       2     142 ..     355     490 ..     354     491 .. 0.93

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 4.3
               Polysacc_synt_C  92 lkpllaalvmgivvylll 109
                                   l ++la +v ++vv+ ++
  gi|15669256|ref|NP_248061.1|  92 LQTILAFIVAFLVVI-FA 108
                                   233333333333322.22 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
               Polysacc_synt_C   4 ilalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgi...vGaaiatvlallvvavlnlyalrrll 81 
                                   + + + ++ s+  ++s+iL+g   q +a    v+ +l  +i++l++i+lf++   + ++++ +l  +v++++  y++ +++
  gi|15669256|ref|NP_248061.1| 136 MAMGYYFLDSIVAFFSNILTGFQLQNYASSTRVVRILSVFIFSLIFIYLFNVhnaYVPSVSYLLMAVVMIIIYGYIVVKKI 216
                                   444556677888**************************************86444889999999999**999999999999 PP

               Polysacc_synt_C  82 gikl.....ellrrllkpllaalvmgivvylllllllgllll 118
                                     k+      + r+l++  l++ +m++++ +  +l+lg l +
  gi|15669256|ref|NP_248061.1| 217 FPKFakekvIFSRKLIRN-LFSYGMYVMIGYAGSLILGYLDG 257
                                   999989997556666654.44445555544477777666654 PP

  == domain 3  score: -5.6 bits;  conditional E-value: 5
               Polysacc_synt_C  52 lfgivGaaiatvlallvvavlnlyalrr.llgikl..ellrrllkpllaalvmgi 103
                                   ++ ++G a + +l++l +++l ++   +    ++   +   ++l +++++++ ++
  gi|15669256|ref|NP_248061.1| 240 MYVMIGYAGSLILGYLDGICLTYFTGLNaVADYRNvaMPTVNILSYFAFSVGAVL 294
                                   4455666666666666666665444322133333333334444444444444433 PP

  == domain 4  score: 93.3 bits;  conditional E-value: 3.8e-30
               Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllg 82 
                                   ++il+++++fl++++++ +iL+g+gr+ i +k+l iga ++li+n+llip+fgi+Gaai tv++++++ ++++++l++ll 
  gi|15669256|ref|NP_248061.1| 355 IQILSFGAMFLTFNSIGFNILNGIGRPNISTKILYIGASFNLIFNILLIPKFGIIGAAITTVFGYFIMWIFQIWFLNKLLE 435
                                   89******************************************************************************* PP

               Polysacc_synt_C  83 iklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                   +++ l ++ + ++l++++  i v+++  l+ +++l    +l+++++v   +Y+l ++ l+
  gi|15669256|ref|NP_248061.1| 436 HQF-LNKKWILVILVGIFSLIPVMFIKDLIDNVIL----QLFVCGVVYFGIYILGIFGLK 490
                                   ***.6677779999999999999988888888776....9999999******99998776 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   8.9   5.4e-09     2e-05      13     137 ..      26     156 ..      18     161 .. 0.87
   2 ?    0.8  11.1     0.096   3.4e+02      69     150 ..     127     207 ..     123     217 .. 0.87
   3 ?    0.2   5.7      0.15   5.4e+02      87     135 ..     171     217 ..     161     247 .. 0.58
   4 !   26.8  12.2   9.3e-10   3.3e-06      13     160 ..     253     400 ..     242     401 .. 0.91
   5 ?   -5.1   5.9         5   1.8e+04     110     131 ..     439     460 ..     405     488 .. 0.50

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.4e-09
                          MatE  13 slidtllvgrlgskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllsliiallvll 92 
                                   +l+ +l ++++++ +++   ++l ++s+l+v  ++gl  al   + ++l +++ +++k +++   il ++l++i+a+lv++
  gi|15669256|ref|NP_248061.1|  26 YLVRVLYANEIPKLDVGLFYAVLDFFSMLVVfRAFGLDQALIRYIPKYLAENRLDMLKSSIVFVGILQTILAFIVAFLVVI 106
                                   667778888888888888888899988888878************************************************ PP

                          MatE  93 fseqilslftqdee....vlelakrylrililgipa.lalqlvlsgilrg 137
                                   f+++i+ ++ +++      l l+ ++l i+++g+ + +++   +s+il g
  gi|15669256|ref|NP_248061.1| 107 FAPYIAEFYINNQGqftgRLDLVINILIIMAMGYYFlDSIVAFFSNILTG 156
                                   *************9999999999999999999875515666666666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.096
                          MatE  69 kealrqglilllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyisl 149
                                     ++++ +i++++ +++ +++  +fs+++  +  q+ + +  + r+l++ i++++++ l++v ++++ ++++  +++++++
  gi|15669256|ref|NP_248061.1| 127 DLVINILIIMAMGYYFLDSIV-AFFSNILTGFQLQNYASSTRVVRILSVFIFSLIFIYLFNVHNAYVPSVSYLLMAVVMII 206
                                   556788899999999999999.9999999999999999*******************************999988887776 PP

                          MatE 150 i 150
                                   i
  gi|15669256|ref|NP_248061.1| 207 I 207
                                   6 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.15
                          MatE  87 allvllfseqilslftqdeevlelakrylrililgipalalqlvlsgil 135
                                   +l v++fs ++++lf+ +++    +  yl+++++ i++++ ++v ++i+
  gi|15669256|ref|NP_248061.1| 171 ILSVFIFSLIFIYLFNVHNA-YVPSVSYLLMAVVMIIIYG-YIVVKKIF 217
                                   55678889999999988887.4445556666666666553.33333333 PP

  == domain 4  score: 26.8 bits;  conditional E-value: 9.3e-10
                          MatE  13 slidtllvgrl.gskalAav.sialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvl 91 
                                   + +d + + ++ g +a+A + ++a++++++l +f++++++ l ++ +  + ++ +k+++  + + ++ +l++  ++a+l+ 
  gi|15669256|ref|NP_248061.1| 253 GYLDGICLTYFtGLNAVADYrNVAMPTVNILSYFAFSVGAVLFPMSSELWEKGYKKALSYGVEKVFLYSLIIVTPLAILMA 333
                                   55666677777788888877579********************************************************** PP

                          MatE  92 lfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplny 160
                                    f+  i+ ++ +++     a+  ++il +g+ +l ++ +  +il+g+g++ +++ i+ i++ +n+++n 
  gi|15669256|ref|NP_248061.1| 334 YFPTVIINILFNPKY--LSAAPAIQILSFGAMFLTFNSIGFNILNGIGRPNISTKILYIGASFNLIFNI 400
                                   **********99884..457889********************************************97 PP

  == domain 5  score: -5.1 bits;  conditional E-value: 5
                          MatE 110 lakrylrililgipalalqlvl 131
                                   l k++++++++gi+ l++ + +
  gi|15669256|ref|NP_248061.1| 439 LNKKWILVILVGIFSLIPVMFI 460
                                   3333333344443333333333 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6  26.1   2.7e-11   9.5e-08      11     293 .]      41     353 ..      36     353 .. 0.79
   2 ?   -2.0   3.7      0.47   1.7e+03      83     169 ..     353     438 ..     350     489 .. 0.66

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.7e-11
               Polysacc_synt_3  11 FGvvaialvvislanlfvdmGlssaliq.......kedlteedlstvft..fnlvlgllialvlfllapliasfynqpe.. 80 
                                    G+   +l ++s++ +f  +Gl++ali+       +++l+  + s vf+  ++ +l++++a++++++ap+ia+fy +++  
  gi|15669256|ref|NP_248061.1|  41 VGLFYAVLDFFSMLVVFRAFGLDQALIRyipkylaENRLDMLKSSIVFVgiLQTILAFIVAFLVVIFAPYIAEFYINNQgq 121
                                   57777788899999*************944333322344555888888544899*********************876533 PP

               Polysacc_synt_3  81 .......lvtvlrvlalv.lilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALv..igtllssl 151
                                          ++++l ++a+   +l ++++  +++l+    ++  +  ++v ++  +i++++  +l     A v  ++ ll ++
  gi|15669256|ref|NP_248061.1| 122 ftgrldlVINILIIMAMGyYFLDSIVAFFSNILTGFQLQNYASSTRVVRILSVFIFSLIFIYLFNVHNAYVpsVSYLLMAV 202
                                   333322234555566665246788888888888776667777777888888889999999888766666664478899999 PP

               Polysacc_synt_3 152 lslvllwlaskwr.......prlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpv 225
                                   ++++++ +++  +        ++ fs+k +++lfs+g+++++      +   ld +   ++ + +a++ Y      +  ++
  gi|15669256|ref|NP_248061.1| 203 VMIIIYGYIVVKKifpkfakEKVIFSRKLIRNLFSYGMYVMIGYAGSLILGYLDGICLTYFTGLNAVADYRNVAMPTVNIL 283
                                   9988887777777454444445668999****************************************9976555555566 PP

               Polysacc_synt_3 226 aeitsviakVlfPalSrlqdd..kkklrelylkvlrlialivlPiavglavvaellvkvllGsqWleavp 293
                                   + +  ++ +VlfP+ S+l +   kk+l   ++kv+  + +iv P+a+++a++ + ++++l+  ++l+a+p
  gi|15669256|ref|NP_248061.1| 284 SYFAFSVGAVLFPMSSELWEKgyKKALSYGVEKVFLYSLIIVTPLAILMAYFPTVIINILFNPKYLSAAP 353
                                   7788999**********9775337899999***********************************99875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.47
               Polysacc_synt_3  83 tvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslvllwlaskw 163
                                   + +++l++  ++ +++s+  ++l+   + +  +ki  ++  + +i+ i+l +  +g+   +i t++  ++++++ +++++ 
  gi|15669256|ref|NP_248061.1| 353 PAIQILSFGAMFLTFNSIGFNILNGIGRPNISTKILYIGASFNLIFNILL-IPKFGIIGAAITTVFGYFIMWIFQIWFLNK 432
                                   56666666666666666666666666666666666666666666666665.356777777777777777777777777666 PP

               Polysacc_synt_3 164 rprlkf 169
                                    ++ +f
  gi|15669256|ref|NP_248061.1| 433 LLEHQF 438
                                   555444 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7  45.9   5.9e-07    0.0021      56     426 ..      89     455 ..      51     484 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.9e-07
                          MurJ  56 vrkvltllilvlllvtligilaapllirllatgf..deetlelavsllrillp.ylllvslsavfgavLnarkkFfapafs 133
                                   v+    l ++++ +v+++ +++ap+++++  + +      l l +++l i++  y +l s++a+f+ +L   +     + +
  gi|15669256|ref|NP_248061.1|  89 VGI---LQTILAFIVAFLVVIFAPYIAEFYINNQgqFTGRLDLVINILIIMAMgYYFLDSIVAFFSNILTGFQLQNYASST 166
                                   333...344555566677778*******9998885456678899999999865499999**********998888888888 PP

                          MurJ 134 PvllNvsvIltllllanklgeeailaLaiGvliGgvlqllvqlpalkkagll..lkprfafrdeglkkflk.lllptllgv 211
                                    v+  +sv ++ l++   ++ ++ ++ +++ l+ +v+ +++  + ++k  +    k+++ f  + +++++   +  ++ + 
  gi|15669256|ref|NP_248061.1| 167 RVVRILSVFIFSLIFIYLFNVHNAYVPSVSYLLMAVVMIIIYGYIVVKKIFPkfAKEKVIFSRKLIRNLFSyGMYVMIGYA 247
                                   888888887777777777776778888899888888888887777777777767566666777888888762589999999 PP

                          MurJ 212 svsqlnllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltllllipv 292
                                   ++ +l+ l  + l+ f   ++v+ +++  +     l+ f+ s+ +vl+P  S+  +++ ++++   +++    +l+++ p+
  gi|15669256|ref|NP_248061.1| 248 GSLILGYLDGICLTYFTGLNAVADYRNVAMPTVNILSYFAFSVGAVLFPMSSELWEKGYKKALSYGVEKVFLYSLIIVTPL 328
                                   9999999999*********************************************************************** PP

                          MurJ 293 sfgllvlskpivsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlnillsllll 373
                                   +++++ +   i+++lf      + +   +a ++ + ++g +++  + +  +++   ++ +  +ki  i +  n+++++ll+
  gi|15669256|ref|NP_248061.1| 329 AILMAYFPTVIINILF------NPKYLSAAPAIQILSFGAMFLTFNSIGFNILNGIGRPNISTKILYIGASFNLIFNILLI 403
                                   ****************......5667788999************************************************* PP

                          MurJ 374 pplgvvglalatslsaliglvllyvllrkrlklteargiktflaklvvllala 426
                                   p++g +g a+ t+ ++ i  ++ +++l+k l+ ++ ++  + +   v++++l+
  gi|15669256|ref|NP_248061.1| 404 PKFGIIGAAITTVFGYFIMWIFQIWFLNKLLEHQFLNKKWILVIL-VGIFSLI 455
                                   *****************************9985544332222222.3344333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1220  (0.0680462); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 3001.40
//
Query:       gi|15669257|ref|NP_248062.1|  [L=392]
Description: galactosyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-39  132.8   0.9    8.7e-39  132.8   0.9    1.7  2  Glycos_transf_1  Glycosyl transferases group 1
    4.1e-24   85.5   0.0    1.8e-23   83.4   0.0    2.0  3  Glyco_trans_1_4  Glycosyl transferases group 1
    4.1e-17   62.7   0.0    5.6e-17   62.2   0.0    1.2  1  Glyco_transf_4   Glycosyltransferase Family 4
    8.7e-07   29.3   0.0    2.3e-06   27.9   0.0    1.7  1  Glyco_trans_1_2  Glycosyl transferases group 1
    1.4e-05   25.2   0.6    2.9e-05   24.1   0.6    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.47   10.6   0.0    1.8  1  DUF357           Protein of unknown function (DUF357)


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.9   5.6e+03       6      30 ..      28      52 ..      23      60 .. 0.78
   2 !  132.8   0.9   2.9e-42   8.7e-39       4     171 ..     201     368 ..     198     369 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.9
                                  HHHTTTTTT-EEEEEESS-TTTTTH CS
               Glycos_transf_1  6 rkklgknekkkiilsvgrlekeKgv 30
                                   k l ++e+  i+++  ++ k+K +
  gi|15669257|ref|NP_248062.1| 28 TKHLSEDENYDIYIFAPNIPKYKEF 52
                                  5666778888899999999888865 PP

  == domain 2  score: 132.8 bits;  conditional E-value: 2.9e-42
                                   HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSS CS
               Glycos_transf_1   4 kkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsre 84 
                                   +++k ++k ++k  +++vgrl k+Kgv+++ika+ +l+k+l++++ l+++G ge++++lkkla ++ + + + f+g+v+ e
  gi|15669257|ref|NP_248062.1| 201 EDKKIKEKFKNKIKLCFVGRLYKWKGVENIIKAYVDLPKDLKEKIILIVVGYGEDLERLKKLAGNYLN-NGIYFTGKVDFE 280
                                   6778888889********************************************************88.9*********99 PP

                                   SHHHHHHCESEEEEEESS.BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHH CS
               Glycos_transf_1  85 dleellknadifvlpsis.EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrer 164
                                   + +++ k++di++++s++  g+  +ll Am +g++++as ++g+ evv dg +G+l k n++e+++++i+kl+e+++lr+ 
  gi|15669257|ref|NP_248062.1| 281 KAIAIVKASDIYIHSSYKgGGLSSSLLQAMCCGKAIVASPYEGADEVVIDGYNGILLKDNSPEEIKRGIIKLIENNNLRKI 361
                                   9******************************************************************************** PP

                                   HHHHHHH CS
               Glycos_transf_1 165 lgenark 171
                                   +gena++
  gi|15669257|ref|NP_248062.1| 362 YGENAKN 368
                                   *****96 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.1   3.3e+03       3      42 ..       6      46 ..       5      65 .. 0.67
   2 ?   -3.5   0.0       4.4   1.3e+04      70      89 ..     157     176 ..     155     178 .. 0.81
   3 !   83.4   0.0   6.1e-27   1.8e-23       3     134 .]     214     355 ..     212     355 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                                  EEEEES---GG.GTHHHHHHHH.HHHH.H.HEEEEEES---. CS
               Glyco_trans_1_4  3 vilfvGrleenvkgvdllleav.pllrkk.dvrlvivGdgpr 42
                                   i+f G + +++ g++  ++++ ++l ++ ++ ++i   +  
  gi|15669257|ref|NP_248062.1|  6 LIIFPGYYIPHIGGLETHVDEFtKHLSEDeNYDIYIFAPN-I 46
                                  5889998888999999999999888886634888887733.3 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.4
                                   HHH-SEEEE-----SHHHHH CS
               Glyco_trans_1_4  70 laaadvfvaPsegfglkllE 89 
                                   +++ad +va s+ +++ +lE
  gi|15669257|ref|NP_248062.1| 157 FKKADYVVAISKAVKNFILE 176
                                   67899999999888888887 PP

  == domain 3  score: 83.4 bits;  conditional E-value: 6.1e-27
                                   EEEEES---GG.GTHHHHHHHHHHHH.H.H..EEEEEES---...HHHHHHHT.T-T.TEEEE---..THHHHHHHH-SEE CS
               Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d..vrlvivGdgp.rpeeleelaa.gleerveftGfv..edlaellaaadvf 76 
                                   +++fvGrl++ +kgv+ +++a   l k+ +  + l++vG g+   e+l++la   l++++ ftG+v  e+  ++++a+d++
  gi|15669257|ref|NP_248062.1| 214 KLCFVGRLYK-WKGVENIIKAYVDLPKDlKekIILIVVGYGEdL-ERLKKLAGnYLNNGIYFTGKVdfEKAIAIVKASDIY 292
                                   799*****75.5**********888866534699*****99765.59998885588899*******888899********* PP

                                   EE--...---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
               Glyco_trans_1_4  77 vaPs...egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                   +  s    g++ +ll+am +g+++Va++ +g+ evv  g ng+l+++++pe++ + i++L+e+
  gi|15669257|ref|NP_248062.1| 293 IHSSykgGGLSSSLLQAMCCGKAIVASPYEGADEVVidGYNGILLKDNSPEEIKRGIIKLIEN 355
                                   ****96559**********************9**999*********999***********987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0   1.9e-20   5.6e-17       1     169 [.      17     194 ..      17     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.9e-20
                Glyco_transf_4   1 vGGverhvleLaraLar.rGheVtvvtpgddgpleeev.....elvvrvprvplpllkrllrslaflrrlrrllkrekpDv 75 
                                   +GG e+hv e++++L +  ++++++++p+ ++  e e      ++++ +    +p+++ + +    ++r+   l + ++D+
  gi|15669257|ref|NP_248062.1|  17 IGGLETHVDEFTKHLSEdENYDIYIFAPNIPKYKEFEIrhnnvKVYRYPAFEIIPNYPVPNIFNIKFWRMFFNLYKIDFDI 97 
                                   7****************889***********9999998764432222222333344444444444445555555556**** PP

                Glyco_transf_4  76 vHahspaal....gaallalrrrlgiplVltvHglye.krllkarlkplsrllralerrllrradrviavSeatadelrer 151
                                   v +++ ++     g+  ++lr  ++++l++  Hg++  k   ++++k+ + + + + + ++++ad v+a+S+a+++ ++e 
  gi|15669257|ref|NP_248062.1|  98 VMTRTRFFSntllGFIFAKLR-FKKKKLIHVEHGSAFvKLESEFKNKLSYFYDKTIGKLIFKKADYVVAISKAVKNFILE- 176
                                   *77765443222122223333.589***********854444445555555666677777********************. PP

                Glyco_transf_4 152 ygvppekitVipnGvDle 169
                                     v+ ++i +i++G  +e
  gi|15669257|ref|NP_248062.1| 177 NFVNDKDIPIIYRGLEIE 194
                                   667889********9887 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   7.6e-10   2.3e-06      11      90 ..     302     383 ..     291     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 7.6e-10
               Glyco_trans_1_2  11 pnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydhraeq 89 
                                   ++  l+ a+ cG  +++++ eg +e + +g  +il +  ++ee+ + i +l++n  +r+  +e+a++++++++++++ +++
  gi|15669257|ref|NP_248062.1| 302 LSSSLLQAMCCGKAIVASPYEGADEVVIDGYNGILLKdnSPEEIKRGIIKLIENNNLRKIYGENAKNFIKENFNWKKSVKE 382
                                   5667899***********99*****************9*************************************998776 PP

               Glyco_trans_1_2  90 l 90 
                                   +
  gi|15669257|ref|NP_248062.1| 383 Y 383
                                   5 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.6   9.6e-09   2.9e-05      11     137 ..      22     165 ..      17     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 9.6e-09
               Glyco_trans_4_2  11 vhtlrlakeLakr.gyeVhvitpkkga.kdele.aegihvhrlkvd...rkgpleylkafklkklik...kikPDvvhahy 82 
                                   +h+ ++ k L++  +y+++++ p+ ++ k++++  ++++v+r +       +p+ ++  +k++++++   ki +D+v + +
  gi|15669257|ref|NP_248062.1|  22 THVDEFTKHLSEDeNYDIYIFAPNIPKyKEFEIrHNNVKVYRYPAFeiiPNYPVPNIFNIKFWRMFFnlyKIDFDIVMTRT 102
                                   677777777765439********8888788887578899999963344244588887555666665433389*****9988 PP

               Glyco_trans_4_2  83 a.kpygllgslaar.lsgvipvvlsvwGldv..lkfpkksklkkl....llklalkkatkvis 137
                                      +  llg ++a+ + ++++++   +G+ +  l++++k+kl ++    + kl +kka+ v +
  gi|15669257|ref|NP_248062.1| 103 RfFSNTLLGFIFAKlRFKKKKLIHVEHGSAFvkLESEFKNKLSYFydktIGKLIFKKADYVVA 165
                                   7677899999999875566999999******9977777777444444469999******9987 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.47      26      56 ..     255     285 ..     250     288 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                        DUF357  26 aaeevlemaesYleDakyflekgdlvnAlas 56 
                                   + e++ ++a++Yl+ + yf  k d+++A+a 
  gi|15669257|ref|NP_248062.1| 255 DLERLKKLAGNYLNNGIYFTGKVDFEKAIAI 285
                                   5578899*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2423.99
//
Query:       gi|15669258|ref|NP_248063.1|  [L=157]
Description: hypothetical protein MJ_1070 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        0.1   13.1   1.6        0.1   13.1   1.6    1.8  2  LPAM_1     Prokaryotic membrane lipoprotein lipid attachment 
        4.9    7.3   9.8       0.23   11.5   2.6    2.3  2  Ibs_toxin  Toxin Ibs, type I toxin-antitoxin system


Domain annotation for each model (and alignments):
>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.6   1.1e-05       0.1       1      16 [.       1      16 [.       1      16 [. 0.96
   2 ?   -2.4   0.5         1     9e+03       8      10 ..     146     148 ..     142     153 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                        LPAM_1  1 MKKillalgalllLsG 16
                                  M+K+l++l++ll Ls+
  gi|15669258|ref|NP_248063.1|  1 MRKYLIILVLLLFLSS 16
                                  **************95 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                        LPAM_1   8 lga 10 
                                   l++
  gi|15669258|ref|NP_248063.1| 146 LLI 148
                                   443 PP

>> Ibs_toxin  Toxin Ibs, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.6   2.5e-05      0.23       1      15 [.       1      15 [.       1      18 [. 0.91
   2 ?   -0.8   0.8      0.19   1.7e+03      11      16 ..     146     151 ..     140     154 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.5e-05
                     Ibs_toxin  1 MMKLVIILVVLLlIS 15
                                  M K +IILV LL +S
  gi|15669258|ref|NP_248063.1|  1 MRKYLIILVLLLFLS 15
                                  6799********998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.19
                     Ibs_toxin  11 LLlISF 16 
                                   LL+I F
  gi|15669258|ref|NP_248063.1| 146 LLIICF 151
                                   777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1006.29
//
Query:       gi|15669259|ref|NP_248064.1|  [L=313]
Description: hypothetical protein MJ_1071 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0091   16.1   0.2      0.018   15.2   0.2    1.4  1  Torsin    Torsin
  ------ inclusion threshold ------
       0.13   12.9   6.5       0.96   10.1   6.5    2.3  1  DUSP      DUSP domain


Domain annotation for each model (and alignments):
>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2     2e-06     0.018      66     114 ..     142     187 ..     136     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-06
                                   HHHHHHHHHHHHSTTGGGSTTEEEEEHHHHS--GGGHHHHHHHHHHHHH CS
                        Torsin  66 knfvaeiiaenlyrdGlrsdyvkkfvatadfPkkkkveeykeelkeqir 114
                                   k++v+    + ly+ G + + vkk++  +++P++k v++yk++l ++i 
  gi|15669259|ref|NP_248064.1| 142 KEYVSA--LNGLYKIGKK-KKVKKLIINMELPDEKDVKKYKKKLAKKIT 187
                                   667765..4889999977.568999999****************99986 PP

>> DUSP  DUSP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   6.5   0.00011      0.96      43      88 ..     189     237 ..      18     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
                                   B...........TTTEB-SS--B.TTTEEEEEHHHHHHHHHHC-T----EE CS
                          DUSP  43 l.kappltk...engrlkpnlqe.grdyeivpeevwkfLvqwYgggpeikr 88 
                                   + k+ +  +   ++ +lk n ++ +++y++v+++vw+++   +g g e+k+
  gi|15669259|ref|NP_248064.1| 189 FnKKLE--NyeiNYFNLKFNNKNfECQYIYVKQSVWDKILGLFGEGIELKY 237
                                   222222..13578999**999999********************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1970.82
//
Query:       gi|15669260|ref|NP_248065.1|  [L=116]
Description: hypothetical protein MJ_1072 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        0.1   12.0   0.0       0.12   11.8   0.0    1.1  1  Glyco_transf_29  Glycosyltransferase family 29 (sialyltransfe
       0.16   12.3   1.2       0.29   11.4   1.2    1.4  1  Cas_Cmr5         CRISPR-associated protein (Cas_Cmr5)
       0.16   11.9   3.9        5.5    7.0   0.4    2.3  2  AvrM_N           Flax-rust effector AvrM N-terminal domain
       0.23   11.3   2.7       0.31   10.8   1.2    1.7  2  EspA             EspA-like secreted protein


Domain annotation for each model (and alignments):
>> Glyco_transf_29  Glycosyltransferase family 29 (sialyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.6e-05      0.12     135     206 ..      29      96 ..       3      98 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
               Glyco_transf_29 135 dllwlpafltkekvslraletlekkvkskik...lnkekvlilnPdflryvakfwlkskglkakrpstGllaltl 206
                                   + ++ +a++   +v ++++ +++++ k+++k   ++ke+++++   +lryv +++ +   l+ k++++G+++l+l
  gi|15669260|ref|NP_248065.1|  29 AEELYNAVV---EVIKEEKIIVKHELKDELKnelATKEDIMLAEERILRYVDNRFNQ---LD-KKMTVGFVILIL 96 
                                   333333333...333444444444455544445799*******************66...44.99*****99876 PP

>> Cas_Cmr5  CRISPR-associated protein (Cas_Cmr5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.2   6.5e-05      0.29      50     112 ..      11      76 ..       4      78 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.5e-05
                                   HHHTC......SSCCCHHHHHHHHHHHHHHHHCTSS...STTTCHHHHHHHHSTHHHHHHHHHHHHHHH CS
                      Cas_Cmr5  50 llskg......kkkkedahkkllehlaewlkkeksaskkkkgendllkelleadlseymratreaLall 112
                                    ++k         k+e+  ++l++++ e++k+e ++  k + +++l +el +++  ++m+a +++L+++
  gi|15669260|ref|NP_248065.1|  11 AYAKLyeiiakYIKDEKRAEELYNAVVEVIKEE-KIIVKHELKDELKNELATKE--DIMLAEERILRYV 76 
                                   55555555555578999999*************.66666777777777777665..9999999999986 PP

>> AvrM_N  Flax-rust effector AvrM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.4    0.0012       5.5      48      64 ..      13      29 ..       8      29 .. 0.92
   2 ?    6.1   0.2    0.0024        11      27      46 ..      67      86 ..      38      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0012
                        AvrM_N 48 rkLykaakeykkaekkA 64
                                   kLy++  +y+k+ek+A
  gi|15669260|ref|NP_248065.1| 13 AKLYEIIAKYIKDEKRA 29
                                  59*************98 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0024
                        AvrM_N 27 LspdeliRYvaerdtnvekm 46
                                  L  ++++RYv +r  ++ k+
  gi|15669260|ref|NP_248065.1| 67 LAEERILRYVDNRFNQLDKK 86
                                  8899*********9999874 PP

>> EspA  EspA-like secreted protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.2     7e-05      0.31      72     112 ..      15      54 ..      11      65 .. 0.83
   2 ?   -0.2   0.0      0.17   7.8e+02      48      61 ..      76      89 ..      54      90 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7e-05
                          EspA  72 mdaviAdltkddpkskeelppdVieYlrengIlvenktidd 112
                                   + ++iA+   +d+k  eel ++V+e ++e+ I v+ +  d+
  gi|15669260|ref|NP_248065.1|  15 LYEIIAKYI-KDEKRAEELYNAVVEVIKEEKIIVKHELKDE 54 
                                   5689***99.688*********************7665555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.17
                          EspA 48 snakfaqmskkaev 61
                                   +++f+q+ kk+ v
  gi|15669260|ref|NP_248065.1| 76 VDNRFNQLDKKMTV 89
                                  57899999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1679  (0.0936472); expected 358.6 (0.02)
Passed bias filter:                      732  (0.0408277); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 721.27
//
Query:       gi|15669261|ref|NP_248066.1|  [L=270]
Description: hypothetical protein MJ_1073 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-56  189.3   0.1    6.6e-56  188.9   0.1    1.1  1  RIO1            RIO1 family
    2.2e-14   53.4   0.1    6.7e-14   51.9   0.0    1.9  2  Rio2_N          Rio2, N-terminal
    5.6e-08   32.5   0.8    6.2e-07   29.1   0.8    2.0  1  Pkinase         Protein kinase domain
    8.8e-06   25.8   0.1    0.00043   20.3   0.0    2.2  2  APH             Phosphotransferase enzyme family
    1.9e-05   24.2   0.1    3.2e-05   23.4   0.1    1.4  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0029   17.2   0.1     0.0044   16.6   0.1    1.6  1  Choline_kinase  Choline/ethanolamine kinase
  ------ inclusion threshold ------
      0.023   13.6   0.0      0.031   13.2   0.0    1.1  1  Haspin_kinase   Haspin like kinase domain
       0.12   11.1   0.1        0.2   10.4   0.0    1.5  2  Pkinase_fungal  Fungal protein kinase
       0.13   13.0   0.3       0.24   12.0   0.3    1.4  1  DUF960          Staphylococcal protein of unknown function (D
       0.21   10.9   0.0        7.4    5.9   0.0    2.1  2  APH_6_hur       Aminoglycoside/hydroxyurea antibiotic resista


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.9   0.1   3.7e-59   6.6e-56       1     185 [.      78     257 ..      78     261 .. 0.95

  Alignments for each domain:
  == domain 1  score: 188.9 bits;  conditional E-value: 3.7e-59
                                   EEEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETT CS
                          RIO1   1 nVyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrh 81 
                                   +Vy++  +dg+e ++K++k+++t+F++ k+y+ + ++    k++++++++++l+ae+Ef++L++l  + v+vP+pie++rh
  gi|15669261|ref|NP_248066.1|  78 DVYTVLLSDGREAVLKFHKHGRTCFTRGKRYRGYLAD----KHHISWLYVSRLTAEREFEILNELFPI-VKVPEPIEWNRH 153
                                   69***********************************....89*************************.************ PP

                                   EEEEE--EETTEEGGBHHHCG.-.HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GTTEEETTSTT CS
                          RIO1  82 vlvmefigedgvaapklkdve.e.eeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvsQaveldhpn 159
                                   +++m  +   g ++++l+  e + +ee+++l+++++ee++k+y e g++H+DLSe+N+l+de+ ++viID++Qav++ hp+
  gi|15669261|ref|NP_248066.1| 154 AIIMGKVV--GEELKRLDLSEfMsKEEIKDLFWKIIEEVKKAY-EIGYIHGDLSEFNILLDENgDFVIIDWPQAVPKYHPD 231
                                   ********..66677666666655*******************.*******************9***************** PP

                                   HHHHHHHHHHHHHHHHHTTC-----H CS
                          RIO1 160 alefLerDveniikfFrrkgvekvde 185
                                   a+ +L+rD++n+i++F++++++k de
  gi|15669261|ref|NP_248066.1| 232 AEFYLKRDIWNVIRYFKKYKIDKEDE 257
                                   ********************997665 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0   3.7e-17   6.7e-14      19      82 .]       1      61 [.       1      61 [. 0.97
   2 ?   -2.2   0.0       2.9   5.2e+03      42      60 ..     162     180 ..     151     197 .. 0.62

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 3.7e-17
                        Rio2_N 19 mrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyLALktlvkr 82
                                  mr+he+Vp ++i + +++ e++v +rl+rl k ++++r+t    GY+++++GyD+LA++++vk+
  gi|15669261|ref|NP_248066.1|  1 MRHHEWVPLDEIVRKAKMPEKDVLYRLKRLNKFGFVVRST---YGYAVSMGGYDALAINAFVKK 61
                                  9*************************************97...7*****************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                        Rio2_N  42 kkrlsrllkaklisrktak 60 
                                    + l+rl   +++s++++k
  gi|15669261|ref|NP_248066.1| 162 GEELKRLDLSEFMSKEEIK 180
                                   4556666666666555443 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.8   3.4e-10   6.2e-07       5     142 ..      69     221 ..      66     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.4e-10
                                   EEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH....................HHHHHHHHHHHHHSCTTB--EEE CS
                       Pkinase   5 eklGeGsfGkVykaveketgkivAvKkikkekakkkke....................kkvlrEikilkklkhpnivrlye 65 
                                   +klG G+ G Vy ++  ++g++ ++K  k+ ++  ++                      ++ rE +il++l    iv++ e
  gi|15669261|ref|NP_248066.1|  69 NKLGVGKEGDVYTVL-LSDGREAVLKFHKHGRTCFTRGkryrgyladkhhiswlyvsrLTAEREFEILNEL--FPIVKVPE 146
                                   678888888888888.6777888888777766543333334556666666666666555566777777776..46888888 PP

                                   EEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SG CS
                       Pkinase  66 vfeekdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDF 142
                                    +e +++ + ++  v g+el++l   +  +s+ee+k+++++i+e ++  ++ g iH Dl   NiL+de+g++ i+D+
  gi|15669261|ref|NP_248066.1| 147 PIEWNRHAI-IMGKVVGEELKRLDL-SEFMSKEEIKDLFWKIIEEVKKAYEIGYIHGDLSEFNILLDENGDFVIIDW 221
                                   888777776.566666688988875.689***********************************************8 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.024        43       5      58 ..      71     148 ..      68     188 .. 0.62
   2 !   20.3   0.0   2.4e-07   0.00043     160     196 ..     190     224 ..     158     229 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.024
                                   E--.SSCEEEEEEETT.--EEEEE.....................E-TTS-HHHHHHHHHHHHHHHHTT-..B--B-C CS
                           APH   5 lsggasnrtylvttpa.gryvlrr.....................npparaaeeirrevallrlLakagv..pvPevl 58 
                                   l+ g + ++y v  ++ ++ vl++                     ++ ++++ +     +++  L+++ +  +vPe++
  gi|15669261|ref|NP_248066.1|  71 LGVGKEGDVYTVLLSDgREAVLKFhkhgrtcftrgkryrgyladkHHISWLYVSRLTAEREFEILNELFPivKVPEPI 148
                                   778999999999999978******555555555555555555554444444444444444444444442234566555 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 2.4e-07
                                   --SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                           APH 160 lpgelptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                                   + ++ + + +HgDl+  N+l+d++++ v  +iD+  a
  gi|15669261|ref|NP_248066.1| 190 VKKAYEIGYIHGDLSEFNILLDENGDFV--IIDWPQA 224
                                   333677899*************999999..****766 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   1.8e-08   3.2e-05      36     199 ..     108     256 ..      83     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.8e-08
                           Kdo  36 yrggllgklskdlyrfk.lgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwael 115
                                   yrg l+ k      ++  ++r++a rEf++l++L    v+vp+p+  +  ++ ++    ++ e+l+   dL +++ k    
  gi|15669261|ref|NP_248066.1| 108 YRGYLADKHH---ISWLyVSRLTAEREFEILNELFPI-VKVPEPIEWNRHAIIMG---KVVGEELKRL-DLSEFMSK---- 176
                                   5666665543...445559***************975.9******9988777665...6899999875.9******8.... PP

                           Kdo 116 aeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlr..adrwrekdLarLkrsflkie 194
                                    ee k   +k +   ++k  ++g  H+dl   nill++++     +++iD  +a ++    a+   ++d+ +  r+f+k +
  gi|15669261|ref|NP_248066.1| 177 -EEIKDLFWK-IIEEVKKAYEIGYIHGDLSEFNILLDENG----DFVIIDWPQAVPKYHpdAEFYLKRDIWNVIRYFKKYK 251
                                   .888888886.5589************************9....9***********9985667788999999999988766 PP

                           Kdo 195 ltead 199
                                   + + d
  gi|15669261|ref|NP_248066.1| 252 IDKED 256
                                   66655 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.4e-06    0.0044     128     172 ..     177     222 ..      51     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.4e-06
                                   HHHHHTHHHHHH..CHGG-EEEE-S--SGGGEEE.-CTTEEEE--GT CS
                Choline_kinase 128 ekelekleklle..elespvvfcHnDlqegNillnkeekklvlIDFE 172
                                   e+  + + k++e  ++ +++ + H Dl e Nill +e+++ v+ID+ 
  gi|15669261|ref|NP_248066.1| 177 EEIKDLFWKIIEevKKAYEIGYIHGDLSEFNILL-DENGDFVIIDWP 222
                                   2222333455542355567***************.9**********6 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.7e-05     0.031     191     254 ..     159     224 ..     135     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                 Haspin_kinase 191 kdkGtdLeev...klkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnvtlidlkls 254
                                   k  G++L+++   ++ s ++++ +fw+i++ ++ a  +  + H dL+  niL+d+n+   +id+  +
  gi|15669261|ref|NP_248066.1| 159 KVVGEELKRLdlsEFMSKEEIKDLFWKIIEEVKKA-YEIGYIHGDLSEFNILLDENGDFVIIDWPQA 224
                                   667888888744567788999*****987766655.345678*********************8766 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00011       0.2     299     343 ..     170     213 ..     114     232 .. 0.89
   2 ?   -3.1   0.0       1.4   2.5e+03     196     217 ..     237     258 ..     235     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                Pkinase_fungal 299 iekaespkellealrDaIkghrsLflkagiLHrDiSenNilitds 343
                                   ++++ s++e+   +   I+  ++ + ++g++H D Se Nil+ ++
  gi|15669261|ref|NP_248066.1| 170 LSEFMSKEEIKDLFWKIIEEVKKAY-EIGYIHGDLSEFNILLDEN 213
                                   678899999999999999999999*.***************9854 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                Pkinase_fungal 196 ergvegvarlvahedveekddd 217
                                   +r++++v r++++ ++ ++d++
  gi|15669261|ref|NP_248066.1| 237 KRDIWNVIRYFKKYKIDKEDEK 258
                                   5789999999999999855554 PP

>> DUF960  Staphylococcal protein of unknown function (DUF960)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   0.00014      0.24      15      71 ..     178     239 ..     174     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHHHHHTTTTS---S....EEEEEE..EEETTEEEEEEEETT---EEEEEEEEE-- CS
                        DUF960  15 elqlllWeiidellkgvvpldy....lqiFeL..kenkgkltiehsqeepeyekeydlplkyd 71 
                                   e+ +l+W+ii+e  k+  +  y    l  F++   en   + i + q +p+y+ + ++ lk d
  gi|15669261|ref|NP_248066.1| 178 EIKDLFWKIIEEV-KKAYEIGYihgdLSEFNIllDENGDFVIIDWPQAVPKYHPDAEFYLKRD 239
                                   899*********9.777888772222568*9666999999************99988875544 PP

>> APH_6_hur  Aminoglycoside/hydroxyurea antibiotic resistance kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.035        62      15      35 ..      76      96 ..      69     106 .. 0.86
   2 ?    5.9   0.0    0.0041       7.4     153     183 ..     190     220 ..     174     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.035
                     APH_6_hur 15 sSlvlkVlradGapAvlKlak 35
                                    +v  Vl  dG  AvlK  k
  gi|15669261|ref|NP_248066.1| 76 EGDVYTVLLSDGREAVLKFHK 96
                                  56899*************987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0041
                     APH_6_hur 153 leepselrpLHgdlhhenvLagerrgWlaid 183
                                   ++++ e++ +Hgdl   n+L  e+    +id
  gi|15669261|ref|NP_248066.1| 190 VKKAYEIGYIHGDLSEFNILLDENGDFVIID 220
                                   67899***************99977777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1876.85
//
Query:       gi|15669262|ref|NP_248067.1|  [L=112]
Description: hypothetical protein MJ_1074 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.059   13.5   0.7       0.42   10.8   0.1    2.0  2  Ku_PK_bind  Ku C terminal domain like


Domain annotation for each model (and alignments):
>> Ku_PK_bind  Ku C terminal domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.017   3.1e+02      29      52 ..      11      35 ..       2      50 .. 0.54
   2 ?   10.8   0.1   2.4e-05      0.42       7      40 ..      49      82 ..      45      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.017
                    Ku_PK_bind 29 vIeqlvedslgd.ssydkaveclka 52
                                   I++ ++d  +  + y+ ++e +k 
  gi|15669262|ref|NP_248067.1| 11 LIHKKIKDEREAdELYNAIIEIIKE 35
                                  4444444444433444444444443 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 2.4e-05
                    Ku_PK_bind  7 kkllaqkdeedlvekavkqlksvIeqlvedslgd 40
                                  k+ la+k+++dlv + +k ++++I + v++ +++
  gi|15669262|ref|NP_248067.1| 49 KDELATKKDIDLVREEMKAMEERILRYVDNRFNQ 82
                                  6678888889*******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1733  (0.096659); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 756.94
//
Query:       gi|15669263|ref|NP_248068.1|  [L=474]
Description: anthranilate synthase component I TrpE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-96  320.8   0.0    8.8e-96  320.4   0.0    1.2  1  Chorismate_bind  chorismate binding enzyme
    3.8e-31  108.2   1.4    2.7e-29  102.2   0.0    2.5  2  Anth_synt_I_N    Anthranilate synthase component I, N termina


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.4   0.0  9.8e-100   8.8e-96       1     258 []     202     461 ..     202     461 .. 0.97

  Alignments for each domain:
  == domain 1  score: 320.4 bits;  conditional E-value: 9.8e-100
                                   .HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEETT. CS
               Chorismate_bind   1 sredYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkvegg. 80 
                                   s+e++ eav+k+ke+i agd+++vvlsrr+++ l+ ++d+l++y+++r+ np+py+++l+++d++++g+SPE+l++++ + 
  gi|15669263|ref|NP_248068.1| 202 SKEEFIEAVKKAKEYIFAGDIFQVVLSRRIEIDLD-NLDHLKIYKKVREINPSPYMYYLDFGDRKIIGSSPEILVRTDYKd 281
                                   5899*****************************65.79*************************************966445 PP

                                   ..SEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEEEEE CS
               Chorismate_bind  81 ..rrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlvsti 159
                                     r + t+piaGT++rgkt+eed++le++ll+deKeraEh+m+vdl+rnd+gk++k+g+v+v++++ +e+ys+v+h+vs++
  gi|15669263|ref|NP_248068.1| 282 nkRLVITRPIAGTIRRGKTEEEDKELEKKLLSDEKERAEHVMLVDLARNDIGKISKFGTVEVTDFMIIEKYSHVQHIVSNV 362
                                   5599***************************************************************************** PP

                                   EEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETTEEEEEEEE CS
               Chorismate_bind 160 egelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdkelrlgaGa 240
                                    gelk++ +++ ++ka+fP+g+++GaPk rameii+elE++ Rg+Y+G vgy++ d+ ++la++IRt v+++++ ++++Ga
  gi|15669263|ref|NP_248068.1| 363 VGELKDNYDSFLAVKATFPAGTLSGAPKVRAMEIIEELEKTWRGPYGGGVGYFGWDDLMDLAITIRTFVISKNKGYIQVGA 443
                                   **********************************************************************9999******* PP

                                   EEETT--HHHHHHHHHHH CS
               Chorismate_bind 241 GIvadSdpeaEyeEtlaK 258
                                   GIvadS pe+E+eEt+ K
  gi|15669263|ref|NP_248068.1| 444 GIVADSIPENEWEETERK 461
                                   ***************998 PP

>> Anth_synt_I_N  Anthranilate synthase component I, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0     3e-33   2.7e-29       2     139 ..       9     156 ..       8     159 .. 0.88
   2 !    4.2   0.4    0.0052        47      90     101 ..     407     418 ..     345     428 .. 0.80

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 3e-33
                 Anth_synt_I_N   2 dltplsvylklaeeehkflLeSaeneggegrySfigldpflelkskngeveveg.......pegeeleeeepldalrelle 75 
                                   d+ pl vy+++++ e++flLeSae+  + +ryS++g ++ +++  kng+++ve        +++ e ++e pldalre+ +
  gi|15669263|ref|NP_248068.1|   9 DVCPLDVYEQIRG-ENTFLLESAEGVPKVARYSILGKAE-GKVIFKNGKLKVESftefgdkAKDLEGKYECPLDALREVRN 87 
                                   578**********.66********99999**********.9999***********9999655555555666********** PP

                 Anth_synt_I_N  76 rfrsaedse..ptelpfvgGlvGylgYDlvreieklp...ksakddlnlpdarlilydtlivfDhkerr 139
                                   ++ ++ d +  +  ++f gGlvGyl+YD++r++ +l+    ++++dl++pda++++++++i fD ke+ 
  gi|15669263|ref|NP_248068.1|  88 EYLKYIDISniEPIPRFKGGLVGYLSYDIIRYWIDLSninPKPINDLKFPDAEFFIVKDFISFDLKEKV 156
                                   ***9998886655566****************99888776779*********************99986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0052
                 Anth_synt_I_N  90 fvgGlvGylgYD 101
                                    +gG vGy+g D
  gi|15669263|ref|NP_248068.1| 407 PYGGGVGYFGWD 418
                                   69********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3141.69
//
Query:       gi|15669264|ref|NP_248069.1|  [L=337]
Description: hypothetical protein MJ_1076 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-61  208.5  10.4    1.3e-61  208.5  10.4    1.8  2  ATPase_2      ATPase domain predominantly from Archaea
    1.1e-11   45.4   0.0    1.6e-11   44.9   0.0    1.3  1  AAA_16        AAA ATPase domain
    1.4e-08   35.1   0.0      3e-08   34.0   0.0    1.5  1  AAA_22        AAA domain
    5.9e-07   29.6   7.7      9e-05   22.5   0.1    3.1  4  AAA_14        AAA domain
    1.4e-05   25.5   0.2    5.4e-05   23.6   0.2    1.9  1  AAA           ATPase family associated with various cellular 
     0.0001   21.2   0.5      0.089   11.5   0.0    2.9  3  RNA12         RNA12 protein
    0.00042   20.2   0.9       0.11   12.3   0.0    3.1  3  TK            Thymidine kinase
    0.00066   18.7   0.1    0.00066   18.7   0.1    1.9  2  AAA_PrkA      PrkA AAA domain
     0.0073   16.7   0.3      0.065   13.6   0.0    2.7  4  RNA_helicase  RNA helicase
  ------ inclusion threshold ------
      0.011   15.2   0.0       0.02   14.4   0.0    1.4  1  AAA_7         P-loop containing dynein motor region
      0.022   14.2   0.1        1.6    8.1   0.0    2.5  2  TniB          Bacterial TniB protein
      0.027   13.7   0.0      0.047   12.9   0.0    1.4  1  DUF2075       Uncharacterized conserved protein (DUF2075)
      0.065   12.7   0.0       0.11   11.9   0.0    1.3  1  RecA          recA bacterial DNA recombination protein
      0.074   13.6   0.1       0.87   10.1   0.0    2.3  2  ABC_tran      ABC transporter
      0.082   12.8   0.0         10    6.0   0.0    2.2  2  NACHT         NACHT domain
      0.093   12.9   0.0       0.26   11.4   0.0    1.8  2  AAA_33        AAA domain
       0.14   11.9   0.0       0.35   10.7   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.5  10.4   1.2e-64   1.3e-61       1     233 []       3     236 ..       3     236 .. 0.97
   2 ?   -0.9   0.6       1.2   1.3e+03      54      85 ..     267     293 ..     247     332 .. 0.49

  Alignments for each domain:
  == domain 1  score: 208.5 bits;  conditional E-value: 1.2e-64
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...eeeekkkl 78 
                                   F++Rekel++l+++++ epn+i+f+YGp++sGK+++++++i++le+++  v++y++lr++++ ++def+    e+++kk+l
  gi|15669264|ref|NP_248069.1|   3 FYNREKELNYLKNYVQLEPNSILFVYGPKSSGKSTVMMRVIKELENSN-IVFFYYNLRKYATPTKDEFLSiffEKSDKKYL 82 
                                   9*******************************************8866.7******************************* PP

                      ATPase_2  79 ekal..giavpkaeleeilk...eksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltk 154
                                    ++l  + ++ k+ +ee ++    k ++vf++i++ ++ + k+gk+++++iDelqkl+++++n+ ++l++eL+nl++sltk
  gi|15669264|ref|NP_248069.1|  83 LNKLeiNLKIFKFGIEENFDfnnIKLNDVFAKINESINTVIKDGKRPVLVIDELQKLKNIYFNSGKSLLNELFNLFVSLTK 163
                                   **99667789999******9999999******************************************************* PP

                      ATPase_2 155 ekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkeleelskedfeeiyryvGGkPkalvel 233
                                    +hlc+vicl+S++lfi+ vy++s l + ++y+l+d+l+k+ ++++lke     e+++k++++++ +y+ + P+++ +l
  gi|15669264|ref|NP_248069.1| 164 MEHLCHVICLTSDTLFIDNVYRNSSLSEASEYYLIDWLKKDDIKKILKE-----EGFNKKEIDYCLNYL-SLPYEISQL 236
                                   *************************************************.....799************.999999876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.2
                      ATPase_2  54 yialreesiskldefieeeeekkklekalgia 85 
                                    ++l+ee+i k+ ++++     +k++   +++
  gi|15669264|ref|NP_248069.1| 267 TSDLNEEEIYKVLSKFK-----DKIKINYKKD 293
                                   33333333333322211.....1111111222 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   1.5e-14   1.6e-11       1     159 [.       2     155 ..       2     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 1.5e-14
                        AAA_16   1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalare 79 
                                   r++ Re+el+ L+++++   +  p ++++++G++ +GKs+++ ++ ++le ++++f++ + +++  a+p    ++++++++
  gi|15669264|ref|NP_248069.1|   2 RFYNREKELNYLKNYVQ--LE--PnSILFVYGPKSSGKSTVMMRVIKELENSNIVFFYYNLRKY--ATPTKDeFLSIFFEK 76 
                                   6999*****88888887..33..338**************************************..9999777*****999 PP

                        AAA_16  80 ellrqlldeaesaeleawrekleealaavpelagaeasrllellkrll.allsrderplvlvlDdlqwade....aslqll 155
                                   +  + ll+++e  +l  ++  +ee++         + +++++++++ +   ++  ++  vlv+D+lq+++     +  +ll
  gi|15669264|ref|NP_248069.1|  77 SDKKYLLNKLEI-NLKIFKFGIEENFD----FNNIKLNDVFAKINESInTVIKD-GKRPVLVIDELQKLKNiyfnSGKSLL 151
                                   999999999888.99999999999999....44445599999999999556666.666*********98876665555555 PP

                        AAA_16 156 aaLl 159
                                    +L+
  gi|15669264|ref|NP_248069.1| 152 NELF 155
                                   5554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   2.8e-11     3e-08       5     126 ..      22     170 ..      18     179 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.8e-11
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellralglelka............. 70 
                                    +il+v+G++ +GK+t++ r+ ++l++        + +v  +++l +  ++++   e+l+++ ++ ++             
  gi|15669264|ref|NP_248069.1|  22 NSILFVYGPKSSGKSTVMMRVIKELEN--------SNIVffYYNLRKYATPTKD--EFLSIFFEKSDKkyllnkleinlki 92 
                                   689**********************74........4444469999999966655..44444444334445789999***** PP

                        AAA_22  71 ...........erlsseellealeqalrarav...ielliiDEaqhlr.....s.....eealeeLrsllnlsrkgvqli 126
                                              ++ ++ ++++++++ +++  +   +++l+iDE q+l      s     +e+++ ++sl +    ++ ++
  gi|15669264|ref|NP_248069.1|  93 fkfgieenfdfNNIKLNDVFAKINESINTVIKdgkRPVLVIDELQKLKniyfnSgksllNELFNLFVSLTK--MEHLCHV 170
                                   ***********8888888888888888888888888***********766665273444444444455554..4444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   8.6e-08     9e-05       2      68 ..      22      82 ..      21      85 .. 0.68
   2 !   10.3   0.9   0.00049      0.52      39      88 ..      98     152 ..      79     182 .. 0.60
   3 ?   -1.2   0.0       1.9     2e+03      66      80 ..     176     190 ..     142     222 .. 0.57
   4 ?   -1.7   0.1       2.6   2.7e+03      57      57 ..     290     290 ..     246     323 .. 0.58

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.6e-08
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyi..nldderdkkladpekllelileklkeekktyl 68
                                  + il++ G++ +GK+t++ ++ikel   +++i+++  nl +  + +   ++++l++++ek    +k+yl
  gi|15669264|ref|NP_248069.1| 22 NSILFVYGPKSSGKSTVMMRVIKELE--NSNIVFFyyNLRKYATPT---KDEFLSIFFEKS---DKKYL 82
                                  5799******************9988..555555500555544432...334788888872...34444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00049
                        AAA_14  39 dderdkkladpe....kllelileklkeekktylflDEiqevpew.ekalkslvd 88 
                                   +++ d ++ + +    k++e i   +k+ k+ +l++DE q+++++ ++  ksl++
  gi|15669264|ref|NP_248069.1|  98 EENFDFNNIKLNdvfaKINESINTVIKDGKRPVLVIDELQKLKNIyFNSGKSLLN 152
                                   333333222222111145555555455579999*********8851355555555 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.9
                        AAA_14  66 tylflDEiqevpewe 80 
                                     lf+D + + ++++
  gi|15669264|ref|NP_248069.1| 176 DTLFIDNVYRNSSLS 190
                                   334444444433333 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 2.6
                        AAA_14  57 l 57 
                                    
  gi|15669264|ref|NP_248069.1| 290 Y 290
                                   1 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.2   5.1e-08   5.4e-05       2     116 ..      26     181 ..      25     192 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.1e-08
                                   EEESSTTSSHHHHHHHHHHHHTHE.......................EEEEETTTCS.SS..................... CS
                           AAA   2 llyGppGtGKTllakavakelgve.......................fleisgsell.sk..................... 37 
                                    +yGp+  GK++++  v+kel+ +                       f+e s ++ l +k                     
  gi|15669264|ref|NP_248069.1|  26 FVYGPKSSGKSTVMMRVIKELENSnivffyynlrkyatptkdeflsiFFEKSDKKYLlNKleinlkifkfgieenfdfnni 106
                                   68******************9533244444455555566666666664444444433344888888888888885555555 PP

                                   ....STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGG CS
                           AAA  38 ....yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdk 114
                                       ++ + +++i+ ++k+     k  +l+iDE+ +l +       +++++++n+L++ +  ++k e+ + vi+ t +   
  gi|15669264|ref|NP_248069.1| 107 klndVFAKINESINTVIKDG----KRPVLVIDELQKLKNIY----FNSGKSLLNELFNLFVSLTKMEHLCHVICLTSDTLF 179
                                   33333333333444444332....469**********6666....678999***********************9988655 PP

                                   ST CS
                           AAA 115 ld 116
                                   +d
  gi|15669264|ref|NP_248069.1| 180 ID 181
                                   55 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   8.4e-05     0.089       1      44 [.       6      48 ..       6      70 .. 0.86
   2 !    5.6   0.0     0.005       5.3     137     194 ..     116     178 ..      76     194 .. 0.79
   3 ?    0.8   0.4      0.15   1.5e+02     271     364 ..     216     301 ..     185     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.4e-05
                         RNA12  1 RkekiedlkewleEnvntFivvkGPrGSGkkeLvldrvlkdrkk 44
                                  R+++ + lk++++ ++n+ + v GP+ SGk+  v+ rv+k+ ++
  gi|15669264|ref|NP_248069.1|  6 REKELNYLKNYVQLEPNSILFVYGPKSSGKST-VMMRVIKELEN 48
                                  7888999***********************87.56789988766 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.005
                         RNA12 137 keedyleahpeakPvvvidnflakaek....ngvvykklaeWaasLvqs.niahVifltedvs 194
                                   +e+     ++ ++Pv+vid+ ++ ++      + + ++l +   sL+++  + hVi lt+d+ 
  gi|15669264|ref|NP_248069.1| 116 NESINTVIKDGKRPVLVIDELQKLKNIyfnsGKSLLNELFNLFVSLTKMeHLCHVICLTSDTL 178
                                   4444555678899*******99876654544678999999999999987258*******9975 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.15
                         RNA12 271 dlkeldealeklGGRltDLealvrrvksgetpkeAveeiieqsaeeilkmflldseeakkakwtkeqaWklikklskkgsi 351
                                   ++ke+d +l+ l     ++ +l++  k g +++e +++ i+  a  i+  +l      +++++++e+ +k+++k  +k +i
  gi|15669264|ref|NP_248069.1| 216 NKKEIDYCLNYLSL-PYEISQLINNKKLGLSVEETIKRWINIEADGIK--YLI-----DTSDLNEEEIYKVLSKFKDKIKI 288
                                   55666666666643.356778888889999999999999999998885..555.....46778899999999999999999 PP

                         RNA12 352 eynellleelfkg 364
                                   +y++ +++e +k 
  gi|15669264|ref|NP_248069.1| 289 NYKKDVKKEEMKY 301
                                   9999888887765 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00011      0.11       2      30 ..      23      51 ..      22      69 .. 0.86
   2 ?    0.5   0.0      0.45   4.7e+02      63      93 ..     113     142 ..      74     144 .. 0.70
   3 ?    4.0   0.0     0.038        40      11      86 ..     145     223 ..     142     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                            TK  2 sielilgpmfaGKsteLlrrvkryqlaek 30
                                  si +++gp  +GKst ++r +k+++ ++ 
  gi|15669264|ref|NP_248069.1| 23 SILFVYGPKSSGKSTVMMRVIKELENSNI 51
                                  689*******************9988765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.45
                            TK  63 tssleeikeeleeedvdvvlvDEaqFfeqdi 93 
                                   ++  e+i++++++ +  v+++DE q ++ +i
  gi|15669264|ref|NP_248069.1| 113 AKINESINTVIKDGKRPVLVIDELQKLK-NI 142
                                   3444567777777788999****99888.55 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.038
                            TK  11 faGKs..teLlrrvkryqlaekkvvvikaakdnRysegkvvthdgisleak..ksktssleeikeeleeedvdvvlvDEa 86 
                                   ++GKs  +eL +    +++ e  + vi  + d+ +   +v+  + +s  ++   ++  + ++ik++l+ee ++   +D +
  gi|15669264|ref|NP_248069.1| 145 NSGKSllNELFNLFVSLTKMEHLCHVICLTSDTLFID-NVYRNSSLSEASEyyLIDWLKKDDIKKILKEEGFNKKEIDYC 223
                                   8999966699999***********************6.699888888777755567777888999999888887777766 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   6.2e-07   0.00066      86     150 ..      20      91 ..       4      99 .. 0.81
   2 ?   -1.9   0.3       1.2   1.2e+03     304     328 ..     285     309 ..     245     321 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.2e-07
                      AAA_PrkA  86 erkqilyllGPvggGksslverlkklleaa....piyal..egsPvfeePlhli.peelrkkleeeygirle 150
                                   e   il++ GP ++Gks+++ r+ k le++      y l    +P ++e l+++  ++++k l ++++i+l+
  gi|15669264|ref|NP_248069.1|  20 EPNSILFVYGPKSSGKSTVMMRVIKELENSnivfFYYNLrkYATPTKDEFLSIFfEKSDKKYLLNKLEINLK 91 
                                   4568*******************999*99954433356676679*********9888999999999999775 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                      AAA_PrkA 304 vvkvPyclrvseekkiyekllkese 328
                                   ++k+ y   v++e+  y k+l e e
  gi|15669264|ref|NP_248069.1| 285 KIKINYKKDVKKEEMKYIKFLIENE 309
                                   4666677777766666666666655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       8.4   8.9e+03      34      49 ..       3      18 ..       2      21 .. 0.84
   2 !   13.6   0.0   6.1e-05     0.065       1      43 [.      25      69 ..      25      81 .. 0.72
   3 ?   -1.3   0.0       2.8   2.9e+03      51      76 ..     129     157 ..     123     180 .. 0.65
   4 ?   -2.1   0.0       4.9   5.2e+03      16      36 ..     165     185 ..     145     225 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8.4
                  RNA_helicase 34 vysrnpeddfwdgYtg 49
                                  +y r++e +++++Y +
  gi|15669264|ref|NP_248069.1|  3 FYNREKELNYLKNYVQ 18
                                  8999999999999976 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.1e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl......klkkkdsvysrnpeddf 43
                                  +++yGp+  GKSt++ +++k+l+++       +     + y+ +++d+f
  gi|15669264|ref|NP_248069.1| 25 LFVYGPKSSGKSTVMMRVIKELENSNivffyyN----LRKYATPTKDEF 69
                                  589*******************97655533321....333444555554 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.8
                  RNA_helicase  51 evvvidDfgqvkdee.nps..dlaelirl 76 
                                   +v+vid++ + k+ + n     l+el++l
  gi|15669264|ref|NP_248069.1| 129 PVLVIDELQKLKNIYfNSGksLLNELFNL 157
                                   67888888888877765432344444444 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 4.9
                  RNA_helicase  16 keLakallkklklkkkdsvys 36 
                                   ++L++ ++ ++++   d+vy 
  gi|15669264|ref|NP_248069.1| 165 EHLCHVICLTSDTLFIDNVYR 185
                                   444444444444444445543 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.9e-05      0.02      34      77 ..      23      66 ..       8      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                         AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanq 77
                                    ++++Gp+ +GK++++++++k+l+++++++   n+ ++ ++++
  gi|15669264|ref|NP_248069.1| 23 SILFVYGPKSSGKSTVMMRVIKELENSNIVFFYYNLRKYATPTK 66
                                  344567***************************99999988764 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.045        47      22      57 ..       9      44 ..       4      50 .. 0.76
   2 ?    8.1   0.0    0.0015       1.6      99     146 ..     107     154 ..      97     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.045
                          TniB 22 rLeeLleypkrkrmpnlllvGdsnnGKtmivekFar 57
                                  +L+ L +y + +  + l ++G+   GK++++ +  +
  gi|15669264|ref|NP_248069.1|  9 ELNYLKNYVQLEPNSILFVYGPKSSGKSTVMMRVIK 44
                                  56666666666666778999*********9988655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0015
                          TniB  99 kararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnal 146
                                   k ++  +k+++ + +++++ k  vL+iDE+++l +   ++ + +ln l
  gi|15669264|ref|NP_248069.1| 107 KLNDVFAKINESINTVIKDGKRPVLVIDELQKLKNIYFNSGKSLLNEL 154
                                   5667778889999999*****************999999999888877 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.4e-05     0.047       2     119 ..      23     154 ..      22     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.4e-05
                       DUF2075   2 avvlVtGvaGtGKtvvllnllaeledde........................eertavylsvNhplvl.vlrealakke.. 55 
                                   ++++V G   +GK+ v+++++ ele+++                        e++ ++yl+   + +l + +  ++++   
  gi|15669264|ref|NP_248069.1|  23 SILFVYGPKSSGKSTVMMRVIKELENSNivffyynlrkyatptkdeflsiffEKSDKKYLLNKLEINLkIFKFGIEENFdf 103
                                   689*********************777688888888888888888899999888888888766665552456667777788 PP

                       DUF2075  56 ekkkkkeafeklssfinnlsefkkaeekkeepkedvvivDEAhrlltksdqaekqseenqlkel 119
                                   ++ k +++f+k ++ in++          ++ k  v+++DE ++l +    +++ s++  l+el
  gi|15669264|ref|NP_248069.1| 104 NNIKLNDVFAKINESINTVI---------KDGKRPVLVIDELQKLKN---IYFN-SGKSLLNEL 154
                                   89999***************.........99999***********98...3333.345555444 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.11      55      81 ..      24      50 ..      19      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                  EEEEEESTTSSHHHHHHHHHHHHHHTT CS
                          RecA 55 iieiyGpessGkttlalhaiaeaqkkg 81
                                  i+ +yGp+ssGk+t+ +++i e ++++
  gi|15669264|ref|NP_248069.1| 24 ILFVYGPKSSGKSTVMMRVIKELENSN 50
                                  7789****************9987765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00083      0.87       6      37 ..      17      48 ..      13     136 .. 0.87
   2 ?    1.2   0.1      0.45   4.7e+02      45      95 ..     202     285 ..     146     302 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00083
                                  EEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  6 lklkegekvaivGenGaGKStLlkllagllkp 37
                                  ++l++++++ + G+  +GKSt+++ ++++l++
  gi|15669264|ref|NP_248069.1| 17 VQLEPNSILFVYGPKSSGKSTVMMRVIKELEN 48
                                  68999*****************9888887764 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.45
                                   TTCEGGG..B-HHHCCHCEEEE-SS--S-TTSB.HHHH..............................HHHTCHHHHHHHS CS
                                   xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx.xxxx..............................xxxxxxxxxxxxx RF
                      ABC_tran  45 dgkdlke..qeleslrkeigvlpqepqlfpelt.vren..............................esdeeiekalskl 92 
                                   +++d+k+  +e+ + +kei ++    +l +e++ + +n                                +eei+k+lsk+
  gi|15669264|ref|NP_248069.1| 202 KKDDIKKilKEEGFNKKEIDYCLNYLSLPYEISqLINNkklglsveetikrwinieadgikylidtsdLNEEEIYKVLSKF 282
                                   556666666666677777777777777777766433336777777777777777777777777776655566677777777 PP

                                   TTG CS
                                   xxx RF
                      ABC_tran  93 glk 95 
                                   ++k
  gi|15669264|ref|NP_248069.1| 283 KDK 285
                                   765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0095        10       2      44 ..      24      60 ..      23      82 .. 0.82
   2 ?    4.7   0.0     0.025        26      67     160 ..     113     211 ..     105     217 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0095
                                  CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTT CS
                         NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslre 44
                                  ++++ G+  sGK+t + +++ ++  ++       ++F+ +lr+
  gi|15669264|ref|NP_248069.1| 24 ILFVYGPKSSGKSTVMMRVIKELENSN------IVFFYYNLRK 60
                                  57899*****************99887......4556666665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.025
                                   SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHH....HCTTSSCE. CS
                         NACHT  67 apvsevwavllelperlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrd....leeqleea. 142
                                   a+++e ++ +++  +r +l++D l +l+++  +++k  +++l++  ++ + +   + ++ +++++l        ++l+ea 
  gi|15669264|ref|NP_248069.1| 113 AKINESINTVIKDGKRPVLVIDELQKLKNIYFNSGKSLLNELFNLFVSLTKMEHLCHVICLTSDTLFIdnvyRNSSLSEAs 193
                                   55667778899999999***********98888555555555544455555666666666666666443444333343336 PP

                                   ..EEEE--TCCHHHHHHH CS
                         NACHT 143 ivlevegfsesrrkqlvr 160
                                   +++ +  ++++++k+++ 
  gi|15669264|ref|NP_248069.1| 194 EYYLIDWLKKDDIKKILK 211
                                   777777777777777765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00025      0.26       2      24 ..      25      47 ..      24     125 .. 0.88
   2 ?   -2.1   0.0       3.7   3.9e+03      21      39 ..     165     185 ..     146     213 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                        AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                                  +++ G++ sGKst+  r++k+l 
  gi|15669264|ref|NP_248069.1| 25 LFVYGPKSSGKSTVMMRVIKELE 47
                                  6889****************997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.7
                        AAA_33  21 kklg.avllssdtlrr.rlfg 39 
                                   ++l  ++ l+sdtl+  +++ 
  gi|15669264|ref|NP_248069.1| 165 EHLChVICLTSDTLFIdNVYR 185
                                   333357778888865424444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00033      0.35      17      39 ..      17      39 ..      11      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                        AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                  ++++++++ ++ Gp  sGKST++
  gi|15669264|ref|NP_248069.1| 17 VQLEPNSILFVYGPKSSGKSTVM 39
                                  67788889999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1581  (0.0881812); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2490.61
//
Query:       gi|15669265|ref|NP_248070.1|  [L=521]
Description: seryl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-55  187.3   4.6    2.8e-55  186.5   4.6    1.4  1  tRNA_bind_4     tRNA-binding domain
    3.1e-09   37.0   0.0    1.6e-08   34.7   0.0    2.0  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
      0.041   13.8   1.4       0.17   11.7   0.4    2.5  2  DNA_pol3_a_NII  DNA polymerase III polC-type N-terminus II


Domain annotation for each model (and alignments):
>> tRNA_bind_4  tRNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.5   4.6   4.7e-59   2.8e-55       1     160 [.       3     165 ..       3     166 .. 0.96

  Alignments for each domain:
  == domain 1  score: 186.5 bits;  conditional E-value: 4.7e-59
                                   EEEEEEEEEEESS-SCC.CHHHHHHHHHHHCCTGGGTTSSTTT.S.SSEEEEEEE-SSEEEEEEEEESSS-HHHHHHHHHH CS
                   tRNA_bind_4   1 lkfelkgklklskdiee.aeeeieefieeanktiLkkGvpegkeeegakitewkiegnelkleieSgryvRahdallrlkk 80 
                                   l+f+l+gk+++sk+++e a++++ee++++a++ i+ kGvp+gke+e++ki+++++egn lkl+i Sg+y+Rah++l+rl+k
  gi|15669265|ref|NP_248070.1|   3 LTFDLDGKIIFSKELSEeAKNAVEEVLKNADS-IFLKGVPKGKENEASKIKSYEFEGNILKLKIASGTYTRAHEGLIRLRK 82 
                                   57*************776*********99776.************************************************ PP

                                   HHHHHCCCCCS--EEEEEEEEEEEEEE-SS--....HH---TTECEEEEETTEEEEEEES--HHHHHTTHHHHHHHHHHHH CS
                   tRNA_bind_4  81 plaeklGkkyriGvRgikveeyeieiesekel....kaekipeveeveveegkitlelkdvdeselkkrvvdRiiklveek 157
                                   plaeklG+++riGvRgi++++y i+ie++++     +  k+pe+e ++ve +ki+l++kd++eselk++++dR+ik+v+++
  gi|15669265|ref|NP_248070.1|  83 PLAEKLGRNFRIGVRGIEIDNYVITIETDEDKakklEGIKVPECE-AKVEGNKIILTFKDIGESELKRNIIDRAIKFVKTE 162
                                   ****************************98877888999*****9.*********************************** PP

                                   HCC CS
                   tRNA_bind_4 158 iek 160
                                   +ek
  gi|15669265|ref|NP_248070.1| 163 LEK 165
                                   997 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.2   1.2e+03      62      93 ..       5      38 ..       4      92 .. 0.77
   2 !   34.7   0.0   2.7e-12   1.6e-08      10     179 .]     310     489 ..     302     489 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.2
                                  EEEEEEEEEESG..GGHHHHHHHHHHHHHHHHHH CS
                                  xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b 62 Fhqkdgyvfhae..aslddslrdlikaisrifer 93
                                  F+ ++  +f++e  +++++ +++++k ++ if +
  gi|15669265|ref|NP_248070.1|  5 FDLDGKIIFSKElsEEAKNAVEEVLKNADSIFLK 38
                                  5666777777755588999999999999999865 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 2.7e-12
                                   EEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEE.EEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  10 eyiLkPtneetfvelirdevlrs.krLPlklyqi.qtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikais 88 
                                    y+L P ++e+f++ +  ev+   k  P+ +++  +  yR E    rGL Rv eF   +++ +++++ +++   + +k ++
  gi|15669265|ref|NP_248070.1| 310 GYVLAPAQCEPFYQFFEGEVIDVdK--PIMFFDRsGWTYRWEGGGARGLDRVNEFLRVECVWIGSPEFVEETRDKTLKYAE 388
                                   599****************886657..***99861679*****98**********************99999999****** PP

                                   HHHHHTT.SCEEEEEE.....GTTSC......BTTSEEEEEEEEETT...TSEEEEEEEEEEEETHHHHHTTEEEECTTSS CS
                                   xxxxxxxxxxxxxxxx.....xxxxx......xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  89 riferlglefraiiel.....msaks......adykdkkefeavses...ltkgieigtiqklgtrlserlgatvldennr 155
                                   ++ e+l le+ + +++      ++k+      +   +k+e+ ++ +     +kg+ + +++  gt+++e ++++      +
  gi|15669265|ref|NP_248070.1| 389 KLAEKLDLEYWVEVGDdpfylEGRKKedrgieFPDVPKYEMRLWLPHikdERKGVAVTSANVHGTHFVEGFRIKD----YK 465
                                   *********9766666565542222255666644555555555555423257888899999999*****999954....47 PP

                                   EEEEEEEEEEEEHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b 156 eksvimicaaigveRllsaileqn 179
                                    ++v ++c + g++R +  +l+q+
  gi|15669265|ref|NP_248070.1| 466 GRRVWTGCTGYGITRWVVGYLAQY 489
                                   8899***********999888775 PP

>> DNA_pol3_a_NII  DNA polymerase III polC-type N-terminus II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.43   2.6e+03      22      39 ..      50      67 ..      46      72 .. 0.79
   2 ?   11.7   0.4   2.9e-05      0.17      23      59 ..     125     160 ..     123     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.43
                DNA_pol3_a_NII 22 kkqepevegnkliikvpn 39
                                  k  ++e+egn l++k+ +
  gi|15669265|ref|NP_248070.1| 50 KIKSYEFEGNILKLKIAS 67
                                  567899****99998766 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.9e-05
                DNA_pol3_a_NII  23 kqepevegnkliikvpneiiaealkkkkldklleeyi 59 
                                   ++e +vegnk+i +++++i  + lk++ +d  ++ ++
  gi|15669265|ref|NP_248070.1| 125 ECEAKVEGNKII-LTFKDIGESELKRNIIDRAIKFVK 160
                                   6999*******6.**************9999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3355.20
//
Query:       gi|15669266|ref|NP_248071.1|  [L=234]
Description: hypothetical protein MJ_1078 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-34  120.4   9.7    1.2e-34  120.3   9.7    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
       0.45    9.9   2.9       0.27   10.6   0.5    1.9  2  DUF5305          Family of unknown function (DUF5305)


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   9.7   1.3e-38   1.2e-34      78     301 .]       1     214 [.       1     214 [. 0.84

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 1.3e-38
               LPG_synthase_TM  78 lfvnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalallllav 158
                                   +f+n+++P++l G+v+r yllk+k++ s s  +++v++er++dl+a++ l++++++l +    +   +l+ + ++++++++
  gi|15669266|ref|NP_248071.1|   1 MFINSLVPAKL-GDVYRGYLLKKKTNESISLGVGTVFIERVFDLVAMISLLFISAYLSFKSDIPKE-ILYSIKWGVIIILF 79 
                                   59*********.***********************************************9999988.77777777766666 PP

               LPG_synthase_TM 159 la...lllllllrrrlarlarvlkrlarllarfarklasakrklvlasprrlllafllslliwllealtlylllralgvdv 236
                                   l+   + +l++  +  ++ +    +l + l  f ++l++        +  +l+l + ls+  w +e+lt+y+++ +l++++
  gi|15669266|ref|NP_248071.1|  80 LIiliFGFLIVNSKINLKNK----KLEAILMNFEKGLKAV-------KLNTLPLLITLSFTGWFIEGLTVYFIFLSLNLNL 149
                                   65331333333333333333....3333333444444443.......2345****************************** PP

               LPG_synthase_TM 237 slallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                    ++  ++  la++l++a+p++P+GlGv+E+al+ +l+l  ++ + a a+ +lyrli+++ ++l+G
  gi|15669266|ref|NP_248071.1| 150 EILFGVFSDLASSLLTAIPLTPSGLGVVEYALIYILKLKNIDYSGAFAVLILYRLISYFSIVLFG 214
                                   **********************************************************9999988 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5     3e-05      0.27     114     161 ..      64     111 ..      23     119 .. 0.88
   2 ?   -1.2   0.1      0.12   1.1e+03     117     143 ..     205     231 ..     189     234 .] 0.55

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3e-05
                       DUF5305 114 aegilliilgllaliglvvlirriiftsskaekyelelekilkeYdew 161
                                   +e+++ i  g++++++l++li+  +  +sk + ++++le il ++++ 
  gi|15669266|ref|NP_248071.1|  64 KEILYSIKWGVIIILFLIILIFGFLIVNSKINLKNKKLEAILMNFEKG 111
                                   4467777789999999999999999999**************999875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.12
                       DUF5305 117 illiilgllaliglvvlirriiftssk 143
                                   i ++ ++l+++i + ++ r+i++++++
  gi|15669266|ref|NP_248071.1| 205 ISYFSIVLFGAIMFYIVERNILKEPKN 231
                                   344444455555555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1505.57
//
Query:       gi|15669267|ref|NP_248072.1|  [L=397]
Description: hypothetical protein MJ_1079 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-49  166.4  44.5      1e-48  166.1  44.5    1.1  1  TctA      Tripartite tricarboxylate transporter TctA family
  ------ inclusion threshold ------
        6.6    4.7   6.9        9.5    4.2   6.9    1.1  1  Hid1      High-temperature-induced dauer-formation protein


Domain annotation for each model (and alignments):
>> TctA  Tripartite tricarboxylate transporter TctA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.1  44.5   1.1e-52     1e-48       1     408 [.       4     383 ..       4     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 166.1 bits;  conditional E-value: 1.1e-52
                          TctA   1 LllvllGvllGtliGllPGlhatlavalllpltfgldpeaalilllgiyvgaifggsipaillgvPGtpssvatvldgypl 81 
                                   Ll+++lG+++Gt++Gl PG+h++++val + + + +     + +l+g++++++f+++ip+++lgvP + ++++++l+ ++l
  gi|15669267|ref|NP_248072.1|   4 LLYLILGIICGTITGLFPGIHPNNIVALSFLILPYFGLDNYIPFLIGLVITHYFINFIPSAFLGVP-DDETAVSALPMHKL 83 
                                   899*************************9999996666669*************************.889999******** PP

                          TctA  82 akqGrageAlrlaaigSfiGglvsvllllllaplla.kvalkfgpaeyfalillglvliailseksllkglialllglllg 161
                                   +++G++ eA+ la +gS +G+++s+l++l+l+ +l  +v     + + f+ ++l+  ++  + + + ++ +++++l++++g
  gi|15669267|ref|NP_248072.1|  84 TLNGNGYEAIVLAGFGSYLGVVFSILISLFLMSILHfDVRAFYCSIKIFIPFILIAFILYQIFTAKSVWEVLVIFLSGIFG 164
                                   ***************************9999988862444444455566655555555555556677899999******** PP

                          TctA 162 tvgldpnsgtpRftfgsielldgislvpvliGlFgiselltsleskskip...lslkdlk.kslptilrgsliGtivG... 235
                                   +  l    +     f       +i+l+++++G+Fgi+ l+++l++  ki+   +   d++ k    +l++s+  ++ G   
  gi|15669267|ref|NP_248072.1| 165 IAVLYCSEA-----F-------NITLTAIFTGMFGIPLLINNLKT-YKIKsqmMAFPDFElK----FLKSSFFASVAGffr 228
                                   ****87753.....3.......3********************86.4444344345555544....666655555555444 PP

                          TctA 236 .ilPgvGas.iaaflayavakrlskkpekfgkgaiegvaapeaannaaaggaliplltlgipgsgvaavllgallihglqp 314
                                    +lPg++++ ++++l+  + +r          + ++++++  +   ++ +++l +++ +g+++sgva ++           
  gi|15669267|ref|NP_248072.1| 229 iFLPGISGAqLNYILSKILNER----------DLKNFIVSQGSIILSNEVFSLLAVIFIGVGRSGVARAIQ---------- 289
                                   4*****9998999999999664..........7889*******************************4443.......... PP

                          TctA 315 gpeLftenpelvyallasllianvlllvlgllliklfakll.kipkelLlpiilvllvigayalnnsl...fdvlvmlifg 391
                                      L++ n   + + ++s+li++ +++++ l+l+k++  ++ k++ ++L+ ++++++ +++++ ++++   + ++v+l+++
  gi|15669267|ref|NP_248072.1| 290 ---LLNANI-NINTAIFSILISSTIAIIILLNLSKYILLFIrKVNFKFLSLFFIIFCSLVVIIGSYNTyliYHIIVYLTAI 366
                                   ...333222.3567899**********************666***************9999887776655599******** PP

                          TctA 392 vlGlllrrlgvplaplv 408
                                    +Gll  + + +l++++
  gi|15669267|ref|NP_248072.1| 367 YIGLLAVKSNTNLSNMM 383
                                   *************9998 PP

>> Hid1  High-temperature-induced dauer-formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   6.9    0.0011       9.5     496     562 ..     295     360 ..     268     369 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0011
                          Hid1 496 vnispylktLsleacskllqLlesfSspsfLlanesNhkllalllealnnviqkqfkgnrnLvYsil 562
                                   +ni   + ++ +++ ++++ Ll ++S+   L+  ++N k+l+l + ++++++    ++n +L+Y i+
  gi|15669267|ref|NP_248072.1| 295 ININTAIFSILISSTIAIIILL-NLSKYILLFIRKVNFKFLSLFFIIFCSLVVIIGSYNTYLIYHII 360
                                   4666666677778888888776.69****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1221  (0.068102); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2551.17
//
Query:       gi|15669268|ref|NP_248073.1|  [L=135]
Description: hypothetical protein MJ_1080 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.16   11.5   0.1       0.22   11.1   0.1    1.1  1  DUF2071     Uncharacterized conserved protein (COG2071)


Domain annotation for each model (and alignments):
>> DUF2071  Uncharacterized conserved protein (COG2071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   1.2e-05      0.22      27      58 ..      91     122 ..      83     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.2e-05
                       DUF2071  27 lelDtfdGkayvslvpFrmedvrvrglpavpg 58 
                                   l+lDt++G  y s+v F m+ v + +l++v +
  gi|15669268|ref|NP_248073.1|  91 LNLDTMKGILYFSVVLFIMTSVIWFYLFRVLF 122
                                   89********************9999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 831.97
//
Query:       gi|15669269|ref|NP_248074.1|  [L=138]
Description: hypothetical protein MJ_1081 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-41  138.6   0.0      1e-40  138.4   0.0    1.0  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.4   0.0   5.8e-45     1e-40       1     115 []      22     134 ..      22     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 5.8e-45
                                   E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGGTTS..THHHHHHHHHH-SE CS
                       UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhnaegpdnadaHlkssllgss 80 
                                   dit+ + +a++es+vk+G+++++++htta++tinEnadp+v++D+ ++l++l+p++ +++h  eg  n+daH+kssl+g+s
  gi|15669269|ref|NP_248074.1|  22 DITPYIISAISESKVKDGIAVIYVPHTTAGITINENADPSVKHDIINFLSHLIPKNwNFTHL-EG--NSDAHIKSSLVGCS 99 
                                   79******************************************************999999.99..************** PP

                                   EEEEEETTEE---TTEEEEEEESS-SSEEEEEEEE CS
                       UPF0047  81 ltipvedgklalGtwqsiylveldgpreRkvvvqv 115
                                   +ti+++dgk  lGtwq+i+++e+dgpr+R+++v++
  gi|15669269|ref|NP_248074.1| 100 QTIIIKDGKPLLGTWQGIFFAEFDGPRRREFYVKI 134
                                   *******************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 964.03
//
Query:       gi|15669270|ref|NP_248075.1|  [L=120]
Description: hypothetical protein MJ_1082 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-21   76.5   0.1    1.7e-21   75.9   0.1    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
    1.6e-05   24.4   0.4      3e-05   23.5   0.1    1.7  2  HTH_24           Winged helix-turn-helix DNA-binding
    1.8e-05   24.6   0.1    7.6e-05   22.5   0.1    1.9  2  MarR_2           MarR family
    0.00013   21.7   0.0    0.00022   20.9   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
    0.00019   21.2   1.4    0.00024   20.9   1.4    1.2  1  TFIIE_alpha      TFIIE alpha subunit
    0.00064   19.3   0.1     0.0012   18.4   0.1    1.4  1  GntR             Bacterial regulatory proteins, gntR family
    0.00071   19.5   0.0     0.0011   18.9   0.0    1.3  1  MarR             MarR family
     0.0011   18.8   0.0     0.0026   17.7   0.0    1.7  1  HTH_36           Helix-turn-helix domain
     0.0015   18.6   0.0     0.0073   16.4   0.0    1.9  2  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
     0.0019   18.0   0.1     0.0048   16.7   0.0    1.6  2  HTH_5            Bacterial regulatory protein, arsR family
     0.0021   17.8   0.0     0.0036   17.0   0.0    1.4  1  HTH_38           Helix-turn-helix domain
     0.0026   17.3   0.0     0.0072   15.9   0.0    1.7  2  HTH_47           winged helix-turn-helix
     0.0076   16.6   0.1      0.011   16.1   0.1    1.3  1  Penicillinase_R  Penicillinase repressor
     0.0095   15.9   0.0       0.03   14.2   0.0    1.9  2  HTH_11           HTH domain
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.068   13.4   0.0    2.1  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.023   14.3   0.0      0.041   13.5   0.0    1.5  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
      0.037   14.3   0.0      0.064   13.5   0.0    1.4  1  Rio2_N           Rio2, N-terminal
      0.039   13.9   0.3      0.067   13.2   0.2    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
       0.04   14.0   0.2      0.084   13.0   0.1    1.5  2  HTH_20           Helix-turn-helix domain
      0.041   13.7   0.1      0.092   12.6   0.1    1.6  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.044   13.9   0.0       0.12   12.5   0.0    1.7  1  HTH_28           Helix-turn-helix domain
      0.044   13.5   0.0      0.095   12.4   0.0    1.4  1  DUF4423          Domain of unknown function (DUF4423)
      0.046   13.1   0.1      0.052   12.9   0.1    1.1  1  PurA             PurA ssDNA and RNA-binding protein
      0.059   13.9   0.2       0.12   12.9   0.1    1.6  1  HTH_27           Winged helix DNA-binding domain
      0.059   12.9   0.5      0.095   12.3   0.1    1.6  2  HTH_CodY         CodY helix-turn-helix domain
       0.06   13.7   0.0      0.097   13.0   0.0    1.3  1  Rrf2             Transcriptional regulator
      0.072   13.1   0.2       0.17   11.9   0.1    1.7  2  HTH_29           Winged helix-turn helix
      0.072   13.1   0.0        0.1   12.6   0.0    1.2  1  Dimerisation2    Dimerisation domain
       0.08   12.6   0.0       0.12   12.0   0.0    1.2  1  RP-C             Replication protein C N-terminal domain
       0.15   12.4   0.0       0.26   11.7   0.0    1.4  1  Ribosomal_L12    Ribosomal protein L7/L12 C-terminal domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.1   2.8e-24   1.7e-21       2      67 ..      19      90 ..      18      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 2.8e-24
                                  H.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....TTEEEE--H CS
                          TrmB  2 q.klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.....pklYravdp 67
                                  +  lGL+e E++vY+ Ll++g+ ++ eiae+++++r++v+++LrsL+++GlV+r+k +     +++Y+avd+
  gi|15669270|ref|NP_248075.1| 19 RcILGLQEIEIRVYFDLLENGEGSVLEIAERVNRDRTTVQKALRSLMNCGLVDRRKVTekvgyKYIYNAVDL 90
                                  5579****************************************************9999**999*****97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   5.1e-08     3e-05       3      47 ..      26      70 ..      24      71 .. 0.93
   2 ?   -2.5   0.0       6.6   3.9e+03       7      14 ..      95     102 ..      92     103 .. 0.53

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5.1e-08
                        HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  e++++++  L +n+  s  e+Aer++  ++tv + l+ L++ Gl+
  gi|15669270|ref|NP_248075.1| 26 EIEIRVYFDLLENGEGSVLEIAERVNRDRTTVQKALRSLMNCGLV 70
                                  78899999999********************************98 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.6
                        HTH_24   7 kILelLqk 14 
                                   +I+e+L +
  gi|15669270|ref|NP_248075.1|  95 DIIEELLD 102
                                   35555554 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   1.3e-07   7.6e-05       7      55 ..      28      74 ..      22      78 .. 0.80
   2 ?   -0.7   0.0       2.3   1.4e+03      23      31 ..      92     100 ..      83     102 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.3e-07
                                  HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                  + rv + L  ++++  +v e+a+r + ++ +v+++l+ L   GLv rr+
  gi|15669270|ref|NP_248075.1| 28 EIRVYFDLLENGEG--SVLEIAERVNRDRTTVQKALRSLMNCGLVDRRK 74
                                  55555555555553..9*****************************996 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.3
                                   EHHHHHHHH CS
                        MarR_2  23 tvgelarrl 31 
                                   +v+++ ++l
  gi|15669270|ref|NP_248075.1|  92 RVSDIIEEL 100
                                   777887776 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   3.7e-07   0.00022      16      50 ..      38      72 ..      34      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.7e-07
                                  BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  ++e ++ e+A+r    ++tv   L++L+++G+v +
  gi|15669270|ref|NP_248075.1| 38 NGEGSVLEIAERVNRDRTTVQKALRSLMNCGLVDR 72
                                  4566899**************************87 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   1.4   4.1e-07   0.00024      15     100 ..      28     112 ..      13     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.1e-07
                                   HHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHHHH CS
                   TFIIE_alpha  15 avlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevvkk 95 
                                    + v + Lle+ge +  ++a+ ++ d++ + k+L  L + +lv+ + ++ e+ + +  y  ++ +++ d++ + l+   ++
  gi|15669270|ref|NP_248075.1|  28 EIRVYFDLLENGEGSVLEIAERVNRDRTTVQKALRSLMNCGLVDRR-KVTEKVGYKYIYNAVDLDRVSDIIEELLDDWYQN 107
                                   4567788999*********************************954.455566666667789***********99999999 PP

                                   HHHHH CS
                   TFIIE_alpha  96 Leekl 100
                                   +++ l
  gi|15669270|ref|NP_248075.1| 108 VKKWL 112
                                   98865 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   2.1e-06    0.0012      27      58 ..      43      74 ..      37      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.1e-06
                                  HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          GntR 27 ereLaaefgVsrttvReALrrLeaeglverrq 58
                                  + e+a++ + +rttv++ALr L   glv rr+
  gi|15669270|ref|NP_248075.1| 43 VLEIAERVNRDRTTVQKALRSLMNCGLVDRRK 74
                                  459*************************9985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.8e-06    0.0011      10      51 ..      33      74 ..      24      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.8e-06
                                  HHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR 10 rilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                  + l e+g+ sv e+a++++ +++tv ++l+ L   Gl++R+k
  gi|15669270|ref|NP_248075.1| 33 FDLLENGEGSVLEIAERVNRDRTTVQKALRSLMNCGLVDRRK 74
                                  567788888999****************************98 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.4e-06    0.0026      29      55 .]      44      70 ..      33      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.4e-06
                        HTH_36 29 etlakrlglsknTvsraikeLeqlGyi 55
                                    +a+r + ++ Tv++a+++L+ +G++
  gi|15669270|ref|NP_248075.1| 44 LEIAERVNRDRTTVQKALRSLMNCGLV 70
                                  579**********************85 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-05    0.0073      17      57 ..      30      70 ..      24      71 .. 0.94
   2 ?   -0.5   0.0       2.4   1.4e+03       4      18 ..      94     108 ..      91     113 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                                  HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                         HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                  +V+  Ll++g  ++ e++++++ +++ V k+L +L++ +lV
  gi|15669270|ref|NP_248075.1| 30 RVYFDLLENGEGSVLEIAERVNRDRTTVQKALRSLMNCGLV 70
                                  68889********************************9999 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.4
                                   HHHHHHCSTTHHHHH CS
                         HTH_9   4 teiieehFGevvakV 18 
                                   + iiee++++  ++V
  gi|15669270|ref|NP_248075.1|  94 SDIIEELLDDWYQNV 108
                                   567888877776666 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     8e-06    0.0048      10      46 ..      35      71 ..      34      72 .. 0.95
   2 ?   -2.8   0.0       9.8   5.9e+03      18      25 ..      93     100 ..      92     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8e-06
                                  HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5 10 lLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  lL++ge +v e+ae ++  + tv   L+ L+++GLV+
  gi|15669270|ref|NP_248075.1| 35 LLENGEGSVLEIAERVNRDRTTVQKALRSLMNCGLVD 71
                                  7999********************************6 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.8
                                   HHHHHHHH CS
                         HTH_5  18 vcelaeel 25 
                                   v+++ eel
  gi|15669270|ref|NP_248075.1|  93 VSDIIEEL 100
                                   89999987 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.9e-06    0.0036      15      42 ..      34      62 ..      22      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.9e-06
                        HTH_38 15 rllaeG.lslreIArrLgrspsTIsRElk 42
                                  +ll+ G  s+ eIA r++r+++T+++ l+
  gi|15669270|ref|NP_248075.1| 34 DLLENGeGSVLEIAERVNRDRTTVQKALR 62
                                  78888856777**************9987 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.2e-05    0.0072      44      77 ..      38      71 ..      30      72 .. 0.92
   2 ?   -1.8   0.0         4   2.4e+03      58      71 ..      88     101 ..      85     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                                  EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                        HTH_47 44 DGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                   G+ s+l+iAer++ +  +v++++r+L + gl+ 
  gi|15669270|ref|NP_248075.1| 38 NGEGSVLEIAERVNRDRTTVQKALRSLMNCGLVD 71
                                  6999*************************99985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4
                                   --HHHHHHHHHHHH CS
                        HTH_47  58 lpfdrvaaiaraLa 71 
                                   ++ drv +i+++L 
  gi|15669270|ref|NP_248075.1|  88 VDLDRVSDIIEELL 101
                                   57889999999986 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.8e-05     0.011       5      95 ..      28     115 ..      24     120 .] 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-05
                                   -SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXX..XXXXXXXXXXXX CS
               Penicillinase_R   5 EaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeea..vasavkqlldkl 83 
                                   E  v+  l e+ge +v e+ e+++++    ++TV+  lr L++ gl++r+k   +  Y    +  ++  v+   ++lld  
  gi|15669270|ref|NP_248075.1|  28 EIRVYFDLLENGEGSVLEIAERVNRD----RTTVQKALRSLMNCGLVDRRKVTEKVGYKYIYNAVDLdrVSDIIEELLDDW 104
                                   55666667788999999999999999....******************998866655544444433311556677777777 PP

                                   XXXXXXXXXXXX CS
               Penicillinase_R  84 fegsvkelvaaf 95 
                                   ++ +vk+ ++ f
  gi|15669270|ref|NP_248075.1| 105 YQ-NVKKWLTYF 115
                                   75.666666655 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   5.1e-05      0.03      17      43 ..      42      68 ..      31      82 .. 0.79
   2 ?   -2.2   0.0         7   4.2e+03       1      10 [.      92     101 ..      92     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-05
                        HTH_11 17 sgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                  s  e+Ae+ n+ r+tv++ +++L   g
  gi|15669270|ref|NP_248075.1| 42 SVLEIAERVNRDRTTVQKALRSLMNCG 68
                                  6779******************98888 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7
                        HTH_11   1 RllqilelLl 10 
                                   R ++i+e Ll
  gi|15669270|ref|NP_248075.1|  92 RVSDIIEELL 101
                                   7789999986 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00011     0.068      23      55 ..      41      73 ..      12      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                                  B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGyveye 55
                                   ++ ++aer n    +V++ l+ L + G+v+  
  gi|15669270|ref|NP_248075.1| 41 GSVLEIAERVNRDRTTVQKALRSLMNCGLVDRR 73
                                  46779*************************965 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.8e-05     0.041      28      69 ..      45      87 ..      34      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.8e-05
                  HrcA_DNA-bdg 28 eiAevlkrneGtvRNqlqsLkalgLvegv.pGPkGGYkPtlka 69
                                  eiAe ++r+  tv   l sL   gLv+ +    k GYk   +a
  gi|15669270|ref|NP_248075.1| 45 EIAERVNRDRTTVQKALRSLMNCGLVDRRkVTEKVGYKYIYNA 87
                                  9*************************96414567777765555 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00011     0.064      30      72 ..      46      89 ..      42      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                        Rio2_N 30 ieeisrlkeeevkkrlsrllkaklisr.ktakydGYkLtyeGyD 72
                                  i+e+ + +++ v+k+l++l++ +l+ r k ++  GYk +y++ D
  gi|15669270|ref|NP_248075.1| 46 IAERVNRDRTTVQKALRSLMNCGLVDRrKVTEKVGYKYIYNAVD 89
                                  66666777899****************7778899******9988 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   0.00011     0.067      25      57 ..      44      75 ..      17      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                  HHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEE CS
                     HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrgrri 57
                                   e+A++++  r tv ++l+ L + gl++r++ +
  gi|15669270|ref|NP_248075.1| 44 LEIAERVNRDRTTVQKALRSLMNCGLVDRRK-V 75
                                  59**************************886.5 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       9.6   5.8e+03      24      34 ..      11      21 ..       7      32 .. 0.75
   2 ?   13.0   0.1   0.00014     0.084      17      59 ..      34      75 ..      28      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 9.6
                                  TB-HHHHHHHH CS
                        HTH_20 24 gltaselaerl 34
                                   +t ++l++++
  gi|15669270|ref|NP_248075.1| 11 KFTIEDLMRCI 21
                                  57888888876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00014
                                  HHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                        HTH_20 17 raLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                  ++L ++++ ++ e+aer+  +++t+ + Lr L   gLv+++++
  gi|15669270|ref|NP_248075.1| 34 DLL-ENGEGSVLEIAERVNRDRTTVQKALRSLMNCGLVDRRKV 75
                                  556.888999*****************************9986 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00015     0.092      12      41 ..      35      64 ..      35      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                 HTH_AsnC-type 12 LqedaRisyaeLAervGlSestvlrRvrrL 41
                                  L e++  s+ e+Aerv+ +++tv++ +r L
  gi|15669270|ref|NP_248075.1| 35 LLENGEGSVLEIAERVNRDRTTVQKALRSL 64
                                  5689999*****************988766 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0002      0.12       9      36 ..      36      64 ..      34      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                        HTH_28  9 laaGh.svreaArelgisrrtvyrWikry 36
                                  l +G+ sv e+A++++ +r+tv++ ++ +
  gi|15669270|ref|NP_248075.1| 36 LENGEgSVLEIAERVNRDRTTVQKALRSL 64
                                  568999*****************999865 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016     0.095      33      72 ..      37      74 ..      29      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                       DUF4423 33 kdfkadpeelakrlrpkisaeevekalefLlklgllkkde 72
                                  ++++ ++ e+a+r++   +   v+kal+ L+++gl+++ +
  gi|15669270|ref|NP_248075.1| 37 ENGEGSVLEIAERVN--RDRTTVQKALRSLMNCGLVDRRK 74
                                  45677999*******..*******************9987 PP

>> PurA  PurA ssDNA and RNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   8.7e-05     0.052      94     151 ..      30      87 ..      22     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.7e-05
                          PurA  94 kyyldlkenqrGrflriaqlvmrgksrgqrqqialPaqGlielrdalteliedygegd 151
                                   + y+dl en  G  l ia  v+r +++ q+    l   Gl++ r++  ++  +y  + 
  gi|15669270|ref|NP_248075.1|  30 RVYFDLLENGEGSVLEIAERVNRDRTTVQKALRSLMNCGLVDRRKVTEKVGYKYIYNA 87 
                                   789*********************9999999999999****99999877766665554 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00021      0.12      18      51 ..      40      73 ..      29      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00021
                        HTH_27 18 rkkladlcgrlnvedshisyslkkLtekGLvert 51
                                  + +  ++++r+n++ +++ ++l+ L + GLv r 
  gi|15669270|ref|NP_248075.1| 40 EGSVLEIAERVNRDRTTVQKALRSLMNCGLVDRR 73
                                  556669*************************443 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         8   4.8e+03      21      27 ..       5      11 ..       2      14 .. 0.68
   2 ?   12.3   0.1   0.00016     0.095       9      51 ..      45      87 ..      37      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8
                      HTH_CodY 21 ivnaLrk 27
                                  i+n L+k
  gi|15669270|ref|NP_248075.1|  5 IINRLKK 11
                                  7777777 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00016
                      HTH_CodY  9 kiaDriGitrsvivnaLrkLesaGiiesrsLGmkGtYlkvlne 51
                                  +ia+r+   r  +  aLr L   G+++ r +  k  Y  + n 
  gi|15669270|ref|NP_248075.1| 45 EIAERVNRDRTTVQKALRSLMNCGLVDRRKVTEKVGYKYIYNA 87
                                  79***************************99998888766665 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00016     0.097      22      57 ..      38      72 ..      25      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                                  TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvks 57
                                  ++e  s+ eiaer+n  ++ ++k l+ L + glv  
  gi|15669270|ref|NP_248075.1| 38 NGE-GSVLEIAERVNRDRTTVQKALRSLMNCGLVDR 72
                                  333.5799*************************975 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00029      0.17       8      35 ..      36      63 ..      34      74 .. 0.82
   2 ?   -2.5   0.0       9.2   5.5e+03      24      35 ..      79      90 ..      78      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                        HTH_29  8 laeGvstvsqiAkllglsrrtvyrwlkr 35
                                  l+ G+++v +iA++++ +r+tv+++l+ 
  gi|15669270|ref|NP_248075.1| 36 LENGEGSVLEIAERVNRDRTTVQKALRS 63
                                  5667778*****************9986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.2
                        HTH_29 24 lsrrtvyrwlkr 35
                                  + ++++y+++++
  gi|15669270|ref|NP_248075.1| 79 VGYKYIYNAVDL 90
                                  678999999875 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00017       0.1      24      75 ..      33      82 ..      25      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                 Dimerisation2 24 FdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYs 75
                                  FdlL++ ++ s+ e+ae+++ +   ++  l+ ++  gL  r+k +e k +Y+
  gi|15669270|ref|NP_248075.1| 33 FDLLEN-GEGSVLEIAERVNRDRTTVQKALRSLMNCGLVDRRKVTE-KVGYK 82
                                  9***99.9999*****************************997776.46664 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.12      76     104 ..      45      73 ..      42      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                          RP-C  76 qLsralglsestlrrhlaaLveaGliirr 104
                                   ++++++++ ++t+++ l++L+++Gl+ rr
  gi|15669270|ref|NP_248075.1|  45 EIAERVNRDRTTVQKALRSLMNCGLVDRR 73 
                                   5779999*******************988 PP

>> Ribosomal_L12  Ribosomal protein L7/L12 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00043      0.26       8      52 ..      50      95 ..      44     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00043
                                  -TT-HHHHHHHHHHHH---HHHHHHHHTTTT.STEEEEE-HHHHHH CS
                 Ribosomal_L12  8 agakKiaVIKaVreitglgLkeaKdlVeaap.kvvkegvskeeAee 52
                                  ++ +++ V Ka+r++++ gL++ +++ e+++ k + ++v+ +   +
  gi|15669270|ref|NP_248075.1| 50 VNRDRTTVQKALRSLMNCGLVDRRKVTEKVGyKYIYNAVDLDRVSD 95
                                  566789999********************97566777776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 760.64
//
Query:       gi|15669271|ref|NP_248076.1|  [L=193]
Description: iron-sulfur flavoprotein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-41  141.6   0.0      2e-41  141.3   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    2.3e-12   47.0   0.0    2.7e-12   46.8   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
      0.028   14.7   0.0      0.042   14.1   0.0    1.3  1  Flavodoxin_5  Flavodoxin domain


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.3   0.0   3.3e-45     2e-41       1     152 [.       1     155 [.       1     158 [. 0.96

  Alignments for each domain:
  == domain 1  score: 141.3 bits;  conditional E-value: 3.3e-45
                                   -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH-SCEE CS
                       FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaaadali 77 
                                   mk+++isGS+r+++nt  l+++a++a++e+g+e+e+i lad+   pc   ++c+++   +++  ddv e+l+k+++ad++i
  gi|15669271|ref|NP_248076.1|   1 MKVIGISGSPRPEGNTTLLVREALNAIAEEGIETEFISLADKeLNPCigcNMCKEEG--KCPIIDDVDEILKKMKEADGII 79 
                                   9***********************************************988888666..679******************* PP

                                   EEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEECSEEEETS CS
                       FMN_red  78 ivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpraavavgk 152
                                   +++P+Y+g++s++lK ++Dr ++ r + +lr+K++++vavg++r+gg++++ q  + +  ++ +ivv++++  +++
  gi|15669271|ref|NP_248076.1|  80 LGSPVYFGGVSAQLKMLMDRSRPLRIGFQLRNKVGGAVAVGASRNGGQETTIQQIHNFFlIHSMIVVGDNDPTAHY 155
                                   ***********************************************************99*******98877765 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   4.6e-16   2.7e-12       1     103 [.       1     100 [.       1     144 [. 0.85

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 4.6e-16
                                   -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHCCHHHHTT..C.HHHHHHHHHHHHC CS
                  Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaaklayeek..p.adveseqieklla 77 
                                   mk+  i ++prpe  ++  l +++++a++++g  e + + L++   +p +  ++       ee+  p +d   e ++k+++
  gi|15669271|ref|NP_248076.1|   1 MKVIGISGSPRPE-GNTTLLVREALNAIAEEG-IETEFISLADKeLNPCIGCNM-----CKEEGkcPiIDDVDEILKKMKE 74 
                                   8999********5.999***************.9*********97788777644.....4566667867777777****** PP

                                   SSEEEEEEE-BTTB--HHHHHHHHHH CS
                  Flavodoxin_2  78 adaivlqfPlwwfgvPailKgwiDrv 103
                                   ad i+l++P+++ gv+a+lK  +Dr 
  gi|15669271|ref|NP_248076.1|  75 ADGIILGSPVYFGGVSAQLKMLMDRS 100
                                   ************************95 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.1e-06     0.042      23      70 ..      54     101 ..      51     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.1e-06
                  Flavodoxin_5  23 reegelvdvedvekesedlesydavvigasvyygkllpelakFvekhr 70 
                                   +eeg+   ++dv++  ++++++d +++g++vy g+++ +l+ + ++ r
  gi|15669271|ref|NP_248076.1|  54 KEEGKCPIIDDVDEILKKMKEADGIILGSPVYFGGVSAQLKMLMDRSR 101
                                   566666666777766689********************9999988874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1311.52
//
Query:       gi|15669272|ref|NP_248077.1|  [L=282]
Description: shikimate 5-dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-33  112.6   0.0    2.1e-32  111.2   0.0    1.8  1  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
    2.1e-15   56.2   0.0    4.6e-15   55.1   0.0    1.6  1  SDH_C            Shikimate 5'-dehydrogenase C-terminal domain
      1e-10   41.8   0.6    1.8e-10   41.0   0.6    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00019   21.7   0.6    0.00041   20.6   0.2    1.7  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0011   19.5   1.0     0.0024   18.4   1.1    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.013   14.9   0.1      0.026   14.0   0.1    1.6  1  adh_short        short chain dehydrogenase
       0.14   12.2   1.7        7.8    6.7   0.2    3.0  3  Peptidase_M60_C  Peptidase M60 C-terminal domain
       0.82    9.8   3.6        2.3    8.3   0.6    2.7  2  RapH_N           response regulator aspartate phosphatase H, 


Domain annotation for each model (and alignments):
>> Shikimate_dh_N  Shikimate dehydrogenase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   0.0   9.3e-36   2.1e-32       1      83 []      11      93 ..      11      93 .. 0.99

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 9.3e-36
                                  EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT--SEE CS
                Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigAvNti 83
                                  +iG+p++hS SP++hnaafk++gln++y+af+v +++l+ ++++++alg+ G+nvTiP+K +++++lde++++A+ igAvNti
  gi|15669272|ref|NP_248077.1| 11 LIGHPVEHSFSPIMHNAAFKDKGLNYVYVAFDVLPENLKYVIDGAKALGIVGFNVTIPHKIEIMKYLDEIDKDAQLIGAVNTI 93
                                  79********************************************************************************8 PP

>> SDH_C  Shikimate 5'-dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   2.1e-18   4.6e-15       1      30 [.     247     276 ..     247     277 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 2.1e-18
                                   HHHHHHHHHHHHHHHHHS----HHHHHHHH CS
                         SDH_C   1 GLgMLveQgaeqFelWTGrepPvevMreal 30 
                                   GLgML++Qga +F++WTG+ep++evM++a+
  gi|15669272|ref|NP_248077.1| 247 GLGMLIYQGAVAFKIWTGVEPNIEVMKNAI 276
                                   9***************************98 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.6     8e-14   1.8e-10       5     111 ..     116     224 ..     112     249 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 8e-14
                                   HHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-....EEEEGCGHHHHHHT-SEEEE CS
                  Shikimate_DH   5 kkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeei....ealkleelkellaeadvvis 81 
                                   ++++++k+k++++ GaG  a+ va  L++   +++++aNRt+e+a++la+e+ ++      e +k++ l+  l+ +d++i 
  gi|15669272|ref|NP_248077.1| 116 EEIGRVKDKNIVIYGAGGAARAVAFELAKD--NNIIIANRTVEKAEALAKEIAEKLNkkfgEEVKFSGLDVDLDGVDIIIN 194
                                   567899*********************955..579***********9999885442211226799**************** PP

                                   -SSS.SS-SB-HHHHHCCHHH.S..EEEEE- CS
                  Shikimate_DH  82 atas.eepilekeeveealkkrkkplllvDi 111
                                   at     p ++ e + +a k r + ++++D+
  gi|15669272|ref|NP_248077.1| 195 ATPIgMYPNIDVEPIVKAEKLR-EDMVVMDL 224
                                   *954134445555555444443.56666675 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   1.8e-07   0.00041       1      54 [.     126     182 ..     126     198 .. 0.78
   2 ?   -2.1   0.0         2   4.4e+03      67      94 ..     215     242 ..     203     253 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.8e-07
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.......TTTCEEEEE- CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.......lgvrfeaial 54 
                                   ++i GaG+ ++ava +la+ +    +i++a r+ ek+eala+++        g+++++  l
  gi|15669272|ref|NP_248077.1| 126 IVIYGAGGAARAVAFELAKDN----NIIIANRTVEKAEALAKEIaeklnkkFGEEVKFSGL 182
                                   89*****************87....68*************998877655554444444444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
                                   HTTSSEEEE-SSGGGHHHHHHHHHHHT- CS
               Sacchrp_dh_NADP  67 lkegdlvvnlsppissldvlkaCietgv 94 
                                   l+e  +v++l+ + +   +lk + +  +
  gi|15669272|ref|NP_248077.1| 215 LREDMVVMDLIYNPLETVLLKEAKKVNA 242
                                   6777888888888887777776655555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.1   1.1e-06    0.0024       2      50 ..     126     169 ..     125     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EE CS
                 F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkv 50 
                                   i i GaG  ++a+a  l++ +    +i++a +r+ ekae+la+e+  k+
  gi|15669272|ref|NP_248077.1| 126 IVIYGAGGAARAVAFELAKDN----NIIIA-NRTVEKAEALAKEIAEKL 169
                                   5666*************9996....99988.************998333 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.2e-05     0.026       1      58 [.     124     184 ..     124     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.....TSEEEEEE-TT CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.....gakalaiqvDv 58 
                                   k +++ Ga+ G  ra+a elak+  ++++++r+ ek+e++ake+ e+     g+++ +  +Dv
  gi|15669272|ref|NP_248077.1| 124 KNIVIYGAG-GAARAVAFELAKD-NNIIIANRTVEKAEALAKEIAEKlnkkfGEEVKFSGLDV 184
                                   567788877.***********98.566677999999999999998876444545555555555 PP

>> Peptidase_M60_C  Peptidase M60 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.4   7.6e+03       9      22 ..      91     103 ..      90     104 .. 0.73
   2 ?    6.7   0.2    0.0035       7.8      18      32 ..     136     148 ..     119     157 .. 0.67
   3 ?    3.4   0.0     0.037        83      17      28 ..     254     265 ..     242     276 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.4
                                   TEEEEEC.TCCCEE CS
               Peptidase_M60_C   9 ktitvknGeeAVaF 22 
                                   +ti +++G +A+++
  gi|15669272|ref|NP_248077.1|  91 NTIKIEDG-KAIGY 103
                                   58999986.57766 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0035
                                   CCCEEEEEETTTTEE CS
               Peptidase_M60_C  18 eAVaFevrknngnkl 32 
                                    AVaFe+ k+n+  +
  gi|15669272|ref|NP_248077.1| 136 RAVAFELAKDNN--I 148
                                   69********94..3 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.037
                                   TCCCEEEEEETT CS
               Peptidase_M60_C  17 eeAVaFevrknn 28 
                                   ++AVaF+++ + 
  gi|15669272|ref|NP_248077.1| 254 QGAVAFKIWTGV 265
                                   48******9765 PP

>> RapH_N  response regulator aspartate phosphatase H, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.23   5.2e+02      30      46 ..      70      86 ..      66      87 .. 0.88
   2 ?    8.3   0.6     0.001       2.3      17      38 ..     149     170 ..     138     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.23
                                  HHHHHHHHCTS---HHH CS
                        RapH_N 30 keeikqeleemeedqdv 46
                                  k ei + l+e+++d ++
  gi|15669272|ref|NP_248077.1| 70 KIEIMKYLDEIDKDAQL 86
                                  789***********987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.001
                                   HHHTT-HHHHHHHHHHHHHHHC CS
                        RapH_N  17 aIkkrsvekAeelkeeikqele 38 
                                    I +r vekAe+l +ei ++l+
  gi|15669272|ref|NP_248077.1| 149 IIANRTVEKAEALAKEIAEKLN 170
                                   68899**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1943.96
//
Query:       gi|15669273|ref|NP_248078.1|  [L=509]
Description: hypothetical protein MJ_1085 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-05   25.4   3.5      1e-05   25.4   3.5    1.8  2  RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
  ------ inclusion threshold ------
      0.059   13.7   0.1       0.16   12.3   0.1    1.7  1  ParBc          ParB-like nuclease domain


Domain annotation for each model (and alignments):
>> RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         1     9e+03      58      76 ..     288     306 ..     282     324 .. 0.55
   2 !   25.4   3.5   1.1e-09     1e-05       2     138 ..     358     479 ..     357     493 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1
                 RNase_Zc3h12a  58 kvsdkealeeLekenlivl 76 
                                   k ++ke l+++ k+ l +l
  gi|15669273|ref|NP_248078.1| 288 KLKEKERLMKIKKDVLNKL 306
                                   4555555555555444433 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.1e-09
                 RNase_Zc3h12a   2 lrtivIDGsnValshgrqkifsvrglaiaveyFvkrgheeitvfvpkfrkealkkekvsdkealeeLekenlivltpskyl 82 
                                   +r ++ID+  V    ++ +  s + ++ +++  ++ g+++i+ ++ ++   +    k++ k++ + L++e  i+++ sk  
  gi|15669273|ref|NP_248078.1| 358 RRIVIIDAISVL---NNMHNLSPNSIENLIKKIKNAGFKNIITVMDTV--TY---YKIKGKDICRFLANECNIKVSKSKDE 430
                                   799*********...44688999999999******************9..34...69************************ PP

                 RNase_Zc3h12a  83 dgkksvsyddrlilelAeekdGvivsndnyrd.llsenkelkdiveerllsftfvkd 138
                                   +         +li+e+ ++  + ++sn  ++d +++++k + + ++e++++f  ++ 
  gi|15669273|ref|NP_248078.1| 431 A--------YKLIIEYIKNFGALVISNASFKDyIIKDSKLFYKDIKEYIIPFIVENG 479
                                   *........9**********************555557999*********9976665 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.7e-05      0.16      14      51 ..     370     407 ..     360     410 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                         ParBc  14 qprkd.spekieelvasIkkkGllqPiivrktrqgryei 51 
                                   +++ + sp++ie l++ Ik++G+++ i+v+ t  ++y+i
  gi|15669273|ref|NP_248078.1| 370 NNMHNlSPNSIENLIKKIKNAGFKNIITVMDTV-TYYKI 407
                                   4444559***********************995.88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1303  (0.0726756); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3349.27
//
Query:       gi|15669274|ref|NP_248079.1|  [L=340]
Description: hypothetical protein MJ_1086 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.3e-08   32.4   0.5    8.3e-08   32.4   0.5    2.2  3  NTP_transf_2  Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.012   15.7   0.2      0.012   15.7   0.2    1.9  2  Polbeta       Polymerase beta, Nucleotidyltransferase
      0.022   13.9   0.0      0.041   13.0   0.0    1.4  1  Lar_N         Lactate racemase N-terminal domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.68     4e+03      72      72 ..      90      90 ..      37     123 .. 0.60
   2 !   32.4   0.5   1.4e-11   8.3e-08       2      85 ..     125     209 ..     117     219 .. 0.74
   3 ?   -2.7   0.0       1.3   7.6e+03      54      74 ..     248     266 ..     228     287 .. 0.46

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.68
                                  E CS
                  NTP_transf_2 72 d 72
                                  +
  gi|15669274|ref|NP_248079.1| 90 H 90
                                  2 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 1.4e-11
                                   HHHHHHHHHHTT.TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCC CS
                  NTP_transf_2   2 kklleelkelep.vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekled 81 
                                   +kl+ +l++    ++++ + GS    +++k+SDiD++++++++++      ++++  ++ +++++l++l  d++ ++++++
  gi|15669274|ref|NP_248079.1| 125 RKLALILEDYGVpIKSMGVSGSLLLKLNNKNSDIDFVIYGKDMHK------KAREALKQAFEDNKLKPLSDDFWKIAYKKR 199
                                   344445554444899****************************85......68999999***************4444443 PP

                                   ......CTEE CS
                  NTP_transf_2  82 ......pllv 85 
                                         ++  
  gi|15669274|ref|NP_248079.1| 200 ikdktlTYEE 209
                                   3335533333 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.3
                                   HHHHHHCCCEEECTTEEEEEE CS
                  NTP_transf_2  54 eklaeiikfleellglevdlv 74 
                                   +k+  +  +  e ++l+ d+ 
  gi|15669274|ref|NP_248079.1| 248 YKNLGF--AKIEGRVLNDDFA 266
                                   333333..3333335555555 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.88   5.3e+03      63      69 ..      94     100 ..      66     124 .. 0.45
   2 ?   15.7   0.2   1.9e-06     0.012       6      60 ..     130     184 ..     125     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.88
                                   EEEEEET CS
                       Polbeta  63 kvDlvdl 69 
                                   k D+  +
  gi|15669274|ref|NP_248079.1|  94 KEDVKRI 100
                                   3333332 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.9e-06
                                   THHHH.HHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.S CS
                       Polbeta   6 ileke.keielaylFGSrakgkareeSDiDlavllkekldleeelelaaeledikl 60 
                                   ile++   i+ + + GS + +  +++SDiD+ ++ k+  +++ +  l++++ed kl
  gi|15669274|ref|NP_248079.1| 130 ILEDYgVPIKSMGVSGSLLLKLNNKNSDIDFVIYGKDM-HKKAREALKQAFEDNKL 184
                                   566663367777788****999***************9.77778888888888733 PP

>> Lar_N  Lactate racemase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.9e-06     0.041      15     105 ..      88     173 ..      76     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-06
                         Lar_N  15 llgvlepkevkeekdeeeaieeaLenpigsekleelvkekekvvivvsDiTRptpskiilpllleelkeagvkdeditilv 95 
                                   l++ + ++ vk+  +++e ++e ++   ++++l+el ++ +k++++ +D   p++s  +   ll +l++   k++di +++
  gi|15669274|ref|NP_248079.1|  88 LMHAIPKEDVKRILRPKERLNEIIN---EENNLNELEEKCRKLALILEDYGVPIKSMGVSGSLLLKLNN---KNSDIDFVI 162
                                   4556667777777788888888888...7788999999999***************************9...999999764 PP

                         Lar_N  96 .AtGlHrkqte 105
                                    ++ +H+k+ e
  gi|15669274|ref|NP_248079.1| 163 yGKDMHKKARE 173
                                   38899988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2656.55
//
Query:       gi|15669275|ref|NP_248080.1|  [L=312]
Description: mevalonate kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-15   54.6   0.0    1.8e-14   53.7   0.0    1.5  1  GHMP_kinases_N   GHMP kinases N terminal domain
    2.6e-14   53.4   0.0      6e-14   52.2   0.0    1.6  1  GHMP_kinases_C   GHMP kinases C terminal
  ------ inclusion threshold ------
       0.02   14.5   2.4      0.025   14.1   2.4    1.2  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
      0.037   13.6   0.0      0.064   12.8   0.0    1.4  1  GalKase_gal_bdg  Galactokinase galactose-binding signature
      0.067   13.3   5.3       0.28   11.3   0.2    3.1  3  Cas6b_C          Cas6b C-terminal domain
      0.074   13.4   0.0       0.13   12.6   0.0    1.5  1  SDH_beta         Serine dehydratase beta chain
      0.085   12.1   1.0       0.38   10.0   0.1    2.1  2  Herpes_U34       Herpesvirus virion protein U34
       0.11   12.8   0.2       0.49   10.7   0.0    2.1  2  Glyco_hydro_67N  Glycosyl hydrolase family 67 N-terminus
        7.6    6.8   7.9         13    6.1   1.2    3.8  4  DASH_Dad1        DASH complex subunit Dad1


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0   8.9e-18   1.8e-14       1      66 []      96     163 ..      96     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 8.9e-18
                                   EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerlaqggngsggDvaasvyGg 66 
                                   +i+i+s iP+++GLGSSA+++ ++++A+  +++++l++   akl++  e+++q g+ s+ D ++++y g
  gi|15669275|ref|NP_248080.1|  96 KINISSKIPISCGLGSSASITIGTIKAVSGFYNKELKDdeiAKLGYMVEKEIQ-GKASITDTSTITYKG 163
                                   699******************************99944479************.************976 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0     3e-17     6e-14       4      81 ..     227     300 ..     215     303 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 3e-17
                GHMP_kinases_C   4 alergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralre 81 
                                   al+ ++ e +g+l++ +++  l+  + i++p l++++++  + G +gakl+GaGgG++v++l+ ++++ ++++ +l++
  gi|15669275|ref|NP_248080.1| 227 ALKIKNKEDFGKLMTKNHE--LLKKLNISTPKLDRIVDIGNRFG-FGAKLTGAGGGGCVIILV-NEEKEKELLKELNK 300
                                   55558999***********..7889*******************.******************.99999999988876 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.4   1.3e-05     0.025     168     245 ..     122     249 ..      22     264 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                                   H...........................................HHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS.. CS
                 UvrD-helicase 168 k...........................................keelslskskaeelrelvskakekqlspkelkkaf.. 203
                                                                                ++++  ++ ++e++e+++++k   + ++++kk+   
  gi|15669275|ref|NP_248080.1| 122 AvsgfynkelkddeiaklgymvekeiqgkasitdtstitykgilEIKNNKFRKIKGEFEEFLKNCKFLIVYAEKRKKKTae 202
                                   044444444444444444444444444556666777777777664444455556788999999999998888888888889 PP

                                   .....TSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHH CS
                 UvrD-helicase 204 .....ekasdlqkkiaeflkeyqeqkkeenalDfsdllhallellee 245
                                         k +++++ ++e++k + e +k++n  Df +l+ +  ell++
  gi|15669275|ref|NP_248080.1| 203 lvnevAKIENKDEIFKEIDKVIDEALKIKNKEDFGKLMTKNHELLKK 249
                                   99988899999*********************************998 PP

>> GalKase_gal_bdg  Galactokinase galactose-binding signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.2e-05     0.064      13      45 ..       2      34 ..       1      38 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                                  EEEEEEEEEEE--S-TTTT-EEEEEEEEEEEEE CS
               GalKase_gal_bdg 13 vasAPGRvnLiGEHtDYngGfVlpmAieqdiyi 45
                                  ++  P  v L GEH    g+  + mAi++  +i
  gi|15669275|ref|NP_248080.1|  2 IIETPSKVILFGEHAVVYGYRAISMAIDLTSTI 34
                                  677899**********************98766 PP

>> Cas6b_C  Cas6b C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00014      0.28      35     113 ..      36     122 ..      27     123 .. 0.62
   2 ?    3.0   0.1     0.052     1e+02      53      88 ..     138     179 ..     135     184 .. 0.61
   3 ?   -1.3   0.1       1.1   2.2e+03      53      68 ..     219     233 ..     192     272 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                       Cas6b_C  35 kkellekiLvgnilsmakglgvtvee..kiev.kiteveekkvklkeq.k..mlafkgeFktnf..liPdylGlGksvsrG 107
                                    ke  e  ++ n+  + k+lg++++e  +i+  ++ +++ + + +k++ +   +  k  Fk+n+  +iP   GlG s+s  
  gi|15669275|ref|NP_248080.1|  36 IKETQEDEIILNLNDLNKSLGLNLNEikNINPnNFGDFKYCLCAIKNTlDylNIEPKTGFKINIssKIPISCGLGSSASIT 116
                                   5666666777777777777777775511333213445555556666652211223356677776336************** PP

                       Cas6b_C 108 fGtvkk 113
                                    Gt+k+
  gi|15669275|ref|NP_248080.1| 117 IGTIKA 122
                                   ****96 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.052
                       Cas6b_C  53 glgvtveekievkiteveekkvkl......keqkmlafkgeF 88 
                                   +lg+ ve++i+ k + +++ ++++      k++k+  +kgeF
  gi|15669275|ref|NP_248080.1| 138 KLGYMVEKEIQGKASITDTSTITYkgileiKNNKFRKIKGEF 179
                                   689999999998874444444665111111556666666666 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.1
                       Cas6b_C  53 glgvtveekievkite 68 
                                   +++  ++e +++k  +
  gi|15669275|ref|NP_248080.1| 219 EIDKVIDEALKIKN-K 233
                                   44444444444443.2 PP

>> SDH_beta  Serine dehydratase beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.6e-05      0.13       7      65 ..     106     165 ..     105     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.6e-05
                                   XXXXXXX-TTTHHHHHHHHHHHHHHHHTT-TTT.--EEEEEEEHHHHHS-TTSSHHHHHH CS
                      SDH_beta   7 kiGiGPSSShTvgpmraaaaFveelkekellee.varirveLyGsLaatgkghgtdeAvl 65 
                                   + G+G S S T+g ++a   F ++  +++ +++    ++ e+ G  ++t +   t++ +l
  gi|15669275|ref|NP_248080.1| 106 SCGLGSSASITIGTIKAVSGFYNKELKDDEIAKlGYMVEKEIQGKASITDTSTITYKGIL 165
                                   579*****************987655555555515599999***9999999999888775 PP

>> Herpes_U34  Herpesvirus virion protein U34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00019      0.38      94     143 ..      28      80 ..      23      91 .. 0.77
   2 ?    0.1   0.1      0.21   4.1e+02     145     176 ..     178     210 ..     139     220 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                                   --------B..--SEEE.E-T...T-EEEE-HHHHHHHSS-SSS-EEEEEEEE CS
                    Herpes_U34  94 vdavsqfghllvdevnvyLkk...nesvvvslsDitkiKasdlgVfnkcvivr 143
                                   +d++s +    ++e +++L+    n+s++++l+ i++i ++++g f+ c+   
  gi|15669275|ref|NP_248080.1|  28 IDLTSTIEIKETQEDEIILNLndlNKSLGLNLNEIKNINPNNFGDFKYCLCAI 80 
                                   67777777777888888887622268********************9998654 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.21
                                   S.SSS-EEEEEEEEE-S-HHH.HHHHHHHHHHH CS
                    Herpes_U34 145 ylrdevvvleflvvgpknekr.ltslLkaiaak 176
                                    + ++  + +fl+v +++ k+ + +l +++a  
  gi|15669275|ref|NP_248080.1| 178 EFEEFLKNCKFLIVYAEKRKKkTAELVNEVAKI 210
                                   457788889999998887665155566888765 PP

>> Glyco_hydro_67N  Glycosyl hydrolase family 67 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00025      0.49      34     105 ..      85     153 ..      76     166 .. 0.84
   2 ?   -1.0   0.0         1   2.1e+03      56      74 ..     194     212 ..     155     241 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                                   HHHHHHHHHHHHHHHTS---EE-SS--SSEEEEE-TTT-HHHHHT--THHHHTTTTT-EEEEEEEETTEEEE CS
               Glyco_hydro_67N  34 evakqELkeglkgilgkelkvsseekkessilvgtleelaeieslalpeeleelgeeGfllktveveekksv 105
                                   +  + E k+g+k  +  ++ +s    +++si++gt+++++ + +++l++  +e+++ G++++  e+++k s+
  gi|15669275|ref|NP_248080.1|  85 DYLNIEPKTGFKINISSKIPISCGLGSSASITIGTIKAVSGFYNKELKD--DEIAKLGYMVEK-EIQGKASI 153
                                   555667788888889999999999999999***********99999999..89********99.88887765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1
                                   -SS--SSEEEEE-TTT-HH CS
               Glyco_hydro_67N  56 seekkessilvgtleelae 74 
                                   +++kk+ + lv +++++++
  gi|15669275|ref|NP_248080.1| 194 EKRKKKTAELVNEVAKIEN 212
                                   3333333333333333333 PP

>> DASH_Dad1  DASH complex subunit Dad1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.2    0.0063        13      18      31 ..      42      55 ..      33      63 .. 0.82
   2 ?   -1.6   0.0       1.6   3.2e+03      11      24 ..     173     186 ..     167     189 .. 0.79
   3 ?    0.6   0.1      0.33   6.6e+02       4      22 ..     211     229 ..     198     233 .. 0.82
   4 ?    0.7   0.0      0.31   6.1e+02      18      41 ..     241     267 ..     234     269 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0063
                     DASH_Dad1 18 eevlnnlnaLNRsL 31
                                  +e++ nln+LN+sL
  gi|15669275|ref|NP_248080.1| 42 DEIILNLNDLNKSL 55
                                  68***********9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                     DASH_Dad1  11 qeIaesmeevlnnl 24 
                                   + I  ++ee+l+n 
  gi|15669275|ref|NP_248080.1| 173 RKIKGEFEEFLKNC 186
                                   56889999999986 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.33
                     DASH_Dad1   4 rqRdrliqeIaesmeevln 22 
                                   + +d++ +eI + ++e l+
  gi|15669275|ref|NP_248080.1| 211 ENKDEIFKEIDKVIDEALK 229
                                   5788888888888888876 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.31
                     DASH_Dad1  18 eevlnnlnaLNRs...LEeviavgkeF 41 
                                    + ++ l +LN+s   L+ ++++g+ F
  gi|15669275|ref|NP_248080.1| 241 TKNHELLKKLNIStpkLDRIVDIGNRF 267
                                   555555666666433399999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1601  (0.0892967); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2656.80
//
Query:       gi|15669276|ref|NP_248081.1|  [L=279]
Description: cobalt transporter ATP-binding subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-35  122.2   0.0    4.8e-35  121.1   0.0    1.5  2  ABC_tran     ABC transporter
    1.8e-14   54.3   0.0    2.1e-09   37.6   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    9.3e-09   35.0   0.0    5.2e-08   32.6   0.0    1.9  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0015   18.2   0.1     0.0028   17.4   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.004   16.9   0.0       0.58    9.8   0.0    2.2  2  AAA_15       AAA ATPase domain
  ------ inclusion threshold ------
      0.016   15.8   0.1      0.028   14.9   0.1    1.4  1  AAA_23       AAA domain
      0.056   13.8   0.0      0.082   13.3   0.0    1.3  1  AAA_16       AAA ATPase domain
      0.077   12.9   0.2       0.17   11.8   0.0    1.6  2  RsgA_GTPase  RsgA GTPase
       0.12   12.4   0.0       0.45   10.5   0.0    2.0  1  TIR-like     Predicted nucleotide-binding protein containing 


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.1   0.0   2.4e-38   4.8e-35       1     137 []      20     168 ..      20     168 .. 0.96
   2 ?   -1.8   0.0         2     4e+03      22      49 ..     173     199 ..     169     252 .. 0.70

  Alignments for each domain:
  == domain 1  score: 121.1 bits;  conditional E-value: 2.4e-38
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..--S-TTSBHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe..pqlfpeltvr 77 
                                   lk +++k+k+ge+v ++G+nGaGKStL+  + g l+pt+Ge+l++gk++k+  ++l ++rk +g ++q+  +q+f  + v+
  gi|15669276|ref|NP_248081.1|  20 LKGINFKVKKGEMVSLLGPNGAGKSTLFLHFNGILRPTKGEVLIKGKPIKYdkKSLVEVRKTVGLVFQNpdDQIFAPT-VK 99 
                                   789************************************************999999************767777777.99 PP

                                   HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                   e              e ++++++al+ +g++++++++     ++LSgGqk+rva+a +l+ +p++++lDEpta
  gi|15669276|ref|NP_248081.1| 100 EDvafgplnlglpkeEVEKRVKEALKAVGMEGFENKPP----HHLSGGQKKRVAIAGILAMQPEVIVLDEPTA 168
                                   999**********9999999*****************9....*****************************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2
                                   SSHHHHHHHHTTSS--SEEEEEETTCEG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  22 aGKStLlkllagllkpteGeilldgkdl 49 
                                    G S ++kll+ l k+ +  i +  +d+
  gi|15669276|ref|NP_248081.1| 173 VGASKIMKLLYDLNKKGMT-IIISTHDV 199
                                   6778888888888765433.33555554 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   8.5e-06     0.017       4      26 ..      35      74 ..      32     126 .. 0.65
   2 !   37.6   0.0   1.1e-12   2.1e-09     231     301 ..     134     201 ..     101     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.5e-06
                        AAA_21  4 liGpNgsGKSnLLdaldllarl.................d 26
                                  l GpNg+GKS+L+  + ++ r                   
  gi|15669276|ref|NP_248081.1| 35 LLGPNGAGKSTLFLHFNGILRPtkgevlikgkpikydkkS 74
                                  89***********999777654444444444444444430 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 1.1e-12
                        AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                   + p+++lS G+k+  a++ +l+ ++    ++++DEp +gL+P   +++++ll +l+++g  +i++TH+  l
  gi|15669276|ref|NP_248081.1| 134 NKPPHHLSGGQKKRVAIAGILAMQP---EVIVLDEPTAGLDPVGASKIMKLLYDLNKKGMTIIISTHDVDL 201
                                   45899******************99...9**************************************9665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   2.6e-11   5.2e-08      25     203 ..      31     203 ..      21     217 .. 0.68

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.6e-11
                                   SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.....BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.....skekasvkkaeveitfdnedkklkiekeevsis 100
                                   ++ +++GpNG+GKs l+       G      lr +k + li+       k++    + +v ++f+n+d+++        ++
  gi|15669276|ref|NP_248081.1|  31 EMVSLLGPNGAGKSTLFLHF---NG-----ILRPTKGEVLIKGkpikyDKKSLVEVRKTVGLVFQNPDDQIFAP--T--VK 99 
                                   57789*********997333...34.....59999999999987664333333444567888889998883222..2..22 PP

                                   EEEETTSEEEEEETTEEE-H..HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                   xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 101 rrvkrkgeseykingkevtk..kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                    + +  g  +  + ++ev+k  ke  + + ++g++ +    LSgG+k+ va+a ++A+q   p+ + +lDe  a LD    
  gi|15669276|ref|NP_248081.1| 100 -EDVAFGPLNLGLPKEEVEKrvKEALKAVGMEGFENKpphHLSGGQKKRVAIAGILAMQ---PE-VIVLDEPTAGLDPVGA 175
                                   .2222344566666666655335555566666666445559**************9987...44.679************* PP

                                   HHHHHHHHHHCTT.SEEEEE-SSHHHCC CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                         SMC_N 177 kkvaellkekskn.aQfivislreemle 203
                                   +k+ +ll   +k+ + +i+ +++ +++ 
  gi|15669276|ref|NP_248081.1| 176 SKIMKLLYDLNKKgMTIIISTHDVDLVP 203
                                   ********99988456666666655554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.4e-06    0.0028      16      39 ..      24      47 ..      18      61 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.4e-06
                        AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                   ++++  +++ l Gp+G+GKSTl+
  gi|15669276|ref|NP_248081.1| 24 NFKVKKGEMVSLLGPNGAGKSTLF 47
                                  4667745599************98 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0065        13      23      47 ..      31      54 ..      21     134 .. 0.78
   2 !    9.8   0.0   0.00029      0.58     324     365 ..     158     198 ..     141     202 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0065
                        AAA_15 23 eeltvliGkNnsGKSsilealdlFl 47
                                  e +  l G+N++GKS++   ++ +l
  gi|15669276|ref|NP_248081.1| 31 E-MVSLLGPNGAGKSTLFLHFNGIL 54
                                  3.78899*********976665555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00029
                        AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                   + +++++EP a L p   + ++kll++l +++   +ii+TH 
  gi|15669276|ref|NP_248081.1| 158 PEVIVLDEPTAGLDPVGASKIMKLLYDLNKKGM-TIIISTHD 198
                                   5789************************99997.9******7 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.4e-05     0.028      15      36 ..      23      47 ..      19      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                        AAA_23 15 idF...skgltlItGpNGaGKTTil 36
                                  i+F   +  ++ + GpNGaGK+T++
  gi|15669276|ref|NP_248081.1| 23 INFkvkKGEMVSLLGPNGAGKSTLF 47
                                  66666555688999**********8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.1e-05     0.082      21      63 ..      29      70 ..      20     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.1e-05
                        AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                  +g  e+v l G+ G GKs+l  ++   l+ ++g + ++gk  ++
  gi|15669276|ref|NP_248081.1| 29 KG--EMVSLLGPNGAGKSTLFLHFNGILRPTKGEVlIKGKPIKY 70
                                  34..89***************99998888887666699988888 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.5e-05      0.17      92     120 ..      22      51 ..       9      66 .. 0.79
   2 ?   -3.3   0.0       3.6   7.2e+03      35      59 ..     178     202 ..     173     212 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.5e-05
                                   HHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                   RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinall 120
                                    ++ ++k+ +++ l+G+ G+GKStL  +++
  gi|15669276|ref|NP_248081.1|  22 GINFKVKKgEMVSLLGPNGAGKSTLFLHFN 51 
                                   56667776699**************86655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.6
                                   HHHHHHHHHHTT-EEEEEEE-GGG- CS
                   RsgA_GTPase  35 ldrfLvlaeekgiepvivlnKiDll 59 
                                   + ++L  +++kg++++i    +Dl+
  gi|15669276|ref|NP_248081.1| 178 IMKLLYDLNKKGMTIIISTHDVDLV 202
                                   5666777777777777766666665 PP

>> TIR-like  Predicted nucleotide-binding protein containing TIR-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00022      0.45      11      98 ..     145     276 ..     139     279 .] 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                      TIR-like  11 eaaeevkelLeklglepiilee...qvnkg.ktiiekleealksvdfaivlltpd.Divakrke................. 69 
                                   + + +++ +L  ++ e+i+l+e   + +    + i kl  +l++  + i++ t d D v    +                 
  gi|15669276|ref|NP_248081.1| 145 KKRVAIAGILA-MQPEVIVLDEptaGLDPVgASKIMKLLYDLNKKGMTIIISTHDvDLVPVYADkvyvmydgkilkegtpk 224
                                   55667888998.999999999987766777788899999999999999999999985444333345666669999999999 PP

                      TIR-like  70 .......................ekkraRqNVifElGlflgklgrenviilk 98 
                                                          e  + ++N+ +E G+ +g + r+ v +lk
  gi|15669276|ref|NP_248081.1| 225 evfsdvetirkanlrlprvahliEILNKKDNIPIEWGFTIGEVRRNIVNYLK 276
                                   9999999999999******99999999****************999988885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1862.71
//
Query:       gi|15669277|ref|NP_248082.1|  [L=268]
Description: cobalt transport protein CbiQ [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-63  211.9   8.9    8.4e-63  211.9   8.9    1.3  2  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.9   8.9   4.7e-67   8.4e-63       2     212 ..      15     226 ..      14     232 .. 0.97
   2 ?   -4.1   0.2      0.55   9.9e+03      64      72 ..     242     250 ..     235     261 .. 0.43

  Alignments for each domain:
  == domain 1  score: 211.9 bits;  conditional E-value: 4.7e-67
                                   SCCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---..HHHHHHHCCCHCHHHHHHHHHHE....... CS
                          CbiQ   2 ksvlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp..rvlaqalilpllflllgllillfqlitteg 80 
                                   ++ l++++p++k+i+ ++lll++v++++++++lii+++  +lll++++   +++a ++++pl+f +l+l+i++f l++t +
  gi|15669277|ref|NP_248082.1|  15 SNKLRHVNPKLKVIFALSLLLISVFSTSFIVPLIIFFINSILLLFKAKVpkKIYAVFVGIPLGFGILNLVIFAF-LFGTVE 94 
                                   6889***********************************999999999889***********************.9***** PP

                                   EECTTEEE....E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHHHHH CS
                          CbiQ  81 efvfaggg.qisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLleevqri 160
                                   +f ++++g +i ++++G+  glll++R+l  +s +l+la+TTp+ el++ +++l++P++l+++++L+yR+if+L+ee++++
  gi|15669277|ref|NP_248082.1|  95 WFKINVFGfEIPVYKDGIELGLLLFGRMLGGVSSMLFLAFTTPMVELFYIFRELKMPDVLVDMMMLIYRYIFVLYEEYEKM 175
                                   ********************************************************************************* PP

                                   HHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS.. CS
                          CbiQ 161 kqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg.s 212
                                   k Aq++Rlg+s  +++++++slg l+a+lf+ra++++e+++++m++R+Y+g +
  gi|15669277|ref|NP_248082.1| 176 KFAQESRLGTS--NLKSTYKSLGALAAHLFIRAWEKGEKLNITMMSRCYDGkI 226
                                   ***********..**************************************44 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.55
                                   HHHHHHHHH CS
                          CbiQ  64 lllgllill 72 
                                   +++ + i+l
  gi|15669277|ref|NP_248082.1| 242 FIAIFDIFL 250
                                   222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1692.86
//
Query:       gi|15669278|ref|NP_248083.1|  [L=95]
Description: cobalt transport protein CbiN [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-28   97.5   0.2      4e-28   97.2   0.2    1.1  1  CbiN      Cobalt transport protein component CbiN


Domain annotation for each model (and alignments):
>> CbiN  Cobalt transport protein component CbiN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.2   2.2e-32     4e-28       2      67 .]       6      74 ..       5      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 2.2e-32
                          CbiN  2 llllllvvllavvplflv..kgae...FgGaDdqaeevIeeiapdyepwfeplweppsGEiESlLFalQAA 67
                                  ++ll++v++++++pl+++  kg+e   FgG+Ddq+ ev+ee+  +y+pwf+p+weppsGEiESlLFalQAA
  gi|15669278|ref|NP_248083.1|  6 IILLAIVAIIIALPLIIYagKGEEegyFGGSDDQGCEVVEEL--GYKPWFHPIWEPPSGEIESLLFALQAA 74
                                  799***************88666689**************97..9*************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 617.19
//
Query:       gi|15669279|ref|NP_248084.1|  [L=233]
Description: cobalt transport protein CbiM [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.1e-54  182.6  15.7    9.2e-54  182.4  15.7    1.0  1  CbiM        Cobalt uptake substrate-specific transmembrane re
  ------ inclusion threshold ------
      0.028   14.0   0.0       0.28   10.8   0.0    2.5  2  ATP-synt_J  ATP synthase j chain
        1.8    6.7   8.4        2.3    6.4   8.4    1.0  1  DUF2070     Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> CbiM  Cobalt uptake substrate-specific transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.4  15.7   1.5e-57   9.2e-54       1     207 []       2     209 ..       2     209 .. 0.94

  Alignments for each domain:
  == domain 1  score: 182.4 bits;  conditional E-value: 1.5e-57
                          CbiM   1 HipdgiLspavllaayavalallalalrrlrkeldear..vpllallaafifaaqminipipggtslHllgavlaaiLlGp 79 
                                   Hi++g+L+p +++++++++++++a+++ +l+k l+e     pl+a+ +a +f+++++++p  +g+++H++g++l a+L+G 
  gi|15669279|ref|NP_248084.1|   2 HIMEGYLPPMWCAVWWVLSGIVIAYGIVKLKKLLEESPemKPLVAISGAYMFILSSLKMPSVTGSCSHPCGNGLGAVLFGV 82 
                                   *******************************999977779***************************************** PP

                          CbiM  80 waaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaallvalel 160
                                    ++++ +a+vll+qal++++GG+t+LGaN ++m+++g+++a +vyrl  +      +  +++f+aal++ +l+++++a++l
  gi|15669279|ref|NP_248084.1|  83 PITAVLAAIVLLFQALFLAHGGLTTLGANDFSMGIVGPAAAVIVYRLCMKA---GLSSTVGIFFAALFGDWLTYVTTAVQL 160
                                   **********************************************66444...6789*********************** PP

                          CbiM 161 als.gleas..lsltaalaamllvhlpvgilEgviTaaivkalkkvrpel 207
                                   al+ +++ s  +++t+++ + + +++p++i+Eg++T++i  ++kk+rp+l
  gi|15669279|ref|NP_248084.1| 161 ALAfPIP-SftAAFTKFIVIYAYTQVPLAIAEGILTVIIWDYIKKLRPDL 209
                                   ***7554.33589999999999**************************97 PP

>> ATP-synt_J  ATP synthase j chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.7e-05      0.28      14      37 ..      18      41 ..       8      43 .. 0.87
   2 ?   -0.3   0.0      0.13     8e+02      15      27 ..     121     133 ..     120     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.7e-05
                                  HHHHHHHHHHHHHHHHHSTTSSSS CS
                    ATP-synt_J 14 faaglivlygvnkaqnammnsdEf 37
                                  + +g++++yg+ k+++++ +s+E 
  gi|15669279|ref|NP_248084.1| 18 VLSGIVIAYGIVKLKKLLEESPEM 41
                                  689******************995 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHH CS
                    ATP-synt_J  15 aaglivlygvnka 27 
                                   aa++iv+ +  ka
  gi|15669279|ref|NP_248084.1| 121 AAAVIVYRLCMKA 133
                                   7999999887776 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   8.4   0.00038       2.3       3     176 ..      30     206 ..      28     226 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00038
                       DUF2070   3 klskyifrlPswkvsllliillalligllaflssk.........lfgillfglp...alvaflltlpvlrilggrltykrs 71 
                                   kl k++ ++P++k  ++++   +++++ l + s             g +lfg+p    l+a++l+ ++l +++g       
  gi|15669279|ref|NP_248084.1|  30 KLKKLLEESPEMKPLVAISGAYMFILSSLKMPSVTgscshpcgnGLGAVLFGVPitaVLAAIVLLFQALFLAHGG------ 104
                                   677777888888888888888888888888877778899999998899999999554444444444444444333...... PP

                       DUF2070  72 lflalltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspe 152
                                   l+   ++ + + i+  +a++++   ++l + a + s + +f+  l+  +++  ++  + +l   i +++a+++ ++++  +
  gi|15669279|ref|NP_248084.1| 105 LTTLGANDFSMGIVGPAAAVIV---YRLCMKAGLSSTVGIFFAALFGDWLTYVTTAVQLALAFPIPSFTAAFTKFIVIYAY 182
                                   4445555555555555555555...56667777777777777777777777777777777777777777777777777777 PP

                       DUF2070 153 sfllllllslifalavylfivvvd 176
                                   + ++l+++  i+ ++++ +i+ + 
  gi|15669279|ref|NP_248084.1| 183 TQVPLAIAEGILTVIIWDYIKKLR 206
                                   9999**************998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1443.51
//
Query:       gi|15669280|ref|NP_248085.1|  [L=214]
Description: urease accesory protein UreH [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-15   56.0  18.0    4.9e-10   39.2   7.7    2.0  2  NicO       High-affinity nickel-transport protein
    1.7e-09   37.9  12.6    2.8e-08   33.9  12.6    2.5  1  DsbD_2     Cytochrome C biogenesis protein transmembrane regi
    8.3e-08   31.9  10.1    8.3e-08   31.9  10.1    1.5  1  DUF2162    Predicted transporter (DUF2162)
  ------ inclusion threshold ------
      0.055   14.1   8.0       0.52   10.9   0.0    3.8  4  DUF2627    Protein of unknown function (DUF2627)
        2.1    8.0   5.5         15    5.2   0.7    2.3  2  PIRT       Phosphoinositide-interacting protein family
        2.2    8.8  13.7       0.98    9.9   0.4    3.6  3  DUF202     Domain of unknown function (DUF202)
        3.3    7.7   7.7       0.25   11.3   0.3    2.5  2  RseC_MucC  Positive regulator of sigma(E), RseC/MucC
        4.4    7.7  11.1       0.96    9.8   5.1    2.7  3  DUF4134    Domain of unknown function (DUF4134)


Domain annotation for each model (and alignments):
>> NicO  High-affinity nickel-transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   7.7   2.2e-13   4.9e-10       4     100 ..       9     103 ..       7     115 .. 0.88
   2 !   22.9   2.5   2.1e-08   4.6e-05     186     270 ..     119     204 ..     106     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2.2e-13
                          NicO   4 liglsflyGvrHAvdagHgkaiirklmqagktalkrGillslgsslvvvlvavllvvaavlvlrltslsetgaaigteias 84 
                                    ++++f++G++HA+++gHgk ++++++   k  lk +ill+   ++++++v  ll +++  +l+  sl+      +++++ 
  gi|15669280|ref|NP_248085.1|   9 YAITAFILGMLHALEPGHGKSVVAAYILGTKADLKDAILLGTTITISHTAVIFLLGILSIYLLE--SLNVDVVHDMMSVVG 87 
                                   5789**************************************9999999999999888888888..888888888999999 PP

                          NicO  85 Fllvilllnllllrkl 100
                                    l++i+++++++   l
  gi|15669280|ref|NP_248085.1|  88 GLILIAVGIWIIRSYL 103
                                   99********996655 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 2.1e-08
                          NicO 186 alfavGlrlcdgadivlmfaalnwaflggrklvyamsitgtsitvalliglivtlklvakkfalsgslwaaiisle...le 263
                                     +++Gl++c++a+ vl++++  + +++g++ v  +si g++i ++ l+ + v  k + kk+ ++ + +++++ ++   + 
  gi|15669280|ref|NP_248085.1| 119 LGLSAGLVPCPAALAVLLLSISSGNLIDGLIYVAIFSI-GLAISLTGLAVAFVESKELIKKYVGNRK-VSKLPLISgsiII 197
                                   6799**********************************.9999999999999999988888888887.3444333323466 PP

                          NicO 264 ivGavlv 270
                                   ++G++ +
  gi|15669280|ref|NP_248085.1| 198 LIGLYTI 204
                                   6666665 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9  12.6   1.3e-11   2.8e-08      34     197 ..      44     200 ..      10     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.3e-11
                        DsbD_2  34 alllynlGRilsYallGalvgllgsvlqlageleglrallgvllgllllllglklllkkkllklerlgkllsrllkklakk 114
                                   + +l  +  ++s +++  l+g+l+  l  + ++++++ +++v+ gl+l+++g++++               +++l +  +k
  gi|15669280|ref|NP_248085.1|  44 DAILLGTTITISHTAVIFLLGILSIYLLESLNVDVVHDMMSVVGGLILIAVGIWII---------------RSYLHPHEHK 109
                                   45555555567777777788888888888888889999999999999999888885...............5677888888 PP

                        DsbD_2 115 lkslasalllGllnGllpCglvysalllalasgsaleGalvmlaFgLGTlpalllfglllgllskklr........kkllr 187
                                   ++++++ ++lGl  Gl+pC+  +++lll+++sg++++G ++ ++F++G  ++l+ +++++   ++ ++         kl  
  gi|15669280|ref|NP_248085.1| 110 VDTKKGVITLGLSAGLVPCPAALAVLLLSISSGNLIDGLIYVAIFSIGLAISLTGLAVAFVESKELIKkyvgnrkvSKLPL 190
                                   8999********************************************999999888887666554442223322233333 PP

                        DsbD_2 188 lagvllillg 197
                                   ++g ++il+g
  gi|15669280|ref|NP_248085.1| 191 ISGSIIILIG 200
                                   5555555555 PP

>> DUF2162  Predicted transporter (DUF2162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9  10.1   3.7e-11   8.3e-08      41     181 ..      55     209 ..      32     214 .] 0.60

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3.7e-11
                       DUF2162  41 lflllalllssldekllesl..lrygmvlhllmAlllialGlytlkkwkk.skkdvssrt......flalvlPCPvCltai 112
                                   + +++++ll+ l++ llesl  +    +++++ +l+lia+G+++++++ + ++++v+++         a ++PCP+ l+++
  gi|15669280|ref|NP_248085.1|  55 SHTAVIFLLGILSIYLLESLnvDVVHDMMSVVGGLILIAVGIWIIRSYLHpHEHKVDTKKgvitlgLSAGLVPCPAALAVL 135
                                   333333333333333333320022344568999999**********9776655555554345555599************* PP

                       DUF2162 113 lfsiillas...slglspvevglvlglv.flilvlvtyllsrkivkltktny.piiLGnlmlfiGlyfLlsali 181
                                   l+si        ++ + ++++gl++ l+ +++  + +  l++k v ++k+++ p i G++ ++iGly+++  ++
  gi|15669280|ref|NP_248085.1| 136 LLSISSGNLidgLIYVAIFSIGLAISLTgLAVAFVESKELIKKYVGNRKVSKlPLISGSIIILIGLYTIAHPIL 209
                                   ****97665122444444555555544312333333334555555544444415566999********997766 PP

>> DUF2627  Protein of unknown function (DUF2627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.055   1.2e+02      19      49 ..      37      68 ..      29      75 .. 0.83
   2 ?   10.9   0.0   0.00023      0.52      30      67 ..      73     110 ..      69     115 .. 0.83
   3 ?   -1.6   0.0       1.9   4.3e+03      42      53 ..     154     165 ..     136     183 .. 0.69
   4 ?    2.6   0.6     0.094   2.1e+02      39      61 ..     187     209 ..     148     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.055
                       DUF2627 19 Gikl.mrdalfgilsspfsslwlqflaGlllf 49
                                  G k+ ++da++  ++ ++s++++ fl+G+l +
  gi|15669280|ref|NP_248085.1| 37 GTKAdLKDAILLGTTITISHTAVIFLLGILSI 68
                                  5554489*********************9976 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00023
                       DUF2627  30 ilsspfsslwlqflaGlllfaiglgfiaGfilhrdrKr 67 
                                   +l+  + + +++++ Gl+l+a+g+++i  ++  ++ K 
  gi|15669280|ref|NP_248085.1|  73 SLNVDVVHDMMSVVGGLILIAVGIWIIRSYLHPHEHKV 110
                                   566677778999****************9999888885 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.9
                       DUF2627  42 flaGlllfaigl 53 
                                   f +Gl++ + gl
  gi|15669280|ref|NP_248085.1| 154 FSIGLAISLTGL 165
                                   445555555554 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.094
                       DUF2627  39 wlqflaGlllfaiglgfiaGfil 61 
                                    l +++G ++++igl+ ia  il
  gi|15669280|ref|NP_248085.1| 187 KLPLISGSIIILIGLYTIAHPIL 209
                                   688999*********99986655 PP

>> PIRT  Phosphoinositide-interacting protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3    0.0074        17      50      97 ..      51      98 ..      38     109 .. 0.80
   2 ?    5.2   0.7    0.0066        15      50      96 ..     151     202 ..     138     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0074
                          PIRT 50 iivlsvGgavfllGvvittlsrnstlknkdkevfklsGpaflslGlml 97
                                   i +s  + +fllG++   l  + +++  ++ ++ + G +++++G+ +
  gi|15669280|ref|NP_248085.1| 51 TITISHTAVIFLLGILSIYLLESLNVDVVHDMMSVVGGLILIAVGIWI 98
                                  5789999********988887777777777777777777777777655 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0066
                          PIRT  50 iivlsvGgavfllGvvittlsrnstlkn..kdkevfk...lsGpaflslGlm 96 
                                   + ++s+G a+ l G++++ +  ++ +k+   +++v+k   +sG +++ +Gl 
  gi|15669280|ref|NP_248085.1| 151 VAIFSIGLAISLTGLAVAFVESKELIKKyvGNRKVSKlplISGSIIILIGLY 202
                                   679999********99999965555544123555665222567777777765 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   6.4      0.61   1.4e+03      19      54 ..      62      98 ..       5      99 .. 0.72
   2 ?    9.9   0.4   0.00044      0.98      17      59 ..      88     139 ..      83     145 .. 0.74
   3 ?    5.5   0.3     0.011        24      17      56 ..     159     205 ..     151     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.61
                        DUF202 19 alialglallrffl.tgepsalgkilglilivlgilt 54
                                  +l++l++ ll + + +  +  ++++ glili++gi++
  gi|15669280|ref|NP_248085.1| 62 LLGILSIYLLESLNvDVVHDMMSVVGGLILIAVGIWI 98
                                  3333444444332233334445677799999999987 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00044
                        DUF202  17 slalialglallrffltgepsa.........lgkilglilivlgiltllvgl 59 
                                   +l lia+g+ ++r+ l++++ +         lg  +gl+  ++++++ll+++
  gi|15669280|ref|NP_248085.1|  88 GLILIAVGIWIIRSYLHPHEHKvdtkkgvitLGLSAGLVPCPAALAVLLLSI 139
                                   5789999999999999666666333333333589999998888888887765 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.011
                        DUF202  17 slalialglallrffl.......tgepsalgkilglilivlgiltll 56 
                                   +++l++l++a++ +            +s+l  i g i+i++g+ t++
  gi|15669280|ref|NP_248085.1| 159 AISLTGLAVAFVESKElikkyvgNRKVSKLPLISGSIIILIGLYTIA 205
                                   57777777777765447778777666666779999999999999986 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00011      0.25      79     117 ..      62     105 ..      44     118 .. 0.76
   2 ?   -0.8   1.6       0.6   1.3e+03      77     106 ..     134     160 ..     123     187 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                     RseC_MucC  79 ilgallgsall.....gssellaalgallglvlgflivrllskr 117
                                   +lg+l +++l      + +++++++g+l+++++g++i+r + + 
  gi|15669280|ref|NP_248085.1|  62 LLGILSIYLLEslnvdVVHDMMSVVGGLILIAVGIWIIRSYLHP 105
                                   344444444435558999********************987665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.6
                     RseC_MucC  77 llilgallgsallgssellaalgallglvl 106
                                   +l+l++  g+++  ++ +++a++++ ++ +
  gi|15669280|ref|NP_248085.1| 134 VLLLSISSGNLI--DGLIYVAIFSIGLA-I 160
                                   334444444444..23333333222221.1 PP

>> DUF4134  Domain of unknown function (DUF4134)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.59   1.3e+03      37      54 ..       3      21 ..       1      24 [. 0.71
   2 ?    9.8   5.1   0.00043      0.96      24      92 ..      35     102 ..       9     103 .. 0.86
   3 ?    0.0   0.2      0.48   1.1e+03      37      53 ..     184     200 ..     149     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.59
                       DUF4134 37 pvtkliyaiaa.vvglvga 54
                                  ++++l+yai a ++g++ a
  gi|15669280|ref|NP_248085.1|  3 MIMELLYAITAfILGMLHA 21
                                  5778999998856676665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00043
                       DUF4134  24 iseatsevasyfdpvtkliyaiaavvglvgalkvYikwnsgdqdvkksiaawfgaciflvvaatvlkaf 92 
                                   i   + +++  + ++t++++   av+ l+g l++Y  ++s + dv   +++++g++i ++v   +++++
  gi|15669280|ref|NP_248085.1|  35 ILGTKADLKDAILLGTTITISHTAVIFLLGILSIYL-LESLNVDVVHDMMSVVGGLILIAVGIWIIRSY 102
                                   55567789999999*********************8.89999*****************9999999886 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.48
                       DUF4134  37 pvtkliyaiaavvglvg 53 
                                    v+kl ++ ++++ l+g
  gi|15669280|ref|NP_248085.1| 184 KVSKLPLISGSIIILIG 200
                                   45555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1354.99
//
Query:       gi|15669281|ref|NP_248086.1|  [L=300]
Description: nifB protein NifB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-18   67.8   0.2      2e-18   67.3   0.2    1.2  1  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.035   14.3   0.3       0.92    9.8   0.0    2.4  2  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.2   2.3e-22     2e-18       2     166 ..      33     215 ..      32     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 2.3e-22
                                   EEESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCC CS
                                   xxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklav 75 
                                   +v + Cn +C+fC r+       +r+++   +l +e+++  + ++  + ++ + + i g g+ l++++  e l+ + ++  
  gi|15669281|ref|NP_248086.1|  33 PVAPRCNIACKFCRRSLGkeaceHRPGVALSVLKPEDVESYLNKVLkEIPNiKVVGIAGPGDSLFNKETFETLKIIDEK-F 112
                                   6789************99*****99999999999999999998888566666777788899999999776666666666.7 PP

                                   CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH................HHHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxx RF
                   Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtf................eevlealeklrea 140
                                   p++  +++tng+l+  ++ ++l++l+v +v+++++a+d+e +lk +   + +                e ++++++k+ + 
  gi|15669281|ref|NP_248086.1| 113 PNLIKCLSTNGLLL-NKYYKKLADLNVKTVTVTVNAIDPE-ILKEI-VEWVYydkkvhygiegakiliENQIDGIKKAYDE 190
                                   **************.*************************.88888.777778889999999999999************* PP

                                   TSETEEEEEEEBTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 141 gikrvvdrivglpGendeeleellel 166
                                   ++  +++++v++p  n+ ++++++++
  gi|15669281|ref|NP_248086.1| 191 DLI-IKINTVLIPEINMNHVVDIAKE 215
                                   ***.******************9986 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.025   2.3e+02      92     107 ..      69      84 ..      64      85 .. 0.88
   2 ?    9.8   0.0    0.0001      0.92      45      91 ..     242     291 ..     207     296 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.025
                                   HHHHHHHHHHCTS--- CS
                  Seryl_tRNA_N  92 eleaeleklllaiPNi 107
                                   ++e+ l+k+l +iPNi
  gi|15669281|ref|NP_248086.1|  69 DVESYLNKVLKEIPNI 84 
                                   68899**********8 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHHHHHHCCCCCCTT...S-TCCCCCCCHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  45 leelqaerNelskeIgkakkkk...edaeeliaevkelkeelkaleaelk 91 
                                    eel++ r e+ k I +  + +   +da  li+e k l e +k+++++l+
  gi|15669281|ref|NP_248086.1| 242 CEELKKVREECEKYIPQFRACGqcrADAVGLIKERKILEEFFKEKNKKLN 291
                                   79********************99***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1770.60
//
Query:       gi|15669282|ref|NP_248087.1|  [L=385]
Description: hypothetical protein MJ_1094 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-76  257.5   0.0    2.6e-76  257.0   0.0    1.2  1  YcaO      YcaO cyclodehydratase, ATP-ad Mg2+-binding


Domain annotation for each model (and alignments):
>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.0   0.0   1.5e-80   2.6e-76       1     323 []      66     363 ..      66     363 .. 0.89

  Alignments for each domain:
  == domain 1  score: 257.0 bits;  conditional E-value: 1.5e-80
                          YcaO   1 nGkGateeaArasalgEalErysaegffrgdekrvrasyrelegegaldpeelglyseeekdaadfvlepfdpdrpidwvp 81 
                                   +GkGa++ +A++sa +Ea+Er+sa      d++ v+++     +++ ++ e+l l+             ++ +++  +wv+
  gi|15669282|ref|NP_248087.1|  66 YGKGANDIQAKVSACMEAIERFSAS----YDKNKVKEK-----PDNPINVEDLILP-------------QYADKNVKEWVE 124
                                   5*********************977....777777554.....5566*********.............78888999**** PP

                          YcaO  82 gwsltdgeevlvPanlvylyeppegearlfletsnGlAaGntleeAilhGllEliERdafalawyerlplpridla..sdp 160
                                   g +++++e++ vPa++v++  p +  ++lf+ ++nGlA+Gn+l+eAilh+ lE+iERda +la  +r  + +i+++  ++p
  gi|15669282|ref|NP_248087.1| 125 GIDIINNETIDVPADAVFY--PTS--GKLFRGNTNGLASGNNLDEAILHATLEIIERDAWSLADLARKIPTKINPEdaKNP 201
                                   *******************..444..47*******************************999988886566799774455* PP

                          YcaO 161 eirellerlreagievrlldatldlgipvvaavlvd..pk.lllvagaGahldpevAlerAltElaqsrltlisgaredpd 238
                                    i+el+e++++ag++++l+d+t++++ipvvaa+++d  ++ l+l++g+G+hl pe+A++rAltE+aqsr+++ +g r d++
  gi|15669282|ref|NP_248087.1| 202 LIHELIEKYEKAGVKIILKDLTSEFEIPVVAAISDDlsKNpLMLCVGVGCHLHPEIAILRALTEVAQSRASQLHGFRRDAK 282
                                   ************************************9743688999*****************************888888 PP

                          YcaO 239 fdeeladvatleradreallwl.peaaakrldfllfaewassgdleedletllerlkaagld.vlvvdltrpdlglpvvkv 317
                                    +ee++++  +er +r+ + w+  e++ + +d+ +  +  +  dl++dl+ + ++l + g+d  ++vdl+  ++g+ +v+v
  gi|15669282|ref|NP_248087.1| 283 LREEFTSKIPYERLKRIHRKWFeFEGEINIADMPN--N--ARYDLKKDLKFIKDKLSEFGFDkLIYVDLN--KVGVDAVRV 357
                                   879*************9999*87777775666644..3..335***************************..7******** PP

                          YcaO 318 ivPgle 323
                                   i+P++e
  gi|15669282|ref|NP_248087.1| 358 IIPKME 363
                                   ****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2331.76
//
Query:       gi|15669283|ref|NP_248088.1|  [L=423]
Description: hypothetical protein MJ_1095 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-41  140.1   0.0    6.4e-41  139.1   0.0    1.6  1  DUF1743          Domain of unknown function (DUF1743)
    1.1e-08   34.9   0.5    2.7e-08   33.7   0.3    1.8  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.003   16.9   0.4      0.003   16.9   0.4    1.7  2  zf_Rg            Reverse gyrase zinc finger
     0.0073   16.2   0.7      0.019   14.9   0.7    1.7  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0087   15.9   2.5      0.016   15.1   2.5    1.4  1  C1_1             Phorbol esters/diacylglycerol binding domain
  ------ inclusion threshold ------
      0.024   14.6   3.1      0.048   13.6   3.1    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.043   13.8   1.5       0.11   12.5   1.5    1.6  1  DZR              Double zinc ribbon
      0.056   14.3   0.4       0.27   12.1   0.2    2.1  2  zf-PARP          Poly(ADP-ribose) polymerase and DNA-Ligase Z
      0.075   13.1   2.3       0.27   11.4   0.7    2.3  2  Ribosomal_L37ae  Ribosomal L37ae protein family
       0.11   12.3   0.0       0.19   11.5   0.0    1.3  1  RMI2             RecQ-mediated genome instability protein 2
       0.31   11.6   4.5       0.98   10.0   4.5    1.8  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.99    9.4   6.3        5.5    7.0   0.3    2.3  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.1   0.0   4.3e-44   6.4e-41       1     116 []     147     258 ..     147     258 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.1 bits;  conditional E-value: 4.3e-44
                                   TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEEEEEE CS
                       DUF1743   1 grgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvlfGir 80 
                                   grgiiGA+ a++  ++   +tyEllaYr++e wg +re+de+svie+d++t+p+tfdn+D+++++++++P+tp+pvlfGir
  gi|15669283|ref|NP_248088.1| 147 GRGIIGALGAISSTPP---YTYELLAYRKKEMWGkKREIDEKSVIEMDKETFPYTFDNYDYENEKILIAPNTPCPVLFGIR 224
                                   89***********776...9************************************************************* PP

                                   ES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                       DUF1743  81 gedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                   g d+e llka+++i+   e+ e++++f+tn+gtd h
  gi|15669283|ref|NP_248088.1| 225 GIDAEILLKAMHKIEG--EKPERFMIFKTNHGTDVH 258
                                   ****************..****************88 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       7.6   1.1e+04      12      24 ..      53      65 ..      48      66 .. 0.73
   2 !   33.7   0.3   1.8e-11   2.7e-08       1      76 []     273     347 ..     273     347 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.6
                                  EEEETTEEEEEEE CS
               tRNA_anti-codon 12 drsggkvifidlr 24
                                  +r++g+v+ ++l+
  gi|15669283|ref|NP_248088.1| 53 TRGNGGVAIHILD 65
                                  5999999988886 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 1.8e-11
                                   EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEEE CS
               tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrrpggelelkveeiell 76 
                                   V v Grv+   +  +g+++ ++l Dgtg+i +++    ++++++  +l +Gd++ v+G+v++ p g   +++e+i++l
  gi|15669283|ref|NP_248088.1| 273 VIVYGRVVEEPRDIEGGHVIFKLSDGTGEIDCMAYEptKGFRDIIRKLIVGDYIAVYGTVREKPLG---INIEKIKIL 347
                                   67899**99998888************************************************866...788888775 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       6.5   9.8e+03      14      25 ..     138     149 ..     138     150 .. 0.87
   2 !   16.9   0.4     2e-06     0.003       5      31 ..     354     380 ..     351     393 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 6.5
                         zf_Rg  14 gGdisdeRlekG 25 
                                   gG+  +++l +G
  gi|15669283|ref|NP_248088.1| 138 GGEFIKYKLGRG 149
                                   799999***999 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2e-06
                         zf_Rg   5 vfeklCPNCgGdisdeRlekGLpCkrC 31 
                                   v  k CP CgG ++++  ++G  Ck+C
  gi|15669283|ref|NP_248088.1| 354 VKDKRCPYCGGTLKAKGKKAGYKCKKC 380
                                   56799********************** PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.7   1.3e-05     0.019      29      56 ..     357     384 ..     343     389 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                OrfB_Zn_ribbon  29 ktCseCgsknkealsgrtfkCpnCgfea 56 
                                   k+C+ Cg ++k + ++  +kC++C+ ++
  gi|15669283|ref|NP_248088.1| 357 KRCPYCGGTLKAKGKKAGYKCKKCKKTI 384
                                   89**********************9875 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   2.5   1.1e-05     0.016       6      37 ..     351     383 ..     349     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                                   E--SS--B-TTT-SB--S.SSS-EEEETTT--E CS
                          C1_1   6 rnfkqptfCkhCgeflwg.kekqglkCswCkll 37 
                                   ++f + ++C +Cg  l+  + k g+kC+ Ck +
  gi|15669283|ref|NP_248088.1| 351 KKFVKDKRCPYCGGTLKAkGKKAGYKCKKCKKT 383
                                   6778899*********98899*********976 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.1   3.2e-05     0.048      17      46 .]     356     383 ..     348     383 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-05
                 Zn_Tnp_IS1595  17 ngfvCPhCgsr.kayriktrglfqCkeCrkq 46 
                                   +++ CP+Cg++ ka   k+   ++Ck+C+k+
  gi|15669283|ref|NP_248088.1| 356 DKR-CPYCGGTlKAKGKKA--GYKCKKCKKT 383
                                   444.*****9966666665..9*******85 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.5   7.4e-05      0.11      12      38 ..     356     384 ..     352     388 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.4e-05
                           DZR  12 arfCseCgtklkavaa..edrCpsCgekv 38 
                                   ++ C++Cg +lka  +   ++C +C++ +
  gi|15669283|ref|NP_248088.1| 356 DKRCPYCGGTLKAKGKkaGYKCKKCKKTI 384
                                   678********9887799*******9875 PP

>> zf-PARP  Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0         2     3e+03      62      80 ..      59      77 ..      45      79 .. 0.77
   2 ?   12.1   0.2   0.00018      0.27       9      27 ..     376     394 ..     368     412 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2
                                  ..EETTTTS-HHHHHHHHH CS
                       zf-PARP 62 eeiegfeeLekedqekvrd 80
                                   +i+ ++eL  +d+e++++
  gi|15669283|ref|NP_248088.1| 59 VAIHILDELYSKDKEEIKN 77
                                  5688899*********986 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00018
                                   B-SSS--B--SSSEEEEE- CS
                       zf-PARP   9 kCkkCkkkIakgelRlgkk 27 
                                   kCkkCkk+Ia +e+++ ++
  gi|15669283|ref|NP_248088.1| 376 KCKKCKKTIAYDEIKMIEV 394
                                   8**************9986 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.49   7.3e+02      20      42 ..      72      94 ..      68      96 .. 0.85
   2 ?   11.4   0.7   0.00018      0.27      23      62 ..     346     385 ..     320     388 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.49
                                  HHHHHHHHHHHHS-BEESSSSSS CS
               Ribosomal_L37ae 20 rkrvkkieisqhakytCpfcgkt 42
                                  + ++k+i is  +kyt  +c++t
  gi|15669283|ref|NP_248088.1| 72 KEEIKNITISLVEKYTDFECENT 94
                                  67899***********9999876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00018
                                   HHHHHHHHHS-BEESSSSSS.EEEEEETTEEEETTTTEEEE CS
               Ribosomal_L37ae  23 vkkieisqhakytCpfcgkt.kvkRkavgiwkCkkcgktva 62 
                                   + k+e++  ++ +Cp cg t k k k +g +kCkkc+kt+a
  gi|15669283|ref|NP_248088.1| 346 ILKLEKKFVKDKRCPYCGGTlKAKGKKAG-YKCKKCKKTIA 385
                                   5567777788889******9777777777.8********98 PP

>> RMI2  RecQ-mediated genome instability protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.19      46     114 ..     277     352 ..     257     358 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                          RMI2  46 Gtvvevdaske....sllldDgtgvfvveglnelpktk...kclkeGkYVmVvGvvqssspepvlkavKvvdLsen 114
                                   G vve  ++ e     + l Dgtg +   + +  +  +   ++l  G+Y+ V G+v+++     ++ +K+ +L ++
  gi|15669283|ref|NP_248088.1| 277 GRVVEEPRDIEgghvIFKLSDGTGEIDCMAYEPTKGFRdiiRKLIVGDYIAVYGTVREKPLGINIEKIKILKLEKK 352
                                   5566544443345567889*****977776666555557889999***********66655566999999999876 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.5   0.00066      0.98       7      34 ..     358     385 ..     358     394 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00066
               Zn_ribbon_recom   7 rCgeCGspmtrrkrkgkrhyYrCstyrr 34 
                                   rC +CG++++ +++k ++ + +C++++ 
  gi|15669283|ref|NP_248088.1| 358 RCPYCGGTLKAKGKKAGYKCKKCKKTIA 385
                                   8***********9999898888888765 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3    0.0037       5.5      26      37 ..     358     369 ..     352     370 .. 0.89
   2 ?    5.7   6.2    0.0096        14       6      35 ..     358     385 ..     358     388 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0037
                Zn_ribbon_SprT  26 rCrrCkgtLrgk 37 
                                   rC++C+gtL+ k
  gi|15669283|ref|NP_248088.1| 358 RCPYCGGTLKAK 369
                                   8********865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0096
                Zn_ribbon_SprT   6 rCtgCgreythhlsirrhn..YrCrrCkgtLr 35 
                                   rC+ Cg     +l+ +  +  Y C++Ck t+ 
  gi|15669283|ref|NP_248088.1| 358 RCPYCG----GTLKAKGKKagYKCKKCKKTIA 385
                                   688888....99999999999******98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2802.79
//
Query:       gi|161579522|ref|NP_248089.2|  [L=341]
Description: N-acetyl-gamma-glutamyl-phosphate reductase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-35  122.7   0.0    1.9e-35  121.9   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    1.8e-31  109.6   0.0    2.5e-31  109.2   0.0    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    0.00019   22.2   0.0    0.00037   21.3   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
  ------ inclusion threshold ------
      0.018   15.2   0.0      0.035   14.2   0.0    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.041   13.3   0.0      0.063   12.7   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
      0.052   12.9   0.0      0.081   12.3   0.0    1.2  1  U79_P34          HSV U79 / HCMV P34
      0.094   13.2   0.0       0.76   10.3   0.0    2.1  2  CoA_binding_2    CoA binding domain
       0.21   11.4   0.0       0.51   10.2   0.0    1.7  2  NAD_binding_10   NAD(P)H-binding


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.9   0.0   8.4e-39   1.9e-35       2     121 .]       4     141 ..       3     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 8.4e-39
                                    EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG...GGTTTECEBEEEGGGGGCTT-SEEEE-SCHHH CS
                 Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk...aleegkdlkvedvdeeelkevdivflalpagv 78 
                                    vai+GatGy+G+ellrlL++h +v++++++s+++ aGk + ++++    +e++k+l ++  d++++ ++ +vf+a+p+g+
  gi|161579522|ref|NP_248089.2|   4 VAIIGATGYTGAELLRLLANHEKVNVTYITSRKE-AGKHVFKVHPhlkGIEKYKNLCFTG-DIDKV-DAYLVFTATPHGA 80 
                                    9*********************************.**********777778889999999.88888.899********** PP

                                    HHHHHHHHHHTTSEEEESSSTTTTST..................TSEBE-HHHHGGGGGGH CS
                 Semialdhyde_dh  79 skelapklaeagvkviDlssdfRlkd..................davyvlpevnreaikka 121
                                    s++++p+++e+g+kviDls+d+R++d                  ++ y+lpe++re+ik+a
  gi|161579522|ref|NP_248089.2|  81 SMDIVPDFIERGMKVIDLSGDYRFEDlslyekyykikhkglpdvKIAYGLPELHREEIKEA 141
                                    **********************************************************986 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.2   0.0   1.1e-34   2.5e-31       2     184 .]     159     312 ..     158     312 .. 0.95

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 1.1e-34
                                    HHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHH CS
                Semialdhyde_dhC   2 kPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkav 81 
                                    +PL+++++  er+i++++++vSGaG k                 +++ ++  +++ N+ py+ + +++++pe+++elk++
  gi|161579522|ref|NP_248089.2| 159 APLVKENIIEERIIFDSKTGVSGAGIK-----------------PTETTHFPNVNENINPYKIT-THRHTPEIEKELKKL 220
                                    7*****88799***************9.................********************.*************** PP

                                    HHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCSTTEEEEESSHCHHSSHHHHTTCSSSEE CS
                Semialdhyde_dhC  82 aetkkileftekvsatcvrVPvlrGhseavtiklk..lkdveveeveellaaapevkvvvneeedrPtpaavaggtnsvs 159
                                     +   +++ft+      +++P++rG+++++++ l+  ++++e+ +++e+++   ev+v++ + e++P++ +v+g tn+++
  gi|161579522|ref|NP_248089.2| 221 GK--AKVSFTP------HLAPITRGILTTAHTFLAkdVDREEIIKIYEKFYGS-EVFVRIFS-EEIPKLTWVRG-TNFCD 289
                                    98..7788889......8****************9999999************.*******6.**********9.9**** PP

                                    EEEEEEETTCTTEEEEEEEEETTTT CS
                Semialdhyde_dhC 160 VGRirkdemgdeglklvvvgDNllk 184
                                    +G ++ de g   l++++++DNl+k
  gi|161579522|ref|NP_248089.2| 290 IGGFEIDEHGR--LVVISAIDNLVK 312
                                    ********666..**********97 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.7e-07   0.00037       2      90 ..       3      96 ..       2      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.7e-07
                                   EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCT...TESEEEE-S-G..GGHHH CS
                   GFO_IDH_MocA  2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladp...eidavivatpn..gthee 77
                                    vaiiGa G+ g + lr   +++++ +v+ + +++++  + +  + +++  +++++l       ++da++v t +  g  ++
  gi|161579522|ref|NP_248089.2|  3 EVAIIGAtGYTGAELLRL-LANHEKVNVTYITSRKEAGKHVFKVHPHLKGIEKYKNLCFTGdidKVDAYLVFTATphGASMD 83
                                   69*****88889999955.55559****************9977776665555554443333448999999766655999** PP

                                   HHHHHHHTT-EEE CS
                   GFO_IDH_MocA 78 lakaaleagkhvl 90
                                   ++ +++e+g++v+
  gi|161579522|ref|NP_248089.2| 84 IVPDFIERGMKVI 96
                                   **********997 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.6e-05     0.035       2      44 ..       3      42 ..       2      96 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                                   EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBH CS
                         DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkda 44
                                   +va++Ga+G  G e+++++ ++e+++++   +rke    gk +
  gi|161579522|ref|NP_248089.2|  3 EVAIIGATGYTGAELLRLLANHEKVNVTYITSRKE---AGKHV 42
                                   69*******************************98...33333 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.8e-05     0.063       2      41 ..       5      45 ..       4      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.8e-05
                                   EEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCH CS
                      Epimerase  2 lVtGatGfiGsalvkallekg.yevigldrlssasntarle 41
                                    ++GatG+ G+ l++ l+++  ++v+ ++++++a+++  + 
  gi|161579522|ref|NP_248089.2|  5 AIIGATGYTGAELLRLLANHEkVNVTYITSRKEAGKHVFKV 45
                                   69******************9777*******9988876544 PP

>> U79_P34  HSV U79 / HCMV P34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.6e-05     0.081      95     156 ..       6      68 ..       2      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                        U79_P34  95 vsqstegrer.lltvssengklqvtfvtlakvskehelknlGdskcveklekegraldrkkad 156
                                    + ++t+     ll +  + +k+ vt++t  k + +h +k +  +k +ek+++ + + d  k d
  gi|161579522|ref|NP_248089.2|   6 IIGATGYTGAeLLRLLANHEKVNVTYITSRKEAGKHVFKVHPHLKGIEKYKNLCFTGDIDKVD 68 
                                    55556655555999999*************************************999987765 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00034      0.76      23      83 ..      35      96 ..       2     110 .. 0.77
   2 ?    0.3   0.0      0.42   9.5e+02      63      88 ..     205     230 ..     203     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00034
                                   HHHHT--EEEESSS-SEETTEES----T.....T--..EEEE-S-HHHHGGGHHHHHHH--SEE CS
                  CoA_binding_2 23 llehglpvvpVnpkeeeilgekvyaslae.dpepvd..lvdvftppeatpeivkealalgakav 83
                                    +e+g +v+ V+p+ + i+  k+   + + d+   d  lv+ +tp  a  +iv +++++g k++
  gi|161579522|ref|NP_248089.2| 35 RKEAGKHVFKVHPHLKGIEKYKNLCFTGDiDKV--DayLVFTATPHGASMDIVPDFIERGMKVI 96
                                   455889999*****9988886655555543444..35599999*****************9986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.42
                                    S-HHHHGGGHHHHHHH--SEEEE-TT CS
                  CoA_binding_2  63 tppeatpeivkealalgakavwlqpg 88 
                                    t   +tpei ke+++lg + v + p+
  gi|161579522|ref|NP_248089.2| 205 TTHRHTPEIEKELKKLGKAKVSFTPH 230
                                    567899**********9888888776 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00023      0.51       1      34 [.       8      41 ..       8      80 .. 0.87
   2 ?   -3.6   0.0         4   9.1e+03      96     122 ..     179     204 ..     178     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHH CS
                 NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklae 34
                                   GAtG +G +l++ l+++++++vt ++ ++e  ++
  gi|161579522|ref|NP_248089.2|  8 GATGYTGAELLRLLANHEKVNVTYITSRKEAGKH 41
                                   9*************9999*****99887776554 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4
                                    EEETTTTSGCGCHHHHHHHHCCHHHHH CS
                 NAD_binding_10  96 vsaigvgdevpgefgewnkellkayla 122
                                    vs++g++    ++f+++n e++++y +
  gi|161579522|ref|NP_248089.2| 179 VSGAGIKPTETTHFPNVN-ENINPYKI 204
                                    788999877777777765.55666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2363.77
//
Query:       gi|15669285|ref|NP_248090.1|  [L=438]
Description: diaminopimelate decarboxylase LysA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-61  207.1   0.1    5.1e-61  206.2   0.1    1.4  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    1.3e-25   89.4   0.0    1.9e-25   89.0   0.0    1.4  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.2   0.1   5.7e-65   5.1e-61       5     247 .]      52     301 ..      49     301 .. 0.97

  Alignments for each domain:
  == domain 1  score: 206.2 bits;  conditional E-value: 5.7e-65
                                   HHHHHHHHHHCT.CCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHHHHHHCTH CS
                 Orn_Arg_deC_N   5 erklkrwkkalp.rikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqreelryalekgv 84 
                                   ++++krw+++ + +  v+Ya Kan +la+ +lla+lG+g d++S +El+++   +v+ ++i+f ++ck++ee+ +  e ++
  gi|15669285|ref|NP_248090.1|  52 IEAFKRWEEETGkEFIVAYAYKANANLAITRLLAKLGCGADVVSGGELYIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANI 132
                                   5789********88999**************************************************************** PP

                                   TEEEESSHHHHHHHHHHHCC....EEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHC..HHHHHHHHHHHHTTEEEEEEE- CS
                 Orn_Arg_deC_N  85 kvvtvdnveeleklaklape....akvllRiktdvsaatcelistggessKFGaale..eavealleaakeenlqlvGvsf 159
                                   + ++vd+ +el  ++++a+e    a+v  Ri+++v+ +t++ istg +++KFG ++e   a++a++ a + e +++vGv++
  gi|15669285|ref|NP_248090.1| 133 RAFNVDSISELILINETAKElgetANVAFRINPNVNPKTHPKISTGLKKNKFGLDVEsgIAMKAIKMALEMEYVNVVGVHC 213
                                   ********************************************************98899******************** PP

                                   --BSSC-SCHHHHHHHHHHHHHHHHHHHHT---SEEE--S-BS-HCSTTSSSSTHHHHHHHHHHHHHHHHHTSSS-EEEE- CS
                 Orn_Arg_deC_N 160 HvGSgvsdleafvkavekalklfdelaelGvklkiLdvGGGfgveyeeeeeplkleeiaekirealeeafpgdkevtiiaE 240
                                   H+GS+++d+++f + ++k++ +++el+e G++++ +++GGG+g+ y ++++    ++ a +i++ + ++  + + +++i+E
  gi|15669285|ref|NP_248090.1| 214 HIGSQLTDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGGLGIPYYKDKQIPTQKDLADAIINTMLKYKDKVEMPNLILE 294
                                   *********************************************99887777779*************99********** PP

                                   -SHHHHG CS
                 Orn_Arg_deC_N 241 pGRalva 247
                                   pGR+lva
  gi|15669285|ref|NP_248090.1| 295 PGRSLVA 301
                                   *****97 PP

>> Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-terminal sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   0.0   2.1e-29   1.9e-25       5      98 .]     131     389 ..      36     389 .. 0.69

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 2.1e-29
                                   E................................................................................ CS
                                   x................................................................................ RF
               Orn_DAP_Arg_deC   5 d................................................................................ 5  
                                   +                                                                                
  gi|15669285|ref|NP_248090.1| 131 Nirafnvdsiselilinetakelgetanvafrinpnvnpkthpkistglkknkfgldvesgiamkaikmalemeyvnvvgv 211
                                   055555555555555555555555555555555566666666666666666666666666666666666666666666666 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Orn_DAP_Arg_deC   6 ................................................................................. 5  
                                                                                                                    
  gi|15669285|ref|NP_248090.1| 212 hchigsqltdispfieetrkvmdfvvelkeegieiedvnlggglgipyykdkqiptqkdladaiintmlkykdkvempnli 292
                                   666666666666666666666667777777777777777777777777777777777777777777777777777777777 PP

                                   .........GGEEEEEEEEEEEEETCEEEEEES--TTTS-HHHHCTT-S-E.ESBTT-SCEEC.EEEEEEEE-SSSSTT-E CS
                                   .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Orn_DAP_Arg_deC   6 .........eagvLvtrViavkesekkkfvivdaGmndllrpalygsfhei.pvkeeeaekeeeeeeevdvvGptCesgDv 76 
                                            +ag+L+ +V ++ke+  +k+v++daGmnd++rpa+y+++h+i + k       ++e+e v+++G +Ces+Dv
  gi|15669285|ref|NP_248090.1| 293 lepgrslvaTAGYLLGKVHHIKETPVTKWVMIDAGMNDMMRPAMYEAYHHIiNCK------VKNEKEVVSIAGGLCESSDV 367
                                   7777777779***************779***********************5553......2344678************* PP

                                   EEEEEEEEE--TT-EEEESS-S CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
               Orn_DAP_Arg_deC  77 lakdrelpelevGdllafedaG 98 
                                   +++drel+++evGd+la+ d+G
  gi|15669285|ref|NP_248090.1| 368 FGRDRELDKVEVGDVLAIFDVG 389
                                   ********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3079.33
//
Query:       gi|15669286|ref|NP_248091.1|  [L=254]
Description: RNA maturase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-33  114.8   2.3    5.2e-33  114.4   2.3    1.2  1  LAGLIDADG_2     LAGLIDADG DNA endonuclease family
    0.00017   21.6   0.1    0.00094   19.2   0.0    1.9  2  LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
    0.00035   20.8   4.2      0.041   14.2   0.3    2.7  2  LAGLIDADG_3     LAGLIDADG-like domain
  ------ inclusion threshold ------
      0.058   13.1   0.0       0.13   12.0   0.0    1.5  1  CRAL_TRIO       CRAL/TRIO domain
        0.1   12.3   0.1       0.21   11.3   0.0    1.6  2  DUF603          Protein of unknown function, DUF603


Domain annotation for each model (and alignments):
>> LAGLIDADG_2  LAGLIDADG DNA endonuclease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4   2.3   1.5e-36   5.2e-33       2     169 .]      57     223 ..      56     223 .. 0.95

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 1.5e-36
                                   HHHHHHHHTT-EEE-SSTTS-BEEEEEE..S-HHHHHHHHHHTGGG--S--EEEEEE-TTS...EEEEEEEE---BGGGHH CS
                   LAGLIDADG_2   2 eiliGlLLGDgslekrkkrknvrfefkqskkhkeYllyvfellkeyllsnpkivkrktrrk...setklrfqtrslpcfne 79 
                                    ++ GlLLGD+++     +++ ++ ++q +k++++l+yv++++++++l+ + ++ +++rr+   +   + ++t  +++f++
  gi|15669286|ref|NP_248091.1|  57 TFIDGLLLGDACI-----TEKGNLLITQ-NKRYDWLEYVKHRFQQFGLNVYFHCYKYKRRTsevIADLYVLSTSRYELFRQ 131
                                   5799*********.....9999999999.9****************************99999999*************** PP

                                   HHHHHBSSSSB---TTHHHH--HHHHHHHHHHHESTT-S-...-EEE--TTS-HHHHHHHHHHHHHHH---EEEEEETTE. CS
                   LAGLIDADG_2  80 laklfyskgkkiipknilklLtplaLAiwimddGskvkkg...gleLntnsfseeevellvkaLkdkfnlkcrvkkkgkk. 156
                                   l++ +y++g+k ip+++   ++ ++LA w+++dGs +k++   +leL+t+ f+ +e+++l++ Lk  +++++r++kk+++ 
  gi|15669286|ref|NP_248091.1| 132 LRERWYPDGIKRIPNDL--VINDEGLAQWYLGDGSLTKQKngyKLELSTHGFTLDENKFLQQKLKLLYGFDFRISKKHQYr 210
                                   ***************76..69*************99999999**************************************9 PP

                                   EEEEE-GGGHHHH CS
                   LAGLIDADG_2 157 yviyikteslkkl 169
                                   y   +k+++++++
  gi|15669286|ref|NP_248091.1| 211 YLRLFKSKQVHAF 223
                                   9999999999876 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.34   1.2e+03       2      48 ..      56     100 ..      55     117 .. 0.67
   2 !   19.2   0.0   2.6e-07   0.00094       9      74 ..     159     227 ..     155     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.34
                LAGLIDADG_WhiA   2 kaflrGaflasGsindpekkyhLEivspdeelaeqlqkllnefelea 48 
                                   + f+ G++l+   i++ + +  L    +  + +e +++  ++f+l+ 
  gi|15669286|ref|NP_248091.1|  56 RTFIDGLLLGDACITE-KGN-LLITQNKRYDWLEYVKHRFQQFGLNV 100
                                   5678888888888887.333.45555566777888888888887765 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.6e-07
                LAGLIDADG_WhiA   9 flasGsindpekkyhLEivsp..deelaeqlqklln.efeleakilerrkkyvvylKkaeqIvdlLkii 74 
                                    l+ Gs+++ +++y LE++++  + +  + lq+ l+  ++++++i+++ ++  + l k++q+  + +i+
  gi|15669286|ref|NP_248091.1| 159 YLGDGSLTKQKNGYKLELSTHgfTLDENKFLQQKLKlLYGFDFRISKKHQYRYLRLFKSKQVHAFCSIV 227
                                   589******8888*******9445788999******555********9999999999999999998887 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.3   1.1e-05     0.041       4      78 ..      56     129 ..      53     154 .. 0.80
   2 !    7.6   0.4    0.0013       4.7       7      80 ..     155     225 ..     150     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEE..EEE-SCCCCECCCHCHCTTCGG CS
                   LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyek..kkakgrgvyrlliisgenlkrF 78 
                                   + f+ Gl  +D +++++++    +   ++ ++ le+v++  +++G++ + +    k++   ++  l + s + ++ F
  gi|15669286|ref|NP_248091.1|  56 RTFIDGLLLGDACITEKGNL---LITQNKRYDWLEYVKHRFQQFGLNVYFHCYkyKRRTSEVIADLYVLSTSRYELF 129
                                   78****************86...77777779***************9998877534444444445555555555544 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0013
                                   HHHHHHHCCECCECSTTTTSEEEEES-.....HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGGGT CS
                   LAGLIDADG_3   7 LrGlfdaDGsvskskkkgvsisltsss.....kelledvqrlLlrlGIestiyekkkakgrgvyrlliisgenlkrFle 80 
                                   L+  + +DGs +k+k++ + ++l+++       ++l++  +lL  +    +i +k     +++ +l+  +++++++F++
  gi|15669286|ref|NP_248091.1| 155 LAQWYLGDGSLTKQKNGYK-LELSTHGftldeNKFLQQKLKLLYGF--DFRISKK-----HQYRYLRLFKSKQVHAFCS 225
                                   677899*********8744.77777767766699999999999666..5666666.....4444588888888888876 PP

>> CRAL_TRIO  CRAL/TRIO domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.7e-05      0.13     110     139 ..     218     247 ..     216     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                     CRAL_TRIO 110 klfkfafklvkpfldektreKikfvspsnt 139
                                   k ++++ ++v pf++++ r+K++++ + ++
  gi|15669286|ref|NP_248091.1| 218 KQVHAFCSIVEPFIPPSYRNKVRCLHDYQW 247
                                   568999*******************88887 PP

>> DUF603  Protein of unknown function, DUF603
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.9e-05      0.21      13      61 ..       4      54 ..       1      64 [. 0.71
   2 ?   -3.7   0.1       2.3   8.1e+03     149     168 ..      87     107 ..      82     115 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.9e-05
                        DUF603 13 ayfregslsdkeiakklgvskvnvwrmrqkwesgesvv..nedsrl.tised 61
                                   y+ eg lsd+eia  +g  k  v r rqk       v   +d  l  ised
  gi|15669286|ref|NP_248091.1|  4 KYIVEG-LSDREIAYLIGCGKATVVRARQKHGIYREDVkmCDDYTLdNISED 54
                                  577776.9**********************8654333301344444245665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.3
                        DUF603 149 eyikec.siremelyyecmkk 168
                                   ey+k       +++y+ c k 
  gi|15669286|ref|NP_248091.1|  87 EYVKHRfQQFGLNVYFHCYKY 107
                                   566653133457788888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1634.82
//
Query:       gi|15669287|ref|NP_248092.1|  [L=235]
Description: hypothetical protein MJ_1099 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-93  311.2   0.3      5e-93  311.0   0.3    1.0  1  4HFCP_synth  4-HFC-P synthase


Domain annotation for each model (and alignments):
>> 4HFCP_synth  4-HFC-P synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.0   0.3   2.8e-97     5e-93       1     228 []       3     231 ..       3     231 .. 0.99

  Alignments for each domain:
  == domain 1  score: 311.0 bits;  conditional E-value: 2.8e-97
                                   EEE--SSHHHHHHHHHHT-SEEEE--GGG-TT----HHHHHHHHHHS-TTSEEEEEEEEE-S-HHHHHHHHHHHHHTT-SE CS
                   4HFCP_synth   1 LLvSvrnleEaelalaggadiiDvKnPaeGsLGalfpevireivevvpgsvpvSaaiGdlpekpgtvslaalgaaaagvdy 81 
                                   LLvS++++eEa++a+aggadiiDvKnP+eGsLGa+fp++i++i+ev+p+++ vSa++Gd+p+kpgt+slaa+gaa +g+dy
  gi|15669287|ref|NP_248092.1|   3 LLVSPIDVEEAKEAIAGGADIIDVKNPKEGSLGANFPWMIKAIREVTPKDLLVSATVGDVPYKPGTISLAAVGAAISGADY 83 
                                   8******************************************************************************** PP

                                   EEEEE-S--SHHHHHHHHHHHHHHHHHH-TTSEEEEEEETTGGGTT---GGGHHHHHHHHT-SEEEEE-SS-SS--HHHHS CS
                   4HFCP_synth  82 vKvGlaglkkeeealealkavvkavkeedkekkvvavlyaDaervasvsplellelaaeagaagvmlDTadKdgkslldfl 162
                                   +KvGl+g+k++ +a+e++k+vv+avk+ d++k vva++yaDa rv++v+pl ++++a++ag++++mlDTa+Kdgk+l+df 
  gi|15669287|ref|NP_248092.1|  84 IKVGLYGVKNYYQAVELMKNVVRAVKDIDENKIVVAAGYADAYRVGAVEPLIVPKIARDAGCDVAMLDTAIKDGKTLFDFQ 164
                                   ********************************************************************************* PP

                                   -HHHHHHHHHHHHHTT-EEEE-SS--GGGHHHHHHTT-SEEEESGGGBTTSSTT.SSB-HHHHHHHH CS
                   4HFCP_synth 163 seeelaefveeareaglltaLAGslkledlpaLkklkpdilGvRgavCeegdRn.gkidaelveklk 228
                                   s+e laefv+ea+++gl++aLAGs+k+e++p Lk++++di+GvRga+C++gdRn g+id+elv++lk
  gi|15669287|ref|NP_248092.1| 165 SKEILAEFVDEAHSYGLKCALAGSIKKEHIPILKEIGTDIVGVRGAACKGGDRNnGRIDRELVKELK 231
                                   *****************************************************999********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1404.63
//
Query:       gi|15669288|ref|NP_248093.1|  [L=448]
Description: phosphomannomutase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.7e-36  123.0   0.3    1.7e-35  121.7   0.1    1.8  2  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    8.4e-25   87.2   0.0    1.6e-24   86.3   0.0    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    8.5e-20   71.3   0.1    3.1e-19   69.5   0.1    2.0  2  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.2e-13   51.0   0.2    4.8e-13   49.1   0.1    2.1  2  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.7   0.1   3.8e-39   1.7e-35       2     136 ..       3     125 ..       2     127 .. 0.95
   2 ?   -2.6   0.0      0.88   3.9e+03      25      46 ..     252     273 ..     250     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: 121.7 bits;  conditional E-value: 3.8e-39
                                   GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHH CS
                     PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPav 82 
                                   ++fgtsG+R k     l p+ ++k+g a+a+  k+      vvvGrDtR++++ +++al ag+++ G ev  ++++ptP++
  gi|15669288|ref|NP_248093.1|   3 RLFGTSGIRMKN----LSPKIAYKVGLAVAKKYKK------VVVGRDTRTTGKLIETALTAGILNGGGEVTTINIVPTPVL 73 
                                   68*******954....689***********98886......**************************************** PP

                                   HHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT-E CS
                     PGM_PMM_I  83 sfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekeee 136
                                    f +r+  +d gimitaSHnppeyngiK++++nG  +++++e++Ie+ii+ke++
  gi|15669288|ref|NP_248093.1|  74 GFNARN--YDVGIMITASHNPPEYNGIKLFNKNGLAFNKKEEDEIEEIIFKEDF 125
                                   *****9..89****************************************9986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.88
                                   HHHHHHHHHCHHCSTS-EEEEE CS
                     PGM_PMM_I  25 klgqaiaeylkaeakkkkvvvG 46 
                                   kl +a+ +y+ +++++kk+v  
  gi|15669288|ref|NP_248093.1| 252 KLLAAFSRYMVEKTGNKKIVTT 273
                                   5678999999999999999865 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0   3.6e-28   1.6e-24       3     111 ..     251     357 ..     249     359 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 3.6e-28
                                   HHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBSS- CS
                   PGM_PMM_III   3 dqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeattk 83 
                                   d+lla +++y+ e+   +++++v+tv  s+++++++k+l++++++tkvGd  v+eem +++av+GgE Sg++i  d + t 
  gi|15669288|ref|NP_248093.1| 251 DKLLAAFSRYMVEK--TGNKKIVTTVDASMIIDEYLKDLDVEIIRTKVGDVAVAEEMIKNSAVFGGEPSGTWIHADIHLTP 329
                                   99*********995..55567************************************************************ PP

                                   -HHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                   PGM_PMM_III  84 DGilaallvleilaetgkslselleell 111
                                   DGil+ l+vle+l   +k+l e+l+e++
  gi|15669288|ref|NP_248093.1| 330 DGILSGLRVLEMLDFYNKKLYEILDEIP 357
                                   ************************7754 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.1     7e-23   3.1e-19       2     103 .]     145     245 ..     144     245 .. 0.91
   2 ?   -3.0   0.0       2.6   1.2e+04      32      48 ..     276     292 ..     263     300 .. 0.80

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 7e-23
                                   HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGG. CS
                    PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkke. 81 
                                    Y+e+++++v    i+++ + vvid++++++  + + l+ +lg++v+++n++ d+ f ++ p+p+e ++lk+ ++++k   
  gi|15669288|ref|NP_248093.1| 145 NYMEHILKNVE---INEK-FNVVIDCANASACLVSPYLFTDLGCHVISVNSHMDGRFIGRLPEPDE-KNLKKTMDMIKGLn 220
                                   6*********9...6555.9**********************************************.88888887777665 PP

                                   ...G-SEEEEE-TTS-BEEEEETTE CS
                    PGM_PMM_II  82 ...gadlglafDgDaDRlgvvderG 103
                                      ++ +g+a+DgDaDR++++de+G
  gi|15669288|ref|NP_248093.1| 221 msgDNYIGIAHDGDADRMVAIDEKG 245
                                   554889*****************98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.6
                                   THHHHHHHHHHTT-EEE CS
                    PGM_PMM_II  32 ggeilkellkelgvdvv 48 
                                   +++i++e lk+l+v+++
  gi|15669288|ref|NP_248093.1| 276 ASMIIDEYLKDLDVEII 292
                                   57788888888888655 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.9   8.3e+03      12      32 ..     246     264 ..     239     277 .. 0.56
   2 !   49.1   0.1   1.1e-16   4.8e-13      23      67 ..     384     435 ..     361     442 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.9
                                   ..EECCCCCTTHHCCCCCCCC CS
                    PGM_PMM_IV  12 vvaalaallkvasikeglkil 32 
                                   ++a++++ll++  ++   + +
  gi|15669288|ref|NP_248093.1| 246 RLADFDKLLAA--FSRYMVEK 264
                                   46666666665..44443333 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 1.1e-16
                                   H........HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHH CS
                    PGM_PMM_IV  23 a........sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlae 67 
                                   +        ++ +g+++ le+G++l +RpSGTep++rv+vEak+ + +++l e
  gi|15669288|ref|NP_248093.1| 384 GeslfktvpETVDGARFNLENGWVL-IRPSGTEPYIRVRVEAKNNKDAKELLE 435
                                   244444557899*************.*****************7777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3260.89
//
Query:       gi|15669289|ref|NP_248094.1|  [L=408]
Description: glucose-1-phosphate thymidylyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-45  153.5   0.1    1.1e-44  152.9   0.1    1.3  1  NTP_transferase  Nucleotidyl transferase
    7.1e-16   57.2  16.2    3.6e-05   23.3   0.8    4.5  4  Hexapep          Bacterial transferase hexapeptide (six repea
    1.9e-12   47.8   0.0    2.4e-12   47.5   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    0.00011   22.0   0.0    0.00018   21.3   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
      0.001   18.8  22.6      0.083   12.7   0.2    5.3  6  Hexapep_2        Hexapeptide repeat of succinyl-transferase
     0.0068   16.7   3.8      0.019   15.3   0.9    2.6  2  Bactofilin       Polymer-forming cytoskeletal
  ------ inclusion threshold ------
      0.014   15.3   0.3      0.036   14.0   0.1    1.7  2  CTP_transf_3     Cytidylyltransferase
      0.029   14.6   1.2      0.052   13.8   1.2    1.4  1  DUF5041          Domain of unknown function (DUF5041)


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.9   0.1   4.8e-48   1.1e-44       2     246 ..       3     222 ..       2     224 .. 0.92

  Alignments for each domain:
  == domain 1  score: 152.9 bits;  conditional E-value: 4.8e-48
                                   EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS CS
               NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepe 82 
                                   a+IL+ G+G+RL+PLt +++k+++p++gk +++q+ ++++    +++ i+ + +++++ + +++k+  k    ++++ + e
  gi|15669289|ref|NP_248094.1|   3 AIILCAGKGERLRPLTENRPKPMIPIAGK-PILQHIIEKVE-DLVDN-IYLIVKYKKEKIVDYFKNHPK----IKFLEQGE 76 
                                   8****************************.*********98.69999.555556778888899999875....77****** PP

                                   --BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEE CS
               NTP_transferase  83 gkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfv 163
                                    +gt +Av+ a+++++de+     lv++gD++++d++ee++k           ++++++v++++++Gv+  d+e+++++++
  gi|15669289|ref|NP_248094.1|  77 IDGTGQAVLTAKDYVDDEF-----LVINGDIIFEDDLEEFLKYK--------YAVAVKEVKNPENFGVVVLDDENNIIELQ 144
                                   ****************988.....9**************99753........357789*********************** PP

                                   CS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHHH CS
               NTP_transferase 164 EKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleanek 244
                                   EKP+++k s+l+++GiY f++++++ + ++ + ++rge e+td+++ +++e+kv+  +  ++  yW+DvG + ++lean+ 
  gi|15669289|ref|NP_248094.1| 145 EKPENPK-SNLINAGIYKFDKKIFELI-EKTKISERGERELTDAIKHLIKEEKVK-GIKLNG--YWNDVGRPWDILEANKY 220
                                   *******.*******************.669999*****************9998.568899..9*************997 PP

                                   HH CS
               NTP_transferase 245 la 246
                                   l+
  gi|15669289|ref|NP_248094.1| 221 LL 222
                                   76 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.6   2.9e-06    0.0065      10      36 .]     233     259 ..     232     259 .. 0.93
   2 !   12.0   0.0     6e-05      0.13       2      35 ..     261     294 ..     260     295 .. 0.90
   3 !   13.9   0.5   1.5e-05     0.034       2      32 ..     296     325 ..     295     329 .. 0.89
   4 !   23.3   0.8   1.6e-08   3.6e-05       2      34 ..     354     386 ..     353     388 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.9e-06
                                   E-TTEEEETTEEE-TTEEEETTEEEES CS
                       Hexapep  10 IgpfaviggnVkIGdnvkIgagvvigg 36 
                                   I  ++vi g V+I +++++ a++vi g
  gi|15669289|ref|NP_248094.1| 233 IEENVVIKGEVIIEEGAIVKANSVIEG 259
                                   889**********************76 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6e-05
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   ++I +++++gp a+i++ +++ +n+ +g+ + ++
  gi|15669289|ref|NP_248094.1| 261 AIIKKGAVVGPLAYIRPYTVLMENTFVGNSSEVK 294
                                   78999***********************999886 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 1.5e-05
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagv 32 
                                   ++I +n++I + +++ g+ +IG+n+  g ++
  gi|15669289|ref|NP_248094.1| 296 SIIMKNTKIPHLSYV-GDSIIGENCNFGCNT 325
                                   5899***********.9999*******9887 PP

  == domain 4  score: 23.3 bits;  conditional E-value: 1.6e-08
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                   ++ G+nv+ g  + ++++Vk+G+n+ Iga + i
  gi|15669289|ref|NP_248094.1| 354 VIMGDNVKTGIQVSFMPGVKVGSNCWIGASCLI 386
                                   789**************************9988 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   1.1e-15   2.4e-12       1     110 [.       3     114 ..       3     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.1e-15
                                   EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCT.S-EEE-TTSS-SHH CS
                  NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggd..eevlaalarlg.vrvvededpgkgpl 73 
                                   a+iL++G++ R+     +++K+++p++gkp+l++++++++++ vd++++++++  e++ ++++ ++ ++++e+  +  g++
  gi|15669289|ref|NP_248094.1|   3 AIILCAGKGERLrplteNRPKPMIPIAGKPILQHIIEKVEDL-VDNIYLIVKYkkEKIVDYFKNHPkIKFLEQG-EIDGTG 81 
                                   79**********5555557***********************.********99767899999877647777775.689*** PP

                                   HHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHC CS
                  NTP_transf_3  74 aslaaalraaadadavlvlacDmPlltpelverllaa 110
                                   +++++a + +  +d +lv+ +D+++  ++ +e++l+ 
  gi|15669289|ref|NP_248094.1|  82 QAVLTAKDYV--DDEFLVINGDIIF--EDDLEEFLKY 114
                                   ********98..8**********99..8888888875 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   7.9e-08   0.00018       3      75 ..       3      76 ..       1     112 [. 0.86

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7.9e-08
                                  EEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGGCCEEEEE--S CS
                          IspD  3 vvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllldksiqlvaGGd 75
                                  ++i  AG+G+R++   +++pK  + ++g+++l+h ++ + +   vd+i ++v+ ++ + +  +  +++i+ ++ G+
  gi|15669289|ref|NP_248094.1|  3 AIILCAGKGERLRpltENRPKPMIPIAGKPILQHIIEKVED--LVDNIYLIVKYKKEKIVDYFKNHPKIKFLEQGE 76
                                  89*********7433389*********************99..9*********99988888888899999988775 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   1.9   0.00087       1.9      13      32 ..     236     257 ..     233     259 .. 0.90
   2 !    8.1   1.1   0.00097       2.2       2      27 ..     243     270 ..     242     275 .. 0.76
   3 ?   -1.5   0.0      0.98   2.2e+03       6      16 ..     283     293 ..     283     298 .. 0.79
   4 !    8.0   1.4    0.0011       2.4       3      15 ..     314     326 ..     313     328 .. 0.89
   5 ?    0.5   0.1      0.23   5.2e+02      17      25 ..     353     361 ..     346     363 .. 0.79
   6 !   12.7   0.2   3.7e-05     0.083       2      20 ..     372     390 ..     371     397 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00087
                                   T-EE.S.EEE-TT-EE-TT-EE CS
                     Hexapep_2  13 nagi.G.vslGdncvvgaGvvi 32 
                                   n +i G v+++++++v a++vi
  gi|15669289|ref|NP_248094.1| 236 NVVIkGeVIIEEGAIVKANSVI 257
                                   6788888**************9 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00097
                                   EEE-TT-EE-TT-EE..SEEE-TT-EE- CS
                     Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvg 27 
                                   viI++  ++ an++i  + ++ +++vvg
  gi|15669289|ref|NP_248094.1| 243 VIIEEGAIVKANSVIegPAIIKKGAVVG 270
                                   7888888888888877448888888887 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.98
                                   TT-EE-TT-EE CS
                     Hexapep_2   6 dnCliGanagi 16 
                                   +n+++G ++++
  gi|15669289|ref|NP_248094.1| 283 ENTFVGNSSEV 293
                                   699***99986 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0011
                                   EE-TT-EE-TT-E CS
                     Hexapep_2   3 iIGdnCliGanag 15 
                                   iIG+nC++G n +
  gi|15669289|ref|NP_248094.1| 314 IIGENCNFGCNTI 326
                                   8********9976 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.23
                                   SEEE-TT-E CS
                     Hexapep_2  17 GvslGdncv 25 
                                   Gv+ Gdn++
  gi|15669289|ref|NP_248094.1| 353 GVIMGDNVK 361
                                   999***985 PP

  == domain 6  score: 12.7 bits;  conditional E-value: 3.7e-05
                                   EEE-TT-EE-TT-EESEEE CS
                     Hexapep_2   2 viIGdnCliGanagiGvsl 20 
                                   v++G nC iGa++ i  ++
  gi|15669289|ref|NP_248094.1| 372 VKVGSNCWIGASCLIDRDI 390
                                   89***********996554 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.9   8.3e-06     0.019      19      83 ..     227     300 ..     221     306 .. 0.73
   2 ?    0.8   0.1      0.27   6.1e+02       2      77 ..     314     387 ..     313     401 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.3e-06
                    Bactofilin  19 lridGkveGdieakgklvvgeggkvegn..ikaeevvvaGtvkG........nveaeekvelkktakveGdikak 83 
                                    +i+Gk+e ++  kg+++++eg+ v++n  i+   ++ +G v G        +v +e +  + ++++v+++i +k
  gi|15669289|ref|NP_248094.1| 227 TDIKGKIEENVVIKGEVIIEEGAIVKANsvIEGPAIIKKGAVVGplayirpyTVLME-NTFVGNSSEVKASIIMK 300
                                   689*************************87777888888****94444444333333.55555666666665555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.27
                    Bactofilin   2 ligegtkikGelevegdlridG.kveGdieakgklvvgeggkvegn.ikaeevvvaGtvkGnveaeekvelkktakve 77 
                                   +ige++++  + +++++lr d   v+ +i++k+   v++ g++ g+ +k + ++v  ++   v++ ++  + +++ ++
  gi|15669289|ref|NP_248094.1| 314 IIGENCNFGCN-TITANLRFDDkPVKVNIKSKRVESVRKLGVIMGDnVK-TGIQV--SFMPGVKVGSNCWIGASCLID 387
                                   67777777766.6777888877567899999888889999999998444.44444..344445555555555555555 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.6e-05     0.036      16      63 ..      23      71 ..      21      99 .. 0.83
   2 ?   -2.6   0.0       1.9   4.3e+03     174     193 ..     152     169 ..     119     201 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                                  GGGSEETTEEHHHHHHHHHHHTTTTSE..EEEEES-HHHHHHHHHTT.SEE CS
                  CTP_transf_3 16 Knlldlggkpliayvleaalkskafek..vivaTDseeiknvakefg.asv 63
                                  K++++++gkp++++++e++ +  ++++  +iv   +e+i++  k++  +++
  gi|15669289|ref|NP_248094.1| 23 KPMIPIAGKPILQHIIEKVED--LVDNiyLIVKYKKEKIVDYFKNHPkIKF 71
                                  9*******************9..6666558888889999998888855554 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                                   TSEEEEEEEEEEHHHHHHHH CS
                  CTP_transf_3 174 lylshagiytfrkeqplkel 193
                                     l  agiy+f k+ +  el
  gi|15669289|ref|NP_248094.1| 152 SNLINAGIYKFDKK-I-FEL 169
                                   45667777777775.2.222 PP

>> DUF5041  Domain of unknown function (DUF5041)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.2   2.3e-05     0.052       9     101 ..      99     188 ..      93     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                       DUF5041   9 mgieifrFdlsellkkeYnvevYvdeYkngkkidrvhefklGkniksleevpeerreairkeeliaekkkeyelikelsiy 89 
                                   +g  if+ dl+e+lk +Y v   v+e kn ++   v  ++  +ni +l+e+pe+ ++++ +    + +kk++eli++  i 
  gi|15669289|ref|NP_248094.1|  99 NGDIIFEDDLEEFLKYKYAVA--VKEVKNPENF-GVVVLDDENNIIELQEKPENPKSNLINAGIYKFDKKIFELIEKTKIS 176
                                   56668999******9999876..79******99.5778999************************************9999 PP

                       DUF5041  90 lrketDstavit 101
                                    r e + t +i+
  gi|15669289|ref|NP_248094.1| 177 ERGERELTDAIK 188
                                   888866666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 2361.68
//
Query:       gi|15669290|ref|NP_248095.1|  [L=161]
Description: deoxycytidine triphosphate deaminase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-09   37.9   0.0    2.1e-09   37.2   0.0    1.3  1  dUTPase   dUTPase
    0.00032   19.6   0.0    0.00036   19.4   0.0    1.2  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   2.3e-13   2.1e-09      20     106 ..      64     149 ..      62     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 2.3e-13
                                   -SSSEEEET.TEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEE CS
                       dUTPase  20 aakdltvkp.getvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiAqL 99 
                                   + kd  +k  ++ ++v++  +ik+p+++a++  pRS+l + g +    v d  y+G  +  + +++  +++i k++RiAq+
  gi|15669290|ref|NP_248095.1|  64 SEKDEHIKLdRGVYIVKVADYIKIPENVAGFAYPRSSLLRMGATLYSAVHDPGYEGRPEYLMQVFN--PITIYKYARIAQI 142
                                   5678889999999*******************************************8888888876..5************ PP

                                   EEEEBEC CS
                       dUTPase 100 ifarilt 106
                                   +f+++ +
  gi|15669290|ref|NP_248095.1| 143 VFVECRD 149
                                   ***9976 PP

>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     4e-08   0.00036      23     111 ..      18     104 ..       3     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4e-08
                           DCD  23 epleeeqiqPaslDLrLgkkayrvrasFlpgkgekvaekleelklheldLtegavlekgcvYivplleslaLpadlsaaan 103
                                   ++leeeqiq   +DLr+  k +++    +   +++ ++  + +++ + +  e+  l++g vYiv++ + +++p+++++ a 
  gi|15669290|ref|NP_248095.1|  18 DNLEEEQIQQCGIDLRVW-KIFKIEGEGVIDFSNEKRKLPNYIEIFNSEKDEHIKLDRG-VYIVKVADYIKIPENVAGFAY 96 
                                   57899***********96.679**9998876555544444557778888899999*998.9******************** PP

                           DCD 104 pksstGRl 111
                                   p+ss  R+
  gi|15669290|ref|NP_248095.1|  97 PRSSLLRM 104
                                   ****9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1115.27
//
Query:       gi|15669291|ref|NP_248096.1|  [L=88]
Description: hypothetical protein MJ_1103 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.2e-11   42.4   0.8    9.1e-11   42.2   0.8    1.0  1  ParE_toxin  ParE toxin of type II toxin-antitoxin system, par


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.8   5.1e-15   9.1e-11       1      90 []       3      84 ..       3      84 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 5.1e-15
                                  EEEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTCCTTEEEEEECTEEEEEEEETSTTEEEEEEE CS
                    ParE_toxin  1 vrltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrprrelglkglrririgdyriiYriddeelvvvilrv 83
                                  v +++++ kdlk+   +i      +kr++  +ee+ ++   n ++    + +g+ +++rir+g+yri  ++ ++++++ + rv
  gi|15669291|ref|NP_248096.1|  3 VLFAKTFVKDLKHVPGHI------RKRIKLIIEECQNSNSLNDLKLDIKKIKGYHNYYRIRVGNYRIGIEV-NGDTII-FRRV 77
                                  6899**************......************************99999*****************9.588899.**** PP

                                  EEHHHHC CS
                    ParE_toxin 84 lhrsedy 90
                                  lhr+ +y
  gi|15669291|ref|NP_248096.1| 78 LHRKSIY 84
                                  ***9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.53
# Mc/sec: 500.39
//
Query:       gi|15669292|ref|NP_248097.1|  [L=300]
Description: homoserine kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-13   49.4   1.6    7.9e-13   48.4   1.6    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain
    1.4e-07   31.7   0.2    3.3e-07   30.6   0.0    1.8  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   1.6   8.9e-17   7.9e-13       1      66 []      82     149 ..      82     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 8.9e-17
                                   EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerlaqggngsggDvaasvyGg 66 
                                   +i+ik+ +  g+GLGSSAA ++++++A+++l+ l+l++   ++ a  +e +   g  + ++va++++Gg
  gi|15669292|ref|NP_248097.1|  82 KITIKKGVKAGSGLGSSAASSAGTAYAINELFKLNLDKlklVDYASYGELASS-GAKHADNVAPAIFGG 149
                                   699*****************************999844466999999996665.999***********8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.5   1.2         2   1.8e+04      55      62 ..      92      99 ..      91     101 .. 0.82
   2 !   30.6   0.0   3.7e-11   3.3e-07       1      84 [.     209     286 ..     209     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 2
                GHMP_kinases_C 55 GaGgGptv 62
                                  G+G+G++ 
  gi|15669292|ref|NP_248097.1| 92 GSGLGSSA 99
                                  99**9986 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 3.7e-11
                GHMP_kinases_C   1 llealergdlellgellnlsqrs....elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvar 77 
                                   ++ al+++d +l+g+ +     s    e+  v+g+l p+  +++e+ ++  ++g  +sG+  Gp+++a+  +++  ++v++
  gi|15669292|ref|NP_248097.1| 209 MVYALYNKDKSLFGRYMM----SdkviEP--VRGKLIPNYFKIKEEVKDK-VYGITISGS--GPSIIAFP-KEEFIDEVEN 279
                                   6789**************....55566**..****************666.6********..*******9.8888888888 PP

                GHMP_kinases_C  78 alreefe 84 
                                    lr ++e
  gi|15669292|ref|NP_248097.1| 280 ILRDYYE 286
                                   8887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 2072.66
//
Query:       gi|15669293|ref|NP_248098.1|  [L=218]
Description: TRK system potassium uptake protein TrkA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-31  109.1   2.1    2.7e-31  108.2   2.1    1.4  1  TrkA_N           TrkA-N domain
    6.8e-16   57.9   0.7    1.8e-15   56.5   0.1    2.1  2  TrkA_C           TrkA-C domain
    1.1e-05   25.8   0.7    2.8e-05   24.5   0.2    1.8  2  NAD_binding_7    Putative NAD(P)-binding
    6.8e-05   22.5   0.6    0.00024   20.8   0.3    2.0  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00044   20.5   0.1    0.00077   19.7   0.1    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00063   19.7   0.1     0.0011   18.9   0.1    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0007   19.7   0.5     0.0012   19.0   0.5    1.4  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
     0.0045   16.9   0.0     0.0098   15.8   0.0    1.6  1  LpxI_N           LpxI N-terminal domain
     0.0054   16.4   0.1      0.014   15.0   0.0    1.8  2  ApbA             Ketopantoate reductase PanE/ApbA
     0.0067   17.0   0.5      0.027   15.0   0.2    2.3  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.021   14.9   0.1      0.033   14.3   0.1    1.4  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.032   14.4   0.1      0.067   13.4   0.1    1.6  1  UPF0180          Uncharacterised protein family (UPF0180)
      0.034   13.7   0.1      0.055   13.0   0.1    1.3  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      0.034   14.1   0.0      0.072   13.1   0.0    1.6  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.048   14.0   0.9       0.26   11.7   0.8    2.2  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
      0.053   13.0   0.2      0.085   12.3   0.2    1.4  1  adh_short        short chain dehydrogenase
      0.075   12.5   0.1       0.11   12.0   0.1    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
      0.094   13.0   0.3       0.29   11.4   0.3    1.8  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.17   11.1   0.0        0.2   10.8   0.0    1.2  1  FAD_binding_3    FAD binding domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   2.1   2.9e-34   2.7e-31       1     116 []       3     118 ..       3     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 2.9e-34
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddeanilav 80 
                                   iii+G GrvG++la+ Lse+g+d+v+id d++ ++++++e  + v++gd+t+ ++Le+agie+ad+ ia+tg+ e+n++ +
  gi|15669293|ref|NP_248098.1|   3 IIIAGIGRVGYTLAKSLSEKGHDIVLIDIDKDICKKASAEIdALVINGDCTKIKTLEDAGIEDADMYIAVTGKEEVNLMSS 83 
                                   89*****************5558**************9888799************************************* PP

                                   HHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                        TrkA_N  81 llakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                   llak+  +  k+iar+++ e+++++++lg+dvv+sp
  gi|15669293|ref|NP_248098.1|  84 LLAKS-YGINKTIARISEIEYKDVFERLGVDVVVSP 118
                                   ****7.77799***********************98 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.6   5.3e+03      50      65 ..      24      39 ..      22      43 .. 0.73
   2 !   56.5   0.1   1.9e-18   1.8e-15       2      69 ..     149     215 ..     148     216 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.6
                                  T-EEEEEEEHHHHHHH CS
                        TrkA_C 50 GDvllvvgspsdlael 65
                                   D++l+  +++  +++
  gi|15669293|ref|NP_248098.1| 24 HDIVLIDIDKDICKKA 39
                                  5999999888876665 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 1.9e-18
                                   EEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                        TrkA_C   2 vevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                    e+ +p+ +++v+k++kel+ ++ + l++ai  g+el ipsgdt+L++GD++lv++++++ +++r+ +
  gi|15669293|ref|NP_248098.1| 149 LEFIIPEKAKVVNKKIKELGRPQ-DYLIIAIYDGDELKIPSGDTELKSGDRVLVLVKKDAADAIRKMF 215
                                   5999**************99999.*****************************************988 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.2     3e-08   2.8e-05      10      87 ..       3      91 ..       2     102 .. 0.71
   2 ?   -1.4   0.0       3.4   3.2e+03      25      25 ..     151     151 ..     113     185 .. 0.51

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3e-08
                 NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvvapev..keeleelvk........laeeele.kdlegadlviaatddrelneriaea 81
                                  ++++G G+v+++ +++l e+g ++++++ +   +++++  ++         + ++le + +e+ad+ ia+t ++e+n     +
  gi|15669293|ref|NP_248098.1|  3 IIIAGIGRVGYTLAKSLSEKGHDIVLIDIDKdiCKKASAEIDalvingdcTKIKTLEdAGIEDADMYIAVTGKEEVNLMSSLL 85
                                  579***********************877733344444334432112221122333324499***************888777 PP

                 NAD_binding_7 82 akarri 87
                                  ak+++i
  gi|15669293|ref|NP_248098.1| 86 AKSYGI 91
                                  777766 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.4
                 NAD_binding_7  25 k 25 
                                    
  gi|15669293|ref|NP_248098.1| 151 F 151
                                   0 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.3   2.5e-07   0.00024       1      38 [.       1      38 [.       1      60 [. 0.89
   2 ?   -0.7   0.0      0.93   8.8e+02     143     158 ..     106     123 ..      75     143 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.5e-07
                                  SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHH CS
                UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdk 38
                                  m i + G G vG + a  l+e+gh+++++Did+   +k
  gi|15669293|ref|NP_248098.1|  1 MYIIIAGIGRVGYTLAKSLSEKGHDIVLIDIDKDICKK 38
                                  679999**************************976665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.93
                                   -..TTCEEEEE------T CS
                UDPG_MGDP_dh_N 143 k..gvdfdvvsnPEflre 158
                                         +dvv++PE ++ 
  gi|15669293|ref|NP_248098.1| 106 VfeRLGVDVVVSPELIAA 123
                                   233677899999998764 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   8.2e-07   0.00077       4      98 ..       5     107 ..       2     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.2e-07
                                   EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSH CS
                 NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........akaaesieelvasldvvitmvkagkavdeviegl 76 
                                   + G+G  G  +a+ l ++g+++++++ +k+ ++++ ae         ++ ++++e++  +   + + v+ +++v+ + + l
  gi|15669293|ref|NP_248098.1|   5 IAGIGRVGYTLAKSLSEKGHDIVLIDIDKDICKKASAEIdalvingdCTKIKTLEDAGIEDADMYIAVTGKEEVNLMSSLL 85 
                                   67***************************999999998677888778777888887765556667889999999999999* PP

                                   CCC--TT-EEEE-S---HHHHH CS
                 NAD_binding_2  77 lealkkgdilidgstsspedtr 98 
                                   ++++  ++++   s ++++d  
  gi|15669293|ref|NP_248098.1|  86 AKSYGINKTIARISEIEYKDVF 107
                                   **************99999875 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.1e-06    0.0011       3      45 ..       4      46 ..       2      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                                  EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHH CS
                       3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdiseealekalekieks 45
                                   + G G +G  +a+ + ++g+++vl+di++++ +ka ++i + 
  gi|15669293|ref|NP_248098.1|  4 IIAGIGRVGYTLAKSLSEKGHDIVLIDIDKDICKKASAEIDAL 46
                                  578***********************************99873 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5   1.3e-06    0.0012      26      95 ..       3      82 ..       1     106 [. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.3e-06
                                  EEEE--SHHHHHHHHHHHHCT-EEEEE-S-H.HH........HHHHHCTT-EE--HHHC.TTT-SEEEE-SSSSSSB-HH CS
                 AdoHcyase_NAD 26 avvaGyGdvGkGcaaslkglGarvivtevdP.ic........alqaameGfevvtleev.vkkadivvtttGnkdiitle 95
                                  +++aG G vG   a+sl ++G  +++ ++d  ic        al    +  +++tle++ +++ad+++++tG +++  + 
  gi|15669293|ref|NP_248098.1|  3 IIIAGIGRVGYTLAKSLSEKGHDIVLIDIDKdICkkasaeidALVINGDCTKIKTLEDAgIEDADMYIAVTGKEEVNLMS 82
                                  689**************************95455322221115555667899*****98689***********9986554 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     1e-05    0.0098       3      69 ..       3      66 ..       1      87 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                        LpxI_N  3 gliAGsGrlPllvaeaakaagrevvvvalegeadeelekivdevaevsvgqlgklikaLkregvtev 69
                                   +iAG Gr    +a+++ ++g+++v++ + + + ++ ++++d+   v  g++ k ik+L+++g++++
  gi|15669293|ref|NP_248098.1|  3 IIIAGIGRVGYTLAKSLSEKGHDIVLIDIDKDICKKASAEIDA--LVINGDCTK-IKTLEDAGIEDA 66
                                  59***************************99888877776663..233344433.567777777665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.5e-05     0.014       1      31 [.       3      33 ..       3      76 .. 0.79
   2 ?   -2.8   0.0       4.8   4.5e+03      67      79 ..     194     206 ..     186     215 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                  i i+G+G +G +la +L+++g+d++li+ ++
  gi|15669293|ref|NP_248098.1|  3 IIIAGIGRVGYTLAKSLSEKGHDIVLIDIDK 33
                                  78*************************9988 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.8
                                   S-ESEEEE-SSGG CS
                          ApbA  67 epidlvivtvKay 79 
                                   +  d v+v vK  
  gi|15669293|ref|NP_248098.1| 194 KSGDRVLVLVKKD 206
                                   4557777777753 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   2.9e-05     0.027       4      52 ..       4      49 ..       2      95 .. 0.82
   2 ?   -1.6   0.0       4.4   4.2e+03      42      48 ..      85      96 ..      53     118 .. 0.49
   3 ?   -2.5   0.0       8.3   7.8e+03      60      76 ..     194     210 ..     188     215 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.9e-05
                                  EE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEEC CS
                 F420_oxidored  4 ii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvta 52
                                  ii G G++g +la+ l+++g   h+iv++ + +++  +++ +e+ + v+ 
  gi|15669293|ref|NP_248098.1|  4 IIaGIGRVGYTLAKSLSEKG---HDIVLI-DIDKDICKKASAEIDALVIN 49
                                  667*****************...****88.88888888888888854444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.4
                                  HHHHHC.....- CS
                 F420_oxidored 42 laeelg.....v 48
                                  la+++g     +
  gi|15669293|ref|NP_248098.1| 85 LAKSYGinktiA 96
                                  333333333333 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8.3
                                   HH-SEEEE-S-HHHHHH CS
                 F420_oxidored  60 eeadvvvlavkpedvee 76 
                                   ++ d v++ vk  ++++
  gi|15669293|ref|NP_248098.1| 194 KSGDRVLVLVKKDAADA 210
                                   56778888888666554 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.5e-05     0.033      18     100 ..      14     110 ..      11     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-05
                                   HHHHHHHHTT--EEEEEEEESSCCCCH..HTTEB-HHHH............CCHCCCHHHHHHCHCHHHH.....EEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx............xxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
                          CbiA  18 nLaralarrglrVllvDaDpqannlai..leglendiep............dlkrllellealgkkkall...lkiagvvl 81 
                                   +La++l+++g++++l+D D +    a+  ++ l+++ ++            d++ ++ +  +   +   l   l+ +++++
  gi|15669293|ref|NP_248098.1|  14 TLAKSLSEKGHDIVLIDIDKDICKKASaeIDALVINGDCtkiktledagieDADMYIAVTGKEEVN---LmssLLAKSYGI 91 
                                   69*******************888887665555555555777778888555444444444333333...234477777777 PP

                                   EEESS...-TTCHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          CbiA  82 nrvdgeneetllkealeel 100
                                   n+   + +e + k+ +e+l
  gi|15669293|ref|NP_248098.1|  92 NKTIARISEIEYKDVFERL 110
                                   7766665555555555554 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.1e-05     0.067      12      52 ..      15      60 ..      13      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.1e-05
                       UPF0180 12 vkeaLrekGYeVvdlet.....eedaqsvdaiVvtGqdtnvmgied 52
                                  +++ L+ekG+++v ++      +++  ++da+V++G+ t++ + ed
  gi|15669293|ref|NP_248098.1| 15 LAKSLSEKGHDIVLIDIdkdicKKASAEIDALVINGDCTKIKTLED 60
                                  6789*********99887899777799*********9999866555 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.8e-05     0.055       6      58 ..      11      60 ..       5      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.8e-05
                                  HHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHH CS
                  adh_short_C2  6 IGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvea 58
                                  +G+ +Ak+l e+G ++vl d++++    ++++ +e++a v++ D t+ +++e+
  gi|15669293|ref|NP_248098.1| 11 VGYTLAKSLSEKGHDIVLIDIDKDI---CKKASAEIDALVINGDCTKIKTLED 60
                                  5899********************9...8888999999999999998887765 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.6e-05     0.072       2      40 ..       3      45 ..       2      81 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.6e-05
                                  EEEE--SHHHHHHHHHHHTTT--EEEE-S-H....HHHHHHHH CS
                NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvree....elieeine 40
                                  i + G G  G +lAk+l+e+gh+++l+  ++    +   ei++
  gi|15669293|ref|NP_248098.1|  3 IIIAGIGRVGYTLAKSLSEKGHDIVLIDIDKdickKASAEIDA 45
                                  66889*************************9444444444555 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.8   0.00027      0.26       2      68 ..       2      75 ..       1     119 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                                  EEEEESTSHHHHHHHHHHHHHT.TCEEEEEE-.T...S-HHHHHHHHHEETTTEC-SS-EEEETTE..EEETTE CS
                       Gp_dh_N  2 kvainGfGRIGrlvlralleek.elevvaind.l...tdletlayllkyDsvhgrfkgeveaeeea..lvvngk 68
                                   + i G GR+G  +++ l e+  ++ ++ i + +   +++e  a +++ D +  +  ++  +e+++  + v+gk
  gi|15669293|ref|NP_248098.1|  2 YIIIAGIGRVGYTLAKSLSEKGhDIVLIDIDKdIckkASAEIDALVINGDCTKIKTLEDAGIEDADmyIAVTGK 75
                                  689***************96665999999988653334556667778888887777666666644412445554 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   9.1e-05     0.085       5      66 ..       4      60 ..       1      74 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.1e-05
                                  EESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHH CS
                     adh_short  5 vtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevea 66
                                  ++ + + +G+ +ak l ++G ++v++d+ ++ ++++ +e+      al+i++D t+ + +e+
  gi|15669293|ref|NP_248098.1|  4 IIAGIGRVGYTLAKSLSEKGHDIVLIDIDKDICKKASAEID-----ALVINGDCTKIKTLED 60
                                  4555556899***********************99999999.....6789999888777665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00011      0.11       1      66 [.       3      67 ..       3     106 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                  EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..EEEE--TT-HHHHHHHHHHHT-S CS
                     Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl..elveldltdrsalerlfkeeqpd 66
                                  i+++G+ G +G  l+k l ekg++++ +d +++  + ++ +++   ++++d t+ + le++  e ++d
  gi|15669293|ref|NP_248098.1|  3 IIIAGI-GRVGYTLAKSLSEKGHDIVLIDIDKDICK-KASAEIdaLVINGDCTKIKTLEDAGIE-DAD 67
                                  688888.*****************888887744333.333334456777777777777776554.344 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3    0.0003      0.29       1      52 [.       3      48 ..       3      82 .. 0.74
   2 ?   -0.8   0.0       1.8   1.7e+03      78     101 ..     141     164 ..      65     174 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                                  EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEE CS
               Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeai 52
                                  ++i G G+vG  +a+ l+++++    i+++d +k+ ++++ a++   ++  i
  gi|15669293|ref|NP_248098.1|  3 IIIAGIGRVGYTLAKSLSEKGHD---IVLIDIDKDICKKASAEI---DALVI 48
                                  7899****************985...*************99765...33333 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                                   SGGGHHHHHHHHHHHT-EEEESS- CS
               Sacchrp_dh_NADP  78 ppissldvlkaCietgvhyvdtsi 101
                                   +    +++l++ i  ++ +v+  i
  gi|15669293|ref|NP_248098.1| 141 VGRGEAEILEFIIPEKAKVVNKKI 164
                                   333455666666666666666555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00022       0.2       4      61 ..       3      66 ..       1     130 [. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                                  EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS....S--EEE..HHHHHHHHHTT-HHH CS
                 FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp....radgln..qrtmellrqlGledr 61
                                  ++I G G +G +la+ Lse+G + vl++  ++  ++      a ++n  ++ + +l+++G+ed 
  gi|15669293|ref|NP_248098.1|  3 IIIAGIGRVGYTLAKSLSEKGHDIVLIDIDKDICKKAsaeiDALVINgdCTKIKTLEDAGIEDA 66
                                  6899***********************9877665555223366666544788899999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1390.55
//
Query:       gi|15669294|ref|NP_248099.1|  [L=185]
Description: hypothetical protein MJ_1106 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-59  198.2   1.8    4.8e-59  197.7   1.8    1.2  1  DUF483    Protein of unknown function (DUF483)
  ------ inclusion threshold ------
       0.11   13.2   1.2       0.11   13.2   1.2    3.2  3  RecG_N    RecG N-terminal helical domain


Domain annotation for each model (and alignments):
>> DUF483  Protein of unknown function (DUF483)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.7   1.8   5.3e-63   4.8e-59       1     121 [.      42     164 ..      42     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 197.7 bits;  conditional E-value: 5.3e-63
                        DUF483   1 ldlqieivkkykkkvrpaidplvseelgiyrrlddleiGkllgyPkCCvksfieekrfaidsehlkeieellkalksk..y 79 
                                   l++qie+v+kyk+kvrpaidp+vs+elgiyrrldd+eiGkll+yP+CC+ksf+e++r+aid+ehlke+ee++++lk+k  y
  gi|15669294|ref|NP_248099.1|  42 LKFQIELVEKYKPKVRPAIDPMVSTELGIYRRLDDFEIGKLLDYPECCIKSFVEDVRVAIDREHLKEVEEMKEELKNKgiY 122
                                   589*********************************************************************99998877* PP

                        DUF483  80 aivlPsgfiPCsikCkkavkrkligkvdkdefekilklekel 121
                                   aivlPsgfiPCs+kC++a+kr++ig+++k+ef+kil+lekel
  gi|15669294|ref|NP_248099.1| 123 AIVLPSGFIPCSLKCEEAIKRGFIGYLTKEEFDKILELEKEL 164
                                   ****************************************99 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.2   1.2e-05      0.11      46      85 ..      14      53 ..       1      55 [. 0.78
   2 ?    0.7   0.0       0.1   9.2e+02       4      16 ..     104     116 ..      73     124 .. 0.62
   3 ?    0.8   0.1     0.091   8.2e+02      37      54 ..     153     170 ..     135     182 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                  HHH.HHHHHHHHHHTTSSSS-HHHHHHHHHHHHHHHHHHH CS
                        RecG_N 46 evlkeklskfldYikpiasLpeeRkikRlknglemieklr 85
                                  +++ e ++ + + i+++++++ +  + Rlk+ +e++ek++
  gi|15669294|ref|NP_248099.1| 14 SGELEGFEVLKEHIQSLDEFQYQQIVERLKFQIELVEKYK 53
                                  33346677778889999**********************9 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.1
                                   HHHHHHHHHHTS- CS
                        RecG_N   4 eFLeelekllkkv 16 
                                   e+L e+e+++++ 
  gi|15669294|ref|NP_248099.1| 104 EHLKEVEEMKEEL 116
                                   2233333333332 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.091
                                   ---GGGG-HHHH.HHHHH CS
                        RecG_N  37 iddplleneevlkeklsk 54 
                                     d++le e+ lkek+ +
  gi|15669294|ref|NP_248099.1| 153 EFDKILELEKELKEKIRH 170
                                   446777777777788765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1047  (0.058397); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1196.64
//
Query:       gi|15669295|ref|NP_248100.1|  [L=149]
Description: hypothetical protein MJ_1107 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.024   15.0   2.2      0.024   15.0   2.2    1.9  2  Syntaxin_2       Syntaxin-like protein
      0.029   14.6   1.2      0.046   14.0   1.2    1.3  1  COX6B            Cytochrome oxidase c subunit VIb
      0.051   13.1   1.5      0.062   12.8   1.5    1.1  1  DUF4481          Domain of unknown function (DUF4481)
      0.062   13.1   1.2        7.6    6.3   0.0    2.6  3  REF              Rubber elongation factor protein (REF)
      0.082   13.1   0.7        1.2    9.4   0.0    2.5  2  DASH_Dad1        DASH complex subunit Dad1
       0.12   12.6   0.3       0.18   12.1   0.3    1.3  1  Arteri_nucleo    Arterivirus nucleocapsid protein
       0.29    9.6   5.3       0.36    9.3   5.3    1.0  1  Herpes_UL6       Herpesvirus UL6 like
       0.74    9.1   2.2          1    8.6   2.2    1.3  1  LCIB_C_CA        Limiting CO2-inducible proteins B/C beta car
        1.2    9.6   5.5        8.6    6.8   0.1    2.3  2  FeoB_associated  FeoB-associated Cys-rich membrane protein
        6.1    7.0  11.9         11    6.2  11.9    1.4  1  Spore_GerAC      Spore germination B3/ GerAC like, C-terminal


Domain annotation for each model (and alignments):
>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.63   1.1e+03      54      56 ..      34      36 ..      10      69 .. 0.48
   2 ?   15.0   2.2   1.4e-05     0.024      16      63 ..      65     120 ..      60     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.63
                    Syntaxin_2 54 kkl 56
                                  k +
  gi|15669295|ref|NP_248100.1| 34 KII 36
                                  222 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.4e-05
                    Syntaxin_2  16 eklvkqLgtkkd........teelreklhelieeinelikktnellkklsqldnss 63 
                                   e+l+k L tk d         + +++k++++ie+in+l kk+ e + +l++  +++
  gi|15669295|ref|NP_248100.1|  65 EELRKELTTKEDleligekiLRYVDNKINQVIEKINQLDKKIDEGFYQLDKKVDTL 120
                                   5788889999998888766666666******************9999998866655 PP

>> COX6B  Cytochrome oxidase c subunit VIb
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.2   2.6e-05     0.046      32      65 ..      22      56 ..      12      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                         COX6B 32 e.kkeeqdekkCkaekkeyesnCaksWveyfkekr 65
                                  + k+e+++e+ Ck  ++ +e++C ++  ++f+e+ 
  gi|15669295|ref|NP_248100.1| 22 NvKDEKEAEELCKIIEEFFEKQCKENVSKKFEEQK 56
                                  23889999999**********************94 PP

>> DUF4481  Domain of unknown function (DUF4481)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.5   3.5e-05     0.062     160     245 ..       3      83 ..       1      96 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
                       DUF4481 160 yfVyfdlerClqaLselleelkteeekklrkrlsqlv.vvvevavseaeeeeedeeeeeaPLLveegsseqkkeltvtelv 239
                                   +fV f +      L el++++k+e+e++      +l+ ++ e  +++ +e+ +++ ee++P+L+ e ++e +kelt++e +
  gi|15669295|ref|NP_248100.1|   3 FFVVFVMAVAYSKLYELIKNVKDEKEAE------ELCkIIEEFFEKQCKENVSKKFEEQKPVLKLELKEELRKELTTKEDL 77 
                                   7999******************999943......44416667777777777777779999******9************** PP

                       DUF4481 240 sLipea 245
                                   +Li e+
  gi|15669295|ref|NP_248100.1|  78 ELIGEK 83 
                                   **9876 PP

>> REF  Rubber elongation factor protein (REF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.2   2.2e+03      25      33 ..      14      22 ..       5      60 .. 0.62
   2 ?    5.9   0.0    0.0056        10      65      84 ..      82     101 ..      75     102 .. 0.87
   3 ?    6.3   0.0    0.0042       7.6      71      98 ..     102     129 ..      99     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                           REF 25 sslYeyAke 33
                                  s+lYe+ k+
  gi|15669295|ref|NP_248100.1| 14 SKLYELIKN 22
                                  444444332 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0056
                           REF  65 lelLkfvDrKvdesvtkldk 84 
                                    ++L +vD+K++++++k+++
  gi|15669295|ref|NP_248100.1|  82 EKILRYVDNKINQVIEKINQ 101
                                   589************99976 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0042
                           REF  71 vDrKvdesvtkldkrvpsvvKevssqal 98 
                                   +D+K+de + +ldk+v ++ +++   al
  gi|15669295|ref|NP_248100.1| 102 LDKKIDEGFYQLDKKVDTLKRDIIIIAL 129
                                   8***************988777665544 PP

>> DASH_Dad1  DASH complex subunit Dad1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.19   3.5e+02       2      25 ..      52      75 ..      51      78 .. 0.82
   2 ?    9.4   0.0   0.00065       1.2       9      33 ..      84     108 ..      81     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.19
                     DASH_Dad1  2 FerqRdrliqeIaesmeevlnnln 25
                                  Fe+q+  l  e+ e++ + l+  +
  gi|15669295|ref|NP_248100.1| 52 FEEQKPVLKLELKEELRKELTTKE 75
                                  9**********9999988777655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00065
                     DASH_Dad1   9 liqeIaesmeevlnnlnaLNRsLEe 33 
                                   +++ + +++++v++++n+L+++++e
  gi|15669295|ref|NP_248100.1|  84 ILRYVDNKINQVIEKINQLDKKIDE 108
                                   667788999*************975 PP

>> Arteri_nucleo  Arterivirus nucleocapsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   9.9e-05      0.18      12      67 ..      24      76 ..      18      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.9e-05
                 Arteri_nucleo 12 gngkrvnqqlcqllgkllaqrnqsrGkkrkkkkpekphfplaeedDlRheltqqer 67
                                  +++k+++ +lc+++ +++  ++q + +  kk +++kp   l  +++lR elt +e 
  gi|15669295|ref|NP_248100.1| 24 KDEKEAE-ELCKIIEEFF--EKQCKENVSKKFEEQKPVLKLELKEELRKELTTKED 76
                                  4556666.8999999999..8899999999999*******************9985 PP

>> Herpes_UL6  Herpesvirus UL6 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.3    0.0002      0.36     293     403 ..      14     121 ..      10     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0002
                    Herpes_UL6 293 kkeLlklliklkenktvggitdvVedfleevsnslvdknklldasqpGfgkggas.aqssekteqglkksvsnsvikclee 372
                                   +k L +l+ ++k+ k+  ++   +e+f e   ++ v k +   +++p +  + +   ++  +t+++l + + +++ + +++
  gi|15669295|ref|NP_248100.1|  14 SK-LYELIKNVKDEKEAEELCKIIEEFFEKQCKENVSKKFE--EQKPVLKLELKEeLRKELTTKEDL-ELIGEKILRYVDN 90 
                                   56.999******************************96665..777866555544244456666666.6899********* PP

                    Herpes_UL6 373 qineqfdtiekLkkenelllkklkelekeLe 403
                                   +in+ +++i++L k+ +    +l ++ + L+
  gi|15669295|ref|NP_248100.1|  91 KINQVIEKINQLDKKIDEGFYQLDKKVDTLK 121
                                   ************9988777777777666666 PP

>> LCIB_C_CA  Limiting CO2-inducible proteins B/C beta carbonyic anhydrases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.2   0.00057         1     120     189 ..      33     101 ..      15     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00057
                                   HHHH---------------TTTHHHHHHHHHHGGGHHHHHH-SSHHHHHHHHHHHHHHHHHHHHHHHTGG CS
                     LCIB_C_CA 120 kelkkeglekeskepgaldelDaeqsiikqrllkrleeiekaeddlveltkvayeaikddlekliekttv 189
                                   +++ +e  ek++k +++ ++ + +  ++k +l+++l++  ++++dl  + + + + ++++++++iek ++
  gi|15669295|ref|NP_248100.1|  33 CKIIEEFFEKQCK-ENVSKKFEEQKPVLKLELKEELRKELTTKEDLELIGEKILRYVDNKINQVIEKINQ 101
                                   5566677888886.4888999****************98999************************9654 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0048       8.6       7      29 ..       5      33 ..       4      45 .. 0.72
   2 ?    4.2   2.1     0.032        57       2      16 ..     123     137 ..     122     149 .] 0.70

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0048
               FeoB_associated  7 liiaaavafv....irrlikkkkkG..sC 29
                                  ++ ++ava+     +++++k+ k+    C
  gi|15669295|ref|NP_248100.1|  5 VVFVMAVAYSklyeLIKNVKDEKEAeeLC 33
                                  45567888889667777777766655555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.032
               FeoB_associated   2 tiIVgliiaaavafv 16 
                                   +iI++++i++++ ++
  gi|15669295|ref|NP_248100.1| 123 DIIIIALIIILANYA 137
                                   677777777766665 PP

>> Spore_GerAC  Spore germination B3/ GerAC like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  11.9    0.0061        11      46     119 ..      30     106 ..       8     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0061
                                   E.......EEEEEEE.EEEEEEE-SSSEEEEEEEEEEEEEE-----.-----HHHHHHHHHHHHHHHHHHHHHHHH..TT- CS
                   Spore_GerAC  46 k......vsveissskskikvkiengkpsfdikiklegdieeskknlleeeelkelekalekeiekeieealkklq..eyk 118
                                   +       ++  ++ k +++ k+e++kp+ ++++k e +     k+l+++e+l+ + +++ +++ ++i+++++k+   + k
  gi|15669295|ref|NP_248100.1|  30 EelckiiEEFFEKQCKENVSKKFEEQKPVLKLELKEELR-----KELTTKEDLELIGEKILRYVDNKINQVIEKINqlDKK 105
                                   24577777888899999*************999999977.....6778888899999999999999999999776635555 PP

                                   - CS
                   Spore_GerAC 119 s 119
                                   +
  gi|15669295|ref|NP_248100.1| 106 I 106
                                   4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2583  (0.144068); expected 358.6 (0.02)
Passed bias filter:                      880  (0.0490825); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 966.19
//
Query:       gi|15669296|ref|NP_248101.1|  [L=548]
Description: phenylalanyl-tRNA synthetase subunit beta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-43  147.0   0.0    7.4e-43  146.5   0.0    1.2  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    1.8e-18   66.6   0.0    2.5e-15   56.5   0.0    3.4  3  B5               tRNA synthetase B5 domain
    1.9e-16   60.2   0.3    5.8e-16   58.7   0.1    1.8  2  B3_4             B3/4 domain
    9.5e-09   35.4   0.8    1.6e-07   31.5   0.0    2.8  3  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain
    7.9e-08   32.1   0.0    1.7e-07   31.0   0.0    1.6  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.5   0.0   2.1e-46   7.4e-43      11     213 ..     358     546 ..     351     547 .. 0.96

  Alignments for each domain:
  == domain 1  score: 146.5 bits;  conditional E-value: 2.1e-46
               tRNA_synthFbeta  11 tegelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNla 91 
                                     geln+ +k  + +r++++g+G+ Evi+  + ++++l k + + ++++ +e++ P s ++ ++R+s+lp l+e+l+ N +
  gi|15669296|ref|NP_248101.1| 358 I-GELNQLEKKCDFIREIMVGFGFYEVINLMLSNDEVLFKKM-RIEDNNYIEVLKPASIEHRIVRKSILPLLMETLRINKH 436
                                   3.459999*****************************99985.45889********************************* PP

               tRNA_synthFbeta  92 rgnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepaehpa 171
                                   ++++  ++FEig+++  d ++e++ +  +++a+v++ ++            +f ++k  ve ll++l+i ++e+++ ehp+
  gi|15669296|ref|NP_248101.1| 437 KELP-QKIFEIGDCVVIDeNAETKSRVVKKIAGVIVDNE-----------TNFNEIKSYVEGLLRELKI-EYELDNFEHPS 504
                                   ****.*********99999********************...........*******************.*********** PP

               tRNA_synthFbeta 172 lhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEld 213
                                   + +gr+A+i  dgk +G++Ge+hpev  +f+l+ +v++fEl+
  gi|15669296|ref|NP_248101.1| 505 FIKGRCAKILKDGKIIGYFGEIHPEVITNFELEFPVVGFELE 546
                                   ****************************************97 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0     0.006        21       2      55 ..       5      62 ..       4      65 .. 0.87
   2 !   56.5   0.0     7e-19   2.5e-15       4      67 .]     283     345 ..     280     345 .. 0.95
   3 ?   -0.6   0.0      0.46   1.7e+03      51      67 .]     364     380 ..     362     380 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.006
                                  EEEHHHHHHHHTS---HHHHHHHHHHTT-E.....EESSTTCEEEE--TT-TT--SHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxx RF
                            B5  2 slrvekinkllGidlseeeiikiLkrlgce....riekdkdlllVtvPswRsDleree 55
                                  +++ + +++l++++l++e i++ +  +g+e     +e++++ ++  + + R+D + +e
  gi|15669296|ref|NP_248101.1|  5 NVKKADLERLVNMPLEDEFIEEKFPMMGVEvegiFEEDGEKIIQFSINPNRPDYLSAE 62
                                  56677899**********************9998779999999*********988776 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 7e-19
                                   EHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            B5   4 rvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                   + e+ink+lG +l++ +ii++L+r  +++ +  +++++V +P++R+D+  e+D++EEva++yGY
  gi|15669296|ref|NP_248101.1| 283 TSEYINKVLGANLTPGTIINYLRRCRLDA-QFVDNKIKVFIPAYRVDIFGEIDIAEEVAIAYGY 345
                                   6799***********************96.999999***************************9 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.46
                                   --SHHHHHHHHHHHH-G CS
                                   xxxxxxxxxxxxxxxxx RF
                            B5  51 lereeDliEEvaRlyGY 67 
                                   le ++D+i E++  +G+
  gi|15669296|ref|NP_248101.1| 364 LEKKCDFIREIMVGFGF 380
                                   7899********99986 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.1   1.6e-19   5.8e-16      35     135 ..     116     242 ..      95     253 .. 0.92
   2 ?   -1.7   0.0      0.55     2e+03      82     112 ..     435     476 ..     418     479 .. 0.70

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 1.6e-19
                                   --HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEE.EEE--TTEEEEBTTS-EEEE-T....................T CS
                          B3_4  35 innvVDitNyvmlelgq.....PlhafDldkiqgdiv.vrlakegeklvtldgkerelde....................e 89 
                                   ++++++++++++  +g+     +++++D+dk+++++  ++ + +g k+v+l+ +  e+++                    +
  gi|15669296|ref|NP_248101.1| 116 LESIINLQEKLHWVMGRdrkkvAIGIHDADKVKPPFYyKEVSGDGIKFVPLNSD-EEMTPreilekhekgikyahlikddK 195
                                   579*********************************989999999******955.5555557******************* PP

                                   SEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HHHHHHH CS
                          B3_4  90 dlviadsekpv.slagvmggeeskvsedTknvfleaaafdpvsirkt 135
                                    ++i dse+ v s++++++ge ++v+ +T+n ++ +++ d+ ++ kt
  gi|15669296|ref|NP_248101.1| 196 FPIILDSEGDVlSMPPIINGELTRVTTETRNLLIDVTGTDKYAVEKT 242
                                   *********999*****************************999987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.55
                                   -EEEE-T.....TSEEEETE.....EEEE.EETTTEEBTTTB CS
                          B3_4  82 kerelde.....edlviads.....ekpv.slagvmggeesk 112
                                   k++el +     +d+v+ d+     +++v  +agv+  +e+ 
  gi|15669296|ref|NP_248101.1| 435 KHKELPQkifeiGDCVVIDEnaetkSRVVkKIAGVIVDNETN 476
                                   455553336666888888854444478889999999877775 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   4.4e-11   1.6e-07       1      76 [.       1      67 [.       1      72 [. 0.97
   2 ?    0.9   0.0      0.15   5.4e+02      54      75 ..     316     337 ..     305     344 .. 0.78
   3 ?   -2.8   0.0       2.1   7.6e+03      58      79 ..     471     493 ..     444     500 .. 0.58

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 4.4e-11
                     PhetRS_B1  1 MPtisvkkeaLfkalgkelteeeledllfefGlElDeiveeeekkkadkkseeviykidipAnryDLLcleglara 76
                                  MPti+vkk++L ++++  l++e +e+ +   G+E+  i ee+          e+i++  i  nr+D L++eglar 
  gi|15669296|ref|NP_248101.1|  1 MPTINVKKADLERLVNMPLEDEFIEEKFPMMGVEVEGIFEEDG---------EKIIQFSINPNRPDYLSAEGLARG 67
                                  *******************************************.........99*******************985 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.15
                     PhetRS_B1  54 viykidipAnryDLLcleglar 75 
                                   + +k+ ipA r D+     +a+
  gi|15669296|ref|NP_248101.1| 316 NKIKVFIPAYRVDIFGEIDIAE 337
                                   568999*******987666665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.1
                     PhetRS_B1  58 idipAnryDLLc.leglaralkv 79 
                                   +d   n   + + +egl r lk+
  gi|15669296|ref|NP_248101.1| 471 VDNETNFNEIKSyVEGLLRELKI 493
                                   44444444444435666666665 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   4.8e-11   1.7e-07      14     216 ..     359     545 ..     353     548 .] 0.81

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 4.8e-11
                                   SB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHH CS
                  tRNA-synt_2d  14 gklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirt 94 
                                   g+l+ l+k  + i+ei++ +gf ev +  + ++   f+ + +++++ +  ++        ++   e++++R    ++ + t
  gi|15669296|ref|NP_248101.1| 359 GELNQLEKKCDFIREIMVGFGFYEVINLMLSNDEVLFKKMRIEDNNYIEVLKP-------AS--IEHRIVRKSILPLLMET 430
                                   778899999999*************9999999999999998887765554443.......33..34789999999**9999 PP

                                   H...TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEE CS
                  tRNA-synt_2d  95 l...ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePs 172
                                   l   ++k++p+ki+ ig +   d+   t++ + +++ g++vd++ +++++k  +e ll++l       +++ +   f  Ps
  gi|15669296|ref|NP_248101.1| 431 LrinKHKELPQKIFEIGDCVVIDENAETKSRVVKKIAGVIVDNETNFNEIKSYVEGLLREL-------KIEYELDNFEHPS 504
                                   99989999****************************************************9.......4455666778888 PP

                                   EEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEE CS
                  tRNA-synt_2d 173 aevdvylvekkkkwlEllgaGmvrpevleavgideevsgfafGl 216
                                   + ++  + +  k+   ++ +G ++pev++++++  e ++++f l
  gi|15669296|ref|NP_248101.1| 505 F-IKGRCAKILKDGKIIGYFGEIHPEVITNFEL--EFPVVGFEL 545
                                   7.4444423333333366788888888888888..777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3437.18
//
Query:       gi|15669297|ref|NP_248102.1|  [L=176]
Description: orotate phosphoribosyl transferase PyrE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.7e-16   58.0   3.3      1e-15   57.6   3.3    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00028   20.4   0.0    0.00047   19.7   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
       0.02   14.4   0.3      0.057   12.9   0.1    1.7  2  PRTase_2      Phosphoribosyl transferase
      0.036   14.4   0.5      0.036   14.4   0.5    1.7  2  PDZ           PDZ domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   3.3   2.3e-19     1e-15       6     133 ..      40     155 ..      35     165 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 2.3e-19
                                   TT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----T CS
                  Pribosyltran   6 lenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpa 86 
                                   ++np+il+ v +++ae +++   + + v+g++ g+vp+a++++     pl +vrk+ ++ ++++++           e+++
  gi|15669297|ref|NP_248102.1|  40 TTNPEILKLVGEIIAEQIKD---EDVKVAGVELGSVPIATAVSIIAQKPLLIVRKKPKDYGTKNKI---------EGELKE 108
                                   689*****************...999****************************************.........789*** PP

                                   TSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHH CS
                  Pribosyltran  87 gkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeev 133
                                   g kV+iV+D+ +tGg++l+a++ ++e g  + ++ v+vd+ ++++e 
  gi|15669297|ref|NP_248102.1| 109 GDKVVIVEDVTTTGGSVLKAVKEIRENGGIVDKVFVVVDRLEGAKEN 155
                                   *****************************999999****99999876 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     1e-07   0.00047     112     157 ..      99     145 ..      76     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1e-07
                       UPRTase 112 ynkLPkki.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvl 157
                                    nk+  ++ + ++v++++ v  TGgs+ +a++ ++e+g  ++k++v+
  gi|15669297|ref|NP_248102.1|  99 KNKIEGELkEGDKVVIVEDVTTTGGSVLKAVKEIRENGGIVDKVFVV 145
                                   4677777767788*************************999999886 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.21   9.5e+02      25      59 ..      39      70 ..      37      88 .. 0.66
   2 ?   12.9   0.1   1.3e-05     0.057     116     157 ..     104     147 ..      94     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.21
                      PRTase_2 25 iPvkpstvreagaaLaellaeakkeelpepvlvig 59
                                    ++p++ + +g+ +ae++++++   ++   + +g
  gi|15669297|ref|NP_248102.1| 39 ATTNPEILKLVGEIIAEQIKDED---VKVAGVELG 70
                                  56789999999999999999543...333333344 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.3e-05
                      PRTase_2 116 ellaaakelvLvDDEistGktalnliralqek..lprkryvvvs 157
                                     l++ +++v+v D  +tG ++l+ +++++e+  + +k +vvv 
  gi|15669297|ref|NP_248102.1| 104 GELKEGDKVVIVEDVTTTGGSVLKAVKEIRENggIVDKVFVVVD 147
                                   5678899***********************99433334444443 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.6   7.1e+03      24      37 ..      58      72 ..      46      84 .. 0.59
   2 ?   14.4   0.5   7.9e-06     0.036      42      77 ..     103     139 ..      95     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                                  SSSSEEEEEECTT.S CS
                           PDZ 24 gdkgifvsevlpg.g 37
                                  +d+ + v+ v+ g  
  gi|15669297|ref|NP_248102.1| 58 KDEDVKVAGVELGsV 72
                                  445666666666642 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.9e-06
                                   HT.SSTTEEEEEETTEETTTSHHHHHHHHHHTTTSEE CS
                           PDZ  42 dg.lkvGDkIlsvNgvdvenvsheeavqaikgskgkv 77 
                                    g lk+GDk++ v +v++++ s+++av++i++ +g v
  gi|15669297|ref|NP_248102.1| 103 EGeLKEGDKVVIVEDVTTTGGSVLKAVKEIRENGGIV 139
                                   688*****************************99833 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1095.69
//
Query:       gi|15669298|ref|NP_248103.1|  [L=486]
Description: hypothetical protein MJ_1110 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-74  249.8  35.1    1.1e-49  169.2  23.5    2.7  2  DUF530     Protein of unknown function (DUF530)
     0.0015   18.3   0.2        1.4    8.7   0.0    2.8  2  SKA2       Spindle and kinetochore-associated protein 2
  ------ inclusion threshold ------
       0.01   16.0   0.1       0.01   16.0   0.1    3.7  4  DUF5388    Family of unknown function (DUF5388)
       0.33   11.1   3.0         14    6.0   0.0    4.1  5  PAH        Paired amphipathic helix repeat


Domain annotation for each model (and alignments):
>> DUF530  Protein of unknown function (DUF530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   4.1   7.9e-28   3.5e-24       3     122 ..       4     127 ..       1     133 [. 0.90
   2 !  169.2  23.5   2.4e-53   1.1e-49     167     520 ..     133     483 ..     127     484 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 7.9e-28
                        DUF530   3 esvLiaksekfLdeikeekiklddl........kdlesflkvyekLknnldkLqdlkekmelkGytaPyrslkrygsklse 75 
                                    s Li+++++fLd+++e + kl+++         d  ++ ++  +L++nl++Lqdlk kme   +++Py+ + ++      
  gi|15669298|ref|NP_248103.1|   4 TSNLIKNANEFLDSLNEINDKLKEVvgkiknktIDKTKLSDIILTLEKNLEILQDLKSKMEFLEFDSPYKNVGKLKG---- 80 
                                   488**************99999999888887444556778999********************************33.... PP

                        DUF530  76 evkaedvseisrhaqyfRikasakKnildrVksAiasHkiAignlee 122
                                     + e ++ei+ +++y+R+ as+kK+il+rV+ A+++HkiA+++l e
  gi|15669298|ref|NP_248103.1|  81 GYDSEGLQEIASYSTYLRRIASEKKGILERVRHALVAHKIALAHLTE 127
                                   356799***************************************87 PP

  == domain 2  score: 169.2 bits;  conditional E-value: 2.4e-53
                        DUF530 167 eiipyLplsGdYmvklSelskyareafkkilrilkqekkGivksislvikvledgkwirkrvkidsedesnyEeelrkryG 247
                                   ++ p Lpl+G+Y+  + e+++y   ++k  l il+ +++Gi+ s ++++ v ++gk+ +kr+k++ +   nyE+++++++G
  gi|15669298|ref|NP_248103.1| 133 NLPPNLPLDGSYKKIMFEFPPYLVTTYKEFLDILEPKGRGILTSYTISLIVIDKGKREFKRIKVEDK---NYEKYIKEKFG 210
                                   66689***********************************************************998...9********** PP

                        DUF530 248 knvriellqfhrkKpsiinDkyvrtalalaYvklaediisekkdeilkeklkdkek..vkkYdeilkeakkeapelleead 326
                                    n++i++++ + +K++ii+D+yvr++la++Y++  +d+i++ ++e +++ l+++ek  +++Y e++  +++ea       d
  gi|15669298|ref|NP_248103.1| 211 -NAIITSIKRNFSKNKIIDDQYVRRVLAIGYLNTYKDEIEKAINEKIDKLLNEEEKkyLNRYLELCLLFREEADISGGILD 290
                                   .**************************************************9998888*********99999765555556 PP

                        DUF530 327 ....eleelreeklkkeLkdkglldkngkldkelkedlkereeiekeiflevpltlilwDilkYYLttSadrRkrysgpFP 403
                                       e  +l+e +lk+ L+++gl+  +g++   lk+ +k+++e+ k+i+ ++ ++  + D++k+YL +  d+R r s+ FP
  gi|15669298|ref|NP_248103.1| 291 vrcmEERKLKELELKEILEKEGLY-RDGEPIEPLKKAIKIKNELSKKISKDILIKRFSEDVFKFYLYKTPDERAR-SNLFP 369
                                   66344455****************.99************************************************.***** PP

                        DUF530 404 nlrpeldrqqlk..vfee.fekkvvel...lekkleekiiaiknldevllkkfelEkklkglnlklnyaalGaailnsese 478
                                   ++  +++r  l    ++     +v++l   le++l+++ i++kn++ v l+ ++  + +   n+k +       +l++   
  gi|15669298|ref|NP_248103.1| 370 SIMITPQRGFLSwmSVDGiNCVDVLDLkfkLEEELPKYQIPLKNIGGVALYLIHDWDAVERFNFKKKDI---EDLLKK--I 445
                                   ********99984334443556777745558999**************444444333344455544422...122222..2 PP

                        DUF530 479 ieieeiakllsvdvkevkkekknikklekpssdkakkFLeli 520
                                   + ie i ++l+ ++ +    + +++k+ k +++k+kkFL+l+
  gi|15669298|ref|NP_248103.1| 446 ALIEPIKEILKDKNVD----VSKLEKFGKVKKEKTKKFLDLL 483
                                   3466666666544444....456999*************986 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.4    0.0017       7.7      38      94 ..       9      64 ..       1      75 [. 0.86
   2 !    8.7   0.0   0.00031       1.4      53      96 ..      89     135 ..      87     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0017
                          SKA2 38 eNpvkLlerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasae 94
                                  +N  + l +l++++++l+++  ++++    k +l d i  tl +n e+lq+L+ ++e
  gi|15669298|ref|NP_248103.1|  9 KNANEFLDSLNEINDKLKEVVGKIKNKTIDKTKLSDIIL-TLEKNLEILQDLKSKME 64
                                  78889999*************************999776.688**********9986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00031
                          SKA2  53 elqaLkeqceellaekkelidkirttlvanrellqqLqasa...elp 96 
                                   e+++ ++ ++ +++ekk + +++r+ lva +  l +L +++   +lp
  gi|15669298|ref|NP_248103.1|  89 EIASYSTYLRRIASEKKGILERVRHALVAHKIALAHLTEDIgniNLP 135
                                   56666777899***************************999744444 PP

>> DUF5388  Family of unknown function (DUF5388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.3     0.072   3.2e+02      16      64 ..       6      56 ..       4      59 .. 0.72
   2 ?    0.3   0.0      0.19   8.4e+02      56      67 ..     158     169 ..     148     171 .. 0.88
   3 ?   16.0   0.1   2.2e-06      0.01      25      57 ..     235     267 ..     219     275 .. 0.82
   4 ?   -2.4   0.2       1.3   5.9e+03      41      64 ..     460     483 ..     434     484 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.072
                       DUF5388 16 NHirNklqALaaiG.laksqkeavkklveslidsLsesdk.krfkkqleiL 64
                                  N i+N+ + L ++  ++   ke+v k+ +++id+ + sd   +++k leiL
  gi|15669298|ref|NP_248103.1|  6 NLIKNANEFLDSLNeINDKLKEVVGKIKNKTIDKTKLSDIiLTLEKNLEIL 56
                                  7788887777766524566799***********988777524666666666 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.19
                       DUF5388  56 rfkkqleiLEek 67 
                                   ++k++l+iLE k
  gi|15669298|ref|NP_248103.1| 158 TYKEFLDILEPK 169
                                   79********87 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 2.2e-06
                       DUF5388  25 LaaiGlaksqkeavkklveslidsLsesdkkrf 57 
                                    +aiG+ ++ k+ ++k++++ id+L ++++k++
  gi|15669298|ref|NP_248103.1| 235 VLAIGYLNTYKDEIEKAINEKIDKLLNEEEKKY 267
                                   579*********************988877776 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.3
                       DUF5388  41 lveslidsLsesdkkrfkkqleiL 64 
                                   +  s +++ ++ +k++ kk+l+ L
  gi|15669298|ref|NP_248103.1| 460 VDVSKLEKFGKVKKEKTKKFLDLL 483
                                   444667777777788878877766 PP

>> PAH  Paired amphipathic helix repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.061   2.7e+02       4      24 ..      12      29 ..      12      43 .. 0.78
   2 ?   -3.4   0.0       2.6   1.2e+04       7      15 ..      53      61 ..      53      86 .. 0.77
   3 ?    6.0   0.0     0.003        14       2      10 ..     158     166 ..     157     168 .. 0.91
   4 ?   -2.4   0.0       1.2   5.6e+03      10      31 ..     241     260 ..     239     265 .. 0.72
   5 ?   -0.4   0.1       0.3   1.3e+03       1      10 [.     474     483 ..     474     484 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.061
                           PAH  4 keFLdiLhdyqkeqidskeVy 24
                                  +eFLd L++ + +    keV+
  gi|15669298|ref|NP_248103.1| 12 NEFLDSLNEINDKL---KEVV 29
                                  69*******99664...4554 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.6
                           PAH  7 LdiLhdyqk 15
                                  L+iL+d ++
  gi|15669298|ref|NP_248103.1| 53 LEILQDLKS 61
                                  678877664 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.003
                           PAH   2 vYkeFLdiL 10 
                                   +YkeFLdiL
  gi|15669298|ref|NP_248103.1| 158 TYKEFLDIL 166
                                   7*******9 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.2
                           PAH  10 LhdyqkeqidskeVyeqVskLF 31 
                                   L++y+ e    k + e++ kL+
  gi|15669298|ref|NP_248103.1| 241 LNTYKDEI--EKAINEKIDKLL 260
                                   89999886..666666666666 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 0.3
                           PAH   1 evYkeFLdiL 10 
                                   e+ k+FLd+L
  gi|15669298|ref|NP_248103.1| 474 EKTKKFLDLL 483
                                   6789****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1515  (0.0845); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 2965.84
//
Query:       gi|15669299|ref|NP_248104.1|  [L=449]
Description: tRNA CCA-pyrophosphorylase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-43  146.5   0.1    6.4e-43  145.6   0.1    1.5  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    5.3e-20   71.5   2.0    7.4e-20   71.1   0.3    2.2  2  NTP_transf_2     Nucleotidyltransferase domain
      6e-08   33.0   0.1      1e-07   32.2   0.1    1.3  1  SMODS            Second Messenger Oligonucleotide or Dinucleo
     0.0009   19.3   0.1     0.0009   19.3   0.1    2.6  3  Polbeta          Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.6   0.1   1.4e-46   6.4e-43       1     112 [.     161     280 ..     161     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 145.6 bits;  conditional E-value: 1.4e-46
                                   HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEE...E..............EEE..-S CS
               tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvi...dleekea........llkkfde 70 
                                   devrllK+flk++g+YGs++k+kGfsGYl+Ell+l+ygsf ++l++a++w+ + +i   d     +        +lkkfde
  gi|15669299|ref|NP_248104.1| 161 DEVRLLKAFLKSLGLYGSDVKTKGFSGYLCELLILHYGSFINLLKEAQNWRIGKKIilkD---IFEiykdvdinKLKKFDE 238
                                   89**************************************************98884443...3334446778889***** PP

                                   S-EEEETTEEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGG CS
               tRNA_NucTransf2  71 plvviDPvDpkRNvaaalsleklaefilaareflkkpseeff 112
                                   p++v+DPvD +RNva+ ls++++++fi+++r+flk+ps+eff
  gi|15669299|ref|NP_248104.1| 239 PFIVYDPVDLNRNVASPLSKDNFCRFIFYSRQFLKNPSIEFF 280
                                   *****************************************9 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.3   1.6e-23   7.4e-20       1      94 [.      35     146 ..      35     147 .. 0.97
   2 ?   -2.5   0.1       1.4   6.4e+03      56      62 ..     287     293 ..     264     329 .. 0.55

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 1.6e-23
                                   HHHHHHHHHHHTT.TSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH................HHHEHHHHHHHHCCCE CS
                  NTP_transf_2   1 lkklleelkelep.vakvvlfGSyarGtalkg.SDiDllvvlpeevsre................kkeegleklaeiikfl 63 
                                   ++k++e+++e+++ + +v l+GS+ar+t+lk+  DiD++v+++++vs++                 +  ++ ++a ++++ 
  gi|15669299|ref|NP_248104.1|  35 IDKIWEIVRENSYpILEVLLVGSSARNTNLKDdYDIDIFVLFDKSVSEDeleeiglkigteaikrLNGSYNINYASHPYVN 115
                                   689********************************************99****************999999********** PP

                                   EECTTEEEEEECEEECCCCTEEEEEECEEEH CS
                  NTP_transf_2  64 eellglevdlvtrekledpllvksileerpl 94 
                                    e+ g+evd+v+++k+ + ++++s+++++pl
  gi|15669299|ref|NP_248104.1| 116 GEVDGYEVDIVPCYKIDFGEKIISAVDRTPL 146
                                   ****************************997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                                   HHHHCCC CS
                  NTP_transf_2  56 laeiikf 62 
                                   l ei ++
  gi|15669299|ref|NP_248104.1| 287 LEEILEN 293
                                   2222222 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.1   2.3e-11     1e-07       3     135 ..       6     133 ..       4     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2.3e-11
                         SMODS   3 vssqFkeflsnielsqttkdsissrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllvvvne 83 
                                   +++ +ke l++i++s+++ ++++ + ++i +++ +  re +  i e llvGS+ar+T +k   d       d+d++v +++
  gi|15669299|ref|NP_248104.1|   6 IEEILKEVLNEIKPSKEDMEKLQLKANEIIDKIWEIVRENSYPILEVLLVGSSARNTNLK---D-----DYDIDIFVLFDK 78 
                                   678899*********************************999*****************9...3.....368888888887 PP

                         SMODS  84 vegd.epsdl.leklkkal.kktyksseirqdrqvvvvelneikidvvPavenkd 135
                                   + ++ e +++ l+   +a+ + + + +    +++ v  e++++++d+vP+ + + 
  gi|15669299|ref|NP_248104.1|  79 SVSEdELEEIgLKIGTEAIkRLNGSYNINYASHPYVNGEVDGYEVDIVPCYKIDF 133
                                   65441333331444455554333333447788999***************98766 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1     2e-07    0.0009       2      57 ..      37      94 ..      36     118 .. 0.76
   2 ?   -2.6   0.1       1.4   6.3e+03      57      73 ..     220     237 ..     212     244 .. 0.63
   3 ?   -3.9   0.1       3.5   1.5e+04      50      69 ..     320     337 ..     311     340 .. 0.48

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2e-07
                                  STTTTHHHHH.HHHSTTEEEEEE-S.------EEEEEEEESS---HHHHHHHHHHHHH CS
                       Polbeta  2 kikeilekek.eielaylFGSrakg.kareeSDiDlavllkekldleeelelaaeled 57
                                  ki ei+++++  i  ++l GS a++ +++++ DiD++vl++++ + +e  e+  ++  
  gi|15669299|ref|NP_248104.1| 37 KIWEIVRENSyPILEVLLVGSSARNtNLKDDYDIDIFVLFDKSVSEDELEEIGLKIGT 94
                                  77788888754788899******661567799***********777777777666654 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                                   HH..SSSEEEEEETTTS- CS
                       Polbeta  57 di.klgkkvDlvdlneap 73 
                                   di ++ k+vD+ +l++ +
  gi|15669299|ref|NP_248104.1| 220 DIfEIYKDVDINKLKKFD 237
                                   333446777777777544 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3.5
                                   HHHHHHHHH.SSSEEEEEET CS
                       Polbeta  50 elaaelediklgkkvDlvdl 69 
                                   +l++ ++++    k ++v+l
  gi|15669299|ref|NP_248104.1| 320 KLQKSINKV--IVKNEFVIL 337
                                   344444444..234444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2838.04
//
Query:       gi|15669300|ref|NP_248105.1|  [L=301]
Description: N-acetylglucosamine-1-phosphate transferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-26   93.4  16.6    1.4e-26   93.4  16.6    2.7  3  Glycos_transf_4  Glycosyl transferase family 4


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.021   3.8e+02      54      88 ..       5      38 ..       1      43 [. 0.78
   2 !   93.4  16.6   7.8e-31   1.4e-26       3     159 ..      69     212 ..      67     213 .. 0.88
   3 ?   -1.9   0.0      0.16     3e+03      58      71 ..     279     292 ..     249     298 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.021
               Glycos_transf_4 54 ltqvlielglilavlltllvivgvtNavNliDGld 88
                                  ++ +l+++++i +++ ++l+ + +  ++N   G+d
  gi|15669300|ref|NP_248105.1|  5 FI-NLFTYTIIAFIFSAVLCKFLMKKMINYKFGYD 38
                                  55.67778889999999999999999999766665 PP

  == domain 2  score: 93.4 bits;  conditional E-value: 7.8e-31
               Glycos_transf_4   3 lllltillilllGflDDvlglkarlKlilqilaalililtldlslttlgllltqvlielglilavlltllvivgvtNavNl 83 
                                   +++l i+ ++++G++DD+ +l+++ Klil +++ li+ ++       +++         + ++ +l++ l i++ +N +N+
  gi|15669300|ref|NP_248105.1|  69 IFVLPIITAGIIGIVDDIAKLSPKEKLILLFISGLIIGIL------FYNNSYV------N-LIEILIIALGIMISSNLTNM 136
                                   56788999***************************98443......3333333......3.56789999************ PP

               Glycos_transf_4  84 iDGldGlaagvsiiialalvvlaavdgrsellllalallgallGfllfNrypAkvFmGDsgslflGlvlavlailg 159
                                   ++G++Gl++g+ +i++++l+++ ++d+ ++  l al++ ++ lG+l+fN+ypAkvF GD+g+l +G++lavla++ 
  gi|15669300|ref|NP_248105.1| 137 LAGFNGLEIGMGVIASISLALVLFLDNYTTGFLSALIFSASYLGLLIFNKYPAKVFPGDVGTLPIGAFLAVLAVVY 212
                                   ***********************9998888888878888889*******************************975 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.16
               Glycos_transf_4  58 lielglilavlltl 71 
                                   l+++ +i+ +++ +
  gi|15669300|ref|NP_248105.1| 279 LVTVLWIIGIFFGI 292
                                   33334444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1951.98
//
Query:       gi|15669301|ref|NP_248106.1|  [L=192]
Description: hypothetical protein MJ_1114 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0022   17.4   0.4     0.0022   17.4   0.4    2.0  2  Form_Nir_trans   Formate/nitrite transporter
  ------ inclusion threshold ------
      0.014   14.6   0.1      0.016   14.4   0.1    1.0  1  7tm_7            7tm Chemosensory receptor
      0.017   15.1   9.9       0.29   11.2   1.5    2.2  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
      0.059   13.6  12.3      0.098   12.9  12.3    1.4  1  EI24             Etoposide-induced protein 2.4 (EI24)
          3    7.8  14.0        3.5    7.5   1.2    2.4  2  DUF2975          Protein of unknown function (DUF2975)


Domain annotation for each model (and alignments):
>> Form_Nir_trans  Formate/nitrite transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4     6e-07    0.0022       2      71 ..       3      75 ..       2      79 .. 0.93
   2 ?    0.3   0.5     0.099   3.6e+02     181     205 ..     128     152 ..     113     178 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6e-07
                                  HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCT...TCHHHHHHHHHCCCHHHHHHHH CS
                Form_Nir_trans  2 ivekvvaagvkkaklsldklfllgilAGafigfgvllalvvaaalaes...npglakllgglvFpvGlilvvl 71
                                  ivekv ++g  k+k ++ +++++ ++AG++  fg+l+ + +a  l +      ++ k +++++ +++li+v+l
  gi|15669301|ref|NP_248106.1|  3 IVEKVYKEGILKLKENIPQIIINLVVAGLIWVFGILVFIPIADMLGNPylfGLTALKPIISAIITIALIIVLL 75
                                  899*****************************************9887*9977888999**********9986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.099
                                   HHHHHHCT---HHHHHHHHHHHHHH CS
                Form_Nir_trans 181 ifafvasgfeHsvanmfliplglll 205
                                   +f+ v+sg + + a ++li+l l++
  gi|15669301|ref|NP_248106.1| 128 FFLPVISGITPVLAGIVLIILVLWA 152
                                   3444555555555555555555544 PP

>> 7tm_7  7tm Chemosensory receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.4e-06     0.016      37     199 ..      23     186 ..      21     192 .] 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.4e-06
                         7tm_7  37 llllvllvllvlflivlkreeyffrrsallevvynlqlvlglltvlvillsllfqrrrlarllnellkldrrlkrlgnrrn 117
                                   +++lv++ l+++f+i  ++    +  +++l  + +l  ++ +++++ +++ ll+  + + +l+  ++++    +  ++   
  gi|15669301|ref|NP_248106.1|  23 IINLVVAGLIWVFGILVFIPIADMLGNPYLFGLTALKPIISAIITIALIIVLLRVTKDFGELMDGIADIIAVKLAGSRVNE 103
                                   67777788888888777777777889999*************************************776444433333333 PP

                         7tm_7 118 k.....rrfnrllllllvliillllvtllgylllsqyftlvlllllyllpylvlqlllllyfllllliyellrllnerLkq 193
                                         rr  r l++l+v+ii +l +  +   ++  ++ l+ ++l+ l++++  ++l+++ + +   i e +r+  e+L++
  gi|15669301|ref|NP_248106.1| 104 EklkkyRRGLRGLAYLIVAIIAYLFFLPV---ISGITPVLAGIVLIILVLWA-VTVLINIGHIFSEEIEEGIRIATEKLEK 180
                                   24765455555555555555555555555...89999999999999999999.7777888887777777777777777777 PP

                         7tm_7 194 lvrelr 199
                                    ++ ++
  gi|15669301|ref|NP_248106.1| 181 ALEKSV 186
                                   776665 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.6   0.00048       1.7      26      84 ..      15      75 ..      13      81 .. 0.63
   2 ?   11.2   1.5   8.1e-05      0.29      29      85 ..     108     156 ..      93     169 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00048
               Phage_holin_3_6 26 lkeeakragsgagllgaagvlallalllllval....alala.a.lwlaalivaavllvlagvla 84
                                  lke+  ++++ ++++g+  v+++l ++ +  +l    +++l+ + + ++a+i     ++l +vl+
  gi|15669301|ref|NP_248106.1| 15 LKENIPQIIINLVVAGLIWVFGILVFIPIADMLgnpyLFGLTaLkPIISAII----TIALIIVLL 75
                                  5677777777777777777777777777777776555588853355555555....444444444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.1e-05
               Phage_holin_3_6  29 eakragsgagllgaagvlallalllllval.alalaalwlaalivaavllvlagvlal 85 
                                   + +r ++g++ l++a +  l+ l++++    +la          + ++ lvl +v +l
  gi|15669301|ref|NP_248106.1| 108 KYRRGLRGLAYLIVAIIAYLFFLPVISGITpVLAG---------IVLIILVLWAVTVL 156
                                   56788888899999988888888888888885555.........22333333333333 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  12.3   2.7e-05     0.098      19     124 ..      22     151 ..      12     160 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                                   HHHHHHHHHHHHHHHHHHHH....-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHH.........HHHHHHHH......... CS
                          EI24  19 lllplllnlllfllllvlll....wvllasllvllllllplwlfplvalllaapf.........ygllaekv......... 77 
                                   +++ l++++l++++++++++    + l  + l+ l++l p++   ++  l++ ++         ++ +a+++         
  gi|15669301|ref|NP_248106.1|  22 IIINLVVAGLIWVFGILVFIpiadM-LGNPYLFGLTALKPIISAIITIALIIVLLrvtkdfgelMDGIADIIavklagsrv 101
                                   5667777777777665555565441.3334444444444433333222222222234444455555566665444444444 PP

                                   .HH.HHCCTTSHHHHHHHHHHHHHHHHHHHHH.........HH.TTHHH....HHHHH CS
                          EI24  78 .ekrhlglvkslaeslkslllllllllvllpl.........li.Pvvglilsplllsw 124
                                    e+  l         +++ l+ l +l+v+++          +i Pv+  i+ ++l +w
  gi|15669301|ref|NP_248106.1| 102 nEE-KL-------KKYRRGLRGLAYLIVAIIAylfflpvisGItPVLAGIVLIILVLW 151
                                   422.23.......344444444444444444443101114533455555555555554 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   5.6    0.0061        22      61     114 ..      21      76 ..      18      79 .. 0.70
   2 ?    7.5   1.2   0.00098       3.5      58     105 ..     112     157 ..     107     176 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0061
                       DUF2975  61 riglaliaaalllaagivalallaelelapgvvllllg..vafaslvigllvlvla 114
                                   +i+  l++a l++++gi+++ ++a++  +p+++ l  +  ++ a + i+l++++l+
  gi|15669301|ref|NP_248106.1|  21 QIIINLVVAGLIWVFGILVFIPIADMLGNPYLFGLTALkpIISAIITIALIIVLLR 76 
                                   5788889999999999*********7789955544444113334466666666664 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00098
                       DUF2975  58 rLrriglaliaaalllaagivalallaelelapgvvllllgvafaslv 105
                                    Lr ++++++a++++l+++ v+  ++    la++v+++l++ a+++l+
  gi|15669301|ref|NP_248106.1| 112 GLRGLAYLIVAIIAYLFFLPVISGITPV--LAGIVLIILVLWAVTVLI 157
                                   5777788888887777776777776666..666666666555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1284  (0.0716158); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1365.58
//
Query:       gi|15669302|ref|NP_248107.1|  [L=261]
Description: hypothetical protein MJ_1115 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.1e-120  401.8   2.6   1.2e-120  401.6   2.6    1.0  1  BtpA            BtpA family
  ------ inclusion threshold ------
      0.066   12.6   0.0        1.2    8.5   0.0    2.0  2  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.6   2.6  1.4e-124  1.2e-120       1     254 []       6     257 ..       6     257 .. 0.99

  Alignments for each domain:
  == domain 1  score: 401.6 bits;  conditional E-value: 1.4e-124
                          BtpA   1 kekpvigvvHLkpLPgsaeykanleevidkAvkeakaleegGvDavilenygdaPflkevdpetvaamtvivkevksdvsi 81 
                                   k+kp+ig+vHLkpLPgs++y++n+++++d+A+keak+lee+G+Dav++en+gdaPf+ke+d++t+a+m+vi+k++k++vs+
  gi|15669302|ref|NP_248107.1|   6 KKKPLIGMVHLKPLPGSYHYNDNFDDIVDFAIKEAKKLEEAGFDAVMIENFGDAPFKKEADKITIASMAVIAKAIKEEVSL 86 
                                   58******************************************************************************* PP

                          BtpA  82 plGvnvLrndavaalaiAkavgakFiRvnvltgvalsdeGilegkaaellrykkllesrvkiladvavkhavplverdles 162
                                   plG+n+Lrnda++a++iA++v+a+FiRvnvl+gva++d+Gi+egka+el+++kkll+s++k++adv+vkha+++++  +es
  gi|15669302|ref|NP_248107.1|  87 PLGINILRNDAIGAYSIAYVVKADFIRVNVLSGVAFTDQGIIEGKAYELAKLKKLLPSKIKVFADVHVKHAYHFID--FES 165
                                   ****************************************************************************..*** PP

                          BtpA 163 avkdtvergladavilsGkatGgevdleelklaketvkvkvlvgsGvseenlekllsiadGvivgtsikkdGkianaiDke 243
                                   +++dtvergladavi+sGk+tG+evd+e+lklake+v+v+v+vgsG++++nl+ l+s+adG+i+gt+ikkdGk++n+iD +
  gi|15669302|ref|NP_248107.1| 166 SLLDTVERGLADAVIISGKRTGKEVDIEKLKLAKELVDVPVIVGSGTNYNNLRILWSYADGFIIGTWIKKDGKANNEIDID 246
                                   ********************************************************************************* PP

                          BtpA 244 rvrkivelaek 254
                                   r++kiv+la+k
  gi|15669302|ref|NP_248107.1| 247 RAKKIVNLANK 257
                                   *******9985 PP

>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00013       1.2      23      62 ..      34      74 ..      13      79 .. 0.78
   2 ?    2.1   0.0     0.012   1.1e+02     167     194 ..     204     234 ..     175     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00013
                Bac_luciferase 23 rylvelaraaEelGfdavwvaehhggpgga.ldaftllaal 62
                                  + +++ a+++Ee+Gfdav++      p+++ +d +t+++++
  gi|15669302|ref|NP_248107.1| 34 DFAIKEAKKLEEAGFDAVMIENFGDAPFKKeADKITIASMA 74
                                  5567789************9888777777787777777665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.012
                Bac_luciferase 167 iPvyvaaas.paglelaarhadglllag..e 194
                                   +Pv+v++++   +l++ +++adg+++    +
  gi|15669302|ref|NP_248107.1| 204 VPVIVGSGTnYNNLRILWSYADGFIIGTwiK 234
                                   8*999999989*************9987542 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1706.07
//
Query:       gi|15669303|ref|NP_248108.1|  [L=544]
Description: asparagine synthetase AsnB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-57  196.0   0.2    8.4e-32  111.2   0.0    2.2  2  Asn_synthase  Asparagine synthase
    2.1e-35  121.8   0.0    4.3e-35  120.8   0.0    1.5  1  GATase_6      Glutamine amidotransferase domain
    1.8e-34  118.3   0.0    3.4e-34  117.4   0.0    1.5  1  GATase_7      Glutamine amidotransferase domain
     0.0022   17.5   0.1     0.0046   16.4   0.1    1.5  1  DUF3700       Aluminium induced protein
  ------ inclusion threshold ------
      0.019   14.9   1.3       0.19   11.6   0.3    2.7  3  Prefoldin     Prefoldin subunit
       0.02   14.0   0.0      0.034   13.3   0.0    1.4  1  NAD_synthase  NAD synthase
      0.095   12.9   0.7       0.26   11.5   0.7    1.8  1  TPR_2         Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   0.0   3.3e-35   8.4e-32       2     146 ..     246     387 ..     245     390 .. 0.96
   2 !   84.2   0.0   5.3e-27   1.4e-23     201     297 ..     386     514 ..     381     543 .. 0.92

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 3.3e-35
                  Asn_synthase   2 lrelLedaVkrrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvltee 82 
                                   l+++L+++V +r+r+  +vG+  SGG+DSSlia la+ +   ++  +++g+  + s+++ ya+++a++l+++ ++ +++ee
  gi|15669303|ref|NP_248108.1| 246 LDRALKNSVLKRVRGLDKVGIICSGGVDSSLIAKLASLYC--EVILYAVGT--ENSEDLIYAERLAKDLNLKLRKKIISEE 322
                                   6789**********************************98..7********..**************************** PP

                  Asn_synthase  83 elldalpdviyhlee..pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaalsrs 146
                                   e ++++ +v+++++e   + +   ip y +s++a+++g+kvvLsG+GaDElfgGY  ++ + ++++
  gi|15669303|ref|NP_248108.1| 323 EYEEYVFKVAKAIDEvdLMKIGVGIPIYVASEMANEDGLKVVLSGQGADELFGGYA-RHERIYRER 387
                                   ****************9999***********************************9.*99987765 PP

  == domain 2  score: 84.2 bits;  conditional E-value: 5.3e-27
                  Asn_synthase 201 legedelhrelyldlktllpgdllrkDrasmahglEaRvPflDhrlvevalrlppelklrg.................... 261
                                    +ge+el++el+ d+ +l++ +l r D+++ma+g+E+RvPflD ++ve al++p+e+k+++                    
  gi|15669303|ref|NP_248108.1| 386 ERGEEELKKELLKDVYNLYKVNLERDDHCTMANGVELRVPFLDEEVVEIALSIPIEYKMSElsnrpyaesnislkseping 466
                                   57899**************************************************************************** PP

                  Asn_synthase 262 ............gieKyiLRealegylPeeileRpKegfsapvgewkl 297
                                                  K iLR ++ +ylP+ i++RpK+++++++g  k+
  gi|15669303|ref|NP_248108.1| 467 lkntnlnikcvrSVRKKILRDVASQYLPDYIAYRPKKAAQYGSGGEKM 514
                                   ****************************************99988754 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.8   0.0   1.7e-38   4.3e-35      13     134 .]      64     177 ..      40     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 1.7e-38
                      GATase_6  13 evalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllalleelGeevlerlr 93 
                                   ++ laH+Rlaivg     g qP+p+ed++++lv+NGeiyny elre l++  +++fr++sD ev+++l+    ee le+l+
  gi|15669303|ref|NP_248108.1|  64 NLSLAHNRLAIVGRY---GVQPIPNEDETIWLVCNGEIYNYIELREYLKQ--NHEFRTDSDNEVIIHLY---EEEKLEELD 136
                                   488***********8...99*****************************9..999**************...68999**** PP

                      GATase_6  94 Gmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                   G++afai+dk++n + lard +gvkpl+y + ++++afase
  gi|15669303|ref|NP_248108.1| 137 GDYAFAIYDKSKNVVRLARDMFGVKPLFYVDRDKYFAFASE 177
                                   ****************************************8 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   0.0   1.3e-37   3.4e-34       1     121 [.      69     181 ..      69     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 1.3e-37
                      GATase_7   1 hrrlsiidseagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllalleaewgeealerlnGmfAfa 81 
                                   h+rl+i+    g QP+  +ed+++++v+nGeiyNy elre L++ +h+frt+sD ev+++l+e+    e le+l+G +Afa
  gi|15669303|ref|NP_248108.1|  69 HNRLAIVG-RYGVQPIP-NEDETIWLVCNGEIYNYIELREYLKQ-NHEFRTDSDNEVIIHLYEE----EKLEELDGDYAFA 142
                                   67877765.5799****.69*********************987.59***************97....899********** PP

                      GATase_7  82 iwdeeekrlllaRDrlGikPLyygedkgdallfaSelkal 121
                                   i+d++++ + laRD +G+kPL+y+ ++ + ++faSe kal
  gi|15669303|ref|NP_248108.1| 143 IYDKSKNVVRLARDMFGVKPLFYVDRD-KYFAFASERKAL 181
                                   **************************6.8**********8 PP

>> DUF3700  Aluminium induced protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.8e-06    0.0046     125     172 ..     131     177 ..     126     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.8e-06
                       DUF3700 125 vvkdleGkfafvlydskaktvfvaldadgsvplyWGiaadgsvvisdd 172
                                    +++l+G++af +yd++++ v +a+d  g  pl++ ++ d + +++ +
  gi|15669303|ref|NP_248108.1| 131 KLEELDGDYAFAIYDKSKNVVRLARDMFGVKPLFY-VDRDKYFAFASE 177
                                   5789*****************************98.677777666655 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.2   5.2e+02      90     115 ..     185     210 ..     164     213 .. 0.69
   2 ?   11.6   0.3   7.5e-05      0.19      67      88 ..     231     252 ..     228     258 .. 0.90
   3 ?   -3.2   0.0         3   7.8e+03      91     116 ..     513     538 ..     512     540 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.2
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  90 ekqlekleeeleklkdqittleanla 115
                                     +++ +e +l++l ++i+tl  n +
  gi|15669303|ref|NP_248108.1| 185 LINIDGCERDLDELNSKIKTLKPNSQ 210
                                   55677788889999999988877655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.5e-05
                                   TTEEEEEEHHHHHHHHHHHHHH CS
                     Prefoldin  67 agyyveksleeAiellkkklee 88 
                                    +y+ e+s+eeA+e+l++ l++
  gi|15669303|ref|NP_248108.1| 231 LNYMKERSYEEAKEYLDRALKN 252
                                   79****************9986 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  91 kqlekleeeleklkdqittleanlaq 116
                                   k++ k+ ++  + k++i+++ ++l +
  gi|15669303|ref|NP_248108.1| 513 KMIYKVAKKYGFSKKRINEFLDMLKR 538
                                   55666666667777777777777665 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.3e-05     0.034      16      82 ..     259     320 ..     242     379 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                                   CTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE---H CS
                  NAD_synthase  16 agakgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievktidik 82 
                                   +g ++v +  SGGvDSsl+a+la           ++l    +++ ed+  a  la++l+++  +  i+
  gi|15669303|ref|NP_248108.1| 259 RGLDKVGIICSGGVDSSLIAKLASLYC------EVILYaVGTENSEDLIYAERLAKDLNLKLRKKIIS 320
                                   3456666667************98766......22222134555666666666666666665544443 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.7    0.0001      0.26      10      29 ..     232     251 ..     231     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                         TPR_2  10 ayyklgdyeeAleafekAle 29 
                                    y+k   yeeA+e++++Al+
  gi|15669303|ref|NP_248108.1| 232 NYMKERSYEEAKEYLDRALK 251
                                   699****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 3325.89
//
Query:       gi|15669304|ref|NP_248109.1|  [L=196]
Description: hypothetical protein MJ_1117 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-14   52.5   0.0    8.2e-14   52.3   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    1.6e-06   27.9   0.0    1.9e-06   27.7   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    2.1e-05   24.4   0.0    0.00028   20.7   0.0    2.0  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    6.7e-05   22.9   0.0     0.0001   22.3   0.0    1.4  1  CTP_transf_3     Cytidylyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.0   1.8e-17   8.2e-14       1     111 [.       3     117 ..       3     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 1.8e-17
                                   EEEEEESS-TTTTT.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..C....HHHHHHTTCTS-EEE-TTSS-SHHH CS
                  NTP_transf_3   1 aviLAGGrSsRmgg.dKallplggkpllervldalraagvdevvvvggd..e....evlaalarlgvrvvededpgkgpla 74 
                                   a+i+AGG+++Rmgg +K+l++l+g+ l+++v+  l +++v+++++++ +  +     + +a+++++  vv d+ +gkg ++
  gi|15669304|ref|NP_248109.1|   3 ALIMAGGKGTRMGGvEKPLIKLCGRCLIDYVVSPLLKSKVNNIFIATSPntPktkeYINSAYKDYKNIVVIDT-SGKGYIE 82 
                                   79********************************************988442333356668889998899987.7****** PP

                                   HHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCH CS
                  NTP_transf_3  75 slaaalraaadadavlvlacDmPlltpelverllaaa 111
                                    l   +     ++++lv++ D++ l++++++ +++ +
  gi|15669304|ref|NP_248109.1|  83 DLNECIGYF--SEPFLVVSSDLINLKSKIINSIVDYF 117
                                   *******98..7******************9998877 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   4.2e-10   1.9e-06       2      86 ..       3      80 ..       2     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 4.2e-10
                                  EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS-- CS
               NTP_transferase  2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegk 84
                                  a+I+aGG+GtR+      + k+l+   g   li++++s l++s++++ i++ t+ + +  +e++++++k + +  +++ ++gk
  gi|15669304|ref|NP_248109.1|  3 ALIMAGGKGTRMG----GVEKPLIKLCGR-CLIDYVVSPLLKSKVNN-IFIATSPNTPKTKEYINSAYK-DYKNIVVIDTSGK 78
                                  79*********97....5799***99999.9****************.*****************9996.3355666666666 PP

                                  BG CS
               NTP_transferase 85 gt 86
                                  g 
  gi|15669304|ref|NP_248109.1| 79 GY 80
                                  55 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   6.1e-08   0.00028       3      71 ..       3      73 ..       1      81 [. 0.84
   2 ?    1.6   0.0     0.045     2e+02     201     220 ..     173     192 ..     160     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.1e-08
                                  EEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG....CCEEEE CS
                          IspD  3 vvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld....ksiqlv 71
                                  ++i A G+G+Rm+ g++K +++l g+ l+   v+ ll+ ++v++i ++ s++  ++ e + ++    k+i+++
  gi|15669304|ref|NP_248109.1|  3 ALIMAGGKGTRMG-GVEKPLIKLCGRCLIDYVVSPLLK-SKVNNIFIATSPNTPKTKEYINSAykdyKNIVVI 73
                                  89**********8.99*********************9.789********99866666666656556666665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.045
                                   TTG----SHHHHHHHHHHHH CS
                          IspD 201 ednlKittpeDlalAeailr 220
                                   e  + i t++Dl lAe++l+
  gi|15669304|ref|NP_248109.1| 173 ELIFNINTKDDLKLAEMLLK 192
                                   5668899*********9997 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.2e-08    0.0001      15      48 ..      18      50 ..       3      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.2e-08
                                  TGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES CS
                  CTP_transf_3 15 gKnlldlggkpliayvleaalkskafekvivaTD 48
                                  +K+l++l g++li+yv+  +lksk+  ++++aT+
  gi|15669304|ref|NP_248109.1| 18 EKPLIKLCGRCLIDYVVSPLLKSKV-NNIFIATS 50
                                  6*********************999.99*****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1191.24
//
Query:       gi|15669305|ref|NP_248110.1|  [L=89]
Description: hypothetical protein MJ_1118 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-15   56.5   0.9    2.4e-15   56.4   0.9    1.0  1  PRC       PRC-barrel domain
  ------ inclusion threshold ------
      0.034   13.9   0.0      0.052   13.3   0.0    1.3  1  Asp4      Accessory secretory protein Sec Asp4


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.9   2.6e-19   2.4e-15       2      76 ..       2      78 ..       1      81 [. 0.92

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2.6e-19
                                  EECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT........-EEEEEGG.CEECCCTEEEETTS- CS
                           PRC  2 defrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi...gekevliPfdlavkigkdriivdapk 76
                                  + + a  l  ++++ ++G  +GkVkD+v+dek gr+++l+v+  ++  i   ++++vliP++  v ++kd++++d++ 
  gi|15669305|ref|NP_248110.1|  2 EKMPAKLLFERSIIGNKGSVIGKVKDIVFDEKVGRLVSLEVEPAEHSPImreEGRNVLIPYK-LVVAIKDVVVIDETN 78
                                  66677789999***********************************655*************.************986 PP

>> Asp4  Accessory secretory protein Sec Asp4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.8e-06     0.052       2      35 ..      26      59 ..      25      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.8e-06
                          Asp4  2 kdlfykeveGrmeslkrrPaekekttrsekinvt 35
                                  kd+ + e  Gr+ sl   Pae     r e  nv 
  gi|15669305|ref|NP_248110.1| 26 KDIVFDEKVGRLVSLEVEPAEHSPIMREEGRNVL 59
                                  9**************************9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 583.24
//
Query:       gi|15669306|ref|NP_248111.1|  [L=295]
Description: diaminopimelate epimerase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-72  239.6   2.9    9.5e-39  132.3   0.1    2.0  2  DAP_epimerase  Diaminopimelate epimerase
    0.00021   20.9   0.0     0.0025   17.3   0.0    2.2  3  PhzC-PhzF      Phenazine biosynthesis-like protein
  ------ inclusion threshold ------
       0.11   12.9   0.6       0.28   11.6   0.6    1.7  1  DUF4258        Domain of unknown function (DUF4258)
       0.19   12.8   0.0         31    5.7   0.0    2.4  2  CopC           CopC domain


Domain annotation for each model (and alignments):
>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.3   0.1   2.1e-42   9.5e-39       1     120 [.       3     129 ..       3     130 .. 0.96
   2 !  107.8   0.5   8.2e-35   3.7e-31       2     121 .]     166     285 ..     165     285 .. 0.93

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 2.1e-42
                                   EEEECSSEEEEEEECCTTCSSHHH...HHHHHHHHTTTTSTT-SEEEEEE..EEETTEEEEEEEETTTEEESTTHCCHHHH CS
                 DAP_epimerase   1 fakshGnpndvvvvddveaelvle...aelvaalcdreagpgadgvlfvk..psgeediklryfnrdgseaemCGnGvrvf 76 
                                   f+k+h+++nd++v++++++e+v+e   ae+ +++c+r++ +gadgv+f++  +s+e+d+++r+fn+dgseaemCGnG+r+f
  gi|15669306|ref|NP_248111.1|   3 FTKMHALGNDYIVINEFDGEKVKEeekAEFSRKICRRGFSVGADGVIFIQkpTSDEYDVRFRIFNSDGSEAEMCGNGIRCF 83 
                                   89**********************9999************************9**************************** PP

                                   HHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSS...EEEEEE--EE CS
                 DAP_epimerase  77 aaylreggletkkevtvetlgGeleievkddgek...vkvdmGkasl 120
                                   ++y++e+  ++k++++vet+gG ++ e++ +g++   +kv+mG +++
  gi|15669306|ref|NP_248111.1|  84 SKYVYERI-MKKNPLKVETKGGLRVSEMEIEGDEvkkIKVYMGVPKF 129
                                   *******6.66*********************99999******9876 PP

  == domain 2  score: 107.8 bits;  conditional E-value: 8.2e-35
                                   EEECSSEEEEEEECCTTCSSHHH....HHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEETTTEEESTTHCC.HHHHH CS
                 DAP_epimerase   2 akshGnpndvvvvddveaelvle....aelvaalcdreagpgadgvlfvkpsgeediklryfnrdgseaemCGnG.vrvfa 77 
                                   ++++Gnp++v++v+d + +l++     + ++++++++ea+p++++v+fvk+ ++++i++ +++r+++++++CG+G ++ ++
  gi|15669306|ref|NP_248111.1| 166 VVNVGNPHAVIFVEDNNIDLDFVrehlDVIGKEIEHHEAFPERINVHFVKVLNPNEIRIVTWERGAGYTTACGTGtTASVI 246
                                   699***********98764444445999***************************************************** PP

                                   HHHHCTTS-S-SEEEEEETTEEEEEEEECTTSSEEEEEE--EEE CS
                 DAP_epimerase  78 aylreggletkkevtvetlgGeleievkddgekvkvdmGkaslv 121
                                   ++++ g+  t+++v  +++gG+leie+kddg   ++++G+a++v
  gi|15669306|ref|NP_248111.1| 247 MAHKLGK--TNNRVLAHLDGGDLEIEIKDDG---VYMIGDAVMV 285
                                   ******9..88*******************9...7******986 PP

>> PhzC-PhzF  Phenazine biosynthesis-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.6e-07    0.0025      39     165 ..      47     180 ..       2     182 .. 0.72
   2 ?    2.5   0.0     0.018        83      10      39 ..     169     203 ..     165     206 .. 0.76
   3 ?   -2.4   0.0      0.59   2.7e+03     254     280 ..     265     285 ..     235     287 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.6e-07
                                   EEEEEE--SSTTSSEEEEEE-S.SSEES--HHHHHHHHHHHHHHCT-S-SCEEEEEETTEEEEE.EEEEETCEECCEEEEE CS
                     PhzC-PhzF  39 eTaFllkpsdekarfrlRyFTP.vaEvdlcGHatlasahalaekglvasaetveletkaGilpvkslkekddgeellielk 118
                                      F+ kp+++++++r R+F    +E ++cG       + + e+ +  +++ +++etk G        e d+ +++ + + 
  gi|15669306|ref|NP_248111.1|  47 GVIFIQKPTSDEYDVRFRIFNSdGSEAEMCGNGIRCFSKYVYERIM--KKNPLKVETKGGLRVSEMEIEGDEVKKIKVYMG 125
                                   567*****************65279*********999999999997..6999999*998865555667889999******* PP

                                   -SEEEEEE-H......HHHHHHHHHCCTSGG..-TTS-BEEEESSSEEEEEEBST CS
                     PhzC-PhzF 119 fPvikteevs......sedlallakllklaa..qkalpiavkstglekvivplss 165
                                   +P +k +++       +ed++ l++ lkl++   +++ + v + g+ + ++ +++
  gi|15669306|ref|NP_248111.1| 126 VPKFKLKDIPmvvdgyKEDDEFLNGELKLKNpyLPKVKLSVVNVGNPHAVIFVED 180
                                   ****998875222221344444455555554666777777777777777777665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.018
                                   SSEEEEEEESTT.....CS-HHHHHHHHHHHTSSE CS
                     PhzC-PhzF  10 kGNpaaVvldad.....elddeelqsiAaelnlse 39 
                                    GNp aV++ +d     +   e+l  i +e+++ e
  gi|15669306|ref|NP_248111.1| 169 VGNPHAVIFVEDnnidlDFVREHLDVIGKEIEHHE 203
                                   5***********87755555677777777777665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.59
                                   EEEEEEEE.E-TTCEEEEEEEE-EEEE CS
                     PhzC-PhzF 254 gtlevevevkvdkekervkvtGkAvtv 280
                                   g le+e++  +      v++ G Av+v
  gi|15669306|ref|NP_248111.1| 265 GDLEIEIK--D----DGVYMIGDAVMV 285
                                   34443332..2....467777777766 PP

>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   6.3e-05      0.28       3      60 ..     172     226 ..     171     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.3e-05
                       DUF4258   3 aHArermaeRgIseedieevle.nGeiieeys.lvlgktsegrplhvvvapdedpvvviT 60 
                                   +HA+   ++++I+ + ++e l+  G+ ie+++ +     +e  ++h+v ++++++++++T
  gi|15669306|ref|NP_248111.1| 172 PHAVIFVEDNNIDLDFVREHLDvIGKEIEHHEaF-----PERINVHFVKVLNPNEIRIVT 226
                                   6999**********************9*****63.....777899***********9999 PP

>> CopC  CopC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.007        31      64      83 ..      53      72 ..       6      75 .. 0.78
   2 ?    4.7   0.0     0.014        62      16      56 ..     203     243 ..     194     288 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.007
                          CopC 64 elaaGtYtVewrvvsaDGHp 83
                                  + ++++Y V++r+  +DG  
  gi|15669306|ref|NP_248111.1| 53 KPTSDEYDVRFRIFNSDGSE 72
                                  55689*************75 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.014
                          CopC  16 aaapeevtLtFsepvelskvkvtdpdgke..evetvdaktvea 56 
                                   +a pe+++++F + ++++++++++ ++ +  +  t+ ++  +a
  gi|15669306|ref|NP_248111.1| 203 EAFPERINVHFVKVLNPNEIRIVTWERGAgyT--TACGTGTTA 243
                                   678**************999999888545351..333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1966.66
//
Query:       gi|15669307|ref|NP_248112.1|  [L=279]
Description: hypothetical protein MJ_1120 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-12   46.4   0.0    4.1e-12   45.9   0.0    1.3  1  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR
  ------ inclusion threshold ------
      0.025   14.1   0.2      0.075   12.6   0.2    1.9  1  HTH_24    Winged helix-turn-helix DNA-binding
      0.044   13.3   0.3       0.28   10.8   0.3    2.2  2  GerE      Bacterial regulatory proteins, luxR family


Domain annotation for each model (and alignments):
>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   6.9e-16   4.1e-12       2      59 ..      17      74 ..      16      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 6.9e-16
                                  HHHHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSEEEE-HHH CS
                         HTH_1  2 rqlrlfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfeRtgrglrLTeaG 59
                                  +q++l++a+ +++s ++AA+ L++ +++   q+krLE+ lgv+L   + +g++LT+aG
  gi|15669307|ref|NP_248112.1| 17 NQIKLLIALHKTKSQNEAAKLLNIKPSSFNIQLKRLENKLGVKLYYSSPNGTVLTDAG 74
                                  79*******************************************************9 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.3e-05     0.075      18      44 ..      29      55 ..      15      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                        HTH_24 18 isqreLAerlglSpstvnrrlkrLeee 44
                                   sq+e A+ l++ ps  n +lkrLe++
  gi|15669307|ref|NP_248112.1| 29 KSQNEAAKLLNIKPSSFNIQLKRLENK 55
                                  69***********************86 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   4.7e-05      0.28       5      48 ..      16      59 ..      12      60 .. 0.86
   2 ?   -0.8   0.0      0.19   1.1e+03      15      28 ..      95     108 ..      93     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.7e-05
                                  HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHHT-S CS
                          GerE  5 kRErevLrllaeGksnkeIAeelniSekTVkvhksnimkKLnvk 48
                                  + + + L  l + ks +e A+ lni++ + +++++++ +KL+vk
  gi|15669307|ref|NP_248112.1| 16 PNQIKLLIALHKTKSQNEAAKLLNIKPSSFNIQLKRLENKLGVK 59
                                  5556666677778999**************************97 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.19
                                   CTTS-HHHHHHHHT CS
                          GerE  15 aeGksnkeIAeeln 28 
                                   ++G+ + eIA++l+
  gi|15669307|ref|NP_248112.1|  95 VSGFVSGEIAKILF 108
                                   6899999****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1779.37
//
Query:       gi|15669308|ref|NP_248113.1|  [L=94]
Description: virulence associated protein C VapC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-05   23.4   0.1    0.00013   22.4   0.1    1.4  1  PIN       PIN domain
  ------ inclusion threshold ------
       0.17   11.5   0.0        0.3   10.7   0.0    1.4  1  TAP_C     TAP C-terminal domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   1.5e-08   0.00013       2      99 ..       4      91 ..       3      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.5e-08
                                  EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHHHH CS
                           PIN  2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeeaaei 84
                                  v+DTsv+i+++rg +++  + ++ +  +++ ++++++ El+ +  +           + +++  ++l  l++d++  ++a+ i
  gi|15669308|ref|NP_248113.1|  4 VIDTSVIIEIFRGNKDT--LYQICD--YNCKITSITVFELYCGNLK-----------ENEMIMIDSLPKLNFDDKSSKIAGNI 71
                                  8**********999966..788888..*******************...........888899999999999*********** PP

                                  HHHHH.....SBHHHHHHHH CS
                           PIN 85 alkyg.....llpnDaliaA 99
                                  ++k++      ++ D+lia+
  gi|15669308|ref|NP_248113.1| 72 FKKLKkegkiPSVKDLLIAS 91
                                  *9999999988888988885 PP

>> TAP_C  TAP C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.4e-05       0.3      31      46 ..      68      83 ..      64      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.4e-05
                                  HHHHHHHHG..GGS-G CS
                         TAP_C 31 AlqvFeelkakgkIPp 46
                                  A ++F++lk++gkIP 
  gi|15669308|ref|NP_248113.1| 68 AGNIFKKLKKEGKIPS 83
                                  999************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 614.01
//
Query:       gi|15669309|ref|NP_248114.1|  [L=77]
Description: hypothetical protein MJ_1122 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-20   72.7   6.9    3.5e-20   72.5   6.9    1.0  1  VAPB_antitox  Putative antitoxin
    0.00075   19.3   0.8    0.00075   19.3   0.8    2.4  2  RHH_1         Ribbon-helix-helix protein, copG family
     0.0053   16.0   0.8     0.0056   15.9   0.8    1.0  1  PLU-1         PLU-1-like protein
     0.0083   15.5   0.5     0.0094   15.3   0.5    1.0  1  DegV          Uncharacterised protein, DegV family COG1307
  ------ inclusion threshold ------
      0.027   14.9   2.2      0.031   14.7   2.2    1.1  1  RIC3          Resistance to inhibitors of cholinesterase homo
      0.039   14.0   0.5       0.05   13.6   0.5    1.3  1  GvpK          Gas vesicle protein K


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   6.9   1.2e-23   3.5e-20       2      68 ..       6      71 ..       5      72 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 1.2e-23
                  VAPB_antitox  2 tIsIsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgilseeeadeiekaskelrkef 68
                                  tI+I+d+vY++L klK+ ++S s++I++Lle++k+++ ++ + +fg++see++++++k++ke++k++
  gi|15669309|ref|NP_248114.1|  6 TITIDDDVYKELLKLKG-RKSVSEFIKELLEERKRKNLDVFMIAFGSRSEEDVEKLKKELKEAEKWM 71
                                  9****************.***********************************************97 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.8   2.5e-07   0.00075       3      38 ..       6      39 ..       6      40 .. 0.89
   2 ?    0.4   0.4      0.24   7.2e+02       8      17 ..      54      63 ..      52      71 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.5e-07
                                  EEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                         RHH_1  3 sirldeellerLdelarrrgrSrSelIReAlreyle 38
                                  +i++d++++++L  l+ ++++S+Se+I+e+l+e++ 
  gi|15669309|ref|NP_248114.1|  6 TITIDDDVYKEL--LKLKGRKSVSEFIKELLEERKR 39
                                  899*******99..556899*************975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.24
                                  HHHHHHHHHH CS
                         RHH_1  8 eellerLdel 17
                                  ee++e+L + 
  gi|15669309|ref|NP_248114.1| 54 EEDVEKLKKE 63
                                  6667776653 PP

>> PLU-1  PLU-1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.8   1.9e-06    0.0056       6      55 ..      14      73 ..      11      77 .] 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-06
                         PLU-1  6 veelleeeekpsLke.lrallneaekikfp..........lkellekLktfvkdaekwvek 55
                                  ++ell+ + + s +e +++ll+e ++++ +          ++++ ekLk+++k+aekw+++
  gi|15669309|ref|NP_248114.1| 14 YKELLKLKGRKSVSEfIKELLEERKRKNLDvfmiafgsrsEEDV-EKLKKELKEAEKWMQS 73
                                  799999888888888469*********88888888888846666.*************986 PP

>> DegV  Uncharacterised protein, DegV family COG1307
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.5   3.1e-06    0.0094     189     250 ..       7      68 ..       5      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-06
                                   EEEETTEEEEEEEESSHHHHHHHHHHHHHHHHTTTSEEEEEEEECS..-HHHHHHHHHHHCCCS CS
                          DegV 189 lkvedgeleplakvrgqkkaleklielikkdeeekkaervavlhag..aeeeaeelkellkakv 250
                                   ++++d +++ l k +g+k++ e + el++  e ++k+ +v+++  g  +ee++e+lk++lk+ +
  gi|15669309|ref|NP_248114.1|   7 ITIDDDVYKELLKLKGRKSVSEFIKELLE--ERKRKNLDVFMIAFGsrSEEDVEKLKKELKEAE 68 
                                   67899*********************774..5555556666666554378**********9975 PP

>> RIC3  Resistance to inhibitors of cholinesterase homologue 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.2     1e-05     0.031      91     144 ..      17      75 ..      13      76 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                          RIC3  91 llKikskkkkekskeakakkkakenakkkte.........teeeLeeLqerLaeTEramekil 144
                                   llK+k +k+ +    +  k+  +e+++k+ +         +ee++e+L++ L+e E+ m++++
  gi|15669309|ref|NP_248114.1|  17 LLKLKGRKSVS----EFIKELLEERKRKNLDvfmiafgsrSEEDVEKLKKELKEAEKWMQSLI 75 
                                   56666666555....3333334444444444556667777999******************98 PP

>> GvpK  Gas vesicle protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   1.7e-05      0.05      20      64 ..      26      75 ..       9      77 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                          GvpK 20 vveLlrqllErqaiRRmea.....gdlsdeeierlgetLmkleeeleelk 64
                                  v e++++llE++  + ++      g++s+e++e+l ++L++ e+ ++ l 
  gi|15669309|ref|NP_248114.1| 26 VSEFIKELLEERKRKNLDVfmiafGSRSEEDVEKLKKELKEAEKWMQSLI 75
                                  6799999999888888775444459*******************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2075  (0.115734); expected 358.6 (0.02)
Passed bias filter:                      972  (0.0542138); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 544.86
//
Query:       gi|15669310|ref|NP_248115.1|  [L=205]
Description: hypothetical protein MJ_1123 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-19   70.5   0.0    3.1e-19   69.4   0.0    1.6  2  Methyltransf_11  Methyltransferase domain
    4.5e-14   52.9   0.0    8.9e-14   52.0   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
      6e-13   49.0   0.0    7.5e-13   48.6   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    3.6e-11   43.1   0.3    8.5e-11   41.9   0.3    1.6  1  Methyltransf_31  Methyltransferase domain
    1.6e-08   35.2   0.0      4e-08   33.9   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
    1.7e-08   34.1   2.2    1.5e-07   31.0   0.2    2.4  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.7e-05   23.4   0.0    6.6e-05   22.6   0.0    1.5  1  MetW             Methionine biosynthesis protein MetW
    0.00019   21.3   0.4    0.00088   19.2   0.4    1.9  1  Methyltransf_8   Hypothetical methyltransferase
    0.00047   19.9   1.2     0.0022   17.7   0.2    2.3  2  N6_N4_Mtase      DNA methylase
     0.0039   17.0   0.5      0.016   15.0   0.1    2.2  2  IF2_N            Translation initiation factor IF-2, N-termin
     0.0065   16.5   0.1      0.018   15.0   0.0    1.7  2  ADH_zinc_N       Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.049   14.3   3.1      0.081   13.6   0.5    2.2  2  PTS_IIB          PTS system, Lactose/Cellobiose specific IIB 
       0.09   11.9   0.0       0.11   11.5   0.0    1.2  1  DREV             DREV methyltransferase
        0.3   11.4   1.5        5.1    7.5   1.5    2.4  1  B5               tRNA synthetase B5 domain
       0.42   10.6   3.3         12    5.9   0.5    2.4  2  DUF5644          Family of unknown function (DUF5644)


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   2.6e-22   3.1e-19       1      96 []      39     124 ..      39     124 .. 0.95
   2 ?   -2.9   0.0       9.4   1.1e+04      73      87 ..     169     183 ..     154     185 .. 0.61

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 2.6e-22
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekal 81 
                                   L++G+GtGr+a+++       +gvD+skem k+a++++      ++++ a  e+lpf+d+ fD+ +++ vl++ e+p+k +
  gi|15669310|ref|NP_248115.1|  39 LEIGVGTGRFAKPFN----IKIGVDISKEMAKIAEKRG------IKVIIAKGEDLPFKDEEFDFFLINTVLEFAENPKKMI 109
                                   89*************....789*********9997777......5669********************************* PP

                                   HHHHHHEEEEEEEEE CS
               Methyltransf_11  82 keiaRvLkpgGllvi 96 
                                   +e++RvLk gG+++i
  gi|15669310|ref|NP_248115.1| 110 EEAKRVLKRGGKIII 124
                                   ************986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.4
                                   C-CCHHHHHHHHHHH CS
               Methyltransf_11  73 hvedpekalkeiaRv 87 
                                   +++  + ++kei +v
  gi|15669310|ref|NP_248115.1| 169 NIKATQTIFKEIDKV 183
                                   345666677777655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   7.4e-17   8.9e-14       2      97 .]      39     120 ..      39     120 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 7.4e-17
                                   EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHH CS
               Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedl 82 
                                   L++G GtGr+++ +  +      +gvDis+em ++a++r       ++++ ++ edlpf+d++fD+ +++ +l++ +  + 
  gi|15669310|ref|NP_248115.1|  39 LEIGVGTGRFAKPFNIK------IGVDISKEMAKIAEKRG------IKVIIAKGEDLPFKDEEFDFFLINTVLEFAE--NP 105
                                   89***********9866......7***************9......9**********************76699976..55 PP

                                   HHHHHHHHHHEEEEE CS
               Methyltransf_25  83 ekalkeiarvLkpgG 97 
                                   +k+++e++rvLk gG
  gi|15669310|ref|NP_248115.1| 106 KKMIEEAKRVLKRGG 120
                                   6*************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   6.3e-16   7.5e-13      12     164 ..      25     171 ..       8     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 6.3e-16
               Methyltransf_23  12 klerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaepqgkfdlIvlre 90 
                                   ++e +l++  ++gr L+iG GtG++++ +  +    +gvD+s e+ +iae  ++k  + + +   + +++++ fd+   + 
  gi|15669310|ref|NP_248115.1|  25 EIE-ALKRHIPKGRGLEIGVGTGRFAKPFNIK----IGVDISKEMAKIAEkrGIKVIIAKGE---DLPFKDEEFDFFLINT 97 
                                   555.5577899****************66555....6************8876666666666...8899************ PP

               Methyltransf_23  91 vlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGlevve 164
                                   vle  ++p + +  +++ lk gG +++  +++++   +++++ +   +  +  +f sa+++ e+l+e G+++++
  gi|15669310|ref|NP_248115.1|  98 VLEFAENPKKMIEEAKRVLKRGGKIIIGIIDRDSFLGKMYEEKKQKSKFYKDANFLSAKEVIEMLKELGFKNIK 171
                                   **********************************9999998887777777888*****************9985 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.3   7.1e-14   8.5e-11       8     134 ..      39     161 ..      35     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 7.1e-14
               Methyltransf_31   8 lDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnala 88 
                                   l++G GtG++++ ++      ++ +G+Dis+e+ + A+++        +++ ++  e+l+  ++de fD+ l n vl    
  gi|15669310|ref|NP_248115.1|  39 LEIGVGTGRFAKPFN------IK-IGVDISKEMAKIAEKR-------GIKVIIAKGEDLP--FKDEEFDFFLINTVLEFAE 103
                                   788999999988888......44.9**************7.......888**********..******************* PP

               Methyltransf_31  89 dpdkileeiervlkpggilliedprllaelpakveeeskay.............evveg 134
                                   +p+k +ee++rvlk gg ++i  ++  + +++k++ee k +             ev+e+
  gi|15669310|ref|NP_248115.1| 104 NPKKMIEEAKRVLKRGGKIIIGIID-RDSFLGKMYEEKKQKskfykdanflsakEVIEM 161
                                   *************************.666666666666644333333333344433333 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   3.3e-11     4e-08       1      99 []      39     122 ..      39     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.3e-11
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                   LeiG GtG++++++  k      +gvDis+++ + a+++  k +         + +dl  +d+   fD  +++ vl+  ++
  gi|15669310|ref|NP_248115.1|  39 LEIGVGTGRFAKPFNIK------IGVDISKEMAKIAEKRGIKVI-------IAKGEDLPFKDE--EFDFFLINTVLEFAEN 104
                                   8*************999......9*********55555555555.......344444444444..8*************** PP

               Methyltransf_12  82 irevldnirklLkpgGrl 99 
                                   +++++++++++Lk gG++
  gi|15669310|ref|NP_248115.1| 105 PKKMIEEAKRVLKRGGKI 122
                                   ****************86 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.2   1.2e-10   1.5e-07      53     150 ..      40     123 ..       1     129 [. 0.74
   2 ?    2.7   0.1     0.057        68     176     218 ..     132     172 ..     126     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.2e-10
                                   EES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HH CS
               Ubie_methyltran  53 DvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDkl 133
                                   ++  Gtg +a  +  +       +++Di+++m k++ek+        i+ + a++e+Lpf+d+ fD++ +   l    + +
  gi|15669310|ref|NP_248115.1|  40 EIGVGTGRFAKPFNIK-------IGVDISKEMAKIAEKR-------GIKVIIAKGEDLPFKDEEFDFFLINTVLEFAENPK 106
                                   5555555444333322.......3689999999999987.......58999***********************999999* PP

                                   HHHHHHHHHEEEEEEEE CS
               Ubie_methyltran 134 kaLkeayrvlkpGGrlv 150
                                   k ++ea rvlk GG+++
  gi|15669310|ref|NP_248115.1| 107 KMIEEAKRVLKRGGKII 123
                                   **************986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.057
                                   HHHHHHHS-HHHHHHHHHHHHHS--HHHHHHHHHHTTEEEEEE CS
               Ubie_methyltran 176 vlGkllakdldsyryLvesirafPdqetlkeliedaGfksvey 218
                                   +lGk+  ++ ++ ++ +++  +f  ++++ e++++ Gfk+++ 
  gi|15669310|ref|NP_248115.1| 132 FLGKMYEEKKQKSKFYKDA--NFLSAKEVIEMLKELGFKNIKA 172
                                   6788888888888887775..79999*************9985 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   5.6e-08   6.6e-05       7     104 ..      29     118 ..      23     192 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.6e-08
                          MetW   7 iaelikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqa 87 
                                   +++ i+ + r l++G G G + + ++    +   G+++++e  + + ++G++vi     +dl  f+d++fd+ +++  l  
  gi|15669310|ref|NP_248115.1|  29 LKRHIP-KGRGLEIGVGTGRFAKPFN----I-KIGVDISKEMAKIAEKRGIKVIIAK-GEDL-PFKDEEFDFFLINTVLEF 101
                                   555554.5688999999999988873....3.368999999999999******9865.4566.69**************** PP

                          MetW  88 trnpkevldellrigrr 104
                                     npk++++e  r+ +r
  gi|15669310|ref|NP_248115.1| 102 AENPKKMIEEAKRVLKR 118
                                   **********9998665 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.4   7.4e-07   0.00088      64     181 ..      26     149 ..       3     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.4e-07
                                   HHHHCTS-TTS-EEEES-TT-HHHHH--S-..E.EEEESS-SST....TEEES-TTS-S--TT-EEEEEEES--.-SS-HH CS
                Methyltransf_8  64 irklkkkkdnlvvadlGcGeakiaeavrekekv.rsfdlvavne....rvvacdlakvPledesvdvavfclsl.mgtnla 138
                                   i+ lk++  +    ++G G  + a+  + k  v +s +++ + e    +v+      +P +de  d  ++   l  ++n +
  gi|15669310|ref|NP_248115.1|  26 IEALKRHIPKGRGLEIGVGTGRFAKPFNIKIGVdISKEMAKIAEkrgiKVIIAKGEDLPFKDEEFDFFLINTVLeFAENPK 106
                                   667777777777778888888888555544444234555554431122466666688*********987766653799*** PP

                                   HHHHHHHHHEEEEEEEEEEEEGGG-S-HHHHHHHHHCTTEEEE CS
                Methyltransf_8 139 dflkeanrvlkvGGllkvaevksrfesvklfaraltklGfevk 181
                                   ++++ea+rvlk GG + +  +      +k+++++ +k  f  +
  gi|15669310|ref|NP_248115.1| 107 KMIEEAKRVLKRGGKIIIGIIDRDSFLGKMYEEKKQKSKFYKD 149
                                   ***************9998776555566667666666666554 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.31   3.7e+02     215     231 .]      45      70 ..      24      70 .. 0.68
   2 !   17.7   0.2   1.9e-06    0.0022      26      83 ..      96     151 ..      80     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.31
                                   E.........EEEEESSHHHHHHHHH CS
                   N6_N4_Mtase 215 k.........fiGieieeeyvelaek 231
                                              iG++i++e +++aek
  gi|15669310|ref|NP_248115.1|  45 TgrfakpfniKIGVDISKEMAKIAEK 70 
                                   04445555557***********9986 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.9e-06
                                   CHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHHHHHTT-EEEEEEEE CS
                   N6_N4_Mtase  26 dsyeeyleflekvlkevrrvLkddgsifiniddseikkelkaladeifggffllnviv 83 
                                   +++ e+ e  +k+++e++rvLk +g i+i i d+  +  l ++++e++ + +++++++
  gi|15669310|ref|NP_248115.1|  96 NTVLEFAENPKKMIEEAKRVLKRGGKIIIGIIDRDSF--LGKMYEEKKQKSKFYKDAN 151
                                   5677899999*************************98..6666666665666666655 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.8   3.3e+03      19      52 ..      63      72 ..      59      75 .. 0.45
   2 !   15.0   0.1   1.3e-05     0.016      15      39 ..     153     176 ..     148     180 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.8
                         IF2_N 19 evikkLfkelGievkshsssLDeetaeliaeefg 52
                                  e                        +++iae+ g
  gi|15669310|ref|NP_248115.1| 63 E------------------------MAKIAEKRG 72
                                  3........................334444433 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.3e-05
                         IF2_N  15 vkskevikkLfkelGievkshsssL 39 
                                   +++kevi+ L kelG++  ++++++
  gi|15669310|ref|NP_248115.1| 153 LSAKEVIEML-KELGFKNIKATQTI 176
                                   689*******.88**********98 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.5e-05     0.018       2      87 ..      41     124 ..      41     146 .. 0.88
   2 ?   -1.5   0.0         2   2.4e+03      25      41 ..     157     173 ..     150     194 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSH.HHHHHHHHCEE CS
                    ADH_zinc_N   2 vGlaavqlAkalGaeviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvGsg.atleaalkllk 80 
                                   +G+ +  +Ak ++++ i+vd+s+e +++a+k G +++i   e+  ++++  +++    ++ v+e++ ++ +++e+a ++lk
  gi|15669310|ref|NP_248115.1|  41 IGVGTGRFAKPFNIK-IGVDISKEMAKIAEKRGIKVIIAKGEDlPFKDEEFDFF---LINTVLEFAENPkKMIEEAKRVLK 117
                                   577777788888887.69**********************99888*********...*********965268899****** PP

                                   EEEEEEE CS
                    ADH_zinc_N  81 pgGrlvv 87 
                                   +gG++ +
  gi|15669310|ref|NP_248115.1| 118 RGGKIII 124
                                   ***9965 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                                   HHHHHHHHTTESEEEET CS
                    ADH_zinc_N  25 eklelakklGadeviny 41 
                                   e +e++k+lG + +  +
  gi|15669310|ref|NP_248115.1| 157 EVIEMLKELGFKNIKAT 173
                                   44577777777665554 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   6.8e-05     0.081      18      85 ..      62     130 ..      60     143 .. 0.73
   2 ?    0.6   0.1       0.8   9.5e+02      15      37 ..     153     175 ..     151     194 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.8e-05
                                   HHHHHHHHHCTEEEEETTEEGGGHHHHHHT-SEEEEEESSGG....CTHHHHTTSEEEEECTTHHHCCHCHH CS
                       PTS_IIB  18 eklekaakelgieaegeagveleaeeiaddaDlvllapqvrv....kdlarfagkpvavinikdalgimdge 85 
                                   + + k+a+++gi++++++g  l  ++  +++D++l+ + +++    k++ + a+ +v ++  k ++gi d +
  gi|15669310|ref|NP_248115.1|  62 KEMAKIAEKRGIKVIIAKGEDLPFKD--EEFDFFLINTVLEFaenpKKMIEEAK-RVLKRGGKIIIGIIDRD 130
                                   689*****************788877..558*******9999865544444444.66666666555555544 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.8
                                   HHHHHHHHHHHHCTEEEEETTEE CS
                       PTS_IIB  15 maaeklekaakelgieaegeagv 37 
                                   + a+ + +++kelg++ + ++++
  gi|15669310|ref|NP_248115.1| 153 LSAKEVIEMLKELGFKNIKATQT 175
                                   55677888888888555544444 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.5e-05      0.11      99     190 ..      39     128 ..      19     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.5e-05
                          DREV  99 ldlGaGdGeitkrvaptfeevyatelsetmrdrlkkkkynvlsal.e.lqetdvkldlilclnlldrcfdplklledirsa 177
                                   l++G G G  +k     f+     ++s++m +  +k++ +v+ a  e l   d ++d  l   +l+   +p k++e+ + +
  gi|15669310|ref|NP_248115.1|  39 LEIGVGTGRFAKP----FNIKIGVDISKEMAKIAEKRGIKVIIAKgEdLPFKDEEFDFFLINTVLEFAENPKKMIEEAKRV 115
                                   6677776655443....444456899**************99765235888899999999999****************** PP

                          DREV 178 lepngrvivalvl 190
                                   l+  g++i+ ++ 
  gi|15669310|ref|NP_248115.1| 116 LKRGGKIIIGIID 128
                                   ********99874 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.5    0.0043       5.1      16      37 ..     153     174 ..      49     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0043
                                   --HHHHHHHHHHTT-E.EESST CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                            B5  16 lseeeiikiLkrlgceriekdk 37 
                                   ls++e+i++Lk+lg++ i+ ++
  gi|15669310|ref|NP_248115.1| 153 LSAKEVIEMLKELGFKNIKATQ 174
                                   799************9555443 PP

>> DUF5644  Family of unknown function (DUF5644)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1      0.02        24       5      30 ..       8      33 ..       5      36 .. 0.91
   2 ?    5.9   0.5      0.01        12       6      37 ..     141     172 ..     136     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.02
                       DUF5644  5 lkkYeeffkkaefltkeereelekyl 30
                                   ++Y+++f++ e + k+e e+l++++
  gi|15669310|ref|NP_248115.1|  8 AEEYDKWFDENEIIYKSEIEALKRHI 33
                                  579********************998 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.01
                       DUF5644   6 kkYeeffkkaefltkeereelekylklnlitp 37 
                                   k+  +f+k a+fl+++e  e+ k l +  i++
  gi|15669310|ref|NP_248115.1| 141 KQKSKFYKDANFLSAKEVIEMLKELGFKNIKA 172
                                   56689**************9999888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1295  (0.0722293); expected 358.6 (0.02)
Passed bias filter:                      767  (0.0427799); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1486.96
//
Query:       gi|15669311|ref|NP_248116.1|  [L=1195]
Description: SKI2 family helicase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-24   86.6   0.0    3.9e-24   85.4   0.0    1.7  1  DEAD             DEAD/DEAH box helicase
    4.1e-19   68.7   1.7    4.9e-17   62.0   0.2    3.8  3  LAGLIDADG_3      LAGLIDADG-like domain
    1.8e-18   66.8   1.3    4.9e-18   65.4   1.3    1.8  1  Intein_splicing  Intein splicing domain
    3.5e-14   53.2   3.2      1e-13   51.7   0.0    3.0  3  ResIII           Type III restriction enzyme, res subunit
    2.3e-10   40.9   1.5    7.9e-10   39.2   1.5    1.9  1  HHH_5            Helix-hairpin-helix domain
    1.3e-05   24.9   0.0    5.2e-05   23.0   0.0    2.1  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    0.00071   19.9   1.4       0.45   10.9   0.3    3.9  3  Helicase_C       Helicase conserved C-terminal domain
     0.0068   16.5   4.5      0.016   15.2   0.1    3.5  3  LAGLIDADG_WhiA   WhiA LAGLIDADG-like domain
     0.0076   15.8   0.0      0.014   14.9   0.0    1.4  1  Hint             Hint module
  ------ inclusion threshold ------
       0.11   12.8   0.4        5.9    7.2   0.0    3.0  3  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0   2.2e-27   3.9e-24       2     170 ..      18     179 ..      17     184 .. 0.90

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 2.2e-27
                                   HHHHHHHHHHH..TTCEEEEEESTTSSHHHHHHHHHHHHHHHS.TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                   xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   2 diQaeaiplil..gggdvlvaaeTGsGKTlaflipvlqivyet.kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                   + Q++a++  l  +++++l++++T+sGKTl+  +++++++++  k+ t++k ++++P+++La + ++++k+  + ++lr+ 
  gi|15669311|ref|NP_248116.1|  18 PPQKKALERGLldKNKNFLISIPTASGKTLIGEMALINHLLDGnKNPTNKKGIFIVPLKALASEKYEEFKSKYERYGLRIA 98 
                                   6699999999988999************************99999************************************ PP

                                   EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH.CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  80 liiggvaardqlskldngvdivvgtpgrlddllstgkln.lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklq 159
                                   l ig+ +++++lsk     +++++t ++ld+l  ++k++ +++v+++V+DE++ + d+ ++ +++ +l++l+    +   +
  gi|15669311|ref|NP_248116.1|  99 LSIGDYDEDEDLSKY----HLIITTAEKLDSLW-RHKIDwINDVSVVVVDEIHLINDETRGGTLEILLTKLK----E--FN 168
                                   ****87776666666....***********966.688888*******************************4....3..44 PP

                                   SEEEEEESSBS CS
                                   xxxxxxxxxxx RF
                          DEAD 160 rqvivlSATlp 170
                                    q+i lSAT+ 
  gi|15669311|ref|NP_248116.1| 169 VQIIGLSATIG 179
                                   67*******96 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.062   1.1e+02       6      23 ..     450     467 ..     448     472 .. 0.82
   2 !   62.0   0.2   2.7e-20   4.9e-17       3      82 ..     541     628 ..     539     629 .. 0.88
   3 ?   -3.6   0.0       8.1   1.5e+04      27      44 ..     889     906 ..     884     908 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.062
                                   HHHHHHHHCCECCECSTT CS
                   LAGLIDADG_3   6 fLrGlfdaDGsvskskkk 23 
                                   +  G+f +DG+  + +k+
  gi|15669311|ref|NP_248116.1| 450 YFIGYFIGDGYTGVIEKN 467
                                   679********8877765 PP

  == domain 2  score: 62.0 bits;  conditional E-value: 2.7e-20
                                   HHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCC.............ECCCH CS
                   LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvy.............rllii 70 
                                    a +++Glfd+DG++  ++k+   i+++s s++l+e++q +Llr+GI+s+i++k k+k  +                l+i 
  gi|15669311|ref|NP_248116.1| 541 LAYLIAGLFDSDGYIYLNRKN---IEFYSISEKLVEQLQFVLLRFGIHSSIRKK-KTKTMV-SptngkeykckdiyVLTIR 616
                                   67789***************9...******************************.333333.2477888899999899999 PP

                                   CHCTTCGGGTTT CS
                   LAGLIDADG_3  71 sgenlkrFleki 82 
                                   +  ++krF+e+i
  gi|15669311|ref|NP_248116.1| 617 DFMSIKRFYENI 628
                                   9*********99 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 8.1
                                   EEEEES-HHHHHHHHHHH CS
                   LAGLIDADG_3  27 isltssskelledvqrlL 44 
                                   i ++ +++++l+ +q l 
  gi|15669311|ref|NP_248116.1| 889 IIVAKNDRDYLRAYQALT 906
                                   788999999999999886 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   1.3   2.7e-21   4.9e-18       3     134 .]     346     838 ..     344     838 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 2.7e-21
                                   ECTTCEEEEHHHHCCECTTEEEEEETTTTE.EEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCTTEEEEEECC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing   3 ledgeekvkieelvekegeevlslnledlk.levksvkkliklklkelyeiklesgrkikaTpeHkllvvrdegivEkrad 82 
                                   l++++ + ki el  +++e+v +l  ++ k +   +v k+ +++++ ++  k+ +g +i +Tp+H +lv +++ + Ek+a+
  gi|15669311|ref|NP_248116.1| 346 LQESGFR-KITEL--NKDEKVFALCGKEIKpVDGWKVHKTPQHEYNIVV--KTVNGLEITTTPNHIFLVKENGSLKEKEAK 421
                                   6677777.88999..6788888877666551444569999999999775..5669***************99********* PP

                                   C--TT-EEEEE...................................................................... CS
                                   xxxxxxxxxxx...................................................................... RF
               Intein_splicing  83 eLkegdliavp...................................................................... 93 
                                   +Lk+gd++a++                                                                      
  gi|15669311|ref|NP_248116.1| 422 DLKVGDYVATVdrirvkekdidlsngdlyfigyfigdgytgviekntlkatpdlafnpkyppnfddselhkkyflkcrisk 502
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669311|ref|NP_248116.1| 503 gvahyiyskklrkifnklnmltkdnknidafcnlpldklayliaglfdsdgyiylnrkniefysiseklveqlqfvllrfg 583
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669311|ref|NP_248116.1| 584 ihssirkkktktmvsptngkeykckdiyvltirdfmsikrfyeniplrheekrrkleeiiknkeigqipsefvalrftpia 664
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669311|ref|NP_248116.1| 665 kiwcdcgfsvdltmfkprtkrqrelnkkrvkllfelldgkklitnykeyyskrknpyfdfivrekingnnyyslnekgrvl 745
                                   ********************************************************************************* PP

                                   ...............................................HSCEEEEEEEEEEEEEC.EEEEEEEEETT...T- CS
                                   ...............................................xxxxxxxxxxxxxxxxx.xxxxxxxxxxx...xx RF
               Intein_splicing  94 ...............................................dadvvwdkvksievede.eeyVYdltved...nh 123
                                                                                  d+d++wd++k+i++ +  ++y Yd++ +d   n+
  gi|15669311|ref|NP_248116.1| 746 msllnkhikdkenleemynflvnlekcpicgkpihkemryswkkecyDGDIYWDRIKEIKKIKVnDKYAYDIELPDdgsNS 826
                                   *************************************************************998799*******9744456 PP

                                   EEEE.CTTEEE- CS
                                   xxxx.xxxxxxx RF
               Intein_splicing 124 NFva.ngiivHN 134
                                    +++ ng+ivHN
  gi|15669311|ref|NP_248116.1| 827 HYIVaNGFIVHN 838
                                   79888******9 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   5.6e-17     1e-13       2     169 ..      14     178 ..      13     180 .. 0.84
   2 ?   -2.4   0.1       2.4   4.3e+03      96     118 ..     364     401 ..     312     427 .. 0.55
   3 ?    0.1   0.4      0.38   6.8e+02      56     116 ..     695     754 ..     678     771 .. 0.72

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 5.6e-17
                                   -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S........-EEEEESSHHHHHHHHHHGGGGT CS
                        ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkee...kflflvprkslleqtleefkkfl 78 
                                   +elr+ Q++a+e+ l  l  +++k++li ++T +GKTl+  ++li +ll  +k+    k +f+vp k+l +  +eefk+ +
  gi|15669311|ref|NP_248116.1|  14 VELRPPQKKALERGL--L--DKNKNFLISIPTASGKTLIGeMALINHLLDGNKNPtnkKGIFIVPLKALASEKYEEFKSKY 90 
                                   589**********98..6..599*************************9876665778*********************** PP

                                   GG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHHHHHT CS
                        ResIII  79 seaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swreilek 156
                                   + +  +i  ++ +  +++   d ++ ++++tt ++ld+        ++    +   v+++DE H +++++   + + +l k
  gi|15669311|ref|NP_248116.1|  91 ERYGLRIALSIGDYDEDE---DLSKYHLIITTAEKLDSLW-----RHKIDWINDVSVVVVDEIHLINDETrggTLEILLTK 163
                                   **9988555544444444...566***************9.....55556666777************7566566666888 PP

                                   ---..SEEEEEESS- CS
                        ResIII 157 fke..avllglTATp 169
                                   +ke    ++gl+AT+
  gi|15669311|ref|NP_248116.1| 164 LKEfnVQIIGLSATI 178
                                   88765789******7 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                                   -......................-SEEEEEHHHHHHTH CS
                        ResIII  96 a...............kekdstnkkilvttiqsldads 118
                                   +               ++  +++ +i+v t++ l    
  gi|15669311|ref|NP_248116.1| 364 FalcgkeikpvdgwkvHKTPQHEYNIVVKTVNGLEITT 401
                                   22222222334444445577788888888888776655 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.38
                                   -EEE.EESSHHHHHHHHHHGGGGTGG.....GEEEESSS-B--.......-SEEEEEHHHHHH CS
                        ResIII  56 kflf.lvprkslleqtleefkkflseayke.igkkvsgdkkkakekdstnkkilvttiqslda 116
                                   k lf l ++k+l+   +e ++k +++++++ + +k++g+++ +    +++ ++l++  ++  +
  gi|15669311|ref|NP_248116.1| 695 KLLFeLLDGKKLITNYKEYYSKRKNPYFDFiVREKINGNNYYS---LNEKGRVLMSLLNKHIK 754
                                   5555588889999999999999999998889999999999988...55555555555554444 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   1.5   4.4e-13   7.9e-10       3      55 ..    1135    1184 ..    1133    1186 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 4.4e-13
                                    HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                         HHH_5    3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilel 55  
                                    eLls++ iG+++A++l++aGi+s+ed+++ ++ ++a+i  iG+k A++i++el
  gi|15669311|ref|NP_248116.1| 1135 ELLSIKYIGRVRARKLYNAGIRSIEDIIN-NPSKVASI--IGEKIAKKILDEL 1184
                                    8****************************.5*******..************9 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   2.9e-08   5.2e-05       3      34 ..    1136    1167 ..    1135    1185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.9e-08
               DNA_pol_lambd_f    3 FtkvyGVGpktAkkwyakGirtledlrakrak 34  
                                    ++++  +G+++A+k+y++Gir++ed+ ++++k
  gi|15669311|ref|NP_248116.1| 1136 LLSIKYIGRVRARKLYNAGIRSIEDIINNPSK 1167
                                    6778889*******************995554 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.3   0.00025      0.45       5      73 ..     229     334 ..     226     339 .. 0.63
   2 ?   -3.2   0.0         6   1.1e+04      19      61 ..     553     599 ..     539     607 .. 0.46
   3 ?    3.6   0.0     0.046        83      76     111 .]     838     881 ..     741     881 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                                   HHHHHH.HHTTTTSEEEEEESSHH....HHHH...HHHHHHHTTSTEEEESTT............................ CS
                    Helicase_C   5 allell.kleeeggkilifvntid....rlek...vklllekkgikvavlhge............................ 49 
                                    +++l+ +  +egg +l+f+nt++    +++k    k+l+e+++i+   +  e                            
  gi|15669311|ref|NP_248116.1| 229 DIYNLVvDCVKEGGCCLVFCNTKRnavnEAKKlnlKKFLTEEEKIRLKEIAEEilsilepptemcktlaecilngsafhha 309
                                   57788668899*************755533335544555444455555555444444444444444444444444455555 PP

                                   .STHHHHHHHHHHHHTTSSSEEEES CS
                    Helicase_C  50 .lpqnereeileqfnkgesdvLiat 73 
                                    l+ ++r+ + ++f+k  ++v+ +t
  gi|15669311|ref|NP_248116.1| 310 gLTYQHRKIVEDAFRKRLIKVICCT 334
                                   5888888888888888888888887 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6
                                   EEEEESSHH.HHHH.....HHHHHHHTTSTEEEESTTSTHHHHHHHHHH CS
                    Helicase_C  19 ilifvntid.rlek.....vklllekkgikvavlhgelpqnereeileq 61 
                                    +i++n+++ ++++     v+ l  ++ +    +h+++ +++ + +++ 
  gi|15669311|ref|NP_248116.1| 553 GYIYLNRKNiEFYSiseklVEQL--QFVLLRFGIHSSIRKKKTKTMVSP 599
                                   55666666663333321122222..222222245666666665555555 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.046
                                   GTSSSTSTTESEEEESSSS..SSH.......HHHHHHHTTSSSTT CS
                    Helicase_C  76 aerGidipkvnlVinfdlp..rnv.......tsyiqriGRtgRag 111
                                   ++ G+++p+ + ++  dl   +n         +++q iGR+gR g
  gi|15669311|ref|NP_248116.1| 838 NSAGLNLPCRRAIV-KDLTrfTNKgmryipiMEIQQCIGRAGRPG 881
                                   57789998666655.33332233134445559999********75 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       8.4   1.5e+04      59      74 ..     508     523 ..     496     533 .. 0.58
   2 !   15.2   0.1   9.1e-06     0.016       3      59 ..     543     597 ..     541     604 .. 0.92
   3 ?    1.1   0.2      0.24   4.2e+02      48      91 ..     602     647 ..     599     649 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 8.4
                LAGLIDADG_WhiA  59 vylKkaeqIvdlLkii 74 
                                   +y Kk ++I + L+++
  gi|15669311|ref|NP_248116.1| 508 IYSKKLRKIFNKLNML 523
                                   4555555555555544 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 9.1e-06
                LAGLIDADG_WhiA   3 aflrGaflasGsindpekkyhLEivspdeelaeqlqkllnefeleakilerrkkyvv 59 
                                   ++++G+f + G i   +k+  +E++s +e+l+eqlq +l +f+++++i+++++k++v
  gi|15669311|ref|NP_248116.1| 543 YLIAGLFDSDGYIYLNRKN--IEFYSISEKLVEQLQFVLLRFGIHSSIRKKKTKTMV 597
                                   56799*********97777..*******************************99887 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.24
                LAGLIDADG_WhiA  48 akilerrkkyvvylKkaeqIvdlLkiiga..hesllkfenirilre 91 
                                    k  + +  yv+++++  +I ++ ++i    +e+ +k+e+i  ++e
  gi|15669311|ref|NP_248116.1| 602 GKEYKCKDIYVLTIRDFMSIKRFYENIPLrhEEKRRKLEEIIKNKE 647
                                   677788999***************9996511567889999988887 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     8e-06     0.014      12     115 ..     338     432 ..     331     445 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Hint  12 CFpgestvtvedgeqkslseLepGdkVlavdesgevvfsevllfldrdseqraefveietengekltlTpaHLvfvsenek 92 
                                   C  ++ ++  e+g  +++ eL+  +kV a+ +++   +++v  +  +++ q++  ++++t ng ++t Tp+H+  v+en +
  gi|15669311|ref|NP_248116.1| 338 CLNANTEILQESG-FRKITELNKDEKVFALCGKE---IKPVDGWKVHKTPQHEYNIVVKTVNGLEITTTPNHIFLVKENGS 414
                                   8888888877777.67799**********99554...567777755555555566789******************99998 PP

                                   XXXXXXXXXXXXXXXXXXXXXX. CS
                          Hint  93 ssseeeeavfaskvregdyvlve 115
                                    ++       a++ + gdyv + 
  gi|15669311|ref|NP_248116.1| 415 LKE-----KEAKDLKVGDYVATV 432
                                   877.....468888999988872 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0033       5.9      79     126 ..     127     172 ..      40     188 .. 0.73
   2 ?   -3.2   0.0       5.2   9.2e+03      52      82 ..     274     306 ..     263     319 .. 0.68
   3 ?    2.4   0.0       0.1   1.8e+02      92     117 ..    1037    1069 ..     983    1079 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0033
                        AAA_22  79 lealeqalrarav.....ielliiDEaqhlr...seealeeLrsllnlsrkgvqli 126
                                   +++               ++++++DE++ ++   +   le L + l+  +++vq+i
  gi|15669311|ref|NP_248116.1| 127 WRHK--------IdwindVSVVVVDEIHLINdetRGGTLEILLTKLK--EFNVQII 172
                                   2233........134444688*********98755999999977777..8888886 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.2
                        AAA_22  52 sskdllrellralglelka.erlsseell.eal 82 
                                    +k++++e+l++l+ +++  ++l +  l  +a+
  gi|15669311|ref|NP_248116.1| 274 RLKEIAEEILSILEPPTEMcKTLAECILNgSAF 306
                                   578999999999998887755555555555555 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.1
                        AAA_22   92 ielliiDEaqhlr..s.....eealeeLrslln 117 
                                     el +iDE++ l   s      ea+++ ++l++
  gi|15669311|ref|NP_248116.1| 1037 EELNLIDEMDSLGikSfeiedLEAFKTAKMLYD 1069
                                    67889*******775255556777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.91u 0.34s 00:00:01.25 Elapsed: 00:00:00.51
# Mc/sec: 7110.33
//
Query:       gi|15669312|ref|NP_248117.1|  [L=60]
Description: hypothetical protein MJ_1125 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 404.38
//
Query:       gi|15669313|ref|NP_248118.1|  [L=402]
Description: GTP1/Obg family GTP-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-21   74.2   1.0    3.1e-20   72.4   1.0    2.0  1  MMR_HSR1      50S ribosome-binding GTPase
    9.7e-20   71.1   0.7      3e-19   69.5   0.7    1.9  1  GTP-bdg_N     GTP-binding GTPase N-terminal
    3.5e-18   66.0   6.9    1.1e-17   64.4   6.9    1.9  1  GTP-bdg_M     GTP-binding GTPase Middle Region
    2.1e-11   43.6   1.5    4.3e-11   42.6   1.5    1.5  1  FeoB_N        Ferrous iron transport protein B
    1.8e-07   31.2   8.5    0.00099   19.0   0.2    3.0  3  RsgA_GTPase   RsgA GTPase
    7.3e-07   29.2   1.5    7.3e-07   29.2   1.5    3.2  3  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    6.8e-06   25.8  10.2    1.8e-05   24.3   3.7    3.2  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    0.00028   21.1   2.2     0.0036   17.5   2.2    2.5  1  Roc           Ras of Complex, Roc, domain of DAPkinase
     0.0018   18.8   2.7     0.0025   18.3   0.4    2.3  3  ABC_tran      ABC transporter
      0.003   17.6   8.4     0.0056   16.8   0.2    3.7  5  Dynamin_N     Dynamin family
     0.0035   16.8   5.4     0.0039   16.6   3.1    2.2  2  SRPRB         Signal recognition particle receptor beta subun
     0.0038   16.8   5.7       0.62    9.6   1.3    2.6  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.021   14.2   3.0       0.08   12.3   3.0    2.1  1  Gtr1_RagA     Gtr1/RagA G protein conserved region
      0.026   14.3   0.6      0.099   12.4   0.6    2.0  1  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
      0.032   14.0   5.0       0.75    9.5   5.0    2.4  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.033   13.8   3.8        0.1   12.2   1.5    2.6  2  Ras           Ras family
       0.15   12.4   0.0       0.46   10.8   0.0    1.8  2  AAA_16        AAA ATPase domain
       0.66   10.1   3.8          3    8.0   0.3    3.2  4  V-ATPase_H_C  V-ATPase subunit H
        5.2    7.3   7.4         40    4.4   3.1    3.2  2  OrfB_IS605    Probable transposase
        9.5    6.5   7.1        7.4    6.9   0.7    2.3  2  DUF4510       Domain of unknown function (DUF4510)


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   1.0   3.5e-23   3.1e-20       2     114 .]     183     301 ..     182     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 3.5e-23
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH..HHHHHHHHHHC....T CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek..glgkaflalee....a 76 
                                   v+++G++N+GK++L+naltge+ + +++ +tT++++++ +k  +++i ++Dt+G+i+  +      + +afl+ +e    +
  gi|15669313|ref|NP_248118.1| 183 VGLIGYTNAGKTSLLNALTGENKESKNQVFTTLTTTTRAIKGIKRKILVTDTVGFID--D--LppFMIEAFLSTIEesadS 259
                                   89**************************************955589********887..3..3346778888755445558 PP

                                   SEEEEEEETTTTCSHHHHHHHHHHHHH......TTSEEEEEEES CS
                      MMR_HSR1  77 dlillvvdaseeklkpldeeleellee......akkplilvlnk 114
                                   dlil+vvdas +++++++++l+    e       k p+i v+nk
  gi|15669313|ref|NP_248118.1| 260 DLILIVVDAS-DDIEEIKRKLKVNH-EilskinCKAPIITVFNK 301
                                   ********99.44666655543332.234446689999****98 PP

>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.7   3.4e-22     3e-19       2      88 ..      13      97 ..      12      98 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 3.4e-22
                     GTP-bdg_N  2 esleEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkViDRtqLI 84
                                  +s+eEl+eLa+ + ++ v+++vq r k dp++ iG+G ve+i+e ++ee++++vi+ + L+psq+ nL k+++v+ViD+ +L+
  gi|15669313|ref|NP_248118.1| 13 KSIEELKELAEVL-YNPVKTIVQIR-KADPKYQIGSGLVERIAENIKEENIEIVIVGNILTPSQKYNLAKKFKVEVIDKIELV 93
                                  689*******976.89999999986.99******************************************************* PP

                     GTP-bdg_N 85 LdIF 88
                                  L IF
  gi|15669313|ref|NP_248118.1| 94 LRIF 97
                                  **** PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   6.9   1.2e-20   1.1e-17       1      79 []     100     177 ..     100     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 1.2e-20
                                   H--SHHHHHHHHHHHHHHHHHHHCXXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.....T CS
                     GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLeglgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelqrkkR 79 
                                   +Artkea+lQV lA+l+y+lpr  + + +l ++g + g+ G G +++e + +++++ ia++k++Lek++++r++ rk R
  gi|15669313|ref|NP_248118.1| 100 HARTKEAQLQVRLAELQYELPRA-REKVRLAKMGEQPGFGGYGDYEVEKYYQKVKREIATIKRKLEKLREHRRVARKGR 177
                                   9**********************.4444444443334589************************************988 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   1.5   4.8e-14   4.3e-11       2     154 ..     182     340 ..     181     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 4.8e-14
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----S.SSSSSSHHHHHHHHHHHCTSSSE CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiY.slsayseeekvardflleeepdv 81 
                                   tv l+G  n+Gkt+l+naltg +++  N   +t   ++ ++k  ++++ ++D  G   +l ++ +e     ++  + + d+
  gi|15669313|ref|NP_248118.1| 182 TVGLIGYTNAGKTSLLNALTGENKESKNQVFTTLTTTTRAIKGIKRKILVTDTVGFIdDLPPFMIEAF-LSTIEESADSDL 261
                                   6889**************************************99***********8625777777655.5566678899** PP

                                   EEEEEEGG....GHHHHHHHHHHHH...HTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHH CS
                        FeoB_N  82 vvnvvdat....nlernLyLtlqll...elgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellk 154
                                   ++ vvda+    +++r+L +  ++l   + ++p++ ++n++d+++k++ +  l++L++ +  p+  +sak   +++ l++
  gi|15669313|ref|NP_248118.1| 262 ILIVVDASddieEIKRKLKVNHEILskiNCKAPIITVFNKVDKITKEKKRKILEELDRYIVNPI-FVSAKYDINMDLLKE 340
                                   ******96433379******999863226899**************999988999998886664.577777777777766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.1     1e+03      34      52 ..      48      66 ..       6     119 .. 0.59
   2 !   19.0   0.2   1.1e-06   0.00099      88     161 ..     167     237 ..     141     239 .. 0.71
   3 !   15.9   0.5     1e-05    0.0094      17     106 ..     260     351 ..     248     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                                  HHHHHHHHHHHTT-EEEEE CS
                   RsgA_GTPase 34 lldrfLvlaeekgiepviv 52
                                  l++r+   ++e++ie+viv
  gi|15669313|ref|NP_248118.1| 48 LVERIAENIKEENIEIVIV 66
                                  3444444444444444443 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.1e-06
                                   TTHHHHHHHCTT..SEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-SS CS
                   RsgA_GTPase  88 egleelkellkd..ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPGf 161
                                   +++++++++ +   +t+ l+G + +GK++L+nal++e++ + ++v ++      TTt++ +  ++++ l+ Dt Gf
  gi|15669313|ref|NP_248118.1| 167 REHRRVARKGRAkfDTVGLIGYTNAGKTSLLNALTGENKESKNQVFTT-----LTTTTRAIKGIKRKILVTDTVGF 237
                                   444455544444247889*******************99988888886.....58888888888889******998 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 1e-05
                                   -EEEEEEESTT..TT--HH.HHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHH CS
                   RsgA_GTPase  17 dqllivvslke..pelsln.lldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelk 94 
                                   d +livv +++  +e++ +  ++  ++   + +++++ v+nK+D +++e+  +++ eel ++ +++++vsak   +++ lk
  gi|15669313|ref|NP_248118.1| 260 DLILIVVDASDdiEEIKRKlKVNHEILSKINCKAPIITVFNKVDKITKEK-KRKILEELDRYIVNPIFVSAKYDINMDLLK 339
                                   55566655542112222221355556666677889999************.999999999999****************** PP

                                   HHCTTSEEEEEC CS
                   RsgA_GTPase  95 ellkdktsvlvG 106
                                   e++ +++ + +G
  gi|15669313|ref|NP_248118.1| 340 EMIIEHLNLSIG 351
                                   *99888777666 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.1     1e+03      64      79 ..       9      24 ..       7      45 .. 0.79
   2 ?    0.2   0.1      0.85   7.6e+02       4      40 ..      33      69 ..      29      91 .. 0.82
   3 !   29.2   1.5   8.2e-10   7.3e-07      56     106 .]     293     348 ..     259     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                  MMR_HSR1_Xtn 64 KiDlisleeldelare 79
                                  K D+ s+eel+ela+ 
  gi|15669313|ref|NP_248118.1|  9 KFDRKSIEELKELAEV 24
                                  8999999999999985 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.85
                  MMR_HSR1_Xtn  4 ikitstvkltkldeetvkkilkeykihnaevliredv 40
                                  ++i++  +  ++    v++i ++ k  n e++i +++
  gi|15669313|ref|NP_248118.1| 33 VQIRKADPKYQIGSGLVERIAENIKEENIEIVIVGNI 69
                                  5566666777788889999999999999999987765 PP

  == domain 3  score: 29.2 bits;  conditional E-value: 8.2e-10
                  MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare.....pnsvviSaekelnldeLkekiweeLnL 106
                                    p ++v+NK+D+i++e+ +++ +e      n +++Sa+ ++n+d Lke+i e+LnL
  gi|15669313|ref|NP_248118.1| 293 APIITVFNKVDKITKEKKRKILEEldryiVNPIFVSAKYDINMDLLKEMIIEHLNL 348
                                   5899***********9999988866666669999********************97 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.5      0.83   7.4e+02     122     151 ..      28      57 ..       8     165 .. 0.58
   2 !   24.3   3.7     2e-08   1.8e-05       7     192 ..     184     346 ..     178     348 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.83
                                   TTEEEEEEESCGSTHHHHHHHHHHHHHHHH CS
                      GTP_EFTU 122 gvpiivfiNKmDrlkaelkeiveevkqkls 151
                                    v++iv i K+D   +  + +ve + ++++
  gi|15669313|ref|NP_248118.1|  28 PVKTIVQIRKADPKYQIGSGLVERIAENIK 57 
                                   344555555555443333333333333332 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2e-08
                                   EEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGG....G CS
                      GTP_EFTU   7 giighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvd....F 83 
                                   g+ig +++GKt+L+ +L+                     +ke +++ +T  ++++    ++ k++i + Dt G +d    F
  gi|15669313|ref|NP_248118.1| 184 GLIGYTNAGKTSLLNALT-------------------GENKESKNQVFTTLTTTTRAI-KGIKRKILVTDTVGFIDdlppF 244
                                   555555566666655555...................223334444444444444443.4889999999999999888888 PP

                                   HHHHHHH....HHT-SEEEEEEETTTB...STHHHHHHHHHHHHTTTE..EEEEEESCGST.HHHHHHHHHHHHHHHHHHH CS
                      GTP_EFTU  84 skevirg....lrvlDgavlvvdaveG...vepqteevlrlalkegvp..iivfiNKmDrl.kaelkeiveevkqklsrke 154
                                   + e   +     +  D+ ++vvda+++   ++ + + + ++++k +++  ii++ NK+D++ k++ ++i ee+  ++    
  gi|15669313|ref|NP_248118.1| 245 MIEAFLStieeSADSDLILIVVDASDDieeIKRKLKVNHEILSKINCKapIITVFNKVDKItKEKKRKILEELD-RY---- 320
                                   88754444444899***********884445556666677777777777799*********5566666666666.44.... PP

                                   HHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
                      GTP_EFTU 155 eklekygekgekevpvvfgSalkgegvktllealvell 192
                                               +v+ +f+Sa+   +++ l e+++e+l
  gi|15669313|ref|NP_248118.1| 321 ------------IVNPIFVSAKYDINMDLLKEMIIEHL 346
                                   ............35679999999999999999999997 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   2.2     4e-06    0.0036       3     120 .]     184     304 ..     182     304 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4e-06
                                   EEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-S..GGCTTTT-HHHHC... CS
                           Roc   3 vlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaG..qerfrslhplylr... 78 
                                    l+G +++GKtsll+ ++ ++ ++k++  + ++++t+    ikg++        k+ + Dt G   +    + + +l+   
  gi|15669313|ref|NP_248118.1| 184 GLIGYTNAGKTSLLNALTGENKESKNQVFTTLTTTTRA---IKGIKR-------KILVTDTVGfiDDLPPFMIEAFLStie 254
                                   69****************99999888887777776654...567532.......456778888432333346677764333 PP

                                   ...TSCEEEEEEEGHHH.....HCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                           Roc  79 ...eaalailvydsrss.....enlkeWlkelkkvagkspvilvgnkiDl 120
                                      +++l+++v+d++++     ++lk   + l+k + k+p+i v nk+D+
  gi|15669313|ref|NP_248118.1| 255 esaDSDLILIVVDASDDieeikRKLKVNHEILSKINCKAPIITVFNKVDK 304
                                   3347889999999443321122455666666777778899*******995 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.6   2.3e+03      28      62 ..      94     127 ..      46     180 .. 0.65
   2 !   18.3   0.4   2.8e-06    0.0025      12      51 ..     181     220 ..     173     290 .. 0.70
   3 ?   -2.5   0.0       7.4   6.6e+03      55      74 ..     344     364 ..     328     397 .. 0.46

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.6
                                   HHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  28 lkllagllkpteGeilldgkdlkeqeleslrkeig 62 
                                   l++++++ + +e +++++ ++l++ el+++r++++
  gi|15669313|ref|NP_248118.1|  94 LRIFYKHARTKEAQLQVRLAELQY-ELPRAREKVR 127
                                   455555555555555555555555.3333333333 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.8e-06
                                   SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51 
                                    +v+++G + aGK++Ll++l+g+ k  + ++    + +++
  gi|15669313|ref|NP_248118.1| 181 DTVGLIGYTNAGKTSLLNALTGENKESKNQVFTTLTTTTR 220
                                   589*************************999444333332 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 7.4
                                   HHCCHCEEEE-SS.--S-TTS CS
                                   xxxxxxxxxxxxx.xxxxxxx RF
                      ABC_tran  55 eslrkeigvlpqe.pqlfpel 74 
                                   e+l+ +ig+++ + p+l + l
  gi|15669313|ref|NP_248118.1| 344 EHLNLSIGTIETDnPRLISYL 364
                                   444444444444433332222 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       7.5   6.7e+03      63      84 ..     143     164 ..     110     175 .. 0.58
   2 !   16.8   0.2   6.2e-06    0.0056       1      35 [.     183     217 ..     183     224 .. 0.80
   3 ?    3.1   0.2     0.099        89     128     157 ..     258     288 ..     252     302 .. 0.72
   4 ?    1.2   0.1      0.38   3.4e+02     123     167 ..     286     330 ..     276     331 .. 0.81
   5 ?   -2.3   0.0       4.5     4e+03     110     135 ..     359     384 ..     337     397 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.5
                                   --CHHHHHHHHHHHHHHHTSSS CS
                     Dynamin_N  63 edfsevreeieketekiagank 84 
                                   ++++++ +++++e ++i+++++
  gi|15669313|ref|NP_248118.1| 143 YEVEKYYQKVKREIATIKRKLE 164
                                   4444444444444444444333 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 6.2e-06
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS---S- CS
                     Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrp 35 
                                   + ++G +++GK+S+lnaL+ge+   + +  tT ++
  gi|15669313|ref|NP_248118.1| 183 VGLIGYTNAGKTSLLNALTGENKESKNQVFTTLTT 217
                                   6789*****************96666666666554 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.099
                                   TTEEEEEEEETTS-CCC-.CHHHHHHHHSTT CS
                     Dynamin_N 128 kadiilavtsanhdlsns.ealflarevdpk 157
                                   ++d+il v++a+ d+ +  ++l++++e+ +k
  gi|15669313|ref|NP_248118.1| 258 DSDLILIVVDASDDIEEIkRKLKVNHEILSK 288
                                   689***********99654666666666554 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.38
                                   HHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEEEEE- CS
                     Dynamin_N 123 keyikkadiilavtsanhdlsnsealflarevdpkgkrtivvltk 167
                                    + i+ ++ i+ v +   ++++ +++++ +e+d    + i+v +k
  gi|15669313|ref|NP_248118.1| 286 LSKINCKAPIITVFNKVDKITKEKKRKILEELDRYIVNPIFVSAK 330
                                   5566666778899999999*************9999999998766 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 4.5
                                   -B-SSSGTTSHHHHHHHSTTEEEEEE CS
                     Dynamin_N 110 Gldsvnkrdqelvkeyikkadiilav 135
                                    l+s   +++e+++ ++++++ i+  
  gi|15669313|ref|NP_248118.1| 359 RLISYLYENTEIIEDILEDNKHIITF 384
                                   45555556777777777666666554 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.3   1.2e+03      84     105 ..       7      31 ..       2      44 .. 0.60
   2 !   16.6   3.1   4.4e-06    0.0039       5     141 ..     182     321 ..     178     347 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                                   ETTS-HH...HHHHHHHHHHHHHHH CS
                         SRPRB  84 DStidpk...evkevAEllyeilli 105
                                   DS  d k   e+ke AE ly+ +  
  gi|15669313|ref|NP_248118.1|   7 DSKFDRKsieELKELAEVLYNPVKT 31 
                                   6666666222456788888874433 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.4e-06
                                   EEEEE-STTSSHHHHHHHHHHS..S---B---S.S-EEETTG...GGTT-SEEEETT-.GC....CSHHHHHHHHHHGGEE CS
                         SRPRB   5 avllvGlsdsGKTslftrLttd..svkktvtSq.essaalkvksekgskltliDfPGh.ek....lrqklleklkaksslk 77 
                                   +v l+G +++GKTsl++ Lt +  +  k ++    ++++  +k+  + k+ + D  G  +     +   +l ++ +++   
  gi|15669313|ref|NP_248118.1| 182 TVGLIGYTNAGKTSLLNALTGEnkE-SKNQVFTtLTTTTRAIKG-IKRKILVTDTVGFiDDlppfMIEAFLSTIEESADSD 260
                                   6779***************988542.233333313333333422.233444455555422211115677888999999999 PP

                                   EEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---HHHHHHHHHHHH CS
                         SRPRB  78 glvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflakspklikdaLEkEl 141
                                    ++ vvD++ d  e+k       eil++      + +i+   nK +  +  ++++i ++L++ +
  gi|15669313|ref|NP_248118.1| 261 LILIVVDASDDIEEIKRKLKVNHEILSKIN---CKAPIITVFNKVDKITKEKKRKILEELDRYI 321
                                   9*************************9887...677899999**************99999876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.2    0.0014       1.2       3      28 ..     183     208 ..     181     214 .. 0.76
   2 !    9.6   1.3    0.0007      0.62      85     164 ..     229     316 ..     213     325 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0014
                                   EEEEESTTCCHHHHHHHHH.CT--SS- CS
                          cobW   3 tvltGflGsGKTtLlnhll.enraglk 28 
                                   ++l G+  +GKT+Lln+l+ e +++ k
  gi|15669313|ref|NP_248118.1| 183 VGLIGYTNAGKTSLLNALTgE-NKESK 208
                                   6789999************53.44443 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0007
                                   EEEEEECTTTTHHHH.HTT..SHHHHHCCCECEEEEEEETTTH....CCHCCHHHHHHHHHHT.SSEE.EEE-HHHHCHC. CS
                          cobW  85 viliEttGlaePapv.aft..eeelksdltldavvavvDaknl...eaeeekieekaedqlaa.adll.vlnKtDlldeea 157
                                   +++  t+G  +  p  +++   +++++++  d ++ vvDa+      +++ k ++++ +++++ a ++ v+nK+D +++e+
  gi|15669313|ref|NP_248118.1| 229 ILVTDTVGFIDDLPPfMIEafLSTIEESADSDLILIVVDASDDieeIKRKLKVNHEILSKINCkAPIItVFNKVDKITKEK 309
                                   67777888544333322334588999**************7655663334444444444554414444489********97 PP

                                   .HHHHHH CS
                          cobW 158 lleklee 164
                                   + + lee
  gi|15669313|ref|NP_248118.1| 310 KRKILEE 316
                                   7444444 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.0   8.9e-05      0.08      79     145 ..     261     326 ..     182     350 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.9e-05
                     Gtr1_RagA  79 vliyVfDvesreleedletlkeilealrqyspeakvfvlihKmDliqedereeifeerkeeireeie 145
                                    ++ V+D++ +++ee  ++lk   e l++++ +a +    +K+D+i+++++++i+ee  + i + i 
  gi|15669313|ref|NP_248118.1| 261 LILIVVDAS-DDIEEIKRKLKVNHEILSKINCKAPIITVFNKVDKITKEKKRKILEELDRYIVNPIF 326
                                   567799998.556666666666666666777777777777*****************9999887665 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.6   0.00011     0.099      15      58 .]     260     303 ..     256     303 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                          NOG1  15 davlFllDpseecgysleeQlsLleeikelfan.kpvivvlnKiD 58 
                                   d++l ++D+s +   +++  l++ +ei ++++  +p+i+v+nK+D
  gi|15669313|ref|NP_248118.1| 260 DLILIVVDASDDI-EEIKRKLKVNHEILSKINCkAPIITVFNKVD 303
                                   789*******885.69***************97689********9 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   5.0   0.00084      0.75       5     141 ..     184     342 ..     181     344 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00084
                     PduV-EutP   5 lliGkvgsGKttLtqalkg..........eelkYkktqaiefsdevi...DtPGeylenrkly.sal...ivtsaeadvia 68 
                                    liG +++GKt+L +al+g               + t ai+  ++ i   Dt G   +   ++ +a+   i  sa++d+i 
  gi|15669313|ref|NP_248118.1| 184 GLIGYTNAGKTSLLNALTGenkesknqvfT-TLTTTTRAIKGIKRKIlvtDTVGFIDDLPPFMiEAFlstIEESADSDLIL 263
                                   59***************9966666544321.1224566666554433334887743333333213331114468999**** PP

                     PduV-EutP  69 lvqdateeesvfppgfa...svfnk.....eviGiitkidlaedeenieaveelLksaGaekifevsavekegieellkyl 141
                                   +v+da++  + +  ++    ++++k     ++i +  k+d+ ++e++ ++  e+L    ++ if vsa  +++++ l++++
  gi|15669313|ref|NP_248118.1| 264 IVVDASDDIEEIKRKLKvnhEILSKinckaPIITVFNKVDKITKEKKRKI-LEELDRYIVNPIF-VSAKYDINMDLLKEMI 342
                                   **999987776665543111233322223489999999999966555554.6678888787777.7888888888877765 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.35   3.1e+02      94     114 ..      49      70 ..      16     111 .. 0.77
   2 ?   12.2   1.5   0.00012       0.1       4     126 ..     185     309 ..     182     347 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.35
                                   HHHHHHHST.TTSEEEEEEETT CS
                           Ras  94 veeikrvae.envpivLvGnKv 114
                                   ve i +  + en++iv+vGn  
  gi|15669313|ref|NP_248118.1|  49 VERIAENIKeENIEIVIVGNIL 70 
                                   5666655555899******955 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00012
                                   EEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTS.GG.....GHHHHHHHHTTESEEEEE CS
                           Ras   4 lvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGq.ee.....fkslrelyyrdaegillv 78 
                                   l+G ++ GKtsll+  + ++ +++ ++ +    +t++  ++g + k+ + DT G  ++      +++ ++  ++a+  l++
  gi|15669313|ref|NP_248118.1| 185 LIGYTNAGKTSLLNALTGENKESK-NQ-VFTTLTTTTRAIKGIKRKILVTDTVGFiDDlppfmIEAFLSTIEESADSDLIL 263
                                   89************9986643332.22.32456888889999************532222211244445555566666666 PP

                                   EETTBHHHHHTHH...HHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHH CS
                           Ras  79 yditsresfenvk...kwveeikrvaeenvpivLvGnKvDleekravstee 126
                                     ++ ++  e++k   k  +ei ++ + + pi+ v nKvD  +k+     +
  gi|15669313|ref|NP_248118.1| 264 IVVDASDDIEEIKrklKVNHEILSKINCKAPIITVFNKVDKITKE-----K 309
                                   667777778888754567789999999899*********976532.....2 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00052      0.46       8     147 ..     162     305 ..     153     320 .. 0.59
   2 ?   -2.2   0.0       5.2   4.7e+03      37      63 ..     310     334 ..     310     357 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00052
                        AAA_16   8 eleqLlsalervrsgrp..elvllsGesGvGKsslvrellralekdg.gif.lrgkcdqlesaipysalaqalareellrq 84 
                                    le+L++  + +r+gr     v l+G+   GK+sl+++l  + ++++  +f + +++++         + + +   + +  
  gi|15669313|ref|NP_248118.1| 162 KLEKLREHRRVARKGRAkfDTVGLIGYTNAGKTSLLNALTGENKESKnQVFtTLTTTTRA-----IKGIKRKILVTDTVGF 237
                                   456666666677777779999*******************88888742333222222222.....1225555544444444 PP

                        AAA_16  85 lldeaesaeleawrekleeala.....avpelagaea..srllellkrllallsrderplvlvlDdlqwa 147
                                   ++d +     ea+  ++ee++      +v +++++++  +r l +  ++l+++ + + p++ v+  ++++
  gi|15669313|ref|NP_248118.1| 238 IDDLPPF-MIEAFLSTIEESADsdlilIVVDASDDIEeiKRKLKVNHEILSKINC-KAPIITVFNKVDKI 305
                                   4444444.66666666666666666663333333333445555555555566666.45566666666655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.2
                        AAA_16  37 Ksslvrellralekdggiflrgkcdql 63 
                                   K ++++el r++     if+++k+d +
  gi|15669313|ref|NP_248118.1| 310 KRKILEELDRYIVNP--IFVSAKYDIN 334
                                   567888999888866..9999999998 PP

>> V-ATPase_H_C  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.35   3.1e+02      34      63 ..       8      36 ..       4      67 .. 0.78
   2 ?   -3.2   0.0       9.8   8.8e+03      87     108 ..     193     214 ..     181     223 .. 0.61
   3 ?    8.0   0.3    0.0034         3      46      99 ..     248     304 ..     239     321 .. 0.79
   4 ?   -3.0   0.0       8.5   7.6e+03      56      78 ..     367     389 ..     354     400 .. 0.47

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.35
                  V-ATPase_H_C 34 ekleeknfkllkkLiklleeskdktvlava 63
                                  +k+++k+++ lk+L+++l+ +  kt++++ 
  gi|15669313|ref|NP_248118.1|  8 SKFDRKSIEELKELAEVLY-NPVKTIVQIR 36
                                  6899999999999999995.3445666665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.8
                  V-ATPase_H_C  87 KekimellehedeevkyeALka 108
                                   K+ +++ l+ e++e k +  ++
  gi|15669313|ref|NP_248118.1| 193 KTSLLNALTGENKESKNQVFTT 214
                                   5555666666665555554444 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0034
                  V-ATPase_H_C  46 kLiklleeskdktvlav...alnDigelvkllpegkkvleklkaKekimellehede 99 
                                   + ++++ees+d+  + +   a  Di+e+ + l+  +++l+k+++K+ i+++ ++ d+
  gi|15669313|ref|NP_248118.1| 248 AFLSTIEESADSDLILIvvdASDDIEEIKRKLKVNHEILSKINCKAPIITVFNKVDK 304
                                   555666677776433331236789**************************9998876 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 8.5
                  V-ATPase_H_C  56 dktvlavalnDigelvkllpegk 78 
                                   +++++  +l D ++++++  + +
  gi|15669313|ref|NP_248118.1| 367 NTEIIEDILEDNKHIITFRAKER 389
                                   33333334444444444433333 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.17   1.6e+02      95     116 ..      48      69 ..      46      71 .. 0.91
   2 ?    4.4   3.1     0.045        40      45      90 ..     100     169 ..      94     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.17
                    OrfB_IS605  95 lathliktlkevgvetLnvgnm 116
                                   l+ +++++ ke+++e ++vgn 
  gi|15669313|ref|NP_248118.1|  48 LVERIAENIKEENIEIVIVGNI 69 
                                   799*****************96 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.045
                    OrfB_IS605  45 rlksdykylakeiaelqsklkkskn........................ykkasrklarlhrkrsrrrkh 90 
                                   ++++++ +l+ + aelq  l++++                         y+k++r++a + rk+ + r h
  gi|15669313|ref|NP_248118.1| 100 HARTKEAQLQVRLAELQYELPRAREkvrlakmgeqpgfggygdyevekyYQKVKREIATIKRKLEKLREH 169
                                   5666777778888888888888877888888888888888888888888999999999999999999998 PP

>> DUF4510  Domain of unknown function (DUF4510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.0      0.19   1.7e+02     118     137 ..     100     119 ..      89     138 .. 0.76
   2 ?    6.9   0.7    0.0082       7.4      22      52 ..     149     179 ..     133     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.19
                       DUF4510 118 aLrsrEavLeaaLerLqgqc 137
                                   + r++Ea L++ L  Lq ++
  gi|15669313|ref|NP_248118.1| 100 HARTKEAQLQVRLAELQYEL 119
                                   5699************9865 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0082
                       DUF4510  22 lelvareLqalqeeLqeaaeaRRaawearvg 52 
                                    ++v+re+ +++ +L++  e+RR+a + r++
  gi|15669313|ref|NP_248118.1| 149 YQKVKREIATIKRKLEKLREHRRVARKGRAK 179
                                   5789**********************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1646  (0.0918066); expected 358.6 (0.02)
Passed bias filter:                      749  (0.0417759); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 2441.88
//
Query:       gi|15669314|ref|NP_248119.1|  [L=280]
Description: hypothetical protein MJ_1127 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-29  103.6   0.0    1.5e-29  103.2   0.0    1.1  1  TatD_DNase    TatD related DNase
      0.003   16.9   0.1     0.0045   16.4   0.1    1.3  1  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   1.6e-33   1.5e-29       1     254 [.      10     274 ..      10     275 .. 0.83

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 1.6e-33
                                   EEEEE-TTS.CCCTTTHHHHHHHHHHTTEEEEEEE-SSG.........GGHHHHHHHHTT..TTTEEEEE---GGGGGC.. CS
                    TatD_DNase   1 iDaHcHlds.kefeedreeileraeeagvaavvvvgtss.........kdskavlelakk.ypnkvyavlGiHPnevde.. 68 
                                   +D+H+H+d+ +     +e++ + +++ag++ ++v +  +            ++ +e+++k  p k +  +G+HP+e++   
  gi|15669314|ref|NP_248119.1|  10 TDNHIHVDDkHG--YGAEKVAKTFYNAGGKVMIVLNKPTfdgnltasmDILVRDVEIINKnTPVKAFGLVGVHPAELTYlm 88 
                                   5********444..47777779999999999996666666666666535666777777776*************9999888 PP

                                   .......C.CCHHHHHHHH.HHCCCTS.EEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES.-HHHHH CS
                    TatD_DNase  69 .......asedlleelkel.anvkhsk.vvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrk.aeedll 139
                                          a+++ +++l+ + + v++++ +v+iGe+G+++y+++e+ ++a +e+++++++lAk+++++++iH+++ +ee++ 
  gi|15669314|ref|NP_248119.1|  89 kfmsleeAKQRIVDALNYAkKLVEEYDfIVGIGEVGRPHYPVSEDVWKASNEILKYCMELAKDIGCAIQIHAESsTEEQFK 169
                                   888888678888899999988896665389*******************************************98888787 PP

                                   HHHHHCGGCCS...EEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTT. CS
                    TatD_DNase 140 eilkeaaeaka...kvvlHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrg. 216
                                   e+ + a+e+++   kvv H+  g++    +    g++ s+ +  +        ++vk+  + r+++ETD  y+++  +r+ 
  gi|15669314|ref|NP_248119.1| 170 EFSEMAKEVGLnpeKVVKHH-CGNMVLEGERY--GIFPSILAS-RV-----NEDVVKK--SLRFVMETD--YIDD-LKRPg 236
                                   77777777777888*****9.66655555555..*******93.22.....3566654..679******..9999.77777 PP

                                   SE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                    TatD_DNase 217 krnepanvayvveklaelkaltleelaeitaeNakrlf 254
                                    +   ++v++v + l e   l++e +++i++eN++r++
  gi|15669314|ref|NP_248119.1| 237 VALGIKTVPRVTRRLIEKGVLDEEGVYKIHKENIERIY 274
                                   ************************************98 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1     5e-07    0.0045      35     159 ..      22     167 ..       9     206 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5e-07
                                   HHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEEESSEGGS.................GCCCSHHHHH CS
                  Amidohydro_1  35 ealesgiktalksGtttvadmgattstgiealleaaeelplglrilggkvsldr.................gsaetskasr 98 
                                   +++e+++kt+ ++G   ++  ++ t   +  l  +++ l+ +++i+ ++++++                   s e  k ++
  gi|15669314|ref|NP_248119.1|  22 YGAEKVAKTFYNAGGKVMIVLNKPT--FDGNLTASMDILVRDVEIINKNTPVKAfglvgvhpaeltylmkfMSLEEAKQRI 100
                                   6677777777777777777777754..555555555556666666666666666777777777777777775566666666 PP

                                   HHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHH.......HHHHHHHHHHHHTTEEEEEETSSCHHH CS
                  Amidohydro_1  99 eklkagaaetikgkadgvvk.valapheapafsde.......elkealkeakkrdlpvaiHaletkgev 159
                                   +  + + a+++ ++ d +v   +++ + ++ +s++        lk ++++ak+++  ++iHa ++++e+
  gi|15669314|ref|NP_248119.1| 101 VDALNY-AKKLVEEYDFIVGiGEVGRP-HYPVSEDvwkasneILKYCMELAKDIGCAIQIHAESSTEEQ 167
                                   666666.35555555666553333332.333333344444449*******************6666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1713.63
//
Query:       gi|15669315|ref|NP_248120.1|  [L=308]
Description: hypothetical protein MJ_1128 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-56  189.5   7.9    6.4e-56  188.8   7.9    1.3  1  C5-epim_C        D-glucuronyl C5-epimerase C-terminus
  ------ inclusion threshold ------
      0.019   13.5   0.6        2.2    6.6   0.0    2.1  2  Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
       0.95   10.2   5.5       0.67   10.6   3.4    2.1  2  DUF3139          Protein of unknown function (DUF3139)


Domain annotation for each model (and alignments):
>> C5-epim_C  D-glucuronyl C5-epimerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.8   7.9   1.1e-59   6.4e-56       3     187 ..     130     307 ..     127     308 .] 0.97

  Alignments for each domain:
  == domain 1  score: 188.8 bits;  conditional E-value: 1.1e-59
                     C5-epim_C   3 klggwrinveyklyegkklspGWlsamaqgqaisvllrAYeltgdekYlkaakkalksfkipvekGGvlktledk...kiw 80 
                                   ++++wr+n+e+ ly+   ls+GW +a++q+ ++++l+ AYe+tgde+Yl++a+ a+++fk+pvekGG+lk   +k   ++w
  gi|15669315|ref|NP_248120.1| 130 TFIVWRYNFEFPLYN---LSKGWRGALCQAGCLKTLYLAYEATGDERYLNYANLAINAFKVPVEKGGLLKIRIYKnksYYW 207
                                   6789*********77...99**************************************************99999999*** PP

                     C5-epim_C  81 yeeYptspksyvLNGfiysligLydlstakkseeakelfkkglkslkallpkydtgswslYdlrhvtlgkapnlarwdYhk 161
                                   + eY+++++ yvLNGfi++++++ d+ +++ +++a  l+k+glks+k++lp+yd+g+ws+Yd       + ++ ++++Y++
  gi|15669315|ref|NP_248120.1| 208 FPEYASENPPYVLNGFITATLWIGDFGNKTGNADALYLYKEGLKSIKTFLPMYDAGDWSYYD-------ALGHRCNKHYEH 281
                                   **************************************************************.......5899999***** PP

                     C5-epim_C 162 lhiellkaLakitndkvfkkyaerwk 187
                                   lh  ++ +L++ t+d+++ ky+++w+
  gi|15669315|ref|NP_248120.1| 282 LHRLQMLWLYNKTGDEIYLKYYKKWR 307
                                   *************************7 PP

>> Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0   0.00038       2.2     182     204 ..     160     182 ..     150     201 .. 0.85
   2 ?    5.3   0.2   0.00095       5.7     171     203 ..     277     306 ..     249     308 .] 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00038
                                   HHHHHHHHHHT-CHHHHHHHHCC CS
               Glyco_hydro_127 182 ealvklyelTgdkrYldlAkrfi 204
                                   ++l+  ye+Tgd+rYl+ A+  i
  gi|15669315|ref|NP_248120.1| 160 KTLYLAYEATGDERYLNYANLAI 182
                                   679999************98765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.00095
                                   HHTTTHHCTHHHHHHHHHHHHT-CHHHHHHHHC CS
               Glyco_hydro_127 171 kalvpehggieealvklyelTgdkrYldlAkrf 203
                                   k+++  h      +++ly+ Tgd+ Yl+  k++
  gi|15669315|ref|NP_248120.1| 277 KHYEHLHR---LQMLWLYNKTGDEIYLKYYKKW 306
                                   44444444...7899************988877 PP

>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.4   0.00011      0.67       1      43 [.       4      42 ..       4     136 .. 0.82
   2 ?   -3.1   0.0       2.1   1.3e+04      42      67 ..     244     267 ..     229     269 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                       DUF3139  1 mkkiiiililliillvivkvflglvgskpikkylankkldkyl 43
                                  mkk+ iil+l+i++l++v  ++ +  s+p+   ++++ + +y 
  gi|15669315|ref|NP_248120.1|  4 MKKFEIILFLFIAVLIFVFGYF-VGASQPL---YSENPVIQYF 42
                                  9****************99998.4444444...4445555554 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.1
                       DUF3139  42 ylqekgykeddIksikpkydskkgsy 67 
                                   yl ++g k+  Ik+  p+yd+ + sy
  gi|15669315|ref|NP_248120.1| 244 YLYKEGLKS--IKTFLPMYDAGDWSY 267
                                   555666665..777777777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 2350.48
//
Query:       gi|15669316|ref|NP_248121.1|  [L=95]
Description: hypothetical protein MJ_1129 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-26   91.0   0.3      5e-26   90.7   0.3    1.1  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
  ------ inclusion threshold ------
      0.014   15.3   0.1      0.031   14.2   0.0    1.6  2  DUF411          Protein of unknown function, DUF
      0.052   12.5   0.0      0.052   12.5   0.0    1.1  1  SBP_bac_5       Bacterial extracellular solute-binding protei


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   0.3   8.4e-30     5e-26       1      74 []       4      78 ..       4      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 8.4e-30
                                  HHHHHHHHTT-B-TTTSSBCCCCT---EEEE-T.-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEEEE CS
                FeS_assembly_P  1 keavlaaLrtVtDPelgvdlvslglvreidieg.gkVsvditltypacslaeairadaeaalralpgvevveVev 74
                                  ke+vl+aL+tV DP++g+++v++gl+r++++++ g+V++++ +t+p c+++ a++ +a++a+++l+gv++veV+v
  gi|15669316|ref|NP_248121.1|  4 KEDVLNALKTVADPHMGISIVDMGLIRDVEVDDeGNVKFKLIPTNPYCMSVMAMAFQAKEAVKSLEGVKKVEVTV 78
                                  79*****************************************************************99999987 PP

>> DUF411  Protein of unknown function, DUF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.76   4.5e+03      45      60 ..       8      24 ..       2      27 .. 0.51
   2 ?   14.2   0.0   5.2e-06     0.031      23      51 ..      66      94 ..      51      95 .] 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.76
                        DUF411 45 krlLaekp.kaaGlavP 60
                                   + L++ +   +G+++ 
  gi|15669316|ref|NP_248121.1|  8 LNALKTVAdPHMGISIV 24
                                  44444444345566655 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.2e-06
                        DUF411 23 aSchtavvggyvieGHVPaadikrlLaek 51
                                  +S   +   + ++eGHV  +di+++L+ek
  gi|15669316|ref|NP_248121.1| 66 KSLEGVKKVEVTVEGHVMEKDINEMLKEK 94
                                  555555555789***************98 PP

>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.7e-06     0.052      36      98 ..       2      60 ..       1      91 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.7e-06
                                  -SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEEEEESSETTTTTTHCHHHHH CS
                     SBP_bac_5 36 ltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvrftlkkpnalfltllaavpa 98
                                  +t eDv  +++ ++dp+ + +  ++      i +ve++d+  v+f+l  +n++ ++++a+  +
  gi|15669316|ref|NP_248121.1|  2 VTKEDVLNALKTVADPHMGISIVDMG----LIRDVEVDDEGNVKFKLIPTNPYCMSVMAMAFQ 60
                                  6889*********************9....5*******************9987776666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 722.72
//
Query:       gi|15669317|ref|NP_248122.1|  [L=535]
Description: O-sialoglycoprotein endopeptidase/protein kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-91  307.1   0.0    1.7e-91  306.7   0.0    1.1  1  Peptidase_M22   Glycoprotease family
    2.5e-06   27.2   0.1    4.4e-06   26.4   0.1    1.3  1  RIO1            RIO1 family
    3.8e-06   26.5   1.2    5.8e-06   25.9   1.2    1.3  1  Pkinase         Protein kinase domain
    5.4e-06   26.5   0.0      0.013   15.5   0.0    2.2  2  APH             Phosphotransferase enzyme family
    0.00031   20.2   0.3     0.0012   18.3   0.2    2.0  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00064   19.1   0.0      0.001   18.4   0.0    1.4  1  Pkinase_Tyr     Protein tyrosine kinase
  ------ inclusion threshold ------
       0.07   12.8   0.0       0.19   11.3   0.0    1.7  1  Carbam_trans_N  Carbamoyltransferase N-terminus
       0.11   12.1   1.7       0.36   10.4   1.4    1.7  2  Choline_kinase  Choline/ethanolamine kinase
       0.12   11.8   0.0       0.21   11.0   0.0    1.3  1  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.7   0.0   8.4e-95   1.7e-91       5     271 .]      27     291 ..      23     291 .. 0.95

  Alignments for each domain:
  == domain 1  score: 306.7 bits;  conditional E-value: 8.4e-95
                                   EEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--EE CS
                 Peptidase_M22   5 nvvasqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnkPlv 85 
                                   n+++ +    +++ G+ P++a+ +H+e++++li+ea++   ++++++d Ia+++gPGl+++Lrv +++A++l+l+l+kP++
  gi|15669317|ref|NP_248122.1|  27 NKTIMY---KPPKQGINPREAADHHAETFPKLIKEAFEV--VDKNEIDLIAFSQGPGLGPSLRVTATVARTLSLTLKKPII 102
                                   444444...48889************************9..7788************************************ PP

                                   EEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCCHHHHHHHCTC. CS
                 Peptidase_M22  86 gVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypggpkieklakeg. 165
                                   gVnh++ah++ ++l+++ e+P+ l+vsGg+tqv+++ +++y+++getld+a+g++ld++ar+++lp+pggp ie+la++g 
  gi|15669317|ref|NP_248122.1| 103 GVNHCIAHIEIGKLTTEAEDPLTLYVSGGNTQVIAYVSKKYRVFGETLDIAVGNCLDQFARYVNLPHPGGPYIEELARKGk 183
                                   ***************77799****************99******************************************6 PP

                                   S.......EETTEEE.CHHHHHHHHHHST.T.HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCHC CS
                 Peptidase_M22 166 kkiefprplkgldfsfsGlktavlkelek.e.vedlaasfqeavvdhlvekteralklpkakelvilGGvaankrLreale 244
                                   k +++p+++kg+d+ fsGl ta++++  + e  ed+++s+qe ++++l+e+teral+++++ e++++GGvaan+rLre+l+
  gi|15669317|ref|NP_248122.1| 184 KLVDLPYTVKGMDIAFSGLLTAAMRAYDAgErLEDICYSLQEYAFSMLTEITERALAHTNKGEVMLVGGVAANNRLREMLK 264
                                   66*************************66547************************************************* PP

                                   CHHHHTTSEEEXXXHHHHSSXCHHHHH CS
                 Peptidase_M22 245 eeaeelglkliiPplkyctdnaamiaw 271
                                   +++e  ++++++Pp+++c dn+amiaw
  gi|15669317|ref|NP_248122.1| 265 AMCEGQNVDFYVPPKEFCGDNGAMIAW 291
                                   *****99*******************9 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   2.2e-09   4.4e-06      23     150 ..     353     469 ..     342     484 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.2e-09
                                   -SS-H.HHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--E..EEEETTEEEEE--EETTEEGGBHHH CS
                          RIO1  23 teFkk.rkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkp..ielkrhvlvmefigedgvaapklkd 100
                                   ++F+  +k++v++ +r  d++      ++ k  + +E r+L  +++ g+p+P    ++l +  ++m++i+  g  a+++ +
  gi|15669317|ref|NP_248122.1| 353 LDFDViIKERVKKGYR--DER---LDENIRKSRTAREARYLALVKDFGIPAPYIfdVDLDNKRIMMSYIN--GKLAKDVIE 426
                                   5555544555555555..332...34456677889*****************98224567899*******..777766655 PP

                                   CG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GT CS
                          RIO1 101 veeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvs 150
                                    +      ++++++ e + kl  ++ ++H DL   N ++d+d ++iID++
  gi|15669317|ref|NP_248122.1| 427 DN-----LDIAYKIGEIVGKLH-KNDVIHNDLTTSNFIFDKD-LYIIDFG 469
                                   44.....457777777666665.99***********888777.*****95 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.2   2.9e-09   5.8e-06      43     152 ..     379     478 ..     337     496 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.9e-09
                                   HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS CS
                       Pkinase  43 kkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrD 123
                                   ++++rE ++l+ +k   i   y +  + d+  +++ y++g+  +d++e        +  +ia++i e +  lH++ +iH D
  gi|15669317|ref|NP_248122.1| 379 SRTAREARYLALVKDFGIPAPYIFDVDLDNKRIMMSYINGKLAKDVIE--------DNLDIAYKIGEIVGKLHKNDVIHND 451
                                   666777777777777777776666667777777888888776666664........55689******************** PP

                                   -SGGGEEEETTTEEEE-SGTTSEESSSSC CS
                       Pkinase 124 lKpeNiLidekgelKitDFGlakelesss 152
                                   l ++N+++d  ++l i+DFGl k  + ++
  gi|15669317|ref|NP_248122.1| 452 LTTSNFIFD--KDLYIIDFGLGKISNLDE 478
                                   *********..89********99877655 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00059       1.2      36     107 ..     380     444 ..     362     448 .. 0.80
   2 !   15.5   0.0   6.4e-06     0.013     168     235 ..     447     515 ..     445     520 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00059
                                   HHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHC CS
                           APH  36 eirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalhq 107
                                   +++re+++l+l+ + g+p+P +++ d d+  i      ++y+ g+ + +    ++  ++++++ge  ++lh 
  gi|15669317|ref|NP_248122.1| 380 RTAREARYLALVKDFGIPAPYIFDVDLDNKRIM-----MSYINGKLAKD--VIEDNLDIAYKIGEIVGKLHK 444
                                   567*********************755555555.....78888888888..566899999999999999996 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 6.4e-06
                                   EE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCH.......HHCSCHCCCHCHHHHHHHHCS-HHHH CS
                           APH 168 llHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavll.......rswtseldpeflaallrayeqeagla 235
                                   ++H+Dl + N+++d  ++    +iDf++ ++++   D av l        s  +e ++e  +++l++y    +++
  gi|15669317|ref|NP_248122.1| 447 VIHNDLTTSNFIFD--KDLY--IIDFGLGKISNLDEDKAVDLivfkkavLSTHHEKFDEIWERFLEGYK--SVYD 515
                                   69************..8886..********999999986655555555422346666666666666665..5555 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.73   1.5e+03      45      78 ..     367     401 ..     358     409 .. 0.78
   2 !   18.3   0.2     6e-07    0.0012     125     207 .]     433     510 ..     420     510 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.73
                           Kdo  45 skdlyrfk.lgrtravrEfrllkrLeeagvavpkp 78 
                                   ++d+   + + + r +rE r l   ++ g+++p++
  gi|15669317|ref|NP_248122.1| 367 YRDERLDEnIRKSRTAREARYLALVKDFGIPAPYI 401
                                   5554444447889999*******99*****99986 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 6e-07
                           Kdo 125 kavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrwrekdLarLkrsflkieltead..weal 203
                                    ++g ++ klh+ +v H dl   n+ ++++      +++iD+  ++     d ++  dL   k+ +l+ +  + d  we++
  gi|15669317|ref|NP_248122.1| 433 YKIGEIVGKLHKNDVIHNDLTTSNFIFDKD------LYIIDFGLGKISN-LDEDKAVDLIVFKKAVLSTHHEKFDeiWERF 506
                                   68*************************999......5*****9998777.99************99966655555459*** PP

                           Kdo 204 lraY 207
                                   l++Y
  gi|15669317|ref|NP_248122.1| 507 LEGY 510
                                   *999 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.2e-07     0.001       9     154 ..     341     475 ..     233     487 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.2e-07
                                   EESSEEEEEEEEETTTTSSEEEEEEEEE.STTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE--TTEBH CS
                   Pkinase_Tyr   9 eGafGkVvegtlkgekekkevkVavKtl.keeateeekeelleeakimkklkhpnivkllgvctkeepllivteyvkgGdL 88 
                                   +Ga +++ + ++       + +V++K   k+++++e+ +e ++  ++ ++ +   +vk  g+     p+++ +++ ++  +
  gi|15669317|ref|NP_248122.1| 341 KGAEADIKRDSYL------DFDVIIKERvKKGYRDERLDENIRKSRTAREARYLALVKDFGIPA---PYIFDVDLDNKRIM 412
                                   4444444444444......667777754366777777777777777777777777777777665...66666677777777 PP

                                   HHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETT CS
                   Pkinase_Tyr  89 lkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardie 154
                                    ++++ k  +k  ++d l++a+++ + +  L++++++H dl++ N + +++    i DfGL +  +
  gi|15669317|ref|NP_248122.1| 413 MSYINGK-LAKDVIEDNLDIAYKIGEIVGKLHKNDVIHNDLTTSNFIFDKD--LYIIDFGLGKISN 475
                                   7777777.8888999********************************9955..5689****88654 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.8e-05      0.19     257     333 ..     208     288 ..     190     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.8e-05
                Carbam_trans_N 257 rlkearekdedlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNiklNsalle..sglFedvwvqP..aanDsGsA 333
                                   r  +a e+ ed+  s+q++   ++ e ++ + ++++     l GGva+N  l   l +  +g   d +v+P  + +D+G+ 
  gi|15669317|ref|NP_248122.1| 208 RAYDAGERLEDICYSLQEYAFSMLTEITERALAHTNKGEVMLVGGVAANNRLREMLKAmcEGQNVDFYVPPkeFCGDNGAM 288
                                   3333333445***************************************999988765226778888***97778999975 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.58   1.2e+03      48      82 ..     412     446 ..     383     448 .. 0.76
   2 ?   10.4   1.4   0.00018      0.36     149     171 ..     449     468 ..     434     476 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.58
                                   EEE--TCEE--TTGGG.CHHHHHHHHHHHHHHTTCH CS
                Choline_kinase  48 ieefiesrtlstedlr.epeiskkiAkklaelHsle 82 
                                   +  +i+++ l ++ ++ + +i  ki++ +++lH+ +
  gi|15669317|ref|NP_248122.1| 412 MMSYINGK-LAKDVIEdNLDIAYKIGEIVGKLHKND 446
                                   55888886.45555541558999**********865 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00018
                                   -S--SGGGEEE.-CTTEEEE--G CS
                Choline_kinase 149 HnDlqegNillnkeekklvlIDF 171
                                   HnDl  +N+++   +k+l++IDF
  gi|15669317|ref|NP_248122.1| 449 HNDLTTSNFIF---DKDLYIIDF 468
                                   ***********...9******** PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.21     184     250 ..     209     273 ..     193     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                   HHHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS...EEEESGGGG-HHHHHHH.....HHHH-S-EE CS
                   BcrAD_BadFG 184 alsggekaedIlaglhraialrvialisrsggvtde..vtltGGvakneaavkelrklvkenygevkin 250
                                   a   ge  edI   l ++  + + ++ +r  + t++  v+l+GGva n    + lr+++k +  + +++
  gi|15669317|ref|NP_248122.1| 209 AYDAGERLEDICYSLQEYAFSMLTEITERALAHTNKgeVMLVGGVAAN----NRLREMLKAMCEGQNVD 273
                                   66778999999999999999999999999988887778**********....66666677766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 3163.05
//
Query:       gi|15669318|ref|NP_248123.1|  [L=310]
Description: GMP synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-39  132.0   0.0    1.3e-38  130.9   0.0    1.6  1  GMP_synt_C       GMP synthase C terminal domain
    1.1e-12   47.7   0.2    1.8e-07   30.6   0.0    2.2  2  NAD_synthase     NAD synthase
    3.7e-06   26.0   0.0    0.00035   19.5   0.0    2.1  2  tRNA_Me_trans    tRNA methyl transferase
      5e-06   26.2   0.1     0.0011   18.5   0.0    2.2  2  QueC             Queuosine biosynthesis protein QueC
    3.4e-05   23.5   0.0    7.4e-05   22.4   0.0    1.5  1  ThiI             Thiamine biosynthesis protein (ThiI)
      7e-05   22.9   0.0    0.00011   22.2   0.0    1.6  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
    0.00033   20.1   0.1    0.00054   19.4   0.1    1.3  1  Arginosuc_synth  Arginosuccinate synthase
     0.0005   19.9   0.0    0.00079   19.2   0.0    1.4  1  ATP_bind_3       PP-loop family
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.016   14.9   0.0    1.3  1  Asn_synthase     Asparagine synthase
      0.031   13.9   0.1      0.063   12.9   0.1    1.5  1  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.9   0.0   7.5e-42   1.3e-38       1      92 []     218     309 ..     218     309 .. 0.99

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 7.5e-42
                                   CCCCTTT-GGGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE CS
                    GMP_synt_C   1 eelkkaglykkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyd 81 
                                   ee+kka+l+k++wQ+fav+l++k++Gv+gd+R+y+++valR+v+s Damta+v e+p+++L++is+ri++e+++v+rvv+d
  gi|15669318|ref|NP_248123.1| 218 EEVKKANLDKDLWQYFAVVLDCKATGVKGDEREYNWIVALRMVKSLDAMTAHVPEIPFDLLKRISKRITSEIPNVARVVFD 298
                                   799****************************************************************************** PP

                                   ---TTTS-S-- CS
                    GMP_synt_C  82 itskPpatiEw 92 
                                   it+kPpatiE+
  gi|15669318|ref|NP_248123.1| 299 ITDKPPATIEF 309
                                   **********7 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   9.8e-11   1.8e-07      10      86 ..       9      89 ..       3     107 .. 0.74
   2 !   15.2   0.0     5e-06    0.0089     148     177 ..     158     187 ..     150     229 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 9.8e-11
                                  HHHHHHCTT....SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHH CS
                  NAD_synthase 10 keyvkkaga....kgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievktidikpivr 86
                                   e v++ +     +++++ lSGGvDSs++a+l+ ka+  ++ +a+ +  + + + e  e  +++ ++lg++  ++d k+   
  gi|15669318|ref|NP_248123.1|  9 DEAVEEIKQqisdRKAIIALSGGVDSSVAAVLTHKAI-GDKLTAVFVDtGLMRKGEREEVEKTFRDKLGLNLIVVDAKDRFL 89
                                  4444433221123799*********************.578899999856666667777788999********999988654 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 5e-06
                                   BETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                  NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpP 177
                                   ++p+ el+K ev+ Lakel+ P++++ ++P
  gi|15669318|ref|NP_248123.1| 158 VEPLRELYKDEVRLLAKELGLPDSIVYRQP 187
                                   68************************9998 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.9e-07   0.00035       2      37 ..      23      59 ..      22      92 .. 0.73
   2 !    4.5   0.0     0.007        12     158     186 ..     151     179 ..     138     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.9e-07
                 tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeq.gyevigvflklwee 37
                                  k ++alSgGVDSsvaa+l +++ g ++++vf+ +   
  gi|15669318|ref|NP_248123.1| 23 KAIIALSGGVDSSVAAVLTHKAiGDKLTAVFVDTGLM 59
                                  6689**************9887368888888876544 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.007
                 tRNA_Me_trans 158 kealekllfPlgeltKeevrkiAkeagla 186
                                   +  + +++ Pl el K+evr +Ake gl+
  gi|15669318|ref|NP_248123.1| 151 HGMVLEVVEPLRELYKDEVRLLAKELGLP 179
                                   556667888****************9986 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   6.4e-07    0.0011       1      62 [.      23      85 ..      23     108 .. 0.77
   2 !    5.7   0.0     0.005       8.9     139     176 ..     144     179 ..     107     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.4e-07
                                  EEEEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-TTSHHHH.HHHHHHHHT--.-EEEEE-G CS
                          QueC  1 kavvllSGGlDSttvlalakke.gkevealtfdYgqrhkkele.aakkiakelgveehkildld 62
                                  ka++ lSGG+DS+++++l +k+ g++++a+ +d g  +k e e + k++ ++lg+ +  ++d +
  gi|15669318|ref|NP_248123.1| 23 KAIIALSGGVDSSVAAVLTHKAiGDKLTAVFVDTGLMRKGEREeVEKTFRDKLGL-NLIVVDAK 85
                                  79************99998876269*********988666655156667788888.77777764 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.005
                                   HHHHHHHHHHTS--EEE-TTTT--HHHHHHHHHHTTHH CS
                          QueC 139 alnkalnlgedkkieieaPlidlsKaeivklgkelgvp 176
                                     n+al +g+   +e++ Pl +l K e+  l+kelg+p
  gi|15669318|ref|NP_248123.1| 144 HHNVALPHGM--VLEVVEPLRELYKDEVRLLAKELGLP 179
                                   4556666666..899*********************76 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   4.1e-08   7.4e-05       4     160 ..      22     177 ..      19     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.1e-08
                          ThiI   4 gkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekv 83 
                                    k++  lSgG+DS Vaa l  k  G +  +v+++  ++ + e +e+ ++  +       +l ++l+vvd k+   + l+ v
  gi|15669318|ref|NP_248123.1|  22 RKAIIALSGGVDSSVAAVLTHKAiGDKLTAVFVDTGLMRKGEREEVEKTFRD-------KLGLNLIVVDAKDRFLNALKGV 95 
                                   578899************99985599*****998666655555544444443.......3458899****99988888888 PP

                          ThiI  84 ..kekltivllkrkmlriAekvaeeegakalvtGesL.....gqVaSqtleNlrvisavvnllilrPLigldKeeiiklAk 157
                                     +e+ + ++ k  ++ + e++ae  +a+ lv+G        +q   +  +N+ +  + + l +++PL  l K+e+  lAk
  gi|15669318|ref|NP_248123.1|  96 tdPEEKRKIIGK-LFIDVFEEIAEDIKAEVLVQGTIApdwieTQGKIKSHHNVAL-PHGMVLEVVEPLRELYKDEVRLLAK 174
                                   656666777766.68899999*************643111112223333456554.3455688899999999999999999 PP

                          ThiI 158 eig 160
                                   e+g
  gi|15669318|ref|NP_248123.1| 175 ELG 177
                                   998 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   6.4e-08   0.00011       2      76 ..      24     100 ..      23     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.4e-08
                                   EEEE--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB-H.HHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-T CS
                   PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.pvvfvdtghefp.etiefvdeleeryglrlkvyepeeevaekinaekhgss 76 
                                    +++ sgG ds+V   L+ ka  ++ + vfvdtg   + e  e  + +++++gl+l+v++ ++++ ++++  + +++
  gi|15669318|ref|NP_248123.1|  24 AIIALSGGVDSSVAAVLTHKAIGDKlTAVFVDTGLMRKgEREEVEKTFRDKLGLNLIVVDAKDRFLNALKGVTDPEE 100
                                   57899*****************99549*******876637777778889999********99999888887777665 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1     3e-07   0.00054       1      65 [.      25      90 ..      25      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3e-07
               Arginosuc_synth  1 vLaysGGlDtsviikllkeklgeeviavavdvGqee.edldevkekalklgavksvvvDakeefve 65
                                  ++a sGG+D sv+  l ++ +g++  av vd G  +  + +ev++  ++   ++ +vvDak+ f +
  gi|15669318|ref|NP_248123.1| 25 IIALSGGVDSSVAAVLTHKAIGDKLTAVFVDTGLMRkGEREEVEKTFRDKLGLNLIVVDAKDRFLN 90
                                  6899*****************************75415777888877777777**********975 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.4e-07   0.00079       2     112 ..      24     137 ..      23     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.4e-07
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H...HHCTTSTCCCH CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv...akkkgknleea 79 
                                   +++A+SgG+DS +  +l++k     g kl+a+ vd gl  + ++e e+ k++ +kl+++l++ +++    ++ kg +  e+
  gi|15669318|ref|NP_248123.1|  24 AIIALSGGVDSSVAAVLTHKAI---GDKLTAVFVDTGLMRKGERE-EVEKTFRDKLGLNLIVVDAKDrflNALKGVTDPEE 100
                                   79***********999999984...559**********9877665.56688999999999999998888844445555555 PP

                                   HHH....HHHHHHHHCHHCCT.CEEE---BHHHHHHH CS
                    ATP_bind_3  80 ARe....lRYevlkealkkegievlllAhhadDqaEt 112
                                    R+    l  +v++e+++  ++evl+ +  a D +Et
  gi|15669318|ref|NP_248123.1| 101 KRKiigkLFIDVFEEIAEDIKAEVLVQGTIAPDWIET 137
                                   5551111567899999999999999999999999998 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   8.8e-06     0.016      12      51 ..      16      55 ..       5      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.8e-06
                  Asn_synthase 12 rrlradvpvGalLSGGlDSSliaalaarqsksplktFsig 51
                                  ++  +d++  + LSGG+DSS+ a l  +    +l+++ ++
  gi|15669318|ref|NP_248123.1| 16 KQQISDRKAIIALSGGVDSSVAAVLTHKAIGDKLTAVFVD 55
                                  57899***************98888877666666666555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.5e-05     0.063     124     185 ..      58     126 ..      29     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.5e-05
                        AAA_25 124 tlltadvdaleaaieevegvrlvviDplsralgg.....densnsdv..galvealeriarrtgaavll 185
                                     ++++ +++e++ ++  g+ l+v+D  +r+l++     d+++++++  + +++ +e+ia+  +a vl+
  gi|15669318|ref|NP_248123.1|  58 LMRKGEREEVEKTFRDKLGLNLIVVDAKDRFLNAlkgvtDPEEKRKIigKLFIDVFEEIAEDIKAEVLV 126
                                   336788999*******999***********99999978888888886689***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1821.52
//
Query:       gi|15669319|ref|NP_248124.1|  [L=118]
Description: hypothetical protein MJ_1132 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-29  101.8   6.1    2.6e-29  101.3   6.1    1.2  1  UPF0058   Uncharacterised protein family UPF0058
  ------ inclusion threshold ------
      0.091   12.6   0.1       0.37   10.6   0.0    1.8  2  Sortase   Sortase domain


Domain annotation for each model (and alignments):
>> UPF0058  Uncharacterised protein family UPF0058
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   6.1   2.9e-33   2.6e-29       1      86 [.       1      92 [.       1      93 [. 0.90

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 2.9e-33
                                  --HHHHHHHHHHHHHHHHHH..T....STT--TTTTHHHHHH---TT-TTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH CS
                       UPF0058  1 MhKdeLieLHqllvevkkel..e....eeevekeefkeYeeLdisPhhihrsKaehkaAifvLgnaiakalsekeessaervs 77
                                  MhK++L++LHq++v+v+ke+  +    +++  k+ fk Ye+Ldi+Phhihr K+e+kaAi++L++++a++l++++++++++++
  gi|15669319|ref|NP_248124.1|  1 MHKEQLMKLHQFFVYVVKEImdDnlenTDNECKKLFKIYEMLDIRPHHIHRLKSEQKAAILLLSACVASYLANNMDNVPKNLA 83
                                  9*****************99751333333555788************************************************ PP

                                  HHHHHHHHH CS
                       UPF0058 78 krlkelaek 86
                                  k+l+e+a+k
  gi|15669319|ref|NP_248124.1| 84 KKLEENAFK 92
                                  ******987 PP

>> Sortase  Sortase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.1e-05      0.37      62     110 ..      22      69 ..       2      78 .. 0.76
   2 ?   -0.3   0.0       0.1     9e+02      50      69 ..      88     107 ..      85     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.1e-05
                                   T-EEEEEESSSEEEEEEEEEEEEEETTHGGGGSHHTTSEEEEEEEESSS CS
                       Sortase  62 gdaivvetkkgksyvYrvfsveivtpdevsvldptpgdaiLtLiTCtpf 110
                                   +d++  ++ ++ ++ ++++++  ++p +++ l+++++ aiL L+ C   
  gi|15669319|ref|NP_248124.1|  22 DDNLENTD-NECKKLFKIYEMLDIRPHHIHRLKSEQKAAILLLSACVAS 69 
                                   55555566.666679********************9**********943 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.1
                                   TSTTGGGGGGHTT-EEEEEE CS
                       Sortase  50 gavFsdLkklekgdaivvet 69 
                                   ++ F++L+  +k+  i+ e+
  gi|15669319|ref|NP_248124.1|  88 ENAFKHLNSCKKNIIILEEN 107
                                   56899999998876666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1117  (0.0623013); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 824.42
//
Query:       gi|15669320|ref|NP_248125.1|  [L=421]
Description: hypothetical protein MJ_1133 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-88  296.2   0.0    4.2e-88  295.9   0.0    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.9   0.0   2.3e-92   4.2e-88      21     405 ..      20     379 ..      11     380 .. 0.90

  Alignments for each domain:
  == domain 1  score: 295.9 bits;  conditional E-value: 2.3e-92
                                   THHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHHHHHS..----EE--GCG-GG CS
                          UbiD  21 lEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklaellepkppippkvvesekapc 101
                                   + ++ i+++    +g+ +  ++v  +  +f+v++nl+ +re + +++++++ e+++  + +++e++++ + k       + 
  gi|15669320|ref|NP_248125.1|  20 FGVSRILKKY---DGKPVYIKDV--N--GFEVVGNLC-SRETLSKIFNVKK-EDFIFFMLDAMEKEKEGKLKIN----NKL 87 
                                   5555555554...599*******..5..5******97.6899******864.8888888899997664444433....345 PP

                                   GSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEEEETTEEEE--TTTHCHHHHHHHHHHCC CS
                          UbiD 102 qeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqvldknklglhwqihkggaehlrkakkkg 182
                                   +e+ ++ +   ++++ P++ ++++D+G+yit+g+v++ d + g  nl+i+R+ v+ ++ l+++++++++ ++ ++ka+k++
  gi|15669320|ref|NP_248125.1|  88 KEKYIV-EIPENIKNWPIPIYYEKDAGAYITSGVVVVYDKDYG-YNLSIHRILVK-DDYLVIRMVEQRHLHFLYNKALKEK 165
                                   544433.35679***************************8866.9**********.688********************** PP

                                   T--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SSSSSEEETT-SEEEEEEEECCEEEECTTTC-TT CS
                          UbiD 183 geplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcetvdlevpadAEivleGeidpgetapEGPfgdht 263
                                      l+va++iGv+Pa++la+++++  + +El+fa+al g ++ +++ + ++l vp +AE+++eG i p e  +EGPf+d+t
  gi|15669320|ref|NP_248125.1| 166 -GYLDVAIVIGVHPAVLLAGSTSADITFDELKFAAALLGGEIGVFELD-NGLLVP-EAEFIIEGKILP-EVDDEGPFVDIT 242
                                   .59******************************************995.69****.************.579********* PP

                                   SCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHHHCHHHHHHHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHH CS
                          UbiD 264 GyysevrdefpvfkVtaithRkdpiypttvvgkppeedallgkalealflpllkkqvpevkdvhlpeeggfhllavvsikk 344
                                   G+y+ vr+ +p++k+++ +++++pi++++++g   e+++l+g++ e+ +l+ ++++vp+vk++ l+e g+++l+avv+i+k
  gi|15669320|ref|NP_248125.1| 243 GTYDIVRK-QPIIKIEKLYRKEKPIFHALLPGGI-EHKTLMGMPQEPRILKGVRNTVPTVKNIVLTEGGCCWLHAVVQIEK 321
                                   ***99988.6*******************99998.********************************************** PP

                                   HTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHHHHHHC--CCCCEEEECCC CS
                          UbiD 345 rypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevlwaiatrvdpdrDlviiegt 405
                                   r++g+ k+++ a++a ++  sl K+vivvD+d++++d+++v++aiatrv+ d+D+vii+g+
  gi|15669320|ref|NP_248125.1| 322 RTEGDGKNAILAAFASHP--SL-KHVIVVDDDINIFDINDVEYAIATRVQGDKDIVIISGA 379
                                   ******************..99.**********************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2712.30
//
Query:       gi|15669321|ref|NP_248126.1|  [L=226]
Description: hypothetical protein MJ_1134 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-14   54.9   9.6    1.2e-13   51.5   9.6    2.1  1  SMC_ScpA       Segregation and condensation protein ScpA
     0.0019   18.1  10.1     0.0031   17.4  10.1    1.3  1  PIN_8          PIN like domain
     0.0096   16.2  16.7      0.014   15.7  16.2    1.5  1  PcfK           PcfK-like protein
  ------ inclusion threshold ------
      0.047   14.2   4.2      0.083   13.3   4.2    1.5  1  Goodbye        fungal STAND N-terminal Goodbye domain
      0.052   13.8   0.1      0.081   13.2   0.1    1.2  1  DUF2267        Uncharacterized conserved protein (DUF2267)
      0.053   12.8   3.2       0.11   11.8   1.7    1.9  2  LCIB_C_CA      Limiting CO2-inducible proteins B/C beta carbo
      0.079   11.1   8.7      0.096   10.8   8.7    1.1  1  HSP70          Hsp70 protein
       0.36   10.8   6.2       0.66    9.9   6.2    1.4  1  Protocadherin  Protocadherin
       0.55   10.5   3.9       0.87    9.9   3.9    1.3  1  PTPRCAP        Protein tyrosine phosphatase receptor type C-a
       0.88    9.2  21.3          1    9.0  21.3    1.1  1  AAA_15         AAA ATPase domain
          2    7.6   4.4        3.4    6.8   4.4    1.3  1  TMPIT          TMPIT-like protein


Domain annotation for each model (and alignments):
>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   9.6   7.4e-17   1.2e-13       3     239 ..      20     222 ..      19     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 7.4e-17
                                   HHHHHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      SMC_ScpA   3 iakeldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqveeeedeeleleelrdkLiarLl 83 
                                    +k+l+++dv++a++ d +++ ik l +k ++  s++ +++a  l+++K++ L++  +veeeed +  ++      i+  +
  gi|15669321|ref|NP_248126.1|  20 EKKNLNPWDVNIAEIADYYIQKIKEL-KKFDIRLSADVILVAGILLRMKSEALYDECKVEEEEDYDYCDDYYDYDDIEEKP 99 
                                   6799**********************.***************************************998888777788888 PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...HHHHHH CS
                      SMC_ScpA  84 eYrkykeeaklfkeleaerlksfskarsdleefikeveevavkieksvfklieafnkllkrakivalaekqiseleisiee 164
                                     +  k+e ++  + +    ks  k++++++e+ik++e++  k+ ks            + +k++ ++e  i+el    e+
  gi|15669321|ref|NP_248126.1| 100 -KKGKKKEKEDKDKNK----KS--KKPVTVDELIKTIEKELNKVKKS---------RKNREKKTNEVEEI-IEEL--IEED 161
                                   .222333333333333....44..999*******************9.........33344555666674.6655..5667 PP

                                   HHHHHH...............HHH..TS-EEGGGSSTT...--HHHHHHHHHHHHHHHHTT-EEEEESSTTS-EEEE CS
                      SMC_ScpA 165 qleellaqleqflqarlkevLldl..rswvdlseLladnkledkkelvgvFlAlLeLiknqavaleQeeflddLqvs 239
                                      +++a           e+L dl   + + ++      k + +++ v  F+  L L ++ + +l Qe+ +++L ++
  gi|15669321|ref|NP_248126.1| 162 DISDIIA-----------ELLDDLmkEGIIVYQ-----EKFKTREDRVRYFIPSLYLANDGKAELIQEKLFGELIIK 222
                                   7888887...........566666322244343.....356668999999999999999999999999999999886 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4  10.1   1.9e-06    0.0031      59     187 ..      92     221 ..      78     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.9e-06
                         PIN_8  59 yedlekeleklkkaaekkleealkkwakkkaldteelrkelkkqleelkeel...kaeleelkksskadkeedpilkklee 136
                                   y+d+e++ +k kk+++   e+++k+++ kk ++++el k ++k+l+++k++    +++++e+++ +++ +eed+i++ ++e
  gi|15669321|ref|NP_248126.1|  92 YDDIEEKPKKGKKKEK---EDKDKNKKSKKPVTVDELIKTIEKELNKVKKSRknrEKKTNEVEEIIEELIEEDDISDIIAE 169
                                   6677766666666666...5677777777778899***************9977777788888888999999********* PP

                         PIN_8 137 llegkigealskeeleelvkegekRyenkiPPGykDekkdede...ekagDlll 187
                                   ll++   e +    ++e +k+ e+R+++ iP  y  ++ + +    + +g l++
  gi|15669321|ref|NP_248126.1| 170 LLDDLMKEGII--VYQEKFKTREDRVRYFIPSLYLANDGKAELiqeKLFGELII 221
                                   ****9999886..578999***************86654443344466777776 PP

>> PcfK  PcfK-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7  16.2   8.7e-06     0.014      34     123 ..      30     146 ..      21     157 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.7e-06
                          PcfK  34 tleeclkYileeakklaesgc........................aavsddevyewaveYfeeddievtk....eeekaek 86 
                                   +++e+ +Y ++++k+l++  +                        + v+++e y+   +Y++ ddie++     +   +ek
  gi|15669321|ref|NP_248126.1|  30 NIAEIADYYIQKIKELKKFDIrlsadvilvagillrmksealydeCKVEEEEDYDYCDDYYDYDDIEEKPkkgkK---KEK 107
                                   788899999999999888888889999999999999999999999*********************766643221...333 PP

                          PcfK  87 radavskkqk..ekkkakkkkp........eeekkkkkkkekkekqg 123
                                   + + ++kk+k           +        e+e +k+kk++k+ +++
  gi|15669321|ref|NP_248126.1| 108 EDKDKNKKSKkpV--------TvdeliktiEKELNKVKKSRKNREKK 146
                                   3333333333232........02333334433333333333333322 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   4.2   5.1e-05     0.083      17      62 ..     112     157 ..     100     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-05
                       Goodbye  17 kdealkelssvedllkqieaekdkfeefrekkeklkealkkilspi 62 
                                   k+++ k++ +v++l+k ie+e +k +++r+++ek ++ +++i++ +
  gi|15669321|ref|NP_248126.1| 112 KNKKSKKPVTVDELIKTIEKELNKVKKSRKNREKKTNEVEEIIEEL 157
                                   467899999******************************9999765 PP

>> DUF2267  Uncharacterized conserved protein (DUF2267)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     5e-05     0.081      63     119 ..     112     174 ..      99     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5e-05
                                   S...-----SHHHHHHHHHHTS........E...HHHHHHHHHHHHHHHS-HHHHHHHHHTS-HHH CS
                       DUF2267  63 e...pgkrfdreeflervaeelg...vdped...aeqaaraVfaalkealsegeiedvaaqLPkdl 119
                                   +    +k+++ +e+++ +++el+       +   +e+ +  V + ++e ++e++i d+ a+L +dl
  gi|15669321|ref|NP_248126.1| 112 KnkkSKKPVTVDELIKTIEKELNkvkK---SrknREKKTNEVEEIIEELIEEDDISDIIAELLDDL 174
                                   13335669**************85434...3466**************************997776 PP

>> LCIB_C_CA  Limiting CO2-inducible proteins B/C beta carbonyic anhydrases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.24   3.9e+02     185     210 ..      46      70 ..      10      85 .. 0.67
   2 ?   11.8   1.7   6.6e-05      0.11     123     199 ..     105     181 ..      97     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.24
                                   HHTGGS-TT--EEEEEEEEEE--TTS CS
                     LCIB_C_CA 185 ekttvdekkaevavvgGiqinspkel 210
                                   +k  + + +a+v++v+Gi + +++e 
  gi|15669321|ref|NP_248126.1|  46 KK-FDIRLSADVILVAGILLRMKSEA 70 
                                   22.34667889999999998887664 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.6e-05
                                   H---------------TTTHHHHHHHHHHGGGHHHHHH-SSHHHHHHHHHHHHHH.HHHHHHHHHTGGS-TT--EEEE CS
                     LCIB_C_CA 123 kkeglekeskepgaldelDaeqsiikqrllkrleeiekaeddlveltkvayeaik.ddlekliekttvdekkaevavv 199
                                   k+++ + + k++++  + D  +++i+++l+k +++ ++ e++  e+ ++++e i+ dd++++i++   d+ ++e ++v
  gi|15669321|ref|NP_248126.1| 105 KEKEDKDKNKKSKKPVTVDELIKTIEKELNKVKKSRKNREKKTNEVEEIIEELIEeDDISDIIAELL-DDLMKEGIIV 181
                                   445556666677777899999*************999***************986268******965.5555554444 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   8.7   5.9e-05     0.096     490     580 ..      77     167 ..      27     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.9e-05
                                   CEEEEEEECCSS.SBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHH..HHHHHHHHHH CS
                         HSP70 490 keeeitieaseg.lseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaek..ekvesaieeL 567
                                   +eee+  +  ++  + ++ie+  k+ ++ ++edk k+++  +  +++el++++ek+l++ ++  ++ ek  ++ve+ ieeL
  gi|15669321|ref|NP_248126.1|  77 VEEEEDYDYCDDyYDYDDIEEKPKKGKKKEKEDKDKNKKSKKPVTVDELIKTIEKELNKVKKSRKNREKktNEVEEIIEEL 157
                                   44444444444446789999999***********************************99544443333346677777776 PP

                                   HCHTTSSCHHHHH CS
                         HSP70 568 keeleeeekeeie 580
                                    ee   +++++i 
  gi|15669321|ref|NP_248126.1| 158 IEE---DDISDII 167
                                   666...4433333 PP

>> Protocadherin  Protocadherin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.2    0.0004      0.66       7     129 ..      14     146 ..       9     165 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0004
                 Protocadherin   7 lveelvarsletpldqdiagdpdve.slskdrlkiliavlaGvvtvilvil...ivvlvRycrqkaksgykagk..Keeed 81 
                                   +++e +++   +p d +ia+ +d+  ++ k+  k  i   a v+ v  ++l     +l  +c+ ++ + y       + +d
  gi|15669321|ref|NP_248126.1|  14 MIKEGIEKKNLNPWDVNIAEIADYYiQKIKELKKFDIRLSADVILVAGILLrmkSEALYDECKVEEEEDYDYCDdyYDYDD 94 
                                   788889999999999999999999944555555555555444433322222000223444444444444443332222222 PP

                 Protocadherin  82 fv.tPkqenkeekgkkkkkkkkkkka...ksekslllnlvtveeskrddvee 129
                                       Pk+++k+ek+ k+k kk+kk++   ++ k++  +l  v++s+++ +++
  gi|15669321|ref|NP_248126.1|  95 IEeKPKKGKKKEKEDKDKNKKSKKPVtvdELIKTIEKELNKVKKSRKNREKK 146
                                   2113445555555544444444444444555555555666666666544444 PP

>> PTPRCAP  Protein tyrosine phosphatase receptor type C-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.9   0.00053      0.87      34     105 ..      64     142 ..      43     174 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00053
                       PTPRCAP  34 lraraedgeedeeeEdqed.........eedeeedsedleggeeeaesqeeeqaeseeageeqaleka.eeakdeekaske 104
                                   lr ++e   ++ ++E++ed          +d ee+    ++g++++++ ++++++s+++   + l k+ e+  ++ k+s++
  gi|15669321|ref|NP_248126.1|  64 LRMKSEALYDECKVEEEEDydycddyydYDDIEEK---PKKGKKKEKEDKDKNKKSKKPVTVDELIKTiEKELNKVKKSRK 141
                                   45555555555566666665544332224444443...3333333333344444444444444444445444444444433 PP

                       PTPRCAP 105 d 105
                                   +
  gi|15669321|ref|NP_248126.1| 142 N 142
                                   3 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  21.3   0.00064         1      77     235 ..      32     190 ..      12     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00064
                        AAA_15  77 ikIdvefaek.ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeekle 156
                                    +I+ ++++k ++ k++   l  + +  a +ll  k+++l++  k+++ +++  ++ d+ ++++++++k +   +k+ek++
  gi|15669321|ref|NP_248126.1|  32 AEIADYYIQKiKELKKFDIRLSADVILVAGILLRMKSEALYDECKVEEEEDY--DYCDDYYDYDDIEEKPKKG-KKKEKED 109
                                   46777776777677777777888899999999999******99999999987..6666666666666665555.5566666 PP

                        AAA_15 157 kekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl... 234
                                   k+k++ +++  ++++lik++e+ l+k ++  ++ +++  +++ i ++   +d+ s+ + +ll+ l+++ +   +qek+   
  gi|15669321|ref|NP_248126.1| 110 KDKNKKSKKPVTVDELIKTIEKELNKVKKSRKNREKKTNEVEEIIEELIEEDDISDIIAELLDDLMKEGII-VYQEKFktr 189
                                   77777778889999999999999999998889999999999999999999999999999999999888877.467766554 PP

                        AAA_15 235 e 235
                                   e
  gi|15669321|ref|NP_248126.1| 190 E 190
                                   1 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.4    0.0021       3.4      10      82 ..      91     164 ..      82     181 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0021
                         TMPIT  10 efkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelkerkkvl 82 
                                   +++++ee+ k+ k+k +e  k ++k sk+  +  + +k ++++l+k+kks k  e++ +evee+ eel e++ + 
  gi|15669321|ref|NP_248126.1|  91 DYDDIEEKPKKGKKKEKE-DKDKNKKSKKPVTVDELIKTIEKELNKVKKSRKnrEKKTNEVEEIIEELIEEDDIS 164
                                   567788888776666555.45555556666677888999999999999885533555556666666666555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3497  (0.195047); expected 358.6 (0.02)
Passed bias filter:                     1066  (0.0594567); expected 358.6 (0.02)
Passed Vit filter:                       166  (0.00925874); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 1529.07
//
Query:       gi|15669322|ref|NP_248127.1|  [L=152]
Description: putative molybdenum cofactor biosynthesis protein MoaC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-50  170.9   3.7    1.8e-50  170.6   3.7    1.0  1  MoaC      MoaC family
  ------ inclusion threshold ------
      0.056   13.3   0.1       0.11   12.3   0.1    1.5  1  DUF3297   Protein of unknown function (DUF3297)


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.6   3.7     2e-54   1.8e-50       1     134 [.      12     150 ..      12     151 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.6 bits;  conditional E-value: 2e-54
                                   E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEETTTT CS
                          MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkveveleleeeee 81 
                                   mvd+s+ke+++r++vAeg +kl++et++like+k+kkG+vl++a+iagi+a+Kkt elip+cHplp+t+v+v++e+   e+
  gi|15669322|ref|NP_248127.1|  12 MVDISKKEDVERICVAEGYIKLKPETIKLIKEQKIKKGNVLTTAQIAGILAVKKTYELIPMCHPLPITSVNVDFEVF--ED 90 
                                   9*************************************************************************987..79 PP

                                   EEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEE CS
                          MoaC  82 sveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKs 134
                                   +++  ++vkt+ ktG+emEALt+vs+a+lt++DmvK+++k+       ++i  +r+veK 
  gi|15669322|ref|NP_248127.1|  91 KIKAICSVKTTYKTGIEMEALTGVSIALLTIWDMVKSAEKDedgqyktAEIFGIRVVEKI 150
                                   ***************************************99999999999*******995 PP

>> DUF3297  Protein of unknown function (DUF3297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.3e-05      0.11      23      49 ..       9      36 ..       4      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                       DUF3297 23 Girfkg.kektnveEYcvsEgWvrvaag 49
                                  G+++ + ++k++ve  cv+Eg+++++  
  gi|15669322|ref|NP_248127.1|  9 GVKMVDiSKKEDVERICVAEGYIKLKPE 36
                                  677666256889************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 993.99
//
Query:       gi|15669323|ref|NP_248128.1|  [L=541]
Description: hypothetical protein MJ_1136 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-28   96.2   1.2    2.3e-27   94.8   0.4    2.1  2  Radical_SAM_C    Radical_SAM C-terminal domain
    1.6e-23   83.9   1.6    4.2e-23   82.5   0.1    2.4  2  Radical_SAM      Radical SAM superfamily
    2.8e-07   30.8   0.3    8.5e-07   29.2   0.1    2.0  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    6.6e-07   29.3   0.1    1.5e-06   28.1   0.1    1.5  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0014   19.0   0.7     0.0031   17.9   0.7    1.6  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.081   13.0   0.0       0.75    9.8   0.0    2.2  2  RHD_dimer        Rel homology dimerisation domain


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.76   2.3e+03      49      62 ..      42      55 ..      33      70 .. 0.78
   2 !   94.8   0.4   7.7e-31   2.3e-27       1      81 [.     304     384 ..     304     385 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.76
                 Radical_SAM_C 49 irvhRltgdipkel 62
                                   r+hR++  +p+++
  gi|15669323|ref|NP_248128.1| 42 LRIHRIGIGHPSNS 55
                                  699***99888765 PP

  == domain 2  score: 94.8 bits;  conditional E-value: 7.7e-31
                 Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlreliekrlk 81 
                                   pd+vK+yp+lvi+gTeL+e++k+geykp+ +ee+++++  +++++p+++r  R+++dip   ++ g++++nl+el+ k+++
  gi|15669323|ref|NP_248128.1| 304 PDMVKIYPCLVIEGTELYEMWKRGEYKPYREEEAIEIISYAKSIMPKWVRTSRIQRDIPATVIVDGVKKSNLGELVYKYME 384
                                   8******************************************************************************97 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.1   1.4e-26   4.2e-23       5     159 ..      94     288 ..      90     296 .. 0.94
   2 ?   -1.3   0.0      0.81   2.4e+03      34      55 ..     495     517 ..     487     527 .. 0.76

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 1.4e-26
                                   SEESS-.-TTTSCCTT....................HHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTH CS
                                   xxxxxx.xxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   5 rgCnlr.CsfCarpet....................vrregrgrslsveeileevkelk.aekgvkevilgggepllypdf 63 
                                   + C+++ C+fC+ +                         + +++  ++ +i+++ k ++  +k ++ +i+gg  p  + ++
  gi|15669323|ref|NP_248128.1|  94 EKCPHGkCIFCPGGVGsvfgdvpqsytgrepatmrgLMFNFDPYLQTKARIEQLEKVGHpTNK-IELIIMGGTFPARDIEY 173
                                   6788888****************************9999999999999999999999987777.99999999999999999 PP

                                   HHHHHHHHHTC.................CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCT CS
                                   xxxxxxxxxxx.................xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  64 vellerlakla.................vpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrg 124
                                   +++  +++  a                  ++ r++  + +t+pd   e+ +  +l+lg +rv+lg++++ +e +l+ ++rg
  gi|15669323|ref|NP_248128.1| 174 QDWFIKRCLDAmngvdassleeaqkineTAEHRCVALCIETRPDycgEKEINQMLKLGATRVELGVQTIYNE-ILEFCKRG 253
                                   99999999999*************************************************************.******** PP

                                   SHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 125 htfeevlealeklreagikrvvdrivglpGendee 159
                                   ht+e++++a+++l+++g+k++++ ++g+pG  +e+
  gi|15669323|ref|NP_248128.1| 254 HTVEDTIKATQLLKDSGLKVSYHLMPGMPGSDMEM 288
                                   ******************************99997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.81
                                   HHHHHHHHH.HHTTSEEEEEESS CS
                                   xxxxxxxxx.xxxxxxxxxxxxx RF
                   Radical_SAM  34 ileevkelk.aekgvkevilggg 55 
                                   +lee+++++ +e g+k +++++g
  gi|15669323|ref|NP_248128.1| 495 LLEEAERIAkEEFGKKKILVTSG 517
                                   67788888777777777777766 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       4.8   1.4e+04      74      94 ..     372     392 ..     370     402 .. 0.71
   2 !   29.2   0.1   2.8e-10   8.5e-07      42     117 .]     439     529 ..     409     529 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.8
                                   TSSHHHHHHHHHHHHHHHTTE CS
                Acetyltransf_1  74 gkGlGsaLlealeerareegi 94 
                                   +++lG + ++++e++  +  +
  gi|15669323|ref|NP_248128.1| 372 KSNLGELVYKYMEKHGIKCKC 392
                                   578888888888887776655 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 2.8e-10
                                   TEEEEEEEEEEEET.....TSTTEEEEEEEEE............SGGGTTSSHHHHHHHHHHHHHHHT.TESEEEEEEETT CS
                Acetyltransf_1  42 geliGfisllkipd.....ekggvayieslaV............speyrgkGlGsaLlealeeraree.gikkivlaveed 104
                                   + li+f++l+  +       + +++ +++l+V              ++++kG+G++Lle++e++a+ee g kki +    +
  gi|15669323|ref|NP_248128.1| 439 DILIAFLRLREPYKpfrkeIDDNTMLVRQLHVcgqekpltkdlkEITWQHKGYGRKLLEEAERIAKEEfGKKKILV---TS 516
                                   447788877777776666644456666666668888888888766678********************999**855...58 PP

                                   EHHHHHHHHHTTE CS
                Acetyltransf_1 105 ndaairlYeklGF 117
                                     + +++Y+klG+
  gi|15669323|ref|NP_248128.1| 517 GIGVREYYRKLGY 529
                                   999*****88**8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   5.1e-10   1.5e-06      63     110 ..     486     533 ..     484     537 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 5.1e-10
               Acetyltransf_10  63 yrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkavg 110
                                   ++++G+g++Lle++e+ a+++ +k+++ v +    +++Y+klG+++vg
  gi|15669323|ref|NP_248128.1| 486 WQHKGYGRKLLEEAERIAKEEFGKKKILVTSGIGVREYYRKLGYERVG 533
                                   89****************9888888********************997 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.7     1e-06    0.0031      36      76 .]     486     531 ..     481     531 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1e-06
                                   GTTSSHHHHHHHH.....TT.SEEEEEEEEETHH..HHHHHHHHTTEEE CS
                Acetyltransf_7  36 yrgkGiGraLlea.....ae.kgiileqlelnae..kaikfYeklGFee 76 
                                   ++ kG+Gr+Lle      +e  g + +   l+++    +++Y+klG+e+
  gi|15669323|ref|NP_248128.1| 486 WQHKGYGRKLLEEaeriaKEeFGKK-K--ILVTSgiGVREYYRKLGYER 531
                                   89*********95354431144411.1..22222334466*******95 PP

>> RHD_dimer  Rel homology dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.29   8.6e+02      42      70 ..     191     220 ..     150     234 .. 0.78
   2 ?    9.8   0.0   0.00025      0.75       4      39 ..     415     449 ..     412     474 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.29
                     RHD_dimer  42 evWeaeaefskedvhkqvaivfkt.PpYrd 70 
                                   +  e++ +++++  h+ va++++t P Y+ 
  gi|15669323|ref|NP_248128.1| 191 SSLEEAQKINETAEHRCVALCIETrPDYCG 220
                                   55678889999999******9998788874 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00025
                     RHD_dimer   4 rlsktsgsveGgeelillcekvqkddikvrFleeee 39 
                                   +l++++  ++Gg+e++l  e v++ di + Fl+ +e
  gi|15669323|ref|NP_248128.1| 415 KLCREEYEASGGTEIFLSYEDVKN-DILIAFLRLRE 449
                                   67889999**************99.******98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3663.39
//
Query:       gi|15669324|ref|NP_248129.1|  [L=191]
Description: hypothetical protein MJ_1137 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.72    9.5  10.1       0.17   11.5   3.1    2.1  2  PRA1       PRA1 family protein
        2.1    7.9   6.6       0.61    9.7   2.0    2.1  2  CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like


Domain annotation for each model (and alignments):
>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.1   1.9e-05      0.17      43     124 ..      11     100 ..       4     103 .. 0.85
   2 ?    2.4   0.6     0.012   1.1e+02      46      81 ..     127     167 ..     111     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.9e-05
                          PRA1  43 livvllvlllslltnplslivllllvlawlflyflr........seplvlfgrelsdrvvlivllvvsvlllfltgavlvl 115
                                   l++ +l+ + +l+++   +i l++ +++ ++lyfl         s+ l l++re +d    i++++  ++ l+l++ + ++
  gi|15669324|ref|NP_248129.1|  11 LVFGVLIAFSVLIFKKQLIIPLIVSIVIGICLYFLCkryyipivSDLLNLCKREKEDGKGAIYFAIGMLISLILIDDIKAV 91 
                                   5666888999999999999999999999999999443677778677777899999999*********************** PP

                          PRA1 116 lwalligll 124
                                   ++++l+ ++
  gi|15669324|ref|NP_248129.1|  92 FFGILVFAV 100
                                   ****99875 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.012
                          PRA1  46 vllvlllslltnplslivllllvlawlflyflr.....sep 81 
                                   +++++ +sl++ p+    +++++l+ +f+ f+      +++
  gi|15669324|ref|NP_248129.1| 127 LAFFISASLILYPFYGTYGIFVALISAFIEFVSkkiriDDN 167
                                   56677788888888888888888888888775423334444 PP

>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.0   6.8e-05      0.61     101     137 ..      11      48 ..       2      84 .. 0.90
   2 ?    0.3   0.5     0.053   4.7e+02     142     164 ..      88     110 ..      57     140 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 6.8e-05
                     CPP1-like 101 avflvlavltlvapaes.vpalllalglgasiyflnrK 137
                                   +vf+vl++++++  +++ +++l++++ +g+++yfl ++
  gi|15669324|ref|NP_248129.1|  11 LVFGVLIAFSVLIFKKQlIIPLIVSIVIGICLYFLCKR 48 
                                   6899999999988888889****************987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.053
                     CPP1-like 142 gravlltlvgLvvGlllGsllas 164
                                   ++av +++++++vG  l++++  
  gi|15669324|ref|NP_248129.1|  88 IKAVFFGILVFAVGDSLATIIGI 110
                                   57888888888888777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1290.41
//
Query:       gi|15669325|ref|NP_248130.1|  [L=174]
Description: hypothetical protein MJ_1138 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-13   49.8   0.1    5.9e-13   49.2   0.1    1.3  1  LEA_2         Late embryogenesis abundant protein
     0.0069   16.6   0.8        0.3   11.3   0.0    2.4  2  DUF3712       Protein of unknown function (DUF3712)
  ------ inclusion threshold ------
      0.014   14.9   0.1       0.02   14.4   0.1    1.2  1  Vac7          Vacuolar segregation subunit 7
      0.014   15.4   0.0       0.05   13.6   0.0    1.9  2  PepSY_2       Peptidase propeptide and YPEB domain
      0.024   15.1   0.1       0.14   12.7   0.0    2.0  2  OsmC          OsmC-like protein
      0.048   13.9   0.7       0.13   12.5   0.1    1.8  2  Kindlin_2_N   Kindlin-2 N-terminal domain
       0.17   12.2   4.2       0.25   11.6   4.2    1.3  1  Calycin_like  Calycin-like beta-barrel domain
       0.18   12.0   6.1      0.046   13.9   2.6    1.7  2  Spore_GerAC   Spore germination B3/ GerAC like, C-terminal


Domain annotation for each model (and alignments):
>> LEA_2  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1   2.7e-16   5.9e-13       2      99 ..      50     143 ..      49     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.7e-16
                                   EEEEESSSS-EEEEEEEEEEE..ESSSEEEEEEECE-EEESSSCEEEEEEEEEEEHHHHHHHHHHHH..HCCSEEEEEEEE CS
                         LEA_2   2 lrvrNPNsfgvrydgleldls..yngqrlasgtspqgfsqpargtttlevpvsvsaddlarelrallagevgleleytlrg 80 
                                   + v+NPN++g+ +d++++d++  ++g+++  g+ +q+    + g tt+++pv++s+++l++ + ++     +++++++++g
  gi|15669325|ref|NP_248130.1|  50 VLVDNPNPIGISIDKISFDIYalVGGDKIYLGHGEQSNIKITSGNTTFTLPVTISNKKLVEVALKEK----STKIPIEIKG 126
                                   78*******************66699999987777776666666677**************999997....9999****** PP

                                   EEE.EEETTTSCEEEEEEE CS
                         LEA_2  81 rlkvlgkpilgsvtvpvkv 99 
                                    + v  ++++++v++p++ 
  gi|15669325|ref|NP_248130.1| 127 DIAV--NLFITKVNIPIDI 143
                                   9997..78889***99986 PP

>> DUF3712  Protein of unknown function (DUF3712)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00014       0.3      96     125 .]      40      69 ..      19      69 .. 0.85
   2 ?    3.6   0.3     0.034        77      35      83 ..     106     163 ..      80     173 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                       DUF3712  96 pedginllatvtlpNpsvvtielGnvtldl 125
                                   ++d+++++++v + Np+++ i+++++++d+
  gi|15669325|ref|NP_248130.1|  40 DADNTKIEIQVLVDNPNPIGISIDKISFDI 69 
                                   3799***********************996 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.034
                       DUF3712  35 tkflealvlsee..fklsvkGk.t.tlklgglkfkgvtldKtvtlkG......lnslkg 83 
                                   +k++e ++++++  +++++kG+ + +l + ++ +  +++  ++ + +      ln+l++
  gi|15669325|ref|NP_248130.1| 106 KKLVEVALKEKStkIPIEIKGDiAvNLFITKVNIP-IDIQQEIDVSAiakeevLNQLNN 163
                                   56777777777655788888985346666777777.88888888876555555444333 PP

>> Vac7  Vacuolar segregation subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   8.9e-06      0.02     307     371 ..       9      71 ..       3      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.9e-06
                          Vac7 307 llllvvsgaigflfattkpLedvevvkiqnvlaseqelmlDlevkAvNpNvvavtvdeldvniFA 371
                                   ll + v  a+gf    ++p  +v  +kiq+v a ++++  +++v   NpN + +++d++  +i+A
  gi|15669325|ref|NP_248130.1|   9 LLAFAVCLAVGFSGCLEQPKIEVVGQKIQKVDADNTKI--EIQVLVDNPNPIGISIDKISFDIYA 71 
                                   34445566899999999**999999********99998..5666668*****************9 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.3e-05      0.05      38      80 ..      28      69 ..      25      72 .. 0.90
   2 ?   -1.9   0.0       1.5   3.4e+03      49      80 ..      88     120 ..      83     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                       PepSY_2 38 kleaqGykvkkievddggcyEvegldkdGkkveikldpatgev 80
                                  k+e  G k++k+++ d+ + E+++l ++ + + i +d+ + ++
  gi|15669325|ref|NP_248130.1| 28 KIEVVGQKIQKVDA-DNTKIEIQVLVDNPNPIGISIDKISFDI 69
                                  78999*********.6669******************998877 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                       PepSY_2  49 ievddggc.yEvegldkdGkkveikldpatgev 80 
                                   i++++g+  + + ++  + k ve+ l  +++++
  gi|15669325|ref|NP_248130.1|  88 IKITSGNTtFTLPVTISNKKLVEVALKEKSTKI 120
                                   666666655666677778888888888888776 PP

>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     6e-05      0.14      10      62 ..       6      70 ..       4      78 .. 0.66
   2 ?   -0.1   0.1      0.61   1.4e+03      30      66 ..     114     146 ..     102     164 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6e-05
                                  HHHHHHHHHHHHHHHHHHTCCCT---..SCE........EEEEEEEEECCECT..CEEEEEEEEE CS
                          OsmC 10 elllaalasCfaitlravakkkgikl..edl........eveveaerdpegak..giteirlkve 62
                                   lll a+a C+a++++  +++ +i++  +++        ++e+++  d+  +    i++i ++++
  gi|15669325|ref|NP_248130.1|  6 KLLLLAFAVCLAVGFSGCLEQPKIEVvgQKIqkvdadntKIEIQVLVDNPNPIgiSIDKISFDIY 70
                                  59**********************99775556344444444444433322222455666666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.61
                                   CCT---SCEEEEEEEEEECCECTCEEEEEEEEEEE-S CS
                          OsmC  30 kkgikledleveveaerdpegakgiteirlkvevkip 66 
                                   k+  k +++ +e++++ + +  + it++++ ++++ +
  gi|15669325|ref|NP_248130.1| 114 KE--KSTKIPIEIKGDIAVN-LF-ITKVNIPIDIQQE 146
                                   44..5566777777777754.44.7777766666433 PP

>> Kindlin_2_N  Kindlin-2 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.85   1.9e+03      18      39 ..      43      64 ..      30      71 .. 0.63
   2 ?   12.5   0.1   5.6e-05      0.13       3      50 ..      94     147 ..      92     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.85
                   Kindlin_2_N 18 kkevelkirvkgdlhiGgvmlk 39
                                  + ++e++++v     iG  + k
  gi|15669325|ref|NP_248130.1| 43 NTKIEIQVLVDNPNPIGISIDK 64
                                  2456777777777777765555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.6e-05
                   Kindlin_2_N   3 dgtWeLkitvtdleik......kevelkirvkgdlhiGgvmlklvekldikkdw 50 
                                   ++t++L +t+ +++        k+++++i +kgd+ +   + k+   +di+++ 
  gi|15669325|ref|NP_248130.1|  94 NTTFTLPVTISNKKLVevalkeKSTKIPIEIKGDIAVNLFITKVNIPIDIQQEI 147
                                   578888888888776567777799*********************99*999975 PP

>> Calycin_like  Calycin-like beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.2   0.00011      0.25      12     119 ..      30     149 ..      25     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                   EETTEE---B-S....-EEEEEE-SSS-EEEEEE-GG.G........------EEEEEEEEE-SS...SSSBEEEEEEEEE CS
                  Calycin_like  12 svggeespsdad....akvtitknedgtvnlsLknfsfg........elplGditvdnvkvtkeg...gsyttfsgsqklt 77 
                                   +v+g++ +++++     ++++  ++ + + +s+++ sf         ++ lG  + +n+k+t+++   +  +t+s+++ ++
  gi|15669325|ref|NP_248130.1|  30 EVVGQKIQKVDAdntkIEIQVLVDNPNPIGISIDKISFDiyalvggdKIYLGHGEQSNIKITSGNttfTLPVTISNKKLVE 110
                                   55666555555556345555556666889999999886666777779*****************94432225889999999 PP

                                   -TT--E...EEEEEEEEEETTEEEEEEEEE..ETT-SS-EEE CS
                  Calycin_like  78 lagggdaeeatvslsGtisgkklnltitikvkdgamtmpikv 119
                                   +a ++++++++++++G+i+ + + ++++i +     +++i+v
  gi|15669325|ref|NP_248130.1| 111 VALKEKSTKIPIEIKGDIAVNLFITKVNIPID---IQQEIDV 149
                                   999999999*********99999999999884...5555554 PP

>> Spore_GerAC  Spore germination B3/ GerAC like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.53   1.2e+03      47      49 ..      48      50 ..      24      92 .. 0.52
   2 ?   13.9   2.6   2.1e-05     0.046      31      95 ..      93     172 ..      70     174 .] 0.71

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.53
                                  .EE CS
                   Spore_GerAC 47 vsv 49
                                  ++v
  gi|15669325|ref|NP_248130.1| 48 IQV 50
                                  222 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.1e-05
                                   ---EEEEE.ETTEEEE.EEEEEEE.EEEEEEE-SS........SEEEEEEEEEEEEEE....-...----.-----HHHH CS
                   Spore_GerAC  31 ksgvitiplpkgkdekvsveissskskikvkieng........kpsfdikiklegdie....e...skknlleeeelkel 95 
                                   +++++t+p++  +++ v+v  +++++ki ++i+++        k+++ i+i+ e d++    e   ++ n l+ ++++++
  gi|15669325|ref|NP_248130.1|  93 GNTTFTLPVTISNKKLVEVALKEKSTKIPIEIKGDiavnlfitKVNIPIDIQQEIDVSaiakEevlNQLNNLNPNQIQSI 172
                                   24455555555555559**********************99998888888888888775544245544555666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1182.33
//
Query:       gi|15669326|ref|NP_248131.1|  [L=232]
Description: hypothetical protein MJ_1139 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-45  155.5   0.5    1.6e-45  155.2   0.5    1.0  1  RNase_P_p30   RNase P subunit p30
  ------ inclusion threshold ------
      0.035   13.6   0.0        1.1    8.7   0.0    2.2  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.2   0.5   1.8e-49   1.6e-45      16     214 ..      11     203 ..       3     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: 155.2 bits;  conditional E-value: 1.8e-49
                                   ..HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H..HHHHHHHHH--EEEE CS
                   RNase_P_p30  16 srtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpskl.qrlskvrqkfdllav 95 
                                   ++ ik l+el+++g ++ +  + e +k++ +         +   e+++lk++s+v++ ++++++l  +++k+r+k++++ +
  gi|15669326|ref|NP_248131.1|  11 EEDIKLLKELKWNGFVFYQYDD-EFSKDRYEEV-------KAIAESYKLKVYSGVKIKTESSKQLrDKVKKFRNKCHIILI 83 
                                   2479*********888877777.6666666666.......45778899****************99*************** PP

                                   E--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEESHHHHHS-HHHHHHHHHHHHHHHHHHHH..- CS
                   RNase_P_p30  96 rPttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEinyspllrdsglaRrnfisnarkllrltrg..k 174
                                   +++  k++raa+e +dvDi+s++  +r+++g++h+++r+A++++va+E+n+++ll+++g++R++++  +r++l+l+++   
  gi|15669326|ref|NP_248131.1|  84 EGGVLKINRAAVELHDVDILSTPELGRKDSGIDHVLARLASNHRVAIELNFKTLLNKDGYERARTLLFFRNNLKLAKKfdV 164
                                   ********************************************************************************* PP

                                   -EEEE--BSSGGG---HHHHHHHHHHHT--HHHHHHTTTH CS
                   RNase_P_p30 175 gvviSSgAesplelRnpydiinLlktlGLeedrakeavse 214
                                   +vviS +Ae++++++npyd++++l+tl +e+ +ak+++++
  gi|15669326|ref|NP_248131.1| 165 PVVISTDAENKYQIKNPYDLRAFLNTL-VEPLYAKKIMET 203
                                   ***************************.8*******9986 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0    0.0069        62      16      46 ..      29      55 ..      14      80 .. 0.72
   2 ?    8.7   0.0   0.00012       1.1      11      88 ..      94     168 ..      88     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0069
                                  CCTCSHHHHCHHHHHHHHHHHHHHTTSEEEE CS
                  AP_endonuc_2 16 grdlvpvselsdeelrelrkaldelglrias 46
                                   +d+      s+++ +e++++++++ l++ s
  gi|15669326|ref|NP_248131.1| 29 QYDDEF----SKDRYEEVKAIAESYKLKVYS 55
                                  222222....5789*************9765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00012
                                   EEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEE CS
                  AP_endonuc_2  11 gvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllv 88 
                                   +vEl+  d  +  el  +d++++++ ++l++++     l++ t  + ++  er+    + + ++++ ++la+++++p+++
  gi|15669326|ref|NP_248131.1|  94 AVELHDVDILSTPELgrKDSGIDHVLARLASNHRVAIELNFKTLLNKDGY-ERA----RTLLFFRNNLKLAKKFDVPVVI 168
                                   789999999999999999*************9999777777666666554.355....55*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1517.41
//
Query:       gi|15669327|ref|NP_248132.1|  [L=257]
Description: hypothetical protein MJ_1140 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-50  171.9   0.5    1.6e-50  171.4   0.5    1.2  1  2-ph_phosp  2-phosphosulpholactate phosphatase
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.39   10.7   0.0    1.7  2  DUF4743     Domain of unknown function (DUF4743)


Domain annotation for each model (and alignments):
>> 2-ph_phosp  2-phosphosulpholactate phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.4   0.5   1.8e-54   1.6e-50       9     225 ..      43     248 ..      36     249 .. 0.91

  Alignments for each domain:
  == domain 1  score: 171.4 bits;  conditional E-value: 1.8e-54
                                   E-GTTTEEEEE-TTTHHHHHHHHHHTT-SEEEEESSHHHHHHTCCH.HGCCEEEEE-BTTB--TTSSB-S-GGGH..HHHH CS
                    2-ph_phosp   9 eeklkdvvvviDvLRAtstivtaLanGakavipvssveealelakklpeekvllaGErgglkiegfdlgnSPley..tkek 87 
                                   e+k  +v++v+DvLRA++ti+t+L+  +++v+++ s +      kk   e+++ +GEr+g+kiegfd+gnSP+e+  +k+ 
  gi|15669327|ref|NP_248132.1|  43 EYKCGNVAIVVDVLRASTTITTLLSF-IDEVYITTSTS------KK---ENAIYIGERKGRKIEGFDFGNSPTEIlaNKDI 113
                                   557889*******************9.99999887654......32...689**********************9654555 PP

                                   HT.....TSEEEEE-CCHHHHHHHCCTSSEEEEE-STTHHHHHHHHHHHTSSEEEEE--BTTB--HHHHHHHHHHHHHHHH CS
                    2-ph_phosp  88 vk.....gktvvltTtNGTralekaasakrvligsllNakavaeklkelakevvivcaGtegefsleDtlcAgalveelek 163
                                   +k     g++v+ltTtNGTr+l+  + a++++ig+++Nak va+++++ ++ v +v  ++e++f+++D++  g+++++l  
  gi|15669327|ref|NP_248132.1| 114 IKeryenGEKVILTTTNGTRVLKSLD-AEHIFIGAIVNAKYVAKAVEDFED-VSLVPCHRENNFAIDDFIGCGVIAKYLNG 192
                                   55667779***************999.8********************998.***************************99 PP

                                   HS.SEE-HHHHHHHHHHHC-STHHHHHHHSHHHHHHHHTT-HHHHHHHTSTSS----EEEET CS
                    2-ph_phosp 164 eeelelsDaalaalalyeskedllealkksshgkrLkelgleeDleycaqldlldvVpvlke 225
                                       e+++  +aal+l ++  d+++++ +ss++++Lk+lg+e+D+++++ ++ +d V ++k+
  gi|15669327|ref|NP_248132.1| 193 ----EFDEFIKAALELTKH--DWMSLILNSSSAENLKNLGYEKDVTFAILENSIDAVGIYKK 248
                                   ....799999******998..**************************************986 PP

>> DUF4743  Domain of unknown function (DUF4743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.4e-05      0.39      45     109 ..      27      87 ..      14      93 .. 0.79
   2 ?   -2.6   0.0      0.56     5e+03      35      46 ..     153     164 ..     131     176 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.4e-05
                                   TTEEE-SS.EEEE-TT--SHHHHHHHHHHHHHHHHHTT...SS----S-EEEE-SSTTS---EEE CS
                       DUF4743  45 dvFevsekeaveLapslktyeeRtaaveevleelreegsfvalkgwRdElYeVrasfsdppllkl 109
                                   ++ +v++  +++L++++++y+    +v+ v++ lr+  ++++l    dE Y  +++ +++  +++
  gi|15669327|ref|NP_248132.1|  27 KIKMVDS--MITLCNRFTEYK--CGNVAIVVDVLRASTTITTLLSFIDEVYITTSTSKKENAIYI 87 
                                   3333333..7*******7775..789999**********************99988887776665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.56
                                   HHHHHHCT-TTT CS
                       DUF4743  35 dvaeklrkfpdv 46 
                                    va+++++f+dv
  gi|15669327|ref|NP_248132.1| 153 YVAKAVEDFEDV 164
                                   244455555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1884.48
//
Query:       gi|15669328|ref|NP_248133.1|  [L=214]
Description: hypothetical protein MJ_1141 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-48  164.1   0.1    2.1e-48  163.7   0.1    1.1  1  DUF116    Protein of unknown function DUF116
  ------ inclusion threshold ------
       0.12   11.7   1.0       0.17   11.2   1.0    1.2  1  MtrE      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> DUF116  Protein of unknown function DUF116
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.7   0.1   2.4e-52   2.1e-48       6     153 ..      65     209 ..      60     211 .. 0.94

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 2.4e-52
                        DUF116   6 lgrllgldkdklkrvfievnnklvrkkfkkvppekrllllPhClraadCpaklteeglnCkrCgkCkigelkklaeklgyk 86 
                                   ++ l+g ++d++ rv ie+ nk+++++fkk  ++kr+l+lPhClr+++Cpaklt++g +C  C++C++ge++k+ae+ gyk
  gi|15669328|ref|NP_248133.1|  65 IFLLIG-TEDTFYRVGIEFYNKYYEDRFKK--AKKRVLILPHCLRDTKCPAKLTPKGVECIFCNRCRVGEIIKVAEEKGYK 142
                                   555556.5667779****************..9************************************************ PP

                        DUF116  87 vyivtggtlarkiikekkpkaiigvaCerdltegiqdlkklpvigqlvllekggCinTkvdveelee 153
                                   vyiv+g+t++++i+ke+kp+a++gvaC+rdl  g+++l++ +++ q+ +l ++gCinT vdv+el +
  gi|15669328|ref|NP_248133.1| 143 VYIVPGSTFLKRILKEEKPEAVFGVACNRDLFYGMNMLSRKGIPSQGQPLLRDGCINTLVDVDELIT 209
                                   ***************************************************************9975 PP

>> MtrE  Tetrahydromethanopterin S-methyltransferase, subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   1.8e-05      0.17     118     168 ..      10      63 ..       7      95 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.8e-05
                          MtrE 118 yldvlkshlgaivahafiavfaivvlsylmtlvlkhpf...plpllaliwGitv 168
                                   +l ++   + ai a afi+++ i+++sy++    k +f   +l l+  ++ i +
  gi|15669328|ref|NP_248133.1|  10 FLQLVGMITIAIFALAFISFILILIISYILLKKNKLIFpslALFLMDNLYSILL 63 
                                   7888889999*******************9988876662114555666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1322.93
//
Query:       gi|15669329|ref|NP_248134.1|  [L=349]
Description: arsenical pump-driving ATPase ArsA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   5.2e-125  416.7   1.3   6.1e-125  416.4   1.3    1.0  1  ArsA_ATPase  Anion-transporting ATPase
    7.3e-12   45.5   0.1    7.9e-11   42.1   0.1    2.9  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    3.4e-11   43.4   0.0    8.3e-11   42.1   0.0    1.8  1  AAA_31       AAA domain
    2.3e-09   37.0   5.6     0.0001   21.9   2.7    3.1  2  ParA         NUBPL iron-transfer P-loop NTPase
    1.6e-06   27.8   0.0    8.8e-06   25.4   0.0    2.0  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    1.1e-05   25.2   2.7      0.001   18.8   0.7    2.7  3  SRP54        SRP54-type protein, GTPase domain
      8e-05   22.2   0.1    0.00021   20.8   0.1    1.7  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    0.00052   19.1   0.3     0.0019   17.3   0.1    1.8  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0025   17.2   0.5       0.39   10.0   0.3    2.2  2  CTP_synth_N  CTP synthase N-terminus
  ------ inclusion threshold ------
       0.03   14.3   0.3      0.081   12.9   0.3    1.8  1  ResIII       Type III restriction enzyme, res subunit
      0.034   13.6   0.2      0.099   12.1   0.1    1.8  2  PhoH         PhoH-like protein
      0.041   13.0   0.4      0.091   11.9   0.0    1.8  2  DUF815       Protein of unknown function (DUF815)
      0.042   13.0   0.7       0.11   11.7   0.7    1.6  1  NB-ARC       NB-ARC domain
      0.043   13.6   0.5       0.11   12.2   0.1    1.9  2  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.043   13.6   0.0      0.087   12.6   0.0    1.5  1  IstB_IS21    IstB-like ATP binding protein
       0.12   11.6   0.1       0.27   10.5   0.1    1.7  1  Zeta_toxin   Zeta toxin
        0.2   11.2   0.3       0.73    9.4   0.3    1.9  1  AAA_25       AAA domain


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.4   1.3  5.8e-128  6.1e-125       1     304 [.      26     333 ..      26     334 .. 0.97

  Alignments for each domain:
  == domain 1  score: 416.4 bits;  conditional E-value: 5.8e-128
                                   -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEET..SSEEEEE--HH..HHHHHHH CS
                   ArsA_ATPase   1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvk..eNLsavEidpe..veleeak 77 
                                   +k+i++gGKGGVGKtt+saat+v+l+ekg kv+++stDPAhsl+D+f+q++g+eptkvk  +NL++vEidp+  +e++++k
  gi|15669329|ref|NP_248134.1|  26 TKYIMFGGKGGVGKTTMSAATGVYLAEKGLKVVIVSTDPAHSLRDIFEQEFGHEPTKVKgyDNLYVVEIDPQkaMEEYKEK 106
                                   699*********************************************************************666666666 PP

                                   CCHHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHHHHHH CS
                   ArsA_ATPase  78 qevqkeeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevleklleklvkl 158
                                    ++q ee+++lg e+led+l++++ s PG+de ++f+ +lky++++e+dvv++DtaPTGhtlr+l +pev++k+++kl+kl
  gi|15669329|ref|NP_248134.1| 107 LKAQIEENPFLG-EMLEDQLEMAALS-PGTDESAAFDVFLKYMDSNEFDVVIFDTAPTGHTLRFLGMPEVMDKYMTKLIKL 185
                                   677777888888.*************.****************************************************** PP

                                   HHHHHHHHHHHCCCSHCHHHHHH....HHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT- CS
                   ArsA_ATPase 159 keklsplakqlvkllglggvsie....ealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLkkygi 235
                                   ++++s ++k+++kll++gg++++    ++leele++ke+i ++++il+dpert+frlVvipE++s+ E+eRa+k+L+kygi
  gi|15669329|ref|NP_248134.1| 186 RKQMSGFMKMMKKLLPFGGKDEDidydKMLEELEKMKERIVRARNILSDPERTAFRLVVIPEEMSILESERAMKALQKYGI 266
                                   *******************99988899****************************************************** PP

                                   EEEEEEEEEE-TTCSSSTSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHHHHHHHHHC CS
                   ArsA_ATPase 236 kvdavivNkllpeeeqenCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekleklselly 304
                                    +davivN+l+pe++q  C+f++ar+++q k+l++i+e+f d++++++pll++E++G+e+l++++++ly
  gi|15669329|ref|NP_248134.1| 267 PIDAVIVNQLIPEDVQ--CDFCRARRELQLKRLEMIKEKFGDKVIAYVPLLRTEAKGIETLKQIAKILY 333
                                   ****************..**************************************************9 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.1   7.5e-14   7.9e-11       3     116 ..      30     281 ..      28     323 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 7.5e-14
                                   EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH...HTTEB-HHHH.......................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx.......................... RF
                          CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai...leglendiep.......................... 54 
                                   + ++kGGvGKTt++a+ +++la++gl+V+ v +Dp  ++  i    +g e+ + +                          
  gi|15669329|ref|NP_248134.1|  30 MFGGKGGVGKTTMSAATGVYLAEKGLKVVIVSTDPAHSLRDIfeqEFGHEPTKVKgydnlyvveidpqkameeykeklkaq 110
                                   679*********************************99999655555555555559999********************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|15669329|ref|NP_248134.1| 111 ieenpflgemledqlemaalspgtdesaafdvflkymdsnefdvvifdtaptghtlrflgmpevmdkymtkliklrkqmsg 191
                                   *********************************************************999999999999999999999999 PP

                                   ..................CCHCCCHHHHHHCHCHHHH.........EEEEEEEEES.S...-TTCHHHHHHHHHHCTS-EE CS
                                   ..................xxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ..................dlkrllellealgkkkall.......lkiagvvlnrvd.geneetllkealeelkqrygvpvl 109
                                                     d +++le le+++++   +           +  +  v  +e+++ l++e   + +q+yg+p+ 
  gi|15669329|ref|NP_248134.1| 192 fmkmmkkllpfggkdediDYDKMLEELEKMKERIVRArnilsdpE---RTAFRLVViPEEMSILESERAMKALQKYGIPID 269
                                   999999999999999999666666666666555444444554332...333333220222355555555555666655554 PP

                                   E.....EEE--C CS
                                   x.....xxxxxx RF
                          CbiA 110 g.....viprde 116
                                   +     +ip+d+
  gi|15669329|ref|NP_248134.1| 270 AvivnqLIPEDV 281
                                   444444555555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   7.8e-14   8.3e-11       9     129 ..      33     163 ..      26     200 .. 0.69

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 7.8e-14
                        AAA_31   9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt....glgiekne......iektlyevli.eeknikeaii..kt 76 
                                    KGGvGKTT s + ++ la++g kv +v  Dp  ++      ++g    +         +ly v i  +k ++e+    k+
  gi|15669329|ref|NP_248134.1|  33 GKGGVGKTTMSAATGVYLAEKGLKVVIVSTDPAHSLRDifeqEFG----HeptkvkGYDNLYVVEIdPQKAMEEYKEklKA 109
                                   6*********************************99984443333....22222325568888877556666666552233 PP

                        AAA_31  77 kvenldlipssidLaeaeielvelekkeeilkellekvkde.YDyiiiDcpPsL 129
                                   ++e++ ++   ++ +     l   +++  +++ +l+ ++++ +D++i+D+ P+ 
  gi|15669329|ref|NP_248134.1| 110 QIEENPFLGEMLEDQLEMAALSPGTDESAAFDVFLKYMDSNeFDVVIFDTAPTG 163
                                   344444443333322222234444455677899999997655**********85 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   2.7   9.5e-08    0.0001       6      41 ..      28      63 ..      25     165 .. 0.69
   2 !   13.7   0.0   3.1e-05     0.032     141     229 ..     242     332 ..     229     348 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 9.5e-08
                          ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaD 41
                                  +++  gKGGVGK+t+++   + La+kglkv ++ +D
  gi|15669329|ref|NP_248134.1| 28 YIMFGGKGGVGKTTMSAATGVYLAEKGLKVVIVSTD 63
                                  56678***************************9998 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.1e-05
                          ParA 141 iVttpqevaladvkkaiemfkkvkvkvlGvveNm...sgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeirea 218
                                   +V  p+e+++ + ++a++ ++k  +++ +v+ N    + ++c+ c+ + e ++ +  e + e++g ++++ +pl  + ++ 
  gi|15669329|ref|NP_248134.1| 242 LVVIPEEMSILESERAMKALQKYGIPIDAVIVNQlipEDVQCDFCRARRE-LQLKRLEMIKEKFGDKVIAYVPLLRTEAKG 321
                                   7889****************************982334466666666655.5778999****************9999999 PP

                          ParA 219 sdegkplvlke 229
                                   +++ k++++  
  gi|15669329|ref|NP_248134.1| 322 IETLKQIAKIL 332
                                   99888754332 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   8.3e-09   8.8e-06       8     125 ..      32     161 ..      27     180 .. 0.73
   2 ?   -0.3   0.0      0.56   5.9e+02      80     125 ..     198     247 ..     178     268 .. 0.62

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.3e-09
                      CBP_BcsQ   8 GvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqr....egwaraeldgapwrqaaleyapgldll.. 82 
                                   G +GGvG+t+++aa +  l e g +v+++ + p+  Lr  F++++ ++    +g+ +  + + + ++a+ ey+++l+    
  gi|15669329|ref|NP_248134.1|  32 GGKGGVGKTTMSAATGVYLAEKGLKVVIVSTDPAHSLRDIFEQEFGHEptkvKGYDNLYVVEIDPQKAMEEYKEKLKAQie 112
                                   669**********************************99999998775222267777777777778888888877754223 PP

                      CBP_BcsQ  83 ..PfGelnveekenlqqlaekaealla...alkelk.eqyrwillDlpa 125
                                     Pf     e++ ++++l + +++ +a   +lk +  ++++ +++D   
  gi|15669329|ref|NP_248134.1| 113 enPFLGEMLEDQLEMAALSPGTDESAAfdvFLKYMDsNEFDVVIFDTAP 161
                                   3399666667777777766665554440005555558899999999754 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.56
                      CBP_BcsQ  80 dllPfGelnve.eken.lqqlaekaeallaalkelk..eqyrwillDlpa 125
                                   +llPfG   ++ +  + l++l++ +e++ +a + l+  e+  + l+ +p+
  gi|15669329|ref|NP_248134.1| 198 KLLPFGGKDEDiDYDKmLEELEKMKERIVRARNILSdpERTAFRLVVIPE 247
                                   699**976544122221555666677777777767666444444444454 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.7   9.5e-07     0.001       2      38 ..      27      63 ..      26      67 .. 0.95
   2 ?    5.3   0.0     0.013        13      63      92 ..     131     160 ..     119     187 .. 0.80
   3 ?   -2.8   0.0       3.9   4.1e+03     100     118 ..     213     231 ..     210     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.5e-07
                                  EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  ++i++ G  G+GKTt  a    +l ++g kv++v++D
  gi|15669329|ref|NP_248134.1| 27 KYIMFGGKGGVGKTTMSAATGVYLAEKGLKVVIVSTD 63
                                  689*********************************9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.013
                                   STTSCHHHHHHHHHHHHHHTTSSEEEEEE- CS
                         SRP54  63 keeadpaavakeavekakeekidvvlvDTa 92 
                                   + ++d+ a     ++ ++++++dvv+ DTa
  gi|15669329|ref|NP_248134.1| 131 SPGTDESAAFDVFLKYMDSNEFDVVIFDTA 160
                                   4556667777777899999**********9 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.9
                                   HHHHHHHHHHHHHSSSEEE CS
                         SRP54 100 elmeelkkikkvvkpdevl 118
                                   +++eel+k+k+ +  ++++
  gi|15669329|ref|NP_248134.1| 213 KMLEELEKMKERIVRARNI 231
                                   6899999999988666555 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1     2e-07   0.00021       3      40 ..      29      66 ..      27      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2e-07
                     Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPka 40
                                  i + GkGG+Gk+t s+ +   lae+g kv+iv  DP +
  gi|15669329|ref|NP_248134.1| 29 IMFGGKGGVGKTTMSAATGVYLAEKGLKVVIVSTDPAH 66
                                  66789*******************************76 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   1.8e-06    0.0019      24      69 ..      21      66 ..       6      69 .. 0.85
   2 ?   -1.7   0.0       1.1   1.2e+03     114     133 ..     144     163 ..     136     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
                                  GG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                          MeaB 24 akaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                  +k   ++ + + G  G+Gk t+  a g+ l+++G +v +++ DP+ 
  gi|15669329|ref|NP_248134.1| 21 EKKDGTKYIMFGGKGGVGKTTMSAATGVYLAEKGLKVVIVSTDPAH 66
                                  455557788899********************************85 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                                   HHHHHHTT-SEEEEEEESST CS
                          MeaB 114 vllleaaGfDvvlietvGvG 133
                                   ++ +++  fDvv+ +t   G
  gi|15669329|ref|NP_248134.1| 144 LKYMDSNEFDVVIFDTAPTG 163
                                   56789999******998776 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.3   0.00037      0.39       2      40 ..      28      64 ..      27      69 .. 0.87
   2 !    5.4   0.0    0.0095        10     108     210 ..     164     274 ..     160     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                                  EEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE- CS
                   CTP_synth_N  2 yilvtGGvvSglGkGiiaaslgallksrglkvtlikiDP 40
                                  yi+  G    g+Gk  ++a++g  l ++glkv ++  DP
  gi|15669329|ref|NP_248134.1| 28 YIMFGG--KGGVGKTTMSAATGVYLAEKGLKVVIVSTDP 64
                                  665533..579***************************9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0095
                                   ----C..CCHHHHHHHHHHHHHH.HC....T-SEEEEEE-S-TTSGGGHHHHHHHHHHHHHH-TTTEEEE..EEEE--B-T CS
                   CTP_synth_N 108 ktvqv..iphvtdeikeriekvakkv....eadvviveigGtvgdieslpfleairqlklelgkenvlli..hvtlvpvlk 180
                                   +t+++  +p+v+d+  +++ k++k++    ++   ++  gG   di+   +le ++++k ++ + + +l     t    + 
  gi|15669329|ref|NP_248134.1| 164 HTLRFlgMPEVMDKYMTKLIKLRKQMsgfmKMMKKLLPFGGKDEDIDYDKMLEELEKMKERIVRARNILSdpERTAFRLVV 244
                                   555553358999998888888887753444455568899********************9976655444312344555555 PP

                                   TTSSB-HHHHHHHHHHHHHHT---SEEEEE CS
                   CTP_synth_N 181 aagelktkptqhsvkelrslGiqpdiivcr 210
                                     +e+     ++++k+l+++Gi  d +++ 
  gi|15669329|ref|NP_248134.1| 245 IPEEMSILESERAMKALQKYGIPIDAVIVN 274
                                   668999999999**********99999875 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   7.7e-05     0.081      16     140 ..      17     159 ..       2     187 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.7e-05
                                   T......TTSEEE.EEESTTSTHHHHHHHHHHHH-S.....-EEEEE..SSHHHHHHHHHHG.......GGGTGG...... CS
                        ResIII  16 leklkskrdkrgl.ikmaTGtGKTlvaaklierllkkgkeekflflv..prkslleqtleef.......kkflseayke.. 84 
                                   ++kl++k+ ++++ +    G+GKT ++a++  +l++kg   k++++   p  sl +  ++ef       k           
  gi|15669329|ref|NP_248134.1|  17 EKKLEKKDGTKYImFGGKGGVGKTTMSAATGVYLAEKGL--KVVIVStdPAHSLRDIFEQEFgheptkvK--------Gyd 87 
                                   3566655555555499********************977..66665422344566666666644332220........122 PP

                                   ..GEEEESSS-B--.......-SEEEEEHHHHHHTH........................HHHTTT-SEEEEET CS
                        ResIII  85 ..igkkvsgdkkkakekdstnkkilvttiqsldadseee................eeeseellrdrfdviiiDE 140
                                        +++ +k ++  + +++ k  +++   l + +e +                +   + +++++fdv+i+D 
  gi|15669329|ref|NP_248134.1|  88 nlYVVEIDPQKAME--EYKEKLKAQIEENPFLGEMLEDQlemaalspgtdesaafDVFLKYMDSNEFDVVIFDT 159
                                   23222233333333..2233333333333333333322244445555666666667788888888888888885 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   9.4e-05     0.099      20      80 ..      27      91 ..      14     115 .. 0.80
   2 ?   -1.9   0.0       1.7   1.8e+03      41      59 ..     171     189 ..     142     241 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.4e-05
                                  SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T....T----SS---------TTT CS
                          PhoH 20 divfaiGpaGtGKtylavalavealkkkkvkriiltrpavea....geelGflpgdleekvdpyl 80
                                  + ++  G+ G GKt ++ a++v + +k+    i+ t pa +     ++e G  p++++ + + y+
  gi|15669329|ref|NP_248134.1| 27 KYIMFGGKGGVGKTTMSAATGVYLAEKGLKVVIVSTDPAHSLrdifEQEFGHEPTKVKGYDNLYV 91
                                  4667789******************9999999999999998777788888888887776666665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                                   HHHHHTTS-SEEEEEE-S- CS
                          PhoH  41 vealkkkkvkriiltrpav 59 
                                   +  +++k ++++i +r ++
  gi|15669329|ref|NP_248134.1| 171 MPEVMDKYMTKLIKLRKQM 189
                                   3444444444444444333 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.6e-05     0.091      33     101 ..       5      74 ..       1     113 [. 0.82
   2 ?   -2.1   0.1       1.6   1.7e+03      86     129 ..     219     262 ..     211     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.6e-05
                        DUF815  33 idkqkealventeqfleglpannvLLw.GarGtGKSslvkallneyaeegLrlievekedlkelpklvel 101
                                   i++  ++l   te+ le++   + +++ G+ G+GK ++  a+   +ae+gL+++ v+ +  ++l +++e+
  gi|15669329|ref|NP_248134.1|   5 IKDSINSLRGITEKKLEKKDGTKYIMFgGKGGVGKTTMSAATGVYLAEKGLKVVIVSTDPAHSLRDIFEQ 74 
                                   666667777778888887777666665156789*********************************9975 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                        DUF815  86 evekedlkelpklvellrerperfilfvDDLsFeeeeeeyksLk 129
                                   e  ke++    ++++  ++++ r+++    +s  e+e+++k+L+
  gi|15669329|ref|NP_248134.1| 219 EKMKERIVRARNILSDPERTAFRLVVIPEEMSILESERAMKALQ 262
                                   55677777888888888888899999999999999999999886 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7    0.0001      0.11      10      38 ..      18      44 ..      10      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                                  HHHHCTTTSCSEEEEEEESTTSSHHHHHH CS
                        NB-ARC 10 ekLlekdelqslvvalvGmgGvGKttlak 38
                                  +kL +kd+ +   + + G+gGvGKtt+++
  gi|15669329|ref|NP_248134.1| 18 KKLEKKDGTK--YIMFGGKGGVGKTTMSA 44
                                  6888899999..9999**********976 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00011      0.11       3      36 ..      33      66 ..      31      74 .. 0.94
   2 ?   -2.1   0.1       2.5   2.6e+03      29      49 ..      91     113 ..      82     159 .. 0.44

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                    ATP_bind_1  3 GpaGsGKttfvgalseilelrgrsvavvNLDPAa 36
                                  G  G+GKtt+  a   +l ++g +v +v  DPA 
  gi|15669329|ref|NP_248134.1| 33 GKGGVGKTTMSAATGVYLAEKGLKVVIVSTDPAH 66
                                  788*****************************96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.5
                    ATP_bind_1  29 vvNLDPAaeelpYe..aavdire 49 
                                   vv +DP     +Y+   +  i+e
  gi|15669329|ref|NP_248134.1|  91 VVEIDPQKAMEEYKekLKAQIEE 113
                                   44445433333332002223333 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.2e-05     0.087      49      84 ..      28      63 ..       8      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.2e-05
                     IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlfvrve 84
                                   i++ G  GvGK+ +++a gv  +++gl+v+ v+++
  gi|15669329|ref|NP_248134.1| 28 YIMFGGKGGVGKTTMSAATGVYLAEKGLKVVIVSTD 63
                                  46778999**********************988864 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00025      0.27      12      53 ..      22      64 ..      13     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                    Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDd 53
                                  +++  k i+ gG  G GK+++++++  +l+ ++ +vv +++D 
  gi|15669329|ref|NP_248134.1| 22 KKDGTKYIMFGGKGGVGKTTMSAATGVYLAeKGLKVVIVSTDP 64
                                  4466688999*******************96777888888885 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.3   0.00069      0.73      36     108 ..      29     111 ..      24     188 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00069
                        AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal....rddarllvld..... 107
                                   +++ G +g+GKtt+    ++ +a+          +  kV++vs++ +   lr  +++ + +     +  ++l+v+      
  gi|15669329|ref|NP_248134.1|  29 IMFGGKGGVGKTTMSAATGVYLAE----------KGLKVVIVSTDPAH-SLRDIFEQEFGHEptkvKGYDNLYVVEidpqk 98 
                                   6889**********9999999984..........34578888875554.67766666554433444444455555544444 PP

                        AAA_25 108 ............l 108
                                               +
  gi|15669329|ref|NP_248134.1|  99 ameeykeklkaqI 111
                                   4444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2431.63
//
Query:       gi|15669330|ref|NP_248135.1|  [L=361]
Description: hypothetical protein MJ_1143 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-66  221.8   5.5    6.4e-66  221.8   5.5    1.7  2  MS_channel     Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.014   15.7   3.3      0.032   14.5   3.3    1.7  1  DUF3382        Domain of unknown function (DUF3382)
       0.02   14.9   0.3       0.02   14.9   0.3    3.1  4  TM_helix       Conserved TM helix
      0.082   12.4   0.1       0.12   11.8   0.1    1.1  1  AflR           Aflatoxin regulatory protein
       0.93    9.4  13.4      0.043   13.7   5.6    2.1  2  7TMR-DISM_7TM  7TM diverse intracellular signalling
        1.2    9.8   2.9          4    8.1   0.0    2.6  3  Ctr            Ctr copper transporter family
        2.1    8.0   8.3       0.24   11.1   3.5    1.7  2  Tetraspanin    Tetraspanin family


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.3       1.2     3e+03       9      31 ..      67      89 ..      63      91 .. 0.84
   2 !  221.8   5.5   2.5e-69   6.4e-66       1     206 []     142     348 ..     142     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                                  HHHHHHHHHHTTT--SCCHHHHH CS
                    MS_channel  9 ivvgilivlsllgvnvsallavl 31
                                  ++++i++  +++gvn+ +ll +l
  gi|15669330|ref|NP_248135.1| 67 VAIAIILSGFYFGVNFLYLLPSL 89
                                  67899999999999999998775 PP

  == domain 2  score: 221.8 bits;  conditional E-value: 2.5e-69
                                   ..HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-S CS
                    MS_channel   1 kkilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedigl 81 
                                   kk+++++++vvg+l++ls+lg+++++lla+lG++gla++la+++l+snl+aG+i+l++kpfkiG+++++++ +G+Vedig+
  gi|15669330|ref|NP_248135.1| 142 KKLVRLVVWVVGLLLILSNLGYDIKTLLAGLGIGGLAVALASQNLVSNLIAGLIILTDKPFKIGNWITFSGGSGIVEDIGI 222
                                   5899***************************************************************************** PP

                                   SEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEE CS
                    MS_channel  82 rttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvlde 162
                                   r+tkir+ d++i+++Pns+l+++ i+N+   ++++++ ++igvty+++v+k++k+ e++k++l+e+p+v+ d++ +v+++e
  gi|15669330|ref|NP_248135.1| 223 RSTKIRATDNSIIVVPNSKLIDEIIQNVPS-KNKWKVSTTIGVTYNTPVEKIRKAEEIIKNILLEHPNVE-DEPITVYFKE 301
                                   ******************************.***************************************.69999***** PP

                                   E-SSSEEEEEEEEEET......TTHHHHHHHHHHHHHHHHHHHT--- CS
                    MS_channel 163 fgdsslnfevrvfvkt...vvpeeylsvqseinlrikkileeegiei 206
                                   fgd+sln++v +++k+   + +++y s+ +e+nl+ik++++++gie+
  gi|15669330|ref|NP_248135.1| 302 FGDWSLNIQVVYYIKNsryNGYQKYISTINEVNLKIKEEFDRKGIEF 348
                                   ****************9999999**********************96 PP

>> DUF3382  Domain of unknown function (DUF3382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   3.3   1.2e-05     0.032      11      95 ..      68     154 ..      60     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                       DUF3382  11 llalvlfvpilGl..qleldgtrlvleprwglvaiavavvfvgqLlrplllqalkarkklkkveskadgvlvltqrwiill 89 
                                   ++a++l+++++G+     l++ ++ ++  + + +i+++vvf+ ++l +l+ + l+   ++k  +  +d++ vlt++++ l+
  gi|15669330|ref|NP_248135.1|  68 AIAIILSGFYFGVnfLYLLPSLKTAVNEGILTAFILCVVVFFDRFLNELVERYLALTISKKTKKDVDDQIVVLTKKLVRLV 148
                                   6899********9655689************************************98888888888888888877777776 PP

                       DUF3382  90 llvvAl 95 
                                   + vv+l
  gi|15669330|ref|NP_248135.1| 149 VWVVGL 154
                                   666665 PP

>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.3   7.7e-06      0.02       6      48 ..      12      54 ..      10      55 .. 0.96
   2 ?   -4.3   0.8         7   1.8e+04      20      29 ..      68      77 ..      67      79 .. 0.69
   3 ?   -3.3   0.0       3.7   9.4e+03      32      43 ..     111     122 ..     100     124 .. 0.69
   4 ?   -0.3   0.6      0.43   1.1e+03      15      24 ..     188     197 ..     172     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.7e-06
                                  XXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS- CS
                      TM_helix  6 llnellsflPnLvgAilILlvGwiiAkfvsrlvtkllaktgid 48
                                  + n++ +++  L+  il  ++G +   ++ rl +kl +k+gi+
  gi|15669330|ref|NP_248135.1| 12 MHNTVYNYILSLISIILFIVIGKYANALIERLADKLHKKSGIE 54
                                  789**************************************97 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 7
                                  HHHHHHHHHH CS
                      TM_helix 20 AilILlvGwi 29
                                  Ai+I l G++
  gi|15669330|ref|NP_248135.1| 68 AIAIILSGFY 77
                                  7888777765 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.7
                                   HHHHHHHHHHHH CS
                      TM_helix  32 kfvsrlvtklla 43 
                                   +f+  lv + la
  gi|15669330|ref|NP_248135.1| 111 RFLNELVERYLA 122
                                   677777777775 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.43
                                   SHHHHHHHHH CS
                      TM_helix  15 PnLvgAilIL 24 
                                    nL++ ++IL
  gi|15669330|ref|NP_248135.1| 188 SNLIAGLIIL 197
                                   4667777766 PP

>> AflR  Aflatoxin regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.6e-05      0.12     233     259 ..      18      44 ..       3      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.6e-05
                          AflR 233 eYllslvsLivlKVlgwYaAAArdaas 259
                                   +Y+lsl+s+i + V+g+Ya A  ++ +
  gi|15669330|ref|NP_248135.1|  18 NYILSLISIILFIVIGKYANALIERLA 44 
                                   7******************99766655 PP

>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.9      0.23   5.8e+02     124     141 ..      16      33 ..       1      43 [. 0.51
   2 ?   13.7   5.6   1.7e-05     0.043      39     119 ..      68     163 ..      59     211 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.23
                 7TMR-DISM_7TM 124 slaqllallvilllllig 141
                                    + ++l+l+ i+l+++ig
  gi|15669330|ref|NP_248135.1|  16 VYNYILSLISIILFIVIG 33 
                                   333344444444444443 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.7e-05
                 7TMR-DISM_7TM  39 lsfllyllslngllfqylwpnappalnnkllyltlllllilfllFarsf......lelkkkp.............rllkll 100
                                   +  +++  +++g  f yl+p + +a+n+ +l+ ++l+++++f  F++++      l ++kk              +l++l+
  gi|15669330|ref|NP_248135.1|  68 AIAIILSGFYFGVNFLYLLPSLKTAVNEGILTAFILCVVVFFDRFLNELverylaLTISKKTkkdvddqivvltkKLVRLV 148
                                   555666678******************************88888*****888888555553368999*8886555555555 PP

                 7TMR-DISM_7TM 101 lllavllsllllllpllpy 119
                                   ++++ l  ll+l+ +l  y
  gi|15669330|ref|NP_248135.1| 149 VWVVGL--LLILS-NLG-Y 163
                                   555544..33333.222.2 PP

>> Ctr  Ctr copper transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0015         4      11      55 ..       6      50 ..       1      67 [. 0.83
   2 ?    1.1   0.2      0.21   5.5e+02      26      49 ..      98     117 ..      75     143 .. 0.61
   3 ?   -0.9   0.0      0.92   2.3e+03     104     134 ..     138     168 ..     121     178 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0015
                           Ctr 11 ilfrsWritskgqlagsciglfllaifyeflralrerlerewdrh 55
                                  ++++ +  +++ ++++s+i ++l+ ++ ++ +al erl+++++++
  gi|15669330|ref|NP_248135.1|  6 MISEILMHNTVYNYILSLISIILFIVIGKYANALIERLADKLHKK 50
                                  556666678899**************************9988765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.21
                           Ctr  26 gsciglfllaifyeflralrerle 49 
                                   ++ ++l ++++f +fl+    +l 
  gi|15669330|ref|NP_248135.1|  98 LTAFILCVVVFFDRFLN----ELV 117
                                   44455555566666665....222 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.92
                           Ctr 104 qqlirallyvvqvllaYilMLlvMtyNvglf 134
                                   + l++ l+++v ++++ +l L+   y +  +
  gi|15669330|ref|NP_248135.1| 138 VVLTKKLVRLVVWVVGLLLILSNLGYDIKTL 168
                                   3578888888888888888888777766554 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.5   9.5e-05      0.24       7     115 ..      16     137 ..      13     147 .. 0.78
   2 ?   -1.5   0.2      0.65   1.7e+03      10      22 ..     147     159 ..     140     197 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.5e-05
                                   XXXXXXXXXXXXXXXX.XXXXXX..........XXX.....................XXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxx.xxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin   7 ffnllfwligivllav.Gvwlrl..........khaeaalacllsesaedpailaillivvGvllfllgflGcigalkenk 76 
                                   ++n+++ li+i+l++v G +++           k++  +l  ll +  + p ++    i+++ + f + fl ++ +lk   
  gi|15669330|ref|NP_248135.1|  16 VYNYILSLISIILFIViGKYANAlierladklhKKSGIELDELLIRALSLPVAI---AIILSGFYFGVNFLYLLPSLKTAV 93 
                                   78***********99987788778899999877444444444444555555555...799999************999854 PP

                                   ..XXXXXXXXXXXXX...XXXXXXXXXXXX--HHH........H CS
                                   ..xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin  77 ..cllltfsllllvl...fllelaagilgfvfsdkargkvseii 115
                                      +l+ f+l+++v+   fl el+   l+++ s+k++++v ++i
  gi|15669330|ref|NP_248135.1|  94 neGILTAFILCVVVFfdrFLNELVERYLALTISKKTKKDVDDQI 137
                                   44*************88889999999999999999766665544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.65
                                   XXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxx RF
                   Tetraspanin  10 llfwligivllav 22 
                                   l++w++g++l+  
  gi|15669330|ref|NP_248135.1| 147 LVVWVVGLLLILS 159
                                   5666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2304.35
//
Query:       gi|15669331|ref|NP_248136.1|  [L=323]
Description: cobalamin biosynthesis protein CbiG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.2e-28   97.7   0.0    1.3e-27   96.6   0.0    1.5  2  CbiG_C       Cobalamin synthesis G C-terminus
    9.7e-15   54.3   0.0      2e-14   53.3   0.0    1.5  1  CbiG_N       Cobalamin synthesis G N-terminal
     0.0035   17.5   0.6       0.12   12.6   0.1    2.5  2  Orthopox_F6  Orthopoxvirus F6 protein


Domain annotation for each model (and alignments):
>> CbiG_C  Cobalamin synthesis G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.5   8.9e+03      14      48 ..      13      46 ..      10      53 .. 0.68
   2 !   96.6   0.0   2.2e-31   1.3e-27       1     116 []     191     319 ..     191     319 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.5
                                  HHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHH CS
                        CbiG_C 14 eeieeaieealeeaglseeavaalatidlKadepg 48
                                  ++i+e i+++l+ ++++ ++v+ +   ++ ++e g
  gi|15669331|ref|NP_248136.1| 13 KKIAEEIKDVLDYYHYD-NKVEPIKDFKIERNEGG 46
                                  67889999999888874.45666665555555555 PP

  == domain 2  score: 96.6 bits;  conditional E-value: 2.2e-31
                                   EEEEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHH...CSCT-C CS
                        CbiG_C   1 lvvGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaave...vpnpse 78 
                                   ++vG+G+r+g+++ ++ +a+++al   ++   +v+a+ati+ K++e+g+le+++k++ pl +f++ee++++      ++se
  gi|15669331|ref|NP_248136.1| 191 IAVGLGARKGIERYKVYWAVKKALFLRNIPVWRVDAFATIEDKKHERGILETVNKFKKPLIIFKREEINEIYekiDLEKSE 271
                                   68*********************************************************************557866**** PP

                                   HHHCCCSSS-HHHHHHHHHC...........EECSCEEEETTEEEEEE CS
                        CbiG_C  79 fvkkevGvpsVaEaaAllaaa..........rllvpKqakggvTvAia 116
                                   fv k++Gv++V+E+a++la++          +l+++K + +gvTvAia
  gi|15669331|ref|NP_248136.1| 272 FVYKHLGVYGVSEPASILAVKkltnkdfdsiKLILKKFKRNGVTVAIA 319
                                   *******************844555566667****************8 PP

>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   3.4e-18     2e-14      10      82 .]      44     116 ..      39     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 3.4e-18
                                   -SEEEEES-HHHHHHHHHHH--.-TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XXXXX. CS
                        CbiG_N  10 ydalvfilaaGivvRliapllk.dKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviTtatd 82 
                                     +++fi+a+Giv R   + +k dK +Dp V+++ e+    i++ls hlgg+n +++ ia+ ++++ + Ttatd
  gi|15669331|ref|NP_248136.1|  44 EGGFIFIMATGIVLRKFLDEIKnDKFKDPFVIICNENK-ELIPILSNHLGGGNYFSKLIANNINGRVIFTTATD 116
                                   5689***********987666549********999875.58********************************8 PP

>> Orthopox_F6  Orthopoxvirus F6 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   1.9e-05      0.12       8      59 ..      56     107 ..      51     117 .. 0.87
   2 ?    2.5   0.0     0.028   1.7e+02      13      54 ..     265     306 ..     258     315 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                   Orthopox_F6   8 vknkiidlikndqikysrvitieesdsllsvdevyanhGfdcvemideniin 59 
                                   v  k +d iknd+ k   vi+ +e   l+++   +   G    ++i +ni  
  gi|15669331|ref|NP_248136.1|  56 VLRKFLDEIKNDKFKDPFVIICNENKELIPILSNHLGGGNYFSKLIANNING 107
                                   67899**************************999999998888899888865 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.028
                   Orthopox_F6  13 idlikndqi.kysrvitieesdsllsvdevyanhGfdcvemid 54 
                                   idl k + + k+  v  + e  s+l+v+++ +n+ fd +++i 
  gi|15669331|ref|NP_248136.1| 265 IDLEKSEFVyKHLGVYGVSEPASILAVKKL-TNKDFDSIKLIL 306
                                   566665544366678889999******986.7999**999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1999.50
//
Query:       gi|15669332|ref|NP_248137.1|  [L=65]
Description: hypothetical protein MJ_1145 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   14.3   0.2      0.041   14.2   0.2    1.1  1  DUF5623   Domain of unknown function (DUF5623)


Domain annotation for each model (and alignments):
>> DUF5623  Domain of unknown function (DUF5623)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   2.3e-06     0.041      15      55 ..      21      61 ..      13      65 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-06
                       DUF5623 15 qevgrllkellesvarskgvssrlsavrstLddWlemEyse 55
                                   e+ r lk l +  + +k+ ++ l+++r  Ld W+ + y++
  gi|15669332|ref|NP_248137.1| 21 DEIERTLKILRNMARIKKRKEKNLKSIRDVLDYWACQAYKS 61
                                  578899999888888889999**************999943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.30u 0.24s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 519.89
//
Query:       gi|15669333|ref|NP_248138.1|  [L=343]
Description: glyceraldehyde-3-phosphate dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-37  128.5   0.2    2.4e-37  128.0   0.2    1.2  1  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
    6.9e-08   32.7   0.1    1.9e-07   31.2   0.1    1.8  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    1.3e-05   25.5   0.3    9.4e-05   22.7   0.1    2.5  2  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
  ------ inclusion threshold ------
      0.019   14.3   0.1      0.045   13.1   0.1    1.6  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.035   14.3   0.0        0.1   12.8   0.0    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.082   13.2   0.4       0.44   10.8   0.0    2.4  3  TrkA_N           TrkA-N domain
        0.1   13.1   0.3       0.34   11.4   0.1    1.9  2  DUF5498          Family of unknown function (DUF5498)
       0.15   12.3   0.0       0.28   11.4   0.0    1.4  1  DUF4154          YfiR/HmsC-like


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   0.2   1.1e-40   2.4e-37       1     158 []     149     305 ..     149     305 .. 0.99

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 1.1e-40
                                   HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT..CSSEEEE-THHHHHHHHSGGGTTTEEEEEEEE CS
                       Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa..eniiptstgaakavglVlpelkgkldglAvrV 79 
                                   L+++++++n+ ++ikk+++++v++++++         +d ++++++a  +n+++++++++++v +V+pe++gk+ ++Av+V
  gi|15669333|ref|NP_248138.1| 149 LCRILYAINSIADIKKARIVLVRRAADP---------NDDKTGPVNAitPNPVTVPSHHGPDVVSVVPEFEGKILTSAVIV 220
                                   89**************************.........9*********99******************************** PP

                                   SSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH....TTTTTTEEEEHSHHHGGGGTTGCS..SEEEEGGGCEEETTTEEEE CS
                       Gp_dh_C  80 Ptpnvsvvdlvvelekevtveevnaalkeaae....galkgilsyteeelvssDlvgdph..ssifdaketivveenlvkv 154
                                   Pt+ ++++ l+ve++ +v+++++ +a+k++++    +a++g+ s+++ +++ +Dl + ++  +++++++e+i+v en++++
  gi|15669333|ref|NP_248138.1| 221 PTTLMHMHTLMVEVDGDVSRDDILEAIKKTPRiitvRAEDGFSSTAKIIEYGRDLGRLRYdiNELVVWEESINVLENEIFL 301
                                   ***********************************************************999******************* PP

                                   EEEE CS
                       Gp_dh_C 155 vawy 158
                                   ++++
  gi|15669333|ref|NP_248138.1| 302 MQAV 305
                                   *986 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.1   8.5e-11   1.9e-07       2      94 ..       4     109 ..       3     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 8.5e-11
                                   EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHH.............HHSSSS.--S-BEBSSHHHHHHH- CS
                        DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdag.............ellglg.klgvavtddleevleka 68 
                                   kv+++G+ G +Gk+v++av+ ++d+e+ ++ ++k+ ++e++ a              e ++l+   g++v+ ++ +++e+a
  gi|15669333|ref|NP_248138.1|   4 KVLINGY-GSIGKRVADAVSMQDDMEVIGVTKTKP-DFEARLAVekgyklfvaipdnERVKLFeDAGIPVEGTILDIIEDA 82 
                                   89*****.**************************9.555554445669*********77777779**************** PP

                                   SEEEE-S-HHHHHHHHHHHHHT.T-EE CS
                        DapB_N  69 dvliDFTtpeavlenlklalek.gvkl 94 
                                   d+++D    +  ++nl+ +++  +vk+
  gi|15669333|ref|NP_248138.1|  83 DIVVDGAPKKIGKQNLENIYKPhKVKA 109
                                   ******999999999998887535555 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   4.2e-08   9.4e-05       2      33 ..       4      35 ..       3      84 .. 0.86
   2 ?   -0.7   0.0      0.83   1.9e+03      27      72 ..     253     301 ..     243     315 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.2e-08
                                  EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-T CS
                       Gp_dh_N  2 kvainGfGRIGrlvlralleekelevvaindl 33
                                  kv inG+G IG+ v+ a+  ++++ev+ + ++
  gi|15669333|ref|NP_248138.1|  4 KVLINGYGSIGKRVADAVSMQDDMEVIGVTKT 35
                                  89***************************984 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.83
                                   EEEEE-TS-HHHHHHHHHEETTTEC-SS-EEEE...TTEEEETTEEEEE CS
                       Gp_dh_N  27 vvaindltdletlayllkyDsvhgrfkgeveae...eealvvngkkikv 72 
                                   +++++     ++ a++++y    gr++ ++++    ee++ v +++i +
  gi|15669333|ref|NP_248138.1| 253 IITVRAEDGFSSTAKIIEYGRDLGRLRYDINELvvwEESINVLENEIFL 301
                                   5555555566667777777777777776666544445555555555554 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     2e-05     0.045      38      71 ..       4      38 ..       2      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                                  EEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHH CS
                  2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk.afgmkviaydrskkk 71
                                  +v i G+G+IG++va+ ++ + +m+vi++ ++k +
  gi|15669333|ref|NP_248138.1|  4 KVLINGYGSIGKRVADAVSmQDDMEVIGVTKTKPD 38
                                  789****************8899******998663 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.6e-05       0.1       1      48 [.       5      50 ..       5      99 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.6e-05
                                  EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTC CS
               Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvr 48
                                  vli G+Gs+G+ va+ ++ ++d+  e++ ++++k   ea +a ++g +
  gi|15669333|ref|NP_248138.1|  5 VLINGYGSIGKRVADAVSMQDDM--EVIGVTKTKPDFEARLAVEKGYK 50
                                  7899*******************..77777777777676666554443 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0002      0.44       1      51 [.       5      58 ..       5      72 .. 0.68
   2 ?   -3.1   0.0       4.1   9.2e+03       9      40 ..      93     123 ..      91     127 .. 0.75
   3 ?   -2.2   0.0       2.1   4.8e+03      46      58 ..     235     247 ..     228     272 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                                  EEEES-SHHHHHHHHHHHH.TTEEEEEEESSH.HH.HHHHHHTTSEEEES-TTS CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkde.er.veelreeglevvvgdatd 51
                                  ++i G+G +G+++a+ +s  + ++v+++ k + +  ++ + e+g++ +v+ + +
  gi|15669333|ref|NP_248138.1|  5 VLINGYGSIGKRVADAVSMqDDMEVIGVTKTKpDFeARLAVEKGYKLFVAIPDN 58
                                  6899**************966678999998873443444457778855443333 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.1
                                   HHHHHHHHHHHTTEEEEEEESSHHHHHHHHHT CS
                        TrkA_N   9 vGrslaeeLseggkdvvvidkdeerveelree 40 
                                   +G++ +e++ + + +v +i +  e+++ ++++
  gi|15669333|ref|NP_248138.1|  93 IGKQNLENIYKPH-KVKAILQGGEKAKDVEDN 123
                                   7888888888877.499998888888887765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.1
                                   ES-TTSHHHHHHT CS
                        TrkA_N  46 vgdatdeevLeea 58 
                                    gd++++++Le++
  gi|15669333|ref|NP_248138.1| 235 DGDVSRDDILEAI 247
                                   5888888888875 PP

>> DUF5498  Family of unknown function (DUF5498)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00015      0.34      16      64 ..      67     115 ..      60     125 .. 0.88
   2 ?   -1.9   0.0       2.1   4.8e+03      17      42 ..     315     340 ..     278     342 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                       DUF5498  16 gvipadnafneavydefikifgtdkkfgifpsenfskpeqtesifqgvv 64 
                                     ip + ++ + + d  i + g+ kk+g    en+ kp + ++i+qg  
  gi|15669333|ref|NP_248138.1|  67 AGIPVEGTILDIIEDADIVVDGAPKKIGKQNLENIYKPHKVKAILQGGE 115
                                   56899999999999********************************965 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                       DUF5498  17 vipadnafneavydefikifgtdkkf 42 
                                    i +  a+ +   d+f  i  t+k +
  gi|15669333|ref|NP_248138.1| 315 NIDCIRAMLQMEEDNFKSIEKTNKAM 340
                                   23333334444445555555555555 PP

>> DUF4154  YfiR/HmsC-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.28      67     124 ..     226     284 ..     211     294 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                   H-SEEEE-S--HHHHHHHHHHHTTS-.-EEEESSTSGGSSS-SEEEEESSSSEEEEEEH CS
                       DUF4154  67 echvlyigesearelaailkalagkp.vLtvsdgegfaeqggminLvredgrlrfeiNl 124
                                   ++h l ++ + + ++++il+a++++p ++tv  ++gf +   +i+  r+ grlr +iN 
  gi|15669333|ref|NP_248138.1| 226 HMHTLMVEVDGDVSRDDILEAIKKTPrIITVRAEDGFSSTAKIIEYGRDLGRLRYDINE 284
                                   47899999999999***********77*******************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2355.28
//
Query:       gi|15669334|ref|NP_248139.1|  [L=462]
Description: hypothetical protein MJ_1147 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-14   53.4  31.4    8.2e-08   32.3   5.5    4.5  4  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
      0.063   13.7   2.0        2.1    8.8   0.4    2.5  2  Rtt106          Histone chaperone Rttp106-like


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2      0.57   5.1e+03      33      44 ..      82      93 ..      79      94 .. 0.57
   2 !   27.7   2.8   2.5e-10   2.2e-06       4      45 ..     104     146 ..     104     149 .. 0.95
   3 !   32.3   5.5   9.1e-12   8.2e-08       1      47 [.     157     203 ..     157     204 .. 0.97
   4 !    9.5   0.9   0.00012       1.1      28      45 ..     205     222 ..     204     225 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.57
                Pentapeptide_3 33 FsgarFtgdvdF 44
                                    ++ F+gd +F
  gi|15669334|ref|NP_248139.1| 82 IYNVEFNGDFRF 93
                                  455666666555 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 2.5e-10
                Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFs 45 
                                   ++F g+a+Fr  tF+g+++F ++ F g++dF +++F+ ++ Fs
  gi|15669334|ref|NP_248139.1| 104 SVFNGNAYFRVITFKGSVYFIRTIFnGDVDFIDTIFEENAYFS 146
                                   68***********************88**********99*997 PP

  == domain 3  score: 32.3 bits;  conditional E-value: 9.1e-12
                Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                   Fsg++F +  +F  +tF+g ++Fs ++F+ a F +++F+  v F++ 
  gi|15669334|ref|NP_248139.1| 157 FSGTIFNKESHFKSTTFEGNTYFSVTTFNIAEFYNSTFKSHVYFDDI 203
                                   9**************************************99***985 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00012
                Pentapeptide_3  28 FgsadFsgarFtgdvdFs 45 
                                   F+  +F ++rF +dv+F+
  gi|15669334|ref|NP_248139.1| 205 FNLLSFTDCRFRDDVSFK 222
                                   566677777777777776 PP

>> Rtt106  Histone chaperone Rttp106-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.4   0.00024       2.1      58      85 ..     207     241 ..     157     245 .. 0.71
   2 ?    3.7   0.0    0.0094        84      37      80 ..     310     353 ..     282     356 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00024
                        Rtt106  58 l....kk...eeveFsmidqeelegidefvkskgi 85 
                                   l    ++   ++v+F+ id+e+++g++ f+k++ +
  gi|15669334|ref|NP_248139.1| 207 LlsftDCrfrDDVSFKKIDKENFKGLAIFLKTQFL 241
                                   255542245589******************99865 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0094
                        Rtt106  37 iesvsfeRvsvtsrtfdlvvelkk..eeveFsmidqeelegidefv 80 
                                   i++ +++  sv     +l +++++  + +e s++ + e+e i+ef 
  gi|15669334|ref|NP_248139.1| 310 IDQFNYK--SVLAEYRNLRISIENnrTYIEASNLYKMEMELIKEFS 353
                                   7889999..88888888888886666999***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3140.88
//
Query:       gi|15669335|ref|NP_248140.1|  [L=108]
Description: transcription-associated protein TFIIS [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-20   72.6   8.0    1.7e-20   72.6   8.0    3.1  3  TFIIS_C          Transcription factor S-II (TFIIS)
      6e-14   51.6   2.4      6e-14   51.6   2.4    3.5  4  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    1.9e-05   23.9  13.8     0.0025   17.2   1.2    3.3  3  zf-ribbon_3      zinc-ribbon domain
    0.00032   20.6  16.2      0.063   13.2   0.5    4.2  3  zinc_ribbon_4    zinc-ribbon domain
    0.00043   20.2  15.3      0.001   19.0   5.5    2.8  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0027   17.7  15.1        0.7   10.0   0.1    4.2  4  UPF0547          Uncharacterised protein family UPF0547
     0.0045   16.5   5.7      0.039   13.5   0.2    3.4  3  RecR             RecR protein
  ------ inclusion threshold ------
      0.016   14.7  13.1        0.5    9.9   3.7    3.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.018   14.9  13.8       0.11   12.4   6.0    2.5  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.028   14.5  13.4       0.26   11.3   1.0    3.0  3  DZR              Double zinc ribbon
      0.028   14.1  20.2       0.87    9.4   0.2    4.1  4  zinc_ribbon_2    zinc-ribbon domain
      0.035   14.1  12.6      0.085   12.8   0.7    2.7  2  zinc-ribbons_6   zinc-ribbons
      0.087   13.0  16.0        2.5    8.3   1.0    4.4  4  Zn-ribbon_8      Zinc ribbon domain
       0.18   11.8   0.3       0.18   11.8   0.3    3.4  3  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
       0.33   10.6  10.2        2.4    7.8   5.1    2.7  2  TackOD1          Thaumarchaeal output domain 1
       0.46   10.5  12.7        2.9    8.0   1.6    2.9  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.47   10.3   6.5      0.066   13.1   0.5    2.5  3  CxC3             CxC3 like cysteine cluster associated with K
       0.63    9.7  11.7        8.1    6.1   0.1    3.9  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.74    9.9   0.0       0.74    9.9   0.0    3.8  4  PriA_CRR         PriA DNA helicase Cys-rich region (CRR) doma
       0.86    9.4  15.1       0.41   10.5   1.2    3.4  3  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
       0.95    9.3  15.9         16    5.3   0.1    3.9  3  A2L_zn_ribbon    A2L zinc ribbon domain
        1.1    9.7  11.7         30    5.1   0.1    4.2  4  zf-IS66          zinc-finger binding domain of transposase IS
        1.3    8.8  13.9        6.9    6.5   0.1    3.5  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
        1.3    8.7   8.7        3.3    7.4   0.3    2.8  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        1.5    8.9  16.0        4.9    7.3   2.3    3.1  3  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        1.9    8.4  16.4        9.9    6.1   0.7    4.3  4  zf-HIT           HIT zinc finger
        2.1    8.6  16.3        7.4    6.8   4.9    3.2  3  DUF2387          Probable metal-binding protein (DUF2387)
        4.5    7.5  14.7        4.9    7.4   0.3    4.1  4  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
        4.9    6.9  13.1        7.7    6.3   2.7    3.7  3  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
          8    7.1   9.0    2.5e+02    2.3   9.0    2.7  1  RPA_interact_C   Replication protein A interacting C-terminal
        9.5    6.6   9.9    1.2e+02    3.1   9.9    2.3  1  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3      0.13        75       2       8 ..       4      10 ..       3      12 .. 0.83
   2 ?    1.8   0.2      0.38   2.2e+02      30      36 ..      20      26 ..      18      31 .. 0.60
   3 !   72.6   8.0   2.9e-23   1.7e-20       1      39 []      67     105 ..      67     105 .. 0.98

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.13
                       TFIIS_C  2 kCpkCgs 8 
                                   CpkC++
  gi|15669335|ref|NP_248140.1|  4 FCPKCNN 10
                                  59***87 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.38
                       TFIIS_C 30 kCtkCgh 36
                                  kC+ Cg+
  gi|15669335|ref|NP_248140.1| 20 KCAVCGY 26
                                  4555554 PP

  == domain 3  score: 72.6 bits;  conditional E-value: 2.9e-23
                       TFIIS_C   1 akCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                   ++CpkCg++eay++ +QtR aDEp+t+fykC+kCgh+Wr
  gi|15669335|ref|NP_248140.1|  67 IECPKCGHNEAYWWLQQTRCADEPETRFYKCKKCGHTWR 105
                                   68************************************8 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   2.4     1e-16     6e-14       1      35 [.       2      32 ..       2      33 .. 0.95
   2 ?   -2.3   0.0       7.5   4.3e+03       9      19 ..      42      52 ..      41      54 .. 0.71
   3 ?    3.0   0.2      0.17        96       4       8 ..      69      73 ..      64      76 .. 0.78
   4 ?    2.8   0.8      0.18   1.1e+02      20      28 ..      92     101 ..      86     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1e-16
                                  EEBESTTTSBEEEEECSCCCEEEESSSS-EEESSC CS
                RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepadq 35
                                  +kFCpkC+Nl+lpk++k++    C+ CgYee++++
  gi|15669335|ref|NP_248140.1|  2 VKFCPKCNNLMLPKDGKLK----CAVCGYEEETTA 32
                                  59*****************....*********986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.5
                                  SBEEEEECSCC CS
                RNA_POL_M_15KD  9 NlLlpkedkeg 19
                                   +L++k+ k +
  gi|15669335|ref|NP_248140.1| 42 EHLENKKEKIT 52
                                  58898887755 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.17
                                  ESTTT CS
                RNA_POL_M_15KD  4 CpkCg 8 
                                  CpkCg
  gi|15669335|ref|NP_248140.1| 69 CPKCG 73
                                  77776 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.18
                                   CE.EEESSSS CS
                RNA_POL_M_15KD  20 kn.feCrqCg 28 
                                   ++ + C +Cg
  gi|15669335|ref|NP_248140.1|  92 TRfYKCKKCG 101
                                   4458999997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.2   4.3e-06    0.0025       3      24 ..       3      26 ..       1      27 [. 0.90
   2 !   10.5   0.4   0.00052       0.3       3      11 ..      67      75 ..      66      77 .. 0.84
   3 ?    4.3   0.6      0.05        29      18      24 ..      96     102 ..      85     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.3e-06
                   zf-ribbon_3  3 vrCPnCGa.p.lssddnvCpyCGt 24
                                  ++CP+C++   ++++  +C+ CG+
  gi|15669335|ref|NP_248140.1|  3 KFCPKCNNlMlPKDGKLKCAVCGY 26
                                  79******868************8 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00052
                   zf-ribbon_3  3 vrCPnCGap 11
                                  ++CP+CG++
  gi|15669335|ref|NP_248140.1| 67 IECPKCGHN 75
                                  68*****97 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.05
                   zf-ribbon_3  18 vCpyCGt 24 
                                   +C++CG+
  gi|15669335|ref|NP_248140.1|  96 KCKKCGH 102
                                   6888886 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   4.5      0.19   1.1e+02      21      32 ..      14      25 ..       4      27 .. 0.73
   2 !    8.2   0.2    0.0039       2.3      25      33 ..      66      74 ..      61      75 .. 0.71
   3 !   13.2   0.5   0.00011     0.063      27      36 .]      96     105 ..      89     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.19
                 zinc_ribbon_4 21 akgvkvrCskCg 32
                                  +k +k++C+ Cg
  gi|15669335|ref|NP_248140.1| 14 PKDGKLKCAVCG 25
                                  555899999998 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0039
                 zinc_ribbon_4 25 kvrCskCgh 33
                                  ++ C+kCgh
  gi|15669335|ref|NP_248140.1| 66 RIECPKCGH 74
                                  566777776 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00011
                 zinc_ribbon_4  27 rCskCghvFr 36 
                                   +C+kCgh++r
  gi|15669335|ref|NP_248140.1|  96 KCKKCGHTWR 105
                                   9********7 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.5     0.034        20      21      45 ..       5      26 ..       2      27 .. 0.81
   2 ?    3.4   0.1      0.13        77      19      27 ..      19      27 ..      12      39 .. 0.63
   3 !   19.0   5.5   1.8e-06     0.001      18      46 .]      66     103 ..      61     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.034
                 Zn_Tnp_IS1595 21 CPhCgsrkayriktrglfqCkeCrk 45
                                  CP+C    +   k+ g+++C+ C++
  gi|15669335|ref|NP_248140.1|  5 CPKCN--NLMLPKD-GKLKCAVCGY 26
                                  *****..6666777.9999999997 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.13
                 Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                    C  Cg++
  gi|15669335|ref|NP_248140.1| 19 LKCAVCGYE 27
                                  456666666 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 1.8e-06
                 Zn_Tnp_IS1595  18 gfvCPhCgsr.kayrikt........rglfqCkeCrkq 46 
                                   +  CP+Cg+   ++ +++         + ++Ck+C+++
  gi|15669335|ref|NP_248140.1|  66 RIECPKCGHNeAYWWLQQtrcadepeTRFYKCKKCGHT 103
                                   356*******6666666699***************996 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.7      0.18     1e+02      15      20 ..       3       8 ..       2       9 .. 0.69
   2 ?    5.8   0.2     0.025        14      16      23 ..      20      27 ..      19      27 .. 0.90
   3 !   10.0   0.1    0.0012       0.7       9      22 ..      61      74 ..      60      75 .. 0.83
   4 ?    7.0   0.5     0.011       6.1      16      25 ..      96     105 ..      95     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.18
                       UPF0547 15 qfCphC 20
                                  +fCp C
  gi|15669335|ref|NP_248140.1|  3 KFCPKC 8 
                                  677777 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.025
                       UPF0547 16 fCphCGyv 23
                                  +C+ CGy+
  gi|15669335|ref|NP_248140.1| 20 KCAVCGYE 27
                                  7******7 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0012
                       UPF0547  9 kvPvaaqfCphCGy 22
                                  ++P+   +Cp CG+
  gi|15669335|ref|NP_248140.1| 61 TLPTTRIECPKCGH 74
                                  67888899*****9 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.011
                       UPF0547  16 fCphCGyvFq 25 
                                   +C  CG+ + 
  gi|15669335|ref|NP_248140.1|  96 KCKKCGHTWR 105
                                   7999****96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   6.7e-05     0.039      16      34 ..       2      24 ..       1      28 [. 0.87
   2 ?    1.9   0.1       0.3   1.7e+02      18      24 ..      68      74 ..      57      76 .. 0.84
   3 ?    2.2   0.2      0.23   1.3e+02      18      24 ..      96     102 ..      92     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.7e-05
                                  -EE-TTT--E...ESSSS.-CCC CS
                          RecR 16 vrhCsrCgnl...teedl.CaIC 34
                                  v++C++C+nl    +  l Ca+C
  gi|15669335|ref|NP_248140.1|  2 VKFCPKCNNLmlpKDGKLkCAVC 24
                                  89********988888767**99 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.3
                                  E-TTT-- CS
                          RecR 18 hCsrCgn 24
                                   C++Cg+
  gi|15669335|ref|NP_248140.1| 68 ECPKCGH 74
                                  6****97 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.23
                                   E-TTT-- CS
                          RecR  18 hCsrCgn 24 
                                    C++Cg+
  gi|15669335|ref|NP_248140.1|  96 KCKKCGH 102
                                   6****98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.9    0.0027       1.6       3      30 ..       5      29 ..       4      32 .. 0.83
   2 ?    9.9   3.7   0.00087       0.5       2      27 ..      68     102 ..      67     108 .] 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0027
                                  ETTTTCEECHEETSTTCEEESSSSBEEE CS
                  TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVle 30
                                  CP+C++ +l   p+ g l C  CG+  e
  gi|15669335|ref|NP_248140.1|  5 CPKCNNLML---PKDGKLKCAVCGYEEE 29
                                  *****9443...688*********9887 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00087
                                   EETTTTCEE.C........HEETSTTCEEESSSSB CS
                  TF_Zn_Ribbon   2 kCPnCgstn.l........veDpergelvCtdCGl 27 
                                    CP+Cg+ + +          +pe+  + C++CG 
  gi|15669335|ref|NP_248140.1|  68 ECPKCGHNEaYwwlqqtrcADEPETRFYKCKKCGH 102
                                   5******9977*******7777999999******7 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.9    0.0083       4.8      31      55 ..       5      27 ..       3      37 .. 0.84
   2 ?   12.4   6.0   0.00019      0.11      27      56 ..      65     104 ..      38     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0083
                OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfe 55
                                  C++C   + +  ++ ++kC  Cg+e
  gi|15669335|ref|NP_248140.1|  5 CPKCNNLMLP--KDGKLKCAVCGYE 27
                                  9999999999..9999999999987 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00019
                OrfB_Zn_ribbon  27 TSktCseCgsknke..........alsgrtfkCpnCgfea 56 
                                   T  +C++Cg++  +          ++++r +kC++Cg+++
  gi|15669335|ref|NP_248140.1|  65 TRIECPKCGHNEAYwwlqqtrcadEPETRFYKCKKCGHTW 104
                                   5679*********9*********999***********997 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.0   0.00045      0.26      13      38 ..       3      28 ..       2      37 .. 0.80
   2 ?    5.4   0.3     0.032        18      28      36 ..      66      74 ..      41      77 .. 0.73
   3 ?    5.5   5.5     0.029        17       1      36 [.      69     102 ..      60     108 .] 0.49

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00045
                           DZR 13 rfCseCgtklkavaaedrCpsCgekv 38
                                  +fC++C++ + +   + +C  Cg++ 
  gi|15669335|ref|NP_248140.1|  3 KFCPKCNNLMLPKDGKLKCAVCGYEE 28
                                  79999999987777799999999875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.032
                           DZR 28 edrCpsCge 36
                                   + Cp+Cg+
  gi|15669335|ref|NP_248140.1| 66 RIECPKCGH 74
                                  556666665 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.029
                           DZR   1 CpqCgee.........lppdarfCseCgtklkavaa.......edrCpsCge 36 
                                   Cp+Cg++                                     ++C +Cg+
  gi|15669335|ref|NP_248140.1|  69 CPKCGHNeaywwlqqtR------------------CadepetrFYKCKKCGH 102
                                   45555544444444440..................14444444555555554 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.5     0.015       8.6      14      19 ..       3       8 ..       2      10 .. 0.76
   2 ?    4.6   7.4     0.048        28       1      22 [.       4      27 ..       4      27 .. 0.76
   3 ?    9.4   0.2    0.0015      0.87      16      21 ..      69      74 ..      60      75 .. 0.72
   4 ?    6.1   0.8     0.016       9.2       1       7 [.      96     102 ..      91     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                 zinc_ribbon_2 14 kFCpyC 19
                                  kFCp+C
  gi|15669335|ref|NP_248140.1|  3 KFCPKC 8 
                                  788888 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.048
                 zinc_ribbon_2  1 fCpnCGael.q.dnakFCpyCGtp 22
                                  fCp+C +   + d+   C  CG++
  gi|15669335|ref|NP_248140.1|  4 FCPKCNNLMlPkDGKLKCAVCGYE 27
                                  9*******954344444****986 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0015
                 zinc_ribbon_2 16 CpyCGt 21
                                  Cp+CG+
  gi|15669335|ref|NP_248140.1| 69 CPKCGH 74
                                  888888 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.016
                 zinc_ribbon_2   1 fCpnCGa 7  
                                   +C++CG+
  gi|15669335|ref|NP_248140.1|  96 KCKKCGH 102
                                   7999987 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   0.00015     0.085       3      26 ..       5      28 ..       3      56 .. 0.88
   2 ?    5.0   5.2     0.041        24       2      37 ..      68     102 ..      67     107 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                                  -SSS-S--EE-SSEEE-TTT--EE CS
                zinc-ribbons_6  3 CpeCqqelekrgeqyhCeaCqedl 26
                                  Cp+C++ +  ++ +++C  C  + 
  gi|15669335|ref|NP_248140.1|  5 CPKCNNLMLPKDGKLKCAVCGYEE 28
                                  *********9999*******8754 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.041
                                   --SSS-S--E.E-SSEEE-TTT--EEEEEEE-SSS-S CS
                zinc-ribbons_6   2 kCpeCqqele.krgeqyhCeaCqedlkkealCpeCeq 37 
                                   +Cp+C ++   +  +q++C   +e  ++   C +C++
  gi|15669335|ref|NP_248140.1|  68 ECPKCGHNEAyWWLQQTRCA--DEPETRFYKCKKCGH 102
                                   79999988777777677665..344445555666654 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.13        76      28      34 ..       3      10 ..       1      16 [. 0.74
   2 ?    1.6   1.4      0.54   3.1e+02       7      19 ..      20      32 ..      18      41 .. 0.74
   3 ?    7.6   0.1    0.0069         4      27      34 ..      67      74 ..      54      78 .. 0.77
   4 ?    8.3   1.0    0.0044       2.5       6      14 ..      95     103 ..      94     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.13
                   Zn-ribbon_8 28 a.CPeCgs 34
                                  + CP+C+ 
  gi|15669335|ref|NP_248140.1|  3 KfCPKCNN 10
                                  55****86 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.54
                   Zn-ribbon_8  7 rCeeCghefevlq 19
                                  +C  Cg e e  +
  gi|15669335|ref|NP_248140.1| 20 KCAVCGYEEETTA 32
                                  8999998877655 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0069
                   Zn-ribbon_8 27 taCPeCgs 34
                                  ++CP+Cg+
  gi|15669335|ref|NP_248140.1| 67 IECPKCGH 74
                                  56999998 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0044
                   Zn-ribbon_8   6 YrCeeCghe 14 
                                   Y+C++Cgh+
  gi|15669335|ref|NP_248140.1|  95 YKCKKCGHT 103
                                   9******97 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.6       0.3   1.7e+02       5       9 ..       5       9 ..       4      10 .. 0.72
   2 ?    0.0   0.1       1.5   8.4e+02      22      28 ..      21      27 ..      12      27 .. 0.79
   3 ?   11.8   0.3   0.00032      0.18       4      29 ..      68     104 ..      61     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.3
                PhnA_Zn_Ribbon 5 CplCa 9
                                 Cp+C+
  gi|15669335|ref|NP_248140.1| 5 CPKCN 9
                                 77776 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.5
                PhnA_Zn_Ribbon 22 CpeCahE 28
                                  C  C++E
  gi|15669335|ref|NP_248140.1| 21 CAVCGYE 27
                                  8888887 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00032
                PhnA_Zn_Ribbon   4 kCplCaSeytY...........edgallvCpeCahEw 29 
                                    Cp+C+  ++Y            ++  + C +C+h w
  gi|15669335|ref|NP_248140.1|  68 ECPKCGHNEAYwwlqqtrcadePETRFYKCKKCGHTW 104
                                   6**********************************88 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   5.1    0.0041       2.4      88     115 ..       3      30 ..       1      88 [. 0.73
   2 ?    2.3   3.4       0.2   1.2e+02      75     155 ..      68     103 ..      60     108 .] 0.43

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0041
                       TackOD1  88 evCpkCkSidieeqelihhftCgnvgpe 115
                                   + CpkC+   + ++  +++  Cg+ +++
  gi|15669335|ref|NP_248140.1|   3 KFCPKCNNLMLPKDGKLKCAVCGYEEET 30 
                                   689*********999*******997764 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.2
                       TackOD1  75 lCpsCksghlnvrevCpkCkSidieeqelihhftCgnvgpeeeflkegkleCpkCktkLrhiGvDYdrplevykCnsCksl 155
                                    Cp+C +++         C   d  e+ +                                            kC++C+++
  gi|15669335|ref|NP_248140.1|  68 ECPKCGHNEAYWWLQQTRCA--DEPETRFY-------------------------------------------KCKKCGHT 103
                                   34444444443333333332..22334444...........................................44444444 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.6    0.0049       2.9      72     103 ..       4      35 ..       1      43 [. 0.78
   2 ?    5.0   9.2     0.042        25      69      96 ..      17      76 ..      14     108 .] 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0049
                                   EETTTS-EEECHHH.HHS-TTTSSS-EEEEESS CS
                          HypA  72 rCreCgkefeleek.alrCpkCgsadveivsGe 103
                                    C +C++ +  + + +l+C  Cg ++ ++ +G+
  gi|15669335|ref|NP_248140.1|   4 FCPKCNNLMLPK-DgKLKCAVCGYEEETTAEGS 35 
                                   699**9887766.44899*****9987777775 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.042
                                  -EEEETTTS-EEECHH..HHH...............................S-TTTSSS- CS
                          HypA 69 vkvrCreCgkefelee..kal...............................rCpkCgsad 96
                                   k++C +Cg+e e+++  +                                 +CpkCg+++
  gi|15669335|ref|NP_248140.1| 17 GKLKCAVCGYEEETTAegS-KeyeykehlenkkekitviesegletlpttriECPKCGHNE 76
                                  6889*****9999665232.2458899999********************99999999875 PP

>> CxC3  CxC3 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.4       1.7   9.8e+02      11      32 ..       4      23 ..       1      25 [. 0.64
   2 ?   13.1   0.5   0.00011     0.066      10      54 ..      29      75 ..      19      94 .. 0.79
   3 ?   -0.6   0.2         2   1.2e+03      46      53 ..      95     102 ..      81     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.7
                          CxC3 11 ccgeCkktgtltlkageesiav 32
                                   c++C++++    k+g+ ++av
  gi|15669335|ref|NP_248140.1|  4 FCPKCNNLM--LPKDGKLKCAV 23
                                  688888866..55555566665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00011
                          CxC3 10 sccgeCkktgt..ltlkageesiavvtkeGrfdlnsaafkCssCsav 54
                                  ++  e++k       l++++e+i+v+  eG   l++++++C +C+ +
  gi|15669335|ref|NP_248140.1| 29 ETTAEGSKEYEykEHLENKKEKITVIESEGLETLPTTRIECPKCGHN 75
                                  444466665555677889999***********************876 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2
                          CxC3  46 fkCssCsa 53 
                                   +kC++C+ 
  gi|15669335|ref|NP_248140.1|  95 YKCKKCGH 102
                                   67877765 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.014       8.1       4      14 ..       4      14 ..       2      16 .. 0.82
   2 ?   -2.5   0.2       6.9     4e+03       4       9 ..      20      25 ..      18      27 .. 0.81
   3 ?    4.8   0.1     0.036        21       3      10 ..      67      74 ..      65      79 .. 0.85
   4 ?    5.1   0.4     0.029        17       3      11 ..      95     103 ..      93     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.014
                        zf_UBZ  4 lCerCgkeipe 14
                                  +C++C+  +++
  gi|15669335|ref|NP_248140.1|  4 FCPKCNNLMLP 14
                                  8*****98875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.9
                        zf_UBZ  4 lCerCg 9 
                                   C+ Cg
  gi|15669335|ref|NP_248140.1| 20 KCAVCG 25
                                  699998 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.036
                        zf_UBZ  3 ylCerCgk 10
                                  + C++Cg+
  gi|15669335|ref|NP_248140.1| 67 IECPKCGH 74
                                  67****98 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.029
                        zf_UBZ   3 ylCerCgke 11 
                                   y C++Cg++
  gi|15669335|ref|NP_248140.1|  95 YKCKKCGHT 103
                                   99*****85 PP

>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.6       2.3   1.3e+03       1       5 [.       5       9 ..       5      12 .. 0.86
   2 ?    9.9   0.0    0.0013      0.74      13      26 ..      15      28 ..      14      28 .. 0.89
   3 ?   -0.2   0.3       1.7     1e+03       1       5 [.      69      73 ..      66      76 .. 0.71
   4 ?    1.6   0.3      0.48   2.8e+02      17      25 ..      95     103 ..      91     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.3
                      PriA_CRR 1 CpnCd 5
                                 Cp C+
  gi|15669335|ref|NP_248140.1| 5 CPKCN 9
                                 ****7 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0013
                      PriA_CRR 13 srnrLrCHyCgyte 26
                                  ++++L+C  Cgy+e
  gi|15669335|ref|NP_248140.1| 15 KDGKLKCAVCGYEE 28
                                  5799********96 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.7
                      PriA_CRR  1 CpnCd 5 
                                  Cp C 
  gi|15669335|ref|NP_248140.1| 69 CPKCG 73
                                  77774 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.48
                      PriA_CRR  17 LrCHyCgyt 25 
                                    +C  Cg+t
  gi|15669335|ref|NP_248140.1|  95 YKCKKCGHT 103
                                   689999997 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.2    0.0007      0.41       4      17 ..       5      18 ..       2      23 .. 0.88
   2 ?    6.8   0.6      0.01       5.9       2       9 ..      67      74 ..      66      76 .. 0.80
   3 ?    0.9   0.2      0.69     4e+02       3       8 ..      96     101 ..      94     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0007
                                  -SSS--EEEEEE-S CS
                zf-C4_Topoisom  4 CPkCggdLvlkrgk 17
                                  CPkC++ ++ k gk
  gi|15669335|ref|NP_248140.1|  5 CPKCNNLMLPKDGK 18
                                  ***********998 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.01
                                  EE-SSS-- CS
                zf-C4_Topoisom  2 ekCPkCgg 9 
                                  ++CPkCg 
  gi|15669335|ref|NP_248140.1| 67 IECPKCGH 74
                                  58****95 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.69
                                   E-SSS- CS
                zf-C4_Topoisom   3 kCPkCg 8  
                                   kC kCg
  gi|15669335|ref|NP_248140.1|  96 KCKKCG 101
                                   8****9 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   3.7     0.054        31       6      32 ..       5      29 ..       3      30 .. 0.77
   2 ?    5.3   0.1     0.028        16       5      16 ..      68      79 ..      66      85 .. 0.75
   3 ?    4.8   1.5     0.042        25       4      11 ..      95     102 ..      94     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.054
                 A2L_zn_ribbon  6 CsvCggngilnseqgylvCieCgasfp 32
                                  C +C++ ++   ++g l C  Cg++++
  gi|15669335|ref|NP_248140.1|  5 CPKCNNLMLP--KDGKLKCAVCGYEEE 29
                                  7778776666..999999999999876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.028
                 A2L_zn_ribbon  5 vCsvCggngiln 16
                                  +C +Cg+n  ++
  gi|15669335|ref|NP_248140.1| 68 ECPKCGHNEAYW 79
                                  688999987666 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.042
                 A2L_zn_ribbon   4 kvCsvCgg 11 
                                   ++C++Cg+
  gi|15669335|ref|NP_248140.1|  95 YKCKKCGH 102
                                   79999998 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.088        51       3      12 ..       4      13 ..       3      20 .. 0.80
   2 ?    2.9   0.3      0.25   1.4e+02       3      33 ..      20      54 ..      18      56 .. 0.58
   3 ?    5.1   0.1     0.052        30       4       9 ..      69      74 ..      67      85 .. 0.84
   4 ?    3.2   0.3       0.2   1.2e+02      41      46 .]      96     101 ..      94     106 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.088
                       zf-IS66  3 tCpcCGgllk 12
                                   Cp+C+ l+ 
  gi|15669335|ref|NP_248140.1|  4 FCPKCNNLML 13
                                  6*****9874 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.25
                       zf-IS66  3 tCpcCGg.llkpigedrvr...eeldipPakfrVi 33
                                  +C+ CG  + + +++ +     e+l+    k+ Vi
  gi|15669335|ref|NP_248140.1| 20 KCAVCGYeEETTAEGSKEYeykEHLENKKEKITVI 54
                                  69999995544444443334556666555555555 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.052
                       zf-IS66  4 CpcCGg 9 
                                  Cp+CG+
  gi|15669335|ref|NP_248140.1| 69 CPKCGH 74
                                  9***98 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.2
                       zf-IS66  41 aCpcCe 46 
                                   +C++C+
  gi|15669335|ref|NP_248140.1|  96 KCKKCG 101
                                   555554 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.7     0.071        41       3      25 ..       5      26 ..       4      27 .. 0.69
   2 ?    6.5   0.1     0.012       6.9      17      25 ..      66      74 ..      60      78 .. 0.85
   3 ?    4.4   3.2     0.054        31      19      25 ..      96     102 ..      85     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.071
                                  -SSS--B----SSS----SSS-- CS
                DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCGh 25
                                  C +C++   l k   ++C  CG+
  gi|15669335|ref|NP_248140.1|  5 CPKCNN-LMLPKDGKLKCAVCGY 26
                                  556654.3456666899999998 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.012
                                  ----SSS-- CS
                DNA_RNApol_7kD 17 piRCkeCGh 25
                                   i C +CGh
  gi|15669335|ref|NP_248140.1| 66 RIECPKCGH 74
                                  699*****9 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.054
                                   --SSS-- CS
                DNA_RNApol_7kD  19 RCkeCGh 25 
                                   +Ck+CGh
  gi|15669335|ref|NP_248140.1|  96 KCKKCGH 102
                                   7999999 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.011       6.6       7      22 ..      19      34 ..      15      37 .. 0.77
   2 ?    7.4   0.3    0.0057       3.3       5      14 ..      93     102 ..      90     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.011
                                  EE-TTT--EEEECC-- CS
               Desulfoferrod_N  7 YkCevCGniVeVleaG 22
                                   kC vCG + e + +G
  gi|15669335|ref|NP_248140.1| 19 LKCAVCGYEEETTAEG 34
                                  59*****876666665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0057
                                   -EEE-TTT-- CS
               Desulfoferrod_N   5 evYkCevCGn 14 
                                     YkC+ CG 
  gi|15669335|ref|NP_248140.1|  93 RFYKCKKCGH 102
                                   57*******5 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.3    0.0086       4.9       2      31 ..       5      33 ..       4      58 .. 0.70
   2 ?    5.4   0.4     0.034        19      16      23 ..      66      73 ..      61      78 .. 0.85
   3 ?    4.6   6.6     0.062        36       2      24 ..      69     102 ..      68     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0086
                      zf-Mss51  2 CPvpkhkqtapkhvdfeCpdCGiptycsee 31
                                  CP ++ +   pk+ +++C  CG+    + e
  gi|15669335|ref|NP_248140.1|  5 CPKCN-NLMLPKDGKLKCAVCGYEEETTAE 33
                                  ****6.5559************97655544 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.034
                      zf-Mss51 16 dfeCpdCG 23
                                  ++eCp+CG
  gi|15669335|ref|NP_248140.1| 66 RIECPKCG 73
                                  78*****9 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.062
                      zf-Mss51   2 CPvpkhkqt...........apkhvdfeCpdCGi 24 
                                   CP + h+++           +p+   ++C++CG 
  gi|15669335|ref|NP_248140.1|  69 CPKCGHNEAywwlqqtrcadEPETRFYKCKKCGH 102
                                   ****99999**********999***********6 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.5      0.17     1e+02      16      20 ..       5       9 ..       4      11 .. 0.89
   2 ?    4.9   0.1     0.041        23       4      11 ..      20      27 ..      18      30 .. 0.83
   3 ?    3.6   0.3      0.11        62      15      20 ..      68      73 ..      64      75 .. 0.81
   4 ?    6.1   0.7     0.017       9.9      14      20 ..      95     101 ..      90     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.17
                                  -TTT- CS
                        zf-HIT 16 CpkCn 20
                                  CpkCn
  gi|15669335|ref|NP_248140.1|  5 CPKCN 9 
                                  ****9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.041
                                  B-TTT-SB CS
                        zf-HIT  4 lCgvCgfp 11
                                  +C+vCg++
  gi|15669335|ref|NP_248140.1| 20 KCAVCGYE 27
                                  7*****95 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.11
                                  E-TTT- CS
                        zf-HIT 15 kCpkCn 20
                                   CpkC+
  gi|15669335|ref|NP_248140.1| 68 ECPKCG 73
                                  6****8 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.017
                                   EE-TTT- CS
                        zf-HIT  14 YkCpkCn 20 
                                   YkC kC+
  gi|15669335|ref|NP_248140.1|  95 YKCKKCG 101
                                   ******8 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.9     0.013       7.4      11      63 ..       5      50 ..       3      59 .. 0.76
   2 ?    5.8   0.5     0.027        16      29      42 ..      65      78 ..      51      96 .. 0.75
   3 ?    5.4   3.6     0.036        21      11      39 ..      69     103 ..      65     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                       DUF2387 11 CPrCsemDkirmweedeveyrECvsCgftdelsekgqsvakelktrvnkdeek 63
                                  CP+C++     m  +d++    C  Cg+ +e +++  s+  e k+++ +++ek
  gi|15669335|ref|NP_248140.1|  5 CPKCNNL----MLPKDGK--LKCAVCGYEEETTAE-GSKEYEYKEHLENKKEK 50
                                  6777653....5555554..67*********9999.78889999999998874 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.027
                       DUF2387 29 eyrECvsCgftdel 42
                                    +EC +Cg+ ++ 
  gi|15669335|ref|NP_248140.1| 65 TRIECPKCGHNEAY 78
                                  56899999999875 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.036
                       DUF2387  11 CPrCsemD......kirmweedeveyrECvsCgft 39 
                                   CP+C +        ++r+ +e e+++  C +Cg+t
  gi|15669335|ref|NP_248140.1|  69 CPKCGHNEaywwlqQTRCADEPETRFYKCKKCGHT 103
                                   99999888777776777777777888899999987 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.76   4.4e+02       2       7 ..       5      10 ..       4      16 .. 0.83
   2 ?    2.6   0.6      0.26   1.5e+02      37      45 ..      20      28 ..      18      42 .. 0.80
   3 ?    7.4   0.3    0.0085       4.9       2      10 ..      69      77 ..      65      86 .. 0.74
   4 ?    4.7   0.3      0.06        35       1       8 [.      96     103 ..      93     108 .] 0.73

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.76
                zinc_ribbon_13  2 CpKCgn 7 
                                  CpKC+n
  gi|15669335|ref|NP_248140.1|  5 CPKCNN 10
                                  ****97 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.26
                zinc_ribbon_13 37 sCknCgYte 45
                                   C  CgY e
  gi|15669335|ref|NP_248140.1| 20 KCAVCGYEE 28
                                  699999988 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0085
                zinc_ribbon_13  2 CpKCgntea 10
                                  CpKCg++ea
  gi|15669335|ref|NP_248140.1| 69 CPKCGHNEA 77
                                  777777765 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.06
                zinc_ribbon_13   1 kCpKCgnt 8  
                                   kC+KCg+t
  gi|15669335|ref|NP_248140.1|  96 KCKKCGHT 103
                                   57777776 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.7     0.013       7.7       5      30 ..       4      27 ..       3      28 .. 0.90
   2 ?    4.7   0.3     0.041        24       6      11 ..      69      74 ..      67      75 .. 0.66
   3 ?    0.6   0.2      0.76   4.4e+02      24      29 ..      97     102 ..      95     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                 zf-NADH-PPase  5 FCgrCGaptepaeggwarvCpaCgle 30
                                  FC++C   + p++g  ++ C+ Cg+e
  gi|15669335|ref|NP_248140.1|  4 FCPKCNNLMLPKDG--KLKCAVCGYE 27
                                  9****999999999..999****997 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.041
                 zf-NADH-PPase  6 CgrCGa 11
                                  C++CG+
  gi|15669335|ref|NP_248140.1| 69 CPKCGH 74
                                  666664 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.76
                 zf-NADH-PPase  24 CpaCgl 29 
                                   C  Cg+
  gi|15669335|ref|NP_248140.1|  97 CKKCGH 102
                                   889998 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   9.0      0.43   2.5e+02       1      44 [.       4      47 ..       4     104 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.43
                RPA_interact_C  1 lCPvCkkrklketsevifCe.Cglrletseesltleelkrrlaet 44
                                  +CP C++  l ++   + C+ Cg + et+ e  +  e k++l+++
  gi|15669335|ref|NP_248140.1|  4 FCPKCNNLMLPKD-GKLKCAvCGYEEETTAEGSKEYEYKEHLENK 47
                                  6****97776654.6699*99**9988865555555555555544 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   9.9       0.2   1.2e+02      46      90 .]       3     101 ..       2     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.2
                                   TB-TTT--B--CTTT.EEEEE.............E-SSS-E........................................ CS
                          Rpr2  46 tvCkkCgsvlipgvt.csvrv.............enkskkkkkkkkka................................. 79 
                                   ++C kC+++++p     ++ v             e            +                                 
  gi|15669335|ref|NP_248140.1|   3 KFCPKCNNLMLPKDGkLKCAVcgyeeettaegskEY-----------Eykehlenkkekitviesegletlpttriecpkc 72 
                                   79**********843134444667766666555422...........2233334444458899999999999888888888 PP

                                   ....................EEEEETTTT CS
                          Rpr2  80 ..................dvlvvtClaCg 90 
                                                      +  ++C++Cg
  gi|15669335|ref|NP_248140.1|  73 ghneaywwlqqtrcadepETRFYKCKKCG 101
                                   88888888888888888866678888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        60  (0.00334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 694.85
//
Query:       gi|15669336|ref|NP_248141.1|  [L=169]
Description: mutator MutT [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-24   84.9   0.0    5.4e-24   84.7   0.0    1.1  1  NUDIX     NUDIX domain
     0.0011   18.5   0.0      0.017   14.7   0.0    2.0  1  DUF4916   Domain of unknown function (DUF4916)
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.17   11.9   0.0    1.4  1  NUDIX_4   NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.0   9.1e-28   5.4e-24       2     129 ..      39     161 ..      38     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 9.1e-28
                                   EEEEEEEE.EEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE CS
                         NUDIX   2 lrravgvv.llnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd 80 
                                   l++av+v  ++++++++Ll++r+++pf+g ++lPgG+ve gEt+eeA++RE++EEtGl+++   llg    ++++++++++
  gi|15669336|ref|NP_248141.1|  39 LHPAVAVDgIIEKDNKILLIKRKNNPFKGcFALPGGFVECGETVEEAVVREIKEETGLIPKVKSLLG----VYSSPDRDPR 115
                                   5889999999999999*************778***********************************....8999999999 PP

                                   EEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHH CS
                         NUDIX  81 eheilyvfl.eevegelepndenevsevrwvpleellkeklaaesrkllp 129
                                    h i++vf  +   gel+ +  ++ +e+++++l+ l  +kla +++k+++
  gi|15669336|ref|NP_248141.1| 116 GHVISIVFIlDVIGGELKAG--DDAKEAEFFDLNNL--PKLAFDHEKIIK 161
                                   *****999989999999988..66669999******..666777766665 PP

>> DUF4916  Domain of unknown function (DUF4916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.8e-06     0.017      57     144 ..      73     149 ..      42     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.8e-06
                                   EEE--TT--HHHHHHHHHHHHH-TT--B---SS---SEEEEEESSTTSSSEE-TT-EEEEEEEEEEB-.S-----TTEEEE CS
                       DUF4916  57 sGrvlyhetvreallrhiekdlGelalpqlPaslqPftvaeyfPtpgvseytdprqhavslayvvpva.Gdceprqdalel 136
                                    G v   etv ea++r+i+++ G      +P+    + v   + +    +  dpr h +s+++++ v  G+ ++ +da e 
  gi|15669336|ref|NP_248141.1|  73 GGFVECGETVEEAVVREIKEETGL-----IPKVKSLLGV---YSS----PDRDPRGHVISIVFILDVIgGELKAGDDAKEA 141
                                   577778888888888888888875.....3443333333...344....459*************8752799********9 PP

                                   EEE-HHHH CS
                       DUF4916 137 eWltpeea 144
                                   e+++ ++ 
  gi|15669336|ref|NP_248141.1| 142 EFFDLNNL 149
                                   99988765 PP

>> NUDIX_4  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.9e-05      0.17       4      49 ..      48      96 ..      45     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.9e-05
                                  EEEECTEEEEEE--TTSSSTT-EE-SEEE.-TTS-HHHHHH...HHHHS- CS
                       NUDIX_4  4 lirddgrvllekRpekgllggLwefPgge.eegeeleeala...reelgi 49
                                  +i +d+++ll kR+++   +g + +Pgg  e ge++eea++   +ee+g+
  gi|15669336|ref|NP_248141.1| 48 IIEKDNKILLIKRKNN-PFKGCFALPGGFvECGETVEEAVVreiKEETGL 96
                                  67788*********97.9********999899999777776555666775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1093.35
//
Query:       gi|15669337|ref|NP_248142.1|  [L=184]
Description: hypothetical protein MJ_1150 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-58  195.3   0.0    6.6e-58  195.1   0.0    1.0  1  DUF99     Protein of unknown function DUF99


Domain annotation for each model (and alignments):
>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.1   0.0   3.7e-62   6.6e-58       2     182 ..       7     180 ..       6     181 .. 0.97

  Alignments for each domain:
  == domain 1  score: 195.1 bits;  conditional E-value: 3.7e-62
                                   GSEEEEEEEEE.....-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSEETTTEE- CS
                         DUF99   2 eirvlGiddsfferkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrleredirvvlldGitiagFNvv 82 
                                   e+ v+G+dd++f+  k d+ ++l+G++mr++r++dg++f++++ dG+D+te+ii++vk++++++i+v++l Git++gFN++
  gi|15669337|ref|NP_248142.1|   7 EVEVIGFDDAPFN--KADKVCILIGTYMRGNRIIDGIYFRKFKKDGMDVTEKIIDIVKEKHYKKIKVIFLAGITFGGFNIA 85 
                                   678**********..569*************************************************************** PP

                                   -HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT....EEEEEESS-HHHHHHHHHHC- CS
                         DUF99  83 DlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevektgeelyvravGieleeaaklvrklt 163
                                   Dl ++ +et+ Pvi+v+ + p+ +k+  aL+k+f+d++eR++li+++ ++ e++e+    +yv++vG+++e ++++++k+ 
  gi|15669337|ref|NP_248142.1|  86 DLWEINKETEKPVIVVIDKYPNKEKIFLALKKYFDDADERIKLINSF-PEPEKMEN----IYVQYVGADKEFVKNVIKKTK 161
                                   ***********************************************.89999999....********************* PP

                                   SSSSS-HHHHHHHHHHHHH CS
                         DUF99 164 legriPEPlRvAhliAsal 182
                                   l+++iPE+lR++hli++++
  gi|15669337|ref|NP_248142.1| 162 LKSKIPECLRISHLIGRGF 180
                                   ****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1189.58
//
Query:       gi|15669338|ref|NP_248143.1|  [L=113]
Description: hypothetical protein MJ_1151 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.043   14.0   1.5      0.043   14.0   1.5    2.1  2  CTK3_C    CTD kinase subunit gamma CTK3 C-terminus
      0.081   10.9   0.3      0.097   10.6   0.3    1.0  1  Prominin  Prominin


Domain annotation for each model (and alignments):
>> CTK3_C  CTD kinase subunit gamma CTK3 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.5   4.8e-06     0.043      15      48 ..      10      43 ..       7      60 .. 0.83
   2 ?    2.2   3.7     0.023     2e+02      12      58 ..      61     104 ..      52     113 .] 0.64

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-06
                        CTK3_C 15 rhKRlrEniWvvprskekslateaEfenlWeets 48
                                  r+K+ +   W+++ +++ + + ++Ef++l+ee+ 
  gi|15669338|ref|NP_248143.1| 10 RNKKFKKPEWLIEVEDKIEKMADEEFDKLFEEIY 43
                                  89**************888888*********975 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.023
                        CTK3_C  12 DRErhKRlrEniWvvprskekslateaEfenlWeetsdlneddeeea 58 
                                   D  + K+ +   W+++ +k  +l + +E  +++  +++ +e+   + 
  gi|15669338|ref|NP_248143.1|  61 DKSKYKKYKKPKWLIEAEK--ELEKAIETGEYFKWLKEQGEKYR-KQ 104
                                   555779999999***9998..45555666555555555444322.22 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   1.1e-05     0.097     188     281 ..      19     110 ..      10     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 1.1e-05
                      Prominin 188 flkdvpqhidhvlvqnyeelekhvsddLddagkhlgldladtlesnvlpaLaelerllenlkeakeqLeqvnklekeLrks 268
                                   +l +v ++i++++++++ +l +++ ++L+  g   +l++++t +s+ +++ ++ ++l+e+ ke ++++e+ +++ k L+++
  gi|15669338|ref|NP_248143.1|  19 WLIEVEDKIEKMADEEFDKLFEEIYEKLNRGGLREVLNVHKTDKSK-YKKYKKPKWLIEAEKELEKAIETGEYF-KWLKEQ 97 
                                   6789******************************************.*********************998876.559999 PP

                      Prominin 269 gsqLrdglrgvkr 281
                                   g+++r+  +++k+
  gi|15669338|ref|NP_248143.1|  98 GEKYRKQKKEIKK 110
                                   9999988777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1715  (0.0956551); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 802.94
//
Query:       gi|15669339|ref|NP_248144.1|  [L=73]
Description: hypothetical protein MJ_1152 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.018   15.1   0.1      0.022   14.9   0.1    1.1  1  Ribonuclease_P   Ribonuclease P
       0.15   12.0   2.7       0.45   10.5   0.7    1.9  2  tRNA_synt_1c_R1  Glutaminyl-tRNA synthetase, non-specific RNA


Domain annotation for each model (and alignments):
>> Ribonuclease_P  Ribonuclease P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   2.4e-06     0.022      60     109 ..       7      59 ..       3      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-06
                Ribonuclease_P  60 rikRllReafrlnkdelpa...gldlvviakkgaaeadfaelekelekllkkl 109
                                   ++kR++++ +   k+e ++     d +v +k+++++++++e+ k+++k+++++
  gi|15669339|ref|NP_248144.1|   7 HVKRIVKKYLGSKKAESEEediLPDWIVKVKNEIENITYEEYVKDVDKFFNEV 59 
                                   69**************9998887899**********************99875 PP

>> tRNA_synt_1c_R1  Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.7     5e-05      0.45     114     153 ..       2      38 ..       1      44 [. 0.87
   2 ?    3.3   0.2     0.008        72     131     153 ..      39      61 ..      26      66 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5e-05
               tRNA_synt_1c_R1 114 evtpeqieeaVekyieenkeeieekryrknlgkllaevkk 153
                                   ++ ++ +++ V+ky+ ++k+e ee+     l++ + +vk+
  gi|15669339|ref|NP_248144.1|   2 VIMKKHVKRIVKKYLGSKKAESEEEDI---LPDWIVKVKN 38 
                                   678999******************987...8888888884 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.008
               tRNA_synt_1c_R1 131 nkeeieekryrknlgkllaevkk 153
                                   + e+i  + y k + k ++evkk
  gi|15669339|ref|NP_248144.1|  39 EIENITYEEYVKDVDKFFNEVKK 61 
                                   44455556667777788888884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1469  (0.0819343); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 475.47
//
Query:       gi|15669340|ref|NP_248145.1|  [L=62]
Description: hypothetical protein MJ_1153 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.025   13.9   0.5      0.025   13.9   0.5    1.0  1  P35       Apoptosis preventing protein
      0.045   13.9   1.2      0.051   13.8   1.2    1.1  1  Ivy       Inhibitor of vertebrate lysozyme (Ivy)


Domain annotation for each model (and alignments):
>> P35  Apoptosis preventing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   2.8e-06     0.025     107     156 ..       2      52 ..       1      60 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-06
                           P35 107 kgsvlkskfakilkshdytdeksieayekyclpklvderkdy.yvavcvlk 156
                                   k ++lk k+aki+k h y   k +   e+ +    ++e k++   a+ v k
  gi|15669340|ref|NP_248145.1|   2 KENILKQKWAKIMKKHKYKKPKWLIKAEQKAEKMTLEEEKEWiEKAIRVYK 52 
                                   6789***************99976555555555555555554145666655 PP

>> Ivy  Inhibitor of vertebrate lysozyme (Ivy)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.2   5.7e-06     0.051       3      41 ..       3      39 ..       1      49 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.7e-06
                                  SCCCHHHHHHHCTTS-.S--CHHHCT-SEEEEEEEEEETT CS
                           Ivy  3 qpeyraawaklvkgek.rlPeWvrsgsgtsspsqavtlag 41
                                  ++ ++++wak++k++k + P+W+++++   + ++++tl++
  gi|15669340|ref|NP_248145.1|  3 ENILKQKWAKIMKKHKyKKPKWLIKAE---QKAEKMTLEE 39
                                  66789*******9998568******94...4444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1912  (0.106643); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 383.33
//
Query:       gi|15669341|ref|NP_248146.1|  [L=451]
Description: hypothetical protein MJ_1154 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-20   71.8   0.2    1.4e-19   70.5   0.2    1.7  1  HD             HD domain
    0.00064   19.3   0.0     0.0014   18.1   0.0    1.6  1  HDOD           HDOD domain
  ------ inclusion threshold ------
      0.024   14.6   0.5        6.2    6.7   0.1    2.4  2  HD_3           HD domain
       0.11   12.3   0.7        4.9    7.0   0.2    2.9  2  Arg_repressor  Arginine repressor, DNA binding domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.2     3e-23   1.4e-19       1     121 [.      50     149 ..      50     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 3e-23
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            HD   1 rleHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldledv 81 
                                   r+eHsl+++ +a ++ae+++  +d+el+++ aLlHDiG++pf+++ e         ++He++g++++++  ++++ + e++
  gi|15669341|ref|NP_248146.1|  50 RFEHSLGTMFIASKIAEKIN--ADVELTRVSALLHDIGHPPFSHTLEI------CGYSHEVFGRKKIKHMNLDNFSKSEII 122
                                   79******************..**********************7776......6789****************8867777 PP

                                   HHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                            HD  82 aklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                     l r+++e +              ++ + +++++D+l +
  gi|15669341|ref|NP_248146.1| 123 KTLNRKNLEGKI-------------ISGDVDADRMDYLLR 149
                                   777777777776.............999*********987 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.2e-07    0.0014      96     138 ..      51      92 ..      40     110 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.2e-07
                                   HHHHHHHHHHHHHHHHHTT-S-HHHHHHHHHTTTHHHHHHHHH CS
                          HDOD  96 wehslavAlvarelaeelgledpeeaflaGLLhdiGklvllsl 138
                                    ehsl + ++a ++ae+++ +  e   +++LLhdiG   + ++
  gi|15669341|ref|NP_248146.1|  51 FEHSLGTMFIASKIAEKINADV-ELTRVSALLHDIGHPPFSHT 92 
                                   69******************99.*************9887766 PP

>> HD_3  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0028        13       3      59 ..      29      84 ..      27      86 .. 0.73
   2 ?    6.7   0.1    0.0014       6.2      73     109 ..     358     397 ..     351     411 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0028
                          HD_3  3 kLKfqkRqgwlq..tgrvreesvaeHmwrvalmalllseelkekvdiarvikmfLiHDl 59
                                  +L+++k +g +    ++  + +  eH++ + ++a  ++e+++  +d++ +   +L+HD+
  gi|15669341|ref|NP_248146.1| 29 RLRNIKQTGLTYlvYPS-ANHTRFEHSLGTMFIASKIAEKIN--ADVELTRVSALLHDI 84
                                  66666666544411444.677789******************..666666667899*97 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0014
                          HD_3  73 lakeekeeeekeaaerilkllpee...laeellalweEFe 109
                                    ++++ke +e+++++ri k+l+e    ++ +l ++++E+ 
  gi|15669341|ref|NP_248146.1| 358 PKEKIKELRENNVKDRINKILKELdvkVESKLIDILKEYG 397
                                   46899*********999999877666699*********96 PP

>> Arg_repressor  Arginine repressor, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0011       4.9       7      33 ..     371     397 ..     365     400 .. 0.90
   2 ?    2.3   0.0     0.032   1.4e+02      49      66 ..     430     447 ..     423     450 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHS---SHHHHHHHHHTTT CS
                 Arg_repressor   7 qklikkiikeekissQkelvelLkeeG 33 
                                   + +i ki+ke +++    l+++Lke+G
  gi|15669341|ref|NP_248146.1| 371 KDRINKILKELDVKVESKLIDILKEYG 397
                                   679**********************99 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.032
                                   T-EEEETTSTSEEEE-B- CS
                 Arg_repressor  49 glvkvraengeyvYvlpa 66 
                                   gl+k r++  +yvY+l +
  gi|15669341|ref|NP_248146.1| 430 GLIKERFNRRTYVYCLNN 447
                                   899************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2862.64
//
Query:       gi|15669342|ref|NP_248147.1|  [L=603]
Description: hypothetical protein MJ_1155 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     1e-113  379.5   0.1   1.5e-113  379.0   0.1    1.3  1  Radical_SAM_N  Radical SAM N-terminal
    6.1e-17   62.3   0.4    1.3e-16   61.3   0.4    1.5  1  DUF3362        Domain of unknown function (DUF3362)
    7.9e-13   49.1   2.0    1.3e-12   48.4   0.7    2.1  3  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
      0.068   13.2   0.4       0.17   11.9   0.4    1.6  1  Arcadin_1      Arcadin 1


Domain annotation for each model (and alignments):
>> Radical_SAM_N  Radical SAM N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.0   0.1  3.4e-117  1.5e-113       1     298 []       2     292 ..       2     292 .. 0.94

  Alignments for each domain:
  == domain 1  score: 379.0 bits;  conditional E-value: 3.4e-117
                 Radical_SAM_N   1 flpvsrkemeergwdelDvilvsgDaYvDhpsfgaaligrlLeaeGfrvgiiaqPdwksaedfkklGkPrlffgvsaGnlD 81 
                                   flp++++em+e gw+elD+i+v+gDaY+Dh  fga+++gr+L ++G+rvgiiaqPdwk+ +d+k+lGkP++ff+v+aGnlD
  gi|15669342|ref|NP_248147.1|   2 FLPTTKEEMDEWGWEELDIIIVTGDAYIDHYLFGASVVGRYLVEHGYRVGIIAQPDWKNLDDIKRLGKPNYFFAVTAGNLD 82 
                                   9******************************************************************************** PP

                 Radical_SAM_N  82 smvnkytaekklrsdDaytpggkagkRPdravivYsnlireaykdvpvvlGgiEaSLRriahYDywsdkvrrsilldskad 162
                                   sm+++yt +k+lr+ D+ +++g   kRPdra+ivY+nli++a+k+vp+ lGgiEaSLRr++hYDyw++kvr+s+l+dskad
  gi|15669342|ref|NP_248147.1|  83 SMLAHYTPQKRLRDFDSMSNEGIR-KRPDRATIVYTNLIKRAFKGVPIALGGIEASLRRFSHYDYWDNKVRKSVLIDSKAD 162
                                   *******************99976.9******************************************************* PP

                 Radical_SAM_N 163 llvyGmgeraiveiakrlakgeeveelkdirgtavllkkea..kake.kevielpsyeevkedkklyaeafrlleeetnpl 240
                                   +l+yGmge++i++i+k+l++ge++++l+ i+gt+v +++++  + ke  e+ elps+eev ++k++yae++r l +     
  gi|15669342|ref|NP_248147.1| 163 ILMYGMGEKSILAITKALESGENIKDLE-INGTVVRVNERKigDIKErYETKELPSHEEVVNSKEKYAEMHRKLMT----- 237
                                   *************************985.******99984446444437899*****************9998865..... PP

                 Radical_SAM_N 241 nakalvqkhgdravvlnppalplsteelDevyelpyarkahpsykkkkipalemikfS 298
                                    +k ++qk g++++v+ pp + l+++e+De+ye+p++r+ahpsy+   +p +  ++fS
  gi|15669342|ref|NP_248147.1| 238 MDKVIYQKVGNQYLVQFPP-IYLTEKEMDEIYEMPFERRAHPSYS--YVPGIVPVQFS 292
                                   457999**99999988765.789*********************5..89999888887 PP

>> DUF3362  Domain of unknown function (DUF3362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.4   2.8e-20   1.3e-16       2      75 ..     510     578 ..     509     602 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 2.8e-20
                       DUF3362   2 qVqtFyPsPmatattmYhtgknpltkvkreeesvdvvrgekerrlhkAllrYhdpknwpllreALkkmGredLi 75 
                                   qVq F P+Pm+++ttmYhtg np+t     +e+v+v+ + +e++++kA+  Y++ +nw+   e  k +G + +i
  gi|15669342|ref|NP_248147.1| 510 QVQVFTPTPMTLSTTMYHTGINPIT-----NEKVYVPYTYREKKIQKAICLYREEENWEKALEGFKMVGYKGVI 578
                                   9************************.....9***************************9988888888877655 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.4   6.5e+03      91     142 ..      58     105 ..       8     117 .. 0.60
   2 !   48.4   0.7   2.9e-16   1.3e-12       1     141 [.     293     469 ..     293     501 .. 0.81
   3 ?   -3.5   0.0       2.7   1.2e+04     116     136 ..     548     571 ..     527     582 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.4
                                   HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  91 eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagi 142
                                   ++ l+ +++lg   + + + a++ +    ++   +t++++l+ ++ + + gi
  gi|15669342|ref|NP_248147.1|  58 WKNLDDIKRLGKPNYFFAVTAGNLD---SML-AHYTPQKRLRDFDSMSNEGI 105
                                   4566666666655555555555555...233.34555555555555555555 PP

  == domain 2  score: 48.4 bits;  conditional E-value: 2.9e-16
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS..................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly..................... 60 
                                   vv+ rgC ++CsfC++ ++  ++++ +++s ++il+e+++l  + + k+vi+  g p+++                     
  gi|15669342|ref|NP_248147.1| 293 VVTHRGCFGGCSFCSILHH--QGKVIQNRSERSILKEIRKLLNHEDFKGVIQDIGAPTANmyrmgckkgladrcpknclyp 371
                                   5788**************8..********************844447777777777************************* PP

                                   ..........TTHHHHHHHHHHTCCCTEEEEEEE.CSSCHG.........HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHH CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.........xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  61 ..........pdfvellerlaklavpgiritvet.ngtlpd.........eeklerllelg.vdrvslgleaaddekvlkl 120
                                             +++++l+++++ +   g  ++v + +g++ d         e+++++l +++   r+ +  e+++++ v k 
  gi|15669342|ref|NP_248147.1| 372 epcenliinhKPLIKLYRKIRDIV--GDDVRVYVrSGVRYDlimydeeygEDYIKELSKYHvSGRLKVAPEHISKK-VCKA 449
                                   **********99999999999995..44444333144444577778******************************.9999 PP

                                   HTCTSHHHHHHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 121 mnrghtfeevlealeklreag 141
                                   +  +++   +++ lek+re  
  gi|15669342|ref|NP_248147.1| 450 I-QKPDGRLFKKFLEKYREIA 469
                                   9.6677777777777777653 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.7
                                   HHHHHHT...CTSHHHHHHHHHHH CS
                                   xxxxxxx...xxxxxxxxxxxxxx RF
                   Radical_SAM 116 kvlklmn...rghtfeevlealek 136
                                   k++k ++     +++e+ le++++
  gi|15669342|ref|NP_248147.1| 548 KIQKAIClyrEEENWEKALEGFKM 571
                                   566666643233445555555544 PP

>> Arcadin_1  Arcadin 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   3.8e-05      0.17      27      87 ..     210     267 ..     199     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                                   EEEE------.------------------------------.--EEEEEEEEEE-HHHHHHH CS
                     Arcadin_1  27 vEerelpgpv.lvasdeedaeiaRevapivqqivrslpllslnkvkvpritLvlteeElekl 87 
                                    E +elp    +v+s e+ ae+ R+++++ ++i ++++   l ++  p i  +lte+E++++
  gi|15669342|ref|NP_248147.1| 210 YETKELPSHEeVVNSKEKYAEMHRKLMTMDKVIYQKVGNQYLVQF--PPI--YLTEKEMDEI 267
                                   589999999889************************998885555..865..89****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 4001.34
//
Query:       gi|15669343|ref|NP_248148.1|  [L=110]
Description: hypothetical protein MJ_1155.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-15   55.5   2.2    5.7e-15   55.3   2.2    1.1  1  AzlD             Branched-chain amino acid transport protein 
  ------ inclusion threshold ------
      0.012   15.9   5.4      0.017   15.4   5.4    1.2  1  TctB             Tripartite tricarboxylate transporter TctB f
       0.55   10.5   5.1        1.9    8.7   0.3    2.5  2  XhlA             Haemolysin XhlA


Domain annotation for each model (and alignments):
>> AzlD  Branched-chain amino acid transport protein (AzlD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   2.2   9.5e-19   5.7e-15       2      98 ..       5     103 ..       4     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 9.5e-19
                          AzlD   2 llaillmalvtyltRylplllfrr.lklppwlq...rllryvPiavLaaliapellaetgklsaslglarllaalvavlva 78 
                                   +lai+++a++tyl+Ry+p+ l+++ ++++++++   ++l y +++v++al++++++  +  +s    l   + +++a++ +
  gi|15669343|ref|NP_248148.1|   5 ILAIIFVAVGTYLIRYIPIHLHSKiKNIDEKVKeinEILIYSSTSVISALFITSFIKFPIIFS--NVLISTISLIFAIVSY 83 
                                   79*******************************99999******************8876644..4555555666666666 PP

                          AzlD  79 lltrnlllsilvGmavyall 98 
                                    + +nl++sil+++++y+l+
  gi|15669343|ref|NP_248148.1|  84 KKWNNLGISILISVVIYYLA 103
                                   66669*************97 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   5.4   2.8e-06     0.017      35     130 ..       6     107 ..       4     108 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.8e-06
                          TctB  35 lgvllallgllllv......aadgekeekearedwrkllklvlallaalllyalllepl...Gfilatalflllllgreer 106
                                   l+++++++g+ l+        ++ ++++++ +e ++ l+     ++ al++  ++  p+     +++t+ ++++++   ++
  gi|15669343|ref|NP_248148.1|   6 LAIIFVAVGTYLIRyipihlHSKIKNIDEKVKEINEILIYSSTSVISALFITSFIKFPIifsNVLISTISLIFAIV---SY 83 
                                   6777777776666688877733333443333333333332222222233332222222233357999995555555...34 PP

                          TctB 107 kwlkalilavvlallvyllFtklL 130
                                   k + +l++++++++++y+l +k+L
  gi|15669343|ref|NP_248148.1|  84 KKWNNLGISILISVVIYYLASKFL 107
                                   469***************988877 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3   0.00032       1.9      31      61 ..      26      56 ..      23      62 .. 0.81
   2 ?    3.6   0.7     0.013        76      54      66 ..      89     101 ..      70     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00032
                          XhlA 31 eekiknleedlkklesnqkWlirtiiGalis 61
                                   +kikn+ e++k++ + +    + +i+al  
  gi|15669343|ref|NP_248148.1| 26 HSKIKNIDEKVKEINEILIYSSTSVISALFI 56
                                  5799999999999999999999999998754 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.013
                          XhlA  54 tiiGalisaviyl 66 
                                   + i++lis+viy+
  gi|15669343|ref|NP_248148.1|  89 LGISILISVVIYY 101
                                   5699*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1169  (0.0652016); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 711.95
//
Query:       gi|15669344|ref|NP_248149.1|  [L=73]
Description: hypothetical protein MJ_1155.2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.97    7.9   4.9       0.98    7.9   4.9    1.0  1  FUSC      Fusaric acid resistance protein family


Domain annotation for each model (and alignments):
>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.9   5.5e-05      0.98     407     460 ..      13      66 ..       1      69 [. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 5.5e-05
                          FUSC 407 vlaallllfvvlPhvdgfplLvlvlapplllgglllarprlagiglglavffal 460
                                     + +l+l++++P+++gf  L ++++ +++l+   ++ p l+++  g++  +++
  gi|15669344|ref|NP_248149.1|  13 FSLTVLFLLLLIPNLKGFGKLSAIIGGFIALIFQYFGYPSLGILFAGILSPIII 66 
                                   557789999*********************************999999877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 494.49
//
Query:       gi|15669345|ref|NP_248150.1|  [L=903]
Description: cell division protein CDC48 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     3e-102  338.3   1.5    1.3e-49  168.0   0.0    3.5  3  AAA              ATPase family associated with various cellul
    5.2e-37  125.4   1.9      1e-17   63.7   0.1    3.3  2  AAA_lid_3        AAA+ lid domain
    1.7e-32  111.4   0.0      1e-31  108.9   0.0    2.3  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    9.1e-18   64.5   0.0    4.5e-08   33.0   0.0    3.0  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.6e-17   63.5   0.1    2.6e-08   34.2   0.0    3.1  2  AAA_2            AAA domain (Cdc48 subfamily)
    4.9e-16   58.3   1.3    5.7e-15   54.8   0.9    2.7  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    2.2e-14   53.6   1.9    8.3e-06   25.8   0.0    4.3  2  AAA_5            AAA domain (dynein-related subfamily)
    3.2e-14   53.7   1.4    3.6e-06   27.5   0.0    4.5  4  AAA_16           AAA ATPase domain
    5.6e-12   45.5   5.5    1.3e-05   24.5   0.0    3.2  2  TIP49            TIP49 P-loop domain
    1.7e-11   44.2   0.1    8.7e-05   22.6   0.0    3.4  3  AAA_14           AAA domain
      2e-11   44.2   0.0    3.4e-05   24.0   0.0    2.6  2  AAA_33           AAA domain
    9.3e-11   41.6   6.7    3.6e-06   26.9   0.1    4.0  3  Vps4_C           Vps4 C terminal oligomerisation domain
    7.3e-10   39.3   6.5     0.0033   17.7   0.1    5.4  3  AAA_22           AAA domain
    1.4e-08   34.7   0.0     0.0037   17.0   0.0    2.5  2  IstB_IS21        IstB-like ATP binding protein
    2.1e-08   34.8   0.0      0.021   15.4   0.0    3.5  2  AAA_18           AAA domain
    5.4e-08   33.3   0.0     0.0031   17.8   0.0    2.6  2  AAA_28           AAA domain
      6e-08   32.6   0.1      0.019   14.7   0.0    3.9  2  Sigma54_activat  Sigma-54 interaction domain
    1.8e-07   30.6   0.0     0.0015   17.8   0.0    2.8  2  DUF815           Protein of unknown function (DUF815)
    4.1e-07   29.6   0.3      0.045   13.1   0.1    3.0  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.4e-06   28.2   5.2      0.038   13.7   0.0    4.1  4  AAA_24           AAA domain
    1.9e-06   27.3   0.4      0.069   12.4   0.0    3.4  3  Zeta_toxin       Zeta toxin
    2.1e-06   27.4   0.0      0.027   14.0   0.0    2.7  2  AAA_7            P-loop containing dynein motor region
    2.8e-06   26.9   2.8       0.21   11.0   0.1    3.6  3  PhoH             PhoH-like protein
    3.3e-06   27.1   0.1       0.16   12.0   0.0    2.9  3  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    5.7e-06   26.7   0.0       0.26   11.7   0.0    3.0  2  RNA_helicase     RNA helicase
    9.3e-06   25.3   1.3        2.1    7.9   0.0    4.0  4  AAA_25           AAA domain
    1.3e-05   25.0   0.0       0.17   11.7   0.0    2.8  2  AAA_3            ATPase family associated with various cellul
    1.5e-05   25.5   0.1        0.3   11.6   0.0    3.2  2  ABC_tran         ABC transporter
    7.7e-05   23.1   2.2       0.59   10.6   0.0    4.0  2  AAA_17           AAA domain
    9.7e-05   22.5   0.0       0.61   10.2   0.0    2.8  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00036   20.3   0.2       0.53   10.0   0.0    2.8  2  AAA_30           AAA domain
    0.00088   18.6   0.7       0.44    9.7   0.0    2.7  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0012   18.8   1.1          1    9.3   0.1    3.2  2  NACHT            NACHT domain
     0.0016   17.6   0.0        1.6    7.8   0.0    2.5  2  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0016   17.8  16.3       0.43    9.9   0.1    5.5  4  ATPase           KaiC
     0.0024   17.1   4.4        1.5    7.9   0.0    4.1  4  NB-ARC           NB-ARC domain
     0.0026   16.9   0.0        3.3    6.8   0.0    3.0  3  MCM              MCM P-loop domain
     0.0026   17.6   9.8        4.7    6.9   0.0    3.7  4  AAA_11           AAA domain
      0.008   16.2   5.3      0.072   13.1   4.2    2.7  1  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
     0.0088   16.2   0.0        3.1    7.9   0.0    3.0  2  Cytidylate_kin2  Cytidylate kinase-like family
  ------ inclusion threshold ------
      0.011   15.1   0.2        2.1    7.7   0.0    2.6  2  IPT              Isopentenyl transferase
      0.012   15.3   0.5        8.3    6.2   0.0    3.3  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.012   15.3   0.0       0.94    9.2   0.0    2.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.014   14.3   0.3        3.3    6.5   0.0    2.8  3  AFG1_ATPase      AFG1-like ATPase
      0.015   14.8   1.3      0.029   13.9   1.3    1.5  1  Allexi_40kDa     Allexivirus 40kDa protein
      0.017   15.2   0.7        2.9    7.9   0.0    3.2  2  ResIII           Type III restriction enzyme, res subunit
      0.017   15.2   0.0      0.058   13.4   0.0    1.9  1  Molydop_binding  Molydopterin dinucleotide binding domain
      0.021   13.8   2.2        1.7    7.5   0.0    3.4  3  AAA_6            Hydrolytic ATP binding site of dynein motor 
      0.028   14.5   2.2        2.4    8.3   0.0    3.8  3  MMR_HSR1         50S ribosome-binding GTPase
      0.032   14.6   0.0        1.1    9.7   0.0    2.9  2  DUF1677          Protein of unknown function (DUF1677)
      0.035   14.2   0.6       0.34   11.1   0.1    2.8  2  Abi_C            Abortive infection C-terminus
      0.036   14.5   1.2      0.036   14.5   1.2    3.2  2  eIF3_N           eIF3 subunit 6 N terminal domain
      0.038   14.0   8.4       0.19   11.8   7.6    2.4  2  THP2             Tho complex subunit THP2
      0.055   13.3   2.9        0.4   10.5   0.0    3.2  3  PhageMin_Tail    Phage-related minor tail protein
      0.067   13.0   5.8       0.19   11.5   5.8    1.7  1  Baculo_p24       Baculovirus P24 capsid protein
      0.068   12.9   0.0         13    5.6   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
        0.1   12.4   8.6       0.22   11.4   6.6    2.4  2  Sec34            Sec34-like family
       0.12   12.2   2.0       0.26   11.1   0.7    2.3  1  Glutaredoxin2_C  Glutaredoxin 2, C terminal domain
       0.12   12.7   7.4        4.1    7.7   0.4    3.3  2  AAA_19           AAA domain
       0.13   13.0  11.2      0.084   13.6   3.0    3.3  2  DUF2203          Uncharacterized conserved protein (DUF2203)
       0.15   12.2   2.1         12    6.0   0.0    3.1  2  SKI              Shikimate kinase
       0.18   11.5   2.6        8.3    6.1   0.1    2.8  2  Cytidylate_kin   Cytidylate kinase
       0.19   11.3   3.4          4    7.0   0.0    3.3  3  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.62   10.4   6.0        0.9    9.8   4.0    2.3  1  Med15_fungi      Mediator complex subunit 15
       0.75   10.2   7.4        0.2   12.0   0.3    3.4  3  DUF2383          Domain of unknown function (DUF2383)
       0.77    9.0   6.3        1.1    8.5   4.3    1.8  1  CorA             CorA-like Mg2+ transporter protein
        1.6    6.6  10.3        2.3    6.0  10.3    1.1  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        2.2    8.4  11.3        5.5    7.2   0.5    4.8  4  YojJ             Bacterial membrane-spanning protein N-termin
        3.5    8.0   6.1        1.8    8.9   0.4    2.5  2  TINF2_N          TERF1-interacting nuclear factor 2 N-terminu
        5.1    7.7  13.2         12    6.5   0.6    3.5  2  Syntaxin-6_N     Syntaxin 6, N-terminal
        5.3    6.9  13.6        8.6    6.2   0.1    4.9  5  NTPase_1         NTPase
        8.3    6.7  14.2        2.1    8.6   6.6    2.8  2  MapZ_EC1         MapZ extracellular domain 1


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.0   0.0   5.4e-52   1.3e-49       1     131 [.     216     345 ..     216     346 .. 0.98
   2 !  166.7   0.0   1.3e-51   3.2e-49       1     131 [.     489     619 ..     489     620 .. 0.96
   3 ?   -0.8   1.4       7.8   1.9e+03      37      94 ..     778     832 ..     744     860 .. 0.57

  Alignments for each domain:
  == domain 1  score: 168.0 bits;  conditional E-value: 5.4e-52
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsesee 81 
                                   vll+GppGtGKTllakava+e+g++f+ i+g+e++skyvge+e+++r++f+ea+e+a psi+fiDEida+a++r++++ e+
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEAGANFYVINGPEIMSKYVGETEENLRKIFEEAEENA-PSIIFIDEIDAIAPKRDEATGEV 295
                                   79******************************************************9.*********************** PP

                                   HHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  82 eervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   e+r+v+qLlt +dg+k + ++v+vigatnrp+ ldpal+r gRfdr+i i+
  gi|15669345|ref|NP_248150.1| 296 ERRLVAQLLTLMDGLKGR-GQVVVIGATNRPNALDPALRRpGRFDREIVIG 345
                                   *****************7.56**************************9886 PP

  == domain 2  score: 166.7 bits;  conditional E-value: 1.3e-51
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgsese 80 
                                   vll+GppGtGKTllakava+e+g++f++++g+e++sk+vgesek ire+f++a+++a p+i+f+DEida+a++r ++ +s 
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANESGANFISVKGPEIFSKWVGESEKAIREIFRKARQSA-PCIIFFDEIDAIAPKRgRDLSSA 568
                                   79******************************************************9.****************66669** PP

                                   HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   ++++vvnqLlteldg+++  ++v+vi+atnrpd +dpallr gR+dr+i ++
  gi|15669345|ref|NP_248150.1| 569 VTDKVVNQLLTELDGMEEP-KDVVVIAATNRPDIIDPALLRpGRLDRVILVP 619
                                   ******************7.55**************************9886 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 7.8
                                   SSTTHHHHHHHHHHHHHHHTS....TS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHH CS
                           AAA  37 kyvgesekkirelfkeakeka....kp.silfiDEidalaksrsgseseeeervvnqLlteld 94 
                                   ky+++   k++e+++++ e +    +    +  +Eid+++k+         +++++ + t ld
  gi|15669345|ref|NP_248150.1| 778 KYLKDILGKLKEMIDNIYELEnklnTLkEQVSAEEIDEIIKTT--------QNIIQRFTTSLD 832
                                   3455555555555555433333344222556667777777777........333333333333 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.2   8.2e-19     2e-16       1      45 []     368     429 ..     368     429 .. 0.80
   2 !   63.7   0.1   4.1e-20     1e-17       1      35 [.     642     676 ..     642     688 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 8.2e-19
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr.................gikeitmedfee 45 
                                   dvdl+ LA  T+G++GADlaalc+eAa++Alrr                 ++ ++tm+df+e
  gi|15669345|ref|NP_248150.1| 368 DVDLDYLADVTHGFVGADLAALCKEAAMRALRRvlpsidleaeeipkevlDNLKVTMDDFKE 429
                                   9********************************66666666666666544444677777765 PP

  == domain 2  score: 63.7 bits;  conditional E-value: 4.1e-20
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgi 35 
                                   dv+l+eLA++TeGy+GAD++alcreAa+lA+r++i
  gi|15669345|ref|NP_248150.1| 642 DVNLEELAKKTEGYTGADIEALCREAAMLAVRESI 676
                                   9********************************87 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.9   0.0   4.2e-34     1e-31       1      84 [.       4      88 ..       4      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 4.2e-34
                                  CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEEC.CCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEE CS
                       CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveieg.krkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrk 82
                                  +L+Vaea+q dvgrgi+ridp +meelgl+pgdv+eieg k k++aiv+++  ed gkgiIr+dg++R+nagv iGd+V+V++
  gi|15669345|ref|NP_248150.1|  4 ELKVAEAYQGDVGRGIARIDPYTMEELGLKPGDVIEIEGpKGKAYAIVYRGFLEDAGKGIIRIDGYLRQNAGVAIGDRVKVKR 86
                                  59********************************************************************************9 PP

                                  E- CS
                       CDC48_N 83 ae 84
                                  +e
  gi|15669345|ref|NP_248150.1| 87 VE 88
                                  97 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   1.8e-10   4.5e-08      34     102 ..     214     290 ..     206     338 .. 0.86
   2 !   28.1   0.0   5.9e-09   1.5e-06      34     118 ..     487     579 ..     449     610 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.8e-10
                        RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsravee 102
                                     vll+GpPG Gkt lak +a+e g+++ +  gP +      e + +l  ++ + ee+   ++fidei  ++++ +e
  gi|15669345|ref|NP_248150.1| 214 KGVLLVGPPGTGKTLLAKAVANEAGANFYVINGPEImskyvgETEENLRKIFEEAEENapSIIFIDEIDAIAPKRDE 290
                                   569*******************************984433334567899999998876447********99988777 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 5.9e-09
                        RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleekd..vlfideihrlsraveevlys 106
                                     vll+GpPG Gkt lak +a+e g+++ +  gP +      e ++ +  ++ + +++   ++f dei  ++++    l s
  gi|15669345|ref|NP_248150.1| 487 KGVLLFGPPGTGKTLLAKAVANESGANFISVKGPEIfskwvgESEKAIREIFRKARQSApcIIFFDEIDAIAPKRGRDLSS 567
                                   569*******************************98544444456677788877766544499********9999999999 PP

                        RuvB_N 107 amedfrldivig 118
                                   a+ d  ++ ++ 
  gi|15669345|ref|NP_248150.1| 568 AVTDKVVNQLLT 579
                                   999998876665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0     1e-10   2.6e-08       6     105 ..     216     309 ..     212     312 .. 0.88
   2 !   25.5   0.0   4.7e-08   1.2e-05       6     105 ..     489     583 ..     484     585 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1e-10
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----. CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk. 83 
                                   +ll+gp g+Gkt+laka+a+   +    ++ +++  e++     + + + ++  ++   +aee+   i+++DEid i+pk 
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEAGA----NFYVINGPEIMS----KYVGETEENLRKIFEEAEENApsIIFIDEIDAIAPKr 288
                                   6899******************96....************....777777777888888888888***************9 PP

                                   ---------HHHHHHHHHHHH- CS
                         AAA_2  84 essgadvSregVqrdLLqileg 105
                                   ++++ +v r  V + LL +++g
  gi|15669345|ref|NP_248150.1| 289 DEATGEVERRLVAQ-LLTLMDG 309
                                   99999999998877.5667765 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 4.7e-08
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----- CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpke 84 
                                   +ll gp g+Gkt+laka+a+   +    ++i +   e+      + + ++++  ++   +a ++   i+++DEid i+p  
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANESGA----NFISVKGPEIFS----KWVGESEKAIREIFRKARQSApcIIFFDEIDAIAP-- 559
                                   5778******************96....9**********9....77777777777888888888899************.. PP

                                   --------...HHHHHHHHHHHH- CS
                         AAA_2  85 ssgadvSr...egVqrdLLqileg 105
                                   + g+d S+   + V++ LL  l+g
  gi|15669345|ref|NP_248150.1| 560 KRGRDLSSavtDKVVNQLLTELDG 583
                                   777777752326888888877765 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       2.3   5.7e+02      45      62 ..      18      35 ..       2      37 .. 0.81
   2 !   54.8   0.9   2.3e-17   5.7e-15       2      63 ..     105     166 ..     104     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.3
                                  CSCEEECTSCCEEESTTC CS
                       CDC48_2 45 gpvgitetTeielgtkpv 62
                                  g+++i++ T+ elg kp 
  gi|15669345|ref|NP_248150.1| 18 GIARIDPYTMEELGLKPG 35
                                  599***********9996 PP

  == domain 2  score: 54.8 bits;  conditional E-value: 2.3e-17
                                   .SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                       CDC48_2   2 idgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                   +  ++++ +kr++lg++++kG +v++ ++g+++++vVvst+P+gpv++t+ T +el ++pv+
  gi|15669345|ref|NP_248150.1| 105 FGPGFEDFVKRKILGQVLSKGSKVTIGVLGTALTFVVVSTTPAGPVRVTDFTHVELKEEPVS 166
                                   6778777*****************************************************98 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   1.8e-07   4.5e-05       1     135 [.     215     333 ..     215     335 .. 0.66
   2 !   25.8   0.0   3.3e-08   8.3e-06       1     135 [.     488     607 ..     488     609 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.8e-07
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--. CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae. 78 
                                   +vlLvGppGtgK+ la+ +a   ++++ ++++++ +++   +g++e           ++ ++a+   ++i+++DE++ +  
  gi|15669345|ref|NP_248150.1| 215 GVLLVGPPGTGKTLLAKAVANEAGANFYVINGPEIMSKY--VGETE-------ENLRKIFEEAEenAPSIIFIDEIDAIAp 286
                                   59*******************************977654..34444.......3335555555556889999999998872 PP

                                   ..HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                         AAA_5  79 ..sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                     +e+++++ + l       +++ +l++  +     ++ vi+++n+++     l+palr
  gi|15669345|ref|NP_248150.1| 287 krDEATGEVERRLV------AQLLTLMDGLKG--RGQVVVIGATNRPN----ALDPALR 333
                                   22234444433333......444444433331..22277888888777....7777776 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 3.3e-08
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--H CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraes 79 
                                   +vlL GppGtgK+ la+ +a   ++++  v +++      ++ ++    g+ +    ++ r+ar   ++i+++DE++ + +
  gi|15669345|ref|NP_248150.1| 488 GVLLFGPPGTGKTLLAKAVANESGANFISVKGPE------IFSKWV---GESEKAIREIFRKARqsAPCIIFFDEIDAIAP 559
                                   59****************************9997......999999...6777777777778887899************* PP

                                   HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                         AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                   +    L s   ++ +    ++el + +++   +++ via++n++d     ++pal+
  gi|15669345|ref|NP_248150.1| 560 KRGRDLSSAVTDKVVN-QLLTELDGMEEP---KDVVVIAATNRPD----IIDPALL 607
                                   *************998.444555444443...24**********9....6667665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.4e-08   3.6e-06      23     139 ..     212     318 ..     183     320 .. 0.77
   2 !   16.2   0.0     4e-05      0.01      24      60 ..     486     519 ..     475     528 .. 0.79
   3 ?    4.7   0.0      0.15        37     122     149 ..     533     559 ..     529     593 .. 0.70
   4 ?   -0.5   0.2       5.8   1.4e+03     134     134 ..     744     744 ..     680     836 .. 0.58

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.4e-08
                        AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawreklee 103
                                    p  vll+G++G+GK+ l++++++++ ++ +++++g    +        ++    +e l +  ++++e+a    + +++++
  gi|15669345|ref|NP_248150.1| 212 PPKGVLLVGPPGTGKTLLAKAVANEAGAN-FYVINGPEIMS-------KYVGET-EENLRKIFEEAEENAPSIIFIDEIDA 283
                                   3599********************99999.99999999888.......333333.44666666666666666677777777 PP

                        AAA_16 104 alaavpelagaeasrllellkrllallsrderplvl 139
                                    +   +e++g+ ++rl ++l  l++ l+ +++ +v+
  gi|15669345|ref|NP_248150.1| 284 IAPKRDEATGEVERRLVAQLLTLMDGLKGRGQ-VVV 318
                                   7778888888888***********99998676.555 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 4e-05
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkc 60 
                                   p  vll G++G+GK+ l+++++++  ++   f++ k 
  gi|15669345|ref|NP_248150.1| 486 PKGVLLFGPPGTGKTLLAKAVANESGAN---FISVKG 519
                                   489*******************866555...666555 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.15
                        AAA_16 122 llkrllallsrderplvlvlDdlqwade 149
                                   +++++++++++ + p ++++D+++ + +
  gi|15669345|ref|NP_248150.1| 533 AIREIFRKARQ-SAPCIIFFDEIDAIAP 559
                                   67889999**9.888*********5544 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 5.8
                        AAA_16 134 e 134
                                   e
  gi|15669345|ref|NP_248150.1| 744 E 744
                                   1 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.5e-07   6.2e-05      51      98 ..     214     259 ..     207     281 .. 0.90
   2 !   24.5   0.0   5.4e-08   1.3e-05      51     106 ..     487     541 ..     477     544 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.5e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev 98 
                                   ++vLl+Gp+gtGkt la a+++e g    f +++g e+ s  v  te 
  gi|15669345|ref|NP_248150.1| 214 KGVLLVGPPGTGKTLLAKAVANEAG--ANFYVINGPEIMSKYVGETEE 259
                                   89*********************99..68**************99984 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 5.4e-08
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                   ++vLl Gp+gtGkt la a+++e g    f++++g e++s  v  +e ++ + +rk+
  gi|15669345|ref|NP_248150.1| 487 KGVLLFGPPGTGKTLLAKAVANESG--ANFISVKGPEIFSKWVGESEkAIREIFRKA 541
                                   89*********************98..78**************99985688999997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   3.5e-07   8.7e-05       5     100 ..     216     321 ..     213     338 .. 0.81
   2 !   15.9   0.0     4e-05    0.0099       5      76 ..     489     557 ..     486     595 .. 0.79
   3 ?   -0.3   1.7       4.1     1e+03      37      92 ..     761     812 ..     731     852 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.5e-07
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev......... 76 
                                   ++++G+  +GKT l+k +++e      ++  in  +   k   ++e++l+ i+e+++e+  +++f+DEi  +         
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEAG---ANFYVINGPEIMSKYVGETEENLRKIFEEAEENAPSIIFIDEIDAIapkrdeatg 293
                                   789****************9999...9*********9998888777778777777666799*********99777777777 PP

                        AAA_14  77 ...pewekalkslvd..egknldvivtGS 100
                                      +++   l  l+d  +g +++v+v G 
  gi|15669345|ref|NP_248150.1| 294 eveRRLVAQLLTLMDglKG-RGQVVVIGA 321
                                   7776677777777775434.667777665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4e-05
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                   +++ G+  +GKT l+k +++e+     +++ ++  +   k   ++ek +++i++k++++   ++f+DEi  +
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANESG---ANFISVKGPEIFSKWVGESEKAIREIFRKARQSAPCIIFFDEIDAI 557
                                   7899***************9999...8888888888777777777777777777766668999******987 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 4.1
                        AAA_14  37 nldderdkkladpekllelileklkeekktylflDEiqevpewekalkslvdegkn 92 
                                   n ++ + +++++ +kl +++++ l   +k   ++D i e+++  ++lk+ v  + +
  gi|15669345|ref|NP_248150.1| 761 NKEELKPSEKDEAQKLAKYLKDIL---GKLKEMIDNIYELENKLNTLKEQVSAE-E 812
                                   333333333333335666666654...334457888888888888888877765.3 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.4e-07   3.4e-05       2      79 ..     216     323 ..     216     371 .. 0.71
   2 !   17.5   0.0   1.4e-05    0.0035       2      46 ..     489     535 ..     489     614 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.4e-07
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrvl 52 
                                   vllvG+pG+GK+ la+ ++++ g  +++++ ++++++++g+ +++++                               +v+
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEAGanFYVINGPEIMSKYVGETEENLRkifeeaeenapsiifideidaiapkrdeATGEVE 296
                                   799******************************999999976666665555555555556666666555555443333455 PP

                        AAA_33  53 drlyqilnelarkalsagrnvildatn 79 
                                    rl ++l  l +    +g+ v++ atn
  gi|15669345|ref|NP_248150.1| 297 RRLVAQLLTLMDGLKGRGQVVVIGATN 323
                                   555555555554444444445555555 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.4e-05
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                                   vll G+pG+GK+ la+ ++++ g  ++ +  ++++++ +g+ ++ ++
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANESGanFISVKGPEIFSKWVGESEKAIR 535
                                   7899*******************766667777766666665444443 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.3   0.00015     0.036      15      45 ..     408     438 ..     403     448 .. 0.84
   2 ?    1.8   0.1      0.96   2.4e+02       3      58 ..     767     821 ..     765     823 .. 0.83
   3 !   26.9   0.1   1.5e-08   3.6e-06      27      61 .]     853     887 ..     833     887 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00015
                        Vps4_C  15 twmdipsdkllePpvtlkDflkalkkarptV 45 
                                     ++ip++ l + +vt++Df++alk + p+ 
  gi|15669345|ref|NP_248150.1| 408 EAEEIPKEVLDNLKVTMDDFKEALKDVEPSA 438
                                   5689998888888****************95 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.96
                        Vps4_C   3 PCspgdpgaiemtwmdipsdkllePpvtlkDflkalkkarptVskeDLekheeFTk 58 
                                   P +++++++  + ++di   kl+e   ++  +++ l++ +  Vs+e+++++++ T+
  gi|15669345|ref|NP_248150.1| 767 PSEKDEAQKLAKYLKDIL-GKLKEMIDNIYELENKLNTLKEQVSAEEIDEIIKTTQ 821
                                   666777778888888888.8888888899999999**************9988776 PP

  == domain 3  score: 26.9 bits;  conditional E-value: 1.5e-08
                        Vps4_C  27 PpvtlkDflkalkkarptVskeDLekheeFTkefG 61 
                                    +++ ++f+kal+k +p+VskeD++ +e+  +e+G
  gi|15669345|ref|NP_248150.1| 853 VKIKKEHFMKALEKIKPSVSKEDMRVYEKLAQEYG 887
                                   48999***************************998 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.3e-05    0.0033       8      41 ..     216     248 ..     211     328 .. 0.63
   2 !   16.2   0.0   3.9e-05    0.0097       8      48 ..     489     520 ..     484     593 .. 0.75
   3 ?   -0.2   0.3       4.6   1.1e+03      74      96 ..     786     809 ..     734     856 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpe 41 
                                   ++++G++GtGKT+l++ +++++ +  +  + +pe
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEAGANFYVIN-GPE 248
                                   689******************954333333.222 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.9e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlp 48 
                                   ++++G++GtGKT+l++ ++++          ++ +++v+ p
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANES---------GANFISVKGP 520
                                   689****************997.........6666665555 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 4.6
                        AAA_22  74 sseellealeqalrarav.ielli 96 
                                   +++e+++ +++  ++  + +e + 
  gi|15669345|ref|NP_248150.1| 786 KLKEMIDNIYELENKLNTlKEQVS 809
                                   233333333333333333333333 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.5e-05    0.0037      46      72 ..     212     238 ..     198     294 .. 0.84
   2 !   14.9   0.0   6.6e-05     0.016      48      72 ..     487     511 ..     475     519 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.5e-05
                     IstB_IS21  46 kkenivllGpsGvGKshlaialgveav 72 
                                     ++++l+Gp+G+GK+ la a++ ea 
  gi|15669345|ref|NP_248150.1| 212 PPKGVLLVGPPGTGKTLLAKAVANEAG 238
                                   56789*****************99985 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.6e-05
                     IstB_IS21  48 enivllGpsGvGKshlaialgveav 72 
                                   ++++l+Gp+G+GK+ la a++ e  
  gi|15669345|ref|NP_248150.1| 487 KGVLLFGPPGTGKTLLAKAVANESG 511
                                   6799****************98865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   8.5e-05     0.021       1      34 [.     216     267 ..     216     328 .. 0.66
   2 !   15.2   0.0   9.8e-05     0.024       1      25 [.     489     534 ..     489     603 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.5e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvake 34 
                                   +ll G+pG+GKt lak+++++  ++                  +nlr+++ e
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEAgANfyvingpeimskyvgetEENLRKIFEE 267
                                   799***************9987433677777666666666663333333333 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 9.8e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................g 25 
                                   +ll G+pG+GKt lak+++++  ++                     
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANESgANfisvkgpeifskwvgesekaI 534
                                   799***************8886322476666666666666664443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.3e-05    0.0031       2      49 ..     216     268 ..     215     308 .. 0.80
   2 !   12.8   0.0   0.00043      0.11       2      34 ..     489     526 ..     488     552 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-05
                        AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakgedalpwv 49 
                                   + ++G+++tGKT l++a a++   ++ v+  pE++ +++ e  ++ +++ +++
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEagaNFYVIngPEIMSKYVGETEENLRKIFEEA 268
                                   689****************87777777888********988877776666554 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00043
                        AAA_28   2 ivitGgestGKTtlleaLaar.gypvv....pEaarei 34 
                                   + ++G+++tGKT l++a a++ g + +    pE++ + 
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANEsGANFIsvkgPEIFSKW 526
                                   6799***************8765544411355554444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0013      0.33      23      58 ..     214     246 ..     199     291 .. 0.84
   2 !   14.7   0.0   7.8e-05     0.019      22     143 ..     486     598 ..     472     603 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0013
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEET CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavnc 58 
                                     vl++G  GtGK+lla+a+ ++     ++f  +n 
  gi|15669345|ref|NP_248150.1| 214 KGVLLVGPPGTGKTLLAKAVANEA---GANFYVING 246
                                   679***************997654...455666665 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 7.8e-05
                                   SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEEEETG CS
               Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlfLDei 102
                                   +  vl+ G  GtGK+lla+a+ ++s    ++f++v   +         +F    G    A +e   + +++   ++f+Dei
  gi|15669345|ref|NP_248150.1| 486 PKGVLLFGPPGTGKTLLAKAVANESG---ANFISVKGPE---------IFSKWVGESEKAIREIFRKARQSAPCIIFFDEI 554
                                   4679****************998776...8899997654.........444455555556666556677888899999999 PP

                                   GGS-HHHHHHHHHHHHHSEEESBTSS...SEEE--EEEEEEESS CS
               Sigma54_activat 103 gelplelQekLlrvlqegevervGss...keikvdvriiaatne 143
                                     + ++    L  ++ ++ v+++ ++    e + dv +iaatn+
  gi|15669345|ref|NP_248150.1| 555 DAIAPKRGRDLSSAVTDKVVNQLLTEldgMEEPKDVVVIAATNR 598
                                   99999999999999999999998754322578899999999997 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0017      0.42      52     115 ..     212     280 ..     173     324 .. 0.80
   2 !   17.8   0.0   5.9e-06    0.0015      20     155 ..     444     602 ..     429     607 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                        DUF815  52 pannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellr...erperfilfvDD 115
                                   p + vLL+G  GtGK  l ka+ ne+ ++   +   e+  + + e ++ ++++    e++   i+f+D 
  gi|15669345|ref|NP_248150.1| 212 PPKGVLLVGPPGTGKTLLAKAVANEAGANFyvINGPEIMSKYVGETEENLRKIFeeaEENAPSIIFIDE 280
                                   56789*******************998776444555777777766655555443122344556888886 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 5.9e-06
                        DUF815  20 eevdevklddLvgidkqkealventeqfleg.........lpannvLLwGarGtGKSslvkallneyaeeg..Lrlievek 89 
                                    ev +vk++d+ g+++ k++l e +e  l+          +p + vLL+G  GtGK  l ka+ ne  ++   ++  e+  
  gi|15669345|ref|NP_248150.1| 444 VEVPNVKWEDIGGLEEVKQELREAVEWPLKAkevfekigvRPPKGVLLFGPPGTGKTLLAKAVANESGANFisVKGPEIFS 524
                                   566778899999999999999887765444311111111257899*********************999984455579999 PP

                        DUF815  90 edlkelpklvellr...erperfilfvD...........DLsFeeeeeeyksLksvLeGsleakpenvliyaTsNrRhLl 155
                                   + + e +k ++++    +++  +i+f D           DLs   +++   +L + L+G   ++p++v++ a +Nr +++
  gi|15669345|ref|NP_248150.1| 525 KWVGESEKAIREIFrkaRQSAPCIIFFDeidaiapkrgrDLSSAVTDKVVNQLLTELDGM--EEPKDVVVIAATNRPDII 602
                                   88888777666664222445679***998888888888889999999999********95..778999999999998887 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   0.00018     0.045      25      42 ..     216     233 ..     212     236 .. 0.90
   2 !   13.1   0.0   0.00019     0.047      24      42 ..     488     506 ..     471     509 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00018
                  Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                   +llvGppG+GKt+lak++
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAV 233
                                   89*************987 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00019
                  Mg_chelatase  24 nlllvGppGsGKtmlakrl 42 
                                    +ll+GppG+GKt+lak++
  gi|15669345|ref|NP_248150.1| 488 GVLLFGPPGTGKTLLAKAV 506
                                   589*************987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00015     0.038       5      77 ..     216     284 ..     213     297 .. 0.71
   2 !    9.3   0.1    0.0035      0.88       5      22 ..     489     506 ..     486     521 .. 0.85
   3 ?    3.6   0.7      0.19        47      91     172 ..     713     789 ..     694     828 .. 0.78
   4 ?   -0.5   0.1       3.5   8.8e+02      49     113 ..     824     888 ..     803     891 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00015
                        AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie......swedfldevvelaaeladyktlviDtidel 77 
                                   +l++Gp+g+GKT lak           e+G+ + +++++p+i       + e++++ ++e +++ +  ++++iD id +
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAV-------ANEAGA-NFYVINGPEIMskyvgeTEENLRKIFEEAEENAP--SIIFIDEIDAI 284
                                   89**************99.......445555.6666666655444444344666666666666555..89999999976 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0035
                        AAA_24   5 iliyGpsgiGKTtlakel 22 
                                   +l++Gp+g+GKT lak  
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAV 506
                                   89*************977 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.19
                        AAA_24  91 kaeskedkgdgkG.ygelaeefrrllkklqelrknvifiahektrkdedpegeakytrlepklgkktanelkeevDlvlra 170
                                   +  +ke  ++ +G ++el++ +++++  l+ +++ + ++ +e  +  e  ++e     l+p++++ ++++ k+  D+++ +
  gi|15669345|ref|NP_248150.1| 713 A--TKERESAEAGeFSELKNAIGKIISVLSPAKEKIEAVEKEIDKFLEVINKE----ELKPSEKDEAQKLAKYLKDILGKL 787
                                   3..23345566789*************************99999999998888....99******************9998 PP

                        AAA_24 171 nl 172
                                   + 
  gi|15669345|ref|NP_248150.1| 788 KE 789
                                   85 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 3.5
                        AAA_24  49 wedfldevvelaaeladyktlviDtideleelclaevirqnekaeskedkgdgkGygelaeefrr 113
                                   ++ f   ++el+  l+d++++ +   ++ ++++++ ++++ ek +   +k d++ y +la+e +r
  gi|15669345|ref|NP_248150.1| 824 IQRFTTSLDELKNILKDIESIRLKVSTKDVKIKKEHFMKALEKIKPSVSKEDMRVYEKLAQEYGR 888
                                   56677777777888999999999999999999999999999999999999999999999999876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00028     0.069      14      50 ..     211     245 ..     203     263 .. 0.87
   2 !   10.5   0.1    0.0011      0.26      14      50 ..     484     518 ..     474     522 .. 0.86
   3 ?   -0.9   0.0       3.3   8.2e+02     151     189 ..     562     600 ..     552     603 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00028
                    Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                   e Pk +ll+G pG GK+ la+++++e   + n+ +++
  gi|15669345|ref|NP_248150.1| 211 EPPKGVLLVGPPGTGKTLLAKAVANEA--GANFYVIN 245
                                   5699**********************8..67776666 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0011
                    Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                   + Pk +ll G pG GK+ la+++++e   + n++ ++
  gi|15669345|ref|NP_248150.1| 484 RPPKGVLLFGPPGTGKTLLAKAVANES--GANFISVK 518
                                   56999*********************8..88888776 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.3
                    Zeta_toxin 151 gRlvpkeehdeafeglresvealeeekqldrvkikdrdg 189
                                   gR  +  + d+++++l  +++ +ee k+++ +  ++r +
  gi|15669345|ref|NP_248150.1| 562 GRDLSSAVTDKVVNQLLTELDGMEEPKDVVVIAATNRPD 600
                                   89999999*****************99888777666655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   0.00011     0.027      31      64 ..     211     244 ..     200     290 .. 0.82
   2 !   10.4   0.0    0.0014      0.35      33      58 ..     486     511 ..     476     523 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00011
                         AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkekyls 64 
                                   +  k vllvGp GtGKt+++k + ++   + y++
  gi|15669345|ref|NP_248150.1| 211 EPPKGVLLVGPPGTGKTLLAKAVANEAGANFYVI 244
                                   55688*****************999988555544 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0014
                         AAA_7  33 kkpvllvGptGtGKtviikdllkkld 58 
                                    k vll Gp GtGKt+++k + ++  
  gi|15669345|ref|NP_248150.1| 486 PKGVLLFGPPGTGKTLLAKAVANESG 511
                                   5789**************99887765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00084      0.21      22      43 ..     216     237 ..     208     245 .. 0.86
   2 !   10.2   0.0    0.0015      0.37      22      41 ..     489     508 ..     475     514 .. 0.87
   3 ?    3.7   0.2      0.15        38      62      92 ..     762     809 ..     749     862 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00084
                                   EEEE--TTSSTTHHHHHHHHHH CS
                          PhoH  22 vfaiGpaGtGKtylavalavea 43 
                                   v  +Gp GtGKt+la a+a ea
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEA 237
                                   7789************999766 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0015
                                   EEEE--TTSSTTHHHHHHHH CS
                          PhoH  22 vfaiGpaGtGKtylavalav 41 
                                   v  +Gp GtGKt+la a+a 
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVAN 508
                                   7789***********99985 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.15
                                   T----SS---------TTTHHHHHHHTTTS.................- CS
                          PhoH  62 geelGflpgdleekvdpylrplydaLkdll.................g 92 
                                   +eel   + d+++k++ yl+ +  +Lk+++                 +
  gi|15669345|ref|NP_248150.1| 762 KEELKPSEKDEAQKLAKYLKDILGKLKEMIdniyelenklntlkeqvS 809
                                   788999999*********************766666664444444443 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00063      0.16      19      51 ..     213     247 ..     186     263 .. 0.75
   2 ?   -0.9   0.0       6.3   1.6e+03      80     107 ..     451     478 ..     448     487 .. 0.73
   3 !   11.6   0.1   0.00082       0.2      21      51 ..     481     520 ..     457     524 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00063
                                   TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                    + +lL G+ G+GKT l++++a++ g +   ++ P
  gi|15669345|ref|NP_248150.1| 213 PKGVLLVGPPGTGKTLLAKAVANEAGANfyVINGP 247
                                   3459*********************9988667776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 6.3
                                   HHHCTTCCCCSTSCEEEEETGGGGCCCS CS
                          TsaE  80 leelgleeyleeeavvlvEWpekleell 107
                                   +e++g  e +++e   +vEWp k++e++
  gi|15669345|ref|NP_248150.1| 451 WEDIGGLEEVKQELREAVEWPLKAKEVF 478
                                   66676666666666889****9988775 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00082
                                   E.......EEEEESTTSSHHHHHHHHHHHTT--..----T CS
                          TsaE  21 v.......ilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                   +       +lL G+ G+GKT l++++a++ g +  +vk P
  gi|15669345|ref|NP_248150.1| 481 IgvrppkgVLLFGPPGTGKTLLAKAVANESGANfiSVKGP 520
                                   123334449********************99987778776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0011      0.26       1      34 [.     216     249 ..     216     281 .. 0.78
   2 !   11.7   0.0     0.001      0.26       1      26 [.     489     514 ..     489     576 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0011
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsv 34 
                                   ++l+Gp+g+GK++lak +a++   ++  ++ +++
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEAGANFYVINGPEI 249
                                   6799*************98888766644444443 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.001
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                   ++l+Gp+g+GK++lak +a++   ++
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANESGANF 514
                                   679**************888776555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0094       2.4      36      52 ..     216     232 ..     196     238 .. 0.89
   2 ?    5.4   0.0      0.05        12     127     177 ..     258     308 ..     239     322 .. 0.84
   3 !    7.9   0.0    0.0084       2.1      36      52 ..     489     505 ..     464     512 .. 0.85
   4 ?   -1.4   0.0       6.1   1.5e+03     129     183 ..     533     592 ..     524     597 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0094
                        AAA_25  36 allaGapgtGKttlald 52 
                                   +ll+G+pgtGKt la  
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKA 232
                                   69***********9965 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.05
                        AAA_25 127 tadvdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                   ++ ++++ +++ee + +  + iD ++++ +   ++  +v ++lv++l  + +
  gi|15669345|ref|NP_248150.1| 258 EENLRKIFEEAEE-NAPSIIFIDEIDAIAPKRDEATGEVeRRLVAQLLTLMD 308
                                   5678899999999.77***************888888887*****9987765 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0084
                        AAA_25  36 allaGapgtGKttlald 52 
                                   +ll+G+pgtGKt la  
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKA 505
                                   689**********9965 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 6.1
                        AAA_25 129 dvdaleaaieevegvrlvviDplsralgg.densnsd.....vgalvealeriarrtgaav 183
                                   +++++ +++++   +  + +D ++++ +  + + +s+     v++l++ l+ +++ +++ v
  gi|15669345|ref|NP_248150.1| 533 AIREIFRKARQ-SAPCIIFFDEIDAIAPKrGRDLSSAvtdkvVNQLLTELDGMEEPKDVVV 592
                                   56666777777.4477777777777666653333333223323555555555555555555 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00068      0.17       2      80 ..     216     290 ..     215     311 .. 0.70
   2 !   10.4   0.0    0.0018      0.44       2     111 ..     489     597 ..     488     617 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00068
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqs 80 
                                   vll g PG++ktll+ka+a+  +++f  i   p+++   + G +  ee+ +++  ++     ++++ dei+  +pk + 
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEAGANFYVIN-GPEIMSKYV-GET--EENLRKIFEEAEENAPSIIFIDEIDAIAPKRDE 290
                                   7999**********************8775.677776544.432..222222222222334466777777777666655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0018
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqsal 82 
                                   vll g PG++ktll+ka+a+  +++f  ++  p+++ s  +G +    + +e+  k+      +++ dei+  +pk    l
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANESGANFISVK-GPEIF-SKWVGESEK--AIREIFRKARQSAPCIIFFDEIDAIAPKRGRDL 565
                                   7999*******************9998876.45555.444454422..222222222222334677777777777777666 PP

                         AAA_3  83 leameerqvt...vegethklpepflvlatqn 111
                                     a+ ++ v    +e + ++ p+  +v+a+ n
  gi|15669345|ref|NP_248150.1| 566 SSAVTDKVVNqllTELDGMEEPKDVVVIAATN 597
                                   66666665541112333444455566666665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0    0.0012       0.3       6      67 ..     208     267 ..     207     308 .. 0.75
   2 !   10.0   0.0    0.0037      0.91       9      67 ..     484     540 ..     480     595 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0012
                                   EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                   l +++ + v +vG+ G+GK+ L+k++a++    +  + ++g ++ ++   +++++++ +++e
  gi|15669345|ref|NP_248150.1| 208 LGIEPPKGVLLVGPPGTGKTLLAKAVANEAGA-NFYV-INGPEIMSKYVGETEENLRKIFEE 267
                                   5678888899****************998653.3333.566666655555555666555555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0037
                                   ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                   ++ + v ++G+ G+GK+ L+k++a+++   +  i ++g ++ ++   +++k i+ ++ +
  gi|15669345|ref|NP_248150.1| 484 RPPKGVLLFGPPGTGKTLLAKAVANESG--ANFISVKGPEIFSKWVGESEKAIREIFRK 540
                                   5666789*****************9975..56677777777777777777777766666 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0024      0.59       1      47 [.     219     266 ..     219     295 .. 0.69
   2 !    9.5   0.0    0.0052       1.3       1      51 [.     492     543 ..     492     608 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0024
                                   EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTTTSHSSHHHHC CS
                        AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeakrgglakardemr 47 
                                   +G+PG GK+ +++ ++ +   +f +++  +++ + + + + ++ r+ ++
  gi|15669345|ref|NP_248150.1| 219 VGPPGTGKTLLAKAVANEAgaNFYVINGPEIMSKYVGETE-ENLRKIFE 266
                                   7**************9998557888887777777665444.23333333 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0052
                                   EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSHH CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrklpl 51 
                                   +G+PG GK+ +++ ++ + g  ++s  G  +++    ++ +  r+ +rk+ +
  gi|15669345|ref|NP_248150.1| 492 FGPPGTGKTLLAKAVANESGANFISVkGPEIFSKWVGESEKAIREIFRKARQ 543
                                   6******************999998767777766655555556666666655 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0025      0.61      24      79 ..     216     282 ..     210     291 .. 0.62
   2 !    9.1   0.0    0.0055       1.4      23      48 ..     488     513 ..     476     595 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0025
                                   EEEEEETT--HHHHHHCC--TTS-EE--SS....TTHHHH-H....HHHHHHT...TTSEEEEEE-T CS
               Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifv....verlaklp....ldlleqa...kggtLylkdia 79 
                                   v+l+G++G+gk+l A++ ++++g +  + +    + + + ++     +++e+a    + ++++ +i+
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEAGANFYVINgpeiMSKYVGETeenlRKIFEEAeenAPSIIFIDEID 282
                                   9*******************99987654331000222222222233444444433355566666666 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0055
                                   -EEEEEETT--HHHHHHCC--TTS-E CS
               Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgpw 48 
                                    v+l G++G+gk+l A++ +++sg +
  gi|15669345|ref|NP_248150.1| 488 GVLLFGPPGTGKTLLAKAVANESGAN 513
                                   59******************999875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0021      0.53      21      40 ..     216     235 ..     203     246 .. 0.82
   2 ?    7.3   0.0     0.014       3.6      21      40 ..     489     508 ..     475     518 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0021
                        AAA_30  21 avltGpAGtGKttalkalre 40 
                                   ++l+Gp+GtGKt + ka+++
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVAN 235
                                   689***********999976 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.014
                        AAA_30  21 avltGpAGtGKttalkalre 40 
                                   ++l Gp+GtGKt + ka+++
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVAN 508
                                   6789*********9999875 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0017      0.44       5      65 ..     217     270 ..     214     298 .. 0.67
   2 ?    6.3   0.0     0.019       4.8       6      25 ..     491     510 ..     487     545 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                       DUF2075   5 lVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafe 65 
                                   l  G +GtGKt+++ ++++e+        a++ + N+p+++  +   ++++ +k ++ea e
  gi|15669345|ref|NP_248150.1| 217 LLVGPPGTGKTLLAKAVANEA-------GANFYVINGPEIMSKYVGETEENLRKIFEEAEE 270
                                   55699*************999.......677777777776654444444443555544444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.019
                       DUF2075   6 VtGvaGtGKtvvllnllael 25 
                                     G +GtGKt+++ ++++e 
  gi|15669345|ref|NP_248150.1| 491 LFGPPGTGKTLLAKAVANES 510
                                   5699*********9999987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1     0.004         1       3      24 ..     216     237 ..     214     241 .. 0.89
   2 ?    6.7   0.1     0.024       6.1       3      23 ..     489     509 ..     487     513 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.004
                                   EEEEC-TTTCHHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                   v+l G++G GKT L++ +a ++
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEA 237
                                   799**************99876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.024
                                   EEEEC-TTTCHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                   v+l G++G GKT L++ +a +
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANE 509
                                   7899************99865 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.011       2.8     117     136 ..     216     235 ..     210     244 .. 0.90
   2 !    7.8   0.0    0.0062       1.6     117     137 ..     489     509 ..     483     513 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                     Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                   v+++Gp+ tGkt la+a a+
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVAN 235
                                   7899*************997 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0062
                     Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                   v+++Gp+ tGkt la+a a+ 
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANE 509
                                   899**************9985 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1    0.0017      0.43      13      37 ..     207     231 ..     202     243 .. 0.84
   2 ?    3.5   0.0      0.16        39     105     154 ..     255     310 ..     243     324 .. 0.69
   3 !    8.3   0.0    0.0052       1.3      15      38 ..     482     505 ..     473     518 .. 0.81
   4 ?    1.2   0.0      0.77   1.9e+02      64     151 ..     649     732 ..     636     740 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0017
                        ATPase  13 kgGipegrvvlitGepGtGKtifal 37 
                                   k Gi   + vl++G pGtGKt++a+
  gi|15669345|ref|NP_248150.1| 207 KLGIEPPKGVLLVGPPGTGKTLLAK 231
                                   558888889**************97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.16
                        ATPase 105 eelieelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                    e  e+l+++ +e ++   + + iD i+++     e++ +v R+ + ql++ + +l
  gi|15669345|ref|NP_248150.1| 255 GETEENLRKIFEEAEEnapSIIFIDEIDAIapkRDEATGEVERRLVAQLLTLMDGL 310
                                   555666777766666544588999**999943223344456899999999988554 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0052
                        ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                   G+   + vl+ G pGtGKt++a+ 
  gi|15669345|ref|NP_248150.1| 482 GVRPPKGVLLFGPPGTGKTLLAKA 505
                                   56666779*************985 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.77
                        ATPase  64 renak.slGwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaRei 143
                                    ++ +   G d+e+l +e   a++ + es ++++  + + +l+eli+ l+++  +++a +v + s+    ++e+e+    +
  gi|15669345|ref|NP_248150.1| 649 AKKTEgYTGADIEALCRE--AAMLAVRES-IGKPW-DIEVKLRELINYLQSISGTFRAAAVELNSVIKA-TKERESAEAGE 724
                                   555553468888888888..333333333.33232.78999************************9999.55555555566 PP

                        ATPase 144 lrqlvrvl 151
                                   + +l++ +
  gi|15669345|ref|NP_248150.1| 725 FSELKNAI 732
                                   77777766 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0061       1.5      23      43 ..     216     236 ..     202     244 .. 0.82
   2 ?    6.5   0.0     0.017       4.2      23      44 ..     489     510 ..     475     518 .. 0.88
   3 ?   -2.4   0.0       8.7   2.2e+03     121     149 ..     616     645 ..     612     655 .. 0.72
   4 ?   -0.4   1.1       2.1   5.2e+02      62     127 ..     743     810 ..     723     824 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0061
                                   EEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                   v lvG +G GKt lak + n+
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANE 236
                                   789**************9997 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.017
                                   EEEEESTTSSHHHHHHHHCCSH CS
                        NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                   v l G +G GKt lak + n+s
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANES 510
                                   6799**************9984 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 8.7
                                   ...HHHHCHTTSEEE.EEESBCCCCCCS-S CS
                        NB-ARC 121 igvvlparenrlrvl.lTTRdeevanavsa 149
                                   i v++p+++ rl +  + TR++++a+ v+ 
  gi|15669345|ref|NP_248150.1| 616 ILVPVPDEKARLDIFkIHTRSMNLAEDVNL 645
                                   567888888888876577888888887765 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.1
                                   XXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCCCT..TEEEEEEEE-SHHH.H.....HHHH CS
                        NB-ARC  62 tdkseeiletilkeLslseddleekeeveslkrklvrlLltk..rfllvlDDVweeed.wdkigvvlpa 127
                                   + k+e + ++i k L+  +++  + +e++  ++kl ++L++   +   ++D ++e e+ ++ ++  ++a
  gi|15669345|ref|NP_248150.1| 743 KEKIEAVEKEIDKFLEVINKEELKPSEKD-EAQKLAKYLKDIlgKLKEMIDNIYELENkLNTLKEQVSA 810
                                   56778888888888888877777777777.899999999887666667888888876657666666654 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.013       3.3      60      87 ..     216     243 ..     173     258 .. 0.89
   2 ?    6.4   0.0     0.017       4.3      46      91 ..     475     519 ..     436     522 .. 0.76
   3 ?   -2.5   0.1       8.8   2.2e+03      64      84 ..     851     871 ..     793     902 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                                   EEEEESSTSTHHHHHHHHHHHSSSEEEE CS
                           MCM  60 vllvgdpgtaKsqlLkyveklapravyt 87 
                                   vllvg pgt+K+ l k+v++ a  + y+
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEAGANFYV 243
                                   9******************999988887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.017
                                   BBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSS CS
                           MCM  46 kkledktklrgdinvllvgdpgtaKsqlLkyveklapravytsgkg 91 
                                   k++ +k+ +r    vll g pgt+K+ l k+v+ + + a+++s kg
  gi|15669345|ref|NP_248150.1| 475 KEVFEKIGVRPPKGVLLFGPPGTGKTLLAKAVA-NESGANFISVKG 519
                                   55566778899999************9999998.667777887775 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8.8
                                   ESSTSTHHHHHHHHHHHSSSE CS
                           MCM  64 gdpgtaKsqlLkyveklapra 84 
                                    d+ + K +++k++ek+ p  
  gi|15669345|ref|NP_248150.1| 851 KDVKIKKEHFMKALEKIKPSV 871
                                   467777777777777776654 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.019       4.7      20      39 ..     216     235 ..     203     271 .. 0.81
   2 ?    6.9   0.0     0.019       4.8      19      40 ..     488     509 ..     461     548 .. 0.76
   3 ?    4.6   3.9     0.094        23     125     202 ..     738     820 ..     699     834 .. 0.75
   4 ?   -1.7   1.7         8     2e+03     121     184 ..     816     885 ..     799     900 .. 0.41

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.019
                        AAA_11  20 tliqGPPGtgKTktivells 39 
                                   +l+ GPPGtgKT    ++ +
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVAN 235
                                   6899********66655555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.019
                        AAA_11  19 itliqGPPGtgKTktivellsq 40 
                                    +l+ GPPGtgKT    ++ ++
  gi|15669345|ref|NP_248150.1| 488 GVLLFGPPGTGKTLLAKAVANE 509
                                   57899********766666555 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.094
                        AAA_11 125 lakeiskeleklakelrafeeeeekeklkkskekskskleqerrklkkerkelskeleeaeesle.......eevldeaei 198
                                     +  ++++e+++ke+++f e+++ke+lk s++++++kl ++++++  + ke+ +++ e e++l+       +   +  ei
  gi|15669345|ref|NP_248150.1| 738 VLSPAKEKIEAVEKEIDKFLEVINKEELKPSEKDEAQKLAKYLKDILGKLKEMIDNIYELENKLNtlkeqvsA--EEIDEI 816
                                   45566789999999******************************99999999999999999998766544221..222345 PP

                        AAA_11 199 vltT 202
                                   + tT
  gi|15669345|ref|NP_248150.1| 817 IKTT 820
                                   5555 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 8
                        AAA_11 121 e...kaqlakeiskeleklakelrafeeeeek...eklkkskekskskleqerrklkkerkelskeleea 184
                                       ++++ ++ + +l++l++ l++ e+   k   + +k +ke++ + le+ +  ++ke +++ ++l ++
  gi|15669345|ref|NP_248150.1| 816 IiktTQNIIQRFTTSLDELKNILKDIESIRLKvstKDVKIKKEHFMKALEKIKPSVSKEDMRVYEKLAQE 885
                                   1222344444444444444444433333332244333333333333344444444444444444444443 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   4.2   0.00029     0.072       4     136 ..     693     829 ..     690     865 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00029
                  Baculo_PEP_C   4 vqqLnggggnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq.... 80 
                                   +q ++g+     ++L+ v++a +  ++  +++ ++l++ai + ++ ls   k+ ++++++++d++l+ +++   + +    
  gi|15669345|ref|NP_248150.1| 693 LQSISGTFRAAAVELNSVIKATKERESAEAGEFSELKNAIGKIISVLSP-AKEKIEAVEKEIDKFLEVINKEELKPSekde 772
                                   6666666666777777777777777777766666655555443333332.2222344444444444444333222223333 PP

                  Baculo_PEP_C  81 .dtlrneLtnlnsiltnLlssvtNinstLnnllqalnnldlgalsqeledaldtvee 136
                                    ++l + L+ +  +l ++  ++  +++ Ln l + + + + +++ ++ +++++  ++
  gi|15669345|ref|NP_248150.1| 773 aQKLAKYLKDILGKLKEMIDNIYELENKLNTLKEQVSAEEIDEIIKTTQNIIQRFTT 829
                                   355555555555555555555555555566665555555555555555555554333 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.012       3.1       8      81 ..     222     299 ..     218     322 .. 0.61
   2 ?    4.7   0.0      0.12        29       8      55 ..     495     542 ..     491     592 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.012
               Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev....eevdersrlssflskllaarvagdtldeklddel 81 
                                    G+g++ +++a+A++ g +fy  + +e ++k  g +ee +    ee++e++++  f++++ a   + d+ + + + +l
  gi|15669345|ref|NP_248150.1| 222 PGTGKTLLAKAVANEAGANFYVINGPEIMSKYVGETEENLrkifEEAEENAPSIIFIDEIDAIAPKRDEATGEVERRL 299
                                   59******************9776666666666666665541145556666666666666555444444444444444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.12
               Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevdersr 55 
                                    G+g++ +++a+A++ g +f++ + +e  +k  g se+ ++e+  ++r
  gi|15669345|ref|NP_248150.1| 495 PGTGKTLLAKAVANESGANFISVKGPEIFSKWVGESEKAIREIFRKAR 542
                                   59**********************999999999999999955444333 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.086        21       5      29 ..     217     241 ..     214     246 .. 0.88
   2 ?    7.7   0.0    0.0083       2.1       5      32 ..     490     517 ..     487     530 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.086
                           IPT   5 lifGatttGKtaeaiklaketgapv 29 
                                   l++G+ +tGKt  a ++a+e ga  
  gi|15669345|ref|NP_248150.1| 217 LLVGPPGTGKTLLAKAVANEAGANF 241
                                   89******************99865 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0083
                           IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                   l+fG+ +tGKt  a ++a+e ga  i++
  gi|15669345|ref|NP_248150.1| 490 LLFGPPGTGKTLLAKAVANESGANFISV 517
                                   89*********************99975 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.033       8.3       2      24 ..     214     236 ..     213     239 .. 0.91
   2 ?    5.5   0.0     0.053        13       2      24 ..     487     509 ..     486     512 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.033
                     PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                   k +ll+G+ g+GKt L++a+ +e
  gi|15669345|ref|NP_248150.1| 214 KGVLLVGPPGTGKTLLAKAVANE 236
                                   669****************9887 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.053
                     PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                   k +ll+G+ g+GKt L++a+ +e
  gi|15669345|ref|NP_248150.1| 487 KGVLLFGPPGTGKTLLAKAVANE 509
                                   569****************9887 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.17        42       5      71 ..     220     281 ..     216     286 .. 0.83
   2 ?    9.2   0.0    0.0038      0.94       5      71 ..     493     554 ..     489     559 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.17
               Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                   G pG GK+ l + ++++   ++ v++   e+ ++ + +++ +  + ++++++++       i+++DE+
  gi|15669345|ref|NP_248150.1| 220 GPPGTGKTLLAKAVANEAgANFYVING-PEIMSKYVGETEENLRKIFEEAEENAP-----SIIFIDEI 281
                                   78***************9988888888.899999998888887888888888764.....49999997 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0038
               Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                   G pG GK+ l + ++++s  ++ +++   e++++++ ++++   + ++++ +++ +     i+++DE+
  gi|15669345|ref|NP_248150.1| 493 GPPGTGKTLLAKAVANESgANFISVKG-PEIFSKWVGESEKAIREIFRKARQSAPC-----IIFFDEI 554
                                   88*****************77777777.8*******99999999999999998764.....9999997 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.056        14      58      79 ..     209     230 ..     172     239 .. 0.80
   2 ?    6.5   0.0     0.013       3.3      49      79 ..     474     503 ..     446     509 .. 0.70
   3 ?   -2.1   0.1       5.6   1.4e+03     308     336 ..     787     815 ..     772     841 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.056
                   AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                     ep++g+ l G+ G GKt l 
  gi|15669345|ref|NP_248150.1| 209 GIEPPKGVLLVGPPGTGKTLLA 230
                                   568****************985 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                   AFG1_ATPase  49 gklfgrkrksvepvrglYlwGgvGrGKtylm 79 
                                    k +++k   v+p++g+ l G+ G GKt l 
  gi|15669345|ref|NP_248150.1| 474 AKEVFEKI-GVRPPKGVLLFGPPGTGKTLLA 503
                                   34444453.678****************985 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.6
                   AFG1_ATPase 308 fiaLvDelYdadvklvvsaevaleelyea 336
                                   +  ++D++Y+ + kl  + e+   e++ +
  gi|15669345|ref|NP_248150.1| 787 LKEMIDNIYELENKLNTLKEQVSAEEIDE 815
                                   55667777777777766655555444443 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.3   0.00012     0.029      56     182 ..     748     880 ..     723     891 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00012
                  Allexi_40kDa  56 hishdvdsiinklnpvslls....qttlLse.lrdalrtltklldklksvekklelsaetasdskllkklesietsleelh 131
                                    +++++d+ ++ +n+ +l      ++++L++ l+d l +l++++d+++++e+kl++ +e+ s +++ + +++ ++ +++  
  gi|15669345|ref|NP_248150.1| 748 AVEKEIDKFLEVINKEELKPsekdEAQKLAKyLKDILGKLKEMIDNIYELENKLNTLKEQVSAEEIDEIIKTTQNIIQRFT 828
                                   57788999999999887765455567777764789999*****************************9************* PP

                  Allexi_40kDa 132 akldelsssetseseg.PsssptkassaeaaasedLpiyqakhPtarCrtyG 182
                                   + ldel +  ++ ++   ++s+++ + ++ +  + L+  +++   +  r y 
  gi|15669345|ref|NP_248150.1| 829 TSLDELKNILKDIESIrLKVSTKDVKIKKEHFMKALEKIKPSVSKEDMRVYE 880
                                   ******9998887665378888888888888888888777777777777765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.011       2.9      17      71 ..     206     254 ..     183     296 .. 0.69
   2 ?    3.6   0.0      0.24        61      21      45 ..     476     507 ..     432     543 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.011
                                   ......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH CS
                        ResIII  17 eklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl 71 
                                   ekl ++  k +l++ + GtGKTl+a +++ +   ++       ++++ +++++  
  gi|15669345|ref|NP_248150.1| 206 EKLGIEPPKGVLLVGPPGTGKTLLAKAVANEAGANF------YVINGPEIMSKYV 254
                                   444447889999***********9988887776653......3566666666665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.24
                                   .........TTSEEEEEESTTSTHHHHHHHHH CS
                        ResIII  21 s.......krdkrglikmaTGtGKTlvaakli 45 
                                   +       +  k +l+  + GtGKTl+a +++
  gi|15669345|ref|NP_248150.1| 476 EvfekigvRPPKGVLLFGPPGTGKTLLAKAVA 507
                                   134444446677888999********996665 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00023     0.058      30      63 ..      18      51 ..       2      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00023
                                  -EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEE CS
               Molydop_binding 30 evveinpedAaalGikdGdlVevesrrGsvevra 63
                                    ++i p ++++lG+k Gd +e+e ++G++ + +
  gi|15669345|ref|NP_248150.1| 18 GIARIDPYTMEELGLKPGDVIEIEGPKGKAYAIV 51
                                  4789************************998765 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.007       1.7      36      69 ..     217     250 ..     210     265 .. 0.88
   2 ?    2.5   0.0      0.24        60      35      63 ..     489     517 ..     470     559 .. 0.85
   3 ?    0.6   0.5      0.86   2.1e+02     212     275 ..     830     895 ..     811     901 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.007
                         AAA_6  36 apaGpagtGKtEtvkdLakalakqvvvfncsdql 69 
                                    + Gp gtGKt   k +a++ +  ++v+n  + +
  gi|15669345|ref|NP_248150.1| 217 LLVGPPGTGKTLLAKAVANEAGANFYVINGPEIM 250
                                   578*************************987765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.24
                         AAA_6  35 gapaGpagtGKtEtvkdLakalakqvvvf 63 
                                     + Gp gtGKt   k +a++ +  ++ +
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANESGANFISV 517
                                   5678********99999999988877765 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.86
                         AAA_6 212 glralksvlkaagelkre..epees.eeelllralrdvnlpklvaeDvplfkglisdlFpgvelpes 275
                                   +l  lk +lk + +++ +  +++ +  +e +++al+++  p + +eD+ ++++l +++   ++++++
  gi|15669345|ref|NP_248150.1| 830 SLDELKNILKDIESIRLKvsTKDVKiKKEHFMKALEKI-KPSVSKEDMRVYEKLAQEYGRATSVEKK 895
                                   56778888888888765422333334788999999988.58999*********99987666665554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0098       2.4       2      52 ..     216     279 ..     215     312 .. 0.78
   2 ?    2.9   0.0      0.45   1.1e+02       2      22 ..     489     509 ..     488     551 .. 0.83
   3 ?   -0.8   0.3       6.1   1.5e+03      87     103 ..     743     759 ..     707     795 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0098
                                   EEEEESTTSSHHHHHHHHHT.........S.TEEESSSTTSSSSEEEEEEE...ETTEEEEEEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg.........e.kaivsdkpgtTrdinegrvk...lkgkeielvD 52 
                                   v++vG p +GK+ L +a  +         +   i+s++ g T +  ++ ++   ++ ++i+++D
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANeaganfyviNgPEIMSKYVGETEENLRKIFEeaeENAPSIIFID 279
                                   789****************866666655533679999999999999988885433336677777 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.45
                                   EEEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                   v+++G p +GK+ L +a  +e
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANE 509
                                   789*************99986 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 6.1
                                   TTCSHHHHHHHHHHHHH CS
                      MMR_HSR1  87 eeklkpldeeleellee 103
                                   +ek++++++e+ ++le 
  gi|15669345|ref|NP_248150.1| 743 KEKIEAVEKEIDKFLEV 759
                                   34444444444444322 PP

>> DUF1677  Protein of unknown function (DUF1677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0045       1.1      11      53 ..     365     407 ..     359     444 .. 0.75
   2 ?    1.0   0.0       2.3   5.7e+02      10      67 ..     638     700 ..     631     716 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0045
                       DUF1677  11 lteectaeYiarvrerfsGkwvCGLCaeavkeelerskkkisv 53 
                                   l e++  +Y+a+v + f G  +  LC ea    l+r  ++i++
  gi|15669345|ref|NP_248150.1| 365 LAEDVDLDYLADVTHGFVGADLAALCKEAAMRALRRVLPSIDL 407
                                   789999*************************999994444433 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 2.3
                       DUF1677  10 glteectaeYiarvrerfsGkwvCGLCaea....vkeeler.skkkisveeAlkahmafckkf 67 
                                   +l e++  e +a+  e ++G  +  LC ea    v+e + +  + ++++ e ++   ++  +f
  gi|15669345|ref|NP_248150.1| 638 NLAEDVNLEELAKKTEGYTGADIEALCREAamlaVRESIGKpWDIEVKLRELINYLQSISGTF 700
                                   57888888888999999***********97222255555553334444445444444444444 PP

>> Abi_C  Abortive infection C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0013      0.34      13      48 ..     765     800 ..     756     804 .. 0.90
   2 ?   -0.2   0.1       4.5   1.1e+03      22      42 ..     807     827 ..     801     845 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0013
                         Abi_C  13 lspddekadapgakeikqilsglasivqglgeLRNk 48 
                                   l+p++++++++ ak +k+il++l+ +++++ eL Nk
  gi|15669345|ref|NP_248150.1| 765 LKPSEKDEAQKLAKYLKDILGKLKEMIDNIYELENK 800
                                   67999999*************************998 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 4.5
                         Abi_C  22 apgakeikqilsglasivqgl 42 
                                   +  a+ei +i++  ++i+q +
  gi|15669345|ref|NP_248150.1| 807 QVSAEEIDEIIKTTQNIIQRF 827
                                   457888888888888888754 PP

>> eIF3_N  eIF3 subunit 6 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.2   0.00015     0.036      76     129 ..     744     797 ..     740     799 .. 0.95
   2 ?    3.9   2.7      0.27        68      45     130 ..     789     883 ..     784     884 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00015
                        eIF3_N  76 eeleeleeeaekvlelledeevvsnlrsdkkqnlefLkeehgitpemidalykf 129
                                   e++e++e+e++k+le++++ee + + + + +++ ++Lk+  g   emid +y++
  gi|15669345|ref|NP_248150.1| 744 EKIEAVEKEIDKFLEVINKEELKPSEKDEAQKLAKYLKDILGKLKEMIDNIYEL 797
                                   68999***********************************************86 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.27
                        eIF3_N  45 nmvdyaadlykelegeee.....vpeelekkreevleeleeleeeaekvlelledeevvsnlrs...dkkqnlefLkeeh. 116
                                   +m+d + +l+++l++ +e       +e+ k  +++++++++  +e +++l+ +e+   + + +     k++ ++ L++   
  gi|15669345|ref|NP_248150.1| 789 EMIDNIYELENKLNTLKEqvsaeEIDEIIKTTQNIIQRFTTSLDELKNILKDIESIRLKVSTKDvkiKKEHFMKALEKIKp 869
                                   799999999999997443343223346677788888888888888888887777776666666666688888888876333 PP

                        eIF3_N 117 gitpemidalykfa 130
                                    ++ e + ++ k+a
  gi|15669345|ref|NP_248150.1| 870 SVSKEDMRVYEKLA 883
                                   67777776666666 PP

>> THP2  Tho complex subunit THP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.59   1.5e+02      11      71 ..     704     764 ..     699     768 .. 0.82
   2 ?   11.8   7.6   0.00077      0.19      36     128 ..     750     847 ..     744     848 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.59
                          THP2  11 svdLakqveisdeevseivvddekppkelqeilekyeeesedaeelraklekYldeiKmer 71 
                                   +v+L + ++ ++e++s  + + ++  + + +i+  ++  +e++e+++++++k+l+ i  e 
  gi|15669345|ref|NP_248150.1| 704 AVELNSVIKATKERESAEAGEFSELKNAIGKIISVLSPAKEKIEAVEKEIDKFLEVINKEE 764
                                   67777888877777776677777888899999999999*****************998765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00077
                          THP2  36 pkelqeilekyeeeseda..eelraklekYldeiKmerakytleNkyllkdklkeltkevnrWr..kewdniEnll..Fgd 110
                                    ke+ + le  ++e+ +   ++  +kl kYl +i + + k  ++N y l++kl++l+++v++    +  +   n++  F  
  gi|15669345|ref|NP_248150.1| 750 EKEIDKFLEVINKEELKPseKDEAQKLAKYLKDI-LGKLKEMIDNIYELENKLNTLKEQVSAEEidEIIKTTQNIIqrFTT 829
                                   56777778877775544400445689********.78999*******************9963311223333444455999 PP

                          THP2 111 gpnslkkllqkveslkak 128
                                   + + lk++l+++es++ k
  gi|15669345|ref|NP_248150.1| 830 SLDELKNILKDIESIRLK 847
                                   9999**********9987 PP

>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       3.1   7.6e+02      23      47 ..     646     672 ..     642     675 .. 0.86
   2 ?   10.5   0.0    0.0016       0.4      92     184 ..     685     804 ..     682     818 .. 0.70
   3 ?    0.5   0.1       1.9   4.7e+02      84     177 ..     822     867 ..     798     882 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.1
                 PhageMin_Tail  23 eelas..aGvsteeilnllegaaklat 47 
                                   eela+   G+++++i++l + aa+la+
  gi|15669345|ref|NP_248150.1| 646 EELAKktEGYTGADIEALCREAAMLAV 672
                                   67788556***********99999997 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0016
                 PhageMin_Tail  92 svedlaealkevgavakaaGlsfeetaaalallaaag.ikgseAgtalknllsrl..tkeaaealkklGis.t........ 160
                                   ++++l+++l+ ++++++aa ++++ +  a     +a   + se  +a+ +++s l   ke  ea++k  i+ +        
  gi|15669345|ref|NP_248150.1| 685 KLRELINYLQSISGTFRAAAVELNSVIKATKERESAEaGEFSELKNAIGKIISVLspAKEKIEAVEK-EIDkFlevinkee 764
                                   689********************************999*****************554444444444.5554477777777 PP

                 PhageMin_Tail 161 ................kdaqgkmksldeiledlsealkkl 184
                                                   kd  gk k + + + +l ++l++l
  gi|15669345|ref|NP_248150.1| 765 lkpsekdeaqklakylKDILGKLKEMIDNIYELENKLNTL 804
                                   7766654444333333333344444444444444455555 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.9
                 PhageMin_Tail  84 aaanngatsvedlaealkevgavakaaGlsfeetaaalallaaagikgseAgtalknllsrltkeaaealkkl.....Gis 159
                                    + +++ ts+                                                     +e ++ lk++      +s
  gi|15669345|ref|NP_248150.1| 822 NIIQRFTTSL-----------------------------------------------------DELKNILKDIesirlKVS 849
                                   3333333333.....................................................355555555444444555 PP

                 PhageMin_Tail 160 tkdaqgkmksldeiledl 177
                                   tkd++ k   ++++le++
  gi|15669345|ref|NP_248150.1| 850 TKDVKIKKEHFMKALEKI 867
                                   566665555555555555 PP

>> Baculo_p24  Baculovirus P24 capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   5.8   0.00076      0.19      70     155 ..     753     843 ..     750     874 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00076
                    Baculo_p24  70 lckyLssynlsds..ahppeyyvlkqLvrDLlvGaqseavdplkdiktqlctlqecleesnvlvn.sttesssn...enie 144
                                   + k+L ++n+++   +++ e + l + ++D+l G+ +e++d++ +++++l+tl+e ++ ++   + +tt++  +   ++++
  gi|15669345|ref|NP_248150.1| 753 IDKFLEVINKEELkpSEKDEAQKLAKYLKDIL-GKLKEMIDNIYELENKLNTLKEQVSAEEIDEIiKTTQNIIQrftTSLD 832
                                   56999999988764678889999999999975.**********************99987754434333333323446666 PP

                    Baculo_p24 145 slreilrseea 155
                                   +l++il+  e+
  gi|15669345|ref|NP_248150.1| 833 ELKNILKDIES 843
                                   66666654333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.054        13      21      39 ..     213     230 ..     204     235 .. 0.77
   2 ?    4.6   0.0      0.11        28      21      39 ..     486     503 ..     475     508 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.054
                        AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                   +kg +ll+Gp G+GK+ l 
  gi|15669345|ref|NP_248150.1| 213 PKG-VLLVGPPGTGKTLLA 230
                                   356.9**********8765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.11
                        AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                   +kg +ll Gp G+GK+ l 
  gi|15669345|ref|NP_248150.1| 486 PKG-VLLFGPPGTGKTLLA 503
                                   456.9**********8765 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       4.6   1.1e+03      11      45 ..     724     758 ..     714     766 .. 0.79
   2 ?   11.4   6.6   0.00089      0.22       8     103 ..     769     869 ..     762     872 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 4.6
                         Sec34  11 ecdelleqtdealeqLeeleekfksvsektsslhe 45 
                                   e+ el + + ++ + L+  +ek ++v+++  ++ e
  gi|15669345|ref|NP_248150.1| 724 EFSELKNAIGKIISVLSPAKEKIEAVEKEIDKFLE 758
                                   66778888888889999999999999998888765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00089
                         Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheac.....eq.lleeqkrleelaeeieekLkyFeeldpitrkLn 82 
                                   +++e ++l + ++++l +L+e+ ++  + ++k ++l+e+      ++ + + q+ +++++ +++e  ++ +++++i  k +
  gi|15669345|ref|NP_248150.1| 769 EKDEAQKLAKYLKDILGKLKEMIDNIYELENKLNTLKEQVsaeeiDEiIKTTQNIIQRFTTSLDELKNILKDIESIRLKVS 849
                                   567778888888888888888888888888888888776422222331445677778888888888899999999999999 PP

                         Sec34  83 spgsslvksesFlemLkklDe 103
                                   ++  + +k+e+F++ L+k+  
  gi|15669345|ref|NP_248150.1| 850 TKDVK-IKKEHFMKALEKIKP 869
                                   99999.************975 PP

>> Glutaredoxin2_C  Glutaredoxin 2, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7     0.001      0.26      41      91 ..     805     855 ..     799     858 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.001
               Glutaredoxin2_C  41 kkeksigdfeellaktpeliaelnalLeelepliksseavngelSvdDill 91 
                                   k++ s+++ +e+++ t+++i+++   L+el++++k  e++  ++S+ D+++
  gi|15669345|ref|NP_248150.1| 805 KEQVSAEEIDEIIKTTQNIIQRFTTSLDELKNILKDIESIRLKVSTKDVKI 855
                                   56667789****************************************986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.4     0.017       4.1      11      32 ..     214     235 ..     210     244 .. 0.81
   2 ?    7.4   0.2     0.021       5.3      11      31 ..     487     507 ..     480     519 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.017
                        AAA_19  11 kvllvtaGpGtGKTrvlkhiva 32 
                                   k +l++++pGtGKT + k++ +
  gi|15669345|ref|NP_248150.1| 214 KGVLLVGPPGTGKTLLAKAVAN 235
                                   56899*********98877655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.021
                        AAA_19  11 kvllvtaGpGtGKTrvlkhiv 31 
                                   k +l+ ++pGtGKT + k++ 
  gi|15669345|ref|NP_248150.1| 487 KGVLLFGPPGTGKTLLAKAVA 507
                                   6689**********8877655 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.4      0.58   1.4e+02       9      76 ..     687     753 ..     680     765 .. 0.66
   2 ?   13.6   3.0   0.00034     0.084       6      81 ..     771     843 ..     769     894 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.58
                       DUF2203   9 nalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvev 76 
                                   ++l+  l+++   +ra++ el+++ ++ +e ++++ + e++el++++ ++ + ++ + e+ie++  e+
  gi|15669345|ref|NP_248150.1| 687 RELINYLQSISGTFRAAAVELNSVIKATKERESAE-AGEFSELKNAIGKIISVLSPAKEKIEAVEKEI 753
                                   57788888888888888888888776666665553.44466666666666666666666666655443 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00034
                       DUF2203   6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdlea 81 
                                   +eA++l   lk++l +l+++ +++ ele++l++ k++ +   a+e  + +++ ++ i+++++ ++el+  +kd+e 
  gi|15669345|ref|NP_248150.1| 771 DEAQKLAKYLKDILGKLKEMIDNIYELENKLNTLKEQVS---AEEIDEIIKTTQNIIQRFTTSLDELKNILKDIES 843
                                   79*********************************9987...5666667777777777777777777777777654 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.13        32       1      21 [.     222     242 ..     222     272 .. 0.67
   2 ?    6.0   0.0     0.048        12       1      23 [.     495     517 ..     495     545 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.13
                                   TTSSHHHHHHHHHHHHTSEEE CS
                           SKI   1 mGaGKstvGkllAkklglefi 21 
                                   +G+GK+ ++k++A++ g +f+
  gi|15669345|ref|NP_248150.1| 222 PGTGKTLLAKAVANEAGANFY 242
                                   69*************998885 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.048
                                   TTSSHHHHHHHHHHHHTSEEEEH CS
                           SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                   +G+GK+ ++k++A++ g +fi +
  gi|15669345|ref|NP_248150.1| 495 PGTGKTLLAKAVANESGANFISV 517
                                   69******************976 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0      0.08        20       4      26 ..     219     241 ..     216     246 .. 0.89
   2 ?    6.1   0.1     0.033       8.3       5      28 ..     493     516 ..     489     519 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.08
                                   E-STTSSHHHHHHHHHHHHT-EE CS
                Cytidylate_kin   4 DGPagsGKssvaralaeklglky 26 
                                    GP g+GK  +a+a+a++ g+++
  gi|15669345|ref|NP_248150.1| 219 VGPPGTGKTLLAKAVANEAGANF 241
                                   59****************99876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.033
                                   -STTSSHHHHHHHHHHHHT-EEEE CS
                Cytidylate_kin   5 GPagsGKssvaralaeklglkyld 28 
                                   GP g+GK  +a+a+a++ g+++++
  gi|15669345|ref|NP_248150.1| 493 GPPGTGKTLLAKAVANESGANFIS 516
                                   9******************99986 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.016         4       4      33 ..     217     245 ..     215     263 .. 0.84
   2 ?    3.4   0.1       0.2        50       4      24 ..     490     510 ..     488     618 .. 0.85
   3 ?   -2.1   0.1       9.7   2.4e+03     146     170 ..     759     784 ..     735     790 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.016
                                   EEEESTTCCHHHHHHHHHCT--SS-EEEEE CS
                          cobW   4 vltGflGsGKTtLlnhllenraglklaviv 33 
                                   +l+G++G+GKT Ll + ++n+ag +  vi 
  gi|15669345|ref|NP_248150.1| 217 LLVGPPGTGKT-LLAKAVANEAGANFYVIN 245
                                   799*******8.666667788999888886 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.2
                                   EEEESTTCCHHHHHHHHHCT- CS
                          cobW   4 vltGflGsGKTtLlnhllenr 24 
                                   +l G++G+GKT L +++ +++
  gi|15669345|ref|NP_248150.1| 490 LLFGPPGTGKTLLAKAVANES 510
                                   6889******98877766554 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 9.7
                                   EEE-HHHHCHC...HHHHHHHHHHHH CS
                          cobW 146 vlnKtDlldee.allekleerlrqln 170
                                   v+nK +l ++e ++++kl+++l+++ 
  gi|15669345|ref|NP_248150.1| 759 VINKEELKPSEkDEAQKLAKYLKDIL 784
                                   78999999988777788888888775 PP

>> Med15_fungi  Mediator complex subunit 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.0    0.0036       0.9       4     102 ..     743     841 ..     740     844 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0036
                   Med15_fungi   4 keklkqiyeevaknavrlkpitnlspeqKaaikqqlqeiqqmlarvdaliplfykltkneeavkrLlqmrimlkeqleklp 84 
                                   kek+  + +e+ k   ++ + ++l p +K++ ++  + ++++l +++++i  +y l ++ + +k+ ++    + e+++ ++
  gi|15669345|ref|NP_248150.1| 743 KEKIEAVEKEIDKFL-EVINKEELKPSEKDEAQKLAKYLKDILGKLKEMIDNIYELENKLNTLKEQVSAE-EIDEIIKTTQ 821
                                   667777777776654.4444455******************************************88776.5789999888 PP

                   Med15_fungi  85 q..dqftikpeyLeklksqi 102
                                   +  ++ft+++++L+++ + i
  gi|15669345|ref|NP_248150.1| 822 NiiQRFTTSLDELKNILKDI 841
                                   8999********99987766 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0         6   1.5e+03       9      52 ..     416     459 ..     413     469 .. 0.77
   2 ?   12.0   0.3   0.00081       0.2      27     104 ..     684     759 ..     682     763 .. 0.91
   3 ?   -1.1   0.2       9.2   2.3e+03      29      48 ..     810     829 ..     782     866 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 6
                                   HHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHH CS
                       DUF2383   9 LietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqs 52 
                                    +++lk  ++ +kea ++v+ ++++++l ++ + + e +  L++
  gi|15669345|ref|NP_248150.1| 416 VLDNLKVTMDDFKEALKDVEPSAMREVLVEVPNVKWEDIGGLEE 459
                                   566777788889************99998887777777666655 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00081
                                   --SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT----------------------------HHHHHHHHHHHHHHHHHH CS
                       DUF2383  27 vkdpqlktlleriaeereeaaeeLqseiralggepedggslagklhrawvdlksaltsndeeaileeleegEdkalee 104
                                   vk  +l ++l++i+   ++aa eL+s i+a ++    + +  ++l++a+ ++ s+l+  +e+  +e++e++ dk le 
  gi|15669345|ref|NP_248150.1| 684 VKLRELINYLQSISGTFRAAAVELNSVIKATKERESAEAGEFSELKNAIGKIISVLSPAKEK--IEAVEKEIDKFLEV 759
                                   666788899***************************************************97..99999998888875 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 9.2
                                   SHHHHHHHHHHHHHHHHHHH CS
                       DUF2383  29 dpqlktlleriaeereeaae 48 
                                    +++ ++ +  ++  +++ +
  gi|15669345|ref|NP_248150.1| 810 AEEIDEIIKTTQNIIQRFTT 829
                                   44444333333332222222 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.3    0.0044       1.1     118     236 ..     688     819 ..     682     831 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0044
                          CorA 118 eivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlk..........rlla.kaddkl 185
                                   e++++l  +  +  +   el + +   ++++  +++e ++l+  ++k+ ++l+p +e ++          ++++  ++++ 
  gi|15669345|ref|NP_248150.1| 688 ELINYLQSISGTFRAAAVELNSVIkaTKERESAEAGEFSELKNAIGKIISVLSPAKEKIEavekeidkflEVINkEELKPS 768
                                   555555555555555555666666777788888999999999999999999999999998888888744433336677777 PP

                          CorA 186 lddedkeylrdlldelerllemlealrerleslqdtyssllserlNrvmkv 236
                                   ++de++++ + l d l +l em++++ e+ ++l+ +  ++++e+  +++k+
  gi|15669345|ref|NP_248150.1| 769 EKDEAQKLAKYLKDILGKLKEMIDNIYELENKLNTLKEQVSAEEIDEIIKT 819
                                   777777777777777777888888888888888888888888887777765 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  10.3    0.0093       2.3      36     176 ..     743     882 ..     729     901 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0093
                    V_ATPase_I  36 erklrfleeeieklekavikeeea..eesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekake 114
                                   ++k++ +e+ei+k+ +++ kee +  e++++++ +k+l+++  +l+++ +++ el+++l++lk+++ +++e  ++++++++
  gi|15669345|ref|NP_248150.1| 743 KEKIEAVEKEIDKFLEVINKEELKpsEKDEAQKLAKYLKDILGKLKEMIDNIYELENKLNTLKEQV-SAEEIDEIIKTTQN 822
                                   566777777777766666555544434556777788899999999999999999999999998876.57899999999999 PP

                    V_ATPase_I 115 fleeeeeeeeeeeseeeeee..keeeeeeeseeeeeeelleeeeelsfvaGvikrekveaferi 176
                                   ++++ +++ +e ++  ++ e  + + ++++++     ++++  ++l+ +   +++e+++ +e++
  gi|15669345|ref|NP_248150.1| 823 IIQRFTTSLDELKNILKDIEsiRLKVSTKDVK----IKKEHFMKALEKIKPSVSKEDMRVYEKL 882
                                   99876433333222222222122222222222....2222223447889999999999988886 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       3.1   7.8e+02      13      53 ..     695     735 ..     687     741 .. 0.82
   2 ?    0.3   0.1         3   7.6e+02      15      36 ..     743     764 ..     738     766 .. 0.90
   3 ?    7.2   0.5     0.022       5.5      12      37 ..     774     799 ..     763     808 .. 0.85
   4 ?    3.1   1.5      0.42     1e+02       8      51 ..     802     849 ..     795     855 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 3.1
                          YojJ  13 klkeeLeqiekeleevlkaldeedeClLcelesirekfael 53 
                                    +   ++ + +el+ v+ka +e ++   +e+ ++++ + ++
  gi|15669345|ref|NP_248150.1| 695 SISGTFRAAAVELNSVIKATKERESAEAGEFSELKNAIGKI 735
                                   566778999999*********99999999999998887776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 3
                          YojJ  15 keeLeqiekeleevlkaldeed 36 
                                   ke++e +eke+++ l+ +++e+
  gi|15669345|ref|NP_248150.1| 743 KEKIEAVEKEIDKFLEVINKEE 764
                                   899************9999986 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.022
                          YojJ  12 eklkeeLeqiekeleevlkaldeede 37 
                                   +kl+++L++i ++l+e+++++ e ++
  gi|15669345|ref|NP_248150.1| 774 QKLAKYLKDILGKLKEMIDNIYELEN 799
                                   79******************988776 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.42
                          YojJ   8 eelkekl.keeLeqiekeleevlk....aldeedeClLcelesirekfa 51 
                                   + lke++ +ee+ +i+k+ +++++    +lde  + +L ++esir k++
  gi|15669345|ref|NP_248150.1| 802 NTLKEQVsAEEIDEIIKTTQNIIQrfttSLDEL-KNILKDIESIRLKVS 849
                                   456666524567777777777665111133433.347777777776665 PP

>> TINF2_N  TERF1-interacting nuclear factor 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.8       2.3   5.6e+02      53     109 ..     744     801 ..     734     811 .. 0.71
   2 ?    8.9   0.4    0.0071       1.8      56     120 ..     828     889 ..     813     895 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 2.3
                       TINF2_N  53 kekaadlkaiqshlerlrasaa.kstkkkdekveeaqenflklvqsLledpeerekfl 109
                                   ++ +a+ k+i+++le +++     s+k + +k+ +  +++l   ++++++  e e++l
  gi|15669345|ref|NP_248150.1| 744 EKIEAVEKEIDKFLEVINKEELkPSEKDEAQKLAKYLKDILGKLKEMIDNIYELENKL 801
                                   3336778888999988888655566677778888888888888888888888877777 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0071
                       TINF2_N  56 aadlkaiqshlerlrasaakstkkkdekveeaqenflklvqsLledpeerekflqeefpeeYGek 120
                                   +++l+++++ l+ +++      k + ++v+  +e+f+k  +++  + ++ +  + e++ +eYG++
  gi|15669345|ref|NP_248150.1| 828 TTSLDELKNILKDIESI---RLKVSTKDVKIKKEHFMKALEKIKPSVSKEDMRVYEKLAQEYGRA 889
                                   56677778888888885...5677778899999************9999999999********85 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.6      0.05        12      15      74 ..     694     766 ..     684     791 .. 0.58
   2 ?    4.0   6.2       0.3        74      37      96 ..     788     849 ..     761     868 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.05
                  Syntaxin-6_N  15 nkaeslyrrwe.rlledtssstseelde..trteLrkalrsiewdledLeetvrivek.........npsk.f 74 
                                   +++ +++r    +l ++ +++++ e+ e    +eL++a+++i   l+  +e +++vek         n+++  
  gi|15669345|ref|NP_248150.1| 694 QSISGTFRAAAvELNSVIKATKERESAEagEFSELKNAIGKIISVLSPAKEKIEAVEKeidkfleviNKEElK 766
                                   4555555555324433333322223322003479***********************9555555555554434 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.3
                  Syntaxin-6_N  37 eeldetrteLrkalrsiewdl..edLeetvriveknpskfkidekelsrrrafveevreevk 96 
                                   +e+ +   eL+++l+++++++  e+++e +++ ++  ++f  + +el++  + +e++r +v+
  gi|15669345|ref|NP_248150.1| 788 KEMIDNIYELENKLNTLKEQVsaEEIDEIIKTTQNIIQRFTTSLDELKNILKDIESIRLKVS 849
                                   45555566788888888887644578888877777778888888888877777777776664 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.035       8.6       2      26 ..     216     240 ..     215     258 .. 0.83
   2 ?    0.4   0.1       2.2   5.5e+02      81     105 ..     257     282 ..     247     305 .. 0.70
   3 ?   -1.8   0.1        10   2.5e+03     103     124 ..     453     474 ..     420     478 .. 0.83
   4 ?    5.4   0.0     0.063        16       2      32 ..     489     519 ..     488     525 .. 0.82
   5 ?   -0.6   0.9       4.5   1.1e+03     100     144 ..     790     841 ..     774     867 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.035
                                   EEEE--TTSSHHHHHHHHHHHH... CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss 26 
                                   v++ GppG+GKt l k v+++   +
  gi|15669345|ref|NP_248150.1| 216 VLLVGPPGTGKTLLAKAVANEAGAN 240
                                   6899************999987554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2.2
                                   HHHHHHHHHHHHH.HHH-EEEE---S CS
                      NTPase_1  81 feelalealrkal.seadviviDEiG 105
                                    ee   +++++a  + + +i iDEi 
  gi|15669345|ref|NP_248150.1| 257 TEENLRKIFEEAEeNAPSIIFIDEID 282
                                   455555666666635667******95 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 10
                                   --STTGGG-HHHHHHHHHHHTT CS
                      NTPase_1 103 EiGkmElkskkfkeaveevLks 124
                                    iG +E   ++++eave  Lk 
  gi|15669345|ref|NP_248150.1| 453 DIGGLEEVKQELREAVEWPLKA 474
                                   59999**9*****999987775 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.063
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                   v++ GppG+GKt l k v+++   + ++v+G
  gi|15669345|ref|NP_248150.1| 489 VLLFGPPGTGKTLLAKAVANESGANFISVKG 519
                                   6788***********9999987666666665 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 4.5
                                   EE---STTGGG-HHHHHHH.....HHHHTTTSEEEEE--SS-..-SHHHHHH CS
                      NTPase_1 100 viDEiGkmElkskkfkeav.....eevLksekpvlavihrrk..dlalveei 144
                                   +iD i ++E k +++ke+v     +e++k+ ++++  +  +    ++++++i
  gi|15669345|ref|NP_248150.1| 790 MIDNIYELENKLNTLKEQVsaeeiDEIIKTTQNIIQRFTTSLdeLKNILKDI 841
                                   5888888998888887654111116777777777766555543333344433 PP

>> MapZ_EC1  MapZ extracellular domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.6    0.0083       2.1      12      78 ..     740     811 ..     734     830 .. 0.85
   2 ?    1.4   1.1       1.5   3.7e+02      30      70 ..     848     888 ..     819     897 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0083
                      MapZ_EC1  12 kkekkalkafekeyaafftddketflknsefaklseLekkLe....klk.gskeYkklkkkldslkkqisai 78 
                                   + +k++++a+eke+++f    +++ lk+se ++ ++L+k L+    klk   ++  +l++kl++lk+q+sa 
  gi|15669345|ref|NP_248150.1| 740 SPAKEKIEAVEKEIDKFLEVINKEELKPSEKDEAQKLAKYLKdilgKLKeMIDNIYELENKLNTLKEQVSAE 811
                                   567899*************************99999998887222256645677889***********9985 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.5
                      MapZ_EC1  30 tddketflknsef.aklseLekkLeklkgskeYkklkkklds 70 
                                   +++k++++k ++f + l++++ ++ k ++   Y+kl +++ +
  gi|15669345|ref|NP_248150.1| 848 VSTKDVKIKKEHFmKALEKIKPSVSK-EDMRVYEKLAQEYGR 888
                                   678999*******999*****99998.556669998888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (903 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1800  (0.100396); expected 358.6 (0.02)
Passed bias filter:                      802  (0.044732); expected 358.6 (0.02)
Passed Vit filter:                       179  (0.00998383); expected 17.9 (0.001)
Passed Fwd filter:                        86  (0.0047967); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              72  [number of targets reported over threshold]
# CPU time: 1.21u 0.32s 00:00:01.53 Elapsed: 00:00:00.51
# Mc/sec: 5305.88
//
Query:       gi|15669346|ref|NP_248151.1|  [L=129]
Description: hypothetical protein MJ_1158 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-05   23.1   6.8     0.0054   16.8   1.1    2.2  2  Elf1            Transcription elongation factor Elf1 like
    0.00042   20.2   8.2      0.083   12.8   0.9    2.1  2  eIF-5_eIF-2B    Domain found in IF2B/IF5
     0.0025   17.8  10.0       0.26   11.3   0.9    3.7  4  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
     0.0043   16.9   9.7      0.067   13.1   1.4    2.3  2  C1_1            Phorbol esters/diacylglycerol binding domain 
     0.0046   16.8   6.1        2.1    8.3   0.1    3.5  4  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0099   15.5  12.2       0.13   12.0   3.6    3.0  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
  ------ inclusion threshold ------
      0.011   15.7   4.6          1    9.4   0.5    2.2  2  DUF1451         Zinc-ribbon containing domain
      0.012   15.7   6.7        0.6   10.3   0.2    2.8  2  Zn-ribbon_8     Zinc ribbon domain
      0.012   15.4   1.5       0.97    9.2   0.1    2.1  2  HydF_tetramer   Hydrogen maturase F tetramerization domain
      0.019   15.3   0.1       0.16   12.3   0.0    2.0  2  CPSase_L_D3     Carbamoyl-phosphate synthetase large chain, o
      0.022   14.4   0.8      0.022   14.4   0.8    1.8  2  DUF1847         Protein of unknown function (DUF1847)
      0.026   14.8   4.9        4.9    7.5   0.0    3.7  4  Ribosomal_L32p  Ribosomal L32p protein family
      0.033   14.3   0.2      0.033   14.3   0.2    3.1  3  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
      0.035   14.2   5.8        1.7    8.8   1.1    2.3  2  PHD_4           PHD-finger
      0.046   13.7   9.0          1    9.4   0.9    2.4  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.087   12.8  11.8        2.1    8.3   0.1    3.5  3  zinc_ribbon_4   zinc-ribbon domain
      0.089   12.4  11.2        8.2    6.1   0.2    4.1  4  Sgf11           Sgf11 (transcriptional regulation protein)
        0.1   12.2   0.3       0.57    9.7   0.0    1.9  2  SipA            SipA N-terminal domain
       0.13   12.1   5.6        2.4    8.1   0.7    2.6  2  zf-CCHC_6       Zinc knuckle
        0.4   10.8  10.6        1.3    9.2   2.7    2.6  2  zf-MYND         MYND finger
       0.44   10.6   5.3        2.3    8.3   0.3    2.6  2  PDCD2_C         Programmed cell death protein 2, C-terminal p
       0.45   10.7  19.1         13    6.0   0.4    4.2  4  zf-CCHC         Zinc knuckle
       0.62    9.5  11.5       0.56    9.6   2.0    2.1  2  NMD3            NMD3 family
       0.81    9.8  11.3        2.5    8.3   2.2    2.4  2  zf-RRPl_C4      Putative ribonucleoprotein zinc-finger pf C4 
        1.5    8.7  10.2       0.23   11.3   0.5    3.4  3  zf-HYPF         HypF finger
        2.3    8.2  14.8        5.4    7.0   0.1    4.1  4  TFIIS_C         Transcription factor S-II (TFIIS)
        2.3    7.7  13.6        1.4    8.4   0.2    4.0  4  zf-ribbon_3     zinc-ribbon domain
        2.5    8.4  14.9    1.1e+04   -3.3  15.0    3.8  0  IBR             IBR domain, a half RING-finger domain
          3    7.8  13.2         24    5.0   0.2    3.7  5  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        3.3    7.5  14.5        1.3    8.8   0.2    4.0  4  zinc_ribbon_2   zinc-ribbon domain
        3.3    7.5   8.6        9.7    6.0   1.0    2.4  2  Ribosomal_S27e  Ribosomal protein S27
        7.6    6.5   8.9          7    6.7   0.6    2.9  3  Nudix_N_2       Nudix N-terminal


Domain annotation for each model (and alignments):
>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.5    0.0015      0.86      19      54 ..      17      50 ..      11      60 .. 0.74
   2 !   16.8   1.1   9.6e-06    0.0054      10      61 ..      72     122 ..      64     127 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                          Elf1 19 ptkFdCpfCnheksvevkldkkekiaevsCkvCges 54
                                  ++   C +C++e    +++   ++ a v+C++Cg++
  gi|15669346|ref|NP_248151.1| 17 KKLAVCFNCKKEADQIIEIY--TNQAFVKCSNCGAT 50
                                  55556889999855555555..5599*******985 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 9.6e-06
                          Elf1  10 rkkkkkkk.lptkFdCpfCnheksvevkldkkekiaevsCkvCgesfetkvna 61 
                                   +k k  +  l+++  C +C++e + ++ ++++  + +v+C++Cg +  ++++ 
  gi|15669346|ref|NP_248151.1|  72 KKHKYEPWfLEKTAVCFNCKKEATQDIAITET--KMIVRCRNCGFTRVYQFHI 122
                                   233333335999**********8877777766..778******9876666554 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.9   0.00015     0.083      85     116 ..      17      49 ..       4      50 .. 0.75
   2 !   11.8   1.2    0.0003      0.17      83     116 ..      80     114 ..      62     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                                   HHHTSTSSSTSTCEEECC.SSSCEEEEESSSTC CS
                  eIF-5_eIF-2B  85 eeyVlCkeCkspetelek.eerllvlkCkaCga 116
                                   ++  +C +Ck+   +++   ++  ++kC++Cga
  gi|15669346|ref|NP_248151.1|  17 KKLAVCFNCKKEADQIIEiYTNQAFVKCSNCGA 49 
                                   66779*****976666665666677*******8 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0003
                                   HHHHHTSTSSSTSTCEE.ECCSSSCEEEEESSSTC CS
                  eIF-5_eIF-2B  83 yieeyVlCkeCkspete.lekeerllvlkCkaCga 116
                                   ++e+  +C +Ck+  t+ + ++e+ ++++C++Cg 
  gi|15669346|ref|NP_248151.1|  80 FLEKTAVCFNCKKEATQdIAITETKMIVRCRNCGF 114
                                   6777789*****999872555666666******95 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.9   0.00046      0.26      10      45 ..      11      49 ..       6      50 .. 0.80
   2 !    8.1   0.1    0.0047       2.7      18      34 ..      40      57 ..      34      62 .. 0.80
   3 !    7.4   2.0    0.0074       4.2      15      45 ..      81     114 ..      67     115 .. 0.77
   4 ?    4.7   0.3     0.052        29      19      32 ..     107     120 ..     101     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00046
                 Zn_Tnp_IS1595 10 LealrWpngfvCPhCgsr..kayrikt.rglfqCkeCrk 45
                                  +e++  +   vC +C+++  ++++i t     +C+ C++
  gi|15669346|ref|NP_248151.1| 11 MEKWELKKLAVCFNCKKEadQIIEIYTnQAFVKCSNCGA 49
                                  56666666699*********999999955666*****97 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0047
                 Zn_Tnp_IS1595 18 gfv.CPhCgsrkayrikt 34
                                   fv C +Cg +++y +++
  gi|15669346|ref|NP_248151.1| 40 AFVkCSNCGATRYYILRR 57
                                  4666*****999998887 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0074
                 Zn_Tnp_IS1595  15 WpngfvCPhCgsr..kayrikt.rglfqCkeCrk 45 
                                      + vC +C+++  + + i+      +C+ C+ 
  gi|15669346|ref|NP_248151.1|  81 LEKTAVCFNCKKEatQDIAITEtKMIVRCRNCGF 114
                                   556789*******775555555688999999986 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.052
                 Zn_Tnp_IS1595  19 fvCPhCgsrkayri 32 
                                   ++C +Cg +++y++
  gi|15669346|ref|NP_248151.1| 107 VRCRNCGFTRVYQF 120
                                   57*****9999975 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   1.5    0.0035       1.9       7      36 ..      15      49 ..       6      51 .. 0.79
   2 !   13.1   1.4   0.00012     0.067       1      36 [.      74     114 ..      74     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0035
                                  --SS--B-TTT-SB-....-S.SSS-EEEETTT-- CS
                          C1_1  7 nfkqptfCkhCgefl....wg.kekqglkCswCkl 36
                                   +k+ + C  C++      +   +   +kCs+C+ 
  gi|15669346|ref|NP_248151.1| 15 ELKKLAVCFNCKKEAdqiiEIyTNQAFVKCSNCGA 49
                                  4588999*****9988887556888999*****86 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00012
                                   --EEEE--SS--B-TTT-SB-.....-SSSS-EEEETTT-- CS
                          C1_1   1 HhwvhrnfkqptfCkhCgefl.....wgkekqglkCswCkl 36 
                                   H++++ ++++++ C  C++        ++ k +++C++C++
  gi|15669346|ref|NP_248151.1|  74 HKYEPWFLEKTAVCFNCKKEAtqdiaITETKMIVRCRNCGF 114
                                   888888999***********9999966699*********97 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.1   3.4e+03      26      31 ..      20      25 ..      18      29 .. 0.79
   2 !    8.3   0.1    0.0037       2.1      13      23 ..      43      53 ..      41      57 .. 0.89
   3 ?    1.6   0.0      0.48   2.7e+02      20      32 ..      79      91 ..      79      96 .. 0.81
   4 !    8.0   0.3    0.0048       2.7      11      23 ..     106     118 ..     105     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.1
                       DUF35_N 26 avCphC 31
                                  avC +C
  gi|15669346|ref|NP_248151.1| 20 AVCFNC 25
                                  789999 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0037
                       DUF35_N 13 rCpdCGtvqfP 23
                                  +C++CG+ +++
  gi|15669346|ref|NP_248151.1| 43 KCSNCGATRYY 53
                                  8********98 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.48
                       DUF35_N 20 vqfPPravCphCg 32
                                  ++  ++avC +C 
  gi|15669346|ref|NP_248151.1| 79 WFLEKTAVCFNCK 91
                                  777889******5 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0048
                       DUF35_N  11 gqrCpdCGtvqfP 23 
                                   + rC++CG  +++
  gi|15669346|ref|NP_248151.1| 106 IVRCRNCGFTRVY 118
                                   66******99876 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   1.4    0.0059       3.3       3      25 ..      22      49 ..      21      53 .. 0.66
   2 !   12.0   3.6   0.00022      0.13      13      29 ..     102     118 ..      86     119 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0059
                                  -SSS--B--.--....SSS----SSS-- CS
                DNA_RNApol_7kD  3 CgeCgaevs.lk....kgdpiRCkeCGh 25
                                  C +C++e   ++    +++ ++C +CG 
  gi|15669346|ref|NP_248151.1| 22 CFNCKKEADqIIeiytNQAFVKCSNCGA 49
                                  66666665543212227899*******6 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00022
                                   -SSS----SSS-----B CS
                DNA_RNApol_7kD  13 kkgdpiRCkeCGhRilY 29 
                                   + + ++RC++CG+  +Y
  gi|15669346|ref|NP_248151.1| 102 ETKMIVRCRNCGFTRVY 118
                                   345689******96666 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3    0.0041       2.3     116     143 ..      21      52 ..       9      57 .. 0.84
   2 ?    9.4   0.5    0.0018         1     114     141 ..      84     115 ..      65     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0041
                       DUF1451 116 vCekCgke....lalkkteeippCpkCgateF 143
                                   vC +C+ke    +++++ +   +C++Cgat++
  gi|15669346|ref|NP_248151.1|  21 VCFNCKKEadqiIEIYTNQAFVKCSNCGATRY 52 
                                   788887763333689**************987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0018
                       DUF1451 114 tlvCekCgke....lalkkteeippCpkCgat 141
                                   t vC +C+ke    +a+++t+ i +C +Cg t
  gi|15669346|ref|NP_248151.1|  84 TAVCFNCKKEatqdIAITETKMIVRCRNCGFT 115
                                   56899998762222689************976 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2    0.0011       0.6       8      34 ..      22      49 ..      15      53 .. 0.89
   2 ?    7.1   2.1     0.011         6       8      34 ..      87     114 ..      75     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                   Zn-ribbon_8  8 CeeCghefevlqsis.dapltaCPeCgs 34
                                  C +C++e +++ +i    + ++C +Cg+
  gi|15669346|ref|NP_248151.1| 22 CFNCKKEADQIIEIYtNQAFVKCSNCGA 49
                                  99*******9999998888888****98 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.011
                   Zn-ribbon_8   8 CeeCghefevlqsisdaplta.CPeCgs 34 
                                   C +C++e ++  +i++ ++++ C +Cg 
  gi|15669346|ref|NP_248151.1|  87 CFNCKKEATQDIAITETKMIVrCRNCGF 114
                                   9999999998887889999999****95 PP

>> HydF_tetramer  Hydrogen maturase F tetramerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0017      0.97      43      93 ..      11      63 ..       3      68 .. 0.74
   2 ?    5.6   0.1     0.022        12      51      81 ..      86     116 ..      76     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0017
                                  HHHHH----EEEEE--SS--..HHHTT-SEEEE-TT----HHHHHHHHHHHHH CS
                 HydF_tetramer 43 lkkktgkelefevaagrefp..eeleeyklvihCggCmitrkellaRikelke 93
                                  ++k   k+l++ ++ ++e +   e+ + +  ++C+ C  tr  +l+R+   +e
  gi|15669346|ref|NP_248151.1| 11 MEKWELKKLAVCFNCKKEADqiIEIYTNQAFVKCSNCGATRYYILRRVGIEDE 63
                                  5566667777777777766622555666899****************977665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.022
                                   -EEEEE--SS--HHHTT-SEEEE-TT----H CS
                 HydF_tetramer  51 lefevaagrefpeeleeyklvihCggCmitr 81 
                                   + f+++++   +  ++e k++++C  C +tr
  gi|15669346|ref|NP_248151.1|  86 VCFNCKKEATQDIAITETKMIVRCRNCGFTR 116
                                   4566666666667899***********8887 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.22   1.2e+02      34      78 ..      12      67 ..      10      78 .. 0.53
   2 ?   12.3   0.0   0.00028      0.16      26      72 ..      69     115 ..      43     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.22
                   CPSase_L_D3 34 dpwFLekleelvelekelkkkkk...........eldeellreakklGfsDkqiae 78
                                  ++w L+kl+  ++++ke  +  +           ++ ++ +  ++++G+ D+ i e
  gi|15669346|ref|NP_248151.1| 12 EKWELKKLAVCFNCKKEADQIIEiytnqafvkcsNCGATRYYILRRVGIEDESIIE 67
                                  56777777777777777666666222222333334444445556666666655543 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00028
                   CPSase_L_D3  26 eiheltkidpwFLekleelvelekelkkkkkeldeellreakklGfs 72 
                                   e ++  k++pwFLek +  ++++ke +++ + ++++++ + ++ Gf+
  gi|15669346|ref|NP_248151.1|  69 EKNKKHKYEPWFLEKTAVCFNCKKEATQDIAITETKMIVRCRNCGFT 115
                                   55667799*****************9988878888889999999996 PP

>> DUF1847  Protein of unknown function (DUF1847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.8   3.9e-05     0.022      48     112 ..       9      71 ..       3      80 .. 0.85
   2 ?    0.9   0.5      0.58   3.2e+02      80     108 ..      79     107 ..      56     124 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-05
                       DUF1847  48 efakrmgykkiGiafCvglleeakalakileakgfevvsviCkvgsvdkeelgieeeekvkkkkk 112
                                   +f+++ + kk+  a+C+  ++ea+++ +i +++ f  +s +  +     +++gie+e+ ++ +k+
  gi|15669346|ref|NP_248151.1|   9 DFMEKWELKKL--AVCFNCKKEADQIIEIYTNQAFVKCSNCGATRYYILRRVGIEDESIIEDEKN 71 
                                   79999999995..89********************9999988888888999****9998876554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.58
                       DUF1847  80 kgfevvsviCkvgsvdkeelgieeeekvk 108
                                     +e ++v+  + + + +++ i+e++++ 
  gi|15669346|ref|NP_248151.1|  79 WFLEKTAVCFNCKKEATQDIAITETKMIV 107
                                   55566666655566666677777766554 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.78   4.4e+02      22      34 ..      15      27 ..      10      29 .. 0.77
   2 ?    7.5   0.0    0.0087       4.9      24      36 ..      39      51 ..      34      53 .. 0.82
   3 ?   -0.2   0.1       2.2   1.2e+03      23      34 ..      83      92 ..      69      99 .. 0.65
   4 ?    5.5   0.1     0.036        20      23      37 ..     103     117 ..      91     122 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.78
                                  ----EEEETTTCC CS
                Ribosomal_L32p 22 kapnlvecpncge 34
                                  + ++l++c nc++
  gi|15669346|ref|NP_248151.1| 15 ELKKLAVCFNCKK 27
                                  5567889****85 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0087
                                  --EEEETTTCCEE CS
                Ribosomal_L32p 24 pnlvecpncgelk 36
                                  +++v+c+ncg+++
  gi|15669346|ref|NP_248151.1| 39 QAFVKCSNCGATR 51
                                  588*******976 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.2
                                  ---EEEETTTCC CS
                Ribosomal_L32p 23 apnlvecpncge 34
                                    +  +c nc++
  gi|15669346|ref|NP_248151.1| 83 KTA--VCFNCKK 92
                                  444..4888874 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.036
                                   ---EEEETTTCCEEC CS
                Ribosomal_L32p  23 apnlvecpncgelkl 37 
                                   ++ +v+c ncg +++
  gi|15669346|ref|NP_248151.1| 103 TKMIVRCRNCGFTRV 117
                                   347899****96665 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   2.0      0.05        28      34      47 ..      40      53 ..      24      62 .. 0.80
   2 ?   -0.5   0.1       2.5   1.4e+03       2      19 ..      87     102 ..      86     106 .. 0.57
   3 ?   14.3   0.2   5.9e-05     0.033      34      51 ..     105     122 ..      97     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.05
                zinc_ribbon_13 34 itvsCknCgYtelY 47
                                   +v C+nCg t  Y
  gi|15669346|ref|NP_248151.1| 40 AFVKCSNCGATRYY 53
                                  689******98877 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.5
                zinc_ribbon_13   2 CpKCgnteaevkevaatG 19 
                                   C  C+++ +  +++a+t 
  gi|15669346|ref|NP_248151.1|  87 CFNCKKEAT--QDIAITE 102
                                   777776654..4455554 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 5.9e-05
                zinc_ribbon_13  34 itvsCknCgYtelYkaet 51 
                                   ++v C+nCg+t +Y+ ++
  gi|15669346|ref|NP_248151.1| 105 MIVRCRNCGFTRVYQFHI 122
                                   689***********9665 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3    0.0054         3       3      38 ..      18      49 ..      16      73 .. 0.81
   2 ?    8.8   1.1    0.0031       1.7       2      36 ..      82     112 ..      81     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0054
                         PHD_4  3 vtaaCivCgedgkedevveeesetpsslmeCsvCye 38
                                    a+C  C+++ ++   +e    t+++++ Cs C  
  gi|15669346|ref|NP_248151.1| 18 KLAVCFNCKKEADQI--IE--IYTNQAFVKCSNCGA 49
                                  5689****9987666..33..478999*******75 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0031
                         PHD_4   2 PvtaaCivCgedgkedevveeesetpsslmeCsvC 36 
                                     ta+C  C+++ ++d   +   +++++++ C  C
  gi|15669346|ref|NP_248151.1|  82 EKTAVCFNCKKEATQDI--A--ITETKMIVRCRNC 112
                                   679*********99993..2..3567788889888 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.9    0.0018         1      70     100 ..      19      55 ..      11      65 .. 0.68
   2 ?    8.5   1.7    0.0034       1.9      58      94 ..      94     114 ..      60     122 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                                   EEEETTTS-EEECHH..HHH.....S-TTTSSS-EEEE CS
                          HypA  70 kvrCreCgkefelee..kal.....rCpkCgsadveiv 100
                                    + C +C+ke ++    + +     +C +Cg+++  i+
  gi|15669346|ref|NP_248151.1|  19 LAVCFNCKKEADQIIeiY-TnqafvKCSNCGATRYYIL 55 
                                   567899998887332131.1345569999999887765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0034
                                   TT-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSS CS
                          HypA  58 egaeLeieevpvkvrCreCgkefeleekalrCpkCgs 94 
                                   +  +++i+e+++ vrCr+Cg                 
  gi|15669346|ref|NP_248151.1|  94 ATQDIAITETKMIVRCRNCG----------------F 114
                                   12344555555555555555................4 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2       2.2   1.2e+03       4      10 ..      21      27 ..      19      28 .. 0.75
   2 ?    8.3   0.1    0.0038       2.1      24      33 ..      40      49 ..      34      50 .. 0.79
   3 ?    7.6   3.5    0.0062       3.5       5      32 ..      87     113 ..      84     115 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.2
                 zinc_ribbon_4  4 tCpsCka 10
                                  +C +Ck+
  gi|15669346|ref|NP_248151.1| 21 VCFNCKK 27
                                  6888987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0038
                 zinc_ribbon_4 24 vkvrCskCgh 33
                                  + v+Cs+Cg+
  gi|15669346|ref|NP_248151.1| 40 AFVKCSNCGA 49
                                  569*****97 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0062
                 zinc_ribbon_4   5 CpsCkakyeiddeklpakgvkvrCskCg 32 
                                   C +Ck++ + +d  ++++++ vrC +Cg
  gi|15669346|ref|NP_248151.1|  87 CFNCKKEAT-QDIAITETKMIVRCRNCG 113
                                   666666644.455788889999999998 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.12        68       4      13 ..      19      28 ..      17      30 .. 0.82
   2 ?    6.1   0.2     0.015       8.2       2      11 ..      39      48 ..      38      50 .. 0.86
   3 ?    3.0   0.1      0.14        78       5      13 ..      85      93 ..      82      96 .. 0.82
   4 ?    5.5   0.1     0.022        12       2      11 ..     104     113 ..     103     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
                                  EEE-TTTSSE CS
                         Sgf11  4 yvtCpnCgRq 13
                                  + +C nC+++
  gi|15669346|ref|NP_248151.1| 19 LAVCFNCKKE 28
                                  568*****86 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.015
                                  C-EEE-TTTS CS
                         Sgf11  2 seyvtCpnCg 11
                                  +++v+C nCg
  gi|15669346|ref|NP_248151.1| 39 QAFVKCSNCG 48
                                  579******8 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.14
                                  EE-TTTSSE CS
                         Sgf11  5 vtCpnCgRq 13
                                   +C nC+++
  gi|15669346|ref|NP_248151.1| 85 AVCFNCKKE 93
                                  58*****86 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.022
                                   C-EEE-TTTS CS
                         Sgf11   2 seyvtCpnCg 11 
                                   ++ v+C nCg
  gi|15669346|ref|NP_248151.1| 104 KMIVRCRNCG 113
                                   6899*****7 PP

>> SipA  SipA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0     0.001      0.57       4      35 ..       9      40 ..       6      47 .. 0.88
   2 ?    0.6   0.0      0.66   3.7e+02      76      95 ..      63      82 ..      51      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.001
                                  GHHHHHHHHHHHHHHCTSS-HHHHHHHHHH-- CS
                          SipA  4 sfaasfkqksldaLfkaskkadaLkevysnsn 35
                                  +f  +++ k l++ f++ k+ad++ e+y+n  
  gi|15669346|ref|NP_248151.1|  9 DFMEKWELKKLAVCFNCKKEADQIIEIYTNQA 40
                                  7888899999*******************975 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.66
                                  HHHHHH---SS-SSSTTS-- CS
                          SipA 76 ariikDgLkeksafGPWlak 95
                                  + ii D+ ++k  + PW  +
  gi|15669346|ref|NP_248151.1| 63 ESIIEDEKNKKHKYEPWFLE 82
                                  6899*************754 PP

>> zf-CCHC_6  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.7    0.0043       2.4       2       9 ..      42      49 ..      42      50 .. 0.95
   2 ?    5.8   0.4     0.022        12       2       8 ..     107     113 ..     106     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0043
                     zf-CCHC_6  2 vKCknCGA 9 
                                  vKC nCGA
  gi|15669346|ref|NP_248151.1| 42 VKCSNCGA 49
                                  8******9 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.022
                     zf-CCHC_6   2 vKCknCG 8  
                                   v+C+nCG
  gi|15669346|ref|NP_248151.1| 107 VRCRNCG 113
                                   8*****9 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.7    0.0023       1.3       1      21 [.      22      52 ..      22      53 .. 0.85
   2 ?    5.9   1.1     0.025        14       1      17 [.      87     113 ..      87     118 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0023
                                  -TTT--...........B-SCE-TTTS-SEE CS
                       zf-MYND  1 CavCgk..........aealkkCagCksvfY 21
                                  C +C+k          ++a  kC++C +++Y
  gi|15669346|ref|NP_248151.1| 22 CFNCKKeadqiieiytNQAFVKCSNCGATRY 52
                                  9*****999999998555555*****99988 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.025
                                   -TTT--.........B-SC...E-TTTS CS
                       zf-MYND   1 CavCgk........aealk...kCagCk 17 
                                   C +C+k        + ++k   +C +C 
  gi|15669346|ref|NP_248151.1|  87 CFNCKKeatqdiaiT-ETKmivRCRNCG 113
                                   99****999999853.444578****96 PP

>> PDCD2_C  Programmed cell death protein 2, C-terminal putative domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.4     0.072        40     102     118 ..      37      53 ..      15      55 .. 0.85
   2 ?    8.3   0.3    0.0041       2.3     102     123 ..     102     123 ..      79     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.072
                       PDCD2_C 102 eesdipkCsnCgskrvF 118
                                   ++++  kCsnCg++r +
  gi|15669346|ref|NP_248151.1|  37 TNQAFVKCSNCGATRYY 53 
                                   4557889******9975 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0041
                       PDCD2_C 102 eesdipkCsnCgskrvFEfQlm 123
                                   e++ i +C+nCg +rv+ f ++
  gi|15669346|ref|NP_248151.1| 102 ETKMIVRCRNCGFTRVYQFHIL 123
                                   3458999**********99875 PP

>> zf-CCHC  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.4     0.023        13       2       9 ..      21      28 ..      20      28 .. 0.84
   2 ?    6.0   0.3     0.024        13       2       8 ..      43      49 ..      42      50 .. 0.84
   3 ?    6.0   0.4     0.023        13       2       9 ..      86      93 ..      85      93 .. 0.84
   4 ?    4.5   1.1     0.071        40       2       7 ..     108     113 ..     107     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.023
                                  CTSSSSSS CS
                       zf-CCHC  2 kCynCGep 9 
                                  +C+nC ++
  gi|15669346|ref|NP_248151.1| 21 VCFNCKKE 28
                                  6****875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.024
                                  CTSSSSS CS
                       zf-CCHC  2 kCynCGe 8 
                                  kC nCG 
  gi|15669346|ref|NP_248151.1| 43 KCSNCGA 49
                                  8*****6 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.023
                                  CTSSSSSS CS
                       zf-CCHC  2 kCynCGep 9 
                                  +C+nC ++
  gi|15669346|ref|NP_248151.1| 86 VCFNCKKE 93
                                  6****875 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.071
                                   CTSSSS CS
                       zf-CCHC   2 kCynCG 7  
                                    C+nCG
  gi|15669346|ref|NP_248151.1| 108 RCRNCG 113
                                   7****9 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.0     0.001      0.56      14      45 ..      20      51 ..       8      75 .. 0.83
   2 ?    5.2   2.3     0.022        12      13      45 ..      84     116 ..      75     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                          NMD3 14 glCedCllkevditegiekievevCkeCgryl 45
                                  ++C +C ++  +i+e+ ++  +  C++Cg+ +
  gi|15669346|ref|NP_248151.1| 20 AVCFNCKKEADQIIEIYTNQAFVKCSNCGATR 51
                                  39***************************987 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.022
                          NMD3  13 nglCedCllkevditegiekievevCkeCgryl 45 
                                   +++C +C ++ ++ + + e+  +  C++Cg  +
  gi|15669346|ref|NP_248151.1|  84 TAVCFNCKKEATQDIAITETKMIVRCRNCGFTR 116
                                   459****99999999988888899*****9765 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.2    0.0044       2.5      77     105 ..      16      44 ..       5      47 .. 0.83
   2 ?    6.4   2.0     0.017       9.5      75     106 ..      79     110 ..      60     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0044
                    zf-RRPl_C4  77 lkklklCkeCkervekvlkndfvknflly 105
                                   lkkl +C +Ck++  ++++   ++ f ++
  gi|15669346|ref|NP_248151.1|  16 LKKLAVCFNCKKEADQIIEIYTNQAFVKC 44 
                                   67889**************9999999877 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.017
                    zf-RRPl_C4  75 eylkklklCkeCkervekvlkndfvknfllyk 106
                                    +l+k  +C +Ck++ ++ +  +  k   +++
  gi|15669346|ref|NP_248151.1|  79 WFLEKTAVCFNCKKEATQDIAITETKMIVRCR 110
                                   47899999999*99999999988888887776 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   0.00041      0.23       1      29 [.      21      49 ..      21      55 .. 0.90
   2 ?    1.0   0.2      0.67   3.8e+02       1       9 [.      86      94 ..      86      97 .. 0.79
   3 ?    1.1   0.2      0.62   3.4e+02      23      28 ..     108     113 ..     106     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00041
                                  --HHHHHHHC-TTSTTTT-TT---TTTS- CS
                       zf-HYPF  1 lCedClrEykdpldRRfhaqfisCtnCGP 29
                                  +C +C++E +     + +  f+ C nCG 
  gi|15669346|ref|NP_248151.1| 21 VCFNCKKEADQIIEIYTNQAFVKCSNCGA 49
                                  6999************************6 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.67
                                  --HHHHHHH CS
                       zf-HYPF  1 lCedClrEy 9 
                                  +C +C++E 
  gi|15669346|ref|NP_248151.1| 86 VCFNCKKEA 94
                                  599999995 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.62
                                   --TTTS CS
                       zf-HYPF  23 sCtnCG 28 
                                    C nCG
  gi|15669346|ref|NP_248151.1| 108 RCRNCG 113
                                   59***9 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.4      0.36     2e+02      29      36 ..      20      27 ..      17      29 .. 0.77
   2 ?    7.0   0.1    0.0097       5.4      28      36 ..      41      49 ..      38      56 .. 0.73
   3 ?    1.9   0.6      0.37   2.1e+02      30      36 ..      86      92 ..      83      95 .. 0.74
   4 ?    5.5   0.1     0.027        15       2      12 ..     108     118 ..     102     122 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.36
                       TFIIS_C 29 ykCtkCgh 36
                                   +C +C++
  gi|15669346|ref|NP_248151.1| 20 AVCFNCKK 27
                                  57999987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0097
                       TFIIS_C 28 fykCtkCgh 36
                                  f+kC +Cg 
  gi|15669346|ref|NP_248151.1| 41 FVKCSNCGA 49
                                  777777775 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.37
                       TFIIS_C 30 kCtkCgh 36
                                  +C +C++
  gi|15669346|ref|NP_248151.1| 86 VCFNCKK 92
                                  7888887 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.027
                       TFIIS_C   2 kCpkCgsreay 12 
                                   +C +Cg +++y
  gi|15669346|ref|NP_248151.1| 108 RCRNCGFTRVY 118
                                   57777777666 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3      0.35     2e+02      18      24 ..      21      27 ..      20      28 .. 0.80
   2 ?    8.4   0.2    0.0025       1.4       3      10 ..      42      49 ..      40      50 .. 0.84
   3 ?    2.0   0.2      0.27   1.5e+02      18      24 ..      86      92 ..      83      94 .. 0.81
   4 ?    2.7   0.2      0.16        90      19      23 ..     109     113 ..     107     114 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.35
                   zf-ribbon_3 18 vCpyCGt 24
                                  vC +C +
  gi|15669346|ref|NP_248151.1| 21 VCFNCKK 27
                                  799**75 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0025
                   zf-ribbon_3  3 vrCPnCGa 10
                                  v+C+nCGa
  gi|15669346|ref|NP_248151.1| 42 VKCSNCGA 49
                                  89999997 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.27
                   zf-ribbon_3 18 vCpyCGt 24
                                  vC +C +
  gi|15669346|ref|NP_248151.1| 86 VCFNCKK 92
                                  7999975 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.16
                   zf-ribbon_3  19 CpyCG 23 
                                   C +CG
  gi|15669346|ref|NP_248151.1| 109 CRNCG 113
                                   77777 PP

>> IBR  IBR domain, a half RING-finger domain
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.25   1.4e+02      44      57 ..      17      30 ..      11      33 .. 0.85
   2 ?    3.5   3.2      0.12        67      31      55 ..      22      50 ..      20      53 .. 0.63
   3 ?    5.0   0.2     0.042        24      29      39 ..      42      52 ..      30      60 .. 0.72
   4 ?    4.5   0.1     0.058        32      44      60 ..      82      98 ..      68     101 .. 0.82
   5 ?    4.3   2.9     0.066        37      31      55 ..      87     115 ..      85     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.25
                OrfB_Zn_ribbon 44 grtfkCpnCgfead 57
                                  +++ +C+nC+ ead
  gi|15669346|ref|NP_248151.1| 17 KKLAVCFNCKKEAD 30
                                  56789*****9987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
                OrfB_Zn_ribbon 31 CseCgsknke....alsgrtfkCpnCgfe 55
                                  C +C ++ ++      ++  +kC+nCg++
  gi|15669346|ref|NP_248151.1| 22 CFNCKKEADQiieiYTNQAFVKCSNCGAT 50
                                  55666666666666666777777777764 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.042
                OrfB_Zn_ribbon 29 ktCseCgsknk 39
                                   +Cs+Cg++ +
  gi|15669346|ref|NP_248151.1| 42 VKCSNCGATRY 52
                                  46888887765 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.058
                OrfB_Zn_ribbon 44 grtfkCpnCgfeadrDv 60
                                  ++t +C+nC+ ea  D+
  gi|15669346|ref|NP_248151.1| 82 EKTAVCFNCKKEATQDI 98
                                  67899******999887 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.066
                OrfB_Zn_ribbon  31 CseCgsknke....alsgrtfkCpnCgfe 55 
                                   C +C ++ ++    + ++  ++C+nCgf+
  gi|15669346|ref|NP_248151.1|  87 CFNCKKEATQdiaiTETKMIVRCRNCGFT 115
                                   8888888888888888899999*****96 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.57   3.2e+02       2       8 ..      22      28 ..      21      31 .. 0.73
   2 ?    8.8   0.2    0.0024       1.3       1       7 [.      43      49 ..      34      50 .. 0.59
   3 ?    1.4   0.1      0.51   2.8e+02       2       8 ..      87      93 ..      84      97 .. 0.75
   4 ?    3.5   0.9      0.11        61       2       6 ..     109     113 ..     108     115 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.57
                 zinc_ribbon_2  2 CpnCGae 8 
                                  C nC +e
  gi|15669346|ref|NP_248151.1| 22 CFNCKKE 28
                                  8888766 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0024
                 zinc_ribbon_2  1 fCpnCGa 7 
                                  +C+nCGa
  gi|15669346|ref|NP_248151.1| 43 KCSNCGA 49
                                  4555554 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.51
                 zinc_ribbon_2  2 CpnCGae 8 
                                  C nC +e
  gi|15669346|ref|NP_248151.1| 87 CFNCKKE 93
                                  7777665 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.11
                 zinc_ribbon_2   2 CpnCG 6  
                                   C nCG
  gi|15669346|ref|NP_248151.1| 109 CRNCG 113
                                   88887 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.0     0.017       9.7      10      35 ..      22      50 ..      19      52 .. 0.63
   2 ?    5.5   1.3     0.025        14      10      34 ..      87     114 ..      80     118 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.017
                                  -TTTS-E..EEE.ESS-SS-EEESSSTCE CS
                Ribosomal_S27e 10 CpdCene..tvv.FshaatvvkCisCgkv 35
                                  C +C++e  +++     +  vkC  Cg +
  gi|15669346|ref|NP_248151.1| 22 CFNCKKEadQIIeIYTNQAFVKCSNCGAT 50
                                  55555432244324567889999999975 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                                   -TTTS-...EEEEESS-SS-EEESSSTC CS
                Ribosomal_S27e  10 CpdCen...etvvFshaatvvkCisCgk 34 
                                   C +C++   + +     + +v C  Cg 
  gi|15669346|ref|NP_248151.1|  87 CFNCKKeatQDIAITETKMIVRCRNCGF 114
                                   66665511145678899999******95 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       3.2   1.8e+03      23      29 ..      20      26 ..      20      33 .. 0.82
   2 ?    4.2   0.3     0.073        41      25      33 ..      44      52 ..      41      54 .. 0.72
   3 ?    6.7   0.6     0.012         7       3      31 ..      87     115 ..      86     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.2
                                  EEETTTT CS
                     Nudix_N_2 23 lvCpaCg 29
                                  +vC +C 
  gi|15669346|ref|NP_248151.1| 20 AVCFNCK 26
                                  5898885 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.073
                                  ETTTTEEE- CS
                     Nudix_N_2 25 CpaCgtihY 33
                                  C++Cg++ Y
  gi|15669346|ref|NP_248151.1| 44 CSNCGATRY 52
                                  666666666 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.012
                                   -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                     Nudix_N_2   3 CsqCGtpvelripdgDnreRlvCpaCgti 31 
                                   C +C ++ ++ i   ++++  +C +Cg++
  gi|15669346|ref|NP_248151.1|  87 CFNCKKEATQDIAITETKMIVRCRNCGFT 115
                                   88999999999999999999*******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 770.13
//
Query:       gi|15669347|ref|NP_248152.1|  [L=341]
Description: hypothetical protein MJ_1157 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-16   59.1   0.0      2e-15   57.0   0.0    1.9  1  ATP_bind_3     PP-loop family
      4e-05   22.6   0.0    5.7e-05   22.1   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
      8e-05   22.7   0.0    0.00032   20.8   0.0    1.9  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
    0.00021   20.8   2.2    0.00021   20.8   2.2    3.3  3  RecR           RecR protein
     0.0036   16.8   2.9     0.0036   16.8   2.9    2.8  3  zn-ribbon_14   Zinc-ribbon
  ------ inclusion threshold ------
      0.092   11.9   0.0       0.15   11.1   0.0    1.5  1  NAD_synthase   NAD synthase


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.0   6.8e-19     2e-15       2     171 ..      85     270 ..      84     280 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 6.8e-19
                                   EEEE--SCHHHHHHHHHHHHHCTTTTT.EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H............. CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgi.klvaihvdhglreeskeeaelvkelckklnikleiekvdv............. 68 
                                   + +++SgG DS+++ ++l++l k+    kl+++ vd g++   +  +++vke+ck++n++l+i k++              
  gi|15669347|ref|NP_248152.1|  85 IGIGISGGKDSLVMAYILKELFKHIPNaKLICFFVDEGIKGFRNIAEKYVKEFCKEYNLDLKIIKFEDeigytldeivknd 165
                                   679******************9987767**************************************999999*99998775 PP

                                   ..HHCTTSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCCEE-CCCT- CS
                    ATP_bind_3  69 ..akkkgknleeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasirlvRPlLkv 147
                                     +k +  +       +R  +l++++ keg+++l+++h+ dD++ t+l++   g+ ++ ++  ke +    ++ + Pl  +
  gi|15669347|ref|NP_248152.1| 166 ylSKLNIGKPCSFCGVVRRYLLNKHALKEGCDYLAIGHNLDDFCQTILMNYVEGNIKNIIQFGKEFEGGGFVKRIKPLKLI 246
                                   443333333344566789999********************************99986665555555445588899***** PP

                                   -HHHHHHHHHHTT---B--CGGGC CS
                    ATP_bind_3 148 skeeleeylkekkikwveDesNad 171
                                     ee++ y++ ++ik+ + +  ++
  gi|15669347|ref|NP_248152.1| 247 PEEEVKLYAEINNIKYQREPCPYS 270
                                   ****************98876555 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.9e-08   5.7e-05       2     124 ..      84     203 ..      83     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.9e-08
                 tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfeef 82 
                                   k+ +++SgG DS v a++lke ++++    l +   ++    +   +   k++++ +++ ++ l++++fe+e   ++ e +
  gi|15669347|ref|NP_248152.1|  84 KIGIGISGGKDSLVMAYILKELFKHIPNAKLICFFVDEGI--KGFRNIAEKYVKEFCKEYNLDLKIIKFEDEIGYTLDEIV 162
                                   6889***********************9999998883333..34555666899******************9776666666 PP

                 tRNA_Me_trans  83 leeye.eGrTPnPdvlCNkeiKfgallekakeelgadalatGH 124
                                    ++y  + +  +P+  C   ++  +l ++a +  g+d+la GH
  gi|15669347|ref|NP_248152.1| 163 KNDYLsKLNIGKPCSFCG-VVRRYLLNKHALK-EGCDYLAIGH 203
                                   666641345568*****7.5777778888887.9********* PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.1e-07   0.00032       6     155 ..      89     262 ..      84     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.1e-07
                                   --SSCTCHHHHHHHHHHCTTH.....EEEEEE-STB.-HHH.HHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHH CS
                   PAPS_reduct   6 vsgGkdslVllhLalkafkpv.....pvvfvdtghe.fpet.iefvdeleeryglrlkvyepeeevaekinaekhgsslye 79 
                                   +sgGkdslV+  ++ + fk +       +fvd g + f+++  ++v+e+ ++y+l+lk+ + e+e+   + +  +  ++y 
  gi|15669347|ref|NP_248152.1|  89 ISGGKDSLVMAYILKELFKHIpnaklICFFVDEGIKgFRNIaEKYVKEFCKEYNLDLKIIKFEDEIGYTLDEIVK--NDYL 167
                                   7*****************9977787779******9867776257************9999999998887776663..4444 PP

                                   C........HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S...........CEEE-CCCT--H CS
                   PAPS_reduct  80 e........aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek...........slrvfPllnWte 141
                                   +         ++ +++ + l+k+  k + d+l +G   d+  +   +++ve + ++             + r+ Pl    e
  gi|15669347|ref|NP_248152.1| 168 SklnigkpcSFCGVVRRYLLNKHALKEGCDYLAIGHNLDDFCQTILMNYVEGNIKNIIqfgkefegggfVKRIKPLKLIPE 248
                                   445777888778777777777766666668888888777777777777766555533367777777886666778888888 PP

                                   HHHHHHHHHCT--B CS
                   PAPS_reduct 142 edvwqyilrenipy 155
                                   e+v  y+  +ni+y
  gi|15669347|ref|NP_248152.1| 249 EEVKLYAEINNIKY 262
                                   88888888888877 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.4      0.44   1.3e+03      17      23 ..      56      62 ..      52      63 .. 0.80
   2 ?    0.0   0.1      0.22   6.5e+02      17      23 ..     174     180 ..     171     184 .. 0.63
   3 !   20.8   2.2   7.2e-08   0.00021      11      35 ..     308     332 ..     302     333 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.44
                                  EE-TTT- CS
                          RecR 17 rhCsrCg 23
                                  + C++C+
  gi|15669347|ref|NP_248152.1| 56 HLCKECF 62
                                  7899997 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.22
                                   EE-TTT- CS
                          RecR  17 rhCsrCg 23 
                                   ++Cs Cg
  gi|15669347|ref|NP_248152.1| 174 KPCSFCG 180
                                   4566665 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 7.2e-08
                                   HHHHH-EE-TTT--EESSSS-CCCC CS
                          RecR  11 eakekvrhCsrCgnlteedlCaICs 35 
                                   ++ke++r+C++Cg  +  ++C +Cs
  gi|15669347|ref|NP_248152.1| 308 NVKEEIRRCEICGFPCSGNICKVCS 332
                                   89**********************8 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.35   1.1e+03      10      18 ..      53      61 ..      52      62 .. 0.81
   2 ?   -2.0   0.1      0.89   2.6e+03       3       7 ..     176     180 ..     167     182 .. 0.67
   3 !   16.8   2.9   1.2e-06    0.0036       1      24 [.     314     337 ..     314     339 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.35
                  zn-ribbon_14 10 SSqkiCkAC 18
                                  S+  +Ck C
  gi|15669347|ref|NP_248152.1| 53 SNRHLCKEC 61
                                  788899988 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.89
                  zn-ribbon_14   3 CerCG 7  
                                   C+ CG
  gi|15669347|ref|NP_248152.1| 176 CSFCG 180
                                   77777 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 1.2e-06
                  zn-ribbon_14   1 gkCerCGylSSqkiCkACvLLegL 24 
                                   ++Ce CG+ +S  iCk C  L +L
  gi|15669347|ref|NP_248152.1| 314 RRCEICGFPCSGNICKVCSWLIKL 337
                                   58****************876555 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.1e-05      0.15      20      43 ..      84     107 ..      66     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.1e-05
                                   EEEEEE-SSHHHHHHHHHHHHHHT CS
                  NAD_synthase  20 gvvlGlSGGvDSslvaalavkalg 43 
                                   ++ +G+SGG DS + a++ ++++ 
  gi|15669347|ref|NP_248152.1|  84 KIGIGISGGKDSLVMAYILKELFK 107
                                   5678****************9993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2256.61
//
Query:       gi|15669348|ref|NP_248153.1|  [L=645]
Description: replication factor A [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-51  169.9  18.5    5.3e-23   80.8   0.7    6.1  6  tRNA_anti-codon  OB-fold nucleic acid binding domain
    4.1e-13   49.6   5.1     0.0001   22.1   0.1    5.1  5  CDC24_OB3        Cell division control protein 24, OB domain 
      7e-11   41.9   9.7    5.8e-06   26.1   1.1    4.5  4  REPA_OB_2        Replication protein A OB domain
      3e-10   40.0   0.1    2.7e-07   30.5   0.0    4.1  4  Rep_fac-A_C      Replication factor-A C terminal domain
    2.9e-06   27.4   2.6       0.19   12.0   0.1    4.1  3  DUF3127          Domain of unknown function (DUF3127)
     0.0051   16.8   0.0        3.2    7.8   0.0    3.0  2  Mucin_bdg        Putative mucin or carbohydrate-binding modul
     0.0086   16.0   0.1       0.75    9.7   0.0    3.9  4  POT1PC           ssDNA-binding domain of telomere protection 
  ------ inclusion threshold ------
       0.01   15.8   5.3        5.2    7.1   0.0    4.9  5  DUF1967          Domain of unknown function (DUF1967)
      0.013   15.3   0.1        3.8    7.4   0.0    2.6  2  POT1             Telomeric single stranded DNA binding POT1/C
      0.018   14.8   2.0        2.7    7.7   0.1    3.5  4  DUF5088          Domain of unknown function (DUF5088)
      0.039   14.0   0.6         28    4.9   0.0    4.0  3  Ribosomal_S17    Ribosomal protein S17
      0.043   13.7   3.4        6.4    6.7   0.1    4.6  4  RNA_pol_Rpb5_C   RNA polymerase Rpb5, C-terminal domain
        0.1   12.7   5.1         33    4.6   0.0    4.8  5  Molydop_binding  Molydopterin dinucleotide binding domain
       0.23   11.2   3.8         17    5.2   0.1    4.2  3  SH3_2            Variant SH3 domain
       0.36   10.5   3.0         11    5.7   1.9    3.5  3  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        1.3    9.1   7.1       0.66   10.1   0.9    3.8  3  DNA_pol_D_N      DNA polymerase delta subunit OB-fold domain
        5.6    6.6   7.3        6.6    6.3   1.5    3.4  2  TF_Zn_Ribbon     TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.5   4.9e-11   5.1e-08       1      71 [.      78     153 ..      78     158 .. 0.92
   2 !   41.0   0.2   1.4e-13   1.4e-10       2      76 .]     187     266 ..     186     266 .. 0.85
   3 !   80.8   0.7   5.1e-26   5.3e-23       1      76 []     291     398 ..     291     398 .. 0.99
   4 !   20.4   0.0   3.6e-07   0.00038      16      62 ..     430     484 ..     420     499 .. 0.77
   5 ?    1.1   0.1      0.37   3.9e+02      38      59 ..     498     519 ..     486     521 .. 0.82
   6 ?    2.4   0.0      0.15   1.6e+02      20      43 ..     562     592 ..     560     630 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 4.9e-11
                                   EEEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEEE CS
               tRNA_anti-codon   1 VtvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkve 71 
                                   V + G +t+is        d+s gk+  i++ D++g+i+ +l++   +    ++k+Gdv++++  r ++++++ lel+ +
  gi|15669348|ref|NP_248153.1|  78 VEITGVITDISeiktfkrrDGSLGKYKRITIADKSGTIRMTLWD---DLAELDVKVGDVIKIErARARKWRNN-LELSST 153
                                   7899****************************************...666667********************.999866 PP

  == domain 2  score: 41.0 bits;  conditional E-value: 1.4e-13
                                   EEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEEC.TTSSEEEEEEEE CS
               tRNA_anti-codon   2 tvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrr.pggelelkveei 73 
                                   t++G+v+s          d+s+gk+ ++++rD+tg+i+v+l++     +  ++ +Gd+vrv+G++++  +gg le +++ +
  gi|15669348|ref|NP_248153.1| 187 TFEGEVISALpikefkraDGSIGKLKSFIVRDETGSIRVTLWD---NLTDIDVGRGDYVRVRGYIREGyYGG-LECTANYV 263
                                   5677777777777888899************************...44445577**************5555.******** PP

                                   EEE CS
               tRNA_anti-codon  74 ell 76 
                                   e+l
  gi|15669348|ref|NP_248153.1| 264 EIL 266
                                   997 PP

  == domain 3  score: 80.8 bits;  conditional E-value: 5.1e-26
                                   EEEEEEEEEEE.......EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTS......... CS
               tRNA_anti-codon   1 VtvaGrvtsis.......drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpgg......... 64 
                                   V+v+Grv++is       d++++kv++i+l++gtgr++v+++r ++t+l+en+keGd+vr+t +rvk+++++         
  gi|15669348|ref|NP_248153.1| 291 VSVKGRVIAISnkksvdlDGEIAKVQDIILDNGTGRVRVSFWR-GKTALLENIKEGDLVRITnCRVKTFYDRegnkrtdlv 370
                                   89*****************************************.*************************999999****** PP

                                   ................SEEEEEEEEEEE CS
               tRNA_anti-codon  65 ................elelkveeiell 76 
                                                   e+elk+++ie++
  gi|15669348|ref|NP_248153.1| 371 atletevikdenieapEYELKYCKIEDI 398
                                   **************************87 PP

  == domain 4  score: 20.4 bits;  conditional E-value: 3.6e-07
                                   TTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEEC..........T CS
               tRNA_anti-codon  16 gkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrr..........p 62 
                                   +kv ++ l+Dgtgri+++l++   +    ++keGd+v++   + k+r          +
  gi|15669348|ref|NP_248153.1| 430 RKVRNLLLEDGTGRIRLSLWD---DLAEIEIKEGDIVEILhAYAKERgdyidlvigkY 484
                                   5788899**************...666667*********9999998854444444433 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.37
                                   HHHHHHTTS-TTSEEEEEEEEE CS
               tRNA_anti-codon  38 eatklaenlkeGdvvrvtGrvk 59 
                                     +k+  +++ G  v+v+G v 
  gi|15669348|ref|NP_248153.1| 498 TNRKFIADIEDGETVEVRGAVV 519
                                   56799999**********9986 PP

  == domain 6  score: 2.4 bits;  conditional E-value: 0.15
                                   EEEEEETTEEEEEEEET.......HHHHHHH CS
               tRNA_anti-codon  20 fidlrDgtgriqvvlfr.......eeatkla 43 
                                   +++++Dgtg++ + + +       +  ++ +
  gi|15669348|ref|NP_248153.1| 562 NFVVDDGTGTLLCRAYDrrvekmlKMNREEL 592
                                   799********99999866655554444445 PP

>> CDC24_OB3  Cell division control protein 24, OB domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   9.7e-08    0.0001       1      83 [.      70     150 ..      70     168 .. 0.73
   2 !   10.8   0.0   0.00027      0.29      30      69 ..     210     246 ..     184     284 .. 0.75
   3 !    7.1   0.1    0.0038         4       9      69 ..     291     352 ..     289     372 .. 0.87
   4 ?    3.8   0.0     0.039        41      22      54 ..     423     455 ..     406     478 .. 0.68
   5 ?    3.6   0.0     0.045        48     150     213 ..     534     595 ..     512     603 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.7e-08
                     CDC24_OB3   1 DLrekmlnvtLlGrvvai.....freknsek.kkmdryslrieDttGaidatlweeagklhfkrlrvGhlvllsgLatset 75 
                                   D++e  ++v + G++++i     f+ +++ +  k++   ++i+D++G+i++tlw+  ++l  k   vG+++ +++    + 
  gi|15669348|ref|NP_248153.1|  70 DIEEGQIGVEITGVITDIseiktFKRRDG-SlGKYK--RITIADKSGTIRMTLWDDLAELDVK---VGDVIKIERARARKW 144
                                   899999************88766544444.434555..9*****************8877666...*****9998644433 PP

                     CDC24_OB3  76 kqskklev 83 
                                   +  ++le+
  gi|15669348|ref|NP_248153.1| 145 R--NNLEL 150
                                   3..44444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00027
                     CDC24_OB3  30 dryslrieDttGaidatlweeagklhfkrlrvGhlvllsg 69 
                                   + +s+ ++D+tG+i++tlw++   l + +++ G++v + g
  gi|15669348|ref|NP_248153.1| 210 KLKSFIVRDETGSIRVTLWDN---LTDIDVGRGDYVRVRG 246
                                   45699***************9...6667789999997766 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0038
                     CDC24_OB3   9 vtLlGrvvaifr.eknsek.kkmdryslrieDttGaidatlweeagklhfkrlrvGhlvllsg 69 
                                   v++ Grv+ai++ +  + + + ++++ + +++ tG +++  w+    l ++ ++ G+lv +++
  gi|15669348|ref|NP_248153.1| 291 VSVKGRVIAISNkKSVDLDgEIAKVQDIILDNGTGRVRVSFWRGKTALLEN-IKEGDLVRITN 352
                                   7899******77455555667888889************************.*******9987 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.039
                     CDC24_OB3  22 knsekkkmdryslrieDttGaidatlweeagkl 54 
                                   ++ e+k+ ++++l +eD tG i++ lw+  ++ 
  gi|15669348|ref|NP_248153.1| 423 IEFEDKVRKVRNLLLEDGTGRIRLSLWDDLAEI 455
                                   33333444556****************996554 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.045
                     CDC24_OB3 150 Cgrpv..sggeleCefCqcsvaevvrefeleitLdddtssaklfalctgqtaielLqispeeFsel 213
                                   C+++v   +g  +C  C+    e+ +   l+ ++dd+t++  l++ + +    ++L++  ee ++l
  gi|15669348|ref|NP_248153.1| 534 CRKRVveIDGIYNCPICGD--VEPEEILRLNFVVDDGTGT--LLCRAYDRRVEKMLKMNREELKNL 595
                                   6666666446677777775..4688999*********777..999999999999999999987776 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   1.1   5.5e-09   5.8e-06       9      94 ..      73     157 ..      68     160 .. 0.80
   2 ?    3.5   0.0     0.065        69      39      62 ..     211     232 ..     188     260 .. 0.66
   3 !   10.4   0.4   0.00046      0.49       1      85 [.     279     361 ..     279     368 .. 0.83
   4 ?    4.1   0.1     0.043        45      27      72 ..     422     463 ..     395     472 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.5e-09
                     REPA_OB_2   9 kdsi.vDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepvvalkgvkvsdFgg.rsl 87 
                                   +++i v + gv+++++e++++ +++++   k + +t+ D+sg ++++tlW++ ae ++ +  +v+ +  ++ + +    +l
  gi|15669348|ref|NP_248153.1|  73 EGQIgVEITGVITDISEIKTFKRRDGS-LGKYKRITIADKSG-TIRMTLWDDLAE-LDVKVGDVIKIERARARKWRNnLEL 150
                                   4444399******************99.777889*******9.59******9776.699************9999763455 PP

                     REPA_OB_2  88 sllssst 94 
                                   s +s ++
  gi|15669348|ref|NP_248153.1| 151 SSTSETK 157
                                   5555444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.065
                     REPA_OB_2  39 kreltlvDesgasvevtlWgkeae 62 
                                    +++ + De+g s++vtlW++  +
  gi|15669348|ref|NP_248153.1| 211 LKSFIVRDETG-SIRVTLWDNL-T 232
                                   45566677776.8******983.3 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00046
                     REPA_OB_2   1 iselenvekdsivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfe.sseepvvalkgvkvs 80 
                                   i++l++ e++++v v g v  +++ +++     + e+ k +  + D+    v+v +W  ++  +e  +e ++v + +++v+
  gi|15669348|ref|NP_248153.1| 279 IEDLTKYEDGELVSVKGRVIAISNKKSVDLD--G-EIAKVQDIILDNGTGRVRVSFWRGKTALLEnIKEGDLVRITNCRVK 356
                                   6889999999999999999999888877654..3.5888888899************77777766479************* PP

                     REPA_OB_2  81 dFggr 85 
                                    F  r
  gi|15669348|ref|NP_248153.1| 357 TFYDR 361
                                   99766 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.043
                     REPA_OB_2  27 eitskstekelkkreltlvDesgasvevtlWgkeaekfesseepvv 72 
                                   ei   +  k  k r+l l D +g+ +++ lW++ ae  e +e ++v
  gi|15669348|ref|NP_248153.1| 422 EIEFED--KVRKVRNLLLEDGTGR-IRLSLWDDLAEI-EIKEGDIV 463
                                   444433..3345699999999986.9******97763.66666666 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.076        80      58      77 ..     106     125 ..     102     177 .. 0.80
   2 ?   -0.1   0.0      0.68   7.2e+02      58      75 ..     214     231 ..     211     237 .. 0.85
   3 ?   -0.4   0.0      0.84   8.9e+02      55      77 ..     432     454 ..     423     471 .. 0.85
   4 !   30.5   0.0   2.5e-10   2.7e-07       3      92 ..     513     597 ..     511     641 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.076
                                   EEEE-SS-EEEEEEEHHHHH CS
                   Rep_fac-A_C  58 ikvsDstgqlwvtlFneaae 77 
                                   i ++D++g++++tl+++ ae
  gi|15669348|ref|NP_248153.1| 106 ITIADKSGTIRMTLWDDLAE 125
                                   789**************998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.68
                                   EEEE-SS-EEEEEEEHHH CS
                   Rep_fac-A_C  58 ikvsDstgqlwvtlFnea 75 
                                   + v D+tg+++vtl+++ 
  gi|15669348|ref|NP_248153.1| 214 FIVRDETGSIRVTLWDNL 231
                                   5689**********9985 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.84
                                   EEEEEEE-SS-EEEEEEEHHHHH CS
                   Rep_fac-A_C  55 ilsikvsDstgqlwvtlFneaae 77 
                                   + ++ ++D tg+++++l+++ ae
  gi|15669348|ref|NP_248153.1| 432 VRNLLLEDGTGRIRLSLWDDLAE 454
                                   5567789*************998 PP

  == domain 4  score: 30.5 bits;  conditional E-value: 2.5e-10
                                   EEEEEEEEEETTTTEEEB--STT---B-EEETTTEEEETTTTEEESS--EEEEEEEEEE-SS-EEEEEEEHHHHHHHHSS- CS
                   Rep_fac-A_C   3 svkatvsfikkdnlvYkACpsedCnkKvveeedgewrCekCdkeveepkyryilsikvsDstgqlwvtlFneaaekllgls 83 
                                   +v+++v++i +d+l+   Cp  +C k+vve  dg + C  C +   ep+  + l++ v D tg+l   +++   ek+l ++
  gi|15669348|ref|NP_248153.1| 513 EVRGAVVKILSDTLFLYLCP--NCRKRVVEI-DGIYNCPICGDV--EPEEILRLNFVVDDGTGTLLCRAYDRRVEKMLKMN 588
                                   689999999999999999**..*******97.8********998..67778889*************************** PP

                                   HHHHHHHCC CS
                   Rep_fac-A_C  84 aeelkklke 92 
                                    eelk+l  
  gi|15669348|ref|NP_248153.1| 589 REELKNLTI 597
                                   ****99864 PP

>> DUF3127  Domain of unknown function (DUF3127)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2   0.00041      0.43       1      73 [.      79     146 ..      79     162 .. 0.82
   2 ?    1.3   0.0      0.38     4e+02       3      63 ..     189     245 ..     187     262 .. 0.78
   3 !   12.0   0.1   0.00018      0.19       2      63 ..     293     351 ..     292     363 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00041
                       DUF3127   1 eitGkiikilptqegssknGefkkrefvleteeqYpkkiclevvgdkideldklqvgdevkvsfnlegrewng 73 
                                   eitG i+ i + ++++ + G+  k + +   ++  +  i ++++ d ++eld ++vgd +k++ + ++r+w +
  gi|15669348|ref|NP_248153.1|  79 EITGVITDISEIKTFKRRDGSLGKYKRITIADK--SGTIRMTLW-DDLAELD-VKVGDVIKIE-RARARKWRN 146
                                   89****************997766555433332..568999999.7799999.*********9.579****98 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.38
                       DUF3127   3 tGkiikilptqegssknG.efkkrefvleteeqYpkkiclevvgdkideldklqvgdevkvs 63 
                                   +G++i+ lp +e++ + G   k ++f++  e     +i ++++ d+++++d +  gd v+v 
  gi|15669348|ref|NP_248153.1| 189 EGEVISALPIKEFKRADGsIGKLKSFIVRDE---TGSIRVTLW-DNLTDID-VGRGDYVRVR 245
                                   899*************996667788998877...345667777.6777777.7777777775 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00018
                       DUF3127   2 itGkiikilptqegssknG.efkkrefvleteeqYpkkiclevvgdkideldklqvgdevkvs 63 
                                   ++G++i+i +++++    G   k ++++l        ++ +++++ k+++l+++++gd v+++
  gi|15669348|ref|NP_248153.1| 293 VKGRVIAISNKKSVDLD-GeIAKVQDIILDNG---TGRVRVSFWRGKTALLENIKEGDLVRIT 351
                                   79************999.94567788888765...679*********************9985 PP

>> Mucin_bdg  Putative mucin or carbohydrate-binding module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.015        16      68     101 ..     124     160 ..      94     166 .. 0.78
   2 !    7.8   0.0     0.003       3.2      68      88 ..     453     473 ..     439     490 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                     Mucin_bdg  68 keisfkeGdvlkiyHaEpk...nrlilskkqeeilks 101
                                    e+++k Gdv+ki  a ++   n l ls+ +e+++k+
  gi|15669348|ref|NP_248153.1| 124 AELDVKVGDVIKIERARARkwrNNLELSSTSETKIKK 160
                                   689**************99999999778777777764 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.003
                     Mucin_bdg  68 keisfkeGdvlkiyHaEpknr 88 
                                    ei++keGd+++i Ha +k+r
  gi|15669348|ref|NP_248153.1| 453 AEIEIKEGDIVEILHAYAKER 473
                                   589*************99977 PP

>> POT1PC  ssDNA-binding domain of telomere protection protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.87   9.2e+02      78     119 ..     114     150 ..     107     168 .. 0.76
   2 ?   -1.0   0.0       1.4   1.5e+03      74     104 ..     218     245 ..     199     246 .. 0.72
   3 !    9.7   0.0   0.00071      0.75      81     115 ..     329     364 ..     309     393 .. 0.78
   4 ?   -1.8   0.0       2.4   2.5e+03      82     103 ..     447     465 ..     440     486 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.87
                                   EEEEEE-HHHHHHHTTT--TT-EEEEEEEEEEE-TTS.-EEE CS
                        POT1PC  78 tlqitlydehaefarenlkpgdfvrLrNvhiklgrkgskleg 119
                                   t+  tl+d+ ae+  + +k+gd+++++  +++  r++  le+
  gi|15669348|ref|NP_248153.1| 114 TIRMTLWDDLAEL--D-VKVGDVIKIERARARKWRNN--LEL 150
                                   6677888877665..3.889*****999998776665..443 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                   SBS-EEEEEE-HHHHHHHTTT--TT-EEEEE CS
                        POT1PC  74 fgkltlqitlydehaefarenlkpgdfvrLr 104
                                    +  ++ +tl+d+  ++    + +gd+vr r
  gi|15669348|ref|NP_248153.1| 218 DETGSIRVTLWDNLTDID---VGRGDYVRVR 245
                                   55668999****976653...5578888765 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00071
                                   EEE-HHHHHHHTTT--TT-EEEEEEEEEE..E-TTS. CS
                        POT1PC  81 itlydehaefarenlkpgdfvrLrNvhik..lgrkgs 115
                                   ++ +    +++++ +k+gd+vr++N ++k  ++r+g+
  gi|15669348|ref|NP_248153.1| 329 VSFWRGKTALLEN-IKEGDLVRITNCRVKtfYDREGN 364
                                   6666666667777.**************977777776 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 2.4
                                   EE-HHHHHHHTTT--TT-EEEE CS
                        POT1PC  82 tlydehaefarenlkpgdfvrL 103
                                   +l+d+    a+ ++k+gd+v +
  gi|15669348|ref|NP_248153.1| 447 SLWDDL---AEIEIKEGDIVEI 465
                                   556654...4456899999988 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.029        31      43      64 ..     116     137 ..     115     140 .. 0.90
   2 ?   -1.3   0.0         2   2.1e+03      46      65 ..     227     246 ..     224     248 .. 0.85
   3 ?    1.6   0.0      0.25   2.7e+02      54      65 ..     341     352 ..     338     356 .. 0.86
   4 ?    7.1   0.0    0.0049       5.2      44      64 ..     446     466 ..     444     469 .. 0.88
   5 ?   -2.6   0.1       5.4   5.7e+03      53      64 ..     504     515 ..     504     518 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.029
                                   HTTHHHHHHTTT--TT-EEEET CS
                       DUF1967  43 klGvedaLrkaGakeGdtVrIg 64 
                                   ++ ++d L ++ +k Gd ++I 
  gi|15669348|ref|NP_248153.1| 116 RMTLWDDLAELDVKVGDVIKIE 137
                                   68899***************97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                                   HHHHHHTTT--TT-EEEETT CS
                       DUF1967  46 vedaLrkaGakeGdtVrIgd 65 
                                   ++d L +  +  Gd Vr+ +
  gi|15669348|ref|NP_248153.1| 227 LWDNLTDIDVGRGDYVRVRG 246
                                   679999999********976 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.25
                                   T--TT-EEEETT CS
                       DUF1967  54 GakeGdtVrIgd 65 
                                    +keGd VrI +
  gi|15669348|ref|NP_248153.1| 341 NIKEGDLVRITN 352
                                   69********76 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0049
                                   TTHHHHHHTTT--TT-EEEET CS
                       DUF1967  44 lGvedaLrkaGakeGdtVrIg 64 
                                   l ++d L +  +keGd V+I 
  gi|15669348|ref|NP_248153.1| 446 LSLWDDLAEIEIKEGDIVEIL 466
                                   6689***************96 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 5.4
                                   TT--TT-EEEET CS
                       DUF1967  53 aGakeGdtVrIg 64 
                                   a +++G+tV++ 
  gi|15669348|ref|NP_248153.1| 504 ADIEDGETVEVR 515
                                   5799*****985 PP

>> POT1  Telomeric single stranded DNA binding POT1/CDC13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0036       3.8      41      89 ..     109     147 ..      68     180 .. 0.76
   2 ?    5.2   0.0     0.016        17      51      93 ..     324     365 ..     277     372 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0036
                                   CTTTSCCHCTTTEEEEEEEECCCCCCCCGGCCCCEEECCCCEEEESTTS CS
                          POT1  41 vDpsknkgdendglrvvlFsknfedLpivkkvgdiirlhraklqsynge 89 
                                   +D+s        ++r +l ++  e L++  kvgd+i+++ra++++++++
  gi|15669348|ref|NP_248153.1| 109 ADKS-------GTIRMTLWDDLAE-LDV--KVGDVIKIERARARKWRNN 147
                                   4444.......7777777777655.677..9***************975 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.016
                                   TTEEEEEEEECCCCCCCCGGCCCCEEECCCCEEEESTTSCECC CS
                          POT1  51 ndglrvvlFsknfedLpivkkvgdiirlhraklqsyngepqgl 93 
                                   +  +rv + + +   L  + k+gd +r+++ +++++ ++  ++
  gi|15669348|ref|NP_248153.1| 324 TGRVRVSFWRGKTALLENI-KEGDLVRITNCRVKTFYDREGNK 365
                                   5568999************.***************99886555 PP

>> DUF5088  Domain of unknown function (DUF5088)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.062        66      20      66 ..     102     146 ..      73     165 .. 0.60
   2 ?    1.1   0.0      0.26   2.8e+02      23      63 ..     213     251 ..     203     287 .. 0.82
   3 ?    7.7   0.1    0.0025       2.7      23      66 ..     317     360 ..     291     415 .. 0.85
   4 ?   -3.8   0.0       8.3   8.8e+03      47     166 ..     456     467 ..     435     477 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.062
                       DUF5088  20 lfffiilstsaglvkvvvWkealrkysslkvGDiivikkfrkkkkie 66 
                                    +  i +  ++g +++ +W         +kvGD+i i++ r++k  +
  gi|15669348|ref|NP_248153.1| 102 KYKRITIADKSGTIRMTLWDDLA--ELDVKVGDVIKIERARARKWRN 146
                                   44445555555556666664322..3456777777777766655433 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.26
                       DUF5088  23 fiilstsaglvkvvvWkealrkysslkvGDiivikkfrkkk 63 
                                   ++i+  ++g ++v +W + l     +  GD++ ++++ ++ 
  gi|15669348|ref|NP_248153.1| 213 SFIVRDETGSIRVTLWDN-L-TDIDVGRGDYVRVRGYIREG 251
                                   79999999999*****75.5.35678889******996654 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0025
                       DUF5088  23 fiilstsaglvkvvvWkealrkysslkvGDiivikkfrkkkkie 66 
                                    iil   +g v+v +W+ +      +k+GD++ i++ r k  ++
  gi|15669348|ref|NP_248153.1| 317 DIILDNGTGRVRVSFWRGKTALLENIKEGDLVRITNCRVKTFYD 360
                                   58999999*********99999**************99997654 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 8.3
                       DUF5088  47 slkvGDiivikkfrkkkkiealskidrntfsetkyfdvkEisvkeilkiellkkkekvkeiFttvvGkveYlsvllrksan 127
                                    +k+GDi+ i                                                                       
  gi|15669348|ref|NP_248153.1| 456 EIKEGDIVEIL---------------------------------------------------------------------- 466
                                   35666666543...................................................................... PP

                       DUF5088 128 gkyeeYvllkvsgikvvLlansdkelydievgksieite 166
                                                                         +
  gi|15669348|ref|NP_248153.1| 467 --------------------------------------H 467
                                   ......................................3 PP

>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.14   1.4e+02      44      56 ..     128     140 ..     102     142 .. 0.82
   2 ?    4.9   0.0     0.026        28      44      56 ..     342     354 ..     338     356 .. 0.90
   3 ?    1.2   0.0      0.38     4e+02      43      52 ..     456     465 ..     450     468 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.14
                                   --TT-EEEEEEEC CS
                 Ribosomal_S17  44 vkvGDiVrieecr 56 
                                   vkvGD+++ie  r
  gi|15669348|ref|NP_248153.1| 128 VKVGDVIKIERAR 140
                                   9********9876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.026
                                   --TT-EEEEEEEC CS
                 Ribosomal_S17  44 vkvGDiVrieecr 56 
                                   +k+GD Vri  cr
  gi|15669348|ref|NP_248153.1| 342 IKEGDLVRITNCR 354
                                   89**********8 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.38
                                   S--TT-EEEE CS
                 Ribosomal_S17  43 svkvGDiVri 52 
                                   ++k+GDiV+i
  gi|15669348|ref|NP_248153.1| 456 EIKEGDIVEI 465
                                   49*******9 PP

>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2         2   2.1e+03      20      37 ..      12      29 ..       9      32 .. 0.85
   2 ?    6.7   0.1    0.0061       6.4      42      60 ..     122     139 ..     102     144 .. 0.82
   3 ?    0.6   0.0       0.5   5.3e+02      48      59 ..     341     352 ..     336     357 .. 0.87
   4 ?    2.2   0.0      0.16   1.6e+02      46      59 ..     454     467 ..     445     477 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2
                                  HHHHHHHTT--TTCSS-E CS
                RNA_pol_Rpb5_C 20 kkellkklkikeeqLPki 37
                                  kk++ + l+i+ee+L ++
  gi|15669348|ref|NP_248153.1| 12 KKKVAEALNISEEELDRM 29
                                  7899999********998 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0061
                                   HHHHCCT--TTSEEEEEEE CS
                RNA_pol_Rpb5_C  42 pvarylglkkGdvvkItrk 60 
                                    +a+ l++k Gdv+kI r 
  gi|15669348|ref|NP_248153.1| 122 DLAE-LDVKVGDVIKIERA 139
                                   5555.99**********96 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.5
                                   T--TTSEEEEEE CS
                RNA_pol_Rpb5_C  48 glkkGdvvkItr 59 
                                   ++k+Gd+v+It+
  gi|15669348|ref|NP_248153.1| 341 NIKEGDLVRITN 352
                                   689*******97 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.16
                                   CCT--TTSEEEEEE CS
                RNA_pol_Rpb5_C  46 ylglkkGdvvkItr 59 
                                   ++++k+Gd+v+I  
  gi|15669348|ref|NP_248153.1| 454 EIEIKEGDIVEILH 467
                                   499*********76 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.75   7.9e+02      37      57 ..     121     141 ..     114     150 .. 0.90
   2 ?   -1.2   0.0       1.9     2e+03      26      55 ..     268     296 ..     253     307 .. 0.74
   3 ?    4.6   0.0     0.031        33      39      56 ..     337     354 ..     334     358 .. 0.82
   4 ?    4.4   0.0     0.036        37      37      52 ..     450     465 ..     430     473 .. 0.90
   5 ?   -0.0   0.0      0.83   8.8e+02      43      55 ..     505     517 ..     490     527 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.75
                                   HHHHHHT--TT-EEEEEETTE CS
               Molydop_binding  37 edAaalGikdGdlVevesrrG 57 
                                   +d+a+l++k Gd +++e +r 
  gi|15669348|ref|NP_248153.1| 121 DDLAELDVKVGDVIKIERARA 141
                                   699************997765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                                   CSSS.-EEEEEHHHHHHHT--TT-EEEEEET CS
               Molydop_binding  26 kpep.evveinpedAaalGikdGdlVevesr 55 
                                   k e+ e  e+n ed+ +++  dG+lV v+ r
  gi|15669348|ref|NP_248153.1| 268 KGEKiESEEVNIEDLTKYE--DGELVSVKGR 296
                                   4444457789999999998..9**9999876 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.031
                                   HHHHT--TT-EEEEEETT CS
               Molydop_binding  39 AaalGikdGdlVevesrr 56 
                                   A   +ik+GdlV++++ r
  gi|15669348|ref|NP_248153.1| 337 ALLENIKEGDLVRITNCR 354
                                   55668**********976 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.036
                                   HHHHHHT--TT-EEEE CS
               Molydop_binding  37 edAaalGikdGdlVev 52 
                                   +d+a+ +ik+Gd+Ve+
  gi|15669348|ref|NP_248153.1| 450 DDLAEIEIKEGDIVEI 465
                                   69*************9 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 0.83
                                   T--TT-EEEEEET CS
               Molydop_binding  43 GikdGdlVevesr 55 
                                   +i+dG++Vev+ +
  gi|15669348|ref|NP_248153.1| 505 DIEDGETVEVRGA 517
                                   79********865 PP

>> SH3_2  Variant SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0       0.1   1.1e+02      15      27 ..     125     137 ..     106     166 .. 0.81
   2 ?    0.6   0.0      0.43   4.5e+02      17      28 ..     341     352 ..     341     376 .. 0.76
   3 ?    5.2   0.1     0.016        17      15      38 ..     454     477 ..     429     490 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.1
                                   B--B-TTEEEEEE CS
                         SH3_2  15 eLsfkkGdvikvl 27 
                                   eL  k+Gdvik+ 
  gi|15669348|ref|NP_248153.1| 125 ELDVKVGDVIKIE 137
                                   5899*******96 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.43
                                   -B-TTEEEEEE. CS
                         SH3_2  17 sfkkGdvikvls 28 
                                   ++k+Gd+++++ 
  gi|15669348|ref|NP_248153.1| 341 NIKEGDLVRITN 352
                                   589*******96 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.016
                                   B--B-TTEEEEEE....EEEECTTEE CS
                         SH3_2  15 eLsfkkGdvikvls..lgskdsdgww 38 
                                   e+++k+Gd++ +l      k++++++
  gi|15669348|ref|NP_248153.1| 454 EIEIKEGDIVEILHayA--KERGDYI 477
                                   59********9998531..4444443 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.6   5.9e+03      14      22 ..     261     269 ..     259     270 .. 0.88
   2 ?    0.8   0.0      0.37   3.9e+02      13      21 ..     460     468 ..     460     470 .. 0.92
   3 ?    5.7   1.9     0.011        11       5      28 ..     543     574 ..     539     578 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.6
                                   -EEEECC-- CS
               Desulfoferrod_N  14 niVeVleaG 22 
                                   n Ve+l++G
  gi|15669348|ref|NP_248153.1| 261 NYVEILKKG 269
                                   88****999 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.37
                                   --EEEECC- CS
               Desulfoferrod_N  13 GniVeVlea 21 
                                   G+iVe+l+a
  gi|15669348|ref|NP_248153.1| 460 GDIVEILHA 468
                                   99*****96 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.011
                                   -EEE-TTT--EEE........ECC--SS-EEE CS
               Desulfoferrod_N   5 evYkCevCGniVe........VleaGgGeLVC 28 
                                    +Y C +CG++          V++ G G+L C
  gi|15669348|ref|NP_248153.1| 543 GIYNCPICGDVEPeeilrlnfVVDDGTGTLLC 574
                                   58*******86312222333477888888888 PP

>> DNA_pol_D_N  DNA polymerase delta subunit OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2      0.98     1e+03     129     129 ..      70      70 ..       5     165 .. 0.69
   2 ?   -3.4   0.0       9.4   9.9e+03      84      99 ..     212     227 ..     202     250 .. 0.64
   3 ?   10.1   0.9   0.00063      0.66      66      99 ..     389     449 ..     258     476 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.98
                   DNA_pol_D_N 129 d 129
                                   d
  gi|15669348|ref|NP_248153.1|  70 D 70 
                                   3 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.4
                   DNA_pol_D_N  84 dellLEDesgrvrLsg 99 
                                   +++++ De+g +r++ 
  gi|15669348|ref|NP_248153.1| 212 KSFIVRDETGSIRVTL 227
                                   5677889999998873 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00063
                   DNA_pol_D_N  66 k..........................edesapqaerkkyvsekdellLEDesgrvrLs.g 99 
                                   +                          ed+  ++ e +  v +  +llLED +gr+rLs  
  gi|15669348|ref|NP_248153.1| 389 ElkyckiediynrdvdwndinliaqvvEDYGVNEIEFEDKVRKVRNLLLEDGTGRIRLSlW 449
                                   055555555666666666666666677889999999999999****************952 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   3.9       0.1   1.1e+02       3      33 ..     531     558 ..     529     560 .. 0.76
   2 ?    6.3   1.5    0.0063       6.6       1      22 [.     545     574 ..     545     576 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.1
                                   ETTTTCEECHEETSTTCEEESSSSBEEEECC CS
                  TF_Zn_Ribbon   3 CPnCgstnlveDpergelvCtdCGlVledns 33 
                                   CPnC  +  v++ + g + C+ CG V  +++
  gi|15669348|ref|NP_248153.1| 531 CPNCRKR--VVEID-GIYNCPICGDVEPEEI 558
                                   9999987..55544.8899999999988775 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0063
                                   EEETTTTCEEC........HEETSTTCEEE CS
                  TF_Zn_Ribbon   1 ykCPnCgstnl........veDpergelvC 22 
                                   y CP+Cg  +         v+D  +g+l+C
  gi|15669348|ref|NP_248153.1| 545 YNCPICGDVEPeeilrlnfVVDDGTGTLLC 574
                                   56*****966347799999*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (645 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 4054.66
//
Query:       gi|15669349|ref|NP_248154.1|  [L=434]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit A [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   2.8e-131  438.6   0.0   3.3e-131  438.4   0.0    1.0  1  Amidase      Amidase
  ------ inclusion threshold ------
        3.8    7.3   5.0        5.6    6.7   0.1    2.4  2  PRKCSH-like  Glucosidase II beta subunit-like
        5.5    7.0   7.0        5.9    6.9   0.7    2.5  3  GP24_25      Tail assembly gene products 24 & 25


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.4   0.0  5.5e-135  3.3e-131       2     451 .]       5     423 ..       4     423 .. 0.98

  Alignments for each domain:
  == domain 1  score: 438.4 bits;  conditional E-value: 5.5e-135
                                   HHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS-- CS
                       Amidase   2 lveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaekDa 82 
                                    ve++l+rie++n+++nal++v +e+ l++A+kl+k+++   +k+pL+G  i+vK ni+v+g+ ++++sk+leny+a++Da
  gi|15669349|ref|NP_248154.1|   5 RVEEYLDRIEKINKDINALIEVKPEKVLEEAKKLEKDEK--AKKKPLYGKIIVVKANINVEGYTISCASKTLENYIAPYDA 83 
                                   599**********************************97..**************************************** PP

                                   HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHHC CS
                       Amidase  83 tvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsfc 163
                                   tv+e++k++G +i+g +nmdefa gss+e+s+fgpt+NP+ k+r+pGGSS+GsAAav+a+l+++a+G+DtGGSiR PAs c
  gi|15669349|ref|NP_248154.1|  84 TVIEKIKENGGLIIGIANMDEFACGSSGETSYFGPTKNPRAKDRIPGGSSSGSAAAVSADLCDMALGSDTGGSIRNPASHC 164
                                   ********************************************************************************* PP

                                   TSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEEEEG CS
                       Amidase 164 glvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglriGvvk 244
                                   g+vG+KP+yg+vSr+g+++l++s+d++Gpl++++ed+ ll   i g+d +d t+         +++ +kk+ kg+++Gvvk
  gi|15669349|ref|NP_248154.1| 165 GVVGFKPSYGVVSRYGLCDLAMSFDQIGPLTKTAEDALLLTNIIKGKDLRDTTTVE-------TKPFEKKDIKGFKVGVVK 238
                                   **************************************************999997.......6899************** PP

                                   GGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS---SS-SCCCCCCCHHH CS
                       Amidase 245 edgvasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvryerlsetkvlsellpksr 325
                                   e+  + +d++++  veka++  +++G+e+ve++ ++++ al++yyli ++e++s ++ry+g+              +  ++
  gi|15669349|ref|NP_248154.1| 239 EFM-DVADEKIRDKVEKAIEVFKDLGCEIVELSYKYVDLALPTYYLINYVEFFSSTRRYDGR-------------RYGYKI 305
                                   **9.89*****************************************************999.............458899 PP

                                   HCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHHHHHGCC CS
                       Amidase 326 aellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktidsytvlynll 406
                                   +e +geev rri+ g++  ++e+s+kyy++a k+r l+r+e+ k+++++D+++  t+p+ +++lgek     +++++y ++
  gi|15669349|ref|NP_248154.1| 306 EEVCGEEVLRRIMIGSMISQKEYSGKYYKNALKARNLMRNEMIKIMKDVDIIVGATVPKLPHKLGEK----LTPMEMYSYD 382
                                   ******************************************************************9....57******** PP

                                   TTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
                       Amidase 407 dftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                                   ++t   vp+n+ gl a  vp+g+ + g PvG+q+ gk+f++e++L
  gi|15669349|ref|NP_248154.1| 383 VLT---VPANICGLCAGVVPCGDIN-GIPVGLQIQGKPFEDEKVL 423
                                   ***...****************996.****************998 PP

>> PRKCSH-like  Glucosidase II beta subunit-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.1     0.033     2e+02     121     161 ..       4      44 ..       2      59 .. 0.74
   2 ?    6.7   0.1   0.00093       5.6      52     103 ..     139     186 ..     107     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.033
                   PRKCSH-like 121 eiarkfeelleeankkvkkglkikeelllaakkkldelkkk 161
                                   e  +++++  e+ nk+++  +++k e +l+ +kkl++ +k 
  gi|15669349|ref|NP_248154.1|   4 ERVEEYLDRIEKINKDINALIEVKPEKVLEEAKKLEKDEKA 44 
                                   56688999999999999999999988888887776654333 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00093
                   PRKCSH-like  52 qvnddycdcPdGsdePGtsacengkfycaneGyisgyiesfkvddgvcdydi 103
                                    v  d cd   Gsd  G+   +n+  +c   G+ ++y    +   g+cd  +
  gi|15669349|ref|NP_248154.1| 139 AVSADLCDMALGSDTGGS--IRNPASHCGVVGFKPSYGVVSR--YGLCDLAM 186
                                   5889**********9885..799**************65554..47777655 PP

>> GP24_25  Tail assembly gene products 24 & 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.7   0.00098       5.9      69     105 ..       6      43 ..       3      59 .. 0.75
   2 ?    3.4   0.2     0.012        73      25      65 ..     213     251 ..     207     274 .. 0.71
   3 ?   -3.5   0.0       1.6   9.5e+03      75     111 ..     346     379 ..     341     384 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00098
                       GP24_25  69 vdeysdelekviakvfrliatdPkklidalde.eedPr 105
                                   v+ey d++ek+ +++  li  +P k++++ ++ e+d +
  gi|15669349|ref|NP_248154.1|   6 VEEYLDRIEKINKDINALIEVKPEKVLEEAKKlEKDEK 43 
                                   78*********************999887665244444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.012
                       GP24_25  25 lsddvtveLkpLLkLgkkareavvellkefeeiaeleedde 65 
                                   l+d  tve kp+ k   k+ +  v ++kef ++a+ +  d+
  gi|15669349|ref|NP_248154.1| 213 LRDTTTVETKPFEKKDIKGFK--VGVVKEFMDVADEKIRDK 251
                                   8999*******9998777776..567899999995444443 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.6
                       GP24_25  75 elekviakvfrliatdPkklidaldeeedPriraely 111
                                   e+ k++++v  ++     kl ++l e+  P   +e+y
  gi|15669349|ref|NP_248154.1| 346 EMIKIMKDVDIIVGATVPKLPHKLGEKLTP---MEMY 379
                                   667777887766654444577777777777...7777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2912.14
//
Query:       gi|15669350|ref|NP_248155.1|  [L=167]
Description: hypothetical protein MJ_1161 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1107.91
//
Query:       gi|15669351|ref|NP_248156.1|  [L=218]
Description: hypothetical protein MJ_1162 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-15   56.7   0.1    6.1e-15   56.3   0.1    1.2  1  Metallophos    Calcineurin-like phosphoesterase
    1.1e-14   54.9   0.1    2.1e-14   54.1   0.1    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    8.9e-09   35.0   0.3    2.2e-07   30.4   0.1    2.5  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.1     1e-18   6.1e-15       1     203 [.       5     180 ..       5     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1e-18
                                   EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHHHH CS
                   Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfeeel 81 
                                   ++i+ i+DlH     g l+ +++ ++d+     +d+++++GD+++ g   + ++e la+l +y   v +++GN++      
  gi|15669351|ref|NP_248156.1|   5 MKIVGITDLH-----GKLPPAVREFKDF-----ADVLVVCGDITHFGKGIE-VIEKLAELSDY-MEVLCVPGNCD-----T 68 
                                   89********.....************9.....799999********5555.55555888887.89*********.....7 PP

                                   HHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE...EEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHH.HHHHT CS
                   Metallophos  82 lnkygylgifsepwrsdaevfnnlplaslgsgs...lkvlllhGgspellvsldklgslnleleapepgdewlkd.lekre 158
                                   ++  ++l+ f+ ++ +++++ +n++ +++g+ +   +++   + +                        +e++++     +
  gi|15669351|ref|NP_248156.1|  69 KEVIDELNSFKLNIDRKVKKIENINFVGIGGSNktpFNTPNEYTE------------------------EEIYNKlINVVK 125
                                   777788888999999999999999999977775433333333333........................444444333477 PP

                                   TCSEEEEEESSESS........CSSSCSCCHHHHHHHHHHTT..ESEEEEESSSS CS
                   Metallophos 159 kadwvivlgHsply........rgsgylfgdealedllkkyg..vdlvisGHtHv 203
                                   + + +++++H p+y          +  + g+++++++ ++++  +  + +GH+H+
  gi|15669351|ref|NP_248156.1| 126 NLKNIFLVSHAPPYntmadivdLDKDIHVGSKSIRKIIEDFNenIRFCACGHIHE 180
                                   7888999***************9999999999999998888778999*******7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.1   3.5e-18   2.1e-14       1     145 [.       5     197 ..       5     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 3.5e-18
                 Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepevleellela...pvlaVrGNnD.............. 62 
                                   Mk++ i+DlH  +++++av e  k+  +d ++++GD+   ++  ev+e+l el    +vl V+GN+D              
  gi|15669351|ref|NP_248156.1|   5 MKIVGITDLH--GKLPPAVREF-KDF-ADVLVVCGDIthFGKGIEVIEKLAELSdymEVLCVPGNCDtkevidelnsfkln 81 
                                   9*********..6777776655.665.599******977666667777777777778**********77766666666555 PP

                 Metallophos_2  63 ........eevveedvlreaaelgtdl................p.eeaelel........agek..vlliHgdpl...... 102
                                           e                                  p e+ e e+        ++ k  +l+ H  p+      
  gi|15669351|ref|NP_248156.1|  82 idrkvkkiE-----------------NinfvgiggsnktpfntPnEYTEEEIynklinvvKNLKniFLVSHAPPYntmadi 145
                                   555554442.................0333444444455555522555555544445555555587888888877999999 PP

                 Metallophos_2 103 ........gvkdalaellkeaeegsdvvvcGHtHvp.evekeggvlvvnPGs 145
                                            +++++++ +++  e+ ++++cGH+H+   ++k+g+++vvnP  
  gi|15669351|ref|NP_248156.1| 146 vdldkdihVGSKSIRKIIEDFNENIRFCACGHIHESrCIDKIGNTIVVNPSP 197
                                   99998887777888888888777777*********9678888*******954 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.011        64      29      44 ..      25      39 ..       1     104 [. 0.61
   2 !   30.4   0.1   3.8e-11   2.2e-07     159     236 ..     112     197 ..      42     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.011
                                  HHH--SEEEEES---- CS
                 Metallophos_3 29 edkdpDllvlvGdlvk 44
                                  +d  +D+lv+ Gd+ +
  gi|15669351|ref|NP_248156.1| 25 KD-FADVLVVCGDITH 39
                                  33.3678888887743 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 3.8e-11
                                   HHHHHHGGGGGGS---EEEEEE.SS--S-SST....BTTBS---S-HHHHHHHHHH--SEEEE..-SS--EE..EEETTEE CS
                 Metallophos_3 159 weveyrLkvlkelkdrrkvlll.atpPigelv....adkglkekgsevvaelvktlnPevvvv..ghavkeh..eelgktl 230
                                    e e   k+++ +k+ + ++l+ + pP   +     +dk+  + gs+ + +++ ++n ++ ++  gh + ++  +++g+t+
  gi|15669351|ref|NP_248156.1| 112 TEEEIYNKLINVVKNLKNIFLVsHAPPYNTMAdivdLDKD-IHVGSKSIRKIIEDFNENIRFCacGHIHESRciDKIGNTI 191
                                   4555667899999999****99345665544344469999.899**************9999877999998899******* PP

                                   EEE--B CS
                 Metallophos_3 231 vvnPGa 236
                                   vvnP  
  gi|15669351|ref|NP_248156.1| 192 VVNPSP 197
                                   ****64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1461.54
//
Query:       gi|15669352|ref|NP_248157.1|  [L=217]
Description: hypothetical protein MJ_1163 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-22   79.6   0.1    3.1e-22   79.2   0.1    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    1.5e-19   70.4   0.0    1.9e-19   70.0   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    5.4e-11   42.9   0.7    1.3e-10   41.6   0.7    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   0.1   5.2e-26   3.1e-22       2     163 .]       2     181 ..       1     181 [. 0.89

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 5.2e-26
                 Lactamase_B_3   2 ltwlghnsflletagarilvDPfka....nlgyeppaeeaDlvlisqaledHa.hletlkqlaenvkvlee.......... 67 
                                   +tw+gh++f ++    ++l+DPf +     l y++  e ++++ ++++++dH  ++e+l++   nv+v+++          
  gi|15669352|ref|NP_248157.1|   2 ITWYGHACFKVD----NVLIDPFVPnplcDLPYDEIMEGVEVIAVTHGHADHLgNAEELAK-TYNVPVVTNheisvylser 77 
                                   9*********97....7******44345678999999***************626677777.8899999998999999999 PP

                 Lactamase_B_3  68 .........geslevggleiravatshdavggser..genngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvg 137
                                            g+++e++g++++ v+++h +   ++   g   gf++++   ++yh G+++   ++e + e+  + + l+P+g
  gi|15669352|ref|NP_248157.1|  78 gvcaegmniGGTIEINGAKLTMVKAEHSSDISPTIsgGVAAGFIIND---RVYHAGDTGLFGDMELIGEIYAPQIALLPIG 155
                                   999999999999***************888665442245899***88...9****************************** PP

                 Lactamase_B_3 138 gpltlgqeealelakrLkpklvlPmh 163
                                   g +t+g +eal +++++ p++v+Pmh
  gi|15669352|ref|NP_248157.1| 156 GRYTMGIDEALVAIELIYPEIVIPMH 181
                                   *************************9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.0   3.1e-23   1.9e-19       2     201 .]      14     182 ..      13     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 3.1e-23
                                   EEEES--TTHHHHHTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHT CS
                 Lactamase_B_2   2 riLiDagpdlrqqalral.qPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylalee 81 
                                   ++LiD++       +++   P    + ++ ++++ +th+H+DHl ++  l+++++  +p++ + +++ +l++++       
  gi|15669352|ref|NP_248157.1|  14 NVLIDPFVP-----NPLCdLPYD--EIMEGVEVIAVTHGHADHLGNAEELAKTYN--VPVVTNHEISVYLSERG------- 78 
                                   677777665.....333322333..345699*********************765..9***************4....... PP

                                   TTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---.HHHHHHHCT-SEEE CS
                 Lactamase_B_2  82 epavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip.eeigerlggadlll 161
                                      v ++ +++g+++e++  g ++t++ a+h+s    +   g ++G++i     rvy++gDtg +   e+  +++ ++++l
  gi|15669352|ref|NP_248157.1|  79 ---VCAEGMNIGGTIEIN--GAKLTMVKAEHSSDISPTISGGVAAGFIIN---DRVYHAGDTGLFGdMELIGEIYAPQIAL 151
                                   ...56789*********9..678************999999*********...7***********95445569999***** PP

                                   EE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                 Lactamase_B_2 162 lditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                   l+i+         + +++ ++ea+ a++ + +++++++H+
  gi|15669352|ref|NP_248157.1| 152 LPIG---------GRYTMGIDEALVAIELIYPEIVIPMHY 182
                                   ****.........899***********************7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.7   2.3e-14   1.3e-10      43     183 ..      35     166 ..      13     209 .. 0.71

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.3e-14
                                   GGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEE CS
                   Lactamase_B  43 kdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrral 123
                                   + v+ + +TH+H+DH G++++l+++++vpv+ ++e+  +l ++++  + +  g           ++ e  ++  ++   + 
  gi|15669352|ref|NP_248157.1|  35 EGVEVIAVTHGHADHLGNAEELAKTYNVPVVTNHEISVYLSERGVCAEGMNIG-----------GTIEINGAKLTMVKAEH 104
                                   67999****************************************77777765...........47777777777777777 PP

                                   EHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC...TTCEEE-SHCHHHHHHHHHH CS
                   Lactamase_B 124 yvtggpghghghgvveygggkvlftGDallagetgridl..tlrgaevrdpsdaekyldsll 183
                                        p+ ++g++  ++ +++v  +GD++l g+ ++i++   +++a  + ++ ++  +d++l
  gi|15669352|ref|NP_248157.1| 105 SSDISPTISGGVAAGFIINDRVYHAGDTGLFGDMELIGEiyAPQIALLPIGGRYTMGIDEAL 166
                                   77777777777777777999999999999999999999877444444333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1441.83
//
Query:       gi|15669353|ref|NP_248158.1|  [L=318]
Description: hypothetical protein MJ_1164 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-14   51.4   0.3    4.8e-13   49.0   0.0    2.4  3  HTH_3     Helix-turn-helix
    5.6e-07   29.5   0.0    4.4e-06   26.6   0.0    2.4  2  HTH_19    Helix-turn-helix domain
    1.3e-06   28.6   0.0    4.9e-06   26.8   0.0    1.9  2  HTH_31    Helix-turn-helix domain
     0.0032   17.4   0.0      0.017   15.0   0.0    2.2  1  HTH_11    HTH domain
     0.0085   16.5   0.0      0.045   14.2   0.0    2.2  2  HTH_26    Cro/C1-type HTH DNA-binding domain
  ------ inclusion threshold ------
      0.066   13.3   0.1        0.2   11.8   0.1    1.8  1  HTH_7     Helix-turn-helix domain of resolvase
       0.14   11.8   1.1        8.9    6.0   0.0    3.2  3  NOD       NOTCH protein


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.8   4.5e+03      40      49 ..      61      70 ..      59      74 .. 0.75
   2 !   49.0   0.0   1.9e-16   4.8e-13       1      52 [.     131     182 ..     131     184 .. 0.98
   3 ?   -2.1   0.0       1.6   4.1e+03      37      48 ..     293     304 ..     291     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.8
                                  HHHHHHHHHT CS
                         HTH_3 40 tlkklakaLg 49
                                   lkk++k L 
  gi|15669353|ref|NP_248158.1| 61 ELKKISKILH 70
                                  6899999885 PP

  == domain 2  score: 49.0 bits;  conditional E-value: 1.9e-16
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEH CS
                         HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsl 52 
                                   lke R++ g+s  +LAe++Gvsr +i+++E   +nPs+++++k++++L+v+l
  gi|15669353|ref|NP_248158.1| 131 LKEVREAMGISVGKLAEVAGVSRKAIYKYETQMANPSVDVALKIEEFLDVPL 182
                                   89************************************************98 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.6
                                   BHHHHHHHHHHH CS
                         HTH_3  37 sletlkklakaL 48 
                                   s+e lkk+ +aL
  gi|15669353|ref|NP_248158.1| 293 SIEELKKMDDAL 304
                                   899999998887 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.73   1.9e+03      28      51 ..      43      68 ..      33      73 .. 0.54
   2 !   26.6   0.0   1.7e-09   4.4e-06       1      56 [.     128     182 ..     128     190 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.73
                        HTH_19 28 kisaiEngkkdvps...aelllkiaea 51
                                   i +i ++ +d +s   +++l+ki+++
  gi|15669353|ref|NP_248158.1| 43 LILKILKN-IDSLSrdqSKELKKISKI 68
                                  55555544.444444445555555544 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 1.7e-09
                        HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidl 56 
                                   G+ Lke+Re  g++  +lae +g+sr+ i+++E+    +ps ++ lki e+l+++l
  gi|15669353|ref|NP_248158.1| 128 GKVLKEVREAMGISVGKLAEVAGVSRKAIYKYETQM-ANPSVDVALKIEEFLDVPL 182
                                   788******************************665.5***************996 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   1.9e-09   4.9e-06       3      57 ..     128     181 ..     128     186 .. 0.95
   2 ?   -2.1   0.0         2     5e+03      41      56 ..     291     306 ..     288     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.9e-09
                        HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57 
                                   G  L++ Re+ G+s   +Ae +gvs+  + ++E+    +ps +v  ++ + l+++
  gi|15669353|ref|NP_248158.1| 128 GKVLKEVREAMGISVGKLAEVAGVSRKAIYKYETQMA-NPSVDVALKIEEFLDVP 181
                                   779**********************************.6*******999999997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
                        HTH_31  41 rpspavlealaralgl 56 
                                   ++s + l ++ +al l
  gi|15669353|ref|NP_248158.1| 291 VVSIEELKKMDDALEL 306
                                   68999*******9976 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   6.8e-06     0.017       5      35 ..     130     159 ..     129     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.8e-06
                        HTH_11   5 ilelLleargpisgeeLAeeLnvSrrtvrrd 35 
                                   +l+ ++ea g is  +LAe  +vSr++++++
  gi|15669353|ref|NP_248158.1| 130 VLKEVREAMG-ISVGKLAEVAGVSRKAIYKY 159
                                   7888999999.******************97 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.5   3.7e+03      41      51 ..      60      70 ..      47      74 .. 0.63
   2 !   14.2   0.0   1.8e-05     0.045       2      53 ..     131     181 ..     130     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                        HTH_26 41 dtLdkiCdaLg 51
                                  ++L ki ++L 
  gi|15669353|ref|NP_248158.1| 60 KELKKISKILH 70
                                  45666666664 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.8e-05
                        HTH_26   2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgct 53 
                                   L+e+  ++gi++ +La+ +g+s+  ++++ ++   ++s d+  ki + L++ 
  gi|15669353|ref|NP_248158.1| 131 LKEVREAMGISVGKLAEVAGVSRKAIYKYETQM-ANPSVDVALKIEEFLDVP 181
                                   899999*************************95.7******99998888875 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   7.6e-05       0.2      21      41 ..     139     159 ..     135     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.6e-05
                                   T--STTTSSSS---SSSS--S CS
                         HTH_7  21 GisiskIAkevnisRsTvYRy 41 
                                   Gis+ k+A+  ++sR  +Y+y
  gi|15669353|ref|NP_248158.1| 139 GISVGKLAEVAGVSRKAIYKY 159
                                   9*******************9 PP

>> NOD  NOTCH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0035       8.9       9      38 ..      43      72 ..      40      85 .. 0.89
   2 ?    0.6   0.1      0.18   4.5e+02      18      32 ..     205     219 ..     203     220 .. 0.89
   3 ?    1.5   0.0     0.087   2.2e+02      26      35 ..     258     271 ..     244     273 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0035
                           NOD  9 LvlvVlidpeellnnskeFLrelsalLrtn 38
                                  L+l +l + + l +++++ L+++s++L+ +
  gi|15669353|ref|NP_248158.1| 43 LILKILKNIDSLSRDQSKELKKISKILHGT 72
                                  899999999*******************65 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.18
                           NOD  18 eellnnskeFLrels 32 
                                   e ++++  +FL el+
  gi|15669353|ref|NP_248158.1| 205 EDFKKEAINFLNELG 219
                                   78999*********8 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.087
                           NOD  26 e....FLrelsalL 35 
                                   +    F rels+lL
  gi|15669353|ref|NP_248158.1| 258 KrkalFVRELSRLL 271
                                   13345*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2034.59
//
Query:       gi|15669354|ref|NP_248159.1|  [L=146]
Description: formylmethanofuran dehydrogenase subunit FwdE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-08   32.8   7.2    0.00017   21.2   0.9    2.3  2  Fer4            4Fe-4S binding domain
      4e-05   23.5   9.4      0.021   14.9   1.2    2.4  2  Fer4_6          4Fe-4S binding domain
    0.00015   21.8   8.1      0.001   19.2   0.7    2.3  2  Fer4_10         4Fe-4S dicluster domain
    0.00031   20.8   7.9      0.017   15.2   1.2    2.3  2  Fer4_21         4Fe-4S dicluster domain
     0.0017   18.4  11.6      0.037   14.1   1.6    2.3  2  Fer4_2          4Fe-4S binding domain
     0.0025   17.8   0.1     0.0049   16.9   0.1    1.5  1  HTH_3           Helix-turn-helix
  ------ inclusion threshold ------
      0.025   14.7   0.2        7.6    6.7   0.1    2.1  2  DUF2250         Uncharacterized protein conserved in archaea 
      0.029   14.5   9.9       0.21   11.8  10.0    2.1  1  Fer4_9          4Fe-4S dicluster domain
      0.055   13.5   0.1        0.1   12.6   0.1    1.4  1  HTH_19          Helix-turn-helix domain
      0.084   13.8   1.8      0.084   13.8   1.8    2.5  2  Fer4_16         4Fe-4S double cluster binding domain
       0.12   12.6   0.0       0.17   12.1   0.0    1.2  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
       0.22   12.2  11.9         10    6.8  12.5    2.2  2  Fer4_7          4Fe-4S dicluster domain
       0.33   11.7   8.8       0.45   11.3   1.1    2.4  2  Fer4_15         4Fe-4S single cluster domain
       0.38   11.3  12.1        3.1    8.4   2.1    2.6  2  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
        8.8    7.0  13.4        5.8    7.5   2.7    2.4  3  Fer4_17         4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.7   1.2e-05     0.015       2      14 ..      93     105 ..      92     107 .. 0.91
   2 !   21.2   0.9   1.4e-07   0.00017       3      23 ..     120     140 ..     118     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                                   EEETTTSSS-THH CS
                          Fer4   2 videekCigCGaC 14 
                                    +de+ Ci+CG C
  gi|15669354|ref|NP_248159.1|  93 FWDENSCIACGSC 105
                                   59*********** PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.4e-07
                                   EETTTSSS-THHHHHSTTTEE CS
                          Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                   ide+ C  C  C+  CP++ +
  gi|15669354|ref|NP_248159.1| 120 IDEDTCHLCASCIFRCPTNSL 140
                                   9*****************976 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   1.6   6.6e-05     0.079       3      15 ..      93     105 ..      91     109 .. 0.91
   2 !   14.9   1.2   1.7e-05     0.021       2      22 ..     118     138 ..     117     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-05
                        Fer4_6   3 eidpdkCigCgdC 15 
                                    +d+++Ci Cg C
  gi|15669354|ref|NP_248159.1|  93 FWDENSCIACGSC 105
                                   79**********9 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.7e-05
                        Fer4_6   2 veidpdkCigCgdCvrvCPeg 22 
                                   v id+d C  C  C+  CP++
  gi|15669354|ref|NP_248159.1| 118 VGIDEDTCHLCASCIFRCPTN 138
                                   679****************98 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   1.4    0.0069       8.2       5      16 ..      95     106 ..      91     110 .. 0.79
   2 !   19.2   0.7   8.4e-07     0.001       2      21 ..     118     137 ..     117     146 .] 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0069
                       Fer4_10   5 dddtCirCgkCv 16 
                                   d+++Ci Cg C 
  gi|15669354|ref|NP_248159.1|  95 DENSCIACGSCL 106
                                   788999999995 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 8.4e-07
                       Fer4_10   2 vvidddtCirCgkCvkaCPa 21 
                                   v id+dtC  C+ C   CP+
  gi|15669354|ref|NP_248159.1| 118 VGIDEDTCHLCASCIFRCPT 137
                                   679****************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.8   0.00095       1.1       4      15 ..      95     106 ..      93     117 .. 0.85
   2 !   15.2   1.2   1.5e-05     0.017       3      27 ..     120     144 ..     118     146 .] 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00095
                       Fer4_21   4 dedkCigCgkCl 15 
                                   de++Ci Cg+Cl
  gi|15669354|ref|NP_248159.1|  95 DENSCIACGSCL 106
                                   899********7 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.5e-05
                       Fer4_21   3 idedkCigCgkCliaCedtshqaie 27 
                                   ided+C  C +C+  C+++s + i+
  gi|15669354|ref|NP_248159.1| 120 IDEDTCHLCASCIFRCPTNSLKFIK 144
                                   9*****************9998886 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.6   3.1e-05     0.037       4      18 ..      93     106 ..      91     110 .. 0.83
   2 !    9.2   2.8    0.0011       1.4       5      22 .]     120     137 ..     118     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                        Fer4_2   4 vvdtdrCigCgaCvs 18 
                                   + d+++Ci+Cg+C  
  gi|15669354|ref|NP_248159.1|  93 FWDENSCIACGSC-L 106
                                   789**********.4 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
                        Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                   +d+d+C  C +C+  CP+
  gi|15669354|ref|NP_248159.1| 120 IDEDTCHLCASCIFRCPT 137
                                   8****************7 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   4.1e-06    0.0049       5      39 ..      17      50 ..      13      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.1e-06
                                  HHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHH CS
                         HTH_3  5 RkqlglsqeeLAeklGvsrstisriEnGernPsle 39
                                  +  +gl q+e+A+ +   rs +s++ +G+  P  +
  gi|15669354|ref|NP_248159.1| 17 LRRKGLLQKEIAKIIKSDRSIVSHYLSGRY-PKEK 50
                                  3357************************55.6655 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0063       7.6      44      63 ..      15      34 ..       6      38 .. 0.87
   2 ?    6.2   0.0    0.0096        11       8      49 ..      49      90 ..      44     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0063
                       DUF2250 44 kkLeelGLlervegktikrt 63
                                   kL++ GLl++  +k+ik  
  gi|15669354|ref|NP_248159.1| 15 MKLRRKGLLQKEIAKIIKSD 34
                                  69****************75 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0096
                       DUF2250  8 elalkvlkhlkkanvdYaksiakeleipleevrellkkLeel 49
                                  e+ l+v k+++++ + Y+    + l  ++e +++l+k+L+ +
  gi|15669354|ref|NP_248159.1| 49 EKILNVAKIIEEMPPQYGAKFIHSLTDNKELAKNLIKELYGI 90
                                  56799********************************99865 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8  10.0   0.00017      0.21       2      49 ..      99     138 ..      64     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   C+ Cg+C   C a +  +  ++            C+ C +C+ +Cp++
  gi|15669354|ref|NP_248159.1|  99 CIACGSCLG-CAALTLDNFTVGIDEDT-------CHLCASCIFRCPTN 138
                                   ********9.*9999999888888775.......************97 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   8.6e-05       0.1      11      49 ..      20      55 ..      17      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.6e-05
                        HTH_19 11 lgltqeelaerlgisrskisaiEngkkdvpsaelllkia 49
                                  +gl q+e+a+ ++ +rs  s++ +g+  +p+ e++l +a
  gi|15669354|ref|NP_248159.1| 20 KGLLQKEIAKIIKSDRSIVSHYLSGR--YPK-EKILNVA 55
                                  7899*********************7..576.4444444 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   3.1       2.1   2.5e+03       2       9 ..      99     106 ..      98     110 .. 0.75
   2 ?   13.8   1.8     7e-05     0.084       1      19 [.     124     142 ..     124     146 .] 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.1
                       Fer4_16   2 CgtCgkCa 9  
                                   C+ Cg C+
  gi|15669354|ref|NP_248159.1|  99 CIACGSCL 106
                                   88888885 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7e-05
                       Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                   +C+ C  C+  CPtn +k 
  gi|15669354|ref|NP_248159.1| 124 TCHLCASCIFRCPTNSLKF 142
                                   5**************9875 PP

>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.17     111     154 ..      19      62 ..      11      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                CobA_CobO_BtuR 111 lglldeeevlellkkkpeklelvlTGrnapeelleaADlvtemk 154
                                    + l ++e+ +++k+ ++ +   l+Gr+++e++l++A ++ em 
  gi|15669354|ref|NP_248159.1|  19 RKGLLQKEIAKIIKSDRSIVSHYLSGRYPKEKILNVAKIIEEMP 62 
                                   45566789******9999************************96 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   3.0     0.087     1e+02      37      44 ..      98     105 ..      65     110 .. 0.79
   2 ?    6.8  12.5    0.0086        10       2      51 ..      99     138 ..      98     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.087
                        Fer4_7  37 kClgCgaC 44 
                                   +C+ Cg+C
  gi|15669354|ref|NP_248159.1|  98 SCIACGSC 105
                                   56666655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0086
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                   Ci Cg C   C   a++ld++       +v id+++C  C +C+ +CPt+
  gi|15669354|ref|NP_248159.1|  99 CIACGSCL-GCA--ALTLDNF-------TVGIDEDTCHLCASCIFRCPTN 138
                                   99999998.566..7888776.......588*****************97 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.3     0.054        64       4      16 ..      95     107 ..      93     115 .. 0.86
   2 ?   11.3   1.1   0.00037      0.45       1      20 [.     118     137 ..     118     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.054
                       Fer4_15   4 DrdaCigcglCva 16 
                                   D++ Ci cg C+ 
  gi|15669354|ref|NP_248159.1|  95 DENSCIACGSCLG 107
                                   999********85 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00037
                       Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                   V +D+d+C  c+ C+ ++p+
  gi|15669354|ref|NP_248159.1| 118 VGIDEDTCHLCASCIFRCPT 137
                                   669************99996 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.7    0.0045       5.4       2      14 ..      95     107 ..      95     114 .. 0.86
   2 ?    8.4   2.1    0.0026       3.1       1      18 [.     120     137 ..     120     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0045
                       Fer4_13   2 DrdtCiacgaCve 14 
                                   D+++Ciacg+C  
  gi|15669354|ref|NP_248159.1|  95 DENSCIACGSCLG 107
                                   789********75 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0026
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   +D+dtC  c++C   +P 
  gi|15669354|ref|NP_248159.1| 120 IDEDTCHLCASCIFRCPT 137
                                   89************9996 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   3.9     0.088   1.1e+02      45      53 ..      98     106 ..      55     110 .. 0.78
   2 ?    4.2   3.1     0.055        66       2      15 ..      99     111 ..      98     119 .. 0.78
   3 ?    7.5   2.7    0.0049       5.8      44      59 ..     123     138 ..     117     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.088
                       Fer4_17  45 lCieCgeCe 53 
                                   +Ci Cg C 
  gi|15669354|ref|NP_248159.1|  98 SCIACGSCL 106
                                   566666664 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.055
                       Fer4_17   2 CiqCgyClpeCpsy 15 
                                   Ci Cg Cl  C  +
  gi|15669354|ref|NP_248159.1|  99 CIACGSCLG-CAAL 111
                                   999999999.8765 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0049
                       Fer4_17  44 slCieCgeCerkCPqg 59 
                                   ++C+ C  C  +CP +
  gi|15669354|ref|NP_248159.1| 123 DTCHLCASCIFRCPTN 138
                                   5799*********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 1170.78
//
Query:       gi|15669355|ref|NP_248160.1|  [L=355]
Description: formylmethanofuran dehydrogenase subunit FwdF [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-57  187.4  96.8    1.3e-08   34.3   4.4    8.3  8  Fer4      4Fe-4S binding domain
    4.6e-39  132.8  64.9    7.3e-12   45.7   5.0    5.3  5  Fer4_7    4Fe-4S dicluster domain
    2.5e-35  119.1  96.9    4.1e-06   26.6   4.0    8.5  8  Fer4_6    4Fe-4S binding domain
    2.7e-33  114.7  61.2    1.7e-05   25.6   1.1    8.2  8  Fer4_16   4Fe-4S double cluster binding domain
    5.6e-30  103.2  67.6    1.7e-07   31.3  10.3    6.9  7  Fer4_10   4Fe-4S dicluster domain
    1.3e-28   98.9  72.2    2.7e-07   30.6   9.5    6.0  6  Fer4_21   4Fe-4S dicluster domain
    4.6e-28   97.1  66.4    8.8e-08   32.2   7.6    6.1  7  Fer4_9    4Fe-4S dicluster domain
    1.5e-27   93.9  75.4    0.00066   19.6   3.2    8.5  8  Fer4_2    4Fe-4S binding domain
    8.9e-16   58.1  66.5    5.6e-05   23.5   8.1    5.9  5  Fer4_8    4Fe-4S dicluster domain
    2.3e-14   52.6  83.9      0.013   15.9   2.5    8.5  8  Fer4_4    4Fe-4S binding domain
    1.6e-11   44.5  75.5    0.00045   20.7  11.5    7.8  8  Fer4_17   4Fe-4S dicluster domain
    6.9e-05   23.3  80.7        1.2    9.8   2.6    8.3  7  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    0.00055   20.7 103.8       0.08   13.9   7.9    8.5  8  Fer4_3    4Fe-4S binding domain
    0.00075   20.3  71.0       0.13   13.2   1.3    8.2  9  Fer4_22   4Fe-4S dicluster domain
     0.0086   16.8  76.5        1.7    9.5   0.6   10.0  9  Fer4_15   4Fe-4S single cluster domain
  ------ inclusion threshold ------
        3.4    7.8  50.9        7.1    6.8   5.1    6.8  7  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   8.4   2.9e-10   3.3e-07       3      23 ..      28      48 ..      26      49 .. 0.95
   2 !   31.5   2.5   9.1e-11     1e-07       3      23 ..      68      88 ..      66      89 .. 0.94
   3 !   29.2   3.2   4.7e-10   5.2e-07       2      23 ..     111     132 ..     110     133 .. 0.93
   4 !   31.3   5.6     1e-10   1.2e-07       2      23 ..     150     171 ..     149     172 .. 0.94
   5 !   31.2   4.6   1.1e-10   1.2e-07       1      24 []     189     212 ..     189     212 .. 0.95
   6 !   25.8   5.3   5.6e-09   6.3e-06       2      24 .]     238     260 ..     237     260 .. 0.96
   7 !   18.9   7.4   8.4e-07   0.00094       2      23 ..     270     291 ..     269     292 .. 0.92
   8 !   34.3   4.4   1.1e-11   1.3e-08       1      24 []     306     329 ..     306     329 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.9e-10
                                  EETTTSSS-THHHHHSTTTEE CS
                          Fer4  3 ideekCigCGaCvevCPvgAI 23
                                  ++ e+C+gCG+C+++CPv+AI
  gi|15669355|ref|NP_248160.1| 28 WNDELCVGCGICADICPVNAI 48
                                  899*****************9 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 9.1e-11
                                  EETTTSSS-THHHHHSTTTEE CS
                          Fer4  3 ideekCigCGaCvevCPvgAI 23
                                  id++ C+ CG C+++CP++A+
  gi|15669355|ref|NP_248160.1| 68 IDKDVCVLCGMCASACPFDAL 88
                                  9*******************8 PP

  == domain 3  score: 29.2 bits;  conditional E-value: 4.7e-10
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                   ++ ++kC+ C +C++vCP gAI
  gi|15669355|ref|NP_248160.1| 111 KVYQDKCVLCEQCEMVCPQGAI 132
                                   7899*****************9 PP

  == domain 4  score: 31.3 bits;  conditional E-value: 1e-10
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                    i++ekC+ CG+C+e CP +AI
  gi|15669355|ref|NP_248160.1| 150 NINKEKCVLCGICAEYCPADAI 171
                                   69*******************9 PP

  == domain 5  score: 31.2 bits;  conditional E-value: 1.1e-10
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                   +++d++kC++C+ C+ vCP++AI+
  gi|15669355|ref|NP_248160.1| 189 IEVDKDKCVFCKVCEFVCPHDAIE 212
                                   589********************6 PP

  == domain 6  score: 25.8 bits;  conditional E-value: 5.6e-09
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   vid++ C+ CG C+ +CP +AI+
  gi|15669355|ref|NP_248160.1| 238 VIDKDACVTCGWCAFICPAEAIE 260
                                   8*********************6 PP

  == domain 7  score: 18.9 bits;  conditional E-value: 8.4e-07
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                   +id + C +CGaC+++CP  A+
  gi|15669355|ref|NP_248160.1| 270 IIDVNACNACGACISICPCSAL 291
                                   79****************9987 PP

  == domain 8  score: 34.3 bits;  conditional E-value: 1.1e-11
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                   +++++++C+ CGaC+++CPv+AI+
  gi|15669355|ref|NP_248160.1| 306 IIVNQNLCVLCGACAKACPVNAIK 329
                                   689********************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   5.0   6.6e-15   7.3e-12       2      52 .]      33      87 ..      32      87 .. 0.89
   2 !   35.3  11.7   1.2e-11   1.3e-08       2      52 .]      73     131 ..      72     131 .. 0.83
   3 !   41.4   9.4   1.5e-13   1.6e-10       1      52 []     155     210 ..     155     210 .. 0.88
   4 !   14.9   3.2   2.7e-05     0.031      18      52 .]     225     258 ..     215     267 .. 0.68
   5 !   34.9  13.9   1.5e-11   1.7e-08       1      52 []     275     327 ..     275     327 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 6.6e-15
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgt....ekveidpekClgCgaCvavCPtga 52
                                  C+gCg C++ Cpv+ai + +    ++     +k++id + C+ Cg+C+++CP++a
  gi|15669355|ref|NP_248160.1| 33 CVGCGICADICPVNAIAMGPLGAIAKGdiiaPKLDIDKDVCVLCGMCASACPFDA 87
                                  *******************986665434677999******************997 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 1.2e-11
                        Fer4_7   2 CigCgaCvaaCpvkaield........eeenekgtekveidpekClgCgaCvavCPtga 52 
                                   C+ Cg C++aCp +a++l+        +e ++k ++++++ ++kC+ C++C+ vCP ga
  gi|15669355|ref|NP_248160.1|  73 CVLCGMCASACPFDALDLKingksikeDERYPKIKRDIKVYQDKCVLCEQCEMVCPQGA 131
                                   *****************987775554334444555889999***************997 PP

  == domain 3  score: 41.4 bits;  conditional E-value: 1.5e-13
                        Fer4_7   1 rCigCgaCvaaCpvkaield....eeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C+ Cg C+++Cp++ai+l+      +n+k++ ++e+d +kC++C++C+ vCP++a
  gi|15669355|ref|NP_248160.1| 155 KCVLCGICAEYCPADAINLKynypTPSNPKPITDIEVDKDKCVFCKVCEFVCPHDA 210
                                   7*****************99444335677788999******************987 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 2.7e-05
                        Fer4_7  18 eldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                      +  +e+ t k++id + C++Cg C+  CP++a
  gi|15669355|ref|NP_248160.1| 225 PQAK-LYEDITGKTVIDKDACVTCGWCAFICPAEA 258
                                   4433.355666778888888888888888888765 PP

  == domain 5  score: 34.9 bits;  conditional E-value: 1.5e-11
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt.ekveidpekClgCgaCvavCPtga 52 
                                   +C  CgaC + Cp +a+e+++ ++++++ +++ ++++ C+ CgaC+++CP++a
  gi|15669355|ref|NP_248160.1| 275 ACNACGACISICPCSALEFPKPKDKAEKvPRIIVNQNLCVLCGACAKACPVNA 327
                                   5******************988776654499999*****************97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   4.5   1.7e-08   1.9e-05       4      24 .]      28      48 ..      28      48 .. 0.97
   2 !   22.6   2.6   6.6e-08   7.4e-05       4      24 .]      68      88 ..      65      88 .. 0.93
   3 !   20.6   2.6   2.9e-07   0.00033       6      24 .]     114     132 ..     110     132 .. 0.93
   4 !   22.2   4.4   9.5e-08   0.00011       2      24 .]     149     171 ..     148     171 .. 0.94
   5 !   19.3   4.8   7.7e-07   0.00086       2      24 .]     189     211 ..     189     211 .. 0.96
   6 !   18.6   3.7   1.2e-06    0.0014       3      24 .]     238     259 ..     236     259 .. 0.95
   7 !   16.2   7.3   7.3e-06    0.0082       4      24 .]     271     291 ..     269     291 .. 0.92
   8 !   26.6   4.0   3.7e-09   4.1e-06       3      24 .]     307     328 ..     305     328 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.7e-08
                        Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                  +++++C+gCg C+++CP +ai
  gi|15669355|ref|NP_248160.1| 28 WNDELCVGCGICADICPVNAI 48
                                  899****************98 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 6.6e-08
                        Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                  id+d C+ Cg C+++CP++a+
  gi|15669355|ref|NP_248160.1| 68 IDKDVCVLCGMCASACPFDAL 88
                                  8*****************996 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 2.9e-07
                        Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                   +dkC+ C+ C++vCP gai
  gi|15669355|ref|NP_248160.1| 114 QDKCVLCEQCEMVCPQGAI 132
                                   69*************9998 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 9.5e-08
                        Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                   + i+++kC+ Cg C+  CP++ai
  gi|15669355|ref|NP_248160.1| 149 ININKEKCVLCGICAEYCPADAI 171
                                   679******************98 PP

  == domain 5  score: 19.3 bits;  conditional E-value: 7.7e-07
                        Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                   +e+d+dkC+ C  C+ vCP++ai
  gi|15669355|ref|NP_248160.1| 189 IEVDKDKCVFCKVCEFVCPHDAI 211
                                   79*******************98 PP

  == domain 6  score: 18.6 bits;  conditional E-value: 1.2e-06
                        Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                   +id+d+C+ Cg C+ +CP+ ai
  gi|15669355|ref|NP_248160.1| 238 VIDKDACVTCGWCAFICPAEAI 259
                                   79*****************998 PP

  == domain 7  score: 16.2 bits;  conditional E-value: 7.3e-06
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   id ++C+ Cg+C+++CP  a+
  gi|15669355|ref|NP_248160.1| 271 IDVNACNACGACISICPCSAL 291
                                   899**************8875 PP

  == domain 8  score: 26.6 bits;  conditional E-value: 3.7e-09
                        Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                    +++++C+ Cg+C+++CP +ai
  gi|15669355|ref|NP_248160.1| 307 IVNQNLCVLCGACAKACPVNAI 328
                                   699*****************98 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.5     3e-07   0.00034       2      20 ..      33      51 ..      32      70 .. 0.85
   2 !   17.9   0.3     4e-06    0.0045       2      26 ..      73      98 ..      72     115 .. 0.70
   3 !   19.6   0.9   1.2e-06    0.0013       1      29 [.     116     142 ..     116     154 .. 0.81
   4 !   19.7   0.9   1.1e-06    0.0012       1      22 [.     155     176 ..     155     194 .. 0.77
   5 !   13.7   3.9   8.3e-05     0.093       1      19 [.     195     213 ..     195     241 .. 0.80
   6 !   18.5   1.2   2.5e-06    0.0028       2      22 ..     244     264 ..     243     271 .. 0.87
   7 !   14.4   4.7   4.9e-05     0.054       2      22 ..     276     296 ..     275     310 .. 0.80
   8 !   25.6   1.1   1.5e-08   1.7e-05       2      32 ..     313     342 ..     312     353 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3e-07
                       Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                  C++Cg Ca++CP+nai + 
  gi|15669355|ref|NP_248160.1| 33 CVGCGICADICPVNAIAMG 51
                                  ****************876 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 4e-06
                       Fer4_16  2 CgtCgkCaevCPtnaikek.kekeie 26
                                  C+ Cg Ca++CP +a++ k + k+i+
  gi|15669355|ref|NP_248160.1| 73 CVLCGMCASACPFDALDLKiNGKSIK 98
                                  ****************9993333333 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 1.2e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeieare 29 
                                   +C+ C++C +vCP++ai  +  +e++ re
  gi|15669355|ref|NP_248160.1| 116 KCVLCEQCEMVCPQGAIVVE--RELAERE 142
                                   5****************999..5555554 PP

  == domain 4  score: 19.7 bits;  conditional E-value: 1.1e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikekke 22 
                                   +C+ Cg Cae CP++ai+ k +
  gi|15669355|ref|NP_248160.1| 155 KCVLCGICAEYCPADAINLKYN 176
                                   5*****************9933 PP

  == domain 5  score: 13.7 bits;  conditional E-value: 8.3e-05
                       Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                   +C+ C+ C  vCP++ai+ 
  gi|15669355|ref|NP_248160.1| 195 KCVFCKVCEFVCPHDAIEV 213
                                   59***************85 PP

  == domain 6  score: 18.5 bits;  conditional E-value: 2.5e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                   C+tCg Ca +CP++ai+ +k 
  gi|15669355|ref|NP_248160.1| 244 CVTCGWCAFICPAEAIEVEKP 264
                                   ****************98854 PP

  == domain 7  score: 14.4 bits;  conditional E-value: 4.9e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                   C  Cg+C+++CP +a++ +k 
  gi|15669355|ref|NP_248160.1| 276 CNACGACISICPCSALEFPKP 296
                                   *****************9832 PP

  == domain 8  score: 25.6 bits;  conditional E-value: 1.5e-08
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecis 32 
                                   C+ Cg+Ca++CP+naik k ++ei+ +++ +
  gi|15669355|ref|NP_248160.1| 313 CVLCGACAKACPVNAIKVK-RTEINFEREPK 342
                                   *****************99.67777666555 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.3   6.3e-06    0.0071       5      33 ..      29      57 ..      26      67 .. 0.76
   2 !   26.8  10.7   3.8e-09   4.2e-06       3      56 .]      67     128 ..      65     128 .. 0.78
   3 !   27.8  10.9   1.8e-09     2e-06       5      56 .]     113     167 ..     109     167 .. 0.94
   4 !   16.6   2.4   5.8e-06    0.0065       2      23 ..     149     170 ..     148     182 .. 0.82
   5 !   10.6   6.8   0.00044      0.49       2      23 ..     189     210 ..     188     234 .. 0.79
   6 !   31.3  10.3   1.5e-10   1.7e-07       2      56 .]     237     287 ..     236     287 .. 0.93
   7 !   24.0   0.8   2.9e-08   3.2e-05       2      38 ..     306     342 ..     305     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.3e-06
                       Fer4_10  5 dddtCirCgkCvkaCPadltsvgakgeas 33
                                  +d+ C++Cg C + CP+++ ++g  g++ 
  gi|15669355|ref|NP_248160.1| 29 NDELCVGCGICADICPVNAIAMGPLGAIA 57
                                  6899*************876665555554 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 3.8e-09
                       Fer4_10   3 vidddtCirCgkCvkaCPadl..........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    id+d C+ Cg C +aCP+d+          ++++ +++++++ +v    +kC  c++C  +CP
  gi|15669355|ref|NP_248160.1|  67 DIDKDVCVLCGMCASACPFDAldlkingksiKEDERYPKIKRDIKV--YQDKCVLCEQCEMVCP 128
                                   599***********************99754444444444444444..459************9 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 1.8e-09
                       Fer4_10   5 dddtCirCgkCvkaCPadl...tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    +d+C+ C++C  +CP+ +   ++  a+ e+  +++++++ ekC  cg C+e CP
  gi|15669355|ref|NP_248160.1| 113 YQDKCVLCEQCEMVCPQGAivvERELAEREKFVIGEININKEKCVLCGICAEYCP 167
                                   579**************99999999*****************************9 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 5.8e-06
                       Fer4_10   2 vvidddtCirCgkCvkaCPadl 23 
                                   + i++++C+ Cg C + CPad+
  gi|15669355|ref|NP_248160.1| 149 ININKEKCVLCGICAEYCPADA 170
                                   6799****************54 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00044
                       Fer4_10   2 vvidddtCirCgkCvkaCPadl 23 
                                   +++d+d+C+ C+ C  +CP d+
  gi|15669355|ref|NP_248160.1| 189 IEVDKDKCVFCKVCEFVCPHDA 210
                                   5789***************955 PP

  == domain 6  score: 31.3 bits;  conditional E-value: 1.5e-10
                       Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    vid+d C+ Cg C   CPa       + e+  +++  ++v +C +cgaC+++CP
  gi|15669355|ref|NP_248160.1| 237 TVIDKDACVTCGWCAFICPA----EAIEVEKPFKGELIIDVNACNACGACISICP 287
                                   69******************....888888888889999***************9 PP

  == domain 7  score: 24.0 bits;  conditional E-value: 2.9e-08
                       Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeav 38 
                                   ++++++ C+ Cg+C kaCP+++ +v+ ++++ e e++
  gi|15669355|ref|NP_248160.1| 306 IIVNQNLCVLCGACAKACPVNAIKVKRTEINFEREPK 342
                                   68899***************88887777777766655 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   2.4   4.1e-08   4.6e-05      32      59 .]      24      50 ..      15      50 .. 0.85
   2 !   30.6   9.5   2.4e-10   2.7e-07       3      57 ..      68     132 ..      66     134 .. 0.73
   3 !   29.4  11.5   5.7e-10   6.4e-07       2      58 ..     150     212 ..     149     213 .. 0.79
   4 !   23.8  14.1   3.2e-08   3.5e-05       2      53 ..     238     288 ..     237     293 .. 0.81
   5 !   16.5  17.4     6e-06    0.0067       3      58 ..     271     329 ..     270     330 .. 0.77
   6 !   14.5   3.3   2.7e-05      0.03       3      28 ..     308     330 ..     305     340 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.1e-08
                       Fer4_21 32 tvlkvvedeCvGCnlCssvCPvedciem 59
                                  + l   ++ CvGC +C+++CPv ++i+m
  gi|15669355|ref|NP_248160.1| 24 RELCWNDELCVGCGICADICPV-NAIAM 50
                                  455567999************9.99998 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 2.4e-10
                       Fer4_21   3 idedkCigCgkCliaCedtshqai....eidaktvl.......kvvedeCvGCnlCssvCPvedci 57 
                                   id+d C+ Cg C+ aC+  + +      +i++++++       kv +d+Cv C+ C  vCP +++i
  gi|15669355|ref|NP_248160.1|  68 IDKDVCVLCGMCASACPFDALDLKingkSIKEDERYpkikrdiKVYQDKCVLCEQCEMVCP-QGAI 132
                                   9****************65555424555222222224444555999***************.6887 PP

  == domain 3  score: 29.4 bits;  conditional E-value: 5.7e-10
                       Fer4_21   2 ridedkCigCgkCliaCedtshqai..........eidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                   +i+++kC+ Cg C+  C+    +ai          + ++ t ++v +d+Cv C++C  vCP +d+ie
  gi|15669355|ref|NP_248160.1| 150 NINKEKCVLCGICAEYCP---ADAInlkynyptpsNPKPITDIEVDKDKCVFCKVCEFVCP-HDAIE 212
                                   599***************...5888554555543333344577999***************.69997 PP

  == domain 4  score: 23.8 bits;  conditional E-value: 3.2e-08
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieidakt..vlkvvedeCvGCnlCssvCPv 53 
                                   +id+d C+ Cg C+  C+    +aie+++     l +  + C +C  C+s+CP 
  gi|15669355|ref|NP_248160.1| 238 VIDKDACVTCGWCAFICP---AEAIEVEKPFkgELIIDVNACNACGACISICPC 288
                                   79****************...6999887654014445579*************6 PP

  == domain 5  score: 16.5 bits;  conditional E-value: 6e-06
                       Fer4_21   3 idedkCigCgkCliaCedtshqaie.idakt...vlkvvedeCvGCnlCssvCPvedcie 58 
                                   id + C  Cg C+  C+ ++ +  + +d+++   ++ v ++ Cv C  C++ CPv ++i+
  gi|15669355|ref|NP_248160.1| 271 IDVNACNACGACISICPCSALEFPKpKDKAEkvpRIIVNQNLCVLCGACAKACPV-NAIK 329
                                   999**************877777752233332224466799*************9.8887 PP

  == domain 6  score: 14.5 bits;  conditional E-value: 2.7e-05
                       Fer4_21   3 idedkCigCgkCliaCedtshqaiei 28 
                                   ++++ C+ Cg C++aC+   ++ai++
  gi|15669355|ref|NP_248160.1| 308 VNQNLCVLCGACAKACP---VNAIKV 330
                                   56677777777777777...455554 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.4   5.7e-07   0.00063      22      51 .]      19      48 ..      10      48 .. 0.76
   2 !   32.2   7.6   7.9e-11   8.8e-08       2      51 .]      73     132 ..      71     132 .. 0.91
   3 !   15.8   2.0   1.1e-05     0.012      33      51 .]     151     171 ..     134     171 .. 0.74
   4 !   28.6   8.6     1e-09   1.1e-06       1      51 []     155     211 ..     155     211 .. 0.91
   5 !   12.8   4.9   9.1e-05       0.1       9      51 .]     216     259 ..     213     259 .. 0.69
   6 !   19.2  15.0     9e-07     0.001       1      50 [.     243     290 ..     243     291 .. 0.87
   7 !   23.9  14.8   3.2e-08   3.6e-05       1      51 []     275     328 ..     275     328 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.7e-07
                        Fer4_9 22 aerkarlraaseeaCigCgaCveaCpkgai 51
                                  +e + r  ++++e C+gCg C+++Cp +ai
  gi|15669355|ref|NP_248160.1| 19 GEVEKRELCWNDELCVGCGICADICPVNAI 48
                                  4444455577889*************9987 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 7.9e-11
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase..........eaCigCgaCveaCpkgai 51 
                                   C+ Cg C +aCp+++   + +++ ++ +++            ++C+ C++C+ +Cp+gai
  gi|15669355|ref|NP_248160.1|  73 CVLCGMCASACPFDALDLKINGKSIKEDERYPkikrdikvyqDKCVLCEQCEMVCPQGAI 132
                                   ****************9999999998765544999***********************98 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1.1e-05
                        Fer4_9  33 e..eaCigCgaCveaCpkgai 51 
                                      e+C+ Cg C+e Cp +ai
  gi|15669355|ref|NP_248160.1| 151 InkEKCVLCGICAEYCPADAI 171
                                   03369************9987 PP

  == domain 4  score: 28.6 bits;  conditional E-value: 1e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase......eaCigCgaCveaCpkgai 51 
                                   kC+ Cg C e Cpa++++ + +  + ++ +         ++C++C+ C+ +Cp++ai
  gi|15669355|ref|NP_248160.1| 155 KCVLCGICAEYCPADAINLKYNYPTPSNPKPITdievdkDKCVFCKVCEFVCPHDAI 211
                                   7*****************9999999887655448999999**************997 PP

  == domain 5  score: 12.8 bits;  conditional E-value: 9.1e-05
                        Fer4_9   9 veaCpagvvvedaaerkarlraase..eaCigCgaCveaCpkgai 51 
                                    + Cp++  +++a+ +++   ++    +aC++Cg C+ +Cp +ai
  gi|15669355|ref|NP_248160.1| 216 YK-CPMMKRIPQAKLYEDITGKTVIdkDACVTCGWCAFICPAEAI 259
                                   44.77776666666555554433225679************9987 PP

  == domain 6  score: 19.2 bits;  conditional E-value: 9e-07
                        Fer4_9   1 kCtgCgaCveaCpagvv.vedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   +C+ Cg C   Cpa+++ ve+ ++++  ++    +aC  CgaC+ +Cp  a
  gi|15669355|ref|NP_248160.1| 243 ACVTCGWCAFICPAEAIeVEKPFKGELIIDV---NACNACGACISICPCSA 290
                                   6****************77788888888766...47************876 PP

  == domain 7  score: 23.9 bits;  conditional E-value: 3.2e-08
                        Fer4_9   1 kCtgCgaCveaCpagvv...vedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   +C+ CgaC++ Cp  +    +++++++k+   + +++ C+ CgaC++aCp +ai
  gi|15669355|ref|NP_248160.1| 275 ACNACGACISICPCSALefpKPKDKAEKVPRIIVNQNLCVLCGACAKACPVNAI 328
                                   6***********77766222555555555555566689************9987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   5.1   1.1e-05     0.012       5      21 ..      28      44 ..      24      45 .. 0.87
   2 !   19.5   2.0   6.3e-07   0.00071       4      21 ..      67      84 ..      64      85 .. 0.89
   3 !   15.7   1.7   1.1e-05     0.012       3      22 .]     110     129 ..     108     129 .. 0.89
   4 !   18.7   2.0   1.2e-06    0.0013       5      22 .]     151     168 ..     149     168 .. 0.95
   5 !   15.2   2.5   1.5e-05     0.017       3      22 .]     189     208 ..     187     208 .. 0.94
   6 !   12.8   2.7   8.7e-05     0.098       4      22 .]     238     256 ..     235     256 .. 0.92
   7 !   19.0   2.6   9.1e-07     0.001       4      21 ..     270     287 ..     267     287 .. 0.93
   8 !   19.6   3.2   5.9e-07   0.00066       1      21 [.     304     324 ..     304     325 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                        Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                   + + C+gCg+C + CP
  gi|15669355|ref|NP_248160.1| 28 WNDELCVGCGICADICP 44
                                  57789************ PP

  == domain 2  score: 19.5 bits;  conditional E-value: 6.3e-07
                        Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                   +d d C+ Cg C saCP
  gi|15669355|ref|NP_248160.1| 67 DIDKDVCVLCGMCASACP 84
                                  589*************** PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.1e-05
                        Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                   ++v  d+C+ C+ C  +CP+
  gi|15669355|ref|NP_248160.1| 110 IKVYQDKCVLCEQCEMVCPQ 129
                                   67889**************6 PP

  == domain 4  score: 18.7 bits;  conditional E-value: 1.2e-06
                        Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                   ++ ++C+ Cg+C   CPa
  gi|15669355|ref|NP_248160.1| 151 INKEKCVLCGICAEYCPA 168
                                   689**************8 PP

  == domain 5  score: 15.2 bits;  conditional E-value: 1.5e-05
                        Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                   ++vd d+C+ C+ C  +CP+
  gi|15669355|ref|NP_248160.1| 189 IEVDKDKCVFCKVCEFVCPH 208
                                   689****************7 PP

  == domain 6  score: 12.8 bits;  conditional E-value: 8.7e-05
                        Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                   v+d d+C+ Cg C   CPa
  gi|15669355|ref|NP_248160.1| 238 VIDKDACVTCGWCAFICPA 256
                                   79****************8 PP

  == domain 7  score: 19.0 bits;  conditional E-value: 9.1e-07
                        Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                                    +d ++C++CgaC+s CP
  gi|15669355|ref|NP_248160.1| 270 IIDVNACNACGACISICP 287
                                   5899*************9 PP

  == domain 8  score: 19.6 bits;  conditional E-value: 5.9e-07
                        Fer4_2   1 apvvvdtdrCigCgaCvsaCP 21 
                                   +++ v+ + C+ CgaC +aCP
  gi|15669355|ref|NP_248160.1| 304 PRIIVNQNLCVLCGACAKACP 324
                                   57899**************** PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   9.4   2.4e-06    0.0027       5      63 ..      33      85 ..      29      87 .. 0.84
   2 !   23.5   8.1     5e-08   5.6e-05       4      64 ..      72     130 ..      69     131 .. 0.63
   3 !   18.3   8.1     2e-06    0.0023       3      64 ..     154     209 ..     152     211 .. 0.73
   4 !    8.0  14.2    0.0036         4       3      63 ..     194     256 ..     193     259 .. 0.70
   5 !   20.1  13.5   5.7e-07   0.00063       2      64 ..     273     326 ..     272     327 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.4e-06
                        Fer4_8  5 CieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                  C++Cg C + Cpv           a+g+ ++ + + ++       + C+ cg+C+++Cp 
  gi|15669355|ref|NP_248160.1| 33 CVGCGICADICPVNAIAMgPLGAIAKGDIIAPKLDIDK-------DVCVLCGMCASACPF 85
                                  ************88777758888899998886666666.......89************6 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 5e-08
                        Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaae.dvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                    C+ Cg+C saCp+     k + ++ +e +   + +++    + + ++C+ c++C+ vCp+g
  gi|15669355|ref|NP_248160.1|  72 VCVLCGMCASACPFDALDLKINGKSIKEDERyPKIKRDI---KVYQDKCVLCEQCEMVCPQG 130
                                   6************53333233222222222221233333...44689*************87 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 2e-06
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaae.dvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   ekC+ Cg C + Cp+     k ++ ++ + +   + e ++       ++C+ c+ C+ vCp +
  gi|15669355|ref|NP_248160.1| 154 EKCVLCGICAEYCPADAINLKYNYPTPSNPKPiTDIEVDK-------DKCVFCKVCEFVCPHD 209
                                   69************65555555555555555521444455.......8*************75 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0036
                        Fer4_8   3 ekCieCgaCqsaCp......vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                   +kC+ C  C+  Cp      ++ +  +++  ++ +  ed   + v       ++C+tcg C+  Cp 
  gi|15669355|ref|NP_248160.1| 194 DKCVFCKVCEFVCPhdaievICYKCPMMKRIPQAKLYEDITGKTV----IDKDACVTCGWCAFICPA 256
                                   69********99988888763333335555555555553444444....44689************7 PP

  == domain 5  score: 20.1 bits;  conditional E-value: 5.7e-07
                        Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   +++C+ CgaC s Cp    +   ++d+ +++      +q        + C+ cgaC+++Cpv+
  gi|15669355|ref|NP_248160.1| 273 VNACNACGACISICPCSALEFPKPKDKAEKVPR-IIVNQ--------NLCVLCGACAKACPVN 326
                                   789************666665665666666555.55555........59************97 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.5   1.2e-05     0.013       2      17 .]      31      46 ..      30      46 .. 0.91
   2 !   14.4   2.7   3.6e-05      0.04       1      16 [.      70      85 ..      70      86 .. 0.91
   3 !   15.8   4.6   1.3e-05     0.014       1      17 []     114     130 ..     114     130 .. 0.95
   4 !   12.5   1.4   0.00015      0.17       1      16 [.     153     168 ..     153     175 .. 0.93
   5 ?    2.3   8.5      0.28   3.1e+02       1      15 [.     193     207 ..     193     221 .. 0.92
   6 ?    5.5   2.7     0.026        29       1      16 [.     241     256 ..     241     258 .. 0.91
   7 !   13.5   4.9     7e-05     0.079       2      15 ..     274     287 ..     274     299 .. 0.91
   8 !   14.5   2.5   3.4e-05     0.038       1      17 []     310     326 ..     310     326 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  e C+gCg C ++CP++
  gi|15669355|ref|NP_248160.1| 31 ELCVGCGICADICPVN 46
                                  67************75 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.6e-05
                        Fer4_4  1 qerCigCgsCvaaCPq 16
                                  ++ C+ Cg C +aCP+
  gi|15669355|ref|NP_248160.1| 70 KDVCVLCGMCASACPF 85
                                  689************7 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1.3e-05
                        Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                   q++C+ C +C+ +CPqg
  gi|15669355|ref|NP_248160.1| 114 QDKCVLCEQCEMVCPQG 130
                                   79*************96 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00015
                        Fer4_4   1 qerCigCgsCvaaCPq 16 
                                   +e+C+ Cg C  +CP 
  gi|15669355|ref|NP_248160.1| 153 KEKCVLCGICAEYCPA 168
                                   69*************6 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.28
                        Fer4_4   1 qerCigCgsCvaaCP 15 
                                   +++C+ C++C+ +CP
  gi|15669355|ref|NP_248160.1| 193 KDKCVFCKVCEFVCP 207
                                   699***********9 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.026
                        Fer4_4   1 qerCigCgsCvaaCPq 16 
                                   ++ C+ Cg C  +CP 
  gi|15669355|ref|NP_248160.1| 241 KDACVTCGWCAFICPA 256
                                   689***********96 PP

  == domain 7  score: 13.5 bits;  conditional E-value: 7e-05
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   + C+ Cg+C+++CP
  gi|15669355|ref|NP_248160.1| 274 NACNACGACISICP 287
                                   57***********9 PP

  == domain 8  score: 14.5 bits;  conditional E-value: 3.4e-05
                        Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                   q+ C+ Cg+C  aCP++
  gi|15669355|ref|NP_248160.1| 310 QNLCVLCGACAKACPVN 326
                                   688************75 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   2.5    0.0015       1.7      44      58 ..      31      45 ..      11      48 .. 0.72
   2 !   16.3   8.7   9.4e-06     0.011       2      58 ..      33      85 ..      32      88 .. 0.88
   3 !   20.7  11.5     4e-07   0.00045       2      59 ..      73     130 ..      72     131 .. 0.76
   4 !   12.4   2.3   0.00016      0.18      42      59 ..     152     169 ..     135     172 .. 0.82
   5 !   12.6  11.1   0.00014      0.15       1      59 [.     155     209 ..     155     211 .. 0.75
   6 !    8.7  14.2    0.0022       2.5       1      59 [.     195     257 ..     195     258 .. 0.70
   7 ?    3.0   6.5      0.13   1.5e+02      45      57 ..     275     287 ..     268     290 .. 0.67
   8 ?    6.6  16.2      0.01        11       1      58 [.     275     325 ..     275     328 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                       Fer4_17 44 slCieCgeCerkCPq 58
                                  +lC++Cg C+  CP 
  gi|15669355|ref|NP_248160.1| 31 ELCVGCGICADICPV 45
                                  567777777777774 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 9.4e-06
                       Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58
                                  C +Cg C++ Cp +++       +l a++ g++ + + +   + C+ Cg+C+++CP 
  gi|15669355|ref|NP_248160.1| 33 CVGCGICADICPVNAIAMG----PLGAIAKGDIIAPKLDIDKDVCVLCGMCASACPF 85
                                  **************99766....8888777888887888899**************6 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 4e-07
                       Fer4_17   2 CiqCgyClpeCpsyeaydn.epkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                   C  Cg+C+ +Cp+ +   + + k++ ++ ++ ++++   + + ++C+ C++Ce++CPqg
  gi|15669355|ref|NP_248160.1|  73 CVLCGMCASACPFDALDLKiNGKSIKEDERYPKIKRD-IKVYQDKCVLCEQCEMVCPQG 130
                                   99**********9888544266777777555444332.346889*************97 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00016
                       Fer4_17  42 kaslCieCgeCerkCPqg 59 
                                   + ++C+ Cg C+++CP++
  gi|15669355|ref|NP_248160.1| 152 NKEKCVLCGICAEYCPAD 169
                                   6689************86 PP

  == domain 5  score: 12.6 bits;  conditional E-value: 0.00014
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepk.kllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                   +C  Cg C++ Cp  +++ +++  ++ +   ++++     e   ++C+ C+ Ce +CP++
  gi|15669355|ref|NP_248160.1| 155 KCVLCGICAEYCPADAINLKYNYpTPSNPKPITDI-----EVDKDKCVFCKVCEFVCPHD 209
                                   6*************999998666223333222333.....346799************97 PP

  == domain 6  score: 8.7 bits;  conditional E-value: 0.0022
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkk.llraakl.glleeaekeeka..slCieCgeCerkCPqg 59 
                                   +C  C+ C+ +Cp  ++   + k  +++++   +l e++  ++++  + C++Cg C+  CP++
  gi|15669355|ref|NP_248160.1| 195 KCVFCKVCEFVCPHDAIEVICYKCpMMKRIPQaKLYEDITGKTVIdkDACVTCGWCAFICPAE 257
                                   6999*********988866666651444443324555555555443399************85 PP

  == domain 7  score: 3.0 bits;  conditional E-value: 0.13
                       Fer4_17  45 lCieCgeCerkCP 57 
                                    C+ Cg C + CP
  gi|15669355|ref|NP_248160.1| 275 ACNACGACISICP 287
                                   5666666666665 PP

  == domain 8  score: 6.6 bits;  conditional E-value: 0.01
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                   +C+ Cg+C+  Cp  +    +pk  ++++   +++        +lC+ Cg C+++CP 
  gi|15669355|ref|NP_248160.1| 275 ACNACGACISICPCSALEFPKPKDKAEKVPRIIVN-------QNLCVLCGACAKACPV 325
                                   5************8888666777777775554333.......38*************6 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   3.0    0.0026       2.9       2      17 ..      30      44 ..      29      46 .. 0.90
   2 !    9.6   2.8    0.0012       1.3       1      17 [.      68      84 ..      68      89 .. 0.97
   3 !    7.1   1.6    0.0071       7.9       3      18 ..     114     129 ..     112     130 .. 0.91
   4 !    9.8   2.6     0.001       1.2       1      17 [.     151     167 ..     151     169 .. 0.94
   5 !    8.4   2.8    0.0028       3.1       1      17 [.     191     207 ..     191     209 .. 0.95
   6 !    7.8   4.0    0.0042       4.7       1      17 [.     239     255 ..     239     257 .. 0.95
   7 ?    6.4  17.4     0.011        13       1      58 []     271     330 ..     271     330 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0026
                       Fer4_13  2 DrdtCiacgaCvelaP 17
                                  D + C++cg+C++++P
  gi|15669355|ref|NP_248160.1| 30 D-ELCVGCGICADICP 44
                                  3.88***********9 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0012
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  +D+d C+ cg C++++P
  gi|15669355|ref|NP_248160.1| 68 IDKDVCVLCGMCASACP 84
                                  8***************9 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0071
                       Fer4_13   3 rdtCiacgaCvelaPd 18 
                                   +d+C+ c++C +++P+
  gi|15669355|ref|NP_248160.1| 114 QDKCVLCEQCEMVCPQ 129
                                   69*************6 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.001
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   +++++C+ cg+C+e +P
  gi|15669355|ref|NP_248160.1| 151 INKEKCVLCGICAEYCP 167
                                   79*************** PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0028
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   VD+d+C+ c++C  ++P
  gi|15669355|ref|NP_248160.1| 191 VDKDKCVFCKVCEFVCP 207
                                   9***************9 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0042
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   +D+d C+ cg C+ ++P
  gi|15669355|ref|NP_248160.1| 239 IDKDACVTCGWCAFICP 255
                                   8**************** PP

  == domain 7  score: 6.4 bits;  conditional E-value: 0.011
                       Fer4_13   1 VDrdtCiacgaCvelaP.dvFee.ddeggasvvaeqptseeekadaeeAadaCPvesIgv 58 
                                   +D + C acgaC +++P    e  +++++a  v++  +++ +  ++ + a+aCPv++I+v
  gi|15669355|ref|NP_248160.1| 271 IDVNACNACGACISICPcSALEFpKPKDKAEKVPRIIVNQNLCVLCGACAKACPVNAIKV 330
                                   68899************434554467899*****************************97 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   5.8   0.00069      0.77       1      15 []      33      47 ..      33      47 .. 0.98
   2 !    9.2   5.5    0.0022       2.5       1      15 []      73      87 ..      73      87 .. 0.96
   3 !   10.8   6.2   0.00069      0.77       1      15 []     117     131 ..     117     131 .. 0.98
   4 ?    7.1   4.5     0.011        12       1      15 []     156     170 ..     156     170 .. 0.94
   5 ?    5.8   4.8     0.029        32       1      15 []     196     210 ..     196     210 .. 0.96
   6 ?    3.2   4.3      0.19   2.1e+02       1      12 [.     244     255 ..     244     258 .. 0.90
   7 ?    4.3   9.0     0.085        95       1      14 [.     276     289 ..     276     290 .. 0.89
   8 !   13.9   7.9   7.2e-05      0.08       1      15 []     313     327 ..     313     327 .. 0.98

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00069
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gCg C + CPv+A
  gi|15669355|ref|NP_248160.1| 33 CVGCGICADICPVNA 47
                                  *************99 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0022
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ Cg C  +CP +A
  gi|15669355|ref|NP_248160.1| 73 CVLCGMCASACPFDA 87
                                  ************998 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00069
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ C++C+ vCP gA
  gi|15669355|ref|NP_248160.1| 117 CVLCEQCEMVCPQGA 131
                                   *************99 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.011
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ Cg C e CP +A
  gi|15669355|ref|NP_248160.1| 156 CVLCGICAEYCPADA 170
                                   ************887 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.029
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ C  C+ vCP +A
  gi|15669355|ref|NP_248160.1| 196 CVFCKVCEFVCPHDA 210
                                   9***9*******998 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.19
                        Fer4_3   1 CtgCgaCvevCP 12 
                                   C+ Cg C   CP
  gi|15669355|ref|NP_248160.1| 244 CVTCGWCAFICP 255
                                   ************ PP

  == domain 7  score: 4.3 bits;  conditional E-value: 0.085
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   C+ CgaC   CP  
  gi|15669355|ref|NP_248160.1| 276 CNACGACISICPCS 289
                                   999*********65 PP

  == domain 8  score: 13.9 bits;  conditional E-value: 7.2e-05
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ CgaC ++CPv+A
  gi|15669355|ref|NP_248160.1| 313 CVLCGACAKACPVNA 327
                                   *************99 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   1.3   0.00011      0.13      78      95 ..      29      46 ..      10      47 .. 0.84
   2 !    8.5   0.3    0.0032       3.5      77      93 ..      68      84 ..      58      87 .. 0.81
   3 ?    6.2   3.1     0.017        19       1      14 [.     116     129 ..     116     143 .. 0.83
   4 !    9.2   1.0    0.0019       2.2      71      94 ..     145     168 ..     134     170 .. 0.78
   5 ?    1.1   5.8      0.66   7.4e+02       1      14 [.     195     208 ..     195     228 .. 0.84
   6 !    7.9   2.7    0.0048       5.4      77      94 ..     239     256 ..     217     258 .. 0.72
   7 ?    1.6   6.4      0.44   4.9e+02      81      93 ..     275     287 ..     265     290 .. 0.66
   8 ?    2.2   5.7      0.29   3.2e+02       2      16 ..     276     289 ..     275     305 .. 0.75
   9 !    9.6   1.4    0.0015       1.7      78      95 ..     309     326 ..     293     327 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                       Fer4_22 78 gesgCvGCgRCieacpvk 95
                                  + + CvGCg C + cpv+
  gi|15669355|ref|NP_248160.1| 29 NDELCVGCGICADICPVN 46
                                  6789***********986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0032
                       Fer4_22 77 fgesgCvGCgRCieacp 93
                                  +++ +Cv Cg C +acp
  gi|15669355|ref|NP_248160.1| 68 IDKDVCVLCGMCASACP 84
                                  57788999999999998 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.017
                       Fer4_22   1 rClsCgaCtlvCpt 14 
                                   +C+ C +C +vCp 
  gi|15669355|ref|NP_248160.1| 116 KCVLCEQCEMVCPQ 129
                                   79**********97 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0019
                       Fer4_22  71 sefkekfgesgCvGCgRCieacpv 94 
                                      + ++++++Cv Cg C e cp+
  gi|15669355|ref|NP_248160.1| 145 VIGEININKEKCVLCGICAEYCPA 168
                                   44555678999*********9997 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.66
                       Fer4_22   1 rClsCgaCtlvCpt 14 
                                   +C+ C  C +vCp 
  gi|15669355|ref|NP_248160.1| 195 KCVFCKVCEFVCPH 208
                                   7***********95 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.0048
                       Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                   +++ +Cv Cg C   cp+
  gi|15669355|ref|NP_248160.1| 239 IDKDACVTCGWCAFICPA 256
                                   477778888888888876 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.44
                       Fer4_22  81 gCvGCgRCieacp 93 
                                   +C  Cg Ci+ cp
  gi|15669355|ref|NP_248160.1| 275 ACNACGACISICP 287
                                   5666666666665 PP

  == domain 8  score: 2.2 bits;  conditional E-value: 0.29
                       Fer4_22   2 ClsCgaCtlvCptCs 16 
                                   C +CgaC  +Cp Cs
  gi|15669355|ref|NP_248160.1| 276 CNACGACISICP-CS 289
                                   889999999998.44 PP

  == domain 9  score: 9.6 bits;  conditional E-value: 0.0015
                       Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                   +++ Cv Cg C +acpv+
  gi|15669355|ref|NP_248160.1| 309 NQNLCVLCGACAKACPVN 326
                                   7899***********986 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.6     0.011        12       6      19 ..      31      44 ..      28      50 .. 0.88
   2 ?    5.4  13.3     0.028        31       3      66 .]      68     134 ..      66     134 .. 0.81
   3 ?    3.9   3.3     0.079        89       2      20 ..     111     129 ..     110     141 .. 0.84
   4 !    9.5   0.6    0.0015       1.7       1      19 [.     149     167 ..     149     174 .. 0.90
   5 ?    4.1   4.9     0.071        79       1      19 [.     189     207 ..     189     208 .. 0.88
   6 ?    1.4   0.1      0.49   5.5e+02      58      66 .]     205     213 ..     204     213 .. 0.91
   7 ?    5.7   5.2     0.022        25       2      19 ..     238     255 ..     237     263 .. 0.88
   8 !    7.2   1.2    0.0077       8.6       3      19 ..     271     287 ..     269     300 .. 0.91
   9 !    7.0   3.6    0.0089        10       1      19 [.     306     324 ..     306     329 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                       Fer4_15  6 daCigcglCvaeap 19
                                  ++C gcg C++ +p
  gi|15669355|ref|NP_248160.1| 31 ELCVGCGICADICP 44
                                  79*********998 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.028
                       Fer4_15   3 vDrdaCigcglCvaeap.evfeldedglasvllddgeiaeg...evpddeeeaaqeAaraCPvdAIrv 66 
                                   +D+d C  cg+C+ ++p +   l+ +g++ ++ d++  + +    v +d+    ++   +CP +AI+v
  gi|15669355|ref|NP_248160.1|  68 IDKDVCVLCGMCASACPfDALDLKINGKS-IKEDERYPKIKrdiKVYQDKCVLCEQCEMVCPQGAIVV 134
                                   8***************6378888889998.7755444333387788888888889999********87 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.079
                       Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                   +v +d+C  c++C  ++p+
  gi|15669355|ref|NP_248160.1| 111 KVYQDKCVLCEQCEMVCPQ 129
                                   66799********999985 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0015
                       Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                   + +++++C  cg C++ +p
  gi|15669355|ref|NP_248160.1| 149 ININKEKCVLCGICAEYCP 167
                                   6799**************8 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.071
                       Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                   ++vD+d+C  c +C  ++p
  gi|15669355|ref|NP_248160.1| 189 IEVDKDKCVFCKVCEFVCP 207
                                   79************77766 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.49
                       Fer4_15  58 aCPvdAIrv 66 
                                   +CP dAI+v
  gi|15669355|ref|NP_248160.1| 205 VCPHDAIEV 213
                                   6******97 PP

  == domain 7  score: 5.7 bits;  conditional E-value: 0.022
                       Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                   v+D+daC  cg C+  +p
  gi|15669355|ref|NP_248160.1| 238 VIDKDACVTCGWCAFICP 255
                                   79************9997 PP

  == domain 8  score: 7.2 bits;  conditional E-value: 0.0077
                       Fer4_15   3 vDrdaCigcglCvaeap 19 
                                   +D +aC  cg+C+  +p
  gi|15669355|ref|NP_248160.1| 271 IDVNACNACGACISICP 287
                                   899***********997 PP

  == domain 9  score: 7.0 bits;  conditional E-value: 0.0089
                       Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                   + v++++C  cg+C++++p
  gi|15669355|ref|NP_248160.1| 306 IIVNQNLCVLCGACAKACP 324
                                   67999************98 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.5     0.059        66      57      90 ..      15      48 ..       6      55 .. 0.78
   2 ?    2.6   0.2      0.13   1.4e+02      62      86 ..      60      84 ..      50      94 .. 0.80
   3 ?    4.5   1.1     0.033        37      65      91 ..     107     133 ..      95     137 .. 0.80
   4 ?    6.0   1.5     0.012        13      56      92 ..     137     173 ..     126     181 .. 0.69
   5 ?    5.9  10.9     0.012        13      42      92 ..     158     213 ..     148     220 .. 0.70
   6 ?    4.8   1.7     0.027        30      66      96 ..     235     265 ..     215     269 .. 0.78
   7 ?    6.8   5.1    0.0063       7.1      45      92 ..     281     330 ..     268     336 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.059
                                  EEETTTTSSEEEEE-CCC--S--HHHHH-TT--E CS
                        ETF_QO 57 ivedeeakekklqinaqnCvhCktCdikdpsqni 90
                                  i +d e ++ +l  n + Cv C  C    p + i
  gi|15669355|ref|NP_248160.1| 15 IYRDGEVEKRELCWNDELCVGCGICADICPVNAI 48
                                  4556688999***************766666666 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                                  TTSSEEEEE-CCC--S--HHHHH-T CS
                        ETF_QO 62 eakekklqinaqnCvhCktCdikdp 86
                                  +  ++kl i+   Cv C  C    p
  gi|15669355|ref|NP_248160.1| 60 DIIAPKLDIDKDVCVLCGMCASACP 84
                                  556789**************86655 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.033
                                   SEEEEE-CCC--S--HHHHH-TT--EE CS
                        ETF_QO  65 ekklqinaqnCvhCktCdikdpsqnie 91 
                                   +  +++    Cv C  C++  p+  i 
  gi|15669355|ref|NP_248160.1| 107 KRDIKVYQDKCVLCEQCEMVCPQGAIV 133
                                   566888999**********99998875 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.012
                                   EEEETTTTSSEEEEE-CCC--S--HHHHH-TT--EEE CS
                        ETF_QO  56 eivedeeakekklqinaqnCvhCktCdikdpsqniew 92 
                                   e++e+e+    +++in + Cv C  C    p + i+ 
  gi|15669355|ref|NP_248160.1| 137 ELAEREKFVIGEININKEKCVLCGICAEYCPADAINL 173
                                   334444555567899***********99999988875 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.012
                                   HS-THHHH-TTS-EEEEE....TT.TTSSEEEEE-CCC--S--HHHHH-TT--EEE CS
                        ETF_QO  42 yagpeqryCPagvyeive....de.eakekklqinaqnCvhCktCdikdpsqniew 92 
                                     g+++ yCPa   ++       +  +  + ++++   Cv Ck+C+   p++ ie 
  gi|15669355|ref|NP_248160.1| 158 LCGICAEYCPADAINLKYnyptPSnPKPITDIEVDKDKCVFCKVCEFVCPHDAIEV 213
                                   5678999****986655411113312345679999*************99999875 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.027
                                   EEEEE-CCC--S--HHHHH-TT--EEE---S CS
                        ETF_QO  66 kklqinaqnCvhCktCdikdpsqniewvvPe 96 
                                    k +i+   Cv C  C    p + ie + P 
  gi|15669355|ref|NP_248160.1| 235 GKTVIDKDACVTCGWCAFICPAEAIEVEKPF 265
                                   456899*******************999885 PP

  == domain 7  score: 6.8 bits;  conditional E-value: 0.0063
                                   THHHH-TTS-EEEEETT..TTSSEEEEE-CCC--S--HHHHH-TT--EEE CS
                        ETF_QO  45 peqryCPagvyeivede..eakekklqinaqnCvhCktCdikdpsqniew 92 
                                    +  +CP +  e+ + +   +k +++ +n + Cv C +C    p + i+ 
  gi|15669355|ref|NP_248160.1| 281 ACISICPCSALEFPKPKdkAEKVPRIIVNQNLCVLCGACAKACPVNAIKV 330
                                   56679*******9985522567789999***********99999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2122.37
//
Query:       gi|15669356|ref|NP_248161.1|  [L=82]
Description: formylmethanofuran dehydrogenase subunit FwdG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-18   65.3  15.7    7.4e-10   38.2   5.1    2.1  2  Fer4       4Fe-4S binding domain
    3.5e-14   53.1  36.5    6.2e-08   33.1  14.8    2.0  3  Fer4_7     4Fe-4S dicluster domain
      4e-12   46.1  20.5    1.5e-08   34.6  10.8    2.1  2  Fer4_10    4Fe-4S dicluster domain
      8e-12   44.7  16.0    7.7e-07   28.9   3.8    2.2  2  Fer4_6     4Fe-4S binding domain
    8.8e-10   39.4   9.7    1.4e-05   25.9   1.6    2.1  2  Fer4_16    4Fe-4S double cluster binding domain
      4e-09   36.0  14.4    5.1e-05   23.1   3.4    2.2  2  Fer4_2     4Fe-4S binding domain
    5.3e-09   36.1   8.4    1.5e-08   34.7   8.5    1.6  1  Fer4_9     4Fe-4S dicluster domain
    5.9e-09   35.9  11.2    2.3e-05   24.4   1.9    2.0  2  Fer4_21    4Fe-4S dicluster domain
    1.1e-06   28.6  13.3    0.00086   19.6   2.8    2.2  2  Fer4_4     4Fe-4S binding domain
      3e-06   27.8  23.4     0.0044   17.8   8.1    2.3  2  Fer4_3     4Fe-4S binding domain
    1.1e-05   25.7  23.3    0.00012   22.5  13.0    1.9  2  Fer4_8     4Fe-4S dicluster domain
    3.2e-05   24.7   7.0      0.012   16.4   0.5    2.1  2  Fer4_22    4Fe-4S dicluster domain
    5.1e-05   23.7  10.3    0.00044   20.7  10.6    1.9  3  Fer4_17    4Fe-4S dicluster domain
    0.00031   21.4  11.3       0.22   12.3   4.7    2.8  2  Fer4_15    4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.023   14.3   4.0       0.45   10.2   0.5    2.2  2  MTHFR_C    Methylene-tetrahydrofolate reductase C terminal
      0.025   15.1  12.8        0.2   12.2   3.2    2.6  3  Fer4_13    4Fe-4S single cluster domain of Ferredoxin I
      0.064   13.4   4.7       0.27   11.4   4.7    1.8  1  Fer4_11    4Fe-4S dicluster domain
       0.07   13.1   7.1       0.55   10.2   0.5    2.3  2  SCIFF      Six-cysteine peptide SCIFF
      0.075   12.8   5.1       0.36   10.6   0.7    2.1  2  Fer4_20    Dihydroprymidine dehydrogenase domain II, 4Fe-4S c
        0.1   12.4   0.1       0.12   12.2   0.1    1.1  1  Arteri_Gl  Arterivirus GL envelope glycoprotein
       0.85    9.8   8.2        3.3    7.9   0.7    2.1  2  Fer4_18    4Fe-4S dicluster domain
          6    6.5   5.8        5.1    6.7   0.1    2.0  2  HCV_NS2    Hepatitis C virus non-structural protein NS2


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   2.8   3.6e-11     3e-08       2      22 ..       7      27 ..       6      29 .. 0.94
   2 !   38.2   5.1   9.1e-13   7.4e-10       2      24 .]      54      76 ..      53      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 3.6e-11
                                  EEETTTSSS-THHHHHSTTTE CS
                          Fer4  2 videekCigCGaCvevCPvgA 22
                                  v+ +e+C gCG+Cv  CPv+A
  gi|15669356|ref|NP_248161.1|  7 VVYPERCHGCGNCVVSCPVNA 27
                                  799*****************9 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 9.1e-13
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  v+++++C gCGaC+e+CPv+AI+
  gi|15669356|ref|NP_248161.1| 54 VVNQDLCGGCGACIEACPVNAIE 76
                                  89********************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   4.0   1.7e-06    0.0014      32      52 .]       7      27 ..       2      27 .. 0.79
   2 !   33.1  14.8   7.6e-11   6.2e-08       1      52 []      12      74 ..      12      74 .. 0.70
   3 !   23.4   2.2     8e-08   6.6e-05       2      21 ..      60      79 ..      59      82 .] 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.7e-06
                        Fer4_7 32 eidpekClgCgaCvavCPtga 52
                                  ++ pe+C gCg+Cv  CP++a
  gi|15669356|ref|NP_248161.1|  7 VVYPERCHGCGNCVVSCPVNA 27
                                  556889999999999999886 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 7.6e-11
                        Fer4_7  1 rCigCgaCvaaCpvkaield.........eeenek.....gt.ekveidpekClgCgaCvavCPtga 52
                                  rC gCg+Cv+ Cpv+a   +         +    +     ++   ++++++ C gCgaC+++CP++a
  gi|15669356|ref|NP_248161.1| 12 RCHGCGNCVVSCPVNAKHPEtwggkgpysD----DvvirvENgVVTVVNQDLCGGCGACIEACPVNA 74
                                  8************99999773344332221....0233333314446789***************97 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 8e-08
                        Fer4_7  2 CigCgaCvaaCpvkaielde 21
                                  C gCgaC +aCpv+aiel  
  gi|15669356|ref|NP_248161.1| 60 CGGCGACIEACPVNAIELVF 79
                                  ****************9865 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6  10.8   1.8e-11   1.5e-08       4      56 .]       8      71 ..       5      71 .. 0.79
   2 !   22.6   2.1     1e-07   8.4e-05       3      22 ..      54      73 ..      52      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.8e-11
                       Fer4_10  4 idddtCirCgkCvkaCPadl...........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  + +++C +Cg+Cv +CP+++            s+++    +++ +  ++ + C gcgaC+eaCP
  gi|15669356|ref|NP_248161.1|  8 VYPERCHGCGNCVVSCPVNAkhpetwggkgpYSDDVVIRVENGVVTVVNQDLCGGCGACIEACP 71
                                  5679**************99********997444444444444444457899***********9 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1e-07
                       Fer4_10  3 vidddtCirCgkCvkaCPad 22
                                  v+++d C +Cg+C +aCP++
  gi|15669356|ref|NP_248161.1| 54 VVNQDLCGGCGACIEACPVN 73
                                  6799**************94 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   4.4   1.9e-07   0.00015       6      23 ..      10      27 ..       7      27 .. 0.93
   2 !   28.9   3.8   9.4e-10   7.7e-07       3      24 .]      54      75 ..      52      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.9e-07
                        Fer4_6  6 pdkCigCgdCvrvCPega 23
                                  p++C gCg+Cv+ CP +a
  gi|15669356|ref|NP_248161.1| 10 PERCHGCGNCVVSCPVNA 27
                                  89*************997 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 9.4e-10
                        Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                  ++++d+C gCg+C+ +CP +ai
  gi|15669356|ref|NP_248161.1| 54 VVNQDLCGGCGACIEACPVNAI 75
                                  79******************98 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.4   3.6e-06    0.0029       1      16 [.      12      27 ..      11      40 .. 0.86
   2 !   25.9   1.6   1.7e-08   1.4e-05       2      20 ..      60      78 ..      59      82 .] 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.6e-06
                       Fer4_16  1 rCgtCgkCaevCPtna 16
                                  rC++Cg+C+ +CP+na
  gi|15669356|ref|NP_248161.1| 12 RCHGCGNCVVSCPVNA 27
                                  6999999999999998 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.7e-08
                       Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                  Cg+Cg+C+e+CP+nai+  
  gi|15669356|ref|NP_248161.1| 60 CGGCGACIEACPVNAIELV 78
                                  ****************965 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   3.3   1.5e-06    0.0012       3      21 ..       6      24 ..       3      25 .. 0.88
   2 !   23.1   3.4   6.2e-08   5.1e-05       4      21 ..      54      71 ..      52      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                   vv ++rC gCg Cv +CP
  gi|15669356|ref|NP_248161.1|  6 LVVYPERCHGCGNCVVSCP 24
                                  57889************** PP

  == domain 2  score: 23.1 bits;  conditional E-value: 6.2e-08
                        Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                  vv+ d C gCgaC+ aCP
  gi|15669356|ref|NP_248161.1| 54 VVNQDLCGGCGACIEACP 71
                                  799*************** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   8.5   1.8e-11   1.5e-08       1      51 []      12      75 ..      12      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.8e-11
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.............eaCigCgaCveaCpkgai 51
                                  +C gCg+Cv +Cp ++  ++  ++k  +  +               + C gCgaC+eaCp +ai
  gi|15669356|ref|NP_248161.1| 12 RCHGCGNCVVSCPVNAKHPETWGGKGPYSDDVVirvengvvtvvnqDLCGGCGACIEACPVNAI 75
                                  6****************999999998885544499999*******99**************987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   2.1   5.4e-06    0.0044      35      54 ..       7      26 ..       1      29 [. 0.79
   2 !   24.4   1.9   2.8e-08   2.3e-05      26      58 ..      45      76 ..      39      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.4e-06
                       Fer4_21 35 kvvedeCvGCnlCssvCPve 54
                                   v  ++C GC  C+  CPv+
  gi|15669356|ref|NP_248161.1|  7 VVYPERCHGCGNCVVSCPVN 26
                                  45689999999999999994 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2.8e-08
                       Fer4_21 26 ieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                  i++++  v+ v +d C GC  C++ CPv ++ie
  gi|15669356|ref|NP_248161.1| 45 IRVENGVVTVVNQDLCGGCGACIEACPV-NAIE 76
                                  4555555556679**************9.9997 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   2.8   1.1e-06   0.00086       1      17 []      10      26 ..      10      32 .. 0.94
   2 !   14.7   2.9   4.1e-05     0.034       1      17 []      57      73 ..      57      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                        Fer4_4  1 qerCigCgsCvaaCPqg 17
                                  +erC gCg Cv +CP++
  gi|15669356|ref|NP_248161.1| 10 PERCHGCGNCVVSCPVN 26
                                  69*************75 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.1e-05
                        Fer4_4  1 qerCigCgsCvaaCPqg 17
                                  q+ C gCg+C+ aCP++
  gi|15669356|ref|NP_248161.1| 57 QDLCGGCGACIEACPVN 73
                                  68899**********85 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   8.1   5.5e-06    0.0044       1      15 []      13      27 ..      13      27 .. 0.98
   2 !   16.0   7.3   2.2e-05     0.018       1      15 []      60      74 ..      60      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.5e-06
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gCg Cv++CPv+A
  gi|15669356|ref|NP_248161.1| 13 CHGCGNCVVSCPVNA 27
                                  **************9 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.2e-05
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C gCgaC e+CPv+A
  gi|15669356|ref|NP_248161.1| 60 CGGCGACIEACPVNA 74
                                  779***********9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5  13.0   1.4e-07   0.00012       3      64 ..      11      73 ..       9      74 .. 0.72
   2 !   14.5   2.5   4.3e-05     0.035       4      17 ..      59      72 ..      56      81 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.4e-07
                        Fer4_8  3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                  e+C++Cg C  +Cpv  +    +  + ++      + e ++ +  + + C +cgaC e+Cpv+
  gi|15669356|ref|NP_248161.1| 11 ERCHGCGNCVVSCPVNAKHPeTWGGKGPYSDDVVIRVENGVVTVVNQDLCGGCGACIEACPVN 73
                                  69************87776545555555544443344444444566899************97 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.3e-05
                        Fer4_8  4 kCieCgaCqsaCpv 17
                                   C++CgaC +aCpv
  gi|15669356|ref|NP_248161.1| 59 LCGGCGACIEACPV 72
                                  47777777777775 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   1.2   0.00036      0.29      80      95 ..      11      26 ..       2      27 .. 0.80
   2 !   16.4   0.5   1.5e-05     0.012      73      95 ..      51      73 ..      38      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00036
                       Fer4_22 80 sgCvGCgRCieacpvk 95
                                  + C GCg C+ +cpv+
  gi|15669356|ref|NP_248161.1| 11 ERCHGCGNCVVSCPVN 26
                                  5699999999999875 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.5e-05
                       Fer4_22 73 fkekfgesgCvGCgRCieacpvk 95
                                  +++ +++  C GCg Cieacpv+
  gi|15669356|ref|NP_248161.1| 51 VVTVVNQDLCGGCGACIEACPVN 73
                                  45567899************986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   3.1   7.2e-05     0.059      44      59 ..      11      26 ..       7      28 .. 0.81
   2 !   20.7  10.6   5.4e-07   0.00044       1      58 [.      12      72 ..      12      75 .. 0.76
   3 !   11.5   2.1   0.00041      0.34       2      16 ..      60      74 ..      59      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.2e-05
                       Fer4_17 44 slCieCgeCerkCPqg 59
                                  ++C++Cg+C+ +CP +
  gi|15669356|ref|NP_248161.1| 11 ERCHGCGNCVVSCPVN 26
                                  6899999999999965 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 5.4e-07
                       Fer4_17  1 rCiqCgyClpeCpsyeaydn.......epkkllraaklglleeaekeekaslCieCgeCerkCPq 58
                                  rC++Cg C+ +Cp ++++++       + + ++ ++++g ++      + +lC +Cg C ++CP 
  gi|15669356|ref|NP_248161.1| 12 RCHGCGNCVVSCPVNAKHPEtwggkgpYSDDVVIRVENGVVTV----VNQDLCGGCGACIEACPV 72
                                  7****************99855444334555666656654444....5789*************6 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00041
                       Fer4_17  2 CiqCgyClpeCpsye 16
                                  C +Cg+C+++Cp ++
  gi|15669356|ref|NP_248161.1| 60 CGGCGACIEACPVNA 74
                                  889999999999765 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.5   0.00036      0.29       6      19 ..      11      24 ..       7      34 .. 0.88
   2 !   12.3   4.7   0.00027      0.22       2      19 ..      54      71 ..      53      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00036
                       Fer4_15  6 daCigcglCvaeap 19
                                  ++C gcg+Cv  +p
  gi|15669356|ref|NP_248161.1| 11 ERCHGCGNCVVSCP 24
                                  79*********998 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00027
                       Fer4_15  2 vvDrdaCigcglCvaeap 19
                                  vv++d+C gcg+C++++p
  gi|15669356|ref|NP_248161.1| 54 VVNQDLCGGCGACIEACP 71
                                  699**************8 PP

>> MTHFR_C  Methylene-tetrahydrofolate reductase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00055      0.45      17      31 ..       8      22 ..       2      32 .. 0.83
   2 ?    5.7   0.2     0.014        11      17      29 ..      55      67 ..      38      75 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00055
                       MTHFR_C 17 vleekCkaCgdCvla 31
                                  v+ e+C+ Cg+Cv++
  gi|15669356|ref|NP_248161.1|  8 VYPERCHGCGNCVVS 22
                                  6789********986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.014
                       MTHFR_C 17 vleekCkaCgdCv 29
                                  v ++ C  Cg C+
  gi|15669356|ref|NP_248161.1| 55 VNQDLCGGCGACI 67
                                  23445*******7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.7    0.0049         4       4      17 ..      11      24 ..       8      27 .. 0.91
   2 ?   12.2   3.2   0.00025       0.2       1      17 [.      55      71 ..      55      73 .. 0.95
   3 ?    6.6   0.1     0.014        11      48      57 ..      67      76 ..      67      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0049
                       Fer4_13  4 dtCiacgaCvelaP 17
                                  ++C +cg+Cv  +P
  gi|15669356|ref|NP_248161.1| 11 ERCHGCGNCVVSCP 24
                                  79***********9 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00025
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  V++d C +cgaC e++P
  gi|15669356|ref|NP_248161.1| 55 VNQDLCGGCGACIEACP 71
                                  899*************9 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.014
                       Fer4_13 48 adaCPvesIg 57
                                  ++aCPv++I+
  gi|15669356|ref|NP_248161.1| 67 IEACPVNAIE 76
                                  689******7 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.7   0.00034      0.27       4      59 ..       7      75 ..       4      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                       Fer4_11  4 lflpeqCrhCleppCvasapse...............aivkdeetGaVlldektkkeevrevveacPykiv 59
                                  ++ pe C+ C +  Cv s+p++                +v + e+G+V + ++    ++ +++eacP +++
  gi|15669356|ref|NP_248161.1|  7 VVYPERCHGCGN--CVVSCPVNakhpetwggkgpysdDVVIRVENGVVTVVNQDLCGGCGACIEACPVNAI 75
                                  678999*99975..8899988888889999999999988888999999765555556**********9875 PP

>> SCIFF  Six-cysteine peptide SCIFF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00067      0.55      17      28 ..      13      24 ..       7      32 .. 0.85
   2 ?    6.0   1.2     0.013        11       8      27 ..      56      70 ..      50      72 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00067
                         SCIFF 17 kggCgeCqtSCq 28
                                   +gCg+C  SC 
  gi|15669356|ref|NP_248161.1| 13 CHGCGNCVVSCP 24
                                  58*********5 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.013
                         SCIFF  8 kkslkktlkkggCgeCqtSC 27
                                  +++l      ggCg C   C
  gi|15669356|ref|NP_248161.1| 56 NQDL-----CGGCGACIEAC 70
                                  4444.....69*****9999 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.7   0.00045      0.36      21      43 ..      10      30 ..       1      33 [. 0.83
   2 ?    4.9   0.3     0.027        22      24      39 ..      60      73 ..      43      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00045
                                  HTT----TT-HHHHCSTT---HH CS
                       Fer4_20 21 AsRClqCkkapcvkgCPveidip 43
                                   +RC  C   +cv +CPv+ + p
  gi|15669356|ref|NP_248161.1| 10 PERCHGC--GNCVVSCPVNAKHP 30
                                  58*****..78*******99877 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.027
                                  ----TT-HHHHCSTT- CS
                       Fer4_20 24 ClqCkkapcvkgCPve 39
                                  C  C    c+++CPv+
  gi|15669356|ref|NP_248161.1| 60 CGGC--GACIEACPVN 73
                                  7777..78******97 PP

>> Arteri_Gl  Arterivirus GL envelope glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.12      99     154 ..       3      59 ..       1      65 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                     Arteri_Gl  99 vysfvvraarlrlclagryaitahtnfvldakGrifrsksqv.vvekpgkteVggkl 154
                                   +y +vv  +r+  c ++  ++   +++ ++  G+ + s++ v  ve++  t V+ +l
  gi|15669356|ref|NP_248161.1|   3 AYELVVYPERCHGCGNCVVSCPVNAKHPETWGGKGPYSDDVViRVENGVVTVVNQDL 59 
                                   68999*****************************99999998456655555666555 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.5     0.013        10      60      74 ..      12      26 ..       5      31 .. 0.88
   2 ?    7.9   0.7    0.0041       3.3      58      73 ..      57      72 ..      36      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                       Fer4_18 60 dcidcescvkvcPtg 74
                                   c  c+ cv  cP++
  gi|15669356|ref|NP_248161.1| 12 RCHGCGNCVVSCPVN 26
                                  6999*********86 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0041
                       Fer4_18 58 agdcidcescvkvcPt 73
                                  +  c  c++c++ cP+
  gi|15669356|ref|NP_248161.1| 57 QDLCGGCGACIEACPV 72
                                  4457777777777776 PP

>> HCV_NS2  Hepatitis C virus non-structural protein NS2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0063       5.1     173     194 ..       6      27 ..       2      28 .. 0.85
   2 ?    2.2   1.7      0.15   1.2e+02     181     194 ..      61      74 ..      43      75 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0063
                       HCV_NS2 173 iirwgadtlaCGdivaGlPVsA 194
                                   +++   +  +CG++v   PV A
  gi|15669356|ref|NP_248161.1|   6 LVVYPERCHGCGNCVVSCPVNA 27 
                                   567778999***********99 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                       HCV_NS2 181 laCGdivaGlPVsA 194
                                    +CG +++  PV A
  gi|15669356|ref|NP_248161.1|  61 GGCGACIEACPVNA 74 
                                   47**********88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 618.15
//
Query:       gi|15669357|ref|NP_248162.1|  [L=133]
Description: formylmethanofuran dehydrogenase subunit FwdD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-22   79.2   0.0    2.6e-22   78.9   0.0    1.1  1  Molydop_binding  Molydopterin dinucleotide binding domain
    1.6e-05   24.9   0.0    3.7e-05   23.8   0.0    1.5  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
  ------ inclusion threshold ------
      0.059   13.6   0.1       0.11   12.6   0.1    1.5  2  Rad9_Rad53_bind  Fungal Rad9-like Rad53-binding


Domain annotation for each model (and alignments):
>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   4.4e-26   2.6e-22       1     109 [.       3     102 ..       3     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 4.4e-26
                                   EEEEEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEE.EEESSB-TTEEEEESSH CS
               Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevra.kvtervrpGvvfmpfgw 80 
                                   + L+tgr+ +q  ++ + ++   + k ++ vv+in+ed+++lG+k+Gd+V+v+s++G+v+v + k ter+++G++++p+g 
  gi|15669357|ref|NP_248162.1|   3 FFLNTGRTIWQGEAMEAGKNLDLYVKAAG-VVYINEEDMEKLGVKEGDKVKVKSEYGEVVVYVkKATERMPEGMIYIPMGP 82 
                                   679*************9999999999898.*********************************999*************** PP

                                   CC.....S-GHCTS--SCSTTT--CSTT- CS
               Molydop_binding  81 weagekggnaNaltddatdplsgtpefks 109
                                   w+        N ++ ++ +  +g+p+fk+
  gi|15669357|ref|NP_248162.1|  83 WA--------NCVV-KPDTHSTGMPTFKG 102
                                   **........9999.66667789999986 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   6.2e-09   3.7e-05      14      61 ..      30      77 ..      24      81 .. 0.84
   2 ?   -2.9   0.0       1.3     8e+03      35      39 ..     108     112 ..      97     126 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.2e-09
                                  TTEEEE-HHHHHHHTS-TTSEEEEEC.CCCEEEEEEEBSTTSTTTTEEE CS
                       CDC48_N 14 rgivridpedmeelglepgdvveieg.krkTvaivwpaepedegkgiIr 61
                                   g+v+i++edme+lg+++gd v+++    + v++v  a +  + +g I 
  gi|15669357|ref|NP_248162.1| 30 AGVVYINEEDMEKLGVKEGDKVKVKSeYGEVVVYVKKATERMP-EGMIY 77
                                  69***********************966668888888877655.77765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                                   EEEEC CS
                       CDC48_N  35 veieg 39 
                                   ve+e+
  gi|15669357|ref|NP_248162.1| 108 VEVEK 112
                                   44443 PP

>> Rad9_Rad53_bind  Fungal Rad9-like Rad53-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.9e-05      0.11      47      82 ..      31      66 ..       8      78 .. 0.80
   2 ?   -2.4   0.0      0.83     5e+03      26      56 ..     103     115 ..      84     121 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
               Rad9_Rad53_bind 47 gavevkkedvkyLdlriGdkvkvdmktyvvrglekk 82
                                  g v +++ed+ +L ++ Gdkvkv+++  +v+ + kk
  gi|15669357|ref|NP_248162.1| 31 GVVYINEEDMEKLGVKEGDKVKVKSEYGEVVVYVKK 66
                                  45889********************86666655554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.83
               Rad9_Rad53_bind  26 Ypakilskgtsqdkvlvkfeegavevkkedv 56 
                                   Yp+  +++                  +k d 
  gi|15669357|ref|NP_248162.1| 103 YPGFYVEV------------------EKTDE 115
                                   55544444..................33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 892.42
//
Query:       gi|15669358|ref|NP_248163.1|  [L=567]
Description: formylmethanofuran dehydrogenase subunit FwdA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-92  310.9   0.1    3.1e-92  310.5   0.1    1.1  1  Amidohydro_3  Amidohydrolase family
    6.4e-08   32.3   0.1    0.00038   19.9   0.0    2.7  2  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.5   0.1   3.5e-96   3.1e-92       1     473 []      40     499 ..      40     499 .. 0.96

  Alignments for each domain:
  == domain 1  score: 310.5 bits;  conditional E-value: 3.5e-96
                  Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerfpyal 80 
                                   +viDa+G++v+PG++DsH+H+ag++vn+ r +r++d++        +++ +++g       + g G+++++++++++ y+ 
  gi|15669358|ref|NP_248163.1|  40 KVIDASGCVVMPGGIDSHSHVAGAKVNVgRIFRPEDSK--------REIYAKKGL------RTGTGFSVPSTYKTGYQYSE 106
                                   69**********************************33........445555555......7999**************** PP

                  Amidohydro_3  81 aeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllregafhlvldlaplareaeaaa 161
                                   +++++v+e+a+++l a++tH+++  ++ +d+            ++   ++n++ ++++l+eg           +++a+aa+
  gi|15669358|ref|NP_248163.1| 107 MGYTTVIEAAMPPLIARHTHEEFMETPQIDK------------AAMPLFGNNWMVLEYLKEG-----------DIKACAAF 164
                                   *******************************............99*****************...........******** PP

                  Amidohydro_3 162 vaaalaalasyGitsv.......eagggnvsslddleplfeltaeeklplrviikelldaaerlglpls..........pg 225
                                   va++l+a +++ i++v       +++g+nv+sldd++p+f++t++e      i  +l++++e lglp+s          pg
  gi|15669358|ref|NP_248163.1| 165 VAWLLKAVKGFAIKIVnpggteaWGWGKNVHSLDDPVPYFDITPRE------IVRGLAEVNELLGLPHSihvhpnnlghPG 239
                                   **********************************************......889************************** PP

                  Amidohydro_3 226 seeltigavklfad......gvlgsrtalltepyf.....tgwpdfedea..laelvaaadergldvaihaigdaavd..d 291
                                   + e+t++++k+ ++      + +++++++ t+ +f     t+w+dfe++a  +ae+v++ +++ +dv+++++++++++  d
  gi|15669358|ref|NP_248163.1| 240 NWETTLETMKCVEGveakprVGERETSYYNTHCQFhsyggTSWKDFESKAieIAEYVNKSKHVVIDVGQVTLDETTTMtaD 320
                                   **************777777667999999999999********************************************** PP

                  Amidohydro_3 292 vldafeaa...aekngnqdrrrlehaegv...tesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellna 366
                                   ++ +++ +   + k++n+d+ +le+++gv    +s++ +v a+q+a+g++                        + + +n+
  gi|15669358|ref|NP_248163.1| 321 GPMEYDLHmtnGLKWANCDV-ELETGSGVvpfIYSPKGPVYAVQWAIGLE------------------------LFLNTNT 376
                                   *******************9.*****************************........................6666666 PP

                  Amidohydro_3 367 gvkvalgsD.apvgpfdpwprigaavmrktrrgg..............evlrpdeelsleealalyTrgpAkalgledrkG 432
                                   + kv l++D ++ gpf+++pr++a++m+k++r++              +v+++d+e++l+e+++ +++++Ak+lgl+++kG
  gi|15669358|ref|NP_248163.1| 377 D-KVLLTTDhPNAGPFTRYPRVIAWLMSKKYRDEwlynkvhkwaqqrsHVADADKEYDLYEIAKITRANQAKVLGLSETKG 456
                                   6.******************************************************************************* PP

                  Amidohydro_3 433 tLevGadADlvvldadpldvdppelaear..vrltvvdGrvvy 473
                                   +L+vGa+AD++++ +dp + d +++ +a   +++++++G+vv+
  gi|15669358|ref|NP_248163.1| 457 HLGVGAEADIAIYAIDPEEKDGKKIEKAFryAKYVLKGGEVVV 499
                                   ***********************99998899**********97 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0     4e-05      0.36       1      17 [.      48      64 ..      48     321 .. 0.88
   2 !   19.9   0.0   4.2e-08   0.00038     273     336 ..     426     489 ..     365     505 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4e-05
                                  EEEE-EEEEEEECETTE CS
                  Amidohydro_1  1 ivlPGlIDaHvHleqsl 17
                                  +v+PG+ID+H H+ +  
  gi|15669358|ref|NP_248163.1| 48 VVMPGGIDSHSHVAGAK 64
                                  69**********97543 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 4.2e-08
                                   TTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT.CGGGTTTCTSEEEEE CS
                  Amidohydro_1 273 yedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldi.laafvglkkdgnvkk 336
                                   + d++   +l+e+ +++  n Ak+lgl++++G + vG +AD+++ + d+  ++  +++k++  +k
  gi|15669358|ref|NP_248163.1| 426 A-DADKEYDLYEIAKITRANQAKVLGLSETKGHLGVGAEADIAIYAIDPeEKDGKKIEKAFRYAK 489
                                   2.556667999*999999**************************977555334444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 4290.38
//
Query:       gi|15669359|ref|NP_248164.1|  [L=89]
Description: hypothetical protein MJ_1170 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-11   45.0   2.4    4.1e-06   27.4   0.3    2.3  2  YbjQ_1           Putative heavy-metal-binding
  ------ inclusion threshold ------
      0.037   14.4   2.3      0.088   13.2   2.3    1.6  1  SeleniumBinding  Selenium binding protein


Domain annotation for each model (and alignments):
>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   5.4e-07    0.0049       1      23 [.       4      26 ..       4      28 .. 0.96
   2 !   27.4   0.3   4.6e-10   4.1e-06      59     104 .]      32      85 ..      29      85 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.4e-07
                        YbjQ_1  1 mivtttesiegkeivevlgivtg 23
                                  mi++tt+++eg +iv++lg+v g
  gi|15669359|ref|NP_248164.1|  4 MITSTTDNLEGFKIVKYLGVVIG 26
                                  9********************98 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 4.6e-10
                        YbjQ_1  59 eeAlerlkeeAeelGAnAvvgvrldtsei....ge..kgm..levlayGTAVkv 104
                                   ++Ale+l + Ae++GAnAv+g+r++ + +    ++   ++  l   ayGTAV+v
  gi|15669359|ref|NP_248164.1|  32 DDALEDLIDVAEDMGANAVIGIRISNELTteiiSDenYAVpeLTYYAYGTAVIV 85 
                                   689********************9866543334332222311445799****86 PP

>> SeleniumBinding  Selenium binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.3   9.9e-06     0.088       7      73 ..       4      83 ..       1      87 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.9e-06
               SeleniumBinding  7 fiittaneiPGvel.yylgivsavvesdnvdkilkaleekvkekkglaligfkltai.dg.............kllGyGtav 73
                                  +i  t++++ G ++  ylg+v     +d+ d+ l+ l + + ++++ a+ig ++                    +  yGtav
  gi|15669359|ref|NP_248164.1|  4 MITSTTDNLEGFKIvKYLGVVIG--YGDDPDDALEDLIDVAEDMGANAVIGIRISNElTTeiisdenyavpelTYYAYGTAV 83
                                  456699******97369****88..99*************************986431112222336777766677788877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 588.74
//
Query:       gi|15669360|ref|NP_248165.1|  [L=273]
Description: formylmethanofuran dehydrogenase subunit FwdC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-10   40.3  21.3    8.3e-10   38.6  21.3    1.9  1  GXGXG     GXGXG motif
  ------ inclusion threshold ------
      0.065   13.4   0.1       0.34   11.0   0.0    1.9  2  DUF2670   Protein of unknown function (DUF2670)


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6  21.3   9.3e-14   8.3e-10      21     168 ..      75     215 ..      64     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 9.3e-14
                                   HHTTT---.-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--TT-SS-GGGSB-S-SSTTTT--S CS
                         GXGXG  21 rygeeglpedtikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpskeskfkaeeniivGnvvlygatg 101
                                   +y+ ++++++  +i ++G aG  +ga + kG ++ ++G+a+  +G++++gG++ ik+++        ++  G+    g+ g
  gi|15669360|ref|NP_248165.1|  75 KYIGSKMTKG--EIVVEGDAGMYVGAEM-KGGKIVVNGNAESWAGQNMKGGELLIKGNAGD---YVGSAYRGDW--RGMSG 147
                                   5666666644..56678***********.******************************54...4445566885..79*** PP

                                   EEEEESSB--SSTTTT-SS-EEEESEB.-SSTTTT-EEEEEEE-S-B-SSBTTT--EEEEEEE-SSST CS
                         GXGXG 102 GklfirgkageRfavrnsgatavvegv.gdhgceYmtGGvvvvLgktgrnfaaGmsgGiayvldedek 168
                                   G++ ++g+ag+ ++  +s+  + ++g+ g +++    GG++++ g++   ++  m+ G++ v+ + e+
  gi|15669360|ref|NP_248165.1| 148 GTIIVEGNAGNEIGEFMSKGLIHIKGNvGIMAGIHQNGGIIIIDGDVDVRVGGEMKAGAIVVYGKVEE 215
                                   *****************99999999998**********************************955544 PP

>> DUF2670  Protein of unknown function (DUF2670)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.8e-05      0.34      40     107 ..      39     105 ..      25     113 .. 0.84
   2 ?   -0.3   0.0      0.12     1e+03      44      97 ..     201     253 ..     194     265 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.8e-05
                       DUF2670  40 tvlglkkigfidyfteetveilstskavaqnciiklklvngklplvefwdclsdpgeykyeevtgakv 107
                                    v g k+i   d f  e ++i  + + v +n  +klk + +k+   e+  +  d g y   e  g k+
  gi|15669360|ref|NP_248165.1|  39 LVQGRKRIKVADIFDVELNDIEGEPRIVIKNSSPKLKYIGSKMTKGEIV-VEGDAGMYVGAEMKGGKI 105
                                   57899**********************************9999877654.556777777777777776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.12
                       DUF2670  44 lkkigfidyfteetveilstsk..avaqnciiklklvngklplvefwdclsdpgey 97 
                                     k g i  +++  +eil + k   + +n +ikl+  ++  p++  +  +s  g+y
  gi|15669360|ref|NP_248165.1| 201 EMKAGAIVVYGK-VEEILPSFKfeGIVENPVIKLSKKDAGTPIAGTFYKFS--GDY 253
                                   556677777765.56777655422789999999998888888765444333..444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1821.58
//
Query:       gi|15669361|ref|NP_248166.1|  [L=84]
Description: hypothetical protein MJ_1172 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-41  139.0  10.1    5.1e-41  138.8  10.1    1.0  1  DUF2683       Protein of unknown function (DUF2683)
  ------ inclusion threshold ------
      0.017   15.0   0.1      0.019   14.8   0.1    1.1  1  DarT          ssDNA thymidine ADP-ribosyltransferase, DarT
       0.02   15.4   0.3      0.024   15.1   0.3    1.2  1  DsrC          DsrC like protein
      0.054   13.8   1.1       0.09   13.1   0.9    1.5  1  TEX12         Testis-expressed 12
      0.061   12.4   1.4      0.062   12.4   1.4    1.0  1  AcMNPV_Ac109  Autographa californica nuclear polyhedrosis vir


Domain annotation for each model (and alignments):
>> DUF2683  Protein of unknown function (DUF2683)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.8  10.1   1.4e-44   5.1e-41       1      78 []       4      81 ..       4      81 .. 1.00

  Alignments for each domain:
  == domain 1  score: 138.8 bits;  conditional E-value: 1.4e-44
                       DUF2683  1 mvqaivdisDesnriieivKakydlkdksaAidllieqyaeyllEaElkPefvekirnimKgeepidigdiedlrkry 78
                                  mv+aivdi+De+nrii+ivKaky+l+dks+Ai+++ie+yae+llE+ElkPe++ekirnimK+e+pi+ig+ie+l+kry
  gi|15669361|ref|NP_248166.1|  4 MVKAIVDITDENNRIINIVKAKYNLRDKSQAINKIIEEYAEFLLEDELKPEYIEKIRNIMKNEKPIYIGSIENLKKRY 81
                                  9****************************************************************************9 PP

>> DarT  ssDNA thymidine ADP-ribosyltransferase, DarT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   5.3e-06     0.019     126     173 ..      16      64 ..       7      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.3e-06
                          DarT 126 eidwdlvyakswknt.eedsdrkerkqAEvLvkdsiplelitgigvrne 173
                                   +  +++v+ak++ ++ ++  +   ++ AE+L +d++ +e+i++i  + +
  gi|15669361|ref|NP_248166.1|  16 NRIINIVKAKYNLRDkSQAINKIIEEYAEFLLEDELKPEYIEKIRNIMK 64 
                                   445789999988888666888888999***************9976555 PP

>> DsrC  DsrC like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.3   6.8e-06     0.024      34      84 ..       8      58 ..       2      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.8e-06
                          DsrC 34 gieLteehwevikflreyyeeygvapairklvkalkkelgeekgnskelye 84
                                   +++t+e  ++i++++++y+ ++++ ai+k++++ ++ l e++ + +++ +
  gi|15669361|ref|NP_248166.1|  8 IVDITDENNRIINIVKAKYNLRDKSQAINKIIEEYAEFLLEDELKPEYIEK 58
                                  4699********************************999998888888876 PP

>> TEX12  Testis-expressed 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.9   2.5e-05      0.09      30      72 ..      27      68 ..      15      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                         TEX12 30 vlndmskeinlllskyakilseraavdasyieeidalfkeast 72
                                  +l d s+ in ++ +ya+ l e   +   yie+i  ++k+ + 
  gi|15669361|ref|NP_248166.1| 27 NLRDKSQAINKIIEEYAEFLLED-ELKPEYIEKIRNIMKNEKP 68
                                  699*****************997.57899*********98654 PP

>> AcMNPV_Ac109  Autographa californica nuclear polyhedrosis virus (AcMNPV) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.4   1.7e-05     0.062     253     306 ..      11      64 ..       4      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                  AcMNPV_Ac109 253 itrsslkilkliqellgisdysdilvdlvkyfkklifnyqlvPkviiklsnide 306
                                   it ++ +i+  ++ + ++ d s+ + ++++ +  ++++ +l P+ i+k+ ni +
  gi|15669361|ref|NP_248166.1|  11 ITDENNRIINIVKAKYNLRDKSQAINKIIEEYAEFLLEDELKPEYIEKIRNIMK 64 
                                   7888889999999999999********************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1165  (0.0649785); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 558.82
//
Query:       gi|15669362|ref|NP_248167.1|  [L=94]
Description: hypothetical protein MJ_1173 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-08   35.2   0.2    1.6e-08   35.1   0.2    1.1  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
    6.7e-06   26.3   3.1    8.1e-06   26.1   3.1    1.1  1  YafQ_toxin       Bacterial toxin of type II toxin-antitoxin s
    0.00043   20.2   4.1     0.0016   18.3   4.1    1.8  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
     0.0032   17.5   1.6     0.0039   17.3   1.6    1.1  1  Toxin_YhaV       Toxin with endonuclease activity, of toxin-a
  ------ inclusion threshold ------
      0.022   15.2   1.6      0.032   14.6   1.6    1.3  1  HigB-like_toxin  RelE-like toxin of type II toxin-antitoxin s
      0.039   14.7   0.1      0.043   14.5   0.1    1.1  1  FliD_N           Flagellar hook-associated protein 2 N-termin
      0.056   13.7   0.1      0.067   13.4   0.1    1.2  1  DUF3369          Domain of unknown function (DUF3369)


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.2   6.2e-12   1.6e-08       7      90 .]      10      86 ..       4      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 6.2e-12
                                  HHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEE.CTSTCCTTEEEEEEC.TEEEEEEEETSTTEEEEEEEEEHH CS
                    ParE_toxin  7 Alkdlkkiadyiardgpaakrfldaleealellaenpalgrp.rrelglkglrririg.dyriiYriddeelvvvilrvlhrs 87
                                    k l+k+ +         k+ l+a+ +++e++ +np+++++ r+   l+++ r++i+  +++++++d+++++v++++  h++
  gi|15669362|ref|NP_248167.1| 10 LDKILQKLSKR-------DKKKLKAILKKMEEITQNPHHYKNlRHP--LNDFKRVHIDkSFVLVFTVDENNKTVIFVDFDHHD 83
                                  45555555554.......999*********************3333..559****************99999999*******9 PP

                                  HHC CS
                    ParE_toxin 88 edy 90
                                   +y
  gi|15669362|ref|NP_248167.1| 84 NIY 86
                                  776 PP

>> YafQ_toxin  Bacterial toxin of type II toxin-antitoxin system, YafQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   3.1   3.1e-09   8.1e-06       1      87 [.       2      86 ..       2      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.1e-09
                                  -EEEEEHHHHHHHHHHHHTT--HHHHHHHHHHHHTT-S--GGG--EE-SSS-TTEEEEEEETTEEEEEEE-SS..EEEEEEEE CS
                    YafQ_toxin  1 ykikptkqfkkdlkrlkkrkkdleklkevlklLaegepLpekyrdHaLkgnwkgyrecHikpDllLiYrledd..elvlvrlG 81
                                  y+i++  + +k l++l+kr  d++klk++lk++ e ++ p++y++  L   +++++ +Hi + ++L+++++++  ++++v+ +
  gi|15669362|ref|NP_248167.1|  2 YEIEIMPSLDKILQKLSKR--DKKKLKAILKKMEEITQNPHHYKN--LRHPLNDFKRVHIDKSFVLVFTVDENnkTVIFVDFD 80
                                  6788888999999999975..678999999999998877777764..55555699***************99777******** PP

                                  -HHHHH CS
                    YafQ_toxin 82 sHself 87
                                   H++++
  gi|15669362|ref|NP_248167.1| 81 HHDNIY 86
                                  **9986 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   4.1   6.3e-07    0.0016       5      87 .]       8      90 ..       4      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.3e-07
               ParE-like_toxin  5 rrfkkalkklkeklka...dldkavkeiiedPelGeeKkGDLsgvfvykfklnkqltllaYeldekkrvlvlllvGtheNfYr 84
                                  +++ k+l+kl+++ k+   ++ k+++ei+++P+  ++    L++   +     ++ + l +++de+++++  + +  h+N Y+
  gi|15669362|ref|NP_248167.1|  8 PSLDKILQKLSKRDKKklkAILKKMEEITQNPHHYKNLRHPLNDFKRV---HIDKSFVLVFTVDENNKTVIFVDFDHHDNIYK 87
                                  67788888988775550115668899********99999888876444...457889999**********************9 PP

               ParE-like_toxin 85 elK 87
                                  + K
  gi|15669362|ref|NP_248167.1| 88 KKK 90
                                  876 PP

>> Toxin_YhaV  Toxin with endonuclease activity, of toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.6   1.5e-06    0.0039      31      98 ..      18      79 ..      11      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-06
                    Toxin_YhaV 31 kkaavkllaaiaklilekipadPtaseyrlgktLgekykhwkrakllqryRLFFRydseskiivlaWv 98
                                  +k++ k l+ai k + e+i+++P + + +l ++L+    ++kr+ + + + L F +d+++k+++++  
  gi|15669362|ref|NP_248167.1| 18 SKRDKKKLKAILKKM-EEITQNPHHYK-NLRHPLN----DFKRVHIDKSFVLVFTVDENNKTVIFVDF 79
                                  5788999****9997.57*****8644.4556666....799*********************99755 PP

>> HigB-like_toxin  RelE-like toxin of type II toxin-antitoxin system HigB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.6   1.3e-05     0.032      21      92 ..      13      81 ..       7      82 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
               HigB-like_toxin 21 iqsklakklrrklqaldaaedekdlrappsnklekLkgdlkglySirvNkqyrlifkfkaeeaevvdlylDy 92
                                  i  kl k+ ++kl+a+ +  + +++   +  ++++L+  l+++  +++ k + l+f+ ++++++v  +  D 
  gi|15669362|ref|NP_248167.1| 13 ILQKLSKRDKKKLKAILK--KMEEITQ-NPHHYKNLRHPLNDFKRVHIDKSFVLVFTVDENNKTVIFVDFDH 81
                                  556666666777777653..4455555.679***************************77776665444555 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.7e-05     0.043       5      49 ..      10      54 ..       9      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHH CS
                        FliD_N  5 tdslvkqlmkaerakldkleqkktklewkqsayrelnsklsnlks 49
                                  +d+++++l k +++kl+ + +k +++++    y++l+  l+++k 
  gi|15669362|ref|NP_248167.1| 10 LDKILQKLSKRDKKKLKAILKKMEEITQNPHHYKNLRHPLNDFKR 54
                                  589****************************************98 PP

>> DUF3369  Domain of unknown function (DUF3369)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.6e-05     0.067      88     140 ..      30      83 ..      10      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                       DUF3369  88 kpleela.deelrelleraleskkslfeddfvvlyfktkegsegvlylettrpl 140
                                   k++ee+  +++  ++l++ l++ k ++ d+++vl f  +e++++v++++ ++  
  gi|15669362|ref|NP_248167.1|  30 KKMEEITqNPHHYKNLRHPLNDFKRVHIDKSFVLVFTVDENNKTVIFVDFDHHD 83 
                                   456666668999*****************9999****************77654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2198  (0.122595); expected 358.6 (0.02)
Passed bias filter:                      955  (0.0532657); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 648.54
//
Query:       gi|15669363|ref|NP_248168.1|  [L=540]
Description: CTP synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.3e-131  437.7   0.2   2.2e-131  437.0   0.2    1.3  1  CTP_synth_N    CTP synthase N-terminus
    1.4e-58  197.8   0.0    2.4e-58  197.0   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    8.2e-05   22.5   0.0    0.00039   20.2   0.0    2.1  1  Peptidase_C26  Peptidase C26
     0.0013   18.8   0.0      0.003   17.6   0.0    1.9  2  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
       0.21   10.8   0.1        0.6    9.4   0.0    1.7  2  DUF1611        Domain of unknown function (DUF1611_C) P-loop 


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.0   0.2  6.1e-135  2.2e-131       1     265 []       5     267 ..       5     267 .. 0.99

  Alignments for each domain:
  == domain 1  score: 437.0 bits;  conditional E-value: 6.1e-135
                                   EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT--- CS
                   CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfldikl 81 
                                   k+i++tGGv+S+lGkGi+aaslg+llk+rg+kv++ikiDPYl++dagt+sp+ehGEvfv++dG+e+DlDlG+YeRf+d++l
  gi|15669363|ref|NP_248168.1|   5 KFIFITGGVISSLGKGITAASLGRLLKARGFKVNMIKIDPYLQIDAGTMSPYEHGEVFVTEDGGESDLDLGHYERFIDENL 85 
                                   8******************************************************************************** PP

                                   -GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHHHHHHHHHH CS
                   CTP_synth_N  82 tkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfleairqlkle 162
                                   tk+nnittGkiy+sv++ker+G+ylGktvqviph+t+eik++i+++ +    d++iveigGtvgdieslpfleairq+k++
  gi|15669363|ref|NP_248168.1|  86 TKNNNITTGKIYWSVLTKERKGEYLGKTVQVIPHITNEIKDWIKNLGE--GYDITIVEIGGTVGDIESLPFLEAIRQFKKD 164
                                   ***********************************************8..8****************************** PP

                                   H-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--GGGEEEEE--S-G CS
                   CTP_synth_N 163 lgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvekeavisvkdvesi 243
                                   +gkenvl+ihv+l+p+++aagelktkptqhsvkelrs+Giqpdi++cr+e++++++++ek+alfc+v+keavi+++d+++i
  gi|15669363|ref|NP_248168.1| 165 VGKENVLYIHVSLLPYIRAAGELKTKPTQHSVKELRSIGIQPDILICRTEMPISDKIREKLALFCDVDKEAVIEARDARTI 245
                                   ********************************************************************************* PP

                                   GGHHHHHHHCTHHHHHHHHTT- CS
                   CTP_synth_N 244 yevpllleeqglaelileklkl 265
                                   yevpl le++gl +l+++kl+l
  gi|15669363|ref|NP_248168.1| 246 YEVPLNLEKEGLGKLVTKKLNL 267
                                   ********************97 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.0   0.0   6.8e-62   2.4e-58       2     189 ..     302     532 ..     301     533 .. 0.93

  Alignments for each domain:
  == domain 1  score: 197.0 bits;  conditional E-value: 6.8e-62
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHH.........HHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS- CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeei.........lellknpdgilvsgGpgspgvegkieaikearenkiP 73 
                                   l+D+y s+te+l+ha+++++ kv++ +i+++ +e+         + + ++ dgilv+gG+g++gvegki+aik+aren+iP
  gi|15669363|ref|NP_248168.1| 302 LKDAYLSITEALIHAGAKNDTKVNINWIHSERLESeefeelldrYREDNQLDGILVPGGFGDRGVEGKINAIKYARENDIP 382
                                   89****************************99999676666543215899******************************* PP

                                   EEEETHHHHHHHHHTTTEEE.......................EEECEEEEEEEEEEEETTT........CGGTTTTSEEE CS
                        GATase  74 iLGICLGmQllaiefgrkvv.......................kekekehhggtmrlgddet........allyglknevi 123
                                   +LGIC+GmQ+++ief+r+v                        ++ke + +ggtmrlg++++         +lyg  +ev+
  gi|15669363|ref|NP_248168.1| 383 FLGICMGMQCAVIEFARNVCgleganstefdentkypvvdllpEQKEIDAKGGTMRLGAYPAilmegtlaYKLYGR-KEVY 462
                                   *****************9999999999999999999999****9999***********************99***9.99** PP

                                   EEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHH CS
                        GATase 124 erhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflik 189
                                   erhrHryevnp+    le++gl++++ks d+ +l+e+ie ++ + f+++Q HPE++s+p++p++lf++l++
  gi|15669363|ref|NP_248168.1| 463 ERHRHRYEVNPEyheILENHGLTISGKSPDG-RLAEFIEISKnRyFIATQAHPEFKSRPNKPHPLFDGLVR 532
                                   *************98789999*******888.8999999888789***********************987 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.1e-07   0.00039      97     216 .]     372     515 ..     367     515 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-07
                 Peptidase_C26  97 LiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe..........q...saashavkve.......... 154
                                    i+ a e+++P lgiC G+q   + +  ++        + t++ e++          q   +        +          
  gi|15669363|ref|NP_248168.1| 372 AIKYARENDIPFLGICMGMQCAVIEFARNVCGLEG--ANSTEFDENTkypvvdllpeQkeiD-------AKggtmrlgayp 443
                                   6788999*************998877666543222..2334444444334554444413342.......333333444667 PP

                 Peptidase_C26 155 ....kgsllaellgseeievnslHhqaike......laeelrveAvaeDg.viEaieseeakafvlgvQwHPE 216
                                       +g+l ++l+g++e+     H+  ++        +++l ++  ++Dg + E+ie+ +++  +++ Q HPE
  gi|15669363|ref|NP_248168.1| 444 ailmEGTLAYKLYGRKEVYERHRHRYEVNPeyheilENHGLTISGKSPDGrLAEFIEISKNR-YFIATQAHPE 515
                                   77779*********99999999999999988999877889*********95679***99977.899******9 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   8.4e-07     0.003       8      55 ..      15      73 ..       7     359 .. 0.78
   2 ?   -3.1   0.0       2.1   7.5e+03     104     118 ..     416     430 ..     406     435 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.4e-07
                                  TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH..............C CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............x RF
                          CbiA  8 GGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep..............d 55
                                  +  GK  +aa+L+r+l+ rg++V +++ Dp    +a   g+    e               d
  gi|15669363|ref|NP_248168.1| 15 SSLGKGITAASLGRLLKARGFKVNMIKIDPYLQIDA---GTMSPYEHgevfvtedggesdlD 73
                                  567***************************865555...33333333455555556666663 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.1
                                   CTS-EEEEEE--CCH CS
                                   xxxxxxxxxxxxxxx RF
                          CbiA 104 ygvpvlgviprdeav 118
                                   ++ pv++++p+ +++
  gi|15669363|ref|NP_248168.1| 416 TKYPVVDLLPEQKEI 430
                                   3899******99987 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00017       0.6      17      51 ..      10      44 ..       3      56 .. 0.84
   2 ?   -3.2   0.0       1.1   4.1e+03     157     183 ..     323     349 ..     302     352 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00017
                       DUF1611 17 vvGTdcavGKrttaleleealeerGlkaafvaTgq 51
                                  ++G  +++GK +ta  l + l++rG+k++++  ++
  gi|15669363|ref|NP_248168.1| 10 TGGVISSLGKGITAASLGRLLKARGFKVNMIKIDP 44
                                  56667899**********************98776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.1
                       DUF1611 157 kvvgislNtknlseeeakealeeleee 183
                                   kv    + ++ l+ ee++e l++++e+
  gi|15669363|ref|NP_248168.1| 323 KVNINWIHSERLESEEFEELLDRYRED 349
                                   455556788889999999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 3619.43
//
Query:       gi|15669364|ref|NP_248169.1|  [L=378]
Description: chorismate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.9e-143  476.5   0.0   3.3e-143  476.3   0.0    1.0  1  Chorismate_synt  Chorismate synthase
  ------ inclusion threshold ------
      0.047   14.1   0.1       0.32   11.5   0.0    2.1  2  G5               G5 domain
      0.049   13.4   0.1      0.077   12.8   0.1    1.3  1  BCIP             p21-C-terminal region-binding protein


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.3   0.0  5.5e-147  3.3e-143       1     327 []      12     368 ..      12     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: 476.3 bits;  conditional E-value: 5.5e-147
                                   SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE-TTS CS
               Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallieNkdq 81 
                                   +rvt+fGeShgka+gav+dg+pa+l+l+eediqkeLdrRrpgqs ++t+rkE+D+veilsG+fegkt+G+pi+ ++ Nk++
  gi|15669364|ref|NP_248169.1|  12 FRVTVFGESHGKAVGAVVDGCPANLPLSEEDIQKELDRRRPGQSIFSTPRKEEDKVEILSGIFEGKTTGAPICSIVYNKNM 92 
                                   89******************************************************************************* PP

                                   -..SSSSSTSBE-TTSTCHHHHHHC-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHT.TTEEEEEEEEEETTE........ CS
               Chorismate_synt  82 rskdyeeikevpRpgHADltyalkYgirdlrgggrsSaReTaarvaaGavakklLke.lgieivayvssigei........ 153
                                   r+kdy++ik++pRpgHADlty lkY++ d+rgggr+S+R T+++v+ Ga+akklL+  ++i+i++y+++ig+i        
  gi|15669364|ref|NP_248169.1|  93 RPKDYSKIKDTPRPGHADLTYRLKYKNYDYRGGGRASGRVTIGHVIGGAIAKKLLSYtYNIKIIGYTIKIGKIegdfsyyk 173
                                   *************************999****************************878************8889999999 PP

                                   ...............CHHHHHTT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHHT CS
               Chorismate_synt 154 ...............ekeaenpvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalms 219
                                                  e  ++np+rcp+ + ++emee++ +a++++ds+Ggvve+v+ +vp+G+G+p+f+kl+++La+alms
  gi|15669364|ref|NP_248169.1| 174 npevfenekslerliEIIESNPLRCPSMN-EKEMEEYVLKAMENKDSVGGVVEIVALNVPVGVGNPIFNKLNGELARALMS 253
                                   999999999998876544889*****987.899************************************************ PP

                                   STTEEEEEETTGGGGGGSBHHHHS--EE......EE.SS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTTS-E- CS
               Chorismate_synt 220 ipAvkgveiGsGfeaaelkGseanDeiv......lr.ktnnaGGieGGisnGepivvrvavKpipsiakeqktvdletkee 293
                                   i+AvkgveiG+Gf+aae+ Gse+nDe++      +r ktnn+GGi+GGis G+piv+r+avKp+psi k+qkt++l+t e+
  gi|15669364|ref|NP_248169.1| 254 INAVKGVEIGAGFKAAEMYGSEMNDEMYfdddknIRfKTNNCGGILGGISCGTPIVLRIAVKPTPSIGKKQKTINLKTLEN 334
                                   ****************************766655338******************************************** PP

                                   EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHHH CS
               Chorismate_synt 294 velevkgrhDpcvvpravvvveamvalvladall 327
                                   ve+e++grhDp++vpr+v+v+eamva++lad+++
  gi|15669364|ref|NP_248169.1| 335 VEIEIEGRHDPVIVPRIVPVAEAMVAITLADLMI 368
                                   *******************************985 PP

>> G5  G5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.3e-05      0.32      21      48 ..      92     119 ..      84     120 .. 0.86
   2 ?   -0.6   0.1      0.32   1.9e+03      33      56 ..     318     341 ..     313     354 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.3e-05
                                   TS-TT-EEEEE--B-EEEEEEEEEEEET CS
                            G5  21 slpkgeekVvqeGknGvkevtyrvtyen 48 
                                     pk+++k++  +++G+ + tyr++y+n
  gi|15669364|ref|NP_248169.1|  92 MRPKDYSKIKDTPRPGHADLTYRLKYKN 119
                                   3689**********************98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.32
                                   -B-EEEEEEEEEEEETTEEEEE-- CS
                            G5  33 GknGvkevtyrvtyenGkevsrev 56 
                                   ++ G+k++t+ +++  ++e++ e 
  gi|15669364|ref|NP_248169.1| 318 PSIGKKQKTINLKTLENVEIEIEG 341
                                   677999999999988888887765 PP

>> BCIP  p21-C-terminal region-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.3e-05     0.077      78     145 ..     181     251 ..     143     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                          BCIP  78 kecikqlkeyllekakksass.kkklkk.lLss.skdkkvglliseRliNiPvevvpplykmLleeiewaq 145
                                   +++++ l+e + ++  +  s  +k++++ +L++ +++ +vg ++    +N+Pv v  p+++ L  e+++a 
  gi|15669364|ref|NP_248169.1| 181 EKSLERLIEIIESNPLRCPSMnEKEMEEyVLKAmENKDSVGGVVEIVALNVPVGVGNPIFNKLNGELARAL 251
                                   467778888887765555554557777779987768899****************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2492.26
//
Query:       gi|15669365|ref|NP_248170.1|  [L=430]
Description: proteasome-activating nucleotidase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-44  151.5   0.0    3.7e-44  150.3   0.0    1.6  1  AAA              ATPase family associated with various cellul
    4.9e-18   64.7   0.4    4.9e-18   64.7   0.4    2.1  2  AAA_lid_3        AAA+ lid domain
    1.9e-10   40.5   0.9      5e-10   39.2   0.9    1.8  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    1.8e-07   31.4   0.0    1.8e-07   31.4   0.0    2.2  1  AAA_2            AAA domain (Cdc48 subfamily)
    9.4e-07   28.7   0.0    2.4e-06   27.4   0.0    1.7  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.2e-06   26.5   0.1    3.6e-05   23.8   0.1    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
    7.8e-06   25.5   0.3    2.4e-05   23.9   0.3    1.8  1  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
    1.8e-05   25.2   2.4    0.00079   19.8   0.0    2.6  2  AAA_16           AAA ATPase domain
    4.5e-05   22.7   0.0    0.00011   21.4   0.0    1.7  1  DUF815           Protein of unknown function (DUF815)
     0.0004   20.7   2.4     0.0078   16.5   0.1    2.8  2  AAA_22           AAA domain
    0.00081   19.7   0.0     0.0054   17.1   0.0    2.3  2  RNA_helicase     RNA helicase
     0.0013   18.0   1.4     0.0022   17.3   0.1    2.1  2  TIP49            TIP49 P-loop domain
      0.002   17.9   0.0     0.0048   16.7   0.0    1.7  1  IstB_IS21        IstB-like ATP binding protein
     0.0024   17.8   0.1     0.0075   16.1   0.0    1.9  1  AAA_3            ATPase family associated with various cellul
     0.0024   17.3   0.6      0.068   12.5   0.6    2.6  1  ATPase           KaiC
     0.0028   18.2   1.5     0.0092   16.5   0.0    2.6  3  AAA_18           AAA domain
      0.006   16.0   0.1      0.016   14.6   0.1    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0062   16.6   2.4      0.012   15.6   0.0    2.5  2  AAA_14           AAA domain
     0.0064   16.7   0.0      0.018   15.2   0.0    1.8  1  AAA_33           AAA domain
     0.0083   16.4   1.1      0.012   15.9   0.0    1.8  2  AAA_28           AAA domain
     0.0091   15.7   4.1     0.0092   15.7   0.1    2.6  3  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.028   14.1   0.1       0.22   11.2   0.1    2.3  1  Sigma54_activat  Sigma-54 interaction domain
      0.028   14.2   1.2       0.64    9.8   0.1    3.1  2  Bac_DnaA         Bacterial dnaA  protein
      0.031   13.6   0.2      0.073   12.3   0.0    1.7  1  Zeta_toxin       Zeta toxin
      0.038   14.0   0.0       0.09   12.8   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.047   13.2   0.2       0.22   11.0   0.0    2.1  2  AAA_7            P-loop containing dynein motor region
      0.056   12.9   0.4       0.19   11.2   0.1    1.9  2  PhoH             PhoH-like protein
        0.1   12.1   0.1       0.42   10.2   0.1    2.0  1  AAA_25           AAA domain
       0.11   13.0   0.1       0.11   13.0   0.1    3.3  2  AAA_17           AAA domain
       0.11   11.6   0.0       0.22   10.6   0.0    1.5  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.24   11.1   1.4       0.53   10.0   0.4    2.1  1  AAA_30           AAA domain
       0.97    9.3   0.0       0.97    9.3   0.0    3.3  3  ATPase_2         ATPase domain predominantly from Archaea
        1.9    8.2   8.0        1.2    8.9   0.0    2.4  2  AAA_11           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.3   0.0   6.8e-47   3.7e-44       1     131 [.     207     339 ..     207     340 .. 0.96

  Alignments for each domain:
  == domain 1  score: 150.3 bits;  conditional E-value: 6.8e-47
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTCC CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgse 78 
                                   +llyGppGtGKTllakava+e++++f+++ gsel++k++ge+++ ++++fk akeka psi+fiDEida+a +r    ++ 
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKA-PSIIFIDEIDAIAAKRtdaLTGG 286
                                   69******************************************************9.****************9876678 PP

                                   CHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  79 seeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   ++e +r++ qLl+e+dg++ + ++v +igatnrpd ldpa+lr gRfdr+ie++
  gi|15669365|ref|NP_248170.1| 287 DREVQRTLMQLLAEMDGFDAR-GDVKIIGATNRPDILDPAILRpGRFDRIIEVP 339
                                   88999999************7.66***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       3.3   1.8e+03       5      18 ..     273     287 ..     270     287 .. 0.77
   2 !   64.7   0.4     9e-21   4.9e-18       1      45 []     362     406 ..     362     406 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.3
                     AAA_lid_3   5 keLAe.rTeGySGAD 18 
                                   +++A+ rT+  +G D
  gi|15669365|ref|NP_248170.1| 273 DAIAAkRTDALTGGD 287
                                   666666***999987 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 9e-21
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfee 45 
                                   dv+l+e+A++TeG++GA+l+a+c eA+++A+r+ ++ +tm+df++
  gi|15669365|ref|NP_248170.1| 362 DVNLEEIAKMTEGCVGAELKAICTEAGMNAIRELRDYVTMDDFRK 406
                                   9******************************************86 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.9   9.2e-13     5e-10       1      57 []      94     149 ..      94     149 .. 0.99

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 9.2e-13
                                   EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                   V+tV++ +++ ++++Vk+s++  ++v+++  v++++L pg +V ++++t  ++++LP
  gi|15669365|ref|NP_248170.1|  94 VGTVVDKVGE-RKVVVKSSTGPSFLVNVSHFVNPDDLAPGKRVCLNQQTLTVVDVLP 149
                                   9*********.*********************************************9 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   3.4e-10   1.8e-07       6     104 ..     207     299 ..     202     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 3.4e-10
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----- CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpke 84 
                                   ill gp g+Gkt+laka+a   ++    ++ir+  sel +    + + +     ++  + a+e+   i+++DEid i++k+
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVATETNA----TFIRVVGSELVK----KFIGEGASLVKDIFKLAKEKApsIIFIDEIDAIAAKR 279
                                   8999******************96....************....88889999999999999999999************86 PP

                                   --------HHHHHHHHHHHH CS
                         AAA_2  85 ssgadvSregVqrdLLqile 104
                                   +        +Vqr L+q+l 
  gi|15669365|ref|NP_248170.1| 280 TDALTGGDREVQRTLMQLLA 299
                                   6667777889*******995 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   4.4e-09   2.4e-06      34      99 ..     205     278 ..     180     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.4e-09
                        RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvleka..gdlaalltnl......eekdvlfideihrlsra 99 
                                     +llyGpPG Gkt lak +a+e ++++    g  l k+  g+ a+l++++      ++  ++fidei  ++ +
  gi|15669365|ref|NP_248170.1| 205 KGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKKfiGEGASLVKDIfklakeKAPSIIFIDEIDAIAAK 278
                                   569**********************997666665554433466666655432222223457*******988765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   6.6e-08   3.6e-05       2     131 ..     207     323 ..     206     329 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.6e-08
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--HHH CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEveraesev 81 
                                   +lL GppGtgK+ la+ +a  +n+++  v +++      l+ +    ++++slv+ +++ a +  ++i+++DE++ +  + 
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVATETNATFIRVVGSE------LVKKFI--GEGASLVKDIFKLAKEkAPSIIFIDEIDAIAAKR 279
                                   89*************************999987......666666..56668888888855556889********999998 PP

                                   HHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS--.-TT-TT CS
                         AAA_5  82 lnsLlslleerrllleeggelvkaknddller..frviatanpldrslnels 131
                                   +++L     e ++ l+++  +++     +  r  + +i+++n++d     l+
  gi|15669365|ref|NP_248170.1| 280 TDALTGGDREVQRTLMQLLAEMDG----FDARgdVKIIGATNRPD----ILD 323
                                   888866655555555555555533....33444699999999988....444 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.3   4.4e-08   2.4e-05       2      56 ..      94     149 ..      93     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.4e-08
                 Prot_ATP_OB_N   2 yGtflavnsqdgtadVlvggrrmrVavsPlvdaeeLrpGqeVlLnEa.lvvVealg 56 
                                   +Gt++  + +++ +  ++ g  + V+vs  v++++L pG +V Ln++ l+vV++l+
  gi|15669365|ref|NP_248170.1|  94 VGTVVDKVGERKVVVKSSTGPSFLVNVSHFVNPDDLAPGKRVCLNQQtLTVVDVLP 149
                                   699999998888999999***************************86367888774 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.5e-06   0.00079      16      55 ..     196     232 ..     190     247 .. 0.79
   2 ?    4.5   0.0     0.075        41     122     155 ..     251     283 ..     247     303 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.5e-06
                        AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggif 55 
                                   +e+v    p  +ll+G++G+GK+ l+++++++ +++   f
  gi|15669365|ref|NP_248170.1| 196 FEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNAT---F 232
                                   56666666799******************9855544...4 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.075
                        AAA_16 122 llkrllallsrderplvlvlDdlqwadeaslqll 155
                                   l+k++++l+++ + p ++++D+++ + +   ++l
  gi|15669365|ref|NP_248170.1| 251 LVKDIFKLAKE-KAPSIIFIDEIDAIAAKRTDAL 283
                                   55667788888.778*********7777655554 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.1e-07   0.00011      17     116 ..     159     272 ..     149     279 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.1e-07
                        DUF815  17 epveevdevklddLvgidkqkealventeqfleg.........lpannvLLwGarGtGKSslvkallneyaeegLrli..e 86 
                                     v+e  +v+ +d+ g++kq +++ e +e  l++         +p + +LL+G  GtGK  l ka+ +e++++ +r++  e
  gi|15669365|ref|NP_248170.1| 159 MEVDERPNVRYEDIGGLEKQMQEIREVVELPLKHpelfekvgiEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVgsE 239
                                   556777788888888888888888777664333211111122368899*****************************9888 PP

                        DUF815  87 vekedlkelpklvellr...erperfilfvDDL 116
                                   + k+ + e  +lv+ +    +++   i+f+D +
  gi|15669365|ref|NP_248170.1| 240 LVKKFIGEGASLVKDIFklaKEKAPSIIFIDEI 272
                                   999999998888886542226677789999975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.4e-05    0.0078       8      40 ..     207     230 ..     202     243 .. 0.83
   2 ?    2.5   0.0       0.3   1.6e+02      84     105 ..     257     279 ..     246     315 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerp 40 
                                   ++++G++GtGKT+l++ ++ +          ++
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVATET---------NA 230
                                   89***************99987.........44 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.3
                        AAA_22  84 qalraravielliiDEaqhlr..s 105
                                   + ++++a  +++ iDE++ +   +
  gi|15669365|ref|NP_248170.1| 257 KLAKEKAP-SIIFIDEIDAIAakR 279
                                   55566666.9*********96652 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     1e-05    0.0054       1      68 [.     207     265 ..     207     279 .. 0.79
   2 ?   -1.2   0.0         5   2.7e+03      51      73 ..     397     416 ..     393     427 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenps 68 
                                   i+lyGp+g+GK++lak +          ++++ +++r + ++ ++++ g+ + ++ D+ +  +e+ ps
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAV---------ATETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPS 265
                                   789**************3.........35567788899999999999999999999998888776666 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5
                  RNA_helicase  51 evvvidDfgqvkdeenpsdlael 73 
                                   ++v +dDf + +++    +++ +
  gi|15669365|ref|NP_248170.1| 397 DYVTMDDFRKAVEK---IMEKKK 416
                                   57899**9999877...344444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       2.9   1.6e+03     150     175 ..      22      47 ..       5     125 .. 0.71
   2 !   17.3   0.1     4e-06    0.0022      51      92 ..     205     244 ..     197     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.9
                                   SS-EEEEEE-HHHHHHHHHHT--TT- CS
                         TIP49 150 akeekklklgskiaeellkekvkegD 175
                                    keek+++ +s++ ++llke+++e+ 
  gi|15669365|ref|NP_248170.1|  22 FKEEKEINDNSNLKNDLLKEELQEKA 47 
                                   45556666666666666666665543 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysle 92 
                                   +++Ll Gp+gtGkt la a++ e +    f+ ++gse+ +  
  gi|15669365|ref|NP_248170.1| 205 KGILLYGPPGTGKTLLAKAVATETN--ATFIRVVGSELVKKF 244
                                   89********************977..78*******997665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.8e-06    0.0048      45      74 ..     202     231 ..     189     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.8e-06
                     IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavra 74 
                                   e  ++i+l Gp+G+GK+ la a+++e+ ++
  gi|15669365|ref|NP_248170.1| 202 EPPKGILLYGPPGTGKTLLAKAVATETNAT 231
                                   556789****************99887555 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-05    0.0075       2      92 ..     207     293 ..     206     304 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqsal 82 
                                   +ll g PG++ktll+ka+a+  +++f r+ + ++l+   i     + ++  ++  +k p   ++++ dei+  ++k   al
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVATETNATFIRV-VGSELVKKFIGEGASLVKDIFKLAKEKAP---SIIFIDEIDAIAAKRTDAL 283
                                   7999************************9.56677766554334444555566666666...6788888888888888888 PP

                         AAA_3  83 leameerqvt 92 
                                       +e q t
  gi|15669365|ref|NP_248170.1| 284 TGGDREVQRT 293
                                   7766666655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.6   0.00013     0.068      12      80 ..     196     261 ..     191     301 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                        ATPase  12 l.kgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleee 80 
                                   + k Gi   + +l++G pGtGKt++a+  + +     +   + v   e  ++++ + +sl  d+ kl +e
  gi|15669365|ref|NP_248170.1| 196 FeKVGIEPPKGILLYGPPGTGKTLLAKAVATET----NATFIRVVGSELVKKFIGEGASLVKDIFKLAKE 261
                                   54668888899**************98765544....233444444444466666666666666666555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       5.7   3.1e+03      25      44 ..      27      46 ..       7     100 .. 0.53
   2 !   16.5   0.0   1.7e-05    0.0092       1      34 [.     207     261 ..     207     320 .. 0.66
   3 ?   -1.7   0.0       7.4     4e+03      16      43 ..     366     395 ..     363     422 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.7
                        AAA_18 25 gvnlrdvakenglllevdpe 44
                                   +n ++++k++ l +e +++
  gi|15669365|ref|NP_248170.1| 27 EINDNSNLKNDLLKEELQEK 46
                                  33444444443333333333 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.7e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvake 34 
                                   Ill G+pG+GKt lak+++ +++                      +  + ++ake
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVATETNAtfirvvgselvkkfigegaslVKDIFKLAKE 261
                                   99****************9997556787775444444444444444444444444 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 7.4
                        AAA_18  16 keLskrl.gf.gvnlrdvakenglllevdp 43 
                                   +e++k++ g+ g +l+ +++e g+   ++ 
  gi|15669365|ref|NP_248170.1| 366 EEIAKMTeGCvGAELKAICTEAGMNAIREL 395
                                   567777777787777777777666543333 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   2.9e-05     0.016      25      43 ..     207     225 ..     199     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.9e-05
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll+GppG+GKt+lak+++
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVA 225
                                   89*************9976 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   1.7         5   2.7e+03      45      45 ..      45      45 ..       2      88 .. 0.52
   2 !   15.6   0.0   2.3e-05     0.012       5      76 ..     207     275 ..     204     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5
                        AAA_14 45 k 45
                                  +
  gi|15669365|ref|NP_248170.1| 45 E 45
                                  1 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.3e-05
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                   +++ G+  +GKT l+k ++ e       ++ +   +  +k + + ++l + i++++ke+  +++f+DEi  +
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVATETN---ATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAI 275
                                   7899**************98877...666666655544444444447888888887777899*******987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.2e-05     0.018       2      28 ..     207     235 ..     207     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-05
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avll 28 
                                   +ll G+pG+GK+ la+ ++ ++   ++++
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVATETNatFIRV 235
                                   6789***************9999555555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.3       9.3     5e+03      43      54 ..      47      51 ..       5      87 .. 0.59
   2 !   15.9   0.0   2.2e-05     0.012       2      39 ..     207     249 ..     206     292 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 9.3
                        AAA_28 43 edalpwvedlla 54
                                          ++ +
  gi|15669365|ref|NP_248170.1| 47 A-------RIAE 51
                                  2.......2222 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.2e-05
                        AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileekl 39 
                                   i + G+++tGKT l++a a +     ++vv  E + +++ e++
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVATEtnatFIRVVgSELVKKFIGEGA 249
                                   7899***************443444777888888887776665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.3       7.9   4.3e+03     127     169 ..      18      58 ..       9      80 .. 0.67
   2 !   15.7   0.1   1.7e-05    0.0092       5      75 ..     207     273 ..     204     288 .. 0.64
   3 ?    0.5   0.0      0.81   4.4e+02      30      63 ..     384     415 ..     378     428 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.9
                        AAA_24 127 fiahektrkdedpegeakytrlepklgkktanelkeevDlvlr 169
                                   f+ + k++k  +++++ k++ l+ +l++k  + + e    +l 
  gi|15669365|ref|NP_248170.1|  18 FTEEFKEEKEINDNSNLKNDLLKEELQEK--ARIAELESRILK 58 
                                   66666777777777777888888888888..555555555555 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.7e-05
                        AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtid 75 
                                   il+yGp+g+GKT lak    + ++ fi + ++    +++        + +++++ +la+e+a  ++++iD id
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVatETNATFIRVVGSELVKKFIG-----EGASLVKDIFKLAKEKA-PSIIFIDEID 273
                                   89**************998777777775555443333333.....22344444444444444.3555555555 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.81
                        AAA_24  30 dtekGlksldadkfpdieswedfldevvel.aael 63 
                                    te+G++++   +  d  +++df+++v+++ + ++
  gi|15669365|ref|NP_248170.1| 384 CTEAGMNAIRELR--DYVTMDDFRKAVEKImE-KK 415
                                   5899999999988..44599999999999952.32 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00041      0.22      23      53 ..     205     232 ..     177     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00041
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpf 53 
                                     +l+ G  GtGK+lla+a+ ++++   + f
  gi|15669365|ref|NP_248170.1| 205 KGILLYGPPGTGKTLLAKAVATETN---ATF 232
                                   679***************9976554...444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0012      0.64      37     113 ..     207     279 ..     201     379 .. 0.70
   2 ?    1.2   0.1       0.5   2.7e+02      51      94 ..     380     422 ..     374     429 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHH.TT-SEEEEE-GGGGTT-H CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkekl.rkvDvLliDDiqflagke 113
                                   +++yg+ G Gkt L ka++ e+ ++    rvv   + e +++++    +  ++ fk    ++  ++ iD+i  +a k 
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVATETNAT--FIRVV---GSELVKKFIGEGASLVKDIFKLAKeKAPSIIFIDEIDAIAAKR 279
                                   79***************99876544..34554...5566666666555555555554330455678888888888875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.5
                                   HHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHH CS
                      Bac_DnaA  51 lkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkek 94 
                                   lkai  e+  na      Y+t ++F  ++v+ +++kk+ + ke 
  gi|15669365|ref|NP_248170.1| 380 LKAICTEAGMNAIRELRDYVTMDDFR-KAVEKIMEKKKVKVKEP 422
                                   677777777776666668******95.67888888888888874 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013     0.073      14      52 ..     202     238 ..     193     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                    Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldpD 52 
                                   e Pk ill G pG GK+ la+++++e+  +  ++r+ + 
  gi|15669365|ref|NP_248170.1| 202 EPPKGILLYGPPGTGKTLLAKAVATET--NATFIRVVGS 238
                                   6799**********************8..8888887665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00017      0.09      21      50 ..     199     235 ..     175     277 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                                   E.......EEEEESTTSSHHHHHHHHHHHTT------ CS
                          TsaE  21 v.......ilLeGdLGaGKTtlvrglakalgveevkS 50 
                                   v       ilL+G+ G+GKT l++++a + + + ++ 
  gi|15669365|ref|NP_248170.1| 199 VgieppkgILLYGPPGTGKTLLAKAVATETNATFIRV 235
                                   133344449******************9998874333 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0004      0.22      34      58 ..     205     229 ..     195     240 .. 0.83
   2 ?   -1.7   0.0       3.3   1.8e+03      68      96 ..     394     422 ..     380     425 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0004
                         AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                   k +ll+Gp GtGKt+++k + ++ +
  gi|15669365|ref|NP_248170.1| 205 KGILLYGPPGTGKTLLAKAVATETN 229
                                   779**************99887776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.3
                         AAA_7  68 nfsaqtsanqlqdiiesklekrrkgvygP 96 
                                   ++  + +  ++++ +e+ +ek++ +v  P
  gi|15669365|ref|NP_248170.1| 394 ELRDYVTMDDFRKAVEKIMEKKKVKVKEP 422
                                   566678889999999999*9999877655 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00034      0.19      23      42 ..     208     227 ..     201     243 .. 0.87
   2 ?   -1.9   0.0       3.5   1.9e+03      92     112 ..     404     424 ..     385     425 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00034
                                   EEE--TTSSTTHHHHHHHHH CS
                          PhoH  23 faiGpaGtGKtylavalave 42 
                                      Gp GtGKt+la a+a e
  gi|15669365|ref|NP_248170.1| 208 LLYGPPGTGKTLLAKAVATE 227
                                   578***********999976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.5
                                   -TTCHHHHHHTTSEEEEEGGG CS
                          PhoH  92 gaekvekllekgkievaplay 112
                                    +++vek++ek+k++v + a+
  gi|15669365|ref|NP_248170.1| 404 FRKAVEKIMEKKKVKVKEPAH 424
                                   467899999999999987766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00077      0.42      36      55 ..     207     226 ..     201     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00077
                        AAA_25  36 allaGapgtGKttlaldlal 55 
                                   +ll+G+pgtGKt la  +a 
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVAT 226
                                   69************977765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   2.7       3.8   2.1e+03      28      55 ..      37      65 ..       1     172 [. 0.74
   2 ?   13.0   0.1   0.00019      0.11       1      50 [.     210     260 ..     210     369 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.8
                                  HHHHHHHHTTTS.HSSHHHHCTSHHHHHH CS
                        AAA_17 28 dllreeakrggl.akardemrklpleekk 55
                                  dll ee +++   a+ ++++ kl+le+k+
  gi|15669365|ref|NP_248170.1| 37 DLLKEELQEKARiAELESRILKLELEKKE 65
                                  45555555553324445555555544443 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00019
                                   EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSH CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrklp 50 
                                   +G+PG GK+ +++ ++ + + t++   G+ l +    +g++  +d ++ ++
  gi|15669365|ref|NP_248170.1| 210 YGPPGTGKTLLAKAVATETNATFIRVvGSELVKKFIGEGASLVKDIFKLAK 260
                                   7*********************99555888888777777654555443222 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00041      0.22     117     137 ..     207     227 ..     201     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00041
                     Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                   +++yGp+ tGkt la+a a+ 
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVATE 227
                                   89***************9975 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4   0.00097      0.53      22      51 ..     208     237 ..     195     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00097
                        AAA_30  22 vltGpAGtGKttalkalreaweaaggrvig 51 
                                   +l Gp+GtGKt + ka++   +a   rv+g
  gi|15669365|ref|NP_248170.1| 208 LLYGPPGTGKTLLAKAVATETNATFIRVVG 237
                                   688*************99887777666665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0018      0.97      17      45 ..     201     229 ..     193     247 .. 0.80
   2 ?    0.7   0.1      0.78   4.2e+02      37     131 ..     252     276 ..     228     301 .. 0.61
   3 ?    1.3   0.2      0.48   2.6e+02      36      69 ..     251     284 ..     246     423 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                      ATPase_2  17 repneiyfiYGpegsGKtaLlkeiienle 45 
                                    ep + +++YGp g GKt L k ++++ +
  gi|15669365|ref|NP_248170.1| 201 IEPPKGILLYGPPGTGKTLLAKAVATETN 229
                                   56777899*************99988764 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.78
                      ATPase_2  37 lkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilkeksklvfkaielllekikkkg 117
                                   +k i +  ++k                                                                      
  gi|15669365|ref|NP_248170.1| 252 VKDIFKLAKEKAP-------------------------------------------------------------------- 264
                                   3334444444444.................................................................... PP

                      ATPase_2 118 kkiiiiiDelqkli 131
                                      ii+iDe+  + 
  gi|15669365|ref|NP_248170.1| 265 --SIIFIDEIDAIA 276
                                   ..556666655444 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.48
                      ATPase_2  36 Llkeiienledkdkyviyyialreesiskldefi 69 
                                   L+k i +  ++k   +i+++++  ++ +++d   
  gi|15669365|ref|NP_248170.1| 251 LVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALT 284
                                   5555555666666666666666666666666553 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   5.8       2.3   1.3e+03     122     183 ..      21      86 ..       3      90 .. 0.42
   2 ?    8.9   0.0    0.0021       1.2      20      38 ..     207     225 ..     180     264 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.3
                        AAA_11 122 kaqlakeiskeleklakelrafeeeeek...............eklkkskekskskleqerrklkkerkelskelee 183
                                   +++  kei+++++ ++           +               e++  + e +k++le+e+ +l ke + l++el++
  gi|15669365|ref|NP_248170.1|  21 EFKEEKEINDNSNLKN-----------DllkeelqekariaelESRILKLELEKKELERENLQLMKENEILRRELDR 86 
                                   1111122221111111...........01111111122233335555666666666777777777777777776665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0021
                        AAA_11  20 tliqGPPGtgKTktivell 38 
                                    l+ GPPGtgKT    ++ 
  gi|15669365|ref|NP_248170.1| 207 ILLYGPPGTGKTLLAKAVA 225
                                   5899********5544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1286  (0.0717274); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 2645.84
//
Query:       gi|15669366|ref|NP_248171.1|  [L=351]
Description: hypothetical protein MJ_1178 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-38  132.0   1.6    6.7e-38  129.9   0.2    2.2  2  Glycos_transf_1  Glycosyl transferases group 1
    6.1e-29  101.1   0.0    1.5e-28   99.9   0.0    1.6  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.9e-24   86.6   0.0    3.2e-24   85.8   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    2.7e-13   50.1   0.6    4.7e-13   49.3   0.6    1.3  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    5.4e-13   49.1   0.0    1.2e-12   48.0   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
    1.1e-05   26.0   0.0      2e-05   25.1   0.0    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    0.00073   19.4   1.7      0.012   15.4   0.1    2.9  3  DUF3492          Domain of unknown function (DUF3492)
  ------ inclusion threshold ------
        6.4    6.6   5.9        0.6    9.9   0.9    1.9  2  Cecropin         Cecropin family


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.13   2.9e+02      20      75 ..      22      78 ..      18      91 .. 0.60
   2 !  129.9   0.2     3e-41   6.7e-38      12     171 ..     176     328 ..     168     329 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.13
                                  EESS-TTT.TTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHH...HHHHHHCTTCGG CS
               Glycos_transf_1 20 svgrleke.KgvdllikafallkkqlnpnvklviaGngeeekelk...klaeelelsdnv 75
                                   v +l+k+ K+++  i  +++ +   ++++k vi+ n++++k+++   +l+ ++++++n+
  gi|15669366|ref|NP_248171.1| 22 HVENLVKRlKDIEFHILTYDSYE---ENEYKNVIIHNVPHLKKFRgisYLINAYKIGKNI 78
                                  55555555566666666666654...4577777777666666643111555566665555 PP

  == domain 2  score: 129.9 bits;  conditional E-value: 3e-41
                                   TTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHC CS
               Glycos_transf_1  12 nekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellkn 92 
                                    ++ ++ l+vg+++++Kgvd li+a+++       ++++ ++G+g+  k++++ + + +l  ++++lg++s +++ +++++
  gi|15669366|ref|NP_248171.1| 176 EGDYNFGLFVGAFVPQKGVDILIDAIKD------IDFNFKLIGDGKLYKKIENFVVKNNL-SHIELLGRKSFDEVASFMRK 249
                                   4678999********************5......6899**********************.89********999******* PP

                                   ESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
               Glycos_transf_1  93 adifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenark 171
                                   ++ +v+ps+sEgfG+v++E ma+ +pvia+ +gg+ e+v dg +Gll ++nn+ +l+e+i +l+++eelr+ lgen+++
  gi|15669366|ref|NP_248171.1| 250 CSFLVVPSRSEGFGMVAVEGMACSKPVIATRVGGLGEIVIDGYNGLLAEKNNPNDLKEKILELINNEELRKTLGENGKE 328
                                   *****************************************************************************97 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.2   9.4e+03      22      46 ..      24      48 ..      12      69 .. 0.57
   2 !   99.9   0.0   6.5e-32   1.5e-28       5     134 .]     183     315 ..     181     315 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.2
                                  HHH.HHHH.HHEEEEEES---...HHH CS
               Glyco_trans_1_4 22 eav.pllrkkdvrlvivGdgp.rpeel 46
                                  e++ ++l+  d++++i   ++ +++e+
  gi|15669366|ref|NP_248171.1| 24 ENLvKRLK--DIEFHILTYDSyEENEY 48
                                  44444444..46666666333333333 PP

  == domain 2  score: 99.9 bits;  conditional E-value: 6.5e-32
                                   EEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHH.T.T-T.TEEEE---..THHHHHHHH-SEEEE-- CS
               Glyco_trans_1_4   5 lfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleela.a.gleerveftGfv..edlaellaaadvfvaPs 80 
                                   lfvG+++ ++kgvd+l++a++ +    +++ ++Gdg+  + ++e+ + + +l +++e++G+   +++a+++++++ +v+Ps
  gi|15669366|ref|NP_248171.1| 183 LFVGAFV-PQKGVDILIDAIKDID---FNFKLIGDGKlYK-KIENFVvKnNL-SHIELLGRKsfDEVASFMRKCSFLVVPS 257
                                   8*****6.56*************9...89*******9765.99987645788.69*****999999*************** PP

                                   ..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
               Glyco_trans_1_4  81 ..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                     egfg++++E ma+ +pv+at+vgg+ e+v  g ngll+++++p++l e+il+L+++
  gi|15669366|ref|NP_248171.1| 258 rsEGFGMVAVEGMACSKPVIATRVGGLGEIVidGYNGLLAEKNNPNDLKEKILELINN 315
                                   999**************************999***********************986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.0   1.4e-27   3.2e-24       1     168 [.      16     170 ..      16     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 1.4e-27
                Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrl.rrllkrekpDvvHahs 80 
                                   +GG+  hv++L+++L +  +e +++t ++ ++ e++    v ++ vp++++ r   +l ++ ++ +++++ e++D++H+h+
  gi|15669366|ref|NP_248171.1|  16 IGGITLHVENLVKRLKD--IEFHILTYDSYEENEYK---NVIIHNVPHLKKFRGISYLINAYKIgKNIIESEGIDLIHSHY 91 
                                   7**************96..5*****98888888888...677777777766666666666666626688888********* PP

                Glyco_transf_4  81 paalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekitV 161
                                   +++ g++++ l+ +l ip++lt+Hg++      a   + s+  r++ +++  ++d++i+vS++++++l e+++   ++  V
  gi|15669366|ref|NP_248171.1|  92 AFPQGCVGALLKNKLSIPHILTLHGSD------ALILKNSIKGRYFFKYATTNSDKIICVSKYIKNQLDENLK---NRAIV 163
                                   ********99999**************......56667778888888999********************555...7999* PP

                Glyco_transf_4 162 ipnGvDl 168
                                   i+nGv+ 
  gi|15669366|ref|NP_248171.1| 164 IYNGVNK 170
                                   *****96 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.6   2.1e-16   4.7e-13      12     138 ..      22     145 ..      17     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2.1e-16
               Glyco_trans_4_2  12 htlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkg.pleyl.kafkl.kklikkikPDvvhahyakpygll 89 
                                   h+ +l+k L++  +e h++t +    +e e +++ +h+++   k+  ++yl +a k+ k++i+ +++D++h hya p g +
  gi|15669366|ref|NP_248171.1|  22 HVENLVKRLKD--IEFHILTYDSY--EENEYKNVIIHNVPHLKKFrGISYLiNAYKIgKNIIESEGIDLIHSHYAFPQGCV 98 
                                   77778888888..999***99988..66667888899999778999999984699************************** PP

               Glyco_trans_4_2  90 gslaarlsgvipvvlsvwGldvlkfpkksklkklllklalkkatkvist 138
                                   g+l++ ++  ip +l+ +G+d l  ++ +   ++ +k+a  +++k+i+ 
  gi|15669366|ref|NP_248171.1|  99 GALLKNKLS-IPHILTLHGSDALILKNSI-KGRYFFKYATTNSDKIICV 145
                                   ****99998.************7777777.5799*************96 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   5.3e-16   1.2e-12       4      86 ..     255     338 ..     252     343 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 5.3e-16
               Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaeht 82 
                                    psrse++ ++ +E +ac  ++++++  gl+e++ +g  ++l+e  ++++l eki +l++n+e+r+ ++e+++e+  ++++
  gi|15669366|ref|NP_248171.1| 255 VPSRSEGFGMVAVEGMACSKPVIATRVGGLGEIVIDGYNGLLAEknNPNDLKEKILELINNEELRKTLGENGKEF-SKKFS 334
                                   59*************************************************************************.99999 PP

               Glyco_trans_1_2  83 ydhr 86 
                                   +++ 
  gi|15669366|ref|NP_248171.1| 335 WEKC 338
                                   9976 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   8.9e-09     2e-05       1     147 [.      17     156 ..      17     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 8.9e-09
               Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlp.vprrpspladlaalralrrllrqrrerpdvvhah 80 
                                   gGi+ +v++l+++L +   e ++lt + +++ +      v +h++p +   ++  +   a+   + ++  ++e++d++h+h
  gi|15669366|ref|NP_248171.1|  17 GGITLHVENLVKRLKDI--EFHILTYDSYEENE---YKNVIIHNVPhLKKFRGISYLINAYKIGKNII--ESEGIDLIHSH 90 
                                   67788888888888754..88888876666666...46677777663333333333333444445667..9********** PP

               Glyco_trans_4_4  81 s.ptaglaarlarrrrgiplvvtlhgll.lrrgsgavrrlyralerrllrradavlvvseaeaeelral 147
                                   + ++ g +++l++ + +ip+++tlhg + l   ++ ++r++    +++ ++ d +++vs ++  +l ++
  gi|15669366|ref|NP_248171.1|  91 YaFPQGCVGALLKNKLSIPHILTLHGSDaLILKNSIKGRYF---FKYATTNSDKIICVSKYIKNQLDEN 156
                                   *8899999*****889*********8541334477777777...5789999999999999999998775 PP

>> DUF3492  Domain of unknown function (DUF3492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   5.2e-06     0.012      11      62 ..      13      61 ..       7      71 .. 0.89
   2 ?    1.0   0.1      0.13   2.9e+02     177     205 ..      88     116 ..      66     117 .. 0.81
   3 ?   -0.3   0.0      0.33   7.4e+02      22      61 ..     194     233 ..     193     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.2e-06
                       DUF3492 11 YPyvsGGVSsWvhqlitklpeveFavlfigsdeeeygelkyelPenVvevee 62
                                  YPy+ GG++  v++l++ l+++eF++l   s ee+  e k  + +nV ++++
  gi|15669366|ref|NP_248171.1| 13 YPYI-GGITLHVENLVKRLKDIEFHILTYDSYEEN--EYKNVIIHNVPHLKK 61
                                  9997.**********************99999877..788888888888876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                       DUF3492 177 HavstGyAgllgallkerkgtpllltEHG 205
                                   H++     g +gallk++ + p +lt HG
  gi|15669366|ref|NP_248171.1|  88 HSHYAFPQGCVGALLKNKLSIPHILTLHG 116
                                   55555555889***************999 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.33
                       DUF3492  22 vhqlitklpeveFavlfigsdeeeygelkyelPenVveve 61 
                                   v+ li ++++++F+   ig  +  ++  ++ + +n++++e
  gi|15669366|ref|NP_248171.1| 194 VDILIDAIKDIDFNFKLIGDGKLYKKIENFVVKNNLSHIE 233
                                   5779***********9999998776667788888888876 PP

>> Cecropin  Cecropin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3       3.7   8.2e+03       8      13 ..      73      78 ..      73      78 .. 0.76
   2 ?    9.9   0.9   0.00027       0.6       1      12 [.     215     227 ..     215     227 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.7
                      Cecropin  8 naGkri 13
                                  ++Gk+i
  gi|15669366|ref|NP_248171.1| 73 KIGKNI 78
                                  678887 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00027
                      Cecropin   1 KfgKKLEn.aGkr 12 
                                   K++KK+En + k+
  gi|15669366|ref|NP_248171.1| 215 KLYKKIENfVVKN 227
                                   99********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 2530.95
//
Query:       gi|15669367|ref|NP_248172.1|  [L=334]
Description: hypothetical protein MJ_1177 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-72  243.4  37.0      4e-72  243.1  37.0    1.0  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.1  37.0   2.2e-76     4e-72       5     325 ..      16     327 ..      11     329 .. 0.95

  Alignments for each domain:
  == domain 1  score: 243.1 bits;  conditional E-value: 2.2e-76
               AI-2E_transport   5 lvllllllalypfiselllplliAlvlayllnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvplliaqltqlvks 85 
                                    +l++ll++++p    ++  l+ ++ +ay++ pv+++L+k++ k+++a l++ +++l ++++++++l++++ ++l+ ++ks
  gi|15669367|ref|NP_248172.1|  16 GLLIMLLYIIWP----FIDVLAYSCAFAYMALPVYNILRKKFNKTISAGLAISIYILPIMTITIYALLTFMEIILSFNTKS 92 
                                   444444444444....66689999********************************************************* PP

               AI-2E_transport  86 lpayidslqnilnelpslleelenliqalkqslskilsnilssilnsllsllasllglilslvlvllllffllldgeklrq 166
                                   ++ yi+++++i+n+++ +   +      ++q ++k++ ++ +++++++++ + +++ li+++++vl+l+f++l+dg+k ++
  gi|15669367|ref|NP_248172.1|  93 IEPYINEILSIYNSFMLERIIN------NEQIIAKYIDEFIKYLVSQFSGKIIDVGYLIVKVIMVLFLTFYFLRDGDKAKN 167
                                   ****************777777......79*************************************************** PP

               AI-2E_transport 167 gilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvglanliPyiGavivlipia 247
                                    i++++p++++e+++ +l+ l+++++++++++v +++ii++l++ig+lilgvpya l+ai++g+++l+P++G+++v+i ia
  gi|15669367|ref|NP_248172.1| 168 LIISFVPDEYKEKMRIYLSYLHDSYKNLFISCVSLSIIITILSYIGYLILGVPYAELFAIITGIFALLPILGGWMVYISIA 248
                                   ********************************************************************************* PP

               AI-2E_transport 248 iialltgg.ikevlivlivvllvqliegnilePklmgkrlglhplvillsllaggklfGlvGlilavpltavikailea 325
                                   i+++l+++ +k+v++++++ l++++  + +++P+l++k++++hp+++++++l++   +Gl G+ ++++++++++a++ a
  gi|15669367|ref|NP_248172.1| 249 IYFFLIHDyTKAVFMFIYGELFLSIAPDFVIRPYLVKKEVDIHPVLVVIAFLMAPLSLGLSGFAIGPLVVGALNAFYLA 327
                                   ********999****************************************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1324  (0.0738468); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2058.63
//
Query:       gi|15669368|ref|NP_248173.1|  [L=149]
Description: glycerol-3-phosphate cytidyltransferase TaqD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-21   76.0   0.0    3.8e-21   75.8   0.0    1.0  1  CTP_transf_like  Cytidylyltransferase-like
     0.0026   17.7   0.1      0.004   17.1   0.1    1.6  1  FAD_syn          FAD synthetase
  ------ inclusion threshold ------
      0.046   14.0   0.0      0.083   13.1   0.0    1.5  1  DUF1884          Domain of unknown function (DUF1884)
      0.078   12.5   0.1      0.091   12.3   0.1    1.2  1  Peripla_BP_2     Periplasmic binding protein


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.0   8.5e-25   3.8e-21       2     142 ..       7     136 ..       6     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 8.5e-25
                                   EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-..SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHT CS
               CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk..kplasaeeRlemlelakevdevisvdpweltrevlkkl 80 
                                   + GtFD++H GH ++l+ ak+l++e liv+v+ de++kk k  kp++++e+R em+e++k vd++i  +      e + +l
  gi|15669368|ref|NP_248173.1|   7 TAGTFDILHPGHYEILKFAKSLGDE-LIVIVARDETVKKLKgrKPIIPEEQRREMVEALKPVDKAILGSLKNKL-EPILEL 85 
                                   78***********************.**************66**************************999888.589999 PP

                                   TTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
               CTP_transf_like  81 kpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                   kpd  ++v+g d+ + f  ++ l++ l++++l  + ++       +   k++++ Ss +i +
  gi|15669368|ref|NP_248173.1|  86 KPD--IIVLGPDQTT-F-DEETLKKELAKYNLYPEIVR-------FRGYKKCPFHSSFDIVK 136
                                   ***..*******966.4.48899999999999999777.......89999999999998865 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   8.8e-07     0.004       6      36 ..       2      32 ..       1     111 [. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.8e-07
                       FAD_syn  6 egavvtlGnFDGvHlGHqallkkaveaakek 36
                                  ++ vvt G FD +H GH ++lk a+++ +e 
  gi|15669368|ref|NP_248173.1|  2 KKRVVTAGTFDILHPGHYEILKFAKSLGDEL 32
                                  5789******************999987654 PP

>> DUF1884  Domain of unknown function (DUF1884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.9e-05     0.083      23      55 ..      85     117 ..      57     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                                   ----EEEE-HHHHHHHHHHHHHHHT------EE CS
                       DUF1884  23 fePdiiLvGkeaieflkealkkeleeeeevtel 55 
                                   ++Pdii++G++   f +e+lkkel + + + e+
  gi|15669368|ref|NP_248173.1|  85 LKPDIIVLGPDQTTFDEETLKKELAKYNLYPEI 117
                                   78*********************9887666555 PP

>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1     2e-05     0.091      49      81 ..      76     106 ..      34     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                                   SB-HHHHHHH--SEEEE-GGG...GGGHHHHHH CS
                  Peripla_BP_2  49 eidvEklaalkPDlvilskglgltdedeellks 81 
                                      +E +++lkPD+++l +++  t+ dee+lk+
  gi|15669368|ref|NP_248173.1|  76 KNKLEPILELKPDIIVLGPDQ--TTFDEETLKK 106
                                   4567*****************..7777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1060.15
//
Query:       gi|15669369|ref|NP_248174.1|  [L=145]
Description: hypothetical protein MJ_1180 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-06   27.9   0.0    2.2e-06   27.6   0.0    1.1  1  NMT1_2     NMT1-like family
  ------ inclusion threshold ------
       0.07   13.1   0.2       0.17   11.8   0.2    1.6  1  SBP_bac_1  Bacterial extracellular solute-binding protein
       0.11   12.5   0.3       0.21   11.7   0.3    1.4  1  DUF3568    Protein of unknown function (DUF3568)


Domain annotation for each model (and alignments):
>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   3.6e-10   2.2e-06       2      96 ..      26     140 ..      25     145 .] 0.84

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.6e-10
                        NMT1_2   2 apekeqlklGfialtdaaplvva.kekglfake..................Glt.v....elekqaswaelrdkllagelD 58 
                                   ++e ++l++++ ++ ++a+l+va  + +lf+++                  G + +     ++ ++++a++++ + +g++D
  gi|15669369|ref|NP_248174.1|  26 TSEVPTLTVAYLPTDHHASLFVAcDNPDLFKDKygiclkavkdkeeyelykGNKkIanvkVVKVTEGGASIMNLMTQGQVD 106
                                   67999***************66516679999999*****************4444444445667889999999999***** PP

                        NMT1_2  59 aahv.ltpapllidlGiggakadmkvlaslnlnGqaitl 96 
                                   +a+   +p+++ id+G+     + kv+++l+++  +++l
  gi|15669369|ref|NP_248174.1| 107 VALLgYPPVIFYIDKGT-----KAKVIMNLHTEVLQLLL 140
                                   *****************.....89999999988777666 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   2.9e-05      0.17     114     244 ..      43     114 ..      22     133 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.9e-05
                                   EEEEEE..ETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT....HH CS
                     SBP_bac_1 114 argliY..NkdlfekagldppwtWdelveaakklkekgkkpiggarggsasgtayyfalalakslggkvfdkdgg....gl 188
                                   a++++   N+dlf+                                                         +++g    + 
  gi|15669369|ref|NP_248174.1|  43 ASLFVAcdNPDLFK---------------------------------------------------------DKYGiclkA- 65 
                                   33333344444444.........................................................443322221. PP

                                   CSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHH CS
                     SBP_bac_1 189 dnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwa 244
                                           ++  ++  +++n+++ +  +++ +++ga+  +l+++G++++a+ g   
  gi|15669369|ref|NP_248174.1|  66 -------VKDKEEYELYKGNKKIANVKVVKVTEGGASIMNLMTQGQVDVALLGYPP 114
                                   .......3334455577889999**************************9988655 PP

>> DUF3568  Protein of unknown function (DUF3568)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   3.4e-05      0.21       4      88 ..       6      96 ..       3     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                       DUF3568  4 lllllsis.lillasCaalvagaa.agagtvayvnGelkae..yean....lkkvykAtlkaiedlnvlsvvekskdsssati 78
                                  +l++l is l+l a+C  + + ++ +++ tvay      a+  + ++    +k+ y  +lka++d++ +++ + +k++ + ++
  gi|15669369|ref|NP_248174.1|  6 MLVALLISsLVLFAGC--VQNETSeVPTLTVAYLPTDHHASlfVACDnpdlFKDKYGICLKAVKDKEEYELYKGNKKIANVKV 86
                                  3333333314899***..8888888*********999988843344344448999********************99988888 PP

                       DUF3568 79 eakaaedktv 88
                                     ++++  +
  gi|15669369|ref|NP_248174.1| 87 VKVTEGGASI 96
                                  7777665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1023.01
//
Query:       gi|15669370|ref|NP_248175.1|  [L=199]
Description: hypothetical protein MJ_1181 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-13   50.7   0.2    2.1e-13   50.5   0.2    1.1  1  NMT1_2    NMT1-like family
  ------ inclusion threshold ------
      0.012   15.2   0.1       0.21   11.1   0.0    2.0  2  DUF5563   Family of unknown function (DUF5563)
      0.071   13.0   0.0      0.098   12.6   0.0    1.3  1  NMT1      NMT1/THI5 like
       0.11   12.6   0.6       0.29   11.2   0.0    1.9  2  Swi5      Swi5


Domain annotation for each model (and alignments):
>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.2   4.7e-17   2.1e-13     140     246 ..       3     125 ..       1     132 [. 0.89

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 4.7e-17
                        NMT1_2 140 rywLaaaGldp.......eadvklvvvpp.pqmvanlkagtidgfcvgePwnaqavaegiGvtaltsqel.......wkdh 205
                                   + +L+a+G+          a v+lv  ++   m++ l+++++d+ ++ eP ++   ++giG  ++ s++l       w +h
  gi|15669370|ref|NP_248175.1|   3 EDALKAEGITYtedpnnkSAMVLLVNCKGqGTMPQMLAQKQLDAVIAWEPMPEIIKNKGIGKVIAHSEDLpsatggtWANH 83 
                                   567888888888888888899999**99999************************************************** PP

                        NMT1_2 206 PekvlgvredfveknpntaralvkalleAtkwlda.kkenra 246
                                   P++ l+++e+ +++++++++ + k+l +At+ +++ ++ + +
  gi|15669370|ref|NP_248175.1|  84 PCCCLAASENALKNKREAVITFAKLLKDATDEINKnRDLAVK 125
                                   *********************************953333333 PP

>> DUF5563  Family of unknown function (DUF5563)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.023     1e+02     119     156 ..      68     105 ..      46     120 .. 0.71
   2 ?   11.1   0.0   4.8e-05      0.21      44      91 ..     120     168 ..     114     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.023
                       DUF5563 119 gatkvprasslrlslhpfamltapkaaeyarkqsvklr 156
                                    ++ +p a+    + hp   l+a+  a  +++++v   
  gi|15669370|ref|NP_248175.1|  68 HSEDLPSATGGTWANHPCCCLAASENALKNKREAVITF 105
                                   456678888888899************99999988543 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.8e-05
                       DUF5563  44 ydlaisvalqwldasedltwlewekvkvplkgrpvypnr.rereamils 91 
                                    dla+  +++wl+++e++     e++k  ++  pv p+  +  eam l 
  gi|15669370|ref|NP_248175.1| 120 RDLAVKASVRWLGTNENVEKDSIEHIKFDYRLEPVIPKViKFVEAMKLQ 168
                                   59***********************************862557888775 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.2e-05     0.098     118     212 ..      20     119 ..       1     123 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                                   -GGG-EEEE-.TT-HHH.HHHCTSSSEEECEETTTHHHHHHHTT-.....-EEEE-GGGTT--.---SEEEEEEHHHHHH- CS
                          NMT1 118 dpsdvtlvnvggtslak.alltgkvDaaiggyenwegvelesegk.....elrifaladlgvp.dyyslvlitnekllken 191
                                   + + v lvn++g  +++  l++++ Da+i++    e +  +++g+     + + ++ a  g   +     l+++e+ lk++
  gi|15669370|ref|NP_248175.1|  20 KSAMVLLVNCKGQGTMPqMLAQKQLDAVIAWEPMPEII--KNKGIgkviaHSEDLPSATGGTWaNHPCCCLAASENALKNK 98 
                                   45568899**999999967899*******555454444..566664466667777777777766899999*********** PP

                                   HHHHHHHHHHHHHHHHHHHHS CS
                          NMT1 192 pelvkkFlrAlkkGyeyalah 212
                                   +e+v  F + lk +++ + ++
  gi|15669370|ref|NP_248175.1|  99 REAVITFAKLLKDATDEINKN 119
                                   ***************998776 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.56   2.5e+03      18      29 ..     108     119 ..      89     146 .. 0.51
   2 ?   11.2   0.0   6.5e-05      0.29      27      49 ..     174     196 ..     162     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.56
                                   HHHHHHHHHHHH CS
                          Swi5  18 elaelkeelkek 29 
                                    l+++++e +++
  gi|15669370|ref|NP_248175.1| 108 LLKDATDEINKN 119
                                   334444444433 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.5e-05
                                   HHHH.HHHHHHHHHHHHHHHHHH CS
                          Swi5  27 kekkdpeetvkrhIklLheYNEi 49 
                                   k k++++e+vk+ I  L++YNEi
  gi|15669370|ref|NP_248175.1| 174 KLKDASSEEVKDIIFDLQTYNEI 196
                                   345679****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1352.24
//
Query:       gi|15669371|ref|NP_248176.1|  [L=366]
Description: hypothetical protein MJ_1182 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0018   18.5   0.1     0.0043   17.3   0.1    1.6  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.069   12.4   0.0       0.11   11.8   0.0    1.2  1  FAD_binding_3  FAD binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   4.7e-07    0.0043       1      27 [.       5      31 ..       5      37 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.7e-07
                                  EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                  I+GaGlsG+ + +lL+++gf + ++++
  gi|15669371|ref|NP_248176.1|  5 IIGAGLSGSILYRLLSEDGFYINIYDH 31
                                  9************************96 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.2e-05      0.11       3      25 ..       2      24 ..       1      35 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.2e-05
                                  EEEEE--SHHHHHHHHHHHHTTH CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGv 25
                                  +V+I+GaG++G +l +lLse G 
  gi|15669371|ref|NP_248176.1|  2 QVCIIGAGLSGSILYRLLSEDGF 24
                                  8*******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 2502.86
//
Query:       gi|15669372|ref|NP_248177.1|  [L=161]
Description: hypothetical protein MJ_1183 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-54  183.9   0.4    1.5e-54  183.7   0.4    1.0  1  DUF2124   Uncharacterized protein conserved in archaea (DUF21
     0.0083   15.4   0.0      0.011   15.0   0.0    1.1  1  TIP49     TIP49 P-loop domain
  ------ inclusion threshold ------
      0.036   13.8   0.0       0.05   13.4   0.0    1.1  1  GATase    Glutamine amidotransferase class-I


Domain annotation for each model (and alignments):
>> DUF2124  Uncharacterized protein conserved in archaea (DUF2124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.7   0.4   2.5e-58   1.5e-54       2     140 ..      15     153 ..      14     154 .. 0.97

  Alignments for each domain:
  == domain 1  score: 183.7 bits;  conditional E-value: 2.5e-58
                                   HHHHHHHHHHHHTTT-..SEEEEEE-TTTTHHHHHHHHHHTTT..SEEEEEETT-GGG-EEEEEETTEEEEEEE-.-S-EE CS
                       DUF2124   2 glsgllrefkelvkes..ekivfvGspgvCtpfaellayaiRdlekelvfvpdldlekarklevtdvGmqleeeaeeekad 80 
                                   gls +lref++lv++s  ek++fvGs gvC+pfael++yaiRd  ke++f+pd dl+k++kl+++d+Gmq+e+  + +k+d
  gi|15669372|ref|NP_248177.1|  15 GLSPMLREFRTLVRDSniEKVAFVGSVGVCQPFAELFGYAIRD--KECYFIPDGDLNKVKKLVIKDIGMQMEDFENLNKVD 93 
                                   99************66569************************..9*********************************** PP

                                   EEEEEGGGGSTTTS--HHHHHHHHHHHEEEEEEEEEETTHHHHTTHHHHS--SEEEEEEE CS
                       DUF2124  81 vvvllGGlampkikveaedvkeliekiekkkviGvcfmsifekagWldkidFdliidakl 140
                                   ++vl+GGlampk++ve++++keli+k++ kkviGvcfmsif+kagW+++idFd+++d+ +
  gi|15669372|ref|NP_248177.1|  94 AIVLFGGLAMPKYGVEVDKIKELINKLSPKKVIGVCFMSIFQKAGWDKEIDFDYLMDGFI 153
                                   *********************************************************987 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.8e-06     0.011     187     265 ..      39     120 ..      28     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-06
                                   EE-SSS-SS--..----S--------S---S----.XXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXX CS
                         TIP49 187 kklGrsearak..efDiekdefvelPkGevekkke.vvqevtLhdlDvanarpqdllslllqllkskkteiteklreeink 264
                                     +G ++  a+   + i ++e   +P+G+++k k+ v++++ +   D  n ++ d + l+  l  +k +   +k++e ink
  gi|15669372|ref|NP_248177.1|  39 GSVGVCQPFAElfGYAIRDKECYFIPDGDLNKVKKlVIKDIGMQMEDFENLNKVDAIVLFGGLAMPKYGVEVDKIKELINK 119
                                   566767666551146679999999********7663789****************************99888999999998 PP

                                   X CS
                         TIP49 265 k 265
                                    
  gi|15669372|ref|NP_248177.1| 120 L 120
                                   6 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.3e-06      0.05      36      79 ..      86     130 ..      68     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.3e-06
                                   HHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCT..STS-EEEETH CS
                        GATase  36 ilellknpdgilvsgGpgspgvegkieaikeare..nkiPiLGICL 79 
                                     e+l+++d+i++ gG   p+++ +++ ike+++  + + ++G+C+
  gi|15669372|ref|NP_248177.1|  86 F-ENLNKVDAIVLFGGLAMPKYGVEVDKIKELINklSPKKVIGVCF 130
                                   2.24789*************************9955555699**96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1008.58
//
Query:       gi|15669373|ref|NP_248178.1|  [L=156]
Description: riboflavin synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-15   55.4   0.0      7e-15   55.1   0.0    1.1  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   3.9e-19     7e-15       2     133 ..       3     126 ..       2     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 3.9e-19
                                   EEEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHHH CS
                 DMRL_synthase   2 lriaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfeyv 82 
                                    +++iV ++f      ++ + a+++lke+  +  +i + tVPG  +lp+a+kkl+e++++ d v+alG  + G+ ++++++
  gi|15669373|ref|NP_248178.1|   3 KKVGIVDTTF---ARVDMASIAIKKLKELSPN-IKIIRKTVPGIKDLPVACKKLLEEEGC-DIVMALG--MPGKAEKDKVC 76 
                                   589******9...77899***********965.799999*****************6445.*******..9********** PP

                                   HHHHHHHHHHHHHHCTS-EEEEEEEESSHHCCHHCCTSTC..CCHHHHHHHHH CS
                 DMRL_synthase  83 aeavskglmrvsldtgvPvifgvltvdteeqaleraggka..gnkGeeaaeaa 133
                                   a+++s glm ++l t++ +i   +   +e++a++  + +   + ++ee+ae++
  gi|15669373|ref|NP_248178.1|  77 AHEASLGLMLAQLMTNKHIIEVFV---HEDEAKDDKELDWlaKRRAEEHAENV 126
                                   ****************76665433...33333333321113377777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 979.56
//
Query:       gi|15669374|ref|NP_248179.1|  [L=622]
Description: putative aldehyde ferredoxin oxidoreductase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-25   88.9   0.0      7e-25   88.1   0.0    1.4  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma
    2.9e-21   75.9   0.0    1.2e-20   73.9   0.0    1.9  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3


Domain annotation for each model (and alignments):
>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.0   7.8e-29     7e-25      31     197 ..      24     201 ..       3     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 7.8e-29
                                   HHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE-TTTSSEEEEEEETCHHHHHHHCT-SEEEEES-- CS
                        AFOR_N  31 glaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaksPltgtlgesnaGgrfgaelkraGydaivieGka 111
                                     +++ + +  ++++d+++++n+++f+ G+l   p+ g +rl++ ++sPl+++++ s++Gg +g+++k++G++ + i G++
  gi|15669374|ref|NP_248179.1|  24 TWGLYWHNKFETWKYDAYDEKNVFCFGSGVL---PVIGGHRLIFSFRSPLWDGFYFSSMGG-AGYQFKSTGLNNVAIIGRC 100
                                   5566777776779*****************9...566************************.******************* PP

                                   SS-EEEEEETT.EEEEEE-TTTTTS.-HHHHHHHHHHHHTS...EEEEE-HHHHTT-TTB-E.EE.........TTEEE-S CS
                        AFOR_N 112 ekpvylviedd.kveiedaedlwgl.dtyettealkeelgd...kvaviGpaGenlvrfAsisvd.........dgraagr 178
                                   e+p++lvie+d + +i  +e  ++l ++ye+ +++ e ++d   + +v+G a++++  ++ +s +         ++  a+r
  gi|15669374|ref|NP_248179.1| 101 ENPSILVIENDgQLRIDFIEVKEELkTVYEVSKYILELYKDknlRSVVVGEAAKRTNMGGLFSQTvrngkfvegSEDWAAR 181
                                   ********7665666666655555449**********7777656666********999999977799998886544467** PP

                                   SSHHHHHH.HTTEEEEEEE- CS
                        AFOR_N 179 gGlGavmg.sKnlkaivvrg 197
                                   gG G+v+  ++n+  iv+ g
  gi|15669374|ref|NP_248179.1| 182 GGGGSVLYrAHNIMGIVFFG 201
                                   ********9********966 PP

>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.0   1.3e-24   1.2e-20      20     279 ..     241     529 ..     220     552 .. 0.71

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 1.3e-24
                                   HHHH-GGGHHHHHHHTT---BTTTTBS-..-TTG..GGGSH.......HHHHHH.TEEEE.E.-TT.-SS--EEEEE.... CS
                        AFOR_C  20 lrkyGTaelvnianetgalptknfqegt..feka..ekisg.......ealeek.ylvkneg.Cfs.CpiaCgrevkveeg 86 
                                    +k G +   n++  ++ +p+ n++  +        +ki +       e ++++ ++ k+ + C   Cp+ C+++ +  + 
  gi|15669374|ref|NP_248179.1| 241 ETKTGGTFGNNWLLYKEKVPIFNWRMPYidK--EdrKKILEkilkfylEIFNKEtIEPKRWAnCGEpCPVLCKKYRN--K- 316
                                   344455566779999999********99542..3234433335557877777755788887799989********87..2. PP

                                   ..ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHH............... CS
                        AFOR_C  87 kkvkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedt............... 152
                                        +  +ye +a+ G+ lgi+dl +  ++ +++d lG+D i++Gn+ a+++el   Gllk+e++               
  gi|15669374|ref|NP_248179.1| 317 -----NKVDYEPYASNGTLLGIFDLYEADRVVKTADALGFDAIEIGNLTAWVFELLDVGLLKEEELnikkpifdykkitnd 392
                                   .....2359************************************************************************ PP

                                   ...TS----TT-THHHHHHHHHHHTT-T.THHHHTT-HHHHHHCTT....-.........GGG--EETTEE--SS-GGG.. CS
                        AFOR_C 153 ...dglelefgdaeallellekiAkreg.igdllAeGvkrlaeklg....a.........eelamhvkGlelpaydprg.. 214
                                      +  e++  +ae+++++++  A++++ + ++l+ G +++a+ l+    +         +++a+ v   +   + p+   
  gi|15669374|ref|NP_248179.1| 393 ddeEIREISKHNAEQAIKFMHNLAENSNdLYKILSLGKRKAAKILNerfkSrvnkigkkfNDFAVYVPFGDWGEIAPNLyw 473
                                   99888899**********************************888843222223333333333333321122222222201 PP

                                   -HHHHHHHHH-TTSS-SGGG-THHHH.....S---TT--.HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH CS
                        AFOR_C 215 akgmalaYatsnrGacHlrayliale.....ekvdplet.egkaelvkwfqdltalvdslglCkftseaee 279
                                   ++g+ + + +               +       + ++++ e+ aelv+ + +l   ++ lg+C+f + + +
  gi|15669374|ref|NP_248179.1| 474 TPGFFMPFVI---------------QgryltYYKPEFNEpEKLAELVVESIKLELPIENLGICRFHRKWLK 529
                                   1222223333...............1333332223334437888888888888888888888888884333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1202  (0.0670422); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.52
# Mc/sec: 3612.53
//
Query:       gi|15669375|ref|NP_248180.1|  [L=346]
Description: molybdate ABC transporter periplasmic substrate-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-32  112.5   0.0    4.6e-32  111.6   0.0    1.4  1  SBP_bac_11  Bacterial extracellular solute-binding protein
    4.3e-18   66.3   0.7    5.6e-18   66.0   0.7    1.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6   0.0   5.1e-36   4.6e-32       1     218 [.      40     313 ..      40     316 .. 0.91

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 5.1e-36
                                   .EEEE-SSTHHHHHHHHHHH.HHHH---EEEEESSHHHHHHHHHHH...-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEE CS
                    SBP_bac_11   1 ltvaaagslaaalrelaaaF.eahtgvkvevsaggsgklarqiadga.rpDvwipassawlellaaaglvqaesavplass 79 
                                   l+++ agsl  +++e  + F ++h++v+ve + +gs +++r+i+d   ++D++++a+   + ++    +++  ++v +a++
  gi|15669375|ref|NP_248180.1|  40 LKIFHAGSLSVPFEEYEKMFeKEHPNVDVEREPAGSVACVRKIIDLGkKADILASADYSLIPQMMMPKYAD--WYVMFARN 118
                                   7899****************5559*******************99766***********************..******** PP

                                   EEEEEESTT-....TT---SHHH.HHHSS--EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHTEEEEESSH........ CS
                    SBP_bac_11  80 plviavpkgn....pkkikgwad.LlkpglklavadPttspsGlaalalleaagaqellkalekkvvklgess........ 147
                                    +v+a+   +      ++++w + L +p++k+++++P+ +p G++++++l+ a+ ++ + +++++ v    ++        
  gi|15669375|ref|NP_248180.1| 119 EIVLAYTDKSkykdEINSTNWYKiLQRPDVKIGFSNPNDDPCGYRTQMVLQLAELYYKDPTIYDNLVLKHSNIkveenngt 199
                                   ******888765433378888772555***************************988888888888855555588888889 PP

                                   ......................HHHHHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--................. CS
                    SBP_bac_11 148 ......................rqlltaveageadagivyeseakaaengdkleavylpeglnl.d............... 190
                                                         ++ll+ +eag  d++++y+s a+    +++l++++lp+++nl                 
  gi|15669375|ref|NP_248180.1| 200 ylilvpkeldvdtnklfvrskeTDLLAPLEAGAFDYLFIYKSVAN----QHHLKYIELPKEINLgYyeyadtykkvalkii 276
                                   9999999999999999999999999999*****************....9*************955*************** PP

                                   ...........EEEEEEEE-TT--HHHHHHHHHTTSH CS
                    SBP_bac_11 191 .........pldypaavlkkaakreaAraFlafLrsp 218
                                            p++y+++v+++a+++++A +F++f++++
  gi|15669375|ref|NP_248180.1| 277 aknktinakPIVYGMTVPTNAPHKKEAIEFVKFVLGH 313
                                   *********************************9986 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.7   6.2e-22   5.6e-18      12     311 ..      50     313 ..      44     316 .. 0.87

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 6.2e-22
                                   HHHHHH....HHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCC CS
                     SBP_bac_1  12 alvaka....fekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkd 88 
                                    ++ ++    fekehp+++Ve e+   gs+a  +++ i  G+++ D+ a+           + +  +  ++ ++ a+++ +
  gi|15669375|ref|NP_248180.1|  50 VPF-EEyekmFEKEHPNVDVEREPA--GSVAC-VRKIIDLGKKA-DILAS-----------ADYSLIPQMMMPKYADWYVM 114
                                   566.4446789********999999..77777.77999999977.*****...........******************** PP

                                   TEEEEHHHHTHHHHCEEEESEEEEEEEEEEE.ETTTHHCTTGGG..SHBHH.HHHHHHHHHHHHCTCT...HCCHCCEEHH CS
                     SBP_bac_1  89 aadklsssvlpkildskvlyvPlyaargliY.Nkdlfekagldp..pwtWd.elveaakklkekgkkp...iggarggsas 162
                                   +a +                       +l+Y +k++++    d+   ++W   l ++++k++ +++++   +++  +  ++
  gi|15669375|ref|NP_248180.1| 115 FARN---------------------EIVLAYtDKSKYK----DEinSTNWYkILQRPDVKIGFSNPNDdpcGYRTQMVLQL 170
                                   *999.....................6688887888888....3334669999***************************** PP

                                   HHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHS.HHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEH CS
                     SBP_bac_1 163 gtayyfalalakslggkvfdkdgggldnpegvt.aatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivgl 242
                                    ++yy + +++ +l  k  +            +   + +++l++v ++ +  ++k    ++++++la +eaG  + ++++ 
  gi|15669375|ref|NP_248180.1| 171 AELYYKDPTIYDNLVLKHSNI-----------KvEENNGTYLILVPKELDVDTNKLFVRSKETDLLAPLEAGAFDYLFIYK 240
                                   *******99999999333222...........23667777888888889******************************** PP

                                   HHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE....EEEEEEEEBTTCSTHHHHHHHHHHHTSH CS
                     SBP_bac_1 243 waalaamkvapkvafaadkekpkeelgvaplPagkggkpgi....lgayglaipkgsknpeaAkkFldfllsp 311
                                   + a+++++++++ + +++  +++  + +  +++   +k++     +++yg+++p++++++++A +F++f+l++
  gi|15669375|ref|NP_248180.1| 241 SVANQHHLKYIELPKEINLGYYEYADTYKKVALKIIAKNKTinakPIVYGMTVPTNAPHKKEAIEFVKFVLGH 313
                                   *************999999999999999988777777777778**************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2556.12
//
Query:       gi|15669376|ref|NP_248181.1|  [L=270]
Description: hypothetical protein MJ_1188 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-24   85.9   0.0    5.3e-24   84.8   0.0    1.5  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.078   13.1   0.1       0.27   11.4   0.0    2.0  2  SAM_2         SAM domain (Sterile alpha motif)
       0.16   11.9   2.8        2.2    8.3   0.1    3.2  3  JmjN          jmjN domain


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.8   0.0   8.9e-28   5.3e-24       1     209 [.      20     217 ..      20     218 .. 0.93
   2 ?   -2.2   0.0      0.39   2.3e+03      55      78 ..     239     265 ..     224     268 .. 0.51

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 8.9e-28
                                   HHHHHHCT-SEEEEECCTCSHHHHC.HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHH CS
                  AP_endonuc_2   1 laaaaeaGfdgvElfgrdlvpvsel.sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaa 80 
                                   +++ +++G++++E+f+ +++ ++++ + +++++lrk + + ++ ++  ++  ++++++   rea+    ++++   iela+
  gi|15669376|ref|NP_248181.1|  20 FDIFRDIGIKCMEFFPENPDFWDNRfDLDYIADLRKEFLKFDVALHNPHIELNPSSLNPYVREAV----IKETLWSIELAK 96 
                                   67889***************************************999999999999877777777....************ PP

                                   HHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTTTEEEE CS
                  AP_endonuc_2  81 aLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavdspnvgvc 159
                                      ++l+++hpG     ++++ +e +e + + l++ +++a  +++++++E++++  +  g+  ee++ +l++ d   + ++
  gi|15669376|ref|NP_248181.1|  97 FYRCKLITIHPG-KRPTNRSPTDEEYEAFFKYLDRTLEVAINKNITICVENMPERINRIGWspEEMEWILKRYDE-LLYMT 175
                                   ************.5588888888***************************************************5.4**** PP

                                   EEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSS CS
                  AP_endonuc_2 160 lDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeGe 209
                                   lD++H+  +   ++++l+ + d+ikh Hi+ +++     r +h p+ + e
  gi|15669376|ref|NP_248181.1| 176 LDFAHAKEY---MEEFLESVIDYIKHTHISGVVN-----RKDHFPLRKSE 217
                                   ******988...*****************99998.....77777777665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.39
                                   TCTHCHTTCS...HHHHHHHHHHHHHH CS
                  AP_endonuc_2  55 ypdederear...reesvdalkraiel 78 
                                    +d++ +e++    ee ++++ + ie+
  gi|15669376|ref|NP_248181.1| 239 ELDDRRLEKNpvtKEEKIEEVIKDIEF 265
                                   333333444455666667777777765 PP

>> SAM_2  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.1   6.4e+03      19      29 ..     182     192 ..     176     198 .. 0.65
   2 ?   11.4   0.0   4.5e-05      0.27      15      63 ..     217     264 ..     213     267 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                                   GGGHHHHHHTT CS
                         SAM_2  19 kqytdnFrdag 29 
                                   k+y + F+++ 
  gi|15669376|ref|NP_248181.1| 182 KEYMEEFLESV 192
                                   56777776654 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 4.5e-05
                                   HTTTGGGHHHHHHTTCSHHHHHTTSCHHHHHHTTHHHHHHHHHHHHHHH CS
                         SAM_2  15 siglkqytdnFrdagitgaelllrlteedLkrlGitsvghrkkilkkiq 63 
                                   +i++  y ++++d+g+ g+   l+l+   L++ ++t+     +++k i+
  gi|15669376|ref|NP_248181.1| 217 EIDFSPYIKALLDYGYNGMFN-LELDDRRLEKNPVTKEEKIEEVIKDIE 264
                                   799***************444.6****************9999999886 PP

>> JmjN  jmjN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00037       2.2       5      19 ..     116     130 ..     115     136 .. 0.91
   2 ?    2.3   0.0     0.029   1.7e+02       7      22 ..     185     201 ..     184     204 .. 0.84
   3 ?   -2.4   0.1      0.85   5.1e+03      12      24 ..     219     231 ..     219     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00037
                                   --HHHHC-HHHHHHH CS
                          JmjN   5 PTeeEFkdplkYiek 19 
                                   PT eE++ + kY+++
  gi|15669376|ref|NP_248181.1| 116 PTDEEYEAFFKYLDR 130
                                   ************987 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.029
                                   HHHH.C-HHHHHHHHHH CS
                          JmjN   7 eeEF.kdplkYiekiep 22 
                                   +eEF +  + Yi++ + 
  gi|15669376|ref|NP_248181.1| 185 MEEFlESVIDYIKHTHI 201
                                   8***88******98765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.85
                                   -HHHHHHHHHHHH CS
                          JmjN  12 dplkYiekieplg 24 
                                   d+  Yi+   ++g
  gi|15669376|ref|NP_248181.1| 219 DFSPYIKALLDYG 231
                                   8899999877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1740.26
//
Query:       gi|15669377|ref|NP_248182.1|  [L=301]
Description: dinitrogenase reductase activating glycohydrolase DraG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-64  218.7   0.0    1.5e-64  218.5   0.0    1.0  1  ADP_ribosyl_GH  ADP-ribosylglycohydrolase


Domain annotation for each model (and alignments):
>> ADP_ribosyl_GH  ADP-ribosylglycohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.5   0.0   8.4e-69   1.5e-64       1     291 []      10     277 ..      10     277 .. 0.97

  Alignments for each domain:
  == domain 1  score: 218.5 bits;  conditional E-value: 8.4e-69
                                   HHHHHHHHHHHHHGGGTT--HHHHHHHTSS--S-----STTTTTS-TT---HHHHHHHHHHHTEET.TEE-HHHHHHHHHH CS
                ADP_ribosyl_GH   1 GallGaavGDAlGlpvefwsydeirrrygelgetpdktgfghfglkpgewtddtqmalllleslleaggldpedlarrfla 81 
                                   G+++Ga++GDAlG+p+e ++++ei+++yg  ++  ++ ++ + +l +gewtddt++a++l++sl++ +g+d++++a+ ++a
  gi|15669377|ref|NP_248182.1|  10 GSVFGAVIGDALGMPTENLTKEEIKKLYGFVDSYVEPKNYLAGKLNKGEWTDDTEQAICLIKSLTK-EGIDIKKFANCLIA 89 
                                   899*****************************99999999999**********************9.78*********999 PP

                                   .HHT....T--SS--HHHHHHHHHTTTT-...-S-B...---BTTTGGG-HHHHHHTSS-HHHHHHHHHHHHHTTB--HHH CS
                ADP_ribosyl_GH  82 eWleepgdteprgignttrealrnlksgepppeaganangsagngalmRaaplgllyagdpeeaaelaeeaarlTHnhpea 162
                                    W +    ++p +ig t   a+++l++++    +g     s+++ga+mR+ plg++++++++++ e +++a+++THn+++a
  gi|15669377|ref|NP_248182.1|  90 -WKN----KNPPDIGLTSLMAIDKLENND---YSGVD---SSSCGAAMRIYPLGIVFHNNLKKLKEEVIKASKITHNNKTA 159
                                   .***....9****************9875...67776...***************************************** PP

                                   HHHHHHHHHHHHHHHTT--STHHHHHH..HHHHTTT-HHHHHHHGGGGG---HHH........HHHHH--SSBHHHHHHHH CS
                ADP_ribosyl_GH 163 vagaaayaaliaaalrgksleealdaaeeelavapaeeelaaalrkalaladsdkdvdvdaeeavdelgsggyavealaaa 243
                                   +aga+a+a ++++al+ ++    ld+    ++ ++ +ee+a++l +++++ + d+         +d +g+g+ + e +++a
  gi|15669377|ref|NP_248182.1| 160 IAGALAIAFFVSSALKDRKDFSLLDEC--YNYIKDIDEEFAKKLLEIKNFNNLDY--------IYDYFGTGVKTDEVVPSA 230
                                   ***************999999999998..799*****************999999........9***************** PP

                                   HHHHHH.-SSHHHHHHHHHTS-SSHHHHHHHHHHHHHHHH-GGGS-HH CS
                ADP_ribosyl_GH 244 lyallhaaddfeeallaavnlGgDtdttgaiaGallGalyGleaiPee 291
                                   ++  l  +d+f+e++l+++n GgDtd+ ++++Ga++Ga+yG+++iP+e
  gi|15669377|ref|NP_248182.1| 231 IATYLL-TDNFKEGMLKCINAGGDTDSLASMYGAMAGAYYGFKNIPKE 277
                                   ******.***************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1915.78
//
Query:       gi|15669378|ref|NP_248183.1|  [L=283]
Description: hypothetical protein MJ_1189 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-19   69.9  32.4    2.2e-19   69.9  32.4    2.8  3  DUF4013   Protein of unknown function (DUF4013)


Domain annotation for each model (and alignments):
>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   1.7     0.031   5.5e+02      82     107 ..      22      47 ..      11      59 .. 0.62
   2 !   69.9  32.4   1.2e-23   2.2e-19       4     165 ..      73     222 ..      70     227 .. 0.74
   3 ?   -0.3   2.5     0.046   8.2e+02      60     111 ..     222     265 ..     215     279 .. 0.38

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.031
                       DUF4013  82 aagallvlallglllalllvllllll 107
                                   +++++l+    g++ a+++++l++ll
  gi|15669378|ref|NP_248183.1|  22 GIVGGLLSSTSGAIGAIFGIILSILL 47 
                                   44455555555556666655555553 PP

  == domain 2  score: 69.9 bits;  conditional E-value: 1.2e-23
                       DUF4013   4 llliiaivlslvllGYlvrvlrdtirgddelPefddwgkllvdGlkafvvslvYlliplii.alltllvalaslaagdsaa 83 
                                   + ++ia+++ ++l GY+vrv+++t+++ d lP++dd+ +ll +G+ +++  +++++i +i+ +l++++++++ +     + 
  gi|15669378|ref|NP_248183.1|  73 FGFLIALIIGFILDGYYVRVMKTTVENYDVLPDWDDIAELLKRGFLYWIGNIILSIIFMIVpILFIIFGVFLIF-----LP 148
                                   5577888888999*********************************9999999886666663222222222222.....22 PP

                       DUF4013  84 gallvlallglllalllvllllllfglllpvalarfartgslsaafnfkeilklikkkigkyiialilllvigivlsllai 164
                                   + ++v++ +g+ll+++    + ++++++  +a +++  +g +s +f+fkei+++i  + ++yii li++ vi+iv+ +++ 
  gi|15669378|ref|NP_248183.1| 149 LVGIVFIGIGFLLLFV----STIALLIYEGLAEVNYSVKG-FSGFFEFKEIFRMI--N-LNYIILLIIVGVIVIVINFVVQ 221
                                   3444444445444444....44433344447889****99.**************..5.599**99999999999999876 PP

                       DUF4013 165 l 165
                                   l
  gi|15669378|ref|NP_248183.1| 222 L 222
                                   5 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.046
                       DUF4013  60 ipliialltllvalaslaagdsaagallvlallglllalllvllllllfgll 111
                                   +p+i+     ++a++ +  ++ + + ++v     ++ a+++++++++  +++
  gi|15669378|ref|NP_248183.1| 222 LPFIL---LKIFAISPARYSTFSSSETIVD----VISAVISAFVGFY-TAVF 265
                                   44444...2223333333333333333333....3333333333444.3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1289  (0.0718947); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 1949.06
//
Query:       gi|15669893|ref|NP_248185.1|  [L=134]
Description: coenzyme F420-reducing hydrogenase subunit delta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-44  150.5   0.1    2.2e-44  150.4   0.1    1.0  1  FlpD      Methyl-viologen-reducing hydrogenase, delta subunit
     0.0017   18.2   0.0     0.0021   17.9   0.0    1.1  1  DFP       DNA / pantothenate metabolism flavoprotein


Domain annotation for each model (and alignments):
>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.4   0.1   2.5e-48   2.2e-44       1     123 []       5     127 ..       5     127 .. 1.00

  Alignments for each domain:
  == domain 1  score: 150.4 bits;  conditional E-value: 2.5e-48
                          FlpD   1 ilaFlCnwcayaaadlagvsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGnekaerrvekl 81 
                                   i+aF+C++  y aadlag+sr+qyp++vri+r+pC+g+ d ++ l+a++kGad+V+v+g ++g+C y++Gn kae+rv+ +
  gi|15669893|ref|NP_248185.1|   5 IIAFCCYQXGYGAADLAGTSRMQYPATVRIVRLPCTGKFDITYALRAFQKGADAVMVVGXKKGECAYETGNLKAEERVRFA 85 
                                   9******************************************************************************** PP

                          FlpD  82 kelleelgiepeRvrleevsaaegekfaevikefvekikeLG 123
                                   k+ll+elgi+ +R+ ++ +saae++kf+++++e+++++++LG
  gi|15669893|ref|NP_248185.1|  86 KQLLDELGIGGDRIDMFFMSAAEADKFVSAVNEMTARVEKLG 127
                                   *****************************************8 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.3e-07    0.0021      19      97 ..      31     113 ..      21     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.3e-07
                                   TTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS--..-T.T-.EEEE--SHHHHHHHHHHHHTT-SEEEE---S--E CS
                           DFP  19 pVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvslet..pe.gv.evvkvesaeemleaveealkeadivimaAAvaDy 95 
                                    VR++  + +Gk  ++ A +a ++Ga+  +v g  + e   ++ ++    +v+ a+++l+++    ++ d+++m+AA aD 
  gi|15669893|ref|NP_248185.1|  31 TVRIVRLPCTGKFDITYALRAFQKGADAVMVVGXKKGECayETgNLkAEERVRFAKQLLDELGIGGDRIDMFFMSAAEADK 111
                                   589999999**********************99976554112213314566888888888887777888***********5 PP

                                   EE CS
                           DFP  96 rp 97 
                                    +
  gi|15669893|ref|NP_248185.1| 112 FV 113
                                   55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1029.73
//
Query:       gi|15669379|ref|NP_248186.1|  [L=288]
Description: methylviologen-reducing hydrogenase subunit VhuG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-34  116.8   0.0    8.3e-34  116.2   0.0    1.3  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.0   4.6e-38   8.3e-34       1     131 []      16     165 ..      16     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 4.6e-38
                                   -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESH CS
                   Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGt 81 
                                   C+Gc+isll+l+++ll++l  +e++y  +++ad+k    e++e ++dv++veG++  +++++ +l++e++ek+k+via+Gt
  gi|15669379|ref|NP_248186.1|  16 CSGCHISLLDLHDKLLEVLPNLEIVY-APIIADPK----EIPE-GIDVFLVEGGI--RNEHDEHLIHEIREKSKIVIAWGT 88 
                                   *******************99*****.9999****....7886.***********..************************ PP

                                   HHHH-TGGGSTT-TEE..........................-.HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHHH CS
                   Oxidored_q6  82 CAafGGipaaannpsv..........................g.eevgellevvpvdinipGCPphpeailetllal 131
                                   CAa+GGip+++n +++                          + e v+++++ ++vd+ ipGCPp+p+ i++++ al
  gi|15669379|ref|NP_248186.1|  89 CAAYGGIPGLGNLYKKeellnyvystdstenkgeipseeippLeEYVKPIKDFIKVDYTIPGCPPTPKMIADAIIAL 165
                                   ************9955688999999999999998887776551677899999********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1980.19
//
Query:       gi|298575368|ref|NP_248187.2|  [L=418]
Description: methylviologen-reducing hydrogenase subunit alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-36  125.8   0.1    1.2e-23   83.8   0.0    3.1  3  NiFeSe_Hases  Nickel-dependent hydrogenase
     0.0066   16.4   0.6      0.015   15.3   0.0    1.8  2  RRF           Ribosome recycling factor


Domain annotation for each model (and alignments):
>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.0   1.3e-27   1.2e-23       1      79 [.      39     117 ..      39     126 .. 0.98
   2 !    5.9   0.0   0.00057       5.1     156     213 ..     143     197 ..     141     226 .. 0.66
   3 !   32.7   0.0   4.1e-12   3.6e-08     285     465 ..     229     408 ..     206     414 .. 0.75

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 1.3e-27
                                    --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHHTTGGGTS CS
                   NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhFYhLhalDwv 79 
                                    RG+E+++ gr  +++  +v RiCG+C t+H lasv+a++ A g++ip+ a+ +r+l++  +++h+h +hFY L+a D+v
  gi|298575368|ref|NP_248187.2|  39 RGFEQFVVGRPAEEVPRIVPRICGICQTAHHLASVKAIDAAWGVEIPEPAKKLRELMHIGNMIHSHALHFYFLAAPDFV 117
                                    9*****************************************************************************9 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.00057
                                    HHHHHHHHTHHHHHHHSSSSS--.EBTTBESSGBGSBSHHHHHHHHHHHHHHHHHHHH CS
                   NiFeSe_Hases 156 aLelqrkaakivaifggknPhpqslvvGGvtcaidllnaerlaevkslikevkefvee 213
                                    a++l++  +kiv   ggk  hp + + GG +  +     e+ +e+ + ++++ e+ ++
  gi|298575368|ref|NP_248187.2| 143 AIALRKFGQKIVEAVGGKAIHPVTGIPGGQAKRLTE---EERDELLKDADQMIEYAKN 197
                                    6778888899*********************99544...3333333333333333332 PP

  == domain 3  score: 32.7 bits;  conditional E-value: 4.1e-12
                                    E-TTSSBS.TS-B-GGG---EB---....EEE--T....TSB-BSS-EEEETTB.....--BESHHHHHHHHHHTT-HHH CS
                   NiFeSe_Hases 285 evkhswYk.ekslhplegetepkyt....leelde....egkYswikaPrykgk.....amevGplarvlvayakgkeev 350
                                    + kh +Y+ +    + +g+++++++    l   +        Y ++k P yk+      ++ vGpla + v  + +++ +
  gi|298575368|ref|NP_248187.2| 229 DGKHNFYDdTLRFLSPDGKEKVEFKpeeyL---NYigeyVVPYNYVKHPYYKKVgypegVYRVGPLAMLNVCDEMETPLA 305
                                    567888885444556678888888874442...332223567999****9985433333899*******9999999**** PP

                                    HHHHHHHHHHHT-HGGGGSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTB---B--TT-SGGGS-SEEEEEEEEEE CS
                   NiFeSe_Hases 351 kelvdkllkklglkvealfstlGRtaaRaleakliaellkewldelvenikkgdtetaneekldkkevpkeakGvglvea 430
                                    +e+ +++l+ +g+++   +  l+ + aR +e   ++e++k  l+   +n  + d       +++ +  pk  +Gvg+v a
  gi|298575368|ref|NP_248187.2| 306 EEYRKEFLEIFGFPA---NQSLAYNHARLIELVEACEKAKILLE---DNDITSD-------DIKADVEPKAGNGVGVVYA 372
                                    *************99...55789999****98777776655444...3333322.......2333344788********* PP

                                    TTEEEEEEEEE.ETTEEEEEEEE-HHHHHH--S-TT CS
                   NiFeSe_Hases 431 pRGaLsHwiki.kdgkienYqavvPsTWnasPrdak 465
                                    pRG+L H  +  ++g + + +++v +T n+   +++
  gi|298575368|ref|NP_248187.2| 373 PRGVLIHNYETdENGIVVKANMIVATTHNVPTMEKA 408
                                    *******99995689999***********8766555 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.7e-06     0.015      85     122 ..     175     215 ..     172     237 .. 0.77
   2 ?   -2.5   0.1      0.48   4.3e+03      44      66 ..     393     412 ..     386     415 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-06
                                    SSSHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHH CS
                            RRF  85 plTeErrkelvkeakkaaekakv...airniRrdankklkk 122
                                     lTeE+r+el k+a +++e ak+    i++  +++++++k 
  gi|298575368|ref|NP_248187.2| 175 RLTEEERDELLKDADQMIEYAKNgveLIKQLNEQYMEQIKT 215
                                    69*********************444444555566666654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.48
                                    TEEEEEESSCCHHHHHHHHHHHS CS
                            RRF  44 rtllitpfdkslvkaiekaIlks 66 
                                    ++++ t    ++v   ekaI+++
  gi|298575368|ref|NP_248187.2| 393 NMIVAT---THNVPTMEKAIQQA 412
                                    444444...58888888888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      728  (0.0406046); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 2926.28
//
Query:       gi|15669380|ref|NP_248188.1|  [L=394]
Description: polyferredoxin MvhB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-54  179.5 122.2    2.5e-07   30.2   2.7   12.2 12  Fer4      4Fe-4S binding domain
    2.2e-45  153.0  88.3    2.1e-10   41.0   7.7    8.1  9  Fer4_7    4Fe-4S dicluster domain
    1.5e-35  121.9  95.8    0.00022   22.1   3.6   11.5 12  Fer4_16   4Fe-4S double cluster binding domain
    1.4e-33  114.8 100.7    6.2e-09   35.8  10.9    8.1  9  Fer4_10   4Fe-4S dicluster domain
    1.4e-33  113.5 122.4    1.3e-05   25.0   1.5   12.0 12  Fer4_6    4Fe-4S binding domain
    3.4e-33  113.6  96.3    8.4e-07   29.1   7.2    7.8  9  Fer4_9    4Fe-4S dicluster domain
    4.2e-29  100.5 102.0      8e-08   32.3  13.6    9.1  9  Fer4_21   4Fe-4S dicluster domain
    1.8e-24   84.3 109.8     0.0011   19.0   2.1   12.2 12  Fer4_2    4Fe-4S binding domain
    3.7e-19   68.9  98.2    1.6e-05   25.2   9.9   10.0  8  Fer4_8    4Fe-4S dicluster domain
    1.8e-14   54.0  94.1     0.0036   17.8   0.4   11.1 11  Fer4_17   4Fe-4S dicluster domain
    2.6e-10   40.5 140.2      0.014   16.3   6.0   12.4 12  Fer4_3    4Fe-4S binding domain
    9.1e-10   38.3 108.4        0.1   13.1   3.1   11.6 12  Fer4_4    4Fe-4S binding domain
    1.2e-06   28.7  98.1      0.065   13.4   2.7    9.7 10  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.15   12.8  88.9        1.2    9.9   1.0   11.3 10  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   3.6   1.9e-06    0.0025       2      23 ..       7      28 ..       6      29 .. 0.92
   2 !   22.5   2.3   5.3e-08   6.8e-05       7      23 ..      35      51 ..      32      52 .. 0.92
   3 !   20.6   3.1   2.2e-07   0.00028       7      22 ..      72      87 ..      68      89 .. 0.90
   4 !   18.5   2.2   9.9e-07    0.0013       5      23 ..      98     116 ..      94     117 .. 0.87
   5 !   28.8   7.2   5.4e-10   6.9e-07       5      24 .]     139     158 ..     135     158 .. 0.92
   6 !   30.2   2.7   1.9e-10   2.5e-07       2      23 ..     165     186 ..     164     187 .. 0.95
   7 !   28.5   3.8   6.8e-10   8.7e-07       2      24 .]     204     226 ..     203     226 .. 0.93
   8 !   19.3   5.3   5.5e-07   0.00071       1      23 [.     233     255 ..     233     256 .. 0.91
   9 !   12.5   0.5   7.7e-05     0.098      13      23 ..     284     294 ..     283     295 .. 0.91
  10 !   21.9   5.0   8.1e-08    0.0001       7      24 .]     305     322 ..     302     322 .. 0.93
  11 !   23.3   1.7   3.1e-08     4e-05       2      21 ..     337     356 ..     336     359 .. 0.85
  12 ?    2.3   1.1      0.12   1.6e+02       7      16 ..     370     379 ..     368     380 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
                                  EEETTTSSS-THHHHHSTTTEE CS
                          Fer4  2 videekCigCGaCvevCPvgAI 23
                                  +i ++ C  C aC   CP+ AI
  gi|15669380|ref|NP_248188.1|  7 TIQKDACLVCYACQAECPTKAI 28
                                  7889*****************9 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 5.3e-08
                                  TSSS-THHHHHSTTTEE CS
                          Fer4  7 kCigCGaCvevCPvgAI 23
                                   C  C++Cv+vCP+gA+
  gi|15669380|ref|NP_248188.1| 35 VCNLCMECVKVCPTGAL 51
                                  5***************8 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 2.2e-07
                                  TSSS-THHHHHSTTTE CS
                          Fer4  7 kCigCGaCvevCPvgA 22
                                  kC +CG+C+e+CP g 
  gi|15669380|ref|NP_248188.1| 72 KCEKCGQCAEACPIGI 87
                                  9************985 PP

  == domain 4  score: 18.5 bits;  conditional E-value: 9.9e-07
                                   TTTSSS-THHHHHSTTTEE CS
                          Fer4   5 eekCigCGaCvevCPvgAI 23 
                                   +  C+ C +C++vCP + I
  gi|15669380|ref|NP_248188.1|  98 KGHCVLCQKCIDVCPIEII 116
                                   678************9998 PP

  == domain 5  score: 28.8 bits;  conditional E-value: 5.4e-10
                                   TTTSSS-THHHHHSTTTEEE CS
                          Fer4   5 eekCigCGaCvevCPvgAIt 24 
                                   ++ C+gCG+Cv  CPv+AIt
  gi|15669380|ref|NP_248188.1| 139 TDACVGCGICVPECPVNAIT 158
                                   79*****************7 PP

  == domain 6  score: 30.2 bits;  conditional E-value: 1.9e-10
                                   EEETTTSSS-THHHHHSTTTEE CS
                          Fer4   2 videekCigCGaCvevCPvgAI 23 
                                   vid++kCi+C +C++ CP +AI
  gi|15669380|ref|NP_248188.1| 165 VIDKSKCIYCSICAQTCPWNAI 186
                                   8********************9 PP

  == domain 7  score: 28.5 bits;  conditional E-value: 6.8e-10
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   +++ ekCi+C +CvevCP + I+
  gi|15669380|ref|NP_248188.1| 204 EVNAEKCIYCLKCVEVCPGDMIK 226
                                   69*****************9996 PP

  == domain 8  score: 19.3 bits;  conditional E-value: 5.5e-07
                                   EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                   +vi +  C +C++Cv++CPv+A+
  gi|15669380|ref|NP_248188.1| 233 IVIPPKSCPACKLCVNICPVDAL 255
                                   5788999***************8 PP

  == domain 9  score: 12.5 bits;  conditional E-value: 7.7e-05
                                   HHHHHSTTTEE CS
                          Fer4  13 aCvevCPvgAI 23 
                                   +C++vCP++AI
  gi|15669380|ref|NP_248188.1| 284 KCASVCPTEAI 294
                                   7*********9 PP

  == domain 10  score: 21.9 bits;  conditional E-value: 8.1e-08
                                   TSSS-THHHHHSTTTEEE CS
                          Fer4   7 kCigCGaCvevCPvgAIt 24 
                                   +Ci CGaC  +CP+gA++
  gi|15669380|ref|NP_248188.1| 305 MCIVCGACTVACPTGALK 322
                                   6***************85 PP

  == domain 11  score: 23.3 bits;  conditional E-value: 3.1e-08
                                   EEETTTSSS-THHHHHSTTT CS
                          Fer4   2 videekCigCGaCvevCPvg 21 
                                   ++ + +C +CG+CvevCP  
  gi|15669380|ref|NP_248188.1| 337 EFSPYLCDKCGKCVEVCPMK 356
                                   577889************75 PP

  == domain 12  score: 2.3 bits;  conditional E-value: 0.12
                                   TSSS-THHHH CS
                          Fer4   7 kCigCGaCve 16 
                                    C+ C +C +
  gi|15669380|ref|NP_248188.1| 370 YCVMCLLCLS 379
                                   6*******76 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.9   1.5e-06    0.0019      30      52 .]       5      27 ..       2      27 .. 0.91
   2 !   31.4  10.3   1.7e-10   2.1e-07       2      52 .]      36      87 ..      35      87 .. 0.88
   3 !   32.2   8.5     9e-11   1.2e-07       1      52 []     100     156 ..     100     156 .. 0.82
   4 !   35.0  12.9   1.2e-11   1.6e-08       1      52 []     141     185 ..     141     185 .. 0.93
   5 !   39.8  10.3   3.9e-13     5e-10       1      50 [.     170     222 ..     170     224 .. 0.87
   6 !   22.7   4.0   8.5e-08   0.00011       2      52 .]     240     293 ..     239     293 .. 0.81
   7 !    9.7   0.3   0.00099       1.3       7      25 ..     284     302 ..     283     305 .. 0.82
   8 !   41.0   7.7   1.6e-13   2.1e-10       2      50 ..     306     355 ..     305     357 .. 0.88
   9 ?   -0.4   0.5       1.4   1.8e+03      38      46 ..     371     379 ..     368     384 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                        Fer4_7 30 kveidpekClgCgaCvavCPtga 52
                                  +++i+ + Cl C+aC+a+CPt+a
  gi|15669380|ref|NP_248188.1|  5 SITIQKDACLVCYACQAECPTKA 27
                                  67999****************87 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 1.7e-10
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeene.kgtekveidpekClgCgaCvavCPtga 52
                                  C  C  Cv++Cp++a+  +e e++ k+ ++v++ + kC  Cg+C+++CP g+
  gi|15669380|ref|NP_248188.1| 36 CNLCMECVKVCPTGALVEEEIEVNgKKLKRVNYLAHKCEKCGQCAEACPIGI 87
                                  99**************99887555144499*******************885 PP

  == domain 3  score: 32.2 bits;  conditional E-value: 9e-11
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt.....ekveidpekClgCgaCvavCPtga 52 
                                   +C+ C++C ++Cp + i+l+ + +++++     +++  + + C+gCg Cv +CP++a
  gi|15669380|ref|NP_248188.1| 100 HCVLCQKCIDVCPIEIISLPGVIDKPKKeikppKEPIAVTDACVGCGICVPECPVNA 156
                                   6*****************9966555433334437777889***************97 PP

  == domain 4  score: 35.0 bits;  conditional E-value: 1.2e-11
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C+gCg Cv+ Cpv+ai+l++        k++id +kC++C  C+++CP++a
  gi|15669380|ref|NP_248188.1| 141 ACVGCGICVPECPVNAITLENN-------KAVIDKSKCIYCSICAQTCPWNA 185
                                   5******************654.......689******************97 PP

  == domain 5  score: 39.8 bits;  conditional E-value: 3.9e-13
                        Fer4_7   1 rCigCgaCvaaCpvkaield...eeenekgtekveidpekClgCgaCvavCPt 50 
                                   +Ci C  C+++Cp++ai +    ++++ k+++k e+++ekC++C +Cv+vCP 
  gi|15669380|ref|NP_248188.1| 170 KCIYCSICAQTCPWNAIFVAgkiPKKRRKEVKKFEVNAEKCIYCLKCVEVCPG 222
                                   7*****************9955545566677999******************5 PP

  == domain 6  score: 22.7 bits;  conditional E-value: 8.5e-08
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenek.gt..ekveidpekClgCgaCvavCPtga 52 
                                   C  C+ Cv+ Cpv+a++l+ + + + ++  e ++i++e+    ++C++vCPt+a
  gi|15669380|ref|NP_248188.1| 240 CPACKLCVNICPVDALDLEVKLSSPhPItdEGLVIVEEDFEVLKKCASVCPTEA 293
                                   99***************9855333322233567999****************87 PP

  == domain 7  score: 9.7 bits;  conditional E-value: 0.00099
                        Fer4_7   7 aCvaaCpvkaieldeeene 25 
                                   +C+++Cp++ai +dee++e
  gi|15669380|ref|NP_248188.1| 284 KCASVCPTEAIVVDEEKKE 302
                                   7**********99998655 PP

  == domain 8  score: 41.0 bits;  conditional E-value: 1.6e-13
                        Fer4_7   2 CigCgaCvaaCpvkaieldee.enekgtekveidpekClgCgaCvavCPt 50 
                                   Ci CgaC++aCp++a++l +  +n k+  ++e++p  C  Cg+Cv+vCP 
  gi|15669380|ref|NP_248188.1| 306 CIVCGACTVACPTGALKLGKIeHNGKEYNRIEFSPYLCDKCGKCVEVCPM 355
                                   *****************99861444677999******************6 PP

  == domain 9  score: -0.4 bits;  conditional E-value: 1.4
                        Fer4_7  38 ClgCgaCva 46 
                                   C+ C  C +
  gi|15669380|ref|NP_248188.1| 371 CVMCLLCLS 379
                                   555555543 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   4.6     0.002       2.6       2      21 ..      13      32 ..      12      37 .. 0.85
   2 !   19.9   1.1   8.2e-07     0.001       2      26 ..      36      59 ..      35      70 .. 0.81
   3 !   14.0   2.5   5.9e-05     0.076       1      15 [.      72      86 ..      72      95 .. 0.87
   4 !   21.0   1.5   3.8e-07   0.00048       1      31 [.     100     128 ..     100     139 .. 0.85
   5 !   22.1   3.6   1.7e-07   0.00022       2      31 ..     142     172 ..     141     173 .. 0.89
   6 !   14.6   3.2   3.7e-05     0.047      49      67 .]     166     184 ..     159     184 .. 0.80
   7 !   12.9   4.1   0.00013      0.16       2      20 ..     171     189 ..     170     208 .. 0.68
   8 !   17.6   1.1   4.3e-06    0.0055       1      25 [.     209     233 ..     209     238 .. 0.86
   9 !   15.3   0.3   2.3e-05     0.029       2      20 ..     240     258 ..     239     279 .. 0.85
  10 !   13.9   1.3   6.3e-05     0.081       6      30 ..     283     306 ..     282     307 .. 0.78
  11 !   19.2   1.3   1.4e-06    0.0018       2      26 ..     306     327 ..     305     338 .. 0.80
  12 !   11.6   7.6   0.00033      0.42       2      20 ..     343     361 ..     342     387 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.002
                       Fer4_16  2 CgtCgkCaevCPtnaikekk 21
                                  C  C +C   CPt+ai+ ++
  gi|15669380|ref|NP_248188.1| 13 CLVCYACQAECPTKAIDIDS 32
                                  999*************9774 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 8.2e-07
                       Fer4_16  2 CgtCgkCaevCPtnaikekkekeie 26
                                  C  C +C++vCPt+a+ e+ e e++
  gi|15669380|ref|NP_248188.1| 36 CNLCMECVKVCPTGALVEE-EIEVN 59
                                  99***************99.44444 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 5.9e-05
                       Fer4_16  1 rCgtCgkCaevCPtn 15
                                  +C +Cg+Cae+CP +
  gi|15669380|ref|NP_248188.1| 72 KCEKCGQCAEACPIG 86
                                  5************76 PP

  == domain 4  score: 21.0 bits;  conditional E-value: 3.8e-07
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeieareci 31 
                                   +C+ C+kC++vCP + i+ +   +i++++++
  gi|15669380|ref|NP_248188.1| 100 HCVLCQKCIDVCPIEIISLP--GVIDKPKKE 128
                                   7******************9..888877754 PP

  == domain 5  score: 22.1 bits;  conditional E-value: 1.7e-07
                       Fer4_16   2 CgtCgkCaevCPtnaikek.kekeieareci 31 
                                   C++Cg C+  CP+nai+ + ++++i++ +ci
  gi|15669380|ref|NP_248188.1| 142 CVGCGICVPECPVNAITLEnNKAVIDKSKCI 172
                                   *****************88678889999997 PP

  == domain 6  score: 14.6 bits;  conditional E-value: 3.7e-05
                       Fer4_16  49 kkqeaitgCdiCqdvCPan 67 
                                     + ++++C iC+++CP+n
  gi|15669380|ref|NP_248188.1| 166 IDKSKCIYCSICAQTCPWN 184
                                   45789*************9 PP

  == domain 7  score: 12.9 bits;  conditional E-value: 0.00013
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C+ C  Ca++CP nai   
  gi|15669380|ref|NP_248188.1| 171 CIYCSICAQTCPWNAIFVA 189
                                   8888888888888887654 PP

  == domain 8  score: 17.6 bits;  conditional E-value: 4.3e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekei 25 
                                   +C+ C kC+evCP + ik ++e+ i
  gi|15669380|ref|NP_248188.1| 209 KCIYCLKCVEVCPGDMIKVDEENLI 233
                                   5*****************9977655 PP

  == domain 9  score: 15.3 bits;  conditional E-value: 2.3e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C  C+ C+++CP++a++ +
  gi|15669380|ref|NP_248188.1| 240 CPACKLCVNICPVDALDLE 258
                                   99**************988 PP

  == domain 10  score: 13.9 bits;  conditional E-value: 6.3e-05
                       Fer4_16   6 gkCaevCPtnaikekkekeiearec 30 
                                   +kCa+vCPt+ai  + e++ e r+c
  gi|15669380|ref|NP_248188.1| 283 KKCASVCPTEAIVVD-EEKKEVRMC 306
                                   69***********99.455555555 PP

  == domain 11  score: 19.2 bits;  conditional E-value: 1.4e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeie 26 
                                   C+ Cg+C+ +CPt+a+k     +ie
  gi|15669380|ref|NP_248188.1| 306 CIVCGACTVACPTGALKLG---KIE 327
                                   ****************988...333 PP

  == domain 12  score: 11.6 bits;  conditional E-value: 0.00033
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C +CgkC+evCP + ++  
  gi|15669380|ref|NP_248188.1| 343 CDKCGKCVEVCPMKTLRLS 361
                                   *************999876 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   3.0   1.5e-05      0.02       2      22 ..       6      26 ..       5      33 .. 0.85
   2 !   31.3  11.0   1.2e-10   1.6e-07       6      56 .]      33      84 ..      27      84 .. 0.86
   3 !   20.0  12.8   4.3e-07   0.00055       8      56 .]     100     153 ..      95     153 .. 0.90
   4 !   11.8   3.5   0.00016       0.2       5      22 ..     138     155 ..     134     162 .. 0.81
   5 !   35.8  10.9   4.8e-12   6.2e-09       1      56 []     163     221 ..     163     221 .. 0.93
   6 !   17.6   0.4   2.5e-06    0.0031       2      23 ..     233     254 ..     232     278 .. 0.81
   7 !   14.8  10.1   1.8e-05     0.023      13      56 .]     283     317 ..     282     317 .. 0.89
   8 !   26.1  13.5   5.5e-09     7e-06       6      56 .]     303     354 ..     299     354 .. 0.90
   9 !   14.4   7.2   2.4e-05     0.031       5      51 ..     339     377 ..     335     383 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                       Fer4_10  2 vvidddtCirCgkCvkaCPad 22
                                  + i++d C+ C +C++ CP++
  gi|15669380|ref|NP_248188.1|  6 ITIQKDACLVCYACQAECPTK 26
                                  6799***************93 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 1.2e-10
                       Fer4_10  6 ddtCirCgkCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   + C  C +Cvk+CP+ +  + + +   ++ ++v+    kC++cg+C+eaCP
  gi|15669380|ref|NP_248188.1| 33 FKVCNLCMECVKVCPTGAlVEEEIEVNGKKLKRVNYLAHKCEKCGQCAEACP 84
                                  467*************8777777788888888999999*************9 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 4.3e-07
                       Fer4_10   8 tCirCgkCvkaCPadl.....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    C+ C+kC ++CP  +       ++ k+e+++ ++   + ++C gcg Cv +CP
  gi|15669380|ref|NP_248188.1| 100 HCVLCQKCIDVCPIEIislpgVIDKPKKEIKPPKEPIAVTDACVGCGICVPECP 153
                                   6*************99***99888888888888888889**************9 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00016
                       Fer4_10   5 dddtCirCgkCvkaCPad 22 
                                    +d C++Cg Cv  CP++
  gi|15669380|ref|NP_248188.1| 138 VTDACVGCGICVPECPVN 155
                                   5799************94 PP

  == domain 5  score: 35.8 bits;  conditional E-value: 4.8e-12
                       Fer4_10   1 kvvidddtCirCgkCvkaCPadl...tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   k+vid+++Ci C  C + CP+++    ++  k+ ++e ++ +++ ekC+ c +Cve+CP
  gi|15669380|ref|NP_248188.1| 163 KAVIDKSKCIYCSICAQTCPWNAifvAGKIPKKRRKEVKKFEVNAEKCIYCLKCVEVCP 221
                                   579******************9999888888888999999999***************9 PP

  == domain 6  score: 17.6 bits;  conditional E-value: 2.5e-06
                       Fer4_10   2 vvidddtCirCgkCvkaCPadl 23 
                                   +vi++++C  C+ Cv+ CP+d+
  gi|15669380|ref|NP_248188.1| 233 IVIPPKSCPACKLCVNICPVDA 254
                                   799****************955 PP

  == domain 7  score: 14.8 bits;  conditional E-value: 1.8e-05
                       Fer4_10  13 gkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +kC ++CP+         ea   ++++k v  C+ cgaC+ aCP
  gi|15669380|ref|NP_248188.1| 283 KKCASVCPT---------EAIVVDEEKKEVRMCIVCGACTVACP 317
                                   58*******.........7777777888899************9 PP

  == domain 8  score: 26.1 bits;  conditional E-value: 5.5e-09
                       Fer4_10   6 ddtCirCgkCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                      Ci Cg+C+ aCP+ + +  + +   +e ++++  ++ C++cg+Cve+CP
  gi|15669380|ref|NP_248188.1| 303 VRMCIVCGACTVACPTGAlKLGKIEHNGKEYNRIEFSPYLCDKCGKCVEVCP 354
                                   567*************88888888888899999999***************9 PP

  == domain 9  score: 14.4 bits;  conditional E-value: 2.4e-05
                       Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaC 51 
                                    +  C +CgkCv++CP+     ++     ++ + ++    C +c  C
  gi|15669380|ref|NP_248188.1| 339 SPYLCDKCGKCVEVCPM-----KTLRLSRGKLPLKG---YCVMCLLC 377
                                   5668*************.....44444444444444...44444444 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   3.0   1.6e-07    0.0002       2      24 .]       6      28 ..       5      28 .. 0.96
   2 !   20.8   4.0   2.3e-07   0.00029       9      24 .]      36      51 ..      35      51 .. 0.96
   3 !   12.1   2.7   0.00013      0.17       7      22 ..      71      86 ..      66      87 .. 0.88
   4 !    7.7   4.8    0.0031         4       9      23 ..     101     115 ..     100     116 .. 0.88
   5 !   18.1   5.9   1.5e-06     0.002       7      24 .]     140     157 ..     135     157 .. 0.93
   6 !   16.8   3.1   4.1e-06    0.0053       1      24 []     163     186 ..     163     186 .. 0.96
   7 !   17.4   3.0   2.6e-06    0.0033       2      21 ..     203     222 ..     202     228 .. 0.89
   8 !   14.7   3.9   1.9e-05     0.025       6      24 .]     237     255 ..     232     255 .. 0.88
   9 !    8.3   0.4    0.0019       2.5      14      24 .]     284     294 ..     283     294 .. 0.92
  10 !   17.6   5.3   2.2e-06    0.0028       9      24 .]     306     321 ..     304     321 .. 0.94
  11 !   25.0   1.5     1e-08   1.3e-05       2      21 ..     336     355 ..     335     358 .. 0.91
  12 ?   -0.5   1.2       1.2   1.5e+03       9      18 ..     371     380 ..     369     380 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.6e-07
                        Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                  ++i++d+C+ C++C + CP++ai
  gi|15669380|ref|NP_248188.1|  6 ITIQKDACLVCYACQAECPTKAI 28
                                  89*******************98 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.3e-07
                        Fer4_6  9 CigCgdCvrvCPegai 24
                                  C+ C++Cv+vCP+ga+
  gi|15669380|ref|NP_248188.1| 36 CNLCMECVKVCPTGAL 51
                                  **************97 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00013
                        Fer4_6  7 dkCigCgdCvrvCPeg 22
                                   kC  Cg C+ +CP g
  gi|15669380|ref|NP_248188.1| 71 HKCEKCGQCAEACPIG 86
                                  59************65 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0031
                        Fer4_6   9 CigCgdCvrvCPega 23 
                                   C+ C +C++vCP  +
  gi|15669380|ref|NP_248188.1| 101 CVLCQKCIDVCPIEI 115
                                   ************655 PP

  == domain 5  score: 18.1 bits;  conditional E-value: 1.5e-06
                        Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                   d+C+gCg Cv  CP +ai
  gi|15669380|ref|NP_248188.1| 140 DACVGCGICVPECPVNAI 157
                                   99**************98 PP

  == domain 6  score: 16.8 bits;  conditional E-value: 4.1e-06
                        Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                   +++id++kCi C  C+  CP +ai
  gi|15669380|ref|NP_248188.1| 163 KAVIDKSKCIYCSICAQTCPWNAI 186
                                   689******************998 PP

  == domain 7  score: 17.4 bits;  conditional E-value: 2.6e-06
                        Fer4_6   2 veidpdkCigCgdCvrvCPe 21 
                                    e++++kCi C +Cv vCP 
  gi|15669380|ref|NP_248188.1| 203 FEVNAEKCIYCLKCVEVCPG 222
                                   69*****************5 PP

  == domain 8  score: 14.7 bits;  conditional E-value: 1.9e-05
                        Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                   p +C  C  Cv++CP +a+
  gi|15669380|ref|NP_248188.1| 237 PKSCPACKLCVNICPVDAL 255
                                   779************9996 PP

  == domain 9  score: 8.3 bits;  conditional E-value: 0.0019
                        Fer4_6  14 dCvrvCPegai 24 
                                   +C++vCP+ ai
  gi|15669380|ref|NP_248188.1| 284 KCASVCPTEAI 294
                                   7*******998 PP

  == domain 10  score: 17.6 bits;  conditional E-value: 2.2e-06
                        Fer4_6   9 CigCgdCvrvCPegai 24 
                                   Ci Cg+C+++CP+ga+
  gi|15669380|ref|NP_248188.1| 306 CIVCGACTVACPTGAL 321
                                   **************97 PP

  == domain 11  score: 25.0 bits;  conditional E-value: 1e-08
                        Fer4_6   2 veidpdkCigCgdCvrvCPe 21 
                                   +e+ p +C+ Cg+Cv vCP+
  gi|15669380|ref|NP_248188.1| 336 IEFSPYLCDKCGKCVEVCPM 355
                                   799999*************7 PP

  == domain 12  score: -0.5 bits;  conditional E-value: 1.2
                        Fer4_6   9 CigCgdCvrv 18 
                                   C+ C  C +v
  gi|15669380|ref|NP_248188.1| 371 CVMCLLCLSV 380
                                   99**999865 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   3.9   0.00033      0.42      29      51 .]       7      28 ..       1      28 [. 0.78
   2 !   13.6  14.0   4.4e-05     0.056       1      50 [.      12      50 ..      12      51 .. 0.90
   3 !   25.9  12.1   6.5e-09   8.3e-06       2      49 ..      36      86 ..      35      87 .. 0.77
   4 !   20.9  14.1   2.4e-07    0.0003       1      50 [.      72     115 ..      72     116 .. 0.90
   5 !   26.6  11.3   3.8e-09   4.8e-06       2      51 .]     101     157 ..     100     157 .. 0.88
   6 !   26.5  12.0     4e-09   5.2e-06       1      51 []     141     186 ..     141     186 .. 0.92
   7 !   29.1   7.2   6.6e-10   8.4e-07       1      50 [.     209     254 ..     190     255 .. 0.95
   8 !   24.5   7.9   1.7e-08   2.2e-05       6      50 ..     283     320 ..     283     321 .. 0.95
   9 !   17.6   6.1   2.4e-06    0.0031       2      44 ..     343     379 ..     342     384 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                        Fer4_9 29 raaseeaCigCgaCveaCpkgai 51
                                  +++++ aC+ C aC + Cp++ai
  gi|15669380|ref|NP_248188.1|  7 TIQKD-ACLVCYACQAECPTKAI 28
                                  44554.8*************987 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.4e-05
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                  +C  C aC++ Cp++++  d+++            C  C++Cv++Cp+ga
  gi|15669380|ref|NP_248188.1| 12 ACLVCYACQAECPTKAIDIDSFKV-----------CNLCMECVKVCPTGA 50
                                  5999*************9998863...........999**********97 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 6.5e-09
                        Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkg 49
                                  C+ C +Cv++Cp+g+ ve++ e   +  +         +C +Cg+C+eaCp g
  gi|15669380|ref|NP_248188.1| 36 CNLCMECVKVCPTGALVEEEIEVNGKKLK--RvnylaHKCEKCGQCAEACPIG 86
                                  ***************98877654443322..12358899************76 PP

  == domain 4  score: 20.9 bits;  conditional E-value: 2.4e-07
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   kC +Cg+C eaCp g+ + d+   + +        C+ C++C+++Cp ++
  gi|15669380|ref|NP_248188.1|  72 KCEKCGQCAEACPIGIKKVDDDFPYSKG------HCVLCQKCIDVCPIEI 115
                                   7****************99988888887......5************775 PP

  == domain 5  score: 26.6 bits;  conditional E-value: 3.8e-09
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase.......eaCigCgaCveaCpkgai 51 
                                   C+ C++C+++Cp ++++   +  k + +++         +aC+gCg Cv  Cp +ai
  gi|15669380|ref|NP_248188.1| 101 CVLCQKCIDVCPIEIISLPGVIDKPKKEIKPPkepiavtDACVGCGICVPECPVNAI 157
                                   ****************9998888877666555779****9*************9987 PP

  == domain 6  score: 26.5 bits;  conditional E-value: 4e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   +C+gCg Cv+ Cp ++++ ++++  +        +Ci C  C++ Cp +ai
  gi|15669380|ref|NP_248188.1| 141 ACVGCGICVPECPVNAITLENNKAVIDKS-----KCIYCSICAQTCPWNAI 186
                                   6********************99999974.....6************9876 PP

  == domain 7  score: 29.1 bits;  conditional E-value: 6.6e-10
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   kC+ C +Cve+Cp ++++ d+ + ++   +    +C  C+ Cv++Cp +a
  gi|15669380|ref|NP_248188.1| 209 KCIYCLKCVEVCPGDMIKVDEENLIVIPPK----SCPACKLCVNICPVDA 254
                                   7*********************99999866....6************987 PP

  == domain 8  score: 24.5 bits;  conditional E-value: 1.7e-08
                        Fer4_9   6 gaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   ++C ++Cp++++v d+ ++++r+       Ci CgaC+ aCp+ga
  gi|15669380|ref|NP_248188.1| 283 KKCASVCPTEAIVVDEEKKEVRM-------CIVCGACTVACPTGA 320
                                   57********************8.......*************97 PP

  == domain 9  score: 17.6 bits;  conditional E-value: 2.4e-06
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCve 44 
                                   C +Cg+Cve+Cp+++ + ++++   +        C++C  C+ 
  gi|15669380|ref|NP_248188.1| 343 CDKCGKCVEVCPMKTLRLSRGKLPLKG------YCVMCLLCLS 379
                                   *******************99999997......3999999986 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8  14.1    0.0014       1.8       3      55 ..       8      49 ..       6      54 .. 0.89
   2 !   14.5  11.9   2.2e-05     0.029       7      53 ..      35      85 ..      30      90 .. 0.81
   3 !   16.5  14.6   5.3e-06    0.0069       7      58 ..      72     117 ..      71     118 .. 0.83
   4 !   20.6   2.8   2.8e-07   0.00036      36      58 ..     137     158 ..     121     159 .. 0.83
   5 !   32.0  12.8     8e-11     1e-07       1      58 [.     164     226 ..     164     227 .. 0.78
   6 !   32.3  13.6   6.2e-11     8e-08       3      56 ..     205     254 ..     203     257 .. 0.93
   7 ?    5.5   0.1     0.014        18      44      57 ..     282     294 ..     267     297 .. 0.73
   8 !   26.6   6.8   3.7e-09   4.8e-06       6      54 ..     304     356 ..     299     360 .. 0.78
   9 ?    3.0   0.4     0.087   1.1e+02      40      50 ..     370     380 ..     364     384 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                       Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPved 55
                                  i++d C+ C  C   C+   ++ai+id+ +v       C  C  C++vCP+ +
  gi|15669380|ref|NP_248188.1|  8 IQKDACLVCYACQAECP---TKAIDIDSFKV-------CNLCMECVKVCPT-G 49
                                  99***************...69****98777.......999*********7.4 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.2e-05
                       Fer4_21  7 kCigCgkCliaCedtsh..qaieidaktvlkvv..edeCvGCnlCssvCPv 53
                                   C  C +C+++C++++   + ie+++k+  +v   +++C  C  C++ CP+
  gi|15669380|ref|NP_248188.1| 35 VCNLCMECVKVCPTGALveEEIEVNGKKLKRVNylAHKCEKCGQCAEACPI 85
                                  6889*********98843378999988766554339**************8 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 5.3e-06
                       Fer4_21   7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                   kC +Cg+C+ aC+      i++  +  +++ + +Cv C+ C++vCP+ + i+
  gi|15669380|ref|NP_248188.1|  72 KCEKCGQCAEACP----IGIKKV-DDDFPYSKGHCVLCQKCIDVCPI-EIIS 117
                                   899**********....345544.45679*****************9.7765 PP

  == domain 4  score: 20.6 bits;  conditional E-value: 2.8e-07
                       Fer4_21  36 vvedeCvGCnlCssvCPvedcie 58 
                                    v+d CvGC +C+  CPv ++i+
  gi|15669380|ref|NP_248188.1| 137 AVTDACVGCGICVPECPV-NAIT 158
                                   479**************9.9997 PP

  == domain 5  score: 32.0 bits;  conditional E-value: 8e-11
                       Fer4_21   1 AridedkCigCgkCliaCedtshqai.........eidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                   A+id++kCi C  C+++C+    +ai         + ++ ++++v +++C+ C  C++vCP  d+i+
  gi|15669380|ref|NP_248188.1| 164 AVIDKSKCIYCSICAQTCPW---NAIfvagkipkkRRKEVKKFEVNAEKCIYCLKCVEVCP-GDMIK 226
                                   89*****************5...66655565553323333566999***************.58886 PP

  == domain 6  score: 32.3 bits;  conditional E-value: 6.2e-11
                       Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedc 56 
                                   ++ +kCi C kC+ +C+    + i++d+++ + +  ++C +C+lC+++CPv d+
  gi|15669380|ref|NP_248188.1| 205 VNAEKCIYCLKCVEVCP---GDMIKVDEENLIVIPPKSCPACKLCVNICPV-DA 254
                                   789**************...5**********9999***************9.65 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.014
                       Fer4_21  44 CnlCssvCPvedci 57 
                                    + C+svCP+ ++i
  gi|15669380|ref|NP_248188.1| 282 LKKCASVCPT-EAI 294
                                   578******7.665 PP

  == domain 8  score: 26.6 bits;  conditional E-value: 3.7e-09
                       Fer4_21   6 dkCigCgkCliaCedtshqa..ieidaktvlkvv..edeCvGCnlCssvCPve 54 
                                    +Ci Cg C++aC++++ +   ie ++k++ ++      C  C  C++vCP++
  gi|15669380|ref|NP_248188.1| 304 RMCIVCGACTVACPTGALKLgkIEHNGKEYNRIEfsPYLCDKCGKCVEVCPMK 356
                                   58************9998862266666666554322789************84 PP

  == domain 9  score: 3.0 bits;  conditional E-value: 0.087
                       Fer4_21  40 eCvGCnlCssv 50 
                                    Cv C lC+sv
  gi|15669380|ref|NP_248188.1| 370 YCVMCLLCLSV 380
                                   69999999887 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   2.7    0.0009       1.1       7      22 .]      10      25 ..       5      25 .. 0.87
   2 !   12.8   1.7   7.5e-05     0.096       9      22 .]      35      48 ..      27      48 .. 0.88
   3 !    9.6   2.4    0.0008         1       9      21 ..      72      84 ..      66      84 .. 0.92
   4 !   12.9   1.7     7e-05      0.09       8      21 ..      99     112 ..      91     112 .. 0.89
   5 !   17.7   5.1   2.1e-06    0.0027       3      21 ..     135     153 ..     132     154 .. 0.89
   6 !   16.0   2.1   7.3e-06    0.0093       3      21 ..     164     182 ..     162     183 .. 0.92
   7 !   19.0   2.1   8.4e-07    0.0011       2      21 ..     202     221 ..     201     221 .. 0.94
   8 !   12.1   3.5   0.00013      0.16       3      21 ..     233     251 ..     230     252 .. 0.91
   9 ?    4.1   1.0     0.043        56      15      22 .]     284     291 ..     283     291 .. 0.89
  10 !   18.1   2.4   1.5e-06     0.002       3      22 .]     294     318 ..     292     318 .. 0.80
  11 !   16.1   1.9   6.7e-06    0.0086       3      21 ..     336     354 ..     334     355 .. 0.87
  12 ?    1.1   0.8       0.4   5.1e+02      10      19 ..     371     380 ..     370     380 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0009
                        Fer4_2  7 tdrCigCgaCvsaCPa 22
                                   d+C+ C aC+  CP+
  gi|15669380|ref|NP_248188.1| 10 KDACLVCYACQAECPT 25
                                  699*******999**7 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.5e-05
                        Fer4_2  9 rCigCgaCvsaCPa 22
                                   C+ C  Cv++CP+
  gi|15669380|ref|NP_248188.1| 35 VCNLCMECVKVCPT 48
                                  7************7 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0008
                        Fer4_2  9 rCigCgaCvsaCP 21
                                  +C  Cg C  aCP
  gi|15669380|ref|NP_248188.1| 72 KCEKCGQCAEACP 84
                                  8***********9 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 7e-05
                        Fer4_2   8 drCigCgaCvsaCP 21 
                                    +C+ C +C+++CP
  gi|15669380|ref|NP_248188.1|  99 GHCVLCQKCIDVCP 112
                                   58***********9 PP

  == domain 5  score: 17.7 bits;  conditional E-value: 2.1e-06
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   + ++td+C+gCg+Cv  CP
  gi|15669380|ref|NP_248188.1| 135 PIAVTDACVGCGICVPECP 153
                                   6789*************** PP

  == domain 6  score: 16.0 bits;  conditional E-value: 7.3e-06
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   +v+d  +Ci C++C + CP
  gi|15669380|ref|NP_248188.1| 164 AVIDKSKCIYCSICAQTCP 182
                                   689**************** PP

  == domain 7  score: 19.0 bits;  conditional E-value: 8.4e-07
                        Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                   +++v++++Ci C +Cv +CP
  gi|15669380|ref|NP_248188.1| 202 KFEVNAEKCIYCLKCVEVCP 221
                                   5789***************9 PP

  == domain 8  score: 12.1 bits;  conditional E-value: 0.00013
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   +v+ + +C +C+ Cv+ CP
  gi|15669380|ref|NP_248188.1| 233 IVIPPKSCPACKLCVNICP 251
                                   688999************* PP

  == domain 9  score: 4.1 bits;  conditional E-value: 0.043
                        Fer4_2  15 aCvsaCPa 22 
                                   +C s+CP+
  gi|15669380|ref|NP_248188.1| 284 KCASVCPT 291
                                   7******7 PP

  == domain 10  score: 18.1 bits;  conditional E-value: 1.5e-06
                        Fer4_2   3 vvvdtd.....rCigCgaCvsaCPa 22 
                                   +vvd++     +Ci CgaC+ aCP+
  gi|15669380|ref|NP_248188.1| 294 IVVDEEkkevrMCIVCGACTVACPT 318
                                   56666666666*************7 PP

  == domain 11  score: 16.1 bits;  conditional E-value: 6.7e-06
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   +++ +  C  Cg+Cv +CP
  gi|15669380|ref|NP_248188.1| 336 IEFSPYLCDKCGKCVEVCP 354
                                   5677889************ PP

  == domain 12  score: 1.1 bits;  conditional E-value: 0.4
                        Fer4_2  10 CigCgaCvsa 19 
                                   C+ C  C+s+
  gi|15669380|ref|NP_248188.1| 371 CVMCLLCLSV 380
                                   9******986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   2.7   0.00078      0.99      49      64 ..      11      26 ..       6      27 .. 0.83
   2 !   15.9  14.0     1e-05     0.013       2      65 .]      33      87 ..      32      87 .. 0.78
   3 !   12.6   0.7   0.00011      0.14      49      65 .]      99     115 ..      88     115 .. 0.85
   4 !   14.1   1.0   3.9e-05      0.05       3      21 ..     140     158 ..     138     165 .. 0.80
   5 !   23.0   7.8   6.5e-08   8.4e-05       3      62 ..     169     221 ..     167     224 .. 0.70
   6 !    9.5  19.8     0.001       1.3       4      64 ..     239     319 ..     238     320 .. 0.64
   7 !   25.2   9.9   1.3e-08   1.6e-05       2      64 ..     303     356 ..     302     357 .. 0.75
   8 ?   -0.3   0.6       1.2   1.5e+03       4      12 ..     370     378 ..     368     382 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00078
                        Fer4_8 49 wsCttcgaCtevCpvg 64
                                  ++C+ c aC+ +Cp++
  gi|15669380|ref|NP_248188.1| 11 DACLVCYACQAECPTK 26
                                  6799999999999986 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1e-05
                        Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                  ++ C+ C+ C + Cp+     +++  + ++  +  ++  +       ++C  cg+C+e+Cp+gi
  gi|15669380|ref|NP_248188.1| 33 FKVCNLCMECVKVCPTGALVEEEIEVNGKK-LK-RVNYLA-------HKCEKCGQCAEACPIGI 87
                                  567************999987665555444.44.445444.......9*************997 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00011
                        Fer4_8  49 wsCttcgaCtevCpvgi 65 
                                   ++C+ c++C +vCp++i
  gi|15669380|ref|NP_248188.1|  99 GHCVLCQKCIDVCPIEI 115
                                   68***********9986 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 3.9e-05
                        Fer4_8   3 ekCieCgaCqsaCpvlrrt 21 
                                   ++C++Cg C  +Cpv   t
  gi|15669380|ref|NP_248188.1| 140 DACVGCGICVPECPVNAIT 158
                                   68***********986555 PP

  == domain 5  score: 23.0 bits;  conditional E-value: 6.5e-08
                        Fer4_8   3 ekCieCgaCqsaCp..vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62 
                                   +kCi C+ C ++Cp  ++       + ++++++e v + +v     ++++C  c +C+evCp
  gi|15669380|ref|NP_248188.1| 169 SKCIYCSICAQTCPwnAIFVA---GKIPKKRRKE-VKKFEV-----NAEKCIYCLKCVEVCP 221
                                   79***********93333334...4444555555.333444.....3799************ PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.001
                        Fer4_8   4 kCieCgaCqsaCp......vlrrtkkhlldargeaae.......dvqeeqvlee...............eealwsCttcga 56 
                                   +C  C +C + Cp       ++ +  h+ + +g ++        +        +               ++ +  C  cga
  gi|15669380|ref|NP_248188.1| 239 SCPACKLCVNICPvdaldlEVKLSSPHPITDEGLVIVeedfevlK--------KcasvcpteaivvdeeKKEVRMCIVCGA 311
                                   799**********55444433333344444444443344443330........2555666666666667899********* PP

                        Fer4_8  57 CtevCpvg 64 
                                   Ct++Cp+g
  gi|15669380|ref|NP_248188.1| 312 CTVACPTG 319
                                   ******87 PP

  == domain 7  score: 25.2 bits;  conditional E-value: 1.3e-08
                        Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   ++ Ci CgaC+ aCp+   +   + ++ +e +     e         + C  cg+C+evCp++
  gi|15669380|ref|NP_248188.1| 303 VRMCIVCGACTVACPTGALKLGKIEHNGKEYNR---IEFS------PYLCDKCGKCVEVCPMK 356
                                   789************999888444444444333...3333......68*************87 PP

  == domain 8  score: -0.3 bits;  conditional E-value: 1.2
                        Fer4_8   4 kCieCgaCq 12 
                                   +C+ C +C 
  gi|15669380|ref|NP_248188.1| 370 YCVMCLLCL 378
                                   466666664 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   4.0     0.039        50      44      58 ..      11      25 ..       4      28 .. 0.80
   2 !    8.7   3.0     0.002       2.5      43      59 ..      33      49 ..      25      50 .. 0.82
   3 !   11.3  14.3   0.00031      0.39       2      60 ..      36      87 ..      35      88 .. 0.76
   4 !    9.9   0.2   0.00081         1      45      59 ..     100     114 ..      90     131 .. 0.78
   5 !   17.8   0.4   2.8e-06    0.0036       1      26 [.     141     166 ..     141     170 .. 0.87
   6 !   17.1  10.4   4.6e-06    0.0059       1      59 [.     170     223 ..     170     225 .. 0.73
   7 !    7.2   0.5    0.0057       7.3      45      58 ..     239     252 ..     229     261 .. 0.83
   8 ?    0.6   0.3      0.68   8.8e+02      50      58 ..     283     291 ..     281     294 .. 0.80
   9 !   11.6   2.2   0.00025      0.32      39      59 ..     299     319 ..     293     323 .. 0.84
  10 !   11.3  12.5   0.00031       0.4       2      59 ..     306     356 ..     305     357 .. 0.85
  11 ?    0.9   0.2      0.54   6.9e+02       5      20 ..     371     385 ..     369     392 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.039
                       Fer4_17 44 slCieCgeCerkCPq 58
                                  + C+ C  C+++CP 
  gi|15669380|ref|NP_248188.1| 11 DACLVCYACQAECPT 25
                                  578888888888886 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.002
                       Fer4_17 43 aslCieCgeCerkCPqg 59
                                  ++ C+ C eC+++CP g
  gi|15669380|ref|NP_248188.1| 33 FKVCNLCMECVKVCPTG 49
                                  6779**********975 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00031
                       Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60
                                  C+ C  C+++Cp+++  ++e + +  +    +l++   +  a++C +Cg+C+++CP g+
  gi|15669380|ref|NP_248188.1| 36 CNLCMECVKVCPTGALVEEEIE-VNGK----KLKR--VNYLAHKCEKCGQCAEACPIGI 87
                                  **************99887333.2222....2222..2568***************876 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00081
                       Fer4_17  45 lCieCgeCerkCPqg 59 
                                    C+ C++C  +CP +
  gi|15669380|ref|NP_248188.1| 100 HCVLCQKCIDVCPIE 114
                                   577777777777644 PP

  == domain 5  score: 17.8 bits;  conditional E-value: 2.8e-06
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkll 26 
                                   +C +Cg C+peCp ++++ +++k ++
  gi|15669380|ref|NP_248188.1| 141 ACVGCGICVPECPVNAITLENNKAVI 166
                                   5****************999888776 PP

  == domain 6  score: 17.1 bits;  conditional E-value: 4.6e-06
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaek.eekaslCieCgeCerkCPqg 59 
                                   +Ci C+ C++ Cp +++          ++  ++ +e++k e +a++Ci C +C+++CP +
  gi|15669380|ref|NP_248188.1| 170 KCIYCSICAQTCPWNAIFVA------GKIPKKRRKEVKKfEVNAEKCIYCLKCVEVCPGD 223
                                   6************9999543......33333333334331349***************87 PP

  == domain 7  score: 7.2 bits;  conditional E-value: 0.0057
                       Fer4_17  45 lCieCgeCerkCPq 58 
                                   +C  C++C+  CP 
  gi|15669380|ref|NP_248188.1| 239 SCPACKLCVNICPV 252
                                   78888888888885 PP

  == domain 8  score: 0.6 bits;  conditional E-value: 0.68
                       Fer4_17  50 geCerkCPq 58 
                                   ++C+++CP 
  gi|15669380|ref|NP_248188.1| 283 KKCASVCPT 291
                                   689999996 PP

  == domain 9  score: 11.6 bits;  conditional E-value: 0.00025
                       Fer4_17  39 keekaslCieCgeCerkCPqg 59 
                                   +++++  Ci Cg C+ +CP g
  gi|15669380|ref|NP_248188.1| 299 EKKEVRMCIVCGACTVACPTG 319
                                   4578899***********976 PP

  == domain 10  score: 11.3 bits;  conditional E-value: 0.00031
                       Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                   Ci Cg+C+ +Cp+++           +++ + +e+   e    lC +Cg+C+++CP++
  gi|15669380|ref|NP_248188.1| 306 CIVCGACTVACPTGALKLG-------KIEHNGKEYNRIEFSPYLCDKCGKCVEVCPMK 356
                                   **************99776.......5555667777778899**************95 PP

  == domain 11  score: 0.9 bits;  conditional E-value: 0.54
                       Fer4_17   5 CgyClpeCpsyeaydn 20 
                                   C +Cl  C s ++ ++
  gi|15669380|ref|NP_248188.1| 371 CVMCLL-CLSVAEKEK 385
                                   445554.555544444 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   5.8      0.13   1.7e+02       4      15 .]      16      27 ..      13      27 .. 0.88
   2 !   16.3   6.0   1.1e-05     0.014       1      15 []      36      50 ..      36      50 .. 0.98
   3 !   11.8   4.4   0.00029      0.37       1      14 [.      73      86 ..      73      87 .. 0.92
   4 !   10.4   3.4    0.0008         1       1      12 [.     101     112 ..     101     115 .. 0.93
   5 !    9.2   7.4     0.002       2.6       1      15 []     142     156 ..     142     156 .. 0.98
   6 !    9.7   3.1    0.0014       1.8       1      15 []     171     185 ..     171     185 .. 0.97
   7 !   10.1   4.2     0.001       1.3       1      13 [.     210     222 ..     210     223 .. 0.92
   8 !    7.9   4.7    0.0051       6.5       4      15 .]     243     254 ..     238     254 .. 0.92
   9 ?    4.6   0.4     0.059        75       6      15 .]     284     293 ..     280     293 .. 0.87
  10 !    9.7   7.3    0.0014       1.8       1      15 []     306     320 ..     306     320 .. 0.92
  11 !   13.8   5.5     7e-05      0.09       1      12 [.     343     354 ..     343     356 .. 0.93
  12 ?    1.0   3.3      0.83   1.1e+03       1      10 [.     371     380 ..     371     380 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.13
                        Fer4_3  4 CgaCvevCPvgA 15
                                  C+aC   CP++A
  gi|15669380|ref|NP_248188.1| 16 CYACQAECPTKA 27
                                  **********98 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.1e-05
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ C+ Cv+vCP+gA
  gi|15669380|ref|NP_248188.1| 36 CNLCMECVKVCPTGA 50
                                  **************9 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00029
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C  Cg+C e+CP g
  gi|15669380|ref|NP_248188.1| 73 CEKCGQCAEACPIG 86
                                  999*********88 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0008
                        Fer4_3   1 CtgCgaCvevCP 12 
                                   C+ C+ C +vCP
  gi|15669380|ref|NP_248188.1| 101 CVLCQKCIDVCP 112
                                   ************ PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.002
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+gCg Cv  CPv+A
  gi|15669380|ref|NP_248188.1| 142 CVGCGICVPECPVNA 156
                                   *************99 PP

  == domain 6  score: 9.7 bits;  conditional E-value: 0.0014
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ C+ C + CP++A
  gi|15669380|ref|NP_248188.1| 171 CIYCSICAQTCPWNA 185
                                   9************98 PP

  == domain 7  score: 10.1 bits;  conditional E-value: 0.001
                        Fer4_3   1 CtgCgaCvevCPv 13 
                                   C+ C  CvevCP 
  gi|15669380|ref|NP_248188.1| 210 CIYCLKCVEVCPG 222
                                   999*99******7 PP

  == domain 8  score: 7.9 bits;  conditional E-value: 0.0051
                        Fer4_3   4 CgaCvevCPvgA 15 
                                   C +Cv+ CPv+A
  gi|15669380|ref|NP_248188.1| 243 CKLCVNICPVDA 254
                                   899*******98 PP

  == domain 9  score: 4.6 bits;  conditional E-value: 0.059
                        Fer4_3   6 aCvevCPvgA 15 
                                    C  vCP+ A
  gi|15669380|ref|NP_248188.1| 284 KCASVCPTEA 293
                                   5******876 PP

  == domain 10  score: 9.7 bits;  conditional E-value: 0.0014
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ CgaC ++CP+gA
  gi|15669380|ref|NP_248188.1| 306 CIVCGACTVACPTGA 320
                                   777***********9 PP

  == domain 11  score: 13.8 bits;  conditional E-value: 7e-05
                        Fer4_3   1 CtgCgaCvevCP 12 
                                   C+ Cg CvevCP
  gi|15669380|ref|NP_248188.1| 343 CDKCGKCVEVCP 354
                                   ************ PP

  == domain 12  score: 1.0 bits;  conditional E-value: 0.83
                        Fer4_3   1 CtgCgaCvev 10 
                                   C++C +C+ v
  gi|15669380|ref|NP_248188.1| 371 CVMCLLCLSV 380
                                   ****99*876 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.0     0.019        24       1      16 [.      10      25 ..      10      26 .. 0.91
   2 !   13.1   3.1   8.2e-05       0.1       3      17 .]      35      49 ..      33      49 .. 0.90
   3 !   10.2   2.1   0.00072      0.93       2      15 ..      71      84 ..      70      94 .. 0.88
   4 !   12.2   1.1   0.00016      0.21       4      15 ..     101     112 ..      96     124 .. 0.92
   5 !   12.5   3.8   0.00013      0.17       2      17 .]     140     155 ..     139     155 .. 0.91
   6 ?    2.2   1.5      0.25   3.2e+02       2      15 ..     169     182 ..     168     196 .. 0.90
   7 !    8.2   1.9     0.003       3.8       2      15 ..     208     221 ..     207     228 .. 0.92
   8 !   11.5   2.7   0.00027      0.35       2      16 ..     238     252 ..     237     255 .. 0.88
   9 ?    4.0   0.7      0.07        90       8      16 ..     283     291 ..     283     292 .. 0.87
  10 !   11.0   3.3   0.00038      0.48       4      17 .]     306     319 ..     300     319 .. 0.91
  11 !   12.1   2.2   0.00018      0.23       4      16 ..     343     355 ..     334     356 .. 0.90
  12 ?   -2.3   0.6       7.2   9.2e+03       4      10 ..     371     377 ..     368     380 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.019
                        Fer4_4  1 qerCigCgsCvaaCPq 16
                                  ++ C+ C +C a CP+
  gi|15669380|ref|NP_248188.1| 10 KDACLVCYACQAECPT 25
                                  689************8 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.2e-05
                        Fer4_4  3 rCigCgsCvaaCPqg 17
                                   C+ C+ Cv +CP+g
  gi|15669380|ref|NP_248188.1| 35 VCNLCMECVKVCPTG 49
                                  6************86 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00072
                        Fer4_4  2 erCigCgsCvaaCP 15
                                   +C  Cg+C  aCP
  gi|15669380|ref|NP_248188.1| 71 HKCEKCGQCAEACP 84
                                  5899*********9 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00016
                        Fer4_4   4 CigCgsCvaaCP 15 
                                   C+ C +C+++CP
  gi|15669380|ref|NP_248188.1| 101 CVLCQKCIDVCP 112
                                   ***********9 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 0.00013
                        Fer4_4   2 erCigCgsCvaaCPqg 17 
                                   + C+gCg Cv  CP++
  gi|15669380|ref|NP_248188.1| 140 DACVGCGICVPECPVN 155
                                   89************75 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.25
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   ++Ci C  C  +CP
  gi|15669380|ref|NP_248188.1| 169 SKCIYCSICAQTCP 182
                                   79***********9 PP

  == domain 7  score: 8.2 bits;  conditional E-value: 0.003
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   e+Ci C +Cv +CP
  gi|15669380|ref|NP_248188.1| 208 EKCIYCLKCVEVCP 221
                                   89***********9 PP

  == domain 8  score: 11.5 bits;  conditional E-value: 0.00027
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   ++C  C+ Cv++CP+
  gi|15669380|ref|NP_248188.1| 238 KSCPACKLCVNICPV 252
                                   67889*********7 PP

  == domain 9  score: 4.0 bits;  conditional E-value: 0.07
                        Fer4_4   8 gsCvaaCPq 16 
                                   ++C ++CP+
  gi|15669380|ref|NP_248188.1| 283 KKCASVCPT 291
                                   68******8 PP

  == domain 10  score: 11.0 bits;  conditional E-value: 0.00038
                        Fer4_4   4 CigCgsCvaaCPqg 17 
                                   Ci Cg+C+ aCP+g
  gi|15669380|ref|NP_248188.1| 306 CIVCGACTVACPTG 319
                                   999*********86 PP

  == domain 11  score: 12.1 bits;  conditional E-value: 0.00018
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   C  Cg+Cv +CP+
  gi|15669380|ref|NP_248188.1| 343 CDKCGKCVEVCPM 355
                                   999*********7 PP

  == domain 12  score: -2.3 bits;  conditional E-value: 7.2
                        Fer4_4   4 CigCgsC 10 
                                   C+ C  C
  gi|15669380|ref|NP_248188.1| 371 CVMCLLC 377
                                   8888666 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3  12.7      0.31   3.9e+02      58      95 ..      10      46 ..       4      48 .. 0.80
   2 ?    3.3  11.4     0.072        93      60      95 ..      35      83 ..      31      83 .. 0.60
   3 !   10.9  11.6   0.00032      0.41      54      95 ..      66     111 ..      52     112 .. 0.72
   4 !   12.6   3.2   9.5e-05      0.12      53      75 ..      93     115 ..      87     122 .. 0.82
   5 ?    2.8  12.7       0.1   1.3e+02      57      95 ..     138     181 ..     120     182 .. 0.73
   6 !    7.0   1.8    0.0052       6.6      51      73 ..     161     183 ..     155     191 .. 0.80
   7 !   12.2   2.2   0.00013      0.16      50      74 ..     199     223 ..     186     235 .. 0.72
   8 !    6.6   3.6    0.0069       8.9      59      74 ..     238     253 ..     226     261 .. 0.84
   9 !    7.9   6.3    0.0026       3.3      65     100 ..     283     321 ..     273     339 .. 0.75
  10 !   13.4   2.7   5.1e-05     0.065      61      95 ..     343     381 ..     323     390 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.31
                       Fer4_18 58 agdcidcescvkvcPtg.idirkGlqleciscllcidac 95
                                  +  c+ c +c + cPt+ idi   ++  c  c++c+  c
  gi|15669380|ref|NP_248188.1| 10 KDACLVCYACQAECPTKaIDID-SFK-VCNLCMECVKVC 46
                                  5679***********9648885.555.499999999999 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.072
                       Fer4_18 60 dcidcescvkvcPtgidir.....kG........lqleciscllcidac 95
                                   c  c  cvkvcPtg  +      +G        l  +c +c++c +ac
  gi|15669380|ref|NP_248188.1| 35 VCNLCMECVKVCPTGALVEeeievNGkklkrvnyLAHKCEKCGQCAEAC 83
                                  5999**********96544111122311111111445788899999998 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00032
                       Fer4_18  54 kekgagdcidcescvkvcPtgid.irkGlql...eciscllcidac 95 
                                    +  a +c +c++c + cP+gi  + + + +   +c+ c++cid c
  gi|15669380|ref|NP_248188.1|  66 VNYLAHKCEKCGQCAEACPIGIKkVDDDFPYskgHCVLCQKCIDVC 111
                                   3445678***************6356666543337**********9 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 9.5e-05
                       Fer4_18  53 rkekgagdcidcescvkvcPtgi 75 
                                       ++g+c+ c++c++vcP++i
  gi|15669380|ref|NP_248188.1|  93 DFPYSKGHCVLCQKCIDVCPIEI 115
                                   5566899*************987 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.1
                       Fer4_18  57 gagdcidcescvkvcPtg.idirkGl....qleciscllcidac 95 
                                    +  c+ c+ cv  cP++ i + +      + +ci c+ c  +c
  gi|15669380|ref|NP_248188.1| 138 VTDACVGCGICVPECPVNaITLENNKavidKSKCIYCSICAQTC 181
                                   4567************86366655441133569********999 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.0052
                       Fer4_18  51 eerkekgagdcidcescvkvcPt 73 
                                   ++++  ++++ci c+ c + cP 
  gi|15669380|ref|NP_248188.1| 161 NNKAVIDKSKCIYCSICAQTCPW 183
                                   4555667899************6 PP

  == domain 7  score: 12.2 bits;  conditional E-value: 0.00013
                       Fer4_18  50 keerkekgagdcidcescvkvcPtg 74 
                                   + ++ e +a +ci c +cv+vcP +
  gi|15669380|ref|NP_248188.1| 199 EVKKFEVNAEKCIYCLKCVEVCPGD 223
                                   22334556778************65 PP

  == domain 8  score: 6.6 bits;  conditional E-value: 0.0069
                       Fer4_18  59 gdcidcescvkvcPtg 74 
                                     c +c+ cv++cP++
  gi|15669380|ref|NP_248188.1| 238 KSCPACKLCVNICPVD 253
                                   5799**********85 PP

  == domain 9  score: 7.9 bits;  conditional E-value: 0.0026
                       Fer4_18  65 escvkvcPtg...idirkGlqleciscllcidacdkvme 100
                                   ++c +vcPt+   +d  k     ci c+ c  ac +   
  gi|15669380|ref|NP_248188.1| 283 KKCASVCPTEaivVDEEKKEVRMCIVCGACTVACPTGAL 321
                                   789999999733355556666679999999999976554 PP

  == domain 10  score: 13.4 bits;  conditional E-value: 5.1e-05
                       Fer4_18  61 cidcescvkvcPtg.idirkG...lqleciscllcidac 95 
                                   c +c++cv+vcP++ + +  G   l+  c+ cllc+   
  gi|15669380|ref|NP_248188.1| 343 CDKCGKCVEVCPMKtLRLSRGklpLKGYCVMCLLCLSVA 381
                                   99**********9735665664335567*******8765 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.1     0.009        12       1      20 [.       6      25 ..       6      33 .. 0.87
   2 ?    0.6   2.7      0.74   9.5e+02       8      20 ..      36      48 ..      28      62 .. 0.81
   3 ?    8.7   3.4    0.0022       2.8       7      31 ..      72      96 ..      70     101 .. 0.88
   4 ?   -0.2   2.2       1.4   1.8e+03       8      19 ..     101     112 ..      96     124 .. 0.80
   5 ?    9.9   1.0   0.00093       1.2       6      19 ..     140     153 ..     139     163 .. 0.88
   6 ?    7.4  10.1    0.0057       7.3       2      66 .]     165     227 ..     164     227 .. 0.80
   7 ?    8.7   5.1    0.0022       2.8       5      66 .]     237     296 ..     233     296 .. 0.69
   8 ?    5.2   0.7     0.028        36       8      20 ..     306     318 ..     302     331 .. 0.90
   9 ?    6.6   0.2     0.011        14       7      20 ..     342     355 ..     336     366 .. 0.80
  10 ?    0.6   0.1      0.77   9.9e+02       8      30 ..     371     389 ..     368     394 .] 0.70

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.009
                       Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                  +++ +daC  c +C ae+p+
  gi|15669380|ref|NP_248188.1|  6 ITIQKDACLVCYACQAECPT 25
                                  7899**************84 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.74
                       Fer4_15  8 CigcglCvaeape 20
                                  C  c  Cv+++p+
  gi|15669380|ref|NP_248188.1| 36 CNLCMECVKVCPT 48
                                  9999999999985 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0022
                       Fer4_15  7 aCigcglCvaeapevfeldedglas 31
                                  +C+ cg+C++++p  +++ +d++++
  gi|15669380|ref|NP_248188.1| 72 KCEKCGQCAEACPIGIKKVDDDFPY 96
                                  7************999999999875 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.4
                       Fer4_15   8 CigcglCvaeap 19 
                                   C  c  C++++p
  gi|15669380|ref|NP_248188.1| 101 CVLCQKCIDVCP 112
                                   888888888886 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.00093
                       Fer4_15   6 daCigcglCvaeap 19 
                                   daC gcg Cv e+p
  gi|15669380|ref|NP_248188.1| 140 DACVGCGICVPECP 153
                                   89***********8 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.0057
                       Fer4_15   2 vvDrdaCigcglCvaea..pevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66 
                                   v+D+++Ci c  C++ +    +f+  +  ++     ++e+++ ev+ ++     + +++CP+d I v
  gi|15669380|ref|NP_248188.1| 165 VIDKSKCIYCSICAQTCpwNAIFVAGKIPKK----RRKEVKKFEVNAEKCIYCLKCVEVCPGDMIKV 227
                                   69***************44456666655554....3456677799999999999*********9987 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.0022
                       Fer4_15   5 rdaCigcglCvaeapevfelded.glasvl.lddgeiaeg..evpddeeeaaqeAaraCPvdAIrv 66 
                                    + C  c lCv  +p v  ld +  l+s + +      ++   + +++ e  ++ a++CP++AI+v
  gi|15669380|ref|NP_248188.1| 237 PKSCPACKLCVNICP-VDALDLEvKLSSPHpI-----TDEglVIVEEDFEVLKKCASVCPTEAIVV 296
                                   67899*********9.5555533133333332.....333366777888899************97 PP

  == domain 8  score: 5.2 bits;  conditional E-value: 0.028
                       Fer4_15   8 CigcglCvaeape 20 
                                   Ci cg+C  ++p+
  gi|15669380|ref|NP_248188.1| 306 CIVCGACTVACPT 318
                                   ***********96 PP

  == domain 9  score: 6.6 bits;  conditional E-value: 0.011
                       Fer4_15   7 aCigcglCvaeape 20 
                                   +C+ cg Cv+++p 
  gi|15669380|ref|NP_248188.1| 342 LCDKCGKCVEVCPM 355
                                   7***********95 PP

  == domain 10  score: 0.6 bits;  conditional E-value: 0.77
                       Fer4_15   8 CigcglCvaeapevfeldedgla 30 
                                   C +c lC+ +a    e++++g++
  gi|15669380|ref|NP_248188.1| 371 CVMCLLCLSVA----EKEKKGKK 389
                                   88888888876....45566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2624.60
//
Query:       gi|15669381|ref|NP_248190.1|  [L=518]
Description: 2-isopropylmalate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-97  326.6   0.6    1.3e-97  326.6   0.6    2.2  2  HMGL-like     HMGL-like
    2.4e-37  127.8   6.1      5e-37  126.8   6.1    1.6  1  LeuA_dimer    LeuA allosteric (dimerisation) domain
     0.0031   17.9   2.7        3.5    8.0   0.1    3.4  3  Radical_SAM   Radical SAM superfamily
     0.0062   16.0   0.1      0.031   13.7   0.0    2.1  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.065   13.1   0.0       0.17   11.7   0.0    1.6  1  EspA          EspA-like secreted protein
       0.27   11.4   5.3       0.13   12.5   0.8    2.8  3  Imm74         Immunity protein 74


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.6   0.6  4.2e-101   1.3e-97       1     264 []      23     281 ..      23     281 .. 0.98
   2 ?   -0.9   0.5      0.33   9.9e+02      78      78 ..     404     404 ..     340     490 .. 0.56

  Alignments for each domain:
  == domain 1  score: 326.6 bits;  conditional E-value: 4.2e-101
                                   B-EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHH CS
                     HMGL-like   1 kvkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaa 81 
                                   +v+i+dttLRDGeq+++++l+ eek+ ia +Ld++gvd+iE+gfp++s ++ e++++i++   +a+i++l+ra++kdi++a
  gi|15669381|ref|NP_248190.1|  23 RVYIFDTTLRDGEQTPGVSLTPEEKIDIAIKLDDLGVDVIEAGFPVSSLGEQEAIKKICSLNLDAEICGLARAVKKDIDVA 103
                                   599****************************************************************************** PP

                                   HH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-SE CS
                     HMGL-like  82 vealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGatr 162
                                   ++    +g++r+h+fiats lh+k+klkk++ee++++a++a+++++++g++ve+s+eda+rt++++l+ev+++a++aGa++
  gi|15669381|ref|NP_248190.1| 104 ID----CGVDRIHTFIATSPLHRKYKLKKSKEEIIDIAVDAIEYIKEHGIRVEFSAEDATRTEIDYLIEVYKKAVDAGADI 180
                                   **....*************************************************************************** PP

                                   EEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHHHH CS
                     HMGL-like 163 iniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelvaal 243
                                   in++DtvGv+ P++++ li++lk+++k  v++svHcHnd+GlAvan+laAveaGa++v +t+nGlGer Gnaalee+v+ l
  gi|15669381|ref|NP_248190.1| 181 INVPDTVGVMIPRAMYYLINELKKEIK--VPISVHCHNDFGLAVANSLAAVEAGAEQVHCTINGLGERGGNAALEEVVMSL 259
                                   ***************************..**************************************************86 PP

                                   .HHTT-B----HHHHHHHHHHH CS
                     HMGL-like 244 .ealgvdtgldlqklrsiaalv 264
                                       gv+t++++qkl++i++lv
  gi|15669381|ref|NP_248190.1| 260 mSIYGVKTNIKTQKLYEISQLV 281
                                   15667***************98 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.33
                                   H CS
                     HMGL-like  78 i 78 
                                   +
  gi|15669381|ref|NP_248190.1| 404 V 404
                                   1 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.8   6.1   1.7e-40     5e-37       2     133 .]     381     513 ..     380     513 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 1.7e-40
                                   XXXXXXXXXXXXXXXX...XX--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHHT-EEE CS
                    LeuA_dimer   2 vtdedlealvkdelle...aeerlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgvdikLl 79 
                                   vtd d+ea+v+d++++   + + ++le+++v++g++  +ta+v+l++ ++e+k++sa+G+GpvdA+++A++ka+g++ikL+
  gi|15669381|ref|NP_248190.1| 381 VTDRDVEAIVEDVVGKlakKDRVVELEQIAVMTGNRVIPTASVALKI-EEEIKKSSAIGVGPVDAAVKAIQKAIGEKIKLK 460
                                   9**************99845599************************.9******************************** PP

                                   EEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHHS CS
                    LeuA_dimer  80 dYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrll 133
                                   +Y+++ait+gtda+aev V+le   g+++++ ++++div+AS++A+i+++n++l
  gi|15669381|ref|NP_248190.1| 461 EYHINAITGGTDALAEVIVTLE-GYGREITTKAASEDIVRASVEAVIDGINKIL 513
                                   **********************.66777***********************986 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1    0.0012       3.5      25     115 ..      38     161 ..       7     192 .. 0.64
   2 !    7.6   0.0    0.0015       4.6      99     148 ..     338     384 ..     230     391 .. 0.84
   3 ?    0.7   0.1       0.2   6.1e+02      91     138 ..     428     475 ..     392     515 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0012
                                   HHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.......................CCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................xxxxxxxx RF
                   Radical_SAM  25 rgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.......................vpgiritv 82 
                                   +g sl++ee ++++ +l  + gv+++    g p     ++e++++++ l                        v+ i++++
  gi|15669381|ref|NP_248190.1|  38 PGVSLTPEEKIDIAIKL-DDLGVDVIEA--GFPVSSLGEQEAIKKICSLNldaeicglaravkkdidvaidcgVDRIHTFI 115
                                   56677777777777777.5665555555..445555567788888888865555555555555556666666666666666 PP

                                   EECSSCHG..............HHHHHHHHHTT-SEEEEEEBSSSHH CS
                                   xxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpd..............eeklerllelgvdrvslgleaadde 115
                                    t++++                 + +e ++e g  rv++++e a+  
  gi|15669381|ref|NP_248190.1| 116 ATSPLHRKyklkkskeeiidiaVDAIEYIKEHG-IRVEFSAEDATRT 161
                                   666666446666666555555555555555555.6666666655554 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0015
                                   HTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  99 elgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdr 148
                                     g+  ++  l+ +  e v k +  ++ f+e+++ +++l ++g + v+dr
  gi|15669381|ref|NP_248190.1| 338 HTGTHAIEAKLKELGIE-VGKDI-NKDQFDEIVKRIKALGDKGKR-VTDR 384
                                   45566677777777778.99***.78****************988.8875 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.2
                                   HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                   Radical_SAM  91 eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklr 138
                                   ee +++    gv  v   ++a+ +  + ++++ + + + ++  ++++l+
  gi|15669381|ref|NP_248190.1| 428 EEEIKKSSAIGVGPVDAAVKAIQKA-IGEKIKlKEYHINAITGGTDALA 475
                                   5555555555555555555555555.55555544444444433333333 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0     1e-05     0.031      25     126 ..      42     150 ..      29     190 .. 0.73
   2 ?   -1.5   0.0      0.47   1.4e+03     103     122 ..     361     380 ..     338     399 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                                   CHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC...........HTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCC. CS
                  AP_endonuc_2  25 lsdeelrelrkaldelglriaslslftrfgypded...........erearreesvdalkraielaaaLGapllvlhpGt. 93 
                                   l++ee  +++  ld+lg+ +    ++  + +  e            e +       +a+k+ i+ a ++G++ +++++ t 
  gi|15669381|ref|NP_248190.1|  42 LTPEEKIDIAIKLDDLGVDVIEAGFPVSSLGEQEAikkicslnldaEICGL----ARAVKKDIDVAIDCGVDRIHTFIATs 118
                                   466677777778888888866666666666655557777777555544444....789*********************98 PP

                                   ...GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSE CS
                  AP_endonuc_2  94 ...agagpkgseeeawerlaeslneladyaekegvk 126
                                      + +  k+s+ee ++ ++++++ + +++     +
  gi|15669381|ref|NP_248190.1| 119 plhRKYKLKKSKEEIIDIAVDAIEYIKEHGI----R 150
                                   8887777888888888888888887777743....2 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.47
                                   HHHHHHHHHHHHHHHHHHHH CS
                  AP_endonuc_2 103 eeawerlaeslneladyaek 122
                                   +++++ +++++++l+d++++
  gi|15669381|ref|NP_248190.1| 361 KDQFDEIVKRIKALGDKGKR 380
                                   47788888888888888765 PP

>> EspA  EspA-like secreted protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.6e-05      0.17      85     163 ..     131     285 ..     124     301 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
                          EspA  85 kskeelppdVieYlrengIlv.......enktiddylkkngq.vGegkldkgd............................ 129
                                   ++  +++ d ieY++e+gI v         ++id +++ + + v  g                                  
  gi|15669381|ref|NP_248190.1| 131 EEIIDIAVDAIEYIKEHGIRVefsaedaTRTEIDYLIEVYKKaVDAG-----Adiinvpdtvgvmipramyylinelkkei 206
                                   445577889************88887655667777777777644444.....23445777999999999999999999999 PP

                          EspA 130 .............................................LtavkasLesdsgrasDfvqQsQlklqkliqnyn 163
                                                                                L++v  sL s  g ++ + +Q+  ++ +l+ +y 
  gi|15669381|ref|NP_248190.1| 207 kvpisvhchndfglavanslaaveagaeqvhctinglgerggnaaLEEVVMSLMSIYGVKTNIKTQKLYEISQLVSKYT 285
                                   9999999999999999999999999999999999999999999999999999999999999999999999999998885 PP

>> Imm74  Immunity protein 74
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2       1.2   3.5e+03      61      79 ..     136     153 ..     127     154 .. 0.73
   2 ?   -2.2   0.0       1.7     5e+03      53      68 ..     358     373 ..     347     381 .. 0.81
   3 ?   12.5   0.8   4.3e-05      0.13      50      80 .]     377     407 ..     357     407 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                         Imm74  61 eIveaiekeftkrgltvaf 79 
                                    +v+aie +++++g++v+f
  gi|15669381|ref|NP_248190.1| 136 IAVDAIE-YIKEHGIRVEF 153
                                   4567774.89999999998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                         Imm74  53 pitkeerqeIveaiek 68 
                                    i k+  +eIv+ i++
  gi|15669381|ref|NP_248190.1| 358 DINKDQFDEIVKRIKA 373
                                   5889999999999976 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 4.3e-05
                         Imm74  50 esepitkeerqeIveaiekeftkrgltvafe 80 
                                   + + +t+ ++++Ive+++++++k++ +v++e
  gi|15669381|ref|NP_248190.1| 377 KGKRVTDRDVEAIVEDVVGKLAKKDRVVELE 407
                                   56679*********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.25s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3446.49
//
Query:       gi|15669382|ref|NP_248191.1|  [L=366]
Description: asoB protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-23   82.3  58.5    5.4e-23   81.5  58.5    1.5  1  AA_permease_2  Amino acid permease
    2.6e-08   32.9  56.2    4.7e-07   28.8  56.2    2.3  1  AA_permease    Amino acid permease
  ------ inclusion threshold ------
        7.6    5.2   6.9        2.4    6.9   0.3    2.3  2  YqfD           Putative stage IV sporulation protein YqfD


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5  58.5   9.1e-27   5.4e-23       1     401 [.       4     362 ..       4     366 .] 0.77

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 9.1e-27
                 AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvafl 79 
                                   l+l +a++l+i+s++g gifv +   ++  g+ +i+w+w   + +sl+++  +a  s++++ sgG+y ++ ++ g+ ++ +
  gi|15669382|ref|NP_248191.1|   4 LTLKDAVFLTITSIVGGGIFVLSplTYLLFGK-SIIWGWALLIFVSLIMASPFAYASTKISESGGVYKFVMKILGREIGVF 83 
                                   567899***************99944444666.55566666666679999999999999********************** PP

                 AA_permease_2  80 sawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliili 160
                                   sa+++w++ v++l s+++++++   n    ++      +  ++ +++++++++++ g ++++++  i gil+i+++  + i
  gi|15669382|ref|NP_248191.1|  84 SAYILWLSGVFAL-SGVVSFFEIVFNT---KF-----NVSYVGLCLIVILTALILGGLRIVGNFVRIFGILTITII--LYI 153
                                   ***********98.8888888887774...33.....35667889999999999******************9633..333 PP

                 AA_permease_2 161 ilglitvdgggfsslstetdtffpngwpg.vllgllivlwsfdGfesaanvseevkk.kdvpkaifigllivlvlyllvni 239
                                        ++++g+          + ++++    +l+++  lw+ +G+e+++  ++  k+ k + +++ +g  i++vlyll+++
  gi|15669382|ref|NP_248191.1| 154 -----VFSNGIKI-------DSIGEFNLKnAILTIYFGLWTATGWEGITMPLSAFKNqKAIAYGLLVGTFIIGVLYLLFSL 222
                                   .....33444443.......223333333269999*********************999********************66 PP

                 AA_permease_2 240 aflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvnkfgs 320
                                   +++      + +nl+++   + ++           ++ +++ l++  ++++++++ s++ + +++d+++P+ f k +k  +
  gi|15669382|ref|NP_248191.1| 223 TIVSL--NVKTNNLDEI---LKILIGD----N--LFLLAGMLLIISSCAFSVLFTLSYMPYGMGKDRIFPKAFIKLRKE-I 291
                                   65554..5555666663...2333332....2..346667889999999*****************************9.* PP

                 AA_permease_2 321 piraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkrpgkilvaiigalfllfllva 401
                                   p++++il+ +++ i+ll+f      +  +l+++s+++ +i y+ll +++++     ++ k +   +  +i  l++lf +++
  gi|15669382|ref|NP_248191.1| 292 PYYGVILNTLLV-IILLIF------DAKTLVDMSMFSTLIAYFLLYLAVFKESSG-KI-KAI-SLISMLITGLLILFRVYN 362
                                   ***********9.655566......469*****************9777653333.22.111.223333334444444444 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8  56.2   7.8e-11   4.7e-07       2     412 ..       9     352 ..       8     366 .] 0.84

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 7.8e-11
                   AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlny 82 
                                   +++ ++ +++G g+fv +  +    G  +++ +++l ++v+++++  +++ +t++++sgg y+++ + lg+e G++ ++++
  gi|15669382|ref|NP_248191.1|   9 AVFLTITSIVGGGIFVLSPLTYLLFGK-SIIWGWALLIFVSLIMASPFAYASTKISESGGVYKFVMKILGREIGVFSAYIL 88 
                                   78999**********************.***************************************************** PP

                   AA_permease  83 lfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillag 163
                                   ++s++++l     +++++++++ ++t+ +   ++g+ ++v+l+++ l g++  g + + ++ i+ i+ii +i+++      
  gi|15669382|ref|NP_248191.1|  89 WLSGVFALS----GVVSFFEIV-FNTKFN-VSYVGLCLIVILTALILGGLRIVGNF-VRIFGILTITIILYIVFS------ 156
                                   *99998754....668888888.566666.9999*********************6.446678889999999999...... PP

                   AA_permease 164 gkpnkgagfrflgdngsifknnlppgfa.keeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviri 243
                                       +g                    ++ +++e+++kn i  + + + ++tG e +++  +  k+ +k+i  + l   ++i
  gi|15669382|ref|NP_248191.1| 157 ----NG----------I---------KIdSIGEFNLKNAILTIYFGLWTATGWEGITMPLSAFKN-QKAIAYGLLVGTFII 213
                                   ....33..........1.........111466789*******************99988888888.79************* PP

                   AA_permease 244 tifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdgla 324
                                   +++Y+l++l+i++l++ ++  +l ++++             +++ + ++ a+ l+ + s+a s l++ s + y + kd+++
  gi|15669382|ref|NP_248191.1| 214 GVLYLLFSLTIVSLNVKTN--NLDEILKI------------LIGDNLFLLAGMLLIISSCAFSVLFTLSYMPYGMGKDRIF 280
                                   *********9999998888..44445544............899999********************************** PP

                   AA_permease 325 PkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrsieelg 405
                                   Pk + k+ k   P+ +++l ++++ ++l+ ++ +         l+ +s++++li + l +l+        k+++ +i+ ++
  gi|15669382|ref|NP_248191.1| 281 PKAFIKLRK-EIPYYGVILNTLLVIILLIFDAKT---------LVDMSMFSTLIAYFLLYLAVF------KESSGKIKAIS 345
                                   ****99965.69*********9999888444443.........357888888877777776655......44455555555 PP

                   AA_permease 406 fkaallp 412
                                    ++ l+ 
  gi|15669382|ref|NP_248191.1| 346 LISMLIT 352
                                   4444444 PP

>> YqfD  Putative stage IV sporulation protein YqfD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.6     0.028   1.7e+02      64     113 ..      60     110 ..      57     116 .. 0.76
   2 ?    6.9   0.3   0.00039       2.4      82     114 ..     203     235 ..     187     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.028
                          YqfD  64 vkivekkGlpfllkrlkkrkglliga.llfllllyllSsfiwsievegnek 113
                                    ki e  G+++++ ++  r + ++ a +l l  ++ lS ++ + e+  n+k
  gi|15669382|ref|NP_248191.1|  60 TKISESGGVYKFVMKILGREIGVFSAyILWLSGVFALSGVVSFFEIVFNTK 110
                                   689999999988888777766555551667778999********9976665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00039
                          YqfD  82 rkglligallfllllyllSsfiwsievegnekv 114
                                    +gll+g +++ +l +l+S +i s +v++n+  
  gi|15669382|ref|NP_248191.1| 203 AYGLLVGTFIIGVLYLLFSLTIVSLNVKTNNLD 235
                                   4789999999*****************997643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2312.78
//
Query:       gi|15669383|ref|NP_248192.1|  [L=624]
Description: threonyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-54  181.9   0.1      1e-53  181.1   0.1    1.5  1  tRNA-Thr_ED     Archaea-specific editing domain of threonyl-t
    1.2e-24   86.3   3.3    2.3e-24   85.4   2.5    2.0  2  HGTP_anticodon  Anticodon binding domain
    3.2e-14   53.3   0.1    7.6e-14   52.1   0.1    1.7  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P


Domain annotation for each model (and alignments):
>> tRNA-Thr_ED  Archaea-specific editing domain of threonyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.1   0.1   1.7e-57     1e-53       1     137 []       5     140 ..       5     140 .. 0.99

  Alignments for each domain:
  == domain 1  score: 181.1 bits;  conditional E-value: 1.7e-57
                                   -EEEEEEEEEEEEEEEEESSSS-.SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEEEEE-ST CS
                   tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeaeeeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvvlypyaH 81 
                                   m++Llih+d+le+eak+k+ k aee+e+ +g+l+e+l +FiavE+eDe+++e ++  av+ei+kva+++k++++v+ypyaH
  gi|15669383|ref|NP_248192.1|   5 MKMLLIHSDYLEFEAKEKT-KIAEETENLKGKLDECLACFIAVEREDENNPEGTAIGAVEEIEKVANQLKVNNIVVYPYAH 84 
                                   9******************.************************************************************* PP

                                   S-SSB--HHHHHHHHHHHHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE- CS
                   tRNA-Thr_ED  82 LssslaspevakeilkkleeklkekglevkraPFGwykefeisckGhpLaelsrei 137
                                   Lss+l+spe+a+++lk++e+ lke+g++v raPFGwyk+f+isckGhpL+elsr+i
  gi|15669383|ref|NP_248192.1|  85 LSSDLSSPETAVKVLKDIESILKERGYNVLRAPFGWYKAFKISCKGHPLSELSRKI 140
                                   ******************************************************97 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.6   9.7e+03      15      30 ..      62      77 ..      56      83 .. 0.75
   2 !   85.4   2.5   3.8e-28   2.3e-24       1      93 [.     507     601 ..     507     602 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.6
                                  HHHHHHHHHHHHTTTS CS
                HGTP_anticodon 15 eeyakklaeeLraagi 30
                                   e+ +k+a++L+ ++i
  gi|15669383|ref|NP_248192.1| 62 VEEIEKVANQLKVNNI 77
                                  5677888998888776 PP

  == domain 2  score: 85.4 bits;  conditional E-value: 3.8e-28
                                   SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEE.. CS
                HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreq.. 79 
                                   qv vip++e   ++ +ya k+ae+Lr+++ir+++dd++es+ kkir+a + ++p++vv+G++e+e++++tv  r++     
  gi|15669383|ref|NP_248192.1| 507 QVRVIPVAE---RHYDYALKVAEKLRENNIRADFDDREESVSKKIRNAGKEWVPYVVVIGDEEMESDKLTVTIREKSTLkk 584
                                   89*******...9****************************************************9999999994443224 PP

                                   ...EEEETTHHHHHHHH CS
                HGTP_anticodon  80 ...ervsldelveklke 93 
                                      e+++ldel+e +k+
  gi|15669383|ref|NP_248192.1| 585 pykEKMTLDELIERIKK 601
                                   6669***********98 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.1   1.3e-17   7.6e-14       1     178 [.     277     486 ..     277     487 .. 0.82

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.3e-17
                                   EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEE.EBTTTS.TBCTTTB-SEEEEEEEEEEES.GGGHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                  tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtk.yRdEks.dsrGLlRvreFhqkdgyvfha.easldd 78 
                                   Y++ + n +e++L+  ++ +   + +d  l ++ LPlkly+++t  +R+E++ ++ GL R+r F++ d + +++  +++ +
  gi|15669383|ref|NP_248192.1| 277 YRFRQGN-KELMLRFAACFGQFMMKKDMYLLPRYLPLKLYELSTYsFRYEQRgELVGLKRLRCFTMPDMHTVCLnLEQAME 356
                                   8898888.9*******************999988*********955******8999******************5587777 PP

                                   HHHHHHHHHHHHHHHTT.SCEEEEEEGTTSC...........BTTSEEEEEEEEETT...................TSEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxx...................xxxxx RF
                  tRNA-synt_2b  79 slrdlikaisriferlglefraiielmsaks...........adykdkkefeavses...................ltkgi 129
                                   ++++ + +  +   +l l++ +i + ++++             +yk+k+  +++ e+                   l++ i
  gi|15669383|ref|NP_248192.1| 357 EFEKQFWECLKTGDDLNLSYSVIFRFTKDFFdehrdwffkiaKEYKNKYGKDVILEIlpkrkhywvgkvdiavidsLGRPI 437
                                   7777777777777889999999999966554678899999995555555555555556666666666666666666***** PP

                                   EEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxx RF
                  tRNA-synt_2b 130 eigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileq 178
                                   e  t+q +  + ++r++++v   n+ e  +i+++ +  g +eR+l+ +le+
  gi|15669383|ref|NP_248192.1| 438 ENPTVQID-VESAKRFDIKV-HTNEGEIYPIILHCSpTGsIERVLCGLLEK 486
                                   ********.99*********.6666666777888877999******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 3683.17
//
Query:       gi|15669384|ref|NP_248193.1|  [L=761]
Description: hypothetical protein MJ_1198 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-08   34.9   0.2    1.4e-08   34.9   0.2    3.5  4  S1               S1 RNA binding domain
    2.1e-08   34.4   7.4    2.1e-08   34.4   7.4    2.6  2  DnaJ_CXXCXGXG    DnaJ central domain
    9.1e-06   25.6   0.5    4.3e-05   23.4   0.5    2.2  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
    0.00024   21.3   0.2    0.00043   20.5   0.2    1.4  1  DHH              DHH family
     0.0028   17.5   0.1     0.0053   16.6   0.1    1.4  1  RMI2             RecQ-mediated genome instability protein 2
  ------ inclusion threshold ------
       0.07   13.1  20.0       0.25   11.3   2.4    3.5  3  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
       0.54   10.1   1.5       0.84    9.5   0.3    1.9  2  CxC3             CxC3 like cysteine cluster associated with K
        4.9    7.5   5.6         22    5.4   0.2    3.6  3  zinc_ribbon_9    zinc-ribbon


Domain annotation for each model (and alignments):
>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.7   6.1e+03      10      22 ..      79      91 ..      78      92 .. 0.85
   2 !   34.9   0.2   6.3e-12   1.4e-08       2      73 ..     132     198 ..     131     200 .. 0.95
   3 ?   -2.6   0.1       3.2   7.1e+03      34      52 ..     219     236 ..     214     244 .. 0.69
   4 ?   -0.7   0.1      0.82   1.8e+03       2      12 ..     471     481 ..     470     485 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.7
                                  EEEEEEETTEEEE CS
                            S1 10 GeVtsvtkgGafV 22
                                  G+V+++++ Ga++
  gi|15669384|ref|NP_248193.1| 79 GKVVKCDRCGAII 91
                                  99*****999976 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 6.3e-12
                                   STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEE CS
                            S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriils 73 
                                   +e g+ ++G+Vt+++k+Gaf++l + v+g++   ++ +      + e l vGde+ v+ ++v+ ++r+i++ 
  gi|15669384|ref|NP_248193.1| 132 VEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISL-----RLENLNVGDEIIVQAIDVRPEKREIDFK 198
                                   578999**************************9999999.....*************************986 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.2
                                   GGGSSSSCEESCHHHCEET CS
                            S1  34 aselsrdarvedpdevlkv 52 
                                   ++++s++  ve +d+v+++
  gi|15669384|ref|NP_248193.1| 219 IKDISQN-LVEMRDQVVHI 236
                                   4566666.88888888876 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.82
                                   STTTCEEEEEE CS
                            S1   2 pekgevveGeV 12 
                                   ++ gevv+G+V
  gi|15669384|ref|NP_248193.1| 471 HFPGEVVDGKV 481
                                   789******99 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   7.4   9.3e-12   2.1e-08       1      67 []       5      79 ..       5      79 .. 0.69
   2 !    9.6  11.4   0.00052       1.2       1      63 [.      57      87 ..      51     110 .. 0.53

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 9.3e-12
                 DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkGsG.v....vree....qkt.lgp.fvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67
                                  C+ C+G+g+k  k ktC+ C+G+G         +    +++  ++      + +Cp+C+GtGkv     kC+ C G+g
  gi|15669384|ref|NP_248193.1|  5 CPICDGTGKKVVKYKTCPVCEGTGfIdefsP--KqhmkRVSkRATyDLDYGEIPCPKCKGTGKVP-VYAKCDFCGGSG 79
                                  9*******988999**********5444321..122221112222123345779*********88.4569******86 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00052
                 DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvikekdkCkkC 63
                                  C+kCkG+g+ +    +C+ C+GsG+                           v+    kC++C
  gi|15669384|ref|NP_248193.1| 57 CPKCKGTGKVP-VYAKCDFCGGSGK---------------------------VV----KCDRC 87
                                  66666666422.2445666666664...........................33....23333 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.5   1.9e-08   4.3e-05       1      68 [.     234     298 ..     234     306 .. 0.93
   2 ?   -2.2   0.0       1.9   4.3e+03      13      36 ..     406     429 ..     397     439 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.9e-08
                                   EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEE CS
               tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelel 68 
                                   V ++G+v++i   ++ +   ++++Dgt+   v +   +  + + ++k+Gd+v v Grv+ r+g+ l++
  gi|15669384|ref|NP_248193.1| 234 VHIRGEVVQI--VQTPGPTVFTITDGTDFAWVAALEIAGLRAHPDVKVGDIVDVIGRVTIRDGR-LQI 298
                                   679*******..**********************999**************************9.766 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                                   EEETTEEEEEEEETTEEEEEEEET CS
               tRNA_anti-codon  13 rsggkvifidlrDgtgriqvvlfr 36 
                                   r  +k+ f++l+D t  +  ++ +
  gi|15669384|ref|NP_248193.1| 406 RRPSKAPFYELEDVTKDLVFSIED 429
                                   7778899999**999888777666 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2   1.9e-07   0.00043       2      57 ..     365     482 ..     364     524 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.9e-07
                                   EEEE-ECSSSHHHHHHHHHHHH........................................................CEC CS
                                   xxxxxxxxxxxxxxxxxxxxxx........................................................xxx RF
                           DHH   2 ilivghknpDtDsigSaialan........................................................llv 26 
                                   i+i   ++ DtD+ +  ial++                                                        +l+
  gi|15669384|ref|NP_248193.1| 365 III--RHHADTDGYCGGIALEKailpiidkfaidvdaiwhffkrrpskapfyeledvtkdlvfsiedalkfgqklpliVLI 443
                                   444..7899*************888888888888888888777777777777777777777777777777777777777** PP

                                   S--TCGGCGCCH..HCCCSEEEEEEE-S---S......S CS
                                   xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx......x RF
                           DHH  27 Dhneksqavege..akeeaedviiiDHHrlge......e 57 
                                   D+++++++  +   ak+ + +vi+iDHH +ge      e
  gi|15669384|ref|NP_248193.1| 444 DNGSTDEDIPAIskAKAYGIEVIVIDHHFPGEvvdgkvE 482
                                   ***9998765433399999*********99975555442 PP

>> RMI2  RecQ-mediated genome instability protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.4e-06    0.0053      38     118 ..     230     313 ..     209     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.4e-06
                          RMI2  38 evsrvWlQGtvvevdaske..sllldDgtgvfvveglnelpktk.kclkeGkYVmVvGvvqssspepvlkavKvvdLsenp 115
                                   + ++v + G vv++ ++     +++ Dgt+ + v +l+   ++  + +k G+ V V+G v+ +  +  ++ +K+++L  ++
  gi|15669384|ref|NP_248193.1| 230 RDQVVHIRGEVVQIVQTPGptVFTITDGTDFAWVAALEIAGLRAhPDVKVGDIVDVIGRVTIRDGRLQIERIKLQKLEGDE 310
                                   55789999*****999887889************9999888877799*************88888899******9998877 PP

                          RMI2 116 dre 118
                                     e
  gi|15669384|ref|NP_248193.1| 311 AEE 313
                                   655 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.4   0.00011      0.25      11      42 ..       3      30 ..       1      46 [. 0.90
   2 ?   10.2   4.2   0.00025      0.57      12      43 ..      20      67 ..      19      70 .. 0.71
   3 ?    4.4   9.9     0.017        38       7      41 ..      51      80 ..      46     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                  EE-TTTTTTSEETTE......E-TTTTTSSEE CS
                     Anti-TRAP 11 tkCdaCngsGkiepeeprasleCPkCsGkgli 42
                                  +kC+ C+g+Gk   +       CP C+G g+i
  gi|15669384|ref|NP_248193.1|  3 VKCPICDGTGKKVVK----YKTCPVCEGTGFI 30
                                  69*********9998....669*******987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00025
                                  E-TTTTTTSEETTE......................E-TTTTTSSEEE CS
                     Anti-TRAP 12 kCdaCngsGkiepe................eprasleCPkCsGkglip 43
                                  +C+ C+g+G i+                     + ++CPkC+G g +p
  gi|15669384|ref|NP_248193.1| 20 TCPVCEGTGFIDEFspkqhmkrvskratydLDYGEIPCPKCKGTGKVP 67
                                  7999999997765444577777766655533457799******99887 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.017
                                  HHCEEE-TTTTTTSEETTE......E-TTTTTSSE CS
                     Anti-TRAP  7 peLEtkCdaCngsGkiepeeprasleCPkCsGkgl 41
                                  +  E +C++C+g+Gk++        +C  C+G g 
  gi|15669384|ref|NP_248193.1| 51 DYGEIPCPKCKGTGKVPVY-----AKCDFCGGSGK 80
                                  5558899999999999988.....67888888764 PP

>> CxC3  CxC3 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3   0.00037      0.84       8      56 ..      17      65 ..      13      82 .. 0.89
   2 ?   -2.6   0.0       2.1   4.8e+03       8      33 ..      99     123 ..      95     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00037
                          CxC3  8 ppsccgeCkktgtltlkageesiavvtkeGrfdlnsaafkCssCsavre 56
                                    ++c+ C+ tg + + + ++++  v+k    dl + ++ C +C+ + +
  gi|15669384|ref|NP_248193.1| 17 KYKTCPVCEGTGFIDEFSPKQHMKRVSKRATYDLDYGEIPCPKCKGTGK 65
                                  5689****************************************98765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.1
                          CxC3   8 ppsccgeCkktgtltlkageesiavv 33 
                                     + c++C k +  ++k+g +++ v+
  gi|15669384|ref|NP_248193.1|  99 DRTLCDKCLKEE-EERKKGLRNVYVF 123
                                   567899999988.7888887777776 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.28   6.3e+02      23      29 ..       4      10 ..       2      12 .. 0.82
   2 ?    5.4   0.2    0.0098        22      22      34 ..      19      32 ..      14      33 .. 0.83
   3 ?    1.3   0.1      0.19   4.3e+02      21      29 ..      55      62 ..      41      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.28
                 zinc_ribbon_9 23 lCPhCgg 29
                                   CP C+g
  gi|15669384|ref|NP_248193.1|  4 KCPICDG 10
                                  5****98 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0098
                 zinc_ribbon_9 22 vlCPhCgg.gFVEe 34
                                  ++CP C+g gF+ e
  gi|15669384|ref|NP_248193.1| 19 KTCPVCEGtGFIDE 32
                                  58****766**987 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.19
                 zinc_ribbon_9 21 dvlCPhCgg 29
                                  ++ CP C+g
  gi|15669384|ref|NP_248193.1| 55 IP-CPKCKG 62
                                  35.****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (761 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 4830.27
//
Query:       gi|15669385|ref|NP_248194.1|  [L=146]
Description: hypothetical protein MJ_1199 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-31  109.0   0.0    1.9e-31  108.6   0.0    1.2  1  DUF2122   RecB-family nuclease (DUF2122)


Domain annotation for each model (and alignments):
>> DUF2122  RecB-family nuclease (DUF2122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.6   0.0     1e-35   1.9e-31       2     106 .]      40     141 ..      39     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 1e-35
                       DUF2122   2 aAAqsGipevlklalklgksllvlpdlkDalellkpekvlllskee.geelleeeeleekgrvllvfsgadegfskkelel 81 
                                   +AAqsGip+++k+a+klgk++l++++l+Da+e+l+pekv+l+ +++ ++e+++++e+   ++ l+vf+ga++gf+k+ele+
  gi|15669385|ref|NP_248194.1|  40 SAAQSGIPTLHKMAYKLGKNVLFFEELDDAIEVLRPEKVFLIGNKSiCDEKVDFNEV--GENDLVVFCGASTGFTKLELEK 118
                                   7*******************************************999*********9..99******************** PP

                       DUF2122  82 getvkvegveadvgelaelavvlye 106
                                   g   ++  ve+++g+l++la++lye
  gi|15669385|ref|NP_248194.1| 119 GLGRYI--VENEIGALGNLAIFLYE 141
                                   *****6..****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 925.29
//
Query:       gi|15669386|ref|NP_248195.1|  [L=366]
Description: type II R/M system modification methyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-48  164.4   0.3    2.8e-33  115.7   0.0    3.1  2  DNA_methylase    C-5 cytosine-specific DNA methylase
     0.0008   19.0   0.0     0.0014   18.2   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   3.5e-13   3.1e-09       1      54 [.       5      58 ..       5      72 .. 0.89
   2 !  115.7   0.0   3.1e-37   2.8e-33      46     334 ..     106     362 ..      86     363 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 3.5e-13
                                  -EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.-SEEEES-TTT CS
                 DNA_methylase  1 lkfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfkkvsigDitkid 54
                                  lkfidLf+G+GGf+ g+ + gfe  +a+e +++aa  Y+ nf+ ++ ++i+  +
  gi|15669386|ref|NP_248195.1|  5 LKFIDLFCGCGGFSRGFVEEGFEPLVAIELNEDAAFSYALNFNGQIYEKIRPGE 58
                                  59****************************************999988887655 PP

  == domain 2  score: 115.7 bits;  conditional E-value: 3.1e-37
                                   EEEES-TTTS-GS--...-SEEEE---GGGTECTSE.......E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGG CS
                 DNA_methylase  46 sigDitkidkkklpe..diDlLvgGfPCqpfSvaGk.......qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkh 117
                                   +i +i+ i+++k+ +  ++D+++gG+PC ++  a          +  +d+ g L  e+iri+ + +Pk+f++ENV+g+++ 
  gi|15669386|ref|NP_248195.1| 106 DIREIHAIEIEKFIKnkKVDVIIGGPPCEGYTGANPkreknpyDRLYKDETGRLVLEYIRIVGDLQPKIFVMENVPGIKEV 186
                                   456677777777766445*************999874555555566789999**************************998 PP

                                   CCSHHHHHHHHHHHHHTEE.EEEEEEEGGGTT-SB--EEEEEEEEEGGG----------SS---GGG.....TSGGGTTS- CS
                 DNA_methylase 118 dkgktlkvilekleelGYe.vsykllnasdyGvpQnReRvfivgirkdlelnvlvkvkefrfpkkkdleasktlrdlleek 197
                                   +       i+++++e+GYe v+++ l+a+dyG p  R+Rvf+  i+            + +++++k  ++++++ dl+ + 
  gi|15669386|ref|NP_248195.1| 187 RG-----AIIKEFREIGYEdVYFNTLRAEDYGNPSVRRRVFVSNIEI-----------NPEKTQPK--TVIEAIGDLMYKG 249
                                   65.....9**********7699*******************988844...........34455554..4789999999985 PP

                                   EE.BTTTB--GGGSSSTT-EE--.......S---HHHTS--B--TTS...-B----S-STT--B-TTS---EEEETTEEE- CS
                 DNA_methylase 198 se.ldeektalsdklvekeekikkttkaseegypkelsrnridkveelkglsatrrksgrgeklekelaeagklqknkerf 277
                                   ++  ++e  al   + ++  k          g+         d + + kg ++   ++ r         +  kl ++++  
  gi|15669386|ref|NP_248195.1| 250 RDvPNHEFAALPARFRKRVHKL---------GWG--------DAFIYFKGANRRLGNYIR--------LHPLKLAETVMGK 305
                                   3333333333333333322222.........344........555555555555556655........5666777777776 PP

                                   -T.TTGGG--B-BHHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHHHH CS
                 DNA_methylase 278 kpviekkriRrLtprEaarlqGfPddfefgskksaaykqiGnsVpvpvieaiakeik 334
                                   + +i++++ R LtprE arl+++Pd   f++   + y qiG+sVpv + +aia+ ik
  gi|15669386|ref|NP_248195.1| 306 RFFIHPYEDRLLTPREQARLMSYPDYHLFAGGIRSCYNQIGESVPVALSRAIARVIK 362
                                   668**************************************************9987 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.6e-07    0.0014       4      83 ..       7     135 ..       4     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-07
               Methyltransf_15   4 ilDlfsGaGGnviqfalv.fekviaieinlekl..acaqhNaevYgvsdkitlvlgdvfe..................... 60 
                                    +Dlf+G+GG +  f ++ fe  +aie n++    +  + N ++Y   +ki +   +++e                     
  gi|15669386|ref|NP_248195.1|   7 FIDLFCGCGGFSRGFVEEgFEPLVAIELNEDAAfsYALNFNGQIY---EKIRPGEFKLKElkgyvgiypfkfpfeeedikw 84 
                                   69*************9999**********9876224556688899...777766666666666777777777777777777 PP

               Methyltransf_15  61 ..............................llaklklekikvdlvflSpPwGG 83 
                                                                 + +++k +k  vd+++  pP+ G
  gi|15669386|ref|NP_248195.1|  85 lkrlgtlnektkklspvvinddireihaieIEKFIKNKK--VDVIIGGPPCEG 135
                                   777777777777777777777777776653333333333..477777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2342.09
//
Query:       gi|15669387|ref|NP_248196.1|  [L=70]
Description: 50S ribosomal protein L24e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-27   95.0   1.8    2.7e-27   94.8   1.8    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
    3.6e-06   26.8   3.0    5.6e-06   26.2   3.0    1.2  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
    0.00026   21.0   1.1    0.00046   20.2   1.1    1.3  1  YHS             YHS domain
     0.0052   17.1   0.1     0.0053   17.1   0.1    1.1  1  NosL            NosL
  ------ inclusion threshold ------
       0.04   13.9   2.9       0.47   10.5   1.2    2.2  2  DUF2116         Uncharacterized protein containing a Zn-ribbo


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   1.8   7.6e-31   2.7e-27       3      64 ..       4      65 ..       2      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 7.6e-31
                                  X-B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTT-XXXXXXXX CS
                Ribosomal_L24e  3 tekCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrnPrklkWTkayRrahkkelt 64
                                  +++CsF+gy+i+PG+Gk+ v++Dg+v+ F+ssKcek +++ rnPrklkWTk+y+ ++++ ++
  gi|15669387|ref|NP_248196.1|  4 WRTCSFCGYEIEPGKGKMVVEKDGTVLYFCSSKCEKSYRMGRNPRKLKWTKVYQDMKAELKK 65
                                  689****************************************************9987655 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   3.0   1.5e-09   5.6e-06       5      41 .]       6      41 ..       5      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.5e-09
                        zf-FCS  5 rCwfCkkyikgkpeftyvlendgvvgqFCStsCldsY 41
                                  +C+fC+ +i+ ++    v+e+dg v +FCS+ C +sY
  gi|15669387|ref|NP_248196.1|  6 TCSFCGYEIEPGK-GKMVVEKDGTVLYFCSSKCEKSY 41
                                  9********6666.467****************9999 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   1.1   1.3e-07   0.00046       6      35 ..      10      39 ..       9      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-07
                           YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCkd 35
                                  cg  ++++k +  +e +G+  yFcS +C+ 
  gi|15669387|ref|NP_248196.1| 10 CGYEIEPGKGKMVVEKDGTVLYFCSSKCEK 39
                                  9***************************86 PP

>> NosL  NosL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.5e-06    0.0053       8      68 ..       5      62 ..       1      70 [] 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                          NosL  8 aecdvCgMliaehpgpkgqifyededepakFcstrdlfafllepeerk.eikaiyvtDmsav 68
                                  ++c++Cg  i+     kg++++e++++++ Fcs+++  ++ + ++ rk + +++y +Dm+a+
  gi|15669387|ref|NP_248196.1|  5 RTCSFCGYEIE---PGKGKMVVEKDGTVLYFCSSKCEKSYRMGRNPRKlKWTKVY-QDMKAE 62
                                  57999998776...4599*************************999998888888.899854 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.02        70       4      16 ..       5      17 ..       2      25 .. 0.87
   2 ?   10.5   1.2   0.00013      0.47      19      34 ..      32      47 ..      28      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.02
                       DUF2116  4 kHCivCGkaIpld 16
                                  + C  CG  I+++
  gi|15669387|ref|NP_248196.1|  5 RTCSFCGYEIEPG 17
                                  67********986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00013
                       DUF2116 19 fCsekCqeeyekkrkk 34
                                  fCs kC++ y+  r+ 
  gi|15669387|ref|NP_248196.1| 32 FCSSKCEKSYRMGRNP 47
                                  9*********988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 454.76
//
Query:       gi|15669388|ref|NP_248197.1|  [L=78]
Description: 30S ribosomal protein S28e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-30  103.9   4.0    3.7e-30  103.7   4.0    1.1  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   4.0   2.1e-34   3.7e-30       2      64 .]      12      74 ..      11      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 2.1e-34
                                  --EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                Ribosomal_S28e  2 eaklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                  ea++AeVi+v+grtG++G+++qVr+++l+gkd+gr+++RnVkGPv++GDi++L+EterEAr L
  gi|15669388|ref|NP_248197.1| 12 EAVAAEVIEVIGRTGVTGGIIQVRCKILGGKDTGRVLVRNVKGPVKVGDIIMLRETEREARPL 74
                                  7899*********************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 484.90
//
Query:       gi|15669389|ref|NP_248198.1|  [L=117]
Description: 50S ribosomal protein L7Ae [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-31  106.8   2.3    4.2e-31  106.5   2.3    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
    2.5e-05   24.1   0.1    4.2e-05   23.3   0.1    1.4  1  PELOTA_1        PELOTA RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.5   2.3   4.7e-35   4.2e-31       4      94 ..      15     105 ..      12     106 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 4.7e-35
                                   HHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSEEE CS
                Ribosomal_L7Ae   4 eevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsala 84 
                                   +e+l +++ka+k+++G++evtka+erg aklvi+Aedv+pee +++l++lc+ek++py +v sk++LG+++g+++++s++a
  gi|15669389|ref|NP_248198.1|  15 KELLDAVAKAQKIKKGANEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLEVAASSVA 95 
                                   578899999************************************************************************ PP

                                   EEESTTTHHH CS
                Ribosomal_L7Ae  85 ikdegdskdl 94 
                                   i++egd+++l
  gi|15669389|ref|NP_248198.1|  96 IINEGDAEEL 105
                                   ******9987 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   4.7e-09   4.2e-05      15      71 ..      20      78 ..       8      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.7e-09
                      PELOTA_1 15 giedinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpdl 71
                                  ++ + + iK g  E T+++ R + + v+++++ +  + +ahl +L++ekg+p+  v+++
  gi|15669389|ref|NP_248198.1| 20 AVAKAQKIKKGANEVTKAVERGIAKLVIIAEDVKpeEVVAHLPYLCEEKGIPYAYVASK 78
                                  5778899***********************987743669*************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 713.61
//
Query:       gi|15669390|ref|NP_248199.1|  [L=288]
Description: ATP phosphoribosyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-53  180.5   0.2    3.3e-53  179.9   0.2    1.3  1  HisG      ATP phosphoribosyltransferase
    1.8e-27   95.2   0.3    4.1e-27   94.1   0.3    1.6  1  HisG_C    HisG, C-terminal domain


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.9   0.2   3.7e-57   3.3e-53       1     159 [.      49     208 ..      49     209 .. 0.95

  Alignments for each domain:
  == domain 1  score: 179.9 bits;  conditional E-value: 3.7e-57
                                   -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESEEEEEEEEETTSS--SGCGG.TT-.EEEEES-HHHHHHH CS
                          HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgkcklvvavpeesevkslkdlvedkgkriaTsypnlakky 81 
                                   ra+dip++V++g++d+G+tG D+v E++ e++v+ lld gfg +klv+a+pe+s+++s++d   ++g+r+aT++pnl+kky
  gi|15669390|ref|NP_248199.1|  49 RARDIPEFVADGVADIGVTGYDLVLERNVEDKVDFLLDFGFGFAKLVLAAPESSNINSIDDI--KEGMRVATEFPNLTKKY 127
                                   899***********************99999*****************************97..3567************* PP

                                   HHHTT-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHH.S..HHHHHHHHHHHH CS
                          HisG  82 feekglkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslk.k..kekieellerlr 159
                                   fe+++ kveii+lsG++E+ap +g+aD+I Dl++tG+TLr n+Lk+i++i++s+++Liank+slk k  +eki++++  ++
  gi|15669390|ref|NP_248199.1| 128 FEKLNKKVEIIELSGATEIAPFIGIADLISDLTSTGTTLRLNRLKVIDEIVSSTTRLIANKNSLKdKekREKINQIVIAIK 208
                                   *****************************************************************5555559999998776 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.3   4.6e-31   4.1e-27       1      73 []     213     286 ..     213     286 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 4.6e-31
                                   TTTEEEEEEEEEGGGHHHHHHH---SSS-EEEE-..SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEEEE-S- CS
                        HisG_C   1 ArkyvllmynvpkesleevlkilPGlrsPTvspla.degwvaVsavveekevaevideLkaaGAsdIlvlpiek 73 
                                   A+ ++l+m+n+pk+++ee+ k++PG+ +PTvs++  d+++va++avv+e+e+++++++L+a+GA+dIlv+pie+
  gi|15669390|ref|NP_248199.1| 213 AETKRLIMMNAPKDKVEEIRKLIPGMAGPTVSKVLsDDNMVAIHAVVNEDEIFTLVPKLHALGARDILVVPIER 286
                                   899******************************9669***********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1771.32
//
Query:       gi|15669391|ref|NP_248200.1|  [L=103]
Description: hypothetical protein MJ_1205 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-32  110.7   2.6    3.2e-32  110.6   2.1    1.2  1  UPF0058   Uncharacterised protein family UPF0058


Domain annotation for each model (and alignments):
>> UPF0058  Uncharacterised protein family UPF0058
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   2.1   1.8e-36   3.2e-32       1      86 [.       1      86 [.       1      87 [. 0.94

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 1.8e-36
                                  --HHHHHHHHHHHHHHHHHHTST.T--TTTTHHHHHH---TT-TTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH CS
                       UPF0058  1 MhKdeLieLHqllvevkkeleee.evekeefkeYeeLdisPhhihrsKaehkaAifvLgnaiakalsekeessaervskrlke 82
                                  MhKdeLi+LHqll++++k++e++ +++++efkeY+eL+i Phhihr+Kaeh ++if+L+++iak+ls++ +  +++vs+ l+ 
  gi|15669391|ref|NP_248200.1|  1 MHKDELIQLHQLLIYLRKYIEKKyNCDNNEFKEYDELNIYPHHIHRTKAEHIYTIFLLSSIIAKILSDNGKI-PRSVSNLLRV 82
                                  9*******************6554********************************************9999.******9998 PP

                                  HHHH CS
                       UPF0058 83 laek 86
                                  + ek
  gi|15669391|ref|NP_248200.1| 83 SGEK 86
                                  7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 667.59
//
Query:       gi|15669392|ref|NP_248201.1|  [L=424]
Description: DNA primase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-13   50.5   0.3    1.1e-12   48.3   0.2    2.4  2  Toprim_4  Toprim domain
    3.4e-07   30.6   0.0    2.1e-05   24.9   0.0    2.5  2  Toprim_2  Toprim-like
    7.3e-05   22.9   3.1    0.00011   22.4   0.1    2.7  3  Toprim    Toprim domain
  ------ inclusion threshold ------
       0.04   13.7   0.4        6.1    6.7   0.1    2.6  2  DRTGG     DRTGG domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.2     1e+04      10      38 ..      44      71 ..      42      89 .. 0.69
   2 !   48.3   0.2   2.4e-16   1.1e-12       2      77 ..     172     259 ..     171     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                      Toprim_4 10 aDvlalekagiknvvavlggalspldgir 38
                                   D+  l k+g  + + v  +++ + + i+
  gi|15669392|ref|NP_248201.1| 44 LDLRELQKTGRVGRIDVELTNI-NGKSIA 71
                                  5778888888888888888888.444444 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 2.4e-16
                      Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklkt.enlve....aekkvkevilaldgDa.....eGeatae 72 
                                    ii+VEg+aDvl+l ++giknv+av g+++ p+  i+++k+k+ + +++    +e ++ke++++ d D      +G+++ e
  gi|15669392|ref|NP_248201.1| 172 DIIVVEGRADVLNLLRCGIKNVIAVEGTSV-PKTIIELSKKKIvTVFTDgdrgGELILKELLQVCDVDFvarapPGKEVEE 251
                                   69****************************.************7777779999999************9999999999998 PP

                      Toprim_4  73 rlae...l 77 
                                     ++   +
  gi|15669392|ref|NP_248201.1| 252 LSKKeimK 259
                                   88874433 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   4.6e-09   2.1e-05       1      69 [.     174     236 ..     174     253 .. 0.78
   2 ?    3.0   0.0      0.03   1.4e+02      20      53 ..     375     405 ..     361     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.6e-09
                      Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellr 69 
                                   +v+Eg  D+l l++ gik   nv+a+ Gt + ++ + +l+++  k v + +D D+ G+   k+l ++  
  gi|15669392|ref|NP_248201.1| 174 IVVEGRADVLNLLRCGIK---NVIAVEGT-SVPKTIIELSKK--KIVTVFTDGDRGGELILKELLQVCD 236
                                   69***************9...********.555555566666..568899**********999988773 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.03
                      Toprim_2  20 ktnvvalgGtalteaalkllerypekkvvlalDn 53 
                                   + +++ ++Gt +t++++++l ++   +++++ D+
  gi|15669392|ref|NP_248201.1| 375 SIDAIIINGT-VTQKLIDILYEK--TNLIFCKDA 405
                                   4578999***.*********999..889999996 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.6   7.4e+03      51      51 ..     118     118 ..      68     144 .. 0.59
   2 !   22.4   0.1   2.4e-08   0.00011       2      92 ..     173     241 ..     172     252 .. 0.85
   3 ?   -0.4   0.1      0.31   1.4e+03      22      63 ..     312     370 ..     268     382 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
                                   H CS
                        Toprim  51 k 51 
                                   +
  gi|15669392|ref|NP_248201.1| 118 E 118
                                   1 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 2.4e-08
                                   EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHH CS
                        Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiawe 82 
                                   +++vEg +d+ ++ +    g ++v+a+ G+ +  +                      ++++ + + + tD+Dr Ge i +e
  gi|15669392|ref|NP_248201.1| 173 IIVVEGRADVLNLLRC---GIKNVIAVEGTSVPKTI--------------------IELSKKKIVTVFTDGDRGGELILKE 230
                                   89**************...9***********98888....................555667789999************* PP

                                   HHHHHT.HHHT CS
                        Toprim  83 llevlk.elle 92 
                                   ll+v++ +++ 
  gi|15669392|ref|NP_248201.1| 231 LLQVCDvDFVA 241
                                   ***99865554 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.31
                                   EEEEEEESSSSEEEHSTTEEEEE..................ECTTTHHHHHHHHHHHHHH CS
                        Toprim  22 fqavtaslGhildletefkpvye..................eiedkkkvlkalkelakra 63 
                                   +++v ++  +  + e+ ++p+y+                  +i+++k+ + +++el  + 
  gi|15669392|ref|NP_248201.1| 312 DVEVSSVECNPSNNEE-LPPKYNkyrkfyeklieledskvlIINGDKEEIVSIEELINNT 370
                                   4555555555555555.5555555555555666666666666666666666666665444 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0014       6.1      41      90 ..     171     218 ..     131     221 .. 0.89
   2 ?    4.5   0.0    0.0064        29      37      71 ..     344     385 ..     336     401 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0014
                                   SEEEEEETT-HHHHHHHTT-TEEEEEEETT----HHHHHHHHHHT--EEE CS
                         DRTGG  41 gdlvivpGDRediqlaaleagiaalilTgglepseevlklaeeaglpvls 90 
                                   +d+++v G R+d+ l +l  gi+ +i  +g  +++++++l +++ ++v++
  gi|15669392|ref|NP_248201.1| 171 DDIIVVEG-RADV-LNLLRCGIKNVIAVEGTSVPKTIIELSKKKIVTVFT 218
                                   78888855.9997.5689999************************99985 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0064
                                   HHHTSEEEEEETT-HHHHHHHTT-T.......EEEEEEETT- CS
                         DRTGG  37 rlkegdlvivpGDRediqlaaleag.......iaalilTggl 71 
                                    l++ +++i+ GD+e+i+    + +       i a+i++g +
  gi|15669392|ref|NP_248201.1| 344 ELEDSKVLIINGDKEEIVSIEELINntdnyksIDAIIINGTV 385
                                   57888999999*****97543333334888889999988864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1193  (0.0665402); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2709.57
//
Query:       gi|15669393|ref|NP_248202.1|  [L=226]
Description: protease synthase and sporulation negative regulator Pai1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-26   92.9   0.5    2.2e-26   92.4   0.5    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.2e-18   67.3   0.1      2e-18   66.5   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    7.6e-17   61.4   0.0    1.2e-16   60.8   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.6e-12   46.5   0.0    5.4e-12   45.9   0.0    1.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    3.9e-11   42.8   0.0    6.1e-11   42.1   0.0    1.3  1  FR47             FR47-like protein
      4e-09   36.8   0.2    5.8e-09   36.3   0.2    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    6.2e-09   35.9   0.0    1.2e-08   34.9   0.0    1.5  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      4e-08   33.0   0.0    7.3e-08   32.1   0.0    1.4  1  Acetyltransf_15  Putative acetyl-transferase
    4.1e-08   34.0   0.1    5.8e-08   33.5   0.1    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    1.5e-07   31.6   0.0    2.4e-07   31.0   0.0    1.3  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
    0.00059   19.5   0.0     0.0013   18.5   0.0    1.5  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.014   15.0   0.1      0.023   14.3   0.1    1.5  1  GNAT_acetyltran  GNAT acetyltransferase
      0.025   14.6   0.0      0.051   13.6   0.0    1.6  1  Acetyltransf_13  ESCO1/2 acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.5   1.6e-29   2.2e-26      11     117 .]      95     210 ..      83     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 1.6e-29
                                   HTH....HHHHHHHHHH.HHHHHHSTTC.EEEEEEETTEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHH CS
                Acetyltransf_1  11 sff....ppnedaseee.feesfsleae.gllvaeedgeliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLl 82 
                                    ++      ++++  ++ +++++ + +e g++v+e +g+++Gf+ +  ++    ek++va+i++++V+p++rg+G+G+aL+
  gi|15669393|ref|NP_248202.1|  95 AYRgfdkYYYKKKKWARwYFKWLMKRDEdGFFVCEVNGKPVGFVACDCNWIsniEKREVAEIHEIFVDPDFRGRGIGTALI 175
                                   444444333333333447778877777769**************777666688**************************** PP

                                   HHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  83 ealeerareegikkivlaveedndaairlYeklGF 117
                                   ++++e+a+++g + ++l+v + n++ai++Y++lGF
  gi|15669393|ref|NP_248202.1| 176 NKAIEYAKKRGRRIVELWVGVENKGAIEFYKRLGF 210
                                   **********88777***************88**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.1   1.5e-21     2e-18       3      76 .]     123     212 ..     121     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 1.5e-21
                                   EEEEEEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHH.HTT.....SEEEEE.EEEE..THHHH CS
                Acetyltransf_7   3 gevfVaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLle.aae.....kgiile.qlel..naeka 65 
                                   + +fV+e +gk+vGf+a+ +++         aei++++Vdp++rg+GiG+aL++ a +     +g + + +l++  +++ a
  gi|15669393|ref|NP_248202.1| 123 DGFFVCEVNGKPVGFVACDCNWisniekrevAEIHEIFVDPDFRGRGIGTALINkA-IeyakkRG-RRIvELWVgvENKGA 201
                                   569**************99999*9999999999999*****************943.22444566.32334555655569* PP

                                   HHHHHHTTEEE CS
                Acetyltransf_7  66 ikfYeklGFee 76 
                                   i+fY++lGFee
  gi|15669393|ref|NP_248202.1| 202 IEFYKRLGFEE 212
                                   *********96 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   8.4e-20   1.2e-16      27     110 ..     119     214 ..      94     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 8.4e-20
               Acetyltransf_10  27 eegealllvaeeggkivGvielrdgs..........hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp. 95 
                                   +  e  ++v+e++gk+vG+++ + ++          +i+ +fVdp++rg+Gig+aL+++++e+a+k+g ++ el v   + 
  gi|15669393|ref|NP_248202.1| 119 KRDEDGFFVCEVNGKPVGFVACDCNWisniekrevaEIHEIFVDPDFRGRGIGTALINKAIEYAKKRGRRIvELWVGVENk 199
                                   4566679*************888888889999999********************************************99 PP

               Acetyltransf_10  96 yavpfYeklGFkavg 110
                                    a++fY++lGF++ +
  gi|15669393|ref|NP_248202.1| 200 GAIEFYKRLGFEEKE 214
                                   ***********9865 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   3.9e-15   5.4e-12       1     126 [.      76     211 ..      76     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 3.9e-15
                                   .EEEE-GGGHHHHHHHHHHHTT----H.......HHHHHHHHHHT..TSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEE CS
                Acetyltransf_9   1 eirelteedldevlellkyaFqdeespl.....eeireyfrklle..esrvlgaedngelvgqlallplelnvpGktlkaa 74 
                                   +ir++t++dld++lel  +a+   ++++     + ++++ + l++  e+ ++++e ng+ vg +a+ ++ +  + ++ ++a
  gi|15669393|ref|NP_248202.1|  76 TIRNVTKDDLDDFLELYFKAYRGFDKYYykkkkWARWYF-KWLMKrdEDGFFVCEVNGKPVGFVAC-DCNWISNIEKREVA 154
                                   59*************************987653333433.3333333568999999******7765.88887777****** PP

                                   EEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-E CS
                Acetyltransf_9  75 gvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGye 126
                                    +  + v+p+ rgrg+ ++L+++a+e+++++g +++ l+       +i++Y+r+G+e
  gi|15669393|ref|NP_248202.1| 155 EIHEIFVDPDFRGRGIGTALINKAIEYAKKRGRRIVELWVgvenkGAIEFYKRLGFE 211
                                   ***************************************999877668********8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   4.5e-14   6.1e-11      14      81 ..     146     214 ..     135     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 4.5e-14
                                   EEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EEEE CS
                          FR47  14 awilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfekie 81 
                                     i ++++ e+  + v+p++r+rG g+ l+++ ++   +rg  ++ l+v+ +N+ +i++y++lGfe+ e
  gi|15669393|ref|NP_248202.1| 146 SNIEKREVAEIHEIFVDPDFRGRGIGTALINKAIEYAKKRGRRIVeLWVGVENKGAIEFYKRLGFEEKE 214
                                   56789999***************************99999986543999****************9874 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.2   4.2e-12   5.8e-09       1     137 [.      77     213 ..      77     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 4.2e-12
                Acetyltransf_4   1 iraateeDakeilaiyaeyvvntaitfeyev.ssveefekflealdsekeyvflvaesdrivGyaylg..qfkkrakdwka 78 
                                   ir +t++D++ +l++y + + + + + +y+  + + ++ k+l ++  ++  +f ++ +++ vG  +     +    k++ a
  gi|15669393|ref|NP_248202.1|  77 IRNVTKDDLDDFLELYFKAY-RGFDKYYYKKkKWARWYFKWLMKR--DEDGFFVCEVNGKPVGFVACDcnWISNIEKREVA 154
                                   89**************6533.3344455555367888999**998..9999999999******998875234444666666 PP

                Acetyltransf_4  79 el.svylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelv 137
                                   e+ ++++ + d + +g+g +li+  ++++k+ + +  +  + ++n+ +i+f+k+lGFe  
  gi|15669393|ref|NP_248202.1| 155 EIhEIFV-DPDFRGRGIGTALINKAIEYAKKRGRRIVELWVGVENKGAIEFYKRLGFEEK 213
                                   6615666.699**********************************************865 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0     9e-12   1.2e-08       2      61 ..     126     190 ..     125     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 9e-12
               Acetyltransf_CG   2 feltldegeevafleYe......vrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglkvv 61 
                                   f ++++ g+ v+f+  +       +k +v +++ ++V++ +rG+Gi+ +L+++a+++a+++g ++v
  gi|15669393|ref|NP_248202.1| 126 FVCEVN-GKPVGFVACDcnwisnIEKREVAEIHEIFVDPDFRGRGIGTALINKAIEYAKKRGRRIV 190
                                   566666.66777776656666665666799**********************************97 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   5.3e-11   7.3e-08      14     118 ..      52     195 ..      42     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 5.3e-11
               Acetyltransf_15  14 kevkkeFrnkrdeeeaitknenkydivqykkkeeLvasvfivkkkyyslvs.............................. 64 
                                   k +   F   +++  ++++ +++y+i + + k+ L   + +  k y+++ +                              
  gi|15669393|ref|NP_248202.1|  52 KSILDDFFRCQNAAMEVYNLIKTYTIRNVT-KDDLDDFLELYFKAYRGFDKyyykkkkwarwyfkwlmkrdedgffvcevn 131
                                   444444544455559***********9965.566766666666666666666666778*********************** PP

               Acetyltransf_15  65 ..............silieknvleiYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHln 118
                                                 s +++++v ei +++v++++rg+G+   l+++++++ kk+       ++ L + 
  gi|15669393|ref|NP_248202.1| 132 gkpvgfvacdcnwiSNIEKREVAEIHEIFVDPDFRGRGIGTALINKAIEYAKKR----GRRIVELWVG 195
                                   ***********************************************9988653....3445555555 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1   4.2e-11   5.8e-08       3     138 .]      76     211 ..      75     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 4.2e-11
                Acetyltransf_3   3 lLrplteeDlealfelrs.dpe.vmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsv..glrdleeede 79 
                                   ++r++t++Dl++++el+    + + +y    ++  +  +w+ + w  + +e+g  + +++ +++ +G+v   ++++++ ++
  gi|15669393|ref|NP_248202.1|  76 TIRNVTKDDLDDFLELYFkAYRgFDKY---YYKKKKWARWYFK-WLMKRDEDG--FFVCEVNGKPVGFVacDCNWISNIEK 150
                                   69***********99655022234444...4444555556664.766556666..77777455468887334446666655 PP

                Acetyltransf_3  80 e..aelg.ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                   +  ae+  + ++p+f+g+G++t   + ++eya ++ g + ++  +  eN++ i  +++lGfe
  gi|15669393|ref|NP_248202.1| 151 RevAEIHeIFVDPDFRGRGIGTALINKAIEYA-KKRGRRIVELWVGVENKGAIEFYKRLGFE 211
                                   56699985777799******************.66669999********************7 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.7e-10   2.4e-07      26     141 ..      80     206 ..      60     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.7e-10
                Acetyltransf_6  26 tdpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrldgrpvAva.......lglrsgdrlyywl 99 
                                    + +dl+ +lel+++ +++  d +  +   ++ r +++ l +r+   ++v +++g+pv+++        ++++++++  + 
  gi|15669393|ref|NP_248202.1|  80 VTKDDLDDFLELYFKAYRGF-DKYY-YKKKKWARWYFKWLMKRDEDGFFVCEVNGKPVGFVacdcnwiSNIEKREVAEIHE 158
                                   479*************9999.5553.5666677777777777777779************9666666567999******** PP

                Acetyltransf_6 100 ggydpelaklspgllllweliedaaeeGlrrfdlgggde......eyK 141
                                   + +dp++++ ++g+ l+ ++ie a+ +G+r ++l  g e       yK
  gi|15669393|ref|NP_248202.1| 159 IFVDPDFRGRGIGTALINKAIEYAKKRGRRIVELWVGVEnkgaieFYK 206
                                   **********************************99876333333466 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   9.2e-07    0.0013      29     143 ..     108     216 ..      99     217 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.2e-07
                                   HHHHHHHHHHC.STTEEEEEEEETTEEEEEEEE..EEGGGCGGGGCS---TT-EEEEEEESSHHHCTTTCHHHHHHHHHHH CS
                Acetyltransf_8  29 eevrellakldadphsepliglldgepvgyfei..YwakedelaeyydaepgdrGiHlligeaeargkglttallralvhy 107
                                   ++ r + + l + ++   ++ +++g+pvg++ +   w+++         +     iH +  ++++rg+g++tal+++ ++y
  gi|15669393|ref|NP_248202.1| 108 KWARWYFKWLMKRDEDGFFVCEVNGKPVGFVACdcNWISNI-------EKREVAEIHEIFVDPDFRGRGIGTALINKAIEY 181
                                   56666666666666777777888888888887611233322.......3555677999999******************** PP

                                   HHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEE CS
                Acetyltransf_8 108 lfadprtrrvvvEPdvrNerairllekaGfekekev 143
                                   + ++ + r v +   v+N+ ai++++++Gfe+++ v
  gi|15669393|ref|NP_248202.1| 182 AKKR-GRRIVELWVGVENKGAIEFYKRLGFEEKEVV 216
                                   9877.6666778899***************988765 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.6e-05     0.023     174     237 ..     146     213 ..      36     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
               GNAT_acetyltran 174 Sysvyekgiei.eidTkedyrrkgLAtivaaalileclkrg..lyPsWDaa.neaSvaLaekLGYefe 237
                                   S +  ++ +ei ei  ++d+r++g  t++ ++ i+ + krg  ++  W    n+ +++ +++LG+e +
  gi|15669393|ref|NP_248202.1| 146 SNIEKREVAEIhEIFVDPDFRGRGIGTALINKAIEYAKKRGrrIVELWVGVeNKGAIEFYKRLGFEEK 213
                                   4445677888867999***********************87447889*8889*************986 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.7e-05     0.051       7      31 ..     156     180 ..     150     195 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.7e-05
               Acetyltransf_13   7 isriWvssshRrkgiAtkLldaare 31 
                                   i+ i+v +++R +gi t+L++ a+e
  gi|15669393|ref|NP_248202.1| 156 IHEIFVDPDFRGRGIGTALINKAIE 180
                                   99*******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1438.09
//
Query:       gi|15669394|ref|NP_248203.1|  [L=406]
Description: S-adenosylmethionine synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.5e-182  606.1   8.5   2.8e-182  605.9   8.5    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
    0.00034   20.6   3.3    0.00088   19.3   0.4    2.5  2  LZ3wCH           Leucine zipper with capping helix domain
  ------ inclusion threshold ------
      0.098   13.3   2.2       0.26   12.0   0.3    2.7  2  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 
       0.14   12.8   1.6       0.28   11.9   0.4    2.1  3  Phage_ABA_S      Phage ABA sandwich domain


Domain annotation for each model (and alignments):
>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  605.9   8.5  6.2e-186  2.8e-182       1     396 []       2     402 ..       2     402 .. 0.99

  Alignments for each domain:
  == domain 1  score: 605.9 bits;  conditional E-value: 6.2e-186
                                   --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEEEEEE CS
               AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGGevie 81 
                                   rni+v++l+ +p+ee+ +EivErKG+GHPDsi+Dgiae+vsral+k+y+ekfg+ilhhn+D+v+lv+G++ pkfgGG +++
  gi|15669394|ref|NP_248203.1|   2 RNIIVKKLDVEPIEERPTEIVERKGLGHPDSICDGIAESVSRALCKMYMEKFGTILHHNTDQVELVGGHAYPKFGGGVMVS 82 
                                   79******************************************************************************* PP

                                   -EEEEEEEEEEEEE.......EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BESS CS
               AdoMet_Synthase  82 pieillsgratkev......egekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevplaND 156
                                   pi+illsgrat+e+      e  k+pv++ a++aakeylk+ lr++d++kdvi+d+++g+gs dL+dvfer+k+evplaND
  gi|15669394|ref|NP_248203.1|  83 PIYILLSGRATMEIldkeknEVIKLPVGTTAVKAAKEYLKKVLRNVDVDKDVIIDCRIGQGSMDLVDVFERQKNEVPLAND 163
                                   *************988776666679******************************************************** PP

                                   SEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHHHHHHHH CS
               AdoMet_Synthase 157 tSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevkeeikeev 237
                                   tSfgvgyapls++e+lvleter+lns+elk+++p+vGeDiKvmglRe+kki+lT+a+a+vdr+vk++eeY+ev e+++++v
  gi|15669394|ref|NP_248203.1| 164 TSFGVGYAPLSTTERLVLETERFLNSDELKNEIPAVGEDIKVMGLREGKKITLTIAMAVVDRYVKNIEEYKEVIEKVRKKV 244
                                   ********************************************************************************* PP

                                   HHHHHHHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-TTT-HHHHHHH CS
               AdoMet_Synthase 238 eelakkltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNPvsHvGKiYnv 318
                                   e+lakk+++ +eve+++NtaD++e+esvyltvtGtsaE+gDdGsvGRGNRvnGlitp rpms+EAa+GKNPv+HvGKiYn+
  gi|15669394|ref|NP_248203.1| 245 EDLAKKIADGYEVEIHINTADDYERESVYLTVTGTSAEMGDDGSVGRGNRVNGLITPFRPMSMEAASGKNPVNHVGKIYNI 325
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT-HHHHHHHHTTT- CS
               AdoMet_Synthase 319 laneiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideelekieeiteeliegk 396
                                   lan ia++i++ +egvke+yvr+lsqiGkpi+eP+++++++i+e++++++++e +++ei++++l++i e++++++egk
  gi|15669394|ref|NP_248203.1| 326 LANLIANDIAK-LEGVKECYVRILSQIGKPINEPKALDIEIITEDSYDIKDIEPKAKEIANKWLDNIMEVQKMIVEGK 402
                                   *********87.9**************************************************************996 PP

>> LZ3wCH  Leucine zipper with capping helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2       0.1   4.6e+02      11      43 ..     217     248 ..     210     267 .. 0.67
   2 !   19.3   0.4     2e-07   0.00088       5      34 ..     372     401 ..     369     403 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.1
                        LZ3wCH  11 kkakeaanrWtdnifdikswikekfpkskkeln 43 
                                    +a   + r+ +ni + k+ i++   k+ ++l 
  gi|15669394|ref|NP_248203.1| 217 TIAMAVVDRYVKNIEEYKEVIEK-VRKKVEDLA 248
                                   56677777778877777776665.444444444 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2e-07
                        LZ3wCH   5 ekkkatkkakeaanrWtdnifdikswikek 34 
                                   ++k+++ kake an W dni++++++i e+
  gi|15669394|ref|NP_248203.1| 372 DIKDIEPKAKEIANKWLDNIMEVQKMIVEG 401
                                   5899999********************985 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   5.7e-05      0.26      11      29 ..      27      45 ..      20     142 .. 0.75
   2 ?   -1.5   0.1      0.92   4.1e+03      21      41 ..     218     238 ..     211     264 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.7e-05
               S-AdoMet_synt_N 11 eGHPDkvadqisdaildai 29
                                   GHPD ++d i++++  a+
  gi|15669394|ref|NP_248203.1| 27 LGHPDSICDGIAESVSRAL 45
                                  6***********9986554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.92
               S-AdoMet_synt_N  21 isdaildailkedpkarvace 41 
                                   i+ a++d+++k+ ++ +  +e
  gi|15669394|ref|NP_248203.1| 218 IAMAVVDRYVKNIEEYKEVIE 238
                                   555555555554333332222 PP

>> Phage_ABA_S  Phage ABA sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         3   1.4e+04      75      89 ..      33      47 ..       8      47 .. 0.72
   2 ?   11.9   0.4   6.2e-05      0.28      28      75 ..     219     273 ..     203     283 .. 0.75
   3 ?   -2.9   0.0       2.6   1.2e+04      15      40 ..     358     384 ..     329     388 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3
                   Phage_ABA_S 75 rvevigetapeAICk 89
                                   +  i+e+   A+Ck
  gi|15669394|ref|NP_248203.1| 33 ICDGIAESVSRALCK 47
                                  566677888888886 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.2e-05
                   Phage_ABA_S  28 flvevfeysedisaAweVveklknegieikvkslekkyqvlveidek........r 75 
                                   +   v +y ++i+   eV+ek++ +++e  +k++ ++y+v+++i+          +
  gi|15669394|ref|NP_248203.1| 219 AMAVVDRYVKNIEEYKEVIEKVR-KKVEDLAKKIADGYEVEIHINTAddyeresvY 273
                                   4455779****************.******************99987555555544 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.6
                   Phage_ABA_S  15 vktsntevldegeflvevfey.sedis 40 
                                    k  + e+++e++  ++  e+ +++i+
  gi|15669394|ref|NP_248203.1| 358 PKALDIEIITEDSYDIKDIEPkAKEIA 384
                                   444466666666666666666566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1389  (0.0774723); expected 358.6 (0.02)
Passed bias filter:                      973  (0.0542696); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 2470.94
//
Query:       gi|298575367|ref|NP_248204.2|  [L=226]
Description: hypothetical protein MJ_1209m [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-40  137.0   1.7    2.1e-40  136.9   0.4    1.7  2  RE_BsaWI  BsaWI restriction endonuclease type 2


Domain annotation for each model (and alignments):
>> RE_BsaWI  BsaWI restriction endonuclease type 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.17     3e+03       5      23 ..      23      41 ..      19      64 .. 0.64
   2 !  136.9   0.4   1.2e-44   2.1e-40       2     106 .]      91     199 ..      90     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.17
                       RE_BsaWI  5 envkrllvikygeesvlpd 23
                                   e++ r+ v +y+++++ +d
  gi|298575367|ref|NP_248204.2| 23 EEYIRNKVEEYLKQGFSKD 41
                                   5666666666666666222 PP

  == domain 2  score: 136.9 bits;  conditional E-value: 1.2e-44
                       RE_BsaWI   2 selenvkrllvikygeesvlpdvDliiykkdknklkliaiIsaKtSlreRvtqtgfwslklkldkktkkikvvlvtpdkd 81 
                                    +el++vkrl++i+yge+ +lpd+D+i+yk+++n++k+iaiIs+K+S+reR ++t++w+lklk+++ t++ikv+l+tpdkd
  gi|298575367|ref|NP_248204.2|  91 EELDKVKRLIAINYGEYLFLPDADVIVYKVENNDIKIIAIISVKNSFRERRFETTYWKLKLKESPVTSHIKVFLATPDKD 170
                                    79****************************************************************************** PP

                       RE_BsaWI  82 nelkkk....kskkervileheldgvyvl 106
                                    ne+++k    k+kk+r+ile+eldg+y l
  gi|298575367|ref|NP_248204.2| 171 NEISYKcpngKPKKMRIILEYELDGIYFL 199
                                    ***************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1459.57
//
Query:       gi|298575372|ref|YP_003727984.1|  [L=194]
Description: type II R/M system modification methylase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.3e-18   65.3   1.0    6.3e-18   65.3   1.0    1.5  2  N6_N4_Mtase  DNA methylase
     0.0081   15.9   0.0      0.011   15.5   0.0    1.2  1  UPF0020      Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.052   12.8   0.0      0.067   12.4   0.0    1.1  1  N6_Mtase     N-6 DNA Methylase
       0.19   11.3   0.1       0.52    9.8   0.1    1.6  1  MTS          Methyltransferase small domain


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.52   2.3e+03      78      99 ..       3      24 ..       1      26 [. 0.80
   2 !   65.3   1.0   1.4e-21   6.3e-18       1     130 [.      32     162 ..      32     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.52
                                      EEEEEEEEESSSTTTSTCCS-B CS
                       N6_N4_Mtase 78 llnvivwkkpnsmpesnkdrlt 99
                                      ++ v +w+k n+++  n+d+l+
  gi|298575372|ref|YP_003727984.1|  3 VIIVKIWNKINGITLINDDFLN 24
                                      6677899999999999998776 PP

  == domain 2  score: 65.3 bits;  conditional E-value: 1.4e-21
                                       EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT.......HHHHHHH CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk.......elkalad 70 
                                       +dlivt+pPYn+g d   ++q ++   yeeyl++ +++lk++  +Lk+dg +++ni   + k        +++++a+
  gi|298575372|ref|YP_003727984.1|  32 IDLIVTSPPYNVGID---YNQHDDTIPYEEYLDWTKQWLKKALTLLKKDGRLCLNIPLDKNKGgikpvyaDIVKIAL 105
                                       89*************...999999999*******************************999999**99998888888 PP

                                       HHTT-EEEEEEEEEEES........SSTTTSTCCS-B--EEEEEEEESSTT-..---GGGSSBSS-HH CS
                       N6_N4_Mtase  71 eifggffllnvivwkkp........nsmpesnkdrltsthEyilvfsknkkyllkfnldaikvpyeek 130
                                       ++ g f+++++i+w+ +        +s+ + ++ ++    E+i+v+ k   +  k+       ++ e+
  gi|298575372|ref|YP_003727984.1| 106 DV-G-FKYQTTIIWNEQnisrrtawGSFMSASAPYVIAPVETIVVLYKESWK--KL-------SKGES 162
                                       88.7.**********9999999998544444445*************99999..33.......22222 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.4e-06     0.011     106     161 ..      16      70 ..      10     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-06
                                       EEEE--GGG--STTS---EEEE----------HHHHHHH.HHHHHHHHHHH-TT..- CS
                           UPF0020 106 efsqadaakLrlkegevdvivtnpPYGerlgskkalekL.Yseflrelkrvlrgggr 161
                                       ++ + d+ ++ l+++++d+ivt pPY   ++ ++  +++ Y+e l++ k+ l++   
  gi|298575372|ref|YP_003727984.1|  16 TLINDDFLNVDLPNESIDLIVTSPPYNVGIDYNQHDDTIpYEEYLDWTKQWLKK--A 70 
                                       455568888888999***************99999965559****999999988..3 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.5e-05     0.067     107     180 ..      15      81 ..       1      87 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                          N6_Mtase 107 vkirlgdtlekpkfekdkkfdvvvaNppfnqkewkektlekderfreavapksnadla..fllhiieslkpkGraa 180
                                       +   ++d l+ +  +  +++d +v+ pp+n     + + ++d      ++ ++  d++  +l  ++  lk++Gr  
  gi|298575372|ref|YP_003727984.1|  15 ITLINDDFLNVDLPN--ESIDLIVTSPPYNVG--IDYNQHDDT-----IPYEEYLDWTkqWLKKALTLLKKDGRLC 81 
                                       445566666666666..9************99..455555555.....888888888778************9976 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00012      0.52      82     136 ..      15      81 ..       8      91 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00012
                                       EEEEE-STTT.TSTTS-EEEEEE---STTTCHCHH...........HHHHHHHHHHHHHEEEEEEEE CS
                               MTS  82 vevvasdvle.eveekkfdlivsNPPfhagkatel...........avaeeliaeAkeaLkegGeLl 136
                                       +++++ d l+ +++++++dliv+ PP+  g + ++           + +++ +++A   Lk++G+L 
  gi|298575372|ref|YP_003727984.1|  15 ITLINDDFLNvDLPNESIDLIVTSPPYNVGIDYNQhddtipyeeylDWTKQWLKKALTLLKKDGRLC 81 
                                       555556655427889************9987544311111111111456677777777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1297.59
//
Query:       gi|15669395|ref|NP_248205.1|  [L=258]
Description: hypothetical protein MJ_1210 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-46  159.5   0.0    1.3e-46  159.3   0.0    1.0  1  PAC2        PAC2 family
  ------ inclusion threshold ------
      0.011   15.8   1.6        2.8    8.1   0.1    3.7  4  HHH_2       Helix-hairpin-helix motif
       0.28   11.8   4.0        8.2    7.1   0.8    2.9  3  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.3   0.0   2.1e-50   1.3e-46       1     212 [.      23     233 ..      23     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: 159.3 bits;  conditional E-value: 2.1e-50
                                   EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEEEEE..TTT.SEEEEEEE... CS
                          PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprlyak..dsgsrdllvlqg... 74 
                                   Li+G+pgiG+Vg la+++L+++++ ek+ e+ + + +p     p+vlv+++   e++  ++ya   +   ++++v+ g   
  gi|15669395|ref|NP_248205.1|  23 LIEGLPGIGHVGRLAAEHLVHEFKGEKFLELFCYD-FP-----PQVLVKDDgtIEYMCAEFYAIreP---KPMIVVLGntq 94 
                                   8**********************************.**.....********9*9*******887744...999999999** PP

                                   .E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT......-CEEEEHHHH CS
                          PAC2  75 .repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees......eyggivgitg 148
                                     +pi+qy  +a++++++  e+g + v++Lgg++ g++      +++kv+ga t++el+++l+e+      ++ggivg++g
  gi|15669395|ref|NP_248205.1|  95 aLSPIGQYH-LAEEIVKIGIEYGANFVYTLGGFGVGKLC-----EEVKVYGATTSKELAKKLKEHdilfrtDGGGIVGAAG 169
                                   *********.*************************9984.....6779**************755567778********** PP

                                   HHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                          PAC2 149 lLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                   l+l+ a+ +gip+++l++e+p+yl dP+aa+a+le++ kl ++e+++e+Le++a+ +e+ +e++
  gi|15669395|ref|NP_248205.1| 170 LMLMFADLNGIPGICLMGETPGYLIDPNAAKAVLEKFCKLENIEINMEELEKRAKGMEQFIEKI 233
                                   ***********************************************************99885 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.1   6.5e+03      18      33 ..       7      22 ..       6      25 .. 0.78
   2 ?    8.1   0.1   0.00047       2.8       7      24 ..      29      46 ..      22      52 .. 0.91
   3 ?    2.2   0.0     0.032   1.9e+02      12      29 ..     139     156 ..     135     162 .. 0.83
   4 ?    1.8   0.0     0.043   2.6e+02      14      30 ..     197     213 ..     194     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.1
                         HHH_2 18 lLakrFksldaLkkas 33
                                  ++ ++ k+++ L++a 
  gi|15669395|ref|NP_248205.1|  7 IITRKVKDIEPLENAL 22
                                  5678889999999985 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00047
                         HHH_2  7 GIrhVGektAklLakrFk 24
                                  GI hVG  +A+ L+++Fk
  gi|15669395|ref|NP_248205.1| 29 GIGHVGRLAAEHLVHEFK 46
                                  9****************8 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.032
                         HHH_2  12 GektAklLakrFksldaL 29 
                                   G++t+k+Lak+ k+ d L
  gi|15669395|ref|NP_248205.1| 139 GATTSKELAKKLKEHDIL 156
                                   99********99976655 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.043
                         HHH_2  14 ktAklLakrFksldaLk 30 
                                   ++Ak+  ++F +l++++
  gi|15669395|ref|NP_248205.1| 197 NAAKAVLEKFCKLENIE 213
                                   689***********986 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0094        56      19      39 ..      26      46 ..      24      52 .. 0.89
   2 ?   -1.8   0.1       0.8   4.8e+03      47      47 ..     134     134 ..      87     156 .. 0.52
   3 ?    7.1   0.8    0.0014       8.2      28      66 ..     196     239 ..     173     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0094
                    5_3_exonuc 19 nipGvpgiGektAakLlkeyg 39
                                   +pG+  +G  +A +L++e++
  gi|15669395|ref|NP_248205.1| 26 GLPGIGHVGRLAAEHLVHEFK 46
                                  689****************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.8
                    5_3_exonuc  47 n 47 
                                   +
  gi|15669395|ref|NP_248205.1| 134 E 134
                                   1 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0014
                    5_3_exonuc  28 ektAakLlkeygsleeilenldelke.....kklkekLeenkee 66 
                                   + +A+++l+++ +le+i  n++el++     ++  ek+++ +ee
  gi|15669395|ref|NP_248205.1| 196 PNAAKAVLEKFCKLENIEINMEELEKrakgmEQFIEKIKKFEEE 239
                                   67899****************98776444444455666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1246  (0.0694963); expected 358.6 (0.02)
Passed bias filter:                     1004  (0.0559987); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 1624.00
//
Query:       gi|15669396|ref|NP_248206.1|  [L=116]
Description: hypothetical protein MJ_1211 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   12.8   0.1       0.08   12.3   0.1    1.3  1  Kdo       Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   4.5e-06      0.08     122     175 ..      23      72 ..       3      78 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-06
                           Kdo 122 allkavgrliaklhragvnHadlya.knillqqeeeeeaeiwliDldkarlrlra 175
                                   + ++++ ++  kl  +g++H  +   +++l+ ++     + ++iD+dka+++ + 
  gi|15669396|ref|NP_248206.1|  23 KVVEDILKITLKLDILGIEHKEIQGgRHFLITNK-----KTYIIDFDKAKEKKTT 72 
                                   5566667777788899999999975378888777.....5**********99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 727.49
//
Query:       gi|15669397|ref|NP_248207.1|  [L=201]
Description: CDP-diacylglycerol--serine O-phosphatidyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-13   48.7   2.1    9.4e-13   48.7   2.1    3.2  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
       0.15   11.5   0.1        0.2   11.1   0.1    1.1  1  Arginase         Arginase family


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   2.1   1.1e-16   9.4e-13       3      66 .]      11      66 ..       9      66 .. 0.90
   2 ?   -9.8  13.1         2   1.8e+04       2       2 ..     158     158 ..      69     195 .. 0.61

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1.1e-16
                                  HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
               CDP-OH_P_transf  3 PnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                   + +T+l+++ ++lail l         + l+ +++++D+lDG++AR++++vs++G+ lDs+ D
  gi|15669397|ref|NP_248207.1| 11 SDYVTMLNIITGLLAIL-L-------NSFSLIYLSIIFDSLDGYVARKTGTVSDFGAELDSISD 66
                                  5789************5.5.......4667899*****************************99 PP

  == domain 2  score: -9.8 bits;  conditional E-value: 2
                                   - CS
               CDP-OH_P_transf   2 l 2  
                                    
  gi|15669397|ref|NP_248207.1| 158 Y 158
                                   1 PP

>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   2.2e-05       0.2     200     238 ..      30      68 ..       5      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.2e-05
                                   TTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHH CS
                      Arginase 200 eedpvylSfDiDvlDpavaPGtGtpepgGltlrellall 238
                                   +   +ylS+  D lD  va  tGt    G +l+ + +++
  gi|15669397|ref|NP_248207.1|  30 SFSLIYLSIIFDSLDGYVARKTGTVSDFGAELDSISDVV 68 
                                   4458**************************999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1297.60
//
Query:       gi|15669398|ref|NP_248208.1|  [L=110]
Description: hypothetical protein MJ_1213 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-08   32.2   1.4    6.9e-08   32.0   1.4    1.0  1  Peptidase_M56  BlaR1 peptidase M56
    2.5e-05   24.4   0.1    2.9e-05   24.2   0.1    1.1  1  DUF45          Protein of unknown function DUF45
    5.1e-05   23.1   0.0    5.4e-05   23.1   0.0    1.2  1  Peptidase_M48  Peptidase family M48
    0.00082   19.2   0.2      0.001   18.9   0.2    1.2  1  SprT-like      SprT-like family
     0.0032   17.4   0.1      0.004   17.1   0.1    1.2  1  Peptidase_M78  IrrE N-terminal-like domain
  ------ inclusion threshold ------
      0.066   13.7   0.1      0.081   13.4   0.1    1.1  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
      0.098   11.2   0.0      0.098   11.2   0.0    1.1  1  XG_FTase       Xyloglucan fucosyltransferase


Domain annotation for each model (and alignments):
>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   1.4   2.7e-11   6.9e-08     139     216 ..       7      83 ..       1      92 [. 0.83

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.7e-11
                 Peptidase_M56 139 raeelkeaLkeakeemqlkrnikirlsssidsPavlgllkprIvlPadflkklsdeeleyillHElaHlkrkDllvnl 216
                                    +e l + ++e + + + k niki++++   + a++ l    I++ +++l+ lsdee+ +il+HEl+Hlk +   +n 
  gi|15669398|ref|NP_248208.1|   7 LNEILSNTINELNLNDK-KANIKIKIKPLKRKIASISLTNKTIYINKNILPYLSDEEIRFILAHELLHLKYGKYHINE 83 
                                   45555666666666666.99**************************************************98777775 PP

>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   1.2e-08   2.9e-05     115     197 ..       6      95 ..       2     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.2e-08
                         DUF45 115 eleerlaklaaklgv....kprsvsikdmktrWGsc.sskgkirlnwrLvk.appevidYVvvHElaHlle.knHskrFwa 188
                                   +l+e l++  ++l++       +++ik  k++ +s   ++++i +n +++  ++ e i+++++HEl Hl++ k H  +F +
  gi|15669398|ref|NP_248208.1|   6 ILNEILSNTINELNLndkkANIKIKIKPLKRKIASIsLTNKTIYINKNILPyLSDEEIRFILAHELLHLKYgKYHINEFEE 86 
                                   45555555555555533325668999**********999********98753799***************85679999999 PP

                         DUF45 189 lvekllPdw 197
                                   ++  l+P+ 
  gi|15669398|ref|NP_248208.1|  87 ELLFLFPNK 95 
                                   999999885 PP

>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.1e-08   5.4e-05      43      78 ..      43      77 ..       2      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.1e-08
                                  SS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTT CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 43 gknkrivltdgLlkqllseeelaaVlGHElGHikhr 78
                                    nk+i++++ +l   ls+ee++++l+HEl H+k +
  gi|15669398|ref|NP_248208.1| 43 LTNKTIYINKNIL-PYLSDEEIRFILAHELLHLKYG 77
                                  4578*********.******************9976 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2     4e-07     0.001      14      76 ..      21      75 ..       5      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4e-07
                     SprT-like 14 ggqaaggvkiiwskrlnttaGranlkratvrhhasIeLseklldsrsedrllntLaHElcHla 76
                                  ++ ++ ++ki+ +  l++++   +l +      ++I +++++l + s+++++ +LaHEl Hl 
  gi|15669398|ref|NP_248208.1| 21 ND-KKANIKIKIK-PLKRKIASISLTN------KTIYINKNILPYLSDEEIRFILAHELLHLK 75
                                  33.3666777666.8888888889998......9***************************95 PP

>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.6e-06     0.004      26      65 ..      42      87 ..      15     103 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.6e-06
                 Peptidase_M78 26 s.etkvivlnsn....hsptrqrftlaHElgHlllhherdkf.ree 65
                                  s ++k+i++n+n    +s+++ rf laHEl Hl  +++ +++ +ee
  gi|15669398|ref|NP_248208.1| 42 SlTNKTIYINKNilpyLSDEEIRFILAHELLHLKYGKYHINEfEEE 87
                                  246999**99765222689***************999987766444 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.1e-05     0.081       7      56 ..       4      62 ..       3      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
                                  HHHHHHHHHHHHHH...HSTTTEEEEEEEE..EETEEEEEEEESSSSSTTHHHT.....G CS
                     HATPase_c  7 rqiisnlvdNavkf...atkageieveika..seddlvisveDnGiGipkedlk.....k 56
                                  r+i++++++N +++   + k+ +i+++ik+  + +  +is ++  i i+k++l+     +
  gi|15669398|ref|NP_248208.1|  4 RKILNEILSNTINElnlNDKKANIKIKIKPlkR-KIASISLTNKTIYINKNILPylsdeE 62
                                  689***********7666699999999998532.68999999999999999998555550 PP

>> XG_FTase  Xyloglucan fucosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.8e-05     0.098     248     278 ..      73     103 ..       7     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.8e-05
                      XG_FTase 248 yfvPslflvpefeeelrklfpeketvfhhla 278
                                   ++  + + + efeeel  lfp+ke+++  l 
  gi|15669398|ref|NP_248208.1|  73 HLKYGKYHINEFEEELLFLFPNKEAILINLI 103
                                   55567899*****************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 774.95
//
Query:       gi|15669399|ref|NP_248209.1|  [L=1018]
Description: type I restriction-modification enzyme 1 subunit R [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      9e-41  140.0   0.2      9e-41  140.0   0.2    2.3  2  SWI2_SNF2  SWI2/SNF2 ATPase
    1.4e-37  129.6   7.4    1.4e-37  129.6   7.4    4.8  6  HSDR_N     Type I restriction enzyme R protein N terminus (HS
    8.5e-18   64.9   0.5    8.5e-18   64.9   0.5    4.2  5  ResIII     Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
       0.79    9.9   6.1          1    9.6   0.2    3.1  3  DUF5448    Family of unknown function (DUF5448)


Domain annotation for each model (and alignments):
>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.0   0.2     2e-44     9e-41       2     223 ..     255     506 ..     254     507 .. 0.82
   2 ?   -2.1   1.3      0.57   2.6e+03     160     219 ..     556     618 ..     538     623 .. 0.66

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 2e-44
                     SWI2_SNF2   2 Qyravekavervke.....gdrkgGviWHtqGSGKsltmvflakkllee.elknpkvvvvtDRkdLdkQlsktfakag... 73 
                                   Qy av+ka er+++     + ++ G++WH qGSGK+++ ++la+   +e + k+p v++++DR++L++Q  + + +++   
  gi|15669399|ref|NP_248209.1| 255 QYWAVKKAYERITNylnnkDYKNRGLVWHWQGSGKTFEILYLAELFYNEfKNKDPIVFIMVDRRELETQFNDDIIALQnan 335
                                   9************9999865599*************************6688999*****************999886222 PP

                     SWI2_SNF2  74 .eekpkqaesrkeLkellek..........esekiifttiqKfeeeek....eklevlsereniivlvDEaHRsqygelak 139
                                    ++  k+++s +eLk  le+          +++++++++++Kf++++     e++  ++++e i++l DEaHR+++g++a+
  gi|15669399|ref|NP_248209.1| 336 fKDCFKKINSVEELKGVLEDikesennpniSEKGVYLVMMHKFDKNKLkdfiESFGSIDKKE-ILILRDEAHRTESGKFAT 415
                                   2333478999999999995333455555445789*********8653333545667766665.****************** PP

                     SWI2_SNF2 140 klrkalpnaafigFTGTPilkkdkktkevFg......eyidkYtikeaveDgavvpilYesrl.aklelkeeekldeefee 213
                                     +k+l+na  igFTGTP++kkd +t +++        y+d++ i+e+++ g ++p+ +     ++++  +ee++++ +e+
  gi|15669399|ref|NP_248209.1| 416 LRNKILKNAIAIGFTGTPVHKKDMSTFKEYAypqegeFYLDRFFIEESIKEGFTLPLIWRVVKpEDIKDISEEEIKNIIEK 496
                                   *****************************965554445******************8887654144555555569*****9 PP

                     SWI2_SNF2 214 iteeleeeek 223
                                   ++ ++e+++k
  gi|15669399|ref|NP_248209.1| 497 LFVDEEDADK 506
                                   9999988765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.57
                     SWI2_SNF2 160 kkdkktkevFgeyidkY...tikeaveDgavvpilYesrl.aklelkeeekldeefeeiteele 219
                                   ++d+k+   F +y+d+Y   +ik+  e  + v i+Y ++  +++e  ++e +++++ + ++el+
  gi|15669399|ref|NP_248209.1| 556 AQDRKSCILFKKYLDEYlkeKIKNYNENWTQVVITYIHNDdVEIENYKKE-IEKKYGKNVDELN 618
                                   46777788899999999444456666666666677765540344444443.7777776666655 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.6   7.4     3e-41   1.4e-37      12     193 ..      15     200 ..       8     201 .. 0.88
   2 ?   -2.9   0.0       1.3   5.7e+03     145     160 ..     258     273 ..     209     281 .. 0.73
   3 ?   -3.0   0.1       1.4   6.1e+03      49      78 ..     334     367 ..     316     388 .. 0.60
   4 ?   -4.4   4.2       3.6   1.6e+04       3      60 ..     486     541 ..     484     632 .. 0.53
   5 ?   -1.4   0.7      0.42   1.9e+03      48      48 ..     746     746 ..     686     790 .. 0.49
   6 ?    0.9   3.5     0.083   3.7e+02      30     111 ..     896     983 ..     882    1002 .. 0.72

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 3e-41
                                   HHHHHHHTT-EE...............----SHHHHHHHHHHHHHHHH..............-HHHHHHHHTT--HHHHHH CS
                        HSDR_N  12 idellrelGyqvlskkdveiegrrpevrkskaevaleknlreqlgaln..............ikkltkrlalsdgnkefye 78 
                                   i e l++lG++ l++ +           ++ +++++++ l+eql+ +n              i    ++l    + +e+++
  gi|15669399|ref|NP_248209.1|  15 IEENLNKLGWKELEGYE----------GEAFSNYIIKPILEEQLKIINdhigeykdefiekaI----NKLINEPKPEEILD 81 
                                   67789******997763..........558899*****************9998777742222....222256679***** PP

                                   HHHTS.-EEEE....TS-EEEEESS-SSSGGGS-EEEEE----SSSS---EEEEEEETTEEEEEEEE--T...T.-HHHHH CS
                        HSDR_N  79 llkeg.kvkfk....egrkknikLiDkknlenNrfqvvnQvtvtgnqkrrpDivlfvnglplvviElKrp...g.tieeAi 150
                                   ++k+g  ++++    ++ ++++kLiD+kn+e+N+f+++++++++gn++++pD++lf+ng+p+++iE+Kr+   + t+eeAi
  gi|15669399|ref|NP_248209.1|  82 YIKNGiLITLDkgrkGQVSNRVKLIDYKNIEKNIFNYAHELKFKGNDNIIPDFTLFINGIPIIIIEAKREfseKeTYEEAI 162
                                   *********666**9999****************************************************98736****** PP

                                   HHHTSS---.---SSSGGGGG--EEEEE-SS-EEEEE--SSSG CS
                        HSDR_N 151 nQikryrkeksdvsipqlfrYlqfgvisngketrfyaktkrre 193
                                   nQi+ry++e     +p lf+Y+qf +++ ++++++++ +++++
  gi|15669399|ref|NP_248209.1| 163 NQINRYERE-----APKLFNYVQFAIVYGDEKLYIPTYPNEEK 200
                                   *******99.....9*********************9998765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                                   -HHHHHHHHTSS---. CS
                        HSDR_N 145 tieeAinQikryrkek 160
                                   ++++A++ i++y ++k
  gi|15669399|ref|NP_248209.1| 258 AVKKAYERITNYLNNK 273
                                   4667777777777654 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHH.-HHHHHHHH...TT--HHHHHH CS
                        HSDR_N  49 knlreqlgaln.ikkltkrla...lsdgnkefye 78 
                                   +n+++ ++++n +++l+  l     s++n ++ e
  gi|15669399|ref|NP_248209.1| 334 ANFKDCFKKINsVEELKGVLEdikESENNPNISE 367
                                   5778888888884444444333224444444433 PP

  == domain 4  score: -4.4 bits;  conditional E-value: 3.6
                                   SHHHHHH.HHHHHHHHTT-EE...............----SHHHHHHHHHHHHHHHH.........- CS
                        HSDR_N   3 sEaeleqelidellrelGyqvlskkdveiegrrpevrkskaevaleknlreqlgaln.........i 60 
                                   sE+e+++  i +l+      v++++  +i  +    +k++ae++ +++l ++  +++         i
  gi|15669399|ref|NP_248209.1| 486 SEEEIKN-IIEKLF------VDEEDADKIVVS----KKEIAEKIKLSDLLKSESSIKeaskyiaehI 541
                                   5665555.666666......444444444443....3334444444444433333333322222220 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 0.42
                                   H CS
                        HSDR_N  48 e 48 
                                    
  gi|15669399|ref|NP_248209.1| 746 F 746
                                   1 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.083
                                   .........----SHHHHHHHHHHHHHHHH.-HHHHHHHH.TT--HHHHHHHHHTS.-EEEE....TS-EEEEESS-SSSG CS
                        HSDR_N  30 eiegrrpevrkskaevaleknlreqlgaln.ikkltkrla.lsdgnkefyellkeg.kvkfk....egrkknikLiDkknl 103
                                     e ++ +  k k+++ + ++l + l+al+ ++++ k l+   +++k+++ +lk+  + ++k     +++ + +L Dkk +
  gi|15669399|ref|NP_248209.1| 896 INELKNAYISKTKKNEYVINELINCLNALKtYEEEEKTLSkSEKAIKNMLFYLKNVeNCNIKklplTEKTLK-NLEDKKLI 975
                                   455666667788899999999*********744444444469999999999999877777444676333333.57777777 PP

                                   GGS-EEEE CS
                        HSDR_N 104 enNrfqvv 111
                                   +  +f+ +
  gi|15669399|ref|NP_248209.1| 976 KPSDFDKI 983
                                   76666655 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3       1.1   4.8e+03      85     125 ..      67     119 ..      43     170 .. 0.51
   2 !   64.9   0.5   1.9e-21   8.5e-18       4     170 ..     251     434 ..     248     435 .. 0.78
   3 ?   -3.3   4.2       1.7   7.8e+03     118     118 ..     599     599 ..     479     645 .. 0.58
   4 ?   -2.6   0.3       1.1   4.9e+03      99     113 ..     719     733 ..     659     791 .. 0.50
   5 ?   -2.0   1.1      0.69   3.1e+03      89     113 ..     852     873 ..     800     973 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                                   GEEEESSS-B--......................-SEEEEEHHHHHHTH....... CS
                        ResIII  85 igkkvsgdkkka...............kekdstnkkilvttiqsldadseeeeees 125
                                   i+k +++ k ++                +k + ++++ ++ ++ + +++    ++ 
  gi|15669399|ref|NP_248209.1|  67 INKLINEPKPEEildyikngilitldkGRKGQVSNRVKLIDYKNIEKNI---FNYA 119
                                   4444444444444444444444444443444555556666666665555...3333 PP

  == domain 2  score: 64.9 bits;  conditional E-value: 1.9e-21
                                   E-HHHHHHHHHHT...........TTSEEEEEESTTSTHHHHHHHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGG CS
                        ResIII   4 lreyQeeaienlleklks.....krdkrglikmaTGtGKTlvaaklierllkkgkee..kflflvprkslleqtleefkkf 77 
                                   +r++Q  a+++  e +++     + ++rgl+++  G+GKT+ ++ l+e +++++k++   ++++v+r++l  q  +++  +
  gi|15669399|ref|NP_248209.1| 251 PRYMQYWAVKKAYERITNylnnkDYKNRGLVWHWQGSGKTFEILYLAELFYNEFKNKdpIVFIMVDRRELETQFNDDIIAL 331
                                   677887777777777777666556666**************************99999888999***********888777 PP

                                   TGG..............GEEEESSS-B--...........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGT CS
                        ResIII  78 lseayke..........igkkvsgdkkka....kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrl 144
                                   ++ ++k+           ++++++    +    ++ ++++k ++++  +++d+++ ++  es    ++++ +i+ DEaHr+
  gi|15669399|ref|NP_248209.1| 332 QNANFKDcfkkinsveeLKGVLED----IkeseNNPNISEKGVYLVMMHKFDKNKLKDFIESFGSIDKKEILILRDEAHRT 408
                                   777776655445533332222222....2344467799*****************7777777777888888********** PP

                                   TS.TTTHHH.HHT---SEEEEEESS-S CS
                        ResIII 145 gakkswrei.lekfkeavllglTATpe 170
                                    +  ++  + ++ +k+a+ +g+T+Tp 
  gi|15669399|ref|NP_248209.1| 409 ES-GKFATLrNKILKNAIAIGFTGTPV 434
                                   **.6666663566799*********95 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.7
                                   H CS
                        ResIII 118 s 118
                                   +
  gi|15669399|ref|NP_248209.1| 599 I 599
                                   1 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1.1
                                   .....-SEEEEEHHH CS
                        ResIII  99 kdstnkkilvttiqs 113
                                   + s+ ++ ++t+ ++
  gi|15669399|ref|NP_248209.1| 719 ETSKIWESFLTKLNE 733
                                   233333333333333 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 0.69
                                   ESSS-B--.......-SEEEEEHHH CS
                        ResIII  89 vsgdkkkakekdstnkkilvttiqs 113
                                   ++ +  ++    +++ +i v+  ++
  gi|15669399|ref|NP_248209.1| 852 INPQLLEN---LKNKDEINVIVADM 873
                                   33333333...33333333333333 PP

>> DUF5448  Family of unknown function (DUF5448)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2     0.048   2.1e+02      13      75 ..     489     549 ..     480     558 .. 0.80
   2 ?   -2.3   0.1       1.1   4.9e+03      72     106 ..     576     610 ..     559     615 .. 0.78
   3 ?    9.6   0.2   0.00023         1       1      32 [.     978    1009 ..     978    1014 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.048
                       DUF5448  13 dlksaierelkrredgpkvltyrvvscitearhfkdldcallclkevvedliehvlespedre 75 
                                   ++k+ ie+     ed  k++  +    i+e+ ++ dl  +   +ke+ + + eh+le  e+ +
  gi|15669399|ref|NP_248209.1| 489 EIKNIIEKLFVDEEDADKIVVSK--KEIAEKIKLSDLLKSESSIKEASKYIAEHILEDTENFK 549
                                   57888888888888888887654..46889999999999999999999999999999887755 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                       DUF5448  72 edreyvnkctgivgvklrveevalddfdakvkeky 106
                                   + ++y ++ t +v + ++ ++v+ ++++  +++ky
  gi|15669399|ref|NP_248209.1| 576 KIKNYNENWTQVVITYIHNDDVEIENYKKEIEKKY 610
                                   45678888999999999999999999998888888 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00023
                       DUF5448    1 sdidklnehelvdlksaierelkrredgpkvl 32  
                                    sd+dk+ +  +vdlk+ai+   krr+   k++
  gi|15669399|ref|NP_248209.1|  978 SDFDKIKKFLFVDLKNAIKETEKRRKVSNKIV 1009
                                    689**********************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1018 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1932  (0.107758); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.94u 0.30s 00:00:01.24 Elapsed: 00:00:00.52
# Mc/sec: 5932.58
//
Query:       gi|15669400|ref|NP_248210.1|  [L=86]
Description: hypothetical protein MJ_1215 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-17   62.1   0.4    5.5e-17   61.8   0.4    1.1  1  NTP_transf_2    Nucleotidyltransferase domain
    1.3e-14   54.1   2.0    1.7e-14   53.6   2.0    1.3  1  Polbeta         Polymerase beta, Nucleotidyltransferase
    0.00031   20.9   0.0    0.00033   20.8   0.0    1.1  1  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
      0.016   15.4   0.1      0.026   14.7   0.1    1.4  1  SMODS           Second Messenger Oligonucleotide or Dinucleot
      0.016   15.1   0.0      0.017   15.0   0.0    1.1  1  Adenyl_cycl_N   Adenylate cyclase NT domain
      0.025   14.7   0.4       0.04   14.0   0.3    1.4  1  Baculo_FP       Baculovirus FP protein
       0.89    9.5   4.0        2.7    8.0   4.0    1.9  1  RBD-FIP         FIP domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.4   2.2e-20   5.5e-17       1      79 [.      15      86 .]      15      86 .] 0.95

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 2.2e-20
                                  HHHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEEC CS
                  NTP_transf_2  1 lkklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekl 79
                                  l+k+++elke+++v+++++fGSyarG+ +++SDiD+ v + e           +k  e ++ le +l ++vdl+t++++
  gi|15669400|ref|NP_248210.1| 15 LRKHKKELKENYKVKSIAIFGSYARGEQKETSDIDIMVEFYET-------PDYLKFFELEDYLENILNIKVDLITKNSI 86
                                  689****************************************.......4469********************99875 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   2.0   6.7e-18   1.7e-14       4      70 ..      12      84 ..       9      86 .] 0.85

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 6.7e-18
                                  TTTHHHHH.......HHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETT CS
                       Polbeta  4 keilekek.......eielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdln 70
                                  keil+k+k       +++ + +FGS+a+g+++e SDiD++v + e+ d+ + +el++ le+i l+ kvDl++ n
  gi|15669400|ref|NP_248210.1| 12 KEILRKHKkelkenyKVKSIAIFGSYARGEQKETSDIDIMVEFYETPDYLKFFELEDYLENI-LNIKVDLITKN 84
                                  555555533334444***********************************************.99*****9866 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.3e-07   0.00033       8      52 ..       9      57 ..       5      85 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.3e-07
                                  HHHHHHHHHHHHHH-TT-E...EEE-HHHHTT-.SEESSEEEEEEBTTB CS
                DNA_pol_B_palm  8 ealealvkkaakeldpeve...vivcGSYRRga.essGDvDvlitkkda 52
                                  ++++++++k+ kel+++++   + + GSY Rg+ +++ D+D+++   ++
  gi|15669400|ref|NP_248210.1|  9 SEIKEILRKHKKELKENYKvksIAIFGSYARGEqKETSDIDIMVEFYET 57
                                  46677777777777777651116799*****9725789*****986665 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1     1e-05     0.026      28      85 ..       8      58 ..       5      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                         SMODS 28 vkaitkrLnkdfrelks..kiaesllvGSyardTaikpvsdkdmlfeldvdllvvvneve 85
                                   ++i++ L+k+++elk+  k+++   +GSyar+      +++     +d+d++v++ e+ 
  gi|15669400|ref|NP_248210.1|  8 LSEIKEILRKHKKELKEnyKVKSIAIFGSYARG-----EQKE----TSDIDIMVEFYETP 58
                                  5799**********99977889999******96.....3444....67888888877665 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   6.6e-06     0.017      72     123 ..       9      59 ..       2      82 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.6e-06
                 Adenyl_cycl_N  72 kelarsaeekekkekakeaaieglylmGStgsiaqsekSDlDiWvchrsels 123
                                   +e+++  ++++k+  +++++++++   GS +   q+e+SD+Di v   ++ +
  gi|15669400|ref|NP_248210.1|   9 SEIKEILRKHKKEL-KENYKVKSIAIFGSYARGEQKETSDIDIMVEFYETPD 59 
                                   44444444444443.4689************************987665555 PP

>> Baculo_FP  Baculovirus FP protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   1.6e-05      0.04     101     137 ..       9      45 ..       5      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                     Baculo_FP 101 akyklLLkkvrkeLkptykyiwickdGvlarkseksr 137
                                   ++ k +L+k +keLk++yk  +i+  G  ar ++k+ 
  gi|15669400|ref|NP_248210.1|   9 SEIKEILRKHKKELKENYKVKSIAIFGSYARGEQKET 45 
                                   5789***************************998875 PP

>> RBD-FIP  FIP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.0    0.0011       2.7      18      27 ..      60      74 ..       7      78 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0011
                                  H.....HHHHHHHHH CS
                       RBD-FIP 18 r.....LedYiDnlL 27
                                  +     LedY++n+L
  gi|15669400|ref|NP_248210.1| 60 YlkffeLEDYLENIL 74
                                  055555********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1129  (0.0629706); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 527.72
//
Query:       gi|15669401|ref|NP_248211.1|  [L=121]
Description: hypothetical protein MJ_1216 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-25   89.1   0.9    2.3e-25   88.8   0.9    1.1  1  DUF86     Protein of unknown function DUF86
  ------ inclusion threshold ------
      0.019   14.6   1.8      0.023   14.3   1.8    1.1  1  AIPR      AIPR protein


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.9   2.6e-29   2.3e-25       1     118 [.      13     108 ..      13     109 .. 0.97

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 2.6e-29
                                   HHHHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHTTSS-HHHHHHHHH CS
                         DUF86   1 ikealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdyifeilaekgviaeepeepwrk 81 
                                   i+e+++++  ft+++++eef++++  ++av r+l+vigEa+++i+k+                      +++++p++p+++
  gi|15669401|ref|NP_248211.1|  13 ILEYMDDIINFTKNMEYEEFINNKAIKYAVVRCLEVIGEAVKKIPKD----------------------IREKYPHIPFKE 71 
                                   689********************************************......................************ PP

                                   HHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHHHH CS
                         DUF86  82 miglRNrLvHgYlgidpeivwsiikenlpdleefles 118
                                   ++g+R++L+H+Y+g+d+ +vw+++k ++p++++  e+
  gi|15669401|ref|NP_248211.1|  72 LAGMRDKLIHQYFGVDYLTVWETAKYEIPEIKKEFEK 108
                                   *******************************998776 PP

>> AIPR  AIPR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.8   2.6e-06     0.023     202     290 ..      25     116 ..       6     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-06
                          AIPR 202 kgskyekifkekltykkliasvilfkklekkikkelkegykanivyyilaalrkllkkk...ldllkiweeqkis.qelek 278
                                   k+ +ye+ +++k+  + ++  + ++ ++ kki k  +e+y  +i ++ la +r  l  +   +d+l++we++k++  e++k
  gi|15669401|ref|NP_248211.1|  25 KNMEYEEFINNKAIKYAVVRCLEVIGEAVKKIPKDIREKY-PHIPFKELAGMRDKLIHQyfgVDYLTVWETAKYEiPEIKK 104
                                   5778888888888888899999999999999999999999.6887777777777666667**************9999999 PP

                          AIPR 279 llekiaeeveds 290
                                    +eki + +e +
  gi|15669401|ref|NP_248211.1| 105 EFEKIIKDIEGK 116
                                   999998887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 764.86
//
Query:       gi|15669402|ref|NP_248212.1|  [L=98]
Description: hypothetical protein MJ_1217 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-21   75.7   2.1    3.1e-21   75.5   2.1    1.1  1  NTP_transf_2    Nucleotidyltransferase domain
    3.1e-14   52.8   3.3    4.4e-14   52.3   3.3    1.3  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0016   18.6   0.0     0.0017   18.5   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
      0.034   14.1   0.0      0.035   14.0   0.0    1.1  1  Adenyl_cycl_N   Adenylate cyclase NT domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   2.1   6.9e-25   3.1e-21       1      94 [.      11      97 ..      11      98 .] 0.97

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 6.9e-25
                                  HHHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCT CS
                  NTP_transf_2  1 lkklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpl 83
                                  l+k++++lke+++v+++++fGSyar + +++SDiD+l+ + e+        +l+kl+e +  l+ llg++vdl+t++++++p+
  gi|15669402|ref|NP_248212.1| 11 LRKHKKILKEKYKVKSIAIFGSYAREEQKETSDIDILIDYYEP-------ISLLKLIELENYLSDLLGIKVDLITKNSIHNPY 86
                                  689****************************************.......779****************************** PP

                                  EEEEEECEEEH CS
                  NTP_transf_2 84 lvksileerpl 94
                                  ++ksi+e+ ++
  gi|15669402|ref|NP_248212.1| 87 VKKSIEEDLIY 97
                                  *******9987 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   3.3   9.7e-18   4.4e-14       4      82 ..      15      93 ..       5      98 .] 0.89

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 9.7e-18
                                  TTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETT.TS-HHHHHHHHH CS
                       Polbeta  4 keilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdln.eapplllyeilk 82
                                  k+il+++ +++ + +FGS+a+++++e SDiD+ + + e  +l + +el++ l+d+ lg kvDl++ n   +p+++++i +
  gi|15669402|ref|NP_248212.1| 15 KKILKEKYKVKSIAIFGSYAREEQKETSDIDILIDYYEPISLLKLIELENYLSDL-LGIKVDLITKNsIHNPYVKKSIEE 93
                                  67888888***********************************************.9********997788999888865 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   3.9e-07    0.0017       9      50 ..       6      51 ..       2      92 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.9e-07
                                  HHHHHHHHHHHHH-TT...-EEEE-HHHHTT.-SEESSEEEEEEBT CS
                DNA_pol_B_palm  9 alealvkkaakeldpe...vevivcGSYRRg.aessGDvDvlitkk 50
                                  +++++++k+ k l+++    ++ + GSY R+ ++++ D+D+li   
  gi|15669402|ref|NP_248212.1|  6 EIKEILRKHKKILKEKykvKSIAIFGSYAREeQKETSDIDILIDYY 51
                                  5556666666666666111556899***886256799*****9765 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.9e-06     0.035      78     132 ..      11      64 ..       1      78 [. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.9e-06
                 Adenyl_cycl_N  78 aeekekkekakeaaieglylmGStgsiaqsekSDlDiWvchrselsaeelelLek 132
                                    ++++k   +++++++++   GS +   q+e+SD+Di + + + +s  +l +Le+
  gi|15669402|ref|NP_248212.1|  11 LRKHKKI-LKEKYKVKSIAIFGSYAREEQKETSDIDILIDYYEPISLLKLIELEN 64 
                                   2233332.236899***********************999888887777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 720.55
//
Query:       gi|15669403|ref|NP_248213.1|  [L=425]
Description: type I restriction-modification enzyme 1 subunit S [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-83  279.2  20.1      1e-45  156.0   5.2    2.1  2  Methylase_S  Type I restriction modification DNA specificity 
  ------ inclusion threshold ------
       0.12   11.7   0.1       0.23   10.8   0.1    1.3  1  TatD_DNase   TatD related DNase


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.4   7.0   1.7e-41   1.5e-37       1     165 [.      22     188 ..      22     191 .. 0.88
   2 !  156.0   5.2   1.1e-49     1e-45       1     168 []     220     404 ..     220     404 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 1.7e-41
                                   ETT-EEEEHHHHEEEEE-----TT.GGTTT--EEEE-HHHCCT.EE-HHHHCCTT---B-TT-EEEE-S.SSTT-EEEESS CS
                   Methylase_S   1 pedwevvkLgdvfeikkgktpkkk.elkengkypyiragilnn.kvvkdglgykkkyilpkgdilissr.atiGkvayrdk 78 
                                   pedwevv++gd++++ kgk+p    +++ +g ypy++++ l++ +++k  + + k+ i++++dil+ ++  ++G++++ +k
  gi|15669403|ref|NP_248213.1|  22 PEDWEVVRIGDFIKYIKGKKPAVMvDEELEGYYPYLSTEYLRDgIASKFVKITNKEIIVNENDILLLWDgSNAGEIFLGKK 102
                                   89********************999**************77776999999999999999**********778899999888 PP

                                   -BEE-TTEEEEEESTTT--HHHHHHHHHHCHHHHHHHCCSSTTT---HHHHCC-EEEE--HHHHHHHHHHHHHHHHHHHHH CS
                   Methylase_S  79 kyylnqsvivlipknkkkineflylylllklkklkslsvgstqpkltkenlkkikIplPpleeQkkIakiLsqldntiele 159
                                     +l++ + +l++knk+ ++ +l++ l+lk + lks+++g+++p+++k+ +++ikIplPpleeQk+IakiLs++dn+i  +
  gi|15669403|ref|NP_248213.1| 103 G-ILSSTMVKLEQKNKIMDDLYLFYSLKLKESFLKSQTKGTGIPHVDKKIFENIKIPLPPLEEQKQIAKILSDFDNLIGTI 182
                                   6.***********87655566666666677779*******************************************55555 PP

                                   HHHHHH CS
                   Methylase_S 160 kkikne 165
                                   +k+++ 
  gi|15669403|ref|NP_248213.1| 183 NKQIEV 188
                                   555554 PP

  == domain 2  score: 156.0 bits;  conditional E-value: 1.1e-49
                                   ETT-EEEEHHHHEEEEE-----TTGGTTT--E...........EEE-HH.HCCTEE-HHHHCCTT---B-TT-EEEE-S.. CS
                   Methylase_S   1 pedwevvkLgdvfeikkgktpkkkelkengky...........pyirag.ilnnkvvkdglgykkkyilpkgdilissr.. 67 
                                   pedwevvkL++v++i++gk++k++e++eng++            ++++  +l++    d+l+++++ +l++gdi+++++  
  gi|15669403|ref|NP_248213.1| 220 PEDWEVVKLKEVVDIQSGKYFKYSEFCENGVKclkidnvgfgkIFWETVsFLPE----DYLNKYPQLVLKSGDIVLALNrp 296
                                   89***********************************************9****....*********************** PP

                                   .....SSTT-EEEESS-BEE-TTEEEEEEST.TT--HHHHHHHHH..HCHHHHHHHCCSSTTT---HHHHCC-EEEE--HH CS
                   Methylase_S  68 .....atiGkvayrdkkyylnqsvivlipkn.kkkineflylyll..lklkklkslsvgstqpkltkenlkkikIplPple 140
                                        ++iG+ + +d++++l+q+v+++i+k+ k+++ +fl+++l+  +++k+l++l++g++qp+++++ l +ikIplP+le
  gi|15669403|ref|NP_248213.1| 297 iiggkIKIGILKDIDEPAILYQRVGRFIFKSeKIDK-QFLFYLLMseYFKKELSKLLIGTDQPYIRTPVLLNIKIPLPHLE 376
                                   *******************************77666.******************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Methylase_S 141 eQkkIakiLsqldntielekkikneier 168
                                   eQk +a++L+++dn+ie+++k+k++ie+
  gi|15669403|ref|NP_248213.1| 377 EQKAMAERLKSIDNLIEIKRKEKEQIEK 404
                                   **************************96 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   2.5e-05      0.23     196     243 ..     347     400 ..     341     414 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.5e-05
                                   -GGGEEE---TTSSEE.........CCCTTSE--GGGHHHHHHHHHHHHTS-HHHHH CS
                    TatD_DNase 196 pldrlLiETDaPyltp.........kpyrgkrnepanvayvveklaelkaltleela 243
                                   +l++lLi+TD Py++              +   e++++a+ ++ + +l +++ +e +
  gi|15669403|ref|NP_248213.1| 347 ELSKLLIGTDQPYIRTpvllnikipL---PHLEEQKAMAERLKSIDNLIEIKRKEKE 400
                                   689***********996777764222...4566666666666666655555544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1380  (0.0769703); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2694.58
//
Query:       gi|15669404|ref|NP_248214.1|  [L=104]
Description: hypothetical protein MJ_1219 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          2    6.6   6.7        2.4    6.3   6.7    1.0  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.7   0.00013       2.4      91     175 ..      17      95 ..       4     100 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00013
                       DUF2070  91 llsall.qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesfllllllslifalavyl 170
                                   +  +ll +++++  ++++ ++   l +  l+++ + +++ ++      ++++ + ++ y++++++l ll++s+i ++++ +
  gi|15669404|ref|NP_248214.1|  17 AGCVLLgYNYYTGNIFCG-VIGSLLLFGALWSLNGGKIWGII------SFIISASIFCYINWDFILNLLFYSIIAFIVMSI 90 
                                   222233466666666666.55555556666666666555554......6677777777789999******99999999988 PP

                       DUF2070 171 fivvv 175
                                   +i ++
  gi|15669404|ref|NP_248214.1|  91 LILIF 95 
                                   88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1166  (0.0650343); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.38s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 561.33
//
Query:       gi|15669405|ref|NP_248215.1|  [L=578]
Description: type I restriction-modification enzyme 1 subunit M [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   2.8e-112  375.0   0.5   4.4e-112  374.4   0.5    1.3  1  N6_Mtase     N-6 DNA Methylase
    2.5e-05   24.1   0.0    0.00034   20.3   0.0    2.3  2  UPF0020      Putative RNA methylase family UPF0020
    0.00036   21.2   1.4    0.00036   21.2   1.4    3.1  4  HsdM_N       HsdM N-terminal domain
     0.0025   17.9   0.5     0.0077   16.3   0.5    1.8  1  HTH_56       Cch helix turn helix domain
     0.0025   17.7   0.4      0.026   14.4   0.1    2.5  2  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0028   18.1   0.1      0.007   16.8   0.1    1.7  1  HTH_27       Winged helix DNA-binding domain
     0.0097   15.8   0.1      0.021   14.7   0.1    1.5  1  MarR         MarR family
  ------ inclusion threshold ------
      0.017   15.0   0.0       0.04   13.8   0.0    1.5  1  Gelsolin     Gelsolin repeat
      0.057   13.4   0.8       0.37   10.8   0.3    2.4  2  PadR         Transcriptional regulator PadR-like family
       0.12   11.7   3.3       0.12   11.6   1.1    2.1  2  CorA         CorA-like Mg2+ transporter protein
        2.5    8.2   9.2         66    3.7   0.2    4.1  4  Cep57_CLD_2  Centrosome localisation domain of PPC89


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  374.4   0.5  2.7e-115  4.4e-112       2     312 .]     226     542 ..     225     542 .. 0.98

  Alignments for each domain:
  == domain 1  score: 374.4 bits;  conditional E-value: 2.7e-115
                      N6_Mtase   2 skdllGdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyG 82 
                                   s d+lGd+YE++l++fa +++k+ Ge++TP evskli++l+epk++e+++DpacGsg++l+++ ++    +g++ ++ + G
  gi|15669405|ref|NP_248215.1| 226 SYDILGDAYEWTLNYFAPTKAKE-GEVYTPIEVSKLIAHLVEPKDDEVILDPACGSGSMLIEQYRF----AGSNPNIVLVG 301
                                   68********************9.*****************************************9....69********* PP

                      N6_Mtase  83 qeknettyrLakmNlllhgieykkvkirlgdtlekpkfe.......kdkkfdvvvaNppfnqkewkektlekderfrea.. 154
                                   qe n+ t+ Lak+N++lhgi+ k++k+ +gd+l +pkfe        + k+d vvaNpp+nq++++e+tl+ +e+++++  
  gi|15669405|ref|NP_248215.1| 302 QERNDVTAVLAKLNFILHGINLKDAKVFIGDSLLNPKFEsfixevkGTGKADKVVANPPWNQDGYDENTLKVNEKYKDIym 382
                                   ********************************************9999*****************************9999 PP

                      N6_Mtase 155 ..vapksnadlafllhiieslkpkGraavvlangvLfrggkegkIrkalvekdlveavialpeklFyntsiptcilvlkke 233
                                     +++k++ad+a++++i +++++  +a++vl++g+Lfrggke++Irk++v++dl+eav+ lpeklFyn+ +p++il+l+k+
  gi|15669405|ref|NP_248215.1| 383 ygFPNKNSADWAWVQLINYYTEK--KAGIVLDSGALFRGGKEKTIRKRFVDDDLIEAVVLLPEKLFYNCPAPGIILILNKN 461
                                   99*********************..9******************************************************* PP

                      N6_Mtase 234 kae.rkgkvlfidaseefkkkd..rkknklteediekildtykekskevdkfskvveleeiaendynlnvgryveteeeee 311
                                   k+e rkgk+lfi+as+e+ k++  +k nkl++e+ieki+++yke+ k+vd+f+kvv++eei++ndynlnv+ y+++ ee+e
  gi|15669405|ref|NP_248215.1| 462 KPEeRKGKILFINASNEYIKHPevKKLNKLSDENIEKIAKAYKEF-KDVDGFCKVVDIEEIRKNDYNLNVSLYISPIEEDE 541
                                   *999*****************9999********************.******************************99988 PP

                      N6_Mtase 312 d 312
                                   d
  gi|15669405|ref|NP_248215.1| 542 D 542
                                   5 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.1e-07   0.00034      21      46 ..     262     287 ..     256     327 .. 0.88
   2 ?    0.9   0.0       0.2   3.2e+02     116     132 ..     347     362 ..     338     373 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.1e-07
                                   HHHTT--TTS-EEETT-TTSHHHHHH CS
                       UPF0020  21 vrlagwkpgepllDPmCGsGtilIEa 46 
                                     l + k++e++lDP CGsG++lIE 
  gi|15669405|ref|NP_248215.1| 262 AHLVEPKDDEVILDPACGSGSMLIEQ 287
                                   567899*******************5 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.2
                                   -STTS---EEEE----- CS
                       UPF0020 116 rlkegevdvivtnpPYG 132
                                   +  +g+ d +v+npP+ 
  gi|15669405|ref|NP_248215.1| 347 K-GTGKADKVVANPPWN 362
                                   4.67899********96 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.65   1.1e+03      88     119 ..      39      69 ..      25      84 .. 0.49
   2 !   21.2   1.4   2.2e-07   0.00036       5     107 ..      91     191 ..      87     223 .. 0.64
   3 ?   -1.8   0.0       2.8   4.5e+03      56      77 ..     372     395 ..     345     414 .. 0.62
   4 ?   -2.4   0.1       4.3     7e+03     100     100 ..     508     508 ..     477     564 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.65
                                   HHHHHHCHHHHCT--STHHHHHHHS.......S CS
                        HsdM_N  88 genlnkafpaleelnkslkgvfmkd.dfnafal 119
                                    en+n+++ +l+++   l+ + + + d+ ++ +
  gi|15669405|ref|NP_248215.1|  39 YENVNEVLSKLADAG-LLEKTAK-KeDKRKKIY 69 
                                   445555555555552.2444443.423333322 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2.2e-07
                                   HHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC..............--..--------.......S-CCCSH CS
                        HsdM_N   5 lwkaadiLRgkvdaseykeyilgLlFlKrlddveeereekllee....yken...aleeleeklksk...eafyipeelrW 75 
                                   l++ ad +R    + +yk ++l +lF K ++d++  + e+l +e     + +            +++   ++   ++ + W
  gi|15669405|ref|NP_248215.1|  91 LKQGADLIR---TQVDYK-VLLLFLFFKAISDKYLLKVEELKKEfedlDE-EdiyV-----LANEEIlelYDVEGKKLYVW 161
                                   677788888...455788.99********************888554322.12331.....33333311133335668889 PP

                                   HHHHHS--HHHHHHHHHHCHHHHCT--ST....HHH CS
                        HsdM_N  76 kelakkkdddelgenlnkafpaleelnks....lkg 107
                                   +e a+++      e++ +a++++ e+nk+    l +
  gi|15669405|ref|NP_248215.1| 162 HEVANNP------EDFINALNKIVEMNKEklsgLDE 191
                                   9988854......45666666666666622223444 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.8
                                   .--------......S-CCCSHHH CS
                        HsdM_N  56 eleeklksk..eafyipeelrWke 77 
                                   +  ek+k++  ++f +++ + W++
  gi|15669405|ref|NP_248215.1| 372 KVNEKYKDIymYGFPNKNSADWAW 395
                                   233444444667788877776654 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 4.3
                                   T CS
                        HsdM_N 100 e 100
                                   +
  gi|15669405|ref|NP_248215.1| 508 D 508
                                   2 PP

>> HTH_56  Cch helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.5   4.7e-06    0.0077      56      93 ..      33      69 ..      26      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.7e-06
                        HTH_56 56 kileeagFedtkvvlkelkekGllesekdrntkkrtvk 93
                                  k+l + ++e+++ vl++l++ Glle+ ++++ k++++ 
  gi|15669405|ref|NP_248215.1| 33 KVL-KDNYENVNEVLSKLADAGLLEKTAKKEDKRKKIY 69
                                  444.55678*************************9993 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.6e-05     0.026      29      66 ..      32      73 ..      11      75 .. 0.80
   2 ?    0.1   0.0      0.45   7.4e+02      28      48 ..     537     557 ..     530     560 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                                  CCCTTSSCHCHHHHHHHHHHCTSEEEESST....TTEEEE-- CS
                          TrmB 29 aeelgvprskvYevLrsLedkGlVerekgr....pklYravd 66
                                   + l+  + +v+evL++L d+Gl e+  ++    +k+Y+  +
  gi|15669405|ref|NP_248215.1| 32 EKVLKDNYENVNEVLSKLADAGLLEKTAKKedkrKKIYKIKP 73
                                  5566777999****************9988899899999887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.45
                                   HCCCTTSSCHCHHHHHHHHHH CS
                          TrmB  28 iaeelgvprskvYevLrsLed 48 
                                   i e+ +v+   vYe L++L +
  gi|15669405|ref|NP_248215.1| 537 IEEDEDVDLGEVYEELNKLHN 557
                                   7888899999********986 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   4.3e-06     0.007      34      64 ..      41      71 ..      33      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.3e-06
                        HTH_27 34 hisyslkkLtekGLvertgdeadrrekrvrl 64
                                  ++ ++l+kL  +GL+e+t++++d+r k +++
  gi|15669405|ref|NP_248215.1| 41 NVNEVLSKLADAGLLEKTAKKEDKRKKIYKI 71
                                  4559***********************9975 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.3e-05     0.021      33      58 ..      41      66 ..      36      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                  HHHHHHHHHHHTTSEEEEEETTSTTS CS
                          MarR 33 tvtrvldrLekkGlieRskspeDrRe 58
                                  +v +vl +L ++Gl+e++ ++eD+R+
  gi|15669405|ref|NP_248215.1| 41 NVNEVLSKLADAGLLEKTAKKEDKRK 66
                                  6889*********************8 PP

>> Gelsolin  Gelsolin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.4e-05      0.04       5      64 ..     124     193 ..     122     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                                   EEEBSSSGGGEETTSEEEEEESS..........EEEEEEHTTSHHHHHHHHHHHHHHHHHCTTTTTSEEE CS
                      Gelsolin   5 pkvvklsssslesgdcyLLdngf..........tiflWiGkessqeeknfaadlaaeldseerfplpeli 64 
                                   +++ k   ++l+++d+y+L n+           ++++W    +++e    a   ++e+++e++++l eli
  gi|15669405|ref|NP_248215.1| 124 VEELKKEFEDLDEEDIYVLANEEilelydvegkKLYVWHEVANNPEDFINALNKIVEMNKEKLSGLDELI 193
                                   67778889**************************************999999999999999999888876 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00023      0.37      36      67 ..      44      73 ..      32      81 .. 0.85
   2 ?   -0.5   0.0      0.76   1.2e+03      28      44 ..     542     558 ..     534     567 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                                  HHHHHHHHTTSEEEEEE-STSSS-EEEEEESH CS
                          PadR 36 paLkrLekeglveseweesgegpprkyYrlTd 67
                                   +L++L + gl+e++ ++  e++++k+Y++ +
  gi|15669405|ref|NP_248215.1| 44 EVLSKLADAGLLEKTAKK--EDKRKKIYKIKP 73
                                  689************998..59******9965 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.76
                                   CTTHHHHHHHHHHHHHT CS
                          PadR  28 elseGslYpaLkrLeke 44 
                                   ++  G++Y  L++L +e
  gi|15669405|ref|NP_248215.1| 542 DVDLGEVYEELNKLHNE 558
                                   67789********9876 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.1   7.5e-05      0.12     105     200 ..     102     195 ..      83     230 .. 0.80
   2 ?   -1.5   0.0      0.75   1.2e+03     187     226 ..     538     577 ..     535     578 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.5e-05
                          CorA 105 pkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlr.rrlvklrralapnrevlkrllakaddk 184
                                   ++ +  ll+ ++ +i d+++  +e+l++e ++l++e      +e++ el++++ ++l  +++++++ ++ +++l +     
  gi|15669405|ref|NP_248215.1| 102 VDYKVLLLFLFFKAISDKYLLKVEELKKEFEDLDEEDIYVLANEEILELYDVEgKKLYVWHEVANNPEDFINALNK---IV 179
                                   5667789******************************9***************999***************65555...66 PP

                          CorA 185 llddedkeylrdllde 200
                                   ++++e+   l++l+ +
  gi|15669405|ref|NP_248215.1| 180 EMNKEKLSGLDELIKR 195
                                   6666664444444444 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.75
                          CorA 187 ddedkeylrdlldelerllemlealrerleslqdtyssll 226
                                   ++++   l ++++el++l+++     e++    ++++ l+
  gi|15669405|ref|NP_248215.1| 538 EEDEDVDLGEVYEELNKLHNEYLEKFEVVKGYLEEINGLI 577
                                   5566677999999999998888888888888888887765 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.2   1.9e+03      34      54 ..      29      49 ..      29      52 .. 0.88
   2 ?    3.6   0.2     0.042        69      45      61 ..     122     142 ..     111     151 .. 0.73
   3 ?    3.6   0.0     0.044        73      25      48 ..     484     507 ..     473     510 .. 0.86
   4 ?    3.7   0.2      0.04        66      40      53 ..     545     558 ..     538     562 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                   Cep57_CLD_2 34 dsalrqLgvAyeelneLkaev 54
                                  d+a++ L + ye++ne  +++
  gi|15669405|ref|NP_248215.1| 29 DMAEKVLKDNYENVNEVLSKL 49
                                  8999999********998876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.042
                   Cep57_CLD_2  45 eelneLkaevealrkE....L 61 
                                   + ++eLk e e l++E    L
  gi|15669405|ref|NP_248215.1| 122 LKVEELKKEFEDLDEEdiyvL 142
                                   6899***********966662 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.044
                   Cep57_CLD_2  25 elkrLnkERdsalrqLgvAyeeln 48 
                                   e k+Lnk+ d+ + ++  Ay e  
  gi|15669405|ref|NP_248215.1| 484 EVKKLNKLSDENIEKIAKAYKEFK 507
                                   789*****************9976 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.04
                   Cep57_CLD_2  40 LgvAyeelneLkae 53 
                                   Lg+ yeeln+L++e
  gi|15669405|ref|NP_248215.1| 545 LGEVYEELNKLHNE 558
                                   8999********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.60
# Mc/sec: 2903.19
//
Query:       gi|15669406|ref|NP_248216.1|  [L=299]
Description: hypothetical protein MJ_1221 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-18   67.5  16.7    1.5e-18   67.2  13.4    2.1  2  DUF389    Domain of unknown function (DUF389)


Domain annotation for each model (and alignments):
>> DUF389  Domain of unknown function (DUF389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.016   2.8e+02      62      88 ..     109     135 ..      77     145 .. 0.72
   2 !   67.2  13.4   8.5e-23   1.5e-18       1     140 [.     146     278 ..     146     280 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.016
                        DUF389  62 tsemlsrtepnlvdllvAlasGaagal 88 
                                    + m ++t+  ++++++A + G++g +
  gi|15669406|ref|NP_248216.1| 109 AKTMVKITKNVIIKVILASIMGVIGLI 135
                                   455666666667788877777776654 PP

  == domain 2  score: 67.2 bits;  conditional E-value: 8.5e-23
                        DUF389   1 MlisPlmgpilaiafglvigdrkllrrglknlliglllallvgflfglllplkvlgeeelptsemlsrtepn.lvdllvAl 80 
                                   M+i+Pl++ +++ a+g+v+gd++l+ +g+k++l+   ++++++f+ +l+++ k     el   + ls t  + +++ +vA+
  gi|15669406|ref|NP_248216.1| 146 MIIAPLVDTVMGSAIGTVLGDKELFIQGMKKELLCSGIVIVCAFIPSLFFVSK-----ELV-LQYLSET--SiILSAIVAI 218
                                   ***********************************************665444.....343.3444443..3699****** PP

                        DUF389  81 asGaagalallsgnssslvGvaIaaaLlPPavnaGlglalgewalalgslllllvNivgI 140
                                   ++G+ g ++++sg+   ++Gv I +++l Pa  +G++la++++ l+++ ++ll++Niv++
  gi|15669406|ref|NP_248216.1| 219 IAGISGGMSIASGKEYEIIGVTIDVSILIPALLMGMALATMDLYLIYITFILLAINIVLL 278
                                   *********************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1846.87
//
Query:       gi|15669407|ref|NP_248217.1|  [L=243]
Description: dolichol-P-glucose synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-28   97.2   0.0    1.1e-27   96.9   0.0    1.1  1  Glycos_transf_2  Glycosyl transferase family 2
    5.7e-07   29.7   0.0    7.2e-07   29.3   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00012   22.5   0.0    0.00021   21.7   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.038   14.1   0.2      0.066   13.3   0.2    1.4  1  UvrA_inter       UvrA interaction domain
       0.31   11.3   3.9         10    6.3   0.0    2.4  2  BLYB             Borrelia hemolysin accessory protein


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.0   3.1e-31   1.1e-27       2     166 ..      21     178 ..      20     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 3.1e-31
                                   EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS. CS
               Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd. 81 
                                   vv+p++Neek++ etl+ l++      + i+vvDDgS D+t ei+++      +v+v+r+  n+G++gal +g++ a    
  gi|15669407|ref|NP_248217.1|  21 VVVPAFNEEKMIGETLKNLKKE---GYKNIVVVDDGSMDKTSEIAKKE-----GVIVCRHILNRGLGGALGTGIKCALLYk 93 
                                   9********************9...8899*******************.....9**********************97777 PP

                                   ..EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCE CS
               Glycos_transf_2  82 ..yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaal 160
                                     +i+++DaD +++p+++ek+v++   +g+d+++g+r+  + e ++++  kr+   + + ++++  + ++ +++  ++ ++
  gi|15669407|ref|NP_248217.1|  94 pkIIITFDADGQHHPKDVEKVVKPVLFEGYDMAIGSRMMDKNELKNMPLVKRI--GNFGLNFITYLMGGYFVTDSQSGLRA 172
                                   77************************************************994..66666666666666666666666666 PP

                                   EEEHHH CS
               Glycos_transf_2 161 lrreal 166
                                   ++ ea+
  gi|15669407|ref|NP_248217.1| 173 FSYEAA 178
                                   666655 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0     2e-10   7.2e-07       4     136 ..      19     143 ..      16     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2e-10
               Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealr 84 
                                   + v+Vp+fnee+ +ge+l +l +  y    +vvv+d+s ++t e a+      ++v +++    ++l  +g   al  +++
  gi|15669407|ref|NP_248217.1|  19 IFVVVPAFNEEKMIGETLKNLKKEGY--KNIVVVDDGSMDKTSEIAKK-----EGV-IVC---RHILN-RGLGGALGTGIK 87 
                                   78******************999544..5678888*********9976.....333.333...34443.344555556666 PP

               Glyco_tranf_2_3  85 a...vksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfll.nrstlvsal 136
                                       +k+++++ +D+D   +P  +++++  +l+++++++ ++++++ n+ + ++ +
  gi|15669407|ref|NP_248217.1|  88 CallYKPKIIITFDADGQHHPKDVEKVVKPVLFEGYDMAIGSRMMDkNELKNMPLV 143
                                   434599*********************************99999974543444444 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   5.9e-08   0.00021       2      45 ..      27      69 ..      26     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5.9e-08
               Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkelpevkl 45
                                  ne+++++e+l+ +++ g+++i+v+d++s D+t++i k+   v +
  gi|15669407|ref|NP_248217.1| 27 NEEKMIGETLKNLKKEGYKNIVVVDDGSMDKTSEIAKKE-GVIV 69
                                  9***********************************995.3333 PP

>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   1.8e-05     0.066      13      56 ..      13      56 ..       2      67 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                    UvrA_inter 13 leegtkllilaPvvrerkgefkkllenlkkkGfvrvri.Dgeiyd 56
                                    ++ +++++ P  +e+k  + ++l+nlkk+G++++++ D+  +d
  gi|15669407|ref|NP_248217.1| 13 EINKDEIFVVVPAFNEEK-MIGETLKNLKKEGYKNIVVvDDGSMD 56
                                  45678999*********9.99*************97653544444 PP

>> BLYB  Borrelia hemolysin accessory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.1     0.013        47      69     114 ..       2      45 ..       1      49 [. 0.77
   2 ?    6.3   0.0    0.0029        10      80     110 ..     172     202 ..     166     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.013
                          BLYB  69 dilekiaklidainsDknkkiiedLkfernklikikikllkkeldk 114
                                   +i++k +  i+ in+D+   ++    f+ +k+i + +k lkke +k
  gi|15669407|ref|NP_248217.1|   2 EIMKKQNSQINEINKDEIFVVVP--AFNEEKMIGETLKNLKKEGYK 45 
                                   57888888888888887666655..588999999999999988877 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0029
                          BLYB  80 ainsDknkkiiedLkfernklikikikllkk 110
                                   a ++++ kkii dLk +r ++  + i l kk
  gi|15669407|ref|NP_248217.1| 172 AFSYEAAKKIIGDLKSDRYEVSSEFIILAKK 202
                                   67999***************99999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1532.76
//
Query:       gi|15669408|ref|NP_248218.1|  [L=92]
Description: hypothetical protein MJ_1223 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.22   11.4   0.9       0.39   10.6   0.9    1.5  1  DUF3767   Protein of unknown function (DUF3767)


Domain annotation for each model (and alignments):
>> DUF3767  Protein of unknown function (DUF3767)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.9   2.2e-05      0.39      36      75 ..      40      81 ..      15      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.2e-05
                       DUF3767 36 gavvGglrfvlkk..nvakaaNWavgafllgsivayeqCrar 75
                                   +v+G+l +v+++  n+a a   a++ f+ g ++a+ +C++ 
  gi|15669408|ref|NP_248218.1| 40 TVVAGTLIVVISQkyNLAFADTIALAIFICGVVGAFAFCKVI 81
                                  35678888888886777788899****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 638.74
//
Query:       gi|15669409|ref|NP_248219.1|  [L=139]
Description: hypothetical protein MJ_1224 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-35  121.7   6.1    2.1e-35  121.5   6.1    1.0  1  DUF61     Protein of unknown function DUF61
  ------ inclusion threshold ------
      0.049   13.3   0.1        0.1   12.3   0.0    1.6  2  NdhN      NADH-quinone oxidoreductase cyanobacterial subunit 
       0.16   11.8   0.1       0.32   10.9   0.1    1.4  1  DUF3944   Domain of unknown function (DUF3944)


Domain annotation for each model (and alignments):
>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.5   6.1   3.6e-39   2.1e-35       1     127 []      12     133 ..      12     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 3.6e-39
                                   -S---SHHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSSSE..EE CS
                         DUF61   1 drilakeiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpelgesvyl 81 
                                   ++i++  ik++n  +  +rktL+elL+eekp+++  +g++hr++++ele+lkei++e+    lk+PI+le+d++lg  +++
  gi|15669409|ref|NP_248219.1|  12 EKIIKGIIKDMNPRF--KRKTLRELLSEEKPHVI-INGKRHRIKRRELEFLKEIASED----LKIPIVLEVDSSLGG-AIK 84 
                                   5899***********..*****************.*********************99....8***********876.9** PP

                                   EES-HHHHHHHHHHT--......-SSEEEHH.HHHHHHHH-ST...TEE CS
                         DUF61  82 vrgkaevkvvskilgke...reeedelviykpevrelrrklptatqliF 127
                                   ++gk+evkv+skilgke   ++e+d ++iykpe++++r++lpt+tqliF
  gi|15669409|ref|NP_248219.1|  85 ISGKEEVKVISKILGKEidiFSEKDVMYIYKPELKIVRKELPTTTQLIF 133
                                   ********************9***************************9 PP

>> NdhN  NADH-quinone oxidoreductase cyanobacterial subunit N
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.7e-05       0.1      93     142 ..      28      77 ..       9      86 .. 0.85
   2 ?   -2.0   0.0      0.43   2.6e+03      84     102 ..     110     128 ..      91     133 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                          NdhN  93 eyqlenLppkskglvlWliegkvlskqEleylvklpkkeprlkvvvElgg 142
                                   +++l++L  ++k+ v+     + + ++Ele+l ++++++ ++ +v+E+ +
  gi|15669409|ref|NP_248219.1|  28 RKTLRELLSEEKPHVIINGKRHRIKRRELEFLKEIASEDLKIPIVLEVDS 77 
                                   4678999999****988888899************************865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.43
                          NdhN  84 evyfvpplveyqlenLppk 102
                                    +y   p+++   ++Lp++
  gi|15669409|ref|NP_248219.1| 110 VMYIYKPELKIVRKELPTT 128
                                   4566677777777777765 PP

>> DUF3944  Domain of unknown function (DUF3944)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   5.3e-05      0.32       7      19 ..      56      68 ..      54      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.3e-05
                       DUF3944  7 LeFLkklssedLe 19
                                  LeFLk+  sedL+
  gi|15669409|ref|NP_248219.1| 56 LEFLKEIASEDLK 68
                                  9***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 945.80
//
Query:       gi|15669410|ref|NP_248220.1|  [L=280]
Description: hypothetical protein MJ_1225 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-58  192.5  15.0    1.4e-13   51.0   0.3    4.1  4  CBS            CBS domain
  ------ inclusion threshold ------
      0.027   14.1   0.1      0.094   12.3   0.0    1.9  2  Peptidase_S51  Peptidase family S51
      0.052   13.6   1.4        2.8    8.0   0.2    2.9  3  Spore_Cse60    Sporulation protein Cse60
       0.18   12.5   0.0         31    5.3   0.0    2.1  2  PRCC           Mitotic checkpoint regulator, MAD2B-interactin


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.1   5.6e-17   2.5e-13       5      55 ..      10      61 ..       5      63 .. 0.89
   2 !   51.0   0.3   3.2e-17   1.4e-13       1      56 [.      86     141 ..      86     142 .. 0.97
   3 !   49.8   0.6   7.4e-17   3.3e-13       3      55 ..     152     203 ..     149     205 .. 0.95
   4 !   50.3   0.4   5.5e-17   2.5e-13       2      55 ..     226     279 ..     223     280 .] 0.94

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 5.6e-17
                                  SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHH CS
                           CBS  5 mtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllral 55
                                   ++++vtv+p+tt+++al +m e++++rlPVV  +++k+vGi+t +D+++++
  gi|15669410|ref|NP_248220.1| 10 QNKKIVTVYPTTTIRKALMTMNENKYRRLPVVnAGNNKVVGIITSMDIVDFM 61
                                  5799*****************7777*******766779**********9986 PP

  == domain 2  score: 51.0 bits;  conditional E-value: 3.2e-17
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   V++im ++v+t+++++++ ea+e++  k+v++ P+V+++++l+ ++t+rD++rall
  gi|15669410|ref|NP_248220.1|  86 VREIMEENVITLKENADIDEAIETFLTKNVGGAPIVNDENQLISLITERDVIRALL 141
                                   89**********************99**********9999**************97 PP

  == domain 3  score: 49.8 bits;  conditional E-value: 7.4e-17
                                   HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   d+ trdv++++p + l++++++m+++g++rlPVV ++g+lvGi+t +D +++l
  gi|15669410|ref|NP_248220.1| 152 DYITRDVIVATPGERLKDVARTMVRNGFRRLPVV-SEGRLVGIITSTDFIKLL 203
                                   789*******************************.9**************987 PP

  == domain 4  score: 50.3 bits;  conditional E-value: 5.5e-17
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   ++im rdv+t+++ + l++++e+m+ +++++lPVVde+ ++ Gi+t++D+l++ 
  gi|15669410|ref|NP_248220.1| 226 EEIMKRDVITAKEGDKLKKIAEIMVTNDIGALPVVDENLRIKGIITEKDVLKYF 279
                                   589*********************8888*******9888************996 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.1e-05     0.094      51     114 ..      22      87 ..      16      90 .. 0.89
   2 ?   -1.8   0.0      0.46   2.1e+03      94     101 ..     125     132 ..      95     150 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                                   HHHHHHHHTT-.EEEE--TTTS-HHHHHHHHHHSSEE.EE--S-HHHHHHHHHHTTHHHHHHHHHH CS
                 Peptidase_S51  51 kvrkaleklgl.evdeLelskdpeeeieeklleadvi.yvgGGntfrLlkllketgldkllreavq 114
                                   ++rkal +++  + + L+++++ ++++   + ++d++ ++gGG +++L+++ +e++  +++ e v+
  gi|15669410|ref|NP_248220.1|  22 TIRKALMTMNEnKYRRLPVVNAGNNKVVGIITSMDIVdFMGGGSKYNLIREKHERNFLAAINEPVR 87 
                                   6788888876669999*********************99*********************999875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.46
                                   HHHHHHHH CS
                 Peptidase_S51  94 frLlkllk 101
                                    +L++l++
  gi|15669410|ref|NP_248220.1| 125 NQLISLIT 132
                                   23444444 PP

>> Spore_Cse60  Sporulation protein Cse60
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2   0.00062       2.8       6      37 ..      69     100 ..      65     110 .. 0.87
   2 ?   -0.9   0.0      0.38   1.7e+03      13      25 ..     101     113 ..      98     129 .. 0.80
   3 ?    3.4   0.1     0.018        81      19      33 ..     137     151 ..     132     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00062
                   Spore_Cse60   6 vFDeeHEkDLekevneFLkkldddqliDikYn 37 
                                   +  e+HE++  +++ne ++++ ++++i +k n
  gi|15669410|ref|NP_248220.1|  69 LIREKHERNFLAAINEPVREIMEENVITLKEN 100
                                   66799**********************99976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.38
                   Spore_Cse60  13 kDLekevneFLkk 25 
                                    D+++++ +FL k
  gi|15669410|ref|NP_248220.1| 101 ADIDEAIETFLTK 113
                                   5889999999976 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.018
                   Spore_Cse60  19 vneFLkkldddqliD 33 
                                   +   L+k+d++++iD
  gi|15669410|ref|NP_248220.1| 137 IRALLDKIDENEVID 151
                                   66789*********9 PP

>> PRCC  Mitotic checkpoint regulator, MAD2B-interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.007        31     117     191 ..      75     148 ..      53     149 .. 0.83
   2 ?    5.3   0.0     0.007        31     126     157 ..     216     252 ..     190     255 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.007
                          PRCC 117 lrqLlGrrggnrkreeikeakiieinedeel.kaneqwlakalteekaekkgnpvrgqakrKHQltyLahqAkene 191
                                    r++l++   n+  +ei+e ++i+ +e + + +a e++l+k+    +    +n++ ++   +  ++ L+ +  ene
  gi|15669410|ref|NP_248220.1|  75 ERNFLAAI--NEPVREIMEENVITLKENADIdEAIETFLTKNVGGAPIVNDENQLISLITERDVIRALLDKIDENE 148
                                   45555555..78899*************99999*********8888887779999888888888888888888887 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.007
                          PRCC 126 g.....nrkreeikeakiieinedeelkaneqwlaka 157
                                         n + eei+++++i+ +e ++lk+ ++ + ++
  gi|15669410|ref|NP_248220.1| 216 NvreitNVRMEEIMKRDVITAKEGDKLKKIAEIMVTN 252
                                   1446779999*******************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1970.02
//
Query:       gi|15669411|ref|NP_248221.1|  [L=805]
Description: plasma membrane ATPase 1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-53  178.8   4.9    7.4e-53  178.8   4.9    2.8  4  E1-E2_ATPase     E1-E2 ATPase
    2.9e-22   80.0   0.6    8.4e-22   78.5   0.6    1.8  1  Hydrolase        haloacid dehalogenase-like hydrolase
    5.6e-17   61.2   0.0    2.1e-16   59.4   0.0    2.1  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    1.3e-05   25.1   2.9    1.3e-05   25.1   2.9    3.1  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
      0.004   17.2   0.1       0.01   15.9   0.1    1.6  1  Cation_ATPase    Cation transport ATPase (P-type)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.4       2.4   8.7e+03     118     143 ..      51      76 ..      42      90 .. 0.45
   2 !  178.8   4.9   2.1e-56   7.4e-53       6     181 .]     114     289 ..     109     289 .. 0.98
   3 ?   -3.5   0.0       1.7   6.1e+03      53      70 ..     478     495 ..     472     504 .. 0.73
   4 ?   -2.2   0.2      0.71   2.5e+03      27      41 ..     587     601 ..     585     603 .. 0.91

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHHHHHHHHHS-STTTSS CS
                  E1-E2_ATPase 118 lgkvlvpvvlliallvflialllgks 143
                                   + ++++  + +++ +++++  +++++
  gi|15669411|ref|NP_248221.1|  51 FLSYFWNPIAWMIEIAAILSAIIKHW 76 
                                   33333333333333333333333333 PP

  == domain 2  score: 178.8 bits;  conditional E-value: 2.1e-56
                                   EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEEEE CS
                  E1-E2_ATPase   6 takvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvekekgdmvfsGtvvvsgeakavV 85 
                                    a+v+rdg+++ i+akelvpGD+v ++ gd+vpaD+++v+g    vdesaLTGEslpvek+ gd ++sG++v++ge++++V
  gi|15669411|ref|NP_248221.1| 114 NARVLRDGKWQIIPAKELVPGDVVRIRIGDIVPADIILVDGDYlVVDESALTGESLPVEKKIGDIAYSGSIVKKGEMTGIV 194
                                   699****************************************************************************** PP

                                   EE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHH CS
                  E1-E2_ATPase  86 tatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLpla 166
                                    atg +t++gk ++lve+a +k ++ qk++ k+g +l++++++++++++++ l++gksl+e+  +al+l+v+aiP a+p++
  gi|15669411|ref|NP_248221.1| 195 KATGLNTYFGKTVKLVEKA-EKVSSYQKMIIKIGDYLIVLAVILIAIMVAVELFRGKSLIETAQFALVLAVSAIPAAMPAV 274
                                   *******************.9************************************************************ PP

                                   HHHHHHHHHHHHHHT CS
                  E1-E2_ATPase 167 vplalalgarrlakk 181
                                   +++++a+ga +lakk
  gi|15669411|ref|NP_248221.1| 275 LSITMAIGALNLAKK 289
                                   *************97 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.7
                                   TTTS---S-EE-G-TTEE CS
                  E1-E2_ATPase  53 saLTGEslpvekekgdmv 70 
                                    ++TG+++++ k+   m+
  gi|15669411|ref|NP_248221.1| 478 KMVTGDHVAIAKNIARML 495
                                   678999999999766665 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 0.71
                                   SEEEEETT-B--SEE CS
                  E1-E2_ATPase  27 DivllkagdrvpaDg 41 
                                   Divll +g +v +D+
  gi|15669411|ref|NP_248221.1| 587 DIVLLSPGISVIVDA 601
                                   9************97 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.6   2.4e-25   8.4e-22       2     210 .]     306     570 ..     305     570 .. 0.74

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 2.4e-25
                                   SEEEEESBTTTBCHHHHHHHHHHHH.....CHHHHHHHHHH..HHCHHHHHHHHHHHHH.......HHHHHHHHHETTTE. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx..xxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxx. RF
                     Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa.....alalaaaletg..sehpigkalvaaakar.......sgaltgfatfigrg. 67 
                                   + ++ Dk+GTLt+ + ++ ++i+ +     ++ l aal+        i  a+ ++ak++            ++ +fi +  
  gi|15669411|ref|NP_248221.1| 306 DILCSDKTGTLTKNQLVCGEIIALNgfskeDVVLFAALASReeDADAIDMAILNEAKKLglmekikN---YKIKKFIPFDp 383
                                   78999**********9999999999877777777777777788999999999999999987553331...33333333335 PP

                                   ...............HHHHTHHHHHHHH.........HCHHHHHHHHHHHHHHCHHHHHHTT..HHHHHHHHHHTHHBHTT CS
                                   ...............xxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                     Hydrolase  68 ...............ayaigkpewltal.........dippdlgaaigsaqsqgrtvallqa..ralavftiadplkvkpe 122
                                                  ++ +g p+ + +l         ++++ +++  +   ++   ++++++  +  +++ + dp  ++++
  gi|15669411|ref|NP_248221.1| 384 vikrteaevtndeefKVSKGAPQVILDLcnadeelrrKVEEIVDKLAENGYRALGVAVYKNGrwHFAGIIPLYDP--PRED 462
                                   5555566666667777777777766666444443333345555555555555555555555544888999999**..**** PP

                                   HHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT................GGGESEEEEHHCES............STTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxx............xxxxx RF
                     Hydrolase 123 aaeavasLkaagievvlltgdnpetaeraanqlG................ddyfdaviasdiet............vakps 175
                                   a  av+++k+ g+ + ++tgd+ + a+ +a+ lG                +        ++i++            +a++ 
  gi|15669411|ref|NP_248221.1| 463 APLAVKKIKELGVIIKMVTGDHVAIAKNIARMLGigdkiisisellkklkR--------GEIKEekfdeiveeadgFAEVF 535
                                   ************************************999998666655552........33333344445555999***** PP

                                   HHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 176 pegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                   pe+k ++++ Lq +++ vam GDgvnDa+al++A+
  gi|15669411|ref|NP_248221.1| 536 PEHKYKIVDSLQKRGHLVAMTGDGVNDAPALKKAD 570
                                   *********************************98 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.0   5.7e-20   2.1e-16       5      69 .]       7      70 ..       5      70 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 5.7e-20
               Cation_ATPase_N  5 sleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                   +ee+ e+++t+ ++GL+++ea++rlk yG Ne+ ++kk+  + k+l+ f+np+ ++ ++aa++s
  gi|15669411|ref|NP_248221.1|  7 NVEEIEEEYKTSIKTGLSTEEAKKRLKIYGYNEI-PEKKVHPIIKFLSYFWNPIAWMIEIAAILS 70
                                  79********************************.8888999999******************98 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.2   4.4e+03      71      94 ..      32      55 ..      25      68 .. 0.78
   2 ?   -0.2   0.1      0.19     7e+02      69     163 ..     322     427 ..     298     449 .. 0.50
   3 !   25.1   2.9   3.5e-09   1.3e-05      83     246 ..     421     593 ..     419     602 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                                  TEEEEE--B-HHHHHHHHHHHHHT CS
                   Hydrolase_3 71 gkilykstiskedvkeiikllken 94
                                   ki+  ++i++++v+ iik+l+ +
  gi|15669411|ref|NP_248221.1| 32 LKIYGYNEIPEKKVHPIIKFLSYF 55
                                  577888999999999999998765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.19
                                   TTTEEEEE--B-HHHHHHHHHHHHHTT....CEEEEEESSEEEESTT........THHHHHHHHHCHCTCEEEESHHHHHC CS
                   Hydrolase_3  69 ekgkilykstiskedvkeiikllkenn....veillytedkvyvlnk.......eksekkkkeeektkkkkeeidseeele 138
                                     g+i++ + +skedv  + +l++ ++    +++++ +e k ++l +       +k+ +    ++ t+ +++++++++  +
  gi|15669411|ref|NP_248221.1| 322 VCGEIIALNGFSKEDVVLFAALASREEdadaIDMAILNEAKKLGLMEkiknykiKKFIPFDPVIKRTEAEVTNDEEFKVSK 402
                                   556666666667666666666666555566666666665444444442232222223333333333333333333333333 PP

                                   HCSESEEE.EES-HHHHHHHHHHHHH CS
                   Hydrolase_3 139 deeiakil.ilkdkekldelekelks 163
                                   +  +  il +++ +e+l +  +e+ +
  gi|15669411|ref|NP_248221.1| 403 G-APQVILdLCNADEELRRKVEEIVD 427
                                   3.222222444444444444444433 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 3.5e-09
                                   HHHHHHHHHHHTT...CEEEEEESSEEEESTT.........THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEE.EES-H CS
                   Hydrolase_3  83 dvkeiikllkenn...veillytedkvyvlnk........eksekkkkeeektkkkkeeidseeeledeeiakil.ilkdk 151
                                   +v+ei++ l en+   + +++y++ ++             e     +k++++     + ++ ++    ++ia +l i ++ 
  gi|15669411|ref|NP_248221.1| 421 KVEEIVDKLAENGyraLGVAVYKNGRWHFAGIiplydpprEDAPLAVKKIKELGVIIKMVTGDHVAIAKNIARMLgIGDKI 501
                                   577777777777777777777777777776667777776655555555666666666666667777777888888888888 PP

                                   HHHHHHHHHHHHHCTTTE...EEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEET CS
                   Hydrolase_3 152 ekldelekelksklnkll...titssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmg 229
                                    +++el k+lk+   k+    +i++  +g+ e+ p++  K++ +  l+         v+  GDg ND + L++a+ g+A+ 
  gi|15669411|ref|NP_248221.1| 502 ISISELLKKLKRGEIKEEkfdEIVEEADGFAEVFPEH--KYKIVDSLQ----KRGHLVAMTGDGVNDAPALKKADCGIAVS 576
                                   8888888887776655556678999999999999986..555555555....566679999******************** PP

                                   TS-HHHHHHSSEEE--G CS
                   Hydrolase_3 230 naseevkkaAdyvtksn 246
                                   na++ + +aAd v  s 
  gi|15669411|ref|NP_248221.1| 577 NATDAARAAADIVLLSP 593
                                   ************98775 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.8e-06      0.01      22      89 ..     351     413 ..     341     414 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.8e-06
                 Cation_ATPase  22 nktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilkrCt 89 
                                   ++ + A+l+ a+kl    +e  +++k+ + ipF+ + Kr    ++++   +   + KGAp++il+ C+
  gi|15669411|ref|NP_248221.1| 351 DAIDMAILNEAKKL--GLMEKIKNYKIKKFIPFDPVIKRTEAEVTND---EEFKVSKGAPQVILDLCN 413
                                   67899999999999..67888899****************9999964...666789***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (805 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1247  (0.0695521); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 4755.65
//
Query:       gi|15669412|ref|NP_248222.1|  [L=240]
Description: pyruvate formate-lyase activating enzyme [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-23   82.6   4.9    4.8e-23   82.4   3.1    1.8  2  Radical_SAM   Radical SAM superfamily
      7e-14   52.3   0.6    1.3e-13   51.4   0.2    1.7  1  Fer4_12       4Fe-4S single cluster domain
    4.8e-09   36.4   0.7    1.7e-08   34.6   0.1    2.0  2  Fer4_14       4Fe-4S single cluster domain
     0.0082   15.6   0.7        2.1    7.7   0.0    2.1  2  ComA          (2R)-phospho-3-sulfolactate synthase (ComA)
  ------ inclusion threshold ------
       0.02   15.1   0.2       0.12   12.6   0.0    2.3  2  Glutaredoxin  Glutaredoxin
      0.025   14.8   0.0      0.071   13.3   0.0    1.8  1  UPF0180       Uncharacterised protein family (UPF0180)
      0.082   12.9   0.0       0.18   11.9   0.0    1.5  1  B12-binding   B12 binding domain
       0.61    9.9   4.0       0.91    9.4   0.5    2.3  2  PADR1         PADR1 (NUC008) domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   3.1   2.2e-26   4.8e-23       1     164 [.      23     180 ..      23     183 .. 0.87
   2 ?    5.3   0.3     0.011        24      80     148 ..     158     232 ..     143     236 .. 0.65

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 2.2e-26
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgirit 81 
                                   v+++ gCn++C++C++ +   + ++ r ++veei + ++ l     ++ ++++ggep+l++d v +++r+ak+  +g+ + 
  gi|15669412|ref|NP_248222.1|  23 VIFLYGCNMKCPYCHNLKF--MLEHKRGMTVEEIFNDIDFLF----ADAIVISGGEPTLQKDAVIEIARYAKE--KGFPVK 95 
                                   57899************98..********************7....99*************************..7***** PP

                                   EEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHH...HHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                   xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  82 vetngtlpdeeklerllelg.vdrvslgleaaddekvlklmn.rghtf...eevlealeklreagikrvvdrivglpGend 157
                                   + tngt+  +e++e+l +   +d+v+++++   d+ +++ ++ r ++     ++l+ +++++++++  v  r++ +p + d
  gi|15669412|ref|NP_248222.1|  96 IDTNGTH--PEVIEELIKNKlIDYVAIDVKCRFDK-YKEFVKcREDGEeikNKILKIIDLCKKNNVF-VECRTTFVPKVMD 172
                                   *******..6********99***************.******8755554456677777777777777.7777777777776 PP

                                   .HHHHHHH CS
                                   .xxxxxxx RF
                   Radical_SAM 158 .eeleell 164
                                    e++e+++
  gi|15669412|ref|NP_248222.1| 173 eEDIEDIA 180
                                   36666665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.011
                                   EEEEECSSCHG....HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSETEEEE CS
                                   xxxxxxxxxxx....xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  80 itvetngtlpd....eeklerllelg..vdrvslgleaaddekvlklmn..rghtfeevlealeklreagikrvvdr 148
                                   ++ve+  t +     ee +e +++    +d +++    + d  + + ++  +++   e+ e+ ++++++ i++vv+r
  gi|15669412|ref|NP_248222.1| 158 VFVECRTTFVPkvmdEEDIEDIAKTVkdCDLYAIQQFEPKDA-YDEEFKklPMPKENELRELGKIAKKY-IDNVVIR 232
                                   333333333333334899999999889999999999999999.99999986666666666666655555.9876665 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.2   5.6e-17   1.3e-13       8     123 ..      22     130 ..      16     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 5.6e-17
                       Fer4_12   8 lslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdi 88 
                                   +++f+ gCn++C++C+n +     +++ +t    eei++d++    + ++++GGEP l  +++a++e++++ ke+++ ++ 
  gi|15669412|ref|NP_248222.1|  22 AVIFLYGCNMKCPYCHNLKFMLE-HKRGMT---VEEIFNDIDFLFADAIVISGGEPTL--QKDAVIEIARYAKEKGF-PVK 95 
                                   689*************9776533.223333...4566666666699************..*****************.899 PP

                       Fer4_12  89 wlytgytleelskkekeellkeidvlvdGkfeesl 123
                                   + ++g+  e +++  k++l++++ + v+ +f++ +
  gi|15669412|ref|NP_248222.1|  96 IDTNGTHPEVIEELIKNKLIDYVAIDVKCRFDKYK 130
                                   ******99999876777777776655555555444 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.1   7.5e-12   1.7e-08       3      96 ..      26     107 ..      23     125 .. 0.76
   2 ?   -0.5   0.1      0.59   1.3e+03      66     112 ..     145     187 ..     139     192 .. 0.63

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 7.5e-12
                       Fer4_14   3 vrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekki 83 
                                   +   gCn++C+ C n + ++ e +   t e++ + +    +  + ++ +v++GGeP    +k++++++ ++ ke++  +++
  gi|15669412|ref|NP_248222.1|  26 L--YGCNMKCPYCHNLK-FMLEHKRGMTVEEIFNDI----DFLF-ADAIVISGGEPT--LQKDAVIEIARYAKEKG--FPV 94 
                                   4..89**********99.777777766666554444....4444.5669*******9..78***************..*** PP

                       Fer4_14  84 wletngtleiele 96 
                                   ++ tngt    +e
  gi|15669412|ref|NP_248222.1|  95 KIDTNGTHPEVIE 107
                                   ******9874444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.59
                       Fer4_14  66 ellklvkrlkeeypekkiwletngtleielektpdlkeklealskid 112
                                   ++lk+++  k++   + + + t  + +  +++ +d +++ ++++  d
  gi|15669412|ref|NP_248222.1| 145 KILKIIDLCKKNN--VFVECRTTFVPK--VMDEEDIEDIAKTVKDCD 187
                                   5666777666666..666666665555..444577777777777554 PP

>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00094       2.1      83     152 ..      50     119 ..      39     128 .. 0.83
   2 !    7.7   0.3   0.00096       2.2      51     137 ..     107     203 ..      98     231 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00094
                                   -HHHHHHHHHHCT-SEEEE--SSS---HHHHHHHHHHHCCTTSEEEEEES-SSHHHHTT--CCHHHHHHH CS
                          ComA  83 kvdeyleeckelgfdviEvsdgtlelpeeeklrliekakkeglkvlpevgkkdgelesesdveklieeak 152
                                    v+e +++++ l  d+i +s g  +l+++  +++ + ak++g+ v+  +   ++e  +e+  +kli+ ++
  gi|15669412|ref|NP_248222.1|  50 TVEEIFNDIDFLFADAIVISGGEPTLQKDAVIEIARYAKEKGFPVKIDTNGTHPEVIEELIKNKLIDYVA 119
                                   78889999999999********************************999888887777777777776665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00096
                                   CHHHHHHHHHHHCTT-EEEE-HHHHHHHHHTT.......-HHHHHHHHHHCT-SEEEE--SSS-..--HHHHHHHHHHHCC CS
                          ComA  51 eeilrekielahehgvyvstGgtlfEaalaqg.......kvdeyleeckelgfdviEvsdgtle..lpeeeklrliekakk 122
                                   ee++++k+  +   +v++ ++  + E +  ++       k+ + ++ ck+ ++  +E+ ++++   ++ee+  ++ +++k+
  gi|15669412|ref|NP_248222.1| 107 EELIKNKLIDYVAIDVKCRFDK-YKEFVKCREdgeeiknKILKIIDLCKKNNV-FVECRTTFVPkvMDEEDIEDIAKTVKD 185
                                   5566666666666666666666.666665555566666677788888888765.788888888777888888888888888 PP

                                   TTSEEEEEES-SSH...H CS
                          ComA 123 eglkvlpevgkkdg...e 137
                                    +l ++ ++  kd+   e
  gi|15669412|ref|NP_248222.1| 186 CDLYAIQQFEPKDAydeE 203
                                   888888888888884430 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.3e-05      0.12       7      29 ..      31      54 ..      23      74 .. 0.79
   2 ?   -0.7   0.0      0.76   1.7e+03      17      31 ..     108     122 ..      83     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                                  TSSHHHHHHHHHH.HHTTGGEEEE CS
                  Glutaredoxin  7 ptCpyCkkakrlL.kelgvkfeei 29
                                    CpyC++ k  L +++g+ +eei
  gi|15669412|ref|NP_248222.1| 31 MKCPYCHNLKFMLeHKRGMTVEEI 54
                                  57***********77777999887 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.76
                                   HHHHHTTGGEEEEEG CS
                  Glutaredoxin  17 rlLkelgvkfeeidv 31 
                                   +l k++ +++  idv
  gi|15669412|ref|NP_248222.1| 108 ELIKNKLIDYVAIDV 122
                                   455666677888877 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.2e-05     0.071      17      77 .]      45     113 ..      37     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                       UPF0180  17 rekGYeVvdleteedaqsvdaiVvtG.....qdtnvmgied..tetkapv.InAsgktaeeIlqeveer 77 
                                   +++G +V+++ ++ d   +daiV++G     q+  v++i    +e + pv I+ +g  +e I++ ++++
  gi|15669412|ref|NP_248222.1|  45 HKRGMTVEEIFNDIDFLFADAIVISGgeptlQKDAVIEIARyaKEKGFPVkIDTNGTHPEVIEELIKNK 113
                                   589*********999***********8999877777777777578889999**************9996 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.9e-05      0.18      41     109 ..      52     119 ..      26     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.9e-05
                   B12-binding  41 edivaairaekpdvvglSal.ltsqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvv 109
                                   e+i + i  + +d++++S   +t q +av e+++ +k+++  vk+ + G+hp++ +e++ +    id+v 
  gi|15669412|ref|NP_248222.1|  52 EEIFNDIDFLFADAIVISGGePTLQKDAVIEIARYAKEKGFPVKIDTNGTHPEVIEELIKN--KLIDYVA 119
                                   89999999999*******9889999999******************************554..6668865 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.5   0.00041      0.91       8      28 ..      25      45 ..      21      49 .. 0.85
   2 ?    1.2   0.2      0.15   3.3e+02      37      51 ..     129     143 ..     121     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00041
                         PADR1  8 mlfGalekCpeCkegqlvfds 28
                                   l+G+  kCp C++ ++ +++
  gi|15669412|ref|NP_248222.1| 25 FLYGCNMKCPYCHNLKFMLEH 45
                                  589**********99988766 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
                         PADR1  37 msewtkCtfktkdpk 51 
                                   ++e++kC    +++k
  gi|15669412|ref|NP_248222.1| 129 YKEFVKCREDGEEIK 143
                                   679****99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1478.20
//
Query:       gi|15669413|ref|NP_248223.1|  [L=132]
Description: translation initiation factor IF-5A [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-08   32.0   0.4      5e-06   26.5   0.1    2.2  2  EFP_N     Elongation factor P (EF-P) KOW-like domain
    2.4e-07   30.7   0.2    7.6e-07   29.1   0.2    1.8  1  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi
  ------ inclusion threshold ------
      0.053   13.6   0.0      0.094   12.8   0.0    1.4  1  EFP       Elongation factor P (EF-P) OB domain


Domain annotation for each model (and alignments):
>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   8.4e-10     5e-06       3      32 ..      10      39 ..       8      45 .. 0.88
   2 !    3.8   0.0    0.0097        58       6      24 ..      74      92 ..      70      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 8.4e-10
                                  GG--TT-EEEETTEEEEEEEEEEEEETTS- CS
                         EFP_N  3 selkkGlvieidgklyvVlefehvkpGkGq 32
                                   +lk G+ ++idg ++ ++++  +kpGk +
  gi|15669413|ref|NP_248223.1| 10 GSLKVGQYVMIDGVPCEIVDISVSKPGKHG 39
                                  689************************865 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0097
                                  -TT-EEEETTEEEEEEEEE CS
                         EFP_N  6 kkGlvieidgklyvVlefe 24
                                  +kG+v+ i g+ +++++ +
  gi|15669413|ref|NP_248223.1| 74 RKGQVLAIMGDMVQIMDLQ 92
                                  9**************9976 PP

>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.2   1.3e-10   7.6e-07       1      67 [.      70     127 ..      70     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.3e-10
                                   --EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG..GB-HHHHTT--TT-E..EEEEEETTEEEEEE CS
                        eIF-5a   1 nVkrkeyqLidIqdDgflsLmd.ddgetkeDlklpegelgkqikekfeegkdvlVtVlsamGeekiia 67 
                                   +++r++ q+++I++D ++++md +++et e l++peg       e +e+g +  V++++a+G+ ki +
  gi|15669413|ref|NP_248223.1|  70 IIDRRKGQVLAIMGD-MVQIMDlQTYETLE-LPIPEG------IEGLEPGGE--VEYIEAVGQYKITR 127
                                   599************.************99.888843......46789****..**********9986 PP

>> EFP  Elongation factor P (EF-P) OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.6e-05     0.094       8      27 ..      81     100 ..      74     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                                   EETTEEEEEETTT--EEEEE CS
                           EFP   8 kdgdeyvFMdnetYeqielp 27 
                                     gd++  Md +tYe +elp
  gi|15669413|ref|NP_248223.1|  81 IMGDMVQIMDLQTYETLELP 100
                                   679***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1067.08
//
Query:       gi|15669414|ref|NP_248224.1|  [L=501]
Description: pyruvate carboxylase subunit A [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-83  277.8   0.7    8.6e-83  277.0   0.7    1.4  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.2e-47  161.0   0.2    3.1e-47  159.7   0.2    1.7  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    1.2e-43  147.6   0.0    2.4e-43  146.6   0.0    1.6  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    4.4e-15   55.8   0.0    1.1e-14   54.4   0.0    1.7  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    2.2e-09   37.2   0.4    2.5e-08   33.7   0.4    2.2  1  RimK             RimK-like ATP-grasp domain
      1e-06   28.7   0.1    2.5e-06   27.4   0.1    1.6  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
      8e-06   26.0   0.1    1.5e-05   25.1   0.1    1.5  1  ATP-grasp_3      ATP-grasp domain
    1.5e-05   24.6   0.4      3e-05   23.6   0.1    1.7  2  ATP-grasp        ATP-grasp domain
    0.00063   19.5   0.0     0.0016   18.2   0.0    1.7  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
     0.0014   18.1   0.1      0.087   12.2   0.0    3.2  3  AP_endonuc_2     Xylose isomerase-like TIM barrel
     0.0031   17.0   0.1     0.0087   15.5   0.0    1.7  2  ATP-grasp_5      ATP-grasp domain
  ------ inclusion threshold ------
      0.015   14.1   0.2        0.4    9.4   0.0    2.2  2  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
       0.14   12.4   0.2       0.36   11.1   0.0    1.7  2  baeRF_family3    Bacterial archaeo-eukaryotic release factor 


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.0   0.7   6.3e-86   8.6e-83       2     209 ..     116     321 ..     115     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: 277.0 bits;  conditional E-value: 6.3e-86
                                   HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS- CS
                   CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkq 82 
                                   k +ak+++kk++vp++p+s++++e+++ea++ia+ ig+Pv++ka++g+GG Gm va+++eel+e++++a++ ak+afg+++
  gi|15669414|ref|NP_248224.1| 116 KINAKKIMKKAGVPLIPGSEGAIEDIDEAIEIAEAIGFPVVVKASAGGGGMGMSVAYSKEELKEVIESARNIAKSAFGDPT 196
                                   7789***************************************************************************** PP

                                   EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEE CS
                   CPSase_L_D2  83 vlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtvefl 163
                                   v++ek+l++p++iE+++l D++gn+i++++re+s+q+r+qk+ie+APs+ +t+e r++++eaa+k+ +++++ +agtvefl
  gi|15669414|ref|NP_248224.1| 197 VFIEKYLENPRHIEIQLLGDKHGNIIHLGDRECSIQRRHQKLIEEAPSPIMTEELRERMGEAAIKAGKAINYDSAGTVEFL 277
                                   ********************************************************************************* PP

                                   EETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                   CPSase_L_D2 164 ldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                   ++  ++++y++E+NtR++ve++++e++TG+dlvk+++kia+ge+L 
  gi|15669414|ref|NP_248224.1| 278 YE--NGNFYFLEMNTRIQVEHTVTEQVTGIDLVKAMIKIAAGEELT 321
                                   **..5**************************************997 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.7   0.2   2.3e-50   3.1e-47       1     110 []       1     110 [.       1     110 [. 0.99

  Alignments for each domain:
  == domain 1  score: 159.7 bits;  conditional E-value: 2.3e-50
                                   ---EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SEEE-- CS
                 Biotin_carb_N   1 kikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgadavhpG 81 
                                   +++kvlianrGeiA+riira+ elgi+tvavyse+d++slh+++adea+++gpa+a++sYlni++i+++a+++++da+hpG
  gi|15669414|ref|NP_248224.1|   1 MFNKVLIANRGEIAIRIIRACWELGIKTVAVYSEADKRSLHATLADEAYCIGPAPAAKSYLNIDAILNVAEKAKVDAIHPG 81 
                                   799****************************************************************************** PP

                                   SSTTTT-HHHHHHHHHTT-EESSS-HHHH CS
                 Biotin_carb_N  82 yGflsEnaefaeaveeagivfiGPsaeal 110
                                   yGfl+Enaefa+av++ag+ fiGP+++a+
  gi|15669414|ref|NP_248224.1|  82 YGFLAENAEFARAVKKAGFEFIGPNPDAI 110
                                   *************************9986 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.6   0.0   1.7e-46   2.4e-43       1     108 []     335     442 ..     335     442 .. 0.99

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 1.7e-46
                                   EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EEESS- CS
                 Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelrieGvk 81 
                                   e+RinaEdp ++f p +Gk++ ++ p+gpgvR+dsgv+ g+e++pyyDs++aKli++g++reea+ar++raL+e++i Gvk
  gi|15669414|ref|NP_248224.1| 335 ECRINAEDPLNDFVPCPGKIKLYRSPGGPGVRIDSGVYGGAEIPPYYDSMIAKLITYGNSREEAIARMKRALREYVIIGVK 415
                                   8******************************************************************************** PP

                                   BSHHHHHHHHH-HHHHHT---TTTCCC CS
                 Biotin_carb_C  82 tnieflrailedeefakgeldtkflee 108
                                   tni+f+ra+le+e+f kg+++t+++e+
  gi|15669414|ref|NP_248224.1| 416 TNIPFHRAVLEEENFLKGNISTHYVEQ 442
                                   ************************985 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   8.2e-18   1.1e-14      28     174 ..     144     290 ..     122     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 8.2e-18
                                   HHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT......-SCEEEEE--.ESEEEEEEEEETSSCEEEEE CS
               Dala_Dala_lig_C  28 lekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky......dekvlvEeai.egreievavlgneklevsev 101
                                     ++ e++g+pv+VK++  G  +G+s + s+eelke ie+a +       d +v++E+++ + r ie+ +lg+ + ++ ++
  gi|15669414|ref|NP_248224.1| 144 AIEIAEAIGFPVVVKASAGGGGMGMSVAYSKEELKEVIESARNIaksafgDPTVFIEKYLeNPRHIEIQLLGDKHGNIIHL 224
                                   347999*********************************99875444455899*******999*********999***999 PP

                                   EEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
               Dala_Dala_lig_C 102 geivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                   g++  +  + + ++k ++ +a       +++e +e++ e+a+ka ka++    + v f+++ +g++++ E+Nt
  gi|15669414|ref|NP_248224.1| 225 GDRECS--IQRRHQKLIE-EAPS---PIMTEELRERMGEAAIKAGKAINYDSAGTVEFLYE-NGNFYFLEMNT 290
                                   998765..5577788863.3322...235789999**********************9987.9*********9 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.4   1.8e-11   2.5e-08      23     186 ..     137     313 ..     114     315 .. 0.69

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.8e-11
                                   EESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH....GGG--........EEEEE--SS-SEEEE CS
                          RimK  23 lardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea....lkeai........lvqeyieeaenediR 91 
                                    ++d ++a ++ e   ++fPvvvK + g  G+++ +a  +++lk+v+e+                 ++ +y+e+   + i 
  gi|15669414|ref|NP_248224.1| 137 AIEDIDEAIEIAEA--IGFPVVVKASAGGGGMGMSVAYSKEELKEVIESarniA---KsafgdptvFIEKYLENP--RHIE 210
                                   33444444444455..58*****************************9965542...133465555778887655..6666 PP

                                   EEEETTEEEEEEEEE--SSS----TTTT..-EEEE-...---HHHHHHHHHHHHHCT-SEEE.EEEEEETTEEEEEEEESS CS
                          RimK  92 vlvvddevvaalrrvskeGdFRsnlhrG..gvaekl...qlseeekelAikaakamelvvaG.vDllrakrgllvlEvnss 166
                                   +  ++d+    ++   +e       ++    + +++   +l e   e Aika ka++ + aG v+ l ++ ++++lE+n+ 
  gi|15669414|ref|NP_248224.1| 211 IQLLGDKHGNIIHLGDRECSIQRRHQKLieEAPSPImteELRERMGEAAIKAGKAINYDSAGtVEFLYENGNFYFLEMNTR 291
                                   677788888888888888776544444300222332111345555689*************9677***************9 PP

                                   --SHH..HHHHHT--HHHHHHH CS
                          RimK 167 pglek..iektlgidiakklie 186
                                    ++e+   e+ +gid+ k +i+
  gi|15669414|ref|NP_248224.1| 292 IQVEHtvTEQVTGIDLVKAMIK 313
                                   99876226899*****999997 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   1.8e-09   2.5e-06       1      91 [.     114     205 ..     114     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.8e-09
                                   HBHHHHHHHHHHTT--B-..-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHH..CTS-TTC CS
                        GARS_A   1 asKsfakdllkkagipta..eyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkei..lekkkfG 77 
                                   +sK  ak+++kkag+p    +  a++d +ea e+ e+ ++++ VvKa+   +g g++va s+ee  +++++   + k +fG
  gi|15669414|ref|NP_248224.1| 114 GSKINAKKIMKKAGVPLIpgSEGAIEDIDEAIEIAEAIGFPV-VVKASAGGGGMGMSVAYSKEELKEVIESArnIAKSAFG 193
                                   68999**********9754566789*****************.****************9999888888765335568888 PP

                                   CCCSSEEEEE---S CS
                        GARS_A  78 eagekvviEelleG 91 
                                       +v iE++le 
  gi|15669414|ref|NP_248224.1| 194 --DPTVFIEKYLEN 205
                                   ..899******984 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   1.1e-08   1.5e-05       4     159 ..     116     293 ..     113     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.1e-08
                                   HHHHHHHHTTT.S-.--............-EESS--SSSEEEEESS-------B--SS--TTE.................. CS
                   ATP-grasp_3   4 KlktykkLkeagvk.vP........tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve........... 64 
                                   K++  k +k+agv+ +P             e +e    ++vvK + G+gg +++v+  kee+++ ie+             
  gi|15669414|ref|NP_248224.1| 116 KINAKKIMKKAGVPlIPgsegaiedIDEAIEIAEAIGFPVVVKASAGGGGMGMSVAYSKEELKEVIESARniaksafgdpt 196
                                   666666666666663357555543222233445555999****************************99899********* PP

                                   .EEEE---S.EEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H.HHHHHHHHHHHHTTSTT--EEEEEEE CS
                   ATP-grasp_3  65 .lvqefieG.kplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietel.keevvelaeevvekleglaGyvGvDl 142
                                     + +++e  +++ ++ll+d++ + +    r+   +++++       +pi te+ +e++ e+a ++ +++ +  +   v++
  gi|15669414|ref|NP_248224.1| 197 vFIEKYLENpRHIEIQLLGDKHGNIIHLGDRECSIQRRHQKLIEEAPSPIMTEElRERMGEAAIKAGKAI-NYDSAGTVEF 276
                                   989999986489********99998888888887777888899999999999988***************.8999989*** PP

                                   EESS.SEEEEEEESS-- CS
                   ATP-grasp_3 143 vlkdeepyviEvNPRlt 159
                                   ++++++ y++E N R++
  gi|15669414|ref|NP_248224.1| 277 LYENGNFYFLEMNTRIQ 293
                                   ***************98 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   2.2e-08     3e-05      13     159 ..     137     291 ..     123     297 .. 0.79
   2 ?   -3.7   0.0       5.5   7.5e+03     108     144 ..     434     470 ..     425     478 .. 0.55

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.2e-08
                                   EECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEEEEE CS
                     ATP-grasp  13 aveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlvvrs 85 
                                   a+e+ +e+ e+ae++g+pvvvK +  g  G G sv  s+e+l++++e +        ++ +v +E++ +  + + +    +
  gi|15669414|ref|NP_248224.1| 137 AIEDIDEAIEIAEAIGFPVVVK-ASAGGGGMGMSVAYSKEELKEVIESArniaksafGDPTVFIEKYLENPRHIEIQLLGD 216
                                   689999****************.677779******************99999999999999*******9999888888889 PP

                                   TTC-EEE-.-EEEEEEETTEEEEEEECEE-.SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS CS
                     ATP-grasp  86 aeGetafy.pvvetvqedgilrlsvapaev.sekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapR 159
                                   ++G++  + +    +q++    +  ap+++ +e+  ++  e a k+ +++++    +vE+ +  +g+ ++ E+  R
  gi|15669414|ref|NP_248224.1| 217 KHGNIIHLgDRECSIQRRHQKLIEEAPSPImTEELRERMGEAAIKAGKAINYDSAGTVEFLYE-NGNFYFLEMNTR 291
                                   999865551444566666666666666665145566777788888888888888888886555.787777777666 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.5
                                   EEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEE CS
                     ATP-grasp 108 svapaevsekaqkkaeeiakkiveeLggvGvfavElF 144
                                   ++  + v+++ +k  e+++k ++e+ + + v++  +F
  gi|15669414|ref|NP_248224.1| 434 NISTHYVEQNMHKLREKMVKYALESRDLYSVVSEKVF 470
                                   4555555555555555555555555555555555555 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.1e-06    0.0016      42     119 ..     248     325 ..     195     337 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.1e-06
                  ATPgrasp_Ter  42 elekdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgys.alaGvnlpylalklllgleteeveep 119
                                   + e +e++ e+a +  ++++ d    v + +++++ + LE+N+R++    ++  ++G++l+++++k + g+ + + ++ 
  gi|15669414|ref|NP_248224.1| 248 TEELRERMGEAAIKAGKAINYDSAGTVEFLYENGNFYFLEMNTRIQVEHTVTeQVTGIDLVKAMIKIAAGE-ELTLKQE 325
                                   5566788999************************************9776662578**************5.3333333 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.019        26      74     178 ..      16     125 ..       9     131 .. 0.68
   2 !   12.2   0.0   6.3e-05     0.087       3      94 ..      94     184 ..      78     289 .. 0.64
   3 ?    0.5   0.0      0.24   3.4e+02      16      42 ..     379     411 ..     369     451 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.019
                                   HHHHHHHHHTBSEEEEEBCC.....GBCTTTSGHH.....HHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHH CS
                  AP_endonuc_2  74 raielaaaLGapllvlhpGt.....agagpkgsee.....eawerlaeslneladyaekegvklalEtlagsgvelgdeel 144
                                   r i+++ +LG++++ + +       +  ++++  +     +  ++ + ++++++ +aek+ v  a++++ g+ +e+  +e+
  gi|15669414|ref|NP_248224.1|  16 RIIRACWELGIKTVAVYSEAdkrslHATLADE--AycigpAPAAKSYLNIDAILNVAEKAKVD-AIHPGYGFLAEN--AEF 91 
                                   66667777777777777554444332222222..13333334444555899999999999988.678888888655..59* PP

                                   HHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHH CS
                  AP_endonuc_2 145 arlldavdspnvgvclDtgHlliaeedvddalra 178
                                   ar +++ + +++g + D   ++  + +  +++++
  gi|15669414|ref|NP_248224.1|  92 ARAVKKAGFEFIGPNPDAIEAMGSKINAKKIMKK 125
                                   *************999998888877777776665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.3e-05
                                   HHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS...HHHHHHHHHHHHHHHH CS
                  AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear...reesvdalkraielaa 80 
                                   a+++aGf+++  +++    + ++        +k+++++g+                         +e +++++ +aie+a+
  gi|15669414|ref|NP_248224.1|  94 AVKKAGFEFIGPNPDAIEAMGSK-----INAKKIMKKAGVP--------------------LipgSEGAIEDIDEAIEIAE 149
                                   34444444444444444444432.....4445555555554....................03334446************ PP

                                   HHTBSEEEEEBCC.....................G CS
                  AP_endonuc_2  81 aLGapllvlhpGt.....................a 94 
                                   a+G p++v  + +                     a
  gi|15669414|ref|NP_248224.1| 150 AIGFPVVVKASAGgggmgmsvayskeelkeviesA 184
                                   *******9887744444443333333333333330 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.24
                                   CCTCSHHHHC......HHHHHHHHHHHHHHTTS CS
                  AP_endonuc_2  16 grdlvpvsel......sdeelrelrkaldelgl 42 
                                   ++++  ++ l       +e+++++++al+e+ +
  gi|15669414|ref|NP_248224.1| 379 PYYDSMIAKLitygnsREEAIARMKRALREYVI 411
                                   555555544455555555555555555555533 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.3e-06    0.0087      13      54 ..     117     160 ..     111     165 .. 0.90
   2 ?   -3.0   0.0       2.9     4e+03     148     169 ..     446     467 ..     412     494 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.3e-06
                   ATP-grasp_5  13 aeakelleaygipvvetrl..assaeeaveaaeeigypvvlKiv 54 
                                    +ak++++  g+p+++     +++ +ea+e+ae+ig+pvv+K  
  gi|15669414|ref|NP_248224.1| 117 INAKKIMKKAGVPLIPGSEgaIEDIDEAIEIAEAIGFPVVVKAS 160
                                   6799***********9887669********************75 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.9
                   ATP-grasp_5 148 plnstlareliertkaskllkg 169
                                    l ++ +++++e+   + ++++
  gi|15669414|ref|NP_248224.1| 446 KLREKMVKYALESRDLYSVVSE 467
                                   3344444444444444444444 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00029       0.4     274     318 ..       4      48 ..       2      79 .. 0.74
   2 ?    2.2   0.1     0.043        59     128     182 ..     109     162 ..      82     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00029
                                   EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS CS
                Oxidored_nitro 274 rvaiygdpdrvvalarllkelGmevvaagtetahrddeerlkael 318
                                   +v+i+  +++++ ++r++ elG+++va+ +e  +r +++ l +e+
  gi|15669414|ref|NP_248224.1|   4 KVLIANRGEIAIRIIRACWELGIKTVAVYSEADKRSLHATLADEA 48 
                                   899********************************9997666644 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.043
                                   HHHHHHHHCTT-TT---SSEEEEEEETTCGHGHHHHHHHHHHHHTEEEEEEECTS CS
                Oxidored_nitro 128 alealvrklvgkkgekeprkvnilgeynlgpgdlrelkelleklGlevnavftgg 182
                                   a+ea+  k+  +k+  ++  v ++++++ + +d++e  e+ e++G+ v++ ++ g
  gi|15669414|ref|NP_248224.1| 109 AIEAMGSKIN-AKKIMKKAGVPLIPGSEGAIEDIDEAIEIAEAIGFPVVVKASAG 162
                                   5566666663.46666777999*****9999***************877666554 PP

>> baeRF_family3  Bacterial archaeo-eukaryotic release factor family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       9.1   1.3e+04     121     141 ..     239     259 ..     231     267 .. 0.63
   2 ?   11.1   0.0   0.00026      0.36      81     128 ..     407     454 ..     396     462 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 9.1
                 baeRF_family3 121 Lreaawplveayaeeeraeal 141
                                   + ea  p++ ++++e++ ea+
  gi|15669414|ref|NP_248224.1| 239 IEEAPSPIMTEELRERMGEAA 259
                                   445556777777777776665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00026
                 baeRF_family3  81 lplvlaGveenlslfrevsknpsliegglegnpaelsaeeLreaawpl 128
                                   +  v++Gv+ n+++ r v + ++ ++g++++++ e+++++Lre++ + 
  gi|15669414|ref|NP_248224.1| 407 REYVIIGVKTNIPFHRAVLEEENFLKGNISTHYVEQNMHKLREKMVKY 454
                                   7789**************************************998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 3183.10
//
Query:       gi|15669415|ref|NP_248225.1|  [L=76]
Description: hypothetical protein MJ_1230 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-29  101.0   2.7    3.2e-29  100.9   2.7    1.0  1  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
    0.00046   19.7   2.8     0.0013   18.2   2.8    1.8  1  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00059   20.2   0.1    0.00077   19.8   0.1    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0027   17.7   1.2      0.026   14.5   1.2    2.0  1  CpXC             CpXC protein
     0.0029   17.5   0.1        0.6   10.1   0.0    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.007   17.0   0.1        1.8    9.3   0.1    2.2  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
     0.0076   16.1   2.9        0.8    9.6   0.3    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
     0.0092   15.6   2.9      0.016   14.9   0.4    2.0  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
     0.0099   15.6   3.6      0.045   13.5   3.6    1.8  1  DUF2225          Uncharacterized protein conserved in bacteri
  ------ inclusion threshold ------
      0.011   16.1   2.5        1.4    9.5   0.3    2.2  2  zf-H2C2_2        Zinc-finger double domain
      0.024   14.3   1.2       0.35   10.6   0.1    2.3  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.041   13.6   2.2        3.9    7.3   0.2    2.5  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.047   13.0   1.2      0.047   13.0   1.2    2.1  2  zf-RanBP         Zn-finger in Ran binding protein and others
      0.058   13.4   2.7       0.87    9.7   0.3    2.2  2  Rubredoxin       Rubredoxin
       0.06   13.3   2.7        6.1    6.9   0.4    2.3  2  zinc_ribbon_4    zinc-ribbon domain
      0.071   13.0   0.1        1.4    8.8   0.0    2.1  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.077   13.4   3.2       0.79   10.1   0.5    2.1  2  DUF4379          Probable Zinc-ribbon domain
      0.089   12.8   3.4        1.7    8.7   0.8    2.2  2  ADK_lid          Adenylate kinase, active site lid
      0.098   12.7   2.6       0.32   11.1   0.3    2.2  2  zf-Sec23_Sec24   Sec23/Sec24 zinc finger
       0.12   12.6   0.2       0.57   10.4   0.1    1.9  2  DUF5319          Family of unknown function (DUF5319)
       0.12   12.2   1.3        3.5    7.5   0.1    2.2  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
       0.13   12.0   2.2        3.6    7.4   0.2    2.3  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.15   12.2   2.6         15    5.8   2.8    2.1  1  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.24   11.1   6.7        2.4    8.0   1.2    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.31   10.5   7.0        4.5    6.8   1.5    2.3  2  zf-ribbon_3      zinc-ribbon domain
       0.47   10.5   2.3        6.6    6.8   0.4    2.1  2  DUF1451          Zinc-ribbon containing domain
       0.91    9.3   9.1        2.4    8.0   2.6    2.2  2  zinc_ribbon_2    zinc-ribbon domain
        2.2    8.2   7.5        8.4    6.4   0.3    2.3  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
        3.7    7.2   5.1        4.9    6.8   0.5    2.2  2  zf_C2H2_10       C2H2 type zinc-finger


Domain annotation for each model (and alignments):
>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   2.7   5.2e-32   3.2e-29       1      63 []      10      76 .]      10      76 .] 0.97

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 5.2e-32
                zinc_ribbon_13  1 kCpKCgnteaevkevaatGsglskifdvqnkkfitvsCknCgYtelYkaetsegk....nilDlllg 63
                                  kCpKCgnte+ +keva+tG+glskifd+q++++i+++Ck+CgY+e+Y++++ + k    nilD+++g
  gi|15669415|ref|NP_248225.1| 10 KCPKCGNTEFFEKEVAMTGTGLSKIFDIQHNEYIVITCKKCGYSEFYDKSIVKSKdnlmNILDIFFG 76
                                  7*************************************************999888999******97 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   2.8   2.1e-06    0.0013       2      27 ..      10      52 ..       9      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.1e-06
                                  EETTTTCEEC..............HEETSTTCE...EESSSSB CS
                  TF_Zn_Ribbon  2 kCPnCgstnl..............veDpergel...vCtdCGl 27
                                  kCP+Cg+t++              ++D  ++e+   +C++CG+
  gi|15669415|ref|NP_248225.1| 10 KCPKCGNTEFfekevamtgtglskIFDIQHNEYiviTCKKCGY 52
                                  8********66*********************96667****96 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   1.2e-06   0.00077       5      42 ..      10      56 ..       6      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.2e-06
               Lar_restr_allev  5 pCPfCggravlersqrvvaeigq...........cvyCadCgastpwfk 42
                                   CP Cg+ +  e++   +  +             +++C++Cg+  ++f+
  gi|15669415|ref|NP_248225.1| 10 KCPKCGNTEFFEKEVAMTGTGLSkifdiqhneyiVITCKKCGY--SEFY 56
                                  6************98888765559*******************..3333 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.2   4.3e-05     0.026       2      51 ..      10      58 ..       9      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.3e-05
                          CpXC  2 tCpaCgkefeaeiwtsidadedpelkeklldgslfeatCpkCgataklea 51
                                  +Cp+Cg++  +e +  ++ +       ++ ++++  +tC kCg++  ++ 
  gi|15669415|ref|NP_248225.1| 10 KCPKCGNTEFFEKEVAMTGTG-LSKIFDIQHNEYIVITCKKCGYSEFYDK 58
                                  7*****998888766665554.455568***************9976665 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00098       0.6      19      29 ..       9      19 ..       2      28 .. 0.75
   2 ?    5.9   0.0      0.02        12      20      30 ..      46      56 ..      30      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00098
                 Zn_Tnp_IS1595 19 fvCPhCgsrka 29
                                    CP+Cg++++
  gi|15669415|ref|NP_248225.1|  9 WKCPKCGNTEF 19
                                  45999998865 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                 Zn_Tnp_IS1595 20 vCPhCgsrkay 30
                                  +C +Cg++++y
  gi|15669415|ref|NP_248225.1| 46 TCKKCGYSEFY 56
                                  68888888877 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1    0.0029       1.8       2      11 ..       8      17 ..       7      27 .. 0.86
   2 ?    6.0   0.0     0.031        19       3      18 ..      45      60 ..      43      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0029
                       zf-ISL3  2 phrCPnCgsk 11
                                  +++CP+Cg++
  gi|15669415|ref|NP_248225.1|  8 RWKCPKCGNT 17
                                  799*****97 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.031
                       zf-ISL3  3 hrCPnCgsktvvkhgk 18
                                  ++C +Cg    ++++ 
  gi|15669415|ref|NP_248225.1| 45 ITCKKCGYSEFYDKSI 60
                                  89******99999874 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.3    0.0013       0.8       2      11 ..      10      19 ..       9      23 .. 0.87
   2 !    6.8   0.2    0.0098       6.1       2       9 ..      46      53 ..      41      57 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                       TFIIS_C  2 kCpkCgsrea 11
                                  kCpkCg++e 
  gi|15669415|ref|NP_248225.1| 10 KCPKCGNTEF 19
                                  8******985 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0098
                       TFIIS_C  2 kCpkCgsr 9 
                                  +C+kCg  
  gi|15669415|ref|NP_248225.1| 46 TCKKCGYS 53
                                  45555554 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.4   2.5e-05     0.016       1      17 [.       5      21 ..       5      23 .. 0.89
   2 ?    1.1   0.1      0.51   3.2e+02       6      11 ..      46      51 ..      44      57 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                       zf-RRN7  1 wekgppCgvCgcrsftl 17
                                  +ek++ C+ Cg+++f++
  gi|15669415|ref|NP_248225.1|  5 MEKRWKCPKCGNTEFFE 21
                                  689************97 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.51
                       zf-RRN7  6 pCgvCg 11
                                   C  Cg
  gi|15669415|ref|NP_248225.1| 46 TCKKCG 51
                                  466665 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   3.6   7.3e-05     0.045       2      61 ..       5      57 ..       4      71 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.3e-05
                       DUF2225  2 ykkkieCPvC.eekfkkkkvkssslrlikrdsdlnakYeevnplfYevvvCpkCgYaalkk 61
                                  ++k+ +CP C +++f +k+v   +  l k        + +++ + Y v +C+kCgY+ + +
  gi|15669415|ref|NP_248225.1|  5 MEKRWKCPKCgNTEFFEKEVAMTGTGLSKI-------F-DIQHNEYIVITCKKCGYSEFYD 57
                                  689999999944578888887766655443.......3.578889************9976 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3    0.0023       1.4      12      21 ..       6      15 ..       5      17 .. 0.87
   2 ?    6.6   0.1     0.018        11      12      23 ..      41      53 ..      33      53 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0023
                     zf-H2C2_2 12 ekpyeCplCd 21
                                  ek+++Cp+C+
  gi|15669415|ref|NP_248225.1|  6 EKRWKCPKCG 15
                                  899******8 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.018
                     zf-H2C2_2 12 ekp.yeCplCdka 23
                                  e +  +C++C+++
  gi|15669415|ref|NP_248225.1| 41 EYIvITCKKCGYS 53
                                  444469*****96 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.16        96      19      24 ..      10      15 ..       5      20 .. 0.85
   2 ?   10.6   0.1   0.00056      0.35      17      27 ..      44      54 ..      32      58 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.16
                                  --SSS- CS
                DNA_RNApol_7kD 19 RCkeCG 24
                                  +C +CG
  gi|15669415|ref|NP_248225.1| 10 KCPKCG 15
                                  699998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00056
                                  ----SSS---- CS
                DNA_RNApol_7kD 17 piRCkeCGhRi 27
                                  +i Ck+CG+  
  gi|15669415|ref|NP_248225.1| 44 VITCKKCGYSE 54
                                  689*****965 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.017        11      24      30 ..      11      17 ..       7      19 .. 0.79
   2 ?    7.3   0.2    0.0063       3.9      24      31 ..      47      54 ..      42      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.017
                 A2L_zn_ribbon 24 CieCgas 30
                                  C++Cg++
  gi|15669415|ref|NP_248225.1| 11 CPKCGNT 17
                                  8888887 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0063
                 A2L_zn_ribbon 24 CieCgasf 31
                                  C++Cg+s+
  gi|15669415|ref|NP_248225.1| 47 CKKCGYSE 54
                                  99999997 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.2   7.7e-05     0.047       2      12 ..       6      16 ..       6      17 .. 0.89
   2 ?    2.5   0.8      0.15        94       6      12 ..      46      52 ..      46      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.7e-05
                                  SSSEE-SSS-- CS
                      zf-RanBP  2 egdWdCskClv 12
                                  e++W+C+kC++
  gi|15669415|ref|NP_248225.1|  6 EKRWKCPKCGN 16
                                  689******96 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.15
                                  E-SSS-- CS
                      zf-RanBP  6 dCskClv 12
                                  +C+kC++
  gi|15669415|ref|NP_248225.1| 46 TCKKCGY 52
                                  6****98 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3    0.0014      0.87      34      42 ..       8      16 ..       5      19 .. 0.84
   2 ?    4.1   0.1     0.078        48       3      12 ..      46      57 ..      44      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                                  T-BBTTTB- CS
                    Rubredoxin 34 dWvCPdCgv 42
                                   W+CP+Cg 
  gi|15669415|ref|NP_248225.1|  8 RWKCPKCGN 16
                                  7******96 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.078
                                  EETTT-BE..EE CS
                    Rubredoxin  3 eCkvCgyv..Yd 12
                                   Ck Cgy   Yd
  gi|15669415|ref|NP_248225.1| 46 TCKKCGYSefYD 57
                                  6******43366 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.4    0.0098       6.1      27      34 ..      10      17 ..       6      17 .. 0.83
   2 ?    6.5   0.1     0.013       7.7      26      33 ..      45      52 ..      39      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0098
                 zinc_ribbon_4 27 rCskCghv 34
                                  +C+kCg++
  gi|15669415|ref|NP_248225.1| 10 KCPKCGNT 17
                                  89999986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                 zinc_ribbon_4 26 vrCskCgh 33
                                  ++C+kCg 
  gi|15669415|ref|NP_248225.1| 45 ITCKKCGY 52
                                  78888875 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0023       1.4      23      35 ..       6      18 ..       2      19 .. 0.79
   2 ?    2.3   0.0      0.26   1.6e+02      13      18 ..      46      51 ..      43      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
                       DUF35_N 23 PPravCphCgsdd 35
                                   +r+ Cp+Cg ++
  gi|15669415|ref|NP_248225.1|  6 EKRWKCPKCGNTE 18
                                  57999****9876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.26
                       DUF35_N 13 rCpdCG 18
                                   C++CG
  gi|15669415|ref|NP_248225.1| 46 TCKKCG 51
                                  599999 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5    0.0013      0.79      30      38 ..       9      17 ..       6      33 .. 0.73
   2 ?    4.2   0.1     0.093        58      31      43 ..      46      60 ..      33      66 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
                       DUF4379 30 WkCakCghe 38
                                  WkC+kCg++
  gi|15669415|ref|NP_248225.1|  9 WKCPKCGNT 17
                                  *******52 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.093
                       DUF4379 31 kCakCg..heWeasv 43
                                  +C+kCg  + + +s+
  gi|15669415|ref|NP_248225.1| 46 TCKKCGysEFYDKSI 60
                                  7*****544666666 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.8    0.0027       1.7       1      10 [.       8      17 ..       8      17 .. 0.91
   2 ?    4.9   0.1     0.044        27       3       9 ..      46      52 ..      45      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0027
                                  EEE-TTT--E CS
                       ADK_lid  1 RrvCpkCGrs 10
                                  R+ CpkCG +
  gi|15669415|ref|NP_248225.1|  8 RWKCPKCGNT 17
                                  9*******75 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.044
                                  E-TTT-- CS
                       ADK_lid  3 vCpkCGr 9 
                                  +C+kCG 
  gi|15669415|ref|NP_248225.1| 46 TCKKCGY 52
                                  8999995 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00051      0.32      17      32 ..       2      17 ..       1      23 [. 0.82
   2 ?    1.8   0.1      0.42   2.6e+02       2       8 ..      45      51 ..      44      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00051
                zf-Sec23_Sec24 17 idfggkrwiCnfCnhk 32
                                  ++f  krw+C+ C++ 
  gi|15669415|ref|NP_248225.1|  2 VIFMEKRWKCPKCGNT 17
                                  57889********986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.42
                zf-Sec23_Sec24  2 irCrrCr 8 
                                  i C++C+
  gi|15669415|ref|NP_248225.1| 45 ITCKKCG 51
                                  8899996 PP

>> DUF5319  Family of unknown function (DUF5319)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.85   5.3e+02      63      77 ..      10      24 ..       8      40 .. 0.83
   2 ?   10.4   0.1   0.00092      0.57      59      81 ..      42      64 ..      21      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.85
                       DUF5319 63 lCedCeeehyydWdl 77
                                  +C  C ++ +++ ++
  gi|15669415|ref|NP_248225.1| 10 KCPKCGNTEFFEKEV 24
                                  699*******99876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00092
                       DUF5319 59 GivllCedCeeehyydWdllaan 81
                                   iv++C+ C  + +yd ++++++
  gi|15669415|ref|NP_248225.1| 42 YIVITCKKCGYSEFYDKSIVKSK 64
                                  599****************9864 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.089        55      14      20 ..       9      15 ..       4      17 .. 0.78
   2 ?    7.5   0.1    0.0056       3.5       4      20 ..      35      51 ..      33      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.089
                     zf-C2H2_3 14 sqCkeCg 20
                                   +C++Cg
  gi|15669415|ref|NP_248225.1|  9 WKCPKCG 15
                                  56****9 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0056
                     zf-C2H2_3  4 LdlgqksfgasqCkeCg 20
                                   d+  +++   +Ck+Cg
  gi|15669415|ref|NP_248225.1| 35 FDIQHNEYIVITCKKCG 51
                                  688788888899****9 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0058       3.6      44      52 ..       8      16 ..       4      18 .. 0.83
   2 ?    4.2   0.1     0.056        35      18      29 ..      40      51 ..      31      54 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0058
                zinc_ribbon_10 44 kyrCpkCga 52
                                  +++CpkCg 
  gi|15669415|ref|NP_248225.1|  8 RWKCPKCGN 16
                                  8******96 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.056
                zinc_ribbon_10 18 knryalICskCh 29
                                  ++   + C+kC 
  gi|15669415|ref|NP_248225.1| 40 NEYIVITCKKCG 51
                                  445567888885 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   2.8     0.024        15      10      30 ..      19      58 ..      11      66 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.024
                      zf-Mss51 10 t...................apkhvdfeCpdCGiptycse 30
                                                      +++ + ++C++CG++ ++++
  gi|15669415|ref|NP_248225.1| 19 FfekevamtgtglskifdiqHNEYIVITCKKCGYSEFYDK 58
                                  3555555555555566655556677789*****9877665 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.2    0.0039       2.4      15      21 ..       9      15 ..       7      17 .. 0.89
   2 ?    6.2   0.4     0.014       8.5       3       9 ..      47      53 ..      46      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0039
                  Rubredoxin_2 15 GrCpsCg 21
                                  ++Cp Cg
  gi|15669415|ref|NP_248225.1|  9 WKCPKCG 15
                                  ******9 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.014
                  Rubredoxin_2  3 CsqCGfe 9 
                                  C++CG++
  gi|15669415|ref|NP_248225.1| 47 CKKCGYS 53
                                  *****98 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.5    0.0073       4.5       5      10 ..      11      16 ..      10      17 .. 0.65
   2 ?    6.4   0.3    0.0096       5.9      17      24 ..      45      52 ..      44      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0073
                   zf-ribbon_3  5 CPnCGa 10
                                  CP+CG+
  gi|15669415|ref|NP_248225.1| 11 CPKCGN 16
                                  777775 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0096
                   zf-ribbon_3 17 nvCpyCGt 24
                                  ++C++CG+
  gi|15669415|ref|NP_248225.1| 45 ITCKKCGY 52
                                  79*****7 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.4     0.011       6.6     134     143 ..      10      19 ..       4      23 .. 0.88
   2 ?    3.9   0.1     0.081        50     132     143 ..      44      55 ..      33      59 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                       DUF1451 134 pCpkCgateF 143
                                   +CpkCg+teF
  gi|15669415|ref|NP_248225.1|  10 KCPKCGNTEF 19 
                                   7********9 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.081
                       DUF1451 132 ippCpkCgateF 143
                                   + +C+kCg +eF
  gi|15669415|ref|NP_248225.1|  44 VITCKKCGYSEF 55 
                                   457999999888 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.6    0.0038       2.4       1       7 [.      10      16 ..      10      17 .. 0.85
   2 ?    5.3   0.5     0.028        17       2       7 ..      47      52 ..      45      53 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0038
                 zinc_ribbon_2  1 fCpnCGa 7 
                                  +Cp+CG+
  gi|15669415|ref|NP_248225.1| 10 KCPKCGN 16
                                  7999998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.028
                 zinc_ribbon_2  2 CpnCGa 7 
                                  C++CG+
  gi|15669415|ref|NP_248225.1| 47 CKKCGY 52
                                  777775 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.8     0.041        25       4       9 ..      11      16 ..      11      17 .. 0.96
   2 ?    6.4   0.3     0.014       8.4      22      31 ..      45      54 ..      38      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.041
                                  ESTTTS CS
                RNA_POL_M_15KD  4 CpkCgN 9 
                                  CpkCgN
  gi|15669415|ref|NP_248225.1| 11 CPKCGN 16
                                  *****9 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                                  EEESSSS-EE CS
                RNA_POL_M_15KD 22 feCrqCgYee 31
                                    C +CgY e
  gi|15669415|ref|NP_248225.1| 45 ITCKKCGYSE 54
                                  67******76 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.5    0.0079       4.9       4       9 ..      10      15 ..       8      17 .. 0.80
   2 ?    2.4   0.4      0.19   1.2e+02       4      10 ..      46      52 ..      45      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0079
                    zf_C2H2_10  4 sCPKCq 9 
                                   CPKC+
  gi|15669415|ref|NP_248225.1| 10 KCPKCG 15
                                  6****8 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.19
                    zf_C2H2_10  4 sCPKCqe 10
                                   C KC++
  gi|15669415|ref|NP_248225.1| 46 TCKKCGY 52
                                  599***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 524.78
//
Query:       gi|15669416|ref|NP_248226.1|  [L=567]
Description: pyruvate carboxylase subunit B [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-63  212.3   0.2    1.7e-62  210.7   0.2    1.8  1  PYC_OADA         Conserved carboxylase domain
    4.1e-49  167.5   0.0    5.6e-49  167.1   0.0    1.2  1  HMGL-like        HMGL-like
    7.8e-20   70.5   6.8    7.8e-20   70.5   6.8    2.2  2  Biotin_lipoyl    Biotin-requiring enzyme
    2.2e-16   59.4   2.0    1.4e-07   31.2   0.1    2.5  2  Biotin_lipoyl_2  Biotin-lipoyl like
    1.3e-05   25.0   2.4    3.9e-05   23.5   1.6    2.2  2  RnfC_N           RnfC Barrel sandwich hybrid domain
    8.9e-05   22.0   1.3    0.00016   21.2   1.3    1.4  1  NQRA             Na(+)-translocating NADH-quinone reductase s
    0.00012   22.7   1.1       0.48   11.2   0.0    2.8  2  HlyD_3           HlyD family secretion protein
    0.00012   21.3   0.6      0.055   12.7   0.1    2.3  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
     0.0021   17.9   1.9     0.0068   16.3   1.3    2.2  2  GCV_H            Glycine cleavage H-protein
     0.0026   17.0   0.0          2    7.5   0.0    2.3  2  DUF561           Protein of unknown function (DUF561)
     0.0046   16.9   0.7      0.016   15.2   0.4    2.0  1  DUF2118          Uncharacterized protein conserved in archaea
     0.0064   15.7   0.0      0.014   14.6   0.0    1.5  1  TGT              Queuine tRNA-ribosyltransferase
  ------ inclusion threshold ------
      0.032   14.1   1.4      0.073   12.9   1.4    1.6  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
      0.036   14.1   1.2       0.73    9.9   0.2    2.7  2  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
      0.069   13.4   1.1       0.96    9.7   0.2    2.5  2  Peptidase_M23    Peptidase family M23
      0.097   12.4   2.5       0.67    9.7   0.4    3.0  3  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
       0.24   11.1   3.1        1.7    8.4   0.2    2.9  3  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
       0.55    9.0  10.3      0.087   11.6   6.0    1.7  2  YqfD             Putative stage IV sporulation protein YqfD


Domain annotation for each model (and alignments):
>> PYC_OADA  Conserved carboxylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.7   0.2   1.8e-65   1.7e-62       1     196 [.     290     476 ..     290     477 .. 0.94

  Alignments for each domain:
  == domain 1  score: 210.7 bits;  conditional E-value: 1.8e-65
                                   HHCCT--CCHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHTT----STTHHHHHHHHHHHHHHH........TS.TTSS-- CS
                      PYC_OADA   1 VykheiPGGqltnlkeqakeqglldkfeevlkeyaevnkllGdivkVTPsSkvvgdlAvfnvlnklteedvleegrykdip 81 
                                   V+++++PGG+l+nl +q+keqg+ldkfeevl+e+++v+k+lG++++VTP+S++vg++Av+nvl+        e +ryk i+
  gi|15669416|ref|NP_248226.1| 290 VLVYQVPGGMLSNLVSQLKEQGALDKFEEVLQEIPRVRKDLGYPPLVTPTSQIVGTQAVLNVLT--------E-ERYKIIT 361
                                   789*************************************************************........6.5****** PP

                                   HHHHHHHTTSS---SS---HHHHHHHHT..-----S-GGGG---.-HHHHHHHTTTTS..SSHHHHHHHHHSHHHHHHHHH CS
                      PYC_OADA  82 dsvvdllkGelGkppggfpeelvkkvlk.geepitsrpadslepedleklrkeleeka..kteedvlsyalypkvaekflk 159
                                   ++vv+++kG +Gkpp+++++el k+vl+ ge+pit+rpad+l+p ++ek++ke+eek   k+eed+l+yalyp++a kfl+
  gi|15669416|ref|NP_248226.1| 362 NEVVNYVKGFYGKPPAPINPELLKRVLDeGEKPITCRPADLLPP-EWEKVKKEAEEKGivKKEEDILTYALYPQIAVKFLR 441
                                   ***************************999**************.***********99667*******************8 PP

                                   HHHHHHHHH..CTTTS......-SEEEEEETTEEEE. CS
                      PYC_OADA 160 freeygdvsvlptkvffeglkvgeeveveveggkyli 196
                                    + +++ +   ++k + + l++++e+ vev+g+k+++
  gi|15669416|ref|NP_248226.1| 442 GELKAEPI--PKEKDIGKILEIPTEYIVEVDGEKFEV 476
                                   66665555..677889999***************984 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.1   0.0   5.6e-52   5.6e-49       2     263 ..       2     267 ..       1     268 [. 0.96

  Alignments for each domain:
  == domain 1  score: 167.1 bits;  conditional E-value: 5.6e-52
                                   -EEEE-TTTHHHHTS.SS---HHHHHHHHHHHHHHT-SEE--........TSGGGT.THHHHHHHS---TT-B........ CS
                     HMGL-like   2 vkivdttLRDGeqal.kaalsveeklaiakaLdeagvdeiEv........gfpaaseddfevvraiakavkka......r. 66 
                                   vkivdtt RD++q+l ++++++e++l+ia+++de+g+ ++Ev        +++ + ed++e++ra++k ++++      r 
  gi|15669416|ref|NP_248226.1|   2 VKIVDTTFRDAQQSLiATRMRTEDMLPIAEKMDEVGFYSMEVwggatfdaCIRYLNEDPWERLRALKKRIQNTplqmllRg 82 
                                   89************9999******************************************************977776625 PP

                                   ...--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-E..TTT-BTTTBS- CS
                     HMGL-like  67 ..ilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkd..velsledasrt 143
                                     +++++++ ++ ++++v +++++g +++++f+a ++              ++++e a+k a++ g++   ++ ++ ++ +
  gi|15669416|ref|NP_248226.1|  83 qnLVGYRHYPDDIVEKFVIKAHENGIDIFRIFDALND--------------VRNMETAIKTAKKVGAEvqGAICYTISPVH 149
                                   57***********************************..............9****************555567899**** PP

                                   -HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBT CS
                     HMGL-like 144 dleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtv 224
                                   ++++ +e+++++ee+G+++i i+D+ G+ltP e +el+++lke+++  +++ vH H + GlA +  l+ +eaGad vd+++
  gi|15669416|ref|NP_248226.1| 150 TIDQYVELAKKLEEMGCDSICIKDMAGLLTPYEGYELVKRLKEEIS--LPIDVHSHCTSGLAPMTYLKVIEAGADMVDCAI 228
                                   **********************************************..********************************* PP

                                   TS--SSBBB-BHHHHHHHHHHTT-B----HHHHHHHHHH CS
                     HMGL-like 225 nGlGeraGnaaleelvaalealgvdtgldlqklrsiaal 263
                                   +    ++  +++e +v+al+++++dtgldl+ l +i+++
  gi|15669416|ref|NP_248226.1| 229 SPFAMGTSQPPTESIVVALKGTKYDTGLDLKLLNEIRDY 267
                                   **********************************99986 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       4.8   4.8e+03      31      46 ..     464     479 ..     463     481 .. 0.85
   2 !   70.5   6.8   7.9e-23   7.8e-20      15      73 .]     507     566 ..     491     566 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.8
                                   SEEEEEECTTEEEEEE CS
                 Biotin_lipoyl  31 qvlaeveamKmemeie 46 
                                   + ++ev   K e++ie
  gi|15669416|ref|NP_248226.1| 464 EYIVEVDGEKFEVKIE 479
                                   6799999999999986 PP

  == domain 2  score: 70.5 bits;  conditional E-value: 7.9e-23
                                   ..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                 Biotin_lipoyl  15 g.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                   g v++++vk+GdkVk+g+v++++eamKme++ie+p++G+v+ il++eGd+v+vgd++++i
  gi|15669416|ref|NP_248226.1| 507 GmVTKIKVKEGDKVKKGDVIVVLEAMKMEHPIESPVEGTVERILIDEGDAVNVGDVIMII 566
                                   46788****************************************************987 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.1   1.4e-10   1.4e-07       5      35 ..     501     531 ..     500     537 .. 0.91
   2 !   27.4   0.2   2.2e-09   2.2e-06       4      33 ..     537     566 ..     535     567 .] 0.96

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.4e-10
               Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLaelDs 35 
                                   +++p+ G V+++ Vk+G+ Vk+Gdv+++l+ 
  gi|15669416|ref|NP_248226.1| 501 VTSPFRGMVTKIKVKEGDKVKKGDVIVVLEA 531
                                   789*************************986 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.2e-09
               Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLael 33 
                                   +I +pv G+V+++++ +G+ V+ Gdv++++
  gi|15669416|ref|NP_248226.1| 537 PIESPVEGTVERILIDEGDAVNVGDVIMII 566
                                   699*************************99 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.7   5.6e+03      30      48 ..     335     353 ..     331     371 .. 0.77
   2 !   23.5   1.6   3.9e-08   3.9e-05       6      80 ..     477     549 ..     472     565 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.7
                        RnfC_N  30 lvlplsqhiGapakplvkv 48 
                                   lv p sq +G++a + v  
  gi|15669416|ref|NP_248226.1| 335 LVTPTSQIVGTQAVLNVLT 353
                                   7889999999999776655 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 3.9e-08
                        RnfC_N   6 GvhppenkelskekpieklplpkelvlplsqhiGapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkai 80 
                                    ++p+ + el ++k++ +++++  ++ p++   G+ +k+ vk+gdkV+kG++i   e+  +  p+ ++v GtV +i
  gi|15669416|ref|NP_248226.1| 477 KIEPKIGTELKRKKEVITAEMEGAVTSPFR---GMVTKIKVKEGDKVKKGDVIVVLEAmKMEHPIESPVEGTVERI 549
                                   5788889999999***************97...6999****************999886679***********988 PP

>> NQRA  Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.3   1.6e-07   0.00016      32      79 ..     501     549 ..     473     567 .] 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                          NQRA  32 lgedyvglkpklkvkegdkVkkGqvlfe.dKknpgvlftspasGevvei 79 
                                   + ++++g+  k+kvkegdkVkkG+v++  +  + +  + sp+ G+v +i
  gi|15669416|ref|NP_248226.1| 501 VTSPFRGMVTKIKVKEGDKVKKGDVIVVlEAMKMEHPIESPVEGTVERI 549
                                   4579********************98761455668899********987 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00048      0.48       2      30 ..     501     529 ..     500     534 .. 0.91
   2 !    9.5   0.1    0.0016       1.5       2      30 ..     538     566 ..     537     567 .] 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00048
                        HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                   +++p+ G v++++v+eg+ v +gd+++ +
  gi|15669416|ref|NP_248226.1| 501 VTSPFRGMVTKIKVKEGDKVKKGDVIVVL 529
                                   89***********************8765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0016
                        HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                   + +pv G+v  + + eg+ v+ gd+++ i
  gi|15669416|ref|NP_248226.1| 538 IESPVEGTVERILIDEGDAVNVGDVIMII 566
                                   679**********************9976 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   5.5e-05     0.055     110     139 ..     500     529 ..     484     534 .. 0.61
   2 !    7.2   0.0    0.0026       2.6     107     139 ..     534     566 ..     529     567 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      HlyD_D23 110 tvkapisGvVteknvreGqyvqpgdtlfti 139
                                    v++p+ G+Vt+ +v eG+ v++gd+++ +
  gi|15669416|ref|NP_248226.1| 500 AVTSPFRGMVTKIKVKEGDKVKKGDVIVVL 529
                                   455666666666666666666666555443 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0026
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      HlyD_D23 107 ktvtvkapisGvVteknvreGqyvqpgdtlfti 139
                                    + ++++p++G+V +  + eG+ v+ gd+++ i
  gi|15669416|ref|NP_248226.1| 534 MEHPIESPVEGTVERILIDEGDAVNVGDVIMII 566
                                   566889999999999999999999999988876 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.95   9.4e+02      32      74 ..     472     512 ..     463     516 .. 0.69
   2 !   16.3   1.3   6.9e-06    0.0068      31      73 ..     507     548 ..     489     559 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.95
                                   SEEEEE-.--TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                         GCV_H  32 dvvfvel.pevgtkvkkgeslaavEsvKaasevyapvsGevvev 74 
                                   +   v++ p+ gt++k ++++ + E     + v +p+ G v+++
  gi|15669416|ref|NP_248226.1| 472 EKFEVKIePKIGTELKRKKEVITAEM---EGAVTSPFRGMVTKI 512
                                   55556663567999999999988885...566778888888765 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 6.9e-06
                                   -SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEE CS
                         GCV_H  31 gdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevve 73 
                                   g v+ ++++e g+kvkkg+ + ++E+ K+  ++ +pv+G+v  
  gi|15669416|ref|NP_248226.1| 507 GMVTKIKVKE-GDKVKKGDVIVVLEAMKMEHPIESPVEGTVER 548
                                   6677788875.9****************************975 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0028       2.8     118     149 ..     138     169 ..      95     176 .. 0.77
   2 !    7.5   0.0     0.002         2      51      86 ..     185     225 ..     181     231 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0028
                        DUF561 118 ktdlsvtiPyiLkleeqvkLakkLeslgvdli 149
                                   +  ++ ti  + ++++ v+LakkLe++g d i
  gi|15669416|ref|NP_248226.1| 138 QGAICYTISPVHTIDQYVELAKKLEEMGCDSI 169
                                   3469************************9987 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.002
                        DUF561  51 klvkkvksvsniPi.....CvsaveakllleavkaGadlve 86 
                                   +lvk++k+ +++Pi     C s++ + + l+ + aGad+v+
  gi|15669416|ref|NP_248226.1| 185 ELVKRLKEEISLPIdvhshCTSGLAPMTYLKVIEAGADMVD 225
                                   79***********99999999******************97 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   1.6e-05     0.016      87     133 ..     504     549 ..     482     558 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                       DUF2118  87 pvegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvVvfi 133
                                   p  g++  + v++Gd+v++gd++  + + k e + +++pveg+V  i
  gi|15669416|ref|NP_248226.1| 504 PFRGMVTKIKVKEGDKVKKGDVIVVLEAMKME-HPIESPVEGTVERI 549
                                   778999*************************9.99********9554 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.4e-05     0.014     147     250 ..     122     228 ..     115     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHHHHHHHHHHSE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-SSSSSSHHHHHHHHHHHHGGGS..-TTS-E CS
                           TGT 147 sverTlrwldrcleahqa.lfgivqGglyedlreesaeelakrdfdgyaigGlsvgeekeellevveavtell..pedkpr 224
                                    +e+ ++ ++++ ++ q  ++  + +    d   e a++l ++++d ++i  +++  +  e +e+v++++e++  p d   
  gi|15669416|ref|NP_248226.1| 122 NMETAIKTAKKVGAEVQGaICYTISPVHTIDQYVELAKKLEEMGCDSICIKDMAGLLTPYEGYELVKRLKEEIslPIDVHS 202
                                   566666666666666655588888888888999999****************99888778899999999886544999999 PP

                                   EETTB-SHHHHHHHHHTT--EEEESH CS
                           TGT 225 ylmGvgtPedlleavalGvDmfdcvy 250
                                   ++     P++ l+ +++G+Dm+dc++
  gi|15669416|ref|NP_248226.1| 203 HCTSGLAPMTYLKVIEAGADMVDCAI 228
                                   99999*******************86 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   7.3e-05     0.073      37      93 ..     511     566 ..     489     567 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-05
                                   EESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEEE.--EEE.E-TTSECEEE CS
               ATP-synt_ab_Xtn  37 kpkvkvgdkvsggdilGtvqeteliehkimvppkvegkvkei.aeege.ytvedtiaev 93 
                                   k kvk+gdkv++gd++ +  e   +eh i  p+  eg+v++i  +eg+  +v d+i+ +
  gi|15669416|ref|NP_248226.1| 511 KIKVKEGDKVKKGDVIVV-LEAMKMEHPIESPV--EGTVERIlIDEGDaVNVGDVIMII 566
                                   569*************65.566666****9998..999998734678669999999877 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00073      0.73      44      69 ..     506     531 ..     483     534 .. 0.85
   2 ?    1.9   0.0      0.24   2.4e+02      50      67 ..     549     566 ..     540     567 .] 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00073
                                   TTTEEEESS-TT-EEETTEEEEEEEE CS
                     QRPTase_N  44 pglevellvkDGervekgdvlleieG 69 
                                   +g+ ++++vk+G++v+kgdv++ +e+
  gi|15669416|ref|NP_248226.1| 506 RGMVTKIKVKEGDKVKKGDVIVVLEA 531
                                   5778999**************99875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.24
                                   ESS-TT-EEETTEEEEEE CS
                     QRPTase_N  50 llvkDGervekgdvllei 67 
                                   +l+++G+ v+ gdv++ i
  gi|15669416|ref|NP_248226.1| 549 ILIDEGDAVNVGDVIMII 566
                                   7899***********987 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00096      0.96      51      69 ..     508     526 ..     484     535 .. 0.78
   2 ?    1.7   0.0      0.31   3.1e+02      11      39 ..     533     565 ..     527     566 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00096
                                   EESEESS-TTEEE-TTCEE CS
                 Peptidase_M23  51 hlskisvkegqkVkaGqvI 69 
                                    + ki+vkeg+kVk+G+vI
  gi|15669416|ref|NP_248226.1| 508 MVTKIKVKEGDKVKKGDVI 526
                                   356799***********99 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.31
                                   TTT-EEEESSSEEE....EEEEEETTTEEEEEE CS
                 Peptidase_M23  11 pkgtpVlAaadGtV....vfagkkegyGnvvii 39 
                                   + + p+ ++ +GtV    +  g+  ++G v++i
  gi|15669416|ref|NP_248226.1| 533 KMEHPIESPVEGTVerilIDEGDAVNVGDVIMI 565
                                   556678888888885533333333355666665 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.67   6.6e+02      77     106 ..     467     498 ..     464     505 .. 0.81
   2 ?    9.7   0.4   0.00067      0.67      79     109 ..     505     535 ..     498     542 .. 0.81
   3 ?   -1.0   0.0       1.4   1.4e+03      81     101 ..     544     564 ..     539     566 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.67
                                   TTTTTTTEEES-..---SEE-SEEEEEEE-HH CS
                    PTS_EIIA_1  77 vklkgegFellv..kegdkVkagdklvevdle 106
                                   v+++ge Fe+++  k g++ k+++++++ ++e
  gi|15669416|ref|NP_248226.1| 467 VEVDGEKFEVKIepKIGTELKRKKEVITAEME 498
                                   78999999999844568999999999988775 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00067
                                   TTTTTEEES----SEE-SEEEEEEE-HHHHG CS
                    PTS_EIIA_1  79 lkgegFellvkegdkVkagdklvevdleaik 109
                                    +g + +++vkegdkVk+gd +v ++  +++
  gi|15669416|ref|NP_248226.1| 505 FRGMVTKIKVKEGDKVKKGDVIVVLEAMKME 535
                                   56778899**************988776665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.4
                                   TTTEEES----SEE-SEEEEE CS
                    PTS_EIIA_1  81 gegFellvkegdkVkagdklv 101
                                   g++ ++l+ egd V+ gd ++
  gi|15669416|ref|NP_248226.1| 544 GTVERILIDEGDAVNVGDVIM 564
                                   444456778888888888776 PP

>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.5   4.5e+03      32      45 ..     125     138 ..     118     144 .. 0.77
   2 ?    8.4   0.2    0.0017       1.7      36      53 ..     512     529 ..     510     539 .. 0.86
   3 ?    1.9   0.1      0.18   1.8e+02      40      53 ..     553     566 ..     548     566 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.5
                                   -EEEES--TT-EEB CS
                        PYNP_C  32 vGielhkklGdkVk 45 
                                   + i+  kk+G +V+
  gi|15669416|ref|NP_248226.1| 125 TAIKTAKKVGAEVQ 138
                                   55788899999997 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0017
                                   ES--TT-EEBTTSEEEEE CS
                        PYNP_C  36 lhkklGdkVkkGeplati 53 
                                   +++k GdkVkkG++++++
  gi|15669416|ref|NP_248226.1| 512 IKVKEGDKVKKGDVIVVL 529
                                   57899**********987 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.18
                                   TT-EEBTTSEEEEE CS
                        PYNP_C  40 lGdkVkkGeplati 53 
                                    Gd+V+ G++++ i
  gi|15669416|ref|NP_248226.1| 553 EGDAVNVGDVIMII 566
                                   69*********987 PP

>> YqfD  Putative stage IV sporulation protein YqfD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       5.3   5.2e+03      17      47 ..      97     127 ..      96     135 .. 0.60
   2 ?   11.6   6.0   8.7e-05     0.087     158     225 ..     467     532 ..     465     548 .. 0.76

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 5.3
                          YqfD  17 erflnllarrgIelwdikrkkdgeleakisl 47 
                                   e+f+ ++ ++gI+++ i    ++   +++ +
  gi|15669416|ref|NP_248226.1|  97 EKFVIKAHENGIDIFRIFDALNDVRNMETAI 127
                                   7777788888887777655444444444444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.7e-05
                          YqfD 158 veikGtrlivevvekeeppeieekdepcnivAkkdGvItkvivesG...eplvkegdtVkkGdvLIsgvie 225
                                   ve++G + +v+++ k+  + + +      i A+++G +t+ +  +G   + +vkegd VkkGdv++  +  
  gi|15669416|ref|NP_248226.1| 467 VEVDGEKFEVKIEPKIGTELKRK---KEVITAEMEGAVTSPF--RGmvtKIKVKEGDKVKKGDVIVVLEAM 532
                                   89*************86644444...579*********9844..44222689*************976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 3939.30
//
Query:       gi|15669417|ref|NP_248227.1|  [L=296]
Description: hypothetical protein MJ_1232 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-38  128.2   1.0    9.5e-38  127.7   0.1    1.7  2  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor
    9.7e-32  109.2   5.2    1.2e-17   64.1   2.3    3.2  3  CBS           CBS domain
    3.7e-07   30.0   0.2    1.2e-06   28.4   0.0    2.0  2  HTH_11        HTH domain
    2.4e-06   27.8   0.0    7.4e-06   26.2   0.0    1.9  2  Rrf2          Transcriptional regulator
     0.0061   16.3   0.4      0.021   14.6   0.4    2.0  1  HTH_38        Helix-turn-helix domain
  ------ inclusion threshold ------
       0.06   12.9   0.6       0.06   12.9   0.6    2.4  3  HTH_24        Winged helix-turn-helix DNA-binding
      0.072   13.2   0.0       0.14   12.2   0.0    1.4  1  HTH_20        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7   0.1   3.7e-41   9.5e-38       1      77 [.       2      78 ..       2      80 .. 0.97
   2 ?   -3.0   0.1       2.3   5.9e+03      27      44 ..     219     236 ..     214     241 .. 0.73

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 3.7e-41
                  HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealkiqt 77
                                  eLt vq+eilq+Li+lyr+k+r++Kg+eiA  l+rn+Gt+RNq+q+L+al+Lv+gvpGPkGGY+Pt+kay+al +++
  gi|15669417|ref|NP_248227.1|  2 ELTVVQREILQELINLYREKNRPIKGTEIALRLNRNPGTIRNQMQALRALDLVDGVPGPKGGYVPTSKAYRALGLED 78
                                  69***********************************************************************9886 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.3
                  HrcA_DNA-bdg  27 eeiAevlkrneGtvRNql 44 
                                   ++iAe ++  +  v+ ++
  gi|15669417|ref|NP_248227.1| 219 HDIAENIDNIDKKVKEVM 236
                                   678888887777777766 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.2   5.7e+03      13      29 ..       6      22 ..       3      26 .. 0.73
   2 !   44.3   0.0   7.1e-15   1.8e-11       1      55 [.     172     225 ..     172     227 .. 0.90
   3 !   64.1   2.3   4.7e-21   1.2e-17       1      56 [.     232     287 ..     232     288 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.2
                                  ETTSBHHHHHHHHHHHT CS
                           CBS 13 ppdttleealelmrekg 29
                                     + l e+++l+rek+
  gi|15669417|ref|NP_248227.1|  6 VQREILQELINLYREKN 22
                                  55667889999998876 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 7.1e-15
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   Vgd+  ++v t++p++tl+e ++l++ek +s+ PVV +++klvG+++l+D+++ +
  gi|15669417|ref|NP_248227.1| 172 VGDVGIKEVWTINPNCTLRETAKLFAEKYISGAPVV-DNDKLVGVISLHDIAENI 225
                                   7788788999***************8888*******.5888**********9876 PP

  == domain 3  score: 64.1 bits;  conditional E-value: 4.7e-21
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   V+++m+rdv+t++ d+ + +al++m +++v+rl +Vd+++k+vGi+t++D+l+ ++
  gi|15669417|ref|NP_248227.1| 232 VKEVMRRDVITIHKDEKIYDALKIMNKNNVGRLVIVDDNNKIVGIITRTDILKIIS 287
                                   89***********************6677****779****************9886 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   4.6e-10   1.2e-06       3      54 ..      12      64 ..       7      65 .. 0.84
   2 ?   -2.9   0.0       2.6   6.7e+03      39      53 ..      76      95 ..      76      97 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 4.6e-10
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GY 54
                                  + ++ l +e++ pi g e+A +Ln+   t+r+ ++aL++l + ++++pg+  GY
  gi|15669417|ref|NP_248227.1| 12 QELINLYREKNRPIKGTEIALRLNRNPGTIRNQMQALRAL-DLVDGVPGPkgGY 64
                                  3445555566666**************************9.7********9999 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.6
                        HTH_11 39 Leelg...vpIesepgr..G 53
                                  Le+ g   vpI+++ ++  G
  gi|15669417|ref|NP_248227.1| 76 LEDEGeiiVPIYKDGKKveG 95
                                  56666666899988877555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   2.9e-09   7.4e-06      11      66 ..      11      65 ..       1      71 [. 0.87
   2 ?   -3.6   0.0       5.7   1.5e+04      26      36 ..     216     226 ..     214     237 .. 0.60

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.9e-09
                                  HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEE CS
                          Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyr 66
                                  l+ l+ L +e+++ p++ +eia r n +p  ++  ++ Lr  +lv  v G++GGy+
  gi|15669417|ref|NP_248227.1| 11 LQELINLYREKNR-PIKGTEIALRLNRNPGTIRNQMQALRALDLVDGVPGPKGGYV 65
                                  5567778877775.6****************************************7 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.7
                                   B-HHHHHHHHT CS
                          Rrf2  26 vsseeiaerqn 36 
                                   +s+++iae+ +
  gi|15669417|ref|NP_248227.1| 216 ISLHDIAENID 226
                                   56667777663 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.4   8.3e-06     0.021      15      39 ..      17      43 ..       2      46 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.3e-06
                        HTH_38 15 rllaeGlslr..eIArrLgrspsTIsR 39
                                    ++++  ++  eIA rL+r+p+TI +
  gi|15669417|ref|NP_248227.1| 17 LYREKNRPIKgtEIALRLNRNPGTIRN 43
                                  233455666699*************87 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   2.4e-05      0.06       6      47 ..       8      54 ..       4      55 .. 0.80
   2 ?   -3.3   0.0       2.8   7.1e+03      15      25 ..     184     194 ..     184     194 .. 0.86
   3 ?   -3.5   0.2       3.1   7.9e+03       4      12 ..     278     286 ..     277     287 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                        HTH_24  6 rkILelLqk.....nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  r+IL++L       n  i  +e+A rl+  p+t++ +++ L    l+
  gi|15669417|ref|NP_248227.1|  8 REILQELINlyrekNRPIKGTEIALRLNRNPGTIRNQMQALRALDLV 54
                                  55565555555556666************************987665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.8
                        HTH_24  15 nprisqreLAe 25 
                                   np+++ re A+
  gi|15669417|ref|NP_248227.1| 184 NPNCTLRETAK 194
                                   8999*999885 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.1
                        HTH_24   4 tdrkILelL 12 
                                   t+ +IL+++
  gi|15669417|ref|NP_248227.1| 278 TRTDILKII 286
                                   677899987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.4e-05      0.14      11      58 ..       6      58 ..       4      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.4e-05
                                  HHHHHHHHH.....STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                        HTH_20 11 vRrrilraL.....araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                  v+r+il++L       +++   +e+a rl   + t+++++++L+  +Lv++v 
  gi|15669417|ref|NP_248227.1|  6 VQREILQELinlyrEKNRPIKGTEIALRLNRNPGTIRNQMQALRALDLVDGVP 58
                                  899*********9999999999***************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1853.57
//
Query:       gi|15669418|ref|NP_248228.1|  [L=288]
Description: hypothetical protein MJ_1233 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-11   43.4   0.0    1.7e-10   41.4   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
    2.4e-10   41.0   0.0    5.6e-10   39.8   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    9.2e-09   35.3   0.0    1.8e-08   34.3   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    3.1e-08   33.4   0.0    4.8e-08   32.7   0.0    1.2  1  MTS              Methyltransferase small domain
    8.4e-08   32.1   0.0    1.5e-07   31.2   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
    4.9e-07   29.3   0.0      4e-06   26.3   0.0    2.1  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.9e-06   26.7   0.1    9.8e-06   25.4   0.0    1.6  2  Met_10           Met-10+ like-protein
    1.4e-05   24.9   0.4     0.0032   17.2   0.0    2.8  3  N6_N4_Mtase      DNA methylase
    1.6e-05   24.8   0.0    3.8e-05   23.6   0.0    1.6  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
    1.9e-05   24.2   0.0    5.1e-05   22.8   0.0    1.6  1  Spermine_synth   Spermine/spermidine synthase domain
    3.2e-05   23.6   0.0    5.8e-05   22.7   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00061   19.7   0.0      0.002   18.0   0.0    1.8  2  Methyltransf_23  Methyltransferase domain
     0.0012   18.6   0.1      0.013   15.2   0.1    2.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0028   17.1   0.0      0.006   16.0   0.0    1.5  1  SAM_MT           Putative SAM-dependent methyltransferase
     0.0085   15.4   0.0      0.015   14.6   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
       0.01   15.1   0.0      0.022   14.1   0.0    1.5  1  N6_Mtase         N-6 DNA Methylase
      0.026   14.3   0.0       0.89    9.4   0.0    2.5  3  DUF1965          Domain of unknown function (DUF1965)
      0.049   14.7   0.0      0.096   13.7   0.0    1.5  1  Methyltransf_24  Methyltransferase domain
      0.077   12.7   0.0       0.14   11.9   0.0    1.4  1  UPF0020          Putative RNA methylase family UPF0020


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       3.4   3.2e+03      44      64 ..      47      64 ..      13      66 .. 0.68
   2 !   41.4   0.0   1.8e-13   1.7e-10       1      95 [.     139     241 ..     139     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.4
                                  EEEETTEECCCTSS-TT-EEE CS
               Methyltransf_11 44 kvefvvadaeklpfednsfDl 64
                                      ++  + k+p  d sfD+
  gi|15669418|ref|NP_248228.1| 47 D---REKKIAKFPEGDVSFDI 64
                                  3...67788888888889997 PP

  == domain 2  score: 41.4 bits;  conditional E-value: 1.8e-13
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-...EEEETTEECCCT..SS-TT-EEEEEEES....-CC CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl...kvefvvadaekl..pfednsfDlvvsse....vlh 72 
                                   Ld  +G G+ a +  +rga+v++++ ++++l+lak +   e+l    ++++ +da ++   f+d+ fD+v+          
  gi|15669418|ref|NP_248228.1| 139 LDTCMGLGYTAIEAYRRGAEVITIEKNPNVLELAKINPYSEELfkgGIKIILGDAYDVikRFKDEEFDVVIHDPprfsLAG 219
                                   6777899***************************999999888999999********5567**********9764443444 PP

                                   C-CCHHHHHHHHHHHEEEEEEEE CS
               Methyltransf_11  73 hvedpekalkeiaRvLkpgGllv 95 
                                   h+   e++ kei RvLkpgG+l+
  gi|15669418|ref|NP_248228.1| 220 HL-YSEEFYKEIFRVLKPGGRLF 241
                                   44.79***************997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   5.9e-13   5.6e-10       1      97 []     138     238 ..     138     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 5.9e-13
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCGB..SSSTTTEEEEEEEST.GG CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaedl..pfedgsfDlvvssga.lh 75 
                                   vLd + G G +++++ +r+  a+v+ ++ +++ le a+ +  +e+l    ++++ gda d+   f+d++fD+v+     ++
  gi|15669418|ref|NP_248228.1| 138 VLDTCMGLGYTAIEAYRRG--AEVITIEKNPNVLELAKINPYSEELfkgGIKIILGDAYDVikRFKDEEFDVVIHDPPrFS 216
                                   9*****************5..*****************88888888899*********9963359**********655666 PP

                                   GSSHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                   +  +   e+++kei+rvLkpgG
  gi|15669418|ref|NP_248228.1| 217 LAGHLYSEEFYKEIFRVLKPGG 238
                                   666667789************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   1.9e-11   1.8e-08       2     108 ..     133     241 ..     132     273 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.9e-11
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAren..aqklgldnveFeqgdiee.leklledekfDlil 79 
                                   +kg +vlD   G G+ ++e+++    +aev+ i+ +++++elA+ n  +++l+   ++   gd+ + ++  ++de fD+++
  gi|15669418|ref|NP_248228.1| 133 KKGEKVLDTCMGLGYTAIEAYR---RGAEVITIEKNPNVLELAKINpySEELFKGGIKIILGDAYDvIKR-FKDEEFDVVI 209
                                   6899*****************4...489*****************6225555555***********7776.9********* PP

               Methyltransf_31  80 snevl...naladpdkileeiervlkpggill 108
                                    + +    +    ++++++ei+rvlkpgg+l 
  gi|15669418|ref|NP_248228.1| 210 HDPPRfslAGHLYSEEFYKEIFRVLKPGGRLF 241
                                   9944455577777899*************985 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   5.1e-11   4.8e-08      26     148 ..     129     254 ..     123     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 5.1e-11
                                   HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC...EEEEE-STT...TTSTTS-EEE CS
                           MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle...vevvasdvl...eeveekkfdl 100
                                   +++ ++ +kvlD + G G+ ++++ ++  e  v  ++++ + le+ak n  +++l    ++++  d++   + +++++fd+
  gi|15669418|ref|NP_248228.1| 129 AVKVKKGEKVLDTCMGLGYTAIEAYRRGAE--VITIEKNPNVLELAKINPYSEELFkggIKIILGDAYdviKRFKDEEFDV 207
                                   456668899**************9998877..999*************9888777669988887665511167779***** PP

                                   EEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEE.EEEETTSCHHHH CS
                           MTS 101 ivsNPPfhagkatelavaeeliaeAkeaLkegGeLl.iVanrklgyesl 148
                                   ++  PP  +     +   ee+ +e  ++Lk+gG+L+  V n   +y+ +
  gi|15669418|ref|NP_248228.1| 208 VIHDPPRFSLAG--HLYSEEFYKEIFRVLKPGGRLFhYVGNPGKKYRGK 254
                                   ******655554..68899***************984688888888755 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   1.6e-10   1.5e-07      40     122 ..     133     213 ..     112     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.6e-10
                                   HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T.TTEEEEES-HHHHCTS--SS-EEEEEEE CS
                 Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee.etaelkedaleallklakkkeefdivfl 119
                                    +g++vLD + G G  ++EA  Rga +++ +ek+++++++ k n  + +l +  ++++  da++ +++   k+eefd+v  
  gi|15669418|ref|NP_248228.1| 133 KKGEKVLDTCMGLGYTAIEAYRRGA-EVITIEKNPNVLELAKINPYSEELFKgGIKIILGDAYDVIKRF--KDEEFDVVIH 210
                                   46789*******************5.6899*********888886555554447************999..899******* PP

                                   --S CS
                 Cons_hypoth95 120 DPP 122
                                   DPP
  gi|15669418|ref|NP_248228.1| 211 DPP 213
                                   *** PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   4.3e-09     4e-06      41     150 ..     128     241 ..     115     246 .. 0.83
   2 ?    0.3   0.0       0.4   3.7e+02     202     228 ..     258     284 ..     249     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.3e-09
                                   HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS..TEEEEE--TTT-..TTS-T-E CS
               Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki..nieflqanaeeL..pfeddsf 117
                                   + v vk+g+kvlD + G g  a++   + ++  +v+ ++ n+n+L+ ++     e      i+ + ++a ++   f+d+ f
  gi|15669418|ref|NP_248228.1| 128 NAVKVKKGEKVLDTCMGLGYTAIE---AYRRGAEVITIEKNPNVLELAKINPYSEELFkgGIKIILGDAYDVikRFKDEEF 205
                                   3456899************99886...5667779**************9876555444379******999874479***** PP

                                   EEEEEE...S-GGG-S-HHHHHHHHHHHEEEEEEEE CS
               Ubie_methyltran 118 Dvvtvs...fGlrnvtDklkaLkeayrvlkpGGrlv 150
                                   Dvv      f l      ++  ke++rvlkpGGrl+
  gi|15669418|ref|NP_248228.1| 206 DVVIHDpprFSLAGHLYSEEFYKEIFRVLKPGGRLF 241
                                   **9863444************************986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.4
                                   HHHHHHHHHTTEEEEEEEEEGGGTEEE CS
               Ubie_methyltran 202 etlkeliedaGfksveyesltgGvvai 228
                                   + + e +++ Gf +v+  + + Gvva+
  gi|15669418|ref|NP_248228.1| 258 KGVMERLRKVGFVNVKRVEEALGVVAV 284
                                   55567789****************997 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.3   3.2e+03      74     107 ..      31      64 ..      16      68 .. 0.62
   2 !   25.4   0.0     1e-08   9.8e-06      97     192 ..     131     235 ..     120     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.3
                                   EEEETTTS---GGGHHHHHHHHTT--TT-EEEET CS
                        Met_10  74 fklDvskvyfsskleaErerlaklveegevVvdv 107
                                   ++lD+ k    +k   +re+ ++++ eg+v  d+
  gi|15669418|ref|NP_248228.1|  31 LNLDLNKTEKKEKILIDREKKIAKFPEGDVSFDI 64 
                                   4555555555556666666666666666666665 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1e-08
                                   T--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-.TTCEEEEES-GGG---...TT-EE... CS
                        Met_10  97 lveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkv.ekvvkpileDgrevir...eqlad... 170
                                   +v++ge V+d   G G+ ai + +  ++ +v++i++nP+  ++ k n    ++ +  +k il+D+ +vi+   ++ +d   
  gi|15669418|ref|NP_248228.1| 131 KVKKGEKVLDTCMGLGYTAIEAYR--RGAEVITIEKNPNVLELAKINPYSEELfKGGIKIILGDAYDVIKrfkDEEFDvvi 209
                                   499*****************9998..99******************98877763678***********9755444455555 PP

                                   ....EEEE--TTTGGGGHHHHHHHEE CS
                        Met_10 171 ....rvvmnlpksaieFldkvlaalk 192
                                       r+ +    +++eF ++++++lk
  gi|15669418|ref|NP_248228.1| 210 hdppRFSLAGHLYSEEFYKEIFRVLK 235
                                   55554444444455666666666665 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1         1   9.6e+02      50      64 ..      27      54 ..       8     100 .. 0.54
   2 !   17.2   0.0   3.4e-06    0.0032     189     230 ..     132     173 ..     121     174 .. 0.93
   3 ?    4.5   0.0     0.026        25      35      62 ..     223     250 ..     220     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1
                                  EEEEEEE-CCCHHT.............H CS
                   N6_N4_Mtase 50 gsifiniddseikk.............e 64
                                    if+n d ++++k             +
  gi|15669418|ref|NP_248228.1| 27 EEIFLNLDLNKTEKkekilidrekkiaK 54
                                  3455555555555433333333333330 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.4e-06
                                   S-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                   N6_N4_Mtase 189 tkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelae 230
                                    kkg+ vlD  +G G+Ta++a + g + i ie++++ +ela+
  gi|15669418|ref|NP_248228.1| 132 VKKGEKVLDTCMGLGYTAIEAYRRGAEVITIEKNPNVLELAK 173
                                   589*********************************999886 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.026
                                   HHHHHHHHHHHEEEEEEEEEEE-CCCHH CS
                   N6_N4_Mtase  35 lekvlkevrrvLkddgsifiniddseik 62 
                                    e++ ke+ rvLk++g +f  ++    k
  gi|15669418|ref|NP_248228.1| 223 SEEFYKEIFRVLKPGGRLFHYVGNPGKK 250
                                   57899*************9988876665 PP

>> Methyltransf_30  S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0     4e-08   3.8e-05      32      89 ..     185     243 ..     163     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4e-08
                                   EEEEEES-HHHHHHHC-.T-EEEEEE-SS-TTTSGGGCSHHHHHHHHHHEEEEEEEEES CS
               Methyltransf_30  32 tlklligdarealkeld.ekadawFlDgFsPaknPelwseellkelarllkkkgtlaty 89 
                                    +k+++gda +++k+ + e++d++ +D+   + +  l+see++ke++r+lk++g+l  y
  gi|15669418|ref|NP_248228.1| 185 GIKIILGDAYDVIKRFKdEEFDVVIHDPPRFSLAGHLYSEEFYKEIFRVLKPGGRLFHY 243
                                   689************999**********9999***********************9877 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   5.4e-08   5.1e-05      75     133 ..     186     245 ..     180     275 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.4e-08
                                   EEEEESTCHHHHCTCSS.-EEEEEEECCSTTCSSCGCSSHHHHHHHHHTEEEEE.EEEEEE CS
                Spermine_synth  75 vklvlgdgfkflkayek.kfdvvivdsldpvgpaenlFskeffdllkkvlkedG.viilqa 133
                                   +k++lgd++ ++k+ ++ +fdvvi d     + a +l+s+ef++ + +vlk++G +++ ++
  gi|15669418|ref|NP_248228.1| 186 IKIILGDAYDVIKRFKDeEFDVVIHDPPR-FSLAGHLYSEEFYKEIFRVLKPGGrLFHYVG 245
                                   5899*************9********988.888888*****************94455555 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   6.2e-08   5.8e-05       3      80 ..     137     213 ..     135     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.2e-08
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgv.sdkitlvlgdvfellaklklekikvdlvflSpP 80 
                                    +lD + G G  +i+  + + +vi+ie+n++ l++a+ N  + +  +  i+++lgd  ++++++k e+   d+v+  pP
  gi|15669418|ref|NP_248228.1| 137 KVLDTCMGLGYTAIEAYRRGAEVITIEKNPNVLELAKINPYSEELfKGGIKIILGDAYDVIKRFKDEEF--DVVIHDPP 213
                                   79*************************************9888776899******************99..*******9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       8.5     8e+03     103     117 ..      63      77 ..      60      80 .. 0.79
   2 !   18.0   0.0   2.1e-06     0.002      20     119 ..     132     244 ..     112     279 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8.5
               Methyltransf_23 103 rqiatllkpgGylll 117
                                   + ++++ k++G++++
  gi|15669418|ref|NP_248228.1|  63 DILKKIAKDEGHIYF 77 
                                   567888899999987 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.1e-06
               Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..........kakkaqkdqfdeqeaaepqgkfdlIvl.. 88 
                                    ++g +vLd   G G+++ ++ ++g++v+ ++ +p+  e+a+          + +k +   ++    +++++ fd+++   
  gi|15669418|ref|NP_248228.1| 132 VKKGEKVLDTCMGLGYTAIEAYRRGAEVITIEKNPNVLELAKinpyseelfkGGIKIILGDAYDVIKRFKDEEFDVVIHdp 212
                                   37888*******************************999998888888888833444444444444445778999999655 PP

               Methyltransf_23  89 .revlehvpdppellrqiatllkpgGylllse 119
                                    r++l    + +e  + i++ lkpgG+l++ +
  gi|15669418|ref|NP_248228.1| 213 pRFSLAGHLYSEEFYKEIFRVLKPGGRLFHYV 244
                                   577777777789****************8766 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.4e-05     0.013      67     205 ..     128     272 ..     122     277 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                   HHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC..SEEEEES-GGGTTGGG..-SE CS
                          PCMT  67 ellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle..nvivvvgDGrkGyeek..aPY 143
                                   + +++kkg++vL+   G Gy +    +  ++ + v++ie+ +++ e ak n   ++l    ++++ gD +   + +    +
  gi|15669418|ref|NP_248228.1| 128 NAVKVKKGEKVLDTCMGLGYTAI---EAYRRGAEVITIEKNPNVLELAKINPYSEELFkgGIKIILGDAYDVIKRFkdEEF 205
                                   56789***************764...445677889*************999777766556788888888876665411357 PP

                                   EEEE.....ESSB....BSS--HHHHHTEEEEEEEEEEESBSSSEEEEEEEEETTTEEEEEEEEEE---B- CS
                          PCMT 144 daih.....vgaa....apeiPealidQLkeGGrlvvPvgeeeeQvlklvdkkadgkvvikkleevrfvpl 205
                                   d+++     ++ a    ++e  +++++ Lk+GGrl   vg+      k+++ k+ +k v+++l +v fv +
  gi|15669418|ref|NP_248228.1| 206 DVVIhdpprFSLAghlySEEFYKEIFRVLKPGGRLFHYVGN----PGKKYRGKDLQKGVMERLRKVGFVNV 272
                                   76542333334442222567788888888888888888884....23333333334556667777777665 PP

>> SAM_MT  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.3e-06     0.006      47     156 ..     110     212 ..     104     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.3e-06
                        SAM_MT  47 aahRrkfgggrgeaiakavglkkgvlptvlDaTaGlGrDafvlaslGckvtliErhpvvaaLLedglkRakqdaeigella 127
                                     hR k  +  ++++ k   +k +   +vlD+  GlG  a+     G++v  iE++p v  L       ak +   +el +
  gi|15669418|ref|NP_248228.1| 110 RMHRTKEVNPYEDTLNKINAVKVKKGEKVLDTCMGLGYTAIEAYRRGAEVITIEKNPNVLEL-------AKINPYSEELFK 183
                                   678888888889999887666666677******************************98665.......455555567778 PP

                        SAM_MT 128 erlkLlaasslealakleeekpdvvYlDP 156
                                     +k++ +++++++++ ++e+ dvv  DP
  gi|15669418|ref|NP_248228.1| 184 GGIKIILGDAYDVIKRFKDEEFDVVIHDP 212
                                   88999999999999999999999998888 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.6e-05     0.015      55     163 ..     127     241 ..     116     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                                   HTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-.SSS-EEEEES-GGG---.....--S CS
                          CMAS  55 leklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeld.lerkvevklldyedlde.....kvd 129
                                   ++ +++k+G+++Ld   G G+++++a +r +++v+ +    +  +lak +  +++ ++   ++ l d  d+ +     ++d
  gi|15669418|ref|NP_248228.1| 127 INAVKVKKGEKVLDTCMGLGYTAIEAYRR-GAEVITIEKNPNVLELAKINPYSEElFKGGIKIILGDAYDVIKrfkdeEFD 206
                                   456789***********************.****99988888888888665544414556777777765554324445788 PP

                                   EEEE.ES-GGGTSGGGHHHHHHHHHHHS-TT-EEE CS
                          CMAS 130 rvvs.vgafehvgkenydtffkklkkllkedGlll 163
                                    v+     f   g+   ++f+k+++++lk++G+l 
  gi|15669418|ref|NP_248228.1| 207 VVIHdPPRFSLAGHLYSEEFYKEIFRVLKPGGRLF 241
                                   76641457888899999999999999999999875 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.3e-05     0.022      40     138 ..     128     218 ..     119     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                      N6_Mtase  40 ellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkf 120
                                   + ++ k+ge+v+D ++G g   ++a +            ++   ekn++  +Lak+N +  +  +  +ki lgd++   k 
  gi|15669418|ref|NP_248228.1| 128 NAVKVKKGEKVLDTCMGLGYTAIEAYRR---------GAEVITIEKNPNVLELAKINPYSEELFKGGIKIILGDAYDVIKR 199
                                   6678999999*******99999999883.........4556678********************************99888 PP

                      N6_Mtase 121 ekdkkfdvvvaNpp.fnqk 138
                                    kd++fdvv+  pp f+ +
  gi|15669418|ref|NP_248228.1| 200 FKDEEFDVVIHDPPrFSLA 218
                                   88**********9966655 PP

>> DUF1965  Domain of unknown function (DUF1965)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.22     2e+02      36      56 ..      79      99 ..      73     102 .. 0.82
   2 ?   -3.5   0.0       9.9   9.4e+03      35      49 ..     147     161 ..     145     168 .. 0.73
   3 ?    9.4   0.0   0.00094      0.89      13      38 ..     205     230 ..     203     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.22
                                  SSHHHHHHHHTSTT------- CS
                       DUF1965 36 etteeFRaaikspgfkklgpn 56
                                  ++ e F+aai++ g+ kl p+
  gi|15669418|ref|NP_248228.1| 79 KDGEVFKAAISNNGYYKLVPT 99
                                  55678**********999775 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.9
                                   ESSHHHHHHHHTSTT CS
                       DUF1965  35 YetteeFRaaikspg 49 
                                   Y+ +e++R   +  +
  gi|15669418|ref|NP_248228.1| 147 YTAIEAYRRGAEVIT 161
                                   888999998776555 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00094
                                   EE--SS-GGG-EEEEEEETTEEESSH CS
                       DUF1965  13 lDvtGRdpskWkvlGwlyngifYett 38 
                                   +Dv   dp + +++G ly ++fY+ +
  gi|15669418|ref|NP_248228.1| 205 FDVVIHDPPRFSLAGHLYSEEFYKEI 230
                                   899999*****************975 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0    0.0001     0.096      18      99 ..     153     238 ..     142     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.0001
               Methyltransf_24  18 lrrngagrlvavdhdpgaeeaaalare.....aglddrvrlikadseealaslaagsiDllfiDgghaa....e.avledl 88 
                                    rr +  ++++++++p   ++ +la+      + ++  +++i +d+ +++++++++++D+++ D +       +    e++
  gi|15669418|ref|NP_248228.1| 153 YRRGA--EVITIEKNP---NVLELAKInpyseELFKGGIKIILGDAYDVIKRFKDEEFDVVIHDPP-RFslagHlYSEEFY 227
                                   34444..699******...8888888543343566777**************************54.33122121233446 PP

               Methyltransf_24  89 eallprlapgg 99 
                                   + + ++l+pgg
  gi|15669418|ref|NP_248228.1| 228 KEIFRVLKPGG 238
                                   77777888777 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.14      65     153 ..     145     235 ..     114     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT.-GGGEEEEE--GGG--..STTS---EEEE----------HHHHH CS
                       UPF0020  65 lkaeaeeearaelklygsDldrrvvqgareNaekag.vgdliefsqadaakLr..lkegevdvivtnpPYGerlgskkale 142
                                   l  +a e+ r+ ++++ ++++++v++ a+ N  + +  ++ i++   da ++    k++e+dv++ +pP   +l  +   e
  gi|15669418|ref|NP_248228.1| 145 LGYTAIEAYRRGAEVITIEKNPNVLELAKINPYSEElFKGGIKIILGDAYDVIkrFKDEEFDVVIHDPPR-FSLAGHLYSE 224
                                   55677788889999*****************8665516899********9998666677**********3.3444455558 PP

                                   HHHHHHHHHHH CS
                       UPF0020 143 kLYseflrelk 153
                                   ++Y+e+ r lk
  gi|15669418|ref|NP_248228.1| 225 EFYKEIFRVLK 235
                                   88888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2062.32
//
Query:       gi|15669419|ref|NP_248229.1|  [L=241]
Description: hypothetical protein MJ_1234 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-26   91.5   6.5    8.9e-26   91.2   5.8    1.5  1  Cas_Cas6  CRISPR associated protein Cas6


Domain annotation for each model (and alignments):
>> Cas_Cas6  CRISPR associated protein Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   5.8     5e-30   8.9e-26       2     145 ..      84     238 ..      83     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 5e-30
                                   HHCS-EEEETTEEEEEEEEEE----S--TCEE.EEESS-BBEEEEEEETTCCEEEEE-T..TSTTHHHHHHHHHHHHHHHH CS
                      Cas_Cas6   2 llknkeirlgnnefkveevellkepeitssevvfktlSPivvrstkkengkkktyylsp..ddeeFsellkenlkkkykal 80 
                                   l + +e++l+n +f+v+e+++++ +++ +   +f t SPiv++  k++++ ++ +++++  d ++F ++l++n+ kkyka+
  gi|15669419|ref|NP_248229.1|  84 LDNLEEVNLNNFKFEVSELKKFDLKVK-N---KFITGSPIVLY--KDKDRGEYIKFYDDdfDLMFFVQRLQDNAVKKYKAF 158
                                   66889*********************7.2...49*********..446777777777555899****************** PP

                                   HSS........SS---EEEEE.EEEE..............TEEEEEEEEEEEE.....EE-HHHHHHHHHC-SCS-CCCT- CS
                      Cas_Cas6  81 ygee......keeklsikpdk.kvkkivvkkk........etyirGylgrfel.....egdpellklaydaGlGeknsqGF 141
                                   y+ee            ++ +  +v++  v  +        e+ + G++ ++       +++++++k+++d+GlGekns+GF
  gi|15669419|ref|NP_248229.1| 159 YNEEpvlngfI-----FDRISpRVRNGRVDVYvriakkgrEFLVVGTTWKLLEkikirKEERKFYKFIMDCGLGEKNSLGF 234
                                   *****766663.....3333333444444444444456784444444433322445569********************** PP

                                   S-EE CS
                      Cas_Cas6 142 Gmve 145
                                   G+++
  gi|15669419|ref|NP_248229.1| 235 GFIN 238
                                   **98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1711.35
//
Query:       gi|15669420|ref|NP_248230.1|  [L=425]
Description: ribulose bisophosphate carboxylase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.8e-104  349.1   0.3   2.3e-104  348.8   0.3    1.1  1  RuBisCO_large    Ribulose bisphosphate carboxylase large chai
    1.5e-37  128.4   0.0    1.3e-36  125.4   0.0    2.3  3  RuBisCO_large_N  Ribulose bisphosphate carboxylase large chai


Domain annotation for each model (and alignments):
>> RuBisCO_large  Ribulose bisphosphate carboxylase large chain, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.8   0.3  2.5e-108  2.3e-104       1     299 []     132     424 ..     132     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 348.8 bits;  conditional E-value: 2.5e-108
                                   .HHHHHHHH...T--EEEEE-SSSS---HHHHHHHHHHHHTT-.SEEE--TT-SSBTTB-HHHHHHHHHHHHHHHHHHHSS CS
                 RuBisCO_large   1 giaverevlnkegrpilGtiiKPklGLspknyarvvyelllgglDfiKdDEnlnsqpfarlkdrieavaeaikraqdetGe 81 
                                   gi++ re+l+ ++rp+lGti+KPk+GL+++++a+v+ye++ gg+D++KdDEnl+sq f++++dri + +e+ ++a++etGe
  gi|15669420|ref|NP_248230.1| 132 GIEGVRETLKIKERPLLGTIVKPKVGLKTEEHAKVAYEAWVGGVDLVKDDENLTSQEFNKFEDRIYKTLEMRDKAEEETGE 212
                                   7999***************************************************************************** PP

                                   --EEEEE---SSHHHHHHHHHHHHHHHGGEEEEEHHHH-HHHHHHHHHHSTTS..EEEEE-TTTHHHHST--SEE-HHHHH CS
                 RuBisCO_large  82 kklyalnitaddleemlrraefvketggeivlvdvlviGfaaitslrkafrknelllHlHraghgaltrqskhGisfrvla 162
                                   +k y+ nita + +em+rrae++ ++g+e v++dv+v+Gf+a++s r++  + ++++H+Hra+h+a+tr+++ Gis+  la
  gi|15669420|ref|NP_248230.1| 213 RKAYMPNITAPY-REMIRRAEIAEDAGSEYVMIDVVVCGFSAVQSFREE--DFKFIIHAHRAMHAAMTRSRDFGISMLALA 290
                                   *********887.9**********************************9..8889************************** PP

                                   HHHHHHT-SEEE---TTSSSBS--GG......GHHHHHHHHSSEEE-SS-EEE-TT----EEEEESS--TTTHHHHHHHHS CS
                 RuBisCO_large 163 kllRLlGvdhlhtgtvgvgklegdesvvkgfkdtlrekmleedeaegiffeqdlaslkavlpvasgGihagqlpellenlg 243
                                   k+ RLlGvd+lh+gtv vgk+eg e+ vk+ +d+++ +++e+d+ e++ff+qd++++k+v+pv sgG+h   +p+++e+lg
  gi|15669420|ref|NP_248230.1| 291 KIYRLLGVDQLHIGTV-VGKMEGGEKEVKAIRDEIVYDKVEADN-ENKFFNQDWFDIKPVFPVSSGGVHPRLVPKIVEILG 369
                                   ****************.************************997.578********************************* PP

                                   ---SEEE-HHHHHTSTT-HHHHHHHHHHHHHHHHHT--HHHHHTT-HHHHHHHHHX CS
                 RuBisCO_large 244 esdvilqaGGGilgHpdgaaaGakalrqaleaaveGadleeyAkehkeLarAlesw 299
                                   + d+i+qaGGG++gHpdg+ aGaka+r a+ea++eG++lee A+e +eL++Ale+w
  gi|15669420|ref|NP_248230.1| 370 R-DLIIQAGGGVHGHPDGTRAGAKAMRAAIEAIIEGKSLEEKAEEVAELKKALEYW 424
                                   *.****************************************************99 PP

>> RuBisCO_large_N  Ribulose bisphosphate carboxylase large chain, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   0.0   1.4e-40   1.3e-36       1     120 []       2     122 ..       2     122 .. 0.97
   2 ?   -0.3   0.0      0.12   1.1e+03      19      51 ..     151     182 ..     137     211 .. 0.67
   3 ?   -4.0   0.0       1.8   1.7e+04     100     116 ..     248     264 ..     248     264 .. 0.84

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 1.4e-40
               RuBisCO_large_N   1 dyvdedyepketdllaafrvePaegvsveeaaaavAaeSStgtwtevsttkdellkklkakvyeieevee....ekelvki 77 
                                   dy++ +y+p+e dll+++ ++   g ++e+ a+++A+eSS+gtwt+v+t+k+++++kl++kvyei+e+ e    +  l+ki
  gi|15669420|ref|NP_248230.1|   2 DYINLNYRPNEGDLLSCMVIK---GENLEKLANEIAGESSIGTWTKVQTMKSDIYEKLRPKVYEIKEIGEengyKVGLIKI 79 
                                   69******************9...99*****************************************99887888899*** PP

               RuBisCO_large_N  78 AYplelFeegsipqllssiaGnifgmkavkalrleDirlPkay 120
                                   AYpl  Fe +++p +l+ iaGnifgmk  k lr+ D+r+P+++
  gi|15669420|ref|NP_248230.1|  80 AYPLYDFEINNMPGVLAGIAGNIFGMKIAKGLRILDFRFPAEF 122
                                   ****************************************986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.12
               RuBisCO_large_N  19 rvePaegvsveeaaaavAaeSStgtwtevsttk 51 
                                    v+P+ g+++ee a +vA e+ +g    v  ++
  gi|15669420|ref|NP_248230.1| 151 IVKPKVGLKTEEHA-KVAYEAWVGGVDLVKDDE 182
                                   47899999988876.688888777654444443 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 1.8
               RuBisCO_large_N 100 ifgmkavkalrleDirl 116
                                   + g++av++ r eD+++
  gi|15669420|ref|NP_248230.1| 248 VCGFSAVQSFREEDFKF 264
                                   57999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2761.28
//
Query:       gi|15669421|ref|NP_248231.1|  [L=634]
Description: putative mRNA 3'-end processing factor 2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-27   96.0   0.0    3.1e-27   95.1   0.0    1.5  1  Beta-Casp      Beta-Casp domain
    1.9e-27   95.0  14.7    1.5e-26   92.1   3.6    4.0  4  KH_7           KH domain
    9.9e-17   60.6   0.0    4.1e-16   58.6   0.0    2.1  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.6e-12   47.9   0.8    3.7e-12   46.7   0.8    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
    3.2e-12   46.3   0.0    5.5e-12   45.5   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    1.6e-10   40.9   0.1    3.4e-10   39.8   0.1    1.6  1  Lactamase_B_2  Beta-lactamase superfamily domain
      6e-05   22.8   1.1      6e-05   22.8   1.1    3.0  2  KH_2           KH domain
     0.0005   20.0   0.0     0.0015   18.4   0.0    1.8  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0016   18.3   0.1     0.0061   16.4   0.1    2.0  1  KH_4           KH domain
  ------ inclusion threshold ------
      0.055   13.9   0.2       0.21   12.0   0.2    1.9  2  DUF2870        Protein of unknown function (DUF2870)
       0.14   12.2   0.0       0.37   10.8   0.0    1.7  1  MOEP19         KH-like RNA-binding domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   0.0   1.9e-30   3.1e-27       1     109 [.     419     542 ..     419     543 .. 0.84

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 1.9e-30
                                   HHHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.......................E-SHH....HHHH.. CS
                     Beta-Casp   1 aqellylLeelwkekkledlklpiyldsplaskatevYkeyae.......................veakslewmeskkee 58 
                                   aqel+++Lee  ++  + + ++p+yld+ ++ +at+++++y+e                       ++   +  +++++ +
  gi|15669421|ref|NP_248231.1| 419 AQELMLVLEEGYNQ--G-IFNAPVYLDG-MIWEATAIHTAYPEylskemrqkifhegdnpflsevfKR---VGSTNERR-K 491
                                   7***********88..5.7789******.************998888877777777777777544322...33344443.2 PP

                                   HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHH CS
                     Beta-Casp  59 lnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrk 109
                                   + +s++p+vila+sgml+gG+s+e+lk+l++d++n++i+vgyqaegTlgrk
  gi|15669421|ref|NP_248231.1| 492 VIDSDEPCVILATSGMLTGGPSVEYLKHLAPDEKNAIIFVGYQAEGTLGRK 542
                                   44789********************************************98 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   3.6   9.3e-30   1.5e-26       1      68 []       4      69 ..       4      69 .. 0.98
   2 ?    5.4   0.2     0.011        18       7      27 ..      75      95 ..      72     127 .. 0.77
   3 ?    2.8   0.4     0.071   1.2e+02      43      65 ..     156     178 ..     151     181 .. 0.86
   4 ?   -3.5   0.0       6.6   1.1e+04      49      59 ..     457     467 ..     450     472 .. 0.73

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 9.3e-30
                          KH_7  1 eevleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                                  eevle+++++i +k Pke+ki dv+FEGPe+V+Y+knp++f+  +++i++lAk+lrkRi iRpDpsvl
  gi|15669421|ref|NP_248231.1|  4 EEVLENIRKEIIKKSPKEAKIVDVQFEGPEVVVYVKNPEIFT--NEIIKSLAKDLRKRISIRPDPSVL 69
                                  689***************************************..89********************98 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
                          KH_7  7 lkekieeklPkevkitdveFE 27
                                   k+ki e +P+e++it+  F 
  gi|15669421|ref|NP_248231.1| 75 AKQKILEIVPEEAEITNFVFD 95
                                  589**************9986 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.071
                          KH_7  43 engdlirklAkelrkRiviRpDp 65 
                                   e ++++r++ + + + iv+R D 
  gi|15669421|ref|NP_248231.1| 156 EVKEILRRIGRRIHRDIVVRGDY 178
                                   56799***************995 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 6.6
                          KH_7  49 rklAkelrkRi 59 
                                   + l+ke+r++i
  gi|15669421|ref|NP_248231.1| 457 EYLSKEMRQKI 467
                                   56788888887 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.8   6.2e+03      20      37 ..     393     413 ..     392     420 .. 0.82
   2 !   58.6   0.0   2.5e-19   4.1e-16       2      62 .]     562     625 ..     561     625 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.8
                         RMMBL  20 nellelirklkprn...vilv 37 
                                   +ell++++ +  r    +i+v
  gi|15669421|ref|NP_248231.1| 393 RELLRVVSETTDRGgkvLIPV 413
                                   799999999999988877777 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 2.5e-19
                         RMMBL   2 ipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvfiP 62 
                                   ip+++++++i+ fSgH+d+ +l+++ir+lkp +  +i vHGee +++++a++ ++ +++ +++P
  gi|15669421|ref|NP_248231.1| 562 IPINLQVYTIEgFSGHSDRKQLIKYIRRLKPSPekIIMVHGEESKCLDFADTVRRLFKKQTYVP 625
                                   89**************************************************976667777666 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.8   2.3e-15   3.7e-12       4     162 ..     191     362 ..     188     412 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 2.3e-15
                                   CSSEEEEEEETTCEEEES--SCHHHHHHHH.HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                   Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal.elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                   ++ ++ +++++++ +LiD+G+  + +++a     a ++ ++d+davi+TH+HlDH+G  +gl +     ++++   ++ l 
  gi|15669421|ref|NP_248231.1| 191 VGRSCLYVQTPDTRVLIDCGINVACEDKAFpHFDAPEFSIEDLDAVIVTHAHLDHCGFIPGLFRYGYDGPVYCTRPTRDLM 271
                                   6789*****************99988877779**********************************999999999999999 PP

                                   CHHHHHHHHHCCHH..........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCC..EEEEEETTCCEEEECTTT CS
                   Lactamase_B  84 meeaddaasrkgll..........lagvsadkpdvdeeeldgnaggrralyvtggpghghg..hgvveygggkvlftGDal 152
                                   +   +d+ +  + +          +++ ++    +d  +++++ + ++++ +  g++ g+   h++++ g  ++++tGD  
  gi|15669421|ref|NP_248231.1| 272 TLLQKDYLEIAKKEgkevpytskdIKTCVKHTIPIDYGVTTDISPTIKLTLHNAGHVLGSAiaHLHIGEGLYNLAYTGDIK 352
                                   999999999988889*******99666666666778888888888888888888887777522666666888*******99 PP

                                   SSHHCCCCCC CS
                   Lactamase_B 153 lagetgridl 162
                                   ++ ++++ + 
  gi|15669421|ref|NP_248231.1| 353 FETSRLLEPA 362
                                   9888877776 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   3.4e-15   5.5e-12       6     170 ..     202     359 ..     197     372 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.4e-15
                 Lactamase_B_6   6 nvkiLlDvGwdes.kvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslld 85 
                                   ++++L+D+G +   ++++   ++  e  i+++d+++++ha l+h G +  +   f  +++ + pvy+t p+  L  ++  d
  gi|15669421|ref|NP_248231.1| 202 DTRVLIDCGINVAcEDKAFPHFDAPEFSIEDLDAVIVTHAHLDHCG-F--IPGLF--RYGYDGPVYCTRPTRDLMTLLQKD 277
                                   789********65133333466777779******************.3..56655..5899*************8887777 PP

                 Lactamase_B_6  86 lyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWki..skesekivYavdwnh 164
                                   + + ++ +g+e     + +di+++ ++ +++ Y  +++++     + +t +naGh+lG +i ++   +++ ++ Y  d+  
  gi|15669421|ref|NP_248231.1| 278 YLEIAKKEGKE--VPYTSKDIKTCVKHTIPIDYGVTTDISP---TIKLTLHNAGHVLGSAIAHLhiGEGLYNLAYTGDIKF 353
                                   77666555544..457899*****************99995...799999**********977611455667777777766 PP

                 Lactamase_B_6 165 akeshL 170
                                   +  ++L
  gi|15669421|ref|NP_248231.1| 354 ETSRLL 359
                                   666555 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.1   2.1e-13   3.4e-10       1     147 [.     203     355 ..     203     384 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 2.1e-13
                                   SEEEES--TTHHHH..HTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHH......... CS
                 Lactamase_B_2   1 rriLiDagpdlrqq..alralqPve.lrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvla......... 68 
                                   +r+LiD+g +++    a +       +  +++++daV++thaH DH+  ++ l + ++  + p+y+++ +++         
  gi|15669421|ref|NP_248231.1| 203 TRVLIDCGINVACEdkAFPHF---DaPEFSIEDLDAVIVTHAHLDHCGFIPGLFRyGY--DGPVYCTRPTRDlmtllqkdy 278
                                   79********88773333333...33677899***************99999999443..479****99888666544444 PP

                                   .....HCCTTCGHHHCHTT.............TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE CS
                 Lactamase_B_2  69 .....vleanfvylaleee.............pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie 131
                                        +            e             +  ++ ++d g ++++  + +++t++ a h  g         ++ l i+
  gi|15669421|ref|NP_248231.1| 279 leiakK------------EgkevpytskdiktCVKHTIPIDYGVTTDIS-PTIKLTLHNAGHVLGS-------AIAHLHIG 339
                                   433222............0345555555666999999999999999998.5789999999999998.......89999999 PP

                                   CTTEEEEEESS-S--- CS
                 Lactamase_B_2 132 gggkrvyyigDtgyip 147
                                   +g  +++y+gD ++ +
  gi|15669421|ref|NP_248231.1| 340 EGLYNLAYTGDIKFET 355
                                   9999*******98544 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.6      0.33   5.4e+02      12      59 ..      21      61 ..       6      78 .. 0.58
   2 !   22.8   1.1   3.7e-08     6e-05      11      55 ..      85     127 ..      72     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.33
                                  CETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                          KH_2 12 kagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdie 59
                                  +a + +v      ++ ++v+++ +p i      + ik++ k+lrk+i 
  gi|15669421|ref|NP_248231.1| 21 EAKIVDVQF----EGPEVVVYVKNPEIF---TNEIIKSLAKDLRKRIS 61
                                  444555555....444455554444442...34457777777777775 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 3.7e-08
                                   ECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHH CS
                          KH_2  11 kkagvskveIertanrviiviresqpgivIGkgGsnikkigkelr 55 
                                   ++a++ +++ +   n  +++i + +pg+vIGk+G+++++i+k++r
  gi|15669421|ref|NP_248231.1|  85 EEAEITNFVFDA--NTGEVIIESKKPGLVIGKEGKTLEMIKKAIR 127
                                   677788888855..88899***********************998 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   9.4e-07    0.0015       6      50 ..     192     246 ..     190     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.4e-07
                 Lactamase_B_3   6 ghnsflletagarilvDPfkanlgyeppa...........eeaDlvlisqaledHa 50 
                                   g +++ ++t+++r+l+D +  n+  e +a           e+ D+v++++a+ dH+
  gi|15669421|ref|NP_248231.1| 192 GRSCLYVQTPDTRVLIDCGI-NVACEDKAfphfdapefsiEDLDAVIVTHAHLDHC 246
                                   89***************883.5555555555667777999***************9 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.7e-06    0.0061      15      54 ..      84     122 ..      73     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.7e-06
                          KH_4  15 peevevteeeeeeeveielnvegedlGrvIGkrGrtldAl 54 
                                   pee e+t     + ++ e+ +e+++ G+vIGk+G+tl  +
  gi|15669421|ref|NP_248231.1|  84 PEEAEITNF-VFDANTGEVIIESKKPGLVIGKEGKTLEMI 122
                                   666677766.234566678889**************9755 PP

>> DUF2870  Protein of unknown function (DUF2870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00013      0.21      18      68 ..     110     160 ..      98     163 .. 0.90
   2 ?   -3.5   0.0       8.9   1.5e+04      19      41 ..     574     595 ..     570     612 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                       DUF2870  18 dyvGkNektkiivklqkkgsgaParepvvseeeqkalmaaayrkqeelkkl 68 
                                    ++Gk  kt  ++k + + +  P r p +++e+ ka+ a+ yr ++e+k++
  gi|15669421|ref|NP_248231.1| 110 LVIGKEGKTLEMIKKAIRWAPKPVRTPPIQSETIKAIRATLYRERHEVKEI 160
                                   589******999*************************************97 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.9
                       DUF2870  19 yvGkNektkiivklqkkgsgaPa 41 
                                   ++G+ ++ ++i    ++ +  P+
  gi|15669421|ref|NP_248231.1| 574 FSGHSDRKQLIKY-IRRLKPSPE 595
                                   5566666555533.333344444 PP

>> MOEP19  KH-like RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00022      0.37       9      69 ..     356     421 ..     351     426 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                        MOEP19   9 eeLkdPlvfy...leawlleaiFGpdgeripeiEqvsqtllev..kaldseglaeilifGrprykk 69 
                                     L +P v +   le+ ++e+ +G  ++ +pe E   + ll+v  ++ d  g++ i +fG  r+++
  gi|15669421|ref|NP_248231.1| 356 SRLLEPAVCQfprLETLIIESTYGAYDDVLPEREEAERELLRVvsETTDRGGKVLIPVFGVGRAQE 421
                                   567777777544489***************************9444566699999999*9998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 4029.20
//
Query:       gi|15669422|ref|NP_248232.1|  [L=224]
Description: proteasome subunit beta PsmB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.8e-58  196.1   0.1    4.6e-58  195.8   0.1    1.1  1  Proteasome  Proteasome subunit
  ------ inclusion threshold ------
      0.053   14.0   0.2       0.42   11.1   0.0    2.2  2  RuvA_C      RuvA, C-terminal domain


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.8   0.1   5.1e-62   4.6e-58       2     190 .]       4     187 ..       3     187 .. 0.97

  Alignments for each domain:
  == domain 1  score: 195.8 bits;  conditional E-value: 5.1e-62
                                   HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHH CS
                    Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipve 82 
                                    kGtt+vG+ ++d v+la+dkra+ g+ +++k+ ++K++kidd+i++++aG+++Da+++vr + aea+ly++r+gr+ip+ 
  gi|15669422|ref|NP_248232.1|   4 MKGTTTVGLICDDAVILATDKRASLGNLVADKE-AKKLYKIDDYIAMTIAGSVGDAQAIVRLLIAEAKLYKMRTGRNIPPL 83 
                                   58***************************7777.8********************************************** PP

                                   HHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHH CS
                    Proteasome  83 rlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleea 163
                                       ++a++l++ + +s++ pf+ +++i+g+d  +g +L+++dp G + eek ++a+Gsgs  a+++le+ y  d+++ee+
  gi|15669422|ref|NP_248232.1|  84 ----ACATLLSNILHSSRMFPFLTQIIIGGYDLLEGAKLFSLDPLGGMNEEKTFTATGSGSPIAYGVLEAGYDRDMSVEEG 160
                                   ....888888888889999*************9999********************************************* PP

                                   HHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                    Proteasome 164 velavkalkealerdklsgknievavi 190
                                   ++la++alk+a+erd++sg++i++avi
  gi|15669422|ref|NP_248232.1| 161 IKLALNALKSAMERDTFSGNGISLAVI 187
                                   *************************97 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.7e-05      0.42      30      46 ..     152     168 ..     145     169 .. 0.82
   2 ?    0.2   0.1      0.12   1.1e+03      16      31 ..     196     211 ..     195     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.7e-05
                                   -TTS-HHHHHHHHHCCT CS
                        RuvA_C  30 npgasveelIraALklL 46 
                                   + ++svee+I++AL +L
  gi|15669422|ref|NP_248232.1| 152 DRDMSVEEGIKLALNAL 168
                                   789***********998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.12
                                   -HHHHHHHHHHHHC-T CS
                        RuvA_C  16 kekeaekAvakvlanp 31 
                                     +e+ek++++ +a+p
  gi|15669422|ref|NP_248232.1| 196 EDEEIEKILDSMKAKP 211
                                   568*******998833 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1428.55
//
Query:       gi|15669423|ref|NP_248233.1|  [L=455]
Description: prolyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-30  104.8   6.9    1.8e-30  104.8   6.9    2.7  2  ProRS-C_2       Prolyl-tRNA synthetase, C-terminal
    1.2e-25   90.6   0.1    2.6e-25   89.4   0.0    1.6  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    2.4e-20   72.5   0.9    5.5e-20   71.3   0.9    1.7  1  HGTP_anticodon  Anticodon binding domain
  ------ inclusion threshold ------
      0.019   14.6   4.4      0.039   13.6   0.0    2.8  3  LEDGF           Lens epithelium-derived growth factor (LEDGF)
      0.024   14.8   0.5       0.43   10.8   0.1    2.5  2  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal


Domain annotation for each model (and alignments):
>> ProRS-C_2  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.47   1.7e+03       4      20 ..     371     386 ..     367     389 .. 0.67
   2 !  104.8   6.9   5.1e-34   1.8e-30       1      66 []     394     455 .]     394     455 .] 0.99

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.47
                                   -SS--....HHHHHHHC CS
                     ProRS-C_2   4 Leaenvnlllenikekl 20 
                                   +e++  n ++enik+  
  gi|15669423|ref|NP_248233.1| 371 VEKT-LNNIMENIKNRA 386
                                   4444.488999999865 PP

  == domain 2  score: 104.8 bits;  conditional E-value: 5.1e-34
                                   EEE-SS--....HHHHHHHCTTT-SEEEEE--GGG-SHHHHHHHSS-EEEEEESSSSEEEEEE-B- CS
                     ProRS-C_2   1 itiLeaenvnlllenikeklsekkGvvLvPfneeiYneefeeeidasvLGeteyeGkkYisiaktY 66 
                                   itiLe++n    +++ik++lsek+Gv+LvPf+eeiYnee+ee+++a++LGetey+G+kYi+iaktY
  gi|15669423|ref|NP_248233.1| 394 ITILEDIN----PDEIKNILSEKRGVILVPFKEEIYNEELEEKVEATILGETEYKGNKYIAIAKTY 455
                                   8*******....*****************************************************9 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.0   7.2e-29   2.6e-25       6     177 ..      91     262 ..      82     264 .. 0.91
   2 ?   -2.2   0.0      0.99   3.6e+03      87     106 ..     299     318 ..     293     401 .. 0.57

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 7.2e-29
                                   TTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEE.EEEEEEEEES.GGGHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxx RF
                  tRNA-synt_2b   6 rndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreF.hqkdgyvfha.easlddslrdl 83 
                                   + d +++L+Pt+e++++ +++ + ++   +LP+k+yqi   +R+E++ +r+L+R+re+ + k+++  h+ ++++++++++ 
  gi|15669423|ref|NP_248233.1|  91 QLDVKLALRPTSETPIYYMMKLW-VKVhTDLPIKIYQIVNTFRYETKHTRPLIRLREImTFKEAHTAHStKEEAENQVKEA 170
                                   457789**************988.877588*****************9*********83579*******99********** PP

                                   HHHHHHHHHHTT.SCEEEEEE..GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  84 ikaisriferlglefraiiel..msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimi 162
                                   i  ++++f +lg++ + i +   +++  + ++++  f+ +++  +++++i+t+++lg+++s+++++ +    + +   + +
  gi|15669423|ref|NP_248233.1| 171 ISIYKKFFDTLGIP-YLISKRpeWDK-FPGAEYTMAFDTIFP-DGRTMQIATVHNLGQNFSKTFEIIFETPTGDKDYAYQT 248
                                   **************.55766677774.499************.9************************99*********** PP

                                   EEEEEHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxx RF
                  tRNA-synt_2b 163 caaigveRllsaile 177
                                   c++i+  R+++ i++
  gi|15669423|ref|NP_248233.1| 249 CYGIS-DRVIASIIA 262
                                   *****.****99987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.99
                                   HHHHHHHTT.SCEEEEEEGT CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  87 isriferlglefraiielms 106
                                   +++i+e+l  +fr+ i + +
  gi|15669423|ref|NP_248233.1| 299 AKEIYEKLKGKFRVHIDDRD 318
                                   56666666555555444422 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.9   1.5e-23   5.5e-20       1      93 [.     280     373 ..     280     374 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 1.5e-23
                                   SEEEEESSSS..HHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEE CS
                HGTP_anticodon   1 qvvviplnek..aeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreq 79 
                                   qvv++pl  k  ++ ++e ak+++e+L+ + +rv++dd++ ++g+k+++++ +g+p++++vG+k++e++++t+ +rdt+e+
  gi|15669423|ref|NP_248233.1| 280 QVVIVPLIFKgkEDIVMEKAKEIYEKLKGK-FRVHIDDRDIRPGRKFNDWEIKGVPLRIEVGPKDIENKKITLFRRDTMEK 359
                                   8*****99998777799***********88.************************************************** PP

                                   EEEETTHHHHHHHH CS
                HGTP_anticodon  80 ervsldelveklke 93 
                                    +v+  +l+e++++
  gi|15669423|ref|NP_248233.1| 360 FQVDETQLMEVVEK 373
                                   **********9987 PP

>> LEDGF  Lens epithelium-derived growth factor (LEDGF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.063   2.3e+02      75      95 ..     157     179 ..     115     196 .. 0.68
   2 ?   13.6   0.0   1.1e-05     0.039      75     100 ..     288     313 ..     285     326 .. 0.86
   3 ?   -1.7   0.2      0.57     2e+03      76      98 ..     376     398 ..     347     413 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.063
                         LEDGF  75 f..kekakeirkkAeeiYnkfks 95 
                                   +  ke+a++  k+A  iY+kf +
  gi|15669423|ref|NP_248233.1| 157 HstKEEAENQVKEAISIYKKFFD 179
                                   13366777777889999999965 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.1e-05
                         LEDGF  75 fkekakeirkkAeeiYnkfkslflvp 100
                                   fk k + +++kA+eiY+k+k  f v+
  gi|15669423|ref|NP_248233.1| 288 FKGKEDIVMEKAKEIYEKLKGKFRVH 313
                                   89999***************999864 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.57
                         LEDGF  76 kekakeirkkAeeiYnkfkslfl 98 
                                   ++  ++i+++A e ++ f +++ 
  gi|15669423|ref|NP_248233.1| 376 NNIMENIKNRAWEKFENFITILE 398
                                   44455666666666666666555 PP

>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.093   3.3e+02      17      33 ..     156     177 ..     147     200 .. 0.77
   2 ?   10.8   0.1   0.00012      0.43       2      38 ..     403     439 ..     402     455 .] 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.093
                                   EESSGHHHHHHHHHHH.....S CS
                     ProRS-C_1  17 pWcgeeecEekIkeet.....g 33 
                                    +  +ee+E+++ke +      
  gi|15669423|ref|NP_248233.1| 156 AHSTKEEAENQVKEAIsiykkF 177
                                   567899********98555554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00012
                                   HHHHHHHHTT-.EEEEEESSGHHHHHHHHHHHS-EEEE CS
                     ProRS-C_1   2 eefkealekkg.fvlapWcgeeecEekIkeetgakslc 38 
                                   +e+k++l++k+ ++l+p+++e  +E +++e++ a++l+
  gi|15669423|ref|NP_248233.1| 403 DEIKNILSEKRgVILVPFKEEIYNE-ELEEKVEATILG 439
                                   89*****99999******9977665.578888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3000.91
//
Query:       gi|15669424|ref|NP_248234.1|  [L=225]
Description: hypothetical protein MJ_1239 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.07   13.2   3.9      0.082   13.0   0.8    2.3  2  DUF3882          Lactococcus phage M3 protein
      0.089   13.6   0.3       0.75   10.6   0.1    2.5  2  GramPos_pilinBB  Gram-positive pilin backbone subunit 2, Cna-


Domain annotation for each model (and alignments):
>> DUF3882  Lactococcus phage M3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2     0.041   3.7e+02      49      81 ..      29      61 ..      22     114 .. 0.68
   2 ?   13.0   0.8   9.1e-06     0.082      36     101 ..     107     173 ..      84     218 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.041
                                  HHHHHHHHHHHHTT-TT-EEEEE-----SSHHH CS
                       DUF3882 49 divdaikevieeydlkdyflaieepiitrkrkg 81
                                   i+da +evi++ ++ +    i + ++t + k 
  gi|15669424|ref|NP_248234.1| 29 YIIDAENEVIKDEEILERLEKISKVVMTVQAKR 61
                                  477888888888888888888888888877664 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.1e-06
                                   ---TTS-HHHHHHHHHHHHHHHHHHTT-TT-EEEEE-----SSHHHHHHHH.HHHHHHHHHHBTTBS CS
                       DUF3882  36 aynkkkdalerakdivdaikevieeydlkdyflaieepiitrkrkgsisli.ranGsflGvidnlvn 101
                                   a   ++d +     +   +k+++ee++l  y+l+ +e  i  kr   +  + + n   l  +++  n
  gi|15669424|ref|NP_248234.1| 107 AMRCSRDIWVGIEGVESLVKDIVEEHNLIAYYLYGQECSINSKRAIYVPYAtKINENALESMKGYLN 173
                                   5666788888888888899*****************9988877776665542567777777777666 PP

>> GramPos_pilinBB  Gram-positive pilin backbone subunit 2, Cna-B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   8.4e-05      0.75      15     100 ..      91     167 ..      83     181 .. 0.69
   2 ?   -1.3   0.0      0.43   3.9e+03      93     111 ..     189     207 ..     183     218 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.4e-05
                                   TT--S--EEEEEEE-TTEEE-TTT--EEEETT.--TTTSEEEEEEE-TTS-EEEEEEE-H.HHHGGGTTT-EEEEEEEEE- CS
               GramPos_pilinBB  15 etakyekykfsDtlskGLtynedvkvkvdekd.vvkdtdytvaekedgktlevevanlkklekvaakageeivvtYsatlN 94 
                                   +++k+++y   D +++ +  ++d+ v +++ + +vkd    + e+++     +++  l   +++  +++++i+v Y  ++N
  gi|15669424|ref|NP_248234.1|  91 KERKFKNYRILDVIKEAMRCSRDIWVGIEGVEsLVKD----IVEEHN-----LIAYYLY-GQECSINSKRAIYVPYATKIN 161
                                   5677888888888888888888888888777756665....233222.....2222222.344678999************ PP

                                   TTS-B- CS
               GramPos_pilinBB  95 enAvie 100
                                   enA+ +
  gi|15669424|ref|NP_248234.1| 162 ENALES 167
                                   ***876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.43
                                   E-TTS-B-SSEEEEEEEEE CS
               GramPos_pilinBB  93 lNenAvienenkNdvkLeY 111
                                   lN++  ie  ++Nd+ + Y
  gi|15669424|ref|NP_248234.1| 189 LNDEESIERIKNNDIVVGY 207
                                   4444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1403.86
//
Query:       gi|15669425|ref|NP_248235.1|  [L=97]
Description: hypothetical protein MJ_1240 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   16.3   0.0      0.016   15.6   0.0    1.4  1  DUF1091   Protein of unknown function (DUF1091)
       0.11   12.7   0.1       0.34   11.1   0.1    1.7  1  ApbA_C    Ketopantoate reductase PanE/ApbA C terminal


Domain annotation for each model (and alignments):
>> DUF1091  Protein of unknown function (DUF1091)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.8e-06     0.016       4      55 ..       2      50 ..       1      66 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-06
                       DUF1091  4 sifkrsngykpflynitldfCkflknpnnnplfkifykslkkysnl.nhtCPy 55
                                  +i k++++yk+ ++n+++ f ++l++     +f ++ + l+ + nl   t Py
  gi|15669425|ref|NP_248235.1|  2 EIKKSYKDYKKLVWNVSTEFTQALAR----IMFFYIVNDLETAKNLaKITSPY 50
                                  6778889*****************44....899999999****9998888998 PP

>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   3.8e-05      0.34       7      55 ..      10      70 ..       6      93 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.8e-05
                        ApbA_C  7 weKllinaainpltalldckngell............espelralvrallkEalavaeaeg 55
                                  ++Kl++n++ + ++al+++++  ++            +sp+l ++  +llkE+++ +e+e 
  gi|15669425|ref|NP_248235.1| 10 YKKLVWNVSTEFTQALARIMFFYIVndletaknlakiTSPYLPKVPSKLLKELSEAIEEEI 70
                                  79*******************9999777777777777777777888888888877775443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2022  (0.112778); expected 358.6 (0.02)
Passed bias filter:                      802  (0.044732); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 793.83
//
Query:       gi|15669426|ref|NP_248236.1|  [L=71]
Description: hypothetical protein MJ_1241 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-05   23.8   0.0    2.5e-05   23.7   0.0    1.0  1  ATPase           KaiC
    5.8e-05   23.5   0.0    6.2e-05   23.5   0.0    1.1  1  AAA_16           AAA ATPase domain
    0.00025   20.8   0.1    0.00029   20.6   0.1    1.1  1  Thymidylate_kin  Thymidylate kinase
     0.0011   18.8   0.0     0.0012   18.6   0.0    1.1  1  AAA_30           AAA domain
     0.0014   18.9   0.1     0.0015   18.8   0.1    1.1  1  AAA_22           AAA domain
     0.0016   18.4   0.0      0.002   18.1   0.0    1.1  1  APS_kinase       Adenylylsulphate kinase
     0.0022   18.2   0.0     0.0026   17.9   0.0    1.1  1  AAA_33           AAA domain
     0.0041   16.2   0.0     0.0044   16.0   0.0    1.0  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0041   17.0   0.0     0.0048   16.8   0.0    1.1  1  NACHT            NACHT domain
     0.0066   16.2   0.0     0.0066   16.2   0.0    1.1  1  IstB_IS21        IstB-like ATP binding protein
     0.0073   16.2   0.1     0.0078   16.1   0.1    1.1  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0097   15.8   0.1      0.012   15.6   0.1    1.2  1  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.014   14.6   0.0      0.014   14.6   0.0    1.1  1  NB-ARC           NB-ARC domain
      0.019   14.6   0.1      0.024   14.2   0.1    1.1  1  SRP54            SRP54-type protein, GTPase domain
      0.023   15.1   0.1      0.028   14.9   0.1    1.2  1  AAA              ATPase family associated with various cellul
      0.027   14.4   0.1      0.033   14.1   0.1    1.2  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.028   14.4   0.0      0.034   14.2   0.0    1.1  1  AAA_5            AAA domain (dynein-related subfamily)
      0.031   14.0   0.0      0.032   13.9   0.0    1.1  1  Sigma54_activat  Sigma-54 interaction domain
      0.032   13.9   0.0      0.034   13.8   0.0    1.0  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.033   14.7   0.1      0.056   14.0   0.1    1.4  1  AAA_18           AAA domain
      0.048   13.4   0.0      0.057   13.2   0.0    1.1  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.056   12.8   0.0       0.07   12.5   0.0    1.1  1  Gtr1_RagA        Gtr1/RagA G protein conserved region
      0.061   13.1   0.0      0.071   12.9   0.0    1.1  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.067   13.7   0.0      0.073   13.6   0.0    1.1  1  ABC_tran         ABC transporter
      0.071   13.2   0.1      0.087   12.9   0.1    1.1  1  AAA_14           AAA domain
      0.074   11.9   0.0      0.087   11.6   0.0    1.0  1  AAA_35           AAA-like domain
      0.076   13.1   0.0      0.085   12.9   0.0    1.1  1  DUF87            Helicase HerA, central domain
       0.12   12.7   0.0       0.12   12.7   0.0    1.2  1  AAA_19           AAA domain
       0.13   11.6   0.0       0.17   11.3   0.0    1.1  1  KTI12            Chromatin associated protein KTI12
       0.15   11.2   0.0       0.16   11.1   0.0    1.0  1  PIF1             PIF1-like helicase
       0.15   12.1   0.1       0.19   11.8   0.1    1.2  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   4.4e-08   2.5e-05       7      64 ..      14      70 ..       8      71 .] 0.89

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.4e-08
                        ATPase  7 glDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlr 64
                                  g+++ l + +  + +  + G +G GKt++a +++++ +++ g ++v+ t +e+++ ++
  gi|15669426|ref|NP_248236.1| 14 GFEDNLIDALNTYGSACVLGLAGMGKTTIA-RYIYTKLRREGVKVVYLTSDEESKTIK 70
                                  66666668888889999***********97.7********************998875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.1e-07   6.2e-05      25      63 ..      27      65 ..      15      71 .] 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.1e-07
                        AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                  ++  + G +G+GK++++r +++ l+++g+ +++ + d+ 
  gi|15669426|ref|NP_248236.1| 27 GSACVLGLAGMGKTTIARYIYTKLRREGVKVVYLTSDEE 65
                                  57789**********************999999888876 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1     5e-07   0.00029       3      37 ..      33      68 ..      31      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5e-07
                                  ESTTSSHHHHHHHHHHHHHHTTE..EEEESSSTTSH CS
               Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik.vvltrepggte 37
                                  Gl G GKtt+a++++ +l++eg k v+lt  +++ +
  gi|15669426|ref|NP_248236.1| 33 GLAGMGKTTIARYIYTKLRREGVKvVYLTSDEESKT 68
                                  899*********************988888776654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.1e-06    0.0012      16      56 ..      26      64 ..      17      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.1e-06
                        AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrviglAptg 56
                                   g   a++ G AG GKtt+ + +   ++++g +v+ l++ +
  gi|15669426|ref|NP_248236.1| 26 YG--SACVLGLAGMGKTTIARYIYTKLRREGVKVVYLTSDE 64
                                  44..58899**************************998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   2.7e-06    0.0015       5      56 ..      26      69 ..      21      71 .] 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.7e-06
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl 56
                                   g+ +v G +G+GKTt +r +  +l         r +v  v+l+s+++sk++
  gi|15669426|ref|NP_248236.1| 26 YGSACVLGLAGMGKTTIARYIYTKLR--------REGVKVVYLTSDEESKTI 69
                                  68899*******************94........555558888888777665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.4e-06     0.002       8      39 ..      32      63 ..      28      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.4e-06
                                  ESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                    APS_kinase  8 tGlsgsGKstianalekkLvekgisvylLdGd 39
                                   Gl+g GK+tia+ + +kL+++g++v+ L  d
  gi|15669426|ref|NP_248236.1| 32 LGLAGMGKTTIARYIYTKLRREGVKVVYLTSD 63
                                  59************************999877 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   4.5e-06    0.0026       4      37 ..      31      69 ..      29      71 .] 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.5e-06
                        AAA_33  4 lvGlpGsGKstlaerllkklg.....avllssdtlrrrl 37
                                  + Gl+G+GK+t a+ ++ kl      +v l+sd++++++
  gi|15669426|ref|NP_248236.1| 31 VLGLAGMGKTTIARYIYTKLRregvkVVYLTSDEESKTI 69
                                  57**************88888888*9999*****99986 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.7e-06    0.0044      23      70 ..      23      67 ..      12      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.7e-06
                                  GGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                          MeaB 23 lakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                  l++ G a v+Gl    G Gk t+   + ++lrr+G +v  l  D  s+
  gi|15669426|ref|NP_248236.1| 23 LNTYGSACVLGLA---GMGKTTIARYIYTKLRREGVKVVYLTSDEESK 67
                                  4566888888776...67********************9999887775 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.3e-06    0.0048       4      29 ..      30      55 ..      28      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.3e-06
                                  EEEC-TTTCHHHHHHHHHHHHCTS-S CS
                         NACHT  4 ilqGeaGsGKTtLlqklalawaegkl 29
                                  ++ G aG+GKTt ++ + ++++++  
  gi|15669426|ref|NP_248236.1| 30 CVLGLAGMGKTTIARYIYTKLRREGV 55
                                  799******************99874 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-05    0.0066      48      84 ..      27      63 ..       6      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                     IstB_IS21 48 enivllGpsGvGKshlaialgveavraglsvlfvrve 84
                                   + ++lG +G+GK+ +a  + ++  r+g++v++++ +
  gi|15669426|ref|NP_248236.1| 27 GSACVLGLAGMGKTTIARYIYTKLRREGVKVVYLTSD 63
                                  56799****************************9875 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.4e-05    0.0078      24      62 ..      30      68 ..      19      71 .] 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                      ATPase_2 24 fiYGpegsGKtaLlkeiienledkdkyviyyialreesi 62
                                   + G  g GKt++ + i+++l+  + +v+y+++ +e+++
  gi|15669426|ref|NP_248236.1| 30 CVLGLAGMGKTTIARYIYTKLRREGVKVVYLTSDEESKT 68
                                  6889**************************999887765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1     2e-05     0.012       4      30 ..      31      57 ..      28      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-05
                                  EE--TTSSHHHHHHHHHHHH...GGGE CS
                      NTPase_1  4 iTGppGvGKtTlvkkvlellkssgvkv 30
                                  + G  G+GKtT+ + ++ +l+++gvkv
  gi|15669426|ref|NP_248236.1| 31 VLGLAGMGKTTIARYIYTKLRREGVKV 57
                                  55889********************99 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.3e-05     0.014      24      44 ..      30      50 ..      16      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                                  EEEESTTSSHHHHHHHHCCSH CS
                        NB-ARC 24 alvGmgGvGKttlakqilnks 44
                                   + G +G+GKtt+a+ i+ k+
  gi|15669426|ref|NP_248236.1| 30 CVLGLAGMGKTTIARYIYTKL 50
                                  578**************9985 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.2e-05     0.024       6      38 ..      31      63 ..      27      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-05
                                  EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  ++Gl G+GKTt +  +  +l++eg kv+  + D
  gi|15669426|ref|NP_248236.1| 31 VLGLAGMGKTTIARYIYTKLRREGVKVVYLTSD 63
                                  79*************************998888 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   4.8e-05     0.028       2      27 ..      30      58 ..      29      69 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.8e-05
                                  EEESSTTSSHHHHHHHHHHHH...THEEE CS
                           AAA  2 llyGppGtGKTllakavakel...gvefl 27
                                  ++ G  G+GKT++a+ + ++l   gv+++
  gi|15669426|ref|NP_248236.1| 30 CVLGLAGMGKTTIARYIYTKLrreGVKVV 58
                                  68899***************933334444 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.7e-05     0.033       3      38 ..      30      65 ..      28      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-05
                          MobB  3 givgksgsGKTtLleklipelkarglrvgtiKhahh 38
                                  ++ g  g+GKTt+   + ++l+++g++v ++  +++
  gi|15669426|ref|NP_248236.1| 30 CVLGLAGMGKTTIARYIYTKLRREGVKVVYLTSDEE 65
                                  678999**********************98876665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.8e-05     0.034       3      41 ..      30      69 ..      28      71 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.8e-05
                                  EEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHH CS
                         AAA_5  3 lLvGppGtgKselaerlaaal.nreveyvqltrdtteedl 41
                                  +++G  G gK+++a+++   l +  v +v lt+d +++++
  gi|15669426|ref|NP_248236.1| 30 CVLGLAGMGKTTIARYIYTKLrREGVKVVYLTSDEESKTI 69
                                  899******************8778888999988877776 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.6e-05     0.032      22      56 ..      26      60 ..      13      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-05
                                  SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEE CS
               Sigma54_activat 22 dlsvlitGesGtGKellaraiheaskrkekpfvav 56
                                    s  ++G  G GK+++ar i+++ +r+  ++v +
  gi|15669426|ref|NP_248236.1| 26 YGSACVLGLAGMGKTTIARYIYTKLRREGVKVVYL 60
                                  4567799*****************99998888766 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.9e-05     0.034       5      54 ..      20      67 ..      17      71 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.9e-05
                                  HHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEEEEESEEHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                   ATP-synt_ab  5 lDalfpivqGqrtlipgafgvGktvisqslskqsnsdd.aiiyvgiGergn 54
                                  +Dal +++     +++g +g+Gkt+i++ +  + + +   ++y    e ++
  gi|15669426|ref|NP_248236.1| 20 IDALNTYG---SACVLGLAGMGKTTIARYIYTKLRREGvKVVYLTSDEESK 67
                                  77777775...68*****************999888876777776666555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   9.8e-05     0.056       2      22 ..      30      50 ..      30      68 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.8e-05
                        AAA_18  2 lltGtpGvGKttlakeLskrl 22
                                  ++ G +G GKtt+a+++  +l
  gi|15669426|ref|NP_248236.1| 30 CVLGLAGMGKTTIARYIYTKL 50
                                  799**************7665 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.8e-05     0.057       4      41 ..      31      68 ..      29      71 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.8e-05
                           PRK  4 vagsSGaGkttvarklekifgrekvkaaeiegdsflrl 41
                                  v g  G Gktt+ar +   ++re+vk ++ + d++ ++
  gi|15669426|ref|NP_248236.1| 31 VLGLAGMGKTTIARYIYTKLRREGVKVVYLTSDEESKT 68
                                  668899********************999988877655 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.07       5      44 ..      32      71 .]      30      71 .] 0.95

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                     Gtr1_RagA  5 mGksgsGKtsmrsiiFdnylardtlrlgatidveksevrf 44
                                  +G  g GKt++ + i+ ++  + +  +  t+d e ++++f
  gi|15669426|ref|NP_248236.1| 32 LGLAGMGKTTIARYIYTKLRREGVKVVYLTSDEESKTIKF 71
                                  799********************************99986 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.071       3      31 ..      35      63 ..      33      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                        CLP1_P  3 kdsGKSTlarlLlNyalrkgrkpvyvDlD 31
                                     GK+T+ar++  ++ r+g k+vy+  D
  gi|15669426|ref|NP_248236.1| 35 AGMGKTTIARYIYTKLRREGVKVVYLTSD 63
                                  578**********************9877 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00013     0.073      15      42 ..      30      57 ..      19      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00013
                                  EEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 15 aivGenGaGKStLlkllagllkpteGei 42
                                   ++G  G GK+t+++ ++ +l+ +  ++
  gi|15669426|ref|NP_248236.1| 30 CVLGLAGMGKTTIARYIYTKLRREGVKV 57
                                  589***************9998765555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00015     0.087       6      43 ..      30      67 ..      26      71 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                        AAA_14  6 vitGaRrvGKTtllkqlikellvkkesilyinldderd 43
                                  ++ G+  +GKTt+++ ++ +l  +  +++y++ d+e++
  gi|15669426|ref|NP_248236.1| 30 CVLGLAGMGKTTIARYIYTKLRREGVKVVYLTSDEESK 67
                                  6889999******9999988888888999999998876 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015     0.087       8      70 ..       5      65 ..       2      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                        AAA_35  8 ldspfYierppieekcyeeiekpGalirikapkkmGKtSLlarilakakqqgyktvsldlqla 70
                                  ++ + Y++r  +e+++++++++ G+   + +   mGKt +   i +k +++g+k+v+l  ++ 
  gi|15669426|ref|NP_248236.1|  5 MEIKWYVKRG-FEDNLIDALNTYGSAC-VLGLAGMGKTTIARYIYTKLRREGVKVVYLTSDEE 65
                                  5667899998.999999*******975.667889************************87665 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00015     0.085      27      56 ..      30      58 ..      21      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                         DUF87 27 AilgsTGsGKSntvavLleellekkgatil 56
                                  ++lg +G+GK++ ++++  +l  + g++++
  gi|15669426|ref|NP_248236.1| 30 CVLGLAGMGKTTIARYIYTKLR-REGVKVV 58
                                  79*****************998.7777776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0002      0.12      12      38 ..      28      54 ..       2      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0002
                        AAA_19 12 vllvtaGpGtGKTrvlkhivallvelg 38
                                    +v++ +G+GKT++ + i + l ++g
  gi|15669426|ref|NP_248236.1| 28 SACVLGLAGMGKTTIARYIYTKLRREG 54
                                  57899**************99999988 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00029      0.17       6      38 ..      31      63 ..      29      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                                  EE--TTSSHHHHHHHHHHHHHHTT--EEEE-TH CS
                         KTI12  6 ltGlPssGKstrakeLakaleeekrsvvvidde 38
                                  + Gl   GK+t+a+ + ++l+ e+ +vv++ ++
  gi|15669426|ref|NP_248236.1| 31 VLGLAGMGKTTIARYIYTKLRREGVKVVYLTSD 63
                                  5788899*******************9998643 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00028      0.16      25      57 ..      29      61 ..      13      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                                  EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEE CS
                          PIF1 25 fFvtGsgGtgKtflwkallkklrsegkivlavA 57
                                    v G +G gKt + + +++klr eg +v+   
  gi|15669426|ref|NP_248236.1| 29 ACVLGLAGMGKTTIARYIYTKLRREGVKVVYLT 61
                                  4588*********************99998765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00034      0.19       9      36 ..      36      63 ..      30      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                                  TSSHHHHHHHHHHHHHHTT--EEEEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  9 GvGKTtlaanLaralarrglrVllvDaD 36
                                  G GKTt+a  + + l r+g +V+ +  D
  gi|15669426|ref|NP_248236.1| 36 GMGKTTIARYIYTKLRREGVKVVYLTSD 63
                                  89********************977666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 448.64
//
Query:       gi|15669427|ref|NP_248237.1|  [L=539]
Description: methyl coenzyme M reductase system subunit AtwA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-54  183.3   0.0    2.8e-26   92.6   0.0    2.5  2  ABC_tran       ABC transporter
    2.8e-07   30.6   0.6      0.014   15.3   0.1    2.6  2  RsgA_GTPase    RsgA GTPase
    6.2e-07   29.1   0.4      0.051   13.0   0.0    3.5  3  SMC_N          RecF/RecN/SMC N terminal domain
    6.2e-06   26.2   3.8       0.63    9.8   0.1    4.1  4  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    6.6e-06   25.8   0.6      0.038   13.7   0.0    2.4  2  AAA_29         P-loop containing region of AAA domain
    0.00014   22.2   0.6       0.57   10.5   0.1    2.9  2  AAA_22         AAA domain
     0.0009   19.7   0.1        1.7    9.0   0.1    2.7  2  AAA_16         AAA ATPase domain
     0.0011   19.6   2.3        0.3   11.6   0.1    3.2  3  AAA_18         AAA domain
     0.0012   18.7   0.6        2.5    7.7   0.0    3.4  4  AAA_15         AAA ATPase domain
     0.0023   18.5   3.0       0.16   12.4   0.0    2.7  2  AAA_23         AAA domain
     0.0027   17.0   4.0        2.4    7.4   0.0    3.9  4  Zeta_toxin     Zeta toxin
     0.0036   16.7   0.0      0.062   12.7   0.0    2.3  2  Mg_chelatase   Magnesium chelatase, subunit ChlI
     0.0049   16.9   1.0         12    6.0   0.0    3.8  4  MMR_HSR1       50S ribosome-binding GTPase
     0.0054   15.9   2.1       0.16   11.1   0.0    2.8  2  NB-ARC         NB-ARC domain
  ------ inclusion threshold ------
      0.013   15.7   0.6       0.59   10.3   0.2    2.9  2  AAA_33         AAA domain
      0.014   15.1   0.6        3.9    7.2   0.0    3.1  3  IstB_IS21      IstB-like ATP binding protein
      0.028   14.1   0.4        2.9    7.6   0.0    2.8  3  AAA_30         AAA domain
      0.031   14.5   0.0        3.2    8.0   0.0    3.0  2  SbcCD_C        Putative exonuclease SbcCD, C subunit
      0.034   14.1   0.3       0.86    9.6   0.0    2.6  2  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
      0.053   13.2   0.0       0.18   11.5   0.0    1.9  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
      0.059   13.8   2.8       0.38   11.2   0.1    3.3  4  AAA            ATPase family associated with various cellular
      0.073   12.8   0.1       0.13   11.9   0.1    1.5  1  DUF2225        Uncharacterized protein conserved in bacteria 
      0.073   12.8   0.0        3.5    7.3   0.0    2.4  2  PRK            Phosphoribulokinase / Uridine kinase family
      0.074   12.8   1.1          4    7.1   0.2    2.5  2  AAA_24         AAA domain
       0.12   12.6   0.5        2.7    8.2   0.0    3.0  3  AAA_28         AAA domain
       0.12   12.7   0.6        9.1    6.7   0.0    2.9  2  RNA_helicase   RNA helicase
       0.15   12.3   0.9         33    4.7   0.0    3.0  2  Roc            Ras of Complex, Roc, domain of DAPkinase
       0.37   11.3   3.2        4.9    7.6   3.2    2.3  1  Terminase_2    Terminase small subunit
       0.38   10.5   5.6        3.8    7.4   0.7    2.4  2  zinc_ribbon_2  zinc-ribbon domain
       0.57   10.1   6.9        5.8    6.8   0.5    3.2  3  NACHT          NACHT domain
       0.85    9.5   6.2        1.3    9.0   0.1    3.2  3  MobB           Molybdopterin guanine dinucleotide synthesis p
        1.5    8.9   9.7        4.4    7.3   0.1    3.4  3  DUF87          Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.0   1.2e-27     7e-25       1     136 [.      24     203 ..      24     204 .. 0.86
   2 !   92.6   0.0   5.1e-29   2.8e-26       1     136 [.     308     463 ..     308     464 .. 0.87

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 1.2e-27
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTS..S--SEEEE...............................EETTCE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx...............................xxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagl..lkpteGei...............................lldgkd 48 
                                   lkn+s++l+ege ++i+G++GaGKS Ll +l g+  ++pteG+i                               +    +
  gi|15669427|ref|NP_248237.1|  24 LKNISFTLEEGESLGILGKSGAGKSVLLHMLRGMdgYEPTEGQIiyhvsycekcgyvdvpskagtpckkcgnelkK---IE 101
                                   79*****************************99755799*********************9999999888885552...33 PP

                                   GGG....B-HHHCCHCEEEE-SS.--S-TTSBHHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHH CS
                                   xxx....xxxxxxxxxxxxxxxx.xxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  49 lke....qeleslrkeigvlpqe.pqlfpeltvren..........esdeeiekalsklglkelkdtvvksspssLSgGqk 114
                                   ++     + +  l+++i+++ q    l  e+tv en          e +e i+ al+ +++++l++++  + ++ LSgG+k
  gi|15669427|ref|NP_248237.1| 102 VDFwndkKYTYNLKRKIAIMLQRtFALYGEKTVLENilealhqagyEGKEAIDMALKLIKMVKLEHRIT-HIARDLSGGEK 181
                                   33344455566889999999999678888888*******999999777777999999999999777776.667******** PP

                                   HHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 115 qrvalarallkkpkllllDEpt 136
                                   qrv+lar ++k+p ++l+DEpt
  gi|15669427|ref|NP_248237.1| 182 QRVVLARQIAKEPFIFLADEPT 203
                                   *********************9 PP

  == domain 2  score: 92.6 bits;  conditional E-value: 5.1e-29
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG......B-HHHCCHCEEEE-SS--S-TTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx......xxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke......qeleslrkeigvlpqepqlfpel 74 
                                   ++nv+l+++e e+ ++vG +GaGK+tL+k++ag l p +G+ +++ g+++ +        + ++++ ig+l+qe  l p+ 
  gi|15669427|ref|NP_248237.1| 308 VDNVTLNIREREIFGLVGTSGAGKTTLAKIIAGVLPPSKGKYWFRvGDEWVDmtkpgpMGRGRAKRYIGILFQEYALYPHR 388
                                   58****************************************99888888888888889999******************* PP

                                   BHHHH..........HHHTCHHHHHHHSTTGG...TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxx..........xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  75 tvren..........esdeeiekalsklglke...lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   t+ en          ++ ++++++ + ++       +++++++ p++LS G++ r ala++l+k+p++++lDEpt
  gi|15669427|ref|NP_248237.1| 389 TILENlteaiglelpDEFARMKAVYTLVSVGFseeEAEEILDKYPHELSVGERHRCALAQVLIKEPRVVILDEPT 463
                                   ************888444444443333332223336899999999*****************************9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   0.00013     0.072      86     122 ..      20      57 ..       6      71 .. 0.82
   2 !   15.3   0.1   2.5e-05     0.014      64     121 ..     282     340 ..     238     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                                   THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                   +k  l++++  l++ +   ++G+SG+GKS L+ +l++ 
  gi|15669427|ref|NP_248237.1|  20 DKVVLKNISFTLEEgESLGILGKSGAGKSVLLHMLRGM 57 
                                   5566788999999888999**************99985 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.5e-05
                                   HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  64 eleelkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                   e++e   +le++  + + v+    +++++++ ++++ ++  lvG SG+GK+tL + +++
  gi|15669427|ref|NP_248237.1| 282 EIKEDIIKLENVSKHYCSVERGVIKAVDNVTLNIRErEIFGLVGTSGAGKTTLAKIIAG 340
                                   466666667777667777777777999*******9989999************988765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.82   4.6e+02      28      42 ..      38      52 ..      14      65 .. 0.83
   2 !   13.0   0.0   9.1e-05     0.051      94     204 ..     109     241 ..      84     253 .. 0.80
   3 !   11.1   0.0   0.00036       0.2      92     205 ..     276     502 ..     253     515 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.82
                                  EEEESTTSSHHHHHH CS
                                  xxxxxxxxxxxxxxx RF
                         SMC_N 28 aivGpNGSGKsnlld 42
                                   i+G+ G+GKs ll 
  gi|15669427|ref|NP_248237.1| 38 GILGKSGAGKSVLLH 52
                                  699********8876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.1e-05
                                   SSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT........................CS-HHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................xxxxxxxxxxxxxxx RF
                         SMC_N  94 keevsisrrvkrkgeseykingkevtkkevsellesagiske........................lLSgGektLvalaLl 150
                                   k  ++++r++    + ++++ g++   +++ e l++ag + +                         LSgGek+ v    +
  gi|15669427|ref|NP_248237.1| 109 KYTYNLKRKIAIMLQRTFALYGEKTVLENILEALHQAGYEGKeaidmalklikmvklehrithiarDLSGGEKQRV----V 185
                                   3457777888888888888889999999999999999988888999999999999999999999999******965....5 PP

                                   HHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH..CTTSEEEEE-SSHHHCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                         SMC_N 151 fAiqkvkpaplyllDeidaaLDeknvkkvaellkek..sknaQfivislreemlek 204
                                   +A q +k   ++l De    LD +  k v + lke   +++  +i +s+  e++++
  gi|15669427|ref|NP_248237.1| 186 LARQIAKEPFIFLADEPTGTLDPQTAKLVHSALKELviKNKISLILTSHWPEVIAE 241
                                   56666666667889********************8732456888888888777765 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00036
                                   SSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT..................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                         SMC_N  92 iekeevsisrrvkrkgeseykingkevtkkevsellesagiske..................................... 135
                                     ++ev+i+                                  +                                     
  gi|15669427|ref|NP_248237.1| 276 KPETEVEIKE---------------------------------Diiklenvskhycsvergvikavdnvtlnirereifgl 323
                                   3333333333.................................23333333333333333333333444444445566677 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|15669427|ref|NP_248237.1| 324 vgtsgagkttlakiiagvlppskgkywfrvgdewvdmtkpgpmgrgrakryigilfqeyalyphrtilenlteaiglelpd 404
                                   777777777777777777777777788888888888888888888888888888888888888888888888888888888 PP

                                   ..............................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                   ..............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 136 ..............................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                                                 +LS Ge+  +ala ++    +k   +++lDe    +D   ++ vae ++++
  gi|15669427|ref|NP_248237.1| 405 efarmkavytlvsvgfseeeaeeildkyphELSVGERHRCALAQVL----IKEPRVVILDEPTGTMDPITRNTVAESIHKS 481
                                   8888888888888888888888888888889**********99885....5556689**********************98 PP

                                   CTT.SE.EEEE-SSHHHCCC- CS
                                   xxx.xx.xxxxxxxxxxxxxx RF
                         SMC_N 187 skn.aQ.fivislreemleka 205
                                   + +  Q +i++s++ +++ ++
  gi|15669427|ref|NP_248237.1| 482 RIElEQtYIIVSHDMDFVLNV 502
                                   876545379999998877665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.089        50       3      22 ..      38      57 ..      36      72 .. 0.84
   2 ?    6.3   0.1     0.013       7.4     236     303 .]     175     240 ..     113     240 .. 0.77
   3 !    9.8   0.1    0.0011      0.63       1      57 [.     320     359 ..     320     404 .. 0.70
   4 ?    5.2   0.1     0.027        15     234     299 ..     433     497 ..     388     501 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.089
                        AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                  ++ G+ g+GKS LL  l+++
  gi|15669427|ref|NP_248237.1| 38 GILGKSGAGKSVLLHMLRGM 57
                                  699***********999887 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                        AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHP...kllrrllellkelsrngaQviltTHSpllld 303
                                   +lS G k+    +++  + +k++ ++l DEp   L+P   kl+++ l+ l ++++  + +ilt+H p++++
  gi|15669427|ref|NP_248237.1| 175 DLSGGEKQR---VVLARQIAKEPFIFLADEPTGTLDPqtaKLVHSALKELVIKNK--ISLILTSHWPEVIA 240
                                   455555554...4444455555588888*********666666666655555555..9*******999885 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0011
                        AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeip 57 
                                   + +l+G  g+GK++L +++ ++                  +++k  + ++ +d+  +
  gi|15669427|ref|NP_248237.1| 320 IFGLVGTSGAGKTTLAKIIAGVL-----------------PPSKGKYWFRVGDEWVD 359
                                   578****************8875.................45555555555544444 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.027
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell...kelsrngaQv.iltTHS.p 299
                                   ++elS G ++  al+  l+  +   +++++DEp   ++P    +++e +   +    ++ Q  i+++H+  
  gi|15669427|ref|NP_248237.1| 433 PHELSVGERHRCALAQVLIKEP---RVVILDEPTGTMDPITRNTVAESIhksR---IELEQTyIIVSHDmD 497
                                   6899999999978888888777...**************77777778884441...344566699999844 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.2    0.0012      0.65      19      39 ..      31      51 ..      23      54 .. 0.76
   2 !   13.7   0.0   6.7e-05     0.038      13      50 ..     309     346 ..     306     351 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                        AAA_29 19 idlkgatlltGpsGsGKSTll 39
                                  +++ ++  + G+sG+GKS ll
  gi|15669427|ref|NP_248237.1| 31 LEEGESLGILGKSGAGKSVLL 51
                                  443337789*********998 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.7e-05
                        AAA_29  13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                   d+ t++i++++++ l+G+sG+GK+Tl   i+ +L p+k
  gi|15669427|ref|NP_248237.1| 309 DNVTLNIREREIFGLVGTSGAGKTTLAKIIAGVLPPSK 346
                                   67889999999999************888888887776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1    0.0024       1.4       7      51 ..      36      86 ..      31     186 .. 0.83
   2 !   10.5   0.1     0.001      0.57       5      70 ..     318     404 ..     315     463 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0024
                        AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee........erpevvfvtlpsst 51
                                  +l + G sG+GK++ll +l+  +   ++++e         + ++ +v++ps+ 
  gi|15669427|ref|NP_248237.1| 36 SLGILGKSGAGKSVLLHMLRGMDG--YEPTEgqiiyhvsYCEKCGYVDVPSKA 86
                                  56688**************99974..333334577666555555577777665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.001
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...................erpevv..fvtlpsstsskdllrellral 64 
                                   + i  ++G sG+GKTtl++ ++  l+  +   +                   + ++++  +++  ++   +++l++l +a+
  gi|15669427|ref|NP_248237.1| 318 REIFGLVGTSGAGKTTLAKIIAGVLPPSKGKYWfrvgdewvdmtkpgpmgrgRAKRYIgiLFQEYALYPHRTILENLTEAI 398
                                   5566699***********988877764433333666666666666666666644444422444444446666666666666 PP

                        AAA_22  65 glelka 70 
                                   glel +
  gi|15669427|ref|NP_248237.1| 399 GLELPD 404
                                   666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1    0.0031       1.7      24      46 ..      34      56 ..      24     230 .. 0.72
   2 !    8.1   0.0    0.0058       3.2      25      51 ..     319     345 ..     305     461 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0031
                        AAA_16 24 pelvllsGesGvGKsslvrellr 46
                                  +e++ + G sG GKs l+ +l+ 
  gi|15669427|ref|NP_248237.1| 34 GESLGILGKSGAGKSVLLHMLRG 56
                                  478889************99884 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0058
                        AAA_16  25 elvllsGesGvGKsslvrellralekd 51 
                                   e+  l+G sG GK++l++ ++  l  +
  gi|15669427|ref|NP_248237.1| 319 EIFGLVGTSGAGKTTLAKIIAGVLPPS 345
                                   677799**********98777555554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.037        21       3      36 ..      39      76 ..      37     125 .. 0.79
   2 ?   -0.2   0.1       2.4   1.4e+03      28      89 ..     231     300 ..     211     320 .. 0.64
   3 !   11.6   0.1   0.00053       0.3       3      19 ..     323     339 ..     322     366 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.037
                        AAA_18  3 ltGtpGvGKttlakeLskrlgf....gvnlrdvakeng 36
                                  + G++G+GK+ l + L+ + g+    g+++ +v + + 
  gi|15669427|ref|NP_248237.1| 39 ILGKSGAGKSVLLHMLRGMDGYepteGQIIYHVSYCEK 76
                                  89**************8877888888666666555444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.4
                        AAA_18  28 lrdvakenglllevdpealdeskrldedkldklldaleenss........aleegknlvidghlaelese 89 
                                   l++ ++e   +l++ + +ld+ +++ e+  ++++++++e  +         + +++ + ++ +  +++s 
  gi|15669427|ref|NP_248237.1| 231 LTSHWPEVIAELTEKAIWLDKGEIIMEGTSEEVVNKFMETVKefkkpeteVEIKEDIIKLENVSKHYCSV 300
                                   4444444444444555588888888888888888888888777777777655555555666666666655 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00053
                        AAA_18   3 ltGtpGvGKttlakeLs 19 
                                   l Gt+G+GKttlak ++
  gi|15669427|ref|NP_248237.1| 323 LVGTSGAGKTTLAKIIA 339
                                   89************984 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.57   3.2e+02      28      75 ..      39     115 ..      24     168 .. 0.71
   2 !    7.7   0.0    0.0044       2.5     318     369 .]     188     239 ..     168     239 .. 0.88
   3 ?   -2.3   0.2       4.9   2.7e+03     261     293 ..     261     289 ..     245     301 .. 0.52
   4 ?    5.8   0.0     0.018       9.8      13      44 ..     307     339 ..     305     428 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.57
                        AAA_15  28 liGkNnsGKSsilealdlFlnnkekkn................................kkvikiekedleifenisesk 75 
                                   + Gk ++GKS +l++l  +   +                                    ++ +kie +++++++++++ k
  gi|15669427|ref|NP_248237.1|  39 ILGKSGAGKSVLLHMLRGMDGYE---PtegqiiyhvsycekcgyvdvpskagtpckkcgNELKKIEVDFWNDKKYTYNLK 115
                                   67999999999999997766533...134667777788888888888888888888888777777777777777666654 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0044
                        AAA_15 318 dekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                   +++ +++ i+l +EP   L pq  k ++ +lkel+ +nk  +i+t+H p +i
  gi|15669427|ref|NP_248237.1| 188 RQIAKEPFIFLADEPTGTLDPQTAKLVHSALKELVIKNKISLILTSHWPEVI 239
                                   56888999*******************************9*******88776 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.9
                        AAA_15 261 kkilkkkidkikkfnykgkkneeieikddeelp 293
                                   +++++k+++++k f+ ++ ++e      ++ ++
  gi|15669427|ref|NP_248237.1| 261 EEVVNKFMETVKEFKKPETEVEI----KEDIIK 289
                                   34555555554444444443333....333333 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.018
                        AAA_15  13 slkdveidlsee.ltvliGkNnsGKSsileald 44 
                                   + ++v++++ e  +  l+G+ ++GK+++++++ 
  gi|15669427|ref|NP_248237.1| 307 AVDNVTLNIREReIFGLVGTSGAGKTTLAKIIA 339
                                   5677888888887889**************996 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.0     0.033        19      15      45 ..      27      60 ..       9     296 .. 0.69
   2 !   12.4   0.0   0.00029      0.16      10      41 ..     296     340 ..     287     343 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.033
                        AAA_23 15 idF...skgltlItGpNGaGKTTildAiklaLyg 45
                                  i F   +     I G+ GaGK+ +l  ++ + + 
  gi|15669427|ref|NP_248237.1| 27 ISFtleEGESLGILGKSGAGKSVLLHMLRGMDGY 60
                                  555555445668************9988866544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00029
                        AAA_23  10 f............rdqeidF.skgltlItGpNGaGKTTildAikl 41 
                                   +            ++++++  ++ ++ ++G  GaGKTT+   i  
  gi|15669427|ref|NP_248237.1| 296 HycsvergvikavDNVTLNIrEREIFGLVGTSGAGKTTLAKIIAG 340
                                   555554444444467778888899***************988865 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.15        84      23      37 ..      41      55 ..      30      67 .. 0.89
   2 ?    5.5   0.0     0.016         9      77     123 ..      99     148 ..      91     169 .. 0.86
   3 ?   -0.7   0.0       1.3   7.3e+02      95     172 ..     251     273 ..     209     297 .. 0.66
   4 !    7.4   0.0    0.0044       2.4      21      40 ..     323     342 ..     309     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.15
                    Zeta_toxin 23 GqpGAGKselaellk 37
                                  G +GAGKs l+++l+
  gi|15669427|ref|NP_248237.1| 41 GKSGAGKSVLLHMLR 55
                                  899********9986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.016
                    Zeta_toxin  77 qkdaselvekllqeaiengyniivegtlrsp...dvvkklaealkkaGYe 123
                                   + ++  + +k  ++ +++++ i + +t++ +    v++++ eal++aGYe
  gi|15669427|ref|NP_248237.1|  99 KIEVDFWNDKKYTYNLKRKIAIMLQRTFALYgekTVLENILEALHQAGYE 148
                                   678899**********************97522156778**********8 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.3
                    Zeta_toxin  95 gyniivegtlrspdvvkklaealkkaGYevevvvvavkkelSrlgvldRyeeevaegRlvpkeehdeafeglresvea 172
                                   + +ii+egt +                                                       e++++++e+v++
  gi|15669427|ref|NP_248237.1| 251 KGEIIMEGTSE-------------------------------------------------------EVVNKFMETVKE 273
                                   55566666633.......................................................333333333333 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0044
                    Zeta_toxin  21 lgGqpGAGKselaellkdel 40 
                                   l+G +GAGK++la+ ++  l
  gi|15669427|ref|NP_248237.1| 323 LVGTSGAGKTTLAKIIAGVL 342
                                   889***********998766 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.35   1.9e+02      24      44 ..      36      56 ..      18      73 .. 0.84
   2 !   12.7   0.0   0.00011     0.062      27      51 ..     323     347 ..     306     355 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.35
                  Mg_chelatase 24 nlllvGppGsGKtmlakrlps 44
                                  +l ++G +G+GK++l + l +
  gi|15669427|ref|NP_248237.1| 36 SLGILGKSGAGKSVLLHMLRG 56
                                  67789**********988876 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00011
                  Mg_chelatase  27 lvGppGsGKtmlakrlpsllpplse 51 
                                   lvG++G+GKt lak ++++lpp + 
  gi|15669427|ref|NP_248237.1| 323 LVGTSGAGKTTLAKIIAGVLPPSKG 347
                                   89*******************9875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.021        12       2      21 ..      37      56 ..      36     123 .. 0.92
   2 ?   -2.0   0.0       6.4   3.6e+03      19      19 ..     190     190 ..     131     229 .. 0.62
   3 ?    5.6   0.1     0.028        16       3      21 ..     322     340 ..     320     354 .. 0.86
   4 ?    1.0   0.0      0.77   4.3e+02      21      58 ..     452     510 ..     444     536 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.021
                                  EEEEESTTSSHHHHHHHHHT CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                   +i+G++ +GKS L+  l g
  gi|15669427|ref|NP_248237.1| 37 LGILGKSGAGKSVLLHMLRG 56
                                  589***********998865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.4
                                   H CS
                      MMR_HSR1  19 l 19 
                                   +
  gi|15669427|ref|NP_248237.1| 190 I 190
                                   2 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.028
                                   EEEESTTSSHHHHHHHHHT CS
                      MMR_HSR1   3 aivGrpNvGKStLinaltg 21 
                                   ++vG + +GK+tL + + g
  gi|15669427|ref|NP_248237.1| 322 GLVGTSGAGKTTLAKIIAG 340
                                   89***********987765 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.77
                                   TS.TEEESSSTTSSSSEEEEEEE...ETTEE....................EEEEECGGCSS CS
                      MMR_HSR1  21 ge.kaivsdkpgtTrdinegrvk...lkgke....................ielvDtpGlie 58 
                                   +e ++ + d+p  T d+++++     +   +                    ++++D +Gl+ 
  gi|15669427|ref|NP_248237.1| 452 KEpRVVILDEPTGTMDPITRNTVaesI---HksrieleqtyiivshdmdfvLNVCDRAGLMR 510
                                   444444555555555554444331221...12334444455555555555567777777643 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.6     0.074        42      22      38 ..      36      52 ..      21     128 .. 0.85
   2 !   11.1   0.0   0.00029      0.16      17      41 ..     317     339 ..     303     363 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.074
                                  EEEEEESTTSSHHHHHH CS
                        NB-ARC 22 vvalvGmgGvGKttlak 38
                                   +++ G+ G GK++l++
  gi|15669427|ref|NP_248237.1| 36 SLGILGKSGAGKSVLLH 52
                                  4789**********986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00029
                                   TSCSEEEEEEESTTSSHHHHHHHHC CS
                        NB-ARC  17 elqslvvalvGmgGvGKttlakqil 41 
                                   e +  + +lvG  G GKttlak i 
  gi|15669427|ref|NP_248237.1| 317 ERE--IFGLVGTSGAGKTTLAKIIA 339
                                   455..99**************9886 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0       0.2   1.1e+02       5      19 ..      40      54 ..      38     140 .. 0.88
   2 ?   10.3   0.2    0.0011      0.59       4      24 ..     323     343 ..     320     532 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.2
                        AAA_33  5 vGlpGsGKstlaerl 19
                                   G +G+GKs l++ l
  gi|15669427|ref|NP_248237.1| 40 LGKSGAGKSVLLHML 54
                                  599*******99876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0011
                        AAA_33   4 lvGlpGsGKstlaerllkklg 24 
                                   lvG +G+GK+tla+ ++  l+
  gi|15669427|ref|NP_248237.1| 323 LVGTSGAGKTTLAKIIAGVLP 343
                                   79***********97776665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.049        27      42      64 ..      28      51 ..      13      72 .. 0.81
   2 ?   -1.2   0.0       2.6   1.4e+03     103     148 ..     187     234 ..     149     247 .. 0.65
   3 ?    7.2   0.0     0.007       3.9      44      67 ..     315     338 ..     295     350 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.049
                     IstB_IS21 42 sf.iekkenivllGpsGvGKshla 64
                                  sf +e+ e++ +lG sG+GKs l 
  gi|15669427|ref|NP_248237.1| 28 SFtLEEGESLGILGKSGAGKSVLL 51
                                  5524788999***********885 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.6
                     IstB_IS21 103 lkrllkvdllilDdlgllpldqaeaellfeviekry..errsiiitsn 148
                                   +++++k   + l d  + +ld + a+l+   +++ +  ++ s+i+ts 
  gi|15669427|ref|NP_248237.1| 187 ARQIAKEPFIFLADEPTGTLDPQTAKLVHSALKELVikNKISLILTSH 234
                                   455666667777777777888888888888888876224456677775 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.007
                     IstB_IS21  44 iekkenivllGpsGvGKshlaial 67 
                                   i+++e + l+G sG+GK+ la  +
  gi|15669427|ref|NP_248237.1| 315 IREREIFGLVGTSGAGKTTLAKII 338
                                   78999999************9766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.099        56      21      41 ..      37      57 ..      27      71 .. 0.79
   2 ?    7.6   0.0    0.0052       2.9      18      42 ..     318     342 ..     306     353 .. 0.81
   3 ?   -1.6   0.0       3.5   1.9e+03      81     114 ..     443     480 ..     409     485 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.099
                        AAA_30 21 avltGpAGtGKttalkalrea 41
                                    + G  G+GK+ +l  lr +
  gi|15669427|ref|NP_248237.1| 37 LGILGKSGAGKSVLLHMLRGM 57
                                  5688***********999865 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0052
                        AAA_30  18 drvavltGpAGtGKttalkalreaw 42 
                                   + +  l+G  G+GKtt+ k ++ ++
  gi|15669427|ref|NP_248237.1| 318 REIFGLVGTSGAGKTTLAKIIAGVL 342
                                   557889***********99988765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.5
                        AAA_30  81 k...grarlepgtllivDE.agmvdtkqlaallkaaek 114
                                   +   +++ +++ +++i DE +g +d  + ++++++++k
  gi|15669427|ref|NP_248237.1| 443 RcalAQVLIKEPRVVILDEpTGTMDPITRNTVAESIHK 480
                                   15565566777799999995567777777777776665 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.23   1.3e+02      30      42 ..     173     185 ..     157     220 .. 0.77
   2 ?    8.0   0.0    0.0057       3.2      62      88 ..     452     478 ..     425     480 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.23
                       SbcCD_C  30 sgtlSGGekqfla 42 
                                   ++ lSGGekq ++
  gi|15669427|ref|NP_248237.1| 173 ARDLSGGEKQRVV 185
                                   6789999998765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0057
                       SbcCD_C  62 palrlvfLDEAFsklDeesiatllell 88 
                                   + +r+v+LDE  +++D+ +++t+ e +
  gi|15669427|ref|NP_248237.1| 452 KEPRVVILDEPTGTMDPITRNTVAESI 478
                                   469**************9999998866 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1       0.5   2.8e+02       7      39 ..      15      54 ..       9      63 .. 0.65
   2 ?    9.6   0.0    0.0015      0.86      19      41 ..     318     340 ..     299     345 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.5
                                  HHHHHHHHHHCH.......TEEEEEEESTTSSHHHHHHHH CS
                          TsaE  7 tealgkklakal.......gdvilLeGdLGaGKTtlvrgl 39
                                  t+++g k+  +        g+ + + G+ GaGK++l + l
  gi|15669427|ref|NP_248237.1| 15 TKKFGDKVVLKNisftleeGESLGILGKSGAGKSVLLHML 54
                                  45555554332234444445558999********998765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                                   TEEEEEEESTTSSHHHHHHHHHH CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglak 41 
                                   ++++ L G  GaGKTtl++ +a 
  gi|15669427|ref|NP_248237.1| 318 REIFGLVGTSGAGKTTLAKIIAG 340
                                   567899*************9875 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00031      0.18       8      49 ..      28     418 ..      22     456 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                                   HS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS..S.EEEEEE..................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x.xxxxxx..................................... RF
                   ATP-synt_ab   8 lfpivqGqrtlipgafgvGktvisqslskqsnsd..d.aiiyvg..................................... 48 
                                    f++ +G+ ++i+g++g Gk+v++++l      +  +  iiy                                       
  gi|15669427|ref|NP_248237.1|  28 SFTLEEGESLGILGKSGAGKSVLLHMLRGMDGYEptEgQIIYHVsycekcgyvdvpskagtpckkcgnelkkievdfwndk 108
                                   58999*******************999876544455447888777888888888888888888887777777777777777 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                   ATP-synt_ab  49 ................................................................................. 48 
                                                                                                                    
  gi|15669427|ref|NP_248237.1| 109 kytynlkrkiaimlqrtfalygektvlenilealhqagyegkeaidmalklikmvklehrithiardlsggekqrvvlarq 189
                                   777777777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                   ATP-synt_ab  49 ................................................................................. 48 
                                                                                                                    
  gi|15669427|ref|NP_248237.1| 190 iakepfifladeptgtldpqtaklvhsalkelviknkisliltshwpeviaeltekaiwldkgeiimegtseevvnkfmet 270
                                   777777777777777777777777777777777777777777777777777777777777777777766666666666666 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                   ATP-synt_ab  49 ................................................................................. 48 
                                                                                                                    
  gi|15669427|ref|NP_248237.1| 271 vkefkkpeteveikediiklenvskhycsvergvikavdnvtlnirereifglvgtsgagkttlakiiagvlppskgkywf 351
                                   666665555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                                   ..................................................................E CS
                                   ..................................................................x RF
                   ATP-synt_ab  49 ..................................................................i 49 
                                                                                                     +
  gi|15669427|ref|NP_248237.1| 352 rvgdewvdmtkpgpmgrgrakryigilfqeyalyphrtilenlteaiglelpdefarmkavytlvsV 418
                                   5555555555555555555555555555555555555555555555555555555555555555554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       8.3   4.7e+03       4      18 ..      40      54 ..      38      68 .. 0.74
   2 ?   -0.7   0.0       3.3   1.8e+03      39      99 ..     257     277 ..     186     291 .. 0.69
   3 ?   11.2   0.1   0.00068      0.38       3      21 ..     323     341 ..     321     381 .. 0.88
   4 ?    0.0   0.0       1.9   1.1e+03      16      66 ..     410     461 ..     406     484 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8.3
                                  ESSTTSSHHHHHHHH CS
                           AAA  4 yGppGtGKTllakav 18
                                   G  G GK+ l + +
  gi|15669427|ref|NP_248237.1| 40 LGKSGAGKSVLLHML 54
                                  577888888777654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.3
                                   TTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
                           AAA  39 vgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                                    g                                         +e+vvn++++ ++++kk 
  gi|15669427|ref|NP_248237.1| 257 EG----------------------------------------TSEEVVNKFMETVKEFKKP 277
                                   22........................................3556666666666666554 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00068
                                   EESSTTSSHHHHHHHHHHH CS
                           AAA   3 lyGppGtGKTllakavake 21 
                                   l+G+ G GKT+lak +a  
  gi|15669427|ref|NP_248237.1| 323 LVGTSGAGKTTLAKIIAGV 341
                                   89**************976 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 1.9
                                   HHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                           AAA  16 kavakelgvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDE 66 
                                   kav + ++v f e ++ e+l+ky  e +   r+  + a+    +p ++++DE
  gi|15669427|ref|NP_248237.1| 410 KAVYTLVSVGFSEEEAEEILDKYPHELSVGERHRCALAQVLIkEPRVVILDE 461
                                   67777778888888999999998888887777777777766677899*9999 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00024      0.13      44      97 ..      67     120 ..      57     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                       DUF2225  44 lfYevvvCpkCgYaalkkdfeklskeekeklkekiskkwksrdfskertldeai 97 
                                   ++Y+v+ C+kCgY  ++++  +  k+  + lk+     w+ ++++ + + + ai
  gi|15669427|ref|NP_248237.1|  67 IIYHVSYCEKCGYVDVPSKAGTPCKKCGNELKKIEVDFWNDKKYTYNLKRKIAI 120
                                   68*******************999999999999999999999999888888776 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.15        85       3      21 ..      38      56 ..      37      77 .. 0.79
   2 ?    7.3   0.0    0.0062       3.5       1      23 [.     320     342 ..     320     357 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.15
                           PRK  3 gvagsSGaGkttvarklek 21
                                  g+ g+SGaGk+ + + l+ 
  gi|15669427|ref|NP_248237.1| 38 GILGKSGAGKSVLLHMLRG 56
                                  899********99888765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0062
                           PRK   1 vIgvagsSGaGkttvarklekif 23 
                                   + g+ g SGaGktt+a+ +  ++
  gi|15669427|ref|NP_248237.1| 320 IFGLVGTSGAGKTTLAKIIAGVL 342
                                   56999**********99887665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.077        43       4      22 ..      36      54 ..      33      64 .. 0.82
   2 ?    7.1   0.2    0.0072         4       6      22 ..     322     338 ..     319     346 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.077
                        AAA_24  4 kiliyGpsgiGKTtlakel 22
                                  ++ i G+sg+GK+ l+ +l
  gi|15669427|ref|NP_248237.1| 36 SLGILGKSGAGKSVLLHML 54
                                  5789*********998876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0072
                        AAA_24   6 liyGpsgiGKTtlakel 22 
                                    ++G sg+GKTtlak +
  gi|15669427|ref|NP_248237.1| 322 GLVGTSGAGKTTLAKII 338
                                   589***********966 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.2   6.7e+02       4      24 ..      39      60 ..      38      64 .. 0.82
   2 ?    8.2   0.0    0.0048       2.7       4      20 ..     323     339 ..     321     360 .. 0.85
   3 ?   -2.1   0.0       7.1     4e+03      14      79 ..     389     460 ..     388     470 .. 0.53

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.2
                        AAA_28  4 itGgestGKTtlleaLaar.gy 24
                                  i+G +++GK+ ll  L  + gy
  gi|15669427|ref|NP_248237.1| 39 ILGKSGAGKSVLLHMLRGMdGY 60
                                  78999********999865455 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0048
                        AAA_28   4 itGgestGKTtlleaLa 20 
                                   ++G++++GKTtl++ +a
  gi|15669427|ref|NP_248237.1| 323 LVGTSGAGKTTLAKIIA 339
                                   79***********9887 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 7.1
                        AAA_28  14 tlleaLaar.gypvvpEaareileekl.akgedalpwvedllafaervleeqleeeaaa....aankvlfcD 79 
                                   t+le+L++  g +   E+ar+     l   g+ + +++e l ++ +++   +++++a a    ++++v+++D
  gi|15669427|ref|NP_248237.1| 389 TILENLTEAiGLELPDEFARMKAVYTLvSVGFSEEEAEEILDKYPHELSVGERHRCALAqvliKEPRVVILD 460
                                   566677766677777777775333222222222222223455555555555666666666677777777777 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0       0.2   1.1e+02       3      18 ..      39      54 ..      37      69 .. 0.88
   2 ?    6.7   0.0     0.016       9.1       3      22 ..     323     342 ..     321     364 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.2
                  RNA_helicase  3 lyGpsgeGKStlakeL 18
                                  + G+sg GKS+l + L
  gi|15669427|ref|NP_248237.1| 39 ILGKSGAGKSVLLHML 54
                                  68*********99875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.016
                  RNA_helicase   3 lyGpsgeGKStlakeLakal 22 
                                   l+G sg GK+tlak +a  l
  gi|15669427|ref|NP_248237.1| 323 LVGTSGAGKTTLAKIIAGVL 342
                                   68************955433 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.058        33       4      21 ..      39      56 ..      37     105 .. 0.80
   2 ?    4.5   0.3     0.068        38       4      17 ..     323     336 ..     321     341 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.058
                                  EESSTTSSHHHHHHCHCT CS
                           Roc  4 lvGdsgvGKtsllkrfve 21
                                  ++G+sg+GK+ ll+ +  
  gi|15669427|ref|NP_248237.1| 39 ILGKSGAGKSVLLHMLRG 56
                                  89***********98764 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.068
                                   EESSTTSSHHHHHH CS
                           Roc   4 lvGdsgvGKtsllk 17 
                                   lvG sg+GKt+l+k
  gi|15669427|ref|NP_248237.1| 323 LVGTSGAGKTTLAK 336
                                   89**********87 PP

>> Terminase_2  Terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   3.2    0.0087       4.9      17     128 ..     137     303 ..     123     319 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0087
                   Terminase_2  17 NatqAaikAgyskktArsigselLrkpkIkkaIreakaereertiie...adeVlqellkiaraeitdeve.......... 84 
                                   N  +A  +Agy+ k A  ++ +l++ +k + +I  +   ++  ++ +   a ++ +e     + e+t +++          
  gi|15669427|ref|NP_248237.1| 137 NILEALHQAGYEGKEAIDMALKLIKMVKLEHRITHIARDLSGGEKQRvvlARQIAKEPFIFLADEPTGTLDpqtaklvhsa 217
                                   888999999999999999999999999999998888777654433332236666666655555555333334444444455 PP

                   Terminase_2  85 ....................................rvklkdseevdkeilrevkegke.gvkvklkDklkAlellakhl. 127
                                                                        +   +seev ++ +++vke k+ +++v++k+ +  le++ kh+ 
  gi|15669427|ref|NP_248237.1| 218 lkelviknkisliltshwpeviaeltekaiwldkgeIIMEGTSEEVVNKFMETVKEFKKpETEVEIKEDIIKLENVSKHYc 298
                                   555555666666666666666666666777777665444567788889999999999999*******************85 PP

                   Terminase_2 128 ....g 128
                                       g
  gi|15669427|ref|NP_248237.1| 299 sverG 303
                                   44431 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.4      0.03        17      14      21 ..      72      79 ..      70      80 .. 0.78
   2 ?    7.4   0.7    0.0067       3.8       2      11 ..      90      99 ..      89     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.03
                 zinc_ribbon_2 14 kFCpyCGt 21
                                   +C++CG+
  gi|15669427|ref|NP_248237.1| 72 SYCEKCGY 79
                                  58999997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0067
                 zinc_ribbon_2  2 CpnCGaelqd 11
                                  C++CG+el++
  gi|15669427|ref|NP_248237.1| 90 CKKCGNELKK 99
                                  *******986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4     0.051        28       5      20 ..      39      54 ..      36      57 .. 0.89
   2 ?   -0.4   0.0       1.7   9.3e+02     101     145 ..     210     249 ..     176     270 .. 0.62
   3 ?    6.8   0.5      0.01       5.8       5      21 ..     323     339 ..     320     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.051
                                  EEC-TTTCHHHHHHHH CS
                         NACHT  5 lqGeaGsGKTtLlqkl 20
                                  + G++G GK++Ll+ l
  gi|15669427|ref|NP_248237.1| 39 ILGKSGAGKSVLLHML 54
                                  78***********865 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.7
                                   ........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..E CS
                         NACHT 101 ekqpvrtlLselirkkllpeasllltvrpralrdleeqleeaivl 145
                                   +++ v+  L+el+ k    + sl+lt++   +  ++e+ e+ai+l
  gi|15669427|ref|NP_248237.1| 210 TAKLVHSALKELVIK---NKISLILTSHWPEV--IAELTEKAIWL 249
                                   555555555555555...44444444443333..66655555444 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.01
                                   EEC-TTTCHHHHHHHHH CS
                         NACHT   5 lqGeaGsGKTtLlqkla 21 
                                   l G +G GKTtL++ +a
  gi|15669427|ref|NP_248237.1| 323 LVGTSGAGKTTLAKIIA 339
                                   78***********9887 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.23   1.3e+02       2      19 ..      37      54 ..      36      57 .. 0.89
   2 ?   -2.4   0.2       7.3   4.1e+03      67     119 ..     228     279 ..     211     290 .. 0.56
   3 ?    9.0   0.1    0.0023       1.3       1      19 [.     320     338 ..     320     347 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.23
                          MobB  2 lgivgksgsGKTtLlekl 19
                                  lgi gksg+GK  Ll+ l
  gi|15669427|ref|NP_248237.1| 37 LGILGKSGAGKSVLLHML 54
                                  799***********9865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.3
                          MobB  67 rlalikeleeaelsleellarlsevDlvlvEGfkkealpkievlraelgkeel 119
                                   +l l+++  e   +l e + +l+    +++EG  +e ++k     +e +k+e+
  gi|15669427|ref|NP_248237.1| 228 SLILTSHWPEVIAELTEKAIWLD-KGEIIMEGTSEEVVNKFMETVKEFKKPET 279
                                   44444444444445555555553.34577888888888886555555555554 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0023
                          MobB   1 vlgivgksgsGKTtLlekl 19 
                                   ++g+vg+sg+GKTtL + +
  gi|15669427|ref|NP_248237.1| 320 IFGLVGTSGAGKTTLAKII 338
                                   689***********98755 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0079       4.4      25      42 ..      36      53 ..      31      55 .. 0.86
   2 ?   -0.8   0.0       2.4   1.3e+03     117     151 ..     260     295 ..     248     320 .. 0.76
   3 ?    4.9   1.6     0.045        25      26      43 ..     321     338 ..     303     342 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0079
                         DUF87 25 HlAilgsTGsGKSntvav 42
                                  +l+ilg++G+GKS +   
  gi|15669427|ref|NP_248237.1| 36 SLGILGKSGAGKSVLLHM 53
                                  689**********98765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.4
                         DUF87 117 qrsvleealdqaka.keekeklssdepveklleelk 151
                                   +++v++++++++k+ k+ ++++ ++e + kl++  k
  gi|15669427|ref|NP_248237.1| 260 SEEVVNKFMETVKEfKKPETEVEIKEDIIKLENVSK 295
                                   678899999999888888888888888887777666 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.045
                         DUF87  26 lAilgsTGsGKSntvavL 43 
                                   ++ +g++G+GK+++++++
  gi|15669427|ref|NP_248237.1| 321 FGLVGTSGAGKTTLAKII 338
                                   899************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1166  (0.0650343); expected 358.6 (0.02)
Passed bias filter:                      936  (0.0522059); expected 358.6 (0.02)
Passed Vit filter:                       131  (0.0073066); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.86u 0.35s 00:00:01.21 Elapsed: 00:00:00.49
# Mc/sec: 3298.90
//
Query:       gi|15669428|ref|NP_248238.1|  [L=123]
Description: hypothetical protein MJ_1243 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-47  159.4   0.1    2.9e-47  159.2   0.1    1.1  1  DUF134        Protein of unknown function  DUF134
    4.9e-05   22.9   0.1    7.6e-05   22.3   0.1    1.3  1  Sigma70_r4_2  Sigma-70, region 4
     0.0018   17.7   0.1     0.0029   17.1   0.1    1.4  1  Sigma70_r4    Sigma-70, region 4
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.021   14.6   0.0    1.5  1  HTH_8         Bacterial regulatory protein, Fis family
      0.046   13.5   0.1       0.12   12.2   0.0    1.7  2  HTH_23        Homeodomain-like domain
      0.058   13.5   0.0       0.25   11.4   0.0    2.0  2  HTH_3         Helix-turn-helix
      0.065   13.4   0.1       0.14   12.3   0.1    1.7  1  HTH_17        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.2   0.1   1.1e-50   2.9e-47       1      97 [.       1      99 [.       1     100 [. 0.98

  Alignments for each domain:
  == domain 1  score: 159.2 bits;  conditional E-value: 1.1e-50
                        DUF134  1 msrkgrprklrdileePkvrifkPeaveetg..kvaisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkkiaka 81
                                  msr+grp+++r+i+eePk+rifkP++v++t+  kv++s+deleairlvdy d++qeea+klmGis+++lw+llte+rkkia+a
  gi|15669428|ref|NP_248238.1|  1 MSRRGRPKIPRFISEEPKFRIFKPHGVSLTEvdKVILSVDELEAIRLVDYLDYTQEEASKLMGISRRVLWSLLTEGRKKIADA 83
                                  99****************************9989************************************************* PP

                        DUF134 82 lveGraiilkGGeykr 97
                                  l++G+ai+++GGeyk+
  gi|15669428|ref|NP_248238.1| 84 LINGKAIVIEGGEYKI 99
                                  **************98 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1     3e-08   7.6e-05      11      54 .]      37      80 ..      36      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3e-08
                                  S-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                  Sigma70_r4_2 11 LperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54
                                  L+ ++ e++ l ++ +++++E+++l+gis +   s l  +rkk+
  gi|15669428|ref|NP_248238.1| 37 LSVDELEAIRLVDYLDYTQEEASKLMGISRRVLWSLLTEGRKKI 80
                                  6778889***********************************96 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.1e-06    0.0029       5      36 ..      37      68 ..      36      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                                  S-HHHHHHHHHHHTTT--HHHHHHHHTS-HHH CS
                    Sigma70_r4  5 LpererevlelrfgeglTleEIgerlgiSrer 36
                                  L+ +e e ++l+ + ++T+eE ++ +giSr  
  gi|15669428|ref|NP_248238.1| 37 LSVDELEAIRLVDYLDYTQEEASKLMGISRRV 68
                                  56678999*********************975 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   8.1e-06     0.021       2      36 ..      39      70 ..      38      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.1e-06
                                  HHHHHHHHHHHHHHHTTT-HHHHHHHHTS-HHHHH CS
                         HTH_8  2 leevEkelIeaALertgGnkskAArlLGisRrtLy 36
                                  ++e+E+  +++ L+ t+    +A++l GisRr L+
  gi|15669428|ref|NP_248238.1| 39 VDELEAIRLVDYLDYTQ---EEASKLMGISRRVLW 70
                                  67899999999999999...**************9 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.5e-05      0.12       8      35 ..      42      70 ..      39      75 .. 0.83
   2 ?   -3.3   0.0       3.5   8.9e+03      20      27 ..      77      84 ..      76      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.5e-05
                        HTH_23  8 lrilllla.eGlsvreIAreLgvsrrTvy 35
                                  l++++l++   ++++e+++++g+srr ++
  gi|15669428|ref|NP_248238.1| 42 LEAIRLVDyLDYTQEEASKLMGISRRVLW 70
                                  67888888537**************9665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.5
                        HTH_23 20 vreIAreL 27
                                  +++IA++L
  gi|15669428|ref|NP_248238.1| 77 RKKIADAL 84
                                  57899987 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.3   3.3e+03       6      19 ..      23      36 ..      20      39 .. 0.72
   2 ?   11.4   0.0   9.6e-05      0.25       8      25 ..      51      68 ..      42      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                                  HHTTHHHHHHHHHH CS
                         HTH_3  6 kqlglsqeeLAekl 19
                                  k +g s++e+ +++
  gi|15669428|ref|NP_248238.1| 23 KPHGVSLTEVDKVI 36
                                  56788888887765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 9.6e-05
                                  TTHHHHHHHHHHTSSHHH CS
                         HTH_3  8 lglsqeeLAeklGvsrst 25
                                  l+++qee+++++G+sr+ 
  gi|15669428|ref|NP_248238.1| 51 LDYTQEEASKLMGISRRV 68
                                  689*************86 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.7e-05      0.14       2      26 ..      53      77 ..      53     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-05
                        HTH_17  2 ltveEaAelLgvsrstvyrlirrge 26
                                  +t eEa++l g+sr+ +  l+ +g+
  gi|15669428|ref|NP_248238.1| 53 YTQEEASKLMGISRRVLWSLLTEGR 77
                                  899****************998663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 815.46
//
Query:       gi|15669429|ref|NP_248239.1|  [L=108]
Description: hypothetical protein MJ_1244 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-49  163.9   0.2      1e-48  163.8   0.2    1.0  1  Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen r


Domain annotation for each model (and alignments):
>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.8   0.2   5.8e-53     1e-48       1     106 [.       1     106 [.       1     107 [. 0.99

  Alignments for each domain:
  == domain 1  score: 163.8 bits;  conditional E-value: 5.8e-53
                 Nit_Regul_Hom   1 mkvllklfvesenlgkvinalseagitGfylieYkGlsPqewkgflleedpesaikiikdlseeavlintvvdeekvekik 81 
                                   mk+ll+lfvesen+gk+inalse+gitGf+l++YkG+sPq+w+gfll+edpe+aik+++dl+++avli+t+v+e+k+++i+
  gi|15669429|ref|NP_248239.1|   1 MKILLYLFVESENVGKAINALSEGGITGFFLYDYKGMSPQDWQGFLLDEDPEMAIKAVSDLAQNAVLIGTIVSENKLMEIE 81 
                                   8******************************************************************************** PP

                 Nit_Regul_Hom  82 eeleeklkderytiieipvekikvn 106
                                   + ++ekl+d++ytiieip+e+i+vn
  gi|15669429|ref|NP_248239.1|  82 KLIDEKLADCKYTIIEIPIEGIIVN 106
                                   ***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 777.94
//
Query:       gi|15669430|ref|NP_248240.1|  [L=112]
Description: hypothetical protein MJ_1245 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-42  142.9   2.7    3.8e-42  142.7   2.7    1.0  1  Nit_Regul_Hom   Uncharacterized protein, homolog of nitrogen 
     0.0087   16.4   0.2      0.011   16.0   0.2    1.1  1  ATP-synt_F      ATP synthase (F/14-kDa) subunit
  ------ inclusion threshold ------
      0.048   13.8   0.0      0.063   13.4   0.0    1.2  1  SpoU_methylase  SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.7   2.7   6.3e-46   3.8e-42       2     106 ..       4     110 ..       3     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 142.7 bits;  conditional E-value: 6.3e-46
                 Nit_Regul_Hom   2 kvllklfvesenlgkvinalseagitGfylieYkGlsPqewkgflle..edpesaikiikdlseeavlintvvdeekveki 80 
                                   +vl++lfve++n+gk+in+++ agitGf+l++Y+GlsP+++k+++ e  ed+e++++ii+d+s++av+i+tvv+eek++ki
  gi|15669430|ref|NP_248240.1|   4 RVLFELFVEEKNVGKAINIMTLAGITGFFLHKYRGLSPDKFKNLSKEelEDIEKVYEIIRDESDKAVVIGTVVKEEKAKKI 84 
                                   899******************************************99888******************************* PP

                 Nit_Regul_Hom  81 keeleeklkderytiieipvekikvn 106
                                   +e l+ek+++er+t+++ip+ k+kv+
  gi|15669430|ref|NP_248240.1|  85 EELLKEKMNNERWTVMKIPILKVKVH 110
                                   ************************98 PP

>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.9e-06     0.011      12      75 ..      22     104 ..      17     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.9e-06
                                   HHHHTTCEEEE................CSSHHHHHHHHHHHHHHTTEEEEE...EEHHHHCCCHHHHHHCTCSSSSEEEEE CS
                    ATP-synt_F  12 gfrlaGvgeve................vtdeeeieealkelleredigiil...itekiaeeirelideykeealPaileI 73 
                                    + laG++++                 +++ e+ie++ + + +++d ++++   ++e+ a++i+el++e  +++  ++++I
  gi|15669430|ref|NP_248240.1|  22 IMTLAGITGFFlhkyrglspdkfknlsKEELEDIEKVYEIIRDESDKAVVIgtvVKEEKAKKIEELLKEKMNNERWTVMKI 102
                                   6899**********************9999*******9999999999999555599************99999******** PP

                                   SC CS
                    ATP-synt_F  74 Ps 75 
                                   P 
  gi|15669430|ref|NP_248240.1| 103 PI 104
                                   96 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.1e-05     0.063       5      91 ..       6      84 ..       3     100 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                                  EEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SE CS
                SpoU_methylase  5 vlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgks 87
                                  +++   +++N+G+++  +  +g+++ +l k r+  l  +++k+++ ++le +e kv+    e++++  ++   +++t  k+++
  gi|15669430|ref|NP_248240.1|  6 LFELFVEEKNVGKAINIMTLAGITGFFLHKYRG--LSPDKFKNLSKEELEDIE-KVY----EIIRDESDK-AVVIGTVVKEEK 80
                                  555667899*******************88666..5888999**999999999.444....555555555.455666554444 PP

                                  GCCS CS
                SpoU_methylase 88 lsei 91
                                   ++i
  gi|15669430|ref|NP_248240.1| 81 AKKI 84
                                  4433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1619  (0.0903006); expected 358.6 (0.02)
Passed bias filter:                      811  (0.045234); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 846.61
//
Query:       gi|15669431|ref|NP_248241.1|  [L=294]
Description: succinyl-CoA synthetase subunit alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-32  112.5   2.8    1.1e-32  112.5   2.8    2.5  3  CoA_binding    CoA binding domain
    3.4e-18   65.9   0.7    6.4e-18   65.0   0.7    1.5  1  Ligase_CoA     CoA-ligase
    2.4e-12   46.8   0.4    5.9e-12   45.6   0.1    1.8  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
      4e-06   27.3   0.1      2e-05   25.1   0.0    2.1  2  CoA_binding_2  CoA binding domain
  ------ inclusion threshold ------
      0.023   14.3   0.4      0.023   14.3   0.4    1.7  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
      0.079   13.3   0.0       0.22   11.8   0.0    1.6  1  PHP            PHP domain
       0.14   13.0   0.6       0.34   11.8   0.1    1.9  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.5   2.8   4.4e-36   1.1e-32       1      96 []      11     104 ..      11     104 .. 0.98
   2 ?   -3.8   0.0         7   1.8e+04      28      48 ..     120     140 ..     117     146 .. 0.67
   3 ?    2.2   0.1      0.11   2.9e+02       9      68 ..     156     210 ..     148     239 .. 0.62

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 4.4e-36
                                   CTTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHH CS
                   CoA_binding   1 dkdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavde 81 
                                   d++tk iv+G++g+  +g +h+k++l++g+k+v+gv+p+k+g++v+g+pv+++v+e++++t+++++vi+vPa++a++av e
  gi|15669431|ref|NP_248241.1|  11 DENTKAIVQGITGR--QGSFHTKKMLECGTKIVGGVTPGKGGQNVHGVPVFDTVKEAVKETDANASVIFVPAPFAKDAVFE 89 
                                   689***********..***************************************************************** PP

                                   HHHTT-SEEEEESST CS
                   CoA_binding  82 lveagikgiviiteg 96 
                                   +++agi++iv+ite+
  gi|15669431|ref|NP_248241.1|  90 AIDAGIELIVVITEH 104
                                   *************95 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7
                                   ECEEEEEEC-TTTTTCEETTE CS
                   CoA_binding  28 ygikavfgvnprkvgtevlgl 48 
                                   +g+k++++ +p+ ++ +v+ l
  gi|15669431|ref|NP_248241.1| 120 VGVKIIGPNTPGIASPKVGKL 140
                                   566777777777777766655 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.11
                                   ETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEE CS
                   CoA_binding   9 iGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavi 68 
                                   +  +g+ + +  h+++k ++g++  +g++++     + gl  + +v +l ek +++ a++
  gi|15669431|ref|NP_248241.1| 156 VSRSGTLTYEIAHQIKKAGFGVSTCVGIGGD----PIVGLRYK-EVLDLFEKDDETEAIV 210
                                   5556666667788899999999999998766....66677666.6666666633444444 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.7   2.5e-21   6.4e-18       1     152 [.     156     275 ..     156     276 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 2.5e-21
                                   EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEE CS
                    Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldi 81 
                                   ++++GtL+ye +++ik+a              g + ++++++G+d            + ++ e l  + +d+e+++i++ +
  gi|15669431|ref|NP_248241.1| 156 VSRSGTLTYEIAHQIKKA--------------GFGVSTCVGIGGDPIV---------GLRYKEVLDLFEKDDETEAIVMIG 213
                                   689***************..............***************8.........999********************* PP

                                   EESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHHHH CS
                    Ligase_CoA  82 vlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraaka 152
                                   ++G g +e++aa++++++k+        pv+ ++aG +a+ ++++++a+a+ e g  +a+sk +al+ a+a
  gi|15669431|ref|NP_248241.1| 214 EIG-GGAEEEAAKFIEKMKK--------PVIGYIAGQSAPEGKRMGHAGAIVEKGKGTAESKMKALEEAGA 275
                                   ***.9999999999987765........79************************************99876 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.3   3.3e+03      52      77 ..      92     119 ..      87     123 .. 0.69
   2 !   45.6   0.1   2.3e-15   5.9e-12       2     131 ..     151     284 ..     150     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
                  Succ_CoA_lig  52 dpetkvillylEsi..rdgrkflsaarr 77 
                                   d  +++i++  E+i  +d  +f++ a+ 
  gi|15669431|ref|NP_248241.1|  92 DAGIELIVVITEHIpvHDTMEFVNYAED 119
                                   6778888888888722456777777665 PP

  == domain 2  score: 45.6 bits;  conditional E-value: 2.3e-15
                  Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsird.grkflsaarraa 79 
                                   G+++++s SG+l  +++++ ++ g+g+s++v +G    + + ++++l+ +++d+et++i++  E  +   ++ ++ +++++
  gi|15669431|ref|NP_248241.1| 151 GSVGMVSRSGTLTYEIAHQIKKAGFGVSTCVGIGGdpIVGLRYKEVLDLFEKDDETEAIVMIGEIGGGaEEEAAKFIEKMK 231
                                   99********************************9334677789*****************99965551455666666664 PP

                  Succ_CoA_lig  80 rkkpvvvlksGrseagaraaashtgala....gsdavvdaafrqaGvlrvdsleel 131
                                     kpv+ + +G+s+   +  + h ga++    g  +   +a+++aG++++++++++
  gi|15669431|ref|NP_248241.1| 232 --KPVIGYIAGQSAPEGKR-MGHAGAIVekgkGTAESKMKALEEAGAYVAKNISDI 284
                                   ..*********97655544.578888872222445566789999999999999875 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   7.7e-09     2e-05      32     114 ..      43     133 ..      21     135 .. 0.86
   2 ?   -1.0   0.0      0.95   2.4e+03       6      30 ..     153     177 ..     151     212 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 7.7e-09
                                   EESSS-..SEETTEES----T......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT....---HHHHHHHHHTT-E CS
                 CoA_binding_2  32 pVnpke..eeilgekvyaslaed..pepvdlvdvftppeatpeivkealalgakavwlqpg....sedeeaaelaeeagir 104
                                    V+p +  + ++g++v+ +++e+  +++  + ++f+p+  + + v ea+++g++ +++  +        e++++ae+ g++
  gi|15669431|ref|NP_248241.1|  43 GVTPGKggQNVHGVPVFDTVKEAvkETDANASVIFVPAPFAKDAVFEAIDAGIELIVVITEhipvHDTMEFVNYAEDVGVK 123
                                   478887779************9535677779****************************9999999999************ PP

                                   EE.ES-HHHH CS
                 CoA_binding_2 105 vvgdrCilve 114
                                   ++g++ ++++
  gi|15669431|ref|NP_248241.1| 124 IIGPNTPGIA 133
                                   ******9986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.95
                                   ET--S-TTSHHHHHHHHHHHHT--E CS
                 CoA_binding_2   6 vGasdnpgkfgykvlryllehglpv 30 
                                   vG+ +++g   y ++++++++g+ v
  gi|15669431|ref|NP_248241.1| 153 VGMVSRSGTLTYEIAHQIKKAGFGV 177
                                   5666666666666666666666443 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   9.1e-06     0.023      11     122 ..      20     132 ..       9     138 .. 0.77
   2 ?   -2.4   0.1       1.2     3e+03       8      51 ..     233     277 ..     227     283 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.1e-06
                                   S.-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEE.EHHHHHHT-S..EEEE-S-HHHHHHHHHHHTGGG--T CS
                          IlvN  11 G.yGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevl.tvaeavkkad..vvmiliPDelqkevyeeeiepnlke 87 
                                   G  G qG  +++++ + g ++v g+  g+      + +g+ v  tv+eavk++d    +i +P  + k+ + e+i   ++ 
  gi|15669431|ref|NP_248241.1|  20 GiTGRQGSFHTKKMLECGTKIVGGVTPGKGG---QNVHGVPVFdTVKEAVKETDanASVIFVPAPFAKDAVFEAIDAGIEL 97 
                                   4359***********************9944...34566666526788888765115678889998888777999999988 PP

                                   T-EEEESSSHHHHTTSS---TTSEEEEEEESS-SH CS
                          IlvN  88 gkalafahGfnihfglikppkdvdvvlvAPkgpGh 122
                                     +++     +  +++++  +dv v ++ P +pG 
  gi|15669431|ref|NP_248241.1|  98 IVVITEHIPVHDTMEFVNYAEDVGVKIIGPNTPGI 132
                                   7777666666667899*****************95 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                                   EEES-.SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EE CS
                          IlvN   8 aviGy.GsqGhaqalnlrdsgldvvvglregsksvkkAkeegfev 51 
                                    viGy   q   +++ +  +g  v  g  + ++++k  +e+g  v
  gi|15669431|ref|NP_248241.1| 233 PVIGYiAGQSAPEGKRMGHAGAIVEKGKGTAESKMKALEEAGAYV 277
                                   578873347777788888888888877777776666666666655 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.4e-05      0.22      17      61 ..      83     125 ..      74     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.4e-05
                                   .HHHHHHHHHCT-SEE.EEEEEEBTTHHHHHHHHHHHHTTTTSEEE CS
                                   xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           PHP  17 ieelvkkakelglkai.aiTDhgnlfgyvefykaakkkykagikpi 61 
                                   +++ v +a++ g++ i  iT+h ++++ +ef+++a   ++ g+k+i
  gi|15669431|ref|NP_248241.1|  83 AKDAVFEAIDAGIELIvVITEHIPVHDTMEFVNYA---EDVGVKII 125
                                   5788999999999976269****************...77889997 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00013      0.34      10      97 ..      24     109 ..      14     125 .. 0.73
   2 ?   -1.4   0.0       1.6   4.1e+03       3      25 ..     209     232 ..     193     278 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                   HHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-... CS
                  GFO_IDH_MocA  10 kigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelakaaleagk... 87 
                                   + gs h +++ e   ++++v+ + p++  +       gv++++ ++e +++++++a ++ +p+   ++ + +a+ ag+   
  gi|15669431|ref|NP_248241.1|  24 RQGSFHTKKMLEC--GTKIVGGVTPGKGGQN----VHGVPVFDTVKEAVKETDANASVIFVPAPFAKDAVFEAIDAGIeli 98 
                                   5555555555554..5566666666664333....3799***************************************777 PP

                                   EEEEES.SS-S CS
                  GFO_IDH_MocA  88 hvllEK.Plat 97 
                                    v+ E+ P+ +
  gi|15669431|ref|NP_248241.1|  99 VVITEHiPVHD 109
                                   77888745433 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                                   EEEETT.SHHHHHHHHHHHHTTTT CS
                  GFO_IDH_MocA   3 vaiiGa.Gkigskhlrplnesqrl 25 
                                   +++iG  G  ++++++++ e+ ++
  gi|15669431|ref|NP_248241.1| 209 IVMIGEiGGGAEEEAAKFIEKMKK 232
                                   456665555566666555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2194.98
//
Query:       gi|15669432|ref|NP_248242.1|  [L=180]
Description: hypothetical protein MJ_1247 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-16   58.5   0.0    7.8e-16   58.1   0.0    1.3  1  SIS             SIS domain
    4.5e-07   30.0   0.6    8.1e-05   22.7   0.2    2.3  2  SIS_2           SIS domain
      0.007   16.0   0.0      0.009   15.6   0.0    1.2  1  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
      0.035   13.5   0.0       0.07   12.5   0.0    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   1.7e-19   7.8e-16       2     106 ..      37     134 ..      36     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.7e-19
                                   HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSE CS
                           SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergak 82 
                                   ++kak+i+++G G+s+ i++ +a+ l+++g++ ++v ++++      +  ++ddl+ilis sg+t +++ +a++ak+ + +
  gi|15669432|ref|NP_248242.1|  37 IIKAKKIFIFGVGRSGYIGRCFAMRLMHLGFKSYFVGETTT------PSYEKDDLLILISGSGRTESVLTVAKKAKNINNN 111
                                   789**************************************......6677****************************** PP

                                   EEEEESSTTSHHHHHSSEEEEEEE CS
                           SIS  83 iiaITdskgsplareadlalyina 106
                                   iiaI ++ g+ ++++adl++ + +
  gi|15669432|ref|NP_248242.1| 112 IIAIVCECGN-VVEFADLTIPLEV 134
                                   *****87665.5677777766655 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0     0.003        13      26      58 ..      31      63 ..      15      77 .. 0.84
   2 !   22.7   0.2   1.8e-08   8.1e-05     102     137 ..      81     116 ..      72     117 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.003
                                  HHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT CS
                         SIS_2 26 eliadslenggkvlvfGsGhSaalaeelaarag 58
                                  + + d + + +k+++fG G S  +   +a r+ 
  gi|15669432|ref|NP_248242.1| 31 DSLIDRIIKAKKIFIFGVGRSGYIGRCFAMRLM 63
                                  5677888999***********998888888776 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.8e-08
                                   -TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                         SIS_2 102 kpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                   ++ D+L+ iS sG+ ++v+ +a++ak++  ++iA++
  gi|15669432|ref|NP_248242.1|  81 EKDDLLILISGSGRTESVLTVAKKAKNINNNIIAIV 116
                                   789*******************************97 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     2e-06     0.009      84     146 ..      51     109 ..      20     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-06
                                   HHHHHHHHHHHHHHTT-EEEEES--SST...........T-S-EEEEE-BS----....-----HH CS
                TM1586_NiRdase  84 aGYygeqlvLkltalGlgtcWvggtykkkkakvelkkgeklvivIalGyaktklv...eakrkple 146
                                    GY+g ++ + l+ lG+++ +vg t+ ++++      +++l+i+I+ G ++t++v   ++k k+++
  gi|15669432|ref|NP_248242.1|  51 SGYIGRCFAMRLMHLGFKSYFVGETTTPSYE------KDDLLILIS-GSGRTESVltvAKKAKNIN 109
                                   7***********************9999888......677777776.8888887644455555544 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.6e-05      0.07      13      73 ..      16      80 ..       9      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                                  HHHHHHHTTCC.HTTCCGSBS-GTTSEEEEES-SH...HHHHHHHHHHHTT-EEEEESSSHHHHH CS
                  2-Hacid_dh_C 13 eadeevregew.ksekallgkelsgktvGiiGlGr...IGqavakrlkafgmkviaydrskkkee 73
                                   +++ + ++ew ++ ++l  + ++ k++ i+G+Gr   IG+ +a rl  +g+k +++  + +++ 
  gi|15669432|ref|NP_248242.1| 16 ILKKFYTNDEWkNKLDSLIDRIIKAKKIFIFGVGRsgyIGRCFAMRLMHLGFKSYFVGETTTPSY 80
                                  56677789999555556777789**********98777***************999988877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1384.11
//
Query:       gi|15669433|ref|NP_248243.1|  [L=154]
Description: hypothetical protein MJ_1248 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1015.09
//
Query:       gi|15669434|ref|NP_248244.1|  [L=361]
Description: 3-dehydroquinate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.5e-149  496.5   3.5   3.9e-149  496.4   3.5    1.0  1  DHQS             3-dehydroquinate synthase II
     0.0032   16.2   2.8       0.64    8.7   0.6    2.2  2  CdhD             CO dehydrogenase/acetyl-CoA synthase delta s
     0.0082   15.7   0.0       0.17   11.4   0.0    2.2  2  Hint             Hint module
  ------ inclusion threshold ------
        0.1   12.4   0.8        1.6    8.6   0.2    2.9  3  DUF1953          Domain of unknown function (DUF1953)
       0.18   11.4   0.1       0.24   10.9   0.1    1.2  1  Glyco_hydr_30_2  O-Glycosyl hydrolase family 30
       0.26   11.1   1.6        8.3    6.3   0.0    3.2  2  eIF-1a           Translation initiation factor 1A / IF-1
       0.52   10.3   4.7         15    5.6   0.0    3.9  4  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain


Domain annotation for each model (and alignments):
>> DHQS  3-dehydroquinate synthase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.4   3.5  1.5e-152  3.9e-149       1     352 []       2     361 .]       2     361 .] 0.97

  Alignments for each domain:
  == domain 1  score: 496.4 bits;  conditional E-value: 1.5e-152
                          DHQS   1 kevwikadeeeweerkelvtaaleagvdavlveeedaekvkelgkikviake.eddavlvgkd.dleklkka....kkvaa 75 
                                   k+ w+++  ++wee+k++vt+ale+++ +v++e ed ek+kelg+ikv++++ + d+vlv+k+ ++e lk+a    k++a+
  gi|15669434|ref|NP_248244.1|   2 KFGWVNVIGDNWEEKKKIVTTALESSIPVVVAEPEDIEKIKELGNIKVASHSlDADIVLVNKNdNIEFLKEAknlgKETAI 82 
                                   678****99*****************************************99555999999984445555557779***** PP

                          DHQS  76 lveikskeeeeeaaeaake..adyvivelkdwtvIPlEnliAalqgeetkiiaavksaeeAklaletLEkGadgvllkted 154
                                   ++ i+ske+ee+a+e+a+   +d++i+e++dwt+IPlEnliA+l ++++ki+a v+s++eAk+a+e+LEkG+dgvll++++
  gi|15669434|ref|NP_248244.1|  83 YIPIESKEDEEFASEVARFgfVDNIILEGRDWTIIPLENLIADLFHRDVKIVASVNSVDEAKVAYEILEKGTDGVLLNPKN 163
                                   ****************997669*********************************************************** PP

                          DHQS 155 veeikelaelleeaeeekleLkeaevtkveevgmgdRvcvDtcslmkegeGmLvGsssrglfLvhsEtlespYvasRPFRV 235
                                    e+ikel++l+ee+++ek+ L+ a+vtkve++g+gdRvc+Dtcslmk geGmL+Gs+sr+lfLvhsEt+e+pYva+RPFRV
  gi|15669434|ref|NP_248244.1| 164 LEDIKELSKLIEEMNKEKVALDVATVTKVEPIGSGDRVCIDTCSLMKIGEGMLIGSYSRALFLVHSETVENPYVATRPFRV 244
                                   ********************************************************************************* PP

                          DHQS 236 NAGavhaYvlvpggkTkYLseLkaGdevlvvdkkGktreavvGRvKiEkRPlllveaeaegkkvstilQnaetirlvtedg 316
                                   NAG+vhaY+l+pg+kTkYLseLkaGd+vl+vdk+G+trea+vGRvKiE+RPl+l+eae++g+ ++tilQnaetirlv+e+g
  gi|15669434|ref|NP_248244.1| 245 NAGPVHAYILCPGNKTKYLSELKAGDKVLIVDKDGNTREAIVGRVKIERRPLVLIEAEYKGDIIRTILQNAETIRLVNEKG 325
                                   ********************************************************************************* PP

                          DHQS 317 kaisvteLkeGdevlvyleekaRHfGikieEtiiEk 352
                                   ++isv++Lk+Gd+vl++ ee aRHfG++i+EtiiEk
  gi|15669434|ref|NP_248244.1| 326 EPISVVDLKPGDKVLIKPEEYARHFGMAIKETIIEK 361
                                   ***********************************8 PP

>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1   0.00054       1.4     132     175 ..      15      60 ..       8      62 .. 0.80
   2 !    8.7   0.6   0.00025      0.64     124     182 ..     133     191 ..      62     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00054
                                   THHHHHHHHHHTT--EEEE-.SSHHHHHHHHH.HHHCTT-.--EEE CS
                          CdhD 132 dykeiaelaleykvpvvllsindleelkelar.kllkagv.kdivl 175
                                   + k+i+  ale   pvv+   +d+e++kel + k+++  +  divl
  gi|15669434|ref|NP_248244.1|  15 EKKKIVTTALESSIPVVVAEPEDIEKIKELGNiKVASHSLdADIVL 60 
                                   447899************************6515555666778887 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00025
                                   EEEEE-TTTHHHHHHHHHHTT--EEEE-.SSHHHHHHHHHHHHCTT---EEEE---SH. CS
                          CdhD 124 llyaAtkddykeiaelaleykvpvvllsindleelkelarkllkagvkdivldPttaal 182
                                   ++++ +  d +++a  +le +++ vll  ++le++kel++ + +++ +++ ld  t++ 
  gi|15669434|ref|NP_248244.1| 133 IVASVNSVDEAKVAYEILEKGTDGVLLNPKNLEDIKELSKLIEEMNKEKVALDVATVTK 191
                                   6777788899999999*************************************999875 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   6.5e-05      0.17      17      47 ..     251     281 ..     247     302 .. 0.88
   2 ?    1.7   0.0      0.06   1.5e+02      22      39 ..     323     340 ..     315     347 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.5e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Hint  17 stvtvedgeqkslseLepGdkVlavdesgev 47 
                                   + +   ++++k lseL+ GdkVl vd++g++
  gi|15669434|ref|NP_248244.1| 251 AYILCPGNKTKYLSELKAGDKVLIVDKDGNT 281
                                   5667788999*****************9986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.06
                                   XXXXXXXXXXXXXXXXXX CS
                          Hint  22 edgeqkslseLepGdkVl 39 
                                   e+ge +s+ +L+pGdkVl
  gi|15669434|ref|NP_248244.1| 323 EKGEPISVVDLKPGDKVL 340
                                   678889999********8 PP

>> DUF1953  Domain of unknown function (DUF1953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.11   2.8e+02       9      26 ..     261     278 ..     256     282 .. 0.77
   2 ?    8.6   0.2   0.00062       1.6      43      62 ..     280     299 ..     276     300 .. 0.88
   3 ?   -2.2   0.0       1.4   3.6e+03      17      31 ..     336     350 ..     332     356 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.11
                                   TTEEEEEETTTEEEEEES CS
                       DUF1953   9 kGlcGfmrGdkvlvivkt 26 
                                   k l  +  Gdkvl++ k 
  gi|15669434|ref|NP_248244.1| 261 KYLSELKAGDKVLIVDKD 278
                                   55667778*****99876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00062
                                   TTTEEEEEEEEE-SS-EEEE CS
                       DUF1953  43 itdetvrGrvkvdklplilv 62 
                                    t e++ Grvk+++ pl+l+
  gi|15669434|ref|NP_248244.1| 280 NTREAIVGRVKIERRPLVLI 299
                                   5889**************97 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.4
                                   TTTEEEEEESSSS-E CS
                       DUF1953  17 Gdkvlvivktlnrdy 31 
                                   Gdkvl+      r +
  gi|15669434|ref|NP_248244.1| 336 GDKVLIKPEEYARHF 350
                                   9***99766666665 PP

>> Glyco_hydr_30_2  O-Glycosyl hydrolase family 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   9.5e-05      0.24     197     324 ..      33     163 ..      12     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.5e-05
                                   --HHHHHHHHHHHHHHHHHHT-S-EEEEEEES.SGGGGS---.-TTS..---HHHHHHSTTSTT--TT-TTEEEEEEE--T CS
               Glyco_hydr_30_2 197 atnediaalvrkLseklsekklktkivlgeag.qldyLykkkeserg..qddqieeffekasanyvanlknvekviaghsy 274
                                   a+ edi ++ +  + k+ +++l++ ivl + + ++++L + k+ +++      ie+  +++ a+ va +  v ++i     
  gi|15669434|ref|NP_248244.1|  33 AEPEDIEKIKELGNIKVASHSLDADIVLVNKNdNIEFLKEAKNLGKEtaIYIPIESKEDEEFASEVARFGFVDNIILEGRD 113
                                   567899999999999***********987655279*****9996555004455677777888899**************** PP

                                   T-SSSHHHHHHHHHHHHHHHHTTSS--EEEE----S--.--TTT-SSSHH CS
               Glyco_hydr_30_2 275 fttspakelvekrkelaakisakepklkyWqseyciLgdkegeingeard 324
                                   +t +p ++l+    + + ki a+ ++++  +  y iL++ ++ +  ++++
  gi|15669434|ref|NP_248244.1| 114 WTIIPLENLIADLFHRDVKIVASVNSVDEAKVAYEILEKGTDGVLLNPKN 163
                                   **********9988888888889999999999999999888777666665 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.5     0.077     2e+02      38      62 ..     288     308 ..     265     309 .. 0.80
   2 ?    6.3   0.0    0.0032       8.3      41      56 ..     333     348 ..     317     361 .] 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.077
                                   T----TT-EEEEEE-TT-TTEEEEE CS
                        eIF-1a  38 kiwikrGdyVlVelspydltkGrIv 62 
                                   +++i r   Vl+e  +y   kG+I+
  gi|15669434|ref|NP_248244.1| 288 RVKIERRPLVLIEA-EY---KGDII 308
                                   68888888899998.44...99998 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0032
                                   --TT-EEEEEE-TT-T CS
                        eIF-1a  41 ikrGdyVlVelspydl 56 
                                    k+Gd+Vl+++ +y+ 
  gi|15669434|ref|NP_248244.1| 333 LKPGDKVLIKPEEYAR 348
                                   69*********99965 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.1       6.6   1.7e+04      41      48 ..      57      64 ..      57      66 .. 0.80
   2 ?    3.1   0.1     0.036        93      15      47 ..     173     205 ..     148     229 .. 0.89
   3 ?    0.8   0.0      0.19   4.9e+02      36      48 ..     265     278 ..     256     281 .. 0.78
   4 ?    5.6   0.0    0.0059        15      32      50 ..     328     346 ..     315     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 6.6
                                  EEEEEETT CS
                Prot_ATP_ID_OB 41 DlVavdkd 48
                                  D V+v+k 
  gi|15669434|ref|NP_248244.1| 57 DIVLVNKN 64
                                  6799*996 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.036
                                   EEE-TTS-EEEEEE-GGGSSST--TTEEEEEET CS
                Prot_ATP_ID_OB  15 iVktssdeevvvslagavpremLrpgDlVavdk 47 
                                   +++  ++e+v + +a   + e++  gD+V +d+
  gi|15669434|ref|NP_248244.1| 173 LIEEMNKEKVALDVATVTKVEPIGSGDRVCIDT 205
                                   677889999999999999999999999999987 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.19
                                   T--TTEEEE.EETT CS
                Prot_ATP_ID_OB  36 mLrpgDlVa.vdkd 48 
                                   +L++gD V+ vdkd
  gi|15669434|ref|NP_248244.1| 265 ELKAGDKVLiVDKD 278
                                   79*****9835555 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0059
                                   GSSST--TTEEEEEETTTT CS
                Prot_ATP_ID_OB  32 vpremLrpgDlVavdkdtg 50 
                                   +   +L+pgD V++ +  +
  gi|15669434|ref|NP_248244.1| 328 ISVVDLKPGDKVLIKPEEY 346
                                   45567********988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2596.75
//
Query:       gi|15669435|ref|NP_248245.1|  [L=166]
Description: hypothetical protein MJ_1249.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.33   11.2  12.3       0.46   10.7  12.3    1.1  1  EI24      Etoposide-induced protein 2.4 (EI24)
        3.8    5.7  12.7        4.8    5.4  12.7    1.1  1  DUF2070   Predicted membrane protein (DUF2070)
        7.9    5.7  13.5        9.1    5.5   8.6    2.0  2  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  12.3   7.7e-05      0.46      28     126 ..      12     111 ..       2     119 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.7e-05
                                   HHHHHHHHHHH-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HH.CCTTSHH....HHHHHHHHHHHHHH CS
                          EI24  28 llfllllvlllwvllasllvllllllplwlfplvalllaapfygllaekvekrhl.glvksla....eslkslllllllll 103
                                    ++l+        +l+sl++ l++  +l+ f l++++l ++     + k+e+ ++ +l+ ++     e+l++l++l+++ +
  gi|15669435|ref|NP_248245.1|  12 SFLLI--------ILVSLILSLFYYNFLFAF-LLSFILFGITWAYCYIKIESTDKgKLLYEIKrpgiETLRFLFILMIISV 83 
                                   22221........122333333333334444.4444444444444444444433333455555666699999999999999 PP

                                   HHHHH.....HHTTHHH....HHHHHHH CS
                          EI24 104 vllpl.....liPvvglilsplllswlt 126
                                   ++  l     ++P++ ++ls l+l+++ 
  gi|15669435|ref|NP_248245.1|  84 FIKSLlhsnsFFPYISFLLSNLILGLVL 111
                                   8888889**888**********999875 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  12.7    0.0008       4.8      15     122 ..      10     112 ..       5     131 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0008
                       DUF2070  15 kvsllliillalligllaflssklfgillfglpalvaflltlpvlrilggr...ltykrslflalltelivviisllaill 92 
                                   k+s+lliil++l+++l ++++  lf++ll ++ + ++ +  +  ++++ +    +++kr  +  l +++i++iis++   l
  gi|15669435|ref|NP_248245.1|  10 KISFLLIILVSLILSLFYYNF--LFAFLLSFILFGITWAYCYIKIESTDKGkllYEIKRPGIETLRFLFILMIISVFIKSL 88 
                                   699*************99988..5788888888888888888999998887888888888555555555555544433333 PP

                       DUF2070  93 sallqalvllalvlslalvfalrllvlvav 122
                                    +      +++++  +++ +++ +l lv++
  gi|15669435|ref|NP_248245.1|  89 LH------SNSFFPYISFLLSNLILGLVLF 112
                                   22......2333333444444444444444 PP

>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   8.6    0.0015       9.1      72     112 ..      12      51 ..       4      55 .. 0.81
   2 ?    3.0   0.2    0.0086        51     188     229 ..      72     109 ..      64     124 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0015
                          UbiA  72 faivllilgllllalllnpltallgllallly.vvYtglrlK 112
                                    ++++++++l+l+++++n+l+a+l+ ++l+   ++Y   + K
  gi|15669435|ref|NP_248245.1|  12 SFLLIILVSLILSLFYYNFLFAFLLSFILFGItWAYC--YIK 51 
                                   45666777777778*********9999999999***9..666 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0086
                          UbiA 188 arillalllavlllallllllalllllylllalllaalallr 229
                                    r+l++    ++++++++  l++ +++++++++ll +l+l  
  gi|15669435|ref|NP_248245.1|  72 LRFLFI----LMIISVFIKSLLHSNSFFPYISFLLSNLILGL 109
                                   333222....22222345678888888888888887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1114  (0.062134); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1038.88
//
Query:       gi|15669436|ref|NP_248246.1|  [L=253]
Description: geranylgeranylglyceryl phosphate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-95  318.1   2.4    3.1e-95  317.9   2.4    1.0  1  PcrB           PcrB family
    4.9e-05   22.9   0.5    0.00023   20.7   0.0    1.9  2  His_biosynth   Histidine biosynthesis protein
    0.00043   19.2   0.2       0.46    9.3   0.0    2.2  2  Trp_syntA      Tryptophan synthase alpha chain
     0.0014   17.9   0.5       0.28   10.3   0.1    2.5  2  NanE           Putative N-acetylmannosamine-6-phosphate epime
     0.0017   17.8   0.4        1.9    7.9   0.1    2.5  2  G3P_antiterm   Glycerol-3-phosphate responsive antiterminator
  ------ inclusion threshold ------
      0.022   13.8   1.4       0.26   10.3   0.2    2.1  2  IMPDH          IMP dehydrogenase / GMP reductase domain
      0.025   14.3   0.5      0.057   13.1   0.5    1.7  1  Spore_YhaL     Sporulation protein YhaL
      0.026   13.8   0.6      0.039   13.2   0.1    1.5  2  DHO_dh         Dihydroorotate dehydrogenase
       0.03   14.0   0.0      0.075   12.7   0.0    1.7  2  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.9   2.4   1.6e-98   3.1e-95       2     225 ..      14     245 ..      13     246 .. 0.98

  Alignments for each domain:
  == domain 1  score: 317.9 bits;  conditional E-value: 1.6e-98
                                   HGGGTS...EEEEE-TTSS-CHHHHHHHHCTT-SEEEEECST.CHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSEE CS
                          PcrB   2 dileer...hltklDPeeenpdEiveiviesgtDavmigGsq.svtldntvrllkkvsriklPivlepsnvegvvryaDal 78 
                                   +i+ee+   +lt+lDPeeen++Ei+e+v ++++Da+m+gGs+ +v+ld+tv+++kk+  +klPi+l+p+nv+g++ryaDa+
  gi|15669436|ref|NP_248246.1|  14 QIIEEEgavYLTLLDPEEENIEEIAENV-KDYADAIMVGGSIgIVNLDETVKKIKKI--TKLPIILFPGNVDGLSRYADAV 91 
                                   889999999*******************.*************9**************..********************** PP

                                   EEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSH..HHHHTTB-.B-TTHHHHHHHHHHHHHHTT-SE CS
                          PcrB  79 FvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdsk..vaavteak.vdlnkediaayallaakllglrl 156
                                   F+msl+nsan++W+v+a++lg++++ k++  +e+++++Yl++eP++k  v++v+e++ +++nk++i+a+++l+ak++g+r+
  gi|15669436|ref|NP_248246.1|  92 FYMSLMNSANTYWVVTAPTLGAITILKYN--LEPIPMAYLCIEPAKKtaVGYVGEIReIPQNKPKITAMYCLSAKFFGMRW 170
                                   *****************************..**************9999******************************** PP

                                   EEEE-.TTSSS-H.HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH...HCHHHHHHHH CS
                          PcrB 157 iYlEa.sGaledv.eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd...erkidailea 225
                                   +YlEa sGa+++v +e+ial+kkl+++++ivGGGir++E+A+e+v a AD+iv+Gn++ee++   e+++dai++a
  gi|15669436|ref|NP_248246.1| 171 AYLEAgSGASYPVnNETIALSKKLSGINIIVGGGIRKPEIAYEKVLAgADAIVTGNLLEENPkavEMMYDAIKKA 245
                                   *************************************************************999********987 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.23   4.5e+02      58      83 ..      30      55 ..       8      76 .. 0.60
   2 !   20.7   0.0   1.2e-07   0.00023      58     120 ..     181     243 ..     172     249 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.23
                                  HHHHHHHHHHHHHH-SSEEEEESSSS CS
                  His_biosynth 58 reanldlveeiaeevfipvqvGGGIr 83
                                  +e+n++ ++e ++     ++vGG I 
  gi|15669436|ref|NP_248246.1| 30 EEENIEEIAENVKDYADAIMVGGSIG 55
                                  44555555555555556688888443 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.2e-07
                                   HHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHC CS
                  His_biosynth  58 reanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfg 120
                                    ++n + ++   +   i++ vGGGIr+ e + e + agad ++ g    +np+ ++ + +++ 
  gi|15669436|ref|NP_248246.1| 181 YPVNNETIALSKKLSGINIIVGGGIRKPEIAYEKVLAGADAIVTGNLLEENPKAVEMMYDAIK 243
                                   5667777777777788**************************************999988765 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00023      0.46     130     202 ..      10      75 ..       7      85 .. 0.90
   2 !    7.9   0.1   0.00062       1.2     189     229 ..     187     228 ..     176     252 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00023
                                   HHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EE CS
                     Trp_syntA 130 eelveaakkkglelvflvapttsderlkevveqaegfvYvvsraGvTgaenavaaevdelverlkkltavPva 202
                                   ++l ++++++g  +++l+ p  ++e ++e++e+++ +  ++ + G  g       ++de+v+++kk+t++P+ 
  gi|15669436|ref|NP_248246.1|  10 KRLNQIIEEEGAVYLTLLDP--EEENIEEIAENVKDYADAIMVGGSIGI-----VNLDETVKKIKKITKLPII 75 
                                   6789999****999999999..999**************9999999997.....46999*********99985 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00062
                                   HHHHHHHCTSS-EEEESSS-SHHHH.HHHHTT-SEEEE-HHH CS
                     Trp_syntA 189 lverlkkltavPvavGFGistkeqv.kqvakvadGvivGSal 229
                                   +++  kkl+   + vG Gi+++e + ++v ++ad+++ G  l
  gi|15669436|ref|NP_248246.1| 187 TIALSKKLSGINIIVGGGIRKPEIAyEKVLAGADAIVTGNLL 228
                                   5566678888889**********8725566********9754 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.1     0.005       9.9       4      36 ..      44      75 ..      41      78 .. 0.87
   2 !   10.3   0.1   0.00014      0.28     136     191 ..     190     243 ..     175     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.005
                                  HHHHHHHHT-SEEEEESHHHHHHHHTT--S-EE CS
                          NanE  4 makaaeqaGavgiriegvedikaikavvdlPii 36
                                   a a   +G++gi ++  e +k+ik++++lPii
  gi|15669436|ref|NP_248246.1| 44 YADAIMVGGSIGI-VNLDETVKKIKKITKLPII 75
                                  6889999999999.688899************9 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00014
                                   HHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHHHHHHT- CS
                          NanE 136 lvkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrleeiakkfveaik 191
                                   l k+l  +g+++i+ G i  Pe a + +  G+da+v G  +    + ++   +aik
  gi|15669436|ref|NP_248246.1| 190 LSKKL--SGINIIVGGGIRKPEIAYEKVLAGADAIVTGNLLEENPKAVEMMYDAIK 243
                                   55555..6899***************************999888888888777776 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0011       2.1      11      68 ..      37      96 ..      29     121 .. 0.72
   2 !    7.9   0.1   0.00097       1.9     131     169 ..     188     226 ..     182     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                                  GCC-...-SSEEEE--.EETTTHHHHHHHHHHTT-EEEEEG.GGEET--SSHHHHHHHHH CS
                  G3P_antiterm 11 lekalesevevvflle.gdilnlkeiveklkkagkkvfvhi.DlieGlskdeaaveflkk 68
                                  + + ++  ++++++     i+nl+e+v+k+kk  k+ ++ +   ++Gls+   av +++ 
  gi|15669436|ref|NP_248246.1| 37 IAENVKDYADAIMVGGsIGIVNLDETVKKIKKITKLPIILFpGNVDGLSRYADAVFYMSL 96
                                  444455555555554326799**************988765379***********99876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00097
                                   HCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE-- CS
                  G3P_antiterm 131 ikeikkelkipiiaGGLietkedveealkaGaiavstsn 169
                                   i+  kk + i+ii GG i++ e   e + aGa+a+ t+n
  gi|15669436|ref|NP_248246.1| 188 IALSKKLSGINIIVGGGIRKPEIAYEKVLAGADAIVTGN 226
                                   555677789**************************9986 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.026        52     101     153 ..      29      81 ..       3      90 .. 0.71
   2 ?   10.3   0.2   0.00013      0.26     203     240 ..     192     229 ..     175     247 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.026
                                   SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEE..EEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                         IMPDH 101 vkedalervkalveagvdvlvvdsahghsekvleavkeikkkveevevi..aGnv 153
                                    +e+++e++++ v+  +d+++v  + g   +  e+vk+ikk + ++ +i   Gnv
  gi|15669436|ref|NP_248246.1|  29 PEEENIEEIAENVKDYADAIMVGGSIGIV-NLDETVKKIKKIT-KLPIIlfPGNV 81 
                                   56677788888888888888888888864.5677888888766.44444336777 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00013
                                   HCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 203 akkagvpviaDGGikysgdivkAlaaGadavmlGslla 240
                                    k  g+++i  GGi++ +     + aGada++ G+ll 
  gi|15669436|ref|NP_248246.1| 192 KKLSGINIIVGGGIRKPEIAYEKVLAGADAIVTGNLLE 229
                                   45569*************9999999***********94 PP

>> Spore_YhaL  Sporulation protein YhaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5   2.9e-05     0.057      18      49 ..       1      31 [.       1      34 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                    Spore_YhaL 18 mavktakeEreldqefIEkEGevylerleeer 49
                                  m +k  k E++l+q  IE+EG vyl+ l  e 
  gi|15669436|ref|NP_248246.1|  1 MKIKIGKVEKRLNQ-IIEEEGAVYLTLLDPEE 31
                                  77899999999976.8*********9998775 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.6   3.1e+03     116     130 ..      36      50 ..      22      72 .. 0.56
   2 ?   13.2   0.1   1.9e-05     0.039     237     292 ..     190     243 ..     177     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.6
                                   HHHHHHGGGESEEEE CS
                        DHO_dh 116 evvrkigpfadilel 130
                                   e++++++ +ad++ +
  gi|15669436|ref|NP_248246.1|  36 EIAENVKDYADAIMV 50 
                                   333333333333333 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.9e-05
                                   HHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHH CS
                        DHO_dh 237 lykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkele 292
                                   l+k+l+  i iI  GGi   e a+ek+ aGA ++  +  l  e+pk+++ + + ++
  gi|15669436|ref|NP_248246.1| 190 LSKKLS-GINIIVGGGIRKPEIAYEKVLAGADAIVTGNLL-EENPKAVEMMYDAIK 243
                                   555565.7************************99888777.788888877777665 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.8e-05     0.075      41     108 ..      28      93 ..      12     163 .. 0.78
   2 ?   -2.0   0.0       1.3   2.6e+03      72      86 ..     236     250 ..     231     252 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
                                   SSHHHHHHHHHHHH.HTSSEEEEESS-SSSTT--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGG CS
                 MoCF_biosynth  41 Ddeeeikeallaal.eeadviittGGtGptpdDvtpealaklfekelegfeeafrrvslkpgkpvgvap 108
                                   D eee  e++++++ ++ad+i + G +G+   D t++ ++k+ + ++ +f+  ++++s+  ++   v  
  gi|15669436|ref|NP_248246.1|  28 DPEEENIEEIAENVkDYADAIMVGGSIGIVNLDETVKKIKKITKLPIILFPGNVDGLSRYADA---VFY 93 
                                   555555555544440556*********************************999999999765...222 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                                   --HHHHHHHHHSEE- CS
                 MoCF_biosynth  72 Dvtpealaklfekel 86 
                                    ++++a++k+++++l
  gi|15669436|ref|NP_248246.1| 236 EMMYDAIKKAGKEKL 250
                                   567788888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1532.29
//
Query:       gi|15669437|ref|NP_248247.1|  [L=251]
Description: GerC2 protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-19   70.8   0.0    2.7e-19   69.6   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    1.6e-16   60.8   0.0    9.2e-16   58.3   0.0    2.1  2  Methyltransf_25  Methyltransferase domain
    1.1e-14   54.6   0.0    1.3e-14   54.4   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    2.1e-11   43.6   2.2      4e-11   42.7   2.1    1.6  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.2e-11   43.8   0.6    4.1e-11   42.9   0.6    1.5  1  Methyltransf_31  Methyltransferase domain
    3.6e-09   37.2   0.0    9.2e-09   35.9   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
    1.4e-07   31.6   2.6    1.8e-06   28.0   0.6    2.1  2  Methyltransf_8   Hypothetical methyltransferase
    5.4e-07   29.2   0.2    1.1e-06   28.1   0.2    1.7  1  CMAS             Mycolic acid cyclopropane synthetase
    7.7e-06   25.6   0.1    1.2e-05   25.0   0.1    1.2  1  MetW             Methionine biosynthesis protein MetW
     0.0012   18.6   4.5       0.28   10.9   1.7    2.5  2  N6_N4_Mtase      DNA methylase
     0.0096   15.0   0.4      0.015   14.4   0.4    1.6  1  RrnaAD           Ribosomal RNA adenine dimethylase
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.021   14.6   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.023   13.5   2.3      0.031   13.0   0.2    1.9  2  p450             Cytochrome P450
      0.024   13.2   0.1      0.068   11.7   0.1    1.7  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
      0.028   14.6   0.6       0.41   10.9   0.0    2.6  3  UPF0180          Uncharacterised protein family (UPF0180)
       0.33   11.5   3.2       0.71   10.5   0.8    2.2  2  DUF3994          Domain of unknown function (DUF3994)


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   2.5e-22   2.7e-19       1      96 []      60     146 ..      60     146 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 2.5e-22
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES.-CCC-CCHHHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse.vlhhvedpeka 80 
                                   Ld+GcGtG  ++ l     + vg+D+s em k+ak+k++++      vva+ae lpf+++sfD  +s++ +l+h+ ++++a
  gi|15669437|ref|NP_248247.1|  60 LDIGCGTGEQLKILN----NAVGLDISLEMAKIAKNKTNKPV-----VVANAEFLPFKNKSFDKAISFFgALNHC-NLKRA 130
                                   8**************....99**************9999997.....****************9999887*****.6**** PP

                                   HHHHHHHEEEEEEEEE CS
               Methyltransf_11  81 lkeiaRvLkpgGllvi 96 
                                   l+e+ RvLk +G++++
  gi|15669437|ref|NP_248247.1| 131 LREVNRVLKDDGIFIF 146
                                   **************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   8.2e-19   9.2e-16       1      97 []      59     142 ..      59     142 .. 0.94
   2 ?   -0.4   0.0       1.8     2e+03      45      74 ..     188     220 ..     169     239 .. 0.66

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 8.2e-19
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGGSSHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhhlsde 80 
                                   vLd+GcGtG+ ++ l ++      +g+Dis em ++a+++      n  +v+++ae lpf+++sfD  +s+++ l+h++  
  gi|15669437|ref|NP_248247.1|  59 VLDIGCGTGEQLKILNNA------VGLDISLEMAKIAKNKT-----NKPVVVANAEFLPFKNKSFDKAISFFGaLNHCN-- 126
                                   9********999999866......79***************.....6679*********************99999987.. PP

                                   HHHHHHHHHHHHEEEEE CS
               Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                    l++al+e+ rvLk++G
  gi|15669437|ref|NP_248247.1| 127 -LKRALREVNRVLKDDG 142
                                   .899***********99 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.8
                                   TTTEEEEESBCCGBS..SSTTTEEEEEEEST.G CS
               Methyltransf_25  45 glnvefvqgdaedlp..fedgsfDlvvssga.l 74 
                                   +++v+ +  d+++++  ++++ f +v+ +g+ +
  gi|15669437|ref|NP_248247.1| 188 KIKVKTRFYDFKEVEdaLKKEGFEVVYTFGTnI 220
                                   446666666776665335777888888876533 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   1.2e-17   1.3e-14       9     163 ..      36     213 ..      13     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.2e-17
               Methyltransf_23   9 lsdklerllpk......lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkf 83 
                                   ++ k++r++++       + g  vLdiGcGtG+ l++l     + +g D+s e+ +ia+++ + + + +++++ ++++++f
  gi|15669437|ref|NP_248247.1|  36 YKNKYMRIVEReiiqkeIKDGDFVLDIGCGTGEQLKIL----NNAVGLDISLEMAKIAKNKTNKPVVVANAEFLPFKNKSF 112
                                   34444444433222223466669*************88....478**************99999999************** PP

               Methyltransf_23  84 dlIvlrevlehvpdppellrqiatllkpgGylllseplasl................kedrllld......wlylvpagrh 142
                                   d ++++++  +  ++ ++lr +++ lk++G +++++ + ++                k++++ ++      +     +g++
  gi|15669437|ref|NP_248247.1| 113 DKAISFFGALNHCNLKRALREVNRVLKDDGIFIFTVANIYDikwiiknilkgnfkkvKNAMKKRKgtitkvI-----DGEK 188
                                   *88888777777799**********************99999999999999888855333333333332222.....4444 PP

               Methyltransf_23 143 i....sffsarslkelleeaGlevv 163
                                   i    +f++ ++++++l++ G+evv
  gi|15669437|ref|NP_248247.1| 189 IkvktRFYDFKEVEDALKKEGFEVV 213
                                   44445******************99 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   2.1   3.6e-14     4e-11       9     151 ..      21     146 ..      13     224 .. 0.70

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 3.6e-14
                                   XXXXXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHH CS
               Ubie_methyltran   9 vkevfesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvge 89 
                                   +ke ++++a++yD++ +    +  r+  + +++ +  k g  vlD+ +Gtg+    l ++       v+lDi+ +m k+++
  gi|15669437|ref|NP_248247.1|  21 IKEYYDKLAKSYDKLYKN---KYMRIVEREIIQ-KEIKDGDFVLDIGCGTGEQLKILNNA-------VGLDISLEMAKIAK 90 
                                   788899999999987543...333444443333.3457899**********975555444.......679**********9 PP

                                   HHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
               Ubie_methyltran  90 kklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                   +k ++        ++anae Lpf+++sfD     fG  n  + ++aL+e+ rvlk  G+++ 
  gi|15669437|ref|NP_248247.1|  91 NKTNK------PVVVANAEFLPFKNKSFDKAISFFGALNHCNLKRALREVNRVLKDDGIFIF 146
                                   99766......4689***************99999***********************8753 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.6   3.7e-14   4.1e-11       3     128 ..      55     175 ..      53     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 3.7e-14
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn.e 82 
                                   +g  vlD+GCGtGe ++ l+       + vG+Dis e+ + A+++      +n  + ++++e l+  ++ ++fD  +s+ +
  gi|15669437|ref|NP_248247.1|  55 DGDFVLDIGCGTGEQLKILN-------NAVGLDISLEMAKIAKNK------TNKPVVVANAEFLP--FKNKSFDKAISFfG 120
                                   66679***************.......489*************96......56667788888899..889*****888757 PP

               Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr..........llaelpakveeeska 128
                                   +ln+ ++++ +l+e+ rvlk++gi++ + ++          +l+ + +kv++ +k+
  gi|15669437|ref|NP_248247.1| 121 ALNH-CNLKRALREVNRVLKDDGIFIFTVANiydikwiiknILKGNFKKVKNAMKK 175
                                   7776.567889***************999996655554333333333444444443 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   8.2e-12   9.2e-09       1      99 []      60     144 ..      60     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 8.2e-12
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas.nvlhhlk 80 
                                   L+iGcGtG+ l+ l ++      +g+Dis ++ + ak+k++k       +v + +   +   +++sfD  +++ ++l+h+ 
  gi|15669437|ref|NP_248247.1|  60 LDIGCGTGEQLKILNNA------VGLDISLEMAKIAKNKTNKPV-----VVANAEFLPF---KNKSFDKAISFfGALNHC- 125
                                   8***************9......**********55555554444.....4444444333...335***999887*****8. PP

               Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                   +++++l+++ ++Lk++G++
  gi|15669437|ref|NP_248247.1| 126 NLKRALREVNRVLKDDGIF 144
                                   *****************85 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.6   1.6e-09   1.8e-06      46     186 ..      27     174 ..      10     189 .. 0.70
   2 ?    3.6   0.1     0.046        51     158     182 ..     190     214 ..     176     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.6e-09
                                   HHHHHHHCTSSS-HHHHHHHHHCTS..-TTS-EEEES-TT-...HHH.HH-..-S-..EEEEESS-SSTTEEES-TTS-S- CS
                Methyltransf_8  46 kgfrsqvkkWPenPldviirklkkk..kdnlvvadlGcGea...kia.eav..rekekvrsfdlvavnervvacdlakvPl 118
                                   k+ +s  k + ++ ++++ r++ +k  kd   v d+GcG     ki  +av    + ++  +     n+ vv+ +   +P 
  gi|15669437|ref|NP_248247.1|  27 KLAKSYDKLYKNKYMRIVEREIIQKeiKDGDFVLDIGCGTGeqlKILnNAVglDISLEMAKIAKNKTNKPVVVANAEFLPF 107
                                   44444445555666666667766552257789******97621244333330033444455555667889*********** PP

                                   -TT-EEEEEEES.---SS-HHHHHHHHHHHEEEEEEEEEEEEGGG-S-HHHHHHHHHCTTEEEEEEE-- CS
                Methyltransf_8 119 edesvdvavfcl.slmgtnladflkeanrvlkvGGllkvaevksrfesvklfaraltklGfevkskdls 186
                                   +++s d a+  + +l   nl+  l+e+nrvlk  G++  + v + + ++k +++++ k  f+ ++  ++
  gi|15669437|ref|NP_248247.1| 108 KNKSFDKAISFFgALNHCNLKRALREVNRVLKDDGIFIFT-V-ANIYDIKWIIKNILKGNFKKVKNAMK 174
                                   ********9665268889*****************97543.3.45778888888888888887766655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.046
                                   EEGGG-S-HHHHHHHHHCTTEEEEE CS
                Methyltransf_8 158 evksrfesvklfaraltklGfevks 182
                                    vk+rf + k ++ al+k Gfev+ 
  gi|15669437|ref|NP_248247.1| 190 KVKTRFYDFKEVEDALKKEGFEVVY 214
                                   599*******************976 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.2     1e-09   1.1e-06      57     181 ..      50     163 ..       8     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1e-09
                                   TTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.--SEEEEES- CS
                          CMAS  57 klelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde.kvdrvvsvga 136
                                   + e+k+G+ +LdiGcG G+ ++        + vgl +S e ak ak++     +++ v v  +++  +++  +d+ +s   
  gi|15669437|ref|NP_248247.1|  50 QKEIKDGDFVLDIGCGTGEQLKILN-----NAVGLDISLEMAKIAKNK-----TNKPVVVANAEFLPFKNkSFDKAIS--F 118
                                   45799**************987554.....469******999877765.....5677899999999998879**9877..4 PP

                                   GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTTCC CS
                          CMAS 137 fehvgkenydtffkklkkllkedGllllhtitslhkkelaerglk 181
                                   f ++ + n+++  ++++++lk+dG+++     +++ k++ ++ lk
  gi|15669437|ref|NP_248247.1| 119 FGALNHCNLKRALREVNRVLKDDGIFIFTVANIYDIKWIIKNILK 163
                                   7788888999999*************9988888887777665555 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1     1e-08   1.2e-05       5     110 ..      47     147 ..      44     173 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1e-08
                          MetW   5 eliaelikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaec.vakGlsviqgdldkdlenfedksfdyvvlsqt 84 
                                   e+i++ ik+g  vld+GcG Ge l++l++     g  + l+ + +a+  ++k + v     + ++  f++ksfd ++    
  gi|15669437|ref|NP_248247.1|  47 EIIQKEIKDGDFVLDIGCGTGEQLKILNNAV---GLDISLEMAKIAKNkTNKPVVVA----NAEFLPFKNKSFDKAISFFG 120
                                   7899***********************8733...34445555555544145555553....4567899******9997776 PP

                          MetW  85 lqatrnpkevldellrigr.raivsfP 110
                                     +  n k+ l+e+ r+ +   i  f 
  gi|15669437|ref|NP_248247.1| 121 ALNHCNLKRALREVNRVLKdDGIFIFT 147
                                   666778888888888885414555555 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0017       1.9     169     230 ..      33      90 ..       8      91 .. 0.74
   2 !   10.9   1.7   0.00025      0.28      35      87 ..     127     177 ..     124     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0017
                                   ----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                   N6_N4_Mtase 169 kkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelae 230
                                   +k+++ +  +   +++I+   k+gd vlD  +G+G  +++   l+ +++G +i+ e +++a+
  gi|15669437|ref|NP_248247.1|  33 DKLYKNKYMRIVEREIIQKEIKDGDFVLDIGCGTGEQLKI---LN-NAVGLDISLEMAKIAK 90 
                                   5566666666666899**************9998865544...55.7889999988888876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00025
                                   HHHHHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHHHHHTT.-EEEEEEEEEEES CS
                   N6_N4_Mtase  35 lekvlkevrrvLkddgsifiniddseikkelkaladeifg.gffllnvivwkkp 87 
                                   l++ l+ev rvLkddg+++  +  ++    +k ++++i++ +f+  + + +k++
  gi|15669437|ref|NP_248247.1| 127 LKRALREVNRVLKDDGIFIFTVANIYD---IKWIIKNILKgNFKKVKNAMKKRK 177
                                   67789***************9999996...677777777744433333333332 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.4   1.3e-05     0.015      22      94 ..      48     113 ..      29     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                                   HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHHH CS
                        RrnaAD  22 IldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfetpeev 94 
                                   I+ + ++++ + vl+ig G+G + ++    +++ v l +  ++ak+ ++  + ++++ v +++fl f+ +++ 
  gi|15669437|ref|NP_248247.1|  48 II-QKEIKDGDFVLDIGCGTGEQLKI----LNNAVGLDISLEMAKIAKN--KTNKPVVVANAEFLPFKNKSFD 113
                                   33.45888*************88555....5667888888999999999..6679999999999999988855 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.9e-05     0.021      51     105 ..      31      84 ..       6     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                                   ETTEEE--HHHHHHHHHHTT..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEE CS
                          PCMT  51 gynatiSaphmvalalelle..lkkgarvLevGsGsGyltavlarlvgekgrvvsie 105
                                   +y++   + +m  +  e ++  +k+g+ vL++G+G+G +  +l + vg +    s+e
  gi|15669437|ref|NP_248247.1|  31 SYDKLYKNKYMRIVEREIIQkeIKDGDFVLDIGCGTGEQLKILNNAVGLDI---SLE 84 
                                   6666677777777788888888********************999998765...554 PP

>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.24   2.7e+02      17      40 ..      16      39 ..       7      49 .. 0.80
   2 ?   13.0   0.2   2.8e-05     0.031     170     234 ..     127     194 ..      90     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.24
                                  TTTCCHHHHHHHHHHHH-SEEEEE CS
                          p450 17 grkeelhevlrklqkkygpifrlk 40
                                  ++k+ ++e+++kl+k+y+++++ k
  gi|15669437|ref|NP_248247.1| 16 REKMGIKEYYDKLAKSYDKLYKNK 39
                                  338999************999866 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.8e-05
                                   HHHHHHHHHHHHH...HHHCHHHHCCCCCHHHTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHCHCHC CS
                          p450 170 lselvkaveelss...llskssvqllllfpllkylptkllrklkeavkklkdlldklieerretldsa 234
                                   l+++++ v+++++   ++ +++ +++++++++k +++  ++k+k+a+kk+k+++ k+i   + +++++
  gi|15669437|ref|NP_248247.1| 127 LKRALREVNRVLKddgIFIFTVANIYDIKWIIKNILKGNFKKVKNAMKKRKGTITKVIDGEKIKVKTR 194
                                   455555555555556788999************************************98887777666 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   6.1e-05     0.068     119     224 ..      57     167 ..      18     194 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.1e-05
               Methyltransf_29 119 rtvlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaLeRgvpailavlgtkrlpyPsrsfdlihCsrCridwteedg 199
                                     vlD+GCg      +l +   l +sl          ++a ++     + v  ++ lp+  +sfd +      +++ +   
  gi|15669437|ref|NP_248247.1|  57 DFVLDIGCGTGEQLKILNNAVGLDISLEMA-------KIAKNKTN-KPVVVANAEFLPFKNKSFDKAISFFGALNHCN-LK 128
                                   457777777665554444333344444333.......33333322.23345567789999999998877777776554.45 PP

               Methyltransf_29 200 illlevdRvlRpgGyfvlsappvy..............e 224
                                     l ev+Rvl+ +G f+++  ++y              +
  gi|15669437|ref|NP_248247.1| 129 RALREVNRVLKDDGIFIFTVANIYdikwiiknilkgnfK 167
                                   6799***************99999666555544433332 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1         3   3.3e+03      47      63 ..      85     101 ..      76     103 .. 0.72
   2 ?    0.7   0.0      0.53   5.9e+02       8      49 ..     130     174 ..     127     191 .. 0.61
   3 ?   10.9   0.0   0.00036      0.41      10      47 ..     199     237 ..     196     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3
                       UPF0180  47 vmgiedtetkapvInAs 63 
                                   + +i +++t+ pv+ A+
  gi|15669437|ref|NP_248247.1|  85 MAKIAKNKTNKPVVVAN 101
                                   66777778888887664 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.53
                       UPF0180   8 gLsnvkeaLrekGYeVvdleteedaqsvdaiVv...tG...qdtnvmg 49 
                                    L +v++ L++ G  + ++ +    ++++ i+    +G   + +n+m+
  gi|15669437|ref|NP_248247.1| 130 ALREVNRVLKDDGIFIFTVAN---IYDIKWIIKnilKGnfkKVKNAMK 174
                                   688999999999988888887...666666665333443322233333 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00036
                       UPF0180  10 snvkeaLrekGYeVv.dleteedaqsvdaiVvtGqdtnv 47 
                                   ++v++aL+++G+eVv +++t+ ++   d +++++  +n+
  gi|15669437|ref|NP_248247.1| 199 KEVEDALKKEGFEVVyTFGTNITNSPLDKFIYKSFLKNF 237
                                   69***********98456777789999999998888877 PP

>> DUF3994  Domain of unknown function (DUF3994)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.63     7e+02      48      64 ..      41      57 ..      15      97 .. 0.59
   2 ?   10.5   0.8   0.00064      0.71      17      84 ..     160     230 ..     153     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.63
                       DUF3994 48 kaGikienvinnvkdGt 64
                                     ++ e +++++kdG 
  gi|15669437|ref|NP_248247.1| 41 MRIVEREIIQKEIKDGD 57
                                  34444455555555553 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00064
                       DUF3994  17 riwkkafkklkaeikiGdGtvssd.dlksldkkaGi.kienvinnv.kdGtelvGnwGidyddgvkvslil 84 
                                   +i k  fkk+k+ +k  +Gt++   d  +++ k+   ++++v + + k+G e+v  +G + +++    +i 
  gi|15669437|ref|NP_248247.1| 160 NILKGNFKKVKNAMKKRKGTITKViDGEKIKVKTRFyDFKEVEDALkKEGFEVVYTFGTNITNSPLDKFIY 230
                                   567789***************96557778888887669*******989**********9988865555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1381  (0.077026); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1548.67
//
Query:       gi|15669438|ref|NP_248248.1|  [L=167]
Description: hypothetical protein MJ_1251 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-62  210.7   0.2    1.1e-62  210.6   0.2    1.0  1  UPF0254     Uncharacterised protein family (UPF0254)
    0.00029   20.8   3.1      0.014   15.4   0.5    3.1  3  Ubiq-assoc  Ubiquitin-associated
  ------ inclusion threshold ------
       0.16   11.5   0.5       0.28   10.7   0.0    1.6  2  CinA        Competence-damaged protein


Domain annotation for each model (and alignments):
>> UPF0254  Uncharacterised protein family (UPF0254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.6   0.2   1.9e-66   1.1e-62       1     163 []       1     162 [.       1     162 [. 0.96

  Alignments for each domain:
  == domain 1  score: 210.6 bits;  conditional E-value: 1.9e-66
                                   -EEEEEEESTTTTHHHHHHHHHHCT-S-.........HHHHHHHTTEEEEEEEE--SHHHHHHHHT------..SSESSSE CS
                       UPF0254   1 mirvataECFthgkigreiHalasgYeeefassl...deekvklknvsvvaalFiPtlsgvksllkielPlepkelikgiK 78 
                                   mi+vataECFth++ig +iH++a+gYe+ f++++   +e+   +knv+v++a+F+P++ gv++ll+i+lP+++ + +k++K
  gi|15669438|ref|NP_248248.1|   1 MITVATAECFTHANIGLTIHKAAAGYED-FEFKYlfsEEDLKLMKNVRVISAMFVPSIIGVEKLLDIKLPEPDFN-YKYAK 79 
                                   9**************************9.8888888766777789*************************99655.9**** PP

                                   E-BHHHHHHHHHHHHHHHHHHHT-SEEEEEE-SEES-EEEEE-SS-EEEE--S--EETTTT..TTHHHHHHHHHHHHHHHH CS
                       UPF0254  79 vYneeeDkevallmakavkkitnadigigttAGiGrGaiaivtdkkellttsdveadlrksdaeeilkRqksgiekalkll 159
                                   +Y+ee+D eva+lma+++kk++n++i+ig+tAG+GrGai+i+td++++l+tsdv+a+l++   e+i++Rqk+giek +k +
  gi|15669438|ref|NP_248248.1|  80 AYSEEKDLEVAKLMAEGLKKKLNVNISIGSTAGVGRGAICILTDNNRYLFTSDVYANLITF--ENIKERQKNGIEKGIKRF 158
                                   *************************************************************..8***************** PP

                                   HHHH CS
                       UPF0254 160 eell 163
                                   +e+l
  gi|15669438|ref|NP_248248.1| 159 LEIL 162
                                   *997 PP

>> Ubiq-assoc  Ubiquitin-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.051   3.1e+02      16      29 ..      15      28 ..      14      35 .. 0.89
   2 !   15.4   0.5   2.4e-06     0.014       4      18 ..      83      97 ..      82      99 .. 0.92
   3 ?    2.2   0.0      0.03   1.8e+02      25      42 ..     132     149 ..     130     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.051
                                  H---SHHHHHHHHH CS
                    Ubiq-assoc 16 LGLsidkAneyYek 29
                                   GL i kA+  Ye+
  gi|15669438|ref|NP_248248.1| 15 IGLTIHKAAAGYED 28
                                  59*******99985 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.4e-06
                                  HHHHHHHHHHHHH-- CS
                    Ubiq-assoc  4 EvkDmEiAkLMSLGL 18
                                  E+kD+E+AkLM  GL
  gi|15669438|ref|NP_248248.1| 83 EEKDLEVAKLMAEGL 97
                                  99*********9888 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.03
                                   HHHHHH-SSHHHHHHHHH CS
                    Ubiq-assoc  25 eyYekGilYedllekrke 42 
                                   + Y + i++e++ e++k+
  gi|15669438|ref|NP_248248.1| 132 DVYANLITFENIKERQKN 149
                                   679999*******99985 PP

>> CinA  Competence-damaged protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2       0.6   3.6e+03      18      34 ..       3      19 ..       2      25 .. 0.71
   2 ?   10.7   0.0   4.7e-05      0.28      76     102 ..      88     114 ..      74     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.6
                          CinA 18 tlatAEScTGGllaaal 34
                                  t+atAE +T   ++ ++
  gi|15669438|ref|NP_248248.1|  3 TVATAECFTHANIGLTI 19
                                  79999999866665555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4.7e-05
                          CinA  76 evaeemaegarerlgadiavavtGiAG 102
                                   eva+ maeg +++l+++i++  t   G
  gi|15669438|ref|NP_248248.1|  88 EVAKLMAEGLKKKLNVNISIGSTAGVG 114
                                   79******************9887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1109.91
//
Query:       gi|15669439|ref|NP_248249.1|  [L=282]
Description: preprotein translocase subunit SecF [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-51  173.0  14.9    6.3e-51  172.5  14.9    1.2  1  SecD_SecF  Protein export membrane protein
    1.7e-07   29.8   9.7    2.4e-07   29.3   9.7    1.2  1  Patched    Patched family
    6.7e-05   22.2   0.1    0.00016   21.1   0.1    1.6  1  Sec_GG     SecD/SecF GG Motif
  ------ inclusion threshold ------
      0.015   13.0  12.1       0.02   12.6  12.1    1.2  1  ACR_tran   AcrB/AcrD/AcrF family


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.5  14.9   1.4e-54   6.3e-51       4     187 ..      91     274 ..      88     276 .. 0.96

  Alignments for each domain:
  == domain 1  score: 172.5 bits;  conditional E-value: 1.4e-54
                                   TTT--SSS.-EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHH.HHHHHHHHHHHHHHTT--- CS
                     SecD_SecF   4 kllkevdk.daekisvetvgpsvskelaekavlallialvliliyvalrFewrvalaaiia.lvhDviitvgvlsllgiev 82 
                                   k++ +vd+ d+ ++s +t+g+++s++++e+++ a+++a+++++i+v+l+F+++v+++aii+ +++D+i+++g++sllgie+
  gi|15669439|ref|NP_248249.1|  91 KEFFHVDSlDKLNYSEKTIGATLSSKFFEEGFKAVGFAFMFMAIVVYLYFRNPVPSGAIILsALSDIIMALGAMSLLGIEL 171
                                   567788888999***********************************************998******************* PP

                                   -HHHHHHHHHHTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHH CS
                     SecD_SecF  83 dlatvaalLtiiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfala 163
                                   ++at+aalL++iGYSv++++++++rv ++l+k+ ++t+ke+++++l++tLt ti+++l+ ll+vv+l++ ++d+l+++a++
  gi|15669439|ref|NP_248249.1| 172 SSATIAALLMVIGYSVDSDILLTTRVLKRLTKSFDETVKEAMKTGLTMTLT-TITAMLI-LLIVVKLFIPVADILANIATV 250
                                   ***************************************************.9999888.99******************* PP

                                   HHHHTSTTTTTHHHHHHHHHHHHH CS
                     SecD_SecF 164 llvGlivgtyssifiasplllllk 187
                                   l+++li+++++++++++++l+++ 
  gi|15669439|ref|NP_248249.1| 251 LILALIADIINTWLLNAGILKYYI 274
                                   ********************9986 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   9.7   5.4e-11   2.4e-07     660     787 ..     122     250 ..      91     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.4e-11
                       Patched 660 iqnivlallcmfvvallfipelitvlvitlsivsidigviGflslWgvdLDpismitiimsiGfsvdlsaHiayafvrsek 740
                                   ++ + +a++ m++v  l   +++ + +i+ls +s  i  +G +sl g++L + ++++++m iG+svd     + +  +   
  gi|15669439|ref|NP_248249.1| 122 FKAVGFAFMFMAIVVYLYFRNPVPSGAIILSALSDIIMALGAMSLLGIELSSATIAALLMVIGYSVDSDILLTTRVLKRLT 202
                                   6678899********************************************************************999999 PP

                       Patched 741 ddakeRvvealea.lgwPvvqgalSTilgvlvLlfvdsymvqvFfktv 787
                                   ++ +e v+ea+++ l + +       il ++v lf++   ++  + tv
  gi|15669439|ref|NP_248249.1| 203 KSFDETVKEAMKTgLTMTLTTITAMLILLIVVKLFIPVADILANIATV 250
                                   99*********8756666666666667777777777766665555555 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   3.5e-08   0.00016       2      25 ..      22      45 ..      21      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.5e-08
                                  HHHHC--EE-TTTS-EEEEEEEE- CS
                        Sec_GG  2 slftkGlNLGlDFtGGthielqfd 25
                                  ++++kG+  ++D tGGt+i++++ 
  gi|15669439|ref|NP_248249.1| 22 LIGFKGIPKSIDITGGTEITIKVN 45
                                  5899*****************996 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  12.1   4.4e-06      0.02     338     452 ..     126     243 ..      83     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-06
                                   HHHHHHHHHHHHHHHSS.HHHHHHHHHHHHHHHHHHHHHHHHTT--BCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      ACR_tran 338 leaivLvvlvvflFLqn.lratlipaiavPlsllgtfavlkalgfslNlltLfgLvlAiGlvvDdAiVvvEnierkleeeg 417
                                     a +  ++vv+l+ +n + +  i++ a+   +++++ ++++lg+ l   t+ +L + iG  vD+ i     + ++l ++ 
  gi|15669439|ref|NP_248249.1| 126 GFAFMFMAIVVYLYFRNpVPSGAIILSAL-SDIIMALGAMSLLGIELSSATIAALLMVIGYSVDSDILLTTRVLKRLTKSF 205
                                   567889999*****999445555555554.47999********************************************77 PP

                                   S-HHHHHHHHHHHHHHHHHHHHHHHHHH...CTGGGGS CS
                      ACR_tran 418 ekpleaalksmkeiqgalvaialvllav...flPilfl 452
                                    + +++a+k+  +++ + +   l+ll+v   f+P++ +
  gi|15669439|ref|NP_248249.1| 206 DETVKEAMKTGLTMTLTTITAMLILLIVvklFIPVADI 243
                                   77777777777777777777777666653447787643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1201  (0.0669864); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1704.51
//
Query:       gi|15669440|ref|NP_248250.1|  [L=469]
Description: hypothetical protein MJ_1254 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-09   36.5   2.1      4e-09   35.9   0.6    2.2  1  HTH_24           Winged helix-turn-helix DNA-binding
    5.2e-06   26.3   0.6    1.5e-05   24.9   0.1    2.0  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    9.6e-06   25.4   1.0    3.4e-05   23.7   0.2    2.3  2  MarR             MarR family
      2e-05   24.4   0.0    4.5e-05   23.2   0.0    1.5  1  MarR_2           MarR family
    8.6e-05   22.3   0.0    0.00016   21.4   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
    0.00035   20.4   1.2     0.0012   18.7   0.1    2.2  2  TrmB             Sugar-specific transcriptional regulator Trm
    0.00074   19.8  19.7     0.0038   17.5   5.1    2.4  2  Csm1_N           Csm1 N-terminal domain
     0.0014   18.1  20.8     0.0019   17.7  20.8    1.2  1  HMMR_N           Hyaluronan mediated motility receptor N-term
     0.0018   18.8   0.6     0.0018   18.8   0.6    3.0  2  Phage_rep_O      Bacteriophage replication protein O
     0.0022   17.8   1.0     0.0022   17.8   1.0    2.5  2  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
     0.0023   18.1  25.4       0.11   12.6  10.5    2.3  2  Tropomyosin_1    Tropomyosin like
     0.0023   16.2  15.9     0.0036   15.6  15.9    1.4  1  FPP              Filament-like plant protein, long coiled-coi
     0.0036   16.7  13.7     0.0069   15.8  13.7    1.4  1  FAM76            FAM76 protein
     0.0046   16.9   0.1      0.019   14.9   0.1    2.1  1  HTH_37           Helix-turn-helix domain
     0.0075   16.7  12.7      0.011   16.2  12.7    1.2  1  Fez1             Fez1
  ------ inclusion threshold ------
       0.01   15.2   3.2      0.012   15.0   0.6    1.9  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.01   15.8   0.0      0.045   13.7   0.0    2.2  1  HTH_36           Helix-turn-helix domain
      0.012   15.2   5.1      0.022   14.4   5.1    1.4  1  Exonuc_VII_L     Exonuclease VII, large subunit
      0.013   15.3   0.2      0.034   13.9   0.2    1.7  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.016   15.0  11.0      0.016   15.0  11.0    2.0  2  ERM              Ezrin/radixin/moesin family
       0.02   15.1   2.4       0.21   11.8   0.2    2.9  2  Rio2_N           Rio2, N-terminal
      0.026   15.2   3.0      0.043   14.4   3.0    1.3  1  HNF-1_N          Hepatocyte nuclear factor 1 (HNF-1), N termi
      0.028   14.2  25.1      0.043   13.6   3.6    3.8  3  DivIC            Septum formation initiator
      0.034   14.1   0.1       0.08   12.9   0.1    1.6  1  DUF977           Bacterial protein of unknown function (DUF97
      0.035   13.6   0.1      0.096   12.2   0.1    1.7  1  Sigma70_r4       Sigma-70, region 4
      0.045   14.0  17.2        1.2    9.3  15.8    2.1  2  ATG16            Autophagy protein 16 (ATG16)
       0.06   13.2   0.1       0.17   11.8   0.1    1.8  1  HTH_5            Bacterial regulatory protein, arsR family
      0.071   13.4  10.3        1.8    8.9   0.6    3.9  2  Mnd1             Mnd1 HTH domain
      0.072   13.5   0.7      0.072   13.5   0.7    2.4  2  Penicillinase_R  Penicillinase repressor
       0.08   13.1  21.6       0.89    9.6   8.8    2.3  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
      0.095   12.7  10.0       0.19   11.8  10.0    1.4  1  Rootletin        Ciliary rootlet component, centrosome cohesi
      0.098   12.8  18.4       0.22   11.7  18.4    1.6  1  Fib_alpha        Fibrinogen alpha/beta chain family
       0.12   12.4   3.4       0.25   11.3   3.4    1.6  1  DUF489           Protein of unknown function (DUF489)
       0.12   13.0   7.6        2.8    8.6   0.2    3.1  3  SlyX             SlyX
       0.14   11.1  23.4       0.51    9.2   8.2    2.1  2  Spc7             Spc7 kinetochore protein
       0.16   11.9   0.1       0.16   11.9   0.1    1.8  1  Cdc6_C           CDC6, C terminal winged helix domain
       0.18   11.1  18.0      0.043   13.1   4.4    2.4  2  TMPIT            TMPIT-like protein
       0.18   11.9   0.0       0.37   10.9   0.0    1.5  1  HTH_29           Winged helix-turn helix
        0.3   11.2  19.7       0.63   10.1   6.4    2.3  2  ADIP             Afadin- and alpha -actinin-Binding
       0.32   11.3  19.3        1.4    9.3   3.1    4.8  5  TSC22            TSC-22/dip/bun family
       0.46   10.9  12.4      0.032   14.6   3.6    2.5  2  Ly49             Ly49-like protein, N-terminal region
        0.5   10.6  18.8        3.1    8.0   7.2    2.3  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
       0.55   10.3  11.9       0.45   10.6   2.5    2.5  2  DUF1664          Protein of unknown function (DUF1664)
       0.56    9.5  10.7       0.14   11.5   1.5    2.2  2  DUF4407          Domain of unknown function (DUF4407)
       0.58   10.1  21.8       0.16   11.9   2.7    3.4  3  Prefoldin        Prefoldin subunit
       0.61    8.7   2.6       0.86    8.2   1.2    1.9  1  Tweety           Tweety
       0.71   10.8  16.5       0.19   12.7  13.1    1.8  1  PRKG1_interact   cGMP-dependent protein kinase interacting do
       0.74   10.0  24.5        1.4    9.1  12.9    3.4  3  Cnn_1N           Centrosomin N-terminal motif 1
       0.78    9.8  18.7        3.6    7.7   9.3    2.4  2  DHR10            Designed helical repeat protein 10 domain
       0.82    8.3   3.8        1.2    7.8   3.8    1.1  1  Med15            ARC105 or Med15 subunit of Mediator complex 
       0.96    8.3  15.7       0.03   13.2   8.8    1.8  2  LMBR1            LMBR1-like membrane protein
          1   10.0  18.1        2.9    8.6   4.8    2.6  2  YabA             Initiation control protein YabA
        1.3   10.0   6.2       0.93   10.5   4.0    1.9  1  CSN5_C           Cop9 signalosome subunit 5 C-terminal domain
        1.3    8.5  13.3       0.15   11.6   7.4    2.2  2  Angiomotin_C     Angiomotin C terminal
        1.5    9.1  19.0        2.1    8.6  19.0    1.2  1  zf-C4H2          Zinc finger-containing protein
        1.5    9.3  10.7      0.059   13.8   2.0    2.5  2  DUF2681          Protein of unknown function (DUF2681)
        1.6    9.0  24.7        2.6    8.3  10.3    3.3  2  XhlA             Haemolysin XhlA
        1.7    8.5  13.7        5.3    6.9   4.2    2.4  2  Sec34            Sec34-like family
        2.1    8.8  24.2       0.65   10.5   7.2    2.8  2  ZapB             Cell division protein ZapB
        2.2    8.6  18.6         11    6.4  18.6    2.0  1  OmpH             Outer membrane protein (OmpH-like)
        2.5    8.6  21.9       0.17   12.3   1.4    3.5  3  FlaC_arch        Flagella accessory protein C (FlaC)
        2.5    8.6  16.1        2.9    8.4   3.5    2.6  2  Snapin_Pallidin  Snapin/Pallidin
        2.8    8.1  12.4        6.1    7.0   2.1    2.6  2  DUF2730          Protein of unknown function (DUF2730)
        2.9    8.0  31.5        3.8    7.6  12.2    2.9  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        3.1    8.5  16.6        7.2    7.3   4.4    2.5  2  BST2             Bone marrow stromal antigen 2
        3.1    8.0  24.3        2.2    8.6   7.3    2.8  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
          4    7.6  24.0        7.4    6.7   8.4    2.5  2  BRE1             BRE1 E3 ubiquitin ligase
        4.4    7.4  19.3        7.8    6.6   6.2    2.2  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
        5.5    6.5  19.3        2.3    7.8   7.2    2.2  2  DUF4795          Domain of unknown function (DUF4795)
        5.7    7.2  19.1        3.2    8.0   8.0    3.2  2  JIP_LZII         JNK-interacting protein  leucine zipper II
          6    6.1  13.4          2    7.7   5.0    2.1  2  DUF3450          Protein of unknown function (DUF3450)
        7.1    6.5  13.1       0.48   10.3   2.3    2.8  2  TRAF_BIRC3_bd    TNF receptor-associated factor BIRC3 binding
          8    6.5   6.9        2.8    8.0   1.8    2.1  2  Noelin-1         Neurogenesis glycoprotein
          9    6.4  19.2       0.96    9.5   6.9    3.3  2  NEMO             NF-kappa-B essential modulator NEMO
        9.6    5.2  24.3         46    2.9  24.3    2.0  1  Atg14            Vacuolar sorting 38 and autophagy-related su


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.6   1.7e-11     4e-09       8      48 .]     409     449 ..     405     449 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.7e-11
                        HTH_24   8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                   I+ l++k+++i+q+e+ e +g+S++ v+r + +Le+  +I+
  gi|15669440|ref|NP_248250.1| 409 IIDLIKKHGHITQKEIVEITGMSKPKVSRIISELEDRKIIR 449
                                   67***********************************9996 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   6.3e-08   1.5e-05      21      57 ..     418     453 ..     397     462 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 6.3e-08
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEE CS
                     HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglisrgrri 57 
                                   ++tq+e+ ++ G++   vsri+seL+++++i++++ i
  gi|15669440|ref|NP_248250.1| 418 HITQKEIVEITGMSKPKVSRIISELEDRKIIRKEK-I 453
                                   79******************************653.2 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       8.6   2.1e+03      37      52 ..     344     359 ..     329     361 .. 0.86
   2 !   23.7   0.2   1.4e-07   3.4e-05       8      51 ..     409     452 ..     402     454 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 8.6
                                   HHHHHHHTTSEEEEEE CS
                          MarR  37 vldrLekkGlieRsks 52 
                                   ++ +L +++ i+++k 
  gi|15669440|ref|NP_248250.1| 344 QIQKLLDENIIYKEKI 359
                                   6889999999999986 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 1.4e-07
                                   HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR   8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                   i+ +++ +g ++++e+ +  g+sk+ v+r++ +Le++  i+++k
  gi|15669440|ref|NP_248250.1| 409 IIDLIKKHGHITQKEIVEITGMSKPKVSRIISELEDRKIIRKEK 452
                                   7889***********************************99986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.9e-07   4.5e-05      12      54 ..     411     451 ..     402     454 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.9e-07
                                   HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                     +  ++   +t++e+++ +g+sk+ vsri+ +L+++  ++++
  gi|15669440|ref|NP_248250.1| 411 DLIKKHGH--ITQKEIVEITGMSKPKVSRIISELEDRKIIRKE 451
                                   55777887..9*****************************987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   6.8e-07   0.00016       8      50 ..     409     450 ..     409     452 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.8e-07
                                   HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                   i+d++ +++   t +e+ + tg++k++v+R+++ L+ ++++++
  gi|15669440|ref|NP_248250.1| 409 IIDLIKKHGH-ITQKEIVEITGMSKPKVSRIISELEDRKIIRK 450
                                   7888888888.8***************************9997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       5.4   1.3e+03      26      58 ..     328     360 ..     321     370 .. 0.72
   2 !   18.7   0.1     5e-06    0.0012      15      57 ..     410     453 ..     402     461 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 5.4
                                   CHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB  26 deiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                   dei + l+   s   + +++L+d  ++++ek +
  gi|15669440|ref|NP_248250.1| 328 DEIISVLNERISEYESQIQKLLDENIIYKEKIE 360
                                   666666666666767778999999999999855 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 5e-06
                                   HHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                          TrmB  15 laLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57 
                                   + L+ k+g  t +ei e++g +++kv +++++Led+ ++++ek 
  gi|15669440|ref|NP_248250.1| 410 IDLIkKHGHITQKEIVEITGMSKPKVSRIISELEDRKIIRKEKI 453
                                   6677799*********************************9984 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.7     0.016       3.9      27      67 ..     287     327 ..     282     330 .. 0.87
   2 !   17.5   5.1   1.6e-05    0.0038      12      70 .]     335     393 ..     331     393 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.016
                        Csm1_N  27 hENsvLsqkletkdqeiesLkeqlaeleekvkeleerrkkq 67 
                                   +E + L++kl+ k++ei++L  +++ le k+++++++  ++
  gi|15669440|ref|NP_248250.1| 287 NELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNK 327
                                   78899***************************999876555 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.6e-05
                        Csm1_N  12 qerldsAdllvsklvhENsvLsqkletkdqeiesLkeqlaeleekvkeleerrkkqeEe 70 
                                    er+ + +  ++kl+ EN + ++k+e+ ++ ie+Lk++ ++l+ kv+el + +kk  Ee
  gi|15669440|ref|NP_248250.1| 335 NERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDIAKKYMEE 393
                                   6788888999***************************************9998887775 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7  20.8   8.2e-06    0.0019     145     275 ..     268     395 ..     265     454 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.2e-06
                        HMMR_N 145 lLksKvsedgtkKklnsLsleLmklrnkleake...kevsvkQedmeaklqvtqknLeeskakvaqLkeklvslekekiee 222
                                   + k+K+s  +   + + +  eL+ l+nkl+ ke   k++++k +d+e kl  ++knL +  + ++ L+e++++ e      
  gi|15669440|ref|NP_248250.1| 268 FVKEKISKRKIIERTKNIKNELTSLKNKLKEKEeeiKNLAIKIKDLEDKLSKANKNLLNKDEIISVLNERISEYES----- 343
                                   67888888876656666666*********9998555778899999************999999******9966655..... PP

                        HMMR_N 223 kseteklleyieelsnvseqlekykldiaqleellkekndeiesLkss.Leeke 275
                                     +++kll+++   ++ +e+l+ky + +++ ++ lk k +e++++ ++ +eek 
  gi|15669440|ref|NP_248250.1| 344 --QIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDIAKKyMEEKR 395
                                   ..4566666666666666666666666666666666666666555333133333 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.2       4.7   1.1e+03      52      83 ..     327     358 ..     269     370 .. 0.69
   2 !   18.8   0.6   7.5e-06    0.0018      45      83 ..     414     452 ..     412     463 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 4.7
                   Phage_rep_O  52 nsqlveltgisrtkvskalkeLirekviikeg 83 
                                   + +++ + +   ++ ++++++L +e++i ke+
  gi|15669440|ref|NP_248250.1| 327 KDEIISVLNERISEYESQIQKLLDENIIYKEK 358
                                   44444444444455667777777777777766 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 7.5e-06
                   Phage_rep_O  45 kksdwisnsqlveltgisrtkvskalkeLirekviikeg 83 
                                   kk  +i+++++ve+tg+s+ kvs+ + eL ++k+i ke+
  gi|15669440|ref|NP_248250.1| 414 KKHGHITQKEIVEITGMSKPKVSRIISELEDRKIIRKEK 452
                                   78899*******************************997 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   1.8       9.3   2.2e+03      21      36 ..     292     307 ..     279     327 .. 0.56
   2 !   17.8   1.0   9.1e-06    0.0022      23      65 ..     336     378 ..     333     379 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 9.3
                        GIT_CC  21 lKkalaaseakiqqLl 36 
                                   lK++l   e  i++L 
  gi|15669440|ref|NP_248250.1| 292 LKNKLKEKEEEIKNLA 307
                                   4445544444444443 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 9.1e-06
                        GIT_CC  23 kalaaseakiqqLlkvNtslsdelrlLQskvqkLqaeNaqlrd 65 
                                   + ++  e++iq+Ll  N   +++++ L + +++L++eN++l+d
  gi|15669440|ref|NP_248250.1| 336 ERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKD 378
                                   567788***********************************97 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6  10.5   0.00047      0.11       6      61 ..     272     327 ..     269     333 .. 0.90
   2 !   11.5   6.7    0.0011      0.25      13      67 ..     335     389 ..     331     396 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00047
                 Tropomyosin_1   6 kleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkea 61 
                                   k+ + +  e+ +++++++ +l ++ +eke+eik+L  k++ le+++ k++++l + 
  gi|15669440|ref|NP_248250.1| 272 KISKRKIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNK 327
                                   566778899****************************************9999765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0011
                 Tropomyosin_1  13 qekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaee 67 
                                    e+ +e+e+++++l +en+   ++i+sL+k +++l +e +kl++k++e  + a++
  gi|15669440|ref|NP_248250.1| 335 NERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDIAKK 389
                                   5899*******************************************99887765 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6  15.9   1.5e-05    0.0036     699     807 ..     270     385 ..     267     466 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                           FPP 699 elksekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnel.. 777
                                   + k +k+++  + k+ +++l slk++l+e+E+ +++l  +++ l++  s+a++ l ++ e+ + l+ r +e e+++++l  
  gi|15669440|ref|NP_248250.1| 270 KEKISKRKIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNKDEIISVLNERISEYESQIQKLld 350
                                   5677899999999***************************************************************99844 PP

                           FPP 778 .....kqkieaLeveLeeekksheeleakckelqe 807
                                        k+kie+L++ +e+ kk   +l+ k++el  
  gi|15669440|ref|NP_248250.1| 351 eniiyKEKIESLNKYIETLKKENDKLKDKVRELSD 385
                                   44444567788887777777777777777777754 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8  13.7   2.9e-05    0.0069     196     298 ..     278     379 ..     261     381 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.9e-05
                         FAM76 196 laeekesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeake 276
                                   + e +++ +++ +sl+ +  ++  ++++L  +i+ l+ +l++ +++ll+kd  i+ l     e e+++++ l + +  +ke
  gi|15669440|ref|NP_248250.1| 278 IIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNKDEIISVLNERISEYESQIQK-LLDENIIYKE 357
                                   3344444444456788888999999*********************************999999999875.66667789** PP

                         FAM76 277 kieklekkirellkevaelskk 298
                                   kie+l+k i++l+ke+ +l+ k
  gi|15669440|ref|NP_248250.1| 358 KIESLNKYIETLKKENDKLKDK 379
                                   ***************9999865 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   7.8e-05     0.019      14      51 ..     392     438 ..     371     446 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.8e-05
                                   HHHHHHHHH........HHHHHH.HCT--HHHHHHHHT--HHHHHHH CS
                        HTH_37  14 kaKaqlala........iaelie.krelsqseaaqllgiaqPkvsrl 51 
                                   + K+ +++         i++li+ + +++q+e+ +++g+++Pkvsr+
  gi|15669440|ref|NP_248250.1| 392 EEKRGVLWSfltedekiIIDLIKkHGHITQKEIVEITGMSKPKVSRI 438
                                   556665555566667778888862568******************97 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  12.7   4.6e-05     0.011      16     145 ..     286     443 ..     281     458 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.6e-05
                          Fez1  16 KqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeel 96 
                                   K+ L   ++ + +k +ei +l  ++++l+ kl++ ++++ + +e ++  ++ + ++e+++q+  +e+ + +ek+e+l++ +
  gi|15669440|ref|NP_248250.1| 286 KNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNKDEIISVLNERISEYESQIQKLLDENIIYKEKIESLNKYI 366
                                   566666666666666666666666677766666666666666666666666688888888888777777777777777777 PP

                          Fez1  97 kelreelselsleeeeaa............................lesdeakaqrqeaeeleelkreverlraeLk 145
                                   + l++e  +l+ + +e +                            ++++ + +q++  e ++  k +v r+ +eL+
  gi|15669440|ref|NP_248250.1| 367 ETLKKENDKLKDKVRELSdiakkymeekrgvlwsfltedekiiidlIKKHGHITQKEIVEITGMSKPKVSRIISELE 443
                                   77777766665554444333333334444444444444444444432222222233334555555556666666665 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.6   4.8e-05     0.012      10     102 ..     255     344 ..     246     353 .. 0.72
   2 ?    1.5   0.3      0.61   1.5e+02      60     100 ..     344     384 ..     339     394 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.8e-05
                          HemX  10 lallvalavgaglyylgqqqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqle 90 
                                   +  + + a+ +gl   ++  + +   ++++++++l++l+++l++   ++e+ ++l+ ++++l++kl++++k+l ++++ ++
  gi|15669440|ref|NP_248250.1| 255 IIAIFGTAIFGGLFVKEKISKRKIIERTKNIKNELTSLKNKLKE---KEEEIKNLAIKIKDLEDKLSKANKNLLNKDEIIS 332
                                   22223344445555555555555555559999999999999999...7888888999999999999999999999999999 PP

                          HemX  91 elqqqlskvsga 102
                                    l++++s+ +++
  gi|15669440|ref|NP_248250.1| 333 VLNERISEYESQ 344
                                   999999887765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.61
                          HemX  60 qkqeleerlqqlaeklealekeleqlqkqleelqqqlskvs 100
                                   q q+l ++    +ek+e+l+k +e+l+k+ ++l++++ ++s
  gi|15669440|ref|NP_248250.1| 344 QIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELS 384
                                   44555555555578888888888888888888888888876 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   0.00019     0.045      27      55 .]     420     448 ..     397     448 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00019
                        HTH_36  27 sqetlakrlglsknTvsraikeLeqlGyi 55 
                                   +q+ + + +g+sk +vsr+i eLe+  +i
  gi|15669440|ref|NP_248250.1| 420 TQKEIVEITGMSKPKVSRIISELEDRKII 448
                                   7999********************98765 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   5.1   9.1e-05     0.022     144     252 ..     277     386 ..     261     426 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.1e-05
                  Exonuc_VII_L 144 eleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlk.. 222
                                   ++ e+ ++++++l+ ++k++l+ek++++++la ++k+ e++l++++++l + ++++ + l++++++ ++++++l ++    
  gi|15669440|ref|NP_248250.1| 277 KIIERTKNIKNELT-SLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLN-KDEIISVLNERISEYESQIQKLLDENIiy 355
                                   33344444444443.334455555555555555555555544444444444.33344445555555555555544222123 PP

                  Exonuc_VII_L 223 .ekleekkerlkklkerlelleekkerleel 252
                                    ek+e+ ++ +++lk++ ++l++k ++l+ +
  gi|15669440|ref|NP_248250.1| 356 kEKIESLNKYIETLKKENDKLKDKVRELSDI 386
                                   3444444444444444444444444333333 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   0.00014     0.034       3      46 ..     407     450 ..     406     454 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00014
                      HTH_DeoR   3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46 
                                   + i++l+k++g+++ +e+ve  g S+  + R ++eLe   ++++
  gi|15669440|ref|NP_248250.1| 407 KIIIDLIKKHGHITQKEIVEITGMSKPKVSRIISELEDRKIIRK 450
                                   679***********************999999999999988876 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   3.0     0.072        17       7      46 ..     275     314 ..     270     315 .. 0.88
   2 ?   15.0  11.0   6.8e-05     0.016       2      99 ..     298     395 ..     297     396 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.072
                           ERM   7 kreleerLkqlqeeaekaqeaLreseetaelLaekarrae 46 
                                   kr++ er k++++e    +++L+e+ee+++ La k + +e
  gi|15669440|ref|NP_248250.1| 275 KRKIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLE 314
                                   678889999***********************99988876 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 6.8e-05
                           ERM   2 eaerekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekekler 82 
                                   e e e ++l  ++k l+++  ka+++L ++ e +  L+e+  + e + ++L  ++   +e+i+ l++  e  ++e +kl++
  gi|15669440|ref|NP_248250.1| 298 EKEEEIKNLAIKIKDLEDKLSKANKNLLNKDEIISVLNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKD 378
                                   567888999************************************************************************ PP

                           ERM  83 klreaeleaarleeese 99 
                                   k+re +  a++ +ee++
  gi|15669440|ref|NP_248250.1| 379 KVRELSDIAKKYMEEKR 395
                                   ************99985 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2       1.3   3.2e+02      24      59 ..     324     359 ..     317     365 .. 0.80
   2 ?   11.8   0.2    0.0009      0.21      19      58 ..     413     452 ..     409     461 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.3
                        Rio2_N  24 vVptelieeisrlkeeevkkrlsrllkaklisrkta 59 
                                   +  +++i ++ + + +e ++++++ll++++i ++++
  gi|15669440|ref|NP_248250.1| 324 LLNKDEIISVLNERISEYESQIQKLLDENIIYKEKI 359
                                   556667777777788999*************99764 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0009
                        Rio2_N  19 mrnhevVptelieeisrlkeeevkkrlsrllkaklisrkt 58 
                                    ++h  + +++i ei+++++ +v++ +s+l ++k+i++++
  gi|15669440|ref|NP_248250.1| 413 IKKHGHITQKEIVEITGMSKPKVSRIISELEDRKIIRKEK 452
                                   58999*******************************9975 PP

>> HNF-1_N  Hepatocyte nuclear factor 1 (HNF-1), N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   3.0   0.00018     0.043      52     172 ..     307     437 ..     271     443 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00018
                       HNF-1_N  52 g.gittlangagksskn.....asssttksklsqtq.rledesssp......gnsydtspils.asqrsfsfe.kaeeled 117
                                   + +i+ l+   +k++kn     +  s+++ ++s+ + ++++  +++       +s++    ++  ++  ++ + k +el d
  gi|15669440|ref|NP_248250.1| 307 AiKIKDLEDKLSKANKNllnkdEIISVLNERISEYEsQIQKLLDENiiykekIESLNK--YIEtLKKENDKLKdKVRELSD 385
                                   3344444444444444444333333333444443332222222222222211333322..2222455555555599***** PP

                       HNF-1_N 118 ldieeaaeqrakveellredswrvkeeikaflqqhrIsQrevvdvTGlsQShlSq 172
                                   ++ + ++e+r +  ++l ed++++   ik+     +I Q+e+v++TG+s  ++S+
  gi|15669440|ref|NP_248250.1| 386 IAKKYMEEKRGVLWSFLTEDEKIIIDLIKK---HGHITQKEIVEITGMSKPKVSR 437
                                   *****************************7...579*************999886 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   7.9     0.036       8.6      17      53 ..     280     315 ..     276     331 .. 0.86
   2 ?    2.3   2.2       0.6   1.4e+02      23      59 ..     321     356 ..     315     357 .. 0.80
   3 ?   13.6   3.6   0.00018     0.043      23      54 ..     356     388 ..     354     394 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.036
                                   XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                         DivIC  17 laykqlkqeiaalqaelaklkaeneeLeaevkdLksd 53 
                                    + k +k+e++ l+++l+++ +e+++L+ ++kdL+ d
  gi|15669440|ref|NP_248250.1| 280 ERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLE-D 315
                                   5678899***************************5.4 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.6
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                         DivIC  23 kqeiaalqaelaklkaeneeLeaevkdLksdedyiee 59 
                                   ++++  + + +  l++++ e e+++++L  de+ i +
  gi|15669440|ref|NP_248250.1| 321 NKNLLNKDEIISVLNERISEYESQIQKL-LDENIIYK 356
                                   666667777889999************9.69998876 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00018
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCC-XX.XX CS
                         DivIC  23 kqeiaalqaelaklkaeneeLeaevkdLks.de 54 
                                   k++i+ l++ +++lk+en++L+++v++L++  +
  gi|15669440|ref|NP_248250.1| 356 KEKIESLNKYIETLKKENDKLKDKVRELSDiAK 388
                                   789*************************64545 PP

>> DUF977  Bacterial protein of unknown function (DUF977)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00034      0.08      16      63 ..     408     454 ..     387     461 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00034
                        DUF977  16 riiGlvkkneritisdleritGvgrtsvrkylvdvlerGdlirpGkyG 63 
                                    ii l+kk++ it ++++ itG+ +  v +++ + le   +ir+ k+G
  gi|15669440|ref|NP_248250.1| 408 IIIDLIKKHGHITQKEIVEITGMSKPKVSRIISE-LEDRKIIRKEKIG 454
                                   589*************************998765.6666777777766 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1    0.0004     0.096       5      42 ..     402     440 ..     400     442 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0004
                                   S-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHH CS
                    Sigma70_r4   5 Lpererevlelrf.geglTleEIgerlgiSrerVrqiek 42 
                                   L+e+e+ ++ l       T++EI e+ g+S+  V++i++
  gi|15669440|ref|NP_248250.1| 402 LTEDEKIIIDLIKkHGHITQKEIVEITGMSKPKVSRIIS 440
                                   99***********97788*******************87 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  15.8    0.0052       1.2     103     184 ..     281     376 ..     274     379 .. 0.77
   2 ?    7.0   2.8     0.027       6.4     103     149 ..     337     383 ..     332     395 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0052
                         ATG16 103 rllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvq..............dlqDElsaLqlqlnq 169
                                   r ++ ++el  l++klke+ee++++l  ++++le+kl++ +++l  k++ +               +l DE +  + + ++
  gi|15669440|ref|NP_248250.1| 281 RTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNKDEIISvlneriseyesqiqKLLDENIIYKEKIES 361
                                   567788888888888888888888888888888888888888888888888877777777777777777888888888888 PP

                         ATG16 170 aEeklrklekENkeL 184
                                   + +  ++l+kEN +L
  gi|15669440|ref|NP_248250.1| 362 LNKYIETLKKENDKL 376
                                   888888888888877 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.027
                         ATG16 103 rllelneelqkleeklkedeerlaeleaeraaletklkdreeelrek 149
                                   r+ e ++++qkl ++    +e++++l++ +++l+++ +++++++re+
  gi|15669440|ref|NP_248250.1| 337 RISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVREL 383
                                   44444444444444444444444444444444444444444444443 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00071      0.17      13      41 ..     415     444 ..     407     450 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00071
                                   T.SSEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                         HTH_5  13 e.gelcvcelaeelglsqstvShHLkkLre 41 
                                   + g  +  e++e++g+s+++vS+  + L++
  gi|15669440|ref|NP_248250.1| 415 KhGHITQKEIVEITGMSKPKVSRIISELED 444
                                   55556678**************97777776 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.9     0.096        23      36      56 ..     345     365 ..     304     366 .. 0.86
   2 ?    8.9   0.6    0.0074       1.8      19      54 ..     422     457 ..     419     458 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.096
                          Mnd1  36 lqsLvdDglveveKiGssnvy 56 
                                   +q+L+d++++ +eKi s n y
  gi|15669440|ref|NP_248250.1| 345 IQKLLDENIIYKEKIESLNKY 365
                                   8**************998876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0074
                          Mnd1  19 klapkekgivsqsVkdvlqsLvdDglveveKiGssn 54 
                                   k++   +g+++  V  ++ +L d +++++eKiG +n
  gi|15669440|ref|NP_248250.1| 422 KEIVEITGMSKPKVSRIISELEDRKIIRKEKIGRIN 457
                                   55666689999**********************998 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2         3   7.1e+02      76     114 ..     330     367 ..     318     368 .. 0.78
   2 ?   13.5   0.7    0.0003     0.072       1      59 [.     402     456 ..     402     465 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 3
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
               Penicillinase_R  76 vkqlldklfegsvkelvaafveeeklseddleeLrelle 114
                                     ++l++ ++ ++++ ++++++e+ + ++ +e L++++e
  gi|15669440|ref|NP_248250.1| 330 IISVLNERIS-EYESQIQKLLDENIIYKEKIESLNKYIE 367
                                   5566666663.8999999999999999999999999987 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.0003
                                   ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTE CS
               Penicillinase_R   1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegra 59 
                                   l+e E+ +++++ ++g++t ke+ve         +  V  +++ L++++++++ek gr 
  gi|15669440|ref|NP_248250.1| 402 LTEDEKIIIDLIKKHGHITQKEIVEITGMS----KPKVSRIISELEDRKIIRKEKIGRI 456
                                   6899*********************98777....6779*****************9996 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.9    0.0088       2.1     139     183 ..     268     314 ..     266     319 .. 0.83
   2 ?    9.6   8.8    0.0037      0.89      67     131 ..     321     385 ..     313     415 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0088
                       UPF0242 139 eleeqLaekq..ellqeyqetieeqrsvlekrqdqieqLeskVrDln 183
                                   +++e++ +++  e+ ++ +++++++++ l++++++i++L +k++Dl 
  gi|15669440|ref|NP_248250.1| 268 FVKEKISKRKiiERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLE 314
                                   567777777733467788999************************95 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0037
                       UPF0242  67 kskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae 131
                                   +++l +k + ++ l+e +++ e ++++l +e+   ke++++ ++ +e lk+en +L+ k  + + 
  gi|15669440|ref|NP_248250.1| 321 NKNLLNKDEIISVLNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSD 385
                                   45566777788888899999999999999999999999******************988766443 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8  10.0   0.00078      0.19      26     126 ..     283     388 ..     274     412 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00078
                     Rootletin  26 lqYkkrcseleqrllektselektkltlllssareleeeesadl...eealakLee....ErqrseklaqvnslLreqlee 99 
                                   ++ k+  ++l ++l+ek+ e ++  ++++    +   ++ +++l   +e+++ L+e       + +kl+++n +++e++e 
  gi|15669440|ref|NP_248250.1| 283 KNIKNELTSLKNKLKEKEEEIKNLAIKIKD--LEDKLSKANKNLlnkDEIISVLNEriseYESQIQKLLDENIIYKEKIES 361
                                   456777778888888877777777765443..2222222333334557777777652221567899*************** PP

                     Rootletin 100 arqaneaLtedlqkltkdwerlreele 126
                                    ++  e+L+++++kl++++++l + ++
  gi|15669440|ref|NP_248250.1| 362 LNKYIETLKKENDKLKDKVRELSDIAK 388
                                   ****************99998776554 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  18.4   0.00091      0.22      27     129 ..     279     384 ..     275     393 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00091
                                   CCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH...HHH CS
                     Fib_alpha  27 lkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe...sni 104
                                    +  k++k++l++l+n+l+e +++ k+    +k+++d+l +++k+  ++d++i+ +++++ e  +++++ +d+++   ++i
  gi|15669440|ref|NP_248250.1| 279 IERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNKDEIISVLNERISEYESQIQKLLDENIiykEKI 359
                                   577899*****************************************99*********99999999999999997777899 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 105 rvLqnvlesneqkiqkLeqdidqke 129
                                   + L + +e+++++  kL+ ++ ++ 
  gi|15669440|ref|NP_248250.1| 360 ESLNKYIETLKKENDKLKDKVRELS 384
                                   9999999999999999999998765 PP

>> DUF489  Protein of unknown function (DUF489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.4     0.001      0.25      37     139 ..     267     364 ..     259     393 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.001
                                   HH--S-SSHHHHTTSGGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHTTHHHHTTS-T CS
                        DUF489  37 lletdpestedvygglanlklGletlleqlekekkkkdaeltryalsllalerkLsknkealaklgerieqierqlehfdl 117
                                   l++ ++ s  ++ ++++n+k+ l+ l++ l+++++    e+  +a+++  le kLsk ++ l + +e i+ ++++ ++++ 
  gi|15669440|ref|NP_248250.1| 267 LFVKEKISKRKIIERTKNIKNELTSLKNKLKEKEE----EIKNLAIKIKDLEDKLSKANKNLLNKDEIISVLNERISEYES 343
                                   56666667778888899999999999999999988....778888888888888877766666556666666666555555 PP

                                   TSHHHHHHHHHHHHHHTGGGSS CS
                        DUF489 118 lhenvlanlasiYsdtiSklgp 139
                                   + +++l + + iY++ i +l++
  gi|15669440|ref|NP_248250.1| 344 QIQKLLDE-NIIYKEKIESLNK 364
                                   55554443.3456666655555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.4      0.37        89      19      50 ..     289     320 ..     280     330 .. 0.54
   2 ?    5.6   0.9       0.1        25      11      50 ..     323     362 ..     310     363 .. 0.81
   3 ?    8.6   0.2     0.012       2.8      17      52 ..     357     392 ..     349     397 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.37
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                          SlyX  19 ieeLndvvaeqqqqidrlqrqlrllaerlkel 50 
                                   + +L + + e +++i+ l  +++ l+++l+++
  gi|15669440|ref|NP_248250.1| 289 LTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKA 320
                                   33444444555555555555555555555444 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.1
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                          SlyX  11 klafqedtieeLndvvaeqqqqidrlqrqlrllaerlkel 50 
                                    l   ++ i  Ln+ + e + qi++l  +    +e++++l
  gi|15669440|ref|NP_248250.1| 323 NLLNKDEIISVLNERISEYESQIQKLLDENIIYKEKIESL 362
                                   566678999*****************99998888888776 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                          SlyX  17 dtieeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                   + ie+Ln+ +    ++ d+l+ ++r+l +  k+  e
  gi|15669440|ref|NP_248250.1| 357 EKIESLNKYIETLKKENDKLKDKVRELSDIAKKYME 392
                                   468999999999999999999999999887766555 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  11.2    0.0024      0.58     198     258 ..     286     346 ..     269     349 .. 0.55
   2 ?    9.2   8.2    0.0021      0.51     139     232 ..     329     422 ..     324     460 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
                          Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervle 258
                                   k+eL +l+++l+e ++ei+++  ++++l+++l + ++++ + +e +s l+e+i+e e+ ++
  gi|15669440|ref|NP_248250.1| 286 KNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNKDEIISVLNERISEYESQIQ 346
                                   4566666666666666666666666666666666655555555555555555555555444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0021
                          Spc7 139 gLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekk 219
                                   ++ ++l+e++++ e++ ++L +++   +e  ++l+++ ++l++e +kl+++++el++i k+++ee r  l +  +e e+  
  gi|15669440|ref|NP_248250.1| 329 EIISVLNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDIAKKYMEEKRGVLWSFLTEDEKII 409
                                   78899**************************************************************99988887777766 PP

                          Spc7 220 kelaelqeqleel 232
                                    +l ++   ++++
  gi|15669440|ref|NP_248250.1| 410 IDLIKKHGHITQK 422
                                   6666666665554 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00068      0.16      33      76 ..     426     463 ..     411     469 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00068
                                   T-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESS CS
                        Cdc6_C  33 gvdpltqrevsdllseLemlgileleksskGrregrtrkisLnv 76 
                                   +++ ++   vs+++seLe++ i++ ek       gr +k +L+ 
  gi|15669440|ref|NP_248250.1| 426 EITGMSKPKVSRIISELEDRKIIRKEKI------GRINKLTLTE 463
                                   567788899*****************99......5556666655 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   8.6     0.078        19      12      83 ..     276     346 ..     269     348 .. 0.79
   2 ?   13.1   4.4   0.00018     0.043       2      86 ..     336     428 ..     335     440 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.078
                         TMPIT  12 keleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk 83 
                                   +++ e+ k++k++l +l++  ++  +eik+   ++k+l+++l+k +k++  +++e+++ l+e+++e +++++
  gi|15669440|ref|NP_248250.1| 276 RKIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNL-LNKDEIISVLNERISEYESQIQ 346
                                   5666777788888888888888888888888888888888888888886.5788899999999999988886 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00018
                         TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.......eeeee.eveelkee 74 
                                   e+++e e+++++l +++  yk+k+e+l+k +++++ke +k k +++el++  kk+ ++++       +e+e+ +++ +k++
  gi|15669440|ref|NP_248250.1| 336 ERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDIAKKYMEEKRgvlwsflTEDEKiIIDLIKKH 416
                                   6788999***********************************************999866788888855555155666666 PP

                         TMPIT  75 lkerkkvlkeve 86 
                                    + ++k + e+ 
  gi|15669440|ref|NP_248250.1| 417 GHITQKEIVEIT 428
                                   666666666665 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0015      0.37       5      37 ..     409     443 ..     407     465 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0015
                        HTH_29   5 llllaeGvs..tvsqiAkllglsrrtvyrwlkrfe 37 
                                   ++ l + ++  t ++i++++g+s+++v r++   e
  gi|15669440|ref|NP_248250.1| 409 IIDLIKKHGhiTQKEIVEITGMSKPKVSRIISELE 443
                                   55555666677*******************98755 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   8.3     0.069        17      79     125 ..     276     324 ..     269     328 .. 0.82
   2 ?   10.1   6.4    0.0026      0.63      59     125 ..     321     387 ..     319     395 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.069
                          ADIP  79 lk..tqleqlerelalvqakerqlekklktleqklknekeelqrlknal 125
                                    k  ++++  ++el+++++k+++ e ++k+l  k+k + ++l++ +++l
  gi|15669440|ref|NP_248250.1| 276 RKiiERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNL 324
                                   4444888999999999999999999999999999999999999998765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0026
                          ADIP  59 netirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknal 125
                                   n+ + +++  i+ l+ +i+  + q ++l  e+  +++k  +l+k ++tl++ + ++k++++ l  ++
  gi|15669440|ref|NP_248250.1| 321 NKNLLNKDEIISVLNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDIA 387
                                   6778889999999*********************************************997665444 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   2.1      0.54   1.3e+02      14      33 ..     301     320 ..     280     327 .. 0.88
   2 ?    9.3   3.1     0.006       1.4      14      45 ..     329     360 ..     324     369 .. 0.89
   3 ?    8.1   0.9     0.014       3.3      20      44 ..     356     380 ..     354     388 .. 0.91
   4 ?    2.6   0.3       0.7   1.7e+02      14      36 ..     371     393 ..     366     396 .. 0.72
   5 ?    2.4   0.0      0.81   1.9e+02       2      18 ..     411     427 ..     410     445 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.54
                         TSC22  14 EeVevLkekIkeLeernsel 33 
                                   Ee+ +L  kIk+Le++ s+ 
  gi|15669440|ref|NP_248250.1| 301 EEIKNLAIKIKDLEDKLSKA 320
                                   88999999999999998875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.006
                         TSC22  14 EeVevLkekIkeLeernseleeENslLkalas 45 
                                   E + vL e+I e e+++++l  EN ++k+ + 
  gi|15669440|ref|NP_248250.1| 329 EIISVLNERISEYESQIQKLLDENIIYKEKIE 360
                                   55789***********************8764 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.014
                         TSC22  20 kekIkeLeernseleeENslLkala 44 
                                   kekI  L + +++l++EN  Lk  +
  gi|15669440|ref|NP_248250.1| 356 KEKIESLNKYIETLKKENDKLKDKV 380
                                   99*******************9865 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.7
                         TSC22  14 EeVevLkekIkeLeernseleeE 36 
                                    e + Lk+k++eL +  +++ eE
  gi|15669440|ref|NP_248250.1| 371 KENDKLKDKVRELSDIAKKYMEE 393
                                   56688888888888877766655 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.81
                         TSC22   2 DLVKsHLmfAVrEeVev 18 
                                   DL+K+H  ++ +E Ve+
  gi|15669440|ref|NP_248250.1| 411 DLIKKHGHITQKEIVEI 427
                                   9************9996 PP

>> Ly49  Ly49-like protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   3.6   0.00014     0.032      18      93 ..     252     330 ..     249     344 .. 0.71
   2 ?   -0.4   3.2       6.1   1.5e+03      55     100 ..     346     389 ..     325     421 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 0.00014
                                   XXXXXXXXXXXXXX..XXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..HHHHHHHHHHHHHHHHHHH CS
                          Ly49  18 lLvtvavLvtkifq..ysqekhel....eetlnlsqnysimqndinlkeelLrnkslecsilkdlleslkreqkrlysktk 92 
                                    L+++a+++t if   + +ek ++    e t n++++ ++++n+ + kee ++n +++++ l+d+l++ +   k+l +k +
  gi|15669440|ref|NP_248250.1| 252 YLLIIAIFGTAIFGglFVKEKISKrkiiERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKAN---KNLLNKDE 329
                                   5889999***999533344443331111555599999**********************98887776555...44445555 PP

                                   T CS
                          Ly49  93 t 93 
                                   +
  gi|15669440|ref|NP_248250.1| 330 I 330
                                   5 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 6.1
                                   XXXXXXXXXXXXXXXXX..HHHHHHHHHHHHHHHHHHHTTTSXSXX CS
                          Ly49  55 dinlkeelLrnkslecsilkdlleslkreqkrlysktktvlkslqn 100
                                   +  l e+++ +  +e  +l++ +e+lk+e ++l +k + +++  ++
  gi|15669440|ref|NP_248250.1| 346 QKLLDENIIYKEKIE--SLNKYIETLKKENDKLKDKVRELSDIAKK 389
                                   333555555555555..45667777888877777777766665554 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   7.2     0.013       3.1      74     129 ..     272     327 ..     269     340 .. 0.82
   2 ?    7.2   5.0     0.023       5.5      94     155 ..     334     395 ..     326     397 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.013
                 Jnk-SapK_ap_N  74 kraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeael 129
                                   k ++++++e  +++++e   l++k+++ eee+++l +k+k+++d+ls+ +++  + 
  gi|15669440|ref|NP_248250.1| 272 KISKRKIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNK 327
                                   557789999999*********************************99887765555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.023
                 Jnk-SapK_ap_N  94 lqekveqleeenrelelkaknaadqlsrleekeaelkkeysklheretellkklkelverqr 155
                                   l+e++++ e+++++l      +++++++l++  + lkke++kl+++ +el    k+++e++r
  gi|15669440|ref|NP_248250.1| 334 LNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDIAKKYMEEKR 395
                                   56666666666666665555566777777777777777777777777777777777666655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.5    0.0019      0.45      77     121 ..     277     321 ..     269     324 .. 0.87
   2 ?    4.1   2.1      0.18        43      64     114 ..     334     384 ..     326     395 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0019
                       DUF1664  77 eqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                   + +e +k+ik+e+t+++++l+e +e+++++   +++le kl++ +
  gi|15669440|ref|NP_248250.1| 277 KIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKAN 321
                                   4568899*********************************98765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.18
                       DUF1664  64 Lssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                   L++ri + ++++++  +     ke+++++++ +++++++ +++k+ v++l 
  gi|15669440|ref|NP_248250.1| 334 LNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELS 384
                                   667777777777777777777777777777777777777777777777775 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   2.3      0.31        74     120     161 ..     275     322 ..     253     327 .. 0.45
   2 ?   11.5   1.5   0.00058      0.14     105     170 ..     327     394 ..     324     407 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.31
                       DUF4407 120 akelkeqlaaa.......ltaelaeleaqiaalqaeidaaearldalra 161
                                   ++++ e+++ +       l+++l+e e++i++l  +i+ +e++l+++++
  gi|15669440|ref|NP_248250.1| 275 KRKIIERTK-NikneltsLKNKLKEKEEEIKNLAIKIKDLEDKLSKANK 322
                                   333333322.201112224455555555555555555555555554444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00058
                       DUF4407 105 ekeIdaelaeeqqeeakelkeqlaaa..ltaelaeleaqiaalqaeidaaearldalraeaqkeldgt 170
                                   ++eI ++l+e+ +e ++++++ l+++  ++++++ l++ i+ l++e d++++++++l + a+k ++ +
  gi|15669440|ref|NP_248250.1| 327 KDEIISVLNERISEYESQIQKLLDENiiYKEKIESLNKYIETLKKENDKLKDKVRELSDIAKKYMEEK 394
                                   57899999999999999999999999*******************************99999887765 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   5.8      0.22        53      80     117 ..     283     320 ..     275     324 .. 0.78
   2 ?    3.4   0.2      0.28        68      76      99 ..     328     351 ..     324     353 .. 0.85
   3 ?   11.9   2.7   0.00067      0.16      81     115 ..     354     388 ..     352     393 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.22
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  80 ellkkkleelekqlekleeeleklkdqittleanlaql 117
                                   + +k++l++l++ l++ eee++ l+ +i+ le++l++ 
  gi|15669440|ref|NP_248250.1| 283 KNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKA 320
                                   55788888888888888888888888888888888765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.28
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  76 eeAiellkkkleelekqlekleee 99 
                                   +e i +l+++++e+e+q++kl +e
  gi|15669440|ref|NP_248250.1| 328 DEIISVLNERISEYESQIQKLLDE 351
                                   66788999***********99876 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00067
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  81 llkkkleelekqlekleeeleklkdqittleanla 115
                                   ++k+k+e+l+k +e+l++e +klkd++ +l +++ 
  gi|15669440|ref|NP_248250.1| 354 IYKEKIESLNKYIETLKKENDKLKDKVRELSDIAK 388
                                   689*************************9998875 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.2    0.0036      0.86      86     167 ..     312     394 ..     309     414 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0036
                        Tweety  86 etndGvlqltyslrkanhtlagikklvseteesleekleeeLtkleeifakrtdlletlrlvqeqveevvqqlselp..fl 164
                                   +++d ++++ + l + +++++ +++++se e+++++ l+e++   e+ +++ ++++etl++ + +++  v++ls+++   +
  gi|15669440|ref|NP_248250.1| 312 DLEDKLSKANKNLLNKDEIISVLNERISEYESQIQKLLDENIIYKEK-IESLNKYIETLKKENDKLKDKVRELSDIAkkYM 391
                                   78899999999******************************776555.577889*********************986555 PP

                        Tweety 165 kkk 167
                                   ++k
  gi|15669440|ref|NP_248250.1| 392 EEK 394
                                   555 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  13.1   0.00078      0.19       9      89 ..     285     379 ..     276     388 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00078
                PRKG1_interact   9 ekeenerLkreLeelekelselkseleklkqq...rqesvskrssllelekrerrslerkisel...........eeelke 75 
                                    k+e   Lk++L+e e+e+++l  +++ l+ +    ++++ ++ +++++ ++  +++e +i++l           e+ +k 
  gi|15669440|ref|NP_248250.1| 285 IKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKlskANKNLLNKDEIISVLNERISEYESQIQKLldeniiykekiESLNKY 365
                                   57788899****************999998663322223334444444444444444444444443334443444555599 PP

                PRKG1_interact  76 leeLraenqrLkdE 89 
                                   +e L++en++Lkd 
  gi|15669440|ref|NP_248250.1| 366 IETLKKENDKLKDK 379
                                   99999999999985 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   7.1      0.38        91      38      70 ..     275     307 ..     268     316 .. 0.79
   2 ?    9.1  12.9    0.0058       1.4      15      70 ..     302     377 ..     300     384 .. 0.90
   3 ?    7.7   1.3     0.016       3.9       6      35 ..     363     392 ..     361     412 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.38
                        Cnn_1N  38 keellkenielkveveslqkelkekkkllreae 70 
                                   k+++++   ++k e+ sl+++lkek++++++++
  gi|15669440|ref|NP_248250.1| 275 KRKIIERTKNIKNELTSLKNKLKEKEEEIKNLA 307
                                   567888888889999999999999998888764 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0058
                        Cnn_1N  15 ENFdLKLriyfLeerleklse....................eqkeellkenielkveveslqkelkekkkllreae 70 
                                   E  +L ++i+ Le++l k ++                    +q+++ll+eni  k+++esl k ++++kk+ ++++
  gi|15669440|ref|NP_248250.1| 302 EIKNLAIKIKDLEDKLSKANKnllnkdeiisvlneriseyeSQIQKLLDENIIYKEKIESLNKYIETLKKENDKLK 377
                                   666999999999999999999999999999999999999999*********************9999999877665 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.016
                        Cnn_1N   6 eeqidkLkKENFdLKLriyfLeerleklse 35 
                                   +++i++LkKEN  LK ++ +L +  +k  e
  gi|15669440|ref|NP_248250.1| 363 NKYIETLKKENDKLKDKVRELSDIAKKYME 392
                                   688999999999999999888776666555 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   9.3     0.015       3.6      48     109 ..     285     346 ..     276     352 .. 0.52
   2 ?    5.3   4.5     0.084        20      22      70 ..     346     394 ..     331     397 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.015
                         DHR10  48 elakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaak 109
                                     ++l + k klke +++++++ i+ ++le k +  ++ l n+ e ++ l e+ +e + + +
  gi|15669440|ref|NP_248250.1| 285 IKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNKDEIISVLNERISEYESQIQ 346
                                   33334444555555555555555555555555555555555555656666666655555555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.084
                         DHR10  22 qakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleeke 70 
                                   q+ +d    +++ ++s+ k +e++++e  kl++  ++l++  ++++e +
  gi|15669440|ref|NP_248250.1| 346 QKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDIAKKYMEEK 394
                                   44556666789999*************************9999998865 PP

>> Med15  ARC105 or Med15 subunit of Mediator complex non-fungal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.8    0.0049       1.2     516     553 ..     351     388 ..     339     394 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0049
                         Med15 516 eeqLYrekyrqltkYiePlkrmiakiendeddikdlsk 553
                                   e+ +Y+ek  +l+kYie lk+   k+++   +  d++k
  gi|15669440|ref|NP_248250.1| 351 ENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDIAK 388
                                   6789******************9999988777777765 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.5       3.8   9.2e+02     404     420 ..      43      58 ..       8      97 .. 0.54
   2 ?   13.2   8.8   0.00013      0.03     195     314 ..     275     393 ..     238     426 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.8
                         LMBR1 404 lieillilYlmlcayvg 420
                                   +i +ll++++++ + ++
  gi|15669440|ref|NP_248250.1|  43 VIIFLLLFFVAFNV-SS 58 
                                   22222222222221.22 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00013
                         LMBR1 195 ksdldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklks........... 264
                                   k+++ e++k+++ e+ +l+++++e+e+e+++l  ++k l++++s+ ++   + +ei++  +e i+e  ++           
  gi|15669440|ref|NP_248250.1| 275 KRKIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNKDEIISVLNERISEYESQiqklldeniiy 355
                                   556666777777777777777777777777777777777777777775555666666666666666533333333223333 PP

                         LMBR1 265 .....nenkteeslaklekqlikalqkrertekqwkrllekalelediiknkssk 314
                                        + nk  e+l+k++ +l+ ++++  ++ k+                   ++
  gi|15669440|ref|NP_248250.1| 356 kekieSLNKYIETLKKENDKLKDKVRELSDIAKK-----------------YMEE 393
                                   3223334444445555555555444444444444.................4444 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   7.1      0.15        35      13      59 ..     278     324 ..     270     337 .. 0.83
   2 ?    8.6   4.8     0.012       2.9       6      58 ..     334     386 ..     325     398 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.15
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXX CS
                          YabA  13 leeqleelleeleelkeelaelleenaeLeleneklrerleeeekke 59 
                                   + e+++++++el++lk++l+e  ee ++L +  + l ++l++++k+ 
  gi|15669440|ref|NP_248250.1| 278 IIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNL 324
                                   6678899999***************************9997666554 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXX CS
                          YabA   6 lfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekk 58 
                                   l ++++e e+q+++ll+e    ke++++l +  ++L+ en+kl+++++e ++ 
  gi|15669440|ref|NP_248250.1| 334 LNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDI 386
                                   56789999**********9999**********************999443332 PP

>> CSN5_C  Cop9 signalosome subunit 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.0    0.0039      0.93      15      73 ..     309     389 ..     304     400 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0039
                        CSN5_C  15 qisDLaeKlekaessvsrsrsaagtlseeaseaeekkk......................kkkedsqLakvvkdstkiase 73 
                                   +i+DL++Kl+ka++++ ++ + ++ l+e+ se e++ +                       kke+++L++ v++ + ia +
  gi|15669440|ref|NP_248250.1| 309 KIKDLEDKLSKANKNLLNKDEIISVLNERISEYESQIQklldeniiykekieslnkyietLKKENDKLKDKVRELSDIAKK 389
                                   79******************999999988877776666899**************99999888888999999988888865 PP

>> Angiomotin_C  Angiomotin C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   7.4   0.00062      0.15     114     171 ..     279     340 ..     270     351 .. 0.78
   2 ?   -1.0   0.7       4.4     1e+03      19      76 ..     356     411 ..     340     429 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00062
                  Angiomotin_C 114 inhSpkask.dssl...ikkeeedlllanrriqemEnrikaLhAqllEkdavikvLqqrsrk 171
                                   i+  ++ ++  +sl   +k++ee+++    +i+++E ++ + + +ll kd +i+vL++r  +
  gi|15669440|ref|NP_248250.1| 279 IERTKNIKNeLTSLknkLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNKDEIISVLNERISE 340
                                   44444444424444665688999***********************************9765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.4
                  Angiomotin_C  19 ceKREqlekrlrtrLErELkslraqqrqksaqeslsdselsasaLqeeLrekEEriLa 76 
                                    eK E+l+k + t L +E ++l+ + r+ s  +++  +e     L   L e E  i+ 
  gi|15669440|ref|NP_248250.1| 356 KEKIESLNKYIET-LKKENDKLKDKVRELSDIAKKY-MEEKRGVLWSFLTEDEKIIID 411
                                   4555555555543.5666666666655555555444.455555555555555555554 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  19.0    0.0088       2.1       2     123 ..     279     401 ..     278     458 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0088
                       zf-C4H2   2 ikeirektleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekeksleka 82 
                                   i+ +++  +el++lknkl+++ e++++    +++ + +l++ ++  ++  e +  +++ i++ Es i++  +e+   +ek+
  gi|15669440|ref|NP_248250.1| 279 IERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNKDEIISVLNERISEYESQIQKLLDENIIYKEKI 359
                                   677889999************************************************************************ PP

                       zf-C4H2  83 kklyeeykklkeevnelrse.lglekledleeeeeellkeei 123
                                   ++l + ++ lk+e ++l+ +   l+ + ++  ee+  +  ++
  gi|15669440|ref|NP_248250.1| 360 ESLNKYIETLKKENDKLKDKvRELSDIAKKYMEEKRGVLWSF 401
                                   *******************98999999999999987665555 PP

>> DUF2681  Protein of unknown function (DUF2681)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.0   0.00025     0.059       4      65 ..     252     315 ..     249     337 .. 0.84
   2 ?   -0.6   2.1       7.6   1.8e+03      30      51 ..     357     378 ..     325     397 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00025
                       DUF2681   4 lallvgliaavlllvaylswqlkkar..kknaklqaekqqlkvekavaeaevknakvkqkneen 65 
                                     l+++++++ +   ++++ ++ k +  ++++++++e   lk + + +e+e+kn  +k k  e 
  gi|15669440|ref|NP_248250.1| 252 YLLIIAIFGTAIFGGLFVKEKISKRKiiERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLED 315
                                   578999999999999********99999******************************887554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 7.6
                       DUF2681  30 kknaklqaekqqlkvekavaea 51 
                                   +k++ l++ ++ lk e    + 
  gi|15669440|ref|NP_248250.1| 357 EKIESLNKYIETLKKENDKLKD 378
                                   3333333333333333333333 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  10.3     0.011       2.6       9      47 ..     278     316 ..     269     318 .. 0.90
   2 ?    6.7   4.7     0.036       8.5       4      47 ..     329     372 ..     326     375 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.011
                          XhlA   9 ietkldnleervdkleekaaeaeekiknleedlkklesn 47 
                                   i ++++n++++++ l++k  e ee+iknl  ++k+le+ 
  gi|15669440|ref|NP_248250.1| 278 IIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDK 316
                                   55899*******************************986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.036
                          XhlA   4 erlerietkldnleervdkleekaaeaeekiknleedlkklesn 47 
                                   e +  +++++ ++e++++kl + +   +eki++l++ ++ l++ 
  gi|15669440|ref|NP_248250.1| 329 EIISVLNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKE 372
                                   6778899********************************99975 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.3     0.032       7.7      13      56 ..     276     319 ..     269     323 .. 0.86
   2 ?    6.9   4.2     0.022       5.3       4      71 ..     323     390 ..     320     395 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.032
                         Sec34  13 delleqtdealeqLeeleekfksvsektsslheaceqlleeqkr 56 
                                   ++++e+t++++++L++l++k k+ +e+ ++l  + ++l ++ ++
  gi|15669440|ref|NP_248250.1| 276 RKIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSK 319
                                   68999*************************99999998777655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.022
                         Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyF 71 
                                   +L +k e +  l e+++e ++q+++l ++    +ek +sl++  e+l +e+++l++ ++e+++  k +
  gi|15669440|ref|NP_248250.1| 323 NLLNKDEIISVLNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDIAKKY 390
                                   5666777788888999**************************************99999988766555 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9  14.0       9.9   2.4e+03      15      66 ..     277     349 ..     271     351 .. 0.65
   2 ?   10.5   7.2    0.0027      0.65      10      55 ..     342     394 ..     335     399 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 9.9
                          ZapB  15 kaidtitlLqmeieeLkeeneelkeenreleeeneqlk.....................eereawqerlkkLL 66 
                                   k i++ +  ++e+  Lk + +e +ee+++l  +++ l+                     e  ++ ++ ++kLL
  gi|15669440|ref|NP_248250.1| 277 KIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEdklskanknllnkdeiisvlnERISEYESQIQKLL 349
                                   6789999999999999999999999999999666666633333333444444444444355566666666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0027
                          ZapB  10 Eskiqkaid.......titlLqmeieeLkeeneelkeenreleeeneqlkeer 55 
                                   Es+iqk++d       +i++L + ie Lk+en +lk++ rel+   ++  ee+
  gi|15669440|ref|NP_248250.1| 342 ESQIQKLLDeniiykeKIESLNKYIETLKKENDKLKDKVRELSDIAKKYMEEK 394
                                   77777777633222226888888888888888888888888887666666655 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  18.6     0.044        11       8     109 ..     276     394 ..     273     442 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.044
                                   HHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.............-HHHHHHHHHHHHHHHHHH CS
                          OmpH   8 qkileespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.e...........keekeqelqkkeqelqqkq 76 
                                    ki+e ++  k+  + l++k k+ ++e+++++ ++++l+++l k++k+l +             e e ++qk+ +e    +
  gi|15669440|ref|NP_248250.1| 276 RKIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLlNkdeiisvlnerISEYESQIQKLLDENII-Y 355
                                   58999*************************************9999998767888777555533333335555555444.3 PP

                                   HHHH.......HHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                          OmpH  77 qqka.......qelqkkqqellkpildkinkaikevakek 109
                                   ++k        + l+k++ +l ++ + ++ ++ k++++ek
  gi|15669440|ref|NP_248250.1| 356 KEKIeslnkyiETLKKENDKLKDK-VRELSDIAKKYMEEK 394
                                   333323322223344444333333.555666667777776 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   9.0       3.6   8.6e+02       1      38 [.     281     322 ..     277     333 .. 0.79
   2 ?    5.6   3.3     0.086        21       1      42 [.     309     350 ..     309     355 .. 0.96
   3 ?   12.3   1.4   0.00069      0.17       7      36 ..     357     386 ..     351     392 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 3.6
                     FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenV....k 38 
                                   r++++ n+l +l+ +l+  ++e+++l  ++++l+++     k
  gi|15669440|ref|NP_248250.1| 281 RTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLskanK 322
                                   678888999999999999999999999999888887744444 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.086
                     FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdlls 42 
                                   +i++lE klsk   +l +  + ++ l++ + e + ++++ll+
  gi|15669440|ref|NP_248250.1| 309 KIKDLEDKLSKANKNLLNKDEIISVLNERISEYESQIQKLLD 350
                                   89*************************************996 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00069
                     FlaC_arch   7 nklsklsteletvkkeneelsksveelken 36 
                                   +k+++l   +et+kken++l+++v el + 
  gi|15669440|ref|NP_248250.1| 357 EKIESLNKYIETLKKENDKLKDKVRELSDI 386
                                   688999999999999999999999999875 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.5     0.035       8.4      30      87 ..     283     339 ..     275     340 .. 0.86
   2 ?    8.4   3.5     0.012       2.9       6      71 ..     329     389 ..     327     393 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.035
               Snapin_Pallidin  30 eeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRae 87 
                                   +  +++l++l++kLke ee+ + ++  ++k   +KL+++ k++ +  e+++ l++R++
  gi|15669440|ref|NP_248250.1| 283 KNIKNELTSLKNKLKEKEEEIK-NLAIKIKDLEDKLSKANKNLLNKDEIISVLNERIS 339
                                   5678999*******97666665.99**************************9999985 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.012
               Snapin_Pallidin   6 gllellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkr 71 
                                   +++++l   + e ++++++l ++    +e++++ln+ ++ l+++++     +lk  ++ L+ i k+
  gi|15669440|ref|NP_248250.1| 329 EIISVLNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKEND-----KLKDKVRELSDIAKK 389
                                   5788999999999*************************99999999.....888888888888765 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   4.0     0.093        22      34      86 ..     274     324 ..     251     334 .. 0.76
   2 ?    7.0   2.1     0.026       6.1      40      98 ..     329     392 ..     321     395 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.093
                       DUF2730  34 dleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaev 86 
                                      k+ e  +++++ lt+l+ k+++   ++++++L ++++dl+ +l+++++++
  gi|15669440|ref|NP_248250.1| 274 SKRKIIERTKNIKNELTSLKNKLKE--KEEEIKNLAIKIKDLEDKLSKANKNL 324
                                   4456667778999999999999997..78999999999999999999988876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.026
                       DUF2730  40 ekveendkrlteletkvenLPt.....akdlekLkllladlrgelkaleaevrqlshqvdLLLe 98 
                                   e+++  ++r++e e+++++L       ++ +e+L++ ++ l+ e ++l+ +vr+ls  ++  +e
  gi|15669440|ref|NP_248250.1| 329 EIISVLNERISEYESQIQKLLDeniiyKEKIESLNKYIETLKKENDKLKDKVRELSDIAKKYME 392
                                   4556678888888888887765112225789999999999999999999999999987765555 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  12.2     0.016       3.8      32      70 ..     286     324 ..     280     328 .. 0.89
   2 ?    3.5  15.4      0.29        70       3      71 ..     320     388 ..     318     394 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.016
                    TMF_DNA_bd  32 nntikkLrkknkelekeikelkkkleklekeleeleerl 70 
                                   +n + +L+ k+ke e+eik+l  k+++le +l++ ++ l
  gi|15669440|ref|NP_248250.1| 286 KNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNL 324
                                   578889**************************9998876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.29
                    TMF_DNA_bd   3 lekklkeKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlk 71 
                                   + k+l +KDe+I  L e   +++++ +kl       ++k++ l+k i++lkk+++kl  ++ el++ +k
  gi|15669440|ref|NP_248250.1| 320 ANKNLLNKDEIISVLNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDIAK 388
                                   568899999999999999999999999999999999999999999999999999999998888887665 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.4      0.03       7.2      56      90 ..     270     304 ..     268     305 .. 0.90
   2 ?    6.2   4.5     0.063        15      21      89 ..     312     380 ..     305     385 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.03
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                          BST2  56 kekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90 
                                   kek  ++k  ++ +++++e+++L++kL+++e+e++
  gi|15669440|ref|NP_248250.1| 270 KEKISKRKIIERTKNIKNELTSLKNKLKEKEEEIK 304
                                   67778899999*********************997 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.063
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                          BST2  21 lLerqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaev 89 
                                    Le +L +a+++l++++  ++  n+ + + ++ ++k  +++   ++k++ l++ i++L+++ ++ + +v
  gi|15669440|ref|NP_248250.1| 312 DLEDKLSKANKNLLNKDEIISVLNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKV 380
                                   589999999999999999999999999999999999999999999999999999999876544444443 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   7.3     0.009       2.2      65     105 ..     271     311 ..     266     314 .. 0.86
   2 ?    3.7   9.4      0.29        69      45     101 ..     331     391 ..     313     395 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.009
                                   TTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS- CS
                  Seryl_tRNA_N  65 kkedaeeliaevkelkeelkaleaelkeleaeleklllaiP 105
                                   +k  + ++i+++k++k+el  l+++lke e+e+++l+ +i 
  gi|15669440|ref|NP_248250.1| 271 EKISKRKIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIK 311
                                   44567789***************************999885 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.29
                                   HHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  45 leelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekll 101
                                   +  l+++  e   +I+k+ +++    e++e+l + +++lk+e ++l+++++el++  +k++
  gi|15669440|ref|NP_248250.1| 331 ISVLNERISEYESQIQKLLDENiiykEKIESLNKYIETLKKENDKLKDKVRELSDIAKKYM 391
                                   4567778888888888888888888888888888888888888888888888887766665 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   7.4     0.045        11       2      41 ..     286     325 ..     285     332 .. 0.89
   2 ?    6.7   8.4     0.031       7.4      20      80 ..     332     392 ..     325     406 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.045
                          BRE1   2 qkELvklekafeelseqlskkvkeltileekklrleaeka 41 
                                   ++EL +l++  +e +e+++++  ++++le+k+++++++  
  gi|15669440|ref|NP_248250.1| 286 KNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLL 325
                                   69********************************998765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.031
                          BRE1  20 skkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLke 80 
                                   s + + ++  e+++++l  e    ++k+ ++++ +++l++e+ kL+ ++   s++ ++  e
  gi|15669440|ref|NP_248250.1| 332 SVLNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDIAKKYME 392
                                   5566678899************************************999988888887766 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  11.1     0.034       8.1      42     114 ..     275     348 ..     269     352 .. 0.85
   2 ?    6.6   6.2     0.032       7.8       5      64 ..     327     388 ..     323     397 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.034
                         Mod_r  42 neslaeknlslepeleelrselqekleelkelekefeekeqeldell.qkfspdallarLqtavaeaeeeSeal 114
                                    +++ e+  + ++el+ l+++l+ek ee+k+l  + +++e +l+++  + +++d + + L++ ++e e + ++l
  gi|15669440|ref|NP_248250.1| 275 KRKIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANkNLLNKDEIISVLNERISEYESQIQKL 348
                                   56777878888999*****************************9999556799999999999999999876665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.032
                         Mod_r   5 keeLqellede.eklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselq 64 
                                   k+e+  +l++  + +e+ +++l +e   +ke+ e+l + +e l ++n +l+++++el++  +
  gi|15669440|ref|NP_248250.1| 327 KDEIISVLNERiSEYESQIQKLlDENIIYKEKIESLNKYIETLKKENDKLKDKVRELSDIAK 388
                                   44444444444444444444444444444555555544444444444444444444444333 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   7.6      0.47   1.1e+02      12      61 ..     278     327 ..     267     330 .. 0.62
   2 ?    7.8   7.2    0.0097       2.3      14      67 ..     329     382 ..     316     391 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.47
                       DUF4795  12 lqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadk 61 
                                   + e  +++++el +l++k ke e++++++  k++ l++++++ +k+  +k
  gi|15669440|ref|NP_248250.1| 278 IIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKNLLNK 327
                                   44555666666666666666666666666666666666666666655555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0097
                       DUF4795  14 eaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveee 67 
                                   e i+ l e++++ e++ ++l ++   +++k+e+l k+ie l+k++++ ++   e
  gi|15669440|ref|NP_248250.1| 329 EIISVLNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRE 382
                                   78999***************************************9874433333 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   8.0     0.013       3.2      26      70 ..     273     317 ..     270     318 .. 0.96
   2 ?    3.2   3.3      0.43     1e+02      47      68 ..     357     378 ..     319     393 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.013
                      JIP_LZII  26 vvkddLIarvdeLtsereiLreEleslqkakerlesrikelEeel 70 
                                   + k+ +I+r+ ++++e ++L++ l++ +++ + l  +ik+lE++l
  gi|15669440|ref|NP_248250.1| 273 ISKRKIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKL 317
                                   789***************************************987 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.43
                      JIP_LZII  47 eEleslqkakerlesrikelEe 68 
                                   e +esl+k  e+l+++  +l +
  gi|15669440|ref|NP_248250.1| 357 EKIESLNKYIETLKKENDKLKD 378
                                   4444444444444433333332 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   3.0      0.31        73      35      79 ..     278     322 ..     270     331 .. 0.58
   2 ?    7.7   5.0    0.0083         2      29      85 ..     328     384 ..     315     399 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.31
                       DUF3450  35 sqkkidklddekqellaeyralkeeleslevyneqlerlvasqeq 79 
                                   + ++ +++++e ++l++++++ +ee+++l+++ + le+ ++++++
  gi|15669440|ref|NP_248250.1| 278 IIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANK 322
                                   444555555555666666666666666666666666655555554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0083
                       DUF3450  29 vaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasle 85 
                                    ++ +  +++i++++ + q+ll+e    ke++esl++y e l++  ++++ ++ +l 
  gi|15669440|ref|NP_248250.1| 328 DEIISVLNERISEYESQIQKLLDENIIYKEKIESLNKYIETLKKENDKLKDKVRELS 384
                                   445555667777777777777777777777777777777777777777777776665 PP

>> TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.3       0.5   1.2e+02      34      60 ..     289     315 ..     279     319 .. 0.81
   2 ?   10.3   2.3     0.002      0.48      18      59 ..     329     370 ..     316     372 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.5
                 TRAF_BIRC3_bd  34 ieaverqrrldqekieaLekKvrqLer 60 
                                   +  ++   ++ +e i+ L  K+++Le 
  gi|15669440|ref|NP_248250.1| 289 LTSLKNKLKEKEEEIKNLAIKIKDLED 315
                                   5667778889999************95 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.002
                 TRAF_BIRC3_bd  18 nIVsVLnrEverssttieaverqrrldqekieaLekKvrqLe 59 
                                    I+sVLn  +   +++i+ +   +   +ekie+L+k ++ L+
  gi|15669440|ref|NP_248250.1| 329 EIISVLNERISEYESQIQKLLDENIIYKEKIESLNKYIETLK 370
                                   69************************************9997 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.8     0.012       2.8      42      89 ..     276     323 ..     271     330 .. 0.92
   2 ?   -0.3   0.4       4.4     1e+03      68      89 ..     358     379 ..     325     394 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.012
                      Noelin-1  42 rqllekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvveed 89 
                                   r++ e+ +n+ +++  l+++ ++  +++++    +k+le+kl++++++
  gi|15669440|ref|NP_248250.1| 276 RKIIERTKNIKNELTSLKNKLKEKEEEIKNLAIKIKDLEDKLSKANKN 323
                                   7899**************************************999876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 4.4
                      Noelin-1  68 yvrktetllktlesklkvveed 89 
                                    +++ ++ ++tl+++ ++++++
  gi|15669440|ref|NP_248250.1| 358 KIESLNKYIETLKKENDKLKDK 379
                                   2333333333333333333333 PP

>> NEMO  NF-kappa-B essential modulator NEMO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   4.5       5.9   1.4e+03      14      65 ..     281     307 ..     272     329 .. 0.57
   2 ?    9.5   6.9     0.004      0.96       6      47 ..     343     394 ..     339     407 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 5.9
                          NEMO  14 eNneLkealkqsNqalkeRlEeLsawqekqkeerefleeklrearellerls 65 
                                     ++                          k e+ +l++kl+e  e +++l+
  gi|15669440|ref|NP_248250.1| 281 RTKNI-------------------------KNELTSLKNKLKEKEEEIKNLA 307
                                   44444.........................4455555555555544444443 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.004
                          NEMO   6 eqlkellteN..........neLkealkqsNqalkeRlEeLsawqekqkeer 47 
                                    q+++ll eN          n+  e+lk++N++lk+ + eLs   +k  ee+
  gi|15669440|ref|NP_248250.1| 343 SQIQKLLDENiiykekieslNKYIETLKKENDKLKDKVRELSDIAKKYMEEK 394
                                   5777777777333333322244458**********************99998 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9  24.3      0.19        46      29     127 ..     280     382 ..     270     460 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.19
                         Atg14  29 erlaklksekeslkkkiekalegke....eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkkla 105
                                   er++++k e  slk+k+++++e+ +    + ++ledk+ + +++l ++   i+ l+er++e + ++++l +e+ + k+k++
  gi|15669440|ref|NP_248250.1| 280 ERTKNIKNELTSLKNKLKEKEEEIKnlaiKIKDLEDKLSKANKNLLNKDEIISVLNERISEYESQIQKLLDENIIYKEKIE 360
                                   78999*************999999999999999999999999999999999999999999999999999999999999999 PP

                         Atg14 106 klsdklkkRrsdleslqnelee 127
                                   +l++ + + +++ ++l+++++e
  gi|15669440|ref|NP_248250.1| 361 SLNKYIETLKKENDKLKDKVRE 382
                                   9999998766665566665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2773  (0.154666); expected 358.6 (0.02)
Passed bias filter:                      842  (0.046963); expected 358.6 (0.02)
Passed Vit filter:                       257  (0.0143343); expected 17.9 (0.001)
Passed Fwd filter:                       109  (0.00607954); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              75  [number of targets reported over threshold]
# CPU time: 1.07u 0.32s 00:00:01.39 Elapsed: 00:00:00.54
# Mc/sec: 2633.46
//
Query:       gi|15669441|ref|NP_248251.1|  [L=398]
Description: hypothetical protein MJ_1255 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-31  109.0   0.1    4.4e-31  108.1   0.1    1.4  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
    1.1e-20   74.1   0.0    5.3e-20   71.9   0.0    1.9  1  Glyco_trans_1_3  Glycosyl transferase family 1
    6.3e-07   28.5   0.0    1.2e-06   27.6   0.0    1.4  1  UDPGT            UDP-glucoronosyl and UDP-glucosyl transferas
     0.0056   16.7   0.1      0.035   14.1   0.0    2.2  2  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.054   13.5   0.0    1.9  3  Glyco_transf_4   Glycosyltransferase Family 4
       0.02   14.4   0.7      0.055   13.0   0.4    2.0  1  Glycos_transf_1  Glycosyl transferases group 1
       0.11   12.7   1.1       0.34   11.0   0.1    2.3  2  KH_5             NusA-like KH domain
       0.22   10.6   0.0        4.6    6.3   0.0    2.1  2  Mito_fiss_Elm1   Mitochondrial fission ELM1


Domain annotation for each model (and alignments):
>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.1     2e-34   4.4e-31       3     166 ..     203     361 ..     201     362 .. 0.91

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 2e-34
                                   EEEE-SSSHHHHHCCCTSHHHHHHHHHHHHCHHHCCT-E.EC---STT..-TTTT.CEEEEEESSSSHHHHHHHH-EEEEC CS
               Glyco_tran_28_C   3 lVtGGSqgaeaLnelvlselkllelksrelqvlhqtGkr.eleevkik..veelt.lkvevfefidkmaeaikaadLvIsR 79 
                                   +V+GG   +e +   +l+el +++lk ++l+v + +G+    ++++ +  +++++ ++ve+++ +++m+e+ik+a+L++s+
  gi|15669441|ref|NP_248251.1| 203 SVIGG---FE-YRYKILEELGKIALK-NNLNVKLVCGSYeVAKKLMRDlnLNSYKnENVEIIPITTNMKELIKNAELIVSH 278
                                   66676...77.8899***********.7***********788888888776666689************************ PP

                                   S-CHHHHHHHHTT--EEEE--TT....S-HHHHHHHHHHHHHHSSEEEE-STTCHHHHHHHHCCS---S---SSCH..CHH CS
               Glyco_tran_28_C  80 AGagtiaEllalgkplIlvplpeaaenhqdnNakelekagaalvleqkeltpekLeeallelaaeklrlaekskasaaskf 160
                                   +G++ti+E+l++gkplI++p  ++   +q nNak++++ g+++ l +kel   +Leea+l+++++k+   + sk+++ +k+
  gi|15669441|ref|NP_248251.1| 279 GGHSTIMEALSFGKPLIVIPDLDHP--EQGNNAKKVHDLGCGIALSYKEL--YRLEEAILDIRNMKMYKRNASKMKELAKK 355
                                   ***********************88..***********************..**************997777777778999 PP

                                   HHHHHH CS
               Glyco_tran_28_C 161 adlaer 166
                                   +d +++
  gi|15669441|ref|NP_248251.1| 356 YDGKKN 361
                                   998876 PP

>> Glyco_trans_1_3  Glycosyl transferase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.0   2.4e-23   5.3e-20       1     308 [.       5     326 ..       5     335 .. 0.76

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 2.4e-23
               Glyco_trans_1_3   1 arilYgvsGeGaGhasRsrvvlehLarghevkvvvsgraldvLeke.fdvneiv.glsivyeenrvrklktllknlqvaak 79 
                                   ++il +v GeG Gh++R  ++ e+L  ++e+  +++g++++++ek  f+v+e +  +++  ++ +   +  +l   +   +
  gi|15669441|ref|NP_248251.1|   5 MKILISVCGEGFGHTTRCVAIGEALKNDYEISYIAYGKSKNFIEKYgFKVFETFpEIKLKGKDGKFDITSSIL---NKEYS 82 
                                   79*****************************************99956**99751566666666666555554...55666 PP

               Glyco_trans_1_3  80 laknvkalvelvedfrpdlvvtDFealtallakrhkLPvisvdnqqvvnrtdyelell...akkdallakavvkaklPkad 157
                                    +k +++ ++ +++++pdl+++D    t+ +ak  k Pvi + nq+  ++   +  +    +k+ + + +   + ++P  +
  gi|15669441|ref|NP_248251.1|  83 PKKAIRREINIIREYNPDLIISDCKYSTVVAAKLLKKPVICISNQNYTRYKLKTDLIVyptMKALNIINERCERFIVPDFP 163
                                   7788999999***********************************988765554444422245555568889999****99 PP

               Glyco_trans_1_3 158 lylvttFfqapvrkkerttlvPpilRkeilaakptegehlLvYlt.....segnealpevLkklg....vefvvYglrrdt 229
                                   l  +   ++  + k  +  ++ p++R ++  + +   + +L  +       +  e+l ++  k +    + +  Y + +  
  gi|15669441|ref|NP_248251.1| 164 LPYTICEYNLKIIK--NMEFIGPLIRYDVDDVDNYGEDYILSVIGgfeyrYKILEELGKIALKNNlnvkLVCGSYEVAK-- 240
                                   98888888888887..6778999***********999999976542111123445566554333311113344455544.. PP

               Glyco_trans_1_3 230 eeekegnlt.yka.....fseegFleDL.ataraviagagftLmtealyLkkPlLavPvarqFeqvlnalyLerlgyGaav 303
                                   +  ++ nl  yk+       ++  +++L ++a  +++ +g++ + eal  +kPl+++P     eq  na  ++ lg+G+a+
  gi|15669441|ref|NP_248251.1| 241 KLMRDLNLNsYKNenveiIPITTNMKELiKNAELIVSHGGHSTIMEALSFGKPLIVIPDLDHPEQGNNAKKVHDLGCGIAL 321
                                   5566666642555111113345556666267999*********************************************99 PP

               Glyco_trans_1_3 304 dakdl 308
                                   + k+l
  gi|15669441|ref|NP_248251.1| 322 SYKEL 326
                                   88876 PP

>> UDPGT  UDP-glucoronosyl and UDP-glucosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   5.5e-10   1.2e-06     344     422 ..     275     353 ..     270     359 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.5e-10
                         UDPGT 344 FvtHaGangvyEaisnGvPmvglPlF..gdqrdNikrmeakgaavtlnvkemtsedllnAlkevindksykenimrLsslh 422
                                    v+H+G  +++Ea+s G P++++P     +q +N+k+++  g +++l  ke+    l++A+  + n k+yk+n+ ++ +l 
  gi|15669441|ref|NP_248251.1| 275 IVSHGGHSTIMEALSFGKPLIVIPDLdhPEQGNNAKKVHDLGCGIALSYKELY--RLEEAILDIRNMKMYKRNASKMKELA 353
                                   699*********************752269*********************96..69*****************9988775 PP

>> Glyco_transf_28  Glycosyltransferase family 28 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.6e-05     0.035       1     115 [.       7     122 ..       7     142 .. 0.76
   2 ?   -0.7   0.1      0.62   1.4e+03      54      87 ..     335     369 ..     320     379 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                                   EEEEE-SSH.HHHHHHHHHHHHHHCTT-EEEEEEETCCCHHHHHHCCT-....EEEE---GHCTT....CHHHHCCHHHHH CS
               Glyco_transf_28   1 ivllggGTg.GhvfPalAlakeLkkegheVrylgtkrgleerlveeagl....efepiageklrrkl..spknlkeilkvl 74 
                                   i+++++G g Gh +  +A+ ++Lk +  e++y++   + ++++ e++g     +f +i++++  +k+  + + l++  +  
  gi|15669441|ref|NP_248251.1|   7 ILISVCGEGfGHTTRCVAIGEALKNDY-EISYIA-YGKSKNFI-EKYGFkvfeTFPEIKLKGKDGKFdiTSSILNKEYSPK 84 
                                   56777787779************8765.9*9665.45567777.8888853334444666655554443888888888888 PP

                                   HHHHHHHHHHHHHHHCCCCCCCCCCCHCCCCCHCCCTTHCC CS
               Glyco_transf_28  75 kavvkakkilkeakpdavvgtggyvslpaviaaplaripvi 115
                                   ka+++ + i++e++pd++++ + y+    v+aa+l++ pvi
  gi|15669441|ref|NP_248251.1|  85 KAIRREINIIREYNPDLIISDCKYS---TVVAAKLLKKPVI 122
                                   9*********************776...5788888888876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.62
                                   --GHCTT...CHHHHCCHHHHHHHHHHHHHHHHHH CS
               Glyco_transf_28  54 ageklrrkl.spknlkeilkvlkavvkakkilkea 87 
                                   +++ ++++    +++ke+ k++ + +++kki+ e+
  gi|15669441|ref|NP_248251.1| 335 DIRNMKMYKrNASKMKELAKKYDGKKNIKKIIDEF 369
                                   55555554447788888888888888888888776 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.4e-05     0.054      57     140 ..      83     160 ..      17     170 .. 0.77
   2 ?   -3.0   0.0       2.8   6.2e+03     137     163 ..     231     260 ..     228     267 .. 0.78
   3 ?   -2.7   0.0       2.2     5e+03      63     100 ..     264     295 ..     237     298 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.4e-05
                Glyco_transf_4  57 slaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrv 137
                                      ++rr  +++++++pD++ +   ++ ++a   +++ l++p+++     y  +++k +  +  +   + ++ +  r+ r+
  gi|15669441|ref|NP_248251.1|  83 PKKAIRREINIIREYNPDLIISDCKYSTVVA---AKL-LKKPVICISNQNY--TRYKLKTDLIVYPTMKALNIINERCERF 157
                                   44567888999*************9999666...343.899*******999..5666666666677777777777777777 PP

                Glyco_transf_4 138 iav 140
                                   i++
  gi|15669441|ref|NP_248251.1| 158 IVP 160
                                   765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.8
                Glyco_transf_4 137 viavSeatadelreryg...vppekitVip 163
                                   +++ S ++a+ l++ ++   +++e++++ip
  gi|15669441|ref|NP_248251.1| 231 LVCGSYEVAKKLMRDLNlnsYKNENVEIIP 260
                                   678888888888888885556669999988 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.2
                Glyco_transf_4  63 rlrrllkrekpDvvHahspaalgaallalrrrlgiplV 100
                                    +++l+k  +  ++ +h+ ++ +  +  l    g+pl+
  gi|15669441|ref|NP_248251.1| 264 NMKELIK--NAELIVSHGGHSTIMEA--LS--FGKPLI 295
                                   4455555..77778788777665443..33..455655 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   2.5e-05     0.055      18     125 ..     202     300 ..     190     356 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                                   EEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES..STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEE CS
               Glycos_transf_1  18 ilsvgrlekeKgvdllikafallkkqlnpnvklviaG.ngeeekelkklaeelelsdnviflgevsredleellknadifv 97 
                                   + ++g +e++  +   +  +a   k+ n nvklv +G  +  +k +++l  +   ++nv+++      +++el+kna ++v
  gi|15669441|ref|NP_248251.1| 202 LSVIGGFEYRYKILEELGKIA--LKN-NLNVKLV-CGsYEVAKKLMRDLNLNSYKNENVEIIPITT--NMKELIKNAELIV 276
                                   555555555433322222222..233.7888875.8966666677788888888899****99998..************* PP

                                   EEESSBSS-HHHHHHHHTT--EEEETTT CS
               Glycos_transf_1  98 lpsisEgfGivllEAmaaglpviasnag 125
                                         g   +++EA+++g+p i+    
  gi|15669441|ref|NP_248251.1| 277 SH----GGHSTIMEALSFGKPLIVIPDL 300
                                   99....88899************98755 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00015      0.34      31      58 ..     240     272 ..     230     273 .. 0.90
   2 ?   -1.9   0.1       1.7   3.7e+03      28      39 ..     360     371 ..     357     378 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                          KH_5  31 kavsseLk.....gekidvvewseDlaefiana 58 
                                   k+++++L+     +e++++++ + +++e+i+na
  gi|15669441|ref|NP_248251.1| 240 KKLMRDLNlnsykNENVEIIPITTNMKELIKNA 272
                                   6778888888999******************98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                          KH_5  28 srikavsseLkg 39 
                                   ++ik++++e+ +
  gi|15669441|ref|NP_248251.1| 360 KNIKKIIDEFFE 371
                                   589999999864 PP

>> Mito_fiss_Elm1  Mitochondrial fission ELM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0021       4.6       2      85 ..      17     124 ..      16     144 .. 0.77
   2 ?    2.3   0.0     0.035        78     232     256 ..     274     298 ..     213     325 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0021
                Mito_fiss_Elm1   2 GaenQalGLaeaLgleievkrislkkllrvlrprg.............................adakeiaklaretlekp 53 
                                   G+++ ++++ eaL+ ++e+  i++ k  + ++++g                              ++k++ + + + +++ 
  gi|15669441|ref|NP_248251.1|  17 GHTTRCVAIGEALKNDYEISYIAYGKSKNFIEKYGfkvfetfpeiklkgkdgkfditssilnkeYSPKKAIRREINIIREY 97 
                                   99************99999999999999999999999999999****9999999999999988877788888888888889 PP

                Mito_fiss_Elm1  54 gPdlviaaGr.rtaslalalkrlaaekvfvVqi 85 
                                    Pdl+i+  + +t+++a +lk+       v++i
  gi|15669441|ref|NP_248251.1|  98 NPDLIISDCKySTVVAAKLLKK------PVICI 124
                                   ******9665155555566665......34444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.035
                Mito_fiss_Elm1 232 ivvTaDSvSMlsEAastgkpVyvlg 256
                                   ++v+    S ++EA+s gkp+ v++
  gi|15669441|ref|NP_248251.1| 274 LIVSHGGHSTIMEALSFGKPLIVIP 298
                                   45666777899***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2663.45
//
Query:       gi|15669442|ref|NP_248252.1|  [L=311]
Description: LPPG:FO 2-phospho-L-lactate transferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-49  167.8   0.5    3.9e-49  167.5   0.5    1.1  1  UPF0052   Uncharacterised protein family UPF0052
  ------ inclusion threshold ------
      0.086   12.6   0.0       0.14   12.0   0.0    1.2  1  AIM24     Mitochondrial biogenesis AIM24


Domain annotation for each model (and alignments):
>> UPF0052  Uncharacterised protein family UPF0052
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.5   0.5   4.3e-53   3.9e-49       1     263 [.       5     277 ..       5     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 167.5 bits;  conditional E-value: 4.3e-53
                                   EEEEE-CHHHHHHHHHHCCSS..CEEEEEE-----SHHHHHHHHHHTS---HHHHHHHHHH...--S-C..........HH CS
                       UPF0052   1 vvvlgGGtGlskllrglkevt..aeltavvtvaDdggssGelrrelgllaigDirnvlval...idder..........ll 66 
                                   ++vl+GGtG++kll+glk+v   +el ++v++++d+++         l+  +D+++vl++l   i++e+          ++
  gi|15669442|ref|NP_248252.1|   5 ITVLSGGTGTPKLLQGLKRVVnnEELAVIVNTGEDTWIGD-------LYLSPDVDTVLYTLadlINEETwygvkedtfyTH 78 
                                   89*******************999**************99.......**************88888888************ PP

                                   HHHCH-B-SS.....SSSSTT-BHHHHHHHHHHHHHS.-HHHHHHHHHHHTT-SSEEEES-SS--EEEEEET.TS-E..EE CS
                       UPF0052  67 eeLfqyRfkg.....dgdlaghslgnllLaalaeltg.sleeaiealskilkvrgrvlPatddpvelsaele.dGee..it 138
                                   e+L ++ f++     d+d a ++ ++ +L+      g +l+e+++  + +l+++++v+P+tdd+ve+++  + dG++  ++
  gi|15669442|ref|NP_248252.1|  79 EQLKNLGFDEvlrigDKDRALKMHKTYYLKR-----GhKLSEVVDMEKVALGIKAKVIPMTDDRVETKILAKvDGKVdlLK 154
                                   ******9999*********************.....99*****************************99885366667788 PP

                                   .STTTGGGG-S...-EEE.EEEESTT----HHHHHHHHH-SEEEE-SS-IIIIIHHHHTSCCHHHHHHH-SSEEEEE--SB CS
                       UPF0052 139 .geskisearklkapikr.vflepegaeaapevleaikeAdlivlgpGslytSiiPiLlvpgiaealreskakkvlvsnim 217
                                    ++ +++++   ++++ + ++ +   a++ ++++eaik++dl+++gp++++tSi+PiL ++gi+e l  +++k+v+vs+i+
  gi|15669442|ref|NP_248252.1| 155 fHDFWVKRK--GDVEVLDvIYENSLYAKPCEKAVEAIKNSDLVIIGPSNPITSIGPILSLNGIKELL--KDKKVVVVSPIV 231
                                   89****333..57999999999999******************************************..5699******** PP

                                   --TTTSTT-BHHHHHHHHHHCH-........SS....S...-SEEEEE-S---HHHH CS
                       UPF0052 218 tqkGetdgfsvsdhvkaieravg........kgvakay...vdavlvntsevpeell 263
                                   +      + +vs+++ ++++a g        ++    y   vd++++++   ++e+ 
  gi|15669442|ref|NP_248252.1| 232 G------NSAVSGPAGKLMKAKGydvsvkgiYEF---YkdiVDVLVIDNV--DKEIA 277
                                   9......****************77666333333...3666999999776..44444 PP

>> AIM24  Mitochondrial biogenesis AIM24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.5e-05      0.14      39     100 ..      14      79 ..       3      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.5e-05
                                   E.--------------EEEEEEES.SS-.EEEEE--SSSEEEEEEE.G.GTT.EEEEEGGGEEEEE CS
                         AIM24  39 t.gllkalkrlltgeslfllkftakiss.gtvllapklpgtivtle.l.gggdwlivqkdafLAat 100
                                   t +ll++lkr++ +e l +  +t++ +  g+++l+p++ + ++tl  l ++++w+ v+ d f  ++
  gi|15669442|ref|NP_248252.1|  14 TpKLLQGLKRVVNNEELAVIVNTGEDTWiGDLYLSPDVDTVLYTLAdLiNEETWYGVKEDTFYTHE 79 
                                   25899******************875559***********9999998888999**99999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2016.45
//
Query:       gi|15669443|ref|NP_248253.1|  [L=349]
Description: hypothetical protein MJ_1257 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-29  100.6   4.8      8e-29  100.6   4.8    2.4  3  THUMP            THUMP domain
    3.9e-11   43.4   0.0    6.7e-11   42.6   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
    5.1e-05   23.2   0.1    0.00032   20.6   0.0    2.2  2  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.058   14.1   0.0       0.18   12.5   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
       0.28   11.2   4.0        3.2    7.9   0.1    2.9  3  Ubiquitin_4      Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   4.8   2.2e-32     8e-29       2     142 ..      20     158 ..      19     160 .. 0.93
   2 ?    0.2   0.4       0.2   7.1e+02      23      78 ..     165     260 ..     159     270 .. 0.46
   3 ?   -3.2   0.0       2.3   8.2e+03      34      44 ..     307     317 ..     279     337 .. 0.60

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 2.2e-32
                                   HHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHC CS
                         THUMP   2 eieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeee 82 
                                   e+++l  ++k+ ++ +++     ++++ +++p+e  +++ke    +++  r+ip +++c++d+++i++a++ +++kk+e+ 
  gi|15669443|ref|NP_248253.1|  20 ELNKLPIKKKILWTPFRG-----ILKVLSQNPYEFLNIIKENKNNLKFSLRIIPLEIGCQTDINEIKKAISFLINKKKEKL 95 
                                   566666666766666666.....678889**************************************************** PP

                                   T-.EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT...-EE-SSS-SEEEEEEEETTEEEEEE CS
                         THUMP  83 ke.tFaVrvkrrgkhfeftsreinrevGkaivektg...lkVdlenPdivvrveiikdkayisi 142
                                   k+ +F Vr++rrg+h efts e++r++G+++ e+++   l+V+l+++d+ +++ei++d+ yisi
  gi|15669443|ref|NP_248253.1|  96 KNkSFVVRCNRRGNH-EFTSEELERIIGEYVLENFKdlnLRVNLKDWDFKINIEILQDESYISI 158
                                   99*************.**********************************************99 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.2
                                   EEEEECTEEEEEETHHHHHHHHHTST....................................TECEEEEE....EEEEESS CS
                         THUMP  23 rivvelkgekpeedeellkealekar....................................giqrvipv....cevcead 63 
                                   ++v+e++ ++++  +++++++l +++                                     +++v+ +    + +++++
  gi|15669443|ref|NP_248253.1| 165 ELVIEENIKNLKNLKRYIERPLNRSErkmqelmekfpfifenincvvdigsspggwakmlskKAKKVYAIdtgeLKIKANN 245
                                   555555555555555555555555543333333333333333333333333333333333333334444444445555555 PP

                                   HHHHHHHHHHHHHHH CS
                         THUMP  64 ledileaakeivkkk 78 
                                   +  i++ a++++ +k
  gi|15669443|ref|NP_248253.1| 246 IIHIKKRAENVDFEK 260
                                   555555555555555 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.3
                                   EETHHHHHHHH CS
                         THUMP  34 eedeellkeal 44 
                                   ++++e l++ l
  gi|15669443|ref|NP_248253.1| 307 KTKKEDLEKVL 317
                                   22222222222 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   1.9e-14   6.7e-11       3      95 ..     187     273 ..     186     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.9e-14
                                   CCHHHHHHHHHHHHT.-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHH.TTEEEECS-CCCSSHHHHHCH CS
                          FtsJ   3 sRsayKLleidekfk.lfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmapl.pgvttiqgditdpetiekike 81 
                                   +Rs  K++e+ ekf  +f++ + vvD+g++PGgw+++l+++    +kv+a+D+++ +   +++  i+    + + ++ i+e
  gi|15669443|ref|NP_248253.1| 187 NRSERKMQELMEKFPfIFENINCVVDIGSSPGGWAKMLSKKA---KKVYAIDTGELKIKaNNIIHIKKRAENVDFEKDINE 264
                                   7999**********957789999******************3...79*********8776888888777777777777775 PP

                                   CHHHSSEEEEEE-- CS
                          FtsJ  82 alserkvdlvvsDg 95 
                                        ++dl++ D 
  gi|15669443|ref|NP_248253.1| 265 -----EIDLITNDT 273
                                   .....578888774 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.26   9.2e+02     131     131 ..      96      96 ..      51     140 .. 0.56
   2 !   20.6   0.0   8.9e-08   0.00032       6     136 ..     190     319 ..     175     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.26
               Methyltransf_23 131 l 131
                                   +
  gi|15669443|ref|NP_248253.1|  96 K 96 
                                   1 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 8.9e-08
               Methyltransf_23   6 eeelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlI 86 
                                   e++++++ e+++   +  + v+diG   G +++ l+++ ++v+++D  +    +a +++  +k  ++ +++++ ++ +dlI
  gi|15669443|ref|NP_248253.1| 190 ERKMQELMEKFPFIFENINCVVDIGSSPGGWAKMLSKKAKKVYAIDTGEL-KIKANNIIHIKKRAENVDFEKDINEEIDLI 269
                                   46777777777776788889***************************755.4456699999999999999999******** PP

               Methyltransf_23  87 vlrevlehvpdppellrqiatllkpgGylllseplaslk.edrllldwlyl 136
                                   ++   l+  +++  +l+ +a++lk +Gy++++  +++lk  +++l+++l +
  gi|15669443|ref|NP_248253.1| 270 TNDTNLYPDESLFLTLK-FAKHLKTNGYIIHTLKARNLKtKKEDLEKVLKI 319
                                   **999998888777766.5667*********99999996555556665444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.4   8.7e+03      36      55 ..     124     143 ..      99     181 .. 0.56
   2 ?   12.5   0.0   5.1e-05      0.18       1      51 [.     210     259 ..     210     295 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.4
                                   HHHHHHHHTTTTEEEEESBC CS
               Methyltransf_25  36 aareraeeeglnvefvqgda 55 
                                   ++ e++++ +l+v++   d+
  gi|15669443|ref|NP_248253.1| 124 YVLENFKDLNLRVNLKDWDF 143
                                   44444544444554444444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.1e-05
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefv 51 
                                   v+d+G  +G ++++l+k+   +kv+++D  e  ++a +  + ++++ nv+f+
  gi|15669443|ref|NP_248253.1| 210 VVDIGSSPGGWAKMLSKKA--KKVYAIDTGELKIKANNIIHIKKRAeNVDFE 259
                                   89****************6..9******988777654433322222355554 PP

>> Ubiquitin_4  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1   0.00089       3.2       7      45 ..      61      99 ..      58     102 .. 0.87
   2 ?    3.8   0.1     0.016        58       9      42 ..     160     194 ..     153     199 .. 0.78
   3 ?   -3.0   0.1       2.1   7.6e+03      15      37 ..     247     269 ..     243     274 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00089
                   Ubiquitin_4  7 kldgeslevvvkqnatvkdLkkaierkvelklkrekekk 45
                                  k++ +++++++  +++++++kkai   +++k+++ k+k+
  gi|15669443|ref|NP_248253.1| 61 KFSLRIIPLEIGCQTDINEIKKAISFLINKKKEKLKNKS 99
                                  677788999999****************99999888776 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.016
                   Ubiquitin_4   9 dgeslevvvkqn.atvkdLkkaierkvelklkrek 42 
                                   ++e+ e+v+++n  ++k+Lk+ ier +++++++++
  gi|15669443|ref|NP_248253.1| 160 QDEFNELVIEENiKNLKNLKRYIERPLNRSERKMQ 194
                                   5566678888886789***********99877765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.1
                   Ubiquitin_4  15 vvvkqnatvkdLkkaierkvelk 37 
                                   + +k+ a+  d+ k i+++++l 
  gi|15669443|ref|NP_248253.1| 247 IHIKKRAENVDFEKDINEEIDLI 269
                                   56788888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1140  (0.0635841); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2186.31
//
Query:       gi|15669444|ref|NP_248254.1|  [L=67]
Description: histone A3 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-17   61.9   1.6    5.8e-17   61.7   1.6    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    4.3e-09   36.8   0.2    4.4e-09   36.8   0.2    1.0  1  Histone        Core histone H2A/H2B/H3/H4
      2e-05   24.6   1.4    2.3e-05   24.4   1.4    1.1  1  TAF            TATA box binding protein associated factor (TA
    7.5e-05   23.0   0.0    8.7e-05   22.8   0.0    1.2  1  CENP-S         CENP-S protein
     0.0016   18.6   0.4     0.0021   18.2   0.4    1.3  1  CENP-T_C       Centromere kinetochore component CENP-T histon
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.013   15.5   0.0    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
      0.029   14.8   0.1      0.035   14.6   0.1    1.2  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 
      0.038   14.0   0.0      0.042   13.9   0.0    1.1  1  Bromo_TP       Bromodomain associated
      0.064   13.3   0.0      0.068   13.2   0.0    1.2  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu
       0.07   13.2   0.0      0.074   13.1   0.0    1.1  1  MU2_FHA        Mutator 2 Fork head associated domain
      0.092   12.9   0.0      0.093   12.9   0.0    1.1  1  Polo_box_2     Polo box domain


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   1.6   3.6e-20   5.8e-17       1      65 []       2      65 ..       2      65 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 3.6e-20
                                  XXXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                 CBFD_NFYB_HMF  1 aeLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                  aeLP+a+  +I+k++ +a++++++A +++ae++ee + e+a+++++++k++krKt+k e++k A+
  gi|15669444|ref|NP_248254.1|  2 AELPVAPCVRILKKA-GAQRVSEAAGKYFAEALEEIALEIARKSVDLAKHAKRKTVKVEDVKAAL 65
                                  69*************.***********************************************97 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.2   2.7e-12   4.4e-09      65     129 ..       4      66 ..       1      67 [] 0.92

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.7e-12
                                   HHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                       Histone  65 lpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                   lp+a  vr ++k     +r+s  a  +++ealE +  e++  +  lakhaKR+T+  +D+++A+r
  gi|15669444|ref|NP_248254.1|   4 LPVAPCVRILKK--AGAQRVSEAAGKYFAEALEEIALEIARKSVDLAKHAKRKTVKVEDVKAALR 66 
                                   677777888887..889**********************************************99 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   1.4   1.4e-08   2.3e-05      17      66 .]      17      66 ..      10      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.4e-08
                                  T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH- CS
                           TAF 17 GitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsALr 66
                                  G + +s+ a +  ae +e+   ei+++++   +h+kR++  v+Dv +ALr
  gi|15669444|ref|NP_248254.1| 17 GAQRVSEAAGKYFAEALEEIALEIARKSVDLAKHAKRKTVKVEDVKAALR 66
                                  6677888899999************************************9 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   5.4e-08   8.7e-05      26      71 ..      25      66 ..       7      67 .] 0.68

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.4e-08
                        CENP-S 26 atkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLlaR 71
                                  a k f +al e+  + +++ + DL   akHAkR+t++++Dv+  +R
  gi|15669444|ref|NP_248254.1| 25 AGKYFAEALEEIALE-IARKSVDL---AKHAKRKTVKVEDVKAALR 66
                                  555555566555543.44445665...9*************98777 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.4   1.3e-06    0.0021      25      75 ..      16      66 ..       3      67 .] 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                      CENP-T_C 25 gskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmk 75
                                  +  ++++++a k   +a+++    +++     akHa+RKt++ +Dv + ++
  gi|15669444|ref|NP_248254.1| 16 AGAQRVSEAAGKYFAEALEEIALEIARKSVDLAKHAKRKTVKVEDVKAALR 66
                                  34556666666666666666666666666679**************98776 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   8.2e-06     0.013      13      67 ..      11      65 ..       5      67 .] 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.2e-06
                   TFIID-31kDa 13 liLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAi 67
                                   iL++ g + ++e   + + +       ++ + +  la+hak+k+v+++dv+ A+
  gi|15669444|ref|NP_248254.1| 11 RILKKAGAQRVSEAAGKYFAEALEEIALEIARKSVDLAKHAKRKTVKVEDVKAAL 65
                                  699999999999999999**********************************997 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.1e-05     0.035      32      62 ..      35      65 ..      17      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                                  HHHHHHHHHHHHHHHHTT-SEE-HHHHHHHH CS
                   TFIID_20kDa 32 dFvesvtkfacklakhRksdklevrDiqlhl 62
                                  +   ++  +++ lakh k +++ v D++  l
  gi|15669444|ref|NP_248254.1| 35 EIALEIARKSVDLAKHAKRKTVKVEDVKAAL 65
                                  55567999*******************9655 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.5e-05     0.042      14      68 ..      11      65 ..       4      67 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                                  HHHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHH CS
                      Bromo_TP 14 qileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvltL 68
                                   il++aG  ++ e+a   + e +++  +e++++    a ha R +++++Dv  +L
  gi|15669444|ref|NP_248254.1| 11 RILKKAGAQRVSEAAGKYFAEALEEIALEIARKSVDLAKHAKRKTVKVEDVKAAL 65
                                  688888888888888877888888888******9999**************9988 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.2e-05     0.068      30      65 ..      31      66 ..      15      67 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                                  HHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXXX CS
                   TFIID-18kDa 30 dlvrgyliellqqaakvaklrgsrkitlEDllfliR 65
                                  + +++   e+  +++++ak+ +++ +++ED++ ++R
  gi|15669444|ref|NP_248254.1| 31 EALEEIALEIARKSVDLAKHAKRKTVKVEDVKAALR 66
                                  556677789**********************99988 PP

>> MU2_FHA  Mutator 2 Fork head associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.5e-05     0.074      40      75 ..       9      44 ..       2      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                       MU2_FHA 40 ativvlraGvvrvaallGkvfvnglekgvadiskkd 75
                                   + ++ +aG  rv+ + Gk f + le++  +i++k 
  gi|15669444|ref|NP_248254.1|  9 CVRILKKAGAQRVSEAAGKYFAEALEEIALEIARKS 44
                                  56678899************************9985 PP

>> Polo_box_2  Polo box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.7e-05     0.093       7      39 ..      13      45 ..       5      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-05
                                  -TT-TT-EEE-SSEEEEEEETTEEEEEEE-TTS CS
                    Polo_box_2  7 ierleGqrvvtaaGryiveddtlvvfevanksn 39
                                  +++ + qrv  aaG+y  e  + + +e+a ks 
  gi|15669444|ref|NP_248254.1| 13 LKKAGAQRVSEAAGKYFAEALEEIALEIARKSV 45
                                  4667889***********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 470.88
//
Query:       gi|15669445|ref|NP_248255.1|  [L=240]
Description: uridylate kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-33  114.7   2.6    7.3e-33  114.1   2.6    1.2  1  AA_kinase       Amino acid kinase family
  ------ inclusion threshold ------
      0.043   13.7   0.0      0.062   13.2   0.0    1.3  1  Ploopntkinase3  P-loop Nucleotide Kinase3
       0.12   12.6   0.0        3.5    7.9   0.0    2.7  2  Mur_ligase_C    Mur ligase family, glutamate ligase domain


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   2.6   1.2e-36   7.3e-33       1     240 [.      15     218 ..      15     219 .. 0.93

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 1.2e-36
                                   TEEEEEE-TTCCCCTCC...HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC....E..HHHHHH CS
                     AA_kinase   1 krvVvKlGGssltdkee...aslrrlaeqiaalkesgnklvvVhGggsftdgllal..ksglssgelaaglrstleeagev 76 
                                   +r+V  lGGs++ +ke+   +++ ++a++ +++k +g+++++V+Ggg+++++++++  + g s+++               
  gi|15669445|ref|NP_248255.1|  15 MRIVFDLGGSVVMPKEGakaEKIMEYANIFKKIKDEGHEVAIVVGGGKTAREYIEIgrELGASESFC-------------- 81 
                                   79999*****99977777**************************************66666666666.............. PP

                                   HHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEE CS
                     AA_kinase  77 atrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgr 157
                                      d+l+++++r++a++l  +l +++++  ++  +                  + e +l+ g++pv++g     ++g+   
  gi|15669445|ref|NP_248255.1|  82 ---DELGIMATRMNAMILITALGDYSIKKVPTSFE------------------EAELILNLGKIPVMGGT----HPGH--- 134
                                   ...9**************************99955..................55669999********5....4888... PP

                                   E-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-E CS
                     AA_kinase 158 gssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaalaaarrggip 236
                                    ++D +aa lAe ++Ad l+i t+VdGVyd+dp+k +da++++++s++e+ +  ++s l  g+  v+++ a+++++r++ +
  gi|15669445|ref|NP_248255.1| 135 -TTDAVAASLAEFINADLLVIGTNVDGVYDKDPNKYEDAKKFDKMSAKELVDlaISSSLKAGSSSVVDLLAAKIIERAKLK 214
                                   .9*****************************************************************************99 PP

                                   EEEE CS
                     AA_kinase 237 vvIt 240
                                   v ++
  gi|15669445|ref|NP_248255.1| 215 VAVV 218
                                   9987 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     1e-05     0.062     120     184 ..     169     233 ..     135     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                Ploopntkinase3 120 hdqadawrkarskklgrvqneswvkgrlsasrkladalikaaekgkvkvlaGhPdelrsileeii 184
                                   +++a+++ k  +k+l      s +k+  s++ +l +a i +++k kv v++G P+el ++ + ii
  gi|15669445|ref|NP_248255.1| 169 YEDAKKFDKMSAKELVDLAISSSLKAGSSSVVDLLAAKIIERAKLKVAVVKGTPEELLNVSKGII 233
                                   67999999999****99999999**99999999999988899999************99888776 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.052   3.1e+02      31      68 ..      41      74 ..      24     105 .. 0.63
   2 ?    7.9   0.0   0.00059       3.5      22      76 ..     134     184 ..     122     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.052
                                  HHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHHHHHHH CS
                  Mur_ligase_C 31 lkalreiapdkrlilvfgpggelgertrtfhdefgrla 68
                                   + +++i ++++ ++++  gg    +t+ ++ e+gr +
  gi|15669445|ref|NP_248255.1| 41 ANIFKKIKDEGHEVAIVV-GGG---KTAREYIEIGREL 74
                                  555566655444444444.334...4555555555544 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00059
                                   -SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEEE CS
                  Mur_ligase_C  22 hnpdslsaalkalreiapdkrlilvfgpggelgertrtfhdefgrlasaladslv 76 
                                   h+ d++ a l+ +     +  l+++ +  +  ++++ +++++ ++  ++ a +lv
  gi|15669445|ref|NP_248255.1| 134 HTTDAVAASLAEF----INADLLVIGTNVDGVYDKDPNKYEDAKKFDKMSAKELV 184
                                   5555555555555....5789***********************99998777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1890.87
//
Query:       gi|15669446|ref|NP_248256.1|  [L=131]
Description: 30S ribosomal protein S6e [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-44  149.1   0.0    6.7e-44  148.9   0.0    1.0  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.9   0.0   3.7e-48   6.7e-44       2     124 ..       5     121 ..       4     122 .. 0.98

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 3.7e-48
                                   EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEETTSSS CS
                 Ribosomal_S6e   2 klnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlskggvg 82 
                                   k++++dp+tg+ ++ie+   + + l+gk+ige +dg+++G  l+gy+l+i gg+d +Gfpm+++++++++vr+Lls   +g
  gi|15669446|ref|NP_248256.1|   5 KFVVADPKTGRCYQIEA---DNTPLVGKKIGEVFDGKIIG--LEGYKLQIRGGTDSSGFPMRPDIHGSRKVRVLLSA-PPG 79 
                                   89*************98...67899***************..***********************************.*** PP

                                   S-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--SS--TTTS CS
                 Ribosomal_S6e  83 yrprrkGerkrksvrGcivsadisqlnlvivkkgekdieglt 124
                                   ++p+rkGer+rk+vrG++++ di+q+n+++v++gek+i++l+
  gi|15669446|ref|NP_248256.1|  80 FKPKRKGERRRKTVRGNTIAPDIVQINVKVVEYGEKSIPELL 121
                                   ****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 985.82
//
Query:       gi|15669447|ref|NP_248257.1|  [L=437]
Description: translation initiation factor IF-2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-34  116.1   0.3    1.8e-33  114.6   0.3    1.8  1  eIF2_C          Initiation factor eIF2 gamma, C terminal
    2.3e-31  108.8   0.3    1.5e-30  106.2   0.3    2.0  1  GTP_EFTU        Elongation factor Tu GTP binding domain
    3.9e-08   33.6   0.9    1.1e-07   32.1   0.9    1.9  1  GTP_EFTU_D2     Elongation factor Tu domain 2
    6.2e-06   26.2   1.7    5.7e-05   23.1   0.2    2.4  2  RsgA_GTPase     RsgA GTPase
    0.00032   20.7   0.0    0.00086   19.4   0.0    1.8  1  MMR_HSR1        50S ribosome-binding GTPase
    0.00054   19.9   2.5      0.001   19.0   2.5    1.4  1  Nop10p          Nucleolar RNA-binding protein, Nop10p family
    0.00072   19.5   0.3    0.00072   19.5   0.3    1.7  1  MMR_HSR1_Xtn    C-terminal region of MMR_HSR1 domain
     0.0022   17.5   2.8     0.0055   16.2   2.8    1.7  1  RecR            RecR protein
     0.0039   17.0   0.2          2    8.1   0.0    2.4  2  PduV-EutP       Ethanolamine utilisation - propanediol utilis
  ------ inclusion threshold ------
      0.011   13.7   0.1      0.012   13.5   0.1    1.1  1  PolC_DP2        DNA polymerase II large subunit DP2
      0.016   14.7   1.0        1.4    8.5   0.2    2.5  2  FeoB_N          Ferrous iron transport protein B
      0.072   13.0   1.7       0.12   12.3   1.7    1.4  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.089   12.8   0.6        2.3    8.3   0.0    2.6  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.17   10.6   0.2       0.25   10.1   0.2    1.2  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.23   10.6   0.6       0.89    8.6   0.1    1.9  2  G-alpha         G-protein alpha subunit
       0.38   10.4   6.8        1.3    8.7   6.8    1.8  1  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding


Domain annotation for each model (and alignments):
>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6   0.3   1.6e-36   1.8e-33       2      86 .]     351     435 ..     350     435 .. 0.99

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 1.6e-36
                                   EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSEEEEE CS
                        eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrWrLiG 82 
                                   +++i+ +ll+r+vg+kee k+e+l+++EvLmlniG+a+t gv+ts+++d a++kLk P+cae+g+++a+sRrv++rWrLiG
  gi|15669447|ref|NP_248257.1| 351 KITIRANLLDRVVGTKEELKIEPLRTGEVLMLNIGTATTAGVITSARGDIADIKLKLPICAEIGDRVAISRRVGSRWRLIG 431
                                   79******************************************************************************* PP

                                   EEEE CS
                        eIF2_C  83 wGei 86 
                                   +G+i
  gi|15669447|ref|NP_248257.1| 432 YGTI 435
                                   **98 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.3   1.3e-33   1.5e-30       4     193 ..      38     226 ..      35     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 1.3e-33
                                   EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.................... CS
                      GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.................... 64 
                                   +nig++ghvDhGKt+Lt +L+                  +D+++eE +rgi+i    + +e                    
  gi|15669447|ref|NP_248257.1|  38 VNIGMVGHVDHGKTSLTKALTGV---------------WTDRHSEELRRGISIRLGYADCEirkcpqcgtyttkprcpncl 103
                                   79******************922...............4788888999999999999999999999999999999999998 PP

                                   .TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESCGST.HHHHHH CS
                      GTP_EFTU  65 .ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKmDrl.kaelke 141
                                    +++  ++++++D+PGH+  + ++  g++ +Dga+lv++a+e  ++pqt+e+l  +  +g+  ii++ NK+D + +++ +e
  gi|15669447|ref|NP_248257.1| 104 aETEFLRRVSFVDSPGHETLMATMLSGASLMDGAILVIAANEPcPQPQTKEHLMALEILGIDkIIIVQNKIDLVdEKQAEE 184
                                   6677889**********************************9879****************9999*********7777888 PP

                                   HHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                      GTP_EFTU 142 iveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                     e++k ++      ++   ++   + p++++Sa +  +++ ll+a+ +++p
  gi|15669447|ref|NP_248257.1| 185 NYEQIK-EF------VKGTIAE---NAPIIPISAHHEANIDVLLKAIQDFIP 226
                                   888888.66......4444433...57********************99998 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.9     1e-10   1.1e-07       1      73 [.     258     339 ..     258     340 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1e-10
                                   EEEEEEEEEESEEETTEEEEEEC.TCTTSEE......EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS...GSSTTC CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke......ivtrissletfhededeavaganaGvivaikgled...aiivGd 71 
                                   G+v +g +++G++k+Gde++i++  ++ + +       +t+i sl + +  ++ a +g+ +Gv++ ++++ +   a ++G+
  gi|15669447|ref|NP_248257.1| 258 GGVLGGAIIQGVFKVGDEIEIRPgIKVTEGNktfwkpLTTKIVSLAAGNTILRKAHPGGLIGVGTTLDPYLTksdA-LTGS 337
                                   8899*******************966644447************************************99886645.7777 PP

                                   EE CS
                   GTP_EFTU_D2  72 tl 73 
                                   ++
  gi|15669447|ref|NP_248257.1| 338 VV 339
                                   75 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.14   1.6e+02     103     136 ..      41      71 ..      10     123 .. 0.75
   2 !   23.1   0.2   5.1e-08   5.7e-05      13      99 ..     131     223 ..     104     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.14
                                   EEECSTTSSHHHHHHHHCTT-----S-------- CS
                   RsgA_GTPase 103 vlvGqSGvGKStLinallpelelktgevseklgr 136
                                    +vG+   GK++L +al++     t   se+l+r
  gi|15669447|ref|NP_248257.1|  41 GMVGHVDHGKTSLTKALTGV---WTDRHSEELRR 71 
                                   37788889*********986...44444444444 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 5.1e-08
                                   EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE--TTT CS
                   RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllvsakt 86 
                                   ++ +d +++v++++ep  ++++ +  L+++e  gi +++iv nKiDl++e++      +++e+ + + a + +++ +sa++
  gi|15669447|ref|NP_248257.1| 131 ASLMDGAILVIAANEPCPQPQT-KEHLMALEILGIdKIIIVQNKIDLVDEKQaeenyeQIKEFVKGTIAENAPIIPISAHH 210
                                   778999********88777765.6679999*****7888999********999996666666677777789999******* PP

                                   HTTHHHHHHHCTT CS
                   RsgA_GTPase  87 kegleelkellkd 99 
                                   +++++ l ++++d
  gi|15669447|ref|NP_248257.1| 211 EANIDVLLKAIQD 223
                                   ***9999998876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   7.7e-07   0.00086       1     113 [.      39     172 ..      39     206 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.7e-07
                                   EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE..ETTEE.........................EEEEEC CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk..lkgke.........................ielvDt 53 
                                   +++ vG+   GK++L +altg  + + s++    + i+ g  +  ++  +                         + +vD 
  gi|15669447|ref|NP_248257.1|  39 NIGMVGHVDHGKTSLTKALTGVwTDRHSEELRRGISIRLGYADceIR--KcpqcgtyttkprcpnclaeteflrrVSFVDS 117
                                   5899****************965455555555555554444442233..12234445555555555555556666****** PP

                                   GGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT...TTCSHHHHHHHHHHHHH.TTSEEEEEEE CS
                      MMR_HSR1  54 pGliegaseekglgkaflalee.adlillvvdas...eeklkpldeeleellee.akkplilvln 113
                                   pG  e       l  ++l+  + +d ++lv+ a+       +p+ +e    le    +++i+v n
  gi|15669447|ref|NP_248257.1| 118 PG-HE------TLMATMLSGASlMDGAILVIAANepcP---QPQTKEHLMALEIlGIDKIIIVQN 172
                                   **.44......788888887776799999998774330...333333333332211123444444 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   2.5   9.3e-07     0.001       4      28 ..      83     107 ..      81     109 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.3e-07
                                   --EE-TTT--EESSSB-TTT-SB-B CS
                        Nop10p   4 ylrkcgkcrvYTLkkvcpecggptk 28 
                                    +rkc++c++YT k +cp+c ++t+
  gi|15669447|ref|NP_248257.1|  83 EIRKCPQCGTYTTKPRCPNCLAETE 107
                                   69******************99885 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   6.4e-07   0.00072      57     100 ..     166     221 ..     164     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.4e-07
                  MMR_HSR1_Xtn  57 pclyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                   + ++v NKiDl+++++ +e +++              +++iSa++e n+d L+++i
  gi|15669447|ref|NP_248257.1| 166 KIIIVQNKIDLVDEKQAEENYEQikefvkgtiaenAPIIPISAHHEANIDVLLKAI 221
                                   5799*******99999988888667888999987668999************9988 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.8   4.9e-06    0.0055      15      35 ..      83     103 ..      76     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.9e-06
                                   H-EE-TTT--EESSSS-CCCC CS
                          RecR  15 kvrhCsrCgnlteedlCaICs 35 
                                   ++r C++Cg++t++  C+ C 
  gi|15669447|ref|NP_248257.1|  83 EIRKCPQCGTYTTKPRCPNCL 103
                                   79******************7 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0018         2       4      23 ..      40      59 ..      37      69 .. 0.88
   2 !    6.6   0.1    0.0053         6      67     142 ..     137     222 ..     106     223 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0018
                     PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                  i ++G+v+ GKt+Lt+al+g
  gi|15669447|ref|NP_248257.1| 40 IGMVGHVDHGKTSLTKALTG 59
                                  5689*************987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0053
                     PduV-EutP  67 ialvqdateeesvfppgfasvfnkeviGi....i..tkidlaed...eenieaveelLksaGaek..ifevsavekegiee 136
                                     lv +  +e +  p++  ++++ e++Gi    i   kidl+++   een e+ +e++k   ae+  i+ +sa ++ +i+ 
  gi|15669447|ref|NP_248257.1| 137 AILVIA-ANEPCPQPQTKEHLMALEILGIdkiiIvqNKIDLVDEkqaEENYEQIKEFVKGTIAENapIIPISAHHEANIDV 216
                                   333333.34445667777777777777744432223688887441115667777777776555443389************ PP

                     PduV-EutP 137 llkyle 142
                                   llk ++
  gi|15669447|ref|NP_248257.1| 217 LLKAIQ 222
                                   999886 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.1e-05     0.012     614     650 ..      80     116 ..      31     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                      PolC_DP2 614 veiarrkCkkCgketlearCeeCgekteeklvCkkce 650
                                   ++ + rkC++Cg+ t++ rC++C ++te   + + ++
  gi|15669447|ref|NP_248257.1|  80 ADCEIRKCPQCGTYTTKPRCPNCLAETEFLRRVSFVD 116
                                   567789********************99876665555 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.022        24       2      23 ..      39      60 ..      38      63 .. 0.90
   2 ?    8.5   0.2    0.0012       1.4     100     156 .]     160     221 ..     132     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.022
                                  EEEEEESTTSSHHHHHHHHHTT CS
                        FeoB_N  2 tvalvGnpnvGkttlfnaltga 23
                                  ++ +vG  + Gkt+l  altg+
  gi|15669447|ref|NP_248257.1| 39 NIGMVGHVDHGKTSLTKALTGV 60
                                  6889****************96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0012
                                   HHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHH......TS-EEEEBTTTTBTHHHHHHHH CS
                        FeoB_N 100 qllelgvpvvlalnmideaekkgieidlkkLsekL......gvpvvktsakkkegieellkai 156
                                   ++l ++ +++++ n+id +++k+ e + ++++e +      + p++++sa+++ +i+ llkai
  gi|15669447|ref|NP_248257.1| 160 EILGID-KIIIVQNKIDLVDEKQAEENYEQIKEFVkgtiaeNAPIIPISAHHEANIDVLLKAI 221
                                   444443.688999******************9988333333489*************999986 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.7   0.00011      0.12      11      34 ..      84     105 ..      83     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                       DUF35_N  11 gqrCpdCGtvqfPPravCphCgsd 34 
                                   +++Cp CGt+     + Cp+C++ 
  gi|15669447|ref|NP_248257.1|  84 IRKCPQCGTYT--TKPRCPNCLAE 105
                                   689*******7..88******764 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.1      0.35     4e+02       4       9 ..      86      91 ..      85      95 .. 0.86
   2 ?    8.3   0.0     0.002       2.3       3      15 ..      97     115 ..      92     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.35
                PhnA_Zn_Ribbon  4 kCplCa 9 
                                  kCp+C+
  gi|15669447|ref|NP_248257.1| 86 KCPQCG 91
                                  899996 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.002
                PhnA_Zn_Ribbon   3 pkCplCaSeytY......e 15 
                                   p Cp+C +e++       +
  gi|15669447|ref|NP_248257.1|  97 PRCPNCLAETEFlrrvsfV 115
                                   99*******9875555551 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00022      0.25     505     537 ..      82     112 ..       8     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                                   --EEEETT.--EESSSB-TTT--BE.EEEEEES CS
                          NRDD 505 pkidvCnecgykgeiekCpkCgseeevevirRi 537
                                    +i  C++cg+  ++ +Cp+C    e+e +rR+
  gi|15669447|ref|NP_248257.1|  82 CEIRKCPQCGTYTTKPRCPNCL--AETEFLRRV 112
                                   56889******999989*****..668999998 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00079      0.89      12      55 ..      27      69 ..      15      79 .. 0.77
   2 ?   -0.2   0.0      0.39   4.4e+02     272     294 ..     167     192 ..     156     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00079
                                  XXXXXXXXE..EEEEEEEESTTSSHHHHHHHHHHHCS----HHH CS
                       G-alpha 12 kaerkarkkkrevkllllGqseSGKsTilkqlkllykkgfseee 55
                                   a++k+  k+ ev++ ++G+ + GK+++ k l  + ++ +see 
  gi|15669447|ref|NP_248257.1| 27 MAKKKQA-KQAEVNIGMVGHVDHGKTSLTKALTGVWTDRHSEEL 69
                                  3444444.458*********************999999999884 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.39
                                   EEEEEE-HHHHHHHCCCS...-GGGC CS
                       G-alpha 272 iiLflnKlDileeKlkkg...klsky 294
                                   ii++ nK+D+  eK  ++   +++++
  gi|15669447|ref|NP_248257.1| 167 IIIVQNKIDLVDEKQAEEnyeQIKEF 192
                                   8999999**99999955512444444 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.8    0.0011       1.3      10      20 ..      84      94 ..      83     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                       zf-tcix 10 vrkCpkCGtyN 20
                                  +rkCp+CGty 
  gi|15669447|ref|NP_248257.1| 84 IRKCPQCGTYT 94
                                  8********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2507.08
//
Query:       gi|15669448|ref|NP_248258.1|  [L=389]
Description: hypothetical protein MJ_1262 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-41  143.0   5.6    1.8e-41  142.5   5.6    1.1  1  NurA      NurA domain


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.5   5.6   9.9e-46   1.8e-41       4     242 .]      71     359 ..      69     359 .. 0.97

  Alignments for each domain:
  == domain 1  score: 142.5 bits;  conditional E-value: 9.9e-46
                                   EEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGGCCSCEEEE CS
                          NurA   4 aAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElklgallleekgedllll 84 
                                   a+ DGS+++ ++ ++ +y ++a+++++g +e++++a++   +d+++p d+ e+rir++m tlElk++++ l++ ++d++++
  gi|15669448|ref|NP_248258.1|  71 AGGDGSCNKLDYISFSFYGVGAVSFIHGRGEKVKKAKEEYIFDITHPLDI-EDRIRRYMLTLELKTALYVLKNYNIDYYIF 150
                                   899***********************************************.****************************** PP

                                   ECSHHCCCH.............................................HHHHHHHHHHHHHHHHHHHHHTT-.TT CS
                          NurA  85 DGsligslv.............................................efdelheeleyeeylyslsrllea.gl 119
                                   DGsl+  l+                                              ++++++  e+ ey+ +l +l+++ + 
  gi|15669448|ref|NP_248258.1| 151 DGSLFSLLIftkkgiemyereleeiyneygkefnkkideetksgeigiiskdlnLELNKKILVEHVEYILTLTKLINEfKD 231
                                   ********************************************************************************* PP

                                   CEEEEESS-SCTCCHCCC......S--HHHHCCHHCCHCH---STTS-HHHHTT...................-HCCHHHH CS
                          NurA 120 nlvgvaKsfrskellnllletlligesisDiallgallrkpgytspllkilrek...................pllreali 181
                                   +++g++K+++ ++++ ++         ++Dia++ ++++k+gy++p+  ++                      ++++ ++ 
  gi|15669448|ref|NP_248258.1| 232 RIIGISKTSKINIYFDKN---------MPDIAIFTKYTDKSGYSEPIDFVNKLGdekkekhkqlssvvkginfIKNKPFYA 303
                                   ******************.........**********************998889************************** PP

                                   HH-.EEEEEEESSTTTTEEEEEHHHHHH.CCHHHHHHHHHH..TTB-SSSBCCHHHHHHHHCC CS
                          NurA 182 dke.iyfaYvrlegggsilrleipaevs.takdedvlsllasqrlsisGYprpLalAhelaki 242
                                   + +  y+++vrle +  ++ l      s  + d++vls+l   ++si+GYp++L++ he ++i
  gi|15669448|ref|NP_248258.1| 304 KIDtAYIQFVRLEDNCGVVGLT-----SfNKIDKEVLSSLK--EISINGYPYILKKSHETVEI 359
                                   ************5555555555.....446***********..*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1050  (0.0585643); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2349.40
//
Query:       gi|15669449|ref|NP_248259.1|  [L=651]
Description: methionyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.5e-161  537.5   0.5     2e-161  537.1   0.5    1.1  1  tRNA-synt_1g    tRNA synthetases class I (M)
    8.9e-33  112.3   0.7    1.6e-32  111.4   0.7    1.5  1  tRNA_bind       Putative tRNA binding domain
    1.5e-27   96.2   4.4    3.5e-10   38.8   0.3    3.9  3  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    2.3e-15   56.7   0.0    4.9e-08   32.7   0.0    2.5  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
    5.2e-08   33.0   0.9    5.2e-08   33.0   0.9    1.9  2  Anticodon_1     Anticodon-binding domain of tRNA
  ------ inclusion threshold ------
      0.013   14.5   0.4       0.26   10.2   0.0    2.6  3  tRNA-synt_1f    tRNA synthetases class I (K)
      0.074   11.7   0.0       0.12   11.0   0.0    1.2  1  ILVD_EDD        Dehydratase family
      0.074   13.1   7.2       0.16   12.0   7.2    1.6  1  DZR             Double zinc ribbon
        0.3   11.1   5.4          2    8.4   0.3    2.7  2  DUF1610         Domain of unknown function (DUF1610)
       0.55   10.2   5.0        2.9    8.0   5.0    2.2  1  zinc-ribbons_6  zinc-ribbons
        2.4    8.1   6.0    1.4e+02    2.5   6.0    2.5  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
        3.4    7.8   8.0        1.6    8.8   2.3    2.6  2  DUF1272         Protein of unknown function (DUF1272)


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  537.1   0.5  1.4e-164    2e-161       1     391 []       3     384 ..       3     384 .. 0.99

  Alignments for each domain:
  == domain 1  score: 537.1 bits;  conditional E-value: 1.4e-164
                                   EEEEE--B--SS---HHHHH.HHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1g   1 vlvttalpYangklHlGhll.evisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkk 80 
                                   +l+ttal+Y+ng+lHlGh++ ++i+aDi+++y +lrge+v++v+gtD+hG+pi+l+Aekeg +pee+vek+h+eike+++ 
  gi|15669449|ref|NP_248259.1|   3 YLITTALAYTNGPLHLGHARsTYIPADIIYKYLKLRGEDVIHVGGTDNHGVPITLTAEKEGKSPEEIVEKYHNEIKEDLDL 83 
                                   69******************9************************************************************ PP

                                   TT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE-TTSSB-E. CS
                  tRNA-synt_1g  81 lnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqceecgkklep 161
                                   l+++fd++g+t+s+ h e++qe++ klke+g+iyekeieq+ycp++++flpdryveg CP+c+  eargd+ce cg++lep
  gi|15669449|ref|NP_248259.1|  84 LGVEFDAFGKTHSQIHIETAQEFYLKLKENGYIYEKEIEQFYCPNCKKFLPDRYVEGICPYCG-GEARGDHCEVCGRHLEP 163
                                   ***************************************************************.67*************** PP

                                   ...............EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EETTECC CS
                  tRNA-synt_1g 162 telinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvPgaek 242
                                    el++p ++i++ kpe+++t+h+ffkls+++k+l+e+i ++ ke++e+vk+++++w+ke L+d++isrd++wG+p+Pg ++
  gi|15669449|ref|NP_248259.1| 164 FELKDPYCVICKGKPEIRKTKHHFFKLSALKKELEEYI-KNAKEMPEHVKNMALNWIKE-LHDWDISRDISWGVPIPG-TN 241
                                   **************************************.8888***************9.*****************6.78 PP

                                   EEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH.TT----S-EEEE--EE CS
                  tRNA-synt_1g 243 kvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillg.aelklpkkvvaheylt 322
                                   +v+YVWl+A+igYis+tk+l       e wk+yW  +k+++++hfigkdi+ +H++fwP +l++  +++lp++vv+ +ylt
  gi|15669449|ref|NP_248259.1| 242 QVMYVWLEAPIGYISFTKMLG------EIWKKYW-LEKDTKIYHFIGKDITVHHAVFWPGMLIAhGSFNLPTAVVSGGYLT 315
                                   9******************97......99*****.889**************************899************** PP

                                   E--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHHHHHHHHH. CS
                  tRNA-synt_1g 323 vegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNseLadklgnlvnRvl 391
                                   +eg+K+S+S+++vv++k++++++dad+lRYyl+++ap  kD+dfs++df +++N+eL++ +gn+ +Rvl
  gi|15669449|ref|NP_248259.1| 316 LEGRKMSTSKRWVVWVKDFVKNFDADYLRYYLIMSAPLFKDCDFSFDDFKNKINNELINIIGNFTHRVL 384
                                   *******************************************************************85 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   0.7   1.1e-35   1.6e-32       1      96 []     556     649 ..     556     649 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 1.1e-35
                                   EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECCESSC CS
                     tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeeldeke 81 
                                   lrvG+v+eae++p+++kLl+l vd+G+e+ rqivsg+k +y+pe+lv+kkv+v++nlkp+kl Gv SeGMil+ae+ de++
  gi|15669449|ref|NP_248259.1| 556 LRVGEVVEAEDIPKSKKLLKLMVDLGDEK-RQIVSGIKGYYKPEDLVGKKVIVICNLKPAKLCGVLSEGMILAAED-DEGN 634
                                   79***************************.*********************************************5.**** PP

                                   EEEEEESST--TTCE CS
                     tRNA_bind  82 vgilelpadveaGek 96 
                                   v++l++++d++aG+k
  gi|15669449|ref|NP_248259.1| 635 VSLLTVDKDIKAGSK 649
                                   *************85 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.3   2.4e-13   3.5e-10      25     175 ..       3     135 ..       1     140 [. 0.88
   2 !   38.2   0.5   3.6e-13   5.4e-10     354     432 ..     160     238 ..     157     273 .. 0.95
   3 !   17.2   0.0   8.1e-07    0.0012     557     601 ..     314     359 ..     303     360 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.4e-13
                   tRNA-synt_1  25 filvdgPPyvtGslHiGhalaktl.kdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefrekv 104
                                   + ++    y +G lH+Gha  + +  di+ +y +++G++v +v G+D +G++i  + ek+ g++                 
  gi|15669449|ref|NP_248259.1|   3 YLITTALAYTNGPLHLGHARSTYIpADIIYKYLKLRGEDVIHVGGTDNHGVPITLTAEKE-GKSP---------------- 66 
                                   6666667799*********9998857****************************999998.3433................ PP

                   tRNA-synt_1 105 rewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktalse 175
                                    e++++y++ei++++  lGv   fd   +T ++   e+ +e + +l ++g iy+ +   ++++++k  l +
  gi|15669449|ref|NP_248259.1|  67 EEIVEKYHNEIKEDLDLLGV--EFDAFGKTHSQIHIETAQEFYLKLKENGYIYEKEIEQFYCPNCKKFLPD 135
                                   378999*************7..577888999999999999************************9987765 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 3.6e-13
                   tRNA-synt_1 354 kaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswleniqdWciSRqrwWGhrip 432
                                   + e++e++ p+c   k   + r t+  f ++++l++++ + +++++ +p+  +++  +w+++ +dW iSR+  WG++ip
  gi|15669449|ref|NP_248259.1| 160 HLEPFELKDPYCVICKGKPEIRKTKHHFFKLSALKKELEEYIKNAKEMPEHVKNMALNWIKELHDWDISRDISWGVPIP 238
                                   57899999*****999999***********************************************************9 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 8.1e-07
                   tRNA-synt_1 557 rdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                   +  eGrKmS s+  v+  +d +k+  ad lR++li +++  +d ++
  gi|15669449|ref|NP_248259.1| 314 LTLEGRKMSTSKRWVVWVKDFVKNFDADYLRYYLImSAPLFKDCDF 359
                                   5669*******************************78888888766 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   3.3e-11   4.9e-08      23     128 ..      16     123 ..       8     132 .. 0.89
   2 !   21.3   0.0   9.6e-08   0.00014     242     282 ..     309     349 ..     268     368 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 3.3e-11
                                   -BHHHHHH.HHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT----SB.--BG CS
                  tRNA-synt_1e  23 shlGhaRs.lvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnvlkptl.eprv 101
                                    hlGhaRs ++  Di+ ++l+ +g dv +v    +    i + a++e+ks +e++ek+ +e k+dl+ L+v    + +++ 
  gi|15669449|ref|NP_248259.1|  16 LHLGHARStYIPADIIYKYLKLRGEDVIHVGGTDNHGVPITLTAEKEGKSPEEIVEKYHNEIKEDLDLLGVEFDAFgKTHS 96 
                                   7******64899******************998888889********************************9755527778 PP

                                   GGGHHHHHHHHHHHHHTTSEEE-TTS- CS
                  tRNA-synt_1e 102 sekvdeiielvekliekgyaYavsdgd 128
                                   + +++   e+  kl e+gy Y+ + ++
  gi|15669449|ref|NP_248259.1|  97 QIHIETAQEFYLKLKENGYIYEKEIEQ 123
                                   889******************988554 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 9.6e-08
                                   EEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                  tRNA-synt_1e 242 lhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                                   +  g+l++eg+kms s + ++ +kd++k+fd+  lR++l+ 
  gi|15669449|ref|NP_248259.1| 309 VSGGYLTLEGRKMSTSKRWVVWVKDFVKNFDADYLRYYLIM 349
                                   5679*********************************9864 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       4.7   6.9e+03      88     108 ..     264     293 ..     263     296 .. 0.69
   2 !   33.0   0.9   3.5e-11   5.2e-08       1      92 [.     406     503 ..     406     575 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.7
                   Anticodon_1  88 lwqr........eeeelgkkesimlae.wp 108
                                   +w++          + +gk+ ++++a  wp
  gi|15669449|ref|NP_248259.1| 264 IWKKywlekdtkIYHFIGKDITVHHAVfWP 293
                                   555555555555447789999999998888 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 3.5e-11
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.raaqevllevletllrllaPf 80 
                                   d+++l++++++++ v++++++++f++a+ ++ ++ ++   + y++  +p+  ++  e++ +++ +++ + ++tl+ ll+P 
  gi|15669449|ref|NP_248259.1| 406 DKELLKKCEETLEAVDKNIRSFKFRDALVNILHLAIE--GNSYFQKMEPWAVDD--EERlKEILYTCCKTVKTLVYLLYPY 482
                                   89*******************************9777..89*********9544..34545699***************** PP

                   Anticodon_1  81 mPfitEelwqr.........e 92 
                                   mP  +  l +          +
  gi|15669449|ref|NP_248259.1| 483 MPKKSLALLELmneeldlelR 503
                                   **9888888223334444442 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.074   1.1e+02      34      69 ..      13      49 ..       3      57 .. 0.84
   2 ?   -3.7   0.0       2.8   4.1e+03     121     244 ..      83      95 ..      61      97 .. 0.62
   3 ?   10.2   0.0   0.00017      0.26     241     325 ..     281     364 ..     265     378 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.074
                  tRNA-synt_1f 34 SGliHiGnlr.evltadlvaralrkrgeevrlilisD 69
                                   G++H+G +r   + ad++++ l+ rge+v ++   D
  gi|15669449|ref|NP_248259.1| 13 NGPLHLGHARsTYIPADIIYKYLKLRGEDVIHVGGTD 49
                                  69********4457799***********998887666 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.8
                  tRNA-synt_1f 121 elgievefisatelYksglydeaikealenrekikeilekyrgeereetyspylpvcekcgrvdttevvevdaeeeeieYk 201
                                                                                                                    
  gi|15669449|ref|NP_248259.1|  83 L-------------------------------------------------------------------------------- 83 
                                   4................................................................................ PP

                  tRNA-synt_1f 202 ceecGeeeevdiregngKLqWkvdwamrWaalgVdfEpaGkDh 244
                                                                  lgV+f ++Gk h
  gi|15669449|ref|NP_248259.1|  84 -------------------------------LGVEFDAFGKTH 95 
                                   ...............................455555555555 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00017
                  tRNA-synt_1f 241 GkDhaaaGgSvdvsskia.eilggeaPekvvY.elillkggekmssSkGnvltledwlevaepevlrflilrrkPk.kakk 318
                                   GkD++   + +  +  ia   ++   P  vv   +++l+g+ kms Sk  v+ ++d ++    + lr++++ + P  k  +
  gi|15669449|ref|NP_248259.1| 281 GKDITVHHAVFWPGMLIAhGSFNL--PTAVVSgGYLTLEGR-KMSTSKRWVVWVKDFVKNFDADYLRYYLIMSAPLfKDCD 358
                                   666666555666666666444444..333333034555555.**************************9999888647778 PP

                  tRNA-synt_1f 319 ldldlei 325
                                   +++d ++
  gi|15669449|ref|NP_248259.1| 359 FSFD-DF 364
                                   8887.55 PP

>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.8e-05      0.12      93     130 ..     292     328 ..     290     361 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.8e-05
                      ILVD_EDD  93 vPgllmaaarlniPaifvsgGpmeagkkkkldlssvfe 130
                                    Pg+l+a  ++n+P+ +vsgG  + +  +k++ s+ + 
  gi|15669449|ref|NP_248259.1| 292 WPGMLIAHGSFNLPTAVVSGGYLTLE-GRKMSTSKRWV 328
                                   5********************98872.23344444443 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   7.2   0.00011      0.16       1      48 [.     126     174 ..     125     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                           DZR   1 CpqCgeelppdar..fCseCgtklkavaaedrCpsCgekvdp...earfCpeC 48 
                                   Cp+C++ lp++     C++Cg + +     d+C  Cg+ ++p   ++ +C  C
  gi|15669449|ref|NP_248259.1| 126 CPNCKKFLPDRYVegICPYCGGEAR----GDHCEVCGRHLEPfelKDPYCVIC 174
                                   ***********9888*********9....8*******9866511156666666 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3    0.0013         2      16      22 ..     123     129 ..     113     129 .. 0.85
   2 ?    4.1   0.8     0.031        46      12      23 ..     135     146 ..     134     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                       DUF1610  16 vFpCPNC 22 
                                    F+CPNC
  gi|15669449|ref|NP_248259.1| 123 QFYCPNC 129
                                   6****** PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.031
                       DUF1610  12 EravvFpCPNCG 23 
                                    r+v+ +CP CG
  gi|15669449|ref|NP_248259.1| 135 DRYVEGICPYCG 146
                                   699********9 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.0    0.0019       2.9       2      40 ..     125     162 ..     109     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0019
                                   --SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S--- CS
                zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqedlkkealCpeCeqele 40 
                                   +Cp+C++ l  r  +  C  C  + +   +C+ C+ +le
  gi|15669449|ref|NP_248259.1| 125 YCPNCKKFLPDRYVEGICPYCGGEAR-GDHCEVCGRHLE 162
                                   68888888888777777888877754.567777777776 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   6.0     0.091   1.4e+02      25      45 ..     153     176 ..     122     180 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.091
                                   E-HHHHHHHHH...TT-B-TTT-- CS
                    zf-C3HC4_3  25 lCeeCaekllk...rkkkCpiCrr 45 
                                    Ce C ++l+    +++ C iC+ 
  gi|15669449|ref|NP_248259.1| 153 HCEVCGRHLEPfelKDPYCVICKG 176
                                   589999999768899999999986 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.3    0.0011       1.6      28      50 ..     122     148 ..     111     151 .. 0.74
   2 ?    1.3   0.3      0.24   3.6e+02       6      18 ..     152     164 ..     149     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                       DUF1272  28 EctFCaeCa....eevlenvCPncgGe 50 
                                   E  +C +C     ++ +e++CP cgGe
  gi|15669449|ref|NP_248259.1| 122 EQFYCPNCKkflpDRYVEGICPYCGGE 148
                                   44577777623335678*********8 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.24
                       DUF1272   6 pnCecCdkdlppd 18 
                                   ++Ce C ++l+p 
  gi|15669449|ref|NP_248259.1| 152 DHCEVCGRHLEPF 164
                                   58******99874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1655  (0.0923086); expected 358.6 (0.02)
Passed bias filter:                      837  (0.0466841); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.78u 0.28s 00:00:01.06 Elapsed: 00:00:00.48
# Mc/sec: 4116.07
//
Query:       gi|15669450|ref|NP_248260.1|  [L=733]
Description: phosphoribosylformylglycinamidine synthase II [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-60  201.9   1.9    1.6e-35  122.6   0.2    2.3  2  AIRS_C          AIR synthase related protein, C-terminal doma
    1.8e-51  172.8   0.3    3.2e-24   85.4   0.0    2.5  2  AIRS            AIR synthase related protein, N-terminal doma
    1.6e-09   38.2   0.4    5.5e-09   36.4   0.1    2.1  2  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe
  ------ inclusion threshold ------
      0.074   13.3   0.0       0.23   11.8   0.0    1.8  1  PurL_C          Phosphoribosylformylglycinamidine synthase II


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6   0.2   3.5e-39   1.6e-35       1     152 [.     192     342 ..     192     346 .. 0.95
   2 !   79.0   0.1   9.1e-26   4.1e-22       1     149 [.     563     700 ..     563     706 .. 0.92

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 3.5e-39
                                   STTEEEEEEET...SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHH CS
                        AIRS_C   1 kpGdvliltgs...lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalae 78 
                                   +pG  lil+gs   +G+gga+ ++++ + ee+++++++vq+gd++ e+ li++++++    g+vka++D+++ GL+ga +e
  gi|15669450|ref|NP_248260.1| 192 EPGLSLILIGStgrDGIGGAS-FASKDLTEESEEERPSVQVGDAFSEKCLIDAVLEAVKT-GKVKAMKDLGAAGLSGASSE 270
                                   6999*****************.666779999999988*****************999996.******************** PP

                                   HHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEE CS
                        AIRS_C  79 mapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeels 152
                                   m+ ++gvg e++l++v ++++l +p+e+++se+++r+l+av+p +++++++i+++++lp a+vIG+++++++  
  gi|15669450|ref|NP_248260.1| 271 MCYGGGVGCELYLENVVLREPL-TPYEIMVSESQERMLLAVEPGSEEEIIEIFKKYELP-ASVIGKTIPEKRII 342
                                   **********************.***********************************7.*********98765 PP

  == domain 2  score: 79.0 bits;  conditional E-value: 9.1e-26
                                   STTEEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHH CS
                        AIRS_C   1 kpGdvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaem 79 
                                   k+Gd li t +  + +gg+ ++++ +  ee  ++     ++d+++e++  +++r+   + glv+ a D+++GGL++ala m
  gi|15669450|ref|NP_248260.1| 563 KEGDILIITNEtkDEMGGSEYYKVIHNTEEGRVP-----RVDLEKEKKIYEEVREVVKE-GLVSEAVDCSRGGLAVALAKM 637
                                   69******************99999888888887.....*******9999999999997.********************* PP

                                   HHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESS CS
                        AIRS_C  80 apasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtake 149
                                   a  +++g+e+dl   +  ++   +  +l+se+sGr ++av+ e++d+vl++l++     a++IG+v +++
  gi|15669450|ref|NP_248260.1| 638 AVLNNIGLEVDLT--EYNKNNLRDDILLFSETSGRIILAVRDENKDKVLSKLSS-----AYIIGKVGGSR 700
                                   *************..7777776788899*************************4.....9******9864 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.1   8.6e-28   3.8e-24       1      94 []      63     180 ..      63     180 .. 0.93
   2 !   85.4   0.0   7.2e-28   3.2e-24       2      94 .]     426     548 ..     425     548 .. 0.93

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 8.6e-28
                                   SSSEE.........EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC............HHHHHHH CS
                          AIRS   1 dDaav.........vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp............wleevvr 60 
                                   dDaav         +++++shn+p++++p+++ +a++v+++++D+++mGA+P+all+ l ++             +e+vv+
  gi|15669450|ref|NP_248260.1|  63 DDAAVirlkndiclAIAMESHNHPSYIDPYNG-AATGVGGIVRDVLSMGAKPIALLDPLRFGdifgkegdkvrwLIEGVVK 142
                                   79994455555555******************.****************************************999***** PP

                                   HHHHHHHHTT-EEEEEEEEEESS....EEEEEEEEEEE CS
                          AIRS  61 glaeaaeelgvplvgGdtsfsne....ptisvtavGlv 94 
                                   g++++++++gvp+vgG+++f+++     +++v++vGlv
  gi|15669450|ref|NP_248260.1| 143 GIGDYGNRIGVPTVGGECEFDSSfdynNLVNVVCVGLV 180
                                   ********************988999999*******97 PP

  == domain 2  score: 85.4 bits;  conditional E-value: 7.2e-28
                                   SSEE...........EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHH CS
                          AIRS   2 Daav...........vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrgl 62 
                                   Daav           ++ttd+++r++ ++p+ + +  ava+++++la++GA+P+a+l++l+++         +l+e+++gl
  gi|15669450|ref|NP_248260.1| 426 DAAVlrinevypmgiALTTDCNSRYCKLNPYVG-AVNAVAEAVRNLATVGAEPIAMLDNLNFGnperperfwQLAECIKGL 505
                                   899444555555555******************.*********************************************** PP

                                   HHHHHHTT-EEEEEEEEEESS...........EEEEEEEEEEE CS
                          AIRS  63 aeaaeelgvplvgGdtsfsne...........ptisvtavGlv 94 
                                   a+aae +++p+vgG++s +ne           pt++++++G v
  gi|15669450|ref|NP_248260.1| 506 ADAAEFFEIPVVGGNVSLYNEtviegkehpinPTPAIFVLGKV 548
                                   *******************999******************986 PP

>> FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransferase linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1   1.2e-12   5.5e-09      12      49 ..       1      35 [.       1      36 [. 0.94
   2 ?   -2.5   0.0       1.8   7.9e+03       4      18 ..     705     719 ..     704     722 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.2e-12
                FGAR-AT_linker 12 LsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrH 49
                                  +++++ +y++++   lgr+P+ +El mf   wSEHC +
  gi|15669450|ref|NP_248260.1|  1 MDENDLKYIEKV---LGRKPNHIELAMFENLWSEHCAY 35
                                  578899******...9********************99 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                FGAR-AT_linker   4 ankelglaLsdeEid 18 
                                   +n++    L+ eE++
  gi|15669450|ref|NP_248260.1| 705 INEKDVVNLDVEEMK 719
                                   78888999******8 PP

>> PurL_C  Phosphoribosylformylglycinamidine synthase II C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.1e-05      0.23      18      83 ..     599     668 ..     596     678 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
                                   -GGGHHHHHHHHHHHHHTT-E..EE--TTSS-HHHH.H.HHHTT-EEEE------..SS-EEEEEEES-- CS
                        PurL_C  18 elerekklWseirklvekgaf..vvsssdyskrttl.e.nalkglklnvklpelrhePvhqlvlvfgetp 83 
                                   +le+ekk+++e+r +v++g     v  s+      l + ++l++++l+v l e  ++ +   +l+f+et 
  gi|15669450|ref|NP_248260.1| 599 DLEKEKKIYEEVREVVKEGLVseAVDCSRGGLAVALaKmAVLNNIGLEVDLTEYNKNNLRDDILLFSETS 668
                                   79**************9985422233333222222312145679***********************953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (733 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 4700.39
//
Query:       gi|15669451|ref|NP_248261.1|  [L=140]
Description: nucleoside diphosphate kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.9e-60  200.4   0.8    1.1e-59  200.3   0.8    1.0  1  NDK             Nucleoside diphosphate kinase
  ------ inclusion threshold ------
      0.053   13.4   0.9      0.053   13.4   0.9    1.6  2  DNA_pol3_a_NII  DNA polymerase III polC-type N-terminus II


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.3   0.8   1.2e-63   1.1e-59       1     135 []       3     137 ..       3     137 .. 0.99

  Alignments for each domain:
  == domain 1  score: 200.3 bits;  conditional E-value: 1.2e-63
                                   EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHHH CS
                           NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedaie 81 
                                   ert+v +KPdavkr+lig+ii+r+e+kg++iva+km++l++e ae++Y+ehkgk+f+e+l++fmtsg ++++v+ege+ai+
  gi|15669451|ref|NP_248261.1|   3 ERTFVALKPDAVKRKLIGKIIERFENKGFEIVAMKMIKLDREMAEKYYEEHKGKEFYERLINFMTSGRMIVMVVEGENAIS 83 
                                   89******************************************************************************* PP

                                   HHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTGGGS CS
                           NDK  82 kvreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFkeeei 135
                                   +vr++iG+tnpaea+pgtiR+df++++ +N++H+Sds+esaereiklfFke+ei
  gi|15669451|ref|NP_248261.1|  84 VVRKMIGKTNPAEAEPGTIRGDFALTTPDNIIHASDSKESAEREIKLFFKEDEI 137
                                   ***************************************************997 PP

>> DNA_pol3_a_NII  DNA polymerase III polC-type N-terminus II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   5.9e-06     0.053      44      92 ..      12      57 ..       9      68 .. 0.79
   2 ?   -3.0   0.1      0.72   6.4e+03      73      85 ..     119     131 ..     112     136 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.9e-06
                DNA_pol3_a_NII 44 ealkkkkldklleeyikfgFgklkidvevdedesseeeieefeeqkeee 92
                                  +a k+k ++k++e+++++gF  + +++   + e++e   + +ee+k +e
  gi|15669451|ref|NP_248261.1| 12 DAVKRKLIGKIIERFENKGFEIVAMKMIKLDREMAE---KYYEEHKGKE 57
                                  5789*****************888887777756643...6788887776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.72
                DNA_pol3_a_NII  73 dedesseeeieef 85 
                                   d +es+e+ei+ f
  gi|15669451|ref|NP_248261.1| 119 DSKESAEREIKLF 131
                                   5556666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 1062.96
//
Query:       gi|15669452|ref|NP_248262.1|  [L=417]
Description: high-affinity branched-chain amino acid transport protein BraC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-35  121.4   0.0      7e-35  121.3   0.0    1.1  1  Peripla_BP_6  Periplasmic binding protein
    1.9e-27   96.3   0.0    2.4e-27   96.0   0.0    1.0  1  ANF_receptor  Receptor family ligand binding region
    0.00015   20.8   0.2      0.001   18.2   0.2    2.0  1  Peripla_BP_5  Periplasmic binding protein domain
  ------ inclusion threshold ------
       0.02   13.7   0.0      0.032   13.0   0.0    1.4  1  LppC          LppC putative lipoprotein
       0.11   11.3   0.0       0.22   10.3   0.0    1.5  2  Fe-ADH        Iron-containing alcohol dehydrogenase


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.3   0.0     2e-38     7e-35       2     307 ..      36     356 ..      35     400 .. 0.84

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 2e-38
                                   EEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETTE..EEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-BSHH CS
                  Peripla_BP_6   2 ikiGlltplsGpyassgksllagaqaafeeiNaaGGinGr..kielverDdaydpdraaeaarrlvdqdgvdalvgplssa 80 
                                   ik+Gll++lsG +a++g +    ++ a e iN+    +G   k++l ++D+  dp   +++++ l   +g++ ++gp+ s+
  gi|15669452|ref|NP_248262.1|  36 IKVGLLVDLSGGLATYGNNEKHICEIAEEKINKYFEEKGMpyKVKLYVEDTRADPNICLQKVQALHA-QGITFFLGPMASG 115
                                   9********************************9889997779**********************99.************* PP

                                   HHHHHHHHHHHHT-EEEESS-HH........CCTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHHHHHH CS
                  Peripla_BP_6  81 vaaavaevlakdgvpvigpaglt........gekcspyvfslgpsysaqasalveylakelggkkvalvyadyafgregia 153
                                    ++ +  +++ +++++i+p++++        + + + yvf++ p+++ q++a+++ +ak+lg k+v ++y  +a+g+ +++
  gi|15669452|ref|NP_248262.1| 116 EVKNIKGFINSNKIVIISPSSTAppqmlgfrTPEEKKYVFRFVPTDNFQGNAIGD-VAKQLGLKNVIVIYRKDAWGDGLER 195
                                   ******************99666433433325699********************.7999********************* PP

                                   HHHHHHHCCTEEEEEEEEE-TTHHHHHHHHH....HHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEE..CCC-C CS
                  Peripla_BP_6 154 alkaaakaaGgevvgeepvplgttdfsaqvl....qikaagadavllagtgadlaallkaaaeaGldakrillv..swsgs 228
                                   a+ + +ka+G+++++e+p++++  d+s++++    +i+ +g d+ ++  + + +a+ll ++ ++    k++ ++  +++ s
  gi|15669452|ref|NP_248262.1| 196 ATVEKLKANGINIIDEIPYDPNIGDWSPIIQtttnKIAGKGNDTGVIFIGYEEVATLLSQIDDNSPLLKHVWIGcdGTANS 276
                                   ****************************887333368889****888889999*********9997777776644467777 PP

                                   HHHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHH....HHHHHHHHCCTH.CCHHHH CS
                  Peripla_BP_6 229 eedlkalggeaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaa....dlllealkaags.ltreav 304
                                      l+ ++  +a +v ++++ f + ++++++++++++++++ g+  p+q+a++ y+a     + ++e l ++g   +++ +
  gi|15669452|ref|NP_248262.1| 277 KKVLEEAKN-KAVKVKLYSTMFQS-ETDEAEKIKEEFKKRGYGE--PDQYALNVYDAFwvgaISYAEMLNKTGGkYDADLL 353
                                   777777776.68889999998877.5889999********8887..99999988877633336678888888742555544 PP

                                   HHH CS
                  Peripla_BP_6 305 raa 307
                                    + 
  gi|15669452|ref|NP_248262.1| 354 SKL 356
                                   444 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.0   6.6e-31   2.4e-27      23     353 ..      77     399 ..      60     400 .. 0.82

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 6.6e-31
                                   EEEEEEEEE-TT-HHHHHHHHHHHCCCCEEEEEE-SSHHHHHHHHHHHCCTT-EEEESS---G...G.GG-TTTTTTEEES CS
                  ANF_receptor  23 iklgyeiidtccdfslaleaaldflkgkvvaviGpssssvsdavaslanlfkiPvisygstsp...e.lsdknryptflrt 99 
                                   +k+ ++++dt  d++  l++++ ++++ +  ++Gp  s++++ ++ + n +ki +is++st+p     ++  ++ ++++r 
  gi|15669452|ref|NP_248262.1|  77 YKVKLYVEDTRADPNICLQKVQALHAQGITFFLGPMASGEVKNIKGFINSNKIVIISPSSTAPpqmLgFRTPEEKKYVFRF 157
                                   5999**********************88********************************876555458999999****** PP

                                   S--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEST.CHHHCHHHHHHHHHHTT.T-- CS
                  ANF_receptor 100 vpsdtsqaqAivdilkhfgWkkvaliysdddygesglqaleeeleergicvalkekipe.ssnddevvrkllkeiks.kar 178
                                   vp+d++q+ Ai d+ k++g k v++iy +d++g ++  a +e+l+++gi++  +  +++  ++ + +++ + ++i+    +
  gi|15669452|ref|NP_248262.1| 158 VPTDNFQGNAIGDVAKQLGLKNVIVIYRKDAWGDGLERATVEKLKANGINIIDEIPYDPnIGDWSPIIQTTTNKIAGkGND 238
                                   ****************************************************99999988555667777777666665667 PP

                                   EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC..HHHHHTT-EEEEE--B-HHHHHHHHHST--CCC CS
                  ANF_receptor 179 vivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpeltgleaaegvlgfrlkdpnspkfsefldkreklsd 259
                                     v+f   e++  ll ++ +     +  vwi+ d+ ++s +++++         +++ ++l++++   f++ +d+ ek++ 
  gi|15669452|ref|NP_248262.1| 239 TGVIFIGYEEVATLLSQIDDNSPLLK-HVWIGCDGTANSKKVLEEA------KNKAVKVKLYSTM---FQSETDEAEKIK- 308
                                   8888888899*******999887775.9*******99999999774......5566666663333...333333335554. PP

                                   SSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSSHCCB-HHHHCCHHHHHHHHHHHT-EEEETTSCEEB-TTSB CS
                  ANF_receptor 260 ekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpgralscntlkpweggqkllrylrnvnfeGltGdvkfdengd 340
                                    +++++   +e+ +y++   Yda+++ a    ++l+k++ ++  + + l+++ +  +++    +   + +tG +k++e +d
  gi|15669452|ref|NP_248262.1| 309 -EEFKKRGYGEPDQYALNV-YDAFWVGAISYAEMLNKTGGKY--DADLLSKLIKENTVKYSEGQFGVKSVTGYIKLNEWND 385
                                   .566777778887777744.***************7765555..33334455555555555666777799*********** PP

                                   BE.-EEEEEEEECT CS
                  ANF_receptor 341 rv.ptydilnlqgs 353
                                   r+ ++y i++++ +
  gi|15669452|ref|NP_248262.1| 386 RAsGNYGIFAVTED 399
                                   **********9976 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   2.8e-07     0.001       1     328 [.      36     378 ..      36     399 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.8e-07
                  Peripla_BP_5   1 ikvGvLhSlsGtmaisekslkdaallaieeinaagGvlg..rkieavvvdpasdwelfaekaeklieedkvevvfGcwtSa 79 
                                   ikvG+L  lsG +a+  ++ k+   +a e+in+    +g   k++  v+d ++d++ + +k ++l + +++++ +G   S 
  gi|15669452|ref|NP_248262.1|  36 IKVGLLVDLSGGLATYGNNEKHICEIAEEKINKYFEEKGmpYKVKLYVEDTRADPNICLQKVQALHA-QGITFFLGPMASG 115
                                   8***************999999999999999985544432289*******************99877.89*********** PP

                  Peripla_BP_5  80 sRkavlpvveelnalLfYpv.....qYEGe...EssknviYtGaapnqqaipavdyllselgakrvflvGsdyvypretnr 152
                                     k+++  +++++ +++ p      q  G+   E  k v+    + n q  +a+  ++++lg k v+++     +     r
  gi|15669452|ref|NP_248262.1| 116 EVKNIKGFINSNKIVIISPSstappQMLGFrtpEEKKYVFRFVPTDNFQG-NAIGDVAKQLGLKNVIVIYRKDAWGDGLER 195
                                   *******9999999888775222224445522255566666555555554.455557788888888888888888888888 PP

                  Peripla_BP_5 153 ilkallkakggevvgeeYlplgssdvqkivakikka....kpdvvlstinGdsnvafykelkeag..ikaekipvvslsva 227
                                    + + lka+g+++++e     +  d++ i++   ++    + d+ +  i  ++++++  +++++   +k+  i    +  +
  gi|15669452|ref|NP_248262.1| 196 ATVEKLKANGINIIDEIPYDPNIGDWSPIIQTTTNKiagkGNDTGVIFIGYEEVATLLSQIDDNSplLKHVWIGCDGTANS 276
                                   888888888888888876666777887777654433232266655555666777788888888751134444444455666 PP

                  Peripla_BP_5 228 eeelaaidaealvGhlaawnYfqsvdtpenkafvakfkar.vge.drvtndpmeaayiqvklwaqAveka.gstdvekvre 305
                                    + l++ +++a++ +l ++  fqs +t+e++++ ++fk+r +ge d+   ++  a +++   +a+ ++k  g+ d++ +++
  gi|15669452|ref|NP_248262.1| 277 KKVLEEAKNKAVKVKLYST-MFQS-ETDEAEKIKEEFKKRgYGEpDQYALNVYDAFWVGAISYAEMLNKTgGKYDADLLSK 355
                                   6777888777777777664.4666.78888888888887734553567777778888888888888888734457777777 PP

                  Peripla_BP_5 306 allgqelkapeGevkidpenhhl 328
                                    + ++++k  eG+  +++ + ++
  gi|15669452|ref|NP_248262.1| 356 LIKENTVKYSEGQFGVKSVTGYI 378
                                   77788888888887777766665 PP

>> LppC  LppC putative lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.9e-06     0.032     215     371 ..      31     204 ..      16     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.9e-06
                                   -------EEEEE--SSTTHHHHHHHHHHHHHHH...........TT--S-EEEEETTTS...-HHHHHHHHHHTT--EEE- CS
                          LppC 215 qqtkltkvalLLPlsGklakvaetirdGFlaak........daetqsnaqvkvfDtaae...slediyaqakaagidlvVG 284
                                   +++++ kv+lL  lsG la+ ++  +   + a+        ++   +++++ v Dt a     l+++ + ++a+gi +  G
  gi|15669452|ref|NP_248262.1|  31 SKENVIKVGLLVDLSGGLATYGNNEKHICEIAEekinkyfeEKGMPYKVKLYVEDTRADpniCLQKV-QALHAQGITFFLG 110
                                   6778999****************99999999987787753333334555666669999866455555.56899******** PP

                                   --SHHHHHHHHHSGG.GTTSEEEES---..TT-...--BT.TEEE----HHHH..HHHHHHHHHHTT-SSEEEEEESSHHH CS
                          LppC 285 PLlkqnvdkllaqeqlvqsidvLaLNss..dns...raia.qlcyfgLspEde..aesaAsklwadgvRnplvlvpqndlG 357
                                   P+  ++v+++  + ++  +i +++  s+  ++    r+++ +   f   p d+  ++++ + + + g++n++v+  ++++G
  gi|15669452|ref|NP_248262.1| 111 PMASGEVKNIKGFINS-NKIVIISPSSTapPQMlgfRTPEeKKYVFRFVPTDNfqGNAIGDVAKQLGLKNVIVIYRKDAWG 190
                                   *********9988887.6666665544411343334665414455888888872234445666666888888888888888 PP

                                   HHHHHHHHHHHHHH CS
                          LppC 358 rRvveAFnerwqql 371
                                   +    A  e+ ++ 
  gi|15669452|ref|NP_248262.1| 191 DGLERATVEKLKAN 204
                                   87777766666655 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   6.2e-05      0.22      13      68 ..     167     219 ..     159     231 .. 0.86
   2 ?   -4.0   0.0       1.3   4.8e+03      28      61 ..     268     296 ..     254     313 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.2e-05
                                   GHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HH CS
                        Fe-ADH  13 elgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptle 68 
                                    +g+ +k+lg+k++++++ k ++   gl +  +e+l+++gi++   d+++ +p + 
  gi|15669452|ref|NP_248262.1| 167 AIGDVAKQLGLKNVIVIYRKDAW-GDGLERATVEKLKANGINII--DEIPYDPNIG 219
                                   68999****************99.99**********99999876..8888888765 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.3
                                   EEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE CS
                        Fe-ADH  28 ivtdkgslkksglldkvlesleeagievtvfdgv 61 
                                   i +d+  +      +kvle+ +++ ++v++++++
  gi|15669452|ref|NP_248262.1| 268 IGCDGT-A----NSKKVLEEAKNKAVKVKLYSTM 296
                                   555555.2....2356666666667777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2832.13
//
Query:       gi|15669453|ref|NP_248263.1|  [L=257]
Description: high-affinity branched-chain amino acid transport ATP-binding protein BraF [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-32  112.4   0.0    2.9e-32  112.0   0.0    1.2  1  ABC_tran      ABC transporter
    2.6e-09   37.3   0.8    1.6e-05   24.9   0.4    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.7e-08   33.5   0.1    4.8e-08   33.1   0.1    1.2  1  AAA_15        AAA ATPase domain
      7e-08   32.1   0.1    2.9e-07   30.1   0.1    2.0  3  AAA_29        P-loop containing region of AAA domain
      1e-07   32.7   0.1    1.4e-07   32.2   0.1    1.3  1  AAA_23        AAA domain
    1.1e-05   25.0   0.8     0.0001   21.9   0.8    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0006   19.8   0.0     0.0011   18.9   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.002   17.8   0.0     0.0031   17.1   0.0    1.2  1  AAA_27        AAA domain
     0.0025   18.2   0.0      0.004   17.6   0.0    1.3  1  AAA_16        AAA ATPase domain
     0.0026   17.8   0.2     0.0098   16.0   0.0    2.0  2  MMR_HSR1      50S ribosome-binding GTPase
     0.0035   17.3   0.0     0.0048   16.8   0.0    1.3  1  ATPase_2      ATPase domain predominantly from Archaea
     0.0041   16.9   0.0     0.0078   16.0   0.0    1.3  1  AAA_30        AAA domain
     0.0076   15.3   0.0      0.013   14.6   0.0    1.3  1  T2SSE         Type II/IV secretion system protein
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.017   15.1   0.0    1.3  1  AAA_5         AAA domain (dynein-related subfamily)
      0.019   15.2   0.0      0.045   14.0   0.0    1.6  1  AAA_22        AAA domain
      0.025   13.4   0.1      0.039   12.8   0.1    1.2  1  ABC_ATPase    Predicted ATPase of the ABC class
      0.028   13.7   0.0      0.037   13.3   0.0    1.1  1  DUF2813       Protein of unknown function (DUF2813)
      0.029   13.7   0.0       0.04   13.3   0.0    1.2  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.041   13.8   0.0       0.19   11.6   0.0    1.9  2  Rad17         Rad17 P-loop domain
      0.059   13.1   0.0        0.1   12.3   0.0    1.4  1  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.06   12.3   0.0        0.1   11.5   0.0    1.3  1  AAA_10        AAA-like domain
      0.088   11.4   0.0       0.15   10.6   0.0    1.3  2  AAA_13        AAA domain
      0.094   12.8   0.0       0.21   11.6   0.0    1.6  1  AAA_14        AAA domain
       0.13   11.9   0.0       0.21   11.2   0.0    1.3  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.14   12.6   0.0       0.29   11.5   0.0    1.6  1  RNA_helicase  RNA helicase
       0.18   11.3   0.0       0.34   10.4   0.0    1.3  1  AAA_7         P-loop containing dynein motor region
        0.2   11.5   0.1       0.32   10.9   0.1    1.5  1  NACHT         NACHT domain
       0.21   11.2   0.0       0.44   10.1   0.0    1.5  1  AAA_25        AAA domain
       0.24   11.6   0.0       0.37   11.0   0.0    1.3  1  AAA_33        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   0.0   4.8e-35   2.9e-32       1     137 []      23     182 ..      23     182 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 4.8e-35
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren. 79 
                                   l+ vs+++++g ++ i+G+nG+GKStL+++++g lk +eG++ +++kd+++ ++ e ++  i   +q+pq  +e+tv en 
  gi|15669453|ref|NP_248263.1|  23 LDGVSISVNKGDVTLIIGPNGSGKSTLINVITGFLKADEGRVYFENKDITNkEPAELYHYGIVRTFQTPQPLKEMTVLENl 103
                                   789**********************************************99899*************************** PP

                                   .........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                   .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                                            e+ e++ k+l+ l+l++l d+++     +LSgGq + v++ ral+++pk++++DEp
  gi|15669453|ref|NP_248263.1| 104 ligeinpgesplnslfykkwipkeeEMVEKAFKILEFLKLSHLYDRKA----GELSGGQMKLVEIGRALMTNPKMIVMDEP 180
                                   ********************9987777777899999999999999998....***************************** PP

                                   TT CS
                                   xx RF
                      ABC_tran 136 ta 137
                                    a
  gi|15669453|ref|NP_248263.1| 181 IA 182
                                   75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.4   2.5e-08   1.6e-05       1      27 [.      35      62 ..      35     104 .. 0.75
   2 !   11.2   0.0   0.00038      0.23     219     294 ..     130     208 ..      83     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.5e-08
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarl.dr 27
                                  ++++iGpNgsGKS+L+  + ++  +  +
  gi|15669453|ref|NP_248263.1| 35 VTLIIGPNGSGKSTLINVITGFLKAdEG 62
                                  69*****************999664422 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00038
                        AAA_21 219 r......gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQv 292
                                           + fl+ ++ +++ a elS G+ +l  +  al   +   + ++ DEp +g  P l + ++  +l+++++ g+ +
  gi|15669453|ref|NP_248263.1| 130 MvekafkILEFLKLSHLYDRKAGELSGGQMKLVEIGRALMTNP---KMIVMDEPIAGVAPGLAHDIFnHVLELKAK-GITF 206
                                   14444468889999******************88888888777...8********************666666666.8888 PP

                        AAA_21 293 il 294
                                   ++
  gi|15669453|ref|NP_248263.1| 207 LI 208
                                   66 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   7.8e-11   4.8e-08      11      69 ..      20      75 ..      19     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 7.8e-11
                        AAA_15 11 FRslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleife 69
                                  F++l+ v+i++++  +t++iG+N+sGKS++++++  Fl+ +    +  +++e++d+ ++e
  gi|15669453|ref|NP_248263.1| 20 FKALDGVSISVNKGdVTLIIGPNGSGKSTLINVITGFLKAD----EGRVYFENKDITNKE 75
                                  99**********999************************88....667777777766554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   4.7e-10   2.9e-07      12      49 ..      23      60 ..      18      68 .. 0.80
   2 ?   -2.6   0.0       7.7   4.8e+03      25      36 ..     102     113 ..      86     115 .. 0.71
   3 ?   -2.9   0.0       9.4   5.8e+03      15      27 ..     195     207 ..     192     209 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.7e-10
                        AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                  +dg +i+++  ++tl++Gp+GsGKSTl+  i+  L ++
  gi|15669453|ref|NP_248263.1| 23 LDGVSISVNKGDVTLIIGPNGSGKSTLINVITGFLKAD 60
                                  577889999666****************8887766655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.7
                        AAA_29  25 tlltGpsGsGKS 36 
                                    ll+G++  G S
  gi|15669453|ref|NP_248263.1| 102 NLLIGEINPGES 113
                                   699999888876 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 9.4
                        AAA_29  15 htieidlkgatll 27 
                                   h++e++ kg+t+l
  gi|15669453|ref|NP_248263.1| 195 HVLELKAKGITFL 207
                                   8899999995554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.1   2.3e-10   1.4e-07       9      46 ..      19      60 ..       8     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2.3e-10
                        AAA_23  9 sf...rdqeidFsk.gltlItGpNGaGKTTildAiklaLyge 46
                                   f   ++++i  +k  +tlI+GpNG+GK+T+++ i+  L  +
  gi|15669453|ref|NP_248263.1| 19 EFkalDGVSISVNKgDVTLIIGPNGSGKSTLINVITGFLKAD 60
                                  3355588899998846*******************9877654 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.8   1.6e-07    0.0001       9      48 ..      19      57 ..      14     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.6e-07
                                  SETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHC CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  9 nFksyagktvilpfsksftaivGpNGSGKsnlldAilFvL 48
                                  +Fk + g +++++    +t i+GpNGSGKs l++ i   L
  gi|15669453|ref|NP_248263.1| 19 EFKALDGVSISVNKG-DVTLIIGPNGSGKSTLINVITGFL 57
                                  688887666666554.49***************9996444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.7e-06    0.0011      98     126 ..      32      60 ..       8      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-06
                                   TTSEEEEECSTTSSHHHHHHHHCTT---- CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelk 126
                                   k+++++++G+ G GKStLin++++ l++ 
  gi|15669453|ref|NP_248263.1|  32 KGDVTLIIGPNGSGKSTLINVITGFLKAD 60 
                                   4599******************9876655 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.1e-06    0.0031      10      50 ..      16      57 ..       7      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.1e-06
                        AAA_27 10 ryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                   +G+f+    +++s ++ d++li+GpN +GKst+++ i+ +l
  gi|15669453|ref|NP_248263.1| 16 YFGEFKALdGVSISVNKGDVTLIIGPNGSGKSTLINVITGFL 57
                                  58888875368888899*****************99988765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   6.4e-06     0.004      20      63 ..      31      73 ..      19     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.4e-06
                        AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                  ++g   ++l++G+ G+GKs+l++ +   l++d+g + ++ k   +
  gi|15669453|ref|NP_248263.1| 31 NKG--DVTLIIGPNGSGKSTLINVITGFLKADEGRVyFENKDITN 73
                                  445..579*****************99999996555344444444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-05    0.0098       3      35 ..      37      70 ..      35      90 .. 0.74
   2 ?   -1.2   0.0       3.4   2.1e+03      65      84 ..     201     221 ..     162     251 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                                  EEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSS CS
                      MMR_HSR1  3 aivGrpNvGKStLinaltge.kaivsdkpgtTrd 35
                                  +i+G   +GKStLin +tg  ka  ++  +  +d
  gi|15669453|ref|NP_248263.1| 37 LIIGPNGSGKSTLINVITGFlKADEGRVYFENKD 70
                                  69****************9544544444444444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.4
                                   HHHHHHHHHHC.TSEEEEEEE CS
                      MMR_HSR1  65 glgkaflalee.adlillvvd 84 
                                     g +fl +e   d++l  +d
  gi|15669453|ref|NP_248263.1| 201 AKGITFLIIEHrLDIVLNYID 221
                                   444455544433566666666 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.7e-06    0.0048      18      56 ..      31      68 ..      21     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.7e-06
                      ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyia 56
                                  ++ ++ +i Gp gsGK++L++ i   l+  d+ ++y+ +
  gi|15669453|ref|NP_248263.1| 31 NKGDVTLIIGPNGSGKSTLINVITGFLKA-DEGRVYFEN 68
                                  567899**************998887755.666777655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.3e-05    0.0078      16      49 ..      32      64 ..      25      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                        AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrv 49
                                  +gd v+++ Gp G+GK+t++++++  ++a++grv
  gi|15669453|ref|NP_248263.1| 32 KGD-VTLIIGPNGSGKSTLINVITGFLKADEGRV 64
                                  454.9*********************99997777 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.1e-05     0.013     125     160 ..      29      64 ..      12      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                         T2SSE 125 avrerglilvsGgTgsGKttllyallkeinksderi 160
                                   +v++  + l+ G+ gsGK+tl++++  ++++++ r+
  gi|15669453|ref|NP_248263.1|  29 SVNKGDVTLIIGPNGSGKSTLINVITGFLKADEGRV 64 
                                   56666778999*******************998876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.7e-05     0.017       3      75 ..      37     109 ..      35     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-05
                                   EEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGG CS
                         AAA_5   3 lLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEve 75 
                                   l++Gp G+gKs+l+  +  +l  +e  ++  ++d+t ++    +++   +t  +++pl+ +++  e l+++E++
  gi|15669453|ref|NP_248263.1|  37 LIIGPNGSGKSTLINVITGFLkADEGRVYFENKDITNKEPAELYHYGIVRTFQTPQPLK-EMTVLENLLIGEIN 109
                                   89*******************99999999999******999999999999999999999.88888888888888 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.2e-05     0.045       6      31 ..      34      59 ..      30     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.2e-05
                        AAA_22  6 gilvvtGesGtGKTtllrrlleqlde 31
                                   +++++G+ G+GK+tl++ ++  l++
  gi|15669453|ref|NP_248263.1| 34 DVTLIIGPNGSGKSTLINVITGFLKA 59
                                  6899*************988887754 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   6.3e-05     0.039     241     264 ..      29      53 ..      19      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.3e-05
                                   EE-SS.EEEEEE-TTSSHHHHHHHH CS
                    ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAl 264
                                    + kG vtlI+G++  GKsTL++ +
  gi|15669453|ref|NP_248263.1|  29 SVNKGdVTLIIGPNGSGKSTLINVI 53 
                                   567899****************987 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.9e-05     0.037      16      88 ..      25      96 ..      17     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.9e-05
                       DUF2813 16 rLSlslee..ntvLiGENaWGKSSLldALslilnvekelyqFtlkDFhvdeseeeeqekhlqlvltfkeeekeee 88
                                    S+s+++   t +iG N  GKS L++ ++ +l++++    F++kD      +e  +  h  +v tf++ ++ +e
  gi|15669453|ref|NP_248263.1| 25 GVSISVNKgdVTLIIGPNGSGKSTLINVITGFLKADEGRVYFENKDITN---KEPAELYHYGIVRTFQTPQPLKE 96
                                  566776651156689***********************999*****984...46777778888888887766555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.5e-05      0.04       8      62 ..      19      73 ..      13     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.5e-05
                  Mg_chelatase  8 qeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakias 62
                                  + +a   + i++  g   l++Gp GsGK+ l++ +++ l + + +  +e + i+ 
  gi|15669453|ref|NP_248263.1| 19 EFKALDGVSISVNKGDVTLIIGPNGSGKSTLINVITGFLKADEGRVYFENKDITN 73
                                  5566677788888888899*******************99888888777777764 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0003      0.19      34      66 ..      22      54 ..      19      79 .. 0.82
   2 ?   -0.6   0.0       1.7   1.1e+03     113     140 ..     153     179 ..     114     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                         Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                  +l+  ++  +k  + Li GP G gkst ++v++
  gi|15669453|ref|NP_248263.1| 22 ALDGVSISVNKGDVTLIIGPNGSGKSTLINVIT 54
                                  566677777888899**************9986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                         Rad17 113 eLkdakylklqklGddlrtdkklilved 140
                                   eL + +  kl   G  l t+ k+i++++
  gi|15669453|ref|NP_248263.1| 153 ELSGGQM-KLVEIGRALMTNPKMIVMDE 179
                                   4455555.56667888888888888776 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017       0.1       1      33 [.      38      70 ..      38      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLD 33
                                  ++Gp GsGK+t+++ ++ +l++ + +v+  N D
  gi|15669453|ref|NP_248263.1| 38 IIGPNGSGKSTLINVITGFLKADEGRVYFENKD 70
                                  79***************9999988888777766 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016       0.1      17      52 ..      29      64 ..      16      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                        AAA_10 17 sktnasasliiGdlGnGKSvlakllvlyisllggka 52
                                  s+++   +liiG+ G GKS l++++  ++ + +g++
  gi|15669453|ref|NP_248263.1| 29 SVNKGDVTLIIGPNGSGKSTLINVITGFLKADEGRV 64
                                  55555567******************9999988876 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00025      0.15      20      53 ..      37      64 ..      28     101 .. 0.69
   2 ?   -4.2   0.0       7.6   4.7e+03     525     537 ..     170     182 ..     167     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                        AAA_13 20 liYGwNGaGKTtLSrllrslelgetepkfangsi 53
                                  li G NG+GK+tL +++  + l++ e +     +
  gi|15669453|ref|NP_248263.1| 37 LIIGPNGSGKSTLINVITGF-LKADEGR-----V 64
                                  899**************998.3333333.....3 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 7.6
                        AAA_13 525 gkdkivviDDPvS 537
                                   ++ k++v+D P+ 
  gi|15669453|ref|NP_248263.1| 170 TNPKMIVMDEPIA 182
                                   57899*****997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00034      0.21       3      48 ..      34      78 ..      32     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkklad 48
                                   + +i G+  +GK+tl++ +    l  +e  +y++ +d ++k+ a+
  gi|15669453|ref|NP_248263.1| 34 DVTLIIGPNGSGKSTLINVIT-GFLKADEGRVYFENKDITNKEPAE 78
                                  6889************97666.555477788888877777766543 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00034      0.21       2      21 ..      35      54 ..      34      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00034
                                  EEEEEESTTCCHHHHHHHHH CS
                          cobW  2 vtvltGflGsGKTtLlnhll 21
                                  vt++ G+ GsGK+tL+n ++
  gi|15669453|ref|NP_248263.1| 35 VTLIIGPNGSGKSTLINVIT 54
                                  799*************9887 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00048      0.29       2      39 ..      37      69 ..      36      86 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00048
                  RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnp 39
                                  ++ Gp+g GKStl++  ++ +l    +  +++vy+ n+
  gi|15669453|ref|NP_248263.1| 37 LIIGPNGSGKSTLINV-ITGFL----KADEGRVYFENK 69
                                  589************9.33333....334467776655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00054      0.34      29      58 ..      29      58 ..      23      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00054
                         AAA_7 29 llknkkpvllvGptGtGKtviikdllkkld 58
                                   ++++  +l++Gp G+GK+++i+ ++  l+
  gi|15669453|ref|NP_248263.1| 29 SVNKGDVTLIIGPNGSGKSTLINVITGFLK 58
                                  57788889**************98776665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00052      0.32       2      22 ..      35      55 ..      34     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00052
                                  CEEEEC-TTTCHHHHHHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLlqklal 22
                                  + ++ G++GsGK+tL+  +  
  gi|15669453|ref|NP_248263.1| 35 VTLIIGPNGSGKSTLINVITG 55
                                  789************988765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00072      0.44      31      50 ..      31      50 ..      26      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00072
                        AAA_25 31 pagelallaGapgtGKttla 50
                                   +g+++l++G+ g+GK+tl 
  gi|15669453|ref|NP_248263.1| 31 NKGDVTLIIGPNGSGKSTLI 50
                                  689***************95 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00059      0.37       1      16 [.      35      50 ..      35      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00059
                        AAA_33  1 lvllvGlpGsGKstla 16
                                  ++l++G++GsGKstl+
  gi|15669453|ref|NP_248263.1| 35 VTLIIGPNGSGKSTLI 50
                                  6799**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1627.89
//
Query:       gi|15669454|ref|NP_248264.1|  [L=191]
Description: high-affinity branched-chain amino acid transport ATP-binding protein BraG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-18   65.5   0.0      1e-17   65.0   0.0    1.2  1  ABC_tran  ABC transporter
    1.6e-05   24.9   0.0    1.8e-05   24.7   0.0    1.2  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
  ------ inclusion threshold ------
      0.017   15.3   0.1       0.21   11.8   0.1    2.2  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
      0.083   13.0   0.0        1.6    8.8   0.0    2.1  2  MotCF     Bacteriophage T4 MotA, C-terminal


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0   2.2e-21     1e-17      32     137 .]       2     116 ..       1     116 [. 0.89

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 2.2e-21
                                   TTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH...........HHHTCHHHHHHHSTTGGTTCB CS
                                   xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  32 agllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren...........esdeeiekalsklglkelkdt 100
                                    gl+k  +Gei +++kd+ +  +++++r +i++lpq++++f +ltv+en           + +e+ie als +      ++
  gi|15669454|ref|NP_248264.1|   2 FGLTKIYSGEIIFKDKDIAKvPPHQKARMKIAYLPQTNNVFANLTVEENlkiagyvldkdKVKERIEIALSVFP---ELKD 79 
                                   5788999*************99**********************************976666666777777665...4568 PP

                                   GESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 101 vvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                   ++k+++ +LSgGq+q +a+ +al++++++l+lDEpta
  gi|15669454|ref|NP_248264.1|  80 ILKRKAGTLSGGQRQFLAMGMALVRDAEVLMLDEPTA 116
                                   888888*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   3.9e-09   1.8e-05     220     282 ..      71     131 ..       7     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.9e-09
                        AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ell 282
                                    +vf e +d  ++ a  lS G++++la+  al r++    +l +DEp + L Pkl + ++ +++
  gi|15669454|ref|NP_248264.1|  71 LSVFPELKDILKRKAGTLSGGQRQFLAMGMALVRDA---EVLMLDEPTAQLSPKLAEVIFeKII 131
                                   444555566667788999******************...9****************99995554 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.8e-05      0.21      25      43 ..      80      98 ..      61     132 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
                       SbcCD_C 25 elsrssgtlSGGekqflay 43
                                   l+r++gtlSGG++qfla+
  gi|15669454|ref|NP_248264.1| 80 ILKRKAGTLSGGQRQFLAM 98
                                  489***********98764 PP

>> MotCF  Bacteriophage T4 MotA, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.051   2.3e+02      39      76 ..      37      72 ..      24      79 .. 0.75
   2 ?    8.8   0.0   0.00036       1.6      23      63 ..     127     168 ..     115     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.051
                                  EEETTEEEEEEETTSEEEEEEES--HHHHHHHHCTT-E CS
                         MotCF 39 krtngirnfeinnngnmrifgykmmehhiqkftdigms 76
                                  +  n   n+ +  + n++i gy + + ++++  +i +s
  gi|15669454|ref|NP_248264.1| 37 QTNNVFANLTV--EENLKIAGYVLDKDKVKERIEIALS 72
                                  44555555555..4579999999999999988888877 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00036
                                   EEEEEEETTEE.EEEEEEEETTEEEEEEETTSEEEEEEES-- CS
                         MotCF  23 lkkveiyrsny.lailekrtngirnfeinnngnmrifgykmm 63 
                                   ++k+   r n+ l+il    n  r +ei +ng m + g   +
  gi|15669454|ref|NP_248264.1| 127 FEKIIEMRDNFgLTILLVEQNAKRALEISDNGYMFVSGRVAF 168
                                   55665567776599********************99886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1342.33
//
Query:       gi|15669455|ref|NP_248265.1|  [L=315]
Description: high-affinity branched-chain amino acid transport protein BraD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.1e-52  175.8  41.1    1.1e-51  175.6  41.1    1.0  1  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.6  41.1   6.1e-56   1.1e-51       4     268 .]      17     293 ..      14     293 .. 0.96

  Alignments for each domain:
  == domain 1  score: 175.6 bits;  conditional E-value: 6.1e-56
                  BPD_transp_2   4 nlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrlkvde 84 
                                     + ++ +l+++AlGl+l+++ ++v+n+++g+ +++G+yva++ll+l++ +++l+l+v ++vga+vgl+++ l l+  +++
  gi|15669455|ref|NP_248265.1|  17 GAIIYSNLLVLLALGLTLTYITTNVPNFAQGSYAIVGSYVALTLLKLFGICPYLSLPVLFVVGAIVGLITY-LALKPLIKR 96 
                                   5678999*************************************************************998.999****** PP

                  BPD_transp_2  85 liitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv.........llalllvlavllllrrtrfGr 156
                                    +++ +l+++ +++ l+ll+ i   ++  s++++ ++ + ++++  ++ +          ++++ll++ ++lll++t+fG 
  gi|15669455|ref|NP_248265.1|  97 NASVEILMIATLAIDLILLGVIGAYSEILSQIVGSTQAKFVFANLDFSLFGfkgilfvstFVVILLLIGLYLLLYKTKFGI 177
                                   **********************************************99999****************************** PP

                  BPD_transp_2 157 alravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGgagsllgtviGali 237
                                   alra +en+++a+ +Gi+v++++l+++++sgalAg+aG ll ++++++p  +g  ++++++aa ++Gg+ ++ g++iG++i
  gi|15669455|ref|NP_248265.1| 178 ALRASMENPSLAQTMGIDVEKTRLFSWILSGALAGVAGGLLPFMQEIVP-ATGDLIIISIFAASIVGGLRHISGALIGGYI 257
                                   **********************************************999.******************************* PP

                  BPD_transp_2 238 igvvksllltllgi.....ptelarvllgallilvl 268
                                   ig+++sl++++l +        + +v++ +++i+ l
  gi|15669455|ref|NP_248265.1| 258 IGISESLITYYLASafgtgFLVYGKVISLIIMIATL 293
                                   ************9966555599**********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2213.08
//
Query:       gi|15669456|ref|NP_248266.1|  [L=345]
Description: high-affinity branched-chain amino acid transport protein BraE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-69  231.7  37.5    1.4e-68  231.0  37.5    1.3  1  BPD_transp_2    Branched-chain amino acid transport system / 
  ------ inclusion threshold ------
        0.3   11.1   0.1        0.3   11.1   0.1    3.2  3  Gly-zipper_Omp  Glycine zipper
        1.1    9.4   7.0         11    6.2   0.0    3.4  2  Pox_A14         Poxvirus virion envelope protein A14
        1.9    8.6  10.1        0.8    9.8   3.6    2.8  2  SirB            Invasion gene expression up-regulator, SirB


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.0  37.5   3.1e-72   1.4e-68       2     268 .]       6     317 ..       5     317 .. 0.99

  Alignments for each domain:
  == domain 1  score: 231.0 bits;  conditional E-value: 3.1e-72
                  BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl............................ 54 
                                   i+++l ++++++i++l+l++ fg+aG++n+g +  +++Ga++++ +l +ll+l                            
  gi|15669456|ref|NP_248266.1|   6 ISMILLWFGLYYIVSLSLNMEFGYAGIPNFGKALSVLVGAIAVGGILDRLLMLyfgiggdfitgttyatsainnliasnpi 86 
                                   789****************************************************************************** PP

                  BPD_transp_2  55 .....lllallvallvgaavglllgllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsfl 130
                                        l+la+++a ++g++vg++++l++++lk+d+l itll++s++v+l+++++ +i++g++g+s+++ l++++g+++ ++
  gi|15669456|ref|NP_248266.1|  87 vgigiLILAIILASILGFVVGAIFILPSAKLKEDYLGITLLAISEAVLLICTYNLNIIGGYYGISTPDILAFVSGEYRGWV 167
                                   ********************************************************************************* PP

                  BPD_transp_2 131 savivllalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp..nig 209
                                   +a+ivl++++lv++++++l++t+fGr lra++ene++++a+G ++++++++t++i++a++++aG+l++l++++i +  +++
  gi|15669456|ref|NP_248266.1| 168 FAWIVLFIAFLVYLFFERLLNTPFGRVLRAMRENENTVKAFGRDIMKLRIKTMAIGSAIGAIAGVLYSLYTVNIIAnaFTR 248
                                   ****************************************************************************99*** PP

                  BPD_transp_2 210 vglgfnaiaavvlGgagsllgtviGaliigvvksllltllgi..........ptelarvllgallilvl 268
                                   v ++f ++++v+lGg g++ g+ +G l++++vk ll+ ++++          p +l+++l+g+l++l+l
  gi|15669456|ref|NP_248266.1| 249 VDWTFFPFLMVLLGGKGNNKGVALGVLCYVIVKVLLDIYKYNikyalgipfePVWLSYMLFGVLMLLIL 317
                                   ************************************************99999*************987 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   1.5      0.57   2.6e+03      21      32 ..      38      50 ..      27      52 .. 0.58
   2 ?   -2.0   2.1      0.86   3.8e+03      27      36 ..      99     108 ..      61     110 .. 0.69
   3 ?   11.1   0.1   6.7e-05       0.3      23      41 ..     219     237 ..     209     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.57
                Gly-zipper_Omp 21 gtGaliGA.avGa 32
                                  +   l+GA avG+
  gi|15669456|ref|NP_248266.1| 38 ALSVLVGAiAVGG 50
                                  4556777733444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.86
                Gly-zipper_Omp  27 GAavGaavGg 36 
                                   + ++G +vG+
  gi|15669456|ref|NP_248266.1|  99 ASILGFVVGA 108
                                   3344444444 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 6.7e-05
                Gly-zipper_Omp  23 GaliGAavGaavGgliGaa 41 
                                     +iG a+Ga++G l++ +
  gi|15669456|ref|NP_248266.1| 219 TMAIGSAIGAIAGVLYSLY 237
                                   579**********998755 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   2.9     0.022        98       7      31 ..      77     101 ..      73     108 .. 0.84
   2 ?    6.2   0.0    0.0025        11       2      38 ..     154     190 ..     153     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.022
                       Pox_A14   7 lknyystvliaGiiLLilacifafv 31 
                                   ++n  ++  i+Gi +Lila+i+a +
  gi|15669456|ref|NP_248266.1|  77 INNLIASNPIVGIGILILAIILASI 101
                                   6677777789***********9965 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0025
                       Pox_A14   2 dilellknyystvliaGiiLLilacifafvdfsksts 38 
                                   dil +++ +y + ++a i+L i+ +++ f++   +t+
  gi|15669456|ref|NP_248266.1| 154 DILAFVSGEYRGWVFAWIVLFIAFLVYLFFERLLNTP 190
                                   899**************************99766666 PP

>> SirB  Invasion gene expression up-regulator, SirB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.6   0.00018       0.8       9      85 ..      94     182 ..      89     196 .. 0.90
   2 ?    1.5   0.5     0.067     3e+02      64      84 ..     298     318 ..     266     322 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00018
                          SirB   9 lllvllslllFilrgllllkgsallqkkllkilphivdtlLllsgiaLlvllglspf.tka...........WltaKlvll 77 
                                   l+++l+s+l+F++ ++  l + +l +  l  +l  i++ +Ll++   L ++ g++ + t++           W+ a +vl+
  gi|15669456|ref|NP_248266.1|  94 LAIILASILGFVVGAIFILPSAKLKEDYLGITLLAISEAVLLICTYNLNIIGGYYGIsTPDilafvsgeyrgWVFAWIVLF 174
                                   578999*************9888888888899999********************996555999999************** PP

                          SirB  78 vvyivlgv 85 
                                   ++++v  +
  gi|15669456|ref|NP_248266.1| 175 IAFLVYLF 182
                                   *9988765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.067
                          SirB  64 pftkaWltaKlvllvvyivlg 84 
                                   pf + Wl ++l+++++ ++l 
  gi|15669456|ref|NP_248266.1| 298 PFEPVWLSYMLFGVLMLLILY 318
                                   77777******9999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2320.45
//
Query:       gi|15669457|ref|NP_248267.1|  [L=170]
Description: 3-isopropylmalate dehydratase LeuD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-22   79.9   0.1    5.4e-22   78.5   0.1    1.8  1  Aconitase_C    Aconitase C-terminal domain
    6.1e-08   32.5   0.4    1.9e-06   27.7   0.4    2.1  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus
     0.0045   17.2   0.2        2.7    8.3   0.1    2.3  2  DUF3006        Protein of unknown function (DUF3006)


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.1   9.1e-26   5.4e-22      63     126 ..      41     103 ..       6     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 9.1e-26
                                   HHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEE CS
                   Aconitase_C  63 vdaaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLpl 126
                                   +d  ++ k+++ +++v++ +nfG+GSSRe+A  a +  Gikavia+SF+rIf++n+i+ gl+p+
  gi|15669457|ref|NP_248267.1|  41 IDENFPKKVKEGDVIVAG-ENFGCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPI 103
                                   667777788888888877.********************************************9 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.4   3.1e-10   1.9e-06      10     177 ..      14     163 ..       7     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.1e-10
                                   EEHHHHS-GGGGGGTTSHHHHHCCTT-S-BTTSHHHHHHHHTTSS-EEEEEEEEEES---THHHHHHHHHHSEEETTEEEE CS
                 Aconitase_2_N  10 tntDdlsPasdAwsRsDiplHakamlkkkaeeelkaieelkkkgvplayvgdvvGtGssRksavnsvlWtigedipyvPnk 90 
                                   ++tD + P++   +    +l +++m   +++ +       k k   ++  g+  G GssR  av ++ +   +        
  gi|15669457|ref|NP_248267.1|  14 VDTDAIIPGPYLRTTDPYELASHCMAGIDENFP------KKVKEGDVIVAGENFGCGSSREQAVIAIKYCGIK-------- 80 
                                   566666666666666666666666655443333......2345567888899999999999998777655433........ PP

                                   EE--EEEEEEE-HHHHHHHHHTT-EEEE---TT--TT-EEEEETTTTEEEETT--EEEE---S-TCHHHH.HHHTSHHHHH CS
                 Aconitase_2_N  91 raggvvlGgkiaPiFfntvedsGalpieadvskletGdvieikpkegkikkeegevvsefklkpetllde.vraggripli 170
                                        v+  + a iF+  + + G +pi a+ ++++ Gd++ei+  +++i   +++  ++ + +p+ l  e + agg ++ +
  gi|15669457|ref|NP_248267.1|  81 ----AVIAKSFARIFYRNAINVGLIPIIANTDEIKDGDIVEIDLDKEEIVITNKNKTIKCE-TPKGLEREiLAAGGLVNYL 156
                                   ....36778899*******************************999999886666666666.4666665515678888888 PP

                                   HHHHHHH CS
                 Aconitase_2_N 171 igrglte 177
                                     r+l +
  gi|15669457|ref|NP_248267.1| 157 KKRKLIQ 163
                                   8887765 PP

>> DUF3006  Protein of unknown function (DUF3006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0012       7.4      26      41 ..      43      58 ..      42      74 .. 0.86
   2 !    8.3   0.1   0.00045       2.7      28      52 ..     106     133 ..      84     138 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0012
                       DUF3006 26 sdLpegakeGdvLeie 41
                                  +++p+++keGdv+   
  gi|15669457|ref|NP_248267.1| 43 ENFPKKVKEGDVIVAG 58
                                  689*********9865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00045
                       DUF3006  28 LpegakeGdvLeie.dd.e.ieldpeet 52 
                                     +++k+Gd++ei+ d+ e ++ ++++t
  gi|15669457|ref|NP_248267.1| 106 NTDEIKDGDIVEIDlDKeEiVITNKNKT 133
                                   5678**********75544566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1150.85
//
Query:       gi|15669458|ref|NP_248268.1|  [L=163]
Description: hypothetical protein MJ_1272 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-25   87.9   0.0    5.8e-25   87.6   0.0    1.1  1  PTPS      6-pyruvoyl tetrahydropterin synthase


Domain annotation for each model (and alignments):
>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0   3.2e-29   5.8e-25       6     121 ..      12     157 ..       8     159 .. 0.91

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 3.2e-29
                                   EEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEEC.CCC-CCHHCCS...... CS
                          PTPS   6 feFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkfl.naddpeleell...... 79 
                                    +F++aH++ +h+  c+ +HGH+y v+v++ ge+  +  +v+df+ +k+++kei++elDhk++  ++++++   l      
  gi|15669458|ref|NP_248268.1|  12 LRFSSAHIVFGHP-TCGVIHGHSYYVDVKLYGERAGDFKFVCDFKIIKKIVKEICDELDHKLIlPKNHEHVYYELrdktly 91 
                                   69**********9.9************************************************98888888777789**** PP

                                   ......................--HHHHHHHHHHHHHHHH...GCCCGCEEEEEEEEETTEEEEEE CS
                          PTPS  80 .....................spTaEnlaklifeelkerl...qekevklskvrvwEtpnswaeyr 121
                                                        s+TaE la ++++e+++rl     ++++  +v++ E  ++ a yr
  gi|15669458|ref|NP_248268.1|  92 fkyenkeysipvedvillpipSTTAEDLAIYFANEIADRLknlGFSNINWIEVSINEGIGQGACYR 157
                                   *******************9999*****************76555666777777779888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1247.57
//
Query:       gi|15669459|ref|NP_248269.1|  [L=350]
Description: hypothetical protein MJ_1273 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-124  414.3   1.1   1.6e-124  414.0   1.1    1.1  1  DUF43            Branched-chain polyamine synthase A C-termin
    3.2e-05   23.8   0.0      8e-05   22.5   0.0    1.6  1  Methyltransf_31  Methyltransferase domain
    0.00039   19.9   0.1    0.00088   18.7   0.1    1.6  1  Spermine_synth   Spermine/spermidine synthase domain
     0.0023   17.3   0.1     0.0043   16.4   0.1    1.4  1  GidB             rRNA small subunit methyltransferase G
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.026   14.4   0.0    1.4  1  N6-adenineMlase  Probable N6-adenine methyltransferase
      0.024   14.3   0.0      0.045   13.4   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.038   14.7   0.0       0.13   13.0   0.0    1.8  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> DUF43  Branched-chain polyamine synthase A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.0   1.1  6.2e-128  1.6e-124       1     243 []     105     349 ..     105     349 .. 0.99

  Alignments for each domain:
  == domain 1  score: 414.0 bits;  conditional E-value: 6.2e-128
                                   HHHHHHHHHHTT-----GGGT---B-HHHHHHHHHHHHHTT-STT-EEEEES-TT-HHHHHHHHT--SEEEEE-S-HHHHH CS
                         DUF43   1 dllekfreiakdRPeaieeyDqgfvtpettvaRvallyerGDLegkeilvlGdDDLtslalaLtglpkkvvvvDiDeRlik 81 
                                   dlle+f+ei+k+RP++++eyDqgfvtpe+t++R+al+++rGDL +k++lvlGdDDLts+al+L++lpkk+vvvDiD+Rli+
  gi|15669459|ref|NP_248269.1| 105 DLLERFKEIVKNRPMPKHEYDQGFVTPECTISRIALMNSRGDLFNKDVLVLGDDDLTSIALMLSNLPKKIVVVDIDDRLIN 185
                                   79******************************************************************************* PP

                                   HHHHHHHHHT--.EEEE---TTS---TTTSS-BSEEEE---SSHHHHHHHHHHHHHTB-STT-EEEEEE-TTT--HHHHHH CS
                         DUF43  82 fiervakelglk.ieaivyDlrkplpeelkekFdvfitDPpetvealkaFlgRGiaaLkgegcagYlgltrressldkWke 161
                                   fi++va++l++k ie+i++Dlrkplpe+++++Fd+fitDPpetv+a+k+F+gRGi+aLkge++agY+g+trressldkW+e
  gi|15669459|ref|NP_248269.1| 186 FIKEVAEQLNYKnIEVITLDLRKPLPEKYSRAFDTFITDPPETVYAVKTFIGRGISALKGERRAGYFGITRRESSLDKWRE 266
                                   ********************************************************************************* PP

                                   HHHHHH.TS--EEEEEEEEEEEB---S-GGGSHHHHHSSS----SS---EEEEEEEE--TT----SSS--S.S-S--XXXX CS
                         DUF43 162 iqklll.emgvvitdlirnFneYenweykeetraikllpvkkkpekiwyksalfrietlkgkrkveeevkkvedlykdees 241
                                   iq++l+ +++vvitd+irnFn+Y+nw+y+eetra+kl+pvkkkpe+iwyks++frietlk++r++eeev+  ++ly+d+es
  gi|15669459|ref|NP_248269.1| 267 IQRTLInDFNVVITDIIRNFNHYVNWGYEEETRAWKLAPVKKKPEDIWYKSYMFRIETLKDSRGFEEEVDVGDELYNDAES 347
                                   ******9*************************************************************************9 PP

                                   XX CS
                         DUF43 242 st 243
                                   st
  gi|15669459|ref|NP_248269.1| 348 ST 349
                                   86 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   3.1e-08     8e-05      28      81 ..     171     224 ..     159     282 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.1e-08
               Methyltransf_31  28 kaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsn 81 
                                    +++v +Di+ + i++ +e a++l+++n+e+   d  + l+++++ + fD  +++
  gi|15669459|ref|NP_248269.1| 171 PKKIVVVDIDDRLINFIKEVAEQLNYKNIEVITLDLRKpLPEKYS-RAFDTFITD 224
                                   5789*************************************8888.8***99987 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   3.4e-07   0.00088      18     101 ..     148     226 ..     132     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.4e-07
                                   ST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEE.EESTCHHHHCTCSS-EEEEE CS
                Spermine_synth  18 npkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvkl.vlgdgfkflkayekkfdvvi 97 
                                    +k+vL++G  D   +  ++  n ++ki++vdiD   i+f k++  +l+ +      +++  l++   + ++y+  fd  i
  gi|15669459|ref|NP_248269.1| 148 FNKDVLVLGDDDLTSIA-LMLSNLPKKIVVVDIDDRLINFIKEVAEQLNYK-----NIEViTLDLRKPLPEKYSRAFDTFI 222
                                   589*****988876554.4444556*************9999888888777.....7777678888888899999999999 PP

                                   EECC CS
                Spermine_synth  98 vdsl 101
                                   +d  
  gi|15669459|ref|NP_248269.1| 223 TDPP 226
                                   8865 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.7e-06    0.0043      64     110 ..     163     209 ..     160     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-06
                                   HHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCCT CS
                          GidB  64 ipLaiarpelkltLleslekkiaFLeevkeelklenveivearaeek 110
                                   i L + +  +k+++++ + + i+F++ev e+l+ +n+e++  ++ + 
  gi|15669459|ref|NP_248269.1| 163 IALMLSNLPKKIVVVDIDDRLINFIKEVAEQLNYKNIEVITLDLRKP 209
                                   67777888899*****************************9998883 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     1e-05     0.026      47      99 ..     171     228 ..     149     294 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
               N6-adenineMlase  47 kkkekvlLleiDkrFealygeekfvfYdlnnpeelp........eelkgkfdviviDPPFl 99 
                                      +k+++ +iD+r  ++++e      +++n e ++        e+++ +fd +++DPP  
  gi|15669459|ref|NP_248269.1| 171 P--KKIVVVDIDDRLINFIKEV-AEQLNYKNIEVITldlrkplpEKYSRAFDTFITDPPET 228
                                   3..899********99998886.888888888833333556666999************64 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.7e-05     0.045      28      90 ..     166     228 ..     159     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                                   HHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEEEE--C CS
               Methyltr_RsmB-F  28 elmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaPCs 90 
                                    l +  +++v vd++++ ++ ++e  ++L+ +n+ v++ D+rk+      + fD  + D P +
  gi|15669459|ref|NP_248269.1| 166 MLSNLPKKIVVVDIDDRLINFIKEVAEQLNYKNIEVITLDLRKPLPEKYSRAFDTFITDPPET 228
                                   34455689***********************************865555579**999999865 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.9e-05      0.13      13      68 ..     165     221 ..     160     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                                   HHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG.BSS.STTTEEEE CS
               Methyltransf_25  13 lalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaed.lpf.edgsfDlv 68 
                                   l+l++  + +k++ vDi++++++ ++e ae+ ++ n+e+++ d+++ lp+  ++ fD  
  gi|15669459|ref|NP_248269.1| 165 LMLSNL-P-KKIVVVDIDDRLINFIKEVAEQLNYkNIEVITLDLRKpLPEkYSRAFDTF 221
                                   444444.4.9*******************998888*********887886244577765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 2806.94
//
Query:       gi|15669460|ref|NP_248270.1|  [L=257]
Description: diphthine synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-18   68.0   0.0    1.3e-18   67.7   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.096   12.9   0.1       0.14   12.3   0.1    1.3  1  Ferritin_2    Ferritin-like domain


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.0   1.5e-22   1.3e-18       1     212 [.       1     224 [.       1     225 [. 0.68

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 1.5e-22
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsr.......aleilldllaeeleleapmgkekepleea.yeeiaeala 73 
                                   +l+l+G+G+ d +++T+++l+  k+a+ ++++  +       ++e +++ l           k+  +l ++  e +  +l+
  gi|15669460|ref|NP_248270.1|   1 MLILAGLGLYDENDMTLKTLKFAKKAEKIYAEF-YtavltgtTTEKIEEVLG----------KKIHVLSRKdVEYNGYKLI 70 
                                   799**************************6444.111112234444444443..........3333333331333344556 PP

                  TP_methylase  74 ealragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.......lpgla 147
                                   e++++ kd+ +l++GDP+v++t+  l+  ++a+++giev +i ++s+ +a+   +g+ l+++g+++s++            
  gi|15669460|ref|NP_248270.1|  71 EEAKD-KDIMFLTAGDPMVATTHVDLA--IEAKKKGIEVLIINAPSIYSAV-GITGLQLYKFGKTTSIVfpeenyfP---- 143
                                   66666.58******************9..77777**********9988766.6889999999999999966555543.... PP

                  TP_methylase 148 keeereleallan....gdtlvll.....kaprk.............laelaelLkealyddttpvavveragtedervvr 206
                                      e+ ++ + +n     +tl ll     +   +             l el  + ke + +++t+++vv+rag  + ++v 
  gi|15669460|ref|NP_248270.1| 144 ---ETPYNVIKENlergLHTLCLLdiridE---NekrfmtaneglkvLLELENRKKEGIINEDTKAVVVARAGSLKPKLVY 218
                                   ...555555555555556899999444441...1444555434444455555555666999999*********98888777 PP

                  TP_methylase 207 gtleel 212
                                   g++++l
  gi|15669460|ref|NP_248270.1| 219 GKIKDL 224
                                   877765 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.6e-05      0.14       3      32 ..      17      59 ..      15     107 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                    Ferritin_2  3 vdiLnfAlnlEyleaafYtaalegasldd.............k 32
                                  ++ L+fA  +E + a+fYta+l+g++ ++              
  gi|15669460|ref|NP_248270.1| 17 LKTLKFAKKAEKIYAEFYTAVLTGTTTEKieevlgkkihvlsR 59
                                  5789*******************99988887777776655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1577.96
//
Query:       gi|15669461|ref|NP_248271.1|  [L=388]
Description: Na(+)/H(+) antiporter NapA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-68  231.9  50.7    1.2e-68  231.7  50.7    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
      0.016   14.5   0.2      0.016   14.5   0.2    2.5  2  CcmF_C          Cytochrome c-type biogenesis protein CcmF C-t


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.7  50.7   1.3e-72   1.2e-68       2     379 ..       9     378 ..       7     380 .. 0.94

  Alignments for each domain:
  == domain 1  score: 231.7 bits;  conditional E-value: 1.3e-72
                                   HHHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHH CS
                Na_H_Exchanger   2 vllillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksilll 82 
                                   +++++++++v+ l++++++p i+  +iaG+++Gp+gl++++ + e l++l+++g i+l+FlaGle+d + l++ +k +l+l
  gi|15669461|ref|NP_248271.1|   9 FIILSIIFIVPNLLKKFNIPAITSIMIAGIIIGPYGLNILQVD-ETLKILADFGAIMLMFLAGLEVDNETLKQEFKNSLIL 88 
                                   4666668888889*****************************9.************************************* PP

                                   HHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHH CS
                Na_H_Exchanger  83 allgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavll 163
                                   +l ++li+ v+ G+l++    lg+ ++ +ll+++i++  ++++v+ail+e++ v++rlgt++l++ ++ D+++++ll+v++
  gi|15669461|ref|NP_248271.1|  89 SLFSLLIPGVG-GYLIGQ--YLGLGFIGSLLYAVIFASHSVAIVYAILEELKMVKTRLGTIILSATIIVDLFTLLLLSVVI 166
                                   ***********.*****8..589********************************************************** PP

                                   HHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHH CS
                Na_H_Exchanger 164 alakeeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallaellgvsgilgafla 244
                                   +l    +gge+    ll ++l+++v++l++  + + +l ++++      ++ +  vl ++++a +++e++g++ i+gaf++
  gi|15669461|ref|NP_248271.1| 167 KLG---IGGENVGTFLLETVLYIGVLLLAIPSLSKNILGVFEKL----HAQRIHYVLFIIFIAIIVGEVIGIHPIVGAFIC 240
                                   **8...*************************************9....788888999999********************* PP

                                   HHHHH..HHHHHTT..HHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSSX CS
                Na_H_Exchanger 245 Glvls..eyefsnk..lseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllgls 321
                                   G+++s   ++++++  l+++l+++++g+f+p+fF+++G+++++ v+ ++ls+l l+l++l++ ++ +++++f++lr+lg++
  gi|15669461|ref|NP_248271.1| 241 GVAVSeaLTKEEHDelLNKNLNAIGYGFFIPIFFLVLGMETNIRVI-FNLSNLELLLITLISAVALKFISGFIALRILGFD 320
                                   *****764444444666666**************************.59******************************** PP

                                   HHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHHHHH CS
                Na_H_Exchanger 322 lrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslkpll 379
                                   +    i g++ +++ + +l++a++g+ lgl+ +e + ++++  ++t  + ++++k ++
  gi|15669461|ref|NP_248271.1| 321 RIKNTIGGLLTVPKISASLVAASIGRELGLIGNEIFVTIVALSVITATITPIVVKHIF 378
                                   ***********************************77777777777776888888776 PP

>> CcmF_C  Cytochrome c-type biogenesis protein CcmF C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.1     0.018   1.6e+02     139     206 ..     188     255 ..     126     269 .. 0.58
   2 ?   14.5   0.2   1.8e-06     0.016      20      68 ..     333     381 ..     326     383 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.018
                        CcmF_C 139 glalavwvvlaalaelaerlrakakellarlrklprsawGmvlA.HlGvavtvlGvalvsayeverdvr 206
                                    l+la+  +   +  ++e+l+ +++  +  +  + + ++G v++ H  v+ +++Gva+++a+++e++ +
  gi|15669461|ref|NP_248271.1| 188 VLLLAIPSLSKNILGVFEKLH-AQRIHYVLFIIFIAIIVGEVIGiHPIVGAFICGVAVSEALTKEEHDE 255
                                   223333344444444444442.222222333345566778888779999*********99999887655 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.8e-06
                        CcmF_C  20 pklksggrfalvSREsaLllnNllLvvaaavVllGTLyPlvldalglgk 68 
                                   pk++++   a + RE  L+ n ++++++a++V+  T+ P+v++ + ++k
  gi|15669461|ref|NP_248271.1| 333 PKISASLVAASIGRELGLIGNEIFVTIVALSVITATITPIVVKHIFVAK 381
                                   677777788999******************************9987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2593.38
//
Query:       gi|15669462|ref|NP_248272.1|  [L=561]
Description: dihydroxy-acid dehydratase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.8e-222  739.5   0.5   2.1e-222  739.3   0.5    1.0  1  ILVD_EDD  Dehydratase family


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  739.3   0.5  1.2e-226  2.1e-222       1     517 []      39     556 ..      39     556 .. 0.98

  Alignments for each domain:
  == domain 1  score: 739.3 bits;  conditional E-value: 1.2e-226
                      ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmleaqllD 81 
                                   +p+ig++ns++e+vp+h hl+++aeavk+g+ ++gg+++efnt++++Dgiamg+egm+ysLpsRe+iad+ve m++a+ +D
  gi|15669462|ref|NP_248272.1|  39 RPFIGVVNSFTEVVPGHIHLRDIAEAVKKGIYANGGTAFEFNTMAICDGIAMGHEGMKYSLPSREIIADTVESMAKAHGFD 119
                                   7******************************************************************************** PP

                      ILVD_EDD  82 alvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaacpgaGsCs 160
                                   +lvli++CDKivPg++m+a+r+ +P+i+v+gGpm +g+ +  k+dl+svfe vga+aagki+eeel+e+e+ acpgaGsC+
  gi|15669462|ref|NP_248272.1| 120 GLVLIPSCDKIVPGMIMGAIRTGLPFIVVTGGPMFPGELRgkKYDLISVFEGVGACAAGKITEEELKEIEDIACPGAGSCA 200
                                   ************************************88545599************************************* PP

                      ILVD_EDD 161 gmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvllalGGStNavlH 241
                                   g++TAntmacl+ea+Glslp++a+ +at+ae+ ++a+++g+riv+lv+++++p +iltkeafeNAi v+lalGGStN++lH
  gi|15669462|ref|NP_248272.1| 201 GLFTANTMACLTEAMGLSLPYCATSHATTAEKIRIAKRSGMRIVDLVRNNITPDKILTKEAFENAILVDLALGGSTNTTLH 281
                                   ********************************************************************************* PP

                      ILVD_EDD 242 llAiAreagve.ltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvltvtgktlaenleeae 321
                                   ++AiA+e++ + +tlddfd+ls +vp++a+l+P g++ + dlhraGG+pavlk L+++  +++++ltv+gkt++e ++e +
  gi|15669462|ref|NP_248272.1| 282 IPAIANEVKPKfITLDDFDRLSGEVPHIASLRPGGEHFIIDLHRAGGIPAVLKVLEEK--IRKECLTVSGKTIGEIIKEVK 360
                                   ********876368******************************************66..*******************99 PP

                      ILVD_EDD 322 vkeqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseeeaveailkgkikagdvvviryeGP 402
                                     + +virp+++p+++++gl++LkG+Lap+GavvK+ av++++ k+egpArvfdseeeav+ail g+i++gdvvviryeGP
  gi|15669462|ref|NP_248272.1| 361 YIDYSVIRPVDNPVHETAGLRILKGSLAPNGAVVKIGAVNPKMYKHEGPARVFDSEEEAVDAILGGDIERGDVVVIRYEGP 441
                                   9******************************************************************************** PP

                      ILVD_EDD 403 kGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGpialvedGDiieidiekrtlelevseee 483
                                    GgpGm+Eml+ptsa++g+gl+++valitDGRfSG+s+g++ighvsPEA++gGpia+vedGDii+id+ +++l+l+++eee
  gi|15669462|ref|NP_248272.1| 442 AGGPGMREMLAPTSAICGMGLDDSVALITDGRFSGGSRGPCIGHVSPEAMAGGPIAIVEDGDIIKIDMINKKLDLALDEEE 522
                                   ********************************************************************************* PP

                      ILVD_EDD 484 laaRraawkp.ekkvktrgllakyaklvssaseGA 517
                                   +++R a+wk+ e+kvk +g+la+yaklvssa+eGA
  gi|15669462|ref|NP_248272.1| 523 IKERLAKWKKpEPKVK-KGYLARYAKLVSSADEGA 556
                                   *********9666654.*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3624.65
//
Query:       gi|15669463|ref|NP_248273.1|  [L=168]
Description: 3-isopropylmalate dehydratase LeuD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-21   74.9   0.0    9.7e-21   74.5   0.0    1.3  1  Aconitase_C    Aconitase C-terminal domain
    0.00015   21.5   0.2    0.00085   19.0   0.0    1.9  2  Aconitase_2_N  Aconitate hydratase 2 N-terminus


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   1.1e-24   9.7e-21      68     123 ..      48     102 ..       4     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 1.1e-24
                                   HHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT- CS
                   Aconitase_C  68 rykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennlikngl 123
                                   + k+++ +++v + knfG+GSSRehA+++l+  Gi  viaeSF+rIf++n+i+ gl
  gi|15669463|ref|NP_248273.1|  48 PKKVKPGDIIVGG-KNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGL 102
                                   4455677777655.****************************************97 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.043   3.8e+02      55      71 ..      55      71 ..       9      76 .. 0.80
   2 !   19.0   0.0   9.4e-08   0.00085      95     169 ..      83     159 ..      75     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.043
                                  -EEEEEEEEEES---TH CS
                 Aconitase_2_N 55 playvgdvvGtGssRks 71
                                   ++  g   G GssR  
  gi|15669463|ref|NP_248273.1| 55 DIIVGGKNFGCGSSREH 71
                                  56777788899999976 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 9.4e-08
                                   EEEEEEE-HHHHHHHHHTT-EEEE--..-TT--TT-EEEEETTTTEEEE.TT--EEEE---S-TCHHHHHHHTSHHHH CS
                 Aconitase_2_N  95 vvlGgkiaPiFfntvedsGalpiead..vskletGdvieikpkegkikk.eegevvsefklkpetlldevraggripl 169
                                    v+  + a iF+  + + G   ie++   +k+++Gd +e++  +g+ik+  +gev++  kl pe +++ + agg +p 
  gi|15669463|ref|NP_248273.1|  83 CVIAESFARIFYRNAINVGLPLIECKgiSEKVNEGDELEVNLETGEIKNlTTGEVLKGQKL-PEFMMEILEAGGLMPY 159
                                   477788999**99999999777888744689******************888888888888.89999*******9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 1462.45
//
Query:       gi|15669464|ref|NP_248274.1|  [L=179]
Description: hypothetical protein MJ_1278 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1181.88
//
Query:       gi|15669465|ref|NP_248275.1|  [L=185]
Description: hypothetical protein MJ_1279 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1141.78
//
Query:       gi|15669466|ref|NP_248276.1|  [L=157]
Description: hypothetical protein MJ_1280 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.043   13.5   0.0      0.063   13.0   0.0    1.3  1  Tetraspanin      Tetraspanin family
       0.08   13.3   9.1        4.5    7.7   9.2    2.2  1  MT0933_antitox   MT0933-like antitoxin protein
        2.1    9.0   7.4        7.1    7.2   7.4    1.9  1  YtxH             YtxH-like protein
        2.8    7.8   4.6          5    7.0   4.6    1.4  1  DUF2976          Protein of unknown function (DUF2976)


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.4e-05     0.063       5      28 ..       4      27 ..       2      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                                  XXXXXXXXXXXXXXXXXXXXXXXX CS
                                  xxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin  5 lfffnllfwligivllavGvwlrl 28
                                  ++ + ++f +ig+++l++G+wl+ 
  gi|15669466|ref|NP_248276.1|  4 ILTLLIIFAIIGLLILIFGIWLIK 27
                                  5667789***************54 PP

>> MT0933_antitox  MT0933-like antitoxin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   9.2     0.001       4.5       4      30 ..     120     146 ..      82     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.001
                MT0933_antitox   4 akdlaekhedkvdqgiDKAgdavddkt 30 
                                   + d ++++ed++d+ ++ A+d+v+d+ 
  gi|15669466|ref|NP_248276.1| 120 VEDIVKEGEDIIDDIVEEAEDFVEDVV 146
                                   468899******************976 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   7.4    0.0016       7.1      30      74 ..     109     149 ..      96     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0016
                          YtxH  30 lkekaddlkekakelleeakekakekaedlkekvkekadelkekv 74 
                                   ++e+ +++ke ++++++e     ++ ++d++e++++ ++++++++
  gi|15669466|ref|NP_248276.1| 109 VAEYGEEIKEEVEDIVKEG----EDIIDDIVEEAEDFVEDVVDDF 149
                                   5677788888888887777....7777777777777777777765 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.6    0.0011         5      64      84 ..       8      28 ..       4      30 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0011
                       DUF2976 64 fgltlvvGvvllvvviwLltk 84
                                  +++++++G ++l++ iwL++k
  gi|15669466|ref|NP_248276.1|  8 LIIFAIIGLLILIFGIWLIKK 28
                                  7899**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1536  (0.0856713); expected 358.6 (0.02)
Passed bias filter:                     1111  (0.0619666); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1201.05
//
Query:       gi|15669467|ref|NP_248277.1|  [L=1048]
Description: hypothetical protein MJ_1281 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        5.1    6.3   9.5         14    4.9   9.5    1.7  1  DUF4763   Domain of unknown function (DUF4763)


Domain annotation for each model (and alignments):
>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   9.5    0.0008        14       6      59 ..     590     642 ..     587     644 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0008
                       DUF4763   6 LpkceleveqklsqvsqseqldveeeisseselpaeqeeeeeeldLdeiydele 59 
                                   L++ce+  e++ +q+++++q++ve+e+++e+++++e  +e +  +L  + +ele
  gi|15669467|ref|NP_248277.1| 590 LENCENVNEEEENQINEEQQTNVENEQQTEQQFENED-KETNTYELPLTWKELE 642
                                   899******************************9855.8888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1048 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2027  (0.113057); expected 358.6 (0.02)
Passed bias filter:                      794  (0.0442858); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.96u 0.32s 00:00:01.28 Elapsed: 00:00:00.48
# Mc/sec: 6538.68
//
Query:       gi|15669468|ref|NP_248278.1|  [L=352]
Description: hypothetical protein MJ_1282 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-47  159.7   5.3    8.3e-47  158.6   5.3    1.6  1  DUF553          Transglutaminase-like domain
    1.6e-08   34.9   0.2    1.6e-08   34.9   0.2    3.1  3  S_layer_C       S-layer like family, C-terminal region
    2.2e-06   28.1   0.0    3.8e-06   27.3   0.0    1.4  1  Transglut_core  Transglutaminase-like superfamily
  ------ inclusion threshold ------
       0.98    9.5   4.1         12    6.1   0.4    2.6  3  TerY_C          TerY-C metal binding domain


Domain annotation for each model (and alignments):
>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.6   5.3   1.8e-50   8.3e-47       1     154 []     173     316 ..     173     316 .. 0.98

  Alignments for each domain:
  == domain 1  score: 158.6 bits;  conditional E-value: 1.8e-50
                        DUF553   1 kklkklaeklkkensketiinvlewvdenikYdyekaevvetllvlWatfftlskvdskilklietpkeilktkkgiCrDY 81 
                                   +k+k+l++klk++++k+ti n+++wv++nikYdy+k++++e+ +++W++++              tp+e++ktkkg+C DY
  gi|15669468|ref|NP_248278.1| 173 EKVKSLSYKLKGKDKKATIENIAKWVANNIKYDYDKCKKIESGKFSWDEYN--------------TPSETVKTKKGVCLDY 239
                                   589***********************************************9..............9*************** PP

                        DUF553  82 aiLTaalLlnlniskvylvsvtfenskvg.....HaavavkidgtyfvlDqklpiikideylkkllkkvkiiteveiy 154
                                   a+LT+alLln+ni + y+++v+++n++++     Ha+vavkid+tyfv+Dq++++i+i+ey++++++++++i+++ ++
  gi|15669468|ref|NP_248278.1| 240 ATLTSALLLNDNIIP-YMLDVALYNTSSLkissyHASVAVKIDNTYFVIDQQPYLIPINEYTAQTFEDNLRIASIVMF 316
                                   ***************.9*********999999****************************************999886 PP

>> S_layer_C  S-layer like family, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.2   3.5e-12   1.6e-08     144     216 ..      57     127 ..      15     130 .. 0.83
   2 ?    0.6   1.0       0.1   4.6e+02      32      73 ..     167     216 ..     139     251 .. 0.67
   3 ?    2.3   0.1     0.033   1.5e+02      27      84 ..     286     343 ..     257     351 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 3.5e-12
                     S_layer_C 144 ldsvdknLiLvGGPvvNkvtkeLedklkvaityeednksaatiavienaangndvlvvAGsDRegTkaAalal 216
                                     +  k+ iLvG P  N +tk+     k++i +  ++k++++i++  +  ng+ v+++AGsD +gT a +  +
  gi|15669468|ref|NP_248278.1|  57 KTTITKDTILVGNPEENPLTKKYIGFFKIKINKTFPGKNKGIIEK--QIINGHTVILLAGSDIQGTYASIITF 127
                                   456789*************************8888********95..89*****************9998766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.1
                     S_layer_C  32 akvvidsg.....itleykde...ekled..kvvglalkykgdkladikdkd 73 
                                   +  ++ +       +l+ kd+      e+  k v  ++ky+ dk ++i++++
  gi|15669468|ref|NP_248278.1| 167 LTPKEIEKvkslsYKLKGKDKkatI--ENiaKWVANNIKYDYDKCKKIESGK 216
                                   3333333332223556666654222..2244778888889999988888876 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.033
                     S_layer_C  27 vldweakvvidsgitleykdeekledkvvglalkykgdkladikdkdkvdianyaklk 84 
                                   v d++ ++   +  t +  +++     +v++ ++++ d ++ ik+k+  +ia y  l 
  gi|15669468|ref|NP_248278.1| 286 VIDQQPYLIPINEYTAQTFEDNLRIASIVMFRVVKERDGIKLIKEKEVPGIAIYGDLI 343
                                   44444444444443333333335556899999*************99999****9664 PP

>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   8.4e-10   3.8e-06       7      66 ..     182     248 ..     176     289 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 8.4e-10
                Transglut_core   7 ltagakdplekakaiyewvrknveys.........aprrtpgsrd.aeavletgkGncedfaslfvallR 66 
                                   l  + kd+++ ++ i++wv++n++y+          + + +++ + ++++++t+kG+c d+a+l +all 
  gi|15669468|ref|NP_248278.1| 182 L--KGKDKKATIENIAKWVANNIKYDydkckkiesGKFSWDEY-NtPSETVKTKKGVCLDYATLTSALLL 248
                                   4..667888999**************99988775223333333.36********************9985 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.9   8.7e+03      39      69 ..      16      46 ..      11      49 .. 0.66
   2 ?    6.1   0.4    0.0026        12      23      70 ..     186     233 ..     170     237 .. 0.85
   3 ?    4.3   0.0    0.0091        41      32      57 ..     263     288 ..     252     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.9
                        TerY_C 39 eeyrlagaypide.dYfelsderasnlkvnts 69
                                  + y ++  y +++  Y++l++ +  ++ v+t+
  gi|15669468|ref|NP_248278.1| 16 NIYAYEKIYDVNHvCYYTLTSVEL-QKFVKTA 46
                                  668888888888867777766544.5555555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0026
                        TerY_C  23 erelqevaleelkleveeyrlagaypidedYfelsderasnlkvntse 70 
                                   +++++ ++++++  +  +y +  + +i++  f++ + ++ +++v+t++
  gi|15669468|ref|NP_248278.1| 186 DKKATIENIAKWVANNIKYDYDKCKKIESGKFSWDEYNTPSETVKTKK 233
                                   457788899999********************************9985 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0091
                        TerY_C  32 eelkleveeyrlagaypidedYfels 57 
                                   ++ +l++++y+ + a +id++Yf   
  gi|15669468|ref|NP_248278.1| 263 NTSSLKISSYHASVAVKIDNTYFVID 288
                                   45678999**************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2371.20
//
Query:       gi|15669469|ref|NP_248279.1|  [L=254]
Description: hypothetical protein MJ_1282.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-21   77.0  23.3    2.1e-20   73.1  23.3    2.3  1  Peptidase_A24  Type IV leader peptidase family
    2.4e-06   28.0   0.1    2.4e-06   28.0   0.1    2.3  2  Arc_PepC_II    Archaeal Peptidase A24 C-terminus Type II


Domain annotation for each model (and alignments):
>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1  23.3   2.3e-24   2.1e-20       2     107 .]       7     148 ..       6     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 2.3e-24
                 Peptidase_A24   2 vlltillvlsviDldtrtlpdeltlpllllgvlfaqllllglpnlaqavlgalvgalvllli................... 63 
                                   + l++ ++++v D+++r+++d+l++++l++gv++   +ll++++l+ ++++++++++++l++                   
  gi|15669469|ref|NP_248279.1|   7 YGLICSIYGAVEDWRKREVTDFLWISMLWVGVFI---HLLYNKSLLLFFIEIFAVLFITLSVryekfnklvyigvflflls 84 
                                   6799****************************99...679***************************************** PP

                 Peptidase_A24  64 ....................slvdeqamGgGDvklaavlgaflgwerlllavlvaillgavlgl 107
                                                       +l+++++mGgGD+k++++l+++ g++++++++l+ail+++++++
  gi|15669469|ref|NP_248279.1|  85 filfksyfalsflvfyligiFLYYLNFMGGGDCKFLMGLSYLKGMFFTFIIFLNAILFVIPYCI 148
                                   *******************999***************************************986 PP

>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   1.0       1.7   1.6e+04      71      81 ..     142     152 ..     140     154 .. 0.81
   2 !   28.0   0.1   2.6e-10   2.4e-06      33      88 ..     180     236 ..     160     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.7
                   Arc_PepC_II  71 ygvPflipita 81 
                                   + +P+ i+i++
  gi|15669469|ref|NP_248279.1| 142 FVIPYCIFILL 152
                                   67999999985 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 2.6e-10
                   Arc_PepC_II  33 gkikrkfisvekeldeelrkelkkykkkgl.ieetvWvtygvPflipitaGfiialv 88 
                                   +k+k+  + ++++ +  l+ ++++ k++++  + +vWvt+ +Pfl++i +++i+ +v
  gi|15669469|ref|NP_248279.1| 180 DKVKKFETIMGDDENLSLIPNINEEKEEKKtYKGKVWVTPQLPFLVFICLSYILYIV 236
                                   44666666667677777777887777665515667******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1541.64
//
Query:       gi|15669470|ref|NP_248280.1|  [L=179]
Description: hypothetical protein MJ_1282.2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1157.53
//
Query:       gi|15669471|ref|NP_248281.1|  [L=220]
Description: hypothetical protein MJ_1283 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   10.9   0.1        0.2   10.4   0.1    1.1  1  PV-1      PV-1 protein (PLVAP)


Domain annotation for each model (and alignments):
>> PV-1  PV-1 protein (PLVAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   1.1e-05       0.2      39      91 ..      18      73 ..       8      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 1.1e-05
                          PV-1 39 iilGlvlfmvyG.nvhvstesnlqaterr..aeslysqvlglsasqanlskelnlt 91
                                  + +Gl+lf + G n ++s  s l + + +   +s+ s +++  +s++nlsk+l++ 
  gi|15669471|ref|NP_248281.1| 18 LSIGLILFFLLGfNSYTSDGSYLTVFKMKdvKNSIESCLINSLTSNSNLSKNLDML 73
                                  3479****999989999999***99877633689*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1390.62
//
Query:       gi|15669472|ref|NP_248282.1|  [L=121]
Description: hypothetical protein MJ_1284 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 797.51
//
Query:       gi|15669473|ref|NP_248283.1|  [L=184]
Description: hypothetical protein MJ_1285 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1260.95
//
Query:       gi|15669474|ref|NP_248284.1|  [L=595]
Description: hypothetical protein MJ_1286 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-25   88.9   0.9    2.3e-15   56.6   0.1    4.3  4  T2SSF     Type II secretion system (T2SS), protein F
     0.0085   15.7   1.4      0.025   14.2   1.4    1.9  1  DUF1449   Protein of unknown function (DUF1449)
  ------ inclusion threshold ------
      0.046   12.9   0.0        0.1   11.8   0.0    1.5  1  SIL1      Nucleotide exchange factor SIL1
       0.64   10.4   0.1       0.64   10.4   0.1    4.3  5  DUF3566   Transmembrane domain of unknown function (DUF3566)


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   5.1       3.8   1.7e+04     108     122 ..      69      83 ..      55      88 .. 0.65
   2 ?   -4.1   4.5       3.2   1.4e+04     106     124 ..      89     107 ..      82     108 .. 0.60
   3 !   39.4   0.1   1.1e-13   5.1e-10       5     124 ..     130     254 ..     126     255 .. 0.93
   4 !   56.6   0.1   5.1e-19   2.3e-15       1     124 [.     399     525 ..     399     526 .. 0.97

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 3.8
                                   XXXXXXXXXXXXXXX CS
                         T2SSF 108 llvvallvllillai 122
                                   +++++l++++i+l++
  gi|15669474|ref|NP_248284.1|  69 SIILGLIIFIIFLIV 83 
                                   455555555555544 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3.2
                                   XXXXXXXXXXXXXXXXXXX CS
                         T2SSF 106 llllvvallvllillaill 124
                                   +++ ++++++++il+++l+
  gi|15669474|ref|NP_248284.1|  89 AIFGLIGGIFIVILIGVLY 107
                                   3445566666666666665 PP

  == domain 3  score: 39.4 bits;  conditional E-value: 1.1e-13
                                   HHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.....SHHHHHCT-TT.TS-HHHHHHHHHHHHHT-HHHH CS
                         T2SSF   5 latllsaGvplveaLellaeeaengplaeelkriarrlraGg.....slsealertpssefpelvvqlirageeggnLaev 80 
                                   ++ l+sa +p+ve++++l++e+ +g +++e k+i+++ +        ++ +  + tps+++++++++++++   g  +  +
  gi|15669474|ref|NP_248284.1| 130 ISALSSANIPVVEIFTSLSKEDIYGGMSKEAKEIVKDTKVFNydiitTFLRRARITPSKKLSSVYYNIVASLIVGAEMKNI 210
                                   68999************************************985555555555589999********************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                         T2SSF  81 Lerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                   ++ + e l+e+r+l+  ++ ++ e l +++v+++ +++l+++++
  gi|15669474|ref|NP_248284.1| 211 FHEIYERLMEDRKLELFEAIEKVEILSEFYVIACGMIPLFVVMT 254
                                   *****************************************985 PP

  == domain 4  score: 56.6 bits;  conditional E-value: 5.1e-19
                                   HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC...T-TT.TS.-HHHHHHHHHHHHHT-H CS
                         T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale...rtpssef.pelvvqlirageeggnL 77 
                                   fl+ l +++++G+ + +a++ +a++  +gpl++++k++a ++++G +++e+++   rt+ s + ++ ++ l + + +gg++
  gi|15669474|ref|NP_248284.1| 399 FLNDLTMAVRSGMDIIRAMQVCARTN-YGPLTKIVKKMAIQMSWGRPVNEVFAdleRTEKSLIaKRIASILKECAVSGGDV 478
                                   8999**********************.**************************99999999******************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                         T2SSF  78 aevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                    ++L  +  +  +  e++r++ a+ + +++++++ +++ +    i++
  gi|15669474|ref|NP_248284.1| 479 KDILTSVTVHAYKLSEMKREISARQFIYVVVIYLSFFLYIGTSYIMV 525
                                   *************************************9998877775 PP

>> DUF1449  Protein of unknown function (DUF1449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.4   5.7e-06     0.025      31     107 ..      40     115 ..      22     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.7e-06
                       DUF1449  31 lldsllpdvdldadvepdvdadgalsklLgWLrvgrvPvLilLvlfLtlFglvGlvlqslvasllgallpallaaai 107
                                   + d+ ++++ l+a +++  ++  +   +L+ + +g + ++i+L++f  +++++Gl+   +++ l+g+l p +la   
  gi|15669474|ref|NP_248284.1|  40 IEDEKFDEILLKAGMNAVSST-YLPVVFLTSIILGLIIFIIFLIVFNIFYAIFGLIGGIFIVILIGVLYPYVLAEEK 115
                                   555555566666666444333.477889999999**************************************99755 PP

>> SIL1  Nucleotide exchange factor SIL1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.3e-05       0.1      70     136 ..     412     481 ..     387     503 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                          SIL1  70 lsariigssLRNNpeavenvlekkp......efvkelfeelselskkksdvliKRylsilqeLlqnsefvtky 136
                                    ++r +  + R N   ++++++k +      + v+e+f++l+    +++++++KR+ sil+e + +  +v++ 
  gi|15669474|ref|NP_248284.1| 412 DIIRAMQVCARTNYGPLTKIVKKMAiqmswgRPVNEVFADLER---TEKSLIAKRIASILKECAVSGGDVKDI 481
                                   57899***************99985567777889999999988...9**************998887776665 PP

>> DUF3566  Transmembrane domain of unknown function (DUF3566)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   5.1      0.22   9.7e+02      16      44 ..      65      93 ..      54      99 .. 0.64
   2 ?   -0.6   0.1      0.37   1.7e+03      22      42 ..      90     110 ..      89     122 .. 0.77
   3 ?   10.4   0.1   0.00014      0.64      55     114 ..     144     207 ..     129     210 .. 0.83
   4 ?   -1.8   0.1      0.86   3.9e+03       8      35 ..     230     257 ..     211     272 .. 0.56
   5 ?   -0.7   0.8       0.4   1.8e+03      17      62 ..     495     540 ..     482     587 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.22
                       DUF3566 16 vlklsfllsvalfivlvvavavlylvlda 44
                                  v+ +s++l++++fi+ ++ + ++y++   
  gi|15669474|ref|NP_248284.1| 65 VFLTSIILGLIIFIIFLIVFNIFYAIFGL 93
                                  44456666666666666666666665544 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.37
                       DUF3566  22 llsvalfivlvvavavlylvl 42 
                                   +++++++i++v+ + vly  +
  gi|15669474|ref|NP_248284.1|  90 IFGLIGGIFIVILIGVLYPYV 110
                                   577889999999999999654 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00014
                       DUF3566  55 vkdlvgee....ssldleevlslgrvlslaalvgvvnvvlltalatlaallYNlvadlvGGlev 114
                                   +++l++e+     s + +e+++ ++v+++ ++  ++    +t    l ++ YN+va+l+ G e+
  gi|15669474|ref|NP_248284.1| 144 FTSLSKEDiyggMSKEAKEIVKDTKVFNYDIITTFLRRARITPSKKLSSVYYNIVASLIVGAEM 207
                                   44444444444456788999**************************************999876 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.86
                       DUF3566   8 lsrvdpwSvlklsfllsvalfivlvvav 35 
                                   +++v+ +S + +     + lf+v+ v v
  gi|15669474|ref|NP_248284.1| 230 IEKVEILSEFYVIACGMIPLFVVMTVPV 257
                                   3444444444444444444444444433 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 0.4
                       DUF3566  17 lklsfllsvalfivlvvavavlylvldalgvfdkvnslvkdlvgee 62 
                                   +k  + +   +++v++   ++ly+  + + v + + +l+k++ g +
  gi|15669474|ref|NP_248284.1| 495 MKREISARQFIYVVVIYLSFFLYIGTSYIMVHSLLPTLLKNIHGLS 540
                                   5555555555666677777788888888888888888888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1308  (0.0729544); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 3886.83
//
Query:       gi|15669475|ref|NP_248285.1|  [L=270]
Description: type II secretion system protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-38  132.2   0.0    2.3e-38  131.8   0.0    1.1  1  T2SSE       Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.059   13.6   0.0       0.21   11.8   0.0    1.9  2  AAA_22      AAA domain
       0.07   13.5   0.0       0.14   12.6   0.0    1.5  1  AAA_16      AAA ATPase domain
      0.076   12.5   0.0       0.14   11.7   0.0    1.4  1  AAA_7       P-loop containing dynein motor region
      0.089   12.5   0.0       0.19   11.5   0.0    1.5  1  AAA_29      P-loop containing region of AAA domain
      0.091   12.0   0.0       0.16   11.2   0.0    1.4  1  Zeta_toxin  Zeta toxin
       0.16   12.5   0.0       0.45   11.0   0.0    1.7  2  ABC_tran    ABC transporter


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.8   0.0   9.2e-42   2.3e-38     107     268 ..       4     167 ..       2     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 131.8 bits;  conditional E-value: 9.2e-42
                         T2SSE 107 dlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnak..... 182
                                   dl+  ++ ++++ + l   ++ + +i+v+G   +GKttll+a   +i+ +  +iv +ED+ Ei+l ++n ++  ++     
  gi|15669475|ref|NP_248285.1|   4 DLIRYGSISPEMLAYLWLLIEYKNSIMVAGEVATGKTTLLNAFSLFIPPQ-MKIVSIEDTPEIRLYHENWIAGTTRsgfgg 83 
                                   67788889999999999*********************************.************************9***** PP

                         T2SSE 183 .kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagalerLeqlgaeveaaelkssilav 262
                                    + ++t+ dll+aaLR+rPD ++vGE+R++e+  + +A+ TGHl  lsT+Ha+s+  +++rL+   +++++ +l++  +  
  gi|15669475|ref|NP_248285.1|  84 eEYEITMMDLLKAALRQRPDYLIVGEVRGEEAKILFQAITTGHLA-LSTIHAKSPEAVIRRLNAEPMNIPKIMLEQLNAI- 162
                                   99******************************999**********.****************998877777777654333. PP

                         T2SSE 263 vdivvr 268
                                     + vr
  gi|15669475|ref|NP_248285.1| 163 -CMQVR 167
                                   .35555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.3e-05      0.21       4      29 ..      25      50 ..      23     110 .. 0.83
   2 ?   -1.6   0.0       1.1   2.9e+03      23      48 ..     219     248 ..     212     262 .. 0.42

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.3e-05
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                  ++++++v Ge+ tGKTtll+ +    
  gi|15669475|ref|NP_248285.1| 25 YKNSIMVAGEVATGKTTLLNAFSLFI 50
                                  7899****************998765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                        AAA_22  23 rrlleqldeeakaee....erpevvfvtlp 48 
                                   rr++e   + +k        r+e+++  ++
  gi|15669475|ref|NP_248285.1| 219 RRIAEFIGISEKEIInelhSRAEFLRNLCK 248
                                   444444332222222334444444444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.4e-05      0.14      25     123 ..      27     122 ..      22     141 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                        AAA_16  25 elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysa.laqalareellrqlldeaesaeleawreklee 103
                                   +++++ Ge ++GK++l++++   +  +  i+ ++ + +       y   ++   +r + +  ++ e +  +l  ++ + + 
  gi|15669475|ref|NP_248285.1|  27 NSIMVAGEVATGKTTLLNAFSLFIPPQMKIVsIEDTPEIR----LYHEnWIAGTTR-SGFGGEEYEITMMDLLKAALRQRP 102
                                   789*****************98888885444244444333....454456666645.555555555555555555555555 PP

                        AAA_16 104 alaavpelagaeasrllell 123
                                    + +v+e++g+ea+ l++++
  gi|15669475|ref|NP_248285.1| 103 DYLIVGEVRGEEAKILFQAI 122
                                   55567777777766666655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.4e-05      0.14      26      56 ..      19      49 ..      12      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.4e-05
                         AAA_7 26 lelllknkkpvllvGptGtGKtviikdllkk 56
                                  l ll++ k+++++ G++ tGKt++++ +   
  gi|15669475|ref|NP_248285.1| 19 LWLLIEYKNSIMVAGEVATGKTTLLNAFSLF 49
                                  56899*******************9987655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.5e-05      0.19      22      49 ..      26      53 ..      20      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.5e-05
                        AAA_29 22 kgatlltGpsGsGKSTllDAiqalLvpa 49
                                  k++++++G+  +GK+Tll A++  + p+
  gi|15669475|ref|NP_248285.1| 26 KNSIMVAGEVATGKTTLLNAFSLFIPPQ 53
                                  56789***************98665554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.3e-05      0.16      15      58 ..      25      69 ..      22      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.3e-05
                    Zeta_toxin 15 rPklillgGqpGAGKselaellkdelerqgnvvrldpD.dlRelh 58
                                  ++ +i+++G  + GK++l++++   + +q ++v ++ + ++R +h
  gi|15669475|ref|NP_248285.1| 25 YKNSIMVAGEVATGKTTLLNAFSLFIPPQMKIVSIEDTpEIRLYH 69
                                  6789*********************99999999995432777777 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.45       8      48 ..      23      63 ..      18      80 .. 0.85
   2 ?   -2.1   0.0         2     5e+03      31      74 ..     106     154 ..     104     199 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                                  EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkd 48
                                  ++  + + + Ge  +GK+tLl++++    p++  + +++++
  gi|15669475|ref|NP_248285.1| 23 IEYKNSIMVAGEVATGKTTLLNAFSLFIPPQMKIVSIEDTP 63
                                  5667778999********************99999888654 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
                                   HTTSS--SEEEEEETTCEGGG.....B-HHHCCHCEEEE-SS--S-TTS CS
                                   xxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  31 lagllkpteGeilldgkdlke.....qeleslrkeigvlpqepqlfpel 74 
                                   + g+++ +e +il++   + +     +  +s ++ i+ l  ep   p++
  gi|15669475|ref|NP_248285.1| 106 IVGEVRGEEAKILFQAITTGHlalstIHAKSPEAVIRRLNAEPMNIPKI 154
                                   5566666666665554444444444455555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1727.66
//
Query:       gi|15669476|ref|NP_248286.1|  [L=252]
Description: type II secretion system protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   11.1   0.8       0.19   10.5   0.8    1.2  1  MreB_Mbl  MreB/Mbl protein


Domain annotation for each model (and alignments):
>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.8     1e-05      0.19     193     264 ..      68     142 ..      57     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 1e-05
                                   SEE--HHHHHHHHHHH-BSS--HHHH.EEEEEEEETTTTCEE..EEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS CS
                      MreB_Mbl 193 nlliGertaekikieigsavkeeeee.kmeikGrdlvtglpk..evevsseevrealkepvsaiveavkevLekt 264
                                   +++iG  ++ek k+ i      ++ee k+ +k r++v+ l      e+++e++++ lke++++i + +k +L+++
  gi|15669476|ref|NP_248286.1|  68 EIIIGYDNVEKTKKYIVIEPILTKEEiKLFLKLRKVVQALLDvpVEEIDKEKLEDYLKEKIKEIFDDLKLTLDDV 142
                                   689************999887777777************97622579*************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1696  (0.0945953); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1646.97
//
Query:       gi|15669477|ref|NP_248287.1|  [L=123]
Description: hypothetical protein MJ_1288.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1345  (0.0750181); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 788.33
//
Query:       gi|15669478|ref|NP_248288.1|  [L=165]
Description: hypothetical protein MJ_1289 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1309  (0.0730102); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1057.23
//
Query:       gi|15669479|ref|NP_248289.1|  [L=312]
Description: hypothetical protein MJ_1290 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1119  (0.0624129); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1946.98
//
Query:       gi|15669480|ref|NP_248290.1|  [L=240]
Description: hypothetical protein MJ_1291 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1646.32
//
Query:       gi|15669481|ref|NP_248291.1|  [L=552]
Description: hypothetical protein MJ_1292 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 3652.05
//
Query:       gi|15669482|ref|NP_248292.1|  [L=237]
Description: hypothetical protein MJ_1292.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1716.47
//
Query:       gi|15669483|ref|NP_248293.1|  [L=231]
Description: hypothetical protein MJ_1293 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.9    9.1   4.9       0.94   10.1   2.0    2.0  2  Renin_r   Renin receptor-like protein


Domain annotation for each model (and alignments):
>> Renin_r  Renin receptor-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.31   5.6e+03      40      45 ..      25      30 ..       2      50 .. 0.43
   2 ?   10.1   2.0   5.2e-05      0.94      48      87 ..      73     112 ..      56     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.31
                       Renin_r 40 klnlak 45
                                  ++n ++
  gi|15669483|ref|NP_248293.1| 25 EVNRTS 30
                                  222222 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 5.2e-05
                       Renin_r  48 ssdYpaiFniiLwlvvvlvlaliaivvalasmdPgrDSii 87 
                                    s Yp + n+i  l++++v+ li+++++l+  +P r  +i
  gi|15669483|ref|NP_248293.1|  73 ISPYPYLLNLIKDLIILFVIGLIITIIGLLMYEPTRPKVI 112
                                   467*******************************997666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1471.05
//
Query:       gi|15669484|ref|NP_248294.1|  [L=285]
Description: fumarate hydratase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.6e-105  350.2   0.2   8.6e-105  350.0   0.2    1.0  1  Fumerase  Fumarate hydratase (Fumerase)


Domain annotation for each model (and alignments):
>> Fumerase  Fumarate hydratase (Fumerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  350.0   0.2  4.8e-109  8.6e-105       3     267 ..       6     275 ..       4     278 .. 0.97

  Alignments for each domain:
  == domain 1  score: 350.0 bits;  conditional E-value: 4.8e-109
                      Fumerase   3 aveealkeastelpedvlealkkalekEesenakevleqlleNaeiAaeeklplCqDTGiavvfvkigeeve.vetgdlee 82 
                                    v e+++ea+++lpedv++al++a++kE+se++k++l++++eN +iA+e+++plCqDTG+++vf+kig++++  e +++ e
  gi|15669484|ref|NP_248294.1|   6 VVVELFREAAIYLPEDVKNALEEAYKKESSEISKNTLKAIIENNKIAEETQVPLCQDTGVPIVFLKIGKNINsSEIMKIIE 86 
                                   6899*******************************************************************9334449999 PP

                      Fumerase  83 aineGvreaykegplRksvvadplerkntgd....nlPavihielvp..gdeleitvlakGgGsenksklkmlnpsdgleg 157
                                    i+eGv++a++e plR++vv +pl+r+n ++    n P  i+ie+ +  + e+ei +++kG+Gsen+s+lkml+psdg+eg
  gi|15669484|ref|NP_248294.1|  87 EIKEGVKKATEEVPLRPNVV-HPLTRENFKTnvglNSP-FINIEFDEslDREIEIIAFPKGAGSENMSALKMLKPSDGIEG 165
                                   9*******************.*********999999**.*****99955689***************************** PP

                      Fumerase 158 vkkfvletvkeagtnaCpPlvlgvgiGgtseeaallakkallrelgeenpdeelaeleeellekinklgiGpqGlGGkttv 238
                                   +k+fvlet+++ag+++CpP+v+g+giGgt++ a +lakkallr++ge+++d+e+a+le+ellekin+lgiG++GlGG+ t+
  gi|15669484|ref|NP_248294.1| 166 IKNFVLETIANAGGKPCPPIVVGIGIGGTADVALKLAKKALLRKIGERHRDKEIANLEKELLEKINSLGIGAMGLGGDITA 246
                                   ********************************************************************************* PP

                      Fumerase 239 ldvkierlprhiAslpvavnvsCsadRra 267
                                   ldv+ie + +h+Aslpv+++++C+adRra
  gi|15669484|ref|NP_248294.1| 247 LDVFIEIAGCHTASLPVGICIQCWADRRA 275
                                   ***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1810.83
//
Query:       gi|15669485|ref|NP_248295.1|  [L=218]
Description: hypothetical protein MJ_1295 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-10   40.0   0.6    2.2e-09   37.9   0.3    2.0  2  PHP          PHP domain
    0.00091   18.8   0.2     0.0021   17.6   0.2    1.6  1  RNase_P_p30  RNase P subunit p30
      0.008   15.7   0.1      0.011   15.2   0.1    1.2  1  PGA_cap      Bacterial capsule synthesis protein PGA_cap
  ------ inclusion threshold ------
      0.043   14.4   0.1      0.084   13.5   0.1    1.4  1  DUF5600      Domain of unknown function (DUF5600)
      0.068   13.2   0.2       0.44   10.6   0.1    2.2  3  B12-binding  B12 binding domain
      0.088   11.9   0.0       0.18   10.9   0.0    1.4  1  Dus          Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.3   7.3e-13   2.2e-09       1      72 [.       4      79 ..       4     140 .. 0.76
   2 ?   -1.1   0.0      0.66     2e+03     148     166 ..     132     149 ..     115     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 7.3e-13
                                  EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHH...HHH...HTTTTSEEEEEEE....... CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx...xxxxxxxxxxxxxxxxxxxx RF
                           PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvefyka...akk...kykagikpiiGleayvadds 72
                                  d+H+Ht +s     l + elv++a+ l++ aiaiTDh+++ +y e +++   ak+   ky ++i +i+G+e++ ++ +
  gi|15669485|ref|NP_248295.1|  4 DFHTHTVFSDG--ELIPAELVRRARVLKHRAIAITDHADFSNYKELIEKttiAKEelkKYWDDIIVIVGVELTHIPPK 79
                                  78999999944..3336************************665555551115554435559*********8766655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.66
                                   HHHHHHHHHC.T-EEEEEG CS
                                   xxxxxxxxxxxxxxxxxxx RF
                           PHP 148 eealeelakifgdyiEint 166
                                   +e++e l+++ ++++Ei +
  gi|15669485|ref|NP_248295.1| 132 KETAENLKEN-DIFVEITS 149
                                   6899999999.*****975 PP

>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   6.9e-07    0.0021      15     145 ..      18     148 ..       6     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.9e-07
                                   ...HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H.HHHHHHHHH..--EE CS
                   RNase_P_p30  15 ksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpsklqrlskvrqk..fdll 93 
                                   +++++++++ l+ +++ai+ + + ++ k+  +++  +++++elkk   ++ +  +v+l+   p+++ + +k ++     ++
  gi|15669485|ref|NP_248295.1|  18 PAELVRRARVLKHRAIAITDHADFSNYKELIEKT--TIAKEELKKYWDDIIVIVGVELTHIPPKSIPKMAKKAKDlgAEIV 96 
                                   5567888888999999999999977777777777..777888888888899999999999999977444444443114466 PP

                                   ......EEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEE CS
                   RNase_P_p30  94 ......avrPttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEin 145
                                         +v+P+ ek +  a  + dvDi+ ++       +++++t+++  e+ +++Ei+
  gi|15669485|ref|NP_248295.1|  97 vvhgetVVEPVEEKTNYYASISEDVDILAHPG------FIDKETAENLKENDIFVEIT 148
                                   113333467899******************99......79****************96 PP

>> PGA_cap  Bacterial capsule synthesis protein PGA_cap
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   3.7e-06     0.011     187     240 ..      58     109 ..      19     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.7e-06
                       PGA_cap 187 ark.eadlvivslHwgeeyqekpadeqrelaralidaGadvviGhhpHvlqgiei 240
                                   ++k + d++++    g e ++ p+++  ++a+++ d Ga +v+ h+  v++++e 
  gi|15669485|ref|NP_248295.1|  58 LKKyWDDIIVI---VGVELTHIPPKSIPKMAKKAKDLGAEIVVVHGETVVEPVEE 109
                                   34323444443...49999*********************************995 PP

>> DUF5600  Domain of unknown function (DUF5600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.8e-05     0.084       9      76 ..      20      91 ..      19      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-05
                       DUF5600  9 dlvkRaRlvkvhalllaelr..kempsvfgkek.kkkeLieelpeiyekvsrk.hnlplgdFPdvekfkekl 76
                                  +lv+RaR++k  a+ +++    ++ ++++ k +  k+eL +  ++i   v  +  ++p++  P+++k ++ l
  gi|15669485|ref|NP_248295.1| 20 ELVRRARVLKHRAIAITDHAdfSNYKELIEKTTiAKEELKKYWDDIIVIVGVElTHIPPKSIPKMAKKAKDL 91
                                  8*************9998886778899**999856*************996552689******999988776 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00015      0.44      40     115 ..      18     102 ..       3     108 .. 0.74
   2 ?   -0.5   0.0       0.4   1.2e+03      69      93 ..      82     106 ..      79     123 .. 0.66
   3 ?   -0.6   0.0      0.43   1.3e+03      12      43 ..     152     183 ..     142     196 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                   B12-binding  40 nedivaairaekpdvvglSalltsqleavkelvel.......lkrirprvkvvvGG....ahpsldpeetleak.lgiddv 108
                                   ++++v+++r +k ++++++    + +++ kel+e        lk++ ++++v+vG     ++p   p++  +ak lg + +
  gi|15669485|ref|NP_248295.1|  18 PAELVRRARVLKHRAIAIT--DHADFSNYKELIEKttiakeeLKKYWDDIIVIVGVelthIPPKSIPKMAKKAKdLG-AEI 95 
                                   589***************5..799999999999999999999************95222244555556655555777.555 PP

                   B12-binding 109 vvgeged 115
                                   vv  ge+
  gi|15669485|ref|NP_248295.1|  96 VVVHGET 102
                                   6666665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.4
                   B12-binding  69 kelvellkrirprvkvvvGGahpsl 93 
                                    ++++ +k  ++++ vv G ++++ 
  gi|15669485|ref|NP_248295.1|  82 PKMAKKAKDLGAEIVVVHGETVVEP 106
                                   5666677777777777766655554 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.43
                   B12-binding  12 lhplGlavlaaalrdagfeVq.llganvenedi 43 
                                    h++   ++a++ r+ g +   +++  ++  d+
  gi|15669485|ref|NP_248295.1| 152 GHNITNGYVANIAREFGLKTLiNTDTHAPE-DL 183
                                   677777799999999998653255555544.33 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     6e-05      0.18     140     176 ..      81     118 ..      75     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6e-05
                                   HHHHHHHHHHCT-SEEEEESSECCCTT-C.G--CHHHH CS
                           Dus 140 alelakiveaaGaqaltvHgRtraqnyeg.tadweaIk 176
                                   + ++ak++++ Ga+ ++vHg t  +  e+ t ++++I+
  gi|15669485|ref|NP_248295.1|  81 IPKMAKKAKDLGAEIVVVHGETVVEPVEEkTNYYASIS 118
                                   5789******************9999999788889886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1419.98
//
Query:       gi|15669486|ref|NP_248296.1|  [L=358]
Description: biotin synthetase BioB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.6e-15   55.4   1.2      3e-13   50.5   0.9    2.6  2  Radical_SAM    Radical SAM superfamily
    3.7e-12   46.2   0.0    9.1e-12   45.0   0.0    1.6  2  BATS           Biotin and Thiamin Synthesis associated domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.037   14.1   0.0    1.9  2  Radical_SAM_C  Radical_SAM C-terminal domain
       0.72    9.7   7.0       0.48   10.3   2.4    2.4  2  UPF0228        Uncharacterised protein family (UPF0228)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.9   6.7e-17     3e-13       6     164 ..      64     251 ..      61     254 .. 0.88
   2 ?    1.7   0.0     0.067     3e+02      26      97 ..     284     352 ..     261     356 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 6.7e-17
                                   EESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE................................ CS
                                   xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                   Radical_SAM   6 gCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilg................................ 53 
                                    C  +C+fC+++   + + + +  +s+ eile +k++  +  +  + ++                                
  gi|15669486|ref|NP_248296.1|  64 KCKEDCIFCSQSIYsKCNIPIYPLKSKKEILEYAKKI-IDE-CSKISSSiergtligaespnlmdvgypnrgfplwverfs 142
                                   6***********9987788888889999999999999.676.888888888888888888888888888888888888888 PP

                                   ...SSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHH CS
                                   ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  54 ...ggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevl 131
                                      +g  + +++f+e++e++  ++ ++ ++ v ++ +l+d+ekl++l++l   r++ +lea  +  +++++  +h++e+ +
  gi|15669486|ref|NP_248296.1| 143 ivtSGKKINDDEFIEIVEAIELIK-EETNLKVCCSLGLLDREKLKELKKLD-VRIHNNLEASKNY-FKNIC-STHSYEDKV 219
                                   8888888888*************7.**************************.*************.*****.9******** PP

                                   HHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 132 ealeklreagikrvvdrivglpGendeeleell 164
                                   ++++ +++++++ v+++ + + Ge+ ee+ +++
  gi|15669486|ref|NP_248296.1| 220 KVIKEAKKLDLE-VCSGGIFGLGESVEERIKMA 251
                                   ************.88888888889999988876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.067
                                   HHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  26 grslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerl 97 
                                    + +sv + l+++  +k  +   e+ l gg     +df+ ++++        + + ++t g  + e+ l+ +
  gi|15669486|ref|NP_248296.1| 284 IKPISVSDALKLIALYKIIMPYAEIRLAGGRIYNLRDFQSYALMVLDG--LMVGNYLTTKGRCL-EDDLKMI 352
                                   5678999999999999977779********999999999999888776..56666666666666.6665555 PP

>> BATS  Biotin and Thiamin Synthesis associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       3.5   1.6e+04       8      27 ..     150     169 ..     147     174 .. 0.71
   2 !   45.0   0.0     2e-15   9.1e-12       1      82 [.     263     354 ..     263     356 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.5
                                   -TCCCCHHHHHHHHHHSTTS CS
                          BATS   8 ikdtpllkiiaalRlllPka 27 
                                   i+d++++ i+ a+ l+  ++
  gi|15669486|ref|NP_248296.1| 150 INDDEFIEIVEAIELIKEET 169
                                   67888888887777766555 PP

  == domain 2  score: 45.0 bits;  conditional E-value: 2e-15
                                   E--B----TCCCC.................HHHHHHHHHHSTTSE.CCCTCHH-HHHHHHHHHCCT--EEE-C---TTTGG CS
                          BATS   1 siprlrpikdtpl.................lkiiaalRlllPkag.illsgResaefrdqlllklGansisagsktevggy 63 
                                   +i++l+pi++t+                  lk+ia++++++P+a+ +l++gR  + ++ q  + +  + +++g+       
  gi|15669486|ref|NP_248296.1| 263 PINILHPIEGTKAyekikngeikpisvsdaLKLIALYKIIMPYAEiRLAGGRIYNLRDFQSYALMVLDGLMVGN------- 336
                                   8**********999999*******************************************6669**********....... PP

                                   GSESSTT-TCCCCHHHHHH CS
                          BATS  64 aflttdgrsleedvkmlee 82 
                                    +ltt+gr le+d+km+++
  gi|15669486|ref|NP_248296.1| 337 -YLTTKGRCLEDDLKMIAD 354
                                   .****************85 PP

>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.2   9.7e+03      28      53 ..      87     113 ..      82     123 .. 0.67
   2 ?   14.1   0.0   8.2e-06     0.037       6      44 ..     264     302 ..     259     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.2
                 Radical_SAM_C  28 plsleeyvdlvadil.ellppdirvhR 53 
                                   + s++e ++ + +i+ e+ +    ++R
  gi|15669486|ref|NP_248296.1|  87 LKSKKEILEYAKKIIdECSKISSSIER 113
                                   556677777777777776666666666 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8.2e-06
                 Radical_SAM_C   6 lypllvikgTeLaelyksgeykplsleeyvdlvadilel 44 
                                   +  l+ i+gT+ +e  k+ge+kp+s+ ++++l+a ++ +
  gi|15669486|ref|NP_248296.1| 264 INILHPIEGTKAYEKIKNGEIKPISVSDALKLIALYKII 302
                                   5567889**************************977655 PP

>> UPF0228  Uncharacterised protein family (UPF0228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2     0.084   3.8e+02     102     115 ..      39      52 ..       2      58 .. 0.65
   2 ?   10.3   2.4   0.00011      0.48      52     116 ..     140     206 ..     138     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.084
                       UPF0228 102 airikneLekneki 115
                                   a +ikn +++n ki
  gi|15669486|ref|NP_248296.1|  39 AFKIKNRIKNNSKI 52 
                                   789******99998 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00011
                       UPF0228  52 eyiievseqaiedeevlaiLekydlqvkk...fvwCyiefgdgsekywineedairikneLeknekil 116
                                   ++ i  s + i+d+e+++i+e  +l  +     v C + + d  +     ++  +ri+n+Le   + +
  gi|15669486|ref|NP_248296.1| 140 RFSIVTSGKKINDDEFIEIVEAIELIKEEtnlKVCCSLGLLDREKLKE-LKKLDVRIHNNLEASKNYF 206
                                   5678899**************99985544222699*****77777554.566669*******988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2292.17
//
Query:       gi|15669487|ref|NP_248297.1|  [L=237]
Description: 6-carboxyhexanoate--CoA ligase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-93  311.6   4.0    3.8e-93  311.5   4.0    1.0  1  BioW      6-carboxyhexanoate--CoA ligase
  ------ inclusion threshold ------
      0.039   14.1   3.3       0.26   11.5   0.4    2.7  3  DUF1492   Protein of unknown function (DUF1492)


Domain annotation for each model (and alignments):
>> BioW  6-carboxyhexanoate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.5   4.0   4.2e-97   3.8e-93       1     241 []       6     236 ..       6     236 .. 0.98

  Alignments for each domain:
  == domain 1  score: 311.5 bits;  conditional E-value: 4.2e-97
                                   EEEEEEEEETTEEEEEEEEEEEGGGHHHHHHHHHHCCCTBTTB--SEEEEEEEE-SSCEEEEE----EEEEE-SSHHHHHH CS
                          BioW   1 ysikmRaskegkHiSGaEriveeeeieevvselleralehekgkadfinikvekvkeeeikkikaLpvetievkskeeare 81 
                                   ysikmRask+gkHiSGaEriv+++eiee+v+el++ral+he+g++dfinik+e++ +eei++i++Lp++ti++k+keeare
  gi|15669487|ref|NP_248297.1|   6 YSIKMRASKNGKHISGAERIVNKDEIEETVKELVRRALTHENGTPDFINIKIEEI-KEEITYINHLPIKTIHCKDKEEARE 85 
                                   9******************************************************.99*********************** PP

                                   HHHHHHHCCT--HHHHHHHHHHHHHGTT-SSBEEEETTTTCE--SSTTT-B---SEEETCHHHHHHHHHHTT---HHHHHH CS
                          BioW  82 lakellkeagvseeaaekalellkelenmrGAvlldaetgerleedkerGvRvtkldledekkekakkeekslskervkeA 162
                                   +ak++l+++g+ +++++ a+e++++  +mrGA++l+++ gerle+dkerGvRv+++d+++e kek+ ke+  l +er+++A
  gi|15669487|ref|NP_248297.1|  86 TAKKILRNEGIPDSVIDYAYEIIDK-GGMRGAAILNLK-GERLEPDKERGVRVKNIDTTKELKEKILKEN--LGTERTVDA 162
                                   *************************.9********999.*************************997654..59******* PP

                                   HHHHHHHHHTTTEEEEEEE-SSTT---EEEEETTTEEEEECTSS-TT----EEEEEE-GC..SGHHHHHHHHHH-EEEE CS
                          BioW 163 lvlaskvaaapgivaElCiSDdpdYttGYvatkklgYvritklKekgeekGgRvffvkkekeadleelieyLekkpvli 241
                                   +++askv+++ g++aElC+SD+++YttGYvatkk gY+rit+lK++ge +GgRvffvk++   d+e+li++Le+kp++i
  gi|15669487|ref|NP_248297.1| 163 IAIASKVIHL-GVIAELCTSDNKSYTTGYVATKK-GYFRITNLKKEGE-SGGRVFFVKDD--VDIEDLINKLENKPFII 236
                                   **********.***********************.9***********9.9*******999..89************997 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   2.8e-05      0.26      26      83 ..      23      82 ..      12      95 .. 0.83
   2 ?    2.3   0.0     0.021   1.9e+02      41      97 ..     138     194 ..     127     196 .. 0.84
   3 ?   -1.8   0.0       0.4   3.5e+03      43      57 ..     217     231 ..     212     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.8e-05
                       DUF1492 26 eLvvakediekktaeaikkklelqrlidklensdsrsvL.rmvyidkltvwqv.idklni 83
                                  e +v k++ie++ +e +++ l  ++   ++ n++   +  +++yi++l +  + +++ + 
  gi|15669487|ref|NP_248297.1| 23 ERIVNKDEIEETVKELVRRALTHENGTPDFINIKIEEIKeEITYINHLPIKTIhCKDKEE 82
                                  6799*******************************99973699****9998874555555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.021
                       DUF1492  41 aikkklelqrlidklensdsrsvLrmvyidkltvwqvidklnisrstyyrllrvavk 97 
                                    i   +el++ i k +    r+v  +    k+    vi +l  s    y++  va+k
  gi|15669487|ref|NP_248297.1| 138 NIDTTKELKEKILKENLGTERTVDAIAIASKVIHLGVIAELCTSDNKSYTTGYVATK 194
                                   577888999999888888899999999999999999999999999999988888876 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.4
                       DUF1492  43 kkklelqrlidklen 57 
                                   k   +++ li+klen
  gi|15669487|ref|NP_248297.1| 217 KDDVDIEDLINKLEN 231
                                   556778889999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1602.68
//
Query:       gi|15669488|ref|NP_248298.1|  [L=372]
Description: 8-amino-7-oxononanoate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-63  214.9   0.0      2e-63  214.8   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.3e-07   30.5   0.0    2.1e-07   29.8   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.005   15.8   0.0     0.0081   15.2   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.013   14.3   0.0      0.074   11.8   0.0    1.9  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
      0.019   14.3   0.0      0.035   13.4   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
       0.02   14.2   0.3        0.1   11.9   0.3    1.9  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.023   13.3   0.1      0.051   12.2   0.1    1.5  1  SHMT             Serine hydroxymethyltransferase
      0.058   13.2   0.2       0.12   12.1   0.2    1.6  1  Tipalpha         TNF-alpha-Inducing protein of Helicobacter
        0.2   11.7   0.1        0.2   11.7   0.1    2.0  2  MMR_HSR1_Xtn     C-terminal region of MMR_HSR1 domain


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.8   0.0     1e-66     2e-63       3     363 .]      29     365 ..      27     365 .. 0.95

  Alignments for each domain:
  == domain 1  score: 214.8 bits;  conditional E-value: 1e-66
                                   EEESSSSSTTSTTSSHHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHH CS
                 Aminotran_1_2   3 vinLgsneylgdsgkptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalie 82 
                                   v++++sn+yl +s++p++ e++k+  + ga+++g++  +g+i  ++ lee++a+f          +e+++v++sG+  +  
  gi|15669488|ref|NP_248298.1|  29 VLDFSSNDYLCLSKHPEVIEAVKEGLKyGAGSTGSRLTSGNIN-HQRLEEKIAEFKE--------TERTLVYSSGYATNVG 100
                                   799****************************************.*************........**************** PP

                                   HHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                 Aminotran_1_2  83 alifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                   ++ +l+k  +gd il++++++as++++++ls++ v  y+       h+d+e+l ++++e+  +   + +i++ ++++++G+
  gi|15669488|ref|NP_248298.1| 101 VISALCK--KGDLILSDKLNHASIIDGCKLSKADVLIYN-------HCDVEHLTNLIEENWGKY-NNLFIVTDGVFSMDGD 171
                                   ******9..******************************.......*************74333.366************* PP

                                   B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHH CS
                 Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlr 244
                                   +a+l +l+k+   a++ n++l++D+a++++v+g+ + +  ++n+++ +n++  g+lsKa G  G   G+++g ++vv++l 
  gi|15669488|ref|NP_248298.1| 172 IAPLRDLKKI---ADEFNAILIIDDAHGTGVLGDGRGTLKHFNLKPSDNIVQIGTLSKAIGGLG---GFVCGIEEVVEYLI 246
                                   **********...********************8854444************************...************** PP

                                   HHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHH CS
                 Aminotran_1_2 245 klsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskkLl 325
                                   + sr+f++s++l++ v++   +a +++ e ++ +++lqk+ k   + +++ +++  ++ + ++++   ++   +e+++ L+
  gi|15669488|ref|NP_248298.1| 247 NTSRSFIFSTALPPHVVEGCIKAFEII-EKTDIVKKLQKNIKIANKVFKKYEFIKEDNLTPIYPFIFKEKT--MEIAEHLI 324
                                   **********************99887.999*****************99999999999******998888..******** PP

                                   HTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHHHHHHHHH CS
                 Aminotran_1_2 326 eevgvyvtpgtsftv...pgrlRitv.Aglteeeleelveal 363
                                   ++ ++ ++ ++++tv    +r+R+++  g+ +e+ e l+e++
  gi|15669488|ref|NP_248298.1| 325 KN-NIFCVGIRYPTVpkgLERIRVSInVGHEKEDFELLCERI 365
                                   **.************988779*****99************98 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   1.1e-10   2.1e-07      49     181 ..      67     200 ..      56     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.1e-10
                                   T--HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHH CS
               Cys_Met_Meta_PP  49 sgnptrsvleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdlee 129
                                   sgn +++ lee+ia+ +++e++l++ssG a+   +i al+k+Gd i++++  + +  + +k     + + ++++d+++l +
  gi|15669488|ref|NP_248298.1|  67 SGNINHQRLEEKIAEFKETERTLVYSSGYATNVGVISALCKKGDLILSDKLNHASIIDGCKLSKADV-LIYNHCDVEHLTN 146
                                   6899****************************************99988877777777776555544.3445556555555 PP

                                   HHHHCCTTEEEEEEESS-TTTT..----HHHHHHHHHHTT-EEEEEGTTTHTTT CS
               Cys_Met_Meta_PP 130 lekaikentklvylEtptnpll..kvvDiekiaklakkagvlvvvDntfaspll 181
                                   l +    + + +++ t +   +  +++ ++++ k+a + ++++++D +  +++l
  gi|15669488|ref|NP_248298.1| 147 LIEENWGKYNNLFIVTDGVFSMdgDIAPLRDLKKIADEFNAILIIDDAHGTGVL 200
                                   544444466667776666555522688888999999999999999999999986 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     4e-06    0.0081      11     179 ..      42     196 ..      41     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-06
                                   --HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEE CS
                   Aminotran_5  11 kpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdei 91 
                                   k +eV++a++e ++  ++++  s++++ +  +   +  +ek+ae+ ++e   ++++ sG   a n+ ++s++   k+gd i
  gi|15669488|ref|NP_248298.1|  42 KHPEVIEAVKEGLK--YGAG--STGSRLTSGNINHQRLEEKIAEFKETER--TLVYSSGY--ATNVGVISAL--CKKGDLI 112
                                   56788888888876..5555..33333334566788999******99996..55555543..5666666663..8****** PP

                                   EEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEE.SBETTTTEB--HHHHHHHHHHTT-E CS
                   Aminotran_5  92 vvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvait.hvsnvtGtiqpveeigklakkkgal 171
                                   +  +++h + +    + +k  +a+v +++  +  +l+ + +e++  +  +l ++t  v ++ G i p+ +++k+a + +a+
  gi|15669488|ref|NP_248298.1| 113 LSDKLNHASII----DGCKLSKADVLIYNHCDVEHLT-NLIEENWGKYNNLFIVTdGVFSMDGDIAPLRDLKKIADEFNAI 188
                                   ***********....5566666777666655555555.5666666666777777725789********************* PP

                                   EEEE-TTT CS
                   Aminotran_5 172 vlvDaaqa 179
                                   +++D a +
  gi|15669488|ref|NP_248298.1| 189 LIIDDAHG 196
                                   ****9865 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.7e-05     0.074      72     129 ..      76     132 ..      64     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                                   HHHHHHHCT-SEEEEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EE CS
                      OKR_DC_1  72 qkyaarvfgadksyfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgat 129
                                   ++ +a+  +++++ +   G + +n  v+ a++++gdl+l d+ +H Si  +  ls a 
  gi|15669488|ref|NP_248298.1|  76 EEKIAEFKETERTLVYSSGYA-TNVGVISALCKKGDLILSDKLNHASIIDGCKLSKAD 132
                                   667777778888887777765.5778999********************998888774 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.8e-05     0.035      29      84 ..      67     122 ..      54     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                   T--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHH CS
               Beta_elim_lyase  29 gedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihf 84 
                                    ++ + +rLe+++ae  ++e +l   +G a n   +++l+++g+ ++ ++ +h   
  gi|15669488|ref|NP_248298.1|  67 SGNINHQRLEEKIAEFKETERTLVYSSGYATNVGVISALCKKGDLILSDKLNHASI 122
                                   5677899*********************************9999888888877644 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   5.2e-05       0.1      19     156 ..      65     204 ..      44     232 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.2e-05
                                   SSS.SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSS CS
               DegT_DnrJ_EryC1  19 lts.gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtyn 98 
                                   lts + + +++E+++a++ +++  +  ssG a++  +++al   +gd ++  +l+ ++ +      g k   +Dv +  ++
  gi|15669488|ref|NP_248298.1|  65 LTSgNINHQRLEEKIAEFKETERTLVYSSGYATNVGVISALCK-KGDLILSDKLNHASIID-----GCKLSKADVLIYNHC 139
                                   4553446677888888888888888888888888888877643.47777777776655444.....444445555555554 PP

                                   B-GGGCGGG--TTE.....EEEE...EB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTE CS
               DegT_DnrJ_EryC1  99 idpaaieaaitert.....kaIl...pVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgk 156
                                    d++++ ++i+e+        I+   +  + G++a +  lk+ia++ + ++i D Ah+ G   +g+
  gi|15669488|ref|NP_248298.1| 140 -DVEHLTNLIEENWgkynnLFIVtdgVFSMDGDIAPLRDLKKIADEFNAILIIDDAHGTGVLGDGR 204
                                   .667777777766655544333312123578***********************999999877774 PP

>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.6e-05     0.051      93     211 ..      92     200 ..      53     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.6e-05
                                   SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHHHHHHHH--SEE CS
                          SHMT  93 lsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydelekkakefkPkli 173
                                    sG  +n+ v +al ++gd il+ +l +   +  G k+++    a   +++ +   v++ t+li+ +       +++  +i
  gi|15669488|ref|NP_248298.1|  92 SSGYATNVGVISALCKKGDLILSDKLNHAS-IIDGCKLSK----ADVLIYNHC--DVEHLTNLIEEN-----WGKYNNLFI 160
                                   699999*************99998887764.456666666....455667655..688889998744.....334444445 PP

                                   EE.E.-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHH CS
                          SHMT 174 va.G.tsaysrlidyarlreiadevgayllvdmahiaGlv 211
                                   v+ G +s    +   + l++iade +a+l++d ah +G++
  gi|15669488|ref|NP_248298.1| 161 VTdGvFSMDGDIAPLRDLKKIADEFNAILIIDDAHGTGVL 200
                                   5413245556666778899****************99986 PP

>> Tipalpha  TNF-alpha-Inducing protein of Helicobacter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   6.2e-05      0.12       9      93 ..     241     327 ..     237     368 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.2e-05
                                   EEGGGBSSCTTSTTEEEEEEE--TT-HHHHHHHHHHH..HHHHHHHHHHHHHHHHHHSTT----S---HHHHHHTHHHHHH CS
                      Tipalpha   9 vpawmiedrseyitqGidsshvidGkversegiarer..arirvaihiankikeiykssqnaekkkiddeifkqitqaiaa 87 
                                   v  ++i+    +i       hv++G ++  e i +     +++  i+iank+ + y   ++ +  +i   ifk+ t  ia+
  gi|15669488|ref|NP_248298.1| 241 VVEYLINTSRSFIFSTALPPHVVEGCIKAFEIIEKTDivKKLQKNIKIANKVFKKYEFIKEDNLTPIYPFIFKEKTMEIAE 321
                                   55677777777777777789*****9999999987752257888999********************************** PP

                                   HEEEEE CS
                      Tipalpha  88 sldkev 93 
                                    l k+ 
  gi|15669488|ref|NP_248298.1| 322 HLIKNN 327
                                   998765 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0001       0.2      22      62 ..     121     162 ..     105     192 .. 0.83
   2 ?   -2.5   0.2       2.6   5.2e+03      18      31 ..     277     290 ..     267     305 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                  MMR_HSR1_Xtn  22 kilkeykihnaevliredvtvDdlidviegnr.vYipclyvl 62 
                                   +i+   k+ +a+vli ++++v+ l + ie+n  +Y + ++v 
  gi|15669488|ref|NP_248298.1| 121 SIIDGCKLSKADVLIYNHCDVEHLTNLIEENWgKYNNLFIVT 162
                                   788999**********************99976888887776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.6
                  MMR_HSR1_Xtn  18 etvkkilkeykihn 31 
                                   + vkk+ k+ ki n
  gi|15669488|ref|NP_248298.1| 277 DIVKKLQKNIKIAN 290
                                   34444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2299.41
//
Query:       gi|15669489|ref|NP_248299.1|  [L=248]
Description: dethiobiotin synthetase BioD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-49  168.0   0.2    2.7e-49  167.7   0.2    1.0  1  AAA_26       AAA domain
      3e-06   27.3   0.0    5.6e-06   26.4   0.0    1.4  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    5.5e-06   25.8   0.3     0.0012   18.2   0.1    2.5  2  DUF1611      Domain of unknown function (DUF1611_C) P-loop do
     0.0099   15.3   2.5      0.084   12.3   0.3    2.4  4  ParA         NUBPL iron-transfer P-loop NTPase
  ------ inclusion threshold ------
      0.012   15.0   2.0          3    7.1   0.2    2.7  2  CTP_synth_N  CTP synthase N-terminus
       0.04   14.1   0.0      0.098   12.9   0.0    1.6  1  CdiA_C       Contact-dependent growth inhibition CdiA C-termi
      0.041   13.8   0.2       0.43   10.5   0.1    2.2  2  NTPase_1     NTPase
      0.053   13.6   0.0      0.096   12.8   0.0    1.4  1  Torsin       Torsin
      0.077   12.3   0.0        0.1   11.9   0.0    1.2  1  MipZ         ATPase MipZ
      0.082   12.8   0.2        1.5    8.7   0.0    2.4  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
        0.2   11.1   0.2        0.6    9.5   0.1    1.8  2  adh_short    short chain dehydrogenase
       0.21   10.7   2.0        5.2    6.1   0.1    2.7  3  ArsA_ATPase  Anion-transporting ATPase
       0.31   10.9   3.2         13    5.7   0.2    2.5  2  AAA_31       AAA domain


Domain annotation for each model (and alignments):
>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.7   0.2     2e-52   2.7e-49       2     193 ..      35     238 ..      34     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 167.7 bits;  conditional E-value: 2e-52
                        AAA_26   2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgieededselikellgldqtyelpeplalsaplspelaarqe 82 
                                    if+tgtdtg+GKT vs +L++ lk+ g++vgy+KP+ tg +  ed+ ++k++l++d++ +l++p+ l+ plsp++a + e
  gi|15669489|ref|NP_248299.1|  35 MIFITGTDTGIGKTYVSSILAENLKKMGINVGYLKPVETGGR--EDTLTLKNILNTDDDLDLMNPINLKLPLSPNIAFDVE 113
                                   69***************************************7..99*********************************** PP

                        AAA_26  83 gedidlekiv.......kelekdadivvVEGagglgvpiteellnadiaknlgapvilVargglgtinqllltiealrqkn 156
                                   +  ++l++i        ++l++++d+++VEGagg++vpi e+ l+ d++k lg++ ++V r+ lgtin++llt+e+lr+k+
  gi|15669489|ref|NP_248299.1| 114 NSPLTLDEIKekiknayETLKEKYDFLIVEGAGGVCVPIKEDFLMSDLIKFLGLDAVVVSRPNLGTINHTLLTVEHLRNKG 194
                                   *****999999999**888************************************************************** PP

                        AAA_26 157 vrvlGvilNkvrnp.......envetlekksgipvlGvvPylpd 193
                                   ++v+Gvi+N++++        ++ et+ek ++i+++G+v + +d
  gi|15669489|ref|NP_248299.1| 195 INVRGVIINCITDLsevlyyeKTFETIEKVGNIEIIGIVKSRED 238
                                   **********766666666655****************988766 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   4.1e-09   5.6e-06       1     118 [.      36     239 ..      36     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.1e-09
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE.EEESSCCCCH.HTTEB-HHHH......................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxx......................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvD.aDpqannlai.leglendiep......................... 54 
                                   i+i++t  G GKT ++  La  l++ g +V  ++ + + +  +++ l+   n  +                          
  gi|15669489|ref|NP_248299.1|  36 IFITGTDTGIGKTYVSSILAENLKKMGINVGYLKpVETGGREDTLtLKNILNTDDDldlmnpinlklplspniafdvensp 116
                                   78********************************9999999999765555555555899********************** PP

                                   ..............................................................CCHCCCHHHHHHCHCHHHH CS
                                   ..............................................................xxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ..............................................................dlkrllellealgkkkall 73 
                                                                                                 ++   l ++e+l++k    
  gi|15669489|ref|NP_248299.1| 117 ltldeikekiknayetlkekydflivegaggvcvpikedflmsdlikflgldavvvsrpnlgTINHTLLTVEHLRNK---G 194
                                   *******************************************************9777444444444444444433...3 PP

                                   ..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  74 lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeav 118
                                   +++ gv++n +    e    ++ +e++++  +++++g+++ +e++
  gi|15669489|ref|NP_248299.1| 195 INVRGVIINCITDLSEVLYYEKTFETIEKVGNIEIIGIVKSREDF 239
                                   ***********99888888888888887666********999987 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   8.7e-07    0.0012      13      47 ..      34      68 ..      30      76 .. 0.89
   2 !    5.3   0.0    0.0074        10      74     105 ..     125     154 ..     116     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.7e-07
                       DUF1611 13 krvlvvGTdcavGKrttaleleealeerGlkaafv 47
                                  k +++ GTd  +GK + + +l+e l++ G++++ +
  gi|15669489|ref|NP_248299.1| 34 KMIFITGTDTGIGKTYVSSILAENLKKMGINVGYL 68
                                  789****************************9876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0074
                       DUF1611  74 aveglvkkaaeeeepdlilveGQgsLthpays 105
                                    + ++ ++++  e+ d+++veG g+++ p+ +
  gi|15669489|ref|NP_248299.1| 125 KIKNAYETLK--EKYDFLIVEGAGGVCVPIKE 154
                                   4455555555..4569**********988755 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.3   6.1e-05     0.084       4      38 ..      34      68 ..      32      75 .. 0.92
   2 ?   -2.3   0.0       1.7   2.4e+03     207     243 ..     100     135 ..      84     138 .. 0.75
   3 ?    0.6   0.1      0.22   3.1e+02     137     173 ..     167     203 ..     126     212 .. 0.81
   4 ?    2.3   0.1     0.071        97     109     172 ..     164     234 ..     150     242 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.1e-05
                          ParA  4 kviavlSgKGGVGKStvavnlAlaLakkglkvgll 38
                                  k+i ++ +  G+GK+ v++ lA +L+k+g++vg l
  gi|15669489|ref|NP_248299.1| 34 KMIFITGTDTGIGKTYVSSILAENLKKMGINVGYL 68
                                  6788999999***********************76 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                          ParA 207 geipldpeireasdegkplvlkepeseaakaleeiae 243
                                    ++pl+p+i+  +++  pl+l+e ++++++a+e++ e
  gi|15669489|ref|NP_248299.1| 100 LKLPLSPNIAFDVENS-PLTLDEIKEKIKNAYETLKE 135
                                   5789999998888765.57777778888888887765 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.22
                          ParA 137 agaviVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                    +av+V+ p+  +++++  ++e +++  ++v Gv+ N
  gi|15669489|ref|NP_248299.1| 167 LDAVVVSRPNLGTINHTLLTVEHLRNKGINVRGVIIN 203
                                   4689999999999999999999999999999999988 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.071
                          ParA 109 wgelDyLiiDlPP.GtgDeqltvaqkl.....plagaviVttpqevaladvkkaiemfkkv.kvkvlGvve 172
                                   +  lD +++  P  Gt   +l  +++l     +++g++i        +   +k++e ++kv +++++G+v+
  gi|15669489|ref|NP_248299.1| 164 FLGLDAVVVSRPNlGTINHTLLTVEHLrnkgiNVRGVIINCITDLSEVLYYEKTFETIEKVgNIEIIGIVK 234
                                   44566666666644666666666666644443444544444444444566677777666654567777775 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2    0.0022         3       1      37 [.      34      69 ..      34      71 .. 0.91
   2 ?    6.5   0.1    0.0033       4.6     114     145 ..     116     149 ..     111     243 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0022
                                  EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEE CS
                   CTP_synth_N  1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlik 37
                                  k+i++tG    g+Gk  +++ l++ lk++g++v  +k
  gi|15669489|ref|NP_248299.1| 34 KMIFITGT-DTGIGKTYVSSILAENLKKMGINVGYLK 69
                                  78999986.57*********************98876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0033
                                   CHHHHHHHHHHHHHH.H.C.T-SEEEEEE-S-TT CS
                   CTP_synth_N 114 phvtdeikeriekvakk.v.eadvviveigGtvg 145
                                   p   deike+i+++ ++ + + d++ive  G v 
  gi|15669489|ref|NP_248299.1| 116 PLTLDEIKEKIKNAYETlKeKYDFLIVEGAGGVC 149
                                   66789*******9998853369******777664 PP

>> CdiA_C  Contact-dependent growth inhibition CdiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.1e-05     0.098      37      66 ..     105     134 ..      99     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.1e-05
                        CdiA_C  37 aknivlnlrdsdlsieeikegieralkwpk 66 
                                   ++ni +++++s+l+ +eike+i++a+++ k
  gi|15669489|ref|NP_248299.1| 105 SPNIAFDVENSPLTLDEIKEKIKNAYETLK 134
                                   689*********************997644 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00031      0.43       2      31 ..      36      66 ..      35      93 .. 0.84
   2 ?    0.9   0.0      0.27   3.7e+02      19      36 ..     186     203 ..     171     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                                  EEEE--.TTSSHHHHHHHHHHHH...GGGEE CS
                      NTPase_1  2 vfiTGp.pGvGKtTlvkkvlellkssgvkvg 31
                                  +fiTG   G+GKt + + ++e+lk+ g++vg
  gi|15669489|ref|NP_248299.1| 36 IFITGTdTGIGKTYVSSILAENLKKMGINVG 66
                                  89***647********************997 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.27
                                   HHHHH...GGGEEEEEEE CS
                      NTPase_1  19 vlellkssgvkvgGfyte 36 
                                    +e l+++g++v+G++ +
  gi|15669489|ref|NP_248299.1| 186 TVEHLRNKGINVRGVIIN 203
                                   5799**********9876 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.9e-05     0.096      61      88 ..      42      69 ..      18      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.9e-05
                                  -TTSSHHHHHHHHHHHHSTTGGGSTTEE CS
                        Torsin 61 wtGtGknfvaeiiaenlyrdGlrsdyvk 88
                                   tG Gk +v++i+aenl + G++  y k
  gi|15669489|ref|NP_248299.1| 42 DTGIGKTYVSSILAENLKKMGINVGYLK 69
                                  589******************9988765 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.2e-05       0.1       3     110 ..      36     147 ..      34     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.2e-05
                                   EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE.--TTT-HHHHHHHHHHHHHHHHT------EEE-SSS-HHHHTTS-. CS
                          MipZ   3 ivlgnekGGsGksttavhvavaLlkkGarvaaid.ldlrqrtlarylenraataerkglsLplpealalseaeeaeveee. 81 
                                   i ++    G Gk+ ++  +a  L k+G +v+ +  +++  r  +  l+n ++t +  +l  p+   l ls + + +ve++ 
  gi|15669489|ref|NP_248299.1|  36 IFITGTDTGIGKTYVSSILAENLKKMGINVGYLKpVETGGREDTLTLKNILNTDDDLDLMNPINLKLPLSPNIAFDVENSp 116
                                   5566667899*********************98546666666666688888887777776666666666666666666542 PP

                                   ..HHHHHHHHHHHHHHHHHH-SEEEEE--SS CS
                          MipZ  82 ..eeaevaeleelvadleaeldfividtPGs 110
                                      ++  ++++++ + l++++df++++  G 
  gi|15669489|ref|NP_248299.1| 117 ltLDEIKEKIKNAYETLKEKYDFLIVEGAGG 147
                                   2223444799****************98886 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0011       1.5       2      36 ..      36      71 ..      35      93 .. 0.86
   2 ?    1.6   0.0      0.17   2.4e+02      76      98 ..     121     144 ..     111     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                          MobB  2 lgivgk.sgsGKTtLleklipelkarglrvgtiKha 36
                                  + i+g+  g GKT   + l + lk+ g++vg++K  
  gi|15669489|ref|NP_248299.1| 36 IFITGTdTGIGKTYVSSILAENLKKMGINVGYLKPV 71
                                  5666664799***********************965 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.17
                          MobB  76 eaelsleellarl.sevDlvlvEG 98 
                                   e + ++++  ++l +++D+++vEG
  gi|15669489|ref|NP_248299.1| 121 EIKEKIKNAYETLkEKYDFLIVEG 144
                                   4456788888899556*******9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00044       0.6       1      27 [.      34      60 ..      34      73 .. 0.87
   2 ?   -1.3   0.0      0.92   1.3e+03      64      87 ..     126     147 ..     114     214 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00044
                                  SEEEEESTTSHHHHHHHHHHHHTT-EE CS
                     adh_short  1 kvvlvtGassGIGraiakelakeGakv 27
                                  k++++tG + GIG+ ++  +++e+ k 
  gi|15669489|ref|NP_248299.1| 34 KMIFITGTDTGIGKTYVSSILAENLKK 60
                                  789*************99999998876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.92
                                   HHHHHHHHHHHHSSESEEEE---S CS
                     adh_short  64 vealvekavkklgkldvLvnNAGi 87 
                                   +++++e+ ++k++ l  +v +AG 
  gi|15669489|ref|NP_248299.1| 126 IKNAYETLKEKYDFL--IVEGAGG 147
                                   445555555444332..3455554 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0038       5.2       2      30 ..      34      63 ..      33      67 .. 0.86
   2 ?   -0.7   0.0      0.46   6.4e+02     180     205 ..     112     137 ..      81     154 .. 0.69
   3 ?    2.8   0.1     0.039        53     210     245 ..     170     205 ..     167     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0038
                                  EEEEEEES.TTSSHHHHHHHHHHHHHHTTS CS
                   ArsA_ATPase  2 kvilvgGK.GGVGKttvsaatavklsekgk 30
                                  k+i+++G   G+GKt vs+ +a +l ++g 
  gi|15669489|ref|NP_248299.1| 34 KMIFITGTdTGIGKTYVSSILAENLKKMGI 63
                                  7899999637************99998875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.46
                                   HHHHHHHHHHHHHHHHHHHHHHTSTT CS
                   ArsA_ATPase 180 ieealeeleetkeeikkveeiltdpe 205
                                   +e+   +l+e ke+ik++ e+l+++ 
  gi|15669489|ref|NP_248299.1| 112 VENSPLTLDEIKEKIKNAYETLKEKY 137
                                   45455567777777777777777654 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.039
                                   EEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE CS
                   ArsA_ATPase 210 rlVvipEklslkEteRaikeLkkygikvdavivNkl 245
                                   ++V+ p   +++ t   +++L + gi+v  vi+N +
  gi|15669489|ref|NP_248299.1| 170 VVVSRPNLGTINHTLLTVEHLRNKGINVRGVIINCI 205
                                   56888888899999999*****************76 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3     0.011        16       2      33 ..      34      65 ..      33      67 .. 0.89
   2 ?    5.7   0.2    0.0092        13      98     124 ..     117     143 ..      87     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.011
                        AAA_31  2 kvIaianqKGGvGKTTtsvnlaaalaklgkkv 33
                                  k+I i+    G+GKT  s  la+ l k+g  v
  gi|15669489|ref|NP_248299.1| 34 KMIFITGTDTGIGKTYVSSILAENLKKMGINV 65
                                  7788888899*****************99765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0092
                        AAA_31  98 velekkeeilkellekvkdeYDyiiiD 124
                                   ++l++ +e +k++ e++k++YD+ i+ 
  gi|15669489|ref|NP_248299.1| 117 LTLDEIKEKIKNAYETLKEKYDFLIVE 143
                                   4556667788*************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      703  (0.0392102); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1595.53
//
Query:       gi|15669490|ref|NP_248300.1|  [L=464]
Description: adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   3.8e-115  384.8   0.0   4.7e-115  384.5   0.0    1.0  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.5   0.0  2.6e-119  4.7e-115       6     406 .]      32     459 ..      25     459 .. 0.96

  Alignments for each domain:
  == domain 1  score: 384.5 bits;  conditional E-value: 2.6e-119
                                   B--SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-. CS
                   Aminotran_3   6 ednlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkg 86 
                                   ++n  l+i+++eG+yl d  g++ylD+vssi+ +++Gh+  ++++a+k+qa+k+ h  +   +n p++ la+kl++++pk+
  gi|15669490|ref|NP_248300.1|  32 SKN--LIIERGEGNYLIDIYGNKYLDAVSSIWCNLFGHSRKEIIEAIKNQADKICHSTLLGCGNVPSILLAKKLVDITPKH 110
                                   334..99************************************************************************** PP

                                   .SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGG CS
                   Aminotran_3  87 ldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeev 167
                                   l kvf+ + G+eAve A+K+a +y++ ++ + +tk+i++k+++HG+t+ga+sv+gs +  +  f+p+l + ++++ p++++
  gi|15669490|ref|NP_248300.1| 111 LTKVFYSEDGAEAVEIAIKMAYQYYVLRGDKGRTKFISVKEGYHGDTVGAMSVGGS-ELFHGVFKPLLFKGYHANPPYCYR 190
                                   ********************************************************.************************ PP

                                   TB-HH.......HHHHHHHHHHHHHH...CHTCCCEEEEEE-S.CETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTT CS
                   Aminotran_3 168 lkene.......eeeaalleeleale...kkkkdevaAvivEp.iqgegGvvvaspeflaklrelckkhdvllivDEvqtG 237
                                   +k+++       +e+ + +e+l++++   +k+++ev  vi+E  i g +G++++++++++++++ ck++dv++i DEv+tG
  gi|15669490|ref|NP_248300.1| 191 CKYHNfkdtderNEKGCEMECLNEMIsliEKHAEEVFCVILEGgIMGSAGMIPYPDGYIEGVAKACKENDVIFILDEVATG 271
                                   ***99999999877788888888888888**************************************************** PP

                                   TTTTSSSSGGGGCTS....--SEEEE-GGGGTT.SS-EEEEEEHHHHTTS-TTS........B--TTTT-HHHHHHHHHHH CS
                   Aminotran_3 238 fGrTGklfAlehagv....spDlmtlaKaltgG.lplsavlataevmqalapgs........hgsTfgGnplacavalavl 305
                                   fGrTGk+f +++ ++    +pD+++l+K+ltgG lpl+a+l+t+e+++++  g+        hg+T++Gn l c++ala+l
  gi|15669490|ref|NP_248300.1| 272 FGRTGKMFFCDNEELkkleKPDILCLGKGLTGGyLPLAATLTTDEIYNQF-LGEfgeskqlyHGHTYTGNQLLCSAALATL 351
                                   ***********996533337******************************.66678999********************** PP

                                   HHHHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC.........HHHHHHHHHCTEE-EEE CS
                   Aminotran_3 306 eiieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke.........keilkkakekGvlilsa 377
                                   ei+e+e+++en+q + + + ++L++l++ + ++++vRg+G+m++iel++++e+ke         +++++k++ekG++++++
  gi|15669490|ref|NP_248300.1| 352 EIFEKENVIENIQPKIKLFHKELRKLKELE-HVGDVRGRGFMVGIELVKDKETKEpypygykagYRVAEKLLEKGIYMRPI 431
                                   ***************************997.*********************999*********99*************** PP

                                   TTTEEEE---TT--HHHHHHHHHHHHHHH CS
                   Aminotran_3 378 Gdnvirllppliitdeeidelleilkkal 406
                                   G nvi l+ppl it++ei  l+++l +a+
  gi|15669490|ref|NP_248300.1| 432 G-NVIILVPPLSITEKEIIYLCDALYEAI 459
                                   *.****************99999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2925.12
//
Query:       gi|15669491|ref|NP_248301.1|  [L=400]
Description: hypothetical protein MJ_1301 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-93  310.4  13.1    2.5e-76  256.6   5.0    2.9  3  ATPase_2       ATPase domain predominantly from Archaea
    1.5e-07   32.0   0.0      5e-07   30.3   0.0    1.9  2  AAA_16         AAA ATPase domain
    3.6e-07   30.3   6.7     0.0017   18.4   0.1    3.3  3  AAA_14         AAA domain
    4.7e-07   30.1   0.0    1.5e-06   28.5   0.0    1.8  2  AAA_22         AAA domain
    6.4e-05   21.9   0.1      0.036   12.9   0.0    2.6  2  AAA_35         AAA-like domain
    0.00048   20.6   0.0      0.013   15.9   0.0    2.7  2  AAA            ATPase family associated with various cellular
  ------ inclusion threshold ------
      0.024   13.8   0.3        1.4    8.0   0.0    2.6  2  NB-ARC         NB-ARC domain
      0.039   13.6   0.1       0.19   11.3   0.0    2.2  3  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.067   13.6   0.4        2.1    8.8   0.0    3.0  3  RNA_helicase   RNA helicase
      0.077   13.1   1.9       0.13   12.4   0.3    2.3  2  MMR_HSR1       50S ribosome-binding GTPase
      0.097   12.7   1.4        1.2    9.2   0.1    2.8  3  Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen r
       0.14   12.7   1.0        1.4    9.5   0.0    2.7  2  RPAP3_C        Potential Monad-binding region of RPAP3
       0.46   10.3   2.3        1.4    8.8   0.0    2.7  4  TK             Thymidine kinase
       0.79    9.5   2.1        1.6    8.5   1.4    1.7  2  FTCD_C         Formiminotransferase-cyclodeaminase


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.6   5.0     2e-79   2.5e-76       1     191 [.      10     214 ..      10     218 .. 0.96
   2 !   57.1   0.0   1.9e-18   2.4e-15     176     233 .]     244     302 ..     238     302 .. 0.92
   3 ?    0.8   0.2      0.29   3.7e+02      92     119 ..     312     339 ..     303     399 .. 0.71

  Alignments for each domain:
  == domain 1  score: 256.6 bits;  conditional E-value: 2e-79
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...eeeekkkl 78 
                                   Ff+Reke+ ++++i+e epn iyfiYG+++sGKtaL++eii+n++dk+ky+++y++lre++isk+d+fie   ee+e +k 
  gi|15669491|ref|NP_248301.1|  10 FFNREKEIHKILSIIEGEPNLIYFIYGSINSGKTALINEIINNRLDKNKYIVFYFDLREIFISKYDDFIEvlfEEYEGDKS 90 
                                   9************************************************************************88877754 PP

                      ATPase_2  79 ekal............giavpkaeleeilk.eksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLl 146
                                      +            gi++pk++l+ei+k +++k+vf++i+++l++ik++gk++iiiiDelqk++d+++n  ++l++eL+
  gi|15669491|ref|NP_248301.1|  91 PIEVikaiindlpslyGIPIPKNTLNEIFKkKTTKNVFRYITNVLMDIKREGKQPIIIIDELQKIGDMKIN--GFLIYELF 169
                                   44446899**********************9****************************************..******** PP

                      ATPase_2 147 nliesltkekhlcvviclsSeglfiervyneselegrhkyilvdd 191
                                   n+++sltk+khlc+v+clsS++lfiervyne++le+r++yilvdd
  gi|15669491|ref|NP_248301.1| 170 NYFVSLTKHKHLCHVFCLSSDSLFIERVYNEAMLEDRVDYILVDD 214
                                   *******************************************98 PP

  == domain 2  score: 57.1 bits;  conditional E-value: 1.9e-18
                      ATPase_2 176 neselegrhkyilvddldketalnflkegfkel.eelskedfeeiyryvGGkPkalvel 233
                                   n++    r +yilvdd+dketal+f+++++ke+  +l++ed+e+iy+yvGGkP  ++++
  gi|15669491|ref|NP_248301.1| 244 NRGFASMRGEYILVDDFDKETALKFMDFLAKENnMSLTNEDKELIYNYVGGKPVLIIKV 302
                                   56777889*************************8889*******************987 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.29
                      ATPase_2  92 eeilkeksklvfkaielllekikkkgkk 119
                                   + il+   k+++++++++le++k++  +
  gi|15669491|ref|NP_248301.1| 312 NDILDFMLKDATQKLKYFLEDVKEEDEE 339
                                   5555555666666666666666665543 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   3.9e-10     5e-07       1     150 [.       9     158 ..       9     175 .. 0.75
   2 ?   -2.6   0.0       4.7   6.1e+03     138     161 ..     254     275 ..     249     288 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 3.9e-10
                        AAA_16   1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellr.alekdggiflrgkcdqlesaipysalaqalare 79 
                                   +++ Re+e++++ls++e    g+p  + +++G   +GK++l++e+ + +l k++ i+++ + ++         +++     
  gi|15669491|ref|NP_248301.1|   9 KFFNREKEIHKILSIIE----GEPnLIYFIYGSINSGKTALINEIINnRLDKNKYIVFYFDLREI--------FISKY-D- 75 
                                   6899*****99999998....999899***************99996477777788888888888........55555.2. PP

                        AAA_16  80 ellrqllde..aesaeleawrekleeala....avpelagaea......srllellkrllallsrderplvlvlDdlqwad 148
                                   ++++ l +e   +++  e  ++ + +  +    ++p+ +  e       + +++ +++ l+ ++r++++ ++++D+lq++ 
  gi|15669491|ref|NP_248301.1|  76 DFIEVLFEEyeGDKSPIEVIKAIINDLPSlygiPIPKNTLNEIfkkkttKNVFRYITNVLMDIKREGKQPIIIIDELQKIG 156
                                   44444444433223345555554444444666844444444445666799999999****999999999*********987 PP

                        AAA_16 149 ea 150
                                   ++
  gi|15669491|ref|NP_248301.1| 157 DM 158
                                   75 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.7
                        AAA_16 138 vlvlDdlqwadeaslqllaaLlrl 161
                                   ++++Dd++  +e+ l+++++L+++
  gi|15669491|ref|NP_248301.1| 254 YILVDDFD--KETALKFMDFLAKE 275
                                   68999999..56667777766665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.3e-06    0.0017       3      62 ..      30      87 ..      28     101 .. 0.79
   2 !   13.1   0.1   5.7e-05     0.073      49     118 ..     124     208 ..     104     213 .. 0.71
   3 ?    0.6   0.5      0.41   5.2e+02      14      62 ..     294     335 ..     285     362 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklke 62
                                   i++i G   +GKT l++++i+++l +k++++ + +d  +    +++++++e+++e++++
  gi|15669491|ref|NP_248301.1| 30 LIYFIYGSINSGKTALINEIINNRL-DKNKYIVFYFDLREIFI-SKYDDFIEVLFEEYEG 87
                                  58999********************.88888888888766653.4455678888887544 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.7e-05
                        AAA_14  49 pekllelileklke....ekktylflDEiqev..........pewekalkslvdegknldvivtGSnskllskeiats.la 114
                                   ++++ ++i + l++     k+ ++++DE q++           e++++  sl ++++ ++v++  S s+++ +  ++  l 
  gi|15669491|ref|NP_248301.1| 124 TKNVFRYITNVLMDikreGKQPIIIIDELQKIgdmkingfliYELFNYFVSLTKHKHLCHVFCLSSDSLFIERVYNEAmLE 204
                                   22344444443222333468899*********999999999988888888999999899********99998866654145 PP

                        AAA_14 115 grva 118
                                   +rv+
  gi|15669491|ref|NP_248301.1| 205 DRVD 208
                                   5555 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.41
                        AAA_14  14 GKTtllkqlikellvkkesilyinldderdkkladpekllelileklke 62 
                                   GK +l+ ++i++l        y nl+d  d +l+d ++ l+++le +ke
  gi|15669491|ref|NP_248301.1| 294 GKPVLIIKVIDKLR-------YENLNDILDFMLKDATQKLKYFLEDVKE 335
                                   55555555554444.......6666666666666555556666666444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.2e-09   1.5e-06       6     128 ..      30     186 ..      25     192 .. 0.88
   2 ?   -2.1   0.0       3.2   4.1e+03      92     116 ..     295     318 ..     254     332 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.2e-09
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka.............. 70 
                                    i +++G   +GKT l++++ ++       ++++  v++++l +    + +d+ + l+++++ +++               
  gi|15669491|ref|NP_248301.1|  30 LIYFIYGSINSGKTALINEIINNRL-----DKNKYIVFYFDLREIFisKYDDFIEVLFEEYEGDKSPievikaiindlpsl 105
                                   5789*****************9984.....34577777999999999999999*********99999************** PP

                        AAA_22  71 ..............erlsseellealeqalrarav...ielliiDEaqhlr..s......eealeeLrsllnlsrkgvqli 126
                                                 + ++++ +++++++ l + ++   ++++iiDE q++   +       e++++++sl +  +k++ ++
  gi|15669491|ref|NP_248301.1| 106 ygipipkntlneifKKKTTKNVFRYITNVLMDIKRegkQPIIIIDELQKIGdmKingfliYELFNYFVSLTK--HKHLCHV 184
                                   ****************************9999999999************6552667777888888888888..8888888 PP

                        AAA_22 127 Lv 128
                                   ++
  gi|15669491|ref|NP_248301.1| 185 FC 186
                                   76 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.2
                        AAA_22  92 ielliiDEaqhlrseealeeLrsll 116
                                   +++lii  +++l + e+l+++ +++
  gi|15669491|ref|NP_248301.1| 295 KPVLIIKVIDKL-RYENLNDILDFM 318
                                   356777777777.777777776554 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0031         4      35      70 ..      33      69 ..       8      85 .. 0.67
   2 !   12.9   0.0   2.8e-05     0.036     207     275 ..     270     340 ..     251     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0031
                        AAA_35 35 rikapkkmGKtSLlarilakakqq.gyktvsldlqla 70
                                   i ++ + GKt L+++i+++  ++ +y ++++dl+++
  gi|15669491|ref|NP_248301.1| 33 FIYGSINSGKTALINEIINNRLDKnKYIVFYFDLREI 69
                                  4777888999999999998765541667778887764 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.8e-05
                        AAA_35 207 qeLaqryglelsekqleqLmslvgGhPylvrlalyhlaqeelt..leelleeaateegiYsdhLrrllvkL 275
                                     La++ +++l++++ e +++ vgG+P l+ + +++l  e+l+  l+ +l++a+++ + + +  ++  ++L
  gi|15669491|ref|NP_248301.1| 270 DFLAKENNMSLTNEDKELIYNYVGGKPVLIIKVIDKLRYENLNdiLDFMLKDATQKLKYFLEDVKEEDEEL 340
                                   459999**********************************8877799999999999888887777766666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     1e-05     0.013       3     101 ..      34     180 ..      32     211 .. 0.71
   2 ?   -2.7   0.0       5.6   7.2e+03      38      56 ..     291     309 ..     270     339 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                                   EESSTTSSHHHHHHHHHHH.H...THEEEEEETTTCS.SS......................................... CS
                           AAA   3 lyGppGtGKTllakavake.l...gvefleisgsell.sk......................................... 37 
                                   +yG    GKT+l++ ++++ l   +  ++ +++ e++ sk                                         
  gi|15669491|ref|NP_248301.1|  34 IYGSINSGKTALINEIINNrLdknKYIVFYFDLREIFiSKyddfievlfeeyegdkspievikaiindlpslygipipknt 114
                                   799999999999999999952433344566666666655566667777777777788888888888888888888888888 PP

                                   ........STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSS CS
                           AAA  38 ........yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkes 101
                                           + ++  + i +++ ++k++ k+ i++iDE+ +++  +       +  ++ +L++ +  ++k+++
  gi|15669491|ref|NP_248301.1| 115 lneifkkkTTKNVFRYITNVLMDIKREGKQPIIIIDELQKIGDMK------INGFLIYELFNYFVSLTKHKH 180
                                   888866667777788888888888888877**********98776......555555555555555555555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.6
                                   STTHHHHHHHHHHHHHHHT CS
                           AAA  38 yvgesekkirelfkeakek 56 
                                   yvg ++  i +++++++ +
  gi|15669491|ref|NP_248301.1| 291 YVGGKPVLIIKVIDKLRYE 309
                                   4444444444444444333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0011       1.4       9      45 ..      18      53 ..      13      81 .. 0.72
   2 ?    3.0   0.2     0.039        50      64     108 ..     336     378 ..     273     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0011
                                  HHHHHC.TTTSCSEEEEEEESTTSSHHHHHHHHCCSHC CS
                        NB-ARC  9 iekLle.kdelqslvvalvGmgGvGKttlakqilnksd 45
                                   + L+  ++e++ l+ +++G   +GKt l+++i+n+  
  gi|15669491|ref|NP_248301.1| 18 HKILSIiEGEPN-LIYFIYGSINSGKTALINEIINN-R 53
                                  344444357888.999*****************998.2 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.039
                                   HHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCCCTTEEEE CS
                        NB-ARC  64 kseeiletilkeLslseddleekeeveslkrklvrlLltkrfllv 108
                                   + ee+ ++++  L+l ++d e+ +  + + +k++++L++++ l++
  gi|15669491|ref|NP_248301.1| 336 EDEELYKKVVDALKLFKEDYEIED-IK-IPKKIREFLIKRNILFL 378
                                   457888999999988877776665.44.799*********99986 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.19       3      28 ..      32      57 ..      30      73 .. 0.78
   2 ?   -2.0   0.0       1.8   2.3e+03      23      46 ..     139     165 ..     131     215 .. 0.53
   3 ?   -3.4   0.0       4.9   6.3e+03     117     149 ..     343     380 ..     333     386 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                  EEEEESTTCCHHHHHHHHHCT--SS- CS
                          cobW  3 tvltGflGsGKTtLlnhllenraglk 28
                                  + + G++ sGKT+L+n++++nr +++
  gi|15669491|ref|NP_248301.1| 32 YFIYGSINSGKTALINEIINNRLDKN 57
                                  67899**************8876654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                                   T--SS-EEEEESS-SS...CHCCCCCC CS
                          cobW  23 nraglklavivNefge...vsiDaell 46 
                                   +r+g++  +i+ e+++   ++i++ l+
  gi|15669491|ref|NP_248301.1| 139 KREGKQPIIIIDELQKigdMKINGFLI 165
                                   567777777777766411144444444 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 4.9
                                   EEEETTTH......CCHCCHHHHHHHHHHTSSEEEEE- CS
                          cobW 117 avvDaknl.....eaeeekieekaedqlaaadllvlnK 149
                                    vvDa +l     e e+ ki++k+++ l + ++l ln 
  gi|15669491|ref|NP_248301.1| 343 KVVDALKLfkedyEIEDIKIPKKIREFLIKRNILFLNP 380
                                   57888776666665566677777777777777777775 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0016       2.1       2      62 ..      33      89 ..      32     134 .. 0.74
   2 ?   -0.0   0.0      0.88   1.1e+03      49      77 ..     143     173 ..     104     183 .. 0.73
   3 ?    0.9   0.0      0.46   5.9e+02      29      62 ..     273     307 ..     248     339 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                  RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvk 62
                                  ++yG+ + GK+ l++e++++ l+k     k  v++   ++ f ++Y++   v++++   +k
  gi|15669491|ref|NP_248301.1| 33 FIYGSINSGKTALINEIINNRLDKN----KYIVFYFDLREIFISKYDDFIEVLFEEYEGDK 89
                                  79**************888887444....33344457777777888777777777666665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.88
                  RNA_helicase  49 gqevvvidDfgqvkdee.nps.dlaelirlv 77 
                                   +q++++id++ ++ d + n   +++ ++  v
  gi|15669491|ref|NP_248301.1| 143 KQPIIIIDELQKIGDMKiNGFlIYELFNYFV 173
                                   6999999999999888766665555555555 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.46
                  RNA_helicase  29 kkkdsvysrnpeddfwdgYt.gqevvvidDfgqvk 62 
                                    k++++   n +++  ++Y  g++v++i  + + +
  gi|15669491|ref|NP_248301.1| 273 AKENNMSLTNEDKELIYNYVgGKPVLIIKVIDKLR 307
                                   34455555888888888888777777776555555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   9.9e-05      0.13       4      26 ..      34      56 ..      32     161 .. 0.84
   2 ?   -1.5   0.1       2.1   2.7e+03     108     108 ..     326     326 ..     275     376 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.9e-05
                                  EEESTTSSHHHHHHHHHTSTEEE CS
                      MMR_HSR1  4 ivGrpNvGKStLinaltgekaiv 26
                                  i+G  N+GK+ Lin +++++   
  gi|15669491|ref|NP_248301.1| 34 IYGSINSGKTALINEIINNRLDK 56
                                  89***************986544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                                   E CS
                      MMR_HSR1 108 l 108
                                   l
  gi|15669491|ref|NP_248301.1| 326 L 326
                                   1 PP

>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00093       1.2      44     105 ..      10      71 ..       6      73 .. 0.91
   2 ?   -3.6   0.0         9   1.1e+04      21      33 ..     155     167 ..     149     169 .. 0.78
   3 ?    1.4   0.0      0.25   3.2e+02      49      91 ..     283     322 ..     265     334 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00093
                 Nit_Regul_Hom  44 gflleedpesaikiikdlseeavlintvvdeekvekikeeleeklkderytiieipvekikv 105
                                    f+ e +++++++ii+ + +   +i   +++ k   i+e ++++l++++y +   ++++i +
  gi|15669491|ref|NP_248301.1|  10 FFNREKEIHKILSIIEGEPNLIYFIYGSINSGKTALINEIINNRLDKNKYIVFYFDLREIFI 71 
                                   5777889999999**999999999********************************999977 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9
                 Nit_Regul_Hom  21 lseagitGfylie 33 
                                   + ++ i Gf ++e
  gi|15669491|ref|NP_248301.1| 155 IGDMKINGFLIYE 167
                                   5678899999987 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.25
                 Nit_Regul_Hom  49 edpesaikiikdlseeavlintvvdeekvekikeeleeklkde 91 
                                   ed e +++ +     + vli  v+d+ + e++++ l+  lkd 
  gi|15669491|ref|NP_248301.1| 283 EDKELIYNYV---GGKPVLIIKVIDKLRYENLNDILDFMLKDA 322
                                   5555555444...56889********99999999998888875 PP

>> RPAP3_C  Potential Monad-binding region of RPAP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0011       1.4      29      83 ..     110     159 ..      78     165 .. 0.87
   2 ?    0.4   0.3      0.74   9.5e+02      48      73 ..     312     348 ..     275     353 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                       RPAP3_C  29 inpkqlpkiFknsledeilsdildalnerlqeekaedsslvleiLdrLskvkRFd 83 
                                   i++++l +iFk++ + +++  i ++l + ++e k++     + i d+L+k+  ++
  gi|15669491|ref|NP_248301.1| 110 IPKNTLNEIFKKKTTKNVFRYITNVLMDIKREGKQP-----IIIIDELQKIGDMK 159
                                   8899****************************9877.....88999999987766 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.74
                       RPAP3_C  48 sdild...........alnerlqeekaedsslvleiL 73 
                                   +dild           ++ e ++ee++e  ++v++ L
  gi|15669491|ref|NP_248301.1| 312 NDILDfmlkdatqklkYFLEDVKEEDEELYKKVVDAL 348
                                   3333333335555555555555555444445555555 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0011       1.4       3      35 ..      31      62 ..      29      72 .. 0.82
   2 ?   -0.6   0.0      0.83   1.1e+03      62      88 ..     131     154 ..     113     165 .. 0.67
   3 ?   -2.1   0.1       2.3   2.9e+03     124     157 ..     165     200 ..     144     207 .. 0.69
   4 ?   -2.3   0.1       2.6   3.4e+03      32      90 ..     297     352 ..     287     360 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                            TK  3 ielilgpmfaGKsteLlrrvkryqlaekkvvvi 35
                                  i++i+g++++GK+ +L++++ + +l + k +v+
  gi|15669491|ref|NP_248301.1| 31 IYFIYGSINSGKT-ALINEIINNRLDKNKYIVF 62
                                  89**********7.5888888877777777665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.83
                            TK  62 ktssleeikeeleeedvdvvlvDEaqF 88 
                                    t+ l +ik+e ++    ++++DE q 
  gi|15669491|ref|NP_248301.1| 131 ITNVLMDIKREGKQ---PIIIIDELQK 154
                                   44555566665555...89999*9985 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.3
                            TK 124 ilkllalaekvkklkavC.mkCgkk.Asftkrlnke 157
                                   i++l+ +  +++k k  C ++C +    f  r+ +e
  gi|15669491|ref|NP_248301.1| 165 IYELFNYFVSLTKHKHLChVFCLSSdSLFIERVYNE 200
                                   667777777888888888335765435666666665 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 2.6
                            TK  32 vvvikaakdnRysegkvvthdgisleakksktssleeikeeleeedvdvvlvDEaqFfe 90 
                                   v++ik     Ry++         +l+  ++k + + e ++e++ee +   +vD  + f+
  gi|15669491|ref|NP_248301.1| 297 VLIIKVIDKLRYENL--NDILDFMLKDATQKLKYFLEDVKEEDEE-LYKKVVDALKLFK 352
                                   566666666666652..2222222333333333333333333332.3333456666666 PP

>> FTCD_C  Formiminotransferase-cyclodeaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.8   2.3e+03      88     135 ..     111     157 ..     108     160 .. 0.80
   2 ?    8.5   1.4    0.0012       1.6      42      93 ..     304     356 ..     301     372 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.8
                                   .........S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS- CS
                        FTCD_C  88 pketeeekaareeaiqealkkavevPlelarkalellelleelaekgn 135
                                   pk+t +e   ++++ ++ ++  ++v +++ r+ ++ + +++el ++g 
  gi|15669491|ref|NP_248301.1| 111 PKNTLNEI-FKKKTTKNVFRYITNVLMDIKREGKQPIIIIDELQKIGD 157
                                   67775544.567788999999999999999999999999999998886 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0012
                                   T-TT-GGGHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHTTTT....... CS
                        FTCD_C  42 gkkkyedveeemeellekl.eelrkellelideDaeaFnevmeayklpketee 93 
                                   +k +ye++++ ++ +l+ + ++l+  l ++ +eD+e +++v++a+kl ke  e
  gi|15669491|ref|NP_248301.1| 304 DKLRYENLNDILDFMLKDAtQKLKYFLEDVKEEDEELYKKVVDALKLFKEDYE 356
                                   677899999999999999856777777778899**************997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1191  (0.0664287); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.63u 0.24s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 2796.84
//
Query:       gi|15669492|ref|NP_248302.1|  [L=168]
Description: ferredoxin [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-13   48.5  15.5    2.8e-07   30.1   4.8    2.3  2  Fer4      4Fe-4S binding domain
    1.4e-09   37.9   8.6    3.8e-06   26.9   1.7    2.2  2  Fer4_21   4Fe-4S dicluster domain
    2.7e-09   37.0  19.1      5e-07   29.7  11.1    1.9  2  Fer4_10   4Fe-4S dicluster domain
    5.6e-09   36.5   8.3    9.4e-09   35.7   8.3    1.3  1  Fer4_7    4Fe-4S dicluster domain
    3.7e-08   33.4   1.9     0.0002   21.5   0.1    2.1  2  Fer4_9    4Fe-4S dicluster domain
    1.8e-07   30.9  13.1      1e-05   25.4   2.8    2.3  2  Fer4_6    4Fe-4S binding domain
    2.1e-07   31.3   1.4      0.011   16.2   0.0    2.2  2  Fer4_8    4Fe-4S dicluster domain
    1.7e-06   28.4   1.4      0.021   15.4   0.1    2.2  2  Fer4_17   4Fe-4S dicluster domain
    2.4e-06   27.3  13.7     0.0041   17.1   3.4    2.3  2  Fer4_2    4Fe-4S binding domain
    8.3e-05   23.4  12.4    0.00045   21.1  12.2    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00017   22.3   1.2      0.043   14.7   0.2    2.2  2  Fer4_22   4Fe-4S dicluster domain
    0.00086   19.6  12.0      0.053   14.0   3.3    2.2  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.013   16.0   9.3       0.46   11.1   2.6    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        0.1   13.6   6.0        0.1   13.6   6.0    2.2  2  Fer4_3    4Fe-4S binding domain
       0.15   12.2   9.0       0.32   11.2   1.5    2.3  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   4.8   2.4e-10   2.8e-07       2      24 .]      52      74 ..      51      74 .. 0.94
   2 !   24.1   2.9   1.7e-08   2.1e-05       1      20 [.      93     112 ..      93     114 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.4e-10
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                  +++ee+CigC  C++vCP+ AI+
  gi|15669492|ref|NP_248302.1| 52 TVIEELCIGCEGCANVCPTKAIE 74
                                  689*******************6 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.7e-08
                                   EEEETTTSSS-THHHHHSTT CS
                          Fer4   1 vvideekCigCGaCvevCPv 20 
                                   ++i++ekC++C +C + CPv
  gi|15669492|ref|NP_248302.1|  93 PKINPEKCVYCLYCHDFCPV 112
                                   68*****************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   1.7   3.2e-09   3.8e-06      33      59 .]      50      75 ..      36      75 .. 0.80
   2 !   15.0   0.8   1.7e-05      0.02      32      53 ..      91     112 ..      78     117 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.2e-09
                       Fer4_21 33 vlkvvedeCvGCnlCssvCPvedciem 59
                                    +v+e+ C+GC+ C++vCP+ ++iem
  gi|15669492|ref|NP_248302.1| 50 PKTVIEELCIGCEGCANVCPT-KAIEM 75
                                  45789***************7.99998 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.7e-05
                       Fer4_21  32 tvlkvvedeCvGCnlCssvCPv 53 
                                   ++ k+  ++Cv C  C++ CPv
  gi|15669492|ref|NP_248302.1|  91 KIPKINPEKCVYCLYCHDFCPV 112
                                   4446667889999999999988 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7  11.1   4.2e-10     5e-07       6      56 .]      55     111 ..      51     111 .. 0.95
   2 !   18.8   1.0   1.1e-06    0.0013       3      24 ..      94     125 ..      92     154 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.2e-10
                       Fer4_10   6 ddtCirCgkCvkaCPadl......tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   ++ Ci+C+ C ++CP+++      + v+ ++ + +++  ++++ekC  c +C + CP
  gi|15669492|ref|NP_248302.1|  55 EELCIGCEGCANVCPTKAiemipiEPVKITDNYVKDKIPKINPEKCVYCLYCHDFCP 111
                                   589*************99******9*******************************9 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.1e-06
                       Fer4_10   3 vidddtCirCgkCvkaCPadl..........t 24 
                                   +i++++C+ C  C ++CP+            +
  gi|15669492|ref|NP_248302.1|  94 KINPEKCVYCLYCHDFCPVFSvfneispihpR 125
                                   79****************95466655554431 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   8.3   7.9e-12   9.4e-09       2      50 ..      58     112 ..      57     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 7.9e-12
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenek......gtekveidpekClgCgaCvavCPt 50 
                                   CigC+ C+++Cp+kaie+ + e  k      + + ++i+pekC++C  C + CP+
  gi|15669492|ref|NP_248302.1|  58 CIGCEGCANVCPTKAIEMIPIEPVKitdnyvKDKIPKINPEKCVYCLYCHDFCPV 112
                                   *****************9975444433333233778******************7 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   1.7e-07    0.0002      33      51 .]      45      73 ..      23      73 .. 0.73
   2 !   11.6   0.2   0.00021      0.25      34      47 ..      98     111 ..      74     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.7e-07
                        Fer4_9 33 e..........eaCigCgaCveaCpkgai 51
                                             e CigC+ C+++Cp++ai
  gi|15669492|ref|NP_248302.1| 45 GtvkipktvieELCIGCEGCANVCPTKAI 73
                                  0444445556679*************987 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00021
                        Fer4_9  34 eaCigCgaCveaCp 47 
                                   e+C+ C  C + Cp
  gi|15669492|ref|NP_248302.1|  98 EKCVYCLYCHDFCP 111
                                   67888888888888 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   2.8   8.5e-09     1e-05       3      24 .]      52      73 ..      51      73 .. 0.94
   2 !   10.9   2.7   0.00032      0.38       1      21 [.      92     112 ..      92     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.5e-09
                        Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                  ++ +++CigC+ C++vCP++ai
  gi|15669492|ref|NP_248302.1| 52 TVIEELCIGCEGCANVCPTKAI 73
                                  6899****************98 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00032
                        Fer4_6   1 vveidpdkCigCgdCvrvCPe 21 
                                   ++ i+p+kC+ C  C + CP 
  gi|15669492|ref|NP_248302.1|  92 IPKINPEKCVYCLYCHDFCPV 112
                                   689*****************5 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.3   3.8e-05     0.045      49      64 ..      56      71 ..      31      76 .. 0.83
   2 !   16.2   0.0   8.9e-06     0.011       3      34 ..      98     130 ..      97     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-05
                        Fer4_8 49 wsCttcgaCtevCpvg 64
                                  + C +c+ C++vCp++
  gi|15669492|ref|NP_248302.1| 56 ELCIGCEGCANVCPTK 71
                                  5688888888888875 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 8.9e-06
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaae 34 
                                   ekC+ C +C + Cpv++ ++   + ++r+  +e
  gi|15669492|ref|NP_248302.1|  98 EKCVYCLYCHDFCPVFSVFNeISPIHPRDVGEE 130
                                   69****************995566777766555 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.8e-05     0.021      44      58 ..      56      70 ..      30      87 .. 0.80
   2 !   12.5   0.1   0.00014      0.17       1      20 [.      99     118 ..      99     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                       Fer4_17 44 slCieCgeCerkCPq 58
                                  +lCi+C++C+ +CP 
  gi|15669492|ref|NP_248302.1| 56 ELCIGCEGCANVCPT 70
                                  678888888888885 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                       Fer4_17   1 rCiqCgyClpeCpsyeaydn 20 
                                   +C  C yC + Cp +   ++
  gi|15669492|ref|NP_248302.1|  99 KCVYCLYCHDFCPVFSVFNE 118
                                   6************9988655 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   3.4   3.4e-06    0.0041       5      22 .]      53      70 ..      50      70 .. 0.88
   2 !   15.7   2.7     1e-05     0.012       3      21 ..      93     111 ..      91     112 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.4e-06
                        Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                  v ++ CigC+ C ++CP+
  gi|15669492|ref|NP_248302.1| 53 VIEELCIGCEGCANVCPT 70
                                  66899****99******7 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1e-05
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   +++++++C+ C  C + CP
  gi|15669492|ref|NP_248302.1|  93 PKINPEKCVYCLYCHDFCP 111
                                   89***************** PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1  12.2   3.8e-07   0.00045       2      66 ..      58     112 ..      57     113 .. 0.71
   2 !    7.7   2.3    0.0058       6.9       1      14 [.      99     112 ..      99     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.8e-07
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                   C++C+ Ca+vCPt+ai++     ie+ + +++   ++k  +++ ek      + +C  C d CP+
  gi|15669492|ref|NP_248302.1|  58 CIGCEGCANVCPTKAIEMI---PIEPVKITDN-YVKDKIPKINPEK------CVYCLYCHDFCPV 112
                                   ******************9...4555554332.2333444444444......66**********6 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0058
                       Fer4_16   1 rCgtCgkCaevCPt 14 
                                   +C+ C  C + CP+
  gi|15669492|ref|NP_248302.1|  99 KCVYCLYCHDFCPV 112
                                   59999999999998 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   3.6e-05     0.043      61      95 ..      37      71 ..      25      72 .. 0.85
   2 ?    6.7   0.1     0.011        13      78      94 ..      96     112 ..      82     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.6e-05
                       Fer4_22 61 rlrqrllhklsefkekfgesgCvGCgRCieacpvk 95
                                   +r+ +l  + ++ +++ e+ C+GC  C ++cp+k
  gi|15669492|ref|NP_248302.1| 37 EMRNAILTGTVKIPKTVIEELCIGCEGCANVCPTK 71
                                  57888888888999999999999999999999975 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                       Fer4_22  78 gesgCvGCgRCieacpv 94 
                                   + ++Cv C  C++ cpv
  gi|15669492|ref|NP_248302.1|  96 NPEKCVYCLYCHDFCPV 112
                                   55666666666666664 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   3.3   4.5e-05     0.053       2      16 ..      56      70 ..      55      71 .. 0.90
   2 !   10.7   1.5   0.00054      0.64       1      15 [.      97     111 ..      97     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  e CigC  C ++CP+
  gi|15669492|ref|NP_248302.1| 56 ELCIGCEGCANVCPT 70
                                  67************8 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00054
                        Fer4_4   1 qerCigCgsCvaaCP 15 
                                   +e+C+ C  C+++CP
  gi|15669492|ref|NP_248302.1|  97 PEKCVYCLYCHDFCP 111
                                   699************ PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.6   0.00039      0.46       2      17 ..      55      69 ..      54      71 .. 0.89
   2 ?    9.0   0.6    0.0017       2.1       1      18 [.      95     112 ..      95     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                       Fer4_13  2 DrdtCiacgaCvelaP 17
                                  + + Ci+c+ C++++P
  gi|15669492|ref|NP_248302.1| 55 E-ELCIGCEGCANVCP 69
                                  5.88************ PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0017
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   ++ ++C+ c  C +++P 
  gi|15669492|ref|NP_248302.1|  95 INPEKCVYCLYCHDFCPV 112
                                   7899*************4 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   6.0   8.8e-05       0.1       1      15 []      58      72 ..      58      72 .. 0.96
   2 ?    0.1   4.5       1.7   2.1e+03       1      13 [.     100     112 ..     100     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.8e-05
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gC+ C +vCP++A
  gi|15669492|ref|NP_248302.1| 58 CIGCEGCANVCPTKA 72
                                  ****99*******98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.7
                        Fer4_3   1 CtgCgaCvevCPv 13 
                                   C+ C  C + CPv
  gi|15669492|ref|NP_248302.1| 100 CVYCLYCHDFCPV 112
                                   899966******7 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.5   0.00026      0.32      54      74 ..      51      71 ..      25      76 .. 0.75
   2 ?    5.2   1.1     0.019        23      52      73 ..      91     112 ..      78     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                       Fer4_18 54 kekgagdcidcescvkvcPtg 74
                                  k+  +  ci ce c +vcPt+
  gi|15669492|ref|NP_248302.1| 51 KTVIEELCIGCEGCANVCPTK 71
                                  4455667************96 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.019
                       Fer4_18  52 erkekgagdcidcescvkvcPt 73 
                                   +  + +  +c+ c +c + cP+
  gi|15669492|ref|NP_248302.1|  91 KIPKINPEKCVYCLYCHDFCPV 112
                                   4455566789999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1211.44
//
Query:       gi|15669493|ref|NP_248303.1|  [L=501]
Description: polyferredoxin MvhB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-70  229.7 149.1      2e-07   30.6   4.1   14.9 15  Fer4      4Fe-4S binding domain
    2.4e-48  162.5 121.5      1e-08   35.6   8.5   10.1 10  Fer4_7    4Fe-4S dicluster domain
    2.3e-40  136.5 126.9    5.6e-08   32.8  11.4   10.8 11  Fer4_9    4Fe-4S dicluster domain
    3.2e-37  125.1 156.3      6e-05   22.9   3.0   14.6 14  Fer4_6    4Fe-4S binding domain
    9.7e-37  124.9 134.0    1.9e-07   31.1   9.9   10.7 11  Fer4_10   4Fe-4S dicluster domain
    3.1e-35  120.9 120.0     0.0032   18.4   1.2   14.0 14  Fer4_16   4Fe-4S double cluster binding domain
    1.1e-32  111.9 131.5    3.3e-07   30.3  13.8   11.0 11  Fer4_21   4Fe-4S dicluster domain
    8.4e-28   94.7 140.8    3.1e-05   23.8   3.4   14.3 14  Fer4_2    4Fe-4S binding domain
    8.7e-21   74.2 127.3    8.8e-06   26.2   4.1   12.7 12  Fer4_17   4Fe-4S dicluster domain
    8.6e-18   64.6 128.9    0.00057   20.3   5.0   12.4 10  Fer4_8    4Fe-4S dicluster domain
    5.2e-16   58.3 163.3      0.016   16.1   6.6   14.4 14  Fer4_3    4Fe-4S binding domain
    1.8e-12   46.7 137.2       0.11   13.0   2.4   14.4 14  Fer4_4    4Fe-4S binding domain
    1.6e-11   44.6 124.6       0.12   13.0   0.7   14.7 14  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    9.1e-06   26.3 104.3      0.023   15.4   0.4   14.6 14  Fer4_15   4Fe-4S single cluster domain
    1.9e-05   24.8 118.3      0.081   13.1   8.7   10.7  9  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.34   11.4   8.0         10    6.8   0.1    5.3  4  TPR_17    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3       1.4   1.6e+03       5      11 ..      17      23 ..      15      23 .. 0.87
   2 !   14.1   0.2   2.7e-05      0.03      13      23 ..      30      40 ..      29      41 .. 0.91
   3 !   16.2   2.4     6e-06    0.0067       8      24 .]      50      66 ..      48      66 .. 0.93
   4 !   27.9   4.7   1.2e-09   1.4e-06       1      24 []      73      96 ..      73      96 .. 0.94
   5 !   21.7   4.3   1.1e-07   0.00013       7      22 ..     109     124 ..     105     126 .. 0.90
   6 !   24.4   2.0   1.6e-08   1.8e-05       1      23 [.     174     196 ..     174     197 .. 0.93
   7 !   17.4   2.9   2.4e-06    0.0027       6      24 .]     202     220 ..     200     220 .. 0.95
   8 !   29.7   2.9   3.3e-10   3.7e-07       3      24 .]     224     245 ..     223     245 .. 0.94
   9 !   26.0   1.8   4.7e-09   5.2e-06       6      23 ..     264     281 ..     262     282 .. 0.92
  10 !   22.3   2.0     7e-08   7.8e-05       2      22 ..     289     309 ..     288     311 .. 0.90
  11 !   11.9   4.4   0.00013      0.15       8      24 .]     352     368 ..     350     368 .. 0.95
  12 !   26.3   3.7   3.8e-09   4.2e-06       3      23 ..     377     397 ..     375     398 .. 0.91
  13 !   19.2   3.0   6.6e-07   0.00074       4      23 ..     408     427 ..     405     427 .. 0.91
  14 !   24.2   6.4   1.8e-08     2e-05       3      23 ..     446     466 ..     444     467 .. 0.92
  15 !   30.6   4.1   1.8e-10     2e-07       2      24 .]     470     492 ..     470     492 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                                  TTTSSS- CS
                          Fer4  5 eekCigC 11
                                  eekC  C
  gi|15669493|ref|NP_248303.1| 17 EEKCQSC 23
                                  89**999 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.7e-05
                                  HHHHHSTTTEE CS
                          Fer4 13 aCvevCPvgAI 23
                                  +C+e+CP++AI
  gi|15669493|ref|NP_248303.1| 30 KCMEACPTDAI 40
                                  6*********9 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 6e-06
                                  SSS-THHHHHSTTTEEE CS
                          Fer4  8 CigCGaCvevCPvgAIt 24
                                  C  CG+C+  CP+ AI+
  gi|15669493|ref|NP_248303.1| 50 CLTCGECARNCPNKAIK 66
                                  999************96 PP

  == domain 4  score: 27.9 bits;  conditional E-value: 1.2e-09
                                  EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                  +++d  +C gCG+C++vCP g I+
  gi|15669493|ref|NP_248303.1| 73 YYVDRRRCNGCGICANVCPIGIIK 96
                                  689******************996 PP

  == domain 5  score: 21.7 bits;  conditional E-value: 1.1e-07
                                   TSSS-THHHHHSTTTE CS
                          Fer4   7 kCigCGaCvevCPvgA 22 
                                    C  CG CvevCP++A
  gi|15669493|ref|NP_248303.1| 109 ICSMCGVCVEVCPYNA 124
                                   5**************9 PP

  == domain 6  score: 24.4 bits;  conditional E-value: 1.6e-08
                                   EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                   ++id +kC+gC +C   CP + I
  gi|15669493|ref|NP_248303.1| 174 IKIDRDKCVGCLRCSYLCPRDTI 196
                                   68******************988 PP

  == domain 7  score: 17.4 bits;  conditional E-value: 2.4e-06
                                   TTSSS-THHHHHSTTTEEE CS
                          Fer4   6 ekCigCGaCvevCPvgAIt 24 
                                   + C+ C++C e CP +AI+
  gi|15669493|ref|NP_248303.1| 202 DACTSCNLCGENCPKDAIK 220
                                   79****************6 PP

  == domain 8  score: 29.7 bits;  conditional E-value: 3.3e-10
                                   EETTTSSS-THHHHHSTTTEEE CS
                          Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                   +d++kCi C +Cve+CP++A++
  gi|15669493|ref|NP_248303.1| 224 VDYNKCILCLKCVEICPNDALK 245
                                   9*******************85 PP

  == domain 9  score: 26.0 bits;  conditional E-value: 4.7e-09
                                   TTSSS-THHHHHSTTTEE CS
                          Fer4   6 ekCigCGaCvevCPvgAI 23 
                                   + Ci+CG+C+e CP gA+
  gi|15669493|ref|NP_248303.1| 264 SYCINCGLCAEHCPSGAL 281
                                   68***************8 PP

  == domain 10  score: 22.3 bits;  conditional E-value: 7e-08
                                   EEETTTSSS-THHHHHSTTTE CS
                          Fer4   2 videekCigCGaCvevCPvgA 22 
                                   ++ ++ C +C++Cv++CP+++
  gi|15669493|ref|NP_248303.1| 289 YYSPDVCWKCMECVKICPNDV 309
                                   6789***************97 PP

  == domain 11  score: 11.9 bits;  conditional E-value: 0.00013
                                   SSS-THHHHHSTTTEEE CS
                          Fer4   8 CigCGaCvevCPvgAIt 24 
                                   C  C +C++ CP +AI+
  gi|15669493|ref|NP_248303.1| 352 CSLCEICINNCPEEAIS 368
                                   99*************96 PP

  == domain 12  score: 26.3 bits;  conditional E-value: 3.8e-09
                                   EETTTSSS-THHHHHSTTTEE CS
                          Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                   i  e Ci CG+C +vCP +AI
  gi|15669493|ref|NP_248303.1| 377 IKDENCILCGTCSNVCPRDAI 397
                                   66799***************9 PP

  == domain 13  score: 19.2 bits;  conditional E-value: 6.6e-07
                                   ETTTSSS-THHHHHSTTTEE CS
                          Fer4   4 deekCigCGaCvevCPvgAI 23 
                                    ++ Ci+C +C+  CP ++I
  gi|15669493|ref|NP_248303.1| 408 FTDNCIACETCAIHCPRDVI 427
                                   579***************98 PP

  == domain 14  score: 24.2 bits;  conditional E-value: 1.8e-08
                                   EETTTSSS-THHHHHSTTTEE CS
                          Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                    d++ Ci+CG+C +vCP+++I
  gi|15669493|ref|NP_248303.1| 446 TDMDFCIKCGLCNKVCPNNCI 466
                                   699*****************9 PP

  == domain 15  score: 30.6 bits;  conditional E-value: 1.8e-10
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   vid+e+C +CGaC+++CP+ AI+
  gi|15669493|ref|NP_248303.1| 470 VIDKERCEFCGACYNICPTKAIY 492
                                   79*******************96 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   3.8    0.0018       2.1      34      52 .]      16      39 ..       8      39 .. 0.82
   2 !   31.4  11.5   1.9e-10   2.1e-07       1      52 []      49      94 ..      49      94 .. 0.93
   3 !   30.4  12.5   3.9e-10   4.4e-07       1      52 []      79     124 ..      79     124 .. 0.91
   4 !   28.4   9.9   1.7e-09   1.9e-06       2      51 ..     110     194 ..     109     195 .. 0.69
   5 !   17.7  11.4   3.5e-06     0.004       1      52 []     203     243 ..     203     243 .. 0.91
   6 !   35.6   8.5     9e-12     1e-08       1      52 []     228     280 ..     228     280 .. 0.90
   7 !   31.4  11.6   1.9e-10   2.1e-07       2      52 .]     266     309 ..     265     309 .. 0.93
   8 !   26.9   9.8     5e-09   5.6e-06       2      52 .]     352     396 ..     351     396 .. 0.91
   9 !   26.8  13.7   5.1e-09   5.7e-06       2      51 ..     412     464 ..     411     465 .. 0.85
  10 !   19.1   0.4   1.3e-06    0.0015      32      52 .]     470     490 ..     466     498 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0018
                        Fer4_7 34 dpekClgC.....gaCvavCPtga 52
                                  ++ekC++C      +C+++CPt+a
  gi|15669493|ref|NP_248303.1| 16 VEEKCQSCpfsqtSKCMEACPTDA 39
                                  5799**996666568*******97 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 1.9e-10
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  +C  Cg C+++Cp+kai+ +e+        +++d ++C gCg C++vCP g+
  gi|15669493|ref|NP_248303.1| 49 SCLTCGECARNCPNKAIKRNEF------GGYYVDRRRCNGCGICANVCPIGI 94
                                  5******************998......469******************885 PP

  == domain 3  score: 30.4 bits;  conditional E-value: 3.9e-10
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   rC gCg C+++Cp + i++ e++   g    ++ +  C+ Cg+Cv+vCP++a
  gi|15669493|ref|NP_248303.1|  79 RCNGCGICANVCPIGIIKIVEKD---G---KKFPMGICSMCGVCVEVCPYNA 124
                                   8******************9973...4...3578999************997 PP

  == domain 4  score: 28.4 bits;  conditional E-value: 1.7e-09
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenek...................................gtekveidpekClgCgaCvav 47 
                                   C  Cg Cv++Cp++a+   +e  +                                    ++++++id +kC+gC +C   
  gi|15669493|ref|NP_248303.1| 110 CSMCGVCVEVCPYNARVSSYELLNTkreglaerylkvlenlmkvklfraeekpgkvvekvERKSIKIDRDKCVGCLRCSYL 190
                                   999***********999775322222344444455555555555555555555555555566889**************** PP

                        Fer4_7  48 CPtg 51 
                                   CP +
  gi|15669493|ref|NP_248303.1| 191 CPRD 194
                                   **75 PP

  == domain 5  score: 17.7 bits;  conditional E-value: 3.5e-06
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C+ C+ C ++Cp +ai+             e+d++kC+ C +Cv+ CP +a
  gi|15669493|ref|NP_248303.1| 203 ACTSCNLCGENCPKDAIKDG-----------EVDYNKCILCLKCVEICPNDA 243
                                   5**************99864...........5799**************987 PP

  == domain 6  score: 35.6 bits;  conditional E-value: 9e-12
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidp.ekClgCgaCvavCPtga 52 
                                   +Ci C +Cv+ Cp++a++++++++ k +e+ + +p ++C++Cg C++ CP+ga
  gi|15669493|ref|NP_248303.1| 228 KCILCLKCVEICPNDALKVENFKVIKVKEDKTSQPtSYCINCGLCAEHCPSGA 280
                                   7********************99999887777775269*************98 PP

  == domain 7  score: 31.4 bits;  conditional E-value: 1.9e-10
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   Ci+Cg C++ Cp++a+++++        +++++p+ C+ C +Cv+ CP ++
  gi|15669493|ref|NP_248303.1| 266 CINCGLCAEHCPSGALRFEN-------GHLYYSPDVCWKCMECVKICPNDV 309
                                   ******************54.......59*******************875 PP

  == domain 8  score: 26.9 bits;  conditional E-value: 5e-09
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   C  C+ C ++Cp +ai+++ +      +  +i+ e+C+ Cg C +vCP +a
  gi|15669493|ref|NP_248303.1| 352 CSLCEICINNCPEEAISITTV------KLEKIKDENCILCGTCSNVCPRDA 396
                                   999***************987......335799***************987 PP

  == domain 9  score: 26.8 bits;  conditional E-value: 5.1e-09
                        Fer4_7   2 CigCgaCvaaCpvkaield...eeenekgtekveidpekClgCgaCvavCPtg 51 
                                   Ci C+ C+  Cp ++i  +   ++ +++++  ++ d++ C+ Cg C +vCP +
  gi|15669493|ref|NP_248303.1| 412 CIACETCAIHCPRDVIPNTtgyKKVVDRENSFIRTDMDFCIKCGLCNKVCPNN 464
                                   ***************985533345567788999******************87 PP

  == domain 10  score: 19.1 bits;  conditional E-value: 1.3e-06
                        Fer4_7  32 eidpekClgCgaCvavCPtga 52 
                                   +id e+C +CgaC + CPt+a
  gi|15669493|ref|NP_248303.1| 470 VIDKERCEFCGACYNICPTKA 490
                                   567788888888888888765 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   5.3     0.029        33      34      51 .]      18      40 ..       4      40 .. 0.65
   2 !   13.3  13.7   6.2e-05     0.069       1      51 []      19      65 ..      19      65 .. 0.88
   3 !   25.5  12.3   9.7e-09   1.1e-05       2      50 ..      50      94 ..      49      95 .. 0.93
   4 !   26.0  10.8   6.7e-09   7.5e-06       1      50 [.      79     124 ..      79     125 .. 0.80
   5 !   20.2  19.8   4.4e-07   0.00049       1      50 [.     180     243 ..     180     244 .. 0.97
   6 !   31.6   8.6   1.2e-10   1.3e-07       1      50 [.     228     280 ..     228     281 .. 0.86
   7 !   27.5  12.2   2.4e-09   2.7e-06       1      49 [.     265     308 ..     265     310 .. 0.93
   8 !   27.7  10.3     2e-09   2.2e-06       2      51 .]     352     397 ..     351     398 .. 0.91
   9 !   32.8  11.4     5e-11   5.6e-08       1      51 []     381     427 ..     381     427 .. 0.94
  10 !   20.5  15.1   3.4e-07   0.00038       1      51 []     411     466 ..     411     466 .. 0.92
  11 !   16.3   1.3   7.2e-06    0.0081      34      51 .]     474     491 ..     467     491 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.029
                        Fer4_9 34 eaCigCga.....CveaCpkgai 51
                                  e+C +C       C+eaCp++ai
  gi|15669493|ref|NP_248303.1| 18 EKCQSCPFsqtskCMEACPTDAI 40
                                  56777754556668888887776 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.2e-05
                        Fer4_9  1 kCtgC.....gaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  kC +C      +C+eaCp++++   +++ +         +C++Cg+C+  Cp++ai
  gi|15669493|ref|NP_248303.1| 19 KCQSCpfsqtSKCMEACPTDAIFLLNNKSF---------SCLTCGECARNCPNKAI 65
                                  799999988777*********988877776.........5*************987 PP

  == domain 3  score: 25.5 bits;  conditional E-value: 9.7e-09
                        Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                  C  Cg+C + Cp++++++ +++++   r+    +C gCg C+++Cp g+
  gi|15669493|ref|NP_248303.1| 50 CLTCGECARNCPNKAIKRNEFGGYYVDRR----RCNGCGICANVCPIGI 94
                                  ************************99987....5************886 PP

  == domain 4  score: 26.0 bits;  conditional E-value: 6.7e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerk.arlraaseeaCigCgaCveaCpkga 50 
                                   +C+gCg C ++Cp g+++  ++ +k   + +     C +Cg Cve+Cp +a
  gi|15669493|ref|NP_248303.1|  79 RCNGCGICANVCPIGIIKIVEKDGKkFPMGI-----CSMCGVCVEVCPYNA 124
                                   6***************966555555045443.....************975 PP

  == domain 5  score: 20.2 bits;  conditional E-value: 4.4e-07
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase..............eaCigCgaCveaCpkga 50 
                                   kC+gC +C + Cp +++v+d+     +++  +e              ++Ci C +Cve+Cp++a
  gi|15669493|ref|NP_248303.1| 180 KCVGCLRCSYLCPRDTIVPDSIDACTSCNLCGEncpkdaikdgevdyNKCILCLKCVEICPNDA 243
                                   7***************************99999****************************997 PP

  == domain 6  score: 31.6 bits;  conditional E-value: 1.2e-10
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase...eaCigCgaCveaCpkga 50 
                                   kC+ C +Cve Cp+++ + ++++ +   + +     + Ci Cg C+e+Cp+ga
  gi|15669493|ref|NP_248303.1| 228 KCILCLKCVEICPNDALKVENFKVIKVKEDKTSqptSYCINCGLCAEHCPSGA 280
                                   7****************999998776655444479999************997 PP

  == domain 7  score: 27.5 bits;  conditional E-value: 2.4e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   +C++Cg C e Cp+g+ + ++++ + + +      C++C++Cv++Cp++
  gi|15669493|ref|NP_248303.1| 265 YCINCGLCAEHCPSGALRFENGHLYYSPDV-----CWKCMECVKICPND 308
                                   6*********************99999754.....************98 PP

  == domain 8  score: 27.7 bits;  conditional E-value: 2e-09
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   C  C  C++ Cp ++++   ++ +   ++    +Ci Cg+C ++Cp++ai
  gi|15669493|ref|NP_248303.1| 352 CSLCEICINNCPEEAISITTVKLEKIKDE----NCILCGTCSNVCPRDAI 397
                                   9****************999999877543....7*************997 PP

  == domain 9  score: 32.8 bits;  conditional E-value: 5e-11
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   +C+ Cg+C ++Cp ++++ d++++++  +     +Ci C++C+ +Cp+++i
  gi|15669493|ref|NP_248303.1| 381 NCILCGTCSNVCPRDAIIIDRSNGEVLFTD----NCIACETCAIHCPRDVI 427
                                   6**************************976....6*************976 PP

  == domain 10  score: 20.5 bits;  conditional E-value: 3.4e-07
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkgai 51 
                                   +C+ C +C   Cp +v+ +  + +k+  r+ s      + Ci+Cg C ++Cp+++i
  gi|15669493|ref|NP_248303.1| 411 NCIACETCAIHCPRDVIPNTTGYKKVVDRENSFirtdmDFCIKCGLCNKVCPNNCI 466
                                   6****************99999999998877779999999*************987 PP

  == domain 11  score: 16.3 bits;  conditional E-value: 7.2e-06
                        Fer4_9  34 eaCigCgaCveaCpkgai 51 
                                   e+C +CgaC+++Cp++ai
  gi|15669493|ref|NP_248303.1| 474 ERCEFCGACYNICPTKAI 491
                                   58*************987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   4.2     0.013        14      14      24 .]      30      40 ..      16      40 .. 0.73
   2 !   12.8   3.8   8.4e-05     0.094       8      24 .]      49      65 ..      49      65 .. 0.92
   3 !   20.6   4.5   2.8e-07   0.00032       4      24 .]      75      95 ..      74      95 .. 0.93
   4 !   13.6   5.3   4.6e-05     0.052       8      23 ..     109     124 ..     107     124 .. 0.93
   5 !   17.1   2.1   3.8e-06    0.0043       2      20 ..     174     192 ..     173     196 .. 0.89
   6 !    8.4   3.8     0.002       2.3       7      24 .]     202     219 ..     200     219 .. 0.94
   7 !   22.9   3.0   5.4e-08     6e-05       3      24 .]     223     244 ..     223     244 .. 0.93
   8 !   17.1   2.5   3.7e-06    0.0042       8      24 .]     265     281 ..     263     281 .. 0.92
   9 !   12.5   2.7   0.00011      0.12       5      20 ..     291     306 ..     288     310 .. 0.84
  10 !   10.0   4.9   0.00065      0.73       9      24 .]     352     367 ..     352     367 .. 0.96
  11 !   19.8   3.7   5.4e-07   0.00061       4      24 .]     377     397 ..     376     397 .. 0.93
  12 !   13.3   3.8   5.9e-05     0.066       7      24 .]     410     427 ..     408     427 .. 0.90
  13 !   13.1   6.1   6.8e-05     0.077       2      23 ..     444     465 ..     443     467 .. 0.86
  14 !   18.7   3.8   1.2e-06    0.0013       3      24 .]     470     491 ..     470     491 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
                        Fer4_6 14 dCvrvCPegai 24
                                  +C+ +CP++ai
  gi|15669493|ref|NP_248303.1| 30 KCMEACPTDAI 40
                                  5********98 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.4e-05
                        Fer4_6  8 kCigCgdCvrvCPegai 24
                                  +C+ Cg+C+r+CP +ai
  gi|15669493|ref|NP_248303.1| 49 SCLTCGECARNCPNKAI 65
                                  69***********9887 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 2.8e-07
                        Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                  +d+ +C+gCg C++vCP g+i
  gi|15669493|ref|NP_248303.1| 75 VDRRRCNGCGICANVCPIGII 95
                                  89***************9876 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 4.6e-05
                        Fer4_6   8 kCigCgdCvrvCPega 23 
                                    C  Cg Cv vCP++a
  gi|15669493|ref|NP_248303.1| 109 ICSMCGVCVEVCPYNA 124
                                   5*************98 PP

  == domain 5  score: 17.1 bits;  conditional E-value: 3.8e-06
                        Fer4_6   2 veidpdkCigCgdCvrvCP 20 
                                   + id+dkC+gC +C   CP
  gi|15669493|ref|NP_248303.1| 174 IKIDRDKCVGCLRCSYLCP 192
                                   78*************9999 PP

  == domain 6  score: 8.4 bits;  conditional E-value: 0.002
                        Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                   d+C++C+ C  +CP +ai
  gi|15669493|ref|NP_248303.1| 202 DACTSCNLCGENCPKDAI 219
                                   89************9998 PP

  == domain 7  score: 22.9 bits;  conditional E-value: 5.4e-08
                        Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                   e+d++kCi C +Cv +CP +a+
  gi|15669493|ref|NP_248303.1| 223 EVDYNKCILCLKCVEICPNDAL 244
                                   69****************8875 PP

  == domain 8  score: 17.1 bits;  conditional E-value: 3.7e-06
                        Fer4_6   8 kCigCgdCvrvCPegai 24 
                                    Ci Cg C+ +CP ga+
  gi|15669493|ref|NP_248303.1| 265 YCINCGLCAEHCPSGAL 281
                                   6**************97 PP

  == domain 9  score: 12.5 bits;  conditional E-value: 0.00011
                        Fer4_6   5 dpdkCigCgdCvrvCP 20 
                                    pd C  C++Cv++CP
  gi|15669493|ref|NP_248303.1| 291 SPDVCWKCMECVKICP 306
                                   5778889********* PP

  == domain 10  score: 10.0 bits;  conditional E-value: 0.00065
                        Fer4_6   9 CigCgdCvrvCPegai 24 
                                   C  C+ C+++CPe ai
  gi|15669493|ref|NP_248303.1| 352 CSLCEICINNCPEEAI 367
                                   999***********98 PP

  == domain 11  score: 19.8 bits;  conditional E-value: 5.4e-07
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   i++++Ci Cg C +vCP +ai
  gi|15669493|ref|NP_248303.1| 377 IKDENCILCGTCSNVCPRDAI 397
                                   789**************9997 PP

  == domain 12  score: 13.3 bits;  conditional E-value: 5.9e-05
                        Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                   d+Ci C+ C+++CP ++i
  gi|15669493|ref|NP_248303.1| 410 DNCIACETCAIHCPRDVI 427
                                   89************8776 PP

  == domain 13  score: 13.1 bits;  conditional E-value: 6.8e-05
                        Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                   ++ d d Ci Cg C +vCP + 
  gi|15669493|ref|NP_248303.1| 444 IRTDMDFCIKCGLCNKVCPNNC 465
                                   6679999************765 PP

  == domain 14  score: 18.7 bits;  conditional E-value: 1.2e-06
                        Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                   +id+++C  Cg+C+++CP++ai
  gi|15669493|ref|NP_248303.1| 470 VIDKERCEFCGACYNICPTKAI 491
                                   69******************98 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1  16.8    0.0025       2.8       6      56 .]      17      61 ..      12      61 .. 0.86
   2 !   11.6   3.1    0.0002      0.23       6      21 ..      47      62 ..      42      71 .. 0.71
   3 !   26.2  11.5   5.6e-09   6.3e-06       3      56 .]      74     121 ..      72     121 .. 0.87
   4 !   12.8  14.4   8.7e-05     0.098       2      56 .]     174     215 ..     173     215 .. 0.91
   5 !    8.1   3.8    0.0025       2.8       7      22 ..     202     217 ..     195     225 .. 0.77
   6 !   31.1   9.9   1.7e-10   1.9e-07       4      56 .]     224     277 ..     221     277 .. 0.85
   7 !   27.7   7.5     2e-09   2.2e-06       2      56 .]     288     363 ..     287     363 .. 0.88
   8 !   20.8  13.5   2.7e-07    0.0003       3      56 .]     376     423 ..     374     423 .. 0.79
   9 !   22.7  12.7   7.2e-08   8.1e-05       6      56 .]     409     462 ..     405     462 .. 0.92
  10 !   21.5  15.0   1.7e-07   0.00019       2      56 .]     444     487 ..     443     487 .. 0.81
  11 !   16.7   2.4   5.4e-06     0.006       3      22 ..     470     489 ..     468     500 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0025
                       Fer4_10  6 ddtCirCg.....kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  +++C  C      kC++aCP+           + +   + k+ +C +cg+C++ CP
  gi|15669493|ref|NP_248303.1| 17 EEKCQSCPfsqtsKCMEACPT-----------DAIFLLNNKSFSCLTCGECARNCP 61
                                  5788888777788********...........77777888888************9 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0002
                       Fer4_10  6 ddtCirCgkCvkaCPa 21
                                  + +C+ Cg+C + CP 
  gi|15669493|ref|NP_248303.1| 47 SFSCLTCGECARNCPN 62
                                  5578888888888887 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 5.6e-09
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   ++d+ +C +Cg C ++CP       ++ ++ e++ ++  ++ C +cg Cve+CP
  gi|15669493|ref|NP_248303.1|  74 YVDRRRCNGCGICANVCPI------GIIKIVEKDGKKFPMGICSMCGVCVEVCP 121
                                   57999**************......666666666677799*************9 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 8.7e-05
                       Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   ++id+d+C++C +C   CP              +  v + +++Ct c  C e CP
  gi|15669493|ref|NP_248303.1| 174 IKIDRDKCVGCLRCSYLCPR-------------DTIVPDSIDACTSCNLCGENCP 215
                                   689***************99.............6677777899***********9 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0025
                       Fer4_10   7 dtCirCgkCvkaCPad 22 
                                   d C+ C+ C + CP d
  gi|15669493|ref|NP_248303.1| 202 DACTSCNLCGENCPKD 217
                                   6899999999999984 PP

  == domain 6  score: 31.1 bits;  conditional E-value: 1.7e-10
                       Fer4_10   4 idddtCirCgkCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +d ++Ci C kCv+ CP d+ +  + k ++ +e++ +   + C++cg C+e+CP
  gi|15669493|ref|NP_248303.1| 224 VDYNKCILCLKCVEICPNDAlKVENFKVIKVKEDKTSQPTSYCINCGLCAEHCP 277
                                   6899**************9965556666677777778899*************9 PP

  == domain 7  score: 27.7 bits;  conditional E-value: 2e-09
                       Fer4_10   2 vvidddtCirCgkCvkaCPadl....................tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                   +++ +d C +C +Cvk CP d+                     s+g+++ +s e++v++ +v+ C  c+ C+  CP
  gi|15669493|ref|NP_248303.1| 288 LYYSPDVCWKCMECVKICPNDVrrikqdfrrlyihkgnlmpkASMGNNKLYSCESPVDDrVVGGCSLCEICINNCP 363
                                   67899*************************************666666666666666665***************9 PP

  == domain 8  score: 20.8 bits;  conditional E-value: 2.7e-07
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                   +i d+ Ci Cg+C ++CP         +++ + +  ++   ++C++c+ C+ +CP
  gi|15669493|ref|NP_248303.1| 376 KIKDENCILCGTCSNVCPR-------DAIIIDRSNGEVlFTDNCIACETCAIHCP 423
                                   58899**************.......444444444444478*************9 PP

  == domain 9  score: 22.7 bits;  conditional E-value: 7.2e-08
                       Fer4_10   6 ddtCirCgkCvkaCPadl...tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +d Ci C++C   CP d+   t+  +k  + e++ +r++++ C++cg C ++CP
  gi|15669493|ref|NP_248303.1| 409 TDNCIACETCAIHCPRDVipnTTGYKKVVDRENSFIRTDMDFCIKCGLCNKVCP 462
                                   589***************99888888889999999******************9 PP

  == domain 10  score: 21.5 bits;  conditional E-value: 1.7e-07
                       Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   ++ d d Ci+Cg C+k+CP         + ++++    ++ e+C++cgaC+ +CP
  gi|15669493|ref|NP_248303.1| 444 IRTDMDFCIKCGLCNKVCPN--------NCIDYGV---IDKERCEFCGACYNICP 487
                                   57899***************........4444433...33369***********9 PP

  == domain 11  score: 16.7 bits;  conditional E-value: 5.4e-06
                       Fer4_10   3 vidddtCirCgkCvkaCPad 22 
                                   vid+++C  Cg+C + CP++
  gi|15669493|ref|NP_248303.1| 470 VIDKERCEFCGACYNICPTK 489
                                   799***************93 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.9    0.0025       2.8       6      17 ..      29      40 ..      18      48 .. 0.79
   2 !   16.5   2.6   1.1e-05     0.012       2      20 ..      50      68 ..      49      78 .. 0.90
   3 !   14.0   3.2   6.8e-05     0.076       1      19 [.      79      97 ..      79     107 .. 0.82
   4 !   18.2   9.0   3.3e-06    0.0037       2      65 ..     110     192 ..     109     194 .. 0.66
   5 !    8.9   1.2    0.0026         3       1      20 [.     180     199 ..     180     202 .. 0.89
   6 !   15.3   3.7   2.6e-05     0.029       2      31 ..     204     230 ..     203     230 .. 0.91
   7 !   18.4   1.2   2.8e-06    0.0032       1      31 [.     228     258 ..     228     264 .. 0.86
   8 !   18.3   0.4   3.1e-06    0.0034       2      20 ..     266     284 ..     265     292 .. 0.89
   9 !   10.9   0.8   0.00062      0.69       2      16 ..     295     309 ..     294     341 .. 0.82
  10 !   11.8   2.3   0.00031      0.35       2      20 ..     352     370 ..     351     381 .. 0.82
  11 !   13.0   2.4   0.00014      0.15       1      19 [.     381     399 ..     381     406 .. 0.86
  12 !   12.7   1.1   0.00016      0.18       1      21 [.     411     431 ..     411     448 .. 0.76
  13 !   11.8   8.1   0.00032      0.36       1      30 [.     450     476 ..     450     477 .. 0.87
  14 !   17.0   1.6   7.7e-06    0.0086       1      25 [.     475     497 ..     475     501 .] 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0025
                       Fer4_16  6 gkCaevCPtnai 17
                                   kC+e+CPt+ai
  gi|15669493|ref|NP_248303.1| 29 SKCMEACPTDAI 40
                                  69*********9 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.1e-05
                       Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                  C tCg+Ca  CP +aik +
  gi|15669493|ref|NP_248303.1| 50 CLTCGECARNCPNKAIKRN 68
                                  9***************987 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 6.8e-05
                       Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                  rC +Cg Ca+vCP + ik 
  gi|15669493|ref|NP_248303.1| 79 RCNGCGICANVCPIGIIKI 97
                                  6999999999999999874 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 3.3e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeieare...cisy.................ntaekkdlaedeekckkq..eaitgCdiC 60 
                                   C  Cg C+evCP na  +  ++ +++++      +                 +++  k +++ e+k  k    ++ gC +C
  gi|15669493|ref|NP_248303.1| 110 CSMCGVCVEVCPYNARVSS-YELLNTKReglA--ErylkvlenlmkvklfraEEKPGKVVEKVERKSIKIdrDKCVGCLRC 187
                                   9**************8888.344444443441..24456666667777787544444555555555443233889****** PP

                       Fer4_16  61 qdvCP 65 
                                      CP
  gi|15669493|ref|NP_248303.1| 188 SYLCP 192
                                   ****9 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0026
                       Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                   +C++C +C   CP + i  +
  gi|15669493|ref|NP_248303.1| 180 KCVGCLRCSYLCPRDTIVPD 199
                                   5**************99876 PP

  == domain 6  score: 15.3 bits;  conditional E-value: 2.6e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeieareci 31 
                                   C++C+ C e CP +aik     e+++++ci
  gi|15669493|ref|NP_248303.1| 204 CTSCNLCGENCPKDAIKDG---EVDYNKCI 230
                                   *****************99...88888885 PP

  == domain 7  score: 18.4 bits;  conditional E-value: 2.8e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeieareci 31 
                                   +C+ C kC+e+CP +a+k ++ k+i+ +e++
  gi|15669493|ref|NP_248303.1| 228 KCILCLKCVEICPNDALKVENFKVIKVKEDK 258
                                   5*******************99988877765 PP

  == domain 8  score: 18.3 bits;  conditional E-value: 3.1e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C++Cg Cae CP++a++ +
  gi|15669493|ref|NP_248303.1| 266 CINCGLCAEHCPSGALRFE 284
                                   ****************977 PP

  == domain 9  score: 10.9 bits;  conditional E-value: 0.00062
                       Fer4_16   2 CgtCgkCaevCPtna 16 
                                   C +C +C+++CP ++
  gi|15669493|ref|NP_248303.1| 295 CWKCMECVKICPNDV 309
                                   99**********986 PP

  == domain 10  score: 11.8 bits;  conditional E-value: 0.00031
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C  C+ C++ CP++ai+ +
  gi|15669493|ref|NP_248303.1| 352 CSLCEICINNCPEEAISIT 370
                                   999*************866 PP

  == domain 11  score: 13.0 bits;  conditional E-value: 0.00014
                       Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                   +C+ Cg C +vCP +ai  
  gi|15669493|ref|NP_248303.1| 381 NCILCGTCSNVCPRDAIII 399
                                   6***************965 PP

  == domain 12  score: 12.7 bits;  conditional E-value: 0.00016
                       Fer4_16   1 rCgtCgkCaevCPtnaikekk 21 
                                   +C+ C+ Ca  CP ++i +++
  gi|15669493|ref|NP_248303.1| 411 NCIACETCAIHCPRDVIPNTT 431
                                   6****************9873 PP

  == domain 13  score: 11.8 bits;  conditional E-value: 0.00032
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearec 30 
                                   +C++Cg C +vCP n+i+     +i++++c
  gi|15669493|ref|NP_248303.1| 450 FCIKCGLCNKVCPNNCIDYG---VIDKERC 476
                                   6****************988...7777766 PP

  == domain 14  score: 17.0 bits;  conditional E-value: 7.7e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekei 25 
                                   rC  Cg+C ++CPt+ai     +++
  gi|15669493|ref|NP_248303.1| 475 RCEFCGACYNICPTKAIYLH--RKW 497
                                   69***************988..444 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.3     0.054        61      37      57 ..      16      40 ..       7      42 .. 0.76
   2 !   30.1   8.0   3.5e-10   3.9e-07       7      58 ..      49      96 ..      45      97 .. 0.92
   3 !    6.3   4.7    0.0093        10      27      53 ..      96     122 ..      92     127 .. 0.74
   4 !   19.9   1.2   5.3e-07   0.00059      25      57 ..     165     196 ..     158     198 .. 0.83
   5 !   13.9   3.4     4e-05     0.045      38      58 ..     201     220 ..     193     221 .. 0.83
   6 !   25.3  10.4   1.1e-08   1.3e-05       3      56 ..     224     280 ..     222     283 .. 0.71
   7 !   19.2   9.3   9.1e-07     0.001       6      52 ..     264     306 ..     261     312 .. 0.88
   8 !   20.6  14.4   3.3e-07   0.00037       8      57 ..     352     397 ..     344     399 .. 0.91
   9 !   30.3  13.8     3e-10   3.3e-07       2      57 ..     376     427 ..     375     429 .. 0.93
  10 !   24.7  14.6   1.7e-08   1.9e-05       5      58 ..     409     467 ..     406     468 .. 0.77
  11 !   10.7   2.2   0.00039      0.44       3      22 ..     471     490 ..     469     499 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.054
                       Fer4_21 37 vedeCvGC.....nlCssvCPvedci 57
                                  ve++C  C       C++ CP+ d+i
  gi|15669493|ref|NP_248303.1| 16 VEEKCQSCpfsqtSKCMEACPT-DAI 40
                                  6899999955544579999996.776 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 3.5e-10
                       Fer4_21  7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                  +C+ Cg+C+  C++   +ai+ ++   + v   +C GC +C++vCP+ + i+
  gi|15669493|ref|NP_248303.1| 49 SCLTCGECARNCPN---KAIKRNEFGGYYVDRRRCNGCGICANVCPI-GIIK 96
                                  6************5...99*99999999******************9.8876 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0093
                       Fer4_21  27 eidaktvlkvvedeCvGCnlCssvCPv 53 
                                   +i +k   k     C  C +C++vCP 
  gi|15669493|ref|NP_248303.1|  96 KIVEKDGKKFPMGICSMCGVCVEVCPY 122
                                   55555555666677************6 PP

  == domain 4  score: 19.9 bits;  conditional E-value: 5.3e-07
                       Fer4_21  25 aieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                    +e+ +++ +k+  d+CvGC  Cs  CP  d i
  gi|15669493|ref|NP_248303.1| 165 VVEKVERKSIKIDRDKCVGCLRCSYLCP-RDTI 196
                                   5667778899999***************.4655 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 4e-05
                       Fer4_21  38 edeCvGCnlCssvCPvedcie 58 
                                    d C+ CnlC + CP +d+i+
  gi|15669493|ref|NP_248303.1| 201 IDACTSCNLCGENCP-KDAIK 220
                                   589************.79986 PP

  == domain 6  score: 25.3 bits;  conditional E-value: 1.1e-08
                       Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvv.......edeCvGCnlCssvCPvedc 56 
                                   +d +kCi C kC+  C++   +a+++++ +v+kv        ++ C+ C lC++ CP +++
  gi|15669493|ref|NP_248303.1| 224 VDYNKCILCLKCVEICPN---DALKVENFKVIKVKedktsqpTSYCINCGLCAEHCP-SGA 280
                                   899**************7...666555555554441111123678************.465 PP

  == domain 7  score: 19.2 bits;  conditional E-value: 9.1e-07
                       Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                   + Ci+Cg+C+  C+     a++++ + +l +  d C  C  C+++CP
  gi|15669493|ref|NP_248303.1| 264 SYCINCGLCAEHCP---SGALRFE-NGHLYYSPDVCWKCMECVKICP 306
                                   57************...5899996.6778999*************** PP

  == domain 8  score: 20.6 bits;  conditional E-value: 3.3e-07
                       Fer4_21   8 CigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                   C  C+ C+  C++   +ai+i++ +  k+ +++C+ C  Cs+vCP  d+i
  gi|15669493|ref|NP_248303.1| 352 CSLCEICINNCPE---EAISITTVKLEKIKDENCILCGTCSNVCP-RDAI 397
                                   7789999999996...9****************************.5776 PP

  == domain 9  score: 30.3 bits;  conditional E-value: 3e-10
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                   +i++++Ci Cg C  +C+    +ai id ++   + +d+C++C+ C++ CP  d+i
  gi|15669493|ref|NP_248303.1| 376 KIKDENCILCGTCSNVCP---RDAIIIDRSNGEVLFTDNCIACETCAIHCP-RDVI 427
                                   599***************...6*******9999999***************.5766 PP

  == domain 10  score: 24.7 bits;  conditional E-value: 1.7e-08
                       Fer4_21   5 edkCigCgkCliaCedtshqai.........eidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                    d+Ci C+ C+i C+    + i            +++ +++  d C+ C lC +vCP ++ci+
  gi|15669493|ref|NP_248303.1| 409 TDNCIACETCAIHCPR---DVIpnttgykkvVDRENSFIRTDMDFCIKCGLCNKVCP-NNCID 467
                                   589***********95...566555565531333455668889**************.7**96 PP

  == domain 11  score: 10.7 bits;  conditional E-value: 0.00039
                       Fer4_21   3 idedkCigCgkCliaCedts 22 
                                   id+++C  Cg C+  C++++
  gi|15669493|ref|NP_248303.1| 471 IDKERCEFCGACYNICPTKA 490
                                   66666666666666666433 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   5.9     0.062        70       7      22 .]      17      37 ..      14      37 .. 0.86
   2 !    7.4   3.8    0.0047       5.2       9      22 .]      49      62 ..      45      62 .. 0.92
   3 !   23.8   3.4   2.7e-08   3.1e-05       3      21 ..      73      91 ..      71      91 .. 0.95
   4 !   15.1   2.1   1.6e-05     0.018       8      22 .]     108     122 ..     103     122 .. 0.87
   5 !   19.8   1.3   5.2e-07   0.00058       3      21 ..     174     192 ..     171     193 .. 0.91
   6 !    7.5   3.4    0.0041       4.6       8      21 ..     202     215 ..     196     216 .. 0.92
   7 !   16.2   1.8   7.2e-06    0.0081       4      22 .]     223     241 ..     221     241 .. 0.92
   8 !   10.0   3.6    0.0007      0.78      10      21 ..     266     277 ..     260     278 .. 0.89
   9 !    7.5   1.9    0.0043       4.8       2      22 .]     287     307 ..     286     307 .. 0.90
  10 !    7.2   3.6    0.0052       5.8      10      22 .]     352     364 ..     348     364 .. 0.92
  11 !   15.9   3.1   8.8e-06    0.0099       7      21 ..     379     393 ..     376     394 .. 0.87
  12 !   10.3   3.1   0.00053       0.6       7      21 ..     409     423 ..     406     424 .. 0.91
  13 !   14.9   1.5   1.8e-05      0.02       6      22 .]     447     463 ..     443     463 .. 0.90
  14 !   14.2   2.2   3.1e-05     0.034       4      22 .]     470     488 ..     467     488 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.062
                        Fer4_2  7 tdrCigC.....gaCvsaCPa 22
                                  +++C +C     ++C  aCP+
  gi|15669493|ref|NP_248303.1| 17 EEKCQSCpfsqtSKCMEACPT 37
                                  89*****887766*******7 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0047
                        Fer4_2  9 rCigCgaCvsaCPa 22
                                  +C+ Cg C  +CP+
  gi|15669493|ref|NP_248303.1| 49 SCLTCGECARNCPN 62
                                  6************5 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 2.7e-08
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  ++vd++rC+gCg+C ++CP
  gi|15669493|ref|NP_248303.1| 73 YYVDRRRCNGCGICANVCP 91
                                  799***************9 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 1.6e-05
                        Fer4_2   8 drCigCgaCvsaCPa 22 
                                    +C  Cg Cv +CP+
  gi|15669493|ref|NP_248303.1| 108 GICSMCGVCVEVCPY 122
                                   58************5 PP

  == domain 5  score: 19.8 bits;  conditional E-value: 5.2e-07
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   +++d+d+C+gC  C   CP
  gi|15669493|ref|NP_248303.1| 174 IKIDRDKCVGCLRCSYLCP 192
                                   79************999*9 PP

  == domain 6  score: 7.5 bits;  conditional E-value: 0.0041
                        Fer4_2   8 drCigCgaCvsaCP 21 
                                   d+C++C+ C  +CP
  gi|15669493|ref|NP_248303.1| 202 DACTSCNLCGENCP 215
                                   79***********9 PP

  == domain 7  score: 16.2 bits;  conditional E-value: 7.2e-06
                        Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                   +vd ++Ci C +Cv  CP+
  gi|15669493|ref|NP_248303.1| 223 EVDYNKCILCLKCVEICPN 241
                                   589***************5 PP

  == domain 8  score: 10.0 bits;  conditional E-value: 0.0007
                        Fer4_2  10 CigCgaCvsaCP 21 
                                   Ci+Cg C   CP
  gi|15669493|ref|NP_248303.1| 266 CINCGLCAEHCP 277
                                   ************ PP

  == domain 9  score: 7.5 bits;  conditional E-value: 0.0043
                        Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                   + ++ +d C  C  Cv+ CP+
  gi|15669493|ref|NP_248303.1| 287 HLYYSPDVCWKCMECVKICPN 307
                                   67899***************5 PP

  == domain 10  score: 7.2 bits;  conditional E-value: 0.0052
                        Fer4_2  10 CigCgaCvsaCPa 22 
                                   C  C++C+++CP+
  gi|15669493|ref|NP_248303.1| 352 CSLCEICINNCPE 364
                                   999*********5 PP

  == domain 11  score: 15.9 bits;  conditional E-value: 8.8e-06
                        Fer4_2   7 tdrCigCgaCvsaCP 21 
                                    ++Ci Cg+C ++CP
  gi|15669493|ref|NP_248303.1| 379 DENCILCGTCSNVCP 393
                                   578************ PP

  == domain 12  score: 10.3 bits;  conditional E-value: 0.00053
                        Fer4_2   7 tdrCigCgaCvsaCP 21 
                                   td+Ci+C++C   CP
  gi|15669493|ref|NP_248303.1| 409 TDNCIACETCAIHCP 423
                                   79********999*9 PP

  == domain 13  score: 14.9 bits;  conditional E-value: 1.8e-05
                        Fer4_2   6 dtdrCigCgaCvsaCPa 22 
                                   d d Ci Cg C ++CP+
  gi|15669493|ref|NP_248303.1| 447 DMDFCIKCGLCNKVCPN 463
                                   889*************5 PP

  == domain 14  score: 14.2 bits;  conditional E-value: 3.1e-05
                        Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                   v+d +rC  CgaC++ CP+
  gi|15669493|ref|NP_248303.1| 470 VIDKERCEFCGACYNICPT 488
                                   89*****99*********7 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8  16.9      0.68   7.6e+02      40      59 ..      44      63 ..       9      64 .. 0.68
   2 !   12.1   1.7    0.0002      0.22       1      17 [.      79      95 ..      79     109 .. 0.78
   3 !   26.2   4.1   7.8e-09   8.8e-06       2      59 ..     110     194 ..     109     196 .. 0.68
   4 !   12.0   3.6   0.00021      0.23      41      59 ..     199     217 ..     193     219 .. 0.87
   5 !   10.3   2.1   0.00072      0.81      42      59 ..     225     242 ..     216     244 .. 0.82
   6 !   16.4   0.9   8.7e-06    0.0097      33      59 ..     253     279 ..     245     280 .. 0.80
   7 !    8.0   2.3    0.0036         4      45      60 ..     294     309 ..     285     310 .. 0.89
   8 !   11.4  11.4   0.00033      0.36       2      59 ..     295     365 ..     294     367 .. 0.66
   9 !   10.0   3.2   0.00088      0.98      44      59 ..     380     395 ..     370     397 .. 0.81
  10 !    9.4   2.7    0.0014       1.5      43      60 ..     409     426 ..     399     427 .. 0.85
  11 !   15.4  13.3   1.8e-05      0.02       1      59 [.     411     464 ..     411     465 .. 0.75
  12 !    6.9   1.4    0.0081       9.1       1      20 [.     475     494 ..     475     500 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.68
                       Fer4_17 40 eekaslCieCgeCerkCPqg 59
                                  ++k  +C++CgeC+r CP++
  gi|15669493|ref|NP_248303.1| 44 NNKSFSCLTCGECARNCPNK 63
                                  56889*************85 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0002
                       Fer4_17  1 rCiqCgyClpeCpsyea 17
                                  rC++Cg C+++Cp +++
  gi|15669493|ref|NP_248303.1| 79 RCNGCGICANVCPIGII 95
                                  69999999999998765 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 7.8e-09
                       Fer4_17   2 CiqCgyClpeCpsyea......ydnepkkllraakl...................glleeaeke...ekaslCieCgeCer 54 
                                   C+ Cg C+++Cp++++       +++++ l++++ l                   + +e++e++      ++C++C +C++
  gi|15669493|ref|NP_248303.1| 110 CSMCGVCVEVCPYNARvssyelLNTKREGLAERY-LkvlenlmkvklfraeekpgKVVEKVERKsikIDRDKCVGCLRCSY 189
                                   ************9777555433444455555553.2245556667777878778756666666643246699********* PP

                       Fer4_17  55 kCPqg 59 
                                    CP +
  gi|15669493|ref|NP_248303.1| 190 LCPRD 194
                                   ***86 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00021
                       Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                   + ++ C++C++C + CP++
  gi|15669493|ref|NP_248303.1| 199 DSIDACTSCNLCGENCPKD 217
                                   57899************87 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00072
                       Fer4_17  42 kaslCieCgeCerkCPqg 59 
                                     ++Ci C +C++ CP++
  gi|15669493|ref|NP_248303.1| 225 DYNKCILCLKCVEICPND 242
                                   5799************97 PP

  == domain 6  score: 16.4 bits;  conditional E-value: 8.7e-06
                       Fer4_17  33 lleeaekeekaslCieCgeCerkCPqg 59 
                                   +++e ++++  s Ci+Cg+C++ CP+g
  gi|15669493|ref|NP_248303.1| 253 KVKEDKTSQPTSYCINCGLCAEHCPSG 279
                                   5566677788999************86 PP

  == domain 7  score: 8.0 bits;  conditional E-value: 0.0036
                       Fer4_17  45 lCieCgeCerkCPqgl 60 
                                    C +C eC++ CP+++
  gi|15669493|ref|NP_248303.1| 294 VCWKCMECVKICPNDV 309
                                   6************997 PP

  == domain 8  score: 11.4 bits;  conditional E-value: 0.00033
                       Fer4_17   2 CiqCgyClpeCpsyea...ydn.....epkkllraakl.....glleeaekeekaslCieCgeCerkCPqg 59 
                                   C +C  C++ Cp   +    d+     ++ +l+ +a++      ++e   ++++++ C+ C+ C   CP++
  gi|15669493|ref|NP_248303.1| 295 CWKCMECVKICPNDVRrikQDFrrlyiHKGNLMPKASMgnnklYSCESPVDDRVVGGCSLCEICINNCPEE 365
                                   99**********74333221112222234466666666443224455556669****************86 PP

  == domain 9  score: 10.0 bits;  conditional E-value: 0.00088
                       Fer4_17  44 slCieCgeCerkCPqg 59 
                                   ++Ci Cg C+ +CP +
  gi|15669493|ref|NP_248303.1| 380 ENCILCGTCSNVCPRD 395
                                   6899999999999975 PP

  == domain 10  score: 9.4 bits;  conditional E-value: 0.0014
                       Fer4_17  43 aslCieCgeCerkCPqgl 60 
                                    ++Ci C+ C+  CP ++
  gi|15669493|ref|NP_248303.1| 409 TDNCIACETCAIHCPRDV 426
                                   578***********9886 PP

  == domain 11  score: 15.4 bits;  conditional E-value: 1.8e-05
                       Fer4_17   1 rCiqCgyClpeCpsyeaydne.pkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                   +Ci C+ C+ +Cp+  + ++   kk++ + +++       ++ ++ Ci+Cg+C+++CP++
  gi|15669493|ref|NP_248303.1| 411 NCIACETCAIHCPRDVIPNTTgYKKVVDR-ENS-----FIRTDMDFCIKCGLCNKVCPNN 464
                                   6*************999555313344444.333.....334689**************97 PP

  == domain 12  score: 6.9 bits;  conditional E-value: 0.0081
                       Fer4_17   1 rCiqCgyClpeCpsyeaydn 20 
                                   rC  Cg+C + Cp+ ++y  
  gi|15669493|ref|NP_248303.1| 475 RCEFCGACYNICPTKAIYLH 494
                                   6999********99887754 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3  17.7       1.4   1.6e+03      11      64 ..      20      63 ..       2      64 .. 0.66
   2 !   12.9   2.7    0.0001      0.12       3      17 ..      78      92 ..      76     108 .. 0.72
   3 !   12.3   1.2   0.00016      0.18      47      64 ..     106     123 ..      95     124 .. 0.82
   4 !   20.3   5.0   5.1e-07   0.00057       5      63 ..     110     193 ..     106     195 .. 0.57
   5 !   10.0   3.6    0.0008       0.9      47      64 ..     200     217 ..     194     218 .. 0.83
   6 !   14.9  12.0   2.5e-05     0.028       3      64 ..     227     279 ..     225     280 .. 0.70
   7 !   13.5   2.9   6.5e-05     0.073       3      18 ..     264     279 ..     261     293 .. 0.78
   8 !   15.9   7.9   1.2e-05     0.013       4      64 ..     294     365 ..     291     366 .. 0.75
   9 ?    5.8  25.3     0.017        19       3      64 ..     380     464 ..     378     465 .. 0.64
  10 !    9.3   0.9    0.0014       1.6       3      17 ..     474     488 ..     472     500 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.4
                        Fer4_8 11 CqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                  Cqs Cp+ +++k +   + +              ++  +sC+tcg+C+++Cp++
  gi|15669493|ref|NP_248303.1| 20 CQS-CPFSQTSKCMEACPTDAIFL-L--------NNKSFSCLTCGECARNCPNK 63
                                  555.66666655333444444333.2........23358*************87 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.0001
                        Fer4_8  3 ekCieCgaCqsaCpv 17
                                  ++C++Cg C + Cp+
  gi|15669493|ref|NP_248303.1| 78 RRCNGCGICANVCPI 92
                                  578888888888874 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00016
                        Fer4_8  47 alwsCttcgaCtevCpvg 64 
                                    ++ C++cg C+evCp +
  gi|15669493|ref|NP_248303.1| 106 PMGICSMCGVCVEVCPYN 123
                                   5788************76 PP

  == domain 4  score: 20.3 bits;  conditional E-value: 5.1e-07
                        Fer4_8   5 CieCgaCqsaCp........................vlrrtkkhlldargeaae.........dvqeeqvlee........ 44 
                                   C  Cg C + Cp                        v                          +        +        
  gi|15669493|ref|NP_248303.1| 110 CSMCGVCVEVCPynarvssyellntkreglaerylkV----------------LenlmkvklfR--------Aeekpgkvv 166
                                   ************5555444433333333333333331................03333333330........033333333 PP

                        Fer4_8  45 ........eealwsCttcgaCtevCpv 63 
                                           +   ++C++c +C+  Cp 
  gi|15669493|ref|NP_248303.1| 167 ekverksiKIDRDKCVGCLRCSYLCPR 193
                                   444444468899**************7 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.0008
                        Fer4_8  47 alwsCttcgaCtevCpvg 64 
                                   ++++Ct+c+ C e+Cp++
  gi|15669493|ref|NP_248303.1| 200 SIDACTSCNLCGENCPKD 217
                                   678999999999999985 PP

  == domain 6  score: 14.9 bits;  conditional E-value: 2.5e-05
                        Fer4_8   3 ekCieCgaCqsaCp..vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   +kCi C  C + Cp  +l+ ++     +  +++e + ++q         +C +cg C+e Cp g
  gi|15669493|ref|NP_248303.1| 227 NKCILCLKCVEICPndALKVEN----FKVIKVKE-DKTSQP------TSYCINCGLCAEHCPSG 279
                                   79***********933333333....33333334.445555......79*************86 PP

  == domain 7  score: 13.5 bits;  conditional E-value: 6.5e-05
                        Fer4_8   3 ekCieCgaCqsaCpvl 18 
                                   ++Ci+Cg+C ++Cp+ 
  gi|15669493|ref|NP_248303.1| 264 SYCINCGLCAEHCPSG 279
                                   6899999999999965 PP

  == domain 8  score: 15.9 bits;  conditional E-value: 1.2e-05
                        Fer4_8   4 kCieCgaCqsaCp............vlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                    C +C+ C + Cp            ++ +++  +++ + g+++ +  e+ v  +++ ++ C+ c+ C ++Cp++
  gi|15669493|ref|NP_248303.1| 294 VCWKCMECVKICPndvrrikqdfrrLYIHKGnLMPKASMGNNKLYSCESPV--DDRVVGGCSLCEICINNCPEE 365
                                   5***********999888777777755555535555555555555555555..5899***************85 PP

  == domain 9  score: 5.8 bits;  conditional E-value: 0.017
                        Fer4_8   3 ekCieCgaCqsaCp.....................vlrrtkkhlldargeaae..................dvqeeqvlee 44 
                                   e+Ci Cg C + Cp                                      e                  +v+++++  +
  gi|15669493|ref|NP_248303.1| 380 ENCILCGTCSNVCPrdaiiidrsngevlftdnciaC----------------EtcaihcprdvipnttgykKVVDREN--S 442
                                   68***********99998655555555555554440................33333333333333444222333333..2 PP

                        Fer4_8  45 ..eealwsCttcgaCtevCpvg 64 
                                     ++ ++ C  cg C++vCp++
  gi|15669493|ref|NP_248303.1| 443 fiRTDMDFCIKCGLCNKVCPNN 464
                                   45999***************87 PP

  == domain 10  score: 9.3 bits;  conditional E-value: 0.0014
                        Fer4_8   3 ekCieCgaCqsaCpv 17 
                                   e+C  CgaC + Cp+
  gi|15669493|ref|NP_248303.1| 474 ERCEFCGACYNICPT 488
                                   567778888888873 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   2.3   0.00075      0.84       1      15 []      20      39 ..      18      39 .. 0.77
   2 !    8.4   4.9    0.0042       4.7       1      15 []      50      64 ..      50      64 .. 0.97
   3 !   11.0   4.8   0.00062      0.69       1      14 [.      80      93 ..      80      94 .. 0.94
   4 !   16.1   6.6   1.4e-05     0.016       1      15 []     110     124 ..     110     124 .. 0.98
   5 ?    5.8   3.5     0.029        32       1      13 [.     181     193 ..     181     194 .. 0.92
   6 !   10.1   3.8    0.0012       1.3       1      15 []     204     218 ..     204     218 .. 0.97
   7 !   13.1   2.5   0.00013      0.15       1      15 []     229     243 ..     229     243 .. 0.96
   8 !   12.8   5.4   0.00016      0.18       1      15 []     266     280 ..     266     280 .. 0.98
   9 !   10.9   3.8   0.00068      0.76       1      14 [.     295     308 ..     295     309 .. 0.93
  10 ?    3.9   2.7      0.12   1.3e+02       1      15 []     352     366 ..     352     366 .. 0.90
  11 !   14.9   3.7   3.4e-05     0.038       1      15 []     382     396 ..     382     396 .. 0.97
  12 ?    1.6   4.0      0.63   7.1e+02       1      14 [.     412     425 ..     412     426 .. 0.91
  13 !    9.5   8.9    0.0019       2.1       1      14 [.     451     464 ..     451     465 .. 0.94
  14 !   11.8   3.8   0.00033      0.37       1      15 []     476     490 ..     476     490 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00075
                        Fer4_3  1 CtgCg.....aCvevCPvgA 15
                                  C+ C       C+e+CP++A
  gi|15669493|ref|NP_248303.1| 20 CQSCPfsqtsKCMEACPTDA 39
                                  77773445558*******98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0042
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ Cg C + CP++A
  gi|15669493|ref|NP_248303.1| 50 CLTCGECARNCPNKA 64
                                  9***********998 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00062
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C+gCg C +vCP g
  gi|15669493|ref|NP_248303.1| 80 CNGCGICANVCPIG 93
                                  ************88 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 1.4e-05
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C +Cg CvevCP++A
  gi|15669493|ref|NP_248303.1| 110 CSMCGVCVEVCPYNA 124
                                   9************98 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.029
                        Fer4_3   1 CtgCgaCvevCPv 13 
                                   C+gC +C   CP 
  gi|15669493|ref|NP_248303.1| 181 CVGCLRCSYLCPR 193
                                   ****99******7 PP

  == domain 6  score: 10.1 bits;  conditional E-value: 0.0012
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   Ct C++C e CP++A
  gi|15669493|ref|NP_248303.1| 204 CTSCNLCGENCPKDA 218
                                   *************98 PP

  == domain 7  score: 13.1 bits;  conditional E-value: 0.00013
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ C  Cve CP++A
  gi|15669493|ref|NP_248303.1| 229 CILCLKCVEICPNDA 243
                                   ****99******998 PP

  == domain 8  score: 12.8 bits;  conditional E-value: 0.00016
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C++Cg+C e CP+gA
  gi|15669493|ref|NP_248303.1| 266 CINCGLCAEHCPSGA 280
                                   **************9 PP

  == domain 9  score: 10.9 bits;  conditional E-value: 0.00068
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   C+ C+ Cv+ CP++
  gi|15669493|ref|NP_248303.1| 295 CWKCMECVKICPND 308
                                   9***********86 PP

  == domain 10  score: 3.9 bits;  conditional E-value: 0.12
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C  C+ C + CP+ A
  gi|15669493|ref|NP_248303.1| 352 CSLCEICINNCPEEA 366
                                   999*********866 PP

  == domain 11  score: 14.9 bits;  conditional E-value: 3.4e-05
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ Cg+C +vCP +A
  gi|15669493|ref|NP_248303.1| 382 CILCGTCSNVCPRDA 396
                                   ************998 PP

  == domain 12  score: 1.6 bits;  conditional E-value: 0.63
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   C+ C++C   CP +
  gi|15669493|ref|NP_248303.1| 412 CIACETCAIHCPRD 425
                                   9**********975 PP

  == domain 13  score: 9.5 bits;  conditional E-value: 0.0019
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   C+ Cg+C +vCP++
  gi|15669493|ref|NP_248303.1| 451 CIKCGLCNKVCPNN 464
                                   ************97 PP

  == domain 14  score: 11.8 bits;  conditional E-value: 0.00033
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C  CgaC + CP++A
  gi|15669493|ref|NP_248303.1| 476 CEFCGACYNICPTKA 490
                                   999**********98 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   4.0     0.016        17       2      16 ..      18      37 ..      17      38 .. 0.83
   2 !   10.2   1.7   0.00081       0.9       3      15 ..      49      61 ..      46      71 .. 0.91
   3 !   11.9   3.7   0.00024      0.27       3      15 ..      79      91 ..      77     108 .. 0.90
   4 !   10.1   3.5   0.00089      0.99       4      17 .]     110     123 ..     107     123 .. 0.92
   5 ?    6.1   3.2     0.017        19       2      16 ..     179     193 ..     178     194 .. 0.91
   6 ?    0.9   3.0      0.79   8.8e+02       2      15 ..     202     215 ..     201     218 .. 0.82
   7 !   12.6   1.0   0.00013      0.15       1      15 [.     226     240 ..     226     250 .. 0.90
   8 !    9.1   2.9    0.0018         2       3      17 .]     265     279 ..     263     279 .. 0.90
   9 !   13.0   2.4   9.9e-05      0.11       1      15 [.     292     306 ..     292     315 .. 0.89
  10 ?    2.9   1.8      0.18     2e+02       4      16 ..     352     364 ..     346     368 .. 0.88
  11 !   12.6   1.6   0.00014      0.15       2      16 ..     380     394 ..     379     400 .. 0.93
  12 !   11.2   1.6   0.00039      0.43       2      16 ..     410     424 ..     409     433 .. 0.91
  13 ?    5.9   3.1      0.02        22       4      16 ..     451     463 ..     440     468 .. 0.91
  14 !   11.5   4.2   0.00031      0.35       1      16 [.     473     488 ..     473     489 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.016
                        Fer4_4  2 erCigCg.....sCvaaCPq 16
                                  e+C+ C+     +C+ aCP+
  gi|15669493|ref|NP_248303.1| 18 EKCQSCPfsqtsKCMEACPT 37
                                  89*****776666******7 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00081
                        Fer4_4  3 rCigCgsCvaaCP 15
                                  +C+ Cg C + CP
  gi|15669493|ref|NP_248303.1| 49 SCLTCGECARNCP 61
                                  6************ PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00024
                        Fer4_4  3 rCigCgsCvaaCP 15
                                  rC+gCg C ++CP
  gi|15669493|ref|NP_248303.1| 79 RCNGCGICANVCP 91
                                  8***********9 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00089
                        Fer4_4   4 CigCgsCvaaCPqg 17 
                                   C  Cg+Cv +CP++
  gi|15669493|ref|NP_248303.1| 110 CSMCGVCVEVCPYN 123
                                   999*********86 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.017
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   ++C+gC +C + CP 
  gi|15669493|ref|NP_248303.1| 179 DKCVGCLRCSYLCPR 193
                                   89***********95 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.79
                        Fer4_4   2 erCigCgsCvaaCP 15 
                                   + C+ C  C   CP
  gi|15669493|ref|NP_248303.1| 202 DACTSCNLCGENCP 215
                                   78999999987787 PP

  == domain 7  score: 12.6 bits;  conditional E-value: 0.00013
                        Fer4_4   1 qerCigCgsCvaaCP 15 
                                   +++Ci C +Cv +CP
  gi|15669493|ref|NP_248303.1| 226 YNKCILCLKCVEICP 240
                                   589************ PP

  == domain 8  score: 9.1 bits;  conditional E-value: 0.0018
                        Fer4_4   3 rCigCgsCvaaCPqg 17 
                                    Ci+Cg C   CP+g
  gi|15669493|ref|NP_248303.1| 265 YCINCGLCAEHCPSG 279
                                   6************85 PP

  == domain 9  score: 13.0 bits;  conditional E-value: 9.9e-05
                        Fer4_4   1 qerCigCgsCvaaCP 15 
                                   ++ C  C+ Cv +CP
  gi|15669493|ref|NP_248303.1| 292 PDVCWKCMECVKICP 306
                                   588************ PP

  == domain 10  score: 2.9 bits;  conditional E-value: 0.18
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   C  C  C++ CP 
  gi|15669493|ref|NP_248303.1| 352 CSLCEICINNCPE 364
                                   89999******95 PP

  == domain 11  score: 12.6 bits;  conditional E-value: 0.00014
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   e+Ci Cg C ++CP 
  gi|15669493|ref|NP_248303.1| 380 ENCILCGTCSNVCPR 394
                                   79************5 PP

  == domain 12  score: 11.2 bits;  conditional E-value: 0.00039
                        Fer4_4   2 erCigCgsCvaaCPq 16 
                                   ++Ci C  C + CP 
  gi|15669493|ref|NP_248303.1| 410 DNCIACETCAIHCPR 424
                                   89************5 PP

  == domain 13  score: 5.9 bits;  conditional E-value: 0.02
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   Ci Cg C  +CP 
  gi|15669493|ref|NP_248303.1| 451 CIKCGLCNKVCPN 463
                                   ************5 PP

  == domain 14  score: 11.5 bits;  conditional E-value: 0.00031
                        Fer4_4   1 qerCigCgsCvaaCPq 16 
                                   +erC  Cg+C+++CP+
  gi|15669493|ref|NP_248303.1| 473 KERCEFCGACYNICPT 488
                                   689999*********8 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   4.5       1.3   1.4e+03      46      56 ..      30      40 ..      12      41 .. 0.84
   2 ?    3.6   1.7     0.086        96       5      18 ..      49      62 ..      47      67 .. 0.91
   3 !   12.9   1.3   0.00011      0.12       1      17 [.      75      91 ..      75     103 .. 0.96
   4 ?    5.5   2.5     0.022        24       6      17 ..     110     121 ..     108     123 .. 0.94
   5 !   11.7   1.3   0.00026      0.29       1      17 [.     176     192 ..     176     193 .. 0.96
   6 ?    6.3   3.8     0.012        14       4      18 ..     202     216 ..     201     217 .. 0.91
   7 !   13.0   0.7    0.0001      0.12       1      18 [.     224     241 ..     224     259 .. 0.96
   8 !    8.7   2.6    0.0023       2.6       5      18 ..     265     278 ..     263     279 .. 0.90
   9 !   10.0   0.1   0.00088      0.99       4      18 ..     293     307 ..     292     337 .. 0.77
  10 ?    3.8   1.7     0.077        86       5      18 ..     351     364 ..     346     367 .. 0.92
  11 !   10.1   2.6   0.00084      0.95       2      17 ..     379     393 ..     377     394 .. 0.91
  12 !    8.9   3.4    0.0019       2.1       4      17 ..     410     423 ..     409     432 .. 0.94
  13 !   10.3   2.1    0.0007      0.79       2      18 ..     447     463 ..     446     464 .. 0.91
  14 !   11.6   2.0   0.00029      0.32       1      17 [.     471     487 ..     471     489 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.3
                       Fer4_13 46 eAadaCPvesI 56
                                  + ++aCP+++I
  gi|15669493|ref|NP_248303.1| 30 KCMEACPTDAI 40
                                  55899999998 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.086
                       Fer4_13  5 tCiacgaCvelaPd 18
                                  +C  cg C+  +P+
  gi|15669493|ref|NP_248303.1| 49 SCLTCGECARNCPN 62
                                  699*********96 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00011
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  VDr +C +cg+C++++P
  gi|15669493|ref|NP_248303.1| 75 VDRRRCNGCGICANVCP 91
                                  9***************9 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.022
                       Fer4_13   6 CiacgaCvelaP 17 
                                   C+ cg+Cve++P
  gi|15669493|ref|NP_248303.1| 110 CSMCGVCVEVCP 121
                                   9**********9 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.00026
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   +Drd+C++c  C  l+P
  gi|15669493|ref|NP_248303.1| 176 IDRDKCVGCLRCSYLCP 192
                                   8**************** PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.012
                       Fer4_13   4 dtCiacgaCvelaPd 18 
                                   d C++c++C+e +P+
  gi|15669493|ref|NP_248303.1| 202 DACTSCNLCGENCPK 216
                                   58************6 PP

  == domain 7  score: 13.0 bits;  conditional E-value: 0.0001
                       Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                   VD ++Ci c +Cve++P+
  gi|15669493|ref|NP_248303.1| 224 VDYNKCILCLKCVEICPN 241
                                   899**************6 PP

  == domain 8  score: 8.7 bits;  conditional E-value: 0.0023
                       Fer4_13   5 tCiacgaCvelaPd 18 
                                    Ci+cg+C+e +P 
  gi|15669493|ref|NP_248303.1| 265 YCINCGLCAEHCPS 278
                                   5************5 PP

  == domain 9  score: 10.0 bits;  conditional E-value: 0.00088
                       Fer4_13   4 dtCiacgaCvelaPd 18 
                                   d C  c+ Cv+++P+
  gi|15669493|ref|NP_248303.1| 293 DVCWKCMECVKICPN 307
                                   67************5 PP

  == domain 10  score: 3.8 bits;  conditional E-value: 0.077
                       Fer4_13   5 tCiacgaCvelaPd 18 
                                    C+ c++C + +P+
  gi|15669493|ref|NP_248303.1| 351 GCSLCEICINNCPE 364
                                   6999********97 PP

  == domain 11  score: 10.1 bits;  conditional E-value: 0.00084
                       Fer4_13   2 DrdtCiacgaCvelaP 17 
                                   D ++Ci cg+C +++P
  gi|15669493|ref|NP_248303.1| 379 D-ENCILCGTCSNVCP 393
                                   5.99************ PP

  == domain 12  score: 8.9 bits;  conditional E-value: 0.0019
                       Fer4_13   4 dtCiacgaCvelaP 17 
                                   d+Ciac++C+  +P
  gi|15669493|ref|NP_248303.1| 410 DNCIACETCAIHCP 423
                                   79***********9 PP

  == domain 13  score: 10.3 bits;  conditional E-value: 0.0007
                       Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                   D d Ci cg+C +++P+
  gi|15669493|ref|NP_248303.1| 447 DMDFCIKCGLCNKVCPN 463
                                   6788************7 PP

  == domain 14  score: 11.6 bits;  conditional E-value: 0.00029
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   +D+++C  cgaC++++P
  gi|15669493|ref|NP_248303.1| 471 IDKERCEFCGACYNICP 487
                                   8**************** PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.8     0.038        43      52      65 ..      28      41 ..      12      42 .. 0.88
   2 ?    2.7   1.0      0.19   2.2e+02      13      64 ..      55      65 ..      49      68 .. 0.60
   3 !   15.4   0.4     2e-05     0.023       2      19 ..      74      91 ..      74     106 .. 0.79
   4 ?    6.7   0.2     0.011        13       8      19 ..     110     121 ..     107     147 .. 0.84
   5 !   12.9   1.8   0.00013      0.14       1      19 [.     174     192 ..     174     201 .. 0.91
   6 ?    4.7   3.1     0.045        51       6      20 ..     202     216 ..     196     222 .. 0.90
   7 !    9.9   0.5    0.0011       1.3       2      20 ..     223     241 ..     223     261 .. 0.83
   8 ?    4.7   0.7     0.045        50       8      20 ..     266     278 ..     263     287 .. 0.86
   9 ?    2.2   0.1      0.27   3.1e+02       6      30 ..     293     317 ..     289     329 .. 0.78
  10 ?    0.6   2.0      0.89     1e+03      15      64 ..     359     367 ..     351     369 .. 0.54
  11 ?    1.3   4.5      0.53     6e+02       5      19 ..     379     393 ..     376     401 .. 0.82
  12 ?    4.6   0.4     0.049        55       6      33 ..     410     437 ..     407     443 .. 0.74
  13 ?    4.2   3.7     0.065        73       1      20 [.     444     463 ..     444     467 .. 0.89
  14 !   13.5   0.7     8e-05      0.09       2      20 ..     470     488 ..     470     493 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.038
                       Fer4_15 52 aqeAaraCPvdAIr 65
                                  + + ++aCP+dAI+
  gi|15669493|ref|NP_248303.1| 28 TSKCMEACPTDAIF 41
                                  567799*******8 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.19
                       Fer4_15 13 lCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAI 64
                                   C                                         ar+CP +AI
  gi|15669493|ref|NP_248303.1| 55 EC-----------------------------------------ARNCPNKAI 65
                                  44.........................................556666665 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 2e-05
                       Fer4_15  2 vvDrdaCigcglCvaeap 19
                                  +vDr +C gcg C+ ++p
  gi|15669493|ref|NP_248303.1| 74 YVDRRRCNGCGICANVCP 91
                                  69***************7 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.011
                       Fer4_15   8 CigcglCvaeap 19 
                                   C +cg+Cv+++p
  gi|15669493|ref|NP_248303.1| 110 CSMCGVCVEVCP 121
                                   ***********7 PP

  == domain 5  score: 12.9 bits;  conditional E-value: 0.00013
                       Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                   +++Drd+C gc +C  ++p
  gi|15669493|ref|NP_248303.1| 174 IKIDRDKCVGCLRCSYLCP 192
                                   79***************98 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.045
                       Fer4_15   6 daCigcglCvaeape 20 
                                   daC++c+lC +++p+
  gi|15669493|ref|NP_248303.1| 202 DACTSCNLCGENCPK 216
                                   89***********86 PP

  == domain 7  score: 9.9 bits;  conditional E-value: 0.0011
                       Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                   +vD ++Ci c  Cv+ +p+
  gi|15669493|ref|NP_248303.1| 223 EVDYNKCILCLKCVEICPN 241
                                   59***************85 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.045
                       Fer4_15   8 CigcglCvaeape 20 
                                   Ci cglC++ +p 
  gi|15669493|ref|NP_248303.1| 266 CINCGLCAEHCPS 278
                                   **********985 PP

  == domain 9  score: 2.2 bits;  conditional E-value: 0.27
                       Fer4_15   6 daCigcglCvaeapevfeldedgla 30 
                                   d C  c  Cv+ +p+ ++  ++++ 
  gi|15669493|ref|NP_248303.1| 293 DVCWKCMECVKICPNDVRRIKQDFR 317
                                   67999********987776666665 PP

  == domain 10  score: 0.6 bits;  conditional E-value: 0.89
                       Fer4_15  15 vaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAI 64 
                                   + +                                         CP++AI
  gi|15669493|ref|NP_248303.1| 359 INN-----------------------------------------CPEEAI 367
                                   555.........................................555555 PP

  == domain 11  score: 1.3 bits;  conditional E-value: 0.53
                       Fer4_15   5 rdaCigcglCvaeap 19 
                                    ++Ci cg C  ++p
  gi|15669493|ref|NP_248303.1| 379 DENCILCGTCSNVCP 393
                                   578999999999997 PP

  == domain 12  score: 4.6 bits;  conditional E-value: 0.049
                       Fer4_15   6 daCigcglCvaeapevfeldedglasvl 33 
                                   d+Ci c+ C+  +p+ +  +  g+++v+
  gi|15669493|ref|NP_248303.1| 410 DNCIACETCAIHCPRDVIPNTTGYKKVV 437
                                   89**********9865555556666555 PP

  == domain 13  score: 4.2 bits;  conditional E-value: 0.065
                       Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                   ++ D d Ci cglC +++p+
  gi|15669493|ref|NP_248303.1| 444 IRTDMDFCIKCGLCNKVCPN 463
                                   56799*************97 PP

  == domain 14  score: 13.5 bits;  conditional E-value: 8e-05
                       Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                   v+D+++C+ cg+C+  +p+
  gi|15669493|ref|NP_248303.1| 470 VIDKERCEFCGACYNICPT 488
                                   69**************985 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   6.7     0.012        14      63      96 ..      27      61 ..       9      73 .. 0.77
   2 ?    6.1   2.8     0.011        13      60      75 ..      79      94 ..      73     102 .. 0.87
   3 !    8.0   2.4    0.0029       3.2      55      74 ..     104     123 ..      95     128 .. 0.80
   4 !    7.0   8.5    0.0058       6.5      40      96 ..     159     215 ..     141     217 .. 0.76
   5 !    9.2  11.0    0.0012       1.4      57      96 ..     200     240 ..     193     247 .. 0.81
   6 !   13.1   8.7   7.2e-05     0.081      44     100 ..     249     310 ..     241     317 .. 0.80
   7 ?    5.4   2.3     0.019        21      54      74 ..     345     365 ..     321     378 .. 0.77
   8 !   10.1  11.6   0.00064      0.72      55      95 ..     376     422 ..     364     435 .. 0.75
   9 ?    5.0  11.3     0.024        27      49      96 ..     439     487 ..     425     489 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                       Fer4_18 63 dcescvkvcPtg.idirkGlqleciscllcidacd 96
                                  + ++c++ cPt+ i + +   ++c++c++c   c 
  gi|15669493|ref|NP_248303.1| 27 QTSKCMEACPTDaIFLLNNKSFSCLTCGECARNCP 61
                                  4578******9648899**************9995 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
                       Fer4_18 60 dcidcescvkvcPtgi 75
                                   c  c+ c +vcP+gi
  gi|15669493|ref|NP_248303.1| 79 RCNGCGICANVCPIGI 94
                                  699***********98 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0029
                       Fer4_18  55 ekgagdcidcescvkvcPtg 74 
                                   + ++g c  c++cv+vcP +
  gi|15669493|ref|NP_248303.1| 104 KFPMGICSMCGVCVEVCPYN 123
                                   557789************75 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0058
                       Fer4_18  40 rkkekkalkekeerk.ekgagdcidcescvkvcPtgidirkGlqleciscllcidacd 96 
                                   ++k  k+++++e+++ + +  +c+ c  c  +cP +  + + +   c sc lc + c 
  gi|15669493|ref|NP_248303.1| 159 EEKPGKVVEKVERKSiKIDRDKCVGCLRCSYLCPRDTIVPDSID-ACTSCNLCGENCP 215
                                   4455555555555551456778**************99999987.7*******99995 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0012
                       Fer4_18  57 gagdcidcescvkvcPtgidirkGl..qleciscllcidacd 96 
                                   +   c++c+ c + cP +  i++G     +ci cl+c++ c 
  gi|15669493|ref|NP_248303.1| 200 SIDACTSCNLCGENCPKD-AIKDGEvdYNKCILCLKCVEICP 240
                                   5678************98.58888522468***********6 PP

  == domain 6  score: 13.1 bits;  conditional E-value: 7.2e-05
                       Fer4_18  44 kkalkekeerkekgagdcidcescvkvcPtg.idirkGlqle....ciscllcidacdkvme 100
                                    k++k ke++++++++ ci+c+ c + cP g +   +G  +     c +c++c+  c + + 
  gi|15669493|ref|NP_248303.1| 249 FKVIKVKEDKTSQPTSYCINCGLCAEHCPSGaLRFENGHLYYspdvCWKCMECVKICPNDVR 310
                                   5678999999*******************98467889976533445***********76555 PP

  == domain 7  score: 5.4 bits;  conditional E-value: 0.019
                       Fer4_18  54 kekgagdcidcescvkvcPtg 74 
                                    ++ +g c  ce c++ cP +
  gi|15669493|ref|NP_248303.1| 345 DDRVVGGCSLCEICINNCPEE 365
                                   4567899************75 PP

  == domain 8  score: 10.1 bits;  conditional E-value: 0.00064
                       Fer4_18  55 ekgagdcidcescvkvcPtg...idirkGlql...eciscllcidac 95 
                                   + ++ +ci c++c +vcP +   id  +G  l   +ci+c  c   c
  gi|15669493|ref|NP_248303.1| 376 KIKDENCILCGTCSNVCPRDaiiIDRSNGEVLftdNCIACETCAIHC 422
                                   446679************754337888896554448*******9888 PP

  == domain 9  score: 5.0 bits;  conditional E-value: 0.024
                       Fer4_18  49 ekeerkekgagdcidcescvkvcPtg.idirkGlqleciscllcidacd 96 
                                   ++++  ++++  ci+c+ c kvcP + id     +  c  c+ c + c 
  gi|15669493|ref|NP_248303.1| 439 RENSFIRTDMDFCIKCGLCNKVCPNNcIDYGVIDKERCEFCGACYNICP 487
                                   444445566777************8647877777889*******99995 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.077        86       4      18 ..      30      44 ..      29      44 .. 0.90
   2 ?   -2.0   0.1       5.9   6.6e+03       4      13 ..      55      64 ..      52      65 .. 0.81
   3 ?    6.8   0.1    0.0092        10       1      13 [.     231     243 ..     231     244 .. 0.93
   4 ?    0.8   0.0      0.72   8.1e+02       2      13 ..     298     309 ..     297     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.077
                        TPR_17  4 kaleldPnnadaynn 18
                                  k++e +P++a ++ n
  gi|15669493|ref|NP_248303.1| 30 KCMEACPTDAIFLLN 44
                                  8*********99876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.9
                        TPR_17  4 kaleldPnna 13
                                  ++++++Pn a
  gi|15669493|ref|NP_248303.1| 55 ECARNCPNKA 64
                                  899****976 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0092
                        TPR_17   1 lylkaleldPnna 13 
                                   l+lk++e++Pn+a
  gi|15669493|ref|NP_248303.1| 231 LCLKCVEICPNDA 243
                                   79**********8 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.72
                        TPR_17   2 ylkaleldPnna 13 
                                   + ++++++Pn++
  gi|15669493|ref|NP_248303.1| 298 CMECVKICPNDV 309
                                   6789999***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.64u 0.24s 00:00:00.88 Elapsed: 00:00:00.40
# Mc/sec: 3732.71
//
Query:       gi|15669494|ref|NP_248304.1|  [L=152]
Description: hypothetical protein MJ_1304 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.1e-33  114.4   0.2    3.9e-33  114.1   0.2    1.0  1  HEPN       HEPN domain
    0.00011   22.4   0.0    0.00081   19.6   0.0    2.0  2  HEPN_AbiV  AbiV
  ------ inclusion threshold ------
      0.051   13.7   0.7       0.31   11.2   0.4    2.1  2  CTK3_C     CTD kinase subunit gamma CTK3 C-terminus


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   0.2   6.5e-37   3.9e-33       2     117 ..      12     141 ..      11     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 6.5e-37
                                   HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHH..... CS
                          HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreel..... 77 
                                   + +++rAeedle A++ll++++y ++++h+qq++eka+KA+l+ +g+   + h ++  ++++  e+k +++++e+l     
  gi|15669494|ref|NP_248304.1|  12 KLFIKRAEEDLEVAKVLLKTNHYPDSVYHSQQCVEKAVKAVLILNGII-FRRHVVSGVFRNVIYEMKIEDSWKEKLlnlip 91 
                                   6799*******************************************5.**************99999999999999999* PP

                                   ..HHHHCCCHHCCCTSS--S........--HHHHHHHHHHHHHHHHHHHH CS
                          HEPN  78 ..eeLekayiesrYpdakee........yteedaeealkdaeevlelvee 117
                                     e Le+++++ rYp+ +++        yt+edaee+lkdae+vle++++
  gi|15669494|ref|NP_248304.1|  92 kiESLEEHWVMPRYPEPYFGelwnpleeYTKEDAEECLKDAENVLEVIKD 141
                                   99********************************************9875 PP

>> HEPN_AbiV  AbiV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.4e-07   0.00081       4      51 ..       9      56 ..       7      96 .. 0.90
   2 ?    0.9   0.0     0.076   4.5e+02     140     163 ..     113     136 ..     105     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.4e-07
                     HEPN_AbiV  4 egakalleNAeeLledAelLaengsyarAysLlilaiEElgKalllyd 51
                                  + ak+ ++ Aee le A++L+++++y+ ++++++ + E ++Ka+l+++
  gi|15669494|ref|NP_248304.1|  9 KYAKLFIKRAEEDLEVAKVLLKTNHYPDSVYHSQQCVEKAVKAVLILN 56
                                  568889999************************************986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.076
                     HEPN_AbiV 140 issPseviskeaaeeiielaeell 163
                                   +++P e  +ke+aee ++ ae++l
  gi|15669494|ref|NP_248304.1| 113 LWNPLEEYTKEDAEECLKDAENVL 136
                                   677888888888888888888776 PP

>> CTK3_C  CTD kinase subunit gamma CTK3 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.15   8.9e+02       6      17 ..      15      26 ..      11      29 .. 0.81
   2 ?   11.2   0.4   5.1e-05      0.31      21      65 ..      97     135 ..      94     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.15
                        CTK3_C  6 lkRiEeDRErhK 17
                                  +kR EeD E  K
  gi|15669494|ref|NP_248304.1| 15 IKRAEEDLEVAK 26
                                  799****88766 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.1e-05
                        CTK3_C  21 EniWvvprskekslateaEfenlWeetsdlneddeeealeeleel 65 
                                   E+ Wv+pr        e  f +lW+ +++++++d ee l+++e++
  gi|15669494|ref|NP_248304.1|  97 EEHWVMPRYP------EPYFGELWNPLEEYTKEDAEECLKDAENV 135
                                   899*****99......889**********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1066.05
//
Query:       gi|15669495|ref|NP_248305.1|  [L=147]
Description: hypothetical protein MJ_1305 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-13   49.8   0.1    4.3e-13   49.4   0.1    1.4  1  NTP_transf_2    Nucleotidyltransferase domain
      5e-08   32.9   0.1      9e-08   32.1   0.1    1.6  1  Polbeta         Polymerase beta, Nucleotidyltransferase
    0.00028   21.1   0.0     0.0007   19.8   0.0    1.8  2  SMODS           Second Messenger Oligonucleotide or Dinucleot
      0.005   17.0   0.0     0.0074   16.5   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.1   9.6e-17   4.3e-13       1      74 [.      10      91 ..      10     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 9.6e-17
                                  HHHHHHHHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH......HHHEHHHHHHHHCCCEEECTTEEEEEE CS
                  NTP_transf_2  1 lkklleelkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsre......kkeegleklaeiikfleellglevdlv 74
                                  l+++l+++k++++   ++++lfGSyarGta ++SD+Dllv+ ++  +r        ++  le + +   +++++l+ + dl+
  gi|15669495|ref|NP_248305.1| 10 LDEFLQKCKQKFGddLISIILFGSYARGTAVEYSDVDLLVIAKNLPKRRidrhkvLRDIVLEFIYRYGINISPILVEPRDLS 91
                                  5799**********99*****************************9987777777333334444444444444444444444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.1     2e-11     9e-08      11      51 ..      23      68 ..       9     115 .. 0.67

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2e-11
                                  HHHHSTTEEEEEE-S------EEEEEEEESS-.....--HHHHHHH CS
                       Polbeta 11 keielaylFGSrakgkareeSDiDlavllkek.....ldleeelel 51
                                  ++++ ++lFGS+a+g+a e SD+Dl v+ k+      ++ +   ++
  gi|15669495|ref|NP_248305.1| 23 DDLISIILFGSYARGTAVEYSDVDLLVIAKNLpkrriDRHKVLRDI 68
                                  57999*************************9975444333333344 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.6e-07    0.0007      30      79 ..       9      49 ..       4      85 .. 0.81
   2 ?   -1.7   0.0      0.65   2.9e+03     127     142 ..     130     145 ..     113     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.6e-07
                         SMODS 30 aitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllv 79
                                   + ++L+k ++++++++++ +l+GSyar+Ta++          +dvdllv
  gi|15669495|ref|NP_248305.1|  9 ILDEFLQKCKQKFGDDLISIILFGSYARGTAVE-Y--------SDVDLLV 49
                                  5789***************************98.3........3444444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.65
                         SMODS 127 vvPavenkdgsyeipd 142
                                   + P++ +++++++i+d
  gi|15669495|ref|NP_248305.1| 130 IKPIFIDEEKEWKIAD 145
                                   5677777777777776 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.6e-06    0.0074      11      67 ..      11      69 ..       4      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-06
                                  HHHHHHHHHHH-TT.-EEEE-HHHHTT-S.EESSEEEEEEBTTBSTTSS--HHHHHHHH CS
                DNA_pol_B_palm 11 ealvkkaakeldpe.vevivcGSYRRgae.ssGDvDvlitkkdakseskklkklleklv 67
                                   ++++k  +++ ++ +++i  GSY Rg + +  DvD+l+  k+  +++ +++k+l+++v
  gi|15669495|ref|NP_248305.1| 11 DEFLQKCKQKFGDDlISIILFGSYARGTAvEYSDVDLLVIAKNLPKRRIDRHKVLRDIV 69
                                  566777777777775788999*****9763689*********99998888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1015.04
//
Query:       gi|15669496|ref|NP_248306.1|  [L=83]
Description: hypothetical protein MJ_1306 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 579.48
//
Query:       gi|15669497|ref|NP_248307.1|  [L=262]
Description: putative monovalent cation/H+ antiporter subunit B [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-21   76.6  14.3      2e-21   76.6  14.3    2.2  2  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.2     0.078   1.4e+03      68      98 ..       9      51 ..       2      82 .. 0.48
   2 !   76.6  14.3   1.1e-25     2e-21       1     123 [.     111     238 ..     111     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.078
                          MnhB 68 eglglllavltgllglll.....g....fltslflelel...l 98
                                  ++++++++ ++ l++l+      g    +lt+++++  +   +
  gi|15669497|ref|NP_248307.1|  9 VAISFFVFGASVLYSLAHmqispGvnevYLTHYIIPNYVcavI 51
                                  4555555555555555553333323345666655554444431 PP

  == domain 2  score: 76.6 bits;  conditional E-value: 1.1e-25
                          MnhB   1 ilrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafgleelekllrvklaprileglglllavltgll 81 
                                   i++ +a  + +l++ +++  +l Gh +PGGGFqgG+++aaa+il ++afg++   ++ ++ l+  +le+lg+l ++l+g++
  gi|15669497|ref|NP_248307.1| 111 IIKFLAFPMSVLMVALGIITVLGGHITPGGGFQGGALIAAAFILSVIAFGSNSPLWFDHKFLE--KLEALGALGYLLLGVA 189
                                   6778888999***************************************************77..**************** PP

                          MnhB  82 glllg..fltslflelel..llg...eve..lgtallfdlgVylvVvggll 123
                                   g+++g  +l + f+e++   ++    e    +g++++++++V+l+V++gl+
  gi|15669497|ref|NP_248307.1| 190 GMFIGgyYLFN-FTEINGftIFPapkE-IitAGIIPYLNIAVGLKVLAGLS 238
                                   ****9986665.555633463333323.258*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1799.96
//
Query:       gi|15669498|ref|NP_248308.1|  [L=108]
Description: hypothetical protein MJ_1308 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.065   12.6   2.1       0.48    9.7   0.9    2.0  2  SLATT_5          SMODS and SLOG-associating 2TM effector doma
          1    9.3   5.2       0.39   10.7   1.1    2.2  2  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> SLATT_5  SMODS and SLOG-associating 2TM effector domain family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0    0.0095        85     142     184 ..       5      46 ..       3      51 .. 0.64
   2 ?    9.7   0.9   5.3e-05      0.48      34      79 ..      54      99 ..      47     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0095
                       SLATT_5 142 iDyklfraknakkseelekskklkwfl.rrylivifllylliil 184
                                   +Dy++f+ k   ++ee++  + + + +   + ++  ++ +++i+
  gi|15669498|ref|NP_248308.1|   5 MDYNDFQKK--LDKEEHGDGITVGAVYtGEFTLYLLFIFGALII 46 
                                   89**99999..477777777777777744444444444444544 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 5.3e-05
                       SLATT_5 34 tfslsllSvylivlsllsnkssestinenlldflsiilSilvlvis 79
                                  +++l+ l++ ++ ls+ +  +++   n+n++++  + lSi++ +i+
  gi|15669498|ref|NP_248308.1| 54 LMTLFGLAALAFSLSVSPLIFKFKEENSNAINYQLFWLSIFLGAIA 99
                                  678899999999999999***********************97776 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2     0.094   8.4e+02      12      26 ..      30      45 ..      29      48 .. 0.54
   2 ?   10.7   1.1   4.4e-05      0.39      17      42 ..      52      80 ..      47      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.094
                                  XXX.XXXXXXXXXXXX CS
               Gram_pos_anchor 12 TGe.ngnifltaaGll 26
                                  TGe +  +++ +++l+
  gi|15669498|ref|NP_248308.1| 30 TGEfTLYLLFIFGALI 45
                                  7774555555555544 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4.4e-05
                                  XXXXXXXXXXXXXXXXXX...XXXXXXXX CS
               Gram_pos_anchor 17 nifltaaGllallggllL...lvkrRKke 42
                                   +++t++Gl+al+++l +    +k + ++
  gi|15669498|ref|NP_248308.1| 52 KTLMTLFGLAALAFSLSVsplIFKFKEEN 80
                                  5789************9988766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 730.37
//
Query:       gi|15669499|ref|NP_248309.1|  [L=481]
Description: hydrogenase subunit F [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-44  151.8  25.8    2.2e-44  151.8  25.8    1.9  2  Proton_antipo_M  Proton-conducting membrane transporter
    1.2e-10   41.1  17.4    1.2e-10   41.1  17.4    2.8  3  NADHdeh_related  NADH dehydrogenase I, subunit N related prot


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.6      0.25   2.2e+03      63      76 ..      76      95 ..      62     117 .. 0.41
   2 !  151.8  25.8   2.5e-48   2.2e-44       1     289 [.     119     404 ..     119     410 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.25
               Proton_antipo_M 63 lefeelskal......elgl 76
                                    + +ls+++       +g 
  gi|15669499|ref|NP_248309.1| 76 AIIVTLSLIAslvlitGMGE 95
                                  44444444433333322222 PP

  == domain 2  score: 151.8 bits;  conditional E-value: 2.5e-48
               Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslel 81 
                                   a+d++ ly+++E+v+++   L+ l +++ ++++A+l +++++ ++  ++Llgi+ l++ tgtl++++++ +  l ++++++
  gi|15669499|ref|NP_248309.1| 119 ADDIFNLYVFFEIVSIVQAGLVFLSGTE-EAYKAGLRYMIMGNVAAALMLLGIAFLLASTGTLNITDMKHY--LLVDNPMI 196
                                   7899********************9888.******************************************..9******* PP

               Proton_antipo_M  82 llllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla...vssneisqlllilaiisml 159
                                     +llll+vgl+  +++ p+h   +d y  +   +sa+l  t +k  + +l+ ++l l+    +   ++ +l++l++++m+
  gi|15669499|ref|NP_248309.1| 197 YGGLLLLIVGLAYGAGLPPFHNVKADLYARSKGFISAML-QTYSKFVLVGLMIIILKLFnglDYFASAHAVLIALGVLAMV 276
                                   ***************************************.999998888888776665556677788999*********** PP

               Proton_antipo_M 160 lgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrdirayggLak 240
                                   +g ++al q+d+K+llAy  is+ Gy+  +la++t  g+ a i+h + h++ k++lFl a   i ++++  ++ ++ggL  
  gi|15669499|ref|NP_248309.1| 277 FGVVMALLQSDYKKLLAYHAISQGGYVATGLALGTPLGIVAGIFHAINHVIYKSALFLGA--YIVSCKRGSNLHKLGGLLP 355
                                   ************************************************************..55689999*********** PP

               Proton_antipo_M 241 kmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavva 289
                                    mP +a ++l++ l+++G+Pp+ gF sk+++ +aa++v++  ++++++ 
  gi|15669499|ref|NP_248309.1| 356 LMPSVAFMVLCAKLAISGIPPFNGFQSKWMLAQAAMQVNMPEIAIIMII 404
                                   ***************************************9988888543 PP

>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.11   9.4e+02      26      44 ..      29      47 ..      19      54 .. 0.87
   2 !   41.1  17.4   1.4e-14   1.2e-10      38     217 ..      65     251 ..      33     253 .. 0.81
   3 ?   -2.1   1.5      0.23   2.1e+03     133     210 ..     330     405 ..     315     415 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.11
               NADHdeh_related 26 tlilfvvalifvilvilsk 44
                                  + i+f++a+i++il+ +s+
  gi|15669499|ref|NP_248309.1| 29 KYITFITAAILIILPFISQ 47
                                  67899999*****999987 PP

  == domain 2  score: 41.1 bits;  conditional E-value: 1.4e-14
               NADHdeh_related  38 ilvilskpekqveiefgkdaiklkvvsldelkirrllaiv...cglatlgav.vtgdvfnftlflaliGianiGivaavkk 114
                                    +++l +p kq  i++ +   +l  ++    k++  + +     g+a++ a+ ++ d+fn  +f  ++ i+  G+v     
  gi|15669499|ref|NP_248309.1|  65 GIAYLYNPAKQAIIVTLSLIASLVLITGMGEKLKNNMFVTlslMGFASIAAIvLADDIFNLYVFFEIVSIVQAGLVFLSGT 145
                                   577888888888888888888888888888888887777521257788776516889*******************99999 PP

               NADHdeh_related 115 efvleaafnyGlvaliatlplfggaalilastGtlsifelakl..agd.vlliaklllvlGvvGetGvaPfyaakaeifra 192
                                   e++ +a  +y ++  +a+  ++ g a +lastGtl i ++ +     + ++    lll++G++  +G+ Pf+ +ka+++ +
  gi|15669499|ref|NP_248309.1| 146 EEAYKAGLRYMIMGNVAAALMLLGIAFLLASTGTLNITDMKHYllVDNpMIYGGLLLLIVGLAYGAGLPPFHNVKADLYAR 226
                                   ****************999999999**************998754333356666788999***999************988 PP

               NADHdeh_related 193 pgapyillihlsslllivrvveill 217
                                   + +    ++   s +++v  + i+l
  gi|15669499|ref|NP_248309.1| 227 SKGFISAMLQTYSKFVLVGLMIIIL 251
                                   8887778888878777777776666 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.23
               NADHdeh_related 133 lplfggaalilastGtlsifelaklagdvlliaklllvlGvvGetGvaPfyaakaeifrapgapyillihlssllliv 210
                                     lf ga ++  + G   ++ l +l   ++ +a ++l + ++   G+ Pf   +++ + a+ a  + +  ++ +++iv
  gi|15669499|ref|NP_248309.1| 330 SALFLGAYIVSCKRGS-NLHKLGGLLPLMPSVAFMVLCAKLAIS-GIPPFNGFQSKWMLAQAAMQVNMPEIAIIMIIV 405
                                   5688888888888886.577777776656667666666666555.888887777777777777776666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1131  (0.0630822); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2960.69
//
Query:       gi|15669500|ref|NP_248310.1|  [L=128]
Description: putative monovalent cation/H+ antiporter subunit C [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-25   89.1   5.5    1.4e-25   88.9   5.5    1.1  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
    0.00019   21.3   3.8    0.00019   21.3   3.8    1.7  2  DUF2108      Predicted membrane protein (DUF2108)
     0.0081   16.2   4.6     0.0098   15.9   4.6    1.2  1  DUF5317      Family of unknown function (DUF5317)


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   5.5   2.4e-29   1.4e-25       3     101 ..      18     122 ..      16     127 .. 0.94

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 2.4e-29
                                   HHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC....................TTSCGGHHHHHHHHH CS
                   Oxidored_q2   3 llliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvi.......tnpatefadplpqalvLtaivi 76 
                                   +++++ll++iGlygv++ +n+lk++i+le+++++vnl+l+++g++  gt++i       +++a+e+a+pl +alvLt ivi
  gi|15669500|ref|NP_248310.1|  18 FITSGLLVIIGLYGVFFVDNVLKKIIALEILGSGVNLALIAIGYNG-GTIPIklpgvsvEVFAKESAYPLTHALVLTNIVI 97 
                                   689*****************************************86.777777**************************** PP

                                   HHHHHHHHHHHHHHHHHHSSS-BCC CS
                   Oxidored_q2  77 gaaetavgLallvrlyreygtddvq 101
                                    a+++av+L++ + ly++y+t++ +
  gi|15669500|ref|NP_248310.1|  98 EASMLAVMLGVSIILYKKYKTLRSS 122
                                   *********************9876 PP

>> DUF2108  Predicted membrane protein (DUF2108)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   3.8   3.2e-08   0.00019       4      46 ..      19      61 ..      16      63 .. 0.95
   2 ?   -1.7   0.1       0.5     3e+03      10      17 ..     103     110 ..      92     116 .. 0.47

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.2e-08
                       DUF2108  4 lvalalaliGaigvillkkpldKlimlalleaGlillivakgY 46
                                  +++++l++iG  gv ++ + l+K+i+l +l +G+ l+++a gY
  gi|15669500|ref|NP_248310.1| 19 ITSGLLVIIGLYGVFFVDNVLKKIIALEILGSGVNLALIAIGY 61
                                  78999************************************99 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.5
                       DUF2108  10 aliGaigv 17 
                                   a++ ++++
  gi|15669500|ref|NP_248310.1| 103 AVMLGVSI 110
                                   22222222 PP

>> DUF5317  Family of unknown function (DUF5317)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   4.6   1.6e-06    0.0098      22     122 ..       6     110 ..       1     123 [. 0.62

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-06
                       DUF5317  22 vltvelleflkklsallsilsylllllflllnrklk.glllialGvllN..flvialNggkMPvsleale.kagle.llel 97 
                                   +l v++++f +       +l+++ l  ++++ + lk  + l +lG+ +N  +++i  Ngg +P++l  ++ ++  + ++  
  gi|15669500|ref|NP_248310.1|   6 YL-VNRMDFQMASFITSGLLVIIGLYGVFFVDNVLKkIIALEILGSGVNlaLIAIGYNGGTIPIKLPGVSvEVFAKeSAYP 85 
                                   33.367777777777777778888877777777776444455555555511678889********9998843333334444 PP

                       DUF5317  98 lkegksgkhtlltestklkfLgDii 122
                                   l++  + + +++++s   ++Lg  i
  gi|15669500|ref|NP_248310.1|  86 LTHALVLTNIVIEASMLAVMLGVSI 110
                                   4444666667776666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 859.12
//
Query:       gi|15669501|ref|NP_248311.1|  [L=293]
Description: hypothetical protein MJ_1311 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-34  118.4   0.2    7.2e-34  117.1   0.1    1.6  2  AP_endonuc_2    Xylose isomerase-like TIM barrel
    0.00084   18.3   0.1     0.0013   17.7   0.1    1.2  1  UxuA            D-mannonate dehydratase (UxuA)
     0.0015   18.2   0.0     0.0034   17.1   0.0    1.6  1  AP_endonuc_2_N  AP endonuclease family 2 C terminus
     0.0075   16.2   0.0       0.02   14.8   0.0    1.9  1  HIRAN           HIRAN domain
  ------ inclusion threshold ------
      0.043   13.1   0.0        8.9    5.5   0.0    2.6  2  Amidohydro_1    Amidohydrolase family
       0.18   11.8   2.5         12    6.0   0.1    3.6  4  DUF4250         Domain of unknown function (DUF4250)


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1   0.1   2.4e-37   7.2e-34       2     210 .]      36     239 ..      35     239 .. 0.93
   2 ?   -1.1   0.0      0.36   1.1e+03       1      12 [.     245     256 ..     240     283 .. 0.63

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 2.4e-37
                                   HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHHHHHH CS
                  AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraielaaa 81 
                                   +++ae+ fd+ E+ + + +  s   +++++ l ++ d++ ++i+++ +f++ +    +   +r r+  v+++++aie a +
  gi|15669501|ref|NP_248311.1|  36 EKIAEHNFDAWEIVCEGTHYLS---PKNIKYLMELRDRYEVEIVVHAPFSDLNPASMN---ERvRKLTVECIRDAIEGAFE 110
                                   679******************9...57***************************9985...445889************** PP

                                   HTBSEEEEEBCCGBCTTTSGHH....HHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTTTE CS
                  AP_endonuc_2  82 LGapllvlhpGtagagpkgsee....eawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavdspnv 156
                                   L+ +++v+hpG    + ++ +     e +++  + l e++++ae++g+k++lE+++++   lg   e l+++++++ds+n+
  gi|15669501|ref|NP_248311.1| 111 LDSEVVVVHPG----YIPELWSnyvsEILDNNFSTLSEIVEIAEDYGIKIGLENMPNFRGVLGItpESLLEIVKDIDSKNL 187
                                   ***********....44444444456**********************************9999***************** PP

                                   EEEEEHHHHHHHTTTHHHHHHHHHGG...EEEEEE.EESSTTTTSSTTEESTTSSSS CS
                  AP_endonuc_2 157 gvclDtgHlliaeedvddalraladr...ikhvHikDakgdlgagrdrhvpigeGei 210
                                   g+++D+gH++ a +++++++++l +    i hvH++D++g     +d+h+ igeG+i
  gi|15669501|ref|NP_248311.1| 188 GITFDIGHANTA-GNPAEFVEKLQNIgigIIHVHAHDNNG----YDDEHLKIGEGNI 239
                                   ************.***************************....***********87 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.36
                                   HHHHHHCT-SEE CS
                  AP_endonuc_2   1 laaaaeaGfdgv 12 
                                   l++++e+G+dgv
  gi|15669501|ref|NP_248311.1| 245 LEKLKEIGYDGV 256
                                   345566666665 PP

>> UxuA  D-mannonate dehydratase (UxuA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   4.3e-07    0.0013     182     314 ..     136     260 ..     126     276 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.3e-07
                                   HHHHHHHHHHHHHHHHHT-EEEE---SSSS-BTTB--SSSSHHHHHHHHHH--STTEEEEEEHHHHTTST.T--HHHHHHH CS
                          UxuA 182 enlayFlkeiiPvaeevgvklaihPDDPPlpifGlpRivstkedlqrlldlvdspangitlCtGslgara.dndlvemike 261
                                   +n    l+ei+ +ae++g+k+ +    P   ++G+  i  t e+l  +++  ds++ git+  G   +     + ve +++
  gi|15669501|ref|NP_248311.1| 136 DNNFSTLSEIVEIAEDYGIKIGLENM-PN--FRGVLGI--TPESLLEIVKDIDSKNLGITFDIGHANTAGnPAEFVEKLQN 211
                                   44444699*************99754.33..4454444..679999*****************986544303456666666 PP

                                   HGGGEEEEE--EEEE-SSTT-EEEE-TTSSSS-HHHHHHHHHHHHHHH-EE-- CS
                          UxuA 262 fadriyFahlRnikreedeksFveaahleGsvdlaevvkalleeeyrrylRpD 314
                                    +  i  +h  + + ++de      ++ eG+++++ev++ l e++y++++ ++
  gi|15669501|ref|NP_248311.1| 212 IGIGIIHVHAHDNNGYDDE----HLKIGEGNINFIEVLEKLKEIGYDGVISIE 260
                                   6667777888887777644....457888******************988765 PP

>> AP_endonuc_2_N  AP endonuclease family 2 C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.1e-06    0.0034       2      22 ..     241     261 ..     240     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                AP_endonuc_2_N   2 wkdifsaLrqiGYdgplSiEw 22 
                                   + +++ +L++iGYdg++SiE 
  gi|15669501|ref|NP_248311.1| 241 FIEVLEKLKEIGYDGVISIEN 261
                                   778999**************5 PP

>> HIRAN  HIRAN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   6.6e-06      0.02      52      83 ..     121     152 ..      38     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.6e-06
                                   EEE-HHHHHHHHHHHHTTSSEEEEEESS-TTT CS
                         HIRAN  52 GrlprevakwlspLldsgfitfegvvvdapek 83 
                                   G++p+ +++ +s++ld++f t++++v  a++ 
  gi|15669501|ref|NP_248311.1| 121 GYIPELWSNYVSEILDNNFSTLSEIVEIAEDY 152
                                   **************************999875 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.003       8.9     130     199 ..      57     124 ..      51     155 .. 0.79
   2 ?    4.1   0.1    0.0081        24     126     191 ..     167     251 ..     155     278 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.003
                                   HHHHHHHHHHHHHHHTTEEEEEE....TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE CS
                  Amidohydro_1 130 sdeelkealkeakkrdlpvaiHa....letkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt 199
                                   s+  +k ++++ +++ + +++Ha    l+    +e +++  +   e+  + +  e++  ld+  ++++h  ++ 
  gi|15669501|ref|NP_248311.1|  57 SPKNIKYLMELRDRYEVEIVVHApfsdLNPASMNERVRKLTV---EC--IRDAIEGAFELDS-EVVVVHPGYIP 124
                                   7889999******************99999999999999999...99..9999999999999.66666655544 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0081
                                   TCCSHHHHHHHHHHHHHHHTTEEEE...EE..TSSCHHHHHHHHHHTTTEEEETTTTSTCC..............HHTTTH CS
                  Amidohydro_1 126 apafsdeelkealkeakkrdlpvai...Ha..letkgevedaeaafgetiehgthlevaes..............lgllde 187
                                     ++++e l e++k  + ++l +++   Ha  +++++e  + ++ +g +i+h +  ++ +               + +l++
  gi|15669501|ref|NP_248311.1| 167 VLGITPESLLEIVKDIDSKNLGITFdigHAntAGNPAEFVEKLQNIGIGIIHVHAHDNNGYddehlkigegninfIEVLEK 247
                                   556677777777777777766666422244663333333344444444555544333322233333333333333333333 PP

                                   CCEE CS
                  Amidohydro_1 188 ikli 191
                                   +k i
  gi|15669501|ref|NP_248311.1| 248 LKEI 251
                                   4444 PP

>> DUF4250  Domain of unknown function (DUF4250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.72   2.2e+03      14      21 ..      65      72 ..      65      73 .. 0.88
   2 ?   -1.7   0.0         1     3e+03      34      45 ..     202     213 ..     199     214 .. 0.86
   3 ?    3.0   0.0     0.032        96      32      47 ..     239     254 ..     234     254 .. 0.83
   4 ?    6.0   0.1    0.0039        12       9      40 ..     257     288 ..     256     291 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.72
                       DUF4250 14 tkLRDeys 21
                                  ++LRD y+
  gi|15669501|ref|NP_248311.1| 65 MELRDRYE 72
                                  89***996 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                       DUF4250  34 keeleekLasig 45 
                                    +e +ekL++ig
  gi|15669501|ref|NP_248311.1| 202 PAEFVEKLQNIG 213
                                   57999****998 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.032
                       DUF4250  32 idkeeleekLasigYe 47 
                                   i+  e+ ekL++igY+
  gi|15669501|ref|NP_248311.1| 239 INFIEVLEKLKEIGYD 254
                                   5666899********5 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0039
                       DUF4250   9 lSivNtkLRDeyssldelcedldidkeeleek 40 
                                   +Si N ++RD  +s + l e+l+i +e++ ek
  gi|15669501|ref|NP_248311.1| 257 ISIENKNIRDAVKSKEILKEYLEIVNEKVAEK 288
                                   6888********************99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2029.51
//
Query:       gi|15669502|ref|NP_248312.1|  [L=321]
Description: hypothetical protein MJ_1312 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.9e-16   59.1   0.7      1e-15   58.5   0.2    1.5  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.2   5.6e-20     1e-15       3     167 .]      23     192 ..      21     192 .. 0.85
   2 ?   -2.6   0.0      0.35   6.3e+03      78      98 ..     258     277 ..     216     287 .. 0.63

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 5.6e-20
                                   EESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHH..HHTT.SEEEEEE.SSTGGGSTTHHHHHHHHHHTCCCTE CS
                                   xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx..xxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpet.vrregrgrslsveeileevkelk..aekg.vkevilg.ggepllypdfvellerlaklavpgi 78 
                                   + ++C+++C++C++++t  ++ +r ++ s+e+i + v+e     ++  +++++++  gep+l+ ++ +++e+l+     +i
  gi|15669502|ref|NP_248312.1|  23 PCKFCSYDCVYCQVGRTiNKTIERREFYSPEDIFKSVEERIgkLNNEkIDYLTFVaDGEPTLDINLSKEVEMLRDF---DI 100
                                   6689**************889999999999999998865544334444999999889******************8...** PP

                                   EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH...HHHHHHHHHHHHTTSET..EEEEEEEBTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                   Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtf...eevlealeklreagikr..vvdrivglpG 154
                                    i+++tn  l+  +   r + l++d vs+ ++++d++ + + +nr+h     +++le++ ++r++   +  + ++i+g   
  gi|15669502|ref|NP_248312.1| 101 PIAIITNSSLIW-REDVRNDILNFDLVSFKVDSVDEK-IWREINRPHKDlvlDKILEGMIAFRDNYKGEliTETMILGSIK 179
                                   ***********5.43334444459*************.77777755554566*************8888************ PP

                                   TSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxx RF
                   Radical_SAM 155 endeeleellell 167
                                   +++e + +++e+l
  gi|15669502|ref|NP_248312.1| 180 YTEESIIKTAEFL 192
                                   **********996 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.35
                                   EEEEEEECSSCHGHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  78 iritvetngtlpdeeklerll 98 
                                     +++++ +++ +ee++++ll
  gi|15669502|ref|NP_248312.1| 258 DILAITSVHPM-REEVIKELL 277
                                   33344444444.377777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2254.49
//
Query:       gi|15669503|ref|NP_248313.1|  [L=403]
Description: hypothetical protein MJ_1313 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.6e-165  548.9   0.0   6.3e-165  548.8   0.0    1.0  1  DUF521    Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.8   0.0  3.5e-169  6.3e-165       1     400 [.       1     400 [.       1     401 [. 0.98

  Alignments for each domain:
  == domain 1  score: 548.8 bits;  conditional E-value: 3.5e-169
                        DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvpttlnpi 81 
                                   m+Ltkeee++l+Ge+Ge+l+ +m++lv+lG+i+gA++L+p++sa++sgvsykti+d glefle++a++++kv+v++tlnp+
  gi|15669503|ref|NP_248313.1|   1 MYLTKEEEKILDGEYGEVLRRCMNLLVSLGDIYGADKLIPISSAQISGVSYKTIKDIGLEFLEDFAKEDVKVKVYATLNPA 81 
                                   9******************************************************************************** PP

                        DUF521  82 gvdlerweelgvdeefaekqeriieayeklGveltftCtpyllgnapkkGehlawsESsavvyaNSvlGarTnreggpsal 162
                                   g+dl+ w+elg+de+fa+kq riiea++k+ ve+++tCtpyl+gn p++Geh++w+ESsav++aNSvlGa+Tnreggpsal
  gi|15669503|ref|NP_248313.1|  82 GMDLDIWRELGIDEKFAKKQLRIIEAFKKMEVEISCTCTPYLTGNLPRFGEHISWAESSAVSFANSVLGAKTNREGGPSAL 162
                                   ********************************************************************************* PP

                        DUF521 163 aaAitGrtpeyGlhldenRkptvlveveae.....sedeadygalGylvGkkvgeriPvlkglekp..sedelKalgAala 236
                                   aaAi+G+tp+yG+hldenRk t+++e++ +     +  e++ygalGylvGk+v+++iP++++l k   ++d+lK+lgAa+a
  gi|15669503|ref|NP_248313.1| 163 AAAIIGKTPYYGYHLDENRKTTHIIELDGQlisnfKYGESFYGALGYLVGKIVKNGIPYFENLYKLnpNNDNLKSLGAAMA 243
                                   **************************9999999999999**********************9999989************* PP

                        DUF521 237 asgavalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlvalGcPhlsleElrelaellkgkk 317
                                   asg++al+h +++T e  +++e +  ++k eki+i  e+++e++e+l ++++e++dl+++GcPh+sl E++++aell  k+
  gi|15669503|ref|NP_248313.1| 244 ASGGIALYHAKNLTAE-CRVKEVV--NDKIEKISIGVEEIKEAYEKL-NTTNEEPDLICIGCPHCSLMEIKKIAELL--KN 318
                                   ****************.6777766..5789*****************.888999***********************..99 PP

                        DUF521 318 kkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYlpgltgvkvalgslee 398
                                   kk + +lwv++s ++k+ a+r+g+++++ekaG+kv++dtCmvvsp+++   +k+vatnSgKaa Ylp+ ++ +v++g++ee
  gi|15669503|ref|NP_248313.1| 319 KKLNADLWVCCSLHIKAIADRMGYTKIIEKAGGKVVKDTCMVVSPIEDLG-YKRVATNSGKAAVYLPSFCKSEVIFGDIEE 398
                                   999********************************************985.*****************************9 PP

                        DUF521 399 cv 400
                                   ++
  gi|15669503|ref|NP_248313.1| 399 LL 400
                                   87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2667.14
//
Query:       gi|15669504|ref|NP_248314.1|  [L=307]
Description: cobalamin biosynthesis protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.2e-85  285.3   0.0    4.8e-85  285.1   0.0    1.1  1  CobD_Cbib   CobD/Cbib protein
  ------ inclusion threshold ------
       0.16   11.7   0.0       0.25   11.0   0.0    1.2  1  Herpes_UL7  Herpesvirus UL7 like


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.1   0.0   5.3e-89   4.8e-85       1     260 [.       7     282 ..       7     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 285.1 bits;  conditional E-value: 5.3e-89
                     CobD_Cbib   1 lllAlllDlllgdprrllhPvvligklisalekrlrk.....akkerlaGvllalllvllallvalllllla.laall..g 73 
                                   l+lA+++D+++g+ ++ +hP v+igkli++le+++++     + ++ l G l++++++l+++++a+++  ++ l + +   
  gi|15669504|ref|NP_248314.1|   7 LFLAIIFDRIIGELPESIHPTVWIGKLIAFLENIFKStncknKYRDFLFGSLTTFITLLVVGVIAFFVDKCImLLP-FplN 86 
                                   689******************************9952244455667779999999999999999999998765222.1357 PP

                     CobD_Cbib  74 lvlealllkltlalrsLleevrkvakal.kgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPlfyfll 153
                                   +++ ++ll++t++++sL e ++k  + + +gdle aR+av++iV+Rd s+ld+e++++AavEs++EN++D+++++lfy+++
  gi|15669504|ref|NP_248314.1|  87 YIIYGFLLSTTIGYKSLFEFCKKPIEYIkNGDLEGARKAVQHIVSRDASKLDKEHVLSAAVESLSENITDSIIGALFYAIF 167
                                   89*********************99999559************************************************** PP

                     CobD_Cbib 154 lglpgalaykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllala.........aalriarrdarkhpSpN 225
                                   +glpga++y+a+nTlD+m+GYkne+y ++G+ aArlDD++n+iP+R++++ll+++         +a+  ++++a+k pSpN
  gi|15669504|ref|NP_248314.1| 168 FGLPGAFVYRAINTLDAMIGYKNEKYLWYGKLAARLDDIANFIPSRIAGILLIITapfykgdvkKAIYGFLKEANKVPSPN 248
                                   ***************************************************9995566666666779999*********** PP

                     CobD_Cbib 226 sgwpeaalAgalgvrLggpnvY.lgkleekptlgdk 260
                                   sg+++a+lA al+++L++ ++Y lg  + k +++++
  gi|15669504|ref|NP_248314.1| 249 SGYTMATLANALNITLEKIGYYkLG--SGKIDVEKS 282
                                   **********************877..444444444 PP

>> Herpes_UL7  Herpesvirus UL7 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.8e-05      0.25     105     177 ..      31     106 ..      22     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.8e-05
                    Herpes_UL7 105 vkllarlrlvkskipvlekvrrlLlngietLlnTlmelldleekdseivl....pahyklykelestelelkdllks 177
                                    kl+a+l+ +++ +++ +k r +L+ + +t +  l+  + +  + ++ +     p  y +y  l st +  k l+++
  gi|15669504|ref|NP_248314.1|  31 GKLIAFLENIFKSTNCKNKYRDFLFGSLTTFITLLVVGV-IAFFVDKCIMllpfPLNYIIYGFLLSTTIGYKSLFEF 106
                                   589***************************997766655.66666665555755599*****999999999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2024.47
//
Query:       gi|15669505|ref|NP_248315.1|  [L=361]
Description: hypothetical protein MJ_1315 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-42  145.9   0.0    1.5e-42  145.5   0.0    1.1  1  CLP1_P      mRNA cleavage and polyadenylation factor CLP1 P-l
    0.00038   20.5   0.1    0.00062   19.8   0.1    1.5  1  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
      0.002   18.1   0.2     0.0045   16.9   0.2    1.6  1  AAA_31      AAA domain
     0.0021   17.5   0.0     0.0044   16.5   0.0    1.6  1  ParA        NUBPL iron-transfer P-loop NTPase
     0.0031   17.2   0.5       0.36   10.4   0.1    2.2  2  SRP54       SRP54-type protein, GTPase domain
      0.004   16.5   0.1      0.013   14.8   0.1    1.8  1  MipZ        ATPase MipZ
  ------ inclusion threshold ------
      0.023   14.4   0.0      0.053   13.3   0.0    1.6  1  PduV-EutP   Ethanolamine utilisation - propanediol utilisatio
      0.026   14.4   0.0      0.053   13.4   0.0    1.5  1  MobB        Molybdopterin guanine dinucleotide synthesis prot
      0.038   14.1   0.2       0.35   11.0   0.2    2.2  1  MMR_HSR1    50S ribosome-binding GTPase
      0.044   13.8   0.1       0.43   10.6   0.0    2.2  2  Dynamin_N   Dynamin family
      0.082   12.8   0.0       0.15   11.9   0.0    1.4  1  APS_kinase  Adenylylsulphate kinase
      0.085   12.1   0.0       0.17   11.1   0.0    1.4  1  Zeta_toxin  Zeta toxin
       0.11   13.0   0.0       0.21   12.0   0.0    1.5  1  AAA         ATPase family associated with various cellular ac
       0.13   11.9   0.0       0.29   10.8   0.0    1.6  2  CoaE        Dephospho-CoA kinase
       0.15   12.2   0.0       0.28   11.3   0.0    1.4  1  Torsin      Torsin


Domain annotation for each model (and alignments):
>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5   0.0   1.3e-45   1.5e-42       1     187 [.      39     214 ..      39     215 .. 0.94

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 1.3e-45
                        CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpidveegfsldaplvyffGdtspsdnpslyl 81 
                                   G++dsGK+Tla++L+N++l+ g k+++vD DvGq++i pP+tisla+ e+++++ +++++ +  +yf+G+t+p +   +++
  gi|15669505|ref|NP_248315.1|  39 GGVDSGKTTLATFLANELLNLGFKVAIVDSDVGQKSILPPATISLAFPETNFNNLYEIKPYK--SYFVGSTAPIQFFGEMI 117
                                   899***************************************************99998887..79*******88777777 PP

                        CLP1_P  82 alvkelareveekleenkkakasgliIntpGwvkglgaellleliealepdvvvvldqeellnelkrdlplskvkvvklpk 162
                                     +k l + +e         ka+++i++t+G+++g ga+l+  +ie+++pd++++l+++++l+++ + ++ +k++v+ l++
  gi|15669505|ref|NP_248315.1| 118 TGTKLLCDYAE--------DKADIIIVDTTGLISGSGADLKRMKIEMIKPDIIIALEKRNELKSILKPFE-NKIRVFYLKV 189
                                   77777777666........58*************************************999999999999.********** PP

                        CLP1_P 163 spgvvqrsreerrelreerireYFy 187
                                    + +++ sreer+e+r e+++eYF+
  gi|15669505|ref|NP_248315.1| 190 YENAKSFSREERKEIRAEKWKEYFK 214
                                   ************************8 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   5.2e-07   0.00062       9      40 ..      42      73 ..      35     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.2e-07
                                  TSSHHHHHHHHHHHHHHTT--EEEEEEEESSC CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  9 GvGKTtlaanLaralarrglrVllvDaDpqan 40
                                  ++GKTtla+ La  l + g++V+ vD D+  +
  gi|15669505|ref|NP_248315.1| 42 DSGKTTLATFLANELLNLGFKVAIVDSDVGQK 73
                                  68**************************9854 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   3.7e-06    0.0045      11      63 ..      39     116 ..      35     183 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.7e-06
                        AAA_31  11 GGv..GKTTtsvnlaaalaklgkkvLlvDlDp.Qan....attglgiekneiektlyev...................l 63 
                                   GGv  GKTT ++ la  l +lg kv +vD D  Q++    at++l + +++  ++lye+                   +
  gi|15669505|ref|NP_248315.1|  39 GGVdsGKTTLATFLANELLNLGFKVAIVDSDVgQKSilppATISLAFPETNF-NNLYEIkpyksyfvgstapiqffgeM 116
                                   676669*************************725442222344444444443.45555555555555555555544441 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.7e-06    0.0044      13      47 ..      39      75 ..      36     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.7e-06
                          ParA 13 GGV..GKStvavnlAlaLakkglkvgllDaDiyGpsi 47
                                  GGV  GK+t+a+ lA +L + g+kv+++D D+   si
  gi|15669505|ref|NP_248315.1| 39 GGVdsGKTTLATFLANELLNLGFKVAIVDSDVGQKSI 75
                                  77777**************************987776 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1    0.0003      0.36       4      39 ..      35      70 ..      32      73 .. 0.87
   2 ?    4.9   0.0     0.015        18      80      97 ..     127     144 ..     118     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                  i+l+G   +GKTt ++ La+ l + g kv++v  D+
  gi|15669505|ref|NP_248315.1| 35 IILLGGVDSGKTTLATFLANELLNLGFKVAIVDSDV 70
                                  667777779**********************99885 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.015
                                   HHTTSSEEEEEE--SSTT CS
                         SRP54  80 keekidvvlvDTaGrlqn 97 
                                    e+k+d+++vDT+G    
  gi|15669505|ref|NP_248315.1| 127 AEDKADIIIVDTTGLISG 144
                                   56789*********8765 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.1e-05     0.013      12      47 ..      43      78 ..      35     159 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                  SSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHH CS
                          MipZ 12 sGksttavhvavaLlkkGarvaaidldlrqrtlary 47
                                  sGk+t a  +a  Ll+ G++va +d d+ q+++   
  gi|15669505|ref|NP_248315.1| 43 SGKTTLATFLANELLNLGFKVAIVDSDVGQKSILPP 78
                                  8******************************98654 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.4e-05     0.053       3      26 ..      34      57 ..      32      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-05
                     PduV-EutP  3 killiGkvgsGKttLtqalkgeel 26
                                  ki+l+G v+sGKttL+  l +e l
  gi|15669505|ref|NP_248315.1| 34 KIILLGGVDSGKTTLATFLANELL 57
                                  8****************9999876 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.4e-05     0.053       3      39 ..      36      72 ..      34      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-05
                          MobB  3 givgksgsGKTtLleklipelkarglrvgtiKhahhg 39
                                   + g  +sGKTtL + l +el + g++v+++  ++ +
  gi|15669505|ref|NP_248315.1| 36 ILLGGVDSGKTTLATFLANELLNLGFKVAIVDSDVGQ 72
                                  5678889***********************9877665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00029      0.35       2      84 ..      35     167 ..      34     209 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                                   EEEEESTTSSHHHHHHHHHT.......STEEE.SSSTTSSSSE.EEEEEEETTEE.......................... CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg.......ekaiv.sdkpgtTrdi.negrvklkgke.......................... 47 
                                   ++++G   +GK+tL   l +       ++aiv sd  ++ + +  ++ +++ +++                          
  gi|15669505|ref|NP_248315.1|  35 IILLGGVDSGKTTLATFLANellnlgfKVAIVdSDVGQKSILPpATISLAFPETNfnnlyeikpyksyfvgstapiqffge 115
                                   788899999999988888875555555345554444444444423333331111123344455555666666666666666 PP

                                   .................EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEE CS
                      MMR_HSR1  48 .................ielvDtpGliegaseekglgkaflaleeadlillvvd 84 
                                                    i++vDt Gli+   ++ +l++   ++++ d+i+ + +
  gi|15669505|ref|NP_248315.1| 116 mitgtkllcdyaedkadIIIVDTTGLIS--GSGADLKRMKIEMIKPDIIIALEK 167
                                   66666666666666666********997..334455666666666677766665 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.47   5.6e+02       1      18 [.      35      52 ..      35      60 .. 0.83
   2 ?   10.6   0.0   0.00036      0.43      64     139 ..      95     169 ..      81     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.47
                                  EEEEEBTTTTHHHHHHHH CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaL 18
                                  i+++G + sGK++++  L
  gi|15669505|ref|NP_248315.1| 35 IILLGGVDSGKTTLATFL 52
                                  7899*********98655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00036
                                   -CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETT CS
                     Dynamin_N  64 dfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikkadiilavtsan 139
                                   +++ ++ ++  +t+ i+  ++ i +   ll++++ ++ ++ +vD+ Gl+s    d + +k  + k dii+a+ + n
  gi|15669505|ref|NP_248315.1|  95 EIKPYKSYFVGSTAPIQFFGEMI-TGTKLLCDYAEDKADIIIVDTTGLISGSGADLKRMKIEMIKPDIIIALEKRN 169
                                   55555556666666666333333.55678999******************99999977777777889999998776 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.15       4      40 ..      34      70 ..      31      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                  EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                    APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                   + l G   sGK+t+a+ l+++L + g +v ++d d+
  gi|15669505|ref|NP_248315.1| 34 KIILLGGVDSGKTTLATFLANELLNLGFKVAIVDSDV 70
                                  567778889************************9986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.17       8      41 ..      23      57 ..      17      75 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                    Zeta_toxin  8 kk.ypsqerPklillgGqpGAGKselaellkdele 41
                                   + ++++++P  i+l G+  +GK++la+ l++el 
  gi|15669505|ref|NP_248315.1| 23 LScIKDSQKPLKIILLGGVDSGKTTLATFLANELL 57
                                  4434477***********************99986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017      0.21       2      73 ..      36     145 ..      35     175 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                   EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS......................................STTH CS
                           AAA   2 llyGppGtGKTllakavakel...gvefleisgsellsk......................................yvge 41 
                                   +l G    GKT+la  +a+el   g++ + i  s++ +k                                      ++ge
  gi|15669505|ref|NP_248315.1|  36 ILLGGVDSGKTTLATFLANELlnlGFK-VAIVDSDVGQKsilppatislafpetnfnnlyeikpyksyfvgstapiqFFGE 115
                                   78899999************7544232.23333333333444455555555555555566678888888888888888999 PP

                                   HHHHHHHHHHHHHHTSTSEEEEEETGGGHHHH CS
                           AAA  42 sekkirelfkeakekakpsilfiDEidalaks 73 
                                   +   ++ l + a+ ka   i+++D    + +s
  gi|15669505|ref|NP_248315.1| 116 MITGTKLLCDYAEDKA--DIIIVDTTGLISGS 145
                                   9999999999888887..88888866666555 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00024      0.29       3      44 ..      35      82 ..      33      93 .. 0.75
   2 ?   -4.1   0.0       8.9   1.1e+04      77      89 ..     166     178 ..     152     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                                  EEEEESTTSSHHHHHHHHHH......TT-EEEEHHHHHHHTTCCTHHH CS
                          CoaE  3 vgltGgiasGKstvanlfad......lgvpivDaDlvArqvvepgsea 44
                                  + l Gg+ sGK+t+a  +a+      ++v ivD D+  +++  p +  
  gi|15669505|ref|NP_248315.1| 35 IILLGGVDSGKTTLATFLANellnlgFKVAIVDSDVGQKSILPPATIS 82
                                  5588*********998877543222457899****9888887776655 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 8.9
                                   HHHHHHHHHHHHH CS
                          CoaE  77 eekkaLnallhPl 89 
                                   e+++ L ++l P+
  gi|15669505|ref|NP_248315.1| 166 EKRNELKSILKPF 178
                                   5666666666664 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00023      0.28      48      94 ..      27      73 ..      20      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                                  SS-SS-EEEEEEE-TTSSHHHHHHHHHHHHSTTGGGSTTEEEEEHHH CS
                        Torsin 48 ekpkkpLvlsfhGwtGtGknfvaeiiaenlyrdGlrsdyvkkfvata 94
                                  ++++kpL + + G   +Gk  +a  +a++l + G +  +v   v+++
  gi|15669505|ref|NP_248315.1| 27 KDSQKPLKIILLGGVDSGKTTLATFLANELLNLGFKVAIVDSDVGQK 73
                                  5799********************************99998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2355.63
//
Query:       gi|15669506|ref|NP_248316.1|  [L=80]
Description: hypothetical protein MJ_1316 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-13   48.7   0.2    1.1e-12   48.5   0.2    1.0  1  MJ1316    MJ1316 RNA cyclic group end recognition domain


Domain annotation for each model (and alignments):
>> MJ1316  MJ1316 RNA cyclic group end recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.2     6e-17   1.1e-12       4      76 .]       6      79 ..       4      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 6e-17
                        MJ1316  4 aqdvlnRirWdkeldkskfvvgyldR..fkgikevpleeiswiedflleeeegelaIPlHRiryikrk..gevvWdR 76
                                   +++ln+i+W +++++++f+v +l+R  +++ k ++l+++   +++l+  ++   +IPlHRi +i++k  ge+++++
  gi|15669506|ref|NP_248316.1|  6 LKEILNKIFWHPDYKREDFEVVILHRgaEENKKAISLDDVELKGNYLIYFDT---YIPLHRILEIRNKktGEILYKK 79
                                  589************************9999999********9997777766...7**********96468888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 603.60
//
Query:       gi|15669507|ref|NP_248317.1|  [L=398]
Description: hypothetical protein MJ_1317 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-37  128.1  34.5    1.5e-20   73.4  11.7    2.0  2  MFS_1         Major Facilitator Superfamily
    3.5e-08   32.7  23.9      9e-07   28.1  23.9    2.1  1  MFS_1_like    MFS_1 like family
  ------ inclusion threshold ------
       0.42    9.6  14.1       0.23   10.4   4.6    3.3  3  PUCC          PUCC protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4  11.7   2.5e-24   1.5e-20       2     230 ..      28     243 ..      27     264 .. 0.79
   2 !   55.9  21.6   5.6e-19   3.3e-15      13     172 ..     235     397 ..     225     398 .] 0.81

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 2.5e-24
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg.lllll 80 
                                    ++ fl+ +++ +++p+lp +l ++ g    +igl+ +l  + + ++++++G+ sd++  r+ +++lg+l+++ + lll+l
  gi|15669507|ref|NP_248317.1|  28 GFTSFLNDMSSEMIMPILP-MLITSVGGGSLSIGLVGGLREFISNILMVLIGYCSDKVRKRKiFVVLGYLTSSMFkLLLGL 107
                                   6899***************.899999********************************99998999999999999555555 PP

                         MFS_1  81 fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgg..llasslgWravfyila 158
                                     s +w   +++  l  +g g+ ++   a+i++  pk   g+++g+  a+  +Gailg  l+   +l+ ++++  + +i+a
  gi|15669507|ref|NP_248317.1| 108 --SKSWlGAVIFSSLERMGKGIRTAPRDAIISESMPK-TLGKGFGIQRAFDTAGAILGSTLSLlfILYLQYSFNQIILIAA 185
                                   ..999989*****************************.*************************544447777********* PP

                         MFS_1 159 ivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltll 230
                                   ++++l ++   l+++ e+p++++++ + +         v ++k l k   l+  ++++++f++ ++++++++
  gi|15669507|ref|NP_248317.1| 186 VIGFLTLI--PLYFVKEKPSPSNNKITFR---------V-GIKNLPKELKLF--ILISAIFTLSNFSYMFYI 243
                                   ******66..4555444444444444333.........1.244444444442..222222223444444443 PP

  == domain 2  score: 55.9 bits;  conditional E-value: 5.6e-19
                         MFS_1  13 silgpalplalaedlgispseigl......lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslw 86 
                                   s+++ ++ ++ a+++ + ++e         l+ ly +++a +s+p+G lsd++Gr++vl +g++++++ +l ++ f +s  
  gi|15669507|ref|NP_248317.1| 235 SNFSYMFYILRAQEFLMIVDEKMAiiipiaLYILYNIFYATFSIPFGILSDKIGRKSVLTIGYIVYGIVSLGFAyF-ISQK 314
                                   444444444445555544444222234555778899*********************************7777767.4444 PP

                         MFS_1  87 lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvl 167
                                    l++l +l G+++++++ +  a+++d+++++ r+ a+gl+++ ++l ++ + l++g+l   ++ + +f+   ++++++++l
  gi|15669507|ref|NP_248317.1| 315 SLILLFALYGIAYALFAGNQKAYVSDLSSEDIRATALGLFYTVVGLTSLPASLIAGYLW-KISPEMTFLYGSVLAIISGLL 394
                                   7**********************************************************.999***************997 PP

                         MFS_1 168 fllll 172
                                     ll+
  gi|15669507|ref|NP_248317.1| 395 --LLF 397
                                   ..443 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1  23.9   1.5e-10     9e-07      18     383 ..      41     381 ..      32     383 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.5e-10
                    MFS_1_like  18 llPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeeskle 98 
                                   ++P l + ++s g     ig++  ++ ++s +   ++g  +D+++krk  v+l+ l s ++ l l                
  gi|15669507|ref|NP_248317.1|  41 IMPILPMLITSVGGGSLSIGLVGGLREFISNILMVLIGYCSDKVRKRKIFVVLGYLTSSMFKLLLG--------------- 106
                                   68889999999999999*****************************************99999333............... PP

                    MFS_1_like  99 vsvaqdvdaektfwilfllvvlasfflaai.lvlldaatlkel.gedrkdyGrqrlfGsvGyaifafitGilidhysvnll 177
                                            +k+ w+ +++ +  + + ++i  +  da++ + + ++  k +G qr f + G ++ ++++ ++i +++ ++ 
  gi|15669507|ref|NP_248317.1| 107 --------LSKS-WLGAVIFSSLERMGKGIrTAPRDAIISESMpKTLGKGFGIQRAFDTAGAILGSTLSLLFILYLQYSFN 178
                                   ........4455.5555555555555555515567888888885556666***********99999999999999999885 PP

                    MFS_1_like 178 pysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienF.lflYLkelga 257
                                   +    ++++aa++   +l++l + + +  ++ +  +++  ++n+ k+ +++i++ +++ l +++ +++   ++ +L     
  gi|15669507|ref|NP_248317.1| 179 Q----IILIAAVIGFLTLIPLYFVKEKPSPSNNKITFRVGIKNLPKELKLFILISAIFTLSNFSYMFYILrAQEFL-MIVD 254
                                   5....56677777777777788888888888888889999************999999888777666554566777.2222 PP

                    MFS_1_like 258 sntllGslvalgvvaeiplfffa...eklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaav 335
                                    ++ + + +al  + +i    f+     l +k+G   +l+i+ ++y +  l+ a++++   ++++ +L+gi+++l+ +   
  gi|15669507|ref|NP_248317.1| 255 EKMAIIIPIALYILYNIFYATFSipfGILSDKIGRKSVLTIGYIVYGIVSLGFAYFISQKSLILLFALYGIAYALFAGNQK 335
                                   3333334444444444432222222267899*************************8888888888*************** PP

                    MFS_1_like 336 eyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                    yvs++ ++ ++at  gl+ ++ +gl +   sli+G+lw++ s+ ++F
  gi|15669507|ref|NP_248317.1| 336 AYVSDLSSEDIRATALGLFYTV-VGLTSLPASLIAGYLWKI-SPEMTF 381
                                   *******************998.9***************95.555555 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1    0.0091        55      28      63 ..      71     102 ..      60     123 .. 0.81
   2 ?   -3.4   0.3      0.62   3.7e+03     281     308 ..     160     187 ..     142     192 .. 0.40
   3 ?   10.4   4.6   3.8e-05      0.23      82     148 ..     307     373 ..     249     396 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.0091
                          PUCC  28 apfraliGfrSDtkralGwkRvpyiwlGslalalgl 63 
                                   ++  +liG+ SD  r    kR  +++lG l+  +  
  gi|15669507|ref|NP_248317.1|  71 NILMVLIGYCSDKVR----KRKIFVVLGYLTSSMFK 102
                                   567799*********....*********99876644 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.62
                          PUCC 281 vllgllsflllilaallenvallvagvl 308
                                   +l+  ls+l+++  +   n+ +l+a+v+
  gi|15669507|ref|NP_248317.1| 160 ILGSTLSLLFILYLQYSFNQIILIAAVI 187
                                   2222333333333333333444444433 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 3.8e-05
                          PUCC  82 aatwaglilaavafllvGlgvslsqTallALladlaeeeerpkvvgllyvmlligivvsaivvgall 148
                                    a  +++  ++++f+l+G++  l      A ++dl++e+ r+ + gl y ++ +    ++++ g l 
  gi|15669507|ref|NP_248317.1| 307 FAYFISQKSLILLFALYGIAYALFAGNQKAYVSDLSSEDIRATALGLFYTVVGLTSLPASLIAGYLW 373
                                   466778889999*************************************999888777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2544.64
//
Query:       gi|15669508|ref|NP_248318.1|  [L=602]
Description: hypothetical protein MJ_1318 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-12   47.2   1.3    4.1e-12   46.1   1.3    1.5  1  Lon_C        Lon protease (S16) C-terminal proteolytic domain
    0.00033   20.5   0.1     0.0046   16.8   0.0    2.3  2  ChlI         Subunit ChlI of Mg-chelatase
  ------ inclusion threshold ------
      0.081   12.1   6.1      0.016   14.5   2.0    1.8  2  DLP_helical  Dynamin-like helical domain
       0.57   10.7   4.8        7.9    7.1   0.2    3.6  3  HSCB_C       HSCB C-terminal oligomerisation domain


Domain annotation for each model (and alignments):
>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   1.3   9.1e-16   4.1e-12      45     172 ..      48     171 ..      34     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 9.1e-16
                                   EEEEEESS-S-EEE.EES--HH.HHHHHHHHHHHHTSS-GGGSS-SS-TTT-EEEEEE-S-B-GGGGGGGHHHHHHHHHHH CS
                         Lon_C  45 ieavllpgkgklkl.tGklgdv.mkesaqaalsyvrsraeelgidkevfekkdihihvPeGavPkdGPsaGvtlatalvsl 123
                                   i  ++++g g++ + t  l ++ m+ sa++a+ +       +g d   ++k++++i v +      GPsaG t++  ++  
  gi|15669508|ref|NP_248318.1|  48 IQINVTKGDGHVFMdTMPLTELdMQGSARIAAKVAGE---VTGKD---MSKYNVYITVRSDVPVVGGPSAGGTMTIGIICE 122
                                   5555566666543325566665577777777655433...23333...4566788888776656789************** PP

                                   HTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEGGG CS
                         Lon_C 124 ltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvilPken 172
                                   l + + +k+v mtG i   G + p+GG+ ek+ aak+a+ + +++Pk  
  gi|15669508|ref|NP_248318.1| 123 LMNWSLNKHVMMTGTINPDGSIGPVGGILEKIEAAKKANCTIMLIPKGQ 171
                                   **********************************************965 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.086   3.9e+02      64     105 ..      45      86 ..      31     100 .. 0.80
   2 !   16.8   0.0     1e-06    0.0046      65     119 ..     115     169 ..     112     171 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.086
                          ChlI  64 piAigilaaleqieaeeetlflGeLsldGslrpvkgvlpial 105
                                   pi i i    ++ ++  +t+ l eL+++Gs r  ++v   + 
  gi|15669508|ref|NP_248318.1|  45 PINIQINVTKGDGHVFMDTMPLTELDMQGSARIAAKVAGEVT 86 
                                   7777777777777788999***********999888876665 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1e-06
                          ChlI  65 iAigilaaleqieaeeetlflGeLsldGslrpvkgvlpialaakkegikkvivpk 119
                                   + igi+++l++ + ++++++ G ++ dGs+ pv g+l+ + aakk++++ +++pk
  gi|15669508|ref|NP_248318.1| 115 MTIGIICELMNWSLNKHVMMTGTINPDGSIGPVGGILEKIEAAKKANCTIMLIPK 169
                                   689**************************************************98 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.0   3.5e-06     0.016      47     173 ..     210     339 ..     206     351 .. 0.78
   2 ?   -2.1   0.1      0.38   1.7e+03     187     220 ..     543     575 ..     516     591 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-06
                   DLP_helical  47 eekikknggelalieetkksvirdvlerqlpeaeerleelekevekleesakriekelaelkkeieearielreel.kayf 126
                                   +++i k+ +e  liee+ k++++++ e+ l++a+e+ e+l+ke+ ++    + +++ l+el    +  +++  e l ++y 
  gi|15669508|ref|NP_248318.1| 210 KKIIMKEYPENPLIEEKYKDIMKELSENVLKTANEKYENLSKELSNSYVGYEYQKALLNELTTSKSLLEKANDEYLkNKYY 290
                                   57899999**************************************98777777766665544444444444444414688 PP

                   DLP_helical 127 sdLilqvkgl.sletieeFlereiGdegi.vvgtkleneferqlekise 173
                                   s      ++l +letie  l+   G+e++ +  t+++n++++  e ++ 
  gi|15669508|ref|NP_248318.1| 291 SATCSAFNALiKLETIEHTLKYLTGEEDVkTFLTEVQNKISHDKEIVYS 339
                                   8888888876489************999625689999999998766655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.38
                   DLP_helical 187 ehfndsssklgkqgikylkksklvkinntsilaa 220
                                   +++n+s+s+   + i+++ ++++ +i++t+ +  
  gi|15669508|ref|NP_248318.1| 543 KELNKSISENISSEINIVTNENV-NIEETTTKEN 575
                                   33333333333333444444333.4444444444 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3     0.032   1.4e+02      29      69 ..     236     291 ..     222     294 .. 0.64
   2 ?   -1.3   0.0      0.74   3.3e+03      38      59 ..     356     380 ..     353     382 .. 0.76
   3 ?    7.1   0.2    0.0018       7.9      25      76 .]     411     469 ..     399     469 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.032
                                   HHHHHHHHHHHHHHHHHHHHHH...............HTT-HHHHHHHHHHHHHHH CS
                        HSCB_C  29 eelkaeveerieeleaeleeaf...............ekkdleaaadllrrlrYle 69 
                                   e++ +  +e+ e+l +el++ +               +k+ le+a d++ + +Y++
  gi|15669508|ref|NP_248318.1| 236 ENVLKTANEKYENLSKELSNSYvgyeyqkallnelttSKSLLEKANDEYLKNKYYS 291
                                   44445555666666666666667666666666655555558889999999999985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.74
                                   HHHHHHHHHHHHHHTT....-HHHHH CS
                        HSCB_C  38 rieeleaeleeafekk....dleaaa 59 
                                   ri+e e+ l++a+ k+    ++++a 
  gi|15669508|ref|NP_248318.1| 356 RIAEAEKLLDNAW-KSyylgNYDEAI 380
                                   8999999999999.555777777775 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0018
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH.......HTT.-HHHHHHHHHHHHHHHHHHHHHH CS
                        HSCB_C  25 keeleelkaeveerieeleaeleeaf.......ekk.dleaaadllrrlrYlekikeeik 76 
                                   +++l+ l+++     e++++ +e++f         + dle a++++    Yl  i+e+i+
  gi|15669508|ref|NP_248318.1| 411 EAKLKSLAQQYLDNAETILTYVETLFpnlptddL-EnDLESAKEAYKDGDYLLTIAESID 469
                                   48999*********************99987642.25********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1373  (0.0765798); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4139.67
//
Query:       gi|15669509|ref|NP_248319.1|  [L=492]
Description: sodium-dependent transporter [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.4e-111  372.1  44.1    4.1e-76  256.8  24.3    2.0  2  SNF       Sodium:neurotransmitter symporter family
  ------ inclusion threshold ------
        3.3    7.7   5.5        5.1    7.1   0.2    2.8  2  LRR19-TM  Leucine-rich repeat family 19 TM domain


Domain annotation for each model (and alignments):
>> SNF  Sodium:neurotransmitter symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.6  12.0   4.2e-39   3.7e-35       1     110 [.       6     115 ..       6     125 .. 0.98
   2 !  256.8  24.3   4.6e-80   4.1e-76     154     509 ..     125     481 ..     117     490 .. 0.89

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 4.2e-39
                           SNF   1 RetwskkldfilsvvGfavgLgnvWRFPYlcyknGGGafliPYlilllvaGiPlfflelalGqytreGaitvwrkicPllk 81 
                                   Re+ws+ l fil++vG+a+gLgn+WRF Y++y+nGGGafliPY+++ll++GiPl+ le+a+G+yt++ a  + +k+    +
  gi|15669509|ref|NP_248319.1|   6 RESWSSNLGFILASVGSAIGLGNIWRFGYMVYTNGGGAFLIPYIVALLCVGIPLMILEFAIGHYTKKSAPLALEKLHKGSE 86 
                                   89******************************************************************************* PP

                           SNF  82 giGyasivvalyvglyYnvilawalfYlf 110
                                     G+ +++  +++  yY+vi+aw l+Yl+
  gi|15669509|ref|NP_248319.1|  87 WTGWFAVISGFIITSYYVVIIAWCLYYLI 115
                                   ***************************97 PP

  == domain 2  score: 256.8 bits;  conditional E-value: 4.6e-80
                           SNF 154 aaeefwerevlklsssieelGelrweltlcllvawvvvylailkGvks....sgkvvyftatfPyvvllvllvrgvlLpGa 230
                                       ++ +++l++ss++e++G +++ ++++ l++w +v l +  G+k+    + k++    +   +++++l++ +++LpGa
  gi|15669509|ref|NP_248319.1| 125 DPNAYFFHNILQISSGVEDIGGVSYGILVSTLAVWGIVALILSAGIKNglekANKIMIPFLL---FLIILLVLNALTLPGA 202
                                   56678999******************************999888887511114555544444...3344566799****** PP

                           SNF 231 vkgikfyltpdlekllepkvWidaatqiffslgigfGvlialasYnkfennvyrdallvslinsltsvlaglvvFsvlGfm 311
                                   ++gi++yltpd++ l + +vW  a +qiffsl++gfG+lia+asY  ++++++ +a+ vsl+n+ +s+lag++vF  lG+m
  gi|15669509|ref|NP_248319.1| 203 LTGIEWYLTPDFSALFNYNVWLSAFSQIFFSLSLGFGILIAYASYLPKKSDLTINAVTVSLLNCGFSFLAGFAVFGTLGYM 283
                                   ********************************************************************************* PP

                           SNF 312 aeeqgekisevaeeGpgLaFiaypealtklpl.splwsvlFFlmlillgldsqfgtvegiitavvDefkvllrrrelltli 391
                                   + ++g ++++  +eG+gLaF+++p+al+ lp+ s l++++FFl l+++g+ s++++ve+ ++a++D+f     +r+   l+
  gi|15669509|ref|NP_248319.1| 284 SYTSGIPLDKAVSEGIGLAFVTFPKALSLLPFaSRLFGIVFFLALVFAGISSAVSIVEASVSAIIDKFSL---SRKKALLA 361
                                   *******************************7378**********************************9...67777778 PP

                           SNF 392 vavlaflvglllvtegGiyvltlldkyaaslsllvvvlleaiavawvyglkkflddikemlgfrpllflklcwkfvsplll 472
                                   v +l ++++ +++t +G+y+l+++d++a+ + l ++++le+i   w++g +k+ ++++++   + ++++k+   +vsp++l
  gi|15669509|ref|NP_248319.1| 362 VLALFIIISPIFTTGAGLYYLDIIDHFASGYLLPIAAILEIIIAIWLFGGDKLREHVNKLSEIKLGVWWKYLAGVVSPIIL 442
                                   8888899999*********************************************************************** PP

                           SNF 473 lvlliasivklkpltynayv..yPkwaealgwllalssv 509
                                    +++   + ++ +++y  y+  y  ++  +  l  ++sv
  gi|15669509|ref|NP_248319.1| 443 TAVVFLDASNVLTSGYGGYKttYVIFGALIIPLAFVVSV 481
                                   *****************9865565555444433333333 PP

>> LRR19-TM  Leucine-rich repeat family 19 TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.2     0.034     3e+02       7      45 ..      79     117 ..      74     123 .. 0.81
   2 ?    7.1   0.2   0.00057       5.1       5      32 ..     420     447 ..     416     454 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.034
                      LRR19-TM   7 ekeksgksWaylvgvvvlalvtsllillaikckllykfl 45 
                                   ek + g  W+   +v+   ++ts  +++++ c  +  +l
  gi|15669509|ref|NP_248319.1|  79 EKLHKGSEWTGWFAVISGFIITSYYVVIIAWCLYYLIIL 117
                                   566779999999999*99******999999997765555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00057
                      LRR19-TM   5 aaekeksgksWaylvgvvvlalvtslli 32 
                                   + ++ k+g  W+yl+gvv  +++t+++ 
  gi|15669509|ref|NP_248319.1| 420 KLSEIKLGVWWKYLAGVVSPIILTAVVF 447
                                   5567789999********9999988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 2981.81
//
Query:       gi|15669510|ref|NP_248320.1|  [L=131]
Description: hypothetical protein MJ_1320 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-26   91.2   1.4    6.1e-26   91.0   1.4    1.0  1  PIN_9          PIN like domain
    3.4e-06   27.4   0.0    4.6e-06   26.9   0.0    1.1  1  Fcf1           Fcf1
    3.4e-06   27.6   1.6    1.4e-05   25.6   1.6    1.8  1  PIN            PIN domain
    7.4e-05   23.0   3.8     0.0015   18.8   3.8    2.0  1  PIN_4          PIN domain
     0.0054   16.5   0.0       0.01   15.6   0.0    1.5  1  DUF5615        Domain of unknown function (DUF5615)
  ------ inclusion threshold ------
      0.013   15.9   0.3      0.021   15.2   0.3    1.3  1  NAD_binding_7  Putative NAD(P)-binding
      0.027   14.2   0.1      0.036   13.7   0.1    1.4  1  DUF188         Uncharacterized BCR, YaiI/YqxD family COG1671
      0.044   13.6   1.2      0.063   13.1   1.1    1.4  1  RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   1.4   2.7e-29   6.1e-26       1     116 []       4     122 ..       4     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 2.7e-29
                         PIN_9   1 vilDtnaLmipvqfgvdifeelerll.gsvelvvpkavleELerlak..agkgkertaakvalsLaerceiveaeeekaDd 78 
                                   ++ Dtn+L+  ++ +++   e+er l  + e+v+++++ eELerl k  + kgke+ a+++al+  +++++v+ ++++aD+
  gi|15669510|ref|NP_248320.1|   4 IVPDTNFLIYVFKHKINFDYEIERALnTKFEIVILSPIKEELERLLKsrDLKGKEKLAVNLALAKIKNYKLVDYTANYADE 84 
                                   577***********************999***************9761157899*************************** PP

                         PIN_9  79 ailelakeldaavlvTnDreLkkrllekgipvilLRqk 116
                                   ail++ake +  +++TnD+eLk++l+e++ipv+++Rqk
  gi|15669510|ref|NP_248320.1|  85 AILNYAKENENVIVATNDKELKEKLMENNIPVMVVRQK 122
                                   *************************************8 PP

>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   2.1e-09   4.6e-06       2      95 ..      28     124 ..      27     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.1e-09
                                   HCTS-EEEEEEHHHHHHHHHCT..........-HHHHHHHTTSEEE----SS---HHHHHHHHH-BTB-TT-EEEE-S-HH CS
                          Fcf1   2 tLqakvkpliTqCviaeleklgkk........lkealkiaktferlkCnhkkptsaddClvsvvkkkknkkryivAtqDkd 74 
                                    L+ k++++i + + +ele+l k+        l   l++ak ++  k    ++ +ad+ +++  k   ++++ ivAt+Dk+
  gi|15669510|ref|NP_248320.1|  28 ALNTKFEIVILSPIKEELERLLKSrdlkgkekLAVNLALAK-IKNYKLVDYTANYADEAILNYAK---ENENVIVATNDKE 104
                                   68888999999999999999884444555533444444444.455555555779**********9...36999******** PP

                                   HHHHHHTSTT--EEEEE--EE CS
                          Fcf1  75 lrrrlrkipgvPilyikrsvm 95 
                                   l+++l +   +P++ ++++++
  gi|15669510|ref|NP_248320.1| 105 LKEKLMEN-NIPVMVVRQKKY 124
                                   *****986.69*****99998 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   1.6   6.2e-09   1.4e-05       1      88 [.       4      92 ..       4     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.2e-09
                                  EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHH CS
                           PIN  1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeeaa 82
                                  iv DT++li+++  + ++  +++++l+   e+v+ + + +El + l++r +k +++ ++ ++l   ++ k+++ +a+ a+ea 
  gi|15669510|ref|NP_248320.1|  4 IVPDTNFLIYVFkHKINFDYEIERALNTKFEIVILSPIKEELERLLKSRDLKGKEKLAVNLALAKIKNYKLVDYTANYADEAI 86
                                  689*********65666667899999999*******************88888888888888888999999999999999886 PP

                                  HHHHHH CS
                           PIN 83 eialky 88
                                    ++k 
  gi|15669510|ref|NP_248320.1| 87 LNYAKE 92
                                  655554 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   3.8   6.9e-07    0.0015       1      80 [.       4     108 ..       4     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.9e-07
                         PIN_4   1 fVlDTnvlLhdpealksf........keehdvviPitVleELdklKkgsse..................relarlarqanr 55 
                                   +V DTn+l++ ++   +f        + + ++vi   + eEL++l k++++                  + +++ a+ a +
  gi|15669510|ref|NP_248320.1|   4 IVPDTNFLIYVFKHKINFdyeieralNTKFEIVILSPIKEELERLLKSRDLkgkeklavnlalakiknyKLVDYTANYADE 84 
                                   699*********9999999*****************************998888888888888888877788888888888 PP

                         PIN_4  56 lldellekesgrlkvqtsaeelpee 80 
                                    + +   ke++++ v t+++el+e+
  gi|15669510|ref|NP_248320.1|  85 AILNYA-KENENVIVATNDKELKEK 108
                                   776554.446677788888788764 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.6e-06      0.01      34      69 ..      80     116 ..      61     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.6e-06
                       DUF5615  34 gasDeeileyAkeedriiv.TkDkDFgellllggppp 69 
                                   +  De+il+yAke++ +iv T+Dk   e l+ +  p 
  gi|15669510|ref|NP_248320.1|  80 NYADEAILNYAKENENVIVaTNDKELKEKLMENNIPV 116
                                   578*********9876665277798877766655554 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.3   9.6e-06     0.021      24      95 ..      26     122 ..      24     128 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.6e-06
                 NAD_binding_7  24 rklleagakvtvvapevkeele..........................elvklaeeelekd....legadlviaatddrel 74 
                                   ++ l+++ ++++++p  keele                          +lv+++ +++++      ++ + vi+at+d+el
  gi|15669510|ref|NP_248320.1|  26 ERALNTKFEIVILSPI-KEELErllksrdlkgkeklavnlalakiknyKLVDYTANYADEAilnyAKENENVIVATNDKEL 105
                                   6778889999999998.56666566666666777777777666665555555555555433333355667*********** PP

                 NAD_binding_7  75 neriaeaakarrilvnvadkp 95 
                                   +e+++e    ++i+v v+ ++
  gi|15669510|ref|NP_248320.1| 106 KEKLME----NNIPVMVVRQK 122
                                   *99886....46666666665 PP

>> DUF188  Uncharacterized BCR, YaiI/YqxD family COG1671
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.6e-05     0.036      26      78 ..      67     121 ..      25     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                        DUF188  26 splvetvvVdsgadaaDdaIveraeagD..lvvTqDipLAarvlekgaaalsprG 78 
                                    +  + + Vd  a+ aD+aI++ a++++  +v T+D  L ++++e+++ ++  r 
  gi|15669510|ref|NP_248320.1|  67 AKIKNYKLVDYTANYADEAILNYAKENEnvIVATNDKELKEKLMENNIPVMVVRQ 121
                                   456678899***************987643677************9999987765 PP

>> RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.1   2.8e-05     0.063      71     123 ..      64     117 ..      33     127 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
                 RNase_Zc3h12a  71 enlivltpskyldgkksvsyddrlilelAeekdGviv.sndn..yrdllsenkelk 123
                                   + l ++++ k +d   +  y d+ il++A+e++ viv +nd+  ++ l+++n  ++
  gi|15669510|ref|NP_248320.1|  64 LALAKIKNYKLVD--YTANYADEAILNYAKENENVIVaTNDKelKEKLMENNIPVM 117
                                   3445555556666..5667************9999984566532334777765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1248  (0.0696079); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 837.68
//
Query:       gi|15669511|ref|NP_248321.1|  [L=713]
Description: hypothetical protein MJ_1321 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-60  204.5   0.6    8.5e-60  202.5   0.0    2.3  3  Piwi      Piwi domain


Domain annotation for each model (and alignments):
>> Piwi  Piwi domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.22   3.9e+03      43      76 ..     177     209 ..     161     219 .. 0.74
   2 ?   -1.6   0.1     0.072   1.3e+03     123     142 ..     368     387 ..     355     395 .. 0.63
   3 !  202.5   0.0   4.8e-64   8.5e-60       1     302 []     426     699 ..     426     699 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.22
                                   HHHHHHHHHHHHHHHTT-BS-EEESSSTTSSE.. CS
                          Piwi  43 kkqtltnvllkinvKlGgknvliveikleldvsp 76 
                                   ++++ ++++ k n K+ ++ + +v+++   ++++
  gi|15669511|ref|NP_248321.1| 177 EEYVGKKIIFKPNPKVRYT-ISLVDAPNPQKIEE 209
                                   6677789999999999999.88888888777744 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.072
                                   CHHHHHHHHHHHHHHHHHHT CS
                          Piwi 123 elleklkeiikellrefkks 142
                                   + l+ +k+ +++++r+++k 
  gi|15669511|ref|NP_248321.1| 368 DELKAIKDKVNKMFRNYNKI 387
                                   33444566666666666664 PP

  == domain 3  score: 202.5 bits;  conditional E-value: 4.8e-64
                                   EEEEEECS.SGHHC.HHHHHHHHHHTCCCCEEEEEHHHHCTCCHHHHHHHHHHHHHHHHTT-BS-EEESSSTTSSE....E CS
                          Piwi   1 lilvilpe.kkkdk.yheikkyletdlgiisqcillktilkrqlkkqtltnvllkinvKlGgknvliveikleldvsptli 79 
                                   ++++i+ + k+kd+ y+ei+k++++dl+iisq+il+++++k+++  ++++n+l++i+ KlG+k ++i+++k+ +d+    i
  gi|15669511|ref|NP_248321.1| 426 CFALIIGKeKYKDNdYYEILKKQLFDLKIISQNILWENWRKDDK-GYMTNNLLIQIMGKLGIK-YFILDSKTPYDY----I 500
                                   688899887777767***************************88.******************.************....* PP

                                   EEEEEEEEECCCSCCCEEEEEEEEEE.TSSEEEEEEEEESSCCCCHHHHHHHHHHHHHHHHHHTTTT-TTSEEEEEESS.. CS
                          Piwi  80 iGidishgtagtvdnpsvaavvasld.kensrylaevstqassqelleklkeiikellrefkksskkkkperiivyRdGvs 159
                                   +G+d+  g+ g+   ++v+++++++d ++++r+++ ++t+a++++l+ +   ++ e+l++  k++ ++++++i++ RdG  
  gi|15669511|ref|NP_248321.1| 501 MGLDTGLGIFGN---HRVGGCTVVYDsEGKIRRIQPIETPAPGERLHLP---YVIEYLEN--KANIDMENKNILFLRDG-- 571
                                   ************...**********************************...********..*****************.. PP

                                   ..S..S-HHHHHHHHHHHHHHHHHCTTTEEEEEEEECSCS--EEESESTCCCEETTTCEEE...TTEEEEEEEECCEEECC CS
                          Piwi 160 eGqfkqvlnsEvkelkealkklkeqyqpkltvivvqkrhhtrfFasdkaeksqnippGtvv...dkkitlpeekdfylcsh 237
                                         ++nsE ++lke++k+l+    ++++vi+++k++++++F+sd++++s++ ++G+++   + ++++p + +++l+++
  gi|15669511|ref|NP_248321.1| 572 -----FIQNSERNDLKEISKELN----SNIEVISIRKNNKYKVFTSDYRIGSVFGNDGIFLphkTPFGSNPVKLSTWLRFN 643
                                   .....***********9999888....7889********************************999*************** PP

                                   CCEEEEEEEEEEEEEEES..S-CCHHHHHHHHHCTGGTTTT....SS-SS-HHHHHHHHHHHHHHTCCC CS
                          Piwi 238 aglqgtvkPtkytvlvdeaklsadelqsltyklchmyqrst....rsvsiPapvyyAhklAkrvrnnlk 302
                                   +g+++++k   ++          +++++l+y+l++m+++++    r+++iPap++yA+k++k++++n+k
  gi|15669511|ref|NP_248321.1| 644 CGNEEGLK---IN----------ESIMQLLYDLTKMNYSALygegRYLRIPAPIHYADKFVKALGKNWK 699
                                   ********...66..........7****************99999**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 4451.69
//
Query:       gi|15669512|ref|NP_248322.1|  [L=1005]
Description: purine NTPase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-27   96.3  16.0    3.2e-27   96.3  16.0    9.3  1  AAA_23           AAA domain
    4.4e-15   55.7  41.5    1.3e-10   41.1   1.6    3.3  3  SMC_N            RecF/RecN/SMC N terminal domain
    4.6e-13   48.8   5.2    4.6e-13   48.8   5.2   13.1 12  Rad50_zn_hook    Rad50 zinc hook motif
    3.2e-08   33.7  43.3    3.2e-08   33.7  43.3    4.4  2  AAA_15           AAA ATPase domain
    4.2e-07   29.6   0.0    7.9e-07   28.7   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
      3e-05   24.2   0.0    7.2e-05   22.9   0.0    1.7  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
      0.001   18.9   6.8      0.001   18.9   6.8    5.1  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      0.002   18.6  64.9        1.7    9.2   0.6   11.3 10  NPV_P10          Nucleopolyhedrovirus P10 protein
     0.0025   17.4   0.0     0.0025   17.4   0.0    4.8  8  AAA_27           AAA domain
     0.0026   17.7  18.7     0.0026   17.7  18.7    5.9  2  CEP63            Centrosomal protein of 63 kDa
     0.0032   18.3  12.7     0.0032   18.3  12.7    8.3  5  PRKG1_interact   cGMP-dependent protein kinase interacting do
     0.0043   17.8   6.7     0.0043   17.8   6.7    9.5 10  Occludin_ELL     Occludin homology domain
  ------ inclusion threshold ------
      0.063   13.6   1.8       0.27   11.6   0.0    3.1  3  AAA_16           AAA ATPase domain
      0.064   12.1 133.7       0.12   11.2  19.3    6.9  8  Spc7             Spc7 kinetochore protein
        0.1   12.9   3.6       0.26   11.6   0.6    3.3  2  zf-AD            Zinc-finger associated domain (zf-AD)
       0.23    9.6 154.5      0.034   12.3  45.5    5.0  5  EzrA             Septation ring formation regulator, EzrA
       0.23   10.0 125.4       0.43    9.2  25.9    6.0  7  AAA_13           AAA domain
       0.69    9.8   7.1        7.7    6.4   0.2    4.2  4  TarH             Tar ligand binding domain homologue
       0.92    9.8   0.0       0.92    9.8   0.0    4.7  4  AAA_22           AAA domain
          1    9.7 128.7      0.019   15.3   4.0   13.3 13  BLOC1_2          Biogenesis of lysosome-related organelles co
        1.4    9.2  19.7        1.7    8.9   0.3    7.9  8  WXG100           Proteins of 100 residues with WXG
        2.5    8.1  13.2       0.36   10.8   0.1    4.7  5  DUF4743          Domain of unknown function (DUF4743)
        6.7    6.1   7.4         13    5.1   0.0    4.1  5  Mce4_CUP1        Cholesterol uptake porter CUP1 of Mce4, puta
        6.8    6.3  82.1      0.032   13.9   5.5    6.9  6  Syntaxin         Syntaxin
        8.8    3.7  95.3       0.94    6.9  16.5    3.4  3  DUF3584          Protein of unknown function (DUF3584)
        9.2    6.3  76.8       0.28   11.2   5.6    9.6  9  DUF1664          Protein of unknown function (DUF1664)
        9.7    5.2  15.9        2.5    7.1   0.5    4.2  4  PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subuni


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3  16.0   4.8e-30   3.2e-27       2     200 .]       8     225 ..       7     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 4.8e-30
                        AAA_23   2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenk 82 
                                   ++++nf+s+ +  i F+kg+++I+G+NG+GK++i++A+ +aL+g         g++f+ + +   ++gk++ yvel+fe +
  gi|15669512|ref|NP_248322.1|   8 IRMNNFKSHVNSRIKFEKGIVAIIGENGSGKSSIFEAVFFALFGA--------GSNFNYDTII--TKGKKSVYVELDFEVN 78 
                                   89******************************************3........5566767765..4569999********* PP

                        AAA_23  83 dgrytrsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkke.......... 153
                                   ++  +++i re    ++ +k +k+ k   ++i++ ++ ++e+lg++ + + ++++++q++ ++f+  +++e          
  gi|15669512|ref|NP_248322.1|  79 GN--NYKIIREYDSGRGGAKLYKNGKPYATTISAVNKAVNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSEkletvakllg 157
                                   99..58999***************************************************777777555555667777777 PP

                        AAA_23 154 ....................rleelekeleeled.ekkllekleqekekekeleeleeeleeilkele 200
                                                       rle +e el+ +e+ ek+l +k  q++ek+k+l e++++l++i+ke e
  gi|15669512|ref|NP_248322.1| 158 idefekcyqkmgeivkeyekRLERIEGELNYKENyEKELKNKMSQLEEKNKKLMEINDKLNKIKKEFE 225
                                   7777788888888777777799999999999998455555555999*****************99976 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   1.6   1.9e-13   1.3e-10       2      50 ..       5      51 ..       4     117 .. 0.79
   2 ?   -3.7   1.0       9.9   6.6e+03      76     128 ..     181     232 ..     156     237 .. 0.59
   3 !   26.1  24.1   7.7e-09   5.1e-06      92     217 ..     578     997 ..     517    1000 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1.9e-13
                                  EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGe 50
                                  lk+++++nFks    +  ++f+k++ ai+G+NGSGKs++++A+ F L  
  gi|15669512|ref|NP_248322.1|  5 LKEIRMNNFKSH--VNSRIKFEKGIVAIIGENGSGKSSIFEAVFFALFG 51
                                  89**********..58999*************************98843 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.9
                                   EEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  76 kaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevselle 128
                                   + e e+ ++++ +k + +++  +++ + k+  e + k+n+ + +++++++l++
  gi|15669512|ref|NP_248322.1| 181 RIEGELNYKENYEK-ELKNKMSQLEEKNKKLMEINDKLNKIKKEFEDIEKLFN 232
                                   44444444444444.44555555555555555566666666667777777766 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 7.7e-09
                                   SSSSCEEEEEEEETTSEEEEEETTEEE-H..HHHHHHHHCTT-STT................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx................................... RF
                         SMC_N  92 iekeevsisrrvkrkgeseykingkevtk..kevsellesagiske................................... 135
                                    + ++++ +   ++k+ s+y ingk v +  ++++++l++ +   +                                   
  gi|15669512|ref|NP_248322.1| 578 LKLKNYKEQLDEINKKISNYVINGKPVDEilEDIKSQLNKFKNFYNqylsavsylnsvdeegirnrikeienivsgwnkek 658
                                   333334444445556668888888888877788888888865444459999999999999999999999999999999999 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|15669512|ref|NP_248322.1| 659 creelnklredereinrlkdklnelknkekelieienrrslkfdkykeylgltekleelknikdgleeiynicnskilaid 739
                                   999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|15669512|ref|NP_248322.1| 740 nikrkynkedieiylnnkilevnkeindieerisyinqkldeinyneeehkkikelyenkrqeldnvreqkteietgieyl 820
                                   999999999999999999999999999999999999999999999999********************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                         SMC_N 136 ................................................................................. 135
                                                                                                                    
  gi|15669512|ref|NP_248322.1| 821 kkdveslkarlkemsnlekekekltkfveyldkvrrifgrngfqaylrekyvpliqkylneafsefdlpysfveltkdfev 901
                                   ********************************************************************************* PP

                                   ............CS-HHHHHHHHHHHHHHHHCC...S--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHH CS
                                   ............xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 136 ............lLSgGektLvalaLlfAiqkv...kpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreem 201
                                               +LSgGe+  val+L++Ai ++   ++    +lDe    LDe++++k+ae++++ ++  Q+i+i++++e+
  gi|15669512|ref|NP_248322.1| 902 rvhapngvltidNLSGGEQIAVALSLRLAIANAligNRVECIILDEPTVYLDENRRAKLAEIFRKVKSIPQMIIITHHREL 982
                                   *****************************87754445666679************************************** PP

                                   CCC-SCEEEEEEEETT CS
                                   xxxxxxxxxxxxxxxx RF
                         SMC_N 202 lekadklvgvtkveng 217
                                      ad ++ v+k + +
  gi|15669512|ref|NP_248322.1| 983 EDVADVIINVKK-DGN 997
                                   **********99.554 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2         1   6.6e+02      35      50 ..     169     184 ..     166     186 .. 0.81
   2 ?   -1.2   0.4       2.8   1.9e+03       6      51 ..     194     206 ..     190     209 .. 0.56
   3 ?    2.2   0.9      0.25   1.7e+02       3      19 ..     236     252 ..     235     253 .. 0.88
   4 ?    0.4   0.2      0.88   5.9e+02      35      49 ..     347     361 ..     341     364 .. 0.85
   5 ?   -1.6   0.6       3.8   2.5e+03      34      48 ..     363     377 ..     356     382 .. 0.58
   6 !   48.8   5.2   6.9e-16   4.6e-13       1      51 [.     481     531 ..     481     532 .. 0.96
   7 ?    1.2   1.2      0.51   3.4e+02       7      17 ..     534     544 ..     530     555 .. 0.57
   8 ?   -1.3   0.6       2.9   1.9e+03      41      45 ..     583     587 ..     570     597 .. 0.53
   9 ?   -2.5   0.0       7.3   4.8e+03      34      48 ..     604     618 ..     601     620 .. 0.81
  10 ?    0.1   1.3       1.1   7.3e+02       3      19 ..     671     687 ..     670     688 .. 0.79
  11 ?   -0.2   0.1       1.3   8.9e+02       1      17 [.     754     770 ..     754     773 .. 0.87
  12 ?   -1.3   1.2       3.1   2.1e+03       4      19 ..     771     786 ..     768     809 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1
                                   HHHHHHHHHHHHHHH. CS
                 Rad50_zn_hook  35 seLikelqsklerlpe 50 
                                    e++ke++++ler++ 
  gi|15669512|ref|NP_248322.1| 169 GEIVKEYEKRLERIEG 184
                                   5899999999999975 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.8
                                   HHHHHHHHHHTT-SEE-TTT--EE-HHHHHHHHHHHHHHHHHHH.. CS
                 Rad50_zn_hook   6 eelnkkieelkeakgcCPlCgReldeehrseLikelqsklerlpee 51 
                                   +e                                 l++k+ +l+e+
  gi|15669512|ref|NP_248322.1| 194 KE---------------------------------LKNKMSQLEEK 206
                                   45.................................55555555554 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.25
                                   HHHHHHHHHHHHHTT-S CS
                 Rad50_zn_hook   3 qeteelnkkieelkeak 19 
                                   +++++++k+i++l+e+k
  gi|15669512|ref|NP_248322.1| 236 NKKLLYEKFINKLEERK 252
                                   6889**********987 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.88
                                   HHHHHHHHHHHHHHH CS
                 Rad50_zn_hook  35 seLikelqsklerlp 49 
                                     L++++++++er++
  gi|15669512|ref|NP_248322.1| 347 DTLLNKIKDEIERVE 361
                                   679*********987 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 3.8
                                   HHHHHHHHHHHHHHH CS
                 Rad50_zn_hook  34 rseLikelqsklerl 48 
                                    ++L++el++  e++
  gi|15669512|ref|NP_248322.1| 363 IKDLLEELKNLNEEI 377
                                   455555555544444 PP

  == domain 6  score: 48.8 bits;  conditional E-value: 6.9e-16
                                   HHHHHHHHHHHHHHHTT-SEE-TTT--EE-HHHHHHHHHHHHHHHHHHH.. CS
                 Rad50_zn_hook   1 lhqeteelnkkieelkeakgcCPlCgReldeehrseLikelqsklerlpee 51 
                                   +++e+++l+k+++elke++g+CPlC+ ++de++++eLi++++++l+++ +e
  gi|15669512|ref|NP_248322.1| 481 INSEIKRLKKILDELKEVEGKCPLCKTPIDENKKMELINQHKTQLNNKYTE 531
                                   699********************************************9887 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 0.51
                                   HHHHHHHHHTT CS
                 Rad50_zn_hook   7 elnkkieelke 17 
                                   e+nkki e+++
  gi|15669512|ref|NP_248322.1| 534 EINKKIREIEK 544
                                   55555555543 PP

  == domain 8  score: -1.3 bits;  conditional E-value: 2.9
                                   HHHHH CS
                 Rad50_zn_hook  41 lqskl 45 
                                   ++++l
  gi|15669512|ref|NP_248322.1| 583 YKEQL 587
                                   33333 PP

  == domain 9  score: -2.5 bits;  conditional E-value: 7.3
                                   HHHHHHHHHHHHHHH CS
                 Rad50_zn_hook  34 rseLikelqsklerl 48 
                                     e++++++s+l+++
  gi|15669512|ref|NP_248322.1| 604 VDEILEDIKSQLNKF 618
                                   579999999999987 PP

  == domain 10  score: 0.1 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHTT-S CS
                 Rad50_zn_hook   3 qeteelnkkieelkeak 19 
                                    e+++l+ k++elk+++
  gi|15669512|ref|NP_248322.1| 671 REINRLKDKLNELKNKE 687
                                   57889999999999876 PP

  == domain 11  score: -0.2 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHHHHHTT CS
                 Rad50_zn_hook   1 lhqeteelnkkieelke 17 
                                   l+++++e nk i+ ++e
  gi|15669512|ref|NP_248322.1| 754 LNNKILEVNKEINDIEE 770
                                   68899999999999987 PP

  == domain 12  score: -1.3 bits;  conditional E-value: 3.1
                                   HHHHHHHHHHHHTT-S CS
                 Rad50_zn_hook   4 eteelnkkieelkeak 19 
                                   +++ +n+k++e++ ++
  gi|15669512|ref|NP_248322.1| 771 RISYINQKLDEINYNE 786
                                   5666777777776554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7  43.3   4.8e-11   3.2e-08       1     279 [.       3     338 ..       3     352 .. 0.69
   2 !    9.6  36.6     0.001      0.69      96     364 ..     652     978 ..     641     982 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 4.8e-11
                        AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsileal.dlFlnnkekkn..kkvikiekedleifeniseskdik 78 
                                   M++k+i+ +NF+s+ +  i++++ +  +iG+N+sGKSsi ea    ++   +++n     +k +k+ + + + + + ++ k
  gi|15669512|ref|NP_248322.1|   3 MILKEIRMNNFKSHVNSRIKFEKGIVAIIGENGSGKSSIFEAVfFALFGAGSNFNydTIITKGKKSVYVELDFEVNGNNYK 83 
                                   9****************************************9702233334677776555566666777778888888888 PP

                        AAA_15  79 Idvef.......................................................aek.ekakeyektlkskekkk 103
                                   I  e+                                                       + + ek ++  k+l  +e +k
  gi|15669512|ref|NP_248322.1|  84 IIREYdsgrggaklykngkpyattisavnkavneilgvdrnmflnsiyikqgeiakflslK-PsEKLETVAKLLGIDEFEK 163
                                   8888899999999999999999999999999999999999999999999888877665432.1466777777777777777 PP

                        AAA_15 104 adlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkee 184
                                   +   + ++ ++  k+++  + +l+  ++ +  +++++k+s  e +++k  + + + +++k+++ed++kl +++e+++  +e
  gi|15669512|ref|NP_248322.1| 164 CYQKMGEIVKEYEKRLERIEGELN--YKENYEKELKNKMSQLEEKNKKLMEINDKLNKIKKEFEDIEKLFNEWENKKLLYE 242
                                   766666666666666666655553..5555556666677777777777777788888899999999999999999998888 PP

                        AAA_15 185 elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl.........eeelteklkeiqeklkeidkkl 256
                                   ++ n+l++  + l+l + + ++ +             ++  +e   +e l          ++l +++ +i++ l+e+++ +
  gi|15669512|ref|NP_248322.1| 243 KFINKLEERKRALELKNQELKILE-----------YDLNTVVEA--RETLnrhkdeyekYKSLVDEIRKIESRLRELKSHY 310
                                   444444444444444444444444...........333333332..22333322222235667777777777777777777 PP

                        AAA_15 257 aeelk.....kilkkkidkikkfnykgk 279
                                   ++ lk     +i+k +i+k+k f +k+k
  gi|15669512|ref|NP_248322.1| 311 EDYLKltkqlEIIKGDIEKLKEFINKSK 338
                                   7777788788777777777655544443 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.001
                        AAA_15  96 lkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkl 176
                                   + ++++k+++ +l+k+++d  ++ + k+  ++ +++ +e i++e++ s k+++ +++  l+++ eelk  k+ l+++++  
  gi|15669512|ref|NP_248322.1| 652 SGWNKEKCRE-ELNKLREDEREINRLKDKLNELKNKEKELIEIENRRSLKFDKYKEYLGLTEKLEELKNIKDGLEEIYNIC 731
                                   4555555555.8888888888888888888888899999999999999999999999999999999999999999999988 PP

                        AAA_15 177 eeslkkeeelknvlksaiiklllisakRnvsd..edsekkssllgklkekileealqekl....eeelteklkeiqeklke 251
                                   ++++   + +k +++++ i+++l+++  +v++  +d e+  s++++++++i+ +  + k          e+  + +++++e
  gi|15669512|ref|NP_248322.1| 732 NSKILAIDNIKRKYNKEDIEIYLNNKILEVNKeiNDIEERISYINQKLDEINYNEEEHKKikelY----ENKRQELDNVRE 808
                                   88888888999999999999999999999999776667777888888888877644444434441....333333333333 PP

                        AAA_15 252 idkklaeelkkilkkkidkik.kfnykgkkneeieik............................................ 287
                                   ++ ++++ ++  lkk+++++k  ++ +++ + e+e                                              
  gi|15669512|ref|NP_248322.1| 809 QKTEIETGIE-YLKKDVESLKaRLKEMSNLEKEKEKLtkfveyldkvrrifgrngfqaylrekyvpliqkylneafsefdl 888
                                   3333333322.2444444433333333333333332233455566666777777777777888888888888888888888 PP

                        AAA_15 288 .................ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkel 351
                                                     +  l++++ + G q ++ l+l ++ a+    + ++  +++++EP ++L  +    l++ ++++
  gi|15669512|ref|NP_248322.1| 889 pysfveltkdfevrvhaPNGVLTIDNLSGGEQIAVALSLRLAIANAL--IGNRVECIILDEPTVYLDENRRAKLAEIFRKV 967
                                   888888***********9*****************************..*******************************9 PP

                        AAA_15 352 andnktQviitTH 364
                                    +    Q ii TH
  gi|15669512|ref|NP_248322.1| 968 KSIP--QMIIITH 978
                                   9999..9*****9 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.2e-09   7.9e-07       1      55 [.       5      57 ..       5      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.2e-09
                        AAA_29  1 LkrlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpakkvrfN 55
                                  Lk++++ N  +  + +i+++ kg++ ++G++GsGKS+++ A+ + L +a   +fN
  gi|15669512|ref|NP_248322.1|  5 LKEIRMNNFKSHVNSRIKFE-KGIVAIIGENGSGKSSIFEAVFFALFGAG-SNFN 57
                                  7889999999999999***8.889************************99.8898 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.1e-07   7.2e-05      29      89 ..     911     965 ..     896     966 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.1e-07
                       SbcCD_C  29 ssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                    + +lSGGe+ ++++l l +a+a ++  +     +++ ++LDE    lDe+++a+l e+++
  gi|15669512|ref|NP_248322.1| 911 TIDNLSGGEQ-IAVALSLRLAIANALIGN-----RVECIILDEPTVYLDENRRAKLAEIFR 965
                                   5789******.9999******99999995.....89**********************998 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   6.8   1.6e-06     0.001       1     216 [.      27     227 ..      27     251 .. 0.83
   2 ?   -0.6   5.3       1.4   9.5e+02     109     213 ..     269     374 ..     235     388 .. 0.68
   3 ?   -2.6   2.0       5.7   3.8e+03     125     165 ..     421     461 ..     380     559 .. 0.55
   4 !   14.6   2.9   3.4e-05     0.022     106     300 ..     786     981 ..     739     984 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.6e-06
                        AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlers 81 
                                   + ++iG NgsGKS++++a  ++ +             g g++  ++  ++ + ++  +e+ +e ++ ++ ++  +++ +r 
  gi|15669512|ref|NP_248322.1|  27 IVAIIGENGSGKSSIFEAVFFALF-------------GAGSNFNYDTIITKGKKSVYVELDFE-VNGNNYKIIREYDSGRG 93 
                                   579****************99864.............66666666666666666666666666.66666666666666666 PP

                        AAA_21  82 qveeklssvetllesgll.ldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldgl 161
                                   +   kl+ ++++  +++  ++k + e   v+ +++ ++  +++++ +k+ls++++++l+ ++ l+ i+++   + ++ +  
  gi|15669512|ref|NP_248322.1|  94 GA--KLYKNGKPYATTISaVNKAVNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSEKLETVAKLLGIDEFEKCYQKMGEIV 172
                                   66..99999999999887589999999999999999999999999999999999999999999999999988877777777 PP

                        AAA_21 162 rkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderl 216
                                    +++++l +i +++ ++ +  + l+  +++l + + +l+ ++++ ++i++++e++
  gi|15669512|ref|NP_248322.1| 173 KEYEKRLERIEGELNYKENYEKELKNKMSQLEEKNKKLMEINDKLNKIKKEFEDI 227
                                   7779999999999999999999999999999999999999999999999999887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                        AAA_21 109 dvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke..rigllnifadyfgfakekrllqr 187
                                    ++  ear++    +++++k +s+ ++++++ ++++ + ++  ++ l+l   l     +i  l  f++  ++ + ++ l+ 
  gi|15669512|ref|NP_248322.1| 269 LNTVVEARETLNRHKDEYEKYKSLVDEIRKIESRLRELKSHYEDY-LKLTKQLEIIkgDIEKLKEFINKSKYRDDIDNLDT 348
                                   344445555555556666666666666666666665555555555.55555555557************************ PP

                        AAA_21 188 lvrslklveielsdlgegeeliasvd 213
                                   l++++k+   +++++++  e+ +  +
  gi|15669512|ref|NP_248322.1| 349 LLNKIKDEIERVETIKDLLEELKNLN 374
                                   *******9999999998887776655 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.7
                        AAA_21 125 fslkelsvsepndlqfgkaltditsrawsllllldglrker 165
                                   ++++e+++++ ++++++ +      +++s++ +l ++ +++
  gi|15669512|ref|NP_248322.1| 421 KKSIEKNINDLETRINKLLEETKNIDIESIENSLKEIEEKK 461
                                   33333333333333333333222222222222222222222 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 3.4e-05
                        AAA_21 106 eeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke..rigllnifadyfgfakekrl 184
                                   eee +++ e ++++ ++ ++++ +++ +e  +++ +k+  ++++r+ +   l  +  k      +l+ +++ fg +  + +
  gi|15669512|ref|NP_248322.1| 786 EEEHKKIKELYENKRQELDNVREQKTEIETGIEYLKKDVESLKARLKEMSNLEKEKEKLtkFVEYLDKVRRIFGRNGFQAY 866
                                   334455666666777777777777777777777777777777777776555555555444433333333333333333333 PP

                        AAA_21 185 lqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkg......s 259
                                   l++ + +l +     +++++++e   + +++++ +++   ++   + l++++lS G + + al + l+ a+  +       
  gi|15669512|ref|NP_248322.1| 867 LREKYVPLIQK----YLNEAFSEFDLPYSFVELTKDFEVRVHAPNGVLTIDNLSGGEQIAVALSLRLAIAN--AlignrvE 941
                                   33333333333....33333333333333333334555666666678*************98888777777..3347799* PP

                        AAA_21 260 llliDEpEngLHPkllrrllell.kelsrngaQviltTHSpl 300
                                    +++DEp   L+  + ++l+e++ k +s    Q i+ TH  +
  gi|15669512|ref|NP_248322.1| 942 CIILDEPTVYLDENRRAKLAEIFrKVKSI--PQMIIITHHRE 981
                                   ***********************666666..********765 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.6    0.0025       1.7      29      66 ..     195     232 ..     170     238 .. 0.62
   2 ?    1.0   0.1      0.89   5.9e+02      25      64 ..     260     299 ..     242     311 .. 0.82
   3 ?    1.8   0.0       0.5   3.3e+02      16      59 ..     292     335 ..     287     338 .. 0.81
   4 ?    5.3   3.1     0.043        28      11      61 ..     341     380 ..     320     388 .. 0.60
   5 ?    2.7   5.4      0.27   1.8e+02      12      63 ..     427     483 ..     415     503 .. 0.52
   6 ?    6.8   2.5     0.014       9.5       7      63 ..     489     544 ..     487     564 .. 0.69
   7 ?    2.7   4.9      0.26   1.7e+02      35      60 ..     571     596 ..     544     653 .. 0.68
   8 ?    4.8   1.3      0.06        40       9      55 ..     640     691 ..     638     741 .. 0.63
   9 !    8.8   2.1    0.0034       2.3       7      62 ..     759     814 ..     754     815 .. 0.90
  10 !    7.5   0.1    0.0084       5.6       9      57 ..     806     860 ..     803     889 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0025
                       NPV_P10  29 dvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                   ++++++ +++e n+kL +++++L++++++ e+I+++ n
  gi|15669512|ref|NP_248322.1| 195 ELKNKMSQLEEKNKKLMEINDKLNKIKKEFEDIEKLFN 232
                                   45555555555555555555555555555555555554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.89
                       NPV_P10  25 qqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                   q+++ ++ +l++v e  e L++  ++ ++ ++ v++I +i
  gi|15669512|ref|NP_248322.1| 260 QELKILEYDLNTVVEARETLNRHKDEYEKYKSLVDEIRKI 299
                                   6677889999999999999999999999999988888876 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.5
                       NPV_P10  16 vddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59 
                                   + d +  +++++ ++++  +d  +l+++L+ +   +++l++ ++
  gi|15669512|ref|NP_248322.1| 292 LVDEIRKIESRLRELKSHYEDYLKLTKQLEIIKGDIEKLKEFIN 335
                                   55677888899999999999999999999999988888887665 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.043
                       NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                   +        +d l++ +++++++++ v+ +++ L+    +L++l++++e+I
  gi|15669512|ref|NP_248322.1| 341 D-------DIDNLDTLLNKIKDEIERVETIKDLLE----ELKNLNEEIEKI 380
                                   3.......445555555555555555554444333....344455555555 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.27
                       NPV_P10  12 dikavddkVdalqqqv.....ddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                   +i++++++++ l ++      +++++ l++++e ++ L++++++  el++k+ +I++
  gi|15669512|ref|NP_248322.1| 427 NINDLETRINKLLEETknidiESIENSLKEIEEKKKVLENLQKEKIELNKKLGEINS 483
                                   455555555554443322222444455555555555555544444444444444443 PP

  == domain 6  score: 6.8 bits;  conditional E-value: 0.014
                       NPV_P10   7 lvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                     I+++ k+v+ k    ++ +d+ + +++ +++ +++L++  ++L+e+++k+ +I++
  gi|15669512|ref|NP_248322.1| 489 KKILDELKEVEGKCPLCKTPIDENK-KMELINQHKTQLNNKYTELEEINKKIREIEK 544
                                   5677777777777777777776643.4666677777777777777777777777753 PP

  == domain 7  score: 2.7 bits;  conditional E-value: 0.26
                       NPV_P10  35 pdvtelnekLdaqsaqLaeletkven 60 
                                    +++el+ kL +  +qL+e+++k++n
  gi|15669512|ref|NP_248322.1| 571 SQIEELELKLKNYKEQLDEINKKISN 596
                                   45666777777777777777774443 PP

  == domain 8  score: 4.8 bits;  conditional E-value: 0.06
                       NPV_P10   9 IradikavddkVdalq.....qqvddvqenlpdvtelnekLdaqsaqLaele 55 
                                   Ir+ ik++++ V+  +     +++++++e+ ++++ l++kL+++ ++ +el 
  gi|15669512|ref|NP_248322.1| 640 IRNRIKEIENIVSGWNkekcrEELNKLREDEREINRLKDKLNELKNKEKELI 691
                                   6666666666665443111115679999999999999999998876544443 PP

  == domain 9  score: 8.8 bits;  conditional E-value: 0.0034
                       NPV_P10   7 lvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                   l + ++i++++++++ ++q++d+++ n ++ ++++e  ++  ++L+++ ++ ++I+
  gi|15669512|ref|NP_248322.1| 759 LEVNKEINDIEERISYINQKLDEINYNEEEHKKIKELYENKRQELDNVREQKTEIE 814
                                   567889****************************************9999888775 PP

  == domain 10  score: 7.5 bits;  conditional E-value: 0.0084
                       NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet......k 57 
                                   +r+  +++++ ++ l++ v+++++ l+++++l+++ +++++ ++ l++       
  gi|15669512|ref|NP_248322.1| 806 VREQKTEIETGIEYLKKDVESLKARLKEMSNLEKEKEKLTKFVEYLDKvrrifgR 860
                                   666778899999****************998777777777666666654445540 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.7e-06    0.0025       1      87 [.       3      87 ..       3     137 .. 0.76
   2 ?   -2.7   0.7       5.7   3.8e+03     158     192 ..     196     229 ..     180     256 .. 0.59
   3 ?   -1.0   0.2       1.6   1.1e+03     157     200 ..     423     467 ..     416     474 .. 0.82
   4 ?   -1.0   0.3       1.6   1.1e+03     155     194 ..     457     496 ..     430     501 .. 0.70
   5 ?   -2.8   1.0       5.9   3.9e+03     158     175 ..     535     552 ..     513     587 .. 0.51
   6 ?   -2.7   0.4       5.6   3.7e+03      78     100 ..     667     689 ..     655     702 .. 0.54
   7 ?   -2.9   0.1       6.4   4.2e+03     158     195 ..     768     808 ..     758     826 .. 0.50
   8 ?   -2.6   0.0       5.2   3.5e+03     153     193 ..     815     854 ..     811     859 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.7e-06
                        AAA_27  1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipertkdnflhdakkLrigavle.eadgeel 82
                                  M l++++++ + +  +++++f+   +++  i+G N +GKs++++A+   lfG   + +++ +  + k  +   l+ e +g++ 
  gi|15669512|ref|NP_248322.1|  3 MILKEIRMNNFKSHVNSRIKFE---KGIVAIIGENGSGKSSIFEAVFFALFGAGSNFNYDTIITKGKKSVYVELDfEVNGNNY 82
                                  8889999999999999999998...89***************************99999988776665555555436666677 PP

                        AAA_27 83 efaRr 87
                                  ++ R+
  gi|15669512|ref|NP_248322.1| 83 KIIRE 87
                                  77765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.7
                        AAA_27 158 lrevleaLeaeadelfkprkskkrainealeelee 192
                                   l++ + +Le++ ++l + + + + +i+++ e++e+
  gi|15669512|ref|NP_248322.1| 196 LKNKMSQLEEKNKKLMEINDKLN-KIKKEFEDIEK 229
                                   33444444444444444444444.44444444443 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.6
                        AAA_27 157 slrevleaLeaeadelfkprkskk.rainealeeleeakkelrea 200
                                   s+++ +++Le++ ++l +++k+ + ++i ++l+e+ee kk l++ 
  gi|15669512|ref|NP_248322.1| 423 SIEKNINDLETRINKLLEETKNIDiESIENSLKEIEEKKKVLENL 467
                                   677888999999999999999999888999999999988887765 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.6
                        AAA_27 155 laslrevleaLeaeadelfkprkskkrainealeeleeak 194
                                   +++ ++vle+L++e+ el k+ ++ + +i++ ++ l+e+k
  gi|15669512|ref|NP_248322.1| 457 IEEKKKVLENLQKEKIELNKKLGEINSEIKRLKKILDELK 496
                                   4455677788888888887777777766666666666655 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 5.9
                        AAA_27 158 lrevleaLeaeadelfkp 175
                                   +++ + ++e++ ++l k+
  gi|15669512|ref|NP_248322.1| 535 INKKIREIEKDIEKLKKE 552
                                   223333333333333333 PP

  == domain 6  score: -2.7 bits;  conditional E-value: 5.6
                        AAA_27  78 dgeelefaRrkgrkktlldaddq 100
                                   +++e e++R k + ++l +++++
  gi|15669512|ref|NP_248322.1| 667 REDEREINRLKDKLNELKNKEKE 689
                                   33444444444444444444433 PP

  == domain 7  score: -2.9 bits;  conditional E-value: 6.4
                        AAA_27 158 lrevleaLeaeadel.fkprkskk.raineal.eeleeakk 195
                                   ++e +  ++++ de+ ++++++kk ++++e + +el+++++
  gi|15669512|ref|NP_248322.1| 768 IEERISYINQKLDEInYNEEEHKKiKELYENKrQELDNVRE 808
                                   55555555566666523333333333333322022222222 PP

  == domain 8  score: -2.6 bits;  conditional E-value: 5.2
                        AAA_27 153 aGlaslrevleaLeaeadelfkprkskkrainealeeleea 193
                                   +G++ l++ +e+L+a+ +e+ + +k+k+ ++++  e l+++
  gi|15669512|ref|NP_248322.1| 815 TGIEYLKKDVESLKARLKEMSNLEKEKE-KLTKFVEYLDKV 854
                                   7899999999999999999988888887.666666655555 PP

>> CEP63  Centrosomal protein of 63 kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7  18.7     4e-06    0.0026      65     168 ..     161     262 ..     146     270 .. 0.87
   2 ?   -0.4  10.7       1.3   8.4e+02      28      95 ..     787     856 ..     783     861 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4e-06
                         CEP63  65 leelekekqelvakyeqqlqklreelsklkrsyekLqrkqlkearekeakskeedrvelsrlnskleefrqkslewekqrl 145
                                    e+  ++  e+v++ye++l++++ el+  k++yek  + ++ + +e ++k+  e + +l++ +++ e+ ++   ewe+++l
  gi|15669512|ref|NP_248322.1| 161 FEKCYQKMGEIVKEYEKRLERIEGELN-YKENYEKELKNKMSQLEE-KNKKLMEINDKLNKIKKEFEDIEKLFNEWENKKL 239
                                   45566667799***************7.699999988999999996.579999**************************** PP

                         CEP63 146 qyqkqvasleaqrkaLaekleli 168
                                   +y k ++ le+ ++aL  k + +
  gi|15669512|ref|NP_248322.1| 240 LYEKFINKLEERKRALELKNQEL 262
                                   **************998776655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
                         CEP63  28 aqtraletrlkireeeLasarnaldekhkEvgllrqqleelekekqelv..akyeqqlqklreelsklkr 95 
                                   ++++ ++   +++ +eL ++r++  e ++ ++ l++ +e+l+++ +e+   +k +++l+k+ e l+k++r
  gi|15669512|ref|NP_248322.1| 787 EEHKKIKELYENKRQELDNVREQKTEIETGIEYLKKDVESLKARLKEMSnlEKEKEKLTKFVEYLDKVRR 856
                                   4555555555667777777777777777777777777777777777765223555667777777777766 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   6.4      0.17   1.1e+02      37      89 ..     171     223 ..     146     231 .. 0.72
   2 ?    1.2  11.8       1.1   7.1e+02       3      88 ..     238     332 ..     236     336 .. 0.72
   3 !   18.3  12.7   4.8e-06    0.0032       3      89 ..     461     552 ..     459     554 .. 0.92
   4 ?   -0.2   7.7       2.8   1.9e+03      18      80 ..     664     721 ..     653     729 .. 0.56
   5 ?    0.3  13.4         2   1.3e+03      16      88 ..     754     829 ..     740     853 .. 0.45

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.17
                PRKG1_interact  37 lkqqrqesvskrssllelekrerrslerkiseleeelkeleeLraenqrLkdE 89 
                                   + ++ ++++++ +  l+ +++ +++l++k+s+lee++k+l e+  + +++k+E
  gi|15669512|ref|NP_248322.1| 171 IVKEYEKRLERIEGELNYKENYEKELKNKMSQLEEKNKKLMEINDKLNKIKKE 223
                                   44444445555566677777888888888889999999999999888888888 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.1
                PRKG1_interact   3 kkLYeeekeenerLkreLeelekelselkseleklkqqrqe..svskrssllelekrerrslerkisel....eeel...k 74 
                                   k LYe+  ++ e+ kr Le  ++el+ l+  l+++ + r++  + +++ +  +    e r++e ++ el    e+ l   k
  gi|15669512|ref|NP_248322.1| 238 KLLYEKFINKLEERKRALELKNQELKILEYDLNTVVEARETlnRHKDEYEKYKSLVDEIRKIESRLRELkshyEDYLkltK 318
                                   789*****************************9998775544444444444444455666677777766333333334447 PP

                PRKG1_interact  75 eleeLraenqrLkd 88 
                                   +le ++ + ++Lk+
  gi|15669512|ref|NP_248322.1| 319 QLEIIKGDIEKLKE 332
                                   88888899999997 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 4.8e-06
                PRKG1_interact   3 kkLYeeekeenerLkreLeelekelselkseleklkqqrqe.....svskrssllelekrerrslerkiseleeelkelee 78 
                                   kk+ e+ ++e+ +L ++L e++ e+++lk+ l++lk+ + +        ++++ +el ++++ +l++k++elee +k+++e
  gi|15669512|ref|NP_248322.1| 461 KKVLENLQKEKIELNKKLGEINSEIKRLKKILDELKEVEGKcplckTPIDENKKMELINQHKTQLNNKYTELEEINKKIRE 541
                                   8999*******************************988655777766678899999************************* PP

                PRKG1_interact  79 LraenqrLkdE 89 
                                   + ++ ++Lk+E
  gi|15669512|ref|NP_248322.1| 542 IEKDIEKLKKE 552
                                   *********99 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.8
                PRKG1_interact  18 reLeelekelselkseleklkqqrqesvskrssllelekrerrslerkis..eleeelkeleeLr 80 
                                   ++L+e e+e+++lk +l++lk       +k+++l+e+e+r + + ++      l e+l+el++++
  gi|15669512|ref|NP_248322.1| 664 NKLREDEREINRLKDKLNELK-------NKEKELIEIENRRSLKFDKYKEylGLTEKLEELKNIK 721
                                   456666677777777777776.......4456677777666665554322124466666666555 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 2
                PRKG1_interact  16 LkreLeelekelselkseleklkqq......rqesvskrssllelekrerrslerkiseleeel....keleeLraenqrL 86 
                                   L +++ e++ke+++++++++ ++q+      ++e+ +k ++l e +++e  ++ ++ +e+e  +    k +e L+      
  gi|15669512|ref|NP_248322.1| 754 LNNKILEVNKEINDIEERISYINQKldeinyNEEEHKKIKELYENKRQELDNVREQKTEIETGIeylkKDVESLK------ 828
                                   566666666666666666666664432221123344444444444444444444444444222222223333333...... PP

                PRKG1_interact  87 kd 88 
                                    +
  gi|15669512|ref|NP_248322.1| 829 -A 829
                                   .2 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5  14.0       3.1   2.1e+03      39      94 ..     180     253 ..     158     264 .. 0.62
   2 !   17.8   6.7   6.4e-06    0.0043      15      97 ..     280     358 ..     267     362 .. 0.85
   3 ?    0.6   3.6       1.4   9.5e+02      37      69 ..     369     397 ..     354     412 .. 0.42
   4 ?    5.7  10.7     0.036        24      16      98 ..     406     487 ..     395     490 .. 0.76
   5 ?    5.7  11.8     0.038        25      11      79 ..     519     593 ..     509     620 .. 0.59
   6 ?    2.7   6.7      0.31     2e+02       3      77 ..     552     627 ..     551     649 .. 0.85
   7 ?   -0.9  10.7       4.3   2.9e+03      29      89 ..     664     724 ..     609     729 .. 0.70
   8 ?    6.8   3.6     0.017        11      19      92 ..     702     782 ..     699     785 .. 0.90
   9 ?    3.1  10.7      0.24   1.6e+02      25      98 ..     759     833 ..     739     836 .. 0.79
  10 ?    0.8   6.2       1.2   8.2e+02       7      69 ..     786     847 ..     782     857 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.1
                  Occludin_ELL  39 seLe..............relkelkegsk...eykkieeeilqeykklkk.dpeyqekkkrceyLkekLshiKk 94 
                                   +++e              +++++l+e++k   e+++  ++i +e+++++k  +e+ +kk   e+  +kL+  K+
  gi|15669512|ref|NP_248322.1| 180 ERIEgelnykenyekelkNKMSQLEEKNKklmEINDKLNKIKKEFEDIEKlFNEWENKKLLYEKFINKLEERKR 253
                                   33333333333333333377777777777666777777788888888888777777777777888888776555 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 6.4e-06
                  Occludin_ELL  15 aeFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKkl 95 
                                   +  ++eY++Yk+l +e+++++++++eL+++ +++ + +k+ + i+ + ++++k++ ++++y+++   ++ L   L+ iK  
  gi|15669512|ref|NP_248322.1| 280 NRHKDEYEKYKSLVDEIRKIESRLRELKSHYEDYLKLTKQLEIIKGD-IEKLKEFINKSKYRDDIDNLDTL---LNKIKDE 356
                                   56789******************************************.899****9999998876655555...6667776 PP

                  Occludin_ELL  96 ik 97 
                                   i+
  gi|15669512|ref|NP_248322.1| 357 IE 358
                                   65 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.4
                  Occludin_ELL  37 kfseLerelkelkegskeykkieeeilqeykkl 69 
                                   ++++L++e+++ +    +yk+i ee  + y+k+
  gi|15669512|ref|NP_248322.1| 369 ELKNLNEEIEKIE----KYKRICEECKEYYEKY 397
                                   3333333333332....4444444422222222 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.036
                  Occludin_ELL  16 eFnkeYkeYkelhaeleevskkfseLerelkelkegsk..eykkieeeilqeykklkkdpeyqek.kkrceyLkekLshiK 93 
                                   e+nk   eY +l +e ++++k++++Le+++++l e++k   +++ie    +++k+++++++ +e+ +k+  +L++kL  i 
  gi|15669512|ref|NP_248322.1| 406 EYNKLTLEYITLLQEKKSIEKNINDLETRINKLLEETKniDIESIE----NSLKEIEEKKKVLENlQKEKIELNKKLGEIN 482
                                   67888889*************************9999944555555....5566665555554441444568999999999 PP

                  Occludin_ELL  94 klike 98 
                                   + ik 
  gi|15669512|ref|NP_248322.1| 483 SEIKR 487
                                   88875 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.038
                  Occludin_ELL  11 erYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegsk......eykkieeeilqeykklkkdpeyqekk 79 
                                   ++ k++ n++Y+e  e++++++e++k++++L++e+++ ++ ++      e ++ +ee+  ++k++k++ +  +kk
  gi|15669512|ref|NP_248322.1| 519 NQHKTQLNNKYTELEEINKKIREIEKDIEKLKKEIDKEENLKTlktlylEKQSQIEELELKLKNYKEQLDEINKK 593
                                   566777777777777777777777777777776666655544444444444555555555555555555544444 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.31
                  Occludin_ELL   3 eIksaeqrerYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqe 77 
                                   eI ++e+ ++ k+ + ++ ++  el+ +l+++++++ e++++++++  + k +++i e+i ++++k+k+  ++y++
  gi|15669512|ref|NP_248322.1| 552 EIDKEENLKTLKTLYLEKQSQIEELELKLKNYKEQLDEINKKISNYVINGKPVDEILEDIKSQLNKFKNfYNQYLS 627
                                   678888888888888888999999999999999999999999999999999****************987777765 PP

  == domain 7  score: -0.9 bits;  conditional E-value: 4.3
                  Occludin_ELL  29 aeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekL 89 
                                   ++l+e ++++++L+++l+elk+++ke  +ie++   ++ k+k+     ek ++++ +k+ L
  gi|15669512|ref|NP_248322.1| 664 NKLREDEREINRLKDKLNELKNKEKELIEIENRRSLKFDKYKEYLGLTEKLEELKNIKDGL 724
                                   3444555667777777777777777777777776666666666666666666555555555 PP

  == domain 8  score: 6.8 bits;  conditional E-value: 0.017
                  Occludin_ELL  19 keYkeYkelhaeleevskkfseLe.......relkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshi 92 
                                   ++YkeY  l ++lee+++    Le       +++ + ++ +++y+k   ei+ + k l+ ++e  + ++r+ y+++kL+ i
  gi|15669512|ref|NP_248322.1| 702 DKYKEYLGLTEKLEELKNIKDGLEeiynicnSKILAIDNIKRKYNKEDIEIYLNNKILEVNKEINDIEERISYINQKLDEI 782
                                   68***********99999999999888888888888888888999999999999999999******************987 PP

  == domain 9  score: 3.1 bits;  conditional E-value: 0.24
                  Occludin_ELL  25 kelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekkkrceyLkekLshiKklike 98 
                                    e+++e++++++++s ++++l+e + +++e+kki+e   ++ ++l +  ++  e ++ +eyLk+  + +K+++ke
  gi|15669512|ref|NP_248322.1| 759 LEVNKEINDIEERISYINQKLDEINYNEEEHKKIKELYENKRQELDNvREQKTEIETGIEYLKKDVESLKARLKE 833
                                   578899999999999999999999999999999998855566666554444455566789***********9987 PP

  == domain 10  score: 0.8 bits;  conditional E-value: 1.2
                  Occludin_ELL   7 aeqrerYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykkl 69 
                                   +e++++ k+ ++++ +e  ++ ++ +e++  ++ L++++++lk + ke++++e+e  +++ k+
  gi|15669512|ref|NP_248322.1| 786 EEEHKKIKELYENKRQELDNVREQKTEIETGIEYLKKDVESLKARLKEMSNLEKE-KEKLTKF 847
                                   6777788888888888888888888888888888888888888888888888888.6666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00041      0.27      22      52 ..      23      53 ..       6     128 .. 0.81
   2 ?   -1.6   0.2       4.6   3.1e+03     111     147 ..     292     330 ..     231     404 .. 0.60
   3 ?   -1.9   0.1       5.8   3.8e+03      53      53 ..     596     596 ..     488     685 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00041
                        AAA_16 22 grpelvllsGesGvGKsslvrellralekdg 52
                                   + ++v ++Ge G+GKss+ ++++ al ++g
  gi|15669512|ref|NP_248322.1| 23 FEKGIVAIIGENGSGKSSIFEAVFFALFGAG 53
                                  44599*****************998887773 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.6
                        AAA_16 111 lagaea...srllellkrllallsrderplvlvlDdlqwa 147
                                   l ++++   srl+el ++  ++l+ +++ l ++  d++++
  gi|15669512|ref|NP_248322.1| 292 LVDEIRkieSRLRELKSHYEDYLKLTKQ-LEIIKGDIEKL 330
                                   3333333324444444444455554333.55544444443 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.8
                        AAA_16  53 g 53 
                                    
  gi|15669512|ref|NP_248322.1| 596 N 596
                                   0 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  16.6     0.023        16     160     250 ..     167     259 ..     153     269 .. 0.50
   2 ?    6.0  19.5    0.0072       4.8     147     265 ..     261     392 ..     256     406 .. 0.61
   3 ?    8.8  18.1     0.001      0.68     169     260 ..     407     502 ..     395     508 .. 0.81
   4 ?   11.2  19.3   0.00018      0.12     133     270 ..     514     649 ..     512     656 .. 0.79
   5 ?    1.3   7.6      0.19   1.2e+02     158     232 ..     611     690 ..     601     707 .. 0.43
   6 ?   -0.4  12.0      0.62   4.1e+02     154     248 ..     636     726 ..     629     749 .. 0.75
   7 ?   -1.8  21.4       1.7   1.1e+03     142     258 ..     674     794 ..     655     798 .. 0.77
   8 ?    4.7  19.7     0.017        11     137     264 ..     717     845 ..     714     861 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.023
                          Spc7 160 kqeeeldellpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkaeieekkkelaelqeqleeleekiee 238
                                   k  e ++e+ ++le+ + el+ + + ++e ++++++++  +++L e+ ++l+++k+e e  +k  +e ++++   e+ i++
  gi|15669512|ref|NP_248322.1| 167 KMGEIVKEYEKRLERIEGELNYKENYEKELKNKMSQLEekNKKLMEINDKLNKIKKEFEDIEKLFNEWENKKLLYEKFINK 247
                                   333333444444444444444444444444444444322255566666666666666666666666666665555566666 PP

                          Spc7 239 lkeqkseleeei 250
                                   l+e+k+ le + 
  gi|15669512|ref|NP_248322.1| 248 LEERKRALELKN 259
                                   665555555444 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0072
                          Spc7 147 nlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles.............idkeeLeelreelaelk.. 212
                                   +l++le d +++ + +e l++ ++e+e+ +++l +e++k++++ +el+s             i k ++e+l+e +++ k  
  gi|15669512|ref|NP_248322.1| 261 ELKILEYDLNTVVEARETLNRHKDEYEK-YKSLVDEIRKIESRLRELKShyedylkltkqleIIKGDIEKLKEFINKSKyr 340
                                   5666777777777777777777777654.4445555555555555555544445555555555577778888777654422 PP

                          Spc7 213 aeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwse 265
                                    +i+++ + l++ ++++e++e+ i++l e+ ++l+eei++ e++++ c++++e
  gi|15669512|ref|NP_248322.1| 341 DDIDNLDTLLNKIKDEIERVET-IKDLLEELKNLNEEIEKIEKYKRICEECKE 392
                                   6788888888888888877754.555556677777777766666655555544 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.001
                          Spc7 169 lpeleeekaeleeeleklqeaaeelesidkeeLeelr....eelaelkaeieekkkelaelqeqleeleekieelkeqkse 245
                                   +++l+ e+ +l +e +++++  ++le+  ++ Lee++    e++++  +eieekkk l++lq+++ el++k+ e+++++++
  gi|15669512|ref|NP_248322.1| 407 YNKLTLEYITLLQEKKSIEKNINDLETRINKLLEETKnidiESIENSLKEIEEKKKVLENLQKEKIELNKKLGEINSEIKR 487
                                   677888888888888888888888888888888888844444777778899999999999999999999999999999999 PP

                          Spc7 246 leeeiaeaervleec 260
                                   l++ + e ++v  +c
  gi|15669512|ref|NP_248322.1| 488 LKKILDELKEVEGKC 502
                                   999999999988777 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00018
                          Spc7 133 RmqllegLkegleenlegleedkelLekqeeeldellpeleeeka.eleeeleklqeaaeelesidkeeLeelreelaelk 212
                                   +m+l+++ k++l++++++lee ++++ + e+ +++l++e+++e++ +  ++l  ++  + ++e++ + +L++++e+l+e++
  gi|15669512|ref|NP_248322.1| 514 KMELINQHKTQLNNKYTELEEINKKIREIEKDIEKLKKEIDKEENlKTLKTLYLEK--QSQIEEL-ELKLKNYKEQLDEIN 591
                                   57788888888888888888888888888888888888888776632333333333..3445554.578999999999999 PP

                          Spc7 213 aeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsr 270
                                   ++i++   + + + e le++++++++ k+ ++++ ++++  ++v ee  + + +e+++
  gi|15669512|ref|NP_248322.1| 592 KKISNYVINGKPVDEILEDIKSQLNKFKNFYNQYLSAVSYLNSVDEEGIRNRIKEIEN 649
                                   9999999999999999999999999999999999999999999999998888888876 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.19
                          Spc7 158 Lekqeeeldellpeleeekaelee.eleklqeaaeeles....idkeeLeelreelaelkaeieekkkelaelqeqleel 232
                                   +++q ++++++++++ +  + l++   e ++++ +e+e+     +ke+ +e  ++l+e + ei+++k++l+el+++ +el
  gi|15669512|ref|NP_248322.1| 611 IKSQLNKFKNFYNQYLSAVSYLNSvDEEGIRNRIKEIENivsgWNKEKCREELNKLREDEREINRLKDKLNELKNKEKEL 690
                                   33333333333333333333332211222333444444422223444444444444444445555555555554444443 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 0.62
                          Spc7 154 dkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleelee 234
                                   d+e + ++ +e+++++   ++  ++ +eel+kl+e ++e++ + k++L+el+++ +    eie+++    ++ ++   l+e
  gi|15669512|ref|NP_248322.1| 636 DEEGIRNRIKEIENIVSGWNK--EKCREELNKLREDEREINRL-KDKLNELKNKEK-ELIEIENRRSLKFDKYKEYLGLTE 712
                                   677777777778887777765..56789999999999997774.788888888744.457888888888888888888888 PP

                          Spc7 235 kieelkeqkselee 248
                                   k+eelk+ k+ lee
  gi|15669512|ref|NP_248322.1| 713 KLEELKNIKDGLEE 726
                                   88888776665554 PP

  == domain 7  score: -1.8 bits;  conditional E-value: 1.7
                          Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles......idkeeLeelreelaelkaeie 216
                                   ++l+++l++l++ +++L + e+   +l+ +  +e+  l+e+le+l++ ++ le+      ++   + +++++ ++ + ei 
  gi|15669512|ref|NP_248322.1| 674 NRLKDKLNELKNKEKELIEIENR-RSLKFDKYKEYLGLTEKLEELKNIKDGLEEiynicnSKILAIDNIKRKYNKEDIEIY 753
                                   45666677777777777766554.445555555666899999999997777777666733445678899999999999999 PP

                          Spc7 217 ekkkelaelqeqleeleekieelkeqkseleeeiaeaervle 258
                                    +++++ e++++++++ee+i+ ++++ +e++ + +e+++++e
  gi|15669512|ref|NP_248322.1| 754 -LNNKILEVNKEINDIEERISYINQKLDEINYNEEEHKKIKE 794
                                   .999999**********************9999999999987 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.017
                          Spc7 137 legLkegleenlegleedkelLekqeeel..dellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaei 215
                                   l+++k+glee++++ ++    +++ + +   +++   l+++  e+++e+++++e+   ++  + +e++   ee +++k+ +
  gi|15669512|ref|NP_248322.1| 717 LKNIKDGLEEIYNICNSKILAIDNIKRKYnkEDIEIYLNNKILEVNKEINDIEERISYIN-QKLDEINYNEEEHKKIKELY 796
                                   678888888888888888888888777773345666677777788899999988877644.47888888888888888888 PP

                          Spc7 216 eekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgws 264
                                   e+k++el++++eq++e+e+ ie lk+  ++l+++++e  ++ +e+++ +
  gi|15669512|ref|NP_248322.1| 797 ENKRQELDNVREQKTEIETGIEYLKKDVESLKARLKEMSNLEKEKEKLT 845
                                   8888888888888888888888888888888888888877777766554 PP

>> zf-AD  Zinc-finger associated domain (zf-AD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   0.00039      0.26      16      73 ..     353     411 ..     340     414 .. 0.76
   2 ?   -1.3   0.1       3.9   2.6e+03      54      73 ..     613     632 ..     612     634 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00039
                         zf-AD  16 ifdtsnss.islaeileeltglele..pddslpekiCesCleklqefyeFrekcveanell 73 
                                   i d+ + + +++ ++leel +l+ e  + +++ + iCe+C+e  ++  e+ ek+ve n+l 
  gi|15669512|ref|NP_248322.1| 353 IKDEIE-RvETIKDLLEELKNLNEEieKIEKYKR-ICEECKEYYEKYLELEEKAVEYNKLT 411
                                   333333.258999999999999888756666666.********************999876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.9
                         zf-AD  54 eklqefyeFrekcveanell 73 
                                   ++l++f +F+++++ a ++l
  gi|15669512|ref|NP_248322.1| 613 SQLNKFKNFYNQYLSAVSYL 632
                                   799*********99887666 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9  32.0     0.074        49     258     427 ..     146     318 ..     110     320 .. 0.88
   2 ?   -3.7  75.7       3.7   2.5e+03      19     327 ..     192     497 ..     173     499 .. 0.87
   3 ?   12.3  45.5   5.2e-05     0.034     220     430 ..     420     622 ..     414     631 .. 0.91
   4 ?    7.4  43.1    0.0016       1.1      90     309 ..     526     746 ..     510     756 .. 0.82
   5 ?   10.9  20.7   0.00013     0.089      99     188 ..     754     842 ..     731     859 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.074
                                   HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGG. CS
                          EzrA 258 ekkieeilerlkeleledveeelktieeeidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlkqsYe. 337
                                   ++k+e++ ++l   e+e++ +++ +i +e+++  + +e E + k+++ek+lk+  ++le+ +k++ e++++l+++k+++e 
  gi|15669512|ref|NP_248322.1| 146 SEKLETVAKLLGIDEFEKCYQKMGEIVKEYEKRLERIEGELNYKENYEKELKNKMSQLEEKNKKLMEINDKLNKIKKEFEd 226
                                   6889999999999999***************************************************************55 PP

                                   ...SSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          EzrA 338 ...LseeeleklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreq 415
                                      L +e+ +k   +ek +++le++ + le k +e k+   +l+  + e+ e+l++ +++ e+++  ++++rk E+r re 
  gi|15669512|ref|NP_248322.1| 227 iekLFNEWENKKLLYEKFINKLEERKRALELKNQELKILEYDLNTVV-EARETLNRHKDEYEKYKSLVDEIRKIESRLREL 306
                                   55588999999999999999999999999999999999888887665.57899***************************9 PP

                                   HHHHHHHHHHHH CS
                          EzrA 416 ldeikkelkeik 427
                                    ++++  lk +k
  gi|15669512|ref|NP_248322.1| 307 KSHYEDYLKLTK 318
                                   999999998887 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.7
                                   XXX-THHHHHHHHHHHHHHHHHHHHHTTTSSS-S---TTTHHHHHHHHHHHHHHHHHHTHHHHHT-GGGT--S-SHHHHHT CS
                          EzrA  19 lrkkikkeideLeerkneiknlpvqeelskvkklnltgeseekfeewkkkwdeiktkklpeieellfeaeelldkykfkka 99 
                                   + k++k++  +Lee+ +++++  ++++l+k+kk    +++e+ f+ew++k + + +k ++++ee+   +e  +++ k+ ++
  gi|15669512|ref|NP_248322.1| 192 YEKELKNKMSQLEEKNKKLME--INDKLNKIKK--EFEDIEKLFNEWENK-KLLYEKFINKLEERKRALELKNQELKILEY 267
                                   679999999********9986..89******97..7899*********99.66777799********************99 PP

                                   T.HHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH------ CS
                          EzrA 100 k.kklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleniekefse 179
                                     +++ e++e+l++ + +++k ++ ++e+++ e++ re  ++  e+Y +l k+l+  + + ++ +e ++k  ++  +++++
  gi|15669512|ref|NP_248322.1| 268 DlNTVVEARETLNRHKDEYEKYKSLVDEIRKIESRLREL-KSHYEDYLKLTKQLEIIKGDIEKLKEFINK--SKYRDDIDN 345
                                   746789*****************************9976.55567899********************99..689999999 PP

                                   -------.---HHHHHHHHHHHHHHHHHHHHHHHHHH...HHTTTTTTSHH..HHHHHHHHHHHSTTS--SG..GGSSSSS CS
                          EzrA 180 feelten.gdyveakeilkkleeeideleevieeiPe...lleelkkelpk..qleelkegykemkeegYal..eelniek 252
                                   +++l ++ +d +e  e++k+l ee+++l+e ie+i +   ++ee+k+ + k  +lee    y++++ e   l  e+++iek
  gi|15669512|ref|NP_248322.1| 346 LDTLLNKiKDEIERVETIKDLLEELKNLNEEIEKIEKykrICEECKEYYEKylELEEKAVEYNKLTLEYITLlqEKKSIEK 426
                                   99976554889999999999999999999988888662226777777777633345666689******9999555569*** PP

                                   HHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGG CS
                          EzrA 253 eieelekkieeilerlkeleledveeelktieeeidsLyddlekEveAkkeveknlkelkeklehlekqnkelke 327
                                   +i++le++i+++le+ k++++e++e+ lk+iee+ +++ + l+kE+    e +k+l e+++++++l+k+++elke
  gi|15669512|ref|NP_248322.1| 427 NINDLETRINKLLEETKNIDIESIENSLKEIEEK-KKVLENLQKEK---IELNKKLGEINSEIKRLKKILDELKE 497
                                   *******************************998.5677999**96...5899999**********999999986 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 5.2e-05
                                   TTTTSHHHHHHHHHHHHHSTTS--SGGGSSSSSHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          EzrA 220 lkkelpkqleelkegykemkeegYaleelniekeieelekkieeilerlkeleledveeelktieeeidsLyddlekEveA 300
                                    kk + k++++l++ ++++ ee  +++  +ie+ ++e+e+k +++le+l++ ++e  +++l +i++ei+ L ++l++    
  gi|15669512|ref|NP_248322.1| 420 EKKSIEKNINDLETRINKLLEETKNIDIESIENSLKEIEEK-KKVLENLQKEKIE-LNKKLGEINSEIKRLKKILDE---- 494
                                   578999********************************998.6788888888885.78999**********999975.... PP

                                   HHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGT CS
                          EzrA 301 kkeveknlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeel 381
                                    keve + + +k+ +++ +k+++ +++  ++l+++Y+  ee  +k+re+ek++++l+k++++ ee+l++ k+ Y e q+++
  gi|15669512|ref|NP_248322.1| 495 LKEVEGKCPLCKTPIDE-NKKMELINQHKTQLNNKYTELEEINKKIREIEKDIEKLKKEIDK-EENLKTLKTLYLEKQSQI 573
                                   68999999999999998.66788999999999999998899999***************998.6789************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                          EzrA 382 eeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrki 430
                                   eele kl++ +e+++ei++++++   + k   e l++ik++l++ k+  
  gi|15669512|ref|NP_248322.1| 574 EELELKLKNYKEQLDEINKKISNYVINGKPVDEILEDIKSQLNKFKNFY 622
                                   ********************************************99865 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0016
                                   -S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHH...HHHHHHHHT--TTTTHHHHHHHHHH CS
                          EzrA  90 lldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklk...ekYrelrkkllanrfsygealeele 167
                                    +++ ++ +++kk++e+e+++++++++i+k  e lk l++   +++++ie+l+   ++Y+e  ++++++  +y    ++++
  gi|15669512|ref|NP_248322.1| 526 NNKYTELEEINKKIREIEKDIEKLKKEIDK-EENLKTLKTLYLEKQSQIEELElklKNYKEQLDEINKKISNYVINGKPVD 605
                                   356678999******************987.4556666666666666666665111667777777777778888888**** PP

                                   HHHHHH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTT.TSHHHHHHHHHHHHHSTTS--SGGG CS
                          EzrA 168 kqleniekefsefeeltengdyveakeilkkleeeideleevieeiPelleelkk.elpkqleelkegykemkeegYalee 247
                                   + le+i++++++f+++   ++y+ a  +l++++ee   +++ i+ei ++++  +k +  ++l++l+e  +e  + + +l e
  gi|15669512|ref|NP_248322.1| 606 EILEDIKSQLNKFKNFY--NQYLSAVSYLNSVDEE--GIRNRIKEIENIVSGWNKeKCREELNKLREDEREINRLKDKLNE 682
                                   **************986..68*************7..6899**********98762699********************** PP

                                   S.SSSSHHHHHHHHHHHHHHHHTT.--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSS CS
                          EzrA 248 l.niekeieelekkieeilerlke.leledveeelktieeeidsLyddlekEveAkkeveknlk 309
                                   l n eke+ e+e++ +  +++ ke l l++  eelk+i++ ++++y++ +  + A ++++++ +
  gi|15669512|ref|NP_248322.1| 683 LkNKEKELIEIENRRSLKFDKYKEyLGLTEKLEELKNIKDGLEEIYNICNSKILAIDNIKRKYN 746
                                   9999***************99988479********************99988888888777655 PP

  == domain 5  score: 10.9 bits;  conditional E-value: 0.00013
                                   TTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH------ CS
                          EzrA  99 akkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleniekefse 179
                                   +++k+ e+++e++++ee+i  i+++l+e+  +ee++++ i++l e+ r+  +++++++ + ++ +e+l+k++e ++ +++e
  gi|15669512|ref|NP_248322.1| 754 LNNKILEVNKEINDIEERISYINQKLDEINYNEEEHKK-IKELYENKRQELDNVREQKTEIETGIEYLKKDVESLKARLKE 833
                                   579999*************************9999876.5666666666667899************************** PP

                                   --------- CS
                          EzrA 180 feeltengd 188
                                   +++l ++++
  gi|15669512|ref|NP_248322.1| 834 MSNLEKEKE 842
                                   ***986654 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1         1   6.8e+02      21      32 ..      30      41 ..      25      67 .. 0.86
   2 ?   -2.1   0.0       1.6   1.1e+03     475     493 ..      71      89 ..      56      94 .. 0.87
   3 ?   -2.0  14.3       1.6     1e+03      87     181 ..     168     258 ..     159     274 .. 0.72
   4 ?    7.6  33.5     0.002       1.3     268     470 ..     274     481 ..     269     494 .. 0.78
   5 ?    9.2  25.9   0.00065      0.43     324     470 ..     455     597 ..     449     620 .. 0.87
   6 ?    7.9  29.8    0.0015         1     255     442 ..     499     693 ..     489     734 .. 0.60
   7 ?    8.3  32.3    0.0012      0.77     278     572 ..     668     981 ..     655     997 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1
                        AAA_13 21 iYGwNGaGKTtL 32
                                  i G NG+GK+++
  gi|15669512|ref|NP_248322.1| 30 IIGENGSGKSSI 41
                                  77********97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                        AAA_13 475 leLkfeeekkgYrivrkgg 493
                                    eL+fe ++++Y+i+r+ +
  gi|15669512|ref|NP_248322.1|  71 VELDFEVNGNNYKIIREYD 89 
                                   589*************855 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.6
                        AAA_13  87 LGeesiekqekieklkkeikkleekleaaeaqlqkaekekkklekeledeawkkivkkknsalsealkglkyeekfkerll 167
                                   +Ge  +e ++++e++++e++ +e+  ++ +++ +++e+++kkl + ++d++ k i kk+ +++++ ++  ++++   e+++
  gi|15669512|ref|NP_248322.1| 168 MGEIVKEYEKRLERIEGELNYKENYEKELKNKMSQLEEKNKKLME-INDKLNK-I-KKEFEDIEKLFNEWENKKLLYEKFI 245
                                   567778888888888888888888888888888888887766666.7888866.5.6788888888888888888888888 PP

                        AAA_13 168 kelkkknrkaaell 181
                                   ++l++  + a el+
  gi|15669512|ref|NP_248322.1| 246 NKLEER-KRALELK 258
                                   888875.2333333 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.002
                        AAA_13 268 erkaaLeahFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelka..eaealeeqLkglqralea 346
                                   e +++L++h d+ + ek+++L + i k+es+ +el+  +++  +  ++ ++ + d+e+lk+  ++++ ++ +++l   l++
  gi|15669512|ref|NP_248322.1| 274 EARETLNRHKDE-Y-EKYKSLVDEIRKIESRLRELKSHYEDYLKLTKQLEIIKGDIEKLKEfiNKSKYRDDIDNLDTLLNK 352
                                   568999999887.5.559*****************************9************97777889999**99888777 PP

                        AAA_13 347 KrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaiek 427
                                    ++e+ +  +++++ ++++++++++++i++  +   e  + +e+  e  +k++e+   ++l+ e+ ++ +++k++ek+i++
  gi|15669512|ref|NP_248322.1| 353 IKDEIERVETIKDLLEELKNLNEEIEKIEKYKRICEECKEYYEKYLELEEKAVEY---NKLTLEYITLLQEKKSIEKNIND 430
                                   7777777667899999999999999888877666555555555555555566666...56666666677788888888888 PP

                        AAA_13 428 lekelkeeeaelkkleee........ikeLekqlrdekpaaeeinkeLkaf 470
                                   le+++++  +e+k+++ e        i+e++k l++ ++   e+nk+L ++
  gi|15669512|ref|NP_248322.1| 431 LETRINKLLEETKNIDIEsienslkeIEEKKKVLENLQKEKIELNKKLGEI 481
                                   888888888877777766655555558888888888888888888888776 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.00065
                        AAA_13 324 eelkaeaealeeqLkglqraleaKrkepfksve.lesvkakiesikklvaeineliakhNekvanleeekeeakkklelhl 403
                                   +e++++ +++ e+L++ + +l++K  e+ ++++ l+++ +++++++ +    ++ i + N+k++ +++ k+++++k     
  gi|15669512|ref|NP_248322.1| 455 KEIEEK-KKVLENLQKEKIELNKKLGEINSEIKrLKKILDELKEVEGKCPLCKTPIDE-NKKMELINQHKTQLNNKYTE-- 531
                                   444444.444567999999************9988********************975.9999******9999998655.. PP

                        AAA_13 404 veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                   +ee+++++ e +k+++kl+k+i k e +lk  ++   +++ +i+eLe +l++ k+  +eink+++++
  gi|15669512|ref|NP_248322.1| 532 LEEINKKIREIEKDIEKLKKEIDKEE-NLKTLKTLYLEKQSQIEELELKLKNYKEQLDEINKKISNY 597
                                   999999****************9988.8899999999999***********************9998 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.0015
                        AAA_13 255 sdtCpFCgqplpaerkaaLeahFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealee 335
                                   +++Cp C+ p++++ k +L +   ++ ++k+ +Le++ +k+ + + + +eklk+ +d+++  +  +  + e ++++e+le 
  gi|15669512|ref|NP_248322.1| 499 EGKCPLCKTPIDENKKMELINQHKTQLNNKYTELEEINKKIREIE-KDIEKLKKEIDKEENLKTLKTLYLEKQSQIEELEL 578
                                   589*************99999989999999999998888876655.45688888888888888888888888888888888 PP

                        AAA_13 336 qLkglqraleaKrkepfk.svelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlv........... 404
                                   +Lk+ +++l++  k++++  ++ + v++ +e ik++++++++    +N++ + +    +  ++ ++  ++           
  gi|15669512|ref|NP_248322.1| 579 KLKNYKEQLDEINKKISNyVINGKPVDEILEDIKSQLNKFKN---FYNQYLSAVSYLNSVDEEGIRN-RIkeienivsgwn 655
                                   888888888888888777556666666666655544444444...4444444444444333334433.4400000112222 PP

                        AAA_13 405 .eeleseldeykkkykklekaieklekelkeeeaelkkl 442
                                    e++++el+++ ++ +++++   kl+ elk++e+el ++
  gi|15669512|ref|NP_248322.1| 656 kEKCREELNKLREDEREINRLKDKLN-ELKNKEKELIEI 693
                                   24444444444333333332222222.333333333333 PP

  == domain 7  score: 8.3 bits;  conditional E-value: 0.0012
                        AAA_13 278 ddefeekqerLekliekveskkselleklkavsde...asensafeedkeelkaeaealeeqLkglqraleaKrkepfksv 355
                                   +d  e++++rL+++++++++k++el+e  +  s +   ++e+    e+ eelk+ ++ lee  +  ++++ a ++++ ++ 
  gi|15669512|ref|NP_248322.1| 668 ED--EREINRLKDKLNELKNKEKELIEIENRRSLKfdkYKEYLGLTEKLEELKNIKDGLEEIYNICNSKILA-IDNIKRKY 745
                                   44..67888999999999888876655444444333225555556777777777777777776666666554.34555555 PP

                        AAA_13 356 elesv....kakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekel 432
                                   + e++    ++ki +++k++++i+e i+  N+k ++++ ++ee kk  el++ +  ++eld+  +++ ++e+ ie l+k++
  gi|15669512|ref|NP_248322.1| 746 NKEDIeiylNNKILEVNKEINDIEERISYINQKLDEINYNEEEHKKIKELYENK--RQELDNVREQKTEIETGIEYLKKDV 824
                                   544441111456679*********************999999988777776554..6677777777777777777777666 PP

                        AAA_13 433 keeeaelkkleeeikeLekqlrdekpaaeeinkeLkafGlgeleLkfeee.........................kkgYri 488
                                   +  +a+lk++ +     ek+ ++ ++ +e + k  + fG+++++  + e+                         +k +++
  gi|15669512|ref|NP_248322.1| 825 ESLKARLKEMSNL----EKEKEKLTKFVEYLDKVRRIFGRNGFQAYLREKyvpliqkylneafsefdlpysfvelTKDFEV 901
                                   5555555544443....3333333333333333333333333333333333333333344444444333333356666655 PP

                        AAA_13 489 ..vrkggsqaaetLSeGEktaIaflYFlkslk.eddseigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfi 566
                                     +  +g    ++LS GE+ a+a+   l+  +   +   +  + +++D P   LD n     +   +++    k++ Q++i
  gi|15669512|ref|NP_248322.1| 902 rvHAPNGVLTIDNLSGGEQIAVALSLRLAIANaLIG---NRVECIILDEPTVYLDENRRAKLAEIFRKV----KSIPQMII 975
                                   00556788899*************988888882222...355889*************99998888888....79****** PP

                        AAA_13 567 LTHnle 572
                                    TH+ e
  gi|15669512|ref|NP_248322.1| 976 ITHHRE 981
                                   ***966 PP

>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.9   2.6e+03      83     107 ..     213     237 ..     198     262 .. 0.73
   2 ?    6.4   0.2     0.012       7.7      62     135 ..     273     319 ..     257     356 .. 0.62
   3 ?   -0.4   0.0       1.4   9.4e+02      85     117 ..     378     410 ..     322     416 .. 0.70
   4 ?    4.0   0.1     0.062        41      37     106 ..     556     627 ..     554     633 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.9
                                   SSHHHHHHHHHHHHHHHHHHHHHTS CS
                          TarH  83 akellaraeeslaqseeawkaYlal 107
                                    ++ l+++++  +++e+ ++++++ 
  gi|15669512|ref|NP_248322.1| 213 INDKLNKIKKEFEDIEKLFNEWENK 237
                                   2777888888888888888888775 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHHHHTTTSSSSSSHHHHHHHHHHHHHHHHHHHHHTS---GGGHH.HHHHHHHHHHHHHHHHHHH CS
                          TarH  62 lqaRltLnragiaaladeaedakellaraeeslaqseeawkaYlalprtaeeeealaaelkakykalqdglapl 135
                                   ++aR tLnr                           ++ +++Y++l  + ++ e+ + elk++y+ +   l  +
  gi|15669512|ref|NP_248322.1| 273 VEARETLNR--------------------------HKDEYEKYKSLVDEIRKIESRLRELKSHYEDY-LKLTKQ 319
                                   445555555..........................55555555555555555555555555555553.234444 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHHHHHHHHHTS---GGGHH.H CS
                          TarH  85 ellaraeeslaqseeawkaYlalprtaeeeeal 117
                                   e +++ ++  ++ +e++++Yl+l+++a e ++l
  gi|15669512|ref|NP_248322.1| 378 EKIEKYKRICEECKEYYEKYLELEEKAVEYNKL 410
                                   5566666677889999****9999998666666 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.062
                                   HHHCHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSS..SHHHHHHHHHHHHHHHHHHHHHT CS
                          TarH  37 ndalrevytnrlqqqaaLaearvsllqaRltLnragiaaladeaeda..kellaraeeslaqseeawkaYla 106
                                    ++l+++ t  l++q+++ e +++l +   +L+ ++  +     ++    e l+ ++++l++ +  +++Yl+
  gi|15669512|ref|NP_248322.1| 556 EENLKTLKTLYLEKQSQIEELELKLKNYKEQLDEINKKISNYVINGKpvDEILEDIKSQLNKFKNFYNQYLS 627
                                   68999999999******************999998877777766666779********************97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0014      0.92       4      25 ..      24      45 ..      20      88 .. 0.89
   2 ?   -1.7   2.0       4.9   3.3e+03      75      75 ..     303     303 ..     208     375 .. 0.54
   3 ?   -1.7   0.4       4.7   3.1e+03      70      70 ..     579     579 ..     500     632 .. 0.54
   4 ?   -2.6   0.0       9.5   6.3e+03      78      99 ..     927     947 ..     922     979 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                        AAA_22  4 tagilvvtGesGtGKTtllrrl 25
                                  ++gi++++Ge G+GK+   + +
  gi|15669512|ref|NP_248322.1| 24 EKGIVAIIGENGSGKSSIFEAV 45
                                  799*************988766 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.9
                        AAA_22  75 s 75 
                                   +
  gi|15669512|ref|NP_248322.1| 303 L 303
                                   2 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.7
                        AAA_22  70 a 70 
                                   +
  gi|15669512|ref|NP_248322.1| 579 K 579
                                   2 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 9.5
                        AAA_22  78 llealeqalraravielliiDE 99 
                                   l+ a+++al   +v e++i+DE
  gi|15669512|ref|NP_248322.1| 927 LRLAIANALIGNRV-ECIILDE 947
                                   55667777777778.8999998 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   7.6     0.062        41      36      92 ..     165     225 ..     159     226 .. 0.61
   2 ?    6.4   7.6     0.017        11      44      82 ..     194     232 ..     186     259 .. 0.89
   3 ?   15.3   4.0   2.9e-05     0.019      10      82 ..     264     335 ..     259     337 .. 0.87
   4 ?    2.6   4.0      0.25   1.7e+02      35      79 ..     338     382 ..     335     386 .. 0.72
   5 ?    4.3   6.1     0.077        51      34      90 ..     388     444 ..     383     449 .. 0.67
   6 ?    3.4   7.1      0.14        92      37      86 ..     448     497 ..     441     501 .. 0.82
   7 ?   11.9   5.3   0.00032      0.21      43      82 ..     515     554 ..     510     563 .. 0.86
   8 ?    2.8   5.5      0.23   1.5e+02      49      94 ..     569     614 ..     556     616 .. 0.74
   9 ?    2.4   0.2       0.3     2e+02      40      81 ..     605     651 ..     602     655 .. 0.64
  10 ?    1.4   3.1      0.58   3.9e+02      47      77 ..     660     690 ..     641     698 .. 0.53
  11 ?    2.0   0.7       0.4   2.7e+02      34      73 ..     705     744 ..     690     752 .. 0.86
  12 ?    1.1   0.4      0.76     5e+02      58      80 ..     756     778 ..     748     783 .. 0.54
  13 ?   10.0  11.5    0.0013      0.84      14      86 ..     781     853 ..     768     856 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.062
                       BLOC1_2  36 ykklkdvaaslekkle....klnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                   y+k+ +++++ ek le    +ln k++  +++++++ q+e++ ++L e+ ++L+++ ke E
  gi|15669512|ref|NP_248322.1| 165 YQKMGEIVKEYEKRLEriegELNYKENYEKELKNKMSQLEEKNKKLMEINDKLNKIKKEFE 225
                                   6666666666666666222223444555566666777777777788888888877777766 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.017
                       BLOC1_2  44 aslekkleklnekyeelqpylqqidqiekqvteLeeavs 82 
                                   ++l++k+++l+ek+++l +  +++++i+k+ +++e++ +
  gi|15669512|ref|NP_248322.1| 194 KELKNKMSQLEEKNKKLMEINDKLNKIKKEFEDIEKLFN 232
                                   78999*************************999999766 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 2.9e-05
                       BLOC1_2  10 yleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavs 82 
                                   +le +l+ +ve  ++L++ ++   ekyk+l d++ ++e+ l +l++ ye   ++ +q++ i+ ++++L+e ++
  gi|15669512|ref|NP_248322.1| 264 ILEYDLNTVVEARETLNR-HKDEYEKYKSLVDEIRKIESRLRELKSHYEDYLKLTKQLEIIKGDIEKLKEFIN 335
                                   677777777777777766.466679*******************************************99887 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.25
                       BLOC1_2  35 kykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                   ky +  d+++ l +k+++  e+ e+++ +l+++++++++++++e+
  gi|15669512|ref|NP_248322.1| 338 KYRDDIDNLDTLLNKIKDEIERVETIKDLLEELKNLNEEIEKIEK 382
                                   555555666666666666666777789999999999999998886 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.077
                       BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyske 90 
                                   e++k++ ++  +le+k+ ++n++  e   +lq+ + iek++++Le+ +++L e +k+
  gi|15669512|ref|NP_248322.1| 388 EECKEYYEKYLELEEKAVEYNKLTLEYITLLQEKKSIEKNINDLETRINKLLEETKN 444
                                   566666777777777777777777777777777777777777777777776555554 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.14
                       BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDe 86 
                                   ++++++++++e+k + l+++++e  ++ +++ +i+ ++++L+++ +eL e
  gi|15669512|ref|NP_248322.1| 448 ESIENSLKEIEEKKKVLENLQKEKIELNKKLGEINSEIKRLKKILDELKE 497
                                   67788889999999999999999999999999999999999998888855 PP

  == domain 7  score: 11.9 bits;  conditional E-value: 0.00032
                       BLOC1_2  43 aaslekkleklnekyeelqpylqqidqiekqvteLeeavs 82 
                                   ++ +++   +ln+ky el++  ++i +iek++++L++ ++
  gi|15669512|ref|NP_248322.1| 515 MELINQHKTQLNNKYTELEEINKKIREIEKDIEKLKKEID 554
                                   5567778899*************************98776 PP

  == domain 8  score: 2.8 bits;  conditional E-value: 0.23
                       BLOC1_2  49 kleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                   k ++++e++ +l++y++q+d+i+k+++    + + +De+  +++++
  gi|15669512|ref|NP_248322.1| 569 KQSQIEELELKLKNYKEQLDEINKKISNYVINGKPVDEILEDIKSQ 614
                                   456777777799************9998777777777776666655 PP

  == domain 9  score: 2.4 bits;  conditional E-value: 0.3
                       BLOC1_2  40 kdvaaslekkleklnekyeelqpylqqidq.....iekqvteLeeav 81 
                                   ++++++++++l+k ++ y++  + ++ ++      i ++++e+e++v
  gi|15669512|ref|NP_248322.1| 605 DEILEDIKSQLNKFKNFYNQYLSAVSYLNSvdeegIRNRIKEIENIV 651
                                   57788888888888888887666555555500034556677777766 PP

  == domain 10  score: 1.4 bits;  conditional E-value: 0.58
                       BLOC1_2  47 ekkleklnekyeelqpylqqidqiekqvteL 77 
                                   +++l+kl+e + e++ +++++++++++ +eL
  gi|15669512|ref|NP_248322.1| 660 REELNKLREDEREINRLKDKLNELKNKEKEL 690
                                   3344444444444444444444444433333 PP

  == domain 11  score: 2.0 bits;  conditional E-value: 0.4
                       BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekq 73 
                                   ++y  l++++++l++  + l+e y+  ++++  id+i+++
  gi|15669512|ref|NP_248322.1| 705 KEYLGLTEKLEELKNIKDGLEEIYNICNSKILAIDNIKRK 744
                                   5788899999999999999999999999999999999876 PP

  == domain 12  score: 1.1 bits;  conditional E-value: 0.76
                       BLOC1_2  58 eelqpylqqidqiekqvteLeea 80 
                                   +++ +  ++i++ie++++ + + 
  gi|15669512|ref|NP_248322.1| 756 NKILEVNKEINDIEERISYINQK 778
                                   34444555555555555544443 PP

  == domain 13  score: 10.0 bits;  conditional E-value: 0.0013
                       BLOC1_2  14 eleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDe 86 
                                   e++   e+ k +++l e+  ++ ++++++  ++e+ +e+l++  e+l+  l+++ ++ek+ ++L++ v+ LD+
  gi|15669512|ref|NP_248322.1| 781 EINYNEEEHKKIKELYENKRQELDNVREQKTEIETGIEYLKKDVESLKARLKEMSNLEKEKEKLTKFVEYLDK 853
                                   67888999****************************************************************8 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3    0.0026       1.7      47      85 ..     190     228 ..     160     229 .. 0.91
   2 ?   -2.0   0.0       6.4   4.2e+03      61      83 ..     290     312 ..     283     313 .. 0.61
   3 ?   -1.9   0.0       6.1     4e+03      37      37 ..     360     360 ..     336     381 .. 0.53
   4 ?    0.1   0.0       1.5   9.9e+02      10      37 ..     468     495 ..     461     497 .. 0.54
   5 ?    0.8   0.1      0.91     6e+02      59      80 ..     524     545 ..     513     557 .. 0.55
   6 ?    0.4   0.1       1.2     8e+02      50      75 ..     570     595 ..     568     599 .. 0.83
   7 ?   -1.4   0.0       4.3   2.9e+03      51      72 ..     664     685 ..     639     690 .. 0.59
   8 ?    4.0   0.1     0.091        61       7      39 ..     797     829 ..     791     836 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0026
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100  47 dafqaefeewkqaaqklvdaLeeisealkqaanafedaD 85 
                                   + +++e+++ + ++++ +++L+ei+++l++++++fed +
  gi|15669512|ref|NP_248322.1| 190 ENYEKELKNKMSQLEEKNKKLMEINDKLNKIKKEFEDIE 228
                                   5677888888888899999*****************988 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.4
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100  61 qklvdaLeeisealkqaanafed 83 
                                   + lvd+  +i++ l++ ++ +ed
  gi|15669512|ref|NP_248322.1| 290 KSLVDEIRKIESRLRELKSHYED 312
                                   55566666666666666666665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 6.1
                                   C CS
                        WXG100  37 l 37 
                                   +
  gi|15669512|ref|NP_248322.1| 360 V 360
                                   2 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                        WXG100  10 rqaaarfqkqaeeledelqrlkaevdal 37 
                                   ++   +++k+ +e+ +e++rlk+ +d+l
  gi|15669512|ref|NP_248322.1| 468 QKEKIELNKKLGEINSEIKRLKKILDEL 495
                                   4444445555556666666666655555 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.91
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100  59 aaqklvdaLeeisealkqaana 80 
                                   ++++ +++Leei+++++++ + 
  gi|15669512|ref|NP_248322.1| 524 QLNNKYTELEEINKKIREIEKD 545
                                   4444444555555555555444 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100  50 qaefeewkqaaqklvdaLeeisealk 75 
                                   q+++ee+  ++++++++L+ei++++ 
  gi|15669512|ref|NP_248322.1| 570 QSQIEELELKLKNYKEQLDEINKKIS 595
                                   57788888899999999999999875 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 4.3
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100  51 aefeewkqaaqklvdaLeeise 72 
                                   + + e  +++++l+d+L+e+ +
  gi|15669512|ref|NP_248322.1| 664 NKLREDEREINRLKDKLNELKN 685
                                   4444445667777777777766 PP

  == domain 8  score: 4.0 bits;  conditional E-value: 0.091
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGC CS
                        WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdalqs 39 
                                   e  rq   ++++q++e+e+ ++ lk++v++l++
  gi|15669512|ref|NP_248322.1| 797 ENKRQELDNVREQKTEIETGIEYLKKDVESLKA 829
                                   556788899********************9976 PP

>> DUF4743  Domain of unknown function (DUF4743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       2.7   1.8e+03      29      86 ..     168     226 ..     159     240 .. 0.61
   2 ?   -2.8   0.0       8.7   5.8e+03      57      80 ..     349     372 ..     305     384 .. 0.70
   3 ?    3.4   0.0      0.11        73      37      81 ..     454     498 ..     449     523 .. 0.86
   4 ?   10.8   0.1   0.00055      0.36      14      97 ..     589     673 ..     576     681 .. 0.85
   5 ?   -2.2   0.2       5.6   3.7e+03      54      82 ..     758     786 ..     750     810 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.7
                                   EEEEEHHHHHHHCT-TTTEEE-SS.EEEE-TT--SHHHHHHHHHHHHHHHHH.TT...S CS
                       DUF4743  29 vGlirpdvaeklrkfpdvFevsekeaveLapslktyeeRtaaveevleelre.egsfva 86 
                                   +G i ++  ++l++ +   +++e+   eL++++++ ee+ +++ e+ ++l++ +++f  
  gi|15669512|ref|NP_248322.1| 168 MGEIVKEYEKRLERIEGELNYKENYEKELKNKMSQLEEKNKKLMEINDKLNKiKKEFED 226
                                   55566666666666666666666656667777777777777777666666542333444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.7
                                   E-TT--SHHHHHHHHHHHHHHHHH CS
                       DUF4743  57 LapslktyeeRtaaveevleelre 80 
                                   L ++ k+  eR + ++++leel++
  gi|15669512|ref|NP_248322.1| 349 LLNKIKDEIERVETIKDLLEELKN 372
                                   445555666777777777777765 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.11
                                   HHHHCT-TTTEEE-SS.EEEE-TT--SHHHHHHHHHHHHHHHHHT CS
                       DUF4743  37 aeklrkfpdvFevsekeaveLapslktyeeRtaaveevleelree 81 
                                   ++++++ ++v e  +ke++eL+++l ++++  ++++++l+el+e 
  gi|15669512|ref|NP_248322.1| 454 LKEIEEKKKVLENLQKEKIELNKKLGEINSEIKRLKKILDELKEV 498
                                   67777888899999999************************9984 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00055
                                   --GCCEEEEEETTEEEEEEEHHHHHHHCT-TTTEEE-SS.EEEE-TT--S..HHHHHHHHHHHHHHHHHTT...SS----S CS
                       DUF4743  14 ssrseflpFvvegqqvGlirpdvaeklrkfpdvFevsekeaveLapslkt..yeeRtaaveevleelreegsfvalkgwRd 92 
                                   + ++++ ++v++g+ v  i +d+ ++l+kf++ ++   + av+  +s ++  + +R +++e++++ +++e+    l+++R+
  gi|15669512|ref|NP_248322.1| 589 EINKKISNYVINGKPVDEILEDIKSQLNKFKNFYNQYLS-AVSYLNSVDEegIRNRIKEIENIVSGWNKEKCREELNKLRE 668
                                   45688999************************9999999.999888887633689999*************9899999998 PP

                                   -EEEE CS
                       DUF4743  93 ElYeV 97 
                                    + e+
  gi|15669512|ref|NP_248322.1| 669 DEREI 673
                                   76665 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 5.6
                                   EEEE-TT--SHHHHHHHHHHHHHHHHHTT CS
                       DUF4743  54 aveLapslktyeeRtaaveevleelreeg 82 
                                    +e++++ +++eeR + +++ l+e++ ++
  gi|15669512|ref|NP_248322.1| 758 ILEVNKEINDIEERISYINQKLDEINYNE 786
                                   67889999999999999999888876544 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.34   2.2e+02      37      70 ..     203     236 ..     198     285 .. 0.78
   2 ?   -2.5   0.0       4.3   2.8e+03      35      70 ..     361     396 ..     358     399 .. 0.84
   3 ?   -2.6   0.0       4.4   2.9e+03      39      64 ..     473     498 ..     465     500 .. 0.68
   4 ?    0.2   0.1      0.64   4.3e+02      41      63 ..     529     551 ..     509     622 .. 0.80
   5 ?    5.1   0.0      0.02        13      36     108 ..     764     836 ..     760     859 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.34
                     Mce4_CUP1  37 ltdlnevLdelNprlpqlredireladladvYad 70 
                                   l++ n+ L e+N++l++++++++++++l + +++
  gi|15669512|ref|NP_248322.1| 203 LEEKNKKLMEINDKLNKIKKEFEDIEKLFNEWEN 236
                                   788999****************999999887766 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.3
                     Mce4_CUP1  35 esltdlnevLdelNprlpqlredireladladvYad 70 
                                   e+++dl e L++lN++++++++  r  ++ ++ Y++
  gi|15669512|ref|NP_248322.1| 361 ETIKDLLEELKNLNEEIEKIEKYKRICEECKEYYEK 396
                                   578888899999999999999988888888888875 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.4
                     Mce4_CUP1  39 dlnevLdelNprlpqlredireladl 64 
                                   +ln+ L e+N+++ +l++ + el+++
  gi|15669512|ref|NP_248322.1| 473 ELNKKLGEINSEIKRLKKILDELKEV 498
                                   56777777777777777666666655 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.64
                     Mce4_CUP1  41 nevLdelNprlpqlredirelad 63 
                                    + L+e+N+++ ++++di++l++
  gi|15669512|ref|NP_248322.1| 529 YTELEEINKKIREIEKDIEKLKK 551
                                   44577777777777777777765 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.02
                     Mce4_CUP1  36 sltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsn 108
                                    ++d++e ++ +N++l++++ + +e ++++++Y++  ++l ++ ++ +   + i+  ++++++l + + ++sn
  gi|15669512|ref|NP_248322.1| 764 EINDIEERISYINQKLDEINYNEEEHKKIKELYENKRQELDNVREQKTEIETGIEYLKKDVESLKARLKEMSN 836
                                   6788999999*****************************9999999999999999999999988888777776 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   4.9     0.097        65      30     195 ..     194     230 ..     159     278 .. 0.59
   2 ?    8.4   1.5    0.0023       1.5       5      57 ..     286     337 ..     282     356 .. 0.85
   3 ?   -0.4   5.8       1.2   7.7e+02       5      88 ..     350     435 ..     341     438 .. 0.63
   4 ?   -0.6  11.7       1.3   8.6e+02       4      77 ..     417     490 ..     412     500 .. 0.88
   5 ?    6.7  20.2    0.0077       5.1       2     172 ..     526     697 ..     525     721 .. 0.73
   6 ?   13.9   5.5   4.9e-05     0.032       4     107 ..     761     878 ..     758     885 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.097
                      Syntaxin  30 eesktstraksvklkkrmesdikeikkraesvkarLeaLdksnkenekksgegsavdRirksqtaaLrkklkevmteynel 110
                                   +e+                                                                              
  gi|15669512|ref|NP_248322.1| 194 KEL------------------------------------------------------------------------------ 196
                                   222.............................................................................. PP

                      Syntaxin 111 rekireeykerieRrlevtGkevseeeieelietgesevflqkllqeqrgarealseieeRhkevlelekslkeLhqlFld 191
                                                                                      ++++s+ ee +k+++e++ +l+++++ F d
  gi|15669512|ref|NP_248322.1| 197 ---------------------------------------------------KNKMSQLEEKNKKLMEINDKLNKIKKEFED 226
                                   ...................................................333334444444444444444444444444 PP

                      Syntaxin 192 mavL 195
                                   +  L
  gi|15669512|ref|NP_248322.1| 227 IEKL 230
                                   3332 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0023
                      Syntaxin   5 fkeveeikkeiekleeevkklkkqneesktstraksvklkkrmesdikeikkr 57 
                                   +++ +++ +ei+k+e+ +++lk++ e++++ t++ ++ +k ++e++ + i+k+
  gi|15669512|ref|NP_248322.1| 286 YEKYKSLVDEIRKIESRLRELKSHYEDYLKLTKQLEI-IKGDIEKLKEFINKS 337
                                   677788999****************************.******999998875 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.2
                      Syntaxin   5 fkeveeikkeiekleeevkklkkqneesktstraksvk..lkkrmesdikeikkraesvkarLeaLdksnkenekksgegs 83 
                                   ++++++  + +e++++++++lk+ nee+ +  + k +    k+  e+  +  +k  e  k  Le +   ++++  +++ + 
  gi|15669512|ref|NP_248322.1| 350 LNKIKDEIERVETIKDLLEELKNLNEEIEKIEKYKRICeeCKEYYEKYLELEEKAVEYNKLTLEYITLLQEKKSIEKNIND 430
                                   455555555667788888888888888888777776644566666666655555566666666666666666655556666 PP

                      Syntaxin  84 avdRi 88 
                                    ++Ri
  gi|15669512|ref|NP_248322.1| 431 LETRI 435
                                   66665 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.3
                      Syntaxin   4 ffkeveeikkeiekleeevkklkkqneesktstraksvk.lkkrmesdikeikkraesvkarLeaLdksnkenek 77 
                                   +++e ++i+k+i++le+ ++kl ++++++     ++s+k + ++ ++  ++ +k+  +++++L +++ ++k+ +k
  gi|15669512|ref|NP_248322.1| 417 LLQEKKSIEKNINDLETRINKLLEETKNIDIESIENSLKeIEEK-KKVLENLQKEKIELNKKLGEINSEIKRLKK 490
                                   5789999********************99999999999988777.999999999999999999999999998776 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.0077
                      Syntaxin   2 eeffkeveeikkeiekleeevkklkkqneesktstraksvklkkrmesdikeikkraesvkarLeaLdksnkenekksgeg 82 
                                   ++ + e eei+k+i+++e++++klkk+ ++  +  + k++ +  + +s+i+e + + ++ k++L++++k++ +   + ++ 
  gi|15669512|ref|NP_248322.1| 526 NNKYTELEEINKKIREIEKDIEKLKKEIDKEENLKTLKTL-YL-EKQSQIEELELKLKNYKEQLDEINKKISNYVINGKPV 604
                                   67799********************998887777777777.33.44799********************999888555666 PP

                      Syntaxin  83 savdRirksqtaaLrkklkevmteynelrekireeykerieRrlev.tG..kevseeeieelietgesevflqkllqeqrg 160
                                     +    ksq +  ++  ++ ++  + l++  +e  ++ri+   ++  G  ke  +ee+++l e+++  + l++ l+e + 
  gi|15669512|ref|NP_248322.1| 605 DEILEDIKSQLNKFKNFYNQYLSAVSYLNSVDEEGIRNRIKEIENIvSGwnKEKCREELNKLREDEREINRLKDKLNELKN 685
                                   66666666666666666666666666667777777777777774442443377889********99866666666789999 PP

                      Syntaxin 161 arealseieeRh 172
                                   + + l eie+R+
  gi|15669512|ref|NP_248322.1| 686 KEKELIEIENRR 697
                                   999*****9996 PP

  == domain 6  score: 13.9 bits;  conditional E-value: 4.9e-05
                      Syntaxin   4 ffkeveeikkeiekleeevkklkkqneeskts...t..ra...ksvk.lkkrmesdikeikkraesvkarLeaLdksnken 75 
                                   + ke+++i++ i+ +++++++++ ++ee k+       ++   ++v+  k ++e+ i+  kk  es+karL+++++  ke+
  gi|15669512|ref|NP_248322.1| 761 VNKEINDIEERISYINQKLDEINYNEEEHKKIkelYenKRqelDNVReQKTEIETGIEYLKKDVESLKARLKEMSNLEKEK 841
                                   5689999**********9999987766665541113112211145677888899999999***************999999 PP

                      Syntaxin  76 ekks...gegsavdRi..rksqtaaLrkklkevmtey 107
                                   ek     +    v Ri  r+   a Lr+k   ++++y
  gi|15669512|ref|NP_248322.1| 842 EKLTkfvEYLDKVRRIfgRNGFQAYLREKYVPLIQKY 878
                                   9988555555555555434455566666666666555 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  16.5    0.0014      0.94     816     958 ..     164     307 ..     155     324 .. 0.71
   2 ?    2.1  38.9      0.04        27     225     492 ..     328     595 ..     310     625 .. 0.81
   3 ?    3.8  27.1     0.012       7.9     242     481 ..     610     855 ..     591     861 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0014
                       DUF3584 816 erpalkeqveelesaaeeleqeltrliedtklerkklekerkalekqldqldenlrklrdllsklaelkldadaeqae... 893
                                     +++ e v+e e+ +e++e el+ ++ ++++e+k+ +++++  +k+l +++++l k++++++ + +l  +++++++    
  gi|15669512|ref|NP_248322.1| 164 CYQKMGEIVKEYEKRLERIEGELNYKE-NYEKELKNKMSQLEEKNKKLMEINDKLNKIKKEFEDIEKLFNEWENKKLLyek 243
                                   557888999999999999999998765.57778888888899999999999999999999999999999999888887555 PP

                       DUF3584 894 ..gelaerlaaleelkrkrerlsedvkkalerfkgvlkdksgsglaetweklreeestlsdkaleld 958
                                      +l+er +ale   ++++ l+ d+++ +e  +   + ++ ++ +e++++l +e ++++ +  el 
  gi|15669512|ref|NP_248322.1| 244 fiNKLEERKRALELKNQELKILEYDLNTVVEARE---TLNRHKDEYEKYKSLVDEIRKIESRLRELK 307
                                   6566777777777777777777777777777666...336667778888887776666655543332 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.04
                       DUF3584 225 qdveeWiediqalaaiekvrpeieklqeefeqleslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelke 305
                                   ++ +e+i+ ++   +i +    ++k++ e+e +e++   L  lk +l +++e++++ +  ++e k+ +++ l+ +e++++ 
  gi|15669512|ref|NP_248322.1| 328 EKLKEFINKSKYRDDIDNLDTLLNKIKDEIERVETIKDLLEELK-NLNEEIEKIEKYKRICEECKEYYEKYLELEEKAVEY 407
                                   56788999999999**********************99999997.68999*******************999999999987 PP

                       DUF3584 306 aidelnq.elsaakaklaakesele.aleeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrr 384
                                   ++ +l+   l ++k+ +++  ++le ++++  ++ ++ die+ ++ l ++++ ++ le+l++e   l +k  +++++ +r+
  gi|15669512|ref|NP_248322.1| 408 NKLTLEYiTLLQEKKSIEKNINDLEtRINKLLEETKNIDIESIENSLKEIEEKKKVLENLQKEKIELNKKLGEINSEIKRL 488
                                   766655324555666677777777644677777778899***************************************999 PP

                       DUF3584 385 kqkikeeleeeleklkerleaireekdrlkaaieealealesqlrk..qleaqkeelneeekelesrlselklrldsatat 463
                                   k+ ++e l+e+  k    + +i e+k+     i+++  +l++++ +  + +++++e++++ ++l++++++++ + +  t  
  gi|15669512|ref|NP_248322.1| 489 KKILDE-LKEVEGKCPLCKTPIDENKKME--LINQHKTQLNNKYTEleEINKKIREIEKDIEKLKKEIDKEENLKTLKTLY 566
                                   876655.5555555555567777776663..34444444444444211667899999************************ PP

                       DUF3584 464 eEeleqieeadealekaqeelekaeaeve 492
                                    E++ qiee + +l++ +e+l + +++ +
  gi|15669512|ref|NP_248322.1| 567 LEKQSQIEELELKLKNYKEQLDEINKKIS 595
                                   ***************99999999888765 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.012
                       DUF3584 242 kvrpeieklqeefeqleslelrLsllk.gelkadeerlaekqeevqeakaelkqqlrtledelkeaidelnqelsaakakl 321
                                    ++ +++k ++ ++q  s++  L ++   ++++ ++++++    ++++      + r++ ++l e + e n +l+++ ++l
  gi|15669512|ref|NP_248322.1| 610 DIKSQLNKFKNFYNQYLSAVSYLNSVDeEGIRNRIKEIENIVSGWNKE------KCREELNKLREDEREIN-RLKDKLNEL 683
                                   455555555666666666666665543134555555555555554433......33444444444444443.456666667 PP

                       DUF3584 322 aakeselealeeqk.kkyed.adieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkikeel.....eee 395
                                   ++ke+el ++e+++  k+++ ++   l ++l++l +i++ lee+ +  +  + ++ ++++ky+++  +i  ++     ++e
  gi|15669512|ref|NP_248322.1| 684 KNKEKELIEIENRRsLKFDKyKEYLGLTEKLEELKNIKDGLEEIYNICNSKILAIDNIKRKYNKEDIEIYLNNkilevNKE 764
                                   777777666665541466663455678888999999999999999999999999999999999888777644311111567 PP

                       DUF3584 396 leklkerleaireekdrl......kaaieealealesqlrkqleaqkeelneeekelesrlselklrldsatateEeleqi 470
                                   +++++er   i ++ d+       +++i+e +e+ +++l  +  +qk+e++   + l++ +++lk rl++++  e e+e++
  gi|15669512|ref|NP_248322.1| 765 INDIEERISYINQKLDEInyneeeHKKIKELYENKRQELD-NVREQKTEIETGIEYLKKDVESLKARLKEMSNLEKEKEKL 844
                                   7777777666666666654433335555555555555555.4445667777777777777777777777777777777777 PP

                       DUF3584 471 eeadealekaq 481
                                   ++++e l+k +
  gi|15669512|ref|NP_248322.1| 845 TKFVEYLDKVR 855
                                   77777776665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.4   0.00053      0.35      50     122 ..     161     236 ..     146     241 .. 0.73
   2 ?    0.0   0.3       1.2   8.1e+02      86     112 ..     269     295 ..     238     312 .. 0.44
   3 ?    6.7   2.8      0.01       6.9      46     108 ..     316     382 ..     310     390 .. 0.67
   4 ?    4.5   8.3      0.05        33      38     113 ..     423     495 ..     404     501 .. 0.66
   5 ?    4.3   2.7     0.059        39      77     119 ..     513     555 ..     506     559 .. 0.67
   6 ?    3.1   1.8      0.14        91      68     108 ..     573     613 ..     556     664 .. 0.51
   7 ?   -1.0   1.4       2.6   1.7e+03      54      64 ..     680     690 ..     645     749 .. 0.56
   8 ?    5.9   1.3     0.018        12      51     123 ..     711     785 ..     696     786 .. 0.79
   9 ?   11.2   5.6   0.00043      0.28      40     121 ..     755     835 ..     753     839 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00053
                       DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevre...dlseigedvesvkeavegleskleriee 122
                                    e+ ++++ +  ++ ++r++r++ +l+  ++  ke+k+++++++e   +l ei+++++++k+ +e++e+  ++ e+
  gi|15669512|ref|NP_248322.1| 161 FEKCYQKMGEIVKEYEKRLERIEGELNYKENYEKELKNKMSQLEEknkKLMEINDKLNKIKKEFEDIEKLFNEWEN 236
                                   5777888888888888888888888888888888888887777651114556777777777777777776666555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
                       DUF1664  86 keevtevredlseigedvesvkeaveg 112
                                    + v e+re l++ +++ e+ k++v +
  gi|15669512|ref|NP_248322.1| 269 LNTVVEARETLNRHKDEYEKYKSLVDE 295
                                   234445555555555554444443332 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.01
                       DUF1664  46 vskqleqvseslaa.....tkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                   ++kqle ++ ++++      k +  ++id++d+ l++ k+ ++ ++  ++++ e+l++++e++e++++
  gi|15669512|ref|NP_248322.1| 316 LTKQLEIIKGDIEKlkefiNKSKYRDDIDNLDTLLNKIKDEIERVE-TIKDLLEELKNLNEEIEKIEK 382
                                   4555555554444411111244566788888888888888888774.688888888888888888876 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.05
                       DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                   s+++ ++++ ++++   + l++tk+   + i++  k+++e k++ +++++e  e++++l ei+++++ +k++  +l
  gi|15669512|ref|NP_248322.1| 423 SIEKNINDLETRIN---KLLEETKNIDIESIENSLKEIEEKKKVLENLQKEKIELNKKLGEINSEIKRLKKILDEL 495
                                   33333333333332...33456666667777777777788888888888888888888888888888887777766 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.059
                       DUF1664  77 eqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                   + +e++++ k ++++   +l+ei+++++++++ +e+l++++++
  gi|15669512|ref|NP_248322.1| 513 KKMELINQHKTQLNNKYTELEEINKKIREIEKDIEKLKKEIDK 555
                                   4566666777777777777777777777777777777766654 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.14
                       DUF1664  68 idrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                   i++++ kl++ ke   ei++++++   + + ++e +e +k+
  gi|15669512|ref|NP_248322.1| 573 IEELELKLKNYKEQLDEINKKISNYVINGKPVDEILEDIKS 613
                                   33333333333333333333333332222222222222222 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 2.6
                       DUF1664  54 seslaatkrhL 64 
                                    ++l++  ++L
  gi|15669512|ref|NP_248322.1| 680 LNELKNKEKEL 690
                                   22222222333 PP

  == domain 8  score: 5.9 bits;  conditional E-value: 0.018
                       DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevte..vredlseigedvesvkeaveglesklerieek 123
                                   ++  e+l++ k+ L++  +  ++k+ +  +i+++ ++e  e  +++++ e++++++ ++e ++ +++kl++i+++
  gi|15669512|ref|NP_248322.1| 711 TEKLEELKNIKDGLEEIYNICNSKILAIDNIKRKYNKEDIEiyLNNKILEVNKEINDIEERISYINQKLDEINYN 785
                                   555677888888888877888888888888887776654441257889999999999999999999999999876 PP

  == domain 9  score: 11.2 bits;  conditional E-value: 0.00043
                       DUF1664  40 sdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                   ++ + +v k+++++ e ++   ++L  +i+  +++ ++ ke+ ++ ++e+++vre+ +ei++ +e +k+ ve+l+++l+++
  gi|15669512|ref|NP_248322.1| 755 NNKILEVNKEINDIEERISYINQKLD-EINYNEEEHKKIKELYENKRQELDNVREQKTEIETGIEYLKKDVESLKARLKEM 834
                                   56677899999999999999999985.69999999999999999***********************************99 PP

                       DUF1664 121 e 121
                                   +
  gi|15669512|ref|NP_248322.1| 835 S 835
                                   6 PP

>> PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.2     0.054        36      48     191 ..     160     294 ..     152     360 .. 0.63
   2 ?    7.1   0.5    0.0038       2.5     180     233 ..     391     446 ..     389     449 .. 0.86
   3 ?    3.2   0.1     0.058        38      79     239 ..     530     566 ..     511     640 .. 0.66
   4 ?   -2.1   0.1       2.4   1.6e+03      64     110 ..     793     839 ..     783     858 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.054
               PHA_synth_III_E  48 aakelmermveqqkayfrlleqfakafadkdasasavedaweqlekaieqlqkafqglisdlad.klyleelqkflafWel 127
                                   ++++ +++m e  k+y + le++  +++ k++ +++ ++ ++qle+  ++l++  ++    l++ k   e+ +k++  We+
  gi|15669512|ref|NP_248322.1| 160 EFEKCYQKMGEIVKEYEKRLERIEGELNYKENYEKELKNKMSQLEEKNKKLMEINDK----LNKiKKEFEDIEKLFNEWEN 236
                                   556677777777777777777777766655555555555555544444444444444....33355569999999999999 PP

               PHA_synth_III_E 128 pldtwqraasslselmpgdllkllelneleaeqdqlresldrvlsaP.alGytREeqeqlqelvr 191
                                       + ++  +l e       ++lel++ e +   l+ +l+ v++a   l  +++e e++++lv+
  gi|15669512|ref|NP_248322.1| 237 KKLLYEKFINKLEE-----RKRALELKNQELKI--LEYDLNTVVEAReTLNRHKDEYEKYKSLVD 294
                                   43344444444443.....45555555444444..555555555543145555555555555555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0038
               PHA_synth_III_E 180 REeqeqlqelvravvdyqqasqeYqalla..avgvksverlreklqeaaekgkqik 233
                                   +E  e++ el +++v+y++ + eY++ll+  + + k++++l+ ++++  e+ k+i+
  gi|15669512|ref|NP_248322.1| 391 KEYYEKYLELEEKAVEYNKLTLEYITLLQekKSIEKNINDLETRINKLLEETKNID 446
                                   68899*********************997225678999999999999999988886 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.058
               PHA_synth_III_E  79 asasavedaweqlekaieqlqkafqglisdladklyleelqkflafWelpldtwqraasslselmpgdllkllelneleae 159
                                   ++ +++++  +                                                                      
  gi|15669512|ref|NP_248322.1| 530 TELEEINKKIRE--------------------------------------------------------------------- 541
                                   444444444444..................................................................... PP

               PHA_synth_III_E 160 qdqlresldrvlsaPalGytREeqeqlqelvravvdyqqasqeYqallaavgvksverlreklqeaaekgkqiksaralf 239
                                                                                          +e+ +ekl+++ +k++++k++++l+
  gi|15669512|ref|NP_248322.1| 542 -------------------------------------------------------IEKDIEKLKKEIDKEENLKTLKTLY 566
                                   .......................................................4555555555555555555555555 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.4
               PHA_synth_III_E  64 frlleqfakafadkdasasavedaweqlekaieqlqkafqglisdla 110
                                    +l+e+ ++++ +   +++++e + e l+k +e l+++++++++ ++
  gi|15669512|ref|NP_248322.1| 793 KELYENKRQELDNVREQKTEIETGIEYLKKDVESLKARLKEMSNLEK 839
                                   56677777778887788888888888888888888888887765444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1005 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4106  (0.229014); expected 358.6 (0.02)
Passed bias filter:                      876  (0.0488594); expected 358.6 (0.02)
Passed Vit filter:                       322  (0.0179597); expected 17.9 (0.001)
Passed Fwd filter:                       197  (0.0109878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 4.52u 0.40s 00:00:04.92 Elapsed: 00:00:00.94
# Mc/sec: 3230.36
//
Query:       gi|15669513|ref|NP_248323.1|  [L=366]
Description: DNA repair protein RAD32 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-15   56.8   0.9    8.6e-15   55.8   0.9    1.5  1  Metallophos    Calcineurin-like phosphoesterase
    9.4e-10   38.9   0.0    1.9e-09   37.9   0.0    1.5  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.9   9.6e-19   8.6e-15       3     203 ..       3     189 ..       1     190 [. 0.69

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 9.6e-19
                                   EEEEESBTB........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHH...TSEEEEEC CS
                   Metallophos   3 ilvigDlHl........algggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvky...pipvylll 71 
                                   +++i+D Hl        +++   +d+++ +++++l+  kpd+vl+ GDl+++  ++ + l+  ++a+ k+   +i+vy+++
  gi|15669513|ref|NP_248323.1|   3 FVHIADNHLgyrqynldDREKDIYDSFKLCIKKILEI-KPDVVLHSGDLFNDLRPPVKALRIaMQAFKKLhenNIKVYIVA 82 
                                   89**************9999999999***********.***************99999999977777777999******** PP

                                   -TTSCHHHHHHHHHHHHHHHHHHHEHH..HCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC.HH CS
                   Metallophos  72 GNHegfeeellnkygylgifsepwrsd..aevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepg.de 149
                                   GNHe     ++++ g++   + ++ +    + ++ +++++      + +++ G ++              ++ +++++  +
  gi|15669513|ref|NP_248323.1|  83 GNHE-----MPRRLGEESPLALLKDYVkiLDGKDVINVNG------EEIFICGTYY--------------HKKSKREEmLD 138
                                   ****.....5555454444422222221133333333333......3333333322..............22222222333 PP

                                   HHHH.HHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                   Metallophos 150 wlkd.lekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHv 203
                                    lk+  ++ ++ + +i++ H +++ ++   ++ e+++     ++  ++  GH+H+
  gi|15669513|ref|NP_248323.1| 139 KLKNfESEAKNYKKKILMLHQGINPYIPLDYELEHFD----LPKFSYYALGHIHK 189
                                   333446667777789*******995555555555555....555569999****7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   2.1e-13   1.9e-09       1     145 [.       1     205 [.       1     218 [. 0.72

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.1e-13
                 Metallophos_2   1 MklaiiSDlH.............snldaleavlealkevgvdaiihaGDl.eeeep.....e.vleellela....pvlaV 57 
                                   M +++i+D H             + +d  + +++++ e ++d ++h+GDl ++  p       +++++++l     +v++V
  gi|15669513|ref|NP_248323.1|   1 MMFVHIADNHlgyrqynlddrekDIYDSFKLCIKKILEIKPDVVLHSGDLfNDLRPpvkalRiAMQAFKKLHenniKVYIV 81 
                                   999**********9988887766666667777*****************87555554555424666666666777****** PP

                 Metallophos_2  58 rGNnD................................eev....veedvlreaaelgtdlp.eeaelelagekvlliHgdp 101
                                    GN++                                e +       +   + +e+ ++l+  e e +  ++k+l++H+  
  gi|15669513|ref|NP_248323.1|  82 AGNHEmprrlgeesplallkdyvkildgkdvinvngeE-IficgTYYHKKSKREEMLDKLKnFESEAKNYKKKILMLHQG- 160
                                   ********************999999866666666531.2233322222233333333332233333335666******8. PP

                 Metallophos_2 102 lgvkdalaellkeaeegsd.vvvcGHtHvpevekeggvlvvnPGs 145
                                    +    l++ l+  + +++ ++++GH+H++ +e+ ++ ++ + Gs
  gi|15669513|ref|NP_248323.1| 161 INPYIPLDYELEHFDLPKFsYYALGHIHKRILERFNDGILAYSGS 205
                                   77777888888887788889*********9877776666667666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2187.31
//
Query:       gi|15669514|ref|NP_248324.1|  [L=234]
Description: putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-26   92.7   1.6    2.4e-26   92.2   1.6    1.3  1  MobB      Molybdopterin guanine dinucleotide synthesis protei
    1.6e-08   34.0   0.5    2.8e-08   33.3   0.5    1.4  1  FeS       Putative Fe-S cluster
    1.3e-05   24.9   0.1    1.3e-05   24.9   0.1    1.8  2  cobW      CobW/HypB/UreG, nucleotide-binding domain
     0.0006   19.4   2.0     0.0011   18.6   0.6    1.9  2  GTP_EFTU  Elongation factor Tu GTP binding domain
     0.0015   18.6   0.4     0.0026   17.8   0.4    1.5  1  AAA_14    AAA domain
  ------ inclusion threshold ------
      0.018   15.1   0.2      0.038   14.1   0.1    1.8  2  MMR_HSR1  50S ribosome-binding GTPase
      0.046   14.2   0.0      0.057   13.9   0.0    1.2  1  ABC_tran  ABC transporter
       0.11   12.9   0.1       0.31   11.4   0.0    1.7  2  AAA_16    AAA ATPase domain


Domain annotation for each model (and alignments):
>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   1.6   1.1e-29   2.4e-26       1     119 [.       3     120 ..       3     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 1.1e-29
                          MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikeleeaelsl 81 
                                   v+g++g+++sGKTtL+e++   lk+++ ++++iKh++++++vdk+g D+yr+ +AGAk +++a+++++  +++    +++l
  gi|15669514|ref|NP_248324.1|   3 VIGVIGYKDSGKTTLIEEI---LKHSDKKIAVIKHTKEDVEVDKKGTDTYRLSNAGAKITVLATDSKTVFFTD----RMDL 76 
                                   799**************87...678899*******************************************99....4789 PP

                          MobB  82 eellarlse..vDlvlvEGfkke....alpkievlraelgkeel 119
                                   e++l+ ls+  +D+v++EGfk++    ++pki++l+++ g++ +
  gi|15669514|ref|NP_248324.1|  77 ENILSVLSDynIDFVIIEGFKEAlkrlNIPKIVMLKDKDGSDLI 120
                                   9****998778*********865333389*******99887544 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.5   1.3e-11   2.8e-08       4      32 ..     153     180 ..     152     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.3e-11
                           FeS   4 tNCgaCGypgCmafAealvegeaqledCp 32 
                                   +NCg CGy +C+ f +a+v+gea+ +dC+
  gi|15669514|ref|NP_248324.1| 153 LNCGHCGY-NCRTFVKAVVKGEARWDDCV 180
                                   7*******.*******************7 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   5.7e-09   1.3e-05       2      58 ..       3      63 ..       2     100 .. 0.67
   2 ?   -1.5   0.2      0.71   1.6e+03      28      65 ..     123     162 ..     116     189 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 5.7e-09
                                  EEEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCC.....HCCCT.EEEETT CS
                          cobW  2 vtvltGflGsGKTtLlnhllenraglklavivNefgevsiDaell.....retgveivelen 58
                                  v+++ G+  sGKTtL++++l++ +++k+avi     +v++D++       +++g++i+ l++
  gi|15669514|ref|NP_248324.1|  3 VIGVIGYKDSGKTTLIEEILKH-SDKKIAVIKHTKEDVEVDKKGTdtyrlSNAGAKITVLAT 63
                                  678999999***********76.89********99999999986633333555555555554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.71
                                   -EEEEESS-SSCHCCCCCC...HCCCT.EEEETTTTECCHC CS
                          cobW  28 klavivNefgevsiDaell...retgveivelenGciCctl 65 
                                   ++a i+ ++   +iD  l    +++ v++++l+ G +  + 
  gi|15669514|ref|NP_248324.1| 123 HTAMIIEDYN-YNIDDVLKviyEKAVVPTMNLNCGHCGYNC 162
                                   5788888888.888875432224446668888877765554 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.6   4.9e-07    0.0011       4      47 ..       2      45 ..       1      78 [. 0.69
   2 ?   -0.1   0.0      0.25   5.5e+02     120     189 ..     102     170 ..      93     215 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.9e-07
                                  EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSH CS
                      GTP_EFTU  4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlk 47
                                  r ig+ig  D+GKtTL++++l+++ +     ++++e+  +D+  
  gi|15669514|ref|NP_248324.1|  2 RVIGVIGYKDSGKTTLIEEILKHSDKKIAVIKHTKEDVEVDKKG 45
                                  789******************98876555333333344444443 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.25
                                   HTTTEEEEEEES...CGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEE.EBTTTTBTHHHHHHHHH CS
                      GTP_EFTU 120 kegvpiivfiNK...mDrlkaelkeiveevkqklsrkeeklekygekgekevpvvf.gSalkgegvktllealv 189
                                   ++++p iv++      D +++   +i+e++++++   ++ l+++ ek+   vp +   ++  g + +t+++a+v
  gi|15669514|ref|NP_248324.1| 102 RLNIPKIVMLKDkdgSDLIDDHTAMIIEDYNYNI---DDVLKVIYEKA--VVPTMNlNCGHCGYNCRTFVKAVV 170
                                   5566644444330223555888888888888888...33333334333..344333034444555555555554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.4   1.1e-06    0.0026       3      50 ..       2      46 ..       1     105 [. 0.69

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe 50
                                  +++ + G + +GKTtl+++++k++    ++i  i+  +e+ +  ++ +
  gi|15669514|ref|NP_248324.1|  2 RVIGVIGYKDSGKTTLIEEILKHSD---KKIAVIKHTKEDVEVDKKGT 46
                                  6899*****************9999...88888877777665444332 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.7e-05     0.038       2      32 ..       4      35 ..       3     112 .. 0.83
   2 ?   -3.3   0.0       4.3   9.6e+03      26      42 ..     200     216 ..     193     225 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                                  EEEEESTTSSHHHHHHHHHTS.TEEESSSTTS CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivsdkpgt 32
                                  ++++G+  +GK+tLi  +++    +++ ++ t
  gi|15669514|ref|NP_248324.1|  4 IGVIGYKDSGKTTLIEEILKHsDKKIAVIKHT 35
                                  89*****************9644444444443 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.3
                                   ESSSTTSSSSEEEEEEE CS
                      MMR_HSR1  26 vsdkpgtTrdinegrvk 42 
                                   vs++ g T++   +++k
  gi|15669514|ref|NP_248324.1| 200 VSKIVGSTIKAMIETLK 216
                                   67777777777666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.6e-05     0.057      13      68 ..       3      67 ..       1     140 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                                  EEEEEESTTSSHHHHHHHHTTSS--.......SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                      ABC_tran 13 kvaivGenGaGKStLlkllagllkp.......teGeilldgkdlkeqeleslrkeigvlpqe..p 68
                                  +++++G   +GK+tL++ +++++++       t++++++d+k +++ +l+ + ++i vl  +  +
  gi|15669514|ref|NP_248324.1|  3 VIGVIGYKDSGKTTLIEEILKHSDKkiavikhTKEDVEVDKKGTDTYRLSNAGAKITVLATDskT 67
                                  7899*******************998888888889999999998889999999999999988642 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.31      28      60 ..       5      36 ..       2      59 .. 0.82
   2 ?   -1.8   0.0       1.6   3.5e+03     129     145 ..      60      75 ..      42      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                        AAA_16 28 llsGesGvGKsslvrellralekdggiflrgkc 60
                                   ++G++ +GK++l++e+l++  k+ + +++ + 
  gi|15669514|ref|NP_248324.1|  5 GVIGYKDSGKTTLIEEILKHSDKK-IAVIKHTK 36
                                  5899999***********999888.66665554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                        AAA_16 129 llsrderplvlvlDdlq 145
                                    l++d++ +v++ D ++
  gi|15669514|ref|NP_248324.1|  60 VLATDSK-TVFFTDRMD 75 
                                   4455466.999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.37s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1263.25
//
Query:       gi|15669515|ref|NP_248325.1|  [L=89]
Description: cadmium resistance protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-22   76.7   0.1    1.4e-21   76.1   0.1    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
    1.5e-14   53.8   0.0    1.8e-14   53.5   0.0    1.1  1  HTH_20           Helix-turn-helix domain
      3e-07   29.9   0.0    4.8e-07   29.2   0.0    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    3.4e-05   23.6   0.0      5e-05   23.1   0.0    1.2  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00048   20.3   0.0    0.00065   19.8   0.0    1.2  1  HTH_34           Winged helix DNA-binding domain
     0.0018   18.6   0.0     0.0022   18.3   0.0    1.1  1  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.018   14.9   0.1    1.3  1  TFIIE_alpha      TFIIE alpha subunit
      0.017   15.0   0.0      0.022   14.7   0.0    1.2  1  MarR             MarR family
      0.022   14.8   0.0      0.032   14.3   0.0    1.3  1  DUF2250          Uncharacterized protein conserved in archaea
      0.026   14.3   0.0        0.1   12.4   0.0    1.9  1  HTH_IclR         IclR helix-turn-helix domain
      0.027   14.8   0.0      0.039   14.3   0.0    1.2  1  Rrf2             Transcriptional regulator
      0.037   13.8   0.1      0.083   12.6   0.0    1.6  2  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.041   13.8   0.0       0.06   13.2   0.0    1.2  1  MarR_2           MarR family
      0.096   12.5   0.0       0.24   11.2   0.0    1.8  2  HTH_23           Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.1   1.1e-24   1.4e-21       1      46 [.      16      62 ..      16      63 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 1.1e-24
                                  SHHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  1 dptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  dptRl ILklLae g++cvc + +el+++q+t+ShHL++L++aG+V+
  gi|15669515|ref|NP_248325.1| 16 DPTRLMILKLLAEnGSMCVCKIIDELKKPQPTISHHLNILKKAGIVK 62
                                  8*********************************************7 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   1.4e-17   1.8e-14       1      60 [.       8      67 ..       8      68 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.4e-17
                                  HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                  ++i++A+++P+R++il++La+++ +++  + ++l  ++ t+s+HL++L +ag+v+ ++eg
  gi|15669515|ref|NP_248325.1|  8 AEIFKAFGDPTRLMILKLLAENGSMCVCKIIDELKKPQPTISHHLNILKKAGIVKARKEG 67
                                  68********************************************************98 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   3.8e-10   4.8e-07       2      48 .]      16      62 ..      15      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 3.8e-10
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  d t++ IL+lL +n++++   + ++l  +++t++ +l+ L+++G++k
  gi|15669515|ref|NP_248325.1| 16 DPTRLMILKLLAENGSMCVCKIIDELKKPQPTISHHLNILKKAGIVK 62
                                  889******************************************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.9e-08     5e-05      16      66 ..      24      76 ..      20      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.9e-08
                                  HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE-- CS
                          TrmB 16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYravd 66
                                  +Ll ++g++ + +i  el+ p++++   L+ L+++G+V+ +k+   ++Y  vd
  gi|15669515|ref|NP_248325.1| 24 KLLaENGSMCVCKIIDELKKPQPTISHHLNILKKAGIVKARKEGtWNFYYIVD 76
                                  4555***********************************99966366887776 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.1e-07   0.00065       2      49 ..      19      66 ..      18      70 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.1e-07
                        HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49
                                  Rl +l +La++ +++  ++ ++l+  +  +s hl++L+kag ++ +ke
  gi|15669515|ref|NP_248325.1| 19 RLMILKLLAENGSMCVCKIIDELKKPQPTISHHLNILKKAGIVKARKE 66
                                  9*******************************************9997 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.7e-06    0.0022       7      65 ..      21      75 ..      17      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                                  HHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE-- CS
               Penicillinase_R  7 evmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYspl 65
                                   ++++l e+g++ v ++++el+++    + T+   l+ L k g+++++keg    Y+ +
  gi|15669515|ref|NP_248325.1| 21 MILKLLAENGSMCVCKIIDELKKP----QPTISHHLNILKKAGIVKARKEGTWNFYYIV 75
                                  58999*******************....99********************999888765 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.4e-05     0.018       7      86 ..      10      84 ..       5      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                  HHHCS-.HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHH CS
                   TFIIE_alpha  7 vrkfyg.eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvk 86
                                  ++k++g      +l+ L+e+g +    +  elk  ++ + + Ln L++a++vk +++     +w  ++++i ++++ +++k
  gi|15669515|ref|NP_248325.1| 10 IFKAFGdPTRLMILKLLAENGSMCVCKIIDELKKPQPTISHHLNILKKAGIVKARKE----GTW--NFYYIVDDRVKEIIK 84
                                  4555662566789***************************************99874....344..455566778888887 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.7e-05     0.022       3      48 ..      17      62 ..      16      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                                  HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR  3 ltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                  +t+++iL +l+e+g++ v ++ + l+  ++t++  l  L k+G ++
  gi|15669515|ref|NP_248325.1| 17 PTRLMILKLLAENGSMCVCKIIDELKKPQPTISHHLNILKKAGIVK 62
                                  6899***************************************996 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.5e-05     0.032       7      59 ..      16      68 ..      11      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.5e-05
                       DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegkt 59
                                  d+  l++lk l++ ++     i +el++p+  +++ l+ L+++G+++  ++ t
  gi|15669515|ref|NP_248325.1| 16 DPTRLMILKLLAENGSMCVCKIIDELKKPQPTISHHLNILKKAGIVKARKEGT 68
                                  678899****************************************9887766 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.8e-05       0.1       6      49 ..      20      62 ..       5      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.8e-05
                                  HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                  l+iL++lae +  + +  + +++  p +t +++L+ L + G+v+
  gi|15669515|ref|NP_248325.1| 20 LMILKLLAENGS-MCVCKIIDELKKPQPTISHHLNILKKAGIVK 62
                                  79**********.78**************************998 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     3e-05     0.039      14      59 ..      20      65 ..      18      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                                  HHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          Rrf2 14 llyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                  l++L++ +e++++ + +i ++ + +++ +++ l+ L+kag+vk+++
  gi|15669515|ref|NP_248325.1| 20 LMILKLLAENGSMCVCKIIDELKKPQPTISHHLNILKKAGIVKARK 65
                                  78889999999999*****************************985 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.5e-05     0.083       5      45 ..      22      62 ..      19      68 .. 0.94
   2 ?   -2.1   0.0       2.6   3.4e+03       1       9 [.      78      86 ..      78      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.5e-05
                      HTH_DeoR  5 ilellkqqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                  il+ll++ g++ v +++++l+  + Ti   Ln+L+++g+++
  gi|15669515|ref|NP_248325.1| 22 ILKLLAENGSMCVCKIIDELKKPQPTISHHLNILKKAGIVK 62
                                  9*************************************964 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                      HTH_DeoR  1 Rieqilell 9 
                                  R ++i++l+
  gi|15669515|ref|NP_248325.1| 78 RVKEIIKLV 86
                                  778898887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.7e-05      0.06       5      55 ..      17      65 ..      13      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.7e-05
                                  HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                  p+ +++L  L+ ++   + v  + ++l+ +++++s +l+ L +aG v  r+
  gi|15669515|ref|NP_248325.1| 17 PTRLMILKLLAENGS--MCVCKIIDELKKPQPTISHHLNILKKAGIVKARK 65
                                  888999999999998..99999*************************8774 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00019      0.24       6      45 ..      18      59 ..      16      67 .. 0.89
   2 ?   -2.7   0.0       4.6   5.9e+03       9      15 ..      81      87 ..      76      88 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                        HTH_23  6 eRlrillllae..GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                   Rl il+llae   ++v +I +eL  ++ T+++ l+  ++ G
  gi|15669515|ref|NP_248325.1| 18 TRLMILKLLAEngSMCVCKIIDELKKPQPTISHHLNILKKAG 59
                                  5999***************************99877765555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.6
                        HTH_23  9 rilllla 15
                                  +i++l++
  gi|15669515|ref|NP_248325.1| 81 EIIKLVD 87
                                  4777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 544.66
//
Query:       gi|15669516|ref|NP_248326.1|  [L=391]
Description: GTP1/Obg family GTP-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-39  131.8   0.9    1.7e-38  130.9   0.9    1.5  1  MMR_HSR1_Xtn    C-terminal region of MMR_HSR1 domain
    1.3e-24   86.0   0.0    2.6e-24   85.0   0.0    1.6  1  TGS             TGS domain
    1.2e-21   76.9   0.2    3.5e-21   75.4   0.0    1.9  2  MMR_HSR1        50S ribosome-binding GTPase
      4e-14   52.4   0.8    2.5e-11   43.4   0.0    2.2  2  FeoB_N          Ferrous iron transport protein B
    1.7e-08   34.6   1.3    0.00083   19.3   0.1    2.6  2  RsgA_GTPase     RsgA GTPase
    0.00077   19.1   0.8       0.39   10.3   0.1    2.5  3  cobW            CobW/HypB/UreG, nucleotide-binding domain
     0.0022   17.6   0.6       0.22   11.0   0.0    3.2  3  GTP_EFTU        Elongation factor Tu GTP binding domain
     0.0058   16.1   0.6     0.0094   15.4   0.6    1.2  1  RRG8            Required for respiratory growth protein 8 mit
      0.009   16.1   0.2        1.5    8.9   0.2    2.4  2  Dynamin_N       Dynamin family
     0.0094   16.1   0.4       0.26   11.5   0.0    2.9  3  YchF-GTPase_C   Protein of unknown function (DUF933)
  ------ inclusion threshold ------
      0.011   15.7   0.2       0.14   12.2   0.0    2.4  2  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
      0.028   14.2   0.2          2    8.1   0.0    2.3  2  ATP_bind_1      Conserved hypothetical ATP binding protein
      0.068   12.6   0.2        4.6    6.7   0.0    2.4  2  Arf             ADP-ribosylation factor family
      0.076   12.4   1.2       0.31   10.5   0.0    2.2  3  SRPRB           Signal recognition particle receptor beta sub
       0.21   11.9   0.2       0.56   10.4   0.2    1.7  1  AAA_28          AAA domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.9   0.9   1.4e-41   1.7e-38       1     105 [.     205     314 ..     205     315 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 1.4e-41
                  MMR_HSR1_Xtn   1 kgGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldelare.. 79 
                                   +gGi+++stv+lt++de+t+++il+ey+ihna+v+ired+t++++idv++gnrvYip+l+v+NKiDl+++e+l+ ++++  
  gi|15669516|ref|NP_248326.1| 205 RGGINVSSTVPLTHIDEDTIEAILNEYRIHNADVVIREDITLEQFIDVVAGNRVYIPSLVVVNKIDLADEEYLKYIKQKle 285
                                   69****************************************************************************878 PP

                  MMR_HSR1_Xtn  80 ...pnsvviSaekelnldeLkekiweeLn 105
                                      ++++ +S +k++nld Lkeki+e+L+
  gi|15669516|ref|NP_248326.1| 286 efgKDYILVSGNKGINLDLLKEKIYEKLG 314
                                   8888***********************97 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0   0.0   2.2e-27   2.6e-24       1      59 [.     316     388 ..     316     389 .. 0.99

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 2.2e-27
                                   EEEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                           TGS   1 irvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                   i++y+ P+Gk+pd      ++rgatv+D++ k+h++++++f+yA+V+G       qrvgldh+Ledgd+++Iv
  gi|15669516|ref|NP_248326.1| 316 IKIYLkPQGKKPDfdepliMRRGATVKDVCEKLHKDFVRNFRYAQVWGksakhpgQRVGLDHKLEDGDILTIV 388
                                   79**********************************************************************9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   2.9e-24   3.5e-21       2      87 ..      87     174 ..      86     204 .. 0.87
   2 ?   -2.2   0.0       3.5   4.2e+03      80      84 ..     266     270 ..     221     296 .. 0.58

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 2.9e-24
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adlill 81 
                                   +a+vG p vGKStL+n+lt++k++v+++++tT++i+ g +++kg +i+l+D pG+i gas++kg g ++l+  + adlill
  gi|15669516|ref|NP_248326.1|  87 AAFVGFPSVGKSTLLNKLTNAKSEVGAYAFTTLTIVPGILEYKGAKIQLLDAPGIIVGASSGKGRGTEVLSAVRsADLILL 167
                                   69****************************************************999******9999999977768***** PP

                                   EEETT.T CS
                      MMR_HSR1  82 vvdas.e 87 
                                    vd+   
  gi|15669516|ref|NP_248326.1| 168 TVDIYtL 174
                                   ***8742 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.5
                                   EEEEE CS
                      MMR_HSR1  80 llvvd 84 
                                   +  +d
  gi|15669516|ref|NP_248326.1| 266 VNKID 270
                                   22223 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   2.1e-14   2.5e-11       2     103 ..      86     186 ..      85     191 .. 0.77
   2 !    7.6   0.2    0.0021       2.5     105     156 .]     259     309 ..     217     309 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2.1e-14
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEE CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdvv 82 
                                   t a+vG p vGk+tl+n+lt+ak++vg ++ +t     g l++kg +++++D PGi  + a s   + ++ + + +++d++
  gi|15669516|ref|NP_248326.1|  86 TAAFVGFPSVGKSTLLNKLTNAKSEVGAYAFTTLTIVPGILEYKGAKIQLLDAPGII-VGASSGKGRGTEVLSAVRSADLI 165
                                   6799***************************************************94.33333333433333345667777 PP

                                   EEEEEGGGHHHHHHHHHHHHH CS
                        FeoB_N  83 vnvvdatnlernLyLtlqlle 103
                                   +  vd  +l+   +L  +l +
  gi|15669516|ref|NP_248326.1| 166 LLTVDIYTLDHLPVLEKELYN 186
                                   777777777666566555555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0021
                                   TSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                        FeoB_N 105 gvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellkai 156
                                    +p ++++n+id a+++ ++  ++kL+e +g + + +s++k+ +++ l+++i
  gi|15669516|ref|NP_248326.1| 259 YIPSLVVVNKIDLADEEYLKYIKQKLEE-FGKDYILVSGNKGINLDLLKEKI 309
                                   57889********************975.8****************999986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   4.1e-05     0.049      99     125 ..      84     109 ..      78     118 .. 0.83
   2 !   19.3   0.1     7e-07   0.00083      44     101 ..     257     313 ..     233     317 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-05
                                   TSEEEEECSTTSSHHHHHHHHCTT--- CS
                   RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelel 125
                                   d t+++vG   vGKStL+n+l++  + 
  gi|15669516|ref|NP_248326.1|  84 DATAAFVGFPSVGKSTLLNKLTNA-KS 109
                                   57999****************986.44 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 7e-07
                                   HTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSE CS
                   RsgA_GTPase  44 ekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdkt 101
                                   +  i+ ++v+nKiDl++ee  l+ +k++le++g + +lvs +++ +l+ lke++ +k+
  gi|15669516|ref|NP_248326.1| 257 RVYIPSLVVVNKIDLADEEY-LKYIKQKLEEFGKDYILVSGNKGINLDLLKEKIYEKL 313
                                   3456899************9.******************************9998775 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0035       4.2       4      25 ..      88     109 ..      85     115 .. 0.83
   2 ?   -3.8   0.0       6.7     8e+03     124     147 ..     141     167 ..     131     171 .. 0.64
   3 !   10.3   0.1   0.00033      0.39     103     167 ..     220     285 ..     176     293 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0035
                                   EEEESTTCCHHHHHHHHHCT-- CS
                          cobW   4 vltGflGsGKTtLlnhllenra 25 
                                    ++Gf+  GK+tLln+l++ ++
  gi|15669516|ref|NP_248326.1|  88 AFVGFPSVGKSTLLNKLTNAKS 109
                                   579**************96654 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.7
                                   H....CCHCCHHHHHHHHHHTSSEEEE CS
                          cobW 124 l...eaeeekieekaedqlaaadllvl 147
                                   +    ++++   +++ + +  adl++l
  gi|15669516|ref|NP_248326.1| 141 IivgASSGKGRGTEVLSAVRSADLILL 167
                                   444445566666677778888888887 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00033
                                   SHHHHHCCCECEEEEEEETTTH.....CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHH CS
                          cobW 103 eeelksdltldavvavvDaknl....eaeeekieekaedqlaaadllvlnKtDlldeeallekleerlr 167
                                   +e++ +++  +  +   D+  +     + e+ i   a++ +   +l+v+nK+Dl+dee l + ++++l+
  gi|15669516|ref|NP_248326.1| 220 DEDTIEAILNEYRIHNADV--ViredITLEQFIDVVAGNRVYIPSLVVVNKIDLADEEYL-KYIKQKLE 285
                                   4444444444444444444..12344455677778889999999************9955.66666655 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.11   1.3e+02      10      29 ..      91     110 ..      85     117 .. 0.78
   2 ?    0.6   0.0      0.29   3.5e+02      66      80 ..     127     141 ..     113     173 .. 0.59
   3 !   11.0   0.0   0.00018      0.22     122     154 ..     259     302 ..     246     369 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                                   ESTTSSHHHHHHHHHHHTTS CS
                      GTP_EFTU  10 ghvDhGKtTLtdrLlyktga 29 
                                   g    GK+TL+ +L+ ++++
  gi|15669516|ref|NP_248326.1|  91 GFPSVGKSTLLNKLTNAKSE 110
                                   55567*********987665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.29
                                   TCSSEEEEEEEESSS CS
                      GTP_EFTU  66 etkkylinliDtPGH 80 
                                   e+k  +i+l+D+PG 
  gi|15669516|ref|NP_248326.1| 127 EYKGAKIQLLDAPGI 141
                                   477888888898885 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00018
                                   TTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH...........H CS
                      GTP_EFTU 122 gvpiivfiNKmDrlkaelkeiveevkqklsrk...........e 154
                                    +p  v++NK+D +++e+ + +++  +++ ++            
  gi|15669516|ref|NP_248326.1| 259 YIPSLVVVNKIDLADEEYLKYIKQKLEEFGKDyilvsgnkginL 302
                                   57899*********999888877777788554455555444440 PP

>> RRG8  Required for respiratory growth protein 8 mitochondrial
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.6   7.9e-06    0.0094     196     263 ..     178     242 ..     154     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.9e-06
                          RRG8 196 erveledrDVvvtydkdnandielrkvksigkkdltvivlNlkvlkepelealvnklrnheegivlkv 263
                                   +++e e  +V ++ d+   +d++++ vk+ g+ ++  + + l  ++e+++ea++n+ r h+ ++v++ 
  gi|15669516|ref|NP_248326.1| 178 PVLEKELYNVGIRLDQT-PPDVKIK-VKERGGINVSST-VPLTHIDEDTIEAILNEYRIHNADVVIRE 242
                                   57888999999999998.9*****9.9*9999776665.58************************985 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.2    0.0012       1.5       2      22 ..      88     108 ..      87     123 .. 0.81
   2 ?    4.8   0.0     0.023        27      96     137 ..     126     170 ..     115     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0012
                                   EEEEBTTTTHHHHHHHHHTS- CS
                     Dynamin_N   2 avvGsqSsGKSSvlnaLlged 22 
                                   a+vG  S GKS++ln+L+ ++
  gi|15669516|ref|NP_248326.1|  88 AFVGFPSVGKSTLLNKLTNAK 108
                                   689999***********9876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.023
                                   EETTS-SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEE CS
                     Dynamin_N  96 lsllvkgltlvDlPGldsvnkrdq...elvkeyikkadiilavts 137
                                   l+ +  ++ l+D PG++  +   +     v +++++ad+il+ ++
  gi|15669516|ref|NP_248326.1| 126 LEYKGAKIQLLDAPGIIVGASSGKgrgTEVLSAVRSADLILLTVD 170
                                   56667899********99888877788999999999999998766 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.6   3.1e+03      61      76 ..     281     296 ..     264     297 .. 0.71
   2 !   11.5   0.0   0.00022      0.26      17      44 ..     335     362 ..     333     368 .. 0.92
   3 ?    0.8   0.0      0.49   5.8e+02      65      81 ..     371     387 ..     364     389 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.6
                 YchF-GTPase_C  61 agklrlegkdyvvqdg 76 
                                   ++kl+  gkdy++  g
  gi|15669516|ref|NP_248326.1| 281 KQKLEEFGKDYILVSG 296
                                   67889999*9998655 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00022
                 YchF-GTPase_C  17 ikkgttapqaAgviHsDfekgFiraevi 44 
                                   +++g+t+++ + + H+Df ++F  a+v 
  gi|15669516|ref|NP_248326.1| 335 MRRGATVKDVCEKLHKDFVRNFRYAQVW 362
                                   689**********************996 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.49
                 YchF-GTPase_C  65 rlegkdyvvqdgDiilf 81 
                                   ++ g d+ ++dgDi+++
  gi|15669516|ref|NP_248326.1| 371 QRVGLDHKLEDGDILTI 387
                                   5678999*******976 PP

>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.14      30      59 ..      17      47 ..      16      62 .. 0.88
   2 ?    0.5   0.0      0.51   6.1e+02      54      83 ..     218     251 ..     211     253 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                  EEEEEESBSS.SSHCHHHHHHHTTSBSSHHH CS
                Lip_prot_lig_C 30 dikiyGDffg.pkdieeleekLigvkyekea 59
                                  +++i GD +g +++i ++ee+L+ ++y+k++
  gi|15669516|ref|NP_248326.1| 17 KFNIVGDVMGiEEEIRRIEEELKKTPYNKAT 47
                                  689*******8999**************976 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.51
                                   BSSHHHHHHHHHTSCHHHHCC....THHHHHHHH CS
                Lip_prot_lig_C  54 kyekeaieealekidlseyfg....gieleelle 83 
                                   ++++++ie++l+++++ +       +i+le++++
  gi|15669516|ref|NP_248326.1| 218 HIDEDTIEAILNEYRIHNADVvireDITLEQFID 251
                                   6789999999997764432112357888888887 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.034        41       2      23 ..      90     111 ..      89     118 .. 0.85
   2 ?    8.1   0.0    0.0017         2     150     187 ..     253     291 ..     237     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.034
                    ATP_bind_1   2 vGpaGsGKttfvgalseilelr 23 
                                   vG +++GK+t+ ++l++  ++ 
  gi|15669516|ref|NP_248326.1|  90 VGFPSVGKSTLLNKLTNAKSEV 111
                                   89************99876665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0017
                    ATP_bind_1 150 samlrlelPhvvvlnkfDllkek.lekeleffedveals 187
                                    a  r+ +P +vv+nk+Dl++e+ l++  + +e++ +  
  gi|15669516|ref|NP_248326.1| 253 VAGNRVYIPSLVVVNKIDLADEEyLKYIKQKLEEFGKDY 291
                                   55667889***********99889888888888876655 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0038       4.6      18      64 ..      88     137 ..      78     142 .. 0.72
   2 ?    3.7   0.1     0.031        37     116     141 ..     260     285 ..     224     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0038
                                   EEEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEETTEEEEEEE CS
                           Arf  18 lllGLDnaGKtTilkklkleelvt...tvPTigfnveeleiknlkftvwD 64 
                                    ++G  + GK+T+l+kl++ + +       T+      le+k+ k+++ D
  gi|15669516|ref|NP_248326.1|  88 AFVGFPSVGKSTLLNKLTNAKSEVgayAFTTLTIVPGILEYKGAKIQLLD 137
                                   689999***********987765434444555555566777777777777 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.031
                                   SEEEEEEE-TTSTTSS-HHHHHHHTT CS
                           Arf 116 vallvlaNKqDlpealseeelrellg 141
                                   ++ lv+ NK+Dl++    + ++++l+
  gi|15669516|ref|NP_248326.1| 260 IPSLVVVNKIDLADEEYLKYIKQKLE 285
                                   56799*******99998888888876 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   0.2       8.5     1e+04     138     154 ..      28      44 ..      27      53 .. 0.72
   2 ?   10.5   0.0   0.00026      0.31       7      58 ..      88     140 ..      83     143 .. 0.82
   3 ?   -0.1   0.0      0.46   5.6e+02     110     139 ..     257     286 ..     245     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 8.5
                                   HHHHHHHHHCHHHHHH- CS
                         SRPRB 138 EkElnkiierrskalke 154
                                   E+E+ +i e  +k + +
  gi|15669516|ref|NP_248326.1|  28 EEEIRRIEEELKKTPYN 44 
                                   88888888887777655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00026
                                   EEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT CS
                         SRPRB   7 llvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPG 58 
                                    +vG    GK +l+++Lt+ + +    +    +++  + + kg k++l+D PG
  gi|15669516|ref|NP_248326.1|  88 AFVGFPSVGKSTLLNKLTNAKSEVGAYAFtTLTIVPGILEYKGAKIQLLDAPG 140
                                   589***************99666655555466777777888***********9 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.46
                                   TT---EEEEEE-TTSTT---HHHHHHHHHH CS
                         SRPRB 110 kdavdiliACnKqelflakspklikdaLEk 139
                                   +  ++ l+  nK +l+     k ik++LE+
  gi|15669516|ref|NP_248326.1| 257 RVYIPSLVVVNKIDLADEEYLKYIKQKLEE 286
                                   4567889999******************95 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00047      0.56       3      25 ..      88     110 ..      86     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
                        AAA_28   3 vitGgestGKTtlleaLaargyp 25 
                                   +++G +s GK+tll++L++ + +
  gi|15669516|ref|NP_248326.1|  88 AFVGFPSVGKSTLLNKLTNAKSE 110
                                   6899*************987544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1021  (0.0569468); expected 358.6 (0.02)
Passed bias filter:                      839  (0.0467957); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 2613.86
//
Query:       gi|15669517|ref|NP_248327.1|  [L=245]
Description: hypothetical protein MJ_1327 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1680.02
//
Query:       gi|15669518|ref|NP_248329.1|  [L=298]
Description: type II R/M system modification methyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-05   23.1   0.4    0.00021   21.3   0.4    2.0  2  TaqI_C    TaqI-like C-terminal specificity domain
  ------ inclusion threshold ------
        1.1    9.9   4.5         21    5.8   4.4    2.2  1  DUF3800   Protein of unknown function (DUF3800)


Domain annotation for each model (and alignments):
>> TaqI_C  TaqI-like C-terminal specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.31   2.8e+03      38      50 ..      28      43 ..       5      99 .. 0.66
   2 !   21.3   0.4   2.4e-08   0.00021      18     115 ..     109     228 ..      75     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.31
                        TaqI_C 38 e...ekpKilvrdisk 50
                                  +   + p++l++di+k
  gi|15669518|ref|NP_248329.1| 28 TkipDFPHVLLKDIAK 43
                                  4555567777777765 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.4e-08
                        TaqI_C  18 gnYldlikkklkneka.........kelfe..............ekpKilvrdisk..kldaaydekayyvlntlylliak 73 
                                   ++Y +++kk lk + +         k++f+              +k++i v+ + +   +++ + + + + + +++ ++ +
  gi|15669518|ref|NP_248329.1| 109 TKYPNIYKKLLKFKDRmenrylpknKKWFNwqalrnykfliknlNKKRIYVPTLDRkpYNRFSLGDDELLPSGDVIFIQPY 189
                                   455555555444444333444456699999999999999999999******9998833566******************** PP

                        TaqI_C  74 delevslkyllgiLNSklikfyykkiystlrggysrlkrkel 115
                                   ++   ++ +llg+LNS+    yy      +rgg + +++k l
  gi|15669518|ref|NP_248329.1| 190 NDD--DIYFLLGYLNSSFFRNYYLANG-GRRGGRVAFTQKLL 228
                                   *99..99*************9987766.34466666655555 PP

>> DUF3800  Protein of unknown function (DUF3800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.4    0.0024        21      13      74 ..      79     275 ..      52     295 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0024
                       DUF3800  13 kdgsspyfvlgg..............kkie.eikkleekikelkkky.................................. 44 
                                   k ++ + fv+ g              ++++ ++ ++++k+ ++k+++                                  
  gi|15669518|ref|NP_248329.1|  79 KAKNCKRFVVEGfvqyiliednlkdeEIFKtKYPNIYKKLLKFKDRMenrylpknkkwfnwqalrnykfliknlnkkriyv 159
                                   556666777777788888888887765666888889999999988888888888888888888888877777777777777 PP

                       DUF3800  45 ................................................................................. 44 
                                                                                                                    
  gi|15669518|ref|NP_248329.1| 160 ptldrkpynrfslgddellpsgdvifiqpyndddiyfllgylnssffrnyylanggrrggrvaftqkllenakiptfsdev 240
                                   777777777777777777777777777777777777777777777777777777777777777776666666666666555 PP

                       DUF3800  45 ....krlleriakflkkn.dliksdeesdesiliv 74 
                                       k++++ i + lk+  d+++++++ d+ i+  
  gi|15669518|ref|NP_248329.1| 241 kekiKNIVKDIIYNLKNGkDIENLERQIDYIIVSA 275
                                   44445555555555544322222434333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2153.98
//
Query:       gi|15669519|ref|NP_248330.1|  [L=294]
Description: methionine aminopeptidase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-40  137.6   0.0    5.3e-40  137.3   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24
  ------ inclusion threshold ------
       0.17   11.4   0.0       0.23   11.0   0.0    1.2  1  ApbE           ApbE family


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.3   0.0   5.9e-44   5.3e-40       2     209 .]       8     286 ..       7     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 137.3 bits;  conditional E-value: 5.9e-44
                                   HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC...SSSB--TTEEEEE CS
                 Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp...ndrvlkegdlvli 79 
                                   +i +a++ias+++e++++ i pgv+  e+a+++e++  +r+ ++++afp  + +++n+ ++hytp   ++ ++k++d+v++
  gi|15669519|ref|NP_248330.1|   8 KIIEAGKIASKVREEAVKLIXPGVKLLEVAEFVENR--IRELGGEPAFP--CNISINEIAAHYTPklnDNLEFKDDDVVKL 84 
                                   7889******************************98..778889*****..8888888888****65334458******** PP

                                   EEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESS. CS
                 Peptidase_M24  80 dagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGl. 159
                                   d+ga++dgy++D++ Tv +   ++ +++l++a ++a++++ik++ p ++++e++++++ev+es+g+ k++ ++ GH + + 
  gi|15669519|ref|NP_248330.1|  85 DLGAHVDGYIADTAITVDL---SNSYKDLVKASEDALYTVIKEINPPMNIGEMGKIIQEVIESYGY-KPISNLSGHVMHRy 161
                                   *****************88...678*****************************************.************99 PP

                                   SSSEE..EEEESSSTTCSSB--TTBEEEEEE......EEEEETTT.................................... CS
                 Peptidase_M24 160 evhde..gpsvsresndgrkleeGmvftiEp......giyfapge.................................... 196
                                   e+h +   p+v+  +++++ +  G+ ++iEp      g++  +g+                                    
  gi|15669519|ref|NP_248330.1| 162 ELHTGisIPNVY--ERTNQYIDVGDLVAIEPfatdgfGMV-KDGNlgniykflakrpirlpqarklldvisknypylpfae 239
                                   ***985555666..568999***********888866333.2333455666666677777888888888888888888888 PP

                                   .................................E.EEEEBEEEEEES CS
                 Peptidase_M24 197 .................................g.gvriedtvlvte 209
                                                                    g + + e+t+l+te
  gi|15669519|ref|NP_248330.1| 240 rwvlkneserlalnslirasciygypilkerenGiVGQAEHTILITE 286
                                   99999999999999999999999999999999977889999999997 PP

>> ApbE  ApbE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.5e-05      0.23     111     137 ..      76     101 ..      15     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.5e-05
                                   EESTT..-----TTTHHHHHHHHHHHH CS
                          ApbE 111 lakkgpgmkLDlggiaKGyavdrvael 137
                                   + k+++ +kLDlg+   Gy++d ++ +
  gi|15669519|ref|NP_248330.1|  76 F-KDDDVVKLDLGAHVDGYIADTAITV 101
                                   3.345579**************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1991.63
//
Query:       gi|15669520|ref|NP_248331.1|  [L=127]
Description: hypothetical protein MJ_1330 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-18   66.7   0.0    2.5e-18   66.5   0.0    1.0  1  PgpA             Phosphatidylglycerophosphatase A
     0.0026   17.4   0.0     0.0039   16.8   0.0    1.2  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
  ------ inclusion threshold ------
       0.13   11.4   0.0       0.22   10.7   0.0    1.3  1  dCache_2         Cache domain


Domain annotation for each model (and alignments):
>> PgpA  Phosphatidylglycerophosphatase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.0   4.1e-22   2.5e-18      42     142 ..      31     126 ..      13     127 .] 0.86

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 4.1e-22
                                   H.HHHHHHHHHHHHHHHHHHT.-S-...HHT-TT--HHHHTTHHHHH........TTHHHHHHHHHHHHS--THHHHTSSS CS
                          PgpA  42 l.llilllflvGiwackktek.elg...ekDpgeiviDEvvgqwiallllpatllalllafilFrlfDivKpgpigwldrk 117
                                     +++++l++++i ++++ ++ +l    ++Dp+ +++DEv+g++ia+       +a + a+++Fr++D+ Kpg+ig ldrk
  gi|15669520|ref|NP_248331.1|  31 SnPNVSTLLIAAILLDNEGRAnNLPfnyNEDPNYVYVDEVIGLAIAN------EIAGTKAIFNFRFYDAKKPGIIGELDRK 105
                                   2468889999999999999986776999*******************......34569**********************7 PP

                                   .-S---TTHHHHHHHHHHHHHHHHH CS
                          PgpA 118 lkgglgvmlDDllAgiaaalvlali 142
                                         ++lDD++Ag++a+++++++
  gi|15669520|ref|NP_248331.1| 106 ----GFMFLDDAIAGLLAGCMSKVF 126
                                   ....4579*************9987 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.6e-07    0.0039      34      68 ..      10      44 ..       8      45 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.6e-07
               Cation_ATPase_N 34 GpNelkekkkkslwvkllkqftnplvilLlvaalv 68
                                  G+Ne  ++ k+ l ++llkq++np v  Ll+aa++
  gi|15669520|ref|NP_248331.1| 10 GSNEERDRVKEKLKEILLKQLSNPNVSTLLIAAIL 44
                                  999999***************************97 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.7e-05      0.22     173     201 ..       6      34 ..       4      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.7e-05
                      dCache_2 173 dwiIGtgaylddieeelkqellktlksir 201
                                   d++IG+ + +d ++e+lk++llk+l++ +
  gi|15669520|ref|NP_248331.1|   6 DLYIGSNEERDRVKEKLKEILLKQLSNPN 34 
                                   89***********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 972.27
//
Query:       gi|15669521|ref|NP_248332.1|  [L=144]
Description: hypothetical protein MJ_1331 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0012   19.2   0.0     0.0022   18.4   0.0    1.4  1  Acylphosphatase  Acylphosphatase
     0.0063   16.8   2.1       0.19   12.1   2.1    2.2  2  RNA_pol_Rpb4     RNA polymerase Rpb4
  ------ inclusion threshold ------
      0.013   15.2   0.2      0.018   14.7   0.2    1.3  1  Snf7             Snf7
      0.055   12.7   0.1       0.06   12.6   0.1    1.1  1  Dynein_C         Dynein heavy chain C-terminal domain
      0.072   13.1   1.0       0.11   12.5   0.4    1.7  2  LOH1CR12         Tumour suppressor protein
      0.079   12.8   1.5       0.47   10.4   0.6    2.3  2  DUF4041          Domain of unknown function (DUF4041)
        0.1   12.8   0.1       0.17   12.1   0.1    1.3  1  DUF2316          Uncharacterized protein conserved in bacteri
       0.19   11.4   0.0       0.28   10.8   0.0    1.2  1  IL11             Interleukin 11
       0.49   10.6   3.1        1.8    8.8   1.0    2.4  2  DASH_Dad1        DASH complex subunit Dad1


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-06    0.0022       1      79 [.       9      90 ..       9      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
               Acylphosphatase  1 vrllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppk....arvdeveveeleeeee 79
                                  ++l+++G+V    F   v +l k l ++G v   +d  V+i+a  + ek +++ +e+ ++ +     ++v+++e  +l++  e
  gi|15669521|ref|NP_248332.1|  9 YELRIYGNVECAEFIDKVESLGKLLDVNGVVYVYKDS-VRILANFPNEKKRQLFKEIIKDLEDdgglIKVERIEERDLNTYIE 90
                                  6799****************************99999.*******87776666666666444445789999999998877655 PP

>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.038        76      43      83 ..      40      80 ..      35      86 .. 0.84
   2 !   12.1   2.1   9.5e-05      0.19      34      73 ..      99     139 ..      55     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.038
                                  HHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTST.STHHHHH CS
                  RNA_pol_Rpb4 43 kilkktleyltnkfsrlkneekfnelvellksfe.LtkaEkl 83
                                  ++ k+++  l n f + k+++ f+e+++ l+  + L k E++
  gi|15669521|ref|NP_248332.1| 40 YVYKDSVRILAN-FPNEKKRQLFKEIIKDLEDDGgLIKVERI 80
                                  567888889998.888888999********988888888876 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 9.5e-05
                                   SHCHTCHHCHHHHHHHHHHHCTHHTTSSHHH.HHHHHHHHT CS
                  RNA_pol_Rpb4  34 keevkgnlnkilkktleyltnkfsrlkneek.fnelvellk 73 
                                    ++  ++ nk l kt++yl+n f++l++++k  +e+++ lk
  gi|15669521|ref|NP_248332.1|  99 STNELKEINKKLDKTISYLENIFNALEKQIKvSEEIRDILK 139
                                   444578999**********************5556666666 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   8.8e-06     0.018      90     132 ..      99     143 ..      76     144 .] 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.8e-06
                                   HHHHHHHHHHCTC..CHHHHHHHHHHHHHHHHHTCHHHHHHHHHT CS
                          Snf7  90 gakamkamnkkvd..idkidklmdeiedqmekaeeisEalsrsld 132
                                   +++++k++nkk+d  i  ++++   +e+q++++eei ++l ++++
  gi|15669521|ref|NP_248332.1|  99 STNELKEINKKLDktISYLENIFNALEKQIKVSEEIRDILKDTFE 143
                                   799*********877999************************985 PP

>> Dynein_C  Dynein heavy chain C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     3e-05      0.06      33     109 ..      57     140 ..      19     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                                   -------------.....----..............-HHHHHHHHHHHHHHHHHHHHHHHHHHHHC---------HHHHHH CS
                      Dynein_C  33 vlelaadileklpe...lfdleeaekk....pteyeeplntvllqElerfnkLleeirrsLkelqkaikGevvmseeleel 106
                                    ++l ++i++ l +   l+++e+ e++      e ++ ln + + El+++nk l++  + L+++ +a++ ++++see++++
  gi|15669521|ref|NP_248332.1|  57 KRQLFKEIIKDLEDdggLIKVERIEERdlntYIEFPNGLNKISTNELKEINKKLDKTISYLENIFNALEKQIKVSEEIRDI 137
                                   44556666666664333335554222245567888999******************************************9 PP

                                   HHH CS
                      Dynein_C 107 ans 109
                                   +++
  gi|15669521|ref|NP_248332.1| 138 LKD 140
                                   986 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.8   3.6e+03     105     119 ..      21      35 ..      16      38 .. 0.77
   2 ?   12.5   0.4   5.5e-05      0.11      72     120 ..      78     127 ..      46     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.8
                      LOH1CR12 105 divpllEtlnelLde 119
                                   + ++ +E l +lLd+
  gi|15669521|ref|NP_248332.1|  21 EFIDKVESLGKLLDV 35 
                                   668888999888886 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.5e-05
                      LOH1CR12  72 lrekqkqyasyaealskvnels.dqlsriqiiledivpllEtlnelLded 120
                                    r +++  + y+e  +++n++s ++l+ i++ l++++  lE++ + L+++
  gi|15669521|ref|NP_248332.1|  78 ERIEERDLNTYIEFPNGLNKIStNELKEINKKLDKTISYLENIFNALEKQ 127
                                   4555666788999999*****8457******************9999865 PP

>> DUF4041  Domain of unknown function (DUF4041)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.21   4.3e+02       8      19 ..      16      27 ..      11      29 .. 0.89
   2 ?   10.4   0.6   0.00024      0.47      15      49 ..      95     129 ..      90     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.21
                       DUF4041  8 NgEcdaaiskVk 19
                                  N Ec+  i kV 
  gi|15669521|ref|NP_248332.1| 16 NVECAEFIDKVE 27
                                  88********95 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00024
                       DUF4041  15 iskVkynnietlekRIeksfeainklgktmnirIt 49 
                                   ++k++ n ++ ++k++ k+ + +++++ +++ +I+
  gi|15669521|ref|NP_248332.1|  95 LNKISTNELKEINKKLDKTISYLENIFNALEKQIK 129
                                   689*************************9987775 PP

>> DUF2316  Uncharacterized protein conserved in bacteria (DUF2316)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.7e-05      0.17      20      64 ..      97     141 ..      80     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.7e-05
                       DUF2316  20 elsgltveevaedLnlttekvekvLelkasrledvWilrdyLeek 64 
                                   ++s+ +++e+ ++L+ t +++e++++  +++++    +rd L+++
  gi|15669521|ref|NP_248332.1|  97 KISTNELKEINKKLDKTISYLENIFNALEKQIKVSEEIRDILKDT 141
                                   56788899********************************99985 PP

>> IL11  Interleukin 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00014      0.28      71     120 ..      83     132 ..      76     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                          IL11  71 tdlksyekHfdWLkkvskkskhslepklgelisklkrLlkslqllmskle 120
                                   +dl+ y +  + L+k+s ++ + +++kl + is l+++ + l+++++  e
  gi|15669521|ref|NP_248332.1|  83 RDLNTYIEFPNGLNKISTNELKEINKKLDKTISYLENIFNALEKQIKVSE 132
                                   689999999999********************************998655 PP

>> DASH_Dad1  DASH complex subunit Dad1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.23   4.6e+02       4      18 ..      55      69 ..      52      71 .. 0.85
   2 ?    8.8   1.0   0.00091       1.8      10      44 ..     103     137 ..     100     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.23
                     DASH_Dad1  4 rqRdrliqeIaesme 18
                                  +++++l +eI + +e
  gi|15669521|ref|NP_248332.1| 55 EKKRQLFKEIIKDLE 69
                                  67899*****99988 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00091
                     DASH_Dad1  10 iqeIaesmeevlnnlnaLNRsLEeviavgkeFesV 44 
                                   ++eI++++++ ++ l+ +   LE+ i+v++e+ ++
  gi|15669521|ref|NP_248332.1| 103 LKEINKKLDKTISYLENIFNALEKQIKVSEEIRDI 137
                                   68*****************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1605  (0.0895198); expected 358.6 (0.02)
Passed bias filter:                      797  (0.0444531); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1006.10
//
Query:       gi|15669522|ref|NP_248333.1|  [L=393]
Description: translation-associated GTPase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-34  116.7   1.8      9e-34  116.4   0.4    1.9  2  MMR_HSR1_C      GTPase of unknown function C-terminal
    7.8e-26   90.4   0.0    3.1e-24   85.2   0.0    2.6  2  MMR_HSR1        50S ribosome-binding GTPase
    1.6e-15   56.8   0.1      3e-15   56.0   0.1    1.4  1  TGS             TGS domain
    2.1e-12   46.8   0.2    1.1e-09   38.0   0.1    2.6  2  FeoB_N          Ferrous iron transport protein B
     0.0014   18.3   2.1       0.92    9.0   0.4    3.2  3  GTP_EFTU        Elongation factor Tu GTP binding domain
     0.0072   17.0   0.5      0.067   13.8   0.1    2.5  2  RTP             Replication terminator protein
     0.0079   16.4   1.5       0.24   11.6   0.0    3.0  3  YchF-GTPase_C   Protein of unknown function (DUF933)
  ------ inclusion threshold ------
      0.011   14.7   0.1       0.31   10.0   0.0    2.4  2  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
      0.036   14.1   0.8        1.3    9.0   0.0    3.4  4  Dynamin_N       Dynamin family
      0.086   12.7   0.2        3.4    7.6   0.0    2.3  2  RsgA_GTPase     RsgA GTPase
      0.088   12.5   1.6       0.95    9.1   0.2    2.3  2  DUF4423         Domain of unknown function (DUF4423)
      0.099   13.2   1.3       0.37   11.3   0.0    2.5  2  AAA_18          AAA domain
       0.11   12.7   0.1        1.9    8.7   0.0    2.9  2  Roc             Ras of Complex, Roc, domain of DAPkinase
       0.14   12.3   3.4       0.79    9.9   0.9    2.5  2  MetOD2          Metanogen output domain 2
       0.14   12.0   0.0       0.31   11.0   0.0    1.6  1  Ploopntkinase3  P-loop Nucleotide Kinase3


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.5   5.4e+03      10      28 ..     147     165 ..     136     173 .. 0.69
   2 !  116.4   0.4   7.5e-37     9e-34       1     112 []     218     323 ..     218     323 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.5
                    MMR_HSR1_C  10 adenieklkekypkdkkvv 28 
                                    ++n++kl+++ +++k++v
  gi|15669522|ref|NP_248333.1| 147 LTKNWDKLARRAQQEKNIV 165
                                   5688888888888777666 PP

  == domain 2  score: 116.4 bits;  conditional E-value: 7.5e-37
                    MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekirdlv 81 
                                   a+NKaD+p+a++nie+lk+++++   v+p+sA++ElaL++a+k+g+ik ++  +dfei +++  +++e++++a ++i+d +
  gi|15669522|ref|NP_248333.1| 218 AANKADHPDAEKNIERLKKEFKDYI-VIPTSAEIELALKRAEKAGIIKRKE--NDFEIIDES--KVNEQMRRAFDYIKD-F 292
                                   89********************665.*********************9875..69***9994..5**************.* PP

                    MMR_HSR1_C  82 lkrygsTGVqealnaavfelldlivVYPVed 112
                                   lk+yg+TGVqe++n+a f+lld+ivVYPVed
  gi|15669522|ref|NP_248333.1| 293 LKKYGGTGVQECINKAYFDLLDMIVVYPVED 323
                                   *****************************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.0   2.6e-27   3.1e-24       2     103 ..       4     138 ..       3     152 .. 0.78
   2 ?    2.0   0.2      0.17   2.1e+02      81     114 .]     185     221 ..     154     221 .. 0.54

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 2.6e-27
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.........................EEEEECGGCS CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.........................ielvDtpGli 57 
                                   +++vG+pNvGKSt++nalt++ a+++++p+tT+++n+g   +   +                         +e++D++Gl+
  gi|15669522|ref|NP_248333.1|   4 IGLVGKPNVGKSTMFNALTEKPAEIGNYPFTTIQPNKGIAYITS-PcpckelgvkcnprnskcidgirhipVEVIDVAGLV 83 
                                   89************************************988442.22344444445555555555556666********99 PP

                                   SHHHHHHHHHHHHHHHHC.TSEEEEEEETT.........TTCSHHHHHHHHHHHHH CS
                      MMR_HSR1  58 egaseekglgkaflalee.adlillvvdas.........eeklkpldeeleellee 103
                                    ga+e++g+g++fl+  + ad+++lvvdas         +e+++p+ e+++ ll+e
  gi|15669522|ref|NP_248333.1|  84 PGAHEGRGMGNKFLDDLRqADAFILVVDASgktdaegnpTENYDPV-EDVKFLLNE 138
                                   9*************977769********998888877775567777.666666654 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.17
                                   EEEETTTT..CSHHHH.HHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  81 lvvdasee..klkpld.eeleelleeakkplilvlnk 114
                                    + d+ e+  k++++d  +l++ l++  kp+i+++nk
  gi|15669522|ref|NP_248333.1| 185 AIRDMDESpiKWTEEDlLNLAKKLRKISKPMIIAANK 221
                                   33333322123333322455555666999*****998 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.1   2.5e-18     3e-15       4      59 ..     334     389 ..     327     390 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 2.5e-18
                                   EETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                           TGS   4 ytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                   ++Pd+ +  +++g+t++D+Ayk+h++l++kfiyA+  +   rvg d++L+++d+++Iv
  gi|15669522|ref|NP_248333.1| 334 VLPDAFL--VKKGSTARDLAYKVHTELGEKFIYAIDAKkkIRVGADYELKHNDIIKIV 389
                                   4566666..*****************************766****************9 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.1   9.5e-13   1.1e-09       3      41 ..       4      42 ..       2      48 .. 0.91
   2 !    6.4   0.0     0.005       5.9      94     144 ..     201     249 ..     177     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 9.5e-13
                                  EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEE CS
                        FeoB_N  3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegk 41
                                  + lvG+pnvGk+t+fnalt++  ++gN+p +t++ ++g 
  gi|15669522|ref|NP_248333.1|  4 IGLVGKPNVGKSTMFNALTEKPAEIGNYPFTTIQPNKGI 42
                                  789******************************988876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.005
                                   HHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHT.S-EEEEBTT CS
                        FeoB_N  94 nLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLg.vpvvktsak 144
                                    L L  +l  +++p+++a n+ d+ ++++   ++++L+++++   v++tsa+
  gi|15669522|ref|NP_248333.1| 201 LLNLAKKLRKISKPMIIAANKADHPDAEK---NIERLKKEFKdYIVIPTSAE 249
                                   588999***************99877655...67778777753667777776 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.02        23       5      31 ..       3      29 ..       1      37 [. 0.87
   2 ?    2.7   0.1     0.068        81      91     105 ..     100     114 ..      92     173 .. 0.85
   3 !    9.0   0.4   0.00077      0.92     114     154 ..     204     254 ..     180     322 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.02
                                  EEEEEESTTSSHHHHHHHHHHHTTSSC CS
                      GTP_EFTU  5 nigiighvDhGKtTLtdrLlyktgais 31
                                   ig++g  + GK+T+  +L++k  +i 
  gi|15669522|ref|NP_248333.1|  3 MIGLVGKPNVGKSTMFNALTEKPAEIG 29
                                  58999**************99877765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.068
                                   HHT-SEEEEEEETTT CS
                      GTP_EFTU  91 lrvlDgavlvvdave 105
                                   lr++D  +lvvda+ 
  gi|15669522|ref|NP_248333.1| 100 LRQADAFILVVDASG 114
                                   89**********984 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00077
                                   HHHHHHHTTTEEEEEEESCGST..HHHHHHHHHHHHHHHHHH..........H CS
                      GTP_EFTU 114 vlrlalkegvpiivfiNKmDrl..kaelkeiveevkqklsrk..........e 154
                                   +++ ++k   p+i++ NK+D++  +++++++++e k+ +  +           
  gi|15669522|ref|NP_248333.1| 204 LAKKLRKISKPMIIAANKADHPdaEKNIERLKKEFKDYI--ViptsaeielaL 254
                                   34455566677**********977666777777766544..133544444441 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   5.6e-05     0.067      15      66 ..     217     268 ..     204     282 .. 0.81
   2 ?    0.1   0.1         1   1.2e+03      28      69 ..     285     326 ..     270     371 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-05
                                   HHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEE CS
                           RTP  15 itlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrke 66 
                                   i   + ++  + k +++lkkeFk++   P+ +ei  al+   + gi+kr+++
  gi|15669522|ref|NP_248333.1| 217 IAANKADHPDAEKNIERLKKEFKDYIVIPTSAEIELALKRAEKAGIIKRKEN 268
                                   555555555677889********************************99875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                                   HHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBT CS
                           RTP  28 lldelkkeFkelgykPnhseiyralhelvedgilkrrkelke 69 
                                     d +k+  k++g +  +  i +a+ +l++  +++ ++  ++
  gi|15669522|ref|NP_248333.1| 285 AFDYIKDFLKKYGGTGVQECINKAYFDLLDMIVVYPVEDENK 326
                                   467777777888888888888888888888877776655543 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.2   1.5e+03      34      75 ..     234     274 ..     217     278 .. 0.67
   2 !   11.6   0.0    0.0002      0.24      14      41 ..     338     365 ..     332     371 .. 0.91
   3 ?    2.1   0.1      0.19   2.3e+02      62      81 ..     369     388 ..     365     390 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.2
                 YchF-GTPase_C  34 fekgFiraevikyedlvelgseaaakeagklrlegkdyvvqd 75 
                                   ++k+F    vi  +  +el   ++a++ag ++++  d+ + d
  gi|15669522|ref|NP_248333.1| 234 LKKEFKDYIVIPTSAEIEL-ALKRAEKAGIIKRKENDFEIID 274
                                   4555555555555555555.5677788888888887777655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0002
                 YchF-GTPase_C  14 aWtikkgttapqaAgviHsDfekgFira 41 
                                   a+ +kkg+ta + A ++H+++ ++Fi a
  gi|15669522|ref|NP_248333.1| 338 AFLVKKGSTARDLAYKVHTELGEKFIYA 365
                                   6789**********************88 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.19
                 YchF-GTPase_C  62 gklrlegkdyvvqdgDiilf 81 
                                   +k  + g dy ++++Dii +
  gi|15669522|ref|NP_248333.1| 369 KKKIRVGADYELKHNDIIKI 388
                                   4445679**********975 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00026      0.31      31      57 ..       3      29 ..       1      32 [. 0.87
   2 ?    2.3   0.0     0.057        68     171     192 ..     216     237 ..     200     318 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00026
                                  EEEEEE-TTSSHHHHHHHHHHHHHCTT CS
                          MeaB 31 vvGltGvPGaGkstlvealglelrrrG 57
                                  ++Gl G P +Gkst+ +al+++ ++ G
  gi|15669522|ref|NP_248333.1|  3 MIGLVGKPNVGKSTMFNALTEKPAEIG 29
                                  69*****************98866655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.057
                                   EEEEE---HHHHHHHHHHHHHH CS
                          MeaB 171 iivvnkaDkkeaekaarelraa 192
                                   ii+ nkaD+++aek  + l++ 
  gi|15669522|ref|NP_248333.1| 216 IIAANKADHPDAEKNIERLKKE 237
                                   7889****99999988777654 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0011       1.3       1      22 [.       4      25 ..       4      40 .. 0.81
   2 ?   -0.2   0.0      0.73   8.8e+02     103     139 ..      74     113 ..      63     127 .. 0.76
   3 ?   -1.4   0.0       1.8   2.2e+03     141     167 ..     195     221 ..     177     222 .. 0.80
   4 ?   -0.2   0.2      0.74   8.8e+02      32      83 ..     246     293 ..     205     326 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                                  EEEEEBTTTTHHHHHHHHHTS- CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                  i +vG+ + GKS++ naL++++
  gi|15669522|ref|NP_248333.1|  4 IGLVGKPNVGKSTMFNALTEKP 25
                                  789***************9987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.73
                                   EEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETT CS
                     Dynamin_N 103 ltlvDlPGldsvnkrdq...elvkeyikkadiilavtsan 139
                                   ++++D+ Gl   +++     +     +++ad++++v++a+
  gi|15669522|ref|NP_248333.1|  74 VEVIDVAGLVPGAHEGRgmgNKFLDDLRQADAFILVVDAS 113
                                   7788888888888777734444444567999999999997 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.8
                                   -CCC-CHHHHHHHHSTTBTTEEEEEE- CS
                     Dynamin_N 141 dlsnsealflarevdpkgkrtivvltk 167
                                   ++++ + l+la+++++ +k +i+  +k
  gi|15669522|ref|NP_248333.1| 195 KWTEEDLLNLAKKLRKISKPMIIAANK 221
                                   688999999999999999999987776 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.74
                                   --S-EEEEECCT---CCS...SSEEEET-EB--CHHHHHHHHHHHHHHHTSS CS
                     Dynamin_N  32 Trrplelqlgeeeeaseravkeelkekekkledfsevreeieketekiagan 83 
                                   T + +el l++ e+    a +++ ke+  ++ d s+v+e+++++++ i++ +
  gi|15669522|ref|NP_248333.1| 246 TSAEIELALKRAEK----AGIIKRKENDFEIIDESKVNEQMRRAFDYIKDFL 293
                                   55555666666555....5566666666666666666666666666666544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0028       3.4     104     122 ..       6      24 ..       2      33 .. 0.85
   2 ?    2.7   0.1     0.087     1e+02      48      82 ..     214     246 ..     176     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0028
                                   EECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase 104 lvGqSGvGKStLinallpe 122
                                   lvG+  vGKSt+ nal+++
  gi|15669522|ref|NP_248333.1|   6 LVGKPNVGKSTMFNALTEK 24 
                                   89999***********976 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.087
                                   EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE- CS
                   RsgA_GTPase  48 epvivlnKiDlleeeeeleelkeelealgyevllv 82 
                                   +++i+ nK+D  + e+++e+lk+e++++   v+ +
  gi|15669522|ref|NP_248333.1| 214 PMIIAANKADHPDAEKNIERLKKEFKDY--IVIPT 246
                                   567899********99999999998864..44444 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2    0.0008      0.95      82     147 ..     174     240 ..     153     244 .. 0.88
   2 ?    2.1   0.1      0.12   1.4e+02      51      76 ..     246     270 ..     242     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0008
                       DUF4423  82 slttssevkseavrsyhkqmlelAiealervpkeeRdiss.ltlaiskedyekikkeirefrkkila 147
                                    l+++++  ++a+r++  + +++  e l ++ k+ R+is  +++a +k+d ++++k+i++++k++ +
  gi|15669522|ref|NP_248333.1| 174 GLNIDEDDIKMAIRDMDESPIKWTEEDLLNLAKKLRKISKpMIIAANKADHPDAEKNIERLKKEFKD 240
                                   56778889999***************************975899*******************9976 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                       DUF4423  51 saeevekalefLlklgllkkdedgky 76 
                                   + +e+e al++ +k+g++k++e++ +
  gi|15669522|ref|NP_248333.1| 246 TSAEIELALKRAEKAGIIKRKEND-F 270
                                   5689999***************84.3 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00031      0.37       1      21 [.       4      24 ..       4      48 .. 0.86
   2 ?   -0.3   0.4       1.2   1.4e+03      54      66 ..     162     174 ..     106     274 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                        AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                  I+l G+p vGK+t+ ++L ++
  gi|15669522|ref|NP_248333.1|  4 IGLVGKPNVGKSTMFNALTEK 24
                                  89****************887 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                        AAA_18  54 edkldklldalee 66 
                                   ++ +++l d+l +
  gi|15669522|ref|NP_248333.1| 162 KNIVKALKDQLSG 174
                                   3333333333333 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0016       1.9       3      24 ..       5      26 ..       3     124 .. 0.87
   2 ?    0.1   0.0      0.72   8.7e+02     100     119 ..     203     223 ..     179     224 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                                  EEESSTTSSHHHHHHCHCT-CC CS
                           Roc  3 vlvGdsgvGKtsllkrfvedkf 24
                                   lvG+ +vGK+++++ ++e+  
  gi|15669522|ref|NP_248333.1|  5 GLVGKPNVGKSTMFNALTEKPA 26
                                  69**************998765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.72
                                   HHHHHHCS.SS-EEEEEE-TT CS
                           Roc 100 kelkkvag.kspvilvgnkiD 119
                                   +  kk ++ ++p+i+ +nk+D
  gi|15669522|ref|NP_248333.1| 203 NLAKKLRKiSKPMIIAANKAD 223
                                   4444444435699******99 PP

>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.9   0.00066      0.79      25      86 ..     151     210 ..     143     212 .. 0.86
   2 ?    2.0   0.1      0.19   2.3e+02       4      20 ..     249     265 ..     247     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00066
                        MetOD2  25 YarLaksvevnkrllslLs.qtydidddkaevseeieaalknlekk.leaqeerlkqikkeles 86 
                                   + +La++++ +k++++ L+ q+++++ d    +++i+ a++++ ++ ++  ee+l ++ k+l +
  gi|15669522|ref|NP_248333.1| 151 WDKLARRAQQEKNIVKALKdQLSGLNID----EDDIKMAIRDMDESpIKWTEEDLLNLAKKLRK 210
                                   789*************997479999977....99*********6644************99976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.19
                        MetOD2   4 diereverAkkaGvdke 20 
                                   +ie +++rA+kaG+ k+
  gi|15669522|ref|NP_248333.1| 249 EIELALKRAEKAGIIKR 265
                                   89999********9654 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00026      0.31       5      26 ..       3      24 ..       1      78 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                Ploopntkinase3  5 liylvGqPGaGkstlmaeltkg 26
                                  +i lvG+P  Gkst+  +lt+ 
  gi|15669522|ref|NP_248333.1|  3 MIGLVGKPNVGKSTMFNALTEK 24
                                  899*****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1195  (0.0666518); expected 358.6 (0.02)
Passed bias filter:                      752  (0.0419432); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 2539.66
//
Query:       gi|15669523|ref|NP_248334.1|  [L=84]
Description: hypothetical protein MJ_1333 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.46   10.2   2.2        2.8    7.7   0.1    2.3  2  Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain


Domain annotation for each model (and alignments):
>> Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3    0.0091   1.6e+02       1      12 [.       5      16 ..       5      17 .. 0.92
   2 ?    7.7   0.1   0.00016       2.8      13      30 ..      54      71 ..      43      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.0091
                                  HHHHHHHHHHTS CS
               Ribosomal_L12_N  1 kieeiieaikel 12
                                  ki+eii+++ +l
  gi|15669523|ref|NP_248334.1|  5 KIQEIINELDNL 16
                                  89*******997 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00016
                                  BHHHHHHHHHHHHHHTTH CS
               Ribosomal_L12_N 13 tvLElseLvkalEekFGV 30
                                  tv ++ eL+ka++ ++G 
  gi|15669523|ref|NP_248334.1| 54 TVEDVYELIKAIKLQLGM 71
                                  999**********99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 576.18
//
Query:       gi|15669524|ref|NP_248335.1|  [L=137]
Description: hypothetical protein MJ_1333.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-24   87.0  22.0    1.4e-24   86.8  22.0    1.0  1  EamA            EamA-like transporter family
    4.8e-05   22.8  11.4      6e-05   22.5  11.4    1.2  1  TPT             Triose-phosphate Transporter family
    0.00071   19.6   8.5     0.0015   18.5   8.5    1.8  1  TMEM234         Putative transmembrane family 234
     0.0052   17.4  10.8     0.0052   17.4  10.8    2.3  2  Multi_Drug_Res  Small Multidrug Resistance protein
  ------ inclusion threshold ------
      0.014   14.5   4.8      0.014   14.5   4.8    2.2  2  Mg_trans_NIPA   Magnesium transporter NIPA
        1.5    7.0  18.8        1.8    6.7  18.8    1.1  1  DUF2070         Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.8  22.0   4.6e-28   1.4e-24       3     136 ..       4     134 ..       2     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 4.6e-28
                          EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllff 83 
                                   +i+l ll+a+f++++++++ki+ +k + ++  +v +   gi+l++i+llk +++  ++ + +l +++++++ +v++ ll++
  gi|15669524|ref|NP_248335.1|   4 AIILGLLVAVFYGVGTFFAKIVCEKNPLFQWIVVNI--VGIILCLIILLKYKNI-IITDQKILTYAIISAVLVVIGSLLLY 81 
                                   79*******************999999998888885..5777777777778888.8************************* PP

                          EamA  84 yalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                   yal k++as++++++s+ P++t+ ls+l+l+e+ltl q++givli++G++l++
  gi|15669524|ref|NP_248335.1|  82 YALYKGKASIVVPLSSIGPAITVALSILFLKETLTLPQMIGIVLIIIGIILLS 134
                                   ***************************************************97 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5  11.4     2e-08     6e-05      36     137 ..      35     135 ..       6     137 .] 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2e-08
                           TPT  36 avqllvgsvlilvlwalglkkrpkisseflkailplalvktlghvlavvslskvaVSfthtvKasePiFtvilsrlllgek 116
                                    v  +vg++l+l+   l++k++   +++ l++ ++ a++ ++g++l   +l k   S    + ++ P+ tv+ls+l+l+e+
  gi|15669524|ref|NP_248335.1|  35 IVVNIVGIILCLI-ILLKYKNIIITDQKILTYAIISAVLVVIGSLLLYYALYKGKASIVVPLSSIGPAITVALSILFLKET 114
                                   3444455555444.3457777777778899999************************************************ PP

                           TPT 117 lsllvylsLlpivgGvalasv 137
                                   l+l  ++ ++ i+ G++l s+
  gi|15669524|ref|NP_248335.1| 115 LTLPQMIGIVLIIIGIILLSI 135
                                   *****************9987 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   8.5   5.2e-07    0.0015      48     115 ..      67     133 ..       9     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.2e-07
                       TMEM234  48 liplllNqsgSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                   +i+ +l + gS+l +++l k + s++vp++ s+  ++Tv  + l  +++l+  +++g++l+++gi+l+
  gi|15669524|ref|NP_248335.1|  67 IISAVLVVIGSLLLYYALYKGKASIVVPLS-SIGPAITVALSILFLKETLTLPQMIGIVLIIIGIILL 133
                                   46778899********************86.9**********999999*****************996 PP

>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.26   7.9e+02      56      73 ..       8      25 ..       3      33 .. 0.78
   2 !   17.4  10.8   1.7e-06    0.0052       2      93 .]      33     126 ..      31     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.26
                                  --HHHHHHHHHHHHHHHH CS
                Multi_Drug_Res 56 svAYavwsGiGtvlivlv 73
                                  ++  av+ G+Gt +  +v
  gi|15669524|ref|NP_248335.1|  8 GLLVAVFYGVGTFFAKIV 25
                                  555699999999887765 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.7e-06
                                   X-HHHHHHHHHHHHHHHH---....-----------HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH CS
                Multi_Drug_Res   2 nwvllvlAillevvgailLkl....segftkltpsllvivgygisfllLskalkslpvsvAYavwsGiGtvlivlvgillf 78 
                                   +w+++ + ++  +   ilLk+    +  ++ lt  ++  v ++i  llL +al + ++s++ ++ s iG +++v+++il++
  gi|15669524|ref|NP_248335.1|  33 QWIVVNIVGIILCL-IILLKYkniiITDQKILTYAIISAVLVVIGSLLLYYALYKGKASIVVPL-SSIGPAITVALSILFL 111
                                   56666666665544.47888866554444555555566668889999**************995.89************** PP

                                   --------HHHHHHH CS
                Multi_Drug_Res  79 geslslkkliglali 93 
                                   +e+l l ++ig++li
  gi|15669524|ref|NP_248335.1| 112 KETLTLPQMIGIVLI 126
                                   *************98 PP

>> Mg_trans_NIPA  Magnesium transporter NIPA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   5.6     0.097   2.9e+02     142     182 ..      32      73 ..      21      81 .. 0.65
   2 ?   14.5   4.8   4.8e-06     0.014      74     121 ..      88     135 ..      76     137 .] 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.097
                 Mg_trans_NIPA 142 paflvyvilvvvvvlvlilyvepr.kGktnilvyitlcsllg 182
                                    +++v  i+ ++++l+++l +++     ++il y ++ ++l 
  gi|15669524|ref|NP_248335.1|  32 FQWIVVNIVGIILCLIILLKYKNIiITDQKILTYAIISAVLV 73 
                                   455666677777777777766654256788999988877653 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.8e-06
                 Mg_trans_NIPA  74 PatLvtPLGalsvivsavlasllLkekLkllgllGcllailGstvlvi 121
                                    a++v PL ++   ++  l+ l+Lke L l +++G++l i+G ++l i
  gi|15669524|ref|NP_248335.1|  88 KASIVVPLSSIGPAITVALSILFLKETLTLPQMIGIVLIIIGIILLSI 135
                                   5899**************************************988765 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  18.8   0.00061       1.8      59     171 ..      22     133 ..       2     136 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00061
                       DUF2070  59 lrilggrltykrslflalltelivviisllaillsall.qalvllalvlslalvfalrllvlvavsdesllkavlpaliqp 138
                                    +i+ ++ ++ ++++++++  ++++i +ll +   +++ q++ l + ++s +lv++ +ll+++a+ + + + +v +++i p
  gi|15669524|ref|NP_248335.1|  22 AKIVCEKNPLFQWIVVNIVGIILCLI-ILLKYKNIIITdQKI-LTYAIISAVLVVIGSLLLYYALYKGKASIVVPLSSIGP 100
                                   33333334444444444444444444.444444444565555.555566669999999*********************** PP

                       DUF2070 139 llailllvlyfspesfllllllslifalavylf 171
                                   ++ ++l++l+++++ +l+ ++ +++++++++l+
  gi|15669524|ref|NP_248335.1| 101 AITVALSILFLKETLTLPQMIGIVLIIIGIILL 133
                                   **********88888887777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1208  (0.0673769); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 822.62
//
Query:       gi|15669525|ref|NP_248336.1|  [L=283]
Description: UDP-glucose pyrophosphorylase GtaB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-31  108.2   0.2    9.8e-31  107.2   0.2    1.5  1  NTP_transferase  Nucleotidyl transferase
    3.7e-10   40.4   0.0    4.4e-10   40.1   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    3.2e-05   23.8   0.0    4.7e-05   23.3   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.038   13.7   0.0      0.069   12.9   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.2   0.2   2.2e-34   9.8e-31       1     217 [.       4     239 ..       4     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 2.2e-34
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT......... CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfg......... 72 
                                   kavI + G GtRL P+t++++k ++pv++k +++q++++ l+++g+++i++v+  + ++ +e+++  +++++         
  gi|15669525|ref|NP_248336.1|   4 KAVIPVAGFGTRLLPITKAQPKEMLPVVNK-PIVQYVVEDLVEAGVKDILFVTG-KGKQAIENHFDVNYELEckleksgky 82 
                                   689999************************.*****************888777.667789999999999999999***** PP

                                   ............SEEEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSSTTSEEEEEE CS
               NTP_transferase  73 ............vevlialepegkgtAdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaiekaakgtvtfgiv 140
                                                ++ ++ ++e+kg+ dA++ ++e++++e+    ++ + gD ++++  +++++k +++++    +++  v
  gi|15669525|ref|NP_248336.1|  83 ellkiikeidrlGNIFYVRQKEQKGLGDAILYGEEFVGEEY----FIAMVGDTIYSKnIVKDLIKAHEKYGC-SVIALERV 158
                                   ********99999999**********************999....688888999988577888888888887.5889999* PP

                                   ESS-CTTSEEEEEC..TTS..BEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTE CS
               NTP_transferase 141 pveeateyGviead..eeg..rverfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegk 216
                                   p+e+  +yGvi  +  e+g  +++++vEKPk ++a s+l+ +G Y+  +++++++ +   + + ge +itd+++ +l+e++
  gi|15669525|ref|NP_248336.1| 159 PKEDVYKYGVIDGEeiEKGvyKIKNMVEKPKVEEApSNLIITGAYLLSPKIFEKI-RETPPGRGGEIQITDAMNLLLKEED 238
                                   ************997755578***********99999******************.6688899999********9999865 PP

                                   E CS
               NTP_transferase 217 v 217
                                    
  gi|15669525|ref|NP_248336.1| 239 I 239
                                   3 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   9.8e-14   4.4e-10       2     123 ..       6     157 ..       5     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 9.8e-14
                                   EEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHH...................... CS
                  NTP_transf_3   2 viLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggd..eevla...................... 53 
                                   vi  +G ++R+      ++K +lp+ +kp++++v++ l +agv++++ v+g   +++++                      
  gi|15669525|ref|NP_248336.1|   6 VIPVAGFGTRLlpitkAQPKEMLPVVNKPIVQYVVEDLVEAGVKDILFVTGKgkQAIENhfdvnyeleckleksgkyellk 86 
                                   66679******8887668*******************************98864555558888899999999999998888 PP

                                   ...HHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEES CS
                  NTP_transf_3  54 ...alarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvpty 123
                                      +++rlg  + + ++++kg + +++ + + + ++++++ + +D+++ ++++v+ l++a+++ g++v+++++
  gi|15669525|ref|NP_248336.1|  87 iikEIDRLGNIFYVRQKEQKGLGDAILYGEEFV-GEEYFIAMVGDTIY-SKNIVKDLIKAHEKYGCSVIALER 157
                                   8888899995555555679*************9.9***********88.9****************9998775 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.1e-08   4.7e-05      41     119 ..      83     160 ..      77     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.1e-08
                                   CHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEE CS
               Glycos_transf_2  41 etveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrpri 119
                                   e+ +i++e+ ++ +++ ++r++e +G++ a+  g + +  +y++ +  D++++++ +++l++a ek g +v++  r+ +
  gi|15669525|ref|NP_248336.1|  83 ELLKIIKEI-DRLGNIFYVRQKEQKGLGDAILYGEEFVGEEYFIAMVGDTIYSKNIVKDLIKAHEKYGCSVIALERVPK 160
                                   677888888.5799*****************************************************999988877655 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.5e-05     0.069       3      53 ..       5      57 ..       3      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                                  EEEECTTSSCTT...-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-G CS
                          IspD  3 vvipAAGsGkRm...kaglpKqflelkgqtllehtvdallaskavdkivvvvse 53
                                  +vip AG+G+R+    + +pK  l + ++++++  v+ l +   v+ i+ v  +
  gi|15669525|ref|NP_248336.1|  5 AVIPVAGFGTRLlpiTKAQPKEMLPVVNKPIVQYVVEDLVE-AGVKDILFVTGK 57
                                  89*********74447899******************9998.556767666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1932.97
//
Query:       gi|15669526|ref|NP_248337.1|  [L=143]
Description: phosphoheptose isomerase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-22   79.5   0.1    3.1e-22   79.1   0.1    1.1  1  SIS_2     SIS domain
      0.001   18.9   0.0     0.0019   18.1   0.0    1.4  1  SIS       SIS domain
  ------ inclusion threshold ------
       0.19   11.6   0.0        9.4    6.0   0.0    2.1  2  PA14      PA14 domain


Domain annotation for each model (and alignments):
>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.1   5.1e-26   3.1e-22      46     138 .]       6      98 ..       5      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 5.1e-26
                                   GHHHHHHTSSSTT-BTTEEEE--GGGSSSSST..THHHHHTT-TTHHHHHHHHTT-..-TT-EEEEE-SS--SHHHHHHHH CS
                         SIS_2  46 Saalaeelaaragglaeferialpalalhtdaeatkssalerdegyakqilrlvrl..kpgDvLlviSnsGnnavvveaae 124
                                   Saa+++++aa+++g++++er +lpa+al+td   ++ +a+ +d g+++++ r+v++  k+gDvL  iS+sGn+++v++aa+
  gi|15669526|ref|NP_248337.1|   6 SAANSQHFAAEIVGRFKLERKGLPAIALTTDI--SILTAIGNDYGFDRIFERQVEAlgKEGDVLAGISTSGNSENVIKAAN 84 
                                   9*****************************98..*******************99888*********************** PP

                                   HHHHHT-EEEEEE- CS
                         SIS_2 125 aakergmkviAlts 138
                                   +ake+g+++i+l++
  gi|15669526|ref|NP_248337.1|  85 KAKEMGIYTIGLLG 98 
                                   ***********986 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.1e-07    0.0019      49     110 ..      59     120 ..      50     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.1e-07
                                   GG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEEEEEEEECHC CS
                           SIS  49 alideddlvilisfsgetkdlvaaaelakergakiiaITdskgsplareadlalyinaepet 110
                                   al +e+d++  is+sg++ ++++aa++ake g  +i++ ++ g  l    dlal +++++ +
  gi|15669526|ref|NP_248337.1|  59 ALGKEGDVLAGISTSGNSENVIKAANKAKEMGIYTIGLLGKGGGKLKDIVDLALVVPSNDTA 120
                                   566899********************************999999999888888888877766 PP

>> PA14  PA14 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0    0.0081        48      41      67 ..       8      34 ..       3      55 .. 0.83
   2 ?    6.0   0.0    0.0016       9.4      55      85 ..      85     117 ..      75     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0081
                                  CGCCSCEEEEEEEEEBSSSEEEEEEET CS
                          PA14 41 eaadnfsarwtGylkppesGtYtFkva 67
                                   + ++f+a++ G++k +++G   ++++
  gi|15669526|ref|NP_248337.1|  8 ANSQHFAAEIVGRFKLERKGLPAIALT 34
                                  6889************99997666665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0016
                                   EBSSSEEEEEEETTCCCEEEE..ETTCCCEETT CS
                          PA14  55 kppesGtYtFkvasddgvrls..idgelvidnn 85 
                                   k++e G Yt+++ +++g +l   +d +lv++ n
  gi|15669526|ref|NP_248337.1|  85 KAKEMGIYTIGLLGKGGGKLKdiVDLALVVPSN 117
                                   78999***************9989999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 968.06
//
Query:       gi|15669527|ref|NP_248338.1|  [L=148]
Description: hypothetical protein MJ_1336 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-07   31.1   0.0    1.5e-07   31.0   0.0    1.1  1  PfkB          pfkB family carbohydrate kinase
    0.00058   19.3   0.0    0.00067   19.1   0.0    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
      0.009   15.8   0.3      0.017   15.0   0.2    1.5  1  RE_MjaI       MjaI restriction endonuclease


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   2.6e-11   1.5e-07     152     238 ..      56     135 ..      15     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.6e-11
                                   HHHHHHTTEEEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCT.HSHHHHHHHHHHHHHTTSSEEEEEEGGGE CS
                          PfkB 152 aeaaknggtfdpnlldplgaqfkeallellaladllkpneeElealtgekl.edieealaalhklkakgaktvvvtlGkeG 231
                                    +++k+ +    +l dp+++       ++   + l+kpn +E+++++g+++ +  +e+ + + + + k+++++v+t+G++G
  gi|15669527|ref|NP_248338.1|  56 DDIKKEFK--GKILIDPKPK------NDFYKDVYLIKPNLKEASQILGREIeNKDDELEKSGLESVDKYNSNFVITRGEKG 128
                                   44555444..5567777774......45666799*****************9999999*********************** PP

                                   EEEEETT CS
                          PfkB 232 alvvekd 238
                                   a + + d
  gi|15669527|ref|NP_248338.1| 129 ATLITVD 135
                                   *998644 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.1e-07   0.00067     114     166 ..      74     128 ..      41     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-07
                                   HHTGGG-SEEE-BHHHHHHHHT---SSHH.HHHHHHHHHHH.TT-SEEEEEEGGS CS
                  Phos_pyr_kin 114 eeLlplatvitPNlpEaeaLlgekiktee.dmkeaakkllk.lgakaVlikGghl 166
                                   +++ + + +i PNl+Ea+++lg++i++++ ++++ + + ++ ++++ V+ +G + 
  gi|15669527|ref|NP_248338.1|  74 NDFYKDVYLIKPNLKEASQILGREIENKDdELEKSGLESVDkYNSNFVITRGEKG 128
                                   55677899*****************966537777776666648888888888874 PP

>> RE_MjaI  MjaI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   2.8e-06     0.017      38     104 ..      74     144 ..      52     148 .] 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.8e-06
                       RE_MjaI  38 kkwYlekl..peaieeatkkiykkieelkeeieevdeedvrkwvedLvinktfeGlkvq..eailkklake 104
                                   +++Y++ +  + +++ea++ + + ie+  +e+e+   e v k+  ++vi++  +G ++   + i+   +++
  gi|15669527|ref|NP_248338.1|  74 NDFYKDVYliKPNLKEASQILGREIENKDDELEKSGLESVDKYNSNFVITRGEKGATLItvDEIFTMFQQK 144
                                   5789998888999***************************************9996543237777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1028.16
//
Query:       gi|15669528|ref|NP_248339.1|  [L=231]
Description: hypothetical protein MJ_1337 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-05   24.4   0.0    2.3e-05   24.0   0.0    1.1  1  Carb_kinase  Carbohydrate kinase
  ------ inclusion threshold ------
       0.18   12.2   3.3       0.41   11.0   0.0    2.9  4  DUF3194      Protein of unknown function (DUF3194)


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.5e-09   2.3e-05      96     242 ..      64     222 ..      48     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.5e-09
                                   -..EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCH.............HCCSHHHHHHHHHHHHTTEEEEE CS
                   Carb_kinase  96 p..lviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivk.............keddrlelarelaqklnavvllk 161
                                   +  ++ DA+g++  +         + + + P ++E + L++                  ++    + r+   k+++  ++k
  gi|15669528|ref|NP_248339.1|  64 SpkIIADAGGMYAAKAA---NIGDKFYLFLPDVGELAFLADEKAShpayvrgfiseidDNEVPKLIERDYKLKMPKYMVVK 141
                                   33688999999988887...5777888999999999999998888899999999764333333456778888999****** PP

                                   STTSEEEECTTEEEEE---..-GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHCCCT-TS-HCHHHHH CS
                   Carb_kinase 162 gekdvivspegevlinstg..ssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaaekkgvgmlatelsk 240
                                   ge d  + +e+ + ++++   +++   GG+GD+L+ ++++l+++  +  ea   ++ ++++ ++ a  +  +  + te+++
  gi|15669528|ref|NP_248339.1| 142 GETDYTIREEKIIDKIKEPkiKAMECIGGTGDTLTEIVSSLISVDFKTEEALSLGCKINRKLGEIANVNPNT--QITEIIN 220
                                   ********9998888877522577889*******************99999999999999999887777665..5555555 PP

                                   HH CS
                   Carb_kinase 241 ii 242
                                   +i
  gi|15669528|ref|NP_248339.1| 221 AI 222
                                   55 PP

>> DUF3194  Protein of unknown function (DUF3194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.92   8.3e+03      19      29 ..      46      56 ..      35      61 .. 0.53
   2 ?   -0.5   0.0      0.19   1.7e+03      61      78 ..     114     131 ..     112     135 .. 0.80
   3 ?   -1.0   0.1      0.26   2.4e+03      20      37 ..     149     166 ..     142     168 .. 0.81
   4 ?   11.0   0.0   4.6e-05      0.41      32      81 ..     177     227 ..     174     229 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.92
                                  HHHHHHHTTS- CS
                       DUF3194 19 viekkifkkvs 29
                                  vi+++i  k+s
  gi|15669528|ref|NP_248339.1| 46 VIIHYIKPKIS 56
                                  34455555554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.19
                                   T----TTHHHHHHHHHHH CS
                       DUF3194  61 lskldqelideavdeaye 78 
                                   +s++d++ + ++++  y+
  gi|15669528|ref|NP_248339.1| 114 ISEIDDNEVPKLIERDYK 131
                                   688888888888888775 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.26
                                   HHHHHHTTS-TTTEEEEE CS
                       DUF3194  20 iekkifkkvskkevldld 37 
                                    e+ki++k+ +  +++++
  gi|15669528|ref|NP_248339.1| 149 REEKIIDKIKEPKIKAME 166
                                   578999999999999887 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 4.6e-05
                                   TEEEEEEEEEEEESSSEEEEEEEEEEE-TT----TT.HHHHHHHHHHHHHH CS
                       DUF3194  32 evldlditvevkeneeLdvdveveleldelskldqe.lideavdeayeeld 81 
                                   e+    i v++k +e L +  +++ +l e+ +++++ +i e++++  ++l+
  gi|15669528|ref|NP_248339.1| 177 EIVSSLISVDFKTEEALSLGCKINRKLGEIANVNPNtQITEIINAIPKALE 227
                                   77777899***********************************99888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1530.88
//
Query:       gi|15669529|ref|NP_248340.1|  [L=353]
Description: H(2)-dependent methylenetetrahydromethanopterin dehydrogenase-like protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-41  141.0   2.7    2.5e-41  139.8   2.7    1.7  1  HMD            H2-forming N5,N10-methylene-tetrahydromethanop
  ------ inclusion threshold ------
      0.014   15.6   1.1       0.04   14.1   0.0    2.1  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd


Domain annotation for each model (and alignments):
>> HMD  H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   2.7   2.8e-45   2.5e-41       1      97 []     205     301 ..     205     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 2.8e-45
                                   HHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-HHHHHHCHHCC-S CS
                           HMD   1 AdlvsaVaDmgslvTAvtlagildyydvvtkilkapkemvekqilesLqtiaslveksGieglekalnpelllksaksmnl 81 
                                   Ad++s VaDmgslvTAv+l+g+ldyy+v++ki++apk+m+e+q++++Lqt+aslve+sGieg++kalnpell++sa+sm+l
  gi|15669529|ref|NP_248340.1| 205 ADVSSVVADMGSLVTAVALSGVLDYYTVGRKIINAPKKMIEQQVIMTLQTMASLVETSGIEGMVKALNPELLIRSASSMKL 285
                                   89******************************************************************************* PP

                                   CCCTCHHHHHHHHHHC CS
                           HMD  82 geeqeeLpaalkvlek 97 
                                    ++q++L+aal++l++
  gi|15669529|ref|NP_248340.1| 286 LDRQKDLDAALEILQN 301
                                   **************85 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.4e-06      0.04      11      94 ..      43     131 ..      42     137 .. 0.87
   2 ?   -0.8   0.2      0.17   1.5e+03      64      87 ..     213     237 ..     164     295 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.4e-06
                                   HHHHHHHHHHTT-EEEEE-SSH.....HHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EE CS
                 NAD_binding_2  11 Gsnmalnllkagykvavynrtk.....ekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkkgdil 86 
                                   Gs ma ++++ag++v++ + +k     +  +++ ++g+k++++  e++++ ++ +++ + gka+  + + ++e++ +++++
  gi|15669529|ref|NP_248340.1|  43 GSRMAIEFAEAGHDVVLAEPNKnimsdDLWKKVEDAGVKVVSDDVEAAKHGEIHVLFTPFGKATFRIAKTIIEHVPENAVI 123
                                   99****************98772222234455555569*****99************************************ PP

                                   EE-S---H CS
                 NAD_binding_2  87 idgstssp 94 
                                    ++ t+sp
  gi|15669529|ref|NP_248340.1| 124 CNTCTVSP 131
                                   **999987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.17
                                   SSHHHHHHHHHS.HCCC--TT-EEE CS
                 NAD_binding_2  64 kagkavdevieg.llealkkgdili 87 
                                     g+ v +v  + +l+++  g+ +i
  gi|15669529|ref|NP_248340.1| 213 DMGSLVTAVALSgVLDYYTVGRKII 237
                                   3344444444333444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2316.68
//
Query:       gi|15669530|ref|NP_248341.1|  [L=154]
Description: protein with ATP/GTP-binding site [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-18   64.6   0.5    8.4e-12   45.0   0.0    2.4  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    2.1e-13   50.4   0.3    2.6e-13   50.0   0.3    1.1  1  MMR_HSR1      50S ribosome-binding GTPase
    3.2e-09   36.6   0.4      4e-09   36.3   0.4    1.2  1  Ras           Ras family
    5.2e-09   36.4   0.1      7e-09   35.9   0.1    1.2  1  Roc           Ras of Complex, Roc, domain of DAPkinase
    1.3e-08   34.5   0.5    3.1e-08   33.3   0.5    1.6  1  Arf           ADP-ribosylation factor family
    1.6e-06   27.7   0.4    9.4e-06   25.2   0.4    2.1  1  FeoB_N        Ferrous iron transport protein B
     0.0001   22.3   0.2      0.012   15.6   0.0    2.1  2  RsgA_GTPase   RsgA GTPase
    0.00033   20.5   0.0       0.02   14.7   0.0    2.2  2  ATP_bind_1    Conserved hypothetical ATP binding protein
     0.0022   17.8   0.4     0.0027   17.5   0.4    1.1  1  AAA_24        AAA domain
      0.003   17.0   0.2     0.0041   16.6   0.2    1.3  1  SRPRB         Signal recognition particle receptor beta subun
     0.0036   17.4   0.2       0.44   10.6   0.1    2.1  2  Dynamin_N     Dynamin family
     0.0052   16.7   0.2       0.01   15.7   0.2    1.4  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
     0.0065   16.2   0.6      0.013   15.2   0.6    1.9  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
  ------ inclusion threshold ------
      0.016   14.2   0.1        3.6    6.5   0.1    2.5  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.017   15.4   0.0      0.021   15.1   0.0    1.2  1  AAA_28        AAA domain
       0.03   14.7   0.1      0.044   14.2   0.1    1.6  1  RNA_helicase  RNA helicase
       0.03   14.2   0.4      0.058   13.3   0.4    1.4  1  NTPase_1      NTPase
      0.042   13.9   0.2      0.064   13.3   0.2    1.5  1  AAA_14        AAA domain
       0.06   13.4   0.7       0.12   12.5   0.1    1.7  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
       0.07   13.4   0.0       0.11   12.7   0.0    1.4  1  AAA_22        AAA domain
      0.072   12.4   0.4       0.34   10.2   0.4    1.8  1  AIG1          AIG1 family
      0.099   12.1   0.1       0.16   11.5   0.1    1.4  1  AAA_7         P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.5e-06    0.0012       4      31 ..       6      33 ..       3      36 .. 0.88
   2 !   45.0   0.0     1e-14   8.4e-12      52     150 ..      35     131 ..      32     154 .] 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                                  EEEEEEESTTSSHHHHHHHHHHHTTSSC CS
                      GTP_EFTU  4 rnigiighvDhGKtTLtdrLlyktgais 31
                                  +++++ig  D GKtTL+++L+ k g+++
  gi|15669530|ref|NP_248341.1|  6 VKVVVIGSSDVGKTTLMENLIDKIGKVE 33
                                  689******************9999876 PP

  == domain 2  score: 45.0 bits;  conditional E-value: 1e-14
                                   HTSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESC CS
                      GTP_EFTU  52 rgiTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKm 132
                                   +giT  +   sl    k+++i++  tPG + F    + +l+ +++a++v+da++G++   ee+++l+ ++++p  +fiNK 
  gi|15669530|ref|NP_248341.1|  35 KGITTAIDYGSLT--IKDKKIHFFGTPGQKRFEFMRELALKGTNFALVVLDASKGITKEDEEIIKLLESKKIPYGIFINKT 113
                                   79***********..****************************************************************** PP

                                   GSTHHHHHHHHHHHHHHH CS
                      GTP_EFTU 133 Drlkaelkeiveevkqkl 150
                                   D  + + +e+ +  + k+
  gi|15669530|ref|NP_248341.1| 114 DVGDIDTSEVYNFCNPKF 131
                                   *99888888877777666 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.3   3.2e-16   2.6e-13       1     114 []       7     112 ..       7     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 3.2e-16
                                   EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEE CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflaleeadlill 81 
                                   +v+++G + vGK+tL+  l+++  +v +++g T+ i +g +++k+k+i++  tpG  +    + ++ ++++ l+ ++ +l+
  gi|15669530|ref|NP_248341.1|   7 KVVVIGSSDVGKTTLMENLIDKIGKV-EYKGITTAIDYGSLTIKDKKIHFFGTPG-QK----RFEFMRELA-LKGTNFALV 80 
                                   699*******************9999.799*************************.43....446666666.5568***** PP

                                   EEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  82 vvdaseeklkpldeeleelleeakkplilvlnk 114
                                   v+das ++++++dee+ +lle++k+p+ + +nk
  gi|15669530|ref|NP_248341.1|  81 VLDAS-KGITKEDEEIIKLLESKKIPYGIFINK 112
                                   ***99.77************9999999999987 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.4     5e-12     4e-09       1     131 [.       7     127 ..       7     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 5e-12
                                   EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEET CS
                           Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvydi 81 
                                   K+v++G+s vGKt+l+ + +++  k ey+     +    ++++++k+++   + T Gq +f+ +rel +++++ +l+v d 
  gi|15669530|ref|NP_248341.1|   7 KVVVIGSSDVGKTTLMENLIDKIGKVEYKGIT-TAIDYGSLTIKDKKIH--FFGTPGQKRFEFMRELALKGTNFALVVLDA 84 
                                   9*******************998888876433.5666677778888766..69*************************997 PP

                                   TBHHHHHTHHHHHHHHHHHST.TTSEEEEEEETTTGGGG-SS-HHHHHHHH CS
                           Ras  82 tsresfenvkkwveeikrvae.envpivLvGnKvDleekravsteegeela 131
                                   ++      ++k  eei +  e +++p  +  nK+D+ +   ++t+e+ +++
  gi|15669530|ref|NP_248341.1|  85 SKG-----ITKEDEEIIKLLEsKKIPYGIFINKTDVGD---IDTSEVYNFC 127
                                   654.....444455666655556688999999999986...6666665555 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.1   8.6e-12     7e-09       1     118 [.       7     113 ..       7     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 8.6e-12
                                   EEEEESSTTSSHHHHHHCHCT-CCC-EEE.TTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                           Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekek.stigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                   Kvv++G s vGKt+l+++++++  + ++k  t+++d+ + ++            k+ k++++ t Gq+rf+ +++l l++ 
  gi|15669530|ref|NP_248341.1|   7 KVVVIGSSDVGKTTLMENLIDKIGKVEYKgITTAIDYGSLTI------------KDKKIHFFGTPGQKRFEFMRELALKGT 75 
                                   9*******************9988877652688889877654............234699********************* PP

                                   CEEEEEEEGHHH..HCHHHHHHHHHHHCSSS-EEEEEE-T CS
                           Roc  81 alailvydsrss..enlkeWlkelkkvagkspvilvgnki 118
                                   + a++v+d+++   ++ +e +k l++  +k+p  + +nk+
  gi|15669530|ref|NP_248341.1|  76 NFALVVLDASKGitKEDEEIIKLLES--KKIPYGIFINKT 113
                                   ********665311222333333332..344555555555 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.5   3.9e-11   3.1e-08      12     173 ..       3     152 ..       1     154 [] 0.85

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 3.9e-11
                                   TTEEEEEEEESTTSSHHHHHHHH..HHSSCEECSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGCTTESEEEEEEE CS
                           Arf  12 kkelrilllGLDnaGKtTilkkl..kleelvttvPTigfnveeleiknlkftvwDvGGqeklRplWknYfektdavifvvD 90 
                                   k e++++++G    GKtT++++l  k ++++    T+  +  +l+ik+ k++++   Gq++   + +  ++ t+  + v+D
  gi|15669530|ref|NP_248341.1|   3 KDEVKVVVIGSSDVGKTTLMENLidKIGKVEYKGITTAIDYGSLTIKDKKIHFFGTPGQKRFEFMRELALKGTNFALVVLD 83 
                                   679********************444467777888999999**********************99999************* PP

                                   TT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBTHHHHHHHH CS
                           Arf  91 sadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkgeglkeglewl 171
                                   +++   +++  ee+ +lle+   k+++  ++ NK D+ ++++++e+ +          ++  i+k +avk++gl+e ++++
  gi|15669530|ref|NP_248341.1|  84 ASK--GITKEDEEIIKLLES---KKIPYGIFINKTDV-GDIDTSEVYNFC--------NPKFIVKGCAVKKDGLDELINKI 150
                                   975..688888999888876...5678999******8.567777776543........355788999**********9999 PP

                                   HH CS
                           Arf 172 se 173
                                   ++
  gi|15669530|ref|NP_248341.1| 151 MS 152
                                   76 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.4   1.2e-08   9.4e-06       2      57 ..       7      61 ..       6     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.2e-08
                                  EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE---- CS
                        FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGi 57
                                  +v+++G  +vGkttl+++l ++  kv  + G+t     g+l++k+k++++   PG 
  gi|15669530|ref|NP_248341.1|  7 KVVVIGSSDVGKTTLMENLIDKIGKV-EYKGITTAIDYGSLTIKDKKIHFFGTPGQ 61
                                  799*******************9999.6***************************6 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.4e-05     0.012     102     147 ..       8      54 ..       2      67 .. 0.79
   2 ?    5.3   0.0      0.02        17      38      63 ..      95     120 ..      76     154 .] 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                                   EEEECSTTSSHHHHHHHHCTT-.----S--------------SEEEE CS
                   RsgA_GTPase 102 svlvGqSGvGKStLinallpel.elktgevseklgrGkhTTtavell 147
                                   +v++G+S vGK+tL+++l+ +  +++ + + ++ + G  T +  +++
  gi|15669530|ref|NP_248341.1|   8 VVVIGSSDVGKTTLMENLIDKIgKVEYKGITTAIDYGSLTIKDKKIH 54 
                                   7899***********99999765889999999999998887776665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.02
                                   HHHHHHHTT-EEEEEEE-GGG--HHH CS
                   RsgA_GTPase  38 fLvlaeekgiepvivlnKiDlleeee 63 
                                   ++ l+e+k+i+  i +nK+D+ + ++
  gi|15669530|ref|NP_248341.1|  95 IIKLLESKKIPYGIFINKTDVGDIDT 120
                                   567899**************987665 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.035        28       1      18 [.      10      27 ..      10      35 .. 0.86
   2 !   14.7   0.0   2.5e-05      0.02      67     136 ..      36      89 ..      27     151 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.035
                    ATP_bind_1  1 vvGpaGsGKttfvgalse 18
                                  v+G   +GKtt++++l++
  gi|15669530|ref|NP_248341.1| 10 VIGSSDVGKTTLMENLID 27
                                  89999********99986 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.5e-05
                    ATP_bind_1  67 alvvaleflresldwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrlt 136
                                   ++++a+++++ ++         ++++ + f+tPGQ ++ +++e         +   ++  v+L  s+ +t
  gi|15669530|ref|NP_248341.1|  36 GITTAIDYGSLTI---------KDKKIHFFGTPGQKRFEFMRELAL------K-GTNFALVVLDASKGIT 89 
                                   7888889888888.........233579*********988877544......4.3444444444444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.4   3.3e-06    0.0027       2      73 ..       5      84 ..       4     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.3e-06
                        AAA_24  2 klkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.swedfldevvelaaeladyktlviDt 73
                                  ++k++++G+s +GKTtl+ +l       ++k +   ++ G+  ++++k+       ++  +++ ela +  ++  +v+D 
  gi|15669530|ref|NP_248341.1|  5 EVKVVVIGSSDVGKTTLMENLidkigkvEYKGITTAIDYGSLTIKDKKIHFFGtPGQKRFEFMRELALKGTNFALVVLDA 84
                                  579******************99999999999999999999999999987555667777788888888888888888885 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2     5e-06    0.0041       4      63 ..       6      65 ..       3     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5e-06
                                  -EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT-GCCS CS
                         SRPRB  4 pavllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfPGheklr 63
                                   +v+++G sd GKT+l++ L  +  k  +  + + + +   + k++k+++   PG++++ 
  gi|15669530|ref|NP_248341.1|  6 VKVVVIGSSDVGKTTLMENLIDKIGKVEYKGITTAIDYGSLTIKDKKIHFFGTPGQKRFE 65
                                  5799*******************88888888888888888888************99864 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00054      0.44       1      33 [.       8      40 ..       8      43 .. 0.85
   2 ?    5.4   0.0     0.021        17     107     165 ..      57     111 ..      35     114 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00054
                                  EEEEEBTTTTHHHHHHHHHTS--S---SSS--- CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTr 33
                                  ++v+Gs   GK++++++L+ +   +  +++tT+
  gi|15669530|ref|NP_248341.1|  8 VVVIGSSDVGKTTLMENLIDKIGKVEYKGITTA 40
                                  89****************998777777777775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.021
                                   E---B-SSSGTTSHHHHHHH.STTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTT.EEEEE CS
                     Dynamin_N 107 DlPGldsvnkrdqelvkeyi.kkadiilavtsanhdlsnsealflarevdpkgkr.tivvl 165
                                    +PG      ++ e ++e++ k  ++ l+v++a++ +++ + + + +++++k+    i+++
  gi|15669530|ref|NP_248341.1|  57 GTPGQ-----KRFEFMRELAlKGTNFALVVLDASKGITKEDEE-IIKLLESKKIPyGIFIN 111
                                   55553.....3357777888899*************9966555.55555555554147776 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.2e-05      0.01       3      29 ..       9      35 ..       7      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                          MobB  3 givgksgsGKTtLleklipelkarglr 29
                                   ++g s+ GKTtL+e+li ++ + +++
  gi|15669530|ref|NP_248341.1|  9 VVIGSSDVGKTTLMENLIDKIGKVEYK 35
                                  689***************998776665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.6   1.6e-05     0.013       3      38 ..       7      45 ..       5     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                     PduV-EutP  3 killiGkvgsGKttLtqalkg..eelkYkk.tqaiefsd 38
                                  k+++iG++++GKttL+++l +   +++Yk  t ai++ +
  gi|15669530|ref|NP_248341.1|  7 KVVVIGSSDVGKTTLMENLIDkiGKVEYKGiTTAIDYGS 45
                                  89****************988444788874366666655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0044       3.6      32      69 ..       8      45 ..       4     116 .. 0.90
   2 ?    5.7   0.0    0.0076       6.2     207     228 ..     132     153 ..     114     154 .] 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0044
                                  EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                          MeaB 32 vGltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                  v + G+  +Gk tl+e+l+ ++ +  ++    a+D +s
  gi|15669530|ref|NP_248341.1|  8 VVVIGSSDVGKTTLMENLIDKIGKVEYKGITTAIDYGS 45
                                  56788999999999999999998888888888888776 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0076
                                   EEEEBCCCTBSHHHHHHHHHHH CS
                          MeaB 207 vlktsavegeGidelvdaieeh 228
                                   ++k  av+++G+del+++i +h
  gi|15669530|ref|NP_248341.1| 132 IVKGCAVKKDGLDELINKIMSH 153
                                   78999**************998 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.5e-05     0.021       1      43 [.       7      56 ..       7      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                        AAA_28  1 kivitGgestGKTtlleaLaar.......gypvvpEaareileeklakge 43
                                  k+v++G +  GKTtl+e+L ++       g+++  +++   +++k    +
  gi|15669530|ref|NP_248341.1|  7 KVVVIGSSDVGKTTLMENLIDKigkveykGITTAIDYGSLTIKDKKIHFF 56
                                  79*****************9666666667899999999999999875444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   5.3e-05     0.044       1      25 [.       8      32 ..       8     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.3e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                  +++ G+s +GK+tl+++L++++ k 
  gi|15669530|ref|NP_248341.1|  8 VVVIGSSDVGKTTLMENLIDKIGKV 32
                                  6899****************99853 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   7.2e-05     0.058       1      35 [.       7      39 ..       7      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.2e-05
                                  EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEE CS
                      NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyt 35
                                  kv++ G++ vGKtTl++++++++    v+++G+ t
  gi|15669530|ref|NP_248341.1|  7 KVVVIGSSDVGKTTLMENLIDKI--GKVEYKGITT 39
                                  58899******************..5689999987 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   7.9e-05     0.064       5      28 ..       8      32 ..       4     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.9e-05
                        AAA_14  5 lvitGaRrvGKTtllkqlikell.v 28
                                  +v+ G   vGKTtl+++li++   v
  gi|15669530|ref|NP_248341.1|  8 VVVIGSSDVGKTTLMENLIDKIGkV 32
                                  6899***************876542 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.1   2.5e+03      13      24 ..      19      30 ..       4      43 .. 0.56
   2 ?   12.5   0.1   0.00014      0.12      46     101 ..      96     151 ..      77     154 .] 0.78

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                  MMR_HSR1_Xtn 13 tkldeetvkkil 24
                                  t+l e+ + ki 
  gi|15669530|ref|NP_248341.1| 19 TTLMENLIDKIG 30
                                  334444444443 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                  MMR_HSR1_Xtn  46 idviegnrvYipclyvlNKiDl..isleeldelarepnsvviSaekelnldeLkekiw 101
                                   i  +e ++  ip  +++NK+D   i+ +e+ ++++ + +v  +a k+ +ldeL +ki 
  gi|15669530|ref|NP_248341.1|  96 IKLLESKK--IPYGIFINKTDVgdIDTSEVYNFCNPKFIVKGCAVKKDGLDELINKIM 151
                                   55554433..788899******6677777778888667777999999********996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00014      0.11       8      33 ..       8      33 ..       3      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                        AAA_22  8 lvvtGesGtGKTtllrrlleqldeea 33
                                  +vv+G s +GKTtl+++l ++  +++
  gi|15669530|ref|NP_248341.1|  8 VVVIGSSDVGKTTLMENLIDKIGKVE 33
                                  58****************99976554 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4   0.00042      0.34       2     108 ..       7     100 ..       6     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                                   EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHHHCTT CS
                          AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrclllsee 82 
                                   ++v++G + +Gk +   ++++k     k++ +++t++    s t ++kki+   TPg    +++      e +r  +l+ +
  gi|15669530|ref|NP_248341.1|   7 KVVVIGSSDVGKTTLMENLIDKI---GKVEYKGITTAIDYGSLTIKDKKIHFFGTPG----QKR-----FEFMR--ELALK 73 
                                   799*********99999999874...566789************************9....333.....33444..47778 PP

                                   -ESEEEEEEETT.B-SHHHHHHHHHHH CS
                          AIG1  83 gihalllvlslg.rfteedekalktlk 108
                                   g ++ l+vl+++  +t+ede+++k l+
  gi|15669530|ref|NP_248341.1|  74 GTNFALVVLDASkGITKEDEEIIKLLE 100
                                   999999999999899999999998775 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00019      0.16      32      66 ..       4      38 ..       1      50 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                         AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylslt 66
                                   + +v+++G++ +GKt+++++l++k+ k +y+ +t
  gi|15669530|ref|NP_248341.1|  4 DEVKVVVIGSSDVGKTTLMENLIDKIGKVEYKGIT 38
                                  67899********************9998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 1200.90
//
Query:       gi|15669531|ref|NP_248342.1|  [L=114]
Description: hypothetical protein MJ_1340 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-24   83.8   1.2    6.6e-24   83.5   1.2    1.1  1  Robl_LC7    Roadblock/LC7 domain
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.018   14.9   0.0    1.1  1  MAPKK1_Int  Mitogen-activated protein kinase kinase 1 interac


Domain annotation for each model (and alignments):
>> Robl_LC7  Roadblock/LC7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   1.2   7.4e-28   6.6e-24       1      91 []       1      90 [.       1      90 [. 0.97

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 7.4e-28
                                  HHHHHHHHCCHHCTECEEEEEETTS-EEEECCSSSS-HHHHHHHHHHHHHHHHHHHHHCTSSSECEEEEEETTEEEEEEECTT CS
                      Robl_LC7  1 lveelleelqsvpgvrgalvvskdGlviatstldnddadqlAalasgllsaakaaarelgegelkelliegkkgelyltpage 83
                                  +++ +l el++++g++g++vv kdGlvia++ +++ da+ ++a+as++++aa++ a e+g g+l++++ieg++g+ +++ age
  gi|15669531|ref|NP_248342.1|  1 MIDRVLLELNKTEGIKGSMVVGKDGLVIASQLPGSVDAELVGAMASAAFGAAERTAAEIGMGTLEQTMIEGEHGKTLMVDAGE 83
                                  57899****************************************************************************** PP

                                  TEEEEEEE CS
                      Robl_LC7 84 galLvvla 91
                                    +Lvvl+
  gi|15669531|ref|NP_248342.1| 84 -GILVVLT 90
                                  .9999985 PP

>> MAPKK1_Int  Mitogen-activated protein kinase kinase 1 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     2e-06     0.018      11     101 ..       9      99 ..       2     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-06
                    MAPKK1_Int  11 lsevdgllaiivtDrDGvvllkvgddssadsalrpslistfvlatdQasKLdlgknksiislyedyqvvqfnklplilsvi 91 
                                   l++ +g+++ +v  +DG v+++    s + + +     ++f  a   a  +++g  ++++   e+     +++ + il v+
  gi|15669531|ref|NP_248342.1|   9 LNKTEGIKGSMVVGKDGLVIASQLPGSVDAELVGAMASAAFGAAERTAAEIGMGTLEQTMIEGEHGKTLMVDAGEGILVVL 89 
                                   6788999999************999998999999999999****************999999999999999********** PP

                    MAPKK1_Int  92 astecNiGli 101
                                   ++ + N Gli
  gi|15669531|ref|NP_248342.1|  90 TDAKVNLGLI 99 
                                   ********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 878.27
//
Query:       gi|15669532|ref|NP_248343.1|  [L=312]
Description: hypothetical protein MJ_1341 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2253.93
//
Query:       gi|15669533|ref|NP_248344.1|  [L=114]
Description: hypothetical protein MJ_1342 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.2   4.5        1.8    8.5   0.3    2.6  3  C1_1      Phorbol esters/diacylglycerol binding domain (C1 do


Domain annotation for each model (and alignments):
>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.48   8.7e+03      24      31 ..       6      13 ..       2      15 .. 0.59
   2 ?    7.1   2.8   0.00027       4.8      12      36 ..      34      58 ..      31      59 .. 0.71
   3 ?    8.5   0.3    0.0001       1.8      12      31 ..      54      73 ..      50      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.48
                                  SSS-EEEE CS
                          C1_1 24 kekqglkC 31
                                  ++k + kC
  gi|15669533|ref|NP_248344.1|  6 GGKKIAKC 13
                                  55666666 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00027
                                  -B-TTT-SB--SSSS-EEEETTT-- CS
                          C1_1 12 tfCkhCgeflwgkekqglkCswCkl 36
                                  +fC+ C++f+   ek g+k + Ck+
  gi|15669533|ref|NP_248344.1| 34 NFCDMCNDFVIDDEKIGIKIDKCKY 58
                                  69********556666666555555 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0001
                                  -B-TTT-SB--S.SSS-EEEE CS
                          C1_1 12 tfCkhCgeflwg.kekqglkC 31
                                   +Ck+C +++ g  e++g +C
  gi|15669533|ref|NP_248344.1| 54 DKCKYCPKQI-GeAEIPGSAC 73
                                  79********.6699999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.88
# Mc/sec: 389.62
//
Query:       gi|15669534|ref|NP_248345.1|  [L=420]
Description: ammonium transporter [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.2e-111  372.4  32.0   2.6e-111  372.2  32.0    1.0  1  Ammonium_transp  Ammonium Transporter Family


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.2  32.0  1.4e-115  2.6e-111       2     399 .]      35     414 ..      34     414 .. 0.95

  Alignments for each domain:
  == domain 1  score: 372.2 bits;  conditional E-value: 1.4e-115
                                   HHHHHHHHHHHH.HHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-.TTTTSCCGCCT CS
               Ammonium_transp   2 flllsaalvifm.qagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfign.lglsaagvqde 80 
                                   f+l+++ +++fm q+gfa+le+g+vr+knv n+++kn++d+++++++++++G +l+ +   ++s+fi +  ++  ++++++
  gi|15669534|ref|NP_248345.1|  35 FFLVVMGVLVFMmQWGFAMLEGGQVRKKNVNNVMMKNMVDWLIGCVAWLFIGGILCSKG-FDLSAFIDWwKQILGTNWPNN 114
                                   5555555555555*******************************************776.59******9999999999996 PP

                                   TCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--.-SSSTTTTHHHHH CS
               Ammonium_transp  81 tlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvliDfAgstvVHlvgg 161
                                    l d++ ++f l+f+ata+tivsg+vaerikfsay+l+s+++++l yp    +v+  g+w a++  ++D+Ags+vVH +gg
  gi|15669534|ref|NP_248345.1| 115 GL-DLASWFFGLVFCATAATIVSGGVAERIKFSAYVLISLIITGLLYPL---FVYL-GPWGASIVPWHDYAGSLVVHGLGG 190
                                   66.7778*****************************************5...8899.************************ PP

                                   HHHHHHHHHHS-STTTTG.TTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.HHHHHHHHHHHHHHHHHHH CS
               Ammonium_transp 162 vagLaaalvlgkregrfe.gkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrararaavtTllAaaagaltalli 241
                                   + +L a+  lg+r+grf  g++  i ghn+p+av+G++ L++gW+gFN+Gs+l++ +++   ++ tT++A+a+g+++al++
  gi|15669534|ref|NP_248345.1| 191 FLALGAIAALGPRIGRFVdGRPVPILGHNIPMAVFGAFALAIGWYGFNVGSSLALGDISGL-VCATTTMAMAGGGIGALIA 270
                                   *************************************************************.******************* PP

                                   HHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTC-CTTHHHHHHHHHHHHHHHHH CS
               Ammonium_transp 242 srlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklkidDsldvvavHgvgGiwGllav 322
                                   sr++     vl++anGi+AGlVAi+++++vv+p+g liiGl+Ag+++ +++k l ek+++dD+++vv+vHg++G++G++++
  gi|15669534|ref|NP_248345.1| 271 SRND-----VLFTANGIVAGLVAICSGTDVVSPIGGLIIGLIAGLQVPIVYK-LVEKAGLDDVCGVVPVHGTAGVIGAILT 345
                                   ****.....******************************************8.**************************** PP

                                   HHHTSHHHCSSHSSTTGGGT-C.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.SB--HHHHHHSHHHHHHSSSSB CS
               Ammonium_transp 323 gifaaekvvaskisggllsgeg.kqlvvqligilvilayafvvtlilllllklllg.LrvseeeeevglDvaehgetay 399
                                   gi++ +          +++g+g  +l+ q+ig++++++y +++++il+++++++lg Lrvseeee++glD+aeh++ ay
  gi|15669534|ref|NP_248345.1| 346 GILGLK----------IFGGAGgVSLIDQIIGAVFCIIYGTGLGYILAKIVGIALGgLRVSEEEEKMGLDMAEHKMPAY 414
                                   ****98..........466666688*****************************999******************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2612.11
//
Query:       gi|15669535|ref|NP_248346.1|  [L=112]
Description: nitrogen regulatory protein P-II GlnB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-40  136.6   3.3    4.2e-40  136.5   3.3    1.0  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.5   3.3   2.3e-44   4.2e-40       1     102 []       4     105 ..       4     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 136.5 bits;  conditional E-value: 2.3e-44
                                   EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHHH-SS CS
                          P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiikaaktg 81 
                                   +eaiirpekle vk+aL++ag+ g+tv+evkGrG q g +e yrg+ey v+l+pkvk+e+vv++edv++v+++i+++a+tg
  gi|15669535|ref|NP_248346.1|   4 VEAIIRPEKLEIVKKALSDAGYVGMTVSEVKGRGVQGGIVERYRGREYIVDLIPKVKIELVVKEEDVDNVIDIICENARTG 84 
                                   79******************************************************************************* PP

                                   STTSEEEEEEEESEEEETTTT CS
                          P-II  82 eiGDGkiFvlpveevirirtg 102
                                   ++GDGkiFv+pve+v+r+rt+
  gi|15669535|ref|NP_248346.1|  85 NPGDGKIFVIPVERVVRVRTK 105
                                   *******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 934.02
//
Query:       gi|15669536|ref|NP_248347.1|  [L=314]
Description: O-linked GlnNAc transferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-54  178.1  38.6    1.2e-09   37.6   0.5    9.1  9  TPR_1            Tetratricopeptide repeat
    1.3e-51  168.6  27.1    9.7e-07   28.4   0.1    9.1  9  TPR_2            Tetratricopeptide repeat
      2e-40  133.6  31.3    5.8e-07   29.2   0.0    8.9  9  TPR_8            Tetratricopeptide repeat
    3.2e-35  120.5  17.5    2.6e-08   34.2   0.0    5.8  8  TPR_19           Tetratricopeptide repeat
    2.4e-33  113.5  23.2      5e-07   29.3   0.2    8.0  8  TPR_11           TPR repeat
    3.7e-33  111.4   0.0    0.00034   21.2   0.0    8.5  9  TPR_14           Tetratricopeptide repeat
    2.6e-32  108.8   8.8    4.5e-05   23.5   0.0    8.3  8  TPR_17           Tetratricopeptide repeat
    6.8e-30  103.4   0.0    1.1e-06   29.2   0.0    6.0  6  TPR_16           Tetratricopeptide repeat
    1.6e-27   95.6  16.9    1.1e-08   35.2   0.1    7.6  7  TPR_12           Tetratricopeptide repeat
    2.5e-25   88.5  11.0    1.4e-07   31.6   1.8    4.6  5  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    5.4e-23   80.9   0.0    7.3e-06   26.1   0.0    5.7  6  TPR_9            Tetratricopeptide repeat
    1.3e-21   77.1   8.0    1.6e-05   24.0   0.2    4.9  4  NARP1            NMDA receptor-regulated protein 1
    1.2e-20   71.9   2.9      0.028   14.5   0.0    8.4  8  TPR_7            Tetratricopeptide repeat
    8.3e-17   60.6  17.0       0.12   13.1   0.0    8.4  8  TPR_6            Tetratricopeptide repeat
    3.8e-14   52.6   0.2    2.6e-06   26.9   0.0    3.0  3  TPR_15           Tetratricopeptide repeat
    1.4e-12   47.0   5.2        0.2   11.6   0.0    7.6  9  TPR_10           Tetratricopeptide repeat
    4.2e-12   45.9  21.5      0.033   14.3   0.0    8.1  8  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    1.6e-09   37.8  12.3      5e-05   23.3   2.0    4.9  5  SRP_TPR_like     Putative TPR-like repeat
    3.1e-09   36.1   0.3     0.0015   17.4   0.0    3.7  3  DUF3808          Protein of unknown function (DUF3808)
    8.1e-08   32.5   0.9        5.9    7.0   0.0    6.0  4  DUF3856          Domain of Unknown Function (DUF3856)
    2.2e-07   30.5   0.0      0.087   12.5   0.0    3.4  3  HrpB1_HrpK       Bacterial type III secretion protein (HrpB1_
    8.1e-07   28.9  15.9        4.4    7.8   0.1    8.3  8  PPR              PPR repeat
    4.5e-06   27.2   0.0       0.77   10.2   0.0    3.5  3  BTAD             Bacterial transcriptional activator domain
    4.5e-06   26.3   0.0       0.13   11.6   0.0    3.9  4  TPR_MalT         MalT-like TPR region
    1.4e-05   24.6   0.1    0.00017   21.1   0.0    2.2  3  Coatomer_E       Coatomer epsilon subunit
    1.6e-05   24.5   0.5       0.42   10.0   0.0    4.3  4  SNAP             Soluble NSF attachment protein, SNAP
    3.5e-05   23.8  11.0      0.045   13.8   0.1    6.6  7  MIT              MIT (microtubule interacting and transport) 
    4.8e-05   23.2   4.1        9.8    6.0   0.0    6.4  7  DUF5113          Domain of unknown function (DUF5113)
    0.00011   21.9   0.7        1.3    8.7   0.0    3.9  4  TPR_21           Tetratricopeptide repeat-like domain
    0.00018   21.5   0.4         13    5.8   0.0    5.1  4  DUF627           Protein of unknown function (DUF627)
    0.00018   21.3   5.7      0.014   15.1   0.4    3.7  4  RPN7             26S proteasome subunit RPN7
     0.0014   18.4   0.4       0.28   11.0   0.0    3.6  4  ATP13            Mitochondrial ATPase expression
     0.0016   17.2   0.0       0.17   10.6   0.0    2.7  3  PknG_TPR         Protein kinase G tetratricopeptide repeat
     0.0034   17.7   0.0        1.7    9.0   0.0    3.4  3  TPR_20           Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.016   14.9   6.9         46    3.8   0.0    6.0  6  SPOB_a           Sensor_kinase_SpoOB-type, alpha-helical doma
      0.022   15.2   0.0         15    6.0   0.0    3.8  4  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
      0.025   14.5   0.8        8.8    6.2   0.0    2.8  3  DUF4919          Domain of unknown function (DUF4919)
       0.05   13.7   0.1        1.9    8.6   0.0    3.3  4  MAS20            MAS20 protein import receptor
      0.066   12.4   0.0       0.83    8.8   0.0    2.3  2  FAT              FAT domain
        0.1   11.6   0.0       0.25   10.3   0.0    1.6  1  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
        0.1   12.2   0.4         51    3.4   0.0    3.3  3  Sec16_C          Sec23-binding domain of Sec16
       0.31   11.3   3.6         41    4.5   0.0    4.1  3  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
       0.31   10.8   5.9        1.4    8.7   0.1    4.0  4  PPTA             Protein prenyltransferase alpha subunit repe


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.14        58      13      31 ..      24      42 ..      22      44 .. 0.83
   2 !   30.4   0.1   5.4e-10   2.2e-07       2      34 .]      46      78 ..      45      78 .. 0.95
   3 ?    6.9   0.0     0.014         6       6      26 ..      84     104 ..      80     112 .. 0.85
   4 !    9.4   0.2    0.0023      0.96       9      33 ..     121     145 ..     117     146 .. 0.91
   5 !   30.1   0.2   6.3e-10   2.6e-07       1      34 []     147     180 ..     147     180 .. 0.96
   6 !   22.3   0.3   1.9e-07     8e-05       4      31 ..     184     211 ..     182     214 .. 0.90
   7 !   26.5   0.3   8.7e-09   3.6e-06       2      34 .]     216     248 ..     215     248 .. 0.94
   8 !   37.6   0.5   2.8e-12   1.2e-09       3      33 ..     251     281 ..     249     282 .. 0.95
   9 !   35.3   0.4   1.5e-11   6.4e-09       1      31 [.     283     313 ..     283     314 .] 0.95

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                                  HTT-HHHHHHHHHHHHHHS CS
                         TPR_1 13 klgkydeAleyyekALeln 31
                                  ++ +y++Al   +k Le++
  gi|15669536|ref|NP_248347.1| 24 EKRNYEKALLLIDKILEVR 42
                                  5689*****9999999986 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 5.4e-10
                                  HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                  +++ +++ +++ lg+ d+Aley++kAL+l P++
  gi|15669536|ref|NP_248347.1| 46 DVYVRKARILRTLGENDKALEYFDKALKLKPKY 78
                                  899****************************97 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.014
                                   HHHHHHHHTT-HHHHHHHHHH CS
                         TPR_1   6 nlGnayfklgkydeAleyyek 26 
                                    +G+++ +lgk++eA e + k
  gi|15669536|ref|NP_248347.1|  84 LKGALLVSLGKLEEAKEVFLK 104
                                   689************998866 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0023
                                   HHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   9 nayfklgkydeAleyyekALelnPn 33 
                                    ++ klg+yd Al+  +k L+ +P+
  gi|15669536|ref|NP_248347.1| 121 FILKKLGEYDYALKIIDKILKKYPK 145
                                   6899****************99997 PP

  == domain 5  score: 30.1 bits;  conditional E-value: 6.3e-10
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   a a+  +G ++++ gk+++ le+++ AL++nP++
  gi|15669536|ref|NP_248347.1| 147 AIAWAEKGEILYREGKLKKSLECFDNALKINPKD 180
                                   679*****************************86 PP

  == domain 6  score: 22.3 bits;  conditional E-value: 1.9e-07
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALeln 31 
                                   l  +G ++fklg+y eAl++ +k+ e n
  gi|15669536|ref|NP_248347.1| 184 LLYKGEILFKLGRYGEALKCLKKVFERN 211
                                   7789********************9988 PP

  == domain 7  score: 26.5 bits;  conditional E-value: 8.7e-09
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   +al  + +++ +lg++++Aley +kAL+lnP++
  gi|15669536|ref|NP_248347.1| 216 RALMYIIQILIYLGRLNQALEYTKKALKLNPDD 248
                                   68899999***********************96 PP

  == domain 8  score: 37.6 bits;  conditional E-value: 2.8e-12
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                    +  +G ++ klgky+eA++y++k+Le+nPn
  gi|15669536|ref|NP_248347.1| 251 LYLYKGIILNKLGKYNEAIKYFDKVLEINPN 281
                                   6899**************************9 PP

  == domain 9  score: 35.3 bits;  conditional E-value: 1.5e-11
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                   ++a+++++ a+ klgk +eA+e+y++AL ++
  gi|15669536|ref|NP_248347.1| 283 PDAWNGKAIALEKLGKINEAIECYNRALDIY 313
                                   68**************************986 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.15        64      12      29 ..      23      40 ..      20      44 .. 0.84
   2 !   26.3   0.1   1.1e-08   4.6e-06       2      33 ..      46      77 ..      45      78 .. 0.94
   3 !   14.5   0.0   6.8e-05     0.028       3      32 ..      81     110 ..      79     112 .. 0.91
   4 !   11.2   0.0   0.00077      0.32       7      33 ..     119     145 ..     115     146 .. 0.91
   5 !   28.4   0.1   2.3e-09   9.7e-07       1      34 []     147     180 ..     147     180 .. 0.96
   6 !   21.9   0.1   2.8e-07   0.00012       4      33 ..     184     213 ..     181     214 .. 0.90
   7 !   22.5   0.1   1.9e-07   7.9e-05      10      34 .]     224     248 ..     223     248 .. 0.94
   8 !   27.1   0.1   6.5e-09   2.7e-06       2      33 ..     250     281 ..     249     282 .. 0.92
   9 !   26.9   0.2   7.5e-09   3.1e-06       1      31 [.     283     313 ..     283     314 .] 0.95

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.15
                         TPR_2 12 yklgdyeeAleafekAle 29
                                  +++ +ye+Al + +k le
  gi|15669536|ref|NP_248347.1| 23 LEKRNYEKALLLIDKILE 40
                                  6789******99999987 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.1e-08
                         TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPn 33
                                  +++ + +++++ lg+ ++Ale+f+kAl+l P+
  gi|15669536|ref|NP_248347.1| 46 DVYVRKARILRTLGENDKALEYFDKALKLKPK 77
                                  7899***************************8 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 6.8e-05
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                   a++  G ++  lg++eeA+e f k  +l+ 
  gi|15669536|ref|NP_248347.1|  81 ANFLKGALLVSLGKLEEAKEVFLKLCRLEK 110
                                   78999*********************9986 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00077
                         TPR_2   7 lGlayyklgdyeeAleafekAleldPn 33 
                                    + ++ klg+y+ Al+  +k l+ +P+
  gi|15669536|ref|NP_248347.1| 119 TAFILKKLGEYDYALKIIDKILKKYPK 145
                                   5899**********************7 PP

  == domain 5  score: 28.4 bits;  conditional E-value: 2.3e-09
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   a a+ + G+++y+ g++++ le+f+ Al+++P++
  gi|15669536|ref|NP_248347.1| 147 AIAWAEKGEILYREGKLKKSLECFDNALKINPKD 180
                                   689*****************************86 PP

  == domain 6  score: 21.9 bits;  conditional E-value: 2.8e-07
                         TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                   l + G++++klg+y eAl++++k+ e + +
  gi|15669536|ref|NP_248347.1| 184 LLYKGEILFKLGRYGEALKCLKKVFERNNK 213
                                   7899********************998876 PP

  == domain 7  score: 22.5 bits;  conditional E-value: 1.9e-07
                         TPR_2  10 ayyklgdyeeAleafekAleldPnn 34 
                                   ++++lg++++Ale+ +kAl+l+P++
  gi|15669536|ref|NP_248347.1| 224 ILIYLGRLNQALEYTKKALKLNPDD 248
                                   799********************97 PP

  == domain 8  score: 27.1 bits;  conditional E-value: 6.5e-09
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                    ++ + G ++ klg+y+eA+++f+k+le++Pn
  gi|15669536|ref|NP_248347.1| 250 LLYLYKGIILNKLGKYNEAIKYFDKVLEINPN 281
                                   57889999999********************9 PP

  == domain 9  score: 26.9 bits;  conditional E-value: 7.5e-09
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                   ++a++  + a++klg+ +eA+e++++Al ++
  gi|15669536|ref|NP_248347.1| 283 PDAWNGKAIALEKLGKINEAIECYNRALDIY 313
                                   689*************************987 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       4.2   1.8e+03      14      29 ..      25      40 ..      22      44 .. 0.65
   2 !   29.2   0.0   1.4e-09   5.8e-07       2      33 ..      46      77 ..      45      78 .. 0.95
   3 !   18.0   0.1   5.4e-06    0.0022       3      33 ..      81     111 ..      80     112 .. 0.92
   4 ?    2.5   0.1      0.52   2.2e+02       9      29 ..     121     141 ..     114     145 .. 0.86
   5 !   18.2   0.2   4.8e-06     0.002       3      34 .]     149     180 ..     147     180 .. 0.95
   6 !   17.8   0.1   6.2e-06    0.0026       7      33 ..     187     213 ..     182     214 .. 0.91
   7 !   16.7   0.1   1.5e-05    0.0062       9      34 .]     223     248 ..     223     248 .. 0.94
   8 !   25.9   0.2   1.6e-08   6.6e-06       7      33 ..     255     281 ..     251     282 .. 0.92
   9 !   22.5   0.1   1.9e-07   8.1e-05       2      31 ..     284     313 ..     283     314 .] 0.94

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 4.2
                                  TT-HHHHHHHHHHHHH CS
                         TPR_8 14 lgdyeeAkeyyekale 29
                                  + +ye+A   + k le
  gi|15669536|ref|NP_248347.1| 25 KRNYEKALLLIDKILE 40
                                  6677777666666666 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 1.4e-09
                                  CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                                  ++y+++++i+++lg+ ++A ey+ kal+l+p+
  gi|15669536|ref|NP_248347.1| 46 DVYVRKARILRTLGENDKALEYFDKALKLKPK 77
                                  69*****************************8 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 5.4e-06
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   a +++g ++ +lg++eeAke++ k ++l+++
  gi|15669536|ref|NP_248347.1|  81 ANFLKGALLVSLGKLEEAKEVFLKLCRLEKS 111
                                   57999*********************99876 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.52
                                   HHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8   9 siylklgdyeeAkeyyekale 29 
                                    i++klg+y+ A + + k l+
  gi|15669536|ref|NP_248347.1| 121 FILKKLGEYDYALKIIDKILK 141
                                   689*******99999999876 PP

  == domain 5  score: 18.2 bits;  conditional E-value: 4.8e-06
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   a+  +g i+   g+++++ e++  al+++p++
  gi|15669536|ref|NP_248347.1| 149 AWAEKGEILYREGKLKKSLECFDNALKINPKD 180
                                   89****************************96 PP

  == domain 6  score: 17.8 bits;  conditional E-value: 6.2e-06
                                   HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                                   +g i++klg+y eA ++++k+ e + +
  gi|15669536|ref|NP_248347.1| 187 KGEILFKLGRYGEALKCLKKVFERNNK 213
                                   799********************9987 PP

  == domain 7  score: 16.7 bits;  conditional E-value: 1.5e-05
                                   HHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   9 siylklgdyeeAkeyyekaleldpdn 34 
                                   +i++ lg++++A ey +kal+l+pd+
  gi|15669536|ref|NP_248347.1| 223 QILIYLGRLNQALEYTKKALKLNPDD 248
                                   68999*******************96 PP

  == domain 8  score: 25.9 bits;  conditional E-value: 1.6e-08
                                   HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                                   +g i+ klg+y+eA++y+ k+le++p+
  gi|15669536|ref|NP_248347.1| 255 KGIILNKLGKYNEAIKYFDKVLEINPN 281
                                   68899*********************8 PP

  == domain 9  score: 22.5 bits;  conditional E-value: 1.9e-07
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                   +a++ ++ +++klg+++eA+e+y++al++ 
  gi|15669536|ref|NP_248347.1| 284 DAWNGKAIALEKLGKINEAIECYNRALDIY 313
                                   79*************************985 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   9.7e-05      0.04       1      57 [.      22      77 ..      22      78 .. 0.92
   2 !   20.3   0.2   1.4e-06   0.00059       5      50 ..      59     104 ..      55     115 .. 0.91
   3 !   13.0   0.0   0.00026      0.11      24      60 ..     112     148 ..     105     156 .. 0.84
   4 !   17.7   0.0   9.1e-06    0.0038       5      58 ..     127     180 ..     123     187 .. 0.92
   5 !   23.6   0.0   1.3e-07   5.5e-05       1      63 [.     157     217 ..     157     224 .. 0.90
   6 !   31.6   0.1   4.1e-10   1.7e-07       1      61 [.     191     251 ..     191     258 .. 0.94
   7 !   20.4   0.2   1.3e-06   0.00054       2      45 ..     226     269 ..     225     269 .. 0.95
   8 !   34.2   0.0   6.3e-11   2.6e-08       5      53 ..     263     311 ..     259     314 .] 0.95

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.7e-05
                        TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57
                                  +l+  +y+ Al l  ++l+   +++++  + A++l  lg+ d+A +  d++++ +p+
  gi|15669536|ref|NP_248347.1| 22 ALEKRNYEKALLLIDKILEV-RESPDVYVRKARILRTLGENDKALEYFDKALKLKPK 77
                                  588999**********9888.7799999999********************999886 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.4e-06
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLda 50 
                                   g  + Al+++ +al+ +pk+  a  l   +l++lg l+eA+++  +
  gi|15669536|ref|NP_248347.1|  59 GENDKALEYFDKALKLKPKYILANFLKGALLVSLGKLEEAKEVFLK 104
                                   67799*************************************9765 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00026
                        TPR_19  24 naearllLAeallalgqldeAealLdalpeedpddar 60 
                                   ++ +++  A +l +lg++d A +++d++++++p++a 
  gi|15669536|ref|NP_248347.1| 112 DLPVKYVTAFILKKLGEYDYALKIIDKILKKYPKSAI 148
                                   56677888999***********************643 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 9.1e-06
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                   g y+ Al++  ++l+++pk+a a++   e+l+  g l++  ++ d +++ +p+d
  gi|15669536|ref|NP_248347.1| 127 GEYDYALKIIDKILKKYPKSAIAWAEKGEILYREGKLKKSLECFDNALKINPKD 180
                                   8999************************************************94 PP

  == domain 5  score: 23.6 bits;  conditional E-value: 1.3e-07
                        TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryas 63 
                                   l+ eg++   l+ + +al+ +pk+   +l+  e+l++lg++ eA ++L+++ e + +d   ++
  gi|15669536|ref|NP_248347.1| 157 LYREGKLKKSLECFDNALKINPKDCQSLLYKGEILFKLGRYGEALKCLKKVFERNNKDI--RA 217
                                   5789999999*******************9***********************999954..44 PP

  == domain 6  score: 31.6 bits;  conditional E-value: 4.1e-10
                        TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                   l++ g+y eAl+ l+++++ ++k+ +a+++ +++l+ lg+l++A +  +++++ +pdd+ +
  gi|15669536|ref|NP_248347.1| 191 LFKLGRYGEALKCLKKVFERNNKDIRALMYIIQILIYLGRLNQALEYTKKALKLNPDDPLL 251
                                   5678*****************************************************9875 PP

  == domain 7  score: 20.4 bits;  conditional E-value: 1.3e-06
                        TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAe 45 
                                   ++ g++ +Al++ ++al+ +p+++ + l+  ++l +lg ++eA+
  gi|15669536|ref|NP_248347.1| 226 IYLGRLNQALEYTKKALKLNPDDPLLYLYKGIILNKLGKYNEAI 269
                                   6779**************************************95 PP

  == domain 8  score: 34.2 bits;  conditional E-value: 6.3e-11
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                   g+y eA++++ ++l+ +p+ ++a+ + A+al +lg ++eA+++ +++++
  gi|15669536|ref|NP_248347.1| 263 GKYNEAIKYFDKVLEINPNIPDAWNGKAIALEKLGKINEAIECYNRALD 311
                                   99*******************************************9987 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   1.5e-07   6.1e-05       2      42 .]      53      93 ..      52      93 .. 0.93
   2 !    7.8   0.0    0.0064       2.7       3      26 ..      88     111 ..      86     113 .. 0.88
   3 ?   -1.6   0.1       5.2   2.2e+03       4      15 ..     123     134 ..     122     134 .. 0.79
   4 !   25.7   0.0   1.6e-08   6.5e-06       1      42 []     154     195 ..     154     195 .. 0.98
   5 !   14.7   0.0   4.5e-05     0.019       1      30 [.     188     217 ..     188     220 .. 0.87
   6 !   23.4   0.6   8.1e-08   3.4e-05       3      42 .]     224     263 ..     223     263 .. 0.93
   7 !   29.3   0.2   1.2e-09     5e-07       3      42 .]     258     297 ..     256     297 .. 0.95
   8 !   17.7   0.2     5e-06    0.0021       6      23 ..     295     312 ..     292     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.5e-07
                        TPR_11  2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                  ++++ +G++++A+e + kAlkl+P++  a +  G+++  +G
  gi|15669536|ref|NP_248347.1| 53 RILRTLGENDKALEYFDKALKLKPKYILANFLKGALLVSLG 93
                                  68899*****************************9998877 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0064
                        TPR_11   3 ayyeqGkyeeAieaYkkAlkldPd 26 
                                   +++++Gk+eeA e++ k ++l  +
  gi|15669536|ref|NP_248347.1|  88 LLVSLGKLEEAKEVFLKLCRLEKS 111
                                   789****************99876 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5.2
                        TPR_11   4 yyeqGkyeeAie 15 
                                   + ++G+y+ A++
  gi|15669536|ref|NP_248347.1| 123 LKKLGEYDYALK 134
                                   6789***99985 PP

  == domain 4  score: 25.7 bits;  conditional E-value: 1.6e-08
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   G ++y  Gk+++++e++ +Alk++P++   ++  G++++k+G
  gi|15669536|ref|NP_248347.1| 154 GEILYREGKLKKSLECFDNALKINPKDCQSLLYKGEILFKLG 195
                                   899*************************************99 PP

  == domain 5  score: 14.7 bits;  conditional E-value: 4.5e-05
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaea 30 
                                   G +++++G+y eA++++kk  + ++++ +a
  gi|15669536|ref|NP_248347.1| 188 GEILFKLGRYGEALKCLKKVFERNNKDIRA 217
                                   899****************98877777665 PP

  == domain 6  score: 23.4 bits;  conditional E-value: 8.1e-08
                        TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   ++  +G++++A+e  kkAlkl+Pd++ +y+  G ++ k+G
  gi|15669536|ref|NP_248347.1| 224 ILIYLGRLNQALEYTKKALKLNPDDPLLYLYKGIILNKLG 263
                                   78899****************************9998887 PP

  == domain 7  score: 29.3 bits;  conditional E-value: 1.2e-09
                        TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   ++ ++Gky+eAi+ + k l+++P+ ++a+++ + a+ k+G
  gi|15669536|ref|NP_248347.1| 258 ILNKLGKYNEAIKYFDKVLEINPNIPDAWNGKAIALEKLG 297
                                   6889**********************************98 PP

  == domain 8  score: 17.7 bits;  conditional E-value: 5e-06
                        TPR_11   6 eqGkyeeAieaYkkAlkl 23 
                                   ++Gk++eAie+Y++Al++
  gi|15669536|ref|NP_248347.1| 295 KLGKINEAIECYNRALDI 312
                                   68**************97 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0         8   3.3e+03      13      36 ..      24      46 ..      15      53 .. 0.67
   2 !   21.2   0.0   8.2e-07   0.00034       2      43 ..      46      87 ..      45      88 .. 0.91
   3 ?    5.9   0.0     0.065        27       8      38 ..      86     116 ..      84     122 .. 0.84
   4 !   11.5   0.0     0.001      0.44       9      43 ..     121     155 ..     115     156 .. 0.89
   5 !   13.6   0.0   0.00022     0.091       3      34 ..     149     180 ..     147     186 .. 0.94
   6 !   14.8   0.0     9e-05     0.038       4      43 ..     184     223 ..     182     224 .. 0.90
   7 !   20.1   0.0   1.9e-06   0.00079       2      42 ..     216     256 ..     215     258 .. 0.92
   8 !   17.8   0.0   9.8e-06    0.0041       4      40 ..     252     288 ..     250     292 .. 0.88
   9 !   11.8   0.0   0.00084      0.35       1      30 [.     283     312 ..     283     314 .] 0.91

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 8
                        TPR_14 13 alGdpdeAiallrralalaPddae 36
                                  + +++++A+ l +++l+   + ++
  gi|15669536|ref|NP_248347.1| 24 EKRNYEKALLLIDKILEVRES-PD 46
                                  467899999999999886554.33 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 8.2e-07
                        TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43
                                  +++ + a++l++lG+ d+A++++++al+l P+   a++l + 
  gi|15669536|ref|NP_248347.1| 46 DVYVRKARILRTLGENDKALEYFDKALKLKPKYILANFLKGA 87
                                  677889*****************************9998876 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.065
                        TPR_14   8 aeallalGdpdeAiallrralalaPddaeaw 38 
                                   +++l  lG+++eA +++ ++++l  +d+ + 
  gi|15669536|ref|NP_248347.1|  86 GALLVSLGKLEEAKEVFLKLCRLEKSDLPVK 116
                                   568999***************9999887665 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.001
                        TPR_14   9 eallalGdpdeAiallrralalaPddaeawlllaq 43 
                                    +l  lG++d A+++ +++l+++P++a aw + ++
  gi|15669536|ref|NP_248347.1| 121 FILKKLGEYDYALKIIDKILKKYPKSAIAWAEKGE 155
                                   568899************************99887 PP

  == domain 5  score: 13.6 bits;  conditional E-value: 0.00022
                        TPR_14   3 allalaeallalGdpdeAiallrralalaPdd 34 
                                   a+++ +e+l++ G++++++++++ al+ +P+d
  gi|15669536|ref|NP_248347.1| 149 AWAEKGEILYREGKLKKSLECFDNALKINPKD 180
                                   89****************************97 PP

  == domain 6  score: 14.8 bits;  conditional E-value: 9e-05
                        TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                   ll  +e+l+ lG++ eA+++l+++ +++ +d +a+++  q
  gi|15669536|ref|NP_248347.1| 184 LLYKGEILFKLGRYGEALKCLKKVFERNNKDIRALMYIIQ 223
                                   566799****************************998766 PP

  == domain 7  score: 20.1 bits;  conditional E-value: 1.9e-06
                        TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                   +al+ + ++l  lG++ +A+++ ++al+l+Pdd+ ++l+ +
  gi|15669536|ref|NP_248347.1| 216 RALMYIIQILIYLGRLNQALEYTKKALKLNPDDPLLYLYKG 256
                                   6888899*****************************99876 PP

  == domain 8  score: 17.8 bits;  conditional E-value: 9.8e-06
                        TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawll 40 
                                   +l  + +l  lG++ eAi++++++l+ +P+ ++aw  
  gi|15669536|ref|NP_248347.1| 252 YLYKGIILNKLGKYNEAIKYFDKVLEINPNIPDAWNG 288
                                   5666899***************************965 PP

  == domain 9  score: 11.8 bits;  conditional E-value: 0.00084
                        TPR_14   1 peallalaeallalGdpdeAiallrralal 30 
                                   p+a+   a al+ lG+  eAi++++ral+ 
  gi|15669536|ref|NP_248347.1| 283 PDAWNGKAIALEKLGKINEAIECYNRALDI 312
                                   6789999********************986 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.018       7.7      12      34 .]      44      66 ..      42      66 .. 0.92
   2 !   13.5   0.1   0.00018     0.073       1      34 []      67     100 ..      67     100 .. 0.96
   3 ?    2.6   0.0      0.53   2.2e+02       2      33 ..     102     133 ..     101     134 .. 0.83
   4 !   14.6   0.0   7.6e-05     0.032       3      32 ..     137     166 ..     135     168 .. 0.90
   5 !   21.9   0.0   3.5e-07   0.00015       1      33 [.     169     201 ..     169     202 .. 0.96
   6 ?    0.4   0.0       2.6   1.1e+03       1      33 [.     203     235 ..     203     236 .. 0.85
   7 !   21.8   0.2   3.7e-07   0.00016       3      34 .]     239     270 ..     237     270 .. 0.95
   8 !   23.5   0.0   1.1e-07   4.5e-05       1      34 []     271     304 ..     271     304 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.018
                        TPR_17 12 nadaynnLAelllknGdlmtArq 34
                                  ++d+y  +A++l+ +G+ ++A++
  gi|15669536|ref|NP_248347.1| 44 SPDVYVRKARILRTLGENDKALE 66
                                  689*****************985 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00018
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   ++ kal+l P++  a ++++ ll ++G+l++A++
  gi|15669536|ref|NP_248347.1|  67 YFDKALKLKPKYILANFLKGALLVSLGKLEEAKE 100
                                   589*****************************86 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.53
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   +lk  +l++++ ++ +  A +l+k+G+++ A+
  gi|15669536|ref|NP_248347.1| 102 FLKLCRLEKSDLPVKYVTAFILKKLGEYDYAL 133
                                   677778888888888999*********99876 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 7.6e-05
                        TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtA 32 
                                    k l+++P++a a+ +++e+l++ G+l++ 
  gi|15669536|ref|NP_248347.1| 137 DKILKKYPKSAIAWAEKGEILYREGKLKKS 166
                                   6899********************999876 PP

  == domain 5  score: 21.9 bits;  conditional E-value: 3.5e-07
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   ++ +al+++P++  ++ +++e+l k+G++++A+
  gi|15669536|ref|NP_248347.1| 169 CFDNALKINPKDCQSLLYKGEILFKLGRYGEAL 201
                                   799****************************97 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 2.6
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   +++k+ e++ ++  a+ +  ++l  +G+l +A+
  gi|15669536|ref|NP_248347.1| 203 CLKKVFERNNKDIRALMYIIQILIYLGRLNQAL 235
                                   567888999999999999999999999999997 PP

  == domain 7  score: 21.8 bits;  conditional E-value: 3.7e-07
                        TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   +kal+l+P+++ +y +++ +l k+G++ +A++
  gi|15669536|ref|NP_248347.1| 239 KKALKLNPDDPLLYLYKGIILNKLGKYNEAIK 270
                                   79****************************85 PP

  == domain 8  score: 23.5 bits;  conditional E-value: 1.1e-07
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   ++ k+le++Pn +da+n +A +l+k+G+  +A++
  gi|15669536|ref|NP_248347.1| 271 YFDKVLEINPNIPDAWNGKAIALEKLGKINEAIE 304
                                   589**************************99986 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.1e-06   0.00047       6      66 ..      21      77 ..      21      79 .. 0.93
   2 ?    1.2   0.0       1.5   6.1e+02       3      24 ..      85     106 ..      83     113 .. 0.75
   3 !   21.9   0.0     5e-07   0.00021       9      66 ..     125     179 ..     120     180 .. 0.93
   4 !   16.1   0.0   3.3e-05     0.014      12      54 ..     162     201 ..     161     209 .. 0.92
   5 !   29.2   0.0   2.6e-09   1.1e-06       5      66 ..     223     281 ..     221     283 .. 0.93
   6 !   26.9   0.0   1.4e-08   5.8e-06       9      64 ..     261     313 ..     256     314 .] 0.95

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.1e-06
                        TPR_16  6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66
                                  +al+ ++y++A+ + +  l+ + +    ++ +  +++++  +g+ ++A++++++al+  p+
  gi|15669536|ref|NP_248347.1| 21 DALEKRNYEKALLLIDKILEVR-E---SPDVYVRKARILRTLGENDKALEYFDKALKLKPK 77
                                  6899******************.4...566**************************99996 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.5
                        TPR_16   3 laraalragdyddAaaaleaal 24 
                                   ++ +++ +g+ ++A +++  + 
  gi|15669536|ref|NP_248347.1|  85 KGALLVSLGKLEEAKEVFLKLC 106
                                   5778899999999999996665 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 5e-07
                        TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   ++g+yd A++  +  lk++   P  a A+ ++g++++r g l++ ++ ++ al+  p+
  gi|15669536|ref|NP_248347.1| 125 KLGEYDYALKIIDKILKKY---PKSAIAWAEKGEILYREGKLKKSLECFDNALKINPK 179
                                   789****************...************************999999998886 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 3.3e-05
                        TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                                   +  + ++ ++ alk +   P + ++ll++g++++++gr+ eA+
  gi|15669536|ref|NP_248347.1| 162 KLKKSLECFDNALKIN---PKDCQSLLYKGEILFKLGRYGEAL 201
                                   6667899*********...***********************7 PP

  == domain 5  score: 29.2 bits;  conditional E-value: 2.6e-09
                        TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   ++++++g+  +A+++ + alk++   Pd++  +l++g ++ ++g + eA+ ++++ l+  p+
  gi|15669536|ref|NP_248347.1| 223 QILIYLGRLNQALEYTKKALKLN---PDDPLLYLYKGIILNKLGKYNEAIKYFDKVLEINPN 281
                                   57899******************...88888*************************999885 PP

  == domain 6  score: 26.9 bits;  conditional E-value: 1.4e-08
                        TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                   ++g+y +A+++++ +l+ +   P  ++A+++++ a+ ++g   eA++ y++al+ +
  gi|15669536|ref|NP_248347.1| 261 KLGKYNEAIKYFDKVLEIN---PNIPDAWNGKAIALEKLGKINEAIECYNRALDIY 313
                                   68*****************...******************************9876 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.8e-05    0.0074      47      74 ..      47      74 ..      21      77 .. 0.56
   2 !   19.3   0.1   2.5e-06    0.0011       5      70 ..      47     104 ..      43     111 .. 0.84
   3 ?    2.0   0.0       0.6   2.5e+02      10      31 ..     120     141 ..     115     147 .. 0.87
   4 !   25.0   0.0   4.1e-08   1.7e-05       3      74 ..     147     210 ..     145     213 .. 0.91
   5 !   20.7   0.2   8.7e-07   0.00036       6      66 ..     184     243 ..     179     247 .. 0.73
   6 !   22.2   0.1   3.1e-07   0.00013       8      75 ..     220     279 ..     213     281 .. 0.89
   7 !   35.2   0.1   2.8e-11   1.1e-08       7      76 ..     253     314 .]     248     314 .] 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-05
                        TPR_12 47 tlrnLgrlyralgryeeAlelleealai 74
                                  ++   +r++r lg+ ++Ale++ +al++
  gi|15669536|ref|NP_248347.1| 47 VYVRKARILRTLGENDKALEYFDKALKL 74
                                  4555566666666666666666666655 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.5e-06
                        TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlellee 70 
                                   ++++ a +lr lg+ d+Ale+++kal +      p++   + + +  g l+  lg++eeA e + +
  gi|15669536|ref|NP_248347.1|  47 VYVRKARILRTLGENDKALEYFDKALKLK-----PKY---ILANFLKGALLVSLGKLEEAKEVFLK 104
                                   68899********************9999.....764...77778888888899999999888766 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.6
                        TPR_12  10 aavlrrlgrydeAlellekale 31 
                                   a +l +lg+yd Al++ +k l 
  gi|15669536|ref|NP_248347.1| 120 AFILKKLGEYDYALKIIDKILK 141
                                   789999********99999875 PP

  == domain 4  score: 25.0 bits;  conditional E-value: 4.1e-08
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   a+a+ + +++l+r g++ ++le+++ al i      p+    +++l   g+++++lgry eAl+ l+++ ++
  gi|15669536|ref|NP_248347.1| 147 AIAWAEKGEILYREGKLKKSLECFDNALKIN-----PK---DCQSLLYKGEILFKLGRYGEALKCLKKVFER 210
                                   6677679************************.....87...59*************************9886 PP

  == domain 5  score: 20.7 bits;  conditional E-value: 8.7e-07
                        TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAle 66 
                                   l   +++l++lgry eAl++l+k+ e+ ++       + +++l+ Lgrl +al+ +++Al+
  gi|15669536|ref|NP_248347.1| 184 LLYKGEILFKLGRYGEALKCLKKVFERNNKDI-RALMYIIQILIYLGRLNQALEYTKKALK 243
                                   5468********************99995443.3456666666666666666666666654 PP

  == domain 6  score: 22.2 bits;  conditional E-value: 3.1e-07
                        TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                    + ++l +lgr+ +Ale+ +kal +      pd pl    +   g+++ +lg+y eA++++ ++l+i 
  gi|15669536|ref|NP_248347.1| 220 YIIQILIYLGRLNQALEYTKKALKLN-----PDDPL---LYLYKGIILNKLGKYNEAIKYFDKVLEIN 279
                                   47788999**************9999.....**999...5*************************985 PP

  == domain 7  score: 35.2 bits;  conditional E-value: 2.8e-11
                        TPR_12   7 nnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                      + +l++lg+y eA+++++k+lei      p+      + ++ ++++++lg+  eA+e +++al+i+e
  gi|15669536|ref|NP_248347.1| 253 LYKGIILNKLGKYNEAIKYFDKVLEIN-----PN---IPDAWNGKAIALEKLGKINEAIECYNRALDIYE 314
                                   45899**********************.....64...6668***************************97 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   1.2e-09     5e-07       1      81 [.      24     104 ..      24     105 .. 0.94
   2 !   18.1   0.1   5.8e-06    0.0024      27      81 ..      83     138 ..      81     139 .. 0.95
   3 !   31.6   1.8   3.3e-10   1.4e-07       5      78 ..     163     237 ..     141     241 .. 0.93
   4 !   23.5   0.2   1.2e-07   4.9e-05      15      81 ..     207     274 ..     205     275 .. 0.86
   5 !   23.3   0.1   1.3e-07   5.6e-05      23      80 ..     246     307 ..     237     309 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.2e-09
                                   HTT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3   1 dqnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                   +++ny++A++l++++l   +esp+    +A  l  +g+ ++A+e+++ka kl++k + + +l++  l+ L+k+eeA  ++ 
  gi|15669536|ref|NP_248347.1|  24 EKRNYEKALLLIDKIL-EVRESPDVYVRKARILRTLGENDKALEYFDKAlKLKPKYILANFLKGALLVSLGKLEEAKEVFL 103
                                   589*************.888888888889***********************************************99987 PP

                                   S CS
                        ANAPC3  81 k 81 
                                   k
  gi|15669536|ref|NP_248347.1| 104 K 104
                                   6 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 5.8e-06
                                   HHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  27 yllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   +l++  l ++g+ ++A e++ k+ +l++++l + y++A  l kL++y+ A+++++k
  gi|15669536|ref|NP_248347.1|  83 FLKGALLVSLGKLEEAKEVFLKLcRLEKSDLPVKYVTAFILKKLGEYDYALKIIDK 138
                                   888999**********************************************9987 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 3.3e-10
                                   HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                        ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                   +k+ + +++ +l+ +++++++++++++ l+++g+y +A++ l+k  + n+k++++++ + q l+ L+++++A+  
  gi|15669536|ref|NP_248347.1| 163 LKKSLECFDNALKINPKDCQSLLYKGEILFKLGRYGEALKCLKKVfERNNKDIRALMYIIQILIYLGRLNQALEY 237
                                   6777889999999***********************************************************975 PP

  == domain 4  score: 23.5 bits;  conditional E-value: 1.2e-07
                                   HH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHH.HTT-HHHHHHHH-S CS
                        ANAPC3  15 llaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcll.kLkkyeeAiaaLek 81 
                                   ++++++++  ++++  + l  +g+ ++A+e+++ka kln+ ++  +yl+    l kL+ky+eAi+ ++k
  gi|15669536|ref|NP_248347.1| 207 VFERNNKDIRALMYIIQILIYLGRLNQALEYTKKAlKLNPDDP-LLYLYKGIILnKLGKYNEAIKYFDK 274
                                   566778888899999********************88888877.77888877777**********9987 PP

  == domain 5  score: 23.3 bits;  conditional E-value: 1.3e-07
                                   HHH..HHHH.HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3  23 ped..ayll.AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                   p+d  +yl+ +  l ++g+y++A+++++k  ++n++ + ++  +A +l kL+k++eAi ++ 
  gi|15669536|ref|NP_248347.1| 246 PDDplLYLYkGIILNKLGKYNEAIKYFDKVlEINPNIPDAWNGKAIALEKLGKINEAIECYN 307
                                   444335555599999*******************************************9986 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       3.6   1.5e+03       6      25 ..      23      42 ..      22      60 .. 0.79
   2 !   12.8   0.0   0.00024     0.099       8      49 ..      58      99 ..      51     103 .. 0.90
   3 !   19.9   0.0   1.4e-06    0.0006      10      62 ..     128     180 ..     122     184 .. 0.93
   4 !   18.7   0.0   3.4e-06    0.0014       8      59 ..     160     211 ..     159     219 .. 0.87
   5 !   26.1   0.0   1.7e-08   7.3e-06       5      65 ..     225     285 ..     221     286 .. 0.92
   6 !   18.7   0.0   3.5e-06    0.0015      12      58 ..     266     312 ..     265     314 .] 0.94

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.6
                         TPR_9  6 ireedweralavverlllla 25
                                  ++++++e+al  ++ +l + 
  gi|15669536|ref|NP_248347.1| 23 LEKRNYEKALLLIDKILEVR 42
                                  67899999999999999883 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00024
                         TPR_9  8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAl 49
                                    ++++al++ +  l l+P+ +   +  G ll+ lG l++A 
  gi|15669536|ref|NP_248347.1| 58 LGENDKALEYFDKALKLKPKYILANFLKGALLVSLGKLEEAK 99
                                  5689***********************************996 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 1.4e-06
                         TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                   +++ al++++ +l   P+++  + + G +l++ G l++ l++++ +l ++p++
  gi|15669536|ref|NP_248347.1| 128 EYDYALKIIDKILKKYPKSAIAWAEKGEILYREGKLKKSLECFDNALKINPKD 180
                                   5788**********************************************987 PP

  == domain 4  score: 18.7 bits;  conditional E-value: 3.4e-06
                         TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                   e +  + l++ +  l ++P+d++ ++  G +l++lG++ +Al++L    + +
  gi|15669536|ref|NP_248347.1| 160 EGKLKKSLECFDNALKINPKDCQSLLYKGEILFKLGRYGEALKCLKKVFERN 211
                                   6677889**************************************8766655 PP

  == domain 5  score: 26.1 bits;  conditional E-value: 1.7e-08
                         TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                   +i   +  +al++    l l+Pddp +++  G++l +lG +++A++ ++  l+++p+ pda
  gi|15669536|ref|NP_248347.1| 225 LIYLGRLNQALEYTKKALKLNPDDPLLYLYKGIILNKLGKYNEAIKYFDKVLEINPNIPDA 285
                                   555678899***********************************************98886 PP

  == domain 6  score: 18.7 bits;  conditional E-value: 3.5e-06
                         TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylal 58 
                                    +a+++ + +l ++P+ p+ +   +++l++lG +++A+++ +++l++
  gi|15669536|ref|NP_248347.1| 266 NEAIKYFDKVLEINPNIPDAWNGKAIALEKLGKINEAIECYNRALDI 312
                                   5799****************************************986 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2   3.9e-08   1.6e-05     189     262 ..      12      79 ..       5     109 .. 0.77
   2 !   21.4   0.1   2.5e-07    0.0001     194     259 ..     115     180 ..     107     182 .. 0.92
   3 !   14.6   0.2   2.8e-05     0.012       5      72 ..     182     249 ..     178     259 .. 0.89
   4 !   17.9   0.0   2.7e-06    0.0011     201     252 ..     258     309 ..     250     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.9e-08
                                   SHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHH CS
                         NARP1 189 sallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyi 262
                                   +++lw  yf A    + +++ekAl +idk +e   ++ ++y++Karil+  G+ +kA e  ++a kl    +yi
  gi|15669536|ref|NP_248347.1|  12 ESILWDEYFDAL---EKRNYEKALLLIDKILEVR-ESPDVYVRKARILRTLGENDKALEYFDKALKLK--PKYI 79 
                                   566777777776...457789********99876.579*************************97774..4455 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2.5e-07
                                   HHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                         NARP1 194 vlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                   v y  A    klg+++ Al++idk +++ p++   +  K++il + G lkk  e+ ++a k+  +D
  gi|15669536|ref|NP_248347.1| 115 VKYVTAFILKKLGEYDYALKIIDKILKKYPKSAIAWAEKGEILYREGKLKKSLECFDNALKINPKD 180
                                   7788899999*************************************************9988877 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 2.8e-05
                                   HHHHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-C CS
                         NARP1   5 ellLyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpens 72 
                                   + lLyk  i+ + g++ eAl+ L+++ ++    +  +    ++l+ Lgr ++A ++ ++ l+ np++ 
  gi|15669536|ref|NP_248347.1| 182 QSLLYKGEILFKLGRYGEALKCLKKVFERNNKDIRALMYIIQILIYLGRLNQALEYTKKALKLNPDDP 249
                                   679**********************9888888888888889************************975 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 2.7e-06
                                   HHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                         NARP1 201 hydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                     +klg++++A++y dk +e +p++ + +  Ka  l++ G +++A+e+ ++a
  gi|15669536|ref|NP_248347.1| 258 ILNKLGKYNEAIKYFDKVLEINPNIPDAWNGKAIALEKLGKINEAIECYNRA 309
                                   57999******************************************99876 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.22        91      12      33 ..      25      46 ..      21      49 .. 0.88
   2 !   14.5   0.0   6.6e-05     0.028       2      28 ..      48      74 ..      47      77 .. 0.85
   3 ?    3.5   0.0       0.2        85       6      32 ..      86     112 ..      83     116 .. 0.83
   4 ?    3.2   0.0      0.27   1.1e+02       5      27 ..     153     175 ..     149     180 .. 0.80
   5 !   12.4   0.0    0.0003      0.13       1      31 [.     183     211 ..     183     216 .. 0.87
   6 ?    3.7   0.0      0.18        75       8      34 ..     224     248 ..     217     250 .. 0.73
   7 !   12.8   0.0   0.00022     0.094       2      28 ..     252     278 ..     251     284 .. 0.82
   8 !    9.5   0.1    0.0026       1.1       2      27 ..     286     311 ..     285     314 .] 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.22
                         TPR_7 12 lGdyeeAielyeqsLaltkdpe 33
                                   ++ye+A+ l  + L+++++p+
  gi|15669536|ref|NP_248347.1| 25 KRNYEKALLLIDKILEVRESPD 46
                                  589**********999999986 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.6e-05
                         TPR_7  2 LlnLarlysrlGdyeeAielyeqsLal 28
                                  +++ ar+ + lG+ ++A+e++ ++L l
  gi|15669536|ref|NP_248347.1| 48 YVRKARILRTLGENDKALEYFDKALKL 74
                                  67789******************6655 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.2
                         TPR_7   6 arlysrlGdyeeAielyeqsL.altkdp 32 
                                   + l ++lG+ eeA e++ + L +l+k++
  gi|15669536|ref|NP_248347.1|  86 GALLVSLGKLEEAKEVFLK-LcRLEKSD 112
                                   668899***********99.55888776 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.27
                         TPR_7   5 LarlysrlGdyeeAielyeqsLa 27 
                                    +++  r+G+ ++ +e++  +L 
  gi|15669536|ref|NP_248347.1| 153 KGEILYREGKLKKSLECFDNALK 175
                                   58898999**********99664 PP

  == domain 5  score: 12.4 bits;  conditional E-value: 0.0003
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                   +Ll+ +++ ++lG+y eA++++++  ++++ 
  gi|15669536|ref|NP_248347.1| 183 SLLYKGEILFKLGRYGEALKCLKK--VFERN 211
                                   69999******************9..88765 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.18
                         TPR_7   8 lysrlGdyeeAielyeqsLaltkdped 34 
                                   +   lG+  +A+e+ ++  al   p+d
  gi|15669536|ref|NP_248347.1| 224 ILIYLGRLNQALEYTKK--ALKLNPDD 248
                                   55668999999999999..55555544 PP

  == domain 7  score: 12.8 bits;  conditional E-value: 0.00022
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLal 28 
                                   +l+ + +  +lG+y eAi+++ ++L++
  gi|15669536|ref|NP_248347.1| 252 YLYKGIILNKLGKYNEAIKYFDKVLEI 278
                                   677889999**************7765 PP

  == domain 8  score: 9.5 bits;  conditional E-value: 0.0026
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLa 27 
                                   ++  a + ++lG+  eAie+y ++L 
  gi|15669536|ref|NP_248347.1| 286 WNGKAIALEKLGKINEAIECYNRALD 311
                                   56668899***************664 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0028       1.2       1      28 [.      46      73 ..      46      77 .. 0.89
   2 ?    1.7   0.0       1.2   4.9e+02       7      26 ..      86     105 ..      81     108 .. 0.77
   3 !   13.1   0.0   0.00028      0.12       7      33 .]     120     146 ..     116     146 .. 0.90
   4 ?    4.7   0.0      0.13        55       7      32 ..     154     179 ..     149     180 .. 0.87
   5 !    9.2   0.1    0.0048         2       1      28 [.     182     209 ..     182     211 .. 0.91
   6 ?    5.9   0.2     0.054        23       2      32 ..     217     247 ..     216     248 .. 0.91
   7 !   12.4   0.0   0.00045      0.19       4      32 ..     253     281 ..     251     281 .. 0.89
   8 ?    8.2   0.0      0.01       4.3       7      30 ..     290     313 ..     288     313 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0028
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6  1 dAlyklalsyrklgdtdkAlealerlik 28
                                  d++ + a+ +r lg+ dkAle++++ +k
  gi|15669536|ref|NP_248347.1| 46 DVYVRKARILRTLGENDKALEYFDKALK 73
                                  6788999*****99***********987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrklgdtdkAlealerl 26 
                                   + ++ +lg+ ++A+e + +l
  gi|15669536|ref|NP_248347.1|  86 GALLVSLGKLEEAKEVFLKL 105
                                   55666789*******99777 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00028
                                   HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                         TPR_6   7 alsyrklgdtdkAlealerlikeYPdS 33 
                                   a  ++klg++d Al++ ++++k+YP+S
  gi|15669536|ref|NP_248347.1| 120 AFILKKLGEYDYALKIIDKILKKYPKS 146
                                   66778999*****************98 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                   ++ +++ g+  k+le +++ +k  P+
  gi|15669536|ref|NP_248347.1| 154 GEILYREGKLKKSLECFDNALKINPK 179
                                   77788877**************9997 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.0048
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                   ++l++ ++ ++klg++ +Al+ l+++ +
  gi|15669536|ref|NP_248347.1| 182 QSLLYKGEILFKLGRYGEALKCLKKVFE 209
                                   589*********************9966 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.054
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                   Al+++ + ++ lg+  +Ale+ ++ +k  Pd
  gi|15669536|ref|NP_248347.1| 217 ALMYIIQILIYLGRLNQALEYTKKALKLNPD 247
                                   8888889999999***************998 PP

  == domain 7  score: 12.4 bits;  conditional E-value: 0.00045
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                                   ++ +  + klg++ +A+++++++++  P+
  gi|15669536|ref|NP_248347.1| 253 LYKGIILNKLGKYNEAIKYFDKVLEINPN 281
                                   67788888999**************9997 PP

  == domain 8  score: 8.2 bits;  conditional E-value: 0.01
                                   HHHHHHHHHHHHHHHHHHHHHHH- CS
                         TPR_6   7 alsyrklgdtdkAlealerlikeY 30 
                                   a +++klg+  +A+e ++r ++ Y
  gi|15669536|ref|NP_248347.1| 290 AIALEKLGKINEAIECYNRALDIY 313
                                   77899999************9988 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   9.3e-08   3.9e-05     141     246 ..      40     145 ..       7     147 .. 0.82
   2 !   26.9   0.0   6.3e-09   2.6e-06     141     267 ..     142     268 ..     140     277 .. 0.78
   3 ?    1.0   0.0      0.49     2e+02     226     269 ..     261     304 ..     254     311 .. 0.63

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 9.3e-08
                        TPR_15 141 aaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselraall..WlliDlgrraeLrellkawkaraesdasLwgp 219
                                   ++++s+ ++++ a++ r  g++d+Al+ + +Al+l+p+   + a++l   ll+ lg+ +e++e+  ++ + ++sd + + +
  gi|15669536|ref|NP_248347.1|  40 EVRESPDVYVRKARILRTLGENDKALEYFDKALKLKPK--YILANFLkgALLVSLGKLEEAKEVFLKLCRLEKSDLPVKYV 118
                                   36799********************************9..666666633478999**************9*9********* PP

                        TPR_15 220 laaAlllLgrpkkALeylrkqakenrk 246
                                    a+ l +Lg+++ AL+ + k +k+ +k
  gi|15669536|ref|NP_248347.1| 119 TAFILKKLGEYDYALKIIDKILKKYPK 145
                                   *****************9998887665 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 6.3e-09
                        TPR_15 141 aaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsse...lraallWlliDlgrraeLrellkawkaraesdasLwg 218
                                   ++ +sa  ++  +e+  +eg+ +++l+++ +Al+ +p++ +    + ++l+ l   gr+ e+ + lk+  +r ++d +   
  gi|15669536|ref|NP_248347.1| 142 KYPKSAIAWAEKGEILYREGKLKKSLECFDNALKINPKDCQsllYKGEILFKL---GRYGEALKCLKKVFERNNKDIRALM 219
                                   567899*******************************9865221345555555...6777766788877777777777777 PP

                        TPR_15 219 plaaAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeA 267
                                        l +Lgr ++ALey +k +k n++dpl  l    +l++ g+ +eA
  gi|15669536|ref|NP_248347.1| 220 YIIQILIYLGRLNQALEYTKKALKLNPDDPLLYLYKGIILNKLGKYNEA 268
                                   7788999***********************9877555555555555555 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.49
                        TPR_15 226 lLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAwr 269
                                   +Lg++++A +y+ k ++ n++ p      A ale+ g+ +eA +
  gi|15669536|ref|NP_248347.1| 261 KLGKYNEAIKYFDKVLEINPNIPDAWNGKAIALEKLGKINEAIE 304
                                   57777777777777777777766555555666666665555544 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       2.1   8.6e+02      16      33 ..      26      43 ..      23      46 .. 0.64
   2 !   10.1   0.0    0.0014      0.58       9      30 ..      52      73 ..      50      75 .. 0.93
   3 ?   -1.3   0.0       5.5   2.3e+03       9      23 ..      86     100 ..      86     105 .. 0.80
   4 ?   -0.8   0.0       3.7   1.5e+03       9      30 ..     120     141 ..     120     143 .. 0.81
   5 ?   -1.1   0.0       4.6   1.9e+03       9      31 ..     154     176 ..     154     177 .. 0.86
   6 !    8.0   0.0    0.0064       2.7       9      31 ..     188     210 ..     182     213 .. 0.87
   7 ?    1.4   0.0      0.75   3.1e+02      12      30 ..     225     243 ..     223     245 .. 0.81
   8 !   11.6   0.0   0.00049       0.2       9      31 ..     256     278 ..     252     279 .. 0.94
   9 !    8.2   0.1    0.0056       2.3       9      33 ..     290     314 .]     287     314 .] 0.94

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 2.1
                        TPR_10 16 grydeAealleealairr 33
                                  ++y++A+ l ++ l++r+
  gi|15669536|ref|NP_248347.1| 26 RNYEKALLLIDKILEVRE 43
                                  466677777666666665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0014
                        TPR_10  9 analrqrgrydeAealleeala 30
                                  a++lr +g+ d+A++++++al 
  gi|15669536|ref|NP_248347.1| 52 ARILRTLGENDKALEYFDKALK 73
                                  899*****************97 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 5.5
                        TPR_10   9 analrqrgrydeAea 23 
                                   +++l ++g+++eA +
  gi|15669536|ref|NP_248347.1|  86 GALLVSLGKLEEAKE 100
                                   5678899*****976 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3.7
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   a +l ++g+yd A+++ ++ l 
  gi|15669536|ref|NP_248347.1| 120 AFILKKLGEYDYALKIIDKILK 141
                                   5678999****99999888776 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 4.6
                        TPR_10   9 analrqrgrydeAealleealai 31 
                                   + +l++ g+++++++ ++ al i
  gi|15669536|ref|NP_248347.1| 154 GEILYREGKLKKSLECFDNALKI 176
                                   56899999999999999999976 PP

  == domain 6  score: 8.0 bits;  conditional E-value: 0.0064
                        TPR_10   9 analrqrgrydeAealleealai 31 
                                   + +l+++gry eA++ l+++ ++
  gi|15669536|ref|NP_248347.1| 188 GEILFKLGRYGEALKCLKKVFER 210
                                   7799*************999876 PP

  == domain 7  score: 1.4 bits;  conditional E-value: 0.75
                        TPR_10  12 lrqrgrydeAealleeala 30 
                                   l  +gr+++A+++ ++al 
  gi|15669536|ref|NP_248347.1| 225 LIYLGRLNQALEYTKKALK 243
                                   55789******99888886 PP

  == domain 8  score: 11.6 bits;  conditional E-value: 0.00049
                        TPR_10   9 analrqrgrydeAealleealai 31 
                                   +++l ++g+y+eA ++++++l+i
  gi|15669536|ref|NP_248347.1| 256 GIILNKLGKYNEAIKYFDKVLEI 278
                                   899******************98 PP

  == domain 9  score: 8.2 bits;  conditional E-value: 0.0056
                        TPR_10   9 analrqrgrydeAealleealairr 33 
                                   a+al ++g+ +eA + + +al+i++
  gi|15669536|ref|NP_248347.1| 290 AIALEKLGKINEAIECYNRALDIYE 314
                                   89999******************97 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.11        45      15      30 ..      26      41 ..      24      44 .. 0.91
   2 ?    5.6   0.0      0.04        17      14      41 ..      58      85 ..      57      88 .. 0.86
   3 !   12.0   0.2    0.0004      0.17      12      33 ..     124     145 ..     116     147 .. 0.87
   4 ?    6.7   0.1     0.018       7.4      12      37 ..     158     183 ..     157     190 .. 0.91
   5 ?    6.5   0.1     0.021       8.7      12      40 ..     192     218 ..     191     224 .. 0.77
   6 ?    5.5   0.1     0.042        17      14      33 ..     228     247 ..     225     249 .. 0.92
   7 !   14.3   0.0   7.8e-05     0.033      13      34 ..     261     282 ..     254     287 .. 0.91
   8 ?   -1.0   0.1       4.6   1.9e+03       8      29 ..     290     311 ..     289     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.11
                                  T-HHHHHHHHHHHHHH CS
                    Fis1_TPR_C 15 geYseArryvdalLei 30
                                  ++Y++A+ ++d +Le+
  gi|15669536|ref|NP_248347.1| 26 RNYEKALLLIDKILEV 41
                                  69************97 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.04
                                  HT-HHHHHHHHHHHHHHTTS-HHHHHHH CS
                    Fis1_TPR_C 14 lgeYseArryvdalLeiEPenrQaqsLk 41
                                  lge ++A++y d  L++ P+   a+ Lk
  gi|15669536|ref|NP_248347.1| 58 LGENDKALEYFDKALKLKPKYILANFLK 85
                                  68889**************988777777 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.0004
                                   HHHT-HHHHHHHHHHHHHHTTS CS
                    Fis1_TPR_C  12 yklgeYseArryvdalLeiEPe 33 
                                    klgeY+ A++ +d +L++ P+
  gi|15669536|ref|NP_248347.1| 124 KKLGEYDYALKIIDKILKKYPK 145
                                   59****************9885 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.018
                                   HHHT-HHHHHHHHHHHHHHTTS-HHH CS
                    Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQa 37 
                                   y+ g+ ++++++ d  L+i P+  Q 
  gi|15669536|ref|NP_248347.1| 158 YREGKLKKSLECFDNALKINPKDCQS 183
                                   8999*****************99885 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.021
                                   HHHT-HHHHHHHHHHHHHHTTS-HHHHHH CS
                    Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQaqsL 40 
                                   +klg+Y eA+++++ + e    n+  ++L
  gi|15669536|ref|NP_248347.1| 192 FKLGRYGEALKCLKKVFERN--NKDIRAL 218
                                   79************997643..6666665 PP

  == domain 6  score: 5.5 bits;  conditional E-value: 0.042
                                   HT-HHHHHHHHHHHHHHTTS CS
                    Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                   lg+ ++A++y++  L++ P+
  gi|15669536|ref|NP_248347.1| 228 LGRLNQALEYTKKALKLNPD 247
                                   7999**************98 PP

  == domain 7  score: 14.3 bits;  conditional E-value: 7.8e-05
                                   HHT-HHHHHHHHHHHHHHTTS- CS
                    Fis1_TPR_C  13 klgeYseArryvdalLeiEPen 34 
                                   klg+Y+eA +y d +Lei P+ 
  gi|15669536|ref|NP_248347.1| 261 KLGKYNEAIKYFDKVLEINPNI 282
                                   9*******************85 PP

  == domain 8  score: -1.0 bits;  conditional E-value: 4.6
                                   HHHHHHHT-HHHHHHHHHHHHH CS
                    Fis1_TPR_C   8 AlGhyklgeYseArryvdalLe 29 
                                   A++  klg+ +eA ++ ++ L 
  gi|15669536|ref|NP_248347.1| 290 AIALEKLGKINEAIECYNRALD 311
                                   7889999999999999998886 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2      0.23        96      29      71 ..      27      71 ..       7      98 .. 0.72
   2 !   11.2   1.5    0.0007      0.29       6      73 ..      69     141 ..      64     149 .. 0.71
   3 !   23.3   2.0   1.2e-07     5e-05       4     109 ..     101     215 ..      98     223 .. 0.78
   4 !   10.5   0.5    0.0011      0.46      23      71 ..     224     275 ..     219     279 .. 0.80
   5 !   10.9   0.1   0.00083      0.34      15      68 ..     250     306 ..     239     311 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.23
                  SRP_TPR_like 29 kyeeaLkllkkgs..alsedvrfEkaYvlYklkkykkalkilkkv 71
                                   ye aL l++k      s dv + ka +l  l +  kal+ ++k+
  gi|15669536|ref|NP_248347.1| 27 NYEKALLLIDKILevRESPDVYVRKARILRTLGENDKALEYFDKA 71
                                  577777777776622345567777777777777777777766654 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0007
                  SRP_TPR_like   6 ekilrlegk.elkkf.kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkvea 73 
                                   +k l+l+ k +l +f k   l++l+k eea ++  k     + +  v++  a++l kl +y  alki++k+ +
  gi|15669536|ref|NP_248347.1|  69 DKALKLKPKyILANFlKGALLVSLGKLEEAKEVFLKLCrleKSDLPVKYVTAFILKKLGEYDYALKIIDKILK 141
                                   55556654413455557777889999999977666655121344569*********************98755 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 1.2e-07
                  SRP_TPR_like   4 eyekilrlegkelkkfkvvali..klekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkv...eaee. 75 
                                    + k+ rle++ l    v+a+i  kl+ y+ aLk+++k       s     Ek  +lY+  k+kk+l+ ++++   + ++ 
  gi|15669536|ref|NP_248347.1| 101 VFLKLCRLEKSDLPVKYVTAFIlkKLGEYDYALKIIDKILkkyPKSAIAWAEKGEILYREGKLKKSLECFDNAlkiNPKDc 181
                                   5668889999999888899988668**********9987633345666778******************986511155665 PP

                  SRP_TPR_like  76 kvkvlksqvlYrlgsyekAYklLskekkedelvv 109
                                   ++   k  +l+ lg y +A k+L k+ + ++ ++
  gi|15669536|ref|NP_248347.1| 182 QSLLYKGEILFKLGRYGEALKCLKKVFERNNKDI 215
                                   6667799****************98766655544 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.0011
                  SRP_TPR_like  23 aliklekyeeaLkllkkgsalsed...vrfEkaYvlYklkkykkalkilkkv 71 
                                    li l++ ++aL+++kk+ +l+ d   +   k  +l kl ky++a k ++kv
  gi|15669536|ref|NP_248347.1| 224 ILIYLGRLNQALEYTKKALKLNPDdplLYLYKGIILNKLGKYNEAIKYFDKV 275
                                   5899999999999999999998763434567888999999999999988775 PP

  == domain 5  score: 10.9 bits;  conditional E-value: 0.00083
                  SRP_TPR_like  15 elkkfkvvaliklekyeeaLkllkkgsalsedv...rfEkaYvlYklkkykkalkil 68 
                                    l  +k + l kl+ky+ea+k+ +k  +++ ++      ka +l kl k ++a +  
  gi|15669536|ref|NP_248347.1| 250 LLYLYKGIILNKLGKYNEAIKYFDKVLEINPNIpdaWNGKAIALEKLGKINEAIECY 306
                                   56668999*****************99777644221678999999999999887765 PP

>> DUF3808  Protein of unknown function (DUF3808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.016       6.8     272     338 ..      48     109 ..      18     132 .. 0.69
   2 !   17.4   0.0   3.6e-06    0.0015     248     333 ..     126     206 ..     115     213 .. 0.76
   3 !   11.9   0.0   0.00016     0.067     272     376 ..     184     282 ..     177     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.016
                       DUF3808 272 llfearieslkgnldeAlelleeiieesqselkqvkhlclfelaltlvylheykeaaesfleLlkls 338
                                    + +ari+++ g+ d+Ale++++++     +lk    l  f ++  lv l + +ea e fl+L++l 
  gi|15669536|ref|NP_248347.1|  48 YVRKARILRTLGENDKALEYFDKAL-----KLKPKYILANFLKGALLVSLGKLEEAKEVFLKLCRLE 109
                                   5678888888888888888888877.....3333345666666666666666666666666666664 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.6e-06
                       DUF3808 248 kapleeleelLlksrkrfPksalwllfearieslkgnldeAlelleeiieesqselkqvkhlclfelaltlvylheykeaa 328
                                    ++ + + +++ k++k++Pksa+   +++ i+  +g+l+++le +++++   +++ k+ ++l++     +l  l +y ea+
  gi|15669536|ref|NP_248347.1| 126 LGEYDYALKIIDKILKKYPKSAIAWAEKGEILYREGKLKKSLECFDNAL---KINPKDCQSLLYKGE--ILFKLGRYGEAL 201
                                   5566778899************************************876...788888888877433..333445555555 PP

                       DUF3808 329 esfle 333
                                   +  ++
  gi|15669536|ref|NP_248347.1| 202 KCLKK 206
                                   55555 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00016
                       DUF3808 272 llfearieslkgnldeAlelleeiieesqselkqvkhlclfelaltlvylheykeaaesfleLlklskwSkalYtYlaaac 352
                                   ll+++ i++  g+  eAl+ l++++   + + k++++l++  +  +l+yl + ++a+e+ ++ lkl+     lY Y ++++
  gi|15669536|ref|NP_248347.1| 184 LLYKGEILFKLGRYGEALKCLKKVF---ERNNKDIRALMY--IIQILIYLGRLNQALEYTKKALKLNPDDPLLYLY-KGII 258
                                   8999******************988...788899999999..567788899999*****************9**99.8999 PP

                       DUF3808 353 llelgreekkaeakekaeelfkev 376
                                   l +lg+ +++ ++ +k+ e+  ++
  gi|15669536|ref|NP_248347.1| 259 LNKLGKYNEAIKYFDKVLEINPNI 282
                                   999999987777777766655555 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.031        13      73     123 ..      56     102 ..      46     111 .. 0.65
   2 ?    4.2   0.0       0.1        42      67      86 ..     125     144 ..     114     213 .. 0.55
   3 ?    7.0   0.0     0.014       5.9      79     129 ..     232     278 ..     204     281 .. 0.78
   4 ?    6.1   0.0     0.026        11     105     128 ..     288     311 ..     282     314 .] 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.031
                                   HHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                       DUF3856  73 ealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkaf 123
                                    +l   dkal+yf++  +l+     ++i a f +++ l +lG+ +ea + f
  gi|15669536|ref|NP_248347.1|  56 RTLGENDKALEYFDKALKLKP----KYILANFLKGALLVSLGKLEEAKEVF 102
                                   445566777777777766654....46777777777777777777777666 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.1
                                   HTT-HHHHHHHHHHHHHHHH CS
                       DUF3856  67 klgrydealesadkalryfn 86 
                                   klg+yd al+ +dk l+ + 
  gi|15669536|ref|NP_248347.1| 125 KLGEYDYALKIIDKILKKYP 144
                                   56666666666665555432 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.014
                                   HHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                       DUF3856  79 dkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                   ++al+y  +  +l+ d+  l++     ++  l++lG+++ea+k+f ++ e+
  gi|15669536|ref|NP_248347.1| 232 NQALEYTKKALKLNPDDPLLYL----YKGIILNKLGKYNEAIKYFDKVLEI 278
                                   4556666666667777776664....58999**************999875 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.026
                                   HHHHHHHHTT-HHHHHHHHHHHHH CS
                       DUF3856 105 sravaleelGrkdealkafrmage 128
                                    +a ale+lG+ +ea++ ++ a +
  gi|15669536|ref|NP_248347.1| 288 GKAIALEKLGKINEAIECYNRALD 311
                                   58999**********999998866 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00021     0.087      30      94 ..      64     128 ..      48     151 .. 0.86
   2 ?    5.8   0.0     0.024        10      40      76 ..     176     212 ..     157     220 .. 0.85
   3 !    8.9   0.0    0.0026       1.1      13      91 ..     217     295 ..     210     299 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                    HrpB1_HrpK  30 aellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyakaLlAlcLaalrD 94 
                                   a +  d    L+P+   +++l g ll++ g++eeA  ++ +++  +++   +k   A+ L+ l++
  gi|15669536|ref|NP_248347.1|  64 ALEYFDKALKLKPKYILANFLKGALLVSLGKLEEAKEVFLKLCRLEKSDLPVKYVTAFILKKLGE 128
                                   55556666679********************************9999999999999999998876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.024
                    HrpB1_HrpK  40 LrPevaeldllegvlliergrweeAlrlLreveaeas 76 
                                   + P+  +  l+ g +l + gr+ eAl+ L++v ++++
  gi|15669536|ref|NP_248347.1| 176 INPKDCQSLLYKGEILFKLGRYGEALKCLKKVFERNN 212
                                   5788899999*********************987654 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0026
                    HrpB1_HrpK  13 gLievlslalasedtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyakaLlAlcLaa 91 
                                   +L+ ++   +  ++ ++a +  +    L P  + l l+ g++l + g+++eA++++ +v + +++ p a    A++L+ 
  gi|15669536|ref|NP_248347.1| 217 ALMYIIQILIYLGRLNQALEYTKKALKLNPDDPLLYLYKGIILNKLGKYNEAIKYFDKVLEINPNIPDAWNGKAIALEK 295
                                   55555555555666666666666666799999****************************9999999888777777765 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       2.4     1e+03      14      28 ..      26      40 ..      23      41 .. 0.85
   2 ?    1.6   0.0         1   4.2e+02      14      26 ..      59      71 ..      57      75 .. 0.81
   3 ?    7.8   0.1     0.011       4.4      10      27 ..      89     106 ..      87     109 .. 0.85
   4 ?    3.1   0.0      0.34   1.4e+02      12      29 ..     125     142 ..     122     143 .. 0.88
   5 ?    2.2   0.0      0.65   2.7e+02      11      24 ..     158     171 ..     156     176 .. 0.88
   6 ?    5.3   0.1     0.066        28      10      29 ..     191     210 ..     189     212 .. 0.86
   7 ?    6.7   0.0     0.023       9.4      12      28 ..     261     277 ..     258     279 .. 0.86
   8 ?    4.2   0.0      0.15        62       9      25 ..     292     308 ..     291     311 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.4
                           PPR 14 GkleeAlelfkeMke 28
                                  +++e+Al l+++++e
  gi|15669536|ref|NP_248347.1| 26 RNYEKALLLIDKILE 40
                                  799******999865 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 1
                           PPR 14 GkleeAlelfkeM 26
                                  G+ ++Ale+f++ 
  gi|15669536|ref|NP_248347.1| 59 GENDKALEYFDKA 71
                                  77799*****985 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.011
                           PPR  10 ycknGkleeAlelfkeMk 27 
                                   +++ GkleeA+e+f ++ 
  gi|15669536|ref|NP_248347.1|  89 LVSLGKLEEAKEVFLKLC 106
                                   6789**********9876 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.34
                           PPR  12 knGkleeAlelfkeMkek 29 
                                   k G+++ Al++++++++k
  gi|15669536|ref|NP_248347.1| 125 KLGEYDYALKIIDKILKK 142
                                   89***********99876 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.65
                           PPR  11 cknGkleeAlelfk 24 
                                    ++Gkl++ le+f+
  gi|15669536|ref|NP_248347.1| 158 YREGKLKKSLECFD 171
                                   699**********8 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.066
                           PPR  10 ycknGkleeAlelfkeMkek 29 
                                   + k G++ eAl+++k+  e+
  gi|15669536|ref|NP_248347.1| 191 LFKLGRYGEALKCLKKVFER 210
                                   6799**********997766 PP

  == domain 7  score: 6.7 bits;  conditional E-value: 0.023
                           PPR  12 knGkleeAlelfkeMke 28 
                                   k Gk+ eA+++f++ +e
  gi|15669536|ref|NP_248347.1| 261 KLGKYNEAIKYFDKVLE 277
                                   89***********9776 PP

  == domain 8  score: 4.2 bits;  conditional E-value: 0.15
                           PPR   9 gycknGkleeAlelfke 25 
                                   ++ k Gk+ eA+e++++
  gi|15669536|ref|NP_248347.1| 292 ALEKLGKINEAIECYNR 308
                                   56799*********987 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.082        34      12     122 ..      51     173 ..      46     180 .. 0.74
   2 ?    6.9   0.0     0.019       7.7      70     118 ..     189     237 ..     182     245 .. 0.86
   3 !   10.2   0.0    0.0018      0.77      74     123 ..     261     310 ..     256     313 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.082
                                   HHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTT............STTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHH CS
                          BTAD  12 agraalaagdpeeaaelleaAlalwrGpaladlea............gewleaererleelrlealealaeaelrlGraee 80 
                                   ++r +   g+ ++a+e +++Al+l     la++ +             +++  ++ rle++ l +    a  + +lG+++ 
  gi|15669536|ref|NP_248347.1|  51 KARILRTLGENDKALEYFDKALKLKPKYILANFLKgallvslgkleeAKEVFLKLCRLEKSDLPVKYVTAFILKKLGEYDY 131
                                   555566666677777777777777666666666665555555555556667777778887777776666667789999999 PP

                                   HHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          BTAD  81 alaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                   al+  +++++++P    ++++  + l+r G+  + Le ++++
  gi|15669536|ref|NP_248347.1| 132 ALKIIDKILKKYPKSAIAWAEKGEILYREGKLKKSLECFDNA 173
                                   999999999999999999999999999999999999998876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.019
                                   HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHH CS
                          BTAD  70 eaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALev 118
                                   e +++lGr+ eal+ l++  + ++ + r+   +++ l ++Gr ++ALe+
  gi|15669536|ref|NP_248347.1| 189 EILFKLGRYGEALKCLKKVFERNNKDIRALMYIIQILIYLGRLNQALEY 237
                                   5678899999999999999999999999999999999999999999985 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0018
                                   HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                          BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                   +lG+++ea+++ ++ ++ +P   +++     Al ++G+ +eA+e Y+r+ 
  gi|15669536|ref|NP_248347.1| 261 KLGKYNEAIKYFDKVLEINPNIPDAWNGKAIALEKLGKINEAIECYNRAL 310
                                   69*********************************************985 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00032      0.13     147     269 ..      30     142 ..      25     149 .. 0.79
   2 ?    2.8   0.0      0.15        62      80     115 ..     147     182 ..     140     213 .. 0.71
   3 !    6.8   0.0    0.0088       3.7      82     113 ..     217     248 ..     209     264 .. 0.84
   4 ?   -1.3   0.0       2.6   1.1e+03      90     109 ..     293     312 ..     286     314 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                      TPR_MalT 147 eGielleql.epeaaldayvllarialaqGdleeAetllekaeelaresnfhvdwlanaeevrvrlwlaqgdlaaaerwle 226
                                   +++ l+++  e + + d yv  ari    G++++A+++++ka +l  +       lan+ +  ++  +  g+l++a++   
  gi|15669536|ref|NP_248347.1|  30 KALLLIDKIlEVRESPDVYVRKARILRTLGENDKALEYFDKALKLKPKY-----ILANFLKGALL--VSLGKLEEAKEVFL 103
                                   66777778645577778*************************9997733.....35677777764..68999999999766 PP

                      TPR_MalT 227 aaelpsdddnhflelelrnlarvllalgrydeAlellerLlka 269
                                   +  + +++d  +++    ++a++l +lg+yd Al++++++lk+
  gi|15669536|ref|NP_248347.1| 104 KLCRLEKSDLPVKY----VTAFILKKLGEYDYALKIIDKILKK 142
                                   66555555666655....799***************9999885 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.15
                      TPR_MalT  80 llallqqaeilvaqGrLheAletyeqalqlateqgl 115
                                   + a    +eil   G+L+++le +  al+  ++ ++
  gi|15669536|ref|NP_248347.1| 147 AIAWAEKGEILYREGKLKKSLECFDNALKINPKDCQ 182
                                   555566788888888888888888888887665554 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0088
                      TPR_MalT  82 allqqaeilvaqGrLheAletyeqalqlateq 113
                                   al+++++il+  GrL +Ale  ++al+l ++ 
  gi|15669536|ref|NP_248347.1| 217 ALMYIIQILIYLGRLNQALEYTKKALKLNPDD 248
                                   67788899999999999999999999987765 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 2.6
                      TPR_MalT  90 lvaqGrLheAletyeqalql 109
                                   l + G+  eA+e y++al  
  gi|15669536|ref|NP_248347.1| 293 LEKLGKINEAIECYNRALDI 312
                                   56679999999999999865 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       0.8   3.3e+02     200     269 ..      44     113 ..      25     136 .. 0.67
   2 ?   -1.4   0.0       2.9   1.2e+03     104     127 ..     115     138 ..     105     149 .. 0.81
   3 !   21.1   0.0   4.1e-07   0.00017     106     229 ..     185     311 ..     160     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.8
                                   -HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHH..HTT--HHHHHHHHHHHHHH-TT- CS
                    Coatomer_E 200 tplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaq..hlgkdaevsernlsqlklshpeh 269
                                    p++   kA +  +lg+ ++A +   +aL+ ++k+   L+N +  a+   lgk +e++e +l+  +l+++++
  gi|15669536|ref|NP_248347.1|  44 SPDVYVRKARILRTLGENDKALEYFDKALKLKPKY--ILANFLKGALlvSLGKLEEAKEVFLKLCRLEKSDL 113
                                   56666667777777888888888888888888887..57777755441156777777777776666666554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.9
                                   HHHHHHHHHHHTT-HHHHHHHHTT CS
                    Coatomer_E 104 lrllaaivflkegdfddalkllkk 127
                                   ++ ++a ++ k g++d alk++ k
  gi|15669536|ref|NP_248347.1| 115 VKYVTAFILKKLGEYDYALKIIDK 138
                                   677889999999999999998865 PP

  == domain 3  score: 21.1 bits;  conditional E-value: 4.1e-07
                                   HHHHHHHHHTT-HHHHHHHHTT-...-SHHHHHHH..HHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHH-TT CS
                    Coatomer_E 106 llaaivflkegdfddalkllkks...enLeavAlk..vqillklhrvdlAekelkkmqdidedatltQLAqawvklavgge 181
                                   l  + +++k g + +alk lkk    +n +++Al   +qil+ l r++ A +  kk+ +++ d+ l+ L +  +      +
  gi|15669536|ref|NP_248347.1| 185 LYKGEILFKLGRYGEALKCLKKVferNNKDIRALMyiIQILIYLGRLNQALEYTKKALKLNPDDPLLYLYKGIILNK--LG 263
                                   5567899999**********997666789999986559*********************************987554..46 PP

                                   HHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                    Coatomer_E 182 kiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLd 229
                                   k+++A   f+ + e  ++ p+  ngkA++  +lg+ +eA +  + aLd
  gi|15669536|ref|NP_248347.1| 264 KYNEAIKYFDKVLEINPNIPDAWNGKAIALEKLGKINEAIECYNRALD 311
                                   9**************9*************************9999997 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.092        39      52     147 ..      42     145 ..      39     177 .. 0.59
   2 ?   -0.1   0.0       1.2     5e+02     113     144 ..     146     176 ..     140     188 .. 0.77
   3 !   10.0   0.0     0.001      0.42      78     128 ..     197     249 ..     193     279 .. 0.75
   4 ?    5.1   0.0     0.031        13     126     146 ..     294     314 .]     285     314 .] 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.092
                                   HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT........-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          SNAP  52 eeAgeaflkaAecqeklkekdeaanayveAakcykkv........speeAvealekAieiytekgrfrraAklkkeiaely 124
                                   +e+ +++++ A++ + l+e+d+a + + +A k   k             +   le+A e++++  r++++    k +   +
  gi|15669536|ref|NP_248347.1|  42 RESPDVYVRKARILRTLGENDKALEYFDKALKLKPKYilanflkgALLVSLGKLEEAKEVFLKLCRLEKSDLPVKYVTAFI 122
                                   567788888888888888888888888888877666544433322333455566666666666666666666666666666 PP

                                   HHTT--HHHHHHHHHHHHHHHHH CS
                          SNAP 125 ekelgdlekAieaYekAaelyeq 147
                                    k+lg+++ A++  +k  + y +
  gi|15669536|ref|NP_248347.1| 123 LKKLGEYDYALKIIDKILKKYPK 145
                                   66666666666655555555544 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHHTT--HHHHHHHHHHHHHH CS
                          SNAP 113 aAklkkeiaelyekelgdlekAieaYekAael 144
                                   +A    e +e++  e g+l+k++e++++A ++
  gi|15669536|ref|NP_248347.1| 146 SAIAWAEKGEILYRE-GKLKKSLECFDNALKI 176
                                   566667788999999.9999999999998776 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.001
                                   HHHHHHHHHHT..-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT CS
                          SNAP  78 yveAakcykkv..speeAvealekAieiytekgrfrraAklkkeiaelyekel 128
                                   y eA kc+kkv  ++++ ++al   i+i++  gr+++a +++k+  +l  ++ 
  gi|15669536|ref|NP_248347.1| 197 YGEALKCLKKVfeRNNKDIRALMYIIQILIYLGRLNQALEYTKKALKLNPDDP 249
                                   89*********8888899*********************99999877766665 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.031
                                   HTT--HHHHHHHHHHHHHHHH CS
                          SNAP 126 kelgdlekAieaYekAaelye 146
                                   ++lg++++Aie+Y++A ++ye
  gi|15669536|ref|NP_248347.1| 294 EKLGKINEAIECYNRALDIYE 314
                                   355899999999999999996 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3      0.58   2.4e+02      29      38 ..      63      72 ..      18      75 .. 0.64
   2 ?    1.6   0.0       0.7   2.9e+02      29      39 ..      63      73 ..      62      82 .. 0.74
   3 ?    0.3   0.0       1.9   7.7e+02      18      39 ..     161     175 ..     145     187 .. 0.62
   4 ?    1.8   0.1       0.6   2.5e+02      26      49 ..     196     218 ..     194     230 .. 0.76
   5 ?    0.6   0.0       1.4     6e+02       1      13 [.     231     243 ..     231     248 .. 0.77
   6 ?    4.3   0.0       0.1        42      26      39 ..     264     277 ..     259     285 .. 0.77
   7 !   13.8   0.1   0.00011     0.045      10      32 ..     289     311 ..     287     313 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.58
                           MIT 29 ealelLlqal 38
                                  +ale++ +al
  gi|15669536|ref|NP_248347.1| 63 KALEYFDKAL 72
                                  3333333333 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.7
                           MIT 29 ealelLlqalk 39
                                  +ale++ +alk
  gi|15669536|ref|NP_248347.1| 63 KALEYFDKALK 73
                                  67888888887 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.9
                           MIT  18 gnyeeAlelYkealelLlqalk 39 
                                   g+ ++ le++ +a       lk
  gi|15669536|ref|NP_248347.1| 161 GKLKKSLECFDNA-------LK 175
                                   5555555555555.......44 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.6
                           MIT  26 lYkealelLlqalkekneerrell 49 
                                    Y eal+ L+++  ++n ++  +l
  gi|15669536|ref|NP_248347.1| 196 RYGEALKCLKKVFERNN-KDIRAL 218
                                   699**********8666.444444 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 1.4
                           MIT   1 ldkAlelvkkAve 13 
                                   l++Ale+ kkA +
  gi|15669536|ref|NP_248347.1| 231 LNQALEYTKKALK 243
                                   6788888888876 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.1
                           MIT  26 lYkealelLlqalk 39 
                                   +Y ea++++ ++l 
  gi|15669536|ref|NP_248347.1| 264 KYNEAIKYFDKVLE 277
                                   68888888888886 PP

  == domain 7  score: 13.8 bits;  conditional E-value: 0.00011
                           MIT  10 kAveeDnagnyeeAlelYkeale 32 
                                   kA+ +++ g++ eA+e+Y  al+
  gi|15669536|ref|NP_248347.1| 289 KAIALEKLGKINEAIECYNRALD 311
                                   8********************98 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.4   5.7e+02      20      36 ..      24      40 ..      18      42 .. 0.85
   2 ?    4.5   0.0     0.066        28      10      37 ..      47      74 ..      41      84 .. 0.88
   3 ?    0.1   0.0       1.5   6.3e+02      20      36 ..     125     141 ..     116     145 .. 0.60
   4 ?    2.4   0.0      0.28   1.2e+02       7      37 ..     146     176 ..     141     180 .. 0.88
   5 ?    1.9   0.0      0.42   1.7e+02      17      40 ..     190     213 ..     179     220 .. 0.84
   6 ?   -0.2   0.0       1.9   7.9e+02      20      36 ..     227     243 ..     216     245 .. 0.81
   7 ?    6.0   0.0     0.023       9.8      11      37 ..     252     278 ..     251     282 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.4
                       DUF5113 20 vegeyeeALeyldsale 36
                                   +++ye+AL ++d+ le
  gi|15669536|ref|NP_248347.1| 24 EKRNYEKALLLIDKILE 40
                                  5789*******999987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.066
                       DUF5113 10 dYanlayylnvegeyeeALeyldsaley 37
                                   Y+  a  l + ge ++ALey+d+al++
  gi|15669536|ref|NP_248347.1| 47 VYVRKARILRTLGENDKALEYFDKALKL 74
                                  689999999999**************85 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.5
                       DUF5113  20 vegeyeeALeyldsale 36 
                                     gey+ AL+++d+ l+
  gi|15669536|ref|NP_248347.1| 125 KLGEYDYALKIIDKILK 141
                                   34666666666666664 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.28
                       DUF5113   7 iandYanlayylnvegeyeeALeyldsaley 37 
                                    a ++a+ +  l+ eg+ +++Le++d+al++
  gi|15669536|ref|NP_248347.1| 146 SAIAWAEKGEILYREGKLKKSLECFDNALKI 176
                                   56689999999*****************985 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.42
                       DUF5113  17 ylnvegeyeeALeyldsaleylNa 40 
                                    l+  g+y eAL++l++++e  N+
  gi|15669536|ref|NP_248347.1| 190 ILFKLGRYGEALKCLKKVFERNNK 213
                                   567789***********9998776 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 1.9
                       DUF5113  20 vegeyeeALeyldsale 36 
                                   + g+ ++ALey ++al+
  gi|15669536|ref|NP_248347.1| 227 YLGRLNQALEYTKKALK 243
                                   5689999*******997 PP

  == domain 7  score: 6.0 bits;  conditional E-value: 0.023
                       DUF5113  11 YanlayylnvegeyeeALeyldsaley 37 
                                   Y   +  ln  g+y+eA++y+d++le+
  gi|15669536|ref|NP_248347.1| 252 YLYKGIILNKLGKYNEAIKYFDKVLEI 278
                                   566778899***************985 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0087       3.6     117     169 ..      49     102 ..      22     114 .. 0.84
   2 !    8.7   0.0    0.0031       1.3     122     179 ..     122     180 ..     115     194 .. 0.83
   3 ?    1.0   0.0      0.71   2.9e+02      90     106 ..     195     211 ..     180     285 .. 0.55
   4 ?    0.2   0.0       1.2   5.1e+02     156     174 ..     293     311 ..     258     313 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0087
                        TPR_21 117 lRLarvllaekkydeAlktLeakkeeafaa.lvaelrGDilvaqgkldeAraaY 169
                                   +R ar+l   ++ d+Al+  +++ + + +  l++ l+G +lv+ gkl+eA++ +
  gi|15669536|ref|NP_248347.1|  49 VRKARILRTLGENDKALEYFDKALKLKPKYiLANFLKGALLVSLGKLEEAKEVF 102
                                   688999999***********9887766655145569**************9866 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0031
                        TPR_21 122 vllaekkydeAlktLeakkeeafaalva.elrGDilvaqgkldeAraaYqaAlaaleek 179
                                   +l + ++yd Alk +++  ++  ++++a   +G+il+++gkl++  + +++Al+ + ++
  gi|15669536|ref|NP_248347.1| 122 ILKKLGEYDYALKIIDKILKKYPKSAIAwAEKGEILYREGKLKKSLECFDNALKINPKD 180
                                   777889**********9998877766653679********************9877666 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.71
                        TPR_21  90 gdlaaAkaqLewvleka 106
                                   g + +A + L++v e +
  gi|15669536|ref|NP_248347.1| 195 GRYGEALKCLKKVFERN 211
                                   33333444444444333 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.2
                        TPR_21 156 lvaqgkldeAraaYqaAla 174
                                   l + gk++eA + Y++Al+
  gi|15669536|ref|NP_248347.1| 293 LEKLGKINEAIECYNRALD 311
                                   5678999999999999986 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.046        19       4      27 ..      21      44 ..      20      61 .. 0.76
   2 ?    1.4   0.0      0.75   3.1e+02       8      50 ..      58      97 ..      51     105 .. 0.76
   3 ?    5.8   0.0     0.032        13       9      47 ..     127     162 ..     121     218 .. 0.66
   4 ?   -0.4   0.0       2.7   1.1e+03      12      47 ..     232     264 ..     222     272 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.046
                        DUF627  4 dllargnhikALeiiedlisrhge 27
                                  d+l+++n+ kAL +i++++ ++++
  gi|15669536|ref|NP_248347.1| 21 DALEKRNYEKALLLIDKILEVRES 44
                                  5789*************9988876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.75
                        DUF627  8 rgnhikALeiiedlisrhgedeksallhrlqGtifvklakkte 50
                                   g+  kALe ++++++ + +     l ++l+G ++v l k  e
  gi|15669536|ref|NP_248347.1| 58 LGENDKALEYFDKALKLKPK---YILANFLKGALLVSLGKLEE 97
                                  57788999999999988888...67888888888888887655 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.032
                        DUF627   9 gnhikALeiiedlisrhgedeksallhrlqGtifvklak 47 
                                   g++  AL+ii++++++  +   sa+   ++G+i+++  k
  gi|15669536|ref|NP_248347.1| 127 GEYDYALKIIDKILKKYPK---SAIAWAEKGEILYREGK 162
                                   5666688888888877777...67777777777776554 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.7
                        DUF627  12 ikALeiiedlisrhgedeksallhrlqGtifvklak 47 
                                    +ALe ++++++ + +d    ll   +G i+ kl k
  gi|15669536|ref|NP_248347.1| 232 NQALEYTKKALKLNPDD---PLLYLYKGIILNKLGK 264
                                   56888888888877774...5666667777777765 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.2   2.6e+03      40      63 ..      49      72 ..      36      80 .. 0.76
   2 ?    0.3   0.0       1.2   4.8e+02      38      63 ..     149     174 ..     130     183 .. 0.89
   3 !   15.1   0.4   3.4e-05     0.014      39     139 ..     184     275 ..     161     281 .. 0.90
   4 ?    5.9   0.0     0.022       9.2      37      64 ..     284     311 ..     277     313 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.2
                                  HHHHHHHHHCT-HHHHHHHHHTCC CS
                          RPN7 40 ldlaehYlkigdleeAlkaysrir 63
                                   ++a+   + g+ ++Al+++ +++
  gi|15669536|ref|NP_248347.1| 49 VRKARILRTLGENDKALEYFDKAL 72
                                  566677777788888888887765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHCT-HHHHHHHHHTCC CS
                          RPN7  38 akldlaehYlkigdleeAlkaysrir 63 
                                   a+ +++e  ++ g+l+++l+++  ++
  gi|15669536|ref|NP_248347.1| 149 AWAEKGEILYREGKLKKSLECFDNAL 174
                                   678999***************98775 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 3.4e-05
                                   HHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHCSSS---.HHHHHHHHHHH CS
                          RPN7  39 kldlaehYlkigdleeAlkaysrireyctslkhkidmllnlirvaiffndwdlvskylekakellekggdwerknrlkvye 119
                                    l ++e  +k g + eAlk++++++e     +  i  l+ +i++ i+++  +++ +y++ka +l  +         l  y+
  gi|15669536|ref|NP_248347.1| 184 LLYKGEILFKLGRYGEALKCLKKVFERN---NKDIRALMYIIQILIYLGRLNQALEYTKKALKLNPD------DPLLYLYK 255
                                   57799*******************9986...5589**************************999998......67899*** PP

                                   HHHHHHTT-HHHHHHHHCTS CS
                          RPN7 120 GlallairkfkeAaellldi 139
                                   G++l + +k++eA + + ++
  gi|15669536|ref|NP_248347.1| 256 GIILNKLGKYNEAIKYFDKV 275
                                   *************9999665 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.022
                                   HHHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                          RPN7  37 rakldlaehYlkigdleeAlkaysrire 64 
                                   +a++ +a    k g+++eA+++y+r+++
  gi|15669536|ref|NP_248347.1| 284 DAWNGKAIALEKLGKINEAIECYNRALD 311
                                   5666667777899************986 PP

>> ATP13  Mitochondrial ATPase expression
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       7.1   2.9e+03      68      82 ..      26      40 ..      22      47 .. 0.83
   2 !   11.0   0.0   0.00068      0.28      62      88 ..     119     147 ..     111     154 .. 0.80
   3 ?    2.0   0.0      0.43   1.8e+02      53      79 ..     214     240 ..     202     250 .. 0.87
   4 ?   -0.0   0.0       1.8   7.5e+02      68      88 ..     263     283 ..     243     288 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 7.1
                         ATP13 68 neiesAlklvdkfsk 82
                                   ++e+Al l+dk+ +
  gi|15669536|ref|NP_248347.1| 26 RNYEKALLLIDKILE 40
                                  48899******9976 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00068
                         ATP13  62 ssfsynn..eiesAlklvdkfskkYpeie 88 
                                   ++f+ ++  e++ Alk++dk+ kkYp+ +
  gi|15669536|ref|NP_248347.1| 119 TAFILKKlgEYDYALKIIDKILKKYPKSA 147
                                   56666655699***************754 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.43
                         ATP13  53 tselLkaivssfsynneiesAlklvdk 79 
                                   + + L  i+++++y +++++Al++ +k
  gi|15669536|ref|NP_248347.1| 214 DIRALMYIIQILIYLGRLNQALEYTKK 240
                                   5678999****************9876 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 1.8
                         ATP13  68 neiesAlklvdkfskkYpeie 88 
                                   +++++A+k+ dk+ ++ p+i+
  gi|15669536|ref|NP_248347.1| 263 GKYNEAIKYFDKVLEINPNIP 283
                                   47899*******999888654 PP

>> PknG_TPR  Protein kinase G tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.089        37      86     154 ..      37     105 ..      17     114 .. 0.71
   2 ?    1.1   0.0      0.31   1.3e+02     105     159 ..      90     144 ..      86     166 .. 0.90
   3 !   10.6   0.0   0.00041      0.17      92     158 ..     213     279 ..     176     283 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.089
                                   ----GCC-SHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHH CS
                      PknG_TPR  86 dgvdaseslevpLaevrahldlGdveearelLdeleeeveedWrldWyrglaeLlegdyeeAaaeFdev 154
                                   + +++ es +v  +++r+   lG+ ++a e++d+  + +++    ++ +g    + g++eeA + F ++
  gi|15669536|ref|NP_248347.1|  37 KILEVRESPDVYVRKARILRTLGENDKALEYFDKALKLKPKYILANFLKGALLVSLGKLEEAKEVFLKL 105
                                   456789999999999999999999999999999887766655555555666666667777777777665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.31
                                   HHCT-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHST CS
                      PknG_TPR 105 ldlGdveearelLdeleeeveedWrldWyrglaeLlegdyeeAaaeFdevlaalp 159
                                   + lG+ eea+e++ +l +  ++d  +++ +++     g+y+ A +  d++l+  p
  gi|15669536|ref|NP_248347.1|  90 VSLGKLEEAKEVFLKLCRLEKSDLPVKYVTAFILKKLGEYDYALKIIDKILKKYP 144
                                   579999******9999999999*****99999999999******99999998776 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00041
                                   C-SHHHHHHHHHHHHCT-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHS CS
                      PknG_TPR  92 eslevpLaevrahldlGdveearelLdeleeeveedWrldWyrglaeLlegdyeeAaaeFdevlaal 158
                                   +++   +  +++ + lG  ++a e+ ++  + +++d  l  y+g+     g+y+eA++ Fd+vl++ 
  gi|15669536|ref|NP_248347.1| 213 KDIRALMYIIQILIYLGRLNQALEYTKKALKLNPDDPLLYLYKGIILNKLGKYNEAIKYFDKVLEIN 279
                                   456666778999***************************************************9875 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       2.4     1e+03       6      50 ..      63     107 ..      58     114 .. 0.81
   2 !    9.0   0.0     0.004       1.7       7      55 ..     166     214 ..     162     234 .. 0.89
   3 ?    3.6   0.0       0.2        85       7      54 ..     234     281 ..     229     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.4
                        TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                   + l+ +++al+ +p+ + a +    +l++ g+ eeA e +l++ +
  gi|15669536|ref|NP_248347.1|  63 KALEYFDKALKLKPKYILANFLKGALLVSLGKLEEAKEVFLKLCR 107
                                   566777888888899999999999999999999999999988876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.004
                        TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                   +l+ +++al+ np+d +  l   + l++ gry eAl+ L ++++r+ k+
  gi|15669536|ref|NP_248347.1| 166 SLECFDNALKINPKDCQSLLYKGEILFKLGRYGEALKCLKKVFERNNKD 214
                                   56778899***********************************998775 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.2
                        TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                    l+  ++al+ npdd  + l     l++ g+y eA++ + ++l+ + +
  gi|15669536|ref|NP_248347.1| 234 ALEYTKKALKLNPDDPLLYLYKGIILNKLGKYNEAIKYFDKVLEINPN 281
                                   677789999**************************9988888877766 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.85   3.5e+02      35      49 ..      57      71 ..      53      73 .. 0.84
   2 ?   -0.1   0.0       1.8   7.6e+02      33      45 ..      89     101 ..      88     107 .. 0.84
   3 ?    3.8   0.0      0.11        46      35      53 ..     125     143 ..     122     147 .. 0.88
   4 ?    1.0   0.0      0.86   3.6e+02      34      52 ..     192     210 ..     190     219 .. 0.85
   5 ?    3.7   0.2      0.12        50      29      49 ..     221     241 ..     218     244 .. 0.88
   6 ?    1.5   0.0      0.57   2.4e+02      35      50 ..     261     276 ..     258     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.85
                        SPOB_a 35 qLgkydkaeeyieev 49
                                  +Lg+ dka ey +++
  gi|15669536|ref|NP_248347.1| 57 TLGENDKALEYFDKA 71
                                  79*********9876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
                        SPOB_a  33 ylqLgkydkaeey 45 
                                   ++ Lgk+++a+e+
  gi|15669536|ref|NP_248347.1|  89 LVSLGKLEEAKEV 101
                                   678********98 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.11
                        SPOB_a  35 qLgkydkaeeyieevvkel 53 
                                   +Lg+yd a ++i+++ k +
  gi|15669536|ref|NP_248347.1| 125 KLGEYDYALKIIDKILKKY 143
                                   79************99875 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.86
                        SPOB_a  34 lqLgkydkaeeyieevvke 52 
                                    +Lg+y +a + +++v + 
  gi|15669536|ref|NP_248347.1| 192 FKLGRYGEALKCLKKVFER 210
                                   689************9986 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.12
                        SPOB_a  29 vIsGylqLgkydkaeeyieev 49 
                                   +I+ ++ Lg++++a ey +++
  gi|15669536|ref|NP_248347.1| 221 IIQILIYLGRLNQALEYTKKA 241
                                   7999*************9886 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.57
                        SPOB_a  35 qLgkydkaeeyieevv 50 
                                   +Lgky++a +y ++v 
  gi|15669536|ref|NP_248347.1| 261 KLGKYNEAIKYFDKVL 276
                                   79*********99986 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.78   3.3e+02      78     119 ..      21      61 ..      11     101 .. 0.60
   2 ?    1.2   0.0       1.1   4.7e+02      82     122 ..     126     166 ..     115     170 .. 0.84
   3 ?    1.0   0.0       1.3   5.4e+02      79     121 ..     157     199 ..     146     244 .. 0.63
   4 ?    6.0   0.0     0.036        15      82     123 ..     262     303 ..     254     310 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.78
                                   HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH CS
               Alkyl_sulf_dimr  78 ealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyq 119
                                   +al++ +y+ a+ l++++++  ++  +    ka++l+ lg+ 
  gi|15669536|ref|NP_248347.1|  21 DALEKRNYEKALLLIDKILEVRESP-DVYVRKARILRTLGEN 61 
                                   5666777777777777777664442.2222244444444443 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.1
                                   TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
               Alkyl_sulf_dimr  82 egdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                    g+y  a++++++++ + p+ a a + k ++l + g+ ++s
  gi|15669536|ref|NP_248347.1| 126 LGEYDYALKIIDKILKKYPKSAIAWAEKGEILYREGKLKKS 166
                                   589****************9999999988888777776655 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.3
                                   HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
               Alkyl_sulf_dimr  79 alkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                                    ++eg+++ ++e  ++++  +p++ +    k ++l +lg+  e
  gi|15669536|ref|NP_248347.1| 157 LYREGKLKKSLECFDNALKINPKDCQSLLYKGEILFKLGRYGE 199
                                   5566666666666666666666665555555555555554333 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.036
                                   TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
               Alkyl_sulf_dimr  82 egdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                    g+y+ a++  +++++ +p+  +a + ka ale+lg+ +e+ 
  gi|15669536|ref|NP_248347.1| 262 LGKYNEAIKYFDKVLEINPNIPDAWNGKAIALEKLGKINEAI 303
                                   589999******************************988865 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       1.2   5.1e+02      67     111 ..     157     201 ..     137     209 .. 0.80
   2 ?    5.4   0.1     0.038        16      68     119 ..     192     243 ..     172     246 .. 0.83
   3 ?    6.2   0.0     0.021       8.8      71     120 ..     263     312 ..     259     314 .] 0.91

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.2
                       DUF4919  67 elseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeak 111
                                    + e +lk+ ++   +alk nP d + l +   ++ +lg+  ea 
  gi|15669536|ref|NP_248347.1| 157 LYREGKLKKSLECFDNALKINPKDCQSLLYKGEILFKLGRYGEAL 201
                                   56788999999999************9999888888888776655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.038
                       DUF4919  68 lseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnk 119
                                    +   + e+++  +++ ++n  d+++l++++ ++  lg+ ++a +y+k+  k
  gi|15669536|ref|NP_248347.1| 192 FKLGRYGEALKCLKKVFERNNKDIRALMYIIQILIYLGRLNQALEYTKKALK 243
                                   5667788999********************************9999998766 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.021
                       DUF4919  71 eelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkl 120
                                    +++e+i++  ++l+ nP  + + n  a+a+++lgk +ea + ++r   +
  gi|15669536|ref|NP_248347.1| 263 GKYNEAIKYFDKVLEINPNIPDAWNGKAIALEKLGKINEAIECYNRALDI 312
                                   689**********************************9999999887665 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.8   7.6e+02      89     106 ..      59      76 ..      48     110 .. 0.61
   2 ?    8.6   0.0    0.0046       1.9      80     107 ..     152     179 ..     145     187 .. 0.89
   3 ?   -1.8   0.0       7.4   3.1e+03      81     100 ..     187     206 ..     183     213 .. 0.87
   4 ?   -1.7   0.0       6.8   2.8e+03      88     105 ..     295     313 ..     288     314 .] 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.8
                         MAS20  89 geeeeaaehlynAlkvcp 106
                                   ge+++a+e + +Alk+ p
  gi|15669536|ref|NP_248347.1|  59 GENDKALEYFDKALKLKP 76 
                                   555556666666655543 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0046
                         MAS20  80 qlGEellaqgeeeeaaehlynAlkvcpq 107
                                   ++GE l ++g+ ++++e++ nAlk+ p+
  gi|15669536|ref|NP_248347.1| 152 EKGEILYREGKLKKSLECFDNALKINPK 179
                                   68**********************9886 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 7.4
                         MAS20  81 lGEellaqgeeeeaaehlyn 100
                                   +GE l++ g++ ea+++l +
  gi|15669536|ref|NP_248347.1| 187 KGEILFKLGRYGEALKCLKK 206
                                   79999999*******99977 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 6.8
                         MAS20  88 q.geeeeaaehlynAlkvc 105
                                   + g+ +ea+e+  +Al ++
  gi|15669536|ref|NP_248347.1| 295 KlGKINEAIECYNRALDIY 313
                                   3589999********9988 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.31   1.3e+02     181     215 ..      39      73 ..      22     148 .. 0.60
   2 ?    8.8   0.0     0.002      0.83     200     290 ..     194     287 ..     119     303 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.31
                                   ...TT.TSSCCCHHHHHHHCCHHHHHSSCCHHHHC CS
                           FAT 181 wlprappevvyaylKylwssgeqkealqkLrefts 215
                                    ++r++p+v++ ++++l + ge ++al+   + ++
  gi|15669536|ref|NP_248347.1|  39 LEVRESPDVYVRKARILRTLGENDKALEYFDKALK 73 
                                   33477889999999999999998888888877776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.002
                                   CCHHHHHSSCCHHHHCCTSSCCC.............SS-SS---............HHHHCCCTCCCCCCCCCCCT.S... CS
                           FAT 200 sgeqkealqkLreftsellekke.............elqsgleaqkeptnleeftkllarcylkkGewqealqkldwseek 267
                                    g+  eal++L++  ++  ++ +             +l+++le+ k++ +l+    l   +yl kG  +++l+k       
  gi|15669536|ref|NP_248347.1| 194 LGRYGEALKCLKKVFERNNKDIRalmyiiqiliylgRLNQALEYTKKALKLNPDDPL---LYLYKGIILNKLGK------- 264
                                   344577777777777755555434444444444444444444444333333333333...6*************....... PP

                                   -SSCCHHHHCCHHCTCCCHSTTC CS
                           FAT 268 ieeilqsysaateidpswykawh 290
                                    +e+ +++ +  ei+p++ +aw+
  gi|15669536|ref|NP_248347.1| 265 YNEAIKYFDKVLEINPNIPDAWN 287
                                   89********************7 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00059      0.25     179     288 ..     123     235 ..     107     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00059
                                   HHHHT-HHHHHHHHHHHHTT-GGGHHHHHH..HHHHTT-HH.HHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHH CS
                         ChAPs 179 vrltkrydralellekLkeeepevvillar..vllladeEv.davkllneeleeeekdaelLllqaefllskkkeelAlev 256
                                   ++   +yd al++++k+ +++p+ +i  a+   +l  +  + ++++   ++l+ ++kd++ Ll + e l +  ++  Al++
  gi|15669536|ref|NP_248347.1| 123 LKKLGEYDYALKIIDKILKKYPKSAIAWAEkgEILYREGKLkKSLECFDNALKINPKDCQSLLYKGEILFKLGRYGEALKC 203
                                   5667789****************9999986332344444442799************************************ PP

                                   HHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                         ChAPs 257 akravksaPsefktWalLvkvYikledienAL 288
                                    k+  +    + +  +++ ++ i l+ +++AL
  gi|15669536|ref|NP_248347.1| 204 LKKVFERNNKDIRALMYIIQILIYLGRLNQAL 235
                                   ****************************9999 PP

>> Sec16_C  Sec23-binding domain of Sec16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.28   1.2e+02     214     237 ..      50      73 ..      47     103 .. 0.81
   2 ?    2.9   0.1      0.17        72     209     239 ..     113     143 ..     106     188 .. 0.83
   3 ?    3.4   0.0      0.12        51     213     238 ..     253     278 ..     224     285 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.28
                                   HHHHHHHHTT-HHHHHHHHHHHHH CS
                       Sec16_C 214 lhAavLaelGlvseAqkYcdaiaa 237
                                    +A +L  lG++++A  Y+d   +
  gi|15669536|ref|NP_248347.1|  50 RKARILRTLGENDKALEYFDKALK 73 
                                   5799***************98665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.17
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                       Sec16_C 209 layKllhAavLaelGlvseAqkYcdaiaasl 239
                                   l++K + A++L  lG+ + A k +d i + +
  gi|15669536|ref|NP_248347.1| 113 LPVKYVTAFILKKLGEYDYALKIIDKILKKY 143
                                   689********************99998753 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.12
                                   HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                       Sec16_C 213 llhAavLaelGlvseAqkYcdaiaas 238
                                   l++  +L  lG+ +eA kY+d + ++
  gi|15669536|ref|NP_248347.1| 253 LYKGIILNKLGKYNEAIKYFDKVLEI 278
                                   78899****************99765 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.15        64      14      35 ..     187     208 ..     176     218 .. 0.85
   2 ?    0.5   0.0       1.7   7.2e+02      21      34 ..     262     275 ..     257     282 .. 0.81
   3 ?    4.5   0.0       0.1        41      12      35 ..     287     310 ..     276     313 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.15
                     NRBF2_MIT  14 kadrllaaGkyeeaischkkaa 35 
                                   k + l+  G+y ea+ c kk  
  gi|15669536|ref|NP_248347.1| 187 KGEILFKLGRYGEALKCLKKVF 208
                                   56778899**********9975 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.7
                     NRBF2_MIT  21 aGkyeeaischkka 34 
                                    Gky+eai    k 
  gi|15669536|ref|NP_248347.1| 262 LGKYNEAIKYFDKV 275
                                   59******987775 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.1
                     NRBF2_MIT  12 srkadrllaaGkyeeaischkkaa 35 
                                   + ka  l   Gk +eai c+++a 
  gi|15669536|ref|NP_248347.1| 287 NGKAIALEKLGKINEAIECYNRAL 310
                                   5677778888**********9985 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.52   2.2e+02       2      15 ..     133     146 ..     132     150 .. 0.89
   2 ?   -0.3   0.1       2.3   9.6e+02       7      15 ..     172     180 ..     171     183 .. 0.85
   3 ?    8.7   0.1    0.0034       1.4       2      15 ..     235     248 ..     234     249 .. 0.91
   4 ?   -1.4   0.1       5.2   2.2e+03       3      20 ..     270     287 ..     268     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.52
                                   HHHHHHHHHH-TT- CS
                          PPTA   2 LeltekliekdpkN 15 
                                   L+ ++k+++k+pk+
  gi|15669536|ref|NP_248347.1| 133 LKIIDKILKKYPKS 146
                                   88999*******96 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.3
                                   HHHHH-TT- CS
                          PPTA   7 kliekdpkN 15 
                                   ++++ +pk+
  gi|15669536|ref|NP_248347.1| 172 NALKINPKD 180
                                   89******7 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0034
                                   HHHHHHHHHH-TT- CS
                          PPTA   2 LeltekliekdpkN 15 
                                   Le+t+k+++++p++
  gi|15669536|ref|NP_248347.1| 235 LEYTKKALKLNPDD 248
                                   9***********85 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 5.2
                                   HHHHHHHHH-TT-CHHHH CS
                          PPTA   3 eltekliekdpkNYsaWn 20 
                                   ++ +k++e +p    aWn
  gi|15669536|ref|NP_248347.1| 270 KYFDKVLEINPNIPDAWN 287
                                   566799999998776776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              43  [number of targets reported over threshold]
# CPU time: 0.93u 0.35s 00:00:01.28 Elapsed: 00:00:00.60
# Mc/sec: 1572.02
//
Query:       gi|15669537|ref|NP_248348.1|  [L=454]
Description: glutamine synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.6e-140  468.0   0.0   1.9e-140  467.8   0.0    1.1  1  Gln-synt_C  Glutamine synthetase, catalytic domain
    8.7e-31  105.5   0.0    1.6e-30  104.6   0.0    1.5  1  Gln-synt_N  Glutamine synthetase, beta-Grasp domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.8   0.0  2.1e-144  1.9e-140       2     345 .]     116     451 ..     115     451 .. 0.97

  Alignments for each domain:
  == domain 1  score: 467.8 bits;  conditional E-value: 2.1e-144
                                   T-HHHHHHHHHHHH.HHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHHHHH CS
                    Gln-synt_C   2 rdPRsvlkralarl.aeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrreivea 81 
                                   +dPRs lk  l++l +e++ +++vgpE+EFfl+++++++            +   pa++ggyf+v+p+d+a d+rr+iv a
  gi|15669537|ref|NP_248348.1| 116 GDPRSRLKAILEELkKEMNGEYFVGPEPEFFLLKRDPHNP-----------HRWVPADDGGYFDVEPLDDAPDIRRDIVLA 185
                                   79************556677**************999955...........45678899********************** PP

                                   HHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTTE CS
                    Gln-synt_C  82 lealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdgk 162
                                   le+lg++veashhEva+gQ+E+++kf++alk+aD+v+tfK+++k++A+khgl+atFmpKp++g nG+gmH+h+S+w  +g+
  gi|15669537|ref|NP_248348.1| 186 LENLGFHVEASHHEVAPGQHEVDFKFDNALKTADSVITFKMTIKNIAKKHGLKATFMPKPFFGMNGNGMHCHQSVW-FNGE 265
                                   ****************************************************************************.**** PP

                                   ESSB-TTSGGG.B-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-TSGGCSTEEEE CS
                    Gln-synt_C 163 nlfadeddeya.lselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipaskekakrvElR 242
                                   + f+d++++y+ lse+++++i+G+l hakal+a+t+ptvnSYkRlvpgyeaPv++aw+++NRsa++R+pa+++ka+r+E+R
  gi|15669537|ref|NP_248348.1| 266 PSFYDPEGPYNgLSETCLSYIAGILSHAKALVAITNPTVNSYKRLVPGYEAPVNIAWANKNRSAIIRVPAARGKATRIEFR 346
                                   ********************************************************************************* PP

                                   CEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHCSHHHCCSS-HHHHHH CS
                    Gln-synt_C 243 lpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealeedellkevlgeeviea 321
                                   +pd+++NPYLa+A++laAgldGi++k++++epve++++++s+ee+  +gie++Pa+l +Al++le de+l+++lg++++e+
  gi|15669537|ref|NP_248348.1| 347 APDPTCNPYLAFACMLAAGLDGIKKKMTAPEPVERNIFKMSEEEKkqLGIESVPANLAAALDELECDEVLQKALGKHIYEN 427
                                   ********************************************9999********************************* PP

                                   HHHHHHHCHHHHHCT--HHHHHHH CS
                    Gln-synt_C 322 ylalkraEleeleeevsdwelery 345
                                   y+++kraE+++++++v+dwe+ +y
  gi|15669537|ref|NP_248348.1| 428 YMEIKRAEWDDFRTAVTDWETGKY 451
                                   ********************9776 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6   0.0   1.8e-34   1.6e-30       1      82 [.      20     108 ..      20     109 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 1.8e-34
                                   T--EEEEEEE-SSS-EEEEEEE.......HHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-..E CS
                    Gln-synt_N   1 evkfvdlqFtDikgklkhvtip.......adelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek.kt 73 
                                   +vkf+++qF+Di g +k+v++p       ++el  +++e+gv FDGSsi gf++ieeSDmlLkPdlst+ ++P+r+e+ ++
  gi|15669537|ref|NP_248348.1|  20 NVKFIRFQFVDILGFPKNVAYPvkagekgIEEL-REIFENGVWFDGSSITGFVGIEESDMLLKPDLSTLSVLPWRPEEkSV 99 
                                   79********************66665555666.899***************************************999** PP

                                   EEEEEEEE- CS
                    Gln-synt_N  74 arvicdvyd 82 
                                   arvicdvy+
  gi|15669537|ref|NP_248348.1| 100 ARVICDVYK 108
                                   ********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2993.09
//
Query:       gi|15669538|ref|NP_248349.1|  [L=235]
Description: ExsB protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-72  243.4   0.1    1.9e-72  243.2   0.1    1.0  1  QueC             Queuosine biosynthesis protein QueC
    6.3e-07   29.4   0.0      1e-06   28.7   0.0    1.2  1  Asn_synthase     Asparagine synthase
    8.8e-07   28.0   0.0    1.3e-06   27.4   0.0    1.2  1  tRNA_Me_trans    tRNA methyl transferase
    7.4e-06   25.3   0.0    1.3e-05   24.4   0.0    1.5  1  NAD_synthase     NAD synthase
    8.4e-06   25.7   0.0    2.4e-05   24.2   0.0    1.8  1  ATP_bind_3       PP-loop family
    5.2e-05   22.9   0.2    0.00075   19.1   0.2    2.2  1  ThiI             Thiamine biosynthesis protein (ThiI)
    0.00088   18.7   0.0     0.0013   18.1   0.0    1.3  1  Arginosuc_synth  Arginosuccinate synthase


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.2   0.1   7.2e-76   1.9e-72       1     208 [.       5     224 ..       5     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 243.2 bits;  conditional E-value: 7.2e-76
                                   EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG-------- CS
                          QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelgveehkildldllkelggsaLtdeeievp 80 
                                   ka+++lSGGlDSt+v+++ak+ g+ev+a+tf+Ygqr +k+e+++akki++ lg+ eh ++dl ++k++g+s+L++e+ e+p
  gi|15669538|ref|NP_248349.1|   5 KAITVLSGGLDSTVVTLIAKDLGYEVTAITFNYGQRaAKREINSAKKICEILGI-EHIVVDLPFVKQFGKSSLITEK-EIP 83 
                                   79**********************************99****************.*******************998.588 PP

                                   ---..........--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHHHTS--EE CS
                          QueC  81 keelee.......eelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlgedkkiei 154
                                   + ++ee       e++++++VpaRN+i++ +a+++aeal+ae+i+iG+n+e+  ++PD++ efv+a+nk+l++g+ +k++i
  gi|15669538|ref|NP_248349.1|  84 TLKMEEldsekayETMKAVWVPARNVIMFGIASGFAEALDAEKIFIGINKEEGVTFPDNTIEFVEAFNKVLEYGTLNKVKI 164
                                   74444445577789******************************************************************* PP

                                   E-TTTT--HHHHHHHHHHTT.....HHHHH-B-STTS..-BTTTTSSSHHHHHHHHHHHH CS
                          QueC 155 eaPlidlsKaeivklgkelg.....vpleetlsCYege.eegkaCgeCdaCalRkkgfee 208
                                   eaPl+d +K+eivklg+el+      +l++++sCY+++ e+  +Cg+C++C++Rk++f +
  gi|15669538|ref|NP_248349.1| 165 EAPLYDKTKEEIVKLGAELEkklgvEVLKYSYSCYHDNgEDFLHCGKCESCMRRKRAFLM 224
                                   *******************999997679********9978999***************76 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   3.9e-10     1e-06      22      78 ..       8      64 ..       5      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.9e-10
                  Asn_synthase 22 alLSGGlDSSliaalaarqsksplktFsigfee.kgsdeakyakevaehlgtehtelv 78
                                  ++LSGGlDS++++ +a+     ++++ +  + + ++  e+  ak+++e lg+eh+ + 
  gi|15669538|ref|NP_248349.1|  8 TVLSGGLDSTVVTLIAKDLGY-EVTAITFNYGQrAAKREINSAKKICEILGIEHIVVD 64
                                  68***************9885.9999999995559*******************8775 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   5.2e-10   1.3e-06       2      70 ..       5      65 ..       4      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.2e-10
                 tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdf 70
                                  k +  lSgG DS+v+ ++ k+ gyev++++++  ++         a+++++ a++++e lgi++ vvd+
  gi|15669538|ref|NP_248349.1|  5 KAITVLSGGLDSTVVTLIAKDLGYEVTAITFNYGQR--------AAKREINSAKKICEILGIEHIVVDL 65
                                  66788************************9987655........57789****************9984 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   5.1e-09   1.3e-05      20      87 ..       5      70 ..       2     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.1e-09
                                  EEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHH CS
                  NAD_synthase 20 gvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievktidikpivra 87
                                  +++  lSGG+DS++v  +a+++    +v+a+ +  ++ + +++++ a++++e lgie  ++d+   v+ 
  gi|15669538|ref|NP_248349.1|  5 KAITVLSGGLDSTVVTLIAKDLG--YEVTAITFNyGQRAAKREINSAKKICEILGIEHIVVDLPF-VKQ 70
                                  56778************999875..6789999988999***********************9843.333 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   9.3e-09   2.4e-05       5      69 ..       9      75 ..       5     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 9.3e-09
                                  E--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H.......H CS
                    ATP_bind_3  5 AvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv.......a 69
                                   +SgGlDS++ +l++++l    g +++ai++++g r+ +k+e +  k++c+ l+i++++ +++        +
  gi|15669538|ref|NP_248349.1|  9 VLSGGLDSTVVTLIAKDL----GYEVTAITFNYGQRA-AKREINSAKKICEILGIEHIVVDLPFvkqfgksS 75
                                  58********99999888....569*********996.68899999***********999988755554440 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   2.9e-07   0.00075       5      58 ..       5      58 ..       3     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.9e-07
                          ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellae 58
                                  k++++lSgG+DS V + ++   G +v +++++     ++++i+  +k+ e+l  
  gi|15669538|ref|NP_248349.1|  5 KAITVLSGGLDSTVVTLIAKDLGYEVTAITFNYGQRAAKREINSAKKICEILGI 58
                                  68999**************************87788888899999999998864 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.2e-07    0.0013       4      59 ..      10      65 ..       7      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.2e-07
               Arginosuc_synth  4 ysGGlDtsviikllkeklgeeviavavdvGqe..eedldevkekalklgavksvvvDa 59
                                   sGGlD +v ++l+++ lg+ev a++ + Gq   + +++++k+  + lg  +++vvD 
  gi|15669538|ref|NP_248349.1| 10 LSGGLDSTV-VTLIAKDLGYEVTAITFNYGQRaaKREINSAKKICEILGI-EHIVVDL 65
                                  69****887.578888999************8224567777666666665.9999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1865.95
//
Query:       gi|15669539|ref|NP_248350.1|  [L=336]
Description: hypothetical protein MJ_1348 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-13   49.2   2.8    8.8e-13   48.0   2.8    1.8  1  TPR_3          Tetratricopeptide repeat
     0.0019   18.1   0.3     0.0067   16.4   0.1    2.1  2  TFIIA_gamma_N  Transcription initiation factor IIA, gamma sub
     0.0063   16.5   4.1      0.067   13.3   0.5    3.0  2  TPR_2          Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.013   15.3   6.6      0.022   14.6   0.6    3.0  2  TPR_1          Tetratricopeptide repeat
      0.027   14.7   4.6      0.045   14.0   0.7    3.3  3  TPR_8          Tetratricopeptide repeat
      0.053   13.0   3.9        1.2    8.6   0.2    2.7  3  SPO22          Meiosis protein SPO22/ZIP4 like
      0.084   13.4   0.9       0.19   12.3   0.5    1.8  1  NLRC4_HD2      NLRC4 helical domain HD2
       0.62   10.8  10.8        0.5   11.1   3.3    3.2  2  RecG_N         RecG N-terminal helical domain


Domain annotation for each model (and alignments):
>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   2.8   3.9e-16   8.8e-13       1      36 []      16      52 ..      16      52 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 3.9e-16
                                  HHHHHHH...HHHHHHTT-HHHHHHH..HHHHHHH-TT- CS
                         TPR_3  1 ldylysy...AaefynkkkyqeArelfsYallaildken 36
                                  +++ly+y   ++efynkk+y++A+e+fs  l+++++ken
  gi|15669539|ref|NP_248350.1| 16 SNFLYKYwlkGCEFYNKKDYDKAIEYFS--LSNKIFKEN 52
                                  79************************99..********9 PP

>> TFIIA_gamma_N  Transcription initiation factor IIA, gamma subunit, helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1     3e-06    0.0067      21      47 ..     207     233 ..     201     234 .. 0.91
   2 ?   -3.1   0.0       3.7   8.2e+03      27      39 ..     319     331 ..     315     335 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-06
                 TFIIA_gamma_N  21 liqegkIspqlamkVLeqFDksineaL 47 
                                    i++ +Is+++++++ ++FDks+++ L
  gi|15669539|ref|NP_248350.1| 207 KIKSCQISNEIVNEIIKRFDKSMSDLL 233
                                   58899*******************998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.7
                 TFIIA_gamma_N  27 IspqlamkVLeqF 39 
                                   +++ l   VL++F
  gi|15669539|ref|NP_248350.1| 319 LNEILDYYVLKEF 331
                                   3444444444444 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.5     3e-05     0.067       4      25 ..      22      43 ..      20      52 .. 0.84
   2 ?    3.2   0.2     0.053   1.2e+02       7      23 ..     233     249 ..     231     250 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                         TPR_2  4 lynlGlayyklgdyeeAleafe 25
                                  ++  G+  y+++dy++A+e+f 
  gi|15669539|ref|NP_248350.1| 22 YWLKGCEFYNKKDYDKAIEYFS 43
                                  6788999**************7 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.053
                         TPR_2   7 lGlayyklgdyeeAlea 23 
                                   l+ a++ + +ye++l +
  gi|15669539|ref|NP_248350.1| 233 LAIAHLLKENYEKCLYY 249
                                   89***********9876 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.6   9.8e-06     0.022       7      25 ..      25      43 ..      24      44 .. 0.93
   2 ?    2.4   0.7     0.069   1.6e+02       7      23 ..     233     249 ..     232     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.8e-06
                                  HHHHHHHTT-HHHHHHHHH CS
                         TPR_1  7 lGnayfklgkydeAleyye 25
                                  +G  ++++++yd+A+ey++
  gi|15669539|ref|NP_248350.1| 25 KGCEFYNKKDYDKAIEYFS 43
                                  7999*************95 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.069
                                   HHHHHHHTT-HHHHHHH CS
                         TPR_1   7 lGnayfklgkydeAley 23 
                                   l+ a++ +++y+++l y
  gi|15669539|ref|NP_248350.1| 233 LAIAHLLKENYEKCLYY 249
                                   899**********9865 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.7     2e-05     0.045       4      28 ..      22      46 ..      22      52 .. 0.86
   2 ?   -3.8   0.0         8   1.8e+04       7      18 ..     104     115 ..     103     116 .. 0.78
   3 ?   -0.3   0.1      0.78   1.7e+03      21      29 ..     240     248 ..     236     249 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2e-05
                                  HHHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_8  4 yynlgsiylklgdyeeAkeyyekal 28
                                  y+++g+   +++dy++A+ey+    
  gi|15669539|ref|NP_248350.1| 22 YWLKGCEFYNKKDYDKAIEYFSLSN 46
                                  889*****************97655 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8
                                   HHHHHHHTT-HH CS
                         TPR_8   7 lgsiylklgdye 18 
                                   ++si  k g+++
  gi|15669539|ref|NP_248350.1| 104 IASIFAKIGKLD 115
                                   788888888875 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.78
                                   HHHHHHHHH CS
                         TPR_8  21 keyyekale 29 
                                   ke yek+l+
  gi|15669539|ref|NP_248350.1| 240 KENYEKCLY 248
                                   7889***96 PP

>> SPO22  Meiosis protein SPO22/ZIP4 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00052       1.2     252     274 ..      23      45 ..      15      82 .. 0.89
   2 ?   -1.6   0.0      0.69   1.5e+03     134     166 ..     118     160 ..      95     185 .. 0.74
   3 ?    4.8   0.2    0.0077        17      88     151 ..     231     298 ..     199     325 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00052
                         SPO22 252 WnkgekhykaknydeAaewyels 274
                                   W kg + y++k+yd+A+e++ ls
  gi|15669539|ref|NP_248350.1|  23 WLKGCEFYNKKDYDKAIEYFSLS 45 
                                   77888889999999999988887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.69
                         SPO22 134 l...........kreadeeeieealeemidsvelseanfklils 166
                                   +           ++ +++ + e++l++++ ++++s +  k il+
  gi|15669539|ref|NP_248350.1| 118 KnflnsggewiyNDVIKDANSEDILKSVL-TFDFSYEERKEILN 160
                                   34555555555677888888999999999.79999988888887 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0077
                         SPO22  88 rllarayleldqeesyekalkavell.......qkeygkkehpsllllklkillkreadeeeieealeemi 151
                                    lla a+l    +e+yek+l +v l        + +  +k++++l++     l++++++ ee+++ l+e+ 
  gi|15669539|ref|NP_248350.1| 231 DLLAIAHLL---KENYEKCLYYVMLFkeyfdldEFNEIEKNKINLIVDIAYNLKNGNVKKEEWLNRLNEIY 298
                                   689999996...9*********9999888887733344577777777666667788888888888887776 PP

>> NLRC4_HD2  NLRC4 helical domain HD2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   8.3e-05      0.19      32     124 ..     149     245 ..     132     250 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.3e-05
                     NLRC4_HD2  32 ekket..kellsls...kkaldkalks.knghldlflrFLfGLlsesnqrlleellgqtklssekkqellkwlkekiqkel 106
                                   + + +  ke+l+++   +k+++  + + ++ ++d++++F++G  + ++  ++ e ++++ +s ++ +e+++ + +  +k++
  gi|15669539|ref|NP_248350.1| 149 DFSYEerKEILNREphlRKLFEDNIYNfNSDFFDFMMMFFIGAGNWKRFLEVYEEFKNKIKSCQISNEIVNEIIKRFDKSM 229
                                   33333323666666666666666555526667*************987777666666555666666666666666666665 PP

                     NLRC4_HD2 107 sserllnlfhcLyElqde 124
                                   s   ll + h L E  ++
  gi|15669539|ref|NP_248350.1| 230 SD--LLAIAHLLKENYEK 245
                                   54..77777777777665 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.3   0.00022       0.5       5      61 ..     197     252 ..     194     261 .. 0.92
   2 ?    2.5   0.4      0.11   2.4e+02      19      59 ..     283     326 ..     271     334 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                                   HHHHHHHHHTS---TTT........HHHHHHH---GGGG-HHHH.HHHHHHHHHHTT CS
                        RecG_N   5 FLeelekllkkvlsgkleteelieeikkkleliddplleneevlkeklskfldYikp 61 
                                   FLe  e+ ++k++s + + +e+++ei k++++   +ll   ++lke  +k l Y+  
  gi|15669539|ref|NP_248350.1| 197 FLEVYEEFKNKIKSCQIS-NEIVNEIIKRFDKSMSDLLAIAHLLKENYEKCLYYVML 252
                                   9***********999995.*******************************9999865 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.11
                                   TTT........HHHHHHH.---GGGG..-HHHH.HHHHHHHHHH CS
                        RecG_N  19 gkleteelieeikkklel.iddplle..neevlkeklskfldYi 59 
                                   g+++ ee ++ +++ +++ i++pl +  +   +++ l+++ldY+
  gi|15669539|ref|NP_248350.1| 283 GNVKKEEWLNRLNEIYKEiIKRPLPNtyKDAHNDDLLNEILDYY 326
                                   44444444444444444313444433113344456778888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1371  (0.0764683); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2027.37
//
Query:       gi|15669540|ref|NP_248351.1|  [L=360]
Description: coenzyme F420-reducing hydrogenase subunit beta [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.1e-36  123.6   0.1    1.1e-35  122.7   0.1    1.4  1  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    1.2e-19   70.2   0.0    2.2e-19   69.3   0.0    1.4  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    9.7e-08   31.5   2.9    9.7e-08   31.5   2.9    3.2  3  Fer4         4Fe-4S binding domain
    1.7e-06   28.3   2.3     0.0058   17.1   1.2    2.8  2  Fer4_8       4Fe-4S dicluster domain
    2.8e-06   27.1   2.7    2.8e-06   27.1   2.7    3.1  2  Fer4_6       4Fe-4S binding domain
    6.8e-05   22.7   4.0    6.8e-05   22.7   4.0    3.7  4  Fer4_2       4Fe-4S binding domain
    0.00018   21.6  18.9    0.00033   20.7  15.4    2.7  3  Fer4_10      4Fe-4S dicluster domain
    0.00027   21.5  16.1    0.00027   21.5  16.1    2.3  2  Fer4_7       4Fe-4S dicluster domain
    0.00077   19.5   0.8    0.00077   19.5   0.8    3.2  4  Fer4_21      4Fe-4S dicluster domain
    0.00086   19.6   4.0    0.00086   19.6   4.0    3.9  4  Fer4_4       4Fe-4S binding domain
     0.0018   18.4   0.7     0.0018   18.4   0.7    3.1  3  Fer4_9       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   16.7   2.5      0.011   16.7   2.5    2.9  4  Fer4_16      4Fe-4S double cluster binding domain
      0.012   16.2   0.4      0.012   16.2   0.4    3.0  2  Fer4_17      4Fe-4S dicluster domain
      0.018   15.2   8.3       0.65   10.2   5.1    2.5  2  Fer4_18      4Fe-4S dicluster domain
      0.031   14.8   9.0      0.098   13.2   0.9    3.3  3  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
      0.035   15.1   7.2      0.035   15.1   7.2    3.5  3  Fer4_3       4Fe-4S binding domain
      0.048   14.5   0.8      0.048   14.5   0.8    3.3  3  Fer4_22      4Fe-4S dicluster domain
      0.098   13.4   5.8       0.35   11.6   2.6    3.0  3  Fer4_15      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.1   1.1e-38   1.1e-35       2     151 ..     190     339 ..     189     342 .. 0.96

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 1.1e-38
                   FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqk......kklkekilltiglfCggnfspealrklleelgvdpedvkklefrgkgkfrvelkd 76 
                                   kk+avvGtPC i+a++++++      k+++e+i+l i lfC ++++++++ k l+e g++p++vkk+++ + gk++++l +
  gi|15669540|ref|NP_248351.1| 190 KKLAVVGTPCVINAIYQILSsdndllKPFREAIRLKIALFCFETYDYSKMIKKLNEDGIEPWEVKKMDI-ESGKLKITLIN 269
                                   89*****************99999**99*****************************************.89*****9999 PP

                   FrhB_FdhB_C  77 ..ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveagelelee 151
                                     ++e++lk++e+++r++CkvC d+t+ ++DisvG+v      g +++g+stvl+r++ ge ++++av +g++++ e
  gi|15669540|ref|NP_248351.1| 270 gnTVEYKLKDVESAMRNGCKVCGDFTGLTSDISVGNV------G-TEKGYSTVLIRNKWGEGFFKRAVYNGYITYDE 339
                                   888899999****************************......8.****************************9876 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.0   2.2e-22   2.2e-19       2      78 .]     106     181 ..     105     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 2.2e-22
                   FrhB_FdhB_N   2 vaArstdkeirkkaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYt.lspnlklLk 78 
                                   v A+++ +  +k+aq GG+vta+l+++++eg+idg+iv+  +k  ++p+ ++a +ke++l++aGskY    p+lk+Lk
  gi|15669540|ref|NP_248351.1| 106 VRAKASIE--IKNAQNGGVVTAILANAFDEGLIDGAIVMMDDKWTLEPESYLALSKEDVLKSAGSKYLwKGPILKALK 181
                                   56777877..9*****************************8864458*********************8899999986 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   2.9   9.7e-11   9.7e-08       2      21 ..      14      33 ..      13      36 .. 0.92
   2 !   10.1   3.1   0.00058      0.58      11      19 ..      78      86 ..      78      87 .. 0.95
   3 ?   -2.2   1.0       4.4   4.4e+03      10      14 ..     287     291 ..     286     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 9.7e-11
                                  EEETTTSSS-THHHHHSTTT CS
                          Fer4  2 videekCigCGaCvevCPvg 21
                                  v+d+++C gCGaCv vCPv+
  gi|15669540|ref|NP_248351.1| 14 VWDTNRCSGCGACVAVCPVN 33
                                  79*****************9 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00058
                                  -THHHHHST CS
                          Fer4 11 CGaCvevCP 19
                                  CGaC+++CP
  gi|15669540|ref|NP_248351.1| 78 CGACYDACP 86
                                  ********* PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.4
                                   S-THH CS
                          Fer4  10 gCGaC 14 
                                   gC+ C
  gi|15669540|ref|NP_248351.1| 287 GCKVC 291
                                   78888 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.2   5.8e-06    0.0058      48      64 ..      17      33 ..       2      34 .. 0.73
   2 !    9.2   0.0    0.0017       1.6       8      22 ..      78      92 ..      76     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.8e-06
                        Fer4_8 48 lwsCttcgaCtevCpvg 64
                                   ++C++cgaC+ vCpv+
  gi|15669540|ref|NP_248351.1| 17 TNRCSGCGACVAVCPVN 33
                                  37899999999999997 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0017
                        Fer4_8  8 CgaCqsaCpvlrrtk 22
                                  CgaC +aCp +++++
  gi|15669540|ref|NP_248351.1| 78 CGACYDACPRIKKSA 92
                                  *********776654 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   2.7   2.8e-09   2.8e-06       3      22 ..      14      33 ..      14      35 .. 0.92
   2 !   11.2   1.9   0.00031       0.3      11      20 ..      77      86 ..      65      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.8e-09
                        Fer4_6  3 eidpdkCigCgdCvrvCPeg 22
                                  ++d ++C gCg+Cv+vCP +
  gi|15669540|ref|NP_248351.1| 14 VWDTNRCSGCGACVAVCPVN 33
                                  69****************87 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00031
                        Fer4_6 11 gCgdCvrvCP 20
                                   Cg+C+++CP
  gi|15669540|ref|NP_248351.1| 77 PCGACYDACP 86
                                  6********* PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   4.0   6.9e-08   6.8e-05       5      21 ..      15      31 ..      12      32 .. 0.92
   2 ?   -0.7   0.7         2     2e+03      10      16 ..      47      52 ..      42      55 .. 0.72
   3 !    9.0   2.5    0.0016       1.6      13      21 ..      78      86 ..      64      87 .. 0.84
   4 ?   -2.0   0.6         5   4.9e+03      11      16 ..     286     291 ..     286     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.9e-08
                        Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                   dt+rC gCgaCv +CP
  gi|15669540|ref|NP_248351.1| 15 WDTNRCSGCGACVAVCP 31
                                  79*************** PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                        Fer4_2 10 CigCgaC 16
                                  C +C+ C
  gi|15669540|ref|NP_248351.1| 47 CDECS-C 52
                                  88886.6 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0016
                        Fer4_2 13 CgaCvsaCP 21
                                  CgaC++aCP
  gi|15669540|ref|NP_248351.1| 78 CGACYDACP 86
                                  ********* PP

  == domain 4  score: -2.0 bits;  conditional E-value: 5
                        Fer4_2  11 igCgaC 16 
                                   +gC+ C
  gi|15669540|ref|NP_248351.1| 286 NGCKVC 291
                                   589998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7  15.4   3.3e-07   0.00033       5      56 .]      16      86 ..      13      86 .. 0.82
   2 !   10.8   1.0   0.00041      0.41      11      38 ..      77     118 ..      63     124 .. 0.66
   3 ?   -2.3   0.1       5.1   5.1e+03      34      49 ..     277     292 ..     268     293 .. 0.54

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.3e-07
                       Fer4_10  5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg.........................cgaCveaCP 56
                                  d+++C +Cg+Cv++CP+      ++ +  ee++v+  +++C                           cgaC++aCP
  gi|15669540|ref|NP_248351.1| 16 DTNRCSGCGACVAVCPV------NNLYFREESPVKFECDECSCiivpadivehpisaefcktvvydvpCGACYDACP 86
                                  899**************......555555555666678888778888888888888888888**************9 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00041
                       Fer4_10  11 rCgkCvkaCPadl..............tsvgakgeaseeeav 38 
                                    Cg+C +aCP                 ++v+ak+ +++++a+
  gi|15669540|ref|NP_248351.1|  77 PCGACYDACPRIKksaipkpkglgnilKAVRAKASIEIKNAQ 118
                                   689999999884466666666666666666666655555555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.1
                       Fer4_10  34 eeeavrkkvekCtgcg 49 
                                    +++++     C  cg
  gi|15669540|ref|NP_248351.1| 277 LKDVESAMRNGCKVCG 292
                                   4555555555555554 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5  16.1   2.7e-07   0.00027       1      49 [.      19      86 ..      19      88 .. 0.69
   2 !    7.6   1.0    0.0059       5.8       5      13 ..      78      86 ..      75     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.7e-07
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek.............gtekveidpekClg......CgaCvavCP 49
                                  rC gCgaCva+Cpv+ ++++ee+  k              + +  i++e C +      CgaC ++CP
  gi|15669540|ref|NP_248351.1| 19 RCSGCGACVAVCPVNNLYFREESPVKfecdecsciivpaDIVEHPISAEFCKTvvydvpCGACYDACP 86
                                  8******************9985544544433333332211223455666665777888********* PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0059
                        Fer4_7  5 CgaCvaaCp 13
                                  CgaC +aCp
  gi|15669540|ref|NP_248351.1| 78 CGACYDACP 86
                                  999999998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.8   7.7e-07   0.00077      37      55 ..      16      34 ..       4      36 .. 0.80
   2 ?    0.5   5.0      0.67   6.7e+02      10      20 ..      77      87 ..      45      93 .. 0.70
   3 ?    5.6   0.7     0.017        17      10      26 ..      77      93 ..      64     110 .. 0.82
   4 ?   -2.1   0.1       4.4   4.4e+03      42      47 ..     286     291 ..     268     294 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.7e-07
                       Fer4_21 37 vedeCvGCnlCssvCPved 55
                                   +++C GC  C++vCPv++
  gi|15669540|ref|NP_248351.1| 16 DTNRCSGCGACVAVCPVNN 34
                                  4789*************75 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.67
                       Fer4_21 10 gCgkCliaCed 20
                                   Cg C+ aC+ 
  gi|15669540|ref|NP_248351.1| 77 PCGACYDACPR 87
                                  46666666654 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.017
                       Fer4_21 10 gCgkCliaCedtshqai 26
                                   Cg C+ aC+     ai
  gi|15669540|ref|NP_248351.1| 77 PCGACYDACPRIKKSAI 93
                                  69999999998777777 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 4.4
                       Fer4_21  42 vGCnlC 47 
                                    GC++C
  gi|15669540|ref|NP_248351.1| 286 NGCKVC 291
                                   588888 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   4.0   8.6e-07   0.00086       2      17 .]      18      33 ..      17      33 .. 0.92
   2 ?   -2.4   1.5        10   9.9e+03       5      10 ..      45      50 ..      45      53 .. 0.80
   3 !   11.2   1.1   0.00044      0.43       7      15 ..      78      86 ..      76      98 .. 0.94
   4 ?    1.2   0.4      0.68   6.7e+02       5      10 ..     286     291 ..     286     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.6e-07
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  +rC gCg+Cva+CP++
  gi|15669540|ref|NP_248351.1| 18 NRCSGCGACVAVCPVN 33
                                  89************75 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 10
                        Fer4_4  5 igCgsC 10
                                  ++C+ C
  gi|15669540|ref|NP_248351.1| 45 FECDEC 50
                                  689988 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00044
                        Fer4_4  7 CgsCvaaCP 15
                                  Cg+C++aCP
  gi|15669540|ref|NP_248351.1| 78 CGACYDACP 86
                                  ********* PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.68
                        Fer4_4   5 igCgsC 10 
                                   +gC++C
  gi|15669540|ref|NP_248351.1| 286 NGCKVC 291
                                   69**** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.7   1.8e-06    0.0018      31      49 ..      15      33 ..       2      35 .. 0.71
   2 ?    1.8   8.9      0.28   2.8e+02      13      48 ..      56      87 ..      45      90 .. 0.64
   3 ?   -2.1   0.1       4.5   4.5e+03      35      40 ..     287     292 ..     269     293 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                        Fer4_9 31 aseeaCigCgaCveaCpkg 49
                                  ++ ++C gCgaCv++Cp +
  gi|15669540|ref|NP_248351.1| 15 WDTNRCSGCGACVAVCPVN 33
                                  3337899*********975 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.28
                        Fer4_9 13 pagvvvedaaerkarlraaseeaCigCgaCveaCpk 48
                                  pa++v+   ++++ +   ++    + CgaC++aCp+
  gi|15669540|ref|NP_248351.1| 56 PADIVEHPISAEFCKTVVYD----VPCGACYDACPR 87
                                  66666666666665555543....68********97 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.5
                        Fer4_9  35 aCigCg 40 
                                    C  Cg
  gi|15669540|ref|NP_248351.1| 287 GCKVCG 292
                                   365555 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.7   2.5   1.1e-05     0.011      50      67 .]      16      33 ..       5      33 .. 0.74
   2 ?   13.8  16.7   8.7e-05     0.087       1      65 [.      19      86 ..      19      87 .. 0.70
   3 ?    7.2   1.4      0.01        10       5      14 ..      78      87 ..      76     118 .. 0.79
   4 ?   -0.6   0.0       2.7   2.7e+03      52      61 ..     283     292 ..     245     294 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                       Fer4_16 50 kqeaitgCdiCqdvCPan 67
                                    +++ gC++C++vCP+n
  gi|15669540|ref|NP_248351.1| 16 DTNRCSGCGACVAVCPVN 33
                                  468999999999999998 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.7e-05
                       Fer4_16  1 rCgtCgkCaevCPtnaikek....kekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                  rC +Cg+C+ vCP+n +  +     ++e + + ci    a+  + ++++e ck       C++C d+CP
  gi|15669540|ref|NP_248351.1| 19 RCSGCGACVAVCPVNNLYFReespVKFECDECSCIIV-PADIVEHPISAEFCKTVVYDVPCGACYDACP 86
                                  6***************985522224455555556555.44445555666667766777**********9 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.01
                       Fer4_16  5 CgkCaevCPt 14
                                  Cg+C ++CP 
  gi|15669540|ref|NP_248351.1| 78 CGACYDACPR 87
                                  999*****96 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.7
                       Fer4_16  52 eaitgCdiCq 61 
                                       gC++C 
  gi|15669540|ref|NP_248351.1| 283 AMRNGCKVCG 292
                                   2236788775 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.2   0.4   1.2e-05     0.012      44      58 ..      18      32 ..       2      44 .. 0.69
   2 ?    7.6   0.0    0.0056       5.6       5      20 ..      78      93 ..      76     126 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                       Fer4_17 44 slCieCgeCerkCPq 58
                                  ++C++Cg C+++CP 
  gi|15669540|ref|NP_248351.1| 18 NRCSGCGACVAVCPV 32
                                  666666666666664 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0056
                       Fer4_17  5 CgyClpeCpsyeaydn 20
                                  Cg+C ++Cp+ ++   
  gi|15669540|ref|NP_248351.1| 78 CGACYDACPRIKKSAI 93
                                  999*****99888544 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   5.1   0.00065      0.65      55      92 ..      14      54 ..       2      73 .. 0.71
   2 ?    5.3   0.1     0.021        21      86     108 ..      76      99 ..      71     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00065
                       Fer4_18 55 ekgagdcidcescvkvcPtg.idirkG..lqleciscllci 92
                                    +++ c  c++cv+vcP++ +  r+   +++ec +c+  i
  gi|15669540|ref|NP_248351.1| 14 VWDTNRCSGCGACVAVCPVNnLYFREEspVKFECDECSCII 54
                                  446789************85377887523788999987444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.021
                       Fer4_18  86 iscllcidacdkvmek.lgkpkgl 108
                                   + c+ c dac ++ ++ + kpkgl
  gi|15669540|ref|NP_248351.1|  76 VPCGACYDACPRIKKSaIPKPKGL 99 
                                   57**********987526677776 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.9   9.9e-05     0.098       2      17 ..      16      31 ..      15      40 .. 0.92
   2 ?    4.2   1.3     0.066        66       8      19 ..      77      88 ..      76      89 .. 0.88
   3 ?   -1.2   0.0         3     3e+03      28      49 ..     264     285 ..     255     293 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.9e-05
                       Fer4_13  2 DrdtCiacgaCvelaP 17
                                  D ++C++cgaCv+++P
  gi|15669540|ref|NP_248351.1| 16 DTNRCSGCGACVAVCP 31
                                  7799************ PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.066
                       Fer4_13  8 acgaCvelaPdv 19
                                   cgaC++++P +
  gi|15669540|ref|NP_248351.1| 77 PCGACYDACPRI 88
                                  5*********75 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3
                       Fer4_13  28 asvvaeqptseeekadaeeAad 49 
                                   +    +++t e + +d+e+A+ 
  gi|15669540|ref|NP_248351.1| 264 KITLINGNTVEYKLKDVESAMR 285
                                   4455577888888888888874 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   7.2   3.5e-05     0.035       1      14 [.      20      33 ..      20      34 .. 0.95
   2 ?   -0.8   2.0         4     4e+03       1       8 [.      47      53 ..      47      55 .. 0.83
   3 ?    9.2   0.8    0.0025       2.5       4      12 ..      78      86 ..      75      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.5e-05
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C gCgaCv vCPv+
  gi|15669540|ref|NP_248351.1| 20 CSGCGACVAVCPVN 33
                                  99**********97 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 4
                        Fer4_3  1 CtgCgaCv 8 
                                  C+ C+ C 
  gi|15669540|ref|NP_248351.1| 47 CDECS-CI 53
                                  9***7.95 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0025
                        Fer4_3  4 CgaCvevCP 12
                                  CgaC ++CP
  gi|15669540|ref|NP_248351.1| 78 CGACYDACP 86
                                  ********* PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.8   4.8e-05     0.048      66      95 ..       3      33 ..       1      34 [. 0.80
   2 ?   -2.0   0.7       6.6   6.6e+03      11      20 ..      46      55 ..      43      72 .. 0.73
   3 ?    0.6   1.3         1     1e+03      83      93 ..      76      86 ..      62      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.8e-05
                       Fer4_22 66 llhklsefkekf.gesgCvGCgRCieacpvk 95
                                  l++ ++++ke++ +++ C GCg C+++cpv+
  gi|15669540|ref|NP_248351.1|  3 LMKSYKNLKEEVwDTNRCSGCGACVAVCPVN 33
                                  5666677777666999************985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.6
                       Fer4_22 11 vCptCsCfdv 20
                                   C  CsC+ v
  gi|15669540|ref|NP_248351.1| 46 ECDECSCIIV 55
                                  6888999766 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1
                       Fer4_22 83 vGCgRCieacp 93
                                  v Cg C +acp
  gi|15669540|ref|NP_248351.1| 76 VPCGACYDACP 86
                                  56777777776 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.6   0.00035      0.35       4      19 ..      16      31 ..      14      51 .. 0.86
   2 ?    1.1   0.1      0.69   6.9e+02      11      21 ..      78      88 ..      76      98 .. 0.86
   3 ?   -2.3   0.0       8.1     8e+03      16      46 ..     235     265 ..     229     269 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                       Fer4_15  4 DrdaCigcglCvaeap 19
                                  D ++C gcg+Cva++p
  gi|15669540|ref|NP_248351.1| 16 DTNRCSGCGACVAVCP 31
                                  899************7 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.69
                       Fer4_15 11 cglCvaeapev 21
                                  cg+C++++p++
  gi|15669540|ref|NP_248351.1| 78 CGACYDACPRI 88
                                  9*******964 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8.1
                       Fer4_15  16 aeapevfeldedglasvllddgeiaegevpd 46 
                                   + ++ + +l+edg+    +++ +i++g ++ 
  gi|15669540|ref|NP_248351.1| 235 DYSKMIKKLNEDGIEPWEVKKMDIESGKLKI 265
                                   5555555677888888888888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2176.18
//
Query:       gi|15669541|ref|NP_248352.1|  [L=261]
Description: formylmethanofuran dehydrogenase subunit C [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-45  154.5   6.3      3e-45  154.2   6.3    1.1  1  GXGXG     GXGXG motif


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.2   6.3   1.7e-49     3e-45       1     186 [.      14     210 ..      14     214 .. 0.93

  Alignments for each domain:
  == domain 1  score: 154.2 bits;  conditional E-value: 1.7e-49
                                   EEE-TT--STTH...........HHHHHHHHHHTTT---.-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ES CS
                         GXGXG   1 leirnldrsvgt...........ilsneiakrygeeglpedtikiklkGsaGqslgaflakGltleleGdandyvGkglsg 70 
                                   +++r+l++++++           +l+n++++r++++g+++++++i+++G +G +lg+f+ +G+t+ ++G+a+++ G+++++
  gi|15669541|ref|NP_248352.1|  14 MHYRELNEKIHEilrenpdikkiVLKNVLGQRFIADGIQKKDLTIEIYGIPGGDLGMFM-SGPTIIVHGNAEFAPGNTMDD 93 
                                   689999999999999999999999***********************************.********************* PP

                                   SEEEEE--TT-SS-GGGSB-S-SSTTTT--SEEEEESSB--SSTTTT-.....SS-EEEESEB.-SSTTTT-EEEEEEE-S CS
                         GXGXG  71 GkivikpskeskfkaeeniivGnvvlygatgGklfirgkageRfavrn.....sgatavvegv.gdhgceYmtGGvvvvLg 145
                                   G+ivi++s+            G+v++++++gGk+f+rg++g+R+++++     +++++v++g  +d+++eYm+GG+++vL+
  gi|15669541|ref|NP_248352.1|  94 GTIVIYGSS------------GDVTAHSMRGGKVFVRGDVGYRSGIHMkaykdKVPVLVIGGRaKDFLGEYMAGGIIIVLN 162
                                   *********............***************************9999999*******99***************** PP

                                   -B..........-SSBTTT--EEEEEEE.-SSSTHHHHB-TTT-EEEES-SH CS
                         GXGXG 146 kt..........grnfaaGmsgGiayvl.dedekfekklnkelvelekvede 186
                                               gr++++G++gG++y++ + d++   +l++++ + e  ++e
  gi|15669541|ref|NP_248352.1| 163 IDekgndlgkvkGRMIGTGIHGGAIYIRgEIDKD---QLGVAADIKEF-TEE 210
                                   9999************************777766...77777776666.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      758  (0.0422779); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1670.91
//
Query:       gi|15669542|ref|NP_248353.1|  [L=510]
Description: glutamate synthase GltB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     4e-151  503.3   0.2     6e-151  502.7   0.2    1.2  1  Glu_synthase     Conserved region in glutamate synthase
    7.9e-15   55.1   0.0    7.1e-08   32.3   0.0    2.3  2  Glu_syn_central  Glutamate synthase central domain
    5.8e-13   48.6   5.6    1.7e-09   37.2   2.2    3.1  3  FMN_dh           FMN-dependent dehydrogenase
    1.2e-09   37.7   4.1    1.3e-07   30.9   2.8    3.0  3  IMPDH            IMP dehydrogenase / GMP reductase domain
    6.1e-08   33.1  13.0    0.00076   20.0   0.5    3.5  3  Fer4_7           4Fe-4S dicluster domain
    1.5e-07   31.1   2.8    2.8e-07   30.3   2.8    1.4  1  NMO              Nitronate monooxygenase
    2.8e-05   23.5   5.7    0.00015   21.1   2.9    2.8  2  DHO_dh           Dihydroorotate dehydrogenase
     0.0001   22.0  22.5    0.00035   20.3   1.9    3.5  3  Fer4             4Fe-4S binding domain
    0.00023   21.2  17.6      0.025   14.7  13.2    3.4  3  Fer4_10          4Fe-4S dicluster domain
    0.00036   20.6   8.3    0.00036   20.6   8.3    2.5  2  Fer4_21          4Fe-4S dicluster domain
    0.00042   20.3   1.6    0.00042   20.3   1.6    3.5  3  Fer4_6           4Fe-4S binding domain
     0.0015   18.6  16.7     0.0026   17.9  10.9    2.8  2  Fer4_9           4Fe-4S dicluster domain
     0.0019   19.1   1.2     0.0019   19.1   1.2    3.4  3  Fer4_16          4Fe-4S double cluster binding domain
     0.0027   17.2   0.2     0.0069   15.9   0.2    1.6  1  His_biosynth     Histidine biosynthesis protein
  ------ inclusion threshold ------
       0.18   12.0  23.1      0.085   13.0   2.3    3.6  3  Fer4_2           4Fe-4S binding domain
       0.47   10.9  16.6        1.4    9.4   3.0    3.4  5  Fer4_8           4Fe-4S dicluster domain
        2.5    8.7  17.0        3.4    8.3   1.9    3.4  4  Fer4_17          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  502.7   0.2  5.7e-154    6e-151       2     368 .]     105     478 ..     104     478 .. 0.99

  Alignments for each domain:
  == domain 1  score: 502.7 bits;  conditional E-value: 5.7e-154
                                   SS-HHHHHHHHHHHHH---HHHHHHHHHHHTS.-S-SGGGGEEE--SS--.........--GGGS--HHHHHTTEE---B- CS
                  Glu_synthase   2 rneievikllqkavqveskesidkyrekleerevlkakrdlleldaaeeal........ikleevepalkikkriltsamS 74 
                                   +++i+++k++ +a+qv +++sid +re++e r+++++k+++le++++ee +        + +++++p+lk++++i++++mS
  gi|15669542|ref|NP_248353.1| 105 EHPIYFDKIVLDACQV-TNPSIDPLREPMELRTYIGKKPKQLEFEFVEEEIdgkkikkaKLKTKIAPNLKLDTPIMIAHMS 184
                                   67899***********.*******************************999999*999877899***************** PP

                                   TTTS-HHHHHHHHHHHHHHT-B-EETTS---GGGGS-----SEEEE-TT-TT--HHHHHH-SEEEEE---TTSTTS--EE- CS
                  Glu_synthase  75 yGalseeahealakamnrlgtksntGEGGedeerlktakdvaikQvasgrFGvteeyLnnakaleikiaQGakpgeGgqlp 155
                                   yGals +ah ++aka++++gt++ tGEGG++++ + +a+++ i+QvasgrFGv+eeyL++++a+eiki+QGakpg+Gg+lp
  gi|15669542|ref|NP_248353.1| 185 YGALSLNAHLSFAKAVKECGTFMGTGEGGLPKALYPYADHI-ITQVASGRFGVNEEYLMKGSAIEIKIGQGAKPGIGGHLP 264
                                   *****************************************.*************************************** PP

                                   GGG--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-.TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEEE- CS
                  Glu_synthase 156 geKvseeiakiRkikpgvdliSPaphhdiysiedlaqliedLkevn.keakvsvKlvaeagvetiaagvakanadiilidG 235
                                   geKv++ei+++R+i++g+d+iSPaphhdiysiedlaql+++Lke++ ++++v+vK++a +++ +ia+g+a+++ad+++idG
  gi|15669542|ref|NP_248353.1| 265 GEKVTAEISATRMIPEGSDAISPAPHHDIYSIEDLAQLVRSLKEATrWKKPVFVKIAAVHNAPAIAVGIATSDADAVVIDG 345
                                   ********************************************************************************* PP

                                   TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHHHHTT--S-- CS
                  Glu_synthase 236 leGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaalialgCimar 316
                                   ++GGTGA+pk++++h+G+P+e+a+a+vdq+l+eeglr+++s+ia+Gg++++adv+ka+alGAdav+igtaa++algC+++ 
  gi|15669542|ref|NP_248353.1| 346 YKGGTGAAPKVFRDHVGIPIEMAIAAVDQRLREEGLRNEISIIASGGIRCSADVFKAIALGADAVYIGTAAMVALGCRVCG 426
                                   ********************************************************************************* PP

                                   -GGGT--TTSSS---HHHH..TT----HHHHHHHHHHHHHHHHHHHHHHT-S CS
                  Glu_synthase 317 vChtntCpvGvatqdpeLrkrlkveekaervvnyikalaeevrellaalgin 368
                                   +C+t+ C++G+atq+peL krl+ e  a+rv+n+ika+++e++ell+a+gin
  gi|15669542|ref|NP_248353.1| 427 RCYTGLCAWGIATQRPELVKRLDPEVGARRVANLIKAWTHEIKELLGAAGIN 478
                                   **************************************************86 PP

>> Glu_syn_central  Glutamate synthase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.3e-07   0.00024      56      87 ..     118     149 ..     103     229 .. 0.81
   2 !   32.3   0.0   6.7e-11   7.1e-08     162     270 ..     356     486 ..     317     496 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.3e-07
                                   --SSS----TTTTGGG-B--EEES----SSS..- CS
               Glu_syn_central  56 AqVTNPpiDpiREelvmsletllGkegnlle..e 87 
                                    qVTNP+iDp+RE   m l+t++Gk+++ le   
  gi|15669542|ref|NP_248353.1| 118 CQVTNPSIDPLREP--MELRTYIGKKPKQLEfeF 149
                                   6************6..89********99988541 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 6.7e-11
                                   -STTEEE--HHHHHHHHHHHHHHTT-GGG-EEEEEESS--SHHHHHHHHHTT-SEEEEHHHHHHH................ CS
               Glu_syn_central 162 vseervpipslLavgavhhhLvrkglrtkvslvvesgearevhhfavllgyGadavnPylaleti................ 226
                                   v +++v ip  +a++av+++L ++glr+++s++  sg +r   ++   +++Gadav+   a  ++                
  gi|15669542|ref|NP_248353.1| 356 VFRDHVGIPIEMAIAAVDQRLREEGLRNEISIIA-SGGIRCSADVFKAIALGADAVYIGTAAMVAlgcrvcgrcytglcaw 435
                                   66799**************************975.7889*****************9888877774554544444333333 PP

                                   HHHHTTTS-..............----HH....HHHHHHHHHHHHHHHHHTT--BHHHHHHS CS
               Glu_syn_central 227 eklveegal..............aeeele....knyrkavekGllKimskmGistlqSYkga 270
                                           +                        +n++ka ++ +   +   Gi  ++S +g 
  gi|15669542|ref|NP_248353.1| 436 G-------IatqrpelvkrldpeV----GarrvANLIKAWTHEIKELLGAAGINSIESLRGN 486
                                   0.......0333333344444322....13346*************************9996 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.02        21      43      93 ..     159     209 ..     156     213 .. 0.83
   2 !   37.2   2.2   1.6e-12   1.7e-09     266     309 ..     379     422 ..     300     424 .. 0.80
   3 !    6.9   0.0    0.0027       2.8     311     342 ..     453     484 ..     451     490 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.02
                                   -SS-B--EEET.TEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEE CS
                        FMN_dh  43 vskvdlsttll.GqklslPvliaPvglaklahpdgelalaraaakagipfvl 93 
                                   ++k++l+t++    kl++P++ia +++  l   ++ l  a+a +++g+ ++ 
  gi|15669542|ref|NP_248353.1| 159 IKKAKLKTKIApNLKLDTPIMIAHMSYGALSL-NAHLSFAKAVKECGTFMGT 209
                                   6667777777645689***********99986.99************99976 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 1.6e-12
                                   HHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHH CS
                        FMN_dh 266 eavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaa 309
                                   e ++++i ++++gGir  +Dv+kA+alGAdav +G +++++l +
  gi|15669542|ref|NP_248353.1| 379 EGLRNEISIIASGGIRCSADVFKAIALGADAVYIGTAAMVALGC 422
                                   345779**********************************9975 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0027
                                   HHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHH CS
                        FMN_dh 311 GeeGvervleilraelertmallGvksvaeld 342
                                   G+++v+++++ +++e+++ +  +G++s+++l+
  gi|15669542|ref|NP_248353.1| 453 GARRVANLIKAWTHEIKELLGAAGINSIESLR 484
                                   899*************************9996 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.024        25      19      43 ..     160     184 ..     150     193 .. 0.91
   2 !   30.9   2.8   1.3e-10   1.3e-07     187     237 ..     360     414 ..     297     420 .. 0.79
   3 ?   -0.5   0.0      0.46   4.8e+02     298     328 ..     456     486 ..     449     497 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.024
                                   GGSB--EESSTTEEESSSEEE-SST CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH  19 kevdlktkltkkiklniPlvsaamd 43 
                                   k+++lktk++ ++kl +P++ a+m 
  gi|15669542|ref|NP_248353.1| 160 KKAKLKTKIAPNLKLDTPIMIAHMS 184
                                   6899******************996 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 1.3e-10
                                   SB---HHHHHHHHHHHHCTCT....-EEEEES---SHHHHHHHHHTT-SEEEESC CS
                                   xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 187 gvGvpqltAvaevaeaakkag....vpviaDGGikysgdivkAlaaGadavmlGs 237
                                    vG+p   A+a+v +  ++ g    + +ia GGi+ s d+ kA+a+Gadav +G 
  gi|15669542|ref|NP_248353.1| 360 HVGIPIEMAIAAVDQRLREEGlrneISIIASGGIRCSADVFKAIALGADAVYIGT 414
                                   59*************9999877777****************************97 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.46
                                   -HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 298 svkevveqlvgglrsgmgylGaktieelkek 328
                                   +v+++++  ++++++ +g +G ++ie+l+ +
  gi|15669542|ref|NP_248353.1| 456 RVANLIKAWTHEIKELLGAAGINSIESLRGN 486
                                   588999999******************9975 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.3   1.3e-05     0.014      28      52 .]       9      33 ..       3      33 .. 0.88
   2 !   20.0   0.5   7.2e-07   0.00076       1      22 [.      47      68 ..      47     131 .. 0.83
   3 ?    4.0   0.3     0.071        75      37      51 ..     421     436 ..     395     462 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                        Fer4_7 28 tekveidpekClgCgaCvavCPtga 52
                                  + kve+dp++C+ C++C  +C +g+
  gi|15669542|ref|NP_248353.1|  9 KYKVEVDPNRCMLCERCTIECSWGV 33
                                  56899*****************996 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 7.2e-07
                        Fer4_7  1 rCigCgaCvaaCpvkaieldee 22
                                  rC  C++Cv++Cp +ai+++e 
  gi|15669542|ref|NP_248353.1| 47 RCGACHRCVVMCPRDAITIKEN 68
                                  7*****************9874 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.071
                        Fer4_7  37 kClgCgaCva.vCPtg 51 
                                    C  Cg+C +  C +g
  gi|15669542|ref|NP_248353.1| 421 GCRVCGRCYTgLCAWG 436
                                   5555555554334433 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   2.8   2.6e-10   2.8e-07     139     231 ..     316     422 ..     293     426 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.6e-10
                           NMO 139 liptissvkearkvearG.....aDalivqGpeaG.GhqGtpevgdkglfaLvpqvldavd...........iPviAaGGi 202
                                   + + i++v++a ++ a G     aDa++++G+++G G    p+v        ++ +  avd           i +iA GGi
  gi|15669542|ref|NP_248353.1| 316 VFVKIAAVHNAPAI-AVGiatsdADAVVIDGYKGGtGAA--PKVFRDHVGIPIEMAIAAVDqrlreeglrneISIIASGGI 393
                                   45567777776544.44556677*********9883344..4555444444566677778889999999************ PP

                           NMO 203 idrrgvaaaLalGAsgvqigtrfLltkes 231
                                       +v  a+alGA +v+igt+ +++  +
  gi|15669542|ref|NP_248353.1| 394 RCSADVFKAIALGADAVYIGTAAMVALGC 422
                                   **********************9987655 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.33   3.5e+02     158     185 ..     157     184 ..     128     201 .. 0.78
   2 !   21.1   2.9   1.4e-07   0.00015     162     277 ..     313     417 ..     287     434 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.33
                                   HHHHSSEEEEEE-SSSSHHHHHHHHHHH CS
                        DHO_dh 158 kevskvpvlvKlaPdltdeekkdiadvl 185
                                   k+++k  +  K+aP+l+  + + ia + 
  gi|15669542|ref|NP_248353.1| 157 KKIKKAKLKTKIAPNLKLDTPIMIAHMS 184
                                   456689999*******999988888765 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.4e-07
                                   SSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHH.HH.HH CS
                        DHO_dh 162 kvpvlvKlaPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdialkvire.ly.kr 240
                                   k+pv+vK+a      +  +ia+ ++    d+++     + + +  + + ++v + + G     ++  +a++ + + l+ + 
  gi|15669542|ref|NP_248353.1| 313 KKPVFVKIAA---VHNAPAIAVGIATSDADAVV-----IDGYKGGTGAAPKVFRDHVG----IPIE-MAIAAVDQrLReEG 380
                                   6666666665...33344555555555555555.....22222223333444433444....4553.45555533144145 PP

                                   TTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHH CS
                        DHO_dh 241 lkkeipiIgvGGiesgeDalekieaGAslvqvytalv 277
                                   l++ei iI++GGi  + D++  i  GA +v ++ta +
  gi|15669542|ref|NP_248353.1| 381 LRNEISIIASGGIRCSADVFKAIALGADAVYIGTAAM 417
                                   899*******************************865 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.0   3.4e-05     0.036       1      19 [.      12      30 ..      12      35 .. 0.87
   2 !   20.3   1.9   3.3e-07   0.00035       6      24 .]      46      64 ..      42      64 .. 0.93
   3 ?   -1.4   3.5       2.4   2.5e+03       8      15 ..     422     429 ..     421     430 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                                  EEEETTTSSS-THHHHHST CS
                          Fer4  1 vvideekCigCGaCvevCP 19
                                  v++d+++C+ C +C   C 
  gi|15669542|ref|NP_248353.1| 12 VEVDPNRCMLCERCTIECS 30
                                  689***************5 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 3.3e-07
                                  TTSSS-THHHHHSTTTEEE CS
                          Fer4  6 ekCigCGaCvevCPvgAIt 24
                                  ++C +C +Cv +CP +AIt
  gi|15669542|ref|NP_248353.1| 46 NRCGACHRCVVMCPRDAIT 64
                                  79****************7 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.4
                                   SSS-THHH CS
                          Fer4   8 CigCGaCv 15 
                                   C  CG+C+
  gi|15669542|ref|NP_248353.1| 422 CRVCGRCY 429
                                   888****7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7  13.2   2.4e-05     0.025       1      56 []      11      59 ..      11      59 .. 0.80
   2 !   12.4   3.0   0.00013      0.13       4      24 ..      43      65 ..      40      94 .. 0.74
   3 ?    4.1   0.1     0.048        50       8      19 ..     421     433 ..     415     468 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                       Fer4_10  1 kvvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  kv++d+++C+ C++C+  C +      + + ++++  ++  + +C +c  Cv  CP
  gi|15669542|ref|NP_248353.1| 11 KVEVDPNRCMLCERCTIECSW------GVYRREGDRIISY-SNRCGACHRCVVMCP 59
                                  5789***************77......4444445555544.899***********9 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00013
                       Fer4_10  4 idddtCirCgkCvkaCPadl..t 24
                                    +++C  C +Cv +CP d+   
  gi|15669542|ref|NP_248353.1| 43 SYSNRCGACHRCVVMCPRDAitI 65
                                  55789************966431 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.048
                       Fer4_10   8 tCirCgkCvka.C 19 
                                    C  Cg+C +  C
  gi|15669542|ref|NP_248353.1| 421 GCRVCGRCYTGlC 433
                                   5999999999668 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   8.3   3.4e-07   0.00036       3      58 ..      14      64 ..      12      65 .. 0.82
   2 ?    0.0   1.2      0.92   9.7e+02      37      47 ..     418     428 ..     392     434 .. 0.48

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.4e-07
                       Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                  +d+++C+ C++C+i C+       + +++++    +++C +C+ C+ +CP  d+i+
  gi|15669542|ref|NP_248353.1| 14 VDPNRCMLCERCTIECSW---GVYRREGDRI-ISYSNRCGACHRCVVMCP-RDAIT 64
                                  89**************94...4445555555.566899************.79998 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.92
                       Fer4_21  37 vedeCvGCnlC 47 
                                   v+  C  C  C
  gi|15669542|ref|NP_248353.1| 418 VALGCRVCGRC 428
                                   33444444444 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   1.6     4e-07   0.00042       1      23 [.      11      33 ..      11      34 .. 0.92
   2 ?    6.2   2.9     0.011        11       7      24 .]      46      63 ..      45      70 .. 0.89
   3 ?    1.1   3.7      0.47   4.9e+02       9      17 ..     422     430 ..     422     437 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4e-07
                        Fer4_6  1 vveidpdkCigCgdCvrvCPega 23
                                  +ve+dp++C  C++C++ C  g+
  gi|15669542|ref|NP_248353.1| 11 KVEVDPNRCMLCERCTIECSWGV 33
                                  79*****************9876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.011
                        Fer4_6  7 dkCigCgdCvrvCPegai 24
                                  ++C  C +Cv+ CP +ai
  gi|15669542|ref|NP_248353.1| 46 NRCGACHRCVVMCPRDAI 63
                                  89999*********8876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.47
                        Fer4_6   9 CigCgdCvr 17 
                                   C  Cg+C++
  gi|15669542|ref|NP_248353.1| 422 CRVCGRCYT 430
                                   889****98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  10.9   2.5e-06    0.0026       1      51 []      18      63 ..      18      63 .. 0.89
   2 ?    3.0   0.4      0.11   1.2e+02      35      44 ..     421     430 ..     393     448 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-06
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  +C+ C +C+  C  gv++++  + +   +     +C  C++Cv  Cp++ai
  gi|15669542|ref|NP_248353.1| 18 RCMLCERCTIECSWGVYRREGDRIISYSN-----RCGACHRCVVMCPRDAI 63
                                  5***************9998888887764.....5*************997 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                        Fer4_9  35 aCigCgaCve 44 
                                    C  Cg+C+ 
  gi|15669542|ref|NP_248353.1| 421 GCRVCGRCYT 430
                                   5777777763 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.3     0.051        54      46      66 ..      11      31 ..       4      32 .. 0.74
   2 !   19.1   1.2   1.8e-06    0.0019       1      25 [.      47      72 ..      47      94 .. 0.78
   3 ?   -0.2   0.7       1.9     2e+03       2       9 ..     422     429 ..     415     446 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.051
                       Fer4_16 46 ekckkqeaitgCdiCqdvCPa 66
                                  + +   ++++ C +C+  C +
  gi|15669542|ref|NP_248353.1| 11 KVEVDPNRCMLCERCTIECSW 31
                                  555566889999999999988 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.8e-06
                       Fer4_16  1 rCgtCgkCaevCPtnaikek.kekei 25
                                  rCg C++C+ +CP +ai+ k ++ ++
  gi|15669542|ref|NP_248353.1| 47 RCGACHRCVVMCPRDAITIKeNAISW 72
                                  6****************987234444 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.9
                       Fer4_16   2 CgtCgkCa 9  
                                   C  Cg+C 
  gi|15669542|ref|NP_248353.1| 422 CRVCGRCY 429
                                   77777775 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   6.6e-06    0.0069     191     222 ..     384     415 ..     371     421 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.6e-06
                                   SSEEEEESS--SHHHHHHHHHTTCSEEEESHH CS
                  His_biosynth 191 kipviasGGvgsledlkelksegvdavivgsa 222
                                   +i++iasGG++  +d+ ++ + g+dav +g+a
  gi|15669542|ref|NP_248353.1| 384 EISIIASGGIRCSADVFKAIALGADAVYIGTA 415
                                   45555555555555555555555555555554 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.3     8e-05     0.085       2      20 ..      11      29 ..      10      31 .. 0.89
   2 ?    8.8   3.0    0.0018       1.9       7      21 ..      45      59 ..      40      60 .. 0.90
   3 ?    1.2   2.6      0.47   4.9e+02      10      19 ..     422     431 ..     416     435 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8e-05
                        Fer4_2  2 pvvvdtdrCigCgaCvsaC 20
                                  +v+vd++rC+ C+ C+  C
  gi|15669542|ref|NP_248353.1| 11 KVEVDPNRCMLCERCTIEC 29
                                  689************9888 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0018
                        Fer4_2  7 tdrCigCgaCvsaCP 21
                                  ++rC +C  Cv  CP
  gi|15669542|ref|NP_248353.1| 45 SNRCGACHRCVVMCP 59
                                  589*******999*9 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.47
                        Fer4_2  10 CigCgaCvsa 19 
                                   C  Cg C++ 
  gi|15669542|ref|NP_248353.1| 422 CRVCGRCYTG 431
                                   5556666553 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   3.5     0.043        46      49      62 ..      17      30 ..      10      33 .. 0.80
   2 ?    5.8   2.7     0.018        19       4      16 ..      18      30 ..      15      46 .. 0.59
   3 ?    7.8   3.4    0.0042       4.4      49      63 ..      46      60 ..      34      62 .. 0.71
   4 ?    9.4   3.0    0.0014       1.4       3      17 ..      46      64 ..      44     122 .. 0.68
   5 ?    2.2   0.1      0.24   2.6e+02       5      13 ..     422     430 ..     403     470 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.043
                        Fer4_8 49 wsCttcgaCtevCp 62
                                  ++C+ c++Ct +C 
  gi|15669542|ref|NP_248353.1| 17 NRCMLCERCTIECS 30
                                  68999999999996 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.018
                        Fer4_8  4 kCieCgaCqsaCp 16
                                  +C+ C++C+ +C 
  gi|15669542|ref|NP_248353.1| 18 RCMLCERCTIECS 30
                                  4555555555553 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0042
                        Fer4_8 49 wsCttcgaCtevCpv 63
                                  ++C +c++C++ Cp 
  gi|15669542|ref|NP_248353.1| 46 NRCGACHRCVVMCPR 60
                                  567777777777765 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0014
                        Fer4_8  3 ekCieCgaCqsaCp....v 17
                                  ++C+ C +C  +Cp    +
  gi|15669542|ref|NP_248353.1| 46 NRCGACHRCVVMCPrdaiT 64
                                  5788888888888866552 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.24
                        Fer4_8   5 CieCgaCqs 13 
                                   C  Cg+C +
  gi|15669542|ref|NP_248353.1| 422 CRVCGRCYT 430
                                   666666664 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   4.1      0.07        73      44      57 ..      17      30 ..       9      34 .. 0.84
   2 ?    8.3   1.9    0.0033       3.4      41      59 ..      43      61 ..      31      63 .. 0.78
   3 ?    6.4   3.0     0.012        13       1      21 [.      47      67 ..      47      95 .. 0.70
   4 ?    2.7   0.0      0.18   1.9e+02      45      53 ..     421     429 ..     398     469 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.07
                       Fer4_17 44 slCieCgeCerkCP 57
                                  ++C+ C++C+ +C 
  gi|15669542|ref|NP_248353.1| 17 NRCMLCERCTIECS 30
                                  79********9997 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0033
                       Fer4_17 41 ekaslCieCgeCerkCPqg 59
                                  ++ ++C  C++C+  CP +
  gi|15669542|ref|NP_248353.1| 43 SYSNRCGACHRCVVMCPRD 61
                                  5678999999999999975 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.012
                       Fer4_17  1 rCiqCgyClpeCpsyeaydne 21
                                  rC  C  C+ +Cp+ +++ +e
  gi|15669542|ref|NP_248353.1| 47 RCGACHRCVVMCPRDAITIKE 67
                                  688888899999987665444 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.18
                       Fer4_17  45 lCieCgeCe 53 
                                    C  Cg+C 
  gi|15669542|ref|NP_248353.1| 421 GCRVCGRCY 429
                                   455555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 3286.77
//
Query:       gi|15669543|ref|NP_248355.1|  [L=259]
Description: NH(3)-dependent NAD+ synthetase NadE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.5e-105  350.1   0.1   5.2e-105  349.9   0.1    1.0  1  NAD_synthase     NAD synthase
    7.2e-13   48.0   0.0      5e-07   28.8   0.0    2.9  3  tRNA_Me_trans    tRNA methyl transferase
    0.00041   19.9   0.0     0.0016   18.0   0.0    1.8  2  QueC             Queuosine biosynthesis protein QueC
      0.004   16.8   0.3      0.014   15.0   0.0    1.9  2  ThiI             Thiamine biosynthesis protein (ThiI)
     0.0067   16.2   0.0      0.045   13.6   0.0    2.3  2  HTH_23           Homeodomain-like domain
     0.0071   16.0   0.0      0.013   15.2   0.0    1.3  1  Asn_synthase     Asparagine synthase
  ------ inclusion threshold ------
      0.011   16.2   0.6      0.041   14.3   0.0    2.2  2  HTH_40           Helix-turn-helix domain
      0.031   14.3   0.0       0.11   12.6   0.0    2.0  2  HTH_7            Helix-turn-helix domain of resolvase
      0.032   13.3   0.0      0.063   12.4   0.0    1.4  2  SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
       0.08   12.7   0.0       0.25   11.1   0.0    1.7  2  ATP_bind_3       PP-loop family
       0.11   12.4   0.0       0.48   10.3   0.0    2.1  2  DUF433           Protein of unknown function (DUF433)
       0.11   12.4   0.1       0.27   11.1   0.1    1.6  1  Cas_APE2256      CRISPR-associated protein (Cas_APE2256)
       0.12   12.4   0.0       0.44   10.6   0.0    1.9  3  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
       0.12   12.4   1.7        9.3    6.4   0.0    3.1  3  DUF3791          Protein of unknown function (DUF3791)
       0.14   10.9   0.1        0.2   10.4   0.1    1.3  1  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
       0.66   10.1   2.2         22    5.3   0.3    2.7  3  HTH_48           HTH domain in Mos1 transposase


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.9   0.1  4.6e-108  5.2e-105       1     242 []      10     254 ..      10     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: 349.9 bits;  conditional E-value: 4.6e-108
                                   HHHHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE--- CS
                  NAD_synthase   1 lieelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidi 81 
                                   +++++++f++e+v++a+a+gvv+GlSGG+DSs++a+l+vkalgk++vl+l++P+++++++dve+a+++aenlgi++   di
  gi|15669543|ref|NP_248355.1|  10 IVNKITKFIREKVEEANANGVVVGLSGGIDSSVTAYLCVKALGKDKVLGLIMPEKNTNPKDVEHAKMVAENLGIKYIISDI 90 
                                   5899***************************************************************************** PP

                                   HHHHHHHHH.HHHHHH..-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-HHHH CS
                  NAD_synthase  82 kpivrafeq.elkeak..edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaellKtev 159
                                   ++i++af +  + +++  +++a+gNlkaRiRm+ily++ank+nllv+gT+nksE++vGy+Tk+GD+a+d++pi++l+Ktev
  gi|15669543|ref|NP_248355.1|  91 TDILKAFGAgGYVPTRefDKIADGNLKARIRMCILYYFANKYNLLVAGTSNKSEIYVGYGTKHGDIACDIRPIGNLFKTEV 171
                                   *******998777776779************************************************************** PP

                                   HHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHTHSSSS...HHHHHTTT--HHHHHHHHHHHHHTGGGGS CS
                  NAD_synthase 160 keLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLklvekkkspeeiikekelpaevvekieklvkksehKrk 240
                                   k+Lak+++vP+++++kpPsA+L++gqtDeeeL+ikY++lD+iLkl+ek+k+peei+ke+++p e+++++++l+kk+ehKr+
  gi|15669543|ref|NP_248355.1| 172 KKLAKYIGVPKEIIEKPPSAGLWEGQTDEEELDIKYETLDTILKLYEKGKTPEEIHKETNIPLETINYVFDLIKKNEHKRT 252
                                   ********************************************************************************9 PP

                                   SS CS
                  NAD_synthase 241 lp 242
                                   lp
  gi|15669543|ref|NP_248355.1| 253 LP 254
                                   98 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   4.4e-10     5e-07       3      72 ..      30      92 ..      28      97 .. 0.81
   2 !   15.4   0.0   5.6e-06    0.0063     133     195 ..     128     192 ..     100     194 .. 0.82
   3 ?   -0.3   0.0      0.32   3.6e+02      78      93 ..     209     224 ..     201     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 4.4e-10
                 tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfek 72
                                  vvv+lSgG+DSsv+a+l  ++    +v g+++  ++         +  +d+++a++vae+lgi++ + d+++
  gi|15669543|ref|NP_248355.1| 30 VVVGLSGGIDSSVTAYLCVKALgkDKVLGLIMPEKN---------TNPKDVEHAKMVAENLGIKYIISDITD 92
                                  9***************99887523567777775332.........4579****************9988776 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 5.6e-06
                 tRNA_Me_trans 133 eknevellrakdkkkDQsyfLsqlskealekllfPlgeltKeevrkiAkeagla..vaekkdSqg 195
                                    +n+++ll a  ++k   y+ + +++ +++  + P+g+l K+ev+k+Ak +g++  + ek+ S g
  gi|15669543|ref|NP_248355.1| 128 FANKYNLLVAGTSNKSEIYVGYGTKHGDIACDIRPIGNLFKTEVKKLAKYIGVPkeIIEKPPSAG 192
                                   468899999999****************************************9877889998887 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.32
                 tRNA_Me_trans  78 vfeefleeyeeGrTPn 93 
                                    ++ +l+ ye+G+TP 
  gi|15669543|ref|NP_248355.1| 209 TLDTILKLYEKGKTPE 224
                                   578899*********6 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.5e-06    0.0016       2      68 ..      30      98 ..      29     123 .. 0.78
   2 ?   -0.8   0.0      0.81   9.1e+02     156     178 ..     161     183 ..     144     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                                  EEEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-.GGGGGGS CS
                          QueC  2 avvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildl.dllkelg 68
                                  +vv lSGG+DS++ ++l  k+   ++v  l +  ++ + k++e ak +a++lg+ +  i d+ d+lk++g
  gi|15669543|ref|NP_248355.1| 30 VVVGLSGGIDSSVTAYLCVKALgkDKVLGLIMPEKNTNPKDVEHAKMVAENLGI-KYIISDItDILKAFG 98
                                  6899*********999999887335566666666666999**************.888877625677766 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.81
                                   -TTTT--HHHHHHHHHHTTHHHH CS
                          QueC 156 aPlidlsKaeivklgkelgvple 178
                                    P+ +l K+e+ kl+k +gvp e
  gi|15669543|ref|NP_248355.1| 161 RPIGNLFKTEVKKLAKYIGVPKE 183
                                   4999999*********9999865 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.2e-05     0.014       5      56 ..      29      81 ..      25      95 .. 0.77
   2 ?   -1.1   0.1         1   1.1e+03     141     161 ..     160     180 ..     156     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                          ThiI  5 kvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaell 56
                                   v++ lSgGiDS V+ayl +k  G   vl  +  e  t+++  e  +++ae l
  gi|15669543|ref|NP_248355.1| 29 GVVVGLSGGIDSSVTAYLCVKAlGKDKVLGLIMPEKNTNPKDVEHAKMVAENL 81
                                  578889************99963665555555567778888888888877765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                          ThiI 141 lrPLigldKeeiiklAkeigt 161
                                   +rP+  l K e+ klAk ig 
  gi|15669543|ref|NP_248355.1| 160 IRPIGNLFKTEVKKLAKYIGV 180
                                   6888889999*******9996 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.8     2e+03       2      16 ..     116     130 ..     115     134 .. 0.79
   2 !   13.6   0.0     4e-05     0.045      10      36 ..     213     239 ..     201     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.8
                        HTH_23   2 asereRlrillllae 16 
                                   +++r+R++il+ +a+
  gi|15669543|ref|NP_248355.1| 116 LKARIRMCILYYFAN 130
                                   5899*****987765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4e-05
                        HTH_23  10 illllaeGlsvreIAreLgvsrrTvyr 36 
                                   il+l+ +G++++eI +e +++  T+  
  gi|15669543|ref|NP_248355.1| 213 ILKLYEKGKTPEEIHKETNIPLETINY 239
                                   999*********************975 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.1e-05     0.013      22      73 ..      32      84 ..      17      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                  Asn_synthase 22 alLSGGlDSSliaalaarqsksplktFsigf..eekgsdeakyakevaehlgte 73
                                  + LSGG+DSS+ a+l  + +  + k   + +  ++   +++++ak vae lg++
  gi|15669543|ref|NP_248355.1| 32 VGLSGGIDSSVTAYLCVKALG-KDKVLGLIMpeKNTNPKDVEHAKMVAENLGIK 84
                                  569***************997.55665555554459999************998 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.9   4.4e+03      50      67 ..      83     100 ..      71     115 .. 0.50
   2 ?   14.3   0.0   3.6e-05     0.041       4      40 ..     212     247 ..     209     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.9
                        HTH_40  50 seeeekeIeeaiekvgse 67 
                                    + +++ I+++++++g  
  gi|15669543|ref|NP_248355.1|  83 IKYIISDITDILKAFGAG 100
                                   444444444444444433 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.6e-05
                        HTH_40   4 etlelleeglsieeIAkerglkesTIegHLaelieeg 40 
                                   + l+l+e+g+++eeI ke ++   TI +++ +li+++
  gi|15669543|ref|NP_248355.1| 212 TILKLYEKGKTPEEIHKETNIPLETI-NYVFDLIKKN 247
                                   6689*********************9.6888888775 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.7   9.7e+03      24      32 ..      90      98 ..      88      98 .. 0.83
   2 ?   12.6   0.0    0.0001      0.11       8      38 ..     207     237 ..     201     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.7
                                  STTTSSSS- CS
                         HTH_7 24 iskIAkevn 32
                                  i++I k+++
  gi|15669543|ref|NP_248355.1| 90 ITDILKAFG 98
                                  899999986 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0001
                                   HHHHGGGGSSTTTT--STTTSSSS---SSSS CS
                         HTH_7   8 kndinrvvkLleeGisiskIAkevnisRsTv 38 
                                    +++++++kL+e+G +  +I ke+ni  +T+
  gi|15669543|ref|NP_248355.1| 207 YETLDTILKLYEKGKTPEEIHKETNIPLETI 237
                                   45789*********************88886 PP

>> SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.6e-05     0.063      39      91 ..       3      55 ..       1      57 [. 0.93
   2 ?   -3.4   0.0       3.6     4e+03     203     221 ..     201     219 ..     173     229 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.6e-05
               SQHop_cyclase_N 39 lgeddeeeeekiakylrsqqredGgWelypggpgdlsttveaYlALkllGdsp 91
                                  +ge  ee  +ki+k++r++ +e  + +++ g +g +  +v aYl  k lG+++
  gi|15669543|ref|NP_248355.1|  3 WGESMEEIVNKITKFIREKVEEANANGVVVGLSGGIDSSVTAYLCVKALGKDK 55
                                  578889999*****************************************875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.6
               SQHop_cyclase_N 203 lswtklflaldkvlkller 221
                                    +++  +++ld++lkl+e+
  gi|15669543|ref|NP_248355.1| 201 EELDIKYETLDTILKLYEK 219
                                   3344447788888888885 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00022      0.25       2      67 ..      30      91 ..      29      99 .. 0.72
   2 ?   -2.6   0.0       3.6   4.1e+03     141     157 ..     160     176 ..     122     181 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                                  EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE-- CS
                    ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvd 67
                                  v+v++SgG+DS +  +l +k   k +  l +i+ +   +++  ++ e+ k ++++l+ik++i++++
  gi|15669543|ref|NP_248355.1| 30 VVVGLSGGIDSSVTAYLCVKALGKDK-VLGLIMPE---KNTNPKDVEHAKMVAENLGIKYIISDIT 91
                                  79**************9999977544.34444444...4445556667777777888888877765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.6
                                   E-CCCT--HHHHHHHHH CS
                    ATP_bind_3 141 vRPlLkvskeeleeylk 157
                                   +RP+ ++ k+e+++++k
  gi|15669543|ref|NP_248355.1| 160 IRPIGNLFKTEVKKLAK 176
                                   68888888888877766 PP

>> DUF433  Protein of unknown function (DUF433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.8   4.3e+03      31      49 ..       4      22 ..       4      26 .. 0.68
   2 ?   10.3   0.0   0.00043      0.48      21      49 ..     210     237 ..     209     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.8
                                  T--HHHHHHHH.TS-HHHH CS
                        DUF433 31 GesieeiledyPdLtledi 49
                                  Ges eei+ +     +e +
  gi|15669543|ref|NP_248355.1|  4 GESMEEIVNKITKFIREKV 22
                                  8899999887655555555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00043
                                   THHHHHHHHTT--HHHHHHHH.TS-HHHH CS
                        DUF433  21 VetilellaaGesieeiledyPdLtledi 49 
                                    +til l+++G+++eei ++  ++ le i
  gi|15669543|ref|NP_248355.1| 210 LDTILKLYEKGKTPEEIHKET-NIPLETI 237
                                   579***************997.7666665 PP

>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00024      0.27      71     120 ..       5      56 ..       2      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                   Cas_APE2256  71 eglrnLveklarevknkkregek..vlinaTgGfKpeiavltlvallladev 120
                                   e ++++v+k+++ +++k++e+++  v++ ++gG  + +++ + v  l++d+v
  gi|15669543|ref|NP_248355.1|   5 ESMEEIVNKITKFIREKVEEANAngVVVGLSGGIDSSVTAYLCVKALGKDKV 56 
                                   5799************988887777**********99999999988888887 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00039      0.44       2      55 ..      30      85 ..      29     103 .. 0.77
   2 ?   -2.8   0.0       5.1   5.7e+03     133     154 ..     160     181 ..     152     187 .. 0.83
   3 ?   -2.2   0.0       3.3   3.7e+03      60      93 ..     189     221 ..     169     234 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                                  EEEE--SSCTCHHHHHHHHHHCTTHE..EEEEE-STB-HHHHHHHHHHHHHTT-EE CS
                   PAPS_reduct  2 lvvsvsgGkdslVllhLalkafkpvp..vvfvdtghefpetiefvdeleeryglrl 55
                                  +vv  sgG+ds+V+  L++ka+ + +   + +  + + p+ +e  + ++e++g++ 
  gi|15669543|ref|NP_248355.1| 30 VVVGLSGGIDSSVTAYLCVKALGKDKvlGLIMPEKNTNPKDVEHAKMVAENLGIKY 85
                                  57889****************99965114455566667777788888888887774 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.1
                                   E-CCCT--HHHHHHHHHHCT-- CS
                   PAPS_reduct 133 vfPllnWteedvwqyilrenip 154
                                   + P+ n  +++v +++++ ++p
  gi|15669543|ref|NP_248355.1| 160 IRPIGNLFKTEVKKLAKYIGVP 181
                                   6799999999999999887776 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.3
                                   -SCHHHHHHHHHH-S-THHHCHHHHHHTHHHHHH CS
                   PAPS_reduct  60 peeevaekinaekhgsslyeeaaeriaKveplkk 93 
                                   p  + +e+ + e+    +ye+ +++i K+++  k
  gi|15669543|ref|NP_248355.1| 189 PSAGLWEGQTDEEELDIKYET-LDTILKLYEKGK 221
                                   455566777777777777777.777777766555 PP

>> DUF3791  Protein of unknown function (DUF3791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0083       9.3      44      60 .]       5      21 ..       1      21 [. 0.91
   2 ?    4.0   0.1     0.045        50      44      58 ..      81      95 ..      77      96 .. 0.89
   3 ?   -2.5   0.1         5   5.6e+03       7      16 ..     125     134 ..     122     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0083
                       DUF3791 44 qSkeyivedideylknk 60
                                  +S e+iv+ i++++++k
  gi|15669543|ref|NP_248355.1|  5 ESMEEIVNKITKFIREK 21
                                  799************97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.045
                       DUF3791 44 qSkeyivedideylk 58
                                  ++++yi+ di+++lk
  gi|15669543|ref|NP_248355.1| 81 LGIKYIISDITDILK 95
                                  6899*********97 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5
                       DUF3791   7 Ieeyarklgl 16 
                                   + ++a+k++l
  gi|15669543|ref|NP_248355.1| 125 LYYFANKYNL 134
                                   4568888886 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00018       0.2      89     175 ..       3      85 ..       1     145 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                                   TTTTHHHHHHHHHHHHTSSEEEEEE--TTSSSHHHHHHHHHHHHHHHCTT-TT---SSEEEEEEETTCGHGHHHHHHHHHH CS
                Oxidored_nitro  89 iGdDieavareaeeelgeipvipvstpgfggsqseGydaalealvrklvgkkgekeprkvnilgeynlgpgdlrelkelle 169
                                    G+ +e +++++++   e +v  ++++g ++  s G+d+ ++a++  +v+ + +k++    i++e n++p d+++ k + e
  gi|15669543|ref|NP_248355.1|   3 WGESMEEIVNKITKFIRE-KVEEANANGVVVGLSGGIDSSVTAYL--CVK-ALGKDKVLGLIMPEKNTNPKDVEHAKMVAE 79 
                                   588889999999999888.9***********************98..444.666777788899****************** PP

                                   HHTEEE CS
                Oxidored_nitro 170 klGlev 175
                                    lG+++
  gi|15669543|ref|NP_248355.1|  80 NLGIKY 85 
                                   ****44 PP

>> HTH_48  HTH domain in Mos1 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       7.7   8.6e+03      15      31 ..       4      20 ..       4      23 .. 0.73
   2 ?    5.3   0.3      0.02        22       3      15 ..     119     131 ..     117     135 .. 0.83
   3 ?    3.7   0.0     0.059        66       8      24 ..     213     229 ..     211     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.7
                        HTH_48 15 gksaaeahrkickvyge 31
                                  g+s +e+  ki k + e
  gi|15669543|ref|NP_248355.1|  4 GESMEEIVNKITKFIRE 20
                                  56778888888887766 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.02
                        HTH_48   3 hlRhciLyefkkg 15 
                                    +R ciLy+f  +
  gi|15669543|ref|NP_248355.1| 119 RIRMCILYYFANK 131
                                   69********766 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.059
                        HTH_48   8 iLyefkkgksaaeahrk 24 
                                   iL  + kgk+ +e+h++
  gi|15669543|ref|NP_248355.1| 213 ILKLYEKGKTPEEIHKE 229
                                   7889***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      715  (0.0398795); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1641.04
//
Query:       gi|15669544|ref|NP_248357.1|  [L=145]
Description: hypothetical protein MJ_1354 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1204  (0.0671538); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1018.73
//
Query:       gi|15669545|ref|NP_248358.1|  [L=571]
Description: hypothetical protein MJ_1355 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.7e-160  535.4  33.6    4.4e-81  273.1  14.1    2.0  2  DUF505       Protein of unknown function (DUF505)
     0.0015   18.3   0.4        0.3   10.9   0.0    4.3  4  HxlR         HxlR-like helix-turn-helix
  ------ inclusion threshold ------
       0.02   15.1   1.6       0.42   10.9   0.1    3.4  3  Rio2_N       Rio2, N-terminal
      0.023   13.9   1.6       0.95    8.7   0.3    3.1  3  MKT1_C       Temperature dependent protein affecting M2 dsRNA
      0.038   14.5   7.6       0.64   10.6   0.4    4.4  4  AAA_assoc_C  C-terminal AAA-associated domain
        6.3    7.5   7.5        1.1    9.9   0.1    3.2  3  DUF573       Protein of unknown function, DUF573


Domain annotation for each model (and alignments):
>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.1  14.1   1.5e-84   4.4e-81       1     315 [.       1     300 [.       1     305 [. 0.98
   2 !  268.8  11.5     3e-83     9e-80     365     620 .]     306     566 ..     301     566 .. 0.97

  Alignments for each domain:
  == domain 1  score: 273.1 bits;  conditional E-value: 1.5e-84
                        DUF505   1 MlikkehaeiLeklkeeeekkeeeeieveeleeeeilleLelagLvrleepekielTyaGkklaelldeliekgklekpee 81 
                                   M++kk+h+eiL+k+ke+e+++e+e++ +ee++++  +leL ++g+++  +++ki +T+aGkkl+e++d++       ++e+
  gi|15669545|ref|NP_248358.1|   1 MFLKKRHLEILKKMKETEMQNEIEKALPEEFKTR--ALELFILGFAE-LKGDKIIFTEAGKKLMEIVDKI-------DLEK 71 
                                   9******************************888..***********.9*********************.......99** PP

                        DUF505  82 wkedfrwvgSeiiamleaaekaggkvgeeaeeaLeeRglaeeveaLteaakalleiYreaepkleitaelaevirklPkGp 162
                                   +++   +v+Seii+++e++e++g +v+e+++ +L+eR+la+e++ Lte++k++l+iYre++p +++t+el ++i+++Pk +
  gi|15669545|ref|NP_248358.1|  72 IPD--IFVDSEIIKIMELLEETG-NVPEDWMLMLKERFLADENG-LTEIGKEILKIYRETHPVVYLTPELLAFIKDMPK-I 147
                                   ***..9****************9.********************.*********************************9.8 PP

                        DUF505 163 ae.......kstlpigeneielLeAmRLlaysvpt..gdvyaltalgqavkkalrkggva.eelvlsedilealakvvdge 233
                                   +        k+t+++g+n+i++L+AmRLl++s++t  g+++++t++ ++v k+ + +++  ++l+l+++++e l++     
  gi|15669545|ref|NP_248358.1| 148 GVydelityKNTKEYGDNIINALQAMRLLLISPKTesGKAFSTTKALNYVLKVASLVPNLsRALILRKEDFEILER----- 223
                                   88889**99*************************999**********************99*************87..... PP

                        DUF505 234 eleeeekeaLealgyvddegeltpaGeklleaykllkekeeekvlsialeeeevevLkaIdelwkkaeenpevlPtlkeik 314
                                       e++e++++ g+++ eg++t+ G++++++yk++++ +eek+l+i++ e+e++vLkaI+e+++k+e+npe++Pt++eik
  gi|15669545|ref|NP_248358.1| 224 ---GETTEEMTESGFYA-EGKVTELGQAMMDTYKEMGK-VEEKTLPIYVLEDEIKVLKAIEEIKEKYETNPEIIPTYDEIK 299
                                   ...899**********9.********************.*****************************************8 PP

                        DUF505 315 r 315
                                   +
  gi|15669545|ref|NP_248358.1| 300 K 300
                                   7 PP

  == domain 2  score: 268.8 bits;  conditional E-value: 3e-83
                        DUF505 365 dlreaLysLesfeLieseveekgkevyvlTeyGekvledqekklrevsaeavkaititekefsaPnaeWveeAkeeglvgt 445
                                   dl++ L++Les+eLi++ev  k+k++y++Te+Gekv +     l evs++++kait+ e++ ++P+aeWv ++keeg+v++
  gi|15669545|ref|NP_248358.1| 306 DLGAVLHTLESKELIKREV-VKNKDTYWMTEFGEKVKD-----LGEVSTDGMKAITYPESG-DVPIAEWVIKGKEEGTVKR 379
                                   7999**************8.59**************99.....89***************9.9****************** PP

                        DUF505 446 geptekGrlyaelaeeierlPfltryelkvlkkiP.krgvsveelveev...deleeeevrealeklearglvevlpdgnv 522
                                   g +tekG+++++l+++i+r+P+lt+y++++l kiP kr+++++elv+ +   ++++e+e++++l ++e++g++++l+++++
  gi|15669545|ref|NP_248358.1| 380 G-ITEKGKYLIKLSKTIKRKPYLTKYDISTLIKIPrKRYIHRDELVKLIqghVGGDEKEIIKSLGEAESKGFIKELQNKMI 459
                                   *.***********************************************99999*************************** PP

                        DUF505 523 vlTeaGelikrAlsgvpe....glgnpvtPlvirvlkalrevgslyvkekkvrilpknlkeai.....kasgLtketfkka 594
                                   +lTe+Ge++k+A+++++     +++++vtP+++++lk++++++++++k +k++++ k++ke +     k+++Lt+e++kk+
  gi|15669545|ref|NP_248358.1| 460 KLTELGEEVKTAIEMAKIqellATKFAVTPTTFNILKTIYDHKEEFDKVWKEKSEGKEHKENEivllaKYLSLTPEEIKKN 540
                                   ****************9989999************************************776669**************** PP

                        DUF505 595 lelaReakflgknsiteaGlkLLeAv 620
                                   l+++++++f+gk+ +t+aG+kL+eA+
  gi|15669545|ref|NP_248358.1| 541 LVILKNVGFIGKKGLTDAGVKLVEAY 566
                                   *************************7 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.18   5.4e+02      65      79 ..      53      67 ..      49      71 .. 0.89
   2 ?   -0.7   0.0      0.44   1.3e+03      59      85 ..     235     261 ..     204     265 .. 0.77
   3 !   10.9   0.0    0.0001       0.3      36      74 ..     307     342 ..     289     352 .. 0.87
   4 ?   -0.8   0.0      0.45   1.4e+03      64      77 ..     460     473 ..     439     482 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.18
                                  E-TCGGGGHHHHHHH CS
                          HxlR 65 ltekGrslepvlqel 79
                                  +te+G++l+++++++
  gi|15669545|ref|NP_248358.1| 53 FTEAGKKLMEIVDKI 67
                                  79*********9986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.44
                                   -EEEEEE-TCGGGGHHHHHHHHHHHHH CS
                          HxlR  59 pkveYsltekGrslepvlqelkkwgee 85 
                                      e ++te G+++++  +e+ k  e+
  gi|15669545|ref|NP_248358.1| 235 FYAEGKVTELGQAMMDTYKEMGKVEEK 261
                                   455668999999999999999887665 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHH CS
                          HxlR  36 LaqrLreLeqdglierevypevPpkveYsltekGrslep 74 
                                   L + L+ Le+++li+rev+++  +   Y +te+G+++++
  gi|15669545|ref|NP_248358.1| 307 LGAVLHTLESKELIKREVVKNKDT---YWMTEFGEKVKD 342
                                   567799************998776...********9986 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.45
                                   EE-TCGGGGHHHHH CS
                          HxlR  64 sltekGrslepvlq 77 
                                   +lte G++++ +++
  gi|15669545|ref|NP_248358.1| 460 KLTELGEEVKTAIE 473
                                   68999999998875 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.7   4.9e+03       4      18 ..     213     227 ..     212     246 .. 0.80
   2 ?   10.9   0.1   0.00014      0.42       6      60 ..     269     326 ..     265     337 .. 0.72
   3 ?    0.9   0.0      0.18   5.3e+02      29      66 ..     525     562 ..     514     567 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                        Rio2_N   4 LskedfrvLtavEmg 18 
                                   L kedf +L+  E++
  gi|15669545|ref|NP_248358.1| 213 LRKEDFEILERGETT 227
                                   7899****9876664 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00014
                        Rio2_N   6 kedfrvLtavEmgmrnhe....vVpt.elieeisrlkeeevkkrlsrllkaklisrktak 60 
                                   +++ +vL+a+E    ++e    ++pt ++i+++++++  ++  +l++l  ++li+r+ +k
  gi|15669545|ref|NP_248358.1| 269 EDEIKVLKAIEEIKEKYEtnpeIIPTyDEIKKRTNID--DLGAVLHTLESKELIKREVVK 326
                                   7899*******99998871222555446888888887..788899999999999995433 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.18
                        Rio2_N  29 lieeisrlkeeevkkrlsrllkaklisrktakydGYkL 66 
                                   l++++ +l+ ee+kk l  l + ++i +k  +  G kL
  gi|15669545|ref|NP_248358.1| 525 LLAKYLSLTPEEIKKNLVILKNVGFIGKKGLTDAGVKL 562
                                   778888999******************99988888887 PP

>> MKT1_C  Temperature dependent protein affecting M2 dsRNA replication
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.86   2.6e+03      57      57 ..     159     159 ..     105     208 .. 0.47
   2 ?    2.6   0.0     0.022        66       8      42 ..     235     268 ..     230     304 .. 0.75
   3 ?    8.7   0.3   0.00032      0.95      30      89 ..     455     539 ..     438     541 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.86
                        MKT1_C  57 e 57 
                                   +
  gi|15669545|ref|NP_248358.1| 159 T 159
                                   1 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.022
                        MKT1_C   8 yvdekheltkwGkaLakalkelkeleealllaleL 42 
                                   +  e  ++t++G+a+++++ke+ + ee++l + +L
  gi|15669545|ref|NP_248358.1| 235 FYAE-GKVTELGQAMMDTYKEMGKVEEKTLPIYVL 268
                                   5555.89****************888888866665 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00032
                        MKT1_C  30 k.......eleealllaleLlrlgvLtgdenekpeys..................gapslgseeekksilLisRvasLlpl 85 
                                   +       el e++  a+e+ +++ L ++++  +++                   +++s+g+e ++++i L+ + +sL p 
  gi|15669545|ref|NP_248358.1| 455 QnkmikltELGEEVKTAIEMAKIQELLATKFAVTPTTfnilktiydhkeefdkvwKEKSEGKEHKENEIVLLAKYLSLTPE 535
                                   223333435567777777777777777776666666677777777777777799988999*******************98 PP

                        MKT1_C  86 rlkp 89 
                                   ++k+
  gi|15669545|ref|NP_248358.1| 536 EIKK 539
                                   8776 PP

>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.6   1.8e+03      79     107 ..      12      40 ..       6      40 .. 0.83
   2 ?   10.6   0.4   0.00022      0.64      23      45 ..      40      62 ..      16      90 .. 0.89
   3 ?   -1.2   0.0      0.93   2.8e+03      10      42 ..     303     339 ..     299     369 .. 0.70
   4 ?    4.3   0.9     0.018        55      18      72 ..     442     498 ..     427     548 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.6
                   AAA_assoc_C  79 krlpeerfldeLeeklseeeaertletai 107
                                   k+++e ++++e+e+ l+ee   r+le +i
  gi|15669545|ref|NP_248358.1|  12 KKMKETEMQNEIEKALPEEFKTRALELFI 40 
                                   67889999999999999998888888765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00022
                   AAA_assoc_C 23 lLglveveegdielTelGrkfve 45
                                  +Lg++e+++++i++Te+G+k++e
  gi|15669545|ref|NP_248358.1| 40 ILGFAELKGDKIIFTEAGKKLME 62
                                  7******************9986 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.93
                   AAA_assoc_C  10 evddLlpiveaaelLglve...v.eegdielTelGrk 42 
                                   ++ddL  +++++e+ +l++   v +++   +Te G+k
  gi|15669545|ref|NP_248358.1| 303 NIDDLGAVLHTLESKELIKrevVkNKDTYWMTEFGEK 339
                                   6777777777777777775222212334456666665 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.018
                   AAA_assoc_C  18 veaaelLglv.eveegdielTelGrkfvea.dikerKeifreqllklvplaaairrv 72 
                                   +  ae+ g++ e+++  i+lTelG+++ +a ++ + +e+++++       +++++++
  gi|15669545|ref|NP_248358.1| 442 LGEAESKGFIkELQNKMIKLTELGEEVKTAiEMAKIQELLATKFAVTPTTFNILKTI 498
                                   555666677634688889999999998665366777888887766555555555554 PP

>> DUF573  Protein of unknown function, DUF573
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.1   6.1e+03      59      75 ..       3      19 ..       2      31 .. 0.66
   2 ?    9.9   0.1   0.00038       1.1       5      45 ..     266     304 ..     264     343 .. 0.83
   3 ?    0.1   0.6      0.42   1.3e+03      30      76 ..     472     518 ..     415     530 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.1
                        DUF573 59 Lkkkyrnavskikkgkd 75
                                  Lkk++ ++++k+k+++ 
  gi|15669545|ref|NP_248358.1|  3 LKKRHLEILKKMKETEM 19
                                  78888888888764332 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00038
                        DUF573   5 WseeDEielLqglldfksktgtspksdldafyeavksslss 45 
                                   +  eDEi++L+++ + k+k +t+  +++   y+++k++++ 
  gi|15669545|ref|NP_248358.1| 266 YVLEDEIKVLKAIEEIKEKYETN--PEIIPTYDEIKKRTNI 304
                                   5679*************999998..7999999999999886 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.42
                        DUF573  30 sdldafyeavksslssdvsksqlseKlrrLkkkyrnavskikkgkdp 76 
                                    +++++ e ++ ++ +  ++ ++ + +   k+ +++++++ ++gk+ 
  gi|15669545|ref|NP_248358.1| 472 IEMAKIQELLATKFAVTPTTFNILKTIYDHKEEFDKVWKEKSEGKEH 518
                                   45666666666666667777777777777777777777765555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3500.46
//
Query:       gi|15669546|ref|NP_248359.1|  [L=189]
Description: hypothetical protein MJ_1356 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-10   39.5   0.6    6.4e-10   39.1   0.6    1.1  1  Protoglobin      Protoglobin
     0.0011   19.2   1.4      0.002   18.4   0.7    1.8  2  IlvC             Acetohydroxy acid isomeroreductase, catalyti
     0.0034   16.7   1.3      0.005   16.1   1.3    1.2  1  DUF2357          Domain of unknown function (DUF2357)
      0.009   16.1   2.0      0.012   15.6   2.0    1.2  1  SecA_SW          SecA Wing and Scaffold domain
  ------ inclusion threshold ------
      0.013   15.4   1.4      0.013   15.4   1.4    2.4  2  ApoC-I           Apolipoprotein C-I (ApoC-1)
       0.11   13.0   0.7       0.19   12.2   0.5    1.6  1  PolyA_pol        Poly A polymerase head domain
       0.13   12.7   3.5       0.21   12.1   1.2    2.1  2  Phage_connect_1  Phage gp6-like head-tail connector protein
       0.27   11.7   1.5       0.66   10.5   1.5    2.0  1  OHCU_decarbox    OHCU decarboxylase
       0.27   11.8   4.6        1.6    9.4   0.9    2.7  2  MCM_N            MCM N-terminal domain
       0.51   10.3   6.8       0.64    9.9   1.2    2.3  2  Kin17_mid        Domain of Kin17 curved DNA-binding protein
       0.84   10.0   3.7         12    6.3   0.1    3.2  3  ACDC             AP2-coincident C-terminal


Domain annotation for each model (and alignments):
>> Protoglobin  Protoglobin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.6   3.9e-13   6.4e-10      15     143 ..      22     152 ..      10     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 3.9e-13
                                   SHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSHHHHHHHCHHCHHHHHHHHHHHHHHHCCCSS...CCHHHHHHHHHHHH CS
                   Protoglobin  15 teedlaaLralapliealipavvdafYekllsfpetarifetssqierlkdflksyllklfsgp...fdsayveyldkvGk 92 
                                   +e+d   L ++++li + i++vv+++++ + s+++t+  f++ s++++l + +k++++ lf+        +++++  k G 
  gi|15669546|ref|NP_248359.1|  22 EEKDFSKLTQYKDLISKTIDEVVEEVFNDIFSYEKTKTLFDE-SKRKELEEDFKNWIKGLFEISndsDLNEFYKEIVKRGI 101
                                   6899************************************99.*****************6544333678999******** PP

                                   HHCHCT--HHHHHHCHHHHHHHHHHHHCCCS.-SHHHHHHHHHHHHHHHHH CS
                   Protoglobin  93 mhtrlgleprwyiaalglvqevlleallekeklsaaektalvkalnKliwl 143
                                    +++ +  p ++ a + ++++ l + l e+ k +a+e+ +++  l K + l
  gi|15669546|ref|NP_248359.1| 102 KYVEKDFLPEYLTAIIIKIEDRLKNKLKEELKEDAQEIVDILDDLLKRVIL 152
                                   ******************************************999998765 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.7   1.2e-06     0.002      52     120 ..       4      74 ..       1     106 [. 0.88
   2 ?   -0.6   0.0      0.89   1.4e+03      82      94 ..     123     134 ..      78     162 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                                   HHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHTTHHHHHHHHH..HHTTSHHHH CS
                          IlvC  52 ivdliyegGiakmresiSdtaeygdltagprviteevkeemkeileeiqsGefakeviee..nkagrpelk 120
                                    +d iy++ i++m +  S++  + +lt ++ +i++ + e+++e++++i s e +k++ +e   k+ ++++k
  gi|15669546|ref|NP_248359.1|   4 TFDGIYNEIIENMHHFASEEKDFSKLTQYKDLISKTIDEVVEEVFNDIFSYEKTKTLFDEskRKELEEDFK 74 
                                   578999****************************************************9943333555555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.89
                                   HHS-HHHHHHHHH CS
                          IlvC  82 rviteevkeemke 94 
                                   r+ +++ kee+ke
  gi|15669546|ref|NP_248359.1| 123 RL-KNKLKEELKE 134
                                   22.3344444444 PP

>> DUF2357  Domain of unknown function (DUF2357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.3   3.1e-06     0.005      92     238 ..       5     166 ..       2     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.1e-06
                       DUF2357  92 LeqalklIlrqpherLveeeevvradklkkldsavleellkepeklgeve...........rlgkkllp...rrvrqekke 158
                                   ++ + ++I + +h+  +ee+   ++ + k+l s+++ e+++e   ++++            + ++k l+   ++ ++  +e
  gi|15669546|ref|NP_248359.1|   5 FDGIYNEIIENMHHFASEEKDFSKLTQYKDLISKTIDEVVEE---VFNDIfsyektktlfdESKRKELEedfKNWIKGLFE 82 
                                   788899************************************...33333566799999*97777777622245678889* PP

                       DUF2357 159 ltvDTpENRFvKyvLerlekkle......dlkealkekereaetklseefleelkelekqlerllrhplfrevgeleglps 233
                                   ++ D   N F+K +++r  k +e       l++ + ++e++ ++kl+ee+ e  +e+ + l+ ll+  ++ +v  +     
  gi|15669546|ref|NP_248359.1|  83 ISNDSDLNEFYKEIVKRGIKYVEkdflpeYLTAIIIKIEDRLKNKLKEELKEDAQEIVDILDDLLKRVILLNVAAYMN--F 161
                                   *****************9999998766777788888888888888888888888888888888888888888877766..6 PP

                       DUF2357 234 eSlVL 238
                                   eS+VL
  gi|15669546|ref|NP_248359.1| 162 ESKVL 166
                                   77777 PP

>> SecA_SW  SecA Wing and Scaffold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.0   7.6e-06     0.012      52     138 ..      30     153 ..       8     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.6e-06
                                   CTHHCHHHHHHHHHHHHHHHHHCHHHHS.SS.C......SHHH.HHHHHHCCCSSSTSST..................... CS
                       SecA_SW  52 egesedlrerildliedvveeiveesvpeeeke......ewdl.eglleelkeefsvele..................... 104
                                   +++++ ++++i +++e+v+++i++ ++++   +      + +l e++++++k  f+++ +                     
  gi|15669546|ref|NP_248359.1|  30 TQYKDLISKTIDEVVEEVFNDIFSYEKTK---TlfdeskRKELeEDFKNWIKGLFEISNDsdlnefykeivkrgikyvekd 107
                                   45555577777777888887777332222...12222222333355555555555555558999***************** PP

                                   ...........HHHHHHHHHHHHHHHHHHHHC.HHHHHHHHHHHHH CS
                       SecA_SW 105 ...........elaeellekaekayekkeeei.ellrelervvlLe 138
                                              +++++l +k+++++++ ++ei ++l++l + v+L 
  gi|15669546|ref|NP_248359.1| 108 flpeyltaiiiKIEDRLKNKLKEELKEDAQEIvDILDDLLKRVILL 153
                                   **************************99999987788855555543 PP

>> ApoC-I  Apolipoprotein C-I (ApoC-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.4   7.8e-06     0.013      12      50 ..      41      81 ..      33      83 .. 0.82
   2 ?    0.2   0.2      0.46   7.5e+02      51      59 ..     126     134 ..     119     142 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.8e-06
                                  .HHHCHHHHHH..HHHHCCHCCCHCTTSSSSCCHHHHHHHH CS
                        ApoC-I 12 pdklkEfgktl..edKaraaieeIkqSelpaktrnWfsetf 50
                                   + ++E+ +++   +K+++++ e k++el ++ +nW++  f
  gi|15669546|ref|NP_248359.1| 41 DEVVEEVFNDIfsYEKTKTLFDESKRKELEEDFKNWIKGLF 81
                                  566777777774459*********************98666 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.46
                                   HHHHHHSSS CS
                        ApoC-I  51 ekvkeklke 59 
                                   +k+ke lke
  gi|15669546|ref|NP_248359.1| 126 NKLKEELKE 134
                                   344444443 PP

>> PolyA_pol  Poly A polymerase head domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   0.00012      0.19      71     125 ..     123     180 ..      62     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                   EEEE---SSHHH.........HHHHHHCTSSBGGGS-EEECTTTCEE-TTSHHHHHHTTEE CS
                     PolyA_pol  71 desdarnpesekste......sleeDlkrRDftiNalaynlnkgkvlDlfgGikdLkskvi 125
                                     +++ ++   + +e      ++ +Dl +R + +N  ay   + kvlD++g  ++Lk++ +
  gi|15669546|ref|NP_248359.1| 123 RLKNKLKE---ELKEdaqeivDILDDLLKRVILLNVAAYMNFESKVLDYIGINQNLKKNAV 180
                                   33333333...322233356699************999999**********9999998876 PP

>> Phage_connect_1  Phage gp6-like head-tail connector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.48   7.8e+02      20      60 ..      34      79 ..      27     109 .. 0.64
   2 ?   12.1   1.2   0.00013      0.21      19      73 ..     110     165 ..     101     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.48
               Phage_connect_1 20 alLesliqaAeeyikdylgrkl.......eadedgielpedlktavle 60
                                  +l++  i+ + e++ +++  +        e  ++ +el+ed+k+ ++ 
  gi|15669546|ref|NP_248359.1| 34 DLISKTIDEVVEEVFNDIFSYEktktlfdE--SKRKELEEDFKNWIKG 79
                                  566666666666665554444444444422..4555666666666654 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00013
               Phage_connect_1  19 DalLesliqaAeeyikdylgrkl.eadedgielpedlktavlelaahryenregts 73 
                                    ++L+ +i + e+ +k++l  +l e  ++  ++ +dl   v +l ++ y n+e   
  gi|15669546|ref|NP_248359.1| 110 PEYLTAIIIKIEDRLKNKLKEELkEDAQEIVDILDDLLKRVILLNVAAYMNFESKV 165
                                   57899999999999999999999977788899999*9999999******9996655 PP

>> OHCU_decarbox  OHCU decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.5    0.0004      0.66     122     152 ..     115     145 ..       5     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0004
                                   HHHHHHHHHTTS-HHHHHHHHHHHHHHHHHH CS
                 OHCU_decarbox 122 eIlaelerRlendpekElrealqemckIard 152
                                    I+ ++e+Rl+n+ ++El+e +qe+ +I  d
  gi|15669546|ref|NP_248359.1| 115 AIIIKIEDRLKNKLKEELKEDAQEIVDILDD 145
                                   69999***********************765 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3     0.058        95      59      97 ..      31      68 ..       6      78 .. 0.57
   2 ?    9.4   0.9   0.00098       1.6      49      77 ..     124     152 ..      70     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.058
                         MCM_N 59 enpkeylplleealkevvkklepsykddakefpaeltrr 97
                                  ++   + +  +e+++ev+++++  +k + + f++ + ++
  gi|15669546|ref|NP_248359.1| 31 QYKDLISKTIDEVVEEVFNDIFSYEKTK-TLFDESKRKE 68
                                  3333333556666666666665533333.3333333333 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00098
                         MCM_N  49 fdeeLaeailenpkeylplleealkevvk 77 
                                    +++L e++ e+ +e++++l++ lk+v+ 
  gi|15669546|ref|NP_248359.1| 124 LKNKLKEELKEDAQEIVDILDDLLKRVIL 152
                                   4679***********************95 PP

>> Kin17_mid  Domain of Kin17 curved DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.2   0.00039      0.64      38      82 ..       3      47 ..       1      77 [. 0.75
   2 ?    3.4   0.4     0.041        67      63     107 ..      88     137 ..      82     152 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00039
                     Kin17_mid 38 veankvYqeyiqdkdHvhmNaTkwtsLteFvkyLgkegkvkveet 82
                                  v+ + +Y+e+i++ +H       ++ Lt++   ++k+    vee 
  gi|15669546|ref|NP_248359.1|  3 VTFDGIYNEIIENMHHFASEEKDFSKLTQYKDLISKTIDEVVEEV 47
                                  677889************************888888766555554 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.041
                     Kin17_mid  63 sLteFvkyLgkegkvkveete.....kgllisyidrspealerkeklekk 107
                                    L+eF k + k+g+  ve++      + ++i+  dr +++l+++ k++++
  gi|15669546|ref|NP_248359.1|  88 DLNEFYKEIVKRGIKYVEKDFlpeylTAIIIKIEDRLKNKLKEELKEDAQ 137
                                   58999999999999999887455565666666666655555555444433 PP

>> ACDC  AP2-coincident C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0072        12      36      71 ..       6      41 ..       1      44 [. 0.88
   2 ?    1.8   0.1      0.19     3e+02      28      52 ..      83     106 ..      64     137 .. 0.73
   3 ?    1.9   0.6      0.18   2.9e+02      14      23 ..     142     151 ..      88     185 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0072
                          ACDC 36 skelkrvieahikyvenakslkelqpylklFstcil 71
                                  + +++++ie+  +++++ k++++l  y +l+s+ i 
  gi|15669546|ref|NP_248359.1|  6 DGIYNEIIENMHHFASEEKDFSKLTQYKDLISKTID 41
                                  56899***************************9986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.19
                          ACDC  28 sslanktsskelkrvieahikyven 52 
                                    s+ ++  ++ +k+++++ ikyve+
  gi|15669546|ref|NP_248359.1|  83 ISNDSDL-NEFYKEIVKRGIKYVEK 106
                                   4444443.27888888888888875 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.18
                          ACDC  14 iLeDLlnncl 23 
                                   iL+DLl+ ++
  gi|15669546|ref|NP_248359.1| 142 ILDDLLKRVI 151
                                   4444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1799  (0.10034); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 1249.26
//
Query:       gi|15669547|ref|NP_248360.1|  [L=343]
Description: potassium channel protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-31  108.7   0.1    3.6e-31  107.8   0.1    1.5  1  TrkA_N           TrkA-N domain
    7.7e-16   57.8  15.8    1.3e-15   57.1  15.8    1.3  1  Ion_trans_2      Ion channel
    2.8e-15   55.9   0.0    5.3e-15   55.0   0.0    1.5  1  TrkA_C           TrkA-C domain
  ------ inclusion threshold ------
      0.032   14.2   1.7      0.076   13.0   0.1    2.3  3  DUF1027          Protein of unknown function (DUF1027)
      0.074   13.8   0.0       0.32   11.8   0.0    2.1  2  Methyltransf_12  Methyltransferase domain
       0.12   12.8   0.0       0.32   11.4   0.0    1.7  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
       0.18   11.0   7.0       0.33   10.1   7.0    1.4  1  Ion_trans        Ion transport protein


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.8   0.1   1.4e-34   3.6e-31       1     116 []     110     228 ..     110     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 1.4e-34
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT...SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg...levvvgdatdeevLeeagiekadaviaatgddeanil 78 
                                   +ii+G+Gr+G+ + e++ e+++++++id +e++++e  e+    + ++vgda +eevL++a+i+ka+++ia++++d++n++
  gi|15669547|ref|NP_248360.1| 110 YIICGYGRLGKVVGEKFIEENIPFIAIDINEDVLKEEYEKYpdkFLYIVGDAKKEEVLKKAKIDKAKGLIATLPSDADNVF 190
                                   79*****************9989*************9999965666*********************************** PP

                                   HHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                        TrkA_N  79 avllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                   ++l+a+elnp++ i a+a+++e +++lk +ga++v+sp
  gi|15669547|ref|NP_248360.1| 191 LTLTARELNPNILITAKADEKEAIRKLKIAGANRVVSP 228
                                   ************************************98 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1  15.8   5.2e-19   1.3e-15       3      78 ..      15      86 ..       9      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 5.2e-19
                                  HHHTCHHHHHHHHT....T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Ion_trans_2  3 lllvlifgaviysleegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkvlt 78
                                  ++l+l+++ +i ++    e+ ++++alYfs++t+tT GYGd++p+t +gr +t+vy+++G++++++++++++++++
  gi|15669547|ref|NP_248360.1| 15 ITLILTYAYLISII----EGVDYFTALYFSVITITTTGYGDFTPKTFLGRTLTVVYLCVGVGIVMYLFSLIAEFIV 86
                                  45666666666666....777***************************************************9986 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   2.1e-18   5.3e-15       2      68 ..     267     335 ..     266     337 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 2.1e-18
                                   EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                        TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                   + +++ ++s l+ k+lk++n+r + g+++++irR+ +++i+p ++++L++GDv++ +g+ ++l+ l++l
  gi|15669547|ref|NP_248360.1| 267 RKFVIEKDSELAYKSLKDANIRGKtGATILGIRREkEFCINPYPEFILKPGDVIYAFGTEENLKYLENL 335
                                   6799***********************************************************999887 PP

>> DUF1027  Protein of unknown function (DUF1027)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.88   2.3e+03      55      70 ..      94     109 ..      85     116 .. 0.66
   2 ?   13.0   0.1     3e-05     0.076      17      44 ..     138     165 ..     135     176 .. 0.89
   3 ?   -3.1   0.0       3.2   8.1e+03      28      55 ..     247     274 ..     240     283 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.88
                       DUF1027  55 nkkakkdnkisaledY 70 
                                    + +k +nki++l+d+
  gi|15669547|ref|NP_248360.1|  94 VRLKKMKNKIKTLKDH 109
                                   4556778888888874 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3e-05
                       DUF1027  17 fdeeeleeryseildkydYivGDigyek 44 
                                   ++e+ l+e+y+++ dk+ YivGD  +e+
  gi|15669547|ref|NP_248360.1| 138 INEDVLKEEYEKYPDKFLYIVGDAKKEE 165
                                   58899******************98876 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.2
                       DUF1027  28 eildkydYivGDigyekLRLkGFykden 55 
                                   ++l+++  i  D   e + L+ F+ ++ 
  gi|15669547|ref|NP_248360.1| 247 DFLSTFIKIAKDEYEEDIELRKFVIEKD 274
                                   5666666677777777777777766554 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.32       5      44 ..     113     151 ..     111     194 .. 0.85
   2 ?   -1.3   0.0       1.4   3.7e+03      64      85 ..     304     335 ..     245     342 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
               Methyltransf_12   5 cGtGsllrallekl..pdieytgvDispsaiedakeklakre 44 
                                   cG G+l +++ ek+  ++i ++++Di+++++   ke+  k+ 
  gi|15669547|ref|NP_248360.1| 113 CGYGRLGKVVGEKFieENIPFIAIDINEDVL---KEEYEKYP 151
                                   *******************************...44444444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
               Methyltransf_12  64 g..........ssfDlvvasnvlhhlkdirev 85 
                                              +  D+++a+++ ++lk ++ +
  gi|15669547|ref|NP_248360.1| 304 FcinpypefilKPGDVIYAFGTEENLKYLENL 335
                                   04444444455566788877777777666655 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.32       5      59 ..     112     168 ..     109     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                   EESTSHHHHHHHHHHHHHT.TCEEEEEE-.TS-HHHHHHHHHEETTTEC-SS-EEEE CS
                       Gp_dh_N   5 inGfGRIGrlvlralleek.elevvaind.ltdletlayllkyDsvhgrfkgeveae 59 
                                   i G+GR+G++v  + +ee+  +  + in+ + + e+ +y  k+ ++ g  k+e   +
  gi|15669547|ref|NP_248360.1| 112 ICGYGRLGKVVGEKFIEENiPFIAIDINEdVLKEEYEKYPDKFLYIVGDAKKEEVLK 168
                                   89**************8887999999**98999999888888877777776665554 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   7.0   0.00013      0.33     178     231 ..      32      79 ..       2      89 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                                   SHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Ion_trans 178 nfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsflllNllia 231
                                   ++ftal++++ ++tt g+gd +++t  ++      ++ ++++ +++ ++ +l+ 
  gi|15669547|ref|NP_248360.1|  32 DYFTALYFSVITITTTGYGDFTPKTFLGR------TLTVVYLCVGVGIVMYLFS 79 
                                   69***************************......4444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2261.65
//
Query:       gi|15669548|ref|NP_248361.1|  [L=152]
Description: hypothetical protein MJ_1358 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.013   15.0   5.8      0.013   15.0   5.8    2.2  2  Intg_mem_TP0381  Integral membrane protein (intg_mem_TP0381)
       0.62   10.8   6.7       0.28   11.9   1.2    2.7  2  DUF2809          Protein of unknown function (DUF2809)
        4.6    6.9   6.9         15    5.2   0.9    2.2  2  DUF4131          Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> Intg_mem_TP0381  Integral membrane protein (intg_mem_TP0381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   5.8   2.2e-06     0.013     132     182 ..      10      60 ..       3      69 .. 0.89
   2 ?    3.9   7.6    0.0055        33       8      93 ..      69     146 ..      61     149 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-06
               Intg_mem_TP0381 132 llliapllllllgkykptlkdiiksvlvlfllvlliflvNlllgtNYfFln 182
                                    l+++ l+ l l +y p++k+ +  +++ +l v+l+fl+N+l+  N+ Fl 
  gi|15669548|ref|NP_248361.1|  10 YLIFIKLTGLKLMDYFPRFKENRLKMIFSILSVILAFLINWLIMKNFSFLI 60 
                                   6788899999999************************************95 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0055
               Intg_mem_TP0381   8 lfl.livillavlllllkrkirrkkkakkkrilkvialillileiflllwalaagypnlweslPLhlCrlaiillaialit 87 
                                   +++ +i+i+l++ +l+lkr  ++++  +kk++ + ++ i ++le+++++ ++   ++n+ +  P+     +++++++++++
  gi|15669548|ref|NP_248361.1|  69 VWIfIILIYLLLRFLFLKRVPLSNY--EKKFMGN-MSAIAIFLELLKIIEYVD--EHNIAS--PITV--ALVFFIPVVVFF 140
                                   5562444444444444555445544..4445554.477777788888877754..556666..5443..455677777777 PP

               Intg_mem_TP0381  88 kkkklf 93 
                                   + k ++
  gi|15669548|ref|NP_248361.1| 141 NCKYFY 146
                                   776665 PP

>> DUF2809  Protein of unknown function (DUF2809)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.5      0.12   7.1e+02      22      50 ..      39      64 ..       3      72 .. 0.61
   2 ?   11.9   1.2   4.6e-05      0.28       6      69 ..      63     131 ..      59     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.12
                       DUF2809 22 lvrllvpkksplllalavllfavliEllQ 50
                                  ++ +++    ++l   ++  f++liE++ 
  gi|15669548|ref|NP_248361.1| 39 ILSVILAFLINWL---IMKNFSFLIEIIH 64
                                  3333333333332...4445566666655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.6e-05
                       DUF2809   6 irkylGdvlvvillyllvrllvpkk.....splllalavllfavliEllQltqlpallglrattlgrlv 69 
                                   i++ +   +++il+yll+r+l+ k+       ++ +  + ++a+++Ell+++++++  ++++   ++lv
  gi|15669548|ref|NP_248361.1|  63 IHPIASVWIFIILIYLLLRFLFLKRvplsnYEKKFMGNMSAIAIFLELLKIIEYVDEHNIASPITVALV 131
                                   555666667899**********9776666644445899999***************9999977666666 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.9    0.0025        15      11      49 ..       2      52 ..       1      55 [. 0.86
   2 ?    5.1   0.6    0.0027        16       5      27 ..      66     107 ..      63     144 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0025
                       DUF4131 11 alllllllllllllrr............rprrrvllllllllllallgfal 49
                                  ++++++ ++l+++++              +r ++++++l ++l++l+ +++
  gi|15669548|ref|NP_248361.1|  2 GVVFAFGFYLIFIKLTglklmdyfprfkENRLKMIFSILSVILAFLINWLI 52
                                  68899999999998889999*999999999999999999999999987765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0027
                       DUF4131   5 lalvllalllllllllllllrr...................r 27 
                                   +a v+++++l+ lll++l+l+r                    
  gi|15669548|ref|NP_248361.1|  66 IASVWIFIILIYLLLRFLFLKRvplsnyekkfmgnmsaiaiF 107
                                   444555555555555555555557774444444433333330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1133  (0.0631937); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1182.89
//
Query:       gi|15669549|ref|NP_248362.1|  [L=242]
Description: hypothetical protein MJ_1359 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-91  305.5   0.0    2.1e-91  305.4   0.0    1.0  1  ATPase    KaiC
    0.00036   19.9   0.1     0.0007   18.9   0.0    1.5  2  Rad51     Rad51
    0.00054   19.6   0.0    0.00094   18.8   0.0    1.6  1  AAA_25    AAA domain
    0.00061   18.5   0.0       0.08   11.5   0.0    2.1  2  GvpD      GvpD gas vesicle protein
     0.0044   15.9   0.0     0.0066   15.3   0.0    1.2  1  PPV_E1_C  Papillomavirus helicase
     0.0066   16.4   0.2      0.023   14.6   0.2    1.8  1  NTPase_1  NTPase
  ------ inclusion threshold ------
      0.011   14.8   0.0      0.017   14.2   0.0    1.2  1  T2SSE     Type II/IV secretion system protein
      0.016   14.6   0.0      0.025   13.9   0.0    1.3  1  DnaB_C    DnaB-like helicase C terminal domain
      0.039   14.3   0.0      0.062   13.6   0.0    1.2  1  HutP      HutP
      0.083   13.3   0.0       0.16   12.3   0.0    1.5  1  AAA_16    AAA ATPase domain
      0.096   11.9   0.0       0.11   11.7   0.0    1.1  1  DUF2075   Uncharacterized conserved protein (DUF2075)
       0.11   12.8   0.0       0.14   12.5   0.0    1.3  1  AAA_19    AAA domain
       0.11   11.9   0.0       0.17   11.4   0.0    1.2  1  AAA_7     P-loop containing dynein motor region
       0.12   12.5   0.0       0.17   11.9   0.0    1.4  1  AAA_14    AAA domain
       0.14   12.4   0.0       0.22   11.8   0.0    1.4  1  AAA_22    AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.4   0.0   1.8e-94   2.1e-91       1     230 [.       4     237 ..       4     238 .. 0.99

  Alignments for each domain:
  == domain 1  score: 305.4 bits;  conditional E-value: 1.8e-94
                        ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                   vktgI+g+Deil+gGipe++vvl++G+pGtGK+if++qFl+kg+++y+ep ++v++ee+++++ren++++Gwd++kleeeg
  gi|15669549|ref|NP_248362.1|   4 VKTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIFCQQFLYKGVVDYNEPSILVALEEHPVQIRENMRQFGWDIRKLEEEG 84 
                                   79******************************************************************************* PP

                        ATPase  82 klaiidasesaeesaee......kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklgv 156
                                   k+aiida++ +++sa++      +d +d +eli+ l++ai++i+akr+ iDs+t+l y++k+++aR++++ l+rv+++lg+
  gi|15669549|ref|NP_248362.1|  85 KFAIIDAFTYGIGSAAKrekyvvNDPNDERELIDVLKTAINDIGAKRIGIDSVTTL-YINKPMLARRTVFLLKRVISGLGC 164
                                   *************9999999*999********************************.************************ PP

                        ATPase 157 TailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvleek 230
                                   Tai++s++s++e+++gg+gve+ +vdg+i+Ldl+ei++el+R+l+++kmRgt+hs k+hpf+It+egi v+++k
  gi|15669549|ref|NP_248362.1| 165 TAIFTSQISVGERGFGGPGVEH-AVDGIIRLDLDEIDGELKRSLIVWKMRGTSHSLKRHPFDITNEGIIVYPDK 237
                                   **********************.************************************************986 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   5.9e-07    0.0007      18      57 ..       3      42 ..       1      49 [. 0.94
   2 ?   -3.7   0.0       4.6   5.5e+03     119     145 ..     115     141 ..     106     144 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.9e-07
                                  EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                         Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57
                                  ++ tG   +De+L+GGi+  ++  + G  ++Gk+ +c+++
  gi|15669549|ref|NP_248362.1|  3 RVKTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIFCQQF 42
                                  689**********************************985 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.6
                                   HHHHHTHHHHHHS-EEEEEEETTTGGG CS
                         Rad51 119 ellqqaaallaedkfallivDsvtaly 145
                                   el++ + + +++   + + +Dsvt+ly
  gi|15669549|ref|NP_248362.1| 115 ELIDVLKTAINDIGAKRIGIDSVTTLY 141
                                   555555556666556666688998888 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   7.9e-07   0.00094      15      58 ..       4      47 ..       1     145 [. 0.75

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.9e-07
                        AAA_25 15 laapppprrwlvkgllpagelallaGapgtGKttlaldlalava 58
                                  +++ +p  + +++g +p+  ++ll G pgtGK+ ++ +  ++ +
  gi|15669549|ref|NP_248362.1|  4 VKTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIFCQQFLYKGV 47
                                  5677888999*************************999887655 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0047       5.7      13      32 ..      25      44 ..      17     141 .. 0.88
   2 !   11.5   0.0   6.7e-05      0.08     162     206 ..     184     227 ..     171     233 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0047
                          GvpD 13 llikGaPGtGktlftlrgld 32
                                  +l+ G PGtGk +f  ++l 
  gi|15669549|ref|NP_248362.1| 25 VLLSGGPGTGKSIFCQQFLY 44
                                  7899***********99984 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.7e-05
                          GvpD 162 leyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftla 206
                                   +e+ vdG++ l++ e   g l+r+l + k+rG +   + +Pf ++
  gi|15669549|ref|NP_248362.1| 184 VEHAVDGIIRLDLDEI-DGELKRSLIVWKMRGTSHSLKRHPFDIT 227
                                   6899*********987.7****************99999999875 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.5e-06    0.0066     254     283 ..      13      43 ..       7      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.5e-06
                      PPV_E1_C 254 efLk.gvPkknclvllGppntGkslfamsli 283
                                   e L+ g+P +n+++l G p tGks+f++ ++
  gi|15669549|ref|NP_248362.1|  13 EILHgGIPERNVVLLSGGPGTGKSIFCQQFL 43 
                                   5666269********************9764 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   1.9e-05     0.023       2     102 ..      25     135 ..      24     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                                   EEEE--TTSSHHHHHHHHHHH.H...GGGEEEEEEEE....E-------EEEEEET.T--EEEEEETT.....---SSEET CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlel.lkssgvkvgGfytee....vreggrrigFkivdlasgeegiLarve.....akreprvg 72 
                                   v+++G pG+GK+ ++++ l + + + + +   +  ee    +re+ r+ g++i +l  +eeg +a  +       + ++ +
  gi|15669549|ref|NP_248362.1|  25 VLLSGGPGTGKSIFCQQFLYKgVVDYNEPSILVALEEhpvqIRENMRQFGWDIRKL--EEEGKFAIIDaftygIGSAAKRE 103
                                   7899***********98664415555666656666652222679************..66666776666688889999*** PP

                                   TEEE-HHHHHHHHHHHHHHHHHHH-..EEEE- CS
                      NTPase_1  73 kyvvdvesfeelalealrkalsead..viviD 102
                                   kyvv+  + e+  +++l++a+++ +   i iD
  gi|15669549|ref|NP_248362.1| 104 KYVVNDPNDERELIDVLKTAINDIGakRIGID 135
                                   ******************99965443355555 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.4e-05     0.017     117     150 ..      10      43 ..       3      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                         T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyall 150
                                    ++e+l+  + er ++l+sGg g+GK+++    l
  gi|15669549|ref|NP_248362.1|  10 GMDEILHGGIPERNVVLLSGGPGTGKSIFCQQFL 43 
                                   58999***********************985544 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.1e-05     0.025       2      67 ..       4      70 ..       3      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                                  BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHH CS
                                  xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRl 67
                                  ++tg   +D++++ G+ + +++++ + p++Gk+ ++ ++  + +v+++ p +++ le +  q+ + +
  gi|15669549|ref|NP_248362.1|  4 VKTGIPGMDEILHgGIPERNVVLLSGGPGTGKSIFCQQFLYKGVVDYNEPSILVALEEHPVQIRENM 70
                                  68999999998752688999*********************99999999999999999888886655 PP

>> HutP  HutP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.2e-05     0.062      15      90 ..      61     135 ..      53     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.2e-05
                                   CH.HHHH.HHHHTTEEEEEEEEEESS...HHHHHHHHHHHHHHTTSS-SSSHHHHHHHHHHHHHHHHHHTTSHHSG CS
                          HutP  15 eeeeelkeklkkegikvaavevggeaeelskkivesavvaAkregvikeehreehavahAvleAlsqvtrkavgln 90 
                                   e+  +++e++++ g+ + + e  g++  ++  ++  +  aAkre+ + +++++e+ ++   + A++++ +k +g+ 
  gi|15669549|ref|NP_248362.1|  61 EHPVQIRENMRQFGWDIRKLEEEGKF-AIIDAFTYGIGSAAKREKYVVNDPNDERELIDVLKTAINDIGAKRIGID 135
                                   5567899999999*************.99***************************************99999875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.16      24      46 ..      20      44 ..      12     131 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                        AAA_16 24 p..elvllsGesGvGKsslvrellr 46
                                  p  ++vllsG +G+GKs   +++l 
  gi|15669549|ref|NP_248362.1| 20 PerNVVLLSGGPGTGKSIFCQQFLY 44
                                  24499*************9999984 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.4e-05      0.11       2      25 ..      23      46 ..      22     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.4e-05
                       DUF2075  2 avvlVtGvaGtGKtvvllnllael 25
                                  +vvl +G++GtGK++   ++l++ 
  gi|15669549|ref|NP_248362.1| 23 NVVLLSGGPGTGKSIFCQQFLYKG 46
                                  799*************99999986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.14      10      30 ..      22      42 ..      14     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                        AAA_19 10 ekvllvtaGpGtGKTrvlkhi 30
                                  ++v+l+ +GpGtGK+   ++ 
  gi|15669549|ref|NP_248362.1| 22 RNVVLLSGGPGTGKSIFCQQF 42
                                  6899**********9876654 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.17      30      56 ..      19      45 ..      11      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                         AAA_7 30 lknkkpvllvGptGtGKtviikdllkk 56
                                  + +++ vll G  GtGK++ ++++l k
  gi|15669549|ref|NP_248362.1| 19 IPERNVVLLSGGPGTGKSIFCQQFLYK 45
                                  567788*****************7654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00015      0.17       2      72 ..      22      91 ..      21     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikell.vkkesilyinldderdkkladpekllelileklkeekktylflDE 72
                                  r++++++G   +GK+ +++q++++     +e  + ++l++++ + +++ +++   i+++ +e + ++ ++D 
  gi|15669549|ref|NP_248362.1| 22 RNVVLLSGGPGTGKSIFCQQFLYKGVvDYNEPSILVALEEHPVQIRENMRQFGWDIRKL-EE-EGKFAIIDA 91
                                  68999*****************9999766788899999999997766665556666664.34.677888885 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.22       5      32 ..      22      49 ..      20     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqldee 32
                                  ++++++ G +GtGK+  ++++l++ + +
  gi|15669549|ref|NP_248362.1| 22 RNVVLLSGGPGTGKSIFCQQFLYKGVVD 49
                                  67899****************9986544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1480.36
//
Query:       gi|15669550|ref|NP_248363.1|  [L=99]
Description: hypothetical protein MJ_1360 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 657.17
//
Query:       gi|15669551|ref|NP_248364.1|  [L=292]
Description: hypothetical protein MJ_1361 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-35  122.6   0.0    2.7e-35  121.9   0.0    1.5  1  F420_ligase  F420-0:Gamma-glutamyl ligase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.9   0.0   1.5e-39   2.7e-35       2     195 ..       6     191 ..       5     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 1.5e-39
                                   ..-----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H.......... CS
                   F420_ligase   2 iktplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfsli 82 
                                   ikt++ik+g+++  ivve++k++g++ledgD vv++ek+v++aegn+++ +++kp+  A      +  +  ++S++ + ++
  gi|15669551|ref|NP_248364.1|   6 IKTRYIKRGENFIPIVVEAIKNSGIKLEDGDFVVLSEKMVSTAEGNFIDESKFKPGVLA------Y--LCYYWSKYLWGYV 78 
                                   89***************************************************999999......2..34489******** PP

                                   .........HHHHHHHHTEEEEEE-S-EEEE.......TTS-E.....EEGGG-B-TTS-TTEEE---S-HHHHHHHHHHH CS
                   F420_ligase  83 Lkalakat.rkvevvlsepsdevgnqlidekytdevlvklGll.....gsnagidesnveegllkllPedpdksaeeikkk 157
                                   L +l+k + +k++ + ++p++e+ +      ++++++  +Gl      +++ g+d +nv++++++ lP++p+k+aee+ k+
  gi|15669551|ref|NP_248364.1|  79 LGKLLKVKeDKIKNLRRMPKEETLK------HKQTIIEIVGLRyalkpYAEGGVDLTNVPGTYACPLPKNPKKWAEELYKE 153
                                   ********77*************99......3456777666665566899******************************* PP

                                   HHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB- CS
                   F420_ligase 158 lkertgkdveVliygkDpegriweladpvvaigtsgle 195
                                   +k+++g+dv V++ ++D+++r+++ + + ++++++g+ 
  gi|15669551|ref|NP_248364.1| 154 IKKELGVDVVVMVADTDATYRVLNFYFTALPYAIDGII 191
                                   ************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1936.60
//
Query:       gi|15669552|ref|NP_248365.1|  [L=322]
Description: NADH ubiquinone oxidoreductase subunit 1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-16   60.5  19.1    1.3e-08   34.5   2.1    2.1  2  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   2.1   7.5e-13   1.3e-08       8     118 ..      13     124 ..       6     127 .. 0.71
   2 !   31.6   9.4   5.7e-12     1e-07     127     288 ..     148     309 ..     144     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 7.5e-13
                                   HHHHHHHH.HHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTTS- CS
                        NADHdh   8 vvlllvva.lltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallafaviP 87 
                                   + l++++  ++ +++Rk+ Ariq+R+GP  + p      +  ++K+l+Ke+ +p++    l++l p+l++++  +++ +  
  gi|15669552|ref|NP_248365.1|  13 A-LAFAIStYIPGIQRKIEARIQQRIGPSILAP-----GFWAFFKFLFKETKAPDANLPKLYNLLPLLSIVVLWALLSITS 87 
                                   3.3444445999****************55444.....477899**************************99999999999 PP

                                   SSS.SSS--TTHHHHHHHH.....HHHCHHHHHHHHH CS
                        NADHdh  88 fge.vladlnvglllilal.....sslgvygillaGw 118
                                   +++  +   ++g++ +l l     + lg +++ ++Gw
  gi|15669552|ref|NP_248365.1|  88 LTSfHILSNEIGIVGLLKLeemmyVILGSLAFSIMGW 124
                                   8866555555666655544000003344455555555 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 5.7e-12
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSC CS
                        NADHdh 127 lGalRsaaqmisyEvalglsllavvllagslslseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaG 207
                                   lGa+Rs  +++    ++ l+ + +++  +s+ l++iv +     f l+ ++++ +++i  ++ ++  PF ++  ++++++G
  gi|15669552|ref|NP_248365.1| 148 LGAVRSFKMITIGSFPFYLATFLPFVQKKSIFLKDIVGEP--FLFSLAGIFGAACYFIGYVIMIKEYPFSITHTKADVIEG 226
                                   8***********************************8754..4678888******************************** PP

                                   CCTT-HCHHHHHHHHHHHHHHHHHHHHHHHHCT.SS-HCCS...HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCC CS
                        NADHdh 208 fhtEYsgmkfalfflaeyanmvlvsalavllFlgGwllpfs...gllwfllKvllllflfiwiratlpRlRydqlmklgwk 285
                                   +++E  +   al+  ++ + ++++ +l+++l+lg +++ ++   +++  ++ +l++ +l++++ra  p l ++q+  +++ 
  gi|15669552|ref|NP_248365.1| 227 PTMELIAKYRALYLASKELLLIALGSLFATLYLG-IAPDIEnpiTIVENFAIALIFPILATFVRAFSPVLLFKQIYPISYV 306
                                   *********************************5.666666666777777888888889999****999999999887765 PP

                                   TCH CS
                        NADHdh 286 vll 288
                                     l
  gi|15669552|ref|NP_248365.1| 307 ATL 309
                                   444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2068.55
//
Query:       gi|15669553|ref|NP_248366.1|  [L=151]
Description: formate hydrogenlyase subunit 7 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-26   90.9   0.9    6.9e-26   90.6   0.9    1.1  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
     0.0058   16.7   0.1       0.01   15.9   0.1    1.5  1  DUF1490      Protein of unknown function (DUF1490)
  ------ inclusion threshold ------
       0.16   12.5   3.8        8.7    6.9   0.3    3.0  3  DUF2367      Uncharacterized conserved protein (DUF2367)


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   0.9   1.1e-29   6.9e-26       1     130 [.      24     142 ..      24     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 1.1e-29
                                   -SHHHHHH.T-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEES CS
                   Oxidored_q6   1 CtGcsisl.laleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavG 80 
                                   C++c+i++ +a+ ++++d+     ++y+  l+ +++         ead+lvv+G vt+  +e l++++e  +++kav+avG
  gi|15669553|ref|NP_248366.1|  24 CNACDIEVvNAIFSPFYDA-----EQYNVFLTFNPR---------EADILVVTGCVTKVVAESLRKIYEKIPEPKAVVAVG 90 
                                   *******************.....***999999999.........9*********************************** PP

                                   HHHHH-TGGGSTT-T..EE-....HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHH CS
                   Oxidored_q6  81 tCAafGGipaaannp..svg....eevgellevvpvdinipGCPphpeailetlla 130
                                   +CA +GG+++  n +  + g    + +g++++ +pvd+++pGC p+pe+i++++++
  gi|15669553|ref|NP_248366.1|  91 ACALMGGVYK--N-IggDLGtsdfV-AGPVENIIPVDVKVPGCAPRPEDIIAGIVK 142
                                   *********4..4.32433233322.58999*********************9986 PP

>> DUF1490  Protein of unknown function (DUF1490)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.7e-06      0.01      12      50 ..      58      96 ..      50     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-06
                       DUF1490 12 ttvvtGvvGvaayevlrkavakaplreaaVaatalglrg 50
                                    vvtG v  ++ e lrk  +k p  +a Va+ a +l g
  gi|15669553|ref|NP_248366.1| 58 ILVVTGCVTKVVAESLRKIYEKIPEPKAVVAVGACALMG 96
                                  579*****************************9999977 PP

>> DUF2367  Uncharacterized conserved protein (DUF2367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.3    0.0014       8.7      51      72 ..      17      38 ..       2      40 .. 0.77
   2 ?    3.1   0.0     0.023   1.4e+02      41      60 ..      46      66 ..      39      76 .. 0.77
   3 ?    2.6   0.1     0.032   1.9e+02      40      59 ..      75      93 ..      65     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0014
                       DUF2367 51 svvvvggCpaCrvgvLeddftc 72
                                   +v  ggC aC + v++  f++
  gi|15669553|ref|NP_248366.1| 17 MLVYTGGCNACDIEVVNAIFSP 38
                                  456679*********9999975 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.023
                       DUF2367 41 tativvqP.aqsvvvvggCpa 60
                                   ++++ +P +++++vv gC +
  gi|15669553|ref|NP_248366.1| 46 NVFLTFNPrEADILVVTGCVT 66
                                  45666789899********75 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.032
                       DUF2367 40 ttativvqPaqsvvvvggCp 59
                                  + +  + +P + vv vg+C 
  gi|15669553|ref|NP_248366.1| 75 KIYEKIPEP-KAVVAVGACA 93
                                  455666677.99*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1064.38
//
Query:       gi|161579521|ref|NP_248367.2|  [L=422]
Description: tRNA pseudouridine synthase D [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-87  292.7   0.3    5.1e-87  292.4   0.3    1.0  1  TruD      tRNA pseudouridine synthase D (TruD)
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.52   10.6   0.0    2.2  1  BRICHOS   BRICHOS domain
       0.34   11.4   1.9          1    9.9   0.2    2.7  3  HSCB_C    HSCB C-terminal oligomerisation domain
          3    7.8   6.2        5.6    6.9   2.4    2.8  2  SWIB      SWIB/MDM2 domain


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.4   0.3   1.1e-90   5.1e-87      13     414 ..      24     409 ..      16     411 .. 0.89

  Alignments for each domain:
  == domain 1  score: 292.4 bits;  conditional E-value: 1.1e-90
                           TruD  13 gigGrlrespeDFiVeEieefsgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisi 92 
                                    g  ++lr +peDFiVeEi +f +      ++ ++++++krn+++l++++ +a++++i  k++g++G+KD++A+TtQ+isi
  gi|161579521|ref|NP_248367.2|  24 GAFMKLRMKPEDFIVEEIIDFNK---IAGDRCYLYKLTKRNIESLKAFSYIAKKFKIPLKDIGYCGLKDRHALTTQYISI 100
                                    8889**************77743...45566699********************************************** PP

                           TruD  93 rk.vepeelealeikdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeileeleekggvPNyfGvQRFGs 171
                                     k   + +   l+ ++++le +g++ + l lGdL+GN+F+i+vr++  ++e++ +++e l+ le +g  PNyf+ QRFGs
  gi|161579521|ref|NP_248367.2| 101 PKkYGKLS---LDEPNLKLELIGES-KFLLLGDLEGNRFTITVRGL--KKEDIPKIKENLKYLE-FG-APNYFDSQRFGS 172
                                    65144444...45699*******77.99*****************7..4566999*****9998.56.9*********** PP

                           TruD 172 rrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareav.aetgdleealeelpkslryErallkrLae..kpkdy 248
                                    + + ++ ++k+++kg++eeAv+++++k +++e++ +++ ++++ +++gd+++ +e ++++    r ++++++e  k++dy
  gi|161579521|ref|NP_248367.2| 173 V-FDKKFIAKEVIKGNYEEAVKILLTKYKKSEKKLIKDLKRFIdKNWGDWDKIWEYIKENNIKSRLYVNMVKElkKSNDY 251
                                    7.999**************************************4459******************877777666669*** PP

                           TruD 249 kkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeerlpdtdrlqlvteknveevkrliergra 328
                                    kkAl+ ++++L+++Fv AyqSyl+N++++e l++++p     e+D+v+++ e       + ++ +k++eev ++++++++
  gi|161579521|ref|NP_248367.2| 252 KKALSYVDDRLKKIFVAAYQSYLWNECVKELLRKYVP-----EEDRVYYEYEC-----GTLMFYKKMDEEVFNILKDKKF 321
                                    *********************************9977.....9*******999.....99******************** PP

                           TruD 329 fvtaplvGtetelaegevgeierevleeegleledFk.lpklpelsskGtrRaillrve........dlelsaeedeltl 399
                                     ++ap + +     +ge++ei++e+l++egl++e+ + + +l ++    + R+il  ++        ++el++ + ++tl
  gi|161579521|ref|NP_248367.2| 322 PTIAPDIEY-----SGEEKEIIEEILKREGLTMEELNnIGELGKFI-YSE-RKILSIPKnlkigefeEDELNKGKYKITL 394
                                    ********9.....8*********************9444433333.233.55555444588998888889999999*** PP

                           TruD 400 eFsLpkGsYATvvlr 414
                                    +++L+kGsYAT++++
  gi|161579521|ref|NP_248367.2| 395 SYELEKGSYATIIIK 409
                                    ************997 PP

>> BRICHOS  BRICHOS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00012      0.52      19      49 ..      45      75 ..      35     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                        BRICHOS 19 rlaskkaCyimkmdkssipsleellrlleek 49
                                       +++Cy+ k++k++i+sl+++   ++++
  gi|161579521|ref|NP_248367.2| 45 NKIAGDRCYLYKLTKRNIESLKAFSYIAKKF 75
                                   567899****************988777775 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.2   9.8e+03      51      67 ..     143     159 ..     138     159 .. 0.73
   2 ?    9.9   0.2   0.00023         1      25      63 ..     189     229 ..     180     257 .. 0.87
   3 ?   -1.3   0.0      0.72   3.2e+03      61      75 ..     298     312 ..     275     312 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                                    HTT-HHHHHHHHHHHHH CS
                         HSCB_C  51 ekkdleaaadllrrlrY 67 
                                    +k+d+ ++++ l +l +
  gi|161579521|ref|NP_248367.2| 143 KKEDIPKIKENLKYLEF 159
                                    56688888888887765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00023
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTT..-HHHHHHHHH CS
                         HSCB_C  25 keeleelkaeveerieeleaeleeafekk..dleaaadllr 63 
                                    +e+++ l  + ++ +++l++ l++ ++k+  d++++++ + 
  gi|161579521|ref|NP_248367.2| 189 EEAVKILLTKYKKSEKKLIKDLKRFIDKNwgDWDKIWEYIK 229
                                    48899999999***************8889****9998876 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.72
                                    HHHHHHHHHHHHHHH CS
                         HSCB_C  61 llrrlrYlekikeei 75 
                                    ++  l++++k++ee+
  gi|161579521|ref|NP_248367.2| 298 ECGTLMFYKKMDEEV 312
                                    567799999999986 PP

>> SWIB  SWIB/MDM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       2.5   1.1e+04      16      33 ..     199     216 ..     193     217 .. 0.62
   2 ?    6.9   2.4    0.0012       5.6      26      37 ..     223     234 ..     221     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.5
                           SWIB  16 kelsrpevvkklweYIke 33 
                                     + s ++ +k l  +I +
  gi|161579521|ref|NP_248367.2| 199 YKKSEKKLIKDLKRFIDK 216
                                    455666777777777665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0012
                           SWIB  26 klweYIkennLq 37 
                                    k+weYIkenn +
  gi|161579521|ref|NP_248367.2| 223 KIWEYIKENNIK 234
                                    8********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1372  (0.0765241); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3233.66
//
Query:       gi|15669555|ref|NP_248368.1|  [L=397]
Description: pheromone shutdown protein TraB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-28  100.4   0.0    2.7e-28   99.6   0.0    1.2  1  TraB            TraB family
  ------ inclusion threshold ------
      0.013   15.8   2.0      0.026   14.8   2.0    1.4  1  DMT_YdcZ        Putative inner membrane exporter, YdcZ
       0.06   13.4   1.2       0.06   13.4   1.2    2.8  3  DUF2540         Protein of unknown function (DUF2540)
       0.13   12.2   0.0       0.19   11.7   0.0    1.4  1  Cofac_haem_bdg  Haem-binding uptake, Tiki superfamily, ChaN


Domain annotation for each model (and alignments):
>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   0.0     6e-32   2.7e-28       8     256 ..      15     233 ..       8     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 6e-32
                          TraB   8 ggttsyLfGTiHvskksvyplspeveealeksdtvvvEldlsdd..tdeatqkelaklkllpdgktlsdllseelyarlqk 86 
                                   + +++yL+GT+Hvsk+s++++++ +     +++ ++vEld ++      ++ k++  +k+l+ +++  ++     +a+ qk
  gi|15669555|ref|NP_248368.1|  15 NECDIYLIGTAHVSKDSIEEVEKIISS--VSPEGIAVELDDRRFfsLITNEEKKVDLKKVLK-EGNFLKFFIYLILANSQK 92 
                                   5566***************99999999..5***********999974444444444455777.8888888999******** PP

                          TraB  87 alakrglplaaldkmkPwllalllslaelakkkagldpelvDrylaktakragkpvgglEtveeqlsllsslpdeeqleal 167
                                   ++ + ++++      kP  ++++  ++e a  k gl++ l+Dr++ +t++r   ++ + E+++  ++ll+  +dee le  
  gi|15669555|ref|NP_248368.1|  93 KIGE-SFGI------KP--GSEMKKAIEIA-SKYGLPIYLIDRDIDITLSRLMDRMTFKEKMKIFWELLN--SDEEDLELD 161
                                   ****.9***......**..77777777764.557997777*****************************4..444444444 PP

                          TraB 168 eetldeleeakdlleelveaykegdlealeleaeaeeefpelkevlldeRnrrwaekieallkepgsvfvaVGagHlaGed 248
                                   +          dll+++v+     + e++   + ++e++p+++evl+deR+r +a+++ +l k+++s +++VGagH+ G+ 
  gi|15669555|ref|NP_248368.1| 162 D----------DLLNDMVK-----NPEKFI--KLLKEISPTIYEVLVDERDRFMAKRLFELSKNKNSLVAVVGAGHVEGIV 225
                                   3..........34455555.....333331..3788************************99999**************** PP

                          TraB 249 gvlalLkk 256
                                    +l++L++
  gi|15669555|ref|NP_248368.1| 226 RYLKKLEN 233
                                   ****9986 PP

>> DMT_YdcZ  Putative inner membrane exporter, YdcZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   2.0   5.9e-06     0.026      28     131 ..     253     354 ..     242     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.9e-06
                      DMT_YdcZ  28 gsplaAalvsflvGlivllllllllrksaalaalksvpwwallGGllGavfvtlnillvpklGaaltvvlvllGqllasll 108
                                   +  l +  +s ++  i+l +++ +l+++ +l ++ + +w++++GGl    ++++   l+ +l a l   +++l  l  +++
  gi|15669555|ref|NP_248368.1| 253 K-KLLTYGISLTIISIFLYMICYALNNP-ELLKMITFQWILFTGGLSALGVLLARGKLITALVAFLSAPITTLVPLPLAAV 331
                                   4.777888999***************97.9999999********************************************* PP

                      DMT_YdcZ 109 iDhfGlfgvekrplsltrllGll 131
                                       Gl++++ r+++ + l+G++
  gi|15669555|ref|NP_248368.1| 332 GTIAGLVELKYREITDKDLVGII 354
                                   *******************9986 PP

>> DUF2540  Protein of unknown function (DUF2540)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.34   1.5e+03      30      65 ..      42      79 ..      30      91 .. 0.57
   2 ?   -2.3   0.0       1.1     5e+03      41      59 ..     199     217 ..     191     222 .. 0.81
   3 ?   13.4   1.2   1.3e-05      0.06      13      46 ..     225     257 ..     220     261 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.34
                                  HHHHHHHS---EEEEEE-.-HHHHHH.HHHHGGGHHHH CS
                       DUF2540 30 tlkkakeaekktkktltL.sdeEkkI.vkklGkaanlL 65
                                     + +  e+  ++  +L ++eEkk+ +kk  k  n+L
  gi|15669555|ref|NP_248368.1| 42 VSPEGIAVELDDRRFFSLiTNEEKKVdLKKVLKEGNFL 79
                                  44445555666677777634455554356666666666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                                   EEEEEE--HHHHHHHHHHG CS
                       DUF2540  41 tkktltLsdeEkkIvkklG 59 
                                    k++ +Ls + + +v   G
  gi|15669555|ref|NP_248368.1| 199 AKRLFELSKNKNSLVAVVG 217
                                   5899999999999998777 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHGGG-----HHHHHHHHHS---EEEEEE CS
                       DUF2540  13 lRYllHklenlenvdvetlkkakeaekktkktlt 46 
                                   +RY l klen + +d   l k+k+++k +kk+lt
  gi|15669555|ref|NP_248368.1| 225 VRY-LKKLENGNDIDLMELIKVKKRKKSLKKLLT 257
                                   565.79**************************98 PP

>> Cofac_haem_bdg  Haem-binding uptake, Tiki superfamily, ChaN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.3e-05      0.19     174     213 ..     194     227 ..     134     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                                   HHHHHHHHHHH-SS.E.....EEEEEEHHHH-TTTSHHHH CS
                Cofac_haem_bdg 174 wDetMAesiaaalkarnpgklvvviaGsgHveyglGipar 213
                                   +D+ MA+++ ++ k+   ++ +v ++G+gHv    Gi+++
  gi|15669555|ref|NP_248368.1| 194 RDRFMAKRLFELSKN---KNSLVAVVGAGHV---EGIVRY 227
                                   8********987774...568**********...566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1127  (0.0628591); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2488.67
//
Query:       gi|15669556|ref|NP_248369.1|  [L=291]
Description: ribose-phosphate pyrophosphokinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-30  105.6   1.1      6e-28   97.1   0.3    2.7  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    2.8e-22   78.9   1.5      2e-21   76.2   0.6    2.2  2  Pribosyltran    Phosphoribosyl transferase domain
      6e-09   36.2   2.8    1.4e-08   35.0   0.8    2.1  2  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    4.6e-07   29.5   0.2    2.9e-06   26.9   0.0    2.1  2  UPRTase         Uracil phosphoribosyltransferase
     0.0014   18.5   1.3      0.054   13.4   0.0    2.9  3  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.019   14.4   0.1      0.058   12.9   0.1    1.7  1  PRTase_2        Phosphoribosyl transferase
       0.05   13.2   0.1       0.14   11.8   0.0    1.7  2  Peptidase_S51   Peptidase family S51


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.3   2.3e-31     6e-28       1     114 [.       8     121 ..       8     122 .. 0.96
   2 !    6.4   0.0    0.0031         8       8      59 ..     172     224 ..     144     253 .. 0.76

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 2.3e-31
                Pribosyltran_N   1 lkifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasakr 81 
                                   + +++gs+s++La k+ak l+++l++++ +rf+d+Ei+v+i +++ +++ +ii++  ++ nd+++e +l++dalr   +k+
  gi|15669556|ref|NP_248369.1|   8 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQ-NDAIVETILLCDALRDEGVKK 87 
                                   689***********************************************999866555.********************* PP

                Pribosyltran_N  82 itaViPylgysrqdrk.ksrepisaklvaklLea 114
                                   it+V Pyl+y+rqd+k ++ e+is + +ak++++
  gi|15669556|ref|NP_248369.1|  88 ITLVAPYLAYARQDKKfNPGEAISIRALAKIYSN 121
                                   *****************************99875 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0031
                Pribosyltran_N   8 sskeLaekiakrlgvelgkakvsrfadgEikveiee.svrgkdvfiiqslskp 59 
                                    + e+a+  +k l+ e    + +r +  Ei++  ++ + +++dvfi+ ++ + 
  gi|15669556|ref|NP_248369.1| 172 GALEFAKTASKILNAEYDYLEKTRLSPTEIQIAPKTlDAKDRDVFIVDDIIST 224
                                   4556777777777999999***************9999*********998754 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.086   2.2e+02     106     133 ..      76     106 ..      72     125 .. 0.76
   2 !   76.2   0.6   7.6e-25     2e-21      13     124 ..     147     249 ..     135     289 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.086
                                   HHHHHHCC-BSEEEEEEEE...E-HHHHHHH CS
                  Pribosyltran 106 alelLkekgpeevriavlv...dkpateeev 133
                                    +++L+++g++++ +++++   ++ ++++++
  gi|15669556|ref|NP_248369.1|  76 LCDALRDEGVKKITLVAPYlayARQDKKFNP 106
                                   5799***********9999775555555544 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 7.6e-25
                                   EEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE CS
                  Pribosyltran  13 davarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliV 93 
                                    ++  ++ae++++ + + ++v+++++g++ fak  ++ L+++++y++k++ +p   + a+        ++ d +++ V+iV
  gi|15669556|ref|NP_248369.1| 147 GDAVPKLAEYVKD-KLNDPIVLAPDKGALEFAKTASKILNAEYDYLEKTRLSPTEIQIAP--------KTLDAKDRDVFIV 218
                                   5555566777777.7999******************************998876666665........899********** PP

                                   -SEESSSHHHHHHHHHHHCC-BSEEEEEEEE CS
                  Pribosyltran  94 DDildtGgTllaalelLkekgpeevriavlv 124
                                   DDi++tGgT+  a++lLke+g++++++a+++
  gi|15669556|ref|NP_248369.1| 219 DDIISTGGTMATAVKLLKEQGAKKIIAACVH 249
                                   *****************************98 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.18   4.7e+02      75     120 ..      46      94 ..      20     111 .. 0.76
   2 !   35.0   0.8   5.4e-12   1.4e-08      81     155 ..     210     284 ..     197     290 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.18
                                   --EES--TTSEEEEEEEEE-S-HHHHHH...HHHHHHTT--EEEEEEEE CS
                Pribosyl_synth  75 ltvvGdvgGriaiivddliddvesfvaa...aevlkerGaykiyvlath 120
                                   + +v +++   a+i++   ++ +++v++    + l++ G  ki  +a +
  gi|15669556|ref|NP_248369.1|  46 VRIVDEINDDEAVIINTQKNQNDAIVETillCDALRDEGVKKITLVAPY 94 
                                   5677777777788888777777777765233578999999999888765 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 5.4e-12
                                   -TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHHHT-T CS
                Pribosyl_synth  81 vgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqklrcs 155
                                    + r   ivdd+i    ++  a ++lke+Ga ki++ + h +l  da ++l ++ ++evv t+t   e+ k+   
  gi|15669556|ref|NP_248369.1| 210 AKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVA 284
                                   5567778*********************************************************99999888765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.15   3.9e+02     171     194 ..      37      60 ..      16      93 .. 0.73
   2 !   26.9   0.0   1.1e-09   2.9e-06     106     159 ..     196     248 ..     171     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.15
                       UPRTase 171 eefpkvkvvtaavDeeldekgyiv 194
                                   ++fp+ ++++  vDe  d++++i+
  gi|15669556|ref|NP_248369.1|  37 KRFPDNEIYVRIVDEINDDEAVII 60 
                                   567777777777777666666665 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 1.1e-09
                       UPRTase 106 lepveyynkLPkki..aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsv 159
                                   l+p e+    Pk++  ++r v+++D +i+TGg++a+a++lLke+g+  +kI+ ++v
  gi|15669556|ref|NP_248369.1| 196 LSPTEIQ-IAPKTLdaKDRDVFIVDDIISTGGTMATAVKLLKEQGA--KKIIAACV 248
                                   4454444.357777768899***********************776..68888776 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   2.1e-05     0.054      55     113 ..      49     108 ..      27     126 .. 0.86
   2 ?    0.1   0.1      0.25   6.4e+02      63      85 ..     220     247 ..     207     252 .. 0.73
   3 ?    1.7   0.1     0.079     2e+02     165     181 ..     275     291 .]     257     291 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                                   HHHHTT-SEEEES---TCCHHHH.HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHH CS
                NAD_binding_10  55 aealkgadaVvsalggggkdeeg.aknivdaakeagvkRfvlvsaigvgdevpgefgewn 113
                                    + +++ +aV++++ ++++d+ + ++ ++da++ +gvk++ lv    ++ +++++f++  
  gi|15669556|ref|NP_248369.1|  49 VDEINDDEAVIINTQKNQNDAIVeTILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGE 108
                                   56788999*******99998777999******************9999999999887754 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.25
                                   EEEES---TCC.....HHHHHHHHHHHH CS
                NAD_binding_10  63 aVvsalggggk.....deegaknivdaa 85 
                                    ++s++g+ ++     +e+gak+i++a+
  gi|15669556|ref|NP_248369.1| 220 DIISTGGTMATavkllKEQGAKKIIAAC 247
                                   4566666666666676777788888887 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.079
                                   --EEEHHHHHHHHHHHC CS
                NAD_binding_10 165 ggsisradVAdvlvavl 181
                                    +++s+ +VA+v+v++l
  gi|15669556|ref|NP_248369.1| 275 LSEVSKVSVAEVIVDLL 291
                                   4689**********987 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.3e-05     0.058     117     151 ..     208     242 ..     197     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                      PRTase_2 117 llaaakelvLvDDEistGktalnliralqeklprk 151
                                   l a+++ + +vDD istG t++  ++ l+e+  +k
  gi|15669556|ref|NP_248369.1| 208 LDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKK 242
                                   4467899******************9999987765 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.1   2.9e+03      58     104 ..      41      84 ..      28      90 .. 0.56
   2 ?   11.8   0.0   5.4e-05      0.14      43     113 ..     178     248 ..     147     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                                   HTT-EEEE--TTTS-HHH.HHHHHHHSSEEEE--S-HHHHHHHHHHTT CS
                 Peptidase_S51  58 klglevdeLelskdpeee.ieeklleadviyvgGGntfrLlkllketg 104
                                   + ++ v++++  +d+e+  i+++ +++d+i+    +t+ L+++l+++g
  gi|15669556|ref|NP_248369.1|  41 DNEIYVRIVDEINDDEAViINTQKNQNDAIV----ETILLCDALRDEG 84 
                                   5555566666666655553444445555554....5555555555555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.4e-05
                                   -S--HHHHHHHHHHHHTT-EEEE--TTTS-HHHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHH CS
                 Peptidase_S51  43 gdddeyvekvrkaleklglevdeLelskdpeeeieeklleadviyvgGGntfrLlkllketgldkllreav 113
                                   ++  +++++ ++ lek  l+++e++++++++++ ++ +   d i+ +GG     +kllke+g+ k++   v
  gi|15669556|ref|NP_248369.1| 178 KTASKILNAEYDYLEKTRLSPTEIQIAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACV 248
                                   56789999**********************************************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2275.30
//
Query:       gi|15669557|ref|NP_248370.1|  [L=297]
Description: sulfate transport ATP-binding protein CysA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-35  122.6   0.0    2.2e-35  122.1   0.0    1.2  1  ABC_tran      ABC transporter
    6.2e-07   29.1   0.2    3.3e-06   26.7   0.2    1.8  1  SMC_N         RecF/RecN/SMC N terminal domain
      4e-06   26.9   3.6      0.019   14.8   0.3    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.2e-05   23.6   0.0    6.7e-05   22.6   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00068   20.2   0.6     0.0016   18.9   0.3    1.9  1  AAA_23        AAA domain
    0.00076   19.4   0.1     0.0025   17.7   0.0    1.8  2  RsgA_GTPase   RsgA GTPase
     0.0012   19.2   0.0     0.0018   18.7   0.0    1.4  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.018   14.4   0.0      0.038   13.4   0.0    1.5  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.031   14.7   0.3       0.28   11.6   0.3    2.1  1  AAA           ATPase family associated with various cellular 
      0.039   13.7   0.0      0.093   12.5   0.0    1.6  1  IstB_IS21     IstB-like ATP binding protein
      0.057   13.7   0.0       0.59   10.4   0.0    2.1  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.097   12.4   0.0       0.26   11.0   0.0    1.6  2  AAA_30        AAA domain
       0.11   11.2   0.1       0.27   10.0   0.0    1.6  2  ABC_ATPase    Predicted ATPase of the ABC class
       0.15   12.3   0.1       0.22   11.8   0.1    1.5  1  AAA_22        AAA domain
       0.17   12.2   0.0        0.4   11.0   0.0    1.7  1  AAA_19        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.1   0.0   1.8e-38   2.2e-35       1     137 []      16     158 ..      16     158 .. 0.97

  Alignments for each domain:
  == domain 1  score: 122.1 bits;  conditional E-value: 1.8e-38
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   lknvs+++ + e  +i+G++GaGKS L+k++ag lkp++G+i l+g+d+++  l+  ++++g++pq+  lfp+++v++n  
  gi|15669557|ref|NP_248370.1|  16 LKNVSFEIDR-EYCVILGPSGAGKSVLIKCIAGILKPDSGRIILNGEDITN--LPPEKRNVGYVPQNYALFPNKNVYKNia 93 
                                   799*****87.6778************************************..**************************** PP

                                   ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                              e d++++++++ l++++l ++ v    ++LSgG++qrvalaral+ +p++lllDEpt+
  gi|15669557|ref|NP_248370.1|  94 ygliikkvnklEIDRKVKEIAEFLNISHLLNRDV----KTLSGGEQQRVALARALILNPSILLLDEPTS 158
                                   **********************************....*****************************96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.2   2.7e-09   3.3e-06      10     213 ..      11     201 ..       5     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.7e-09
                                   ETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTT.TTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  10 FksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakk.lrseklsdlihkskekasvkkaeveitfdnedkk 89 
                                   +k ++ k+v+ +++++  +i+Gp G+GKs l+  i  +L  +s +  l  e++++l  +     + + ++v   +      
  gi|15669557|ref|NP_248370.1|  11 WKDFKLKNVSFEIDREYCVILGPSGAGKSVLIKCIAGILKPDSGRIiLNGEDITNLPPE-----KRNVGYVPQNYAL---- 82 
                                   6899999****************************888887777541344455555444.....4444555544322.... PP

                                   SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  90 lkiekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                   ++ ++   +i   ++ k+ ++ +i++k  + +e  ++ +  + + ++LSgGe++ vala  + +   +  ++ llDe  +a
  gi|15669557|ref|NP_248370.1|  83 FPNKNVYKNIAYGLIIKKVNKLEIDRKVKEIAEFLNISHLLNRDVKTLSGGEQQRVALARALIL---N-PSILLLDEPTSA 159
                                   23334446677777777788899**999888888888888888999********9999866443...3.46889******* PP

                                   S-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 171 LDeknvkkvaellkeksknaQfivislreemlekadklvgvtk 213
                                    D k  + + + lk+ + +  ++ i+++    +   + vg+++
  gi|15669557|ref|NP_248370.1| 160 VDIKIKESIISELKKIK-HIPVLHITHDLAEARTLGEKVGIFM 201
                                   *****999999999877.8889999988888877777788877 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.2   6.5e-05     0.077       3      24 ..      29      50 ..      28      74 .. 0.73
   2 !   14.8   0.3   1.6e-05     0.019     211     297 ..     105     185 ..      78     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.5e-05
                        AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                  v+ Gp g+GKS L++++ ++  
  gi|15669557|ref|NP_248370.1| 29 VILGPSGAGKSVLIKCIAGILK 50
                                  89***************99864 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.6e-05
                        AAA_21 211 svderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQ 291
                                   ++d+  +e    fl  ++  ++++  lS G ++  al+ al+  +   s+ll+DEp +  + k+ ++++  lk+ +   + 
  gi|15669557|ref|NP_248370.1| 105 EIDRKVKE-IAEFLNISHLLNRDVKTLSGGEQQRVALARALILNP---SILLLDEPTSAVDIKIKESIISELKKIKH--IP 179
                                   33333333.777888888888889999***999999999999999...*********************88866544..55 PP

                        AAA_21 292 viltTH 297
                                   v+  TH
  gi|15669557|ref|NP_248370.1| 180 VLHITH 185
                                   555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   5.6e-08   6.7e-05       9      53 ..      11      57 ..       5      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.6e-08
                        AAA_29  9 Wgtfdghtieidlkg.atlltGpsGsGKSTllDAiqalLvpak.kvr 53
                                  W  f+ + ++++ +   +++ GpsG+GKS l+  i+ +L p++ ++ 
  gi|15669557|ref|NP_248370.1| 11 WKDFKLKNVSFEIDReYCVILGPSGAGKSVLIKCIAGILKPDSgRII 57
                                  77777766666666668**********************99986655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   1.4e-06    0.0016       5      47 ..       5      53 ..       2     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.4e-06
                        AAA_23  5 enfrsf......rdqeidFskgltlItGpNGaGKTTildAiklaLyget 47
                                  +n+ ++      ++++++ ++   +I Gp GaGK+ ++ +i  +L  ++
  gi|15669557|ref|NP_248370.1|  5 NNLSKIwkdfklKNVSFEIDREYCVILGPSGAGKSVLIKCIAGILKPDS 53
                                  5555555444557777888**********************99986554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.1e-06    0.0025      89     122 ..      15      48 ..       4      59 .. 0.86
   2 ?   -1.7   0.0         2   2.4e+03      53      85 ..     101     133 ..      88     151 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                                   THHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  89 gleelkellkdktsvlvGqSGvGKStLinallpe 122
                                   +l++++ +++ + +v++G+SG+GKS Li+ +++ 
  gi|15669557|ref|NP_248370.1|  15 KLKNVSFEIDREYCVILGPSGAGKSVLIKCIAGI 48 
                                   57888999999******************99875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2
                                   EE-GGG--HHHHHHHHHHHHHHTTSEEEE--TT CS
                   RsgA_GTPase  53 lnKiDlleeeeeleelkeelealgyevllvsak 85 
                                   +nK+++  + +e+ e+ +  + l+ +v ++s  
  gi|15669557|ref|NP_248370.1| 101 VNKLEIDRKVKEIAEFLNISHLLNRDVKTLSGG 133
                                   344444444445555555556666666666555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.5e-06    0.0018      25      67 ..      26      73 ..      16     175 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
                        AAA_16 25 elvllsGesGvGKsslvrellralekd.ggiflrgkcdql....esai 67
                                  e++++ G+sG GKs l+++++  l+ d g i l+g+   +    ++++
  gi|15669557|ref|NP_248370.1| 26 EYCVILGPSGAGKSVLIKCIAGILKPDsGRIILNGEDITNlppeKRNV 73
                                  789******************999999424446665555545444444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.2e-05     0.038      26      62 ..      29      65 ..      25      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                  Mg_chelatase 26 llvGppGsGKtmlakrlpsllpplseeealevakias 62
                                  +++Gp+G+GK++l+k+++++l p s + +l+ + i+ 
  gi|15669557|ref|NP_248370.1| 29 VILGPSGAGKSVLIKCIAGILKPDSGRIILNGEDITN 65
                                  689******************9988877777666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00023      0.28       2      38 ..      29     126 ..      28     189 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                   EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................... CS
                           AAA   2 llyGppGtGKTllakavakelg..vefleisgsellsk........................................... 37 
                                   ++ Gp G GK+ l+k +a  l+  +  + ++g ++++                                            
  gi|15669557|ref|NP_248370.1|  29 VILGPSGAGKSVLIKCIAGILKpdSGRIILNGEDITNLppekrnvgyvpqnyalfpnknvykniaygliikkvnkleidrk 109
                                   578*****************9744445666666666434455544444444444444444444444444444444444444 PP

                                   ................S CS
                           AAA  38 ................y 38 
                                                    
  gi|15669557|ref|NP_248370.1| 110 vkeiaeflnishllnrD 126
                                   44444444444444441 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.8e-05     0.093      37      67 ..      15      45 ..       7      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.8e-05
                     IstB_IS21 37 eLatlsfiekkenivllGpsGvGKshlaial 67
                                  +L + sf  ++e +v+lGpsG+GKs l   +
  gi|15669557|ref|NP_248370.1| 15 KLKNVSFEIDREYCVILGPSGAGKSVLIKCI 45
                                  57888999999**************997665 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00049      0.59      26      47 ..     123     141 ..     102     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00049
                       SbcCD_C  26 lsrssgtlSGGekqflaylala 47 
                                   l+r+++tlSGGe+q +a   la
  gi|15669557|ref|NP_248370.1| 123 LNRDVKTLSGGEQQRVA---LA 141
                                   899**********6543...33 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00021      0.26      18      50 ..      25      57 ..      20      64 .. 0.86
   2 ?   -1.9   0.0       1.9   2.3e+03      47      68 ..     178     199 ..     123     243 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                        AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvi 50
                                  + ++v+ Gp G+GK+ ++k ++ +++ + gr+i
  gi|15669557|ref|NP_248370.1| 25 REYCVILGPSGAGKSVLIKCIAGILKPDSGRII 57
                                  45899*****************99998866766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.9
                        AAA_30  47 grviglAptgkaAkvLaeelgi 68 
                                    +v+ +++  + A++L+e++gi
  gi|15669557|ref|NP_248370.1| 178 IPVLHITHDLAEARTLGEKVGI 199
                                   4566666666666677776665 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   1.4e+03     247     265 ..      28      46 ..      22      49 .. 0.84
   2 ?   10.0   0.0   0.00023      0.27     323     382 ..     130     189 ..     101     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                                   EEEEE-TTSSHHHHHHHHH CS
                    ABC_ATPase 247 tlIvGggfhGKsTLLeAle 265
                                    +I G+   GKs L++ ++
  gi|15669557|ref|NP_248370.1|  28 CVILGPSGAGKSVLIKCIA 46 
                                   7999***********9985 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00023
                                   --HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHH CS
                    ABC_ATPase 323 ASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvre 382
                                    SG   q +++++al ++ ++lL+DE tsA+ + i+ + ++el + ++ p+  +++ ++e
  gi|15669557|ref|NP_248370.1| 130 LSGGEQQRVALARALILNPSILLLDEPTSAVDIKIKESIISELKKIKHIPVLHITHDLAE 189
                                   59999999*******************************999998888787776665554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00018      0.22       8      29 ..      28      49 ..      23     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                        AAA_22  8 lvvtGesGtGKTtllrrlleql 29
                                  +v+ G+sG+GK++l++ ++  l
  gi|15669557|ref|NP_248370.1| 28 CVILGPSGAGKSVLIKCIAGIL 49
                                  799************9877655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00034       0.4       7     124 ..      22     171 ..      16     183 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                        AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkp...eeillvaftgrAakelrerlaalgae.........atTiHrl 75 
                                   ++ ++ ++++++ G GK+ ++k+i  +l+   g+     e+i+ + + +r +  + ++  al  +                
  gi|15669557|ref|NP_248370.1|  22 EIDREYCVILGPSGAGKSVLIKCIAGILKPDSGRIIlngEDITNLPPEKRNVGYVPQNY-ALFPNknvykniayG------ 95 
                                   788999******************99998777654355577777777777777777776.333332444444331...... PP

                        AAA_19  76 al.......ldfddlltealelle....................eaeeekklqeeellivDE.fqdvd.elqyrLlka 124
                                    l       l++d++++e +e+l+                        +  + +  +l+ DE ++ vd +   +++++
  gi|15669557|ref|NP_248370.1|  96 -LiikkvnkLEIDRKVKEIAEFLNishllnrdvktlsggeqqrvA-LARALILNPSILLLDEpTSAVDiKIKESIISE 171
                                   .03333333566666666666666666666666666566555432.22333335556666664455565555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2041.11
//
Query:       gi|15669558|ref|NP_248371.1|  [L=249]
Description: sulfate transport system permease CysT [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-21   75.4  13.1    4.4e-21   75.4  13.1    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.011   16.1   1.3      0.021   15.3   0.4    1.8  2  DUF2231       Predicted membrane protein (DUF2231)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   3.5     0.012   1.1e+02      24      62 ..       9      58 ..       4      62 .. 0.53
   2 !   75.4  13.1   4.9e-25   4.4e-21       1     176 [.      63     244 ..      63     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.012
                  BPD_transp_1 24 iivllslPsfvlaillvlvf...........vilsilghlilpviillll 62
                                  + +l ++  f+++++++++             ++ +++++ l++++++l+
  gi|15669558|ref|NP_248371.1|  9 TVFLVMIFLFIFLPIIYMLSnpgdlnqlldkEVIEAFKTTLLAGAVATLI 58
                                  33444555555555555433777777777775555666666665544444 PP

  == domain 2  score: 75.4 bits;  conditional E-value: 4.9e-25
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.......vilsilghlilpviillllsaapyvrlirra 74 
                                   gi++G+++a ++ +k++ ++  + ++++++P+ v++i+++ ++       +i  ++ + ++++++++l+  +p+++  +r+
  gi|15669558|ref|NP_248371.1|  63 GIPTGYILA-RYDFKFKSFVEAVLDLPMAIPHSVIGIIILSFIygidiinFIGRYVVDNFWGIVTVYLFVGIPFMVNSIRD 142
                                   89*******.****************************998889****9989999999*********************** PP

                  BPD_transp_1  75 alrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtllleailgydyseis 154
                                   ++ s++++ + ++r+lGas++++f+ + lP+++  ii+g+il+f++ + +  ++++++ +p  +  l+ e  +++ +++  
  gi|15669558|ref|NP_248371.1| 143 GFLSVDEEIEYVSRTLGASKIRTFFEISLPLIKNNIISGIILSFARGISEVGAILIIAYYPKtVPILIYERFMSFGLDASK 223
                                   **********************************************************99955444455555555555444 PP

                  BPD_transp_1 155 nggvlalviavlllnlvadilq 176
                                     +++ ++++ ++l ++++ + 
  gi|15669558|ref|NP_248371.1| 224 -PISVGMILISIALFALLRMFG 244
                                   .555555555555555555444 PP

>> DUF2231  Predicted membrane protein (DUF2231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.4   2.3e-06     0.021       9      85 ..      49     137 ..      47     145 .. 0.87
   2 ?   -3.7   0.0       1.8   1.6e+04      76      84 ..     229     237 ..     220     245 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-06
                       DUF2231   9 lvaalvigflaalaGlvelllaepsi..........rakktallHavggvlllalivaltvWrfvlrlreee..qvsplyl 77 
                                   l+a++v++++a ++G+   ++  ++            + ++a+ H v+g+++l++i ++ + +f+ r+  ++   +  +yl
  gi|15669558|ref|NP_248371.1|  49 LLAGAVATLIALIFGIPTGYILARYDfkfksfveavLDLPMAIPHSVIGIIILSFIYGIDIINFIGRYVVDNfwGIVTVYL 129
                                   789************9777766577799999999988999***************************98888779999999 PP

                       DUF2231  78 alslvvvv 85 
                                   ++++ ++v
  gi|15669558|ref|NP_248371.1| 130 FVGIPFMV 137
                                   99886665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.8
                       DUF2231  76 ylalslvvv 84 
                                   ++++s+++ 
  gi|15669558|ref|NP_248371.1| 229 MILISIALF 237
                                   333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1609.85
//
Query:       gi|15669559|ref|NP_248372.1|  [L=155]
Description: hypothetical protein MJ_1369 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.095   12.5   0.1       0.21   11.3   0.1    1.6  1  Scm3      Centromere protein Scm3


Domain annotation for each model (and alignments):
>> Scm3  Centromere protein Scm3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   1.2e-05      0.21       7      27 ..      34      54 ..      32      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.2e-05
                                  HHHHHHHHHHHHHHHHHHSG. CS
                          Scm3  7 esderlkkrwesifeKYerid 27
                                   + e+ kk w s++ KY++i 
  gi|15669559|ref|NP_248372.1| 34 NAGEKQKKNWRSFIRKYNQIK 54
                                  566888*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1048.12
//
Query:       gi|15669560|ref|NP_248373.1|  [L=328]
Description: hypothetical protein MJ_1370 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0072   15.5   1.2      0.034   13.3   1.2    1.8  1  DUF1464   Protein of unknown function (DUF1464)
  ------ inclusion threshold ------
      0.036   14.0   0.6      0.082   12.9   0.1    1.7  2  DUF1910   Domain of unknown function (DUF1910)


Domain annotation for each model (and alignments):
>> DUF1464  Protein of unknown function (DUF1464)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.2   3.8e-06     0.034       1     301 [.       5     314 ..       5     320 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-06
                       DUF1464   1 GiDPGtksydvvvvddlgkvvlekeiptdevekdpsvlvkaieearadivalpSGyGlPlkriselae.reillltlaees 80 
                                   GiD Gt+       d+ +k++++ +    + + + + l k i  + +d++al    G  + +i  +++ +++ +l+++   
  gi|15669560|ref|NP_248373.1|   5 GIDHGTSGITTCIKDNDKKIIFKLKRTELKEKSYLEELEKHISLEDIDLIALTYSMGDGINKILPIEKvKNRGVLSIEGAG 85 
                                   899999999988888889999988876666666777888999999999999999999999998888875667788888888 PP

                       DUF1464  81 eeglvGLrellkelaskelnaftiPgVie.LptvPewRKvnkiDmGtADKlasavlavadeaeeeeyrelsFilvEvGsgf 160
                                   e++  G  ++  e++++ l+a++iPg    ++ + e  +     +   +K+ +a  a      ++ +   +F+l ++ s+ 
  gi|15669560|ref|NP_248373.1|  86 EKVG-GGTKVYDEIKESGLPAVVIPGLHRgIECLDERFRALYSHIASPEKVSIAYYA------YKLFGFNDFVLSDISSN- 158
                                   8776.8899999999**********98543666665555556677888888888882......33344459******987. PP

                       DUF1464 161 naviaVknGkivDGlGgti.lpGflsaGalDgEvAyllgkvakiekslifs.gGvasiagea........elekklsee.. 229
                                   +  + +k+Gki  G+ + i   G +  G +D E+   +    ki+ ++ fs +G+  ia           e          
  gi|15669560|ref|NP_248373.1| 159 TVTLLIKDGKIFGGFDACIgAIG-MLHGPIDLEMIRDID-AGKITANEAFSkAGAVKIAKLYkgventkeE-------Iin 230
                                   677889*************8899.889******999988.5577777777527888888776655443332.......233 PP

                       DUF1464 230 ..........aferlke.vvksvaellssky.kleeiivSGrlkrikelgkklesrleev.kllelaskaKeaaqGaAiia 297
                                             a + l   v   + +ll+    + + ++++G   ++++   ++ +r++e+ + +     +  +a+G A+ia
  gi|15669560|ref|NP_248373.1| 231 nyfndencrlAVDSLILsVSMEINSLLPLLDkNKRRVVLAGSIGTLRN-PIDIPKRIKEFvEAKIFVLYGESGAIGGALIA 310
                                   445555444433333333444445555443212334888887764443.44566666666333334445667899999999 PP

                       DUF1464 298 nala 301
                                   + + 
  gi|15669560|ref|NP_248373.1| 311 EDIL 314
                                   8765 PP

>> DUF1910  Domain of unknown function (DUF1910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.1e-06     0.082      19      71 ..      15      67 ..       8      70 .. 0.82
   2 ?   -2.7   0.0      0.63   5.7e+03      43      56 ..     221     234 ..     200     237 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-06
                       DUF1910 19 eriaklkekieelsedeeksiqaeikilklsifkykleliiakYSlGesieel 71
                                  ++i++ ++ki  + ++ e   +++ + l ++i  + ++li ++YS+G+ i+++
  gi|15669560|ref|NP_248373.1| 15 TCIKDNDKKIIFKLKRTELKEKSYLEELEKHISLEDIDLIALTYSMGDGINKI 67
                                  678888888776666666556677899***********************998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.63
                       DUF1910  43 ikilklsifkykle 56 
                                   ++++k +i++++++
  gi|15669560|ref|NP_248373.1| 221 VENTKEEIINNYFN 234
                                   66777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2233.71
//
Query:       gi|15669561|ref|NP_248374.1|  [L=244]
Description: methlytransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.005   16.7   0.0     0.0099   15.8   0.0    1.4  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
       0.12   11.8   0.0       0.48    9.9   0.0    1.9  2  DUF3343          Protein of unknown function (DUF3343)


Domain annotation for each model (and alignments):
>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-06    0.0099      15      44 ..       7      36 ..       5      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-06
                                  EEETTHHHHHHHHHHHHHTTTTCEEEEE-S CS
               Transketolase_C 15 vayGsmveealeAaeeLekegisaeVvdlr 44
                                  ++ G   ee+l+A e+L++egi++e++d +
  gi|15669561|ref|NP_248374.1|  7 IGIGDNKEEVLKAYEKLKEEGIEVELIDNP 36
                                  67888899*******************965 PP

>> DUF3343  Protein of unknown function (DUF3343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   5.3e-05      0.48       9      33 ..      13      37 ..      10      39 .. 0.89
   2 ?   -2.5   0.0      0.42   3.7e+03      50      63 ..     112     125 ..     109     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 5.3e-05
                       DUF3343  9 thhAiaaekalkeggiearliplPr 33
                                    ++++a++ lke+gie++li  P+
  gi|15669561|ref|NP_248374.1| 13 KEEVLKAYEKLKEEGIEVELIDNPK 37
                                  56899****************9886 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.42
                       DUF3343  50 ieeasrllseaeip 63 
                                   ie as++l++ +i+
  gi|15669561|ref|NP_248374.1| 112 IEFASNFLKNYNIK 125
                                   67788888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1770.74
//
Query:       gi|15669562|ref|NP_248375.1|  [L=280]
Description: hypothetical protein MJ_1372 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-82  275.4   0.1    3.8e-82  275.2   0.1    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase
  ------ inclusion threshold ------
        0.2   11.9   2.3       0.69   10.2   2.3    2.0  1  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.2   0.1   4.2e-86   3.8e-82       1     224 []      55     279 ..      55     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: 275.2 bits;  conditional E-value: 4.2e-86
                                   EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHHHHHHHHH.HHHHH CS
                  Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellkeellkee.lkell 80 
                                   imDGNrR A+  g ++r +Gh  Gae+++e+l+++ +lg++vvt+YafSteNf+R+keevd+lmel+++++ +    +e++
  gi|15669562|ref|NP_248375.1|  55 IMDGNRRAAEIYG-KDRYYGHYLGAEKVREVLRWARDLGINVVTLYAFSTENFRRPKEEVDKLMELFEKKFYEIAdDEEIH 134
                                   9************.99999************************************************97777655234778 PP

                                   HTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHHCTS CS
                  Prenyltransf  81 kegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeideetlekhl 160
                                   + +vrvr+iG+++llp++v++a++ aee+tk+ nk + +nia++Yg+++ei++av+++++++++ + + e+id+e ++khl
  gi|15669562|ref|NP_248375.1| 135 RYEVRVRAIGRINLLPKNVQKAIKYAEERTKNYNK-FFVNIAIAYGGQQEIIDAVKKIAEKVKRGEIEpEDIDKELIDKHL 214
                                   88*****************************6666.**********************999987776668899******** PP

                                   TT..T.SSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                  Prenyltransf 161 ytaka.lpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                   yta+  +p+pDl+iRtsGeeR+SnFl+wq++yselyf+d +WP f++ d+l+a+++yq+r+rrfg
  gi|15669562|ref|NP_248375.1| 215 YTANLpFPNPDLIIRTSGEERISNFLIWQSSYSELYFCDIYWPLFRRVDFLRAVRDYQRRQRRFG 279
                                   **77799********************************************************98 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.3   7.7e-05      0.69      29     108 .]     144     220 ..     102     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.7e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS---- CS
                  Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllaiPNip 108
                                    ++  l ++ +++++ +ee  ++ N+   +I+ a       +e+i+ vk++ e++k+ e e +++++el ++ l   N+p
  gi|15669562|ref|NP_248375.1| 144 GRINLLPKNVQKAIKYAEERTKNYNKFFVNIAIAYG---GQQEIIDAVKKIAEKVKRGEIEPEDIDKELIDKHLYTANLP 220
                                   555566677777777788888888888888888886...5799**************************99988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2311.33
//
Query:       gi|15669563|ref|NP_248376.1|  [L=162]
Description: hypothetical protein MJ_1373 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-12   48.0   3.7      1e-12   48.0   3.7    1.8  2  PrcB_C           PrcB C-terminal
  ------ inclusion threshold ------
       0.29   11.1   1.4       0.31   11.0   0.0    1.6  2  CDP-OH_P_tran_2  CDP-alcohol phosphatidyltransferase 2


Domain annotation for each model (and alignments):
>> PrcB_C  PrcB C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       0.4   3.6e+03      13      25 ..      32      44 ..      24      53 .. 0.73
   2 !   48.0   3.7   1.1e-16     1e-12       1      57 [.      96     150 ..      96     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.4
                        PrcB_C 13 gGYsievdkvyet 25
                                  g+Y i+ +++ ++
  gi|15669563|ref|NP_248376.1| 32 GNYNIKNNSCINS 44
                                  7899999988743 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 1.1e-16
                        PrcB_C   1 lyivvgyGeqptgGYsievdkvyetenaiyvkttllgPepgeevtqaltyPyvvvki 57 
                                   ++iv+++ e+pt GY+i++ +++et n+i+v+++++   p+e++++++tyPy+ +++
  gi|15669563|ref|NP_248376.1|  96 TIIVINLEEMPTAGYKIKIINITETANKITVYYKVIP--PKEFAAMVVTYPYIKLSV 150
                                   689*******************************554..69************8876 PP

>> CDP-OH_P_tran_2  CDP-alcohol phosphatidyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.3      0.55   4.9e+03       5      12 ..       7      14 ..       5      17 .. 0.49
   2 ?   11.0   0.0   3.5e-05      0.31      13      27 ..     136     150 ..     136     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.55
               CDP-OH_P_tran_2  5 Pllllvgl 12
                                  +l+l++++
  gi|15669563|ref|NP_248376.1|  7 ILFLFTAI 14
                                  34444443 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.5e-05
               CDP-OH_P_tran_2  13 faAlLityPWltLsv 27 
                                   faA+ +tyP++ Lsv
  gi|15669563|ref|NP_248376.1| 136 FAAMVVTYPYIKLSV 150
                                   8************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1453  (0.0810419); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1100.55
//
Query:       gi|15669564|ref|NP_248377.1|  [L=266]
Description: hypothetical protein MJ_1374 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-14   54.4   0.0    1.5e-14   53.9   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.3e-05   25.2   0.0    2.3e-05   24.4   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0016   18.5   0.3     0.0051   16.8   0.3    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.061   13.6   0.1       0.11   12.8   0.1    1.3  1  FHA_2          FHA domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   3.5e-18   1.5e-14       2     201 .]      35     222 ..      34     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 3.5e-18
                                   EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC....C--EEEEEE.EEHHHHHHCCTTCGHH CS
                 Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre....lrpkklply.apkgvlavleanfvyl 77 
                                   r  +D+gp+     l  l     + ++ + +a++++h+H DH+++   + e    ++ kk  ++ ++++v +   +   y 
  gi|15669564|ref|NP_248377.1|  35 RMHVDPGPGAIVR-LNEL-----KISPWRTNALFISHCHPDHYTDGEIIVEaitqGMTKKRGVFlGSLSVVEGFGEY-EYV 108
                                   6789*****7777.3343.....23344569**************99999998663333333443777777766666.344 PP

                                   HCHTT..TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT CS
                 Lactamase_B_2  78 aleee..pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlgg 156
                                   +++ +  + ++v+ l +g+s el d   +i+at  +h+ +          +G+r+ +    + y+ Dt++ip+ i+  ++g
  gi|15669564|ref|NP_248377.1| 109 VSKYHqsKLEEVRVLYPGDSAELYD--TTIKATHTKHGDPF--------GIGFRLSTIYGDIGYTSDTEFIPQLIE-DFDG 178
                                   4444457788999999*******85..68************........9******99*************96665.**** PP

                                   -SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSS..SSEEEEESB CS
                 Lactamase_B_2 157 adllllditayeddemirhmgHltpeeaveaaadlg..akrlvliHi 201
                                   + +l+ +i + ++++     gHl  ++a+++++ ++  ++ l++ H+
  gi|15669564|ref|NP_248377.1| 179 VRILIANIVRKKNER---IKGHLCSNDAIDLINSMNkkPELLIMNHM 222
                                   *****9999888877...68***************955556666665 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   5.1e-09   2.3e-05      10     138 ..      27     188 ..      24     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.1e-09
                 Lactamase_B_3  10 flletagarilvDPf.....kanlgyeppaeeaDlvlisqaledHahletlkql........................... 58 
                                   f++ t++ r+ vDP+     +   ++++++ + +++ is+ ++dH++  ++                              
  gi|15669564|ref|NP_248377.1|  27 FRIHTNELRMHVDPGpgaivR-LNELKISPWRTNALFISHCHPDHYTDGEIIVEaitqgmtkkrgvflgslsvvegfgeye 106
                                   8999***********555541.345666667899*************9987544679************************ PP

                 Lactamase_B_3  59 ..........aenvkvleegeslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrv 129
                                              e+v+vl +g+s+e+ ++ i+a++t+h    g ++g  +gf+l+     i++  ++      + ++ +  v
  gi|15669564|ref|NP_248377.1| 107 yvvskyhqskLEEVRVLYPGDSAELYDTTIKATHTKH----GDPFG--IGFRLSTIYGDIGYTSDTEF--IPQLIEDFDGV 179
                                   *********999*************************....66666..89999999999999999887..34455778888 PP

                 Lactamase_B_3 130 DvvltPvgg 138
                                    +++++++ 
  gi|15669564|ref|NP_248377.1| 180 RILIANIVR 188
                                   888888876 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   1.1e-06    0.0051      20      67 ..      38      80 ..      38     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-06
                                  ES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH CS
                   Lactamase_B 20 iDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglvea 67
                                  +D+G ++   +       l++ p +  a++++H H+DH+ + + +vea
  gi|15669564|ref|NP_248377.1| 38 VDPGPGAIVRLNE-----LKISPWRTNALFISHCHPDHYTDGEIIVEA 80
                                  8999999999998.....7*******************9877766665 PP

>> FHA_2  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.4e-05      0.11      23      94 ..     186     264 ..     177     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                         FHA_2  23 iGRgpetkikdkkcSrnqvelkadlekk..lvkvkqlGanps..svngkklkknesvel...kegqtlelleekypytv 94 
                                   i R ++ +ik + cS + + l   ++kk  l+ + ++G++ +  +++   +++n+ +e+   + g ++ell++ky+y++
  gi|15669564|ref|NP_248377.1| 186 IVRKKNERIKGHLCSNDAIDLINSMNKKpeLLIMNHMGVKMTnpQIEAEYISQNTGIEVipaRLGLKVELLNGKYKYQL 264
                                   55999****************988877533788899**987633799999***9887753337899***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1933.96
//
Query:       gi|15669565|ref|NP_248378.1|  [L=415]
Description: SpoVB protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-59  202.1  27.2    1.1e-59  202.1  27.2    2.0  2  Polysacc_synt    Polysaccharide biosynthesis protein
    1.6e-19   70.4  38.7    4.9e-16   59.1  15.8    4.0  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    4.8e-05   23.1  18.9    4.8e-05   23.1  18.9    4.1  3  MatE             MatE


Domain annotation for each model (and alignments):
>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.1  27.2   1.8e-63   1.1e-59       1     273 [.       3     282 ..       3     283 .. 0.98
   2 ?   -3.2  15.6      0.72   4.3e+03      83     197 ..     302     413 ..     281     415 .] 0.61

  Alignments for each domain:
  == domain 1  score: 202.1 bits;  conditional E-value: 1.8e-63
                 Polysacc_synt   1 llkgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnv 81 
                                   l+k++i++l+s+l++k++a+++++++a++lg+e fG+++ +++i+ +l+i++++G++ a+ ++ a+++e   ++++++  +
  gi|15669565|ref|NP_248378.1|   3 LCKDSIYILMSNLYSKGMAYLFYFITAFLLGTEAFGILKGLMPIADTLTIFFSSGIPPAIAKFLAEEKE--VDINKYIPIL 81 
                                   69*******************************************************************..9********* PP

                 Polysacc_synt  82 llvllvlvllfllllliaaflglpelavlylilalmll..llvgvasfrrglfqglermkyaavsqvveqlsrvilvliav 160
                                   +l++l++v+ f+l+++i+++lg+++l+++++++++++l  ++ +v++f rg++qgl +mky++++++ve+++ vilv+i++
  gi|15669565|ref|NP_248378.1|  82 YLMILLSVVGFILTPYIKYILGGHYLNLPNILYFAVGLcvVASTVIAFSRGILQGLLKMKYLSLTWIVEYTAKVILVFILT 162
                                   *************************************99999*************************************** PP

                 Polysacc_synt 161 flfldivaavlgavlaalvggivslavlrkkfr..prfvils.lklvrellsfsapltisslaillytyidsi.llglllg 237
                                   ++ + i++++l+++la+lvggi++l++++k+++  ++f++l   k+++++++ +++l i +++i++  +++s+ l+g + +
  gi|15669565|ref|NP_248378.1| 163 LYLG-IFGSLLSISLAYLVGGIFGLYLIYKALKgkFDFKKLIdIKNTTKNIFSNFNLDILRYSIPIALTSSSYrLFGDIDN 242
                                   ****.***************************54699999999************************************** PP

                 Polysacc_synt 238 aea....vGiYnaayqllvaisgllapivtaalfPvfsel 273
                                    +      G+++++y ++++is+ ++++++a+ +P++ ++
  gi|15669565|ref|NP_248378.1| 243 IVImsimGGFWSGIYGYSSLISRGIFMFASAVSIPLLPRI 282
                                   ************************************9986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.72
                 Polysacc_synt  83 lvllvlvllfllllliaaflg..lpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavf 161
                                   +++ v   lf+   ++ af+   +pe  + ++ila++ l    ++s+++ +  +l+   ya +s  +   + v  +++ ++
  gi|15669565|ref|NP_248378.1| 302 SSIFVIGCLFFPEIPLIAFFKtaNPEGILCLRILAISSL----FMSYYTLISSALQGLGYAKISFYIILFGLVLNIILNLI 378
                                   233344444444344446555115555555555555555....99******************988888888877777777 PP

                 Polysacc_synt 162 lfldivaavlgavlaalvggivslavlrkkfrprfv 197
                                   l++  +++v+g ++  ++++ v+l+ ++ ++r +++
  gi|15669565|ref|NP_248378.1| 379 LVN-AYGIVGGSLATLITSISVFLIGVFAILRIKKH 413
                                   777.55555555555566666666666655555554 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   3.1      0.11   6.4e+02      82     133 ..      73     123 ..      46     130 .. 0.60
   2 !   25.1  14.9   2.4e-09   1.4e-05       7      92 ..     119     203 ..     113     266 .. 0.82
   3 ?   -0.8   0.8      0.25   1.5e+03      54      71 ..     255     274 ..     232     321 .. 0.46
   4 !   59.1  15.8   8.2e-20   4.9e-16       2      80 ..     332     410 ..     331     414 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.11
               Polysacc_synt_C  82 giklellrrllkpllaalvmgivvylllllllgllllaal..alllavlvgalv 133
                                    i+   +  l+ ++l+++v +i++ ++ ++l g+ l+  l  +l +av++++++
  gi|15669565|ref|NP_248378.1|  73 DINK-YIPILYLMILLSVVGFILTPYIKYILGGHYLN--LpnILYFAVGLCVVA 123
                                   4444.45556666777777777766566666555554..323444444444433 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 2.4e-09
               Polysacc_synt_C   7 lsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllgiklel 87 
                                   l ++ ++++ ++ +iLqgl + k++ +  ++   +k+il ++l+ ++gi G ++++ la+lv+ ++ ly++++ l+ k++ 
  gi|15669565|ref|NP_248378.1| 119 LCVVASTVIAFSRGILQGLLKMKYLSLTWIVEYTAKVILVFILTLYLGIFGSLLSISLAYLVGGIFGLYLIYKALKGKFD- 198
                                   5678889999******************************************************************9994. PP

               Polysacc_synt_C  88 lrrll 92 
                                   +++l+
  gi|15669565|ref|NP_248378.1| 199 FKKLI 203
                                   44443 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.25
               Polysacc_synt_C  54 givG..aaiatvlallvvav 71 
                                   gi+G   +i+  + ++++av
  gi|15669565|ref|NP_248378.1| 255 GIYGysSLISRGIFMFASAV 274
                                   45552222222222222222 PP

  == domain 4  score: 59.1 bits;  conditional E-value: 8.2e-20
               Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrl 80 
                                   L+ila+s +f+s++t+ ss Lqglg++ki ++++++g+++++ilnl+l+  +givG ++at+++ + v+++ ++a+ r+
  gi|15669565|ref|NP_248378.1| 332 LRILAISSLFMSYYTLISSALQGLGYAKISFYIILFGLVLNIILNLILVNAYGIVGGSLATLITSISVFLIGVFAILRI 410
                                   89***********************************************************************999885 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   8.5      0.02   1.2e+02      24     158 ..      33     157 ..      10     160 .. 0.67
   2 ?   -1.0   0.3       0.2   1.2e+03     143     161 .]     161     179 ..     152     179 .. 0.79
   3 !   23.1  18.9     8e-09   4.8e-05       1     161 []     226     378 ..     226     378 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.02
                          MatE  24 gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseqilslftqd 104
                                   g++a + +   ++i+  l++   ++s+++ + ++++l +++  ++++++  +l+l++lls++ ++l    +++i ++++ +
  gi|15669565|ref|NP_248378.1|  33 GTEAFGILKGLMPIADTLTI---FFSSGIPPAIAKFLAEEKEVDINKYIP-ILYLMILLSVVGFIL----TPYIKYILGGH 105
                                   55555555555555555544...456889999999999999888888765.455666665555555....66666666554 PP

                          MatE 105 eevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllnipl 158
                                      l+l + +  +++l+++a  +   ++gil+g  k+k      ++ +   ++l
  gi|15669565|ref|NP_248378.1| 106 Y--LNLPNILYFAVGLCVVASTVIAFSRGILQGLLKMKYLSLTWIVEYTAKVIL 157
                                   4..666666777788888888888899999999999988777777766665555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.2
                          MatE 143 vplyislislllniplnyl 161
                                   ++ly+ ++++ll i l+yl
  gi|15669565|ref|NP_248378.1| 161 LTLYLGIFGSLLSISLAYL 179
                                   5678888888888888886 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 8e-09
                          MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilll 80 
                                   Pial++  + l++ id+++++++ g    + +++++ i+  +f+f+ ++s+ l +++++    k+       l  g+i ++
  gi|15669565|ref|NP_248378.1| 226 PIALTSSSYRLFGDIDNIVIMSImGGFWSGIYGYSSLISRGIFMFASAVSIPLLPRISKT---KDL----SLLKEGIIQNT 299
                                   899999999999999999999999999999999999999999999999999999999864...343....34666777788 PP

                          MatE  81 llsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplnyl 161
                                   ++s i+++  l+f+e+ l  f ++++  + +   lril+++ +++++++++s++l+g g++k+++yi+l++l+lni+ln +
  gi|15669565|ref|NP_248378.1| 300 IFSSIFVIGCLFFPEIPLIAFFKTAN--PEGILCLRILAISSLFMSYYTLISSALQGLGYAKISFYIILFGLVLNIILNLI 378
                                   88888888778899887777766554..89999*********************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2655.56
//
Query:       gi|15669566|ref|NP_248379.1|  [L=245]
Description: cell division protein FtsJ [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-57  192.4   0.0    8.3e-57  192.1   0.0    1.1  1  FtsJ             FtsJ-like methyltransferase
    1.6e-06   28.0   0.6    2.2e-05   24.3   0.6    2.4  1  Methyltransf_31  Methyltransferase domain
    0.00019   22.1   0.1     0.0017   19.0   0.0    2.4  2  Methyltransf_25  Methyltransferase domain
     0.0002   21.3   0.0    0.00048   20.0   0.0    1.8  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.014   15.1   0.0       0.03   14.1   0.0    1.5  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.1   0.0   2.3e-60   8.3e-57       1     176 [.      26     205 ..      26     206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 192.1 bits;  conditional E-value: 2.3e-60
                                   CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHH..TTEEEECS-CCCSSHHHHH CS
                          FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmapl..pgvttiqgditdpetieki 79 
                                   yrsR+++KL++++ekf+++kpgk v+Dlg+aPGgw+qv+ + +g kg v+++Dlqp++p+  ++v  i+gd+t +e+ +ki
  gi|15669566|ref|NP_248379.1|  26 YRSRASFKLMQLNEKFNVIKPGKIVLDLGCAPGGWMQVAREIVGDKGFVIGIDLQPVKPFeyDNVVAIKGDFTLEENLNKI 106
                                   9***********************************************************999****************** PP

                                   CHCHHH..SSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCEEEEEEE CS
                          FtsJ  80 kealse..rkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfFekvsvv 158
                                   +e++ +  +kvd+v+sD +p++sg +d+d++++++L+  al++a+++lk+ g+fv+k+f g+ ++++++ +kk+Fekv+++
  gi|15669566|ref|NP_248379.1| 107 RELIPNdeKKVDVVISDASPNISGYWDIDHARSIDLVTTALQIATEMLKERGNFVAKVFYGDMIDDYVNLVKKYFEKVYIT 187
                                   *98866679************************************************************************ PP

                                   E-SS--CCG-EEEEEEEE CS
                          FtsJ 159 kPkssrsesseeflvcrg 176
                                   kP++sr+es+e+++++++
  gi|15669566|ref|NP_248379.1| 188 KPQASRKESAEVYVIAKR 205
                                   ***************997 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.6   6.2e-09   2.2e-05       2     114 ..      45     176 ..      44     238 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.2e-09
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled.........e 73 
                                   + g+ vlDlGC+ G    ++ e +g+k+ v+GiD ++             ++dnv   +gd++  e+l ++         +
  gi|15669566|ref|NP_248379.1|  45 KPGKIVLDLGCAPGGWMQVAREIVGDKGFVIGIDLQPVK---------PFEYDNVVAIKGDFTLEENL-NKirelipndeK 115
                                   56788******************************9963.........45567777777777765553.333456777779 PP

               Methyltransf_31  74 kfDlilsnevl...........naladpdkileeiervlkpggilliedpr.........l 114
                                   k+D+++s++               +     +l+ +++ lk+ g +++  +          l
  gi|15669566|ref|NP_248379.1| 116 KVDVVISDASPnisgywdidhaRSIDLVTTALQIATEMLKERGNFVAKVFYgdmiddyvnL 176
                                   ********76667777777665666677778889999999999999876664433333332 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.6e-07    0.0017       1      71 [.      50     123 ..      50     158 .. 0.73
   2 ?    1.2   0.0      0.17   6.2e+02      26      55 ..     139     169 ..     125     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.6e-07
                                   EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG.BSSSTTTEEEEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaed.lpfedgsfDlvvss 71 
                                   vLdlGc +G +++ + + +g k+ v+g+D+++    +  + ++ +g   +e    ++++ +p +++++D+v+s 
  gi|15669566|ref|NP_248379.1|  50 VLDLGCAPGGWMQVAREIVGdKGFVIGIDLQPVKPFEYDNVVAIKGDfTLEENLNKIRElIPNDEKKVDVVISD 123
                                   9**********99998888779**********998888887765543355556677777347788899999993 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.17
                                   EEESSHHHHHHHHHHHHHTTT.TEEEEESBC CS
               Methyltransf_25  26 gvDiseemleaareraeeegl.nvefvqgda 55 
                                    +D+  ++l++a e ++e+g   +++  gd+
  gi|15669566|ref|NP_248379.1| 139 SIDLVTTALQIATEMLKERGNfVAKVFYGDM 169
                                   5788888888888888776655666666666 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.3e-07   0.00048      20      87 ..      44     121 ..      14     220 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.3e-07
               Methyltransf_23  20 lraggrvLdiGcGtGillevlren.gf..svtgvDlspeaveiae...............kakkaqkdqfdeqeaae.... 78 
                                    ++g+ vLd+Gc+ G +++v+re  g    v+g+Dl p++  ++                +               +    
  gi|15669566|ref|NP_248379.1|  44 IKPGKIVLDLGCAPGGWMQVAREIvGDkgFVIGIDLQPVKPFEYDnvvaikgdftleenlN---------------Kirel 109
                                   68899****************9973434457899999887766644433333222222220...............12222 PP

               Methyltransf_23  79 ...pqgkfdlIv 87 
                                      +++k d+++
  gi|15669566|ref|NP_248379.1| 110 ipnDEKKVDVVI 121
                                   222444555555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.4e-06      0.03      48     107 ..      22      80 ..       5      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.4e-06
                                   EEEETTEEE--HHHHHHHHHHTT.--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESB CS
                          PCMT  48 lsigynatiSaphmvalalelle.lkkgarvLevGsGsGyltavlarlvgekgrvvsieri 107
                                    ++ y +  S   m  l  ++ + +k+g+ vL++G+  G    v  ++vg+kg v++i+ +
  gi|15669566|ref|NP_248379.1|  22 KKLKYRSRASFKLM-QLNEKF-NvIKPGKIVLDLGCAPGGWMQVAREIVGDKGFVIGIDLQ 80 
                                   55555555554443.233334.359*********************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1268  (0.0707234); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1593.66
//
Query:       gi|15669567|ref|NP_248380.1|  [L=553]
Description: glutamyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-86  287.9   0.4    1.1e-85  287.4   0.0    1.5  2  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    6.7e-33  114.0   0.4    1.3e-32  113.1   0.4    1.5  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo
    0.00065   18.7   0.1       0.56    9.1   0.0    2.2  2  tRNA-synt_1f    tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       0.7   4.2e+03      82     110 ..      44      72 ..      25      81 .. 0.45
   2 !  287.4   0.0   1.8e-89   1.1e-85       1     313 [.      91     393 ..      91     394 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.7
                                   HHHHHHHHHTTSEEEE-STHHHHHHHHCC CS
                  tRNA-synt_1c  82 kkyaeeLikkGkAYvcectkeeleeeree 110
                                   + ++e+++++      ++ k +lee+ e+
  gi|15669567|ref|NP_248380.1|  44 MPIVEKVVEEVNKLSLDEIKKKLEELGED 72 
                                   34444444444444444444444444443 PP

  == domain 2  score: 287.4 bits;  conditional E-value: 1.8e-89
                                   S-EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGGGHHHH CS
                  tRNA-synt_1c   1 kVrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwdekptyqsdrfdel 81 
                                   kV+ RfaP+P+G LHiGha+aa+ln +f k+++Gk+ilR+eDTdp+r  +ea + i+edl+wlg+k  ++++ qsdr + +
  gi|15669567|ref|NP_248380.1|  91 KVVMRFAPNPSGPLHIGHARAAVLNDYFVKKYGGKLILRLEDTDPKRVLPEAYDMIKEDLDWLGVKV-DEVVIQSDRIELY 170
                                   799****************************************************************.6699********* PP

                                   HHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTTSS.GGGSST CS
                  tRNA-synt_1c  82 kkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkideess.vefrDl 161
                                   ++y  +Li+ G+AYvc+c++ee +e+r++   + +k rdr +e+nl+l+ e+m +g+   e++ vRlk d +++   +rD 
  gi|15669567|ref|NP_248380.1| 171 YEYGRKLIEMGHAYVCDCNPEEFRELRNK--GVPCKCRDRAIEDNLELW-EKMLNGEL--ENVAVRLKTDIKHKnPSIRDF 246
                                   ***************************99..99999*************.99998766..56889***99998889***** PP

                                   EEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EEEEEE--EEETTS CS
                  tRNA-synt_1c 162 vrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevppfiheylrlnlekk 242
                                    + r++ +p   h+++++k+++yP  +f v++dD+l ++thvlr+++++ nt+k+  +++++g+e+p+fih y +l +e+ 
  gi|15669567|ref|NP_248380.1| 247 PIFRVEKTP---HPRTGDKYCVYPLMNFSVPVDDHLLGMTHVLRGKDHIVNTEKQAYIYKYFGWEMPEFIH-YGILKIEDI 323
                                   *********...*********************************************************99.7899***** PP

                                   B-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHHHHHHHHH CS
                  tRNA-synt_1c 243 klSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksleafdrkkLe 313
                                   +lS   +   ++e  + +wdd r+ +l++lrr+G++pe++ e+++r+++ +++ ++ ++++l a++++ ++
  gi|15669567|ref|NP_248380.1| 324 VLSTSSMYKGIKEGLYSGWDDVRLGTLRALRRRGIKPEAIYEIMKRIGIKQAD-VKFSWENLYAINKELID 393
                                   *************************************************9999.*********99998765 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1   0.4   2.2e-36   1.3e-32       1     174 []     396     539 ..     396     539 .. 0.94

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 2.2e-36
                tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelynikveevekde 81 
                                   A+R+++V++p k++ie+    ++++l++ +hp++pe g+r+++f+ e+y+  +    l+++++ rL+el+ni ve+v    
  gi|15669567|ref|NP_248380.1| 396 ARRFFFVWNPKKLIIEGA---EKKVLKLRMHPDRPEFGERELIFDGEVYVVGDE---LEENKMYRLMELFNIVVEKV---- 466
                                   89**************54...579***************************877...88899***************.... PP

                tRNA-synt_1c_C  82 sgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepalanlkkgd 161
                                    ++++   ++y++++++ ark+k+ iihW++ +++v++                ++l pd++  ++eg+ae+++a+++++d
  gi|15669567|ref|NP_248380.1| 467 -DDIAL--AKYHSDDFKIARKNKAkIIHWIPVKDSVKV----------------KVLMPDGE--IKEGFAEKDFAKVEVDD 526
                                   .35666..99****************************................*******9..59*************** PP

                tRNA-synt_1c_C 162 ivQfeRiGyfrvd 174
                                   i+QfeR+G++r+d
  gi|15669567|ref|NP_248380.1| 527 IIQFERFGFVRID 539
                                   ***********98 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   9.3e-05      0.56      21      81 ..      88     143 ..      66     173 .. 0.72
   2 !    7.4   0.1    0.0003       1.8     239     283 ..     286     326 ..     278     336 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 9.3e-05
                  tRNA-synt_1f  21 ekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvpenl 81 
                                    kd+vv+     pSG++HiG +r  +  d+ ++++       +lil  +d D+ R +pe  
  gi|15669567|ref|NP_248380.1|  88 VKDKVVMRFAPNPSGPLHIGHARAAVLNDYFVKKY-----GGKLILRLEDTDPKRVLPEAY 143
                                   478999999999**********9776666665554.....357888888888888888754 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0003
                  tRNA-synt_1f 239 paGkDhaaaGgSvdvsskiaeilggeaPekvvYelillkggekms 283
                                     GkDh+    +++ ++ i + +g+e Pe + Y ++ ++    +s
  gi|15669567|ref|NP_248380.1| 286 LRGKDHIV---NTEKQAYIYKYFGWEMPEFIHYGILKIEDI-VLS 326
                                   67******...***********************9999876.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3650.09
//
Query:       gi|15669568|ref|NP_248381.1|  [L=482]
Description: carbamoyl-phosphate synthase subunit CarB1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-77  259.6   0.2    2.6e-77  259.1   0.2    1.2  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    3.9e-17   62.7   0.9    1.6e-16   60.8   0.9    2.0  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    2.6e-08   33.7   0.1    8.3e-08   32.0   0.1    1.7  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    5.5e-06   26.2   0.0    1.1e-05   25.1   0.0    1.4  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    7.2e-05   22.4   0.1    0.00016   21.3   0.1    1.6  1  ATP-grasp        ATP-grasp domain
    0.00012   22.2   0.3    0.00025   21.1   0.3    1.6  1  ATP-grasp_3      ATP-grasp domain
     0.0048   16.7   0.1      0.012   15.4   0.1    1.7  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
  ------ inclusion threshold ------
      0.022   14.6   0.0        2.4    8.1   0.0    2.8  2  DUF433           Protein of unknown function (DUF433)
      0.027   13.9   0.1       0.19   11.1   0.1    2.2  2  ATP-grasp_5      ATP-grasp domain
      0.059   12.8   0.0       0.11   12.0   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.1   0.2   1.4e-80   2.6e-77       1     210 [.     125     330 ..     125     331 .. 0.99

  Alignments for each domain:
  == domain 1  score: 259.1 bits;  conditional E-value: 1.4e-80
                                   SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS CS
                   CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnk 81 
                                   D+e ++ea+++in+pv + +a+  ++++ea+++a+eigyPvi+++af+lGG+G+++a+n+eel+++++k+l+ +      +
  gi|15669568|ref|NP_248381.1| 125 DRELFAEAMAEINEPVTKCKAV--NSVDEAVEFAEEIGYPVIVRPAFTLGGTGGGIAHNKEELIDITSKGLKYSI----IN 199
                                   9*******************99..**************************************************6....9* PP

                                   -EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEE CS
                   CPSase_L_D2  82 qvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtv 160
                                   qvl+++s+ g+ke E+ev+rD+k+++i+vc +en++++  +t+++i+v P qtL de +q+lr+aa+k++r++g++g++++
  gi|15669568|ref|NP_248381.1| 200 QVLIDESVLGWKEFELEVMRDRKDTCIIVCGMENIDPMgiHTGESIVVSPIQTLPDEFYQKLRNAAIKIIRHLGIEGGCNI 280
                                   ********************************************************************************* PP

                                   EEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                   CPSase_L_D2 161 eflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                   +f+++++ +ey viEvN+R+s++sala+kaTG++++ +aakia g++L+e
  gi|15669568|ref|NP_248381.1| 281 QFAVNKEMTEYRVIEVNPRVSRSSALASKATGYPIARIAAKIAIGKTLDE 330
                                   ************************************************97 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.9   8.9e-20   1.6e-16       3      58 ..     422     477 ..     420     481 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 8.9e-20
                   CPSase_L_D3   3 lkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkkel 58 
                                   lk+ptdeRif+ia+al++g+sve+i elt+id++F++k++++v+++kel+k k+e+
  gi|15669568|ref|NP_248381.1| 422 LKNPTDERIFVIAKALEKGWSVEKIVELTDIDEFFIKKIKNIVDMKKELEKLKEEI 477
                                   89************************************************998755 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.1   4.6e-11   8.3e-08      26     174 ..     150     298 ..     137     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 4.6e-11
                                   HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-..SCEEEEE--.ESEEEEEEEEETSSCEEEEEEE CS
               Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd..ekvlvEeai.egreievavlgneklevsevge 103
                                   +   +  ee+gypv+V+pa +    G   ++++eel +  ++ +ky   ++vl++e +   +e+e  v+ + k ++  v  
  gi|15669568|ref|NP_248381.1| 150 DEAVEFAEEIGYPVIVRPAFTLGGTGGGIAHNKEELIDITSKGLKYSiiNQVLIDESVlGWKEFELEVMRDRKDTCIIVC- 229
                                   344567899**********98888888999***************97668****9999899*********6665544332. PP

                                   EE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEE.ETTTEEEEEEEES CS
               Dala_Dala_lig_C 104 ivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDffl.teegeivlnEvNt 174
                                        + +d    ++++++ +    +l++e ++k++++a+k+ + l+++G + + f + +e  e  + EvN+
  gi|15669568|ref|NP_248381.1| 230 ---GMENIDPMGIHTGESIVVSPIQTLPDEFYQKLRNAAIKIIRHLGIEGGCNIQFAVnKEMTEYRVIEVNP 298
                                   ...333344444456666666666789*******************************66667888999996 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   6.4e-09   1.1e-05      47     116 ..     259     331 ..     249     346 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 6.4e-09
                  ATPgrasp_Ter  47 eelielaerlaeefgldglvnvQvrededg..pkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteev 116
                                   ++l ++a ++++++g++g  n+Q+  +++   ++++E+NpR+s      s ++G  ++++a+k + g+  +e+
  gi|15669568|ref|NP_248381.1| 259 QKLRNAAIKIIRHLGIEGGCNIQFAVNKEMteYRVIEVNPRVSRSSAlASKATGYPIARIAAKIAIGKTLDEI 331
                                   678899******************988876579*********96555156777************99744443 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1     9e-08   0.00016       5     161 ..     137     301 ..     133     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9e-08
                                   T--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEEEEE CS
                     ATP-grasp   5 glpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekElsvl 81 
                                   + pv++  av+s +e+ e+aee+g+pv+v+ +     G G  + +++e+l ++++        ++v++ e v   kE  + 
  gi|15669568|ref|NP_248381.1| 137 NEPVTKCKAVNSVDEAVEFAEEIGYPVIVR-PAFTLGGTGGGIAHNKEELIDITSKGlkysIINQVLIDESVLGWKEFELE 216
                                   668899999*********************.999************99987776655566677889999888888888888 PP

                                   EEEETTC-EEE--EEEEEEETTEEE...EEEECEE.-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCT.EEEEEEE CS
                     ATP-grasp  82 vvrsaeGetafypvvetvqedgilr...lsvapae.vsekaqkkaeeiakkiveeLggvGvfavElFvledge.llvnEla 157
                                   v+r+++ +  ++  +e++   gi     ++v p + ++++  +k ++ a ki+++Lg+ G   + + v ++ +   v E+ 
  gi|15669568|ref|NP_248381.1| 217 VMRDRKDTCIIVCGMENIDPMGIHTgesIVVSPIQtLPDEFYQKLRNAAIKIIRHLGIEGGCNIQFAVNKEMTeYRVIEVN 297
                                   8999998889999999999999974333678886625677899999999***************99998666678999999 PP

                                   SS-- CS
                     ATP-grasp 158 pRpH 161
                                   pR+ 
  gi|15669568|ref|NP_248381.1| 298 PRVS 301
                                   9985 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   1.4e-07   0.00025      27     158 ..     156     300 ..     123     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.4e-07
                                   SS--SSSEEEEESS-------B--SS--TTE................EEEE---S.EEEEEEEEE.SSSEEEEEEEEEEEE CS
                   ATP-grasp_3  27 leeeekklvvKprdGaggesvrvveekeeaeaaieeve.........lvqefieG.kplSvsllsdgekvlvlavnrqlie 97 
                                   +ee  ++++v p+   gg++  ++++kee+  +  +           l+ e + G k++ ++++ d ++  ++++  + i+
  gi|15669568|ref|NP_248381.1| 156 AEEIGYPVIVRPAFTLGGTGGGIAHNKEELIDITSK-GlkysiinqvLIDESVLGwKEFELEVMRDRKDTCIIVCGMENID 235
                                   455699********************9887654443.3468887787777777776899*********************9 PP

                                   T....TEEEEE...EES----H...HHHHHHHHHHHHTTSTT--EEEEEEEEESS...SEEEEEEESS- CS
                   ATP-grasp_3  98 kaekefvyaGn...vtpietel...keevvelaeevvekleglaGyvGvDlvlkd..eepyviEvNPRl 158
                                     +   + +G+   v+pi+t      ++++++a +++++l g+ G   + + +++   e  viEvNPR+
  gi|15669568|ref|NP_248381.1| 236 PMG---IHTGEsivVSPIQTLPdefYQKLRNAAIKIIRHL-GIEGGCNIQFAVNKemTEYRVIEVNPRV 300
                                   754...455552225777765533478999999999****.**********9999888999*******8 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   6.7e-06     0.012       8     147 ..     131     262 ..     125     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.7e-06
                                   HHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE- CS
                        GARS_A   8 dllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEel 88 
                                   + +++++ p ++ +a+++++ea e+ ee + ++ +v+++   +g g  +a+++ee +++ ++ l+   + +  ++v+i+e 
  gi|15669568|ref|NP_248381.1| 131 EAMAEINEPVTKCKAVNSVDEAVEFAEEIGYPV-IVRPAFTLGGTGGGIAHNKEELIDITSKGLK---Y-SIINQVLIDES 206
                                   5688999999***********************.8999988999*************99999997...3.35679999887 PP

                                   --S.EEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEES-TTS-HHHHHHHH CS
                        GARS_A  89 leG.eEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGayspapvvteellekik 147
                                   + G +E+ l ++ d k++  +    +         g  TG   ++sp+ ++++e ++k +
  gi|15669568|ref|NP_248381.1| 207 VLGwKEFELEVMRDRKDTCIIVCGMENI----DPMGIHTGESIVVSPIQTLPDEFYQKLR 262
                                   777589******9999877666544321....1245566666666666666666665555 PP

>> DUF433  Protein of unknown function (DUF433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0013       2.4      16      41 ..     310     335 ..     294     349 .. 0.83
   2 ?    3.4   0.0     0.038        68      23      39 ..     432     448 ..     429     459 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                                   TT--BTHHHHHHHHTT--HHHHHHHH CS
                        DUF433  16 gtRipVetilellaaGesieeiledy 41 
                                    t +p+++i++ +a G++ +eil d 
  gi|15669568|ref|NP_248381.1| 310 ATGYPIARIAAKIAIGKTLDEILNDV 335
                                   6999*******************986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.038
                                   HHHHHHHTT--HHHHHH CS
                        DUF433  23 tilellaaGesieeile 39 
                                   +i+  l++G+s+e i+e
  gi|15669568|ref|NP_248381.1| 432 VIAKALEKGWSVEKIVE 448
                                   58999**********98 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.085   1.5e+02      12      49 ..      98     140 ..      90     141 .. 0.83
   2 ?   11.1   0.1   0.00011      0.19      20      52 ..     134     166 ..     127     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.085
                   ATP-grasp_5  12 eaeakelleaygipvvetrl.....assaeeaveaaeeigypv 49 
                                   e   + +l+ ygi+++ + +     a++ e  +ea++ei+ pv
  gi|15669568|ref|NP_248381.1|  98 ELHRRGILDKYGIKLLGSNIrtieiAEDRELFAEAMAEINEPV 140
                                   6677899*******99988877787999999999999999998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00011
                   ATP-grasp_5  20 eaygipvvetrlassaeeaveaaeeigypvvlK 52 
                                   + ++ pv++ + ++s++eave aeeigypv ++
  gi|15669568|ref|NP_248381.1| 134 AEINEPVTKCKAVNSVDEAVEFAEEIGYPVIVR 166
                                   566668999999******************875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     6e-05      0.11       9      73 ..      25      88 ..      22     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6e-05
                                  HHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.EEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                     Epimerase  9 fiGsalvkallekgyevigldrlssasntarledl.elveldltdrsalerlfkeeqpdavihlAa 73
                                  f Gs+ +kal+e+g+  i +++++ + +t  +    + v+l+ ++++ +e+++++e+pda++   +
  gi|15669568|ref|NP_248381.1| 25 FSGSQACKALKEEGIYTILVNSNPATIQTDTD--MaDKVYLEPLHPTIVEKIIEKERPDAILPTMG 88
                                  67************555555555444444432..24889**********************98744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1165  (0.0649785); expected 358.6 (0.02)
Passed bias filter:                      801  (0.0446762); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 3080.08
//
Query:       gi|15669569|ref|NP_248382.1|  [L=100]
Description: hypothetical protein MJ_1379 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-25   86.7   1.7    1.1e-24   86.5   1.7    1.1  1  NTP_transf_2    Nucleotidyltransferase domain
    6.1e-17   61.5   2.9    8.4e-17   61.0   2.9    1.3  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0015   18.8   0.2     0.0024   18.1   0.2    1.5  1  SMODS           Second Messenger Oligonucleotide or Dinucleot
     0.0031   17.7   0.0     0.0035   17.5   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.012   15.6   0.0    1.1  1  Adenyl_cycl_N   Adenylate cyclase NT domain
      0.045   13.6   0.9       0.05   13.4   0.9    1.1  1  DUF4422         Domain of unknown function (DUF4422)
      0.073   12.9   0.0      0.081   12.7   0.0    1.2  1  DUF294          Putative nucleotidyltransferase DUF294


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   1.7   4.3e-28   1.1e-24       1      94 [.      11      99 ..      11     100 .] 0.96

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 4.3e-28
                                  HHHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCT CS
                  NTP_transf_2  1 lkklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpl 83
                                  l+k++++lk++++v++++lfGSyarG+ +++SDiD+ v ++e+ +      +  ++ e i+ le++lgl+vdl+t++++++p+
  gi|15669569|ref|NP_248382.1| 11 LRKHKKILKDKYKVKSIALFGSYARGEQTEESDIDIMVEFDENNY-----PSFSEYLELIEYLEKILGLKVDLITKKSIHNPY 88
                                  689****************************************55.....999****************************** PP

                                  EEEEEECEEEH CS
                  NTP_transf_2 84 lvksileerpl 94
                                  ++ksi+e+ ++
  gi|15669569|ref|NP_248382.1| 89 VKKSIEEDLIY 99
                                  *******9987 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   2.9   3.3e-20   8.4e-17       4      82 ..      15      95 ..       5     100 .] 0.88

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 3.3e-20
                                  TTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS-..--HHHHHHHHHHHHHH.SSSEEEEEETT.TS-HHHHHHHHH CS
                       Polbeta  4 keilekekeielaylFGSrakgkareeSDiDlavllkek..ldleeelelaaelediklgkkvDlvdln.eapplllyeilk 82
                                  k+il+++ +++ + lFGS+a+g+++eeSDiD++v ++e+   +++e+lel + le+i lg kvDl++ +   +p+++++i +
  gi|15669569|ref|NP_248382.1| 15 KKILKDKYKVKSIALFGSYARGEQTEESDIDIMVEFDENnyPSFSEYLELIEYLEKI-LGLKVDLITKKsIHNPYVKKSIEE 95
                                  67777778*************************************************.9********987777888888755 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   9.3e-07    0.0024      28      96 ..       4      65 ..       1      94 [. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 9.3e-07
                         SMODS 28 vkaitkrLnkdfrelks..kiaesllvGSyardTaikpvsdkdmlfeldvdllvvvnevegdepsdllekl 96
                                   ++i++ L+k+++ lk+  k+++  l+GSyar+      +++    e+d+d++v+++e++  + s++le +
  gi|15669569|ref|NP_248382.1|  4 LSEIKEILRKHKKILKDkyKVKSIALFGSYARG-----EQTE----ESDIDIMVEFDENNYPSFSEYLELI 65
                                  5789999999998887755778999******96.....3344....8999999999998888888888755 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.4e-06    0.0035       9      55 ..       6      56 ..       2      95 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-06
                                  HHHHHHHHHHHHH-TT-E...EEE-HHHHTT-SE.ESSEEEEEEBTTBSTT CS
                DNA_pol_B_palm  9 alealvkkaakeldpeve...vivcGSYRRgaes.sGDvDvlitkkdakse 55
                                  +++++++k+ k l+++++   +   GSY Rg+++   D+D+++  ++ +  
  gi|15669569|ref|NP_248382.1|  6 EIKEILRKHKKILKDKYKvksIALFGSYARGEQTeESDIDIMVEFDENNYP 56
                                  5667777777777777651115689*****9875268******98877763 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   4.5e-06     0.012      79     128 ..      12      56 ..       1      96 [. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.5e-06
                 Adenyl_cycl_N  79 eekekkekakeaaieglylmGStgsiaqsekSDlDiWvchrselsaeele 128
                                   ++++k   +++++++++ l GS +   q+e+SD+Di v  +    ++++ 
  gi|15669569|ref|NP_248382.1|  12 RKHKK-ILKDKYKVKSIALFGSYARGEQTEESDIDIMVEFD----ENNYP 56 
                                   22222.233689************************88544....44444 PP

>> DUF4422  Domain of unknown function (DUF4422)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9     2e-05      0.05     105     186 ..       5      89 ..       1      93 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                       DUF4422 105 eeiekllkkydiilpkkrklkieslyeqYkka..hhiedldllreiikekypeyleafekvlkkkslylfNm.fimkkelf 182
                                   +ei+++l+k++ il +k k+k   l  +Y++   ++++d+d++ e  +++yp++ e++e +   +++  + + +i+kk++ 
  gi|15669569|ref|NP_248382.1|   5 SEIKEILRKHKKILKDKYKVKSIALFGSYARGeqTEESDIDIMVEFDENNYPSFSEYLELIEYLEKILGLKVdLITKKSIH 85 
                                   789*****************999******987557799******************9998887777655544378888888 PP

                       DUF4422 183 deYc 186
                                   + Y+
  gi|15669569|ref|NP_248382.1|  86 NPYV 89 
                                   8886 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.2e-05     0.081      52      77 ..      27      52 ..       5      73 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                        DUF294 52 llvmGSeGReEqtlktDqDnalvled 77
                                     +GS +R+Eqt ++D D    +++
  gi|15669569|ref|NP_248382.1| 27 IALFGSYARGEQTEESDIDIMVEFDE 52
                                  5679**************98766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 732.32
//
Query:       gi|15669570|ref|NP_248383.1|  [L=78]
Description: hypothetical protein MJ_1380 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-14   52.1   0.2    6.4e-14   51.8   0.2    1.1  1  DUF86     Protein of unknown function DUF86


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.2   3.6e-18   6.4e-14       1      88 [.      13      78 .]      13      78 .] 0.98

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 3.6e-18
                                  HHHHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHHHHHHTTSS-HHHHHHHHHHH CS
                         DUF86  1 ikealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdyifeilaekgviaeepeepwrkmi 83
                                  i+e+++++ eft+++d++ef+++++ ++av+r+l++igEa   i ++                      ++++ p++pw++m+
  gi|15669570|ref|NP_248383.1| 13 ILESANDVIEFTKDIDYNEFINNKMIRYAVIRALEIIGEASRYINND----------------------FREKFPNVPWKEMV 73
                                  689999*****************************************......................************** PP

                                  CCHHH CS
                         DUF86 84 glRNr 88
                                  glRN+
  gi|15669570|ref|NP_248383.1| 74 GLRNI 78
                                  ****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 528.02
//
Query:       gi|15669571|ref|NP_248384.1|  [L=618]
Description: carbamoyl-phosphate synthase subunit CarB2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-40  138.3   0.1    3.8e-40  137.7   0.1    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    2.9e-26   91.5   0.7    1.3e-24   86.2   0.1    3.4  4  MGS              MGS-like domain
    2.3e-24   86.1   0.2      8e-24   84.3   0.1    2.0  2  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
      7e-10   38.7   0.1    1.4e-09   37.8   0.1    1.4  1  ATP-grasp        ATP-grasp domain
    2.3e-09   37.1   0.0    8.8e-09   35.2   0.0    2.0  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    4.7e-09   36.1   0.1    8.9e-09   35.2   0.1    1.4  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    9.5e-08   32.2   0.1    2.2e-07   31.0   0.1    1.6  1  ATP-grasp_3      ATP-grasp domain
    2.5e-06   27.4   0.2    8.6e-06   25.7   0.2    1.9  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
     0.0025   17.3   0.1     0.0082   15.6   0.0    1.8  2  ATP-grasp_5      ATP-grasp domain
  ------ inclusion threshold ------
      0.039   13.5   0.0       0.13   11.8   0.0    1.9  1  ATP-grasp_2      ATP-grasp domain
      0.073   12.5   0.0       0.16   11.4   0.0    1.6  1  GSH-S_ATP        Prokaryotic glutathione synthetase, ATP-gras


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   0.1   2.3e-43   3.8e-40       1     210 [.     203     405 ..     203     406 .. 0.95

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 2.3e-43
                                   SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS CS
                   CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnk 81 
                                   D+e+++++lkk+n+p +++ +a   t eeal+iak+igyPv++++++ lGG+ m+++++e+el+e +++a++ ++    ++
  gi|15669571|ref|NP_248384.1| 203 DREEFSKLLKKLNIPQAEGGTA--YTKEEALEIAKRIGYPVLVRPSYVLGGRAMQIVYSEDELIEYMEEAVKVSE----EH 277
                                   9*******************99..9*************************************************6....9* PP

                                   -EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEE CS
                   CPSase_L_D2  82 qvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtv 160
                                    vl++k+l+   e++v+ + D +   i  + +e + +   + +++ +v P qtL +e  +++   ++k++r++++vg  +v
  gi|15669571|ref|NP_248384.1| 278 PVLIDKFLEDAIELDVDAVCDGESVLI-GAIMEHIEEAgvHSGDSATVIPPQTLPKEIIDTVIDYTAKLARALNIVGLLNV 357
                                   *********************876555.456788877778***************************************** PP

                                   EEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                   CPSase_L_D2 161 eflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                   +++++  ++  yv+E N+R s+  +  +k  G++l+k a ki lg+kLee
  gi|15669571|ref|NP_248384.1| 358 QYAVK--DGVVYVLEANPRASRTVPYVSKSVGIPLAKLATKIMLGKKLEE 405
                                   ****9..5****************************************97 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.89   1.5e+03      51      72 ..     109     130 ..      79     141 .. 0.76
   2 ?    0.9   0.0      0.33   5.4e+02       3      19 ..     177     193 ..     175     219 .. 0.90
   3 ?   -3.6   0.0         8   1.3e+04      79      91 ..     400     412 ..     391     415 .. 0.78
   4 !   86.2   0.1   7.9e-28   1.3e-24       2      95 .]     496     582 ..     495     582 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.89
                                   HHHHHHHTTSCCEEEEE--THH CS
                           MGS  51 eildaikngeidlvintlypfk 72 
                                   + + a+k+ +i+++i++ +p++
  gi|15669571|ref|NP_248384.1| 109 HAVLALKEMGIEAIIINNNPET 130
                                   5667899999998888877765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.33
                                   HHHHHHHHHTTCEEEEE CS
                           MGS   3 velakklkelgfellAT 19 
                                   ++la klk++g+++l T
  gi|15669571|ref|NP_248384.1| 177 INLAMKLKNAGVNILGT 193
                                   78999*********998 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 8
                                   HHHHHHHHHHTTS CS
                           MGS  79 gykirraaenidI 91 
                                   g+k+++++ ++d+
  gi|15669571|ref|NP_248384.1| 400 GKKLEELIKDYDV 412
                                   7889999999988 PP

  == domain 4  score: 86.2 bits;  conditional E-value: 7.9e-28
                                   HHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHHCHHHHH CS
                           MGS   2 lvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatvakdgyki 82 
                                   +v++akkl+elgf+++AT+GTak+l+e+gip++ v ++ +++ + +    il+++++g+++l+int +++ka+   dgy i
  gi|15669571|ref|NP_248384.1| 496 IVDVAKKLHELGFTIYATEGTAKVLRENGIPAILVKKISESP-NDN----ILKLMRDGKMHLIINTSSGKKAKS--DGYYI 569
                                   89*****************************66555555555.555....*********************997..9**** PP

                                   HHHHHHTTSHEES CS
                           MGS  83 rraaenidIplpt 95 
                                   rraa++ +Ip++t
  gi|15669571|ref|NP_248384.1| 570 RRAAVDLGIPYIT 582
                                   ***********98 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.1   4.9e-27     8e-24      60     122 .]       7      68 ..       2      68 .. 0.94
   2 ?   -3.5   0.0       7.8   1.3e+04      57      71 ..     225     239 ..     207     240 .. 0.73

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 4.9e-27
                   CPSase_L_D3  60 eellreakklGfsDkqiaelleeeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                   +e+l +akklGfsDkqia+ll+  +e evr+lrkkl+i p yk+vDtcAaeFea+tpY+Ys+Y
  gi|15669571|ref|NP_248384.1|   7 KEILLKAKKLGFSDKQIANLLG-MDEIEVRDLRKKLNIIPLYKMVDTCAAEFEAKTPYYYSAY 68 
                                   689*****************87.78889**********************************9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.8
                   CPSase_L_D3  57 eldeellreakklGf 71 
                                    ++ee+l+ ak+ G+
  gi|15669571|ref|NP_248384.1| 225 YTKEEALEIAKRIGY 239
                                   457889999999998 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.1   8.6e-13   1.4e-09       2     160 ..     212     375 ..     211     379 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 8.6e-13
                                   HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEE CS
                     ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekEl 78 
                                   +kl++p ++  ++ +kee+ e+a+++g+pv+v+ +     G+  ++v se++l + +e++    +e++v++ +f +   El
  gi|15669571|ref|NP_248384.1| 212 KKLNIPQAEGGTAYTKEEALEIAKRIGYPVLVR-PSYVLGGRAMQIVYSEDELIEYMEEAvkvsEEHPVLIDKFLEDAIEL 291
                                   788899999999999******************.99999***********999888888778879**************** PP

                                   EEEEEEETTC-EEE--EEEEEEETTE....EEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEE CS
                     ATP-grasp  79 svlvvrsaeGetafypvvetvqedgi....lrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnE 155
                                    v +v + e  + + +++e+++e g+      +++ p+++++++  ++ ++++k++++L++vG++ v   v+ dg ++v E
  gi|15669571|ref|NP_248384.1| 292 DVDAVCDGES-VLIGAIMEHIEEAGVhsgdSATVIPPQTLPKEIIDTVIDYTAKLARALNIVGLLNVQYAVK-DGVVYVLE 370
                                   **99988776.7788888898876651111679999*******************************98877.999***** PP

                                   EESS- CS
                     ATP-grasp 156 lapRp 160
                                     pR 
  gi|15669571|ref|NP_248384.1| 371 ANPRA 375
                                   **996 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   5.4e-12   8.8e-09      47     126 ..     336     413 ..     275     419 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 5.4e-12
                  ATPgrasp_Ter  47 eelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgysala.Gvnlpylalklllgleteeveepeeglrvr 126
                                   + +i+++++la+++++ gl nvQ+  +++  ++LE NpRas ++ y   + G+ l++la k +lg+   + ee  ++++v+
  gi|15669571|ref|NP_248384.1| 336 DTVIDYTAKLARALNIVGLLNVQYAVKDGVVYVLEANPRASRTVPYVSKSvGIPLAKLATKIMLGK---KLEELIKDYDVE 413
                                   6899****************************************9877666**************5...444555555555 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   5.5e-12   8.9e-09      24     174 ..     226     373 ..     213     398 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 5.5e-12
                                   H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-SC..EEEEE--.ESEEEEE.EEEETSSCEEEE CS
               Dala_Dala_lig_C  24 kkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkydek..vlvEeai.egreiev.avlgneklevse 100
                                   +ke   ++ +++gypv+V+p+       ++ v se+el e++eea+k  e+  vl+++++ ++ e++v av + e++ +  
  gi|15669571|ref|NP_248384.1| 226 TKEEALEIAKRIGYPVLVRPSYVLGGRAMQIVYSEDELIEYMEEAVKVSEEhpVLIDKFLeDAIELDVdAVCDGESVLIGA 306
                                   456678999************9888889*****************99765444*******99******7788889999999 PP

                                   EEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
               Dala_Dala_lig_C 101 vgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                   + e++ + g+       s+d+a++  p +l+ke+ +++ ++  k  +al++ Gl  v + ++ +g +++ E N+
  gi|15669571|ref|NP_248384.1| 307 IMEHIEEAGVH------SGDSATVIPPQTLPKEIIDTVIDYTAKLARALNIVGLLNVQYAVK-DGVVYVLEANP 373
                                   ****9999985......689999************************************998.9*********7 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1   1.4e-10   2.2e-07       3     158 ..     203     375 ..     201     378 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.4e-10
                                   SHHHHHHHHTTT.S---.........-EESS--....SSSEEEEESS-------B--SS--TTE...............EE CS
                   ATP-grasp_3   3 dKlktykkLkeagvkvP.....tkleaeeleee....ekklvvKprdGaggesvrvveekeeaeaaieeve........lv 66 
                                   d  ++ k Lk+   ++P     t +++ee+ e      +++ v p++  gg ++ +v  ++e+ + +ee          l+
  gi|15669571|ref|NP_248384.1| 203 DREEFSKLLKKL--NIPqaeggTAYTKEEALEIakriGYPVLVRPSYVLGGRAMQIVYSEDELIEYMEEAVkvseehpvLI 281
                                   556666777777..88888999566665555554555999**********************999999988999******* PP

                                   EE---.SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H..HHHHHHHHHHHHTTST...T--EEEEEE CS
                   ATP-grasp_3  67 qefie.GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietel..keevvelaeevvekle...glaGyvGvD 141
                                    +f+e   +l v++++dge vl+ a+ + + e      v +G ++ +   +   +e+++++ + ++kl    +++G++ v 
  gi|15669571|ref|NP_248384.1| 282 DKFLEdAIELDVDAVCDGESVLIGAIMEHIEEA----GVHSGDSATVIPPQtlPKEIIDTVIDYTAKLAralNIVGLLNVQ 358
                                   ****9468**********999998888776655....888888776654333499999999999999987779999999** PP

                                   EEESS.SEEEEEEESS- CS
                   ATP-grasp_3 142 lvlkdeepyviEvNPRl 158
                                     +kd+  yv+E NPR 
  gi|15669571|ref|NP_248384.1| 359 YAVKDGVVYVLEANPRA 375
                                   ****************6 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.2   5.3e-09   8.6e-06       8     108 ..     209     305 ..     204     377 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 5.3e-09
                                   HHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE- CS
                        GARS_A   8 dllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEel 88 
                                   +llkk +ip ae  +    eea e+ ++ + ++  v+++ + +g+ + ++ se+e +++++e ++     + ++ v+i+++
  gi|15669571|ref|NP_248384.1| 209 KLLKKLNIPQAEGGTAYTKEEALEIAKRIGYPV-LVRPSYVLGGRAMQIVYSEDELIEYMEEAVK----VSEEHPVLIDKF 284
                                   599******************************.9****************************98....34689******* PP

                                   --.SEEEEEEEEECTTEEEE- CS
                        GARS_A  89 le.GeEvsllalvdgktvkpl 108
                                   le  +E+ + a++dg++v   
  gi|15669571|ref|NP_248384.1| 285 LEdAIELDVDAVCDGESVLIG 305
                                   *8368***********98653 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.8   4.5e+03      81     104 ..     148     171 ..     147     181 .. 0.80
   2 !   15.6   0.0   5.1e-06    0.0082      13      51 ..     205     243 ..     198     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.8
                   ATP-grasp_5  81 aeeilervkekspeariegvlVqe 104
                                   +ee+l+ +++++++ ++ gv+Vq 
  gi|15669571|ref|NP_248384.1| 148 FEEVLNIAEREKEKGELLGVIVQF 171
                                   577788888888899999999995 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.1e-06
                   ATP-grasp_5  13 aeakelleaygipvvetrlassaeeaveaaeeigypvvl 51 
                                   +e  +ll+ ++ip +e   a ++eea+e+a++igypv +
  gi|15669571|ref|NP_248384.1| 205 EEFSKLLKKLNIPQAEGGTAYTKEEALEIAKRIGYPVLV 243
                                   68899*******************************976 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.1e-05      0.13       9      72 ..     209     267 ..     205     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.1e-05
                                   HHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHH CS
                   ATP-grasp_2   9 eilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaa 72 
                                   ++l+k +++ +eg  a ++eea e+ak++g  +  v+     GGR     +++v+s++e+ e++
  gi|15669571|ref|NP_248384.1| 209 KLLKKLNIPQAEGGTAYTKEEALEIAKRIGYPV-LVRPSYVLGGRA----MQIVYSEDELIEYM 267
                                   79*****************************99.677777789985....55666666665555 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.6e-05      0.16      26      95 ..     232     301 ..     211     357 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.6e-05
                                   HHHHHHSS.EEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTTTS-EEEEE--GGGGG-EEEEEEETTEE CS
                     GSH-S_ATP  26 afleeqgd.vilKPldgkgGegvfrvkksdpnlksilellteegkepviaqrylpeikeGDkRillvdGep 95 
                                   +++++ g  v+++P +  gG+++  v ++d+ ++ + e++  ++++pv++ ++l+++ e D+   + dGe 
  gi|15669571|ref|NP_248384.1| 232 EIAKRIGYpVLVRPSYVLGGRAMQIVYSEDELIEYMEEAVKVSEEHPVLIDKFLEDAIELDVDA-VCDGES 301
                                   455555554999*********************************************9998865.356665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 4087.47
//
Query:       gi|15669572|ref|NP_248385.1|  [L=146]
Description: hypothetical protein MJ_1382 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-28   97.4   1.7    8.1e-28   97.3   1.7    1.0  1  EVE             EVE domain
    0.00079   19.3   0.0     0.0012   18.7   0.0    1.3  1  Dev_Cell_Death  Development and cell death domain


Domain annotation for each model (and alignments):
>> EVE  EVE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   1.7     9e-32   8.1e-28       1     144 [.       2     143 ..       2     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 9e-32
                                   -EEEEEEBHHTSHHHHHCHHHCEEE-EE-GHHHHHHHCC--TT-EEEEE...ETSSS..S-EEEEEEEEECEEEE-GGGG- CS
                           EVE   1 ayWllksepdefsiddlkrkkeegWdgvrnyqarnllramkkGDlvlfY...hsgek..lqaivgiaeVvseaypdetqfd 76 
                                   ayWl+++++d  +++ +  k +++W gv + +++n++ ++k+GD++++Y    sg++  ++ i g++eVvse+y+d++++ 
  gi|15669572|ref|NP_248385.1|   2 AYWLCITNED--NWKVI--KDKKIW-GVAE-RHKNTINKVKVGDKLIIYeiqRSGKDykPPYIRGVYEVVSEVYKDSSKI- 75 
                                   6*********..*****..99****.**99.9*******************97777788******************999. PP

                                   TTSTT--TTTBTTS-.-EEEEEEEEEEEEEEEEHHHHTTHG.TCTTSHHHHCC..T-SEEEE-HHHHHHHHH CS
                           EVE  77 pkskyydpkskkekp.wlrvdvkpvkklkrplslkelkaep.elegmkllrkg..rlsvrpvteedwelile 144
                                       ++   ++++++ ++rv++k vk + +p+++k+l ++  +++++k ++ +    ++r+++eed++li+e
  gi|15669572|ref|NP_248385.1|  76 ----FKPTPRNPNEKfPYRVKLKEVKVFVPPINFKDLIPKLkFITNKKKWSGHlmGKAMREIPEEDYKLIIE 143
                                   ....445566677778*********************995348899999999988999************98 PP

>> Dev_Cell_Death  Development and cell death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.4e-07    0.0012       8      99 ..       9     108 ..       4     134 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-07
                Dev_Cell_Death   8 nketkkecfrkklfglpaeklslvkkikpglkLfLfdyder.......kLyGvfeAasdGglniepkafts....ekskfp 77 
                                   n++  k   +kk+ g++++++++++k+k g kL ++++++         + Gv+e  s+   + ++k f+      ++kfp
  gi|15669572|ref|NP_248385.1|   9 NEDNWKVIKDKKIWGVAERHKNTINKVKVGDKLIIYEIQRSgkdykppYIRGVYEVVSEVYKD-SSKIFKPtprnPNEKFP 88 
                                   556666677899************************876532222222699****99986443.44455434555899*** PP

                Dev_Cell_Death  78 aQvrfkikkkckPLaesefkea 99 
                                     v++k +k + P    +fk++
  gi|15669572|ref|NP_248385.1|  89 YRVKLKEVKVFVPPI--NFKDL 108
                                   *****9888777632..34444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 1112.06
//
Query:       gi|15669573|ref|NP_248386.1|  [L=256]
Description: hypothetical protein MJ_1383 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-19   69.5   0.2    3.4e-19   69.2   0.2    1.1  1  TatD_DNase  TatD related DNase


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.2   1.9e-23   3.4e-19       1     206 [.       2     213 ..       2     253 .. 0.68

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.9e-23
                                   EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSG..........GGHH.HHHHHHTT.TTTEEEEE---GGGGGCC. CS
                    TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtss..........kdsk.avlelakkypnkvyavlGiHPnevdeas 70 
                                   iD+H+H d++ +   ++ +l ++   gv +++    ++          ++   + le akk   ++++++G+HP  +  + 
  gi|15669573|ref|NP_248386.1|   2 IDTHIHSDTRGL---EDLELMAMCLDGVITLAHDPFEMknikvweahvEKLLiNELERAKKVGLNLFICVGMHPRAIPPEI 79 
                                   89******9776...44444444444444444322222333333332254446888999999999************9999 PP

                                   CCHHHHHHHHHHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES.-HHHHHHHHHHCG.GCC CS
                    TatD_DNase  71 edlleelkelanvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrk.aeedlleilkeaa.eak 149
                                   ++ l+++k++    +s+vv+iGeiGL +        ++ +evF +ql lA+el+ p v+H+ +  +e++ +i+ ++    +
  gi|15669573|ref|NP_248386.1|  80 DEALDKIKSY-INYNSRVVGIGEIGLEK------ATKEEKEVFIKQLLLAEELNMPAVVHTPRrNKEEVTKIILDEIsTLN 153
                                   9999999999.33678************......3456899********************88766677666633331333 PP

                                   S....EEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-G..GGEEE---T CS
                    TatD_DNase 150 a....kvvlHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpl..drlLiETDa 206
                                   +     v+ H+   ++e+ k +l+  +y++l++   +    e+ e+vk+ ++  d++L+ +D+
  gi|15669573|ref|NP_248386.1| 154 LknrdIVIEHC---NKETTKWVLDEEFYVGLTIQPGKLTPLEAVEIVKEYKDfaDKILLNSDC 213
                                   355557888**...889999999********98666666788888998777444899999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1607.37
//
Query:       gi|15669574|ref|NP_248387.1|  [L=198]
Description: NADH oxidase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-28  100.5   0.0    1.3e-28  100.2   0.0    1.1  1  Nitroreductase  Nitroreductase family
    0.00018   21.2   0.0      0.057   13.0   0.1    2.8  2  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.0   1.4e-32   1.3e-28       2     170 .]      22     195 ..      21     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 1.4e-32
                                   HH--B---B-S----HHHHHHHHHHH.........HTS--GGG---EEEEEE..-CCCH....HHHHHHHHHHHHHHHTT- CS
                Nitroreductase   2 rkRrSiRkFddepvpkeelekileaa.........rraPsagnlqpwrfvvv.qdkelr....yklaeaalelllkaeaqa 68 
                                    kRrS+R++ + p+++ el++il aa          ++Psag ++p++++v  +d        yk+ +  ++ ++ ++++ 
  gi|15669574|ref|NP_248387.1|  22 IKRRSVREYCSSPLTLRELSHILFAAygvtdergfKTVPSAGATYPLEIYVNvRDVVGVeegvYKYIPERHSIVRILDEEV 102
                                   58*****************************999999**************977665557777999999998888888888 PP

                                   SS-GGGGGGHHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHH CS
                Nitroreductase  69 elaqryrkeelklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaee 149
                                    +        l +++q ++a ap++++i+a++++ +r +++r+ ry ++++g++aqn++L+At+lGlg++ +g+f++ +  
  gi|15669574|ref|NP_248387.1| 103 GHELA-----LAALKQMFIAIAPIVLIIAANYERTTRVYGDRGFRYVHMEVGHVAQNVYLMATSLGLGTVSVGAFYDNE-- 176
                                   77777.....45*******************************************************************.. PP

                                   HHHHHT-S..SEEEEEEEEE- CS
                Nitroreductase 150 vrkllglpdeeeivvliavGy 170
                                   +r++l ++  e +++l++vG+
  gi|15669574|ref|NP_248387.1| 177 IREILKIK--EYPLLLMPVGR 195
                                   ********..9********95 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0022        19       5      40 ..      20      55 ..      16      64 .. 0.81
   2 !   13.0   0.1   6.4e-06     0.057      78     113 ..     142     177 ..      83     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0022
                                  HHHH--B---B--S---HHHHHHHHH-----S...S CS
                TM1586_NiRdase  5 aiekRhsvRkYkdealeeelleelkeaieeinkesg 40
                                   + kR+svR+Y + +l+ + l+ +  a+  + +e g
  gi|15669574|ref|NP_248387.1| 20 VLIKRRSVREYCSSPLTLRELSHILFAAYGVTDERG 55
                                  5679***********999999888887777776665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.4e-06
                                   HHHHHHHHHHHHHHHHHHHHTT-EEEEES--SST.. CS
                TM1586_NiRdase  78 edleekaGYygeqlvLkltalGlgtcWvggtykkkk 113
                                   + +++++G + +++ L +t+lGlgt  vg+ y+++ 
  gi|15669574|ref|NP_248387.1| 142 RYVHMEVGHVAQNVYLMATSLGLGTVSVGAFYDNEI 177
                                   567899***********************9998843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1290.82
//
Query:       gi|15669575|ref|NP_248388.1|  [L=179]
Description: tRNA 2'-O-methylase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-54  183.2   0.2    1.7e-54  182.8   0.2    1.2  1  Trm56          tRNA ribose 2'-O-methyltransferase, aTrm56
    0.00025   20.5   0.1    0.00032   20.1   0.1    1.3  1  SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
     0.0068   16.0   0.0        1.9    8.0   0.0    2.1  2  AA_kinase      Amino acid kinase family


Domain annotation for each model (and alignments):
>> Trm56  tRNA ribose 2'-O-methyltransferase, aTrm56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.8   0.2   2.9e-58   1.7e-54       1     119 []      54     173 ..      54     173 .. 0.97

  Alignments for each domain:
  == domain 1  score: 182.8 bits;  conditional E-value: 2.9e-58
                                   H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC..-SE.EEEEE------TCHHHHSSEEEESSSS-- CS
                         Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikk..kekdllvvvGaekvprevyeladynvsvgnqPh 79 
                                   wGg+f++ v+k+++k+i+efk ++givvhltmyG ni+e++ ei++  ++kd+lv+vGaekvp+evyeladynvsvgnqPh
  gi|15669575|ref|NP_248388.1|  54 WGGNFEFVVEKHWRKYIREFK-KRGIVVHLTMYGANINEIMPEIREisRDKDILVIVGAEKVPKEVYELADYNVSVGNQPH 133
                                   *********************.79*********************9545669***************************** PP

                                   -HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EEE CS
                         Trm56  80 sevaalaifldrllegkelekefedaklkviPsergkkvv 119
                                   sevaalaifldrl+egk+l+++fedak+k++Ps+ gk v+
  gi|15669575|ref|NP_248388.1| 134 SEVAALAIFLDRLFEGKTLYRDFEDAKIKIVPSKDGKVVI 173
                                   *************************************985 PP

>> SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   5.4e-08   0.00032      86     148 ..      68     128 ..      42     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.4e-08
                 SPOUT_MTase_2  86 qlvrkrrkkellivtdPeGeeisevkeelaealrkakevvvlvGsReGiPkGlfrfadfvvDl 148
                                   +++r+ +k+ +++ +   G +i+e++ e+ e   + k + v+vG+   +Pk ++++ad+ v +
  gi|15669575|ref|NP_248388.1|  68 KYIREFKKRGIVVHLTMYGANINEIMPEIREI-SRDKDILVIVGAE-KVPKEVYELADYNVSV 128
                                   689999999999****************9875.5778899****95.5***********9876 PP

>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0011       6.8     164     191 ..      22      49 ..      12      53 .. 0.84
   2 !    8.0   0.0   0.00031       1.9      18      63 ..      87     132 ..      72     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0011
                                   HHHHHHHCTSSEEEEEESSSSCESSTTT CS
                     AA_kinase 164 aallAealgAdkliiltdVdGVydadpk 191
                                    al A algAdk+i+ t+ ++V ++  k
  gi|15669575|ref|NP_248388.1|  22 VALTARALGADKIIFTTEDEHVENSVKK 49 
                                   5899*************99998666555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00031
                                   HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH.TCCCCCHHHC CS
                     AA_kinase  18 aslrrlaeqiaalkesgnklvvVhGggsftdgllal.ksglssgela 63 
                                   a++++++ +i+++ ++++++ v++G+ ++  + ++l ++++s g + 
  gi|15669575|ref|NP_248388.1|  87 ANINEIMPEIREI-SRDKDILVIVGAEKVPKEVYELaDYNVSVGNQP 132
                                   579**********.999***********9999999976677666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1133.40
//
Query:       gi|15669576|ref|NP_248389.1|  [L=74]
Description: hypothetical protein MJ_1386 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 496.87
//
Query:       gi|15669577|ref|NP_248390.1|  [L=379]
Description: hypothetical protein MJ_1387 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   9.4e-115  383.7   0.0   1.1e-114  383.5   0.0    1.0  1  DUF111    Protein of unknown function DUF111


Domain annotation for each model (and alignments):
>> DUF111  Protein of unknown function DUF111
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.5   0.0  5.9e-119  1.1e-114       2     372 ..       3     368 ..       2     369 .. 0.96

  Alignments for each domain:
  == domain 1  score: 383.5 bits;  conditional E-value: 5.9e-119
                        DUF111   2 yldcssGisGDmllgALldlgadkeeleealeklgleeveleiekvkksgisatkvdveeeehehehrslaeieeiieaas 82 
                                   +ld++sGisGDm+l+A++d  +dke + ++++k+   +ve+ei+kvkk++i a kv+++ +  + + +++++i+++i++++
  gi|15669577|ref|NP_248390.1|   3 LLDPFSGISGDMFLSAMIDF-VDKEDFINTIKKVI--DVEIEIKKVKKCHILANKVNIIPKCINCNANTYKDIKNVIKSSD 80 
                                   58*****************9.8999999****964..68********************99999999************** PP

                        DUF111  83 lsekvkekalaiferlaeAeakvhgvpleevhfhEvGavDaivdivgaalaldeLgv.ekvvasplalGsGtvrcahGilP 162
                                   ++e++k +al+i+++laeAe+kvh+v++e+vhfhEvG+ D+i+divgaa+++++L++ ++++ +p+++G+G+vr++hG lP
  gi|15669577|ref|NP_248390.1|  81 IQEDIKITALEILKILAEAESKVHNVDVENVHFHEVGNYDTIADIVGAAYIINKLNLkNNCLYKPINVGNGFVRTEHGLLP 161
                                   *********************************************************667999****************** PP

                        DUF111 163 vPaPAvlellkelklklgevegElvTPTGaAilaalaeefgslpamkvekiGyGaGkrdleeipnvlRvlleeeeeeleke 243
                                   vPaPA++e+lk+lk+  +++++El+TPTG Ai++++  ++ +  a+ +++++yGaG++dl ++ n lRv+     e+ ++e
  gi|15669577|ref|NP_248390.1| 162 VPAPATAEILKGLKIFFSDINEELTTPTGSAIIKYINPKLAK-GAFIIKEVSYGAGDKDL-NLLNALRVFR---VEDIKRE 237
                                   ***************99*******************777765.49***************.8********9...58999** PP

                        DUF111 244 evvvletniDDlspevlgyvlerLleaGAlDvfltpilmKKgRpavllsvlckeedaeeleellfretttlGvReseverl 324
                                   ++v+letn+DD+s+e+lgy++e L +   +D +++p++mKK+Rpa++++++++++ aee++++++ret++lGvR + +er+
  gi|15669577|ref|NP_248390.1| 238 DIVLLETNVDDISAEILGYLYEVL-DGKVRDLHFIPTYMKKNRPAYTIRAIVDRDIAEEVAKIIMRETGSLGVRIFDIERI 317
                                   *********************987.5669**************************************************** PP

                        DUF111 325 vlereietvetelgevrvKva...eevvkvkpEyedvkkiAeetglplkev 372
                                   +++re++t+++  ++vr+Kv+   +e+++ kpE+ed+k+iA++ g+plk++
  gi|15669577|ref|NP_248390.1| 318 TADREFKTIKLFDESVRLKVGrvnDEIISQKPEFEDLKNIAKKYGIPLKDL 368
                                   *********************99767**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2500.94
//
Query:       gi|15669578|ref|NP_248391.1|  [L=415]
Description: S-adenosyl-L-homocysteine hydrolase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-68  228.9   0.0    7.4e-38  130.4   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    8.3e-55  185.3   1.6    8.3e-55  185.3   1.6    1.7  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    3.9e-10   39.4   0.2    1.6e-09   37.4   0.2    2.0  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    1.8e-06   27.7   0.1    3.5e-06   26.7   0.1    1.5  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
     0.0061   15.9   1.9      0.019   14.2   1.8    1.8  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.055   12.7   0.3       0.35   10.1   0.1    1.8  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      0.095   13.0   0.3       0.33   11.2   0.1    2.0  2  TrkA_N         TrkA-N domain


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   0.0   2.9e-41   7.4e-38       2     138 ..       2     133 ..       1     137 [. 0.97
   2 !   97.6   0.0   2.7e-31   6.9e-28     174     287 ..     136     410 ..     132     415 .] 0.98

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 2.9e-41
                                   -B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--HH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase   2 ykvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqde 82 
                                   y+v+di+l + G ++i+ a++ mp l  +re+++eekp+kg  i  +lh+ ++tavL etL++ Gae+  + Cn  stqd+
  gi|15669578|ref|NP_248391.1|   2 YEVRDINLWKEGERKIQWAKQHMPVLNLIRERFKEEKPFKGITIGMALHLEAKTAVLAETLMEGGAEIAITGCNPLSTQDD 82 
                                   99******************************************************************************* PP

                                   HHHHHCCTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase  83 aaaaiaeagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhk 138
                                   +aaa a++g+ v+aw+get eey + ++++l++     +p++++DdG Dl  l+h+
  gi|15669578|ref|NP_248391.1|  83 VAAACAKKGMHVYAWRGETVEEYYENLNKVLDH-----KPDIVIDDGCDLIFLLHT 133
                                   *******************************55.....7*************9997 PP

  == domain 2  score: 97.6 bits;  conditional E-value: 2.7e-31
                                   CCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH.................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                     AdoHcyase 174 tellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD.................................. 220
                                   tell++i G  eetttG+ rL+ ++k+g L++p ++vnd+ tk  fD                                  
  gi|15669578|ref|NP_248391.1| 136 TELLDNIMGGCEETTTGIIRLKAMEKEGALKFPVMDVNDAYTKHLFDnrygtgqsaldgilratnlliagktvvvagygwc 216
                                   78999**************************************************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                     AdoHcyase 221 ................................................................................. 220
                                                                                                                    
  gi|15669578|ref|NP_248391.1| 217 grgvamrakglgaevvvtevnpiralearmdgfrvmkmekaaeigdifitttgckdvirkehilkmrngailanaghfdne 297
                                   ********************************************************************************* PP

                                   ..............................................S-HHHHHHHHHHHHHHHHHHHHTTSSS-SSEEE-- CS
                                   ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase 221 ..............................................hpsfvmsasftnqvlaqielfkkekkyekkvyvlp 255
                                                                                 hp  vm++sf+nq+la   + k+++k e +vy +p
  gi|15669578|ref|NP_248391.1| 298 inkkhleelaksikevrncvteydlgnkkiyllgegrlvnlacadgHPCEVMDMSFANQALAAEYILKNHEKLEPRVYNIP 378
                                   ********************************************************************************* PP

                                   CHHHHHHHHHCCCCCT-------HHHHHCCTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase 256 kklDekvarlhleklgaklteltkeqaeyigv 287
                                    + D  +a+l+l+++g++++eltkeq +y++ 
  gi|15669578|ref|NP_248391.1| 379 YEQDLMIASLKLKAMGIEIDELTKEQKKYLED 410
                                   *****************************975 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.8   4.6e+03      39      58 ..      59      78 ..      57      90 .. 0.79
   2 !  185.3   1.6   3.3e-58   8.3e-55       1     162 []     183     343 ..     183     343 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.8
                                  HHHHHHCT-EEEEE-S-HHH CS
                 AdoHcyase_NAD 39 aaslkglGarvivtevdPic 58
                                  a++l + Ga + +t  +P++
  gi|15669578|ref|NP_248391.1| 59 AETLMEGGAEIAITGCNPLS 78
                                  66788889999999888876 PP

  == domain 2  score: 185.3 bits;  conditional E-value: 3.3e-58
                                   HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SE CS
                 AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadi 81 
                                   n yg+ +s +dgi rat++l+aGk++vvaGyG  G+G a   kglGa v+vtev+Pi al a m+Gf+v+++e++++ +di
  gi|15669578|ref|NP_248391.1| 183 NRYGTGQSALDGILRATNLLIAGKTVVVAGYGWCGRGVAMRAKGLGAEVVVTEVNPIRALEARMDGFRVMKMEKAAEIGDI 263
                                   78******************************************************************************* PP

                                   EEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSBCHHHTS-- CS
                 AdoHcyase_NAD  82 vvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrllnlgcatg 162
                                   ++tttG+kd+i++eh+ km++ ai++n Ghfd+ei+ ++le+ a++++ev+  v ++ l + kki ll eGrl+nl+ca g
  gi|15669578|ref|NP_248391.1| 264 FITTTGCKDVIRKEHILKMRNGAILANAGHFDNEINKKHLEELAKSIKEVRNCVTEYDLGN-KKIYLLGEGRLVNLACADG 343
                                   ***********************************************************98.6799************975 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.51   1.3e+03      50      71 ..      82     103 ..      66     131 .. 0.75
   2 !   37.4   0.2   6.1e-13   1.6e-09      33     128 ..     202     293 ..     179     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.51
                                   HHHHHHHHTT-EEEEESSSHHH CS
                  2-Hacid_dh_C  50 avakrlkafgmkviaydrskkk 71 
                                    va  +++ gm+v+a+     +
  gi|15669578|ref|NP_248391.1|  82 DVAAACAKKGMHVYAWRGETVE 103
                                   5888899999999999766442 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 6.1e-13
                                   -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHH CS
                  2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaee 113
                                    ++gktv + G+G  G+ va r+k++g++v+++++++ +  e++  g++++++e++ +  Di + ++      +++i +e+
  gi|15669578|ref|NP_248391.1| 202 LIAGKTVVVAGYGWCGRGVAMRAKGLGAEVVVTEVNPIRALEARMDGFRVMKMEKAAEIGDIFITTT----GCKDVIRKEH 278
                                   589*********************************998889999****************998755....5789****** PP

                                   HHCSTTTEEEEESS- CS
                  2-Hacid_dh_C 114 lakmkkgailiNtaR 128
                                   + km++gail N++ 
  gi|15669578|ref|NP_248391.1| 279 ILKMRNGAILANAGH 293
                                   ************985 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.1   1.4e-09   3.5e-06       2      97 ..     203     294 ..     202     307 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.4e-09
                                   HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTG CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeie 82 
                                   + gk+++v GyG  G+  a+  +  g +vvv+  +    + +A+ +gf+v+++++a++  d+ ++ +     k+v+++e  
  gi|15669578|ref|NP_248391.1| 203 IAGKTVVVAGYGWCGRGVAMRAKGLGAEVVVTEVNPI-RALEARMDGFRVMKMEKAAEIGDIFITTT---GCKDVIRKEHI 279
                                   789***************************9988887.6778****************999876654...56777777777 PP

                                   GG--TT-EEEESSSH CS
                          IlvN  83 pnlkegkalafahGf 97 
                                    ++++g++la a  f
  gi|15669578|ref|NP_248391.1| 280 LKMRNGAILANAGHF 294
                                   889999998887666 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.8   7.6e-06     0.019      29     123 ..     206     287 ..     187     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.6e-06
                                   -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS---S CS
                   AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipGkkaPkL 109
                                    +v+v G G  G   +  akglga+V+v++v+p r+ + +  g +          ++++a++  d+ i+t   +G     +
  gi|15669578|ref|NP_248391.1| 206 KTVVVAGYGWCGRGVAMRAKGLGAEVVVTEVNPIRALEARMDGFR--------VMKMEKAAEIGDIFITT---TGC--KDV 273
                                   579999**************************9887666655555........22345555666777777...333..357 PP

                                   C-HHHHHTS-TTEE CS
                   AlaDh_PNT_C 110 vteemvksMkpgsV 123
                                   +++e++ +M++g++
  gi|15669578|ref|NP_248391.1| 274 IRKEHILKMRNGAI 287
                                   77777777777776 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00014      0.35     142     209 ..     197     273 ..     151     286 .. 0.69
   2 ?    9.5   0.3    0.0002      0.52       2      86 ..     207     328 ..     206     338 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00014
                                   T........SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEE CS
                                   x........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 142 p........krivvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkei 209
                                   +        k +vv G G +G  +A+ ++ lg+ev++ e +++   +a  + ++ + +e+  + G  + + t  k++
  gi|15669578|ref|NP_248391.1| 197 RatnlliagKTVVVAGYGWCGRGVAMRAKGLGAEVVVTEVNPIRAlEARMDGFRVMKMEKAAEIGDIFITTTGCKDV 273
                                   03444466789999*********************999999876655444555555555555555555555555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0002
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEE......TTHCHHHCSHHHHCHHHHHHHHHHHHH................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx................... RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve......legtclnggcllskallgvaedaeias................... 57 
                                    vvv G G+ G  +a++++  ga+v++ e      le  + +++++  ++++++++   + +                   
  gi|15669578|ref|NP_248391.1| 207 TVVVAGYGWCGRGVAMRAKGLGAEVVVTEvnpiraLEARMDGFRVMKMEKAAEIGDIFITTTgckdvirkehilkmrngai 287
                                   578888888888888888888888888876676664444444444443333333333322225555555544444777777 PP

                                   .............HHHHCHHHHCCCCHCCTCEEEEESCEEEE CS
                                   .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 .............evvkklnqgielllgeevvkidpgkkkvk 86 
                                                +++++l ++i+ + +  v+++d g+kk+ 
  gi|15669578|ref|NP_248391.1| 288 lanaghfdneinkKHLEELAKSIKEVRN-CVTEYDLGNKKIY 328
                                   7777777777777777777777665555.6777777777665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         2   5.1e+03      32      57 ..     107     132 ..     100     174 .. 0.80
   2 ?   11.2   0.1   0.00013      0.33       1      47 [.     208     254 ..     208     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2
                                   HHHHHHHHTTSEEEES-TTSHHHHHH CS
                        TrkA_N  32 erveelreeglevvvgdatdeevLee 57 
                                   e+++++ +++ ++v+ d+ d  +L +
  gi|15669578|ref|NP_248391.1| 107 ENLNKVLDHKPDIVIDDGCDLIFLLH 132
                                   66777888888888888888777765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvg 47 
                                   ++++G+G  Gr +a + +  g  +vvv + ++ r+ e+r +g++v++ 
  gi|15669578|ref|NP_248391.1| 208 VVVAGYGWCGRGVAMRAKGlGA-EVVVTEVNPIRALEARMDGFRVMKM 254
                                   79*****************777.5******************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2578.75
//
Query:       gi|15669579|ref|NP_248392.1|  [L=134]
Description: hypothetical protein MJ_1389 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-16   59.8   0.0    2.1e-16   59.5   0.0    1.2  1  Robl_LC7        Roadblock/LC7 domain
  ------ inclusion threshold ------
      0.017   14.6   0.9      0.027   13.9   0.9    1.3  1  Fijivirus_P9-2  Fijivirus P9-2 protein


Domain annotation for each model (and alignments):
>> Robl_LC7  Roadblock/LC7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.0   2.3e-20   2.1e-16       2      89 ..      13      98 ..      12     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 2.3e-20
                                  HHHHHHHCCHHCTECEEEEEETTS-EEEECCSSSS-HHHHHHHHHHHHHHHHHHHHHCTSSSECEEEEEETTEEEEEEECTTT CS
                      Robl_LC7  2 veelleelqsvpgvrgalvvskdGlviatstldnddadqlAalasgllsaakaaarelgegelkelliegkkgelyltpageg 84
                                  +e ll + +++++v+g+++vskd lv+   ++d++d+++++ +++ +++ +++++++++ +e++++ i+gkk++++l++ +++
  gi|15669579|ref|NP_248392.1| 13 NEILLPLSKNLKNVEGFVIVSKDSLVKVG-NIDGEDLEIISRHMAVVMGSSEMLYKRFN-DEVEYIEIKGKKHKIILYNLDDF 93
                                  5789999**********************.*****************************.**********************6 PP

                                  EEEEE CS
                      Robl_LC7 85 alLvv 89
                                  ++ vv
  gi|15669579|ref|NP_248392.1| 94 IFAVV 98
                                  65555 PP

>> Fijivirus_P9-2  Fijivirus P9-2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.9     3e-06     0.027      10      64 ..      69     123 ..      59     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-06
                Fijivirus_P9-2  10 fecpfelakvemkaisntmhkvddfvstidvnfsdselddkvddleikiekvsgp 64 
                                   f+  +e  +++ k     ++++ddf+ ++  n+   e+ dkv +l+ k++++ g 
  gi|15669579|ref|NP_248392.1|  69 FNDEVEYIEIKGKKHKIILYNLDDFIFAVVGNIKADEIKDKVMELKFKVNNIDGL 123
                                   555566666777777778999*****************************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 866.53
//
Query:       gi|15669580|ref|NP_248393.1|  [L=109]
Description: DNA-directed RNA polymerase subunit I [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 741.99
//
Query:       gi|15669581|ref|NP_248394.1|  [L=418]
Description: aspartate aminotransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-44  151.7   0.0    3.7e-44  151.4   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
        0.1   13.0   0.0       0.36   11.2   0.0    2.0  2  DUF3991        Protein of unknown function (DUF3991)


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.4   0.0   4.1e-48   3.7e-44       3     334 ..      46     369 ..      44     388 .. 0.92

  Alignments for each domain:
  == domain 1  score: 151.4 bits;  conditional E-value: 4.1e-48
                                   EEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCT.TCHTTGGEGEEEESHHHHHHH CS
                 Aminotran_1_2   3 vinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrse.klklkreaavvvgsGagalie 82 
                                   +i++g++e++ +      pev++   e  +++ ++  y ++   +el+ a+  ++ + + ++++++  +v+ + G++ +++
  gi|15669581|ref|NP_248394.1|  46 LIDMGVGEPDEM----ADPEVIRVLCE-EAKKWENRGYADNG-IQELKDAVPPYMEKVYgVKDIDPVNEVIHSIGSKPALA 120
                                   799********9....66666666666.666899999**998.*************55537889***************** PP

                                   HHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                 Aminotran_1_2  83 alifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                    ++ ++ +npgd+ l+  p y+   +  +++ggev+  pl +e+df  dle++ e++k+      + k+++++ p+NPtG+
  gi|15669581|ref|NP_248394.1| 121 YITSAF-INPGDVCLMTVPGYPVTATHTKWYGGEVYNLPLLEENDFLPDLESIPEDIKK------RAKILYLNYPNNPTGA 194
                                   ******.****************************************************......99************** PP

                                   B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSS..HTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHH CS
                 Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsl..davatranveeepn.llivgslsKafGlaGeRvGyilgnaavvs 241
                                    at++ +++++d+a +++++++ D aY+++v++ +  +     + v+++ +  +   s+sKaf+++G+R+++++gn+ +++
  gi|15669581|ref|NP_248394.1| 195 QATKKFYKEVVDFAFENEVIVVQDAAYGALVYDGKplS----FLSVKDAKEvGVEIHSFSKAFNMTGWRLAFLVGNELIIK 271
                                   ********************************976322....56666666677999************************* PP

                                   HHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH..... CS
                 Aminotran_1_2 242 qlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae..... 315
                                   + + ++ +f s    + q+a    l++++     +e  rq++++r +++++ L+e g+k  ++ ++++l++  + +     
  gi|15669581|ref|NP_248394.1| 272 AFATVKDNFDSgqFIPIQKAGIYCLQHPEI----TERVRQKYERRLRKMVKILNEVGFKARMPGGTFYLYVKSPTKangie 348
                                   ***********9999************995....799**************************9999999998888***** PP

                                   ..CHHHHHHHHHHTCTEEEEE CS
                 Aminotran_1_2 316 ..takelskkLleevgvyvtp 334
                                     ta+++s+ L++e+ +  +p
  gi|15669581|ref|NP_248394.1| 349 fkTAEDFSQYLIKEKLISTVP 369
                                   **************7666665 PP

>> DUF3991  Protein of unknown function (DUF3991)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.7   1.5e+04      42      54 ..      70      81 ..      68      86 .. 0.71
   2 ?   11.2   0.0     4e-05      0.36      15      67 ..     357     416 ..     346     418 .] 0.74

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.7
                       DUF3991 42 vvgaekrgttyek 54
                                  ++ +e rg+  ++
  gi|15669581|ref|NP_248394.1| 70 AKKWENRGY-ADN 81
                                  678999998.444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4e-05
                       DUF3991  15 aefaekkllye...deyg.....NavFvykDengkvvgaekrgttyekpfkglasGgsell 67 
                                   + ++++kl+ +   d  g      a+Fv kDeng++++ ek      ++fk   +G  +l+
  gi|15669581|ref|NP_248394.1| 357 QYLIKEKLISTvpwDDAGhylrlAACFVAKDENGNPTTEEKYEDMVLEEFKRRLEG-MDLE 416
                                   566677777776663333466679****************9888888888877777.6655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2608.08
//
Query:       gi|15669582|ref|NP_248395.1|  [L=491]
Description: (R)-citramalate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-83  279.4   0.6      3e-83  279.4   0.6    1.9  2  HMGL-like   HMGL-like
    1.7e-31  108.9   2.5    3.8e-31  107.7   2.5    1.6  1  LeuA_dimer  LeuA allosteric (dimerisation) domain


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.4   0.6   3.4e-87     3e-83       2     264 .]       3     260 ..       2     260 .. 0.99
   2 ?   -0.8   0.2       0.1   8.9e+02      38      85 ..     435     482 ..     424     488 .. 0.78

  Alignments for each domain:
  == domain 1  score: 279.4 bits;  conditional E-value: 3.4e-87
                                   -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHH CS
                     HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaav 82 
                                   v+i+dttLRDGeq+++++l+ ++kl+iak+Lde+gvd+iE+g +  s++++e ++ i k++ +a+i++ vra   di+aa 
  gi|15669582|ref|NP_248395.1|   3 VRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKEGLNAEICSFVRALPVDIDAAL 83 
                                   79******************************************************************************* PP

                                   H....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-SEE CS
                     HMGL-like  83 ealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGatri 163
                                   e    + +++vh++++ts +h+k+kl+k+ +ev++ a +av++a+++g  vels+eda+r+d++fl+++ ++ e++Ga+r+
  gi|15669582|ref|NP_248395.1|  84 E----CDVDSVHLVVPTSPIHMKYKLRKTEDEVLETALKAVEYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRV 160
                                   *....**************************************************************************** PP

                                   EEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHHHHH CS
                     HMGL-like 164 niaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelvaale 244
                                    + DtvGvltP++ +el++++ e+v+  +++svHcHnd+G+A+ant  Av  Ga +  +tvnG+GeraGna+lee+vaal+
  gi|15669582|ref|NP_248395.1| 161 CVCDTVGVLTPQKSQELFKKITENVN--LPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEVVAALK 239
                                   **************************..***************************************************** PP

                                   HTT.-B----HHHHHHHHHHH CS
                     HMGL-like 245 alg.vdtgldlqklrsiaalv 264
                                    l  +dt+++++kl++++++v
  gi|15669582|ref|NP_248395.1| 240 ILYgYDTKIKMEKLYEVSRIV 260
                                   9977*************9987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.1
                                   SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH.. CS
                     HMGL-like  38 deiEvgfpaaseddfevvraiakavkkarilalvrarekdikaaveal 85 
                                   + +E  + a + +  + ++ ++k  k ++i+ +++++ + i+a v+a+
  gi|15669582|ref|NP_248395.1| 435 KLVEYRVEAIGGGTDALIEVVVKLRKGTEIVEVRKSDADIIRASVDAV 482
                                   567777888886666777778888888889999999999999999965 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   2.5   4.3e-35   3.8e-31       2     133 .]     356     490 ..     355     490 .. 0.95

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 4.3e-35
                                   XXXXXXXXXXXXXXXXXX.--EEEEEEEEEEETTCEEEEEEEEEE.TTEE..EEEEEE-SSHHHHHHHHHHHHHHH..T-E CS
                    LeuA_dimer   2 vtdedlealvkdelleae.erlkleklqvssgedelstatvklevkdgee..keasaeGnGpvdAllnAlrkalgv..dik 77 
                                   ++d+dl a+v++++++   e++kl++l+v+sg++ ++ a+vkl++ +ge+    ++a G+GpvdA++nA+rka++   dik
  gi|15669582|ref|NP_248395.1| 356 ISDADLLAIVREVTGKLVeEKIKLDELTVVSGNKITPIASVKLHY-KGEDitLIETAYGVGPVDAAINAVRKAISGvaDIK 435
                                   79**************777**************************.666656899*******************9889*** PP

                                   EEEEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHHS CS
                    LeuA_dimer  78 LldYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrll 133
                                   L +Y+v+ai++gtda+ ev V+l+ +++++v+ +  d+di++AS+ A+++++n+ll
  gi|15669582|ref|NP_248395.1| 436 LVEYRVEAIGGGTDALIEVVVKLR-KGTEIVEVRKSDADIIRASVDAVMEGINMLL 490
                                   ************************.99999***********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3140.98
//
Query:       gi|15669583|ref|NP_248396.1|  [L=608]
Description: hypothetical protein MJ_1393 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.066   13.2   4.1      0.068   13.2   1.1    2.7  2  BACON     Putative binding domain, N-terminal


Domain annotation for each model (and alignments):
>> BACON  Putative binding domain, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.1   3.8e-06     0.068      16      37 ..     243     266 ..     230     282 .. 0.82
   2 ?   -3.4   0.1      0.56     1e+04      10      23 ..     485     502 ..     480     505 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.8e-06
                         BACON  16 pas..tltvtvaaNtsgeeRtati 37 
                                   +++  t+t++++ N ++++Rt+t+
  gi|15669583|ref|NP_248396.1| 243 TTKnaTITINITGNNTYTNRTGTL 266
                                   33346*****************97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.56
                         BACON  10 dWltvspas....tltvt 23 
                                   +W+  s++     ++t+t
  gi|15669583|ref|NP_248396.1| 485 EWVNQSSMLiaegNHTIT 502
                                   488554333666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3987.19
//
Query:       gi|15669584|ref|NP_248397.1|  [L=987]
Description: hypothetical protein MJ_1394 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.6   3.7         19    5.9   0.2    4.0  3  MORN_2    MORN repeat variant
       0.14   12.1   2.3        5.1    7.1   0.2    2.8  2  DUF2808   Protein of unknown function (DUF2808)


Domain annotation for each model (and alignments):
>> MORN_2  MORN repeat variant
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.4   1.2e+04       8      21 ..      49      62 ..      48      63 .. 0.84
   2 ?    5.9   0.2    0.0021        19       9      22 .]     167     180 ..     164     183 .. 0.84
   3 ?    5.2   0.0    0.0037        33       4      18 ..     528     542 ..     522     546 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                        MORN_2  8 YyenGklkeeltYk 21
                                   y +G +++  +Y 
  gi|15669584|ref|NP_248397.1| 49 NYSSGAVEQSSNYA 62
                                  5999*999999995 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0021
                        MORN_2   9 yenGklkeeltYkn 22 
                                   y nG+l+ e++Y+n
  gi|15669584|ref|NP_248397.1| 167 YSNGTLRLEVYYEN 180
                                   88999999999987 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0037
                        MORN_2   4 eekeYyenGklkeel 18 
                                   ++ +Yy+nG l   +
  gi|15669584|ref|NP_248397.1| 528 TFSTYYQNGSLAATV 542
                                   5789*****998766 PP

>> DUF2808  Protein of unknown function (DUF2808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2    0.0061        54     105     141 ..     146     181 ..     135     184 .. 0.87
   2 ?    7.1   0.2   0.00057       5.1     101     141 ..     496     536 ..     494     539 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0061
                       DUF2808 105 tvvlknvrNPrfgGtYlFgvtafppgdnplgqylGtw 141
                                   t+v+ n+ NP     Y+F+  +++ g   l  y   +
  gi|15669584|ref|NP_248397.1| 146 TLVITNW-NPPENQWYYFKFYIYSNGTLRLEVYYENG 181
                                   7888899.99999*************99988887665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00057
                       DUF2808 101 gktvtvvlknvrNPrfgGtYlFgvtafppgdnplgqylGtw 141
                                   g+  ++  + + NP  +  Y+F+ ++++ g ++ + y   +
  gi|15669584|ref|NP_248397.1| 496 GNPTEISPEVYWNPPEDEWYYFELKIYSNGTITFSTYYQNG 536
                                   777888888889********************999997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (987 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 6006.08
//
Query:       gi|15669585|ref|NP_248398.1|  [L=132]
Description: hypothetical protein MJ_1395 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.13   12.4   0.0    1.2  1  Antig_Caf1  Caf1 Capsule antigen
       0.17   12.1   0.9       0.18   12.0   0.0    1.5  2  DUF4330     Domain of unknown function (DUF4330)


Domain annotation for each model (and alignments):
>> Antig_Caf1  Caf1 Capsule antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.4e-05      0.13      46      87 ..      58      99 ..      17     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                                  GEEEEETT--TT-EEEEESSSS--EEEEEEEEE-TTS-EE-- CS
                    Antig_Caf1 46 svnftdaagdpmyltftsqdgnnhqfttkvigkdsrdfdisp 87
                                    nf      p ylt+   dgnn q+  k +     +f i p
  gi|15669585|ref|NP_248398.1| 58 IKNFHINFVSPYYLTYQEPDGNNFQIPKKTLLIINAEFSILP 99
                                  4466666678****************9998877777777655 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     2e-05      0.18     117     159 ..      23      65 ..       3      68 .. 0.87
   2 ?   -3.3   0.2         1   9.1e+03      25      34 ..     115     124 ..     112     129 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                       DUF4330 117 pylkdllvtlegkakitedglvlggqkvkvGkevelegknyef 159
                                   ++ k++++ +e +a i ++g+ + + ++ +G +++++ +  +f
  gi|15669585|ref|NP_248398.1|  23 DGGKNITLIIEYDADIVDNGILFKTVSIPIGGDLNIKNFHINF 65 
                                   6889**********************************99998 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1
                       DUF4330  25 ilavivgifl 34 
                                   il++++ if+
  gi|15669585|ref|NP_248398.1| 115 ILCILIIIFV 124
                                   4444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 864.48
//
Query:       gi|15669586|ref|NP_248399.1|  [L=2894]
Description: hypothetical protein MJ_1396 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-71  238.1  17.7    1.1e-37  130.0   6.3    5.7  6  Bact_lectin      Bacterial lectin
    1.9e-21   76.6 149.1    1.3e-12   47.8  35.1   13.0 15  Beta_helix       Right handed beta helix region
    6.1e-06   25.7   5.3      0.022   14.1   0.6    3.2  2  Lectin_leg-like  Legume-like lectin family
    4.5e-05   23.7   5.9    9.2e-05   22.6   2.9    3.3  3  SdrD_B           SdrD B-like domain
      0.005   17.3   0.0        1.4    9.4   0.0    3.0  2  MG2              MG2 domain
  ------ inclusion threshold ------
        2.5    7.9  10.8        4.7    7.1   0.5    3.2  3  ESPR             Extended Signal Peptide of Type V secretion 


Domain annotation for each model (and alignments):
>> Bact_lectin  Bacterial lectin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   1.5      0.38   1.1e+03       3      46 ..      29      70 ..      26      98 .. 0.75
   2 ?   -2.2   0.6       1.2   3.5e+03     129     149 ..     987    1058 ..     897    1100 .. 0.63
   3 !  124.6   3.5   1.7e-39   4.9e-36       8     195 ..    1477    1675 ..    1471    1676 .. 0.82
   4 ?   -2.5   0.5       1.4   4.2e+03      92     115 ..    1728    1754 ..    1723    1799 .. 0.69
   5 !  130.0   6.3   3.6e-41   1.1e-37       9     195 ..    1808    2008 ..    1804    2009 .. 0.83
   6 ?   -3.4   0.7       2.7     8e+03      88     130 ..    2813    2866 ..    2758    2883 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.38
                                  TTTHHHHEEEEET-E...E..EEEEE-SSTT-EEEEEESSEEETTS CS
                   Bact_lectin  3 kdnfqdyfnlngtatkksk..ivtltedkknqaGavtlknkiDlsk 46
                                  ++n +++f+ln +     +    +lt++ +n +G++  +n  D +k
  gi|15669586|ref|NP_248399.1| 29 TTNNNSNFELNNSLI---YklNNSLTNT-TNNSGSIIINNTTDTNK 70
                                  556666677776443...1234455555.78899999999999886 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                    -............................................-SSS--EEEEEEE..-TTT.......E CS
                   Bact_lectin  129 s............................................ledgkwhpitisYdastkt.......t 149 
                                    +                                            + dg w  i+ +Yd ++++       t
  gi|15669586|ref|NP_248399.1|  987 GeeifynitlynfgvggrfdinityltkgwttkiynnsiliaedaNGDGIWDYINPNYDLNSNNlpdiyvpT 1058
                                    044444455555555555555555555555555555556666666777889999999998888666333331 PP

  == domain 3  score: 124.6 bits;  conditional E-value: 1.7e-39
                                    HHEEEEET-E...EEEEEE-SSTT-EEEEEESSEEETTS-EEEEEEEE--S...B.--EEEEEEES...T----SGGGT CS
                   Bact_lectin    8 dyfnlngtatkkskivtltedkknqaGavtlknkiDlskdFtlkgsvnlgqsnaggaDGigFalqp...gqlGssGggl 83  
                                    +++ +ng+a+  ++ + lt+d  + aG+v++ ++++ls+d  ++++++lg +n  gaDGi+F+lq+   ++lG +Gg+l
  gi|15669586|ref|NP_248399.1| 1477 SQWIANGNASIFPDKLLLTTDDYGEAGSVWYYKPVNLSEDLVVEFYAYLG-DNPDGADGITFTLQSlgtNELGGTGGDL 1554
                                    579999*999999999999999****************************.69999**********87555999***** PP

                                    TTTTSTT-EEEEEE-S--.......SS-EEEEEEE...............-TT-........-SSS--EEEEEEE..-T CS
                   Bact_lectin   84 GigglpnafgfklDtyyN.....kagkpygafvktdangsletvkss...ssks........ledgkwhpitisYdast 146 
                                    G+gg+++++++++Dt+ N     + ++ +   +  d ng+++ + +s      +         edg++h i+i ++a+t
  gi|15669586|ref|NP_248399.1| 1555 GYGGISPSVAVEVDTWLNdfdapA-TTDH---IAIDVNGNINHTYNSltyP--TpnpydlgnVEDGREHLIKIVWNATT 1627
                                    ******************777642.2222...2223334444433333222..14466788899*************** PP

                                    TT.EEEET.HHHT-.............SEEEEEEEEE-SSSB--EEEEEEE CS
                   Bact_lectin  147 kt.tvtyd.dgsstvsidltkkvtkgktyvafgiaastGgatnlqqvkits 195 
                                    kt +v++d + s t+++d+t+ +   +++ +fg++++tGga+nlq+vk+ +
  gi|15669586|ref|NP_248399.1| 1628 KTlQVYFDgNLSLTWNKDITQII---GNSAYFGFTGGTGGAKNLQYVKPIY 1675
                                    *9999999766666677776666...7899*****************9876 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.4
                                    EEEEEE-S--.....SS-EEEEEEE.. CS
                   Bact_lectin   92 fgfklDtyyN...kagkpygafvktda 115 
                                    fgf +D   N   + + ++  f+k+ +
  gi|15669586|ref|NP_248399.1| 1728 FGFSFDVITNtksTGQGSFSQFIKNAN 1754
                                    9*********66644445555555533 PP

  == domain 5  score: 130.0 bits;  conditional E-value: 3.6e-41
                                    HEEEEET-E...E...EEEEE-SSTT-EEEEEESSEEETTS-EEEEEEEE--S...B.--EEEEEEES...T----SGG CS
                   Bact_lectin    9 yfnlngtatkksk...ivtltedkknqaGavtlknkiDlskdFtlkgsvnlgqsnaggaDGigFalqp...gqlGssGg 81  
                                    ++ +ng+a+ +++   ++ lt+d  nq+G+v++ ++++ls+d  ++++++lg +n  gaDGi+F+lq+   ++lG +Gg
  gi|15669586|ref|NP_248399.1| 1808 QWIANGNAYINNSnnlTLILTPDDYNQKGSVWYYKPVNLSEDLVVEFYAYLG-DNPDGADGITFTLQSlgtNELGGTGG 1885
                                    577899999887799*************************************.69999**********87555999*** PP

                                    GTTTTTSTT-EEEEEE-S--.......SS-EEEEEEE...............-TT-........-SSS--EEEEEEE.. CS
                   Bact_lectin   82 glGigglpnafgfklDtyyN.....kagkpygafvktdangsletvkss...ssks........ledgkwhpitisYda 144 
                                    +lG+gg+++++++++Dt+ N     + +++ +  v    +g+l+ + +s   s  +         edg++h i+i ++a
  gi|15669586|ref|NP_248399.1| 1886 DLGYGGISPSVAVEVDTWLNdfdspATTDHIAIDV----DGNLNHTYNSltyS--TpnpydlgnVEDGREHLIKIVWNA 1958
                                    ********************877653333333334....44444444443222..13466788899************* PP

                                    -TTT.EEEET.HHHT-.............SEEEEEEEEE-SSSB--EEEEEEE CS
                   Bact_lectin  145 stkt.tvtyd.dgsstvsidltkkvtkgktyvafgiaastGgatnlqqvkits 195 
                                    +tkt +v++d + + t+++d+t+ +   +++++fg++++tGga+nlq+vk+t+
  gi|15669586|ref|NP_248399.1| 1959 TTKTlQVYFDgNLALTWNKDITQII---GNSTYFGFTGGTGGAKNLQYVKPTY 2008
                                    ***9999999866777777777776...8899******************997 PP

  == domain 6  score: -3.4 bits;  conditional E-value: 2.7
                                    STT-EEEEEE-S--..SS-EEEEEEE.............-TT-...........- CS
                   Bact_lectin   88 lpnafgfklDtyyNkagkpygafvktdangsletvkss.ssks...........l 130 
                                    lpn+  + +  y N+  + y+ + k d+ + +++ +++ ++ +            
  gi|15669586|ref|NP_248399.1| 2813 LPNGYNITIKSY-NTTRDVYVYWYKPDNIEVINISGDYdENGTygntywfkfnvI 2866
                                    555555555555.556677777777777777777666632222444444444442 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4  14.3       2.6   7.9e+03      52     102 ..      31      85 ..      19      96 .. 0.76
   2 ?   -4.1   2.1       4.3   1.3e+04      54      86 ..     270     302 ..     219     337 .. 0.56
   3 ?   -1.1   0.4       0.5   1.5e+03      13      43 ..     526     555 ..     486     591 .. 0.63
   4 ?   -6.4   4.6         6   1.8e+04      70     114 ..     900     958 ..     878    1005 .. 0.58
   5 ?   -4.7   3.8         6   1.8e+04      50      85 ..    1011    1049 ..     982    1055 .. 0.63
   6 ?   -6.1   7.8         6   1.8e+04      85     132 ..    1236    1286 ..    1116    1320 .. 0.64
   7 ?   -3.0   1.9       1.9   5.7e+03     102     149 ..    1404    1459 ..    1333    1466 .. 0.62
   8 ?   -7.1  10.8         6   1.8e+04      35      94 ..    1734    1801 ..    1714    1829 .. 0.61
   9 ?   -2.1   1.4         1   3.1e+03     106     147 ..    2036    2079 ..    1980    2086 .. 0.67
  10 !   24.9  27.5     5e-09   1.5e-05      11     154 ..    2088    2234 ..    2072    2238 .. 0.89
  11 !   28.2  32.8     5e-10   1.5e-06       3     144 ..    2197    2333 ..    2196    2343 .. 0.84
  12 !   47.8  35.1   4.4e-16   1.3e-12      10     147 ..    2343    2502 ..    2340    2508 .. 0.88
  13 !   25.6  29.7   3.2e-09   9.5e-06      54     147 ..    2512    2634 ..    2500    2638 .. 0.88
  14 ?   -4.0  12.9       3.9   1.2e+04      79     120 ..    2640    2681 ..    2636    2774 .. 0.59
  15 ?   -7.5   6.3         6   1.8e+04      24      73 ..    2817    2867 ..    2794    2888 .. 0.41

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.6
                                   -TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-.....SEE-TT-S- CS
                    Beta_helix  52 lgssnntisnntisdnngggialfgasnnlienneitdnggs.....Giylnyssn 102
                                   ++ sn+ + n+ i+  n++  +++++s+++i nn+   n++       i++n  ++
  gi|15669586|ref|NP_248399.1|  31 NNNSNFELNNSLIYKLNNSLTNTTNNSGSIIINNTTDTNKEKnecylNITIN-GYR 85 
                                   4559*********************************996544443444333.344 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 4.3
                                   T-S-EEES-EEE---SEEE-TT--S--EEES-E CS
                    Beta_helix  54 ssnntisnntisdnngggialfgasnnlienne 86 
                                   ++nn+i + +++  + + i  ++ ++n+i +n 
  gi|15669586|ref|NP_248399.1| 270 TPNNKIIHLKVHKKGKFYILSTKLKKNVILGNY 302
                                   255555555555555555555555555554443 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.5
                                   EESEEEES-SS-SEEE-SSS-.EEES-EEES CS
                    Beta_helix  13 iknntisnsggyGiylrgssnvvienneian 43 
                                   +  n+is +  +G  +++ +   ienn+++ 
  gi|15669586|ref|NP_248399.1| 526 VIRNNISINRLTGEVIGEVRW-YIENNTLYF 555
                                   333333333444444444444.444444444 PP

  == domain 4  score: -6.4 bits;  conditional E-value: 6
                                   EEE-TT--S--EEES-EEES-SS-..........SEE-TT....-S--EEES-EEESTT CS
                    Beta_helix  70 ggialfgasnnlienneitdnggs..........Giylny....ssnntienNiidnna 114
                                   + i++++ +++ i+ n    n ++           +++++    ++n+ti+ N  ++ +
  gi|15669586|ref|NP_248399.1| 900 VSINITQINGTYIYTNSTLINLSVpyeeeklvsfPVNISNmpygAYNITIKTNLPNDQN 958
                                   55555555555555555555533322222333332222225556777777666655554 PP

  == domain 5  score: -4.7 bits;  conditional E-value: 6
                                    EE-TT-S-EEES-EE...E---SEEE-TT--S--EEES- CS
                    Beta_helix   50 yilgssnntisnnti...sdnngggialfgasnnlienn 85  
                                    y+++++ ++i+nn+i   +d ng+gi+ + + n  ++ n
  gi|15669586|ref|NP_248399.1| 1011 YLTKGWTTKIYNNSIliaEDANGDGIWDYINPNYDLNSN 1049
                                    334446666677776666666666766665555444444 PP

  == domain 6  score: -6.1 bits;  conditional E-value: 6
                                    -EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT....---EEES- CS
                    Beta_helix   85 neitdnggsGiylnyssnntienNiidnnagsGividdss....snvtvtnN 132 
                                    n i+ n+   iy n+++   i+ N+ + ++ + i+ d +      nvt++ N
  gi|15669586|ref|NP_248399.1| 1236 NQISSNSI-NIYHNSTYPSNITLNTTTYVNVYNIFSDKNVylpnENVTIFAN 1286
                                    33333322.2333322223333333333333333333333333334444444 PP

  == domain 7  score: -3.0 bits;  conditional E-value: 1.9
                                    -...-EEES-EEESTT.....--SEE---TT.---EEES-EEES-SSEEEE-TT-SS CS
                    Beta_helix  102 n...ntienNiidnna.....gsGividdss.snvtvtnNtitnnkgaGiavvgsss 149 
                                    n    +i + i+++ +     ++ + +++ss + ++v n++ ++    G++  +s++
  gi|15669586|ref|NP_248399.1| 1404 NdgiPDIGDTIVNSTTtdifgHYSFLVYNSSkTYFVVVNSRTVGTT-RGLNPQYSKN 1459
                                    2344344444444444444456666666666666666666666664.6666666666 PP

  == domain 8  score: -7.1 bits;  conditional E-value: 6
                                    EEES-EEES........-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-....S CS
                    Beta_helix   35 vienneian........nsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggs....G 94  
                                    vi+n++ ++         + + iy +  s++ i n    ++n    ++ ++s+n i +n  + ng++     
  gi|15669586|ref|NP_248399.1| 1734 VITNTKSTGqgsfsqfiKNANAIYGKDESYFRIPNIDAKNGN----HYIYTSGNKILDNLTIVNGSTqingT 1801
                                    555544444444444555788888888899999999998888....77777777777777777765533331 PP

  == domain 9  score: -2.1 bits;  conditional E-value: 1
                                    ES-EEESTT--SEE---TT.---EEES-EEES-S.SEEEE-TT- CS
                    Beta_helix  106 enNiidnnagsGividdss.snvtvtnNtitnnk.gaGiavvgs 147 
                                     +Ni+ +n   Gi  ++++ +n+t + + i++   +aG+++v++
  gi|15669586|ref|NP_248399.1| 2036 IGNIFFENVSVGILGNETGlNNLTLKSCGIYGKIlNAGVKLVDY 2079
                                    45666666667777666667777777766665445666666655 PP

  == domain 10  score: 24.9 bits;  conditional E-value: 5e-09
                                    .EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT....-S-EEES-EEE---SEEE-TT--S--EEES- CS
                    Beta_helix   11 vtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgs....snntisnntisdnngggialfgasnnlienn 85  
                                    + i+n ti+ sggyGi   +   + + n+ i+  +g Giy  +      n+ti+n tis +n+g + ++++++  + n+
  gi|15669586|ref|NP_248399.1| 2088 LYIDNLTINASGGYGISMLNKIWAMLYNSQISLKNGVGIYWANWaggfGNITIYNITISSCNQGLVLYKDGNGIKLINS 2166
                                    579********************9999*****98899998888799****************7777777********** PP

                                    EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS...--EEE CS
                    Beta_helix   86 eitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsss...nvtvr 154 
                                     i +    G+y + +s + i n+ i nn+  Gi+ + ss  + v+n+ i++n+ +G+ + +sss   n  + 
  gi|15669586|ref|NP_248399.1| 2167 QIKNSVYEGVYSK-NSTLEILNSSIINNS-IGIYANISS--ILVNNSLIYKNRYEGLLLENSSSsilNSNIM 2234
                                    ******99**987.699************.999999999..99**************999999955555555 PP

  == domain 11  score: 28.2 bits;  conditional E-value: 5e-10
                                    EEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--E CS
                    Beta_helix    3 isingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnl 81  
                                    i+ n ss   ++n+ i+++ + G+ l++ss+  i n++i n +  Giy+++   ++i++++is n  +gi + ++sn+ 
  gi|15669586|ref|NP_248399.1| 2197 IYANISSI-LVNNSLIYKNRYEGLLLENSSS-SILNSNIMN-NSIGIYLKENYISKIQKSNISYNA-YGIEIVNSSNVY 2271
                                    55555555.8999999999999999999999.666688888.899999999999999999999999.999999999999 PP

                                    EES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE- CS
                    Beta_helix   82 ienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiav 144 
                                    i+ ++i++ +++Gi +++ +n+++en+ ++nn+ + i  + + sn+ v n+ + ++ +++i++
  gi|15669586|ref|NP_248399.1| 2272 INSSNIFNASTDGIAIFNGENVSVENSLLYNNN-YSILSYGNLSNLSVLNSLLRDSINNSIDI 2333
                                    999999999999999999999999999999999.88888888889999999999888888876 PP

  == domain 12  score: 47.8 bits;  conditional E-value: 4.4e-16
                                    E.EEESEEEES-SS-SEEE-SSS-....EEES-EEES-SS-SEEE-TT-S-EEES-EEE---.......SEEE-TT..- CS
                    Beta_helix   10 nvtiknntisnsggyGiylrgssn...vvienneiannsgsGiyilgssnntisnntisdnn.......gggialf..g 76  
                                    n+++ n+ + nsg+yG+++++ ++   v i+++ i++++ +Giyi+g++ ++i nn+i++n+       g+gi+++  +
  gi|15669586|ref|NP_248399.1| 2343 NLKLYNSSVLNSGSYGLFIYSLGSasnVNISKSLINGSYKDGIYIYGVNAINIVNNNITNNGliggdpaGSGIKISgnY 2421
                                    568899999*********99877766699999*************************************6666666559 PP

                                    -S--EEES-EEES-SS-SEE-TT..........-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-T CS
                    Beta_helix   77 asnnlienneitdnggsGiylny..........ssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavv 145 
                                    ++++li nn+i++n g+Gi+l++           +nn+i+nN i++n+g+Gi+i     nv ++nNti  ++  +i + 
  gi|15669586|ref|NP_248399.1| 2422 TKGVLILNNNISHNLGNGISLEGlwsrtlcdvkVENNIISNNGIEENSGNGIYIGGRVENVSIFNNTIQYSDAQAILIQ 2500
                                    9*********************89*99977777777777777777777*********9***********9999988776 PP

                                    T- CS
                    Beta_helix  146 gs 147 
                                    + 
  gi|15669586|ref|NP_248399.1| 2501 EA 2502
                                    55 PP

  == domain 13  score: 25.6 bits;  conditional E-value: 3.2e-09
                                    T-S-EEES-EEE---...............SEEE-TT--S--EEES-EEES-SS-..........SEE-TT......-S CS
                    Beta_helix   54 ssnntisnntisdnn...............gggialfgasnnlienneitdnggs..........Giylny......ss 101 
                                    ++n+ i nnti  n+               ++g++ +++++ +ie+n+i++n+ +          Gi++++      s 
  gi|15669586|ref|NP_248399.1| 2512 GTNISIINNTIQYNGltvtignitagitvgAYGVYNQDNGYIIIEGNKIINNNLCpnptyggkvgGIEVYGlneswiSL 2590
                                    489*************************************************555556666667799999666666666 PP

                                    --EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT- CS
                    Beta_helix  102 nntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgs 147 
                                       i++Nii nn+++Gi i +s+ ++++ nNti+nn  +Gi++ ++
  gi|15669586|ref|NP_248399.1| 2591 EFNISKNIIANNSAYGILIGASK-DINIINNTIFNNE-KGITIPNW 2634
                                    6**********************.************8.***98665 PP

  == domain 14  score: -4.0 bits;  conditional E-value: 3.9
                                    --EEES-EEES-SS-SEE-TT-S--EEES-EEESTT.--SEE- CS
                    Beta_helix   79 nnlienneitdnggsGiylnyssnntienNiidnna.gsGivi 120 
                                    n +i++n i++n+  Gi l++ +n+t+++  ++ n+ ++Gi +
  gi|15669586|ref|NP_248399.1| 2640 NIIISKNSIYNNSLLGIDLDD-DNVTLNDGLLNYNEaNHGIDY 2681
                                    445555555555555555543.455555444444444344433 PP

  == domain 15  score: -7.5 bits;  conditional E-value: 6
                                    -SEEE-SSS-.EEES-EEES-SS-SEEE-TT.....-S-EEES-EEE---SEEE- CS
                    Beta_helix   24 yGiylrgssnvvienneiannsgsGiyilgs.....snntisnntisdnngggia 73  
                                    y i++++ ++   ++ ++++   ++i++ +      +n t  n ++  +n   i+
  gi|15669586|ref|NP_248399.1| 2817 YNITIKSYNT--TRDVYVYWYKPDNIEVINIsgdydENGTYGNTYWFKFN--VIN 2867
                                    2222222222..22233333344444443333334333333333332222..222 PP

>> Lectin_leg-like  Legume-like lectin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.4   3.1e-05     0.093      22     217 ..    1477    1668 ..    1464    1677 .. 0.70
   2 !   14.1   0.6   7.5e-06     0.022      23     130 ..    1808    1922 ..    1796    2005 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                                    TTEEEEET-EEESSEEEEE-SSTTEEEEEEESS-BEESSEEEEEEEEEESS--SS-S-EEEEEEESSSSSCCSBTTB-S CS
               Lectin_leg-like   22 pnWeyggsaildsnqirltsdeqskkGslwtkspvaleswevevsFrvtgseselegdglaiwytsergkegpvFgskd 100 
                                     +W   g+a++  +++ lt d+  ++Gs+w ++pv+l++ ++ v+F +   ++  ++dg+ + + s  ++e    g+  
  gi|15669586|ref|NP_248399.1| 1477 SQWIANGNASIFPDKLLLTTDDYGEAGSVWYYKPVNLSE-DLVVEFYAYLGDNPDGADGITFTLQSLGTNELGGTGGDL 1554
                                    48**********************************977.7888888877779999****9988776666555567777 PP

                                    S-EE....EEEEEE-S-TS.CTTTSS-SSEEEEEEEESSC---GGGTTTTTESEEEE---BTESSEEEEEEEEETTEEE CS
               Lectin_leg-like  101 kfdG....lailldtydnd.ngpdkknkptisamlndgsleydhekdgkaqelasCtadfrnkdvetlikikYdknalt 174 
                                     + G    +a+ +dt+ nd ++p  + +++i +  n  +  y+  + ++ ++    +++  ++++  +i  +   ++l+
  gi|15669586|ref|NP_248399.1| 1555 GYGGispsVAVEVDTWLNDfDAPATTDHIAIDVNGN-INHTYNSLTYPTPNPYDLGNVE-DGREHLIKIVWNATTKTLQ 1631
                                    777733335788999988844566677777766544.4556777777777777666666.5666665555555556666 PP

                                    EEEETSCCSCCCTTEEEEEESSEE--SSBEEEEEEEESSSGGE CS
               Lectin_leg-like  175 vlidsgllenkndyklCfqvkevelPtgyyfgvsaatgdlsdn 217 
                                    v +d +l   +  +++  ++++ ++ +  yfg++  tg++++ 
  gi|15669586|ref|NP_248399.1| 1632 VYFDGNL---SLTWNK--DITQ-IIGNSAYFGFTGGTGGAKNL 1668
                                    6666443...444444..3444.35677777777777777765 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.5e-06
                                    TEEEEET-EEE.SSE..EEEE-SSTTEEEEEEESS-BEESSEEEEEEEEEESS--SS-S-EEEEEEESSSSSCCSBTTB CS
               Lectin_leg-like   23 nWeyggsaild.snq..irltsdeqskkGslwtkspvaleswevevsFrvtgseselegdglaiwytsergkegpvFgs 98  
                                    +W   g+a ++ sn+  + lt+d+ ++kGs+w ++pv+l++ ++ v+F +   ++  ++dg+ + + s  ++e    g+
  gi|15669586|ref|NP_248399.1| 1808 QWIANGNAYINnSNNltLILTPDDYNQKGSVWYYKPVNLSE-DLVVEFYAYLGDNPDGADGITFTLQSLGTNELGGTGG 1885
                                    69999999888677622578******************977.7788888877778899999999877655554444566 PP

                                    -SS-EE....EEEEEE-S-TS.CTTTSS-SSEEEEEE CS
               Lectin_leg-like   99 kdkfdG....lailldtydnd.ngpdkknkptisaml 130 
                                       + G    +a+ +dt+ nd ++p  + +++i +  
  gi|15669586|ref|NP_248399.1| 1886 DLGYGGispsVAVEVDTWLNDfDSPATTDHIAIDVDG 1922
                                    6666663222467777777763345556666655543 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.6   1.4e+04      38      56 ..     899     917 ..     892     934 .. 0.76
   2 ?   -3.2   0.0       3.3   9.7e+03      49      66 ..    1333    1350 ..    1333    1361 .. 0.77
   3 !   22.6   2.9   3.1e-08   9.2e-05       2      69 ..    1369    1447 ..    1368    1475 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.6
                        SdrD_B  38 vvatttTdasGkYkFtnlt 56 
                                    v+  +T+ +G+Y +tn t
  gi|15669586|ref|NP_248399.1| 899 NVSINITQINGTYIYTNST 917
                                   5567789999999999866 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.3
                        SdrD_B   49 kYkFtnltpGeYkVefta 66  
                                    +Y+F+  ++G+Y +++t 
  gi|15669586|ref|NP_248399.1| 1333 NYSFSLPESGKYLITITG 1350
                                    69***********99875 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 3.1e-08
                        SdrD_B    2 siGdfVweDanknGiqdagekgisgvtVtL.........kdakgevvatttTdasGkYkFtnltpGe.YkVefta.pag 69  
                                    +i  +V eD    G+ d+++kgi gv+V+L          d  +++v++ttTd  G+Y+F   ++ + Y V + + + g
  gi|15669586|ref|NP_248399.1| 1369 EIQGYVKEDFGTLGKEDSEDKGIYGVNVSLledsnndgiPDIGDTIVNSTTTDIFGHYSFLVYNSSKtYFVVVNSrTVG 1447
                                    67889999**********************99888877555556667*************9988776699988653444 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00049       1.4      32      83 ..     260     307 ..     238     326 .. 0.79
   2 ?    4.2   0.0     0.019        57       4      28 ..    1268    1292 ..    1266    1344 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00049
                                   --EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEEC CS
                           MG2  32 aklplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsad 83 
                                   +++p +++i++p++k ++ +  ++ ++  +  + +l+++  lG+ysv++  d
  gi|15669586|ref|NP_248399.1| 260 NFKPHTAYIVTPNNKIIHLKVHKKGKF--YILSTKLKKNVILGNYSVVV--D 307
                                   349*************99999666665..999****************9..3 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.019
                                    EEES-SEE-TT-EEEEEEEEESTTC CS
                           MG2    4 vytDRglYrPgetVslkallrdetl 28  
                                    +++D+++Y P+e+V + a + d+ +
  gi|15669586|ref|NP_248399.1| 1268 IFSDKNVYLPNENVTIFANITDPIG 1292
                                    799************9998888544 PP

>> ESPR  Extended Signal Peptide of Type V secretion system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.5    0.0016       4.7       6      18 ..    1620    1632 ..    1620    1632 .. 0.94
   2 ?    7.1   0.5    0.0016       4.7       6      18 ..    1953    1965 ..    1953    1965 .. 0.94
   3 ?   -2.8   0.2         2   6.1e+03       7      13 ..    2483    2489 ..    2483    2490 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0016
                          ESPR    6 RlIwnktrgqlva 18  
                                    +++wn+t+++l++
  gi|15669586|ref|NP_248399.1| 1620 KIVWNATTKTLQV 1632
                                    79*********98 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0016
                          ESPR    6 RlIwnktrgqlva 18  
                                    +++wn+t+++l++
  gi|15669586|ref|NP_248399.1| 1953 KIVWNATTKTLQV 1965
                                    79*********98 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2
                          ESPR    7 lIwnktr 13  
                                    +I+n+t 
  gi|15669586|ref|NP_248399.1| 2483 SIFNNTI 2489
                                    5****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2894 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 1.10u 0.29s 00:00:01.39 Elapsed: 00:00:00.49
# Mc/sec: 17770.47
//
Query:       gi|15669587|ref|NP_248400.1|  [L=486]
Description: hypothetical protein MJ_1397 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.018   13.8   4.5      0.027   13.3   4.5    1.2  1  Tim54       Inner membrane protein import complex subunit Tim
      0.057   13.6   1.5      0.082   13.1   1.5    1.2  1  CPSF100_C   Cleavage and polyadenylation factor 2 C-terminal
      0.069   11.9   0.3      0.099   11.4   0.3    1.2  1  Presenilin  Presenilin
       0.11   12.8   2.6       0.66   10.3   1.2    2.5  2  A2M_BRD     Alpha-2-macroglobulin bait region domain
       0.12   11.8   0.4       0.19   11.2   0.4    1.2  1  NOZZLE      Plant transcription factor NOZZLE
        1.3    8.7   5.6        2.1    8.1   5.6    1.3  1  Connexin    Connexin


Domain annotation for each model (and alignments):
>> Tim54  Inner membrane protein import complex subunit Tim54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   4.5   9.1e-06     0.027     199     268 ..     301     376 ..     279     394 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.1e-06
                         Tim54 199 eeaeeeeeeeeeekeeeeeeeeeeeeekeeekeeekeeeeeeeekekkkkvpkpyispedYasaelppe......i 268
                                   +e+++++ee+e+e+++++ ++ ++++++e+++++e+++ +++e ++++k+   p i +e++++   +        i
  gi|15669587|ref|NP_248400.1| 301 REIKKKKEEKENEESSKTINQMQRHKKEEKSQTQETKKPSKNEMNKQEKERKYPLIIEEKFKKVAAAIAtvtttsI 376
                                   3444444444444444444443444444444444445555555555577777889999999988777664433330 PP

>> CPSF100_C  Cleavage and polyadenylation factor 2 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.5   2.8e-05     0.082      34      84 ..     292     353 ..     254     376 .. 0.42

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
                     CPSF100_C  34 a........eeaeeeekeeeeeeeeeeeeeeeaskkqkl...aeksekeaseeeseekkesl 84 
                                   +         e +++++e+e+ee++++ ++++++kk+++   +e+++ +++e +++ek++++
  gi|15669587|ref|NP_248400.1| 292 NipyynymeREIKKKKEEKENEESSKTINQMQRHKKEEKsqtQETKKPSKNEMNKQEKERKY 353
                                   03344453322222233333333333333333333333322122222233333333333333 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   3.3e-05     0.099     234     279 ..     305     350 ..     286     418 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.3e-05
                    Presenilin 234 eseeeeeaekkkeeasesskeeeseeesseksaqsseseeeseees 279
                                   +++ee+e+e++++++++ ++++++e+++++++++ s++e +++e++
  gi|15669587|ref|NP_248400.1| 305 KKKEEKENEESSKTINQMQRHKKEEKSQTQETKKPSKNEMNKQEKE 350
                                   1111111111111111111111111111111111111222222221 PP

>> A2M_BRD  Alpha-2-macroglobulin bait region domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.23   6.8e+02      73     121 ..      33      82 ..      29      95 .. 0.75
   2 ?   10.3   1.2   0.00022      0.66      17      80 ..     168     262 ..     160     320 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.23
                                   EEEE..E--CEEEEEEE----.-GGGB-EEEEE..EE...-SSS.EEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx.xxxxxxx RF
                       A2M_BRD  73 vvyyirrdgevvadsvqlpvekdfenklsvsle..synetrPge.evtlkvk 121
                                   vv+y  ++g   +d+ +l ++ +  +  s+ ++  + ++++P + ++tl++ 
  gi|15669587|ref|NP_248400.1|  33 VVFY--PNGSQTVDVSKLHIDYENPDAFSIYISyrNSSFYLPYSkNITLNLP 82 
                                   8999..9999999999999998888888888877546677888437777765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00022
                                   EEEEE-SS-....EE-TT-....BSS-----.-S..........................................S.... CS
                                   xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx.......................................xxxxxx RF
                       A2M_BRD  17 kltvkstfa....tverdstlylvlsrgnivssgek.......................................veeids 54 
                                   kl ++++ +     +++++    +ls+g                                               + e ++
  gi|15669587|ref|NP_248400.1| 168 KLMIRYSLPipfsIIKSNK----ILSNGS------IewtaiyiikndknvslnvnasywavvnntkidfgnysyiI-EPNE 237
                                   5555555543343344444....444444......33344446666667777777777777777666666655531.5667 PP

                                   -EEEEEE--TT-----EE.EEEE..E- CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                       A2M_BRD  55 stsfsfpvtadmaPnarv.vvyyirrd 80 
                                   + s sf +t+d++P +++ +++   rd
  gi|15669587|ref|NP_248400.1| 238 NVSQSFNITSDYVPIFYLkFYAW--RD 262
                                   88****************55444..44 PP

>> NOZZLE  Plant transcription factor NOZZLE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   6.3e-05      0.19      43     111 ..     324     396 ..     303     410 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.3e-05
                        NOZZLE  43 grkpgsktgqqkqkkptlrgmgvaklerv...iieeekkktlva..atvgdtsavasisnnatrllpvlvdrgv 111
                                     k   k+  q+ kkp+   m     er+   iiee+ kk ++a  atv  ts +a + +   r    +vd+g+
  gi|15669587|ref|NP_248400.1| 324 RHKKEEKSQTQETKKPSKNEMNKQEKERKyplIIEEKFKK-VAAaiATVTTTSITAMLIPPIFRRRSYIVDKGI 396
                                   4566788999*****************9744356666555.544136888888888888888888888888887 PP

>> Connexin  Connexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.6    0.0007       2.1      92     146 ..     297     351 ..     289     383 .. 0.44

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0007
                      Connexin  92 vyvlhkiakeekekek.eeeekeeeekeeekkkkkekkkkkkkeeekekkkeegkr 146
                                    y+  +i+k+++eke+ e+++++++ ++++k++k+++ +++kk +++e +k+e++r
  gi|15669587|ref|NP_248400.1| 297 NYMEREIKKKKEEKENeESSKTINQMQRHKKEEKSQT-QETKKPSKNEMNKQEKER 351
                                   3444444444443332133333333333333332222.222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3300  (0.184059); expected 358.6 (0.02)
Passed bias filter:                     1322  (0.0737353); expected 358.6 (0.02)
Passed Vit filter:                       283  (0.0157845); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.87u 0.31s 00:00:01.18 Elapsed: 00:00:00.46
# Mc/sec: 3147.51
//
Query:       gi|15669588|ref|NP_248401.1|  [L=391]
Description: hypothetical protein MJ_1398 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-18   66.1   1.3    3.1e-11   42.7   0.1    2.5  2  HTH_24           Winged helix-turn-helix DNA-binding
    5.1e-15   55.1   0.1    5.5e-07   29.3   0.0    2.5  2  HTH_5            Bacterial regulatory protein, arsR family
    1.7e-13   50.4   0.0    3.3e-06   27.0   0.0    2.3  2  HTH_20           Helix-turn-helix domain
    1.3e-08   34.6   2.4     0.0019   18.0   0.4    2.9  3  TrmB             Sugar-specific transcriptional regulator Trm
      3e-07   30.0   0.2     0.0092   15.4   0.0    2.5  2  RepL             Firmicute plasmid replication protein (RepL)
      9e-07   29.2   0.1       0.05   14.0   0.0    2.7  2  Penicillinase_R  Penicillinase repressor
    5.7e-05   23.0   0.1       0.11   12.5   0.0    2.5  2  MarR             MarR family
    0.00018   21.8   0.0       0.17   12.2   0.0    2.4  2  Rrf2             Transcriptional regulator
    0.00051   19.9   0.2       0.08   12.9   0.1    2.8  2  HTH_12           Ribonuclease R winged-helix domain
     0.0014   18.4   0.2       0.27   11.0   0.0    3.0  3  DUF4423          Domain of unknown function (DUF4423)
     0.0034   17.5   0.1       0.29   11.4   0.0    3.2  3  HTH_34           Winged helix DNA-binding domain
     0.0034   17.5   0.7      0.066   13.3   0.3    2.5  2  DUF2250          Uncharacterized protein conserved in archaea
      0.008   16.1   0.0       0.13   12.2   0.0    2.7  2  HTH_Crp_2        Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.021   14.9   0.3       0.48   10.6   0.1    2.5  2  MerR_1           MerR HTH family regulatory protein
      0.025   14.5   0.1      0.025   14.5   0.1    2.4  1  HTH_36           Helix-turn-helix domain
      0.025   15.2   0.0        4.7    7.9   0.0    2.4  2  RPA_C            Replication protein A C terminal
      0.028   14.7   1.8       0.07   13.5   0.1    2.5  2  HTH_WhiA         WhiA C-terminal HTH domain
      0.031   14.7   0.1       0.13   12.7   0.0    2.1  2  FaeA             FaeA-like protein
      0.036   13.9   0.0       0.08   12.8   0.0    1.5  1  HTH_30           PucR C-terminal helix-turn-helix domain
      0.043   14.0   0.2       0.23   11.7   0.0    2.3  2  PaaX             PaaX-like protein
       0.05   13.6   2.9       0.08   12.9   0.1    2.7  3  HTH_11           HTH domain
      0.056   13.2   0.0       0.36   10.6   0.0    2.1  2  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.065   13.1   0.0         11    6.0   0.0    2.3  2  MarR_2           MarR family
      0.074   13.1   0.2       0.22   11.6   0.2    1.8  1  DUF2089          Protein of unknown function (DUF2089)
       0.18   12.4   0.0       0.92   10.1   0.0    2.1  2  HTH_27           Winged helix DNA-binding domain
        3.9    7.5   7.8       0.72    9.9   0.7    3.3  4  HTH_45           Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.1   4.5e-14   3.1e-11       1      48 []     251     298 ..     251     298 .. 0.98
   2 !   22.2   0.1   1.1e-07   7.5e-05       2      48 .]     325     370 ..     324     370 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 4.5e-14
                        HTH_24   1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                   l++t+r+I++++ +np++  reL++ l+ ++st++++l+ Le++ lIk
  gi|15669588|ref|NP_248401.1| 251 LNDTRREIYNYILDNPGCHLRELSKNLNKPVSTLTWHLRILEKANLIK 298
                                   79*********************************************7 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.1e-07
                        HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                   +et++ I e+L k +    r +A+ l+l + tv++ lk+Le+ G++k
  gi|15669588|ref|NP_248401.1| 325 NETQKSIFEYLLK-SPAHLRKIAKDLNLNVETVRYNLKKLENLGIVK 370
                                   7888999999999.88999**************************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0     8e-10   5.5e-07       2      47 .]     253     299 ..     252     299 .. 0.96
   2 !   23.4   0.1   5.8e-08     4e-05       2      47 .]     326     371 ..     325     371 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 8e-10
                                   HHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5   2 ptRlkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                    tR++I ++  +++ +   el++ l+++ st+  HL++L++a+L+++
  gi|15669588|ref|NP_248401.1| 253 DTRREIYNYILDNPgCHLRELSKNLNKPVSTLTWHLRILEKANLIKS 299
                                   79************999***************************985 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 5.8e-08
                                   HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5   2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                   +t+  I  +L ++++    +a++l+l+  tv++ LkkL+++G+V++
  gi|15669588|ref|NP_248401.1| 326 ETQKSIFEYLLKSPAHLRKIAKDLNLNVETVRYNLKKLENLGIVKS 371
                                   67778899************************************86 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   4.8e-09   3.3e-06       5      59 ..     248     302 ..     243     304 .. 0.95
   2 !   21.1   0.0   3.5e-07   0.00024       9      60 ..     325     375 ..     321     376 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.8e-09
                                   HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                        HTH_20   5 eALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59 
                                   ++L++ +Rr+i+ ++ ++ g  + el + l  + +tl  HLr+Le+a L+++ + 
  gi|15669588|ref|NP_248401.1| 248 KVLLNDTRREIYNYILDNPGCHLRELSKNLNKPVSTLTWHLRILEKANLIKSKKF 302
                                   689***********************************************98775 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 3.5e-07
                                   -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20   9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                   ++++  i+ +L  + ++ +  +a+ l l   t++y+L++Le  g+v++ +eg
  gi|15669588|ref|NP_248401.1| 325 NETQKSIFEYL-LKSPAHLRKIAKDLNLNVETVRYNLKKLENLGIVKSKEEG 375
                                   899********.**********************************999887 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       8.1   5.6e+03       6      22 ..     135     151 ..     130     157 .. 0.71
   2 !   15.2   0.0   2.1e-05     0.015      12      67 ..     257     313 ..     248     314 .. 0.93
   3 !   18.0   0.4   2.8e-06    0.0019       8      63 ..     326     381 ..     325     384 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.1
                                   HHHHCCCHCHHHHHHCC CS
                          TrmB   6 LseyEakvYlaLlklgp 22 
                                   L++ E+++   L ++g+
  gi|15669588|ref|NP_248401.1| 135 LKQSEVEALYELPEKGE 151
                                   77788888777766665 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.1e-05
                                   CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE--H CS
                          TrmB  12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravdp 67 
                                   ++Y ++l +     +e++++l+ p s+    Lr Le++ l++ +k g++ +Y ++d+
  gi|15669588|ref|NP_248401.1| 257 EIYNYILDNPGCHLRELSKNLNKPVSTLTWHLRILEKANLIKSKKfGNRLIYYPADM 313
                                   799******************************************99999****997 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 2.8e-06
                                   HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEE CS
                          TrmB   8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYr 63 
                                   e+  +++ +Ll + pa  ++ia++l++   +v   L++Le+ G+V+ +++  + +Y 
  gi|15669588|ref|NP_248401.1| 326 ETQKSIFEYLL-KSPAHLRKIAKDLNLNVETVRYNLKKLENLGIVKSKEEGnRIVYY 381
                                   66778899999.889*******************************98855255664 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00014     0.097      40     114 ..     234     306 ..     229     329 .. 0.81
   2 !   15.4   0.0   1.3e-05    0.0092      78     120 ..     342     387 ..     337     389 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                          RepL  40 kvwienliatld....liGnkktrlvyylidnlnsnntliatnRelaeetgislktvsetlkileeanilkkkanGvlv 114
                                   kv+i + i+ ld    l+ + + ++ +y++dn        +  Rel+++ +  + t +  l+ile+an++k k  G  +
  gi|15669588|ref|NP_248401.1| 234 KVFILSRINLLDeekvLLNDTRREIYNYILDNPG------CHLRELSKNLNKPVSTLTWHLRILEKANLIKSKKFGNRL 306
                                   5555555555555555677788888888888864......778****************************99888655 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-05
                          RepL  78 nRelaeetgislktvsetlkileeanilkkkanG...vlvinPdll 120
                                    R++a++ ++ ++tv+  lk le+ +i+k k +G   v+ in  +l
  gi|15669588|ref|NP_248401.1| 342 LRKIAKDLNLNVETVRYNLKKLENLGIVKSKEEGnriVYYINESIL 387
                                   59*****************************999766788887765 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   7.2e-05      0.05       6      65 ..     256     311 ..     251     318 .. 0.91
   2 !   12.3   0.0   0.00024      0.17      26      63 ..     344     381 ..     337     386 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.2e-05
                                   SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE-- CS
               Penicillinase_R   6 aevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYspl 65 
                                   +e+++++ ++  +  +e+ + l+++     sT +  lr L+k +l++++k g++ iY+p+
  gi|15669588|ref|NP_248401.1| 256 REIYNYILDNPGCHLRELSKNLNKP----VSTLTWHLRILEKANLIKSKKFGNRLIYYPA 311
                                   7899999999999999999999999....99***************************96 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00024
                                   T--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE CS
               Penicillinase_R  26 eleeekelaysTVktllrrLvkKgllsrekegrafiYs 63 
                                   +++++ +l+ +TV+  l++L++ g++++++eg++++Y+
  gi|15669588|ref|NP_248401.1| 344 KIAKDLNLNVETVRYNLKKLENLGIVKSKEEGNRIVYY 381
                                   567788899****************************8 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00015      0.11      14      50 ..     264     300 ..     260     302 .. 0.92
   2 !    7.7   0.0    0.0047       3.2      18      50 ..     340     372 ..     336     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                   HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR  14 eqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                   +++++ + eL k l+   st+t  l+ Lek++li+++
  gi|15669588|ref|NP_248401.1| 264 DNPGCHLRELSKNLNKPVSTLTWHLRILEKANLIKSK 300
                                   679999****************************986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0047
                                   EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR  18 lsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                   + + ++ak l+++  tv   l++Le  G ++++
  gi|15669588|ref|NP_248401.1| 340 AHLRKIAKDLNLNVETVRYNLKKLENLGIVKSK 372
                                   56789***********************99865 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.011       7.7      26      59 ..     268     301 ..     260     306 .. 0.91
   2 !   12.2   0.0   0.00025      0.17      25      58 ..     339     372 ..     331     377 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                                   B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          Rrf2  26 vsseeiaerqnispsylekilakLrkaglvksvr 59 
                                   + ++e++++ n + s l   l+ L+ka+l+ks++
  gi|15669588|ref|NP_248401.1| 268 CHLRELSKNLNKPVSTLTWHLRILEKANLIKSKK 301
                                   6789****************************86 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00025
                                   -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2  25 pvsseeiaerqnispsylekilakLrkaglvksv 58 
                                   p+ +++ia+  n++ + ++  l+kL++ g+vks+
  gi|15669588|ref|NP_248401.1| 339 PAHLRKIAKDLNLNVETVRYNLKKLENLGIVKSK 372
                                   67899***************************97 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.072        49      34      55 ..     283     304 ..     270     308 .. 0.79
   2 !   12.9   0.1   0.00012      0.08      19      53 ..     345     374 ..     335     380 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.072
                        HTH_12  34 avRyrLrkleergltrrvgyag 55 
                                   ++  +Lr+le+ +l++ +  + 
  gi|15669588|ref|NP_248401.1| 283 TLTWHLRILEKANLIKSKKFGN 304
                                   5678***********9776655 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00012
                        HTH_12  19 iaeeLkkrgydigeravRyrLrkleergltrrvgy 53 
                                   ia+     + ++  ++vRy L+kle+ g+++ +  
  gi|15669588|ref|NP_248401.1| 345 IAK-----DLNLNVETVRYNLKKLENLGIVKSKEE 374
                                   444.....44566799************9986655 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.1   7.3e+02      35      75 ..     122     160 ..     118     176 .. 0.84
   2 ?    3.1   0.0       0.1        69      40      73 ..     271     302 ..     264     306 .. 0.82
   3 !   11.0   0.0   0.00038      0.27      37      75 ..     340     376 ..     331     384 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                       DUF4423  35 fkadpeelakrlrpkisaeevekalefLlklgllkkdedgk 75 
                                   +++++ ++++ l+  ++++eve+  e+ +k +++ + +dgk
  gi|15669588|ref|NP_248401.1| 122 GNKTIIWIKDPLK--LKQSEVEALYELPEKGEVIARYKDGK 160
                                   568999*******..*******9999999999999999887 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.1
                       DUF4423  40 eelakrlrpkisaeevekalefLlklgllkkded 73 
                                   +el+k l+   +++     l++L+k++l+k ++ 
  gi|15669588|ref|NP_248401.1| 271 RELSKNLN--KPVSTLTWHLRILEKANLIKSKKF 302
                                   79999999..566667778***********9875 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00038
                       DUF4423  37 adpeelakrlrpkisaeevekalefLlklgllkkdedgk 75 
                                   a  +++ak l+  +++e v+  l+ L++lg++k +e+g+
  gi|15669588|ref|NP_248401.1| 340 AHLRKIAKDLN--LNVETVRYNLKKLENLGIVKSKEEGN 376
                                   56789******..***********************986 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.9   1.3e+03      37      60 ..     180     203 ..     178     207 .. 0.86
   2 !   11.4   0.0   0.00041      0.29       4      48 ..     257     301 ..     254     305 .. 0.90
   3 ?    1.4   0.0      0.53   3.7e+02      13      47 ..     338     372 ..     330     379 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.9
                        HTH_34  37 kLekagYievdkefkgkkprtllr 60 
                                   +L +  Yi++ k+ ++  p +l++
  gi|15669588|ref|NP_248401.1| 180 VLANLIYIHIVKKTSNPLPYILFT 203
                                   688889*********999998877 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00041
                        HTH_34   4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdk 48 
                                   ++  y +++     +el++ l+   + L  hl++Leka+ i+ +k
  gi|15669588|ref|NP_248401.1| 257 EIYNYILDNPGCHLRELSKNLNKPVSTLTWHLRILEKANLIKSKK 301
                                   67788899999999***************************9887 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.53
                        HTH_34  13 deadfvelkealeatdgnLsvhlkkLekagYievd 47 
                                   + a  +++ + l+++      +lkkLe+ g ++ +
  gi|15669588|ref|NP_248401.1| 338 SPAHLRKIAKDLNLNVETVRYNLKKLENLGIVKSK 372
                                   45788899999999999999*********988765 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.47   3.3e+02      24      56 ..     269     301 ..     248     310 .. 0.85
   2 !   13.3   0.3   9.6e-05     0.066      21      57 ..     338     374 ..     322     388 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.47
                       DUF2250  24 YaksiakeleipleevrellkkLeelGLlerve 56 
                                   + + ++k+l++p++  +  l+ Le++ L++ ++
  gi|15669588|ref|NP_248401.1| 269 HLRELSKNLNKPVSTLTWHLRILEKANLIKSKK 301
                                   5688999*********************99775 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 9.6e-05
                       DUF2250  21 nvdYaksiakeleipleevrellkkLeelGLlerveg 57 
                                    + + + iak l++++e vr  lkkLe+lG+++ +e+
  gi|15669588|ref|NP_248401.1| 338 SPAHLRKIAKDLNLNVETVRYNLKKLENLGIVKSKEE 374
                                   4678899*************************98873 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.2   8.2e+02      35      53 ..     281     300 ..     269     310 .. 0.72
   2 !   12.2   0.0   0.00019      0.13      17      57 ..     335     378 ..     320     384 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHTTSEE.E CS
                     HTH_Crp_2  35 retvsrilseLkreglis.r 53 
                                    +t++  l+ L++++li+ +
  gi|15669588|ref|NP_248401.1| 281 VSTLTWHLRILEKANLIKsK 300
                                   6788889999*******964 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00019
                                   EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E..TEEE CS
                     HTH_Crp_2  17 eielpltqeelAsmlGltretvsrilseLkreglis.r..grri 57 
                                    ++ p   + +A  l+l+ etv   l++L++ g+++ +  g+ri
  gi|15669588|ref|NP_248401.1| 335 LLKSPAHLRKIAKDLNLNVETVRYNLKKLENLGIVKsKeeGNRI 378
                                   4556777789**************************75323334 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.44     3e+02       5      42 ..     272     312 ..     269     315 .. 0.62
   2 ?   10.6   0.1   0.00069      0.48       5      46 ..     344     389 ..     341     391 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.44
                                   HHHHHHTS-HHH....HHHHHHHTT-S-EE-TTS-EEEEHHH CS
                        MerR_1   5 evakilgvttht....lrywekegllkpkrteggrryYtded 42 
                                   e++k l+ +++t    lr  ek  l+k k+  g+r +Y ++d
  gi|15669588|ref|NP_248401.1| 272 ELSKNLNKPVSTltwhLRILEKANLIKSKK-FGNRLIYYPAD 312
                                   555555555555112267788888899999.77776666666 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00069
                                   HHHHHHTS-HHHHHHHHHHTT.-S-EE..-TTS-.EEEEHHHHHHH CS
                        MerR_1   5 evakilgvtthtlrywekegl.lkpkr..teggr.ryYtdedierL 46 
                                   + ak l++++ t+ry  k+   l + +   eg+r  yY +e i  +
  gi|15669588|ref|NP_248401.1| 344 KIAKDLNLNVETVRYNLKKLEnLGIVKskEEGNRiVYYINESILKF 389
                                   689***************999977777779999999**99998766 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.6e-05     0.025      29      55 .]     343     369 ..     333     369 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                        HTH_36  29 etlakrlglsknTvsraikeLeqlGyi 55 
                                   + +ak+l+l+++Tv+  +k+Le lG++
  gi|15669588|ref|NP_248401.1| 343 RKIAKDLNLNVETVRYNLKKLENLGIV 369
                                   68***********************85 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.065        45      48      90 ..     252     290 ..     242     297 .. 0.81
   2 ?    7.9   0.0    0.0068       4.7      69      97 ..     341     369 ..     327     371 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.065
                                   XHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHH CS
                         RPA_C  48 talaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavde 90 
                                   +++ ++++n+i +    + G h++e++++l+ +v++++  ++ 
  gi|15669588|ref|NP_248401.1| 252 NDTRREIYNYILD----NPGCHLRELSKNLNKPVSTLTWHLRI 290
                                   5677888999888....89***************999866655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0068
                                   EHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                         RPA_C  69 hvdeiaqklrlsvndvkqavdeLsneGii 97 
                                   h++ ia+ l+l+v++v+  +++L+n Gi+
  gi|15669588|ref|NP_248401.1| 341 HLRKIAKDLNLNVETVRYNLKKLENLGIV 369
                                   899************************97 PP

>> HTH_WhiA  WhiA C-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1    0.0001      0.07      23      69 ..     238     282 ..     230     294 .. 0.90
   2 ?   -1.6   0.1         5   3.5e+03      57      57 ..     351     351 ..     314     374 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHHT-GGGS-HHHHHHHHHHHH-TTS-HHHHHHTT..T-- CS
                      HTH_WhiA  23 ieaielieekkgleklpeklkevaelRlenpdaSLkeLgelleppis 69 
                                   + +i+l++e+k    l++  +e+ ++ l+np + L+eL++ l++p+s
  gi|15669588|ref|NP_248401.1| 238 LSRINLLDEEKV--LLNDTRREIYNYILDNPGCHLRELSKNLNKPVS 282
                                   578999999988..9******************************98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5
                                   H CS
                      HTH_WhiA  57 L 57 
                                   L
  gi|15669588|ref|NP_248401.1| 351 L 351
                                   2 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       6.3   4.3e+03       5      43 ..     258     295 ..     255     301 .. 0.57
   2 ?   12.7   0.0   0.00019      0.13       3      46 ..     329     370 ..     327     380 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.3
                                   HHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHS CS
                          FaeA   5 IleylnsikapckTreiAdalglsaYQaRyYLeqLekeg 43 
                                   I +y+ + + +c+ re+ + l          L  Lek+ 
  gi|15669588|ref|NP_248401.1| 258 IYNYILD-NPGCHLRELSKNLNKPVSTLTWHLRILEKAN 295
                                   6667766.6677777766655444444444555555555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00019
                                   HHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                          FaeA   3 eeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkik 46 
                                    +I eyl +  +p++ r iA+ l l    +Ry L++Le  g +k
  gi|15669588|ref|NP_248401.1| 329 KSIFEYLLK--SPAHLRKIAKDLNLNVETVRYNLKKLENLGIVK 370
                                   689999987..9****************************9997 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012      0.08       9      39 ..     336     366 ..     331     370 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                                   HHTTT-HHHHHHHHTS-HHHHHHHHHHHHHH CS
                        HTH_30   9 lenggnisatAkaLhvHrnTlryRLrrieel 39 
                                   l++   +++ Ak L++ + T+ry L+++e l
  gi|15669588|ref|NP_248401.1| 336 LKSPAHLRKIAKDLNLNVETVRYNLKKLENL 366
                                   66778899********************986 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       6.3   4.3e+03       6      24 ..      16      34 ..      15      37 .. 0.84
   2 ?   11.7   0.0   0.00033      0.23      26      66 ..     342     382 ..     330     386 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.3
                          PaaX  6 ivtlygdyveprggaiwlg 24
                                  iv +yg yv+ +g +++l+
  gi|15669588|ref|NP_248401.1| 16 IVHVYGIYVHIYGINVSLE 34
                                  8899*****9999888876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00033
                          PaaX  26 LirllaelGiseslvRaalsRlakaGwlvrekegrrsfYrL 66 
                                   L ++ ++l ++ ++vR  l  l++ G +++++eg+r +Y  
  gi|15669588|ref|NP_248401.1| 342 LRKIAKDLNLNVETVRYNLKKLENLGIVKSKEEGNRIVYYI 382
                                   6678999****************************998865 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.3   1.6e+03      32      49 ..      73      91 ..      73      93 .. 0.75
   2 ?   -1.9   0.1         5   3.5e+03      17      40 ..     269     292 ..     254     301 .. 0.51
   3 ?   12.9   0.1   0.00012      0.08       3      46 ..     329     369 ..     327     377 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.3
                        HTH_11 32 vrrdIkaLeelg.vpIese 49
                                  v rdI+ L +++ ++Ie +
  gi|15669588|ref|NP_248401.1| 73 VDRDIAPLIKKLrFKIENK 91
                                  6799*99955555999865 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5
                        HTH_11  17 sgeeLAeeLnvSrrtvrrdIkaLe 40 
                                      eL++ Ln   +t   ++++Le
  gi|15669588|ref|NP_248401.1| 269 HLRELSKNLNKPVSTLTWHLRILE 292
                                   444555555555555555555555 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00012
                        HTH_11   3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46 
                                   ++i e Ll++       ++A+ Ln+   tvr  +k+Le lg  +
  gi|15669588|ref|NP_248401.1| 329 KSIFEYLLKSP--AHLRKIAKDLNLNVETVRYNLKKLENLG-IV 369
                                   66777775555..5689************************.44 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.8   1.2e+03       4      43 ..     257     296 ..     255     300 .. 0.73
   2 ?   10.6   0.0   0.00052      0.36       3      44 ..     329     369 ..     328     375 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.8
                      HTH_DeoR   4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqgl 43 
                                   +i  ++ +   +++ el+  l+    T    L++Le+++l
  gi|15669588|ref|NP_248401.1| 257 EIYNYILDNPGCHLRELSKNLNKPVSTLTWHLRILEKANL 296
                                   7888999999999999999998666665555666666655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00052
                      HTH_DeoR   3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44 
                                   + i e+l ++   ++ +++  l+   +T+R  L++Le+ g++
  gi|15669588|ref|NP_248401.1| 329 KSIFEYLLKS-PAHLRKIAKDLNLNVETVRYNLKKLENLGIV 369
                                   5677777776.46999************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.038        26      12      53 ..     260     299 ..     251     305 .. 0.90
   2 ?    6.0   0.0     0.015        11      13      54 ..     334     372 ..     325     377 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.038
                                   HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2  12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53 
                                   +++ ++pg  +  +el + l+ + s+++ +l+ L++a L+  
  gi|15669588|ref|NP_248401.1| 260 NYILDNPG--CHLRELSKNLNKPVSTLTWHLRILEKANLIKS 299
                                   579999*9..*****************************975 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.015
                                   HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                   +L  +p      + +a+ l+l   +v + lk+L+  G v  +
  gi|15669588|ref|NP_248401.1| 334 YLLKSP---AHLRKIAKDLNLNVETVRYNLKKLENLGIVKSK 372
                                   566666...477889**********************99755 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00032      0.22      31      84 ..     320     373 ..     314     389 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                       DUF2089  31 farLskeql.efvelfikarGnlkevekelgisYpTvrnrldeileaLgyeeeee 84 
                                   + +L++e++ +  e ++k+  +l++++k l++   Tvr  l+++ e+Lg+ +++e
  gi|15669588|ref|NP_248401.1| 320 LLYLKNETQkSIFEYLLKSPAHLRKIAKDLNLNVETVRYNLKKL-ENLGIVKSKE 373
                                   55677775515668889************************995.7899988866 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.5   3.8e+03      20      50 ..     269     299 ..     261     302 .. 0.81
   2 ?   10.1   0.0    0.0013      0.92      18      58 ..     339     377 ..     335     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.5
                        HTH_27  20 kladlcgrlnvedshisyslkkLtekGLver 50 
                                   +l++l++ ln   s+    l+ L+++ L+++
  gi|15669588|ref|NP_248401.1| 269 HLRELSKNLNKPVSTLTWHLRILEKANLIKS 299
                                   7889999999988888888999999999944 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0013
                        HTH_27  18 rkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58 
                                   +++l+ +++ ln++  ++ y+lkkL++ G v++  +e+  r
  gi|15669588|ref|NP_248401.1| 339 PAHLRKIAKDLNLNVETVRYNLKKLENLGIVKS--KEEGNR 377
                                   7899***************************33..344444 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2       3.7   2.6e+03      27      40 ..      27      40 ..      26      43 .. 0.90
   2 ?   -2.5   0.0       7.5   5.2e+03      53      63 ..     141     151 ..     105     155 .. 0.63
   3 ?   -0.8   0.0       2.2   1.5e+03      25      52 ..     273     300 ..     254     305 .. 0.69
   4 ?    9.9   0.7     0.001      0.72      10      54 ..     330     374 ..     324     384 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.7
                        HTH_45 27 ykanLsykllnkYL 40
                                  y  n s +++++YL
  gi|15669588|ref|NP_248401.1| 27 YGINVSLENVSQYL 40
                                  899**********9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.5
                        HTH_45  53 kekYvlTekGl 63 
                                   +  Y+l ekG+
  gi|15669588|ref|NP_248401.1| 141 EALYELPEKGE 151
                                   44566666665 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.2
                        HTH_45  25 imykanLsykllnkYLdmLvekglikks 52 
                                   + ++ n   ++l   L +L + +lik +
  gi|15669588|ref|NP_248401.1| 273 LSKNLNKPVSTLTWHLRILEKANLIKSK 300
                                   5556666667778889999999999776 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.001
                        HTH_45  10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkske 54 
                                   +I e++ ++ a+  ki ++ nL+ ++++  L++L + g++k ++e
  gi|15669588|ref|NP_248401.1| 330 SIFEYLLKSPAHLRKIAKDLNLNVETVRYNLKKLENLGIVKSKEE 374
                                   57788888999999**************************77654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1162  (0.0648112); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2617.48
//
Query:       gi|15669589|ref|NP_248402.1|  [L=197]
Description: hypothetical protein MJ_1399 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-18   65.0   0.0    1.5e-17   64.3   0.0    1.3  1  AAA_17           AAA domain
    8.8e-15   55.4   0.5    6.6e-14   52.6   0.1    1.9  2  AAA_18           AAA domain
     0.0011   19.1   0.0     0.0019   18.3   0.0    1.5  1  ADK              Adenylate kinase
     0.0074   16.2   0.0      0.017   15.0   0.0    1.5  1  P-mevalo_kinase  Phosphomevalonate kinase
     0.0098   16.1   0.2       0.19   11.9   0.2    2.3  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.015   15.2   0.9       0.73    9.6   0.0    2.5  3  dNK              Deoxynucleoside kinase
       0.03   13.3   0.2      0.094   11.7   0.0    1.8  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.057   12.9   0.6        1.1    8.6   0.1    2.3  2  KTI12            Chromatin associated protein KTI12
      0.093   12.4   0.1       0.47   10.1   0.0    2.0  2  CoaE             Dephospho-CoA kinase
       0.16   11.8   0.0        1.5    8.6   0.0    2.1  2  AAA_26           AAA domain


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   8.2e-21   1.5e-17       1     132 [.       7     131 ..       7     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 8.2e-21
                                   EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHH.....HHHHHH.HSSEEE CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaae.....kiaeea.kkkgvl 75 
                                   +G+PG+GK+ +  ++++ky+++++s+Gd++r e k++gl+ + +++ +  ++ ++e+  ea++      i+e+  +k+ v+
  gi|15669589|ref|NP_248402.1|   7 TGMPGAGKSSAY-EIAKKYNLPIVSMGDVVRYETKKRGLELTPENVGNTAIKLREEFGNEAIAvaclkYIEENLkDKEIVI 86 
                                   7********999.**********************************8888888888777765222213444433555577 PP

                                   EEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SH CS
                        AAA_17  76 vdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddne 132
                                   v+g  ++         ++++ +++ kp ++i ++ +p + +er++k   rgr+dd++
  gi|15669589|ref|NP_248402.1|  87 VEGIRSL---------YEVNYFRKHKPLVLIAIHSSPLTRFERLKK---RGREDDSA 131
                                   7777665.........7789999**************999988876...67766654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.1   3.7e-17   6.6e-14       1     120 [.       4     131 ..       4     142 .. 0.92
   2 ?    1.5   0.1      0.22   3.9e+02      17      67 ..     140     186 ..     135     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 3.7e-17
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssaleegk 75 
                                   I++tG+pG+GK++  +  +k  ++     g+++r   k++gl+l+ ++   +  ++r++ ++ + ++ +l+ + ++l + +
  gi|15669589|ref|NP_248402.1|   4 IGITGMPGAGKSSAYEIAKKY-NLpivsmGDVVRYETKKRGLELTPENVgNTAIKLREEFGNEAIAVACLKYIEENLKDKE 83 
                                   89***********99999776.4566************************9999*******************9999**** PP

                        AAA_18  76 nlvidghlaeleseaakdikk...vvLtaspeelleRlekRgyeeaki 120
                                    ++++g+++ +e  +++++k    + ++ sp +++eRl+kRg+e++  
  gi|15669589|ref|NP_248402.1|  84 IVIVEGIRSLYEVNYFRKHKPlvlIAIHSSPLTRFERLKKRGREDDSA 131
                                   *****************9888*********************998773 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.22
                        AAA_18  17 eLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleen 67 
                                    L+++   g+ +++ ++  + +  +++  +++++   ++ l+++l++le+ 
  gi|15669589|ref|NP_248402.1| 140 DLREL---GFSIGHAIALADFVVVNEKS-FEDCLNQLDNILQEILNNLEKY 186
                                   56555...77778888888888777777.8999999999999999999875 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     1e-06    0.0019       1      37 [.       6      41 ..       6      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1e-06
                                  EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHC CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevks 37
                                  + G PgaGK   a +++kky+l+ +s Gd++R e+k+
  gi|15669589|ref|NP_248402.1|  6 ITGMPGAGKS-SAYEIAKKYNLPIVSMGDVVRYETKK 41
                                  679******6.6899*****************99876 PP

>> P-mevalo_kinase  Phosphomevalonate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   9.6e-06     0.017      57     111 ..      49     102 ..      45     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.6e-06
               P-mevalo_kinase  57 ekyRkemikwgeekrkkdpglFcraaiekieaakkdvliisDiRrktdleyfkea 111
                                   e++ ++ ik+ ee  ++  ++ c + ie+ + ++k+++i+ +iR   +++yf+++
  gi|15669589|ref|NP_248402.1|  49 ENVGNTAIKLREEFGNEAIAVACLKYIEE-NLKDKEIVIVEGIRSLYEVNYFRKH 102
                                   677888999999999************97.7999******************986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.2   0.00011      0.19       4     124 ..       6     130 ..       3     139 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                        AAA_33   4 lvGlpGsGKstlaerllkklg......avllssdtlrrrlfgtdqqsktdytrvldr......lyqilnelarkalsagrn 72 
                                   + G+pG+GKs  +e ++kk        + +++  t +r l+ t ++  +  ++++++      + ++l ++++++l+ +  
  gi|15669589|ref|NP_248402.1|   6 ITGMPGAGKSSAYE-IAKKYNlpivsmGDVVRYETKKRGLELTPENVGNTAIKLREEfgneaiAVACL-KYIEENLKDKEI 84 
                                   67999999999998.56666654555555555555555554444444444444443333334355566.888888887654 PP

                        AAA_33  73 vildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangdd 124
                                   vi   + +s  e     + +r+++ p  ++++++++ t  eRl+kR ++ d+
  gi|15669589|ref|NP_248402.1|  85 VI-VEGIRSLYEV----NYFRKHK-PLVLIAIHSSPLTRFERLKKRGREDDS 130
                                   44.5567766665....5556666.8999******************98654 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.009        16       1      85 [.       4      94 ..       4      99 .. 0.68
   2 ?    9.6   0.0   0.00041      0.73      98     149 ..      76     130 ..      65     141 .. 0.81
   3 ?   -1.5   0.1         1   1.8e+03      31      52 ..     165     186 ..     151     195 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.009
                                  EEEEESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSSHHHHHHHHSHHHHHHHHHHHHHHHHH.....HHHHCHHSSS-EE CS
                           dNK  1 ivveGnIgaGKstlvklLskklgvkvfeEpvdkwtnvqknlLekfYkdpsrwsfalqtyvllsrl.....kqqlealatkqvv 78
                                  i + G  gaGKs+  ++ +k +   v    v ++ +++k  Le+  +++ + +++l  ++ ++ +     k+++e l+ k++v
  gi|15669589|ref|NP_248402.1|  4 IGITGMPGAGKSSAYEIAKKYNLPIVSMGDVVRY-ETKKRGLELTPENVGNTAIKLREEFGNEAIavaclKYIEENLKDKEIV 85
                                  6689999********9988876544444566688.667788999999999999999888777665111114444444777777 PP

                                  EEE..S-HH CS
                           dNK 79 vle..Rsiy 85
                                  ++e  Rs y
  gi|15669589|ref|NP_248402.1| 86 IVEgiRSLY 94
                                  777556665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00041
                                   TTSS-HHHHHHHHHHHHHHH.HHCCH..-SEEEEEE--HHHHHHHHHHCTTCCCT CS
                           dNK  98 kgtlseeelkiykelldnll.eelak..pdlliYLkasletclerikkRgreeek 149
                                   ++ l+++e+ i + +++ +  +++ k  p +li ++ s+ t +er+kkRgre++ 
  gi|15669589|ref|NP_248402.1|  76 EENLKDKEIVIVEGIRSLYEvNYFRKhkPLVLIAIHSSPLTRFERLKKRGREDDS 130
                                   5667777888877777777766666666999********************9875 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1
                                   HHHCCSSSSHHHHHHHHSHHHH CS
                           dNK  31 vdkwtnvqknlLekfYkdpsrw 52 
                                    ++  n+  n+L+ + ++ +++
  gi|15669589|ref|NP_248402.1| 165 FEDCLNQLDNILQEILNNLEKY 186
                                   3333344445555555555444 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.3e-05     0.094      31      47 ..       3      19 ..       1      33 [. 0.87
   2 ?   -1.1   0.0      0.41   7.4e+02     166     194 ..     152     181 ..     149     190 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.3e-05
                                  EEEEEE-TTSSHHHHHH CS
                          MeaB 31 vvGltGvPGaGkstlve 47
                                   +G+tG+PGaGks + e
  gi|15669589|ref|NP_248402.1|  3 LIGITGMPGAGKSSAYE 19
                                  69***********8765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.41
                                   HHH-SEEEEE---.HHHHHHHHHHHHHHHH CS
                          MeaB 166 leiaDiivvnkaD.kkeaekaarelraale 194
                                   + +aD +vvn    +   ++  + l+ +l+
  gi|15669589|ref|NP_248402.1| 152 IALADFVVVNEKSfEDCLNQLDNILQEILN 181
                                   568999999987634445555556665555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00062       1.1       1      77 [.       1      88 [.       1     100 [. 0.67
   2 ?    2.1   0.0      0.06   1.1e+02     183     209 ..     160     186 ..     151     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00062
                                  E.EEEEE--TTSSHHHHHHHHHHHHHH............TT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHHHHHHHTT. CS
                         KTI12  1 MpLvvltGlPssGKstrakeLakalee............ekrsvvviddeslgiekdsykdsakekalRsslrsavkrdLske 71
                                  M L+ +tG+P +GKs+ a e+ak+ +             +k++   +  e +g +  + +++   +a+  +  + ++++L+ +
  gi|15669589|ref|NP_248402.1|  1 MLLIGITGMPGAGKSS-AYEIAKKYNLpivsmgdvvryeTKKRGLELTPENVGNTAIKLREEFGNEAIAVACLKYIEENLKDK 82
                                  88999**********7.455666555556656666666544444444455555555556666666777777777788888888 PP

                                  SEEEE- CS
                         KTI12 72 kvVIvD 77
                                  ++VIv 
  gi|15669589|ref|NP_248402.1| 83 EIVIVE 88
                                  888876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.06
                                   -------HHHHHHHHHHHHHHHHHHH. CS
                         KTI12 183 skplaeanflqeLdketseivkeilea 209
                                    + ++ ++ l++Ld++ +ei++++ + 
  gi|15669589|ref|NP_248402.1| 160 VNEKSFEDCLNQLDNILQEILNNLEKY 186
                                   566788999************998764 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00026      0.47       2      35 ..       3      36 ..       2      69 .. 0.80
   2 ?    0.2   0.0      0.29   5.1e+02     159     176 ..     147     164 ..      64     167 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00026
                                  EEEEEESTTSSHHHHHHHHHHTT-EEEEHHHHHH CS
                          CoaE  2 ivgltGgiasGKstvanlfadlgvpivDaDlvAr 35
                                  ++g+tG  ++GKs + ++ +++++piv    v r
  gi|15669589|ref|NP_248402.1|  3 LIGITGMPGAGKSSAYEIAKKYNLPIVSMGDVVR 36
                                  79************************98644444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.29
                                   -HHHHHHH-SEEEE-.SS CS
                          CoaE 159 seeerlaladvvldNdss 176
                                   s    +alad+v+ N+ s
  gi|15669589|ref|NP_248402.1| 147 SIGHAIALADFVVVNEKS 164
                                   445566788888888766 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.18   3.3e+02     115     133 ..      12      30 ..       4      59 .. 0.81
   2 ?    8.6   0.0   0.00085       1.5      83     112 ..      66      95 ..      47     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.18
                        AAA_26 115 teellnadiaknlgapvil 133
                                   + + + ++iak+ ++p++ 
  gi|15669589|ref|NP_248402.1|  12 AGKSSAYEIAKKYNLPIVS 30 
                                   5567899*********995 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00085
                        AAA_26  83 gedidlekivkelekdadivvVEGagglgv 112
                                     +++  k+++e+ kd++iv+VEG+ +l +
  gi|15669589|ref|NP_248402.1|  66 AIAVACLKYIEENLKDKEIVIVEGIRSLYE 95 
                                   44555667779**************99873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1156  (0.0644765); expected 358.6 (0.02)
Passed bias filter:                      859  (0.0479112); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1222.11
//
Query:       gi|15669590|ref|NP_248403.1|  [L=67]
Description: hypothetical protein MJ_1400 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-11   43.3   2.4      3e-11   42.9   2.4    1.2  1  Class_IIIsignal  Class III signal peptide
      0.001   18.8   1.0     0.0012   18.6   1.0    1.1  1  ABC_membrane     ABC transporter transmembrane region


Domain annotation for each model (and alignments):
>> Class_IIIsignal  Class III signal peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   2.4   3.3e-15     3e-11       1      27 []      11      37 ..      11      37 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 3.3e-15
               Class_IIIsignal  1 kKGQiSlEyiLLilavlviaiiaiyyy 27
                                  +KGQiSlE++LL+++v+++aii++yy+
  gi|15669590|ref|NP_248403.1| 11 NKGQISLEFSLLVMVVVLSAIIVSYYL 37
                                  8************************95 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.0   1.3e-07    0.0012     140     190 ..      16      66 ..      13      67 .] 0.95

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-07
                                   SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTH CS
                  ABC_membrane 140 gwkltlvllailpliilvsaviakilkklkkkeqkavakassvaeEslsgi 190
                                   +  ++l+++++++  i+vs+++ k+  + ++ +++ ++++s+vae sls++
  gi|15669590|ref|NP_248403.1|  16 SLEFSLLVMVVVLSAIIVSYYLIKTAIETRNANMDVINQSSNVAEKSLSNV 66 
                                   66799*********************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 495.19
//
Query:       gi|15669591|ref|NP_248404.1|  [L=808]
Description: putative ATP dependent RNA helicase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-23   83.6   0.2    4.6e-23   81.9   0.0    2.0  3  DEAD        DEAD/DEAH box helicase
    8.5e-17   61.5   0.1    3.9e-16   59.4   0.0    2.3  2  Helicase_C  Helicase conserved C-terminal domain
    6.3e-11   42.6   0.3    2.4e-10   40.7   0.0    2.1  2  ResIII      Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   7.7e-27   4.6e-23       2     172 ..     214     375 ..     213     379 .. 0.86
   2 ?   -3.2   0.0       1.1   6.3e+03      65     104 ..     449     488 ..     415     492 .. 0.53
   3 ?   -3.7   0.0       1.5   8.7e+03      76     112 ..     718     755 ..     701     763 .. 0.59

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 7.7e-27
                                   HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   ++Q  ++++ l +g+d+l+  +T sGKTl+  ++ +++++    ktg+k l+++P+ +La+q + ++k++ ++++ +v+l 
  gi|15669591|ref|NP_248404.1| 214 PVQTLSVKAGLlNGDDLLIISATSSGKTLIGELAGIKNLI----KTGKKFLFLVPLVALANQKYLEFKERYEKLGFKVSLR 290
                                   678888888776999************************5....8****************************99999988 PP

                                   ETTSSHHHHHHHHH.TTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSE CS
                                   xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskld.ngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrq 161
                                   +g  +  +++++    ++di+vgt + +d l++t++  l+++ ++V+DE++ l  ++++  ++ ++ +l+   ++     q
  gi|15669591|ref|NP_248404.1| 291 VGLGRIGKKVDVETsLDADIIVGTYEGIDYLIRTKR--LKDIGTVVIDEIHSLNLEERGARLDGLIGRLRFLFKE----AQ 365
                                   77444433333332156****************999..*******************************766555....45 PP

                                   EEEEESSBSHH CS
                                   xxxxxxxxxxx RF
                          DEAD 162 vivlSATlpkd 172
                                    i lSAT+  +
  gi|15669591|ref|NP_248404.1| 366 KIYLSATIG-N 375
                                   *******97.4 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.1
                                   HHHHHHTTTSTSEEEEEETTSSHHHHHHHHH....TTCSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxx RF
                          DEAD  65 nnlkkfkkyidlrvlliiggvaardqlskld....ngvdivvgt 104
                                   + lk+ +     +++   gg ++ + +++ d    +++++vv+t
  gi|15669591|ref|NP_248404.1| 449 KALKSKGI----KAEFYHGGMEYIKRRKVEDdfanQKIQCVVTT 488
                                   33333333....33344444443333332222221347777766 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 1.5
                                   SEEE.EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH CS
                                   xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  76 lrvl.liiggvaardqlskldngvdivvgtpgrlddll 112
                                   l++  + ++gv+ ++++ ++  +++i   tpg++ + l
  gi|15669591|ref|NP_248404.1| 718 LTLIiMEFEGVEVEEKILEMIINLRISGKTPGQISKTL 755
                                   33332345566666666555577888888888877754 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       2.8   1.7e+04       6      37 ..      63      88 ..      59      97 .. 0.61
   2 !   59.4   0.0   6.6e-20   3.9e-16      12     111 .]     427     530 ..     409     530 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.8
                                  HHHHHHHTTTTSEEEEEESSHHHHHHHHHHHH CS
                    Helicase_C  6 llellkleeeggkilifvntidrlekvkllle 37
                                  +lell    + +ki i  ++ +++e  ++l++
  gi|15669591|ref|NP_248404.1| 63 VLELL----KSDKIFILKENEEEIE--EVLKS 88
                                  55665....6778888888888886..55532 PP

  == domain 2  score: 59.4 bits;  conditional E-value: 6.6e-20
                                   HTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESS CS
                    Helicase_C  12 leeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfd 92 
                                   +   +g++lif+ +++r+e +   l++kgik+  +hg ++  +r+++ ++f +++++++++t +++ G+d+p +++Vi  +
  gi|15669591|ref|NP_248404.1| 427 KFGYRGQCLIFTYSRKRAEYLAKALKSKGIKAEFYHGGMEYIKRRKVEDDFANQKIQCVVTTAALSAGVDFP-ASTVILES 506
                                   456799************76444457789******************************************9.88899888 PP

                                   SS.....SSHHHHHHHHTTSSSTT CS
                    Helicase_C  93 lp.....rnvtsyiqriGRtgRag 111
                                   l       n+++++q+ GR+gR g
  gi|15669591|ref|NP_248404.1| 507 LAmgadwLNPAEFQQMCGRAGRKG 530
                                   887877778*************76 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.62   3.7e+03      80     118 ..       8      46 ..       5      77 .. 0.74
   2 !   40.7   0.0   4.1e-14   2.4e-10      25     169 ..     228     373 ..     178     375 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.62
                                   G....GEEEESSS-B--.......-SEEEEEHHHHHHTH CS
                        ResIII  80 eaykeigkkvsgdkkkakekdstnkkilvttiqsldads 118
                                   +++k++ ++v+  +k++  ++ +n++ ++++++++  + 
  gi|15669591|ref|NP_248404.1|   8 KKKKDEIEIVKVGGKIEDGIEVKNNQKIFANYKKVGDKY 46 
                                   555667777777777777888889999999998887665 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 4.1e-14
                                   SEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.............GEEEESSS-B- CS
                        ResIII  25 krglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayke.........igkkvsgdkkk 95 
                                     +li  aT +GKTl+  ++ i++l k gk  kflflvp  +l +q + efk+ +++   +         igkkv+ +   
  gi|15669591|ref|NP_248404.1| 228 DDLLIISATSSGKTLIGeLAGIKNLIKTGK--KFLFLVPLVALANQKYLEFKERYEKLGFKvslrvglgrIGKKVDVE--- 303
                                   57899**********************988..*********************9999876677775544444444444... PP

                                   -.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT---SEEEEEESS- CS
                        ResIII  96 akekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekfkeavllglTATp 169
                                        s +++i+v t++ +d  +        +++ + +  ++iDE H l+ ++        + ++   fkea +++l+AT+
  gi|15669591|ref|NP_248404.1| 304 ----TSLDADIIVGTYEGIDYLI-------RTKRLKDIGTVVIDEIHSLNLEErgarldgLIGRLRFLFKEAQKIYLSATI 373
                                   ....4556**************9.......677788889***********986444344444444666799********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (808 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1103  (0.0615204); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.74u 0.25s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 5256.27
//
Query:       gi|15669592|ref|NP_248405.1|  [L=346]
Description: hypothetical protein MJ_1402 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.026   14.2   0.2      0.041   13.6   0.2    1.2  1  MtrD            Tetrahydromethanopterin S-methyltransferase, 
      0.037   14.9   2.2      0.064   14.2   1.0    2.0  2  Pilin_N         Archaeal Type IV pilin, N-terminal
       0.11   13.1   0.2         15    6.3   0.1    2.8  2  Mannosidase_ig  Mannosidase Ig/CBM-like domain


Domain annotation for each model (and alignments):
>> MtrD  Tetrahydromethanopterin S-methyltransferase, subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   6.9e-06     0.041      77     131 ..      17      71 ..       9      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.9e-06
                          MtrD  77 amlmlaitmlvgnliyvygvGvvaasakvekdpitgdkqekyvsqGteGhgiPtv 131
                                     ++l++t++vg + y +g G+   s++ ++  + g++     + G+ G g+P  
  gi|15669592|ref|NP_248405.1|  17 LLIVLGVTIVVGAVFYAWGSGLFNNSQQSTQSALEGTTSTITYAAGAIGVGVPKE 71 
                                   56899************************************9***********76 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.0   1.1e-05     0.064       1      45 [.       9      53 ..       9      74 .. 0.82
   2 ?   -2.9   0.0       2.3   1.4e+04      29      51 ..     309     331 ..     303     343 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                       Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievk 45
                                  +A+Sp+   ++ + +t+++ Av+ a   gl +n+++++q ++e +
  gi|15669592|ref|NP_248405.1|  9 KAISPILALLIVLGVTIVVGAVFYAWGSGLFNNSQQSTQSALEGT 53
                                  69****************************777777777776444 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                       Pilin_N  29 glasneekapqasievkidssas 51 
                                   g++++++ ++ ++i vk+ s+++
  gi|15669592|ref|NP_248405.1| 309 GFQEEPSGETTVKIPVKVVSDQG 331
                                   44566666666777666555444 PP

>> Mannosidase_ig  Mannosidase Ig/CBM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0024        15      33      72 ..     117     156 ..      23     158 .. 0.84
   2 ?    4.1   0.0     0.012        70      25      62 ..     177     217 ..     176     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0024
                Mannosidase_ig  33 etsttpvtvgansstevaeidvdellaatggadpravvlv 72 
                                   +++ t+v+++  ++teva +++++++ + +g++++a++l+
  gi|15669592|ref|NP_248405.1| 117 DSTLTNVKIESDGATEVAGLTLKKITLNYNGQNYDAYLLC 156
                                   334479*******************998899999999875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.012
                Mannosidase_ig  25 dltgkllaetsttpvtvgansstevaeidvdellaat...g 62 
                                   ++tg++ +  ++    +++ns t va +d ++ l+ t   +
  gi|15669592|ref|NP_248405.1| 177 TWTGDDGNNYTSVYYILAPNSVTGVAAVDGSKDLSVTtakK 217
                                   699999999998999*************9888877543552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2375.39
//
Query:       gi|15669593|ref|NP_248406.1|  [L=374]
Description: hypothetical protein MJ_1403 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.007   17.3   0.2      0.018   15.9   0.2    1.7  1  Pilin_N   Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
       0.14   12.0   0.2        0.2   11.4   0.2    1.2  1  SurA_N_3  SurA N-terminal domain


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2     2e-06     0.018       1      45 [.      26      70 ..      26      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-06
                       Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievk 45
                                  +A+Sp+   ++ + +t+++ Av+ a   +l +n+++++qa++e +
  gi|15669593|ref|NP_248406.1| 26 KAISPILALLIVLGVTIVVGAVFYAWGSNLFGNSQEKTQAAVEGT 70
                                  69**********************999999999999999999655 PP

>> SurA_N_3  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   2.2e-05       0.2       1      47 [.      18      70 ..      18      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.2e-05
                      SurA_N_3  1 Mleflrknaks...wiakillgliila.Fv..lwGvgsylsgsgnsvakVnge 47
                                  M+++l++++     ++++i+lg+ i++  v   wG + ++++++++ a V g+
  gi|15669593|ref|NP_248406.1| 18 MMDWLKNKKAIspiLALLIVLGVTIVVgAVfyAWGSNLFGNSQEKTQAAVEGT 70
                                  9******9765677666777777776654432599988988888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2604.72
//
Query:       gi|15669594|ref|NP_248407.1|  [L=421]
Description: hypothetical protein MJ_1404 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-51  172.5  14.7    1.4e-15   57.4   0.8    4.7  5  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.2     7e-16   1.3e-11       1      54 [.       9      64 ..       9      66 .. 0.86
   2 !   32.1   0.0   6.7e-12   1.2e-07       9      53 ..      78     122 ..      71     126 .. 0.86
   3 !   57.4   0.8     8e-20   1.4e-15       1      55 [.     135     189 ..     135     191 .. 0.95
   4 !   45.2   0.6   5.2e-16   9.4e-12       4      56 ..     216     267 ..     213     268 .. 0.91
   5 ?   -2.9   0.0      0.56     1e+04      16      29 ..     379     391 ..     373     396 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 7e-16
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTB.EEEEEEHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgk.lvGivtlrDllra 54
                                  V++imt+dvvtv+pdt++++al +m+e+g+++l VV  +dgk    ++++rDll a
  gi|15669594|ref|NP_248407.1|  9 VKEIMTKDVVTVTPDTPVSKALGIMEENGFHHLIVVdKKDGKeEYYLISMRDLLLA 64
                                  89***********************9999****99975555525599999999976 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 6.7e-12
                                   CEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                           CBS   9 vvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                    ++v++dt+  +a+ +m ++g ++ P+V++ gk vGi+t+ D++ 
  gi|15669594|ref|NP_248407.1|  78 AHCVHEDTPFLDAVCEMLDSGQRAAPIVNNVGKMVGIITDYDIMA 122
                                   569******888888888****9********************86 PP

  == domain 3  score: 57.4 bits;  conditional E-value: 8e-20
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   V+ imtr+v+t+++++++++a  lmr+++++rl VVd++g++vG+vt+ D+l+++
  gi|15669594|ref|NP_248407.1| 135 VTKIMTRNVITINENDSIGKARALMRDNNIGRLVVVDDEGNPVGMVTEVDILKKV 189
                                   6789*****************************889****************986 PP

  == domain 4  score: 45.2 bits;  conditional E-value: 5.2e-16
                                   HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   im+++++tv+ d++ ++a++ m e++++++PVV + + l Givt+ D++++++
  gi|15669594|ref|NP_248407.1| 216 IMNTPLITVDVDASAADAARVMQEYDIRGVPVV-KGKSLRGIVTRLDIIKYIA 267
                                   7*********************9999*******.444599***********97 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 0.56
                                   SBHHHHHHHHHHHT CS
                           CBS  16 ttleealelmrekg 29 
                                   ++le +l+++ e++
  gi|15669594|ref|NP_248407.1| 379 ESLESVLRQL-EAD 391
                                   6899999999.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 3063.33
//
Query:       gi|15669595|ref|NP_248408.1|  [L=75]
Description: hypothetical protein MJ_1405 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-12   47.7   0.0    1.7e-12   47.6   0.0    1.1  1  Acylphosphatase  Acylphosphatase


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   9.5e-17   1.7e-12       1      55 [.       9      63 ..       9      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 9.5e-17
               Acylphosphatase  1 vrllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfle 55
                                  ++++++Gr+Q vgFR+ + +l + lg++G v N +dg+V+i+a  + e  +k+ +
  gi|15669595|ref|NP_248408.1|  9 YEIIIYGRIQHVGFRERIENLGHALGIDGIVYNYEDGTVRILANFPSERKKKLFK 63
                                  689******************************************9888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 488.34
//
Query:       gi|15669596|ref|NP_248409.1|  [L=149]
Description: aspartate carbamoyltransferase regulatory subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-31  106.1   8.6    1.4e-30  105.4   8.6    1.3  1  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    5.5e-17   61.4   6.4    9.8e-17   60.6   6.4    1.4  1  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me


Domain annotation for each model (and alignments):
>> PyrI  Aspartate carbamoyltransferase regulatory chain, allosteric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   8.6   1.5e-34   1.4e-30       1      92 [.       7      95 ..       7      97 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 1.5e-34
                                  X-----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EEEEEE CS
                          PyrI  1 lkvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnatiniIk 83
                                  lkvkki nG+ViDHI agkal v+k+L++ k +++  v+i++nv+skk gkKdi+kieg el++e++dk++li+p++tiniI+
  gi|15669596|ref|NP_248409.1|  7 LKVKKITNGTVIDHIDAGKALMVFKVLNVPK-ETS--VMIAINVPSKKKGKKDILKIEGIELKKEDVDKISLISPDVTINIIR 86
                                  69****************************7.666..********************************************** PP

                                  TTEEEEEE- CS
                          PyrI 84 dgevveKkk 92
                                  +g+vveK k
  gi|15669596|ref|NP_248409.1| 87 NGKVVEKLK 95
                                  *******87 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   6.4   1.1e-20   9.8e-17       1      45 [.     101     145 ..     101     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 1.1e-20
                                   EEESSS--S-TTBGGGTTS-.-EEEEEETTTTEEEETTT--EEEH CS
                        PyrI_C   1 eiegvlkCpNpnCItnnepveskFkvedkekvklkCkYCekeise 45 
                                   eieg lkC+NpnCItn+e+v+ kFk+e+k+++k++C YCek ++e
  gi|15669596|ref|NP_248409.1| 101 EIEGTLKCTNPNCITNKEKVRGKFKIESKNPLKIRCYYCEKFLNE 145
                                   69***************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 994.61
//
Query:       gi|15669597|ref|NP_248410.1|  [L=129]
Description: hypothetical protein MJ_1407 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-28   96.0   0.0    1.8e-27   94.9   0.0    1.6  1  DUF126    Aconitase X swivel domain


Domain annotation for each model (and alignments):
>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   0.0     1e-31   1.8e-27       1      80 []      24     101 ..      24     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 1e-31
                                   --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT--EE CS
                        DUF126   1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadiPlv 80 
                                   +Sflggvd e+G++idk+++l+gqs++gki+v+p+g+GStvgsyv++ lak+g+  ++++++e++pi+a+Gai+ +iPlv
  gi|15669597|ref|NP_248410.1|  24 FSFLGGVD-EEGNIIDKDSDLYGQSLKGKIFVFPYGRGSTVGSYVIYGLAKRGIL-KGIVNKECEPIVATGAILGGIPLV 101
                                   79******.89********************************************.**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.53
# Mc/sec: 729.37
//
Query:       gi|15669598|ref|NP_248411.1|  [L=350]
Description: GTP1/Obg family GTP-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-41  140.2   1.4    5.6e-41  140.2   1.4    1.7  2  NOG1_N          NOG1 N-terminal helical domain
    1.3e-23   82.5   1.1    3.1e-23   81.3   1.1    1.7  1  NOG1            Nucleolar GTP-binding protein 1 (NOG1)
    1.9e-21   76.2   0.0      5e-21   74.9   0.0    1.7  1  MMR_HSR1        50S ribosome-binding GTPase
    2.3e-17   63.0   0.4    3.9e-17   62.2   0.4    1.4  1  FeoB_N          Ferrous iron transport protein B
    1.8e-12   47.2   0.1    4.9e-12   45.8   0.1    1.7  1  PduV-EutP       Ethanolamine utilisation - propanediol utilis
    4.3e-11   43.0   1.4    4.6e-05   23.4   0.9    2.7  2  RsgA_GTPase     RsgA GTPase
    2.3e-07   30.4   3.1    0.00013   21.5   1.2    2.4  2  Arf             ADP-ribosylation factor family
    3.5e-07   30.2   0.8      9e-07   28.9   0.8    1.6  1  MMR_HSR1_Xtn    C-terminal region of MMR_HSR1 domain
    1.1e-06   28.3   0.4    0.00031   20.3   0.1    2.5  2  GTP_EFTU        Elongation factor Tu GTP binding domain
    9.7e-06   25.3   0.6     0.0047   16.5   0.1    2.3  2  cobW            CobW/HypB/UreG, nucleotide-binding domain
     0.0001   21.8   0.7     0.0002   20.8   0.7    1.5  1  SRPRB           Signal recognition particle receptor beta sub
     0.0012   18.9   0.3       0.57   10.2   0.0    2.7  2  Dynamin_N       Dynamin family
     0.0073   15.9   1.1       0.53    9.9   0.2    2.4  2  Ras             Ras family
  ------ inclusion threshold ------
      0.017   14.5   0.1       0.28   10.6   0.0    2.8  3  TniB            Bacterial TniB protein
      0.019   14.9   3.0       0.47   10.4   0.1    2.7  2  DUF1967         Domain of unknown function (DUF1967)
      0.019   15.2   0.1          1    9.6   0.0    2.6  2  Roc             Ras of Complex, Roc, domain of DAPkinase
       0.03   13.9   0.2       0.16   11.5   0.3    2.0  2  PPS_PS          Phosphopantothenate/pantothenate synthetase
      0.066   12.6   0.1        0.2   11.1   0.0    1.8  2  KTI12           Chromatin associated protein KTI12
      0.071   13.7   3.5       0.13   12.8   1.7    2.5  1  AAA_18          AAA domain
      0.091   11.7   0.4        3.3    6.6   0.0    2.3  2  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
        0.1   12.3   0.2        1.3    8.7   0.1    2.3  2  ATP_bind_1      Conserved hypothetical ATP binding protein
       0.12   12.8   2.0        3.3    8.1   0.8    3.1  2  AAA             ATPase family associated with various cellula
       0.15   12.0   0.6         21    5.0   0.0    2.9  3  NACHT           NACHT domain
       0.26   11.3   1.6        1.9    8.5   0.0    2.8  3  AAA_14          AAA domain
       0.28   10.9   2.5          2    8.1   0.1    2.7  3  AAA_24          AAA domain
       0.52   10.6   6.2       0.73   10.1   5.3    1.7  1  Phage_TAC_8     Phage tail assembly chaperone protein Gp14 ()
       0.92   10.5   0.1       0.92   10.5   0.1    3.1  3  HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-compon
        5.2    7.6   7.0         14    6.2   4.0    3.0  2  HTH_40          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.2   1.4   8.7e-44   5.6e-41       1     158 [.       8     166 ..       8     168 .. 0.97
   2 ?   -1.9   0.1       4.5   2.9e+03      81      92 ..     319     330 ..     282     336 .. 0.57

  Alignments for each domain:
  == domain 1  score: 140.2 bits;  conditional E-value: 8.7e-44
                        NOG1_N   1 Fekiptvptseelidkalrrakraakttkkkknei.krlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrelldv 80 
                                   F+k+pt++ ++el+ kalrr ++ a+++++k+     ++r +e++kvrt++ +++d+L+++++k+P + +l++Fy+e+++v
  gi|15669598|ref|NP_248411.1|   8 FKKMPTILMPDELMAKALRRGEKVANEMRQKELPWlLKARFVEEHKVRTIASVVADNLQKVIDKTPPVRKLPKFYQEMVEV 88 
                                   9***************************9997643489******************************************* PP

                        NOG1_N  81 lvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLrkLpa 158
                                   lv++d +kks+++ kwa++l+rk+g+ey++k++ka+++++a +lr+e++grv s+l++++++++f++ +r+kL++Lp+
  gi|15669598|ref|NP_248411.1|  89 LVGIDDFKKSMGAFKWASELVRKLGNEYARKIRKARTPQQAGKLRKEFVGRVKSILEQIHPEMAFVAVAREKLKDLPT 166
                                   *****************************************************************************7 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.5
                        NOG1_N  81 lvdkdelkksLa 92 
                                    ++ delk++L 
  gi|15669598|ref|NP_248411.1| 319 DIGLDELKERLK 330
                                   233345555554 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   1.1   4.8e-26   3.1e-23       1      58 []     233     289 ..     233     289 .. 0.99

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 4.8e-26
                          NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                   +IE+qAi+AL++la+++lF++D+se cgy++eeQ++Ll+eik+lf+ +p++v++nKiD
  gi|15669598|ref|NP_248411.1| 233 DIELQAILALNYLANLILFIIDASEFCGYTIEEQINLLKEIKDLFK-APIVVAINKID 289
                                   6*********************************************.9*********9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   7.8e-24     5e-21       2     114 .]     173     287 ..     172     287 .. 0.76

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 7.8e-24
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS...HHHHHH.HHHHHHHHHHC.TS CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie...gaseek.glgkaflalee.ad 77 
                                   v+i+G+pNvGKStL+++ltg+ ++++++p+tT+ in g +     ei++vDtpGl++      e++  + +a+lal+  a+
  gi|15669598|ref|NP_248411.1| 173 VVIAGYPNVGKSTLLKKLTGADVEINSYPFTTKGINVGYIG----EIQMVDTPGLLDrplY--ERNdIELQAILALNYlAN 247
                                   89************************************996....7********9753221..22235666677666669* PP

                                   EEEEEEETT.......TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  78 lillvvdas.......eeklkpldeeleelleeakkplilvlnk 114
                                   lil+++das       ee++ +l +e+++l    k p+++++nk
  gi|15669598|ref|NP_248411.1| 248 LILFIIDASefcgytiEEQI-NLLKEIKDL---FKAPIVVAINK 287
                                   *******9966654432222.222444444...57999999998 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.4   6.1e-20   3.9e-17       2     155 ..     172     328 ..     171     329 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 6.1e-20
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH.CTSSSE CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll.eeepdv 81 
                                   tv+++G pnvGk+tl+ +ltga+ ++  +p +t   + g++     e+++vD PG  +   y +++   + +l+ +  +++
  gi|15669598|ref|NP_248411.1| 172 TVVIAGYPNVGKSTLLKKLTGADVEINSYPFTTKGINVGYIG----EIQMVDTPGLLDRPLYERNDIELQAILAlNYLANL 248
                                   689**************************************9....9********97765555555444444433555799 PP

                                   EEEEEEGGG.....HHHHHHHHHHHHHT.TSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                        FeoB_N  82 vvnvvdatn.....lernLyLtlqllel.gvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellka 155
                                   ++ ++da++     +e ++ L+ ++ +l ++p+v+a+n+id +++++++  ++kL+e    +++k+sa k  g++el+++
  gi|15669598|ref|NP_248411.1| 249 ILFIIDASEfcgytIEEQINLLKEIKDLfKAPIVVAINKIDLVDEERVKEIEEKLKEVGIEEILKISADKDIGLDELKER 328
                                   *******85333348************74689***************9988999988766789**************985 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.1   7.7e-15   4.9e-12       4     142 ..     173     330 ..     171     331 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 7.7e-15
                     PduV-EutP   4 illiGkvgsGKttLtqalkgeelk...Yk.ktqaief....sdeviDtPGe.....ylenrklysalivtsaeadvialvq 71 
                                   +++ G  ++GK tL ++l+g +++   Y   t+ i++    + +++DtPG      y  n    +a+ ++ + a++i ++ 
  gi|15669598|ref|NP_248411.1| 173 VVIAGYPNVGKSTLLKKLTGADVEinsYPfTTKGINVgyigEIQMVDTPGLldrplYERNDIELQAILALNYLANLILFII 253
                                   67889999************7776112533477787633323478*****5334447777777899*************99 PP

                     PduV-EutP  72 date.......eesvfppgfasvfnkeviGiitkidlaedeenieaveelLksaGaekifevsavekegieellkyle 142
                                   da+e       e+  + +++  +f+ +++  i kidl+ dee+++  ee+Lk++G+e+i ++sa +++g++el++ l+
  gi|15669598|ref|NP_248411.1| 254 DASEfcgytieEQINLLKEIKDLFKAPIVVAINKIDLV-DEERVKEIEEKLKEVGIEEILKISADKDIGLDELKERLK 330
                                   9975222222155567788999****************.***********************************9997 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.2e-06    0.0033      66     126 ..     138     196 ..     129     228 .. 0.80
   2 !   23.4   0.9   7.2e-08   4.6e-05      46      99 ..     278     331 ..     229     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.2e-06
                                   HHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT---- CS
                   RsgA_GTPase  66 eelkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpelelk 126
                                    ++k+ le++  e+ +v +  +e+l++l +  +  t+v++G   vGKStL+++l++  +++
  gi|15669598|ref|NP_248411.1| 138 GRVKSILEQIHPEMAFVAVA-REKLKDLPTFKDLPTVVIAGYPNVGKSTLLKKLTGA-DVE 196
                                   56788999999999999776.8999999988888********************997.444 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 7.2e-08
                                   T-EEEEEEE-GGG--HHHHHHHHHHHHHHTTS.EEEE--TTTHTTHHHHHHHCTT CS
                   RsgA_GTPase  46 giepvivlnKiDlleeeeeleelkeelealgy.evllvsaktkegleelkellkd 99 
                                   ++++v+++nKiDl++ee+ ++e++e+l+++g+ e+l++sa++  gl+elke+lk+
  gi|15669598|ref|NP_248411.1| 278 KAPIVVAINKIDLVDEER-VKEIEEKLKEVGIeEILKISADKDIGLDELKERLKK 331
                                   568999************.************835889***************997 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0022       1.4      16      50 ..     172     209 ..     158     219 .. 0.73
   2 !   21.5   1.2     2e-07   0.00013      83     172 ..     247     330 ..     242     333 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0022
                                   EEEEEESTTSSHHHHHHHHHHSSCEE.CSS..SSSEEE CS
                           Arf  16 rilllGLDnaGKtTilkklkleelvt.tvP..Tigfnv 50 
                                    +++ G  n GK+T+lkkl+  +++    P  T g nv
  gi|15669598|ref|NP_248411.1| 172 TVVIAGYPNVGKSTLLKKLTGADVEInSYPftTKGINV 209
                                   58999**************9988764244433555555 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2e-07
                                   SEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBT CS
                           Arf  83 davifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkgeg 163
                                   + ++f++D+++    +  +e+++ l e ++l +++++v  NK+Dl +    +e++e+l+   ++     ei k sa k  g
  gi|15669598|ref|NP_248411.1| 247 NLILFIIDASEFCGYT-IEEQINLLKEIKDLFKAPIVVAINKIDLVDEERVKEIEEKLKEVGIE-----EILKISADKDIG 321
                                   5689999999887654.567788888899*********************************99.....888889999888 PP

                                   HHHHHHHHH CS
                           Arf 164 lkeglewls 172
                                   l+e  e+l 
  gi|15669598|ref|NP_248411.1| 322 LDELKERLK 330
                                   888888876 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.8   1.4e-09     9e-07      41     100 ..     262     329 ..     253     332 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.4e-09
                  MMR_HSR1_Xtn  41 tvDdlidvieg.nrvY.ipclyvlNKiDlisleeldelare......pnsvviSaekelnldeLkeki 100
                                   t+++ i+ +++ +  +  p ++++NKiDl+++e ++e++++      ++++ iSa+k+++ldeLke++
  gi|15669598|ref|NP_248411.1| 262 TIEEQINLLKEiKDLFkAPIVVAINKIDLVDEERVKEIEEKlkevgiEEILKISADKDIGLDELKERL 329
                                   66666666655333331578999*****************877888789999*************985 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.017        11       3      27 ..     170     194 ..     168     208 .. 0.83
   2 !   20.3   0.1   4.9e-07   0.00031      72     150 ..     215     307 ..     210     339 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.017
                                   EEEEEEEESTTSSHHHHHHHHHHHT CS
                      GTP_EFTU   3 irnigiighvDhGKtTLtdrLlykt 27 
                                   + +++i+g  + GK+TL+ +L+ + 
  gi|15669598|ref|NP_248411.1| 170 LPTVVIAGYPNVGKSTLLKKLTGAD 194
                                   568999**************98655 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4.9e-07
                                   EEEEEESSSGG...GHHHHHHH......HHT-SEEEEEEETTTBSTHHHHHHHHHHHH....TTTEEEEEEESCGST.HHH CS
                      GTP_EFTU  72 inliDtPGHvd...Fskevirg......lrvlDgavlvvdaveGvepqteevlrlalk....egvpiivfiNKmDrl.kae 138
                                   i+++DtPG  d   + ++ i+          +++ ++++da+e      ee ++l+++     + pi+v+iNK+D + +++
  gi|15669598|ref|NP_248411.1| 215 IQMVDTPGLLDrplYERNDIELqailalNYLANLILFIIDASEFCGYTIEEQINLLKEikdlFKAPIVVAINKIDLVdEER 295
                                   66677777666666666544432232223467889999***9875555555555554411116788***********7778 PP

                                   HHHHHHHHHHHH CS
                      GTP_EFTU 139 lkeiveevkqkl 150
                                   +kei e++k+  
  gi|15669598|ref|NP_248411.1| 296 VKEIEEKLKEVG 307
                                   888888887543 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0065       4.2       1      21 [.     171     191 ..     171     199 .. 0.87
   2 !   16.5   0.1   7.3e-06    0.0047     109     169 ..     243     306 ..     215     312 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0065
                                   EEEEEEESTTCCHHHHHHHHH CS
                          cobW   1 pvtvltGflGsGKTtLlnhll 21 
                                   p++v++G++  GK+tLl++l+
  gi|15669598|ref|NP_248411.1| 171 PTVVIAGYPNVGKSTLLKKLT 191
                                   689***************997 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 7.3e-06
                                   CCCECEEEEEEETTTH.....CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHH CS
                          cobW 109 dltldavvavvDaknl....eaeeekieekaedqlaaadllvlnKtDlldeeallekleerlrql 169
                                   ++ ++ +++++Da+++     +e+ +  ++++d ++a  ++ +nK+Dl+dee+ ++++ee+l+++
  gi|15669598|ref|NP_248411.1| 243 NYLANLILFIIDASEFcgytIEEQINLLKEIKDLFKAPIVVAINKIDLVDEER-VKEIEEKLKEV 306
                                   56778899**********887778888899999999999999*********95.59999998876 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.7   3.2e-07    0.0002       4     160 ..     171     327 ..     168     345 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.2e-07
                                   -EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG.....GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEE CS
                         SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkv..ksekgskltliDfPGheklrqklleklkaksslkglvf 81 
                                   p+v+++G  + GK +l+++Lt   v+        + +   +  + +   +  l+D P  e+   +l   l  +  +  ++f
  gi|15669598|ref|NP_248411.1| 171 PTVVIAGYPNVGKSTLLKKLTGADVEINSYPFtTKGINVGYigEIQMVDTPGLLDRPLYERNDIELQAILALNYLANLILF 251
                                   89*******************88665443333244444444112233333445555556777777766665666688899* PP

                                   EEETTS-H.HHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---HHHHHHHH.HHHHHHHHHCHHHHHH------T CS
                         SRPRB  82 vvDStidp.kevkevAEllyeilliteklkdavdiliACnKqelflakspklikdaL.EkElnkiierrskalkeldeeed 160
                                   ++D++ +    ++e   ll ei         + +i++A nK +l+     k i ++L E  +++i +  +    +lde ++
  gi|15669598|ref|NP_248411.1| 252 IIDASEFCgYTIEEQINLLKEIKDLF-----KAPIVVAINKIDLVDEERVKEIEEKLkEVGIEEILKISADKDIGLDELKE 327
                                   ***98875257888888888875444.....589*********************99444566666655555444444443 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00089      0.57       1      33 [.     173     205 ..     173     211 .. 0.84
   2 ?    6.1   0.0     0.016        10     102     164 ..     214     283 ..     211     288 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00089
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS--- CS
                     Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTr 33 
                                   +++ G  + GKS++l +L+g+d+  ++   tT 
  gi|15669598|ref|NP_248411.1| 173 VVIAGYPNVGKSTLLKKLTGADVEINSYPFTTK 205
                                   678888999*************98888777776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
                                   SEEEEE---B-SSSGTTS.....HHHHHHHSTTEEEEEEEETTS..-CCC-CHHHHHHHHSTTBTTEEEE CS
                     Dynamin_N 102 gltlvDlPGldsvnkrdq.....elvkeyikkadiilavtsanh..dlsnsealflarevdpkgkrtivv 164
                                   ++ +vD+PGl +++  +      + +  +   a++il++ +a+     +  e+ +l +e+++  k  ivv
  gi|15669598|ref|NP_248411.1| 214 EIQMVDTPGLLDRPLYERndielQAILALNYLANLILFIIDASEfcGYTIEEQINLLKEIKDLFKAPIVV 283
                                   5789******998766665676644444446688999999999844556667777777777777776665 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.035        22       2      21 ..     173     192 ..     172     223 .. 0.84
   2 !    9.9   0.2   0.00083      0.53      89     156 ..     265     329 ..     234     335 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.035
                                   EEEEESTTSSHHHHHHHHHH CS
                           Ras   2 lvlvGdsavGKtslllrfvk 21 
                                   +v+ G  +vGK++ll + + 
  gi|15669598|ref|NP_248411.1| 173 VVIAGYPNVGKSTLLKKLTG 192
                                   7999***********98875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00083
                                   THHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHT.SEEEEEBTTTTCTHHHHHHHH CS
                           Ras  89 nvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelg.lkfletSAktnenveeafeel 156
                                   +  ++++eik+  +   piv+  nK+Dl +++ v++ e +   ke+g  + l++SA ++ +++e+ e+l
  gi|15669598|ref|NP_248411.1| 265 EQINLLKEIKDLFK--APIVVAINKIDLVDEERVKEIEEK--LKEVGiEEILKISADKDIGLDELKERL 329
                                   44477888888888..69**************99877744..777884678999999999998875555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.8   1.2e+03      54      94 ..      47      89 ..      44     118 .. 0.71
   2 ?   10.6   0.0   0.00044      0.28      24      56 ..     159     191 ..     139     226 .. 0.84
   3 ?   -0.0   0.0      0.76   4.9e+02     139     159 ..     263     283 ..     250     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.8
                          TniB 54 kFarlhppek..dedaekvpvlvvqappkpdekrlyaaiLeal 94
                                  +F ++h+ ++  +  a++++ ++ ++pp  +  ++y++++e l
  gi|15669598|ref|NP_248411.1| 47 RFVEEHKVRTiaSVVADNLQKVIDKTPPVRKLPKFYQEMVEVL 89
                                  6666666654213445667777778888888888888887765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00044
                          TniB  24 eeLleypkrkrmpnlllvGdsnnGKtmivekFa 56 
                                   e+L + p+ k+ p ++++G +n+GK+++++k +
  gi|15669598|ref|NP_248411.1| 159 EKLKDLPTFKDLPTVVIAGYPNVGKSTLLKKLT 191
                                   678899999********************9976 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.76
                          TniB 139 qreflnalksLgnelkipivl 159
                                    +e +n+lk +++ +k piv+
  gi|15669598|ref|NP_248411.1| 263 IEEQINLLKEIKDLFKAPIVV 283
                                   567789999999999999986 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00073      0.47      23      51 ..     285     313 ..     279     315 .. 0.92
   2 ?    4.8   0.5     0.043        28      26      57 ..     314     345 ..     311     348 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00073
                                   HTTEEE-TGGGHHHHHHHHHHTTHHHHHH CS
                       DUF1967  23 vkqtnfeneeavrrfarrLkklGvedaLr 51 
                                   ++++++ +ee v+ ++++Lk+ G+e+ L+
  gi|15669598|ref|NP_248411.1| 285 INKIDLVDEERVKEIEEKLKEVGIEEILK 313
                                   789***********************997 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.043
                                   EEE-TGGGHHHHHHHHHHTTHHHHHHTTT--T CS
                       DUF1967  26 tnfeneeavrrfarrLkklGvedaLrkaGake 57 
                                   +  +++ ++  +++rLkk+ + + L+++ a++
  gi|15669598|ref|NP_248411.1| 314 ISADKDIGLDELKERLKKIAIKEFLKDKDAEN 345
                                   66778889999*****************9986 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0016         1       2      28 ..     173     199 ..     172     222 .. 0.76
   2 ?    2.8   0.0       0.2   1.3e+02      81     120 .]     247     290 ..     239     290 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0016
                                   EEEESSTTSSHHHHHHCHCT-CCC-EE CS
                           Roc   2 vvlvGdsgvGKtsllkrfvedkfseke 28 
                                   vv+ G  +vGK++llk+++  +++ ++
  gi|15669598|ref|NP_248411.1| 173 VVIAGYPNVGKSTLLKKLTGADVEINS 199
                                   7999**************998876443 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.2
                                   CEEEEEEEGHHH..HCHHHHHHHHHHHCS..SS-EEEEEE-TTT CS
                           Roc  81 alailvydsrss..enlkeWlkelkkvag..kspvilvgnkiDl 120
                                   +l+++++d++++   +++e ++ lk+  +  k+p+++ +nkiDl
  gi|15669598|ref|NP_248411.1| 247 NLILFIIDASEFcgYTIEEQINLLKEIKDlfKAPIVVAINKIDL 290
                                   6777788877664456777777777776655899********95 PP

>> PPS_PS  Phosphopantothenate/pantothenate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.2   1.4e+03      26      43 ..     187     204 ..     182     208 .. 0.82
   2 ?   11.5   0.3   0.00025      0.16      40      78 ..     290     327 ..     263     339 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.2
                        PPS_PS  26 LaealgaklevNlfyrte 43 
                                   L++ +ga++e+N +  t+
  gi|15669598|ref|NP_248411.1| 187 LKKLTGADVEINSYPFTT 204
                                   78999*******987776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00025
                        PPS_PS  40 yrteeRvekiaellkeagaeevlgleedaripeleseRa 78 
                                     +eeRv++i+e lke g+ee+l +++d++i +l++ ++
  gi|15669598|ref|NP_248411.1| 290 LVDEERVKEIEEKLKEVGIEEILKISADKDI-GLDELKE 327
                                   3579*********************999966.4544444 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.8   2.4e+03     230     252 ..     119     141 ..      58     151 .. 0.59
   2 ?   11.1   0.0   0.00032       0.2       2      24 ..     171     193 ..     170     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.8
                                   .......HHHHHHHHHHHHHHHT CS
                         KTI12 230 lpakkltlaeLsrlrrqFvklnk 252
                                     +k+ t ++  +lr++Fv   k
  gi|15669598|ref|NP_248411.1| 119 KIRKARTPQQAGKLRKEFVGRVK 141
                                   33334555666677777776555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00032
                                   .EEEEE--TTSSHHHHHHHHHHH CS
                         KTI12   2 pLvvltGlPssGKstrakeLaka 24 
                                   p vv+ G+P +GKst+ k+L  a
  gi|15669598|ref|NP_248411.1| 171 PTVVIAGYPNVGKSTLLKKLTGA 193
                                   88****************99865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.7    0.0002      0.13       1      21 [.     173     193 ..     173     349 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0002
                        AAA_18   1 IlltGtpGvGKttlakeLskr 21 
                                   ++++G+p vGK+tl k L   
  gi|15669598|ref|NP_248411.1| 173 VVIAGYPNVGKSTLLKKLTGA 193
                                   79***************9443 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0051       3.3      32      50 ..     173     191 ..     154     197 .. 0.89
   2 ?    2.7   0.1     0.078        50     173     227 ..     284     331 ..     269     347 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0051
                                   EEEEE-TTSSHHHHHHHHH CS
                          MeaB  32 vGltGvPGaGkstlvealg 50 
                                   v + G P +Gkstl+++l+
  gi|15669598|ref|NP_248411.1| 173 VVIAGYPNVGKSTLLKKLT 191
                                   6699************997 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.078
                                   EEE---HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHH CS
                          MeaB 173 vvnkaDkkeaekaarelraaleleeekekeWrpkvlktsavegeGidelvdaiee 227
                                   ++nk D+ + e+++       e+ee+ ++    ++lk+sa++  G+del +++++
  gi|15669598|ref|NP_248411.1| 284 AINKIDLVDEERVK-------EIEEKLKEVGIEEILKISADKDIGLDELKERLKK 331
                                   55555555555544.......34444455556789**************998876 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.47     3e+02       1      17 [.     175     191 ..     175     199 .. 0.88
   2 ?    8.7   0.1     0.002       1.3     155     179 ..     277     305 ..     234     346 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.47
                    ATP_bind_1   1 vvGpaGsGKttfvgals 17 
                                   ++G + +GK+t+ ++l+
  gi|15669598|ref|NP_248411.1| 175 IAGYPNVGKSTLLKKLT 191
                                   68999*******99986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.002
                    ATP_bind_1 155 lelPhvvvlnkfDllkek....lekelef 179
                                    + P vv++nk+Dl++e+     e++l+ 
  gi|15669598|ref|NP_248411.1| 277 FKAPIVVAINKIDLVDEErvkeIEEKLKE 305
                                   578*************8753222222222 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.57   3.6e+02      58     104 ..      11      55 ..       2      82 .. 0.67
   2 ?    8.1   0.8    0.0052       3.3       2      75 ..     174     297 ..     173     324 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.57
                                   TSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHHHHHHHHTTTSSSTEE CS
                           AAA  58 kpsilfiDEidalaksr.sgseseeeervvnqLlteldgvkkkeskvi 104
                                    p+il+ DE+ a a +r ++ ++e +++ ++ Ll++   +++k   v 
  gi|15669598|ref|NP_248411.1|  11 MPTILMPDELMAKALRRgEKVANEMRQKELPWLLKARFVEEHK---VR 55 
                                   3799999999999999966667777777777777655444443...33 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0052
                                   EEESSTTSSHHHHHHHHHHH...HTHE...................................................EEE CS
                           AAA   2 llyGppGtGKTllakavake...lgve...................................................fle 28 
                                   ++ G p +GK++l k +      +  +                                                   ++ 
  gi|15669598|ref|NP_248411.1| 174 VIAGYPNVGKSTLLKKLTGAdveI--NsypfttkginvgyigeiqmvdtpglldrplyerndielqailalnylanliLFI 252
                                   68999*********9999886552..2334444555566666655666666666666666666666666666666666677 PP

                                   EETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH.T CS
                           AAA  29 isgsellskyvgesekkirelfkeakeka.kpsilfiDEidalaksr.s 75 
                                   i++se++    g + ++  +l+ke+k    +p ++ i  id + ++r +
  gi|15669598|ref|NP_248411.1| 253 IDASEFC----GYTIEEQINLLKEIKDLFkAPIVVAINKIDLVDEERvK 297
                                   7777777....44444444444444443334788888888888777742 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.9   1.2e+03      45     114 ..      48     110 ..      28     137 .. 0.69
   2 ?    5.0   0.0     0.033        21       2      20 ..     172     190 ..     171     194 .. 0.91
   3 ?    3.8   0.2     0.076        49      79     142 ..     245     306 ..     223     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.9
                                   TTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHC CS
                         NACHT  45 lsrsgnarsladllfsqlpepaapvsevwavllelperlLlilDglDelvtdlgqkekqpvrtlLselir 114
                                   + ++ ++r++a +++++l++ +++ ++ +  l +  + ++ +l g+D++++ +g+       ++ sel+r
  gi|15669598|ref|NP_248411.1|  48 FVEEHKVRTIASVVADNLQKVIDKTPP-VRKLPKFYQEMVEVLVGIDDFKKSMGA------FKWASELVR 110
                                   334445667788888888777777777.555666667777677777777777777......455555554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.033
                                   CEEEEC-TTTCHHHHHHHH CS
                         NACHT   2 lvilqGeaGsGKTtLlqkl 20 
                                   +v++ G + +GK+tLl+kl
  gi|15669598|ref|NP_248411.1| 172 TVVIAGYPNVGKSTLLKKL 190
                                   799**************98 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.076
                                   SCCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE CS
                         NACHT  79 lperlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqleea 142
                                   l++ +L+i+D+ + +    ++  + ++ + +++l+++ ++     +  v  ++++++ee+l+e 
  gi|15669598|ref|NP_248411.1| 245 LANLILFIIDASEFCGYTIEE--QINLLKEIKDLFKAPIVVAINKIDLVDEERVKEIEEKLKEV 306
                                   567799******999987666..89999999999999888888888888888888888888776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       1.3   8.3e+02      36      90 ..      60     112 ..      42     144 .. 0.61
   2 ?    8.5   0.0     0.003       1.9       4      26 ..     172     194 ..     170     256 .. 0.90
   3 ?   -1.1   0.9       2.8   1.8e+03      36      75 ..     288     327 ..     265     346 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.3
                        AAA_14  36 inldderdkkladpe..kllelileklkeekktylflDEiqevpewekalkslvdeg 90 
                                   +  d+ ++   ++p   kl+++++e++    + ++ +D  +++ +++k+  +lv++ 
  gi|15669598|ref|NP_248411.1|  60 VVADNLQKVIDKTPPvrKLPKFYQEMV----EVLVGIDDFKKSMGAFKWASELVRKL 112
                                   444444443333322346777777764....46889999999999999888888754 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.003
                        AAA_14   4 ilvitGaRrvGKTtllkqlikel 26 
                                    +vi G   vGK+tllk+l    
  gi|15669598|ref|NP_248411.1| 172 TVVIAGYPNVGKSTLLKKLTGAD 194
                                   589**************997555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.8
                        AAA_14  36 inldderdkkladpekllelilek.lkeekktylflDEiqe 75 
                                   i+l de+  k+ + ekl e+  e+ lk + ++ + lDE +e
  gi|15669598|ref|NP_248411.1| 288 IDLVDEERVKEIE-EKLKEVGIEEiLKISADKDIGLDELKE 327
                                   4444433322222.223333333312223344466777654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.1     2e+03     105     133 ..     130     159 ..      64     166 .. 0.61
   2 ?    8.1   0.1    0.0031         2       4      22 ..     172     190 ..     171     217 .. 0.87
   3 ?    1.5   0.1      0.32     2e+02     109     149 ..     264     300 ..     259     315 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.1
                        AAA_24 105 gelaeefrrllkklqelrk.nvifiahekt 133
                                   g+l++ef+  +k + e  +    f+a +++
  gi|15669598|ref|NP_248411.1| 130 GKLRKEFVGRVKSILEQIHpEMAFVAVARE 159
                                   456666766666655555555555554444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0031
                        AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                    ++i G + +GK+tl+k+l
  gi|15669598|ref|NP_248411.1| 172 TVVIAGYPNVGKSTLLKKL 190
                                   589**************99 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.32
                        AAA_24 109 eefrrllkklqelrknvifiahektrkdedpegeakytrle 149
                                   ee ++llk +++l k  i++a  k++ +++++ +     +e
  gi|15669598|ref|NP_248411.1| 264 EEQINLLKEIKDLFKAPIVVAINKIDLVDEERVK----EIE 300
                                   678899999999999***********99999776....333 PP

>> Phage_TAC_8  Phage tail assembly chaperone protein Gp14 ()A118
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.3    0.0011      0.73      24      92 ..     276     344 ..     261     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                   Phage_TAC_8  24 vfkvplGdearlelikageeykkavdklekieiddpeelttddyialeekvkellkealnkllddekay 92 
                                   +fk p+   + +  +  +e+ k+  +kl+++ i++  ++++d+ i l+e  + l k+a++  l+d +a 
  gi|15669598|ref|NP_248411.1| 276 LFKAPIVVAINKIDLVDEERVKEIEEKLKEVGIEEILKISADKDIGLDELKERLKKIAIKEFLKDKDAE 344
                                   56666665554444445778899999***************************************9985 PP

>> HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       2.4   1.5e+03      23      38 ..      54      69 ..      18      90 .. 0.73
   2 ?   10.5   0.1    0.0014      0.92      17      53 ..     103     138 ..      92     157 .. 0.83
   3 ?   -1.3   0.4       6.8   4.4e+03       8      12 ..     323     327 ..     293     342 .. 0.56

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.4
                HK97-gp10_like 23 lkkaAkevldkakkrt 38
                                  ++  A +v+d+++k +
  gi|15669598|ref|NP_248411.1| 54 VRTIASVVADNLQKVI 69
                                  5555666655555544 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0014
                HK97-gp10_like  17 kaikkalkkaAkevldkakk.rtpsvdtggdLrdsitv 53 
                                   k++ + ++k ++e+++k++k rtp     g+Lr+ ++ 
  gi|15669598|ref|NP_248411.1| 103 KWASELVRKLGNEYARKIRKaRTP-QQA-GKLRKEFVG 138
                                   899***************872566.455.****99876 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 6.8
                HK97-gp10_like   8 eklse 12 
                                   ++l+e
  gi|15669598|ref|NP_248411.1| 323 DELKE 327
                                   23333 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0         2   1.3e+03      42      63 ..      39      63 ..      23      87 .. 0.73
   2 ?    6.2   4.0     0.022        14      46      77 ..     288     330 ..     236     337 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 2
                        HTH_40 42 eidl...erlvseeeekeIeeaiek 63
                                  e+++    r+v+e++ ++I++++++
  gi|15669598|ref|NP_248411.1| 39 ELPWllkARFVEEHKVRTIASVVAD 63
                                  4666666788999999999988876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.022
                        HTH_40  46 erlvseeeekeIeeaiekvgsek...........lkpikealp 77 
                                    +lv+ee+ keIee +++vg e+           l ++ke+l+
  gi|15669598|ref|NP_248411.1| 288 IDLVDEERVKEIEEKLKEVGIEEilkisadkdigLDELKERLK 330
                                   4679**************9988888888889999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2206.97
//
Query:       gi|15669599|ref|NP_248412.1|  [L=268]
Description: hypothetical protein MJ_1409 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1514  (0.0844442); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1695.47
//
Query:       gi|15669600|ref|NP_248413.1|  [L=159]
Description: hypothetical protein MJ_1410 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-21   75.2   0.9    6.2e-21   74.4   0.9    1.4  1  UPF0113          UPF0113 PUA domain
    4.9e-10   39.8   2.3      1e-09   38.8   2.3    1.5  1  UPF0113_N        UPF0113 Pre-PUA domain
  ------ inclusion threshold ------
      0.056   13.4   1.0       0.27   11.3   0.1    2.5  3  Methyltranf_PUA  RNA-binding PUA-like domain of methyltransfe


Domain annotation for each model (and alignments):
>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.9     1e-24   6.2e-21       1      76 []      94     157 ..      94     157 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 1e-24
                       UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdtkaspgkivvknlaDiGeYlRr 76 
                                   +++v+ekae lFLYGrd++kesi+++++     ++++V+n+n+e+lGiG +        +++++kn+ D+G+YlR+
  gi|15669600|ref|NP_248413.1|  94 YAIVNEKAEALFLYGRDIFKESIIEVKG----FGRIAVFNKNREFLGIGLF--------DGKIIKNIKDKGWYLRE 157
                                   689************************3....447****************........99**************5 PP

>> UPF0113_N  UPF0113 Pre-PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   2.3   1.7e-13     1e-09       1      82 []       4      80 ..       4      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.7e-13
                     UPF0113_N  1 RklseeetrivfekLtkyigdnvkelldrkdgtycfrlkkkrVyyvseellklaetikpenlisaGtclGkftktkkFrlsi 82
                                  Rkl++ e+++++e+L+ky+ +++++ ++  ++  ++  k+ +V+y + e +k++ ++  + ++s+G ++G++  ++kFrls+
  gi|15669600|ref|NP_248413.1|  4 RKLKNAEINLIEEELSKYTDKDFVKSFK-YENLIVLEGKWLTVCYTNIETIKKLNMF--QDIFSVGNVFGEI--KRKFRLSL 80
                                  99****************6666666666.444677888999******9999999998..66***********..7*****97 PP

>> Methyltranf_PUA  RNA-binding PUA-like domain of methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.48   2.9e+03      19      27 ..      41      49 ..      30      50 .. 0.78
   2 ?   -1.3   0.0      0.38   2.2e+03      31      43 ..      82      94 ..      82      95 .. 0.86
   3 ?   11.3   0.1   4.5e-05      0.27       4      48 ..     105     153 ..     103     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.48
               Methyltranf_PUA 19 GwvlVcydg 27
                                   w+ Vcy +
  gi|15669600|ref|NP_248413.1| 41 KWLTVCYTN 49
                                  499999965 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.38
               Methyltranf_PUA 31 GwgKlvggrlKNk 43
                                  G+  ++ + ++N+
  gi|15669600|ref|NP_248413.1| 82 GFTLISPNIINNY 94
                                  7888999999997 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 4.5e-05
               Methyltranf_PUA   4 YlkGetielep..dlkkGwvlVcy...dgyplGwgKlvggrlKNkyPkgl 48 
                                   +l G++i+ e+  + k G+  +++   + + lG g ++g+ +KN   kg+
  gi|15669600|ref|NP_248413.1| 105 FLYGRDIFKESiiEVK-GFGRIAVfnkNREFLGIGLFDGKIIKNIKDKGW 153
                                   7888888888876554.4444444222699**************999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1000.10
//
Query:       gi|15669601|ref|NP_248414.1|  [L=463]
Description: glyceraldehyde-3-phosphate dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   9.2e-158  525.5   0.3   1.1e-157  525.3   0.3    1.0  1  Aldedh    Aldehyde dehydrogenase family
     0.0035   16.8   0.1     0.0076   15.7   0.1    1.5  1  DUF1487   Protein of unknown function (DUF1487)
     0.0042   16.2   0.0     0.0089   15.1   0.0    1.6  1  LuxC      Acyl-CoA reductase (LuxC)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.3   0.3  1.9e-161  1.1e-157       3     462 .]       9     459 ..       7     459 .. 0.98

  Alignments for each domain:
  == domain 1  score: 525.3 bits;  conditional E-value: 1.9e-161
                                   T-SSSEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---H CS
                        Aldedh   3 esesetievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkpl 83 
                                   ++  e ++vinP++ evi k+pa ++e++++a+++A++ ++ +++lp+++R +iL+++a+ ++e+keela+++++++Gkp+
  gi|15669601|ref|NP_248414.1|   9 NR--EDMDVINPYSLEVIKKIPALSREEAKEAIDTAEKYKEVMKNLPITKRYNILMNIAKQIKEKKEELAKILAIDAGKPI 87 
                                   44..459************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TT CS
                        Aldedh  84 aearaeveeaidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaee 164
                                   ++ar eve++i +++++a ++++ ++ev+ps+ ++l+++rreP+G+vgaItP+NfPl+l+a+k+apa+a+GN++v+ P+++
  gi|15669601|ref|NP_248414.1|  88 KQARVEVERSIGTFKLAAFYVKEHRDEVIPSD-DRLIFTRREPVGIVGAITPFNFPLNLSAHKIAPAIATGNVIVHHPSSK 167
                                   *******************************6.9*********************************************** PP

                                   SHHHHHHHHHHHHHT....TS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EE CS
                        Aldedh 165 tplsalllaelfeea....glPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknp 241
                                   +pl+++ la+++e+a    ++P gv n++tg g+ vg+++v +++v+++sftGs++vg+ i k+a+  +k+++lElGG np
  gi|15669601|ref|NP_248414.1| 168 APLVCIELAKIIENAlkkyNVPLGVYNLLTGAGEVVGDEIVVNEKVNMISFTGSSKVGELITKKAG--FKKIALELGGVNP 246
                                   ***************9999***********************************************..************* PP

                                   EEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHH CS
                        Aldedh 242 livledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvek 322
                                   +ivl+daDl+kav+a++kg+f++aGQvCi++  +lv esi+d+f+e +v++ak l+vg+plde+tdvGPlis +++e vek
  gi|15669601|ref|NP_248414.1| 247 NIVLKDADLNKAVNALIKGSFIYAGQVCISVGMILVDESIADKFIEMFVNKAKVLNVGNPLDEKTDVGPLISVEHAEWVEK 327
                                   ********************************************************************************* PP

                                   HHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE- CS
                        Aldedh 323 yveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvft 403
                                   +ve+a++eg klllGg      +++ +++ Pt+l+ v++d+ ++++E+F+PV+++i+ + eee+i+iaN+teyGL++++ft
  gi|15669601|ref|NP_248414.1| 328 VVEKAIDEGGKLLLGG------KRDKALFYPTILE-VDRDNILCKTETFAPVIPIIRTN-EEEMIDIANSTEYGLHSAIFT 400
                                   ****************......67899*******9.9********************85.69******************* PP

                                   SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                        Aldedh 404 kdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                   +d+++ +++ae+le+G v iNds+ ++ +++pfgGvk+SglGreg k+++ee++++kt+
  gi|15669601|ref|NP_248414.1| 401 NDINKSLKFAENLEFGGVVINDSSLFRQDNMPFGGVKKSGLGREGVKYAMEEMSNIKTI 459
                                   *********************************************************96 PP

>> DUF1487  Protein of unknown function (DUF1487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.3e-06    0.0076       9      59 ..     248     300 ..     246     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-06
                       DUF1487   9 vifedgDlnsalealve..slkePfaegavatvlveesirdefvervrsklkp 59 
                                   ++++d+Dln+a++al++   +     + +v ++lv+esi+d+f+e   +k k 
  gi|15669601|ref|NP_248414.1| 248 IVLKDADLNKAVNALIKgsFIYAGQVCISVGMILVDESIADKFIEMFVNKAKV 300
                                   799*************7324667788999****************98777665 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.5e-06    0.0089      74     255 ..     113     289 ..      32     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-06
                          LuxC  74 deflktke.ksyekaqprglvlhvlsgNvpl.lpvmsilqglLvknvnllkvSssdpflaaallksladvdenhtladsls 152
                                   de ++ ++   + ++ p g+v  +++ N pl l    i+ ++ ++nv++  +Ss  p + ++l+k + +  ++      l 
  gi|15669601|ref|NP_248414.1| 113 DEVIPSDDrLIFTRREPVGIVGAITPFNFPLnLSAHKIAPAIATGNVIVHHPSSKAPLVCIELAKIIENALKKY--NVPLG 191
                                   6777777656799*****************868999***************************99988877754..44567 PP

                          LuxC 153 vvyf.ksgdtkleeeiv..qnaDvvvawGgeeaikaiseklkpgkqlikfGakvSfavvdkealeeealdkaaeraAkDii 230
                                   v +   +  + + +eiv  +++  ++  G+++  ++i +k+  +k  ++ G  v   +v k+a    +l+ka++++ k + 
  gi|15669601|ref|NP_248414.1| 192 VYNLlTGAGEVVGDEIVvnEKVNMISFTGSSKVGELITKKAGFKKIALELGG-VNPNIVLKDA----DLNKAVNALIKGSF 267
                                   7776477778889999988889999****************99999999997.5556666777....9************* PP

                          LuxC 231 vfdQqAClspqvvfvekddkieide 255
                                   ++  q C+s  +++v+++    +d+
  gi|15669601|ref|NP_248414.1| 268 IYAGQVCISVGMILVDES---IADK 289
                                   ***************955...4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2938.81
//
Query:       gi|15669602|ref|NP_248415.1|  [L=498]
Description: hypothetical protein MJ_1412 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00011   22.5   0.1        0.4   10.9   0.0    3.4  3  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso
     0.0032   17.3   0.1       0.01   15.7   0.1    1.9  1  PASTA          PASTA domain


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0046        41      74     126 ..      42      94 ..       4     101 .. 0.68
   2 ?    3.0   0.0     0.012   1.1e+02     117     135 ..     276     294 ..     213     309 .. 0.70
   3 !   10.9   0.0   4.5e-05       0.4      10      32 ..     368     390 ..     359     452 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0046
                 Pro_isomerase  74 raipdEitsklkhkrGalamartgkepnsagsqFfItlke.....aphldgkytvFGk 126
                                   ++ip+ +   +k ++G +  a t+   n  +  FfI+  +       ++ g  ++FG 
  gi|15669602|ref|NP_248415.1|  42 EKIPKKF--LIKTTKGNITIAITE---NNETAKFFINNYKdfvkkLRWVSGMDVAFGS 94 
                                   3444444..778899******995...899999***7544355445577777788885 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.012
                 Pro_isomerase 117 ldgkytvFGkVveGmdvve 135
                                      ++tv G+V eG+++++
  gi|15669602|ref|NP_248415.1| 276 SSLSHTVVGRVKEGIELID 294
                                   33369**********9997 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 4.5e-05
                 Pro_isomerase  10 GrivieLfadkaPktvenFlklv 32 
                                   + ivieLf+dkaP+t+  F+k +
  gi|15669602|ref|NP_248415.1| 368 KIIVIELFEDKAPITAWYFRKTT 390
                                   679****************9987 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.1e-06      0.01       7      59 ..     313     361 ..     313     362 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-06
                                   TTSBHHHHHHHHHHTT--CCCEEE.ECTCCGTTBEEEECS-TTSEECTTS-EEE CS
                         PASTA   7 tGmsvdeAkatLkalGlkiktvee.tsddvpeGtVisQsPeaGtevskgskvtl 59 
                                   +G++++eA+++ k++++     e+ +  d +   V++Q Pe+   v+k +kv++
  gi|15669602|ref|NP_248415.1| 313 IGLTIEEAEEMFKKYNI-----EVeKEGDLENAIVVEQEPEYTLDVLKEKKVKI 361
                                   69***************.....221556667777******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3299.70
//
Query:       gi|15669603|ref|NP_248416.1|  [L=103]
Description: hypothetical protein MJ_1413 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-21   74.9   4.1    1.1e-19   71.0   4.1    2.0  1  YbjQ_1    Putative heavy-metal-binding
  ------ inclusion threshold ------
      0.087   11.7   0.0      0.096   11.6   0.0    1.1  1  Tannase   Tannase and feruloyl esterase
      0.098   13.0   0.1       0.13   12.7   0.1    1.3  1  DUF4156   Domain of unknown function (DUF4156)
       0.12   12.8   1.4       0.34   11.5   1.4    1.8  1  SRR       Seven Residue Repeat


Domain annotation for each model (and alignments):
>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   4.1   2.3e-23   1.1e-19       1     104 []       4      99 ..       4      99 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 2.3e-23
                        YbjQ_1   1 mivtttesiegkeivevlgivtgetvrsrnvlkdilaglrslvGGelkayeeeleeareeAlerlkeeAeelGAnAvvgvr 81 
                                   mi+ttt++iegk+i ++lg+v+g  v s  v+ +  +++++       aye++l+e+ ++Al r++++A++lGAnA++g++
  gi|15669603|ref|NP_248416.1|   4 MITTTTPYIEGKKIIKYLGFVHG--VASVYVTVKYYEDVKD-------AYERALRESEDTALIRMVDNAKKLGANAIIGIN 75 
                                   9*********************9..5677777777777775.......8******************************** PP

                        YbjQ_1  82 ldtseige.kgmlevlayGTAVkv 104
                                    ++  +ge + m++v +yGTAV+v
  gi|15669603|ref|NP_248416.1|  76 SNYAMVGEkGDMIMVGIYGTAVVV 99 
                                   ******9999************96 PP

>> Tannase  Tannase and feruloyl esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.1e-05     0.096     347     393 ..      14      60 ..       7      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.1e-05
                       Tannase 347 gGklilyhgtaDpvvspadsikyyesveaklgadleeleeFarlylv 393
                                   g k+i y g   +v s++ ++kyye v+ ++  +l e e+ a + +v
  gi|15669603|ref|NP_248416.1|  14 GKKIIKYLGFVHGVASVYVTVKYYEDVKDAYERALRESEDTALIRMV 60 
                                   779*****************************999988876665555 PP

>> DUF4156  Domain of unknown function (DUF4156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.8e-05      0.13      43      84 ..      49      89 ..      19      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.8e-05
                       DUF4156 43 kelvrgaandLrneAaalGgntivlvtstatetessqtdvtm 84
                                  +e++ +a+  + ++A++lG+n i++++s+ +  +++  d+ m
  gi|15669603|ref|NP_248416.1| 49 RESEDTALIRMVDNAKKLGANAIIGINSNYAMVGEK-GDMIM 89
                                  5677788888999**************995544332.35555 PP

>> SRR  Seven Residue Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.4   7.6e-05      0.34       1      11 [.      35      45 ..      35      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.6e-05
                           SRR  1 enfekVknaYe 11
                                  +++e+Vk+aYe
  gi|15669603|ref|NP_248416.1| 35 KYYEDVKDAYE 45
                                  69********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 695.43
//
Query:       gi|15669604|ref|NP_248417.1|  [L=241]
Description: hypothetical protein MJ_1414 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00022   20.4   0.1    0.00033   19.8   0.1    1.2  1  Phage_GPA   Bacteriophage replication gene A protein (GPA)
  ------ inclusion threshold ------
      0.035   14.1   0.0      0.079   12.9   0.0    1.5  1  HTH_6       Helix-turn-helix domain, rpiR family
       0.21   11.3   2.2         18    5.1   0.4    2.6  2  Spore_YhaL  Sporulation protein YhaL


Domain annotation for each model (and alignments):
>> Phage_GPA  Bacteriophage replication gene A protein (GPA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   5.6e-08   0.00033     146     235 ..      45     142 ..      21     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.6e-08
                     Phage_GPA 146 eevvkksvsNPaiRraelmvrlrgleriaeekGdvavFlTlT.apskyha..t..ykngkg...nskwngatprdaqdYlv 218
                                   +  ++ svsNPai ++++   + g+ +   +kG   v++T+     + +   +  +++g++   + kw++ t +d++++  
  gi|15669604|ref|NP_248417.1|  45 KVFINLSVSNPAINKVNMKMDIDGYSDGKLSKGIIHVYYTVRyFNGRNETipFyvNEEGTFiklEGKWQKITNNDLSNHTW 125
                                   334578***********************************98787776522321455554111458************** PP

                     Phage_GPA 219 kvwavlraelnkaeirv 235
                                   ++ a ++  ++k++i++
  gi|15669604|ref|NP_248417.1| 126 NILAYIKDLIEKNDIKI 142
                                   ***************96 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.3e-05     0.079      40      68 ..      46      74 ..      27      75 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                                  HHHHTT--HHHHHHHH---S-SSHHHH-- CS
                         HTH_6 40 lAkaaavSeativrfakkLGfkGFselkl 68
                                  +  +++vS+++i+++  k+++ G+s+ kl
  gi|15669604|ref|NP_248417.1| 46 VFINLSVSNPAINKVNMKMDIDGYSDGKL 74
                                  56689********************9765 PP

>> Spore_YhaL  Sporulation protein YhaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1    0.0034        20       3      26 ..       6      29 ..       4      38 .. 0.83
   2 ?    5.1   0.4     0.003        18      28      50 ..     136     158 ..     126     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0034
                    Spore_YhaL  3 wWvYlviagIlfSgymavktakeE 26
                                  w ++lv + I fSg +  + +keE
  gi|15669604|ref|NP_248417.1|  6 WAIFLVLLTITFSGCLNKEISKEE 29
                                  669***********9988888887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.003
                    Spore_YhaL  28 eldqefIEkEGevylerleeere 50 
                                   e+++  IE+E + y+ rl+ e +
  gi|15669604|ref|NP_248417.1| 136 EKNDIKIEEENNHYIIRLKDENA 158
                                   566778*************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1524.00
//
Query:       gi|15669605|ref|NP_248418.1|  [L=370]
Description: tryptophanyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-63  213.7   0.0    4.1e-63  213.4   0.0    1.0  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.4   0.0   2.3e-67   4.1e-63       2     293 .]      63     349 ..      62     349 .. 0.96

  Alignments for each domain:
  == domain 1  score: 213.4 bits;  conditional E-value: 2.3e-67
                                   HHS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHT CS
                  tRNA-synt_1b   2 kerplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldp 82 
                                   ++++++v+sG++P+gk+H G+ +++  l   qk++ ++ + iaDl+A++ +++ + e + + + +++      ++a gldp
  gi|15669605|ref|NP_248418.1|  63 NNKEFAVVSGMMPSGKMHFGHKMVVDLLKFYQKYTDNINIPIADLEAYWARNM-SFETTKELALNEYITN---YIALGLDP 139
                                   6899****************8888888888888********************.7777777777777777...******** PP

                                   TTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSS.S.C--BHHHHHHHHHHHHHHHHTCHSEEEEEGGGH CS
                  tRNA-synt_1b  83 ekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrlee.g.egislgeftYplLqaaDilllkadlvpgGsDQk 161
                                   ek++v+lqs++++ ++la +l++ +++ +++ ++ fk  ++++ +   + ++++++++p+L+++ +   k+ +vp+G DQ+
  gi|15669605|ref|NP_248418.1| 140 EKINVYLQSKYQKVKDLALILSKRTNWSEMKAIYGFKG-ETNIGHvFaPIVQVADILHPQLDENLSPEPKPVVVPVGIDQD 219
                                   **************************************.******6379******************************** PP

                                   HHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHHHH CS
                  tRNA-synt_1b 162 qnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllklk 240
                                    +i+l+rd+a+r+++  +f +p++++++++tgl G+ KmS+S++++aIfL+d++++vkkki +a+t  +e  e +k + + 
  gi|15669605|ref|NP_248418.1| 220 PHIRLTRDIANRAKEF-KFIPPSSTYHRFMTGLLGG-KMSSSKPETAIFLTDDEKTVKKKIFSAKTGGREtlEEHKKYGGV 298
                                   ***************9.*******************.*********************************99999****** PP

                                   HTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1b 241 telsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnelle 293
                                   +e +  ++e + +++  ++ +e+ e++++++++++++g++kk + e + e+l+
  gi|15669605|ref|NP_248418.1| 299 PEECV-VYELFLYHLILDD-KELAEIYQKCRSGELTCGKCKKMAYERVVEFLK 349
                                   *****.************9.9****************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2298.87
//
Query:       gi|15669606|ref|NP_248419.1|  [L=452]
Description: hypothetical protein MJ_1416 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-14   54.0   0.1    4.1e-14   53.0   0.1    1.6  1  AIRS_C    AIR synthase related protein, C-terminal domain
    1.3e-08   35.4   2.6    2.9e-08   34.2   2.6    1.6  1  AIRS      AIR synthase related protein, N-terminal domain
  ------ inclusion threshold ------
        3.7    7.6   6.5        0.5   10.4   0.5    2.2  2  NYD-SP28  Sperm tail


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.1   6.9e-18   4.1e-14       1     154 [.     242     388 ..     242     390 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 6.9e-18
                                   STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH..HTTECEEEE--TTHHHHHHHHH CS
                        AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal..kglvkaahDvTgGGLlgalaem 79 
                                   ++Gdv+++t+++G g ++t +   +  +         +  + l    i+++++l+++   ++++a++DvT+GGL g++ e+
  gi|15669606|ref|NP_248419.1| 242 EVGDVILMTEGSGGGTITTTALYYGWFD---------VIYETLNVDFIKACQNLIRSglIKKIHAMTDVTNGGLRGDAYEI 313
                                   58****************9998877765.........56678888************999********************* PP

                                   HHTTTEEEEEECG......THHHHHHHH.HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEEE CS
                        AIRS_C  80 apasgvgaeidld......kvpifdele.splemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeelsv 153
                                    + ++v++ +d +      ++++++ le + +++l + +   l++++p+e ad ++++ +      a ++G v+++ee+++
  gi|15669606|ref|NP_248419.1| 314 SKTAKVSLIFDKEkvyktiNPKVLEMLEvLNIDPLGVSTDS-LMIICPEEYADDIKKVTG------AIEVGYVEEGEESYL 387
                                   *************7777777777776667777777777777.99********99988888......568999999998877 PP

                                   E CS
                        AIRS_C 154 i 154
                                   +
  gi|15669606|ref|NP_248419.1| 388 V 388
                                   5 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   2.6   4.9e-12   2.9e-08       1      93 [.     117     229 ..     117     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 4.9e-12
                                   SSSE........EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHH CS
                          AIRS   1 dDaa........vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaae 67 
                                   dDa+        +v+++d+  + +   p+ + G  +  ++l+D+++mGA+ +al+  + l       ++ ++ +g+ +  e
  gi|15669606|ref|NP_248419.1| 117 DDAGivradakyIVAAIDGTHSRLSDFPFLG-GFHVTRAALRDIYVMGAEAVALISDVHLAddgdvgKIFDFTAGICAVSE 196
                                   7888444444444888887777777777777.9*******************8777777777*****99************ PP

                                   HTT-EEEEEEEEEESS.......EEEEEEEEEE CS
                          AIRS  68 elgvplvgGdtsfsne.......ptisvtavGl 93 
                                   +++vpl+gG t +  +       ++ +v+a+G+
  gi|15669606|ref|NP_248419.1| 197 AVNVPLIGGSTLRVGGdmvigdrLVSAVGAIGV 229
                                   ***********9886667888888888888887 PP

>> NYD-SP28  Sperm tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.9      0.22   1.3e+03      65      89 ..      26      50 ..      12      67 .. 0.59
   2 ?   10.4   0.5   8.4e-05       0.5      48      81 ..     414     447 ..     408     451 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.22
                      NYD-SP28 65 ceelideKdklikelqeeLkekdeq 89
                                  ++++++ K+++ +e+ +++ ++  +
  gi|15669606|ref|NP_248419.1| 26 FKRILEIKEDVDEEFAKKFIKAILE 50
                                  5666666655554444444333333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 8.4e-05
                      NYD-SP28  48 knkpqeLrkeleeqkqaceelideKdklikelqe 81 
                                   + kp +  ++ e++++ac+e i++Kd +++ l+e
  gi|15669606|ref|NP_248419.1| 414 ERKPGDFEEMKEKVRRACDEAIKKKDFVVELLKE 447
                                   779999********************99988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2846.51
//
Query:       gi|15669607|ref|NP_248420.1|  [L=649]
Description: ATP-dependent protease LA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-27   95.4   0.2    6.3e-27   94.5   0.2    1.4  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    7.1e-17   61.4   0.0    5.5e-14   51.8   0.0    2.2  2  AAA_32           AAA domain
    3.7e-13   49.3   0.0    3.3e-06   26.7   0.0    2.9  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.1e-10   41.5   0.0    9.1e-07   28.7   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
    4.6e-08   32.9   0.1    1.1e-07   31.8   0.1    1.7  1  ChlI             Subunit ChlI of Mg-chelatase
    7.8e-08   31.7   0.5     0.0066   15.6   0.0    2.9  2  MCM              MCM P-loop domain
      1e-06   28.8   0.0      0.042   13.8   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
      5e-05   23.1   0.0       0.25   11.1   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00022   21.6   0.0       0.02   15.3   0.0    2.5  2  AAA              ATPase family associated with various cellul
    0.00064   19.0   0.1        1.1    8.4   0.0    3.1  3  TIP49            TIP49 P-loop domain
     0.0017   18.8   0.0     0.0034   17.8   0.0    1.5  1  AAA_16           AAA ATPase domain
     0.0029   17.3   0.0     0.0059   16.4   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.033   13.7   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
      0.015   15.7   0.0       0.14   12.5   0.0    2.3  2  AAA_19           AAA domain
      0.032   13.8   0.1        4.7    6.7   0.0    3.2  3  FeoB_N           Ferrous iron transport protein B
      0.047   14.0   0.0       0.39   11.0   0.0    2.3  2  AAA_22           AAA domain
       0.06   13.1   0.0       0.19   11.4   0.0    1.8  1  AAA_30           AAA domain
       0.07   12.3   0.0       0.12   11.5   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
       0.13   12.2   0.0        3.8    7.4   0.0    2.6  2  NTPase_1         NTPase
       0.59   10.5   3.9       0.89    9.9   0.0    2.8  2  PRANC            PRANC domain


Domain annotation for each model (and alignments):
>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.2     7e-30   6.3e-27      13     200 ..     445     634 ..     434     638 .. 0.86

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 7e-30
                                   S-SS--SSSSS--BSSEEEEEEEETTEE..EEEEEEEEEESS-S.-EEEEES--HHHHHHHHHHHHHHTSS-GGGSS.... CS
                         Lon_C  13 kkrfrseeaekedqvGvvtGlawtevGG..dlltieavllpgkg.klkltGklgdvmkesaqaalsyvrsraeelgi.... 86 
                                    kr+++   + e +vGv+ Gla   +GG  d+  i +++l+ k    +l    gd+ k s++ a ++ ++ ++e ++    
  gi|15669607|ref|NP_248420.1| 445 FKRYKHIVPNDEPKVGVIYGLAVLGAGGigDVTKIIVQILESKNpGTHLLNISGDIAKHSITLASALSKKLVAEKKLplpk 525
                                   57888888999***************9544999999999987763667777779********9998877655544331111 PP

                                   -SS-TTT-EEEEEE-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEE CS
                         Lon_C  87 dkevfekkdihihvPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvi 167
                                   ++  +++k+i+i + +     dG sa  +++ a++s+l +++ ++d a+tG + L+G+vl+iGG+ ek+ aakr g k+vi
  gi|15669607|ref|NP_248420.1| 526 KDIDLNNKEIYIQFSQSYSKIDGDSATAAVCLAIISALLDIPLKQDFAITGSLDLSGNVLAIGGVNEKIEAAKRYGFKRVI 606
                                   4556899************************************************************************** PP

                                   EEGGGGGGTTTS-HHHHTS-B--EESBHHHHHH CS
                         Lon_C 168 lPkenekdlediPeevreeleiilveevdevlk 200
                                   +P++n  d+ +      e++eii+v+++de++ 
  gi|15669607|ref|NP_248420.1| 607 IPEANMIDVIE-----TEGIEIIPVKTLDEIVP 634
                                   *****999987.....5899*********9985 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0023         2       7      52 ..      20      62 ..      15      98 .. 0.80
   2 !   51.8   0.0   6.1e-17   5.5e-14     290     492 ..     188     386 ..     182     393 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0023
                        AAA_32  7 leeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlle 52
                                  ++++igqe Av+ +  ++   k++ N+ +lG++g+G++++vk + e
  gi|15669607|ref|NP_248420.1| 20 IDQVIGQEEAVKIVLSAV---KNKRNVILLGDPGVGKSMIVKAVGE 62
                                  57899**98887765555...5666***************998755 PP

  == domain 2  score: 51.8 bits;  conditional E-value: 6.1e-17
                        AAA_32 290 egaPVvvednptyanLfGkieyesemg..al.vtdftlIkaGaLhkAnGGyLildaedlLeeplaWeaLkraLrskeikie 367
                                   ++ P v  + ++++ L+G i +    g   l +  +++I  Ga+h+A+ G+L +d  + +    + + +  aL+ k++ i+
  gi|15669607|ref|NP_248420.1| 188 KKRPLVRASAYNVTRLLGDIKHCPLGGrpPLgTPPHKRIILGAIHEAHRGILYVDEIKTMP-LEVQDYILTALQDKQLPIS 267
                                   6889*******************9999664425679**************99998887764.5688999************ PP

                        AAA_32 368 sleeqlglistvsLkPepipldvKViLiGsrelYylLseyDpdfkklFkvkadFddemerteenekkyarfiasivkkekl 448
                                     ++    +s  + + +pip+d   i+ G+ +  y L +   d       k  ++++m+ t en +k+++fi + +k+++l
  gi|15669607|ref|NP_248420.1| 268 GRNP---NSSGATVETNPIPCDFILIMSGNMDDVYNLRAPLLD---RIDYKIVLKNKMDNTLENRDKLLQFIVQEIKNNNL 342
                                   6555...5688999****************8877777664333...234466799************************** PP

                        AAA_32 449 lpfdrsavarlieyssrlaedqeklstrfseiadllrEAdywak 492
                                    p++ +++ ++++ +  la++++kl++r++ +a++++ A+ +a 
  gi|15669607|ref|NP_248420.1| 343 NPMTYDGCCEVVRIAQYLAGSKDKLTLRLRLLANIIKMANDVAM 386
                                   *************************************9998875 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   3.6e-09   3.3e-06       3      49 ..      21      67 ..      19     123 .. 0.89
   2 !   19.3   0.0   6.3e-07   0.00057      98     201 ..     227     317 ..     219     323 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.6e-09
                  Mg_chelatase  3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllppl 49
                                   +v+Gqeea + +  a+  + n++l+G pG GK+m+ k++ ++l++ 
  gi|15669607|ref|NP_248420.1| 21 DQVIGQEEAVKIVLSAVKNKRNVILLGDPGVGKSMIVKAVGEILSDF 67
                                  689*****************************************986 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 6.3e-07
                  Mg_chelatase  98 kpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklkdkekectcsekei 178
                                     G+i  ah+G+L++DE+  +  +v + + + l+d+++ is  +       +    + +Np pc  +         s +  
  gi|15669607|ref|NP_248420.1| 227 ILGAIHEAHRGILYVDEIKTMPLEVQDYILTALQDKQLPISGRNP-----NSSGATVETNPIPCDFILIM------SGNMD 296
                                   569*************************************97764.....44455567899999877633......33444 PP

                  Mg_chelatase 179 erYlsklsgplldRidlqvevkk 201
                                   + Y  +l +plldRid ++ +k+
  gi|15669607|ref|NP_248420.1| 297 DVY--NLRAPLLDRIDYKIVLKN 317
                                   445..678999999999988765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00049      0.44      10      42 ..      28      60 ..      20      78 .. 0.86
   2 !   28.7   0.0     1e-09   9.1e-07      87     126 ..     229     268 ..     221     279 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00049
                                  HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHH CS
               Sigma54_activat 10 elleqikkvaktdlsvlitGesGtGKellarai 42
                                  e+++ + +++k++ +v+++G+ G+GK+++ +a+
  gi|15669607|ref|NP_248420.1| 28 EAVKIVLSAVKNKRNVILLGDPGVGKSMIVKAV 60
                                  5667778889999****************9987 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 1e-09
                                   HHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBT CS
               Sigma54_activat  87 GlfekadgGtlfLDeigelplelQekLlrvlqegevervG 126
                                   G++++a+ G+l++Dei+++ple+Q  +l++lq++++   G
  gi|15669607|ref|NP_248420.1| 229 GAIHEAHRGILYVDEIKTMPLEVQDYILTALQDKQLPISG 268
                                   99*******************************9986555 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.1   1.2e-10   1.1e-07      35     121 .]     525     611 ..     497     611 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.2e-10
                          ChlI  35 nsgfefpakkitvnLaPadlkkeGsafDLpiAigilaaleqieaeeetlflGeLsldGslrpvkgvlpialaakkegikkv 115
                                   + + ++++k+i +  + +  k +G +   ++ ++i++al +i+ ++++ + G L+l+G++  + gv + + aak+ g+k+v
  gi|15669607|ref|NP_248420.1| 525 KKDIDLNNKEIYIQFSQSYSKIDGDSATAAVCLAIISALLDIPLKQDFAITGSLDLSGNVLAIGGVNEKIEAAKRYGFKRV 605
                                   5677889999999999999999*********************************************************** PP

                          ChlI 116 ivpken 121
                                   i+p++n
  gi|15669607|ref|NP_248420.1| 606 IIPEAN 611
                                   ***998 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   7.4e-06    0.0066      52      81 ..      35      64 ..      19      74 .. 0.79
   2 !   12.6   0.2   5.8e-05     0.052     115     213 ..     229     324 ..     224     337 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.4e-06
                                  SBBCSS-EEEEEESSTSTHHHHHHHHHHHS CS
                           MCM 52 tklrgdinvllvgdpgtaKsqlLkyvekla 81
                                  + ++ + nv+l+gdpg++Ks ++k+v +++
  gi|15669607|ref|NP_248420.1| 35 SAVKNKRNVILLGDPGVGKSMIVKAVGEIL 64
                                  4588999******************98875 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 5.8e-05
                                   THHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSCC..TTS-HHHHSSSSHH CS
                           MCM 115 GalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagryd..kkksvaeninlsaa 193
                                   Ga+  a++G++++De+  m  e +++++ a+ ++++ i+        +  +     +np+   +    + ++ +  nl a+
  gi|15669607|ref|NP_248420.1| 229 GAIHEAHRGILYVDEIKTMPLEVQDYILTALQDKQLPISGRN-----PNSSGATVETNPIPCDFIliMSGNMDDVYNLRAP 304
                                   9999********************************998555.....3334444567888777752256667777899999 PP

                                   HHHHSSEEEEE-SSTTHHHH CS
                           MCM 194 lLsrFDlifvllDkvdeekD 213
                                   lL+r D  +vl++k+d++ +
  gi|15669607|ref|NP_248420.1| 305 LLDRIDYKIVLKNKMDNTLE 324
                                   99999999999999887544 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   4.7e-05     0.042       1      23 [.      42      64 ..      42      84 .. 0.81
   2 !   12.5   0.0   0.00012      0.11      66     137 ..     236     308 ..     185     309 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.7e-05
                                  EEEEE--SSSSHHHHHHHGGGGB CS
                         AAA_5  1 dvlLvGppGtgKselaerlaaal 23
                                  +v+L+G+pG+gKs++++ + + l
  gi|15669607|ref|NP_248420.1| 42 NVILLGDPGVGKSMIVKAVGEIL 64
                                  69**************9988877 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00012
                                   -SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---............-EEEEEESS--.-TT-TTHHHHTT CS
                         AAA_5  66 geilvlDEveraesevlnsLlslleerrllleeggelvkaknddller......frviatanpldrslnelspalrsR 137
                                     il++DE+++++ ev++  l+ l +++l++  ++   + +     e+      f +i+++n  d  + +l ++l++R
  gi|15669607|ref|NP_248420.1| 236 RGILYVDEIKTMPLEVQDYILTALQDKQLPISGRNPNSSGAT---VETnpipcdFILIMSGNMDD--VYNLRAPLLDR 308
                                   569***************************655555554444...23345889999999999988..77778888877 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0     0.001      0.91       3      55 ..      17      62 ..      16      81 .. 0.82
   2 !   11.1   0.0   0.00028      0.25      84     153 ..     235     309 ..     221     315 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.001
                        RuvB_N  3 PksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiak 55
                                  P+ +++ igqe+    +ki+++a k++++    v+l G PG+Gk+ + k + +
  gi|15669607|ref|NP_248420.1| 17 PRLIDQVIGQEE---AVKIVLSAVKNKRN----VILLGDPGVGKSMIVKAVGE 62
                                  888999999985...68999999998765....89*********999887765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00028
                        RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldivigkGpsarsikldlpk....ftlv..gattragllssPlrdrf 153
                                   ++ +l++dei  +  +v++++ +a++d +l i  g+ p++   +++ ++    f l+  g    +  l +Pl dr+
  gi|15669607|ref|NP_248420.1| 235 HRGILYVDEIKTMPLEVQDYILTALQDKQLPIS-GRNPNSSGATVETNPipcdFILImsGNMDDVYNLRAPLLDRI 309
                                   4679**************************986.444444443333322111255552233344455667777775 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.2e-05      0.02       1      34 [.      43      81 ..      43     119 .. 0.76
   2 ?    3.8   0.0     0.082        73      54     130 ..     232     315 ..     220     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                                  EEEESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTC CS
                           AAA  1 vllyGppGtGKTllakavakelg.....vefleisgsel 34
                                  v+l G pG+GK++++kav + l+     ++++ i  ++l
  gi|15669607|ref|NP_248420.1| 43 VILLGDPGVGKSMIVKAVGEILSdfgefTPYYVIAKPNL 81
                                  689***************999854444455555555555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.082
                                   HHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESS..GGG CS
                           AAA  54 kekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..................eskvivigatnr..pdk 114
                                    e     il +DEi  +  +           v++ +lt+l++ +                      ++i+i+ +n   + +
  gi|15669607|ref|NP_248420.1| 232 HEAH-RGILYVDEIKTMPLE-----------VQDYILTALQDKQLPisgrnpnssgatvetnpiPCDFILIMSGNMddVYN 300
                                   3333.589999999999555...........5999999999999889999999999999999996669*******977888 PP

                                   STHHHHSTTSSEEEET CS
                           AAA 115 ldpallrgRfdrkiei 130
                                   l  +ll +R+d ki +
  gi|15669607|ref|NP_248420.1| 301 LRAPLL-DRIDYKIVL 315
                                   999999.9*9999865 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0012       1.1      25      88 ..      22      81 ..       9      97 .. 0.74
   2 !    5.6   0.0    0.0089         8     279     309 ..     236     266 ..     229     282 .. 0.90
   3 ?    0.7   0.1      0.27   2.4e+02      36      76 ..     477     517 ..     463     538 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXX CS
                         TIP49 25 glvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelg...edvpfvalsgsev 88
                                   ++Gq+   ea+ ++++ +k+k+     v+l G++g Gk+ +  a+ + l+   e +p+ +++  ++
  gi|15669607|ref|NP_248420.1| 22 QVIGQE---EAVKIVLSAVKNKR----NVILLGDPGVGKSMIVKAVGEILSdfgEFTPYYVIAKPNL 81
                                  466776...57889999999997....78899**********9888776652226677777766555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0089
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49 279 pGvlfiDevhmlDiecfsylnraleselaPi 309
                                   +G+l++De++ + +e+  y+  al ++  Pi
  gi|15669607|ref|NP_248420.1| 236 RGILYVDEIKTMPLEVQDYILTALQDKQLPI 266
                                   7*************************99998 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.27
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  36 agvivelikekklaGravLlaGpsgtGktalaiaiskelge 76 
                                   + +iv+++++k+ + + + ++G+ +     la a+sk+l +
  gi|15669607|ref|NP_248420.1| 477 TKIIVQILESKNPGTHLLNISGDIAKHSITLASALSKKLVA 517
                                   6799********9989999******************9973 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.8e-06    0.0034       3      51 ..      24      66 ..      22     118 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.8e-06
                        AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51
                                  +G ee ++ +lsa+++      ++v+l G++GvGKs +v+++ + l+ d
  gi|15669607|ref|NP_248420.1| 24 IGQEEAVKIVLSAVKNK-----RNVILLGDPGVGKSMIVKAVGEILS-D 66
                                  66667776666666633.....89****************9996444.3 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.6e-06    0.0059      41      71 ..      34      64 ..      17      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.6e-06
                     IstB_IS21 41 lsfiekkenivllGpsGvGKshlaialgvea 71
                                  ls +++k n++llG +GvGKs +  a+g   
  gi|15669607|ref|NP_248420.1| 34 LSAVKNKRNVILLGDPGVGKSMIVKAVGEIL 64
                                  67799*********************99765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.7e-05     0.033      28      55 ..      35      62 ..      26      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
                         AAA_7 28 lllknkkpvllvGptGtGKtviikdllk 55
                                    +knk++v+l G+ G+GK++i+k + +
  gi|15669607|ref|NP_248420.1| 35 SAVKNKRNVILLGDPGVGKSMIVKAVGE 62
                                  5799*******************98655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015      0.14       8      43 ..      38      73 ..      26      94 .. 0.80
   2 ?    0.1   0.0         1   9.1e+02     103     127 ..     236     261 ..     127     268 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                        AAA_19  8 lkekvllvtaGpGtGKTrvlkhivallvelggvkpe 43
                                   +++++++++ pG GK+ ++k++ ++l + g+  p 
  gi|15669607|ref|NP_248420.1| 38 KNKRNVILLGDPGVGKSMIVKAVGEILSDFGEFTPY 73
                                  46789*********************9999987543 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                        AAA_19 103 eellivDEfqdvd.elqyrLlkallg 127
                                   + +l vDE+  +  e+q  +l al +
  gi|15669607|ref|NP_248420.1| 236 RGILYVDEIKTMPlEVQDYILTALQD 261
                                   34899***999999999999999884 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0052       4.7       2      52 ..      42      92 ..      41      97 .. 0.78
   2 ?    2.2   0.0      0.13   1.1e+02      47     133 ..     421     514 ..     390     519 .. 0.61
   3 ?   -0.0   0.0      0.62   5.5e+02     111     125 ..     609     623 ..     600     635 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0052
                                  EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEE CS
                        FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveiv 52
                                  +v+l+G+p vGk++++ a+ +  ++ g ++   v  k    ++++  ve++
  gi|15669607|ref|NP_248420.1| 42 NVILLGDPGVGKSMIVKAVGEILSDFGEFTPYYVIAKPNLKNMERPIVEVI 92
                                  689****************99999999988777666665555555555555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                                   EEEEEEE----SSS.....SSSSHHHHHHHHHHHCTSSSEEE....EEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHH CS
                        FeoB_N  47 keveivDlPGiYsl.....sayseeekvardflleeepdvvv....nvvdatnlernLyLtlqllelgvpvvlalnmidea 118
                                   +  ++ D  GiYs+      +y ++ k  ++++ ++ep+v v     v+ a  +     +++q+le + p    ln++  +
  gi|15669607|ref|NP_248420.1| 421 HVRKVFDT-GIYSMekqvaLNYIKNFKRYKHIVPNDEPKVGViyglAVLGAGGIGDVTKIIVQILESKNPGTHLLNISGDI 500
                                   34455564.777773332223334444445556666666533223268888888888889999999999999999999999 PP

                                   HHTTEEE-HHHHHHH CS
                        FeoB_N 119 ekkgieidlkkLsek 133
                                    k+ i++   +Ls+k
  gi|15669607|ref|NP_248420.1| 501 AKHSITLAS-ALSKK 514
                                   998888753.45555 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.62
                                   EEETHHHHHHTTEEE CS
                        FeoB_N 111 alnmideaekkgiei 125
                                     nmid++e++giei
  gi|15669607|ref|NP_248420.1| 609 EANMIDVIETEGIEI 623
                                   46***********97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00044      0.39       4      29 ..      39      64 ..      36     123 .. 0.79
   2 ?   -0.3   0.0       1.3   1.2e+03      81     112 ..     226     255 ..     180     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00044
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                  +++ +++ G +G+GK++ ++ + e l
  gi|15669607|ref|NP_248420.1| 39 NKRNVILLGDPGVGKSMIVKAVGEIL 64
                                  688899**************998876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.3
                        AAA_22  81 aleqalraravielliiDEaqhlrseealeeL 112
                                    +  a++++++ ++l +DE+  + + e+  ++
  gi|15669607|ref|NP_248420.1| 226 IILGAIHEAHR-GILYVDEIKTM-PLEVQDYI 255
                                   56667888888.9******9988.65555444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021      0.19       5      44 ..      25      66 ..      24      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                        AAA_30  5 eQaaaveallt..sgdrvavltGpAGtGKttalkalreawea 44
                                  +Q++av+ +l+  +++r ++l G +G GK++++ka+ e++ +
  gi|15669607|ref|NP_248420.1| 25 GQEEAVKIVLSavKNKRNVILLGDPGVGKSMIVKAVGEILSD 66
                                  5777777665422566799*****************999876 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.12      52      75 ..      39      62 ..      10      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                        DUF815 52 pannvLLwGarGtGKSslvkalln 75
                                  + +nv+L G+ G+GKS +vka+ +
  gi|15669607|ref|NP_248420.1| 39 NKRNVILLGDPGVGKSMIVKAVGE 62
                                  5689*****************965 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0042       3.8       1      25 [.      42      66 ..      42      70 .. 0.88
   2 ?    1.5   0.0      0.28   2.5e+02      81     114 ..     223     254 ..     188     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0042
                                  EEEEE--TTSSHHHHHHHHHHHH.. CS
                      NTPase_1  1 kvfiTGppGvGKtTlvkkvlellks 25
                                  +v++ G pGvGK+ +vk v e l++
  gi|15669607|ref|NP_248420.1| 42 NVILLGDPGVGKSMIVKAVGEILSD 66
                                  58999*************9999865 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.28
                                   HHHHHHHHHHHHHHHH-EEEE---STTGGG-HHH CS
                      NTPase_1  81 feelalealrkalseadviviDEiGkmElkskkf 114
                                    ++++l a+++a  + +++ +DEi  m l+++ +
  gi|15669607|ref|NP_248420.1| 223 HKRIILGAIHEA--HRGILYVDEIKTMPLEVQDY 254
                                   577888888875..899********999998875 PP

>> PRANC  PRANC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0     0.001      0.89      71      92 ..     243     264 ..     224     267 .. 0.85
   2 ?    0.4   0.2       0.9     8e+02      41      82 ..     315     340 ..     304     348 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
                         PRANC  71 lWnlLPiEIkykIleyLndkdL 92 
                                    ++++P+E++ +Il+ L+dk+L
  gi|15669607|ref|NP_248420.1| 243 EIKTMPLEVQDYILTALQDKQL 264
                                   6789****************98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.9
                         PRANC  41 ikkiik.sakkrykliekaievlnnicskkslWnlLPiEIkyk 82 
                                   +k+ ++ ++++r+kl++ +++ ++n                 +
  gi|15669607|ref|NP_248420.1| 315 LKNKMDnTLENRDKLLQFIVQEIKN-----------------N 340
                                   4444431344555555555555544.................3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      790  (0.0440627); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.52
# Mc/sec: 3760.66
//
Query:       gi|15669608|ref|NP_248421.1|  [L=145]
Description: hypothetical protein MJ_1417.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0016   18.8  17.1     0.0016   18.8  17.1    1.9  2  NBD94            Nucleotide-Binding Domain 94 of RH
     0.0028   18.0   0.9     0.0033   17.8   0.9    1.2  1  DUF4378          Domain of unknown function (DUF4378)
     0.0039   17.4  10.1     0.0039   17.4  10.1    1.5  2  Mlp              Mlp lipoprotein family
  ------ inclusion threshold ------
       0.01   14.5  10.3      0.013   14.2  10.3    1.0  1  FapA             Flagellar Assembly Protein A
      0.011   15.7   3.0      0.012   15.6   3.0    1.1  1  PBECR5           phage-Barnase-EndoU-ColicinE5/D-RelE like nu
       0.02   14.4   0.1      0.029   13.9   0.1    1.2  1  E1-E2_ATPase     E1-E2 ATPase
      0.031   13.5   2.1      0.072   12.3   2.0    1.6  1  DUF3150          Protein of unknown function (DUF3150)
      0.043   13.8   1.3      0.056   13.5   1.3    1.1  1  DUF2278          Uncharacterized conserved protein (DUF2278)
       0.06   13.5   1.1       0.09   13.0   1.1    1.3  1  FAA_hydrolase_N  Fumarylacetoacetase N-terminal
       0.06   14.0   2.5      0.081   13.6   2.5    1.3  1  DUF3800          Protein of unknown function (DUF3800)
      0.063   13.6   0.7       0.13   12.6   0.7    1.6  1  PSII_Pbs27       Photosystem II Pbs27
       0.13   11.8   0.9       0.47   10.0   0.9    2.0  1  KNOX2            KNOX2 domain
       0.15   12.4   5.0       0.31   11.4   3.0    2.5  2  MLD              Membrane Localization Domain
       0.19   11.2   1.8       0.21   11.1   1.8    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
        0.2   12.3   5.3       0.71   10.6   5.3    1.9  1  Ribosomal_S20p   Ribosomal protein S20
       0.22   11.3  10.7        1.3    8.8  10.7    2.0  1  Synaptobrevin    Synaptobrevin
       0.29   10.2   3.0        6.4    5.8   3.0    2.1  1  Complex1_49kDa   Respiratory-chain NADH dehydrogenase, 49 Kd 
       0.58   10.5   6.7        0.3   11.4   1.4    2.4  3  DUF948           Bacterial protein of unknown function (DUF94
       0.65   10.1   4.5       0.87    9.7   4.0    1.5  2  DUF4337          Domain of unknown function (DUF4337)
        1.4    8.9  13.6       0.18   11.8   7.3    2.4  2  DUF1043          Protein of unknown function (DUF1043)
        1.9    9.0   3.8         29    5.3   3.8    2.2  1  YtxH             YtxH-like protein
        2.2    8.7   8.3         11    6.5   8.3    2.2  1  DUF4413          Domain of unknown function (DUF4413)
        2.6    7.9   9.1        3.3    7.6   4.3    2.1  2  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
        6.5    7.4  12.2         39    5.0  12.2    2.0  1  YabA             Initiation control protein YabA


Domain annotation for each model (and alignments):
>> NBD94  Nucleotide-Binding Domain 94 of RH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8  17.1   2.2e-06    0.0016      11      87 ..      12      89 ..       9      96 .. 0.85
   2 ?   -0.9   0.2       3.1   2.3e+03      41      52 ..     130     141 ..     111     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.2e-06
                         NBD94 11 idkkkkiyeniekllnEleeiekektsleevknie.lsYgrsLikllvqkIdeekkkaenlieeiekyienideikkk 87
                                  +d ++ki ++i+kl++ l+ei++ ++ + +v+  e +  +  + k l qkId+  ++ +++++e+eky+++  e k++
  gi|15669608|ref|NP_248421.1| 12 KDLTNKILDEIKKLYEQLDEIKDKNINSSNVQLNEfMRQNVNMLKELNQKIDKYLENNNEILKEMEKYVKEDIEHKNR 89
                                  78899**************************966635666678899**********************8764344555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.1
                         NBD94  41 vknielsYgrsL 52 
                                     +i ++Y +sL
  gi|15669608|ref|NP_248421.1| 130 YIQIAIQYLKSL 141
                                   447888888887 PP

>> DUF4378  Domain of unknown function (DUF4378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.9   4.5e-06    0.0033      65     141 ..      13      90 ..      12     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.5e-06
                       DUF4378  65 DlvneiLaeilalelkrslaepsskvssakkr..rkkklsgeqLleevwseieewlsseelvvde...lvdkdlsrrsgkw 140
                                   Dl n+iL+ei +l+   +l e + k+  +++    + + ++ ++l+e+ ++i+++l++++ ++ e    v++d++++  + 
  gi|15669608|ref|NP_248421.1|  13 DLTNKILDEIKKLYE--QLDEIKDKNINSSNVqlNEFMRQNVNMLKELNQKIDKYLENNNEILKEmekYVKEDIEHK--NR 89 
                                   99********77663..334444443333333245556677788*************99666666666*******99..33 PP

                       DUF4378 141 l 141
                                   +
  gi|15669608|ref|NP_248421.1|  90 M 90 
                                   3 PP

>> Mlp  Mlp lipoprotein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4  10.1   5.3e-06    0.0039      37     115 ..      15      91 ..      11     100 .. 0.80
   2 ?   -2.2   0.0       5.6   4.2e+03      63      80 ..     125     142 ..     118     144 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.3e-06
                           Mlp  37 savfkytiekltneiqgcsddnkskcnnfldWLk.tdiqkqkelaqafkkvykFLeskkekdksfdtyiKseldckkgkd 115
                                   ++     i+kl++++++ +d n +  n +l+    ++++  k   +  +k++k+Le+++e  k++++y+K++++ k+  +
  gi|15669608|ref|NP_248421.1|  15 TNKILDEIKKLYEQLDEIKDKNINSSNVQLNEFMrQNVNMLK---ELNQKIDKYLENNNEILKEMEKYVKEDIEHKNRME 91 
                                   55555679****************999999865515555555...55679*************************99864 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.6
                           Mlp  63 nnfldWLktdiqkqkela 80 
                                   ++ ++++++ iq  k l+
  gi|15669608|ref|NP_248421.1| 125 TQLFNYIQIAIQYLKSLL 142
                                   566777777777777766 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2  10.3   1.7e-05     0.013     337     447 ..      13     127 ..       8     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                          FapA 337 eklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelk.elkeeleskkeea. 415
                                   + ++++ +e+++l e+l+++k+k + +++  + +++  +  ++lk+l ++  k+ e+ +e+ +e++ ++ke +e+k++++ 
  gi|15669608|ref|NP_248421.1|  13 DLTNKILDEIKKLYEQLDEIKDK-NINSSNVQLNEFMRQNVNMLKELNQKIDKYLENNNEILKEMEkYVKEDIEHKNRMEr 92 
                                   5568999****************.333332356777778888888888888888888888888887788888888888888 PP

                          FapA 416 kikvnkeiypgvkikig...kkkliikreysnttf 447
                                   k+k  +++   v i ig   +++ i+++ey  t++
  gi|15669608|ref|NP_248421.1|  93 KLKQISMLLLIVIIAIGltiSYMVILNNEYLSTQL 127
                                   89999999999999999988888888888766655 PP

>> PBECR5  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   3.0   1.6e-05     0.012     137     226 ..      10      97 ..       5     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                        PBECR5 137 sekeLaekllndeavkaaYLadkGeevevayvekek....tfteeqvevlekltdalgddeeegeelaekiieekaeiaks 213
                                   ++k+L +k+l +       L+++ +e++++++++ +    +f  ++v+ l++l+ +++++ e+++e+ +++++  +e    
  gi|15669608|ref|NP_248421.1|  10 GQKDLTNKILDEIK----KLYEQLDEIKDKNINSSNvqlnEFMRQNVNMLKELNQKIDKYLENNNEILKEMEKYVKEDI-- 84 
                                   66667666665544....35677777777777776666679999**************************999888877.. PP

                        PBECR5 214 eakdrketekdkm 226
                                   e+k+r+e +++++
  gi|15669608|ref|NP_248421.1|  85 EHKNRMERKLKQI 97 
                                   5778888887776 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   3.9e-05     0.029      94     156 ..      73     135 ..      57     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.9e-05
                                   TTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHH CS
                  E1-E2_ATPase  94 lgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallv 156
                                   l+++ + v+e  + k ++++kl++++  l +v+++i+l++  + +l+++ l + l++ +++++
  gi|15669608|ref|NP_248421.1|  73 LKEMEKYVKEDIEHKNRMERKLKQISMLLLIVIIAIGLTISYMVILNNEYLSTQLFNYIQIAI 135
                                   667778899999****************************99999999999888888887775 PP

>> DUF3150  Protein of unknown function (DUF3150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.0   9.7e-05     0.072      95     141 ..      45      95 ..      18     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.7e-05
                       DUF3150  95 qeFekekqeFLarydravedWinenp....ewaeiIraavpsaetvaerls 141
                                   +eF++++ ++L+++++++++++++n     e+++ ++++++ +++++++l+
  gi|15669608|ref|NP_248421.1|  45 NEFMRQNVNMLKELNQKIDKYLENNNeilkEMEKYVKEDIEHKNRMERKLK 95 
                                   47**********************996666779999999999999999986 PP

>> DUF2278  Uncharacterized conserved protein (DUF2278)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.3   7.5e-05     0.056      63     135 ..      12      88 ..       8     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.5e-05
                       DUF2278  63 edfehpitakLaaleegfhelesepkgl...aL.Dyirsklldlkkgrvlphdkpgedndildklepilkkaieeka 135
                                   +d++++i++++++l e + e+++++ +    +L  ++r+++  lk+      +  +++n+il+++e+++k++ie+k 
  gi|15669608|ref|NP_248421.1|  12 KDLTNKILDEIKKLYEQLDEIKDKNINSsnvQLnEFMRQNVNMLKELNQKIDKYLENNNEILKEMEKYVKEDIEHKN 88 
                                   78999*****************55443344577469999988888888888899999****************9984 PP

>> FAA_hydrolase_N  Fumarylacetoacetase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.1   0.00012      0.09      38      96 ..      26      91 ..      13     101 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                  S-STGG...SSSGTTSSSSSHHHHHT-HHHHHHHHHHHHHHHBT.SHHHHT-HH.......HHHHHE CS
               FAA_hydrolase_N 38 fsqleedaeekesvfsqptLnafaalgrevwravRaalqelLsa.eeelrdnee.......lreeal 96
                                   +ql+e +++k+   s+ +Ln+f+ ++ ++ +++ +++ + L++ +e l++ e+       +++++ 
  gi|15669608|ref|NP_248421.1| 26 YEQLDE-IKDKNINSSNVQLNEFMRQNVNMLKELNQKIDKYLENnNEILKEMEKyvkedieHKNRME 91
                                  444333.333444447799***********************9865577777774433433444444 PP

>> DUF3800  Protein of unknown function (DUF3800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.5   0.00011     0.081      21      78 ..       6      87 ..       3     142 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                       DUF3800 21 vlgg......kkie.eikkleekikelkkky...................krlleriakflkkndliksdeesdesilivldk 77
                                  ++gg      +ki  eikkl+e+++e+k+k                    k+l ++i+k+l++n      +e  +++  ++++
  gi|15669608|ref|NP_248421.1|  6 IIGGgqkdltNKILdEIKKLYEQLDEIKDKNinssnvqlnefmrqnvnmlKELNQKIDKYLENN------NEILKEMEKYVKE 82
                                  5666787777444459***********************9999999999966666666666553......2222222222222 PP

                       DUF3800 78 ....k 78
                                      k
  gi|15669608|ref|NP_248421.1| 83 diehK 87
                                  22111 PP

>> PSII_Pbs27  Photosystem II Pbs27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.7   0.00017      0.13      31      76 ..      52      97 ..      13     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                    PSII_Pbs27 31 nektkadkalpkaYlkdarevvktlresleldkkddakreraakaa 76
                                  ++ +k+ ++  ++Yl++  e+ k++++++++d++ ++++er+ k++
  gi|15669608|ref|NP_248421.1| 52 VNMLKELNQKIDKYLENNNEILKEMEKYVKEDIEHKNRMERKLKQI 97
                                  333344444889*********************9999999999986 PP

>> KNOX2  KNOX2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.9   0.00062      0.47       5      42 ..      41      78 ..      38      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00062
                         KNOX2  5 dpELDqFMeaYcdvLvkYkeeLtrpveEAteFlreieq 42
                                  +  L +FM + +++L++  +   + +e   e l+e+e+
  gi|15669608|ref|NP_248421.1| 41 NVQLNEFMRQNVNMLKELNQKIDKYLENNNEILKEMEK 78
                                  56799**********************99999999996 PP

>> MLD  Membrane Localization Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.0   0.00041      0.31      29      61 ..      36      68 ..      15      71 .. 0.75
   2 ?   -0.6   0.0       2.3   1.7e+03      24      33 ..      73      82 ..      67     101 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00041
                           MLD 29 eyhellgnmkllkleqvealfeLrkqiehYlle 61
                                  ++  +  +++    ++v+ l eL+++i++Yl+ 
  gi|15669608|ref|NP_248421.1| 36 NINSSNVQLNEFMRQNVNMLKELNQKIDKYLEN 68
                                  344445556677889****************86 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.3
                           MLD 24 ldkLdeyhel 33
                                  l ++++y + 
  gi|15669608|ref|NP_248421.1| 73 LKEMEKYVKE 82
                                  4444444333 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.8   0.00028      0.21     159     232 ..      17      90 ..       9     139 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                  Exonuc_VII_L 159 aikrlleekkqrlekla.srlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlkekleekkerl 232
                                   +i   +++  ++l++++ ++++s++ +l++  ++  ++ ++l+++++k l++++e l+e+++ +ke++e+k++ +
  gi|15669608|ref|NP_248421.1|  17 KILDEIKKLYEQLDEIKdKNINSSNVQLNEFMRQNVNMLKELNQKIDKYLENNNEILKEMEKYVKEDIEHKNR-M 90 
                                   3333344444444444312233333344444333333344555555555555555555555444322222221.1 PP

>> Ribosomal_S20p  Ribosomal protein S20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   5.3   0.00095      0.71       7      77 ..      32      97 ..      12     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00095
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-HHHHHHHHHHHHHHHHHHHCTTSSTCCHHHHHHHHH CS
                Ribosomal_S20p  7 kKrirqnekrrlrNrsyksavrtaiKkvraaieadkekaqealkkaiskidkaakkgvihkNtAaRkkSrl 77
                                  +K   +n ++ + N++++++v +++K++++ i    +k  e+ +++ +++ k +k  + hkN+  Rk  ++
  gi|15669608|ref|NP_248421.1| 32 IKDKNINSSNVQLNEFMRQNV-NMLKELNQKI----DKYLENNNEILKEMEKYVKEDIEHKNRMERKLKQI 97
                                  566666666666677766666.4667777777....788999***********************997665 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  10.7    0.0018       1.3       7      86 ..      36     114 ..      16     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                                   HHHHHHHCCCCHHCCHHHHCHCCCCCHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHTXXXXXXXXXXXXXXXXXXXXX CS
                 Synaptobrevin   7 kikaevdevkdimkeNidkvlergekldeLvdktenLqssaqqFkkqarklkrkmwwknmkliiililvvlililiiiiv 86 
                                   +i++   +  + m++N++ + e ++k+d+  +  +++ ++ +++ k+  + k++m  k  k i +l l+v+i i + i++
  gi|15669608|ref|NP_248421.1|  36 NINSSNVQLNEFMRQNVNMLKELNQKIDKYLENNNEILKEMEKYVKEDIEHKNRMERKL-KQISMLLLIVIIAIGLTISY 114
                                   455555677899*******************************************8544.44444444444444333332 PP

>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   3.0    0.0086       6.4      34      63 ..       4      33 ..       1     111 [. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0086
                                  TBESSBBSS---TTHHHHHHHHHHHHHHHH CS
                Complex1_49kDa 34 yiriGGvarDlpegllekikeflkelekkl 63
                                  + +iGG ++Dl++++l++ik++ ++l++  
  gi|15669608|ref|NP_248421.1|  4 IWIIGGGQKDLTNKILDEIKKLYEQLDEIK 33
                                  567999999****99999999998887644 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.51   3.8e+02      56      73 ..      15      32 ..      11      41 .. 0.60
   2 ?   11.4   1.4    0.0004       0.3      23      66 ..      43      87 ..      40     101 .. 0.81
   3 ?   -2.1   0.1       6.6   4.9e+03       4      11 ..     104     111 ..      97     119 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.51
                        DUF948 56 vnelledvneklekvdpl 73
                                  +n++l+++++  e++d++
  gi|15669608|ref|NP_248421.1| 15 TNKILDEIKKLYEQLDEI 32
                                  455555555555555544 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0004
                        DUF948 23 klkktldeaaatieelekqvdpilkevedllakvne.lledvnek 66
                                  +l++ ++++ ++++el++++d++l++ +++l+++++ + ed+++k
  gi|15669608|ref|NP_248421.1| 43 QLNEFMRQNVNMLKELNQKIDKYLENNNEILKEMEKyVKEDIEHK 87
                                  788999999999*******************99999555677665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 6.6
                        DUF948   4 lIaAiAFv 11 
                                   +I+Ai + 
  gi|15669608|ref|NP_248421.1| 104 VIIAIGLT 111
                                   45555544 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1         2   1.5e+03      80      99 ..      16      35 ..      11      49 .. 0.76
   2 ?    9.7   4.0    0.0012      0.87      52     130 ..      29     108 ..      22     135 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2
                       DUF4337 80 akykkkiarykkekkeikkk 99
                                  +k+ ++i++  ++ +eik+k
  gi|15669608|ref|NP_248421.1| 16 NKILDEIKKLYEQLDEIKDK 35
                                  66777888888888888775 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                       DUF4337  52 laeleleqlelllkakaeelaaavdkkiakykkkiarykkekkeikkkAkeleaerdeaneasdk..fdlasalLqiaIvl 130
                                   l e++ ++++  + + +e  +++v +  +++++ki++y ++ +ei k+ +++ +e  e++ + ++   +++++lL + I++
  gi|15669608|ref|NP_248421.1|  29 LDEIKDKNINSSNVQLNEFMRQNV-NMLKELNQKIDKYLENNNEILKEMEKYVKEDIEHKNRMERklKQISMLLLIVIIAI 108
                                   555544444444444454555555.68999****************99998866655554444444444555555444443 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   7.3   0.00023      0.18      10      92 ..       6      88 ..       4     100 .. 0.68
   2 ?   -0.4   0.5       1.4   1.1e+03       2      16 ..     103     117 ..      99     145 .] 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                       DUF1043 10 iiGalilrltnsklkkqkklekelekaka.eleeqkqeledHfaqsaelLetlaedyqkLyqhlaksseeL..lpeleeqelf 89
                                  iiG     ltn+ l + kkl ++l++ k+ +++  + +l++++ q+ ++L++l+++ +k   +l++++e L  + +  ++++ 
  gi|15669608|ref|NP_248421.1|  6 IIGGGQKDLTNKILDEIKKLYEQLDEIKDkNINSSNVQLNEFMRQNVNMLKELNQKIDK---YLENNNEILkeMEKYVKEDIE 85
                                  56666667889999999********998526999*******************976655...555555555221222222222 PP

                       DUF1043 90 qqk 92
                                   ++
  gi|15669608|ref|NP_248421.1| 86 HKN 88
                                  222 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                       DUF1043   2 liglvvGiiiGalil 16 
                                   ++++ +G+ i ++++
  gi|15669608|ref|NP_248421.1| 103 IVIIAIGLTISYMVI 117
                                   445556666666554 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   3.8     0.039        29      49      69 ..      33      86 ..      11      98 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.039
                          YtxH 49 keka.................................kekaedlkekvkekade 69
                                  k+k                                  +e  +++ + vke++++
  gi|15669608|ref|NP_248421.1| 33 KDKNinssnvqlnefmrqnvnmlkelnqkidkylennNEILKEMEKYVKEDIEH 86
                                  444444445555555555555554444444555555555555555555555554 PP

>> DUF4413  Domain of unknown function (DUF4413)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   8.3     0.014        11      13      55 ..      20      73 ..      10     145 .] 0.70

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.014
                       DUF4413 13 neilevkkllkewaks..eddlls.............kmaekmqekfdkywkksnlll 55
                                  +ei +  ++l+e +++  +    s             +m++++++k+dky+++ n +l
  gi|15669608|ref|NP_248421.1| 20 DEIKKLYEQLDEIKDKniN----SsnvqlnefmrqnvNMLKELNQKIDKYLENNNEIL 73
                                  5555555555544333221....0223344555589999999999*****98655443 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.7      0.11        79     113     133 ..      15      35 ..      10      54 .. 0.76
   2 ?    7.6   4.3    0.0044       3.3     111     172 ..      53     114 ..      36     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.11
                   EMP24_GP25L 113 letleselkkleekldsikre 133
                                    +++ +e+kkl e+ld+ik++
  gi|15669608|ref|NP_248421.1|  15 TNKILDEIKKLYEQLDEIKDK 35 
                                   4668999***********975 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0044
                   EMP24_GP25L 111 ekletleselkkleekldsikreqkylrereerlrdtnestnsrvvwwsilqllvlvlvavl 172
                                   + l++l+++++k+ e+ ++i +e++ + +   ++++ +e   + +    ++ ++++ l+  +
  gi|15669608|ref|NP_248421.1|  53 NMLKELNQKIDKYLENNNEILKEMEKYVKEDIEHKNRMERKLKQISMLLLIVIIAIGLTISY 114
                                   56788999999999999999999999999988888888877777777666666666665544 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  12.2     0.052        39       3      60 ..      34      92 ..      11     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.052
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHXXXXXXXX CS
                          YabA  3 kkelfdkleeleeqleelleeleelkeelaelleenaeLelenek.lrerleeeekkek 60
                                  +k++ ++  +l+e +++ ++ l+el++++ + le+n+e+  e ek ++e +e++++ e+
  gi|15669608|ref|NP_248421.1| 34 DKNINSSNVQLNEFMRQNVNMLKELNQKIDKYLENNNEILKEMEKyVKEDIEHKNRMER 92
                                  46677777888899999999999999999999999888877765426666644443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3841  (0.214234); expected 358.6 (0.02)
Passed bias filter:                     1031  (0.0575046); expected 358.6 (0.02)
Passed Vit filter:                       162  (0.00903564); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 889.69
//
Query:       gi|15669609|ref|NP_248422.1|  [L=181]
Description: fuculose-1-phosphate aldolase FucA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.1e-42  143.7   0.0    6.8e-42  143.5   0.0    1.0  1  Aldolase_II  Class II Aldolase and Adducin N-terminal domain


Domain annotation for each model (and alignments):
>> Aldolase_II  Class II Aldolase and Adducin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.5   0.0   3.8e-46   6.8e-42       2     185 ..       5     173 ..       4     174 .. 0.93

  Alignments for each domain:
  == domain 1  score: 143.5 bits;  conditional E-value: 3.8e-46
                                   HHHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHHHHHH CS
                   Aldolase_II   2 elaeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHlaiyk 82 
                                   + ++++r+l++r++v g gGn+Sv+ + +d+++ tp+g  ++ l+++d++++dld g+v++     gkp+se  lHl+iy+
  gi|15669609|ref|NP_248422.1|   5 QFIKICRKLYDRKYVVGSGGNVSVK-E-GDKIYLTPTGSILGFLKEDDIAEMDLD-GNVIK-----GKPTSEKNLHLMIYR 77 
                                   5789*********************.5.79************************9.****4.....49************* PP

                                   H-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEEETTTEEEE CS
                   Aldolase_II  83 arpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavllrnHGllt 163
                                   +r d++a++HtHs   + ls++  +++++ lt+e++ +l  +++++++y++ g+ +l+e++a+   +d ++++l+nHG+++
  gi|15669609|ref|NP_248422.1|  78 KRNDINAIIHTHSLISTFLSTI--NKEIELLTPEGKIFL--KKIGYVDYYEAGSLKLAEETAK---RDEDVIILKNHGVVC 151
                                   ********************76..677*99*******77..88**********9999888888...3567*********** PP

                                   EESSHHHHHHHHHHHHHHHHHH CS
                   Aldolase_II 164 vGetleeAvalaetleeaaeiq 185
                                    G++l +A+  +e+lee a++ 
  gi|15669609|ref|NP_248422.1| 152 LGKDLIDAYIKVEVLEEQAKLT 173
                                   *******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1080.58
//
Query:       gi|15669610|ref|NP_248423.1|  [L=101]
Description: hypothetical protein MJ_1419 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-34  116.7   0.9    4.2e-34  116.4   0.9    1.1  1  UPF0147      Uncharacterised protein family (UPF0147)
     0.0038   17.5   0.1        1.3    9.4   0.1    2.2  2  UPF0253      Uncharacterised protein family (UPF0253)
  ------ inclusion threshold ------
       0.19   12.2   0.4        3.5    8.1   0.3    2.1  2  Caskin-tail  C-terminal region of Caskin


Domain annotation for each model (and alignments):
>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.9   7.1e-38   4.2e-34       2      81 .]      21     100 ..      20     100 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 7.1e-38
                                   HHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
                       UPF0147   2 eekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEti 81 
                                   ee +k v+ +L+eii+dt+vPrniR aa++ake++ +e e++ vr+atai iLdeisnDpnmPlh+Rt+iw++vs+LE++
  gi|15669610|ref|NP_248423.1|  21 EEILKGVALMLDEIINDTTVPRNIRAAAEKAKEAVLKEGEEPIVRSATAIHILDEISNDPNMPLHTRTQIWSIVSELERV 100
                                   6889999***********************************************************************87 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00021       1.3      27      51 ..      24      48 ..       5      56 .. 0.84
   2 !    6.3   0.0     0.002        12      29      50 ..      68      89 ..      59      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00021
                       UPF0253 27 iscalktLdevaanealpeevrekA 51
                                  ++ +   Lde+ ++  +p+++r  A
  gi|15669610|ref|NP_248423.1| 24 LKGVALMLDEIINDTTVPRNIRAAA 48
                                  5667789***************877 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.002
                       UPF0253 29 calktLdevaanealpeevrek 50
                                   a++ Lde+ ++ ++p ++r +
  gi|15669610|ref|NP_248423.1| 68 TAIHILDEISNDPNMPLHTRTQ 89
                                  6899************999865 PP

>> Caskin-tail  C-terminal region of Caskin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.046   2.7e+02      32      53 ..      13      34 ..       9      38 .. 0.85
   2 ?    8.1   0.3   0.00059       3.5      16      48 ..      50      78 ..      37      79 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.046
                   Caskin-tail 32 saaevksaknILdDIgnMFDdL 53
                                  saa++k+ ++IL  ++ M D++
  gi|15669610|ref|NP_248423.1| 13 SAASEKTPEEILKGVALMLDEI 34
                                  567899999*********9985 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00059
                   Caskin-tail 16 kavEkkikqeesessssaaevksaknILdDIgn 48
                                  ka E  +k+ e      + ++ +a +ILd I+n
  gi|15669610|ref|NP_248423.1| 50 KAKEAVLKEGE----EPIVRSATAIHILDEISN 78
                                  33333333222....34567899*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 662.55
//
Query:       gi|15669611|ref|NP_248424.1|  [L=1102]
Description: glucosamine--fructose-6-phosphate aminotransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-39  134.1   3.8    2.9e-39  134.1   3.8    3.0  3  Intein_splicing  Intein splicing domain
    3.2e-35  120.8   3.1    5.7e-21   74.7   0.6    2.4  2  SIS              SIS domain
    3.2e-24   85.1   6.1    4.4e-17   62.2   0.8    3.6  3  LAGLIDADG_3      LAGLIDADG-like domain
    3.4e-19   68.9   0.0      1e-18   67.4   0.0    1.8  1  GATase_7         Glutamine amidotransferase domain
    1.1e-17   64.5   0.0    2.2e-17   63.5   0.0    1.5  1  GATase_6         Glutamine amidotransferase domain
    9.7e-10   38.4   0.4    4.1e-09   36.4   0.4    2.2  1  HTH_3            Helix-turn-helix
    9.2e-09   35.2   8.2    1.2e-08   34.8   1.6    4.0  3  HTH_19           Helix-turn-helix domain
    1.1e-06   28.8   0.0    2.3e-06   27.8   0.0    1.4  1  HTH_31           Helix-turn-helix domain
      2e-05   24.4   0.3    8.2e-05   22.4   0.1    2.3  1  HTH_25           Helix-turn-helix domain
    0.00065   20.1   0.1     0.0017   18.7   0.1    1.7  1  HTH_26           Cro/C1-type HTH DNA-binding domain
     0.0085   16.0   0.0       0.02   14.8   0.0    1.6  1  HTH_37           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.019   15.1   0.4          1    9.5   0.0    3.6  3  LAGLIDADG_WhiA   WhiA LAGLIDADG-like domain
      0.027   13.4   0.1      0.066   12.1   0.1    1.6  2  GATase_4         Glutamine amidotransferases class-II
      0.064   12.8   0.0       0.13   11.8   0.0    1.4  1  Hint             Hint module
        9.6    6.4   7.8       0.99    9.5   0.1    3.1  3  ARL2_Bind_BART   The ARF-like 2 binding protein BART


Domain annotation for each model (and alignments):
>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.1   3.8   2.5e-42   2.9e-39       1     134 []      82     573 ..      82     573 .. 1.00
   2 ?   -0.8   0.6       1.2   1.4e+03     105     125 ..     720     740 ..     591     749 .. 0.50
   3 ?   -2.0   0.0       2.7   3.3e+03      27      64 ..    1010    1047 ..     948    1048 .. 0.74

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 2.5e-42
                                   EEECTTCEEEEHHHHCCECTTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCTTEEEEEEC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing   1 iiledgeekvkieelvekegeevlslnledlklevksvkkliklklkelyeiklesgrkikaTpeHkllvvrdegivEkra 81 
                                   +il dg++k ki+e+   +++evls+n+edlkl++k++kk+ +++ k ly+ik ++++++++T+eHkl+vv++++ivEk++
  gi|15669611|ref|NP_248424.1|  82 VILPDGRMK-KISEI---DEDEVLSVNFEDLKLYNKKIKKFKHKAPKILYKIK-TAFSELITTGEHKLFVVENGKIVEKCV 157
                                   799******.*****...89*********************************.89***************99******** PP

                                   CC--TT-EEEEE..................................................................... CS
                                   xxxxxxxxxxxx..................................................................... RF
               Intein_splicing  82 deLkegdliavp..................................................................... 93 
                                   ++L+ ++li v+                                                                     
  gi|15669611|ref|NP_248424.1| 158 KDLNGSELIGVVrklnysfndnvefkdvyverhykldetirnklrkvreklgltrkdveklcgvkeiyivkietgklesie 238
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669611|ref|NP_248424.1| 239 eerlkklcslyginfeeiiyrdnlhytnpvkfpktptpelmqiigyiigdghfpsnrmlrlkderkevleeynqlfktvfn 319
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669611|ref|NP_248424.1| 320 legnikkgdgnyyileinskylidwfrenipelfnktgnertpefvfrlnndlvasylrgifdaegyiraeakqigigmts 400
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669611|ref|NP_248424.1| 401 kcfikeiqflllrfgilasyskikrkeenwnnthkllisdkksfelfkkyigftakdkmekleailnkmkglnfryisipl 481
                                   ********************************************************************************* PP

                                   ...................................................HSCEEEEEEEEEEEEECEEEEEEEEETTT- CS
                                   ...................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing  94 ...................................................dadvvwdkvksievedeeeyVYdltvednh 123
                                                                                      dad+vw+k+k  eve++ eyVYdl+ved+h
  gi|15669611|ref|NP_248424.1| 482 tkkeirefvgvplktikngdnyctdytiekiieelnskglydkaeylkrflDADIVWTKFKIEEVESDVEYVYDLEVEDYH 562
                                   ********************************************************************************* PP

                                   EEEECTTEEE- CS
                                   xxxxxxxxxxx RF
               Intein_splicing 124 NFvangiivHN 134
                                   NF++n ii+HN
  gi|15669611|ref|NP_248424.1| 563 NFIGNLIINHN 573
                                   **********9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                   EEEEECEEEEEEEEETTT-EE CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing 105 ievedeeeyVYdltvednhNF 125
                                   + v +++e+ Y +t+e+n N 
  gi|15669611|ref|NP_248424.1| 720 VVVIKKKENGYEVTIENNGNT 740
                                   333444444566666666665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.7
                                    ETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing   27 nledlklevksvkkliklklkelyeiklesgrkikaTp 64  
                                    n++++ +  ++ ++++++ l+++ e+k + g+ i +Tp
  gi|15669611|ref|NP_248424.1| 1010 NMDTVAIVPPRDSAVFNSILSNIEEVKARGGKVIAITP 1047
                                    45555555555566666677788888888888888886 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.6   4.8e-24   5.7e-21       5     130 ..     796     918 ..     793     919 .. 0.93
   2 !   46.2   0.1   3.1e-15   3.7e-12       6      89 ..     962    1048 ..     959    1085 .. 0.76

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 4.8e-24
                                   SSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEE CS
                           SIS   5 akriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiia 85 
                                    +r+y++++Gts ++a+ + + ++++g+ v  + dase+ +   +++d+++lvi i++sget d+++a++ ak+++ak+ a
  gi|15669611|ref|NP_248424.1| 796 YDRVYFVAMGTSLHAAMVVEYLFAKLGKLVI-ACDASEFLNK--GVVDDKTLVIGITQSGETYDTLKALRFAKKNKAKTGA 873
                                   579**********************987665.5678886666..8************************************ PP

                                   EESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                           SIS  86 ITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                   I +  gs++ read+++++ a+ e+ v +tk++t+ql+ l+ l++
  gi|15669611|ref|NP_248424.1| 874 IVNVLGSTATREADITVMMGAGIEIAVCATKTYTSQLMILYRLFI 918
                                   **************************************9988875 PP

  == domain 2  score: 46.2 bits;  conditional E-value: 3.1e-15
                                    SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHH..HHHHHHHH.HHHHTTS CS
                           SIS    6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsget..kdlvaaae.lakerga 81  
                                    ++ +++ +G + a+a+e+alk++ei++ ++e+ + + lkhg+++lide++  ++i + + +  +++++++  ++k+rg+
  gi|15669611|ref|NP_248424.1|  962 NNYIFISKGINIASALEGALKFKEITYLHAEGMSGGLLKHGTISLIDENMDTVAIVPPRDSavFNSILSNIeEVKARGG 1040
                                    6778999*************************************************5555423455555555******* PP

                                    EEEEEESS CS
                           SIS   82 kiiaITds 89  
                                    k+iaIT  
  gi|15669611|ref|NP_248424.1| 1041 KVIAITPT 1048
                                    ******33 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   2.9e-08   3.4e-05       4      82 ..     278     349 ..     275     350 .. 0.89
   2 !   62.2   0.8   3.7e-20   4.4e-17       2      83 .]     372     452 ..     371     452 .. 0.96
   3 ?   -2.9   0.1       7.4   8.8e+03      56      72 ..     654     672 ..     640     673 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.9e-08
                                   HHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHH.HCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGGGTTT CS
                   LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLl.rlGIestiyekkkakgrgvyrlliisgenlkrFleki 82 
                                   ++ + G++ +DG++  ++     ++l+   ke+le++ +l +  +++e +i++       ++y l i s+  +  F+e+i
  gi|15669611|ref|NP_248424.1| 278 LMQIIGYIIGDGHFPSNRM----LRLKDERKEVLEEYNQLFKtVFNLEGNIKKG----DGNYYILEINSKYLIDWFRENI 349
                                   67899*************6....9******************99**********....5556668888888899999998 PP

  == domain 2  score: 62.2 bits;  conditional E-value: 3.7e-20
                                   HHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEE..EEE-SCCCCECCCHCHCTTCGGGT CS
                   LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyek..kkakgrgvyrlliisgenlkrFle 80 
                                    +a +LrG fda+G+++ + k    i ++++sk +++++q lLlr+GI ++  +   k+++++++++lli+++++++ F +
  gi|15669611|ref|NP_248424.1| 372 LVASYLRGIFDAEGYIRAEAKQ---IGIGMTSKCFIKEIQFLLLRFGILASYSKIkrKEENWNNTHKLLISDKKSFELFKK 449
                                   6899****************99...************************999999999*********************** PP

                                   TTX CS
                   LAGLIDADG_3  81 kig 83 
                                   +ig
  gi|15669611|ref|NP_248424.1| 450 YIG 452
                                   *98 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 7.4
                                   E..EEE-SCCCCECCCHCH CS
                   LAGLIDADG_3  56 k..kkakgrgvyrlliisg 72 
                                       ++k +g+y l+ii++
  gi|15669611|ref|NP_248424.1| 654 VknAIKKLKGTYALVIINK 672
                                   3446788899999999987 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0   8.5e-22     1e-18      11     122 ..     585     706 ..     575     707 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 8.5e-22
                      GATase_7  11 agaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea..............ewgeealerlnGm 77 
                                   ++a P + + ++++++v+nG i Nykel++eL +kgh+f++++Dtev+ +l+e+              + +++a+++l+G 
  gi|15669611|ref|NP_248424.1| 585 ENAHPHT-DCKEEIAVVHNGIISNYKELKDELMKKGHKFKSETDTEVVPHLIEEelkkfkeineenyiKAVKNAIKKLKGT 664
                                   5667777.57889******************************************************999*********** PP

                      GATase_7  78 fAfaiwdeeekrl.llaRDrlGikPLyygedkgdallfaSelkall 122
                                   +A++i++++  +l + aR+   + PL++g ++ d+++++S + a+l
  gi|15669611|ref|NP_248424.1| 665 YALVIINKNFPNLlIGARN---ESPLILGIND-DGYFLGSDITAFL 706
                                   *******998865156899...8********6.7********9997 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.0   1.8e-20   2.2e-17      14     133 ..     568     700 ..     553     701 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 1.8e-20
                      GATase_6  14 valaHv.RlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.........eel 84 
                                   +++ H+ R+a++g+  +e a+P +  ++++++vhNG i+nykel++el + kg++f+s++Dtev+ +l+            
  gi|15669611|ref|NP_248424.1| 568 LIINHNsRWATHGNVCKENAHPHTDCKEEIAVVHNGIISNYKELKDELMK-KGHKFKSETDTEVVPHLIeeelkkfkeI-- 645
                                   6788888*******988888******************************.******************9777666440.. PP

                      GATase_6  85 G........eevlerlrGmfafaiwdk.rentlilardrlgvkplyyavdesglafas 133
                                            + ++++l+G +a +i++k  +n li ar   +++pl+ +++++g   +s
  gi|15669611|ref|NP_248424.1| 646 NeenyikavKNAIKKLKGTYALVIINKnFPNLLIGAR---NESPLILGINDDGYFLGS 700
                                   26666778888999*************8888888885...559******988887777 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.4   3.4e-12   4.1e-09       1      55 []     201     256 ..     201     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 3.4e-12
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHHTSEHHHH CS
                         HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklakaLgvsldel 55 
                                   l++ R++lgl+++++ +++Gv+  +i +iE G   ++  e+lkkl+  +g+ ++e+
  gi|15669611|ref|NP_248424.1| 201 LRKVREKLGLTRKDVEKLCGVKEIYIVKIETGkLESIEEERLKKLCSLYGINFEEI 256
                                   89*******************************666****************9986 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   1.6     1e-11   1.2e-08       3      59 ..     200     256 ..     199     261 .. 0.95
   2 ?   -1.6   0.0       2.4   2.8e+03      33      63 ..     466     501 ..     460     502 .. 0.71
   3 ?    1.1   0.1      0.34   4.1e+02      11      25 ..     948     962 ..     926     987 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1e-11
                        HTH_19   3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyl 59 
                                   +L+++Re+lglt +++++ +g+   +i +iE+gk + ++ e+l+k++ ++gi+ e++
  gi|15669611|ref|NP_248424.1| 200 KLRKVREKLGLTRKDVEKLCGVKEIYIVKIETGKLESIEEERLKKLCSLYGINFEEI 256
                                   79**************************************************98776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.4
                        HTH_19  33 Eng....kkdvpsaell.lkiaealgidleyllqge 63 
                                    n     ++ ++s++l  + i e++g++l+ + +g+
  gi|15669611|ref|NP_248424.1| 466 LNKmkglNFRYISIPLTkKEIREFVGVPLKTIKNGD 501
                                   555555666677777776889999999999888876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.34
                        HTH_19  11 lgltqeelaerlgis 25 
                                   ++ t++e+a++l+++
  gi|15669611|ref|NP_248424.1| 948 KKETIKEIANNLKVN 962
                                   456677777777664 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.9e-09   2.3e-06       6      56 ..     201     251 ..     199     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.9e-09
                        HTH_31   6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56 
                                   Lr  Re+ GL++++v +++gv e ++ ++E+G+     ++ l +l+ ++g 
  gi|15669611|ref|NP_248424.1| 201 LRKVREKLGLTRKDVEKLCGVKEIYIVKIETGKLESIEEERLKKLCSLYGI 251
                                   99***********************************************96 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   6.8e-08   8.2e-05       2      41 ..     201     240 ..     200     255 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.8e-08
                                   HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--TTSS-H CS
                        HTH_25   2 LraaRearglsleevaketkIrkdylealEeddfdalpep 41 
                                   Lr+ Re++gl++++v+k   +++ y+ ++E +++++++e+
  gi|15669611|ref|NP_248424.1| 201 LRKVREKLGLTRKDVEKLCGVKEIYIVKIETGKLESIEEE 240
                                   9**********************************99876 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.4e-06    0.0017       1      58 [.     200     257 ..     200     260 .. 0.97

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-06
                        HTH_26   1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLl 58 
                                   kLr++  + g+t++++++ +g+ +  + ++ +gk e++  ++L k+C   g+++++++
  gi|15669611|ref|NP_248424.1| 200 KLRKVREKLGLTRKDVEKLCGVKEIYIVKIETGKLESIEEERLKKLCSLYGINFEEII 257
                                   79******************************************************98 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.7e-05      0.02      22      67 ..     200     245 ..     188     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                   HHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT--HHHHHHH CS
                        HTH_37  22 aiaeliekrelsqseaaqllgiaqPkvsrllrgklsrfsldkLlnl 67 
                                   ++++++ek++l+ +++ +l+g+++  +++++ gkl+++++++L +l
  gi|15669611|ref|NP_248424.1| 200 KLRKVREKLGLTRKDVEKLCGVKEIYIVKIETGKLESIEEERLKKL 245
                                   4899***************************************876 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.41   4.9e+02       4      30 ..     313     340 ..     310     355 .. 0.88
   2 ?    9.5   0.0   0.00086         1       2      56 ..     374     426 ..     373     434 .. 0.89
   3 ?   -2.2   0.0       3.7   4.4e+03      28      50 ..     453     476 ..     441     479 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.41
                LAGLIDADG_WhiA   4 flrGaflasGsindpekk.yhLEivspd 30 
                                   +++ +f  +G i++   + y LEi s++
  gi|15669611|ref|NP_248424.1| 313 LFKTVFNLEGNIKKGDGNyYILEINSKY 340
                                   577889999******9999*****9986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00086
                LAGLIDADG_WhiA   2 kaflrGaflasGsindpekkyhLEivspdeelaeqlqkllnefeleakilerrkk 56 
                                   +++lrG+f a+G i+ ++k+  + i ++++ +++++q ll +f++ a+ ++ ++k
  gi|15669611|ref|NP_248424.1| 374 ASYLRGIFDAEGYIRAEAKQ--IGIGMTSKCFIKEIQFLLLRFGILASYSKIKRK 426
                                   68**************6665..9********************999988887765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.7
                LAGLIDADG_WhiA  28 spdeelaeqlqkllnef.eleaki 50 
                                   ++ ++ +e+l  +ln++ +l+++ 
  gi|15669611|ref|NP_248424.1| 453 FTAKDKMEKLEAILNKMkGLNFRY 476
                                   567788899999999888888876 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       4.3   5.2e+03     148     199 ..     118     174 ..      96     188 .. 0.65
   2 ?   12.1   0.1   5.5e-05     0.066      71     162 ..     566     661 ..     556     673 .. 0.70

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4.3
                      GATase_4 148 aepsaeeleralaelakeiaelGvfnlllsdgralfahas.....trLvyilRkaPf 199
                                    + +a ++   +++ ++e+ ++G+  l + +  +++  +      ++L+ ++Rk  +
  gi|15669611|ref|NP_248424.1| 118 FKHKAPKILYKIKTAFSELITTGEHKLFVVENGKIVEKCVkdlngSELIGVVRKLNY 174
                                   455566666777777888888888876666666666666523333447777776655 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.5e-05
                      GATase_4  71 sknvvaH.iRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCelleelasrfe 146
                                    ++++ H  R at+G+v +en+hp +    ++e+   HnG +++yk+      ++ ++   +TD+E++   + eel++  e
  gi|15669611|ref|NP_248424.1| 566 GNLIINHnSRWATHGNVCKENAHPHTD--CKEEIAVVHNGIISNYKELKdelmKKGHKFKSETDTEVVPHLIEEELKKFKE 644
                                   56778884599*************986..57889999*****99876554446455556679***9987777677776554 PP

                      GATase_4 147 .kaepsaeeleralael 162
                                    ++e+ ++++++a+++l
  gi|15669611|ref|NP_248424.1| 645 iNEENYIKAVKNAIKKL 661
                                   23344455555555544 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.13      10     111 ..      73     185 ..      68     209 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Hint  10 ggCFpgestvtvedgeqkslseLepGdkVlavd.esgevvfsevllfldrds....eqraefveietengekltlTpaHLv 85 
                                   g C   +  v + dg+ k++se+   d+Vl+v+ e+ ++  ++++ f ++ +    + ++ f e+ t  ++kl + ++  +
  gi|15669611|ref|NP_248424.1|  73 GHCLHPDTYVILPDGRMKKISEIDE-DEVLSVNfEDLKLYNKKIKKFKHKAPkilyKIKTAFSELITTGEHKLFVVENGKI 152
                                   78*********************97.9******8888999999******99955555566666666666666666555444 PP

                                   XXXXXXXXXXXXX...............XXXXXXXXXXXXX CS
                          Hint  86 fvsenekssseee...............eavfaskvregdy 111
                                      ++                       +++f ++v+  d+
  gi|15669611|ref|NP_248424.1| 153 VE-KC-------VkdlngseligvvrklNYSFNDNVEFKDV 185
                                   32.22.......12222333567777777777777776664 PP

>> ARL2_Bind_BART  The ARF-like 2 binding protein BART
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00082      0.99      32      77 ..     175     228 ..     153     259 .. 0.85
   2 ?   -0.7   0.6       1.2   1.5e+03      34      76 ..     591     635 ..     568     666 .. 0.57
   3 ?   -3.5   0.1       9.2   1.1e+04      44      67 ..     914     937 ..     911     959 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00082
                                   TT--SS-SSTTHHHHHHHHHHHHHHHHHHHHTT-SSS--THHHHH......... CS
                ARL2_Bind_BART  32 vFddeeenkleytdihkeYkklveklleslleeigismeefleal........e 77 
                                    F+d+ e k +y + h +  +++ + l+++ e++g++ +++++ +        +
  gi|15669611|ref|NP_248424.1| 175 SFNDNVEFKDVYVERHYKLDETIRNKLRKVREKLGLTRKDVEKLCgvkeiyivK 228
                                   6*******************************************9655555541 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                                   --.SS-SSTTHHHHHHHHHHHHHHHHHH.HHTT-SSS--THHHHH CS
                ARL2_Bind_BART  34 dd.eeenkleytdihkeYkklveklles.lleeigismeefleal 76 
                                   +d +ee  ++++ i  +Yk+l ++l+++    + + + e + + +
  gi|15669611|ref|NP_248424.1| 591 TDcKEEIAVVHNGIISNYKELKDELMKKgHKFKSETDTEVVPHLI 635
                                   554566666666666777777666666522222233332222222 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 9.2
                                   HHHHHHHHHHHHHHHHHHHTT-SS CS
                ARL2_Bind_BART  44 tdihkeYkklveklleslleeigi 67 
                                   + ++ eY kl+ + ++++ +ei  
  gi|15669611|ref|NP_248424.1| 914 YRLFIEYGKLLGRDMSEYEKEIDK 937
                                   567777777777777777777632 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.86u 0.31s 00:00:01.17 Elapsed: 00:00:00.49
# Mc/sec: 6726.56
//
Query:       gi|15669612|ref|NP_248425.1|  [L=443]
Description: cobyrinic acid a,c-diamide synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-36  126.1   0.1    1.8e-36  125.6   0.1    1.3  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
    6.5e-19   68.5   1.6    9.4e-16   58.2   1.5    2.6  2  AAA_26    AAA domain
    1.1e-18   67.5   0.2    1.9e-18   66.7   0.2    1.4  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.068   13.0   0.0       0.17   11.7   0.0    1.6  1  Csm1_B    Csm1 subunit domain B
      0.098   12.5   0.0       0.27   11.0   0.0    1.7  1  SNO       SNO glutamine amidotransferase family
       0.18   11.1   0.3       0.29   10.4   0.3    1.5  1  DUF1611   Domain of unknown function (DUF1611_C) P-loop domai


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.6   0.1     6e-40   1.8e-36       1     193 [.     248     430 ..     248     433 .. 0.90

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 6e-40
                      GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvl 79 
                                   kiav++++a+++y+  ++++L++++++  +f+plkd+++ +dad+++++Gg++++++ +l+r++++ e+ike+   +g ++
  gi|15669612|ref|NP_248425.1| 248 KIAVAYDKAFNFYYwdNFEALKENKAKIEFFSPLKDSEV-PDADILYIGGGYPELFKEELSRNKEMIESIKEF---DGYIY 324
                                   79*************************************.56*****************************96...79*** PP

                      GATase_3  80 giCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel........aaegeevkGyEiHsGrtilk 152
                                   g+CGGl++  ++i           +v+++glL+++ +++k  ++    ++v++         ++g ++kG+E+H+++ ++ 
  gi|15669612|ref|NP_248425.1| 325 GECGGLMYITKSID----------NVPMVGLLNCSAVMTK-HVQ--GLSYVKAefledcliGRKGLKFKGHEFHYSKLVNI 392
                                   ************87..........489*************.444..445544455889*998899**************** PP

                      GATase_3 153 ekakpllkvkv.ggnngekdGavkksedgnvlGtYlHglfdn 193
                                   ++++ ++k+++ +g +++ dG++++    +vl+ YlH ++ +
  gi|15669612|ref|NP_248425.1| 393 KEERFAYKIERgRGIINNLDGIFNG----KVLAGYLHNHAVA 430
                                   *********88444455******77....********99765 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   1.5   3.2e-19   9.4e-16       1     193 [.       4     183 ..       4     187 .. 0.82
   2 ?   -2.9   0.0       1.7   4.9e+03      24      47 ..     267     290 ..     266     311 .. 0.81

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 3.2e-19
                        AAA_26   1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgieededselikellgldqtyelpeplalsaplspelaarq 81 
                                   ++++++gt+ +vGKTv+s+g+++al +k+++v+ +K    +i     + ++ ++++ +++++ ++++ +          ++
  gi|15669612|ref|NP_248425.1|   4 KRVVIAGTSSEVGKTVISTGIMKAL-SKKYNVQGYKVGPDYI-----DPTYHTIATGNKSRN-LDSFFM----------NK 67 
                                   5799*********************.6666666666433333.....578888887777777.445544..........44 PP

                        AAA_26  82 egedidlekivkelekdadivvVEGagglgvpit..ee.llnadiaknlgapvilVargglgtinqllltiealrqknvrv 159
                                   e+ +       ++ +kd+di v+EG+ gl ++i+  ++  ++a +ak+l++p+il++++++ t  ++++   ++   nv++
  gi|15669612|ref|NP_248425.1|  68 EQIKYLF----QKHSKDKDISVIEGVRGLYEGISaiDDiGSTASVAKALDSPIILLVNAKSLTRSAIAIIKGFMSFDNVKI 144
                                   5544444....5669*****************6511456799************************9999999999***** PP

                        AAA_26 160 lGvilNkvrnpenvetlekksg.....ipvlGvvPylpd 193
                                   +Gvi+N vr+++ +++l+ + +     i+++G +P ++d
  gi|15669612|ref|NP_248425.1| 145 KGVIFNFVRSENHIKKLKDAMSyylpdIEIIGFIPRNED 183
                                   ************9999999999777788*******9987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                        AAA_26  24 alkrkgvkvgyfKPiqtgieeded 47 
                                   alk++++k+ +f P+    + d d
  gi|15669612|ref|NP_248425.1| 267 ALKENKAKIEFFSPLKDSEVPDAD 290
                                   789999999999999887765555 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.2   6.4e-22   1.9e-18       1     125 [.       6     190 ..       6     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 6.4e-22
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH..HTTEB-HHHH......................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx......................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai..leglendiep......................... 54 
                                   ++ia+t+++vGKT++++++++al++ +++V+ ++++p+    ++  +        +                         
  gi|15669612|ref|NP_248425.1|   6 VVIAGTSSEVGKTVISTGIMKALSK-KYNVQGYKVGPDYIDPTYhtIA-------Tgnksrnldsffmnkeqikylfqkhs 78 
                                   68***********************.************7666655422.......133333468999999*********** PP

                                   ..........................................CCHCCCHHHHHHCHCHHHH....EEEEEEEEESS...-T CS
                                   ..........................................xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                          CbiA  55 ..........................................dlkrllellealgkkkall..lkiagvvlnrvdgeneet 91 
                                                                             ++k+l +++ a+ k++  +  +ki+gv++n v++en+++
  gi|15669612|ref|NP_248425.1|  79 kdkdisviegvrglyegisaiddigstasvakaldspiillvNAKSLTRSAIAIIKGFMSFdnVKIKGVIFNFVRSENHIK 159
                                   ***********************************************************99******************** PP

                                   TCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  92 llkealeelkqrygvpvlgviprdeavaeaparg 125
                                   +lk+a+  ++    ++++g+ipr+e++ + + r+
  gi|15669612|ref|NP_248425.1| 160 KLKDAMSYYLP--DIEIIGFIPRNEDF-KVEGRH 190
                                   *******9987..************98.665555 PP

>> Csm1_B  Csm1 subunit domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.7e-05      0.17      29      82 ..     281     333 ..     278     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                                   HHHTT--CCCEEEEETTEEEEEEE--HHHHHHHHHHHHHHHHHCCCCTSSS-EE CS
                        Csm1_B  29 leklelsranllYagGGhfylLlpntekvkekleeiekelnewllkefkgkLyl 82 
                                   l++ e+++a +lY+gGG   l+ ++ +++ke +e+i+ e++  ++ e++g +y+
  gi|15669612|ref|NP_248425.1| 281 LKDSEVPDADILYIGGGYPELFKEELSRNKEMIESIK-EFDGYIYGECGGLMYI 333
                                   678899*********************9999999885.5777777777666666 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.2e-05      0.27      33      97 ..     288     347 ..     266     360 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.2e-05
                                   C-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTBSS-SS--CC CS
                           SNO  33 evdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelenelvktlellk 97 
                                   + d l i GG    ++  + r +   ++ e +k+ +  ++G C Gl++++k ++n   + ++ll+
  gi|15669612|ref|NP_248425.1| 288 DADILYIGGGYPELFKEELSRNK---EMIESIKEFDGYIYGECGGLMYITKSIDNV--PMVGLLN 347
                                   55666666666655555444444...78899999999**************99875..4445554 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   9.7e-05      0.29      12      40 ..       3      31 ..       1     107 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.7e-05
                       DUF1611 12 akrvlvvGTdcavGKrttaleleealeer 40
                                  +krv++ GT+++vGK + ++ + +al ++
  gi|15669612|ref|NP_248425.1|  3 MKRVVIAGTSSEVGKTVISTGIMKALSKK 31
                                  69**************9999888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2749.80
//
Query:       gi|15669613|ref|NP_248426.1|  [L=1847]
Description: replication factor C small subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-60  201.0   0.0    6.4e-21   74.7   0.0    4.1  3  Intein_splicing  Intein splicing domain
    8.8e-56  186.2  20.4    4.3e-22   78.2   0.2    7.2  6  LAGLIDADG_3      LAGLIDADG-like domain
    7.6e-24   83.9   4.1    1.2e-23   83.3   0.1    3.6  2  Rep_fac_C        Replication factor C C-terminal domain
    2.9e-07   30.5   0.8    8.4e-06   25.8   0.2    3.7  3  HTH_3            Helix-turn-helix
    5.8e-07   29.7   0.2        3.4    7.9   0.1    5.0  5  Hom_end          Homing endonuclease
    4.5e-06   26.5   3.7      0.036   13.8   0.0    4.8  4  DNA_pol3_delta2  DNA polymerase III, delta subunit
    1.9e-05   24.5   0.1    0.00016   21.5   0.0    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00055   20.2   2.9     0.0023   18.2   0.1    3.4  3  AAA_assoc_2      AAA C-terminal domain
     0.0033   17.5   0.9       0.17   12.0   0.1    4.0  2  LAGLIDADG_WhiA   WhiA LAGLIDADG-like domain
     0.0063   16.5   0.0     0.0063   16.5   0.0    3.1  3  Rad17            Rad17 P-loop domain
     0.0074   16.7   3.2        1.6    9.2   0.0    4.2  4  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.011   15.8   7.4      0.011   15.7   0.4    4.7  4  HTH_19           Helix-turn-helix domain
      0.057   13.2   2.7        1.6    8.6   0.0    4.2  4  IF2_N            Translation initiation factor IF-2, N-termin
      0.058   13.8   0.2         18    5.8   0.0    3.5  3  HTH_26           Cro/C1-type HTH DNA-binding domain
       0.08   13.3   0.0       0.77   10.1   0.0    2.4  2  AAA_16           AAA ATPase domain
       0.11   12.2   0.3       0.46   10.1   0.1    2.1  2  CAP59_mtransfer  Cryptococcal mannosyltransferase 1
        3.5    8.1   6.6        6.2    7.3   0.1    4.5  4  Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_


Domain annotation for each model (and alignments):
>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.0     6e-24   6.4e-21       5     134 .]      64     601 ..      61     601 .. 0.97
   2 !   61.8   0.0   5.9e-20   6.2e-17      13     134 .]     661    1062 ..     638    1062 .. 0.95
   3 !   57.2   2.4   1.5e-18   1.6e-15       1     134 []    1132    1667 ..    1132    1667 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 6e-24
                                   TTCEEEEHHHHCC...........ECTTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCT. CS
                                   xxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
               Intein_splicing   5 dgeekvkieelve...........kegeevlslnledlklevksvkkliklklkelyeiklesgrkikaTpeHkllvvrd. 73 
                                   +ge++ +i+e++e           +++ +vl+++ ed k+    v+ + k k+++l++ik++ gr++k+T  H+ll+ ++ 
  gi|15669613|ref|NP_248426.1|  64 NGEIR-EIGEVIEeisngkfgvtlTNNLKVLGID-EDGKIREFDVQYVYKDKTNTLIKIKTKMGRELKVTTYHPLLINHKn 142
                                   66777.8888888888899999999999999999.889999999*********************************9887 PP

                                   TEEEEEECCC--TT-EEEEE............................................................. CS
                                   xxxxxxxxxxxxxxxxxxxx............................................................. RF
               Intein_splicing  74 egivEkradeLkegdliavp............................................................. 93 
                                   ++i   +a++Lk+gd +a+p                                                             
  gi|15669613|ref|NP_248426.1| 143 GEIKWEKAENLKVGDKLATPryilfnesdyneelaewlgyfigdghadkesnkitftngdeklrkrfaelteklfkdakik 223
                                   776669*************************************************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669613|ref|NP_248426.1| 224 erihkdrtpdiyvnskeavefidklglrgkkadkvripkeimrsdalraflrayfdcdggiekhsivlstaskemaedlvy 304
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669613|ref|NP_248426.1| 305 allrfgiiaklrekvnknnnkvyyhivisnssnlrtfldnigfsqerklkklleiikdenpnldvitidkekiryirdrlk 385
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669613|ref|NP_248426.1| 386 vkltrdiekdnwsynkcrkitqellkeiyyrleelkeiekaleenilidwdevaerrkeiaektgirsdrileyirgkrkp 466
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
               Intein_splicing  94 ................................................................................. 93 
                                                                                                                    
  gi|15669613|ref|NP_248426.1| 467 slknyikiantlgkniekiidamrifakkyssyaeigkmlnmwnssikiylesntqeiekleeirktelklvkeilndekl 547
                                   ********************************************************************************* PP

                                   ...........HSCEEEEEEEEEEEEECEEEEEEEEETTT-EEEE.CT.TEEE- CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxx RF
               Intein_splicing  94 ...........dadvvwdkvksievedeeeyVYdltvednhNFva.ng.iivHN 134
                                               ++++wd++++ie+ + e ++Ydl v+++hNF++ n   i+HN
  gi|15669613|ref|NP_248426.1| 548 idsigyvlflaSNEIYWDEIVEIEQLNGEFTIYDLHVPRYHNFIGgNLpTILHN 601
                                   **********9999*******************************754246998 PP

  == domain 2  score: 61.8 bits;  conditional E-value: 5.9e-20
                                    HHHCCE.CTTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EE CS
                                    xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing   13 eelvek.egeevlslnledlklevksvkkliklklkelyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdli 90  
                                    +e+++k ++ evl ++ e++++ + +v+++i++k+ ++++ik e g  i +T++H++++++++g+v k+a+++k+gd  
  gi|15669613|ref|NP_248426.1|  661 NEMYKKvDNLEVLTVD-ENFRVRWRKVSTIIRHKVDKILRIKFE-GGYIELTGNHSIMMLDENGLVAKKASDIKVGDCF 737 
                                    3566541345666666.8999*********************66.556************99***************98 PP

                                    EEE............................................................................ CS
                                    xxx............................................................................ RF
               Intein_splicing   91 avp............................................................................ 93  
                                                                                                                   
  gi|15669613|ref|NP_248426.1|  738 LSFvaniegekdrldlkefepkditsrvkiindfdidedtawmlglyvaegavgfkgktsgqviytlgshehdlinkln 816 
                                    87689************************************************************************** PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669613|ref|NP_248426.1|  817 divdkkgfskyenftgsgfdrkrlsakqirilntqlarfveenfydgngrrarnkripdiifelkenlrveflkgladg 895 
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669613|ref|NP_248426.1|  896 dssgnwrevvrissksdnllidtvwlarisgiessifenearliwkggmkwkksnllpaepiikmikklenkingnwry 974 
                                    ******************************************************************************* PP

                                    .............................................HSCEEEEEEEEEEEEECEEEEEEEEETTT-EEEE CS
                                    .............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing   94 .............................................dadvvwdkvksievedeeeyVYdltvednhNFva 127 
                                                                                 + +++   vk+ie  d+++ VYd++v++n+ F+a
  gi|15669613|ref|NP_248426.1|  975 ilrhqlyegkkrvskdkikqilemvnveklsdkekevydllkklsKTELYALVVKEIEIIDYNDFVYDVSVPNNEMFFA 1053
                                    ********************************************9999******************************9 PP

                                    .CTTE.EE- CS
                                    .xxxx.xxx RF
               Intein_splicing  128 .ngii.vHN 134 
                                     n  i +HN
  gi|15669613|ref|NP_248426.1| 1054 gNVPIlLHN 1062
                                    8665559*9 PP

  == domain 3  score: 57.2 bits;  conditional E-value: 1.5e-18
                                    EEECTTCEEEEHHHHCC..ECTTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCTTEEE CS
                                    xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing    1 iiledgeekvkieelve..kegeevlslnledlklevksvkkliklklkelyeiklesgrkikaTpeHkllvvrdegiv 77  
                                    i+l d++e  kie++++  +e + + +ln + + l  + vk   k+  +++y++ lesgr+i aT++Hk+l+   +g+ 
  gi|15669613|ref|NP_248426.1| 1132 ITLPDERE-IKIEDFIKmfEERKLKHVLNRNGEDLVLAGVKFNSKIVNHKVYRLVLESGREIEATGDHKFLTR--DGW- 1206
                                    56778555.599999997655555667999*********9999999999************************..9**. PP

                                    EEECCC--TT-EEEEE............................................................... CS
                                    xxxxxxxxxxxxxxxx............................................................... RF
               Intein_splicing   78 EkradeLkegdliavp............................................................... 93  
                                     k++ eLke d + v                                                                
  gi|15669613|ref|NP_248426.1| 1207 -KEVYELKEDDEVLVYpalegvgfevderriiglnefyefltnyeiklgykplgkaksykelitrdkekilsrvlelsd 1284
                                    .**********999889************************************************************** PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669613|ref|NP_248426.1| 1285 kyskseirrkieeefgikislttiknlingkidgfalkyvrkikelgwdeityddekagifarllgfiigdghlskske 1363
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669613|ref|NP_248426.1| 1364 grilitatinelegikkdleklgikasniiekdiehkldgreikgktsfiyinnkafylllnfwgveignktingynip 1442
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669613|ref|NP_248426.1| 1443 kwikygnkfvkreflrglfgadgtkpyikkyningiklgirveniskdktleffeevkkmleefevesyikvskidnkn 1521
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669613|ref|NP_248426.1| 1522 ltelivkannknylkylsrisyayekdnfarlvgeylrikeaykdiilkeiaenalkeadgekslrelarkynvpvdfi 1600
                                    ******************************************************************************* PP

                                    ...........................HSCEEEEEEEEEEEEECEEEEEEEEETTT-EEEECTTEEE- CS
                                    ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing   94 ...........................dadvvwdkvksievedeeeyVYdltvednhNFvangiivHN 134 
                                                               d+  v +++ + e  ++++ VYd+t+++   F+ang++ HN
  gi|15669613|ref|NP_248426.1| 1601 inqlkgkdiglprnfmtfeeflkekvvDGKYVSERIIKKECIGYRD-VYDITCHKDPSFIANGFVSHN 1667
                                    ***************************999***************9.********************9 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1   1.8e-11   1.9e-08       3      83 .]     175     249 ..     173     249 .. 0.90
   2 !   78.2   0.2   4.1e-25   4.3e-22       2      83 .]     269     346 ..     268     346 .. 0.97
   3 ?    5.2   0.1     0.024        26       3      51 ..     776     826 ..     774     858 .. 0.80
   4 !   12.1   0.0   0.00018      0.18       4      61 ..     886     936 ..     883     989 .. 0.88
   5 !   13.3   0.2   7.5e-05      0.08       4      53 ..    1345    1391 ..    1342    1424 .. 0.79
   6 !   52.1   1.0   5.8e-17   6.1e-14       2      82 ..    1452    1541 ..    1451    1542 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.8e-11
                                   HHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEE.EEE-SCCCCECCCHCHCTTCGGGTTT CS
                   LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyek.kkakgrgvyrlliisgenlkrFleki 82 
                                   ++a + G+f +DG+++k+++k   i++t+ +++l + +++l ++l   ++i+e+ +k+  +++y    ++++++  F +k+
  gi|15669613|ref|NP_248426.1| 175 ELAEWLGYFIGDGHADKESNK---ITFTNGDEKLRKRFAELTEKLFKDAKIKERiHKDRTPDIY----VNSKEAVEFIDKL 248
                                   567789***************...******************************6666666666....9999999999887 PP

                                   X CS
                   LAGLIDADG_3  83 g 83 
                                   g
  gi|15669613|ref|NP_248426.1| 249 G 249
                                   6 PP

  == domain 2  score: 78.2 bits;  conditional E-value: 4.1e-25
                                   HHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEE.EEE-SCCCCECCCHCHCTTCGGGTT CS
                   LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyek.kkakgrgvyrlliisgenlkrFlek 81 
                                     +afLr++fd+DG ++k +     i l+++ske++ed+ + Llr+GI+++++ek +k++++++y+++i++++nl++Fl++
  gi|15669613|ref|NP_248426.1| 269 ALRAFLRAYFDCDGGIEKHS-----IVLSTASKEMAEDLVYALLRFGIIAKLREKvNKNNNKVYYHIVISNSSNLRTFLDN 344
                                   579*****************.....******************************9999999999**************** PP

                                   TX CS
                   LAGLIDADG_3  82 ig 83 
                                   ig
  gi|15669613|ref|NP_248426.1| 345 IG 346
                                   *8 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHCCECCECSTTTTS..EEEEES-HHHHHHHHHHHHHCT.HS CS
                   LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvs..isltssskelledvqrlLlrlGIes 51 
                                     a+  Gl+ a+G v  ++k++++   +l+s++ +l++++  +  + G   
  gi|15669613|ref|NP_248426.1| 776 DTAWMLGLYVAEGAVGFKGKTSGQviYTLGSHEHDLINKLNDIVDKKGFSK 826
                                   568889*********99998877799999**********999988777655 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00018
                                   HHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-S CS
                   LAGLIDADG_3   4 aafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakg 61 
                                    +fL+Gl d+D s ++++     ++++s+s +ll d   l    GIes+i e+   + 
  gi|15669613|ref|NP_248426.1| 886 VEFLKGLADGDSSGNWREV----VRISSKSDNLLIDTVWLARISGIESSIFEN---EA 936
                                   68****************4....****************************99...33 PP

  == domain 5  score: 13.3 bits;  conditional E-value: 7.5e-05
                                    HHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCE CS
                   LAGLIDADG_3    4 aafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIesti 53  
                                     a L G++ +DG+ sksk+++  i+ t ++   le++++ L++lGI+++ 
  gi|15669613|ref|NP_248426.1| 1345 FARLLGFIIGDGHLSKSKEGRILITATINE---LEGIKKDLEKLGIKASN 1391
                                    689***************996545444444...6899999******9764 PP

  == domain 6  score: 52.1 bits;  conditional E-value: 5.8e-17
                                    HHHHHHHHHHHHCCECCECSTTTTS.....EEEEES-....HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHC CS
                   LAGLIDADG_3    2 vkaafLrGlfdaDGsvskskkkgvs.....isltsss....kelledvqrlLlrlGIestiyekkkakgrgvyrlliis 71  
                                    vk++fLrGlf aDG+    kk++ +     i++ + s    +e+ e+v+++L+++++es+i+ +k+++++ +  ++  +
  gi|15669613|ref|NP_248426.1| 1452 VKREFLRGLFGADGTKPYIKKYNINgiklgIRVENISkdktLEFFEEVKKMLEEFEVESYIKVSKIDNKNLTELIVKAN 1530
                                    799*********************9*777777777779999************************************** PP

                                    HCTTCGGGTTT CS
                   LAGLIDADG_3   72 genlkrFleki 82  
                                    ++n+ ++l++i
  gi|15669613|ref|NP_248426.1| 1531 NKNYLKYLSRI 1541
                                    ********998 PP

>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         3   3.2e+03       5      30 ..     481     509 ..     479     514 .. 0.83
   2 !   83.3   0.1   1.1e-26   1.2e-23       2      88 .]    1756    1841 ..    1755    1841 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3
                                   HHHHHHHHHHH.....T-HHHHHHHHHHHHH CS
                     Rep_fac_C   5 eieeileacln.....gdfeeaykklrellv 30 
                                    ie+i++a++      ++++e++k l+  ++
  gi|15669613|ref|NP_248426.1| 481 NIEKIIDAMRIfakkySSYAEIGKMLN--MW 509
                                   699******879999999999999985..66 PP

  == domain 2  score: 83.3 bits;  conditional E-value: 1.1e-26
                                    -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-HHH CS
                     Rep_fac_C    2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGasehl 80  
                                    +p+e+++++e +l g+f ea++ l +l+ve G+s+edil+q++r + +  +++e+ k+e+ + +ge+++r+veGa+e++
  gi|15669613|ref|NP_248426.1| 1756 RPEEVKKMMELALDGKFMEARDLLYKLMVEWGMSGEDILNQMFREINSL-DIDERKKVELADAIGETDFRIVEGANERI 1833
                                    79*********************************************96.7**************************** PP

                                    HHHHHHHH CS
                     Rep_fac_C   81 qlsallar 88  
                                    qlsalla+
  gi|15669613|ref|NP_248426.1| 1834 QLSALLAK 1841
                                    ******96 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.2   7.9e-09   8.4e-06      12      53 ..     442     483 ..     441     485 .. 0.95
   2 ?   -0.9   0.0       1.7   1.8e+03      20      33 ..    1300    1315 ..    1292    1326 .. 0.81
   3 ?   -1.0   0.0       1.9     2e+03      41      54 ..    1586    1599 ..    1583    1600 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 7.9e-09
                                   HHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                         HTH_3  12 qeeLAeklGvsrstisriEnGernPsletlkklakaLgvsld 53 
                                   ++e+Aek+G+    i  +++G+r+Psl++ +k+a++Lg  ++
  gi|15669613|ref|NP_248426.1| 442 RKEIAEKTGIRSDRILEYIRGKRKPSLKNYIKIANTLGKNIE 483
                                   69************************************9887 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                                    T..SSHHHHHHHHTTS CS
                         HTH_3   20 G..vsrstisriEnGe 33  
                                    G  +s +ti +++nG+
  gi|15669613|ref|NP_248426.1| 1300 GikISLTTIKNLINGK 1315
                                    555999********96 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.9
                                    HHHHHHHHTSEHHH CS
                         HTH_3   41 lkklakaLgvslde 54  
                                    l +la+ ++v+ d+
  gi|15669613|ref|NP_248426.1| 1586 LRELARKYNVPVDF 1599
                                    66777777777765 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.5   1.6e+03      20      64 ..     181     224 ..     178     239 .. 0.80
   2 !    6.9   0.0    0.0063       6.6      13      97 ..     270     345 ..     259     357 .. 0.81
   3 !    7.4   0.0    0.0045       4.8      13      66 ..     884     935 ..     873     943 .. 0.84
   4 !    7.9   0.1    0.0032       3.4      18      66 ..    1348    1395 ..    1341    1419 .. 0.81
   5 ?   -2.3   0.0       4.7     5e+03       3      28 ..    1442    1467 ..    1440    1476 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.5
                       Hom_end  20 GLvdsdgyvkkekedsatvktedksvmegivklarsLGikasvkt 64 
                                   G  ++dg+ +ke++ ++t +  d+++ ++  +l+++L   a++k+
  gi|15669613|ref|NP_248426.1| 181 GYFIGDGHADKESN-KITFTNGDEKLRKRFAELTEKLFKDAKIKE 224
                                   77899*******55.999999999999999999999866666666 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0063
                       Hom_end  13 vREaFlaGLvdsdgyvkkekedsatvktedksvmegivklarsLGikasvktkeekidakgvkhqfcyaitlsggdalksv 93 
                                    R aFl    d dg  +k+   s+ ++t +k+  e++v      Gi a+  +k      ++ ++++ y i++s+++ l+  
  gi|15669613|ref|NP_248426.1| 270 LR-AFLRAYFDCDGGIEKH---SIVLSTASKEMAEDLVYALLRFGIIAKLREK-----VNKNNNKVYYHIVISNSSNLRTF 341
                                   35.8899999999999999...***************************9997.....4556677889*****99999888 PP

                       Hom_end  94 lskc 97 
                                   l + 
  gi|15669613|ref|NP_248426.1| 342 LDNI 345
                                   7765 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0045
                       Hom_end  13 vREaFlaGLvdsdgyvkkekedsatvktedksvmegivklarsLGikasvktke 66 
                                    R  Fl GL d+d + + +  +++ +++ + +++ ++v lar+ Gi+ s+ + e
  gi|15669613|ref|NP_248426.1| 884 LRVEFLKGLADGDSSGNWR--EVVRISSKSDNLLIDTVWLARISGIESSIFENE 935
                                   4556*****9999887776..69***********************99986655 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0032
                       Hom_end   18 laGLvdsdgyvkkekedsatvktedksvmegivklarsLGikasvktke 66  
                                    l+G++++dg+ +k ke+ + ++++ ++ +egi k  ++LGikas   ++
  gi|15669613|ref|NP_248426.1| 1348 LLGFIIGDGHLSKSKEGRILITATINE-LEGIKKDLEKLGIKASNIIEK 1395
                                    89***************8888777776.59************9976643 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 4.7
                       Hom_end    3 psflaseaievREaFlaGLvdsdgyv 28  
                                    p+ + + +  v+  Fl GL  +dg++
  gi|15669613|ref|NP_248426.1| 1442 PKWIKYGNKFVKREFLRGLFGADGTK 1467
                                    55555544445558*********975 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.17   1.8e+02       1      33 [.      23      54 ..      23      59 .. 0.91
   2 ?   -3.3   1.9       6.6     7e+03     100     100 ..     389     389 ..     220     458 .. 0.64
   3 !   13.8   0.0   3.4e-05     0.036      77     139 ..    1064    1124 ..     984    1135 .. 0.80
   4 !    7.6   0.0    0.0028       2.9     143     162 ..    1671    1690 ..    1667    1691 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.17
               DNA_pol3_delta2  1 gqeealkilskalksgrlahayLfeGdegigkk 33
                                  gq+e++k l+k ++++ + h +Lf+G+ g+gk 
  gi|15669613|ref|NP_248426.1| 23 GQDEIVKRLKKYVEKKSMPH-LLFSGPPGVGKC 54
                                  68999***********9999.8********995 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.6
               DNA_pol3_delta2 100 r 100
                                   +
  gi|15669613|ref|NP_248426.1| 389 T 389
                                   1 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 3.4e-05
               DNA_pol3_delta2   77 eekersikldqir.elieelsrkpre.skkkiiiiedaekmtksAaNalLktlEEPsenaifiLi 139 
                                    +    +  +d ir ++++++  kp+     kii +++ + +t+ A+Nal +t+E  s+   fiL 
  gi|15669613|ref|NP_248426.1| 1064 D----ERGIDVIRtKVKDFARTKPIGdVPFKIIFLDESDALTADAQNALRRTMEKYSDVCRFILS 1124
                                    3....3479999944555555555554578*************************9999999985 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0028
               DNA_pol3_delta2  143 tnklLktirSRcqelkfspl 162 
                                    ++k++++i+SRc +++fspl
  gi|15669613|ref|NP_248426.1| 1671 PSKIIPPIQSRCAVFRFSPL 1690
                                    789***************98 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.5e-07   0.00016       2      49 ..      14      56 ..      13     132 .. 0.73
   2 ?   -1.6   0.0       1.9     2e+03      86     111 ..    1090    1115 ..    1087    1119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.5e-07
                        RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttl 49
                                  rPk+l++ +gq+++ ++lk ++e     ++++ h+l++GpPG+Gk   
  gi|15669613|ref|NP_248426.1| 14 RPKTLDDIVGQDEIVKRLKKYVE-----KKSMPHLLFSGPPGVGKCLT 56
                                  9******************9997.....57899************633 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                        RuvB_N   86 dvlfideihrlsraveevlysamedf 111 
                                    +++f+de   l+  +++ l  +me +
  gi|15669613|ref|NP_248426.1| 1090 KIIFLDESDALTADAQNALRRTMEKY 1115
                                    699*********************98 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.3   5.5e+03      23      61 ..     350     387 ..     332     397 .. 0.73
   2 ?   -0.6   0.1       1.7   1.8e+03      41      73 ..     982    1015 ..     959    1020 .. 0.70
   3 !   18.2   0.1   2.2e-06    0.0023       3      39 ..    1706    1742 ..    1704    1768 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.3
                                   XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXX CS
                   AAA_assoc_2  23 aRkaLnlLElaaeaaeakegkieitledleealqrkalr 61 
                                    Rk+ +lLE++ + + +  + i+i++e+++ + +r  ++
  gi|15669613|ref|NP_248426.1| 350 ERKLKKLLEIIKDENPN-LDVITIDKEKIRYIRDRLKVK 387
                                   68888899998888775.899999999999887776655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                                    XXXXXXXXXXXXXXXXXXXXX.XXXXXXXHHHHH CS
                   AAA_assoc_2   41 egkieitledleealqrkalr.yDkagdehYdli 73  
                                    egk+++++++++++l+  ++     ++ e Ydl+
  gi|15669613|ref|NP_248426.1|  982 EGKKRVSKDKIKQILEMVNVEkLSDKEKEVYDLL 1015
                                    789999*******996555433555567788875 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 2.2e-06
                                    X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   AAA_assoc_2    3 kklkleddalealaeladGDaRkaLnlLElaaeaaea 39  
                                    + l+l+++ lea++ +++GD+Rka+n+L++aa+ ++ 
  gi|15669613|ref|NP_248426.1| 1706 EGLNLTESGLEAIIYVSEGDMRKAINVLQTAAALSDV 1742
                                    5688999**********************98877654 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00016      0.17       2      79 ..     271     350 ..     270     382 .. 0.82
   2 ?    1.1   0.0       0.4   4.3e+02      30      51 ..    1492    1513 ..    1453    1533 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                LAGLIDADG_WhiA   2 kaflrGaflasGsindpekkyhLEivspdeelaeqlqkllnefeleakiler......rkkyvvylKkaeqIvdlLkiiga 76 
                                   +aflr+ f   G i++    + + +++ ++e+ae+l  +l +f++ ak++e+      + +y +++ ++++  ++L +ig 
  gi|15669613|ref|NP_248426.1| 271 RAFLRAYFDCDGGIEK----HSIVLSTASKEMAEDLVYALLRFGIIAKLREKvnknnnKVYYHIVISNSSNLRTFLDNIGF 347
                                   7899999999999988....67789**********************99875332111224666799999*******9997 PP

                LAGLIDADG_WhiA  77 hes 79 
                                    ++
  gi|15669613|ref|NP_248426.1| 348 SQE 350
                                   665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.4
                LAGLIDADG_WhiA   30 deelaeqlqkllnefeleakil 51  
                                    + e++e+++k+l+efe+e+ i+
  gi|15669613|ref|NP_248426.1| 1492 TLEFFEEVKKMLEEFEVESYIK 1513
                                    4589999999999999987554 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     6e-06    0.0063       7      60 ..       7      55 ..       5      82 .. 0.87
   2 ?   -2.7   0.1       4.6   4.8e+03      24      47 ..     988    1011 ..     985    1077 .. 0.60
   3 ?   -0.6   0.6         1   1.1e+03      76     175 ..    1474    1572 ..    1467    1584 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6e-06
                         Rad17  7 elWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkst 60
                                  ++W+eky+P++++++    + ++ +k++++ +++++     LL sGP+G gk  
  gi|15669613|ref|NP_248426.1|  7 KPWVEKYRPKTLDDIVGQDEIVKRLKKYVEKKSMPH-----LLFSGPPGVGKCL 55
                                  69*************999999999999999999886.....6*********974 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.6
                         Rad17   24 hkkkieevkewlkadvLesrkkri 47  
                                     k ki+++ e+++ + L  ++k++
  gi|15669613|ref|NP_248426.1|  988 SKDKIKQILEMVNVEKLSDKEKEV 1011
                                    455555555555555555444432 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1
                         Rad17   76 wlnpvsl..kepdnqksdfkgltekesrflsqiesfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrdsdal 152 
                                    ++n+++l  +  +  k+ ++  +e  +++l   e+ + +++ +  ++ l  l  +++ +  l ++  +   +  + d++
  gi|15669613|ref|NP_248426.1| 1474 NINGIKLgiRVENISKDKTLEFFEEVKKMLEEFEVESYIKVSKIDNKNLTELIVKANNKNYLKYLSRISYAY--EKDNF 1550
                                    566666522444447777888888888777776666666666666666887888888888888888886555..55689 PP

                         Rad17  153 revirkylrssealplilvitei 175 
                                      ++ +ylr++ea+  i ++ ei
  gi|15669613|ref|NP_248426.1| 1551 ARLVGEYLRIKEAYKDI-ILKEI 1572
                                    999********998433.34444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3     0.032        34       1      14 [.      43      56 ..      43      63 .. 0.89
   2 ?   -2.3   0.0       5.3   5.6e+03      40      65 ..     347     373 ..     325     374 .. 0.76
   3 !    9.2   0.0    0.0015       1.6      54     106 ..    1080    1122 ..    1018    1141 .. 0.72
   4 ?   -2.5   0.0         6   6.4e+03     109     129 ..    1668    1687 ..    1663    1690 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.032
                                  EEEESSTTSSHHHH CS
                           AAA  1 vllyGppGtGKTll 14
                                  +l++GppG+GK l+
  gi|15669613|ref|NP_248426.1| 43 LLFSGPPGVGKCLT 56
                                  69*********876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.3
                                   THHHHHHHHHHHHHHHTS.TSEEEEEE CS
                           AAA  40 gesekkirelfkeakeka.kpsilfiD 65 
                                     +e+k+++l++ +k ++ +  ++ iD
  gi|15669613|ref|NP_248426.1| 347 FSQERKLKKLLEIIKDENpNLDVITID 373
                                   467889999999999888666899888 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0015
                                    HHTS...TS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEE CS
                           AAA   54 keka...kp.silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivi 106 
                                    ++k     p +i+f+DE dal+ +            +n+L + ++++++    + +i
  gi|15669613|ref|NP_248426.1| 1080 RTKPigdVPfKIIFLDESDALTADA-----------QNALRRTMEKYSDV---CRFI 1122
                                    22225576779**********9888...........99999999999885...3333 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 6
                                    ESSGGGSTHHHHSTTSSEEEE CS
                           AAA  109 tnrpdkldpallrgRfdrkie 129 
                                    +n+p+k+ p++  +R+ +  +
  gi|15669613|ref|NP_248426.1| 1668 CNYPSKIIPPIQ-SRCAVFRF 1687
                                    899*********.9**98766 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.4   1.1e-05     0.011      16      60 ..     443     486 ..     441     489 .. 0.94
   2 ?   -3.0   0.0       7.1   7.5e+03      27      56 ..     739     775 ..     728     779 .. 0.70
   3 ?   -0.8   0.2       1.5   1.6e+03      21      40 ..    1300    1319 ..    1285    1334 .. 0.73
   4 ?   -2.9   0.0       6.9   7.3e+03      45      62 ..    1586    1603 ..    1580    1605 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                        HTH_19  16 eelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyll 60 
                                   +e+ae++gi+  +i +++ gk+ +ps +++ kia++lg ++e ++
  gi|15669613|ref|NP_248426.1| 443 KEIAEKTGIRSDRILEYIRGKR-KPSLKNYIKIANTLGKNIEKII 486
                                   89********************.***************9998876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.1
                        HTH_19  27 skisaiEngkkdvpsaell........lkiaealgidl 56 
                                   s+ ++iE++ kd ++ +++         ki + ++id+
  gi|15669613|ref|NP_248426.1| 739 SFVANIEGE-KDRLDLKEFepkditsrVKIINDFDIDE 775
                                   778899965.6699988887766666666666666665 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.5
                        HTH_19   21 rlgisrskisaiEngkkdvp 40  
                                     ++is + i +++ngk+d +
  gi|15669613|ref|NP_248426.1| 1300 GIKISLTTIKNLINGKIDGF 1319
                                    45677999*******99866 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 6.9
                        HTH_19   45 llkiaealgidleyllqg 62  
                                    l+ +a++++++++ ++++
  gi|15669613|ref|NP_248426.1| 1586 LRELARKYNVPVDFIINQ 1603
                                    677999******999886 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       9.4   9.9e+03      17      26 ..      24      33 ..      22      40 .. 0.70
   2 ?    1.5   0.0      0.24   2.6e+02       7      22 ..     443     458 ..     443     462 .. 0.92
   3 ?   -3.3   0.2       7.9   8.3e+03      11      23 ..    1383    1395 ..    1383    1395 .. 0.89
   4 ?    8.6   0.0    0.0015       1.6       4      26 ..    1584    1605 ..    1582    1612 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.4
                         IF2_N 17 skevikkLfk 26
                                    e++k+L+k
  gi|15669613|ref|NP_248426.1| 24 QDEIVKRLKK 33
                                  679*****54 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.24
                         IF2_N   7 yeLAkeLgvkskevik 22 
                                   +e+A++ g++s ++++
  gi|15669613|ref|NP_248426.1| 443 KEIAEKTGIRSDRILE 458
                                   69************98 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 7.9
                         IF2_N   11 keLgvkskevikk 23  
                                    ++Lg+k+  +i+k
  gi|15669613|ref|NP_248426.1| 1383 EKLGIKASNIIEK 1395
                                    689*******996 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0015
                         IF2_N    4 irVyeLAkeLgvkskevikkLfk 26  
                                    ++ +eLA++ +v++  +i +L k
  gi|15669613|ref|NP_248426.1| 1584 KSLRELARKYNVPVDFIINQL-K 1605
                                    8999*****************.5 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.017        18      13      59 ..     442     487 ..     437     489 .. 0.93
   2 ?   -2.6   0.0       7.5   7.9e+03      33      46 ..     640     653 ..     638     653 .. 0.91
   3 ?    3.8   0.0     0.076        80      11      41 ..    1285    1322 ..    1276    1327 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                        HTH_26  13 kseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLle 59 
                                   ++e a++tgi ++ +  +  gk + +sl+   ki+++Lg +++ +++
  gi|15669613|ref|NP_248426.1| 442 RKEIAEKTGIRSDRILEYIRGK-RKPSLKNYIKIANTLGKNIEKIID 487
                                   57899****************9.9***************99998885 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.5
                        HTH_26  33 gkpervsldtLdki 46 
                                   gk++r ++++Ldki
  gi|15669613|ref|NP_248426.1| 640 GKVKRTTFEELDKI 653
                                   899**********8 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.076
                        HTH_26   11 i.tkseLar......gtgisaatlsrlvkgkpervsld 41  
                                      +kse +r      g+ is +t+++l +gk++   l+
  gi|15669613|ref|NP_248426.1| 1285 KySKSEIRRkieeefGIKISLTTIKNLINGKIDGFALK 1322
                                    448899988555555667*************9887775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00073      0.77       3      37 ..      22      53 ..      20      56 .. 0.89
   2 ?   -0.2   0.0       1.1   1.1e+03     118     160 ..    1066    1113 ..     992    1123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00073
                        AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGK 37
                                  vG +e +++L+ ++e+ ++   + +l+sG++GvGK
  gi|15669613|ref|NP_248426.1| 22 VGQDEIVKRLKKYVEKKSM---PHLLFSGPPGVGK 53
                                  899***********95554...79**********9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                        AAA_16  118 rllellkrll.allsrder....p.lvlvlDdlqwadeaslqllaaLlr 160 
                                    r  ++++  + +++++ ++    p  +++lD+ + + ++ +++l+ +++
  gi|15669613|ref|NP_248426.1| 1066 RGIDVIRTKVkDFART-KPigdvPfKIIFLDESDALTADAQNALRRTME 1113
                                    5555555555444444.3345555579***************9998876 PP

>> CAP59_mtransfer  Cryptococcal mannosyltransferase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.3   2.5e+03      84     121 ..     518     557 ..     477     575 .. 0.70
   2 ?   10.1   0.1   0.00043      0.46      39      95 ..    1484    1540 ..    1478    1544 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.3
               CAP59_mtransfer  84 kkelkRIeyLaelRNkaLepLeelakegkekfdk...vlFl 121
                                   +++++ Ie+L e+R + L+ ++e+ +++ + +d+   vlFl
  gi|15669613|ref|NP_248426.1| 518 ESNTQEIEKLEEIRKTELKLVKEILNDE-KLIDSigyVLFL 557
                                   4577889*********999998876322.234444458887 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00043
               CAP59_mtransfer   39 yesgskdgtkeaLraleaelealgversivlneeteleldelesgkkelkRIeyLae 95  
                                    +e+ skd+t e  +++++ le+ +ve++i++++ ++++l+el  ++++++ ++yL++
  gi|15669613|ref|NP_248426.1| 1484 VENISKDKTLEFFEEVKKMLEEFEVESYIKVSKIDNKNLTELIVKANNKNYLKYLSR 1540
                                    79***************************9999999999999988888888888886 PP

>> Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_LLH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       5.7     6e+03      33      66 ..     227     259 ..     211     265 .. 0.73
   2 ?   -1.9   0.0       4.4   4.7e+03      74      94 ..     838     858 ..     837     861 .. 0.90
   3 ?    0.3   0.2       0.9   9.5e+02      62      87 ..     982    1008 ..     975    1012 .. 0.85
   4 ?    7.3   0.1    0.0059       6.2      64      92 ..    1691    1719 ..    1688    1728 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.7
               Phage_holin_6_1  33 qgekakkiaeiaknaVkaveqvakedakgeeKke 66 
                                    ++ + +i    k+aV++  +++ + +k ++K +
  gi|15669613|ref|NP_248426.1| 227 HKDRTPDIYVNSKEAVEFIDKLGLR-GKKADKVR 259
                                   45555566666799*********99.99999976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.4
               Phage_holin_6_1  74 ellkekgisitddeleglIEa 94 
                                   ++l+ k+i i +++l+ ++E 
  gi|15669613|ref|NP_248426.1| 838 KRLSAKQIRILNTQLARFVEE 858
                                   67999**************96 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.9
               Phage_holin_6_1   62 eeKkeeAleklkellkekgi.sitdde 87  
                                    e Kk+  ++k+k++l++++  +++d+e
  gi|15669613|ref|NP_248426.1|  982 EGKKRVSKDKIKQILEMVNVeKLSDKE 1008
                                    569999999999999999999999987 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0059
               Phage_holin_6_1   64 KkeeAleklkellkekgisitddeleglI 92  
                                    Kke   +klke++++ g+++t++ le++I
  gi|15669613|ref|NP_248426.1| 1691 KKEDIAKKLKEIAEKEGLNLTESGLEAII 1719
                                    999999*******************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1847 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1210  (0.0674884); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 1.20u 0.35s 00:00:01.54 Elapsed: 00:00:00.53
# Mc/sec: 10505.51
//
Query:       gi|15669614|ref|NP_248427.1|  [L=352]
Description: vanadium nitrogenase-associated protein N [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-15   54.5   0.0      1e-14   54.1   0.0    1.2  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
  ------ inclusion threshold ------
      0.017   15.1   0.7        1.3    9.1   0.0    2.7  3  Nit_Regul_Hom   Uncharacterized protein, homolog of nitrogen 


Domain annotation for each model (and alignments):
>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.0   1.2e-18     1e-14      16     138 ..      23     143 ..       8     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 1.2e-18
                                   EEEEEES-HHHHHCCCCHHHCHHSS-HS-EEEE--HHHHSSSSHHHHHHHHHHHHHHC-T......SEEEEEE-HHHHHTT CS
                Oxidored_nitro  16 alplvhGpqGCatyaralltrhfrepiplastdltekdavfGgeekLkeaikeivkrykp......kaIgVittClteliG 90 
                                     +++hGp GC++ + +ll       + +++++++e+++vfG+ e+Lk+a++ +++  k        +Ig++ tC++ +iG
  gi|15669614|ref|NP_248427.1|  23 DAIILHGPSGCCFRTARLLELD---GVRVFTSNIDENAIVFGASENLKKALDYAIEYLKKelkkerPMIGIVGTCASMIIG 100
                                   5789*********999999655...458************************9999777666667789************* PP

                                   TTHHHHHHHHHHHHTSSEEEEEE--TTSSSHHHHHHHHHHHHHHHCTT CS
                Oxidored_nitro  91 dDieavareaeeelgeipvipvstpgfggsqseGydaalealvrklvg 138
                                   +D+  ++   +       +ipv++ + +g+ + G  +a+e+ ++  + 
  gi|15669614|ref|NP_248427.1| 101 EDLWEFVDDDR---A--IIIPVEVHSGSGDNTIGAIKAMESALKLGII 143
                                   ***99887654...3..4**********************99986555 PP

>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.69   6.2e+03      55      61 ..      74      80 ..      58     120 .. 0.50
   2 ?    9.1   0.0   0.00015       1.3      33      76 ..     163     206 ..     160     214 .. 0.91
   3 ?    3.4   0.0    0.0082        74      52      84 ..     268     300 ..     260     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.69
                 Nit_Regul_Hom 55 ikiikdl 61
                                  i+ +k++
  gi|15669614|ref|NP_248427.1| 74 IEYLKKE 80
                                  3333333 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00015
                 Nit_Regul_Hom  33 eYkGlsPqewkgflleedpesaikiikdlseeavlintvvdeek 76 
                                   + +G++ +e+ + + ++d + aik++kdl e+   i++v++ +k
  gi|15669614|ref|NP_248427.1| 163 KKRGMAKKEYIKPTYDDDLNEAIKVLKDLKEKDGKIACVLNAKK 206
                                   569*****************************999999998875 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.0082
                 Nit_Regul_Hom  52 esaikiikdlseeavlintvvdeekvekikeel 84 
                                   e a++i+kdl  +a++++ v +   +e+i + +
  gi|15669614|ref|NP_248427.1| 268 ERAVEILKDLDVDAIVVSGVPHALPIEEIDKDI 300
                                   789****************99888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2229.81
//
Query:       gi|15669615|ref|NP_248428.1|  [L=179]
Description: tRNA-splicing endonuclease subunit alpha [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-31  105.9   0.5    2.1e-30  104.6   0.4    1.6  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    6.5e-20   70.6   0.2    1.3e-19   69.7   0.2    1.5  1  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
     0.0012   19.1   0.1     0.0022   18.3   0.0    1.6  2  Sen15            Sen15 protein


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.68   4.1e+03      48      64 ..      64      80 ..      60      83 .. 0.80
   2 !  104.6   0.4   3.5e-34   2.1e-30       2      85 .]      86     171 ..      85     171 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.68
                                  ETTSEEEHHHHHHHHHH CS
                 tRNA_int_endo 48 sedeeldwpdlsaavrl 64
                                  +++++l++++l + +r 
  gi|15669615|ref|NP_248428.1| 64 KDNKPLSFEELYEYARN 80
                                  78999999999998886 PP

  == domain 2  score: 104.6 bits;  conditional E-value: 3.5e-34
                                   HHHHHHHHHHHHTT-EEEECGGGTSSEEEE..TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEETTT CS
                 tRNA_int_endo   2 alkyavyrdLrekGyvvrsGlkFGadFrvY..qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivdae 80 
                                   +lky vy+dLr++Gy+v++Glk+GadFr+Y  + + ++ehs ylV v++ed+ + +++l++ vr+ahsv+Kkl++aivda+
  gi|15669615|ref|NP_248428.1|  86 CLKYLVYKDLRTRGYIVKTGLKYGADFRLYerGANIDKEHSVYLVKVFPEDSSFLLSELTGFVRVAHSVRKKLLIAIVDAD 166
                                   68****************************66667789******************************************* PP

                                   SCEEE CS
                 tRNA_int_endo  81 gdvty 85 
                                   gd+ y
  gi|15669615|ref|NP_248428.1| 167 GDIVY 171
                                   **988 PP

>> tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.2   2.1e-23   1.3e-19       2      67 .]      11      75 ..      10      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 2.1e-23
                                  EEEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEE.TTSEEE-HHHHH CS
               tRNA_int_endo_N  2 egeLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevv.kggeplsfeell 67
                                  +g L gdrv+v+d++++++ ++ ++YG+  +++ L LslvEAlYL+  G+lev+ k+++plsfeel+
  gi|15669615|ref|NP_248428.1| 11 TGLLDGDRVIVFDKNGISK-LSARHYGN-VEGNFLSLSLVEALYLINLGWLEVKyKDNKPLSFEELY 75
                                  689****************.56678***.************************************96 PP

>> Sen15  Sen15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.5   8.7e+03      13      53 ..      59      71 ..      54      87 .. 0.56
   2 !   18.3   0.0   3.6e-07    0.0022      54      91 ..     142     175 ..      90     179 .] 0.77

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                         Sen15 13 tdveikeeeelklvllkGrpkkklsedelvlPlelteklsl 53
                                   +v++k+++ l                            s+
  gi|15669615|ref|NP_248428.1| 59 LEVKYKDNKPL----------------------------SF 71
                                  55555544443............................33 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3.6e-07
                         Sen15  54 ekldkvfkelkeekserkkrivLaivddDsTvvYYkvt 91 
                                   ++l  +++  +    +  k++++aivd D+ +vYY++t
  gi|15669615|ref|NP_248428.1| 142 SELTGFVRVAH----SVRKKLLIAIVDADGDIVYYNMT 175
                                   45544444432....2479****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1145.63
//
Query:       gi|15669616|ref|NP_248429.1|  [L=344]
Description: malate dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.9e-125  418.4   0.0   2.2e-125  418.3   0.0    1.0  1  Ldh_2     Malate/L-lactate dehydrogenase
  ------ inclusion threshold ------
       0.12   12.3   0.1       0.52   10.3   0.0    2.2  2  RHH_3     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> Ldh_2  Malate/L-lactate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.3   0.0  2.4e-129  2.2e-125       3     333 .]       5     329 ..       3     329 .. 0.97

  Alignments for each domain:
  == domain 1  score: 418.3 bits;  conditional E-value: 2.4e-129
                                   HHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHTT-GGGTGGGHHHHHHHHHTTSSBSS---EEEEEETTEEEEEETTE- CS
                         Ldh_2   3 aeelralveavleaagvseedAeivadvlveadlrGvdsHGvarlpryverlkkgkinpkaepevvketpavavvDgdngl 83 
                                    e+ ++l+ +vl+++gv+eedA+i+adv+v+adl+G++sHG+ r+p+y+  lk g+inpk+++++vke+pa+av+Dgd gl
  gi|15669616|ref|NP_248429.1|   5 PENEKKLIIDVLKKFGVPEEDAKITADVFVDADLKGFTSHGIGRFPQYITALKLGNINPKPDIKIVKESPATAVIDGDLGL 85 
                                   5778999************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHSEEEEEEEEEE--SSHHHHHHHHHHTTSEEEEEEEESSEB--TTBSS--BE--EEEEEEEET CS
                         Ldh_2  84 GqvvakkamelaiekakehGigivavrnsnhfGaagyyaemaaeaGligiaftnssplvaptggkeavlGtNPiafaaPak 164
                                   Gqvv+kkamelai+kak+ G+g+va+rn+nhfG+agyy e a+++++igi++tn++p++ap+ggke++lGtNPia+a+ + 
  gi|15669616|ref|NP_248429.1|  86 GQVVGKKAMELAIKKAKNVGVGVVATRNANHFGIAGYYSELAMNQDMIGITITNTEPAMAPFGGKEKILGTNPIAIAFKG- 165
                                   *******************************************************************************9. PP

                                   TSSEEEEEEESBSS-HHHHHHHHHCT---STTSEEETTSSEES-HHHHHCCCEE-BTTTHHHHHHHHHHHHHHTCTTTS-H CS
                         Ldh_2 165 eeepfvlDmAtSvvargkievaarkgkpiPegwalDadGnpttDPaaaleggallplGghKGyglalmvelLagvLsgaat 245
                                   ++++f lDmAt+ +argki +a rk+ +iPeg+a+D+dG+pttDPa+ale g +lp+Gg KGyglal++e+L+ ++ ga++
  gi|15669616|ref|NP_248429.1| 166 NKYKFSLDMATASIARGKILEALRKKIKIPEGCAVDKDGKPTTDPAKALE-GCILPFGGPKGYGLALAIEMLS-AIGGAEV 244
                                   78************************************************.*********************6.58***** PP

                                   GGGSSSSSSCTSS-SSEEEEEEEEEGGGTT.HHHHHHHHHHHHHHHHTS-BSTTTSS---TTHHHHHHHHHHHHH-EEEEH CS
                         Ldh_2 246 gkevsgsedeekkpaklghffiaidpeafgdaeefkervdalldelrasppaegadevllPGereaaaraerlkeGiplde 326
                                   g++v+g++++e++++k g +fiai+pe f+++eefk++vd+llde+++s+pae + e+l+PGe e +++ + +k+G ++d+
  gi|15669616|ref|NP_248429.1| 245 GTKVKGTANPEERCTK-GDLFIAINPEFFMGKEEFKRKVDELLDEIKNSEPAE-GFEILIPGEIEERNKMK-RKDGFEIDK 322
                                   **************99.***********************************8.689********877665.689****** PP

                                   HHHHHHH CS
                         Ldh_2 327 avleelk 333
                                   +++++lk
  gi|15669616|ref|NP_248429.1| 323 NLYNQLK 329
                                   ****995 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.43   3.8e+03      17      27 ..     185     195 ..     183     196 .. 0.87
   2 ?   10.3   0.0   5.8e-05      0.52       1      33 [.     312     344 .]     312     344 .] 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.43
                         RHH_3  17 LkaLSekTrIp 27 
                                   L+aL +k++Ip
  gi|15669616|ref|NP_248429.1| 185 LEALRKKIKIP 195
                                   88999999998 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 5.8e-05
                         RHH_3   1 nktrttvsidpelaekLkaLSekTrIprSklld 33 
                                   +k++ ++ id++l++ Lk++ ++++ ++ ++++
  gi|15669616|ref|NP_248429.1| 312 MKRKDGFEIDKNLYNQLKEICNELGLNIEDYIE 344
                                   788999*****************9999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 2637.57
//
Query:       gi|15669617|ref|NP_248430.1|  [L=168]
Description: inosine-5'-monophosphate dehydrogenase GuaB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      8e-35  119.1   8.7    4.5e-20   71.8   1.5    2.3  2  CBS            CBS domain
     0.0017   18.4   1.7        0.6   10.2   0.1    2.6  2  PRC            PRC-barrel domain
     0.0096   15.8   1.8       0.47   10.4   0.2    2.5  2  DUF3659        Protein of unknown function (DUF3659)
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.023   14.3   0.0    1.4  1  Blt1_C         Get5 carboxyl domain
      0.031   15.2   0.2       0.47   11.3   0.0    2.1  2  Trypsin_2      Trypsin-like peptidase domain
      0.064   12.4   0.0       0.85    8.8   0.0    2.0  2  Peptidase_S32  Equine arteritis virus serine endopeptidase S3
       0.22   10.1   0.0       0.22   10.1   0.0    1.8  3  Peptidase_S46  Peptidase S46
        3.2    8.4   6.7       0.61   10.7   0.9    2.3  2  DUF643         Protein of unknown function (DUF643)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.9   4.7e-17   1.1e-13       1      55 [.      17      70 ..      17      72 .. 0.90
   2 !   71.8   1.5     2e-23   4.5e-20       1      55 [.     113     167 ..     113     168 .] 0.98

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 4.7e-17
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                  ++dim +++ +v++d +l ++++l+r++++s+ PV+++dgklvGi++++D+++ +
  gi|15669617|ref|NP_248430.1| 17 IKDIMKKPI-VVYEDNDLIDVIRLFRKNKISGAPVLNKDGKLVGIISESDIVKTI 70
                                  589996655.***************7777**********************9976 PP

  == domain 2  score: 71.8 bits;  conditional E-value: 2e-23
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   V+d+mtr+v++++pd+t+ +a++lm+++++ rlPVVd++g+l+Givt+ Dl++al
  gi|15669617|ref|NP_248430.1| 113 VRDVMTRKVIVAKPDMTINDAAKLMVKNNIKRLPVVDDEGNLIGIVTRGDLIEAL 167
                                   89***************************************************98 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00027       0.6       4      27 ..      40      65 ..      38      70 .. 0.85
   2 !    6.8   0.3    0.0031         7       7      26 ..     140     159 ..     138     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00027
                                  CCS---TT-EEEETTSSEEEEE..EE CS
                           PRC  4 frasdliGkeVytedGeklGkV..kD 27
                                  fr +++ G +V + dG+ +G +  +D
  gi|15669617|ref|NP_248430.1| 40 FRKNKISGAPVLNKDGKLVGIIseSD 65
                                  77899****************95555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0031
                                   ---TT-EEEETTSSEEEEEE CS
                           PRC   7 sdliGkeVytedGeklGkVk 26 
                                   ++++ ++V++++G  +G V+
  gi|15669617|ref|NP_248430.1| 140 NNIKRLPVVDDEGNLIGIVT 159
                                   689**************996 PP

>> DUF3659  Protein of unknown function (DUF3659)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.018        41      14      30 ..      50      66 ..      46      78 .. 0.76
   2 !   10.4   0.2   0.00021      0.47      14      30 ..     147     163 ..     146     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.018
                       DUF3659 14 vvdeeGnvvGrvveGdl 30
                                  v++++G+ vG + e d+
  gi|15669617|ref|NP_248430.1| 50 VLNKDGKLVGIISESDI 66
                                  78888888888888754 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00021
                       DUF3659  14 vvdeeGnvvGrvveGdl 30 
                                   vvd+eGn +G v+ Gdl
  gi|15669617|ref|NP_248430.1| 147 VVDDEGNLIGIVTRGDL 163
                                   89***********9997 PP

>> Blt1_C  Get5 carboxyl domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     1e-05     0.023      13      34 ..      95     116 ..      91     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                        Blt1_C  13 VLatEeFWdDLegFleqRvKDe 34 
                                    L+ EeF +DL++ l+++v+D 
  gi|15669617|ref|NP_248430.1|  95 ALKIEEFMEDLKNALKTKVRDV 116
                                   5899*****************6 PP

>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.47     136     150 .]      46      60 ..      42      60 .. 0.95
   2 ?    1.7   0.1       0.2   4.4e+02     139     150 .]     146     157 ..     146     157 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                     Trypsin_2 136 SGGplfdsdGrvvGl 150
                                   SG+p++++dG++vG+
  gi|15669617|ref|NP_248430.1|  46 SGAPVLNKDGKLVGI 60 
                                   9*************8 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.2
                     Trypsin_2 139 plfdsdGrvvGl 150
                                   p++d++G+++G+
  gi|15669617|ref|NP_248430.1| 146 PVVDDEGNLIGI 157
                                   9**********8 PP

>> Peptidase_S32  Equine arteritis virus serine endopeptidase S32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00038      0.85     204     231 ..      40      67 ..      33     117 .. 0.81
   2 ?    1.7   0.0     0.052   1.2e+02     213     226 ..     146     159 ..     143     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00038
                                   ---GGGTT-EEEETTE.EEEEEEEEETT CS
                 Peptidase_S32 204 ftkcGDsGspvvdedgelvGvhtGsnkk 231
                                   f k   sG+pv+++dg+lvG+   s+  
  gi|15669617|ref|NP_248430.1|  40 FRKNKISGAPVLNKDGKLVGIISESDIV 67 
                                   5566669**************9888754 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.052
                                   EEEETTE.EEEEEE CS
                 Peptidase_S32 213 pvvdedgelvGvht 226
                                   pvvd++g+l+G+ t
  gi|15669617|ref|NP_248430.1| 146 PVVDDEGNLIGIVT 159
                                   9***********88 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   9.9e-05      0.22     636     653 ..      46      63 ..      44      70 .. 0.89
   2 ?   -3.2   0.1       1.1   2.4e+03     489     507 ..     101     120 ..      92     144 .. 0.41
   3 ?   -1.7   0.1      0.36   8.1e+02     639     651 ..     146     158 ..     145     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.9e-05
                                   TT-EEE-TTS-EEEEEEE CS
                 Peptidase_S46 636 SGSPvlngkgelvGlaFD 653
                                   SG+Pvln++g+lvG++  
  gi|15669617|ref|NP_248430.1|  46 SGAPVLNKDGKLVGIISE 63 
                                   9*************9865 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.1
                                   HT-SHHCHHHH.CC-HHHHH CS
                 Peptidase_S46 489 lleeakaavea.skDpliel 507
                                   ++e  k+a+++  +D +++ 
  gi|15669617|ref|NP_248430.1| 101 FMEDLKNALKTkVRDVMTRK 120
                                   33333333333333333332 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.36
                                   EEE-TTS-EEEEE CS
                 Peptidase_S46 639 PvlngkgelvGla 651
                                   Pv++++g+l+G++
  gi|15669617|ref|NP_248430.1| 146 PVVDDEGNLIGIV 158
                                   9**********97 PP

>> DUF643  Protein of unknown function (DUF643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.5      0.44   9.9e+02      57      78 ..       4      26 ..       1      44 [. 0.77
   2 ?   10.7   0.9   0.00027      0.61      47      82 ..      91     126 ..      81     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.44
                        DUF643 57 iindi.iepekefikdvlkdknl 78
                                  i+n++ i+ e  +ikd++k+  +
  gi|15669617|ref|NP_248430.1|  4 ILNKLnINGEIMLIKDIMKKPIV 26
                                  55554478888999999997655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00027
                        DUF643  47 kiktGksveeiindiiepekefikdvlkdknlikky 82 
                                     kt   +ee ++d+ ++ k  ++dv+ +k ++ k 
  gi|15669617|ref|NP_248430.1|  91 PLKTALKIEEFMEDLKNALKTKVRDVMTRKVIVAKP 126
                                   679999**************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1064.90
//
Query:       gi|15669618|ref|NP_248431.1|  [L=328]
Description: hypothetical protein MJ_1427 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-06   26.2   0.3    1.3e-05   25.3   0.3    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain
     0.0029   17.9   0.0     0.0072   16.7   0.0    1.6  1  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
      0.034   14.2   0.1      0.055   13.5   0.1    1.3  1  YqeY            Yqey-like protein
      0.084   12.9   0.0       0.14   12.2   0.0    1.2  1  Nop16           Ribosome biogenesis protein Nop16


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.3   2.9e-09   1.3e-05       2      66 .]      88     148 ..      87     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.9e-09
                                   EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                   ++i s +P ++GLGS++ l++a+ + + + +++     + a+++ ++ ++g +sg+ + a+ yGg
  gi|15669618|ref|NP_248431.1|  88 LKILSLFPAHSGLGSGTQLSLAVGKLISKIYNK----EMNAYNIAKITGRGGTSGIGIGAFEYGG 148
                                   6777889************************75....4679999999999**************8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.6e-06    0.0072       1      74 [.     231     301 ..     231     310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.6e-06
                GHMP_kinases_C   1 llealergdlellgellnlsqrs.elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeq 74 
                                   +++a+ +++l+ +ge +n +q +  +k ++   ++++++l+++l   +  +a+l  +++Gpt++a++++k  +e+
  gi|15669618|ref|NP_248431.1| 231 MMPAVVEKNLDDFGEVINKLQYLgFKKVELSLQSDIVKDLINEL-HKD-VYAGL--SSFGPTIYAFGDKKLIVEK 301
                                   78999*******************9999***************9.444.24555..556********77765555 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.2e-05     0.055      77     141 ..     203     269 ..     200     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHGGGS-----H.HHHHHHH.HHHHHHTT--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHH CS
                          YqeY  77 kaEievleeYlPeqlse.eeiealv.keaiaevgaesmkdmGkvmkalkpkvkGkaDgkkvsalvke 141
                                   k+E+++ ++Y P +l+e e+i +lv  +++ +v +++  d+G+v+++l+     k++ +  s +vk+
  gi|15669618|ref|NP_248431.1| 203 KKEVDIFKKYCPVPLNEvEKICHLVlMKMMPAVVEKNLDDFGEVINKLQYLGFKKVELSLQSDIVKD 269
                                   79*************874556655426778888999************9999999999999999987 PP

>> Nop16  Ribosome biogenesis protein Nop16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     3e-05      0.14     173     194 ..      52      73 ..      37      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                         Nop16 173 erLvekhGdDyeaMarDrkLNp 194
                                   ++L+ek+G+Dy + +rDr  N 
  gi|15669618|ref|NP_248431.1|  52 KKLIEKYGEDYIKSVRDRVYNT 73 
                                   79****************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2210.64
//
Query:       gi|15669619|ref|NP_248432.1|  [L=567]
Description: O-linked GlnNAc transferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-51  168.9  40.9    2.8e-07   30.2   0.2   11.8 12  TPR_2         Tetratricopeptide repeat
    1.2e-47  157.8  48.2    3.7e-08   32.9   0.3   11.5 11  TPR_1         Tetratricopeptide repeat
    9.6e-33  111.6  44.3    7.7e-13   47.9   4.9    8.7  9  TPR_11        TPR repeat
      7e-32  107.0  59.9    8.2e-06   25.6   1.9   12.2 12  TPR_8         Tetratricopeptide repeat
    6.8e-29  100.0  18.3    1.1e-05   25.6   0.0    8.8  8  TPR_12        Tetratricopeptide repeat
    1.6e-27   95.8   0.0    5.7e-07   30.1   0.0    5.9  6  TPR_16        Tetratricopeptide repeat
    4.4e-26   91.2   5.8      1e-05   25.9   0.1    6.0  6  TPR_19        Tetratricopeptide repeat
    2.7e-24   83.8   0.0      0.023   15.5   0.0    9.9 10  TPR_14        Tetratricopeptide repeat
    1.3e-23   83.0  29.7    6.9e-07   29.4   1.2    6.4  6  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    1.6e-19   68.8  25.3    0.00015   21.9   1.2    9.0  8  TPR_17        Tetratricopeptide repeat
    1.9e-17   62.6  18.8     0.0044   17.6   0.0   10.1 10  TPR_6         Tetratricopeptide repeat
    1.4e-14   53.0   9.7       0.19   11.8   0.0    9.0  9  TPR_7         Tetratricopeptide repeat
    3.7e-13   49.4   0.0      0.014   15.5   0.0    5.7  6  TPR_9         Tetratricopeptide repeat
    3.6e-12   46.4   1.8    6.1e-05   22.8   0.1    5.2  5  TPR_21        Tetratricopeptide repeat-like domain
      4e-12   45.8  17.4    0.00011   21.3   3.1    4.5  4  NARP1         NMDA receptor-regulated protein 1
    2.2e-11   43.5   4.7    0.00068   18.9   0.0    5.0  4  TPR_15        Tetratricopeptide repeat
    1.1e-09   37.8   5.5       0.19   11.7   0.0    8.2  9  TPR_10        Tetratricopeptide repeat
    6.7e-09   35.7  24.0    0.00069   19.6   0.5    7.7  7  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
    1.7e-06   28.0   1.8       0.37   10.9   0.0    5.4  4  ANAPC5        Anaphase-promoting complex subunit 5
    1.9e-06   28.1   0.4        6.4    7.2   0.0    4.9  4  TPR_20        Tetratricopeptide repeat
    1.3e-05   24.8   0.0        4.8    6.4   0.0    4.5  4  TPR_MalT      MalT-like TPR region
    3.5e-05   23.8  36.1     0.0038   17.2   3.6    5.1  4  SRP_TPR_like  Putative TPR-like repeat
    0.00012   22.1   2.6       0.19   11.7   0.0    5.2  3  DUF627        Protein of unknown function (DUF627)
      0.003   17.0   2.6        1.2    8.5   0.0    4.0  4  Coatomer_E    Coatomer epsilon subunit
  ------ inclusion threshold ------
       0.01   15.9   6.5        6.6    6.8   1.1    6.1  3  DUF3856       Domain of Unknown Function (DUF3856)
      0.021   14.1   0.2      0.021   14.1   0.2    2.3  3  DUF247        Plant protein of unknown function
      0.021   15.0   0.0        7.3    6.8   0.0    3.6  3  HemY_N        HemY protein N-terminus
      0.093   12.8  32.3       0.38   10.8   0.5    8.4  8  TPR_3         Tetratricopeptide repeat
       0.15   11.5   2.1        1.2    8.7   0.0    3.6  3  SHNi-TPR      SHNi-TPR
       0.18   11.9  30.1         16    5.6   0.0    8.5  9  MIT           MIT (microtubule interacting and transport) dom
       0.42   10.2  20.9       0.17   11.5   0.5    5.8  4  HTH_Bact      Helix-turn-helix bacterial domain
       0.82    9.4   4.0        4.9    6.9   0.1    2.8  2  Leptin        Leptin
        2.5    7.7  27.6        4.5    7.0   0.5    5.3  4  DUF2225       Uncharacterized protein conserved in bacteria (


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.5   7.9e-07   0.00043       3      33 ..      16      46 ..      14      47 .. 0.89
   2 !   30.2   0.2   5.1e-10   2.8e-07       3      34 .]      50      81 ..      48      81 .. 0.95
   3 ?    7.2   1.2     0.011       6.1       5      29 ..      86     110 ..      83     114 .. 0.90
   4 !   14.3   0.3   6.2e-05     0.033       7      30 ..     121     144 ..     116     147 .. 0.87
   5 !   16.8   0.1   9.5e-06    0.0052       3      34 .]     152     183 ..     150     183 .. 0.95
   6 !   11.1   0.0   0.00064      0.35       8      33 ..     208     233 ..     205     234 .. 0.91
   7 ?    6.7   0.1     0.016       8.8       4      31 ..     238     265 ..     236     268 .. 0.86
   8 !   25.3   0.6   1.8e-08   9.8e-06       3      34 .]     270     301 ..     268     301 .. 0.92
   9 !   17.0   0.1   8.3e-06    0.0045       1      29 [.     302     330 ..     302     333 .. 0.94
  10 ?   -1.9   0.0       9.6   5.2e+03      16      28 ..     361     373 ..     360     377 .. 0.61
  11 !   29.8   0.1   6.8e-10   3.7e-07       2      34 .]     380     412 ..     379     412 .. 0.96
  12 !   11.2   0.0   0.00058      0.31       6      30 ..     418     442 ..     414     445 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.9e-07
                         TPR_2  3 alynlGlayyklgdyeeAleafekAleldPn 33
                                   +   ++ y+  g y++A+e++ kAle   +
  gi|15669619|ref|NP_248432.1| 16 DWVTEANYYLDEGIYDKAVECYLKALEKKNT 46
                                  68899*********************98765 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 5.1e-10
                         TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                                   ++nl++a+y+l +y+ Alea ++Al++ P n
  gi|15669619|ref|NP_248432.1| 50 DWFNLAYALYHLEKYDSALEAINEALKISPSN 81
                                  5*****************************87 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.011
                         TPR_2   5 ynlGlayyklgdyeeAleafekAle 29 
                                   y  Gl++yk+g+   A ++++kA e
  gi|15669619|ref|NP_248432.1|  86 YLKGLIHYKRGEIILAYKYLKKASE 110
                                   899*******************965 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 6.2e-05
                         TPR_2   7 lGlayyklgdyeeAleafekAlel 30 
                                   lG++  k g+yeeAl+++ k+ + 
  gi|15669619|ref|NP_248432.1| 121 LGDISVKYGRYEEALKYYLKSYKM 144
                                   8999999*************9876 PP

  == domain 5  score: 16.8 bits;  conditional E-value: 9.5e-06
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                   al+  G++y+  gd ++A +af++ l+ +P +
  gi|15669619|ref|NP_248432.1| 152 ALFKAGKIYLLFGDIDKAYDAFNEILQQNPSH 183
                                   89****************************86 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.00064
                         TPR_2   8 GlayyklgdyeeAleafekAleldPn 33 
                                   Gl  +k++dy  Al+ f+k+l++d+n
  gi|15669619|ref|NP_248432.1| 208 GLTMIKNKDYIGALKIFNKVLQIDEN 233
                                   88999*******************98 PP

  == domain 7  score: 6.7 bits;  conditional E-value: 0.016
                         TPR_2   4 lynlGlayyklgdyeeAleafekAleld 31 
                                   +y+   +++   +y++Ale+ +k++++ 
  gi|15669619|ref|NP_248432.1| 238 YYYKSVIAEIFEEYKKALEYIDKSISIF 265
                                   788888888889************9986 PP

  == domain 8  score: 25.3 bits;  conditional E-value: 1.8e-08
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                   ++   G+++yklgd e A+ea++kA++l+ +n
  gi|15669619|ref|NP_248432.1| 270 YYAKKGDILYKLGDEEGAIEAYNKAIKLNSQN 301
                                   78899***********************9876 PP

  == domain 9  score: 17.0 bits;  conditional E-value: 8.3e-06
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAle 29 
                                   ++a++ l+ +yy++g++e+  ++f+k+le
  gi|15669619|ref|NP_248432.1| 302 PYAYFGLAILYYRKGELEKSSNFFDKVLE 330
                                   589************************98 PP

  == domain 10  score: -1.9 bits;  conditional E-value: 9.6
                         TPR_2  16 dyeeAleafekAl 28 
                                    y eA ++ +  +
  gi|15669619|ref|NP_248432.1| 361 YYHEAMKYVDNLI 373
                                   4667777766655 PP

  == domain 11  score: 29.8 bits;  conditional E-value: 6.8e-10
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +++y  G++yyklg+y++A e f  Al+ +P++
  gi|15669619|ref|NP_248432.1| 380 RWWYVKGYIYYKLGNYKDAYESFMNALRVNPKD 412
                                   79*****************************86 PP

  == domain 12  score: 11.2 bits;  conditional E-value: 0.00058
                         TPR_2   6 nlGlayyklgdyeeAleafekAlel 30 
                                    l+ +++k+g+ +eA+  + k l++
  gi|15669619|ref|NP_248432.1| 418 SLAIVLEKSGKIDEAITTYTKILKI 442
                                   699*******************997 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.4   2.2e-06    0.0012       8      30 ..      21      43 ..      15      47 .. 0.89
   2 !   29.7   0.4   6.6e-10   3.6e-07       4      34 .]      51      81 ..      49      81 .. 0.98
   3 !    7.5   1.3    0.0071       3.9       5      27 ..      86     108 ..      84     111 .. 0.94
   4 !   10.9   0.4   0.00058      0.31       8      26 ..     122     140 ..     120     145 .. 0.82
   5 !   16.2   0.2   1.2e-05    0.0066       3      34 .]     152     183 ..     151     183 .. 0.91
   6 !    7.9   0.0    0.0053       2.9      13      33 ..     213     233 ..     206     234 .. 0.92
   7 ?    5.2   0.2     0.036        19      16      30 ..     250     264 ..     244     265 .. 0.91
   8 !   24.9   1.6   2.2e-08   1.2e-05       4      34 .]     271     301 ..     268     301 .. 0.93
   9 !   16.3   0.1   1.2e-05    0.0063       2      29 ..     303     330 ..     302     332 .. 0.95
  10 !   32.9   0.3   6.8e-11   3.7e-08       2      34 .]     380     412 ..     379     412 .. 0.95
  11 !   14.2   0.0   5.3e-05     0.029       3      30 ..     415     442 ..     413     443 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.2e-06
                                  HHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1  8 GnayfklgkydeAleyyekALel 30
                                  +n y+  g yd+A+e+y kALe 
  gi|15669619|ref|NP_248432.1| 21 ANYYLDEGIYDKAVECYLKALEK 43
                                  899******************95 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 6.6e-10
                                  HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1  4 lynlGnayfklgkydeAleyyekALelnPnn 34
                                  ++nl++a+++l+kyd Ale+ ++AL++ P+n
  gi|15669619|ref|NP_248432.1| 51 WFNLAYALYHLEKYDSALEAINEALKISPSN 81
                                  9****************************97 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0071
                                   HHHHHHHHHTT-HHHHHHHHHHH CS
                         TPR_1   5 ynlGnayfklgkydeAleyyekA 27 
                                   y +G++++k g+   A +y +kA
  gi|15669619|ref|NP_248432.1|  86 YLKGLIHYKRGEIILAYKYLKKA 108
                                   789*******************9 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00058
                                   HHHHHHTT-HHHHHHHHHH CS
                         TPR_1   8 GnayfklgkydeAleyyek 26 
                                   G +  k g+y+eAl+yy k
  gi|15669619|ref|NP_248432.1| 122 GDISVKYGRYEEALKYYLK 140
                                   5555689**********88 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                   al+  G +y+  g+ d+A +++++ L+ nP++
  gi|15669619|ref|NP_248432.1| 152 ALFKAGKIYLLFGDIDKAYDAFNEILQQNPSH 183
                                   5666799***********************86 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.0053
                                   HTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1  13 klgkydeAleyyekALelnPn 33 
                                   k+++y  Al+ ++k+L++++n
  gi|15669619|ref|NP_248432.1| 213 KNKDYIGALKIFNKVLQIDEN 233
                                   789****************98 PP

  == domain 7  score: 5.2 bits;  conditional E-value: 0.036
                                   -HHHHHHHHHHHHHH CS
                         TPR_1  16 kydeAleyyekALel 30 
                                   +y++Aley +k +++
  gi|15669619|ref|NP_248432.1| 250 EYKKALEYIDKSISI 264
                                   8**********9987 PP

  == domain 8  score: 24.9 bits;  conditional E-value: 2.2e-08
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                   +  +G +++klg+ + A+e+y+kA++ln +n
  gi|15669619|ref|NP_248432.1| 271 YAKKGDILYKLGDEEGAIEAYNKAIKLNSQN 301
                                   7789************************886 PP

  == domain 9  score: 16.3 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALe 29 
                                   +a+++l+ +y+++g++++   +++k+Le
  gi|15669619|ref|NP_248432.1| 303 YAYFGLAILYYRKGELEKSSNFFDKVLE 330
                                   89*************************8 PP

  == domain 10  score: 32.9 bits;  conditional E-value: 6.8e-11
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   + +y +G++y+klg+y++A e +  AL++nP++
  gi|15669619|ref|NP_248432.1| 380 RWWYVKGYIYYKLGNYKDAYESFMNALRVNPKD 412
                                   57*****************************86 PP

  == domain 11  score: 14.2 bits;  conditional E-value: 5.3e-05
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                   +l+ l+ ++ k gk deA+  y k L++
  gi|15669619|ref|NP_248432.1| 415 TLKSLAIVLEKSGKIDEAITTYTKILKI 442
                                   6889*********************997 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   1.6   5.4e-09   2.9e-06       2      39 ..      22      59 ..      21      61 .. 0.94
   2 !   20.7   2.9   4.6e-07   0.00025       2      42 .]      56      96 ..      55      96 .. 0.95
   3 !    7.7   2.3    0.0052       2.8       1      39 [.     122     161 ..     122     164 .. 0.88
   4 ?   -0.4   0.0       1.8   9.8e+02       1      25 [.     157     181 ..     157     182 .. 0.88
   5 ?    5.5   0.1     0.026        14       8      32 ..     215     239 ..     208     241 .. 0.87
   6 ?    0.3   0.0         1   5.6e+02      15      23 ..     249     257 ..     248     266 .. 0.81
   7 !   47.9   4.9   1.4e-15   7.7e-13       1      42 []     275     316 ..     275     316 .. 0.99
   8 !   22.1   0.1   1.6e-07   8.6e-05       1      42 []     386     427 ..     386     427 .. 0.96
   9 ?    6.3   0.0     0.015       7.9       6      23 ..     425     442 ..     422     445 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.4e-09
                        TPR_11  2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39
                                  + y + G y++A+e+Y kAl+ +++n+  ++nL++a+y
  gi|15669619|ref|NP_248432.1| 22 NYYLDEGIYDKAVECYLKALEKKNTNPIDWFNLAYALY 59
                                  66999*******************************99 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 4.6e-07
                        TPR_11  2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                  +a+y + ky+ A+ea ++Alk++P+n  + y  Gl++yk G
  gi|15669619|ref|NP_248432.1| 56 YALYHLEKYDSALEAINEALKISPSNIYFAYLKGLIHYKRG 96
                                  68999*********************************976 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0052
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkl.dPdnaeayynLGlayy 39 
                                   Gd+ ++ G+yeeA++ Y k  k  +++n +a+++ G++y+
  gi|15669619|ref|NP_248432.1| 122 GDISVKYGRYEEALKYYLKSYKMaNSKNLNALFKAGKIYL 161
                                   8888999************999658889999999999986 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.8
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldP 25 
                                   G++y   G++++A  a+++ l+ +P
  gi|15669619|ref|NP_248432.1| 157 GKIYLLFGDIDKAYDAFNEILQQNP 181
                                   8899999******999999888888 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.026
                        TPR_11   8 GkyeeAieaYkkAlkldPdnaeayy 32 
                                    +y +A++ ++k l++d+++   yy
  gi|15669619|ref|NP_248432.1| 215 KDYIGALKIFNKVLQIDENSDISYY 239
                                   67889**************999999 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 1
                        TPR_11  15 eaYkkAlkl 23 
                                   e+YkkAl++
  gi|15669619|ref|NP_248432.1| 249 EEYKKALEY 257
                                   79*****97 PP

  == domain 7  score: 47.9 bits;  conditional E-value: 1.4e-15
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   Gd++y++G+ e+AieaY+kA+kl+++n+ ay++L+ +yy++G
  gi|15669619|ref|NP_248432.1| 275 GDILYKLGDEEGAIEAYNKAIKLNSQNPYAYFGLAILYYRKG 316
                                   9***************************************98 PP

  == domain 8  score: 22.1 bits;  conditional E-value: 1.6e-07
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   G++yy++G+y++A e++ +Al+ +P++ + +  L+ ++ k G
  gi|15669619|ref|NP_248432.1| 386 GYIYYKLGNYKDAYESFMNALRVNPKDISTLKSLAIVLEKSG 427
                                   99*********************************9999987 PP

  == domain 9  score: 6.3 bits;  conditional E-value: 0.015
                        TPR_11   6 eqGkyeeAieaYkkAlkl 23 
                                   + Gk++eAi+ Y k lk+
  gi|15669619|ref|NP_248432.1| 425 KSGKIDEAITTYTKILKI 442
                                   57**********886665 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.4   0.00035      0.19       6      29 ..      19      42 ..      17      46 .. 0.90
   2 !   21.9   0.5   2.3e-07   0.00013       4      34 .]      51      81 ..      51      81 .. 0.97
   3 ?    4.4   2.1     0.094        51       5      29 ..      86     110 ..      83     110 .. 0.94
   4 !   12.4   0.8   0.00027      0.15       7      32 ..     121     146 ..     116     148 .. 0.89
   5 !   12.4   0.1   0.00027      0.15       2      34 .]     151     183 ..     150     183 .. 0.93
   6 ?    5.1   0.0     0.058        31      12      33 ..     212     233 ..     208     234 .. 0.89
   7 ?    3.4   0.6       0.2   1.1e+02       7      30 ..     241     264 ..     237     267 .. 0.79
   8 !   25.6   1.9   1.5e-08   8.2e-06       3      34 .]     270     301 ..     269     301 .. 0.95
   9 !   11.4   0.2   0.00056      0.31       3      29 ..     304     330 ..     302     333 .. 0.95
  10 ?   -0.9   0.1       4.8   2.6e+03      15      30 ..     360     375 ..     360     378 .. 0.76
  11 !   25.0   0.2   2.4e-08   1.3e-05       4      34 .]     382     412 ..     379     412 .. 0.96
  12 !    8.2   0.0    0.0057       3.1       7      30 ..     419     442 ..     418     442 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00035
                                  HHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8  6 nlgsiylklgdyeeAkeyyekale 29
                                    ++ yl+ g y++A+e+y kale
  gi|15669619|ref|NP_248432.1| 19 TEANYYLDEGIYDKAVECYLKALE 42
                                  56889*****************97 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.3e-07
                                  HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8  4 yynlgsiylklgdyeeAkeyyekaleldpdn 34
                                  ++nl++++  l++y++A e++++al+++p+n
  gi|15669619|ref|NP_248432.1| 51 WFNLAYALYHLEKYDSALEAINEALKISPSN 81
                                  9****************************86 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.094
                                   HHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8   5 ynlgsiylklgdyeeAkeyyekale 29 
                                   y++g+i+ k g++  A +y++ka e
  gi|15669619|ref|NP_248432.1|  86 YLKGLIHYKRGEIILAYKYLKKASE 110
                                   89********************975 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00027
                                   HHHHHHHTT-HHHHHHHHHHHHHHHH CS
                         TPR_8   7 lgsiylklgdyeeAkeyyekaleldp 32 
                                   lg+i  k g+yeeA +yy k  +++ 
  gi|15669619|ref|NP_248432.1| 121 LGDISVKYGRYEEALKYYLKSYKMAN 146
                                   89999999*************99986 PP

  == domain 5  score: 12.4 bits;  conditional E-value: 0.00027
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                    a+++ g+iyl  gd+++A  ++++ l+ +p++
  gi|15669619|ref|NP_248432.1| 151 NALFKAGKIYLLFGDIDKAYDAFNEILQQNPSH 183
                                   5899***********************999975 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.058
                                   HHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8  12 lklgdyeeAkeyyekaleldpd 33 
                                   +k +dy  A + ++k+l++d++
  gi|15669619|ref|NP_248432.1| 212 IKNKDYIGALKIFNKVLQIDEN 233
                                   6789999*************97 PP

  == domain 7  score: 3.4 bits;  conditional E-value: 0.2
                                   HHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_8   7 lgsiylklgdyeeAkeyyekalel 30 
                                   ++ i +  ++y++A ey+ k +++
  gi|15669619|ref|NP_248432.1| 241 KSVIAEIFEEYKKALEYIDKSISI 264
                                   56666777899*********9998 PP

  == domain 8  score: 25.6 bits;  conditional E-value: 1.5e-08
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   +y ++g+i+ klgd e A+e+y+ka++l+ +n
  gi|15669619|ref|NP_248432.1| 270 YYAKKGDILYKLGDEEGAIEAYNKAIKLNSQN 301
                                   699*************************9875 PP

  == domain 9  score: 11.4 bits;  conditional E-value: 0.00056
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekale 29 
                                   ay+ l+ +y  +g++e++  ++ k+le
  gi|15669619|ref|NP_248432.1| 304 AYFGLAILYYRKGELEKSSNFFDKVLE 330
                                   8************************98 PP

  == domain 10  score: -0.9 bits;  conditional E-value: 4.8
                                   T-HHHHHHHHHHHHHH CS
                         TPR_8  15 gdyeeAkeyyekalel 30 
                                   + y+eA++y    + l
  gi|15669619|ref|NP_248432.1| 360 KYYHEAMKYVDNLINL 375
                                   5799****98776666 PP

  == domain 11  score: 25.0 bits;  conditional E-value: 2.4e-08
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   +y +g+iy klg+y+ A e+++ al+ +p++
  gi|15669619|ref|NP_248432.1| 382 WYVKGYIYYKLGNYKDAYESFMNALRVNPKD 412
                                   9****************************96 PP

  == domain 12  score: 8.2 bits;  conditional E-value: 0.0057
                                   HHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_8   7 lgsiylklgdyeeAkeyyekalel 30 
                                   l+ +++k g+++eA+ +y k l++
  gi|15669619|ref|NP_248432.1| 419 LAIVLEKSGKIDEAITTYTKILKI 442
                                   5668899*************9997 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   2.6   0.00012     0.064      11      75 ..      22      78 ..      17      80 .. 0.75
   2 !   14.7   0.9     5e-05     0.027       8      76 ..      87     146 ..      80     147 .. 0.83
   3 !   21.8   0.3   3.1e-07   0.00017      17      73 ..     129     178 ..     117     182 .. 0.88
   4 !    9.3   0.0    0.0026       1.4       8      74 ..     206     264 ..     198     267 .. 0.74
   5 !   13.5   0.2   0.00013     0.069      17      74 ..     249     297 ..     236     300 .. 0.69
   6 !   23.1   0.2   1.2e-07   6.7e-05       7      76 ..     271     333 ..     267     334 .. 0.88
   7 !   15.8   0.1   2.4e-05     0.013       6      54 ..     305     353 ..     301     357 .. 0.88
   8 !   25.6   0.0     2e-08   1.1e-05       9      75 ..     385     443 ..     378     445 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                        TPR_12 11 avlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75
                                  + ++  g yd+A e++ kale  +     ++    +  +nL+ +++ l++y+ Ale+ +eal+i 
  gi|15669619|ref|NP_248432.1| 22 NYYLDEGIYDKAVECYLKALEKKN-----TN---PIDWFNLAYALYHLEKYDSALEAINEALKIS 78
                                  566666777777777777766662.....23...2346999***99***************9986 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5e-05
                        TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                     +++++++g+   A ++l+ka e +     + ++++ ++l +++  y   gryeeAl+++ +++++a 
  gi|15669619|ref|NP_248432.1|  87 LKGLIHYKRGEIILAYKYLKKASEKI-----K-NEELFEILGDISVKY---GRYEEALKYYLKSYKMAN 146
                                   6899999999************4444.....3.456888888888888...***************986 PP

  == domain 3  score: 21.8 bits;  conditional E-value: 3.1e-07
                        TPR_12  17 grydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                   gry+eAl+++ k++ +a+     +    +++l+  g +y+++g+ ++A ++++e l+
  gi|15669619|ref|NP_248432.1| 129 GRYEEALKYYLKSYKMAN----SK---NLNALFKAGKIYLLFGDIDKAYDAFNEILQ 178
                                   9****************3....23...589***********************9886 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0026
                        TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   n +++  + ++y  Al++++k+l+i +     ++    ++++  + + + +++y++Ale+  +++ i
  gi|15669619|ref|NP_248432.1| 206 NNGLTMIKNKDYIGALKIFNKVLQIDE-----NS---DISYYYKSVIAEIFEEYKKALEYIDKSISI 264
                                   6677778899***************94.....44...245555566666777777777777777766 PP

  == domain 5  score: 13.5 bits;  conditional E-value: 0.00013
                        TPR_12  17 grydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   ++y +Ale+ +k++ i+       +   + ++   g+++++lg+ e A+e++++a+++
  gi|15669619|ref|NP_248432.1| 249 EEYKKALEYIDKSISIF-------N--RSLYYAKKGDILYKLGDEEGAIEAYNKAIKL 297
                                   45666666666666666.......4..5566777788888888888888888888765 PP

  == domain 6  score: 23.1 bits;  conditional E-value: 1.2e-07
                        TPR_12   7 n.nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                   + + +++l++lg+ + A+e ++ka+ +       ++p+   ++++L++ly++ g++e+  +++ ++l+ + 
  gi|15669619|ref|NP_248432.1| 271 YaKKGDILYKLGDEEGAIEAYNKAIKLN-----SQNPY---AYFGLAILYYRKGELEKSSNFFDKVLETYL 333
                                   43589*******************9999.....44544...7*************************9885 PP

  == domain 7  score: 15.8 bits;  conditional E-value: 2.4e-05
                        TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrl 54 
                                   +  la +++r g+++++  +++k+le + + l ++   +++ +  +g +
  gi|15669619|ref|NP_248432.1| 305 YFGLAILYYRKGELEKSSNFFDKVLETYLEELSEEDISALNLYSLIGKA 353
                                   547999**********************888899999999999999976 PP

  == domain 8  score: 25.6 bits;  conditional E-value: 2e-08
                        TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                    + ++++lg+y +A e +  al++      p+    ++tl  L+++++++g+ +eA+  +++ l+i 
  gi|15669619|ref|NP_248432.1| 385 KGYIYYKLGNYKDAYESFMNALRVN-----PK---DISTLKSLAIVLEKSGKIDEAITTYTKILKIV 443
                                   6899*****************9999.....87...59**************************9986 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   2.7e-08   1.5e-05       3      67 ..      20      81 ..      18      82 .. 0.90
   2 !   16.4   0.1   1.9e-05      0.01       2      49 ..      53      97 ..      52     105 .. 0.90
   3 !   15.7   0.0   3.3e-05     0.018      11      67 ..     129     183 ..     121     184 .. 0.90
   4 ?    3.9   0.0      0.16        87       9      59 ..     213     260 ..     205     266 .. 0.85
   5 !   30.1   0.0   1.1e-09   5.7e-07       2      52 ..     273     320 ..     272     332 .. 0.92
   6 !   12.7   0.0   0.00028      0.15       2      61 ..     384     440 ..     383     444 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.7e-08
                        TPR_16  3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                                  +a+++l+ g yd+A++ +  al++      ++  +++l+ a++++  ++ A++++++al+ +p++
  gi|15669619|ref|NP_248432.1| 20 EANYYLDEGIYDKAVECYLKALEKK---NTNPIDWFNLAYALYHLEKYDSALEAINEALKISPSN 81
                                  79****************7777777...446679****************************986 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.9e-05
                        TPR_16  2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgr 49
                                  +la+a++ + +yd A++a ++alk     P +  +++l+g++++++g+
  gi|15669619|ref|NP_248432.1| 53 NLAYALYHLEKYDSALEAINEALKIS---PSNIYFAYLKGLIHYKRGE 97
                                  78999999999999999999999999...9999999999999999987 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 3.3e-05
                        TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                   g+y++A++++    k++   + +  Al+  g ++l +g+ ++A +++++ l++ p++
  gi|15669619|ref|NP_248432.1| 129 GRYEEALKYYLKSYKMA--NSKNLNALFKAGKIYLLFGDIDKAYDAFNEILQQNPSH 183
                                   9**************99..577*****************************999975 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.16
                        TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyra 59 
                                   +++dy  A++ ++ +l  d        +++++ ++a  + ++++A++++++
  gi|15669619|ref|NP_248432.1| 213 KNKDYIGALKIFNKVLQID---ENSDISYYYKSVIAEIFEEYKKALEYIDK 260
                                   6778888888899999999...77889*******************99987 PP

  == domain 5  score: 30.1 bits;  conditional E-value: 1.1e-09
                        TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlae 52 
                                   +++++++++gd + A++a++ a+k++   ++++ A+++l+ +++r+g+l++
  gi|15669619|ref|NP_248432.1| 273 KKGDILYKLGDEEGAIEAYNKAIKLN---SQNPYAYFGLAILYYRKGELEK 320
                                   689***********************...*******************997 PP

  == domain 6  score: 12.7 bits;  conditional E-value: 0.00028
                        TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                    ++++++++g+y dA + +  al+ +   P +   l  l+ ++ + g  +eA+  y + l
  gi|15669619|ref|NP_248432.1| 384 VKGYIYYKLGNYKDAYESFMNALRVN---PKDISTLKSLAIVLEKSGKIDEAITTYTKIL 440
                                   5799**********************...999999******************8888766 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.5e-05    0.0083       2      66 ..      25      89 ..      24      91 .. 0.93
   2 ?    4.6   0.0     0.086        47      10      46 ..     101     136 ..      93     138 .. 0.80
   3 !   18.7   0.2   3.3e-06    0.0018       3      57 ..     127     182 ..     125     186 .. 0.91
   4 ?    6.3   0.0     0.026        14       2      31 ..     212     240 ..     211     275 .. 0.76
   5 !   25.9   0.1   1.9e-08     1e-05       2      54 ..     279     331 ..     278     338 .. 0.92
   6 !   20.9   0.0   6.9e-07   0.00038       4      53 ..     392     441 ..     389     444 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-05
                        TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66
                                  l+eg y+ A++ + +al++++ n+  + +LA al+ l  +d A ++++++++  p + + a L++
  gi|15669619|ref|NP_248432.1| 25 LDEGIYDKAVECYLKALEKKNTNPIDWFNLAYALYHLEKYDSALEAINEALKISPSNIYFAYLKG 89
                                  78999**************************************************9988888876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.086
                        TPR_19  10 AlalleqalqedpknaearllLAeallalgqldeAea 46 
                                   A ++l++a +e+ kn+e+   L ++ ++ g+++eA +
  gi|15669619|ref|NP_248432.1| 101 AYKYLKKA-SEKIKNEELFEILGDISVKYGRYEEALK 136
                                   89999**9.555557777777**************76 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 3.3e-06
                        TPR_19   3 aegdyaeAlalleqalqe.dpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                   + g+y+eAl+++ + ++  + kn++a+    +++l  g++d+A ++ +++++++p 
  gi|15669619|ref|NP_248432.1| 127 KYGRYEEALKYYLKSYKMaNSKNLNALFKAGKIYLLFGDIDKAYDAFNEILQQNPS 182
                                   569*****99999988765999*******************************997 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.026
                        TPR_19   2 laegdyaeAlalleqalqedpknaearllL 31 
                                   ++++dy  Al+++ ++lq d  n+++ +++
  gi|15669619|ref|NP_248432.1| 212 IKNKDYIGALKIFNKVLQIDE-NSDISYYY 240
                                   6789***************87.66666644 PP

  == domain 5  score: 25.9 bits;  conditional E-value: 1.9e-08
                        TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpee 54 
                                   ++ gd + A++++ +a++ + +n++a  +LA++++  g+l++  +  d+++e 
  gi|15669619|ref|NP_248432.1| 279 YKLGDEEGAIEAYNKAIKLNSQNPYAYFGLAILYYRKGELEKSSNFFDKVLET 331
                                   56789999**************************************9999986 PP

  == domain 6  score: 20.9 bits;  conditional E-value: 6.9e-07
                        TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                    g+y +A + + +al  +pk+   +  LA++l ++g +deA+ +  ++++
  gi|15669619|ref|NP_248432.1| 392 LGNYKDAYESFMNALRVNPKDISTLKSLAIVLEKSGKIDEAITTYTKILK 441
                                   69*****************************************9998875 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0      0.02        11       7      42 ..      20      55 ..      15      56 .. 0.87
   2 !   14.2   0.0   0.00011     0.058       4      36 ..      51      83 ..      48      91 .. 0.87
   3 ?   -0.4   0.0       5.2   2.8e+03       8      30 ..      89     111 ..      83     123 .. 0.80
   4 ?    0.4   0.0       2.9   1.6e+03      12      26 ..     126     140 ..     115     145 .. 0.77
   5 !   14.4   0.0   9.8e-05     0.053       2      34 ..     151     183 ..     150     184 .. 0.93
   6 ?    0.7   0.0       2.4   1.3e+03      13      34 ..     213     234 ..     208     244 .. 0.82
   7 !   15.5   0.0   4.2e-05     0.023       5      43 ..     272     310 ..     267     311 .. 0.90
   8 ?    5.8   0.0     0.054        29       3      31 ..     304     332 ..     302     344 .. 0.89
   9 !   10.2   0.0    0.0021       1.1       4      39 ..     382     417 ..     379     420 .. 0.87
  10 ?    7.9   0.0     0.011       6.2       4      29 ..     416     441 ..     413     445 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.02
                        TPR_14  7 laeallalGdpdeAiallrralalaPddaeawllla 42
                                   a ++l  G +d+A++++ +al++  +++  w+ la
  gi|15669619|ref|NP_248432.1| 20 EANYYLDEGIYDKAVECYLKALEKKNTNPIDWFNLA 55
                                  5889999999*************9999999999888 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00011
                        TPR_14  4 llalaeallalGdpdeAiallrralalaPddae 36
                                  +  la al++l+++d A+++ ++al+  P++  
  gi|15669619|ref|NP_248432.1| 51 WFNLAYALYHLEKYDSALEAINEALKISPSNIY 83
                                  7779*************************9865 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 5.2
                        TPR_14   8 aeallalGdpdeAiallrralal 30 
                                   + +++ +G+   A ++l++a ++
  gi|15669619|ref|NP_248432.1|  89 GLIHYKRGEIILAYKYLKKASEK 111
                                   567888999999******99875 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 2.9
                        TPR_14  12 lalGdpdeAiallrr 26 
                                      G+++eA++++ +
  gi|15669619|ref|NP_248432.1| 126 VKYGRYEEALKYYLK 140
                                   56799******9965 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 9.8e-05
                        TPR_14   2 eallalaeallalGdpdeAiallrralalaPdd 34 
                                   +al ++++++l  Gd d+A ++++++l+++P++
  gi|15669619|ref|NP_248432.1| 151 NALFKAGKIYLLFGDIDKAYDAFNEILQQNPSH 183
                                   688999*************************86 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 2.4
                        TPR_14  13 alGdpdeAiallrralalaPdd 34 
                                    + d+ +A+++++++l+ + ++
  gi|15669619|ref|NP_248432.1| 213 KNKDYIGALKIFNKVLQIDENS 234
                                   5778999**********99876 PP

  == domain 7  score: 15.5 bits;  conditional E-value: 4.2e-05
                        TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                   ++ +++l+ lGd ++Ai+++++a++l+ +++ a++ la 
  gi|15669619|ref|NP_248432.1| 272 AKKGDILYKLGDEEGAIEAYNKAIKLNSQNPYAYFGLAI 310
                                   456899*****************************9995 PP

  == domain 8  score: 5.8 bits;  conditional E-value: 0.054
                        TPR_14   3 allalaeallalGdpdeAiallrralala 31 
                                   a+  la ++++ G+++++ + ++++l+++
  gi|15669619|ref|NP_248432.1| 304 AYFGLAILYYRKGELEKSSNFFDKVLETY 332
                                   67789*********************987 PP

  == domain 9  score: 10.2 bits;  conditional E-value: 0.0021
                        TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawl 39 
                                   ++  + +++ lG++++A + +  al+ +P+d  ++ 
  gi|15669619|ref|NP_248432.1| 382 WYVKGYIYYKLGNYKDAYESFMNALRVNPKDISTLK 417
                                   7778999***********************987665 PP

  == domain 10  score: 7.9 bits;  conditional E-value: 0.011
                        TPR_14   4 llalaeallalGdpdeAiallrrala 29 
                                   l+ la +l+ +G+ deAi+ + ++l+
  gi|15669619|ref|NP_248432.1| 416 LKSLAIVLEKSGKIDEAITTYTKILK 441
                                   5679****************999887 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   2.6   2.8e-06    0.0015      18      81 ..       9      73 ..       1      74 [. 0.87
   2 !   29.4   1.2   1.3e-09   6.9e-07      16      80 ..      75     139 ..      68     141 .. 0.89
   3 !   11.1   0.3   0.00066      0.36      17      58 ..     143     185 ..     137     204 .. 0.85
   4 ?    6.1   0.1     0.024        13      30      81 ..     208     260 ..     186     261 .. 0.75
   5 !    7.8   0.2    0.0069       3.8       6      49 ..     285     328 ..     280     337 .. 0.88
   6 !   27.6   0.2   4.5e-09   2.5e-06       5      81 ..     362     438 ..     360     439 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.8e-06
                                  HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3 18 aetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                   + +s+ed    A  ++  g y++A e + ka +++++++  ++ +A +l+ L+ky+ A+ a+ +
  gi|15669619|ref|NP_248432.1|  9 EKLKSYEDWVTEANYYLDEGIYDKAVECYLKAlEKKNTNPIDWFNLAYALYHLEKYDSALEAINE 73
                                  55678899999999**************999999999999*******************999876 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1.3e-09
                                   H.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3  16 laaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                   l+ ++ + + ayl++l +y++g+   Ay++l+ka ++ k+++   +++  ++k+++yeeA++ + 
  gi|15669619|ref|NP_248432.1|  75 LKISPSNIYFAYLKGLIHYKRGEIILAYKYLKKASEKIKNEELFEILGDISVKYGRYEEALKYYL 139
                                   44567788889**************************************************9876 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00066
                                   ..HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHH CS
                        ANAPC3  17 a.aetespedayllAlclylngqykrAyellrka.klnskslgc 58 
                                   + a+++++++++  ++ ++l g+ ++Ay+ +++  ++n++++ c
  gi|15669619|ref|NP_248432.1| 143 KmANSKNLNALFKAGKIYLLFGDIDKAYDAFNEIlQQNPSHE-C 185
                                   33899*****************************77766664.5 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.024
                                   HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   +l++ +n++y  A+++++k  +++++s  + y +   +   ++y++A+  ++k
  gi|15669619|ref|NP_248432.1| 208 GLTMIKNKDYIGALKIFNKVlQIDENSDISYYYKSVIAEIFEEYKKALEYIDK 260
                                   788999**************777777765555555555555999999988776 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0069
                                   HHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                        ANAPC3   6 knAiflaerllaaetespedayllAlclylngqykrAyellrka 49 
                                   + Ai  ++++ + ++++p++ + lA  +y+ g+ ++  ++++k 
  gi|15669619|ref|NP_248432.1| 285 EGAIEAYNKAIKLNSQNPYAYFGLAILYYRKGELEKSSNFFDKV 328
                                   5699999**************************99988887776 PP

  == domain 6  score: 27.6 bits;  conditional E-value: 4.5e-09
                                   HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   y++A+ + + l     +s+   y +++ +y++g+yk Aye + +a + n+k++  +  +A +l k +k++eAi+++ k
  gi|15669619|ref|NP_248432.1| 362 YHEAMKYVDNLI-NLENSSRWWYVKGYIYYKLGNYKDAYESFMNAlRVNPKDISTLKSLAIVLEKSGKIDEAITTYTK 438
                                   899999999999.666677777888*************************************************9865 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.2   2.8e-07   0.00015       1      34 []      36      69 ..      36      69 .. 0.96
   2 !    8.2   0.0    0.0066       3.6       3      29 ..      72      98 ..      70     103 .. 0.90
   3 ?    4.6   0.6     0.095        51       2      32 ..     138     169 ..     137     171 .. 0.88
   4 ?    5.0   0.0     0.067        37       2      33 ..     224     255 ..     223     256 .. 0.91
   5 ?    3.0   0.1      0.31   1.7e+02       2      33 ..     251     288 ..     250     289 .. 0.66
   6 !   21.4   0.7   4.1e-07   0.00022       1      31 [.     290     320 ..     290     321 .. 0.94
   7 ?    6.6   0.1     0.021        12      16      32 ..     382     398 ..     376     400 .. 0.89
   8 !    9.2   0.0    0.0031       1.7       2      33 ..     402     433 ..     401     434 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.8e-07
                        TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtArq 34
                                  +ylkale+  +n+  ++nLA++l+++ +++ A++
  gi|15669619|ref|NP_248432.1| 36 CYLKALEKKNTNPIDWFNLAYALYHLEKYDSALE 69
                                  8*****************************9975 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0066
                        TPR_17  3 lkaleldPnnadaynnLAelllknGdl 29
                                   +al++ P+n ++ ++++ +++k+G+ 
  gi|15669619|ref|NP_248432.1| 72 NEALKISPSNIYFAYLKGLIHYKRGEI 98
                                  689*********************975 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.095
                        TPR_17   2 ylkalel.dPnnadaynnLAelllknGdlmtA 32 
                                   ylk+ +  + +n +a++  ++++l  Gd ++A
  gi|15669619|ref|NP_248432.1| 138 YLKSYKMaNSKNLNALFKAGKIYLLFGDIDKA 169
                                   77777777999*****************9998 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.067
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   + k+l++d n+  +y+++ ++ +   ++++A+
  gi|15669619|ref|NP_248432.1| 224 FNKVLQIDENSDISYYYKSVIAEIFEEYKKAL 255
                                   889*****************999999999987 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.31
                        TPR_17   2 ylkalel.dPnn.....adaynnLAelllknGdlmtAr 33 
                                   y+kale+ d++      +  y  ++ +l+k+Gd + A+
  gi|15669619|ref|NP_248432.1| 251 YKKALEYiDKSIsifnrSLYYAKKGDILYKLGDEEGAI 288
                                   55555554443345555777888899999999988887 PP

  == domain 6  score: 21.4 bits;  conditional E-value: 4.1e-07
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                   +y ka++l+  n++ay+ LA l++++G+l++
  gi|15669619|ref|NP_248432.1| 290 AYNKAIKLNSQNPYAYFGLAILYYRKGELEK 320
                                   59*************************9875 PP

  == domain 7  score: 6.6 bits;  conditional E-value: 0.021
                        TPR_17  16 ynnLAelllknGdlmtA 32 
                                   ++ ++++++k+G++++A
  gi|15669619|ref|NP_248432.1| 382 WYVKGYIYYKLGNYKDA 398
                                   999************99 PP

  == domain 8  score: 9.2 bits;  conditional E-value: 0.0031
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   + +al+ +P++   +  LA +l+k G+ ++A+
  gi|15669619|ref|NP_248432.1| 402 FMNALRVNPKDISTLKSLAIVLEKSGKIDEAI 433
                                   679**************************997 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.97   5.3e+02      11      28 ..      24      42 ..      21      43 .. 0.76
   2 ?    7.3   0.0     0.015       8.2       4      32 ..      52      80 ..      51      81 .. 0.90
   3 ?   -0.7   0.2       5.4   2.9e+03       4      26 ..      86     108 ..      85     111 .. 0.84
   4 ?    0.1   0.0       2.9   1.6e+03      12      23 ..     127     138 ..     115     140 .. 0.78
   5 !   17.6   0.0   8.1e-06    0.0044       2      32 ..     152     182 ..     151     183 .. 0.93
   6 ?    3.3   0.0      0.29   1.6e+02       7      28 ..     208     229 ..     206     234 .. 0.86
   7 !   10.4   0.1    0.0015      0.83       6      29 ..     274     297 ..     271     301 .. 0.87
   8 !   12.6   0.3   0.00031      0.17       1      30 [.     303     332 ..     303     332 .. 0.96
   9 ?    6.6   0.0     0.025        14       7      32 ..     386     411 ..     381     412 .. 0.86
  10 ?    5.1   0.0     0.076        41       6      28 ..     419     441 ..     418     442 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.97
                                  HH.HHHHHHHHHHHHHHHH CS
                         TPR_6 11 rk.lgdtdkAlealerlik 28
                                  +   g +dkA+e + + ++
  gi|15669619|ref|NP_248432.1| 24 YLdEGIYDKAVECYLKALE 42
                                  444789******9988776 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.015
                                  HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6  4 yklalsyrklgdtdkAlealerlikeYPd 32
                                  ++la++++ l ++d Alea ++ +k  P 
  gi|15669619|ref|NP_248432.1| 52 FNLAYALYHLEKYDSALEAINEALKISPS 80
                                  89*******88**********99998875 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 5.4
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   4 yklalsyrklgdtdkAlealerl 26 
                                   y+ +l ++k g+   A ++l++ 
  gi|15669619|ref|NP_248432.1|  86 YLKGLIHYKRGEIILAYKYLKKA 108
                                   77899999988999999999886 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 2.9
                                   HHHHHHHHHHHH CS
                         TPR_6  12 klgdtdkAleal 23 
                                   k g++++Al+++
  gi|15669619|ref|NP_248432.1| 127 KYGRYEEALKYY 138
                                   5479*****998 PP

  == domain 5  score: 17.6 bits;  conditional E-value: 8.1e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                   Al+k+++ y+  gd dkA +a+++++++ P 
  gi|15669619|ref|NP_248432.1| 152 ALFKAGKIYLLFGDIDKAYDAFNEILQQNPS 182
                                   9**********66***************997 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.29
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                   +l ++k +d+  Al++++++++
  gi|15669619|ref|NP_248432.1| 208 GLTMIKNKDYIGALKIFNKVLQ 229
                                   67889988************98 PP

  == domain 7  score: 10.4 bits;  conditional E-value: 0.0015
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   6 lalsyrklgdtdkAlealerlike 29 
                                    +  ++klgd + A+ea+++ ik 
  gi|15669619|ref|NP_248432.1| 274 KGDILYKLGDEEGAIEAYNKAIKL 297
                                   588999*99************985 PP

  == domain 8  score: 12.6 bits;  conditional E-value: 0.00031
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                         TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeY 30 
                                   +A++ la +y++ g+ +k+   ++++++ Y
  gi|15669619|ref|NP_248432.1| 303 YAYFGLAILYYRKGELEKSSNFFDKVLETY 332
                                   7***********99*************998 PP

  == domain 9  score: 6.6 bits;  conditional E-value: 0.025
                                   HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                   ++ y+klg++ +A e + + ++  P+
  gi|15669619|ref|NP_248432.1| 386 GYIYYKLGNYKDAYESFMNALRVNPK 411
                                   899***9********99998887775 PP

  == domain 10  score: 5.1 bits;  conditional E-value: 0.076
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                   la  ++k g+ d+A++++ +++k
  gi|15669619|ref|NP_248432.1| 419 LAIVLEKSGKIDEAITTYTKILK 441
                                   577788867***********987 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00075      0.41       6      31 ..      21      44 ..      21      49 .. 0.81
   2 ?    2.0   0.0      0.48   2.6e+02       2      28 ..      51      75 ..      51      82 .. 0.81
   3 !    9.7   0.0    0.0017      0.91       5      31 ..     121     147 ..     118     151 .. 0.85
   4 ?   -0.9   0.0       4.1   2.2e+03       1      20 [.     152     171 ..     152     178 .. 0.82
   5 ?    0.5   0.0       1.4   7.7e+02      14      26 ..     250     262 ..     246     269 .. 0.83
   6 ?    1.7   0.0       0.6   3.3e+02       6      28 ..     275     295 ..     271     302 .. 0.81
   7 ?    5.9   0.1     0.028        15       1      32 [.     304     335 ..     304     340 .. 0.86
   8 ?    5.4   0.0     0.039        21       6      33 ..     386     411 ..     383     414 .. 0.81
   9 !   11.8   0.0   0.00035      0.19       1      31 [.     415     445 ..     415     448 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00075
                         TPR_7  6 arlysrlGdyeeAielyeqsLaltkd 31
                                  a+ y ++G y++A+e+y +  al+k 
  gi|15669619|ref|NP_248432.1| 21 ANYYLDEGIYDKAVECYLK--ALEKK 44
                                  677999999**********..66655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.48
                         TPR_7  2 LlnLarlysrlGdyeeAielyeqsLal 28
                                  ++nLa +   l +y+ A+e   +  al
  gi|15669619|ref|NP_248432.1| 51 WFNLAYALYHLEKYDSALEAINE--AL 75
                                  589***************98877..44 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0017
                         TPR_7   5 LarlysrlGdyeeAielyeqsLaltkd 31 
                                   L+++ ++ G+yeeA+++y +s  ++++
  gi|15669619|ref|NP_248432.1| 121 LGDISVKYGRYEEALKYYLKSYKMANS 147
                                   77788888************9988876 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 4.1
                         TPR_7   1 aLlnLarlysrlGdyeeAie 20 
                                   aL+  + +y   Gd ++A +
  gi|15669619|ref|NP_248432.1| 152 ALFKAGKIYLLFGDIDKAYD 171
                                   5677799**********976 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 1.4
                         TPR_7  14 dyeeAielyeqsL 26 
                                   +y++A+e+  +s+
  gi|15669619|ref|NP_248432.1| 250 EYKKALEYIDKSI 262
                                   899***9988865 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.6
                         TPR_7   6 arlysrlGdyeeAielyeqsLal 28 
                                   +++  +lGd e Aie y +  a+
  gi|15669619|ref|NP_248432.1| 275 GDILYKLGDEEGAIEAYNK--AI 295
                                   788999***********99..44 PP

  == domain 7  score: 5.9 bits;  conditional E-value: 0.028
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                   a++ La ly r G+ e+   ++ ++L++  ++
  gi|15669619|ref|NP_248432.1| 304 AYFGLAILYYRKGELEKSSNFFDKVLETYLEE 335
                                   7899********************99876665 PP

  == domain 8  score: 5.4 bits;  conditional E-value: 0.039
                         TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpe 33 
                                   + +y +lG+y++A e +    al+  p 
  gi|15669619|ref|NP_248432.1| 386 GYIYYKLGNYKDAYESFMN--ALRVNPK 411
                                   6799*********999988..7666665 PP

  == domain 9  score: 11.8 bits;  conditional E-value: 0.00035
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                   +L  La + ++ G+ +eAi+ y++ L + ++
  gi|15669619|ref|NP_248432.1| 415 TLKSLAIVLEKSGKIDEAITTYTKILKIVNS 445
                                   6889********************8887766 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.5e-05     0.014       5      62 ..      24      81 ..      21      92 .. 0.92
   2 !    9.4   0.0    0.0021       1.2       7      53 ..      60     106 ..      54     110 .. 0.86
   3 ?    1.3   0.0      0.71   3.9e+02      11      61 ..     131     182 ..     122     190 .. 0.76
   4 !    8.9   0.0    0.0031       1.7       9      65 ..     249     304 ..     244     311 .. 0.90
   5 !    7.9   0.0    0.0061       3.3      12      53 ..     285     326 ..     282     346 .. 0.81
   6 !   14.4   0.0   5.7e-05     0.031      12      62 ..     363     412 ..     359     435 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-05
                         TPR_9  5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62
                                  ++ e  +++a +++   l  +   p +++  + +l++l+ +  Al++ + +l ++p++
  gi|15669619|ref|NP_248432.1| 24 YLDEGIYDKAVECYLKALEKKNTNPIDWFNLAYALYHLEKYDSALEAINEALKISPSN 81
                                  7788889**********************************************99975 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0021
                         TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLe 53 
                                     e+++ al++++  l + P  ++  +  Gl+++++G +  A + L 
  gi|15669619|ref|NP_248432.1|  60 HLEKYDSALEAINEALKISPSNIYFAYLKGLIHYKRGEIILAYKYLK 106
                                   56899********************************9877777765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.71
                         TPR_9  11 weralavverllll.aPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                   +e+al+++     + +++    ++  G ++   G++ +A ++++  l+++p+
  gi|15669619|ref|NP_248432.1| 131 YEEALKYYLKSYKMaNSKNLNALFKAGKIYLLFGDIDKAYDAFNEILQQNPS 182
                                   5666665555544436667778888899999999999999999999999996 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0031
                         TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                   e++ +al++++  + ++ ++ + +   G +l++lG+ ++A+++ + ++ l+ ++p a
  gi|15669619|ref|NP_248432.1| 249 EEYKKALEYIDKSISIFNRSLY-YAKKGDILYKLGDEEGAIEAYNKAIKLNSQNPYA 304
                                   57889************99977.7889*********************998887765 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0061
                         TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLe 53 
                                   e a+++++  + l+++ p+ ++  ++l+++ G l++  + ++
  gi|15669619|ref|NP_248432.1| 285 EGAIEAYNKAIKLNSQNPYAYFGLAILYYRKGELEKSSNFFD 326
                                   67999****************************998876544 PP

  == domain 6  score: 14.4 bits;  conditional E-value: 5.7e-05
                         TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                    +a+++v+ l+ l   + + ++  G ++++lG+++ A + +  +l+++p++
  gi|15669619|ref|NP_248432.1| 363 HEAMKYVDNLINLENSS-RWWYVKGYIYYKLGNYKDAYESFMNALRVNPKD 412
                                   6799*********9888.******************************976 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0038       2.1      83     179 ..      21     115 ..      13     121 .. 0.81
   2 !   11.2   0.1   0.00041      0.22      88     185 ..      94     190 ..      92     198 .. 0.77
   3 !   22.8   0.1   1.1e-07   6.1e-05      42     179 ..     169     301 ..     165     311 .. 0.81
   4 ?    4.8   0.0     0.036        20     127     179 ..     360     412 ..     298     425 .. 0.70
   5 ?   -1.9   0.0       4.3   2.3e+03     156     173 ..     423     440 ..     422     447 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0038
                        TPR_21  83 AkaaveagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLeakke.eafaalvaelrGDilvaqgkl 162
                                   A+   ++g +++A + + ++lek+   + + +    La  l   +kyd Al++++++ + +  +  +a l+G i++++g++
  gi|15669619|ref|NP_248432.1|  21 ANYYLDEGIYDKAVECYLKALEKK---NTNPIDWFNLAYALYHLEKYDSALEAINEALKiSPSNIYFAYLKGLIHYKRGEI 98 
                                   666777777888887777777776...456888899******************8876614556678999*********** PP

                        TPR_21 163 deAraaYqaAlaaleek 179
                                     A +  ++A ++++++
  gi|15669619|ref|NP_248432.1|  99 ILAYKYLKKASEKIKNE 115
                                   99999999999998887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00041
                        TPR_21  88 eagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlkt.Leakkeeafaalvael.rGDilvaqgkldeAr 166
                                   ++g++  A + L+++ ek k+eel ++    L  + ++ + y+eAlk  L++ k ++ + l a    G i++  g++d+A 
  gi|15669619|ref|NP_248432.1|  94 KRGEIILAYKYLKKASEKIKNEELFEI----LGDISVKYGRYEEALKYyLKSYKMANSKNLNALFkAGKIYLLFGDIDKAY 170
                                   567777788999999999999988888....78999999******996254444444333333331699************ PP

                        TPR_21 167 aaYqaAlaaleeka.rellq 185
                                   +a+++ l+++ +++ +++++
  gi|15669619|ref|NP_248432.1| 171 DAFNEILQQNPSHEcKKIVE 190
                                   *******9999998877776 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 1.1e-07
                        TPR_21  42 lYqqlqeaveakdaakakeaaeeladeyggtaYaalaaLllAkaaveagdlaaAkaqLewvlekakdeelkalarlRLarv 122
                                   +Y++ +e ++++ +++ k+ +e +++  +     ++  L    ++++++d+  A + +++vl+  ++ +++   +  +a++
  gi|15669619|ref|NP_248432.1| 169 AYDAFNEILQQNPSHECKKIVECMENVVNAI--NSYEDLNNGLTMIKNKDYIGALKIFNKVLQIDENSDISYYYKSVIAEI 247
                                   4444444445555555555555554444333..566788889999999********************9999999999999 PP

                        TPR_21 123 llaekkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaaleek 179
                                       ++y++Al+ ++++ +   ++l+   +GDil++ g+ + A +aY++A++ ++++
  gi|15669619|ref|NP_248432.1| 248 F---EEYKKALEYIDKSISIFNRSLYYAKKGDILYKLGDEEGAIEAYNKAIKLNSQN 301
                                   7...78999**********999****************************9877665 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.036
                        TPR_21 127 kkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaaleek 179
                                   k y eA+k +++  + + +++   ++G i+++ g+ ++A + + +Al+ + ++
  gi|15669619|ref|NP_248432.1| 360 KYYHEAMKYVDNLINLENSSRWWYVKGYIYYKLGNYKDAYESFMNALRVNPKD 412
                                   568999999999999999999999**********************9876665 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 4.3
                        TPR_21 156 lvaqgkldeAraaYqaAl 173
                                   l + gk+deA + Y++ l
  gi|15669619|ref|NP_248432.1| 423 LEKSGKIDEAITTYTKIL 440
                                   678899999999998755 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.7   5.8e-06    0.0031     196     253 ..      52     109 ..       8     116 .. 0.87
   2 !    8.7   0.3    0.0013      0.69      13      72 ..     124     184 ..     112     215 .. 0.84
   3 !   21.3   3.1     2e-07   0.00011       2     103 ..     232     332 ..     231     346 .. 0.83
   4 !    6.9   0.0    0.0047       2.6     208     255 ..     362     408 ..     337     438 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.8e-06
                                   HHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                         NARP1 196 yflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeear 253
                                   + lA+   +l++++ Ale i++a++ +p+ + + + K+ i+ + G++  A++ +++a 
  gi|15669619|ref|NP_248432.1|  52 FNLAYALYHLEKYDSALEAINEALKISPSNIYFAYLKGLIHYKRGEIILAYKYLKKAS 109
                                   5578888899******************************************999985 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0013
                                   HHHHHTHHHHHHHH.HHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-C CS
                         NARP1  13 iieeagkleeAleh.LeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpens 72 
                                   i  + g++eeAl+  L++++     +l+ + + ++++l  g+ ++A  +++++l++np ++
  gi|15669619|ref|NP_248432.1| 124 ISVKYGRYEEALKYyLKSYKMANSKNLNALFKAGKIYLLFGDIDKAYDAFNEILQQNPSHE 184
                                   566889******95488999999**********************************9876 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 2e-07
                                   HHHHHHHHHHHHHHH.HTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHH CS
                         NARP1   2 eesellLyknqiiee.agkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyegleka 81 
                                   e+s++  y +++i+e  +++++Ale ++++  +i+++  +  +k+++l kLg++e A ++y++ ++ n++n   y gl   
  gi|15669619|ref|NP_248432.1| 232 ENSDISYYYKSVIAEiFEEYKKALEYIDKS-ISIFNRSLYYAKKGDILYKLGDEEGAIEAYNKAIKLNSQNPYAYFGLAIL 311
                                   78898888888877735999******9975.67999**********************************98777777655 PP

                                   T..SSS-HHHHHHHHHHTTTS- CS
                         NARP1  82 kklskedeeallalydelaeky 103
                                     ++k++ e+  +++d++ e+y
  gi|15669619|ref|NP_248432.1| 312 Y-YRKGELEKSSNFFDKVLETY 332
                                   5.46677888888888877766 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0047
                                   SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                         NARP1 208 rekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                   +++A++y+d+ i+ + ++   +++K+ i+ + G+ k+A+e   +a ++
  gi|15669619|ref|NP_248432.1| 362 YHEAMKYVDNLINLENSS-RWWYVKGYIYYKLGNYKDAYESFMNALRV 408
                                   568999999999998766.57788999999999999999877666555 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.02        11     149     178 ..      17      46 ..       5      49 .. 0.89
   2 !   15.1   0.3   1.8e-05    0.0098     149     246 ..      51     148 ..      45     172 .. 0.77
   3 ?    0.1   0.0      0.69   3.8e+02      17      48 ..     210     240 ..     198     246 .. 0.78
   4 !   18.9   0.0   1.3e-06   0.00068     143     270 ..     298     435 ..     286     444 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.02
                        TPR_15 149 llaraelyrqegqtdaAlrdyreAlalapd 178
                                   ++  a++y++eg  d+A+++y +Al+++ +
  gi|15669619|ref|NP_248432.1|  17 WVTEANYYLDEGIYDKAVECYLKALEKKNT 46 
                                   9999*********************99876 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.8e-05
                        TPR_15 149 llaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara..esdasLwgplaaAlllL 227
                                   ++ +a +     + d Al+++ eAl+ +p   ++  a+l  li ++r +    + k +k+++   ++++L + l+  +++ 
  gi|15669619|ref|NP_248432.1|  51 WFNLAYALYHLEKYDSALEAINEALKISPS--NIYFAYLKGLIHYKRGEI-ILAYKYLKKASekIKNEELFEILGDISVKY 128
                                   5556666666778899*************9..8999*******9998874.33333333333557899************* PP

                        TPR_15 228 grpkkALeylrkqak.enrk 246
                                   gr+++AL+y+ k +k +n+k
  gi|15669619|ref|NP_248432.1| 129 GRYEEALKYYLKSYKmANSK 148
                                   ***********977613444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.69
                        TPR_15  17 llykqgdvkkAlevLkeaaqkaapskdteyWr 48 
                                   ++ k++d+ +Al++ ++ +q     +d  y++
  gi|15669619|ref|NP_248432.1| 210 TMIKNKDYIGALKIFNKVLQID-ENSDISYYY 240
                                   67899**********8776666.688877765 PP

  == domain 4  score: 18.9 bits;  conditional E-value: 1.3e-06
                        TPR_15 143 e.qsaafllaraelyrqegqtdaAlrdyreAlal...apdsselraallWlliDlgrraeLrellkawkara......... 210
                                   + q+++ ++ +a ly ++g+ +++ + + ++l+    +  ++++ a  l+ li   +++     + ++  +a         
  gi|15669619|ref|NP_248432.1| 298 NsQNPYAYFGLAILYYRKGELEKSSNFFDKVLETyleELSEEDISALNLYSLIGKAETTG----IPKYYHEAmkyvdnlin 374
                                   447788888889999999999999999999998622244567888888999996655554....22222222244456678 PP

                        TPR_15 211 .esdasLwgplaaAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAwrl 270
                                    e++++ w + +  + +Lg++k A e + + ++ n+kd++ l + A +le++g+ deA + 
  gi|15669619|ref|NP_248432.1| 375 lENSSRWWYVKGYIYYKLGNYKDAYESFMNALRVNPKDISTLKSLAIVLEKSGKIDEAITT 435
                                   899*******************************************************876 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0       0.2   1.1e+02      22      37 ..      27      42 ..      21      50 .. 0.64
   2 !    7.8   0.4    0.0057       3.1       7      31 ..      53      77 ..      53      78 .. 0.94
   3 ?    4.5   0.0     0.061        33      16      31 ..     129     144 ..     129     146 .. 0.89
   4 ?   -0.4   0.0       2.2   1.2e+03      16      31 ..     215     230 ..     209     233 .. 0.88
   5 ?   -1.5   0.0       4.8   2.6e+03      17      31 ..     250     264 ..     249     269 .. 0.82
   6 ?   -0.6   0.0       2.5   1.3e+03      11      30 ..     277     296 ..     274     299 .. 0.85
   7 !   11.7   0.0   0.00034      0.19       8      37 ..     308     337 ..     307     341 .. 0.92
   8 ?    0.3   0.1       1.3     7e+02       9      21 ..     386     398 ..     386     406 .. 0.92
   9 ?    1.4   0.0      0.59   3.2e+02       4      22 ..     415     433 ..     413     442 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.2
                        TPR_10 22 ealleealairrrllG 37
                                  e ++++a++++ ++l+
  gi|15669619|ref|NP_248432.1| 27 EGIYDKAVECYLKALE 42
                                  4466777777777766 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0057
                        TPR_10  7 NLanalrqrgrydeAealleealai 31
                                  NLa al+++ +yd A++   eal i
  gi|15669619|ref|NP_248432.1| 53 NLAYALYHLEKYDSALEAINEALKI 77
                                  9****************99999987 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.061
                        TPR_10  16 grydeAealleealai 31 
                                   gry+eA++++ +++ +
  gi|15669619|ref|NP_248432.1| 129 GRYEEALKYYLKSYKM 144
                                   8*********999876 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.2
                        TPR_10  16 grydeAealleealai 31 
                                   ++y +A++++ ++l+i
  gi|15669619|ref|NP_248432.1| 215 KDYIGALKIFNKVLQI 230
                                   7899******999997 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 4.8
                        TPR_10  17 rydeAealleealai 31 
                                   +y++A+++ +++++i
  gi|15669619|ref|NP_248432.1| 250 EYKKALEYIDKSISI 264
                                   6899****9999998 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 2.5
                        TPR_10  11 alrqrgrydeAealleeala 30 
                                   +l+++g+ ++A + + +a+ 
  gi|15669619|ref|NP_248432.1| 277 ILYKLGDEEGAIEAYNKAIK 296
                                   79999999999999999986 PP

  == domain 7  score: 11.7 bits;  conditional E-value: 0.00034
                        TPR_10   8 LanalrqrgrydeAealleealairrrllG 37 
                                   La+++++ g+++++ ++++++l+++ + l 
  gi|15669619|ref|NP_248432.1| 308 LAILYYRKGELEKSSNFFDKVLETYLEELS 337
                                   9***********************988886 PP

  == domain 8  score: 0.3 bits;  conditional E-value: 1.3
                        TPR_10   9 analrqrgrydeA 21 
                                   + +++++g+y++A
  gi|15669619|ref|NP_248432.1| 386 GYIYYKLGNYKDA 398
                                   679*******998 PP

  == domain 9  score: 1.4 bits;  conditional E-value: 0.59
                        TPR_10   4 slnNLanalrqrgrydeAe 22 
                                   +l  La++l + g+ deA 
  gi|15669619|ref|NP_248432.1| 415 TLKSLAIVLEKSGKIDEAI 433
                                   5667999999999999996 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.5   1.3e-06   0.00069       5      46 ..      52      93 ..      51      96 .. 0.94
   2 ?    1.4   0.6      0.63   3.4e+02      12      23 ..     126     137 ..     125     141 .. 0.89
   3 ?    4.6   0.0     0.062        34      12      34 ..     212     233 ..     208     237 .. 0.87
   4 ?    2.3   0.1      0.34   1.8e+02      15      26 ..     249     260 ..     239     264 .. 0.87
   5 ?    4.3   0.4     0.078        43       7      29 ..     308     330 ..     303     350 .. 0.91
   6 ?    5.4   0.1     0.035        19      17      32 ..     362     377 ..     360     380 .. 0.87
   7 !    8.7   0.1    0.0033       1.8      11      34 ..     389     412 ..     383     425 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-06
                                  HHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHH CS
                    Fis1_TPR_C  5 YylAlGhyklgeYseArryvdalLeiEPenrQaqsLkelied 46
                                  + lA++ y l +Y+ A++ ++  L+i P+n   + Lk li+ 
  gi|15669619|ref|NP_248432.1| 52 FNLAYALYHLEKYDSALEAINEALKISPSNIYFAYLKGLIHY 93
                                  78****************************999999999985 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.63
                                   HHHT-HHHHHHH CS
                    Fis1_TPR_C  12 yklgeYseArry 23 
                                    k g+Y+eA++y
  gi|15669619|ref|NP_248432.1| 126 VKYGRYEEALKY 137
                                   699********9 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.062
                                   HHHT-HHHHHHHHHHHHHHTTS- CS
                    Fis1_TPR_C  12 yklgeYseArryvdalLeiEPen 34 
                                   +k ++Y  A++  + +L+i+ en
  gi|15669619|ref|NP_248432.1| 212 IKNKDYIGALKIFNKVLQID-EN 233
                                   799****************9.44 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.34
                                   T-HHHHHHHHHH CS
                    Fis1_TPR_C  15 geYseArryvda 26 
                                    eY++A++y+d 
  gi|15669619|ref|NP_248432.1| 249 EEYKKALEYIDK 260
                                   69********97 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.078
                                   HHHHHHHHT-HHHHHHHHHHHHH CS
                    Fis1_TPR_C   7 lAlGhyklgeYseArryvdalLe 29 
                                   lA+ +y+ ge +++ ++ d +Le
  gi|15669619|ref|NP_248432.1| 308 LAILYYRKGELEKSSNFFDKVLE 330
                                   8999****************998 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.035
                                   HHHHHHHHHHHHHHTT CS
                    Fis1_TPR_C  17 YseArryvdalLeiEP 32 
                                   Y eA++yvd l+++E 
  gi|15669619|ref|NP_248432.1| 362 YHEAMKYVDNLINLEN 377
                                   9***********9994 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.0033
                                   HHHHT-HHHHHHHHHHHHHHTTS- CS
                    Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPen 34 
                                   +yklg+Y++A +     L++ P+ 
  gi|15669619|ref|NP_248432.1| 389 YYKLGNYKDAYESFMNALRVNPKD 412
                                   8******************99975 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00067      0.37      37      71 ..      44      78 ..       4      91 .. 0.80
   2 ?    6.3   0.0     0.018       9.8      41      73 ..     150     179 ..     120     200 .. 0.69
   3 ?    2.5   0.2      0.27   1.5e+02      50      71 ..     277     298 ..     207     334 .. 0.61
   4 ?    2.0   0.0      0.41   2.2e+02      50      71 ..     388     409 ..     384     425 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00067
                        ANAPC5 37 kksyqyalLnlaslhadfghneeAvkaleeairlA 71
                                  k++ ++  +nla   +++++++ A++a++ea +++
  gi|15669619|ref|NP_248432.1| 44 KNTNPIDWFNLAYALYHLEKYDSALEAINEALKIS 78
                                  456677789***********************997 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.018
                        ANAPC5  41 qyalLnlaslhadfghneeAvkaleeairlAre 73 
                                     al++   +   fg+ ++A++a++e     ++
  gi|15669619|ref|NP_248432.1| 150 LNALFKAGKIYLLFGDIDKAYDAFNEIL---QQ 179
                                   34799999*****************965...44 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.27
                        ANAPC5  50 lhadfghneeAvkaleeairlA 71 
                                   + +++g++e A++a + ai+l 
  gi|15669619|ref|NP_248432.1| 277 ILYKLGDEEGAIEAYNKAIKLN 298
                                   3445555555555555555554 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.41
                        ANAPC5  50 lhadfghneeAvkaleeairlA 71 
                                   + +++g++++A++++ +a r+ 
  gi|15669619|ref|NP_248432.1| 388 IYYKLGNYKDAYESFMNALRVN 409
                                   57899*************9984 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.12        64      13      51 ..      39      77 ..      28      81 .. 0.86
   2 ?    7.2   0.0     0.012       6.4      17      55 ..     145     183 ..     133     201 .. 0.90
   3 ?    4.0   0.0      0.11        62       6      43 ..     286     323 ..     283     339 .. 0.87
   4 ?    6.5   0.0     0.019        11       9      50 ..     400     441 ..     394     447 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.12
                        TPR_20 13 aalaanpddldarldlAlallaagryeeAleqLleilkr 51
                                  +al+++ ++    ++lA al++ ++y+ Ale++ e lk 
  gi|15669619|ref|NP_248432.1| 39 KALEKKNTNPIDWFNLAYALYHLEKYDSALEAINEALKI 77
                                  6778888888889*******************9999885 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                        TPR_20  17 anpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                   an ++l+a ++  + +l  g+ ++A +++ eil+++ + 
  gi|15669619|ref|NP_248432.1| 145 ANSKNLNALFKAGKIYLLFGDIDKAYDAFNEILQQNPSH 183
                                   7899******************************99765 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.11
                        TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAle 43 
                                     +++  +a++ n ++  a + lA +++ +g+ e++ +
  gi|15669619|ref|NP_248432.1| 286 GAIEAYNKAIKLNSQNPYAYFGLAILYYRKGELEKSSN 323
                                   57899999************************998755 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.019
                        TPR_20   9 aeleaalaanpddldarldlAlallaagryeeAleqLleilk 50 
                                   +++ +al  np+d+ +   lA +l + g+ +eA++   +ilk
  gi|15669619|ref|NP_248432.1| 400 ESFMNALRVNPKDISTLKSLAIVLEKSGKIDEAITTYTKILK 441
                                   667789999*************************99988887 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.069        38     239     265 ..      47      73 ..      11      78 .. 0.78
   2 !    6.4   0.0    0.0089       4.8      45     117 ..     120     187 ..      85     197 .. 0.84
   3 ?    5.4   0.0     0.019        10     123     190 ..     269     331 ..     248     346 .. 0.75
   4 ?    2.9   0.0      0.11        57      45     110 ..     384     443 ..     362     448 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.069
                      TPR_MalT 239 lelelrnlarvllalgrydeAleller 265
                                   + +++ nla++l++l +yd+Ale +++
  gi|15669619|ref|NP_248432.1|  47 NPIDWFNLAYALYHLEKYDSALEAINE 73 
                                   456788999999999999999887765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0089
                      TPR_MalT  45 vlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqq 117
                                   +lG +s+  G+ e+Al+ + + +k+a + ++l+    al + ++i+   G+ ++A++ ++++lq+ + ++ ++
  gi|15669619|ref|NP_248432.1| 120 ILGDISVKYGRYEEALKYYLKSYKMA-NSKNLN----ALFKAGKIYLLFGDIDKAYDAFNEILQQNPSHECKK 187
                                   68899999999999999999999999.555555....788899999999999999999999999888777664 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.019
                      TPR_MalT 123 fllvlladllyEwndLeeAeqhlqeGielleqlepeaaldayvllarialaqGdleeAetllekaeel 190
                                   +++++ +d+ly  +d e+A ++ +++i+l  q        ay  la +++ +G+le++ + ++k  e+
  gi|15669619|ref|NP_248432.1| 269 LYYAKKGDILYKLGDEEGAIEAYNKAIKLNSQN-----PYAYFGLAILYYRKGELEKSSNFFDKVLET 331
                                   577788888888888888888888888887776.....457888888888888888888888776665 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.11
                      TPR_MalT  45 vlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqla 110
                                   v G+++   G+ ++A ++++ a ++          + +l ++a +l + G+ +eA+ ty+++l+ +
  gi|15669619|ref|NP_248432.1| 384 VKGYIYYKLGNYKDAYESFMNALRVN----PK--DISTLKSLAIVLEKSGKIDEAITTYTKILKIV 443
                                   55677777777777777776666654....22..24455667888999999*******99999876 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.6     7e-06    0.0038      34     103 ..      38     110 ..      28     121 .. 0.74
   2 ?    3.0   2.7      0.18        98      25      93 ..     126     204 ..     118     226 .. 0.59
   3 ?    0.7   9.2      0.96   5.2e+02       5      71 ..     224     294 ..     213     349 .. 0.62
   4 !   16.5   0.4   1.2e-05    0.0063      30      70 ..     362     404 ..     356     448 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7e-06
                  SRP_TPR_like  34 LkllkkgsalsedvrfEkaYvlYklkkykkalkilkkv...eaee.kvkvlksqvlYrlgsyekAYklL...skekk 103
                                   Lk+l+k++ ++    f  aY+lY+l+ky  al+ ++++   + ++     lk  + Y  g+   AYk+L   s   +
  gi|15669619|ref|NP_248432.1|  38 LKALEKKN-TNPIDWFNLAYALYHLEKYDSALEAINEAlkiSPSNiYFAYLKGLIHYKRGEIILAYKYLkkaS---E 110
                                   66677776.6667789*****************999761114444567789******************5532...2 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.18
                  SRP_TPR_like  25 iklekyeeaLkllkkgs......alsedvrfEkaYvlYkl..kkykkalkilkkveaee..kvkvlksqvlYrlgsyek 93 
                                   +k ++yeeaLk+  k        +l+   +  k Y l+    k y +  +il++  ++e  k+ +    v+  ++sye+
  gi|15669619|ref|NP_248432.1| 126 VKYGRYEEALKYYLKSYkmanskNLNALFKAGKIYLLFGDidKAYDAFNEILQQNPSHEckKIVECMENVVNAINSYED 204
                                   67899******99888733333333333444455555531224455555666666665533333444455555555555 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.96
                  SRP_TPR_like   5 yekilrlegke.lkkf.kvvaliklekyeeaLkllkkgs.alsedvrf.EkaYvlYklkkykkalkilkkv 71 
                                   ++k+l+++++  ++ + k v     e y+ aL++++k     + ++ +  k  +lYkl   + a +  +k+
  gi|15669619|ref|NP_248432.1| 224 FNKVLQIDENSdISYYyKSVIAEIFEEYKKALEYIDKSIsIFNRSLYYaKKGDILYKLGDEEGAIEAYNKA 294
                                   677777765431333355444445899********998624566666634678999998877776655543 PP

  == domain 4  score: 16.5 bits;  conditional E-value: 1.2e-05
                  SRP_TPR_like  30 yeeaLkllkkgsal..sedvrfEkaYvlYklkkykkalkilkk 70 
                                   y+ea+k++++  +l  s+   + k Y++Ykl +yk+a + + +
  gi|15669619|ref|NP_248432.1| 362 YHEAMKYVDNLINLenSSRWWYVKGYIYYKLGNYKDAYESFMN 404
                                   889999999877551145567999**********999876554 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.27   1.4e+02      62     106 ..      33      77 ..      29      79 .. 0.93
   2 !   11.7   0.0   0.00035      0.19       4      53 ..     210     259 ..     208     296 .. 0.83
   3 ?    5.1   0.1     0.041        22      11      48 ..     251     284 ..     249     377 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.27
                        DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakraLsv 106
                                   +vec+ +a e +       f+la  l    +Y  a++  ++aL++
  gi|15669619|ref|NP_248432.1|  33 AVECYLKALEKKNTNPIDWFNLAYALYHLEKYDSALEAINEALKI 77 
                                   89************************9999********9999988 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00035
                        DUF627   4 dllargnhikALeiiedlisrhgedeksallhrlqGtifvklakktedpd 53 
                                   ++++++++i AL+i++++++  ++++ s   + + ++if ++ k +e  d
  gi|15669619|ref|NP_248432.1| 210 TMIKNKDYIGALKIFNKVLQIDENSDISYYYKSVIAEIFEEYKKALEYID 259
                                   57899**********************************99998877555 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.041
                        DUF627  11 hikALeiiedlisrhgedeksallhrlqGtifvklakk 48 
                                   + kALe i+++is  ++    +l   ++G+i++kl ++
  gi|15669619|ref|NP_248432.1| 251 YKKALEYIDKSISIFNR----SLYYAKKGDILYKLGDE 284
                                   78999999999988877....57888899999998765 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.046        25     190     263 ..       4      76 ..       2      88 .. 0.75
   2 ?    0.4   0.0      0.64   3.5e+02      94     131 ..     108     144 ..      86     212 .. 0.65
   3 !    8.5   0.0    0.0022       1.2     213     263 ..     391     441 ..     385     453 .. 0.90
   4 ?   -0.6   0.0       1.3     7e+02      42      91 ..     512     558 ..     470     562 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.046
                                   HHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHHHHHH CS
                    Coatomer_E 190 fqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernlsqlk 263
                                   f  +sek ks  +  + +A   l  g y++A +   +aL+k++ ++    Nl  a  hl+k + + e   + lk
  gi|15669619|ref|NP_248432.1|   4 FRKISEKLKSYEDWVT-EANYYLDEGIYDKAVECYLKALEKKNTNPIDWFNLAYALYHLEKYDSALEAINEALK 76 
                                   5566666666555544.56777888999******************999**********999766555444444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.64
                                   HS----S-HHHHHHHHHHHHHTT-HHHHHHHHTT--SH CS
                    Coatomer_E  94 adseiesnevlrllaaivflkegdfddalkllkksenL 131
                                   a+++i+++e +++l+  + +k g +++alk   ks ++
  gi|15669619|ref|NP_248432.1| 108 ASEKIKNEELFEILGD-ISVKYGRYEEALKYYLKSYKM 144
                                   6677777777777754.577888888988877666555 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0022
                                   HTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHHHHHH CS
                    Coatomer_E 213 llgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernlsqlk 263
                                   +lg+y++A ++  +aL  ++kd  tL  l ++ ++ gk +e+++ + + lk
  gi|15669619|ref|NP_248432.1| 391 KLGNYKDAYESFMNALRVNPKDISTLKSLAIVLEKSGKIDEAITTYTKILK 441
                                   689***************************************998877666 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.3
                                   HHHHHHTT-HHHHHHHS-TTS-HHHHHHHHHHHHHH-STTHHHHHHHHHH CS
                    Coatomer_E  42 yrsylAlgsaqiviseIkesaatelqAvrllaeylnspsrkeeilaelke 91 
                                     sy+ l++    +++Ik++ + e+    ++ e ++  ++ e++l ++ke
  gi|15669619|ref|NP_248432.1| 512 IESYISLDEISQMVNDIKSKLSLEM---YRYCELIDDYKSDESVLMQIKE 558
                                   4689999999999999976655443...2333444444445566666665 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.1     0.012       6.6      58      83 ..      51      76 ..      11     155 .. 0.81
   2 ?    1.4   0.0      0.56     3e+02      69      87 ..     249     267 ..     237     301 .. 0.75
   3 ?    2.1   0.1      0.35   1.9e+02     100     129 ..     413     442 ..     384     447 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                                  HHHHHHHHHHTT-HHHHHHHHHHHHH CS
                       DUF3856 58 haglsealaklgrydealesadkalr 83
                                  +  l+ al +l +yd+ale++++al+
  gi|15669619|ref|NP_248432.1| 51 WFNLAYALYHLEKYDSALEAINEALK 76
                                  4579999****************997 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.56
                                   T-HHHHHHHHHHHHHHHHH CS
                       DUF3856  69 grydealesadkalryfnr 87 
                                    +y++ale +dk++  fnr
  gi|15669619|ref|NP_248432.1| 249 EEYKKALEYIDKSISIFNR 267
                                   5677888888888888877 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.35
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                       DUF3856 100 iaavfsravaleelGrkdealkafrmagem 129
                                   i+++ s a  le+ G+ dea+ ++ ++  +
  gi|15669619|ref|NP_248432.1| 413 ISTLKSLAIVLEKSGKIDEAITTYTKILKI 442
                                   556666777788888888888887776655 PP

>> DUF247  Plant protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.9     1e+03     330     366 ..     166     205 ..     145     264 .. 0.64
   2 ?   14.1   0.2   3.8e-05     0.021     279     364 ..     370     463 ..     361     498 .. 0.79
   3 ?   -3.1   0.0       6.4   3.5e+03     331     366 ..     519     549 ..     512     559 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.9
                        DUF247 330 deevaklfnklckgvvfdeddsy......lskvieklnkyyrs 366
                                    +++ + fn++ ++ + +e   +      +++v++++n+y + 
  gi|15669619|ref|NP_248432.1| 166 IDKAYDAFNEILQQNPSHE---CkkivecMENVVNAINSYEDL 205
                                   5556666666655433311...111234466666666666543 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.8e-05
                        DUF247 279 rNliAlEqchs..........egpeelvvtsYvvfmdqLidtaeDvelLrekgiienrlgsdeevaklfnklckgvvfded 349
                                    Nli lE ++           +     +  +Y +fm+ L  +++D+ +L++  i+ ++ g+ +e+ + ++k+ k v   + 
  gi|15669619|ref|NP_248432.1| 370 DNLINLENSSRwwyvkgyiyyK--LGNYKDAYESFMNALRVNPKDISTLKSLAIVLEKSGKIDEAITTYTKILKIVNSLQF 448
                                   6888888888888888766442..3345779*****************************999***999999985544333 PP

                        DUF247 350 dsy.lskvieklnkyy 364
                                   + + +++++ekl++++
  gi|15669619|ref|NP_248432.1| 449 T-CeIDNILEKLRSRK 463
                                   3.35999999998877 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 6.4
                        DUF247 331 eevaklfnklckgvvfdeddsylskvieklnkyyrs 366
                                   +e+++++n++++++++     ++++ +e +++y+++
  gi|15669619|ref|NP_248432.1| 519 DEISQMVNDIKSKLSL-----EMYRYCELIDDYKSD 549
                                   5888999999988766.....466777777777654 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.013       7.3      62      92 ..      85     115 ..      80     122 .. 0.86
   2 ?    2.8   0.0      0.24   1.3e+02      68     100 ..     124     156 ..     119     158 .. 0.90
   3 ?    0.2   0.0       1.6   8.8e+02      59      96 ..     201     238 ..     199     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                        HemY_N  62 alseGlialaeGdfarAekaaakaaklseap 92 
                                   a ++Gli++  G+   A k ++ka+++ +++
  gi|15669619|ref|NP_248432.1|  85 AYLKGLIHYKRGEIILAYKYLKKASEKIKNE 115
                                   6789*********************998874 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.24
                        HemY_N  68 ialaeGdfarAekaaakaaklseapllayllaA 100
                                   i++  G++++A k   k+ k+++++ l++l +A
  gi|15669619|ref|NP_248432.1| 124 ISVKYGRYEEALKYYLKSYKMANSKNLNALFKA 156
                                   67888*******************99**99987 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.6
                        HemY_N  59 arealseGlialaeGdfarAekaaakaaklseapllay 96 
                                   ++e l++Gl+ + + d+  A k ++k ++ +e++ + y
  gi|15669619|ref|NP_248432.1| 201 SYEDLNNGLTMIKNKDYIGALKIFNKVLQIDENSDISY 238
                                   57899******************999998887765655 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.3       2.5   1.4e+03      17      36 .]      30      45 ..      22      45 .. 0.72
   2 ?   10.8   0.5   0.00069      0.38       3      23 ..      50      70 ..      50      71 .. 0.95
   3 ?    0.2   0.6       1.5   7.9e+02      15      26 ..     129     138 ..     128     146 .. 0.84
   4 ?    2.5   0.1      0.29   1.6e+02      15      24 ..     164     173 ..     150     177 .. 0.81
   5 ?   -1.6   0.1       5.5     3e+03      12      32 ..     279     297 ..     277     301 .. 0.60
   6 ?    4.1   0.5     0.091        49       5      33 ..     306     333 ..     303     336 .. 0.84
   7 ?    5.6   0.6     0.029        16       8      23 ..     386     401 ..     382     406 .. 0.88
   8 ?    5.7   0.0     0.027        14       4      26 ..     416     436 ..     415     438 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.5
                                  HHHHHHH..HHHHHHH-TT- CS
                         TPR_3 17 yqeArelfsYallaildken 36
                                  y++A+e     +l +l+k+n
  gi|15669619|ref|NP_248432.1| 30 YDKAVEC----YLKALEKKN 45
                                  8888888....556666655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00069
                                  HHHHHHHHHHHTT-HHHHHHH CS
                         TPR_3  3 ylysyAaefynkkkyqeArel 23
                                  +++ +A+++y  +ky+ A+e+
  gi|15669619|ref|NP_248432.1| 50 DWFNLAYALYHLEKYDSALEA 70
                                  79****************986 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.5
                                   T-HHHHHHH..H CS
                         TPR_3  15 kkyqeArelfsY 26 
                                   ++y+eA+ +  Y
  gi|15669619|ref|NP_248432.1| 129 GRYEEALKY--Y 138
                                   89*******..5 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.29
                                   T-HHHHHHH. CS
                         TPR_3  15 kkyqeArelf 24 
                                   +++++A+++f
  gi|15669619|ref|NP_248432.1| 164 GDIDKAYDAF 173
                                   9*******97 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 5.5
                                   HHTT-HHHHHHH..HHHHHHH CS
                         TPR_3  12 ynkkkyqeArelfsYallail 32 
                                   y  ++ + A+e+  Y  + +l
  gi|15669619|ref|NP_248432.1| 279 YKLGDEEGAIEA--YNKAIKL 297
                                   566666778888..5455555 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.091
                                   HHHHHHHHHTT-HHHHHHH..HHHHHHH- CS
                         TPR_3   5 ysyAaefynkkkyqeArelfsYallaild 33 
                                   +++A  +y k+++++  ++f+ ++l ++ 
  gi|15669619|ref|NP_248432.1| 306 FGLAILYYRKGELEKSSNFFD-KVLETYL 333
                                   678************999999.8886665 PP

  == domain 7  score: 5.6 bits;  conditional E-value: 0.029
                                   HHHHHHTT-HHHHHHH CS
                         TPR_3   8 AaefynkkkyqeArel 23 
                                   ++ +y  ++y +A+e 
  gi|15669619|ref|NP_248432.1| 386 GYIYYKLGNYKDAYES 401
                                   89************96 PP

  == domain 8  score: 5.7 bits;  conditional E-value: 0.027
                                   HHHHHHHHHHTT-HHHHHHH..H CS
                         TPR_3   4 lysyAaefynkkkyqeArelfsY 26 
                                   l+s+A ++  ++k++eA+ +  Y
  gi|15669619|ref|NP_248432.1| 416 LKSLAIVLEKSGKIDEAITT--Y 436
                                   7899999999*********9..5 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       5.6   3.1e+03      15      30 ..      62      77 ..      62      77 .. 0.86
   2 ?    8.7   0.0    0.0022       1.2       3      22 ..     117     136 ..     116     141 .. 0.86
   3 ?   -0.9   0.0       2.1   1.1e+03      22      30 ..     249     257 ..     248     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.6
                      SHNi-TPR 15 enFpqAveDlrkaLeL 30
                                  e+++ A+e  ++aL++
  gi|15669619|ref|NP_248432.1| 62 EKYDSALEAINEALKI 77
                                  8999999999999987 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0022
                      SHNi-TPR   3 vydlLGEislEnenFpqAve 22 
                                    ++ LG+is+  +++++A++
  gi|15669619|ref|NP_248432.1| 117 LFEILGDISVKYGRYEEALK 136
                                   5789**************98 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.1
                      SHNi-TPR  22 eDlrkaLeL 30 
                                   e+++kaLe+
  gi|15669619|ref|NP_248432.1| 249 EEYKKALEY 257
                                   89*****95 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.5     0.034        18       8      32 ..      18      42 ..      16      43 .. 0.86
   2 ?    2.8   0.2      0.23   1.2e+02      24      41 ..      61      80 ..      61     114 .. 0.77
   3 ?    1.9   1.5      0.43   2.3e+02      18      30 ..     129     141 ..     127     144 .. 0.85
   4 ?    3.0   0.3      0.19     1e+02      27      64 ..     217     259 ..     215     260 .. 0.74
   5 ?    1.7   0.2       0.5   2.7e+02      24      38 ..     248     262 ..     240     275 .. 0.77
   6 ?    2.8   0.2      0.22   1.2e+02      18      33 ..     282     297 ..     271     300 .. 0.89
   7 ?   -2.2   0.1       8.6   4.7e+03      25      41 ..     360     377 ..     360     380 .. 0.75
   8 ?    4.7   0.0     0.058        31      18      39 ..     393     407 ..     391     419 .. 0.56
   9 ?    5.6   0.0      0.03        16       9      29 ..     418     438 ..     414     442 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.034
                           MIT  8 vkkAveeDnagnyeeAlelYkeale 32
                                  v++A  +  +g y++A+e+Y +ale
  gi|15669619|ref|NP_248432.1| 18 VTEANYYLDEGIYDKAVECYLKALE 42
                                  677777888999***********98 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.23
                           MIT 24 lelYkealelLlqalk.e.k 41
                                  le+Y +ale +++alk   +
  gi|15669619|ref|NP_248432.1| 61 LEKYDSALEAINEALKiSpS 80
                                  689**********9995444 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.43
                           MIT  18 gnyeeAlelYkea 30 
                                   g yeeAl++Y ++
  gi|15669619|ref|NP_248432.1| 129 GRYEEALKYYLKS 141
                                   78********876 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.19
                           MIT  27 YkealelLlqalk.ekne....errellrekieeYleRaeeLk 64 
                                   Y  al++++++l+  +n+      +  + e  eeY +  e++ 
  gi|15669619|ref|NP_248432.1| 217 YIGALKIFNKVLQiDENSdisyYYKSVIAEIFEEYKKALEYID 259
                                   7778999999999743333666668888888888888888875 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.5
                           MIT  24 lelYkealelLlqal 38 
                                   +e Yk+ale++ + +
  gi|15669619|ref|NP_248432.1| 248 FEEYKKALEYIDKSI 262
                                   567888888887765 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.22
                           MIT  18 gnyeeAlelYkealel 33 
                                   g+ e A+e+Y +a++l
  gi|15669619|ref|NP_248432.1| 282 GDEEGAIEAYNKAIKL 297
                                   78899********986 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 8.6
                           MIT  25 elYkealelLlqalk.ek 41 
                                   ++Y ea+++   +++ e+
  gi|15669619|ref|NP_248432.1| 360 KYYHEAMKYVDNLINlEN 377
                                   589999999999988553 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.058
                           MIT  18 gnyeeAlelYkealelLlqalk 39 
                                   gn       Yk+a e ++ al+
  gi|15669619|ref|NP_248432.1| 393 GN-------YKDAYESFMNALR 407
                                   44.......5555555555554 PP

  == domain 9  score: 5.6 bits;  conditional E-value: 0.03
                           MIT   9 kkAveeDnagnyeeAlelYke 29 
                                   + A+ ++++g+++eA+  Y++
  gi|15669619|ref|NP_248432.1| 418 SLAIVLEKSGKIDEAITTYTK 438
                                   5699***************86 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   0.00031      0.17       1      37 [.      63     100 ..      63     115 .. 0.78
   2 ?   -1.3   0.2       3.1   1.7e+03       1      11 [.     130     140 ..     130     149 .. 0.80
   3 ?    3.7   2.6     0.086        47       1      47 [.     250     289 ..     250     291 .. 0.69
   4 ?    4.8   0.8      0.04        22       5      45 ..     287     327 ..     285     332 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                                   -HHHHHHHHHHHHHHHHHTTB-TTH.HHHHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAieiSirinsMsLl.GQLyYqkgecle 37 
                                   +Y++aLe +n A++iS  +   + l G + Y +ge + 
  gi|15669619|ref|NP_248432.1|  63 KYDSALEAINEALKISPSNIYFAYLkGLIHYKRGEIIL 100
                                   6***************8777776554999*****9874 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.1
                                   -HHHHHHHHHH CS
                      HTH_Bact   1 rYeeaLeqvnk 11 
                                   rYeeaL++  k
  gi|15669619|ref|NP_248432.1| 130 RYEEALKYYLK 140
                                   7*****99766 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.086
                                   -HHHHHHHHHHHHHHHHHTTB-TTHHHHHH.HHHHHHHHTT--HHHHH CS
                      HTH_Bact   1 rYeeaLeqvnkAieiSirinsMsLlGQLyY.qkgecleklgfseeeIk 47 
                                   +Y +aLe+++k i   i + s      LyY  kg+ l klg +e  I+
  gi|15669619|ref|NP_248432.1| 250 EYKKALEYIDKSIS--IFNRS------LYYaKKGDILYKLGDEEGAIE 289
                                   59999999999874..44444......566356888888887777765 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.04
                                   HHHHHHHHHHHHHHTTB-TT.HHHHHHHHHHHHHHTT--HHH CS
                      HTH_Bact   5 aLeqvnkAieiSirinsMsL.lGQLyYqkgecleklgfseee 45 
                                   a+e  nkAi++  ++    + l  LyY kge lek  + ++ 
  gi|15669619|ref|NP_248432.1| 287 AIEAYNKAIKLNSQNPYAYFgLAILYYRKGE-LEKSSNFFDK 327
                                   778888888887655443333557*******.5666655555 PP

>> Leptin  Leptin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.009       4.9      47      90 ..     160     203 ..     148     238 .. 0.80
   2 ?    3.0   0.1      0.15        82      49      83 ..     425     460 ..     412     462 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.009
                                   -SSHHHHHHHHHHHHHHHHTS--HHHHHHHHHHHHHHHHHHHHH CS
                        Leptin  47 leslskmdqtLavyqqilsslpseevvqisnDlenLrallklla 90 
                                   ++ ++++d+  + +++il + ps+e ++i + +en+ + +++  
  gi|15669619|ref|NP_248432.1| 160 YLLFGDIDKAYDAFNEILQQNPSHECKKIVECMENVVNAINSYE 203
                                   667899*****************************988777655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.15
                                   SHHHHHHHHHHHHHHHHTS--.HHHHHHHHHHHHHH CS
                        Leptin  49 slskmdqtLavyqqilsslps.eevvqisnDlenLr 83 
                                     +k+d+ +++y +il  + s + +  i n le Lr
  gi|15669619|ref|NP_248432.1| 425 KSGKIDEAITTYTKILKIVNSlQFTCEIDNILEKLR 460
                                   5579************99887355667888888887 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.5    0.0082       4.5     134     176 ..      23      63 ..       4      81 .. 0.84
   2 ?    6.3   1.4     0.013       7.1     151     199 ..     101     149 ..      97     162 .. 0.87
   3 ?    1.5   2.0      0.38   2.1e+02     141     196 ..     244     299 ..     165     304 .. 0.75
   4 ?    5.0   5.0     0.032        17     107     194 ..     291     408 ..     287     463 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0082
                       DUF2225 134 eekeklflkkAlelykeayekesfpvegideatvlYLiaeLer 176
                                    +  +  + kA+e+y +a+ek+++  ++id ++++Y ++ Le+
  gi|15669619|ref|NP_248432.1|  23 YYLDEGIYDKAVECYLKALEKKNT--NPIDWFNLAYALYHLEK 63 
                                   566777899**********99988..99********9999984 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                       DUF2225 151 ayekesfpvegideatvlYLiaeLerrlgnkeealrwlskvigskkask 199
                                   ay+  ++ +e+i++ ++  ++++ + ++g++eeal+++ k +++ ++++
  gi|15669619|ref|NP_248432.1| 101 AYKYLKKASEKIKNEELFEILGDISVKYGRYEEALKYYLKSYKMANSKN 149
                                   6777788899999999***********************9999999887 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.38
                       DUF2225 141 lkkAlelykeayekesfpvegideatvlYLiaeLerrlgnkeealrwlskvigskk 196
                                   + +  e yk+a+e  ++++++ +++      ++  ++lg++e a+++++k i+ ++
  gi|15669619|ref|NP_248432.1| 244 IAEIFEEYKKALEYIDKSISIFNRSLYYAKKGDILYKLGDEEGAIEAYNKAIKLNS 299
                                   44456778888888888887777766666678889999999999999888887765 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.032
                       DUF2225 107 yelkkekkskkAklalrlAWlyrdkedeekeklflkkAlelykeayekesfpvegideat..................... 166
                                   y+   + +s+  + +  lA ly  k++ ek+ +f  k le+y e +++e+ +  ++   +                     
  gi|15669619|ref|NP_248432.1| 291 YNKAIKLNSQNPYAYFGLAILYYRKGELEKSSNFFDKVLETYLEELSEEDISALNLY--Sligkaettgipkyyheamkyv 369
                                   555555666777888889999999999999999********9999999988544444..4447888889999999999999 PP

                       DUF2225 167 ...........vlYLiaeLerrlgnkeealrwlskvigs 194
                                                Y  ++  ++lgn+++a + + + ++ 
  gi|15669619|ref|NP_248432.1| 370 dnlinlenssrWWYVKGYIYYKLGNYKDAYESFMNALRV 408
                                   999999999999999999999999999888888776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.87u 0.33s 00:00:01.20 Elapsed: 00:00:00.57
# Mc/sec: 3001.55
//
Query:       gi|15669620|ref|NP_248433.1|  [L=503]
Description: hypothetical protein MJ_1429 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-49  166.7   0.3    1.5e-48  165.9   0.3    1.4  1  DUF87          Helicase HerA, central domain
    1.1e-07   30.9   0.1    0.00021   20.0   0.0    2.3  2  DUF853         Bacterial protein of unknown function (DUF853)
    2.7e-07   29.8   0.0    1.4e-05   24.2   0.0    2.4  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    1.7e-06   28.1   4.0    1.7e-06   28.1   4.0    2.4  3  HAS-barrel     HAS barrel domain
    0.00032   19.8   0.0      0.033   13.1   0.0    2.4  2  AAA_10         AAA-like domain
  ------ inclusion threshold ------
      0.013   15.6   1.6      0.033   14.2   0.0    2.5  2  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.9   0.3   4.9e-52   1.5e-48       2     226 ..     100     325 ..      99     326 .. 0.98

  Alignments for each domain:
  == domain 1  score: 165.9 bits;  conditional E-value: 4.9e-52
                         DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitps 82 
                                   +iG+ll++++v+vyld nklv+rH+Ail  TG GKSnt++vL++el+ kk++t++++DpHGEY +++++ +++k+kvi+p 
  gi|15669620|ref|NP_248433.1| 100 NIGHLLTRDNVRVYLDTNKLVSRHFAILSITGGGKSNTASVLCRELA-KKNGTVIMIDPHGEYISLYHEDMEGKIKVINP- 178
                                   79*********************************************.********************************. PP

                         DUF87  83 psakdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdepveklleelk............ 151
                                            inp +l p e+++l+++   +++ ++r ++e a++++k  +e  ++++ e++ek+++ l+            
  gi|15669620|ref|NP_248433.1| 179 --------IINPVLLAPSEFANLIGI--GDNEIEKRVYVEFAYHTVK--HECPDAKGIEFIEKIENLLYewskiasvgwei 247
                                   ........9*****************..8898889************..******************************** PP

                         DUF87 152 .........kekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlvvsvi 223
                                            + +++l+k++  + ++l+d+++++++++++    + d+i++      + gki+i++lsg++  ++ ++v++i
  gi|15669620|ref|NP_248433.1| 248 kyynplrrnYDRRKLEKEDFVILMSLIDTISKFKLDYALN-IGDRDVIEEF-----EIGKINIVNLSGLEIPQMVTFVGFI 322
                                   ********88888***************************.9*********.....************************* PP

                         DUF87 224 lrr 226
                                    ++
  gi|15669620|ref|NP_248433.1| 323 AKH 325
                                   987 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00022      0.66      16      63 ..     116     163 ..     103     175 .. 0.85
   2 !   20.0   0.0     7e-08   0.00021     256     362 ..     367     467 ..     364     480 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00022
                        DUF853  16 alklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsg 63 
                                   + kl+ rh  i   tG Gk  t  vl+ +l++   +v++ d  G+  +
  gi|15669620|ref|NP_248433.1| 116 TNKLVSRHFAILSITGGGKSNTASVLCRELAKKNGTVIMIDPHGEYIS 163
                                   457899***********************************9998665 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 7e-08
                        DUF853 256 kPklvfffdeahLLf..ndapkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavka 334
                                   kP l +  +eah++   n+  ++    + ++ r  r  GvG+ +v+q P  l  +vL+q  +++   l+   p+dqk ++ 
  gi|15669620|ref|NP_248433.1| 367 KPVL-LIVEEAHIFIpvNE-QNSASLWLGKIAREGRKFGVGLGLVSQRPKQLHPDVLSQTNTKI--ILKIVEPEDQKYIQR 443
                                   5655.45688887752222.22333357788899999***********************9999..5999*********** PP

                        DUF853 335 aadtfranpefdveeaiteLgvGealvs 362
                                   a++ + +    d+ + + +Lg+Gea++ 
  gi|15669620|ref|NP_248433.1| 444 ASEELGE----DLVKDLASLGIGEAVIV 467
                                   *998865....7889999*******984 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   4.7e-09   1.4e-05      13      70 ..     119     178 ..     114     183 .. 0.86
   2 ?    2.8   0.0     0.014        43     263     327 ..     394     453 ..     391     463 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.7e-09
                 TrwB_AAD_bind  13 retqhilivGttGsGKtqalekllrairargdraivlDltGafvsrfydegk..dillnP 70 
                                      +h++i+  tG GK+++++ l r++ +++ ++i +D++G+++s ++++ +    ++nP
  gi|15669620|ref|NP_248433.1| 119 LVSRHFAILSITGGGKSNTASVLCRELAKKNGTVIMIDPHGEYISLYHEDMEgkIKVINP 178
                                   5689********************************************976521345666 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.014
                 TrwB_AAD_bind 263 sllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilr...vsdaetAeelsellGeqev 327
                                   +++ egRkfG+ + l  q  +ql+          +ls +ntk+il+    +d++  +++se lGe  v
  gi|15669620|ref|NP_248433.1| 394 KIAREGRKFGVGLGLVSQRPKQLHP--------DVLSQTNTKIILKivePEDQKYIQRASEELGEDLV 453
                                   5667788888888888888888862........35566666666663224577777778888887655 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   4.0   5.8e-10   1.7e-06       1      91 [.       3      64 ..       3      65 .. 0.89
   2 ?   -2.4   0.1       1.9   5.7e+03      40      80 ..     341     367 ..     329     376 .. 0.58
   3 ?   -3.7   0.0       4.5   1.3e+04      16      31 ..     452     467 ..     440     468 .. 0.67

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 5.8e-10
                    HAS-barrel  1 iGevigestssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalatedtg 83
                                  + +v+g +t + ++f + +  ++++GeyV++++ dg+ vlG++ ++++                       d e +++ +   
  gi|15669620|ref|NP_248433.1|  3 VMKVVGKTTTTHFTFESLE--KIRFGEYVIAKNVDGRDVLGVIKNVVA-----------------------DVEKFVGEV--- 57
                                  57899****9777776666..9**************************.......................999999999... PP

                    HAS-barrel 84 vkvlGeve 91
                                   kv+G ++
  gi|15669620|ref|NP_248433.1| 58 -KVIGVLD 64
                                  .9999876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.9
                    HAS-barrel  40 lGmvtdirrgnselsndlalvlsleeleeangddevalate 80 
                                   +              ++ ++++++ ++  ++ ++ ++++t 
  gi|15669620|ref|NP_248433.1| 341 Y--------------SINEEIRRVAQSNLNIIESHYKVVTK 367
                                   3..............33344445666666666666666665 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.5
                    HAS-barrel  16 rvegskdvkvGeyVei 31 
                                    v+ ++ +++Ge V++
  gi|15669620|ref|NP_248433.1| 452 LVKDLASLGIGEAVIV 467
                                   4566668888888875 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   1.1e-05     0.033      18      78 ..     118     176 ..     108     195 .. 0.78
   2 !    3.9   0.0    0.0067        20     243     290 ..     370     420 ..     282     442 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                        AAA_10  18 ktnasasliiGdlGnGKSvlakllvlyisllggkaliiDpkke.rekfketlpeiakkinvv 78 
                                   k  + + +i+  +G+GKS +a +l   ++  +g +++iDp  e    + e +    +ki+v+
  gi|15669620|ref|NP_248433.1| 118 KLVSRHFAILSITGGGKSNTASVLCRELAKKNGTVIMIDPHGEyISLYHEDM---EGKIKVI 176
                                   55577899999********************************333344444...2344444 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0067
                        AAA_10 243 vvifDEawiftssaeGkk..l.lkelvRiGRsynaavylvtqsadDvlkee 290
                                     i+ Ea if  ++e +   l l ++ R GR++   + lv+q ++ + ++ 
  gi|15669620|ref|NP_248433.1| 370 LLIVEEAHIFIPVNEQNSasLwLGKIAREGRKFGVGLGLVSQRPKQLHPDV 420
                                   347889999988777554113257899***************999876654 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   1.4       1.5   4.5e+03      79     110 ..      29      61 ..       8      74 .. 0.60
   2 ?   14.2   0.0   1.1e-05     0.033       2      55 ..     125     232 ..     124     375 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                                   EEEEEESS...-TTCHHHHHHHHHHC..TS-EEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                          CbiA  79 vvlnrvdgeneetllkealeelkqry..gvpvlg 110
                                   v++  vdg++    +k+ ++++++ +  +v+v+g
  gi|15669620|ref|NP_248433.1|  29 VIAKNVDGRDVLGVIKNVVADVEK-FvgEVKVIG 61 
                                   455555555555555555555542.335555555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.1e-05
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH..HTTEB-HHHH.......................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.......................... RF
                          CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai..leglendiep.......................... 54 
                                   ai s +GG GK+ +a  L+r la+++  V+++D   +  +l +   eg+ + i+p                          
  gi|15669620|ref|NP_248433.1| 125 AILSITGG-GKSNTASVLCRELAKKNGTVIMIDPHGEYISLYHedMEGKIKVINPiinpvllapsefanligigdneiekr 204
                                   56777777.************************665544444455555555555566667777777777777777777777 PP

                                   ...........................C CS
                                   ...........................x RF
                          CbiA  55 ...........................d 55 
                                                              +
  gi|15669620|ref|NP_248433.1| 205 vyvefayhtvkhecpdakgiefiekieN 232
                                   7777777777777764444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3110.43
//
Query:       gi|15669621|ref|NP_248434.1|  [L=127]
Description: phosphoribosyl-AMP cyclohydrolase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-34  116.5   0.5    5.2e-34  115.9   0.5    1.3  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.024   14.7   0.0    1.3  1  BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
       0.13   12.5   0.1       0.65   10.3   0.0    2.0  2  GAD       GAD domain


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.5   8.6e-38   5.2e-34       1      74 []      36     109 ..      36     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 8.6e-38
                                   EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
                        PRA-CH   1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74 
                                   m+a+mn+eal+ktletg+++yyS+srkklW+KGe+Sgnvqk+ +++ DcD+Dall+ veqkg+aCH g++sCF+
  gi|15669621|ref|NP_248434.1|  36 MVAFMNEEALKKTLETGYMHYYSTSRKKLWRKGEESGNVQKLIKFYRDCDGDALLFIVEQKGVACHEGYYSCFH 109
                                   9************************************************************************6 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     4e-06     0.024      34     103 ..      26      97 ..      10     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-06
                      BBS2_Mid  34 aeitetekvvslarlekerfayaleNGtvgvyek.kerlWrvkskne.vvalaaydingdgtkelivgwsnG 103
                                    ++ e+++v ++a +++e +  +le G +  y+  +++lWr  +++  v +l+ +  + dg   l +  ++G
  gi|15669621|ref|NP_248434.1|  26 ITCDENKNVLMVAFMNEEALKKTLETGYMHYYSTsRKKLWRKGEESGnVQKLIKFYRDCDGDALLFIVEQKG 97 
                                   4567999999**********************8625789**9887765889999888888877777766666 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.22   1.3e+03      67      87 ..      20      40 ..       3      51 .. 0.55
   2 ?   10.3   0.0   0.00011      0.65      64      92 ..      72     100 ..      69     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.22
                                  HHHHHHCT--TTEEEEEEEEE CS
                           GAD 67 kklleavgaeegDillfvAdk 87
                                  ++l+ a+  +e+  +l+vA  
  gi|15669621|ref|NP_248434.1| 20 ERLILAITCDENKNVLMVAFM 40
                                  455555555555555555544 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHCT--TTEEEEEEEEEHHHHH CS
                           GAD  64 eevkklleavgaeegDillfvAdkkktvn 92 
                                    +v+kl++ +   +gD+llf++++k +++
  gi|15669621|ref|NP_248434.1|  72 GNVQKLIKFYRDCDGDALLFIVEQKGVAC 100
                                   689********************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 868.15
//
Query:       gi|15669622|ref|NP_248435.1|  [L=359]
Description: FO synthase subunit 2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-18   67.5   0.6    2.8e-17   63.6   0.3    2.1  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.019   14.7   1.2        0.1   12.4   0.0    2.8  3  SinI         Anti-repressor SinI
      0.093   12.6   0.1        3.8    7.4   0.0    2.7  3  PASTA        PASTA domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.3   4.7e-21   2.8e-17       1     161 [.      53     224 ..      53     229 .. 0.83
   2 ?    1.9   0.0     0.042   2.5e+02      21      41 ..     324     344 ..     306     354 .. 0.78

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 4.7e-21
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC...... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla...... 74 
                                   +++t+ C ++C+fCa++   ++ +++++l+++ei++ + e+ ++ g ++++i+gg +p  +  ++ ++++++++a      
  gi|15669622|ref|NP_248435.1|  53 INFTNICVGNCRFCAFRAN-ENDKHAYFLDIDEIAKRAVEA-KKFGcTEVCIQGGLHPKIDTYYQAEILKAVHEAtkpygd 131
                                   689***************7.*********************.69999*****************************77555 PP

                                   .......CCTEEEEEEECSSCHG.........HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHH CS
                                   .......xxxxxxxxxxxxxxxx.........xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                   Radical_SAM  75 .......vpgiritvetngtlpd.........eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealekl 137
                                            ++                     +e l+ l+e g        +e++dd+ ++  ++  +   +e++  ++ +
  gi|15669622|ref|NP_248435.1| 132 ihihafsPMEVY----------FgaenagldiKEALKILKENGlNSMPGTAAEILDDD-IRAELCpNKIKTKEWIYIIKEA 201
                                   555555444444..........2555555555***********888888889999999.9999999*************** PP

                                   HHTTSETEEEEEEEBTTTSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 138 reagikrvvdrivglpGendeele 161
                                   +++gi+ + ++++g+  e + +++
  gi|15669622|ref|NP_248435.1| 202 HKLGIPTTATMMYGHIEEYK-HWV 224
                                   ******66666666665554.444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.042
                                   HHHHHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  21 rregrgrslsveeileevkel 41 
                                   +  ++g ++sveei + +k++
  gi|15669622|ref|NP_248435.1| 324 AGAEHGVYMSVEEIRDMIKRV 344
                                   567889999999999999887 PP

>> SinI  Anti-repressor SinI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.71   4.2e+03       9      14 ..     153     158 ..     148     159 .. 0.68
   2 ?   12.4   0.0   1.7e-05       0.1       3      17 ..     192     206 ..     192     207 .. 0.95
   3 ?   -1.3   0.0      0.34     2e+03      17      24 ..     332     339 ..     332     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.71
                                   HHHHHH CS
                          SinI   9 ikEAke 14 
                                   ikEA++
  gi|15669622|ref|NP_248435.1| 153 IKEALK 158
                                   677766 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.7e-05
                                   HHHHHHHHHHHHHT- CS
                          SinI   3 eEWveLikEAkesGl 17 
                                   +EW+++ikEA + G+
  gi|15669622|ref|NP_248435.1| 192 KEWIYIIKEAHKLGI 206
                                   7************98 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.34
                                   --SHHHHH CS
                          SinI  17 lskeEfRe 24 
                                   +s+eE+R 
  gi|15669622|ref|NP_248435.1| 332 MSVEEIRD 339
                                   699***95 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.2   7.3e+03      10      23 ..      12      25 ..      10      28 .. 0.85
   2 ?    7.4   0.0   0.00064       3.8       7      24 ..     149     168 ..     148     181 .. 0.80
   3 ?    1.8   0.0     0.036   2.2e+02       9      24 ..     332     347 ..     329     355 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.2
                                  BHHHHHHHHHHTT- CS
                         PASTA 10 svdeAkatLkalGl 23
                                  s++eA ++ +++++
  gi|15669622|ref|NP_248435.1| 12 SKKEALELFEDNEI 25
                                  78999999999987 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00064
                                   TTSBHHHHHHHHHHTT-..- CS
                         PASTA   7 tGmsvdeAkatLkalGl..k 24 
                                   +G++++eA ++Lk++Gl  +
  gi|15669622|ref|NP_248435.1| 149 AGLDIKEALKILKENGLnsM 168
                                   599**************554 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.036
                                   SBHHHHHHHHHHTT-- CS
                         PASTA   9 msvdeAkatLkalGlk 24 
                                   msv+e ++++k +Gl 
  gi|15669622|ref|NP_248435.1| 332 MSVEEIRDMIKRVGLI 347
                                   9**************3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2454.66
//
Query:       gi|15669623|ref|NP_248436.1|  [L=162]
Description: putative RNA-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-24   84.1   2.5      5e-24   84.1   2.5    1.7  2  PUA       PUA domain
    2.5e-15   56.5   5.4    5.7e-15   55.4   5.4    1.7  1  DUF1947   Domain of unknown function (DUF1947)
    3.3e-09   37.3   0.3    5.9e-09   36.5   0.3    1.4  1  Pre-PUA   Pre-PUA-like domain
    2.1e-05   24.7   0.3    2.1e-05   24.7   0.3    1.7  2  UPF0113   UPF0113 PUA domain
  ------ inclusion threshold ------
      0.054   12.3   0.3        0.6    8.8   0.1    2.0  2  DUF3103   Protein of unknown function (DUF3103)


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   4.6e+03      55      65 ..      10      20 ..       8      26 .. 0.75
   2 !   84.1   2.5   1.4e-27     5e-24       3      73 ..      81     152 ..      79     153 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                                  -HHHHHHHCTS CS
                           PUA 55 sseelakikgg 65
                                  s ++++kik+ 
  gi|15669623|ref|NP_248436.1| 10 SKKDVKKIKKE 20
                                  67888888875 PP

  == domain 2  score: 84.1 bits;  conditional E-value: 1.4e-27
                                   EEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                           PUA   3 vvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveierv 73 
                                   vvvd gA+k+l +ga+++apG+v+++++++e dvV +vde+  ++++vG+a+++++e++++++gk++++ ++
  gi|15669623|ref|NP_248436.1|  81 VVVDIGAIKFLINGADVMAPGIVDADENIKEEDVVFVVDENhKKPICVGIALMNGKEMKEADKGKAIKNLHY 152
                                   8****************************************99**************************997 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   5.4   1.6e-18   5.7e-15       1      65 [.       5      73 ..       5      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.6e-18
                                  --EE--HHHHHHHHHHHHTTT---T....T--..-EEEE-SS-EEEEETTEEEEEE.SSSEEE-HHHHHH CS
                       DUF1947  1 kRHfLSkKeakeileklkekyisis....lesdkiEieeekkeklYlingvpilfe.eekliPtLklLlk 65
                                  kR+fLSkK+ k+i+++l+ + ++++     +++ +Ei+ ++++ ++l+++ pi+f+ ++k+iPtLklLlk
  gi|15669623|ref|NP_248436.1|  5 KRYFLSKKDVKKIKKELEVFFENVDeiipKKGN-VEIAITDDFEIILVDKEPIAFKkDDKVIPTLKLLLK 73
                                  7****************9888776521104444.**********************************98 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.3   1.6e-12   5.9e-09       7      85 ..       3      73 ..       1      74 [. 0.90

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.6e-12
                       Pre-PUA  7 vksntqlksSdrrkLraklleqfpslseeqleellpkkeevkvvklqgehvelyvvdgeplffqdregellPtlytlwk 85
                                  + ++  l+++d +k++++l   f+++     +e++pkk +v+++ ++ +  e+++vd+ep+ f++ +++++Ptl++l k
  gi|15669623|ref|NP_248436.1|  3 IRKRYFLSKKDVKKIKKELEVFFENV-----DEIIPKKGNVEIA-IT-DDFEIILVDKEPIAFKK-DDKVIPTLKLLLK 73
                                  566677999**********9998888.....9********9877.66.6****************.**********987 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.8   6.5e+03      24      38 ..      15      25 ..       9      43 .. 0.57
   2 !   24.7   0.3     6e-09   2.1e-05       7      69 ..      86     152 ..      80     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.8
                       UPF0113 24 lkitesvkenqvvvV 38
                                  +ki+++++    v++
  gi|15669623|ref|NP_248436.1| 15 KKIKKELE----VFF 25
                                  44444433....333 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 6e-09
                       UPF0113   7 kaeklFLYGrdvlkesilkitesvkenqvvvVlnen.geplGiGkirkdt...kaspgkivvknlaD 69 
                                    a k ++ G dv+  +i+  +e++ke++vv+V++en ++p+ +G++  ++   k  ++++ +knl  
  gi|15669623|ref|NP_248436.1|  86 GAIKFLINGADVMAPGIVDADENIKEEDVVFVVDENhKKPICVGIALMNGkemKEADKGKAIKNLHY 152
                                   444555679***********************99983568888888778887547889999999865 PP

>> DUF3103  Protein of unknown function (DUF3103)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.02        72     117     151 ..      70     104 ..      57     112 .. 0.81
   2 ?    8.8   0.1   0.00017       0.6     125     159 ..     113     148 ..     101     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.02
                       DUF3103 117 LdvyklPerPvlvvdadskkelkaGlkamraelka 151
                                   L   +lP++  +vvd+ + k l  G  +m   +  
  gi|15669623|ref|NP_248436.1|  70 LLLKSLPDKNLVVVDIGAIKFLINGADVMAPGIVD 104
                                   556799************99999999998766655 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00017
                       DUF3103 125 rPvlvvdadskkelkaGlkamr.aelkalgqktalk 159
                                     v+vvd + kk + +G+++m+ +e+k++++ +a+k
  gi|15669623|ref|NP_248436.1| 113 DVVFVVDENHKKPICVGIALMNgKEMKEADKGKAIK 148
                                   569******************857899988877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1039.47
//
Query:       gi|15669624|ref|NP_248437.1|  [L=247]
Description: hypothetical protein MJ_1433 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1168  (0.0651459); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1819.96
//
Query:       gi|15669625|ref|NP_248438.1|  [L=220]
Description: endonuclease III [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-22   80.6   0.0    1.6e-22   80.0   0.0    1.3  1  HhH-GPD         HhH-GPD superfamily base excision DNA repair 
    3.4e-05   23.5   0.0    9.4e-05   22.1   0.0    1.7  1  HHH             Helix-hairpin-helix motif
     0.0067   17.0   0.2      0.021   15.4   0.1    1.9  2  HHH_5           Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.021   14.9   0.0      0.089   12.9   0.0    2.1  1  HHH_2           Helix-hairpin-helix motif
       0.51   10.4   4.5       0.45   10.5   1.5    2.1  2  Alpha-2-MRAP_N  Alpha-2-macroglobulin RAP, N-terminal domain
        1.2    8.5   6.9      0.081   12.4   0.4    2.2  2  Pox_F16         Poxvirus F16 protein


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   5.5e-26   1.6e-22       1     107 [.      36     181 ..      36     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 5.5e-26
                                   HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                       HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv............... 66 
                                   v+ail+q+ts+++++r+i++l+ +   ++  +++++de+kL+elir++Gfy+ Kak++k++ + +v               
  gi|15669625|ref|NP_248438.1|  36 VGAILTQNTSWKNVERAINNLKMED-LLEEVKILNVDEDKLKELIRPAGFYNLKAKRLKNVTKFIVenygnteemaktdkd 115
                                   799*********************8.79***************************************************** PP

                                   ...........................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                   ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD  67 ...........................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                              ++  + +vvD +++r+++rl+ i+ek +++++++ +e+ l+
  gi|15669625|ref|NP_248438.1| 116 tlilraellsingvgketadsillyalDR--ESFVVDAYTKRMFSRLGVINEKAKYDEIKEIFEKNLP 181
                                   ************************98644..68******************************99876 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.1e-08   9.4e-05      10      30 .]     120     140 ..     119     140 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.1e-08
                                   HHHHHTSTT-SHHHHHHHHHH CS
                           HHH  10 reeLlalPGVGpktAeaIlsy 30 
                                   r+eLl++ GVG++tA++Il y
  gi|15669625|ref|NP_248438.1| 120 RAELLSINGVGKETADSILLY 140
                                   68*****************87 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.1   6.3e+03      30      40 ..      68      78 ..      56      96 .. 0.61
   2 !   15.4   0.1   7.1e-06     0.021      18      53 ..      99     139 ..      93     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
                                  HHS-HHHHHTS CS
                         HHH_5 30 aaadveeLaki 40
                                  ++ d+++L ++
  gi|15669625|ref|NP_248438.1| 68 LNVDEDKLKEL 78
                                  44455555553 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 7.1e-06
                                   HHTTT--SHHHHHHS-HHH......HHTSTTS-HHHHHHHHH CS
                         HHH_5  18 llsaGiesvedlaaadvee......LakipGiGkktAeriil 53 
                                   ++++ ++  e+ a+ d+++      L +i G+Gk+tA++i+l
  gi|15669625|ref|NP_248438.1|  99 IVEN-YGNTEEMAKTDKDTlilraeLLSINGVGKETADSILL 139
                                   6666.77777777777555555555**************986 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     3e-05     0.089      17      54 ..      97     140 ..      93     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                         HHH_2  17 klLakrFksldaLkkasle......eLlevddiGeeiAqsivef 54 
                                   k +++++++ ++++k++ +      eLl+++++G+e+A+si  +
  gi|15669625|ref|NP_248438.1|  97 KFIVENYGNTEEMAKTDKDtlilraELLSINGVGKETADSILLY 140
                                   6677888888888888765222222789*************866 PP

>> Alpha-2-MRAP_N  Alpha-2-macroglobulin RAP, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.5   0.00015      0.45      43     113 ..      43     112 ..      39     116 .. 0.82
   2 ?    0.1   0.1      0.27   7.9e+02      40      69 ..     158     188 ..     151     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                Alpha-2-MRAP_N  43 nlvWeKAkrrltevklksLysdLkihdkeelawkklkaegldkdgekEaelrrkligilskYgllehfddk 113
                                   n  W+  +r + + k+++L ++ ki + +e ++k+l         +k ++l++  + i+++Yg  e+++++
  gi|15669625|ref|NP_248438.1|  43 NTSWKNVERAINNLKMEDLLEEVKILNVDEDKLKELIRP-AGFYNLKAKRLKNVTKFIVENYGNTEEMAKT 112
                                   6679999***************************99744.4455678888888888888888877776664 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.27
                Alpha-2-MRAP_N  40 aklnlvWeKAkr.rltevklksLysdLkihd 69 
                                    +l ++ eKAk  ++ e   k+L +dL i +
  gi|15669625|ref|NP_248438.1| 158 SRLGVINEKAKYdEIKEIFEKNLPKDLEIYK 188
                                   5777888899888888888888888887765 PP

>> Pox_F16  Poxvirus F16 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   2.7e-05     0.081     121     178 ..      71     130 ..      41     178 .. 0.82
   2 ?   -0.9   1.4      0.32   9.4e+02      20      41 ..     195     216 ..     189     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                       Pox_F16 121 nrkkirdlia...linmktldkkilkdfvrenfGsvekLlkiikknvlwlklvlaksekrr 178
                                      k+++li    + n+k++  k +++f+ en+G+ e++ k+ +k++l+l+ +l + +  +
  gi|15669625|ref|NP_248438.1|  71 DEDKLKELIRpagFYNLKAKRLKNVTKFIVENYGNTEEMAKT-DKDTLILRAELLSINGVG 130
                                   467889998644478999999999**************9886.999****99998777644 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.32
                       Pox_F16  20 lkvCrdyCeslslqvvkeikef 41 
                                   ++ C+++C++ +l+    ikef
  gi|15669625|ref|NP_248438.1| 195 VEHCKKFCRKKALCDNCPIKEF 216
                                   568***********99999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1529.26
//
Query:       gi|15669626|ref|NP_248439.1|  [L=71]
Description: hypothetical protein MJ_1435 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-07   29.4   0.1    6.2e-07   29.0   0.1    1.1  1  Hfq            Hfq protein
     0.0017   18.6   0.0     0.0031   17.8   0.0    1.4  1  S1             S1 RNA binding domain
  ------ inclusion threshold ------
      0.026   14.3   0.0      0.026   14.3   0.0    1.1  1  Flag1_repress  Repressor of phase-1 flagellin
      0.035   14.1   0.2      0.045   13.7   0.2    1.1  1  DUF5608        Domain of unknown function (DUF5608)


Domain annotation for each model (and alignments):
>> Hfq  Hfq protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.1   1.4e-10   6.2e-07      11      57 ..      23      69 ..      19      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.4e-10
                                  HCT-EEEEEETTS-EEEEEEEEE-SSEEEEEETTEEEEEEGGGEEEE CS
                           Hfq 11 kekipvtifLvnGiklkGviksfDnftvlLesdgkqqlvYKhaisti 57
                                   +  +v+ifL nG  l   +++  n+ ++++  ++  lv+Khai  i
  gi|15669626|ref|NP_248439.1| 23 LNGKKVKIFLRNGEVLDAEVTGVSNYEIMVKVGDRNLLVFKHAIDYI 69
                                  56679**************************999999*******766 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.8e-07    0.0031       4      37 ..      34      66 ..      32      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.8e-07
                                  TTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGS CS
                            S1  4 kgevveGeVtsvtkgGafVelgngvegfvpasel 37
                                   gev+++eVt v+++ + V +g +   +v ++ +
  gi|15669626|ref|NP_248439.1| 34 NGEVLDAEVTGVSNYEIMVKVG-DRNLLVFKHAI 66
                                  69********************.99999988877 PP

>> Flag1_repress  Repressor of phase-1 flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.7e-06     0.026     121     158 ..      24      61 ..       6      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.7e-06
                 Flag1_repress 121 qqksikvymkdGrvleGkssGvdacqvtlrtsdGrktv 158
                                    +k +k+++++G+vl+ + +Gv   ++ ++++d + +v
  gi|15669626|ref|NP_248439.1|  24 NGKKVKIFLRNGEVLDAEVTGVSNYEIMVKVGDRNLLV 61 
                                   4789****************************987654 PP

>> DUF5608  Domain of unknown function (DUF5608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2     1e-05     0.045       3      46 ..      19      63 ..      18      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                                  GGGS-TTSEEEEEETTEEE.EEEEEEE-SSEEEEXETTEEEEEEG CS
                       DUF5608  3 yakvPkGiGvtvylanGrv.qGrlidiGvyevlvevGGdiiyihk 46
                                  ya+   G  v ++l nG v    +  +  ye++v+vG   + + k
  gi|15669626|ref|NP_248439.1| 19 YARRLNGKKVKIFLRNGEVlDAEVTGVSNYEIMVKVGDRNLLVFK 63
                                  788888999*********93467888999********87666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 456.39
//
Query:       gi|15669627|ref|NP_248440.1|  [L=97]
Description: hypothetical protein MJ_1436 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-40  135.3   2.3    3.1e-39  132.9   2.3    1.8  1  Ehbp      Energy-converting hydrogenase B subunit P (EhbP)


Domain annotation for each model (and alignments):
>> Ehbp  Energy-converting hydrogenase B subunit P (EhbP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   2.3   1.7e-43   3.1e-39       1      77 []       6      93 ..       6      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 1.7e-43
                          Ehbp  1 lrPkliislgGYivet...........efpyrnvivvnktdepikievPvfdeeWieehrkLgLevvPveeeddflslfkkak 72
                                  l+P+++++lgGYi+et            fpyrnviv+n+tdepikievP+++e+Wie+h+kLgL+vvPv+e+ddf++lf+++k
  gi|15669627|ref|NP_248440.1|  6 LLPRMTMALGGYIRETtfpyeeddevkPFPYRNVIVGNPTDEPIKIEVPAYNEGWIERHKKLGLIVVPVNEDDDFVGLFQMVK 88
                                  68********************************************************************************* PP

                          Ehbp 73 akldk 77
                                  +k+++
  gi|15669627|ref|NP_248440.1| 89 EKVKN 93
                                  ***85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 646.08
//
Query:       gi|15669628|ref|NP_248441.1|  [L=228]
Description: L-2-haloalkanoic acid dehalogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-32  111.3   0.3    8.8e-32  110.6   0.3    1.3  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.3e-16   61.6   0.0      7e-16   59.2   0.0    1.9  1  Hydrolase       haloacid dehalogenase-like hydrolase
      8e-12   45.1   0.0    1.4e-11   44.3   0.0    1.4  1  Hydrolase_like  HAD-hyrolase-like
    1.2e-05   25.8   0.0    1.7e-05   25.3   0.0    1.2  1  HAD             haloacid dehalogenase-like hydrolase
     0.0095   16.0   0.0       0.53   10.4   0.0    2.4  2  Hydrolase_6     Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   0.3   2.4e-35   8.8e-32       1     177 [.       5     193 ..       5     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 2.4e-35
                         HAD_2   1 iiFDlDgTlldteeliiqafnelleey.............glselseeelrkliglslrellrklgeseeeeekieellrk 68 
                                   i+FDlD+Tl++++e++  a +e+++++             ++ +   ++  + +g + ++l++ +  +++  ++i++ + +
  gi|15669628|ref|NP_248441.1|   5 ILFDLDDTLYNSSEFVEIARREAVKSMidaglnidfeeamNILNKIIKDKGSNYGKHFDDLVKAVLGKYD-PKIITTGIIT 84 
                                   89************************99998888777655333444455555566666667766666655.3488888888 PP

                         HAD_2  69 yneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklk 149
                                   y++ k    ++py++ +++L eLk++g+klg++T++ + +++ekl +lgi+ +Fd ++tse+++  KP+ e ++  l++++
  gi|15669628|ref|NP_248441.1|  85 YHNVKVA-LLRPYPHTIKTLMELKAMGLKLGVITDGLTIKQWEKLIRLGIHPFFDDVITSEEFGLGKPHLEFFKYGLKRMG 164
                                   8888888.************************************************************************* PP

                         HAD_2 150 lkkeeviyvGDsp.tDieaakkagikvia 177
                                   lk+ee++yvGD   +Di+ ak++g+ ++ 
  gi|15669628|ref|NP_248441.1| 165 LKAEETVYVGDRVdKDIKPAKELGMITVR 193
                                   *************************8875 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.0   1.9e-19     7e-16       1     210 []       2     188 ..       2     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.9e-19
                                   SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH.HHHHHETTTEHHHHTHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgal.tgfatfigrgayaigkpewltal 80 
                                   ik ++fD+d TL++++  ve + ++a                 k ++ a  ++ ++   ++       ++ + k     ++
  gi|15669628|ref|NP_248441.1|   2 IKGILFDLDDTLYNSSEFVEIARREA----------------VKSMIDAGLNIDFEEaMNILN-----KIIKDKGSNYGKH 61 
                                   799*************7777777777................444444444443333355555.....5555555555555 PP

                                   HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                     Hydrolase  81 dippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyf 160
                                    + + ++a  g++  +  t  +    ++ v  +     ++p + +++ +Lka+g++++++t +    +++ + +lG + +f
  gi|15669628|ref|NP_248441.1|  62 -FDDLVKAVLGKYDPKIITTGII--TYHNVKVALLR--PYPHTIKTLMELKAMGLKLGVITDGLTIKQWEKLIRLGiHPFF 137
                                   .7777777799999999999999..88888888888..9******************************99999**99999 PP

                                   SEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                     Hydrolase 161 daviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                   d vi+s++ + +kp+ e +++ +++++ k ee++ VGD+v  D++ +++ g
  gi|15669628|ref|NP_248441.1| 138 DDVITSEEFGLGKPHLEFFKYGLKRMGLKAEETVYVGDRVDkDIKPAKELG 188
                                   ********************************************9999865 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   3.9e-15   1.4e-11       2      74 ..     148     217 ..     147     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3.9e-15
                                   .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                   lgKP+ e++++ l+++g++ ee++++GDr++ Di+ A++ G+ +v +l G++++ +     +  +y +++l+e
  gi|15669628|ref|NP_248441.1| 148 LGKPHLEFFKYGLKRMGLKAEETVYVGDRVDKDIKPAKELGMITVRILKGKYKDMEDD---EYSDYTINSLQE 217
                                   69***************************************************96533...567888888877 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   4.7e-09   1.7e-05       1     181 [.       5     177 ..       5     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4.7e-09
                           HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllal......frellrldraglaelleallaglseelaaeler 75 
                                   +lfD+D TL +++ + +++r+ + ++  +  + l+  +++a+      +++ +++  ++++ l+ a l+ ++++++     
  gi|15669628|ref|NP_248441.1|   5 ILFDLDDTLYNSSEFVEIARREAVKSMID--AGLNIDFEEAMnilnkiIKDKGSNYGKHFDDLVKAVLGKYDPKIITTGII 83 
                                   79**********99997777333333333..2333332222234455579999999****************999999999 PP

                           HAD  76 fvaevirpklldp..galellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegk 154
                                    ++ v+    l+p  +  + l + +a G ++ v++ gl +  +++l +lg++ + +       ++t e ++ gkp  +  k
  gi|15669628|ref|NP_248441.1|  84 TYHNVKVAL-LRPypHTIKTLMELKAMGLKLGVITDGLTIKQWEKLIRLGIHPFFDD------VITSEEFGLGKPHLEFFK 157
                                   997777665.444448888888899***************9999999***7777777......777777777777776222 PP

                           HAD 155 vaalrewlaaegegidleevvayGDsp 181
                                          ++ +  g++ ee+v++GD +
  gi|15669628|ref|NP_248441.1| 158 -------YGLKRMGLKAEETVYVGDRV 177
                                   .......23444677777899999975 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.029     1e+02       1      27 [.       5      32 ..       5      52 .. 0.80
   2 !   10.4   0.0   0.00015      0.53      14      67 ..      94     144 ..      88     147 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.029
                                  EEEESTTTSEETTEE-TTHH.HHHHHHH CS
                   Hydrolase_6  1 flfDidGvLwrgdkaipgaa.ealnalr 27
                                  +lfD+d +L++ ++ ++ a  ea++ + 
  gi|15669628|ref|NP_248441.1|  5 ILFDLDDTLYNSSEFVEIARrEAVKSMI 32
                                  69**********9999887525555555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00015
                                   EE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHH CS
                   Hydrolase_6  14 kaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsa 67 
                                   +++p+  ++l  l+a+g ++ ++T + + +     +kl +lg++   ++v+ts 
  gi|15669628|ref|NP_248441.1|  94 RPYPHTIKTLMELKAMGLKLGVITDGLTIK---QWEKLIRLGIHPFFDDVITSE 144
                                   699***********************9987...7899********999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1489.14
//
Query:       gi|15669629|ref|NP_248442.1|  [L=258]
Description: cobalamin (5'-phosphate) synthase CobS [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-41  141.8  10.1    3.6e-41  141.6  10.1    1.0  1  CobS      Cobalamin-5-phosphate synthase


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6  10.1     2e-45   3.6e-41       2     204 .]      13     243 ..      12     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 2e-45
                          CobS   2 lsflTrlPvp....elaralaff...PlvGlllGlll.llallllllll.llaallavaalvlltgglHlDGlaDtaDglg 73 
                                   lsf+Tr+P+     ++++++ +f    l+G++ G++  +l +++++ll+  l+a+l++ ++ +l g++H+DGl+D++Dg++
  gi|15669629|ref|NP_248442.1|  13 LSFFTRIPIYvedfDFENIANYFyliILIGYVFGIFSlILGYIFSFLLPnFLSAVLILFFIEYLNGFHHIDGLIDFGDGWM 93 
                                   89*******766665566555554449*********988888888887776789998877789*****************9 PP

                          CobS  74 sgrdrerrleImkDsrvGafGvlalvlvlllkvaalaala......lllapvlsRlaallaiallpyaeeglgalfaeaqk 148
                                   + +d+ ++l +mkD  +G +Gv++++++ l+ v++l+ ++      ll+ +v+++l++l + +++++  eg+g++f+++++
  gi|15669629|ref|NP_248442.1|  94 AVGDKRKKLMAMKDRYIGCGGVVFAIFFNLMAVISLSYILdinilyLLVGEVCAKLGMLSCSTFGNPLIEGTGRYFVKKAD 174
                                   999******************************99855546677788899****************8878*******9555 PP

                          CobS 149 k......lvllal...............avlllllalllaallvalllrrlarrklggvtGDvlGavieltellvll 204
                                   +      +    +               + ++   +++++++++ l+++++a+r++ggv+GDvlGa++e+t+++vll
  gi|15669629|ref|NP_248442.1| 175 EkfltigI----IlslplllifsgierkI-VI---IAIITTIITGLCMAKIAKRHFGGVNGDVLGASNEITRVVVLL 243
                                   54544331....12334444455544422.11...345666777888999************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1704.00
//
Query:       gi|15669630|ref|NP_248443.1|  [L=207]
Description: thermonuclease [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-32  111.9   0.2    2.8e-32  111.4   0.2    1.2  1  SNase     Staphylococcal nuclease homologue


Domain annotation for each model (and alignments):
>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   0.2   1.6e-36   2.8e-32       1     108 []      78     204 ..      78     204 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 1.6e-36
                                   EEEETTEE-STSSBTTT................TTSTTHHHHHHHHHHHHHHCSSEEEEE-S...SBSTTSEEEEEEEET. CS
                         SNase   1 kvrLvgidaPetakpkk................tvqpfgkeAkeflkklvlqkkvvvleldk...kkDkygrllayvyln. 61 
                                   k+rL+g+d+Pe +k+++                +++++g++Ak+f++k+++ +k+v++++d+   kkDkygr+lay+++n 
  gi|15669630|ref|NP_248443.1|  78 KIRLLGVDTPEIHKRNNpyeyyllngtpitdtkYLKEWGYKAKHFAEKELK-NKTVIIVFDNeapKKDKYGRYLAYIFINn 157
                                   79*************************************************.77777777777*****************9 PP

                                   ...TEEHHHHHHHTTSSEE---BTTSTTTHHHHHHHHHHHHHTT-GGGCT CS
                         SNase  62 ...kknineeLvkeGlArvyevyekneekkkellkaeeeAkkkrkglWse 108
                                       +n+neeL+k+G+Ar   vy +n+e k+e+l++e+eAk++r+glW++
  gi|15669630|ref|NP_248443.1| 158 snnLINFNEELLKYGYAR---VYISNFELKDEFLNVEREAKENRVGLWNW 204
                                   99999*************...77799**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1267.42
//
Query:       gi|15669631|ref|NP_248444.1|  [L=282]
Description: shikimate kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-12   45.0   0.1    3.7e-11   43.1   0.1    1.9  2  GHMP_kinases_N  GHMP kinases N terminal domain
    1.2e-05   25.6   0.0    2.3e-05   24.6   0.0    1.6  1  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.27   2.4e+03      17      40 ..      10      36 ..       9      49 .. 0.66
   2 !   43.1   0.1   4.1e-15   3.7e-11       2      66 .]      79     147 ..      78     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.27
                                  HHHHHHHHHHHHHHHTTEHHHH...HH CS
                GHMP_kinases_N 17 SAAlavalvaAllallglslee...ak 40
                                  S++++ a+++   +++gl+l+    +k
  gi|15669631|ref|NP_248444.1| 10 SGTIINAIATGKGSAFGLDLKVyakVK 36
                                  788888888888888887764333344 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 4.1e-15
                                   EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH.HH..HHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
                GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl.ee..aklaleaerlaqggngsggDv.aasvyGg 66 
                                   +++k+eiP+++GL+SS+A + a+v+A  ++lg ++ +e  ++l++++     +++++  D+ +as+yGg
  gi|15669631|ref|NP_248444.1|  79 VETKTEIPIKSGLSSSSATSNAVVLATFDALGEKIdDEliLNLGIKSSFDEKLTVTGAYDDaTASYYGG 147
                                   7899***************************99974337*********999889988888879999998 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   2.6e-09   2.3e-05      39      84 ..     227     268 ..     196     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.6e-09
                GHMP_kinases_C  39 llealselGalgaklsGaGgGptvfalfkdkdeaeqvaralreefe 84 
                                   +++al ++Ga+ a+lsG+  Gp+ +a++ +++++e+v+++l+++++
  gi|15669631|ref|NP_248444.1| 227 AIDAL-DAGAITAGLSGT--GPSYIAMV-EDENVEKVKEKLNRYGK 268
                                   55665.99**********..********.************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1863.26
//
Query:       gi|15669632|ref|NP_248445.1|  [L=1226]
Description: cobaltochelatase subunit CobN [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
          0 1172.7   0.0          0 1172.4   0.0    1.0  1  CobN-Mg_chel  CobN/Magnesium Chelatase
  ------ inclusion threshold ------
      0.048   13.3   0.0       0.16   11.6   0.0    1.9  1  2-Hacid_dh    D-isomer specific 2-hydroxyacid dehydrogenase, 
       0.18   11.6   1.2       0.38   10.5   0.0    2.1  2  DUF1965       Domain of unknown function (DUF1965)
       0.85    9.9   5.8       0.82    9.9   3.1    2.5  2  DUF5071       Domain of unknown function (DUF5071)
        4.1    7.6   5.9        1.1    9.4   0.7    2.7  2  DUF4145       Domain of unknown function (DUF4145)
        6.2    7.6   8.7          1   10.1   0.1    3.4  4  RraB          Regulator of ribonuclease activity B


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1172.4   0.0         0         0       3    1087 ..      97    1177 ..      95    1179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1172.4 bits;  conditional E-value: 0
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel    3 YlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilfyrahl 81  
                                    ++++gg +N+kn++ yl+ k          ++v+ p +giy     +++e+lee+l+     + +k+ tvgilf+r++l
  gi|15669632|ref|NP_248445.1|   97 FITYGGLDNFKNMVLYLMGKDK--------DVVKHPFQGIYY--RGKIYEELEEFLKD---VEFNKKYTVGILFSRHYL 162 
                                    6799************986653........6899*******7..6789****999987...589999************ PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel   82 lagntavidaliraleerglnvlpvfvssl...d...seaqealeelftkegeekvdalinttsfalvkgpaeeeeeea 154 
                                    ++++++vi++l+++l+++ +nv+pvf++++   d     + e + ++f k++++ +dalin++sf l + +++ + ++ 
  gi|15669632|ref|NP_248445.1|  163 VNDDMDVIEKLLNRLDKE-FNVIPVFSYGAkceDlnaLGSGESVLKYFLKDDKPIIDALINLLSFPLGTVKDKANLNKI 240 
                                    ***************997.**********98862556778899999999******************988866555444 PP

                                    xxxx.xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  155 eeea.lkelnvPvlqa.ilssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeeeeetevekyepiperv 231 
                                    +  + lk+l+vPv+++ +++++s+e+W++++qGls  d+ +++alpE++G+iep++i+++e   +e+++ek   i+er+
  gi|15669632|ref|NP_248445.1|  241 SGVEiLKKLDVPVFHPiMSYYKSYEDWKKDEQGLS-ADIGWTIALPEFEGVIEPIIIGTTE---NENGLEKKFGIEERI 315 
                                    33338***********9999**************6.9**********************54...4789*********** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  232 ervadlaarwarLrrkpnaekkvaiilanypp..gegrlgnavgLdvpaSlvnlLkalkeeGYdveelpesgdeLiell 308 
                                    ++v+++++rw++L+ kp++++kv +il+n+ +   e+++g+a++Ld+++S++n++k+lkeeGY ve++pe+g+eL++l+
  gi|15669632|ref|NP_248445.1|  316 DKVVRRIKRWIELKYKPKKDRKVIFILHNNACasVEATVGSAAHLDSFQSVINIMKKLKEEGYYVENIPENGEELAQLI 394 
                                    *******************************98889******************************99*********** PP

                                    xxxxx.xxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  309 leggt.ndpeweelkv.....gaaallpaeeYeewfeeLpeelreeveerWgeppge.....mveeeksgekklvipgl 376 
                                    +++++ ++++w++++      g + l+++eeY e+f++Lpe++++++ e+Wg+ +g+     m++ + +g++k+vi+gl
  gi|15669632|ref|NP_248445.1|  395 MQKKAiSEFRWTTVNEiiakgGYLYLMDEEEYYEYFNTLPENVKNKILETWGDLNGKdipagMIY-KVNGKNKIVITGL 472 
                                    *****99****6665556667************************************9**97777.68899******** PP

                                    xxxxxxxxxxxxxx...xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  377 qlGnvfvgvQParg...yeedps..klyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwlPGKqvglseecy 450 
                                    ++Gnv+v+vQP+rg   +++d +  k++hdp +pPthqY+A+Y++ ++   ad+++HvG+HGtlE+lPGK+vgls+ecy
  gi|15669632|ref|NP_248445.1|  473 KFGNVYVCVQPKRGcagARCDGRvcKILHDPYCPPTHQYIASYKYFNDI--ADIIIHVGTHGTLEFLPGKNVGLSNECY 549 
                                    **************87778886678**********************96..9*************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  451 PdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeaesldperlkalreqil 529 
                                    Pdi++gd+PhlY+Y+ +np EGt+AKRRsyA+iidH++++m++a +y+el++L++ i+eY +  ++d++r+++l++ i+
  gi|15669632|ref|NP_248445.1|  550 PDICIGDIPHLYIYNSDNPPEGTIAKRRSYATIIDHMQTVMVDA-FYEELETLDSYIEEYLK--EMDASRRHQLEHLIV 625 
                                    ********************************************.9**************99..58899********** PP

                                    xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx RF
                  CobN-Mg_chel  530 elveelnldkdlg...leeakeeeeeefeellekldgyleelkeaqirdglhilGeapegeqlvdlvvailrl...ene 602 
                                    e v+++nl k  +   + e++ + +e+f+e++++l++ le +k+++++dg+hi+Ge p+ge++v+++++il++   +n+
  gi|15669632|ref|NP_248445.1|  626 EEVKKTNLLKIKEkieKIEKEGKIHENFKEIFDELRDILEMIKNSKCNDGMHIFGELPSGEKRVEFIKSILEAifiQNN 704 
                                    *******965333444555677889**********************************************65443555 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  603 egesltealaealgldldeleeksekelrtagdalealeeeaeelveelleeeaeeeeaeaeeleeeeeeeeeeteeEi 681 
                                    + +s ++ +ae+    +++ + ++  +       +e  +++ ++ v+++l+ ++ e+++  ee+ ++ +e+  e+++Ei
  gi|15669632|ref|NP_248445.1|  705 TMNSKRRGIAERS-EAMHPGYPNRGLP----PMEFEYKDKNLKKKVSDVLNGKSIEDKK-LEEKIKDINERI-EKSDEI 776 
                                    6777777777772.3333322222222....2344555777888999999875544433.333333333332.4559** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  682 tallraLdGeyippgpsGdptrgraevLPTGrNfysvDpraiPteaAwevGkklaeellerylqehgeyPekvglslwg 760 
                                     +llr++d++yi+pgpsG +trg+ ++LPTGrNfys+Dp++iPt++A++vG  lae+l++ryl+e+g+yPe+++l++++
  gi|15669632|ref|NP_248445.1|  777 GSLLRGIDAKYIEPGPSGLITRGNYDILPTGRNFYSLDPYRIPTKSAYRVGVLLAEKLINRYLEEEGRYPENIALYWMA 855 
                                    ******************************************************************************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  761 tetmrteGediAqiLallGvrPvwdaagrvvdlelipleeLgRPRiDVtvriSGffRDafpnlielldkavelvaeldE 839 
                                    ++ m+ +Ge ++ iL+llGv+Pv+ + grvv+le+ipleeLgRPRiDVt+r+SG+ RD+fpn+iel+d+a+ +va+ldE
  gi|15669632|ref|NP_248445.1|  856 SDIMWADGEGMGMILYLLGVKPVYRG-GRVVGLEVIPLEELGRPRIDVTIRVSGITRDMFPNCIELVDEAIMKVANLDE 933 
                                    ************************77.**************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  840 peedNfvrkhvleeeaeleekeeaeeratyRvFgskpGaYgagvqeliessnWedeedLaeaYlnwssyaYgkgaegee 918 
                                    p e+Nfv+khv e+ ++      + +++t+R+F+s+pG+Yg+gv+ ++ +s+We++edL++a++ w+syaYgk+++g++
  gi|15669632|ref|NP_248445.1|  934 PLEMNFVKKHVVENLNKGL----SFRESTFRIFCSPPGTYGNGVKYAVYASAWENDEDLKDAFIYWNSYAYGKDVYGKK 1008
                                    **************99987....569***************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  919 aeeafearLkrvdvvvqnqdsrehdlldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvrtlkeeiarelrs 997 
                                    a +afe+ Lk+vd+++++  ++e+dl+ +++y+ ++GGlt+a+r l+g++++ay+gd++np+n++vrtlkeei+r+  +
  gi|15669632|ref|NP_248445.1| 1009 AINAFENILKTVDLTFNKVVTDEYDLFGCCCYFGTHGGLTNAARVLKGEEVKAYYGDTRNPNNVEVRTLKEEIERVSLT 1087
                                    ******************************************************************************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  CobN-Mg_chel  998 rvlNPkWiegmmrhGykGafelaatvdnlfgwdatadvvddwvyeevaetYvlDeevrefleekNpwAlreiaerLlEa 1076
                                    ++lNPkWiegm+rhGykGa ++a+++  ++gw+at++ v++w+++e+ +t+v++ee+r+f++e+N +Al+eia+rLlEa
  gi|15669632|ref|NP_248445.1| 1088 KLLNPKWIEGMKRHGYKGAGDIAKRIGRVYGWSATTKEVENWIFDEIFNTFVKNEENRKFFKEHNIYALEEIARRLLEA 1166
                                    ******************************************************************************* PP

                                    xxxxxxxxxxx RF
                  CobN-Mg_chel 1077 arrglWeasee 1087
                                     +rglW+++e 
  gi|15669632|ref|NP_248445.1| 1167 YQRGLWKTTEG 1177
                                    *******9875 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.5e-05      0.16      30      84 ..      19      73 ..       9      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.5e-05
                                  HHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh 30 teellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerG 84
                                   +el+++  d++  i+ +++++++e+le +++  ++  + +  D +Dl+ +k+ +
  gi|15669632|ref|NP_248445.1| 19 LDELKKEGVDVEYKIYSNRNPIDDEFLEDAKDYDLVFIYRTSSDDIDLEKIKKFN 73
                                  4677777778888888899999999999999999999999999999999888755 PP

>> DUF1965  Domain of unknown function (DUF1965)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00013      0.38      19      43 ..     119     143 ..     108     152 .. 0.79
   2 ?   -2.2   0.3       1.3   3.8e+03      24      35 ..    1125    1136 ..    1116    1154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                                   -GGG-EEEEEEETTEEESSHHHHHH CS
                       DUF1965  19 dpskWkvlGwlyngifYetteeFRa 43 
                                   d  k  ++G++y g+ Ye +eeF +
  gi|15669632|ref|NP_248445.1| 119 DVVKHPFQGIYYRGKIYEELEEFLK 143
                                   45577799***************76 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                                    EEEEEEETTEEE CS
                       DUF1965   24 kvlGwlyngifY 35  
                                    +v++w++++if 
  gi|15669632|ref|NP_248445.1| 1125 EVENWIFDEIFN 1136
                                    689999999984 PP

>> DUF5071  Domain of unknown function (DUF5071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.7   8.2e+03      28      72 ..     136     182 ..     133     184 .. 0.69
   2 ?    9.9   3.1   0.00027      0.82      46     118 ..     591     663 ..     586     664 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.7
                                   HHHHGGGS-TTSTTHHHHHHHHHHT..GGGTHHHHHHHHHSS-HHHH CS
                       DUF5071  28 peLLeWlqDlNwPiaspiaelLarf..peelvkeiaeiLeknDeewk 72 
                                   +eL e+l+D+ +     +  l  r+  +++ ++ i+++L++ D+e++
  gi|15669632|ref|NP_248445.1| 136 EELEEFLKDVEFNKKYTVGILFSRHylVNDDMDVIEKLLNRLDKEFN 182
                                   56666777776666666666666665567788889999999988875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00027
                                   HHHHHHTGGGTHHHHHHHHHSS-HHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHTS--SSHHHHHHHHHHHHH CS
                       DUF5071  46 aelLarfpeelvkeiaeiLeknDeewkyfvleflveklpveskkklkeelerlveeptedEkeeeldelAkei 118
                                   ++   + +e+l + i+e L++ D   ++++ +++ve++   + +k+ke++e++ +e + +E+ +e+ ++ ++i
  gi|15669632|ref|NP_248445.1| 591 VDAFYEELETLDSYIEEYLKEMDASRRHQLEHLIVEEVKKTNLLKIKEKIEKIEKEGKIHENFKEIFDELRDI 663
                                   556667889999**************************************************99998776666 PP

>> DUF4145  Domain of unknown function (DUF4145)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.7   0.00037       1.1      19      64 ..     617     663 ..     604     663 .. 0.87
   2 ?   -1.5   0.4      0.95   2.9e+03      33      53 ..     737     757 ..     733     772 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00037
                       DUF4145  19 RraLEkllkdkgiakgkdL...knkiealvekgvipeklkelldairvi 64 
                                   R  LE+l+++    k+++L   k+kie+  ++g i e+ ke  d++r+i
  gi|15669632|ref|NP_248445.1| 617 RHQLEHLIVEEV--KKTNLlkiKEKIEKIEKEGKIHENFKEIFDELRDI 663
                                   778999999999..44554455************************986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.95
                       DUF4145  33 kgkdLknkiealvekgvipek 53 
                                   k+k+Lk+k+++  + + i++k
  gi|15669632|ref|NP_248445.1| 737 KDKNLKKKVSDVLNGKSIEDK 757
                                   667899999998888876543 PP

>> RraB  Regulator of ribonuclease activity B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00034         1      23      91 ..       2      81 ..       1      85 [. 0.81
   2 ?   -3.0   0.0       4.1   1.2e+04      70      95 ..     158     183 ..     134     184 .. 0.66
   3 ?    0.8   0.0      0.27   8.1e+02      24      59 ..     354     389 ..     334     405 .. 0.75
   4 ?   -1.6   0.9       1.5   4.5e+03      37      90 ..     587     644 ..     583     650 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00034
                          RraB 23 eiehhfyfedeedlekfaeeleklgyevedaeede.........edge..evycldlskemsldaeeIdaiteeleelae 91
                                   i ++  ++  + l+k+++el+k+g +ve + +++         ed +  + ++++ ++ +  d+e+I++++e+ + +a+
  gi|15669632|ref|NP_248445.1|  2 KITFYMWASYCSILKKALDELKKEGVDVEYKIYSNrnpiddeflEDAKdyDLVFIYRTSSDDIDLEKIKKFNENVIVVAQ 81
                                  57778888888899*********************878755555332245777777788999***********9998887 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.1
                          RraB  70 kemsldaeeIdaiteeleelaekfgg 95 
                                   + ++l ++++d i++ l++l ++f++
  gi|15669632|ref|NP_248445.1| 158 SRHYLVNDDMDVIEKLLNRLDKEFNV 183
                                   45677778888888888888777775 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.27
                          RraB  24 iehhfyfedeedlekfaeeleklgyevedaeedeed 59 
                                   +   ++ ++++ + +++++l+++gy ve + e+ e+
  gi|15669632|ref|NP_248445.1| 354 VGSAAHLDSFQSVINIMKKLKEEGYYVENIPENGEE 389
                                   55567788899999999**********999887654 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.5
                          RraB  37 ekfaeeleklgyevedaeede....edgeevycldlskemsldaeeIdaiteeleela 90 
                                   + ++++++ +++e  d + +e     d + + +l+   +++++  ++ +i e++e++ 
  gi|15669632|ref|NP_248445.1| 587 QTVMVDAFYEELETLDSYIEEylkeMDASRRHQLEHLIVEEVKKTNLLKIKEKIEKIE 644
                                   5555555555555555555554432233455555555566666666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1243  (0.069329); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.97u 0.33s 00:00:01.30 Elapsed: 00:00:00.51
# Mc/sec: 7200.62
//
Query:       gi|15669633|ref|NP_248446.1|  [L=202]
Description: hypothetical protein MJ_1442 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0077   15.2   0.0      0.012   14.5   0.0    1.3  1  YceG_bac  Putative component of 'biosynthetic module'


Domain annotation for each model (and alignments):
>> YceG_bac  Putative component of 'biosynthetic module'
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   6.8e-07     0.012     146     228 ..      10      98 ..       5     112 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.8e-07
                      YceG_bac 146 yyGdikkheayFLilLallgvDVlylnpegkdkfekideekkltkvinypesl...el.eefpkeekvvrks......TvA 216
                                   +yG++ ++ ++FLi+L+ lg+ + +  + g +++e+i++ ++   +++ +e++   +  +e ++ ++            +A
  gi|15669633|ref|NP_248446.1|  10 FYGGTMRKFLIFLIFLSVLGCGITISGCIGGKNVEEIQNMQEQVVQQQQNENQeeyQNeDEGVDYNS----IrdvqpiGTA 86 
                                   8*************************99555555555443332222222222200022022222222....1222344677 PP

                      YceG_bac 217 ykasreleevly 228
                                   ++a +++  +l+
  gi|15669633|ref|NP_248446.1|  87 KEADEKIRPILN 98 
                                   778877777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2075  (0.115734); expected 358.6 (0.02)
Passed bias filter:                     1050  (0.0585643); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1184.21
//
Query:       gi|15669634|ref|NP_248447.1|  [L=110]
Description: hypothetical protein MJ_1443 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-06   27.8   5.1      3e-06   27.3   5.1    1.2  1  DUF4870   Domain of unknown function (DUF4870)
     0.0067   16.2   1.6      0.013   15.3   1.6    1.5  1  TIC20     Chloroplast import apparatus Tic20-like
  ------ inclusion threshold ------
       0.23   11.5   0.2       0.23   11.5   0.2    2.1  3  FixQ      Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   5.1     5e-10     3e-06      19     106 ..      21     101 ..      13     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 5e-10
                       DUF4870  19 plgniilPlviwllkkdksefvdeqgkealNFqislliysiilivlsllvligflllllllllllnlvlviiaaikanege 99 
                                    l+++i  ++ ++l+k++ +fv+ ++ +++     l+++siil+++      g+  +l +l+ l++++l i+ ++ka++ge
  gi|15669634|ref|NP_248447.1|  21 YLFGVITGILFYILEKES-KFVKFHAVQSIILFGGLWVLSIILAFI----PYGW--MLSGLVNLAAFILWIVCMYKAYKGE 94 
                                   456778887777777777.*********987777777666666555....6788..99*********************** PP

                       DUF4870 100 eyryplt 106
                                   +++ p++
  gi|15669634|ref|NP_248447.1|  95 KFKLPVI 101
                                   *****87 PP

>> TIC20  Chloroplast import apparatus Tic20-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.6   2.1e-06     0.013     104     180 ..      35     104 ..      14     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-06
                         TIC20 104 kelprylRFhvmlailLdvalqvvllesnfnPligfklklgmylwagvalalivtllecvrsaLlGkyprlPlvsea 180
                                   ++ +++++Fh++++i+L  +l v+ +   f P           l   v la +++ + c+  a  G+  +lP++ + 
  gi|15669634|ref|NP_248447.1|  35 EKESKFVKFHAVQSIILFGGLWVLSIILAFIPYG-------WMLSGLVNLAAFILWIVCMYKAYKGEKFKLPVIGDI 104
                                   34589**************************954.......223344778888888889999999999999999876 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   3.8e-05      0.23      15      46 ..      19      51 ..      17      52 .. 0.91
   2 ?    0.7   0.2     0.088   5.2e+02       4      25 ..      44      65 ..      42      72 .. 0.79
   3 ?   -1.9   0.2      0.56   3.3e+03      21      21 ..      77      77 ..      61      88 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                          FixQ 15 llflvllfygvviyafrpgnr.kdfedaAnlpL 46
                                  l +l+++  g+++y++ ++++  +f +   ++L
  gi|15669634|ref|NP_248447.1| 19 LCYLFGVITGILFYILEKESKfVKFHAVQSIIL 51
                                  779*****************9999999988887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.088
                          FixQ  4 ealrgfadswgllflvllfygv 25
                                   a++ ++ + gl +l ++++ +
  gi|15669634|ref|NP_248447.1| 44 HAVQSIILFGGLWVLSIILAFI 65
                                  5778888888888888888765 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.56
                          FixQ 21 l 21
                                  l
  gi|15669634|ref|NP_248447.1| 77 L 77
                                  2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 747.89
//
Query:       gi|15669635|ref|NP_248448.1|  [L=326]
Description: flap endonuclease-1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-27   94.4   0.4    9.5e-27   93.2   0.0    1.8  2  XPG_I     XPG I-region
    1.9e-17   63.6   0.0    3.6e-17   62.7   0.0    1.4  1  XPG_N     XPG N-terminal domain
    0.00098   18.8  10.8     0.0015   18.2   9.1    2.2  2  UVR       UvrB/uvrC motif
  ------ inclusion threshold ------
       0.13   12.8   5.4       0.13   12.8   0.3    2.9  3  HSCB_C    HSCB C-terminal oligomerisation domain
       0.13   11.8   0.2        0.4   10.2   0.0    1.8  2  DUF1002   Protein of unknown function (DUF1002)


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       2.2     8e+03      67      71 ..     102     106 ..      85     126 .. 0.45
   2 !   93.2   0.0   2.7e-30   9.5e-27       2      94 .]     141     224 ..     140     224 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.2
                                   EEEHH CS
                         XPG_I  67 vidle 71 
                                   +++++
  gi|15669635|ref|NP_248448.1| 102 ELKMK 106
                                   11111 PP

  == domain 2  score: 93.2 bits;  conditional E-value: 2.7e-30
                                   HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT.ECECTT..EEECEEEEEEHHHHHHHHT--HH CS
                         XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnlskkkskkkkekekkkvevidlekvlkelgltre 82 
                                   lmgipyv+Ap+E+EAq++y++kkg+v+av+s+D+D+ll+Gap+v+rnl+  + k+        +e i+l++vl+ l+++ +
  gi|15669635|ref|NP_248448.1| 141 LMGIPYVEAPSEGEAQASYMAKKGDVWAVVSQDYDALLYGAPRVVRNLT--TTKE-------MPELIELNEVLEDLRISLD 212
                                   8***********************************************9..4333.......59***************** PP

                                   HHHHHHHHHCET CS
                         XPG_I  83 qlidlaillgcD 94 
                                   +lid+ai++g+D
  gi|15669635|ref|NP_248448.1| 213 DLIDIAIFMGTD 224
                                   **********99 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.0     1e-20   3.6e-17      20     100 ..      15     100 ..       4     101 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 1e-20
                                   EGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE--S--GGGHHHHHHHH CS
                         XPG_N  20 siealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFdgkapdlkkeelekrs 95 
                                   s e l+gkk+aiD+   ly+fl+++r ++g  l+n     ts   g+f++++ ll++ i+Pi VFdg++p+lk+++ + r+
  gi|15669635|ref|NP_248448.1|  15 SFEDLKGKKVAIDGMNALYQFLTSIRLRDGSPLRNrkgeiTSAYNGVFYKTIHLLENDITPIWVFDGEPPKLKEKTRKVRR 95 
                                   67999***************************************************************************9 PP

                                   HHHHH CS
                         XPG_N  96 errqe 100
                                   e +++
  gi|15669635|ref|NP_248448.1|  96 EMKEK 100
                                   98876 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.7      0.16   5.8e+02       1      13 [.      87      99 ..      87     102 .. 0.87
   2 !   18.2   9.1   4.1e-07    0.0015       2      26 ..      96     120 ..      95     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.16
                           UVR  1 kklikeLeeemee 13
                                  k++ +++++em+e
  gi|15669635|ref|NP_248448.1| 87 KEKTRKVRREMKE 99
                                  68999******98 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 4.1e-07
                           UVR   2 klikeLeeemeeAaenedFEkAAkl 26 
                                   ++ ++ e +m+eA+++edFE+AAk+
  gi|15669635|ref|NP_248448.1|  96 EMKEKAELKMKEAIKKEDFEEAAKY 120
                                   677899*****************98 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   3.7e-05      0.13      35      69 ..      94     128 ..      78     129 .. 0.79
   2 ?    0.8   0.2       0.2   7.1e+02       8      20 ..     196     208 ..     194     218 .. 0.73
   3 ?   -1.6   0.0       1.1   3.9e+03      34      45 ..     300     311 ..     287     323 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                                   HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                        HSCB_C  35 veerieeleaeleeafekkdleaaadllrrlrYle 69 
                                    +e+ e+ e +++ea++k+d+e+aa+ + r  Yl+
  gi|15669635|ref|NP_248448.1|  94 RREMKEKAELKMKEAIKKEDFEEAAKYAKRVSYLT 128
                                   3567778999******999**************96 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.2
                                   HHHHHHHHHHCGG CS
                        HSCB_C   8 evMelrEeleeae 20 
                                   e  el+E le+++
  gi|15669635|ref|NP_248448.1| 196 ELIELNEVLEDLR 208
                                   6789*******95 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHH CS
                        HSCB_C  34 eveerieeleae 45 
                                   +v++++++l++ 
  gi|15669635|ref|NP_248448.1| 300 RVKKHVDKLYNL 311
                                   333333444433 PP

>> DUF1002  Protein of unknown function (DUF1002)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.4       0.6   2.1e+03     134     160 ..      94     122 ..      85     134 .. 0.61
   2 ?   10.2   0.0   0.00011       0.4     146     219 ..     232     306 ..     221     310 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.6
                       DUF1002 134 neeLvttsela..ekigsekaaelvaevk 160
                                   + e++  +el+  e i++e+ +e+ + +k
  gi|15669635|ref|NP_248448.1|  94 RREMKEKAELKmkEAIKKEDFEEAAKYAK 122
                                   45666666663336666666666655554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00011
                       DUF1002 146 kigsekaaelva.evkeevakeklkteeeikkivee..vanelninlsdeqiqqivnllkkiqkldldlkelkkqlk 219
                                    ig ++a elv   v ++v k++ +  +eik+i +e  v++++ ++l+  +++ i+++l + ++ ++  + +kk+++
  gi|15669635|ref|NP_248448.1| 232 GIGFKRAYELVRsGVAKDVLKKEVEYYDEIKRIFKEpkVTDNYSLSLKLPDKEGIIKFLVDENDFNY--DRVKKHVD 306
                                   56666677777525999*****************964499*******************98777765..46666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1454  (0.0810977); expected 358.6 (0.02)
Passed bias filter:                      778  (0.0433934); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1994.23
//
Query:       gi|15669636|ref|NP_248449.1|  [L=176]
Description: hypothetical protein MJ_1445 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-10   42.0   2.0    1.6e-10   41.8   2.0    1.1  1  Metallophos    Calcineurin-like phosphoesterase
    1.4e-08   35.1   0.0    3.1e-08   34.0   0.0    1.5  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   2.0   1.8e-14   1.6e-10       2     141 ..       5     137 ..       4     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.8e-14
                                   EEEEEESBTB......TTCCTHHHHHHHHHHHHHHH.....TTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC CS
                   Metallophos   2 rilvigDlHl......algggqlddllkllddllre.....ekpdlvllaGDlvdrgdlekellellaalvkypipvylll 71 
                                   +i +i+D+H+      ++++ ++++++++ + l+++      + d+v ++GDl+   +  k+  ell+ l      +++++
  gi|15669636|ref|NP_248449.1|   5 KIYLISDTHFnhaniiKYCNRPFSNVEEMNKTLIKNwnnvvRDKDIVYFLGDLILSKNKAKKARELLELLNG---EIVFIR 82 
                                   899***************************99988876677777*********9999999989999988888...9***** PP

                                   -TTS..CHHHHHHHHHHHHHHH.HHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSC CS
                   Metallophos  72 GNHe..gfeeellnkygylgif.sepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnlel 141
                                   GNH+  g   e ++  +y+g+    +++ d    + + l+       + +++hG+     ++ + l+ ++++ 
  gi|15669636|ref|NP_248449.1|  83 GNHDkfG---EKFRVIEYNGYKfMLIHNPD----SSYTLNF------DGWIIHGH-----HHANHLDEYPFIN 137
                                   ****222...34444333333324444444....4445555......99999999.....5555555555554 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   3.4e-12   3.1e-08       2     132 ..       5     130 ..       4     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 3.4e-12
                 Metallophos_2   2 klaiiSDlH...................snldaleavlealkevgvdaiihaGDl..eeeepevleellela..pvlaVrG 59 
                                   k+ +iSD+H                    n  +++++ + +++   d ++++GDl   + + +  +ellel+  +++ +rG
  gi|15669636|ref|NP_248449.1|   5 KIYLISDTHfnhaniikycnrpfsnveeMNKTLIKNWNNVVRDK--DIVYFLGDLilSKNKAKKARELLELLngEIVFIRG 83 
                                   6889*******************88888888888889999999*..********9877777779999999999******** PP

                 Metallophos_2  60 NnDeevveedvlreaaelgtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpev 132
                                   N+D             ++g+++   +++e +g k+ liH  +++++      ++        +++GH H  ++
  gi|15669636|ref|NP_248449.1|  84 NHD-------------KFGEKF---RVIEYNGYKFMLIHNPDSSYT----LNFDG------WIIHGHHHANHL 130
                                   ***.............555555...666677777777777622222....22222......455555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1216.27
//
Query:       gi|15669637|ref|NP_248450.1|  [L=257]
Description: dihydroorotate dehydrogenase electron transfer subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-13   50.3   9.1    3.6e-13   49.1   9.1    1.7  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
    1.6e-07   32.0   0.1    6.8e-07   29.9   0.1    1.9  1  NAD_binding_1    Oxidoreductase NAD-binding domain
     0.0033   17.6   0.0       0.41   10.8   0.0    2.2  2  NAD_binding_6    Ferric reductase NAD binding domain
  ------ inclusion threshold ------
      0.032   14.6   0.0       0.18   12.2   0.0    2.1  1  FAD_binding_6    Oxidoreductase FAD-binding domain
      0.048   12.7   0.0       0.84    8.6   0.0    2.1  2  Peptidase_M42    M42 glutamyl aminopeptidase
      0.076   13.0   0.6       0.16   11.9   0.6    1.5  1  LAMTOR5          Ragulator complex protein LAMTOR5
       0.11   12.6   0.0       0.17   11.9   0.0    1.3  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   9.1   1.4e-16   3.6e-13       1      41 [.     203     237 ..     203     238 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.4e-16
                                   ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
               DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                   e++M+CG+G+C++C+v+ +g       +vCkdGPvF++d++
  gi|15669637|ref|NP_248450.1| 203 ERYMKCGIGICGQCCVDDEG------LCVCKDGPVFWGDKL 237
                                   89****************64......9************97 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   2.7e-10   6.8e-07       2     107 ..      97     187 ..      96     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.7e-10
                                   EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHHHH CS
                 NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqdall 82 
                                   +agG G aP+   ++++ ++     +++ + G+rt+e+ll+ +++e++     +rl++      +++g+ g kg+ ++++ 
  gi|15669637|ref|NP_248450.1|  97 VAGGIGAAPIITAVEEFSKQ---GIEITTILGARTKEELLFLDRFEKV-----SRLEIC-----TDDGSFGFKGFTTEKMK 164
                                   8***************9997...79*********************99.....334333.....46888999********6 PP

                                   HHHHHHSSTTEEEEEECSHHHHHHH CS
                 NAD_binding_1  83 eellslkkeethvyvCGppgMikav 107
                                   e l +  ++ ++++ CGp+ M+k v
  gi|15669637|ref|NP_248450.1| 165 EVLKE--EKFDLIITCGPEIMMKKV 187
                                   66666..9999***********988 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00016      0.41       2      26 ..      92     116 ..      91     149 .. 0.90
   2 ?    4.9   0.0      0.01        26     139     155 ..     175     191 ..     153     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                 NAD_binding_6   2 envllvagGiGitpfisilkdllkk 26 
                                   + vl vagGiG++p+i  + ++ k+
  gi|15669637|ref|NP_248450.1|  92 DKVLAVAGGIGAAPIITAVEEFSKQ 116
                                   689**************99999876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.01
                                   xxxxxxxxxxxxxxxxx RF
                 NAD_binding_6 139 vfvCGppklvkevkklv 155
                                   +++CGp++++k+v +++
  gi|15669637|ref|NP_248450.1| 175 IITCGPEIMMKKVVEIA 191
                                   679**********9887 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.9e-05      0.18      71      97 ..      60      86 ..       7      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.9e-05
                                  TT-HHHHHHHCS-TT-EEEEEEEE-SE CS
                 FAD_binding_6 71 pgGkmsqaLdelkigdtleikGPlGkf 97
                                  + G++++ ++elk gd + ++GP+G++
  gi|15669637|ref|NP_248450.1| 60 RVGEFTKKMHELKEGDIIGVRGPYGTY 86
                                  569**********************86 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.044   1.1e+02     137     167 ..     101     131 ..      99     133 .. 0.93
   2 ?    8.6   0.0   0.00033      0.84     225     247 ..     183     205 ..     172     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.044
                                   HHHHHHHHHHHHHCTSS-SSEEEEEEESTCT CS
                 Peptidase_M42 137 agvavllellkelkeeeleatvylvatvqEE 167
                                   +g a ++++++e++++ +e+t++l a ++EE
  gi|15669637|ref|NP_248450.1| 101 IGAAPIITAVEEFSKQGIEITTILGARTKEE 131
                                   688999************************9 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00033
                                   HHHHHHHHHHHTT--EEEEEESS CS
                 Peptidase_M42 225 lrkkllelAkknnipyqlevlsg 247
                                   + kk++e+A+++nip+q+++ ++
  gi|15669637|ref|NP_248450.1| 183 MMKKVVEIANEYNIPVQVSMERY 205
                                   789***************76554 PP

>> LAMTOR5  Ragulator complex protein LAMTOR5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   6.4e-05      0.16      17      37 ..     211     231 ..     195     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-05
                       LAMTOR5  17 gvvGvlcaDeqGLclgsrGtl 37 
                                   g+ G +c+D++GLc++  G +
  gi|15669637|ref|NP_248450.1| 211 GICGQCCVDDEGLCVCKDGPV 231
                                   67899***********99975 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.6e-05      0.17      17      83 ..     110     180 ..     104     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.6e-05
               Glyco_trans_4_2  17 akeLakrgyeVhvitpkkgakdeleaegi.hvhrl...kvdrkgpleylkafklkklikkikPDvvhahya 83 
                                   ++e++k+g+e++ i     +++ l+ +++ +v rl   ++d ++ ++ ++  k+k+++k++k+D+++++ +
  gi|15669637|ref|NP_248450.1| 110 VEEFSKQGIEITTILGARTKEELLFLDRFeKVSRLeicTDDGSFGFKGFTTEKMKEVLKEEKFDLIITCGP 180
                                   7889999999998888666677777666657777744444578899999999***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1846.03
//
Query:       gi|15669638|ref|NP_248451.1|  [L=381]
Description: bifunctional formaldehyde-activating enzyme/3-hexulose-6-phosphate synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      8e-34  116.9   0.3    1.5e-33  116.0   0.1    1.6  2  Fae        Formaldehyde-activating enzyme (Fae)
    1.2e-20   74.1   0.1    1.4e-19   70.6   0.1    2.0  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> Fae  Formaldehyde-activating enzyme (Fae)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   0.1   1.7e-37   1.5e-33       1     158 [.       4     150 ..       4     151 .. 0.96
   2 ?   -3.3   0.0      0.85   7.6e+03      69      94 ..     238     264 ..     232     268 .. 0.55

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 1.7e-37
                           Fae   1 vGEalvgegeevAhidliiGekdgpvgtAfanalanqskghtpllavlrpnllvkPatlmvnkvtiknekqaellfGpaQa 81 
                                   +GEa++g++  +A +++ +G k++ ++++f+nal+   +g++ ++a lrpnl+vkP tl+v++++i++e q el+ G++Q+
  gi|15669638|ref|NP_248451.1|   4 FGEAVLGNEI-KAIVNVALG-KGELIENTFTNALT---RGNC-VFANLRPNLIVKPLTLVVPRHNIESEIQDELFQGVIQY 78 
                                   59***99998.9********.99************...7766.9************************************* PP

                           Fae  82 avakavadaveegiipkeeaddlviivsvfidpea....kdkkkiyeynyeAtklAikrAlkeePsidevleekdkakhpf 158
                                   avakavad         +  +dl ++vsv + pe+     +k+k+++y y+++klAi+rAl+e+Ps ++v +ek +a hp+
  gi|15669638|ref|NP_248451.1|  79 AVAKAVADL--------DLDEDLKVVVSVNV-PEVpitnLNKRKLFQYFYASAKLAINRALNEYPSKEKVKKEKYRALHPL 150
                                   ********9........7889**********.88889999***************************************97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.85
                           Fae  69 ekqaellfGpa.Qaavakavadaveeg 94 
                                   +++a+++ G+a  + + ka+ ++ + g
  gi|15669638|ref|NP_248451.1| 238 TANAVAISGVApKSTIIKAIHECQKCG 264
                                   445555556552334566666666555 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.1   1.5e-23   1.4e-19       2     223 ..     163     354 ..     162     356 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 1.5e-23
                                   EEEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT.SEEEEEEEE-S-HHHHHHHHHSTC CS
                     OMPdecase   2 nLclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg.flifeDrKfaDIGntvekqatags 80 
                                    L++alDv+t+++l  l++++ +  +++l+ +++l++++g      ++++ +r+ +   i++D+K+ D G ++ + a    
  gi|15669638|ref|NP_248451.1| 163 YLQIALDVPTMENLEFLLQTIPNsDHIILEAGTPLIKKFG-----LEVIEIMREYFdGFIVADLKTLDTGRVEVRLA---- 234
                                   69*********************99***************.....**********99********************.... PP

                                   HHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH..H.SHHHHHHHHHHHHHHHTTESEEECC CS
                     OMPdecase  81 arikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe..k.gytqacveaarehkaedfvmGfvaq 158
                                     +++ a++v +++va k+++ +++++ +k+g   +  l++m+  + ++l +  k + +  ++++  +++     +G+   
  gi|15669638|ref|NP_248451.1| 235 --FEATANAVAISGVAPKSTIIKAIHECQKCG--LISYLDMMNVSEPQKLYDslKlKPDVVILHRGIDEE----TFGIK-- 305
                                   ..9****************************9..9*****************755888888888888877....23332.. PP

                                   CHTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHH CS
                     OMPdecase 159 etlnateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeae 223
                                              + +++++ + l   + ++g+  +++e+l ++   +i+ivGR+I+k++dp   ++
  gi|15669638|ref|NP_248451.1| 306 -----------KEWKFKENCLL---AIAGGVGVENVEELLKE--YQILIVGRAITKSKDPGRVIR 354
                                   ...........33678999998...99999999999***995..69**************87765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2511.76
//
Query:       gi|15669639|ref|NP_248452.1|  [L=530]
Description: type II R/M system modification methyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-35  123.1   0.0    1.2e-14   54.6   0.1    3.1  3  N6_N4_Mtase      DNA methylase
    8.1e-05   22.3   0.8      0.055   13.0   0.2    2.8  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0017   18.1   0.6       0.18   11.5   0.1    2.9  3  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
       0.14   11.8   4.3        1.6    8.3   3.1    2.5  2  LepB_N           LepB N-terminal domain
       0.16   11.7   0.0       0.32   10.8   0.0    1.4  1  CDC48_2          Cell division protein 48 (CDC48), domain 2


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.1   3.3e-18   1.2e-14     121     229 ..      54     167 ..      19     169 .. 0.74
   2 !   44.9   0.0   3.1e-15   1.1e-11      63     215 ..     168     394 ..     163     404 .. 0.90
   3 !   20.7   0.1   7.6e-08   0.00027       1      72 [.     406     495 ..     406     527 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 3.3e-18
                                   GGSSBSS-HHHHHHHHHHCHHHCC-B--BSE.....EE-SCCCTTSTTS-CHH..----SS---HHHHHHHHHHHS-TT-E CS
                   N6_N4_Mtase 121 daikvpyeekdklekrgaytskkkgkkiedi.....Wdlseiqsnekkskgdt..kkkHpaqkPvallerlIklstkkgdi 194
                                   +++ v  +e ++ +k+   + +k+++++e++     Wdl +   +ek++++ +     ++ ++  +l+e+ +k   + gdi
  gi|15669639|ref|NP_248452.1|  54 NRVYVDIDEVENYYKKL--FFEKRKEWEEKLgfkldWDLAFDLLSEKERTKHVhgIHPYKGKFIPQLVEYFLKRHFNVGDI 132
                                   44444444444444444..5555555666556667777666666777777666344445899******************* PP

                                   EEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHH CS
                   N6_N4_Mtase 195 vlDpFaGSGtTavaakelgrkfiGieieeeyvela 229
                                   ++DpF+GSGtT+v ++e+g ++iGi+i++  + +a
  gi|15669639|ref|NP_248452.1| 133 IIDPFMGSGTTLVQCMEMGINSIGIDISPFNCLIA 167
                                   ***************************99877766 PP

  == domain 2  score: 44.9 bits;  conditional E-value: 3.1e-15
                                   THHHHHHHHHTT.-EEEEEEEEEEESSSTTTSTCCS-B--EEEEEEEESSTT-...............---GGGSSBSS-H CS
                   N6_N4_Mtase  63 kelkaladeifg.gffllnvivwkkpnsmpesnkdrltsthEyilvfsknkkyl.............lkfnldaikvpyee 129
                                   + +k++ ++i++ + +ll++++++k+ s++  ++++++++ ++i  ++k++ +l             ++++++ +++ y e
  gi|15669639|ref|NP_248452.1| 168 E-VKLQKYDIQKlKKILLDMLNKTKEFSKNLGDDEFVKEMDKLIEKYNKKYFTLeykrklskkeideDSYSEKIMEMFYLE 247
                                   4.8999999************************************************************************ PP

                                   HHHHHHHHHCHHHCC-B--BSEE.......................................E-SCCCTTSTTS-CHH... CS
                   N6_N4_Mtase 130 kdklekrgaytskkkgkkiediW.......................................dlseiqsnekkskgdt... 168
                                   ++kl++++    +k++++++di+                                        ls++ ++++ +++++   
  gi|15669639|ref|NP_248452.1| 248 YKKLKEKY----CKNDDEFDDIFkdkpflykwyspriraelnfylnlikdcrdetikkvamiILSRTARSVRGTTHFDlat 324
                                   ********....**********9999999999***************************9996666666666666666677 PP

                                   ............----SS---HHHHHHHHHHHS-T........T-EEEETT....-TTTHHHHHHHHTT-E CS
                   N6_N4_Mtase 169 ............kkkHpaqkPvallerlIklstkk........gdivlDpF....aGSGtTavaakelgrk 215
                                               k k +++ Pv+++ r+++ +t++         +i  D++     G   T+++ +el+++
  gi|15669639|ref|NP_248452.1| 325 lkepvfdpyycyKHK-KICRPVQTILRHLEEYTNDvisrieefSKIRKDAYyliiNGDSRTVDIEEELKKH 394
                                   777776555554444.9**********************************9*999************987 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 7.6e-08
                                   EEEEEE--SSSSSCS..........................GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCC CS
                   N6_N4_Mtase   1 vdlivtdpPYntgkdy.....................endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddse 60 
                                   +d i+t+pPY  + dy                       +++   ++  +ey+e +  vl +++r L +d  ifi + d++
  gi|15669639|ref|NP_248452.1| 406 IDGIFTSPPYLGQIDYheqhayayelfdiprldeleiGPKFKGSSKKAQKEYIEGISDVLINMKRFLNEDAKIFIVVNDKK 486
                                   688***************99999999999999999886777777777899**************************99998 PP

                                   HHTHHHHHHHHH CS
                   N6_N4_Mtase  61 ikkelkaladei 72 
                                       l++ + e+
  gi|15669639|ref|NP_248452.1| 487 N---LYKEIFEK 495
                                   5...33444444 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.2   1.5e-05     0.055       3      65 ..     132     193 ..     130     375 .. 0.87
   2 !    7.1   0.0     0.001       3.8      66      94 ..     402     429 ..     377     455 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellakl 65 
                                   +i+D+f G+G   +q  +++ + i+i+i++ ++ +a+   + Y+++ k++ +l d+++ ++++
  gi|15669639|ref|NP_248452.1| 132 IIIDPFMGSGTTLVQCMEMGINSIGIDISPFNCLIAEVKLQKYDIQ-KLKKILLDMLNKTKEF 193
                                   89*****************999*********************996.6777777877755544 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.001
               Methyltransf_15  66 klekikvdlvflSpPw.GGpsYkkqekfdl 94 
                                   k  + k+d +f+SpP  G ++Y++q+++  
  gi|15669639|ref|NP_248452.1| 402 K--NKKIDGIFTSPPYlGQIDYHEQHAYAY 429
                                   2..3357********64779*****99864 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   5.1e-05      0.18      27      65 ..     128     170 ..     125     284 .. 0.79
   2 ?    3.4   0.0     0.015        52     111     142 ..     396     426 ..     380     433 .. 0.79
   3 ?   -2.7   0.0       1.1   3.9e+03     149     176 ..     465     492 ..     452     501 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.1e-05
                                   -TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SS....H CS
                       UPF0020  27 kpgepllDPmCGsGtilIEaallganiapgllrefvle....l 65 
                                   + g+ ++DP+ GsGt l+    +g n + + + +f +     +
  gi|15669639|ref|NP_248452.1| 128 NVGDIIIDPFMGSGTTLVQCMEMGINSIGIDISPFNCLiaevK 170
                                   57999*************9999999999766666665554441 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.015
                                   -GGG--STTS---EEEE----------HHHHH CS
                       UPF0020 111 daakLrlkegevdvivtnpPYGerlgskkale 142
                                   ++ +L  k++++d i t pPY   ++ +++  
  gi|15669639|ref|NP_248452.1| 396 NFYELY-KNKKIDGIFTSPPYLGQIDYHEQHA 426
                                   556677.8889***********9999887765 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.1
                                   HHHHHHH-TT..-EEEEEESSHHHHHCC CS
                       UPF0020 149 lrelkrvlrgggrlvlltsenkalekal 176
                                   l  +kr l++++++ ++++++k+l k +
  gi|15669639|ref|NP_248452.1| 465 LINMKRFLNEDAKIFIVVNDKKNLYKEI 492
                                   5679999999999999999999887654 PP

>> LepB_N  LepB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.046   1.6e+02      50      83 ..      84     117 ..      70     127 .. 0.84
   2 ?    8.3   3.1   0.00046       1.6      93     155 ..     176     239 ..     171     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.046
                        LepB_N  50 ariDwGaafrnfakpeNnedilspleyqGlfnlk 83 
                                    ++Dw  af+ + ++e  + +   + y+G f ++
  gi|15669639|ref|NP_248452.1|  84 FKLDWDLAFDLLSEKERTKHVHGIHPYKGKFIPQ 117
                                   479*************************988775 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00046
                        LepB_N  93 ykkikglfpaiaekakklkekldekllkdivskalkkipadlldketkkelaky.lgidsfkev 155
                                    +k+k ++ ++++k k+++++l ++++ + ++k ++k  ++++  e k++l+k+ +  ds++e+
  gi|15669639|ref|NP_248452.1| 176 IQKLKKILLDMLNKTKEFSKNLGDDEFVKEMDKLIEKYNKKYFTLEYKRKLSKKeIDEDSYSEK 239
                                   58899999********************************************984556666655 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     9e-05      0.32       2      32 ..     110     140 ..     109     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9e-05
                                   .SCCCCHHHHCCCTTEEE-TTEEEEECCTCC CS
                       CDC48_2   2 idgdemaylkrqFlgrpvtkGdlvvfefkgq 32 
                                   + g ++ +l  +Fl+r + +Gd++  +f+g 
  gi|15669639|ref|NP_248452.1| 110 YKGKFIPQLVEYFLKRHFNVGDIIIDPFMGS 140
                                   6677667999**************7777743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1533  (0.0855039); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 3489.16
//
Query:       gi|15669640|ref|NP_248453.1|  [L=370]
Description: hypothetical protein MJ_1449 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-55  188.8   4.7    1.9e-55  188.1   4.7    1.3  1  RE_TdeIII    Type II restriction endonuclease, TdeIII
     0.0086   15.7   1.2       0.25   10.9   0.1    2.4  2  RE_EcoO109I  Type II restriction endonuclease EcoO109I
  ------ inclusion threshold ------
       0.14   11.7   0.4          1    9.0   0.1    2.4  2  ATP-grasp_4  ATP-grasp domain


Domain annotation for each model (and alignments):
>> RE_TdeIII  Type II restriction endonuclease, TdeIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.1   4.7   3.2e-59   1.9e-55       2     241 ..       5     265 ..       4     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 188.1 bits;  conditional E-value: 3.2e-59
                     RE_TdeIII   2 kaieekvkevlekvlekrlesfleeesrek.kpfheallpk..............evlklssferslnTslGktifEkvAk 67 
                                   k+++ek++   ++vl++r++  ++e  + + +pfh a+l +              ++l+ls++ ++l+T+lG++ fE++A+
  gi|15669640|ref|NP_248453.1|   5 KNVIEKISIETIRVLKSRFDTISDEDIKIRnMPFHMAFLRAfygkiginddtealKFLTLSQWFHGLSTTLGQSYFENIAH 85 
                                   68899***********************999************************************************** PP

                     RE_TdeIII  68 iiAkeefkeaksqkevsgtiseeaqerIdeildeltkskkkpdleeeleaire..aqegeekkaksvkaDlylksedgeky 146
                                   i++++e++ +k+      +i+   + +I+ei+++l++ ++ p++e+e++ +re   +++e  +  +++aD+y++++d +  
  gi|15669640|ref|NP_248453.1|  86 ILSNGEKRTFKN-----YKIKRSVRDKISEIINDLKSGERLPNVEKENKELREatSKNSEYVNGLEFTADVYFEDKD-KVV 160
                                   *******87765.....578888999***************************6333344455679*******9998.99* PP

                     RE_TdeIII 147 lfelKtvkPNkgqtkeekrklLelkaillkkepkaeiktyialpYnPygd...ekeYsks.......tvkklfdldeevli 217
                                   ++elKtv+PN g+++ ek+k+L  ka + +++p+++++ +i++pY+P+++   ++ Y k          +k+fd ++evli
  gi|15669640|ref|NP_248453.1| 161 MIELKTVRPNAGEMRGEKQKILYGKAYMMETKPNKKVYYFIGFPYDPTENpenPCGYDKDrfmssliEFSKYFD-KREVLI 240
                                   *************************************************9888899*99997777766778888.****** PP

                     RE_TdeIII 218 geefWdflgge.gtyeelldifeev 241
                                   +ee+W fl+ge +t++++ldi++++
  gi|15669640|ref|NP_248453.1| 241 AEELWSFLSGEeNTMKKILDIINSI 265
                                   **********************986 PP

>> RE_EcoO109I  Type II restriction endonuclease EcoO109I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.3   0.1    0.0092        55      64     122 ..      72     129 ..      63     151 .. 0.75
   2 !   10.9   0.1   4.2e-05      0.25      94     196 ..     150     267 ..     142     269 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0092
                   RE_EcoO109I  64 etifGe.fleklaifisekvygGvksgiegidlef.ekdeekyiv.qvKsGpnwgnkdqvkk 122
                                    t +G+ ++e++a++ s    +G k + +  +++   +d+   i+  +KsG    n ++ +k
  gi|15669640|ref|NP_248453.1|  72 STTLGQsYFENIAHILS----NGEKRTFKNYKIKRsVRDKISEIInDLKSGERLPNVEKENK 129
                                   6899999********99....788888888777664455555555269***99988776644 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.2e-05
                   RE_EcoO109I  94 dlefekdeekyivqvKsGpnwgnkdqvkklkenfkkakkllrtnnikleieavvGvcYGkdkekdk............... 159
                                   d+ fe  ++ +++++K      n+ +++  k+++  +k  + + + ++++   +G  Y  ++++++               
  gi|15669640|ref|NP_248453.1| 150 DVYFEDKDKVVMIELKTV--RPNAGEMRGEKQKILYGKAYMMETKPNKKVYYFIGFPYDPTENPENpcgydkdrfmsslie 228
                                   555666666666666643..3445555555556666666667777777777777888877777777776665444444433 PP

                   RE_EcoO109I 160 ..gkdkeyikliGqefWefisgdeelyvelieplgekak 196
                                     ++  +  +li +e+W+f+sg+e+   ++++ +++ ak
  gi|15669640|ref|NP_248453.1| 229 fsKYFDKREVLIAEELWSFLSGEENTMKKILDIINSIAK 267
                                   3222334457899********************999887 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.17     1e+03     105     135 ..      11      42 ..       4      52 .. 0.70
   2 ?    9.0   0.1   0.00017         1      59      83 ..     140     164 ..     105     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.17
                   ATP-grasp_4 105 vieetlealeellkevn.allglknfpvHiEl 135
                                   ++ et++ l++ +++++ + ++++n+p+H+ +
  gi|15669640|ref|NP_248453.1|  11 ISIETIRVLKSRFDTISdEDIKIRNMPFHMAF 42 
                                   5555666666666666525799*******865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00017
                   ATP-grasp_4  59 eyieGeEfavdayfdeeGepvilni 83 
                                   ey++G Ef  d+yf+ + + v++++
  gi|15669640|ref|NP_248453.1| 140 EYVNGLEFTADVYFEDKDKVVMIEL 164
                                   8*************88877776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2478.51
//
Query:       gi|15669641|ref|NP_248454.1|  [L=371]
Description: hypothetical protein MJ_1450 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-06   27.7   0.1    6.8e-06   25.5   0.0    2.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.1e-05   25.2   0.0    4.9e-05   23.1   0.0    1.8  2  DAO            FAD dependent oxidoreductase
    0.00014   22.0   0.4    0.00033   20.8   0.2    1.7  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00041   19.2   0.0       0.62    8.7   0.0    2.5  2  HI0933_like    HI0933-like protein
     0.0036   16.6   2.0        0.3   10.3   0.0    2.9  3  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      0.005   15.9   0.0      0.008   15.3   0.0    1.3  1  Lycopene_cycl  Lycopene cyclase protein
     0.0053   15.9   0.0      0.017   14.3   0.0    1.7  2  FAD_binding_2  FAD binding domain
     0.0091   16.5   0.0       0.03   14.9   0.0    1.8  2  GMC_oxred_C    GMC oxidoreductase
  ------ inclusion threshold ------
      0.011   15.6   1.1      0.019   14.8   1.1    1.4  1  Fer4           4Fe-4S binding domain
      0.014   14.7   0.0       0.02   14.2   0.0    1.2  1  FAD_binding_3  FAD binding domain
      0.016   14.6   0.1       0.24   10.7   0.0    2.7  2  GMC_oxred_N    GMC oxidoreductase
      0.024   14.9   0.2      0.084   13.1   0.1    2.0  2  TrkA_N         TrkA-N domain
       0.06   12.8   1.4       0.71    9.4   1.7    2.2  2  Mu-like_Com    Mu-like prophage protein Com
       0.12   12.5   1.6       0.23   11.6   1.6    1.4  1  Fer4_2         4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   5.3e-09   6.8e-06       1     115 [.       2     193 ..       2     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5.3e-09
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE......................TTHCHHHCSHHHHCHHHHHHHHHHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve......................legtclnggcllskallgvaedaeias.. 57 
                                   +d ++iG+G+AG ++a++l+   +kv+++e                       +  +   g  +++++ g++ d++i +  
  gi|15669641|ref|NP_248454.1|   2 YDFAIIGSGVAGATLAKELRY-RYKVAVIEkgkkpsyasegknveinyvyglGGSGVYSLGNAIKTEIKGYKIDKDIYKei 81 
                                   5789***************86.*******65565555555555555566664333344445566777777777777777** PP

                                   ........................................................HHHHCHHHHCCCCHCCTCEEEEESC CS
                                   ........................................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 ........................................................evvkklnqgielllgeevvkidpgk 82 
                                                                                           + +k+ n++i++  +  + +i + +
  gi|15669641|ref|NP_248454.1|  82 weelkikapkddflndidkafielgfekmekfidfdrcnkcgecarkickakwtplNYLKESNANIITEFN--IKAINYSN 160
                                   ********************************************************999999999999999..77776666 PP

                                   EEEEETEEECTCEEEEEESEEEE---E..EE-BC..T CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx..x RF
                   Pyr_redox_2  83 kkvklekkkegdeekiaydklvlAtGs..sprdl..g 115
                                     +++    +++++ki++++l++  G+  spr+l   
  gi|15669641|ref|NP_248454.1| 161 -YYEIL---DDKGRKIKAKNLIISAGGinSPRILkkM 193
                                   .55553...37799************86677777543 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.8e-08   4.9e-05       1      41 [.       3      44 ..       3      86 .. 0.88
   2 ?   -0.6   0.0      0.62     8e+02     158     209 ..     142     193 ..     137     206 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.8e-08
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSE CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrns 41
                                  d +iiG+G++G++ A eL      V+++ekg+ ++ ++ g+n 
  gi|15669641|ref|NP_248454.1|  3 DFAIIGSGVAGATLAKELRY-RykVAVIEKGKKPSYASEGKNV 44
                                  789***************54.346***********99999886 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.62
                                   HTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE...EEE--GGGHH.HH.HT CS
                           DAO 158 alGveilegtevtgleeedgkvwgverttp.gendaada...vVnaaGawsd.ll.gl 209
                                   +  ++i+++ +++++ +++   +++    + g++  ++a   ++ a G+ s  +l ++
  gi|15669641|ref|NP_248454.1| 142 ESNANIITEFNIKAI-NYS-NYYEI--LDDkGRK--IKAknlIISAGGINSPrILkKM 193
                                   566788888888888.332.23444..2333766..3444469999999998655444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   2.6e-07   0.00033       1      40 [.       6      44 ..       6      65 .. 0.80
   2 ?   -3.4   0.0       9.3   1.2e+04      27      36 ..     318     327 ..     314     341 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.6e-07
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev 40
                                  I+G+G++G+++A +L+  +++v ++ek+ +++  +  ++v
  gi|15669641|ref|NP_248454.1|  6 IIGSGVAGATLAKELRY-RYKVAVIEKGKKPSYASEGKNV 44
                                  9**************96.5*********999866665555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.3
                                   SSSSSSGGG- CS
                 NAD_binding_8  27 krdrlGGraa 36 
                                   +++++GG ++
  gi|15669641|ref|NP_248454.1| 318 RGSHPGGSLS 327
                                   5789999765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0   0.00048      0.62       2      35 ..       3      35 ..       2      38 .. 0.91
   2 !    7.8   0.0   0.00094       1.2     117     169 ..     138     188 ..     126     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00048
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35
                                  d ++iG G AG   A ++ +   +V+++ek+kk+
  gi|15669641|ref|NP_248454.1|  3 DFAIIGSGVAGATLAKEL-RYRYKVAVIEKGKKP 35
                                  789**************9.7889********997 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00094
                                   HHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GG CS
                   HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPk 169
                                   + lke++ ++ +e ++k++++  ++ +++  +++++++a++l+++ GG   P+
  gi|15669641|ref|NP_248454.1| 138 NYLKESNANIITEFNIKAINY--SNYYEILDDKGRKIKAKNLIISAGGINSPR 188
                                   6789999************55..6667887789***************99887 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.02        25       2      31 ..       6      33 ..       5      37 .. 0.89
   2 !   10.3   0.0   0.00023       0.3      91     144 ..     140     193 ..     136     212 .. 0.84
   3 ?    0.1   0.1      0.31   3.9e+02     204     276 ..     239     306 ..     215     318 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.02
                   Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgn 31
                                  IiG G aG + a el+      + ++Ekg+
  gi|15669641|ref|NP_248454.1|  6 IIGSGVAGATLAKELRYRYK--VAVIEKGK 33
                                  9**************98775..89****96 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00023
                   Pyr_redox_3  91 aksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnip 144
                                    k+ + +i ++ ++++++ ++   +++ + ++++Ak++ii++G  + P+ l+  
  gi|15669641|ref|NP_248454.1| 140 LKESNANIITEFNIKAINYSNYYEILDDKGRKIKAKNLIISAGGINSPRILKKM 193
                                   6777889999999****99987777777777*****************988755 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.31
                   Pyr_redox_3 204 sdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkk 276
                                   +++s  l   i++  +++ +++ +       + +ik++++ + +  + +k+++++d+  la G    ++ l k
  gi|15669641|ref|NP_248454.1| 239 THYSKLLINEIKKDYKDVKEKDIVG-----IMIKIKDENNGVVLDNDVKKEITKEDFKTLARGICKATKYLYK 306
                                   5555555556666666554433222.....2557899999999999999999999999999887777776655 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.2e-06     0.008       1      40 [.       3      39 ..       3      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.2e-06
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpn 40
                                  D ++iG+G Ag  lA++l   +++ kv +ie ++++ ++ 
  gi|15669641|ref|NP_248454.1|  3 DFAIIGSGVAGATLAKEL---RYRYKVAVIEKGKKPSYAS 39
                                  889***************...************9998765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.3e-05     0.017       1      43 [.       3      41 ..       3      42 .. 0.86
   2 ?   -2.1   0.0       1.2   1.5e+03     188     204 ..     170     186 ..     163     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqG 43
                                  D  +iGsG+AG + A e++ + + vav+ek+++    + +s+G
  gi|15669641|ref|NP_248454.1|  3 DFAIIGSGVAGATLAKELRYRYK-VAVIEKGKK---PSYASEG 41
                                  778***************98876.*******99...6666665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                                   EEEEESEEEE-----GG CS
                 FAD_binding_2 188 vrirakavvlatgGfgr 204
                                   ++i+ak++++ +gG++ 
  gi|15669641|ref|NP_248454.1| 170 RKIKAKNLIISAGGINS 186
                                   57899999*****9997 PP

>> GMC_oxred_C  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.6   4.7e+03      21      48 ..     280     307 ..     266     335 .. 0.66
   2 !   14.9   0.0   2.3e-05      0.03     115     143 ..     337     365 ..     310     366 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.6
                                   E--TT-SHHHHHHHHHHHHHHHHHCTSG CS
                   GMC_oxred_C  21 dpnylsdprdlaalvealkaarkilaaa 48 
                                   d++   +++d ++l++++ +a k l + 
  gi|15669641|ref|NP_248454.1| 280 DVKKEITKEDFKTLARGICKATKYLYKL 307
                                   5555667778888888877777776665 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.3e-05
                                   CSEEE-SGGGSSS--SS-THHHHHHHHHH CS
                   GMC_oxred_C 115 dnLrVvDaSvfPsapganptltilalAek 143
                                   ++L+V+DaS+f +a+g+ p ++i+al  k
  gi|15669641|ref|NP_248454.1| 337 EGLYVCDASLFKEALGVPPIVSIIALSKK 365
                                   69***********************9876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.1   1.5e-05     0.019       3      16 ..     114     127 ..     112     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                                   EETTTSSS-THHHH CS
                          Fer4   3 ideekCigCGaCve 16 
                                   id ++C +CG+C+ 
  gi|15669641|ref|NP_248454.1| 114 IDFDRCNKCGECAR 127
                                   9***********85 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-05      0.02       3      43 ..       3      42 ..       1      57 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS-- CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlprad 43
                                  d +I+G+G aG++la++L+ +  +v ++ek ++ ++ + ++
  gi|15669641|ref|NP_248454.1|  3 DFAIIGSGVAGATLAKELRYR-YKVAVIEKGKKPSYASEGK 42
                                  568***************999.9**********99988765 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.21   2.7e+02       1      36 [.       2      35 ..       2      57 .. 0.78
   2 ?   10.7   0.0   0.00019      0.24     236     265 ..     167     192 ..      63     207 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.21
                   GMC_oxred_N  1 vdelveggGsagsvvAaRLsedpstsvlvleaggre 36
                                  +d+ ++g+G+ag+++A+ L    + +v v+e g + 
  gi|15669641|ref|NP_248454.1|  2 YDFAIIGSGVAGATLAKELRY--RYKVAVIEKGKKP 35
                                  688899********9998854..6788888888654 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00019
                   GMC_oxred_N 236 kkgtvkrlvvaakevvvaaGalnsPqlLqr 265
                                   +k     ++++ak+ +++aG +nsP +L++
  gi|15669641|ref|NP_248454.1| 167 DK----GRKIKAKNLIISAGGINSPRILKK 192
                                   33....357899****************86 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.5e-05     0.084       1      33 [.       4      35 ..       4      53 .. 0.75
   2 ?   -2.2   0.0       3.6   4.6e+03     102     112 ..     301     311 ..     263     314 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                                  EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHH CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeer 33
                                  ++iiG G  G +la+eL+ ++k v vi+k ++ 
  gi|15669641|ref|NP_248454.1|  4 FAIIGSGVAGATLAKELRYRYK-VAVIEKGKKP 35
                                  68*****************995.*****97654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.6
                                   HHHHHHHTTSE CS
                        TrkA_N 102 aellkklgadv 112
                                    ++l+klg+d 
  gi|15669641|ref|NP_248454.1| 301 TKYLYKLGVDD 311
                                   34556666665 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.47     6e+02      20      35 ..      82      97 ..      79     101 .. 0.81
   2 ?    9.4   1.7   0.00055      0.71       6      18 ..     121     133 ..     117     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.47
                   Mu-like_Com 20 lDeltiKCPRCGtLnH 35
                                   +el+iK P+   Ln 
  gi|15669641|ref|NP_248454.1| 82 WEELKIKAPKDDFLND 97
                                  689******9888886 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00055
                   Mu-like_Com   6 RCGeCaRLLaKae 18 
                                   +CGeCaR ++Ka 
  gi|15669641|ref|NP_248454.1| 121 KCGECARKICKAK 133
                                   7**********95 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.6   0.00018      0.23       4      21 ..     113     131 ..     111     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                        Fer4_2   4 vvdtdrCigCgaCv.saCP 21 
                                   ++d drC+ Cg C  + C 
  gi|15669641|ref|NP_248454.1| 113 FIDFDRCNKCGECArKICK 131
                                   699**********537786 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2344.37
//
Query:       gi|15669642|ref|NP_248455.1|  [L=484]
Description: hypothetical protein MJ_1451 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.5e-227  754.2   3.1   4.1e-227  754.0   3.1    1.0  1  DUF2114   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2114  Uncharacterized protein conserved in archaea (DUF2114)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  754.0   3.1  2.3e-231  4.1e-227       1     449 []      34     476 ..      34     476 .. 0.99

  Alignments for each domain:
  == domain 1  score: 754.0 bits;  conditional E-value: 2.3e-231
                       DUF2114   1 eyyivasvelGntttkciltatnletgktyllnktvkmtrdvrkpkegeevfgktlagveltresvaelvrdtlleslkka 81 
                                   +yyivasvelGntttk+i+tatn++tgkty+++k+vkmtrdvrkpk+geevfg+tl+gveltre+va++v+++lleslkka
  gi|15669642|ref|NP_248455.1|  34 PYYIVASVELGNTTTKSIITATNMDTGKTYIVSKHVKMTRDVRKPKKGEEVFGETLWGVELTREAVADMVKEVLLESLKKA 114
                                   7******************************************************************************** PP

                       DUF2114  82 kldieedldfvvrstGvvagfdspeevgelikaladGCleagvppkkmtpamskenlpeklrkyslldkvvfdGavasvvp 162
                                    l+++ dl+fvvrstGv+agf+speevge+i+ala+GC++agvpp kmtpam+ke++p+ ++kys+ldk++fdGav++v+p
  gi|15669642|ref|NP_248455.1| 115 GLTVD-DLHFVVRSTGVTAGFASPEEVGEMIIALAQGCMKAGVPPAKMTPAMTKEQIPKPFDKYSFLDKIIFDGAVTGVLP 194
                                   ****9.*************************************************************************** PP

                       DUF2114 163 PkgktgvevvanemegeLvtaGikegakwtdvdfrnPcisidfGttLdGrivndeePyaktvgnfcGlaGaipdaivrGtg 243
                                   P+gk   evvanemegeLvtaGik+g+kwtdvdfrnPc+sidfGttL+Gri+nd+ Pyak++gn+cGlaGai+dai+rG+g
  gi|15669642|ref|NP_248455.1| 195 PTGK---EVVANEMEGELVTAGIKVGSKWTDVDFRNPCMSIDFGTTLAGRITNDTLPYAKVIGNLCGLAGAIADAIARGSG 272
                                   ****...************************************************************************** PP

                       DUF2114 244 lvdkklgaaldlfkekkkkkkkkkkikeyaekihelidiekvPkdrerfGtvPvdakaaeeagvvliGcdvgengsdlekl 324
                                   ++d+k+gaaldl++ k   k +++ +keyae++h++i i++vPkd++rfGtvPvd+k+ae+ag++liGcdvg+ngsdl kl
  gi|15669642|ref|NP_248455.1| 273 KIDEKTGAALDLANIKG--KPNEELAKEYAEEMHKYIIIKEVPKDVDRFGTVPVDPKSAEKAGTTLIGCDVGKNGSDLIKL 351
                                   **************777..899*********************************************************** PP

                       DUF2114 325 eeigaeilekeglkvllavldevsakivkrlievaveeglveektaiGitGragitGkkpelilekieelglyddkeenvv 405
                                   ee+g+e++ek+++++l+ +ld+v++++v+rl+e a ++gl++ek+a+GitGragitG+kpeli+ek+++l+++d++eenvv
  gi|15669642|ref|NP_248455.1| 352 EELGRELVEKSDIPTLMCCLDYVMSEVVRRLVELAYKKGLISEKSAVGITGRAGITGRKPELIIEKLKTLEIWDKVEENVV 432
                                   ********************************************************************************* PP

                       DUF2114 406 fvddgLarGaavmarCmnslGtpknPlGGvrggkCilkkriklq 449
                                   fv+dgLa+Ga+vmarCmn+lGtp+ P+GGvrgg Cil+ r+k+q
  gi|15669642|ref|NP_248455.1| 433 FVEDGLALGASVMARCMNCLGTPQVPIGGVRGGGCILGLRRKWQ 476
                                   *****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3216.01
//
Query:       gi|15669643|ref|NP_248456.1|  [L=259]
Description: hypothetical protein MJ_1452 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-17   61.8   1.2    6.9e-17   61.8   1.2    1.5  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
    4.4e-13   49.4   1.4    5.6e-13   49.1   0.5    1.6  1  Met_10           Met-10+ like-protein
    4.9e-09   36.8   0.0    8.8e-09   36.0   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.3e-08   34.7   0.3    1.7e-08   34.4   0.3    1.2  1  Methyltransf_31  Methyltransferase domain
    1.1e-07   32.4   0.0    1.9e-07   31.6   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    2.8e-07   29.9   0.1    7.3e-07   28.5   0.0    1.6  2  RrnaAD           Ribosomal RNA adenine dimethylase
      7e-07   28.9   0.1    1.3e-06   28.0   0.1    1.4  1  MTS              Methyltransferase small domain
    2.3e-06   27.6   0.2    4.2e-06   26.8   0.2    1.5  1  Methyltransf_18  Methyltransferase domain
      8e-06   25.8   0.0    1.4e-05   25.0   0.0    1.3  1  PRMT5            PRMT5 arginine-N-methyltransferase
    6.4e-05   22.8   0.0    0.00013   21.8   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00094   18.7   0.0     0.0017   17.9   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
     0.0027   18.4   0.0     0.0053   17.5   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
     0.0028   17.3   0.1     0.0051   16.5   0.1    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0037   16.3   0.1     0.0057   15.7   0.1    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
     0.0042   16.4   0.1     0.0085   15.4   0.1    1.5  1  GidB             rRNA small subunit methyltransferase G
     0.0069   16.0   0.1      0.011   15.4   0.1    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.026   14.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      0.029   14.1   0.1      0.043   13.5   0.1    1.2  1  N6_N4_Mtase      DNA methylase
       0.03   13.4   0.1      0.037   13.1   0.1    1.2  1  DREV             DREV methyltransferase
      0.056   13.1   0.0       0.14   11.8   0.0    1.5  1  RolB_RolC        RolB/RolC glucosidase family
      0.081   12.6   0.0       0.12   12.0   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.082   12.2   0.5       0.14   11.4   0.1    1.5  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family


Domain annotation for each model (and alignments):
>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   1.2   8.5e-20   6.9e-17     154     240 ..      27     113 ..      22     154 .. 0.81
   2 ?   -2.0   0.0       2.3   1.9e+03      33      73 ..     158     198 ..     138     213 .. 0.60

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 8.5e-20
                          PrmA 154 aleklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk...eekadviv 231
                                   a+e++v e++ v+D+GtGSGiLa+ aak  akkv+a+ +D+ + + akeN+++N+ ++   +  ++++ +   +ekadv++
  gi|15669643|ref|NP_248456.1|  27 AIERVVDEDDVVFDLGTGSGILAMIAAK-KAKKVYAIELDPFTYDYAKENIKVNGFNNIEII--EGDASTynfKEKADVVI 104
                                   89*********************98888.69**************************95534..34444233569****** PP

                          PrmA 232 aNILaevli 240
                                   a  L ++li
  gi|15669643|ref|NP_248456.1| 105 AELLDTALI 113
                                   ***988775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.3
                          PrmA  33 dsklleeedifepaleeeelkeevkvkalfkeeteakelia 73 
                                   d+++ +ee   e+ +ee++++++  ++  ++ e e ++ ++
  gi|15669643|ref|NP_248456.1| 158 DEDIKSEEVSEEVIYEEVDFHKTNPIEVSYNIELELEKSCE 198
                                   33322333333566666666666667666666666666555 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.5   6.9e-16   5.6e-13      91     180 ..      25     111 ..       5     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 6.9e-16
                                   HHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEE CS
                        Met_10  91 rerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladr 171
                                   ++ + ++v+e++vV d+  G G +a+ +ak  kak+v+ai+l+P ++ y kenik N  ++ ++ i++D+ ++  +++ad 
  gi|15669643|ref|NP_248456.1|  25 KNAIERVVDEDDVVFDLGTGSGILAMIAAK--KAKKVYAIELDPFTYDYAKENIKVNGFNN-IEIIEGDASTYNFKEKADV 102
                                   5667889***********************..**************************987.679********99*****9 PP

                                   EEE--TTTG CS
                        Met_10 172 vvmnlpksa 180
                                   v+ +l ++a
  gi|15669643|ref|NP_248456.1| 103 VIAELLDTA 111
                                   999998887 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   1.1e-11   8.8e-09       1      73 [.      38     108 ..      38     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.1e-11
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEEST CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssga 73 
                                   v dlG+G+G l++ +ak+   +kv+++++++   ++a+e+++ +g+ n+e+++gda++++f++ + D+v++   
  gi|15669643|ref|NP_248456.1|  38 VFDLGTGSGILAMIAAKKA--KKVYAIELDPFTYDYAKENIKVNGFnNIEIIEGDASTYNFKE-KADVVIAELL 108
                                   78**************996..9********************9******************97.9*****9544 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.3     2e-11   1.7e-08       3      96 ..      34     123 ..      32     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2e-11
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                   ++ +v DlG+G+G l+  +a++    ++v+ i+ +++   +A+en + +g++n+e  +gd+ + +  ++ ek D++++  +
  gi|15669643|ref|NP_248456.1|  34 EDDVVFDLGTGSGILAMIAAKK---AKKVYAIELDPFTYDYAKENIKVNGFNNIEIIEGDASTYN--FK-EKADVVIAE-L 107
                                   577899**************66...567***********************************99..88.9****9995.5 PP

               Methyltransf_31  84 l...naladpdkilee 96 
                                   l     +  + k++++
  gi|15669643|ref|NP_248456.1| 108 LdtaLIIEPQVKVMNS 123
                                   5443334444455554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   2.3e-10   1.9e-07       2      69 ..      40     107 ..      39     125 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.3e-10
                                   EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES CS
               Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvsse 69 
                                   d+G+G+G+la   ak++++v++++l++ + ++ake+++ +g+ ++e++++da++ +f++ + D+v++  
  gi|15669643|ref|NP_248456.1|  40 DLGTGSGILAMIAAKKAKKVYAIELDPFTYDYAKENIKVNGFnNIEIIEGDASTYNFKE-KADVVIAEL 107
                                   9********************************************************99.99***9875 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   8.9e-10   7.3e-07      28      94 ..      32     100 ..      21     125 .. 0.87
   2 ?   -1.5   0.0       1.3     1e+03      17      55 ..     119     154 ..     114     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 8.9e-10
                                   GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHHHH CS
                        RrnaAD  28 leekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpeev 94 
                                   + e++ v ++g+G Gil  + ak ak+v ++Eld+  +   +++++    +++++++ D+ +++++e++
  gi|15669643|ref|NP_248456.1|  32 VDEDDVVFDLGTGSGILAMIAAKKAKKVYAIELDPFTYDYAKENIKvnGFNNIEIIEGDASTYNFKEKA 100
                                   3499**************************************998876789*************99965 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                                   HHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEE CS
                        RrnaAD  17 kvineIldklnleekltvleigpGkGilTeeLakrakqv 55 
                                   kv+n+I++   l+e+ +++   p k+i T +L++   ++
  gi|15669643|ref|NP_248456.1| 119 KVMNSIIERGFLKEDVKII---PAKAISTIQLVEAKMSH 154
                                   7899999999999988876...66667776666655555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   1.6e-09   1.3e-06      31     102 ..      34     104 ..      22     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.6e-09
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEE CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdliv 102
                                   +++ v DlG+G G+l++ +ak+ ++  v +++ d    + aken++ n+++ +e+++ d+     ++k d+++
  gi|15669643|ref|NP_248456.1|  34 EDDVVFDLGTGSGILAMIAAKKAKK--VYAIELDPFTYDYAKENIKVNGFNnIEIIEGDASTYNFKEKADVVI 104
                                   456799***************9888..9********************************998888*****98 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.2   5.1e-09   4.2e-06       7      87 ..      27     104 ..      20     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.1e-09
               Methyltransf_18   7 aiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvv 87 
                                   ai ++v+++++v D Gt  g+l++ ++  +kakkv+a+++ +  ++ akeni+ +g+ ++ie++ +d  +   +e++d+v+
  gi|15669643|ref|NP_248456.1|  27 AIERVVDEDDVVFDLGTGSGILAMIAA--KKAKKVYAIELDPFTYDYAKENIKVNGF-NNIEIIEGDASTYNFKEKADVVI 104
                                   68899*****************99887..78999*********************99.67******997655555577665 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.7e-08   1.4e-05      63     146 ..      33     108 ..      13     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.7e-08
                                   .-EEEEEEES-TTSHHHHHHHHHHHHHCCCEEEEEEEES-HHHHHHHHHHHHHHTTCCGCEEEES-CCCCCHCC-ECEEEE CS
                         PRMT5  63 ekklvilvvGaGRGplvdralkaleetkvtkvkivavEKnpnavvtLqkkvneekWeekveviksdmrelkaeekvdllvs 143
                                   +++ v++ +G+G G l    + a++++k    k++a+E  p ++ + +++++++ + +++e+i+ d  +++ +ek+d++++
  gi|15669643|ref|NP_248456.1|  33 DEDDVVFDLGTGSGILA---MIAAKKAK----KVYAIELDPFTYDYAKENIKVNGF-NNIEIIEGDASTYNFKEKADVVIA 105
                                   55667777888888774...44555555....8***********************.99********************** PP

                                   --- CS
                         PRMT5 144 ELL 146
                                   ELL
  gi|15669643|ref|NP_248456.1| 106 ELL 108
                                   **9 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.6e-07   0.00013      70     134 ..      29      92 ..      19     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.6e-07
                                   T..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                          PCMT  70 e..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                   e  +++ + v ++G+GsG+l+ + a+  +++    +ie  +  ++ ak+n+k ++ +n+ +++gD  
  gi|15669643|ref|NP_248456.1|  29 ErvVDEDDVVFDLGTGSGILAMIAAKKAKKVY---AIELDPFTYDYAKENIKVNGFNNIEIIEGDAS 92 
                                   555788899************99998776665...******************************64 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     2e-06    0.0017       4      62 ..      37      93 ..      34     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-06
                                  EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCC CS
                Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalk 62
                                  vv ++G+G+G + + +A k++ k++ +iE+     +++ ++i+ ++++N++i++gda +
  gi|15669643|ref|NP_248456.1| 37 VVFDLGTGSGILAM-IAAKKA-KKVYAIELDPFTYDYAKENIKVNGFNNIEIIEGDAST 93
                                  78899999996554.444444.56779******************************54 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.5e-06    0.0053       2      73 ..      40     106 ..      39     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.5e-06
               Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas 73 
                                   ++G+G+G l++  ++k   +++++++++p   + ake ++ ++   +nn+e+ + d++    +++ D+v+a 
  gi|15669643|ref|NP_248456.1|  40 DLGTGSGILAMIAAKK--AKKVYAIELDPFTYDYAKENIKVNG---FNNIEIIEGDASTYNFKEKADVVIAE 106
                                   99***********999..**************77777766666...677888888888888889*****974 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   6.2e-06    0.0051      29     102 ..      20      93 ..      15     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.2e-06
                                   HHHHH.HHHCCCHCC.-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HH CS
                 Cons_hypoth95  29 realF.nilaaeieg.arvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedale 102
                                   r a+F n ++  +++   v Dl  GsG l++ A+  +akk++++e d+ ++   ken++  ++++ ++++  da+ 
  gi|15669643|ref|NP_248456.1|  20 RLAIFkNAIERVVDEdDVVFDLGTGSGILAMIAA-KKAKKVYAIELDPFTYDYAKENIKVNGFNN-IEIIEGDAST 93 
                                   67777456666655415678***********886.789************************997.6666665543 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1     7e-06    0.0057     194     255 ..      27      88 ..      20     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7e-06
               tRNA_U5-meth_tr 194 alevtqeskgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiir 255
                                   a+e + ++++ +++l  G G +++  a++ +kv a e+   + + a+ ni+ n  +n++ii 
  gi|15669643|ref|NP_248456.1|  27 AIERVVDEDDVVFDLGTGSGILAMIAAKKAKKVYAIELDPFTYDYAKENIKVNGFNNIEIIE 88 
                                   66777777888899**********************************************96 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     1e-05    0.0085      44     121 ..      31     105 ..      19     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                                   CS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCCTTTTT-EEEEEE CS
                          GidB  44 llkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaeekqeeekydvvts 121
                                   +++e++  v D+G+G G+ +++   a++ +k++ +e +     + +e ++  + +n+ei+e +a +++ +ek dvv++
  gi|15669643|ref|NP_248456.1|  31 VVDEDD-VVFDLGTGSGILAMI--AAKKAKKVYAIELDPFTYDYAKENIKVNGFNNIEIIEGDASTYNFKEKADVVIA 105
                                   566666.6*********74443..4577788********************************************986 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.3e-05     0.011       3      63 ..      37      96 ..      35     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
               Methyltransf_15  3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfella 63
                                  v+ Dl +G+G  ++  a++ +kv+aie ++ +   a++N +v g  ++i ++ gd  +   
  gi|15669643|ref|NP_248456.1| 37 VVFDLGTGSGILAMIAAKKAKKVYAIELDPFTYDYAKENIKVNGF-NNIEIIEGDASTYNF 96
                                  6889999999999999999***********************976.68*******987333 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.2e-05     0.026      11      59 ..      26      71 ..      14     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
               Methyltransf_23 11 dklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeavei 59
                                   ++er++   +++  v d+G+G+Gil+ +++++ ++v++++l+p   + 
  gi|15669643|ref|NP_248456.1| 26 NAIERVV---DEDDVVFDLGTGSGILAMIAAKKAKKVYAIELDPFTYDY 71
                                  5566666...57789**************************99854444 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.2e-05     0.043     180     230 ..      23      73 ..      21      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.2e-05
                                   HHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                   N6_N4_Mtase 180 llerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelae 230
                                   + + +I+   +++d+v+D   GSG  a++a++  +k + ie ++  ++ a+
  gi|15669643|ref|NP_248456.1|  23 IFKNAIERVVDEDDVVFDLGTGSGILAMIAAKKAKKVYAIELDPFTYDYAK 73 
                                   66889999***********************************99988887 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.6e-05     0.037      93     162 ..      33     109 ..      16     181 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-05
                          DREV  93 qedkklldlGaGdGeitkrvaptfeevyatels....etmrdrlkkkkynvlsalelqetdvkl....dlilclnlld 162
                                    ed  ++dlG+G G ++ + a+  ++vya el        ++++k  ++n + ++e + + +++    d++   +lld
  gi|15669643|ref|NP_248456.1|  33 DEDDVVFDLGTGSGILAMIAAKKAKKVYAIELDpftyDYAKENIKVNGFNNIEIIEGDASTYNFkekaDVVI-AELLD 109
                                   467889*************************97222234567888899999999986555555421213443.35555 PP

>> RolB_RolC  RolB/RolC glucosidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.14     100     170 ..      56     133 ..      48     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                     RolB_RolC 100 nsgilattlpPYredvtqeelrqal.nrve.....vsyyqgpedlsyFvailpskafvrksal..etsgekygffarsl 170
                                    ++++a+ l P+  d+ +e+++    n++e     +s+y+ +e+ +  +a l+ +a+  ++++   +s    gf++ ++
  gi|15669643|ref|NP_248456.1|  56 AKKVYAIELDPFTYDYAKENIKVNGfNNIEiiegdASTYNFKEKADVVIAELLDTALIIEPQVkvMNSIIERGFLK-ED 133
                                   689******************97655999999**********************9999999987544555555555.55 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00015      0.12       8      74 ..      34      97 ..      30     127 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                                  TT-EEEESS-TTSHHHHHHHHH.TTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHH CS
               Methyltr_RsmB-F  8 eeetilDlcaaPGgKTthiael.mknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkv 74
                                  e++ ++Dl ++ G     +a +  k++++v+A++ +    +  +en+k  g +n+ ++e+Da+ ++  
  gi|15669643|ref|NP_248456.1| 34 EDDVVFDLGTGSGI----LAMIaAKKAKKVYAIELDPFTYDYAKENIKVNGFNNIEIIEGDASTYNFK 97
                                  56667777665542....33333478999*********************************988533 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00017      0.14      47     116 ..      34     100 ..      17     107 .. 0.81
   2 ?   -2.6   0.0       3.4   2.8e+03      70     113 ..     115     158 ..     108     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                   -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T- CS
               Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfedds 116
                                   +   v+D+ +G+g la+  +++     kv  +++++   + +++ +k +g+ nie + ++a   +f++++
  gi|15669643|ref|NP_248456.1|  34 EDDVVFDLGTGSGILAMIAAKK---AKKVYAIELDPFTYDYAKENIKVNGFNNIEIIEGDASTYNFKEKA 100
                                   4557899999999998865555...55788899999999*************************999865 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.4
                                   HHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS CS
               Ubie_methyltran  70 gekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfe 113
                                   + + kv+   i+   Lk+  k +  ++ + i+++ a+  ++ ++
  gi|15669643|ref|NP_248456.1| 115 EPQVKVMNSIIERGFLKEDVKIIPAKAISTIQLVEAKMSHIYYD 158
                                   55666666677777788877777888888888887776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 1750.75
//
Query:       gi|15669644|ref|NP_248457.1|  [L=192]
Description: hypothetical protein MJ_1453 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-49  167.4   0.2    2.8e-49  167.3   0.2    1.0  1  DUF447    Protein of unknown function (DUF447)
  ------ inclusion threshold ------
      0.018   15.4   0.4      0.046   14.0   0.4    1.7  1  PRD       PRD domain


Domain annotation for each model (and alignments):
>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.3   0.2   3.1e-53   2.8e-49       1     175 [.       3     186 ..       3     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: 167.3 bits;  conditional E-value: 3.1e-53
                                   EEEEEEEE-TT-EEEEEEEEEESSSEEEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEEETTTCTT. CS
                        DUF447   1 yEvivtTksekrpnaaPiGvivkgdkvvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfdsetkpakia 81 
                                   +Ev+vtT++++r+n aPiGv++k++kv+++lf+gs+T+eNll+++++++nv+  p+++aka+l+d ++  + ++++     
  gi|15669644|ref|NP_248457.1|   3 SEVVVTTRKNNRDNKAPIGVYFKDKKVIMHLFSGSHTYENLLTEDYFSVNVVP-PIEIAKAVLDDEDDYLYYNDIP----- 77 
                                   6********99******************************************.**********888887766665..... PP

                                   EETT-SEEEEEEEEEE........CTCECCEEEEEEEEEEEEETTB---B-HHHHHHHHHHHHHHCCCC.......SHHHH CS
                        DUF447  82 vlksaeawveveveev........egdsealelelepvkeeileervkpfnRgdaaviEaaVlatRldi.......edkek 147
                                   +lks+++ + ++v e+         g++++++le e +k+ +l++++kp+nR+d++++E+aV ++Rl         +dk++
  gi|15669644|ref|NP_248457.1|  78 YLKSSYYAIFYKVIERkfvdredkFGKNRLMILEGEEIKRIYLNNIPKPYNRADGLLVEIAVIYSRLANknikineDDKKE 158
                                   *******************************************************************5555688999**** PP

                                   HHHHHHHHHHHHHHH--HHHHHHHHHHH CS
                        DUF447 148 lleeieylssvikktggerekealellk 175
                                   + ++i++++s+ikk+gg+++k+++e++ 
  gi|15669644|ref|NP_248457.1| 159 MINDIRKYFSIIKKVGGREHKQLAEIML 186
                                   *************************996 PP

>> PRD  PRD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   5.1e-06     0.046      10      64 ..     118     174 ..     111     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.1e-06
                                   HHTS-B.TTCHHHHHHHHHHHHHHHHHHTT.--HHHHHHHHHHHHTHHHHHHHHHHH CS
                           PRD  10 klqikl.eddslyerLitHlkfaieRlkeg.itienplleeikekypkefeiakeil 64 
                                   ++  ++ +  +   +L++ ++  + Rl ++ i+i++++++e+ ++ +k f i+k++ 
  gi|15669644|ref|NP_248457.1| 118 IYLNNIpKPYNRADGLLVEIAVIYSRLANKnIKINEDDKKEMINDIRKYFSIIKKVG 174
                                   5555556666677899999*******87777***********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1339.79
//
Query:       gi|15669645|ref|NP_248458.1|  [L=220]
Description: 3-dehydroquinate dehydratase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      8e-64  216.0   0.1      9e-64  215.9   0.1    1.0  1  DHquinase_I  Type I 3-dehydroquinase
  ------ inclusion threshold ------
      0.038   14.1   0.0      0.073   13.2   0.0    1.5  1  BBE          Berberine and berberine like


Domain annotation for each model (and alignments):
>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.9   0.1     1e-67     9e-64       1     228 [.       3     213 ..       3     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 215.9 bits;  conditional E-value: 1e-67
                                   EEEE--SSHHHHHHHHHHHTTS-SEEEEEGGG-.TT.THHHHHHHHHHHHHHTTS-EEEE---GGGT-S.SSS-HHHHHHH CS
                   DHquinase_I   1 cvpitgktleeilaelesgkekaDlvElRlDllketseaedvseeleelrstsdlpliftlrtkaeggrfkrkseeeylel 81 
                                   c+p++++++e++++ +e++ e aD+vE+R+D+lke s     +e++e++ +    p+i+t+r ++egg + ++++ee+l+l
  gi|15669645|ref|NP_248458.1|   3 CLPVVEDSVEKAIKTAEKYLEIADIVEFRIDMLKEVS-----EEDIEKFAK---YPCIITVRADWEGGYW-KGNNEERLNL 74 
                                   9********************************8764.....478998855...9**************9.8********* PP

                                   HHHHHHCT-SEEEEEGG.-.HHGHHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSHHH CS
                   DHquinase_I  82 lrtaielgadyvDvElt.eapeeskkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksieD 161
                                   +++aie +a++vD+El  e ++ +  + ++e+  ++tk+I+Syhdfe+tps+e+l++++ek+ ++g Di+K+a+ma+s+eD
  gi|15669645|ref|NP_248458.1|  75 IKKAIECNAKFVDIELReEKNK-ELVKFRDEI-GSKTKIIISYHDFEKTPSKEKLVEIVEKALSIG-DIAKFATMANSKED 152
                                   ****************732222.222455555.799******************************.************** PP

                                   HHHHHHHHHHHHHHT-SS-EEEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHHHH CS
                   DHquinase_I 162 vlrllsltseakeekdeaplIamamGelGkiSRilgevfGspvtfasleeakasapGqltarelrei 228
                                   vl++l++++     k + ++I + mGe+Gk++Rilg +fGs +tfas  ++k sapGq+++++l+ei
  gi|15669645|ref|NP_248458.1| 153 VLNILEVIN-----KYPGKIIGIGMGEKGKLTRILGVYFGSILTFASY-KGKSSAPGQVDIDTLKEI 213
                                   *******95.....4579*****************************5.5568***********998 PP

>> BBE  Berberine and berberine like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.1e-06     0.073      11      33 ..      44      79 ..      26      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.1e-06
                                  -...........H.HHHHHHHG.GGHHHHHHHHHHH CS
                           BBE 11 g...........k.ewgerYFg.gNferLvkvKtky 33
                                              + +w+  Y++ +N erL  +K+++
  gi|15669645|ref|NP_248458.1| 44 EkfakypciitvRaDWEGGYWKgNNEERLNLIKKAI 79
                                  245555566666449*******777********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1594.17
//
Query:       gi|15669646|ref|NP_248459.1|  [L=305]
Description: hypothetical protein MJ_1455 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.039   13.5   0.0      0.072   12.6   0.0    1.3  1  Alpha-amylase  Alpha amylase, catalytic domain
      0.067   13.2   0.1       0.17   11.9   0.1    1.6  1  DUF1128        Protein of unknown function (DUF1128)


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.1e-06     0.072      47      69 ..     130     152 ..     123     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.1e-06
                                   CC--CCCCCCHHHHHHCTT-EEE CS
                 Alpha-amylase  47 efGtnedlkeLiskahekgikvi 69 
                                   efGt ++l+eLi++a+e +ik+i
  gi|15669646|ref|NP_248459.1| 130 EFGTLDELEELIKAAKEEDIKII 152
                                   8*********************9 PP

>> DUF1128  Protein of unknown function (DUF1128)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.9e-05      0.17      35      52 ..     262     279 ..     257     288 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                       DUF1128  35 eekyedlkdlYemVmkke 52 
                                   e ky dl dlY+m+mkk+
  gi|15669646|ref|NP_248459.1| 262 EVKYRDLIDLYAMIMKKS 279
                                   689*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2120.13
//
Query:       gi|15669647|ref|NP_248460.1|  [L=429]
Description: histidinol dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   7.1e-173  575.3   2.7   8.1e-173  575.1   2.7    1.0  1  Histidinol_dh  Histidinol dehydrogenase
     0.0035   17.9   0.9        1.9    9.0   0.1    2.4  2  3-dmu-9_3-mt   3-demethylubiquinone-9 3-methyltransferase
  ------ inclusion threshold ------
      0.031   14.3   0.6        5.8    6.9   0.0    2.2  2  DUF2278        Uncharacterized conserved protein (DUF2278)
      0.038   13.5   5.6        1.2    8.6   1.1    2.3  2  UvrD-helicase  UvrD/REP helicase N-terminal domain
        3.6    8.0   6.4        3.9    7.8   0.5    2.7  2  TetR_C_26      Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  575.1   2.7  2.3e-176  8.1e-173       2     409 .]      23     428 ..      22     428 .. 0.98

  Alignments for each domain:
  == domain 1  score: 575.1 bits;  conditional E-value: 2.3e-176
                                   -------HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC CS
                 Histidinol_dh   2 krseedseeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaq 82 
                                   +r++++ ee+  tv eil+dv+e+Gdeal+ yt+kFD+v+  e+++v++eeieea++++d +++ea+e+a+eni  fh++q
  gi|15669647|ref|NP_248460.1|  23 NRNKANFEEILPTVMEILKDVKEKGDEALKYYTKKFDGVE-IEDFKVTDEEIEEAYNSVDYKVVEAIERAKENIYFFHKKQ 102
                                   6899999******************************875.789************************************* PP

                                   ----EEEEEECTTEEEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SS.GG.--HHHHHHHHHCT- CS
                 Histidinol_dh  83 keseeevketepgvvlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpq.dgkvnpavlaaaklagv 162
                                   +e+ + ++ +++g++lgq vr+ie+vG+YvPgG+a ypStvlm+++pAkvAg++ei++++Pp+ dgk npa+l+a +++gv
  gi|15669647|ref|NP_248460.1| 103 MEQIKDLNVENNGIILGQVVRAIEKVGCYVPGGRAFYPSTVLMTTIPAKVAGCEEIYITSPPTkDGKGNPATLIAGDIVGV 183
                                   *98888899************************************************************************ PP

                                   SEEEE--HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHHHHHHHHHTT CS
                 Histidinol_dh 163 deiykvGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvAaDLlsqaEH 243
                                   ++iykvGG+qAi+alAyGte+ipkvd+ivGPGniyV++AK++v+gev+iD++aGPsEvl+iaDeta++efvA+D+++qaEH
  gi|15669647|ref|NP_248460.1| 184 SAIYKVGGVQAIGALAYGTETIPKVDIIVGPGNIYVTTAKKMVYGEVAIDFLAGPSEVLIIADETANAEFVALDFIAQAEH 264
                                   ********************************************************************************* PP

                                   -TT-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCCH-EEEE-SSHHHHHHHHHHH--SEEEEESTTHHHHGGG- CS
                 Histidinol_dh 244 dedaqavlvttseelaeaveeevekqleelprkeiaekslekqsaiilvedleeaielaneyApEHlelqvedpeelleki 324
                                   d++a++v+ ttse+ ae++++++ +++e+++rkei+ k+le+   +il+ dlee+ie++n+yApEHle+ +++pee+l+ki
  gi|15669647|ref|NP_248460.1| 265 DPNASCVITTTSEKKAEEIKNKIFEEIEKAERKEIILKALEN--SAILIGDLEECIEFSNKYAPEHLEILTKNPEEVLNKI 343
                                   ******************************************..678999******************************* PP

                                   -S-SEEEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                 Histidinol_dh 325 knaGaiflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkelaeavetlAeaEgLeaHaeav 405
                                   k+aG++flGeysp+++gDYa+GtnhvLPTs++Ar+ssgl+ve+Flkki++q+l+ke+lk++a+ v+tlAeaEgL  Haeav
  gi|15669647|ref|NP_248460.1| 344 KHAGSVFLGEYSPVPVGDYASGTNHVLPTSQFARMSSGLNVETFLKKITYQKLDKESLKNIADIVITLAEAEGLFGHAEAV 424
                                   ********************************************************************************* PP

                                   HHHH CS
                 Histidinol_dh 406 kvRl 409
                                   + Rl
  gi|15669647|ref|NP_248460.1| 425 RRRL 428
                                   *996 PP

>> 3-dmu-9_3-mt  3-demethylubiquinone-9 3-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0021       7.7      11      45 ..      45      79 ..      32      93 .. 0.83
   2 !    9.0   0.1   0.00054       1.9      44      96 ..     239     291 ..     219     299 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0021
                  3-dmu-9_3-mt 11 geaeeAaefYvsvfenseilsvarypeeepskegk 45
                                  ++ +eA+++Y++ f+  ei++++ ++ee ++  ++
  gi|15669647|ref|NP_248460.1| 45 EKGDEALKYYTKKFDGVEIEDFKVTDEEIEEAYNS 79
                                  6778*******************999987664444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00054
                  3-dmu-9_3-mt  44 gkvltveFtlagqefvalnggpefkfneavSllveckdqeevdrlwnalseeg 96 
                                    +vl +  + a+ efval+   + ++++  S +++++++++ +++ n++ ee 
  gi|15669647|ref|NP_248460.1| 239 SEVLIIADETANAEFVALDFIAQAEHDPNASCVITTTSEKKAEEIKNKIFEEI 291
                                   5667777788999***********************************99884 PP

>> DUF2278  Uncharacterized conserved protein (DUF2278)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2    0.0041        15      80     143 ..      40     101 ..      11     116 .. 0.80
   2 ?    6.9   0.0    0.0016       5.8      87     134 ..     251     298 ..     234     314 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0041
                       DUF2278  80 fhelesepkglaLDyirsk..lldlkkgrvlphdkpgedndildklepilkkaieekatvyvFGek 143
                                   +++++ e+++ aL y+ +k   +++++++v  +++++  n +  k+ + +++a   k ++y F +k
  gi|15669647|ref|NP_248460.1|  40 LKDVK-EKGDEALKYYTKKfdGVEIEDFKVTDEEIEEAYNSVDYKVVEAIERA---KENIYFFHKK 101
                                   34444.78899*****999889*******************************...8899999665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0016
                       DUF2278  87 pkglaLDyirsklldlkkgrvlphdkpgedndildklepilkkaieek 134
                                   ++ +aLD+i +   d+++ +v+ ++ +++ ++i +k+ + ++ka +++
  gi|15669647|ref|NP_248460.1| 251 AEFVALDFIAQAEHDPNASCVITTTSEKKAEEIKNKIFEEIEKAERKE 298
                                   34459***********************************99996554 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.1   0.00034       1.2     211     269 ..       8      70 ..       6      95 .. 0.91
   2 ?    7.0   0.2     0.001       3.6      37      77 ..     258     299 ..     252     336 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00034
                                   HHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHH....CHHHHHHHHHHSSEEEESSGGG-B CS
                 UvrD-helicase 211 kkiaeflkeyqeqkkeenalDfsdllhallellee....neelaealrerykeiliDEyQDTn 269
                                   kki+e+ ke +e+  ++n + f+++l  ++e+l++    ++e+++++ ++++ + i ++  T+
  gi|15669647|ref|NP_248460.1|   8 KKIKELTKEEEEKIINRNKANFEEILPTVMEILKDvkekGDEALKYYTKKFDGVEIEDFKVTD 70 
                                   578888999999999***********************99************99999987776 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.001
                                   HHHTSSSTGGG.EEEEESSHHHHHHHHHHHHHHHHHCCHHCT CS
                 UvrD-helicase  37 likeeeiepdr.ilvvTFTnkAaeElkeRieealkkaeqess 77 
                                    i+++e +p+   ++ T  +k aeE+k++i e ++kae++++
  gi|15669647|ref|NP_248460.1| 258 FIAQAEHDPNAsCVITTTSEKKAEEIKNKIFEEIEKAERKEI 299
                                   57777778777245555668****************987653 PP

>> TetR_C_26  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.5    0.0011       3.9      71      97 ..      83     109 ..      62     118 .. 0.78
   2 ?    2.2   0.8     0.061   2.2e+02      49     108 ..     290     346 ..     269     346 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHHHHHT.S---SS-HHHH CS
                     TetR_C_26  71 lligliEsaaEqlylydeeeeeeveek 97 
                                    ++++iE a E++y++++++ e++++ 
  gi|15669647|ref|NP_248460.1|  83 KVVEAIERAKENIYFFHKKQMEQIKDL 109
                                   5899****************9999865 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.061
                                   HHHHHHHTTSB-TT--HHHHHHHHHHHHHHHHHHHHT.S---SS-HHHHHHHHHHHHHHH CS
                     TetR_C_26  49 lleeakkkeeireeieveataklligliEsaaEqlylydeeeeeeveekkkellkflkra 108
                                    +e+a++ke i +   +   + +lig +E+  E    y+ e+ e ++++ +e+l+ +k+a
  gi|15669647|ref|NP_248460.1| 290 EIEKAERKEIILK---ALENSAILIGDLEECIEFSNKYAPEHLEILTKNPEEVLNKIKHA 346
                                   3444444444444...44566789999999999999999999999999999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1229  (0.0685482); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2843.05
//
Query:       gi|15669648|ref|NP_248461.1|  [L=135]
Description: hypothetical protein MJ_1457 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-07   29.8   0.1    6.4e-07   29.7   0.1    1.1  1  DUF2076         Uncharacterized protein conserved in bacteria
  ------ inclusion threshold ------
      0.037   13.7   0.0      0.047   13.4   0.0    1.2  1  Tetraspanin     Tetraspanin family
      0.056   13.7   3.7      0.086   13.1   3.7    1.2  1  DUF5082         Domain of unknown function (DUF5082)
      0.086   11.7   0.1      0.095   11.6   0.1    1.1  1  Phage_min_cap2  Phage minor capsid protein 2
        0.1   11.8   0.0       0.13   11.5   0.0    1.1  1  Zip             ZIP Zinc transporter
        4.7    6.9   4.8        9.2    6.0   4.8    1.5  1  Neurensin       Neurensin


Domain annotation for each model (and alignments):
>> DUF2076  Uncharacterized protein conserved in bacteria (DUF2076)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.1   2.1e-10   6.4e-07     150     208 ..      51     107 ..      33     133 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.1e-10
                       DUF2076 150 ggGggFLggAlqtAAGVaGGvllangleslfsgksgeegaasasqsaeeeeiinnyyss 208
                                   +  +  Lg+A++ A GV++G l+ +++e+++++++++e  a++ +s+++e++i+++ ++
  gi|15669648|ref|NP_248461.1|  51 RDSSNLLGTAAAVAGGVIAGELITDAIEDVINNNENNE--ADGYNSEGIETTIEDTIEE 107
                                   667889***************************87555..4446888999999888722 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.6e-05     0.047      77     119 ..       8     101 ..       2     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXX--HHH................................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                   Tetraspanin  77 cllltfsllllvlfllelaagilgfvfsdk................................................... 106
                                   +ll +f+ l ++l+ + l++g l+f  ++k                                                   
  gi|15669648|ref|NP_248461.1|   8 TLLILFFGLAFILVGFGLILGYLIFSRKNKtvngtanrtvvverdssnllgtaaavaggviagelitdaiedvinnnenne 88 
                                   799***************************888888888888888888888888887666655555555555555555544 PP

                                   ........HHHHH CS
                                   xxxxxxxxxxxxx RF
                   Tetraspanin 107 argkvseiinnai 119
                                   a+g  se i+++i
  gi|15669648|ref|NP_248461.1|  89 ADGYNSEGIETTI 101
                                   3333344444444 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.7   2.9e-05     0.086      62     105 ..      86     131 ..      70     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                       DUF5082  62 Gkeennydgirs.....nlessyqtyvdkldelidaieeEIerLenqis 105
                                   ++e++ y+   s      +e+ ++++ + +d++i  i +EI ++ n+i 
  gi|15669648|ref|NP_248461.1|  86 NNEADGYN---SegietTIEDTIEEIDKGVDNVIEDITDEIDNITNDIG 131
                                   33444444...333466*****************************996 PP

>> Phage_min_cap2  Phage minor capsid protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.2e-05     0.095      72     135 ..      71     131 ..      46     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.2e-05
                Phage_min_cap2  72 kelrkllkeagdkaiksddkelaiykeaglepkplekseelqqlveaylkqtegelkNltntta 135
                                   + + ++++++ +++ ++++   + y+++g+e++  ++ ee+++ v+++++++++e++N+tn ++
  gi|15669648|ref|NP_248461.1|  71 ELITDAIEDVINNNENNEA---DGYNSEGIETTIEDTIEEIDKGVDNVIEDITDEIDNITNDIG 131
                                   4445555555555555555...8999999999999999**********************9886 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.2e-05      0.13       5      69 ..      12      89 ..       7     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.2e-05
                           Zip  5 ilaiiaililsllgllgpllvpkiskl.............lsklllslllafavGvllgtaflhLlPealealeesql 69
                                  +   +a++++++  +lg l++++++k+              s++ll  + a a+Gv+ g  + + + +++++ e+ + 
  gi|15669648|ref|NP_248461.1| 12 LFFGLAFILVGFGLILGYLIFSRKNKTvngtanrtvvverDSSNLLGTAAAVAGGVIAGELITDAIEDVINNNENNEA 89
                                  4445677778888888999999999999*******************************9999999999998887665 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.8    0.0031       9.2      43      66 ..       3      26 ..       1      70 [. 0.74

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0031
                     Neurensin 43 vslvvgtlvlllGvtallvGylvp 66
                                  v++++ +l+l +G++++lvG+ + 
  gi|15669648|ref|NP_248461.1|  3 VMTALTLLILFFGLAFILVGFGLI 26
                                  678889999999999999999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1204  (0.0671538); expected 358.6 (0.02)
Passed bias filter:                      741  (0.0413297); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 885.34
//
Query:       gi|15669649|ref|NP_248462.1|  [L=218]
Description: hypothetical protein MJ_1458 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-74  249.0   4.6    1.1e-74  249.0   4.6    1.9  2  DUF5612       Domain of unknown function (DUF5612)
      1e-09   38.0   0.0    1.4e-08   34.3   0.0    2.4  2  ACT           ACT domain
    0.00031   21.3   0.0    0.00078   20.0   0.0    1.7  2  ACT_4         ACT domain
  ------ inclusion threshold ------
      0.039   13.7   1.0          1    9.1   0.1    2.2  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
       0.17   11.3   2.0        0.7    9.3   0.7    2.2  2  PcrB          PcrB family


Domain annotation for each model (and alignments):
>> DUF5612  Domain of unknown function (DUF5612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.088   3.2e+02      76     104 ..      24      52 ..       3      59 .. 0.74
   2 !  249.0   4.6     3e-78   1.1e-74       1     142 [.      75     216 ..      75     217 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.088
                                   SB--THHHHHHHHHHHT.T-EEEEES-BS CS
                       DUF5612  76 slmGGkiteavkklkeekdiivislnmaG 104
                                   s +GG+it + + +k++ +i  i +++ G
  gi|15669649|ref|NP_248462.1|  24 SELGGNITYTQQFIKDDGKIGFIYMEVEG 52 
                                   558*************9999999888776 PP

  == domain 2  score: 249.0 bits;  conditional E-value: 3e-78
                                   E--HHHHT-EEEEEEE-HHHHHHHHHHHHHHHHHHHCTSS-EEEEEEE--SHHHHHHHHHHGGGSTTEEEEEEESSB--TH CS
                       DUF5612   1 hkslkeifGkrviilGGGaqvaqvalGaiseadrhnirGerisvdtiplvGeeelaeaveavsrlprvkvlvlaGslmGGk 81 
                                   h+slk+i+Gkrvii+GGGaqva+va GaiseadrhnirGerisvdt+p+vGee+l+eav+av++lprv +lvlaGslmGGk
  gi|15669649|ref|NP_248462.1|  75 HSSLKKIYGKRVIIIGGGAQVAEVARGAISEADRHNIRGERISVDTLPIVGEENLYEAVKAVATLPRVGILVLAGSLMGGK 155
                                   689****************************************************************************** PP

                                   HHHHHHHHHHT.T-EEEEES-BSSHHHHSSEEESSHHHHHHHHHHHH-TTS---GGGCSS- CS
                       DUF5612  82 iteavkklkeekdiivislnmaGsvtevadlvvtdpvqaGvlavmavadtavfdiervkgk 142
                                   iteavk+lke+++i+visl+m+Gsv++vadlvv dp+qaGvlavma+a+ta+fdi++vkg+
  gi|15669649|ref|NP_248462.1| 156 ITEAVKELKEKTGIPVISLKMFGSVPKVADLVVGDPLQAGVLAVMAIAETAKFDINKVKGR 216
                                   **********************************************************997 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0     4e-12   1.4e-08       3      65 ..       5      66 ..       4      68 .. 0.94
   2 ?    1.0   0.0       0.1   3.7e+02      40      65 ..     111     136 ..      96     141 .. 0.62

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 4e-12
                                  EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                           ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65
                                  +++++++++G+L++++g+l+++g Ni+  +q+  +d+    ++ ++v++ +d+ee++++ ++ 
  gi|15669649|ref|NP_248462.1|  5 ISIEAENKVGVLHKLTGILSELGGNITYTQQFIKDDG-KIGFIYMEVEGIKDIEELKRRMESC 66
                                  789*********************************9.999***************9998875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.1
                                   ECEEEEEEEEEEHHHHHHHHHHHHTT CS
                           ACT  40 vagivfvvivvdeedleevlealkkl 65 
                                   + g+ ++v++    + e++ ea+k++
  gi|15669649|ref|NP_248462.1| 111 IRGERISVDTLPIVGEENLYEAVKAV 136
                                   56666666666666666666666665 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.2e-07   0.00078       7      76 ..       3      70 ..       1      73 [. 0.81
   2 ?   -3.7   0.0         5   1.8e+04      26      38 ..     201     214 ..     197     216 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.2e-07
                         ACT_4  7 vrleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVi 76
                                  + +++eae++ g+L ++t ++se ++ni+  +   +  d    + i +eV+ +++++++ +++++ + V+
  gi|15669649|ref|NP_248462.1|  3 IGISIEAENKVGVLHKLTGILSELGGNITYTQQFIK--DDGKIGFIYMEVEGIKDIEELKRRMESCECVK 70
                                  689**************************9999985..44566777777777777777777777777775 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5
                         ACT_4  26 visee.kanivsvn 38 
                                   +i+e+ k +i++v+
  gi|15669649|ref|NP_248462.1| 201 AIAETaKFDINKVK 214
                                   34444488888776 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.019        67      13      40 ..      84     111 ..      78     112 .. 0.83
   2 ?    9.1   0.1   0.00028         1      16      54 ..     146     182 ..     129     207 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.019
                                   SEEEEE-CHHCHTTGHHHHHHHHHHHT- CS
                  TPP_enzyme_M  13 rpvilvGggvarsgaseelrelaeklgi 40 
                                   + vi++Ggg++ +++++ + + a++++i
  gi|15669649|ref|NP_248462.1|  84 KRVIIIGGGAQVAEVARGAISEADRHNI 111
                                   569********99988888777777776 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00028
                                   EEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-T CS
                  TPP_enzyme_M  16 ilvGggvarsgaseelrelaeklgiPvvttlmgkgvipe 54 
                                   +l+G+     + +e+++el ek+giPv++  m  g++p+
  gi|15669649|ref|NP_248462.1| 146 VLAGS-LMGGKITEAVKELKEKTGIPVISLKM-FGSVPK 182
                                   33443.3346899**************96444.455555 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.7    0.0002       0.7     167     204 ..      71     108 ..      42     136 .. 0.85
   2 ?    1.3   0.1     0.053   1.9e+02      16      62 ..     126     172 ..     124     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0002
                                   -HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCCSSE CS
                          PcrB 167 dveevialkkklekarlivGGGirsaEkAkevveaADv 204
                                     e    lkk   k  +i+GGG + aE A+  +  AD 
  gi|15669649|ref|NP_248462.1|  71 SFEIHSSLKKIYGKRVIIIGGGAQVAEVARGAISEADR 108
                                   5577778999999********************99994 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.053
                                   SS-CHHHHHHHHCTT-SEEE.EECST.CHHHHHHHHHHHHHCTSSS-EE CS
                          PcrB  16 eenpdEiveiviesgtDavm.igGsq.svtldntvrllkkvsriklPiv 62 
                                   een  E+v++v+     +++ ++Gs  + +  ++v+ lk+   +++P++
  gi|15669649|ref|NP_248462.1| 126 EENLYEAVKAVATLPRVGILvLAGSLmGGKITEAVKELKEK--TGIPVI 172
                                   577788899997776666651689988999999****9998..999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1557.39
//
Query:       gi|15669650|ref|NP_248463.1|  [L=556]
Description: adenine deaminase AdeC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-50  169.2   0.0    1.4e-49  167.7   0.0    1.7  2  Adenine_deam_C  Adenine deaminase C-terminal domain
    4.9e-34  118.2   0.6    1.8e-32  113.0   0.6    2.2  1  Amidohydro_1    Amidohydrolase family
      2e-09   37.5   0.0    0.00023   20.8   0.0    2.2  2  Amidohydro_3    Amidohydrolase family


Domain annotation for each model (and alignments):
>> Adenine_deam_C  Adenine deaminase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.48   2.8e+03     109     127 ..     206     224 ..     204     235 .. 0.81
   2 !  167.7   0.0   2.3e-53   1.4e-49       3     164 ..     392     547 ..     390     550 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.48
                                   TTBBSS-HHHHHHHHHHHH CS
                Adenine_deam_C 109 GlmSdepaeevaekleele 127
                                   G+mSd++  +  e+le+l+
  gi|15669650|ref|NP_248463.1| 206 GIMSDHESVDEDEALEKLR 224
                                   9****99888888888887 PP

  == domain 2  score: 167.7 bits;  conditional E-value: 2.3e-53
                                   S-EEEEEEEEEETTEEE-..-TTEEEEEEE--SSSS--EEEEEEESS--BSSEEEES--TTT--EEEEESSHHHHHHHHHH CS
                Adenine_deam_C   3 iTkelevelpvkdgvvvadlekdllkiavveRhgktgnvgvgfvkgfglkkgAiAssvahDshniivvGtndedmalAvnr 83 
                                   iT+el+ + +  + ++    e+ + ki+v+eRh++tgn+g+g++ +f l++gA+Ass+ahDshn+i++G+n++d+alAvn+
  gi|15669650|ref|NP_248463.1| 392 ITEELIFSTE--EIKILL-NENAINKIFVIERHKNTGNIGKGLIYNF-LEEGALASSYAHDSHNVIAIGNNEKDLALAVNK 468
                                   5555555532..222222.3899************************.99******************************* PP

                                   HHHTTSEEEEEETTEEEEEEE-TBTTTBBSS-HHHHHHHHHHHHHHHHTTS-.TTTBSGGGGGSTT-TTSSSEEEETTSEE CS
                Adenine_deam_C  84 vielgGGivvvedgkvlaelpLpiaGlmSdepaeevaekleeleaalkelgv.kledpfmtlsflalpviPelkltdkGlv 163
                                   ++++gGG+++++dg+v++ lpLp++G+m d +++ +aek+++l +  +  g  ++e+pf+++sf++lpviPelk+tdkGlv
  gi|15669650|ref|NP_248463.1| 469 LKDIGGGFIAAKDGEVVEYLPLPVGGIMGD-DGKYIAEKINALYKKIE--GWsSFENPFLSMSFFSLPVIPELKITDKGLV 546
                                   *****************************9.89***********9998..4437**************************9 PP

                                   E CS
                Adenine_deam_C 164 d 164
                                   +
  gi|15669650|ref|NP_248463.1| 547 K 547
                                   6 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.6     3e-36   1.8e-32       2     342 ..      59     332 ..      58     334 .. 0.88

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 3e-36
                                   EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEEE CS
                  Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilgg 82 
                                   + P +ID H+H+e+s+l         +p e+ +++l+sg+++ + +++++++ +g+    gi ++l+ a+ l  +++++++
  gi|15669650|ref|NP_248463.1|  59 LSPTFIDGHIHIESSHL---------IPSEFEKFVLKSGVSKVVIDPHEIANIAGKE---GILFMLNDAKIL--DVYVMLP 125
                                   78**************9.........******************************7...**********97..******* PP

                                   SSEGGS.GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE..TSSCHHH CS
                  Amidohydro_1  83 kvsldr.gsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHa..letkgev 159
                                   ++++++  +++  + ++e++++ +        d v+   +++ ++a+ ++dee+ + +++akk+++ ++ H+  l   + +
  gi|15669650|ref|NP_248463.1| 126 SCVPATnLETSGAEITAENIEELI------LLDNVLGlGEVMNYPAVINEDEEMLKKIEVAKKYNKLIDGHCpkLKGWELN 200
                                   *****8877777777777775554......68889999******************************************* PP

                                   HHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHH.. CS
                  Amidohydro_1 160 edaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkalde.. 238
                                   +++++++ +++e+    e +e+          l  g  l+  e                       ++++  l+ + +   
  gi|15669650|ref|NP_248463.1| 201 KYISHGIMSDHESVDEDEALEK----------LRLGLKLMIREG--------------------TASKNIYLLNICKKIkd 251
                                   *************999999888..........999999996621....................12333333333333320 PP

                                   TSCEEEEEECT....TSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EE CS
                  Amidohydro_1 239 GvkvglgtDga....asgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlv 315
                                     +++l++D++      g  ln+   lr a+           ++ +s+ ea++m+Tin+A ++g+  +vG i++G +A +v
  gi|15669650|ref|NP_248463.1| 252 FRNIMLVSDDVcikdLDGYMLNI---LRKAT-----------NY-VSPIEAIQMVTINPANYFGF--DVG-IKAGNEASFV 314
                                   33489999999999999999999...99999...........77.********************..9**.********** PP

                                   EECCCTCGGGTTTCTSEEEEEEEETTE CS
                  Amidohydro_1 316 vvdldilaafvglkkdgnvkkvivkGk 342
                                   ++         ++ ++++v + ++kG+
  gi|15669650|ref|NP_248463.1| 315 IF---------EDLDNFKVYNIVIKGR 332
                                   **.........***************7 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.8e-08   0.00023       1      23 [.      50      72 ..      50      82 .. 0.87
   2 !   14.5   0.0   3.1e-06     0.019     403     447 ..     277     319 ..     267     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.8e-08
                  Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlag 23
                                  +viD+kG+++ P F+D H+H+ +
  gi|15669650|ref|NP_248463.1| 50 KVIDLKGKYLSPTFIDGHIHIES 72
                                  69******************654 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.1e-06
                  Amidohydro_3 403 rpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.a 447
                                   ++ + +s  ea++++T +pA  +g +    ++++G +A++v+++  
  gi|15669650|ref|NP_248463.1| 277 KATNYVSPIEAIQMVTINPANYFGFDV---GIKAGNEASFVIFEdL 319
                                   566778889******************...5************842 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3546.99
//
Query:       gi|15669651|ref|NP_248464.1|  [L=162]
Description: hypothetical protein MJ_1460 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-18   65.7   0.1    3.9e-18   65.2   0.1    1.3  1  V4R       V4R domain
    3.4e-05   23.8   0.0    4.8e-05   23.3   0.0    1.2  1  DUF2507   Protein of unknown function (DUF2507)
  ------ inclusion threshold ------
       0.03   14.0   0.0       0.04   13.6   0.0    1.1  1  TRAPP     Transport protein particle (TRAPP) component


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.1   6.6e-22   3.9e-18       3      61 ..      97     155 ..      95     156 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 6.6e-22
                                   EEEEEES-S-TT---SS---HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEEEE CS
                           V4R   3 lsieespelaglpgkeePvCyleaGllagalsellgkrveveEveCaaeGhdhCeFeve 61 
                                   ++i+ s+   ++++keeP++ + aG+lag+l+e+++k++ v+EveC ++G+d+C+Fev+
  gi|15669651|ref|NP_248464.1|  97 YKIKLSNPPYQWVSKEEPIHDFIAGILAGCLEEIFKKKFVVNEVECVSQGKDKCVFEVK 155
                                   578889999************************************************98 PP

>> DUF2507  Protein of unknown function (DUF2507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0     8e-09   4.8e-05      22     122 ..      50     154 ..      43     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8e-09
                       DUF2507  22 eilYwaGkelArkfplesledlieffekagwGtLellkek....kkelefeLsgeiveerlkekeekefqLEaGflAeqie 98 
                                   + lY +G e  + ++ +++e+l + f+ +++G+Le+ ++k    +  ++ +Ls +  +    +kee+   + aG+lA ++e
  gi|15669651|ref|NP_248464.1|  50 TSLYEIGEEFGKMLSPKNIEELKKIFKLMNFGDLEIDENKillkNPPYKIKLSNPPYQ--WVSKEEPIHDFIAGILAGCLE 128
                                   459*********************************9997332244556666666665..566899999999*******99 PP

                       DUF2507  99 qq..kevvaeakeekkkkkkkveitv 122
                                   +   k++v++ +e +++ k+k+ ++v
  gi|15669651|ref|NP_248464.1| 129 EIfkKKFVVNEVECVSQGKDKCVFEV 154
                                   85214455555555555555666666 PP

>> TRAPP  Transport protein particle (TRAPP) component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.6e-06      0.04      59     144 ..      55     155 ..      34     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.6e-06
                         TRAPP  59 ickdlWkllfgkqidnlktn....hrgeyvltdnefpltrf......velpke....ls....ylaflcGiirGaLenlgf 121
                                   i +++ k+l  k+i++lk+     + g++ +++n+ +l++        +        +s    +  f++Gi+ G+Le +  
  gi|15669651|ref|NP_248464.1|  55 IGEEFGKMLSPKNIEELKKIfklmNFGDLEIDENKILLKNPpykiklSN---PpyqwVSkeepIHDFIAGILAGCLEEIFK 132
                                   5567778888999999998876667788999999999997766643333...33346335789**************9976 PP

                         TRAPP 122 pakVtahelps.delrgrttfeik 144
                                   +  V   e++  ++ +++++fe+k
  gi|15669651|ref|NP_248464.1| 133 KKFVVN-EVECvSQGKDKCVFEVK 155
                                   644444.44334568899999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1152.86
//
Query:       gi|15669652|ref|NP_248465.1|  [L=199]
Description: hypothetical protein MJ_1461 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          2    8.7   7.7          1    9.6   0.4    3.0  3  DUF5442   Family of unknown function (DUF5442)


Domain annotation for each model (and alignments):
>> DUF5442  Family of unknown function (DUF5442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4   5.7e-05         1      36      69 ..      24      58 ..       8      67 .. 0.79
   2 ?    0.3   0.1     0.043   7.8e+02      11      23 ..      94     106 ..      70     122 .. 0.62
   3 ?    1.5   1.3     0.019   3.4e+02      32      54 ..     136     158 ..      91     194 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 5.7e-05
                       DUF5442 36 lkk.sekeklkeylkdisirtvnciikrfeddpqa 69
                                  +kk  e +k  + lk+   ++vn  i+rf ++p  
  gi|15669652|ref|NP_248465.1| 24 VKKyEEIKKHEDILKKDLLNAVNVFIERFRNNPCI 58
                                  444156788899999999**************975 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.043
                       DUF5442  11 engandflkfvak 23 
                                   e+  n+f+k++ak
  gi|15669652|ref|NP_248465.1|  94 EEKLNEFFKIIAK 106
                                   2223333333333 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.019
                       DUF5442  32 iseelkksekeklkeylkdisir 54 
                                   + eel + e  k+ e + d++ r
  gi|15669652|ref|NP_248465.1| 136 LKEELPTEEYLKVMEEFDDLIER 158
                                   45566666666666666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1479  (0.0824921); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1298.34
//
Query:       gi|15669653|ref|NP_248466.1|  [L=83]
Description: hypothetical protein MJ_1462 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        0.1   12.7   0.1       0.13   12.4   0.1    1.3  1  TetR_C_27  Tetracyclin repressor-like, C-terminal domain
       0.13   11.8   0.0       0.16   11.5   0.0    1.2  1  PGM1_C     PGM1 C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.4e-05      0.13      40      64 ..      10      34 ..       7      78 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                                  HHHHHHHHHHHHHHHHHHHHHHCT- CS
                     TetR_C_27 40 vvekhieeleeqlaeIireGvaaGe 64
                                  + ekh ++ e+++ +Ii eG+a+G+
  gi|15669653|ref|NP_248466.1| 10 IPEKHATKYEDLIRRIIGEGIARGD 34
                                  5689*******************95 PP

>> PGM1_C  PGM1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.8e-05      0.16      32      53 .]      45      66 ..      27      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.8e-05
                        PGM1_C 32 grveyliiAesleeAeelerrl 53
                                  g v ++ +A+s+ +Ae ++++l
  gi|15669653|ref|NP_248466.1| 45 GDVAFVMLARSRRAAEKVYQQL 66
                                  99******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 559.52
//
Query:       gi|15669654|ref|NP_248467.1|  [L=233]
Description: hypothetical protein MJ_1463 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.3e-109  363.2   1.4   5.3e-109  362.9   1.4    1.0  1  UPF0128   Uncharacterised protein family (UPF0128)


Domain annotation for each model (and alignments):
>> UPF0128  Uncharacterised protein family (UPF0128)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.9   1.4    3e-113  5.3e-109       1     221 []      10     230 ..      10     230 .. 0.99

  Alignments for each domain:
  == domain 1  score: 362.9 bits;  conditional E-value: 3e-113
                       UPF0128   1 llentlvfetlGqpekerefklkdlkkWGfdlvlGkkdGketyfaskaeereeGekyeeegkeyeieevlkelPknaklla 81 
                                   ++ ntlvfetlG+pekerefklk+lk+WGfdl++Gk+dGketyf+++ +er++G+k++++gkeye++evl+elPkn++l+a
  gi|15669654|ref|NP_248467.1|  10 MI-NTLVFETLGNPEKEREFKLKSLKRWGFDLIFGKVDGKETYFTVELDERKAGDKFSKDGKEYEVIEVLQELPKNTELYA 89 
                                   56.9***************************************************************************** PP

                       UPF0128  82 rieieeGkaylvleleeed.knlevlrvparelllaflkkkklaelikavksvGlatelvkdrgeeskPlpyeelPpvarr 161
                                   +ie+e+Gkay+v++l++ed kn+evlrvpa++lllaflkk+kla++ika+k+vG+++el++++g+ +kPl+yeelP+varr
  gi|15669654|ref|NP_248467.1|  90 HIEMEMGKAYIVCQLRDEDgKNTEVLRVPAATLLLAFLKKNKLANIIKAIKNVGISLELSMQNGVGGKPLSYEELPNVARR 170
                                   *******************99************************************************************ PP

                       UPF0128 162 flreakkvekdmGfGrlalayfGetkekearyrlsWllPtialfdveiaekidkalaelk 221
                                   f+r+a+kvek++GfGrl++ay+Getk++e+ryr+sWllPtialfd++ia+k++++l++lk
  gi|15669654|ref|NP_248467.1| 171 FIRSARKVEKETGFGRLSFAYYGETKDGEPRYRFSWLLPTIALFDLDIAKKVEQTLGILK 230
                                   *********************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1449.29
//
Query:       gi|15669655|ref|NP_248468.1|  [L=373]
Description: GTP-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-21   75.0   4.0      2e-16   60.1   0.0    3.1  3  MMR_HSR1      50S ribosome-binding GTPase
    6.9e-12   45.2   1.6    4.7e-08   32.7   0.1    2.3  2  FeoB_N        Ferrous iron transport protein B
    8.1e-10   39.0   3.5     0.0021   18.1   0.1    3.5  3  Dynamin_N     Dynamin family
    1.5e-09   38.0   0.2    3.9e-09   36.6   0.2    1.7  1  RsgA_GTPase   RsgA GTPase
    7.2e-06   25.7   3.8    0.00011   21.8   0.2    3.7  5  GTP_EFTU      Elongation factor Tu GTP binding domain
    5.3e-05   23.2   0.1    0.00022   21.2   0.1    2.0  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0014   18.0   0.1      0.007   15.7   0.0    2.2  2  AIG1          AIG1 family
     0.0048   16.7   0.3       0.54   10.1   0.0    2.5  2  DUF86         Protein of unknown function DUF86
     0.0074   16.8   1.2      0.026   15.0   1.2    2.1  1  ABC_tran      ABC transporter
     0.0087   16.4   5.4      0.019   15.3   0.5    3.1  3  DUF5376       Family of unknown function (DUF5376)
     0.0099   14.9   0.9      0.034   13.1   0.2    2.1  3  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
  ------ inclusion threshold ------
      0.013   15.7   0.9       0.48   10.6   0.1    2.5  2  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.015   15.2   0.1      0.065   13.1   0.0    2.0  2  TraB          TraB family
        2.9    8.3   7.0        1.3    9.5   1.7    2.3  2  AAA_23        AAA domain


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.3   3.6e-05     0.046      73     114 .]      21      61 ..       7      61 .. 0.79
   2 !   60.1   0.0   1.6e-19     2e-16       1      64 [.     112     173 ..     112     236 .. 0.80
   3 ?    1.0   0.0      0.34   4.4e+02      48     103 ..     296     345 ..     240     356 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-05
                                   HHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  73 leeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                   ++e+d+illv+da++ +++++ +ele+ ++ ++k+li+vlnk
  gi|15669655|ref|NP_248468.1|  21 IDECDVILLVLDARDPEMTRN-RELEKKIKAKGKKLIYVLNK 61 
                                   456*********994456665.9999999999*********8 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 1.6e-19
                                   EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek 64 
                                   +v+ivG+pNvGKS++inaltg+ ka +++ +g T+  ++ r++   k+i+l+DtpG++e+ +e+ 
  gi|15669655|ref|NP_248468.1| 112 KVGIVGYPNVGKSSIINALTGKrKALTGSVAGLTKGEQWVRLT---KNIKLMDTPGVLEMRDEDD 173
                                   69*******************988******************9...69********988444443 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.34
                                   EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHH CS
                      MMR_HSR1  48 ielvDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldeeleellee 103
                                    +l D  Gl++      +++k +l  ee d  ++vv+  e++ ++ ++++e+l +e
  gi|15669655|ref|NP_248468.1| 296 THLKDFDGLYK------KIKKPVLGSEEIDGNIVVVSFGEKTKDACRKKVENLCRE 345
                                   45667777766......788888888999999999986644444455666666544 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.3   0.00013      0.16      77     154 ..      22      97 ..       9      99 .. 0.80
   2 !   32.7   0.1   3.6e-11   4.7e-08       2      61 ..     112     169 ..     111     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                   TSSSEEEEEEEGG..GHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHH CS
                        FeoB_N  77 eepdvvvnvvdat..nlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellk 154
                                   +e dv++ v+da   ++ rn  L  ++   g++++ +ln+ d + k+ +    +k +e +g + v +sak++ g++ l++
  gi|15669655|ref|NP_248468.1|  22 DECDVILLVLDARdpEMTRNRELEKKIKAKGKKLIYVLNKADLVPKDIL----EKWKEVFGENTVFVSAKRRLGTKILRE 97 
                                   689*********833578*************************998754....577788888888888888877776665 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 3.6e-11
                                   EEEEEESTTSSHHHHHHHHHTTSEE.EEESTTSSSEEEEEEEEETTEEEEEEE----SSSS CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqk.vgNwpGvtvekkegklklkgkeveivDlPGiYsls 61 
                                   +v +vG pnvGk++++naltg+++   g  +G t  ++ ++l+   k+++++D PG+ ++ 
  gi|15669655|ref|NP_248468.1| 112 KVGIVGYPNVGKSSIINALTGKRKAlTGSVAGLTKGEQWVRLT---KNIKLMDTPGVLEMR 169
                                   5789*****************997626999****999999998...9*********98775 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   1.7e-06    0.0021     120     168 .]      15      62 ..       7      62 .. 0.90
   2 !   13.1   0.1   5.9e-05     0.076       1      26 [.     113     138 ..     113     149 .. 0.86
   3 !    7.0   0.0    0.0042       5.4      99     123 ..     153     177 ..     143     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-06
                                   HHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEEEEE-C CS
                     Dynamin_N 120 elvkeyikkadiilavtsanhdlsnsealflarevdpkgkrtivvltkl 168
                                   ++v+++i+++d+il+v++a    + +++++l+++++ kgk+ i vl+k+
  gi|15669655|ref|NP_248468.1|  15 KIVNKIIDECDVILLVLDARDPEM-TRNRELEKKIKAKGKKLIYVLNKA 62 
                                   6999****************9877.78999*****************95 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.9e-05
                                   EEEEEBTTTTHHHHHHHHHTS--S-- CS
                     Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilpr 26 
                                   + +vG  + GKSS++naL+g++   +
  gi|15669655|ref|NP_248468.1| 113 VGIVGYPNVGKSSIINALTGKRKALT 138
                                   679999**************985555 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0042
                                   TS-SEEEEE---B-SSSGTTSHHHH CS
                     Dynamin_N  99 lvkgltlvDlPGldsvnkrdqelvk 123
                                   l k+++l+D+PG+ ++ ++d  ++ 
  gi|15669655|ref|NP_248468.1| 153 LTKNIKLMDTPGVLEMRDEDDLVIS 177
                                   5789***********9999974444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.2     3e-12   3.9e-09      12     163 ..      20     167 ..       7     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 3e-12
                                   TEES--EEEEEEESTTTT--HH.HHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHH CS
                   RsgA_GTPase  12 kvaNvdqllivvslkepelsln.lldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegle 91 
                                    +  +d +l+v+ + +pe++ n  l++    +++kg +++ vlnK+Dl+ ++  le++ke + +    +++vsak++ g++
  gi|15669655|ref|NP_248468.1|  20 IIDECDVILLVLDARDPEMTRNrELEK---KIKAKGKKLIYVLNKADLVPKDI-LEKWKEVFGEN---TVFVSAKRRLGTK 93 
                                   466778899999999888876414666...45778889999***********9.99999887665...6667777666665 PP

                                   HHHHHCTTSE.........EEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-SSSS CS
                   RsgA_GTPase  92 elkellkdkt.........svlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPGfre 163
                                    l+e++k+++         + +vG   vGKS++inal+++ ++ tg+v   l +G       + ++l ++  l+DtPG+ e
  gi|15669655|ref|NP_248468.1|  94 ILREMIKQSLkemgkkegkVGIVGYPNVGKSSIINALTGKRKALTGSVAG-LTKG------EQWVRLTKNIKLMDTPGVLE 167
                                   555555443311111111156899999*********************98.4555......5677777788889****866 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.2   8.9e-08   0.00011      91     146 ..      21      76 ..      13     110 .. 0.80
   2 ?    1.5   0.0      0.15   1.9e+02       5      29 ..     112     136 ..     108     149 .. 0.85
   3 ?   -1.5   0.0       1.2   1.6e+03      69      79 ..     154     164 ..     133     169 .. 0.85
   4 ?   -1.5   0.0       1.2   1.6e+03     129     154 ..     199     252 ..     192     310 .. 0.54
   5 ?   -0.1   0.0      0.45   5.8e+02      84     113 ..     308     337 ..     239     352 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.9e-08
                                   HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHH CS
                      GTP_EFTU  91 lrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveev 146
                                   +  +D+ +lv+da++  +++ +e+ + ++++g ++i ++NK+D + +++ e  +ev
  gi|15669655|ref|NP_248468.1|  21 IDECDVILLVLDARDPEMTRNRELEKKIKAKGKKLIYVLNKADLVPKDILEKWKEV 76 
                                   6689*****************************************66655555444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
                                   EEEEEESTTSSHHHHHHHHHHHTTS CS
                      GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktga 29 
                                   ++gi+g  + GK++++ +L+ k +a
  gi|15669655|ref|NP_248468.1| 112 KVGIVGYPNVGKSSIINALTGKRKA 136
                                   589***************9976655 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.2
                                   SEEEEEEEESS CS
                      GTP_EFTU  69 kylinliDtPG 79 
                                   +++i+l+DtPG
  gi|15669655|ref|NP_248468.1| 154 TKNIKLMDTPG 164
                                   46899*****9 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.2
                                   EESCGST..HHHHHHHHHHHHHHHHHH..........................H CS
                      GTP_EFTU 129 iNKmDrl..kaelkeiveevkqklsrk..........................e 154
                                   iN  D+   k+ +    eev ++l +k                           
  gi|15669655|ref|NP_248468.1| 199 INNFDNSiiKEYFGVDYEEVDEELLKKignkrsyltkggevdlvrtaktiikeY 252
                                   566666555333444444444444444222244444444444444443333330 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.45
                                   HHHHHHHHHT-SEEEEEEETTTBSTHHHHH CS
                      GTP_EFTU  84 skevirglrvlDgavlvvdaveGvepqtee 113
                                   +k+   g + +Dg ++vv+  e  +   ++
  gi|15669655|ref|NP_248468.1| 308 IKKPVLGSEEIDGNIVVVSFGEKTKDACRK 337
                                   555556778889999999987765555444 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   1.7e-07   0.00022      57     104 ..      54     103 ..      37     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.7e-07
                  MMR_HSR1_Xtn  57 pclyvlNKiDlisleeldelare..pnsvviSaekelnldeLkekiweeL 104
                                   + +yvlNK+Dl+ ++ l++ ++   +n+v++Sa+++l+ + L e+i ++L
  gi|15669655|ref|NP_248468.1|  54 KLIYVLNKADLVPKDILEKWKEVfgENTVFVSAKRRLGTKILREMIKQSL 103
                                   789*******************7668******************998776 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.77   9.9e+02      84     105 ..      24      46 ..      10      84 .. 0.60
   2 !   15.7   0.0   5.4e-06     0.007       5      72 ..     115     178 ..     112     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.77
                                   ESEEEEEEETT..B-SHHHHHHHH CS
                          AIG1  84 ihalllvlslg..rfteedekalk 105
                                    +++llvl+++  ++t +++++ k
  gi|15669655|ref|NP_248468.1|  24 CDVILLVLDARdpEMT-RNRELEK 46 
                                   5677777777632222.3333333 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 5.4e-06
                                   EESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHH CS
                          AIG1   5 lvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiske 72 
                                   +vG   +GkS+ +N++ gk+   +     sv    + +++++  k+i+  DTPg++++ +++d ++  
  gi|15669655|ref|NP_248468.1| 115 IVGYPNVGKSSIINALTGKRKALTG----SVAGLTKGEQWVRLTKNIKLMDTPGVLEMRDEDDLVISG 178
                                   699999************9987776....45555566666777889*************999877655 PP

>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.03        38      52     111 ..      46     105 ..      40     109 .. 0.86
   2 !   10.1   0.0   0.00042      0.54      79     107 ..     196     224 ..     167     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.03
                                   TT----SSCHHHHHHHTTSS-HHHHHHHHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHH CS
                         DUF86  52 lgikkpgdyifeilaekgviaeepeepwrkmiglRNrLvHgYlgidpeivwsiikenlpd 111
                                   ++ik++g++ + +l ++++ +++  e+w+++ g   + v+   ++  +i++++ik+ l++
  gi|15669655|ref|NP_248468.1|  46 KKIKAKGKKLIYVLNKADLVPKDILEKWKEVFGENTVFVSAKRRLGTKILREMIKQSLKE 105
                                   56888888899********************99998988888888888888888888776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00042
                                   HHHHHCCHHHHHT-CCCTTHHHHHHHHHH CS
                         DUF86  79 wrkmiglRNrLvHgYlgidpeivwsiike 107
                                   +++++ + N ++ +Y+g+d+e+v + + +
  gi|15669655|ref|NP_248468.1| 196 LSRINNFDNSIIKEYFGVDYEEVDEELLK 224
                                   6789999****************887655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.2     2e-05     0.026      11      43 ..     110     144 ..     105     357 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                                   TSEEEEEESTTSSHHHHHHHHTTSS--SEEEE..E CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                      ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGei..l 43 
                                     kv+ivG    GKS+++++l+g+ k   G++  l
  gi|15669655|ref|NP_248468.1| 110 EGKVGIVGYPNVGKSSIINALTGKRKALTGSVagL 144
                                   5689***********************99999331 PP

>> DUF5376  Family of unknown function (DUF5376)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.74   9.5e+02      84     104 ..      41      61 ..       8      82 .. 0.67
   2 ?    1.2   0.0      0.36   4.6e+02      19      55 ..     193     229 ..     181     236 .. 0.80
   3 !   15.3   0.5   1.4e-05     0.019       4      72 ..     249     323 ..     246     357 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.74
                       DUF5376  84 deedekevlidrkeliYllek 104
                                   + e ek+++ + k+liY+l+k
  gi|15669655|ref|NP_248468.1|  41 NRELEKKIKAKGKKLIYVLNK 61 
                                   455556666666777777776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.36
                       DUF5376  19 vnevsgeskedesylaeylsdldlelakkvldklkdk 55 
                                    +  s  ++ d+s++ ey      e+ ++ l+k+ +k
  gi|15669655|ref|NP_248468.1| 193 LKILSRINNFDNSIIKEYFGVDYEEVDEELLKKIGNK 229
                                   4667788899999999999999999999999999997 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.4e-05
                       DUF5376   4 iFkYkksenklikicvnevsgeskedesylaeylsdld.lelakkvldklkd.....keieeedigseawdaeie 72 
                                   i +Y++ + +++k+  +++ ++ ++d s++++yl+d++ +e ak ++ +lkd     k+i++  +gse++d +i 
  gi|15669655|ref|NP_248468.1| 249 IKEYQDGKLNYYKVDLKKYGQDRERDISFITKYLKDFPfIEDAKMIVTHLKDfdglyKKIKKPVLGSEEIDGNIV 323
                                   55799999999***9999********************9999********9955555678888888888776653 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.4   4.3e+03     171     180 ..      56      65 ..      55      74 .. 0.75
   2 !   13.1   0.2   2.7e-05     0.034      16      51 ..      96     132 ..      79     144 .. 0.77
   3 ?   -1.1   0.0      0.59   7.5e+02     208     246 ..     208     247 ..     164     254 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.4
                                   EEEEE---HH CS
                          MeaB 171 iivvnkaDkk 180
                                   i+v+nkaD+ 
  gi|15669655|ref|NP_248468.1|  56 IYVLNKADLV 65 
                                   89******53 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.7e-05
                                   HHHHHHHGGG-S-SE.EEEEEE-TTSSHHHHHHHHHH CS
                          MeaB  16 kellerllakaGraq.vvGltGvPGaGkstlvealgl 51 
                                   +e++++ l++ G+ + +vG+ G P +Gks +++al+ 
  gi|15669655|ref|NP_248468.1|  96 REMIKQSLKEMGKKEgKVGIVGYPNVGKSSIINALTG 132
                                   45666667777876439*****************985 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.59
                                   EEEBCCCTBSHH.HHHHHHHHHHHHHHHTTHHHHHHHHHH CS
                          MeaB 208 lktsavegeGid.elvdaieehrevlkktGllekrrrera 246
                                    +  +v  e +d el+++i + r++l+k G+++  r +++
  gi|15669655|ref|NP_248468.1| 208 KEYFGVDYEEVDeELLKKIGNKRSYLTKGGEVDLVRTAKT 247
                                   4445555555652689999999999999999888877665 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.074        95      77     119 ..      21      63 ..      13      64 .. 0.74
   2 ?   10.6   0.1   0.00038      0.48       1      24 [.     112     135 ..     112     168 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.074
                                   HCTSCEEEEEEEGHHHHCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                           Roc  77 lreaalailvydsrssenlkeWlkelkkvagkspvilvgnkiD 119
                                   + e ++++lv+d+r+ e  ++   e k +a+ +++i v nk+D
  gi|15669655|ref|NP_248468.1|  21 IDECDVILLVLDARDPEMTRNRELEKKIKAKGKKLIYVLNKAD 63 
                                   56788999****9987766654444455566778999****99 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00038
                                   EEEEESSTTSSHHHHHHCHCT-CC CS
                           Roc   1 KvvlvGdsgvGKtsllkrfvedkf 24 
                                   Kv +vG  +vGK+s+++ ++ ++ 
  gi|15669655|ref|NP_248468.1| 112 KVGIVGYPNVGKSSIINALTGKRK 135
                                   899***************996543 PP

>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.1e-05     0.065      26      81 ..      11      64 ..       5     111 .. 0.85
   2 ?   -1.2   0.0       1.2   1.5e+03     157     197 ..     212     261 ..     207     291 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-05
                          TraB 26 yplspeveealeksdtvvvEldlsddtdeatqkelaklkllpdgktlsdllseely 81
                                   p+++ v+++++++d++++ ld +d+  e+t ++  ++k+  +gk+l  +l+++++
  gi|15669655|ref|NP_248468.1| 11 VPVKKIVNKIIDECDVILLVLDARDP--EMTRNRELEKKIKAKGKKLIYVLNKADL 64
                                  589999*****************999..9999999999999999999888877664 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                          TraB 157 slpdeeqlealeetldeleea.........kdlleelveaykegdleale 197
                                   ++++ee++e+l + + +++++           + +++++ y++g+l+  +
  gi|15669655|ref|NP_248468.1| 212 GVDYEEVDEELLKKIGNKRSYltkggevdlVRTAKTIIKEYQDGKLNYYK 261
                                   46778888888888866665544444433333377999999999998774 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.4      0.35   4.4e+02      94     157 ..      38     105 ..      31     113 .. 0.69
   2 ?    9.5   1.7   0.00099       1.3      22      90 ..     113     218 ..     109     310 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.35
                        AAA_23  94 relskkkgkttkkaklelleideleqfisellgsk.kiil.nlilflgqer....feefelkdkkerlee 157
                                    +++++ +k++k + ++l+++ ++ +++++ +  k k+ + ++ +f  ++r    +  ++++  k+ l+e
  gi|15669655|ref|NP_248468.1|  38 MTRNRELEKKIKAKGKKLIYVLNKADLVPKDILEKwKEVFgENTVFVSAKRrlgtK--ILREMIKQSLKE 105
                                   56788888889999999999999999999988777344567888888887767541..334444444444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00099
                        AAA_23  22 tlItGpNGaGKTTildAikl...aLygetprlsrksgrgfeksdveiesegkvkayveltfenkdgry............. 86 
                                   + I+G    GK++i++A++    aL+g +++l +  g+ +++   +i+   ++++++e++ e++  ++             
  gi|15669655|ref|NP_248468.1| 113 VGIVGYPNVGKSSIINALTGkrkALTGSVAGLTK--GEQWVRLTKNIKLM-DTPGVLEMRDEDDLVISgalrlekvenpip 190
                                   569999999*********96666*******9999..55566666666553.555555555333222223333333333444 PP

                        AAA_23  87 ........................trsi 90 
                                                           ++++
  gi|15669655|ref|NP_248468.1| 191 palkilsrinnfdnsiikeyfgvdYEEV 218
                                   4444444444444444444444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2177.81
//
Query:       gi|15669656|ref|NP_248469.1|  [L=405]
Description: threonine synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-81  273.0   0.1    3.6e-81  272.8   0.1    1.0  1  PALP           Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.014   15.5   0.1       0.75   10.0   0.0    2.7  3  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
      0.051   13.8   0.1        1.3    9.3   0.0    2.3  2  PK_C           Pyruvate kinase, alpha/beta domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.8   0.1   6.1e-85   3.6e-81       2     294 .]      69     372 ..      68     372 .. 0.95

  Alignments for each domain:
  == domain 1  score: 272.8 bits;  conditional E-value: 6.1e-85
                                   GGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EE CS
                          PALP   2 tlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkv 81 
                                   +l +g+TPl r+++l+kelg++ l++K+E+ nptgSfKdRg++  ++r+ e  g ++v +as+GN+ ++lAa++a+ G k+
  gi|15669656|ref|NP_248469.1|  69 SLCEGGTPLYRCNNLEKELGIKeLYVKNEGANPTGSFKDRGMTVGVTRANEL-GVEVVGCASTGNTSASLAAYSARSGKKC 148
                                   6789************************************************.**************************** PP

                                   EEEEETTS-H.HHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT.TTEEE CS
                          PALP  82 tivvpadasp.ekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlg.gkpda 160
                                   ++++p+++ + +k+a+   +Ga+v++v+g++d+a++++++la+e + +yl+++  np + eg++ti++Ei++ql+ ++pd 
  gi|15669656|ref|NP_248469.1| 149 IVLLPEGKVAlGKLAQAMFYGAKVIQVKGNFDDALDMVKQLAKE-KLIYLLNSI-NPFRLEGQKTIAFEICDQLNwQVPDR 227
                                   *********88*********************************.999999999.9************************* PP

                                   EEEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTTCGGTTCC..S..S.SS..B.SSS.CCSTCS..CGTTCCHH CS
                          PALP 161 vvvpvGgGgliaGiaaglke....rrpd..vrvigvepegsdalarsl..ragrrvtvpvsdtiadglavg..spselafe 231
                                   v+vpvG++g+i++i++g+ke    +  d  +++ g++++g+ ++ +++  ra++  +++ ++tia+++++g  +++++a++
  gi|15669656|ref|NP_248469.1| 228 VIVPVGNAGNISAIWKGFKEfeitGIIDelPKMTGIQADGAKPIVEAFrkRAKDIIPYKNPETIATAIRIGnpVNAPKALD 308
                                   ********************8876333378******************5555555555566**********9999****** PP

                                   HHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                          PALP 232 lldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                   ++  +++++ +v+dee++ea++llar+egi+vep+sa ++a+l kl+e g +++++r+v+i tg
  gi|15669656|ref|NP_248469.1| 309 AIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLkKLLEEGIIDRDERIVCITTG 372
                                   *************************************************************998 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.98   5.8e+03      43      51 ..     128     136 ..     123     139 .. 0.80
   2 ?    2.1   0.0     0.036   2.1e+02      23      50 ..     212     240 ..     207     242 .. 0.85
   3 ?   10.0   0.0   0.00013      0.75      49      81 ..     343     375 ..     342     383 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.98
                                   HHH-B-GGG CS
                 ACP_syn_III_C  43 deyGntsaa 51 
                                   + +Gntsa+
  gi|15669656|ref|NP_248469.1| 128 ASTGNTSAS 136
                                   689***995 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.036
                                   HHHHHHHHHT--.GGGB--THHHH-B-GG CS
                 ACP_syn_III_C  23 iidavakklglp.eekvvvnldeyGntsa 50 
                                   i  +++++l+++ +++v+v + + Gn+sa
  gi|15669656|ref|NP_248469.1| 212 IAFEICDQLNWQvPDRVIVPVGNAGNISA 240
                                   555699999999789************99 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00013
                                   GGGHHHHHHHHHHHTTSS-TT-EEEEEEEETTT CS
                 ACP_syn_III_C  49 saasiplaLdeaveegklkpgdlvllvgfGaGl 81 
                                   ++as++  L++++eeg +++ ++++ +++G Gl
  gi|15669656|ref|NP_248469.1| 343 ASASSIAGLKKLLEEGIIDRDERIVCITTGHGL 375
                                   58******************************8 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00022       1.3       8      88 ..     114     193 ..     110     215 .. 0.77
   2 ?    2.0   0.0      0.04   2.4e+02      80     101 ..     349     370 ..     316     378 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00022
                                   HHHHHHHT-SEEEEE-SSSHHHHHHH.HT-TSSEEEEEESHHHH.HHHHH..HCTTEEHHH.HHHHH...TTSHHHHHHHH CS
                          PK_C   8 veaaeelgakaIvvltesGetArlis.kyrpkvpiiavtpnelt.arqla..lyrGvypvlvekaktaestdellreavkv 84 
                                   v++a+elg++ + ++++  ++A l++   r++ + i++ p+ ++   +la  ++ G   ++v     + ++d++l+++ + 
  gi|15669656|ref|NP_248469.1| 114 VTRANELGVEVVGCASTGNTSASLAAySARSGKKCIVLLPEGKVaLGKLAqaMFYGAKVIQV-----KGNFDDALDMVKQL 189
                                   789************99999988765256666888888887777544555568889888876.....45788888877777 PP

                                   HHHT CS
                          PK_C  85 akea 88 
                                   ake+
  gi|15669656|ref|NP_248469.1| 190 AKEK 193
                                   7774 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.04
                                   HHHHHHHHTTSS-STSEEEEEE CS
                          PK_C  80 eavkvakeaglvkkgdevvvta 101
                                   +++k ++e+g++++++++v+++
  gi|15669656|ref|NP_248469.1| 349 AGLKKLLEEGIIDRDERIVCIT 370
                                   3489999*********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2353.90
//
Query:       gi|15669657|ref|NP_248470.1|  [L=214]
Description: transposase, IS240 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-16   58.4   0.1    1.7e-15   57.5   0.1    1.4  1  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.028   14.6   0.0      0.073   13.3   0.0    1.6  2  rve            Integrase core domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.1   1.9e-19   1.7e-15       5     137 ..      82     211 ..      79     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.9e-19
                 DDE_Tnp_IS240   5 rvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasalkelkregelf 84 
                                   ++DET +k+  k  Y + a+D e++  l++++sk R+   +++f + +lk    +  +i++D+ + y+ al++l+ e+e  
  gi|15669657|ref|NP_248470.1|  82 AIDETKLKVGDKYIYAWSAIDVETKeCLGVYISKTRNYLDTILFVKSILKFC-SNKPKILVDGGKWYPWALRKLGLEFE-- 159
                                   79********************9999*************************9.566689*****************755.. PP

                 DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrl.rptrgf...kslksaaktlagfeavknlrk 137
                                       +v+   l+n +Es ++ lK+r+    + f    +++++ ++++ f +++n  k
  gi|15669657|ref|NP_248470.1| 160 ----RVKF-GLRNCVESFFSVLKRRTkVFYNRFpnnSKFDTVISWIKSFMMFYNWMK 211
                                   ....3443.67*************995345666222557888888888888888776 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.2e-06     0.073       6      76 ..      79     145 ..      74     155 .. 0.86
   2 ?   -1.9   0.0      0.41   3.6e+03     107     118 ..     168     179 ..     165     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.2e-06
                           rve   6 elwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngs 76 
                                    l+ +D t+++   g++ +y   ++d+ ++++l++++s+  +  +++ +++  +++  ++ p ++l D g+
  gi|15669657|ref|NP_248470.1|  79 NLIAIDETKLK--VGDKYIYAWSAIDVETKECLGVYISKTRNYLDTILFVKSILKFCSNK-P-KILVDGGK 145
                                   67889999999..55666*********************************999999996.4.66777766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.41
                           rve 107 kvErfhrtlkde 118
                                    vE+f+  lk++
  gi|15669657|ref|NP_248470.1| 168 CVESFFSVLKRR 179
                                   59*****99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1403.14
//
Query:       gi|15669658|ref|NP_248471.1|  [L=184]
Description: hypothetical protein MJ_1467 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0014   17.1   0.2     0.0019   16.7   0.2    1.1  1  SKN1      Beta-glucan synthesis-associated protein (SKN1)
  ------ inclusion threshold ------
      0.056   13.6   0.4      0.099   12.7   0.4    1.4  1  DHHC      DHHC palmitoyltransferase


Domain annotation for each model (and alignments):
>> SKN1  Beta-glucan synthesis-associated protein (SKN1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   2.1e-07    0.0019      20      94 ..      26     102 ..      15     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.1e-07
                          SKN1  20 eakadkkkkvkdlklldkrgllnv.lgllllvlgllllfivlPvltylgkkekestkseaaeiltk.aqvpllsair 94 
                                   + k +kk++  + + ++krg l+v ++l++l+l l+ lfi + +lt++++++ +    ++++i ++ +++++ls ++
  gi|15669658|ref|NP_248471.1|  26 NVKLEKKRFNMNKNKIKKRGQLSVdFVLAILFLMLVSLFIYYNALTFTNNTTDALIVDRMYSIADTfENYAILSYTK 102
                                   5678999999999999***9999935678999****************99998888777777765524667777665 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   1.1e-05     0.099      62     128 ..      12      78 ..       9      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                          DHHC  62 lilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfhlylilrnlTti 128
                                   ++l+ + + +++ ++v+ ekk ++ + +++kk +++ + ++ ++++l+l++l++++  l+++n Tt 
  gi|15669658|ref|NP_248471.1|  12 ILLYDYSINFSIKDNVKLEKKRFNMNKNKIKKRGQLSVDFVLAILFLMLVSLFIYYNALTFTNNTTD 78 
                                   5667777788888999999999999999999999999999999999999999*********999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1181.67
//
Query:       gi|15669659|ref|NP_248472.1|  [L=1009]
Description: surface antigen [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-66  218.1  40.0    4.7e-16   58.4   0.1    9.5  9  PKD       PKD domain
    9.6e-05   21.8   3.5        1.1    8.8   0.0    4.9  5  TcfC      E-set like domain
  ------ inclusion threshold ------
       0.15   12.6   1.0        3.2    8.4   0.0    3.9  5  Ig_3      Immunoglobulin domain


Domain annotation for each model (and alignments):
>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.7   4.3e-05      0.25      10      54 ..      51     101 ..      48     106 .. 0.76
   2 !   23.4   0.0   6.6e-09   3.9e-05       8      68 ..     192     248 ..     185     250 .. 0.90
   3 !    4.9   0.9    0.0039        23      27      47 ..     325     345 ..     309     351 .. 0.74
   4 !   20.0   0.0   7.7e-08   0.00046       3      68 ..     442     503 ..     439     505 .. 0.90
   5 !   14.9   0.8     3e-06     0.018       3      62 ..     525     588 ..     523     594 .. 0.73
   6 ?    2.8   0.1     0.017     1e+02      53      70 ..     694     711 ..     665     712 .. 0.77
   7 !   57.3   0.2   1.8e-19   1.1e-15       8      70 ..     735     798 ..     728     799 .. 0.95
   8 !   47.8   0.4   1.6e-16   9.7e-13      12      67 ..     821     875 ..     817     879 .. 0.93
   9 !   58.4   0.1   7.9e-20   4.7e-16      10      69 ..     904     966 ..     899     968 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.3e-05
                                   SSEEEEEEEES.-......SS-SEEEEE--SS--EEEEETTEEEEEE-SSE CS
                           PKD  10 pgatvaftaavpd......ganvtysWdfgdgsvvqvlseptvthtYlspG 54 
                                   ++ t++f+a  pd       +n    Wdfgd + +  +  +t+thtY+ p 
  gi|15669659|ref|NP_248472.1|  51 VNDTITFEALAPDsvaqdiLDNGVVKWDFGDLTETDYGNYRTTTHTYTFPF 101
                                   6899*******884555555555556*****777778899*******9765 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 6.6e-09
                                   -BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-E CS
                           PKD   8 lvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgs 68 
                                   +v g tv f+ +v + +++   W fgd   ++ + e+ + htY++ G Y  +v++ ++ g+
  gi|15669659|ref|NP_248472.1| 192 IVEGDTVKFNFSV-SRNIIFCVWSFGD---GTFSFEKFPEHTYTKSGLYYPRVLVVDDSGR 248
                                   67899********.88888888*****...************************9999887 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0039
                                   EEEEE--SS--EEEEETTEEE CS
                           PKD  27 tysWdfgdgsvvqvlseptvt 47 
                                    + Wdfgdg+ +  +  + +t
  gi|15669659|ref|NP_248472.1| 325 YWKWDFGDGTETPYTYKSYFT 345
                                   589*****8665555555544 PP

  == domain 4  score: 20.0 bits;  conditional E-value: 7.7e-08
                                   ---S--BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-E CS
                           PKD   3 asptvlvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgs 68 
                                   a +t ++++++v+f  +   g+++   W fgd   ++ + e+++th Y+s G Y  +v + ++ g+
  gi|15669659|ref|NP_248472.1| 442 ADKTQVSVNENVRFDCSP-YGNPIFIMWCFGD---GTCSFEKSPTHRYSSSGLYYPHVFVIDDNGN 503
                                   55778999******9888.*************...*******************999999998887 PP

  == domain 5  score: 14.9 bits;  conditional E-value: 3e-06
                                   ---S--BSSEEEEEEEES.-SS-SEEEE...E--SS--EEEEETT...EEEEEE-SSEEEEEEEEE CS
                           PKD   3 asptvlvpgatvaftaavpdganvtysW...dfgdgsvvqvlsep...tvthtYlspGeYeVtvta 62 
                                   aspt +++  +++ t++   +a+ t+ W   +fgdg+ v+++  +   t+thtY+s+G Y + +++
  gi|15669659|ref|NP_248472.1| 525 ASPTIAPTYYPINITIVE--PASWTWYWhhiYFGDGGSVWIKPKKspyTFTHTYTSEGVYPIYMKV 588
                                   667777777777777777..445555555558****88887766534489**********998776 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.017
                                   SEEEEEEEEEE-SS-EEE CS
                           PKD  53 pGeYeVtvtasnavgsat 70 
                                    G+Y++++++++  g ++
  gi|15669659|ref|NP_248472.1| 694 IGNYTAKLVVWDGMGGVN 711
                                   59***********99987 PP

  == domain 7  score: 57.3 bits;  conditional E-value: 1.8e-19
                                   -BSSEEEEEEEES...-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                           PKD   8 lvpgatvaftaav..pdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsat 70 
                                   ++p++ v+f +++  p g+++ y W+fgd ++v  ++   v h+Y++pG Y+Vt+t+++ +++++
  gi|15669659|ref|NP_248472.1| 735 PEPNEDVEFVSQSydPEGEIAYYIWNFGD-GTVINTTDTIVHHKYERPGYYTVTLTVFDKYNASS 798
                                   799***********99*************.99****************************99886 PP

  == domain 8  score: 47.8 bits;  conditional E-value: 1.6e-16
                                   EEEEEEEES...-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS- CS
                           PKD  12 atvaftaav..pdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavg 67 
                                    tv+f+ ++  ++g++++++Wdfgd   + +++e+++ htY+++G Y Vt+t++ + +
  gi|15669659|ref|NP_248472.1| 821 NTVRFEDTSvvAPGKIISWHWDFGD---GSTSTEQNPIHTYSKEGAYFVTLTVKSDTN 875
                                   589***99999**************...*************************98765 PP

  == domain 9  score: 58.4 bits;  conditional E-value: 7.9e-20
                                   SSEEEEEEEES....-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EE CS
                           PKD  10 pgatvaftaav...pdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsa 69 
                                    g+tv+f+a +   +dg +  y Wdfgdg+++ ++++p + h+Y+++G Y Vt+t+ ++++++
  gi|15669659|ref|NP_248472.1| 904 NGTTVEFNANLsydEDGYIKYYIWDFGDGTPANTTTNPIIIHKYKKEGVYPVTLTVIDNDNLS 966
                                   79*********************************************************9987 PP

>> TcfC  E-set like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.32   1.9e+03      43      56 ..     579     592 ..     578     596 .. 0.85
   2 !    7.7   0.0   0.00041       2.5      39      64 ..     690     715 ..     683     718 .. 0.76
   3 ?    0.1   0.0     0.093   5.6e+02      44      61 ..     782     799 ..     781     805 .. 0.74
   4 ?    0.1   0.0     0.098   5.9e+02      43      66 ..     861     884 ..     860     885 .. 0.87
   5 !    8.8   0.0   0.00019       1.1      43      67 ..     950     974 ..     949     974 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.32
                          TcfC  43 sGiYeveirvyeng 56 
                                   +G+Y++  +vy ++
  gi|15669659|ref|NP_248472.1| 579 EGVYPIYMKVYTAE 592
                                   6*********9865 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00041
                          TcfC  39 ssLPsGiYeveirvyengqvvrteqq 64 
                                   +s+P G+Y+++++v ++ + v++++ 
  gi|15669659|ref|NP_248472.1| 690 KSFPIGNYTAKLVVWDGMGGVNSTTV 715
                                   79**************5555555444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.093
                          TcfC  44 GiYeveirvyengqvvrt 61 
                                   G Y+v++ v+++ +  ++
  gi|15669659|ref|NP_248472.1| 782 GYYTVTLTVFDKYNASSS 799
                                   99*******997665555 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.098
                          TcfC  43 sGiYeveirvyengqvvrteqqkf 66 
                                   +G Y v++ v ++ +++ + ++++
  gi|15669659|ref|NP_248472.1| 861 EGAYFVTLTVKSDTNLTDSVTKIV 884
                                   699**********99998887765 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.00019
                          TcfC  43 sGiYeveirvyengqvvrteqqkft 67 
                                   +G+Y+v++ v++n+++  ++++ ++
  gi|15669659|ref|NP_248472.1| 950 EGVYPVTLTVIDNDNLSDSRTKLIN 974
                                   6****************99999775 PP

>> Ig_3  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         3   1.8e+04      63      74 ..      80      91 ..      51      92 .. 0.76
   2 ?   -3.5   0.0       2.8   1.6e+04       6      25 ..     185     204 ..     182     224 .. 0.73
   3 ?    8.4   0.0   0.00054       3.2       4      42 ..     438     478 ..     437     505 .. 0.69
   4 ?   -2.3   0.1       1.2   7.2e+03      32      56 ..     838     864 ..     822     879 .. 0.52
   5 ?   -2.7   0.0       1.6   9.7e+03      13      44 ..     902     934 ..     897     964 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3
                                  SS--GGG-EEEE CS
                          Ig_3 63 snvtksdsGtYt 74
                                   ++t++d G+Y+
  gi|15669659|ref|NP_248472.1| 80 GDLTETDYGNYR 91
                                  457888999985 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.8
                                   CCCSCEEEETTS-EEEEEEE CS
                          Ig_3   6 vppsstvvtegesvtLtCea 25 
                                   v+ s  ++ eg++v+++ ++
  gi|15669659|ref|NP_248472.1| 185 VNVSRDEIVEGDTVKFNFSV 204
                                   44444556899999987666 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00054
                                   EECCCSCEEEETTS-EEEEEEEEEES--EEEEEETTS..... CS
                          Ig_3   4 ItvppsstvvtegesvtLtCeaegnppptitWykngek...l 42 
                                   It++  +t+v  +e+v++ C+  gnp   i W +++++   +
  gi|15669659|ref|NP_248472.1| 438 ITATADKTQVSVNENVRFDCSPYGNPI-FIMWCFGDGTcsfE 478
                                   899999999*************77775.57887777764432 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.2
                                   EEEEEETTS...TTCSEEE.....SSEECC CS
                          Ig_3  32 titWykngeklssnstsss.....issegs 56 
                                   +++W ++++   s+st+++     ++++ +
  gi|15669659|ref|NP_248472.1| 838 SWHWDFGDG---STSTEQNpihtySKEGAY 864
                                   345555555...222222233333333333 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 1.6
                                   EETTS-EEEEEEEEEES--....EEEEEETTS...T CS
                          Ig_3  13 vtegesvtLtCeaegnppp....titWykngeklss 44 
                                   v +g +v+++ +  ++++      + W +++++  +
  gi|15669659|ref|NP_248472.1| 902 VINGTTVEFNANL-SYDEDgyikYYIWDFGDGT--P 934
                                   5677778877777.3333334445577776663..2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1009 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.81u 0.27s 00:00:01.08 Elapsed: 00:00:00.49
# Mc/sec: 6227.91
//
Query:       gi|15669660|ref|NP_248473.1|  [L=75]
Description: hypothetical protein MJ_1469 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-10   38.2   2.1    1.3e-09   37.7   2.1    1.3  1  Class_IIIsignal  Class III signal peptide
  ------ inclusion threshold ------
      0.016   14.7   0.0      0.017   14.7   0.0    1.1  1  DUF3959          Protein of unknown function (DUF3959)


Domain annotation for each model (and alignments):
>> Class_IIIsignal  Class III signal peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   2.1   1.5e-13   1.3e-09       1      27 []       9      35 ..       9      35 .. 0.98

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.5e-13
               Class_IIIsignal  1 kKGQiSlEyiLLilavlviaiiaiyyy 27
                                  +K+QiSlE+ LL++a++v+a i+++yy
  gi|15669660|ref|NP_248473.1|  9 NKAQISLELALLLGALVVAASIVGFYY 35
                                  8*************************9 PP

>> DUF3959  Protein of unknown function (DUF3959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.9e-06     0.017      13      42 ..      10      40 ..       4      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-06
                       DUF3959 13 lkqiplelslflggllfftsl.gsyytkkts 42
                                    qi+lel+l+lg l+  +s+ g yy k ++
  gi|15669660|ref|NP_248473.1| 10 KAQISLELALLLGALVVAASIvGFYYLKSVT 40
                                  57***************99973666766543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.64
# Mc/sec: 350.67
//
Query:       gi|15669661|ref|NP_248474.1|  [L=154]
Description: hypothetical protein MJ_1469.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0015   18.1   6.3     0.0018   17.8   6.3    1.1  1  Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)


Domain annotation for each model (and alignments):
>> Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   6.3     1e-07    0.0018     111     253 ..      13     142 ..       5     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1e-07
               Exosortase_EpsH 111 llalPlpavlvaqlslpLqllvaavagfllsllgipvereGnviqlptgqveVaeaCsGlrsllallalglllallfrrrl 191
                                   l+++ ++ ++++ l  +++ l +   ++ll+l  ++     n i +++  +e+ + C+   sl + l+lg++++  +++ +
  gi|15669661|ref|NP_248474.1|  13 LIYFFIFYYILKMLEGNIMDLLTITLSKLLNLKFYK-----NEIIVGKNIIEISSPCTC--SLEMALFLGYIFG--TPDVP 84 
                                   444555556666666666666666555555554333.....44445566699******9..6666666666655..55556 PP

               Exosortase_EpsH 192 wkrklllllaavpiaflaNlvRilllvllayhygpeaaegllHeiaGwllfgvalllllgll 253
                                    k k+   ++++ i+ + N++Ri+l++      ++  +  ++H+++ +++f +al+l +  +
  gi|15669661|ref|NP_248474.1|  85 IKYKISYSVFGLSIITISNILRIILIINYS---NMINY-NVVHDVISFIIFPIALFLNWFWI 142
                                   6888******************99887554...45555.89*************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1008.87
//
Query:       gi|15669662|ref|NP_248475.1|  [L=624]
Description: hypothetical protein MJ_1470 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-29  101.4   0.5    3.1e-29  101.4   0.5    3.8  3  DUF2341   Domain of unknown function (DUF2341)


Domain annotation for each model (and alignments):
>> DUF2341  Domain of unknown function (DUF2341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3     0.038   6.9e+02      62      73 ..      89     100 ..      76     103 .. 0.85
   2 !  101.4   0.5   1.7e-33   3.1e-29       1      83 [.     264     346 ..     264     347 .. 0.96
   3 ?   -1.7   0.5      0.26   4.6e+03      24      56 ..     373     402 ..     360     411 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.038
                       DUF2341  62 datfelFDdfsg 73 
                                   ++tf+lF++fs+
  gi|15669662|ref|NP_248475.1|  89 EKTFDLFNNFSE 100
                                   78********98 PP

  == domain 2  score: 101.4 bits;  conditional E-value: 1.7e-33
                       DUF2341   1 dgsdiRfvdsdgttLpywieswdantekaliWvkvpsipangnktikiyygnptatstsngdatfel.FDdfsgteldttk 80 
                                   d++d+Rfvd+dg++L+ywie+ +++t ++++Wvkv +++ n++k i+++ygnptat+t+ngd+tf l FDdfs+++ld+tk
  gi|15669662|ref|NP_248475.1| 264 DCGDVRFVDEDGNPLSYWIEPNTIDTPHTVAWVKV-NLAPNEHKLIYMLYGNPTATTTANGDNTFPLfFDDFSKGNLDNTK 343
                                   89*********************************.6888************************97659************ PP

                       DUF2341  81 Wtv 83 
                                   Wt 
  gi|15669662|ref|NP_248475.1| 344 WTY 346
                                   *85 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.26
                       DUF2341  24 antekaliWvkvpsipangnktikiyygnptat 56 
                                   + +++ +i  ++   ++   ++i  yy n+++ 
  gi|15669662|ref|NP_248475.1| 373 YYNNHNYIIYDI---NNTHISSISTYYPNTSVR 402
                                   444455555555...356677888899988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3943.02
//
Query:       gi|15669663|ref|NP_248476.1|  [L=178]
Description: hypothetical protein MJ_1471 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.068   13.3   0.0       0.12   12.5   0.0    1.3  1  DUF3898   Domain of unknown function (DUF3898)


Domain annotation for each model (and alignments):
>> DUF3898  Domain of unknown function (DUF3898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.7e-06      0.12      46      80 ..      22      55 ..      13      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.7e-06
                       DUF3898 46 klhiakvndrYvlliegdslqfekgvsPvellkPe 80
                                  ++ i ++n+ Yv ++ +d + f+kg+s +e l  +
  gi|15669663|ref|NP_248476.1| 22 TVSIVEHNNNYVDIVKSDYI-FDKGISTMEHLSED 55
                                  578999***********976.*********98755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1119.10
//
Query:       gi|15669664|ref|NP_248477.1|  [L=544]
Description: hypothetical protein MJ_1472 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-19   70.8   3.2    5.1e-19   68.6   3.2    2.3  1  DUF2341   Domain of unknown function (DUF2341)


Domain annotation for each model (and alignments):
>> DUF2341  Domain of unknown function (DUF2341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   3.2   2.9e-23   5.1e-19       4      83 ..     220     307 ..     217     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 2.9e-23
                       DUF2341   4 diRf....vdsdgtt.Lpywiesw.dantekaliWvkvpsip....angnktikiyygnptatstsngdatfelFDdfsgt 74 
                                   ++R+      s++   Lpyw+++w + n++ ++iWv+ ++++    +ng+++i+i+y+++t ++++++++tf++FDdf+  
  gi|15669664|ref|NP_248477.1| 220 ELRVigwdSVSNKIIlLPYWVQTWrEGNNDVSVIWVRANKNEiynyNNGQGYIYILYNSTTPVDRQDPEHTFIFFDDFNY- 299
                                   5666666556788888********99***************9**************************************. PP

                       DUF2341  75 eldttkWtv 83 
                                    ++ +kW++
  gi|15669664|ref|NP_248477.1| 300 -FNPDKWDS 307
                                   .77789975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3463.56
//
Query:       gi|15669665|ref|NP_248478.1|  [L=311]
Description: methionine synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.5e-54  183.0   1.4    1.9e-52  178.6   1.4    2.0  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
    0.00064   19.3   0.1     0.0011   18.6   0.1    1.3  1  Meth_synt_1  Cobalamin-independent synthase, N-terminal domai
     0.0017   17.6   1.0      0.082   12.0   1.0    2.5  1  URO-D        Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.6   1.4   3.1e-56   1.9e-52       1     323 [.       4     307 ..       4     308 .. 0.89

  Alignments for each domain:
  == domain 1  score: 178.6 bits;  conditional E-value: 3.1e-56
                                   S-BB--SB---SS-----------------HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTEE--SS CS
                   Meth_synt_2   1 lpTttiGSfPqtaevrearaevkkgelseeeyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgfaftkn 81 
                                   ++Tt++GS+P  ++ ++   +vkk ++     ++ ++ +ie++v++q ++gv ++++g+ +Rgdmve f +++ gf     
  gi|15669665|ref|NP_248478.1|   4 MITTVVGSYPVVKKEETFLDKVKKVFGL----YDEYKYAIERAVKDQVKAGVNIISDGQ-VRGDMVEIFTNNMYGFD--G- 76 
                                   79*********************99887....7888999********************.6***********99982..2. PP

                                   --EEEETTEEE---EE-SS---SS-SSTHHHHHHTTS-SS-.....BEEEEE-HHHHHHTSEE-...TTS-HHHHHHHHHH CS
                   Meth_synt_2  82 gwvqsygsrcvrppiivgdvsrpaamtvkesalaqsltdkp.....vkglltGpvtilnwsfvr...ddvdraeaaaqial 154
                                          +r+      vg v++ +++t+k + +a+s+ +k      +kg++tGp ti +  +v+    d   ++ +++ia 
  gi|15669665|ref|NP_248478.1|  77 -------KRV------VGRVEFIKPITLKDILYAKSIAKKLnpnveIKGIITGPCTIASSVRVEscySDNRDENLIYDIAK 144
                                   .......232......3444455555555555555554443334449**********999999988889999999****** PP

                                   HHHHHHHHHHHTT-SEEEEE-TTSSTT--SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCHHHHHTT--S CS
                   Meth_synt_2 155 alrdevkdLeaaGikviQiDepalreGlplkkadwaayldwaveafrldtiaaaddtqvhtHlCyselndilsaiaaldvD 235
                                   alr+ev++L++  + +iQiDep l++G+ +            v+  ++d i+ + +++ ++H+C++ +n i +++++++vD
  gi|15669665|ref|NP_248478.1| 145 ALRKEVEALKKH-VPIIQIDEPILSTGMYDFD----------VARKAIDIIVDGLNIKFAMHVCGNVYNII-DELNKFNVD 213
                                   ***********9.**************98777..........999********************999977.********* PP

                                   EEEESBSSS-SSGGGGTTTT---SEEEEBSS-TTSSS--THHHHHHHHHCHHCT.........S-STSB-BB-SS-STTS- CS
                   Meth_synt_2 236 vitieasrsdeellealeevkygrgvglGvydihsprvpsmeeiaalikkaldv.........apkerlwvnPdCGLktrk 307
                                   +++ e++ ++ ++l  le   ++++vg+G+++++  +v+s+eei++li++ +++          + +++ ++PdCG++ ++
  gi|15669665|ref|NP_248478.1| 214 ILDHEFASNK-KNLVILES--MEKKVGFGCVNTKVKKVESVEEIKSLIEEGIEIlknneklnkNLSDNILIDPDCGMRLLP 291
                                   *******999.99999999..9*******************************9999**9999889*************** PP

                                   HHHHHHHHHHHHHHHH CS
                   Meth_synt_2 308 reearaalknmvdaAk 323
                                    + a+++lknmv+a+k
  gi|15669665|ref|NP_248478.1| 292 IDVAFNKLKNMVEATK 307
                                   *************987 PP

>> Meth_synt_1  Cobalamin-independent synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.8e-07    0.0011     140     290 ..     100     243 ..      87     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.8e-07
                                   HHHHHHTTGGEEEEEE-HHHHHHT-EETTCC...-HCHHHHHHHHHHHHHHHHHHHTT-SEEEEE-GGGGSSGCHHHHHHH CS
                   Meth_synt_1 140 vkeakalgieakpvllGpltflkLskakeek..veklellekLlpvYkelleeLkeagvewvqidEPalvldlekeeleal 218
                                   + +  + ++e k ++ Gp+t  +  + ++     + ++l+ ++ ++ ++ +e Lk++ v ++qidEP+l++ +   + +++
  gi|15669665|ref|NP_248478.1| 100 IAKKLNPNVEIKGIITGPCTIASSVRVESCYsdNRDENLIYDIAKALRKEVEALKKH-VPIIQIDEPILSTGM--YDFDVA 177
                                   55556678899999****998665555443322366779999999999999999987.9***********985..678888 PP

                                   HHHHHHHTCCTTTSEEEEE--.SS-.CCHHHHHTTSSTSEEEEETSSHCHHHHHHHHCTT.TTSEEEEEEE-S CS
                   Meth_synt_1 219 keaYeelakekkelklllaty.FdsvaealellaelpveglglDlvraeenlealkkaglpedkvLsaGvidG 290
                                   ++a + +    ++l++ +a+   ++v + +++l +++v+ l  ++ ++++nl  l++     +k +  G+++ 
  gi|15669665|ref|NP_248478.1| 178 RKAIDII---VDGLNIKFAMHvCGNVYNIIDELNKFNVDILDHEFASNKKNLVILES----MEKKVGFGCVNT 243
                                   9999998...4555555554316999**************************99998....567777788775 PP

>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   1.0   1.4e-05     0.082     127     343 ..      98     306 ..      80     308 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                                   HHHHHH.--SS-EEEEEE-HHHHHHHHHCTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEETT CS
                         URO-D 127 kllkkelggevpligfvgaPftlasylveGgskgfekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifDsw 207
                                   k + k+l+ +v + g +++P t+as++           ++ +y+d  + + l+  +++++ + ++a+ ++ + +iqi +  
  gi|15669665|ref|NP_248478.1|  98 KSIAKKLNPNVEIKGIITGPCTIASSVR----------VESCYSDNRD-ENLIYDIAKALRKEVEALKKH-VPIIQIDEP- 165
                                   4455669999999999999999999999..........6667766655.567777777777777776555.778888875. PP

                                   GGGS-HHHHH.HHTHHHHHHHHHHHHH.H--S-EEEEESSHH.HHHHHHTTS--SEEE--TTS-HHHHHH..SS....EEE CS
                         URO-D 208 agllspedfe.efvlpylkrivdevkaegpkvpvilfikgagaeiledlaelgadvlsldwtvdlkeaar..evgdkvalq 285
                                     +ls  +++ +++ +++  ivd+++     ++  ++++g+   i+++l++ ++d+l  + + + k+ +   ++ +k++  
  gi|15669665|ref|NP_248478.1| 166 --ILSTGMYDfDVARKAIDIIVDGLN-----IKFAMHVCGNVYNIIDELNKFNVDILDHEFASNKKNLVIleSM-EKKVGF 238
                                   ..588888874455556666666665.....5899******988**********99887666655333334233.778889 PP

                                   --B-G.GGGG.S-HHHHHHHHHHHHT.........T---SSSEEB-BSS-...--TTS-HHHHHHHHHHH CS
                         URO-D 286 GnldPialLl.gspeeiekevkeile........kgaggkkgyilnlGhg...ippetppenvkalveav 343
                                   G +++ ++   +s eei+  ++e +e        + ++   ++ + + +g   +p ++  +++k +vea+
  gi|15669665|ref|NP_248478.1| 239 GCVNT-KVKKvESVEEIKSLIEEGIEilknneklN-KNLSDNILIDPDCGmrlLPIDVAFNKLKNMVEAT 306
                                   99999.56666999999998888888776666532.3335677788888855557788888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1931.56
//
Query:       gi|15669666|ref|NP_248479.1|  [L=197]
Description: hypothetical protein MJ_1474 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-16   60.4   0.0    2.8e-16   59.8   0.0    1.3  1  PIN_6     PIN domain of ribonuclease
      2e-05   24.1   0.2    5.3e-05   22.7   0.1    1.6  1  PIN_5     PINc domain ribonuclease
    0.00014   22.1   0.0    0.00021   21.6   0.0    1.3  1  PIN_2     PIN domain
     0.0037   17.8   0.1      0.029   14.9   0.1    2.0  1  PIN       PIN domain
     0.0061   16.5   1.6     0.0061   16.5   1.6    1.7  2  ADK_lid   Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   7.9e-20   2.8e-16       2      89 .]      35     118 ..      35     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 7.9e-20
                         PIN_6   2 VlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellplelevrePspesvkkvtefakktGDlsvLSktDiev 82 
                                   VlDa+a+i+  ++++ + +e+ yttpeV++Ei  kk   + +l   +l++++P++e++kkv+e+ kktGD   LS++Di v
  gi|15669666|ref|NP_248479.1|  35 VLDASAIIHG-YNPIIEEGEH-YTTPEVLEEIESKKIIVEQALDFGKLKIMSPNREYIKKVEEVVKKTGD--NLSQQDIGV 111
                                   89******99.8888877766.799***********9998888778***********************8..69******* PP

                         PIN_6  83 lALtyeL 89 
                                   lAL+++L
  gi|15669666|ref|NP_248479.1| 112 LALALNL 118
                                   ****987 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.5e-08   5.3e-05     156     190 ..     105     139 ..      99     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.5e-08
                         PIN_5 156 saeDldvllLAkELdaavvssDeGikkwaeklGlr 190
                                   s++D+ vl LA  L+a + ++D Gi+++a+kl ++
  gi|15669666|ref|NP_248479.1| 105 SQQDIGVLALALNLNAILYTDDYGIQNVAKKLNIE 139
                                   899*****************************987 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   5.7e-08   0.00021      47     113 ..      61     127 ..      29     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.7e-08
                         PIN_2  47 vkksklseeeleellelletkikiveeslyeskikeAkeriarvDpdDtpfvAlaLlleapiWTeDk 113
                                   +++ + ++  +e++l+  + ki + ++++++++++  k+  ++  ++D+ ++AlaL l+a + T+D 
  gi|15669666|ref|NP_248479.1|  61 LEEIESKKIIVEQALDFGKLKIMSPNREYIKKVEEVVKKTGDNLSQQDIGVLALALNLNAILYTDDY 127
                                   555555566678899999999********************************************95 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   8.1e-06     0.029      49     122 .]      61     135 ..      34     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.1e-06
                                   CHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHHHHHHHHH..SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHHC CS
                           PIN  49 kskrekaaelvelllllsalkilpidaeiaeeaaeialkyg..llpnDaliaAtAkehgikliatfDedfrrvakl 122
                                   ++++e ++ +ve+ l+   lki++ + e  ++++e+ +k g  l+  D  ++A+A+  ++ +++t D  + +vak+
  gi|15669666|ref|NP_248479.1|  61 LEEIESKKIIVEQALDFGKLKIMSPNREYIKKVEEVVKKTGdnLSQQDIGVLALALNLNA-ILYTDDYGIQNVAKK 135
                                   44455667779999999*******************************************.677******999985 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.9   6.9e+03      21      34 ..      94     107 ..      92     108 .. 0.69
   2 !   16.5   1.6   1.7e-06    0.0061       1      32 [.     155     182 ..     155     184 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.9
                                   TTB-TTT--.-B-- CS
                       ADK_lid  21 eglCDkCGepLvqR 34 
                                   e +  k+G +L q 
  gi|15669666|ref|NP_248479.1|  94 EEVVKKTGDNLSQQ 107
                                   55556899999885 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.7e-06
                                   EEE-TTT--EEETTTB--SSTTB-TTT--.-B CS
                       ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLv 32 
                                   R +C+ C++ Y v +    +e +C  CG+pL 
  gi|15669666|ref|NP_248479.1| 155 RKICEGCKKLYPVDY----EEDICEICGSPLK 182
                                   789*********999....***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1173.52
//
Query:       gi|15669667|ref|NP_248480.1|  [L=125]
Description: hypothetical protein MJ_1475 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-06   25.5   0.1    1.6e-05   24.5   0.1    1.6  1  Sigma70_r4_2    Sigma-70, region 4
     0.0035   16.8   1.4     0.0042   16.6   0.1    1.7  2  GerE            Bacterial regulatory proteins, luxR family
  ------ inclusion threshold ------
      0.028   14.0   0.0      0.099   12.2   0.0    2.0  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.085   13.4   0.9      0.085   13.4   0.9    2.1  2  PNPase          Polyribonucleotide nucleotidyltransferase, RN
      0.094   12.6   0.0       0.12   12.2   0.0    1.2  1  KR              KR domain
       0.15   11.8   4.1        0.2   11.4   0.5    2.0  2  DNA_pol3_delta  DNA polymerase III, delta subunit


Domain annotation for each model (and alignments):
>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   5.3e-09   1.6e-05      24      53 ..      93     122 ..      89     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 5.3e-09
                                   TS---HHHHHHHHT--HHHHHHHHHHHHHH CS
                  Sigma70_r4_2  24 leglsykEIAellgisegtVksrlsRArkk 53 
                                   + +++ kEIAe++gi+ +tV++++++ +kk
  gi|15669667|ref|NP_248480.1|  93 YLDKKPKEIAEITGINIKTVEYHYYKLKKK 122
                                   678999********************9997 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.97   2.9e+03      42      54 ..       1      13 [.       1      15 [. 0.80
   2 !   16.6   0.1   1.4e-06    0.0042      18      44 ..      96     122 ..      93     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.97
                                  HHHHT-SSHHHHH CS
                          GerE 42 mkKLnvksrvelv 54
                                  mkKL +k + el+
  gi|15669667|ref|NP_248480.1|  1 MKKLIAKTKEELI 13
                                  8999998888887 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.4e-06
                                   S-HHHHHHHHTS-HHHHHHHHHHHHHH CS
                          GerE  18 ksnkeIAeelniSekTVkvhksnimkK 44 
                                   k+ keIAe+ +i  kTV++h   + kK
  gi|15669667|ref|NP_248480.1|  96 KKPKEIAEITGINIKTVEYHYYKLKKK 122
                                   6679*****************999998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.4   4.1e+03       6      12 ..      60      66 ..      57      67 .. 0.69
   2 ?   12.2   0.0   3.3e-05     0.099      20      44 ..      98     122 ..      95     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.4
                        HTH_24  6 rkILelL 12
                                  +kI+++L
  gi|15669667|ref|NP_248480.1| 60 KKIIKAL 66
                                  6888877 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.3e-05
                        HTH_24  20 qreLAerlglSpstvnrrlkrLeee 44 
                                    +e+Ae +g+ + tv ++  +L+++
  gi|15669667|ref|NP_248480.1|  98 PKEIAEITGINIKTVEYHYYKLKKK 122
                                   58****************9998887 PP

>> PNPase  Polyribonucleotide nucleotidyltransferase, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2      0.38   1.1e+03      32      49 ..       7      23 ..       2      42 .. 0.60
   2 ?   13.4   0.9   2.9e-05     0.085      15      66 ..      71     122 ..      55     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.38
                                  HHHHHHHHHHH...HHST CS
                        PNPase 32 eikekvveafaaeleeed 49
                                  + ke+ +e++  e e+e+
  gi|15669667|ref|NP_248480.1|  7 KTKEELIEKIK-ECENEE 23
                                  34455555554.222222 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.9e-05
                                   HHHTTSSSHHHHHHHHHHHHHHHHHHHH...HHSTTS-HHHHHHHHHHHHHH CS
                        PNPase  15 sealtiteKqeRyaaldeikekvveafaaeleeedeedekeikeifkalekk 66 
                                    e++ i+ K +R +++d+i +k + +  +e++e   ++ k +++ +++l+kk
  gi|15669667|ref|NP_248480.1|  71 VEVIPIKAKTGRPTNVDKIIKKYLDKKPKEIAEITGINIKTVEYHYYKLKKK 122
                                   578899********************************************98 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.2e-05      0.12      14      84 ..      33     103 ..      30     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.2e-05
                                   HHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS.S---E CS
                            KR  14 lelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee.ppikG 84 
                                   + +a  l+e+++ + ++l +s + +++sk+ i++le  ++ev  ++a    +++v ++++++ +++ ++i+ 
  gi|15669667|ref|NP_248480.1|  33 RDVAIALLESCEPKKIYLPKS-KYKRSSKKIIKALEGVDVEVIPIKAKTGRPTNVDKIIKKYLDKKpKEIAE 103
                                   678899999998888888888.67888888*******************************99888655554 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   6.7e-05       0.2       9      50 ..       3      44 ..       2      52 .. 0.93
   2 ?    1.8   0.3     0.058   1.7e+02     105     148 ..      57     103 ..      46     105 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.7e-05
                                  HHHHHHHHHHHHHHHTTTEEEEEEEE-STTS-HHH.HTTTST CS
                DNA_pol3_delta  9 llleeskdqilkqalkqgfedlnyikfdlnedwiddvleece 50
                                  +l++++k+++++++++ + e+  yi+++l+ d + ++le+ce
  gi|15669667|ref|NP_248480.1|  3 KLIAKTKEELIEKIKECENEEEIYINLELDRDVAIALLESCE 44
                                  699****************************99999999998 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.058
                                   -HHHHHHHHHTT...TEEEEEE----TTTHHHHHHHHHHHTT-EE-H CS
                DNA_pol3_delta 105 derkklvklLkk...katvveaktlkeeelkkwiqkraqelglkiek 148
                                   ++ kk++k L+    +++ ++akt +  ++ k i+k++ ++ ++i +
  gi|15669667|ref|NP_248480.1|  57 RSSKKIIKALEGvdvEVIPIKAKTGRPTNVDKIIKKYLDKKPKEIAE 103
                                   34455888888876677777888888889999999999988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1442  (0.0804284); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 844.67
//
Query:       gi|15669668|ref|NP_248481.1|  [L=230]
Description: hypothetical protein MJ_1476 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-38  130.4   0.0    8.3e-38  129.8   0.0    1.3  1  SpoU_methylase  SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.8   0.0   4.6e-42   8.3e-38       2     142 .]       5     155 ..       4     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 129.8 bits;  conditional E-value: 4.6e-42
                                   EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEEEEEE CS
                SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfalvat 81 
                                   + v+lv++++ gN+G+iaR++ +fg++el++v+++s  ++n+ea+ +a++a+e+l+ +k +++++ea+ +l+ + +a+ ++
  gi|15669668|ref|NP_248481.1|   5 ISVILVNPKYSGNVGSIARVMMNFGFEELRIVGDKS--IINNEAYMMAVHAREILDnAKFYNTFDEAIGDLDFV-IATSGA 82 
                                   789******************************777..5***********************************.888888 PP

                                   STT-SEGCCS............HHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS
                SpoU_methylase  82 slkgkslsei............dlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142
                                    +++++l+++            ++k+++ +vfG+Ed+Gl+ne+++++d lv+Ip+s++++ +N+++Ava++ly
  gi|15669668|ref|NP_248481.1|  83 RGGDRNLKRVpitpkeladkilEVKGNIGIVFGREDDGLRNEEIDKCDLLVSIPTSEKYPIMNLSHAVAVILY 155
                                   8888888855445555566556666**********************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1518.95
//
Query:       gi|15669669|ref|NP_248482.1|  [L=346]
Description: hypothetical protein MJ_1477 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-33  114.3   3.1    6.6e-33  113.9   3.1    1.1  1  Glyco_hydro_114  Glycoside-hydrolase family GH114
  ------ inclusion threshold ------
       0.15   12.3   0.9        5.8    7.1   0.0    2.9  3  Flavodoxin_NdrI  NrdI Flavodoxin like


Domain annotation for each model (and alignments):
>> Glyco_hydro_114  Glycoside-hydrolase family GH114
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   3.1   7.4e-37   6.6e-33       2     228 ..      71     334 ..      70     337 .. 0.77

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 7.4e-37
               Glyco_hydro_114   2 wqyqlqgple...tspdavdvydiDlf.dts.......aatiaalkakgkkviCYfsaGevedwrp..daddf..npasvl 67 
                                   w+yqlq+ ++    + ++++   iD++ d         +++i++lk++gk  i+Y+s+Ge+ed+r   d++ +  np + l
  gi|15669669|ref|NP_248482.1|  71 WAYQLQN-ADideIANSNFTLIVIDYSkD-GtengkysEEEIEKLKKAGKIPIAYISIGEAEDYRFywDNE-WlkNPPKWL 148
                                   9***993.333343344466666888852.33577999****************************85444.459999999 PP

               Glyco_hydro_114  68 gkkldgWpgerwldirtaakrsskvrsimkaridlaaakGfdgvepDnvDsye...sndtgfl..ltaadqlayvkflaae 143
                                   g +  +W+g + +++++++++     +i+ +++d+++++Gf gv++D+vD +e   +n+  ++   ta++ ++++  ++++
  gi|15669669|ref|NP_248482.1| 149 GDENPEWEGCYAVKYWHPEWK-----KIIFSYLDKIIQQGFCGVYLDKVDEFEywaENG--YDedFTAKEMIKFIVEISNY 222
                                   99989****************.....6*************************9764333..33235555555555555555 PP

               Glyco_hydro_114 144 aha...rglaiglknagelise.....lvdafdfavnEeca...........eyseCdtyepfiaagkpVfhiEYp...vs 202
                                    +    + + i+++n++ l++      l++++ +++ E+++            ++  + ++++ + gk+V+ ++Y    ++
  gi|15669669|ref|NP_248482.1| 223 CRNktnNSFIIIPQNGERLLEYdkhgkLLNTVSGWAVEDLFydgveqkteeeINERIKLLDKVKDSGKFVLVVDYVddgTK 303
                                   5557777*************5566778**************99999887664224566688899***********987733 PP

               Glyco_hydro_114 203 aaedaaacaa...asraagfstvvk..dldL 228
                                   ++e+ + +++   +s ++g+ ++v   d++L
  gi|15669669|ref|NP_248482.1| 304 TNENLKRVEDfinKSLDKGYVPYVAksDREL 334
                                   33333333335669999*****998455555 PP

>> Flavodoxin_NdrI  NrdI Flavodoxin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.056     5e+02      12      54 ..      52     103 ..      42     117 .. 0.58
   2 ?    0.8   0.0     0.059   5.3e+02      33      75 ..     209     254 ..     188     257 .. 0.78
   3 ?    7.1   0.0   0.00065       5.8      25      69 ..     278     321 ..     261     331 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.056
                                   HHHHHH-S.-EEEE-SS........TT--.---SS-EEEEEE--TTSSSSTS CS
               Flavodoxin_NdrI  12 rFveklel.eaqriple........ekeeelevdepyvlivptygegeekka 54 
                                   r  e+l++ ++++++l+        +++ +   ++++ liv  y++ +++++
  gi|15669669|ref|NP_248482.1|  52 RNAENLTNiSKNSNNLKflwayqlqNADIDEIANSNFTLIVIDYSKDGTENG 103
                                   5555554433333333355555443333336678899999999998887554 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.059
                                   ---SS-EEEEEE--TTSSSSTS...S-HHHHHHHTSHHHHHCEEEE CS
               Flavodoxin_NdrI  33 levdepyvlivptygegeekka...vpkqvieflnkeknrkllrGv 75 
                                   +++  ++++ +  y  ++++++   +p++ ++ l++ k+ kll  v
  gi|15669669|ref|NP_248482.1| 209 AKEMIKFIVEISNYCRNKTNNSfiiIPQNGERLLEYDKHGKLLNTV 254
                                   5556689999999999998887899999999999999999998877 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.00065
                                   -SSTT--.---SS-EEEEEE--TTSSSSTSS-HHHHHHHTSHHHH CS
               Flavodoxin_NdrI  25 pleekeeelevdepyvlivptygegeekkavpkqvieflnkeknr 69 
                                   ++ +  ++++ + ++vl+v   ++g+++++  k+v++f+nk+ ++
  gi|15669669|ref|NP_248482.1| 278 RI-KLLDKVKDSGKFVLVVDYVDDGTKTNENLKRVEDFINKSLDK 321
                                   22.23345888899******99***9999999********87665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2150.33
//
Query:       gi|15669670|ref|NP_248483.1|  [L=303]
Description: hypothetical protein MJ_1478 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-11   44.6   0.0    5.7e-11   42.5   0.0    1.9  2  ATP_bind_3      PP-loop family
    3.9e-06   26.6   0.0    6.2e-06   25.9   0.0    1.3  1  ThiI            Thiamine biosynthesis protein (ThiI)
    1.8e-05   23.7   0.0    4.5e-05   22.4   0.0    1.7  1  tRNA_Me_trans   tRNA methyl transferase
    4.2e-05   23.1   0.1    0.00012   21.6   0.0    1.8  2  QueC            Queuosine biosynthesis protein QueC
     0.0007   19.7   0.0      0.002   18.2   0.0    1.9  1  PAPS_reduct     Phosphoadenosine phosphosulfate reductase fam
     0.0021   17.2   0.0      0.004   16.3   0.0    1.4  1  NAD_synthase    NAD synthase
     0.0072   16.8   0.0      0.014   15.9   0.0    1.4  1  Rhodanese       Rhodanese-like domain
  ------ inclusion threshold ------
      0.047   13.3   1.3      0.047   13.3   1.3    2.8  3  RecR            RecR protein
      0.057   13.7  10.6        7.9    6.9   0.0    3.4  3  C1_2            C1 domain


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   2.9e-14   5.7e-11       1     163 [.      53     217 ..      53     222 .. 0.79
   2 ?    0.5   0.0      0.22   4.4e+02      46      94 ..     202     258 ..     199     264 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 2.9e-14
                                   EEEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H......HHCTTST CS
                    ATP_bind_3   1 kvlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv......akkkgkn 75 
                                   k+lvAvSgG D  a  ++l+kl    g ++ ++h++ g+   s+e  ++vkel++kl+++l++ +++       +  +gk+
  gi|15669670|ref|NP_248483.1|  53 KILVAVSGGKDGHAAAWVLKKL----GYNIELFHINLGIEGFSEESLKAVKELAEKLEVPLHVVNLKDitgktmEDIRGKK 129
                                   689*****************99....559*************************************988988776667888 PP

                                   CCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETT..CCEE-CCCT--HHHHHH CS
                    ATP_bind_3  76 leeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseias..irlvRPlLkvskeelee 154
                                         ++RY ++++   ++g++v++++h+ dD +  +l +l++  +++ la  +++ + ++   + v  +++++ e + +
  gi|15669670|ref|NP_248483.1| 130 CSICGTTKRY-LMNKFGYENGFDVIVTGHNLDDEVSFILNNLFNW-NIRYLAKHEPVLPAHDkfLKKVKIFFEIEEELILK 208
                                   8888999999.6789999*****************9999888773.33445444444444332344455556666666666 PP

                                   HHHHTT--- CS
                    ATP_bind_3 155 ylkekkikw 163
                                   y++ ++i++
  gi|15669670|ref|NP_248483.1| 209 YAEAEEIPY 217
                                   666666655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.22
                                   HHHHHHHHHHHTT-EEEEEE--H........HHCTTSTCCCHHHHHHHHHHHHCHHC CS
                    ATP_bind_3  46 eaelvkelckklnikleiekvdv........akkkgknleeaARelRYevlkealkk 94 
                                   e+el+ ++++  +i++++ +++         ++   ++le++   + Y++l+ ++k+
  gi|15669670|ref|NP_248483.1| 202 EEELILKYAEAEEIPYTTVECKYaeraitlkHRAYLNELEKERPGIKYQFLSGYMKN 258
                                   677888888888999988888887777777655568888888888999999888876 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   3.1e-09   6.2e-06       4     129 ..      52     170 ..      49     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 3.1e-09
                          ThiI   4 gkvlaLlSgGiDSpVaaylllkRGcrvvlvhlkn.epgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekv 83 
                                   +k+l+ +SgG D   aa++l k G +++l h++    g see  + v++lae+l       ev l vv++k++  + +e +
  gi|15669670|ref|NP_248483.1|  52 EKILVAVSGGKDGHAAAWVLKKLGYNIELFHINLgIEGFSEESLKAVKELAEKL-------EVPLHVVNLKDITGKTMEDI 125
                                   789999*************************95313345666666666666654.......689****************9 PP

                          ThiI  84 kekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNl 129
                                   + k   +    +   + +k   e+g + +vtG +L    S  l+Nl
  gi|15669670|ref|NP_248483.1| 126 RGKKCSIC-GTTKRYLMNKFGYENGFDVIVTGHNLDDEVSFILNNL 170
                                   87765554.4444445578999**************9999999998 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.2e-08   4.5e-05       2      72 ..      53     116 ..      52     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.2e-08
                 tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfek 72 
                                   k++va+SgG D   aa +lk+ gy+++ ++++l  e         +ee lk +++ aekl++pl+vv++++
  gi|15669670|ref|NP_248483.1|  53 KILVAVSGGKDGHAAAWVLKKLGYNIELFHINLGIE-------GFSEESLKAVKELAEKLEVPLHVVNLKD 116
                                   89*************************999988776.......367899*******************986 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.6   7.1e+03     132     144 ..      26      38 ..      13      44 .. 0.66
   2 !   21.6   0.0   6.1e-08   0.00012       1      63 [.      53     116 ..      53     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.6
                                   GSHHHHHHHHHHH CS
                          QueC 132 crdefvkalnkal 144
                                   c+++fv+ +++ +
  gi|15669670|ref|NP_248483.1|  26 CKEHFVEYFENKV 38 
                                   6666666666655 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 6.1e-08
                                   EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE-GG CS
                          QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqr..hkkeleaakkiakelgveehkildldl 63 
                                   k++v +SGG D  +++++ kk g+++e+ +++ g     ++ l+a+k++a++l+v   ++++l+ 
  gi|15669670|ref|NP_248483.1|  53 KILVAVSGGKDGHAAAWVLKKLGYNIELFHINLGIEgfSEESLKAVKELAEKLEV-PLHVVNLKD 116
                                   57999*****************************998778889************.999988873 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   9.9e-07     0.002       2     114 ..      54     164 ..      53     224 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.9e-07
                                   EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB..-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHC CS
                   PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghe..fpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyee 80 
                                   + v+vsgGkd+ +    + k  +++++++++ g e   +e ++ v+el+e++++ l+v++ ++   + ++  + g++    
  gi|15669670|ref|NP_248483.1|  54 ILVAVSGGKDGHAAAWVLKKLGYNIELFHINLGIEgfSEESLKAVKELAEKLEVPLHVVNLKDITGKTMEDIR-GKKC--- 130
                                   789******************************986447899*************988876666444444444.2333... PP

                                   HHHHHHTHHHHHHHHHCTTECEEE----CCCTTT CS
                   PAPS_reduct  81 aaeriaKveplkkaLekldedalltGaRrdesks 114
                                    ++  +K + ++k   ++++d+++tG   d++ s
  gi|15669670|ref|NP_248483.1| 131 SICGTTKRYLMNKFGYENGFDVIVTGHNLDDEVS 164
                                   5799999999999999999999999988777765 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     2e-06     0.004       4      94 ..      37     127 ..      31     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2e-06
                                   HHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHH CS
                  NAD_synthase   4 elvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpi 84 
                                   ++++++ +y   ++ +++++ +SGG D   +a + +k+  + + + + l  +  see++++ ++lae+l++  +++++k+i
  gi|15669670|ref|NP_248483.1|  37 KVKKSIDKYKMLSKDEKILVAVSGGKDGHAAAWVLKKLGYNIELFHINLGIEGFSEESLKAVKELAEKLEVPLHVVNLKDI 117
                                   4556666666667779****************9999998899999****999999*************************9 PP

                                   HHHHHHHHHH CS
                  NAD_synthase  85 vrafeqelke 94 
                                   +    + ++ 
  gi|15669670|ref|NP_248483.1| 118 TGKTMEDIRG 127
                                   9777666655 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   6.8e-06     0.014      48     106 ..      35      92 ..      21      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.8e-06
                     Rhodanese  48 eapllelpeellelgidnkktvvvycdgggraaaaaallkklGykn.vsvldGGfkawke 106
                                   e++ ++ +++++ l  ++++++ v  +gg++  aaa+ lkklGy+  +++++ G+++++e
  gi|15669670|ref|NP_248483.1|  35 ENKVKKSIDKYKML--SKDEKILVAVSGGKDGHAAAWVLKKLGYNIeLFHINLGIEGFSE 92 
                                   44455556666666..8888888888888888888999999**9889**********997 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       3.7   7.4e+03      31      34 ..       7      10 ..       4      13 .. 0.62
   2 ?    3.9   0.1      0.02        40      30      39 ..     129     138 ..     121     138 .. 0.65
   3 ?   13.3   1.3   2.4e-05     0.047      17      35 ..     272     290 ..     270     291 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.7
                                  -CCC CS
                          RecR 31 CaIC 34
                                  C +C
  gi|15669670|ref|NP_248483.1|  7 CKFC 10
                                  5555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.02
                                   S-CCCCSTTS CS
                          RecR  30 lCaICsdprR 39 
                                    C+IC  ++R
  gi|15669670|ref|NP_248483.1| 129 KCSICGTTKR 138
                                   3666666555 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 2.4e-05
                                   EE-TTT--EESSSS-CCCC CS
                          RecR  17 rhCsrCgnlteedlCaICs 35 
                                   r C++Cg  +   +C++C+
  gi|15669670|ref|NP_248483.1| 272 RECEVCGMTSAGKICSFCR 290
                                   89****************7 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.9     0.017        33      18      37 ..       4      28 ..       2      33 .. 0.76
   2 ?    6.9   0.0     0.004       7.9      14      33 ..     123     146 ..     107     147 .. 0.61
   3 ?    6.1   1.4    0.0072        14      13      39 ..     266     290 ..     257     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
                          C1_2 18 sfnCsaCgrk.....idgffYsCse 37
                                  +++C+ C++k      ++++Y C+e
  gi|15669670|ref|NP_248483.1|  4 TMKCKFCDKKsyiklKSPKMYLCKE 28
                                  689*******876654455599975 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.004
                          C1_2  14 dssesfnCsaCgrk....idgffY 33 
                                   ++   ++Cs+Cg++    +++f Y
  gi|15669670|ref|NP_248483.1| 123 EDIRGKKCSICGTTkrylMNKFGY 146
                                   344459******996666666656 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0072
                          C1_2  13 edssesfnCsaCgrkidgffYsCseCd 39 
                                   e++ + ++C++Cg ++ g+  +Cs C+
  gi|15669670|ref|NP_248483.1| 266 EEDFQFRECEVCGMTSAGK--ICSFCR 290
                                   44555689*******9998..899896 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1858.43
//
Query:       gi|15669671|ref|NP_248484.1|  [L=432]
Description: aminotransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-36  126.4   0.0      2e-36  126.0   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0011   17.8   0.0     0.0034   16.2   0.0    1.7  2  Aminotran_MocR   Alanine-glyoxylate amino-transferase
  ------ inclusion threshold ------
      0.066   12.5   0.0       0.12   11.6   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
      0.098   12.4   0.0        0.3   10.8   0.0    1.8  2  LUD_dom          LUD domain


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.0   4.4e-40     2e-36      18     349 ..      47     408 ..      33     421 .. 0.88

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 4.4e-40
                                   HHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEE CS
                 Aminotran_1_2  18 ptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilv 98 
                                   + +p+++k  +  + ++     y p++gl e +e la+ ++++ ++++++e  +++ +G g +i+ +  llk  ++ +++ 
  gi|15669671|ref|NP_248484.1|  47 EKIPDWIKDIIAEIVKNDCSYAYCPTKGLLETREFLAEQVNKRGGVQITAE-DIIFFNGLGDAIAKIYGLLK--RQVRVIN 124
                                   5677888887775666666678*****************************.*******************9..******* PP

                                   EESS-THHHHH.HHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHH CS
                 Aminotran_1_2  99 pdptyasykni.lrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlak 178
                                   p+p+y+ ++ + + ++g++ v+y l++ + +  d+++le+ +k +p     + +ilv +p NPtG+v++++ l +++dla+
  gi|15669671|ref|NP_248484.1| 125 PSPSYSTHSSAeASHAGSPPVTYFLDPYNYWYPDIDDLEKRIKYNP----AVSGILVINPDNPTGAVYPKKILNEIVDLAN 201
                                   ********98747888999************************966....789**************************** PP

                                   HTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEE.EH....HHHHHHHHHHHHHTS.. CS
                 Aminotran_1_2 179 kynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilg.na....avvsqlrklsrpfls.. 252
                                   +y l++++De+Y  +v++ ++   ++++v +++  l + + sK +  +G R+G+i + na    +++++++++  + l+  
  gi|15669671|ref|NP_248484.1| 202 EYDLFIICDEIYCNLVYNGKKQ-HLLCEVIDDVCGLSLKGISKELPWPGARCGWIEIyNAdkdeEFKKYVESIYKAKLIev 281
                                   ******************8753.448888888889********************99999888855555555555555577 PP

                                   .SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH................ CS
                 Aminotran_1_2 253 .ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae................ 315
                                    s+ l++++   +     ++++lee+ + ++kr+ + +++L++l g++  + ++++++ ++++                  
  gi|15669671|ref|NP_248484.1| 282 cSTTLPQMAIPRIMGHRNYKKYLEERNRFFEKRSNTAYKKLKDLdGVIANKANGAFYMSVVFEDNylngnnsikieneklk 362
                                   79999999999999999999*********************999999999999*********999*************999 PP

                                   ...........CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECT CS
                 Aminotran_1_2 316 ...........takelskkLleevgvyvtpgtsftv..pgrlRitvA 349
                                               +k++   Ll   g+ v+p tsf     g +R+t+ 
  gi|15669671|ref|NP_248484.1| 363 efiehqikdasIDKKFVYYLLASTGICVVPLTSFCSqlNG-FRVTLL 408
                                   999998877777777777799999**********998455.999984 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.7e-07    0.0034     123     217 ..     118     214 ..      88     234 .. 0.78
   2 ?   -1.5   0.0      0.18     8e+02      68     115 ..     325     372 ..     316     379 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.7e-07
                                   .--EEEEEES--HHHHHH.HHHHT-EEEEEEE...ETTEE-HHHHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHH CS
                Aminotran_MocR 123 ekvkllvtvpGydrhfll.leelGielltvdl...qddGpdvdaveklvaedasvkGilavpkysnptGetiseevarrla 199
                                    +v+++ ++p y  h      + G   +t  l   +   pd+d +ek +  +++v Gil++ +  nptG ++ ++   +++
  gi|15669671|ref|NP_248484.1| 118 RQVRVINPSPSYSTHSSAeASHAGSPPVTYFLdpyNYWYPDIDDLEKRIKYNPAVSGILVI-NPDNPTGAVYPKKILNEIV 197
                                   479999999999999765156677766666551115567*******************977.568**************** PP

                                   T---SSTT-EEEEE-TTS CS
                Aminotran_MocR 200 alkaaapdfrifaddaya 217
                                    l     d+ i  d+ y 
  gi|15669671|ref|NP_248484.1| 198 DLAN-EYDLFIICDEIYC 214
                                   9954.5788888999996 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.18
                                   TT--HHHHHHHHHHTTS-GGGEEE-SS-HHHHHHHHHHHHHHC--TT- CS
                Aminotran_MocR  68 laGlpelralfaelldvkaenvlvqnnsslelqglvltlallhGvrds 115
                                   l+G+   +a  a ++ v  e+ + ++n s+++ ++ l   + h ++d+
  gi|15669671|ref|NP_248484.1| 325 LDGVIANKANGAFYMSVVFEDNYLNGNNSIKIENEKLKEFIEHQIKDA 372
                                   7888888999999999999999**********9999998888888886 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.8e-05      0.12     109     167 ..     157     210 ..     123     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.8e-05
                                   E-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
               Beta_elim_lyase 109 mdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                    d+++le+ ik   +  + ++ i++ +  n   G v++ + l+e+ ++a++y++ +++D
  gi|15669671|ref|NP_248484.1| 157 PDIDDLEKRIKY--N--PAVSGILVINPDNP-TGAVYPKKILNEIVDLANEYDLFIICD 210
                                   589999999998..5..89999999999995.9*********************99999 PP

>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.7   7.8e+03     128     143 ..     153     168 ..     143     172 .. 0.76
   2 ?   10.8   0.0   6.6e-05       0.3      13      62 ..     255     302 ..     251     343 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.7
                       LUD_dom 128 nkivpdledavkrlkt 143
                                   n  +pd++d++kr+k 
  gi|15669671|ref|NP_248484.1| 153 NYWYPDIDDLEKRIKY 168
                                   5568999****99997 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 6.6e-05
                       LUD_dom  13 aevyyaktaeealelilellkeksvvseggstdlgeiglapalhsgreev 62 
                                   +e+y+a++ ee +++++++ k k   +e++st+l ++ +   +   ++++
  gi|15669671|ref|NP_248484.1| 255 IEIYNADKDEEFKKYVESIYKAK--LIEVCSTTLPQMAIPRIMGHRNYKK 302
                                   589********************..89*********99944443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2666.51
//
Query:       gi|15669672|ref|NP_248485.1|  [L=129]
Description: hypothetical protein MJ_1479.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0029   18.3  10.7       0.36   11.6  10.6    2.3  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6  10.6     2e-05      0.36       2      63 ..      49      90 ..      48     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                      CxxCxxCC  2 CkeCgaCCkelkvklteedlerlkaaevaeeeeeskkiakadgrCvfldeetklCkiYeeR.p 63
                                  C++Cg CC      l ++++e+  ++ +                C +ld+etklCk+Y++R  
  gi|15669672|ref|NP_248485.1| 49 CERCGRCCI-----LHAYKTEDGIKTIY----------------CEHLDPETKLCKVYKDRfK 90
                                  *********.....77777777777666................9999999999999998842 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 863.30
//
Query:       gi|15669673|ref|NP_248486.1|  [L=423]
Description: hypothetical protein MJ_1480 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-38  129.9   0.0    9.7e-38  128.6   0.0    1.7  1  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
     0.0038   17.0   0.0     0.0098   15.6   0.0    1.7  1  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
       0.15   11.3   0.4        7.8    5.6   0.1    3.0  4  DS              Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.6   0.0   1.6e-41   9.7e-38       2     100 .]       4     102 ..       3     102 .. 0.99

  Alignments for each domain:
  == domain 1  score: 128.6 bits;  conditional E-value: 1.6e-41
                                   EEEEEEEXXTTSSHHHHHHHHHHHTTXEEEEEEEEXXSSTTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSCCCCEEEEC CS
                Saccharop_dh_N   2 reveleGhliDsgilnkvldlileaggsfevlefevGkkkkdtSyaelevsaedeevLeeileeltelgaelveeedvkle 82 
                                   re+el+Gh+iDs+il+kv+d+il++gg+++vlefe+Gk+k+d+Sya++ v ++de++++eil+el +lgae++e e+v+l+
  gi|15669673|ref|NP_248486.1|   4 REIELRGHIIDSLILPKVFDKILDMGGDYKVLEFEIGKRKTDPSYAKILVIGRDERHVDEILNELRDLGAEIPEIEEVELQ 84 
                                   89******************************************************************************* PP

                                   ESSCTTB--TTB----SS CS
                Saccharop_dh_N  83 kaekdgvlpedFYsttnh 100
                                   +aekd+vlpe+FYsttnh
  gi|15669673|ref|NP_248486.1|  85 PAEKDMVLPEGFYSTTNH 102
                                   *****************8 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-06    0.0098      68     136 ..     334     403 ..     315     404 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-06
                                   CHHHHHHHHH-SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC....--SEEEECTHHHHHHH CS
                  TPP_enzyme_M  68 skaanealeeaDlvlalGarfddirttgsepefapeakiihididpaeigkny....qvdlaivgdvketlea 136
                                   +++ +e+l+  D vl+l + ++ i t++  p +    k i +di+pa + k        +l+iv dv+ +l  
  gi|15669673|ref|NP_248486.1| 334 QEKMRELLKGKDMVLMLSTMLHSIATGNLLPSWV---KTICVDINPAVVTKLMdrgtSQALGIVTDVGVFLPM 403
                                   56788999***************99888888887...57*******9999988444347799***99999865 PP

>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0    0.0067        40     185     228 ..     181     224 ..     171     234 .. 0.79
   2 ?    5.6   0.1    0.0013       7.8      22      80 ..     196     254 ..     187     267 .. 0.75
   3 ?    1.4   0.0     0.025   1.5e+02     149     206 ..     297     355 ..     279     363 .. 0.63
   4 ?   -2.2   0.0      0.31   1.9e+03     268     286 ..     388     406 ..     380     408 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0067
                            DS 185 ekkklkldivkDirelndialkakktgaiilGGGvpKhhilnan 228
                                    k++++  i+k++ e+++   k  k g++++GG  + h  + ++
  gi|15669673|ref|NP_248486.1| 181 PKETIIRRIAKEMYEIREKYRKTGKGGIVVVGGPAIIHTGAGWA 224
                                   44556667999**********************88877766655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0013
                            DS  22 ilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgk 80 
                                   i +k rk  k  i++    ++i +G    +a+l++ ++v+++ +  +  ++D+   l  
  gi|15669673|ref|NP_248486.1| 196 IREKYRKTGKGGIVVVGGPAIIHTGAGWALAKLIRMGYVQALFAGNALATHDIESVLYG 254
                                   44444555555666666678999999999999999999999999999999999777655 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.025
                            DS 149 eeSilywAykndipvfcpalt..DgslGdqlllfhsvk.ekkklkldivkDirelndialk 206
                                   +e+++y + kn+ip    +    Dg l d +++   vk ++k  +l   kD+  + + +l+
  gi|15669673|ref|NP_248486.1| 297 KEGVMYECIKNNIPYVLAGSIrdDGPLPD-VITDV-VKaQEKMRELLKGKDMVLMLSTMLH 355
                                   689***********655543223677766.33333.3334454555555666555555555 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 0.31
                            DS 268 aksvkvyaDaTivlPLlva 286
                                   ++   +++D+ ++lP+lv 
  gi|15669673|ref|NP_248486.1| 388 SQALGIVTDVGVFLPMLVE 406
                                   56677999*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2740.50
//
Query:       gi|15669674|ref|NP_248487.1|  [L=213]
Description: hypothetical protein MJ_1481 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-87  292.0  18.9    3.4e-87  291.9  18.9    1.0  1  DUF2100          Uncharacterized protein conserved in archaea
  ------ inclusion threshold ------
       0.19   11.6   0.4       0.47   10.4   0.1    1.9  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> DUF2100  Uncharacterized protein conserved in archaea (DUF2100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.9  18.9   3.8e-91   3.4e-87       1     217 []       2     212 ..       2     212 .. 0.99

  Alignments for each domain:
  == domain 1  score: 291.9 bits;  conditional E-value: 3.8e-91
                                   HHHHHHHHHHHHHHHHHHHHHHXXXXXXXXX---GGG--SEE--HHHHHHHHHHHHHHTHHHHHTTTT-EE-HHHHHHHHH CS
                       DUF2100   1 rleqseeLlkkavesiskiksaktqeekkknkktvkdaeegkidieelkkavyelieadeylykkaPehelkkeeAeefck 81 
                                   r+e+s++L++k++++is++k+ak+++ek+++k+++kda++gkid++e+kka+y liead++lykkaP+hel++eeA+efck
  gi|15669674|ref|NP_248487.1|   2 RVEYSKDLIRKGISTISQLKKAKIRVEKDDKKISYKDAKPGKIDVNEFKKAIYLLIEADDFLYKKAPKHELNEEEAKEFCK 82 
                                   79******************************************************************************* PP

                                   HHHHHHHHHHHHHHTTT---XX..XXXXSSSEEEESXHHHHHHHHHHXSSSXEEEXSSXSSSHHHHTT..XXXSTTTTTSH CS
                       DUF2100  82 illkakkklekvLeefgveeeedieeldkdalyivsnkkvlKaLkeinvdlniisteGvLeieDmkeiNPkipekalkgie 162
                                   +++k++++l+k+L++fg+e ee  +e+d++alyivsnkk++K+Lk++n++l++++teG+L+ieDm++i   +pekal+g++
  gi|15669674|ref|NP_248487.1|  83 LIIKCQEHLNKILANFGFEFEE--KEIDEGALYIVSNKKLFKKLKNKNPNLKVVCTEGMLDIEDMRAI--GVPEKALEGLK 159
                                   **********************..********************************************..*********** PP

                                   HHHHHHHHHHHHHHHHHXXSXEEEEXS..SHHHHHHHHHHHHHHXXEEXSTTXXX CS
                       DUF2100 163 KkveivkeeieklikklkpekvvvvveeddkadellakrAeelynakkldaeeiL 217
                                   Kkvei+++++e++i+k+kpek++vvve  d++dell+ rA++lyna+klda+eiL
  gi|15669674|ref|NP_248487.1| 160 KKVEIARKNVERFIEKYKPEKIFVVVE--DDKDELLYLRAKNLYNAEKLDADEIL 212
                                   **************************9..799*********************98 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   5.2e-05      0.47       2      27 ..      61      86 ..      60     118 .. 0.91
   2 ?   -3.6   0.0       1.2   1.1e+04       7      18 ..     200     211 ..     198     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.2e-05
                                  HHHHHHHTT.---HHHHHHHHHHHHT CS
               Glycos_trans_3N  2 diikklrdgeeLtaeeirfaihgilk 27
                                  d++ k+  ++eL++ee++++ + i+k
  gi|15669674|ref|NP_248487.1| 61 DFLYKKAPKHELNEEEAKEFCKLIIK 86
                                  7889******************9987 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.2
                                   HHTT.---HHHH CS
               Glycos_trans_3N   7 lrdgeeLtaeei 18 
                                   l + e+L+a+ei
  gi|15669674|ref|NP_248487.1| 200 LYNAEKLDADEI 211
                                   566688999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1100  (0.0613531); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1387.40
//
Query:       gi|15669675|ref|NP_248488.1|  [L=309]
Description: 2-phosphoglycerate kinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-07   31.1   1.3      1e-06   29.2   0.1    2.2  2  ATP-cone         ATP cone domain
      7e-07   29.8   0.0    1.3e-06   29.0   0.0    1.4  1  AAA_18           AAA domain
    9.2e-05   21.8   0.1     0.0073   15.6   0.1    2.3  1  Zeta_toxin       Zeta toxin
  ------ inclusion threshold ------
      0.012   15.8   0.0       0.04   14.1   0.0    1.9  2  AAA_33           AAA domain
      0.065   13.7   0.1       0.28   11.6   0.0    2.2  2  AAA_17           AAA domain
      0.077   13.2   0.1       0.16   12.2   0.1    1.5  1  AAA_28           AAA domain
       0.15   12.2   3.3       0.16   12.1   0.0    2.4  3  Cytidylate_kin2  Cytidylate kinase-like family


Domain annotation for each model (and alignments):
>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1   4.1e-10     1e-06       4      81 ..       9      85 ..       7      87 .. 0.94
   2 ?    0.0   0.2      0.51   1.3e+03      17      49 ..     249     291 ..     241     303 .. 0.57

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4.1e-10
                                  E-TTS-EEE--HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS-HHHHHHHHHHH CS
                      ATP-cone  4 iKRdGtvepfdvekIkraiekAcegseeeideiaeeveaevrkrlrdgisteeIqdlvektliehpdyavaaayilyr 81
                                  ++ + ++ pf+++ ++r++++A  + +  +++ia+ + + ++k++ + i+  +++  v  +li +++ +va++y+l+r
  gi|15669675|ref|NP_248488.1|  9 VRGKSYEMPFSKGILARSLTAAGLK-PSIAYRIAWDIYEMLKKENIRVIDKADLRRRVYYYLISKNYDEVAKKYLLWR 85
                                  55566789**************999.***************************************************9 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.51
                                   HHHHHHHHHHHH..........-HHHHHHHHHHHHHHHHHHHI CS
                      ATP-cone  17 kIkraiekAceg..........seeeideiaeeveaevrkrlr 49 
                                   kI+r+i+  + +          ++ +i+e +++  + + +rl+
  gi|15669675|ref|NP_248488.1| 249 KIIRMINDYMVEtakkkgipvvENIKISETVDKCLNIITERLK 291
                                   7888888776664444444444444455555554444444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   4.9e-10   1.3e-06       1     120 [.      95     240 ..      95     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 4.9e-10
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.........gvnlrdvakenglllevdpealdeskrldedkldklldaleenss... 69 
                                   Il+ G++GvG +t+a e+++rlg+          ++ r+v++ + + + ++   +   k+l++d  +k ++++e++s+   
  gi|15669675|ref|NP_248488.1|  95 ILIGGASGVGTSTIAFEIASRLGIpsvigtdsiREVMRKVISRDLIPTLYESS-YTAWKVLRDDEGNKYIKGFERHSEavl 174
                                   99**************************9888744444444444444444444.6667799999999*********99999 PP

                        AAA_18  70 .........aleegknlvidghlaeleseaakdikk.....vvLtasp.eelleRlekRgyeeaki 120
                                             l eg++++i+g +  +   ++k +       + Lt  + e ++ R+ +Rg+ + ++
  gi|15669675|ref|NP_248488.1| 175 tgvegvidrCLVEGQSVIIEGTHLVPTLLKDKYLENshvvfIMLTIYNeELHKMRFYARGRVSSRP 240
                                   99999999*99**********987777666665555889999999988355566888888777665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.8e-06    0.0073      14     184 ..      90     275 ..      85     289 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-06
                    Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilk..................adpkkaselt 76 
                                   +rP++il+gG++G G s++a +++ +l   g   ++ +D++Re  +++ + ++                  ++ +k+ + +
  gi|15669675|ref|NP_248488.1|  90 RRPIVILIGGASGVGTSTIAFEIASRL---GIPSVIGTDSIREVMRKVIS-RDliptlyessytawkvlrdDEGNKYIKGF 166
                                   79************************9...67777888888887766433.112333333444566665543444444444 PP

                    Zeta_toxin  77 q...kdaselvekllqeaiengyniivegtlrspdvvkklaealkkaGYevevvvvavkkelSrlgvldRyeeevae.gRl 153
                                   +   +++ + ve +++  + +g+++i+egt   p  +k   +++ ++ + v +++ + ++el   + ++R + ++    R+
  gi|15669675|ref|NP_248488.1| 167 ErhsEAVLTGVEGVIDRCLVEGQSVIIEGTHLVPTLLK---DKYLENSHVVFIMLTIYNEELHKMRFYARGRVSSRPtERY 244
                                   41114455557788888888888888888888877777...7777778888888888888888888888888884443477 PP

                    Zeta_toxin 154 vpkeehdeafeglresvealeeekqldrvki 184
                                    +  +++++ +  + ++++ +    ++++ki
  gi|15669675|ref|NP_248488.1| 245 LKYFKIIRMINDYMVETAKKKGIPVVENIKI 275
                                   7777777766666666666444445555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.7   4.3e+03      19      40 ..      47      68 ..      44      85 .. 0.72
   2 ?   14.1   0.0   1.6e-05      0.04       1     120 [.      94     235 ..      94     253 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                        AAA_33 19 llkklgavllssdtlrrrlfgt 40
                                  +lkk+   ++++ +lrrr+++ 
  gi|15669675|ref|NP_248488.1| 47 MLKKENIRVIDKADLRRRVYYY 68
                                  5777778899999999999873 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.6e-05
                        AAA_33   1 lvllvGlpGsGKstlaerllkklg.avllssdtlrrrlfg........tdqqskt.....................dytrv 51 
                                   ++l+ G++G+G st a +++ +lg   ++ +d++r+ +++        t                              r 
  gi|15669675|ref|NP_248488.1|  94 VILIGGASGVGTSTIAFEIASRLGiPSVIGTDSIREVMRKvisrdlipT-----LyessytawkvlrddegnkyikGFERH 169
                                   78999****************************8887776666544441.....133444555555565666444333445 PP

                        AAA_33  52 ldrlyqilnelarkalsagrnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaa 120
                                   ++ +   ++++++++l +g++vi+  t l +   +  +k +++ +  v i+     ee++k R  +R +
  gi|15669675|ref|NP_248488.1| 170 SEAVLTGVEGVIDRCLVEGQSVIIEGTHLVPTLLK--DKYLENSH-VVFIMLTIYNEELHKMRFYARGR 235
                                   666999999***************99988776553..23333222.44555555555555555555555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.28       2      37 ..      99     134 ..      98     246 .. 0.74
   2 ?   -2.6   0.0       2.7     7e+03      28      44 ..     256     271 ..     248     299 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                   E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT CS
                        AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrg 37 
                                   G  G+G +t++ +++ ++g++ +   d +re++++ 
  gi|15669675|ref|NP_248488.1|  99 GASGVGTSTIAFEIASRLGIPSVIGTDSIREVMRKV 134
                                   899**************************9998765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.7
                                   HHHHHHHHTTTSHSSHH CS
                        AAA_17  28 dllreeakrgglakard 44 
                                   d++ e+ak++g  +  +
  gi|15669675|ref|NP_248488.1| 256 DYMVETAKKKGI-PVVE 271
                                   555555555554.2222 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.1e-05      0.16       2      36 ..      95     136 ..      94     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.1e-05
                        AAA_28   2 ivitGgestGKTtlleaLaar.......gypvvpEaareile 36 
                                   i i G+++ G++t++ ++a+r       g+  ++E++r++++
  gi|15669675|ref|NP_248488.1|  95 ILIGGASGVGTSTIAFEIASRlgipsviGTDSIREVMRKVIS 136
                                   778899*************99955555555566666666665 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4      0.35     9e+02     139     163 ..      49      73 ..      37      83 .. 0.74
   2 ?   12.1   0.0   6.3e-05      0.16       1      40 [.      94     134 ..      94     197 .. 0.67
   3 ?   -2.8   0.0       2.4   6.1e+03     126     141 ..     288     303 ..     260     306 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.35
               Cytidylate_kin2 139 eeearekiketDkrrakyykkytgq 163
                                   ++e  + i++ D rr+ yy  ++++
  gi|15669675|ref|NP_248488.1|  49 KKENIRVIDKADLRRRVYYYLISKN 73 
                                   5666788999999999999777655 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6.3e-05
               Cytidylate_kin2   1 iITIsreyGsgGetigeaLAekLglpfy.dreiieevakel 40 
                                   +I I++  G g +ti+ ++A +Lg+p +   + i+ev+++ 
  gi|15669675|ref|NP_248488.1|  94 VILIGGASGVGTSTIAFEIASRLGIPSViGTDSIREVMRKV 134
                                   6889*********************9652445555555543 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.4
               Cytidylate_kin2 126 drvkrvaereglseee 141
                                   +r+k++ e eglsee+
  gi|15669675|ref|NP_248488.1| 288 ERLKTMIELEGLSEED 303
                                   4556666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2050.12
//
Query:       gi|15669676|ref|NP_248489.1|  [L=152]
Description: hypothetical protein MJ_1483 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       950  (0.0529868); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 955.74
//
Query:       gi|15669677|ref|NP_248490.1|  [L=150]
Description: hypothetical protein MJ_1484 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1150.74
//
Query:       gi|15669678|ref|NP_248491.1|  [L=474]
Description: TRK system potassium uptake protein TrkG [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-53  179.4  30.5    1.2e-27   96.6  11.7    2.1  2  TrkH             Cation transport protein
  ------ inclusion threshold ------
      0.091   12.8   2.7       0.32   11.0   0.5    2.7  2  Phage_holin_3_7  Putative 3TM holin, Phage_holin_3


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6  11.7   1.3e-31   1.2e-27       4     245 ..      46     264 ..      44     281 .. 0.92
   2 !   87.8  12.1   6.2e-29   5.5e-25     307     492 ..     283     463 ..     264     467 .. 0.94

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 1.3e-31
                          TrkH   4 nifkggiitialgavllfldkeskyplalkddfqivkaaeialsvdgtlklllesaslafldalfeavsgltttglsvivv 84 
                                   n+++ g +++++g vl+ ++k +k +l+l++ ++    a+++ s++g+++l+l+   + + da++e++s++tttg+++i++
  gi|15669678|ref|NP_248491.1|  46 NFLIPGLFFSIFGFVLKRATK-PK-NLKLHHTMVASALAWLIASFIGAIPLYLSIDYFSYVDAVYESMSAWTTTGMTLIPN 124
                                   677788899999999998844.44.79999999*******************99999999********************* PP

                          TrkH  85 eeslprsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkelrslselikilvvyyvgleilafvll 165
                                   +e lp+s+l++r++ q+iGg+g++vl+ l+l++ g   + ly sea    +++  ++s   +ik+++ +y++++il+++ll
  gi|15669678|ref|NP_248491.1| 125 VEVLPKSILFWRSFQQWIGGVGILVLSALVLARSGTVAYLLYTSEA----RQERIMPSAIGTIKTIIWIYILYTILGVLLL 201
                                   **********************************************....88999************************** PP

                          TrkH 166 vvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivillvaiifiilGni.gFpillrviiaik 245
                                            y +++      + w+a++ +m++++++G+s+   S+ ++n   + ++v+i ++++G++ +F+i+ +++  + 
  gi|15669678|ref|NP_248491.1| 202 ---------YLSGL------SFWDALNLTMTGISTGGMSISNYSF-PYND--FAKIVMIGIMMVGGVmSFSIHHKLLTGKY 264
                                   .........****9......**********************999.7788..89999999999998648****99887655 PP

  == domain 2  score: 87.8 bits;  conditional E-value: 6.2e-29
                          TrkH 307 vksipkgsrvlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekep 386
                                   + si+    ++++lF +vs+ t  GF+++  +nl+   ++l+++ m igg +g t+gg+++++++++ + ++yei++   p
  gi|15669678|ref|NP_248491.1| 283 IISIKDKVPIIDSLFTVVSAMTStGFTTINVGNLSSLSLFLIIFLMLIGGGAGTTTGGVKIIRFLVILKALLYEIKEIIYP 363
                                   55666677799********99999********************************************************* PP

                          TrkH 387 k.avskksidgkhlerqllvdlwslflvlliilileglklsdvqepdfsffdiLfevvSaygtvGLSlGaknaslsaqltt 466
                                   k av +  +d   l+ +++++ + +f+++ +  +l+ l     +   ++  d++f  vS   ++G SlG     ++ + + 
  gi|15669678|ref|NP_248491.1| 364 KsAVIHEHLDDMDLNYRIIREAFVVFFLYCLSSFLTALIFIALG---YNPYDSIFDAVSFTSNIGISLG----VVTLKTPV 437
                                   ************************************77777777...9*********************....99****** PP

                          TrkH 467 isklvlialmirGrlrglpvlldrai 492
                                   i+k+  i++m++Grl+++pvl+++a 
  gi|15669678|ref|NP_248491.1| 438 IGKIAGIIAMWIGRLEIIPVLVLFAT 463
                                   ************************94 PP

>> Phage_holin_3_7  Putative 3TM holin, Phage_holin_3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5   3.6e-05      0.32      21      53 ..      72     104 ..      68     121 .. 0.83
   2 ?    0.3   0.1     0.082   7.3e+02      62      79 ..     148     165 ..     133     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.6e-05
               Phage_holin_3_7  21 arhrrgiswlAyllivasgsvairillglyrev 53 
                                    +h + +s lA+l++ + g++++ + ++   +v
  gi|15669678|ref|NP_248491.1|  72 LHHTMVASALAWLIASFIGAIPLYLSIDYFSYV 104
                                   589*******************98877666655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.082
               Phage_holin_3_7  62 vvLlvlvlrarGNvarll 79 
                                   +vL +lvl++ G va ll
  gi|15669678|ref|NP_248491.1| 148 LVLSALVLARSGTVAYLL 165
                                   79999*********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2850.25
//
Query:       gi|15669679|ref|NP_248492.1|  [L=393]
Description: phosphoribosylglycinamide formyltransferase 2 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-63  211.9   0.0    7.8e-63  211.1   0.0    1.3  1  ATP-grasp        ATP-grasp domain
      4e-12   46.1   0.1    2.4e-11   43.6   0.0    2.2  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    5.4e-08   32.8   0.1    2.6e-07   30.6   0.0    2.1  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    7.6e-08   32.1   0.0    1.8e-07   30.9   0.0    1.7  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.9e-07   31.3   0.1    1.1e-06   28.8   0.0    2.3  2  ATP-grasp_3      ATP-grasp domain
      1e-05   25.2   0.0    6.9e-05   22.5   0.0    2.1  1  RimK             RimK-like ATP-grasp domain
    0.00031   20.3   0.0    0.00074   19.0   0.0    1.6  2  Epimerase        NAD dependent epimerase/dehydratase family
     0.0023   17.5   0.1      0.006   16.2   0.1    1.7  1  ATP-grasp_4      ATP-grasp domain
     0.0063   15.9   0.3      0.015   14.7   0.1    1.8  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0075   15.9   0.0      0.018   14.7   0.0    1.6  1  PurK_C           Phosphoribosylaminoimidazole carboxylase C-t
  ------ inclusion threshold ------
      0.043   13.1   0.1       0.33   10.1   0.0    2.3  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
      0.055   14.0   1.8       0.14   12.7   0.1    2.6  3  ATPgrasp_N       ATP-grasp N-terminal domain
      0.061   13.4   0.1        1.9    8.5   0.0    2.4  2  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
       0.51   10.5   2.6       0.36   11.0   0.2    2.1  2  LAL_C2           L-amino acid ligase C-terminal domain 2


Domain annotation for each model (and alignments):
>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.1   0.0   6.1e-66   7.8e-63       2     170 ..     126     297 ..     125     298 .. 0.97

  Alignments for each domain:
  == domain 1  score: 211.1 bits;  conditional E-value: 6.1e-66
                                   HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC......GTTCEEEEE----SE CS
                     ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal......keekvivEefvpfek 76 
                                   eklgl+++++ +++s eel++a+e+lglp+vvK ++++++GkGqsvvrseed+e+a++ +       +++vivEef++f++
  gi|15669679|ref|NP_248492.1| 126 EKLGLKTAKYEFADSLEELRDAVEKLGLPCVVK-PIMSSSGKGQSVVRSEEDIEKAWKIAkegargIGNRVIVEEFINFDY 205
                                   799******************************.**************************999998899************ PP

                                   EEEEEEEEETTC-EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCT.EEEEEE CS
                     ATP-grasp  77 ElsvlvvrsaeGetafypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledge.llvnEl 156
                                   E+++l++r+aeG t+f++++++vq dg++++s++p+++s++ +++a++iakk++++Lgg+G+f+vElFv+  g+ ++++E+
  gi|15669679|ref|NP_248492.1| 206 EITLLTARTAEG-TKFCEPIGHVQIDGDYHESWQPHNMSAELKEQAQDIAKKVTDALGGYGIFGVELFVK--GDeVIFSEV 283
                                   ************.*********************************************************..555****** PP

                                   ESS--GGGGGHHHH CS
                     ATP-grasp 157 apRpHnsGhvtlda 170
                                   +pRpH++G+vt+ +
  gi|15669679|ref|NP_248492.1| 284 SPRPHDTGMVTMIT 297
                                   ************87 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   1.9e-14   2.4e-11      16     179 ..     139     290 ..     125     311 .. 0.75
   2 ?   -0.4   0.0      0.53   6.8e+02      21      70 ..     297     346 ..     289     352 .. 0.67

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.9e-14
                                   ETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHT....T-SCEEEEE--ESEEEEEEEEE CS
               Dala_Dala_lig_C  16 ekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafk....ydekvlvEeaiegreievavlg 92 
                                   ++        e l++ +e+lg+p++VKp  + S  G s v+see++++a + a +      ++v+vEe+i+  + e+++l 
  gi|15669679|ref|NP_248492.1| 139 DSL-------EELRDAVEKLGLPCVVKPIMSSSGKGQSVVRSEEDIEKAWKIAKEgargIGNRVIVEEFINF-DYEITLLT 211
                                   322.......4456779******************************998665442222789********86.67888998 PP

                                   TSSCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEE CS
               Dala_Dala_lig_C  93 neklevsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvN 173
                                       +++e  +     g  +++  y     +   p ++++e +e+ q++a+k+ +al++ G+  v +f++  +e++++Ev 
  gi|15669679|ref|NP_248492.1| 212 ---ARTAEGTKFCEPIGHVQIDGDYH----ESWQPHNMSAELKEQAQDIAKKVTDALGGYGIFGVELFVK-GDEVIFSEVS 284
                                   ...44444444444555556666664....4456889999999**************************9.788999***9 PP

                                   SS---S CS
               Dala_Dala_lig_C 174 tlPGfT 179
                                   + P  T
  gi|15669679|ref|NP_248492.1| 285 PRPHDT 290
                                   999554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.53
                                   CH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHT CS
               Dala_Dala_lig_C  21 keekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafk 70 
                                   ++e++e+  +v + lg+pv  K  + G S  +++  ++   k  ie+a+k
  gi|15669679|ref|NP_248492.1| 297 TQEMSEFEIHVRAILGLPVSTKLIHPGASHVIKAEINKYAPKYHIEDALK 346
                                   45555667778888888888888888887766665555555555555555 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.1   1.4e+03      77      94 ..      24      41 ..      19      58 .. 0.81
   2 !   30.6   0.0   2.1e-10   2.6e-07      11      99 ..     126     212 ..     116     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                                  CCCCSSEEEEE---SEEE CS
                        GARS_A 77 GeagekvviEelleGeEv 94
                                  Ge g++vviE +  G+E 
  gi|15669679|ref|NP_248492.1| 24 GELGKEVVIEAQRLGIEC 41
                                  88899*****99888885 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 2.1e-10
                                   HHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE---. CS
                        GARS_A  11 kkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEelle. 90 
                                   +k g++ta+ye  ++ ee+++ +e+++ +  VvK+   ++gKg +v++see+ ++ + +i ++ + G  g++v++Ee+++ 
  gi|15669679|ref|NP_248492.1| 126 EKLGLKTAKYEFADSLEELRDAVEKLGLPC-VVKPIMSSSGKGQSVVRSEED-IEKAWKIAKEGARG-IGNRVIVEEFINf 203
                                   6889**************************.****************98655.66677899999999.99********983 PP

                                   SEEEEEEEE CS
                        GARS_A  91 GeEvsllal 99 
                                     E++ll+ 
  gi|15669679|ref|NP_248492.1| 204 DYEITLLTA 212
                                   468877664 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   1.4e-10   1.8e-07       8      91 ..     124     203 ..     117     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.4e-10
                                   HHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE- CS
                   CPSase_L_D2   8 alkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlveks 88 
                                   a++k++ ++++ + a  ++lee  ++++++g P+++k+ ++  GkG  v+r+ee+++++ k a + a+   g ++v ve++
  gi|15669679|ref|NP_248492.1| 124 AAEKLGLKTAKYEFA--DSLEELRDAVEKLGLPCVVKPIMSSSGKGQSVVRSEEDIEKAWKIAKEGAR-GIG-NRVIVEEF 200
                                   567888888888888..9**********************************************9996.666.57999**9 PP

                                   -SS CS
                   CPSase_L_D2  89 lkg 91 
                                   ++ 
  gi|15669679|ref|NP_248492.1| 201 INF 203
                                   975 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.7   2.1e+03      69      98 ..      94     122 ..      72     151 .. 0.73
   2 !   28.8   0.0   8.2e-10   1.1e-06      29     159 ..     150     288 ..     119     290 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.7
                                   ---SEEEEEEEEE.SSSEEEEEEEEEEEET CS
                   ATP-grasp_3  69 fieGkplSvsllsdgekvlvlavnrqliek 98 
                                    i+ +++  +++ +  ++  +++nr+li +
  gi|15669679|ref|NP_248492.1|  94 LIDAEKMGYTVIPT-AEATKITMNRELIRR 122
                                   67777777777774.478889999999965 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 8.2e-10
                                   --SSSEEEEESS-------B--SS--TTE.................EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET. CS
                   ATP-grasp_3  29 eeekklvvKprdGaggesvrvveekeeaeaaieeve..........lvqefieGkplSvsllsdgekvlvlavnrqlieka 99 
                                   +   ++vvKp+ ++ g++ +vv+ +e+ e+a +  +          +v efi+  ++ ++ll  + ++    +++ + +  
  gi|15669679|ref|NP_248492.1| 150 KLGLPCVVKPIMSSSGKGQSVVRSEEDIEKAWKIAKegargignrvIVEEFINF-DYEITLLT-ARTAEGTKFCEPIGHV- 227
                                   346789*******************999988877778999*****9******96.46666666.4455555666554433. PP

                                   ...TEEEEEEES..----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS-- CS
                   ATP-grasp_3 100 ekefvyaGnvtp..ietelkeevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPRlt 159
                                   + +  y  +  p  +  elke+++++a++v+ +l g  G++Gv+l +k +e ++ Ev PR+ 
  gi|15669679|ref|NP_248492.1| 228 QIDGDYHESWQPhnMSAELKEQAQDIAKKVTDAL-GGYGIFGVELFVKGDEVIFSEVSPRPH 288
                                   3345566655551155677***************.*************************85 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.4e-08   6.9e-05      14     172 ..     128     292 ..     116     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.4e-08
                                   TT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.......GGG--EEEEE--SS-S CS
                          RimK  14 akikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.......lkeailvqeyieeaen 87 
                                    ++k+ + ++a + e++++ +ek+  + P vvK +++s G +  + + e+++++  +        + ++++v e+i++  +
  gi|15669679|ref|NP_248492.1| 128 LGLKTAKYEFADSLEELRDAVEKL--GLPCVVKPIMSSSGKGQSVVRSEEDIEKAWKIakegargIGNRVIVEEFINFDYE 206
                                   3578899999999*********99..69**********99887777777666655443334677788999********987 PP

                                   EEEEEE..EETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT.-SEEEEEEEEETTEEEEEEEES CS
                          RimK  88 ediRvl..vvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakame.lvvaGvDllrakrgllvlEvns 165
                                     +       + +    +  v  +Gd+    +  ++   ++l+e+ +++A k+++a++   + Gv+l+ + +++++ Ev  
  gi|15669679|ref|NP_248492.1| 207 ITLLTArtAEGTKFCEPIGHVQIDGDYHESWQPHNM--SAELKEQAQDIAKKVTDALGgYGIFGVELFVKGDEVIFSEVSP 285
                                   44433211346678888999999****999988776..57899************99625799****************98 PP

                                   S--SHHH CS
                          RimK 166 spgleki 172
                                    p  +++
  gi|15669679|ref|NP_248492.1| 286 RPHDTGM 292
                                   8876665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   5.8e-07   0.00074       6      70 ..      22      84 ..      19     103 .. 0.91
   2 ?   -3.0   0.0       3.2   4.1e+03       5      35 ..     187     217 ..     187     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.8e-07
                                  TTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                     Epimerase  6 atGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavih 70
                                  ++G +G+ +v + ++ g+e+i++dr+++a + +  +  + + +d++d +al +++++e+pd+++ 
  gi|15669679|ref|NP_248492.1| 22 GSGELGKEVVIEAQRLGIECIAVDRYQNAPAMQVAH--KSYVIDMKDYDALMAIIEREEPDYIVP 84
                                  57999*********************9999888777..899**********************86 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.2
                                   TTTSHHHHHHHHHHHHCTSEEEEEES-STTT CS
                     Epimerase   5 GatGfiGsalvkallekgyevigldrlssas 35 
                                   Ga+G   + +v+++ + +ye++ l+ ++ ++
  gi|15669679|ref|NP_248492.1| 187 GARGIGNRVIVEEFINFDYEITLLTARTAEG 217
                                   6677777789999999999999999986655 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   4.7e-06     0.006       2     151 ..     152     286 ..     151     294 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.7e-06
                   ATP-grasp_4   2 slPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGe.EfavdayfdeeGepvil 81 
                                    lP+v+KP++ ++  G +++++ee+ ++a +  +e         + + + +++++vEe+i+ + E+ +    + eG++   
  gi|15669679|ref|NP_248492.1| 152 GLPCVVKPIMSSSGKGQSVVRSEEDIEKAWKIAKEG--------A-RGI-GNRVIVEEFINFDyEITLLTARTAEGTKFCE 222
                                   58***********************99987644433........3.234.78899*****954477777777899999988 PP

                   ATP-grasp_4  82 nilkkefaseedvsdrlyvtsakvieetlealeellkevnallglknfpvHiElrvsedgkiipiEvnpl 151
                                    i + +   + + s + + +sa++ e+ ++  ++++++++      ++ + +El v+ d  i+  Ev p+
  gi|15669679|ref|NP_248492.1| 223 PIGHVQIDGDYHESWQPHNMSAELKEQAQDIAKKVTDALG-----GYGIFGVELFVKGDEVIF-SEVSPR 286
                                   8864444444445556688888886666555555555444.....577888999999886555.488886 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.2e-05     0.015      40      84 ..      19      66 ..      14     130 .. 0.83
   2 ?   -3.5   0.0       4.5   5.7e+03      51      73 ..     359     381 ..     356     390 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                  EEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH...CHHHHTCEECS CS
                  2-Hacid_dh_C 40 GiiGlGrIGqavakrlkafgmkviaydrskkkee...eeeelgvelvs 84
                                   ++G G++G++v   ++ +g++ ia+dr++++ +   + +++ +++ +
  gi|15669679|ref|NP_248492.1| 19 LLLGSGELGKEVVIEAQRLGIECIAVDRYQNAPAmqvAHKSYVIDMKD 66
                                  689**************************9977743333333334444 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.5
                                   HHHHHHHTT-EEEEESSSHHHHH CS
                  2-Hacid_dh_C  51 vakrlkafgmkviaydrskkkee 73 
                                    ak+ + +g+ + + d  +k++e
  gi|15669679|ref|NP_248492.1| 359 NAKVGRRMGVALAYADSVEKARE 381
                                   57788889999999998887665 PP

>> PurK_C  Phosphoribosylaminoimidazole carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.4e-05     0.018      14      54 ..     340     380 ..     327     382 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                        PurK_C  14 kleellaipgahlHlYgKeearpgRKmGHitvvgdsaeele 54 
                                   ++e++l++p+++l l gK +a+ gR mG   + +ds e+++
  gi|15669679|ref|NP_248492.1| 340 HIEDALKVPNTKLRLFGKPNAKVGRRMGVALAYADSVEKAR 380
                                   56789***********************7777777777766 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00026      0.33      44     134 ..     136     208 ..     109     216 .. 0.66
   2 ?   -0.7   0.0      0.51   6.5e+02      56      78 ..     246     268 ..     224     312 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00026
                   ATPgrasp_ST  44 keqaeiseleafvkeleegvviKpakgsgGkGilviteredqdylkssgksalldelerhvsnilagLyslggkpdvalve 124
                                   +  ++++el++ v++l    v+Kp+ +s+GkG +v+ ++ed ++ + + ++  ++ +                  ++++ve
  gi|15669679|ref|NP_248492.1| 136 EFADSLEELRDAVEKLGLPCVVKPIMSSSGKGQSVVRSEEDIEK-AWKIAKEGARGIG-----------------NRVIVE 198
                                   3448899999999999555*****************66444332.2222233333333.................556666 PP

                   ATPgrasp_ST 125 elikqdpele 134
                                   e+i++d e++
  gi|15669679|ref|NP_248492.1| 199 EFINFDYEIT 208
                                   6666665555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.51
                   ATPgrasp_ST  56 vkeleegvviKpakgsgGkGilv 78 
                                   +ke  +++++K ++  gG Gi  
  gi|15669679|ref|NP_248492.1| 246 LKEQAQDIAKKVTDALGGYGIFG 268
                                   33333557888888888888754 PP

>> ATPgrasp_N  ATP-grasp N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00011      0.14       3      51 ..      33      77 ..      31      94 .. 0.83
   2 ?   -2.6   0.1       6.4   8.2e+03      74      81 ..     124     131 ..     123     132 .. 0.67
   3 ?   -2.6   0.0       6.8   8.7e+03      74      81 ..     147     154 ..     144     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                  HHHHTT-EEEEEEETTS----S-TT.EEEEEEE-TTT-HHHHHHHHHHH CS
                    ATPgrasp_N  3 aAkaLGikvvlvdeedewapeelaelvekfipldlaqdpdaaleavral 51
                                  +A++LGi+ + vd+ + +ap++  +  +k  ++d++ d da+++++++ 
  gi|15669679|ref|NP_248492.1| 33 EAQRLGIECIAVDRYQ-NAPAMQVA--HKSYVIDMK-DYDALMAIIERE 77
                                  69***********999.67755544..79999****.899999999875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.4
                                   HHHHTT-S CS
                    ATPgrasp_N  74 laeaLgLP 81 
                                   +ae+LgL 
  gi|15669679|ref|NP_248492.1| 124 AAEKLGLK 131
                                   67777774 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.8
                                   HHHHTT-S CS
                    ATPgrasp_N  74 laeaLgLP 81 
                                   + e+LgLP
  gi|15669679|ref|NP_248492.1| 147 AVEKLGLP 154
                                   679****9 PP

>> Glyco_transf_28  Glycosyltransferase family 28 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0015       1.9      16     121 ..       5     112 ..       2     125 .. 0.82
   2 ?    2.2   0.0      0.13   1.7e+02      19      85 ..     197     255 ..     195     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0015
                                   HHHHHHHHCTT-EEEEEEETCCCHHHHHHCCT-EEEE---GHCTT...CHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCC CS
               Glyco_transf_28  16 lAlakeLkkegheVrylgtkrgleerlveeaglefepiageklrrkl.spknlkeilkvlkavvkakkilkeakpdavvgt 95 
                                   +A+   L k  ++   lg+ +  +e ++e + l +e ia++++++    +   k+    +k + +  +i+++++pd++v  
  gi|15669679|ref|NP_248492.1|   5 MAIGTPLLKGSIKFLLLGSGELGKEVVIEAQRLGIECIAVDRYQNAPaMQVAHKSYVIDMKDYDALMAIIEREEPDYIVPE 85 
                                   56666666666555577888888888899999*********9999886666778888899********************* PP

                                   CCCCCHCCCCCHCCCTTHCC.CCCHCT CS
               Glyco_transf_28  96 ggyvslpaviaaplaripvi.ihEqna 121
                                      ++++a+i+a +++  vi ++E+ +
  gi|15669679|ref|NP_248492.1|  86 IEAINTDALIDAEKMGYTVIpTAEATK 112
                                   *************99987764566655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                                   HHHHHCTT-EEEEEEETCCCHHHHHHCCT-EEEE---GHCTT..CHHHHCCHHHHHHHHHHHHHHHH CS
               Glyco_transf_28  19 akeLkkegheVrylgtkrgleerlveeaglefepiageklrrklspknlkeilkvlkavvkakkilk 85 
                                   ++e++  ++e++ l t r +e +    +++ +++i+g+ +++  +p+n+++ lk+     +a+ i k
  gi|15669679|ref|NP_248492.1| 197 VEEFINFDYEIT-LLTARTAEGTK-FCEPIGHVQIDGDYHES-WQPHNMSAELKE-----QAQDIAK 255
                                   68999999***9.99999988875.7899*********7777.999999888877.....4444444 PP

>> LAL_C2  L-amino acid ligase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       7.5   9.6e+03      59      70 ..     247     258 ..     243     261 .. 0.59
   2 ?   11.0   0.2   0.00028      0.36      46      76 ..     363     393 .]     357     393 .] 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.5
                        LAL_C2  59 aeeaeaaaeeaa 70 
                                   +e+a+++a+++ 
  gi|15669679|ref|NP_248492.1| 247 KEQAQDIAKKVT 258
                                   566777776665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00028
                        LAL_C2  46 gdrlGyviatgdtaeeaeaaaeeaaaeirie 76 
                                   g r G  +a +d+ e+a++ ae+ a ++rie
  gi|15669679|ref|NP_248492.1| 363 GRRMGVALAYADSVEKARELAEKCAHAVRIE 393
                                   579**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2378.59
//
Query:       gi|15669680|ref|NP_248493.1|  [L=426]
Description: hypothetical protein MJ_1487 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-28   98.3   0.4    1.4e-27   97.2   0.4    1.6  1  Radical_SAM   Radical SAM superfamily
      2e-16   60.1   0.0    5.2e-16   58.8   0.0    1.8  1  B12-binding   B12 binding domain
     0.0068   17.0   0.0      0.025   15.1   0.0    2.0  1  POTRA         Surface antigen variable number repeat
  ------ inclusion threshold ------
      0.018   14.5   0.0        0.1   12.1   0.0    2.1  3  AP_endonuc_2  Xylose isomerase-like TIM barrel
       0.15   11.6   0.0       0.35   10.4   0.0    1.6  1  POTRA_3       POTRA domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.4   3.8e-31   1.4e-27       1     165 [.     177     353 ..     177     355 .. 0.92

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 3.8e-31
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS..........TTHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly..........pdfvellerla 71 
                                   +++trgC+++C fC++p+    +++ r+++ve+i + v+++ ae++ k + +   + + y          +++++lle ++
  gi|15669680|ref|NP_248493.1| 177 IEITRGCPYKCYFCQTPRI--FGKKIRHRDVENIYKYVEIM-AERNLKDIRFITPNAFGYgskdgktlniDKIEKLLESIR 254
                                   689***************7..********************.677799999998888888777777777677777777777 PP

                                   HTCCCTEEEEEEECSSCHG.....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEE CS
                                   xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  72 klavpgiritvetngtlpd.....eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvv 146
                                   ++  ++ ri++ t +  ++      e ++++l++     + +g+++++++ vl+l++rght+e+v++a++ +r+ag+ + v
  gi|15669680|ref|NP_248493.1| 255 EILGNNGRIFFGTFPSEVRpehvnIETVDLILRYAdNKNLVIGAQSGSEK-VLELCHRGHTVEDVYNAVRVARKAGLGVDV 334
                                   777999999999999999999*****************************.***************************99* PP

                                   EEEEEBTTTSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 147 drivglpGendeeleelle 165
                                   d+i+glpGe++e++e++++
  gi|15669680|ref|NP_248493.1| 335 DFIFGLPGETEEDVEKTIK 353
                                   ****************987 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   1.4e-19   5.2e-16       4     120 ..       6     126 ..       3     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.4e-19
                   B12-binding   4 llatvggdlhplGlavlaaalrdagfeVqllganven.edivaairae.kpdv..vglSalltsqleavkelvel....lk 76 
                                    l++++++lh+  +++l +al+ +    ++l + + n +di +  + + k+d   +++S+ +t++l+++ el+++     +
  gi|15669680|ref|NP_248493.1|   6 ALVVYYTKLHKNSFNALIGALEIDE-YFDNLPIYFANkKDIFNLKEVLkKYDKvvIAISF-FTTELWKTYELINElkakYQ 84 
                                   678899999**************54.4557776666667777766666666664488899.**************999999 PP

                   B12-binding  77 rirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                   ++r++++ ++GG+hp+ dp+ tl+  lg+d+v++gege++++++
  gi|15669680|ref|NP_248493.1|  85 SYRNKIIYLAGGPHPTGDPKGTLK--LGFDVVCIGEGEETFPEF 126
                                   ***********************8..9**************998 PP

>> POTRA  Surface antigen variable number repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     7e-06     0.025      25      61 ..     235     274 ..     201     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7e-06
                                   SSTTSBHCHHHHHHHHHHHHHHHHCTT-EE.EE...EEEE CS
                         POTRA  25 lkegdvynpekleadkealksryanlGyfdasV...qvel 61 
                                    k g+++n +k+e+ +e +++ ++n+G +++     +v++
  gi|15669680|ref|NP_248493.1| 235 SKDGKTLNIDKIEKLLESIREILGNNGRIFFGTfpsEVRP 274
                                   499*************************665554654444 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.96   3.5e+03      30      55 ..      45      70 ..      32      90 .. 0.75
   2 ?   -1.6   0.0      0.43   1.5e+03      68     116 ..     204     256 ..     190     265 .. 0.57
   3 ?   12.1   0.0   2.8e-05       0.1      26     122 ..     278     364 ..     263     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.96
                                  HHHHHHHHHHTTSEEEEEEECCCHST CS
                  AP_endonuc_2 30 lrelrkaldelglriaslslftrfgy 55
                                  +  l++ l++++  + ++s+ft   +
  gi|15669680|ref|NP_248493.1| 45 IFNLKEVLKKYDKVVIAISFFTTELW 70
                                  55678888888888888888876655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.43
                                   HHHHHHHHHHHHHHHTBSEEEEEBCC.GBCTTTSGHH...HHHHHHHHHHHHH CS
                  AP_endonuc_2  68 svdalkraielaaaLGapllvlhpGt.agagpkgsee...eawerlaeslnel 116
                                    v+++ + +e++a+ + + + + + + +g+g+k+++    + +e+l es++e+
  gi|15669680|ref|NP_248493.1| 204 DVENIYKYVEIMAERNLKDIRFITPNaFGYGSKDGKTlniDKIEKLLESIREI 256
                                   36666666666666665555555333433444444444455556666666655 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 2.8e-05
                                   HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC.HTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHH CS
                  AP_endonuc_2  26 sdeelrelrkaldelglriaslslftrfgypded.erearreesvdalkraielaaaLGapllvlhpGtagagpkgseeea 105
                                     e+++ + + +d  +l    + ++++++ ++e  +r +     v+++ +a++ a++ G  + v ++     g +g+ ee+
  gi|15669680|ref|NP_248493.1| 278 NIETVDLILRYADNKNLV---IGAQSGSEKVLELcHRGHT----VEDVYNAVRVARKAGLGVDVDFIF----GLPGETEED 347
                                   55789999**********...7777777777775556666....*************99998666644....7999***** PP

                                   HHHHHHHHHHHHHHHHH CS
                  AP_endonuc_2 106 werlaeslneladyaek 122
                                   +e+ ++++++l+++++k
  gi|15669680|ref|NP_248493.1| 348 VEKTIKVMKDLIKMGAK 364
                                   *************9775 PP

>> POTRA_3  POTRA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   9.7e-05      0.35      23      50 ..     234     261 ..     218     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.7e-05
                                   TT-TT-B--HHHHHHHHHHHTSSSEE.E CS
                       POTRA_3  23 PaskGdvLnLrdiEQGleqlnRlpsnqa 50 
                                   +++ G+ Ln+ +iE  le ++   +n+ 
  gi|15669680|ref|NP_248493.1| 234 GSKDGKTLNIDKIEKLLESIREILGNNG 261
                                   4569****************98777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      715  (0.0398795); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2670.83
//
Query:       gi|15669681|ref|NP_248494.1|  [L=393]
Description: hypothetical protein MJ_1488 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-10   40.0   0.3    2.3e-09   37.3   0.4    2.2  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0013   18.1   0.0     0.0038   16.6   0.0    1.8  1  Amino_oxidase   Flavin containing amine oxidoreductase
  ------ inclusion threshold ------
      0.067   12.4   0.2       0.16   11.1   0.3    1.6  2  FAD_binding_3   FAD binding domain
       0.11   12.5   0.0        4.6    7.2   0.0    2.9  3  Glyco_transf_4  Glycosyltransferase Family 4
       0.13   11.3   0.2       0.24   10.4   0.2    1.3  1  FAD_binding_2   FAD binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.4   6.5e-13   2.3e-09       1      58 [.       5      61 ..       5      71 .. 0.87
   2 ?    0.5   0.0       0.2   7.1e+02      10      27 ..      63      80 ..      62      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 6.5e-13
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHH CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyy 58
                                  IvGaGl+Gl+a +lL+k+ ++v+++ek + lGGr +  +++g+ + +ga  + + g++
  gi|15669681|ref|NP_248494.1|  5 IVGAGLGGLLAGALLSKN-HEVVVFEKLPFLGGRFTNLKYEGFQLTTGALHMIPHGND 61
                                  9****************6.**************************9998777665555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.2
                                  HHHHHHHCCTEEEEEE-S CS
                 NAD_binding_8 10 vaAylLakagfdvlllek 27
                                  ++A++L+kag++v ++ +
  gi|15669681|ref|NP_248494.1| 63 YLAQALRKAGANVKIINS 80
                                  5799*********99865 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-06    0.0038       7      93 ..      15     102 ..      10     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-06
                                   HHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET..TTHHHHHHHHHTTCCCCEEEESCCGCEEEEETTEEC CS
                 Amino_oxidase   7 ArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg..agnpllellkelgledslslpdpgapkrvlskggre 85 
                                   A  Lls++++V+v+E  + +GGR    + +G+ + +Ga  + +  ++  l + l++ g + + + ++p+   ++l  +g+e
  gi|15669681|ref|NP_248494.1|  15 AGALLSKNHEVVVFEKLPFLGGRFTNLKYEGFQLTTGALHMIPhgNDGYLAQALRKAGANVKIINSKPD--GTFLI-NGKE 92 
                                   55689999******************************9998888999999999999999888754444..33433.3444 PP

                                   C..TTEECHH CS
                 Amino_oxidase  86 f..pgdlspv 93 
                                   +  ++++s +
  gi|15669681|ref|NP_248494.1|  93 YlyKELFSLL 102
                                   4344444444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   4.6e-05      0.16       4      32 ..       3      30 ..       1      33 [. 0.88
   2 ?   -3.8   0.0       1.6   5.9e+03      16      32 ..      64      80 ..      63      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.6e-05
                                  EEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                 FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvek 32
                                  + IVGaG+ Gl+++ lLs+   +vv+ ek
  gi|15669681|ref|NP_248494.1|  3 IGIVGAGLGGLLAGALLSKN-HEVVVFEK 30
                                  56****************99.88888887 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.6
                                  HHHHHHHTTHHEEEEES CS
                 FAD_binding_3 16 lallLseaGvrvvlvek 32
                                  la+ L++aG +v +++ 
  gi|15669681|ref|NP_248494.1| 64 LAQALRKAGANVKIINS 80
                                  7999******9999986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.15   5.3e+02      11      25 ..      14      28 ..      13      53 .. 0.85
   2 ?    7.2   0.0    0.0013       4.6      10      63 ..      63     118 ..      62     150 .. 0.74
   3 ?    0.0   0.0       0.2   7.3e+02      63      90 ..     320     347 ..     286     354 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.15
                Glyco_transf_4 11 LaraLarrGheVtvv 25
                                  La aL  ++heV+v+
  gi|15669681|ref|NP_248494.1| 14 LAGALLSKNHEVVVF 28
                                  8999**********9 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0013
                Glyco_transf_4  10 eLaraLarrGheVtvvtpgddgpleeev..elvvrvprvplpllkrllrslaflrr 63 
                                   +La+aL+++G +V ++ +++dg +  +   +l++++ +   ++ k   + la  ++
  gi|15669681|ref|NP_248494.1|  63 YLAQALRKAGANVKIINSKPDGTFLINGkeYLYKELFSLLGFKEKAKAFKLATKLK 118
                                   69*******************99999954444444444444444444444444444 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.2
                Glyco_transf_4  63 rlrrllkrekpDvvHahspaalgaalla 90 
                                   ++ +l+k  ++ ++H++s+   + + +a
  gi|15669681|ref|NP_248494.1| 320 DIENLFKGKDYKILHIQSYRDDWPVNHA 347
                                   4566777889********9999877555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   6.7e-05      0.24       4      36 ..       5      36 ..       3      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.7e-05
                                  EE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                 FAD_binding_2  4 ViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                  ++G+Gl+GL A++ +  ++++v+v ek +  gg
  gi|15669681|ref|NP_248494.1|  5 IVGAGLGGLLAGA-LLSKNHEVVVFEKLPFLGG 36
                                  8***********9.6788888******998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2502.70
//
Query:       gi|15669682|ref|NP_248495.1|  [L=682]
Description: cell division control protein 47 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-78  262.1   0.1    4.4e-78  261.4   0.1    1.3  1  MCM              MCM P-loop domain
      6e-24   84.3   5.7    6.9e-24   84.1   3.6    2.2  2  MCM_lid          MCM AAA-lid domain
    1.9e-15   56.8   0.4    4.2e-15   55.7   0.1    1.8  2  MCM_OB           MCM OB domain
    5.8e-09   35.6   0.1    2.3e-06   27.1   0.0    2.8  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    5.7e-06   26.4   0.0    3.5e-05   23.8   0.0    2.4  3  AAA_5            AAA domain (dynein-related subfamily)
    0.00069   19.5   0.0     0.0018   18.1   0.0    1.7  1  AAA_3            ATPase family associated with various cellul
     0.0021   17.8   0.0      0.088   12.5   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.017   15.1   0.1      0.064   13.2   0.1    2.0  1  Imm51            Immunity protein 51
      0.069   13.7   0.1      0.069   13.7   0.1    2.9  2  MCM_N            MCM N-terminal domain
      0.071   12.8   0.7       0.17   11.6   0.7    1.6  1  Cas_NE0113       CRISPR-associated protein NE0113 (Cas_NE0113
      0.096   12.4   1.2       0.22   11.2   0.1    2.2  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.78    9.3   5.8          2    8.0   5.8    1.7  1  AIPR             AIPR protein
       0.88    9.5   7.0        1.1    9.3   0.7    3.2  3  Peroxin-22       Peroxisomal biogenesis protein family
        5.1    7.8   9.4         53    4.6   5.8    3.1  2  FYDLN_acid       Protein of unknown function (FYDLN_acid)


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.4   0.1   3.4e-81   4.4e-78       1     224 []     271     490 ..     271     490 .. 0.96

  Alignments for each domain:
  == domain 1  score: 261.4 bits;  conditional E-value: 3.4e-81
                                   HHHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHS CS
                           MCM   1 eveeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyvekla 81 
                                   ++e+ik++ak+kd++++l++ ++p+i gh+++kka+llq+++gvkk  +     r+di++ll++dpg++K+ +L++++  +
  gi|15669682|ref|NP_248495.1| 271 DIENIKKIAKRKDVVNILADRLIPEIKGHSAIKKAVLLQQIKGVKK--PG---KRADIHILLITDPGIGKTVILRKIA-EI 345
                                   5799*****************************************7..33...59**********************9.78 PP

                                   SSEEEEESSSSSSSHSSSEEEEESSSSS...EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEE CS
                           MCM  82 pravytsgkgssaagLtaavvrdeetge...fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGiva 159
                                   p + y s ++++++gLtaavvr++++     +v++ G lv a+kG +ciDe+  +ke  +s+++EamE+qti+i+K+Gi+a
  gi|15669682|ref|NP_248495.1| 346 PGNLYGSVTTATGVGLTAAVVREKTEIGedtWVIKPGLLVKAHKGTACIDELTVNKE-LQSYVLEAMESQTIHISKGGINA 425
                                   ***********************98754467*********************99988.*********************** PP

                                   EEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                           MCM 160 tLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                   +L+a++++laA+np++gr++++ svae+in++a+lLsrFDlif ++D +d++kD+++ae+iv+lh
  gi|15669682|ref|NP_248495.1| 426 KLPAECAILAACNPRWGRFNPEVSVAEQINIPAPLLSRFDLIFPIRDVSDKDKDKDIAEYIVDLH 490
                                   **************************************************************987 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.9     5e+03      24      52 ..      77     101 ..      75     109 .. 0.73
   2 !   84.1   3.6   5.4e-27   6.9e-24       1      86 [.     517     593 ..     517     594 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.9
                                   HHHHHHHHHHHHHHTSSTSSSST--HHHH CS
                       MCM_lid  24 eklseaYvelRkeeedskrksipitvRqL 52 
                                   e  ++aY  lR+e  ++    + i v++L
  gi|15669682|ref|NP_248495.1|  77 ECYNDAYYTLRNEYPTN----VIIAVKNL 101
                                   667899*****988534....77777776 PP

  == domain 2  score: 84.1 bits;  conditional E-value: 5.4e-27
                                   HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHH CS
                       MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeair 81 
                                   e++ kYi yar + kP++se+ake ++++Yve+Rk++        +it+RqLe+ iR++eA+Ak +l++vv+eed++eai+
  gi|15669682|ref|NP_248495.1| 517 EFIIKYIYYAR-QKKPIISEKAKELFVNYYVEMRKKH--------QITARQLEAAIRIAEAHAKAKLKDVVDEEDAKEAIN 588
                                   5788*******.***********************55........5*********************************** PP

                                   HHHHH CS
                       MCM_lid  82 llkes 86 
                                   +++e+
  gi|15669682|ref|NP_248495.1| 589 IITEC 593
                                   **987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.1   3.3e-18   4.2e-15       3     105 ..     117     221 ..     115     239 .. 0.76
   2 ?   -3.4   0.0       6.2     8e+03      26      60 ..     399     438 ..     393     449 .. 0.58

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 3.3e-18
                                   GG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE..S---....-SB-..TTT-HHH-EEE-GGGSEEEEE CS
                        MCM_OB   3 RdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev..elee....PrkCeekeCeskdpfkletekskfvdf 77 
                                    d+rs+++gklv+ eGi++ as+++p lkka++ c+kcg++v    ++ +       C   eC+   +++l  +ks ++df
  gi|15669682|ref|NP_248495.1| 117 EDIRSKTLGKLVEFEGIIVMASKIRPMLKKAYYICPKCGREVVReiDILNtdseKAVC---ECG--AELNLIEHKSIYTDF 192
                                   689************************************9766323333333223356...566..799************ PP

                                   EEEEEE------.-------EEEEEEEGG CS
                        MCM_OB  78 qklklQEspeev.paGelPrsleviledd 105
                                   q++k+Q   + +  + e P+ ++v+le++
  gi|15669682|ref|NP_248495.1| 193 QEIKVQQPLDLMeNPEEPPKYITVFLENS 221
                                   ******99998834456677777777764 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.2
                                   -EEEEEEEEEEETTT-.-EEE.....S----SB-...TTT- CS
                        MCM_OB  26 vkpklkkavfeckkcgktvev.....eleePrkCe.ekeCe 60 
                                   v+++l++ v+e  + ++ +++     + + P +C    +C+
  gi|15669682|ref|NP_248495.1| 399 VNKELQSYVLEAMESQT-IHIskggiNAKLPAECAiLAACN 438
                                   55666666666666664.33223322444498886434555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.1    0.0082        10      24      45 ..     324     345 ..     295     358 .. 0.87
   2 !   27.1   0.0   1.8e-09   2.3e-06      92     202 ..     373     473 ..     365     478 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0082
                  Mg_chelatase  24 nlllvGppGsGKtmlakrlpsl 45 
                                   ++ll+  pG GKt++ ++++++
  gi|15669682|ref|NP_248495.1| 324 HILLITDPGIGKTVILRKIAEI 345
                                   799*************999887 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 1.8e-09
                  Mg_chelatase  92 Gggs.kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklkdkekec 171
                                   G  +  +kpG + +ah+G   +DEl+  +++    + e +e+++++is+   +++ pa++ ++aa Np   g+++    e+
  gi|15669682|ref|NP_248495.1| 373 GEDTwVIKPGLLVKAHKGTACIDELT-VNKELQSYVLEAMESQTIHISKGGINAKLPAECAILAACNPR-WGRFN---PEV 448
                                   55555789****************97.688888888899****************************94.45444...222 PP

                  Mg_chelatase 172 tcsekeierYlsklsgplldRidlqvevkkl 202
                                   +         + ++ +pll R+dl + ++ +
  gi|15669682|ref|NP_248495.1| 449 S------VAEQINIPAPLLSRFDLIFPIRDV 473
                                   2......122345777888888877777665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.2   6.7e+03      62      85 ..     107     127 ..     101     129 .. 0.77
   2 !   23.8   0.0   2.7e-08   3.5e-05       1     124 [.     324     441 ..     324     464 .. 0.88
   3 ?   -1.6   0.0         2   2.5e+03      16      59 ..     534     577 ..     530     595 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.2
                                   ---G-SEEEEESGGG--HHHHHHH CS
                         AAA_5  62 aaregeilvlDEveraesevlnsL 85 
                                     r+g+i+ ++++    s++l++L
  gi|15669682|ref|NP_248495.1| 107 TTRKGKIFTIEDIR---SKTLGKL 127
                                   56899******998...7776666 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 2.7e-08
                                   EEEEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--H CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaal..nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraes 79 
                                   ++lL+ +pG+gK+ + +++a+        ++ +   ++t++ ++ ++ei ++t + +++ lv+a  ++ ++++DE++ +++
  gi|15669682|ref|NP_248495.1| 324 HILLITDPGIGKTVILRKIAEIPgnLYGSVTTATGVGLTAAVVREKTEIGEDTWVIKPGLLVKA--HKGTACIDELT-VNK 401
                                   689999*****************86667788888899************999999*******55..567899*****.*** PP

                                   HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                         AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                   e ++ +l  +e +++++ +gg   k +++       ++a++np+ 
  gi|15669682|ref|NP_248495.1| 402 ELQSYVLEAMESQTIHISKGGINAKLPAE-----CAILAACNPRW 441
                                   ********************999999987.....99999999986 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2
                                   HHHGGGGBS--EEEEE--TT--HHHHH--B--.........--- CS
                         AAA_5  16 aerlaaalnreveyvqltrdtteedlkgrreikngttslvdspl 59 
                                   +e+ ++++ + ++++  + ++t+++l   ++i++ +++ + + +
  gi|15669682|ref|NP_248495.1| 534 SEKAKELFVNYYVEMRKKHQITARQLEAAIRIAEAHAKAKLKDV 577
                                   56667777666666777777999999999999855555444444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.4e-06    0.0018       1     112 [.     324     439 ..     324     444 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.4e-06
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfan...llladeinrappkt 78 
                                   h+ll   PG++kt++ +++a++ +  +  +  ++ +  +  +  e  e  e ++ +k+G +++        de+   +   
  gi|15669682|ref|NP_248495.1| 324 HILLITDPGIGKTVILRKIAEIPGNLYGSVTTATGVGLTAAVVREKTEIGEDTWVIKPGLLVKAhkgTACIDELT-VNKEL 403
                                   9***************************9998877755555556667888899******9886522256778886.45679 PP

                         AAA_3  79 qsalleameerqvtv..egethklpepflvlatqnP 112
                                   qs +leame +++ +  +g + klp    +la+ nP
  gi|15669682|ref|NP_248495.1| 404 QSYVLEAMESQTIHIskGGINAKLPAECAILAACNP 439
                                   *********99876611578899************9 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.076        98      12      43 ..     311     343 ..     300     357 .. 0.74
   2 !   12.5   0.0   6.9e-05     0.088      85     142 ..     380     438 ..     375     450 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.076
                                   HHHHHH.HCTSSS-EEEECSTTSSHHHHHHHHH CS
               Sigma54_activat  12 leqikk.vaktdlsvlitGesGtGKellaraih 43 
                                   ++ +kk   + d+++l+  + G GK+++ r+i 
  gi|15669682|ref|NP_248495.1| 311 IKGVKKpGKRADIHILLITDPGIGKTVILRKIA 343
                                   3333331345679**************998885 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.9e-05
                                   BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEES CS
               Sigma54_activat  85 kkGlfekadgGtlfLDeigelplelQekLlrvlqegev..ervGsskeikvdvriiaatn 142
                                   k Gl+ ka++Gt  +De++ ++ elQ+ +l++++++++  ++ G +++ ++++ i+aa n
  gi|15669682|ref|NP_248495.1| 380 KPGLLVKAHKGTACIDELT-VNKELQSYVLEAMESQTIhiSKGGINAKLPAECAILAACN 438
                                   679**************95.89***********999862267888999999999999987 PP

>> Imm51  Immunity protein 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     5e-05     0.064      55      95 ..     592     638 ..     588     647 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5e-05
                         Imm51  55 elleklefDpEagmFvay......sedkealkelaellkelledeek 95 
                                   e l+++ +DpE g+F +       ++++++l  + e++kel e +e+
  gi|15669682|ref|NP_248495.1| 592 ECLKEIAYDPETGIFDVDkilgvsKKERDKLTTVYEIIKELSEKSEL 638
                                   56899************99****99****************998876 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.4e-05     0.069      30      87 ..      36     107 ..      12     154 .. 0.72
   2 ?   -1.2   2.1       2.4   3.1e+03      29      61 ..     530     563 ..     461     631 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-05
                         MCM_N  30 emaerekttLevdlddLaafde.eLaeailenpkeylplleealkevvkklepsykdd.............a 87 
                                   e +  +++++ vdl+ L+++   e++e +++np++ +++ +e+ ++ + +l ++y  +             +
  gi|15669682|ref|NP_248495.1|  36 EDIILDNERVVVDLNQLYNYGLmEFVEFLINNPQKGIDFIKECYNDAYYTLRNEYPTNviiavknlpkifkT 107
                                   345568899***********655*************************999999988766655555555550 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.4
                         MCM_N  29 qemaerekttLevdl.ddLaafdeeLaeailenp 61 
                                   + ++ ++ ++L v++   +++  +  a++++   
  gi|15669682|ref|NP_248495.1| 530 KPIISEKAKELFVNYyVEMRKKHQITARQLEAAI 563
                                   3333333333333321233333333333333333 PP

>> Cas_NE0113  CRISPR-associated protein NE0113 (Cas_NE0113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.7   0.00013      0.17      36     100 ..     534     605 ..     502     607 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                    Cas_NE0113  36 lelLleeflkdyga........kikldesaihviedvsgeelaDirteedneallqlivrlvrelrenegerl 100
                                   +e   +e+  +y+         +++  e+ai++ e+ ++ +l+D+  eed+++++++i + ++e   ++++ +
  gi|15669682|ref|NP_248495.1| 534 SEKA-KELFVNYYVemrkkhqiTARQLEAAIRIAEAHAKAKLKDVVDEEDAKEAINIITECLKEIAYDPETGI 605
                                   3333.3333333333555554488888999********************************99988776655 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       6.6   8.5e+03      74      89 ..      25      40 ..      18      50 .. 0.76
   2 ?   11.2   0.1   0.00017      0.22       8      55 ..     295     344 ..     288     370 .. 0.79
   3 ?   -3.3   0.0         5   6.4e+03      90     116 ..     394     419 ..     383     426 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.6
                        RuvB_N 74 dlaalltnleekdvlf 89
                                   l+a l n++++d+++
  gi|15669682|ref|NP_248495.1| 25 YLTAYLRNIHQEDIIL 40
                                  3889999999999986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00017
                        RuvB_N   8 eyigqekvkeklki.fieaakkreeald.hvllyGpPGlGkttlakiiak 55 
                                   e  g +++k+ + +  i+  kk ++  d h+ll+  PG+Gkt + + ia+
  gi|15669682|ref|NP_248495.1| 295 EIKGHSAIKKAVLLqQIKGVKKPGKRADiHILLITDPGIGKTVILRKIAE 344
                                   66677788776544279999999988888*************99887775 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5
                        RuvB_N  90 ideihrlsraveevlysamedfrldiv 116
                                   ide+  ++++++ ++  ame  ++ i 
  gi|15669682|ref|NP_248495.1| 394 IDEL-TVNKELQSYVLEAMESQTIHIS 419
                                   6776.4788888899999999888774 PP

>> AIPR  AIPR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.8    0.0016         2     164     273 ..     513     651 ..     473     670 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                          AIPR 164 kitktdlakvlnalflqkPhqaskgkaklekkyekeeekgskyekifkekltykkliasvilfkklekkikkelkegyk.. 242
                                   ki+k+ ++k+++ + ++kP+ + k k+   + y ++++k ++  ++ +  + ++++ a+++l +++++   ke   +++  
  gi|15669682|ref|NP_248495.1| 513 KIDKEFIIKYIYYARQKKPIISEKAKELFVNYYVEMRKKHQITARQLEAAIRIAEAHAKAKLKDVVDEEDAKE---AINii 590
                                   79**********5555569999988888666666666555555555544444555555555555555554444...33344 PP

                          AIPR 243 ............................anivyyilaalrkllkkk..ldllkiweeqkis 273
                                                               ++ ++ +++++++l +k   ++ ++i ee+k++
  gi|15669682|ref|NP_248495.1| 591 teclkeiaydpetgifdvdkilgvskkeRDKLTTVYEIIKELSEKSelVEHEDIAEEAKKK 651
                                   4555566666666666666666666666555555555555555555555556666666665 PP

>> Peroxin-22  Peroxisomal biogenesis protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.11   1.3e+02      73     113 .]      28      66 ..      17      66 .. 0.87
   2 ?   -2.2   0.1         3   3.9e+03      60      74 ..     251     265 ..     237     308 .. 0.73
   3 ?    9.3   0.7   0.00082       1.1      67     112 ..     621     666 ..     571     667 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.11
                    Peroxin-22  73 avvkqLkpsslivdedeleseeektefvkedLkrFvkeiie 113
                                   a +++++ + +i+d++ +  +  +++  +++L +Fv+ +i+
  gi|15669682|ref|NP_248495.1|  28 AYLRNIHQEDIILDNERVVVD--LNQLYNYGLMEFVEFLIN 66 
                                   678999999999999999987..999999********9996 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3
                    Peroxin-22  60 yKiilcdssdglsav 74 
                                    K ++c+  dg++++
  gi|15669682|ref|NP_248495.1| 251 VKALHCEVLDGEVKI 265
                                   566666666666554 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00082
                    Peroxin-22  67 ssdglsavvkqLkpsslivdedeleseeektefvkedLkrFvkeii 112
                                       +++++k+L+ +s +v  +++ +e +k+ + +++L++ +k++i
  gi|15669682|ref|NP_248495.1| 621 KLTTVYEIIKELSEKSELVEHEDIAEEAKKKGIKEDELENIIKKLI 666
                                   5677899********************8888888889*****9998 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.18   2.3e+02      23      39 ..     145     161 ..     144     180 .. 0.77
   2 ?    4.6   5.8     0.042        53      19      82 ..     524     586 ..     521     672 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.18
                    FYDLN_acid  23 nkdPivcpkcgeefepe 39 
                                   +k   +cpkcg e+  e
  gi|15669682|ref|NP_248495.1| 145 KKAYYICPKCGREVVRE 161
                                   566679*****999766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.042
                    FYDLN_acid  19 FYDLnkdPivcpkcgeefepeevlksraaaaeaeeakkkkeeeedeedeeeeedvsdedadeee 82 
                                   +Y  +k+Pi++ k +e f   +v + r++ + ++++ +++ + ++++++++ +dv de++ +e+
  gi|15669682|ref|NP_248495.1| 524 YYARQKKPIISEKAKELFVNYYV-EMRKKHQITARQLEAAIRIAEAHAKAKLKDVVDEEDAKEA 586
                                   677799*************9999.4555555555554555555555555555555554444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1126  (0.0628033); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 4408.15
//
Query:       gi|15669683|ref|NP_248496.1|  [L=139]
Description: hypothetical protein MJ_1489.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.96    9.1   9.9        1.2    8.8   9.9    1.2  1  Cation_ATPase_C  Cation transporting ATPase, C-terminus


Domain annotation for each model (and alignments):
>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   9.9   6.9e-05       1.2      55     149 ..      21     110 ..      12     133 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 6.9e-05
               Cation_ATPase_C  55 liqgllqalvtllvffltlllfgisekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglf.snkllllaill 134
                                   +++ ++ + + ++  f+  ++f+++ +           +aF   v++ ifn+l+  s +  l++  +lf  +k + + + +
  gi|15669683|ref|NP_248496.1|  21 IFMVIVGLGLLFAFQFILGYGFEMHRQI-----TIKDRIAFRNYVVGKIFNVLVEHSYYGLLLSTFNLFvYKKAITIRLCF 96 
                                   3333333333333334444445555544.....679************************999999999877889999999 PP

               Cation_ATPase_C 135 slllqvlivyvpgln 149
                                   ++++ ++i ++ g +
  gi|15669683|ref|NP_248496.1|  97 IFAISIVIFWILG-G 110
                                   9999999988853.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 935.36
//
Query:       gi|15669684|ref|NP_248497.1|  [L=423]
Description: dihydroorotase PyrC [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-17   63.3   0.3    1.9e-16   60.3   0.3    2.1  1  Amidohydro_1  Amidohydrolase family
    6.4e-07   29.2   0.0      0.026   14.0   0.0    2.2  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.3   2.1e-20   1.9e-16       1     342 [.      47     414 ..      47     416 .. 0.72

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 2.1e-20
                                   EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.....HHHHHHHHHHT.SSS CS
                  Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.....giealleaaee.lpl 75 
                                   +v+PG IDaHvH++++              e+ +e + sg  + +++G+ +++dm+++ ++      +   le +++   +
  gi|15669684|ref|NP_248497.1|  47 LVIPGVIDAHVHFRWG--------------EEKKEDFLSGSLAGINGGVCFAIDMPNNKPPittkeLFYKKLEDCKKdSKI 113
                                   59***********977..............99*************************9999*9999555555555555544 PP

                                   EEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSC CS
                  Amidohydro_1  76 glrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletk 156
                                   ++ + +g       ++++ + ++e  ka+     k++   +vk        +   ++ lk++l     +++ ++iHa + +
  gi|15669684|ref|NP_248497.1| 114 NVFLNFG------VTENNYLGTVEDAKAY-----KIF---MVK---SVGDLFIEDYSKLKDIL----NQNKLFCIHAEHKD 173
                                   6666666......7778888888888888.....222...344...22233444445677777....58999999995544 PP

                                   HHHHHHHHHHTTTEEEETTTTSTCC..........HHTTTHCCEE........EHCTCEEEHH....HHHHHHHHHHHHCE CS
                  Amidohydro_1 157 gevedaeaafgetiehgthlevaes..........lglldeikli........lahgvhltpt....eaellkerlkeagv 215
                                    ++ + +++++     ++  + ++             +++ +k+i         +h +h++ +     ++ +++ lk++++
  gi|15669684|ref|NP_248497.1| 174 VIN-ENLKKYQ----LNSWIDHCKIrdekseveavKEVIKNLKIIdrqsnkkpHVHFCHISTKealyLIKKVRQELKNIKI 249
                                   444.4445554....222333333223333444443333333444777777778899999966456656666666777777 PP

                                   E......HHHHHHHH...............SEHHHHHHHHHHHHTSCEEEEEECT.........TSSCCGGHHHHHHHHHH CS
                  Amidohydro_1 216 a......hcpfsnsi...............lrsgrealrkaldeGvkvglgtDga.........asgnslnlleelrlalk 266
                                   +      h+  + +                 +++ +al k + +    ++++D+a         +  n+++ + ++   ++
  gi|15669684|ref|NP_248497.1| 250 TvevtphHIYLNKDMaeelkgfgkfnpplrEKDDNIALIKGIVNKDVDIIASDHAphlledklkNVKNCPSGIPGIETIVP 330
                                   766666644444443888899999999999666666777777777889*************99988888888888888886 PP

                                   HHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC....CT..........CGGGTTTCTSEE CS
                  Amidohydro_1 267 lqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl....di..........laafvglkkdgn 333
                                   l+  l   + +g +sl +a+r+ + n+Ak++++     +ie+G  A+l+++dl    +i           ++f g++ +g 
  gi|15669684|ref|NP_248497.1| 331 LTLNL---VNKGLISLFDAIRVLSKNPAKIFNI---NNKIEEGNLANLTIIDLkkegKInaelfkskakFSPFDGWEVKGF 405
                                   55544...5599*********************...688**************7555337788888888888889999999 PP

                                   EEEEEETTE CS
                  Amidohydro_1 334 vkkvivkGk 342
                                   ++ ++++G+
  gi|15669684|ref|NP_248497.1| 406 PIYTVINGT 414
                                   999999986 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   2.9e-06     0.026       1      21 [.      39      59 ..      39      77 .. 0.86
   2 !   13.1   0.0   5.6e-06      0.05     406     467 ..     339     411 ..     315     415 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-06
                  Amidohydro_3  1 eviDakGrlvlPGFvDsHtHl 21
                                  e+iD k+ lv+PG +D+H H 
  gi|15669684|ref|NP_248497.1| 39 EIIDIKNSLVIPGVIDAHVHF 59
                                  68******************4 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.6e-06
                  Amidohydro_3 406 eelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear..............vrltvv 467
                                     +sl +a++ ++++pAk+++   +   +e+G  A+l+++d ++  ++ ++ l++ +              + +tv+
  gi|15669684|ref|NP_248497.1| 339 GLISLFDAIRVLSKNPAKIFNINNK---IEEGNLANLTIIDlKKEGKINAE-LFKSKakfspfdgwevkgfPIYTVI 411
                                   4799********************8...*************8554455443.3333334444455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3164.27
//
Query:       gi|15669685|ref|NP_248498.1|  [L=127]
Description: hypothetical protein MJ_1491 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-06   26.0  29.7    1.2e-05   25.5  29.7    1.2  1  DUF5518      Family of unknown function (DUF5518)
  ------ inclusion threshold ------
       0.95    9.8  17.0    9.1e+02    0.1  17.0    2.1  1  DUF4199      Protein of unknown function (DUF4199)
        3.5    7.8  17.2         19    5.5   3.7    3.2  3  DUF5326      Family of unknown function (DUF5326)
        7.1    7.2  19.5        2.8    8.5   0.6    2.3  2  FtsX         FtsX-like permease family


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5  29.7   2.6e-09   1.2e-05       2     114 ..      14     120 ..      13     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.6e-09
                       DUF5518   2 raaliGavvaivlslllglllpsvgsllgllvgGlvaGylagg.....dskdgavaGalaGligaipvlvlllvlllglva 77 
                                   ++a+iG+++  +l+++           l  ++gG+va+ l+ +     d+++  ++Ga++G+ig++++ +l++++++++++
  gi|15669685|ref|NP_248498.1|  14 KPAVIGGIINGILGAICC---------LCYVIGGAVAAHLYVNaggicDYENCGLVGAISGVIGGVIASILSFLFMSAYLS 85 
                                   79****************.........999********9986433344799*****************9999999985555 PP

                       DUF5518  78 aigglagfvallvalllvvllllvvllvilgaiGGai 114
                                   a+g  a +++++ +++ +  + ++++++ilga+GG+i
  gi|15669685|ref|NP_248498.1|  86 ALGLKAAMFTGASFIIGF--ITAIIFGAILGAVGGVI 120
                                   544444444433333333..6999***********98 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1  17.0       0.2   9.1e+02      27     164 ..      13     119 ..       1     123 [. 0.58

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.2
                       DUF4199  27 lstgpllglla.llllllv...pflvylalkkyrkknlgGfisfgqafgfgflislvagllsavfqyiyfnfidpdfieny 103
                                   l+  ++ g+++ +l ++++   ++++ +a   y ++  gG + +  + ++g +  +++g++ +++ +++++ +        
  gi|15669685|ref|NP_248498.1|  13 LKPAVIGGIINgILGAICClcyVIGGAVAAHLYVNA--GGICDYENCGLVGAISGVIGGVIASILSFLFMSAY-------- 83 
                                   444466666664333333365577777777777443..88999999999999999999999999999998522........ PP

                       DUF4199 104 iaeilekleeakeesaeeenaemseeeikealeslspiivalqsflgnliiGlilsliiAl 164
                                   + ++l            + +a+m++               ++++f++ +i+G+il+++ + 
  gi|15669685|ref|NP_248498.1|  84 L-SAL------------GLKAAMFTGAS------------FIIGFITAIIFGAILGAVGGV 119
                                   1.111............21222222222............566677777777777666655 PP

>> DUF5326  Family of unknown function (DUF5326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3    0.0044        20      23      43 ..      16      36 ..      11      47 .. 0.80
   2 ?    5.4   2.3    0.0045        20      24      38 ..      66      80 ..      59     101 .. 0.66
   3 ?    5.5   3.7    0.0042        19      32      59 ..     100     125 ..      91     127 .] 0.76

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0044
                       DUF5326 23 vvfGgliasvvgvligllfkv 43
                                  +v Gg+i  ++g++  l + +
  gi|15669685|ref|NP_248498.1| 16 AVIGGIINGILGAICCLCYVI 36
                                  699***********9998755 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0045
                       DUF5326 24 vfGgliasvvgvlig 38
                                  v Gg+ias++++l+ 
  gi|15669685|ref|NP_248498.1| 66 VIGGVIASILSFLFM 80
                                  789999999999864 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0042
                       DUF5326  32 vvgvligllfkvLvlvalvggliyvvrk 59 
                                   ++g++ +++f +++    vgg+iyvv k
  gi|15669685|ref|NP_248498.1| 100 IIGFITAIIFGAILG--AVGGVIYVVIK 125
                                   678888888877654..59******976 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.6   0.00062       2.8      17      49 ..      18      47 ..      13      54 .. 0.76
   2 ?    3.1  12.5     0.029   1.3e+02      30      85 ..      59     115 ..      56     125 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00062
                          FtsX 17 vlllllteillitlvalviGlglgllaaqllsd 49
                                  + +++ + + +i+++++viG   g++aa l  +
  gi|15669685|ref|NP_248498.1| 18 IGGIINGILGAICCLCYVIG---GAVAAHLYVN 47
                                  55667777889*********...8888887554 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.029
                          FtsX  30 lvalviGlglgllaaqllsdvllssvfs.selkisidlitvliiivlllllallagl 85 
                                   lv++++G++ g++a+ l++ ++++++++ +  + ++ + +++i+++ ++++  + g+
  gi|15669685|ref|NP_248498.1|  59 LVGAISGVIGGVIASILSFLFMSAYLSAlGLKAAMFTGASFIIGFITAIIFGAILGA 115
                                   566666666688888888888888877766666666666666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 778.67
//
Query:       gi|15669686|ref|NP_248499.1|  [L=156]
Description: hypothetical protein MJ_1492 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-34  116.3   1.4    6.4e-34  116.3   1.4    2.0  2  DUF2085          Predicted membrane protein (DUF2085)
  ------ inclusion threshold ------
        1.6    9.2   7.6       0.53   10.7   3.1    2.3  2  Caps_synth_CapC  Capsule biosynthesis CapC


Domain annotation for each model (and alignments):
>> DUF2085  Predicted membrane protein (DUF2085)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   1.6      0.15   1.3e+03      25      49 ..      15      38 ..       4      49 .. 0.54
   2 !  116.3   1.4   7.1e-38   6.4e-34       1      89 [.      50     141 ..      50     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.15
                       DUF2085 25 iylGlllgllllllkaklsklslll 49
                                  +yl+++l+ ++++l+ + s+++ ++
  gi|15669686|ref|NP_248499.1| 15 FYLSIFLAPYFAYLG-ETSNFWKFI 38
                                  466677766666663.222222222 PP

  == domain 2  score: 116.3 bits;  conditional E-value: 7.1e-38
                       DUF2085   1 ChqrpeRSfflkgyqfpvCaRctgiylGlllgllllll.k..aklsklsllllvllllpmaiDgltqllglyestnllRli 78 
                                   Chq+p+RSff++g++++vCaRc+giy+G+l+g++++ + k   +++  + ++l+++l+pma+Dg+tql+gl+es n+lR+i
  gi|15669686|ref|NP_248499.1|  50 CHQMPQRSFFIFGHKMAVCARCFGIYTGVLVGMIIYPFiKklDDFKIPNKWYLIIALIPMAVDGTTQLIGLRESFNELRFI 130
                                   ************************************998458889999999****************************** PP

                       DUF2085  79 tGllaGlalal 89 
                                   tG++aG+++++
  gi|15669686|ref|NP_248499.1| 131 TGFIAGFTVVF 141
                                   *******9986 PP

>> Caps_synth_CapC  Capsule biosynthesis CapC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3     0.099   8.9e+02      38      58 ..       6      26 ..       2      32 .. 0.62
   2 ?   10.7   3.1   5.9e-05      0.53      31     106 ..      32     107 ..      18     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.099
               Caps_synth_CapC 38 vtllialltylivrllsrfli 58
                                  +++li++l++++  +l+ ++ 
  gi|15669686|ref|NP_248499.1|  6 LIVLISFLIFYLSIFLAPYFA 26
                                  566677777766666666655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.9e-05
               Caps_synth_CapC  31 dqplsllvtllialltylivrllsrflilyGrrrfvavlllgvlvklllelllllllpaelveeleviGlivpgLi 106
                                    ++++ + + l a+  +++ ++ +r ++++G +  v + ++g+   +l+ +++ +++++  + ++    +++++Li
  gi|15669686|ref|NP_248499.1|  32 SNFWKFISICLYAVYSLICHQMPQRSFFIFGHKMAVCARCFGIYTGVLVGMIIYPFIKKLDDFKIPNKWYLIIALI 107
                                   67888899999999999999999999*****************************999999886666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1025.28
//
Query:       gi|15669687|ref|NP_248500.1|  [L=231]
Description: hypothetical protein MJ_1493 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-06   26.6   0.7    5.8e-06   25.9   0.7    1.4  1  SWIM          SWIM zinc finger
    1.2e-05   24.3   2.2    6.4e-05   21.9   2.1    1.9  1  Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
  ------ inclusion threshold ------
      0.024   14.2   0.2      0.039   13.5   0.2    1.3  1  INTS5_N       Integrator complex subunit 5 N-terminus
      0.075   13.4   0.8       0.11   12.8   0.2    1.6  2  Cornichon     Cornichon protein
       0.12   12.6   0.5          2    8.7   0.1    2.3  2  DUF2316       Uncharacterized protein conserved in bacteria (


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.7   1.6e-09   5.8e-06       3      39 ..      45      75 ..      43      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.6e-09
                          SWIM  3 VtlddervrlnkatCsCpefqkngipCkHalAvllal 39
                                  V +d++  +  +  C+C+    +++ CkHa+A++ a+
  gi|15669687|ref|NP_248500.1| 45 VKVDLD--NNYFGLCTCQ----YKYNCKHAYALIEAY 75
                                  555554..568888****....***********9997 PP

>> Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   2.1   1.8e-08   6.4e-05     132     198 ..      67     132 ..      60     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.8e-08
                                   HHHHHHHHHHCT-HHHHHHHHHHHHHH.H--SHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                  Cas_Cas02710 132 eaaqakelfNkgefgsalriledlvqrlperkeYaaykllaegylaWdsldhkeAldalskvleldl 198
                                    a   +e++ ++++  a++i+++++ + p++++ +++k+l+  y  Wd++     l +    l +++
  gi|15669687|ref|NP_248500.1|  67 HAYALIEAYENNNYVDAEEIFKEIEDK-PKEEILKILKNLVVKYYLWDEFLNTDSLLNKAIGLIKLI 132
                                   566789*********************.*********************977665544333333333 PP

>> INTS5_N  Integrator complex subunit 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   1.1e-05     0.039       3     103 ..      98     202 ..      95     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                       INTS5_N   3 ilnelknFlaease.kkklseeelvrsalnlLkklPaaRsaVleylaqlfeeavery.....leevetepilkesqinael 77 
                                   il+ lkn++ +     + l++++l+ +a+ l+k +P  R+ ++++ + l ++ v++      ++ +++      ++   + 
  gi|15669687|ref|NP_248500.1|  98 ILKILKNLVVKYYLwDEFLNTDSLLNKAIGLIKLIPLERKNIYTFKSFLRNQFVKNAddeelIKVIDEM---IRADLDFNN 175
                                   5666777776666677889**************************999999999765333321222222...333444455 PP

                       INTS5_N  78 deaieeiqtvleelv.eenpkawapli 103
                                    ++ie ++ +l+e++ +en++a ++li
  gi|15669687|ref|NP_248500.1| 176 SDIIEALTIILDEIFrRENKEAIKKLI 202
                                   666777777777777689999999988 PP

>> Cornichon  Cornichon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   3.2e-05      0.11      77     120 ..      68     110 ..      49     112 .. 0.77
   2 ?   -2.8   0.0       2.2   7.9e+03      94     107 ..     200     213 ..     178     215 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                     Cornichon  77 ayniyrvmskqglydpteifnqlkkhkkesmiklafylllffiy 120
                                   ay + + +++++++d+ eif++++   ke ++k+   l++  +y
  gi|15669687|ref|NP_248500.1|  68 AYALIEAYENNNYVDAEEIFKEIEDKPKEEILKILKNLVV-KYY 110
                                   4444457899************************998884.444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.2
                     Cornichon  94 eifnqlkkhkkesm 107
                                   +++n   khkke +
  gi|15669687|ref|NP_248500.1| 200 KLINLYRKHKKELW 213
                                   34455566666666 PP

>> DUF2316  Uncharacterized protein conserved in bacteria (DUF2316)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.088   3.2e+02      20      46 ..     158     184 ..     151     190 .. 0.85
   2 ?    8.7   0.1   0.00055         2      36      63 ..     194     221 ..     191     225 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.088
                       DUF2316  20 elsgltveevaedLnlttekvekvLel 46 
                                   el ++  e++ +dL+++++++ + L +
  gi|15669687|ref|NP_248500.1| 158 ELIKVIDEMIRADLDFNNSDIIEALTI 184
                                   56788899***********99888865 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00055
                       DUF2316  36 ttekvekvLelkasrledvWilrdyLee 63 
                                   ++e ++k+++l  ++ ++ Wi+ dyL e
  gi|15669687|ref|NP_248500.1| 194 NKEAIKKLINLYRKHKKELWIVGDYLIE 221
                                   578999********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1269  (0.0707792); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1465.95
//
Query:       gi|15669688|ref|NP_248501.1|  [L=371]
Description: AAA ATPase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-40  138.8   0.0    3.1e-40  137.7   0.0    1.6  1  AAA              ATPase family associated with various cellul
    2.9e-09   37.3   0.0    5.7e-09   36.3   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
    3.9e-09   36.5   0.0    1.2e-08   34.9   0.0    1.8  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    7.3e-07   28.7   0.0    1.1e-06   28.1   0.0    1.3  1  TIP49            TIP49 P-loop domain
    1.4e-06   28.0   0.0    2.6e-06   27.1   0.0    1.5  1  AAA_lid_3        AAA+ lid domain
    1.9e-06   27.3   0.0    8.1e-05   21.9   0.0    2.2  2  DUF815           Protein of unknown function (DUF815)
      1e-05   26.0   0.0    0.00083   19.8   0.0    2.5  1  AAA_16           AAA ATPase domain
    1.2e-05   25.4   0.0    8.6e-05   22.6   0.0    2.4  1  AAA_5            AAA domain (dynein-related subfamily)
    3.9e-05   24.0   0.1     0.0029   17.9   0.1    2.7  2  AAA_22           AAA domain
    8.9e-05   22.7   0.0    0.00014   22.1   0.0    1.3  1  AAA_33           AAA domain
    0.00057   19.7   0.0     0.0012   18.6   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
    0.00087   18.7   0.0     0.0021   17.5   0.0    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0033   17.0   0.0       0.02   14.4   0.0    2.2  3  AAA_7            P-loop containing dynein motor region
     0.0062   16.9   0.0      0.012   15.9   0.0    1.6  1  RNA_helicase     RNA helicase
     0.0063   16.4   0.0      0.017   15.0   0.0    1.7  1  Bac_DnaA         Bacterial dnaA  protein
     0.0064   17.0   0.0      0.016   15.7   0.0    1.8  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.015   14.4   0.0      0.024   13.7   0.0    1.2  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.016   15.5   0.0       0.03   14.6   0.0    1.5  1  AAA_28           AAA domain
      0.023   14.0   0.1       0.76    9.1   0.0    2.4  2  ATPase           KaiC
      0.031   14.1   0.0      0.068   13.0   0.0    1.5  1  AAA_lid_2        AAA lid domain
      0.033   13.9   0.0      0.078   12.7   0.0    1.7  1  AAA_24           AAA domain
      0.039   13.4   0.0      0.069   12.6   0.0    1.3  1  PhoH             PhoH-like protein
      0.057   13.1   0.0       0.15   11.8   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
      0.061   13.4   0.0       0.14   12.2   0.0    1.7  1  AAA_14           AAA domain
      0.084   12.0   0.0        6.2    5.9   0.0    2.9  3  DAP3             Mitochondrial ribosomal death-associated pro
      0.087   12.7   0.0       0.16   11.8   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
       0.11   12.1   0.0        0.3   10.6   0.0    1.7  2  AAA_25           AAA domain
       0.12   12.3   0.0       0.33   11.0   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.13   12.1   0.1         19    5.0   0.0    2.9  3  DNA_pol3_delta2  DNA polymerase III, delta subunit
       0.16   11.8   0.0       0.29   10.9   0.0    1.4  1  AAA_11           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   0.0   5.2e-43   3.1e-40       1     131 [.     157     285 ..     157     286 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 5.2e-43
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgsese 80 
                                   vl+yGppGtGKTl+a+a+a+e++++f+ ++++el+ ++vg+++k irel ++a+e+a p+i+fiDE+da++ sr  +s ++
  gi|15669688|ref|NP_248501.1| 157 VLFYGPPGTGKTLMARALATETNSSFILVKAPELIGEHVGDASKMIRELYQRASESA-PCIVFIDELDAIGLSReYQSLRG 236
                                   79******************************************************9.****************999999* PP

                                   HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                           AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieie 131
                                   + ++vvn+Llteldg k++e+ v+ i+atn+p +ldpa++ +Rf+++ie++
  gi|15669688|ref|NP_248501.1| 237 DVSEVVNALLTELDGIKENEG-VVTIAATNNPAMLDPAIR-SRFEEEIEFK 285
                                   ******************866.******************.*******986 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   9.5e-12   5.7e-09       5     105 ..     156     251 ..     153     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 9.5e-12
                                   -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                         AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                   ++l+ gp g+Gkt++a+ala   +    +++i + a el+     eh+ +  +  ++ y++a e+   iv++DE+d i  +
  gi|15669688|ref|NP_248501.1| 156 NVLFYGPPGTGKTLMARALATETN----SSFILVKAPELIG----EHVGDASKMIRELYQRASESApcIVFIDELDAIGLS 228
                                   799******************999....5************....*********************************987 PP

                                   ...---------HHHHHHHHHHHH- CS
                         AAA_2  84 ...essgadvSregVqrdLLqileg 105
                                      +s + dvS  +V+++LL  l+g
  gi|15669688|ref|NP_248501.1| 229 reyQSLRGDVS--EVVNALLTELDG 251
                                   7899999***9..9******98887 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0     2e-11   1.2e-08       4      96 ..     121     225 ..     118     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2e-11
                        RuvB_N   4 ksleeyigqekvkeklkifieaakk...ree.aldhvllyGpPGlGkttlakiiakelgvklkitsgPvl..ekagdlaal 78 
                                    +++e igqe+ k+k +i+++  ++    +e a   vl+yGpPG Gkt +a+ +a+e ++++    +P l  e+ gd + +
  gi|15669688|ref|NP_248501.1| 121 AKFSEIIGQEEAKKKCRIIMKYLENpklFGEwAPKNVLFYGPPGTGKTLMARALATETNSSFILVKAPELigEHVGDASKM 201
                                   5789**************987654411144437899********************************8867899****** PP

                        RuvB_N  79 ltnleekd......vlfideihrl 96 
                                   + +l ++       ++fide+  +
  gi|15669688|ref|NP_248501.1| 202 IRELYQRAsesapcIVFIDELDAI 225
                                   999976543345558999998765 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.8e-09   1.1e-06      24      93 ..     124     195 ..     109     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.8e-09
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  24 eglvGqkkareaagvivelikekklaG....ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslev 93 
                                   + ++Gq++a++ + +i++ +++ kl G    + vL+ Gp+gtGkt +a a++ e +    f+ +++ e+    v
  gi|15669688|ref|NP_248501.1| 124 SEIIGQEEAKKKCRIIMKYLENPKLFGewapKNVLFYGPPGTGKTLMARALATETN--SSFILVKAPELIGEHV 195
                                   579*******************99977555589*******************9987..4577777777766555 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   4.4e-09   2.6e-06       3      44 ..     310     352 ..     308     353 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.4e-09
                     AAA_lid_3   3 dlkeLAerTeGySGADlaa.lcreAallAlrrgikeitmedfe 44 
                                   +lke +e+T+G+SG D+++   + A ++A+ ++++ +++ed+e
  gi|15669688|ref|NP_248501.1| 310 NLKEFVEKTKGFSGRDIKEkFLKPALHRAILEDRDYVSKEDLE 352
                                   89***************777*********************97 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.4e-07   8.1e-05      22     129 ..     118     235 ..     103     270 .. 0.77
   2 ?    3.3   0.0     0.064        38     183     237 ..     275     324 ..     252     334 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.4e-07
                        DUF815  22 vdevklddLvgidkqkea...l...venteqfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlke 94 
                                   +++ k+++++g ++ k++   +   +en + f    + +nvL++G  GtGK  + +al +e++++   ++  e+  e++ +
  gi|15669688|ref|NP_248501.1| 118 FKKAKFSEIIGQEEAKKKcriImkyLENPKLF-GEWAPKNVLFYGPPGTGKTLMARALATETNSSFilVKAPELIGEHVGD 197
                                   56677777888777776522121113444444.3445689***********************9997778889******** PP

                        DUF815  95 lpklvellrerp...erfilfvDDLsFeeeeeeyksLk 129
                                    +k++++l +r+     +i+f+D L      +ey+sL+
  gi|15669688|ref|NP_248501.1| 198 ASKMIRELYQRAsesAPCIVFIDELDAIGLSREYQSLR 235
                                   ******998665111679******98888888887776 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.064
                        DUF815 183 sdRFGlwlgFykldqeeYleiveklakklglelekeeleeeAlewalergsrsgR 237
                                     RF   + F+ ++ ee l+i+e +akk+ l+++  +      e+  +  + sgR
  gi|15669688|ref|NP_248501.1| 275 RSRFEEEIEFKLPNDEERLKIMELYAKKMPLPVKA-N----LKEFVEKTKGFSGR 324
                                   579999********************999998874.3....33455555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.4e-06   0.00083      24      63 ..     154     190 ..     140     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.4e-06
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                   p +vl++G++G+GK+ ++r+l+++ + +   f+  k+ +l
  gi|15669688|ref|NP_248501.1| 154 PKNVLFYGPPGTGKTLMARALATETNSS---FILVKAPEL 190
                                   689*******************977766...666666665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.4e-07   8.6e-05       1     138 []     156     278 ..     156     278 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.4e-07
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--. CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae. 78 
                                   +vl  GppGtgK+ +a+ la  +n+++  v  ++      l+g+     g++s    +l++ a    ++i+++DE++ +  
  gi|15669688|ref|NP_248501.1| 156 NVLFYGPPGTGKTLMARALATETNSSFILVKAPE------LIGEHV---GDASKMIRELYQRASesAPCIVFIDELDAIGl 227
                                   699************************9998876......999988...5666666677766665778999*****99887 PP

                                   HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                         AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                   s   +sL    +e       ++el + k++   e +  ia++n++      l+pa+rsRf
  gi|15669688|ref|NP_248501.1| 228 SREYQSLRGDVSEVVNA--LLTELDGIKEN---EGVVTIAATNNPA----MLDPAIRSRF 278
                                   77777776655554444..33444444443...2366666666666....6899999998 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   4.8e-06    0.0029       8      51 ..     157     191 ..     153     261 .. 0.75
   2 ?   -1.7   0.0       5.5   3.3e+03      48      70 ..     287     309 ..     245     363 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.8e-06
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51 
                                   ++ +G++GtGKT+ +r l+ +          ++++++v++p++ 
  gi|15669688|ref|NP_248501.1| 157 VLFYGPPGTGKTLMARALATET---------NSSFILVKAPELI 191
                                   6789*****************9.........9999999999865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.5
                        AAA_22  48 psstsskdllrellralglelka 70 
                                   p+++++ ++++  ++++ l+ ka
  gi|15669688|ref|NP_248501.1| 287 PNDEERLKIMELYAKKMPLPVKA 309
                                   44444444444444444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   2.3e-07   0.00014       2      51 ..     157     209 ..     157     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.3e-07
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt.dytrv 51 
                                   vl+ G+pG+GK+  a+ l+ ++   ++l+  ++l+  ++g+  + ++  y+r+
  gi|15669688|ref|NP_248501.1| 157 VLFYGPPGTGKTLMARALATETNssFILVKAPELIGEHVGDASKMIReLYQRA 209
                                   799****************99999************99996655444222333 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     2e-06    0.0012      47      78 ..     154     182 ..     110     245 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2e-06
                     IstB_IS21  47 kenivllGpsGvGKshlaialgveavraglsv 78 
                                    +n+++ Gp+G+GK+ +a al++e+   + s 
  gi|15669688|ref|NP_248501.1| 154 PKNVLFYGPPGTGKTLMARALATET---NSSF 182
                                   579******************8764...4444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.5e-06    0.0021      23      43 ..     155     175 ..     122     180 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.5e-06
                  Mg_chelatase  23 HnlllvGppGsGKtmlakrlp 43 
                                    n+l++GppG+GKt++a++l+
  gi|15669688|ref|NP_248501.1| 155 KNVLFYGPPGTGKTLMARALA 175
                                   69****************996 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.3e-05      0.02      34      59 ..     155     180 ..     120     190 .. 0.89
   2 ?   -1.1   0.0         2   1.2e+03      99     110 ..     212     223 ..     198     227 .. 0.81
   3 ?   -3.0   0.0       7.6   4.5e+03     147     170 ..     256     279 ..     248     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                         AAA_7  34 kpvllvGptGtGKtviikdllkkldk 59 
                                   k+vl++Gp GtGKt++++ l ++ ++
  gi|15669688|ref|NP_248501.1| 155 KNVLFYGPPGTGKTLMARALATETNS 180
                                   89***************998888773 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2
                         AAA_7  99 gkklvvFvDDln 110
                                   +  ++vF+D+l+
  gi|15669688|ref|NP_248501.1| 212 SAPCIVFIDELD 223
                                   5679*****996 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 7.6
                         AAA_7 147 kdvqlvaamgppgggrneitpRll 170
                                   + v+ +aa ++p+     i +R+ 
  gi|15669688|ref|NP_248501.1| 256 EGVVTIAATNNPAMLDPAIRSRFE 279
                                   678899999999999999999985 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.1e-05     0.012       1      26 [.     157     182 ..     157     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                   +++yGp+g+GK+++a+ La++  +++
  gi|15669688|ref|NP_248501.1| 157 VLFYGPPGTGKTLMARALATETNSSF 182
                                   689****************9988776 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.9e-05     0.017      37     208 ..     157     329 ..     144     339 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.9e-05
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHH..HHHHHHHHHTT-HHH..HHHHHTT-SEE.EEE-GGGGTT- CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeF..lnelvkalrdkkaee..fkeklrkvDvL.liDDiqflagk 112
                                   +++yg+ G Gkt + +a++ e+ +++   +   l +e+   ++++++ l +++ e+     ++ ++D++ l  + q l g 
  gi|15669688|ref|NP_248501.1| 157 VLFYGPPGTGKTLMARALATETNSSFILVKAPELIGEHVgdASKMIRELYQRASESapCIVFIDELDAIgLSREYQSLRGD 237
                                   799***********************9999999999986445678887776555441144566677766466678888765 PP

                                   .HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT----TTHHH CS
                      Bac_DnaA 113 .ektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaeklevpeevle 192
                                    +++ + l++ ++ + e++  v +++  +P     l+  +rsrfe  +  + + p+ e rl+i++  +++  l v+ ++ e
  gi|15669688|ref|NP_248501.1| 238 vSEVVNALLTELDGIKENEGVVTIAATNNPAM---LDPAIRSRFEEEI--EFKLPNDEERLKIMELYAKKMPLPVKANLKE 313
                                   25677788888888899999999*******76...6899******976..566689999********************** PP

                                   HHHHH--S-HHHHHHH CS
                      Bac_DnaA 193 fiaervtdnvRelega 208
                                   f+ ++   + R+++  
  gi|15669688|ref|NP_248501.1| 314 FVEKTKGFSGRDIKEK 329
                                   **99999999988765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.7e-05     0.016       1      25 [.     157     195 ..     157     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.7e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf..............g 25 
                                   +l  G+pG+GKt +a++L+ ++++              +
  gi|15669688|ref|NP_248501.1| 157 VLFYGPPGTGKTLMARALATETNSsfilvkapeligehV 195
                                   6789**************999866677777777774443 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     4e-05     0.024     114     137 ..     155     177 ..     145     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-05
                     Parvo_NS1 114 rntvwfyGpantGktnlaeaIaka 137
                                   +n v+fyGp+ tGkt +a+a+a+ 
  gi|15669688|ref|NP_248501.1| 155 KN-VLFYGPPGTGKTLMARALATE 177
                                   55.89****************975 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.1e-05      0.03       2      31 ..     157     191 ..     156     232 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.1e-05
                        AAA_28   2 ivitGgestGKTtlleaLaar.gypvv....pEaa 31 
                                   + + G+++tGKT +++aLa + + + +    pE  
  gi|15669688|ref|NP_248501.1| 157 VLFYGPPGTGKTLMARALATEtNSSFIlvkaPELI 191
                                   889****************6544443311344444 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0013      0.76      20      38 ..     155     173 ..     150     182 .. 0.84
   2 ?    2.5   0.0      0.13        80      99     151 ..     193     245 ..     174     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                        ATPase  20 rvvlitGepGtGKtifalq 38 
                                   + vl +G pGtGKt++a  
  gi|15669688|ref|NP_248501.1| 155 KNVLFYGPPGTGKTLMARA 173
                                   57899***********976 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                        ATPase  99 kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvl 151
                                   ++  d++++i+el +  +e     v iD ++++  + + + +R  + ++v+ l
  gi|15669688|ref|NP_248501.1| 193 EHVGDASKMIRELYQRASESAPCIVFIDELDAIGLSREYQSLRGDVSEVVNAL 245
                                   45678999*************************77888888999999999887 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.068      28      55 ..     336     363 ..     330     368 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                     AAA_lid_2  28 AlAalegrdyVtpeDvkeaaplVLaHRl 55 
                                    +A le rdyV++eD++ a + +L  R 
  gi|15669688|ref|NP_248501.1| 336 HRAILEDRDYVSKEDLEWALKKILGNRR 363
                                   579*****************99999886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013     0.078       2      23 ..     154     177 ..     153     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                        AAA_24   2 klkiliyGpsgiGKTtlakel..g 23 
                                   ++++l yGp+g+GKT +a+ l  +
  gi|15669688|ref|NP_248501.1| 154 PKNVLFYGPPGTGKTLMARALatE 177
                                   57899*************988552 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012     0.069      22      66 ..     157     196 ..     143     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                   EEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT---- CS
                          PhoH  22 vfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelG 66 
                                   v   Gp GtGKt++a ala e       + +il+++   +ge++G
  gi|15669688|ref|NP_248501.1| 157 VLFYGPPGTGKTLMARALATETN-----SSFILVKAPELIGEHVG 196
                                   6678***********99987653.....44555555555555555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00025      0.15      22      47 ..     154     179 ..     126     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                                   SS-EEEECSTTSSHHHHHHHHHHHST CS
               Sigma54_activat  22 dlsvlitGesGtGKellaraiheask 47 
                                   + +vl  G  GtGK+l+ara+ ++++
  gi|15669688|ref|NP_248501.1| 154 PKNVLFYGPPGTGKTLMARALATETN 179
                                   479****************9976554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00023      0.14       4      77 ..     156     236 ..     153     286 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                        AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev........ 76 
                                    ++  G+  +GKT +++ l+ e     +s++ ++  +   +   d +k+++++ ++++e+   ++f+DE   +        
  gi|15669688|ref|NP_248501.1| 156 NVLFYGPPGTGKTLMARALATETN---SSFILVKAPELIGEHVGDASKMIRELYQRASESAPCIVFIDELDAIglsreyqs 233
                                   57789999***********98877...7787777776555555566667777776666678899*****988766666655 PP

                        AAA_14  77 ..p 77 
                                      
  gi|15669688|ref|NP_248501.1| 234 lrG 236
                                   552 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0      0.01       6.2      23      59 ..     154     189 ..     134     200 .. 0.81
   2 ?    0.3   0.0      0.51   3.1e+02     145     169 ..     201     225 ..     197     235 .. 0.86
   3 ?    1.6   0.0      0.21   1.2e+02     260     305 ..     280     325 ..     252     332 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.01
                                   --EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES- CS
                          DAP3  23 vkrlvltGekgsGKSvlLlqalayAlekgwvvlhvpe 59 
                                    k ++++G +g+GK++ ++ ala  +++ +++++ pe
  gi|15669688|ref|NP_248501.1| 154 PKNVLFYGPPGTGKTL-MARALATETNSSFILVKAPE 189
                                   566889********85.78888888888888887775 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.51
                                   HHHHHHHHTTSS--EEEEEE-GGGG CS
                          DAP3 145 llkeLkaqskgrvpvlvtvDglnal 169
                                   +++eL + +++  p +v +D+l+a+
  gi|15669688|ref|NP_248501.1| 201 MIRELYQRASESAPCIVFIDELDAI 225
                                   6899***9999***********997 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.21
                                   .EEE-----GGGTHHHHHHHHHTT---STTSSHHHHHHHHHTTSS- CS
                          DAP3 260 epieveglskeEarslleyyadsgvlqekvneelveeklslsgngn 305
                                   e+ie +  ++eE  +++e+ya++  l  k n + + ek +  +++ 
  gi|15669688|ref|NP_248501.1| 280 EEIEFKLPNDEERLKIMELYAKKMPLPVKANLKEFVEKTKGFSGRD 325
                                   5666666789999*************99966666666655444444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00027      0.16       2      36 ..     157     190 ..     156     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdl 36 
                                   vl+ g PG++ktl+++ala+  + +f  ++ +p+l
  gi|15669688|ref|NP_248501.1| 157 VLFYGPPGTGKTLMARALATETNSSFILVK-APEL 190
                                   78899*****************99997765.3555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0005       0.3      26      55 ..     149     176 ..     144     181 .. 0.80
   2 ?   -2.6   0.0       5.8   3.5e+03     143     169 ..     214     246 ..     195     263 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0005
                        AAA_25  26 vkgllpagelallaGapgtGKttlaldlal 55 
                                   ++++ p  + +l++G+pgtGKt +a  la 
  gi|15669688|ref|NP_248501.1| 149 FGEWAP--KNVLFYGPPGTGKTLMARALAT 176
                                   556655..45789************99986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.8
                        AAA_25 143 vrlvviDplsralggdensn..sd...v.galv 169
                                   +  v iD l+++    e  +   d   v +al+
  gi|15669688|ref|NP_248501.1| 214 PCIVFIDELDAIGLSREYQSlrGDvseVvNALL 246
                                   677777777765444333322233222224444 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00055      0.33      19      51 ..     154     188 ..     129     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00055
                                   TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                    + +l++G+ G+GKT ++r+la + + +   vk P
  gi|15669688|ref|NP_248501.1| 154 PKNVLFYGPPGTGKTLMARALATETNSSfiLVKAP 188
                                   4569******************9987765556555 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.8   2.8e+03     114     130 ..     131     146 ..      84     152 .. 0.60
   2 ?    5.0   0.0     0.032        19      22      43 ..     157     178 ..     150     183 .. 0.88
   3 ?    3.5   0.0     0.093        56     121     156 ..     243     280 ..     194     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.8
               DNA_pol3_delta2 114 kmtksAaNalLktlEEP 130
                                   + +k+   +++k lE+P
  gi|15669688|ref|NP_248501.1| 131 EAKKKC-RIIMKYLENP 146
                                   333332.2556666666 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.032
               DNA_pol3_delta2  22 yLfeGdegigkkelalnlakal 43 
                                    Lf+G+ g+gk  +a +la++ 
  gi|15669688|ref|NP_248501.1| 157 VLFYGPPGTGKTLMARALATET 178
                                   7*****************9876 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.093
               DNA_pol3_delta2 121 NalLktlEEPsen..aifiLitsdtnklLktirSRcqe 156
                                   NalL  l   +en  ++ i  t+++  l + irSR  e
  gi|15669688|ref|NP_248501.1| 243 NALLTELDGIKENegVVTIAATNNPAMLDPAIRSRFEE 280
                                   6666666654444226888899999999999****863 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00049      0.29      19      42 ..     156     179 ..     133     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00049
                        AAA_11  19 itliqGPPGtgKTktivellsqll 42 
                                    +l+ GPPGtgKT +  +l  + +
  gi|15669688|ref|NP_248501.1| 156 NVLFYGPPGTGKTLMARALATETN 179
                                   47999********99998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 2252.71
//
Query:       gi|15669689|ref|NP_248502.1|  [L=292]
Description: hypothetical protein MJ_1495 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.5e-161  536.0   3.1   1.8e-161  535.8   3.1    1.0  1  SDH_sah         Serine dehydrogenase proteinase
    4.3e-05   23.5   1.1    0.00029   20.8   0.1    2.0  2  CLP_protease    Clp protease
    7.6e-05   22.1   0.0    0.00011   21.6   0.0    1.2  1  ECH_1           Enoyl-CoA hydratase/isomerase
     0.0013   18.7   0.1     0.0023   17.9   0.1    1.3  1  Peptidase_S49   Peptidase family S49
  ------ inclusion threshold ------
      0.014   15.9   0.1      0.044   14.3   0.1    1.8  1  FliG_N          FliG N-terminal domain
       0.04   13.6   0.0      0.062   13.0   0.0    1.4  1  Glyco_transf_5  Starch synthase catalytic domain
      0.065   13.8   0.3        2.6    8.7   0.1    2.7  2  PepSY           Peptidase propeptide and YPEB domain
       0.12   12.5   0.1       0.23   11.6   0.1    1.4  1  Ku_PK_bind      Ku C terminal domain like


Domain annotation for each model (and alignments):
>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  535.8   3.1  7.9e-165  1.8e-161       2     286 .]      10     292 .]       9     292 .] 0.99

  Alignments for each domain:
  == domain 1  score: 535.8 bits;  conditional E-value: 7.9e-165
                       SDH_sah   2 eksdplsslssllwfllflylllapqlkrkqlllarlkvlrkleekrksrvitmihrqesigflGipiykfitiedseevl 82 
                                   ++ d+++s +++++fl++++l+++p++++++++++rl+++r++e++r++rvi+mihrqe+++flGipiykfitiedsee+l
  gi|15669689|ref|NP_248502.1|  10 IMGDEMTS-MDMFFFLFIFLLFIYPEMMMRYRIMKRLRCIREIERQRGTRVIAMIHRQEALTFLGIPIYKFITIEDSEEIL 89 
                                   689*****.9*********************************************************************** PP

                       SDH_sah  83 rairltpkdkpidliihtpGGlvlaatqiakalkehkaktrvivphyamsGGtlialaadeiildenavlGpvdpqlgqyp 163
                                   rairltp+d+pidliihtpGGl+la++qia alkehkakt+vi+phyamsGG+lialaadeii+d+nav+Gpvdpq+gqyp
  gi|15669689|ref|NP_248502.1|  90 RAIRLTPEDMPIDLIIHTPGGLALASEQIALALKEHKAKTTVIIPHYAMSGGSLIALAADEIIMDKNAVMGPVDPQIGQYP 170
                                   ********************************************************************************* PP

                       SDH_sah 164 aasilkvvekkeakdiddktliladiakkaikqveefvyellkdkydeekakeiakklteGrwthdypltveelkelGlev 244
                                   aasil+++++k+ ++++d+tlil+di+kkaikq+eefvyellkdky++ekakeiakklt+G+wthdypltv++lkelG+ev
  gi|15669689|ref|NP_248502.1| 171 AASILEAYYRKG-EKVSDETLILVDISKKAIKQMEEFVYELLKDKYGDEKAKEIAKKLTSGTWTHDYPLTVSKLKELGIEV 250
                                   ************.9******************************************************************* PP

                       SDH_sah 245 ntnvpeevyellelyeqplgqrpsveyipvpvkkkeqeknak 286
                                   ntnvp++vyellely+qp+g++psv+yipvp++kke+eknak
  gi|15669689|ref|NP_248502.1| 251 NTNVPRKVYELLELYPQPMGAKPSVYYIPVPYSKKESEKNAK 292
                                   ****************************************97 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.3e-07   0.00029      38      98 ..      90     150 ..      53     161 .. 0.79
   2 ?    1.2   0.1      0.13     3e+02     125     164 ..     193     233 ..     183     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.3e-07
                                   HHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEETHHHHHHHTS-T CS
                  CLP_protease  38 llLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticlGlaaSmgslllaagek 98 
                                    ++  + +d +i l+i++pGG   a+  I+ +++ +k++ ++i    a+S gsl+++a+++
  gi|15669689|ref|NP_248502.1|  90 RAIRLTPEDMPIDLIIHTPGGLALASEQIALALKEHKAKTTVIIPHYAMSGGSLIALAADE 150
                                   34455678899*****************************99999*************986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHHHHTS.-HHHHHHHHCSTEEE CS
                  CLP_protease 125 ieieaeellkikerlneilakhtgq.slekiekdldrdtfl 164
                                   ++i  + +++++e + e+l+++ g  ++++i+k+l+  t++
  gi|15669689|ref|NP_248502.1| 193 VDISKKAIKQMEEFVYELLKDKYGDeKAKEIAKKLTSGTWT 233
                                   6788899***********99988751567899988877775 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0     5e-08   0.00011      98     143 ..     136     181 ..     115     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5e-08
                                   EEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHH CS
                         ECH_1  98 aaigGGlelalacDiviaadnasfglnelklGlipgaggtqilark 143
                                   +a+ GG ++ala+D +i+++na+ g    ++G +p+a + + + rk
  gi|15669689|ref|NP_248502.1| 136 YAMSGGSLIALAADEIIMDKNAVMGPVDPQIGQYPAASILEAYYRK 181
                                   89***********************************999998886 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1     1e-06    0.0023       2      40 ..     122     160 ..     121     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1e-06
                                   HHHTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                 Peptidase_S49   2 akkakkPvvasaenvaaSggYylasaadkivanpstivg 40 
                                   +k+ k + ++++  +a Sgg ++a aad+i+++++++ g
  gi|15669689|ref|NP_248502.1| 122 LKEHKAKTTVIIPHYAMSGGSLIALAADEIIMDKNAVMG 160
                                   577888999***************************988 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     2e-05     0.044      49      98 ..     181     230 ..     171     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                                   HHHHHHHHHHHHHHCCCCHHCHHHHHHHHHHHHHHSHHHHHHHCHHHHXX CS
                        FliG_N  49 eveaVleefleeleaqeylseggeeyarelLekalgeekaeellerltae 98 
                                   + e+V +e l  +  +++++++ ee++ elL+  +g+eka+e+ ++lt++
  gi|15669689|ref|NP_248502.1| 181 KGEKVSDETLILVDISKKAIKQMEEFVYELLKDKYGDEKAKEIAKKLTSG 230
                                   568999999999999999*****************************986 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.7e-05     0.062      16      45 ..     109     138 ..      94     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                Glyco_transf_5  16 GGLadvvgaLpkaLaklghdvrvilPryga 45 
                                   GGLa ++++++ aL+++  + +vi+P+y  
  gi|15669689|ref|NP_248502.1| 109 GGLALASEQIALALKEHKAKTTVIIPHYAM 138
                                   ****************************43 PP

>> PepSY  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0       0.1   2.3e+02       5      25 ..     115     135 ..     114     145 .. 0.84
   2 ?    8.7   0.1    0.0012       2.6       2      35 ..     215     260 ..     214     278 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.1
                                   HHHHHHHHHHSTTEEEEEEEE CS
                         PepSY   5 eqAlaiAlaavpgkiieiele 25 
                                   ++ +a Al+++++k ++i++ 
  gi|15669689|ref|NP_248502.1| 115 SEQIALALKEHKAKTTVIIPH 135
                                   578999*********999975 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                                   S-HHHHHHHHHHHSTTEEEEEEEEEEE............TTEEEEE CS
                         PepSY   2 iseeqAlaiAlaavpgkiieieleded............dgrlvYe 35 
                                   +  e+A++iA++  +g++++ ++                 +r vYe
  gi|15669689|ref|NP_248502.1| 215 YGDEKAKEIAKKLTSGTWTHDYPLTVSklkelgievntnVPRKVYE 260
                                   5679*********999998866654334555666666666666666 PP

>> Ku_PK_bind  Ku C terminal domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0001      0.23      18      50 ..     195     227 ..     185     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                    Ku_PK_bind  18 lvekavkqlksvIeqlvedslgdssydkavecl 50 
                                     +ka+kq+++ + +l++d++gd++ +++++ l
  gi|15669689|ref|NP_248502.1| 195 ISKKAIKQMEEFVYELLKDKYGDEKAKEIAKKL 227
                                   5689*******************9888877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1876.93
//
Query:       gi|15669690|ref|NP_248503.1|  [L=117]
Description: hypothetical protein MJ_1496 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-13   49.6   0.0    3.8e-13   49.4   0.0    1.1  1  DUF192    Uncharacterized ACR, COG1430
  ------ inclusion threshold ------
      0.023   14.8   0.1      0.044   13.9   0.1    1.5  1  DUF220    Domain of unknown function DUF220


Domain annotation for each model (and alignments):
>> DUF192  Uncharacterized ACR, COG1430
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.0   4.2e-17   3.8e-13       2      83 ..      20     103 ..      19     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 4.2e-17
                                   EEEEE-SHHHHHHTTTT-----TTEEEEEEECCEEEEEE--TT--S-EEEEEE-TTSBEEEEEEEE-TT-.......ECEE CS
                        DUF192   2 tvevAdteeerarGLmgreslpedegmlfvfdkerehsfwMkntripLdiifldadgriveieealkpqs.......vryv 75 
                                   +v +Ad++ +ra GLm r+    d++mlf +++ +   ++ +++++p+diif+d+++ + +++  lkp++         ++
  gi|15669690|ref|NP_248503.1|  20 EVVLADNFIKRAFGLMLRD--IGDKAMLFLYKRRK-IAMHTFFMLYPIDIIFIDKNRVVEAVR--LKPWKtykcknySTAM 95 
                                   7889**************7..5689*******999.7777888**********9888888888..5799433343334448 PP

                                   EEEETTHH CS
                        DUF192  76 LElpaGaa 83 
                                   LE +   +
  gi|15669690|ref|NP_248503.1|  96 LEFKCSDI 103
                                   88776555 PP

>> DUF220  Domain of unknown function DUF220
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     5e-06     0.044      16      61 ..      43      87 ..      34      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5e-06
                        DUF220 16 dltvkykkekvmfmkvfeGsykveplyvDserlckkrkpksreeYk 61
                                   +   yk++k   m +f   y ++ +++D++r+ ++ + k ++ Yk
  gi|15669690|ref|NP_248503.1| 43 AMLFLYKRRK-IAMHTFFMLYPIDIIFIDKNRVVEAVRLKPWKTYK 87
                                  4445566666.579**********************9999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 787.82
//
Query:       gi|15669691|ref|NP_248504.1|  [L=346]
Description: acetylornithine deacetylase ArgE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-18   67.1   0.0    3.8e-18   66.0   0.0    1.6  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.6e-14   53.7   0.0    2.8e-14   52.9   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   4.2e-22   3.8e-18       1     205 [.      61     341 ..      61     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 4.2e-22
                                   EEEEES-BSSTTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20   1 llgsHlDvVpeeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakal 81 
                                   +l+sH+D+V  +       +f+ +  d+++yG G+ d kg v+ +++a+ +   +      +  l++ pdEE+ ++G+ ++
  gi|15669691|ref|NP_248504.1|  61 ILNSHIDTVKIQS------NFKKD--DNNFYGTGVIDAKGNVVLMIHAFLN--SN------NSLLVISPDEETESNGIYNF 125
                                   589*******222......68888..899********************55..44......4579*******999****** PP

                                   HHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE............................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
                 Peptidase_M20  82 legleerekvdavfelhieepgileagklaigvv............................................... 115
                                   ++ l+++ k++  + ++++ep+ l+     + ++                                               
  gi|15669691|ref|NP_248504.1| 126 CQYLRNKNKIQRGIKCIVGEPTDLN-----VCIGhkgrfeyivesfgearhassqglnpieilsrvildlknlplekikvd 201
                                   **888889*****************.....555589********************************************* PP

                                   .......................................................EEEEEEEEEESHEEEC.CHHHHHHHH CS
                                   .......................................................xxxxxxxxxxxxxxxx.xxxxxxxxx RF
                 Peptidase_M20 116 .......................................................kvevelleggapvtln.dsplvkala 140
                                                                                          k ++ +++++a + +  +++l+++l+
  gi|15669691|ref|NP_248504.1| 202 kiysssitptiikggiqsniipdyayvlfdvrsvekdiikkiddflsqknyskhiKSSLNPERHYANFYMLeNKELINKLS 282
                                   ******************************************999998888877634444444444444434677777777 PP

                                   HHHHHHHTSCEEEEEESSSBHTHHHHTTT..EEEEEEESSG.GCTTSTTTEEEHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 141 eaaeelfgekvelivsgpggtdarffagi..ptvmifgpgs.glaHspnEyvdledlekgikvlarll 205
                                   +  +              ++ +a +f++      +i+g g+ +laHs +Ey++l+d+ +gik +++l+
  gi|15669691|ref|NP_248504.1| 283 KHFKIS--------FFN-ATCEAYYFNKFlkADTIIYGVGKlELAHSKEEYLNLNDFDRGIKEVEKLA 341
                                   764332........555.9*******7777435578999988*******************9888776 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   3.2e-18   2.8e-14       1     104 [.     153     250 ..     153     255 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 3.2e-18
                                   SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEE CS
                     M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakid 81 
                                   ighkG  ++ ++  g+a H++    g N+ie+l+r++ +l++++ ++ +   +  +++++t+i+gG ++n+ipd+a++ +d
  gi|15669691|ref|NP_248504.1| 153 IGHKGRFEYIVESFGEARHAS--SQGLNPIEILSRVILDLKNLPLEKIKVDKIYSSSITPTIIKGGIQSNIIPDYAYVLFD 231
                                   69*******************..99*********************999******************************** PP

                                   EEHHHHHHHHHHHHHHHHHHTSC CS
                     M20_dimer  82 iRllpgedpeevleeieeileke 104
                                   +R +     ++++++i ++l+++
  gi|15669691|ref|NP_248504.1| 232 VRSVE----KDIIKKIDDFLSQK 250
                                   **888....66666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2356.19
//
Query:       gi|15669692|ref|NP_248505.1|  [L=292]
Description: type II R/M system modification methyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-55  187.6   1.0    3.6e-55  187.2   1.0    1.1  1  N6_N4_Mtase      DNA methylase
    2.1e-05   24.3   0.0       0.16   11.7   0.0    2.2  2  UPF0020          Putative RNA methylase family UPF0020
    3.4e-05   24.4   0.0       0.12   13.1   0.0    3.1  2  Methyltransf_11  Methyltransferase domain
     0.0048   17.6   0.0        2.3    9.0   0.0    2.8  2  Methyltransf_25  Methyltransferase domain
     0.0091   15.6   0.1       0.52    9.9   0.0    2.3  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
      0.018   14.9   0.1      0.064   13.1   0.0    1.9  2  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
      0.032   13.9   0.0       0.46   10.1   0.0    2.1  2  Cons_hypoth95    Conserved hypothetical protein 95
       0.04   13.2   0.0       0.23   10.7   0.0    2.0  2  N6_Mtase         N-6 DNA Methylase
      0.061   13.4   0.1       0.36   10.9   0.1    2.1  2  VPR              VPR/VPX protein


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.2   1.0   1.8e-58   3.6e-55       1     231 []      23     264 ..      23     264 .. 0.90

  Alignments for each domain:
  == domain 1  score: 187.2 bits;  conditional E-value: 1.8e-58
                                   EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHHHHHTT.-EEEEE CS
                   N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikkelkaladeifg.gfflln 80 
                                   vd++vt+pPYn+g +   +++y ++ s e+yl+++e+v+ke++rvLkddgs+fin+++    +++   +++++  +f+l+n
  gi|15669692|ref|NP_248505.1|  23 VDVVVTSPPYNIGIK---YNKYSDNLSREDYLNWIEEVVKEIKRVLKDDGSFFINVGYTAKDPWIAFDVANVIRkHFKLQN 100
                                   799************...*********************************************888889999999****** PP

                                   EEEEEES.....................SSTTTSTCCS-B--EEEEEEEESSTT-..---GGGSSBSS-HHHHHHHHHHCH CS
                   N6_N4_Mtase  81 vivwkkp.....................nsmpesnkdrltsthEyilvfsknkkyllkfnldaikvpyeekdklekrgayt 140
                                   +i+w k+                     + +p +++++l+ +hEyi++f+kn++   k+++ ai vpy++k+++++ +   
  gi|15669692|ref|NP_248505.1| 101 TIHWVKSiaiqkedvgnypniigdiavgHYKPINSDRFLSIMHEYIFHFTKNGNV--KLDKLAIGVPYQDKSNIKRFN--- 176
                                   *******9999999977777777777763333333349*****************..*********************... PP

                                   HHCC-B--BSEE..E-SCCCTTSTTS-CHH----SS---HHHHHHHH.HHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEE CS
                   N6_N4_Mtase 141 skkkgkkiediW..dlseiqsnekkskgdtkkkHpaqkPvallerlI.klstkkgdivlDpFaGSGtTavaakelgrkfiG 218
                                   +k + ++ ++ W  + + iqs+ek++       Hpa++P +l+e +I ++  kk  +vlDpF+G G+Ta+a+++lg ++iG
  gi|15669692|ref|NP_248505.1| 177 RKGDLRDRGNTWfiPYETIQSKEKER------PHPATFPPKLPEMCIkLHGVKKTNLVLDPFMGIGSTAIACIRLGIDYIG 251
                                   99999999999944555555555555......5**************5568999*************************** PP

                                   EESSHHHHHHHHH CS
                   N6_N4_Mtase 219 ieieeeyvelaek 231
                                   +ei+e+y++ ae+
  gi|15669692|ref|NP_248505.1| 252 FEIDEYYCRVAEE 264
                                   *********9985 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   7.9e-05      0.16     113     158 ..      16      60 ..       4      79 .. 0.81
   2 !   10.5   0.0   0.00018      0.36       5      50 ..     201     246 ..     198     289 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.9e-05
                                   GG--STTS---EEEE----------HHHHHHHHHH.HHHHHHHH-TT CS
                       UPF0020 113 akLrlkegevdvivtnpPYGerlgskkalekLYse.flrelkrvlrg 158
                                   ++L+  ++ vdv+vt pPY + ++ +k  ++L +e  l+++++v+++
  gi|15669692|ref|NP_248505.1|  16 KQLK--DKTVDVVVTSPPYNIGIKYNKYSDNLSREdYLNWIEEVVKE 60 
                                   4555..558******************99999875467777777765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00018
                                   -SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHH CS
                       UPF0020   5 efngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallg 50 
                                   e+ +pa+  ++L    ++l g+k+++  lDP+ G G+ +I    lg
  gi|15669692|ref|NP_248505.1| 201 ERPHPATFPPKLPEMCIKLHGVKKTNLVLDPFMGIGSTAIACIRLG 246
                                   56799********************************999655555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   5.9e-05      0.12      75      96 .]      52      73 ..       3      73 .. 0.65
   2 !    7.0   0.0    0.0044       8.9       5      42 ..     233     270 ..     229     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.9e-05
                                  CCHHHHHHHHHHHEEEEEEEEE CS
               Methyltransf_11 75 edpekalkeiaRvLkpgGllvi 96
                                  +  e+++kei+RvLk +G ++i
  gi|15669692|ref|NP_248505.1| 52 NWIEEVVKEIKRVLKDDGSFFI 73
                                  46789*************9986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0044
                                   -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT CS
               Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseeg 42 
                                   +G G+ a a+ + g +++g++++++  ++a+e++++e 
  gi|15669692|ref|NP_248505.1| 233 MGIGSTAIACIRLGIDYIGFEIDEYYCRVAEERIKKEL 270
                                   79999999999**********************99986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.013        26      82      97 .]      54      69 ..       4      69 .. 0.69
   2 !    9.0   0.0    0.0011       2.3       1      45 [.     228     270 ..     228     285 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.013
                                  HHHHHHHHHHHEEEEE CS
               Methyltransf_25 82 lekalkeiarvLkpgG 97
                                  +e+++kei+rvLk++G
  gi|15669692|ref|NP_248505.1| 54 IEEVVKEIKRVLKDDG 69
                                  5899*********998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0011
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTT CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeg 45 
                                   vLd   G G +++a+ + +   +++g++i+e +++ a+er+++e 
  gi|15669692|ref|NP_248505.1| 228 VLDPFMGIGSTAIACIRLG--IDYIGFEIDEYYCRVAEERIKKEL 270
                                   89999***********995..********************8764 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00026      0.52      54      89 ..       7      41 ..       2      67 .. 0.79
   2 ?    3.2   0.0     0.029        57       2      39 ..     226     263 ..     225     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00026
               Methyltransf_15 54 vlgdvfellaklklekikvdlvflSpPwG.GpsYkkq 89
                                   + d++e +++lk +++  d+v++SpP   G++Y+k 
  gi|15669692|ref|NP_248505.1|  7 YCMDCLEGMKQLKDKTV--DVVVTSPPYNiGIKYNKY 41
                                  35599999999999988..********8559999875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.029
               Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaq 39 
                                   +++lD+f G G  +i+  + +   i+ ei++  + +a+
  gi|15669692|ref|NP_248505.1| 226 NLVLDPFMGIGSTAIACIRLGIDYIGFEIDEYYCRVAE 263
                                   579*************9999999999999998887765 PP

>> HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.2e-05     0.064      11      41 ..      43      73 ..      39      76 .. 0.91
   2 ?   -3.3   0.0       4.2   8.4e+03      52      65 ..     142     155 ..     139     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-05
               HU-CCDC81_bac_2 11 egisyeeAlqkiekeveelkqeLeeegrvel 41
                                   ++s e+ l++ie+ v+e+k+ L+++g++ +
  gi|15669692|ref|NP_248505.1| 43 DNLSREDYLNWIEEVVKEIKRVLKDDGSFFI 73
                                  589************************9976 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.2
               HU-CCDC81_bac_2  52 egkleFepseagnl 65 
                                    + ++F+ +++gn 
  gi|15669692|ref|NP_248505.1| 142 MHEYIFHFTKNGNV 155
                                   56788888888876 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00023      0.46      96     151 ..       7      60 ..       2      69 .. 0.80
   2 ?    1.5   0.0       0.1   2.1e+02      42      99 ..     225     283 ..     196     290 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00023
                                   EEES-HHHHCTS--SS-EEEEEEE--SSSTTCH.HHHHHHHHHTT-EEEEEEEEEE CS
                 Cons_hypoth95  96 lkedaleallklakkkeefdivflDPPyakellieevlelleekkllkenalvvve 151
                                   + +d le +++l  k++ +d+v   PPy+ +  +++  + l ++  l+    vv e
  gi|15669692|ref|NP_248505.1|   7 YCMDCLEGMKQL--KDKTVDVVVTSPPYNIGIKYNKYSDNLSREDYLNWIEEVVKE 60 
                                   556667777777..77889************99********999999866665555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.1
                                   C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCC..CT--TTTEEEEES CS
                 Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenlee..lkleeetaelked 99 
                                    + vLD f G G+ ++ ++  g++  + +e d+  +++ +e +++  lk++++++++k++
  gi|15669692|ref|NP_248505.1| 225 TNLVLDPFMGIGSTAIACIRLGID-YIGFEIDEYYCRVAEERIKKelLKTDGKFDNVKNK 283
                                   45699********99988866654.45567777777777776654224444466666655 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00012      0.23     109     138 ..       6      35 ..       1      73 [. 0.74
   2 ?   -0.4   0.0      0.27   5.3e+02      31      62 ..     209     240 ..     206     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                      N6_Mtase 109 irlgdtlekpkfekdkkfdvvvaNppfnqk 138
                                   i   d le  k+ kdk++dvvv+ pp+n+ 
  gi|15669692|ref|NP_248505.1|   6 IYCMDCLEGMKQLKDKTVDVVVTSPPYNIG 35 
                                   67778888888889**************85 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.27
                      N6_Mtase  31 PrevsklivellepksgesvyDpacGsggllv 62 
                                   P ++ ++ ++l   k+ + v+Dp +G g+  +
  gi|15669692|ref|NP_248505.1| 209 PPKLPEMCIKLHGVKKTNLVLDPFMGIGSTAI 240
                                   7778889999999999999*******999765 PP

>> VPR  VPR/VPX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00018      0.36      11      32 ..      43      64 ..      37      69 .. 0.88
   2 ?   -1.0   0.0      0.95   1.9e+03      65      83 ..     135     153 ..     124     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                           VPR 11 eepqrEpfdeWleetleeikee 32
                                  ++++rE + +W+ee+++eik+ 
  gi|15669692|ref|NP_248505.1| 43 DNLSREDYLNWIEEVVKEIKRV 64
                                  6899****************96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.95
                           VPR  65 aykylrllqkalfvHfrag 83 
                                     ++l ++   +f   ++g
  gi|15669692|ref|NP_248505.1| 135 SDRFLSIMHEYIFHFTKNG 153
                                   5789999999999555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1934.76
//
Query:       gi|15669693|ref|NP_248506.1|  [L=160]
Description: hypothetical protein MJ_1499 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0012   17.8   2.4     0.0061   15.5   0.4    2.1  2  Phage_min_cap2  Phage minor capsid protein 2
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.027   14.5   0.0    1.3  1  MutS_V          MutS domain V


Domain annotation for each model (and alignments):
>> Phage_min_cap2  Phage minor capsid protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   6.8e-07    0.0061     244     291 ..      27      75 ..       5      90 .. 0.72
   2 !    2.5   0.1    0.0059        53     109     133 ..     111     135 ..     101     160 .] 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.8e-07
                Phage_min_cap2 244 rsgkeeteekkk.pdllsetgyGegdGllginCrHnlfpfipGvnskre 291
                                   + +++++++  k ++ +++++y   +G++gi Cr ++  +i+G+n  ++
  gi|15669693|ref|NP_248506.1|  27 IAQNQNVQTGTKeYYQVEAVKYLLNNGHCGIDCRAKISDIIKGINYPKN 75 
                                   44444444444446667***************************65543 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.0059
                Phage_min_cap2 109 seelqqlveaylkqtegelkNltnt 133
                                   ++e++++ ++++k++e+el+Nl  +
  gi|15669693|ref|NP_248506.1| 111 NDEIKKVAKQVFKRIESELENLEGS 135
                                   6677777777777777777777543 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     3e-06     0.027      15      75 ..      87     152 ..      85     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-06
                                   HHHHHHHHHHH....HHT--BSSSEEEEE.--SEEEEEE--------SS-HHHHHHHHHHHHHTT- CS
                        MutS_V  15 lrqvalivlla....qiGsfvpaekaeis.ivdkiftRvgasDdlakgkstFmvEmlEtasilkna 75 
                                   l+q ++i+ l     + G f+p+++ ei+ +++++f R+ ++ +  +g++t +++++++a+ lk++
  gi|15669693|ref|NP_248506.1|  87 LKQYGIIATLVypgrKGGVFIPCNNDEIKkVAKQVFKRIESELENLEGSATGVQNIKNLANSLKTT 152
                                   5677777766512224589*********735689**************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1373  (0.0765798); expected 358.6 (0.02)
Passed bias filter:                      856  (0.0477439); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1020.96
//
Query:       gi|15669694|ref|NP_248507.1|  [L=230]
Description: hypothetical protein MJ_1500 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.078   12.8   0.8       0.13   12.1   0.8    1.5  1  CBM_11     Carbohydrate binding domain (family 11)
        0.6   11.2   3.1       0.72   10.9   0.7    2.5  3  RNase_J_C  Ribonuclease J C-terminal domain


Domain annotation for each model (and alignments):
>> CBM_11  Carbohydrate binding domain (family 11)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   1.5e-05      0.13      49      99 ..      96     148 ..      49     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                                   E.--SSSEEEEE.EE-S----TTT-EEEEEEEES..SS---EEEEEEEE-SSS CS
                        CBM_11  49 dingsngywldvakeldrqdwskfqglsFwvkgd..gsgnevrleIkdkeeng 99 
                                   d+ +  gy+ + + ++++q   ++  + Fw+kg+    g+ v +eIk+ +e+ 
  gi|15669694|ref|NP_248507.1|  96 DVLNKYGYAITPKTKKGKQKSTGYPDIEFWYKGKkeRDGRVVYIEIKTFNEKN 148
                                   5667789999999999999999***********97789*********987653 PP

>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.6   1.4e+04      19      32 ..       7      20 ..       2      25 .. 0.64
   2 ?   10.9   0.7   8.1e-05      0.72      12      45 ..      45      78 ..      43     108 .. 0.78
   3 ?   -2.8   0.0       1.6   1.4e+04      37      53 ..     195     211 ..     191     220 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
                     RNase_J_C 19 ieeakkvvretiee 32
                                   ee+++++r++++ 
  gi|15669694|ref|NP_248507.1|  7 YEEIESILRQILQP 20
                                  56777777777664 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.1e-05
                     RNase_J_C 12 vkeseeLieeakkvvretieealeekesdwnelk 45
                                  +ke++eLi++++k++ e+iee++++++++++e k
  gi|15669694|ref|NP_248507.1| 45 KKEDKELINDLAKACNEVIEEIKKTGGVKTKEGK 78
                                  699*******************999776666544 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.6
                     RNase_J_C  37 kesdwnelkrkirealk 53 
                                   k++d ++lk  i+++ +
  gi|15669694|ref|NP_248507.1| 195 KIIDLSKLKGGIKREFN 211
                                   56788888888887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1468.49
//
Query:       gi|15669695|ref|NP_248508.1|  [L=223]
Description: hypothetical protein MJ_1501 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-22   78.4   3.2    5.7e-22   78.1   0.8    2.1  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    9.1e-05   22.9   1.4    0.00039   20.8   0.2    2.0  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    0.00021   21.6   0.6     0.0011   19.2   0.1    2.1  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00045   20.2   0.0    0.00077   19.5   0.0    1.4  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    0.00052   19.1   0.1     0.0011   18.0   0.1    1.6  1  PDH              Prephenate dehydrogenase
      0.008   16.9   4.7       0.18   12.5   0.6    2.3  2  PTS_IIB          PTS system, Lactose/Cellobiose specific IIB 
  ------ inclusion threshold ------
      0.028   14.3   5.0        2.2    8.2   1.7    2.1  2  RcpB             Rough colony protein B, tight adherence - ta
      0.032   13.7   0.0        3.5    7.0   0.0    2.1  2  Rep_1            Replication protein
      0.055   13.4   0.1       0.11   12.5   0.1    1.4  1  Peptidase_S24    Peptidase S24-like
      0.061   13.1   0.3       0.23   11.2   0.0    2.0  2  FMN_red          NADPH-dependent FMN reductase
      0.068   12.2   0.0      0.087   11.9   0.0    1.2  1  Exo70            Exo70 exocyst complex subunit
      0.069   13.0   0.1       0.11   12.4   0.1    1.3  1  Complex1_51K     Respiratory-chain NADH dehydrogenase 51 Kd s
      0.097   12.1   0.8       0.27   10.7   0.4    1.8  2  adh_short        short chain dehydrogenase
       0.14   11.8   0.7       0.36   10.5   0.3    1.8  2  ApbA             Ketopantoate reductase PanE/ApbA
       0.17   11.9   0.1       0.42   10.6   0.1    1.6  1  DUF218           DUF218 domain


Domain annotation for each model (and alignments):
>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.8   4.8e-25   5.7e-22       1      97 []       2     102 ..       2     102 .. 0.97
   2 ?   -0.1   0.0       1.2   1.4e+03      84      96 ..     164     176 ..     135     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 4.8e-25
                                   EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE-S-H CS
                 F420_oxidored   1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvlavkp 71 
                                   ki+i+ G+G++g++la++l++++    +i+++ sr++ekaee+a++++         +++++ +n++aa+e dvv+l++++
  gi|15669695|ref|NP_248508.1|   2 KIAILgGTGDQGFGLALRLAKNN----KIIIG-SRKKEKAEEAAKKAKeilkqrgieADIIGLENKDAAKEGDVVILSLPY 77 
                                   7*********************7....99978.*************999******************************** PP

                                   HHHHHHHHHCGHHHHTTSEEEEESSS CS
                 F420_oxidored  72 edveevlselakdalkgklvisvlag 97 
                                   e++ +++++l k++lkgk+v+s+ ++
  gi|15669695|ref|NP_248508.1|  78 EYTLSTIKQL-KEELKGKIVVSIGVP 102
                                   **********.999********9875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                                   HHHTTSEEEEESS CS
                 F420_oxidored  84 dalkgklvisvla 96 
                                   d+ ++k+vi+ ++
  gi|15669695|ref|NP_248508.1| 164 DEEAKKVVIDLAN 176
                                   6788999999988 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   3.3e-07   0.00039       1      94 [.       2      97 ..       2     101 .. 0.75
   2 ?    0.9   0.1      0.48   5.8e+02      49      86 ..     140     175 ..     120     188 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.3e-07
                                  EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTT.TTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHH CS
                Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssr.saGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvskel 82
                                  k+ai+G+tG  G  l+ +L+++ ++ +     ++  +a kk +e  k+   ++d+   + ++++ ke d+v+l+lp +++ + 
  gi|15669695|ref|NP_248508.1|  2 KIAILGGTGDQGFGLALRLAKNNKIIIGSRKKEKAeEAAKKAKEILKQRGIEADIIGLE-NKDAAKEGDVVILSLPYEYTLST 83
                                  79*************99999987766655444443477777777777655555555555.78899****************** PP

                                  HHHHHH..TTSEEE CS
                Semialdhyde_dh 83 apklae..agvkvi 94
                                   ++l e  +g +v+
  gi|15669695|ref|NP_248508.1| 84 IKQLKEelKGKIVV 97
                                  **996511355665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.48
                                   TTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHHHH CS
                Semialdhyde_dh  49 eegkdlkvedvdeeelkevdivflalpagvskelapkl 86 
                                   ++++  ++ed   ++  ++di+++  ++++ k + + +
  gi|15669695|ref|NP_248508.1| 140 QNVCHAVLED--LDNPVDCDILVCGNDEEAKKVVIDLA 175
                                   4555666666..44445677777666655555444433 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   9.4e-07    0.0011       1      85 [.       3      83 ..       3     102 .. 0.83
   2 ?    0.3   0.0      0.65   7.8e+02       9      42 ..     142     173 ..     139     199 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.4e-07
                                  EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGGH CS
               Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppiss 82
                                  + i+G+ G  G ++a  la+++    +i++ +r+kek+e++a+k +++ ++++ + a+ +    + + kegd+v+  +p+ ++
  gi|15669695|ref|NP_248508.1|  3 IAILGGtGDQGFGLALRLAKNN----KIIIGSRKKEKAEEAAKK-AKEILKQRGIEADIIGLENKDAAKEGDVVILSLPYEYT 80
                                  6799999*************98....68*********9988876.56667777777777777777779999999977777676 PP

                                  HHH CS
               Sacchrp_dh_NADP 83 ldv 85
                                  l+ 
  gi|15669695|ref|NP_248508.1| 81 LST 83
                                  655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.65
                                   HHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHC CS
               Sacchrp_dh_NADP   9 vGqavaellarhfdvdaeitvadrskeklealaa 42 
                                   v++av+e+l +  d   +i v++ ++e  + +++
  gi|15669695|ref|NP_248508.1| 142 VCHAVLEDLDNPVDC--DILVCGNDEEAKKVVID 173
                                   677888888877777..78888877777544443 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   6.5e-07   0.00077       1      99 [.       2      96 ..       2     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.5e-07
                                  -EEEE-.-SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHHH CS
                NAD_Gly3P_dh_N  1 kiavlG.aGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsqal 82
                                  kia+lG +G  G  lA  la+n+ ++ + +r++e +ee   +++ ++ L++  +++++   ++ ++a+k+ d+++l +P +++
  gi|15669695|ref|NP_248508.1|  2 KIAILGgTGDQGFGLALRLAKNN-KIIIGSRKKEKAEEA--AKKAKEILKQRGIEADIIGLEN-KDAAKEGDVVILSLPYEYT 80
                                  79999736**************9.888999999999975..5667789999999999988766.788899************* PP

                                  HHHHHHHCCC--TT-EE CS
                NAD_Gly3P_dh_N 83 revlkklkgllkkkail 99
                                   +++k+lk+ lk k  +
  gi|15669695|ref|NP_248508.1| 81 LSTIKQLKEELKGKI-V 96
                                  *********996553.3 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   9.4e-07    0.0011       1      74 [.      14      96 ..      14     100 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.4e-07
                                  HHHHHHHTT--SEEEEE-SSHHHHHHHHH.......TTSSSEE..ES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-E CS
                           PDH  1 laralrrkgfkvtvigydideekaeaale.......lglvdea..tddieavkeadivvlavPvevilevlkelaphlkedal 74
                                  +++alr    ++++ig  ++e++ eaa++       +g++ +    ++ +a+ke+d+v+l+ P e +l ++k+l++ lk + +
  gi|15669695|ref|NP_248508.1| 14 FGLALRLAKNNKIIIGSRKKEKAEEAAKKakeilkqRGIEADIigLENKDAAKEGDVVILSLPYEYTLSTIKQLKEELKGKIV 96
                                  5788888888899999876665554443311111113444332111225799************************9987765 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.6   0.00015      0.18      16      68 ..      39      94 ..      33     111 .. 0.70
   2 ?    6.1   0.2     0.015        18      16      66 ..     122     170 ..     121     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                  HHHHHHHHHHHCTEEEEETTEEGGGHHHHHHT-SEEEEEESSGG.....CTHHHHTT.S CS
                       PTS_IIB 16 aaeklekaakelgieaegeagveleaeeiaddaDlvllapqvrv.....kdlarfag.k 68
                                  aa+k ++++k++giea +     le+++ a++ D+v+l+   ++     k+l++  + k
  gi|15669695|ref|NP_248508.1| 39 AAKKAKEILKQRGIEADIIG---LENKDAAKEGDVVILSLPYEYtlstiKQLKEELKgK 94
                                  57888888888888886654...469999999*******98888765554444444433 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.015
                                   HHHHHHHHHHHCT.EEEEETTEE.GGGHHHHHHT-SEEEEEESSGGCTHHHHT CS
                       PTS_IIB  16 aaeklekaakelg.ieaegeagv.eleaeeiaddaDlvllapqvrvkdlarfa 66 
                                   +ae +++++ke   + a  + +   le+ +++ d+D+++++ + +     +++
  gi|15669695|ref|NP_248508.1| 122 VAEMVQNVLKESKvVSAFQNVCHaVLEDLDNPVDCDILVCGNDEEA----KKV 170
                                   67899999999998777666666799****************8874....222 PP

>> RcpB  Rough colony protein B, tight adherence - tad - subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.7    0.0018       2.2      76     118 ..      22      65 ..      18      70 .. 0.79
   2 ?    7.2   0.1    0.0035       4.2      53     127 ..     130     204 ..     122     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0018
                          RcpB  76 kdkqihiissdk.eakklakkirkrLkakgvkaksiklekkatk 118
                                   k+++i i s++k +a+++akk ++ Lk++g++a  i le+k+  
  gi|15669695|ref|NP_248508.1|  22 KNNKIIIGSRKKeKAEEAAKKAKEILKQRGIEADIIGLENKDAA 65 
                                   556666666655268999***************99999988754 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0035
                          RcpB  53 ladksdv.ayenlltevlrdvgsdkdkqihiissdkeakklakkirkrLkakgvkaksiklekkatknklYPiYve 127
                                   l +   v a++n+ + vl d+    d  i +  +d+eakk   ++ +++   +      +lek++ ++++ P+ + 
  gi|15669695|ref|NP_248508.1| 130 LKESKVVsAFQNVCHAVLEDLDNPVDCDILVCGNDEEAKKVVIDLANQIDGVRAID-CGNLEKSRIIEAITPLLIG 204
                                   5444444369***********************************99987655444.4678899999998888775 PP

>> Rep_1  Replication protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.013        16     150     205 ..      28     103 ..      14     113 .. 0.69
   2 ?    7.0   0.0    0.0029       3.5     166     204 ..     122     189 ..     108     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.013
                         Rep_1 150 vravkekkkkkkkekaveeiakYtvkpsdl.....................ekdeevleeLekalkgkRlialggll 205
                                   + + k+ +k++++ k+++ei+k    ++d+                     e   + +++L++ lkgk ++++g  l
  gi|15669695|ref|NP_248508.1|  28 IGSRKK-EKAEEAAKKAKEILKQRGIEADIiglenkdaakegdvvilslpyEYTLSTIKQLKEELKGKIVVSIGVPL 103
                                   444444.333335699******99999999998766665555555555554444455*********99999888655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0029
                         Rep_1 166 veeiakYtvkpsdl.............................ekdeevleeLekalkgkRlialggl 204
                                   v+e+++ + k+s++                             e+ ++v+ +L++++ g R+i +g l
  gi|15669695|ref|NP_248508.1| 122 VAEMVQNVLKESKVvsafqnvchavledldnpvdcdilvcgndEEAKKVVIDLANQIDGVRAIDCGNL 189
                                   5566666666666666666666666666666777788888888888999**************99865 PP

>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   9.3e-05      0.11      15      56 ..      55      97 ..      52     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.3e-05
                                  XEEEEECTS---TTSEEEEEETTCE.-EEEEEEEEETTEEEEE CS
                 Peptidase_S24 15 dlilVdkfsepkrGdivvfrlpgee.eayiKrviglpgdrvll 56
                                  d+i  +  + +k Gd+v+  lp e    +iK+++++ ++++ +
  gi|15669695|ref|NP_248508.1| 55 DIIGLENKDAAKEGDVVILSLPYEYtLSTIKQLKEELKGKIVV 97
                                  899999999****************99*******877777664 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00019      0.23       5      44 ..      26      65 ..      25      98 .. 0.80
   2 ?   -0.9   0.0         1   1.2e+03      19      55 ..     122     160 ..     120     184 .. 0.41

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                  EEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..- CS
                       FMN_red  5 visGSlrkgsntrklaewaaealkeagaevelidladl.il 44
                                  +i+GS  k+ + + +a+ a+e lk++g+e+++i l ++ ++
  gi|15669695|ref|NP_248508.1| 26 IIIGSR-KKEKAEEAAKKAKEILKQRGIEADIIGLENKdAA 65
                                  689995.8899************************997544 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                                   HHHHHHCCT-T....T-CEEEEE......TTTS.--..---HCHGH CS
                       FMN_red  19 laewaaealkea...gaevelid......ladlilpcalcdkdles 55 
                                   +ae++++ lke+         ++      l dl+ p   +d+d   
  gi|15669695|ref|NP_248508.1| 122 VAEMVQNVLKESkvvS----AFQnvchavLEDLDNP---VDCDILV 160
                                   6777777777763320....2222222334444333...3333322 PP

>> Exo70  Exo70 exocyst complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.2e-05     0.087     123     170 ..     105     152 ..      73     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.2e-05
                         Exo70 123 esikkdsskspvppdggvheltrnvmnylrkLleykdtlssllkdlkd 170
                                    +i  ++++  +ppdg+v e+++nv+   +  + ++++++ +l+dl++
  gi|15669695|ref|NP_248508.1| 105 TAIGDKPTRLLFPPDGSVAEMVQNVLKESKVVSAFQNVCHAVLEDLDN 152
                                   555566677899*******************************99887 PP

>> Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   9.1e-05      0.11      59     137 ..      13     105 ..      12     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.1e-05
                  Complex1_51K  59 Glkiaaealgaekgvigvrdekpeaiealekalaeakaagl...............ldievvklagkYpaGeekaLieslt 124
                                   G+ +a ++ + +k++ig r++ ++a ea +ka +  k++g+                d+ + +l+  Y+    k+L e+l+
  gi|15669695|ref|NP_248508.1|  13 GFGLALRLAKNNKIIIGSRKK-EKAEEAAKKAKEILKQRGIeadiiglenkdaakeGDVVILSLPYEYTLSTIKQLKEELK 92 
                                   788999999999****99877.44444455554444444444557788888888889************************ PP

                  Complex1_51K 125 grevprgkppadv 137
                                   g+ v + + p+  
  gi|15669695|ref|NP_248508.1|  93 GKIVVSIGVPLAT 105
                                   **77777777443 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4   0.00022      0.27       3      58 ..       3      56 ..       2      68 .. 0.78
   2 ?   -3.6   0.0       5.3   6.3e+03      27      47 ..     158     177 ..     153     187 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                                  EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TT CS
                     adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDv 58
                                  + + G+++  G  +a +lak+  k+++ +r++ek+ee+ak+ ke   k   i++D+
  gi|15669695|ref|NP_248508.1|  3 IAILGGTGDQGFGLALRLAKN-NKIIIGSRKKEKAEEAAKKAKEI-LKQRGIEADI 56
                                  567777777788889999988.788999**************997.4566677666 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.3
                                   EEEEESCHHHHHHHHHHHHHT CS
                     adh_short  27 vvvvdrseekleevakelkee 47 
                                   ++v+++  e++++v+  l ++
  gi|15669695|ref|NP_248508.1| 158 ILVCGND-EEAKKVVIDLANQ 177
                                   5555555.4456666666655 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3    0.0003      0.36       2     100 ..       4      98 ..       3     100 .. 0.72
   2 ?   -1.3   0.0       1.3   1.6e+03      84     104 ..     122     142 ..     118     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                                   EEE.S-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT..CEEEEEECEEECCHSCCCCS-ESEEEE-SSG CS
                          ApbA   2 ail.GaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg..geeilrppealsaeekselepidlvivtvKa 78 
                                   ail G+G +G  la +Lak ++++++  r++ ++e+  k+  ++ + +  +  i+  +++        +++ d+vi++++ 
  gi|15669695|ref|NP_248508.1|   4 AILgGTGDQGFGLALRLAK-NNKIIIGSRKKeKAEEAAKKAKEILKQRgiEADIIGLENKD------AAKEGDVVILSLPY 77 
                                   555268999*99*****77.67788888888788886555555555553534444333333......34589********* PP

                                   GGHHHHHHHHGGGECTCEEEEE CS
                          ApbA  79 yqteealeeikplldpntvvll 100
                                     t + ++++k+ l+ + +v++
  gi|15669695|ref|NP_248508.1|  78 EYTLSTIKQLKEELKGK-IVVS 98 
                                   ************99998.6665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                                   HHHHHGGGECTCEEEEEESSS CS
                          ApbA  84 aleeikplldpntvvlllqNG 104
                                   ++e ++++l++  vv  +qN 
  gi|15669695|ref|NP_248508.1| 122 VAEMVQNVLKESKVVSAFQNV 142
                                   567788899999999999985 PP

>> DUF218  DUF218 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00035      0.42      17      65 ..      14      62 ..       2      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00035
                        DUF218 17 ldeaaelyragkiivsGggadedvseaeamaeylrelgvpeeailledr 65
                                     a++l++++kii+   ++++ ++ a+ ++e+l+++g++++ i le++
  gi|15669695|ref|NP_248508.1| 14 FGLALRLAKNNKIIIGSRKKEKAEEAAKKAKEILKQRGIEADIIGLENK 62
                                  55699******977765555567777888***********855656665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      713  (0.039768); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1471.56
//
Query:       gi|15669696|ref|NP_248509.1|  [L=324]
Description: hypothetical protein MJ_1502 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-20   72.7   0.0    4.1e-19   68.9   0.0    2.0  1  Lactamase_B_2  Beta-lactamase superfamily domain
    8.6e-10   38.9   0.3    7.9e-09   35.8   0.0    2.3  3  Lactamase_B    Metallo-beta-lactamase superfamily
    3.3e-05   23.5   0.0    6.8e-05   22.5   0.0    1.5  1  Lactamase_B_4  tRNase Z endonuclease


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.0   6.8e-23   4.1e-19       3     201 .]      41     281 ..      40     281 .. 0.82

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 6.8e-23
                                   EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.....C--EEEEEEEEHHHHHHCCTTCGHHH CS
                 Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.....lrpkklplyapkgvlavleanfvyla 78 
                                   +L+D+g ++  q+l +        ++ +i+ +++th H DH+ g++ l +     +r+k+l++++p+g+ +++e++++   
  gi|15669696|ref|NP_248509.1|  41 FLFDCGENIQRQMLFTE------VSPMKINHIFITHLHGDHILGIPGLLQsmgffGREKELKIFGPEGTKEIIENSLKLGT 115
                                   79******988866555......34679*************************9888888*****************9999 PP

                                   CHTTTTEEEEEE-TTSEEEE.CSTTEEEEEEEE-EE--C...........TCCE-TTTSEEEEEECTTEE........... CS
                 Lactamase_B_2  79 leeepavnvheldwgesfel.gdggleitatparhksgr...........rldrnagdtlGlriegggkr........... 136
                                      e++++v e+ ++e++++ ++++ ei a p +h+ +            rld ++ + lG+ i+ + k+           
  gi|15669696|ref|NP_248509.1| 116 HYIEFPIKVYEIYTKEPITIyKEENYEIIAYPTEHGIPSyayifkeikkpRLDIEKAKKLGVKIGPDLKKlkngeavkniy 196
                                   9999*****************88899******************9999995555555555555553333333344455566 PP

                                   ..................EEEESS-S---HHHHHHHCT..-SEEEEE-S-SSTTHHHH.HHT---STSHHHHCTTSSSSEE CS
                 Lactamase_B_2 137 ..................vyyigDtgyipeeigerlgg..adllllditayeddemir.hmgHltpeeaveaaadlgakrl 196
                                                     ++y+gDt  ++ + g+ l+   +d+l++++t+ ++ +  + ++ H+t+++av +a+ +++k l
  gi|15669696|ref|NP_248509.1| 197 geiikpeyvllppkkgfcLAYSGDTLPLE-DFGKYLKElgCDVLIHEATFDDSAKDAAkENMHSTIGDAVNIAKLANVKAL 276
                                   666666666666666666********999.4455555444*********9888775559********************** PP

                                   EEESB CS
                 Lactamase_B_2 197 vliHi 201
                                   +l+Hi
  gi|15669696|ref|NP_248509.1| 277 ILTHI 281
                                   ****8 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   1.3e-12   7.9e-09      14      68 ..      37      86 ..      33     153 .. 0.84
   2 ?   -2.9   0.0      0.99   5.9e+03     146     162 ..     216     232 ..     215     257 .. 0.71
   3 ?    0.5   0.1     0.088   5.3e+02      41      52 ..     269     280 ..     257     281 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.3e-12
                                  TTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHH CS
                   Lactamase_B 14 dggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveat 68
                                  +g+v+L+D+G   ++++++      ++ p ++ ++++THlH DHi g +gl +  
  gi|15669696|ref|NP_248509.1| 37 GGEVFLFDCGENIQRQMLF-----TEVSPMKINHIFITHLHGDHILGIPGLLQSM 86
                                  699***************9.....9*************************99865 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.99
                                   EEECTTTSSHHCCCCCC CS
                   Lactamase_B 146 lftGDallagetgridl 162
                                   +++GD+l+ ++ g+  +
  gi|15669696|ref|NP_248509.1| 216 AYSGDTLPLEDFGKYLK 232
                                   68999998888776655 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.088
                                   GGGGEEEEE-SB CS
                   Lactamase_B  41 kpkdvdavilTH 52 
                                   k+ +v+a+ilTH
  gi|15669696|ref|NP_248509.1| 269 KLANVKALILTH 280
                                   6789******** PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.1e-08   6.8e-05      14      63 .]      31      78 ..      19      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-08
                 Lactamase_B_4 14 lllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkvswssigG 63
                                   +++++  + +lf ++gE +QR +   +v+  k+++iF+t+ +  ++i G
  gi|15669696|ref|NP_248509.1| 31 GIAFKFGGEVFLF-DCGENIQRQMLFTEVSPMKINHIFITHLH-GDHILG 78
                                  5777777889***.***************************99.777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2061.43
//
Query:       gi|15669697|ref|NP_248510.1|  [L=132]
Description: hypothetical protein MJ_1503 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-21   74.9   0.0    4.9e-21   74.4   0.0    1.2  1  TrmB             Sugar-specific transcriptional regulator Trm
    3.2e-07   29.8   0.0    5.1e-07   29.2   0.0    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
    9.6e-07   28.6   0.0    1.3e-06   28.2   0.0    1.2  1  MarR_2           MarR family
    6.7e-06   25.9   0.4    8.7e-06   25.6   0.4    1.1  1  TFIIE_alpha      TFIIE alpha subunit
      9e-06   25.5   0.0    1.4e-05   24.9   0.0    1.3  1  MarR             MarR family
      1e-05   25.2   0.0    1.4e-05   24.8   0.0    1.2  1  HTH_IclR         IclR helix-turn-helix domain
    0.00017   21.5   0.1     0.0005   20.0   0.0    1.7  2  HTH_36           Helix-turn-helix domain
    0.00027   21.0   0.1    0.00078   19.6   0.0    1.8  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    0.00077   19.2   0.0     0.0013   18.5   0.0    1.3  1  HTH_38           Helix-turn-helix domain
    0.00079   19.4   0.0     0.0012   18.8   0.0    1.3  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00091   19.1   0.0     0.0015   18.5   0.0    1.4  1  HTH_11           HTH domain
     0.0015   18.1   0.1     0.0024   17.5   0.1    1.3  1  GntR             Bacterial regulatory proteins, gntR family
     0.0027   18.0   0.0     0.0047   17.3   0.0    1.4  1  Rrf2             Transcriptional regulator
     0.0031   18.0   0.0     0.0063   17.0   0.0    1.5  1  HTH_27           Winged helix DNA-binding domain
     0.0031   17.1   0.0     0.0044   16.7   0.0    1.3  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
     0.0066   16.8   0.1     0.0085   16.4   0.1    1.2  1  Penicillinase_R  Penicillinase repressor
     0.0085   16.1   0.0      0.015   15.3   0.0    1.3  1  Dimerisation2    Dimerisation domain
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.026   14.4   0.0    1.5  1  HTH_Tnp_Tc3_1    Tc3 transposase
      0.015   15.2   0.0      0.026   14.4   0.0    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
       0.03   13.9   0.0      0.054   13.1   0.0    1.5  1  HTH_47           winged helix-turn-helix
      0.032   14.5   0.4       0.04   14.2   0.4    1.2  1  ESCRT-II         ESCRT-II complex subunit
      0.034   14.3   0.5      0.066   13.4   0.4    1.7  1  FPRL1_inhibitor  Formyl peptide receptor-like 1 inhibitory pr
      0.049   13.4   0.0      0.096   12.5   0.0    1.4  1  HTH_23           Homeodomain-like domain
      0.057   13.1   0.1      0.099   12.3   0.1    1.4  1  DUF4423          Domain of unknown function (DUF4423)
      0.065   13.3   1.4        3.8    7.7   0.5    2.3  2  DUF148           Domain of unknown function DUF148
      0.076   13.0   0.3       0.16   12.0   0.1    1.6  2  HTH_45           Winged helix-turn-helix
       0.08   12.6   0.0       0.12   12.1   0.0    1.2  1  RP-C             Replication protein C N-terminal domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   7.4e-24   4.9e-21       2      68 .]      20      93 ..      19      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 7.4e-24
                                  H.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE--HH CS
                          TrmB  2 q.klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYravdpe 68
                                  + ++G++  ++kvY+ +lk+gp+++++iae+++++rs+v++++++L+++GlV+r++ +      +++Y+a+++e
  gi|15669697|ref|NP_248510.1| 20 AcVFGIKVSDVKVYFDILKNGPSKINDIAERINRDRSTVQRAVQNLMNAGLVKRKQVNikdggyYYVYEAIPFE 93
                                  558************************************************************999******87 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   7.6e-10   5.1e-07       7      48 .]      31      72 ..      27      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 7.6e-10
                        HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  k++  + kn+   ++++Aer++  +stv r +++L+++Gl+k
  gi|15669697|ref|NP_248510.1| 31 KVYFDILKNGPSKINDIAERINRDRSTVQRAVQNLMNAGLVK 72
                                  6666689*********************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.9e-09   1.3e-06      15      54 ..      37      74 ..      24      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.9e-09
                                  HCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2 15 grrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                    +++    ++++a+r + ++s+v+r+++ L  aGLv r+
  gi|15669697|ref|NP_248510.1| 37 LKNGP--SKINDIAERINRDRSTVQRAVQNLMNAGLVKRK 74
                                  55565..589***************************997 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.4   1.3e-08   8.7e-06      15     101 ..      29     115 ..      17     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.3e-08
                                   HHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHHHH CS
                   TFIIE_alpha  15 avlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevvkk 95 
                                    v+v + +l++g  + +d+a+ ++ d+  + +++ +L +a+lvk k+    + + y +y  i  e+  +++k+ +ee   +
  gi|15669697|ref|NP_248510.1|  29 DVKVYFDILKNGPSKINDIAERINRDRSTVQRAVQNLMNAGLVKRKQVNIKDGGYYYVYEAIPFEETKKIIKKTMEEWCNN 109
                                   4677777888**********************************8877779999999999*****************9999 PP

                                   HHHHHC CS
                   TFIIE_alpha  96 Leekle 101
                                   +++ +e
  gi|15669697|ref|NP_248510.1| 110 MKKWVE 115
                                   998655 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   2.1e-08   1.4e-05      12      51 ..      36      75 ..      28      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.1e-08
                                  HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                  +  +gp ++ ++a++++ ++stv r++  L  +Gl++R++
  gi|15669697|ref|NP_248510.1| 36 ILKNGPSKINDIAERINRDRSTVQRAVQNLMNAGLVKRKQ 75
                                  66789999******************************97 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.1e-08   1.4e-05      16      50 ..      39      73 ..      34      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.1e-08
                                  BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  +++ ++ ++A+r+   +Stv R +q L++ G+v++
  gi|15669697|ref|NP_248510.1| 39 NGPSKINDIAERINRDRSTVQRAVQNLMNAGLVKR 73
                                  456689***************************98 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   7.6e-07    0.0005      28      55 .]      44      71 ..      36      71 .. 0.92
   2 ?   -1.8   0.0       4.7   3.1e+03      40      50 ..     108     118 ..      92     118 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.6e-07
                        HTH_36 28 qetlakrlglsknTvsraikeLeqlGyi 55
                                    ++a+r + +++Tv+ra+++L+ +G++
  gi|15669697|ref|NP_248510.1| 44 INDIAERINRDRSTVQRAVQNLMNAGLV 71
                                  579***********************85 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.7
                        HTH_36  40 nTvsraikeLe 50 
                                   n   +++ eLe
  gi|15669697|ref|NP_248510.1| 108 NNMKKWVEELE 118
                                   55667777775 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.2e-06   0.00078      22      55 ..      41      74 ..      31      77 .. 0.88
   2 ?   -2.2   0.1       7.3   4.8e+03       4      13 ..     121     130 ..     118     130 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-06
                                  SB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                Fe_dep_repress 22 vvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                  + k  d+aer+n   s+V+  ++ L ++G+v+ +
  gi|15669697|ref|NP_248510.1| 41 PSKINDIAERINRDRSTVQRAVQNLMNAGLVKRK 74
                                  56778**************************866 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.3
                                   HHHHHHHHHH CS
                Fe_dep_repress   4 estEdYLetI 13 
                                   ++  +YLe I
  gi|15669697|ref|NP_248510.1| 121 DVVKEYLENI 130
                                   5677999987 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.9e-06    0.0013      23      42 ..      44      63 ..      35      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
                        HTH_38 23 lreIArrLgrspsTIsRElk 42
                                  + +IA r++r++sT++R ++
  gi|15669697|ref|NP_248510.1| 44 INDIAERINRDRSTVQRAVQ 63
                                  679**************985 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.8e-06    0.0012      25      61 ..      45      80 ..      35      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.8e-06
                                  HHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES- CS
                     HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrgrririld 61
                                   ++A++++  r+tv r+ + L ++gl++r++ + i+d
  gi|15669697|ref|NP_248510.1| 45 NDIAERINRDRSTVQRAVQNLMNAGLVKRKQ-VNIKD 80
                                  69**************************997.99998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.2e-06    0.0015      13      46 ..      39      76 ..      32      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-06
                        HTH_11 13 rgpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpI 46
                                  +gp  ++++Ae++n+ r+tv+r ++ L  +g     ++
  gi|15669697|ref|NP_248510.1| 39 NGPSKINDIAERINRDRSTVQRAVQNLMNAGlvkrKQV 76
                                  4556899********************99886555444 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.6e-06    0.0024      27      58 ..      44      75 ..      42      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.6e-06
                                  HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          GntR 27 ereLaaefgVsrttvReALrrLeaeglverrq 58
                                   +++a++++ +r+tv++A ++L  +glv r+q
  gi|15669697|ref|NP_248510.1| 44 INDIAERINRDRSTVQRAVQNLMNAGLVKRKQ 75
                                  5899**************************98 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     7e-06    0.0047      23      58 ..      39      74 ..      32      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7e-06
                                  CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvksv 58
                                  ++p ++++iaer n  +s +++ +++L +aglvk +
  gi|15669697|ref|NP_248510.1| 39 NGPSKINDIAERINRDRSTVQRAVQNLMNAGLVKRK 74
                                  56789****************************865 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   9.5e-06    0.0063      16      52 ..      39      75 ..      28      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.5e-06
                        HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertg 52
                                  ++++k+ d+++r n++ s++  ++  L ++GLv+r++
  gi|15669697|ref|NP_248510.1| 39 NGPSKINDIAERINRDRSTVQRAVQNLMNAGLVKRKQ 75
                                  78999****************************7664 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.6e-06    0.0044      22      65 ..      40      85 ..      29     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.6e-06
                  HrcA_DNA-bdg 22 ravKgeeiAevlkrneGtvRNqlqsLkalgLvegv..pGPkGGYkP 65
                                   + K ++iAe ++r+  tv   +q L   gLv+ +      GGY  
  gi|15669697|ref|NP_248510.1| 40 GPSKINDIAERINRDRSTVQRAVQNLMNAGLVKRKqvNIKDGGYYY 85
                                  566899**************************86511456788865 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.3e-05    0.0085      12      83 ..      36     110 ..      27     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                                   HHHHS-EEHHHHHHT--GGG---HHHHHHHHHH.HHHTTS-EEEEETTEEEEE---..-XXXXXXXXXXXXXXXX CS
               Penicillinase_R  12 lwekgeatvkevveeleeekelaysTVktllrr.LvkKgllsrekegrafiYsplv..seeeavasavkqlldkl 83 
                                   + ++g+ +++++ e++++++++ +  V+ l++  Lvk++ ++ +  g  ++Y +    + ++++++++++  +++
  gi|15669697|ref|NP_248510.1|  36 ILKNGPSKINDIAERINRDRSTVQRAVQNLMNAgLVKRKQVNIKDGGYYYVYEAIPfeETKKIIKKTMEEWCNNM 110
                                   778999*************88888888888885588888888888899999987641144455666666655554 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.2e-05     0.015      24      73 ..      34      82 ..      25      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                 Dimerisation2 24 FdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkal 73
                                  Fd+Lk+ +p + +++ae+++ + + ++r ++ ++  gL +r++ + k+++
  gi|15669697|ref|NP_248510.1| 34 FDILKN-GPSKINDIAERINRDRSTVQRAVQNLMNAGLVKRKQVNIKDGG 82
                                  9****9.*******************************998755445454 PP

>> HTH_Tnp_Tc3_1  Tc3 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.9e-05     0.026      13      40 ..      34      61 ..      23      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-05
                                  HHHHHHTT--HHHHHHHHT--HHHHHHH CS
                 HTH_Tnp_Tc3_1 13 llvmkllnvklsEiarklsRsRnCIrry 40
                                   + +k   +k+ +ia +++R R  ++r 
  gi|15669697|ref|NP_248510.1| 34 FDILKNGPSKINDIAERINRDRSTVQRA 61
                                  68889999**************998875 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.9e-05     0.026      10      46 ..      36      72 ..      35      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-05
                                  HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5 10 lLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  +L +g+ ++ ++ae ++  +stv +    L++aGLV+
  gi|15669697|ref|NP_248510.1| 36 ILKNGPSKINDIAERINRDRSTVQRAVQNLMNAGLVK 72
                                  5889********************************7 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.1e-05     0.054      45      77 ..      40      72 ..      26      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.1e-05
                                  EEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                        HTH_47 45 GkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                  G   + diAeri+ +  +v+ ++++L +agl++
  gi|15669697|ref|NP_248510.1| 40 GPSKINDIAERINRDRSTVQRAVQNLMNAGLVK 72
                                  777888*************************97 PP

>> ESCRT-II  ESCRT-II complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4     6e-05      0.04      66     119 ..      60     123 ..      42     131 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6e-05
                      ESCRT-II  66 ledirevleelvkkgraewv..dkek..........skalvywrtpeewasliyewveetgqkgsv 119
                                   ++  + + + lvk+++++ +  +             ++  ++ +t+eew + + +wvee   +++v
  gi|15669697|ref|NP_248510.1|  60 RAVQNLMNAGLVKRKQVNIKdgG--YyyvyeaipfeETKKIIKKTMEEWCNNMKKWVEELEFEDVV 123
                                   33333333446666666666440..2444444445355569******************9988877 PP

>> FPRL1_inhibitor  Formyl peptide receptor-like 1 inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   9.9e-05     0.066      55      94 ..      66     102 ..      35     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.9e-05
               FPRL1_inhibitor  55 lsqgdvkkavvrikdggprdyytfdltrpleenrknikvv 94 
                                   ++ g vk+  v ikdgg   yy ++ + p+ee +k ik  
  gi|15669697|ref|NP_248510.1|  66 MNAGLVKRKQVNIKDGGY--YYVYE-AIPFEETKKIIKKT 102
                                   46799***********94..66665.68*******99965 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014     0.096      22      46 ..      46      70 ..      43      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                        HTH_23 22 eIAreLgvsrrTvyrwlkryreeGl 46
                                  +IA++ ++ r+Tv+r ++   + Gl
  gi|15669697|ref|NP_248510.1| 46 DIAERINRDRSTVQRAVQNLMNAGL 70
                                  8***************998877775 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00015     0.099      33      73 ..      38      76 ..      34     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                       DUF4423 33 kdfkadpeelakrlrpkisaeevekalefLlklgllkkded 73
                                  k++ ++++ +a+r++   + + v++a++ L+++gl+k+++ 
  gi|15669697|ref|NP_248510.1| 38 KNGPSKINDIAERIN--RDRSTVQRAVQNLMNAGLVKRKQV 76
                                  66678999*******..*********************975 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.053        35       4      26 ..      31      53 ..      28      77 .. 0.79
   2 ?    7.7   0.5    0.0057       3.8      14      45 ..     100     131 ..      91     132 .] 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.053
                        DUF148  4 keffaIlknenltiaeieeqlea 26
                                  k +f+Ilkn    i+ i e+++ 
  gi|15669697|ref|NP_248510.1| 31 KVYFDILKNGPSKINDIAERINR 53
                                  66999999999999999998875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0057
                        DUF148  14 nltiaeieeqleawaekygvtdeykefeakvk 45 
                                   + t++e  +++++w+e+ +++d +ke+ ++++
  gi|15669697|ref|NP_248510.1| 100 KKTMEEWCNNMKKWVEELEFEDVVKEYLENIE 131
                                   468999999******************99986 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00024      0.16       3      53 ..      28      75 ..      26      86 .. 0.90
   2 ?   -1.8   0.0       4.9   3.3e+03      38      44 ..     112     118 ..      93     131 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                        HTH_45  3 skleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikksk 53
                                  s +++++dIL+   +g +k   i  + n + +++++ ++ L++ gl+k ++
  gi|15669697|ref|NP_248510.1| 28 SDVKVYFDILK---NGPSKINDIAERINRDRSTVQRAVQNLMNAGLVKRKQ 75
                                  56899*****9...9********************************7765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.9
                        HTH_45  38 kYLdmLv 44 
                                   k+++ L 
  gi|15669697|ref|NP_248510.1| 112 KWVEELE 118
                                   3333333 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00018      0.12      76     104 ..      46      74 ..      41      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                          RP-C  76 qLsralglsestlrrhlaaLveaGliirr 104
                                   ++++++++ +st++r +++L++aGl+ r+
  gi|15669697|ref|NP_248510.1|  46 DIAERINRDRSTVQRAVQNLMNAGLVKRK 74 
                                   678999********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1814  (0.101177); expected 358.6 (0.02)
Passed bias filter:                     1009  (0.0562775); expected 358.6 (0.02)
Passed Vit filter:                       132  (0.00736237); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 811.64
//
Query:       gi|15669698|ref|NP_248511.1|  [L=366]
Description: lipopolysaccharide biosynthesis protein WbpI [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.6e-127  424.0   0.2   4.1e-127  423.8   0.2    1.0  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
    1.6e-05   24.9   0.0    3.5e-05   23.8   0.0    1.6  1  Glyco_trans_4_2  Glycosyl transferase 4-like
     0.0017   18.4   0.0     0.0046   17.0   0.0    1.8  1  Glyco_transf_4   Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.8   0.2  6.9e-131  4.1e-127       4     346 ..      24     361 ..      21     362 .. 0.96

  Alignments for each domain:
  == domain 1  score: 423.8 bits;  conditional E-value: 6.9e-131
                                   TTS-..EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSHHHHHHH CS
                   Epimerase_2   4 kaeselelqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDtnetlaga 84 
                                   + +++++ ++++t qH++++m++++feel++++p+y+ln +s++++++tg++li++e+vl +ekpD+v+v+GDtn++laga
  gi|15669698|ref|NP_248511.1|  24 E-KTNIDWHIIHTNQHYSENMDKIFFEELNLPNPKYNLNIGSGTHGEQTGKMLIEIEKVLLKEKPDVVVVQGDTNTVLAGA 103
                                   4.4589*************************************************************************** PP

                                   HHHHHTT-EEEEET-----S-TT..SHHHHHHHHHHHT-SEEEESSHHHHHHHHHTT--GGGEEE---HHHHHHHHHHHHH CS
                   Epimerase_2  85 laAfklripvaHveAGlRsfdltegmpeEinRhlidklsdlhfapteearenLlkegeeeerifvvGntviDalllskeei 165
                                   l+A+kl+i+vaHveAGlRsfd++  mpeEinR+l+d++s+++fapte a++nLl+eg+ee++ifvvGnt++Da l++ + +
  gi|15669698|ref|NP_248511.1| 104 LVASKLKIDVAHVEAGLRSFDRN--MPEEINRVLTDHISSYLFAPTEIAKNNLLREGIEENKIFVVGNTIVDATLQNLKIA 182
                                   ***********************..******************************************************** PP

                                   H...T-HHHHHH.--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHHH.....HHHHHH-T CS
                   Epimerase_2 166 eeklkaseilke.lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkrl.....leeleele 240
                                   e++ + + + ++ + +++y+l+tlHr+en+d++erlk+i+e + ++ + +d ++++++h  prt+krl     +++l++ +
  gi|15669698|ref|NP_248511.1| 183 EKNENVRAFFNSvVIDDDYFLLTLHRAENVDNKERLKNIVEGIFEIIEIYDKAIIFSIH--PRTKKRLkefnlFDKLKSNK 261
                                   98887777767699***********************************9999******..*******9987777777778 PP

                                   TEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT-HHHHHHHHHHHCT-.. CS
                   Epimerase_2 241 nvtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvnlReeteRpegveagtnvlvgtdkeeIvaaleklledkk 321
                                   ++++iep+gyl+fl+l kna+l+ltdSgG+qeEa++l+vp+++lR++teRpe+ve g+n+lvg +ke++++a+e +l++  
  gi|15669698|ref|NP_248511.1| 262 KIKIIEPVGYLEFLMLEKNAELILTDSGGVQEEACILKVPCITLRDNTERPETVEVGANILVGDNKEKLIKAVEIMLNK-- 340
                                   *****************************************************************************77.. PP

                                   --......--TT-SS-HHHHHHHHH CS
                   Epimerase_2 322 elekmanaknpYgdGkaseriveil 346
                                        +n+knp+g+Gk+ eriv+il
  gi|15669698|ref|NP_248511.1| 341 ----KRNWKNPFGNGKSGERIVRIL 361
                                   ....678899*************98 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   5.9e-09   3.5e-05      13     117 ..      16     128 ..       5     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.9e-09
               Glyco_trans_4_2  13 tlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvd........rkgpleyl..kaf.klkklikkikPDvvhahy 82 
                                   ++ ++++L k +++ h+i  ++++++  ++++i + +l+++         +g+ ++   k++ ++ k++ k+kPDvv ++ 
  gi|15669698|ref|NP_248511.1|  16 LSPIIRALEKTNIDWHIIHTNQHYSE--NMDKIFFEELNLPnpkynlniGSGTHGEQtgKMLiEIEKVLLKEKPDVVVVQG 94 
                                   566899*****************544..67889999997777788887644466555465544****************** PP

               Glyco_trans_4_2  83 akpygllgslaarlsgvipvvlsvwGldvlkfpkk 117
                                    +  +l+g+l+a +++ i v+    Gl  ++ + +
  gi|15669698|ref|NP_248511.1|  95 DTNTVLAGALVASKLK-IDVAHVEAGLRSFDRNMP 128
                                   *************998.887766667666666555 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   7.8e-07    0.0046      13     166 ..      21     171 ..      16     174 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.8e-07
                Glyco_transf_4  13 raLarrGheVtvv.tpgddgpleeev....elvvrvprvplpll.krllrslaflrrlrrllkrekpDvvHahspaalgaa 87 
                                   raL + +++ +++ t ++  +  ++      ++ ++++    ++     ++  +l  + ++l +ekpDvv +++    ++a
  gi|15669698|ref|NP_248511.1|  21 RALEKTNIDWHIIhTNQHYSENMDKIffeeLNLPNPKYNLNIGSgTHGEQTGKMLIEIEKVLLKEKPDVVVVQGDTNTVLA 101
                                   56666666666664222222222222333334444444433333034456667788999***********99987777776 PP

                Glyco_transf_4  88 llalrrrlgiplVltvHglyekrllkarlkplsrllralerrl.lrradrviavSeatadelrerygvppekitVipnGv 166
                                   ++  + +l+i + +   gl          ++ +++ +++ r l  + +  ++a++e ++++l++  g++++ki V+ n +
  gi|15669698|ref|NP_248511.1| 102 GALVASKLKIDVAHVEAGLR---------SFDRNMPEEINRVLtDHISSYLFAPTEIAKNNLLR-EGIEENKIFVVGNTI 171
                                   66666568877666666665.........444445555444443445889**************.***********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2503.76
//
Query:       gi|15669699|ref|NP_248512.1|  [L=778]
Description: Hef nuclease [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-24   85.6   3.0    2.2e-23   83.2   0.2    2.7  2  ERCC4          ERCC4 domain
    4.2e-24   85.0   0.3    4.2e-24   85.0   0.3    4.0  4  Helicase_C     Helicase conserved C-terminal domain
    2.7e-21   76.3   0.2    2.7e-21   76.3   0.2    3.8  3  ResIII         Type III restriction enzyme, res subunit
    2.8e-19   69.6   0.3    2.8e-19   69.6   0.3    3.0  3  DEAD           DEAD/DEAH box helicase
      2e-10   40.6   0.1      9e-10   38.5   0.1    2.2  1  HHH_2          Helix-hairpin-helix motif
    2.5e-09   37.6   0.6    1.8e-08   34.8   0.1    2.9  1  HHH_5          Helix-hairpin-helix domain
    1.6e-08   34.0   2.2    7.8e-07   28.7   0.1    3.3  3  HHH            Helix-hairpin-helix motif
     0.0093   15.3   4.6      0.073   12.4   0.0    2.7  2  SecA_DEAD      SecA DEAD-like domain
  ------ inclusion threshold ------
      0.012   15.9   0.9      0.012   15.9   0.9    2.6  2  PND            FANCM pseudonuclease domain
      0.012   15.9   1.9       0.98    9.8   0.2    3.0  2  HHH_8          Helix-hairpin-helix domain
      0.013   15.7   7.2       0.12   12.5   0.1    3.8  4  Helicase_C_2   Helicase C-terminal domain
      0.015   15.5   1.4       0.21   11.9   0.0    3.4  3  HHH_3          Helix-hairpin-helix motif
      0.065   13.3   1.1       0.29   11.2   0.1    2.6  2  bact-PGI_C     Bacterial phospho-glucose isomerase C-terminal
      0.069   13.5   0.7        0.4   11.0   0.1    2.7  2  Rol_Rep_N      Rolling Circle replication initiation protein 
      0.085   13.0   5.3        7.7    6.7   0.0    4.0  3  SpoIIID        Stage III sporulation protein D
       0.25   11.2   0.0       0.25   11.2   0.0    3.2  4  Helicase_RecD  Helicase
       0.75   10.3   2.9        4.8    7.7   0.0    3.4  3  HhH-GPD        HhH-GPD superfamily base excision DNA repair p


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3      0.23   2.4e+02      79     120 ..     477     523 ..     423     561 .. 0.73
   2 !   83.2   0.2   2.1e-26   2.2e-23       2     154 ..     579     689 ..     578     691 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.23
                                   HHHHHHH.H-SEEEEEEES.-GGGTT.....................T CS
                         ERCC4  79 qvsrlkrngykkpillveg.ldqykrknknsrnkqykakvrq.....i 120
                                   + +++kr  +k+ ++l+   l++ ++ +++ + k  + ++ +      
  gi|15669699|ref|NP_248512.1| 477 KEREMKR-LLKNMCYLLNKrLQKKFEEKSKEEIKEETEEIKEkeiesK 523
                                   5578888.8999999995556666666666666665555554554440 PP

  == domain 2  score: 83.2 bits;  conditional E-value: 2.1e-26
                                   EGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSHHHHHHHH CS
                         ERCC4   2 Dsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgrleeqvsr 82 
                                   D re  +++ +     + ++++ +tl++gdy ++   +++               v+verk+a+d+v+si+d+rl++q++ 
  gi|15669699|ref|NP_248512.1| 579 DVRE--KNMAKL--LHNYANIELKTLEVGDY-VL---SDR---------------VVVERKTAEDFVNSIIDKRLFSQLKN 636
                                   6677..445554..45556************.**...9**...............************************** PP

                                   HHH.H-SEEEEEEES-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHHHH CS
                         ERCC4  83 lkrngykkpillvegldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaewla 154
                                   lk+   +kp+l+veg + ++r                ++++++++a++++ ldfg++i++t++a+eta++l 
  gi|15669699|ref|NP_248512.1| 637 LKK--VEKPLLIVEG-ENFSR----------------LHENALKGAILSIILDFGIPIIFTKNAEETADLLI 689
                                   *88..99********.56666................99999***************************985 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.1      0.01        11      11      62 ..      52     107 ..      41     146 .. 0.80
   2 ?   -2.6   0.0       6.4   6.7e+03       6      31 ..     283     304 ..     275     322 .. 0.60
   3 !   85.0   0.3     4e-27   4.2e-24       4     110 ..     341     452 ..     338     453 .. 0.93
   4 ?   -2.1   0.1       4.5   4.8e+03       7      57 ..     689     719 ..     673     725 .. 0.44

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.01
                                   HHTTTTSEEEEEESSHHHHHH....HHHHHHHTTSTEEEESTTSTHHHHHHHHHHH CS
                    Helicase_C  11 kleeeggkilifvntidrlek....vklllekkgikvavlhgelpqnereeileqf 62 
                                    l++++gk+li ++++  +e+    +k +l+  + k+++l+g+++ ++r e  ++ 
  gi|15669699|ref|NP_248512.1|  52 ILTKKDGKVLILAPSRPLVEQhynrLKQVLNIDEDKIIALTGKIQPKKRAELYKKG 107
                                   5799*************887775554444455599**************9988765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.4
                                   HHHHHHHTTTTSEEEEEESSHHHHHH CS
                    Helicase_C   6 llellkleeeggkilifvntidrlek 31 
                                    +ell   e++gk+ +f+n+i++l++
  gi|15669699|ref|NP_248512.1| 283 AKELL---ESQGKS-VFLNYINKLSM 304
                                   44554...444444.78888887743 PP

  == domain 3  score: 85.0 bits;  conditional E-value: 4e-27
                                   HHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTT.......STHHHHHHHHHHHHTTSSSEEEESGGGT CS
                    Helicase_C   4 eallellkleeeggkilifvntidrlekvklllekkgikvavlhge.......lpqnereeileqfnkgesdvLiatdvae 77 
                                   ++++++l +++++++i+if++++d++ek+  ll+++gik++++ g+       ++q+e++e++e+f k+e  vL++t+v e
  gi|15669699|ref|NP_248512.1| 341 DMVKNIL-EKNKDERIIIFAQYRDTVEKIVNLLTQNGIKAIRFIGQankegkgMSQKEQIEAIERF-KKEGSVLVSTSVSE 419
                                   6678888.99*****************955556899******************************.56889********* PP

                                   SSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                    Helicase_C  78 rGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                   +Gidip+vn++i++++  +  ++iqr+GR++R+
  gi|15669699|ref|NP_248512.1| 420 EGIDIPSVNYIIFYEPVPSEIRFIQRRGRAMRG 452
                                   ********************************7 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 4.5
                                   HHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHH CS
                    Helicase_C   7 lellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqneree 57 
                                   +++ +                     + ++ek+ + v +    ++ +e+++
  gi|15669699|ref|NP_248512.1| 689 IKIAE--------------------KEQIKEKRTVMVRYGKTAMSLKEQQK 719
                                   22222....................33333444444444444455555554 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.2   2.5e-24   2.7e-21      13     169 ..      24     168 ..       9     170 .. 0.86
   2 ?    4.1   0.4      0.04        42      44     110 ..     342     415 ..     338     423 .. 0.78
   3 ?   -1.0   4.6       1.5   1.6e+03      68     118 ..     494     554 ..     478     595 .. 0.54

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 2.5e-24
                                   HHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEES CS
                        ResIII  13 enlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke...igkkvs 90 
                                    n         +k+ l ++ TG GKT +a+ +i+ +l+k++  k+l+l+p++ l+eq ++++k++l+ + ++    ++k++
  gi|15669699|ref|NP_248512.1|  24 AN-------ALKKKTLCVLSTGLGKTAIAILVIAGILTKKD-GKVLILAPSRPLVEQHYNRLKQVLNIDEDKiiaLTGKIQ 96 
                                   33.......34689999************999999999855.5***********************999877777666677 PP

                                   SS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---.SEEEEEESS- CS
                        ResIII  91 gdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfke.avllglTATp 169
                                    +k+ +     ++ ki+++t q + +d+        +   d+f ++i DEaH++++++++  +++kfk+ + +lglTA p
  gi|15669699|ref|NP_248512.1|  97 PKKRAE---LYKKGKIFIATPQVIENDI-----IAGRINVDEFILLIADEAHHTTGDHAYAFVAKKFKDkCHILGLTASP 168
                                   777776...899****************.....9*****************************999966599******98 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.04
                                   HHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEESSS-B--...........-SEEEEE CS
                        ResIII  44 lierllkkgkeekflflvprkslleqtleefkkflseayke...igkkvsgdkkka....kekdstnkkilvtt 110
                                   +++++l+k+k e+++++++ ++ +e+  + +++   +a  +   ++k+ +g ++k+     e+++++ ++lv+t
  gi|15669699|ref|NP_248512.1| 342 MVKNILEKNKDERIIIFAQYRDTVEKIVNLLTQNGIKAIRFigqANKEGKGMSQKEqieaIERFKKEGSVLVST 415
                                   6789999**************************99999998777444433333333444778888888888887 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.5
                                   HHHHHHGGGGTGG....GEEEESSS-B--................-SEEEE.EHHHHHHTH CS
                        ResIII  68 eqtleefkkflseaykeigkkvsgdkkka.........kekdstnkkilvt.tiqsldads 118
                                   ++++++f++ ++e+ ke+++++++++ ++         +e+++t+k +++   i+++  ++
  gi|15669699|ref|NP_248512.1| 494 KRLQKKFEEKSKEEIKEETEEIKEKEIESktavkeetkEEEEKTKKPVTILdFIKQIEVKE 554
                                   5555555555555555533333333333333344443333333443333320344444444 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.3   2.7e-22   2.8e-19       4     174 ..      19     173 ..      16     175 .. 0.79
   2 ?    0.8   0.1      0.34   3.6e+02      35     104 ..     342     415 ..     334     432 .. 0.67
   3 ?   -2.2   0.3       2.9     3e+03      69     110 ..     545     586 ..     508     628 .. 0.68

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 2.7e-22
                                   HHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.SEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                          DEAD   4 QaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid.lrvlliig 83 
                                   Q+ +  ++l +++ l+   TG GKT+++++ +  i+    +k+  k+li++P+r L+eq++n+lk++++ id  ++ + ++
  gi|15669699|ref|NP_248512.1|  19 QQIIAANAL-KKKTLCVLSTGLGKTAIAILVIAGIL----TKKDGKVLILAPSRPLVEQHYNRLKQVLN-IDeDKIIA-LT 92 
                                   566666666.67899999***********9999999....46666************************.55234444.45 PP

                                   TSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  84 gvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqviv 164
                                   g+ + +++++l ++ +i+++tp+ + + +  g++n++++ +l+ DEa+    +    f+ + ++             +++ 
  gi|15669699|ref|NP_248512.1|  93 GKIQPKKRAELYKKGKIFIATPQVIENDIIAGRINVDEFILLIADEAHHTTGDHAYAFVAKKFKDK----------CHILG 163
                                   56666677777699************97778******************99997777777644433..........23777 PP

                                   EESSBSHHHH CS
                                   xxxxxxxxxx RF
                          DEAD 165 lSATlpkdvk 174
                                   l+A + +d++
  gi|15669699|ref|NP_248512.1| 164 LTASPGSDID 173
                                   7777666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.34
                                   HHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.ST..SEEEEEETTSSHHHHHHHHH...TTCSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx..xxxxxxxxxxxxxxxxxxxx...xxxxxxxxx RF
                          DEAD  35 vlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.id..lrvlliiggvaardqlskld...ngvdivvgt 104
                                   ++++++e  +++  +++i +  r  +e+++n l++ + + i+   +++   +g ++++q+++++   ++  ++v+t
  gi|15669699|ref|NP_248512.1| 342 MVKNILE--KNKDERIIIFAQYRDTVEKIVNLLTQNGIKaIRfiGQANKEGKGMSQKEQIEAIErfkKEGSVLVST 415
                                   4555555..5566699999999999999999998888753443223333344677777777774332556777766 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.9
                                   HHTTTSTSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  69 kfkkyidlrvlliiggvaardqlskldngvdivvgtpgrldd 110
                                    f+k+i++++ +  ++++ +++++  ++ ++i+v   ++ + 
  gi|15669699|ref|NP_248512.1| 545 DFIKQIEVKERSKSEEDKIKQEIKIPKKPIKIIVDVREKNMA 586
                                   455666667766666666666666665557777776665554 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.1   8.5e-13     9e-10       8      57 ..     725     774 ..     720     777 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 8.5e-13
                         HHH_2   8 IrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFen 57 
                                   +++VG + A+ L k+Fk++++  +a++eeL +v+++G+e A++i+e ++ 
  gi|15669699|ref|NP_248512.1| 725 LPDVGGALAERLLKHFKTVENVFTAKEEELMKVEGVGKERAKKIREVLTA 774
                                   699******************************************98876 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.1   1.7e-11   1.8e-08       5      54 ..     723     771 ..     720     774 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.7e-11
                                   HTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHH CS
                         HHH_5   5 lsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriile 54 
                                    s++ +G ++A +ll++ +++ve +  a +eeL k+ G+Gk++A++i + 
  gi|15669699|ref|NP_248512.1| 723 ESLPDVGGALAERLLKH-FKTVENVFTAKEEELMKVEGVGKERAKKIREV 771
                                   6899*************.*****************************885 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2       9.7     1e+04      22      28 ..      41      47 ..      41      49 .. 0.86
   2 ?    3.8   0.0     0.056        59      14      29 ..     723     738 ..     722     739 .. 0.89
   3 !   28.7   0.1   7.4e-10   7.8e-07       2      29 ..     743     770 ..     742     771 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 9.7
                                  HHHHHHH CS
                           HHH 22 ktAeaIl 28
                                  ktA aIl
  gi|15669699|ref|NP_248512.1| 41 KTAIAIL 47
                                  8*****9 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.056
                                   HTSTT-SHHHHHHHHH CS
                           HHH  14 lalPGVGpktAeaIls 29 
                                   ++lP VG + Ae+ l 
  gi|15669699|ref|NP_248512.1| 723 ESLPDVGGALAERLLK 738
                                   58**********9986 PP

  == domain 3  score: 28.7 bits;  conditional E-value: 7.4e-10
                                   HHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                           HHH   2 leglipasreeLlalPGVGpktAeaIls 29 
                                   +e++++a +eeL++++GVG+++A +I++
  gi|15669699|ref|NP_248512.1| 743 VENVFTAKEEELMKVEGVGKERAKKIRE 770
                                   79************************87 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   6.9e-05     0.073      76     171 ..      15     110 ..       8     135 .. 0.83
   2 ?    1.1   3.4      0.18   1.9e+02      24      54 ..     494     524 ..     473     598 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.9e-05
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SecA_DEAD  76 mrhydvQliGglvlhegkiaemkTGEGKtlvatlpay.lnaltgkgvhvvtvndYLakrdaewmgpvyeflGlsvgviese 155
                                    r y  Q+i++ +l++ ++  ++TG GKt +a+l ++ +   ++ +v +++ +  L ++  + +++v ++   ++ +++ +
  gi|15669699|ref|NP_248512.1|  15 ARLY-QQIIAANALKKKTLCVLSTGLGKTAIAILVIAgILTKKDGKVLILAPSRPLVEQHYNRLKQVLNIDEDKIIALTGK 94 
                                   5555.59************************99876514555666799999999*************99999999999999 PP

                                   xxxxxxxxxxxxxxxx RF
                     SecA_DEAD 156 leseerreaYeaditY 171
                                   +++++r e Y++  ++
  gi|15669699|ref|NP_248512.1|  95 IQPKKRAELYKKGKIF 110
                                   9999999999975554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.18
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SecA_DEAD  24 neleeelkalsdeeLrakteelkerlaegea 54 
                                   ++l++++++ s+ee++++tee+ke+  e+++
  gi|15669699|ref|NP_248512.1| 494 KRLQKKFEEKSKEEIKEETEEIKEKEIESKT 524
                                   4678899999999999999999887654433 PP

>> PND  FANCM pseudonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       3.3   3.5e+03      62      89 ..     227     254 ..     220     272 .. 0.82
   2 ?   15.9   0.9   1.1e-05     0.012       3     123 ..     568     691 ..     566     693 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.3
                                   TTHHHHHHHHTSSS-EEEEEEE--TTTG CS
                           PND  62 gykrkLvklrkaeklrgivlvektklse 89 
                                    +k +L  l+ a +++ i+ v kt+l e
  gi|15669699|ref|NP_248512.1| 227 ALKERLKILKDAGVINSIADVTKTELIE 254
                                   5788999999999999999999998754 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.1e-05
                                   XXSTTEEEEEGGGTTSHHHHHHTTTSEEEEESS-S.SSEECSSSEEEEEEEHHHHHH-STTHHHHHHHHTSSS-EE.EEEE CS
                           PND   3 kvPlGhilasekWrnsslvqklkdkikvlfedelgvvDfylsndtavlyiseadiiegngykrkLvklrkaeklrg.ivlv 82 
                                   k+P   i +    r+ ++++ l++  ++   + l+v D+ ls+++ v   ++ d++++   kr + +l++ +k+++ +++v
  gi|15669699|ref|NP_248512.1| 568 KIPKKPIKIIVDVREKNMAKLLHNYANIEL-KTLEVGDYVLSDRVVVERKTAEDFVNSIIDKRLFSQLKNLKKVEKpLLIV 647
                                   566666666666677888888888888876.68**************************************8886548999 PP

                                   E--TTTGGGHHHHHHH...HHTTC--EEEEESSHHHHHHHHHHH CS
                           PND  83 ektklseqyfsaLqkf...vvleLglkLlpvaeqteaaklliql 123
                                   e  + s  +  aL+     ++l++g+ ++  ++ +e+a+lli++
  gi|15669699|ref|NP_248512.1| 648 EGENFSRLHENALKGAilsIILDFGIPIIFTKNAEETADLLIKI 691
                                   999999999888886422278*********************97 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.045        47       3      62 ..     683     735 ..     681     741 .. 0.81
   2 ?    9.8   0.2   0.00092      0.98      44      67 ..     749     772 ..     737     773 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.045
                                   HHHHHHHHHHHHHHHCT--CCCHHHHHHHHCCCCC-SS-HHHHTTHCTTSTT--HHHHHH CS
                         HHH_8   3 eiadaLeeladllelkgedpfrvraYrrAaraiealpeeitsleeeltklpgiGkkiaak 62 
                                   e ad+L ++a+ +++k e       Y + a++++++ + i +      +lp +G ++a++
  gi|15669699|ref|NP_248512.1| 683 ETADLLIKIAEKEQIK-EKRTVMVRYGKTAMSLKEQQKFIVE------SLPDVGGALAER 735
                                   7889999999999999.7777777799999999998886665......699999999987 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00092
                                   HHTTHCTTSTT--HHHHHHHHHHH CS
                         HHH_8  44 sleeeltklpgiGkkiaakieeil 67 
                                     eeel k+ g+Gk  a+ki+e l
  gi|15669699|ref|NP_248512.1| 749 AKEEELMKVEGVGKERAKKIREVL 772
                                   32447*****************98 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.023        24       4      57 ..      52     105 ..      49     119 .. 0.72
   2 ?   12.5   0.1   0.00011      0.12       5      81 ..     347     425 ..     343     438 .. 0.74
   3 ?   -2.0   0.0       3.4   3.6e+03     131     164 ..     442     475 ..     432     483 .. 0.75
   4 ?   -1.7   0.8       2.7   2.8e+03      36      58 ..     503     517 ..     478     544 .. 0.44

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.023
                  Helicase_C_2   4 llevvpggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeyk 57 
                                   +l+++ g+vl++ pS  l+e+ ++rlk+ l+ ++ +i+  +++ + +k  e yk
  gi|15669699|ref|NP_248512.1|  52 ILTKKDGKVLILAPSRPLVEQHYNRLKQVLNIDEDKIIALTGKIQPKKRAELYK 105
                                   677899**********************88666656655544444444444444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00011
                  Helicase_C_2   5 levvp.ggvlvffpSyklleevverlkeeleskkieifvee.......keesrekvleeykekkkkgaillavcrGklsEG 77 
                                   le+ + +++++f +  +++e++v+ l +++  k i+++ +        +++++ + +e++k+   +g++l+++      EG
  gi|15669699|ref|NP_248512.1| 347 LEKNKdERIIIFAQYRDTVEKIVNLLTQNGI-KAIRFIGQAnkegkgmSQKEQIEAIERFKK---EGSVLVSTS--VSEEG 421
                                   555552667777777789***********97.789999987766655545555555555555...*******99..8899* PP

                  Helicase_C_2  78 idfs 81 
                                   id++
  gi|15669699|ref|NP_248512.1| 422 IDIP 425
                                   **97 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.4
                  Helicase_C_2 131 vnQaiGRliRhkdDygaivllDeRfakeeirekl 164
                                   + Q  GR++R +  +  +++      ++ +r+ l
  gi|15669699|ref|NP_248512.1| 442 FIQRRGRAMRGEGGKVYVLIAKGTADEAYYRSAL 475
                                   67999*****998887777766665555555555 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 2.7
                  Helicase_C_2  36 kkieifveekeesrekvleeyke 58 
                                   k++e ++e          ee+ke
  gi|15669699|ref|NP_248512.1| 503 KSKEEIKE--------ETEEIKE 517
                                   22222222........2222222 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       3.8     4e+03      21      37 ..     568     584 ..     560     588 .. 0.81
   2 ?   -1.2   0.1       2.3   2.5e+03      28      50 ..     623     641 ..     612     642 .. 0.70
   3 ?   11.9   0.0    0.0002      0.21      10      30 ..     748     768 ..     741     772 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.8
                         HHH_3  21 GlgpklAknIvayRekn 37 
                                   ++ +k +k Iv+ Rekn
  gi|15669699|ref|NP_248512.1| 568 KIPKKPIKIIVDVREKN 584
                                   577888899*****998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.3
                         HHH_3  28 knIvayReknGpfksreeLlkvk 50 
                                   + I++ R     f+ ++ L+kv+
  gi|15669699|ref|NP_248512.1| 623 NSIIDKR----LFSQLKNLKKVE 641
                                   3455555....999999999997 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.0002
                         HHH_3  10 tAsaeeLqklpGlgpklAknI 30 
                                   tA++eeL+k++G+g+  Ak+I
  gi|15669699|ref|NP_248512.1| 748 TAKEEELMKVEGVGKERAKKI 768
                                   9*******************9 PP

>> bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00028      0.29      70     121 ..     321     372 ..     281     382 .. 0.83
   2 ?   -2.0   0.1       3.2   3.4e+03      32     119 ..     495     539 ..     486     563 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                                   TEEEEEESSHH........HHHHHHHHTTTSSEEEEE---SSSHHHHHHHHH CS
                    bact-PGI_C  70 rlrlvllrdeeehprvkkraeivkelaeergvrvtevkaegesplerlasli 121
                                   +   +l++++ ehp+  k++++vk+++e+++++ + + a+    +e++++l 
  gi|15669699|ref|NP_248512.1| 321 EAVNLLMKSDVEHPKLGKVVDMVKNILEKNKDERIIIFAQYRDTVEKIVNLL 372
                                   333444445569***********************************99986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.2
                                   HHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESSHH........HHHHHHHHTTTSSEEEEE---SSS CS
                    bact-PGI_C  32 RfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrdeeehprvkkraeivkelaeergvrvtevkaeges 112
                                   R++++++e +K                                            ++ e ++e+ e++  + t vk e ++
  gi|15669699|ref|NP_248512.1| 495 RLQKKFEEKSKE-------------------------------------------EIKEETEEIKEKEIESKTAVKEETKE 532
                                   555555555554...........................................33344444444444444444444444 PP

                                   HHHHHHH CS
                    bact-PGI_C 113 plerlas 119
                                     e++ +
  gi|15669699|ref|NP_248512.1| 533 EEEKTKK 539
                                   4444444 PP

>> Rol_Rep_N  Rolling Circle replication initiation protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00038       0.4      10      58 ..     231     279 ..     228     302 .. 0.83
   2 ?   -2.9   0.1       8.5   8.9e+03       8      25 ..     610     627 ..     604     633 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00038
                     Rol_Rep_N  10 tfktldveeviedllkiklelfteeekgikgYerllkfgeikvlvskkk 58 
                                   ++k+l++  vi+++ ++ ++++ e ++++ +Y++++k++ ikv +++ k
  gi|15669699|ref|NP_248512.1| 231 RLKILKDAGVINSIADVTKTELIELNNKLFSYDEEVKYELIKVCSEALK 279
                                   678899999**********************************998655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.5
                     Rol_Rep_N   8 ritfktldveeviedllk 25 
                                   r++++ +++e++++++++
  gi|15669699|ref|NP_248512.1| 610 RVVVERKTAEDFVNSIID 627
                                   78999999*****99986 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.013        14      51      68 ..     339     356 ..     333     359 .. 0.87
   2 ?   -1.6   0.5       2.9   3.1e+03       1      27 [.     505     531 ..     505     535 .. 0.87
   3 ?    6.7   0.0    0.0073       7.7       3      47 ..     594     637 ..     590     644 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
                       SpoIIID  51 lakqvkevLeknkaeRhi 68 
                                   + + vk++Leknk eR i
  gi|15669699|ref|NP_248512.1| 339 VVDMVKNILEKNKDERII 356
                                   5678***********976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.9
                       SpoIIID   1 kdyieeRvleiakyiveskatvRkaak 27 
                                   k+ i+e + ei +  +esk+ v++  k
  gi|15669699|ref|NP_248512.1| 505 KEEIKEETEEIKEKEIESKTAVKEETK 531
                                   678999999***999****99998776 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0073
                       SpoIIID   3 yieeRvleiakyiveskatv.RkaakvfgvskstvhkDvterLkki 47 
                                    ie ++le+++y++  +  v Rk+a+ f    s + k +  +Lk++
  gi|15669699|ref|NP_248512.1| 594 NIELKTLEVGDYVLSDRVVVeRKTAEDFV--NSIIDKRLFSQLKNL 637
                                   48999************999899***996..456777776666665 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00024      0.25       7      58 ..      38      94 ..      35     142 .. 0.69
   2 ?   -3.1   0.0       5.7     6e+03     127     159 ..     288     320 ..     282     324 .. 0.75
   3 ?   -1.0   0.0       1.3   1.3e+03      22      53 ..     347     380 ..     338     410 .. 0.65
   4 ?   -2.5   1.0       3.7   3.9e+03      57      58 ..     519     526 ..     484     566 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                 Helicase_RecD  7 GRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke......e 58
                                  G GK+a++ l++a ++ +++ ++l+ aps+  v++ +++l++ l+  +  +      +
  gi|15669699|ref|NP_248512.1| 38 GLGKTAIAILVIAGILTKKDGKVLILAPSRPLVEQHYNRLKQVLNIDED-KiialtgK 94
                                  88**************************************998864432.23543321 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.7
                 Helicase_RecD 127 EGtGrgfslkflkqlkkekkrelreleleepiR 159
                                   E  G++  l ++++l+ +++++++++  +e +R
  gi|15669699|ref|NP_248512.1| 288 ESQGKSVFLNYINKLSMQRTKSAKSIVNDEKVR 320
                                   566888888888888888777777777666666 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.3
                 Helicase_RecD  22 iaegk.snilvtapskenvktlfeflak.gleal 53 
                                   ++++k  +i++ a  +++v+++++ l++ g++a+
  gi|15669699|ref|NP_248512.1| 347 LEKNKdERIIIFAQYRDTVEKIVNLLTQnGIKAI 380
                                   4444449999*9*999999999998754134444 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 3.7
                 Helicase_RecD  57 e......e 58 
                                   e       
  gi|15669699|ref|NP_248512.1| 519 EiesktaV 526
                                   12222222 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.8   5.1e+03      58      82 ..     271     322 ..     220     342 .. 0.53
   2 ?    0.3   0.1       0.9   9.5e+02      52      92 ..     583     640 ..     550     647 .. 0.82
   3 ?    7.7   0.0    0.0046       4.8      17      61 ..     732     771 ..     727     774 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.8
                                   HHHHHHHHH...........................S-SSS--TTSHHHHHH CS
                                   xxxxxxxxx...........................xxxxxxxxxxxxxxxx RF
                       HhH-GPD  58 ikelArilv...........................gkpdvlivvDvhvrri 82 
                                   ik ++++l                             k  + iv D  vr +
  gi|15669699|ref|NP_248512.1| 271 IKVCSEALKlmhakellesqgksvflnyinklsmqrTKSAKSIVNDEKVREA 322
                                   3333333334444444444444444444444444432222344444444444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.9
                                   HHHHHHHHHHHHHHH.................S-SSS--TTSHHHHHHHHHHTTSSSS CS
                                   xxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD  52 rrKakyikelArilv.................gkpdvlivvDvhvrrilkrlrsikek 92 
                                   +++ak +++ A i +                 +k+ + +v  + ++r++++l+ +k+ 
  gi|15669699|ref|NP_248512.1| 583 KNMAKLLHNYANIELktlevgdyvlsdrvvveRKTAEDFVNSIIDKRLFSQLKNLKKV 640
                                   5789999999999888999988888888888866667788888888888888888876 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0046
                                   HHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD  17 iierlferfgfptpedladadeekLrelirelGfyrrKakyikel 61 
                                   + erl + f+  t+e +  a ee+L++     G+++ +ak i+e+
  gi|15669699|ref|NP_248512.1| 732 LAERLLKHFK--TVENVFTAKEEELMKV---EGVGKERAKKIREV 771
                                   5688888866..****************...9999*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (778 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3055  (0.170394); expected 358.6 (0.02)
Passed bias filter:                      840  (0.0468515); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.67u 0.24s 00:00:00.91 Elapsed: 00:00:00.41
# Mc/sec: 5693.29
//
Query:       gi|15669700|ref|NP_248513.1|  [L=437]
Description: hypothetical protein MJ_1506 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-08   32.8   1.6       0.14   12.5   0.1    3.4  3  CARDB           CARDB
    0.00051   20.2   0.0      0.061   13.6   0.0    3.0  3  NPCBM_assoc     NPCBM-associated, NEW3 domain of alpha-galact
     0.0036   17.7   4.1       0.16   12.4   0.1    3.4  3  Arrestin_C      Arrestin (or S-antigen), C-terminal domain


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0   0.00093       5.6      50      87 ..     119     158 ..      77     168 .. 0.84
   2 !   12.5   0.1   2.3e-05      0.14      11      63 ..     193     249 ..     185     272 .. 0.73
   3 !   10.6   0.1     9e-05      0.54      17      69 ..     311     362 ..     304     390 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00093
                                   EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEESTT CS
                         CARDB  50 gtvtvpsLaagesttvsftwtte..ategevtltvvvDpd 87 
                                   g++t++ L++ges tv f+  ++  a + ++ + v+v  d
  gi|15669700|ref|NP_248513.1| 119 GKATISHLNPGESDTVYFKLHVDenAPSRDYRIDVKVSYD 158
                                   7899*****************9976666777777777544 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.3e-05
                                   C-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEE CS
                         CARDB  11 npseafvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagest 63 
                                     ++  +g++ ti++ +kN Gt++++  ++ l+ +++ +    + + v  L+a++++
  gi|15669700|ref|NP_248513.1| 193 DDTSIIPGKTKTIKLDIKNVGTGNAKYLNLYLIGNDKINilggSLIFVGCLKANNQY 249
                                   5677889************************99999876664433444555555555 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 9e-05
                                   TTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEE CS
                         CARDB  17 vgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftw 69 
                                   +g+ ++it+ ++N Gt + + + ++l+++g +  t ++  L+ +++ t  f +
  gi|15669700|ref|NP_248513.1| 311 KGDYIEITIGIANRGTTKIKHCVMTLTANGRN-YTKYIGDLDEDDYDTSIFEI 362
                                   678899**************************.77999999988887766654 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0     1e-05     0.061       3      78 ..      77     157 ..      75     158 .. 0.77
   2 ?    2.9   0.0     0.021   1.3e+02       2      26 ..     198     222 ..     197     226 .. 0.84
   3 ?   -1.1   0.0       0.4   2.4e+03       3      29 ..     311     337 ..     310     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                   NPCBM_assoc   3 pGetvtltltvtndg.taaatnvslslsl..PeGWt.vvevsp.asaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                   pG++v l + + nd  +  ++n+ ++++   P + + v  +++ a+++ l pGe+ ++ +k+ + ++a   dy++ +k+++
  gi|15669700|ref|NP_248513.1|  77 PGDDVDLWIKINNDNyDNEVKNIVVEVTPhyPFELRqVNPIKGkATISHLNPGESDTVYFKLHVDENAPSRDYRIDVKVSY 157
                                   677777777777777677777777777665577766666655426788******************************997 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.021
                   NPCBM_assoc   2 epGetvtltltvtndgtaaatnvsl 26 
                                    pG+t+t++l ++n gt  a+ ++l
  gi|15669700|ref|NP_248513.1| 198 IPGKTKTIKLDIKNVGTGNAKYLNL 222
                                   59**************988877666 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.4
                   NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslsls 29 
                                   +G+  ++t+ ++n gt+ +++  ++l+
  gi|15669700|ref|NP_248513.1| 311 KGDYIEITIGIANRGTTKIKHCVMTLT 337
                                   5777889999*******9999887775 PP

>> Arrestin_C  Arrestin (or S-antigen), C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   2.6e-05      0.16      14      62 ..      73     122 ..      69     180 .. 0.72
   2 !    4.2   0.1    0.0094        56       5      32 ..     186     213 ..     183     229 .. 0.81
   3 ?    0.3   0.1      0.15   8.8e+02      19      45 ..     312     338 ..     311     402 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.6e-05
                                   SEEETT--EEEEEEEEE.-SSSEEEEEEEEEEEEEEEESS..SEEEEEEE CS
                    Arrestin_C  14 kgyvpGetipvtvkidn.dskkkvkkikvslvqhvdvcafnrsnkkeknv 62 
                                   + ++pG+++++++ki+n +   +vk+i v+++ h+ +  ++ +  k k +
  gi|15669700|ref|NP_248513.1|  73 NVIHPGDDVDLWIKINNdNYDNEVKNIVVEVTPHYPFELRQVNPIKGKAT 122
                                   5789************9455599*********999998886544444333 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0094
                                   EEEEEEES-SEEETT--EEEEEEEEE-S CS
                    Arrestin_C   5 vsleaslpkkgyvpGetipvtvkidnds 32 
                                    s e++++ ++++pG t +++++i+n  
  gi|15669700|ref|NP_248513.1| 186 ASFEINIDDTSIIPGKTKTIKLDIKNVG 213
                                   6789********************9855 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.15
                                   T--EEEEEEEEE-SSSEEEEEEEEEEE CS
                    Arrestin_C  19 Getipvtvkidndskkkvkkikvslvq 45 
                                   G+ i++t+ i+n    k+k+  ++l+ 
  gi|15669700|ref|NP_248513.1| 312 GDYIEITIGIANRGTTKIKHCVMTLTA 338
                                   778999999999999999988887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3078.15
//
Query:       gi|15669701|ref|NP_248514.1|  [L=399]
Description: hypothetical protein MJ_1507 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-32  111.8   0.8    1.9e-31  109.9   0.0    2.0  2  MacB_PCD      MacB-like periplasmic core domain
    4.8e-14   52.6  15.1    1.5e-12   47.8   5.3    3.3  3  FtsX          FtsX-like permease family
  ------ inclusion threshold ------
       0.12   12.3   6.7        5.7    6.9   0.1    3.5  3  TMEM65        Transmembrane protein 65
        0.9    9.1   2.6        8.1    6.0   0.3    2.2  2  CD34_antigen  CD34/Podocalyxin family
        6.2    7.4   6.6       0.44   11.1   0.2    2.2  3  DUF1218       Protein of unknown function (DUF1218)
        7.3    6.9  22.1        8.2    6.8  11.2    3.4  4  DUF4064       Protein of unknown function (DUF4064)


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.9   0.0   6.4e-35   1.9e-31       1     194 [.      25     237 ..      25     238 .. 0.72
   2 ?   -1.7   1.8       1.1   3.2e+03       8      22 ..     270     284 ..     262     309 .. 0.70

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 6.4e-35
                      MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgk....gsges....lsdpdvealrrevp.veavapv 72 
                                   sllt++Gi+iGv a+++++slg g+q+++ +++ ++g  + +t+ +    g   +    ++  +++a+      v++v  v
  gi|15669701|ref|NP_248514.1|  25 SLLTIIGIVIGVLAMVSLISLGYGVQNYIHEEMMKMGS-NKITILPmkqfG--VPpshlFTKKEIKAI----KnVKGVDTV 98 
                                   89******************************999974.555555433442..331233455555443....447777776 PP

                      MacB_PCD  73 v.......tvrgggsgeee.vtvvg..vdpdyfk...vfglklaeGrffteadlrggpnvvvigeelaerlf....pvGdt 136
                                   +       ++ ++g  e++ v+ ++  ++ ++ +     g++++eGr+++++    +++++vig+++a++lf    +vGd+
  gi|15669701|ref|NP_248514.1|  99 MygwyggcEIEYNG--EKKfVSYYYaiPS-KLREvykDSGYDIEEGRWLEDN----DKYACVIGYGTAHNLFdreiKVGDV 172
                                   54444444222222..3332444445444.33332225788889****9664....6889**************999**** PP

                      MacB_PCD 137 irl..kpftVvGvledppgsgsalgddavylp........lttlqrrsitvrlkdgadleaaaaelek 194
                                   i++  k+f+VvG+l++  g    ++d++++l+         ++ ++++i v++k+g+d+e++++e++k
  gi|15669701|ref|NP_248514.1| 173 IKIkdKKFRVVGILKQI-G--NQQDDNSIILNidvgeklfGNEGKYNFISVTVKEGEDIEKVSEEIKK 237
                                   **************776.4..345799*****7765555322338999******************98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                      MacB_PCD   8 iaiGvaaviaivslg 22 
                                    ++Gvaa++++v+ +
  gi|15669701|ref|NP_248514.1| 270 FVVGVAAISLLVGAV 284
                                   478888888888654 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0021       6.4      27      67 ..      26      70 ..      18      81 .. 0.53
   2 ?    3.1   0.2     0.046   1.4e+02      65      93 ..     262     291 ..     234     294 .. 0.57
   3 !   47.8   5.3   5.1e-16   1.5e-12       1      96 []     298     392 ..     298     392 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0021
                          FtsX 27 litlvalviGlgl...gllaaqllsdvllssvfs.selkisidli 67
                                  l+t++++viG+++   ++ + + +++++++++ + ++ ki+i ++
  gi|15669701|ref|NP_248514.1| 26 LLTIIGIVIGVLAmvsLISLGYGVQNYIHEEMMKmGSNKITILPM 70
                                  455555555533311122233335555555544446777766655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.046
                          FtsX  65 dlitvliiivlllllalla.gllsiskilk 93 
                                   +++ v++i+v+++  ++l  g++ is+ ++
  gi|15669701|ref|NP_248514.1| 262 SVLGVITIFVVGVAAISLLvGAVGISNTMH 291
                                   344445555544443333225555555555 PP

  == domain 3  score: 47.8 bits;  conditional E-value: 5.1e-16
                          FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllal 81 
                                   ++ igil+alG+++ ++l ++++e+ +++l++ ++Gl+lg+l+a+++ ++ +++    ++   i+++ ++ ++++++l+ +
  gi|15669701|ref|NP_248514.1| 298 RKDIGILKALGAETTDILAIFVVESGFLGLFGGIVGLVLGILLAEVIEALAHKMGY-LMVNAWISWELIVGVLIFSFLVGV 377
                                   689***********************************************999987.899999****************** PP

                          FtsX  82 lagllsiskilkkep 96 
                                   ++g+++++  +k +p
  gi|15669701|ref|NP_248514.1| 378 ISGYFPARSGAKLNP 392
                                   *******99888876 PP

>> TMEM65  Transmembrane protein 65
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2      0.21   6.3e+02      82     105 ..      20      42 ..       8      46 .. 0.71
   2 ?    6.9   0.1    0.0019       5.7      34      65 ..     248     279 ..     230     318 .. 0.78
   3 ?    6.3   0.1    0.0031       9.2      42      67 ..     328     353 ..     325     361 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.21
                        TMEM65  82 vrlasalgkalGvtiGcllGmlpL 105
                                    +++++l +++G++iG+ l m+ L
  gi|15669701|ref|NP_248514.1|  20 QKRTQSLLTIIGIVIGV-LAMVSL 42 
                                   45667777889999985.556665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0019
                        TMEM65  34 lstlaaAalGnlvsdvaGvvlggvvealaerl 65 
                                   +s+l+a  l+++vs v+Gv++  vv  +a  l
  gi|15669701|ref|NP_248514.1| 248 FSVLTAEQLAKTVSSVLGVITIFVVGVAAISL 279
                                   799****************9998887776654 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0031
                        TMEM65  42 lGnlvsdvaGvvlggvvealaerlgl 67 
                                   +G +v  v+G++l++v+eala+++g+
  gi|15669701|ref|NP_248514.1| 328 FGGIVGLVLGILLAEVIEALAHKMGY 353
                                   6899999***************9986 PP

>> CD34_antigen  CD34/Podocalyxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3    0.0027       8.1      95     126 ..      16      47 ..       3      54 .. 0.77
   2 ?    3.0   0.1     0.022        67      57     126 ..     221     284 ..     207     293 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0027
                  CD34_antigen  95 edirseqdyskkllialvtsglllaiLlvagy 126
                                   ++i+++ + s +++i +v++ l+++ L+  gy
  gi|15669701|ref|NP_248514.1|  16 KNIKQKRTQSLLTIIGIVIGVLAMVSLISLGY 47 
                                   67889999***********6666666665444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.022
                  CD34_antigen  57 vlagetetkevlellkdk.rsdLeklgIqnltsvkeaqeedirseqdyskkllialvtsglllaiLlvagy 126
                                   +++  +++++v e +k+  ++++ + + + lt       e+  ++   s + +i++ + g++++ Llv+++
  gi|15669701|ref|NP_248514.1| 221 TVKEGEDIEKVSEEIKKAlKKSFGDEDFSVLT------AEQ-LAKTVSSVLGVITIFVVGVAAISLLVGAV 284
                                   44444466666666654324455555555444......222.4566788999****************986 PP

>> DUF1218  Protein of unknown function (DUF1218)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.84   2.5e+03      31      51 ..      27      43 ..      10      59 .. 0.49
   2 ?   11.1   0.2   0.00015      0.44      31      63 ..     257     291 ..     235     297 .. 0.83
   3 ?   -4.2   0.7         6   1.8e+04      41      56 ..     360     376 ..     350     379 .. 0.47

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.84
                       DUF1218 31 krtlavvlfvlswivfaiAva 51
                                   +++++v+ vl+++     ++
  gi|15669701|ref|NP_248514.1| 27 LTIIGIVIGVLAMV----SLI 43
                                  33333333322222....222 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00015
                       DUF1218  31 krtlavvlfvlswivfaiAvalllvGa..avnaeh 63 
                                    +t++ vl v++++v+++A++ llvGa  ++n++h
  gi|15669701|ref|NP_248514.1| 257 AKTVSSVLGVITIFVVGVAAISLLVGAvgISNTMH 291
                                   689999*********************55566666 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 6
                       DUF1218  41 lsw.ivfaiAvalllvG 56 
                                   +sw +++++ ++ +lvG
  gi|15669701|ref|NP_248514.1| 360 ISWeLIVGVLIFSFLVG 376
                                   44412222333344444 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0035        11       4      26 ..      23      45 ..      20     104 .. 0.65
   2 ?    4.0   2.1     0.019        58      43      81 ..     246     285 ..     217     295 .. 0.53
   3 ?    6.8  11.2    0.0027       8.2       3      94 ..     259     356 ..     252     362 .. 0.72
   4 ?   -1.7   5.9       1.2   3.5e+03       9      89 ..     326     351 ..     325     386 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0035
                       DUF4064  4 aeiiLglIGgilgillglllllf 26
                                  +  +L++IG+++g+l+ + l+  
  gi|15669701|ref|NP_248514.1| 23 TQSLLTIIGIVIGVLAMVSLISL 45
                                  56689999998888876655544 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.019
                       DUF4064  43 qalsgedasavleflstllivlgvi.aliaivlgivgall 81 
                                   + +s+  a++ +  +s++l v++++ + +a++  +vga+ 
  gi|15669701|ref|NP_248514.1| 246 EDFSVLTAEQLAKTVSSVLGVITIFvVGVAAISLLVGAVG 285
                                   4455555555554444444433333133333333444433 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0027
                       DUF4064   3 kaeiiLglIGgilgillglllllflfllssgefsqeltee.......qalsgedasavleflstllivlgvialiaivlgi 76 
                                   ++  +Lg+I + +  ++++ ll+   + +s+ +  + +e+       +al +e ++  + f+ +++++ ++++++ +vlgi
  gi|15669701|ref|NP_248514.1| 259 TVSSVLGVITIFVVGVAAISLLVG-AVGISNTMHMSILERrkdigilKALGAETTDILAIFVVESGFLGLFGGIVGLVLGI 338
                                   555667777664444444444433.44445555555555579999978888888888888888888888888********* PP

                       DUF4064  77 vgalllkknkkvsGilfi 94 
                                   + a +++    ++G+l++
  gi|15669701|ref|NP_248514.1| 339 LLAEVIEALAHKMGYLMV 356
                                   *******99999999997 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.2
                       DUF4064   9 glIGgilgillglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgivgalllkknkkvs 89 
                                   gl Ggi+g++lg+ll                                                       a +++    ++
  gi|15669701|ref|NP_248514.1| 326 GLFGGIVGLVLGILL-------------------------------------------------------AEVIEALAHKM 351
                                   555555555555554.......................................................44444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1411  (0.0786993); expected 358.6 (0.02)
Passed bias filter:                      785  (0.0437838); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 2517.06
//
Query:       gi|15669702|ref|NP_248515.1|  [L=224]
Description: ABC transporter ATP-binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-37  127.0   0.0    9.4e-37  126.6   0.0    1.2  1  ABC_tran      ABC transporter
      2e-08   33.9   0.3    6.6e-07   29.0   0.3    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    3.7e-06   27.0   0.1      0.025   14.4   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    9.7e-06   25.6   0.0    2.2e-05   24.4   0.0    1.6  1  RsgA_GTPase   RsgA GTPase
    2.1e-05   24.6   0.0    3.5e-05   23.9   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
    6.5e-05   22.9   0.1        0.2   11.6   0.0    2.2  2  NTPase_1      NTPase
    8.9e-05   22.2   0.0    0.00017   21.3   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00011   22.7   0.0    0.00013   22.4   0.0    1.2  1  AAA_16        AAA ATPase domain
    0.00017   21.6   0.1     0.0005   20.1   0.1    1.7  2  Rad17         Rad17 P-loop domain
    0.00038   20.1   0.0     0.0011   18.6   0.0    1.7  2  AAA_25        AAA domain
    0.00042   19.6   0.1    0.00046   19.4   0.1    1.1  1  G-alpha       G-protein alpha subunit
    0.00079   19.7   0.1     0.0033   17.7   0.1    2.0  1  AAA_22        AAA domain
     0.0011   17.8   0.0      0.061   12.0   0.0    2.0  2  AAA_13        AAA domain
     0.0014   19.0   0.0     0.0047   17.3   0.0    1.9  2  RNA_helicase  RNA helicase
     0.0022   18.6   0.4     0.0033   17.9   0.4    1.6  1  AAA_23        AAA domain
     0.0026   18.0   0.1     0.0071   16.6   0.0    1.7  2  AAA_28        AAA domain
     0.0057   17.2   0.2      0.064   13.8   0.1    2.2  2  AAA_18        AAA domain
     0.0068   16.8   0.4       0.13   12.7   0.4    2.4  1  AAA           ATPase family associated with various cellular 
     0.0074   16.0   0.3      0.028   14.1   0.1    1.8  2  AAA_15        AAA ATPase domain
  ------ inclusion threshold ------
      0.012   15.7   0.2      0.022   14.8   0.2    1.9  1  MMR_HSR1      50S ribosome-binding GTPase
      0.018   14.1   0.2       0.11   11.5   0.0    1.9  2  T2SSE         Type II/IV secretion system protein
      0.027   14.6   0.0      0.049   13.8   0.0    1.6  1  AAA_33        AAA domain
      0.039   13.3   0.2       0.13   11.6   0.0    1.9  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.041   13.6   0.0       0.24   11.1   0.0    2.0  2  IstB_IS21     IstB-like ATP binding protein
      0.044   13.1   0.0      0.074   12.3   0.0    1.3  1  Septin        Septin
      0.047   13.7   0.0      0.086   12.9   0.0    1.6  1  AAA_14        AAA domain
      0.052   13.3   0.2        0.6    9.8   0.0    2.2  2  AAA_24        AAA domain
      0.053   13.4   0.0      0.098   12.6   0.0    1.6  1  NACHT         NACHT domain
      0.079   12.7   0.0       0.24   11.2   0.0    1.7  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
       0.12   11.9   0.0       0.22   11.0   0.0    1.5  1  AAA_7         P-loop containing dynein motor region
       0.17   11.6   0.0       0.46   10.2   0.0    1.7  2  AAA_30        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.6   0.0   1.6e-39   9.4e-37       1     136 [.      21     169 ..      21     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 1.6e-39
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCE.EEE-SS--S-TTSBHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkei.gvlpqepqlfpeltvr 77 
                                   lkn++lk++ege v i+G++G+GKStLl++la l +pt+Ge+ ++g+ +++   +e+ ++r++i g+++q+ +l ++lt+ 
  gi|15669702|ref|NP_248515.1|  21 LKNINLKIEEGEFVMIMGPSGCGKSTLLNILALLDTPTKGEVYYKGRRTSSmseNERAIFRRKIsGFIFQQFHLIKTLTAL 101
                                   79*******************************************8888777886666666555279************** PP

                                   HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   en             +++++++k+l+ +gl +      ++ p++LSgGq+qrva+aral+++pk++++DEpt
  gi|15669702|ref|NP_248515.1| 102 ENvelpmmlderdksYRRKRAKKLLEMVGLGDRL----NHYPHQLSGGQQQRVAIARALANNPKIIFADEPT 169
                                   *********9997766666788888888887744....4556*****************************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.3   1.1e-09   6.6e-07      14     212 ..      20     214 ..      14     219 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.1e-09
                                   ECEEEEEETTS.SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSS CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  14 agktvilpfsk.sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkie 93 
                                   a k++ l++++ +f +i+Gp G+GKs ll+ +  +L + +          ++ +k  ++ s+++ +   +f+ + + +  +
  gi|15669702|ref|NP_248515.1|  20 ALKNINLKIEEgEFVMIMGPSGCGKSTLLNIL-ALLDTPT--------KGEVYYK-GRRTSSMSENERAIFRRKISGFIFQ 90 
                                   556666666652699*************9977.3444222........2333333.3344444444444455555555555 PP

                                   SSCEEEEEEEETTSEEEEEETTEEE-H..HHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  94 keevsisrrvkrkgeseykingkevtk..kevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDe 166
                                   + ++  + ++ ++ e  +++++++ ++  k  ++lle++g+         +LSgG+++ va+a  +A    +p+ + + De
  gi|15669702|ref|NP_248515.1|  91 QFHLIKTLTALENVELPMMLDERDKSYrrKRAKKLLEMVGLGDRlnhyphQLSGGQQQRVAIARALAN---NPK-IIFADE 167
                                   55555566666666677777765544333777888888887665556666***********9988773...455.5557** PP

                                   TTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 167 idaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvt 212
                                      +LD k   +v ++lk  +++   +i++++++e+++ a+k+++++
  gi|15669702|ref|NP_248515.1| 168 PTGNLDSKSGMAVMSILKGLNEKgITIIMVTHEQELTKYASKIIKLR 214
                                   ******************777665999***************99875 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   4.4e-05     0.025       1      22 [.      33      54 ..      33      85 .. 0.82
   2 !   11.1   0.0   0.00042      0.25     220     301 ..     125     203 ..      61     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.4e-05
                        AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                  + ++ Gp g+GKS+LL +l ll
  gi|15669702|ref|NP_248515.1| 33 FVMIMGPSGCGKSTLLNILALL 54
                                  56899**************999 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00042
                        AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                    +  +  gd+ +  +++lS G+++  a++ al+  +   ++++ DEp  +L+ k    ++ +lk l+++g+ +i++TH  +
  gi|15669702|ref|NP_248515.1| 125 LLEMVGLGDRLNHYPHQLSGGQQQRVAIARALANNP---KIIFADEPTGNLDSKSGMAVMSILKGLNEKGITIIMVTHEQE 202
                                   44455556777778999*******989999999888...9***********************999999*********766 PP

                        AAA_21 301 l 301
                                   l
  gi|15669702|ref|NP_248515.1| 203 L 203
                                   5 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   3.8e-08   2.2e-05      88     141 ..      19      70 ..       5      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.8e-08
                                   TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S------------- CS
                   RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTT 141
                                    +l++++ ++++ ++++++G+SG GKStL+n l+  ++   gev     +G+ T+
  gi|15669702|ref|NP_248515.1|  19 IALKNINLKIEEgEFVMIMGPSGCGKSTLLNILALLDTPTKGEVYY---KGRRTS 70 
                                   56777888888879******************98766655566544...466665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0     6e-08   3.5e-05       8      81 ..      21      91 ..      18     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6e-08
                      ATPase_2  8 lkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkkleka 81
                                  lk+++  +e+   e+++i Gp g+GK++Ll+ i+  l+   k  +yy   r++s s+ ++ i   + + ++ ++
  gi|15669702|ref|NP_248515.1| 21 LKNINLKIEE--GEFVMIMGPSGCGKSTLLN-ILALLDTPTKGEVYYKGRRTSSMSENERAIFRRKISGFIFQQ 91
                                  6677766666..899**************97.7778889999************99999986544444444444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0015      0.85       2      43 ..      34      77 ..      33      85 .. 0.73
   2 !   11.6   0.0   0.00034       0.2      77     156 ..     141     222 ..     119     224 .] 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0015
                                  EEEE--TTSSHHHHHH..HHHHHH...GGGEEEEEEEEE----- CS
                      NTPase_1  2 vfiTGppGvGKtTlvk..kvlellkssgvkvgGfyteevreggr 43
                                  v+i Gp+G GK+Tl++   +l++  + +v ++G  t+ + e++r
  gi|15669702|ref|NP_248515.1| 34 VMIMGPSGCGKSTLLNilALLDTPTKGEVYYKGRRTSSMSENER 77
                                  7899**********861134455566678888888888877766 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00034
                                   -HHHHHHHHHHHHHHHHHHH-EEEE--.-STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS--SHHHHHHHT-TT-EEEE- CS
                      NTPase_1  77 dvesfeelalealrkalseadviviDE.iGkmElkskkfkeaveevLk.sekpvlavihrrkdlalveeirerkdvkvfev 155
                                   ++   ++  +++ r   +++ +i  DE  G++  ks     ++ + L+ ++  +++v h+++  +   +i + +d++++e+
  gi|15669702|ref|NP_248515.1| 141 QLSGGQQQRVAIARALANNPKIIFADEpTGNLDSKSGMAVMSILKGLNeKGITIIMVTHEQELTKYASKIIKLRDGEIVEI 221
                                   555555555555555569999******88*******************8999999******9889999999999****998 PP

                                   - CS
                      NTPase_1 156 t 156
                                   +
  gi|15669702|ref|NP_248515.1| 222 I 222
                                   7 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.9e-07   0.00017      17      49 ..      26      58 ..      19      65 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.9e-07
                        AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                  ++i++ ++++++GpsG GKSTll  ++ l +p+
  gi|15669702|ref|NP_248515.1| 26 LKIEEGEFVMIMGPSGCGKSTLLNILALLDTPT 58
                                  56775559***************5554444554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.2e-07   0.00013      23     106 ..      30     118 ..      15     195 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.2e-07
                        AAA_16  23 rpelvllsGesGvGKsslvrellralekd...ggiflrgkcdql....esa.ipy...sa.laqalareellrqlldeaes 91 
                                   ++e v++ G+sG+GKs+l++ l+  l +    ++++ +g+ +++    e+a   +   s  + q++   +l++ l +  e+
  gi|15669702|ref|NP_248515.1|  30 EGEFVMIMGPSGCGKSTLLNILA-LLDTPtkgEVYY-KGRRTSSmsenERAiF-RrkiSGfIFQQF---HLIKTLTAL-EN 103
                                   4589***************7777.444444322333.3333333221133331.233355445555...777777655.33 PP

                        AAA_16  92 aeleawrekleeala 106
                                    el+   ++ +++++
  gi|15669702|ref|NP_248515.1| 104 VELPMMLDERDKSYR 118
                                   344444444444444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   8.6e-07    0.0005      35      67 ..      21      53 ..      13      87 .. 0.84
   2 ?   -1.4   0.0       3.2   1.9e+03     126     172 ..     153     198 ..      93     205 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.6e-07
                         Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                  lk   L+ ++ + ++i GPsGCgkst +++L+ 
  gi|15669702|ref|NP_248515.1| 21 LKNINLKIEEGEFVMIMGPSGCGKSTLLNILAL 53
                                  56666666777799****************985 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.2
                         Rad17 126 GddlrtdkklilvedlPnkfyrdsdalrevirkylrssealplilvi 172
                                      l  + k+i+ ++   +    s      i+k l+ ++  ++i+v 
  gi|15669702|ref|NP_248515.1| 153 ARALANNPKIIFADEPTGNLDSKSGMAVMSILKGLNEKGI-TIIMVT 198
                                   4455666677777665544444443333334445554444.566655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.9e-06    0.0011      30     125 ..      28     117 ..      20     131 .. 0.69
   2 ?   -2.1   0.0         4   2.3e+03     169     188 ..     181     199 ..     166     201 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                        AAA_25  30 lpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlra.vgealrddarllvldla 109
                                   + +ge+++++G++g+GK+tl+  lal  +   p  g+v   +g+      E+ ++ +rr+++  +++++ + ++l++l   
  gi|15669702|ref|NP_248515.1|  28 IEEGEFVMIMGPSGCGKSTLLNILALLDT---PTKGEVY-YKGRRTSSMSENERAIFRRKISGfIFQQFHLIKTLTALE-- 102
                                   789*****************998887555...4445443.344444444488888888888885557777777777775.. PP

                        AAA_25 110 gveslpLfakdrggtl 125
                                   +v +lp++ ++r+ + 
  gi|15669702|ref|NP_248515.1| 103 NV-ELPMMLDERDKSY 117
                                   55.6777777766665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4
                        AAA_25 169 vealeriarrtgaavllvhH 188
                                   ++ l+ +  ++g+++++v H
  gi|15669702|ref|NP_248515.1| 181 MSILKGL-NEKGITIIMVTH 199
                                   4444444.678999999999 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1     8e-07   0.00046      26     104 ..      34     128 ..      16     220 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8e-07
                                   EEEEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHHHHHHHHHHHHHHH..HHHHHHTT......... CS
                       G-alpha  26 llllGqseSGKsTilkqlkllykkg.............fseeelatwraviqlnivrsikti..lealesleselsesf.. 89 
                                   ++++G s++GKsT+l+ l ll +++             +se+e+a++r  i   i +++++i  l ale+ e ++   +  
  gi|15669702|ref|NP_248515.1|  34 VMIMGPSGCGKSTLLNILALLDTPTkgevyykgrrtssMSENERAIFRRKISGFIFQQFHLIktLTALENVELPM---Mld 111
                                   7899******************99999**********999999999***********987652233444433333...234 PP

                                   ..HHHC-SS-SCCCS-H CS
                       G-alpha  90 ..elqelkerldplkkv 104
                                     +++ +++r+++l+++
  gi|15669702|ref|NP_248515.1| 112 erDKSYRRKRAKKLLEM 128
                                   45444444444444443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   5.8e-06    0.0033       4      30 ..      30      56 ..      27     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.8e-06
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleqld 30
                                  +  +++++G+sG+GK+tll+ l+  ++
  gi|15669702|ref|NP_248515.1| 30 EGEFVMIMGPSGCGKSTLLNILALLDT 56
                                  56799**************99988763 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.026        15      20      66 ..      35      80 ..      22     147 .. 0.74
   2 !   12.0   0.0   0.00011     0.061     525     582 ..     158     212 ..     147     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.026
                        AAA_13 20 liYGwNGaGKTtLSrllrslelgetepkfangsieitngeeldirVf 66
                                  +i G  G GK+tL ++l+ l +    + + +g  ++++ +e +  +f
  gi|15669702|ref|NP_248515.1| 35 MIMGPSGCGKSTLLNILALLDTPTKGEVYYKG-RRTSSMSENERAIF 80
                                  79999**************9765544444333.34445555555555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00011
                        AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkntk 582
                                   ++ ki++ D P   LDs+s + v+s +k      +k   ++  TH  e+ k+++k +k
  gi|15669702|ref|NP_248515.1| 158 NNPKIIFADEPTGNLDSKSGMAVMSILKGLN---EKGITIIMVTHEQELTKYASKIIK 212
                                   6789*************************96...666679999********9998766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   8.1e-06    0.0047       1      42 [.      34      70 ..      34      77 .. 0.78
   2 ?   -2.0   0.0       8.1   4.7e+03      69      99 ..     179     209 ..     140     212 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.1e-06
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpedd 42
                                  +++ Gpsg+GKStl + L  all   ++++k++vy+++ +++
  gi|15669702|ref|NP_248515.1| 34 VMIMGPSGCGKSTLLNIL--ALL---DTPTKGEVYYKGRRTS 70
                                  689**************3..444...7789999999665554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.1
                  RNA_helicase  69 dlaelirlvsstpyplnmasleekgtlftSk 99 
                                    ++ +++  + + +++ m   e+  t ++Sk
  gi|15669702|ref|NP_248515.1| 179 AVMSILKGLNEKGITIIMVTHEQELTKYASK 209
                                   4444444444444444555555444555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.4   5.7e-06    0.0033      15      44 ..      24      56 ..       9     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.7e-06
                        AAA_23 15 idF...skgltlItGpNGaGKTTildAiklaLy 44
                                  i++   +  ++ I Gp G+GK+T+l+ + l  +
  gi|15669702|ref|NP_248515.1| 24 INLkieEGEFVMIMGPSGCGKSTLLNILALLDT 56
                                  555665567899**************9987655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.2e-05    0.0071       2      30 ..      34      62 ..      33      87 .. 0.82
   2 ?   -1.6   0.0       4.8   2.8e+03      63      79 ..     148     166 ..      97     169 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
                        AAA_28  2 ivitGgestGKTtlleaLaargypvvpEa 30
                                  ++i+G++++GK+tll+ La  ++p+  E+
  gi|15669702|ref|NP_248515.1| 34 VMIMGPSGCGKSTLLNILALLDTPTKGEV 62
                                  78*****************7777766665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.8
                        AAA_28  63 qleeeaaa..aankvlfcD 79 
                                   q+ + a+a  +++k++f D
  gi|15669702|ref|NP_248515.1| 148 QRVAIARAlaNNPKIIFAD 166
                                   2222222222667777776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   0.00011     0.064       1      19 [.      34      52 ..      34     125 .. 0.82
   2 ?    1.6   0.0      0.66   3.8e+02      47      95 ..     167     212 ..     120     219 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
                        AAA_18  1 IlltGtpGvGKttlakeLs 19
                                  ++++G++G+GK+tl + L+
  gi|15669702|ref|NP_248515.1| 34 VMIMGPSGCGKSTLLNILA 52
                                  79*************9995 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.66
                        AAA_18  47 deskrldedkldklldaleenssaleegknlvidghlaeleseaakdik 95 
                                   +++  ld +  ++++++l++ +   e+g ++++  h +el ++a k+ik
  gi|15669702|ref|NP_248515.1| 167 EPTGNLDSKSGMAVMSILKGLN---EKGITIIMVTHEQELTKYASKIIK 212
                                   4556777777888999999986...588899999998888888877665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.4   0.00023      0.13       1      66 [.      34     167 ..      34     212 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00023
                                   EEEESSTTSSHHHHHHHHHHH.......HTHE.....................................EEEEETTTCSSS CS
                           AAA   1 vllyGppGtGKTllakavake.......lgve.....................................fleisgsellsk 37 
                                   v+++Gp G+GK++l + +a         +  +                                     +          +
  gi|15669702|ref|NP_248515.1|  34 VMIMGPSGCGKSTLLNILALLdtptkgeV--YykgrrtssmseneraifrrkisgfifqqfhliktltaL----------E 102
                                   6899***********99987644433330..122333333344444433334444444443333333331..........0 PP

                                   ...................................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                           AAA  38 ...................................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                                      y  + +   ++ ++ a++ a +p+i+f DE
  gi|15669702|ref|NP_248515.1| 103 nvelpmmlderdksyrrkrakkllemvglgdrlnhYPHQLSGGQQQRVAIARALAnNPKIIFADE 167
                                   34444444445555555555555555555555555555555555555555555555577777777 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   4.9e-05     0.028      14      49 ..      21      57 ..      20     125 .. 0.78
   2 ?    0.5   0.0      0.69     4e+02     295     365 ..     140     200 ..      66     204 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.9e-05
                        AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnn 49
                                  lk++ ++++e  +  + G+ ++GKS++l++l l+ + 
  gi|15669702|ref|NP_248515.1| 21 LKNINLKIEEGeFVMIMGPSGCGKSTLLNILALLDTP 57
                                  788777777778*******************766544 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.69
                        AAA_15 295 nknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                   ++ + G+q+ + ++  ++         ++++i++ +EP  +L  +  + ++  lk l +++   +i+ TH 
  gi|15669702|ref|NP_248515.1| 140 HQLSGGQQQRVAIARALA---------NNPKIIFADEPTGNLDSKSGMAVMSILKGLNEKGI-TIIMVTHE 200
                                   555555555555543333.........34567888888888888888888888888888887.78888885 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   3.8e-05     0.022       2      20 ..      34      52 ..      33     224 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.8e-05
                                  EEEEESTTSSHHHHHHHHH CS
                      MMR_HSR1  2 vaivGrpNvGKStLinalt 20
                                  v+i+G +  GKStL+n l 
  gi|15669702|ref|NP_248515.1| 34 VMIMGPSGCGKSTLLNILA 52
                                  89**************986 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019      0.11     116     149 ..      18      51 ..       5      62 .. 0.79
   2 ?    0.7   0.0      0.39   2.3e+02      78     178 ..      99     212 ..      72     220 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                         T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyal 149
                                       + ++  ++e   +++ G+ g GK+tll++l
  gi|15669702|ref|NP_248515.1|  18 TIALKNINLKIEEGEFVMIMGPSGCGKSTLLNIL 51 
                                   4556678888999999***************986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.39
                         T2SSE  78 vrlrvvllPvvag.ealviR.kksakeltlddlgaeealk.......ekiaevlrkavrerglilvs.GgTgs..GKttll 146
                                   + l+ v lP++ +    + R k+++k l++  lg + +         ++++ ++++a++++  i+++  +Tg    K+ ++
  gi|15669702|ref|NP_248515.1|  99 TALENVELPMMLDeRDKSYRrKRAKKLLEMVGLGDRLNHYphqlsggQQQRVAIARALANNPKIIFAdEPTGNldSKSGMA 179
                                   556667777777743455563555555544444333333334444446677777777777766666524666422333332 PP

                         T2SSE 147 .yallkeinksderivtvEDpvEiqleganqvq 178
                                     ++lk +n++   i++v    E+   + + ++
  gi|15669702|ref|NP_248515.1| 180 vMSILKGLNEKGITIIMVTHEQELTKYASKIIK 212
                                   266677777777777777666666665555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.4e-05     0.049       2      33 ..      34      78 ..      33     212 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.4e-05
                        AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdt...................l 33
                                  v++ G++G+GKstl+  l+      ll+++t                   +
  gi|15669702|ref|NP_248515.1| 34 VMIMGPSGCGKSTLLNILA------LLDTPTkgevyykgrrtssmsenerA 78
                                  899***********99887......66666644444444444444444440 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00022      0.13      22      66 ..      31      75 ..       9     101 .. 0.70
   2 ?   -1.8   0.0       2.9   1.7e+03       6      29 ..     143     166 ..     134     210 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                  Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagk 66
                                  g  ++++Gp+G+GK+ l + l+ l +p + e   + ++ +s++++
  gi|15669702|ref|NP_248515.1| 31 GEFVMIMGPSGCGKSTLLNILALLDTPTKGEVYYKGRRTSSMSEN 75
                                  5568999**********9988777666666666666666666663 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.9
                  Mg_chelatase   6 kGqeeakraleiaaaGgHnlllvG 29 
                                    G ++++ a+  a a + +++++ 
  gi|15669702|ref|NP_248515.1| 143 SGGQQQRVAIARALANNPKIIFAD 166
                                   445555555555555555555544 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00041      0.24      44      73 ..      28      57 ..      11      84 .. 0.79
   2 ?   -0.1   0.0       1.2   6.8e+02     107     156 ..     157     208 ..     132     213 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00041
                     IstB_IS21 44 iekkenivllGpsGvGKshlaialgveavr 73
                                  ie+ e ++++GpsG GKs l   l+     
  gi|15669702|ref|NP_248515.1| 28 IEEGEFVMIMGPSGCGKSTLLNILALLDTP 57
                                  789999************998777765555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                     IstB_IS21 107 lkvdllilDdlgllpldqaeaellfeviekryerrs..iiitsnlpfaewde 156
                                   ++   +i  d  + +ld+++   ++ +++   e+    i++t ++++ ++ +
  gi|15669702|ref|NP_248515.1| 157 ANNPKIIFADEPTGNLDSKSGMAVMSILKGLNEKGItiIMVTHEQELTKYAS 208
                                   4444455555567789999999999999999998651145677777777655 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013     0.074       7      32 ..      34      59 ..      30      87 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                  EEEEEBTTSSCCCCCCTTSSSS---- CS
                        Septin  7 lmvvGesglGkttlintlfetdliee 32
                                  +m++G sg Gk+tl+n l   d  ++
  gi|15669702|ref|NP_248515.1| 34 VMIMGPSGCGKSTLLNILALLDTPTK 59
                                  8***************9876665544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00015     0.086       3      44 ..      32      72 ..      30     129 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                        AAA_14  3 kilvitGaRrvGKTtllkqlikell.vkkesilyinldderdk 44
                                  + ++i+G+  +GK+tll+ l+  ll ++ +  +y++  + +  
  gi|15669702|ref|NP_248515.1| 32 EFVMIMGPSGCGKSTLLNILA--LLdTPTKGEVYYKGRRTSSM 72
                                  6799************98887..44446666666666665553 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0     0.001       0.6       5      22 ..      34      51 ..      31      62 .. 0.86
   2 ?    0.7   0.0      0.62   3.6e+02     111     133 ..     180     202 ..     174     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.001
                        AAA_24  5 iliyGpsgiGKTtlakel 22
                                  ++i+Gpsg GK+tl++ l
  gi|15669702|ref|NP_248515.1| 34 VMIMGPSGCGKSTLLNIL 51
                                  79************9866 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.62
                        AAA_24 111 frrllkklqelrknvifiahekt 133
                                   ++++lk l+e + ++i++ he++
  gi|15669702|ref|NP_248515.1| 180 VMSILKGLNEKGITIIMVTHEQE 202
                                   6788889999999********98 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00017     0.098       3      22 ..      34      53 ..      32      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                                  EEEEC-TTTCHHHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqklal 22
                                  v++ G++G+GK+tLl  lal
  gi|15669702|ref|NP_248515.1| 34 VMIMGPSGCGKSTLLNILAL 53
                                  899************98775 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00041      0.24      21      54 ..      19      52 ..      12      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00041
                        RuvB_N 21 ifieaakkreealdhvllyGpPGlGkttlakiia 54
                                  i+++  + + e+ + v+++Gp G Gk+tl +i+a
  gi|15669702|ref|NP_248515.1| 19 IALKNINLKIEEGEFVMIMGPSGCGKSTLLNILA 52
                                  677777778888999*****************98 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00037      0.22      27      52 ..      25      50 ..      16      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
                         AAA_7 27 elllknkkpvllvGptGtGKtviikd 52
                                  +l ++++  v+++Gp+G+GK+++++ 
  gi|15669702|ref|NP_248515.1| 25 NLKIEEGEFVMIMGPSGCGKSTLLNI 50
                                  566888999*************9875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0008      0.46      18      47 ..      31      60 ..      20      74 .. 0.82
   2 ?   -1.6   0.0       3.4   1.9e+03      93      93 ..     164     164 ..     120     205 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0008
                        AAA_30 18 drvavltGpAGtGKttalkalreaweaagg 47
                                    ++++ Gp G GK+t+l+ l+ + +  +g
  gi|15669702|ref|NP_248515.1| 31 GEFVMIMGPSGCGKSTLLNILALLDTPTKG 60
                                  35899**************99877766655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.4
                        AAA_30  93 i 93 
                                    
  gi|15669702|ref|NP_248515.1| 164 F 164
                                   3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 1420.40
//
Query:       gi|15669703|ref|NP_248516.1|  [L=153]
Description: hypothetical protein MJ_1509 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-43  147.6   5.2    2.7e-43  147.4   5.2    1.0  1  DUF1931        Domain of unknown function (DUF1931)
     0.0048   17.1   5.2       0.01   16.1   1.8    2.4  2  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
  ------ inclusion threshold ------
      0.096   12.8   1.2        2.9    8.1   0.1    2.6  2  SAM_Exu        Exuperantia SAM-like domain
        0.1   13.0   5.0       0.48   10.8   0.3    3.0  3  DNTTIP1_dimer  DNTTIP1 dimerisation domain
        0.1   12.4   0.1       0.17   11.7   0.1    1.3  1  DUF1810        Protein of unknown function (DUF1810)
       0.11   13.0   2.0       0.27   11.7   0.1    2.3  3  GlutR_dimer    Glutamyl-tRNAGlu reductase, dimerisation domai
       0.24   11.1   4.8       0.15   11.7   1.3    1.9  2  GrpE           GrpE
       0.26   10.3   1.2       0.28   10.2   1.2    1.2  1  tRNA-synt_2    tRNA synthetases class II (D, K and N)


Domain annotation for each model (and alignments):
>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4   5.2   1.2e-46   2.7e-43       1     138 []      11     150 ..      11     150 .. 0.99

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 1.2e-46
                                   HHHHHHHHHS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HHHHHHHHHHHTT..TS--SHHHHH CS
                       DUF1931   1 lerlfreaagLdvdkedlkrisdfVekklydLllvaeenAkangrdviepaDLPiTkglqesireFrkl..eeeleleeil 79 
                                   l++++++++++d++k+++++i+d+Vekkl+dL++va++nAk+++ ++i+++++P+Tkg+ +s++ Fr++  ee++ +e+i+
  gi|15669703|ref|NP_248516.1|  11 LKKIMKTTCEIDLYKTEAEDIMDVVEKKLADLFEVAHRNAKEENAKIIKMRHIPLTKGFLNSMELFRSVieEENIVAETIK 91 
                                   689*******************************************************************999******** PP

                                   HHHTTS-S-SSEE-HHHHCCHHHHHHHHHHHHHHHHHHHSTTSSS--HHHHHHHHHHHH CS
                       DUF1931  80 eqlaalppldlelseeleaelpeivGgLsvalArvikaidpevknpqtehieraeevld 138
                                   +++++++p dl+l++ + ++lp i+G+++++++rvika++++++++++ehie+a++vld
  gi|15669703|ref|NP_248516.1|  92 KYVMKKIPGDLPLDDIVVDNLPLITGTIFIVVGRVIKALHEDIERIRKEHIEEAKKVLD 150
                                   *********************************************************98 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.8   4.6e-06      0.01       3      61 ..       6      63 ..       4      66 .. 0.93
   2 ?    1.8   0.1      0.13     3e+02       8      24 ..     123     140 ..     122     151 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                                  XXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHH CS
                 CBFD_NFYB_HMF  3 LPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehi 61
                                  +P  + kkImk + ++     +A +++ ++ve  + +l + A + +k+e++K+ik  hi
  gi|15669703|ref|NP_248516.1|  6 IPYPQLKKIMKTTCEIDLYKTEAEDIM-DVVEKKLADLFEVAHRNAKEENAKIIKMRHI 63
                                  677889*******99**9999**9988.79****************************9 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.13
                                   HHHHHHCC.TTXS-B-HH CS
                 CBFD_NFYB_HMF   8 vkkImksd.pdarkiakd 24 
                                   v +++k   +d+++i k+
  gi|15669703|ref|NP_248516.1| 123 VGRVIKALhEDIERIRKE 140
                                   677888877888887765 PP

>> SAM_Exu  Exuperantia SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0013       2.9      26      69 ..       2      45 ..       1      48 [. 0.95
   2 ?    2.9   0.1     0.052   1.2e+02      48      71 ..     127     150 ..     124     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                       SAM_Exu 26 AEngidyesLkeiweekkkeGlekllkekitslkeedkeeLlel 69
                                  AE  i y +Lk+i ++  +  l k+ +e i ++ e+++++L e+
  gi|15669703|ref|NP_248516.1|  2 AEMIIPYPQLKKIMKTTCEIDLYKTEAEDIMDVVEKKLADLFEV 45
                                  8999*************************************997 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.052
                       SAM_Exu  48 ekllkekitslkeedkeeLlelLd 71 
                                    k+l e i+++ +e +ee  ++Ld
  gi|15669703|ref|NP_248516.1| 127 IKALHEDIERIRKEHIEEAKKVLD 150
                                   68999*************999998 PP

>> DNTTIP1_dimer  DNTTIP1 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00021      0.48      16      41 ..      29      54 ..      25      63 .. 0.90
   2 ?    1.8   0.1      0.14   3.1e+02       2      26 ..      72      94 ..      71      98 .. 0.69
   3 ?    0.7   0.1       0.3   6.7e+02      49      64 ..     132     147 ..     126     150 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                 DNTTIP1_dimer 16 kevdevikkylrkvfkpAveNireNl 41
                                  ++++ v++k l ++f+ A +N++e +
  gi|15669703|ref|NP_248516.1| 29 EDIMDVVEKKLADLFEVAHRNAKEEN 54
                                  79*********************854 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.14
                 DNTTIP1_dimer  2 sLdLLrkvlQpainkevdevikkyl 26
                                  s++L r+v+ ++  + v e ikky+
  gi|15669703|ref|NP_248516.1| 72 SMELFRSVIEEE--NIVAETIKKYV 94
                                  899999998764..44666777776 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.3
                 DNTTIP1_dimer  49 advqklcrsiLeeakk 64 
                                   +d+++++ + +eeakk
  gi|15669703|ref|NP_248516.1| 132 EDIERIRKEHIEEAKK 147
                                   5666666666666665 PP

>> DUF1810  Protein of unknown function (DUF1810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.4e-05      0.17      58     124 ..      27      94 ..       4      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.4e-05
                                   HHHHHHHSTTHHHHHHHHHHHHHH--S--HHHHS-T...THHHHHHHHHHHHHHH-S--HHHHHHHHHHS CS
                       DUF1810  58 earaylahpvLgkrlreiteallaleeksaeeilGs...idalKlrssmtLFaevaedekvfkevldkyf 124
                                   ea++ +  +v++k+l ++ e+ ++ ++++  +i+     + ++ +  sm LF++v e+e++ +e ++ky 
  gi|15669703|ref|NP_248516.1|  27 EAEDIM--DVVEKKLADLFEVAHRNAKEENAKIIKMrhiPLTKGFLNSMELFRSVIEEENIVAETIKKYV 94 
                                   455544..57889999999999888777777776543334556699*********************997 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.86   1.9e+03      47      47 ..      42      42 ..      13      83 .. 0.60
   2 ?   -1.0   0.0       1.1   2.5e+03      29      42 ..      83      96 ..      63     110 .. 0.65
   3 ?   11.7   0.1   0.00012      0.27      23      49 ..     124     150 ..     122     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.86
                                  - CS
                   GlutR_dimer 47 k 47
                                   
  gi|15669703|ref|NP_248516.1| 42 L 42
                                  1 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                                  HHHHHHHHHHHHHH CS
                   GlutR_dimer 29 lrekaeeireeele 42
                                   +  ae+i++  ++
  gi|15669703|ref|NP_248516.1| 83 ENIVAETIKKYVMK 96
                                  33344444444444 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00012
                                   HHHHHHHHHHHHHHHHHHHHHHHS-S. CS
                   GlutR_dimer  23 vptIkalrekaeeireeeleralkkla 49 
                                     +Ikal+e +e+ir+e +e+a+k l+
  gi|15669703|ref|NP_248516.1| 124 GRVIKALHEDIERIRKEHIEEAKKVLD 150
                                   579********************9875 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.3   6.9e-05      0.15      13      91 ..      13      93 ..       8      98 .. 0.81
   2 ?    0.6   0.1      0.17   3.8e+02      37      59 ..     129     151 ..     125     153 .] 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.9e-05
                                  HHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC...HHH-HHHH CS
                          GrpE 13 eeeeleeeleelekevkelkekllrllaefenlrkrt.ekekeeakkfaiekfakdLLpvlDnleralksak.eneeeksl 91
                                  ++ +   e++  ++e++++ + ++++la++ ++  r  ++e +++ k     + k +L+ ++ ++ +++  +  +e++k++
  gi|15669703|ref|NP_248516.1| 13 KIMKTTCEIDLYKTEAEDIMDVVEKKLADLFEVAHRNaKEENAKIIKMRHIPLTKGFLNSMELFRSVIEEENiVAETIKKY 93
                                  5666677899999****************87666555166777*********************99999766666666654 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.17
                                   TTTTTTTTHHHHHHHHHHHHHHH CS
                          GrpE  37 rllaefenlrkrtekekeeakkf 59 
                                    l++++e +rk + +e++++ ++
  gi|15669703|ref|NP_248516.1| 129 ALHEDIERIRKEHIEEAKKVLDY 151
                                   46678888888888888887776 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.2   0.00012      0.28     116     167 ..      17      68 ..      15     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                                   EEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTSEE-SSS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 116 tqieaemsfieeedimqvleelikslvkevlessakdiefvirrnskdlkkp 167
                                   t++e+ +  +e edim+v+e+ + +l++ ++++ +++  + i+    +l+k 
  gi|15669703|ref|NP_248516.1|  17 TTCEIDLYKTEAEDIMDVVEKKLADLFEVAHRNAKEENAKIIKMRHIPLTKG 68 
                                   789************************9997777666666666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1061.40
//
Query:       gi|15669704|ref|NP_248517.1|  [L=193]
Description: hypothetical protein MJ_1510 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.2e-44  149.3   0.0    1.1e-43  149.1   0.0    1.1  1  TYW3        Methyltransferase TYW3
  ------ inclusion threshold ------
      0.075   13.0   0.0       0.16   12.0   0.0    1.5  1  Pept_S41_N  Peptidase S41 N-terminal domain


Domain annotation for each model (and alignments):
>> TYW3  Methyltransferase TYW3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.1   0.0   1.3e-47   1.1e-43       2     212 ..       6     189 ..       5     190 .. 0.95

  Alignments for each domain:
  == domain 1  score: 149.1 bits;  conditional E-value: 1.3e-47
                                   HHHHHHHHH....HHHHHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE............EESSTT-STT-EEEEEE CS
                          TYW3   2 rKakiLeeLsvpdtdkspkGsvDekirelideinsledlvTtSSCsGRvsvflegrksaeaeeeaaksggkkgggkwlfvs 82 
                                    K+++L +L    + + ++G vDe+i++++++in+ ++++TtSSC GRv ++           e  k ++ k  ++wl ++
  gi|15669704|ref|NP_248517.1|   6 DKKRTLMNL----ELAIREGLVDEEIIPILNKINEIDNYYTTSSCIGRVGIM-----------EIPKDKNPKLYSRWLGKW 71 
                                   688999999....7889***********************************...........688888899999****** PP

                                   SS---HHHHHHHHCS--..............SSEEEEEEE--EEEEEESSHHHHHHHHHHHHHCT-TT-EEEEECTTEEEE CS
                          TYW3  83 HdpvkeeellaelfgleeeegsaksseseeeerlilfkfePmILHvlcrslesAqkllsaAleaGfreSGivslkkkkviv 163
                                   H+ ++ +el+++l++++              e++i+f ++++ILH++c+++esA+k+l++A+++G++ S+i+s++ k+viv
  gi|15669704|ref|NP_248517.1|  72 HHYASYDELFNALKNKK--------------EGYIVFVMNSPILHIACKDIESAKKMLELAIHSGLKASSIKSISDKRVIV 138
                                   *************9997..............79************************************************ PP

                                   EEE---EEEEEEE..STS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS
                          TYW3 164 airsglklevpig..kellvseeylkllvklanerfeenkkrierfeealk 212
                                   +i ++ k+++pig  +e++v+++ylk+l++ +n+++++ ++ + r  ++l+
  gi|15669704|ref|NP_248517.1| 139 EILTTYKVDTPIGedGEIFVDNNYLKFLLDYSNSKLKRAREILMRWANRLD 189
                                   *************9755************************9999998886 PP

>> Pept_S41_N  Peptidase S41 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.8e-05      0.16      19      45 ..      54      90 ..      53      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                    Pept_S41_N 19 evpdlidpr..........kfssPedfFksLlykkdd 45
                                  e+p+ ++p+           ++s++++F++L++kk++
  gi|15669704|ref|NP_248517.1| 54 EIPKDKNPKlysrwlgkwhHYASYDELFNALKNKKEG 90
                                  7899888889999999999**************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1301.30
//
Query:       gi|15669705|ref|NP_248518.1|  [L=107]
Description: hypothetical protein MJ_1511 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.9e-14   51.9   0.0      7e-14   51.6   0.0    1.1  1  CMD         Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
      0.042   14.7   0.5      0.053   14.4   0.5    1.1  1  Csm2_III-A  Csm2 Type III-A
      0.081   12.7   0.0       0.17   11.6   0.0    1.5  1  ubiquitin   Ubiquitin family
      0.089   11.5   0.0        0.1   11.3   0.0    1.0  1  HPS3_Mid    Hermansky-Pudlak syndrome 3, middle region
        0.1   12.7   0.1       0.24   11.5   0.1    1.6  1  La          La domain
       0.13   12.2   0.0         16    5.4   0.0    2.1  2  HNOB        Haem-NO-binding


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   2.3e-17     7e-14       1      83 [.      18      99 ..      18     101 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 2.3e-17
                                  HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHHHH CS
                           CMD  1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAlaaa 83
                                  pe+++a+++l + +++ + +Ld k + L+ lav a++g e  v+  t++++e+G+t eei++v+ +  + ag+p++ +A++a 
  gi|15669705|ref|NP_248518.1| 18 PEFYEAVANLQKEVFS-GKKLDEKMQRLVLLAVVATLGDEKAVKRQTKKLMEMGATIEEIQDVMKVVYIGAGMPRFIKAVEAI 99
                                  9**************9.999*********************99**********************************999986 PP

>> Csm2_III-A  Csm2 Type III-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.5   1.8e-05     0.053      30     106 ..      19     100 ..       8     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHHHHHHHHHTHHHHHHHTHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHH--SH.......HHHHHHHHHH CS
                    Csm2_III-A  30 kfydevkrieekikkkkeeeseeilrklkllkpklaYaagr..eeavkelsevlkkaidkvkksk......ekfkrfvdff 102
                                   +fy++v+++++++ ++k+ +  e +++l+ll + +    ++  ++++k+l+e + + i+++++        + + rf++ +
  gi|15669705|ref|NP_248518.1|  19 EFYEAVANLQKEVFSGKKLD--EKMQRLVLLAVVATLGDEKavKRQTKKLME-MGATIEEIQDVMkvvyigAGMPRFIKAV 96 
                                   69************998866..778889999888777766645688888876.56666666666555556689999***** PP

                                   HHHH CS
                    Csm2_III-A 103 EAiv 106
                                   EAi+
  gi|15669705|ref|NP_248518.1|  97 EAIL 100
                                   *997 PP

>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.8e-05      0.17      17      51 ..       6      40 ..       2      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.8e-05
                                  TTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE-TT CS
                     ubiquitin 17 esdtveelKekiaekegipaeqqrLiysGkvLede 51
                                  + +t+e +K+ + e  +  a+ q+ ++sGk L+++
  gi|15669705|ref|NP_248518.1|  6 PAETIEVVKKNCPEFYEAVANLQKEVFSGKKLDEK 40
                                  779****************************9765 PP

>> HPS3_Mid  Hermansky-Pudlak syndrome 3, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.5e-05       0.1     157     223 ..       8      71 ..       4      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.5e-05
                      HPS3_Mid 157 pyiDttlkacPpvtkdvcalrlqlFiglkalchfknhviLlskadseaeeErrkskrksrkktssks 223
                                   + i+ ++k+cP++ + v  l+ ++F g k+l    ++++Ll+ + +    ++++ kr+++k   +  
  gi|15669705|ref|NP_248518.1|   8 ETIEVVKKNCPEFYEAVANLQKEVFSG-KKLDEKMQRLVLLAVVAT--LGDEKAVKRQTKKLMEMGA 71 
                                   5789999********************.999999999999999883..4455555566666555544 PP

>> La  La domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   7.9e-05      0.24       6      46 ..      19      59 ..      18      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.9e-05
                                  HHHHHTT-TTT-HHHHHHHTTSTTS---HHHHHTSSHHHHH CS
                            La  6 EfYFSdeNLpkDkFLrkkmdkdpegwVplsliasfkrmkkl 46
                                  EfY + +NL+k  F  kk+d++ +  V l+++a+    k++
  gi|15669705|ref|NP_248518.1| 19 EFYEAVANLQKEVFSGKKLDEKMQRLVLLAVVATLGDEKAV 59
                                  89999***************************987544433 PP

>> HNOB  Haem-NO-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0064        19      83     108 ..       8      33 ..       3      44 .. 0.88
   2 ?    5.4   0.0    0.0054        16      84     119 ..      58      92 ..      45      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0064
                                   HHHTHTTCSHHHHHHHHHHHHHHHHH CS
                          HNOB  83 kllrvlgrnlfeFLknldnlHvevlk 108
                                   + ++v+++n+ eF++ + nl++ev++
  gi|15669705|ref|NP_248518.1|   8 ETIEVVKKNCPEFYEAVANLQKEVFS 33 
                                   578999***************99976 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0054
                                   HHTHTTCSHHHHHHHHHHHHHHHHHHHSTTSS--EE CS
                          HNOB  84 llrvlgrnlfeFLknldnlHvevlklsypkakpPsf 119
                                    ++   ++l+e+ + +++++ +v+k+ y +a +P+f
  gi|15669705|ref|NP_248518.1|  58 AVKRQTKKLMEMGATIEEIQ-DVMKVVYIGAGMPRF 92 
                                   5565677999999*******.**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 705.45
//
Query:       gi|15669706|ref|NP_248519.1|  [L=1613]
Description: reverse gyrase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-75  252.3   7.8    1.5e-48  165.8   1.3    4.1  3  Topoisom_bac     DNA topoisomerase
    5.9e-40  136.3   0.1    1.2e-35  122.4   2.9    3.8  2  Intein_splicing  Intein splicing domain
    3.7e-25   88.1   3.3    4.9e-25   87.7   0.3    3.0  2  Toprim           Toprim domain
    2.2e-15   56.7   8.7    2.6e-13   50.1   0.5    4.5  4  LAGLIDADG_3      LAGLIDADG-like domain
    2.2e-13   50.5   3.6    1.9e-05   25.0   0.3    5.0  3  Helicase_C       Helicase conserved C-terminal domain
    8.7e-12   45.2   0.1    2.5e-11   43.7   0.1    1.8  1  DEAD             DEAD/DEAH box helicase
    1.5e-10   41.9   4.4    1.5e-10   41.9   4.4    5.8  4  LAGLIDADG_1      LAGLIDADG endonuclease
    2.2e-10   39.7   3.7      5e-10   38.6   3.7    1.7  1  zf_Rg            Reverse gyrase zinc finger
    7.2e-08   32.6   1.8    7.2e-08   32.6   1.8    3.5  3  ResIII           Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.013   15.8   1.6        3.6    8.0   0.2    4.5  4  BRCT             BRCA1 C Terminus (BRCT) domain
      0.044   13.1   0.9       0.12   11.7   0.1    2.2  2  SecA_DEAD        SecA DEAD-like domain
      0.056   11.9   1.1       0.11   11.0   0.3    1.8  2  FHIPEP           FHIPEP family
       0.12   11.8   0.0         18    4.8   0.0    2.4  2  E1-E2_ATPase     E1-E2 ATPase
       0.13   10.9   0.0       0.27    9.9   0.0    1.4  1  SNF2_N           SNF2 family N-terminal domain
       0.13   12.5   1.4         11    6.4   0.1    3.3  2  Img2             Mitochondrial large subunit ribosomal protei
       0.96    9.7   5.1        4.7    7.4   0.7    4.1  3  Sep15_SelM       Sep15/SelM redox domain


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.28   3.1e+02      63     119 ..     606     662 ..     602     668 .. 0.78
   2 !   86.0   0.0   2.3e-27   2.6e-24       2     160 ..     732     866 ..     731     873 .. 0.81
   3 !  165.8   1.3   1.4e-51   1.5e-48     161     412 ..    1361    1602 ..    1355    1603 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.28
                  Topoisom_bac  63 peeyweveatlkkekkekekkkkkkkerikdkeeaeaileklkkkeakvesvekkek 119
                                   +e ++ v+++ +      ++ kk + e+++d+++ e+++++l +k  +v++++ ke+
  gi|15669706|ref|NP_248519.1| 606 KEGFYGVKIENNLYIPIYTSIKKVNGEQFTDQKDLEELIKQLMEKGERVNAMDAKEN 662
                                   5667777777544444444789999*****************886678888888876 PP

  == domain 2  score: 86.0 bits;  conditional E-value: 2.3e-27
                  Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkgkkvlsaGRVqtptLaliveRereienFvpeeyweveatlkkekkekek 82 
                                   ++en v+ + +Rr+ D++iG++ls+ l++ +++k+ lsaGRVqtp+L++i+eR++e++   + +y +++++   ++     
  gi|15669706|ref|NP_248519.1| 732 LDENKVKGQVVRRIEDRWIGFRLSQKLWE-VFNKNYLSAGRVQTPVLGWIIERYNEHKI--KVPYLSLKLE---ND----- 801
                                   689*************************8.8889*********************9885..5789999876...22..... PP

                  Topoisom_bac  83 kkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYekagl 160
                                         ++i++ +e ++   ++        +v+  ek+ pp  pf+t+tL++ea++++gls ++++siaq+L+e  gl
  gi|15669706|ref|NP_248519.1| 802 ---IYIGKIWE-DEFDKDEVEV--------EVKVYEKEIPPLPPFTTDTLLEEATKRFGLSTDEIMSIAQELFEL-GL 866
                                   ...23345553.3333322223........4566677786666*******************************5.65 PP

  == domain 3  score: 165.8 bits;  conditional E-value: 1.4e-51
                  Topoisom_bac  161 itYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpklkels...... 233 
                                     tY+RT str+s +  ++ ++e+l+ ++ ++yl+   +     ++   +   + +aHe+IrPt+ +++ +el+      
  gi|15669706|ref|NP_248519.1| 1361 CTYHRTSSTRVSLDG-MRVAREYLKLNNLEDYLK---N-----REY--F--ME-GAHECIRPTKPMNT-DELIeflken 1424
                                    6*************9.9********986655655...2.....211..2..23.8********99995.5555666688 PP

                  Topoisom_bac  234 .....ddekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegee 307 
                                         +++ k+Y+lI+rrf+as+mk+a++e  ++ ++  +e+++     i+++G+ ++y+ + k+     lp++++   
  gi|15669706|ref|NP_248519.1| 1425 nikltKNHIKVYDLIFRRFIASQMKEAVVEYEEIYIKDLDEKVEGY-VDIKFDGWSRIYNLKLKK-----LPRIEKSSL 1497
                                    8888888889**************************9987776554.4579********965444.....899988766 PP

                  Topoisom_bac  308 vkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkk..kslvptelGkalvell.ekfk 383 
                                     kv +   + +k  + + y e++++k+m+++giG+p+T+a+ii+kl++rgYv+++k  ++l+pt+lG+++++ l ++++
  gi|15669706|ref|NP_248519.1| 1498 -KVLD--KKLRKIPKVPLYDEGEVVKLMKERGIGRPSTYAQIIKKLLDRGYVVKSKdkNKLIPTKLGIEVYNYLiNNYP 1573
                                    .3433..578999999************************************99954478**************9999* PP

                  Topoisom_bac  384 dlvspelTaeleekLdeIaegkadakevl 412 
                                     l+s+e T+elee +d+I++g+ d+ evl
  gi|15669706|ref|NP_248519.1| 1574 HLISEERTRELEEIMDKIENGEVDYIEVL 1602
                                    *************************9998 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0068       7.6      40      94 ..     132     250 ..      63     748 .. 0.77
   2 !  122.4   2.9   1.1e-38   1.2e-35       1     134 []     874    1360 ..     874    1360 .. 0.99

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0068
                                   EEEEEEEEEEEEEEETTS-EEEEETT-EEEECCT.TEEEEEECCC--TT-EEEEE.......................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.......................... RF
               Intein_splicing  40 kliklklkelyeiklesgrkikaTpeHkllvvrd.egivEkradeLkegdliavp.......................... 93 
                                    l+k  ++++  ++ +++ +i++ + H+ l++++ +++  k+  e +  d++++                           
  gi|15669706|ref|NP_248519.1| 132 LLVKQTYEKISSLTEKNNLNIRVVAYHSELSTKEkKEV--KERIENNDYDVLITTsnyltknmpkckfdfvfvddvdallk 210
                                   57788999************************984444..44334444455554456666667777777776666666666 PP

                                   .......................................H CS
                                   .......................................x RF
               Intein_splicing  94 .......................................d 94 
                                                                          +
  gi|15669706|ref|NP_248519.1| 211 asknidrtlkllgfdeeiineaykiiylikigkiedamkK 250
                                   6666666666666666666666555555555555555551 PP

  == domain 2  score: 122.4 bits;  conditional E-value: 1.1e-38
                                    EEECTTCEEEEHHHHCCECTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCT..TEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
               Intein_splicing    1 iiledgeekvkieelvekegeevlslnledlklevksvkkliklklk.elyeiklesgrkikaTpeHkllvvrd..egi 76  
                                    ++l dg+++ +ie++v++++++vlsl+l++l+++ ++  k++kl+++ +l +i+l++++++kaTp+H+llv+rd   ++
  gi|15669706|ref|NP_248519.1|  874 VVLGDGRIE-TIEDIVNAKERNVLSLDLDNLSIKIDTAIKFWKLRYNgNLSKITLSNNYELKATPDHCLLVLRDnqLKW 951 
                                    6899*****.***************************************************************977788 PP

                                    EEEECCC--TT-EEEEE.............................................................. CS
                                    xxxxxxxxxxxxxxxxx.............................................................. RF
               Intein_splicing   77 vEkradeLkegdliavp.............................................................. 93  
                                        a+++ke+d+ia+p                                                              
  gi|15669706|ref|NP_248519.1|  952 --IPAKDIKENDYIAMPfnykverkpisllnllkylditdvliefdenstifekiaeyirnniktstkykylrnrrvpl 1028
                                    ..9**************************************************************************** PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669706|ref|NP_248519.1| 1029 kyliewnfdldeiekeakyiyksvagtkkiplfklderfwyfaglvlgdgsiqdskiriaqtplkdvksildetfpflh 1107
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669706|ref|NP_248519.1| 1108 nwisgnqviisnpiiaeileklgmrngklngiifslpesyinaliagyfdtdgcfsllydkkakkhnlrmvltskrrdv 1186
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
               Intein_splicing   94 ............................................................................... 93  
                                                                                                                   
  gi|15669706|ref|NP_248519.1| 1187 lekigiylnsigilntlhksrevysliisnksletfkekiakylkirkeafingyktykkeheerfecdllpvkevfkk 1265
                                    ******************************************************************************* PP

                                    ......................................................HSCEEEEEEEEEEEEECEEEEEEEE CS
                                    ......................................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
               Intein_splicing   94 ......................................................dadvvwdkvksievedeeeyVYdlt 118 
                                                                                          ++d+++ +vk++e+  +++yVYdl+
  gi|15669706|ref|NP_248519.1| 1266 ltfekgrkeilkdskihienwykektnnipreklktvlryannsehkeflekivNGDISFVRVKKVENIPYDGYVYDLS 1344
                                    ******************************************************************************* PP

                                    ETTT-EEEECTTEEE- CS
                                    xxxxxxxxxxxxxxxx RF
               Intein_splicing  119 vednhNFvangiivHN 134 
                                    +++n+NF++ng+i HN
  gi|15669706|ref|NP_248519.1| 1345 IKHNQNFISNGVISHN 1360
                                    ***************9 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       8.8   9.8e+03      39      63 ..     229     261 ..     204     269 .. 0.60
   2 !   87.7   0.3   4.4e-28   4.9e-25       1     103 []     551     712 ..     551     712 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.8
                                   TEEEEE........ECTTTHHHHHHHHHHHHHH CS
                        Toprim  39 fkpvye........eiedkkkvlkalkelakra 63 
                                   ++++y+        +ied+ k+ ++lk+  ++ 
  gi|15669706|ref|NP_248519.1| 229 INEAYKiiylikigKIEDAMKKREILKKKISKI 261
                                   445555666674444555555555555554444 PP

  == domain 2  score: 87.7 bits;  conditional E-value: 4.4e-28
                                   EEEEESSHHHHHHHHHTHT..................STEEEEEEESSSSEEEHS.......................... CS
                        Toprim   1 elvivEgpsdaktiakalg..................sgfqavtaslGhildlet.......................... 37 
                                   +l++vE+p++a+tia+++g                  + ++++tas Gh++dl+t                          
  gi|15669706|ref|NP_248519.1| 551 VLMVVESPNKARTIANFFGkpsvrkinnrnvyevcigDLNLIITASGGHVFDLVTkegfygvkiennlyipiytsikkvng 631
                                   69*****************************************************************66666655555555 PP

                                   .......TTEEEEE..............ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEE CS
                        Toprim  38 .......efkpvye..............eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellenkigr 97 
                                          +                    + +d+k+++++++e+a ++d i++atD D+eGe+i+++++ ++ ++++n i+r
  gi|15669706|ref|NP_248519.1| 632 eqftdqkD-----LeelikqlmekgervNAMDAKENIEIIREIADEVDAIFIATDIDTEGEKIGYDIAINALPFNRN-IYR 706
                                   55555552.....0555557778*********************************************9999*****.*** PP

                                   EEESSS CS
                        Toprim  98 vefsei 103
                                   v f+ei
  gi|15669706|ref|NP_248519.1| 707 VGFNEI 712
                                   ****98 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.41   4.6e+02      35      60 ..     336     361 ..     319     374 .. 0.79
   2 !    7.3   0.0    0.0054         6       4      33 ..    1067    1091 ..    1064    1103 .. 0.82
   3 !   50.1   0.5   2.3e-16   2.6e-13       2      82 ..    1147    1226 ..    1146    1227 .. 0.95
   4 ?   -2.7   0.2       6.6   7.4e+03      56      82 ..    1284    1318 ..    1278    1318 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.41
                                   HHHHHHHHHHHHCT.HSCEEEEEEE- CS
                   LAGLIDADG_3  35 elledvqrlLlrlGIestiyekkkak 60 
                                   e ++++ ++Ll+ +I++++ ++k +k
  gi|15669706|ref|NP_248519.1| 336 EKAQEIEKYLLENNIKAKLIHSKDKK 361
                                   6699**************99995444 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0054
                                    HHHHHHHHHHCCECCECSTTTTSEEEEES- CS
                   LAGLIDADG_3    4 aafLrGlfdaDGsvskskkkgvsisltsss 33  
                                      + +Gl  +DGs++ sk     i+++++ 
  gi|15669706|ref|NP_248519.1| 1067 FWYFAGLVLGDGSIQDSK-----IRIAQTP 1091
                                    6789**************.....9999985 PP

  == domain 3  score: 50.1 bits;  conditional E-value: 2.3e-16
                                    HHHHHHHHHHHHCCECCECSTTTTS.....EEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTT CS
                   LAGLIDADG_3    2 vkaafLrGlfdaDGsvskskkkgvs.....isltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisgenl 75  
                                    ++ a+++G+fd+DG++s   +k+ +     + lts+ +++le++  +L+ +GI +t++++     r vy  liis+++l
  gi|15669706|ref|NP_248519.1| 1147 YINALIAGYFDTDGCFSLLYDKKAKkhnlrMVLTSKRRDVLEKIGIYLNSIGILNTLHKS-----REVY-SLIISNKSL 1219
                                    6789*************999998889999*******************************.....9999.********* PP

                                    CGGGTTT CS
                   LAGLIDADG_3   76 krFleki 82  
                                    ++F eki
  gi|15669706|ref|NP_248519.1| 1220 ETFKEKI 1226
                                    *****99 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 6.6
                                    E..EEE-SCCCC......ECCCHCHCTTCGGGTTT CS
                   LAGLIDADG_3   56 k..kkakgrgvy......rlliisgenlkrFleki 82  
                                    +  +k+k ++++       l++ ++++ k Fleki
  gi|15669706|ref|NP_248519.1| 1284 EnwYKEKTNNIPreklktVLRYANNSEHKEFLEKI 1318
                                    44455555555566666677888888888888887 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.3   1.7e-08   1.9e-05       6      74 ..     112     185 ..     108     189 .. 0.84
   2 !   17.2   0.0   4.3e-06    0.0048      20     110 ..     326     478 ..     310     479 .. 0.80
   3 ?    4.3   0.1     0.043        48      44      79 ..     652     686 ..     622     704 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.7e-08
                                   HHHHHHHTTTTSEEEEEESSHHHHHH....HHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESG CS
                    Helicase_C   6 llellkleeeggkilifvntidrlek....vklllekk..gikvavlhgelpqnereeileqfnkgesdvLiatd 74 
                                   l+ l+ l ++g++++i+++t+  +++    ++ l+ek+  +i+v+++h+el+++e++e+ e+  ++++dvLi+t+
  gi|15669706|ref|NP_248519.1| 112 LMSLF-LAKKGKRCYIILPTTLLVKQtyekISSLTEKNnlNIRVVAYHSELSTKEKKEVKERIENNDYDVLITTS 185
                                   55665.78999999999999996655554567777777799********************************97 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 4.3e-06
                                   EEEESSHHHHHH....HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG....GTSSSTST.TESEEEES CS
                    Helicase_C  20 lifvntidrlek....vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdv....aerGidip.kvnlVinf 91 
                                   ++fv     +ek     k+lle++ ik+  +h+     + ++ +++f++g++dvLi        + rG+d+p +v++ i++
  gi|15669706|ref|NP_248519.1| 326 IVFVSIDYGVEKaqeiEKYLLENN-IKAKLIHS-----KDKKGFDDFREGKIDVLIGVASyygvLVRGLDMPeRVRYAIFY 400
                                   555544444444444668887777.***99999.....78899************88775555599*****977******* PP

                                   SSS.SSH..........................................................HHHHHHHTTSSST CS
                    Helicase_C  92 dlp.rnv..........................................................tsyiqriGRtgRa 110
                                   ++p +++                                                          ++yiq++GRt R+
  gi|15669706|ref|NP_248519.1| 401 GIPkFKIrlkeyinslkekgelkediniegkteeeirqiiteklkiknfslrkeddeylllipdvKTYIQASGRTSRM 478
                                   ***7223555668888999999999999999999999999999999999999999999999999999*******9996 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.043
                                   EEESTTSTHHHHHHHHHHHHTTSSS.EEEESGGGTSS CS
                    Helicase_C  44 avlhgelpqnereeileqfnkgesd.vLiatdvaerG 79 
                                    ++++ + ++e++ei+++  ++e+d + iatd+  +G
  gi|15669706|ref|NP_248519.1| 652 ERVNA-MDAKENIEIIREI-ADEVDaIFIATDIDTEG 686
                                   44455.999**********.778898******97776 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.1   2.2e-14   2.5e-11       2     147 ..      81     220 ..      80     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 2.2e-14
                                   HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST..SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx RF
                          DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid..lrvll 80 
                                   +iQ+   + +l+++++ +  +TG GK+   ++  l  ++    k+g+++ i+ Pt+ L++qt++++++++++ +  +rv++
  gi|15669706|ref|NP_248519.1|  81 SIQKMWAKRVLKNKSFSIVVPTGVGKSFFGILMSL--FL---AKKGKRCYIILPTTLLVKQTYEKISSLTEKNNlnIRVVA 156
                                   5999999********************98777777..43...59999************************8553355554 PP

                                   E...ETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHH CS
                                   x...xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  81 i...iggvaardqlskldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinriln 147
                                       ++ +++++ +++++n+ +d++++t   l + +        ++ f+ +D +d ll+   s+ i+r l+
  gi|15669706|ref|NP_248519.1| 157 YhseLSTKEKKEVKERIENNdYDVLITTSNYLTKNMP-----KCKFDFVFVDDVDALLKA--SKNIDRTLK 220
                                   422255777788888888667*********9999664.....345889999*****9997..666666655 PP

>> LAGLIDADG_1  LAGLIDADG endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.9       1.1   1.3e+03      27      65 ..     422     459 ..     404     470 .. 0.68
   2 ?    0.5   0.2       1.1   1.2e+03      36      62 ..     995    1019 ..     977    1037 .. 0.74
   3 !   41.9   4.4   1.3e-13   1.5e-10       1     101 [.    1152    1247 ..    1152    1248 .. 0.91
   4 ?   -2.4   0.8       8.5   9.5e+03      27      89 ..    1299    1367 ..    1278    1377 .. 0.56

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.1
                                   EEEEEEEEEE.GGGHHHHHHHHHHHTECEEEEETTTEEEE CS
                   LAGLIDADG_1  27 vqlefqielk.kkdesllekikeylglgsikkrkkdkyvs 65 
                                   ++  ++i  + k +e++ + i e l++++++ rk+d  + 
  gi|15669706|ref|NP_248519.1| 422 LKEDINI--EgKTEEEIRQIITEKLKIKNFSLRKEDDEYL 459
                                   3333444..455899999****************997554 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.1
                                    EGGGHHHHHHHHHHHTECEEEEETTTE CS
                   LAGLIDADG_1   36 kkkdesllekikeylglgsikkrkkdk 62  
                                    + ++ ++ eki+ey+   +ik+ +k k
  gi|15669706|ref|NP_248519.1|  995 D-ENSTIFEKIAEYIR-NNIKTSTKYK 1019
                                    4.67788888888888.7777766633 PP

  == domain 3  score: 41.9 bits;  conditional E-value: 1.3e-13
                                    HHHHHHHHEEEEEEEEETTTTTTSEEEEEEEEEEEEGGGHHHHHHHHHHHT.ECEEEEETTTE.EEEEEE-SHHHHHHT CS
                   LAGLIDADG_1    1 laGFiDgdGsfsitvtkskskktslkvqlefqielkkkdesllekikeylg.lgsikkrkkdk.yvsyiisnsskslki 77  
                                    +aG++D+dG+fs+ ++k+         ++++++ l++k+ ++leki  yl+ +g++++ +k++ ++s+iisn  ksl++
  gi|15669706|ref|NP_248519.1| 1152 IAGYFDTDGCFSLLYDKKA-------KKHNLRMVLTSKRRDVLEKIGIYLNsIGILNTLHKSReVYSLIISN--KSLET 1221
                                    79*****************.......79****************************9999988899999999..***** PP

                                    HHHHHHHST..-SSTHHHHHHHHHHH CS
                   LAGLIDADG_1   78 lipyfdkyp..llssKyldyldfkkv 101 
                                    + + + ky    +++ ++ y+++kk 
  gi|15669706|ref|NP_248519.1| 1222 FKEKIAKYLkiRKEAFINGYKTYKKE 1247
                                    ********866667778888888875 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 8.5
                                    EEEEEEEEEEGGGHHHHHHHHH....HHTECEEEEETTTE.EEEEEE-S.HHHHHHTHHHHHHHST-SS CS
                   LAGLIDADG_1   27 vqlefqielkkkdesllekike....ylglgsikkrkkdk.yvsyiisn.sskslkilipyfdkyplls 89  
                                    ++  ++ + +++  ++leki +    ++ ++++++   d+ ++++ i++ ++ + + +i++  +y+  s
  gi|15669706|ref|NP_248519.1| 1299 LKTVLRYANNSEHKEFLEKIVNgdisFVRVKKVENIPYDGyVYDLSIKHnQNFISNGVISHNCTYHRTS 1367
                                    445555555566666666665411114446666666666667777777733345556666666666655 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   3.7   4.4e-13     5e-10       1      46 [.       1      44 [.       1      53 [. 0.85

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 4.4e-13
                         zf_Rg  1 MikavfeklCPNCgGdisdeRlekGLpCkrClPkegdvckaLkege 46
                                  Mi  ++++ CPNC+G+i++eRl  G  C++Cl ke++v+++Lk  e
  gi|15669706|ref|NP_248519.1|  1 MIPMIYKEMCPNCNGEITSERLAIGV-CEKCL-KEENVFEKLKLCE 44
                                  9************************6.*****.5667888877544 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   1.8   6.4e-11   7.2e-08       7     141 ..      82     232 ..      49     274 .. 0.74
   2 ?   -2.3   0.1       3.5     4e+03      21      39 ..     256     276 ..     240     286 .. 0.73
   3 ?   -0.0   0.4      0.69   7.7e+02      56      95 ..     487     534 ..     446     543 .. 0.60

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 6.4e-11
                                   HHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....... CS
                        ResIII   7 yQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke... 84 
                                    Q+   +++       ++k + i+ +TG+GK++  + +   l+kkgk  ++ ++ p++ l++qt+e++++++++++ +   
  gi|15669706|ref|NP_248519.1|  82 IQKMWAKRV------LKNKSFSIVVPTGVGKSFFGILMSLFLAKKGK--RCYIILPTTLLVKQTYEKISSLTEKNNLNirv 154
                                   344444444......4789999***********99999999999877..9************************9998999 PP

                                   ...GEEEESSS-B--........-SEEEEEHHHHHHTH.........................HHHTTT-SEEEEETG CS
                        ResIII  85 ...igkkvsgdkkka.kekdstnkkilvttiqsldadseee.................eeeseellrdrfdviiiDEa 141
                                      +++  +++kk+  +++++++ ++l+tt + l++++++                  ++ + +l+   fd  ii Ea
  gi|15669706|ref|NP_248519.1| 155 vayHSELSTKEKKEVkERIENNDYDVLITTSNYLTKNMPKCkfdfvfvddvdallkasKNIDRTLKLLGFDEEIINEA 232
                                   98644444444444468889***************9996556666666666665555555555555555555555555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.5
                                   ....TTSEEEEEESTTSTHHH CS
                        ResIII  21 s..krdkrglikmaTGtGKTl 39 
                                   +   + k+g++ +a  tGK++
  gi|15669706|ref|NP_248519.1| 256 KkiSKIKHGCLIIASATGKSY 276
                                   133677899999999999986 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.69
                                   -EEEEESSHHHHHHHHHHGGGGTGG............GEEEESSS-B- CS
                        ResIII  56 kflflvprkslleqtleefkkflseayke........igkkvsgdkkk 95 
                                     ++lv++k++ e +++ +  ++++++k+          kk+++d++k
  gi|15669706|ref|NP_248519.1| 487 ASIVLVDEKEIFEALKKYMLFMYESEFKRidevnleeLIKKIDEDREK 534
                                   568899999999988855544444444432222221244444444433 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0033       3.6       5      71 ..      90     156 ..      87     158 .. 0.94
   2 ?   -2.3   0.0       5.4     6e+03       4      29 ..    1274    1303 ..    1272    1306 .. 0.86
   3 ?    3.2   0.0       0.1   1.1e+02       6      40 ..    1399    1432 ..    1394    1448 .. 0.87
   4 ?   -3.1   0.0       9.5   1.1e+04      31      64 ..    1559    1592 ..    1558    1594 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0033
                                   TTTTEEEEE...EESTSSHHHHHHHHHHHHTTCEEESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEE CS
                          BRCT   5 lfhgckfvi...tgvldnftrdeleelikehGGkvttevskktthlvvgepesrslkylealklnipivh 71 
                                   ++++++f i   tgv ++f    +  ++ + G ++  ++   tt+lv +++ ++ + ++e+++lni++v 
  gi|15669706|ref|NP_248519.1|  90 VLKNKSFSIvvpTGVGKSFFGILMSLFLAKKGKRC--YIILPTTLLVKQTY-EKISSLTEKNNLNIRVVA 156
                                   78999999999***********************9..99************.9***************95 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.4
                                    TTTTTEEEEE....EESTSSHHHHHHHHHH CS
                          BRCT    4 llfhgckfvi....tgvldnftrdeleeli 29  
                                     ++++ k++i    + + +n++r++l++++
  gi|15669706|ref|NP_248519.1| 1274 EILKDSKIHIenwyKEKTNNIPREKLKTVL 1303
                                    689999999999999999999999999876 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.1
                                    TTTEEEEEEESTSSHHHHHHHHHHHHTTCEEESSC CS
                          BRCT    6 fhgckfvitgvldnftrdeleelikehGGkvttev 40  
                                    ++g + +i  + + +++del e++ke+  k+t+ +
  gi|15669706|ref|NP_248519.1| 1399 MEGAHECI-RPTKPMNTDELIEFLKENNIKLTKNH 1432
                                    67778899.9*****************99997765 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 9.5
                                    HTTCEEESSCSTTSSEEEESSSHSHHHHHHHHHH CS
                          BRCT   31 ehGGkvttevskktthlvvgepesrslkylealk 64  
                                    ++G  v +++ ++  hl+  e +++ ++ + +++
  gi|15669706|ref|NP_248519.1| 1559 KLGIEVYNYLINNYPHLISEERTRELEEIMDKIE 1592
                                    6899999999999999998887666666665555 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00011      0.12      97     210 ..     100     209 ..      30     276 .. 0.80
   2 ?   -3.0   0.1       3.1   3.5e+03     233     258 ..     408     433 ..     403     444 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                     SecA_DEAD  97 mkTGEGKtlvatlpaylnaltgkgvhvvtvndYLakrdaewmgpvyeflGlsvgviese..leseerreaYeaditYgtnn 175
                                   + TG GK+   +l  ++ a +gk + ++     L k+  e+++++ e   l++ v+  +  l+++e++e  +  i     +
  gi|15669706|ref|NP_248519.1| 100 VPTGVGKSFFGILMSLFLAKKGKRCYIILPTTLLVKQTYEKISSLTEKNNLNIRVVAYHseLSTKEKKE-VKERI-----E 174
                                   57**********************************************999999998773333333332.23333.....3 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SecA_DEAD 176 elgfdyLrDnlalskeelvqrglnfaivDEvDsvL 210
                                   +  +d L    +  ++++ + +++f+ vD+vD +L
  gi|15669706|ref|NP_248519.1| 175 NNDYDVLITTSNYLTKNMPKCKFDFVFVDDVDALL 209
                                   33466666666666666677778888888888776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SecA_DEAD 233 eakklvkeleeeedakegveieeesq 258
                                   ++k+++++l+e+ + ke+++ie +++
  gi|15669706|ref|NP_248519.1| 408 RLKEYINSLKEKGELKEDINIEGKTE 433
                                   57889999999*******99998765 PP

>> FHIPEP  FHIPEP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.5   2.8e+03     527     563 ..     987    1023 ..     983    1030 .. 0.80
   2 ?   11.0   0.3   9.5e-05      0.11     348     510 ..    1169    1331 ..    1160    1333 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.5
                                    HHHHHHHHTTTXXSHHHHHHHHHHHTHHHHHHHHH.T CS
                        FHIPEP  527 IletlaeaakktkdvellteavRqaLkrqivqklaee 563 
                                    I + l+e  ++++  e ++e++R+++k +   k++++
  gi|15669706|ref|NP_248519.1|  987 ITDVLIEFDENSTIFEKIAEYIRNNIKTSTKYKYLRN 1023
                                    7888889998999999999999999998877777754 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9.5e-05
                                    HT.......HHHHHHHHHHHHHSS---SEEEEE-TT--TTEEEEEETTEEEEEEE--TTSEEET.........--EEEE CS
                        FHIPEP  348 eeqggeLlerikalrkqlaeelGlvvpeirirdnlelkpneyrikikgvevaegelkpdkllalnpgev.ee.legeet 424 
                                    ++++++L   +++ r+++ e++G+ + +i i + l+ +++ y++ i++ ++++ + k+ k+l ++++   +   + +++
  gi|15669706|ref|NP_248519.1| 1169 KAKKHNLRMVLTSKRRDVLEKIGIYLNSIGILNTLHKSREVYSLIISNKSLETFKEKIAKYLKIRKEAFiNGyKTYKKE 1247
                                    44678999999*****************************************************665554334466777 PP

                                    ETTE...EEEEE-HHHHHHHHTTT--EEEHHHHHHHHHHHHHHHCHHHCHCHHHHHHHHHHH.HTTHHHHHHHHH.HHS CS
                        FHIPEP  425 kepafglpavwieeeqreeaeaagytvvdpssvlathlsevikrhaaellgrqevkklldel.kkeapklveelvpkll 502 
                                    +e+ f+ + + ++e  ++   ++g + + + s +  h+++  k++++++  r+++k++l    ++e+++ +e++v+  +
  gi|15669706|ref|NP_248519.1| 1248 HEERFECDLLPVKEVFKKLTFEKGRKEILKDSKI--HIENWYKEKTNNI-PREKLKTVLRYAnNSEHKEFLEKIVNGDI 1323
                                    8899999999999998888888887777666655..7888888887775.56666666665515667788888888888 PP

                                    -HHHHHHH CS
                        FHIPEP  503 slgelqkv 510 
                                    s  +++kv
  gi|15669706|ref|NP_248519.1| 1324 SFVRVKKV 1331
                                    88888776 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.016        18       3      34 ..     936     968 ..     934     972 .. 0.82
   2 ?    4.4   0.0     0.021        23       6      48 ..    1301    1345 ..    1297    1353 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.016
                                   S--EEEEE.-TTS-EEEEGGG--TTSEEEEETT CS
                  E1-E2_ATPase   3 lpptakvi.rdgteeeidakelvpGDivllkag 34 
                                   +p+++ ++ rd++++ i+ak+++ +D++ ++ +
  gi|15669706|ref|NP_248519.1| 936 TPDHCLLVlRDNQLKWIPAKDIKENDYIAMPFN 968
                                   566666666*******************99876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.021
                                    EEEEE-TTS-EEEEGGG--TTSE..EEEETT-B--SEEEEEEE-S CS
                  E1-E2_ATPase    6 takvirdgteeeidakelvpGDi..vllkagdrvpaDgrivegsa 48  
                                    t+ ++ +++e++   +++v GDi  v +k+ +++p Dg + + s 
  gi|15669706|ref|NP_248519.1| 1301 TVLRYANNSEHKEFLEKIVNGDIsfVRVKKVENIPYDGYVYDLSI 1345
                                    455668999999999*******977889999********987665 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00024      0.27     101     163 ..     126     191 ..      49     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00024
                                   EE--H.HHHHHHHHHHHHH-TTS-EE..E--SSHHHH-----------------EEEE-HHHHHHH CS
                                   xxxxx.xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 101 ivvPa.slldqWeneierhvsssalr..vlvyggqkkmkkkntkvapklladydvvittYdvlsre 163
                                   i+ P+  l++q +++i + +++ +l+  v++y+++ ++k+k+++  +   +dydv+itt ++l ++
  gi|15669706|ref|NP_248519.1| 126 IILPTtLLVKQTYEKISSLTEKNNLNirVVAYHSELSTKEKKEVKERIENNDYDVLITTSNYLTKN 191
                                   7788867889999999999998876511666666665666666666667789*******9999844 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.096   1.1e+02      39      78 ..     404     443 ..     401     444 .. 0.83
   2 ?    6.4   0.1      0.01        11      27      73 ..     623     675 ..     615     681 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.096
                          Img2  39 alredLrkaleelvkvnevtgkieikGdrveevkkfLesk 78 
                                   +++  L++++++l +  e ++ i+i+G+ +ee+++++++k
  gi|15669706|ref|NP_248519.1| 404 KFKIRLKEYINSLKEKGELKEDINIEGKTEEEIRQIITEK 443
                                   56677888888777778899***************99875 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.01
                          Img2  27 ltvirkieGDiaalredLrkalee......lvkvnevtgkieikGdrveevkk 73 
                                   +t i+k++G+    ++dL++ +++       v+   ++++iei  +  +ev +
  gi|15669706|ref|NP_248519.1| 623 YTSIKKVNGEQFTDQKDLEELIKQlmekgeRVNAMDAKENIEIIREIADEVDA 675
                                   699******99988888888888754444336666678888887777777665 PP

>> Sep15_SelM  Sep15/SelM redox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.7    0.0042       4.7      47      75 ..     416     444 ..     412     445 .. 0.93
   2 ?   -1.8   0.1       3.1   3.5e+03      43      62 ..     505     524 ..     498     530 .. 0.86
   3 ?    0.7   0.0      0.53   5.9e+02      60      75 ..    1410    1425 ..    1407    1426 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0042
                                   E-SSS---EEEE-SSS-HHHHHHHHHHHT CS
                    Sep15_SelM  47 ldedgeeverislekwdrdeieelleekg 75 
                                   l+e+ge +e i++e  +++ei++ ++ek+
  gi|15669706|ref|NP_248519.1| 416 LKEKGELKEDINIEGKTEEEIRQIITEKL 444
                                   6899***********************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.1
                                   EEEEE-SSS---EEEE-SSS CS
                    Sep15_SelM  43 kLilldedgeeverislekw 62 
                                   +L +++++ +++++++le++
  gi|15669706|ref|NP_248519.1| 505 MLFMYESEFKRIDEVNLEEL 524
                                   799**************986 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.53
                                    SSS-HHHHHHHHHHHT CS
                    Sep15_SelM   60 ekwdrdeieelleekg 75  
                                    +++++de++e+l+e +
  gi|15669706|ref|NP_248519.1| 1410 KPMNTDELIEFLKENN 1425
                                    589**********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1507  (0.0840538); expected 358.6 (0.02)
Passed bias filter:                      729  (0.0406604); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 1.16u 0.36s 00:00:01.52 Elapsed: 00:00:00.52
# Mc/sec: 9273.36
//
Query:       gi|15669707|ref|NP_248520.1|  [L=335]
Description: hypothetical protein MJ_1513 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.051   14.1   0.2        1.8    9.1   0.0    2.9  3  HTH_27    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.034   6.1e+02      16      40 ..      94     118 ..      90     123 .. 0.84
   2 ?   -1.3   0.1      0.18   3.2e+03      19      43 ..     229     253 ..     221     259 .. 0.65
   3 ?    9.1   0.0   9.9e-05       1.8      37      68 .]     298     327 ..     295     327 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.034
                        HTH_27  16 rrrkkladlcgrlnvedshisyslk 40 
                                   ++rk+  d+ ++ nv++ +++ ++ 
  gi|15669707|ref|NP_248520.1|  94 HERKEFGDVKFYINVSSGSTIGCIA 118
                                   6788889**********99998876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.18
                        HTH_27  19 kkladlcgrlnvedshisyslkkLt 43 
                                    ++++l++++ +  s   +s+kk+ 
  gi|15669707|ref|NP_248520.1| 229 ESIKELIKAVERKESVSNSSVKKMK 253
                                   4566677776665554447777775 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 9.9e-05
                        HTH_27  37 yslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                   ++++kL e +L+e+ ++   +++k +r+++kG
  gi|15669707|ref|NP_248520.1| 298 NVVEKLLELELIEKPEKI--GKSKYIRISEKG 327
                                   689*********888888..***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1637  (0.0913046); expected 358.6 (0.02)
Passed bias filter:                      876  (0.0488594); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2017.24
//
Query:       gi|15669708|ref|NP_248521.1|  [L=120]
Description: hypothetical protein MJ_1514 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-27   96.8   0.3    1.5e-27   96.6   0.3    1.0  1  GGACT     Gamma-glutamyl cyclotransferase, AIG2-like
    1.5e-05   25.3   0.0    2.2e-05   24.7   0.0    1.3  1  AIG2_2    AIG2-like family
  ------ inclusion threshold ------
       0.02   15.3   0.0      0.029   14.8   0.0    1.3  1  GCK       GCK domain


Domain annotation for each model (and alignments):
>> GGACT  Gamma-glutamyl cyclotransferase, AIG2-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.3   2.5e-31   1.5e-27       1     120 [.       4     116 ..       4     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 2.5e-31
                                   EEESSTTSTTSCCCHHHHCSECEEEEEEEECCTBEEEE.ETTTEEEETTSSE..EEEEEEEE-HHHHHHHHHCT.TTTTSE CS
                         GGACT   1 vFvYGtLkrgepnhqrlllgarflesgpatlkgyrlydlggkypalvpgdge.kVkGelyevddeelarLDelEpeepseY 80 
                                   vFvYG+L++g++nh  +l++++f++ g+ t ++y++y+     p++v++++  +++Ge+yevd+++l+r+D lE ++p++Y
  gi|15669708|ref|NP_248521.1|   4 VFVYGSLRKGFWNHEPYLKNSKFIGKGK-TKEKYAMYV--NIIPYVVENEKIsHIVGEVYEVDEKTLKRIDCLE-GHPDYY 80 
                                   8*******************9*******.********8..479****7777679********************.****** PP

                                   EEEEEEEEC..TTS-EEEEEEEEETT..GGGCCS-S-SS-- CS
                         GGACT  81 ereevkvev.ledgeqveawvYvyageeeegdrliesgdWr 120
                                   +r+  kv++ l++g+++eaw+Y+y++     + l+esgd++
  gi|15669708|ref|NP_248521.1|  81 RRK--KVSIiLDSGKEIEAWLYFYPE---SCGILVESGDYK 116
                                   ***..776667*************55...667779999997 PP

>> AIG2_2  AIG2-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   3.7e-09   2.2e-05       1      51 [.      54     103 ..      54     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.7e-09
                        AIG2_2   1 eVfGvlweidlenlkdLDkqEgvedgiyrpievrVstatgeevlaraYvls 51 
                                   ++ G ++e+d++ lk++D  Eg +d  yr+ +v++   +g+e++a++Y + 
  gi|15669708|ref|NP_248521.1|  54 HIVGEVYEVDEKTLKRIDCLEGHPD-YYRRKKVSIILDSGKEIEAWLYFYP 103
                                   6889******************776.**********************875 PP

>> GCK  GCK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.9e-06     0.029       6      58 ..      24      81 ..      21      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.9e-06
                           GCK  6 ceFmkgGgCkesfiawekcveeaeknke..dlvekcaev...tatlkkCmeahsdYYe 58
                                  ++F+ +G+ ke++  + + +  + +n++   +v +  ev   t +   C+e h+dYY 
  gi|15669708|ref|NP_248521.1| 24 SKFIGKGKTKEKYAMYVNIIPYVVENEKisHIVGEVYEVdekTLKRIDCLEGHPDYYR 81
                                  689999*****9999999884444333223666666555100555567*********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 839.94
//
Query:       gi|15669709|ref|NP_248522.1|  [L=355]
Description: hypothetical protein MJ_1515 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-79  264.7   0.0    7.8e-79  264.4   0.0    1.1  1  GATase_4  Glutamine amidotransferases class-II
    7.9e-07   29.3   0.0      3e-06   27.5   0.0    1.8  2  GATase_6  Glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.022   14.9   2.2        2.8    8.1   0.1    2.5  2  DUF613    Protein of unknown function (DUF613)
       0.14   12.1   0.8       0.33   10.9   0.8    1.6  1  HTH_12    Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.4   0.0   1.7e-82   7.8e-79       1     258 [.       1     255 [.       1     266 [. 0.95

  Alignments for each domain:
  == domain 1  score: 264.4 bits;  conditional E-value: 1.7e-82
                      GATase_4   1 mceLLgmssnvptdisfsftgfaarggltdahadGwGiafyegkaarvfkdpepsaesplaelvreypiksknvvaHiRka 81 
                                   mceLLg+++n+++++ +s+++f++r      h +GwGiafy++ ++rv+k+p    e+ lae vr  +iks++++aHiRka
  gi|15669709|ref|NP_248522.1|   1 MCELLGICFNKKVNVELSLNSFKHRSED---HPNGWGIAFYPDGFVRVIKEPIKMNEALLAECVRWTKIKSNIFIAHIRKA 78 
                                   9***********************8877...************************************************** PP

                      GATase_4  82 tqGevklenthpFvRelwgrewifAHnGdlkeykpklegrfePvGsTDsElafCelleelasrfekaepsaeeleralael 162
                                   + G+ ++ nthpFvR+l ++e+ fAHnG+l +y++   + + P+G+TDsE++fC+ll+++++r     +  +e ++ + ++
  gi|15669709|ref|NP_248522.1|  79 SAGSESYVNTHPFVRKLEDKEIAFAHNGTLLGYEDLELDGYYPIGETDSEYVFCYLLSQIEKRE---IEWNKEGFDEMLDI 156
                                   ***********************************9999************************9...45678888888899 PP

                      GATase_4 163 akeiaelGvfnlllsdgralfahas....trLvyilRkaPfgeaelkdedlevdfeevttkedrvavvatepLtrdetWkk 239
                                   + +i+ +G fn l+sdg++lfa+ +    ++L+++ Rk+P+g+++l ded+ +++ +v++ +++  ++at+pLt +e+Wk+
  gi|15669709|ref|NP_248522.1| 157 LLDINYYGAFNCLFSDGEYLFAYKDyrgrRELHFLKRKPPYGRIRLEDEDYIINLGDVKSVREEGFIIATNPLT-NEDWKS 236
                                   99**********************9776667*******************************************.99**** PP

                      GATase_4 240 lepGellvfrdGalvatas 258
                                   +e+Gel+vf++G+++ +++
  gi|15669709|ref|NP_248522.1| 237 FENGELMVFKNGEMIYSNK 255
                                   *************988754 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   6.7e-10     3e-06      10      83 ..      66     137 ..      57     158 .. 0.81
   2 ?   -1.4   0.0      0.56   2.5e+03      37      54 ..     237     254 ..     225     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 6.7e-10
                      GATase_6  10 vedevalaHvRlaivglaeeega.qPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevlla.llee 83 
                                   +++++ +aH R a+ g + +  + +Pf  + ed++++++hNG+   y    e+l+  +g+   +++D+e ++  ll++
  gi|15669709|ref|NP_248522.1|  66 IKSNIFIAHIRKASAGSE-SYVNtHPFvrKLEDKEIAFAHNGTLLGY----EDLEL-DGYYPIGETDSEYVFCyLLSQ 137
                                   37789************9.55666***9999****************....59999.9999999*****998856544 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.56
                      GATase_6  37 sedgrlllvhNGeiynyk 54 
                                    e+g+l++  NGe+   +
  gi|15669709|ref|NP_248522.1| 237 FENGELMVFKNGEMIYSN 254
                                   488999999999975444 PP

>> DUF613  Protein of unknown function (DUF613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.3     0.003        13      22      78 ..     137     193 ..     125     210 .. 0.79
   2 ?    8.1   0.1   0.00062       2.8       7      64 ..     228     286 ..     223     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.003
                        DUF613  22 yvnkkkvgkekeniteleYilLDlflfGPlkikvseyekitkiikkrtkrykkllee 78 
                                    + k+++  +ke   e+  ilLD+  +G +++ +s+ e    +  +r +r  ++l++
  gi|15669709|ref|NP_248522.1| 137 QIEKREIEWNKEGFDEMLDILLDINYYGAFNCLFSDGEYLFAYKDYRGRRELHFLKR 193
                                   5677788888888999999***************99777777777776666666665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00062
                        DUF613   7 lkekeyWeefsl..lplyvnkkkvgkekeniteleYilLDlflfGPlkikvseyekitki 64 
                                   + ++e W++f +  l ++ n++ +   ++ +t+le  +L ++   P ++ ++++ ++ ++
  gi|15669709|ref|NP_248522.1| 228 PLTNEDWKSFENgeLMVFKNGEMIY-SNKRLTDLELKILKILRESPHRVSLKKIIENLEY 286
                                   557899******7667777888888.****************999999999886555554 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   7.3e-05      0.33       2      53 ..     263     316 ..     262     320 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.3e-05
                        HTH_12   2 eILkilaesdkpigakeiaeeLkkrgydigera..vRyrLrkleergltrrvgy 53 
                                   +ILkil es + ++ k+i e+L+    +i+  a  vR  +r+l ++g++++ ++
  gi|15669709|ref|NP_248522.1| 263 KILKILRESPHRVSLKKIIENLEYLSRNIRHDAsvVRIGIRSLLDKGYIKQDSR 316
                                   6***********************999999877669*99****99999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2533.67
//
Query:       gi|15669710|ref|NP_248523.1|  [L=99]
Description: hypothetical protein MJ_1516 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-10   41.0   2.9    2.4e-10   40.6   2.9    1.2  1  TM2       TM2 domain
  ------ inclusion threshold ------
      0.028   14.6   0.4        0.1   12.8   0.1    1.8  2  Pox_A28   Poxvirus A28 family


Domain annotation for each model (and alignments):
>> TM2  TM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   2.9   2.7e-14   2.4e-10       2      50 ..      32      79 ..      31      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.7e-14
                           TM2  2 kksklvaylLwffLGglGvHRFYlGktgsGvlqlltfv.Gglgiwwlidl 50
                                  kks ++a+lL+f+  + G+   YlG++g+G++ llt++  +++i++++d 
  gi|15669710|ref|NP_248523.1| 32 KKSVGIAVLLSFI--IPGAGQMYLGRVGKGIILLLTCWlIIPWIYSIYDA 79
                                  9***********6..99******************************995 PP

>> Pox_A28  Poxvirus A28 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.12     1e+03      60      84 ..      11      35 ..       3      41 .. 0.71
   2 ?   12.8   0.1   1.2e-05       0.1      16      47 ..      66      97 ..      59      99 .] 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.12
                       Pox_A28 60 DpnDevldvkqkWrCvkyenkyvsv 84
                                     D v d+ +  r v ye+k  sv
  gi|15669710|ref|NP_248523.1| 11 QIKDFVKDMDKNQRIVYYEQKKKSV 35
                                  5567777888888888887666555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.2e-05
                       Pox_A28 16 vcllllqlyaiyenydnikefndahsaleysk 47
                                    l++  +y+iy+ y++ k++n++  ++ +sk
  gi|15669710|ref|NP_248523.1| 66 CWLIIPWIYSIYDAYKSAKDYNAQLYSIIFSK 97
                                  34667789****************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 694.98
//
Query:       gi|15669711|ref|NP_248524.1|  [L=155]
Description: hypothetical protein MJ_1516.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1100.38
//
Query:       gi|15669712|ref|NP_248525.1|  [L=278]
Description: hypothetical protein MJ_1517 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1854.45
//
Query:       gi|15669713|ref|NP_248526.1|  [L=374]
Description: hypothetical protein MJ_1518 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.063   13.2   0.0       0.19   11.7   0.0    1.8  1  Gag_p10       Retroviral GAG p10 protein
      0.088   12.8   0.1       0.21   11.6   0.1    1.6  1  DUF3338       Domain of unknown function (DUF3338)
          1    9.5   6.5        1.7    8.7   0.3    3.5  3  Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)


Domain annotation for each model (and alignments):
>> Gag_p10  Retroviral GAG p10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.1e-05      0.19       2      37 ..     267     302 ..     266     314 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
                                   HHHHHHHHHHHHHTTT----HHHHHHHHHHHHHH-T CS
                       Gag_p10   2 kelflsllkallkerGlkvskkklekflqfveevcP 37 
                                   ke+f +++ ++l++ G kv++  +++ l +++e  P
  gi|15669713|ref|NP_248526.1| 267 KEMFNHVIFKILRNGGFKVKEYDIIETLLNIRENLP 302
                                   799***************************999776 PP

>> DUF3338  Domain of unknown function (DUF3338)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.5e-05      0.21       5      58 ..     315     368 ..     312     371 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.5e-05
                       DUF3338   5 elissssgsllssgskssessekqkkekvaalkkkqkaleerLelkleelkklC 58 
                                   eli+   g++ +s ++   +++k +ke v++l++ +k+l e+ +  l++l+kl 
  gi|15669713|ref|NP_248526.1| 315 ELIKIIRGIVRESKKDVFYNNMKRLKEFVEELREMEKKLSEANNITLHDLRKLG 368
                                   67777789999*****************************************96 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.084     5e+02      83     122 ..      92     131 ..      35     148 .. 0.69
   2 ?    8.7   0.3   0.00029       1.7       6     115 ..     191     296 ..     189     308 .. 0.72
   3 ?    1.3   0.1     0.055   3.3e+02      46      75 ..     311     351 ..     298     368 .. 0.49

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.084
                                   S-HHHHHHHHHHHHGGGS---HHHHHHHHHHHHHHT--SH CS
                  Spore_III_AB  83 esfeeaweeavekllkklaLkkedkeilkelgeslgysdr 122
                                   +++e +++   ++ l+  +++++++ei+k+l e    +d+
  gi|15669713|ref|NP_248526.1|  92 NAVEIIFKVVSNEILRTESIDDKELEIIKKLHELVVLTDK 131
                                   4445555555566677788888889998888887776665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00029
                                   XXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHH.-SS-HHHHHHHHHHCS-TTHHHHHHHHHHHHH.STSS-H CS
                  Spore_III_AB   6 llillactgiGfalakrlkrrlkeleelkralellegeiry.gatpLpealeklaeksesplseffeevaerleekegesf 85 
                                   +li++ +  + ++l+k+ k+r+k   e+k+++e+l  +  y     + e   k+ +++   +  ++ +  ++    e++  
  gi|15669713|ref|NP_248526.1| 191 VLIICLSKFYNLYLSKDKKEREKLADEIKNLIEYLYFDWYYdFIDNIGEYEFKFIKNIAA-MC-LLYDYTKE---LEKDGS 266
                                   79*********************************9888885555566633333322222.22.23333444...367777 PP

                                   HHHHHHHHHHHGGGS---HHHHHHHHHHHH CS
                  Spore_III_AB  86 eeaweeavekllkklaLkkedkeilkelge 115
                                   +e+++  + k l++ ++k ++ +i+ +l +
  gi|15669713|ref|NP_248526.1| 267 KEMFNHVIFKILRNGGFKVKEYDIIETLLN 296
                                   788888888888888888888777777655 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.055
                                   H-SS-HHHHHHHHHHCS-T........THHHH...HHHHHH CS
                  Spore_III_AB  46 ygatpLpealeklaekses........plsef...feevae 75 
                                   y  + L ++++ + ++s++        +l+ef   ++e+ +
  gi|15669713|ref|NP_248526.1| 311 YFDKELIKIIRGIVRESKKdvfynnmkRLKEFveeLREMEK 351
                                   55555555555555444444433322222222111222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1672  (0.0932567); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2266.19
//
Query:       gi|15669714|ref|NP_248527.1|  [L=1175]
Description: exodeoxyribonuclease V RecD [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-31  109.5   1.1    3.9e-31  108.4   0.1    2.2  1  AAA_19           AAA domain
    1.7e-29  103.0   0.0      3e-29  102.1   0.0    1.3  1  AAA_30           AAA domain
    5.2e-16   58.2   0.0    9.7e-16   57.3   0.0    1.5  1  UvrD_C_2         UvrD-like helicase C-terminal domain
      1e-12   47.9   0.1    5.6e-12   45.5   0.1    2.4  1  HHH_4            Helix-hairpin-helix containing domain
    3.3e-11   43.4   0.0    2.8e-05   24.0   0.0    3.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    1.9e-06   27.6   0.5    1.6e-05   24.6   0.2    2.8  2  SH3_13           ATP-dependent RecD-like DNA helicase SH3 dom
    5.3e-06   26.8   0.0    2.4e-05   24.6   0.0    2.1  1  AAA_22           AAA domain
    5.6e-06   26.3   5.5      0.048   13.5   0.0    3.6  3  AAA_11           AAA domain
    6.5e-05   22.5  12.2    6.5e-05   22.5  12.2    4.2  2  UvrD_C           UvrD-like helicase C-terminal domain
    0.00013   21.2   0.2    0.00026   20.2   0.2    1.4  1  T2SSE            Type II/IV secretion system protein
    0.00016   21.6   0.0    0.00039   20.3   0.0    1.7  1  Helicase_RecD    Helicase
    0.00057   19.8   0.1     0.0021   18.0   0.1    2.0  1  RsgA_GTPase      RsgA GTPase
     0.0013   19.1   1.2      0.022   15.2   0.0    3.4  3  AAA              ATPase family associated with various cellul
      0.004   16.9   2.6     0.0078   16.0   0.2    2.8  3  DEAD             DEAD/DEAH box helicase
     0.0049   16.4   0.3      0.047   13.1   0.3    2.5  1  PhoH             PhoH-like protein
     0.0067   15.4   1.3       0.68    8.8   0.1    2.4  2  AAA_6            Hydrolytic ATP binding site of dynein motor 
     0.0082   16.1   0.7      0.049   13.6   0.7    2.4  1  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.032   14.6   0.0    1.8  1  AAA_16           AAA ATPase domain
      0.013   15.5   0.3      0.013   15.5   0.3    4.0  2  ResIII           Type III restriction enzyme, res subunit
      0.017   15.7   0.0      0.017   15.7   0.0    4.5  3  AAA_18           AAA domain
       0.02   14.4   1.0       0.12   11.9   0.5    2.4  2  AAA_7            P-loop containing dynein motor region
       0.03   14.8   1.2       0.13   12.7   0.0    2.7  2  ABC_tran         ABC transporter
      0.031   14.0   0.3        3.8    7.2   0.0    2.7  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.031   14.6   0.3        0.6   10.5   0.0    2.9  2  RNA_helicase     RNA helicase
      0.073   11.6   0.1       0.12   10.9   0.1    1.2  1  DUF853           Bacterial protein of unknown function (DUF85
      0.077   13.0   0.0       0.37   10.8   0.0    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
      0.097   12.4   0.1       0.22   11.3   0.1    1.5  1  AAA_29           P-loop containing region of AAA domain
       0.11   12.5   0.1       0.35   10.9   0.1    1.9  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.12   12.3   0.3       0.33   10.9   0.3    1.7  1  NACHT            NACHT domain
       0.24   11.0   0.0       0.45   10.1   0.0    1.4  1  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.4   0.1   6.5e-34   3.9e-31       1     145 [.     569     715 ..     569     716 .. 0.88

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 6.5e-34
                        AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldf 80 
                                   q+eav   lk++v ++t+++GtGKT+v+k+i++l++e+ g+  ++i+++++tg++a+ ++e+l + +a a+TiHr    +f
  gi|15669714|ref|NP_248527.1| 569 QTEAVVnLLKNRVGILTGPAGTGKTTVIKTIMELMKEVLGL--NKIYILTPTGKSAMVVNEKL-NNLATAKTIHRYIAEEF 646
                                   7899955********************************98..8*******************.66899*****9988889 PP

                        AAA_19  81 ddlltealelle..eaeeekklqeeellivDEfqdvd.elqyrLlkallgek.kklllvGDpdQliyvf 145
                                   +d  +    ++   ++ + ++ +e ++li+DE+++vd e++ rLl +++ ++ k+l++vGD++Ql++v+
  gi|15669714|ref|NP_248527.1| 647 KDYFEGDNYFILrlDKITGNDKKEIDALIIDESSMVDiETMGRLLGTIKLDNlKYLIFVGDINQLPPVG 715
                                   98887777766557333344443557**************************999************98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.0     5e-32     3e-29       5     182 ..     568     769 ..     565     775 .. 0.88

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 5e-32
                        AAA_30   5 eQaaavealltsgdrvavltGpAGtGKttalkalreaweaa.g.grviglAptgkaAkvLaeelg..ieastiakllkrlk 81 
                                    Q +av +ll+++  v +ltGpAGtGKtt++k++ e++++  g  ++ +l+ptgk A v++e+l+  ++a+ti++++ +  
  gi|15669714|ref|NP_248527.1| 568 MQTEAVVNLLKNR--VGILTGPAGTGKTTVIKTIMELMKEVlGlNKIYILTPTGKSAMVVNEKLNnlATAKTIHRYIAEEF 646
                                   599******9888..9***********************9988899******************9656*********6555 PP

                        AAA_30  82 ..................grarlepgtllivDEagmvdtkqlaallkaaekag.akvilvGDerQlasVeaGgvlrdlvea 143
                                                     g ++ ++ + li+DE++mvd++++ +ll  ++ ++   +i+vGD +Ql++V+aG+++ d+ + 
  gi|15669714|ref|NP_248527.1| 647 kdyfegdnyfilrldkitG-NDKKEIDALIIDESSMVDIETMGRLLGTIKLDNlKYLIFVGDINQLPPVGAGKPFYDIYNY 726
                                   9*************98852.3444559************************996779*********************876 PP

                        AAA_30 144 ....agigtaeLtevvRqkeseeraaalalregdaeealeala 182
                                       + +   +L+ v R +++++ ++++ + + d ee ++ l+
  gi|15669714|ref|NP_248527.1| 727 lekvNPQSICKLEIVLRADSKKIVELSKLFLDIDKEERIKILN 769
                                   66555668899*******9999999999888877777666655 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   1.6e-18   9.7e-16       1      52 []     959    1007 ..     959    1007 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 1.6e-18
                      UvrD_C_2    1 hayaltihkaQGsefpaVivfdpdlaaarmgelrrrlLYtavTRAreklilv 52  
                                    haya+tihk+QGs f++Vi++ p   +     +++++LYta+TRA+++l+++
  gi|15669714|ref|NP_248527.1|  959 HAYAITIHKSQGSGFENVILIIPKGLNKF---VSKEMLYTAITRAKKRLYVI 1007
                                    89*************************99...57****************96 PP

>> HHH_4  Helix-hairpin-helix containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.1   9.4e-15   5.6e-12       8      91 ..     354     447 ..     346     448 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 9.4e-15
                         HHH_4   8 imeflqeygisaklaekiykkygee..aleilkenPYrliedvegig......FktaDkiakkl...gieedsprRikagi 77 
                                   + ++   y++sa ++eki ++y++e   l+ + +nPY+l+ed+++ +      F+++D++ ++    ++++ sp+R++a++
  gi|15669714|ref|NP_248527.1| 354 LKNYAVYYELSAFKLEKIKEQYEKEfiNLDNIIKNPYILVEDLKENDsferiiFEELDSWERRRlgdKFNPYSPYRVRALL 434
                                   5567778999***************666777************9988999999********9888888************* PP

                         HHH_4  78 lyvlkeaaneeGht 91 
                                   +++lk+++ ++G+t
  gi|15669714|ref|NP_248527.1| 435 VEILKRHL-SSGNT 447
                                   ********.7***9 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   9.8e-05     0.059       2     129 ..     583     738 ..     582     792 .. 0.80
   2 !   24.0   0.0   4.6e-08   2.8e-05     177     233 ..     954    1007 ..     916    1008 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.8e-05
               Viral_helicase1   2 vvhGvpGcGKStlirkllrts.........liltvnrptaelltegk....................pklpnlsvrtvdsf 53 
                                   +  G +G GK+t+i+++++           +ilt+  ++a +++e +                     +  n  + ++d++
  gi|15669714|ref|NP_248527.1| 583 ILTGPAGTGKTTVIKTIMELMkevlglnkiYILTPTGKSAMVVNEKLnnlataktihryiaeefkdyFEGDNYFILRLDKI 663
                                   56799**********999888888999888666666666666666667777777799999999988778888999999999 PP

               Viral_helicase1  54 lmalvkstkgkililDEylllh...aGyilllaalskaklvilfGDplQipfhsrnasfllahlpsslshrvgrrttyl 129
                                   + +++k+   + li+DE  +++   +G +l  ++l+++k +i +GD +Q p        +  +++  l+++ ++++++l
  gi|15669714|ref|NP_248527.1| 664 TGNDKKE--IDALIIDESSMVDietMGRLLGTIKLDNLKYLIFVGDINQLPPVGAG--KPFYDIYNYLEKVNPQSICKL 738
                                   9999987..89*******999744367777789999*************9998644..488888888888888887776 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 4.6e-08
               Viral_helicase1  177 kealgvrevttvhevqGltfdkVtlvllketdlelisesrenllvAlTRhrkslvil 233 
                                     +++ +  + t h  qG+ f++V+l++ k   ++ +  s+e l++A+TR++k+l+++
  gi|15669714|ref|NP_248527.1|  954 EKEMEHAYAITIHKSQGSGFENVILIIPKG-LNKFV--SKEMLYTAITRAKKRLYVI 1007
                                    3334444579******************66.56644..58*************9875 PP

>> SH3_13  ATP-dependent RecD-like DNA helicase SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.2   2.6e-08   1.6e-05      27      55 ..     884     933 ..     863     943 .. 0.80
   2 ?   -2.3   0.0         7   4.2e+03      27      38 ..    1144    1155 ..    1135    1159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.6e-08
                        SH3_13  27 rvgDkVmqlkNnydk..............gvfNGDiGiikei.......d 55 
                                   +v DkV+q++Nny+k              gvfNG +G+  ++       +
  gi|15669714|ref|NP_248527.1| 884 KVADKVIQIRNNYKKwvydterrkwvkehGVFNGMMGFAYTFkkwnkyqK 933
                                   688**********************************9988855544333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7
                        SH3_13   27 rvgDkVmqlkNn 38  
                                    + gDkV+ +   
  gi|15669714|ref|NP_248527.1| 1144 KLGDKVLIISTS 1155
                                    78****998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0     4e-08   2.4e-05       6     104 ..     580     683 ..     577     710 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4e-08
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee........erpevvfvtlpsstsskdllrellralglelkaerlsseel 78 
                                   +++++tG++GtGKTt++++++e  +e+   ++        +++ vv  +l+++ + k++ r +++++++  ++  ++   l
  gi|15669714|ref|NP_248527.1| 580 RVGILTGPAGTGKTTVIKTIMELMKEVLGLNKiyiltptgKSAMVVNEKLNNLATAKTIHRYIAEEFKDYFEG--DNYFIL 658
                                   789*********************99999988******7777777788888888**************53333..555555 PP

                        AAA_22  79 l.ealeqalraravielliiDEaqhlr 104
                                   + ++++ + ++   i +liiDE   ++
  gi|15669714|ref|NP_248527.1| 659 RlDKITGNDKKE--IDALIIDESSMVD 683
                                   533333333333..4799999987774 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.7       2.7   1.6e+03      90     189 ..     473     503 ..     434     570 .. 0.49
   2 !   13.1   0.3    0.0001     0.061       5      42 ..     568     607 ..     564     641 .. 0.67
   3 !   13.5   0.0     8e-05     0.048     215     257 ..     668     714 ..     659     716 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.7
                        AAA_11  90 ivRvgnee.eriseavksvsleekvekrlekeekaqlakeiskeleklakelrafeeeeekeklkkskekskskleqerrk 169
                                   ++R+  e  + ise+v+ v+                                                             
  gi|15669714|ref|NP_248527.1| 473 FLRIIEEYkDIISEKVEIVK------------------------------------------------------------- 492
                                   33333333344444444444............................................................. PP

                        AAA_11 170 lkkerkelskeleeaeesle 189
                                            ke+++ e++  
  gi|15669714|ref|NP_248527.1| 493 ---------KEVKNNENKEI 503
                                   .........33333333322 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.0001
                        AAA_11   5 sqreaiksalseseitliqGPPGtgKT...ktivellsqll 42 
                                    q ea+ + l+++   ++ GP GtgKT   kti+el++++l
  gi|15669714|ref|NP_248527.1| 568 MQTEAVVNLLKNRV-GILTGPAGTGKTtviKTIMELMKEVL 607
                                   68899999999985.************55555555555443 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 8e-05
                        AAA_11 215 akkfdvviIDEAaqavEpstliPlrlga.....kkvvLvGDpkQLpat 257
                                   +k++d++iIDE ++ v ++t+  l+  +     k ++ vGD +QLp++
  gi|15669714|ref|NP_248527.1| 668 KKEIDALIIDESSM-VDIETMGRLLGTIkldnlKYLIFVGDINQLPPV 714
                                   4589********99.78999888866666677899************7 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5  12.2   1.1e-07   6.5e-05      61     348 ..     598    1010 ..     592    1011 .. 0.59
   2 ?   -2.7   0.5       4.8   2.9e+03      34      66 ..    1129    1172 ..    1101    1174 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-07
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrD_C   61 tikallekneklediavLvRsnkdadkiskaLkkeg....ipfnvvdeekfFkreeikdilaylkllankqdkialkri 135 
                                    ti++l+++   l++i +L+ + k a  ++++L+++     i+  + +e+k +       il + k++ n++ +i    i
  gi|15669714|ref|NP_248527.1|  598 TIMELMKEVLGLNKIYILTPTGKSAMVVNEKLNNLAtaktIHRYIAEEFKDYFEGDNYFILRLDKITGNDKKEIDALII 676 
                                    5555555555555555555555555555555555555554444445544444444444455555555555555555555 PP

                                    xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                        UvrD_C  136 lkrlvlgigk..atveriseelkklglsltDfikedtleygeeFieliraleeknl....................... 189 
                                     ++ +++i++  +++ +i  +  k+ + + D  +   +  g +F+   + le+ n                        
  gi|15669714|ref|NP_248527.1|  677 DESSMVDIETmgRLLGTIKLDNLKYLIFVGDINQLPPVGAGKPFYDIYNYLEKVNPqsickleivlradskkivelskl 755 
                                    5555555543224555554445555555666666666666666665555555555466666666666666666666666 PP

                                    ............................................................................... RF
                        UvrD_C  190 ............................................................................... 189 
                                                                                                                   
  gi|15669714|ref|NP_248527.1|  756 fldidkeerikilnemfknketlgdneiyrikeniggiekeiitievvkdgnikkslenaietilkenntedffdfavf 834 
                                    6666666666666666666666666666666666666666666666666666666666666666666666666666666 PP

                                    .............................xxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrD_C  190 .............................elllkkiektaeer............qalvskyadlfkelaeklaelkek 227 
                                                                 +                              k ad+  +++++ +++   
  gi|15669714|ref|NP_248527.1|  835 ndklqilvptktkgefgsyminlfikqesK-----------FIpdkyknkmlenwFFGDGKVADKVIQIRNNYKKWVYD 902 
                                    666666666666666664444333333321...........11222222222212222234567777788888888888 PP

                                    xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrD_C  228 seskr..kkeeklenlreLysllkelekkeeeeeveeklneileia..tLseseleeskkkekipiiTiHqAKGlEFdv 302 
                                    +e+++  k++   + ++ +  ++k+ +k  +++++e+  + i++     +++ ++  +k+ e  + iTiH++ G++F++
  gi|15669714|ref|NP_248527.1|  903 TERRKwvKEHGVFNGMMGFAYTFKKWNK--YQKKYEN--KTIIRFYypKIEAYTD--EKEMEHAYAITIHKSQGSGFEN 975 
                                    88777766666999**************..6666655..5566655113444333..444499999************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrD_C  303 VflagleegtfPsyrskkekrleEEkRlfYVaiTRAkkrLfisysk 348 
                                    V+l+       P+  +k        k ++Y aiTRAkkrL++++ +
  gi|15669714|ref|NP_248527.1|  976 VILII------PKGLNKFV-----SKEMLYTAITRAKKRLYVIVEE 1010
                                    ***87......98776654.....5789**************9865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.8
                                    x...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        UvrD_C   34 k...........ktvekgekivvleaeteeeEaekiaatikall 66  
                                    +           ++ + g+k+ ++++ ++ +  +++ +++k+l+
  gi|15669714|ref|NP_248527.1| 1129 NgfeiiklseinENTKLGDKVLIISTSEDLKNNSQVLEKLKTLQ 1172
                                    14444445544466677778888888888888888888888776 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   4.3e-07   0.00026      16     155 ..     464     605 ..     454     615 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.3e-07
                         T2SSE  16 dihvekper.vkvrervdgielreveelekaalerlisr.iaalakldiseerplqdarlp..ekgvrlrvvllPvvagea 92 
                                   di+  + ++ +++ e   +i +++ve ++k+  +   ++ i   + ++i e + +++ +++   k+   ++ l P+   e+
  gi|15669714|ref|NP_248527.1| 464 DIVKITFDEfLRIIEEYKDIISEKVEIVKKEVKNNENKEiIELFTLKEIREYEEIIENTINylLKSKAPNIDLNPLEIREK 544
                                   56656666666666666776667776666666555544414566778899999999999998878888899999******* PP

                         T2SSE  93 lviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeink 155
                                   l i ++++k   +d+  +e+al+ + ++v++    ++ + +++G+ g+GKtt++ ++++ +++
  gi|15669714|ref|NP_248527.1| 545 LRIKNENKKPAGVDNEEYEKALDMQTEAVVNLL--KNRVGILTGPAGTGKTTVIKTIMELMKE 605
                                   ****9999999**************99999999..6666788*************99988775 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   6.6e-07   0.00039       1     112 [.     583     692 ..     583     740 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.6e-07
                 Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegk.snilvtapskenvktlfeflakglealglke..eekkkkaekaelrvrkqriey 78 
                                   +lt+  G+GK++++  +++ + +    ++i++  p+ +++  + e l++  +a ++++   e    + k  ++ ++  i  
  gi|15669714|ref|NP_248527.1| 583 ILTGPAGTGKTTVIKTIMELMKEVLGlNKIYILTPTGKSAMVVNEKLNNLATAKTIHRyiAE----EFKDYFEGDNYFILR 659
                                   589999********99888888776679******************9777766665542222....222233444444443 PP

                 Helicase_RecD  79 iapdellklkeqadllvvDEAAaiplpllkklle 112
                                   +   +  ++ ++ d+l++DE+++++++++ +ll 
  gi|15669714|ref|NP_248527.1| 660 LDKITGNDK-KEIDALIIDESSMVDIETMGRLLG 692
                                   444444443.367****************99964 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   3.6e-06    0.0021      64     121 ..     544     601 ..     487     622 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.6e-06
                                   HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  64 eleelkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallp 121
                                   +l+  +e+ + +g++    ++    ++e++ +llk+++ +l G+ G GK+t+i+++++
  gi|15669714|ref|NP_248527.1| 544 KLRIKNENKKPAGVDNEEYEKALDMQTEAVVNLLKNRVGILTGPAGTGKTTVIKTIME 601
                                   3555666777788888888889999*****************************9986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.9   1.1e+03      38      99 ..     260     330 ..     249     350 .. 0.77
   2 ?   -1.8   0.1       6.6   3.9e+03      62      95 ..     405     440 ..     391     476 .. 0.61
   3 !   15.2   0.0   3.7e-05     0.022       2      28 ..     583     616 ..     582     703 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.9
                                   STTHHHHHHHHHHHHHHHTS.....TSEEEEEETGGGHHHHH....TTCCCHHHHHHHHHHHHHHHHTTTS CS
                           AAA  38 yvgesekkirelfkeakeka.....kpsilfiDEidalaksr....sgseseeeervvnqLlteldgvkkk 99 
                                    + e +++i+++++e++ ++      p +l +  ++   ++     +++ ++ ee++ n+L++ l++ k++
  gi|15669714|ref|NP_248527.1| 260 KFDEFAENIKKVIAELEGSKykypgLPGVLYFLGMEDAYSRYielwKNEGEKGEEKLYNALIESLENRKEN 330
                                   56788888888888887766778866788888888887766678888888999999999999999999986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.6
                                   EEEETGGGHHHHH..TTCCCHHHHHHHHHHHHHHHH CS
                           AAA  62 lfiDEidalaksr..sgseseeeervvnqLlteldg 95 
                                   ++++E+d+  ++r  ++ +  +  rv + L++ l++
  gi|15669714|ref|NP_248527.1| 405 IIFEELDSWERRRlgDKFNPYSPYRVRALLVEILKR 440
                                   778888888888864333444444444444444444 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 3.7e-05
                                   EEESSTTSSHHHHHHHHHHHH.......THEEEE CS
                           AAA   2 llyGppGtGKTllakavakel.......gvefle 28 
                                   +l+Gp GtGKT+++k +++ +       ++++l+
  gi|15669714|ref|NP_248527.1| 583 ILTGPAGTGKTTVIKTIMELMkevlglnKIYILT 616
                                   699***************9983333222233333 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.8   2.9e+03      65     134 ..     348     414 ..     345     423 .. 0.66
   2 !   16.0   0.2   1.3e-05    0.0078       2     127 ..     567     704 ..     566     705 .. 0.67
   3 ?   -2.8   0.0       7.6   4.5e+03      37      69 ..    1137    1170 ..    1129    1173 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.8
                                   HHHHHHTTTST.SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHH CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  65 nnlkkfkkyid.lrvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrll 134
                                   +++++f+k++  + +l+ ++ ++ ++q++k   ++d ++ +p  l++ l+++    ++++ +++ E d   
  gi|15669714|ref|NP_248527.1| 348 EEFREFLKNYAvYYELSAFKLEKIKEQYEKEFINLDNIIKNPYILVEDLKEN----DSFERIIFEELDSWE 414
                                   6788888864424444556666666666655568999999999999877533....477778888888765 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT......TST. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxx. RF
                          DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk......yid. 75 
                                   d+Q ea+ ++l+++  ++ ++ G+GKT++  i  + +++++     +k+ i++Pt + a  + ++l+++        yi  
  gi|15669714|ref|NP_248527.1| 567 DMQTEAVVNLLKNRVGILTGPAGTGKTTV--IKTIMELMKE-VLGLNKIYILTPTGKSAMVVNEKLNNLATaktihrYIAe 644
                                   68**************************9..5555556553.344444555555544433333333333322223331113 PP

                                   .............SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEE CS
                                   .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  76 .............lrvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVl 127
                                                lr+  i+g+++++ +   +d++  + + t grl+  ++     l+++++l++
  gi|15669714|ref|NP_248527.1| 645 efkdyfegdnyfiLRLDKITGNDKKEIDALIIDESSMVDIETMGRLLGTIK-----LDNLKYLIF 704
                                   3333334556777999999999999999999998899999******98554.....999999986 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.6
                                    HHHHHSTTSTS-EEEEEESSHHHHH..HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          DEAD   37 qivyetkgktgpkalivePtreLae..qtlnnlkk 69  
                                    +++ e ++k g k+li++ ++ L +  q+l++lk+
  gi|15669714|ref|NP_248527.1| 1137 SEINE-NTKLGDKVLIISTSEDLKNnsQVLEKLKT 1170
                                    44544.77888899999999999653367777766 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.3   7.9e-05     0.047       8      57 ..     568     617 ..     563     753 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.9e-05
                                   HHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT..TS-SEEEEEE- CS
                          PhoH   8 eQkeylealkkndivfaiGpaGtGKtylavalavealkk..kkvkriiltrp 57 
                                    Q+e++ +l kn + + +GpaGtGKt +     +  l+k    +++i ++ p
  gi|15669714|ref|NP_248527.1| 568 MQTEAVVNLLKNRVGILTGPAGTGKTTV--IKTIMELMKevLGLNKIYILTP 617
                                   6999999999***************965..3333333331234456655555 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.017        10      69     141 ..     449     521 ..     442     534 .. 0.78
   2 !    8.8   0.1    0.0011      0.68      32      56 ..     579     603 ..     570     611 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
                         AAA_6  69 ldykslgkifkGlaqsGaWgCfdeFnrielevLSvvaqqiktiqqalkekkkkfvfegkeiklnksvgifitm 141
                                   +++k l+ +f+ + +  + + fdeF ri  e   +++++++ +++ +k++++k ++e  ++k  ++++ +i  
  gi|15669714|ref|NP_248527.1| 449 ISTKDLKDFFEKMDKDIVKITFDEFLRIIEEYKDIISEKVEIVKKEVKNNENKEIIELFTLKEIREYEEIIEN 521
                                   667777788888888888899****************************999988877666666666655555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                         AAA_6  32 klggapaGpagtGKtEtvkdLakal 56 
                                   +  g ++GpagtGKt  +k + + +
  gi|15669714|ref|NP_248527.1| 579 NRVGILTGPAGTGKTTVIKTIMELM 603
                                   667999*********9999876655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.7   8.1e-05     0.049       3      25 ..     583     605 ..     581     616 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.1e-05
                                   EEE--TTSSHHHHHHHHHHHH.. CS
                      NTPase_1   3 fiTGppGvGKtTlvkkvlellks 25 
                                   ++TGp G+GKtT++k ++el+k+
  gi|15669714|ref|NP_248527.1| 583 ILTGPAGTGKTTVIKTIMELMKE 605
                                   79*****************9975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.4e-05     0.032      26      51 ..     581     605 ..     565     696 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.4e-05
                        AAA_16  26 lvllsGesGvGKsslvrellralekd 51 
                                   + +l+G++G+GK+++++++++ l k+
  gi|15669714|ref|NP_248527.1| 581 VGILTGPAGTGKTTVIKTIME-LMKE 605
                                   5689***************95.4444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   2.0      0.81   4.8e+02      64     106 ..     463     504 ..     444     553 .. 0.67
   2 ?   15.5   0.3   2.2e-05     0.013       6     105 ..     567     672 ..     562     704 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.81
                                   HHHHHHHHHHGGGGTGG....GEEEESSS-B--.......-SE CS
                        ResIII  64 kslleqtleefkkflseaykeigkkvsgdkkkakekdstnkki 106
                                   k++++ t +ef ++++e+++ i++kv+  kk+  ++++++  i
  gi|15669714|ref|NP_248527.1| 463 KDIVKITFDEFLRIIEEYKDIISEKVEIVKKEV-KNNENKEII 504
                                   577777888888888887776555555555555.222222222 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.2e-05
                                   HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH............... CS
                        ResIII   6 eyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl............... 71 
                                   ++Q+ea+ nll      +++ g++  + GtGKT v+  ++e +++  + +k+ +l p+ +                     
  gi|15669714|ref|NP_248527.1| 567 DMQTEAVVNLL------KNRVGILTGPAGTGKTTVIKTIMELMKEVLGLNKIYILTPTGKSAMVVNeklnnlataktihry 641
                                   67888888887......4667************************999998888888864333333000122222222222 PP

                                   ..HHGGGGTGG....GEEEESSS-B--.............-S CS
                        ResIII  72 ..eefkkflseaykeigkkvsgdkkka......kekdstnkk 105
                                     eefk++++ ++ +           +      + +d+++++
  gi|15669714|ref|NP_248527.1| 642 iaEEFKDYFEGDNYF-----------IlrldkiTGNDKKEID 672
                                   223333333333333...........3333333333333334 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         7   4.2e+03      51      86 ..     373     414 ..     319     467 .. 0.54
   2 ?   -1.1   0.5       4.3   2.5e+03      47      84 ..     456     509 ..     416     567 .. 0.56
   3 ?   15.7   0.0   2.8e-05     0.017       2      43 ..     583     626 ..     583     702 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 7
                        AAA_18  51 rldedkldklldaleenss.......aleegknlvidghlael 86 
                                   +  e+    +ld++ +n+         +++ + ++++ + ++ 
  gi|15669714|ref|NP_248527.1| 373 EQYEKEFI-NLDNIIKNPYilvedlkENDSFERIIFEELDSWE 414
                                   22222222.2222222222344433323333444444444444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.3
                        AAA_18  47 deskrldedkldklldaleenss.................aleegknlvidghla 84 
                                   d ++++d+d ++  +d++ ++++                 ++ e+k  +i+ +  
  gi|15669714|ref|NP_248527.1| 456 DFFEKMDKDIVKITFDEFLRIIEeykdiisekveivkkevKNNENKE-IIELFTL 509
                                   45555555555555555555554333333333333333433333333.4444444 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 2.8e-05
                        AAA_18   2 lltGtpGvGKttlakeLskrl.gf.gvnlrdvakenglllevdp 43 
                                   +ltG++G+GKtt+ k + +++ ++ g n + +++  g + +v +
  gi|15669714|ref|NP_248527.1| 583 ILTGPAGTGKTTVIKTIMELMkEVlGLNKIYILTPTGKSAMVVN 626
                                   79***************999866675554444444443333333 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.5    0.0002      0.12      33      60 ..     579     605 ..     567     624 .. 0.79
   2 ?   -0.8   0.0       1.5     9e+02      43      65 ..     617     640 ..     615     647 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                         AAA_7  33 kkpvllvGptGtGKtviikdllkkldke 60 
                                   ++  +l+Gp+GtGKt++ik++++ ++ e
  gi|15669714|ref|NP_248527.1| 579 NRVGILTGPAGTGKTTVIKTIMELMK-E 605
                                   4445789*************998777.4 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                         AAA_7  43 GtGKtviikd.llkkldkekylsl 65 
                                    tGK++++ +  l++l + k++  
  gi|15669714|ref|NP_248527.1| 617 PTGKSAMVVNeKLNNLATAKTIHR 640
                                   59****99999*****98887765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       8.8   5.3e+03      79      96 ..     132     197 ..      76     211 .. 0.61
   2 ?   12.7   0.0   0.00022      0.13      11      37 ..     579     605 ..     571     650 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8.8
                                   H................................................HHHTCHHHHHHHSTTGG CS
                                   x................................................xxxxxxxxxxxxxxxxx RF
                      ABC_tran  79 n................................................esdeeiekalsklglke 96 
                                                                                    ++++eie++l++++l+ 
  gi|15669714|ref|NP_248527.1| 132 VkikeiidgskdyirkkqspnrvgrgivfdvendvifalpyqelleyckNKNKEIEEILKEFNLIF 197
                                   144444444444444445555555555555566666666666777777778888888888888765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00022
                                   TSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  11 gekvaivGenGaGKStLlkllagllkp 37 
                                   +++  ++G+ G+GK+t++k++++l+k 
  gi|15669714|ref|NP_248527.1| 579 NRVGILTGPAGTGKTTVIKTIMELMKE 605
                                   5555689***************99876 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.065        39      10      72 ..     444     507 ..     441     534 .. 0.76
   2 ?    7.2   0.0    0.0064       3.8       4      49 ..     584     633 ..     581     652 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.065
                           PRK  10 aGkttva.rklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfd 72 
                                   +G tt++ + l++ f++  +  ++i+ d+flr+ + +kd+ +e+ +  k++  +  + e +++ 
  gi|15669714|ref|NP_248527.1| 444 SGNTTIStKDLKDFFEKMDKDIVKITFDEFLRIIEEYKDIISEKVEIVKKEVKNNENKEIIELF 507
                                   7999986256***************************999998887777555455555555444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0064
                           PRK   4 vagsSGaGkttvarklekifgre.kvkaaei...egdsflrldraekdle 49 
                                   ++g+ G Gkttv +++ ++++++ +++  +i   +g+s + +++ +++l+
  gi|15669714|ref|NP_248527.1| 584 LTGPAGTGKTTVIKTIMELMKEVlGLNKIYIltpTGKSAMVVNEKLNNLA 633
                                   69*************99998843123333335556666666665555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.8   1.1e+03      20      78 ..     435     492 ..     429     503 .. 0.73
   2 ?   10.5   0.0     0.001       0.6       3      39 ..     584     617 ..     583     631 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.8
                  RNA_helicase  20 kallkklklkkkdsvysrnpeddfwdgYt.gqevvvidDfgqvkdeenps.dlaelirlvs 78 
                                    ++lk+  l + ++++s +  +df+++ + +   + +d+f ++ +e  ++ +++e++++v+
  gi|15669714|ref|NP_248527.1| 435 VEILKRH-LSSGNTTISTKDLKDFFEKMDkDIVKITFDEFLRIIEE--YKdIISEKVEIVK 492
                                   4555444.34557777788888999888845555779999999999..7769999998886 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.001
                  RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkkdsvysrnp 39 
                                   l+Gp+g+GK+t++k++++ l+k++     +++y+ +p
  gi|15669714|ref|NP_248527.1| 584 LTGPAGTGKTTVIKTIME-LMKEV--LGLNKIYILTP 617
                                   89*************555.55444..23345666444 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0002      0.12      12      45 ..     570     603 ..     559     610 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                        DUF853  12 elalalklanrhGliaGatGtGktvtLqvlaesl 45 
                                     a+   l nr G+++G +GtGkt  ++++ e +
  gi|15669714|ref|NP_248527.1| 570 TEAVVNLLKNRVGILTGPAGTGKTTVIKTIMELM 603
                                   445555689*******************998866 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00061      0.37       3      24 ..     583     608 ..     582     700 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00061
                                   EEE--SSSSHHHHHHHGGGGB....S CS
                         AAA_5   3 lLvGppGtgKselaerlaaal....n 24 
                                   +L Gp GtgK+++++ + +++    +
  gi|15669714|ref|NP_248527.1| 583 ILTGPAGTGKTTVIKTIMELMkevlG 608
                                   89***************999955444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00037      0.22      23      46 ..     580     603 ..     568     605 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                        AAA_29  23 gatlltGpsGsGKSTllDAiqalL 46 
                                    + +ltGp G+GK+T++  i+ l+
  gi|15669714|ref|NP_248527.1| 580 RVGILTGPAGTGKTTVIKTIMELM 603
                                   3789*************9888876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00059      0.35      14      43 ..     573     603 ..     559     618 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00059
                                   HHHCH.TEEEEEEESTTSSHHHHHHHHHHHT CS
                          TsaE  14 lakal.gdvilLeGdLGaGKTtlvrglakal 43 
                                   + + l ++v +L+G+ G+GKTt ++ +++ +
  gi|15669714|ref|NP_248527.1| 573 VVNLLkNRVGILTGPAGTGKTTVIKTIMELM 603
                                   33333457889***************99876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00055      0.33       2      26 ..     581     605 ..     580     611 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00055
                                   CEEEEC-TTTCHHHHHHHHHHHHCT CS
                         NACHT   2 lvilqGeaGsGKTtLlqklalawae 26 
                                   + il+G+aG GKTt ++ ++++++e
  gi|15669714|ref|NP_248527.1| 581 VGILTGPAGTGKTTVIKTIMELMKE 605
                                   6699****************98875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00075      0.45      29      50 ..     576     596 ..     551     683 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00075
                        AAA_25  29 llpagelallaGapgtGKttla 50 
                                   ll ++ +++l+G+ gtGKtt+ 
  gi|15669714|ref|NP_248527.1| 576 LL-KNRVGILTGPAGTGKTTVI 596
                                   54.799**************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1514  (0.0844442); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.88u 0.31s 00:00:01.19 Elapsed: 00:00:00.52
# Mc/sec: 6861.45
//
Query:       gi|15669715|ref|NP_248528.1|  [L=387]
Description: bacteriochlorophyll synthase 43 kDa subunit ChlP [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-13   48.7   0.0    9.9e-12   44.8   0.0    2.4  1  FAD_binding_3   FAD binding domain
    4.1e-05   22.8   0.0    7.3e-05   22.0   0.0    1.4  1  Lycopene_cycl   Lycopene cyclase protein
    0.00029   19.8   0.1      0.017   14.0   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
     0.0025   17.5   2.2     0.0051   16.4   1.9    1.6  1  DAO             FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.036   13.3   0.2       0.06   12.6   0.2    1.4  1  Thi4            Thi4 family
      0.044   12.5   0.4      0.076   11.7   0.4    1.4  1  HI0933_like     HI0933-like protein
       0.35   10.7   3.3        8.3    6.3   0.0    2.7  3  BTHB            Basic tilted helix bundle domain


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   3.9e-15   9.9e-12       2     309 ..       6     285 ..       5     311 .. 0.76

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 3.9e-15
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCC CS
                 FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynelsd 82 
                                   +dV+I+G+Gp+G +++   ++   rv++ve +++  v  +          l+ + G+++    +g++n++ g   y +   
  gi|15669715|ref|NP_248528.1|   6 YDVVIIGGGPVGCITGEYIKNG--RVLIVEEHQSIGVPLQCA-------GLISKNGVKELGNPKGVVNKVRGAYIYSK--- 74 
                                   79*****************999..******998765555554.......568999**********************9... PP

                                   CCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--G CS
                 FAD_binding_3  83 tpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDG 163
                                     ++++++    ++ r +++  + ++++++ + +++ +++  k+ +  +e+d++g + e++    ge+ t++ k +vGaDG
  gi|15669715|ref|NP_248528.1|  75 --NSMVKIG--NEGIRAYIFERKVMDKDIAIR-AAKKCDFLLKA-YGKIEKDKNGYKVEITHL--GEKITLNPKIIVGADG 147
                                   ..7777776..889999999999999999988.45557777666.45599*****99999877..8999************ PP

                                   TT-HHHHHHTGGEEEEEEEEE...EEEEEEEEEC-SCCCTTCCEEEEECCTTEE.EEEECCETEEEEEEEEECCE-GGGSC CS
                 FAD_binding_3 164 grStvrktlgiefegeetvye...agvldvlfdadlsdiveplvlilsaesrgv.mviPlentlerfyvqvearaekeers 240
                                   +++++ k+lg+  + ++++     ++++++ +d+d+      ++l ++ ++r++  +iP+ + ++ ++ +++ ++  ++  
  gi|15669715|ref|NP_248528.1| 148 AKTITGKKLGLVNNKNREILSscqFEMVNAEVDDDFV---Y-IFLDRKYSERFFtWIIPMGK-DRVRVGLIDRGNCYNKLI 223
                                   ***********98888777540114444444444444...2.3555566666667899****.554555555555443333 PP

                                   CCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHHHHH CS
                 FAD_binding_3 241 ekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNtaiq 309
                                     ++e+++++++ +       ++ i+e+s+  +   + +k  k++v+l+GDAa  + P  G Gl  +++
  gi|15669715|ref|NP_248528.1| 224 RFINENKIAKEILK-------NATITEFSTGSLPIGYLDKTFKDNVLLVGDAACHVKPLSGGGLYFGAM 285
                                   33333333333333.......2367788888888899****************999***9999977776 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.8e-08   7.3e-05       1     323 [.       7     334 ..       7     347 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.8e-08
                 Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlgaleecvehsWs..gtivylddgkkillg. 78 
                                   Dvv+iG+Gp g+   + +    ++ +v+++e  +s+  p +      ++++++l +  + + +  g+ +y ++   + +g 
  gi|15669715|ref|NP_248528.1|   7 DVVIIGGGPVGCITGEYI----KNGRVLIVEEHQSIGVPLQCAGLISKNGVKELGNPKGVVNKvrGAYIYSKNSMVK-IGn 82 
                                   9***********999999....6679**********99999999999999999887665555500555555544443.444 PP

                 Lycopene_cycl  79 ...raYgrvsskrlkeellerlvengvklleakvesveeeea.geslvvleggr.kirarlvvdarglaslkkarrlglQt 154
                                      raY   ++k + + ++ r + ++  +l     ++e++++  ++ ++  g++ +++ +++v a g a+   +++lgl  
  gi|15669715|ref|NP_248528.1|  83 egiRAYI-FERKVMDKDIAIRAA-KKCDFLLKAYGKIEKDKNgYKVEITHLGEKiTLNPKIIVGADG-AKTITGKKLGLVN 160
                                   7878885.799999999999999.566666666789999999445666666666889999*******.8888888899888 PP

                 Lycopene_cycl 155 fyGvevevdnppfdldkmvlMDfr....veqklkgltFlYalPldsdrllvEeTelaskpeLpadalkkrlaaylralglk 231
                                       e+ ++ + f++ ++++ D      +  k  +  F +++P+++dr+ v    l ++ +   ++++    +++++  lk
  gi|15669715|ref|NP_248528.1| 161 NKNREILSSCQ-FEMVNAEVDDDFvyifLDRKYSERFFTWIIPMGKDRVRV---GLIDRGNCYNKLIRFINENKIAKEILK 237
                                   88888888887.8888888766443665555557889************87...68999988888888777888888999* PP

                 Lycopene_cycl 232 vkevveeEqgviPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres....slsarawatlw 308
                                    +++ e  +g +P+  g   + ++ +vl +G aa  v+P  G  +       ++  ++i+++l+e+    +l+++ w++  
  gi|15669715|ref|NP_248528.1| 238 NATITEFSTGSLPI--GYLDKTFKDNVLLVGDAACHVKPLSGGGLYFGAMGGKIAGEVISKYLNEDienlELYDKRWKETF 316
                                   **************..7777888999**************9998888888888888********88999999999999999 PP

                 Lycopene_cycl 309 prerkrq...reffrllg 323
                                   + e+k+    r++f  lg
  gi|15669715|ref|NP_248528.1| 317 GSEIKNGlrvRKLFLKLG 334
                                   999886422255554555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.2     0.009        23       1      20 [.       7      26 ..       7      41 .. 0.79
   2 !   14.0   0.0   6.6e-06     0.017     282     341 ..     229     285 ..     197     322 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.009
                                  EEEEE--SHHHHHHHHHHHH CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalak 20
                                  ++vi+GGG+ G ++  ++++
  gi|15669715|ref|NP_248528.1|  7 DVVIIGGGPVGCITGEYIKN 26
                                  69***********9988865 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6.6e-06
                                   HHHHHHHHHHCT--TTTS-EEEE---EEES-SEETTEEE-CCCTEE--CCCS-HHHHHHH CS
                Trp_halogenase 282 deAlaellaeldgkleaeprkirfttGrrkqawvknvvalGlasgfvePlestsihliqa 341
                                   ++ ++e+l++   +   e +  ++  G+  ++++ nv+++G+a++ v Pl + ++++   
  gi|15669715|ref|NP_248528.1| 229 NKIAKEILKNATIT---EFSTGSLPIGYLDKTFKDNVLLVGDAACHVKPLSGGGLYFGAM 285
                                   44444444443322...223445556789************************9998665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.9     2e-06    0.0051       1      33 [.       7      39 ..       7      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2e-06
                                  EEEEECTSHHHHHHHHHHHHTT.EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg.Vtllekgdiag 33
                                  dvviiGGG +G+ t  +  + g V+++e +  +g
  gi|15669715|ref|NP_248528.1|  7 DVVIIGGGPVGCITGEYI-KNGrVLIVEEHQSIG 39
                                  9*****************.9999******97765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   2.4e-05      0.06      17      59 ..       5      44 ..       1      95 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTT CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawl 59
                                  + Dvvi+G+G+ G  ++ y+ +    +v+i+e++ s+G     
  gi|15669715|ref|NP_248528.1|  5 DYDVVIIGGGPVGCITGEYIKNG---RVLIVEEHQSIGVPLQC 44
                                  57******************888...9*********9966555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4     3e-05     0.076       1      43 [.       6      46 ..       6      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3e-05
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                  +dv++iGgG+ G  + + +  ++ rVl++e+ +++g  ++ +G
  gi|15669715|ref|NP_248528.1|  6 YDVVIIGGGPVGCITGEYI--KNGRVLIVEEHQSIGVPLQCAG 46
                                  59*************9999..6789***********9888887 PP

>> BTHB  Basic tilted helix bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.014        35      31      64 ..      87     120 ..      73     125 .. 0.85
   2 ?   -3.2   0.1         3   7.7e+03      20      37 ..     222     230 ..     220     238 .. 0.60
   3 ?    6.3   0.0    0.0032       8.3      13      29 ..     343     359 ..     341     361 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.014
                          BTHB  31 sFLkenkLlGniknVaKtankeqLieaYkklfes 64 
                                   +++ e+k+  +  +++  ++++ L++aY k+ ++
  gi|15669715|ref|NP_248528.1|  87 AYIFERKVMDKDIAIRAAKKCDFLLKAYGKIEKD 120
                                   6788999999999***************987655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3
                          BTHB  20 likfLqenAaesFLkenk 37 
                                   li+f+ e         nk
  gi|15669715|ref|NP_248528.1| 222 LIRFINE---------NK 230
                                   5555555.........44 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0032
                          BTHB  13 dalpKkdlikfLqenAa 29 
                                   ++l+K dli+++ ++++
  gi|15669715|ref|NP_248528.1| 343 EKLSKSDLIDYINKHGD 359
                                   689***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2523.27
//
Query:       gi|15669716|ref|NP_248529.1|  [L=422]
Description: Na+/H+ antiporter [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-54  184.3  40.1    3.4e-54  184.1  40.1    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.1  40.1   1.9e-58   3.4e-54       8     378 ..      12     401 ..       5     412 .. 0.86

  Alignments for each domain:
  == domain 1  score: 184.1 bits;  conditional E-value: 1.9e-58
                                   HHHHHH.....HHHHTTSXHHHHHHHHHHHHTTTTTS.......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHH CS
                Na_H_Exchanger   8 allvgl.....larrlklpeivgliiaGlllGpsglglieps..eedlevlselglilllFlaGleldlrelrknlksill 81 
                                   +l++g      +a+++++p+i++l+i+Gl+l    +    ++  e+ ++++ ++gli+llF  ++e++++ ++++l  i++
  gi|15669716|ref|NP_248529.1|  12 ILFAGGaiiakIAKKIGIPDIPLLLIFGLILSILNVI--PKNivESSFDFIGNFGLIILLFIGSFEMEWNIMKRVLDVIIK 90 
                                   333333344433******************9776555..44478999********************************** PP

                                   HHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHH CS
                Na_H_Exchanger  82 lallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavl 162
                                   l +l +li ++++G+++++++ l+i  l +llfgai+satdp+++++i+  ++ ++ +++++l++esv+nD +++v++ ++
  gi|15669716|ref|NP_248529.1|  91 LDILALLIVWIISGIVFNFVFHLPILSLIGLLFGAIVSATDPATLIPIF-SSMDIDPEVAITLEAESVFNDPLGIVVTLIC 170
                                   ******************75669999***********************.******************************* PP

                                   HHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS...CTHHHHHHHHHHHHHHHH..HHHHHTS.XXXH CS
                Na_H_Exchanger 163 lalakeeaggetslllllliflvvavgglllglvigwllrlitrft...dddrelevllvlllalla..allaell.gvsg 237
                                   l+++     g +++ +++l+f+ +avgg++lg++ g ++++i+  +   d+++ + + l+++++++a   + +     +sg
  gi|15669716|ref|NP_248529.1| 171 LSAL-----GLAKAENPILEFFSLAVGGIILGVIAGKFYEIIISKIkfeDYIAPFTLGLAIAFWYFAegIFPSITGyEISG 246
                                   ***9.....9*************************************99999999************76555555579*** PP

                                   HHHHHHHHHHHHHHHHHTTHHHH....HHHHHH...HHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHH CS
                Na_H_Exchanger 238 ilgaflaGlvlseyefsnklsek....lesfre...glfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilav 311
                                    +++ ++Gl+++++ +++k ++k    +  f++    ++ +l+Fvl+G+s+ +++l+   + l++ l++l +ill+r+++v
  gi|15669716|ref|NP_248529.1| 247 FMAVAIMGLYIGNVIVHKKEHKKdmekVAVFMDelsIFIRILIFVLLGASISIPLLE--KYALPAFLCALGSILLARPVGV 325
                                   ************666666644445555999999999********************7..********************** PP

                                   HHHTTTX.SSXHHHHHHCCCCSS.BHHHHHHHHHHHHHH........XHHHH.........TTSSTTTCSTSXHHHHHHHH CS
                Na_H_Exchanger 312 flllrll.glslrealiigfgglqrgavalalaalgpal........gllar.........elyallivvvlftvlvqGls 374
                                   ++++ +  + +l e++++++ g  rg v + laa++ ++        +   +         el  +++v++++t++     
  gi|15669716|ref|NP_248529.1| 326 LIATAIPpIRPLTERIYLALEGP-RGVVPATLAAMVYTEimkhpnivP---KniaslmpptELAGTILVATFMTII----- 397
                                   ****9997799************.***************666665440...1555566655556666666666666..... PP

                                   HHHH CS
                Na_H_Exchanger 375 lkpl 378
                                   ++++
  gi|15669716|ref|NP_248529.1| 398 VSVV 401
                                   4333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3041.75
//
Query:       gi|15669717|ref|NP_248530.1|  [L=211]
Description: cobalt-precorrin-6Y C(5)-methyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-36  124.9   0.0    4.8e-36  124.7   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.049   13.9   0.0       0.12   12.7   0.0    1.7  1  DUF5461       Family of unknown function (DUF5461)


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.7   0.0   5.3e-40   4.8e-36       1     212 [.       1     192 [.       1     193 [. 0.89

  Alignments for each domain:
  == domain 1  score: 124.7 bits;  conditional E-value: 5.3e-40
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleea.yeeiaealaealragk 80 
                                   ++y+VG+GpGd+e+lT++A++++++ad+v+g++ rale++   ++         + +k +l+++   e  e ++ ++ + k
  gi|15669717|ref|NP_248530.1|   1 MIYIVGIGPGDREYLTLKAIKIVENADLVVGSK-RALELFN--ID---------EDKKITLTKNlIGELKELIKNENIKNK 69 
                                   79*******************************.******3..22.........223335555578999999*99999999 PP

                  TP_methylase  81 dVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeereleallang 161
                                   ++++l++GDP+++g    l+++ +++e   ++e i G+ss+q aaa+l+i++++ + ++ +     ++e++++l +l++n 
  gi|15669717|ref|NP_248530.1|  70 KIAILSTGDPCFSGLLKTLLKIGAKKE---DIEAISGISSIQIAAAKLKISWEDYYIITLHG----KEENRKKLLNLIKNH 143
                                   9*******************7776655...5****************************999....567888888999*9* PP

                  TP_methylase 162 dtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                   + +++l  p +l+e a++L+   + +dt +++v e++++e+e++   +l+e+
  gi|15669717|ref|NP_248530.1| 144 EKVIFL--PNNLKEDAKFLINNgINPDT-KIWVLENLTYENEKISLKSLKEI 192
                                   ******..889***********777766.***************99999987 PP

>> DUF5461  Family of unknown function (DUF5461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.3e-05      0.12      17      50 ..     141     173 ..     127     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                       DUF5461  17 kkiekilllpseedvkkdyiigrvgiirisktyi 50 
                                   k+ ek+++lp++++  ++++i   gi++ +k ++
  gi|15669717|ref|NP_248530.1| 141 KNHEKVIFLPNNLKEDAKFLI-NNGINPDTKIWV 173
                                   45699****************.99********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1439.67
//
Query:       gi|15669718|ref|NP_248531.1|  [L=124]
Description: camphor resistance protein CrcB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-26   91.4   9.8    3.9e-26   91.2   9.8    1.0  1  CRCB      CrcB-like protein, Camphor Resistance (CrcB)


Domain annotation for each model (and alignments):
>> CRCB  CrcB-like protein, Camphor Resistance (CrcB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   9.8   2.2e-30   3.9e-26       2      94 ..       7     115 ..       6     116 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 2.2e-30
                                   HHHHHHHHHHHHHHHH.HHHHBE...BHHHHHHHHHHHHHHHHHHH.............HHTTTHHHHHS-SHHHHHHHHH CS
                          CRCB   2 lvalggalGallRyllssllnkr...plgtlavNvlGsfllgllla.............llttGflGglTTfStfvlelvs 66 
                                   l+++gg++Ga++Ryl+s+++  +   p+gtlavN++Gsf+lg+ll+             +++tGf+G+lTTfStf++e++ 
  gi|15669718|ref|NP_248531.1|   7 LIGVGGFFGAIFRYLISGIVPVKfglPTGTLAVNLIGSFILGFLLYcslfapipteyklFIGTGFCGALTTFSTFSYETFV 87 
                                   799*************9988888**989***************99988888888888888********************* PP

                                   HHHHT-HHHHHHHHHHHHHHHHHHHHHH CS
                          CRCB  67 lleegellaallyvllsvvlgllavvlg 94 
                                   l++eg l++all++l++vv++l++v++g
  gi|15669718|ref|NP_248531.1|  88 LVDEGLLFKALLNILINVVGCLIMVYFG 115
                                   ************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 932.19
//
Query:       gi|15669719|ref|NP_248532.1|  [L=108]
Description: hypothetical protein MJ_1524 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-29  100.7   0.1    4.8e-29  100.5   0.1    1.0  1  DUF190    Uncharacterized ACR, COG1993
  ------ inclusion threshold ------
       0.16   11.9   0.0        1.3    9.0   0.0    1.9  2  MinC_N    Septum formation inhibitor MinC, N-terminal domain


Domain annotation for each model (and alignments):
>> DUF190  Uncharacterized ACR, COG1993
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   0.1   5.3e-33   4.8e-29       1      97 []       5     101 ..       5     101 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 5.3e-33
                                   EEEEEEEETT-EETTEEHHHHHHHHHHHTT-S--EEEE-S---------------------EEEEEEEE-HHHHHHHHHHH CS
                        DUF190   1 klLrIyigesdrlegkplyeaivelareeglagatvlrGieGfgassrihtakllelsedlPvvieivdteekieaflpel 81 
                                   k+L+Iy+ e d++eg+ +y++i++++++eg++gatv++Gi G+g ++ + + ++++ls +lPv+ie+vd ee+i+++lp+l
  gi|15669719|ref|NP_248532.1|   5 KILKIYLREGDKFEGELMYKHIMKILKREGISGATVYKGICGYGVRG-VAEFDIFRLSVNLPVIIECVDIEENINRVLPKL 84 
                                   589*****************************************888.8999***************************** PP

                                   HT----.SEEEEEEEE- CS
                        DUF190  82 kelvke.glvtlekvev 97 
                                    e++k+ gl+++++++v
  gi|15669719|ref|NP_248532.1|  85 YEVIKNnGLIIITDCHV 101
                                   ****988******9987 PP

>> MinC_N  Septum formation inhibitor MinC, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.05   4.5e+02      53      74 ..      15      36 ..      11      44 .. 0.85
   2 ?    9.0   0.0   0.00015       1.3      45      77 ..      63      97 ..      56     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.05
                        MinC_N 53 skleekvdlkaLkelisraglr 74
                                  +k+e+++ +k + ++++r g+ 
  gi|15669719|ref|NP_248532.1| 15 DKFEGELMYKHIMKILKREGIS 36
                                  57899999*********99986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00015
                        MinC_N 45 napvvldvskleekvd..lkaLkelisraglrivg 77
                                  n pv+++  ++ee+++  l++L e+i++ gl+i+ 
  gi|15669719|ref|NP_248532.1| 63 NLPVIIECVDIEENINrvLPKLYEVIKNNGLIIIT 97
                                  78************997789***********9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 756.61
//
Query:       gi|15669720|ref|NP_248533.1|  [L=933]
Description: putative transmembrane oligosaccharyl transferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.5e-182  607.9  34.0   2.1e-182  607.4  34.0    1.2  1  STT3      Oligosaccharyl transferase STT3 subunit


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.4  34.0  1.2e-186  2.1e-182       1     488 []      33     650 ..      33     650 .. 0.99

  Alignments for each domain:
  == domain 1  score: 607.4 bits;  conditional E-value: 1.2e-186
                                   HHHHHHHHHHCCCCCHCC.........CCCCCCT--S--SSCHHHHHHHCCCHHHT-C........CCHHSSEETTSSTTT CS
                          STT3   1 vlilvifalialvavasr........dlFtdedglsylsefDpYYnyRltenllnnGfpG...dvvikkknwfdhsqyyPp 70 
                                   +l++v+f+l+a++a++++        d+F+de+g++yl+++DpYY++Rl+enl+nnG++G   +vv++k++++d +qy+Pp
  gi|15669720|ref|NP_248533.1|  33 MLMFVSFQLRAQTADMKFaqdneflkDMFSDEHGRMYLLALDPYYYLRLSENLYNNGHCGdtiKVVDGKETPYDLYQYAPP 113
                                   89**********************************************************99999**************** PP

                                   -EEESTTCCHCCC.CHHHHHHCCHHC..HHHHHHHHCCHHHHHHHHCHHHHHHH.HHHS-CCCHHHHHHHCCC-CCCCCTT CS
                          STT3  71 GsrvdygplivlLamlasaiinhsld..vsirevclwlpallgsLlaIpiyflv.relksdiaGllAAlllaiaPgYlsrt 148
                                   G++++++p++++La+la+++i+hs+d  v+i+++++w+pa+lg+Ll+Ipiyf+v r+++s+i+G+++A++l++aPg+l++t
  gi|15669720|ref|NP_248533.1| 114 GHPLPWEPPVICLATLAIYYIWHSIDltVTIMNAAFWVPAVLGMLLGIPIYFVVrRVTNSNIGGIAGAIALISAPGLLYKT 194
                                   ******************************************************9999*********************** PP

                                   STT--STCCCCHHHHHHHHHHHHHHHHCCS..........TTCHHHHHHHHHHHHHHTTSCCGG.........HHHHCCHH CS
                          STT3 149 vaGfyDtdmfeivlllfvlffflkaiktks..........nkislaviaaliiflivlaWggya.........iliyalll 210
                                   +aGf+Dt++fe++++lf+++f+l++i++++          n+isl+viaalii+li++a++++a         il+y+++l
  gi|15669720|ref|NP_248533.1| 195 CAGFADTPIFEVLPILFIVWFILESIHSQEktalfkkdlkNPISLFVIAALIIELIIGAYLNIAsgesvviasILFYTVSL 275
                                   ********************************************************************************* PP

                                   HHHHHHHCTTT..........S-CCHHHHH...............HHHHHHHHHH..CCCCCCCTTCHHH..STTTCHHCC CS
                          STT3 211 lfilalLiigr..........felklkiav...............tfsviiaflviaiivllflgfqvva..vseiigalg 264
                                   +fila+Lii++          fel++++av               +f+vi+aflvi+ii+l++l++qv++  +++i+++++
  gi|15669720|ref|NP_248533.1| 276 AFILAGLIIAGikklkgneleFELFALLAViltavspkmwgawwyGFDVITAFLVIYIIALALLKSQVKIkeFINIGNLKN 356
                                   *********************99999999999*************************************9*********** PP

                                   CCHHHHHHHHCCCHHC..CCCCCHHCC.....CHHTT.HHHHTT--..GGGHHHHHHHHHHHHC................. CS
                          STT3 265 ifgllqlvafgsvvvlvaelkfyqfis.....lfqpgilsevlgli..gevvtalavlglialw................. 321
                                   i++l+++++fgs+v+lva+++++++is     l++++ils++++++  ++v+t++a+l+++++w                 
  gi|15669720|ref|NP_248533.1| 357 IVYLSIFYIFGSFVLLVAIYGMGIAISpitspLGYNQILSTYTQTTgwPNVYTTVAELAKPSSWseiftnaigsdtiaivg 437
                                   ********************************************************************************* PP

                                   .CCCCCTS---..--TTHHHHHHHHHS---S--CCHHHCCSSST.TTTCCCHH...HCHHCCHHCTCHHHHHHH....... CS
                          STT3 322 .lgilyslldl..eyaklkikiiilvsvwlpvgllaltkglrfl.iftvPlgi...ifvgllleflavfvkiys....... 388
                                    lgil+s+l+l  e++kl+ik++il+++wl+v+l+a+tkg+rf+ ++t+Pl+i   ifvg+l++fl+++++i++       
  gi|15669720|ref|NP_248533.1| 438 iLGILLSFLSLryEKVKLDIKYSILLAIWLAVTLYAATKGIRFAaLATPPLAIglgIFVGQLERFLKMKSDIAIfgigipa 518
                                   **********999******************************************************************** PP

                                   ..............HHHHHHCCC-SCHCCCCCHHHHHHHCCCHHHHHHHHCCHHHHHHHHH.....HHHHH.......... CS
                          STT3 389 ..............vsqilfsgvvvillmltllpvlallaavkiskifstykdekeakikv.....aakav.......... 440
                                                 +sqil+++++v+++++++l+vlalla++kis+i+st +d+ke++ikv     ++++v          
  gi|15669720|ref|NP_248533.1| 519 gifgllilskysakISQILLPTTYVPIIAYGFLIVLALLAIYKISDIISTLNDKKETIIKVstlllCIGVVipplsavvpf 599
                                   *************************************************************9999988888999999999* PP

                                   ..HHHHCT.TTTTHHH.TTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHCCS CS
                          STT3 441 ..aptksnglkeslew.kantnrdsvvitwwdyghilaveadrpVtfdggs 488
                                     apt++ng+ke+l+w kant+++sv+++wwd+ghi+++ea+r+Vtfdggs
  gi|15669720|ref|NP_248533.1| 600 svAPTFNNGWKEGLDWiKANTPNNSVITCWWDNGHIYTYEARRMVTFDGGS 650
                                   *************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (933 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.44
# Mc/sec: 6399.97
//
Query:       gi|15669721|ref|NP_248534.1|  [L=244]
Description: hypothetical protein MJ_1526 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.099   12.1   3.6        1.1    8.7   3.6    2.1  1  ApbE      ApbE family


Domain annotation for each model (and alignments):
>> ApbE  ApbE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.6   6.3e-05       1.1     216     240 ..     162     187 ..      81     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 6.3e-05
                                   ECEEEEEESC.HHHHHHHHHHHHHHH CS
                          ApbE 216 lasvtViads.alADalaTalfvlge 240
                                     +vtV+a+s a ADa+aTa++ +++
  gi|15669721|ref|NP_248534.1| 162 ADAVTVFAKSsAIADAAATAICNASR 187
                                   679****9866*********998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1698.15
//
Query:       gi|15669722|ref|NP_248535.1|  [L=140]
Description: hypothetical protein MJ_1527 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-07   30.7   8.6    2.6e-07   30.7   8.6    1.4  1  DUF4870   Domain of unknown function (DUF4870)


Domain annotation for each model (and alignments):
>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   8.6   1.4e-11   2.6e-07      17     105 ..      44     126 ..      26     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.4e-11
                       DUF4870  17 liplgniilPlviwllkkdksefvdeqgkealNFqislliysiilivlsllvligflllllllllllnlvlviiaaikane 97 
                                   l+ l+ +i  l+ +ll++++  f++ ++ +++   +sl +++ii+ +   + +ig+  ++ +l+ ++ ++l i+++ika++
  gi|15669722|ref|NP_248535.1|  44 LCYLLFWISGLIFLLLERED-DFIRFHAMQSFITFLSLNLIAIIVSA---IPIIGW--VASTLINIAIIILWIVGMIKAYN 118
                                   45566788888888888888.**********9777777766666555...59***9..9********************** PP

                       DUF4870  98 geeyrypl 105
                                   ge y++p+
  gi|15669722|ref|NP_248535.1| 119 GERYKFPV 126
                                   ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 895.01
//
Query:       gi|15669723|ref|NP_248536.1|  [L=219]
Description: triosephosphate isomerase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-15   55.2   1.5    7.6e-14   51.7   0.4    2.2  2  TIM             Triosephosphate isomerase
    1.1e-06   28.3   0.6    1.5e-06   27.8   0.6    1.2  1  NMO             Nitronate monooxygenase
    3.4e-05   23.0   1.2    4.6e-05   22.6   0.3    1.6  2  FMN_dh          FMN-dependent dehydrogenase
    5.5e-05   22.7   0.7    0.00042   19.8   0.2    2.2  2  His_biosynth    Histidine biosynthesis protein
      8e-05   22.1   0.7      8e-05   22.1   0.7    2.1  2  ThiG            Thiazole biosynthesis protein ThiG
    0.00028   20.1   0.3    0.00054   19.2   0.3    1.5  1  IGPS            Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
      0.018   14.2   0.4      0.034   13.3   0.4    1.5  1  Glu_synthase    Conserved region in glutamate synthase
      0.055   13.5   0.1       0.57   10.3   0.1    2.1  2  Hydrolase_like  HAD-hyrolase-like
       0.12   12.4   0.1       0.33   11.1   0.1    1.8  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.4   3.8e-17   7.6e-14       2     125 ..       2     120 ..       1     129 [. 0.82
   2 ?    3.0   0.1     0.028        56     156     201 ..     131     170 ..     118     198 .. 0.69

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 3.8e-17
                                   EEEEE-TBTS-HHHHHHH.HHHHHHHCHG.CTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHHHHH CS
                           TIM   2 liagNwKmnktleeakel.lkklkaklke.ekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsaemlk 80 
                                   li+ N+K++ +    + l ++k+++k++e + +++ +ap+f+ l+++   +e+ ++ ++aq ++  + G++TG + ae +k
  gi|15669723|ref|NP_248536.1|   2 LIVINYKTYNESIGNRGLeIAKIAEKVSEeSGITIGVAPQFVDLRMI---VENVNIPVYAQHIDNINPGSHTGHILAEAIK 79 
                                   68899999886655554414556666666589************985...55668************************** PP

                                   HTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE-- CS
                           TIM  81 dlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCvGE 125
                                   d+g+k ++i HsE+r l+ + +++++    ++++ gl++i+C  +
  gi|15669723|ref|NP_248536.1|  80 DCGCKGTLINHSEKRMLLADIEAVIN----KCKNLGLETIVCTNN 120
                                   ******************98766665....467789999999765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.028
                                   GCEEEEE--GGGSSSS----HHHHHHHHHHHHHHHHHHSTHHHHTT CS
                           TIM 156 knvviAYePvWAiGtgktatpeqaqevhaairkelaekvskevaek 201
                                   +  +iA eP   iGtg ++++ + + v  ++r +      ke++++
  gi|15669723|ref|NP_248536.1| 131 SPDYIAVEPPELIGTGIPVSKANPEVVEGTVRAV------KEINKD 170
                                   55589*****9****9877766666555555544......233334 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.6   7.6e-10   1.5e-06     126     229 ..     101     206 ..      95     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 7.6e-10
                           NMO 126 eevvarlkeagvvliptissvkearkvearGaDalivqGpeaGGh.qG..tpevgd....kglfaLvpqvldavdiPviAa 199
                                   e v+++ k++g+  i+ +  ++  ++v+a+ +D + v+ pe  G  ++  +   ++    +g+++ v+++ +   + v+  
  gi|15669723|ref|NP_248536.1| 101 EAVINKCKNLGLETIVCTNNINTSKAVAALSPDYIAVEPPELIGTgIPvsK---ANpevvEGTVRAVKEINKD--VKVLCG 176
                                   57899999********************************97664144331...2222346666666666653..779999 PP

                           NMO 200 GGiidrrgvaaaLalGAsgvqigtrfLltk 229
                                    Gi ++++v+aaL lGA+gv +++  + +k
  gi|15669723|ref|NP_248536.1| 177 AGISKGEDVKAALDLGAEGVLLASGVVKAK 206
                                   9*********************99877666 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.89   1.8e+03     125     143 ..     100     118 ..      97     127 .. 0.84
   2 !   22.6   0.3   2.3e-08   4.6e-05     264     308 ..     163     207 ..     149     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.89
                                   HHHHHHHHHHCTESEEEEE CS
                        FMN_dh 125 teellkraeaagykalvlt 143
                                   +e+++++++++g++++v t
  gi|15669723|ref|NP_248536.1| 100 IEAVINKCKNLGLETIVCT 118
                                   5789999999999999988 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 2.3e-08
                                   HHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHH CS
                        FMN_dh 264 iveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflygla 308
                                    v++++++++vl+  Gi++G+Dv  Al lGA++vll+  ++ + +
  gi|15669723|ref|NP_248536.1| 163 AVKEINKDVKVLCGAGISKGEDVKAALDLGAEGVLLASGVVKAKN 207
                                   3444556899*************************9988876654 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.17   3.4e+02     145     168 ..      96     119 ..      74     122 .. 0.80
   2 !   19.8   0.2   2.1e-07   0.00042      62     115 ..     161     212 ..     149     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.17
                                   EEEEHHHHHHHHHHTT-SEEEEEE CS
                  His_biosynth 145 tgldavelakkleelgageilltd 168
                                      d++ +++k+++lg+++i++t+
  gi|15669723|ref|NP_248536.1|  96 LLADIEAVINKCKNLGLETIVCTN 119
                                   45678889999999****999995 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.1e-07
                                   HHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHH CS
                  His_biosynth  62 ldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikel 115
                                     +v+ei +   ++v  G GI++ edv+++l++ga+ v +++ +vk +++ + +
  gi|15669723|ref|NP_248536.1| 161 VRAVKEINKD--VKVLCGAGISKGEDVKAALDLGAEGVLLASGVVKAKNVEEAI 212
                                   5677777777..99******************************9988765544 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.33   6.6e+02     167     179 ..      45      57 ..      28      91 .. 0.59
   2 !   22.1   0.7     4e-08     8e-05     167     213 ..     161     208 ..      90     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.33
                                   HHHHHHH-SS-BE CS
                          ThiG 167 lkiiieeakvPvi 179
                                   l++i+e++++Pv 
  gi|15669723|ref|NP_248536.1|  45 LRMIVENVNIPVY 57 
                                   6777777777764 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 4e-08
                                   HHHHHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSH CS
                          ThiG 167 lkiiieea.kvPvivDAGigspsdaaqamelGadavllntavaeakdp 213
                                   ++ + e   +v v+  AGi + +d+ +a++lGa++vll++ v +ak+ 
  gi|15669723|ref|NP_248536.1| 161 VRAVKEINkDVKVLCGAGISKGEDVKAALDLGAEGVLLASGVVKAKNV 208
                                   444444335899*********************************986 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   2.7e-07   0.00054     152     254 .]     105     215 ..      94     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.7e-07
                                   HHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE..-......CHHHHHHCHCC-TTSEEEEESSS-SHHHH CS
                          IGPS 152 eaakslglevLvEvhdeeeleralklgakiiGvNnRnLktlev..d......lntteeLaklvpkdvllvaeSGiktredv 224
                                   +  k+lgle +v +++ ++ +++ +l  + i v   +L    +  +      ++ t + +k+++kdv + +  Gi++ edv
  gi|15669723|ref|NP_248536.1| 105 NKCKNLGLETIVCTNNINTSKAVAALSPDYIAVEPPELIGTGIpvSkanpevVEGTVRAVKEINKDVKVLCGAGISKGEDV 185
                                   5566666666666666666666666666666666666643333002111111344667778899***************** PP

                                   HHHCCTT-SEEEESHHHHC-TTHHHHHHHH CS
                          IGPS 225 eklkeegvnafLvGeslmrqedvekairel 254
                                   ++  + g++++L  + ++++++ve+airel
  gi|15669723|ref|NP_248536.1| 186 KAALDLGAEGVLLASGVVKAKNVEEAIREL 215
                                   ****************************97 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   1.7e-05     0.034     251     306 ..     145     202 ..      98     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                                   B---HHHHHHHHHHHHHH..TT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHH CS
                  Glu_synthase 251 aGlPlelalaevdqtlke..eglrdrvsliadGglktgadvvkalalGAdavgigtaa 306
                                   +G+P+  a +ev++  ++  +++ + v++    g+  g+dv  al lGA+ v ++++ 
  gi|15669723|ref|NP_248536.1| 145 TGIPVSKANPEVVEGTVRavKEINKDVKVLCGAGISKGEDVKAALDLGAEGVLLASGV 202
                                   89********998754432368999***************************999876 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.33   6.6e+02      39      69 ..     108     136 ..      97     139 .. 0.85
   2 ?   10.3   0.1   0.00029      0.57      33      60 ..     183     210 ..     180     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.33
                                   HHCT-EEEEESSSSS-TTTHHHHHHHHT--- CS
                Hydrolase_like  39 nnaGwksvLVltGvtrpedleepehkptyva 69 
                                   +n G++++  +  +++ ++++  + +p+y+a
  gi|15669723|ref|NP_248536.1| 108 KNLGLETIVCTNNINTSKAVA--ALSPDYIA 136
                                   689999999999999998876..67899986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00029
                                   THHHHHHHCT-EEEEESSSSS-TTTHHH CS
                Hydrolase_like  33 tDiagAnnaGwksvLVltGvtrpedlee 60 
                                    D+++A + G+++vL ++Gv +++ +ee
  gi|15669723|ref|NP_248536.1| 183 EDVKAALDLGAEGVLLASGVVKAKNVEE 210
                                   6*******************88877664 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00017      0.33       5      45 ..      83     126 ..      81     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                                   STTTSEE...TTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HH CS
                   Hydrolase_6   5 idGvLwr...gdkaipgaaealnalraagkpvvllTNnssksee 45 
                                   + G+L++   ++ ++   + ++n +++ g +++++TNn + s+ 
  gi|15669723|ref|NP_248536.1|  83 CKGTLINhseKRMLLADIEAVINKCKNLGLETIVCTNNINTSKA 126
                                   999**98443555899**********************887733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1394.44
//
Query:       gi|15669724|ref|NP_248537.1|  [L=167]
Description: methylated-DNA-protein-cysteine methyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-26   91.2   0.0    4.7e-26   90.7   0.0    1.2  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b
  ------ inclusion threshold ------
      0.029   14.0   0.0      0.069   12.8   0.0    1.6  1  Sigma70_r4_2   Sigma-70, region 4


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   0.0   5.3e-30   4.7e-26       1      80 [.      79     155 ..      79     156 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 5.3e-30
                                   HHHHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHHHTT CS
                 DNA_binding_1   1 afqqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLeaEg 80 
                                   +f+++V+++++ I +Gk+ tYg+iAk+l+  +++raVg al++npl++++PcHRVv+++  lggy+ gl++k+ +Le+E+
  gi|15669724|ref|NP_248537.1|  79 EFTKKVLDIVKDIEFGKTLTYGDIAKKLN--TSPRAVGMALKRNPLPLIIPCHRVVAKNS-LGGYSYGLDKKKFILERER 155
                                   699**************************..*************************9998.*****************96 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.7e-06     0.069      27      49 ..      97     119 ..      94     119 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.7e-06
                                   --HHHHHHHHT--HHHHHHHHHH CS
                  Sigma70_r4_2  27 lsykEIAellgisegtVksrlsR 49 
                                   l+y +IA++l++s+++V  +l+R
  gi|15669724|ref|NP_248537.1|  97 LTYGDIAKKLNTSPRAVGMALKR 119
                                   89***************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1085.41
//
Query:       gi|15669725|ref|NP_248538.1|  [L=156]
Description: ribosomal protein S18 alanine acetyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-23   81.5   0.1      7e-23   81.1   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.4e-14   54.3   0.3    1.9e-14   53.9   0.3    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.4e-14   53.4   0.0    2.6e-14   53.2   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
      4e-07   30.3   0.1    5.1e-07   30.0   0.1    1.3  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    2.1e-05   24.2   0.0      7e-05   22.5   0.0    1.6  2  Acetyltransf_8   Acetyltransferase (GNAT) domain
    9.5e-05   22.3   0.0    0.00015   21.7   0.0    1.3  1  FR47             FR47-like protein
    0.00021   22.0   0.1    0.00042   21.0   0.1    1.6  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0023   18.0   0.1      0.098   12.7   0.1    2.4  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.053   13.7   0.0        0.1   12.7   0.0    1.4  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
       0.12   12.1   0.0       0.14   11.9   0.0    1.2  1  PanZ             Acetyltransferase (GNAT) domain, PanZ


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.1   3.9e-26     7e-23       4     117 .]      14     121 ..      11     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 3.9e-26
                                   HHHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHH CS
                Acetyltransf_1   4 lvellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlea 84 
                                   + e+++e f  p++++       ++s  +++++vae dg+++G+i +++++     +++i+slaV++e+rg G+G+aLl++
  gi|15669725|ref|NP_248538.1|  14 VEEIEREAFKTPYPTSL---ILGFWSMYPNCFYVAEIDGRVVGYILGSMDWG----NGHIISLAVKKECRGLGIGTALLKT 87 
                                   44455544333333332...33455668889*********************....9************************ PP

                                   HHHHHHHT.TESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  85 leeraree.gikkivlaveedndaairlYeklGF 117
                                   le + ++  ++++ivl+v+++n+ a+r+Y ++G+
  gi|15669725|ref|NP_248538.1|  88 LENYYFNIaNCNYIVLEVRVSNVLARRFYYRMGY 121
                                   *********************************8 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.3     1e-17   1.9e-14       3      75 ..      40     122 ..      38     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1e-17
                                   EEEEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH......TTSEEE.EE.EEEETHHHHHHHHHHTT CS
                Acetyltransf_7   3 gevfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLlea......aekgii.le.qlelnaekaikfYeklG 73 
                                   ++++Vae dg++vG+i  s ++  ++i+ laV++e+rg GiG+aLl+       ++ +++ ++ ++++++  a++fY ++G
  gi|15669725|ref|NP_248538.1|  40 NCFYVAEIDGRVVGYILGSMDWgnGHIISLAVKKECRGLGIGTALLKTlenyyfNIANCNyIVlEVRVSNVLARRFYYRMG 120
                                   68*************99999989888888*****************964444442233433234455555589******** PP

                                   EE CS
                Acetyltransf_7  74 Fe 75 
                                   ++
  gi|15669725|ref|NP_248538.1| 121 YR 122
                                   *7 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   1.5e-17   2.6e-14      32     124 ..      41     141 ..      13     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1.5e-17
               Acetyltransf_10  32 lllvaeeggkivGvi..el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl..eltvnasp.yavpfYeklGF 106
                                    ++vae +g++vG+i  ++   ++hi  l+V++e+rg Gig+aLl+++e+++ +  + +   l+v+ s+  a++fY ++G+
  gi|15669725|ref|NP_248538.1|  41 CFYVAEIDGRVVGYIlgSMdWGNGHIISLAVKKECRGLGIGTALLKTLENYYFNIANCNyiVLEVRVSNvLARRFYYRMGY 121
                                   699************877755555***************************5444444448********9*********** PP

               Acetyltransf_10 107 kav..geeqeenGirfvpMe 124
                                   ++    ++ +e+G   + M 
  gi|15669725|ref|NP_248538.1| 122 RDRklLPKYYEDGEDAILMI 141
                                   99866677788877777665 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   2.8e-10   5.1e-07      46     147 ..      36     134 ..       3     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.8e-10
                Acetyltransf_4  46 sekeyvflvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvl.keqnienllaeiaspnen 124
                                   s++ + f vae ++r+vGy  ++ +++    +  ++s  ++ + ++  g+g +l++ le++     n ++++ e+ ++n  
  gi|15669725|ref|NP_248538.1|  36 SMYPNCFYVAEiDGRVVGYILGS-MDW---GNGHIISLAVK-KECRGLGIGTALLKTLENYYfNIANCNYIVLEVRVSNVL 111
                                   66778999***********9887.***...56668999998.89***************999899**************** PP

                Acetyltransf_4 125 siqfhkalGFelvgifkkcikkn 147
                                   +  f+ ++G++  + + k+++++
  gi|15669725|ref|NP_248538.1| 112 ARRFYYRMGYRDRKLLPKYYEDG 134
                                   **********9777777666665 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         1   1.8e+03      47      59 ..      43      55 ..      39      56 .. 0.89
   2 !   22.5   0.0   3.9e-08     7e-05      88     141 ..      72     125 ..      59     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1
                                  EEEEETTEEEEEE CS
                Acetyltransf_8 47 liglldgepvgyf 59
                                  +++++dg+ vgy+
  gi|15669725|ref|NP_248538.1| 43 YVAEIDGRVVGYI 55
                                  8999*******96 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 3.9e-08
                                   SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                Acetyltransf_8  88 eaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                                   ++e rg g++tall++l +y f+   ++ +v+E +v+N  a+r++ ++G++ +k
  gi|15669725|ref|NP_248538.1|  72 KKECRGLGIGTALLKTLENYYFNIANCNYIVLEVRVSNVLARRFYYRMGYRDRK 125
                                   57899*********************************************9876 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   8.2e-08   0.00015      22      80 ..      64     124 ..      49     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 8.2e-08
                                   SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH..S-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                          FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiae..rgktvllvvvasNtpsirlyeklGfeki 80 
                                   g + +l v++e r+ G g+ l k l +   +  + + ++l v+ sN  ++r+y ++G++ +
  gi|15669725|ref|NP_248538.1|  64 GHIISLAVKKECRGLGIGTALLKTLENYYFNiaNCNYIVLEVRVSNVLARRFYYRMGYRDR 124
                                   899**********************98665543455677899****************986 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   2.3e-07   0.00042      54     137 ..      40     121 ..       1     122 [. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.3e-07
                Acetyltransf_3  54 ygwaivlkdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvlek 134
                                    ++ + + d++v+G++ l ++++ ++   +++ ++++++g G++t  ++ l +y+f+  + +++v ++  +N   +r + +
  gi|15669725|ref|NP_248538.1|  40 NCFYVAEIDGRVVGYI-LGSMDWGNG-HIISLAVKKECRGLGIGTALLKTLENYYFNIANCNYIVLEVRVSNVLARRFYYR 118
                                   346666788878****.888999988.89999*********************************************9999 PP

                Acetyltransf_3 135 lGf 137
                                   +G+
  gi|15669725|ref|NP_248538.1| 119 MGY 121
                                   997 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   5.5e-05     0.098       3     126 ..       4     122 ..       2     123 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-05
                                   EEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETT.EEEEEEEEEEEEE- CS
                Acetyltransf_9   3 relteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpG.ktlkaagvtgVava 82 
                                   r+  ++dld+v e+ ++aF+   +    +   f  ++ ++ +++ae +g++vg          + G   +  + + + av+
  gi|15669725|ref|NP_248538.1|   4 RKFSSKDLDAVEEIEREAFKTPYPTS--LILGFWSMY-PNCFYVAEIDGRVVGY---------ILGsMDWGNGHIISLAVK 72 
                                   55555666666666666665555553..222223333.2345566666666653.........2232556678999***** PP

                                   CCGTTS-HHHHHHHHHHHHHHHT.T--EEEE--.....SSHHHHHTTT-E CS
                Acetyltransf_9  83 pehrgrgvlskLlaraleemree.gqplsllfP.....ssipiYrrfGye 126
                                    e rg g+ ++Ll+++ +++    + + ++l        ++++Y r+Gy+
  gi|15669725|ref|NP_248538.1|  73 KECRGLGIGTALLKTLENYYFNIaNCNYIVLEVrvsnvLARRFYYRMGYR 122
                                   *************9998888764577777777777677678999999995 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.8e-05       0.1      73     117 ..      42      86 ..      39      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.8e-05
                Acetyltransf_6  73 lyvlrldgrpvAvalglrsgdrlyywlggydpelaklspgllllw 117
                                   +yv++ dgr+v+++lg ++ +  +    ++  e ++l++g+ ll 
  gi|15669725|ref|NP_248538.1|  42 FYVAEIDGRVVGYILGSMDWGNGHIISLAVKKECRGLGIGTALLK 86 
                                   799**************************************9985 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.8e-05      0.14      34      95 ..      36      97 ..       3     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.8e-05
                          PanZ 34 lteegalfaarFNdRlLgAvkveledkeaelsdlcVRevTRrRGVgsyLleearrqaPevks 95
                                      + +++a    R  g +   ++ + +++ +l V+++ R  G+g  Ll+   +   ++ +
  gi|15669725|ref|NP_248538.1| 36 SMYPNCFYVAEIDGRVVGYILGSMDWGNGHIISLAVKKECRGLGIGTALLKTLENYYFNIAN 97
                                  555678999*****************************************887766555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1031.47
//
Query:       gi|15669726|ref|NP_248539.1|  [L=425]
Description: type I restriction-modification enzyme subunit S [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-68  228.8  18.3    2.5e-35  122.2   9.2    2.1  2  Methylase_S     Type I restriction modification DNA specifici
  ------ inclusion threshold ------
      0.051   13.4   0.9      0.051   13.4   0.9    1.9  2  Chordopox_A30L  Chordopoxvirus A30L protein


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.2   9.2   2.8e-39   2.5e-35       1     165 [.      22     203 ..      22     206 .. 0.86
   2 !  112.3   1.7     3e-36   2.7e-32       1     168 []     235     407 ..     235     407 .. 0.92

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 2.8e-39
                                   ETT-EEEEHHHHEEEEE-----TTGGTTT--EEEE-HH.HCCT...EE-HHHHCCTT---B-TT-EEEE-S........SS CS
                   Methylase_S   1 pedwevvkLgdvfeikkgktpkkkelkengkypyirag.ilnn...kvvkdglgykkkyilpkgdilissr........at 69 
                                   pedwev++L+d+ e+ ++    k ++k++ +yp+ r++ i+++   +++ ++++ +k++++ k +++i+ +        ++
  gi|15669726|ref|NP_248539.1|  22 PEDWEVRELKDILEVIRNGLTAK-QNKDKIGYPITRIEtISDSkidITKLGYVEDIKQEDIAKYRLIIGDIlfshinseEH 101
                                   89*************66666655.89************66666**************************99********** PP

                                   TT-EEEESS.-BEE-TTEEEEEEST.TT--HHHHHHHHHHCHHHHHHH....CCSSTTT---HHHHCC-EEEE--HHHHHH CS
                   Methylase_S  70 iGkvayrdk.kyylnqsvivlipkn.kkkineflylylllklkklksl....svgstqpkltkenlkkikIplPpleeQkk 144
                                   iGkva+ +  + +l ++++ l +++ k+ki+ +++lyll + k+ + +    +++++q+++++++lk++kIplPpleeQk+
  gi|15669726|ref|NP_248539.1| 102 IGKVAIYEGkPEFLLHGMNLLLLRPnKNKIEPYYLLYLLRHFKQKNIFkyiaKRAVNQSSINQTQLKHLKIPLPPLEEQKQ 182
                                   *****9998468**********999899997777777774444333334689***************************** PP

                                   HHHHHHHHHHHHHHHHHHHHH CS
                   Methylase_S 145 IakiLsqldntielekkikne 165
                                   IakiLs++dn+i  ++k+++ 
  gi|15669726|ref|NP_248539.1| 183 IAKILSDFDNLIGTINKQIEV 203
                                   **********55555555554 PP

  == domain 2  score: 112.3 bits;  conditional E-value: 3e-36
                                   ETT-EEEEHHH..HEEEEE-----TT.GGTTT--EEEE-HH.HCCTEE-HHHHCCTT-..--B-TT-EEEE-SSSTT-EEE CS
                   Methylase_S   1 pedwevvkLgd..vfeikkgktpkkk.elkengkypyirag.ilnnkvvkdglgykkk..yilpkgdilissratiGkvay 75 
                                   pedwevv+Lg    f+i +g +p+++  +ke++++p++  +    n ++ + + y++k  ++++ +dilis ra++G+v++
  gi|15669726|ref|NP_248539.1| 235 PEDWEVVELGNekYFKIIMGQSPPSSsYNKEGEGVPFLQGKaEFGN-IYPNPVLYTNKplKVVDDEDILISVRAPVGDVNI 314
                                   89*******96558************777777788******88888.99999999988335678***************** PP

                                   ESS-BEE-TTEEEEEESTTT--HHHHHHHHHHCHHHHHHHCCSSTTT---HHHHCC-EEEE--HHHHHHHHHHHHHHHHHH CS
                   Methylase_S  76 rdkkyylnqsvivlipknkkkineflylylllklkklkslsvgstqpkltkenlkkikIplPpleeQkkIakiLsqldnti 156
                                   +++k++ + ++  ++++++k +n f ++yl++++ k++ l +g  ++ +tk++l++ikIplPpleeQk Iak+L+++d++i
  gi|15669726|ref|NP_248539.1| 315 APFKLCIGRGLAGIKSNKEKVDNFFVFYYLSYIKPKIEYLGGGAVFKAITKKDLESIKIPLPPLEEQKAIAKRLKAIDDLI 395
                                   ****************777777899999999************************************************** PP

                                   HHHHHHHHHHHH CS
                   Methylase_S 157 elekkikneier 168
                                   e+++k+k++ie+
  gi|15669726|ref|NP_248539.1| 396 EIKRKEKEQIEK 407
                                   **********96 PP

>> Chordopox_A30L  Chordopoxvirus A30L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   5.6e-06     0.051       4      52 ..     162     210 ..     159     218 .. 0.90
   2 ?   -4.8   1.6         2   1.8e+04      44      52 ..     395     403 ..     382     412 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.6e-06
                Chordopox_A30L   4 inEsnflHLLsnLsnnkdDsefaatlsvikElisqINlkvleinKKsKK 52 
                                   in   + HL + L   ++ +++a +ls    li  IN ++  +nK  K 
  gi|15669726|ref|NP_248539.1| 162 INQTQLKHLKIPLPPLEEQKQIAKILSDFDNLIGTINKQIEVLNKAKKG 210
                                   999*************************************999997664 PP

  == domain 2  score: -4.8 bits;  conditional E-value: 2
                Chordopox_A30L  44 leinKKsKK 52 
                                   +ei +K K 
  gi|15669726|ref|NP_248539.1| 395 IEIKRKEKE 403
                                   344444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1311  (0.0731218); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2729.74
//
Query:       gi|15669727|ref|NP_248540.1|  [L=237]
Description: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase HisA1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-74  250.5   5.6    1.5e-74  250.3   5.6    1.0  1  His_biosynth    Histidine biosynthesis protein
    2.5e-11   43.2   0.6    0.00013   21.2   0.1    2.2  2  Dus             Dihydrouridine synthase (Dus)
    1.6e-09   37.5   0.5    0.00041   19.7   0.1    2.1  2  ThiG            Thiazole biosynthesis protein ThiG
    2.5e-07   29.8   1.1       0.01   14.7   0.2    2.2  2  Trp_syntA       Tryptophan synthase alpha chain
    1.2e-06   28.2   0.1    0.00031   20.3   0.0    2.2  2  NMO             Nitronate monooxygenase
      5e-06   25.8   0.4     0.0098   15.1   0.1    2.4  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
      6e-06   25.7   1.6     0.0023   17.2   0.2    3.0  3  DHO_dh          Dihydroorotate dehydrogenase
    6.4e-06   25.8   4.0    0.00025   20.6   0.2    2.2  2  PcrB            PcrB family
    8.8e-06   25.2   0.9     0.0074   15.7   0.1    2.3  2  G3P_antiterm    Glycerol-3-phosphate responsive antiterminato
    2.4e-05   23.7   0.9      0.026   13.9   0.0    2.3  2  TMP-TENI        Thiamine monophosphate synthase
    4.1e-05   22.9   0.1     0.0077   15.4   0.0    2.6  2  IGPS            Indole-3-glycerol phosphate synthase
    0.00018   20.6   2.6      0.049   12.6   0.6    2.2  2  IMPDH           IMP dehydrogenase / GMP reductase domain
     0.0015   18.1   0.0      0.038   13.4   0.0    2.1  2  PEP_mutase      Phosphoenolpyruvate phosphomutase
      0.005   15.9   2.3      0.078   12.0   0.3    2.2  2  FMN_dh          FMN-dependent dehydrogenase
     0.0063   16.0   0.9      0.082   12.4   0.0    2.9  5  CutC            CutC family
  ------ inclusion threshold ------
      0.021   14.2   4.6          3    7.2   0.1    3.1  3  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
       0.18   12.1   1.5        3.2    8.1   0.1    2.2  2  Radical_SAM     Radical SAM superfamily


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.3   5.6   1.4e-77   1.5e-74       2     228 ..       3     226 ..       2     227 .. 0.99

  Alignments for each domain:
  == domain 1  score: 250.3 bits;  conditional E-value: 1.4e-77
                                   EEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSS CS
                  His_biosynth   2 iipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGI 82 
                                   iipa+Dlkd k+V+l++Gd ++++ + ++pve+ak++ +ega++lh++Dldaa+ g+++n d++++i++ev++pv+vGGGI
  gi|15669727|ref|NP_248540.1|   3 IIPAVDLKDKKCVQLIQGDPNKKHLELNNPVEVAKKFVDEGAEYLHIIDLDAAF-GTGNNRDVIKNIIKEVNVPVEVGGGI 82 
                                   9****************************************************8.************************** PP

                                   SSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHHTT-SE CS
                  His_biosynth  83 rsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakkleelgage 163
                                   r+le ++el+++g+d+vi+gt+a+ +p++i++l +++g++kiv+a+++++g kv+ikgw+e+++ +++e++k++e++ +g 
  gi|15669727|ref|NP_248540.1|  83 RNLEIAKELISLGVDRVIVGTKAILEPKFIDDLNKEIGKDKIVLAVECKEG-KVVIKGWKEKVDKTPIEVIKEFEDK-VGY 161
                                   ***************************************************.**********************986.9** PP

                                   EEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                  His_biosynth 164 illtdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegel 228
                                   il+t++d +G l+G++++++kel e+++ip+i+sGG+++led+k+lk+ g+++v++gsaly+g +
  gi|15669727|ref|NP_248540.1| 162 ILFTNVDVEGLLKGINVDIIKELIEKTDIPIIYSGGITTLEDIKALKELGIYGVVIGSALYKGLI 226
                                   **************************************************************976 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   1.9e-07    0.0002     172     232 ..      62     122 ..      28     161 .. 0.83
   2 !   21.2   0.1   1.2e-07   0.00013     170     217 ..     176     222 ..     168     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.9e-07
                                   CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHHHHS CS
                           Dus 172 weaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.stavktg 232
                                    + Ik++ ++v++pv + G+I+++e a++ ++  G+d v++g  a  +P +++  ++++ ++
  gi|15669727|ref|NP_248540.1|  62 RDVIKNIIKEVNVPVEVGGGIRNLEIAKELISL-GVDRVIVGTKAILEPKFIDDlNKEIGKD 122
                                   578**************************9999.*****************99555444443 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.2e-07
                                   --CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC CS
                           Dus 170 adweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgal 217
                                   ++ + Ike+ ++  ip+i  G+I+++ed++a  +e G+ gv+ig + +
  gi|15669727|ref|NP_248540.1| 176 INVDIIKELIEKTDIPIIYSGGITTLEDIKAL-KELGIYGVVIGSALY 222
                                   68899************************985.666********9876 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   3.9e-07   0.00041     135     205 ..      34     103 ..      28     110 .. 0.87
   2 !   16.1   0.1     5e-06    0.0053     163     208 ..     177     222 ..     169     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.9e-07
                                   HHHHHHHHTT-S..EBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESH CS
                          ThiG 135 vlarrleevGca..avmPlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllnt 205
                                    +a+++ + G++   ++ l a+ G+g   +n+ ++k ii+e++vPv v  Gi++ + a + + lG+d v++ t
  gi|15669727|ref|NP_248540.1|  34 EVAKKFVDEGAEylHIIDLDAAFGTG---NNRDVIKNIIKEVNVPVEVGGGIRNLEIAKELISLGVDRVIVGT 103
                                   57999999999733478999999998...5999*************************************987 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5e-06
                                   -HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHH CS
                          ThiG 163 nkealkiiieeakvPvivDAGigspsdaaqamelGadavllntava 208
                                   n   +k +ie++++P+i   Gi + +d+ +  elG+ +v++ +a+ 
  gi|15669727|ref|NP_248540.1| 177 NVDIIKELIEKTDIPIIYSGGITTLEDIKALKELGIYGVVIGSALY 222
                                   56679999*********************************99975 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   9.7e-06      0.01     188     230 ..      63     106 ..      57     135 .. 0.83
   2 !   13.9   0.0   1.7e-05     0.018     189     234 ..     180     226 ..     172     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.7e-06
                                   HHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHH CS
                     Trp_syntA 188 elverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalv 230
                                   ++++++ k  +vPv vG Gi++ e +k+++  + d vivG + +
  gi|15669727|ref|NP_248540.1|  63 DVIKNIIKEVNVPVEVGGGIRNLEIAKELIsLGVDRVIVGTKAI 106
                                   67888888899******************98999******9876 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.7e-05
                                   HHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHH CS
                     Trp_syntA 189 lverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkkie 234
                                   ++++l + t+ P+    Gi t e++k++   +  Gv++GSal k + 
  gi|15669727|ref|NP_248540.1| 180 IIKELIEKTDIPIIYSGGITTLEDIKALKeLGIYGVVIGSALYKGLI 226
                                   7899999**********************88999*******988665 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0057         6     181     227 ..      61     107 ..      48     145 .. 0.88
   2 !   20.3   0.0   2.9e-07   0.00031     184     225 ..     180     221 ..     167     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0057
                           NMO 181 lfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLl 227
                                      +++++ + v++Pv   GGi + +  +  ++lG   v +gt+ +l
  gi|15669727|ref|NP_248540.1|  61 NRDVIKNIIKEVNVPVEVGGGIRNLEIAKELISLGVDRVIVGTKAIL 107
                                   5578999999**************999999*************8665 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 2.9e-07
                           NMO 184 LvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                   ++++  +  diP+i  GGi + ++++a   lG  gv ig+++
  gi|15669727|ref|NP_248540.1| 180 IIKELIEKTDIPIIYSGGITTLEDIKALKELGIYGVVIGSAL 221
                                   5667777889******************************97 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1   0.00075      0.79     135     180 ..      63     110 ..      52     120 .. 0.79
   2 !   15.1   0.1   9.3e-06    0.0098     133     177 ..     177     222 ..     151     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00075
                                   HHHHHH.HHTT--EEEES---SHHHHHHHHTT--SEEEE-H.HHH-HH CS
                          NanE 135 alvkal.seaglkviaeGrintPekakkaieiGvdavvvGs.aitrle 180
                                   +++k++ +e ++ v + G i   e ak+ i +Gvd v+vG+ ai  ++
  gi|15669727|ref|NP_248540.1|  63 DVIKNIiKEVNVPVEVGGGIRNLEIAKELISLGVDRVIVGTkAILEPK 110
                                   5667651566899999************************64666555 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 9.3e-06
                                   -HHHHHHHHH.TT--EEEES---SHHHHHHHHTT--SEEEE-HHHH CS
                          NanE 133 Dfalvkalse.aglkviaeGrintPekakkaieiGvdavvvGsait 177
                                   +++++k+l e +++ +i  G i t e  k   e+G++ vv+Gsa+ 
  gi|15669727|ref|NP_248540.1| 177 NVDIIKELIEkTDIPIIYSGGITTLEDIKALKELGIYGVVIGSALY 222
                                   678899987626899*****************************95 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.023        24       7      38 ..      25      56 ..      21      61 .. 0.90
   2 ?    2.3   0.1     0.078        82     233     292 ..      64     120 ..      60     122 .. 0.86
   3 !   17.2   0.2   2.2e-06    0.0023     226     282 ..     173     226 ..     142     236 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.023
                                  TTEEESSSEEE-TTSSTTSSSHHHHHCTTSSE CS
                        DHO_dh  7 lglkfknpiglAaGfdkegeeilkllklgfga 38
                                  ++l+++np+ +A  f  eg e+l++++l++++
  gi|15669727|ref|NP_248540.1| 25 KHLELNNPVEVAKKFVDEGAEYLHIIDLDAAF 56
                                  799************************99655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.078
                                   HHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHH CS
                        DHO_dh 233 virelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkele 292
                                   vi ++ k+++  +p+   GGi   e a e i  G   v v+t     +pk ++++ ke+ 
  gi|15669727|ref|NP_248540.1|  64 VIKNIIKEVN--VPVEVGGGIRNLEIAKELISLGVDRVIVGTKA-ILEPKFIDDLNKEIG 120
                                   6788888888..999999************************99.567888888888875 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 2.2e-06
                                   GHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTC CS
                        DHO_dh 226 lkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpk 282
                                   lk i + +i el ++++  ipiI +GGi++ eD     e G   v +++al ++g  
  gi|15669727|ref|NP_248540.1| 173 LKGINVDIIKELIEKTD--IPIIYSGGITTLEDIKALKELGIYGVVIGSAL-YKGLI 226
                                   78999***********9..**************999999999999999999.77765 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   2.4e-07   0.00025     135     214 ..      28     110 ..      19     123 .. 0.75
   2 !    6.7   0.6    0.0042       4.4     169     214 ..     179     224 ..     134     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.4e-07
                                   -TTHHHHHHHHHHHHHHTT-SEEEEE-.TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-C..HH CS
                          PcrB 135 dlnkediaayallaakllglrliYlEa.sGaledveevialkkklekarlivGGGirsaEkAkevvea.ADvivvGn..vv 211
                                   +ln +  +a   + +    l +i l+a  G+ ++ + ++++ k ++   + vGGGir+ E+Ake +    D ++vG+  ++
  gi|15669727|ref|NP_248540.1|  28 ELNNPVEVAKKFVDEGAEYLHIIDLDAaFGTGNNRDVIKNIIKEVN-VPVEVGGGIRNLEIAKELISLgVDRVIVGTkaIL 107
                                   5566666666666666667889999997788888888888888875.6789*****************9*******83233 PP

                                   HHH CS
                          PcrB 212 eek 214
                                   e k
  gi|15669727|ref|NP_248540.1| 108 EPK 110
                                   333 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0042
                                   HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHH CS
                          PcrB 169 eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveek 214
                                   + +++l  k +++ +i+ GGi   E+ k   e     +v+G ++++ 
  gi|15669727|ref|NP_248540.1| 179 DIIKELIEK-TDIPIIYSGGITTLEDIKALKELgIYGVVIGSALYKG 224
                                   445555544.67899***********999999888999999999975 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0015       1.6     129     171 ..      63     105 ..      58     107 .. 0.91
   2 !   15.7   0.1     7e-06    0.0074     117     167 ..     167     217 ..     153     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0015
                                   HHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE--HH CS
                  G3P_antiterm 129 kvikeikkelkipiiaGGLietkedveealkaGaiavstsnke 171
                                   +vik+i ke+++p+  GG i++ e  +e+++ G++ v +++k+
  gi|15669727|ref|NP_248540.1|  63 DVIKNIIKEVNVPVEVGGGIRNLEIAKELISLGVDRVIVGTKA 105
                                   79*********************************99988776 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 7e-06
                                   -SEEEEESGGGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                  G3P_antiterm 117 pdavevlPglvpkvikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                   +d+  +l g+  ++ike+ ++++ipii +G i+t ed++++ + G+ +v  
  gi|15669727|ref|NP_248540.1| 167 VDVEGLLKGINVDIIKELIEKTDIPIIYSGGITTLEDIKALKELGIYGVVI 217
                                   566667778999*********************************999975 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2    0.0012       1.2     140     177 ..      63     101 ..      58     105 .. 0.85
   2 !   13.9   0.0   2.5e-05     0.026     135     181 .]     174     221 ..     149     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
                      TMP-TENI 140 eglkelaealeiPvvaiGGit.lenvaevleagadgvav 177
                                   + +k++ +++++Pv + GGi+ le ++e++  g+d+v v
  gi|15669727|ref|NP_248540.1|  63 DVIKNIIKEVNVPVEVGGGIRnLEIAKELISLGVDRVIV 101
                                   56899***************62577789*******9987 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.5e-05
                      TMP-TENI 135 eplgleglkelaealeiPvvaiGGit.lenvaevleagadgvavvsai 181
                                   + ++++ +kel e++ iP++  GGit le+++++ e g+ gv + sa+
  gi|15669727|ref|NP_248540.1| 174 KGINVDIIKELIEKTDIPIIYSGGITtLEDIKALKELGIYGVVIGSAL 221
                                   6678999******************7369*************998875 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.014        14      59     114 ..      22      78 ..      14     133 .. 0.74
   2 !   15.4   0.0   7.3e-06    0.0077     199     243 ..     181     223 ..     172     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                                   TTTEESBSS--HHHHHHHHTTT.-SEEEEE-.-CCCC---C.CHHHHHHHH-SS-EEE CS
                          IGPS  59 PskgliredfdpaeiAkkyeeagAsaiSVLt.eekyFqGsl.edLrevrqavslpvlr 114
                                   P k  ++ + +p+e+Akk+ + gA+ + ++  +  +  G++ + ++++ ++v++pv  
  gi|15669727|ref|NP_248540.1|  22 PNKKHLELN-NPVEVAKKFVDEGAEYLHIIDlDAAFGTGNNrDVIKNIIKEVNVPVEV 78 
                                   666677776.899999999999999999885266666787624577888889888865 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 7.3e-06
                                   HHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC CS
                          IGPS 199 teeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmr 243
                                    +eL++  ++d+ ++   Gi+t ed+++lke g+ ++ +G++l +
  gi|15669727|ref|NP_248540.1| 181 IKELIE--KTDIPIIYSGGITTLEDIKALKELGIYGVVIGSALYK 223
                                   344444..2458999999************************976 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.6   4.6e-05     0.049     107     173 ..      34     102 ..      28     105 .. 0.74
   2 !    8.1   0.1    0.0011       1.2     199     239 ..     181     221 ..     150     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                                   HHHHHHHHTT-SEE...EEE-STSSSHHHHHHHHHHHHHTTTSEE.EEEEE-SHHHHHHHHHTT-SEEEE- CS
                                   xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 107 ervkalveagvdvl...vvdsahghsekvleavkeikkkveevev.iaGnvataegakaLieagadavkvG 173
                                   e +k++v++g++ l    +d+a g   +  +++k+i k+v+ v v ++G + + e ak+Li+ g+d v vG
  gi|15669727|ref|NP_248540.1|  34 EVAKKFVDEGAEYLhiiDLDAAFGTG-NNRDVIKNIIKEVN-VPVeVGGGIRNLEIAKELISLGVDRVIVG 102
                                   55677777777655200456676654.45789999999995.54438**********************99 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0011
                                   HHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 199 vaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsll 239
                                   + e  +k+++p+i  GGi++ +di     +G   v++Gs l
  gi|15669727|ref|NP_248540.1| 181 IKELIEKTDIPIIYSGGITTLEDIKALKELGIYGVVIGSAL 221
                                   45667788888888888888888743335777788888765 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   3.6e-05     0.038     155     223 ..      29     105 ..      16     108 .. 0.82
   2 ?    2.4   0.0     0.083        88     184     225 ..     181     223 ..     168     234 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                    PEP_mutase 155 leeaieRaraYaeAGAdgvfvpgl.......qkdaeiaelvaavdvplnvvpl.kgtlsvaelaelGvarislgnhl 223
                                   l++ +e a+ +++ GA+ + ++ l       ++++ i++++++v+vp+ v  + ++    +el  lGv r+++g+++
  gi|15669727|ref|NP_248540.1|  29 LNNPVEVAKKFVDEGAEYLHIIDLdaafgtgNNRDVIKNIIKEVNVPVEVGGGiRNLEIAKELISLGVDRVIVGTKA 105
                                   556667788999999999999988888888666677****************6465556789************976 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.083
                    PEP_mutase 184 iaelvaavdvplnvvpl.kgtlsvaelaelGvarislgnhllr 225
                                   i+el++++d+p++   + ++  ++++l+elG+  +++g++l++
  gi|15669727|ref|NP_248540.1| 181 IKELIEKTDIPIIYSGGiTTLEDIKALKELGIYGVVIGSALYK 223
                                   6666666666666666423336677788888777777777776 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.02        21     206     243 ..      63     101 ..      23     107 .. 0.74
   2 !   12.0   0.3   7.4e-05     0.078     201     243 ..     174     217 ..     122     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.02
                                   HHHHHHHHHHSSEEEEE.EE-SHHHHHHHHHTTESEEEE CS
                        FMN_dh 206 ddikwlreqtklplvvK.GvltaedakraveaGvdgivv 243
                                   d ik++ +++++p+ v  G+ + e ak+++ +Gvd ++v
  gi|15669727|ref|NP_248540.1|  63 DVIKNIIKEVNVPVEVGgGIRNLEIAKELISLGVDRVIV 101
                                   457777777777776642577777777777777777776 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.4e-05
                                   TC--HHHHHHHHHHHSSEEEEE.EE-SHHHHHHHHHTTESEEEE CS
                        FMN_dh 201 psltwddikwlreqtklplvvK.GvltaedakraveaGvdgivv 243
                                   + ++ d ik+l e+t++p++   G+ t ed+k + e+G+ g+v+
  gi|15669727|ref|NP_248540.1| 174 KGINVDIIKELIEKTDIPIIYSgGITTLEDIKALKELGIYGVVI 217
                                   5678999***********9985379*****************98 PP

>> CutC  CutC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.3   1.4e+03      18      55 ..      41      78 ..      31      86 .. 0.68
   2 ?   -0.5   0.1       0.7   7.4e+02     176     186 ..      79      89 ..      53     104 .. 0.52
   3 ?   -0.5   0.0      0.69   7.3e+02     134     146 ..      89     101 ..      80     139 .. 0.67
   4 ?   -1.0   0.0      0.98     1e+03     156     180 ..     177     199 ..     173     201 .. 0.71
   5 !   12.4   0.0   7.8e-05     0.082      75     109 ..     201     235 ..     194     237 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                          CutC 18 aagadRvELCaalavgGltPslgvlkeaaeeakipvyv 55
                                  + ga+ + + +  a  G+     v+k++ +e+++pv v
  gi|15669727|ref|NP_248540.1| 41 DEGAEYLHIIDLDAAFGTGNNRDVIKNIIKEVNVPVEV 78
                                  55666666666666667777777888888888777754 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.7
                          CutC 176 gaGvnaenvae 186
                                   g+G++   +a+
  gi|15669727|ref|NP_248540.1|  79 GGGIRNLEIAK 89 
                                   44444333332 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.69
                          CutC 134 eqlielgvervLt 146
                                    +li+lgv+rv+ 
  gi|15669727|ref|NP_248540.1|  89 KELISLGVDRVIV 101
                                   4566777777654 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.98
                          CutC 156 gleklaeLveqaaerieimagaGvn 180
                                   +++ ++eL+e+++  i i+ ++G++
  gi|15669727|ref|NP_248540.1| 177 NVDIIKELIEKTD--IPIIYSGGIT 199
                                   5778888888765..5557777775 PP

  == domain 5  score: 12.4 bits;  conditional E-value: 7.8e-05
                          CutC  75 leDieaarelgldgvvlGaltadgeiDlkalekli 109
                                   leDi+a++elg+ gvv+G    +g iDlk+  +++
  gi|15669727|ref|NP_248540.1| 201 LEDIKALKELGIYGVVIGSALYKGLIDLKKALEIV 235
                                   69**************************9887766 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.95     1e+03      62      85 ..      25      48 ..      11      56 .. 0.73
   2 ?    7.0   0.4    0.0032       3.4     156     195 ..      65     103 ..      58     106 .. 0.77
   3 ?    7.2   0.1    0.0029         3     116     198 .]     147     222 ..     138     222 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.95
                                  EEEESSSHHHCHHHHHHCT-SEEE CS
                Ribul_P_3_epim 62 vHLmveevdrivpefaeagasiis 85
                                   HL ++++ +++++f++ ga+++ 
  gi|15669727|ref|NP_248540.1| 25 KHLELNNPVEVAKKFVDEGAEYLH 48
                                  577777777888888887777654 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0032
                                   HHHHHHHHT---EEEEESS-.-TTTCHHHHHHT--EEEESH CS
                Ribul_P_3_epim 156 vrklidekeldlkievDGGv.kldnieqiaeagadvlVags 195
                                   ++++i+e  +++ +ev GG+ +l+ ++++++ g+d +++g+
  gi|15669727|ref|NP_248540.1|  65 IKNIIKE--VNVPVEVGGGIrNLEIAKELISLGVDRVIVGT 103
                                   4555554..9999*******44577789*******999997 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0029
                                   --GGGGTTTCCC-SEEEEESS-TT-SS----CCHHHHHHHHHHHHHHHT---EEEEESS--.TTTCHHHHHHT--EEEESH CS
                Ribul_P_3_epim 116 tplealeyllekldlvllmsvePgfgGQkFipevlekikkvrklidekeldlkievDGGvk.ldnieqiaeagadvlVags 195
                                   tp+e+++++ +k+  +l   v+   +G   ++    ++  +++li++  +d+ i   GG++ l+ i+++ e g+  +V+gs
  gi|15669727|ref|NP_248540.1| 147 TPIEVIKEFEDKVGYILFTNVDV--EG--LLKG--INVDIIKELIEK--TDIPIIYSGGITtLEDIKALKELGIYGVVIGS 219
                                   66666666666666666655543..22..1221..246667888887..8999999***963699**************** PP

                                   HHH CS
                Ribul_P_3_epim 196 avf 198
                                   a++
  gi|15669727|ref|NP_248540.1| 220 ALY 222
                                   *97 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1     0.003       3.2      26     115 ..      24     109 ..      10     146 .. 0.78
   2 ?    3.5   0.1      0.08        84      36     106 ..     150     216 ..     130     220 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.003
                                   HHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  26 grslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvs 106
                                    ++l + + +e +k++ ++ g++++++   +  +     +++ + + +   ++++ ve+ g+  + e++++l  lgvdrv 
  gi|15669727|ref|NP_248540.1|  24 KKHLELNNPVEVAKKF-VDEGAEYLHIIDLDAAFGTGNNRDVIKNIIK---EVNVPVEVGGGIRNLEIAKELISLGVDRVI 100
                                   5566666777778888.7778888888888888888888888888887...999999999999889999*******99999 PP

                                   EEEBSSSHH CS
                                   xxxxxxxxx RF
                   Radical_SAM 107 lgleaadde 115
                                   +g +a+ + 
  gi|15669727|ref|NP_248540.1| 101 VGTKAILEP 109
                                   998887665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.08
                                   HHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  36 eevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvs 106
                                   e +ke+ ++k v++++++  ++    +    ++ +++l  ++  i ++ +g+  + e +++l+elg+  v 
  gi|15669727|ref|NP_248540.1| 150 EVIKEF-EDK-VGYILFTNVDVEGLLKG-INVDIIKEL-IEKTDIPIIYSGGITTLEDIKALKELGIYGVV 216
                                   555666.566.88888886666665533.444444444.3688888999999999*********9965555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 1412.34
//
Query:       gi|15669728|ref|NP_248541.1|  [L=642]
Description: ATPase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-12   47.1   0.0    3.3e-12   46.0   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
    1.5e-08   35.1   0.2    4.4e-08   33.6   0.2    1.9  1  PIN              PIN domain
    2.9e-08   33.4   0.6    1.3e-07   31.3   0.6    2.2  1  KH_1             KH domain
    0.00013   22.4   0.0     0.0003   21.2   0.0    1.6  1  AAA_16           AAA ATPase domain
    0.00029   21.1   0.3     0.0019   18.5   0.0    2.3  2  PIN_4            PIN domain
    0.00044   20.0   0.0     0.0047   16.7   0.0    2.4  3  AAA_30           AAA domain
    0.00045   19.3   0.0     0.0011   18.0   0.0    1.6  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    0.00081   19.2   0.1     0.0017   18.2   0.1    1.5  1  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0013   19.2   0.1     0.0058   17.2   0.0    2.2  1  ABC_tran         ABC transporter
     0.0019   18.1   0.0       0.01   15.7   0.0    2.4  1  NTPase_1         NTPase
     0.0021   18.6   0.9      0.013   16.1   0.0    2.9  3  AAA_18           AAA domain
     0.0035   17.0   0.0      0.021   14.6   0.0    2.3  2  AAA_29           P-loop containing region of AAA domain
     0.0056   16.5  10.4     0.0056   16.5   4.7    3.2  2  KH_2             KH domain
     0.0093   15.8   6.4     0.0094   15.8   0.6    4.0  4  KH_4             KH domain
     0.0094   15.6   3.1      0.031   14.0   0.0    3.4  4  Thymidylate_kin  Thymidylate kinase
  ------ inclusion threshold ------
       0.01   16.3   0.2       0.01   16.3   0.2    3.4  4  PIN_12           PIN domain
      0.015   15.3   0.0      0.047   13.7   0.0    1.9  1  AAA_5            AAA domain (dynein-related subfamily)
      0.026   14.8   0.0      0.066   13.5   0.0    1.7  1  AAA_22           AAA domain
      0.034   14.3   0.0      0.086   13.0   0.0    1.7  1  AAA_33           AAA domain
      0.056   13.2   0.0       0.12   12.1   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
      0.057   13.8   0.0       0.28   11.6   0.0    2.2  2  AAA              ATPase family associated with various cellul
      0.068   12.4   0.0       0.16   11.2   0.0    1.6  1  Zeta_toxin       Zeta toxin
      0.081   12.1   0.0       0.18   10.9   0.0    1.5  1  PIF1             PIF1-like helicase
      0.088   13.1   0.0       0.23   11.7   0.0    1.8  1  AAA_28           AAA domain
      0.088   12.7   0.0       0.17   11.8   0.0    1.4  1  Ploopntkinase3   P-loop Nucleotide Kinase3
       0.11   12.4   0.0       0.36   10.7   0.0    1.9  1  NACHT            NACHT domain
       0.13   12.6   0.0       0.34   11.3   0.0    1.7  1  RNA_helicase     RNA helicase
       0.92    9.6   6.5       0.15   12.2   0.7    2.8  1  KH_5             NusA-like KH domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   5.2e-15   3.3e-12      43     245 ..     204     397 ..     188     417 .. 0.74

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 5.2e-15
                         T2SSE  43 ekaalerlisriaalakldiseerplqdar..lpekgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiae 120
                                   +k+++e +i +i   a+++    ++   ++  ++ +++r+ ++ +P +++ e  ++R   ++  +l+d+  + +l e+   
  gi|15669728|ref|NP_248541.1| 204 TKEEMEDIIDNIIKYAEQNNGFFEIQRKGAtvIQLGNIRISIARPPFSEAlEVTAVRPVVKA--SLEDYELSDKLMER--- 279
                                   556666666666666655544444333333114478999***********999999955544..57788766554444... PP

                         T2SSE 121 vlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnakkakvtfadllraaLRlrPD 201
                                    l++       i vsG+ gsGK+t++ al ++  ++ + + t+E p+ +q++++  +q  +   + ++++    +L  rPD
  gi|15669728|ref|NP_248541.1| 280 -LKER---AEGIFVSGPPGSGKSTFVAALAEFYRSQGKIVKTMESPRDLQVSKEI-TQYAPL--EGDMEKTCDILLLVRPD 353
                                   .3334...47899*************999999999977777**********7653.344443..568999999999***** PP

                         T2SSE 202 rimvGEiRdketleilkAvnTGHlgslsTlHansaagalerLeq 245
                                     +  E+R +  +ei   +     g ++ +Ha ++++a++rL  
  gi|15669728|ref|NP_248541.1| 354 YTIYDEVRKTRDFEIFADMRMAGVGMVGVVHASKPIDAIQRLIG 397
                                   ***************666666666669**************964 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.2   6.9e-11   4.4e-08       1     120 [.      29     143 ..      29     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 6.9e-11
                                   EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHH CS
                           PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidaeiaee 80 
                                   +++DT v+i   +g+      r  l +  +++++++v++El y ++ +++  +k +e+++ l++ +s+++i     + + +
  gi|15669728|ref|NP_248541.1|  29 VCVDTCVVI---DGRITELIERGKLKD-ATIIIPEAVVSELEYQANMGREIGYKGIEELRKLIEkASEHNIKVEYYGERPT 105
                                   689999999...777766666666654.*******************888888888888888888**************** PP

                                   HHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                           PIN  81 aaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                    +ei+l +  + +Da+i  +Ake++ +l+ t D   +++a
  gi|15669728|ref|NP_248541.1| 106 REEIFLAK-SGEIDAMIRKVAKETNSILL-TSDWIQYNLA 143
                                   ******99.*****************999.***8877766 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.6     2e-10   1.3e-07       3      46 ..     514     559 ..     512     562 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2e-10
                                   EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.STT....T.- CS
                          KH_1   3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpk.sedeg.sder 46 
                                    ++vP +++g+iIGkgG+ I ++++  g kI v + +++e+ ++er
  gi|15669728|ref|NP_248541.1| 514 DLIVPEKYIGAIIGKGGKEISKLEDMLGLKISVKEkEKEEEkDMER 559
                                   579**********************66*****99644444355555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   4.7e-07    0.0003      17      58 ..     278     319 ..     269     399 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.7e-07
                        AAA_16  17 ervrsgrpelvllsGesGvGKsslvrellralekdggif.lrg 58 
                                   er+++ r e +++sG++G+GKs+ v +l++ ++ +g i+ + +
  gi|15669728|ref|NP_248541.1| 278 ERLKE-RAEGIFVSGPPGSGKSTFVAALAEFYRSQGKIVkTME 319
                                   44444.4599*******************98887764443333 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.9e-06    0.0019       3     127 ..      31     150 ..      29     153 .. 0.68
   2 ?   -0.4   0.1       2.1   1.3e+03       2      33 ..     407     438 ..     406     440 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.9e-06
                         PIN_4   3 lDTnvlLhdpealksf.....keehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqts...ae 75 
                                   +DT+v+++    + ++      ++  ++iP  V++EL+ + +  +  e++++  + +r l e  ++++ ++    +   +e
  gi|15669728|ref|NP_248541.1|  31 VDTCVVIDGR--ITELiergkLKDATIIIPEAVVSELEYQANMGR--EIGYKGIEELRKLIEKASEHNIKVEYYGErptRE 107
                                   6899988764..33333445679999***********98888887..9999976666544444444444444433322333 PP

                         PIN_4  76 elpeeeseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgiea 127
                                   e+    ++s + D +I +va e        + +L++ D    + Aka+giea
  gi|15669728|ref|NP_248541.1| 108 EIFL--AKSGEIDAMIRKVAKET-------NSILLTSDWIQYNLAKAQGIEA 150
                                   3332..34568999999988554.......5699***************987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.1
                         PIN_4   2 VlDTnvlLhdpealksfkeehdvviPitVleE 33 
                                   V+DT ++++d ++ k  + +  v +P+  +eE
  gi|15669728|ref|NP_248541.1| 407 VVDTVIFIKDGKIQKVYEIDFTVKVPYGMVEE 438
                                   99********9886666667889999988887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.4     9e+02      96     124 ..      74     102 ..      73     105 .. 0.90
   2 ?   -1.9   0.0       3.6   2.3e+03      99     134 ..     111     146 ..     107     166 .. 0.75
   3 !   16.7   0.0   7.3e-06    0.0047      20      49 ..     286     315 ..     274     335 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.4
                        AAA_30  96 EagmvdtkqlaallkaaekagakvilvGD 124
                                   E+g  ++++l++l+++a+++++kv   G 
  gi|15669728|ref|NP_248541.1|  74 EIGYKGIEELRKLIEKASEHNIKVEYYGE 102
                                   8889999****************988775 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
                        AAA_30  99 mvdtkqlaallkaaekagakvilvGDerQlasVeaG 134
                                   ++ + +++a++++++k+  +++l  D  Q +  +a 
  gi|15669728|ref|NP_248541.1| 111 LAKSGEIDAMIRKVAKETNSILLTSDWIQYNLAKAQ 146
                                   566778899999999999999999999998755555 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 7.3e-06
                        AAA_30  20 vavltGpAGtGKttalkalreaweaaggrv 49 
                                     ++ Gp+G+GK+t ++al+e ++++g+ v
  gi|15669728|ref|NP_248541.1| 286 GIFVSGPPGSGKSTFVAALAEFYRSQGKIV 315
                                   56899********************99655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.7e-06    0.0011      14      60 ..     272     315 ..     256     319 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-06
                                   HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--E CS
                          MeaB  14 eakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrv 60 
                                    + +l+erl     ra+ + + G PG+Gkst+v al++ +r++Gk v
  gi|15669728|ref|NP_248541.1| 272 LSDKLMERLK---ERAEGIFVSGPPGSGKSTFVAALAEFYRSQGKIV 315
                                   3445555554...47899**************************977 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.7e-06    0.0017       1      28 [.     289     316 ..     289     320 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.7e-06
                    ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsva 28 
                                   v Gp+GsGK+tfv al+e+++++g+ v+
  gi|15669728|ref|NP_248541.1| 289 VSGPPGSGKSTFVAALAEFYRSQGKIVK 316
                                   78*******************9988766 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     9e-06    0.0058      12      55 ..     285     325 ..     281     406 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9e-06
                                   SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqele 55 
                                   e + + G+ G+GKSt++++la+ ++  +G+i   +++ ++  l+
  gi|15669728|ref|NP_248541.1| 285 EGIFVSGPPGSGKSTFVAALAEFYR-SQGKIVKTMESPRD--LQ 325
                                   557789******************9.69999333333333..33 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.6e-05      0.01       2      31 ..     287     316 ..     286     330 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                   +f++GppG+GK+T+v  ++e  +s+g  v+
  gi|15669728|ref|NP_248541.1| 287 IFVSGPPGSGKSTFVAALAEFYRSQGKIVK 316
                                   89********************99998887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       7.8     5e+03     104     115 ..     274     285 ..     273     286 .. 0.85
   2 !   16.1   0.0     2e-05     0.013       1      21 [.     287     307 ..     287     347 .. 0.76
   3 ?   -1.9   0.1       7.1   4.5e+03      71      79 ..     576     584 ..     531     640 .. 0.54

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 7.8
                        AAA_18 104 eelleRlekRgy 115
                                   ++l+eRl++R +
  gi|15669728|ref|NP_248541.1| 274 DKLMERLKERAE 285
                                   689******975 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskr 21 
                                   I+++G+pG+GK+t+  +L++ 
  gi|15669728|ref|NP_248541.1| 287 IFVSGPPGSGKSTFVAALAEF 307
                                   99****************874 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 7.1
                        AAA_18  71 leegknlvi 79 
                                   +e  k +v+
  gi|15669728|ref|NP_248541.1| 576 YETDKYVVV 584
                                   333333333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.2   3.4e+03      44      57 ..     130     143 ..     128     147 .. 0.76
   2 !   14.6   0.0   3.2e-05     0.021      22      43 ..     285     305 ..     273     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.2
                        AAA_29  44 alLvpakkvrfNka 57 
                                    +L+ + ++++N a
  gi|15669728|ref|NP_248541.1| 130 SILLTSDWIQYNLA 143
                                   57888889****98 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.2e-05
                        AAA_29  22 kgatlltGpsGsGKSTllDAiq 43 
                                   +g ++++Gp GsGKST++ A++
  gi|15669728|ref|NP_248541.1| 285 EG-IFVSGPPGSGKSTFVAALA 305
                                   45.99************98875 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3       0.4   2.6e+02      30      67 ..      65      96 ..      41     104 .. 0.68
   2 !   16.5   4.7   8.8e-06    0.0056      15      65 ..     502     551 ..     487     626 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.4
                                  EEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEE CS
                          KH_2 30 viresqpgivIGkgGsnikkigkelrkdieklegkkVk 67
                                   ++ +++g+ IG +G  i++++k ++k      + ++k
  gi|15669728|ref|NP_248541.1| 65 LEYQANMGREIGYKG--IEELRKLIEKAS----EHNIK 96
                                  577788888888887..556666665554....45555 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 8.8e-06
                                   EEEEEEECCS.CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC CS
                          KH_2  15 vskveIerta.nrviiviresqpgivIGkgGsnikkigkelrkdieklegkk 65 
                                   +  v++  t  n + +++ e   g +IGkgG++i k++  l+ +i + e+ k
  gi|15669728|ref|NP_248541.1| 502 KPMVKV--TGdNSIDLIVPEKYIGAIIGKGGKEISKLEDMLGLKISVKEKEK 551
                                   555556..333899999****************************8666655 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2         2   1.3e+03      38      48 ..      69      79 ..      64     100 .. 0.82
   2 ?   -2.2   0.0       6.1   3.9e+03       8      35 ..      83     111 ..      80     114 .. 0.70
   3 !   15.8   0.6   1.5e-05    0.0094       1      52 [.     486     534 ..     486     556 .. 0.88
   4 ?   -2.5   0.0       7.4   4.8e+03      13      38 ..     577     602 ..     573     604 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2
                          KH_4 38 edlGrvIGkrG 48
                                   ++Gr IG++G
  gi|15669728|ref|NP_248541.1| 69 ANMGREIGYKG 79
                                  79999999999 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.1
                          KH_4   8 lkalvddpeevevtee.eeeeeveielnv 35 
                                   l++l++++ e ++++e ++e+ ++ e+ +
  gi|15669728|ref|NP_248541.1|  83 LRKLIEKASEHNIKVEyYGERPTREEIFL 111
                                   56778888888888887777766666655 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1.5e-05
                          KH_4   1 kelvedilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtld 52 
                                   +e +e+ilk+l+  +++  v+++    +++i+l v ++ +G +IGk G+ ++
  gi|15669728|ref|NP_248541.1| 486 EEKLEEILKKLLPRKAKPMVKVT---GDNSIDLIVPEKYIGAIIGKGGKEIS 534
                                   5889********99999999998...6789******************9887 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 7.4
                          KH_4  13 ddpeevevteeeeeeeveielnvege 38 
                                   +  + v v++ e+  +++i+++++g+
  gi|15669728|ref|NP_248541.1| 577 ETDKYVVVDVGEDFAGENIRIYIDGK 602
                                   55566888888889999999999875 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         3   1.9e+03      72     112 ..      44      85 ..      40      89 .. 0.79
   2 ?   -1.7   0.0       3.1     2e+03      36      89 ..     115     168 ..     110     170 .. 0.81
   3 !   14.0   0.0   4.8e-05     0.031       3      55 ..     291     343 ..     289     362 .. 0.81
   4 ?   -2.7   0.3         6   3.9e+03     144     168 ..     549     574 ..     544     585 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3
                                   HHHHHHHTT-EEEEES-HHHHHHHHHT.TTTTTCHHHHHHGG CS
               Thymidylate_kin  72 kikpalkqgktvivdRylfSslaYqga.kegvdldlvlslne 112
                                   +i++   ++ t+i+  +++S l Yq+  +++++++ + +l++
  gi|15669728|ref|NP_248541.1|  44 LIERGKLKDATIIIPEAVVSELEYQANmGREIGYKGIEELRK 85 
                                   55555556689999999********98788999998888775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                                   SHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT-EEEEES-H CS
               Thymidylate_kin  36 teiGekirelllkeeeleeqteallfaadriehleekikpalkqgktvivdRyl 89 
                                   +ei  +ir++ ++++ +   +  + +  ++++ +e +  +a +++  +++d+y 
  gi|15669728|ref|NP_248541.1| 115 GEIDAMIRKVAKETNSILLTSDWIQYNLAKAQGIEAYFLEAAEEEVELVLDKYF 168
                                   667778888888777777777888888888899999999999999999999985 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 4.8e-05
                                   ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HH CS
               Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeq 55 
                                   G  G+GK+t++++l+e ++++g+ v +   p++ ++ + i ++   e ++e+ 
  gi|15669728|ref|NP_248541.1| 291 GPPGSGKSTFVAALAEFYRSQGKIVKTMESPRDLQVSKEITQYAPLEGDMEKT 343
                                   778*******************6577777799*********998756666554 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 6
                                   SHHHHHHHHHHHHHHHHHHHH.TTST CS
               Thymidylate_kin 144 eeeeqldflrkvrerylelak.eder 168
                                   +e+e++++ +++ ++y  + + e +r
  gi|15669728|ref|NP_248541.1| 549 KEKEEEKDMERIYRKYEYVNElESTR 574
                                   45555555555555555444433333 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   0.2   1.6e-05      0.01       1     106 [.      29     134 ..      29     190 .. 0.62
   2 ?   -1.3   0.0       4.2   2.7e+03      81     110 ..     204     233 ..     193     252 .. 0.61
   3 ?   -2.2   0.0       8.1   5.2e+03     104     131 ..     472     500 ..     451     513 .. 0.68
   4 ?   -1.0   2.0       3.4   2.2e+03      77     117 ..     534     574 ..     489     583 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-05
                        PIN_12   1 ifiDTnifldeffrlseeealkklleliesgkiklivpdivldE..flknrekkiees..kklekalkslsklksakkkln 77 
                                   +++DT++ +d          +++l e+ + +++++i+p+ v+ E  ++ n  ++i ++  ++l+k +++ s+ + + + + 
  gi|15669728|ref|NP_248541.1|  29 VCVDTCVVID--------GRITELIERGKLKDATIIIPEAVVSEleYQANMGREIGYKgiEELRKLIEKASEHNIKVEYYG 101
                                   79*******9........4799999****************9862256777999999988666666666444444444444 PP

                        PIN_12  78 ekkkll.slkeikkkieekvees...lkkllek 106
                                   e+++ + ++ +++ +i+  ++++    +++l  
  gi|15669728|ref|NP_248541.1| 102 ERPTREeIFLAKSGEIDAMIRKVakeTNSILLT 134
                                   444332022222222222222222223333333 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.2
                        PIN_12  81 kllslkeikkkieekveeslkklleklea.i 110
                                   ++++ ++i ++i +++e+ ++ ++e   + +
  gi|15669728|ref|NP_248541.1| 204 TKEEMEDIIDNIIKYAEQ-NNGFFEIQRKgA 233
                                   344445555555555444.555555544444 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 8.1
                        PIN_12 104 leklea.ikvipetndevkkilerafkkk 131
                                   +e+ ++ +++  + ++++++il++ + +k
  gi|15669728|ref|NP_248541.1| 472 KEEGGKkAPIYGYAEEKLEEILKKLLPRK 500
                                   55555557777777778888888777655 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 3.4
                        PIN_12  77 nekkkllslkeikkkieekveeslkkllekleaikvipetn 117
                                   +++++ l lk   k+ e++ e+ ++++++k+e ++++++t 
  gi|15669728|ref|NP_248541.1| 534 SKLEDMLGLKISVKEKEKEEEKDMERIYRKYEYVNELESTR 574
                                   44444444444444444444444999999998866666554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.3e-05     0.047       2      39 ..     287     327 ..     286     371 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.3e-05
                                   EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HH CS
                         AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdttee 39 
                                   +++ GppG+gKs+++  la+++   ++ v ++  +rd++ +
  gi|15669728|ref|NP_248541.1| 287 IFVSGPPGSGKSTFVAALAEFYrsqGKIVKTMESPRDLQVS 327
                                   6889******************7666666666666666554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0    0.0001     0.066       5      34 ..     284     313 ..     279     348 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0001
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeak 34 
                                   a  ++v G++G+GK+t ++ l+e +  + k
  gi|15669728|ref|NP_248541.1| 284 AEGIFVSGPPGSGKSTFVAALAEFYRSQGK 313
                                   56689*****************99965544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00013     0.086       2      21 ..     287     306 ..     287     327 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                        AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                   +++ G+pGsGKst++  l++
  gi|15669728|ref|NP_248541.1| 287 IFVSGPPGSGKSTFVAALAE 306
                                   6789***********99974 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.12      45      80 ..     282     317 ..     261     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                     IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavraglsvlf 80 
                                   e++e+i + Gp+G GKs + +al+     +g+ v  
  gi|15669728|ref|NP_248541.1| 282 ERAEGIFVSGPPGSGKSTFVAALAEFYRSQGKIVKT 317
                                   7899*******************9877777776655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.7   5.6e+03      66      74 ..     116     124 ..      78     164 .. 0.64
   2 ?   11.6   0.0   0.00044      0.28       2      22 ..     288     308 ..     287     334 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.7
                                   TGGGHHHHH CS
                           AAA  66 Eidalaksr 74 
                                   Eida++++ 
  gi|15669728|ref|NP_248541.1| 116 EIDAMIRKV 124
                                   333333333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00044
                                   EEESSTTSSHHHHHHHHHHHH CS
                           AAA   2 llyGppGtGKTllakavakel 22 
                                    ++GppG GK++++ a+a+  
  gi|15669728|ref|NP_248541.1| 288 FVSGPPGSGKSTFVAALAEFY 308
                                   689**************9865 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00025      0.16      14      48 ..     282     316 ..     271     319 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                    Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvr 48 
                                   er   i+++G pG+GKs+  ++l++  ++qg++v+
  gi|15669728|ref|NP_248541.1| 282 ERAEGIFVSGPPGSGKSTFVAALAEFYRSQGKIVK 316
                                   666779*****************999999999985 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00029      0.18      19      56 ..     281     318 ..     267     321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                                   .HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEE CS
                          PIF1  19 nekgklfFvtGsgGtgKtflwkallkklrsegkivlav 56 
                                   +e+++ +Fv+G  G+gK+ +  al ++ rs+gkiv ++
  gi|15669728|ref|NP_248541.1| 281 KERAEGIFVSGPPGSGKSTFVAALAEFYRSQGKIVKTM 318
                                   567788****************************9775 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00036      0.23       2      22 ..     287     307 ..     286     339 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                        AAA_28   2 ivitGgestGKTtlleaLaar 22 
                                   i ++G++++GK+t ++aLa+ 
  gi|15669728|ref|NP_248541.1| 287 IFVSGPPGSGKSTFVAALAEF 307
                                   779****************63 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00026      0.17       6      30 ..     287     311 ..     282     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                Ploopntkinase3   6 iylvGqPGaGkstlmaeltkgfdrs 30 
                                   i++ G PG+Gkst++a+l++ +  +
  gi|15669728|ref|NP_248541.1| 287 IFVSGPPGSGKSTFVAALAEFYRSQ 311
                                   899***************9988654 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00056      0.36       3      22 ..     287     306 ..     285     317 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00056
                                   EEEEC-TTTCHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                   +++ G++GsGK+t+++ la+
  gi|15669728|ref|NP_248541.1| 287 IFVSGPPGSGKSTFVAALAE 306
                                   789*************9986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00053      0.34       1      20 [.     287     306 ..     287     332 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00053
                  RNA_helicase   1 iwlyGpsgeGKStlakeLak 20 
                                   i+++Gp+g GKSt++  La+
  gi|15669728|ref|NP_248541.1| 287 IFVSGPPGSGKSTFVAALAE 306
                                   789*************9886 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.7   0.00023      0.15       8      47 ..     516     549 ..     509     560 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                          KH_5   8 aVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvew 47 
                                   +V ++      +Gai+gk+G+ i+++++ L g ki v e+
  gi|15669728|ref|NP_248541.1| 516 IVPEKY-----IGAIIGKGGKEISKLEDML-GLKISVKEK 549
                                   555555.....9******************.***998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1109  (0.0618551); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.44
# Mc/sec: 4408.39
//
Query:       gi|15669729|ref|NP_248542.1|  [L=331]
Description: methylenetetrahydromethanopterin reductase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-71  241.7   0.0    1.5e-71  241.4   0.0    1.0  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
      0.047   14.1   0.0       0.12   12.8   0.0    1.8  1  FlgM            Anti-sigma-28 factor, FlgM


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.4   0.0   1.7e-75   1.5e-71      21     314 .]      12     303 ..       3     303 .. 0.97

  Alignments for each domain:
  == domain 1  score: 241.4 bits;  conditional E-value: 1.7e-75
                Bac_luciferase  21 slrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRf 101
                                   +++ l  ++++aE+ Gf+++w+++h+++    ++ ++ l+a+a+ T++i+lg +vt++y+r+Pa++A ++atLd+lsgGR+
  gi|15669729|ref|NP_248542.1|  12 PIQKLCYYVKLAEDNGFEYCWITDHYNN----RNVYMALTAIAMNTNKIKLGPGVTNPYVRSPAITASAIATLDELSGGRA 88 
                                   677777899******************9....************************************************* PP

                Bac_luciferase 102 glglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyvaaaspaglela 182
                                   +lg+g g  a+  ++ G+++ +++  l+E +ev+r+l++ge+v++eG+ ++++ga l  +p q+++Pvy++a +p++le a
  gi|15669729|ref|NP_248542.1|  89 VLGIGPGDKATF-DALGIEWVKPVTTLKESIEVIRKLLAGERVSYEGKVVKIAGAALAVKPIQKAVPVYMGAQGPKMLETA 168
                                   *******99888.999***************************************************************** PP

                Bac_luciferase 183 arhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraea...raliagldfyaldsegagr 260
                                   + +adg+l++ + p++ +++i+ +++ga++agr+ ++i+v++ +  +v++++++A++ a    a+ia +      +++  +
  gi|15669729|ref|NP_248542.1| 169 GMIADGVLINASNPKDFEAAIPLIKKGAEAAGRSMDEIDVAAYACMSVDKNADKAKQAAvpvVAFIAAGSPPVVLERHGID 249
                                   ***********************************************************999999988889999999999* PP

                Bac_luciferase 261 eaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvde 314
                                   +++ ++i+++ +++++ +a++ v+d +++a+ + Gtpe+v+e+ + +ae+gv++
  gi|15669729|ref|NP_248542.1| 250 MEKVEAIRNALKSGNFPEAFKNVDDTMLEAFSIYGTPEDVVEKCKKLAEMGVTQ 303
                                   ***************************************************985 PP

>> FlgM  Anti-sigma-28 factor, FlgM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.3e-05      0.12      24      42 ..     247     265 ..     215     278 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                          FlgM  24 evreekVaelKeaIasGtY 42 
                                    +++ekV+++++a++sG++
  gi|15669729|ref|NP_248542.1| 247 GIDMEKVEAIRNALKSGNF 265
                                   59***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2129.70
//
Query:       gi|15669730|ref|NP_248543.1|  [L=299]
Description: hypothetical protein MJ_1535 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.097   12.3   0.0       0.19   11.4   0.0    1.4  1  Crr6      Chlororespiratory reduction 6


Domain annotation for each model (and alignments):
>> Crr6  Chlororespiratory reduction 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.1e-05      0.19      21     103 ..      26     108 ..      16     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.1e-05
                          Crr6  21 llkeealaeleqqlkleieypreeedprElsEipevRlwfirldavyPwlpllldwkaGelaryaamlvpHqfsrkeGiqf 101
                                   + +e ++ + e++ +le e   ++++++ l+ i e++  +i  +     + + l  ++G+lar +   v  ++   +G+ f
  gi|15669730|ref|NP_248543.1|  26 VNNEININKIETNKTLENESLIQKTEKNQLAKIKEIKYMYIVKEGNKTKIQFALAYENGSLARVSNGKVVLKIFDDSGLLF 106
                                   45566777778888888888889999**************************************99999999999999999 PP

                          Crr6 102 np 103
                                   n+
  gi|15669730|ref|NP_248543.1| 107 NK 108
                                   86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1414  (0.0788666); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1854.61
//
Query:       gi|15669731|ref|NP_248544.1|  [L=301]
Description: thioredoxin reductase TrxB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-44  152.1   3.4      2e-44  152.0   3.4    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    4.3e-27   95.2   9.0    9.7e-23   80.9   0.8    2.0  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    4.7e-12   46.3   7.5    7.5e-12   45.6   1.4    3.1  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.9e-08   33.8   5.6    0.00042   19.5   0.4    3.2  4  FAD_binding_2  FAD binding domain
    0.00013   20.8   5.9      0.014   14.1   1.2    3.6  4  HI0933_like    HI0933-like protein
    0.00031   20.2   1.0       0.12   11.7   0.0    2.6  3  FAD_oxidored   FAD dependent oxidoreductase
     0.0047   16.3   0.0     0.0082   15.5   0.0    1.3  1  GMC_oxred_N    GMC oxidoreductase
     0.0084   15.4   1.7      0.013   14.8   0.3    1.9  2  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.014   15.6   0.3      0.023   14.9   0.3    1.3  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.015   14.4   7.8       0.32   10.0   0.1    3.5  4  GIDA           Glucose inhibited division protein A
      0.019   15.0   0.2        5.9    6.9   0.0    3.0  3  NAD_binding_9  FAD-NAD(P)-binding
      0.037   13.6   0.9         16    5.0   1.3    2.9  3  DAO            FAD dependent oxidoreductase
       0.12   11.5   0.3        6.2    5.9   0.0    2.5  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
       0.13   11.5   0.0       0.18   11.0   0.0    1.2  1  FAD_binding_3  FAD binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.0   3.4   1.6e-47     2e-44       2     294 .]       4     287 ..       3     287 .. 0.91

  Alignments for each domain:
  == domain 1  score: 152.0 bits;  conditional E-value: 1.6e-47
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.HHHHCHHHHCCCCHC....CTCEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx....xxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.evvkklnqgielllg....eevvk 77 
                                   d ++iG+Gp+Gl+a +++ + +++ +++  e++  +g++  + +++++++++ei+  e  +k++++ e+++      ev+k
  gi|15669731|ref|NP_248544.1|   4 DTIIIGAGPGGLTAGIYAMRGKLNALCI--EKENAGGRIAEAGIVENYPGFEEIRGyELAEKFKNHAEKFKLpiiyDEVIK 82 
                                   789*************************..66679******************999*555555555444444444458*** PP

                                   EEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  78 idpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvElA 158
                                   i+++++ +k+ +k    + ++  +++v+AtG +p++lg+  + +  g+++++++ ++a+ + +++  ++v+G    ++  A
  gi|15669731|ref|NP_248544.1|  83 IETKERPFKVITK----NSEYLTKTIVIATGTKPKKLGLNED-KFIGRGISYCTMCDAFFYLNKE--VIVIGRDTPAIMSA 156
                                   *999999999654....469********************99.9********************9..************** PP

                                   HHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEETTE..EEE.EEETTSCEEEESEEEE-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx..xxx.xxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 159 aalaklgkevtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidgnge..kle.vvledgeeidadlvvvav 235
                                   + l++++k+v ++ + ++l     k+++ ++ ++l++  +ve+  ++++ ei g+++   ++  v++++e i+ad ++++ 
  gi|15669731|ref|NP_248544.1| 157 INLKDIAKKVIVITDKSEL-----KAAESIMLDKLKEAnNVEIIYNAKPLEIVGEERaeGVKiSVNGKEEIIKADGIFISL 232
                                   *******************.....589999999999988*****************998777677777777********** PP

                                   -EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 236 GvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                   G  p+te+l +++g+eld++g+i++de++rtn++giya+GDv    gg++++ +Av  G
  gi|15669731|ref|NP_248544.1| 233 GHVPNTEFL-KDSGIELDKKGFIKTDENCRTNIDGIYAVGDVR---GGVMQVAKAVGDG 287
                                   *********.*********************************...********99876 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.9   5.5e-07   0.00071       1      36 [.       6      40 ..       6      43 .. 0.91
   2 !   80.9   0.8   7.5e-26   9.7e-23      76     305 .]      53     271 ..      42     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.5e-07
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnignsi 36
                                  iIiGaGP Gl+a+i + + +l + l +Ek+n+g  i
  gi|15669731|ref|NP_248544.1|  6 IIIGAGPGGLTAGIYAMRGKL-NALCIEKENAGGRI 40
                                  8********************.689*****998655 PP

  == domain 2  score: 80.9 bits;  conditional E-value: 7.5e-26
                   Pyr_redox_3  76 eklsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek..lvkhys 154
                                   e++++ e++e +++ a++f+lpi ++ eV +++ +++ f+v t++++y +k+++iAtG   kP+kl+ +  +     + y 
  gi|15669731|ref|NP_248544.1|  53 EEIRGYELAEKFKNHAEKFKLPIIYD-EVIKIETKERPFKVITKNSEYLTKTIVIATGT--KPKKLGLNEDKFigRGISYC 130
                                   67889999***************876.6889***************************9..******99887523466666 PP

                   Pyr_redox_3 155 kvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaev 235
                                   ++ ++  y +++v+ViG    a+  A++l +  ++V v+t++se+++ e         ++ ++l+e+   +++++++na+ 
  gi|15669731|ref|NP_248544.1| 131 TMCDAFFYLNKEVIVIGRDTPAIMSAINLKDIAKKVIVITDKSELKAAE--------SIMLDKLKEA---NNVEIIYNAKP 200
                                   666666677**********************************988875........5677788876...44888888887 PP

                   Pyr_redox_3 236 keik..ekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                    ei   e+ e +k++ + ++++ + d +++ +G  p+++flk+s++eld++g+++  +e++ tn++g++ +G
  gi|15669731|ref|NP_248544.1| 201 LEIVgeERAEGVKISVNGKEEIIKADGIFISLGHVPNTEFLKDSGIELDKKGFIKT-DENCRTNIDGIYAVG 271
                                   7775225556778888877788777777777*****************99999875.56799*******998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       2.3     3e+03       3      17 ..       6      20 ..       4      35 .. 0.79
   2 ?    2.8   0.0      0.13   1.7e+02      11      72 ..      57     121 ..      55     125 .. 0.64
   3 !   45.6   1.4   5.9e-15   7.5e-12       2      79 ..     143     215 ..     142     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.3
                                  EEECSSHHHHHHHHH CS
                     Pyr_redox  3 vvvGgGyiglElAga 17
                                  +++G+G  gl ++ +
  gi|15669731|ref|NP_248544.1|  6 IIIGAGPGGLTAGIY 20
                                  89****999876655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHTT.........SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                     Pyr_redox  11 glElAgalaelg.........kkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg 72 
                                   g ElA+ +++++         ++V  +e ++++      ++ +   e+l+k  i + ++tk++++  +ed+
  gi|15669731|ref|NP_248544.1|  57 GYELAEKFKNHAekfklpiiyDEVIKIETKERPF-----KVITKNSEYLTKT-IVIATGTKPKKLGLNEDK 121
                                   6788888888884444444444555555555555.....4444446666666.889999999988888876 PP

  == domain 3  score: 45.6 bits;  conditional E-value: 5.9e-15
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEEEE CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvklk 79 
                                   v+v+G ++ +++ A +l++++kkV v+  +++l      +a++i+ +kl++  ++e+++n+k+ ei+g+e+  e+vk++
  gi|15669731|ref|NP_248544.1| 143 VIVIGRDTPAIMSAINLKDIAKKVIVITDKSELK-----AAESIMLDKLKEAnNVEIIYNAKPLEIVGEER-AEGVKIS 215
                                   89********************************.....**********6555*****************9.6999886 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.4   3.3e-07   0.00042       1      39 [.       4      41 ..       4      51 .. 0.87
   2 ?    0.2   0.0      0.24     3e+02       2      33 ..     143     174 ..     142     183 .. 0.87
   3 ?   -1.9   0.0         1   1.3e+03     147     202 ..     182     235 ..     170     244 .. 0.74
   4 !   14.6   0.1     1e-05     0.013     376     410 ..     254     282 ..     250     288 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.3e-07
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                                  D i+iG+G +GL+A++ a +  l+ +++eke++ gg +a
  gi|15669731|ref|NP_248544.1|  4 DTIIIGAGPGGLTAGIYAMRGKLNALCIEKENA-GGRIA 41
                                  89**************8888888********98.66554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.24
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                   viViG      ++A+++++  +kv+v++ ++e
  gi|15669731|ref|NP_248544.1| 143 VIVIGRDTPAIMSAINLKDIAKKVIVITDKSE 174
                                   89999999999****************98876 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1
                                   HHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE----- CS
                 FAD_binding_2 147 lvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGf 202
                                   +++++++a+ v++  +++ +e++  ++r+ G+ ++   +g+e+ i+a+++ +  g +
  gi|15669731|ref|NP_248544.1| 182 MLDKLKEANnVEIIYNAKPLEIV-GEERAEGVKIS--VNGKEEIIKADGIFISLGHV 235
                                   55666666667777777777774.47799999999..99999999999887766655 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 1e-05
                                   EEBETTSBESTTEEESSBTEEE-STCEESSSSTTS CS
                 FAD_binding_2 376 vetdengrvldadgqpipGLYAaGevaaggvhgan 410
                                   ++tden+r+      +i+G YA+G v +g ++ a 
  gi|15669731|ref|NP_248544.1| 254 IKTDENCRT------NIDGIYAVGDVRGGVMQVAK 282
                                   79*******......************88887665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.2   1.1e-05     0.014       2      37 ..       4      39 ..       3      45 .. 0.88
   2 ?    3.6   0.0     0.017        21     131     165 ..      79     111 ..      58     118 .. 0.77
   3 ?    3.0   0.1     0.026        33       2      33 ..     142     173 ..     141     178 .. 0.89
   4 ?   -1.2   0.0      0.49   6.3e+02     115     163 ..     183     233 ..     175     237 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37
                                  d+i+iG+G+ Gl a i a + + + l +ek+++ gr
  gi|15669731|ref|NP_248544.1|  4 DTIIIGAGPGGLTAGIYAMRGKLNALCIEKENAGGR 39
                                  89****************************977665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.017
                                   -EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                   HI0933_like 131 evksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                   ev ++e++e   f+v t +++e+ ++++v+AtG +
  gi|15669731|ref|NP_248544.1|  79 EVIKIETKERP-FKVIT-KNSEYLTKTIVIATGTK 111
                                   56677665555.99999.899999*********76 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.026
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekak 33 
                                   +viviG     +m Ai++++  k+V+++  ++
  gi|15669731|ref|NP_248544.1| 142 EVIVIGRDTPAIMSAINLKDIAKKVIVITDKS 173
                                   79************************997765 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.49
                                   HHHHHHHHT-EEE-S--EEEE.ECETTE.EEEEE..TTEEEEESEEEE--- CS
                   HI0933_like 115 llkelkeagvklrletevksv.ekeedgkfrvkt.kseeeleadklvlAtG 163
                                   l k  ++++v++ ++ +  ++  +e+ + +++++  +ee ++ad + +++G
  gi|15669731|ref|NP_248544.1| 183 LDKLKEANNVEIIYNAKPLEIvGEERAEGVKISVnGKEEIIKADGIFISLG 233
                                   444445578999888877666434444446666644778889999999888 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   9.1e-05      0.12       1      39 [.       4      41 ..       4      71 .. 0.81
   2 ?   -0.1   0.0      0.35   4.5e+02       1      32 [.     142     173 ..     142     175 .. 0.90
   3 !    6.0   0.1     0.005       6.4      85     137 ..     174     226 ..     161     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.1e-05
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39
                                  D +++G+gp+G++A i A r   + l +e+++  GG  +
  gi|15669731|ref|NP_248544.1|  4 DTIIIGAGPGGLTAGIYAMRGKLNALCIEKENA-GGRIA 41
                                  779*****************8888888887765.55544 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.35
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                   +v+V+G ++  ++ Ai  +   +kv+++ ++ 
  gi|15669731|ref|NP_248544.1| 142 EVIVIGRDTPAIMSAINLKDIAKKVIVITDKS 173
                                   59***********************9998765 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.005
                  FAD_oxidored  85 epevakavleeml.aeagvtvllntrlvevekegkriesvtveskegrktirAk 137
                                   e ++a++++ + l + ++v++++n+++ e++ e+ r e+v++  + +++ i+A+
  gi|15669731|ref|NP_248544.1| 174 ELKAAESIMLDKLkEANNVEIIYNAKPLEIVGEE-RAEGVKISVNGKEEIIKAD 226
                                   567788888888845589*************997.9******655568888886 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.4e-06    0.0082     197     268 ..     181     246 ..     167     255 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.4e-06
                   GMC_oxred_N 197 awLrpalerpnleiltgakaekiilegrkkravGVeasdkkgtvkrlvvaakevvvaaGalnsPqlLqrSGl 268
                                    +L++  e++n+ei+++ak   i+    ++ra GV++s ++++    +++a+ + ++ G + + ++L+ SG+
  gi|15669731|ref|NP_248544.1| 181 IMLDKLKEANNVEIIYNAKPLEIVG---EERAEGVKISVNGKE---EIIKADGIFISLGHVPNTEFLKDSGI 246
                                   4566666999*************54...5********998888...99999********************9 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   9.8e-06     0.013      18      55 ..       3      38 ..       1      49 [. 0.82
   2 ?   -1.3   0.0       0.8     1e+03      11      47 ..     134     169 ..     125     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.8e-06
                                  EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                          Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                   D +i+GaG+ GLta+ y  +  +l+ + +e++ +  G
  gi|15669731|ref|NP_248544.1|  3 HDTIIIGAGPGGLTAGIYAMRG-KLNALCIEKENAG-G 38
                                  799*************998877.9**9999998664.3 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.8
                                   HHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEE CS
                          Thi4  11 dllkyaesDvvivGaGssGLtaayylakkpdlkvail 47 
                                   d   y + +v+++G  +  + +a  l      kv+++
  gi|15669731|ref|NP_248544.1| 134 DAFFYLNKEVIVIGRDTPAIMSAINLKDI-AKKVIVI 169
                                   55567778888888777666666665544.4455555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.3   1.8e-05     0.023       1      38 [.       7      43 ..       7      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                  I+GaG +Gl+a  ++ + +++ l++ek    GGr+a +
  gi|15669731|ref|NP_248544.1|  7 IIGAGPGGLTAGIYAMRGKLNALCIEKE-NAGGRIAEA 43
                                  9****************99********6.789998875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.5    0.0074       9.5       1      28 [.       4      31 ..       4      52 .. 0.78
   2 ?   10.0   0.1   0.00025      0.32     109     151 ..      71     116 ..      53     191 .. 0.73
   3 ?   -1.0   0.0      0.54     7e+02      98     134 ..     179     215 ..     139     240 .. 0.68
   4 ?    1.9   0.0     0.072        92     354     389 ..     263     299 ..     253     301 .] 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0074
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                  d i+iG+G  G+ A + a r  ++ l i
  gi|15669731|ref|NP_248544.1|  4 DTIIIGAGPGGLTAGIYAMRGKLNALCI 31
                                  579**************99988877666 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00025
                                   TTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT.....- CS
                          GIDA 109 pnleiieeeveeliveekkvkgvvtedgetikakavviatGt.....f 151
                                    +l ii +ev +++++e+  k++++  ++++ +k++viatGt      
  gi|15669731|ref|NP_248544.1|  71 FKLPIIYDEVIKIETKERPFKVITK--NSEYLTKTIVIATGTkpkklG 116
                                   57999********886666665543..45677999*******444440 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.54
                                   HHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEET CS
                          GIDA  98 skevteklenepnleiieeeveeliveekkvkgvvte 134
                                   ++ + +kl++ +n+eii +     iv e++ +gv+ +
  gi|15669731|ref|NP_248544.1| 179 ESIMLDKLKEANNVEIIYNAKPLEIVGEERAEGVKIS 215
                                   4557788888888888766544333556666666543 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.072
                                   SSBTEEE-CGGGTB-SHHH.HHHHHHHHHHHHHHHHC CS
                          GIDA 354 kvkgLflAGqinGteGYeE.aaaqGllAGinaarkak 389
                                   +++g+++ G++ G   +++ a++ G++A  n+ ++++
  gi|15669731|ref|NP_248544.1| 263 NIDGIYAVGDVRGGVMQVAkAVGDGCVAMANIIKYLQ 299
                                   499*********99766652667********998877 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.5     0.042        54       2      40 ..       7      39 ..       6      44 .. 0.69
   2 ?    6.9   0.0    0.0046       5.9     108     155 ..      65     110 ..      58     111 .. 0.81
   3 ?   -0.1   0.0      0.66   8.5e+02     129     155 ..     207     234 ..     182     235 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.042
                 NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepgagr 40
                                  i+GaGp Gl++    ++ +     l+  +++++++g gr
  gi|15669731|ref|NP_248544.1|  7 IIGAGPGGLTAGIYAMRGK-----LNALCIEKENAG-GR 39
                                  9********9877666653.....555666666666.55 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0046
                 NAD_binding_9 108 larlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                     +  e++++ ++ +ev+++e++++ ++v  ++++++  + +v+A+G 
  gi|15669731|ref|NP_248544.1|  65 K-NHAEKFKLPIIYDEVIKIETKERPFKV-ITKNSEYLTKTIVIATGT 110
                                   4.34468999****************999.5667788899999***96 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.66
                 NAD_binding_9 129 eradgqavlladgas.laadaVvLAlGh 155
                                   era+g+++  +++++ ++ad +++ lGh
  gi|15669731|ref|NP_248544.1| 207 ERAEGVKISVNGKEEiIKADGIFISLGH 234
                                   45677777666665526**********9 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.3     0.012        16       1      33 [.       4      37 ..       4      46 .. 0.85
   2 ?    3.5   0.0     0.034        44     139     205 ..      51     113 ..      39     132 .. 0.74
   3 ?    0.9   0.0      0.22   2.8e+02     157     202 ..     188     234 ..     175     257 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.012
                                  EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg...Vtllekgdiag 33
                                  d +iiG+G  Gl++  ++  rg    + +ek+  ag
  gi|15669731|ref|NP_248544.1|  4 DTIIIGAGPGGLTAGIYA-MRGklnALCIEKE-NAG 37
                                  789***************.5566999999999.655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.034
                                   TEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH CS
                           DAO 139 dtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd 205
                                   +   +  ++l+  + + ae+    i++  ev ++e + ++  +v  t++ +   + +++V+a+G   +
  gi|15669731|ref|NP_248544.1|  51 GFEEIRGYELAEKFKNHAEKFKLPIIYD-EVIKIETK-ERPFKV-ITKNsEY-LT-KTIVIATGTKPK 113
                                   5556777888889999999999999999.*****765.466777.3554343.34.78******7654 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.22
                                   HHTT-EEEESECEEEE..EEEETCEEEEE...EECTEEEEEEEEEEE--GG CS
                           DAO 157 ealGveilegtevtgl..eeedgkvwgve...rttpgendaadavVnaaGa 202
                                   ea+ vei+++++  ++  e   +++ gv+   +  ++e+ +ad + ++ G+
  gi|15669731|ref|NP_248544.1| 188 EANNVEIIYNAKPLEIvgE---ERAEGVKisvN-GKEEIIKADGIFISLGH 234
                                   6788******999998332...45677766433.22333234558888775 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.034        44       2      36 ..       2      34 ..       1      38 [. 0.75
   2 ?    5.9   0.0    0.0049       6.2     118     161 ..      79     113 ..      61     115 .. 0.79
   3 ?   -2.5   0.0       1.7   2.2e+03     130     160 ..     209     236 ..     184     238 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.034
                   K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalflerq 36
                                  i+D i+iG+Gp  L+  i +   k  l+al +e++
  gi|15669731|ref|NP_248544.1|  2 IHDTIIIGAGPGGLTAGIYAMRGK--LNALCIEKE 34
                                  79*********9998666555444..777777766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0049
                   K_oxygenase 118 eveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepk 161
                                   ev ++e +e+     ++v +     +++e+ ++++v+++Gt+pk
  gi|15669731|ref|NP_248544.1|  79 EVIKIETKER----PFKVIT-----KNSEYLTKTIVIATGTKPK 113
                                   4555666654....488888.....6899*************96 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.7
                   K_oxygenase 130 eelltveskdaegeeeelearnlvlgvGtep 160
                                    e +++++   +g+ee ++a  + ++ G  p
  gi|15669731|ref|NP_248544.1| 209 AEGVKISV---NGKEEIIKADGIFISLGHVP 236
                                   34566665...78888999999999988877 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00014      0.18       3      66 ..       4      68 ..       3     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                  EEEEE--SHHHHHHHHHHHHTT.HHEEEEESSSSSCCSSS--EEEH.HHHHHHHHTT-HHHHHHHS CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaG.vrvvlvekrsttvvlpradglnq.rtmellrqlGledrilaeg 66
                                  d++I+GaGp Gl+++   +++G  + +++ek +   +   a+++++   +e +r   l++++++++
  gi|15669731|ref|NP_248544.1|  4 DTIIIGAGPGGLTAGIY-AMRGkLNALCIEKENAGGRIAEAGIVENyPGFEEIRGYELAEKFKNHA 68
                                  789********988765.555515688999999888888777775514677777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1898.07
//
Query:       gi|15669732|ref|NP_248545.1|  [L=343]
Description: hypothetical protein MJ_1537 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2128.63
//
Query:       gi|15669733|ref|NP_248546.1|  [L=252]
Description: chromatin associated protein KTI12 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-59  201.3   9.2      1e-57  195.7   9.2    2.0  1  KTI12            Chromatin associated protein KTI12
    5.3e-17   62.3   0.0      1e-16   61.4   0.0    1.5  1  AAA_33           AAA domain
    2.8e-11   44.1   2.3    1.2e-10   42.1   0.1    2.4  2  AAA_18           AAA domain
    3.4e-06   27.5   0.0      8e-06   26.3   0.0    1.6  1  AAA              ATPase family associated with various cellul
    8.1e-06   25.8   0.2    3.2e-05   23.9   0.0    2.1  2  APS_kinase       Adenylylsulphate kinase
    1.2e-05   24.7   0.1    3.3e-05   23.2   0.0    1.8  2  Zeta_toxin       Zeta toxin
    2.3e-05   24.0   0.0    4.7e-05   23.0   0.0    1.5  1  ParA             NUBPL iron-transfer P-loop NTPase
    2.8e-05   24.2   0.1    6.9e-05   22.9   0.1    1.7  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    3.1e-05   24.4   4.4    0.00091   19.7   0.0    3.4  2  AAA_17           AAA domain
    6.2e-05   23.0   0.4    6.2e-05   23.0   0.4    2.4  3  AAA_14           AAA domain
    7.8e-05   22.4   3.4       0.13   11.9   0.4    2.8  2  Thymidylate_kin  Thymidylate kinase
    0.00022   20.9   0.1    0.00077   19.1   0.0    2.0  2  SRP54            SRP54-type protein, GTPase domain
    0.00048   20.1   9.5     0.0019   18.1   1.6    2.9  3  dNK              Deoxynucleoside kinase
    0.00069   19.0   0.5      0.042   13.2   0.0    2.6  3  DnaB_C           DnaB-like helicase C terminal domain
    0.00074   19.7   1.3     0.0024   18.0   1.2    2.1  1  SKI              Shikimate kinase
     0.0011   18.9   0.0     0.0011   18.9   0.0    2.3  2  NTPase_1         NTPase
     0.0016   18.5   0.0      0.005   16.8   0.0    1.9  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0025   17.1   5.8     0.0048   16.1   0.1    2.4  2  ArsA_ATPase      Anion-transporting ATPase
     0.0028   16.7   0.5     0.0096   14.9   0.0    1.9  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0035   17.7   2.1      0.011   16.1   0.2    2.3  2  RNA_helicase     RNA helicase
     0.0044   17.4   0.0      0.019   15.3   0.0    2.0  2  AAA_16           AAA ATPase domain
     0.0058   16.5   0.1       0.55   10.1   0.1    2.3  1  CPT              Chloramphenicol phosphotransferase-like prot
     0.0067   16.3   0.0        0.2   11.5   0.0    2.3  2  AAA_3            ATPase family associated with various cellul
  ------ inclusion threshold ------
       0.01   15.2   0.0       0.01   15.2   0.0    3.0  3  6PF2K            6-phosphofructo-2-kinase
      0.011   15.5   0.0      0.023   14.4   0.0    1.5  1  AAA_30           AAA domain
      0.012   15.9   0.0      0.043   14.1   0.0    2.0  2  AAA_22           AAA domain
       0.02   14.7   1.4       0.14   11.9   0.0    2.5  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.04   13.3   0.1      0.076   12.4   0.1    1.4  1  Fringe           Fringe-like
      0.044   13.5   0.0       0.11   12.3   0.0    1.7  1  IstB_IS21        IstB-like ATP binding protein
      0.053   13.2   0.4      0.053   13.2   0.4    2.4  2  AAA_24           AAA domain
      0.056   12.9   1.0       0.33   10.4   0.0    2.3  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
      0.083   13.0   0.1       0.57   10.3   0.1    2.1  2  MCD_N            Malonyl-CoA decarboxylase N-terminal domain
      0.086   13.1   0.0       0.19   11.9   0.0    1.7  1  AAA_28           AAA domain
      0.087   12.6   1.5       0.94    9.2   0.0    2.6  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
       0.09   12.5   0.0       0.19   11.5   0.0    1.6  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
        0.1   12.9   0.1         17    5.7   0.0    3.1  3  AAA_19           AAA domain
       0.11   12.4   0.1        0.3   11.0   0.0    1.7  2  NACHT            NACHT domain
       0.12   12.9   1.0       0.28   11.7   0.5    1.9  1  Raf1_N           Rubisco accumulation factor 1 alpha helical 
       0.18   12.3   2.7       0.81   10.2   2.7    2.1  1  ABC_tran         ABC transporter
       0.21   10.9   0.0       0.36   10.2   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
        1.1    9.1   8.9      0.057   13.3   0.5    2.4  2  AAA_31           AAA domain
        1.1    9.3   8.8       0.41   10.7   0.6    3.2  3  MMR_HSR1         50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.7   9.2   2.4e-60     1e-57       1     272 []       5     250 ..       4     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: 195.7 bits;  conditional E-value: 2.4e-60
                                   E.EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHHHHHHHTT.SEEEE-S--- CS
                         KTI12   1 MpLvvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslrsavkrdLskekvVIvDslny 81 
                                   M L++ltGlP +GKst++k+Lak l++++++v+v+ ++ ++ e+ +++++++e+ +++s+++ ++ +L++  +VIvD++ny
  gi|15669733|ref|NP_248546.1|   5 M-LIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIR-ESFPVWKEKYEEFIKKSTYRLIDSALKN-YWVIVDDTNY 82 
                                   4.9**************************************.9*************************87.********** PP

                                   SHHHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHHHHTT-S..S-HHHHHHHHHH---TTSS-GGGS-SEEEE.TTS---H CS
                         KTI12  82 ikgfRYeLyciakaakttlcvvyvvapldvlvkwneereekeeyekelldaLiqRyeePdsknrWDsPlftvlsaeeklpl 162
                                   ++++R++L++iak+++++++++y++a+ldvl+++n er ek  +++e++++++++++eP +k++WD+P++ ++ +++++++
  gi|15669733|ref|NP_248546.1|  83 YNSMRRDLINIAKKYNKNYAIIYLKASLDVLIRRNIERGEK--IPNEVIKKMYEKFDEPGKKYKWDEPFLIID-TTKDIDF 160
                                   ***************************************99..******************************.******* PP

                                   HHHHHHHHHHHTS--SSSTT----.---HHHHHHHHHHHHHHHHHHH....HTT--HHH................HHHHHH CS
                         KTI12 163 deilkaliekkklkpnqatlskpl.aeanflqeLdketseivkeileaqksavaidkltlpgsseslelpakkltlaeLsr 242
                                   +ei+k+liek+k+ p+  +l++++ +++n+ +++dket++iv+e+++    +++ dk +                ++e+ +
  gi|15669733|ref|NP_248546.1| 161 NEIAKKLIEKSKEIPKFYVLEENKnKNNNISDKIDKETRKIVSEYIK----SKKLDKDK----------------IKEVVE 221
                                   ********************999856778999***************....44444444................889*** PP

                                   HHHHHHHHHT.TSSS--HHHHHHHHHHHHH CS
                         KTI12 243 lrrqFvklnkaklenvdeekiaklFvdyLn 272
                                   lr++F+k  k k+e+vd++++ k F d Ln
  gi|15669733|ref|NP_248546.1| 222 LRKEFLKKIK-KMEEVDADRVLKEFKDLLN 250
                                   **********.****************998 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.0   2.3e-19     1e-16       1     143 []       6     139 ..       6     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 2.3e-19
                        AAA_33   1 lvllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvild 76 
                                   l++l GlpG+GKst++++l+k l      +++l sd +r+   +     k++y ++ ++    + +l+++al +++ vi+d
  gi|15669733|ref|NP_248546.1|   6 LIILTGLPGVGKSTFSKNLAKILSknnidVIVLGSDLIRESFPVW----KEKYEEFIKK---STYRLIDSAL-KNYWVIVD 78 
                                   799****************88888888989999999877777653....2334554444...4444455544.5677**** PP

                        AAA_33  77 atnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrsevpeealdrqkarferp 143
                                    tn  ++ r++++++a++++ + +i++++++ ++l +R+ +R ++       p e+++++ ++f++p
  gi|15669733|ref|NP_248546.1|  79 DTNYYNSMRRDLINIAKKYNKNYAIIYLKASLDVLIRRNIERGEK------IPNEVIKKMYEKFDEP 139
                                   ********************************************7......9********9999987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.1   2.7e-13   1.2e-10       1     116 [.       7     123 ..       7     135 .. 0.75
   2 ?    1.3   0.4       1.1   4.6e+02      34      67 ..     187     226 ..     160     248 .. 0.59

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 2.7e-13
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdv.akenglllevdpealdeskrldedkldklldaleenssaleegknlvid 80 
                                   I+ltG pGvGK+t++k+L+k l  + n +dv +  ++l  e +p + ++++++ ++ + +l+d   +n+       ++++d
  gi|15669733|ref|NP_248546.1|   7 IILTGLPGVGKSTFSKNLAKIL--SKNNIDViVLGSDLIRESFPVWKEKYEEFIKKSTYRLIDSALKNY-------WVIVD 78 
                                   9*******************99..555555416777888888888666666666666666777777764.......78888 PP

                        AAA_18  81 ghlaele.seaakdikk........vvLtaspeelleRlekRgye 116
                                   +    +    +++ i k        ++L+as ++l++R  +Rg++
  gi|15669733|ref|NP_248546.1|  79 DTNYYNSmRRDLINIAKkynknyaiIYLKASLDVLIRRNIERGEK 123
                                   8887766333333333389999*********************65 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.1
                        AAA_18  34 englllevdpe......aldeskrldedkldklldaleen 67 
                                   +n++++  d+e      ++ +sk+ld+dk ++++++ +e 
  gi|15669733|ref|NP_248546.1| 187 NNNISDKIDKEtrkivsEYIKSKKLDKDKIKEVVELRKEF 226
                                   3344444444466666666777777777777776665554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.9e-08     8e-06       1     120 [.       7     168 ..       7     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.9e-08
                                   EEEESSTTSSHHHHHHHHHHHHTHE.E.EEEETTTCSSS....................................STTHHH CS
                           AAA   1 vllyGppGtGKTllakavakelgve.f.leisgsellsk....................................yvgese 43 
                                   ++l+G pG+GK+++ k +ak l+ + + + + gs+l+ +                                    y   + 
  gi|15669733|ref|NP_248546.1|   7 IILTGLPGVGKSTFSKNLAKILSKNnIdVIVLGSDLIREsfpvwkekyeefikkstyrlidsalknywvivddtnYYNSMR 87 
                                   689******************953322334444444433355555555555556666666679****************** PP

                                   HHHHHHHHHHHHTSTSEEEEEE.TGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS...SSTEEEEEEESS..GGGSTHH CS
                           AAA  44 kkirelfkeakekakpsilfiD.EidalaksrsgseseeeervvnqLlteldgvkkk...eskvivigatnr..pdkldpa 118
                                   +++ ++ k+  ++    i+ +   +d l++++ ++ ++  ++v++++++++d+  kk   ++++++i +t++   +++ ++
  gi|15669733|ref|NP_248546.1|  88 RDLINIAKKYNKNY--AIIYLKaSLDVLIRRNIERGEKIPNEVIKKMYEKFDEPGKKykwDEPFLIIDTTKDidFNEIAKK 166
                                   *******9987775..777775279****9998889999***************999999888******999556666666 PP

                                   HH CS
                           AAA 119 ll 120
                                   l+
  gi|15669733|ref|NP_248546.1| 167 LI 168
                                   66 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   7.4e-08   3.2e-05       4     117 ..       6     116 ..       3     124 .. 0.74
   2 ?   -2.4   0.0       9.3     4e+03      28      43 ..     203     218 ..     183     241 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 7.4e-08
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEEEE---- CS
                    APS_kinase   4 vvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivlvafisP 84 
                                    + ltGl g GKst +++l+k L +++i v++L  d +R+      +  +e+ +e i++ +      a ++  v+v     
  gi|15669733|ref|NP_248546.1|   6 LIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESF----PVWKEKYEEFIKKSTYRLIDSALKNYWVIVDDTNY 82 
                                   689************************************864....55566666666665555555555666677777777 PP

                                   SHHHHHHHHHHHHCH.TEEEEEEEE--HHHHHHH CS
                    APS_kinase  85 yreeReaarelleea.lkfievfvdtplevceer 117
                                   y++ R++  ++ ++  +++  ++++++l+v  +r
  gi|15669733|ref|NP_248546.1|  83 YNSMRRDLINIAKKYnKNYAIIYLKASLDVLIRR 116
                                   7777766666666554667777777777776665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9.3
                                   HTT--EEEEEHHHHTT CS
                    APS_kinase  28 ekgisvylLdGdnvRh 43 
                                   ++ i+ + Ld d++++
  gi|15669733|ref|NP_248546.1| 203 SEYIKSKKLDKDKIKE 218
                                   3444444444444443 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   7.8e-08   3.3e-05      18      88 ..       6      70 ..       5     144 .. 0.71
   2 ?   -1.7   0.1       3.3   1.4e+03     153     172 ..     210     229 ..     160     244 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 7.8e-08
                    Zeta_toxin 18 lillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdaselvekll 88
                                  li+l G pG GKs+ ++ l++ l  ++ +v++l  D +Re +P  +e       k+ e ++k +++l +++l
  gi|15669733|ref|NP_248546.1|  6 LIILTGLPGVGKSTFSKNLAKILSkNNIDVIVLGSDLIRESFPVWKE-------KYEEFIKKSTYRLIDSAL 70
                                  79********************9978889**************9999.......555555555555444443 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.3
                    Zeta_toxin 153 lvpkeehdeafeglresvea 172
                                   + +k++++e++e  +e +++
  gi|15669733|ref|NP_248546.1| 210 KLDKDKIKEVVELRKEFLKK 229
                                   34444444444444444444 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.1e-07   4.7e-05       6      50 ..       6      50 ..       3      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.1e-07
                          ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprl 50
                                  +++l g  GVGKSt++ nlA  L+k++++v +l  D++  s p  
  gi|15669733|ref|NP_248546.1|  6 LIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVW 50
                                  67899999*****************************99999865 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   1.6e-07   6.9e-05       3      82 ..       8     181 ..       6     240 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.6e-07
                                   EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH............................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx............................ RF
                          CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep............................ 54 
                                   i  +  GvGK+t++ nLa++l++++ +V+++  D  +++  +  e+ e++i++                            
  gi|15669733|ref|NP_248546.1|   8 ILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVwKEKYEEFIKKstyrlidsalknywvivddtnyynsmrr 88 
                                   566666******************************999996555555555559999999999999999999999999999 PP

                                   ....................................................................CCHCCCHHHHHHC CS
                                   ....................................................................xxxxxxxxxxxxx RF
                          CbiA  55 ....................................................................dlkrllellealg 67 
                                                                                                       d+  + e++++l 
  gi|15669733|ref|NP_248546.1|  89 dliniakkynknyaiiylkasldvlirrniergekipnevikkmyekfdepgkkykwdepfliidttkDI-DFNEIAKKLI 168
                                   9999999999999999999999999999777777777776666666666666666666666666666533.2233333333 PP

                                   HCHHHH..EEEEEEE CS
                                   xxxxxxxxxxxxxxx RF
                          CbiA  68 kkkalllkiagvvln 82 
                                   +k +    ++++vl 
  gi|15669733|ref|NP_248546.1| 169 EKSK--EIPKFYVLE 181
                                   3321..233333333 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.1e-06   0.00091       1     122 [.      10     120 ..      10     132 .. 0.60
   2 ?    1.2   2.2       1.1   4.6e+02      42      69 ..     207     234 ..     179     245 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.1e-06
                                   EE-TTSSHHHHHHHHHHHH...TEEEEEHH.HHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH.HSSEEEE CS
                        AAA_17   1 lGgPGsGKgtqceklveky...gfthlsaG.dllreeakrgglakardemrklpleekkelqkeaaekiaeea.kkkgvlv 76 
                                   +G+PG+GK+t +++l++ +   ++ ++  G dl+re       +++ +e+ k           +   ++ + a k+  v+v
  gi|15669733|ref|NP_248546.1|  10 TGLPGVGKSTFSKNLAKILsknNIDVIVLGsDLIRESF--PVWKEKYEEFIK-----------KSTYRLIDSAlKNYWVIV 77 
                                   7**************98665559999988626666653..222233333322...........222222222212344666 PP

                                   EE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH CS
                        AAA_17  77 dghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd 122
                                   d     + +++ l ++ k+  +++   aii+l+a+ +++++r +++
  gi|15669733|ref|NP_248546.1|  78 DDTNYYNSMRRDLINIAKKYNKNY---AIIYLKASLDVLIRRNIER 120
                                   666655566665666666555555...7777777777777776654 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.1
                                   SHHHHCTSHHHHHHHHHHHHHHHHHHHH CS
                        AAA_17  42 ardemrklpleekkelqkeaaekiaeea 69 
                                   + ++++k +++e  el+ke  +ki++++
  gi|15669733|ref|NP_248546.1| 207 KSKKLDKDKIKEVVELRKEFLKKIKKME 234
                                   3355667777777788888888887765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.4   1.5e-07   6.2e-05       4     107 ..       6     116 ..       4     124 .. 0.67
   2 ?   -0.4   0.9       2.5   1.1e+03      63      92 ..     145     173 ..     105     201 .. 0.55
   3 ?   -0.8   2.2       3.4   1.4e+03      22      62 ..     163     204 ..     150     242 .. 0.51

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.5e-07
                        AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla..dpekllelileklke.....ekktylflDEiqevp 77 
                                   ++++tG+  vGK+t+ k+l+k l  ++ +++ +  d  r+  +    +ek++e+i+++ ++      k+++++ D   +++
  gi|15669733|ref|NP_248546.1|   6 LIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRE--SFpvWKEKYEEFIKKSTYRlidsaLKNYWVIVDDTNYYN 84 
                                   589*****************87774444444444444444..22222334445555543335556678899********** PP

                        AAA_14  78 ewekalkslvdeg.knldv.ivtGSnskllsk 107
                                   ++++ l ++ +++ kn+ + ++  S+  l+ +
  gi|15669733|ref|NP_248546.1|  85 SMRRDLINIAKKYnKNYAIiYLKASLDVLIRR 116
                                   ****9999999776666550555555555554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.5
                        AAA_14  63 ekktylflDEiqevpewekalkslvdegkn 92 
                                    ++ +l++D  +   ++ ++ k+l++++k+
  gi|15669733|ref|NP_248546.1| 145 WDEPFLIIDTTKD-IDFNEIAKKLIEKSKE 173
                                   3444566664433.3455555555555433 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3.4
                        AAA_14  22 likellvkkesilyin.ldderdkkladpekllelileklke 62 
                                   ++k+l+ k+++i  +  l+++++k+++ ++k++++ ++ ++e
  gi|15669733|ref|NP_248546.1| 163 IAKKLIEKSKEIPKFYvLEENKNKNNNISDKIDKETRKIVSE 204
                                   444444444444444313444444444344444444444322 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00091      0.39       3      27 ..      11      36 ..       9      40 .. 0.88
   2 !   11.9   0.4   0.00031      0.13      68     179 ..      61     159 ..      57     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00091
                                  ESTTSSHHHHHHHHHHHHHHTTE..E CS
               Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik.v 27
                                  Gl G+GK+t++++l++ l+++ i  +
  gi|15669733|ref|NP_248546.1| 11 GLPGVGKSTFSKNLAKILSKNNIDvI 36
                                  999******************99844 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00031
                                   TTHHHHHHHHHTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHH CS
               Thymidylate_kin  68 hleekikpalkqgktvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeq 148
                                   +++++i  alk+ ++vivd     + +Y+++ +    dl+   ++    k +++++l+ + +v ++R  +r+e     +  
  gi|15669733|ref|NP_248546.1|  61 STYRLIDSALKN-YWVIVD----DTNYYNSMRR----DLINIAKKYN--KNYAIIYLKASLDVLIRRNIERGE-----KIP 125
                                   577888899988.888887....5778999888....5655555553..7799********************.....667 PP

                                   HHHHHHHHHHHHHHHH.T..TSTEEEEETTS-HH CS
               Thymidylate_kin 149 ldflrkvrerylelak.e..deriliidasksie 179
                                    ++ +k+ e+++e  k +  de +liid++k i+
  gi|15669733|ref|NP_248546.1| 126 NEVIKKMYEKFDEPGKkYkwDEPFLIIDTTKDID 159
                                   7777788888887665432267899999998875 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.8e-06   0.00077       3      42 ..       6      45 ..       4      91 .. 0.93
   2 ?   -0.7   0.0       2.1   9.1e+02     134     134 ..     165     165 ..     108     233 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.8e-06
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSST CS
                         SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRa 42
                                  +i+l Gl G+GK t    La++l+k++ +v++   D  R 
  gi|15669733|ref|NP_248546.1|  6 LIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRE 45
                                  689*********************************9995 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.1
                                   H CS
                         SRP54 134 k 134
                                   k
  gi|15669733|ref|NP_248546.1| 165 K 165
                                   2 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.022       9.3       1      23 [.       7      29 ..       7      38 .. 0.84
   2 !   18.1   1.6   4.4e-06    0.0019     109     200 ..      83     172 ..      70     176 .. 0.76
   3 ?   -0.8   0.1       2.8   1.2e+03      74     118 ..     185     228 ..     172     239 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.022
                                  EEEEESTTSSHHHHHHHHHCCST CS
                           dNK  1 ivveGnIgaGKstlvklLskklg 23
                                  i + G  g+GKst+ k L+k l 
  gi|15669733|ref|NP_248546.1|  7 IILTGLPGVGKSTFSKNLAKILS 29
                                  5678999***********99875 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 4.4e-06
                                   HHHHHHHHH...HHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS.-EEEEETSS.-T CS
                           dNK 109 ykelldnll...eelakpdlliYLkasletclerikkRgreeekkieldYlekLhekyeewlkklnev.pvlvidveeldl 185
                                   y++++  l+   ++ +k   +iYLkasl+++ +r  +Rg+    ki+ + ++k+ ek+ e  kk+++  p l+id  + d+
  gi|15669733|ref|NP_248546.1|  83 YNSMRRDLIniaKKYNKNYAIIYLKASLDVLIRRNIERGE----KIPNEVIKKMYEKFDEPGKKYKWDePFLIIDTTK-DI 158
                                   44444443323366666889**********9987666664....689999*****************989*******9.86 PP

                                   TTHCCHHHHHHHHHH CS
                           dNK 186 vaeeekredvveevk 200
                                   +++e   ++++e+ k
  gi|15669733|ref|NP_248546.1| 159 DFNE-IAKKLIEKSK 172
                                   6555.5556666655 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.8
                                   SS-EEEEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHH CS
                           dNK  74 tkqvvvleRsiysdryiFakalaekgtlseeelkiykelldnlle 118
                                   +k++++ ++   + r+i  +  +++++l++ ++k   el++  l+
  gi|15669733|ref|NP_248546.1| 185 NKNNNISDKIDKETRKIVSE-YIKSKKLDKDKIKEVVELRKEFLK 228
                                   44444555444444444333.444555555555555555555554 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   9.7e-05     0.042      21      56 ..       6      40 ..       1      50 [. 0.82
   2 ?    3.0   0.0      0.13        54      42     121 ..      92     167 ..      84     180 .. 0.78
   3 ?   -0.0   0.2       1.1   4.5e+02      60      95 ..     187     222 ..     160     242 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.7e-05
                                  EEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEES CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C 21 liiiAarpsmGktalalniaenaavkeklpvavfsl 56
                                  lii+ + p++Gk+++  n+a+    k+++ v+v   
  gi|15669733|ref|NP_248546.1|  6 LIILTGLPGVGKSTFSKNLAKILS-KNNIDVIVLGS 40
                                  9*******************9665.68888888655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.13
                                   HHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHTTSXHHHHHHHHHHHHHHHHSEEEEEEXSSXCHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  42 naavkeklpvavfslemsaeqlvqRllsseaeidskklrtgklkeedweklteaieelseaklfiddtpaltvseirska 121
                                   n+a+k++++ a++ l  s + l++R +    +i+++ +++    e ++++  ++  +  e  l+id t+++  +ei +k+
  gi|15669733|ref|NP_248546.1|  92 NIAKKYNKNYAIIYLKASLDVLIRRNIERGEKIPNEVIKKMY--E-KFDEPGKKY-KWDEPFLIIDTTKDIDFNEIAKKL 167
                                   57778889999999*******************999998743..2.444544443.356777889999999999998875 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHTXXHHHHHHTTSXHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  60 aeqlvqRllsseaeidskklrtgklkeedwekltea 95 
                                   ++++ +++  ++ +i s+ +++ kl++++++++ e 
  gi|15669733|ref|NP_248546.1| 187 NNNISDKIDKETRKIVSEYIKSKKLDKDKIKEVVEL 222
                                   344566666666677777777777777777776664 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.2   5.6e-06    0.0024       1     107 [.      13     122 ..      13     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.6e-06
                                   TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGSHHHHHH CS
                           SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsevlkelleeeglViatGGGavlseenrel 81 
                                   +G+GKst+ k lAk l+ + iD+  l ++ ++ s +   e + ee  ++   +++++ l++   Vi   +    ++  r+l
  gi|15669733|ref|NP_248546.1|  13 PGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKE-KYEEFIKKSTYRLIDSALKNY-WVIVD-DTNYYNSMRRDL 90 
                                   69*********************99999999999986655.446666677778888888886.44443.445555555555 PP

                                   HH......HHSEEEEEE--HHHHHHHHHHTTS CS
                           SKI  82 lk......ekgiviyLdvsleellerlkadke 107
                                   ++      ++  +iyL++sl++l++r  ++ e
  gi|15669733|ref|NP_248546.1|  91 INiakkynKNYAIIYLKASLDVLIRRNIERGE 122
                                   555559988888*************9877766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.5e-06    0.0011       2      30 ..       7      35 ..       6      45 .. 0.92
   2 ?   -0.9   0.8       3.1   1.3e+03     123     123 ..     207     207 ..     152     250 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.5e-06
                                  EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                  +++TG pGvGK+T+ k++++ l+++++ v
  gi|15669733|ref|NP_248546.1|  7 IILTGLPGVGKSTFSKNLAKILSKNNIDV 35
                                  89*********************999876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.1
                                   T CS
                      NTPase_1 123 k 123
                                   k
  gi|15669733|ref|NP_248546.1| 207 K 207
                                   1 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.2e-05     0.005       2      39 ..       7      45 ..       6      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-05
                                  EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HH CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvqltrdttee 39
                                  ++L G pG+gKs++++ la+ l ++++ ++ l +d+ +e
  gi|15669733|ref|NP_248546.1|  7 IILTGLPGVGKSTFSKNLAKILsKNNIDVIVLGSDLIRE 45
                                  69********************98888888888776655 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.1e-05    0.0048       3      38 ..       6      41 ..       4      44 .. 0.94
   2 ?    2.6   1.4      0.15        63     157     205 ..     193     241 ..     152     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                   ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                  +i+++G  GVGK+t s  +a  ls+++ +v+++  D
  gi|15669733|ref|NP_248546.1|  6 LIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSD 41
                                  6899****************************9887 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.15
                                   HHHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT CS
                   ArsA_ATPase 157 klkeklsplakqlvkllglggvsieealeeleetkeeikkveeiltdpe 205
                                   k+ ++ ++++++  k  +l + +i+e++e  +e++++ikk+ee+  d  
  gi|15669733|ref|NP_248546.1| 193 KIDKETRKIVSEYIKSKKLDKDKIKEVVELRKEFLKKIKKMEEVDADRV 241
                                   4455566677777777777888888888888999999999888866655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.2e-05    0.0096      30      64 ..       5      39 ..       1      43 [. 0.85
   2 ?   -0.2   0.1       0.9   3.8e+02     243     259 ..     191     207 ..     100     249 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                                  EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEE CS
                          MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavla 64
                                    + ltG+PG+Gkst+ ++l+  l ++   v vl 
  gi|15669733|ref|NP_248546.1|  5 MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLG 39
                                  56789*****************9999988888875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.9
                                   HHHHHHHHHHHHHHHHH CS
                          MeaB 243 rerakeelrelvedell 259
                                    ++  +e+r++v++ + 
  gi|15669733|ref|NP_248546.1| 191 SDKIDKETRKIVSEYIK 207
                                   33333333333333333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   2.6e-05     0.011       1      58 [.       7      80 ..       7     103 .. 0.70
   2 ?    0.8   0.2       1.5   6.3e+02      16      64 ..     161     211 ..     158     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.6e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl................klkkkdsvysrnpeddfwdgYtgqevvvidDf 58
                                  i+l+G +g+GKSt++k+Lak l+k+                   k+k + ++++++    d+  ++  v++dD 
  gi|15669733|ref|NP_248546.1|  7 IILTGLPGVGKSTFSKNLAKILSKNNidvivlgsdliresfpVWKEKYEEFIKKSTYRLIDSALKNYWVIVDDT 80
                                  6899****************999776677777777666666633333333345555556666666666666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.5
                  RNA_helicase  16 keLakallkklklkkkdsvys..rnpeddfwdgYtgqevvvidDfgqvkde 64 
                                   +e+ak+l +k+k++ k  v    +n+++++ d+ ++++  ++ +  ++k+ 
  gi|15669733|ref|NP_248546.1| 161 NEIAKKLIEKSKEIPKFYVLEenKNKNNNISDKIDKETRKIVSEYIKSKKL 211
                                   577888888887777666666556777888888888888888887777644 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.5e-05     0.019      24      55 ..       4      37 ..       1     117 [. 0.81
   2 ?    0.3   0.0       1.9   8.1e+02      72     127 ..     190     249 ..     122     252 .] 0.59

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.5e-05
                        AAA_16 24 pelvllsGesGvGKsslvrellralekd..ggif 55
                                    l++l+G +GvGKs+  + l++ l+k+  ++i+
  gi|15669733|ref|NP_248546.1|  4 IMLIILTGLPGVGKSTFSKNLAKILSKNniDVIV 37
                                  56899******************99999443433 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.9
                        AAA_16  72 laqalareellrqlldeaesaeleawrekleeala.......avpelagaeasrllellkrll 127
                                   + + +++ e  + + +  +s++l+ ++ k     +        +++++  +a r+l ++k+ll
  gi|15669733|ref|NP_248546.1| 190 ISDKIDK-ETRKIVSEYIKSKKLDKDKIKEVV--ElrkeflkKIKKMEEVDADRVLKEFKDLL 249
                                   4444433.332333322333233322222222..23366666666666666677777777666 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1    0.0013      0.55       3     135 ..       6     125 ..       4     171 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
                                   EEEEEE-TTSSHHHHHHHHHHHSSS-EEE...EEHHHHHHHS-GGGGTSTTSEEEETTSEEE-HHHHHHHHHHHHHHHHHH CS
                           CPT   3 iilLnGgsssGKsslaralqevldepwlh...lgvDafvealppkrqdeadglefeteleeigpeldlllaalyeavaama 80 
                                   +i+L G +  GKs+ ++ l ++l +  ++   lg+D   e  p           ++      ++  + + ++ y+ + + +
  gi|15669733|ref|NP_248546.1|   6 LIILTGLPGVGKSTFSKNLAKILSKNNIDvivLGSDLIRESFPV----------WK------EKYEEFIKKSTYRLIDSAL 70 
                                   67777777777777777777777665332111222322222222..........22......3444555666777776666 PP

                                   HTT-EEEEE..E--TTTHH.HHHHHHHHHTTS-EEEEEEE--HHHHHHHHHHHTSSST CS
                           CPT  81 raGnnvivD..dvilekew.lvdllrrllsgldvllVGvrcplevlerRelergdRep 135
                                   ++   vivD  +++ + +  l +++++     +  ++ ++++l+vl rR++erg++ p
  gi|15669733|ref|NP_248546.1|  71 KN-YWVIVDdtNYYNSMRRdLINIAKKYN--KNYAIIYLKASLDVLIRRNIERGEKIP 125
                                   55.44666623334443333666665554..444555678888888888888888766 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00047       0.2       2      37 ..       7      43 ..       6      83 .. 0.82
   2 ?    2.6   0.0      0.26   1.1e+02      77     115 ..     123     160 ..      90     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00047
                         AAA_3  2 vllegvPGlaktllvkalakaldl.efkriqftpdll 37
                                  ++l+g+PG++k ++ k+lak+l+  +++ i + +dl+
  gi|15669733|ref|NP_248546.1|  7 IILTGLPGVGKSTFSKNLAKILSKnNIDVIVLGSDLI 43
                                  689******************9761566777777776 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.26
                         AAA_3  77 ktqsalleameerqvtvegethklpepflvlatqnPieq 115
                                   k+   +++ m e+     g+++k +epfl++ t   i+ 
  gi|15669733|ref|NP_248546.1| 123 KIPNEVIKKMYEK-FDEPGKKYKWDEPFLIIDTTKDIDF 160
                                   5555666677664.56778999***********998876 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.4e-05      0.01      14      58 ..       5      49 ..       2      65 .. 0.79
   2 ?    2.6   0.8      0.16        69     101     145 ..      76     120 ..      71     143 .. 0.79
   3 ?   -0.8   2.5       1.8   7.8e+02     155     188 ..     195     228 ..     151     252 .] 0.49

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-05
                                  EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHS CS
                         6PF2K 14 lvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreask 58
                                  ++i+l GLp  gK++ sk+l + l+ + ++  v     +r+++  
  gi|15669733|ref|NP_248546.1|  5 MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPV 49
                                  68**********************999988777766666666655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.16
                                   EEES---SHHHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHHHHH CS
                         6PF2K 101 ifDAtNttrerRklilefveennlkvlflesicsdeeiikeNike 145
                                   i D tN     R+ +++++++ n +  ++   +s   +i++Ni+ 
  gi|15669733|ref|NP_248546.1|  76 IVDDTNYYNSMRRDLINIAKKYNKNYAIIYLKASLDVLIRRNIER 120
                                   7799**999999999999999985555555556667899999976 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.8
                                   TS-HHHHHHHHHHHHHHHHTT-----TTTTTTSE CS
                         6PF2K 155 dketeeaikdflkRlenyekqyeplddeedeels 188
                                   dket + + +++k  +  + + + + +   e l+
  gi|15669733|ref|NP_248546.1| 195 DKETRKIVSEYIKSKKLDKDKIKEVVELRKEFLK 228
                                   3333333333333333333333333223333333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.3e-05     0.023      20      53 ..       6      39 ..       2      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.3e-05
                        AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglA 53
                                  + +ltG +G GK+t  k l++++ +++ +vi+l 
  gi|15669733|ref|NP_248546.1|  6 LIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLG 39
                                  6799**************************9985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0    0.0001     0.043       7      30 ..       6      29 ..       4     101 .. 0.89
   2 ?   -0.7   0.0       3.7   1.6e+03      91      91 ..     172     172 ..     114     250 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.0001
                        AAA_22  7 ilvvtGesGtGKTtllrrlleqld 30
                                  ++++tG +G+GK+t  ++l++ l 
  gi|15669733|ref|NP_248546.1|  6 LIILTGLPGVGKSTFSKNLAKILS 29
                                  689****************99874 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.7
                        AAA_22  91 v 91 
                                   +
  gi|15669733|ref|NP_248546.1| 172 K 172
                                   1 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00032      0.14       2      29 ..      10      37 ..       9      49 .. 0.87
   2 ?    0.6   0.6      0.95   4.1e+02     157     215 ..     147     201 ..     140     235 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00032
                    ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvav 29
                                  +G +G+GK+tf ++l++il++++ +v v
  gi|15669733|ref|NP_248546.1| 10 TGLPGVGKSTFSKNLAKILSKNNIDVIV 37
                                  699*****************99777766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.95
                    ATP_bind_1 157 lPhvvvlnkfDllkek.lekeleffedvealslllekee......ekykklaeaiaelleefalvl 215
                                    P++++ ++ D+  ++ ++k +e  +++ ++  l+e+++      +            +++ ++ +
  gi|15669733|ref|NP_248546.1| 147 EPFLIIDTTKDIDFNEiAKKLIEKSKEIPKFYVLEENKNknnnisD-----------KIDKETRKI 201
                                   5666666666664444677778888888888777775544443332...........333333322 PP

>> Fringe  Fringe-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00018     0.076      82     134 ..      66     120 ..      43     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                        Fringe  82 fleskkkWfchvDDDnylnv..eaLlklLskynhtqdvylGkpsldrpieatert 134
                                   + +  k+++++vDD ny n   + L+++ +kyn++  +   k sld +i+   + 
  gi|15669733|ref|NP_248546.1|  66 IDSALKNYWVIVDDTNYYNSmrRDLINIAKKYNKNYAIIYLKASLDVLIRRNIER 120
                                   444456899*********973356************99999****9999875443 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00025      0.11      50     122 ..       7      85 ..       3     111 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00025
                     IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkr..arrd....gklaralkrllkvdllilDdlgllpl 122
                                   i+l+G +GvGKs ++  l++   ++++ v+ +  + + e+  +  ++ +     +  r +++ lk   +i+Dd  + + 
  gi|15669733|ref|NP_248546.1|   7 IILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVwkEKYEefikKSTYRLIDSALKNYWVIVDDTNYYNS 85 
                                   89***************************98776555555543113333111144556667777777799999988653 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   0.00012     0.053       5      94 ..       7      99 ..       5     108 .. 0.64
   2 ?   -0.8   3.3       2.5   1.1e+03      51     121 ..     166     236 ..      93     242 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                        AAA_24  5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.swedfldevvel.........aaeladyktlviDtidel 77
                                  i+++G +g+GK+t+ k+l  k  ++  ++  + +     + i+ s++ ++++++e+         + +l++y ++v Dt    
  gi|15669733|ref|NP_248546.1|  7 IILTGLPGVGKSTFSKNL-AK--ILSKNN-IDVIVL-GSDLIReSFPVWKEKYEEFikkstyrliDSALKNYWVIVDDT--NY 82
                                  7899**************.44..444444.322222.223344477777777777777777778888888887777775..44 PP

                        AAA_24 78 eelclaevirqnekaes 94
                                  ++ +++++i+ ++k ++
  gi|15669733|ref|NP_248546.1| 83 YNSMRRDLINIAKKYNK 99
                                  55555555555555555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.5
                        AAA_24  51 dfldevvel......aaeladyktlviDtideleelclaevirqnekaeskedkgdgkGygelaeefrrllkklqel 121
                                   +++++ +e+      +++++  +  + D id+  + ++ e i+ ++  ++k  ++     +el++ef + +kk++e+
  gi|15669733|ref|NP_248546.1| 166 KLIEKSKEIpkfyvlEENKN-KNNNISDKIDKETRKIVSEYIKSKKLDKDK--IKE---VVELRKEFLKKIKKMEEV 236
                                   33333333355555333333.344456888877665555555444442333..222...577778887777777776 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00076      0.33       3      38 ..       7      42 ..       5      55 .. 0.89
   2 ?    0.1   0.7       1.1   4.5e+02     222     262 ..     172     212 ..     150     226 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00076
                     Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCDP 38
                                  i + G  G+Gkst s+nl++ l++++  v+++G D 
  gi|15669733|ref|NP_248546.1|  7 IILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDL 42
                                  5567888**************************995 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                     Fer4_NifH 222 ktvieyapeseqakeyrelarkilenkklviPkplsedeLe 262
                                   k + ++   +e  ++ +++++ki ++ + ++ + +++++L+
  gi|15669733|ref|NP_248546.1| 172 KEIPKFYVLEENKNKNNNISDKIDKETRKIVSEYIKSKKLD 212
                                   33333333444456667777777777777766666666654 PP

>> MCD_N  Malonyl-CoA decarboxylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       2.4     1e+03      55      68 ..      85      98 ..      79     113 .. 0.81
   2 ?   10.3   0.1    0.0013      0.57      47      83 ..     213     251 ..     179     252 .] 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.4
                                  HHHHHHHHHTTT-G CS
                         MCD_N 55 dmRadllallkkek 68
                                  +mR+dl++  kk +
  gi|15669733|ref|NP_248546.1| 85 SMRRDLINIAKKYN 98
                                  69*****9988755 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0013
                                   TTHHHHHHHHHHHHHHHTTT-G..CHHHHHHHHHHHHHH CS
                         MCD_N  47 pgGvkfLVdmRadllallkkek..elraldadlehllss 83 
                                   ++ +k++V++R++ l+ +kk++  + + + +++++ll+s
  gi|15669733|ref|NP_248546.1| 213 KDKIKEVVELRKEFLKKIKKMEevDADRVLKEFKDLLNS 251
                                   66789***************9966667799999999988 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00045      0.19       2      26 ..       7      35 ..       6      78 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00045
                        AAA_28  2 ivitGgestGKTtlleaLa....argypv 26
                                  i++tG ++ GK+t +++La    ++++ v
  gi|15669733|ref|NP_248546.1|  7 IILTGLPGVGKSTFSKNLAkilsKNNIDV 35
                                  89*****************5554224443 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0022      0.94       4      32 ..      14      42 ..      11      49 .. 0.86
   2 ?    1.8   0.3      0.43   1.9e+02      82     166 ..     127     211 ..     115     230 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0022
                        CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDv 32
                                   +GKST++++L+  + +++  ++++  D+
  gi|15669733|ref|NP_248546.1| 14 GVGKSTFSKNLAKILSKNNIDVIVLGSDL 42
                                  69************999999999999987 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.43
                        CLP1_P  82 alvkelareveekleenkkakasgliIntpGwvkglga.elllelie.alepdvvvvldq.eellnelkrdlp.lskvkvv 158
                                   +++k+++++++e  ++  k  + +liI+t+   k++ + e+ ++lie   e+   +vl++ ++ +n+++++    ++  v 
  gi|15669733|ref|NP_248546.1| 127 EVIKKMYEKFDEPGKK-YKWDEPFLIIDTT---KDIDFnEIAKKLIEkSKEIPKFYVLEEnKNKNNNISDKIDkETRKIVS 203
                                   5778888888854444.5778899999999...555432566665541445566777777455555555555533344444 PP

                        CLP1_P 159 klpkspgv 166
                                   ++ ks+++
  gi|15669733|ref|NP_248546.1| 204 EYIKSKKL 211
                                   55555555 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00044      0.19       1      60 [.       7      68 ..       7      96 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00044
               Viral_helicase1  1 ivvhGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvks 60
                                  i+  G pG GKSt  ++l++     ++ v++    l++e++p  + +  + +++ +  l++s
  gi|15669733|ref|NP_248546.1|  7 IILTGLPGVGKSTFSKNLAKILskNNIDVIVLGSDLIRESFPVWKEKYEEFIKKSTYRLIDS 68
                                  5789***************9855555555555555555555333333333333333333333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0      0.04        17      12      38 ..       6      32 ..       3      39 .. 0.85
   2 ?    1.5   0.0      0.82   3.5e+02      92     126 ..      59      95 ..      47     105 .. 0.71
   3 ?    1.6   0.0      0.75   3.2e+02     100     124 ..     145     170 ..     117     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.04
                        AAA_19 12 vllvtaGpGtGKTrvlkhivallvelg 38
                                  ++++t+ pG GK++  k   ++l +++
  gi|15669733|ref|NP_248546.1|  6 LIILTGLPGVGKSTFSKNLAKILSKNN 32
                                  57899*********9999999888765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.82
                        AAA_19  92 e...eaeeekklqeeellivDEfqdvdelqyrLlkall 126
                                   +   ++  ++ l +++++ivD +   + +   L++  +
  gi|15669733|ref|NP_248546.1|  59 KkstYRLIDSAL-KNYWVIVDDTNYYNSMRRDLINIAK 95 
                                   444445566778.899*****99988888888877655 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.75
                        AAA_19 100 lqeeellivDEfqdvd..elqyrLlka 124
                                     +e  li+D + d+d  e +++L+++
  gi|15669733|ref|NP_248546.1| 145 W-DEPFLIIDTTKDIDfnEIAKKLIEK 170
                                   3.4459**********86667777765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0007       0.3       2      28 ..       6      32 ..       5      36 .. 0.89
   2 ?   -2.5   0.0       9.7   4.2e+03     144     159 ..     205     220 ..     164     243 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0007
                                  CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                         NACHT  2 lvilqGeaGsGKTtLlqklalawaegk 28
                                  l+il+G +G+GK+t+ + la  + +++
  gi|15669733|ref|NP_248546.1|  6 LIILTGLPGVGKSTFSKNLAKILSKNN 32
                                  689*****************9998876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.7
                                   .EEEE--TCCHHHHHH CS
                         NACHT 144 vlevegfsesrrkqlv 159
                                   +++ + + ++++k++v
  gi|15669733|ref|NP_248546.1| 205 YIKSKKLDKDKIKEVV 220
                                   3333334444444433 PP

>> Raf1_N  Rubisco accumulation factor 1 alpha helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   0.00066      0.28      16      53 ..     195     232 ..     193     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00066
                        Raf1_N  16 sqeqRaaaAelivekkldakeakelakaikdfsrlrke 53 
                                   ++e R  ++e+i +kkld +++ke++   k+f +  k+
  gi|15669733|ref|NP_248546.1| 195 DKETRKIVSEYIKSKKLDKDKIKEVVELRKEFLKKIKK 232
                                   5789**********************999999765554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.7    0.0019      0.81      14      63 ..       7      56 ..       5     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0019
                                  EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 14 vaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigv 63
                                  + ++G  G GKSt+ k la+ l++++ ++ + g dl +++ ++++++ + 
  gi|15669733|ref|NP_248546.1|  7 IILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKEKYEE 56
                                  6799*******************999999888888888555555555443 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00084      0.36      25      49 ..       7      31 ..       3      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00084
                  Mg_chelatase 25 lllvGppGsGKtmlakrlpsllppl 49
                                  ++l+G pG GK+   k l+++l++ 
  gi|15669733|ref|NP_248546.1|  7 IILTGLPGVGKSTFSKNLAKILSKN 31
                                  789*******************875 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   0.00013     0.057      12      45 ..      14      47 ..       6     138 .. 0.63
   2 ?   -1.0   2.5       3.4   1.4e+03      65      96 ..     181     214 ..     149     247 .. 0.44

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                        AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanat 45
                                  GvGK+T s nla+ l+k++  v++   D    + 
  gi|15669733|ref|NP_248546.1| 14 GVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESF 47
                                  9***********************9998755444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.4
                        AAA_31  65 eeknikeaiiktk..venldlipssidLaeaeie 96 
                                   ee++ k+  i++k   e+ +++  +i+  +++++
  gi|15669733|ref|NP_248546.1| 181 EENKNKNNNISDKidKETRKIVSEYIKSKKLDKD 214
                                   2222222222222113334565555555555543 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   0.00096      0.41       2      21 ..       7      26 ..       6      69 .. 0.86
   2 ?    2.1   0.1      0.45   1.9e+02      69     112 ..      62     105 ..      43     108 .. 0.67
   3 ?    0.1   0.6       1.9   8.3e+02      86      86 ..     183     183 ..     124     243 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00096
                                  EEEEESTTSSHHHHHHHHHT CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                  +++ G p vGKSt+ + l +
  gi|15669733|ref|NP_248546.1|  7 IILTGLPGVGKSTFSKNLAK 26
                                  7899***********99986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.45
                                   HHHHHHCT.SEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEE CS
                      MMR_HSR1  69 aflaleea.dlillvvdaseeklkpldeeleelleeakkplilvl 112
                                   +++ +++a +   ++vd + + ++ ++++l ++ ++ +k++ +++
  gi|15669733|ref|NP_248546.1|  62 TYRLIDSAlKNYWVIVDDT-NYYNSMRRDLINIAKKYNKNYAIIY 105
                                   3333333336666777744.67999********999777766554 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.9
                                   T CS
                      MMR_HSR1  86 s 86 
                                   +
  gi|15669733|ref|NP_248546.1| 183 N 183
                                   0 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2740  (0.152825); expected 358.6 (0.02)
Passed bias filter:                      770  (0.0429472); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.76u 0.36s 00:00:01.12 Elapsed: 00:00:00.50
# Mc/sec: 1529.97
//
Query:       gi|15669734|ref|NP_248547.1|  [L=109]
Description: hypothetical protein MJ_1539 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0073   16.7   2.5       0.26   11.8   0.3    2.1  2  NPV_P10    Nucleopolyhedrovirus P10 protein
  ------ inclusion threshold ------
      0.034   13.8   3.1      0.036   13.7   3.1    1.0  1  DUF4559    Domain of unknown function (DUF4559)
       0.05   13.2   5.2      0.056   13.1   5.2    1.1  1  Spb1_C     Spb1 C-terminal domain
      0.085   12.7   0.7       0.22   11.4   0.3    1.8  2  EF-hand_8  EF-hand domain pair
       0.13   12.7   1.5       0.14   12.6   1.5    1.1  1  FlgN       FlgN protein
       0.15   12.3   0.0        7.1    6.9   0.1    2.2  2  SgrR_N     Sugar transport-related sRNA regulator N-term
       0.17   12.0   5.2       0.22   11.6   5.2    1.2  1  Imm3       Immunity protein Imm3
       0.39   10.4   2.0       0.47   10.2   2.0    1.1  1  ZapD       Cell division protein
       0.64   10.3   6.0       0.82    9.9   6.0    1.2  1  UPF0122    Putative helix-turn-helix protein, YlxM / p13 like
          1    9.8   8.8         14    6.1   0.1    2.7  2  FlaC_arch  Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.3   0.00015      0.26      25      65 ..       9      52 ..       6      54 .. 0.83
   2 !    7.0   0.4    0.0045       8.1      36      66 ..      47      77 ..      41      91 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                       NPV_P10 25 qqvddvqenlpdvtelnekLdaqsaqLaelet.....kvenIqdiL 65
                                  ++v++++ ++p+  e+ +k+++++  L++l++     + e+I+++L
  gi|15669734|ref|NP_248547.1|  9 KEVKEIKVEIPK--EIADKIEKITSFLNSLKDkkemvSKEKIEEML 52
                                  689999999999..****************9966655446677777 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0045
                       NPV_P10 36 dvtelnekLdaqsaqLaeletkvenIqdiLn 66
                                  +++e+ + +d+  ++L +l+  +e+  +iL 
  gi|15669734|ref|NP_248547.1| 47 KIEEMLKLIDEVKDKLPKLNVDIEKLAKILE 77
                                  4566666667777777777777777777765 PP

>> DUF4559  Domain of unknown function (DUF4559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.1     2e-05     0.036     221     290 ..       5      75 ..       1      90 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                       DUF4559 221 llslqklkeleeellkedatkldelvlraeeqkiskeel.lkelqvlkeflnknkd.Lkenlkedvkklqei 290
                                   + +++++ke++ e  ke a k++++++  ++ k +ke +  ++++ + ++++++kd L  +l+ d++kl +i
  gi|15669734|ref|NP_248547.1|   5 MSEEKEVKEIKVEIPKEIADKIEKITSFLNSLKDKKEMVsKEKIEEMLKLIDEVKDkLP-KLNVDIEKLAKI 75 
                                   7899*************999****988888777666655677899***********555.999999999887 PP

>> Spb1_C  Spb1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   5.2   3.1e-05     0.056     108     171 ..       6      69 ..       1      92 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.1e-05
                        Spb1_C 108 rpiKKVaEAkaRKklkaakkleklkkkaeliaededlsekeKakqieklmkkaakkkkkkkvkv 171
                                      K V E k    +  a k+ek+ +  +++ +++++  keK++++ kl++++++k +k +v++
  gi|15669734|ref|NP_248547.1|   6 SEEKEVKEIKVEIPKEIADKIEKITSFLNSLKDKKEMVSKEKIEEMLKLIDEVKDKLPKLNVDI 69 
                                   55688999999999999************************************98877777665 PP

>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00012      0.22       9      40 ..      35      60 ..      27      60 .. 0.81
   2 ?   -1.3   0.0       1.1     2e+03      23      38 ..      78      93 ..      68      95 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                     EF-hand_8  9 elrrilrilglkkglseeevdilfrefDtdgd 40
                                  +l++     ++++ +s+e+++++++++D+ +d
  gi|15669734|ref|NP_248547.1| 35 SLKD-----KKEM-VSKEKIEEMLKLIDEVKD 60
                                  3444.....7777.**************9887 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                     EF-hand_8 23 lseeevdilfrefDtd 38
                                   s +ev i+f+++ +d
  gi|15669734|ref|NP_248547.1| 78 GSGSEVKIVFNKLTID 93
                                  6668899999987555 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.5   8.1e-05      0.14       7      71 ..      18      82 ..       6     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.1e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-- CS
                          FlgN  7 LielleeelelleeLlelleeEteaLkagdieaLeelleekqellekleqleqkrakllaelgls 71
                                  + + +++++e + ++l  l+ ++e+ ++++ie++ +l++e ++ l kl+   +k+ak+l+  g +
  gi|15669734|ref|NP_248547.1| 18 IPKEIADKIEKITSFLNSLKDKKEMVSKEKIEEMLKLIDEVKDKLPKLNVDIEKLAKILEGSGSE 82
                                  66778999999**********************************************99998876 PP

>> SgrR_N  Sugar transport-related sRNA regulator N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0039       7.1      77     102 ..      39      64 ..      25      67 .. 0.87
   2 ?    4.1   0.0      0.03        53      19      44 ..      66      91 ..      63      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0039
                        SgrR_N  77 aeklleqgkiekalalldkdkaalak 102
                                    +++++++kie++l+l+d+ k++l k
  gi|15669734|ref|NP_248547.1|  39 KKEMVSKEKIEEMLKLIDEVKDKLPK 64 
                                   5799**************99998866 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.03
                        SgrR_N 19 evtLqelAdvlfCsrRhartlLkkmq 44
                                  +v +++lA++l  s   ++++ +k+ 
  gi|15669734|ref|NP_248547.1| 66 NVDIEKLAKILEGSGSEVKIVFNKLT 91
                                  7899*******************996 PP

>> Imm3  Immunity protein Imm3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   5.2   0.00012      0.22      56     116 ..      12      70 ..       8      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                          Imm3  56 geialkhakvfvklkegiikrLsslnleelkgelteeeikdlleRrdkVledlekvevDyk 116
                                    ei+++ +k     +e+i+  L+sl   + k+ +++e+i+++l+ +d+V ++l k++vD++
  gi|15669734|ref|NP_248547.1|  12 KEIKVEIPKEIADKIEKITSFLNSLK--DKKEMVSKEKIEEMLKLIDEVKDKLPKLNVDIE 70 
                                   68999999999999*********975..667889*************************87 PP

>> ZapD  Cell division protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.0   0.00026      0.47      38      91 ..      15      69 ..       4      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00026
                                  CS-HHHHHHHHHHHHHHHHHCTTT-TT.S-HHHHHHHHHHHHHHHHHHHH--.ST CS
                          ZapD 38 RadlksellkeLerqkqkLkalrenpg.vdeealeelleeleqalsaLeaaegkl 91
                                  ++++ +e+   +e+ ++ L++l+++++ v++e++ee+l+ +++++++L +++  +
  gi|15669734|ref|NP_248547.1| 15 KVEIPKEIADKIEKITSFLNSLKDKKEmVSKEKIEEMLKLIDEVKDKLPKLNVDI 69
                                  566677777788999999999997654389******************9988655 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.0   0.00046      0.82      48     100 ..      20      74 ..       3      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00046
                       UPF0122  48 qavydnikrtekllekyEekLkllekyk..kreellekikdkllkqkelekklke 100
                                   + + d+i++++++l+++ +k ++++k k  +  +l++++kdkl k +  ++kl++
  gi|15669734|ref|NP_248547.1|  20 KEIADKIEKITSFLNSLKDKKEMVSKEKieEMLKLIDEVKDKLPKLNVDIEKLAK 74 
                                   4699*******************9876511667999*******999988888775 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   5.5     0.018        32       3      35 ..      20      53 ..       6      58 .. 0.84
   2 ?    6.1   0.1     0.008        14       2      30 ..      55      83 ..      53      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.018
                     FlaC_arch  3 delEnklsklsteletvkkeneelsks.veelke 35
                                  +e+  k++k+ + l+++k++ e +sk+ +ee+ +
  gi|15669734|ref|NP_248547.1| 20 KEIADKIEKITSFLNSLKDKKEMVSKEkIEEMLK 53
                                  588899*****************98743776655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.008
                     FlaC_arch  2 idelEnklsklsteletvkkeneelsksv 30
                                  ide+  kl+kl + +e + k +e   ++v
  gi|15669734|ref|NP_248547.1| 55 IDEVKDKLPKLNVDIEKLAKILEGSGSEV 83
                                  78999999999999999888887777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2172  (0.121145); expected 358.6 (0.02)
Passed bias filter:                      931  (0.051927); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.54
# Mc/sec: 605.53
//
Query:       gi|15669735|ref|NP_248548.1|  [L=136]
Description: hypothetical protein MJ_1540 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   14.1   0.4      0.059   13.3   0.3    1.4  1  UPF0158   Uncharacterised protein family (UPF0158)
       0.19   11.7   0.8        0.2   11.6   0.8    1.1  1  MSA-2c    Merozoite surface antigen 2c


Domain annotation for each model (and alignments):
>> UPF0158  Uncharacterised protein family (UPF0158)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   6.6e-06     0.059      67     113 ..      26      72 ..      20      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.6e-06
                       UPF0158  67 vyeskklmesFlnekvedidakeklldilqskkalenFlefiydfea 113
                                    + s+++  +++   +e+i++ + +++++ sk a ++ + f+++ e 
  gi|15669735|ref|NP_248548.1|  26 NIFSLGISRDYITINIENIKTLKEIMEAVSSKSANKKLKSFLEKIED 72 
                                   556789999***********************987665555544333 PP

>> MSA-2c  Merozoite surface antigen 2c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8   2.2e-05       0.2      34      77 ..      48      91 ..      26     136 .] 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.2e-05
                        MSA-2c 34 aevleelstkddeellkallesikgmkiileklnkflkelrkns 77
                                  +e++e +s k+ +++lk++le+i+ +ki l +  k  + l  n 
  gi|15669735|ref|NP_248548.1| 48 KEIMEAVSSKSANKKLKSFLEKIEDLKIFLSEASKIAEILVNNR 91
                                  47999***********************9998877655444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1257  (0.0701099); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 916.06
//
Query:       gi|15669736|ref|NP_248549.1|  [L=420]
Description: N-ethylammeline chlorohydrolase TrzA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-87  292.8   0.1    4.5e-87  292.6   0.1    1.1  1  Amidohydro_1  Amidohydrolase family
    2.7e-16   60.1   0.0    1.6e-12   47.7   0.0    2.1  2  Amidohydro_3  Amidohydrolase family
      0.007   15.8   0.1      0.024   14.0   0.0    1.8  2  TatD_DNase    TatD related DNase
  ------ inclusion threshold ------
      0.047   13.0   0.0      0.092   12.1   0.0    1.4  1  A_deaminase   Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.6   0.1     1e-90   4.5e-87       1     344 []      46     393 ..      46     393 .. 0.95

  Alignments for each domain:
  == domain 1  score: 292.6 bits;  conditional E-value: 1e-90
                                   EEEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHH CS
                  Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgieall 67 
                                   i +PGlI++H+H++++l+rg+    +l++wl          +++e++++++  g+ ++++sGttt++dm++     +e ++
  gi|15669736|ref|NP_248549.1|  46 IAIPGLINTHTHIPMTLFRGVaddlPLMEWLnnyiwpmeakLNEEIVYWGTLLGCIEMIRSGTTTFNDMYF----FLEGIA 122
                                   579********************************************************************....9***** PP

                                   HHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEE CS
                  Amidohydro_1  68 eaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpv 148
                                   +a++e   g+r++++++++d +++e ++ + ++ ++++ + i   +++++++al+ph+++++s+e+l e+ ++akk+++p+
  gi|15669736|ref|NP_248549.1| 123 KAVDES--GMRAVLAYGMIDLFDEERRERELKNAEKYI-NYINSLNNSRIMPALGPHAPYTCSKELLMEVNNLAKKYNVPI 200
                                   *****9..*************88888888888888885.888*************************************** PP

                                   EEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSEHHH CS
                  Amidohydro_1 149 aiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgr 229
                                   +iH+ et  e+++++++ g     + ++ ++ s+g++d++++i+ah+vhlt++e++++k++  +++v+h p sn++l+sg+
  gi|15669736|ref|NP_248549.1| 201 HIHLNETLDEIKMVKEKTG-----MEPFIYLNSFGFFDDVRAIAAHCVHLTDEEIKIMKQK--NINVSHNPISNLKLASGV 274
                                   *******************.....66***********************************..****************** PP

                                   HHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTS CS
                  Amidohydro_1 230 ealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGk 310
                                   +++ k+l eG++v+lgtDg++s+n+lnl+ee+++ + l++g++  ++++ ++++ea+++aT ngAkal++  k+G+i +G+
  gi|15669736|ref|NP_248549.1| 275 APIPKLLAEGINVTLGTDGCGSNNNLNLFEEIKVSAILHKGVNL-NPTV-VKAEEAFNFATKNGAKALNI--KAGEIREGY 351
                                   ****************************************9999.5677.********************..********* PP

                                   B--EEEECC.CT........CGGGTTTCTSEEEEEEEETTEEE CS
                  Amidohydro_1 311 dADlvvvdl.di........laafvglkkdgnvkkvivkGklv 344
                                    AD+v+++l ++         +++v+  + + v+ vi++G++v
  gi|15669736|ref|NP_248549.1| 352 LADIVLINLdKPylypkeniMSHLVYAFNGF-VDDVIIDGNIV 393
                                   *********8336677888899999997766.********998 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   6.7e-05       0.3       1      21 [.      38      58 ..      38      69 .. 0.88
   2 !   47.7   0.0   3.5e-16   1.6e-12     260     472 ..     181     393 ..     124     394 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.7e-05
                  Amidohydro_3  1 eviDakGrlvlPGFvDsHtHl 21
                                  e+iD k+++ +PG++  HtH+
  gi|15669736|ref|NP_248549.1| 38 EIIDGKNKIAIPGLINTHTHI 58
                                  68******************5 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 3.5e-16
                  Amidohydro_3 260 fedealaelvaaadergldvaihaigdaavddvldafeaa.....aekngnqdrr..rlehaegvtesqiervaalqvaag 333
                                   +++e l e+ ++a+++ ++++ih +++ +   ++++ +        +  g+ d +   ++h+  +t+++i+ ++  ++  +
  gi|15669736|ref|NP_248549.1| 181 CSKELLMEVNNLAKKYNVPIHIHLNETLDEIKMVKEKTGMepfiyLNSFGFFDDVraIAAHCVHLTDEEIKIMKQKNINVS 261
                                   55555889999**************9999885555444445888877777777774666666666**************** PP

                  Amidohydro_3 334 vqpvfnfedelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeelsleeal 414
                                     p++n            + a+g++p+  ll+ g++v+lg+D  +g+ +++  ++    +   ++  v      +  eea+
  gi|15669736|ref|NP_248549.1| 262 HNPISNL-----------KLASGVAPIPKLLAEGINVTLGTD-GCGSNNNLNLFEEIKVSAILHK-GVNLNPTVVKAEEAF 329
                                   *******...........899*********************.5555555555555555555555.5777888******** PP

                  Amidohydro_3 415 alyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear.......vrltvvdGrvv 472
                                      T+++Akal+     G +++G+ AD+v+++ ++p   +++++ + +       v  +++dG++v
  gi|15669736|ref|NP_248549.1| 330 NFATKNGAKALNIKA--GEIREGYLADIVLINlDKPYLYPKENIMSHLvyafngfVDDVIIDGNIV 393
                                   ***************..***************88888888888888889999***********998 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   5.4e-06     0.024     109     183 ..     182     269 ..     174     283 .. 0.80
   2 ?   -3.5   0.0       1.2   5.5e+03     200     218 ..     356     369 ..     351     384 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-06
                                   HHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCS.............EEEETT--S-HHHHHHHHHTTEEEEE CS
                    TatD_DNase 109 qeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeaka.............kvvlHsfsgsaeeakkflklgyyisl 176
                                    +e++ e  +lAk+++ p+ iHl ++ +++  + ++++ +++             ++  H+   + ee+k + ++++ +s 
  gi|15669736|ref|NP_248549.1| 182 SKELLMEVNNLAKKYNVPIHIHLNETLDEIKMVKEKTGMEPFiylnsfgffddvrAIAAHCVHLTDEEIKIMKQKNINVSH 262
                                   678899999****************999777777666644445666666666679999************99999999999 PP

                                   -GGGGTT CS
                    TatD_DNase 177 sglltfk 183
                                   + +++ k
  gi|15669736|ref|NP_248549.1| 263 NPISNLK 269
                                   9887665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.2
                                   EEE---TTSSEECCCTTSE CS
                    TatD_DNase 200 lLiETDaPyltpkpyrgkr 218
                                   +Li  D Pyl pk     +
  gi|15669736|ref|NP_248549.1| 356 VLINLDKPYLYPK-----E 369
                                   6777799999993.....3 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     2e-05     0.092     234     279 ..     253     294 ..     239     314 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                                   HHHCT-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSC CS
                   A_deaminase 234 lalaqiplevcPlSNvalgafleyaenPlkeflerglnvslntDDP 279
                                   + +++i +   P+SN +l    +    P++++l +g+nv+l+tD  
  gi|15669736|ref|NP_248549.1| 253 MKQKNINVSHNPISNLKL----ASGVAPIPKLLAEGINVTLGTDGC 294
                                   5788999999********....77889*****************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 3104.23
//
Query:       gi|15669737|ref|NP_248550.1|  [L=808]
Description: hypothetical protein MJ_1542 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-15   58.4   5.1    3.2e-09   37.0   0.0    3.1  3  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    3.2e-13   50.1  41.5    3.2e-13   50.1  41.5    3.7  2  AAA_15         AAA ATPase domain
    0.00041   20.9   0.0     0.0016   19.0   0.0    2.1  2  ABC_tran       ABC transporter
    0.00084   18.8   3.1     0.0044   16.5   0.7    2.3  2  SMC_N          RecF/RecN/SMC N terminal domain
     0.0044   17.6   9.6     0.0044   17.6   9.6    3.3  2  AAA_23         AAA domain
  ------ inclusion threshold ------
      0.024   14.7   0.0       0.12   12.5   0.0    2.2  1  FAD_binding_8  FAD-binding domain
      0.083   13.3   0.1        7.8    6.9   0.0    3.4  3  zf-H3C2        Zinc-finger like, probable DNA-binding
        0.3   11.4   2.7       0.73   10.1   0.7    2.7  3  DUF1828        Domain of unknown function DUF1828


Domain annotation for each model (and alignments):
>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.4   3.8e-08   8.4e-05       3      68 ..      32      89 ..      30     103 .. 0.69
   2 !   37.0   0.0   1.4e-12   3.2e-09     223     303 .]     461     539 ..     397     539 .. 0.83
   3 ?   -2.8   0.2       1.9   4.3e+03     133     223 ..     689     779 ..     675     790 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.8e-08
                        AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsq 68
                                   + GpN++GK+nL++ l+ll+ +        +e+ + +++ ++ +  +l++ +i++   ++ + ++
  gi|15669737|ref|NP_248550.1| 32 TIFGPNNVGKTNLFRVLKLLRNI-------INEKISAVDLEIYLHNKNLKAAKIEVDVIFD-KSDK 89
                                  699*****************654.......3455555566666666666666666666665.4444 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 1.4e-12
                        AAA_21 223 flengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpllld 303
                                   +++++ + e+p++ ++ G+k++l +lt+++   +  +++l+D p n L Pk ++r+ ++lk++++ ++Qv++  HSp++++
  gi|15669737|ref|NP_248550.1| 461 IVVYSEDIEIPLNMVGLGVKKILEILTLVFGYES--KVILLDTPFNQLYPKYQKRFSKILKDTENIDSQVFIILHSPYFIN 539
                                   56788899**********************9998..7*****************************************986 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.9
                        AAA_21 133 sepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvd 213
                                   +    +++++ ++++++ + ++l+ +++ + e    +  +++++ ++ + +l+++l++ l++  +  +  ++++ ++ + +
  gi|15669737|ref|NP_248550.1| 689 NRHPFWISKEEFDKVINIYIKTLEAHREKLIELGYIYLSSKEEVVKYCIEPLRKQLEDILRKKLFIFTVPTDFIIEPQDLK 769
                                   444445555555555555555555555555554444445555555555666666666666666666666666666666666 PP

                        AAA_21 214 erlrergvvf 223
                                   + ++e++ ++
  gi|15669737|ref|NP_248550.1| 770 NIQIEKDKYI 779
                                   6666664444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1  41.5   1.4e-16   3.2e-13       1     369 []       5     538 ..       5     538 .. 0.70
   2 ?   -5.3   6.7         8   1.8e+04      54     130 ..     694     771 ..     651     806 .. 0.39

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.4e-16
                        AAA_15   1 MkIkkikikNFRslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikId 80 
                                   MkIk+i  kN  s++d++i +++  + ++ G+Nn+GK+++ ++l+l+ n     n    ki + dlei+ ++++ k  kI+
  gi|15669737|ref|NP_248550.1|   5 MKIKSIAAKNLLSFDDFKITFEDGdVVTIFGPNNVGKTNLFRVLKLLRNII---N---EKISAVDLEIYLHNKNLKAAKIE 79 
                                   ***********************9999999**************9999966...3...45666666666666666666666 PP

                        AAA_15  81 vef......................................................................aek.ekak 90 
                                   v                                                                        +e+ ek k
  gi|15669737|ref|NP_248550.1|  80 VDVifdksdkeviakflkiffkinapdlirlcnnlklniinsiidyfsagsyiwecselrcyrpyfmlrlrslEEDiEKIK 160
                                   66666888888888888999999999999999999999999999999*******************999998755567788 PP

                        AAA_15  91 eyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisve.kkkskkelpkekeeklekekeelkidkedlk 170
                                   +y+k+ + +e+  + ++  k + +l+  ++  +  ++ ++++++++++   + +k+e   +++    ke+ ++ i + +++
  gi|15669737|ref|NP_248550.1| 161 IYLKERELSEITPDLIDHSKVIHELDRNVEIIEVTNDLKNIITSSVNALiTIYEKNEKLFFSTLIDGKENITTRIGDGNIE 241
                                   888888888888888888888888888888777777666666666654414555777777888888888888888888888 PP

                        AAA_15 171 klikkleeslkkee................................................................... 184
                                   ++ +   + ++k+                                                                    
  gi|15669737|ref|NP_248550.1| 242 NIVEISMKDFTKDIekyedcfkrltmdknilrafvvllaldkllankmsiyvkkvleyskenpwdkeiiedlkyivrfcgf 322
                                   888755555555557777888888899999999999999999888866666666555555555555444444444444444 PP

                        AAA_15 185 ...........................elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl.... 234
                                                                                                                    
  gi|15669737|ref|NP_248550.1| 323 dyrdiyeisdislndillkiyenslifY------------------------------------------------Edylp 355
                                   4444444444422222222222222220................................................13345 PP

                        AAA_15 235 ........................eeelteklkeiqeklkeidkklaeelk....kilkkkidkikkfnykgkkneeieik 287
                                                           e+++++k+ e+ +  +++d+ +   l+    k++ + ++ +k+  + +  + + +ik
  gi|15669737|ref|NP_248550.1| 356 negkvmipdymivellaglknnslEKNVKSKILELFKTSTTKDDLYLGILSmpseKWIPSYLFYLKNNANLKLRKRYMKIK 436
                                   555555555555555555554444333333333333333333333333333555544444444443333333333333333 PP

                        AAA_15 288 .............................ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpq 339
                                                                +d e+pln++G+Gv+ +l +++l + +e k        ++l++ P + L+p+
  gi|15669737|ref|NP_248550.1| 437 emfeyifnsgslsfdvilannkpdivvysEDIEIPLNMVGLGVKKILEILTLVFGYESK--------VILLDTPFNQLYPK 509
                                   44444445666666666666667777777******************************........************** PP

                        AAA_15 340 aqkvlikllkelandnktQviitTHSphii 369
                                    qk + k lk+  n ++ Qv+i  HSp++i
  gi|15669737|ref|NP_248550.1| 510 YQKRFSKILKDTENIDS-QVFIILHSPYFI 538
                                   ****************9.**********98 PP

  == domain 2  score: -5.3 bits;  conditional E-value: 8
                        AAA_15  54 n..kkvikiekedleifeniseskdikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkkne 130
                                      k+++++  + + ++ +  ++k i++ + +  ++k+++   + ++ +k+ +d+l kk+   ++ t +  + ++ kn 
  gi|15669737|ref|NP_248550.1| 694 WisKEEFDKVINIYIKTLEAHREKLIELGYIY-LSSKEEVVKYCIEPLRKQLEDILRKKLFIFTVPTDFIIEPQDLKNI 771
                                   13322222222222222233333333333333.1122222222222222222222222222222222222222222222 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   6.9e-07    0.0016       2      67 ..      19      86 ..      18     205 .. 0.86
   2 ?   -2.7   0.0       3.5   7.8e+03     112     137 .]     478     504 ..     460     504 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.9e-07
                                  EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET..TCEGGGB-HHHCCHCEEEE-SS CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilld..gkdlkeqeleslrkeigvlpqe 67
                                  ++ +++++ g +v i+G+n  GK+ L+++l  l +  +++i     +  l++++l+ ++ e+ v++ +
  gi|15669737|ref|NP_248550.1| 19 DDFKITFEDGDVVTIFGPNNVGKTNLFRVLKLLRNIINEKISAVdlEIYLHNKNLKAAKIEVDVIFDK 86
                                  678999**********************************9554133334448888888888888876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.5
                                   HHHHHHHHHHHHHH.TSSEEEEESTTT CS
                                   xxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                      ABC_tran 112 Gqkqrvalarallk.kpkllllDEpta 137
                                   G k+ +++  +++  ++k++llD p++
  gi|15669737|ref|NP_248550.1| 478 GVKKILEILTLVFGyESKVILLDTPFN 504
                                   6677777777776537899****9986 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.7   1.9e-06    0.0044       2      91 ..       7      92 ..       6     106 .. 0.77
   2 ?    2.5   0.1     0.037        82     161     206 ..     496     542 ..     180     556 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-06
                                  EEEEEEESETTEECEEEEEET.TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  2 lkrleienFksyagktvilpf.sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitf 83
                                  +k++  +n  s+     ++ f +  +  i GpN  GK+nl+  ++  L +  ++k+ + +l+  +h+  ++ ++ k ev+++f
  gi|15669737|ref|NP_248550.1|  7 IKSIAAKNLLSFD--DFKITFeDGDVVTIFGPNNVGKTNLFRVLKL-LRNIINEKISAVDLEIYLHN--KNLKAAKIEVDVIF 84
                                  89999*******5..4444440445899**************9965.44455668888888888887..78888899****** PP

                                  EETTEESS CS
                                  xxxxxxxx RF
                         SMC_N 84 dnedkklk 91
                                  d++dk++ 
  gi|15669737|ref|NP_248550.1| 85 DKSDKEVI 92
                                  ****9944 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.037
                                   EEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                         SMC_N 161 lyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekad 206
                                   + llD    +L  k+ k+++++lk +++  +Q+++i ++  ++++ +
  gi|15669737|ref|NP_248550.1| 496 VILLDTPFNQLYPKYQKRFSKILKDTENIdSQVFIILHSPYFINNEN 542
                                   45677777788889999999***97766449*****99988887754 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   9.6     2e-06    0.0044       3     173 ..      11     273 ..       9     314 .. 0.53
   2 ?   -1.4   0.7       1.2   2.8e+03     156     197 ..     705     749 ..     634     797 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                        AAA_23   3 kienfrsfrdqeidF.skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvelt..fe 80 
                                     +n+ sf+d++i F +  ++ I+GpN  GKT +++ +kl           +++ ++++ ++ +++++ ++a +e++  f 
  gi|15669737|ref|NP_248550.1|  11 AAKNLLSFDDFKITFeDGDVVTIFGPNNVGKTNLFRVLKLLRNII------NEKISAVDLEIYLHNKNLKAAKIEVDviFD 85 
                                   569************5558********************975542......225677888888888766666655553365 PP

                        AAA_23  81 nkdgry.........................................................trsiererelskkkgktt 104
                                   + d++                                                           rs+e+++e++k   k++
  gi|15669737|ref|NP_248550.1|  86 KSDKEViakflkiffkinapdlirlcnnlklniinsiidyfsagsyiwecselrcyrpyfmlrLRSLEEDIEKIKIYLKER 166
                                   555555777777777777777888888888888888888888888888888888888877777444444444444322222 PP

                        AAA_23 105 ..kkaklelleideleqfisellgskkiilnlilflgqer.......feefelkdkke....................... 153
                                     ++ + +l+++++   ++++++++ +  ++l  ++ ++        +       k+e                       
  gi|15669737|ref|NP_248550.1| 167 elSEITPDLIDHSKVIHELDRNVEIIEVTNDLKNIITSSVnalitiyE-------KNEklffstlidgkenittrigdgni 240
                                   112222222222222222222111111111111111111111111110.......00011111111112222222333333 PP

                        AAA_23 154 .............rleelekeleeledekklle 173
                                                 +e++e++++ l+ +k+ l+
  gi|15669737|ref|NP_248550.1| 241 eniveismkdftkDIEKYEDCFKRLTMDKNILR 273
                                   333333111111155555555555555555544 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                        AAA_23 156 eelekeleeledekkllekl......eqekekekeleeleeeleeilk 197
                                   + ++k le   ++  +   l       +e+  +  +e l+++le+il 
  gi|15669737|ref|NP_248550.1| 705 NIYIKTLEAHREKLIE---LgyiylsSKEEVVKYCIEPLRKQLEDILR 749
                                   2222222222222222...23424333333333366666666666654 PP

>> FAD_binding_8  FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.3e-05      0.12      32      78 ..     673     718 ..     665     749 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-05
                 FAD_binding_8  32 aGqyvyinipslsklfwqsHPFtiasapeddklslvikvksgltkkl 78 
                                    G+y  i  ++l+ +f + HPF i  +++d+ ++++ik+ +   +kl
  gi|15669737|ref|NP_248550.1| 673 KGKYHKIVEERLN-FFKNRHPFWISKEEFDKVINIYIKTLEAHREKL 718
                                   5777777777788.77899*******************998887776 PP

>> zf-H3C2  Zinc-finger like, probable DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.2   1.2e+04      64      80 ..     139     154 ..     137     161 .. 0.69
   2 ?    2.0   0.0      0.12   2.7e+02      15      50 ..     338     377 ..     325     400 .. 0.65
   3 ?    6.9   0.0    0.0035       7.8      51      86 ..     625     660 ..     612     667 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.2
                                   TST-SSEETTHHHHHHH CS
                       zf-H3C2  64 rshspyymlnrdrtlkn 80 
                                   r + py+ml r r+l++
  gi|15669737|ref|NP_248550.1| 139 RCYRPYFML-RLRSLEE 154
                                   6789***99.4566655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.12
                                   HHT-EEETT....TTEEEETTEEEE-HHHHHHHHHHHHHH CS
                       zf-H3C2  15 klgaiydkt....kkywvyqgkpvmpdqftfelldflhql 50 
                                    l  iy+++    + y   +gk ++pd + +ell  l++ 
  gi|15669737|ref|NP_248550.1| 338 ILLKIYENSlifyEDYLPNEGKVMIPDYMIVELLAGLKNN 377
                                   55566665422224566779**************988754 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0035
                                   H---HHHHHHHHHTST-SSEETTHHHHHHHHHHT-H CS
                       zf-H3C2  51 thlsfskmkallershspyymlnrdrtlknitetck 86 
                                     lsf k  all+ +  py ++ r   l n+ e  k
  gi|15669737|ref|NP_248550.1| 625 NTLSFGKYYALLQYTSIPYILMLRSWILYNLYEEIK 660
                                   679***************************999877 PP

>> DUF1828  Domain of unknown function DUF1828
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.8   1.1e+04       4      15 ..      24      35 ..      23      44 .. 0.76
   2 ?   10.1   0.7   0.00033      0.73       5      72 ..     153     223 ..     151     231 .. 0.83
   3 ?   -1.9   0.0       1.8   4.1e+03      10      50 ..     703     743 ..     697     754 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.8
                       DUF1828  4 ldedgDsiqiyv 15
                                  ++edgD ++i+ 
  gi|15669737|ref|NP_248550.1| 24 TFEDGDVVTIFG 35
                                  689******996 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00033
                       DUF1828   5 dedgDsiqiyvkkkegdei..rLtDdGltlmdLsysgidldl.skkRkellesilakfgvtledgelsvkv 72 
                                    ed + i+iy+k++e +ei   L D+++++++L+ +   ++  ++ ++ +++s+ a   + +++++l+ ++
  gi|15669737|ref|NP_248550.1| 153 EEDIEKIKIYLKERELSEItpDLIDHSKVIHELDRNVEIIEVtNDLKNIITSSVNALITIYEKNEKLFFST 223
                                   578889*****99999999888************9999999855556677777778889999999888765 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.8
                       DUF1828  10 siqiyvkkkegdeirLtDdGltlmdLsysgidldlskkRke 50 
                                    i+iy+k+ e  + +L + G++    +++ +++ +++ Rk+
  gi|15669737|ref|NP_248550.1| 703 VINIYIKTLEAHREKLIELGYIYLSSKEEVVKYCIEPLRKQ 743
                                   58899999998888999999988777666666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (808 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 5164.77
//
Query:       gi|15669738|ref|NP_248551.1|  [L=348]
Description: ketol-acid reductoisomerase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-75  249.8   0.6    1.3e-74  249.3   0.6    1.2  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    2.1e-64  216.1   1.0    3.3e-64  215.5   1.0    1.2  1  IlvC            Acetohydroxy acid isomeroreductase, catalytic
    1.2e-06   28.9   0.1    2.8e-06   27.8   0.1    1.6  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    1.8e-06   27.4   0.0      3e-06   26.7   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    1.5e-05   25.3   0.0    3.5e-05   24.0   0.0    1.6  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    2.3e-05   24.5   0.2    5.2e-05   23.4   0.1    1.5  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
     0.0091   16.7   0.1      0.025   15.2   0.1    1.8  1  CoA_binding     CoA binding domain
  ------ inclusion threshold ------
      0.065   12.9   0.0       0.11   12.1   0.0    1.3  1  YfaZ            YfaZ precursor
       0.37   10.8   2.1         17    5.4   0.1    3.0  4  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen


Domain annotation for each model (and alignments):
>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.3   0.6   6.4e-78   1.3e-74       2     165 .]      33     196 ..      32     196 .. 0.99

  Alignments for each domain:
  == domain 1  score: 249.3 bits;  conditional E-value: 6.4e-78
                                   HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTG CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeie 82 
                                   +k+k+iaviGyGsqG+aqaln++dsgl+v+vglr +++s++kA ++g++v+t++ea++kad+++iliPDe+q +vy+++ie
  gi|15669738|ref|NP_248551.1|  33 VKDKTIAVIGYGSQGRAQALNMKDSGLNVIVGLRPNGASWNKAIKDGHKVMTIEEAAEKADIIHILIPDEVQPAVYKKQIE 113
                                   79******************************************************************************* PP

                                   GG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHHHHHHTTHHH CS
                          IlvN  83 pnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelalayakgiGatr 163
                                   p+l+egk+++f+hG+nih+g+i+pp++v++++vAPk+pG +vr++yeeg+Gvp l+ave+d++g+a ++al +akgiG t+
  gi|15669738|ref|NP_248551.1| 114 PYLTEGKTISFSHGYNIHYGFIRPPENVNITMVAPKSPGAMVRKTYEEGFGVPGLVAVERDYTGDALQIALGMAKGIGLTK 194
                                   ********************************************************************************9 PP

                                   H- CS
                          IlvN 164 aG 165
                                    G
  gi|15669738|ref|NP_248551.1| 195 VG 196
                                   88 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.5   1.0   1.6e-67   3.3e-64       1     142 [.     202     343 ..     202     344 .. 0.99

  Alignments for each domain:
  == domain 1  score: 215.5 bits;  conditional E-value: 1.6e-67
                                   HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHH CS
                          IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdltagp 81 
                                   F+eEtetDlfgEq+vLcGgv+el++a+FetlveaGy pe+Ayfe++helklivdliy++G+++m+e++S+taeyg+lt++ 
  gi|15669738|ref|NP_248551.1| 202 FREETETDLFGEQVVLCGGVTELIKAAFETLVEAGYAPEMAYFETCHELKLIVDLIYQKGLQGMWENVSNTAEYGGLTRRA 282
                                   99******************************************************************************* PP

                                   HHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHTTSHHHHHHHHHHHTSHHHHHHHHHHHCH CS
                          IlvC  82 rviteevkeemkeileeiqsGefakevieenkagrpelkklrkeeaeheiekvgkklralm 142
                                   rvi+ee++++mkeil+eiq+G+fake+ +e +ag p+l++lr+ e+eh iekvgk+lr+++
  gi|15669738|ref|NP_248551.1| 283 RVINEESRKAMKEILKEIQDGRFAKEWSLEREAGFPHLNALRRLEKEHLIEKVGKELRKMC 343
                                   ***********************************************************96 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   1.4e-09   2.8e-06       1      81 [.      37     111 ..      37     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.4e-09
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
                 F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel 81 
                                   +i++iG+G++g+a a+++  +g    +++v+ ++n  + +++ ++   kv++   eeaae+ad++ + ++ e+ ++v ++ 
  gi|15669738|ref|NP_248551.1|  37 TIAVIGYGSQGRAQALNMKDSG---LNVIVGLRPNGASWNKAIKDG-HKVMT--IEEAAEKADIIHILIPDEVQPAVYKKQ 111
                                   59********************...****9*999999888887774.46666..9*************9999988887654 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.5e-09     3e-06      27     100 ..      26     100 ..      13     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.5e-09
                                   CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEE.ESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S- CS
                  2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkvia.ydrskkkeeeeeelgvelvsleellaesDivslhlp 100
                                   k+++   +++kt+++iG+G+ G+a a  +k  g++vi+   ++  + +++ + g +++++ee+ +++Di+ + +p
  gi|15669738|ref|NP_248551.1|  26 KDVTFDAVKDKTIAVIGYGSQGRAQALNMKDSGLNVIVgLRPNGASWNKAIKDGHKVMTIEEAAEKADIIHILIP 100
                                   56677789**************************998714555554458888899****************9999 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.7e-08   3.5e-05       1      86 [.      37     122 ..      37     130 .. 0.84
   2 ?   -3.3   0.0       4.6   9.2e+03      31      61 ..     225     255 ..     220     276 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.7e-08
                                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSH.HHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC- CS
                 NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtk.ekveelvaegakaaesieelvasldvvitmvkagkavdevieglleal 80 
                                   +i++iG G  G+  aln++++g +v+v  r + ++ ++++++g   + +iee+++++d++ ++++++ +     +++ ++l
  gi|15669738|ref|NP_248551.1|  37 TIAVIGYGSQGRAQALNMKDSGLNVIVGLRPNgASWNKAIKDGH-KVMTIEEAAEKADIIHILIPDEVQPAVYKKQIEPYL 116
                                   59***********************9988765266777777766.67799***************9877665555699999 PP

                                   -TT-EE CS
                 NAD_binding_2  81 kkgdil 86 
                                    +g+++
  gi|15669738|ref|NP_248551.1| 117 TEGKTI 122
                                   999875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.6
                                   SHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE CS
                 NAD_binding_2  31 tkekveelvaegakaaesieelvasldvvit 61 
                                    k+++e+lv++g  +     e +++l++++ 
  gi|15669738|ref|NP_248551.1| 225 IKAAFETLVEAGYAPEMAYFETCHELKLIVD 255
                                   5677777888876666666667777666654 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   2.6e-08   5.2e-05      22      82 ..      34      95 ..      25     101 .. 0.87
   2 ?   -3.9   0.0       6.5   1.3e+04      20      30 ..     209     219 ..     201     236 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.6e-08
                                  TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHH..HHHHCTT-EE--HHHCTTT-SEE CS
                 AdoHcyase_NAD 22 aGkvavvaGyGdvGkGcaaslkglGarvivtevdPica..lqaameGfevvtleevvkkadiv 82
                                    k++ v+GyG  G+  a  +k  G  viv  + P  a   +a+ +G++v+t+ee+++kadi+
  gi|15669738|ref|NP_248551.1| 34 KDKTIAVIGYGSQGRAQALNMKDSGLNVIVG-LRPNGAswNKAIKDGHKVMTIEEAAEKADII 95
                                  57999***********************996.666665225899*****************97 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.5
                                   --TTSEEEEE- CS
                 AdoHcyase_NAD  20 llaGkvavvaG 30 
                                    l G ++v++G
  gi|15669738|ref|NP_248551.1| 209 DLFGEQVVLCG 219
                                   45566666665 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.3e-05     0.025       2      77 ..      34     106 ..      33     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                                   TTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEET...TEEEESCHHHHHHHCTTTEEEEES-HHHHHH CS
                   CoA_binding   2 kdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevl...glpvyksvdeleektevdvavitvPaesaqe 77 
                                   kd+ ++viG g +g+a ++++k+    g+++++g  p+ ++ +     g +v+ +++e+ ek  +d+  i++P e   +
  gi|15669738|ref|NP_248551.1|  34 KDKTIAVIGYGSQGRAQALNMKDS---GLNVIVGLRPNGASWNKAikdGHKVM-TIEEAAEK--ADIIHILIPDEVQPA 106
                                   7999********999988887766...9**********7775555778*****.********..999888888876555 PP

>> YfaZ  YfaZ precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.6e-05      0.11      54     123 ..     172     241 ..     157     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.6e-05
                          YfaZ  54 rsDddGdvagvglglnlpvGpltatvGakgvylsadegdeGsavavGgglalaigksfslfgeayyaPee 123
                                     D  Gd ++++lg+   +G  ++ v        ++    G  v + gg++  i  +f    ea yaPe 
  gi|15669738|ref|NP_248551.1| 172 ERDYTGDALQIALGMAKGIGLTKVGVIQTTFREETETDLFGEQVVLCGGVTELIKAAFETLVEAGYAPEM 241
                                   57999****************9999999999999999999****************************96 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0085        17       2      27 ..      38      63 ..      37      81 .. 0.87
   2 ?    3.2   0.0     0.039        78      62      98 ..      84     120 ..      80     130 .. 0.74
   3 ?   -1.4   0.0         1     2e+03      97     132 ..     181     219 ..     173     235 .. 0.79
   4 ?   -3.0   0.0       3.3   6.5e+03     106     120 ..     285     299 ..     245     303 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0085
                                  EEEE--SHHHHHHHHHHHTTT--EEE CS
                NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrl 27
                                  iav+G Gs G a A  +++ g +v +
  gi|15669738|ref|NP_248551.1| 38 IAVIGYGSQGRAQALNMKDSGLNVIV 63
                                  9*****************99988765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.039
                                   -HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-E CS
                NAD_Gly3P_dh_N  62 dlaealkgadiivlvvPsqalrevlkklkgllkkkai 98 
                                    ++ea+++adii + +P ++   v kk  +   ++ +
  gi|15669738|ref|NP_248551.1|  84 TIEEAAEKADIIHILIPDEVQPAVYKKQIEPYLTEGK 120
                                   689*****************99998764443334444 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1
                                   -EEEE---SEET.TTEEHHHHHHHHH-S--...EEEEES CS
                NAD_Gly3P_dh_N  97 ailvsliKGieegtlkllsevieeelkeek...vavlsG 132
                                   +i++ ++KGi   ++ ++++  +ee++++     +vl G
  gi|15669738|ref|NP_248551.1| 181 QIALGMAKGIGLTKVGVIQTTFREETETDLfgeQVVLCG 219
                                   567788999988889999999888888876555566655 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 3.3
                                   EET.TTEEHHHHHHH CS
                NAD_Gly3P_dh_N 106 ieegtlkllseviee 120
                                   i+e++ k ++e+++e
  gi|15669738|ref|NP_248551.1| 285 INEESRKAMKEILKE 299
                                   455566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2128.37
//
Query:       gi|15669739|ref|NP_248552.1|  [L=441]
Description: hypothetical protein MJ_1544 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-37  126.3   0.5    7.4e-37  126.3   0.5    2.2  2  AAA_14    AAA domain
    2.5e-12   47.0   1.5    5.5e-12   45.9   1.5    1.6  1  DUF4143   Domain of unknown function (DUF4143)
  ------ inclusion threshold ------
      0.038   13.7   0.1       0.18   11.5   0.1    1.9  2  AAA_24    AAA domain
        0.1   12.6   0.0       0.75    9.8   0.0    2.4  3  NCD1      NAB conserved region 1 (NCD1)
       0.12   12.0   1.5         20    4.7   0.1    3.2  3  Ras       Ras family


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   0.5   2.1e-40   7.4e-37       2     131 .]      50     174 ..      49     174 .. 0.90
   2 ?   -2.1   0.1         1   3.8e+03      51      59 ..     373     381 ..     335     411 .. 0.48

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 2.1e-40
                        AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqevpewek 81 
                                   +ki+vi G+Rr GKT++l+q+i++++  k++++yin++der+ ++a  e l+ ++l+  l+ ++++ lf+DEiq v++w k
  gi|15669739|ref|NP_248552.1|  50 NKIKVIYGVRRGGKTYFLFQIINKHF--KDDFIYINFEDERLINIALDE-LN-ELLKIaLSIKNTKNLFFDEIQSVDNWDK 126
                                   79************************..9*************9999653.33.33333233356777************** PP

                        AAA_14  82 alkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                   ++++l d+g  +++++tGS+skllskeiatsl+gr  + e+ pl+f+Efl
  gi|15669739|ref|NP_248552.1| 127 FVRRLNDSG--FNIFITGSSSKLLSKEIATSLRGRNLKTEILPLNFKEFL 174
                                   *******99..99************************************7 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1
                        AAA_14  51 kllelilek 59 
                                   +l++++ e+
  gi|15669739|ref|NP_248552.1| 373 ELIQVCYEL 381
                                   233333332 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   1.5   1.5e-15   5.5e-12       2     120 ..     232     378 ..     216     380 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1.5e-15
                                   xxxxxxxxxxxxxxxxx............................................xxxxxxxxxxxxxxxxxxxx RF
                       DUF4143   2 rDirklagvrdpeelrk............................................glverlppwsespnskkrlr 38 
                                   rD+ + + +r+++e++                                             +l++ l+++      k++ +
  gi|15669739|ref|NP_248552.1| 232 RDVVERHSIRNIKEIKVlrnilinlfaneisikkianllkefntkisreciynyleyfsdaYLIFLLNNF----SYKTKTI 308
                                   677777777777777667778888888888888888888899999999**********************....89***** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  39 kspKlyfvDtGLlvallgldkeelledsenkGallEnlVaqeLlkysekegaklyyyrdkngaEvDfvielkggkivpiEv 119
                                   +  Kly++D G+ +  l+++k        nkG++lEnlV+ eL+++  +e+ +l+y ++ +++EvDf+i    ++  +i+v
  gi|15669739|ref|NP_248552.1| 309 SYSKLYVID-GMWNFSLSFSK--------NKGRILENLVFLELRRRGFVENENLFYVKR-KNYEVDFLIFG--ENKELIQV 377
                                   *********.99999887774........67**************98888889998888.59*******84..44456776 PP

                                   x RF
                       DUF4143 120 K 120
                                    
  gi|15669739|ref|NP_248552.1| 378 C 378
                                   5 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.9e-05      0.18       6      47 ..      54      98 ..      50     133 .. 0.69
   2 ?   -0.4   0.0      0.23   8.2e+02     109     130 ..     122     143 ..      91     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.9e-05
                        AAA_24  6 liyGpsgiGKTtlakel.....gpkplfidtekGlksldadkfpdie 47
                                  +iyG    GKT+++ ++     ++++++i++e+   +l ++ +++++
  gi|15669739|ref|NP_248552.1| 54 VIYGVRRGGKTYFLFQIinkhfKDDFIYINFED--ERLINIALDELN 98
                                  8*******************************9..555555554333 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.23
                        AAA_24 109 eefrrllkklqelrknvifiah 130
                                   + + +++++l++ + n+ +++ 
  gi|15669739|ref|NP_248552.1| 122 DNWDKFVRRLNDSGFNIFITGS 143
                                   4567788888888888887775 PP

>> NCD1  NAB conserved region 1 (NCD1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00021      0.75      10      31 ..     184     205 ..     178     222 .. 0.87
   2 ?   -4.3   0.0         5   1.8e+04      15      25 ..     265     275 ..     261     278 .. 0.62
   3 ?   -1.4   0.0      0.69   2.5e+03      33      72 ..     362     401 ..     353     407 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00021
                          NCD1  10 lyrvLqranLlqYydvliaqGG 31 
                                    y  +++a+Ll+Y + +i+ GG
  gi|15669739|ref|NP_248552.1| 184 RYSTIEKAELLKYLNEFIKFGG 205
                                   58899****************9 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 5
                          NCD1  15 qranLlqYydv 25 
                                   + anLl+ +++
  gi|15669739|ref|NP_248552.1| 265 KIANLLKEFNT 275
                                   45777777766 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.69
                          NCD1  33 dveqlleaeeeefleimelvGmaskPLhvrRlqkaLqewv 72 
                                   +v+ l+  e++e++++   +  + k   ++   ka+++ +
  gi|15669739|ref|NP_248552.1| 362 EVDFLIFGENKELIQVCYELNETNKEREIKAYEKAIKDLK 401
                                   6888999999999999988888888888888888888866 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0055        20       3      44 ..      54      95 ..      51     111 .. 0.77
   2 ?    4.7   0.0    0.0059        21      88     157 ..     119     189 ..     102     193 .. 0.89
   3 ?   -1.2   0.1      0.37   1.3e+03      72     110 ..     372     410 ..     367     426 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0055
                                  EEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEET CS
                           Ras  3 vlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievd 44
                                  v+ G +  GKt +l++ ++++Fk++++    +d+   +i +d
  gi|15669739|ref|NP_248552.1| 54 VIYGVRRGGKTYFLFQIINKHFKDDFIYINFEDERLINIALD 95
                                  67799999****************998766555555556555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0059
                                   HTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHT.SEEEEEBTTTTCTHHHHHHHHH CS
                           Ras  88 envkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelg.lkfletSAktnenveeafeell 157
                                   ++v++w + ++r  ++ ++i + G  + l +k+  +  +g++l  e+  l+f e    +n nv++ + ++ 
  gi|15669739|ref|NP_248552.1| 119 QSVDNWDKFVRRLNDSGFNIFITGSSSKLLSKEIATSLRGRNLKTEILpLNFKEFLKFKNFNVKKRYSTIE 189
                                   6788999999999999***************9999999*******9999******9999****99988875 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.37
                                   ESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEE CS
                           Ras  72 aegillvyditsresfenvkkwveeikrvaeenvpivLv 110
                                    e i ++y++++++  +++k + + ik+ + +nv++ ++
  gi|15669739|ref|NP_248552.1| 372 KELIQVCYELNETNKEREIKAYEKAIKDLKLDNVNLKII 410
                                   566779999999999999999999999988888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 3475.61
//
Query:       gi|15669740|ref|NP_248553.1|  [L=241]
Description: hypothetical protein MJ_1545 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-10   41.2   0.1    4.4e-10   39.5   0.0    1.9  2  HTH_3           Helix-turn-helix
    2.2e-05   24.4   1.1    0.00049   20.1   0.1    2.8  3  HTH_19          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.021   13.6   0.0      0.032   13.0   0.0    1.2  1  Aminotran_MocR  Alanine-glyoxylate amino-transferase
      0.025   14.9   0.0      0.039   14.3   0.0    1.3  1  HTH_31          Helix-turn-helix domain
       0.09   12.6   0.1       0.34   10.7   0.1    1.9  2  DRTGG           DRTGG domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   1.2e-13   4.4e-10       1      46 [.      32      78 ..      32      81 .. 0.94
   2 ?   -2.6   0.0       1.7   6.2e+03      11      24 ..      91     104 ..      86     105 .. 0.59

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.2e-13
                                  HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHH CS
                         HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklak 46
                                  lk++R+  +++q eLA++l+vs+s is++E G + nP + ++kk+  
  gi|15669740|ref|NP_248553.1| 32 LKKWRNLFNIQQIELAKYLNVSPSVISDYEVGrRKNPGVNIIKKYVL 78
                                  89****************************************99865 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                                   HHHHHHHHHTSSHH CS
                         HTH_3  11 sqeeLAeklGvsrs 24 
                                   +++ L + l+ s+s
  gi|15669740|ref|NP_248553.1|  91 TIKALKRILDKSPS 104
                                   45566666666665 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   1.4e-07   0.00049       1      52 [.      29      80 ..      29      86 .. 0.95
   2 ?   -1.2   0.0       0.6   2.1e+03      11      34 ..      88     116 ..      82     123 .. 0.68
   3 ?    1.6   0.0      0.08   2.9e+02      36      56 ..     204     224 ..     199     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.4e-07
                        HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaeal 52
                                  G+ Lk+ R  +++ q ela+ l +s+s is +E g++++p+ + ++k++ al
  gi|15669740|ref|NP_248553.1| 29 GKALKKWRNLFNIQQIELAKYLNVSPSVISDYEVGRRKNPGVNIIKKYVLAL 80
                                  899********************************999*******9998765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.6
                        HTH_19  11 lgltqeelaerlgis.....rskisaiEn 34 
                                    g t+++l + l+ s     + +i ++En
  gi|15669740|ref|NP_248553.1|  88 GGQTIKALKRILDKSpsmkaILSIKEYEN 116
                                   45588888888888855555556666666 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.08
                        HTH_19  36 kkdvpsaelllkiaealgid.l 56 
                                   +kd+++ +l lk+ae+ +i+ +
  gi|15669740|ref|NP_248553.1| 204 NKDKID-SLALKLAEIDNIPlI 224
                                   677775.899*********944 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.9e-06     0.032     140     186 ..      72     118 ..      67     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.9e-06
                                   HHHHHT-EEEEEEEETTEE-HHHHHHHHHC-TTEEEEEE-SSS-TTT CS
                Aminotran_MocR 140 lleelGielltvdlqddGpdvdaveklvaedasvkGilavpkysnpt 186
                                   +++++ + l+ +d ++ G  ++a++++  + +s+k il++ +y np 
  gi|15669740|ref|NP_248553.1|  72 IIKKYVLALIEIDKEKGGQTIKALKRILDKSPSMKAILSIKEYENPI 118
                                   78889999*************************************95 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.1e-05     0.039       3      45 ..      29      71 ..      28     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                        HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspa 45
                                  G  L+ +R+  ++ q e+A+ l+vs+s +s++E Grr +p   
  gi|15669740|ref|NP_248553.1| 29 GKALKKWRNLFNIQQIELAKYLNVSPSVISDYEVGRRKNPGVN 71
                                  6678899999999999*********************988655 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.47   1.7e+03       3      26 ..     124     147 ..     122     156 .. 0.73
   2 ?   10.7   0.1   9.5e-05      0.34      72     104 ..     207     239 ..     182     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.47
                                   HHHTT-EEEE--..SS--E-EEEE CS
                         DRTGG   3 aealgaevlnggeeelrrvekvvv 26 
                                   ++++++e+ +g+++++   +++vv
  gi|15669740|ref|NP_248553.1| 124 VNIIDGEIAVGDNSDTPIYGHTVV 147
                                   789999999999766655555554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 9.5e-05
                                   ---HHHHHHHHHHT--EEE-SS-HHHHHHHHHT CS
                         DRTGG  72 epseevlklaeeaglpvlsveldtfttakrinq 104
                                   ++++  lklae  ++p+++++ldt + +kr+n+
  gi|15669740|ref|NP_248553.1| 207 KIDSLALKLAEIDNIPLITTHLDTKELIKRLNE 239
                                   577778999**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1363.48
//
Query:       gi|15669741|ref|NP_248554.1|  [L=345]
Description: hypothetical protein MJ_1546 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-11   42.0   0.0    2.5e-10   40.4   0.0    1.8  2  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    2.1e-05   24.0   0.1    3.4e-05   23.3   0.1    1.2  1  Thiolase_N      Thiolase, N-terminal domain
     0.0001   22.0   0.2      0.006   16.2   0.0    2.1  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
    0.00012   22.0   0.1    0.00016   21.6   0.1    1.2  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
      0.001   18.9   0.9     0.0027   17.5   0.9    1.7  1  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
  ------ inclusion threshold ------
      0.039   13.1   0.1      0.057   12.5   0.1    1.2  1  Phosphatase     Phosphatase


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.6   1.1e+04       1      14 [.      62      75 ..      62      77 .. 0.82
   2 !   40.4   0.0   8.5e-14   2.5e-10       1      81 [.     218     298 ..     218     304 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.6
                                  HHHTT--GGG-SEE CS
                 ACP_syn_III_C  1 Lekagltpedidal 14
                                  L++a+++p+di a+
  gi|15669741|ref|NP_248554.1| 62 LKRAEIDPKDIGAV 75
                                  68899999999876 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 8.5e-14
                                   HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEET CS
                 ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvllvgfGa 79 
                                   +ek g +ped d++v+hq n +++  vak lg++ee++ + l    +Gnt +  +pl L++ ++  + + g+++l v+ G 
  gi|15669741|ref|NP_248554.1| 218 MEKMGTKPEDYDYCVFHQPNGKFYIRVAKILGFKEEQYKIGLltPYIGNTYSGAVPLGLSNVLD--NCEGGERILAVSYGS 296
                                   57899*******************************77666655899*****************..89**********999 PP

                                   TT CS
                 ACP_syn_III_C  80 Gl 81 
                                   G 
  gi|15669741|ref|NP_248554.1| 297 GA 298
                                   96 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   1.1e-08   3.4e-05      24     113 ..      51     140 ..      45     152 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.1e-08
                                   HHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSH CS
                    Thiolase_N  24 eeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaagea 104
                                     ++ ea++++l++a++dp+++  v+vG   +  + +  a  +a +++   + +a  ++ +c  g +++ ++++ + +g +
  gi|15669741|ref|NP_248554.1|  51 ATIAVEAARNALKRAEIDPKDIGAVYVGSESHPYAVKPTATIVAEAIDATPDLTAADLEFACKAGTAGIQMCMGLVESGLI 131
                                   56778999************************************************************************* PP

                                   SEEEEEEEE CS
                    Thiolase_N 105 dvvvagGvE 113
                                   +  +a+G+ 
  gi|15669741|ref|NP_248554.1| 132 KYGLAIGAD 140
                                   *******86 PP

>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.014        41      65      82 ..     223     240 ..     204     251 .. 0.72
   2 !   16.2   0.0     2e-06     0.006     150     209 ..     260     315 ..     241     333 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.014
                                   --GGG-SEEEE--SSHHH CS
                HMG_CoA_synt_C  65 ftlddfdyvifhsPfckl 82 
                                   +  +d+dy++fh P  k+
  gi|15669741|ref|NP_248554.1| 223 TKPEDYDYCVFHQPNGKF 240
                                   455899********9986 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2e-06
                                   HHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STTS CS
                HMG_CoA_synt_C 150 vptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvseds 209
                                   ++  +Gn Y  ++   l  +l    +++  g+ri++ sYGsG  +  f ++v++  ++ +
  gi|15669741|ref|NP_248554.1| 260 LTPYIGNTYSGAVPLGLSNVL----DNCEGGERILAVSYGSGAGSDAFDITVTDRINKVK 315
                                   455689999999988888888....777788**********************9988744 PP

>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   5.5e-08   0.00016       6     171 ..       3     165 ..       1     168 [. 0.92

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.5e-08
                HMG_CoA_synt_N   6 gilaleiylpaqyvdqaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrlevgtetii 86 
                                   gi++   y+p   ++  e+ +  + +      gl   + +  s  ed  ++++   ++ l+r ++d + ig + vg+e+  
  gi|15669741|ref|NP_248554.1|   3 GIVGYGAYIPKYRIKVEEIARVWNKDPESIKKGLLVYEKAVPSLDEDTATIAVEAARNALKRAEIDPKDIGAVYVGSESHP 83 
                                   8999999****99******9999999999999*999999****************************************99 PP

                HMG_CoA_synt_N  87 dksksvksvlmqlfeesgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsgna.rptggagava 166
                                      k   +++ + ++     d+   d   ac  gta +  ++  +es     +y l +  d a  + g+a   t  ag  a
  gi|15669741|ref|NP_248554.1|  84 YAVKPTATIVAEAIDA--TPDLTAADLEFACKAGTAGIQMCMGLVESGLI--KYGLAIGADTAQGAPGDAlEYTAAAGGAA 160
                                   9999999999999887..78***************************986..799999******99998835689999999 PP

                HMG_CoA_synt_N 167 lligp 171
                                    +ig 
  gi|15669741|ref|NP_248554.1| 161 YIIGK 165
                                   99986 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.9   8.9e-07    0.0027       2      64 ..     107     166 ..     106     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.9e-07
                                   EEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-EEEEEEEEEEE CS
                   ACP_syn_III   2 DlnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGDGAgAvvleas 64 
                                   Dl+ aC++ ++++++  +l+esg +k+ L iga+t          +  ++ + G++A ++++s
  gi|15669741|ref|NP_248554.1| 107 DLEFACKAGTAGIQMCMGLVESGLIKYGLAIGADTAQG---APGDALEYTAAAGGAAYIIGKS 166
                                   8999*******************************766...3445666677788888888776 PP

>> Phosphatase  Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.9e-05     0.057     165     208 ..      81     121 ..      41     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                   Phosphatase 165 aHtHsplpvravlaelaeageelPdLvvaDHGwagaAgqagiea 208
                                    H +  +p  +++   aea +++PdL  aD  +a+ Ag agi+ 
  gi|15669741|ref|NP_248554.1|  81 SHPYAVKPTATIV---AEAIDATPDLTAADLEFACKAGTAGIQM 121
                                   4555555555555...5555689*******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2117.32
//
Query:       gi|15669742|ref|NP_248555.1|  [L=122]
Description: hypothetical protein MJ_1547 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-11   43.8   0.6      6e-11   42.3   0.3    1.9  2  Polbeta       Polymerase beta, Nucleotidyltransferase
    9.1e-10   38.7   0.2    1.2e-09   38.3   0.2    1.3  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.3   6.7e-15     6e-11      15      90 ..       6      73 ..       2      76 .. 0.87
   2 ?   -1.1   0.0      0.23     2e+03      43      59 ..      79      95 ..      72     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 6.7e-15
                                  STTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS-EEEES- CS
                       Polbeta 15 laylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeilkegkllysk 90
                                   ++l+GS+ak++++++SDiD++++  ++   +++le+  +l      +k D+ +++e p++++ ei+k+ k+++  
  gi|15669742|ref|NP_248555.1|  6 GILLYGSYAKNEYTKRSDIDICLVGVDR---NTYLEILGKLG-----NKYDIKIFEELPLYIKMEIIKNHKVIFGD 73
                                  689**********************999...66666666555.....669***********************975 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.23
                                  --HHHHHHHHHHHHHH. CS
                       Polbeta 43 ldleeelelaaeledik 59
                                  +++++  +++ ++e++ 
  gi|15669742|ref|NP_248555.1| 79 EHFYKFRKIWRDMEKRI 95
                                  45677777888877772 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.2   1.4e-13   1.2e-09      14      89 ..       4      97 ..       1     111 [. 0.81

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.4e-13
                                  TSEEEEEHHHHCTTSCTTSSEEEEEEE.STTCHHH.............HHHEHHHHHHHHCCCEEECTTEEEEEE....CEEE CS
                  NTP_transf_2 14 vakvvlfGSyarGtalkgSDiDllvvl.peevsre.............kkeegleklaeiikfleellglevdlv....trek 78
                                  v  + l+GSya+++++k SDiD+++v+ +++++ e             + e  l+ ++eiik+++ ++g e  l+        
  gi|15669742|ref|NP_248555.1|  4 VFGILLYGSYAKNEYTKRSDIDICLVGvDRNTYLEilgklgnkydikiFEELPLYIKMEIIKNHKVIFGDELELSehfyK--- 83
                                  56789******************998626666666***********99777778999****************9985542... PP

                                  CCC...CTEEEEEE CS
                  NTP_transf_2 79 led...pllvksil 89
                                  +++   ++ +++++
  gi|15669742|ref|NP_248555.1| 84 FRKiwrDMEKRIRE 97
                                  44444466666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 757.11
//
Query:       gi|15669743|ref|NP_248556.1|  [L=122]
Description: hypothetical protein MJ_1548 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-14   53.4   0.7    2.8e-14   53.0   0.7    1.2  1  DUF86        Protein of unknown function DUF86
     0.0044   17.1   0.4     0.0062   16.6   0.4    1.2  1  DUF4145      Domain of unknown function (DUF4145)
  ------ inclusion threshold ------
      0.019   15.2   0.2      0.034   14.3   0.2    1.3  1  COG5         Golgi transport complex subunit 5
      0.026   13.3   0.1      0.028   13.2   0.1    1.1  1  Calici_PP_N  Viral polyprotein N-terminal
      0.038   13.6   0.2      0.044   13.4   0.2    1.2  1  DUF4795      Domain of unknown function (DUF4795)


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.7   7.7e-18   2.8e-14      33     116 ..      11      94 ..       2      97 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 7.7e-18
                                   HHHHHHHHHHHHHHHHHHHTT----SSC.HHHHHHHTTSS-HHHHHHHHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHH CS
                         DUF86  33 nlqvigEaaidiakhlakklgikkpgdy.ifeilaekgviaeepeepwrkmiglRNrLvHgYlgidpeivwsiikenlpdl 112
                                    lqv+++ ++d+ ++l+k+ g+  ++dy  +++l +++vi+++++  +++ ++lRN++vH+Y ++++e v + +k+ +++l
  gi|15669743|ref|NP_248556.1|  11 SLQVCVDITMDVVAMLVKDIGLNVEDDYtNIKKLLKHDVITKDEATLLKQYNRLRNAIVHKYDKLNLEVVKEGLKR-IDEL 90 
                                   79************************************************************************98.8999 PP

                                   HHHH CS
                         DUF86 113 eefl 116
                                    e++
  gi|15669743|ref|NP_248556.1|  91 YEIA 94 
                                   8876 PP

>> DUF4145  Domain of unknown function (DUF4145)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.4   1.7e-06    0.0062      24      85 ..      25      85 ..      15      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                       DUF4145 24 kllkdkgiakgkdLknkiealvekgvipeklkelldairviGNdgaHelkditkedaedlle 85
                                  +l+kd g + + d +++i++l +++vi+++ + ll++   ++N+ +H++++++ e +++ l+
  gi|15669743|ref|NP_248556.1| 25 MLVKDIGLNVE-DDYTNIKKLLKHDVITKDEATLLKQYNRLRNAIVHKYDKLNLEVVKEGLK 85
                                  67777776665.5599********************************9**99988877766 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   9.4e-06     0.034      83     127 ..      56     102 ..      42     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.4e-06
                                   XXXXXXXXXX-TTHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHH CS
                          COG5  83 sLsasyerlkskvlepyeea..eklqsalkrlhqtldLlrralrflh 127
                                    L + y+rl++ ++ +y+++  e +++ lkr+ + ++++++++r++ 
  gi|15669743|ref|NP_248556.1|  56 TLLKQYNRLRNAIVHKYDKLnlEVVKEGLKRIDELYEIAYESMRVMK 102
                                   57789************97622678899***************9985 PP

>> Calici_PP_N  Viral polyprotein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.8e-06     0.028     213     276 ..      10      73 ..       4     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-06
                   Calici_PP_N 213 fhlqgpedlardlvpivlggiglaigftrdkvskmmknavdglraatqlgqygleifsllkkyf 276
                                   + lq   d++ d+v +++  igl +     ++ k++k  v     at l qy     ++++ky 
  gi|15669743|ref|NP_248556.1|  10 ISLQVCVDITMDVVAMLVKDIGLNVEDDYTNIKKLLKHDVITKDEATLLKQYNRLRNAIVHKYD 73 
                                   5689999*********************************************988888888884 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   1.2e-05     0.044     104     151 ..      50      96 ..      14     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                       DUF4795 104 leeqeealkkaldtLqeelkekldrlelepLkeqleerlkelqkelqe 151
                                   +++ e+ l k ++ L++++ +k d+l+le +ke l+ r++el +   e
  gi|15669743|ref|NP_248556.1|  50 ITKDEATLLKQYNRLRNAIVHKYDKLNLEVVKEGLK-RIDELYEIAYE 96 
                                   6799*******************************8.66666654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 823.19
//
Query:       gi|15669744|ref|NP_248557.1|  [L=392]
Description: acetyl-CoA acetyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-28   98.3   0.4    4.7e-28   98.3   0.4    1.8  2  Thiolase_N       Thiolase, N-terminal domain
    6.2e-12   45.3   0.3    4.8e-11   42.4   0.1    2.3  2  Thiolase_C       Thiolase, C-terminal domain
    2.4e-08   33.9   4.3    4.8e-07   29.6   2.7    2.6  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    9.5e-06   25.4   0.7     0.0013   18.6   0.4    2.4  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
     0.0015   18.5   0.5      0.087   12.8   0.1    2.9  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.4   1.3e-31   4.7e-28       1     259 [.       4     221 ..       4     222 .. 0.95
   2 ?   -3.4   0.1       1.4   4.9e+03      22      46 ..     255     279 ..     240     283 .. 0.65

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 1.3e-31
                                   EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-TTSEEE CS
                    Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipeevpav 79 
                                   v+i++   t++g+    l + s + L  ea+ +++e ag+d +++de++vGn+ ++ + gq  ia  +a +ag+ +++p++
  gi|15669744|ref|NP_248557.1|   4 VAIIGYGQTKFGE----LWERSFRSLIVEAGVKAVEAAGIDGKDIDEMYVGNMSAGlFVGQEhIASLIAEHAGL-NPIPST 79 
                                   7899999999999....99999999*************************************9***********.****** PP

                                   EEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHH CS
                    Thiolase_N  80 tvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGltae 160
                                   +v+ +c+Sg  a+ +a+ ++a+g++dvv++gGvE+m+++  a+s ++ s   ++ e + + + p+           ++ a+
  gi|15669744|ref|NP_248557.1|  80 RVEAACASGSLALRQAVLNVASGASDVVLVGGVEKMTDVVDATS-AISSASDQEWEALFGATFPS---------LYAMMAQ 150
                                   ***************************************99998.88888888899999******.........999**** PP

                                   HHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-BT CS
                    Thiolase_N 161 nlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvtA 241
                                   ++  +y+++ ee+  + v  h++a+++  a+ F  ++              + ++ ++s+ +ae+L+ l            
  gi|15669744|ref|NP_248557.1| 151 RYMYEYGLTLEELSMWSVIMHENASKNRYAQ-FPFKV--------------TLEQVLNSSPVAEPLRLL------------ 204
                                   *******************************.76655..............678899999*********............ PP

                                   TSB--BEEEEEEEEEEEH CS
                    Thiolase_N 242 gnasqisDGaaavllmse 259
                                     +s++sDGaaa++++++
  gi|15669744|ref|NP_248557.1| 205 -HCSPVSDGAAALIVCEA 221
                                   .9*************986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.4
                                   -HHHHHHHHHHHHHHHHTS-GGGCC CS
                    Thiolase_N  22 saeeLlaealkallekagvdpeevd 46 
                                   ++ + ++ a +++ + a+++p++vd
  gi|15669744|ref|NP_248557.1| 255 TSLKAAKVASEKAYKMANIEPKDVD 279
                                   3334445566777777888888877 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.18   6.6e+02      27      47 ..      29      49 ..      22      74 .. 0.81
   2 !   42.4   0.1   1.3e-14   4.8e-11      24     102 ..     260     358 ..     236     383 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.18
                                  HHHHHHHHHT--GGGESEEEE CS
                    Thiolase_C 27 aikkvlkkagltvedidlfEi 47
                                  a  k+++ ag++ +did + +
  gi|15669744|ref|NP_248557.1| 29 AGVKAVEAAGIDGKDIDEMYV 49
                                  667999**********97755 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 1.3e-14
                                   HHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G....................GGBSTT--HHHH-B-TTT CS
                    Thiolase_C  24 PayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl....................ekvNvnGGaialGHPlGa 84 
                                      a++k+ k a ++ +d+d+ E+++ Fa   L  +++l++ +                      vN  GG  a GH lGa
  gi|15669744|ref|NP_248557.1| 260 AKVASEKAYKMANIEPKDVDVAEVHDCFAINGLILMEELGFCKkgeagkivydkkiaidydgfPAVNPSGGLKAAGHALGA 340
                                   567999***********************************999*******************9***************** PP

                                   HHHHHHHHHHHHHHHCTT CS
                    Thiolase_C  85 sGaRivvtllselkkegg 102
                                   +G R+v  +  +lk++++
  gi|15669744|ref|NP_248557.1| 341 TGIRQVGEIYWQLKQDKE 358
                                   **************9764 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.014        50      90     119 ..      24      53 ..      20      71 .. 0.75
   2 !   29.6   2.7   1.3e-10   4.8e-07     153     208 ..      62     118 ..      54     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.014
                                   HHHHHHHHHHHHHHTS-HHTCTTGGEEEEE CS
                 ketoacyl-synt  90 rllleaawealedagltpeeldgsrvgvfi 119
                                    l +ea  +a+e ag++ +++d+  vg++ 
  gi|15669744|ref|NP_248557.1|  24 SLIVEAGVKAVEAAGIDGKDIDEMYVGNMS 53 
                                   58899****************887765543 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1.3e-10
                                   HHHHHHHHHHT--S.SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SH CS
                 ketoacyl-synt 153 viagrisyalglrG.psvtvdtACsSslvavhaavqslrsgeadvalaGGvellltp 208
                                    ia+ i+ + gl   ps  v++AC+S+  a+ +av ++ sg +dv+l+GGve ++  
  gi|15669744|ref|NP_248557.1|  62 HIASLIAEHAGLNPiPSTRVEAACASGSLALRQAVLNVASGASDVVLVGGVEKMTDV 118
                                   6777888888887548999*********************************99865 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.4   3.5e-07    0.0013       3      45 ..      81     123 ..      80     139 .. 0.86
   2 !    4.4   0.0    0.0094        34      51      68 ..     208     225 ..     195     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.5e-07
                                   EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTT CS
                   ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkd 45 
                                   ++aaC++   al +A   ++sga   vLv g e++++++D + 
  gi|15669744|ref|NP_248557.1|  81 VEAACASGSLALRQAVLNVASGASDVVLVGGVEKMTDVVDATS 123
                                   689*************************************973 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0094
                                   TB-EEEEEEEEEEESSSS CS
                   ACP_syn_III  51 lfGDGAgAvvleaseeeg 68 
                                    ++DGA+A+++ + e+ +
  gi|15669744|ref|NP_248557.1| 208 PVSDGAAALIVCEAEKAK 225
                                   579*******98875443 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.8   6.5e+03      32      45 ..      32      45 ..      27      51 .. 0.81
   2 !   12.8   0.1   2.4e-05     0.087      18      51 ..     252     285 ..     228     287 .. 0.83
   3 ?    2.6   0.0     0.038   1.4e+02      87     109 ..     334     356 ..     331     364 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.8
                                  HHHHHHT--GGGEE CS
               Ketoacyl-synt_C 32 kalaeagvdpedvd 45
                                  ka++ ag+d +d+d
  gi|15669744|ref|NP_248557.1| 32 KAVEAAGIDGKDID 45
                                  78899999999997 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.4e-05
                                   STSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS CS
               Ketoacyl-synt_C  18 ltapngeaqaraiekalaeagvdpedvdyveahg 51 
                                       + +a++ a eka+++a+++p+dvd+ e h+
  gi|15669744|ref|NP_248557.1| 252 ESITSLKAAKVASEKAYKMANIEPKDVDVAEVHD 285
                                   444568899999********************97 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.038
                                   H-B-GGGHHHHHHHHHHHHHHHT CS
               Ketoacyl-synt_C  87 iGHleaAaGvaelikvvlalkhg 109
                                    GH+++A G+ ++  +  +lk++
  gi|15669744|ref|NP_248557.1| 334 AGHALGATGIRQVGEIYWQLKQD 356
                                   6***********99999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2784.00
//
Query:       gi|15669745|ref|NP_248558.1|  [L=61]
Description: hypothetical protein MJ_1550 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 422.85
//
Query:       gi|15669746|ref|NP_248559.1|  [L=57]
Description: hypothetical protein MJ_1551 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-20   71.7   4.5      5e-20   71.5   4.5    1.0  1  CooT      CO dehydrogenase accessory protein CooT
  ------ inclusion threshold ------
      0.067   13.2   2.3       0.21   11.6   0.1    2.1  2  KOW       KOW motif
       0.08   13.1   0.4       0.11   12.7   0.2    1.4  1  SpoVG     SpoVG


Domain annotation for each model (and alignments):
>> CooT  CO dehydrogenase accessory protein CooT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   4.5   8.4e-24     5e-20       1      61 []       1      56 [.       1      56 [. 0.97

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 8.4e-24
                          CooT  1 MCeanvyllkngkeeelvmedVdkiepeedgvvltdifGeekevegkIkeidLvehkiile 61
                                  MC +n+y+     ++elvmedV+ +e+++d+v+++d+fG++ke+ g+Ik+idL+e+ki++e
  gi|15669746|ref|NP_248559.1|  1 MCSCNLYF-----NGELVMEDVMIVEKKGDKVIAIDLFGDKKEFVGEIKKIDLNENKIFIE 56
                                  *******9.....568*******************************************97 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4     0.052   3.1e+02      18      28 ..      18      28 ..      16      31 .. 0.70
   2 ?   11.6   0.1   3.6e-05      0.21      13      32 .]      37      56 ..      32      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.052
                                  EEEEEETTTTE CS
                           KOW 18 kVvkvdqhkvr 28
                                  ++v+   +kv+
  gi|15669746|ref|NP_248559.1| 18 MIVEKKGDKVI 28
                                  77877777754 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.6e-05
                                  TTCEEEEEEEETTTTEEEEE CS
                           KOW 13 kGktGkVvkvdqhkvrVfvd 32
                                  k ++G+++k+d + +++f++
  gi|15669746|ref|NP_248559.1| 37 KEFVGEIKKIDLNENKIFIE 56
                                  679***************97 PP

>> SpoVG  SpoVG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   1.8e-05      0.11      21      46 ..       4      29 ..       1      49 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                         SpoVG 21 asvtlddsfvirdikiiegkkglfva 46
                                  +++ +++++v++d++i+e+k + ++a
  gi|15669746|ref|NP_248559.1|  4 CNLYFNGELVMEDVMIVEKKGDKVIA 29
                                  8899**************88776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.30u 0.24s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 458.00
//
Query:       gi|15669747|ref|NP_248560.1|  [L=141]
Description: hypothetical protein MJ_1552 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-24   84.0   0.0    7.5e-24   83.5   0.0    1.2  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    8.8e-10   38.3   2.3    1.3e-09   37.7   2.3    1.3  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.002   18.0   2.6       0.68    9.9   0.2    2.5  2  zinc_ribbon_4  zinc-ribbon domain
  ------ inclusion threshold ------
      0.029   14.5   2.6      0.063   13.5   2.6    1.6  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
      0.067   13.2   1.5       0.12   12.5   1.5    1.4  1  DZR            Double zinc ribbon
       0.14   12.1   1.0       0.24   11.4   1.0    1.4  1  HypA           Hydrogenase/urease nickel incorporation, metal
       0.34   10.8   0.2       0.34   10.8   0.2    2.0  2  zf-C2H2_3      zinc-finger of acetyl-transferase ESCO
        1.3    8.5   4.8        3.6    7.1   4.8    1.6  1  zf-ribbon_3    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   0.0   3.4e-27   7.5e-24       3      65 .]      57     119 ..      55     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 3.4e-27
                                   EE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                 OB_aCoA_assoc   3 elsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                    lsg+G+vy+++vvh ap  f+++aPyv++++eL+eg ri++++v++ p++v iGm V+avfr
  gi|15669747|ref|NP_248560.1|  57 KLSGKGKVYTYSVVHVAPKDFEKQAPYVIAIIELEEGARITGQIVDCKPEDVYIGMQVEAVFR 119
                                   79************************************************************7 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   2.3   5.8e-13   1.3e-09       5      34 ..      21      50 ..      17      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 5.8e-13
                       DUF35_N  5 aegrLvgqrCpdCGtvqfPPravCphCgsd 34
                                   ++ L+g rC++CGtv+fP r +Cp+C+++
  gi|15669747|ref|NP_248560.1| 21 ERYCLIGVRCKNCGTVYFPSREICPKCRRK 50
                                  566699*********************654 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.2    0.0003      0.68      26      35 ..      28      37 ..      26      38 .. 0.71
   2 !    7.6   0.2    0.0015       3.5       5      24 ..      44      63 ..      43      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0003
                 zinc_ribbon_4 26 vrCskCghvF 35
                                  vrC++Cg+v 
  gi|15669747|ref|NP_248560.1| 28 VRCKNCGTVY 37
                                  7777777764 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0015
                 zinc_ribbon_4  5 CpsCkakyeiddeklpakgv 24
                                  Cp+C  k e+++ kl++kg+
  gi|15669747|ref|NP_248560.1| 44 CPKCRRKTEFEEIKLSGKGK 63
                                  ***************99986 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.6   2.8e-05     0.063      11      39 ..      23      47 ..      19      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-05
                 Auto_anti-p27 11 wtMLaetCpvCgvPLmrdrkggkvyCvaC 39
                                  +++ +  C++Cg++ + +r   + +C+ C
  gi|15669747|ref|NP_248560.1| 23 YCLIGVRCKNCGTVYFPSR---E-ICPKC 47
                                  889999***********86...4.***** PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.5   5.2e-05      0.12      30      48 ..      29      47 ..      15      55 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-05
                           DZR 30 rCpsCgekvdpearfCpeC 48
                                  rC +Cg+   p  ++Cp+C
  gi|15669747|ref|NP_248560.1| 29 RCKNCGTVYFPSREICPKC 47
                                  5555555555555555555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.0   0.00011      0.24      70      95 ..      27      50 ..      12      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                  EEEETTTS-EEECHHHHHS-TTTSSS CS
                          HypA 70 kvrCreCgkefeleekalrCpkCgsa 95
                                   vrC++Cg+ +  +++   CpkC ++
  gi|15669747|ref|NP_248560.1| 27 GVRCKNCGTVYFPSRE--ICPKCRRK 50
                                  589*****99987744..7****875 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00015      0.34      14      26 ..      28      40 ..      24      43 .. 0.86
   2 ?    0.0   0.1      0.34   7.6e+02      15      19 ..      42      47 ..      38      48 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                     zf-C2H2_3 14 sqCkeCgMvYnpg 26
                                  ++Ck+Cg vY p+
  gi|15669747|ref|NP_248560.1| 28 VRCKNCGTVYFPS 40
                                  68********998 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.34
                     zf-C2H2_3 15 q.CkeC 19
                                  + C++C
  gi|15669747|ref|NP_248560.1| 42 EiCPKC 47
                                  35**** PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.8    0.0016       3.6       3      22 ..      28      47 ..      27      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0016
                   zf-ribbon_3  3 vrCPnCGaplssddnvCpyC 22
                                  vrC nCG++  ++  +Cp+C
  gi|15669747|ref|NP_248560.1| 28 VRCKNCGTVYFPSREICPKC 47
                                  79******88********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 938.27
//
Query:       gi|15669748|ref|NP_248561.1|  [L=157]
Description: ArsR family transcriptional regulator [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-18   64.1   0.4    1.1e-17   63.5   0.4    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
    1.4e-06   28.1   0.2    2.9e-06   27.1   0.2    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    3.2e-06   26.6   0.2    5.7e-06   25.8   0.2    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    4.9e-06   26.5   0.0    7.3e-06   26.0   0.0    1.2  1  HTH_20          Helix-turn-helix domain
    9.9e-06   25.4   1.1    0.00048   19.9   0.1    2.4  2  DUF4364         Domain of unknown function (DUF4364)
    2.8e-05   24.2   0.2    7.7e-05   22.8   0.2    1.8  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    2.8e-05   23.9   0.2    4.4e-05   23.2   0.2    1.3  1  HxlR            HxlR-like helix-turn-helix
    4.7e-05   23.8   0.0    8.5e-05   23.0   0.0    1.4  1  HTH_27          Winged helix DNA-binding domain
    9.6e-05   22.1   0.0    0.00015   21.5   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
    0.00011   22.1   0.1    0.00018   21.3   0.1    1.3  1  MarR            MarR family
    0.00033   20.6   4.6    0.00033   20.6   4.6    1.5  1  HTH_45          Winged helix-turn-helix
    0.00055   19.8   0.0    0.00093   19.0   0.0    1.3  1  MarR_2          MarR family
    0.00055   19.6   0.2     0.0011   18.7   0.2    1.4  1  HTH_38          Helix-turn-helix domain
    0.00058   19.8   0.2    0.00091   19.1   0.2    1.4  1  HTH_11          HTH domain
    0.00067   19.7   0.3     0.0015   18.5   0.2    1.7  1  HTH_3           Helix-turn-helix
     0.0008   19.2   0.0     0.0014   18.4   0.0    1.4  1  HTH_10          HTH DNA binding domain
    0.00092   19.3   2.6      0.053   13.6   0.2    2.5  2  DUF2250         Uncharacterized protein conserved in archaea 
     0.0018   18.7   0.2     0.0022   18.4   0.2    1.3  1  HTH_40          Helix-turn-helix domain
     0.0028   17.9   0.3     0.0081   16.4   0.3    1.8  1  NUMOD1          NUMOD1 domain
     0.0035   17.1   0.0     0.0074   16.1   0.0    1.5  1  HTH_23          Homeodomain-like domain
     0.0046   16.7   0.3      0.032   14.1   0.3    2.2  1  DUF1495         Winged helix DNA-binding domain (DUF1495)
     0.0049   15.3   0.4     0.0059   15.0   0.4    1.2  1  DUF505          Protein of unknown function (DUF505)
     0.0055   17.0   0.3     0.0095   16.2   0.3    1.4  1  DUF2513         Hypothetical protein (DUF2513)
     0.0062   16.5   0.3      0.014   15.3   0.3    1.7  1  HTH_36          Helix-turn-helix domain
     0.0069   16.3   0.1      0.036   14.0   0.1    2.0  1  HTH_12          Ribonuclease R winged-helix domain
      0.009   16.1   0.1      0.018   15.2   0.1    1.5  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
     0.0095   16.1   0.4     0.0095   16.1   0.4    1.6  1  HTH_34          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.023   14.7   0.0    1.3  1  HTH_29          Winged helix-turn helix
      0.036   13.8   0.2      0.051   13.3   0.2    1.2  1  DUF4423         Domain of unknown function (DUF4423)
      0.036   14.0   0.0      0.059   13.4   0.0    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.036   13.6   0.0      0.072   12.6   0.0    1.4  1  Sigma70_r4      Sigma-70, region 4
      0.037   14.3   0.2      0.076   13.3   0.2    1.5  1  Mnd1            Mnd1 HTH domain
       0.04   14.1   0.0      0.083   13.1   0.0    1.5  1  HTH_17          Helix-turn-helix domain
      0.043   13.7   0.0      0.076   12.9   0.0    1.4  1  PuR_N           Bacterial purine repressor, N-terminal
      0.054   13.5   0.9       0.13   12.2   0.9    1.7  1  PadR            Transcriptional regulator PadR-like family
      0.055   13.9   0.1       0.11   12.9   0.1    1.5  1  HTH_26          Cro/C1-type HTH DNA-binding domain
      0.074   13.1   0.4       0.23   11.6   0.1    2.0  2  SpoIIID         Stage III sporulation protein D
      0.086   12.6   0.1       0.24   11.2   0.0    1.7  1  LexA_DNA_bind   LexA DNA binding domain
      0.089   13.1   0.1       0.15   12.4   0.1    1.5  1  DUF4476         Domain of unknown function (DUF4476)
        1.7    8.8   8.1          2    8.6   1.9    2.5  2  DUF4234         Domain of unknown function (DUF4234)


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.4   2.6e-20   1.1e-17       2      47 .]       7      52 ..       6      52 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 2.6e-20
                                  HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  +t+++ILk L+e++++++el+++lg+s+st+S+HL++L+e+GLV+k
  gi|15669748|ref|NP_248561.1|  7 KTKIEILKKLNERNYTISELSKILGKSKSTISEHLNALYEMGLVDK 52
                                  89******************************************87 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.2   6.4e-09   2.9e-06      18      63 ..      16      61 ..       2      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 6.4e-09
                                  HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                          TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63
                                  l++ + t++e++++lg ++s++ e L+ L ++GlV++e  ++ +Y 
  gi|15669748|ref|NP_248561.1| 16 LNERNYTISELSKILGKSKSTISEHLNALYEMGLVDKENYSKWVYY 61
                                  468899********************************97766654 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.2   1.3e-08   5.7e-06      10      47 ..      11      50 ..       6      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.3e-08
                        HTH_24 10 elLqk.npr.isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  e+L+k n r  +++eL++ lg S+st++++l+ L e+Gl+
  gi|15669748|ref|NP_248561.1| 11 EILKKlNERnYTISELSKILGKSKSTISEHLNALYEMGLV 50
                                  56666766669***************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.6e-08   7.3e-06       9      56 ..       6      52 ..       2      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.6e-08
                                  -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                  +++  +il+ L  ++  t sel + l+ sk+t+s HL++L e gLv+ 
  gi|15669748|ref|NP_248561.1|  6 SKTKIEILKKL-NERNYTISELSKILGKSKSTISEHLNALYEMGLVDK 52
                                  6778899****.**********************************86 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.1e-06   0.00048      35      77 ..      36      78 ..      12      81 .. 0.92
   2 ?    4.1   0.1     0.078        35       3      30 ..      90     117 ..      88     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-06
                       DUF4364 35 dlqqalseLvesglieeeekenktlykiTekGketlelfenri 77
                                  ++++ l+ L e gl+++e+ ++  +ykiT+kGk++le +e  i
  gi|15669748|ref|NP_248561.1| 36 TISEHLNALYEMGLVDKENYSKWVYYKITNKGKKVLENLEALI 78
                                  58899********************************999766 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.078
                       DUF4364   3 llilYllkkvkfpltnsqlseiileney 30 
                                   l i Y++k++k++  +  ls+ ++e+++
  gi|15669748|ref|NP_248561.1|  90 LWIYYIFKQIKYQAREVVLSKTVVERGI 117
                                   6799********************9885 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.2   1.7e-07   7.7e-05      25      58 ..      23      56 ..      12      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.7e-07
                                  HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                Fe_dep_repress 25 tkdlaerLnvspssVsemlkkLekdGyveyekyk 58
                                   ++l+++L+ s+s++se l+ L ++G+v+ e y+
  gi|15669748|ref|NP_248561.1| 23 ISELSKILGKSKSTISEHLNALYEMGLVDKENYS 56
                                  589**************************99995 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.2   9.8e-08   4.4e-05       5      80 ..       7      78 ..       3      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 9.8e-08
                                  TTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHH CS
                          HxlR  5 kWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelk 80
                                  k k+ il +l + +   sel+++l + s+++++++L +L + gl+++e y++    v Y++t+kG+++ + l++l 
  gi|15669748|ref|NP_248561.1|  7 KTKIEILKKLNERNYTISELSKIL-GKSKSTISEHLNALYEMGLVDKENYSKW---VYYKITNKGKKVLENLEALI 78
                                  6678899*****************.569**********************986...67**********99999986 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.9e-07   8.5e-05       8      68 .]      12      67 ..       6      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.9e-07
                        HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  +L  ++  +r  ++++l++ l  ++s+is+ l++L e+GLv ++ +    + + +++T kG
  gi|15669748|ref|NP_248561.1| 12 ILKKLN--ERNYTISELSKILGKSKSTISEHLNALYEMGLVDKENYS---KWVYYKITNKG 67
                                  666666..788899***************************666665...77999999998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   3.4e-07   0.00015      12      50 ..      16      52 ..      10      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.4e-07
                                  -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  l+e++   t+sel++ +g +kSt + +L+ L e+G+v +
  gi|15669748|ref|NP_248561.1| 16 LNERN--YTISELSKILGKSKSTISEHLNALYEMGLVDK 52
                                  44444..47****************************86 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   4.1e-07   0.00018       2      49 ..       6      52 ..       5      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.1e-07
                                  -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                  + t ++iL +l e+ + ++seL k lg skst+++ l +L++ Gl+++
  gi|15669748|ref|NP_248561.1|  6 SKTKIEILKKLNER-NYTISELSKILGKSKSTISEHLNALYEMGLVDK 52
                                  56788888888765.79*****************************87 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   4.6   7.3e-07   0.00033       9      75 ..      10      80 ..       6      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.3e-07
                        HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdmLvekgli...kk.skekYvlTekGlelleklkeleel 75
                                  ++IL++++e + + +++ +    s +++++ L+ L e gl+   +  +   Y++T+kG+++le+l+ l+ +
  gi|15669748|ref|NP_248561.1| 10 IEILKKLNERNYTISELSKILGKSKSTISEHLNALYEMGLVdkeNYsKWVYYKITNKGKKVLENLEALILM 80
                                  58***************************************753222446799************998765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.1e-06   0.00093      22      54 ..      21      53 ..       8      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.1e-06
                                  EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   t++el + lg sks++s +l+ L + GLv ++
  gi|15669748|ref|NP_248561.1| 21 YTISELSKILGKSKSTISEHLNALYEMGLVDKE 53
                                  59****************************986 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   2.4e-06    0.0011      12      38 ..      12      38 ..       6      42 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.4e-06
                        HTH_38 12 eIerllaeGlslreIArrLgrspsTIs 38
                                   + +l +++++++e  ++Lg+s+sTIs
  gi|15669748|ref|NP_248561.1| 12 ILKKLNERNYTISELSKILGKSKSTIS 38
                                  344555799*****************9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2     2e-06   0.00091       6      45 ..      10      49 ..       6      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2e-06
                        HTH_11  6 lelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                  +e+L++ ++   +++eL++ L+ S++t+  ++ aL e+g  
  gi|15669748|ref|NP_248561.1| 10 IEILKKLNERnYTISELSKILGKSKSTISEHLNALYEMG-L 49
                                  566666666669************************999.2 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   3.4e-06    0.0015       3      28 ..      14      39 ..      12      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.4e-06
                                  HHHHHTTHHHHHHHHHHTSSHHHHHH CS
                         HTH_3  3 elRkqlglsqeeLAeklGvsrstisr 28
                                  ++++++++++ eL++ lG s+stis 
  gi|15669748|ref|NP_248561.1| 14 KKLNERNYTISELSKILGKSKSTISE 39
                                  78899*******************95 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.2e-06    0.0014      22      46 ..      19      43 ..      17      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.2e-06
                        HTH_10 22 RrvtlkeLAkelGIskstlsehLrk 46
                                  R+ t++eL+k+lG skst+sehL++
  gi|15669748|ref|NP_248561.1| 19 RNYTISELSKILGKSKSTISEHLNA 43
                                  899********************85 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2   0.00012     0.053       9      56 ..       8      54 ..       3      59 .. 0.81
   2 ?    6.3   0.1     0.023        10      75      92 ..      56      73 ..      52      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00012
                       DUF2250  9 lalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                   ++++lk l++ n   +  ++k l ++++ ++e l++L+e+GL+++ +
  gi|15669748|ref|NP_248561.1|  8 TKIEILKKLNERNYTIS-ELSKILGKSKSTISEHLNALYEMGLVDKEN 54
                                  56788888887665444.578999********************9987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.023
                       DUF2250 75 khHtYYrltreGelllre 92
                                   +  YY++t++G+ +l +
  gi|15669748|ref|NP_248561.1| 56 SKWVYYKITNKGKKVLEN 73
                                  5678*********99965 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2     5e-06    0.0022       7      48 ..      15      55 ..       8     107 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5e-06
                        HTH_40  7 elleeglsieeIAkerglkesTIegHLaelieegeeidlerl 48
                                  +l e +++i e +k+ g ++sTI +HL  l+e g  +d e++
  gi|15669748|ref|NP_248561.1| 15 KLNERNYTISELSKILGKSKSTISEHLNALYEMGL-VDKENY 55
                                  566999***************************96.555444 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   1.8e-05    0.0081      18      37 .]      22      41 ..      21      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.8e-05
                        NUMOD1 18 SireAakyLgishntInkyl 37
                                  +i+e++k+Lg+s++tI+ +l
  gi|15669748|ref|NP_248561.1| 22 TISELSKILGKSKSTISEHL 41
                                  79***************997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.6e-05    0.0074       6      35 ..       8      38 ..       5      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-05
                        HTH_23  6 eRlrillllae.GlsvreIAreLgvsrrTvy 35
                                   +++il+ l e  ++++e +++Lg s++T++
  gi|15669748|ref|NP_248561.1|  8 TKIEILKKLNErNYTISELSKILGKSKSTIS 38
                                  6899******99******************8 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.3   7.1e-05     0.032      57      89 ..      42      73 ..       6      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.1e-05
                       DUF1495 57 ssLielGLveeeeeseglklYklteeGieivev 89
                                  ++L e+GLv  +e+ +   +Yk+t++G+++ e 
  gi|15669748|ref|NP_248561.1| 42 NALYEMGLVD-KENYSKWVYYKITNKGKKVLEN 73
                                  6899*****6.67788889**********9886 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.4   1.3e-05    0.0059       7     407 ..       9      77 ..       3     105 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                        DUF505   7 haeiLeklkeeeekkeeeeieveeleeeeilleLelagLvrleepekielTyaGkklaelldeliekgklekpeewkedfr 87 
                                    +eiL+kl+e +                                                                     
  gi|15669748|ref|NP_248561.1|   9 KIEILKKLNERNY-------------------------------------------------------------------- 21 
                                   5555555544332.................................................................... PP

                        DUF505  88 wvgSeiiamleaaekaggkvgeeaeeaLeeRglaeeveaLteaakalleiYreaepkleitaelaevirklPkGpaekstl 168
                                                                                                                    
  gi|15669748|ref|NP_248561.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                        DUF505 169 pigeneielLeAmRLlaysvptgdvyaltalgqavkkalrkggvaeelvlsedilealakvvdgeeleeeekeaLealgyv 249
                                                                                                                    
  gi|15669748|ref|NP_248561.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                        DUF505 250 ddegeltpaGeklleaykllkekeeekvlsialeeeevevLkaIdelwkkaeenpevlPtlkeikrelidrkikeYkelle 330
                                                                                                                    
  gi|15669748|ref|NP_248561.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                        DUF505 331 kYGRkleempkkkeeiakkfeeakdlekWy.ednfdlreaLysLesfeLieseveekgkevyvlTeyGekvledqekk 407
                                                        ++ +l+k + +++ ++ e L  L  ++L+++e +     +y +T++G+kvle++e+ 
  gi|15669748|ref|NP_248561.1|  22 ---------------------TISELSKILgKSKSTISEHLNALYEMGLVDKE-NYSKWVYYKITNKGKKVLENLEAL 77 
                                   .....................22222222213334445555555555555555.233334444555555555544433 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   2.1e-05    0.0095      24      85 ..      19      74 ..       7      77 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.1e-05
                       DUF2513 24 lddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtweGhdFLdsi 85
                                   ++++++ls+i g sk +i++hl  l e gL++ e+ +      ++v++++t +G + L+++
  gi|15669748|ref|NP_248561.1| 19 RNYTISELSKILGKSKSTISEHLNALYEMGLVDKENYS------KWVYYKITNKGKKVLENL 74
                                  2444555669**********************976643......377788888888888876 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   3.1e-05     0.014      20      54 ..      18      49 ..       8      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-05
                        HTH_36 20 knggcfpsqetlakrlglsknTvsraikeLeqlGy 54
                                  ++++   + + l+k lg+sk+T+s +++ L + G+
  gi|15669748|ref|NP_248561.1| 18 ERNY---TISELSKILGKSKSTISEHLNALYEMGL 49
                                  5666...8899*******************99998 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1     8e-05     0.036      19      66 .]      12      71 ..       8      71 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8e-05
                        HTH_12 19 iaeeLkkrgydige.........ravRyrLrkleergltrrvgya...greltEkGleeL 66
                                  i ++L++r+y i+e          ++  +L +l e+gl+ +  y+     ++t+kG + L
  gi|15669748|ref|NP_248561.1| 12 ILKKLNERNYTISElskilgkskSTISEHLNALYEMGLVDKENYSkwvYYKITNKGKKVL 71
                                  4445555555554322222222267999*****************555578****99876 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     4e-05     0.018      19      54 ..      21      56 ..      18      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-05
                B-block_TFIIIC 19 itqsdLakeskqdprslfyrlksLekkgLIvkqsii 54
                                  +t s+L+k+++++++ +  +l++L + gL+ k ++ 
  gi|15669748|ref|NP_248561.1| 21 YTISELSKILGKSKSTISEHLNALYEMGLVDKENYS 56
                                  6789*****************************995 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   2.1e-05    0.0095      12      70 ..      18      72 ..       8      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.1e-05
                        HTH_34 12 vdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafk 70
                                  +++ + +el++ l+ +++ +s hl++L + g +  dke  +k     ++iT++G++  +
  gi|15669748|ref|NP_248561.1| 18 ERNYTISELSKILGKSKSTISEHLNALYEMGLV--DKENYSK--WVYYKITNKGKKVLE 72
                                  5677899************************75..7887777..799*******98665 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.1e-05     0.023       2      36 ..      10      44 ..       9      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.1e-05
                        HTH_29  2 aqallllaeGvstvsqiAkllglsrrtvyrwlkrf 36
                                  +++l +l+e  +t+s++ k+lg s++t+  +l++ 
  gi|15669748|ref|NP_248561.1| 10 IEILKKLNERNYTISELSKILGKSKSTISEHLNAL 44
                                  799*************************9988865 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   0.00011     0.051      31      77 ..      15      59 ..       4      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                       DUF4423 31 plkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyr 77
                                  +l++ + +++el+k+l+   s++ +++ l+ L ++gl++k++  k++
  gi|15669748|ref|NP_248561.1| 15 KLNERNYTISELSKILG--KSKSTISEHLNALYEMGLVDKENYSKWV 59
                                  57777889*********..***********************99887 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00013     0.059      21      54 ..      20      53 ..       6      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrg 54
                                  + t  el+ +lG + +t+s  l++L + gl++++
  gi|15669748|ref|NP_248561.1| 20 NYTISELSKILGKSKSTISEHLNALYEMGLVDKE 53
                                  67889**************************953 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00016     0.072      12      40 ..      12      40 ..       9      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                                  HHHHHHTTT--HHHHHHHHTS-HHHHHHH CS
                    Sigma70_r4 12 vlelrfgeglTleEIgerlgiSrerVrqi 40
                                  +l+   ++++T +E++++lg S+++++ +
  gi|15669748|ref|NP_248561.1| 12 ILKKLNERNYTISELSKILGKSKSTISEH 40
                                  566666899*****************976 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   0.00017     0.076      10      56 ..      19      61 ..      10      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00017
                          Mnd1 10 efytlKeleklapkekgivsqsVkdvlqsLvdDglveveKiGssnvy 56
                                    yt+ el k++ k k     ++ ++l++L + glv++e      +y
  gi|15669748|ref|NP_248561.1| 19 RNYTISELSKILGKSK----STISEHLNALYEMGLVDKENYSKWVYY 61
                                  56************55....5******************98777766 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00019     0.083       2      21 ..      21      40 ..      20      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00019
                        HTH_17  2 ltveEaAelLgvsrstvyrl 21
                                  +t++E++++Lg s+st+ + 
  gi|15669748|ref|NP_248561.1| 21 YTISELSKILGKSKSTISEH 40
                                  9****************876 PP

>> PuR_N  Bacterial purine repressor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00017     0.076      12      45 ..      12      45 ..       8      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00017
                         PuR_N 12 iLlenPnklisltyfaerfeaAKSsiSeDlaiik 45
                                  iL +  ++ ++++++++ ++ +KS+iSe l+++ 
  gi|15669748|ref|NP_248561.1| 12 ILKKLNERNYTISELSKILGKSKSTISEHLNALY 45
                                  5556667889999***************998765 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.9    0.0003      0.13      27      74 ..      24      72 ..       9      73 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0003
                                  CCTT......HHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                          PadR 27 lels......eGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                   els      ++++   L+ L + glv++e+       +  yY++T++G++ l+
  gi|15669748|ref|NP_248561.1| 24 SELSkilgksKSTISEHLNALYEMGLVDKENYS-----KWVYYKITNKGKKVLE 72
                                  3333444444999999**************886.....699**********997 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00025      0.11       4      32 ..      14      42 ..      11      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00025
                        HTH_26  4 elmadrgitkseLargtgisaatlsrlvk 32
                                  + + +r++t+seL++ +g s++t+s +++
  gi|15669748|ref|NP_248561.1| 14 KKLNERNYTISELSKILGKSKSTISEHLN 42
                                  6789*********************9987 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00052      0.23       8      40 ..       9      41 ..       4      76 .. 0.87
   2 ?   -1.2   0.0         5   2.2e+03      21      38 ..      98     115 ..      87     122 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00052
                       SpoIIID  8 vleiakyiveskatvRkaakvfgvskstvhkDv 40
                                   +ei k + e++ t+ +  k++g skst+   +
  gi|15669748|ref|NP_248561.1|  9 KIEILKKLNERNYTISELSKILGKSKSTISEHL 41
                                  689999999*******************97654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5
                       SpoIIID  21 tvRkaakvfgvskstvhk 38 
                                    ++  a++  +sk  v +
  gi|15669748|ref|NP_248561.1|  98 QIKYQAREVVLSKTVVER 115
                                   455556666666665554 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00053      0.24      27      59 ..      22      53 ..      10      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00053
                                  -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                 LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyierd 59
                                  +i e+++ lg kS s++ ehL+aL   G+++ +
  gi|15669748|ref|NP_248561.1| 22 TISELSKILG-KSKSTISEHLNALYEMGLVDKE 53
                                  6788888888.89****************9976 PP

>> DUF4476  Domain of unknown function (DUF4476)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00032      0.15      16      79 ..       2      64 ..       1      84 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00032
                       DUF4476 16 kasfdddklklleqalankaftcsqvvqllk.lfsfdddrlkalkllapnivDkqns.etiidsft 79
                                  k+ f+++k+++l+ +l+++++t s++ ++l    s  ++ l+al  +   +vDk+n+ + ++ ++t
  gi|15669748|ref|NP_248561.1|  2 KFLFSKTKIEILK-KLNERNYTISELSKILGkSKSTISEHLNALYEM--GLVDKENYsKWVYYKIT 64
                                  5789*********.9****************4444456777777666..59999999777777766 PP

>> DUF4234  Domain of unknown function (DUF4234)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.9    0.0045         2      17      66 ..      55     103 ..      55     105 .. 0.75
   2 ?    3.5   0.5      0.18        80      45      64 ..     133     154 ..     108     157 .] 0.52

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0045
                       DUF4234  17 YslyWlykltrelnrlsgrkkttslllvflllslitcgiysivwayklgk 66 
                                   Ys + +yk+t++ +++ ++  +   l+v  +++li ++iy i+   k++ 
  gi|15669748|ref|NP_248561.1|  55 YSKWVYYKITNKGKKVLEN-LEALILMVSSIFALIGLWIYYIFKQIKYQA 103
                                   888899*************.22222222355999******9988777765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.18
                       DUF4234  45 flllsl..itcgiysivwaykl 64 
                                   fl++ +   ++ i+ ++++yk+
  gi|15669748|ref|NP_248561.1| 133 FLIFLIisTFLIIFIVYLVYKI 154
                                   2222221133334455566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1798  (0.100284); expected 358.6 (0.02)
Passed bias filter:                      835  (0.0465726); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); expected 17.9 (0.001)
Passed Fwd filter:                        46  (0.00256568); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1122.66
//
Query:       gi|15669749|ref|NP_248562.1|  [L=622]
Description: hypothetical protein MJ_1554 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   2.1e-114  383.2   6.0   8.1e-114  381.3   6.0    1.8  1  Beta_propel  Beta propeller domain


Domain annotation for each model (and alignments):
>> Beta_propel  Beta propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.3   6.0  4.5e-118  8.1e-114       1     510 [.      93     599 ..      93     603 .. 0.89

  Alignments for each domain:
  == domain 1  score: 381.3 bits;  conditional E-value: 4.5e-118
                   Beta_propel   1 ySeTNvqvegVdEaDivktDGkyiyvvsgskvvivd.aeaeelklvseikleekfkieelyldgdrLvvisseeeeeesea 80 
                                   +S+TNvqv+gVdEaDi kt+G+ i + s++k++ ++  +++ +k++++i+         lyl++++L+vis +        
  gi|15669749|ref|NP_248562.1|  93 FSKTNVQVKGVDEADILKTNGNIIAF-SQNKIYLIKpLPPKYAKIIKNISECG-----YLYLTNNTLIVISWN-------- 159
                                   69*******************98765.699******99999999999997766.....8***********987........ PP

                   Beta_propel  81 eeeeepilskeetkvliyDisdkenpkllreleldGsyvssRkigdklylvsskeaeeeeenekeaeeakleellPkvsee 161
                                                k++ y++s++e pk++ +++l+Gsyv+sR+ +++lylv++k++                   P v   
  gi|15669749|ref|NP_248562.1| 160 -------------KITSYNVSNPEMPKIIWQMDLNGSYVDSRLYNGTLYLVVRKNSID----------------CPIV--W 209
                                   .............7999************************************22222................3433..2 PP

                   Beta_propel 162 eeklvacediylpdesesss.....ylvvtsldlak.dkavdskavlgsgeevYvseenlYlas................. 219
                                   ++  + +++ y+p+ ++  s     + +++ +++++ + + ++++v ++++++Y+s++nlY a+                 
  gi|15669749|ref|NP_248562.1| 210 NNYKIGYDKYYIPELPPIYSmdfdtTYIISRINIKSgKVENSIAIVGNYKTTLYMSKNNLYFAYnlkinekklmlnflnes 290
                                   2222244444444444433333332469********6666666666689999***************************** PP

                   Beta_propel 220 ..........................................................eeyeeeeeksedkTeiykfalsd 242
                                                                                             e+y ee+ ++ ++T i k++l++
  gi|15669749|ref|NP_248562.1| 291 adkyfptevadkikrvienedfgdnakfveitetierylsslpsekrhnlmkklqndfENYLEEHWEEFEYTGIAKINLDS 371
                                   **********************************************************889999999************99 PP

                   Beta_propel 243 gkveyaasgeVpGtllnqFsldeydgyLRvattleteeseaetsnnvyvLdeklkevGkleglapgEriysvRFmgdraYl 323
                                    +v+   sg+V+G+lln+F++dey+gyLRvatt  +++ +++ +nn+y+Ld++l++vGkl+gl +gEriy+vRFmgd+aY+
  gi|15669749|ref|NP_248562.1| 372 FEVK---SGKVSGHLLNNFAMDEYNGYLRVATTIGDWRFRDKMTNNIYILDSDLNVVGKLTGLEKGERIYAVRFMGDKAYI 449
                                   8876...8************************************************************************* PP

                   Beta_propel 324 VTfrqtDPLFviDLsdpanPkilGeLkIpGySeYLhpydenhLlGiGkeadeegeeeqglklslFDVsDpanpkevakvvi 404
                                   VT+++tDPL viDL++p+nPk+lGeLkIpGyS+YLhp+++n+ +GiGk+       + +lk+slF++sD +npkev+k+++
  gi|15669749|ref|NP_248562.1| 450 VTYKETDPLLVIDLKNPKNPKVLGELKIPGYSTYLHPIGNNLFIGIGKDD------DGKLKISLFNISDLNNPKEVDKYKL 524
                                   ************************************************93......2569********************* PP

                   Beta_propel 405 gdrgsdsealydhkAllfdkeknllaipvseesnsessssqgayvykvdaekgfklkgkitheelakeetlkkakdlyeys 485
                                   +    +s+a +d++A+l+d++ +++ +p++          + ayv+kv+ +++++ +++ +h                  +
  gi|15669749|ref|NP_248562.1| 525 NVW--WSPAFRDYHAFLWDEKYKIFFLPAY----------NHAYVFKVE-DNKIEMVKDDEH------------------K 574
                                   555..5************************..........89*******.666666666666..................4 PP

                   Beta_propel 486 skvrRslyigdklytvseskiksad 510
                                   ++v R+l+i+++lyt+s s+++  d
  gi|15669749|ref|NP_248562.1| 575 TNVLRALFINNYLYTFSLSEMHILD 599
                                   579**************99887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3934.09
//
Query:       gi|15669750|ref|NP_248563.1|  [L=438]
Description: aspartyl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-95  318.4   0.1      5e-95  318.2   0.1    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
      2e-15   56.5   0.3    4.2e-15   55.5   0.3    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0066   16.0   0.4       0.11   12.0   0.0    2.4  3  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.2   0.1   8.4e-99     5e-95       3     313 ..     124     432 ..     122     433 .. 0.96

  Alignments for each domain:
  == domain 1  score: 318.2 bits;  conditional E-value: 8.4e-99
                                   CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E-S-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx RF
                   tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLtqsp 79 
                                   ++rl+nr+ldlr++kv++++++rs+++k+vr+ l ++gfie++tP L+ s te+g +lF +       ++f    +L qsp
  gi|15669750|ref|NP_248563.1| 124 DTRLENRFLDLRRPKVQAIFKIRSEMLKSVRNTLYNEGFIEVNTPKLVASCTEGGTELFPI-------SYFereaFLGQSP 197
                                   79***********************************************************.......44444445***** PP

                                   HHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  80 qlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrn 160
                                   qly+++l++ g+drvf+ia+ FRaE+++t+rhl+E t+i++em+f++++d m++le+++ + + +v e+ +k+ie+   + 
  gi|15669750|ref|NP_248563.1| 198 QLYKQMLMATGLDRVFEIAPIFRAEEHNTRRHLNEATSIDIEMAFADDKDAMDILEKVVYNAFVDVYENRKKEIETLGIE- 277
                                   **********************************************************************9999888776. PP

                                   SEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 161 skdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddkkltesyDlli 235
                                   ++ ++++f r+ty+eai+++n +      g+dl+++ e+a  + e    +f+td+P+e++pFy+  +e+++++ +++Dl++
  gi|15669750|ref|NP_248563.1| 278 FELPPEKFDRITYDEAIDIANAKgveiswGEDLSREAEKAIGE-EMEGLYFITDWPSEIRPFYTMPDEKNPNICKAFDLMY 357
                                   5566778************9999*******************9.9999********************************* PP

                                   TTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 236 ngvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFPkl 313
                                   +++E+ +G++Ri+ +++l e++k+kgl+   ++ f  ylea++yG+pph+G+glG dR++m+l+++e+Ir+ ++FP+ 
  gi|15669750|ref|NP_248563.1| 358 KDLEISSGAQRIHLYDLLVENIKKKGLN---PDGFTYYLEAFKYGMPPHAGWGLGADRFTMVLTQQENIRECVLFPRD 432
                                   ****************************...*********************************************96 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.3     7e-19   4.2e-15       1      76 []      25     104 ..      25     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 7e-19
                                   EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEEEE CS
               tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrr...pggelelkveeie 74 
                                   V + G+v+si  r+ gk+if++lrD++g++q+v+ +    +e +++ ++l  +dv+ v+G+v +    p+g +e+   e+e
  gi|15669750|ref|NP_248563.1|  25 VIIMGWVHSI--RALGKIIFVILRDREGTVQIVAPKqkvgDELFSQIKKLGAEDVIAVKGKVIANekaPNG-FEILPLELE 102
                                   789*******..*************************99999999999999**************999999.999888888 PP

                                   EE CS
               tRNA_anti-codon  75 ll 76 
                                   ++
  gi|15669750|ref|NP_248563.1| 103 VI 104
                                   75 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       1.3   7.8e+03      20      42 ..     147     169 ..     139     172 .. 0.79
   2 ?    1.4   0.1     0.032   1.9e+02     102     154 ..     210     265 ..     195     279 .. 0.68
   3 !   12.0   0.0   1.8e-05      0.11     212     234 ..     404     426 ..     393     435 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHHCTTCEESSTTS CS
                  tRNA-synt_2d  20 tkvleeikeiflelgfeevegpe 42 
                                   +++l+ +++++ + gf ev+ p+
  gi|15669750|ref|NP_248563.1| 147 SEMLKSVRNTLYNEGFIEVNTPK 169
                                   67888999999999999988775 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.032
                                   EEEEEEEEEEBSST.-SSSB-SEEEE..EEEEEEETT--HHHHHHHHHHHHHHHCT CS
                  tRNA-synt_2d 102 ikiisigrvfRrda.vDathlaeFhq..veglvvdenvsladlkgvleellkklfg 154
                                    +++ i  +fR ++   ++hl e ++  +e+ ++d++  ++ l +v+ + + ++++
  gi|15669750|ref|NP_248563.1| 210 DRVFEIAPIFRAEEhNTRRHLNEATSidIEMAFADDKDAMDILEKVVYNAFVDVYE 265
                                   58899999999999556667766554115667777777777777776666655555 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 1.8e-05
                                   EEEEEEHHHHHHHHHT-SSGHHH CS
                  tRNA-synt_2d 212 fafGlGveRlamlkygieDiRel 234
                                   +++GlG +R++m+ ++ e+iRe 
  gi|15669750|ref|NP_248563.1| 404 AGWGLGADRFTMVLTQQENIREC 426
                                   68*******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 3000.02
//
Query:       gi|15669751|ref|NP_248564.1|  [L=312]
Description: hypothetical protein MJ_1556 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   11.6   8.6      0.056   13.7   3.8    2.2  2  EI24      Etoposide-induced protein 2.4 (EI24)
        4.7    7.5  21.5       0.29   11.4   6.5    3.8  3  Gate      Nucleoside recognition


Domain annotation for each model (and alignments):
>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.16   1.5e+03      54      72 ..      13      31 ..       3      73 .. 0.62
   2 ?   13.7   3.8   6.2e-06     0.056      19     108 ..     109     312 .]      99     312 .] 0.67

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.16
                                  HHHHHHHHHHHHHHHHHHH CS
                          EI24 54 plwlfplvalllaapfygl 72
                                  + +l+  + +l++++f ++
  gi|15669751|ref|NP_248564.1| 13 FTFLYYSIPMLIVGLFISQ 31
                                  2223333333333333332 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.2e-06
                                   HHHHHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHH...........................................HH CS
                          EI24  19 lllplllnlllfllllvlllwvllasllvllllllp...........................................lw 56 
                                   +llp+ll+ l f++++++++ vl+ ++ +l+++++                                             +
  gi|15669751|ref|NP_248564.1| 109 SLLPILLATLGFFGIIYFIILVLIGFIQTLIFMAIGkitlknreykedntdkkiklnkdvvytafkntikygipiirdiTI 189
                                   499**********999999877788888887777779999*******************************9998888555 PP

                                   HHHHHHHHHHHHHHHHHHHHHHH.H......................H..............................CCT CS
                          EI24  57 lfplvalllaapfygllaekvekrh......................l..............................glv 85 
                                    + ++++l+   f++ + e+++ +                                                         
  gi|15669751|ref|NP_248564.1| 190 ASIITSFLIEFGFFDYITEIIKNKAyylplsveeitvavtqpinyigAfvlageflnrgildeievvralllgsilssI-- 268
                                   5557777777778999999996654444444444444444444444404444444444444555444555555333330.. PP

                                   TSHH........................HHHHHHHHHHHHHHHHHHH CS
                          EI24  86 ksla........................eslkslllllllllvllpl 108
                                      +                        ++l ++l++ l+++++l+l
  gi|15669751|ref|NP_248564.1| 269 ---PalrflapyyigiygfkdgfnlmmiSTLVRILITALFVIITLIL 312
                                   ...23333334444444444444555558888888888888888775 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   6.5   3.3e-05      0.29       4      92 ..      19      98 ..      16     137 .. 0.81
   2 ?   -1.5   1.3      0.33     3e+03       5      22 ..     122     139 ..     117     149 .. 0.67
   3 ?    0.5   5.1     0.078     7e+02       8      32 ..     187     211 ..     181     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.3e-05
                          Gate  4 agpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtpksal 86
                                   +p++++++++ ++l +s+++++i  +++++f +l  +l+ ++ ++++t+f++  ++  +l  +y       ++g+ ++k+ +
  gi|15669751|ref|NP_248564.1| 19 SIPMLIVGLFISQILIESNIIKKIY-FIGKIFTRLA-NLPEECGIAITTSFIEPRMANIMLVDFY-------KKGIINKKELY 92
                                  589******************9986.5689999987.8**************6666666666888.......77887777776 PP

                          Gate 87 afllfv 92
                                  +  l+ 
  gi|15669751|ref|NP_248564.1| 93 ISSLID 98
                                  665554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.33
                          Gate   5 gpiillasiliwflssss 22 
                                   g i +++++li+f++   
  gi|15669751|ref|NP_248564.1| 122 GIIYFIILVLIGFIQTLI 139
                                   556777788888877544 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.078
                          Gate   8 illasiliwflssssllgrigklle 32 
                                   i +asi+ +fl +++++++i  +++
  gi|15669751|ref|NP_248564.1| 187 ITIASIITSFLIEFGFFDYITEIIK 211
                                   88999********999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1947.50
//
Query:       gi|15669752|ref|NP_248565.1|  [L=249]
Description: hypothetical protein MJ_1557 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-78  261.0   2.6    8.4e-78  260.7   2.6    1.1  1  Met_10           Met-10+ like-protein
    0.00032   20.3   0.0    0.00065   19.3   0.0    1.6  1  MTS              Methyltransferase small domain
    0.00068   18.8   0.0    0.00087   18.4   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0027   17.6   0.1      0.005   16.7   0.1    1.5  1  PRMT5            PRMT5 arginine-N-methyltransferase
      0.003   16.9   0.2      0.011   15.0   0.0    1.9  2  GidB             rRNA small subunit methyltransferase G
     0.0033   16.8   0.0     0.0059   16.0   0.0    1.4  1  DNA_methylase    C-5 cytosine-specific DNA methylase
     0.0045   17.7   0.0     0.0088   16.7   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
     0.0051   16.5   0.0      0.069   12.8   0.0    2.3  3  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.035   13.6   0.0    1.8  2  Methyltransf_4   Putative methyltransferase
      0.023   14.3   0.0      0.041   13.5   0.0    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.027   14.4   0.0      0.077   12.9   0.0    1.9  1  Methyltransf_18  Methyltransferase domain
      0.027   14.1   0.0      0.043   13.5   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.054   12.9   0.0      0.081   12.3   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
       0.13   12.0   0.0       0.25   11.1   0.0    1.5  1  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.7   2.6   6.6e-81   8.4e-78       2     199 .]       4     194 ..       3     194 .. 0.98

  Alignments for each domain:
  == domain 1  score: 260.7 bits;  conditional E-value: 6.6e-81
                                   EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS- CS
                        Met_10   2 kfeiiGdvvilnlreelkeykkvigevildktkvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskvy 82 
                                   k+++iGdvvi++++ + +e++++++++     k+k++l ++++++gefRt+++++l+G++ tetihkE+gc fklDv+k++
  gi|15669752|ref|NP_248565.1|   4 KYQKIGDVVIVKKELSEDEIREIVKRT-----KCKAILLYTTQITGEFRTPHVKILYGKE-TETIHKEYGCLFKLDVAKIM 78 
                                   8******************88877665.....****************************.******************** PP

                                   --GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG- CS
                        Met_10  83 fsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrev 163
                                   +s+++++Er+r+a + +e+evVvd+fAGiG+f+ip+akysk+k v+ai++nP++++yl+eniklNk+++v+ pil+D+r+v
  gi|15669752|ref|NP_248565.1|  79 WSQGNIEERKRMAFISNENEVVVDMFAGIGYFTIPLAKYSKPKLVYAIEKNPTAYHYLCENIKLNKLNNVI-PILADNRDV 158
                                   **********************************************************************9.********* PP

                                   --TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                        Met_10 164 ireqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                     +++adrv+m++++++++Fldk++++lkd+gvihy
  gi|15669752|ref|NP_248565.1| 159 ELKDVADRVIMGYVHKTHKFLDKTFEFLKDRGVIHY 194
                                   ***********************************9 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.1e-07   0.00065      31     103 ..      96     169 ..      88     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.1e-07
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivs 103
                                   +++ v+D+ +G+G+ ++ lak s+   v +++++  A +   en++ nkl+  + ++a +   e++ +  d +++
  gi|15669752|ref|NP_248565.1|  96 ENEVVVDMFAGIGYFTIPLAKYSKPKLVYAIEKNPTAYHYLCENIKLNKLNnvIPILADNRDVELK-DVADRVIM 169
                                   56789*****************99999************************988899999988888.77788776 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   6.8e-07   0.00087      29      92 ..      85     162 ..      60     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.8e-07
                                   G..........TTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHH CS
                        RrnaAD  29 e..........ekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpe 92 
                                   e          e+  v+++ +G G +T +Lak++  k v ++E+ +  +  l ++++  k +++  + +D  + e++ 
  gi|15669752|ref|NP_248565.1|  85 EerkrmafisnENEVVVDMFAGIGYFTIPLAKYSkpKLVYAIEKNPTAYHYLCENIKlnKLNNVIPILADNRDVELKD 162
                                   44444445557999********************999999*******9999999888444445555777877777766 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   3.9e-06     0.005      93     140 ..     120     166 ..      74     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.9e-06
                                   EEEEEEEES-HHHHHHHHHHHHHHTTCCGCEEEES-CCCCCHCC-ECE CS
                         PRMT5  93 kvkivavEKnpnavvtLqkkvneekWeekveviksdmrelkaeekvdl 140
                                      ++a+EKnp+a+ +L ++++ +k ++ +  i  d r+++ +  +d 
  gi|15669752|ref|NP_248565.1| 120 PKLVYAIEKNPTAYHYLCENIKLNKLNNVIP-ILADNRDVELKDVADR 166
                                   4569**********************55555.5567788887776665 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.52   6.7e+02     139     166 ..       6      33 ..       3      48 .. 0.75
   2 !   15.0   0.0   8.7e-06     0.011      40     144 ..      88     192 ..      62     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.52
                                   EEEEEEEEEESS--HHHHHCCHCCCCCC CS
                          GidB 139 kegglilalKGksaedeleekekalqls 166
                                   ++ g ++++K + +ede++e  k+ + +
  gi|15669752|ref|NP_248565.1|   6 QKIGDVVIVKKELSEDEIREIVKRTKCK 33 
                                   5778999999999999999877666555 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 8.7e-06
                                   HHGGCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCCTTTTT-EEEEE CS
                          GidB  40 svlellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaeekqeeekydvvt 120
                                   + + +++++++ v+D  +G G   ipLa + + + ++ +e++    ++L e ++  kl+nv  + a+  + + ++  d v+
  gi|15669752|ref|NP_248565.1|  88 KRMAFISNENEVVVDMFAGIGYFTIPLAKYSKPKLVYAIEKNPTAYHYLCENIKLNKLNNVIPILADNRDVELKDVADRVI 168
                                   567888899967******************************************************99999999999**** PP

                                   EC-SSSHHHHHHHHCCCEEEEEEE CS
                          GidB 121 sRAlaslnelteillkllkeggli 144
                                   +  + + +++ + + ++lk++g+i
  gi|15669752|ref|NP_248565.1| 169 MGYVHKTHKFLDKTFEFLKDRGVI 192
                                   ****************99999987 PP

>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.6e-06    0.0059       3      49 ..     100     148 ..      99     171 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.6e-06
                                   EEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-..-SEEEE CS
                 DNA_methylase   3 fidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk.kvsigD 49 
                                   ++d+faGiG f++ l++ +  + v+a+e++++a   ++ n+k ++ ++ 
  gi|15669752|ref|NP_248565.1| 100 VVDMFAGIGYFTIPLAKYSkPKLVYAIEKNPTAYHYLCENIKlNKLNNV 148
                                   79**************99889********************97333333 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.9e-06    0.0088       1      97 []     100     190 ..     100     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.9e-06
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                   v+d+ +G G +t+ lak  + + v++++ ++++  +  e+++ ++l nv  + +d +d++++d   D v++     +++  
  gi|15669752|ref|NP_248565.1| 100 VVDMFAGIGYFTIPLAKYSKPKLVYAIEKNPTAYHYLCENIKLNKLnNVIPILADNRDVELKD-VADRVIMG----YVH-- 173
                                   899**************9878********************999999*************998.99999993....333.. PP

                                   HHHHHHHHHHHHEEEEE CS
               Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                   +++k+l++ ++ Lk+ G
  gi|15669752|ref|NP_248565.1| 174 KTHKFLDKTFEFLKDRG 190
                                   45689999999998877 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.9   7.6e+03     121     138 ..      23      40 ..       7      41 .. 0.59
   2 !   12.8   0.0   5.4e-05     0.069       7      84 ..      95     168 ..      90     171 .. 0.87
   3 ?    2.7   0.0     0.065        84     107     138 ..     165     196 ..     156     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.9
                                   HHHHCCCEEEEEEEEEEE CS
               Methyltr_RsmB-F 121 lsaaidllkkgGvlvYsT 138
                                   +  +++ +k   +l+Y+T
  gi|15669752|ref|NP_248565.1|  23 IREIVKRTKCKAILLYTT 40 
                                   444555566666777766 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.4e-05
                                   -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEE CS
               Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriL 84 
                                   +e+e ++D+ a+ G  T  +a+  ++ + v+A+++n +  + + en+k   ++n+i + aD r ++     ++ Dr++
  gi|15669752|ref|NP_248565.1|  95 NENEVVVDMFAGIGYFTIPLAKY-SKPKLVYAIEKNPTAYHYLCENIKLNKLNNVIPILADNRDVELK---DVADRVI 168
                                   799*******************9.77789*******************99999*********998543...3457776 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.065
                                   HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEE CS
               Methyltr_RsmB-F 107 ekdiaqlaklqkellsaaidllkkgGvlvYsT 138
                                   ++ i+ ++++ ++ l+ +++ lk  Gv+ Y  
  gi|15669752|ref|NP_248565.1| 165 DRVIMGYVHKTHKFLDKTFEFLKDRGVIHYHE 196
                                   566888999*******************9964 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.7e-05     0.035       2      60 ..      97     155 ..      96     171 .. 0.88
   2 ?   -1.3   0.0         1   1.3e+03      97     116 ..     176     195 ..     174     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                                   -EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                Methyltransf_4   2 apvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                                   + vv+++  G G f++ lAk    k++ +iE++ +  +++ ++i+ ++l+N+  +  d 
  gi|15669752|ref|NP_248565.1|  97 NEVVVDMFAGIGYFTIPLAKYSKPKLVYAIEKNPTAYHYLCENIKLNKLNNVIPILADN 155
                                   57899**********************************************98776665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1
                                   HHHHHHHHHHEEEEEEEEEE CS
                Methyltransf_4  97 pellkelarvLkkgGvlela 116
                                   +++l++  + Lk +Gv++  
  gi|15669752|ref|NP_248565.1| 176 HKFLDKTFEFLKDRGVIHYH 195
                                   57888888999999999864 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.2e-05     0.041       2      59 ..      98     156 ..      97     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
               Methyltransf_15   2 rvilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvf 59 
                                   +v++D+f+G G  +i +a++   + v+aie+n+       +N ++    +++ ++l+d  
  gi|15669752|ref|NP_248565.1|  98 EVVVDMFAGIGYFTIPLAKYskPKLVYAIEKNPTAYHYLCENIKLN-KLNNVIPILADNR 156
                                   689****************855567*******************98.5566777777755 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     6e-05     0.077      12      74 ..      94     155 ..      87     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6e-05
               Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdG 74 
                                    +++++v+D  +  gy +i l+k +k k v+a++ n+ +++   eni+ ++l++ i +  +d 
  gi|15669752|ref|NP_248565.1|  94 SNENEVVVDMFAGIGYFTIPLAKYSKPKLVYAIEKNPTAYHYLCENIKLNKLNNVIPIL-ADN 155
                                   3456799*********************************************8766554.444 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.4e-05     0.043      41     106 ..      96     162 ..      86     219 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.4e-05
                                   CC-EEEETT-TTSHHHHH..HHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCT CS
                 Cons_hypoth95  41 egarvLDlfaGsGalglE..AlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallk 106
                                   e++ v+D+faG G   +     S   k ++++ek+++a++ l en++  kl++ + +l +++  +l+ 
  gi|15669752|ref|NP_248565.1|  96 ENEVVVDMFAGIGYFTIPlaKYSK-PKLVYAIEKNPTAYHYLCENIKLNKLNNVIPILADNRDVELKD 162
                                   56789********88775203344.48899********************998555555555444443 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.3e-05     0.081     159     255 ..      94     191 ..      67     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.3e-05
                          PrmA 159 vkegeevlDvGtGSGiLaiaaakLga.kkvvavDiDevAvkvakeNaelNkveaklevalseellk.eekadvivaNILae 237
                                    +e+e v+D+ +G G  +i  ak    k v+a+  ++ A +   eN++lNk+++ + + + ++ ++ +  ad ++   + +
  gi|15669752|ref|NP_248565.1|  94 SNENEVVVDMFAGIGYFTIPLAKYSKpKLVYAIEKNPTAYHYLCENIKLNKLNNVIPILADNRDVElKDVADRVIMGYVHK 174
                                   46678899***********98888652779************************998855444443356677777655433 PP

                          PrmA 238 vlielaedikklvkeggl 255
                                      ++++++ +++k+ g+
  gi|15669752|ref|NP_248565.1| 175 -THKFLDKTFEFLKDRGV 191
                                   .35566666666666665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00019      0.25       2     106 ..      95     191 ..      94     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                   +++ +v+D  +G G++t+ la+   + + v+ i+ +++a  +  en + ++l+nv    +d  + e  l+d   D ++   
  gi|15669752|ref|NP_248565.1|  95 NENEVVVDMFAGIGYFTIPLAK-YSKPKLVYAIEKNPTAYHYLCENIKLNKLNNVIPILADNRDVE--LKD-VADRVIM-- 169
                                   67899****************4.333455*************************999999999988..552.3333333.. PP

               Methyltransf_31  83 vlnaladpdkileeiervlkpggi 106
                                      ++    k+l + ++ lk+ g+
  gi|15669752|ref|NP_248565.1| 170 --GYVHKTHKFLDKTFEFLKDRGV 191
                                   ..2333334444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1621.04
//
Query:       gi|15669753|ref|NP_248566.1|  [L=90]
Description: hypothetical protein MJ_1558 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-19   70.3   0.8    1.1e-19   70.1   0.8    1.0  1  ACT_6     ACT domain
    3.1e-11   42.9   0.6    3.9e-11   42.5   0.6    1.2  1  ACT       ACT domain
    5.9e-07   30.0   1.8    7.4e-07   29.7   1.8    1.2  1  ACT_4     ACT domain
    1.2e-05   25.1   0.5    1.9e-05   24.4   0.5    1.5  1  ACT_7     ACT domain


Domain annotation for each model (and alignments):
>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.8   2.5e-23   1.1e-19       2      75 ..       3      78 ..       2      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 2.5e-23
                         ACT_6  2 illitvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgp.ed.alarlekaLlflakelgltvef 75
                                   ++++v+G+dr+G++a +++vlae+++nilDi q +  + ++ ++lv+++ ++ ++a l+k+L+++ +elg++v +
  gi|15669753|ref|NP_248566.1|  3 RVVVSVIGQDRTGIVAGISKVLAENNANILDISQTIMDNLFAMIMLVDISnAKvDFATLKKELEKAGEELGVQVIV 78
                                  689***********************************************7446*******************987 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.6   8.8e-15   3.9e-11       2      66 ..       5      69 ..       4      70 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 8.8e-15
                                  EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                           ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66
                                  v++v  +Dr G+ a ++ +la+++ Ni  i+q+ ++  +a+i+ v i     d ++++++l+k +
  gi|15669753|ref|NP_248566.1|  5 VVSVIGQDRTGIVAGISKVLAENNANILDISQTIMDNLFAMIMLVDISNAKVDFATLKKELEKAG 69
                                  899********************************999************************975 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   1.8   1.7e-10   7.4e-07       7      60 ..       4      55 ..       2      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.7e-10
                         ACT_4  7 vrleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdve 60
                                  v ++v+++dr+g++a i++v++e++ani +++ +    d+l+ + + v +++++
  gi|15669753|ref|NP_248566.1|  4 VVVSVIGQDRTGIVAGISKVLAENNANILDISQTI--MDNLFAMIMLVDISNAK 55
                                  6689****************************999..689**********9975 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.5   4.2e-09   1.9e-05       8      43 ..       5      37 ..       3      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.2e-09
                                  EEEE-S-.---SS--HHHHHHHHHHTTT---EEEE.- CS
                         ACT_7  8 klsvvgsglpfdvtGivaklaspLaeagIsifqiS.t 43
                                  ++sv+g+    d tGiva+++++Lae++ +i+ iS t
  gi|15669753|ref|NP_248566.1|  5 VVSVIGQ----DRTGIVAGISKVLAENNANILDISqT 37
                                  5677777....9**********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 676.08
//
Query:       gi|15669754|ref|NP_248567.1|  [L=188]
Description: putative NTPase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-59  198.8   2.0    6.7e-59  198.6   2.0    1.0  1  NTPase_1         NTPase
      7e-08   32.2   0.0    2.7e-07   30.3   0.0    1.7  1  DUF2478          Protein of unknown function (DUF2478)
    2.1e-07   31.5   0.2      4e-07   30.6   0.2    1.7  1  AAA_18           AAA domain
    1.1e-06   29.1   1.3    3.2e-06   27.6   1.3    1.8  1  AAA              ATPase family associated with various cellul
    1.9e-06   27.1   0.1    3.5e-06   26.2   0.1    1.5  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    3.6e-05   23.8   3.1    6.3e-05   23.0   2.6    1.7  1  ATPase_2         ATPase domain predominantly from Archaea
    5.6e-05   23.0   0.4      0.021   14.5   0.1    2.2  2  IstB_IS21        IstB-like ATP binding protein
      6e-05   22.3   0.3    0.00011   21.5   0.3    1.3  1  NB-ARC           NB-ARC domain
    7.1e-05   22.5   1.6     0.0081   15.8   0.4    2.1  2  SRP54            SRP54-type protein, GTPase domain
    7.3e-05   22.6   0.9    0.00022   21.0   0.9    1.7  1  AAA_30           AAA domain
    0.00011   22.6   2.8     0.0002   21.8   1.9    2.1  1  AAA_17           AAA domain
    0.00016   21.3   1.5     0.0012   18.3   1.5    2.0  1  KdpD             Osmosensitive K+ channel His kinase sensor d
    0.00017   21.5   0.1    0.00026   20.9   0.1    1.3  1  APS_kinase       Adenylylsulphate kinase
    0.00019   20.9   0.3     0.0065   15.8   0.3    2.1  1  DnaB_C           DnaB-like helicase C terminal domain
    0.00022   21.0   0.1      0.015   15.1   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00034   20.2   0.4     0.0023   17.5   0.4    2.1  1  KTI12            Chromatin associated protein KTI12
    0.00043   20.7   0.1    0.00095   19.6   0.1    1.8  1  AAA_16           AAA ATPase domain
    0.00051   20.3   0.6     0.0037   17.6   0.5    2.2  1  AAA_22           AAA domain
    0.00066   19.0   0.7     0.0021   17.4   0.7    1.7  1  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00072   19.3   3.5     0.0018   18.0   3.5    1.8  1  AAA_24           AAA domain
    0.00086   19.3   0.4      0.002   18.1   0.2    1.7  2  NACHT            NACHT domain
     0.0012   18.5   1.4      0.004   16.8   0.7    2.1  2  Thymidylate_kin  Thymidylate kinase
      0.002   18.2   1.3     0.0075   16.3   0.2    2.0  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0022   17.9   0.6     0.0097   15.8   0.1    2.0  2  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0037   17.2   0.8      0.025   14.5   0.2    2.2  2  AAA_31           AAA domain
     0.0042   16.6   0.2     0.0061   16.0   0.2    1.3  1  PhoH             PhoH-like protein
     0.0062   16.5   1.8      0.074   13.0   0.2    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0081   16.3   0.2      0.016   15.4   0.2    1.7  1  AAA_33           AAA domain
     0.0086   15.5   0.1      0.018   14.5   0.1    1.5  1  ParA             NUBPL iron-transfer P-loop NTPase
  ------ inclusion threshold ------
      0.012   15.9   0.2      0.022   15.0   0.2    1.5  1  AAA_28           AAA domain
      0.013   15.5   1.4      0.074   13.1   1.3    2.2  1  AAA_14           AAA domain
       0.02   14.6   0.4       0.19   11.4   0.4    2.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.021   14.0   0.1       0.04   13.1   0.1    1.4  1  ArsA_ATPase      Anion-transporting ATPase
      0.023   15.0   2.5       0.35   11.2   2.4    2.4  1  AAA_19           AAA domain
      0.026   14.1   1.0       0.22   11.1   0.1    2.2  2  AAA_25           AAA domain
      0.028   14.3   1.1       0.27   11.1   0.2    2.1  2  Bac_DnaA         Bacterial dnaA  protein
      0.028   14.8   0.1       0.18   12.2   0.0    2.1  2  RNA_helicase     RNA helicase
      0.029   14.5   0.5       0.07   13.2   0.5    1.8  1  MMR_HSR1         50S ribosome-binding GTPase
      0.038   13.6   1.1      0.094   12.3   1.1    1.7  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.083   12.2   2.2       0.15   11.3   2.2    1.6  1  ATPase           KaiC
      0.085   12.1   1.1        1.1    8.5   1.1    2.6  1  MipZ             ATPase MipZ
       0.16   11.8   0.8       0.36   10.6   0.2    1.8  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.21   11.6   2.3       0.68    9.9   2.0    2.0  1  ResIII           Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.6   2.0   1.6e-61   6.7e-59       1     168 []      20     180 ..      20     180 .. 0.99

  Alignments for each domain:
  == domain 1  score: 198.6 bits;  conditional E-value: 1.6e-61
                                   EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE-HHHH CS
                      NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvvdvesf 81 
                                   ++fiTG+pGvGKtTl  k++e+lk+ g+kvgGf+t+e+r+gg+r+gFki++l+++ee+iLa v+   +++vgky v++e++
  gi|15669754|ref|NP_248567.1|  20 RIFITGMPGVGKTTLALKIAEKLKELGYKVGGFITKEIRDGGKRVGFKIITLDTNEETILAYVG-DGKIKVGKYAVFIENL 99 
                                   69**************************************************************.9*************** PP

                                   HHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE--TTTTTT CS
                      NTPase_1  82 eelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdvkvfevteenrda 162
                                   +++++ea+++al++ad+i+iDE G mE+ks+kf+e v+ev+ks+kp+la++hr+    +v++++++  ++++++t enr++
  gi|15669754|ref|NP_248567.1| 100 DNVGVEAIKRALKDADIIIIDELGAMEFKSRKFSEVVDEVIKSDKPLLATLHRN----WVNKFKDK--GELYTLTIENREK 174
                                   ******************************************************....******97..************* PP

                                   HHHHHH CS
                      NTPase_1 163 lleeil 168
                                   l+eeil
  gi|15669754|ref|NP_248567.1| 175 LFEEIL 180
                                   ****97 PP

>> DUF2478  Protein of unknown function (DUF2478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   6.5e-10   2.7e-07      14     140 ..      33     160 ..      22     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 6.5e-10
                       DUF2478  14 alLaafaerlraeGlrvaGvvqenaeeaegkkcdmeledlatgeririsq.dlgsgsqg.CrLdpeaLaea.aaaverala 91 
                                   +l  ++ae+l++ G++v+G++ ++ +++ gk+   +++ l+t+e+  +     g+   g   +  e+L ++ ++a++ral 
  gi|15669754|ref|NP_248567.1|  33 TLALKIAEKLKELGYKVGGFITKEIRDG-GKRVGFKIITLDTNEETILAYvGDGKIKVGkYAVFIENLDNVgVEAIKRAL- 111
                                   455689***************9999876.6778*******9999876654123333333235666888877256777777. PP

                       DUF2478  92 egadlvivnkFGkqEaeGrGlreeiaaalaagiPvltaVseklleaWra 140
                                   ++ad++i+   G  E + r ++e++ ++++++ P+l ++++++++++++
  gi|15669754|ref|NP_248567.1| 112 KDADIIIIDELGAMEFKSRKFSEVVDEVIKSDKPLLATLHRNWVNKFKD 160
                                   99*******************************************9986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.2   9.5e-10     4e-07       1      91 [.      21     131 ..      21     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 9.5e-10
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf...................gvnlrdvakenglllevdpe...aldeskrldedkld 58 
                                   I++tG+pGvGKttla  ++++l ++                   g++++ + +++++ l +  +   ++ ++ ++ e+ ++
  gi|15669754|ref|NP_248567.1|  21 IFITGMPGVGKTTLALKIAEKLkELgykvggfitkeirdggkrvGFKIITLDTNEETILAYVGDgkiKVGKYAVFIENLDN 101
                                   9********************877788998888888888888888888888888877777777776655555555566655 PP

                        AAA_18  59 klldaleenssaleegknlvidghlaeleseaa 91 
                                   + ++a++++   l +++ ++id + a  ++ + 
  gi|15669754|ref|NP_248567.1| 102 VGVEAIKRA---LKDADIIIIDELGAMEFKSRK 131
                                   556666664...678999999998887776655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   1.3   7.6e-09   3.2e-06       2      76 ..      22     134 ..      21     184 .. 0.57

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 7.6e-09
                                   EEESSTTSSHHHHHHHHHHHH......................THEEEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTS.. CS
                           AAA   2 llyGppGtGKTllakavakel......................gvefleisgsell.skyvgesekkirelfkeakeka.. 57 
                                    ++G pG+GKT+la  +a++l                      g+++++++  e +   yvg+++ k+ ++   +++    
  gi|15669754|ref|NP_248567.1|  22 FITGMPGVGKTTLALKIAEKLkelgykvggfitkeirdggkrvGFKIITLDTNEETiLAYVGDGKIKVGKYAVFIENLDnv 102
                                   579*****************8444444433333333333322234455555555444467777777777766666555455 PP

                                   ..........TSEEEEEETGGGHHHHH...TT CS
                           AAA  58 ..........kpsilfiDEidalaksr...sg 76 
                                             +  i++iDE+ a+  ++   s+
  gi|15669754|ref|NP_248567.1| 103 gveaikralkDADIIIIDELGAMEFKSrkfSE 134
                                   566666667444**********9655524422 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   8.5e-09   3.5e-06      24      61 ..      13      50 ..       7      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 8.5e-09
                                  GG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EE CS
                          MeaB 24 akaGraqvvGltGvPGaGkstlvealglelrrrGkrva 61
                                  + +G++ ++ +tG+PG+Gk tl  +++++l++ G++v+
  gi|15669754|ref|NP_248567.1| 13 KGCGETMRIFITGMPGVGKTTLALKIAEKLKELGYKVG 50
                                  679*********************************97 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   2.6   1.5e-07   6.3e-05      19     144 ..      17     138 ..       7     168 .. 0.63

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.5e-07
                      ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie....eeeekkklekalgiavpkaeleeil 95 
                                   + + +fi+G  g+GKt+L  +i+e+l++++++v  +i  + ++  k   f +    +++     e++++  v+  ++    
  gi|15669754|ref|NP_248567.1|  17 ETMRIFITGMPGVGKTTLALKIAEKLKELGYKVGGFITKEIRDGGKRVGF-KiitlDTN-----EETILAYVGDGKI---- 87 
                                   55679*************************98875555555555555555.22233333.....4444344443333.... PP

                      ATPase_2  96 k.eksklvfkaiell.lekikkkgkk.iiiiiDelqklidlglngaellvke 144
                                   k  k +   ++++++  e+ik+  k   iiiiDel  +  +++++  ++v+e
  gi|15669754|ref|NP_248567.1|  88 KvGKYAVFIENLDNVgVEAIKRALKDaDIIIIDELGAME-FKSRKFSEVVDE 138
                                   22333445555655525666666666789*****98776.666644444333 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   5.2e-05     0.021      49      78 ..      20      49 ..       9      58 .. 0.88
   2 ?    6.7   0.0     0.013       5.3     102     128 ..     107     133 ..      96     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.2e-05
                     IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsv 78
                                   i ++G +GvGK+ la  ++ +  + g++v
  gi|15669754|ref|NP_248567.1| 20 RIFITGMPGVGKTTLALKIAEKLKELGYKV 49
                                  6899***********************999 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.013
                     IstB_IS21 102 alkrllkvdllilDdlgllpldqaeae 128
                                   + ++l  +d++i+D+lg  ++++ + +
  gi|15669754|ref|NP_248567.1| 107 IKRALKDADIIIIDELGAMEFKSRKFS 133
                                   45667788**********999766543 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.3   2.6e-07   0.00011      21      48 ..      19      46 ..       9      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.6e-07
                                  EEEEEEESTTSSHHHHHHHHCCSHCCCC CS
                        NB-ARC 21 lvvalvGmgGvGKttlakqilnksdeve 48
                                  + +++ Gm+GvGKttla +i +k++e+ 
  gi|15669754|ref|NP_248567.1| 19 MRIFITGMPGVGKTTLALKIAEKLKELG 46
                                  5699*******************99875 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   1.9e-05    0.0081       4      33 ..      21      50 ..      18      61 .. 0.90
   2 ?    6.1   0.0     0.019       7.8      71     113 ..     102     141 ..      84     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvl 33
                                  i + G+ G+GKTt + K+a++lk+ g+kv 
  gi|15669754|ref|NP_248567.1| 21 IFITGMPGVGKTTLALKIAEKLKELGYKVG 50
                                  7899*********************99985 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.019
                                   HHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHS CS
                         SRP54  71 vakeavekakeekidvvlvDTaGrlqndkelmeelkkikkvvk 113
                                   v  ea+++a + ++d++++D  G ++ +++ ++e+    +v+k
  gi|15669754|ref|NP_248567.1| 102 VGVEAIKRALK-DADIIIIDELGAMEFKSRKFSEVV--DEVIK 141
                                   55678888777.78***************9999974..34444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.9   5.3e-07   0.00022      21     112 ..      21     139 ..       9     148 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.3e-07
                        AAA_30  21 avltGpAGtGKttalkalreaweaaggrviglAptgka..AkvLae...elgieastiakllkrlk............... 81 
                                    ++tG +G GKtt+  +++e +++ g++v g+  ++     k+++     l+++ +ti  ++   k               
  gi|15669754|ref|NP_248567.1|  21 IFITGMPGVGKTTLALKIAEKLKELGYKVGGFITKEIRdgGKRVGFkiiTLDTNEETILAYVGDGKikvgkyavfienldn 101
                                   579***********************999988655432113444432222223555555555444488888888888888* PP

                        AAA_30  82 ......grarlepgtllivDEagmv..dtkqlaallkaa 112
                                         +  +l++++++i+DE g +   ++++ ++++++
  gi|15669754|ref|NP_248567.1| 102 vgveaiK-RALKDADIIIIDELGAMefKSRKFSEVVDEV 139
                                   *999853.578888*********9944556666666665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.9   4.8e-07    0.0002       1      39 [.      24      62 ..      24     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.8e-07
                                  EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS CS
                        AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrggl 39
                                  +G+PG+GK+t++ k++ek++   +  G  + +e+++gg 
  gi|15669754|ref|NP_248567.1| 24 TGMPGVGKTTLALKIAEKLKELGYKVGGFITKEIRDGGK 62
                                  7*********************************99984 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.5     3e-06    0.0012       4     133 ..      18     161 ..      16     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3e-06
                          KdpD   4 rlkiflGaapGvGktyamLeeaqelkeegvdvviglvethgrketealleglevi................prkeveykgk 68 
                                   +++if+  +pGvGkt   L+ a++lke g +v  g++ ++ r+  +++  ++ ++                +  ++++  +
  gi|15669754|ref|NP_248567.1|  18 TMRIFITGMPGVGKTTLALKIAEKLKELGYKVG-GFITKEIRDGGKRVGFKIITLdtneetilayvgdgkiKVGKYAVFIE 97 
                                   589***************************985.88888888776666544444455566677777764433333334445 PP

                          KdpD  69 eleeldldaila..rkpevvlvDelahtnapgsrhekryqdveelLeagidVittvnvqhleslndv 133
                                   +l+++ ++ai +  ++ +++++Del+  +    + +k  + v+e+++++   ++t++ + ++ ++d 
  gi|15669754|ref|NP_248567.1|  98 NLDNVGVEAIKRalKDADIIIIDELGAMEF---KSRKFSEVVDEVIKSDKPLLATLHRNWVNKFKDK 161
                                   556666777765445778999999988774...4455556667777777777776666666666655 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   6.3e-07   0.00026       3      44 ..      19      60 ..      17      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.3e-07
                                  EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTT CS
                    APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhg 44
                                  + +++tG+ g GK+t+a ++++kL+e g++v      ++R g
  gi|15669754|ref|NP_248567.1| 19 MRIFITGMPGVGKTTLALKIAEKLKELGYKVGGFITKEIRDG 60
                                  679***************************999988888876 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   1.6e-05    0.0065      12      45 ..      11      44 ..       2     151 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                                  HCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C 12 ltsGlqkgdliiiAarpsmGktalalniaenaav 45
                                   ++G  +   i i + p++Gkt+lal+iae+  +
  gi|15669754|ref|NP_248567.1| 11 QFKGCGETMRIFITGMPGVGKTTLALKIAEKLKE 44
                                  566777777799*****************99775 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.5e-05     0.015      35      58 ..      20      43 ..       4      59 .. 0.81
   2 ?    4.0   0.0     0.091        38      75      97 ..     104     126 ..      74     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.5e-05
                        RuvB_N 35 hvllyGpPGlGkttlakiiakelg 58
                                   ++++G PG+Gkttla  ia++l+
  gi|15669754|ref|NP_248567.1| 20 RIFITGMPGVGKTTLALKIAEKLK 43
                                  5899****************9886 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.091
                        RuvB_N  75 laalltnleekdvlfideihrls 97 
                                   + a+   l++ d++ ide+  ++
  gi|15669754|ref|NP_248567.1| 104 VEAIKRALKDADIIIIDELGAME 126
                                   5689999***********97665 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.4   5.4e-06    0.0023       4      79 ..      21     122 ..      19     127 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.4e-06
                                   EEEE--TTSSHHHHHHHHHHHHHH..............................TT--EEEE-THHHH.TTSSS--GGGHH CS
                         KTI12   4 vvltGlPssGKstrakeLakalee..............................ekrsvvviddeslgiekdsykdsakek 54 
                                   + +tG+P +GK+t+a ++a++l+e                              e+    ++ d ++++ k         +
  gi|15669754|ref|NP_248567.1|  21 IFITGMPGVGKTTLALKIAEKLKElgykvggfitkeirdggkrvgfkiitldtnEETILAYVGDGKIKVGKYA----VFIE 97 
                                   789*********************7777777777777777766544444444333333333444444433322....3345 PP

                                   HHHHHHHHHHHHHHTT.SEEEE-S- CS
                         KTI12  55 alRsslrsavkrdLskekvVIvDsl 79 
                                   +l +   +a+kr+L+  +++I+D+l
  gi|15669754|ref|NP_248567.1|  98 NLDNVGVEAIKRALKDADIIIIDEL 122
                                   5556666777777777777777765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   2.3e-06   0.00095      23      57 ..      17      54 ..       7     153 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.3e-06
                        AAA_16 23 rpelvllsGesGvGKsslvrellralekd...ggiflr 57
                                  ++  ++++G++GvGK++l+ ++++ l++     g f++
  gi|15669754|ref|NP_248567.1| 17 ETMRIFITGMPGVGKTTLALKIAEKLKELgykVGGFIT 54
                                  456799*************9999988776443344454 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.5   8.8e-06    0.0037       8      38 ..      21      62 ..      17     162 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.8e-06
                        AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaee...........e 38
                                  +++tG +G+GKTtl+ +++e+l+e  +              +
  gi|15669754|ref|NP_248567.1| 21 IFITGMPGVGKTTLALKIAEKLKELGYKVGgfitkeirdggK 62
                                  78*******************965433322566666655443 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.7   4.9e-06    0.0021       4      96 ..      21     121 ..      19     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.9e-06
                       DUF2075   4 vlVtGvaGtGKtvvllnllael...............eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklss 69 
                                   +++tG +G GKt ++l+++ +l               +d  ++   ++++   ++  +l           + k ++ k++ 
  gi|15669754|ref|NP_248567.1|  21 IFITGMPGVGKTTLALKIAEKLkelgykvggfitkeiRDGGKRVGFKIITLDTNEETILAYV-------GDGKIKVGKYAV 94 
                                   79********************7777777776644221111222222222333333333222.......233568899999 PP

                       DUF2075  70 finnlsefkkaeekkeepkedvvivDE 96 
                                   fi+nl++   ++ k++ +++d++i+DE
  gi|15669754|ref|NP_248567.1|  95 FIENLDNVGVEAIKRALKDADIIIIDE 121
                                   999999887778888889999999999 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   3.5   4.3e-06    0.0018       3      83 ..      19     131 ..      17     182 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-06
                        AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfi..........................dtek.Glksldadkfpdieswedfldev 56 
                                   ++i+i+G +g+GKTtla+++ +k   +                          dt++    +  +d   ++ +++ f++ +
  gi|15669754|ref|NP_248567.1|  19 MRIFITGMPGVGKTTLALKIAEKLKELgykvggfitkeirdggkrvgfkiitlDTNEeTILAYVGDGKIKVGKYAVFIENL 99 
                                   79******************5555555555566666655555555555555555555233333333333344999999999 PP

                        AAA_24  57 vel.....aaeladyktlviDtideleelcla 83 
                                   + +     +++l+d ++++iD ++ +e   ++
  gi|15669754|ref|NP_248567.1| 100 DNVgveaiKRALKDADIIIIDELGAMEFKSRK 131
                                   999**999**************9998655444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   4.8e-06     0.002       3      26 ..      21      44 ..      19      52 .. 0.89
   2 ?   -1.5   0.0       5.1   2.1e+03     117     117 ..     140     140 ..     100     182 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.8e-06
                                  EEEEC-TTTCHHHHHHHHHHHHCT CS
                         NACHT  3 vilqGeaGsGKTtLlqklalawae 26
                                  ++++G +G+GKTtL+ k+a++++e
  gi|15669754|ref|NP_248567.1| 21 IFITGMPGVGKTTLALKIAEKLKE 44
                                  89*******************997 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.1
                                   T CS
                         NACHT 117 l 117
                                   +
  gi|15669754|ref|NP_248567.1| 140 I 140
                                   1 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.7   9.6e-06     0.004       2      86 ..      24     120 ..      23     123 .. 0.70
   2 ?   -1.2   0.0       3.2   1.4e+03      12      46 ..     150     184 ..     147     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.6e-06
                                   EESTTSSHHHHHHHHHHHHHHTTE...EEEESS..STTSHHHHHHHHHHHTCS---HHH........HHHHHHHHHHHTTH CS
               Thymidylate_kin   2 EGlDGaGKttqaellkerlkeegik..vvltre..pggteiGekirelllkeeeleeqt........eallfaadriehle 70 
                                    G+ G+GKtt a +++e+lke g+k   ++t+e  +gg ++G ki  l ++ee++  +             f  +     +
  gi|15669754|ref|NP_248567.1|  24 TGMPGVGKTTLALKIAEKLKELGYKvgGFITKEirDGGKRVGFKIITLDTNEETILAYVgdgkikvgKYAVFIENLDNVGV 104
                                   6999*********************77799999444556778777777667777766666666554433344444434444 PP

                                   HHHHHHHHTT-EEEEE CS
               Thymidylate_kin  71 ekikpalkqgktvivd 86 
                                   e ik+alk+ +++i+d
  gi|15669754|ref|NP_248567.1| 105 EAIKRALKDADIIIID 120
                                   7777777777777766 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.2
                                   HHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHH CS
               Thymidylate_kin  12 qaellkerlkeegikvvltrepggteiGekirell 46 
                                    +++ ++++k++g+ + lt e+++  + e ++++l
  gi|15669754|ref|NP_248567.1| 150 LHRNWVNKFKDKGELYTLTIENREKLFEEILNKIL 184
                                   55666788888887788888888887777777776 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   1.8e-05    0.0075       6      30 ..      25      49 ..      21      52 .. 0.87
   2 ?    0.9   0.1         1   4.3e+02      57      99 ..     130     174 ..      62     186 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-05
                                  SSTTSSHHHHHHHHHHHHHHTT--E CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  6 tkGGvGKTtlaanLaralarrglrV 30
                                  +  GvGKTtla+++a  l++ g++V
  gi|15669754|ref|NP_248567.1| 25 GMPGVGKTTLALKIAEKLKELGYKV 49
                                  5569********************9 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1
                                   HCCCHHH.HHHCHCHHHH..EEEEEEEEESS....-TTCHHHHHH CS
                                   xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                          CbiA  57 krllell.ealgkkkalllkiagvvlnrvdge.neetllkealee 99 
                                    +++e++ e+++  k+ll ++++  +n+++ + + +tl +e+ e+
  gi|15669754|ref|NP_248567.1| 130 RKFSEVVdEVIKSDKPLLATLHRNWVNKFKDKgELYTLTIENREK 174
                                   566777744444444444666666666665440333444444444 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   2.3e-05    0.0097       2      31 ..      21      50 ..      20      59 .. 0.93
   2 ?   -0.1   0.0       1.9   8.1e+02      78      96 ..     101     119 ..      76     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.3e-05
                          MobB  2 lgivgksgsGKTtLleklipelkarglrvg 31
                                  + i+g+ g GKTtL  k+ ++lk+ g++vg
  gi|15669754|ref|NP_248567.1| 21 IFITGMPGVGKTTLALKIAEKLKELGYKVG 50
                                  6799*************************8 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.9
                          MobB  78 elsleellarlsevDlvlv 96 
                                   ++ +e + + l+++D++++
  gi|15669754|ref|NP_248567.1| 101 NVGVEAIKRALKDADIIII 119
                                   3455555555667777766 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   6.1e-05     0.025      12      33 ..      28      49 ..      21      50 .. 0.95
   2 ?    0.6   0.0       1.1   4.5e+02     108     125 ..     104     121 ..      85     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.1e-05
                        AAA_31 12 GvGKTTtsvnlaaalaklgkkv 33
                                  GvGKTT ++++a+ l +lg+kv
  gi|15669754|ref|NP_248567.1| 28 GVGKTTLALKIAEKLKELGYKV 49
                                  9********************9 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                        AAA_31 108 kellekvkdeYDyiiiDc 125
                                    e++++  ++ D+iiiD 
  gi|15669754|ref|NP_248567.1| 104 VEAIKRALKDADIIIIDE 121
                                   467888889999999996 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.5e-05    0.0061      12      99 ..       8      98 ..       3     133 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                                  HHHHHH...H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHHHHHHTTTS CS
                          PhoH 12 ylealk...kndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelGflpgdleekvdpylrplydaLkdll 91
                                  y+++ k   +   +f++G  G GKt la+ +a ++ + +      +t+ + + g+++Gf   +l++  + +l+++ d   ++ 
  gi|15669754|ref|NP_248567.1|  8 YIHQFKgcgETMRIFITGMPGVGKTTLALKIAEKLKELGYKVGGFITKEIRDGGKRVGFKIITLDTNEETILAYVGDGKIKVG 90
                                  555555554555689*****************9888876555666799999**************999999999998755555 PP

                                  -TTCHHHH CS
                          PhoH 92 gaekvekl 99
                                  + + + + 
  gi|15669754|ref|NP_248567.1| 91 KYAVFIEN 98
                                  44333333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.2   0.00018     0.074       2      24 ..      21      43 ..      20      50 .. 0.87
   2 ?    2.6   0.1      0.31   1.3e+02      58      75 ..     106     123 ..     100     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00018
                                  EEEE--SSSSHHHHHHHGGGGBS CS
                         AAA_5  2 vlLvGppGtgKselaerlaaaln 24
                                  +++ G pG+gK++la ++a+ l+
  gi|15669754|ref|NP_248567.1| 21 IFITGMPGVGKTTLALKIAEKLK 43
                                  6899***************9984 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.31
                                   -------G-SEEEEESGG CS
                         AAA_5  58 plvraaregeilvlDEve 75 
                                   +++ra + ++i+++DE+ 
  gi|15669754|ref|NP_248567.1| 106 AIKRALKDADIIIIDELG 123
                                   5689999********985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   3.8e-05     0.016       2      24 ..      21      43 ..      21     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-05
                        AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                                  +++ G+pG+GK+tla ++++kl+
  gi|15669754|ref|NP_248567.1| 21 IFITGMPGVGKTTLALKIAEKLK 43
                                  5789**************99887 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   4.2e-05     0.018      10      36 ..      24      50 ..      17      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
                          ParA 10 SgKGGVGKStvavnlAlaLakkglkvg 36
                                   g  GVGK+t+a ++A +L++ g+kvg
  gi|15669754|ref|NP_248567.1| 24 TGMPGVGKTTLALKIAEKLKELGYKVG 50
                                  5777**********************9 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   5.3e-05     0.022       1      26 [.      20      49 ..      20      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.3e-05
                        AAA_28  1 kivitGgestGKTtlleaLaar....gypv 26
                                  +i itG ++ GKTtl+ ++a++    gy+v
  gi|15669754|ref|NP_248567.1| 20 RIFITGMPGVGKTTLALKIAEKlkelGYKV 49
                                  799*************88886655568875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.3   0.00018     0.074       5      28 ..      21      47 ..      17     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00018
                        AAA_14  5 lvitGaRrvGKTtllkqlikell...v 28
                                  ++itG+  vGKTtl+ +++++l     
  gi|15669754|ref|NP_248567.1| 21 IFITGMPGVGKTTLALKIAEKLKelgY 47
                                  78*****************88875441 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   0.00047      0.19       1      21 [.      21      41 ..      21     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00047
               Viral_helicase1  1 ivvhGvpGcGKStlirkllrt 21
                                  i + G+pG GK+tl  k++++
  gi|15669754|ref|NP_248567.1| 21 IFITGMPGVGKTTLALKIAEK 41
                                  5799*************9987 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.6e-05      0.04       4      32 ..      21      49 ..      18      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.6e-05
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                   ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkv 32
                                  i+++G  GVGKtt++  +a kl e g+kv
  gi|15669754|ref|NP_248567.1| 21 IFITGMPGVGKTTLALKIAEKLKELGYKV 49
                                  9***********************99987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.4   0.00085      0.35      13     113 ..      21     124 ..      15     159 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00085
                        AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal.......ldfddllte 86 
                                   +++t+ pG GKT++  +i + l+elg        +    +   k++  ++ +l+ + +Ti +  +               +
  gi|15669754|ref|NP_248567.1|  21 IFITGMPGVGKTTLALKIAEKLKELGYK--VGGFITKEIRDGGKRVGFKIITLDTNEETILAY-VgdgkikvG-------K 91 
                                   789***********99999999998833..222333333444455555555555555555544.122222220.......2 PP

                        AAA_19  87 alelle......eaeeekklqeeellivDEfqd 113
                                    + ++e       ++ ++ l++++++i+DE   
  gi|15669754|ref|NP_248567.1|  92 YAVFIEnldnvgVEAIKRALKDADIIIIDELGA 124
                                   222333444444334555665666666666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00053      0.22      35      54 ..      20      39 ..      10      52 .. 0.87
   2 ?    1.4   0.1      0.47     2e+02     131     155 ..     105     126 ..      93     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00053
                        AAA_25 35 lallaGapgtGKttlaldla 54
                                   + ++G pg+GKttlal +a
  gi|15669754|ref|NP_248567.1| 20 RIFITGMPGVGKTTLALKIA 39
                                  6789*************987 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.47
                        AAA_25 131 daleaaieevegvrlvviDplsral 155
                                   +a+    ++ ++++ ++iD l ++ 
  gi|15669754|ref|NP_248567.1| 105 EAIK---RALKDADIIIIDELGAME 126
                                   3333...444568******998875 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.38   1.6e+02      37      59 ..      21      43 ..      13      49 .. 0.84
   2 ?   11.1   0.2   0.00064      0.27      79     136 ..      95     149 ..      70     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.38
                                  EEEE-SSSSSHHHHHHHHHHHHH CS
                      Bac_DnaA 37 lfiygevGlGktHLlkaignevl 59
                                  +fi g  G+Gkt L   i+ +++
  gi|15669754|ref|NP_248567.1| 21 IFITGMPGVGKTTLALKIAEKLK 43
                                  799**********9888877765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00064
                                   HHHHHHTT-HHHHHHHHTT-SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEEEE CS
                      Bac_DnaA  79 lvkalrdkkaeefkeklrkvDvLliDDiqflagkektqeelfhtfnalleegkqvvls 136
                                   +++ l +  +e++k+ l+++D+++iD++  ++ k+    ++  +++++++++k ++ +
  gi|15669754|ref|NP_248567.1|  95 FIENLDNVGVEAIKRALKDADIIIIDELGAMEFKS---RKFSEVVDEVIKSDKPLLAT 149
                                   7888999999*********************9999...66777778888887777665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00043      0.18       1      23 [.      21      43 ..      21      76 .. 0.87
   2 ?    0.3   0.0       2.2   9.1e+02      48      69 ..     112     132 ..     105     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00043
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakall 23
                                  i+++G +g+GK+tla ++a++l 
  gi|15669754|ref|NP_248567.1| 21 IFITGMPGVGKTTLALKIAEKLK 43
                                  789**************999887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2.2
                  RNA_helicase  48 tgqevvvidDfgqvkdee.npsd 69 
                                   ++ ++++id++g+++ ++ +   
  gi|15669754|ref|NP_248567.1| 112 KDADIIIIDELGAMEFKSrK--F 132
                                   56789999999999855222..2 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   0.00017      0.07       1      40 [.      20      61 ..      20     182 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                                  EEEEEESTTSSHHHHHHHHHTSTEEESSST..TSSSSEEEEE CS
                      MMR_HSR1  1 evaivGrpNvGKStLinaltgekaivsdkp..gtTrdinegr 40
                                  ++ i G+p vGK+tL  ++ ++  + + k   + T++i+ g 
  gi|15669754|ref|NP_248567.1| 20 RIFITGMPGVGKTTLALKIAEKLKELGYKVggFITKEIRDGG 61
                                  689****************99855554444336777776653 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.1   0.00023     0.094       3      92 ..      21     123 ..      19     145 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                                   EEEEESTTCCHHHHHHHHHCT--SS-EEE...EESS-SS..CHCCCCCCHCCCT....EEEETTTTECCHCTT-HHHHHHH CS
                          cobW   3 tvltGflGsGKTtLlnhllenraglklav...ivNefge..vsiDaellretgve...ivelenGciCctlredllkelea 75 
                                   + +tG +G GKTtL  ++ e+ ++l + v   i+ e+ +    +  ++++ +++e   +  + +G+i       ++++l++
  gi|15669754|ref|NP_248567.1|  21 IFITGMPGVGKTTLALKIAEKLKELGYKVggfITKEIRDggKRVGFKIITLDTNEetiLAYVGDGKIKVGKYAVFIENLDN 101
                                   679***************966555544443337777765333344444433322223444455555444433333333333 PP

                                   HHHHH.....TT-SEEEEEECT CS
                          cobW  76 leere.....erldviliEttG 92 
                                   +  +      ++ d+i+i   G
  gi|15669754|ref|NP_248567.1| 102 VGVEAikralKDADIIIIDELG 123
                                   3222222333666666666666 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.2   0.00037      0.15      15      65 ..      14      59 ..       2     146 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                        ATPase 15 GipegrvvlitGepGtGKtifalqFlikgaekygep.gvfvtveepaedlre 65
                                  G  e   + itG pG GKt++al+ + + +++ g++ g f+t e +      
  gi|15669754|ref|NP_248567.1| 14 GCGETMRIFITGMPGVGKTTLALKIA-EKLKELGYKvGGFITKEIR-----D 59
                                  666777899**************955.5668889883468886543.....3 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.1    0.0025       1.1      11     126 ..      28     140 ..      21     146 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0025
                                   TSSHHHHHHHHHHHHHTTT--EEE.EE--TTT-HHHHHHHHHHHHH.HHHT------EEE-SSS-HHHHTT.S-HHHHHHH CS
                          MipZ  11 GsGksttavhvavaLlkkGarvaa.idldlrqrtlarylenraata.erkglsLplpealalseaeeaeve.eeeeaevae 88 
                                   G Gk+t a+ +a  L + G +v+  i  ++r     + ++ +  t  ++++  L+     +++ ++ a    + ++     
  gi|15669754|ref|NP_248567.1|  28 GVGKTTLALKIAEKLKELGYKVGGfITKEIRDG--GKRVGFKIITLdTNEETILAYVGDGKIKVGKYAVFIeNLDNVG--- 103
                                   89********************97244444443..3334444333303444455555555565555443330333333... PP

                                   HHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEE CS
                          MipZ  89 leelvadleaeldfividtPGsdsalsrlahsladtlv 126
                                   + e+++++ +++d+i+id  G  +  sr   ++ d ++
  gi|15669754|ref|NP_248567.1| 104 V-EAIKRALKDADIIIIDELGAMEFKSRKFSEVVDEVI 140
                                   3.456666678899999999999999998888888776 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00086      0.36       1      27 [.      23      49 ..      23      51 .. 0.91
   2 ?   -1.1   0.0       3.2   1.3e+03      75     104 ..      95     127 ..      70     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00086
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsv 27
                                  ++G++G+GKtt+  +++e l++ g++v
  gi|15669754|ref|NP_248567.1| 23 ITGMPGVGKTTLALKIAEKLKELGYKV 49
                                  68****************999998876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.2
                    ATP_bind_1  75 lresldwl.deeleke.ed.dyllfDtPGQiel 104
                                   + e+ld++  e++++  +d d +++D  G +e+
  gi|15669754|ref|NP_248567.1|  95 FIENLDNVgVEAIKRAlKDaDIIIIDELGAMEF 127
                                   556666665455544444447777776555554 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.0    0.0016      0.68      25      57 ..      19      49 ..       1     147 [. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0016
                                  SEEEEEESTTSTHHHHHHHHHHHH-S.....-E CS
                        ResIII 25 krglikmaTGtGKTlvaaklierllkkgkeekf 57
                                   r++i    G+GKT +a+k++e+l++ g+  k+
  gi|15669754|ref|NP_248567.1| 19 MRIFITGMPGVGKTTLALKIAEKLKELGY--KV 49
                                  388899999***************99877..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                       140  (0.00780858); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              43  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 1200.31
//
Query:       gi|15669755|ref|NP_248568.1|  [L=386]
Description: multidrug-efflux transporter [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-56  191.6  57.3    1.3e-53  182.2  45.3    2.0  2  MFS_1       Major Facilitator Superfamily
    9.4e-10   37.9  41.3    1.2e-07   31.0  18.0    2.1  2  MFS_1_like  MFS_1 like family
    2.9e-08   33.0  20.4    2.9e-08   33.0  20.4    3.6  2  Sugar_tr    Sugar (and other) transporter
    2.1e-06   26.4  22.0    1.1e-05   24.0  22.0    1.9  1  MFS_3       Transmembrane secretion effector
    0.00025   20.2  23.6    0.00031   19.9   5.7    2.7  3  PUCC        PUCC protein
  ------ inclusion threshold ------
          3    6.3  53.8       0.22   10.0   3.0    3.0  3  MFS_2       MFS/sugar transport protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.2  45.3   4.2e-57   1.3e-53       1     353 []      11     350 ..      11     350 .. 0.92
   2 !   23.0   4.1   1.1e-08   3.2e-05     117     173 ..     329     383 ..     327     386 .] 0.91

  Alignments for each domain:
  == domain 1  score: 182.2 bits;  conditional E-value: 4.2e-57
                         MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll. 80 
                                   +++++f ++l+ ++++p++  ++a++lg++  eigl+++ +al+  va++p+G+lsd +G + ++++g ++++++ +l+  
  gi|15669755|ref|NP_248568.1|  11 IWITTFTTMLGVGFIAPIMA-IYAQTLGATNLEIGLIFGSFALARTVAQIPVGVLSDIYGKKFFIVCGTFFYGVS-TLMYn 89 
                                   699*****************.9*****************************************************.88888 PP

                         MFS_1  81 fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                   f+s++  +l++r+++G+++++++p+++++ia+++pk++ g ++g++++++ lG+ +gp +gg+la+ +g   +fy++++++
  gi|15669755|ref|NP_248568.1|  90 FVSTVLGFLIVRIFTGIFSAFVTPVAGSYIAAIAPKTRLGEYMGIFNSAITLGFGIGPFIGGILADMYGIKMPFYFCGFLG 170
                                   989999*************************************************************************** PP

                         MFS_1 162 llafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsg 242
                                   +la+++   ++  e+    ++++k +   ++ + l++ ++ l++++ + + +i+ +++ ++++g++++l ly    ++++ 
  gi|15669755|ref|NP_248568.1| 171 ILAAII--SYMKLEDIVFNKNKEKID--VKKISTLFS-FEFLKNRN-FSSSFIINVSNVMINAGIYAYLALY-AINYNIT- 243
                                   ***998..666555555444444444..347777777.77777777.3367777777789************.*******. PP

                         MFS_1 243 lllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpslla 323
                                     ++g+++al+ +++a l+  +g+l d+lg+    ++++++++++++g++ll+++++ + +l++l +i +g+++ +++ ++
  gi|15669755|ref|NP_248568.1| 244 ISQVGFMIALTNILMALLQRSFGKLYDKLGN----IMIIIGIFIISFGMYLLSTSTTFLTILASLTIIAVGSSISSTATTS 320
                                   9*****************************8....9999999*************888888889999************** PP

                         MFS_1 324 lasdlappeeagtasglfntagslggalgp 353
                                   la++ +p+++ g a+glf+t  ++g+++g+
  gi|15669755|ref|NP_248568.1| 321 LAVKDIPTHRKGEAMGLFTTSINIGMFIGA 350
                                   ****************************96 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.1e-08
                         MFS_1 117 eergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllp 173
                                    ++g a+gl+++++++G+ +g++  g+la+ lg   ++ + ai+s++++++   +l+
  gi|15669755|ref|NP_248568.1| 329 HRKGEAMGLFTTSINIGMFIGAVSFGFLADILGIANMYKFSAIFSIVVGII--SYLR 383
                                   6899*********************************************98..6665 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0  18.0     4e-11   1.2e-07     223     384 ..       6     164 ..       1     165 [. 0.91
   2 !   12.5  16.0   1.6e-05     0.047     200     384 ..     184     367 ..     164     368 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 4e-11
                    MFS_1_like 223 knpeviifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilr 303
                                   kn  vi++ +++++lg  +g+i   + +Y + lga+n  +G +    ++a  +  +    l +++G  + ++ + ++y + 
  gi|15669755|ref|NP_248568.1|   6 KNVFVIWITTFTTMLG--VGFIAPIMAIYAQTLGATNLEIGLIFGSFALARTVAQIPVGVLSDIYGKKFFIVCGTFFYGVS 84 
                                   6667888888888888..599****************9998888877777777777789999******************* PP

                    MFS_1_like 304 fllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                    l+y++++ +   l++ ++ gi  + +  +a +y++ iapk   + ++g+++++ + lG ++G +iGG+l d+++ ++ F+
  gi|15669755|ref|NP_248568.1|  85 TLMYNFVSTVLGFLIVRIFTGIFSAFVTPVAGSYIAAIAPKTRLGEYMGIFNSA-ITLGFGIGPFIGGILADMYGIKMPFY 164
                                   ****************************************************99.89***************999988886 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.6e-05
                    MFS_1_like 200 lnetekesklkvtkslqv.llnilknpeviifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfff 279
                                   +   + ++k++v+k+ +   ++ lkn++    +++ +   m+++ i+++l lY  +++ + + +G ++al+ ++   l   
  gi|15669755|ref|NP_248568.1| 184 IVFNKNKEKIDVKKISTLfSFEFLKNRNFSSSFIINVSNVMINAGIYAYLALYAINYNITISQVGFMIALTNILMALLQRS 264
                                   444455556666665543147899999999999999999999*******************************99999999 PP

                    MFS_1_like 280 aeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfg 360
                                     kl +klG + ++ii+++++ +   l+++ + +  +l   ++ ++   +   a ++ + k +p + ++  +gl+++  + 
  gi|15669755|ref|NP_248568.1| 265 FGKLYDKLGNI-MIIIGIFIISFGMYLLSTSTTFLTILASLTIIAVGSSISSTATTSLAVKDIPTHRKGEAMGLFTTS-IN 343
                                   9********76.78899998888888888888888888888888888888888999999****************975.89 PP

                    MFS_1_like 361 lGralGsliGGllwdlksaiflFr 384
                                   +G ++G++  G+l d+ + + +++
  gi|15669755|ref|NP_248568.1| 344 IGMFIGAVSFGFLADILGIANMYK 367
                                   ************999887777665 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0  20.4   9.8e-12   2.9e-08      40     188 ..      35     177 ..       9     183 .. 0.91
   2 ?    1.8  22.9     0.028        84      45     183 ..     244     379 ..     206     382 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 9.8e-12
                                   HHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                      Sugar_tr  40 skeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                   +  ++++ +gli+++f + +++ ++ +g l+d++G+k  ++++++++ +++++  +     +v  +++ R+++Gi+  +++
  gi|15669755|ref|NP_248568.1|  35 TLGATNLEIGLIFGSFALARTVAQIPVGVLSDIYGKKFFIVCGTFFYGVSTLMYNFVS---TVLGFLIVRIFTGIFSAFVT 112
                                   44557889*********************************************99999...89****************** PP

                                   HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG CS
                      Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill 188
                                    ++  yi+ iApk+  g  ++++++ait+G+ ++ ++g +l+++ +    +++++++ ++ +l +i+ 
  gi|15669755|ref|NP_248568.1| 113 PVAGSYIAAIAPKTRLGEYMGIFNSAITLGFGIGPFIGGILADMYG---IKMPFYFCGFLGILAAIIS 177
                                   *****************************************88888...89*********99998876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.028
                                   ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPm 125
                                    +++g++ +++++  ++ +  +g+l d++G+   ++i++++ + g  l  +++   ++  ++++  ++ +g  + s+ ++ 
  gi|15669755|ref|NP_248568.1| 244 ISQVGFMIALTNILMALLQRSFGKLYDKLGNIM-IIIGIFIISFGMYLLSTST---TFLTILASLTIIAVGSSISSTATTS 320
                                   456677777777777777777888888888643.3444444445555555555...8888888888888888899988888 PP

                                   HHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-.TTHHHHHHHCCHHHHHH CS
                      Sugar_tr 126 yisEiApkklRgalvslyqlaitfGilvaaifglglnktsn.adgwrillglqlvpall 183
                                   ++ +  p++  g  ++l+ ++i +G++++a++  +l+++ + a+ +++   +++v  ++
  gi|15669755|ref|NP_248568.1| 321 LAVKDIPTHRKGEAMGLFTTSINIGMFIGAVSFGFLADILGiANMYKFSAIFSIVVGII 379
                                   88888899888999999999999999999888888877777777777777777777654 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0  22.0   3.8e-09   1.1e-05       7     391 ..       4     381 ..       1     385 [. 0.73

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.8e-09
                         MFS_3   7 lrqkvFrviWiaslvsnlGt.liqevaasWlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqllla 86 
                                   l+++vF viWi++  + lG  +i  + ++    ++ a++l + l+  + +L   +  i++G+l+D++ ++ +++ + ++  
  gi|15669755|ref|NP_248568.1|   4 LEKNVF-VIWITTFTTMLGVgFIAPI-MAIYAQTLGATNLEIGLIFGSFALARTVAQIPVGVLSDIYGKKFFIVCG-TFFY 81 
                                   567777.79**********7255555.5566788*********************************987665555.5666 PP

                         MFS_3  87 lvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavG 167
                                    vs+l+  ++     ++   l++ +++gi +a+ +P     +  + ++  + + + +    i +   +GP +gG+l  + G
  gi|15669755|ref|NP_248568.1|  82 GVSTLMYNFV----STVLGFLIVRIFTGIFSAFVTPVAGSYIAAIAPKTRLGEYMGIFNSAITLGFGIGPFIGGILADMYG 158
                                   6666654433....3455678889999******************************999********************* PP

                         MFS_3 168 aalafavnalsylalivallr.wkrevrksslprEkll.ealraglRfta.asreikavlvRaalFglsasavlaLLPlva 245
                                     + f +    +l +++a++  +k e    +  +Ek+  + ++  + f     r+  ++++  +   +  + ++a L l  
  gi|15669755|ref|NP_248568.1| 159 IKMPFYFC--GFLGILAAIISyMKLEDIVFNKNKEKIDvKKISTLFSFEFlKNRNFSSSFIINVSNVMINAGIYAYLALY- 236
                                   **999874..4566666554314555555555566664133444444432123555555555555556666666666665. PP

                         MFS_3 246 rdqldgdalvyGillgalGvGAilgalllsrLRerlss......erlvlla..avalAlvllslalasslwvavlvlllgG 318
                                          a+ y i ++ +G    l+ +l++ L +++++      + ++ +    + + + lls++ +  + +a l+++  G
  gi|15669755|ref|NP_248568.1| 237 -------AINYNITISQVGFMIALTNILMALLQRSFGKlydklgNIMIIIGifIISFGMYLLSTSTTFLTILASLTIIAVG 310
                                   .......56677777777776666667777666666543311212233333013455666666666666777777777777 PP

                         MFS_3 319 aaWitalstlnvavqlavPrWvvgRalavYltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaaill 391
                                   ++ i + +t   av+  +P   +g a+ ++ t ++ g+  G++ +G +a+ l++++  + +a+  +++++i++
  gi|15669755|ref|NP_248568.1| 311 SS-ISSTATTSLAVK-DIPTHRKGEAMGLFTTSINIGMFIGAVSFGFLADILGIANMYKFSAIFSIVVGIISY 381
                                   65.666666666665.57*********************************************9999998876 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.9      0.13   3.9e+02     309     364 ..      12      69 ..       7      91 .. 0.75
   2 !    7.5   7.7   0.00058       1.7     258     366 ..      43     160 ..      33     188 .. 0.66
   3 !   19.9   5.7     1e-07   0.00031      54     171 ..     272     380 ..     262     386 .] 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.13
                          PUCC 309 llGlasGlfavaaltlmldlaaeerag..lalGaWGaaQaiaaglavllggalrdllk 364
                                    +  ++ +++v+ ++ ++++ a+   +  l +G+     a+a+ +a +  g+l d+  
  gi|15669755|ref|NP_248568.1|  12 WITTFTTMLGVGFIAPIMAIYAQTLGAtnLEIGLIFGSFALARTVAQIPVGVLSDIYG 69 
                                   5556777888888888888887765554578888777889999999999999999864 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00058
                          PUCC 258 vGlllaglvlsrglkkarlasl....gvllglls.flllilaallenvallvagvlllGlasGlf....avaaltlmldla 329
                                   +Gl+ ++++l+r + +  + +l    g    +++  ++  +++l+ n +  v+g l++ +++G+f    +  a + + ++a
  gi|15669755|ref|NP_248568.1|  43 IGLIFGSFALARTVAQIPVGVLsdiyGKKFFIVCgTFFYGVSTLMYNFVSTVLGFLIVRIFTGIFsafvTPVAGSYIAAIA 123
                                   466666666666666665555411113333333303344456666665555555555555555551000567778999*** PP

                          PUCC 330 aeeraglalGaWGaaQaiaaglavllggalrdllkal 366
                                   ++ r g  +G+   a ++  g++ ++gg+l+d+  + 
  gi|15669755|ref|NP_248568.1| 124 PKTRLGEYMGIFNSAITLGFGIGPFIGGILADMYGIK 160
                                   ********************************97664 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 1e-07
                          PUCC  54 lGslalalglaiaplalivlsgkgeaeaaatwaglilaavafllvGlgvslsqTallALladlaeeeerpkvvgllyvmll 134
                                   lG +++++g++i+++++ +ls+        t++ +ila +  ++vG ++  s+Ta   L++     +++ ++ gl    + 
  gi|15669755|ref|NP_248568.1| 272 LGNIMIIIGIFIISFGMYLLST-------STTFLTILASLTIIAVGSSI--SSTATTSLAVKDIPTHRKGEAMGLFTTSIN 343
                                   799*******************.......77788888888877777765..566666677777888999************ PP

                          PUCC 135 igivvsaivvgallkdytearLirvvqgvalitlvln 171
                                   ig+ ++a+ +g l + +  a++ ++ +  ++++ +++
  gi|15669755|ref|NP_248568.1| 344 IGMFIGAVSFGFLADILGIANMYKFSAIFSIVVGIIS 380
                                   *************999999998888776666666655 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9  20.4     0.044   1.3e+02     226     387 ..       9     160 ..       3     164 .. 0.80
   2 ?    7.9  14.5   0.00033         1     181     337 ..     169     320 ..     162     326 .. 0.74
   3 ?   10.0   3.0   7.4e-05      0.22     257     308 ..     331     382 ..     327     385 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.044
                         MFS_2 226 flillllfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvl 305
                                   f+i++++f +++l++g+ + +++ y++  lg ++ ++ ++++ + ++ +++ + + +l   +gkk  +++g+ ++ v +++
  gi|15669755|ref|NP_248568.1|   9 FVIWITTF-TTMLGVGFIAPIMAIYAQT-LGaTNLEIGLIFGSFALARTVAQIPVGVLSDIYGKKFFIVCGTFFYGVSTLM 87 
                                   55555544.5566666666667777765.555**********************************999999999998888 PP

                         MFS_2 306 vlllqpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgllLsafgy 386
                                     ++  s +l fl++ + +g++ ++ + ++ s +a +        +k r g++++++  +  l+ gig ++ g+l +++g+
  gi|15669755|ref|NP_248568.1|  88 YNFV--STVLGFLIVRIFTGIFSAFVTPVAGSYIAAI-------APKTRLGEYMGIFNSAITLGFGIGPFIGGILADMYGI 159
                                   7777..7788888888888888666666666665555.......477889**************************99998 PP

                         MFS_2 387 r 387
                                   +
  gi|15669755|ref|NP_248568.1| 160 K 160
                                   6 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00033
                         MFS_2 181 LmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillllfllaalalgvlnglllYyltyvlgngsaa 261
                                   L +l++ii+++   + v ++k++++ + +k+s+l  + e+++nr f     +f++++  +++++g+++Y + y ++ +  +
  gi|15669755|ref|NP_248568.1| 169 LGILAAIISYMKLEDIV-FNKNKEKIDVKKISTLFSF-EFLKNRNFS---SSFIINVSNVMINAGIYAYLALYAINYNITI 244
                                   55666666655555443.3566666777777777766.467776665...57889999999***************99999 PP

                         MFS_2 262 svfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpws 337
                                   s + +++ + ++l+++l   + k ++k   +++ + + i+ + + ll + +  l+ l+ l+i+ +g  ++ ++ +s
  gi|15669755|ref|NP_248568.1| 245 SQVGFMIALTNILMALLQRSFGKLYDKLGNIMIIIGIFIISFGMYLLSTSTTFLTILASLTIIAVGSSISSTATTS 320
                                   9999999*********************777777766666655444445666666666777777776666666655 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 7.4e-05
                         MFS_2 257 ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvll 308
                                   +g+a+ +f++ + i++++g++ +  la  lg  n+y ++a++ iv +++ +l
  gi|15669755|ref|NP_248568.1| 331 KGEAMGLFTTSINIGMFIGAVSFGFLADILGIANMYKFSAIFSIVVGIISYL 382
                                   688999******************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 2349.44
//
Query:       gi|15669756|ref|NP_248569.1|  [L=553]
Description: hypothetical protein MJ_1561 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-14   52.9   0.0      0.008   16.4   0.0    5.1  5  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
    6.4e-12   45.6  18.2    0.00031   21.0   0.1    5.4  7  CARDB            CARDB
    8.1e-06   26.1   5.3        1.6    9.1   0.1    4.9  4  DUF11            Domain of unknown function DUF11
    2.4e-05   24.6   5.3        0.1   12.9   0.2    4.0  3  DUF4352          Domain of unknown function (DUF4352)
    4.9e-05   22.8   7.8       0.11   11.8   0.0    4.1  5  TRAP_beta        Translocon-associated protein beta (TRAPB)
     0.0022   18.1   0.2          1    9.6   0.0    3.4  4  Ig_GlcNase       Exo-beta-D-glucosaminidase Ig-fold domain
     0.0074   16.6   1.6        2.4    8.4   0.0    3.8  4  AP3B1_C          Clathrin-adaptor complex-3 beta-1 subunit C-
     0.0099   16.2   4.3      0.062   13.6   0.1    4.1  5  CBM49            Carbohydrate binding domain CBM49
  ------ inclusion threshold ------
      0.043   14.1   0.0        4.4    7.7   0.0    3.4  4  Alpha_adaptinC2  Adaptin C-terminal domain
      0.046   13.5   0.0         20    5.0   0.0    3.4  3  Ig_mannosidase   Ig-fold domain
      0.058   12.5   0.1          2    7.5   0.0    2.2  2  PHTB1_C          PTHB1 C-terminus
      0.077   13.0   0.1       0.37   10.8   0.1    2.2  1  WD40_3           WD domain, G-beta repeat
      0.086   13.0   0.0         21    5.3   0.0    3.4  3  Fn3-like         Fibronectin type III-like domain
       0.13   12.7   0.3       0.13   12.7   0.3    3.9  4  Arrestin_C       Arrestin (or S-antigen), C-terminal domain
        2.3    8.2   9.4        3.2    7.7   0.5    3.9  4  DUF2393          Protein of unknown function (DUF2393)


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.7e-06     0.008       2      78 ..      35     116 ..      34     117 .. 0.88
   2 ?    1.9   0.0      0.23   2.8e+02       5      26 ..     159     180 ..     155     183 .. 0.89
   3 ?   -3.0   0.0       7.6   9.1e+03      46      77 ..     236     267 ..     233     268 .. 0.84
   4 !   14.3   0.0   3.1e-05     0.037       7      78 ..     311     384 ..     304     385 .. 0.88
   5 !   13.6   0.0   5.2e-05     0.062       1      77 [.     417     494 ..     417     496 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.7e-06
                   NPCBM_assoc   2 epGetvtltltvtndg.taaatnvslslsl..PeGWt.vvevsp.asaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                    pG++v l + +tnd  +  ++n+ +++s   P + + v  +++ a+++ l pGe+ ++ +k+ + ++a   dye+ +k++
  gi|15669756|ref|NP_248569.1|  35 HPGDDVDLWIKITNDNyDNEVKNIVVEVSPhyPFELRqVNPIKGkATISHLNPGESDTVYFKLHVDENAPSRDYEIDVKVS 115
                                   6899999999999999899999999999987799988777776525777******************************99 PP

                   NPCBM_assoc  78 l 78 
                                   +
  gi|15669756|ref|NP_248569.1| 116 Y 116
                                   7 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.23
                   NPCBM_assoc   5 etvtltltvtndgtaaatnvsl 26 
                                   +t+t+ +++ n+gt +a++v+l
  gi|15669756|ref|NP_248569.1| 159 KTQTVPIEIINTGTGTAKEVNL 180
                                   799****************998 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 7.6
                   NPCBM_assoc  46 slapGetveatvkVtppagaaaGdyevtakar 77 
                                   +l+p+ +   ++k+   ++ + G y++ a+++
  gi|15669756|ref|NP_248569.1| 236 ALKPDNSRVINLKLYTASNLVEGCYQIPAVIT 267
                                   68899999999999999999999999998887 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 3.1e-05
                   NPCBM_assoc   7 vtltltvtndgtaaatnvslslsl..P..eGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                   v++++t+tn+g a a++v+l+l +  P  + W+  +   + +  l pG + ++ + V + + a a  y++ +++++
  gi|15669756|ref|NP_248569.1| 311 VRIDVTITNNGHAEAKDVKLKLITnkPfkDSWS--NCNIKDVGNLLPGVSKTVSFYVDVDKYASAKHYKLPIEISY 384
                                   6899******************98677556788..88889999**************************9999886 PP

  == domain 5  score: 13.6 bits;  conditional E-value: 5.2e-05
                   NPCBM_assoc   1 vepGetvtltltvtndgtaaatnvslslslPeGWt.vvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                   v++G+++t+ +t++n g++ a++v++s+   +G      ++ +++ +l p++t +  + + + ++a+   y +t+++r
  gi|15669756|ref|NP_248569.1| 417 VTAGKENTVYITIKNVGSEKAERVKISAIRNSGQPfDYPIKSDTIGTLYPNQTGTGVIVIDVDKNAESKPYIITIEIR 494
                                   689***********************9976555443355999*************************999****9998 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0034       4.1      50      87 ..      78     117 ..      35     127 .. 0.83
   2 !    9.3   1.8    0.0011       1.3      15      70 ..     155     214 ..     148     224 .. 0.71
   3 ?   -2.5   0.0       5.1   6.1e+03      51      83 ..     231     265 ..     221     279 .. 0.69
   4 ?   -0.7   0.0       1.5   1.8e+03      30      62 ..     272     309 ..     260     311 .. 0.78
   5 !   21.0   0.1   2.6e-07   0.00031      12      78 ..     301     376 ..     289     391 .. 0.76
   6 !   15.2   1.2   1.6e-05     0.019       9      49 ..     411     451 ..     402     507 .. 0.76
   7 ?   -1.5   0.0       2.5     3e+03      17      44 ..     483     510 ..     472     517 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0034
                                   EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEESTT CS
                         CARDB  50 gtvtvpsLaagesttvsftwtte..ategevtltvvvDpd 87 
                                   g++t++ L++ges tv f+  ++  a + ++++ v+v  d
  gi|15669756|ref|NP_248569.1|  78 GKATISHLNPGESDTVYFKLHVDenAPSRDYEIDVKVSYD 117
                                   7899******************976666778777776544 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
                                   EETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE CS
                         CARDB  15 afvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwt 70 
                                   + + ++ t+ +++ N+Gt++++++++ +  + ++v    ++v+v++    ++ + ++ ++
  gi|15669756|ref|NP_248569.1| 155 LIPSKTQTVPIEIINTGTGTAKEVNLYIGYSLNSVnagsESVEVSAYGTTKTQEKTIYYP 214
                                   5678999***************99998887777776644444444444444444444444 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.1
                                   EEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEE CS
                         CARDB  51 tvtvpsLaagesttvsftwtte..ategevtltvv 83 
                                   ++++ +L++++s+ ++++  t+  + eg +++ +v
  gi|15669756|ref|NP_248569.1| 231 KFYLGALKPDNSRVINLKLYTAsnLVEGCYQIPAV 265
                                   56677788888877777777765555566665554 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.5
                                   -SSS-EEEEEEEEEETTEEE.EEEEE....SEE-CTEE CS
                         CARDB  30 qGtaasgatkvalyldgelv.gtvtv....psLaages 62 
                                    Gt+ ++++++  y+ g+   g ++v    +++++g++
  gi|15669756|ref|NP_248569.1| 272 DGTKRAEQITIGAYVKGDILlGISNVvtdpKEIKPGTT 309
                                   69999999999999999987755555667777777776 PP

  == domain 5  score: 21.0 bits;  conditional E-value: 2.6e-07
                                   -SEEETTSE.EEEEEEEEE-SSS-EEEEEEEEEETTEEE......EEEEESEE-CTEEEEEEEEEE-S..-S-CEE CS
                         CARDB  12 pseafvgee.ntitvtvkNqGtaasgatkvalyldgelv......gtvtvpsLaagesttvsftwtte..ategev 78 
                                   p+e  +g++ ++i vt++N+G+a+++++k++l+ ++  +      +  +v +L +g s+tvsf + ++  a+++ +
  gi|15669756|ref|NP_248569.1| 301 PKEIKPGTTyVRIDVTITNNGHAEAKDVKLKLITNKPFKdswsncNIKDVGNLLPGVSKTVSFYVDVDkyASAKHY 376
                                   555555544279************************99966644444456*************9888754444444 PP

  == domain 6  score: 15.2 bits;  conditional E-value: 1.6e-05
                                   EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE CS
                         CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv 49 
                                   ++++ ++++g+ent+++t+kN G+++++ +k++ + +  + 
  gi|15669756|ref|NP_248569.1| 411 ITKEVNVTAGKENTVYITIKNVGSEKAERVKISAIRNSGQP 451
                                   56777899**********************99877765554 PP

  == domain 7  score: -1.5 bits;  conditional E-value: 2.5
                                   TTSEEEEEEEEEE-SSS-EEEEEEEEEE CS
                         CARDB  17 vgeentitvtvkNqGtaasgatkvalyl 44 
                                   + + + it++++  G+ ++g+ +v +y 
  gi|15669756|ref|NP_248569.1| 483 ESKPYIITIEIRCAGDSDEGDNNVYVYQ 510
                                   5666778999999999999999999985 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.014        16       8      81 ..      32     102 ..      24     108 .. 0.76
   2 ?    0.8   0.3      0.53   6.3e+02      15      35 ..     160     180 ..     154     221 .. 0.82
   3 !    7.6   0.0    0.0038       4.5       8      36 ..     302     331 ..     297     376 .. 0.68
   4 !    9.1   0.1    0.0013       1.6       8      35 ..     415     442 ..     410     448 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                         DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtlP......aglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrt 81 
                                     + pGd v+  +  tN   ++  +  v  + P       +++ ++++a+         +  L++ges t+ f++ v   
  gi|15669756|ref|NP_248569.1|  32 NVIHPGDDVDLWIKITNDNYDNEVKNIVVEVSPhypfelRQVNPIKGKAT---------ISHLNPGESDTVYFKLHVDEN 102
                                   478899**********9888887555555566655577777777777777.........569*********999998765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.53
                         DUF11  15 tvtytltvtNtgpasangvvv 35 
                                   t t+ +   Ntg+ +a++v +
  gi|15669756|ref|NP_248569.1| 160 TQTVPIEIINTGTGTAKEVNL 180
                                   667888889999999999876 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0038
                         DUF11   8 sevrpGdt.vtytltvtNtgpasangvvvt 36 
                                   +e++pG t v+  +t tN+g a a++v+++
  gi|15669756|ref|NP_248569.1| 302 KEIKPGTTyVRIDVTITNNGHAEAKDVKLK 331
                                   566677642566799************996 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0013
                         DUF11   8 sevrpGdtvtytltvtNtgpasangvvv 35 
                                   ++v++G + t+ +t +N g  +a++v++
  gi|15669756|ref|NP_248569.1| 415 VNVTAGKENTVYITIKNVGSEKAERVKI 442
                                   4789*******************99987 PP

>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.89   1.1e+03      47      93 ..     189     241 ..     170     244 .. 0.76
   2 !   12.9   0.2   8.5e-05       0.1      34     114 ..     305     380 ..     292     391 .. 0.74
   3 !   10.3   0.4   0.00054      0.65      42     110 ..     425     485 ..     412     498 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.89
                                   EE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB......--EEEE-TT- CS
                       DUF4352  47 kNkgkealtvnssqfkLkdgdgkeydadlsasskadd......lflgtlnpGk 93 
                                    N g+e++ v+++ ++ ++++  +y +++ +s+   +      + lg l+p++
  gi|15669756|ref|NP_248569.1| 189 VNAGSESVEVSAYGTTKTQEKTIYYPTAVPISNLPISpvgetkFYLGALKPDN 241
                                   58999999999998877778878888877777766446666777777777776 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.5e-05
                                   T-.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB.--EEEE-TT-EEEEEEEEEESTT-CG..EE CS
                       DUF4352  34 daggeflivdvtvkNkgkealtvnssqfkLkdgdgkeydadlsasskadd.lflgtlnpGkkvtGklvFdvpkgkkk..le 111
                                   ++g +++ +dvt++N+g  + +  + + kL+   +k ++ + s    + + ++ g+l pG + t + + dv+k ++   ++
  gi|15669756|ref|NP_248569.1| 305 KPGTTYVRIDVTITNNGHAEAK--DVKLKLI--TNKPFKDSWS----NCNiKDVGNLLPGVSKTVSFYVDVDKYASAkhYK 377
                                   7899*************98764..3556665..3344444444....33337899*********99999999998876677 PP

                                   EEE CS
                       DUF4352 112 Ley 114
                                   L +
  gi|15669756|ref|NP_248569.1| 378 LPI 380
                                   655 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00054
                                   EEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB--EEEE-TT-EEEEEEEEEESTT-CGE CS
                       DUF4352  42 vdvtvkNkgkealtvnssqfkLkdgdgkeydadlsasskaddlflgtlnpGkkvtGklvFdvpkgkkkl 110
                                   v +t+kN g+e+      + + +++ g+ +d+ ++       +  gtl p+++ tG++v dv+k+++  
  gi|15669756|ref|NP_248569.1| 425 VYITIKNVGSEKAER--VKISAIRNSGQPFDYPIKS------DTIGTLYPNQTGTGVIVIDVDKNAESK 485
                                   667777766666554..3334455555666655553......4579*******************9864 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.1   2.5e+03      75     129 ..      80     139 ..      77     148 .. 0.61
   2 ?    4.7   0.0     0.014        17      37      56 ..     161     180 ..     154     183 .. 0.88
   3 !    8.5   0.0     0.001       1.2      33      57 ..     307     331 ..     301     401 .. 0.85
   4 !   11.8   0.0   9.5e-05      0.11      31      57 ..     417     443 ..     409     466 .. 0.84
   5 ?   -3.5   0.1         5     6e+03     155     174 ..     530     549 ..     523     552 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.1
                     TRAP_beta  75 akwerlapge..nvshsfvvepkksgsfngtaavvtY..resekgaelqlals.sepgeg 129
                                   a++  l+pge  +v++++ v   ++   +  ++ v+Y   + e+g+e   ++  +++ ++
  gi|15669756|ref|NP_248569.1|  80 ATISHLNPGEsdTVYFKLHVDENAPSRDYEIDVKVSYdeINKEDGKETIHHYEiTKIYYL 139
                                   566677777623466777777777777777788888844345566665555555555555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.014
                     TRAP_beta  37 ltveytiyNvGssaAldVsl 56 
                                    tv ++i+N G+ +A +V+l
  gi|15669756|ref|NP_248569.1| 161 QTVPIEIINTGTGTAKEVNL 180
                                   5899**************98 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.001
                     TRAP_beta  33 egedltveytiyNvGssaAldVslv 57 
                                   +   + +++ti+N G ++A dV+l+
  gi|15669756|ref|NP_248569.1| 307 GTTYVRIDVTITNNGHAEAKDVKLK 331
                                   55668899**************985 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 9.5e-05
                     TRAP_beta  31 lvegedltveytiyNvGssaAldVslv 57 
                                   + +g+++tv++ti NvGs++A  V+++
  gi|15669756|ref|NP_248569.1| 417 VTAGKENTVYITIKNVGSEKAERVKIS 443
                                   5689*****************999986 PP

  == domain 5  score: -3.5 bits;  conditional E-value: 5
                     TRAP_beta 155 ilpvvgiplllwvaskskye 174
                                   i+ v++i+l++ ++ k+k +
  gi|15669756|ref|NP_248569.1| 530 IIVVIAIVLVVGYVFKRKNS 549
                                   45566777777777777655 PP

>> Ig_GlcNase  Exo-beta-D-glucosaminidase Ig-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.9   4.6e+03      73      92 ..      84     103 ..      72     114 .. 0.72
   2 ?   -2.4   0.0       4.3   5.2e+03      72      92 ..     153     173 ..     151     181 .. 0.67
   3 ?    4.1   0.0     0.041        49      31      88 ..     309     367 ..     295     381 .. 0.74
   4 !    9.6   0.0   0.00085         1      19      96 ..     411     486 ..     398     494 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.9
                    Ig_GlcNase  73 tLlPgEsltltveypaaalk 92 
                                   +L PgEs t+ ++ + ++++
  gi|15669756|ref|NP_248569.1|  84 HLNPGESDTVYFKLHVDENA 103
                                   57899999998887655544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.3
                    Ig_GlcNase  72 vtLlPgEsltltveypaaalk 92 
                                   ++L+P  ++t+ +e+ ++ + 
  gi|15669756|ref|NP_248569.1| 153 FSLIPSKTQTVPIEIINTGTG 173
                                   688899999988887555544 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.041
                    Ig_GlcNase  31 eetkvtvtLenkssvpAffvrlnlvdaa.geevlPvlwsDNyvtLlPgEsltltveypa 88 
                                   +  +++vt++n++++ A  v+l+l+ ++  ++    +   +  +LlPg s+t+++ ++ 
  gi|15669756|ref|NP_248569.1| 309 TYVRIDVTITNNGHAEAKDVKLKLITNKpFKDSWSNCNIKDVGNLLPGVSKTVSFYVDV 367
                                   478899******************99987666666666666667777777777765554 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00085
                    Ig_GlcNase  19 pkakvsvtakkkeetkvtvtLenkssvpAffvrlnlvdaageevlPvlwsDNyvtLlPgEsltltveypaaalkgkkp 96 
                                    + +v+vta   +e++v +t++n +s  A  v++++++++g+     + sD   tL P+++ t  + ++ ++++++kp
  gi|15669756|ref|NP_248569.1| 411 ITKEVNVTAG--KENTVYITIKNVGSEKAERVKISAIRNSGQPFDYPIKSDTIGTLYPNQTGTGVIVIDVDKNAESKP 486
                                   4555566665..699*****************************99999*********99987555554444444444 PP

>> AP3B1_C  Clathrin-adaptor complex-3 beta-1 subunit C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       0.3   3.6e+02      93     137 ..      43      93 ..      30      98 .. 0.71
   2 !    8.4   0.0     0.002       2.4      87     142 ..     308     366 ..     303     369 .. 0.84
   3 ?    2.6   0.1      0.12   1.4e+02      84     142 ..     417     477 ..     410     481 .. 0.74
   4 ?   -2.4   0.0       4.4   5.2e+03      56      81 ..     520     547 ..     505     549 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.3
                       AP3B1_C  93 eltltNts.dseiknihigek.....klqagmeihefaeiesLepgasttv 137
                                    +++tN + d+e+kni ++       +l +   i+  a+i+ L+pg+s tv
  gi|15669756|ref|NP_248569.1|  43 WIKITNDNyDNEVKNIVVEVSphypfELRQVNPIKGKATISHLNPGESDTV 93 
                                   578888665999999999865311122344455788889999999998777 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.002
                       AP3B1_C  87 pkmvsveltltNtsdseiknih...igekklqagmeihefaeiesLepgasttvvlGid 142
                                   ++ v + +t+tN++ +e+k+++   i++k+ + + +  + + + +L pg s tv+  +d
  gi|15669756|ref|NP_248569.1| 308 TTYVRIDVTITNNGHAEAKDVKlklITNKPFKDSWSNCNIKDVGNLLPGVSKTVSFYVD 366
                                   56799****************94444688999999999999999999999999887776 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.12
                       AP3B1_C  84 lyspkmvsveltltNtsdseiknihigek.klqag..meihefaeiesLepgasttvvlGid 142
                                   ++  k  +v +t++N ++++++ ++i+   +  +     i ++++i +L p+++ t+v+ id
  gi|15669756|ref|NP_248569.1| 417 VTAGKENTVYITIKNVGSEKAERVKISAIrNSGQPfdYPI-KSDTIGTLYPNQTGTGVIVID 477
                                   5555666899***********9999987633333321333.578999999999999999998 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 4.4
                       AP3B1_C  56 vpvkkkelln..kvtGegLsveyrFtRq 81 
                                   +++k++++l    v +  L v y F R+
  gi|15669756|ref|NP_248569.1| 520 SNSKSYWILGiiVVIAIVLVVGYVFKRK 547
                                   5778888887445567779999999997 PP

>> CBM49  Carbohydrate binding domain CBM49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.7   4.4e+03      30      60 ..     125     154 ..     112     166 .. 0.69
   2 ?   -1.5   0.0       2.7   3.3e+03      22      41 ..     164     183 ..     158     195 .. 0.80
   3 ?    0.2   0.0      0.82   9.8e+02      14      47 ..     208     241 ..     195     257 .. 0.80
   4 !   13.6   0.1   5.2e-05     0.062      15      50 ..     307     343 ..     303     352 .. 0.86
   5 ?   -2.8   0.1       6.8   8.2e+03      21      39 ..     425     443 ..     420     447 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.7
                         CBM49  30 sktiksltlkienlapgeiWgvek.vskntys 60 
                                   ++ti++++  i+++++ +++g+   + + ++s
  gi|15669756|ref|NP_248569.1| 125 KETIHHYE--ITKIYYLHVYGIASfEINGNFS 154
                                   55665554..5567888899988765555665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                         CBM49  22 evtitNnssktiksltlkie 41 
                                    + i+N+++ t k+++l i 
  gi|15669756|ref|NP_248569.1| 164 PIEIINTGTGTAKEVNLYIG 183
                                   57899999999999999876 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.82
                         CBM49  14 ngktyyqvevtitNnssktiksltlkienlapge 47 
                                   +++ yy  +v i+N   +++ + ++ +  l+p++
  gi|15669756|ref|NP_248569.1| 208 EKTIYYPTAVPISNLPISPVGETKFYLGALKPDN 241
                                   445799999*************999999888654 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 5.2e-05
                         CBM49  15 gktyyqvevtitNnssktiksltlkie.nlapgeiWg 50 
                                   g+ty++++vtitNn+++  k+++lk+  n  +++ W+
  gi|15669756|ref|NP_248569.1| 307 GTTYVRIDVTITNNGHAEAKDVKLKLItNKPFKDSWS 343
                                   78**********************9765666888885 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 6.8
                         CBM49  21 vevtitNnssktiksltlk 39 
                                   v +ti+N +s+  + ++++
  gi|15669756|ref|NP_248569.1| 425 VYITIKNVGSEKAERVKIS 443
                                   5589999999888888776 PP

>> Alpha_adaptinC2  Adaptin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.49   5.9e+02      30     105 ..      44     128 ..      30     133 .. 0.66
   2 ?   -2.8   0.0       6.6   7.9e+03      74     106 ..     160     197 ..     152     199 .. 0.60
   3 ?    7.7   0.0    0.0036       4.4      26      96 ..     311     385 ..     282     398 .. 0.76
   4 ?    0.5   0.0      0.62   7.4e+02      27      94 ..     424     494 ..     411     512 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.49
                                   EEEEE-S.SS-EEEEEEEEEEBTTCEEE.EEEES-S-B-TT....CEEEEEEEEEE.ESCTTS-EEEEEEEEEE.CTC.EE CS
               Alpha_adaptinC2  30 lsftNks.sqpisnfsfqaavpkslklq.lqppsstvlppn....pggqitqvlli.enpskkplrmrlrisyk.vgq.ai 101
                                   +++tN   +++++n++ +++   +++l+ ++p+++     +    +++++  +l + en+ + +    +++sy   ++ ++
  gi|15669756|ref|NP_248569.1|  44 IKITNDNyDNEVKNIVVEVSPHYPFELRqVNPIKGKATISHlnpgESDTVYFKLHVdENAPSRDYEIDVKVSYDeINKeDG 124
                                   667777777788888888888888887766666555544333422555555555555558888999999999997444477 PP

                                   EEEE CS
               Alpha_adaptinC2 102 keqi 105
                                   ke i
  gi|15669756|ref|NP_248569.1| 125 KETI 128
                                   7766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.6
                                   EEEEEEES...CTTS-EEEEEEEEEE.CTC.EEEEEEE CS
               Alpha_adaptinC2  74 tqvllien...pskkplrmrlrisyk.vgq.aikeqid 106
                                   tq+++ie     ++ +  ++l i y+ +   a++e+++
  gi|15669756|ref|NP_248569.1| 160 TQTVPIEIintGTGTAKEVNLYIGYSlNSVnAGSESVE 197
                                   34444433335677777888888888443367776665 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0036
                                   EEEEEEEEE-SSS-EEEEEEEEEEBTTCEEEEEEES-S-B-.TTCEEEEEEEEEEES...CTTS-EEEEEEEEEE CS
               Alpha_adaptinC2  26 iritlsftNkssqpisnfsfqaavpkslklqlqppsstvlp.pnpggqitqvllien...pskkplrmrlrisyk 96 
                                   +ri++++tN+  ++ +++++++  +k++k + ++ +  ++    pg + t ++ ++    +s+k  ++ ++isy+
  gi|15669756|ref|NP_248569.1| 311 VRIDVTITNNGHAEAKDVKLKLITNKPFKDSWSNCNIKDVGnLLPGVSKTVSFYVDVdkyASAKHYKLPIEISYL 385
                                   89**************************98877777776663336777777777777778888888888888888 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.62
                                   EEEEEEEE-SSS-EEEEEEEEEEBTTCEEE..EEEES-S-B-TTCEEEEEEEEEEES...CTTS-EEEEEEEE CS
               Alpha_adaptinC2  27 ritlsftNkssqpisnfsfqaavpkslklq..lqppsstvlppnpggqitqvllien...pskkplrmrlris 94 
                                   +++++++N  s++ + ++++a  ++++ +   +++ +  +l p  +++ t v+ i+    + +kp   +++i 
  gi|15669756|ref|NP_248569.1| 424 TVYITIKNVGSEKAERVKISAIRNSGQPFDypIKSDTIGTLYP--NQTGTGVIVIDVdknAESKPYIITIEIR 494
                                   5788999999999999999999998776663355555555555..7777777777664334455544555554 PP

>> Ig_mannosidase  Ig-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.029        35      47      66 ..      84     103 ..      83     118 .. 0.73
   2 ?   -2.3   0.0       3.2   3.8e+03      46      60 ..     153     167 ..     147     182 .. 0.57
   3 ?    5.0   0.0     0.016        20      47      62 ..     352     367 ..     309     381 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.029
                Ig_mannosidase  47 dLlpgesktvtftvnedttl 66 
                                   +L+pges tv f+ + d ++
  gi|15669756|ref|NP_248569.1|  84 HLNPGESDTVYFKLHVDENA 103
                                   79***********9444443 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.2
                Ig_mannosidase  46 FdLlpgesktvtftv 60 
                                   F L+p ++ tv ++ 
  gi|15669756|ref|NP_248569.1| 153 FSLIPSKTQTVPIEI 167
                                   566666666665443 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.016
                Ig_mannosidase  47 dLlpgesktvtftvne 62 
                                   +Llpg sktv f+v+ 
  gi|15669756|ref|NP_248569.1| 352 NLLPGVSKTVSFYVDV 367
                                   69***********933 PP

>> PHTB1_C  PTHB1 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0016         2      11      70 ..      54     120 ..      44     132 .. 0.76
   2 ?    2.8   0.0     0.043        51       2      69 ..     315     385 ..     314     402 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0016
                       PHTB1_C  11 tlenvqlsvqvdkplaask.....stfviesldesasteliisvflkgslipaslevevvasYt..s 70 
                                   +++n+ + v+ ++p+++ +      + +i+ l++++s +++++ ++ ++++  + e++v +sY   +
  gi|15669756|ref|NP_248569.1|  54 EVKNIVVEVSPHYPFELRQvnpikGKATISHLNPGESDTVYFKLHVDENAPSRDYEIDVKVSYDeiN 120
                                   5666666666666666554211226789***********************************8443 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.043
                       PHTB1_C   2 vkvtlkssttlenvqlsvqvdkplaaskstfviesl...desasteliisvflkgslipaslevevvasYt 69 
                                   v +t + +++ ++v+l + ++kp++ s s++ i+++    ++ s+++++ v + + +     +  + +sY 
  gi|15669756|ref|NP_248569.1| 315 VTITNNGHAEAKDVKLKLITNKPFKDSWSNCNIKDVgnlLPGVSKTVSFYVDVDKYASAKHYKLPIEISYL 385
                                   7899999***************************9942224566666666666777777778888888886 PP

>> WD40_3  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00031      0.37       8      29 ..     459     480 ..     456     482 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                        WD40_3   8 vgIkklfpnpsGtrlvfiDekg 29 
                                   + I  l+pn++Gt +++iD ++
  gi|15669756|ref|NP_248569.1| 459 DTIGTLYPNQTGTGVIVIDVDK 480
                                   67889**************776 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.017        21      28      44 ..      84     100 ..      77     109 .. 0.87
   2 ?    3.0   0.0     0.093   1.1e+02      29      48 ..     353     372 ..     348     396 .. 0.77
   3 ?   -1.6   0.0       2.6   3.1e+03      27      42 ..     415     430 ..     413     431 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                                   EE-TT-EEEEEEEEECG CS
                      Fn3-like  28 eLapGesktvtftldrk 44 
                                   +L+pGes tv f+l ++
  gi|15669756|ref|NP_248569.1|  84 HLNPGESDTVYFKLHVD 100
                                   6************9875 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.093
                                   E-TT-EEEEEEEEECGGG-E CS
                      Fn3-like  29 LapGesktvtftldrkdlsv 48 
                                   L pG sktv+f +d++  ++
  gi|15669756|ref|NP_248569.1| 353 LLPGVSKTVSFYVDVDKYAS 372
                                   88*********999987554 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.6
                                   EEE-TT-EEEEEEEEE CS
                      Fn3-like  27 veLapGesktvtftld 42 
                                   v++ +G++ tv +t++
  gi|15669756|ref|NP_248569.1| 415 VNVTAGKENTVYITIK 430
                                   8899*******99986 PP

>> Arrestin_C  Arrestin (or S-antigen), C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   0.00011      0.13      14      81 ..      32     110 ..      28     156 .. 0.66
   2 ?    4.8   0.2      0.03        36      14      55 ..     302     346 ..     295     402 .. 0.69
   3 ?    1.9   0.2      0.24   2.8e+02      15      46 ..     416     447 ..     405     449 .. 0.87
   4 ?   -3.1   0.3       8.4     1e+04      13      41 ..     504     532 ..     503     552 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                   SEEETT--EEEEEEEEE.-SSSEEEEEEEEEEEEEEEESS..SEEEEEEEEEEEEE---..........B-TTEE.EEE CS
                    Arrestin_C  14 kgyvpGetipvtvkidn.dskkkvkkikvslvqhvdvcafnrsnkkeknvvaksdsvkv..........tsaakdklet 81 
                                   + ++pG+++++++ki+n +   +vk+i v++  h+ +  ++ +  k k +++   +++           ++a+++ +e+
  gi|15669756|ref|NP_248569.1|  32 NVIHPGDDVDLWIKITNdNYDNEVKNIVVEVSPHYPFELRQVNPIKGKATISHLNPGESdtvyfklhvdENAPSRDYEI 110
                                   5789************9455699***********999999765555555554433222233455555554455555554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.03
                                   SEEETT--.EEEEEEEEE-SSSEEEEEEEEEEEEEEEESS....S CS
                    Arrestin_C  14 kgyvpGet.ipvtvkidndskkkvkkikvslvqhvdvcafnr..s 55 
                                   k + pG t +++ v+i+n+ + + k +k++l+ +  ++++ +  +
  gi|15669756|ref|NP_248569.1| 302 KEIKPGTTyVRIDVTITNNGHAEAKDVKLKLITNKPFKDSWSncN 346
                                   555566554899********************9988888876663 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.24
                                   EEETT--EEEEEEEEE-SSSEEEEEEEEEEEE CS
                    Arrestin_C  15 gyvpGetipvtvkidndskkkvkkikvslvqh 46 
                                    ++ G + +v ++i+n  + k +++k+s++++
  gi|15669756|ref|NP_248569.1| 416 NVTAGKENTVYITIKNVGSEKAERVKISAIRN 447
                                   578899999*******************9986 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 8.4
                                   -SEEETT--EEEEEEEEE-SSSEEEEEEE CS
                    Arrestin_C  13 kkgyvpGetipvtvkidndskkkvkkikv 41 
                                    + yv  e ++v v+  n +++ +  i v
  gi|15669756|ref|NP_248569.1| 504 NNVYVYQEPLKVVVNNSNSKSYWILGIIV 532
                                   56788888888888888766554444433 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.22   2.6e+02      75     143 ..      53     114 ..      35     116 .. 0.69
   2 ?   -2.0   0.0       2.8   3.3e+03      64      93 ..     162     191 ..     144     250 .. 0.66
   3 ?    7.7   0.5    0.0027       3.2      63      94 ..     311     353 ..     306     411 .. 0.65
   4 ?    1.7   0.6      0.19   2.3e+02      53      83 ..     413     443 ..     378     447 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.22
                       DUF2393  75 ftikeCkleiklvnkshnkkskellkklkplvsksevikedlkpgeske..Frviidyfpyfknysvkltl 143
                                   +++k+ ++e++ + + + +       +++p++ k  +i+  l+pges +  F++ +d+   +++y++ +++
  gi|15669756|ref|NP_248569.1|  53 NEVKNIVVEVSPHYPFELR-------QVNPIKGKA-TIS-HLNPGESDTvyFKLHVDENAPSRDYEIDVKV 114
                                   4555555555555555555.......677888777.454.5899888755599999999999999998887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                       DUF2393  64 vvdgtitNeGkftikeCkleiklvnkshnk 93 
                                    v ++i N+G  t ke+ l i    +s n 
  gi|15669756|ref|NP_248569.1| 162 TVPIEIINTGTGTAKEVNLYIGYSLNSVNA 191
                                   566778888888888888866444444433 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0027
                       DUF2393  63 fvvdgtitNeGkftikeCkleiklvnkshnk...........k 94 
                                   + +d+titN+G+ + k +kl++   ++ +++            
  gi|15669756|ref|NP_248569.1| 311 VRIDVTITNNGHAEAKDVKLKLITNKPFKDSwsncnikdvgnL 353
                                   6699***************988554444444333544444440 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.19
                       DUF2393  53 sqkrllyteafvvdgtitNeGkftikeCkle 83 
                                   +   ++  +   v +ti+N G+ +   +k++
  gi|15669756|ref|NP_248569.1| 413 KEVNVTAGKENTVYITIKNVGSEKAERVKIS 443
                                   334445556778999******9999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 3726.57
//
Query:       gi|15669757|ref|NP_248570.1|  [L=388]
Description: hypothetical protein MJ_1562 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-37  128.2   0.1    4.3e-37  127.8   0.1    1.2  1  MMPL            MMPL family
    2.9e-09   35.6  10.0    8.1e-08   30.8   7.4    2.1  2  Patched         Patched family
    5.7e-07   29.1   4.9    1.1e-06   28.2   4.9    1.4  1  SecD_SecF       Protein export membrane protein
    9.7e-06   23.6   6.1    2.2e-05   22.3   6.1    1.6  1  ACR_tran        AcrB/AcrD/AcrF family
    0.00022   21.1   0.2    0.00022   21.1   0.2    1.6  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
  ------ inclusion threshold ------
        3.2    7.4  10.4        1.3    8.6   0.5    3.1  3  Wzy_C           O-Antigen ligase


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.8   0.1   1.4e-40   4.3e-37      76     302 ..     151     372 ..      50     386 .. 0.82

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 1.4e-40
                          MMPL  76 vaaafvSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvi 156
                                    ++ +  +D + + +  ++++  ++++ ++ ++++ + +ee++ + g++v  tG++++ + + ++ +++  ++++v+l+ i
  gi|15669757|ref|NP_248570.1| 151 KRKRIFNSDYSMTVVNAYTDAGGDQKKLMRVMDDVNERIEETPFPPGVEVIATGTPPMRKLMDELMKESQSFTTTVGLIGI 231
                                   555555567777788888888888899999*************************************************** PP

                          MMPL 157 lviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedre 237
                                   l+iL+i +r ++  ++pll v++ ++ + g       ll + l ++++g+ ++ +++ G+DY + L+ Ry ee+++g   +
  gi|15669757|ref|NP_248570.1| 232 LIILIIYFRKPLSSIMPLLPVLIAVIWTGGA----MGLLDIPLDMATAGIGSL-ILGLGIDYGIHLMHRYDEERRKGMPID 307
                                   ***************************9999....678899********9875.68************************* PP

                          MMPL 238 eaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvll 302
                                   +a+ +av  tg +v+a ++t ++ +l+Lv+a lp++a++G ++alG+ + + +vlTllPAl+v+ 
  gi|15669757|ref|NP_248570.1| 308 KAIETAVVETGTAVMATTATTVVGFLALVLAPLPMMANLGKVCALGISFCMVVVLTLLPALIVIE 372
                                   **************************************************************985 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0014       4.1     441     496 ..      13      69 ..       2     107 .. 0.77
   2 !   30.8   7.4   2.7e-11   8.1e-08     251     386 ..     239     375 ..     221     379 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0014
                       Patched 441 llnksvrlvvlllfvvylaiaiyGcv..nikegLepkklvledsplvevlkliekeiw 496
                                   +++ s +   l+l+++ ++  + G++  n+k++   +k++ +d+p++++l+++  e +
  gi|15669757|ref|NP_248570.1|  13 VAHFSEQKPFLMLLIILIITVFAGISatNVKSQTAFEKMLPQDNPIIKTLYEVRDE-F 69 
                                   555566666778888888888888743399******************99988544.3 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 2.7e-11
                       Patched 251 rskpilailgvlspvlAivsslGlllwlGfrfnsivtvtPFLvLaiGvDd.mflmvaawkrteaklsvkkrigealseagv 330
                                   + kp+ +i+ +l  ++A++   G++ +l ++    +  +  L+L++G+D  ++lm    ++ ++  ++ k i+ a++e+g 
  gi|15669757|ref|NP_248570.1| 239 FRKPLSSIMPLLPVLIAVIWTGGAMGLLDIPLDMATAGIGSLILGLGIDYgIHLMHRYDEERRKGMPIDKAIETAVVETGT 319
                                   679**********************************************7255555555555556679************* PP

                       Patched 331 aitiTslTdvlsFgiGaittlpaiqlFciytavailfdfiYqitffaavlaiaaka 386
                                   a++ T+ T v+ F + ++++lp ++   ++ a+ i f+ +  +t++ a+++i +++
  gi|15669757|ref|NP_248570.1| 320 AVMATTATTVVGFLALVLAPLPMMANLGKVCALGISFCMVVVLTLLPALIVIEERH 375
                                   **************************************************998765 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   4.9   3.6e-10   1.1e-06      29     169 ..     216     355 ..     209     370 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.6e-10
                                   HHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHH.HHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSSHHHHHHHHHH CS
                     SecD_SecF  29 laekavlallialvliliyvalrFewrvalaaiia.lvhDviitvgvlsllgievdlatvaalLtiiGYSvndtvvvfdrv 108
                                   ++e+  +   + l++ili + ++F++++ +   ++ ++  vi t g++ ll i++d+at +    i+G  ++  + ++ r 
  gi|15669757|ref|NP_248570.1| 216 MKESQSFTTTVGLIGILIILIIYFRKPLSSIMPLLpVLIAVIWTGGAMGLLDIPLDMATAGIGSLILGLGIDYGIHLMHRY 296
                                   4455667888999*************9986654444999*****************99966666799************** PP

                                   HHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTS CS
                     SecD_SecF 109 renlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGli 169
                                    e++rk   ++++++i++++ +t t  ++t++tt++  +al+l +  +++++  +  +G+ 
  gi|15669757|ref|NP_248570.1| 297 DEERRK--GMPIDKAIETAVVETGTAVMATTATTVVGFLALVLAPLPMMANLGKVCALGIS 355
                                   ***776..9******************************************9999999886 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   6.1   7.5e-09   2.2e-05     826    1016 ..     175     368 ..     153     372 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 7.5e-09
                                    HHHHHHHHHHHCTT.....SSTTEEEEEEHH....HHHHHHHHCHHHHHHHHHHHHHHHHHHHHHTSSSTCHHHHTTHH CS
                      ACR_tran  826 lseaeeavekiakkv...klpegvtiewtgq....aeqeqeasnsllilvalalllvflvLaalyeslsepllilltvP 897 
                                    + + + +++++++++    +p+gv++  tg+        ++ ++s+++   + l+ + ++L + +   +  ++ ll v 
  gi|15669757|ref|NP_248570.1|  175 QKKLMRVMDDVNERIeetPFPPGVEVIATGTppmrKLMDELMKESQSFTTTVGLIGILIILIIYFRKPLSSIMPLLPVL 253 
                                    44444444443333311179****999999822212345567788999999**************99999888888888 PP

                                    HHHHHHHHHHHHTT--BSHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHHHCHHHHHHHHHHHHH CS
                      ACR_tran  898 lalvGallalllrglelsvi.aqvGlilliGlavkNaillvefakelrekegksleeaileaakeRLrPiLMTalaail 975 
                                    +a++    a+ l +++l+++ a +G ++l Gl    +i l+  + e+r+ +g+ +++ai  a+ e   +++ T+ ++++
  gi|15669757|ref|NP_248570.1|  254 IAVIWTGGAMGLLDIPLDMAtAGIGSLIL-GLGIDYGIHLMHRYDEERR-KGMPIDKAIETAVVETGTAVMATTATTVV 330 
                                    9998888899999*****85267998765.9*****************9.99*************************** PP

                                    HHHHHHCT-STTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ACR_tran  976 GvlPLalstgaGselqqplgivvlgGlvtstvLtLllvPvl 1016
                                    G+l L+l+      +   lg v   G+   +v  L l+P+l
  gi|15669757|ref|NP_248570.1|  331 GFLALVLAP---LPMMANLGKVCALGISFCMVVVLTLLPAL 368 
                                    *******96...45777777777777777777777777776 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1         3     9e+03       7      17 ..      22      32 ..      18      43 .. 0.51
   2 !   21.1   0.2   7.5e-08   0.00022      13     138 ..     249     374 ..     241     382 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3
                                  HHHHHHHHHHH CS
                Sterol-sensing  7 gLglagviivl 17
                                  +L+l +++i++
  gi|15669757|ref|NP_248570.1| 22 FLMLLIILIIT 32
                                  44444444443 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 7.5e-08
                                   HHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCH.HHHHHHHHHHHCCCCHHCCCHH CS
                Sterol-sensing  13 viivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrslde.seriaealgevgpsilltslte 92 
                                   ++ vl++v+ + g + +l+++l + ++  +  l+l  g+d    l++ +++  r+    ++ i  a+ e+g+++++t++t 
  gi|15669757|ref|NP_248570.1| 249 LLPVLIAVIWTGGAMGLLDIPLDMATA-GIGSLILGLGIDYGIHLMHRYDEERRKGMPiDKAIETAVVETGTAVMATTATT 328
                                   67799*********************9.6778*****************9998887666********************** PP

                                   HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHH CS
                Sterol-sensing  93 llalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldir 138
                                   ++ +l  +l  +p + +    +a+++ +  ++ +t+  a++ +++r
  gi|15669757|ref|NP_248570.1| 329 VVGFLALVLAPLPMMANLGKVCALGISFCMVVVLTLLPALIVIEER 374
                                   ****9777*****************999999999999999999887 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.013        39      38      59 ..      13      63 ..       1     177 [. 0.66
   2 ?    8.6   0.5   0.00044       1.3      14      52 ..     220     258 ..     216     305 .. 0.78
   3 ?   -1.5   2.7      0.58   1.7e+03       9      55 ..     320     364 ..     312     383 .. 0.47

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.013
                         Wzy_C 38 i.......pfllllgilvgvilliilfv......................l 59
                                  +       pfl+ll+il++++++ i ++                       
  gi|15669757|ref|NP_248570.1| 13 VahfseqkPFLMLLIILIITVFAGISATnvksqtafekmlpqdnpiiktlY 63
                                  244455557888888888888888777655555555555555555544440 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00044
                         Wzy_C  14 tsRsgiigllvalivlliifykrripfllllgilvgvil 52 
                                   +s +  +gl+++li+l+i f k++ + + ll +l++vi 
  gi|15669757|ref|NP_248570.1| 220 QSFTTTVGLIGILIILIIYFRKPLSSIMPLLPVLIAVIW 258
                                   56678899999************9933333334444443 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.58
                         Wzy_C   9 alflstsRsgiigllvalivlliifykrripfllllgilvgvillii 55 
                                   a++++t+   ++g+l al+++ + ++ ++ + + l + +++v++l +
  gi|15669757|ref|NP_248570.1| 320 AVMATTAT-TVVGFL-ALVLAPLPMMANLGKVCALGISFCMVVVLTL 364
                                   44444444.455553.3333333333333323333333332333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2565.83
//
Query:       gi|15669758|ref|NP_248571.1|  [L=152]
Description: hypothetical protein MJ_1563 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-13   50.9   1.7    3.9e-13   49.1   0.1    2.6  2  HTH_5           Bacterial regulatory protein, arsR family
    7.7e-10   38.5   1.0    4.8e-09   36.0   0.2    2.2  2  TrmB            Sugar-specific transcriptional regulator TrmB
    7.4e-09   35.4   0.0    1.7e-08   34.2   0.0    1.7  1  MarR_2          MarR family
    3.7e-07   30.1   0.0    9.8e-07   28.7   0.0    1.8  1  HTH_20          Helix-turn-helix domain
    4.8e-07   29.2   0.7    8.6e-06   25.2   0.0    3.2  4  HTH_24          Winged helix-turn-helix DNA-binding
    7.5e-06   25.8   0.3    3.7e-05   23.6   0.1    2.3  2  HTH_11          HTH domain
    1.5e-05   24.8   0.7    5.2e-05   23.1   0.0    2.2  2  MarR            MarR family
    2.5e-05   24.0   0.0    0.00031   20.5   0.0    2.4  2  HTH_IclR        IclR helix-turn-helix domain
     0.0001   22.7   0.0    0.00023   21.6   0.0    1.8  1  HTH_27          Winged helix DNA-binding domain
    0.00024   21.3   0.1    0.00071   19.7   0.1    1.8  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00034   20.7   0.0    0.00097   19.3   0.0    1.8  1  HTH_34          Winged helix DNA-binding domain
    0.00072   19.7   1.0     0.0013   18.8   1.0    1.4  1  DUF5343         Family of unknown function (DUF5343)
    0.00077   19.4   2.0      0.033   14.2   0.1    3.0  3  PadR            Transcriptional regulator PadR-like family
     0.0019   18.1   0.6     0.0092   15.9   0.0    2.4  2  HTH_36          Helix-turn-helix domain
     0.0021   17.7   0.4      0.012   15.3   0.0    2.4  2  HTH_41          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.6   2.3      0.017   14.8   0.0    2.2  2  DUF4423         Domain of unknown function (DUF4423)
      0.018   14.6   0.5      0.058   13.0   0.1    1.9  2  SMC_ScpB        Segregation and condensation complex subunit 
       0.02   15.2   0.3      0.085   13.2   0.0    2.2  3  Rrf2            Transcriptional regulator
      0.023   14.9   0.4      0.042   14.0   0.4    1.7  1  FUR             Ferric uptake regulator family
       0.08   12.9   1.8       0.29   11.1   0.0    2.6  2  HTH_12          Ribonuclease R winged-helix domain
      0.081   12.9   0.0       0.11   12.5   0.0    1.3  1  PAX             'Paired box' domain
      0.086   13.0   0.1       0.15   12.2   0.1    1.5  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.12   12.6   2.8       0.93    9.7   1.3    2.2  2  NusB            NusB family
       0.14   12.1   3.1       0.27   11.2   0.0    2.6  3  TBPIP           TBPIP/Hop2 winged helix domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.89   6.6e+02      18      30 ..      15      27 ..      14      33 .. 0.86
   2 !   49.1   0.1   5.2e-16   3.9e-13       6      47 .]      32      73 ..      27      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.89
                                  HHHHHHHHTS-HH CS
                         HTH_5 18 vcelaeelglsqs 30
                                  ++ela++ gl++s
  gi|15669758|ref|NP_248571.1| 15 FSELAKIHGLNKS 27
                                  6899999999987 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 5.2e-16
                                  HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                    + +L++++l++++++eel++s+++vS+ LkkL+e+G+V+k
  gi|15669758|ref|NP_248571.1| 32 YAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEELGFVRK 73
                                  56889***********************************86 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.2   6.4e-12   4.8e-09       3      66 ..      21      88 ..      18      89 .. 0.89
   2 ?    0.9   0.0      0.56   4.2e+02      27      49 ..      95     117 ..      89     118 .. 0.74

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 6.4e-12
                                  HCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST...TTEEEE-- CS
                          TrmB  3 klGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr...pklYravd 66
                                   +GL++    vY+ L  + +p+t+++i eel++++ +v  +L++Le+ G+V+++  +   +++Y+avd
  gi|15669758|ref|NP_248571.1| 21 IHGLNKSVGAVYAILYlSDKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIKgerKNYYEAVD 88
                                  7899999999*****77***********************************9875555677999997 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.56
                                   HHCCCTTSSCHCHHHHHHHHHHC CS
                          TrmB  27 eiaeelgvprskvYevLrsLedk 49 
                                   +ia++     +k Ye L++Le+k
  gi|15669758|ref|NP_248571.1|  95 DIAKRKHDLIAKTYEDLKKLEEK 117
                                   5555555556899999***9987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   2.3e-11   1.7e-08       9      54 ..      32      74 ..      22      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.3e-11
                                  HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   ++++L + p   lt++++ ++l++sk++vs  lk+L++ G+v+++
  gi|15669758|ref|NP_248571.1| 32 YAILYLSDKP---LTISDIMEELKISKGNVSMSLKKLEELGFVRKV 74
                                  5667777777...9*****************************986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.3e-09   9.8e-07      19      57 ..      35      74 ..      15      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.3e-09
                                  H.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                        HTH_20 19 L.araegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                  L  ++++lt s+++e+l +sk ++s  L++Lee g+v+ v
  gi|15669758|ref|NP_248571.1| 35 LyLSDKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKV 74
                                  4449*********************************987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.5   3.4e+03      27      34 ..      24      31 ..      16      36 .. 0.66
   2 !   25.2   0.0   1.1e-08   8.6e-06      15      48 .]      39      72 ..      24      72 .. 0.88
   3 ?   -1.1   0.0       1.9   1.4e+03      16      26 ..      89      99 ..      86      99 .. 0.81
   4 ?   -0.0   0.1      0.89   6.7e+02       3      13 ..     138     148 ..     136     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.5
                        HTH_24 27 lglSpstv 34
                                  l+ S+++v
  gi|15669758|ref|NP_248571.1| 24 LNKSVGAV 31
                                  56677766 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.1e-08
                        HTH_24 15 nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +  ++++++ e+l +S+++v+  lk+Lee G+++
  gi|15669758|ref|NP_248571.1| 39 DKPLTISDIMEELKISKGNVSMSLKKLEELGFVR 72
                                  6679***************************996 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.9
                        HTH_24 16 prisqreLAer 26
                                  +  s++++A+r
  gi|15669758|ref|NP_248571.1| 89 GFSSIKDIAKR 99
                                  56799****97 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.89
                        HTH_24   3 etdrkILelLq 13 
                                   ++  kILe+L 
  gi|15669758|ref|NP_248571.1| 138 KISEKILEALN 148
                                   78889**9995 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1     5e-08   3.7e-05       6      54 ..      32      84 ..      30      85 .. 0.93
   2 ?   -1.9   0.0       4.5   3.4e+03      33      42 ..     108     117 ..     108     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5e-08
                        HTH_11  6 lelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpIesepgrGY 54
                                  + +L+ +++p+++++++eeL++S+  v   +k+Leelg    v I +e++ +Y
  gi|15669758|ref|NP_248571.1| 32 YAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEELGfvrkVWIKGERKNYY 84
                                  67999*********************************999999999999887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.5
                        HTH_11  33 rrdIkaLeel 42 
                                   + d+k+Lee+
  gi|15669758|ref|NP_248571.1| 108 YEDLKKLEEK 117
                                   5699999985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   6.9e-08   5.2e-05      16      49 ..      40      73 ..      33      82 .. 0.91
   2 ?   -1.7   0.1         4     3e+03      21      44 ..      94     117 ..      92     117 .. 0.53

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.9e-08
                                  TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieR 49
                                   pl++s++ + l++sk++v+  l++Le+ G++++
  gi|15669758|ref|NP_248571.1| 40 KPLTISDIMEELKISKGNVSMSLKKLEELGFVRK 73
                                  589*****************************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4
                                   HHHHHHHTS-HHHHHHHHHHHHHT CS
                          MarR  21 seLakklgvskstvtrvldrLekk 44 
                                   +++ak+ +  ++ + + l++Le+k
  gi|15669758|ref|NP_248571.1|  94 KDIAKRKHDLIAKTYEDLKKLEEK 117
                                   566665544444444446777765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.71   5.3e+02      21      33 ..      15      27 ..      13      28 .. 0.91
   2 !   20.5   0.0   4.2e-07   0.00031      16      50 ..      39      73 ..      30      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.71
                                  HHHHHHHHTS-HH CS
                      HTH_IclR 21 lselArrtglpkS 33
                                  +selA+  gl+kS
  gi|15669758|ref|NP_248571.1| 15 FSELAKIHGLNKS 27
                                  59*********99 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 4.2e-07
                                  BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  + +lt+s++ +++ ++k +v+  L+ L+elG+v++
  gi|15669758|ref|NP_248571.1| 39 DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRK 73
                                  679******************************97 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   3.1e-07   0.00023      16      50 ..      39      73 ..      16      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.1e-07
                        HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                  + + +++d+++ l++++ ++s slkkL+e G+v +
  gi|15669758|ref|NP_248571.1| 39 DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRK 73
                                  67899****************************55 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   9.5e-07   0.00071      12      53 ..      30      72 ..      28      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.5e-07
                                  HHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress 12 tIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                  ++Y +   + k+ + +d+ e+L++s+  Vs +lkkLe+ G+v 
  gi|15669758|ref|NP_248571.1| 30 AVYAILYlSDKPLTISDIMEELKISKGNVSMSLKKLEELGFVR 72
                                  678888888999999*************************996 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.3e-06   0.00097       5      45 ..      31      72 ..      30      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-06
                        HTH_34  5 vlsyLas.vdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                  v ++L+  ++  + +++ e+l++++gn s  lkkLe+ g++ 
  gi|15669758|ref|NP_248571.1| 31 VYAILYLsDKPLTISDIMEELKISKGNVSMSLKKLEELGFVR 72
                                  56777774667899*************************985 PP

>> DUF5343  Family of unknown function (DUF5343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.0   1.8e-06    0.0013      27     113 ..      45     137 ..      33     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.8e-06
                       DUF5343  27 qdflktlglkssnasliiplLkflGflde...dGkptelykelrn...edtskkalaeaikeaYsdlFelnedaqnldkee 101
                                   +d++++l+++++n s+ ++ L  lGf+ +   +G + + y+ +      +   k+  ++i ++Y+dl +l+e+ ++ +ke 
  gi|15669758|ref|NP_248571.1|  45 SDIMEELKISKGNVSMSLKKLEELGFVRKvwiKGERKNYYEAVDGfssIKDIAKRKHDLIAKTYEDLKKLEEKCNEEEKEF 125
                                   699************************98666899999888877643444445556789********************** PP

                       DUF5343 102 lknlfrtvtgks 113
                                   +k++++ +   +
  gi|15669758|ref|NP_248571.1| 126 IKQKIKGIERMK 137
                                   *****9766544 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.091        68      13      39 ..      12      36 ..       1      42 [. 0.81
   2 !   14.2   0.1   4.4e-05     0.033      22      64 ..      47      85 ..      42      89 .. 0.85
   3 ?   -1.3   0.1       2.9   2.2e+03      35      44 ..     108     117 ..     104     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.091
                                  HHHHHHHHCCSTT-CCTTHHHHHHHHH CS
                          PadR 13 yeiikeleelsegllelseGslYpaLk 39
                                   e+ +el++  +g l+ s G +Y +L 
  gi|15669758|ref|NP_248571.1| 12 IELFSELAKI-HG-LNKSVGAVYAILY 36
                                  6888999998.78.8*********995 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.4e-05
                                  CSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEE CS
                          PadR 22 lsegllelseGslYpaLkrLekeglveseweesgegpprkyYr 64
                                   +e+ l++s+G++   Lk+Le+ g+v + w +   g +++yY+
  gi|15669758|ref|NP_248571.1| 47 IMEE-LKISKGNVSMSLKKLEELGFVRKVWIK---GERKNYYE 85
                                  4544.799***********************7...79999998 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.9
                                   HHHHHHHHHT CS
                          PadR  35 YpaLkrLeke 44 
                                   Y  Lk+Le++
  gi|15669758|ref|NP_248571.1| 108 YEDLKKLEEK 117
                                   8889999876 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.2e-05    0.0092      27      54 ..      43      70 ..       6      71 .. 0.84
   2 ?   -0.3   0.1       1.4   1.1e+03      27      51 ..      92     116 ..      83     119 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                        HTH_36 27 sqetlakrlglsknTvsraikeLeqlGy 54
                                  + +++++ l++sk  vs  +k+Le+lG+
  gi|15669758|ref|NP_248571.1| 43 TISDIMEELKISKGNVSMSLKKLEELGF 70
                                  489************************8 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                        HTH_36  27 sqetlakrlglsknTvsraikeLeq 51 
                                   s +++akr      + +  +k+Le+
  gi|15669758|ref|NP_248571.1|  92 SIKDIAKRKHDLIAKTYEDLKKLEE 116
                                   6777777754444444455555555 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.6e-05     0.012       8      36 ..      43      71 ..      38      78 .. 0.91
   2 ?   -1.0   0.1         2   1.5e+03       4      11 ..     134     141 ..     129     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                        HTH_41  8 tIeelakeleLSvGlvQkALklLeddkai 36
                                  tI+++ +el +S G v   Lk+Le+ + +
  gi|15669758|ref|NP_248571.1| 43 TISDIMEELKISKGNVSMSLKKLEELGFV 71
                                  9***********************98877 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2
                        HTH_41   4 dRlktIee 11 
                                   +R+k I+e
  gi|15669758|ref|NP_248571.1| 134 ERMKKISE 141
                                   68888877 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.3e-05     0.017      25      71 ..      30      74 ..      25     102 .. 0.82
   2 ?    0.1   0.6      0.79   5.9e+02     132     150 ..     109     127 ..      91     145 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                       DUF4423 25 virellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkd 71
                                  +++++l l d+  +++ + + l+  is+  v+ +l+ L++lg+++k 
  gi|15669758|ref|NP_248571.1| 30 AVYAILYLSDKPLTISDIMEELK--ISKGNVSMSLKKLEELGFVRKV 74
                                  6889999999999**********..*******************986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.79
                       DUF4423 132 ekikkeirefrkkilaiae 150
                                   e++kk  +++ ++  ++++
  gi|15669758|ref|NP_248571.1| 109 EDLKKLEEKCNEEEKEFIK 127
                                   3333333333332222222 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   7.8e-05     0.058       3      39 ..      31      67 ..      29      70 .. 0.94
   2 ?   -0.7   0.0       1.3   9.5e+02      29      46 ..     106     123 ..      84     150 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.8e-05
                      SMC_ScpB  3 iEAiLfvageplsleeLakilelskeeveealeeLke 39
                                  + AiL+++++pl+++++ + l++sk +v+  l++L+e
  gi|15669758|ref|NP_248571.1| 31 VYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEE 67
                                  77*******************************9986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                      SMC_ScpB  29 eveealeeLkeeyeeedr 46 
                                   ++ e l++L+e+++ee++
  gi|15669758|ref|NP_248571.1| 106 KTYEDLKKLEEKCNEEEK 123
                                   455556666666655544 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00011     0.085      13      57 ..      33      73 ..      16      83 .. 0.84
   2 ?   -2.5   0.0       8.9   6.6e+03      26      35 ..      91     100 ..      85     113 .. 0.69
   3 ?   -1.6   0.0       4.7   3.5e+03      27      44 ..     129     146 ..     120     149 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                  HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                  a+lyL+    ++p+++++i e+ +is+  ++  l+kL++ g+v+ 
  gi|15669758|ref|NP_248571.1| 33 AILYLS----DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRK 73
                                  444443....4579*****************************86 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.9
                                   B-HHHHHHHH CS
                          Rrf2  26 vsseeiaerq 35 
                                    s+++ia+r 
  gi|15669758|ref|NP_248571.1|  91 SSIKDIAKRK 100
                                   5677777764 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.7
                                   -HHHHHHHHTS-HHHHHH CS
                          Rrf2  27 sseeiaerqnispsylek 44 
                                   +++ i ++ +is+++le 
  gi|15669758|ref|NP_248571.1| 129 KIKGIERMKKISEKILEA 146
                                   566777777777777764 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   5.6e-05     0.042      13      85 ..      31     100 ..      24     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.6e-05
                                   HHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET.TSEEEEEESS.SSSEEEEEETT CS
                           FUR  13 ilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefe.dgesryelak.kehhdhlicek 85 
                                   ++++l+ s++ l++ ++++elk  + ++s+      Lk lee+g+v+++ ++ + +++ye ++  + ++ +  +k
  gi|15669758|ref|NP_248571.1|  31 VYAILYLSDKPLTISDIMEELKISKGNVSM-----SLKKLEELGFVRKVWIKgERKNYYEAVDgFSSIKDIAKRK 100
                                   677788888888888888888766666666.....6***************945555666665445555555555 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00039      0.29       6      52 ..      34      75 ..      30      80 .. 0.79
   2 ?    0.1   0.4         1   7.7e+02      44      51 ..     122     129 ..      94     147 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                        HTH_12  6 ilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvg 52
                                  il  sdkp+    i eeLk     i++  v   L+klee g++r+v 
  gi|15669758|ref|NP_248571.1| 34 ILYLSDKPLTISDIMEELK-----ISKGNVSMSLKKLEELGFVRKVW 75
                                  6777888888888888886.....556666789************85 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                        HTH_12  44 ergltrrv 51 
                                   e+++++++
  gi|15669758|ref|NP_248571.1| 122 EKEFIKQK 129
                                   22244444 PP

>> PAX  'Paired box' domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014      0.11      28      95 ..      36     104 ..      24     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                           PAX  28 elahsgvrpcvisrqlrvshgcvskilgryqetgsirpgviggskpk.vatpevvkkieeykrenpsif 95 
                                    l+ + +   +i   l++s+g vs  l + +e g +r   i g + +   + +  + i+++ ++   ++
  gi|15669758|ref|NP_248571.1|  36 YLSDKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIKGERKNyYEAVDGFSSIKDIAKRKHDLI 104
                                   556666667789999***********************9998876553555555566666655555555 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1    0.0002      0.15      20      53 ..      43      76 ..      41     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                B-block_TFIIIC 20 tqsdLakeskqdprslfyrlksLekkgLIvkqsi 53
                                  t sd+  e+k+++ ++   lk+Le+ g++ k+ i
  gi|15669758|ref|NP_248571.1| 43 TISDIMEELKISKGNVSMSLKKLEELGFVRKVWI 76
                                  66999************************99877 PP

>> NusB  NusB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.24   1.8e+02      95     129 ..       2      35 ..       1      45 [. 0.81
   2 ?    9.7   1.3    0.0012      0.93      21      70 ..      98     147 ..      80     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.24
                                   TTS-SSHHHHHHH.HHHHHHHHS-HHHHHHHHHHH CS
                          NusB  95 lylddvPakvaineavelakkygdeksakFvNgVL 129
                                   +++ +  +k +i    elak+ g  ks + v ++L
  gi|15669758|ref|NP_248571.1|   2 IIM-EEAKKLIIELFSELAKIHGLNKSVGAVYAIL 35 
                                   556.6778889999999999999999988888887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                                   HHHHHHHHHHHT-.......--HHHHHHHHHHHHHHHHTHHHHHHHHHHT CS
                          NusB  21 eeekeailqealnklleeedldeedkafltelvkgvlrnleelDeliekl 70 
                                   +++ + i++ + + ++ ee+++ee+k+f+++ +kg+ r ++  ++++e l
  gi|15669758|ref|NP_248571.1|  98 KRKHDLIAKTYEDLKKLEEKCNEEEKEFIKQKIKGIERMKKISEKILEAL 147
                                   566666666666767799********************999998888875 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00037      0.27       4      45 ..      29      68 ..      26      77 .. 0.84
   2 ?   -0.1   0.7       1.2   8.9e+02      39      58 ..     111     130 ..      91     134 .. 0.65
   3 ?   -1.1   0.2       2.5   1.9e+03      32      44 ..     137     149 ..     124     151 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                         TBPIP  4 elvleylqeqnrPfsvqdvvanlqkklgKtavqkaLdeLvde 45
                                  ++v++ l+ + +P+ ++d+++ l+  ++K +v   L +L++ 
  gi|15669758|ref|NP_248571.1| 29 GAVYAILYLSDKPLTISDIMEELK--ISKGNVSMSLKKLEEL 68
                                  689*******************96..8888888777777664 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                         TBPIP  39 LdeLvdegkiieKeyGKqki 58 
                                   L +L+++    eKe+ Kqki
  gi|15669758|ref|NP_248571.1| 111 LKKLEEKCNEEEKEFIKQKI 130
                                   44455555556799999988 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.5
                         TBPIP  32 KtavqkaLdeLvd 44 
                                   K+   k+L+ L d
  gi|15669758|ref|NP_248571.1| 137 KKISEKILEALND 149
                                   5555688888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2022  (0.112778); expected 358.6 (0.02)
Passed bias filter:                      823  (0.0459033); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1210.93
//
Query:       gi|15669759|ref|NP_248572.1|  [L=170]
Description: hypothetical protein MJ_1564 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.8e-13   49.1   0.9    5.8e-13   49.1   0.9    2.5  2  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.9   3.3e-17   5.8e-13       2     114 ..       3     104 ..       2     110 .. 0.80
   2 ?   -0.5   0.3      0.08   1.4e+03      31      31 ..     136     136 ..     103     164 .. 0.52

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 3.3e-17
                                   EEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH.....HHHH CS
                   RNA_binding   2 ievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei.....keLl 77 
                                   + ++a v++TEd+ kV++a+ n++p+   +++  e    +g        e e+  + k+++kl+ellr++ i     ++L+
  gi|15669759|ref|NP_248572.1|   3 VIIKAKVKPTEDKYKVKKAILNIFPKA--KLTFIEKDNEFG--------EWEG--KTKSVEKLKELLRSQSIldaarMVLE 71 
                                   8899*********************77..466666677777........4444..46889999999999999877777888 PP

                                   HCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS.EEE CS
                   RNA_binding  78 keleervdekgklylrldKQaaylgklslvegdd.vIk 114
                                   k++ e     + + + l+KQaay+g +++  + +  I 
  gi|15669759|ref|NP_248572.1|  72 KGMTE-----NATKFYLNKQAAYVGAVNFDIDTHgGIF 104
                                   88887.....9999**************9543335554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.08
                                   - CS
                   RNA_binding  31 e 31 
                                   e
  gi|15669759|ref|NP_248572.1| 136 E 136
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1097  (0.0611858); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1120.73
//
Query:       gi|15669760|ref|NP_248573.1|  [L=513]
Description: hypothetical protein MJ_1565 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-53  181.9   3.6    3.3e-53  181.1   3.6    1.4  1  DUF87          Helicase HerA, central domain
    3.5e-14   52.7   0.5      8e-14   51.6   0.5    1.6  1  HAS-barrel     HAS barrel domain
    3.6e-10   39.1   0.0    1.4e-06   27.2   0.0    2.1  2  DUF853         Bacterial protein of unknown function (DUF853)
    1.4e-05   24.2   0.0    6.1e-05   22.1   0.0    1.8  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    0.00069   18.6   0.5        0.7    8.8   0.2    2.7  2  AAA_10         AAA-like domain
  ------ inclusion threshold ------
      0.049   13.0   0.2        4.5    6.6   0.0    2.3  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
       0.15   12.1   0.1       0.33   11.0   0.1    1.6  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
        5.7    7.3   7.8        2.1    8.7   0.7    3.4  3  ATP-synt_E_2   ATP synthase epsilon subunit


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.1   3.6   1.5e-56   3.3e-53       2     226 ..     129     338 ..     128     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: 181.1 bits;  conditional E-value: 1.5e-56
                         DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitps 82 
                                   +iG+l+++++v+v+ld+nkl++rHlAil++TG+GKSntvavLl+el  k +at+l++D+HGEY++++ +  + +v++i+p 
  gi|15669760|ref|NP_248573.1| 129 KIGHLVTREDVEVKLDANKLCSRHLAILAMTGMGKSNTVAVLLRELN-KLKATVLVFDMHGEYKDIYCESEKLRVHIIEP- 207
                                   8**********************************************.*******************999999******9. PP

                         DUF87  83 psakdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqaka.keekeklssdepveklleelk.kekeelrklk 161
                                           kin+ +++ ++l+dl+++  +++a++qr ++++a++++k+ ++e    ++d++++ +  +l+ ++++++ k++
  gi|15669760|ref|NP_248573.1| 208 --------KINIYRINDDDLCDLAGV--DAQATKQRPYIRKAIKEIKEeRKEHDFSTVDDYINAIIGKLEeYKSNDNYKKD 278
                                   ........9*****************..********************999999999*************55555999999 PP

                         DUF87 162 nqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlvvsvilrr 226
                                   +++i++ + +led+l+ ++++++ ++++i+++     +e+ i+ii++ ++de+a+++vvs+i + 
  gi|15669760|ref|NP_248573.1| 279 ESSIQTAIFRLEDMLQFRKNIITLHYNPINDI-----REHYINIIPMEELDENAVDIVVSYIAKA 338
                                   99******************************.....*************************986 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.5   3.6e-17     8e-14       1      92 []       7      91 ..       7      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 3.6e-17
                    HAS-barrel  1 iGevigestssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalatedtg 83
                                  iG+ ige+ +++l+f +++   +kvG+yV+i+++ ++++lGmv++  +gn  l+++l+ ++ ++++e +++ ++++l+++   
  gi|15669760|ref|NP_248573.1|  7 IGYTIGETRIDELTFLAKE--APKVGDYVKINYD-DSELLGMVESTIQGNMALEDILNIEHLEKIREFEDNSSYYILGKI--- 83
                                  8*****************9..*************.*********************************************... PP

                    HAS-barrel 84 vkvlGeved 92
                                   kvlG+++d
  gi|15669760|ref|NP_248573.1| 84 -KVLGDIRD 91
                                  .****9986 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00014      0.31      16      64 ..     145     193 ..     132     212 .. 0.85
   2 !   27.2   0.0   6.2e-10   1.4e-06     253     361 ..     353     455 ..     347     466 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00014
                        DUF853  16 alklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgi 64 
                                   a kl  rh  i   tG Gk  t+ vl  +l +   +v++ d+ G+  +i
  gi|15669760|ref|NP_248573.1| 145 ANKLCSRHLAILAMTGMGKSNTVAVLLRELNKLKATVLVFDMHGEYKDI 193
                                   357889**************************************98776 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 6.2e-10
                        DUF853 253 dldkPklvfffdeahLLfndapkall.ekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkav 332
                                   d  kP + + f+eahL+  +  k+   + + ++ r  r  GvG+ +v+q P  l  + L+q  n +   l    p dqk v
  gi|15669760|ref|NP_248573.1| 353 DFAKPIF-MIFEEAHLIAPQHRKTRAkHYLSRIAREGRKFGVGLCLVSQRPKTLDAETLSQCSNLIISKL--IEPTDQKHV 430
                                   6678865.678******99888876515689999********************************9877..68******* PP

                        DUF853 333 kaaadtfranpefdveeaiteLgvGealv 361
                                   + a++ +      d+ + +t+L++Gea++
  gi|15669760|ref|NP_248573.1| 431 QMASENLS----EDLVKQLTSLNIGEAII 455
                                   **998665....5899***********98 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   2.7e-08   6.1e-05      15      63 ..     150     198 ..     143     207 .. 0.90
   2 ?   -1.1   0.0       0.3   6.7e+02     261     287 ..     381     407 ..     377     448 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.7e-08
                 TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairargdraivlDltGafvsrfydeg 63 
                                    +h++i+  tG+GK++++  llr++++ + +++v+D++G++ + + +++
  gi|15669760|ref|NP_248573.1| 150 SRHLAILAMTGMGKSNTVAVLLRELNKLKATVLVFDMHGEYKDIYCESE 198
                                   68***************************************99887765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.3
                 TrwB_AAD_bind 261 lksllaegRkfGgavvlglqsiaqlre 287
                                   l +++ egRkfG+ + l  q  + l +
  gi|15669760|ref|NP_248573.1| 381 LSRIAREGRKFGVGLCLVSQRPKTLDA 407
                                   677889999999999998888887764 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00066       1.5      17      81 ..     146     215 ..     139     222 .. 0.76
   2 !    8.8   0.2   0.00031       0.7     113     293 ..     222     412 ..     202     438 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00066
                        AAA_10  17 sktnasasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekf.ketlpe....iakkinvvtLd 81 
                                   +k  + + +i+  +G GKS ++ +l   +  l+  +l+ D   e +    e  +     i  kin+ +++
  gi|15669760|ref|NP_248573.1| 146 NKLCSRHLAILAMTGMGKSNTVAVLLRELNKLKATVLVFDMHGEYKDIyCESEKLrvhiIEPKINIYRIN 215
                                   56677899************************************77642332222334466678877775 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00031
                        AAA_10 113 llgvkkkesekkaalseaveavle.gkqrgllavieelrkedekvareiarhlesvvkkslaklvfsdgsveeaislekkv 192
                                   l gv  +++++++ +++a+++ +e +k++++  v + ++    k+ +  ++ + +  + s+   +f  ++    ++++k++
  gi|15669760|ref|NP_248573.1| 222 LAGVDAQATKQRPYIRKAIKEIKEeRKEHDFSTVDDYINAIIGKLEEYKSNDNYKKDESSIQTAIFRLED---MLQFRKNI 299
                                   6677778888888888888888753666777766666655555555555555555566677777776665...47787877 PP

                        AAA_10 193 tvlevedLdLPd.kderlerlteekllsvavlfviaafarefassdkkef..k........vvifDEawift...ssaeGk 259
                                     l+ + ++  d +++ ++ + +e+l   av +v++ +a+ +    k+++  k         +if Ea  ++        k
  gi|15669760|ref|NP_248573.1| 300 ITLHYNPIN--DiREHYINIIPMEELDENAVDIVVSYIAKAVLDDRKRIIidKgrdfakpiFMIFEEAHLIApqhRKTRAK 378
                                   777666543..3235667777777777777777777777766544333321111111122246899999886221345678 PP

                        AAA_10 260 kllkelvRiGRsynaavylvtqsadDvlkeelkn 293
                                   + l+ + R GR++   + lv+q ++ ++ e+l++
  gi|15669760|ref|NP_248573.1| 379 HYLSRIAREGRKFGVGLCLVSQRPKTLDAETLSQ 412
                                   889999*******************999998543 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.002       4.5      27      60 ..     137     171 ..     115     177 .. 0.79
   2 ?    4.1   0.0     0.011        25     206     241 ..     367     402 ..     358     404 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.002
                                   TS-EEEEEGGGS-..SEEEE--TTSSHHHHHHHHH CS
                  FtsK_SpoIIIE  27 sgnplvldlkkma.shllvaGatgsGKStalntLi 60 
                                    +  ++ld++k    hl ++  tg GKS+++ +L+
  gi|15669760|ref|NP_248573.1| 137 EDVEVKLDANKLCsRHLAILAMTGMGKSNTVAVLL 171
                                   355666777777689****************9997 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.011
                                   HHHHHH....HHHHHHHHHHHCGGGTEEEEEEES-- CS
                  FtsK_SpoIIIE 206 laapkdssvlvedaivRlarkgraaglHlllatqrl 241
                                   l ap+  + +++ +++R+ar gr+ g+ l l  qr+
  gi|15669760|ref|NP_248573.1| 367 LIAPQHRKTRAKHYLSRIAREGRKFGVGLCLVSQRP 402
                                   667888899******************999999997 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00015      0.33       8      36 ..     159     187 ..     154     346 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                                   TTSSHHHHHHHHHHHHHHTT--EEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA   8 GGvGKTtlaanLaralarrglrVllvDaD 36 
                                    G GK+ ++a L+r l++ +  Vl++D+ 
  gi|15669760|ref|NP_248573.1| 159 TGMGKSNTVAVLLRELNKLKATVLVFDMH 187
                                   699************************85 PP

>> ATP-synt_E_2  ATP synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.49   1.1e+03      33      54 ..     161     182 ..     142     183 .. 0.72
   2 ?    8.7   0.7   0.00094       2.1       4      25 ..     250     271 ..     248     277 .. 0.90
   3 ?   -0.4   0.2      0.63   1.4e+03       1      28 [.     320     348 ..     320     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.49
                  ATP-synt_E_2  33 mEYEKlLKqRLdeLeklKrkvL 54 
                                   m    ++   L eL+klK  vL
  gi|15669760|ref|NP_248573.1| 161 MGKSNTVAVLLRELNKLKATVL 182
                                   555566666799******9998 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00094
                  ATP-synt_E_2   4 idkstiDKYlniLkskLdeKKs 25 
                                    d st+D Y+n +  kL+e Ks
  gi|15669760|ref|NP_248573.1| 250 HDFSTVDDYINAIIGKLEEYKS 271
                                   589****************998 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.63
                  ATP-synt_E_2   1 mdeidkstiDKYln.iLkskLdeKKsElL 28 
                                   m+e+d  ++D  +  i k  Ld++K  ++
  gi|15669760|ref|NP_248573.1| 320 MEELDENAVDIVVSyIAKAVLDDRKRIII 348
                                   89999999998885488999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 3114.74
//
Query:       gi|15669761|ref|NP_248574.1|  [L=447]
Description: hypothetical protein MJ_1566 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2896.94
//
Query:       gi|15669762|ref|NP_248575.1|  [L=175]
Description: hypothetical protein MJ_1567 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.016   15.1   0.1      0.026   14.4   0.1    1.3  1  Chordopox_A35R  Chordopoxvirus A35R protein
       0.17   11.6   0.4        0.4   10.4   0.4    1.6  1  DUF434          Protein of unknown function (DUF434)


Domain annotation for each model (and alignments):
>> Chordopox_A35R  Chordopoxvirus A35R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.9e-06     0.026      36      95 ..     107     166 ..      93     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-06
                Chordopox_A35R  36 pyliasleleevsvelikqkdledCYiavnGvilkcsednklrlpvtkiyaa.yrsknsii 95 
                                   +y   + + e+++ +l+++  l++  i+ nG+i+k s+++kl++++tki  + y+sk+ i+
  gi|15669762|ref|NP_248575.1| 107 DYNFNQKDKETIDKTLLENGRLKEIQITKNGIIIK-SKNEKLEIEITKIDKIsYKSKSYIM 166
                                   68888888999*********************998.67899********865388887665 PP

>> DUF434  Protein of unknown function (DUF434)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   4.5e-05       0.4       4      18 ..      69      83 ..      68      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.5e-05
                        DUF434  4 eAaeDlryLLnRGYp 18
                                  eA+ Dl+yLL+++Y 
  gi|15669762|ref|NP_248575.1| 69 EAINDLNYLLDNNYL 83
                                  8*************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1196.70
//
Query:       gi|15669763|ref|NP_248576.1|  [L=173]
Description: hypothetical protein MJ_1568 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-36  123.6   0.0    1.3e-17   63.7   0.0    2.0  2  LigT_PEase       LigT like Phosphoesterase
    4.6e-10   39.6   0.0    5.5e-10   39.4   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    1.5e-09   38.1   2.0    4.6e-09   36.5   2.0    1.7  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain


Domain annotation for each model (and alignments):
>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0   2.2e-21   1.3e-17       1      87 []       7      85 ..       7      85 .. 0.95
   2 !   58.2   0.0   1.2e-19   6.9e-16       8      87 .]      90     167 ..      86     167 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 2.2e-21
                                  EE-CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCSC CS
                    LigT_PEase  1 lgppeeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlrp 83
                                  +++pe+i+ee+a+++++++     +g+k+v+++n+HiT++flgevdeek++e+l+   +i    +p+++k++ +g+fp+ ++ 
  gi|15669763|ref|NP_248576.1|  7 IDIPENIKEEIAKFQEQFK----MKGIKLVEKENLHITVKFLGEVDEEKLKEILNLDLSI----QPIKIKLKYIGTFPNSNYI 81
                                  789****************....89****************************9888767....7999*************** PP

                                  CEEE CS
                    LigT_PEase 84 rviy 87
                                  rvi+
  gi|15669763|ref|NP_248576.1| 82 RVIW 85
                                  ***9 PP

  == domain 2  score: 58.2 bits;  conditional E-value: 1.2e-19
                                   HHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEES.HHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC.SCCEE CS
                    LigT_PEase   8 aeelarlaaeleralaklglkpvrpfnpHiTLaflgevd.eekvpellealaeiasgaepfelkvdgvglfpsrl.rprvi 86 
                                    ++l ++++e++++l+ lg+k +r++ pH+T+++++ +d ++k+++ +e+++++++g     ++++++ l++s+l ++++i
  gi|15669763|ref|NP_248576.1|  90 NNNLVEIFKEIDEKLSNLGFKKEREYVPHLTIGRVKFIDnKKKLKDRIEKYKDVDFGE----FEAKHIKLYKSTLtPNGPI 166
                                   47899*************************************************9995....******************* PP

                                   E CS
                    LigT_PEase  87 y 87 
                                   y
  gi|15669763|ref|NP_248576.1| 167 Y 167
                                   9 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   9.1e-14   5.5e-10       2     147 ..      10     157 ..       9     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 9.1e-14
               2_5_RNA_ligase2   2 ppslaapiealr...rslydkayprwppHitLlypfvededladlaellsrlaketepfevrldgfgvFeh.kks.vvyls 77 
                                   p++++++i++++   + ++ k++++  +Hit++++++ de  ++l+e l   + +++p+++ l+ +g+F+      v+++ 
  gi|15669763|ref|NP_248576.1|  10 PENIKEEIAKFQeqfKMKGIKLVEKENLHITVKFLGEVDE--EKLKEILNLDL-SIQPIKIKLKYIGTFPNsNYIrVIWIG 87 
                                   677777888888555577788899***************9..67777776666.*****************644479**** PP

               2_5_RNA_ligase2  78 vsdsealqalraallealpeagdkedsgeftPHlTiaqsadstsaaellekl..aqalpplefevdevallr 147
                                   +   + l+++ +++ e+l   g k++ +e++PHlTi++ +     ++l++++   ++ +  efe +++ l++
  gi|15669763|ref|NP_248576.1|  88 A-YNNNLVEIFKEIDEKLSNLGFKKE-REYVPHLTIGRVKFIDNKKKLKDRIekYKDVDFGEFEAKHIKLYK 157
                                   *.*********************986.**********98755555555555522255555557877777765 PP

>> AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   2.0   7.7e-13   4.6e-09      13     203 ..      11     171 ..       3     173 .] 0.77

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 7.7e-13
                                   H.HHHHHHHHHHHHHHH-GGGGGGB.--TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS--EEEEEEEEEE. CS
                     AKAP7_NLS  13 k.lrkklekfqesvlsklpgldeslfikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkplslrlkGletfn 92 
                                   + +++++ kfqe+   k+     +l +++e+lH+T+  l    + + ++ ke+L+         +  +p++++lk ++tf 
  gi|15669763|ref|NP_248576.1|  11 EnIKEEIAKFQEQFKMKGI----KL-VEKENLHITVKFLG---EVDEEKLKEILNLD-----LSI--QPIKIKLKYIGTFP 76 
                                   3377777777777655444....56.8999*****98875...45555555555432.....222..888**********7 PP

                                   ....TTTEEEEEE--SHHHHHHHHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHTT--S--GG.GGGGGTT CS
                     AKAP7_NLS  93 ddpakarVlYakveeesneekLqeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkkqakskesfdareilkqfkd 173
                                   ++++  rV++++      +++L e+ + i +++++ g+++e++   + +H+T+  +++  +k++ ++        ++++kd
  gi|15669763|ref|NP_248576.1|  77 NSNY-IRVIWIGAY----NNNLVEIFKEIDEKLSNLGFKKERE---YVPHLTIGRVKFIDNKKKLKD-------RIEKYKD 142
                                   6665.9*******9....999************9999987766...88*********9999888777.......4789*** PP

                                   -EEEEEE--EEEEEESSS---TTS--EEEE CS
                     AKAP7_NLS 174 fefgeekineihLsqlesddesdgyYkvia 203
                                    +fge +++ i+L + + + +    Y+vi+
  gi|15669763|ref|NP_248576.1| 143 VDFGEFEAKHIKLYKSTLTPN-GPIYEVIK 171
                                   *************98887766.67777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1108.98
//
Query:       gi|15669764|ref|NP_248577.1|  [L=222]
Description: cobalt transport protein CbiM [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-59  200.9   9.4    2.3e-59  200.7   9.4    1.0  1  CbiM       Cobalt uptake substrate-specific transmembrane reg
  ------ inclusion threshold ------
        2.7    8.4  18.2        9.8    6.5  15.2    2.9  2  DUF4199    Protein of unknown function (DUF4199)


Domain annotation for each model (and alignments):
>> CbiM  Cobalt uptake substrate-specific transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.7   9.4   2.5e-63   2.3e-59       1     207 []       2     209 ..       2     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: 200.7 bits;  conditional E-value: 2.5e-63
                          CbiM   1 HipdgiLspavllaayavalallalalrrlrkeldearvpllallaafifaaqminipipggtslHllgavlaaiLlG.pw 80 
                                   Hipdg+L p +++++y++++++++ ++++l+k  d +++pll++l+af f+++m+n+p+p gt++H++g++l+aiL+  pw
  gi|15669764|ref|NP_248577.1|   2 HIPDGYLGPITCAFFYLIMIPIWYKSIKELKKL-DPRKLPLLGVLTAFSFLVMMFNLPVPDGTTAHMVGGTLIAILMDnPW 81 
                                   *******************************99.9999***************************************99** PP

                          CbiM  81 aaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaallvalela 161
                                   +a +a+++vl++qa++fgdGGit +GaN++nm+v+ ++++y+vy++l+     k  +++a+ ++a++++v+aa+++++e++
  gi|15669764|ref|NP_248577.1|  82 VATIAISIVLIIQAIFFGDGGITCIGANCFNMGVVLPFVGYYVYKFLR----DKVGEVIASGIGAYVGIVAAAIVAGFEFG 158
                                   *********************************************884....45889************************ PP

                          CbiM 162 lsgleas....lsltaalaamllvhlpv.gilEgviTaaivkalkkvrpel 207
                                   l++  +     +++t++++am+ +hl+  g + +v+Ta++v ++kkvrp+l
  gi|15669764|ref|NP_248577.1| 159 LQPFIEPgycpYPFTVSVPAMAFAHLITaGPAAAVVTAIVVWYVKKVRPDL 209
                                   **7654589*******************9999*****************97 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  15.2    0.0011       9.8       8      99 ..      86     167 ..       6     179 .. 0.84
   2 ?   -0.6   0.1      0.17   1.5e+03      39      55 ..     189     205 ..     170     215 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0011
                       DUF4199   8 lvwilifllilyllglhqilstg.pllglla..llllllvpflvylalkkyrkknlgGfisfgqafgfgflislvagllsa 85 
                                   +++i++++ +++++g +     g + +g  a  + + ++ pf++y+  k  r+k+ g++i    a g+g ++ +va+ ++a
  gi|15669764|ref|NP_248577.1|  86 AISIVLII-QAIFFGDG-----GiTCIG--AncFNMGVVLPFVGYYVYKFLRDKV-GEVI----ASGIGAYVGIVAAAIVA 153
                                   34444444.44444443.....213333..2447777777*********99***9.8866....8999999999******* PP

                       DUF4199  86 vfqyiyfnfidpdf 99 
                                    f + +  fi+p++
  gi|15669764|ref|NP_248577.1| 154 GFEFGLQPFIEPGY 167
                                   ************98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.17
                       DUF4199  39 lllllvpflvylalkky 55 
                                    ++++v ++v++++kk 
  gi|15669764|ref|NP_248577.1| 189 PAAAVVTAIVVWYVKKV 205
                                   33333344555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1455.51
//
Query:       gi|15669765|ref|NP_248578.1|  [L=115]
Description: hypothetical protein MJ_1570 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-07   29.8   0.0    5.3e-07   29.4   0.0    1.2  1  PDGLE     PDGLE domain
  ------ inclusion threshold ------
       0.03   14.4   5.8       0.79    9.8   0.2    2.3  2  DUF3309   Protein of unknown function (DUF3309)
      0.069   13.5   1.5       0.11   12.9   0.1    1.8  2  DUF3262   Protein of unknown function (DUF3262)


Domain annotation for each model (and alignments):
>> PDGLE  PDGLE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   8.9e-11   5.3e-07      14      85 ..      31     102 ..      15     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 8.9e-11
                         PDGLE  14 ASanPdGLEwsiekvagtaeleasgdlhealaeiqektalLpDYsfkgaeekk...agtsvAgivGvlltlalag 85 
                                     ++++G Ew  e+va++     + +   +la+i    a+LpDY+++g ++     +g+++++ivGv+l ++ ++
  gi|15669765|ref|NP_248578.1|  31 NYGDAWG-EWGPEDVAEKVGED-KVSGLLHLADIW-SYAPLPDYDIPGWDDPFhasIGYIISAIVGVILCVGAYY 102
                                   45899**.*******8876433.333444566776.59***********9965888*************998765 PP

>> DUF3309  Protein of unknown function (DUF3309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.2    0.0013       7.6       5      26 ..      16      37 ..      12      44 .. 0.79
   2 ?    9.8   0.2   0.00013      0.79      16      39 ..      73      98 ..      72     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0013
                       DUF3309  5 liiLillLiGalptwpysrgwG 26
                                  + ++il  +G l +w y   wG
  gi|15669765|ref|NP_248578.1| 16 VAMVILCPLGILLVWNYGDAWG 37
                                  345677779************9 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00013
                       DUF3309 16 lptw..pysrgwGYgPsGglGlvlvi 39
                                  +p w  p+ ++ GY  s ++G++l +
  gi|15669765|ref|NP_248578.1| 73 IPGWddPFHASIGYIISAIVGVILCV 98
                                  67788899***************986 PP

>> DUF3262  Protein of unknown function (DUF3262)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.8e-05      0.11      20      53 ..      12      45 ..       7      50 .. 0.90
   2 ?   -0.9   0.1      0.36   2.2e+03      26      35 ..      90      99 ..      79     107 .. 0.43

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                       DUF3262 20 lklliagillvvllLwaaWalvsvYkgWaeekis 53
                                  l l++a+++l  l ++++W + +++  W+ e++ 
  gi|15669765|ref|NP_248578.1| 12 LYLIVAMVILCPLGILLVWNYGDAWGEWGPEDVA 45
                                  7899************************998876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.36
                       DUF3262 26 gillvvllLw 35
                                  +i+ v+l + 
  gi|15669765|ref|NP_248578.1| 90 AIVGVILCVG 99
                                  2222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 792.15
//
Query:       gi|15669766|ref|NP_248579.1|  [L=292]
Description: cobalt transport protein CbiQ [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-65  220.7   8.0    2.9e-65  219.9   8.0    1.3  1  CbiQ      Cobalt transport protein
  ------ inclusion threshold ------
       0.16   11.8   0.0       0.38   10.6   0.0    1.6  1  SplA      Transcriptional regulator protein (SplA)


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.9   8.0   3.3e-69   2.9e-65       2     217 ..      23     260 ..      22     262 .. 0.98

  Alignments for each domain:
  == domain 1  score: 219.9 bits;  conditional E-value: 3.3e-69
                                   SCCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---......HHHHHHHCCCHCHHHHHHHHHHE... CS
                          CbiQ   2 ksvlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp......rvlaqalilpllflllgllillf... 73 
                                   k+++h++++ +++i++ ++++++ l++n++++++ii+l+++l+++v+++      +++++alil++l++++ l++l++   
  gi|15669766|ref|NP_248579.1|  23 KTIEHVIKYLNENIFFEKYTRISGLLQNIESRIKIISLVIFLVGSVLSKhiltliIFNSIALILAYLSNIPLLQYLKRvyv 103
                                   899****************************************************************************** PP

                                   .....................EECTTEEE.....E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HH CS
                          CbiQ  74 ..............qlittegefvfaggg..qisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPle 138
                                                 ++++t+g++vf++++  +isit+eGl+++++++lR++t++s+++l+++TT+++++ts++++lgvP++
  gi|15669766|ref|NP_248579.1| 104 fipifagiiaipvmFNFMTPGKDVFVILNnpHISITYEGLIYAITFTLRVATCVSFAVLIPITTQWNKVTSAIHKLGVPEV 184
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS.....S CS
                          CbiQ 139 lalillLayRfiflLleevqrikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtgseerth 217
                                   +++i++LayR+iflLl++v ++++++k+R++++ lg+++s++++gk+i+alf+++++++e+ ++Am +RGY+g  e +h
  gi|15669766|ref|NP_248579.1| 185 VITITNLAYRYIFLLLNFVLDMMYSRKSRVVNK-LGMVESWKEAGKAIGALFIKTYQMGEDXYYAMLSRGYNG--EIKH 260
                                   *********************************.***************************************..4444 PP

>> SplA  Transcriptional regulator protein (SplA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.2e-05      0.38       5      20 ..     121     136 ..     118     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.2e-05
                          SplA   5 lkagdeVyViyrNPHt 20 
                                   + +g  V+Vi +NPH 
  gi|15669766|ref|NP_248579.1| 121 MTPGKDVFVILNNPHI 136
                                   6789***********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1848.01
//
Query:       gi|15669767|ref|NP_248580.1|  [L=278]
Description: cobalt transport ATP-binding protein CbiO [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.9e-31  107.8   0.0    8.4e-31  107.3   0.0    1.2  1  ABC_tran     ABC transporter
    7.5e-17   62.1   0.3    3.4e-08   33.7   0.0    2.5  3  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.6e-11   43.4   0.0    5.3e-11   42.4   0.0    1.5  1  SMC_N        RecF/RecN/SMC N terminal domain
    4.2e-05   24.1   0.1    5.3e-05   23.8   0.2    1.5  1  AAA_23       AAA domain
    9.4e-05   21.3   0.0       0.21   10.2   0.0    2.5  3  AAA_13       AAA domain
    0.00026   20.8   2.1      0.001   18.9   2.1    2.1  1  AAA_15       AAA ATPase domain
    0.00079   19.5   0.2      0.017   15.1   0.0    2.5  2  AAA_14       AAA domain
     0.0018   18.1   0.2       0.12   12.1   0.0    2.2  2  AAA_24       AAA domain
     0.0024   17.5   0.0     0.0047   16.6   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0044   17.2   0.0       0.13   12.5   0.0    2.6  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.053   13.4   0.0    1.8  2  RsgA_GTPase  RsgA GTPase
      0.027   15.0   0.0       0.28   11.7   0.0    2.2  2  AAA_18       AAA domain
      0.029   14.0   0.0      0.052   13.1   0.0    1.3  1  AAA_27       AAA domain
       0.03   14.2   0.1       0.33   10.8   0.0    2.3  2  ATPase_2     ATPase domain predominantly from Archaea
      0.041   13.3   0.1       0.53    9.7   0.0    2.1  2  TniB         Bacterial TniB protein
      0.046   13.4   0.0        0.1   12.3   0.0    1.5  2  AAA_30       AAA domain
      0.052   13.8   0.0      0.075   13.3   0.0    1.6  1  AAA_28       AAA domain
      0.096   12.0   0.0        6.7    6.0   0.0    2.2  2  ATPase       KaiC
        0.1   12.9   0.1       0.86    9.9   0.0    2.1  2  AAA_22       AAA domain
       0.11   12.4   0.1       0.21   11.5   0.1    1.4  1  NACHT        NACHT domain
       0.12   12.1   0.0        0.6    9.8   0.0    2.0  2  IstB_IS21    IstB-like ATP binding protein
       0.18   10.5   0.0          2    7.1   0.0    2.0  2  ABC_ATPase   Predicted ATPase of the ABC class
       0.21   12.0   0.0       0.49   10.7   0.0    1.6  2  AAA_16       AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.3   0.0   1.1e-33   8.4e-31       1     137 []      21     172 ..      21     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 1.1e-33
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG......B-HHHCCHCEEEE-SS..--S-TT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx..xxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke......qeleslrkeigvlpqe..pqlfpe 73 
                                   l+nv+l+++++e+vai+G+nGaGK+tLlk+l gl+ p++Ge+ ++gk+l++      + ++++r+++g+++q+    lf+ 
  gi|15669767|ref|NP_248580.1|  21 LDNVNLNIYKNEVVAILGPNGAGKTTLLKILDGLVFPDKGEVYFEGKKLTDeilrdkELMKEFRRKVGFVFQNpdVMLFNP 101
                                   79*************************************************9**9988899************85555555 PP

                                   SBHHHH........HHHTC....HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xxxxxx........xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  74 ltvren........esdee....iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                   + v ++        +s+e+     +k l+ +++ +lkd++     ++LSgG+k++v++ ++l  +p+++l+DEpt+
  gi|15669767|ref|NP_248580.1| 102 T-VWDEvafsplhlYSKEKaievTDKTLKDMKIYHLKDRHP----YNLSGGEKKKVSISCILSVEPEVILMDEPTS 172
                                   5.88888******9555553444677777777777777777....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.2   1.2e-08   9.6e-06       2      30 ..      34      59 ..      33      93 .. 0.71
   2 !   33.7   0.0   4.4e-11   3.4e-08     220     301 ..     127     205 ..     104     207 .. 0.80
   3 ?   -2.1   0.0       3.5   2.7e+03     171     208 ..     215     252 ..     209     261 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.2e-08
                        AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdve 30
                                   ++ GpNg+GK++LL++ld+l       +
  gi|15669767|ref|NP_248580.1| 34 VAILGPNGAGKTTLLKILDGL---VFPDK 59
                                  689***************999...32333 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 4.4e-11
                        AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                   ++  ++  + +++ +++lS G k+   +  +l   +    ++l DEp + L+Pk  ++++ l+k+ ++ g  v+l+TH+  
  gi|15669767|ref|NP_248580.1| 127 TLKDMKIYHLKDRHPYNLSGGEKKKVSISCILSVEP---EVILMDEPTSALDPKSRAEIMNLIKSFKECGKTVVLVTHDLN 204
                                   55667777888888999********66666665555...9***********************88888888********87 PP

                        AAA_21 301 l 301
                                   l
  gi|15669767|ref|NP_248580.1| 205 L 205
                                   6 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.5
                        AAA_21 171 ifadyfgfakekrllqrlvrslklveielsdlgegeel 208
                                   + ++ +++ k+k+l++  +++l+l+ +e+s+l ++ ++
  gi|15669767|ref|NP_248580.1| 215 LNKKVIFEGKVKDLFSLNLDELNLDVPEISKLFIKLKN 252
                                   55667778888888888888888888888888766554 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   6.8e-14   5.3e-11      23     212 ..      30     216 ..      18     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 6.8e-14
                                   TSSEEEEEESTTSSHHHHHHHHH.HHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE..SSSSSSCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                         SMC_N  23 sksftaivGpNGSGKsnlldAil.FvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk..lkiekeevsis 100
                                   ++++ ai+GpNG+GK+ ll  +   v+ ++    +  +kl+d i + ke  +  + +v  +f+n+d     ++  +ev  s
  gi|15669767|ref|NP_248580.1|  30 KNEVVAILGPNGAGKTTLLKILDgLVFPDKGEVYFEGKKLTDEILRDKELMKEFRRKVGFVFQNPDVMlfNPTVWDEVAFS 110
                                   56789***********876555324899999999********999978888888999**********94334445566666 PP

                                   EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvae 181
                                        ++e  +++ +k+ +  ++ +l  +   ++ +LSgGek+ v+++ ++++   +p+ + l+De  +aLD k ++++ +
  gi|15669767|ref|NP_248580.1| 111 PLHLYSKEKAIEVTDKTLKDMKIYHLKDR---HPYNLSGGEKKKVSISCILSV---EPE-VILMDEPTSALDPKSRAEIMN 184
                                   66666666677777777777777666544...5779************99876...565.569****************** PP

                                   HHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 182 llkekskn.aQfivislreemlekadklvgvt 212
                                   l+k+ ++    ++ ++++ ++   ad+++ + 
  gi|15669767|ref|NP_248580.1| 185 LIKSFKECgKTVVLVTHDLNLACLADRCYVLN 216
                                   ****9999556677899999999999888665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.2   6.7e-08   5.3e-05      11      48 ..      22      60 ..      16     260 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.7e-08
                        AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildAiklaLygetp 48
                                  ++++++  ++ +++I GpNGaGKTT+l  +    + +++
  gi|15669767|ref|NP_248580.1| 22 DNVNLNIyKNEVVAILGPNGAGKTTLLKILDGLVFPDKG 60
                                  556666677899***************988777776654 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00026      0.21      21      40 ..      36      55 ..      28     110 .. 0.71
   2 !    8.6   0.0   0.00084      0.66     524     573 ..     160     205 ..     112     212 .. 0.84
   3 ?   -2.5   0.0       1.8   1.4e+03     345     397 ..     222     273 ..     213     277 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00026
                        AAA_13 21 iYGwNGaGKTtLSrllrsle 40
                                  i G NGaGKTtL ++l+ l 
  gi|15669767|ref|NP_248580.1| 36 ILGPNGAGKTTLLKILDGLV 55
                                  88*************99884 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00084
                        AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnlef 573
                                   + + +++ +D P S LD +s   +++liks     +  k + + TH l++
  gi|15669767|ref|NP_248580.1| 160 V-EPEVILMDEPTSALDPKSRAEIMNLIKSFK---ECGKTVVLVTHDLNL 205
                                   4.789*************************97...99999******9875 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.8
                        AAA_13 345 eaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakk 397
                                   e K+k++f+ ++l++++ ++ +i+kl  +++++  + Ne+   l+e+++ + k
  gi|15669767|ref|NP_248580.1| 222 EGKVKDLFS-LNLDELNLDVPEISKLFIKLKNMGYNINEIPVTLDEAVNIISK 273
                                   779999998.9999999999999999999999888888888888888877665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   2.1   1.3e-06     0.001      15     176 ..      22     257 ..      20     278 .] 0.49

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                        AAA_15  15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnk..ekkn...................................... 54 
                                   ++v +++ ++ +  + G+N++GK+++l++ld +   +  e ++                                      
  gi|15669767|ref|NP_248580.1|  22 DNVNLNIYKNeVVAILGPNGAGKTTLLKILDGLVFPDkgEVYFegkkltdeilrdkelmkefrrkvgfvfqnpdvmlfnpt 102
                                   6667777666799******************77765512222244444444444444444444444444444444443333 PP

                        AAA_15  55 ......kkvikiekedleifeniseskdikIdvef.............................................. 83 
                                         +                                                                          
  gi|15669767|ref|NP_248580.1| 103 vwdevaF---------------------------Splhlyskekaievtdktlkdmkiyhlkdrhpynlsggekkkvsisc 156
                                   3333332...........................03333222222222222233333333336666666666666666666 PP

                        AAA_15  84 .............aekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkek 151
                                                       + ++ + + e++   + +k++ +  +    d +l++ +++ ++ +++v  + + k+l++++
  gi|15669767|ref|NP_248580.1| 157 ilsvepevilmdeP-----TSALDPKSRAEIMNLIKSFKECGKTVVLVTHDLNLACLADRCYVLNKKVIFEGKVKDLFSLN 232
                                   55554444433220.....22222223333333333444444455555555555555555555555555555566666666 PP

                        AAA_15 152 eeklekekeelkidkedlkklikkl 176
                                    ++l+++ +e+++ + +lk+  + +
  gi|15669767|ref|NP_248580.1| 233 LDELNLDVPEISKLFIKLKNMGYNI 257
                                   6666666666666666666665555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.2e-05     0.017       2      59 ..      31      86 ..      30     111 .. 0.81
   2 ?    1.6   0.2      0.34   2.7e+02      10      22 ..     189     201 ..     180     273 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek 59
                                  +++++i G+  +GKTtllk +++ l  +++  +y++ ++ +d+ l+d+ +l++++++k
  gi|15669767|ref|NP_248580.1| 31 NEVVAILGPNGAGKTTLLK-ILDGLVFPDKGEVYFEGKKLTDEILRDK-ELMKEFRRK 86
                                  789**************85.556777899999*****99999988877.588888776 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.34
                        AAA_14  10 aRrvGKTtllkql 22 
                                    + +GKT++l + 
  gi|15669767|ref|NP_248580.1| 189 FKECGKTVVLVTH 201
                                   6788888887443 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00016      0.12       3      27 ..      32      55 ..      30      71 .. 0.83
   2 ?    3.9   0.0     0.049        38     108     130 ..     179     201 ..     177     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                        AAA_24  3 lkiliyGpsgiGKTtlakelgpkpl 27
                                    ++i Gp+g+GKTtl+k l +  +
  gi|15669767|ref|NP_248580.1| 32 EVVAILGPNGAGKTTLLKIL-DGLV 55
                                  5799*************988.5444 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.049
                        AAA_24 108 aeefrrllkklqelrknvifiah 130
                                   ++e+++l+k ++e++k+v+++ h
  gi|15669767|ref|NP_248580.1| 179 RAEIMNLIKSFKECGKTVVLVTH 201
                                   57999****************99 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.1e-06    0.0047      14      50 ..      23      59 ..      19      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.1e-06
                        AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                  +  ++i  ++++ + Gp+G+GK+Tll  +  l  p+k
  gi|15669767|ref|NP_248580.1| 23 NVNLNIYKNEVVAILGPNGAGKTTLLKILDGLVFPDK 59
                                  566777777899*************976666666665 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00017      0.13      32      89 ..     143     187 ..     117     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                       SbcCD_C  32 tlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                   +lSGGek+++   +++       s        ++++++DE  s lD++s+a++++l++
  gi|15669767|ref|NP_248580.1| 143 NLSGGEKKKVSISCIL-------S------VEPEVILMDEPTSALDPKSRAEIMNLIK 187
                                   6677777555555554.......2......35899********************986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.8e-05     0.053      96     121 ..      28      53 ..       3      68 .. 0.81
   2 ?   -1.8   0.0       3.1   2.4e+03      57      94 ..     235     272 ..     208     277 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-05
                                   HCTTSEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallp 121
                                     k+++++++G+ G+GK+tL++ l++
  gi|15669767|ref|NP_248580.1|  28 IYKNEVVAILGPNGAGKTTLLKILDG 53 
                                   34669****************99976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.1
                                   GG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHH CS
                   RsgA_GTPase  57 Dlleeeeeleelkeelealgyevllvsaktkegleelk 94 
                                   +l  +  e+++l  +l+++gy++  + ++  e+++ ++
  gi|15669767|ref|NP_248580.1| 235 ELNLDVPEISKLFIKLKNMGYNINEIPVTLDEAVNIIS 272
                                   44444446777788888888888887777666666555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00036      0.28       1      21 [.      34      54 ..      34      97 .. 0.73
   2 ?    1.1   0.0      0.71   5.5e+02      45     116 ..     173     256 ..     135     269 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                        AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                  +++ G+ G+GKttl k L  +
  gi|15669767|ref|NP_248580.1| 34 VAILGPNGAGKTTLLKILDGL 54
                                  689**************9443 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.71
                        AAA_18  45 aldeskrldedkldklldaleenss.................aleegknlvidghlaeleseaakdikkvvLtasp.eell 107
                                   ald++ r+++++   l++ ++e+ +                  +  +k ++++g + +l+s ++ +     L++++ ++l+
  gi|15669767|ref|NP_248580.1| 173 ALDPKSRAEIMN---LIKSFKECGKtvvlvthdlnlacladrCYVLNKKVIFEGKVKDLFSLNLDE---LNLDVPEiSKLF 247
                                   444444444444...777777765555566666666655566555556666666666666666665...446666666666 PP

                        AAA_18 108 eRlekRgye 116
                                     l++ gy+
  gi|15669767|ref|NP_248580.1| 248 IKLKNMGYN 256
                                   666666655 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.6e-05     0.052      18      51 ..      23      56 ..      15      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-05
                        AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdllf 51
                                  +++++  ++++  i+GpN AGK+t+l+ +  l+f
  gi|15669767|ref|NP_248580.1| 23 NVNLNIYKNEVVAILGPNGAGKTTLLKILDGLVF 56
                                  5666667899999*************99999988 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00042      0.33      19      38 ..      30      49 ..      21     138 .. 0.85
   2 ?    1.3   0.0      0.36   2.8e+02      29      70 ..     190     230 ..     179     277 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                      ATPase_2 19 pneiyfiYGpegsGKtaLlk 38
                                  +ne++ i Gp g GKt+Llk
  gi|15669767|ref|NP_248580.1| 30 KNEVVAILGPNGAGKTTLLK 49
                                  6899**************98 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.36
                      ATPase_2  29 egsGKtaLlkeiienledkdkyviyyialreesiskldefie 70 
                                   + +GKt +l     nl  +  ++ y+ + + +++ k+++ + 
  gi|15669767|ref|NP_248580.1| 190 KECGKTVVLVTHDLNLACLA-DRCYVLNKKVIFEGKVKDLFS 230
                                   56888877765555553433.567777777777777766654 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.25     2e+02      37      53 ..      33      49 ..      26      54 .. 0.87
   2 ?    9.7   0.0   0.00068      0.53      94     153 ..     136     192 ..     121     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.25
                          TniB 37 nlllvGdsnnGKtmive 53
                                   + ++G+   GKt++++
  gi|15669767|ref|NP_248580.1| 33 VVAILGPNGAGKTTLLK 49
                                  5789**********986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00068
                          TniB  94 lgaplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnel 153
                                   l+ ++  + +  ++++  ++++ +++++v+++DE  ++l    +++ e++n++ks+++ +
  gi|15669767|ref|NP_248580.1| 136 LKDRHPYNLSGGEKKKVSISCILSVEPEVILMDEPTSAL--DPKSRAEIMNLIKSFKE-C 192
                                   5666666777789999999********************..88999********9864.4 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013       0.1      18      41 ..      31      54 ..      24      64 .. 0.82
   2 ?   -3.1   0.0       6.7   5.3e+03      90     122 ..     163     199 ..     154     202 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                        AAA_30 18 drvavltGpAGtGKttalkalrea 41
                                  + v+++ Gp G+GKtt+lk l  +
  gi|15669767|ref|NP_248580.1| 31 NEVVAILGPNGAGKTTLLKILDGL 54
                                  56999*************998765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.7
                        AAA_30  90 tllivDEagmv....dtkqlaallkaaekagakvilv 122
                                   ++++ DE   +    + +++ +l+k+ ++ g +v+lv
  gi|15669767|ref|NP_248580.1| 163 EVILMDEPTSAldpkSRAEIMNLIKSFKECGKTVVLV 199
                                   5677777544444334444455555555567777766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.6e-05     0.075       2      20 ..      34      52 ..      33     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.6e-05
                        AAA_28  2 ivitGgestGKTtlleaLa 20
                                  ++i+G+ ++GKTtll+ L 
  gi|15669767|ref|NP_248580.1| 34 VAILGPNGAGKTTLLKILD 52
                                  89**************996 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0086       6.7      15      35 ..      27      47 ..      16      50 .. 0.85
   2 ?    3.7   0.0     0.044        34     138     163 ..     176     201 ..     149     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0086
                        ATPase 15 GipegrvvlitGepGtGKtif 35
                                   i++++vv i G  G+GKt++
  gi|15669767|ref|NP_248580.1| 27 NIYKNEVVAILGPNGAGKTTL 47
                                  58999**************97 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.044
                        ATPase 138 avaReilrqlvrvlkklgvTailvse 163
                                    + R+++++l++ +k+ g T +lv+ 
  gi|15669767|ref|NP_248580.1| 176 PKSRAEIMNLIKSFKECGKTVVLVTH 201
                                   4679******************9975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0011      0.86       6      24 ..      32      50 ..      28      55 .. 0.86
   2 ?    0.5   0.0      0.88   6.9e+02      92     127 ..     162     198 ..     112     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                        AAA_22  6 gilvvtGesGtGKTtllrr 24
                                   ++++ G+ G+GKTtll+ 
  gi|15669767|ref|NP_248580.1| 32 EVVAILGPNGAGKTTLLKI 50
                                  57899***********985 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.88
                        AAA_22  92 ielliiDEaqh.lr..s.eealeeLrsllnlsrkgvqliL 127
                                   +e+++ DE    l+  s +e+++ ++s+ +   +g +++L
  gi|15669767|ref|NP_248580.1| 162 PEVILMDEPTSaLDpkSrAEIMNLIKSFKE---CGKTVVL 198
                                   678888888887877634777777766655...4444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00027      0.21       2      18 ..      33      49 ..      32      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                                  CEEEEC-TTTCHHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLlq 18
                                  +v++ G++G GKTtLl+
  gi|15669767|ref|NP_248580.1| 33 VVAILGPNGAGKTTLLK 49
                                  799************97 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00077       0.6      44      70 ..      28      54 ..      20     132 .. 0.73
   2 ?   -0.2   0.0      0.94   7.3e+02     108     151 ..     161     205 ..     148     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00077
                     IstB_IS21 44 iekkenivllGpsGvGKshlaialgve 70
                                  i k+e +++lGp G+GK+ l   l   
  gi|15669767|ref|NP_248580.1| 28 IYKNEVVAILGPNGAGKTTLLKILDGL 54
                                  678999************997666554 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.94
                     IstB_IS21 108 kvdllilDdlgllpldqaeaellfevie..kryerrsiiitsnlpf 151
                                   +++++++D+  +  ld +++++++++i+  k  +++ +++t +l++
  gi|15669767|ref|NP_248580.1| 161 EPEVILMDEP-TSALDPKSRAEIMNLIKsfKECGKTVVLVTHDLNL 205
                                   5577777774.67889999999999998333556777777877665 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0026         2     243     268 ..      30      55 ..      24      59 .. 0.84
   2 ?    1.1   0.0      0.18   1.4e+02     324     354 ..     145     175 ..     141     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0026
                                   -SSEEEEEE-TTSSHHHHHHHHHHCC CS
                    ABC_ATPase 243 pkGvtlIvGggfhGKsTLLeAlekGv 268
                                   ++ v++I G++  GK+TLL+ l+  v
  gi|15669767|ref|NP_248580.1|  30 KNEVVAILGPNGAGKTTLLKILDGLV 55 
                                   45699***************998655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.18
                                   -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HH CS
                    ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtN 354
                                   SG   + ++i   l ++ +++L+DE tsA  
  gi|15669767|ref|NP_248580.1| 145 SGGEKKKVSISCILSVEPEVILMDEPTSALD 175
                                   77777888899999999***********975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00063      0.49      25      45 ..      32      52 ..      20      97 .. 0.81
   2 ?   -1.8   0.0       4.7   3.6e+03     113     144 ..     176     203 ..     116     216 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00063
                        AAA_16 25 elvllsGesGvGKsslvrell 45
                                  e+v + G+ G GK++l++ l 
  gi|15669767|ref|NP_248580.1| 32 EVVAILGPNGAGKTTLLKILD 52
                                  7899************97665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.7
                        AAA_16 113 gaeasrllellkrllallsrderplvlvlDdl 144
                                   ++++  + +l+k++    ++ ++++vlv  dl
  gi|15669767|ref|NP_248580.1| 176 PKSRAEIMNLIKSFK---EC-GKTVVLVTHDL 203
                                   444444444444443...44.44455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1842.55
//
Query:       gi|15669768|ref|NP_248581.1|  [L=112]
Description: hypothetical protein MJ_1572.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-18   65.8   0.0    5.7e-18   65.5   0.0    1.1  1  DUF1998   Domain of unknown function (DUF1998)


Domain annotation for each model (and alignments):
>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   3.2e-22   5.7e-18       1      83 []       4      86 ..       4      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 3.2e-22
                       DUF1998  1 lehalinalplflqcdesdlgteckapedep.rkrpariliydavpgGaGiaekaaelleellraalelieecdCeeaGCpaC 82
                                  +eh +i++ p+f  +d++++g++++++++++  k++a i+iyd+ +gG G+ae ++e +e+ll++ le++++c+C+ +GCp C
  gi|15669768|ref|NP_248581.1|  4 IEHNIIKITPIFTYIDSREIGGYSYERFNRNlFKDKAVIFIYDGNEGGFGLAEILYENAEKLLNKSLEHLKNCNCA-DGCPLC 85
                                  589**********************8777668999****************************************8.****** PP

                       DUF1998 83 l 83
                                  +
  gi|15669768|ref|NP_248581.1| 86 I 86
                                  7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 739.81
//
Query:       gi|15669769|ref|NP_248582.1|  [L=61]
Description: hypothetical protein MJ_1573 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 463.71
//
Query:       gi|15669770|ref|NP_248583.1|  [L=684]
Description: EIF-4a family ATP-dependent RNA helicase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-24   86.8   0.0    3.7e-24   85.4   0.0    1.7  2  DEAD            DEAD/DEAH box helicase
      8e-23   80.9   0.5    2.7e-20   72.7   0.0    3.7  3  Helicase_C      Helicase conserved C-terminal domain
    2.6e-08   34.0   0.3    6.7e-08   32.7   0.3    1.7  1  ResIII          Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
       0.17   11.6   0.1       0.32   10.7   0.1    1.4  1  PHF12_MRG_bd    PHD finger protein 12 MRG binding domain
        3.7    8.1   6.5         56    4.3   0.8    3.5  3  Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0     1e-27   3.7e-24       3     174 ..      49     225 ..      47     227 .. 0.85
   2 ?   -3.7   0.0       2.4   8.7e+03     113     135 ..     551     573 ..     508     581 .. 0.75

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 1e-27
                                   HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT...TST...SE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx...xx RF
                          DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk...yid...lr 77 
                                    Q +a++ +++++dv+v   T+sGK+++f +++++++++   ++  + l++ Ptr+L+++++++++   +   +i+   ++
  gi|15669770|ref|NP_248583.1|  49 HQVKALKYLYNKKDVVVTTSTASGKSEIFRLAIFDNFLS---NPDDRYLLIYPTRALINNQYEKFSMENElfyKITnkrVK 126
                                   59999********************************86...88889******************5444433244455555 PP

                                   EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHH.HH..HCTSSH....CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx..xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  78 vlliiggvaardqlskldngvdivvgtpgrldd.ll..stgkln....lsqvrflVlDEadrlldqgfsdfinrilnqlpq 151
                                   ++ ++g+v  ++ ++ l+ +++++++tp++l+  +l  ++   n    l+++++lV+DE + +    f+  +  ++++l +
  gi|15669770|ref|NP_248583.1| 127 AEILTGDVGLEKRREILKDKPNVLFTTPDMLHYqILknHN---NylwlLKNLKLLVVDELHVYRGV-FGTNMVYVFKRLLK 203
                                   55668889999999999999*************4444322...34457*****************9.************99 PP

                                   HCTTSTTTSEEEEEESSBSHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 152 itcdgklqrqvivlSATlpkdvk 174
                                     ++ +++ q+++lSATl+ ++k
  gi|15669770|ref|NP_248583.1| 204 LLKRLNNNLQILCLSATLK-NPK 225
                                   9999999999********8.554 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.4
                                   HCTSSHCTTEEEEEEETHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 113 stgklnlsqvrflVlDEadrlld 135
                                    + k+ ++++ f+  DE d++ d
  gi|15669770|ref|NP_248583.1| 551 AKDKIGIRKFHFIFADELDMFWD 573
                                   55677788888888888887755 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.032   1.1e+02      18      61 ..     100     145 ..      78     155 .. 0.62
   2 ?    0.3   0.1      0.24   8.5e+02       4      56 ..     199     249 ..     196     265 .. 0.76
   3 !   72.7   0.0   7.6e-24   2.7e-20       8     109 ..     267     372 ..     260     374 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.032
                                   EEEEEESSHH.HHHHHHHH..HHHTTSTEEEESTTSTHHHHHHHHHH CS
                    Helicase_C  18 kilifvntid.rlekvkll..lekkgikvavlhgelpqnereeileq 61 
                                   ++li  ++ + ++e  +l+   ++k +k+ +l+g+   ++r+eil++
  gi|15669770|ref|NP_248583.1| 100 RALINNQYEKfSME-NELFykITNKRVKAEILTGDVGLEKRREILKD 145
                                   33333333333222.33333222448******************987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.24
                                   HHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHH CS
                    Helicase_C   4 eallellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnere 56 
                                   ++ll+llk+ +++ +il+ + t ++ ++ vkll   ++  + v++ + + ++r+
  gi|15669770|ref|NP_248583.1| 199 KRLLKLLKRLNNNLQILCLSATLKNPKEfVKLL---FNRDFEVVDKSYNPSSRK 249
                                   678899999999999999999999776434554...777777788887777776 PP

  == domain 3  score: 72.7 bits;  conditional E-value: 7.6e-24
                                   HHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTE CS
                    Helicase_C   8 ell.kleeeggkilifvntidrlek.vklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkv 85 
                                   +l+ +l  ++ k+l+f  t+++ ek +++ll++k  +k  ++ g+lp+  reei e+f++ge+  L++t+++e Gidi ++
  gi|15669770|ref|NP_248583.1| 267 RLIeNLVDNNIKTLVFFDTRKETEKlMRFLLNSKvFYKLSTYKGTLPKYVREEIEEKFKNGEILALLTTNALELGIDIGDL 347
                                   33355688999************9988888877778********************************************* PP

                                   SEEEESSSSSS.HHHHHHHHTTSSS CS
                    Helicase_C  86 nlVinfdlprn.vtsyiqriGRtgR 109
                                   + Vin+++p + + s+iqr GR+gR
  gi|15669770|ref|NP_248583.1| 348 DAVINYGIPPDgIFSLIQRFGRAGR 372
                                   *********555************* PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.3   1.9e-11   6.7e-08       3     170 ..      45     222 ..      29     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.9e-11
                                   EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                        ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                   +l+ +Q +a++ l      +++k +++   T +GK+ +  +++ +++l++ + ++ l++ p+++l++  +e+f+   +  y
  gi|15669770|ref|NP_248583.1|  45 KLYLHQVKALKYL------YNKKDVVVTTSTASGKSEIFrLAIFDNFLSN-PDDRYLLIYPTRALINNQYEKFSMENELFY 118
                                   4555555555555......68899***************66666666665.778****************99955555444 PP

                                   .......GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....T...TT CS
                        ResIII  83 ke.....igkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...k...sw 150
                                   k      + ++++gd   +  +e+ +++ ++l+tt ++l+ ++  ++ ++   l ++ +++++DE H +++    +    +
  gi|15669770|ref|NP_248583.1| 119 KItnkrvKAEILTGDVGLEkrREILKDKPNVLFTTPDMLHYQI-LKNHNNYLWLLKNLKLLVVDELHVYRGVfgtNmvyVF 198
                                   443334566666666555566678899**************99.777777788888888********99986655144445 PP

                                   HHH....HHT---SEEEEEESS-S CS
                        ResIII 151 rei....lekfkeavllglTATpe 170
                                   +++    ++ +++  +l l+AT++
  gi|15669770|ref|NP_248583.1| 199 KRLlkllKRLNNNLQILCLSATLK 222
                                   554222233334588899999986 PP

>> PHF12_MRG_bd  PHD finger protein 12 MRG binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   8.9e-05      0.32       5      24 ..     208     227 ..     206     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.9e-05
                  PHF12_MRG_bd   5 kesPldlLirAAslmNPkQF 24 
                                   +++ l+ L+  A+l+NPk+F
  gi|15669770|ref|NP_248583.1| 208 LNNNLQILCLSATLKNPKEF 227
                                   67889**************9 PP

>> Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.15   5.3e+02      21      53 ..     109     140 ..     103     149 .. 0.80
   2 ?    4.3   0.8     0.016        56      35      63 ..     445     473 ..     443     475 .. 0.92
   3 ?    3.5   0.1     0.028     1e+02      22      75 ..     595     646 ..     575     656 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.15
                                   -B-TT-BBSS---HHHHHHHHHHHT-----GGG CS
                Ribosomal_L9_C  21 kagedgklFGsVtakdIaealkkklgieidkkk 53 
                                   k + +++lF ++t+k + +++ +  ++ ++k++
  gi|15669770|ref|NP_248583.1| 109 KFSMENELFYKITNKRVKAEILTG-DVGLEKRR 140
                                   5667889**********9999887.77777765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHT-----GGGEE-TTT-SBS CS
                Ribosomal_L9_C  35 kdIaealkkklgieidkkkieleepiktl 63 
                                   k+I+++l+ + +i+i k+ i+ +++i+++
  gi|15669770|ref|NP_248583.1| 445 KEIVKELEREGKIKIYKNPITNKTEIRNV 473
                                   89********99*********99999875 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.028
                                   B-TT-BBSS---HHHHHHHHHHHT-----GGGEE-TTT-SBSSEEEEEEESSSS CS
                Ribosomal_L9_C  22 agedgklFGsVtakdIaealkkklgieidkkkieleepiktlGeyevtvkLhke 75 
                                    ++ +  +G    ++I e +    g+++dk   el  ++k  G  +++++L k+
  gi|15669770|ref|NP_248583.1| 595 YKDIDIYYGRLRVRKIYEGFIVR-GVDVDKYYQEL-LALKDNGILDAEIDLFKD 646
                                   45566789999999******999.*********99.45*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (684 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 4515.35
//
Query:       gi|15669771|ref|NP_248584.1|  [L=188]
Description: GMP synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-48  164.9   0.2    1.9e-48  164.8   0.2    1.0  1  GATase         Glutamine amidotransferase class-I
    3.3e-18   66.2   0.7      1e-15   58.1   0.3    2.5  2  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.8   0.2   2.1e-52   1.9e-48       2     187 ..       4     180 ..       3     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 2.1e-52
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEETHHHH CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGICLGmQ 82 
                                   ++Dn+ ++++ ++++l  +gv+ ++vp++++ eei+  +k+++gi++sgGp   +++++i+++ +   +k+PiLGICLG+Q
  gi|15669771|ref|NP_248584.1|   4 ILDNGGQYVHRIHRSLKYIGVSSKIVPNTTPLEEIE-SNKEVKGIILSGGPDIEKAKNCIDIALN---AKLPILGICLGHQ 80 
                                   89*********************************6.599************9999999999776...688********** PP

                                   HHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTT CS
                        GATase  83 llaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknp 163
                                   l+a+++g++v +++ +e+   +  +++ e++l+++ ++e++++ +H++ev++   +p+g+e++a+s d ++++++ +k++p
  gi|15669771|ref|NP_248584.1|  81 LIALAYGGEVGRAEAEEYALTKVYVDK-ENDLFKNVPREFNAWASHKDEVKK---VPEGFEILAHS-DICQVEAMKHKTKP 156
                                   **************7777777777766.88**********************...*******9999.889*********** PP

                                   EEEESSBTTSTTSTTHHHHHHHHH CS
                        GATase 164 fvgvQFHPEststpegpellfnfl 187
                                   ++gvQFHPE+ +t+ g+e+l+nf+
  gi|15669771|ref|NP_248584.1| 157 IYGVQFHPEVAHTEYGNEILKNFC 180
                                   **********************96 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0   0.00097       8.7      23      71 ..      10      56 ..       3      61 .. 0.76
   2 !   58.1   0.3   1.1e-19     1e-15      99     216 .]      63     165 ..      56     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00097
                 Peptidase_C26 23 sylaasyveavekagglpvllpieedeedvkaildkldgllltGgqdve 71
                                  +y+++   ++ +  g+ + ++p +++ e++++  +++ g++l+Gg+d+e
  gi|15669771|ref|NP_248584.1| 10 QYVHR-IHRSLKYIGVSSKIVPNTTPLEEIES-NKEVKGIILSGGPDIE 56
                                  56665.66677777888888888888888776.589***********97 PP

  == domain 2  score: 58.1 bits;  conditional E-value: 1.1e-19
                 Peptidase_C26  99 raalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaik 179
                                     al++++PilgiC+G+ql++ a+GG++ ++  e           ++a   +v v+k+  l + +  +e++    H+  +k
  gi|15669771|ref|NP_248584.1|  63 DIALNAKLPILGICLGHQLIALAYGGEVGRAEAE-----------EYA-LTKVYVDKENDLFKNVP-REFNAWASHKDEVK 130
                                   568999********************98776553...........334.45677776665555555.599999******** PP

                 Peptidase_C26 180 elaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                   ++ e++++ A+++   +Ea+++++  ++++gvQ+HPE
  gi|15669771|ref|NP_248584.1| 131 KVPEGFEILAHSDICQVEAMKHKT--KPIYGVQFHPE 165
                                   **********************99..47********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1167.75
//
Query:       gi|15669772|ref|NP_248585.1|  [L=189]
Description: LemA protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-48  162.1   4.5    9.2e-48  161.9   4.5    1.1  1  LemA             LemA family
    0.00034   20.8   7.5       0.12   12.7   2.6    2.6  3  DUF948           Bacterial protein of unknown function (DUF94
      0.002   17.5   0.1     0.0025   17.1   0.1    1.1  1  DUF3535          Domain of unknown function (DUF3535)
     0.0028   16.8   0.2     0.0033   16.6   0.2    1.1  1  AIP3             Actin interacting protein 3
     0.0086   16.0   1.4      0.011   15.6   0.7    1.5  1  EC042_2821       EC042_2821-lke REase
  ------ inclusion threshold ------
      0.017   15.4   1.0        2.2    8.6   0.2    2.8  2  TcdB_N           TcdB toxin N-terminal helical domain
       0.03   14.5   0.0      0.067   13.4   0.0    1.6  1  Phenyl_P_gamma   Phenylphosphate carboxylase gamma subunit (P
      0.056   13.5   0.2       0.16   12.1   0.1    1.7  2  DUF1877          Domain of unknown function (DUF1877)
      0.058   12.4   0.0      0.084   11.9   0.0    1.2  1  Mtc              Tricarboxylate carrier
      0.065   13.6   0.1      0.084   13.2   0.1    1.5  1  Comm             Commissureless
      0.074   13.4   1.7       0.14   12.6   1.7    1.5  1  RPN6_N           26S proteasome regulatory subunit RPN6 N-ter
      0.081   12.6   5.3       0.27   10.8   1.4    2.1  2  Mt_ATP-synt_B    Mitochondrial ATP synthase B chain precursor
      0.082   13.0   1.4       0.16   12.1   0.2    2.2  1  Col_cuticle_N    Nematode cuticle collagen N-terminal domain
       0.11   13.1   1.3        0.5   11.0   1.3    1.8  1  AATF-Che1        Apoptosis antagonizing transcription factor
       0.14   12.2   5.5       0.22   11.6   0.2    2.2  2  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
       0.15   11.8   4.0       0.28   10.9   4.0    1.5  1  BAR_3            BAR domain of APPL family
       0.15   12.9   2.5         14    6.6   0.4    2.9  3  DUF4845          Domain of unknown function (DUF4845)
       0.15   12.1   5.4       0.34   11.0   3.6    2.0  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.16   12.0   2.7       0.32   11.1   1.1    1.9  2  NYD-SP28         Sperm tail
        0.2   11.6   5.7        2.5    8.2   0.1    2.2  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
       0.41   11.1   2.6       0.93   10.0   2.6    1.6  1  FeoB_associated  FeoB-associated Cys-rich membrane protein
        1.9    8.5   8.2        1.1    9.3   5.9    1.7  1  TNFR_16_TM       Tumor necrosis factor receptor member 16 tra
        2.4    8.3   5.7         19    5.4   3.8    2.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
          9    5.3  11.7         76    2.3   9.3    2.7  2  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.9   4.5   1.2e-50   9.2e-48       3     149 .]      43     189 .]      41     189 .] 0.99

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 1.2e-50
                          LemA   3 sqidvqlkrRaDlipnLvetvkgyakhEketleevteaRakaaeaesveekaeaenqlssalsrllavaEnYPdLkanenf 83 
                                    qi v+lk+R D+i++Lve+vk ya++Eketl+++te+R+++ +a++ ee ++ e++ ++ l+++l+ +EnYP+Lk++e++
  gi|15669772|ref|NP_248585.1|  43 GQIRVALKKRLDMINQLVEAVKSYASFEKETLTKITELRSSVLKANTAEEIQNIERESRNILGNILVAVENYPELKTSETV 123
                                   69******************************************************************************* PP

                          LemA  84 leLqeelegtEnriavaRrrYneavreyntkiesfpsnivaklfgfkekelfeaeeaereapkVkF 149
                                   +eL++ ++++E++ia +R  Yn+ v+e+ntki++fpsniva+lfgf++++++++ee+  e+pk++F
  gi|15669772|ref|NP_248585.1| 124 KELMDAIKEIEDEIARHRYTYNNIVQEFNTKIDTFPSNIVANLFGFRKMDYLQFEEEIYERPKISF 189
                                   ******************************************************99889*****99 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   2.6   0.00015      0.12       1      75 [.       8      82 ..       8      98 .. 0.83
   2 !    7.6   0.7     0.006       4.5      30      84 ..      88     137 ..      74     139 .. 0.79
   3 !    9.8   0.2    0.0012       0.9      23      69 ..     118     157 ..     106     164 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                        DUF948  1 IAglIaAiAFvvLviflivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplte 75
                                  I glI+A+ ++ +vi+++ + ++ + + + a+at+ +++  +++ l+ +++l++ v+  ++  +e l k+ +l +
  gi|15669772|ref|NP_248585.1|  8 IVGLILALIVLGIVIYIVSIYNRFQTLKNGAEATLGQIRVALKKRLDMINQLVEAVKSYASFEKETLTKITELRS 82
                                  679****************************************************99966555555555555555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.006
                        DUF948  30 eaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                   ++a+ i+++e++ ++il ++  ++++  e      + +e+v++l++a++++ + +
  gi|15669772|ref|NP_248585.1|  88 NTAEEIQNIERESRNILGNILVAVENYPE-----LKTSETVKELMDAIKEIEDEI 137
                                   56777888888888888888888888888.....568999999999999998877 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0012
                        DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklek 69 
                                   k        ++t++el++ +++i +e+++   + n+++++ n k+++
  gi|15669772|ref|NP_248585.1| 118 KT-------SETVKELMDAIKEIEDEIARHRYTYNNIVQEFNTKIDT 157
                                   44.......55566666666666666666666666666666656654 PP

>> DUF3535  Domain of unknown function (DUF3535)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   3.3e-06    0.0025     242     366 ..      58     173 ..      28     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.3e-06
                       DUF3535 242 klvttdyekllkslslkqkllaekqLeerrrrlqaaieeakeeqealhvrvqaalAgAlvalkelPk.KLnpvikpLMeSi 321
                                   +lv+      +ks+++ +k +   ++ e r+++++a  +++ee ++++ + +  l   lva+++ P+ K +  +k LM++i
  gi|15669772|ref|NP_248585.1|  58 QLVEA-----VKSYASFEKETL-TKITELRSSVLKA--NTAEEIQNIERESRNILGNILVAVENYPElKTSETVKELMDAI 130
                                   33333.....444443333333.2788888888886..678888899999999*************989************ PP

                       DUF3535 322 KkEeneeLQqrsAkalakLielcvdrkpcpndKIvkNLctflcsD 366
                                   K+ e+e+ ++r   +  + ++++ ++     + Iv NL++f  +D
  gi|15669772|ref|NP_248585.1| 131 KEIEDEIARHRY--TYNNIVQEFNTKIDTFPSNIVANLFGFRKMD 173
                                   *******99995..5679999999998888899999999999988 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   4.4e-06    0.0033      73     168 ..      41     161 ..      11     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.4e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX........................... CS
                          AIP3  73 pldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekasesla.........................kk 128
                                   +l +++  +++ l  + + ++ +ks  + +k++l++++e +++  k ++ e ++                         ++
  gi|15669772|ref|NP_248585.1|  41 TLGQIRVALKKRLDMINQLVEAVKSYASFEKETLTKITELRSSVLKANTAEEIQnieresrnilgnilvavenypelktSE 121
                                   566777778888888888888888777666666666666666666555555555677788888899999999*****9999 PP

                                   .......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          AIP3 129 elkaqlkevqslrrdLavlrqlysefkseikeslselrek 168
                                   + k+ ++ +++++ ++a  r +y++  +e+++++ ++ ++
  gi|15669772|ref|NP_248585.1| 122 TVKELMDAIKEIEDEIARHRYTYNNIVQEFNTKIDTFPSN 161
                                   999*******************************998665 PP

>> EC042_2821  EC042_2821-lke REase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.7   1.5e-05     0.011      86     125 ..     124     164 ..     106     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                    EC042_2821  86 dakvkivkelkDpnkthpYtykevikkvnerLkkknikl.k 125
                                   ++ +  +ke++D  + h Yty++++++ n ++    +++  
  gi|15669772|ref|NP_248585.1| 124 KELMDAIKEIEDEIARHRYTYNNIVQEFNTKIDTFPSNIvA 164
                                   4555689999999999**************88774444443 PP

>> TcdB_N  TcdB toxin N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.047        35      22      42 ..      49      69 ..      42      83 .. 0.89
   2 ?    8.6   0.2     0.003       2.2      18      45 ..     119     146 ..     107     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.047
                                  HHHHHHHHHHHHHHHHHHHHH CS
                        TcdB_N 22 skkkyellkklkkeidnYnnl 42
                                  +kk+++ +++l++++++Y + 
  gi|15669772|ref|NP_248585.1| 49 LKKRLDMINQLVEAVKSYASF 69
                                  5799999***********987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.003
                                   TTS-HHHHHHHHHHHHHHHHHHHHHSTT CS
                        TcdB_N  18 seeqskkkyellkklkkeidnYnnlykk 45 
                                   ++e++k+  + +k++ +ei +++ +y +
  gi|15669772|ref|NP_248585.1| 119 TSETVKELMDAIKEIEDEIARHRYTYNN 146
                                   899********************99865 PP

>> Phenyl_P_gamma  Phenylphosphate carboxylase gamma subunit (Phenyl_P_gamma)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.9e-05     0.067      17      56 ..     124     165 ..     109     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.9e-05
                Phenyl_P_gamma  17 kelelsvrtlndgl..kkytyqrvkvelsskldkfpdrlqvr 56 
                                   kel  +++ ++d +  ++yty+ +  e  +k+d fp ++   
  gi|15669772|ref|NP_248585.1| 124 KELMDAIKEIEDEIarHRYTYNNIVQEFNTKIDTFPSNIVAN 165
                                   778888888888654489******************987654 PP

>> DUF1877  Domain of unknown function (DUF1877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.9   2.1e+03       6      31 ..      65      91 ..      60     107 .. 0.58
   2 ?   12.1   0.1   0.00021      0.16      83     119 ..     112     148 ..      89     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.9
                       DUF1877  6 sylrlteeelekllkdped.ledflee 31
                                  sy + ++e+l+k+ + ++  l     e
  gi|15669772|ref|NP_248585.1| 65 SYASFEKETLTKITELRSSvLKANTAE 91
                                  566666777777777666642222222 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00021
                       DUF1877  83 ygparlltpeqVkevaeaLaeldfeelrerfdaeele 119
                                   + + +l+t+e+Vke+ +a++e+++e +r r+  +++ 
  gi|15669772|ref|NP_248585.1| 112 ENYPELKTSETVKELMDAIKEIEDEIARHRYTYNNIV 148
                                   567899*************************998775 PP

>> Mtc  Tricarboxylate carrier
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011     0.084      26      91 ..      50     112 ..      41     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                           Mtc  26 eaeleeakelvekykkgklppelteeelwkakklvdSavHPdtgekillpfRmsafvpvnllitgg 91 
                                   +++l+  ++lve++k+ +   ++++e l k  +l  S++ ++t e i  + R s  +++n+l+++ 
  gi|15669772|ref|NP_248585.1|  50 KKRLDMINQLVEAVKSYA---SFEKETLTKITELRSSVLKANTAEEIQNIERESRNILGNILVAVE 112
                                   678999999999999987...78999***********************************99875 PP

>> Comm  Commissureless
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   0.00011     0.084      10      45 ..       7      60 ..       2     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                          Comm 10 vwigivltLlilslvFclcsCflyrkfrtWkkkkt....................a 45
                                  + +g +l L++l++v  ++s  +y++f+t k++ +                    +
  gi|15669772|ref|NP_248585.1|  7 IIVGLILALIVLGIVIYIVS--IYNRFQTLKNGAEatlgqirvalkkrldminqlV 60
                                  789***************99..567******9988555555444444333333330 PP

>> RPN6_N  26S proteasome regulatory subunit RPN6 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.7   0.00018      0.14      29      96 ..      68     142 ..      38     154 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                        RPN6_N  29 ealreqeqalleLgelyrdqkkaeeLaelikesrsflssi.......aKaKtaKlvrtLldlfskipnslelqie 96 
                                   +  +e  + ++eL +   +++ aee++++ +esr++l +i       +  Kt+  v++L+d +++i++       
  gi|15669772|ref|NP_248585.1|  68 SFEKETLTKITELRSSVLKANTAEEIQNIERESRNILGNIlvavenyPELKTSETVKELMDAIKEIEDEIARHRY 142
                                   34555666788888888999999999999999999987652222222677*****************98776555 PP

>> Mt_ATP-synt_B  Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.4   0.00037      0.27      19     112 ..       4      94 ..       2      98 .. 0.87
   2 ?    3.0   0.1     0.095        71      74     118 ..     117     158 ..     106     163 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00037
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHH CS
                 Mt_ATP-synt_B  19 valcfigflilvakslgpsikefldkriekiqeelnqsrnlkeealkerieqekklqslveltkslfevskeqvaleaeaf 99 
                                   ++l ++g++++++  +   +  ++++r ++ ++  ++   +  +alk+r+++  +l+   e  ks   ++ke++  + e +
  gi|15669772|ref|NP_248585.1|   4 LLLIIVGLILALIVLGIVIYIVSIYNRFQTLKNGAEATLGQIRVALKKRLDMINQLV---EAVKSYASFEKETLTKITELR 81 
                                   567778888888888888888899999999999999999999999999999988887...999****************** PP

                                   HHHHHHHHHHHHH CS
                 Mt_ATP-synt_B 100 erelqaklareik 112
                                   ++ l+a++a ei+
  gi|15669772|ref|NP_248585.1|  82 SSVLKANTAEEIQ 94 
                                   **********997 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.095
                                   CCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Mt_ATP-synt_B  74 lqslveltkslfevskeqvaleaeaferelqaklareikkkldtl 118
                                   l+ ++e+ k+l+++ ke    +a  ++    +++ +e+++k+dt 
  gi|15669772|ref|NP_248585.1| 117 LK-TSETVKELMDAIKEIEDEIARHRYT--YNNIVQEFNTKIDTF 158
                                   44.7788888888888877777766664..689999999999986 PP

>> Col_cuticle_N  Nematode cuticle collagen N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00021      0.16       8      32 ..      14      38 ..       7      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                 Col_cuticle_N  8 tvailsslitlpsiyndiqsfqsev 32
                                  ++ +l+++i++ siyn  q++++  
  gi|15669772|ref|NP_248585.1| 14 ALIVLGIVIYIVSIYNRFQTLKNGA 38
                                  7889****************99865 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.3   0.00067       0.5      20     123 ..      44     135 ..      40     158 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00067
                     AATF-Che1  20 elRIklQkaltaanqLp.qpetlkefles.............seefeealeeaekalkklleslleLreelleqneikkla 86 
                                   ++R+ l+k l  +nqL    +++ +f ++             +++++e+++++e +++++l ++l   e+     +     
  gi|15669772|ref|NP_248585.1|  44 QIRVALKKRLDMINQLVeAVKSYASFEKEtltkitelrssvlKANTAEEIQNIERESRNILGNILVAVENY----P----- 115
                                   57888888888888888522233333222333333334445544555555555555555544444322222....1..... PP

                     AATF-Che1  87 eskeeeekkkskrkrkkkkkeetsleelwkeleklek 123
                                                    + k++++++el++++++ e+
  gi|15669772|ref|NP_248585.1| 116 -----------------ELKTSETVKELMDAIKEIED 135
                                   .................12222333333333333333 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.1      0.16   1.2e+02      47      76 ..      57      86 ..      26     113 .. 0.44
   2 ?   11.6   0.2   0.00029      0.22      30      69 ..     118     157 ..     111     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.16
                     ApoLp-III 47 eelkkksdeleealkevkkkieetadklse 76
                                  ++l ++    ++  ke+ +ki+e + ++ +
  gi|15669772|ref|NP_248585.1| 57 NQLVEAVKSYASFEKETLTKITELRSSVLK 86
                                  111112222222223333333333333333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00029
                     ApoLp-III  30 nsenlvdqlkqvikslqeelkkksdeleealkevkkkiee 69 
                                   ++++ v++l + ik++++e++++  + +++++e+++ki  
  gi|15669772|ref|NP_248585.1| 118 KTSETVKELMDAIKEIEDEIARHRYTYNNIVQEFNTKIDT 157
                                   58999********************************975 PP

>> BAR_3  BAR domain of APPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.0   0.00037      0.28      20     110 ..      38     160 ..      30     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
                         BAR_3  20 vEaeleelekklkkllKlckrlieagkaysaaqkqfaqsLrelkkes...kgdeetd........................ 73 
                                    Ea+l +++ +lkk l  +++l+ea k+y +  k+  +++ el+      ++ ee++                        
  gi|15669772|ref|NP_248585.1|  38 AEATLGQIRVALKKRLDMINQLVEAVKSYASFEKETLTKITELRSSVlkaNTAEEIQnieresrnilgnilvavenypelk 118
                                   69999**************************************99986655555555667766666666666666666666 PP

                         BAR_3  74 ..esLkkfsellqelene...htilldqaqrsikkpLekFrk 110
                                     e+ k+++++++e+e+e   h+   +++ + + +++++F  
  gi|15669772|ref|NP_248585.1| 119 tsETVKELMDAIKEIEDEiarHRYTYNNIVQEFNTKIDTFPS 160
                                   666666666666666554222444555555555555555555 PP

>> DUF4845  Domain of unknown function (DUF4845)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.057        43      12      43 ..      24      55 ..      21      60 .. 0.82
   2 ?    6.6   0.4     0.019        14      12      52 ..      59      99 ..      56     106 .. 0.90
   3 ?   -0.6   0.0       3.4   2.5e+03      15      40 ..     129     154 ..     114     159 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.057
                       DUF4845 12 ikkalkslekesglegmsvaeirsaldkrldi 43
                                  i ++ +  ++ ++ ++++  +ir al+krld+
  gi|15669772|ref|NP_248585.1| 24 IVSIYNRFQTLKNGAEATLGQIRVALKKRLDM 55
                                  556666667779999***************96 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.019
                       DUF4845 12 ikkalkslekesglegmsvaeirsaldkrldinnirsikge 52
                                  + +a+ks ++ ++++ ++ +e+rs++ k  + ++i++i+ e
  gi|15669772|ref|NP_248585.1| 59 LVEAVKSYASFEKETLTKITELRSSVLKANTAEEIQNIERE 99
                                  56899999*****************************9987 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.4
                       DUF4845  15 alkslekesglegmsvaeirsaldkr 40 
                                   a+k++e+e + +  + ++i ++++ +
  gi|15669772|ref|NP_248585.1| 129 AIKEIEDEIARHRYTYNNIVQEFNTK 154
                                   55555666666666666666666655 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.6   0.00045      0.34      31     137 ..      26     133 ..      17     136 .. 0.67
   2 ?    6.6   3.1      0.01       7.6      24     101 ..      76     155 ..      71     172 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00045
                  Baculo_PEP_C  31 qilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq......dtlrneLtnlnsil..tnLlssvtN 103
                                   +i +  +tl++  e +L+++             +l++ l+ +++ + a++      ++  +++t l s +  +n + ++ N
  gi|15669772|ref|NP_248585.1|  26 SIYNRFQTLKNGAEATLGQIRV-----------ALKKRLDMINQLVEAVKsyasfeKETLTKITELRSSVlkANTAEEIQN 95 
                                   4444444444444444555444...........444444444444444444445557777899999998877899999999 PP

                  Baculo_PEP_C 104 in....stLnnllqalnnldlgalsqeledaldtveei 137
                                   i+    + L n+l a++n+ + ++s++ ++++d ++ei
  gi|15669772|ref|NP_248585.1|  96 IEresrNILGNILVAVENYPELKTSETVKELMDAIKEI 133
                                   973333579999*******9999999999999988876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                  Baculo_PEP_C  24 airlqnvqil.aqlatlldaietqLnalsedlksllaeldt.rldtlltnLtdalnalqdtlrneLtnlnsiltnLlssv 101
                                    i  + +++l a+ a+ +++ie++  ++  ++  ++++  + + ++++++L da+++++d++  +  + n+i+ + ++++
  gi|15669772|ref|NP_248585.1|  76 KITELRSSVLkANTAEEIQNIERESRNILGNILVAVENYPElKTSETVKELMDAIKEIEDEIARHRYTYNNIVQEFNTKI 155
                                   55444444432455555666666555555555554444433466788888888888888777777777777777766544 PP

>> NYD-SP28  Sperm tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4      0.24   1.8e+02      18      56 ..      57      95 ..      44      97 .. 0.84
   2 ?   11.1   1.1   0.00043      0.32      14      83 ..      86     155 ..      75     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.24
                      NYD-SP28 18 qerkekleeeaksseekfeeinekWreilrknkpqeLrk 56
                                  +++ e ++  a++ +e + +i+e  +++l+ n+++e+++
  gi|15669772|ref|NP_248585.1| 57 NQLVEAVKSYASFEKETLTKITELRSSVLKANTAEEIQN 95
                                  567778888899999999999999999999999999976 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00043
                      NYD-SP28  14 eelrqerkekleeeaksseekfeeinekWreilrknkpqeLrkeleeqkqaceelideKdklikelqeeL 83 
                                   + +++e  + +e+e+++   +     e++ e+++ ++ +eL ++++e +  +++   + +++++e+++++
  gi|15669772|ref|NP_248585.1|  86 KANTAEEIQNIERESRNILGNILVAVENYPELKTSETVKELMDAIKEIEDEIARHRYTYNNIVQEFNTKI 155
                                   5556666788899999999999999999*************************************99876 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.0     0.029        22       7      54 ..      49      98 ..      43     103 .. 0.81
   2 ?    8.2   0.1    0.0034       2.5      28      51 ..     116     139 ..     114     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.029
                    TMF_DNA_bd  7 lkeKDeqIaqLmeEGekLskkelklnntikkLrkknkele..keikelkk 54
                                  lk++ ++I+qL e  + +++ e +  ++i +Lr+ + +++  +ei++ ++
  gi|15669772|ref|NP_248585.1| 49 LKKRLDMINQLVEAVKSYASFEKETLTKITELRSSVLKANtaEEIQNIER 98
                                  5666689***************************9988774556665554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0034
                    TMF_DNA_bd  28 elklnntikkLrkknkelekeike 51 
                                   elk ++t+k+L   +ke e ei++
  gi|15669772|ref|NP_248585.1| 116 ELKTSETVKELMDAIKEIEDEIAR 139
                                   99******************9987 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.6    0.0012      0.93       3      27 ..      11      37 ..       5      39 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
               FeoB_associated  3 iIVgliiaaavafv..irrlikkkkkG 27
                                  +I +li++++v+++  i++ ++  k+G
  gi|15669772|ref|NP_248585.1| 11 LILALIVLGIVIYIvsIYNRFQTLKNG 37
                                  245555556666667777777777776 PP

>> TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.9    0.0015       1.1      13      26 ..      12      25 ..      11      36 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                    TNFR_16_TM 13 ILaaVvvgLlaYvi 26
                                  ILa++v+g+++Y++
  gi|15669772|ref|NP_248585.1| 12 ILALIVLGIVIYIV 25
                                  9************6 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   3.8     0.026        19      35     119 ..      54     138 ..      21     139 .. 0.67
   2 ?    5.1   3.1     0.032        24      32      95 ..      99     160 ..      69     177 .. 0.44

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.026
                                   HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHHHHHHHHHHHH CS
                     Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.snirvLqnvlesn 114
                                   + +++l + ++++++ +ke+ + ++e+++s+ ++++ ++  +n+ ++s++ l +  + +++    +  +++++L + +++ 
  gi|15669772|ref|NP_248585.1|  54 DMINQLVEAVKSYASFEKETLTKITELRSSVLKANTAEE-IQNIERESRNILGNILVAVENYPELKTsETVKELMDAIKEI 133
                                   335555555556666666666666666666665555555.48888888888886666666666555557788888888877 PP

                                   HHHHH CS
                     Fib_alpha 115 eqkiq 119
                                   e +i+
  gi|15669772|ref|NP_248585.1| 134 EDEIA 138
                                   77775 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.032
                                   CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH CS
                     Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlke 95 
                                   + ++ l ++   +e++ +   +++e+vke++d ++e + + + +  +++++ +e +++i ++  
  gi|15669772|ref|NP_248585.1|  99 ESRNILGNILVAVENYPEL--KTSETVKELMDAIKEIEDEIARHRYTYNNIVQEFNTKIDTFPS 160
                                   3333333333333333221..2223333333333333333333333333333333333334444 PP

>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   9.3       0.1        76      55     140 ..       7      84 ..       1     130 [. 0.45
   2 ?    0.9   0.0      0.27     2e+02      90     129 ..     123     166 ..     111     171 .. 0.51

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.1
               AI-2E_transport  55 lvlllllvllvllvlllvplliaqltqlvkslpayidslqnilnelpslleelenliqalkqslskilsnilssilnslls 135
                                   +++ l+l+l+vl        +++ + ++ + ++++ ++ ++ l ++   l+++ ++i++l  ++  + +++++++l+ +++
  gi|15669772|ref|NP_248585.1|   7 IIVGLILALIVLG-------IVIYIVSIYNRFQTLKNGAEATLGQIRVALKKRLDMINQLVEAVK-SYASFEKETLTKITE 79 
                                   3333333333333.......444444444444444444444444444444444212222222222.222223333333333 PP

               AI-2E_transport 136 llasl 140
                                   l +s+
  gi|15669772|ref|NP_248585.1|  80 LRSSV 84 
                                   22222 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.27
               AI-2E_transport  90 idslqnilnelpslleele.n...liqalkqslskilsnilssi 129
                                   +++l + ++e++++  ++  +    +q+++ ++++  sni+ ++
  gi|15669772|ref|NP_248585.1| 123 VKELMDAIKEIEDEIARHRyTynnIVQEFNTKIDTFPSNIVANL 166
                                   33444444444444444432233345555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2298  (0.128172); expected 358.6 (0.02)
Passed bias filter:                     1122  (0.0625802); expected 358.6 (0.02)
Passed Vit filter:                       167  (0.00931452); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 1180.47
//
Query:       gi|15669773|ref|NP_248586.1|  [L=598]
Description: hypothetical protein MJ_1577 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-70  237.0  24.7      4e-70  237.0  24.7    1.5  2  DUF2207          Predicted membrane protein (DUF2207)
  ------ inclusion threshold ------
      0.033   14.5   0.4      0.085   13.2   0.4    1.7  1  DUF4476          Domain of unknown function (DUF4476)
       0.12   12.7   4.2       0.68   10.3   0.6    2.6  2  Phage_holin_5_2  Phage holin family Hol44, in holin superfami
       0.24   11.6   4.9         20    5.4   0.2    3.1  3  EI24             Etoposide-induced protein 2.4 (EI24)
          1    8.9   5.7        3.1    7.4   0.0    3.0  3  SUR7             SUR7/PalI family


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2      0.35   1.3e+03     383     401 ..       7      25 ..       2      33 .. 0.51
   2 !  237.0  24.7   1.1e-73     4e-70       2     492 .]      38     544 ..      37     544 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.35
                       DUF2207 383 lsalglgliilglililla 401
                                   ++++ l+++i+g+++i+l+
  gi|15669773|ref|NP_248586.1|   7 IIIVCLLIFIVGVVGIFLT 25 
                                   4444444555555544443 PP

  == domain 2  score: 237.0 bits;  conditional E-value: 1.1e-73
                       DUF2207   2 IesydvdatvqedGsldvtEtitydf..dgsrhgiyrdrdlplrtydvdgsgnsvriki.....rddvtepyykessddg. 74 
                                   I++y++++++ ++ +l  +E + y++   ++++++yrd++ pl++   +gs n  ++k+      +++++ y ++ ++d  
  gi|15669773|ref|NP_248586.1|  38 IKDYEANLYIGKNLTL--EEIYSYEVleGRKYRMLYRDWKAPLVY---NGSLNTPYVKVlnlstSSKDMVGYVVDYKGDIf 113
                                   99**************..***********************8754...667777777776668655555777777777778 PP

                       DUF2207  75 ................................tlstgthtyeisYtvknavtkykdvaelywnvigngwdvpienvtitvt 123
                                                                      +g +t  +++ ++++++ ++   +++ ++  +  + p++nv+i+v 
  gi|15669773|ref|NP_248586.1| 114 vfsdedwikrnieeivdkyyirnevgfynplyIRNPGIYTTSYKFVIYPPIETDNVFYHINLKLADE--HLPYKNVKINV- 191
                                   888888888888888999999999999****9999***************************77655..48*********. PP

                       DUF2207 124 lPseaksggdlrawlHgldgsttvkkddgsvtftarnlppgeglevrvlf.ptnnarktsgnklde.ilkeeqkntreraa 202
                                       ++++++l +++++   st ++ ++   ++  ++ p+++++ev++l+ p      +s n+    +++ e+k t ++++
  gi|15669773|ref|NP_248586.1| 192 ---IDENNSILDLFVYP---STFKVYKTYFGYTIEGSSPKNDPIEVEMLLkP------NSVNGFTRyVYNVEGK-TISAYK 259
                                   ...568999******99...5555555555578899**************53......3444433314455555.99**** PP

                       DUF2207 203 rlslallillilllilllllllllliklllwkkygrepkvkevdpeYerdvP.edlsPavvgylvkg..dkvdengltAtl 280
                                   +++++ +i++ l ++l++++ll++li++++++k+g+e+ +  v+peY   vP ++ +P++v++++ g  + +d++g++Atl
  gi|15669773|ref|NP_248586.1| 260 KYTFVSNIVMTLKYLLMAIILLFPLIAYIIYLKFGKEKFY--VVPEYLSYVPnKNRKPWIVNLIFAGdaGFFDKEGFYATL 338
                                   ***************************************9..579************************99********** PP

                       DUF2207 281 ldLavkgyitieeekkkkkkgkdtltilkkndeeldpyEkalldlLfdkseeg.ks...lkeikkyakkskkkakkfkkal 357
                                   ldL+++gyi+i  + k         +ilk++ e+ld yE +++++L ++s+++  +   +k++ ++ k+sk+k kk+k++l
  gi|15669773|ref|NP_248586.1| 339 LDLHNRGYIKIMNGGKI--------EILKTDLENLDVYESDVMKFLMKYSKNNvFDpeyIKSLAQKYKSSKDKLKKLKDEL 411
                                   ***********988666........899*************************8888886667666666666888888888 PP

                       DUF2207 358 kkwksavkk...kergyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllg 435
                                   +k+++  +    + + +++++gkk++  l +++++l+++++++  ++      +++  ++l++++++++ii++l +++l+g
  gi|15669773|ref|NP_248586.1| 412 DKIMEYPRYsskVVNAFLETRGKKIIIALLVISILLAVFLYFIPKYS-----QTFNEVFYLSIVFVVQNIILALTPTSLFG 487
                                   88888777788777778888877777555555555555555554444.....44*************************** PP

                       DUF2207 436 rrteeGaellakwkgFkkyLeDfsefkerppedlelweryLvYAtalGvadkvakql 492
                                   r+++++++++ +w++Fk++L++ +++k+++ped+++w+++L Y+talGv+dkv +++
  gi|15669773|ref|NP_248586.1| 488 RWKANYYKEKLEWDAFKNFLSNLAMIKKYSPEDISIWKDWLIYGTALGVGDKVVEAM 544
                                   ******************************************************998 PP

>> DUF4476  Domain of unknown function (DUF4476)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   2.4e-05     0.085      18      78 ..     367     428 ..     350     437 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                       DUF4476  18 sfdddklklleqalankaftcsqvvqllklfsfdddrlkalkllapnivDkqns.etiidsf 78 
                                     ++d +k+l ++++n+ f  +++++l + +++++d+lk lk   ++i+    + ++++++f
  gi|15669773|ref|NP_248586.1| 367 VYESDVMKFLMKYSKNNVFDPEYIKSLAQKYKSSKDKLKKLKDELDKIMEYPRYsSKVVNAF 428
                                   5678999******************************************9988889999998 PP

>> Phage_holin_5_2  Phage holin family Hol44, in holin superfamily V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2      0.04   1.4e+02      22      51 ..      12      38 ..       4      57 .. 0.68
   2 ?   10.3   0.6   0.00019      0.68      21      66 ..     434     483 ..     421     490 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.04
               Phage_holin_5_2 22 yIPlilgiiGiilgvvivfta..dfqaedili 51
                                  + ++i+g++Gi+l+     t+   ++  +i+i
  gi|15669773|ref|NP_248586.1| 12 LLIFIVGVVGIFLT-----TSfnGMKYTSIYI 38
                                  45678888888888.....2223555555555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
               Phage_holin_5_2  21 kyIPlilgiiGiilgvvivft.a...dfqaedilifgaiiqGilsggast 66 
                                   k I++ l++i+i+l+v  +f+ +   +f++   l +  ++q i+ ++  t
  gi|15669773|ref|NP_248586.1| 434 KKIIIALLVISILLAVFLYFIpKysqTFNEVFYLSIVFVVQNIILALTPT 483
                                   89*************99999966876666666666668888888887655 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.055     2e+02     103     136 ..       9      43 ..       7      73 .. 0.78
   2 ?    5.4   0.2    0.0055        20      90     118 ..     262     290 ..     230     329 .. 0.85
   3 ?    4.9   0.1    0.0079        28      41      78 ..     437     474 ..     373     536 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.055
                                   HHHHHH.HHTTHHH....HHHHHHHHHHHHHHHHH CS
                          EI24 103 lvllpl.liPvvglilsplllswltayfycfeyld 136
                                   +v+l++ ++ vvg++l + +++  +  +y  +y +
  gi|15669773|ref|NP_248586.1|   9 IVCLLIfIVGVVGIFLTTSFNGMKYTSIYIKDYEA 43 
                                   56666635599999999999998888888877755 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0055
                                   HHHHHHHHHHHHHHHHHHHHHTTHHH... CS
                          EI24  90 eslkslllllllllvllplliPvvglils 118
                                   + + +++++l +ll++++ll+P++  i+ 
  gi|15669773|ref|NP_248586.1| 262 TFVSNIVMTLKYLLMAIILLFPLIAYIIY 290
                                   5678999************88*9987664 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0079
                                   THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          EI24  41 llasllvllllllplwlfplvalllaapfygllaekve 78 
                                   ++a+l++ +ll+++l+++p  +  ++++fy  ++  v+
  gi|15669773|ref|NP_248586.1| 437 IIALLVISILLAVFLYFIPKYSQTFNEVFYLSIVFVVQ 474
                                   44555555555555555556666666666666665553 PP

>> SUR7  SUR7/PalI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.6      0.15   5.5e+02      10      57 ..       9      60 ..       7      63 .. 0.43
   2 ?    2.2   0.1     0.032   1.2e+02     103     139 ..     253     307 ..     235     328 .. 0.75
   3 ?    7.4   0.0   0.00087       3.1     123     180 ..     438     491 ..     383     511 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.15
                          SUR7 10 laalilllfailgsiknstplt.........siylskfdlsgldlaqigladvysfg 57
                                  +++l+++++ ++g++     lt         siy+ +++     ++++ l+++ys+ 
  gi|15669773|ref|NP_248586.1|  9 IVCLLIFIVGVVGIF-----LTtsfngmkytSIYIKDYEANLYIGKNLTLEEIYSYE 60
                                  333333333333333.....2221123434466666665553333444577777765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.032
                          SUR7 103 ktlsklnnltkalfilhiialvlsfislvvgllaic..................v 139
                                   kt+s++++ t ++ i++     l++i l++ l+a +                   
  gi|15669773|ref|NP_248586.1| 253 KTISAYKKYTFVSNIVMTLKYLLMAIILLFPLIAYIiylkfgkekfyvvpeylsY 307
                                   6788889999999999999999999999999998875666666666666666653 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00087
                          SUR7 123 lvlsfislvvgllaicvspdnsrllsflnlllsvlsflatllaalldtllfvfvrkki 180
                                   ++l +is++++++  +  p+ s  +++ ++ ls++ ++ +++ al+ t lf   r k 
  gi|15669773|ref|NP_248586.1| 438 IALLVISILLAVFLYF-IPKYSQ-TFNEVFYLSIVFVVQNIILALTPTSLFG--RWKA 491
                                   6788899999888887.677777.9***********************9998..4334 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1606  (0.0895755); expected 358.6 (0.02)
Passed bias filter:                      809  (0.0451224); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.79u 0.33s 00:00:01.12 Elapsed: 00:00:00.50
# Mc/sec: 3574.89
//
Query:       gi|15669774|ref|NP_248587.1|  [L=259]
Description: cobalamin biosynthesis precorrin-3 methylase CbiF [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-55  186.9   0.2    5.1e-55  186.7   0.2    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
    4.8e-06   27.1   0.2    1.3e-05   25.7   0.2    1.6  1  Radical_SAM   Radical SAM superfamily
     0.0098   16.3   0.1       0.02   15.3   0.1    1.5  1  Cyt_b-c1_8    Cytochrome b-c1 complex subunit 8
  ------ inclusion threshold ------
      0.035   14.1   2.1       0.64   10.0   0.1    3.0  3  HU-DNA_bdg    DNA-binding domain
      0.069   12.9   0.1       0.18   11.5   0.1    1.7  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.7   0.2   1.4e-58   5.1e-55       1     212 [.       6     212 ..       6     213 .. 0.95

  Alignments for each domain:
  == domain 1  score: 186.7 bits;  conditional E-value: 1.4e-58
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkd 81 
                                   k+++VG+GpGdpel+T+++ +a+++adv+++++s++ e ll++ ++       +++  ++++ + eei + +++a+++gk+
  gi|15669774|ref|NP_248587.1|   6 KVIIVGAGPGDPELITIKGKKAIEEADVIIYAGSLVNEKLLEYNKK-------NAEIYNSANMNLEEIIDVMVKAVNQGKK 79 
                                   79*******************************99******99976.......57778889999***************** PP

                  TP_methylase  82 VvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl....lpglakeeereleall 158
                                   Vv+l++GDP++yg+  e +++l++   gi+ve+iPGvssl aa a+l+++lt  +++++v+    + ++ ++e+++l++l+
  gi|15669774|ref|NP_248587.1|  80 VVRLHTGDPSIYGAIKEQIDELSK--YGIDVEIIPGVSSLFAATASLKVELTLPEVSQTVIitrpEGRTPMPEKEKLRDLA 158
                                   ************************..**************************************97778899********* PP

                  TP_methylase 159 angdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                   +++ t++++ +++ +++++++L+e  +++ +tpvavv +a+++de++vrgtl+++
  gi|15669774|ref|NP_248587.1| 159 KHQSTMAIFLGVSMIDKVVKELIEGgYRE-ETPVAVVYHASWDDEKIVRGTLKDI 212
                                   *************************6666.66********************997 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.2   3.5e-09   1.3e-05      24     151 ..      56     230 ..      48     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3.5e-09
                                   HHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC........................CCTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................xxxxxx RF
                   Radical_SAM  24 grgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla........................vpgiri 80 
                                   + ++++ +eei++ + ++ +++g+k+v l+ g+p+ y  + e +++l+k                           p+++ 
  gi|15669774|ref|NP_248587.1|  56 YNSANMNLEEIIDVMVKA-VNQGKKVVRLHTGDPSIYGAIKEQIDELSKYGidveiipgvsslfaataslkveltLPEVSQ 135
                                   67889*************.9*****************99999999999988999999999999988888888888333333 PP

                                   EEEECSSCHG.....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHH...................HHHHHHHHH CS
                                   xxxxxxxxxx.....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx...................xxxxxxxxx RF
                   Radical_SAM  81 tvetngtlpd.....eeklerllelg.vdrvslgleaaddekvlklmnrghtf...................eevlealek 136
                                   tv++  +  +     +ekl+ l++   +  + lg+  +d+  v++l+++g+                       +++  ek
  gi|15669774|ref|NP_248587.1| 136 TVIITRPEGRtpmpeKEKLRDLAKHQsTMAIFLGVSMIDKV-VKELIEGGYREetpvavvyhaswddekivrGTLKDIAEK 215
                                   3333333333567779********8899999*********8.999998666667778888888888888888888888888 PP

                                   HHHTTSETEEEEEEE CS
                                   xxxxxxxxxxxxxxx RF
                   Radical_SAM 137 lreagikrvvdrivg 151
                                    ++ gik++  +ivg
  gi|15669774|ref|NP_248587.1| 216 VKKEGIKKTALIIVG 230
                                   888888855444443 PP

>> Cyt_b-c1_8  Cytochrome b-c1 complex subunit 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   5.7e-06      0.02      10      70 ..     192     250 ..     187     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.7e-06
                    Cyt_b-c1_8  10 evvYtlSPmqqkvmrglfkdlpkkiakkvkenwvsavlllvplvGtygYaenykeqeklsh 70 
                                   +vvY  S    k++rg++kd+++k++k        a++++  ++ ++ Ya      +  +h
  gi|15669774|ref|NP_248587.1| 192 AVVYHASWDDEKIVRGTLKDIAEKVKKEG--IKKTALIIVGEVLNPKYYAYSKLYDKNFEH 250
                                   69**********************99854..344555557788888888877666666666 PP

>> HU-DNA_bdg  DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00018      0.64      10      42 ..      44      74 ..      35     110 .. 0.87
   2 ?    1.4   0.2     0.082   2.9e+02      53      76 ..     169     192 ..     157     219 .. 0.77
   3 ?    0.7   0.1      0.13   4.8e+02      30      43 ..     208     221 ..     194     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00018
                                  ---------EEEEE----EE-HHHHHHHHHHH- CS
                    HU-DNA_bdg 10 kltkdkksdyiaqvessgsltledIidemvkeg 42
                                  kl   +++ ++a++ +s++++le+Iid mvk  
  gi|15669774|ref|NP_248587.1| 44 KLL--EYNKKNAEIYNSANMNLEEIIDVMVKAV 74
                                  444..678999*******************974 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.082
                                   HHHHHHHHHHHHHTTT-EEE-SSE CS
                    HU-DNA_bdg  53 ilnlykrevseaileGysVntglg 76 
                                    +++++++v e+i+ Gy  +t++ 
  gi|15669774|ref|NP_248587.1| 169 GVSMIDKVVKELIEGGYREETPVA 192
                                   567888899999999988887765 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.13
                                   -HHHHHHHHHHH-T CS
                    HU-DNA_bdg  30 tledIidemvkegt 43 
                                   tl+dI+++++keg 
  gi|15669774|ref|NP_248587.1| 208 TLKDIAEKVKKEGI 221
                                   68999999999985 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1     5e-05      0.18      70     137 .]      23     101 ..      15     101 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5e-05
                                   HHHHHHHH-SEEEEES-SSSTCCCTTTTTTTTTT............-EEEEEESSCCCCTTCC....--SEEEECTHHHHH CS
                  TPP_enzyme_M  70 aanealeeaDlvlalGarfddirttgsepefape............akiihididpaeigkny....qvdlaivgdvketl 134
                                   ++++a+eeaD+++  G+  ++        e++++            ++ii + +++ + gk +    + d +i+g +ke +
  gi|15669774|ref|NP_248587.1|  23 KGKKAIEEADVIIYAGSLVNEKLL-----EYNKKnaeiynsanmnlEEIIDVMVKAVNQGKKVvrlhTGDPSIYGAIKEQI 98 
                                   5789************99888322.....2222211122233443335999999998888877444457788888888887 PP

                                   HHH CS
                  TPP_enzyme_M 135 eaL 137
                                   ++L
  gi|15669774|ref|NP_248587.1|  99 DEL 101
                                   766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      715  (0.0398795); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1617.57
//
Query:       gi|15669775|ref|NP_248588.1|  [L=70]
Description: hypothetical protein MJ_1579 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1923  (0.107256); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 462.35
//
Query:       gi|15669776|ref|NP_248589.1|  [L=124]
Description: hypothetical protein MJ_1580 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-29   99.8   9.0    1.1e-28   99.6   9.0    1.1  1  DUF2304        Uncharacterized conserved protein (DUF2304)
  ------ inclusion threshold ------
        0.1   12.1   0.6        0.1   12.1   0.6    2.2  2  YvrJ           YvrJ protein family
       0.14   12.5   6.0      0.076   13.3   2.8    1.8  2  Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
        0.4   10.9  12.7      0.088   13.0   6.8    2.1  2  Spore_YabQ     Spore cortex protein YabQ (Spore_YabQ)


Domain annotation for each model (and alignments):
>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   9.0   2.4e-32   1.1e-28       2     104 ..      14     116 ..      13     118 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 2.4e-32
                       DUF2304   2 lqiiliivsvllllliirlvrkkklkleysllwlllalilivlslfpqiltvlanllGvgrgtnllfllgivfllvilfsl 82 
                                   +qi+ +i+++++l  ++ +++++ +++++ l+w++++ +++++ +fp+++ ++a++lGvgrg+++l++++iv+l++++++l
  gi|15669776|ref|NP_248589.1|  14 IQIVGVIFALFALSRVVLQLKRRSISFNEGLFWIFVWGFVVIFLVFPEFFGYVAEVLGVGRGVDALIYISIVVLFYLIYRL 94 
                                   9******************************************************************************** PP

                       DUF2304  83 slklskleekikeLaqeiAlle 104
                                   ++k+++le++i+++++eiA+++
  gi|15669776|ref|NP_248589.1|  95 YAKINNLERQITHIVREIAIRD 116
                                   ********************86 PP

>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.6      0.13   5.7e+02      19      28 ..       6      15 ..       2      17 .. 0.84
   2 ?   12.1   0.6   2.3e-05       0.1       9      31 ..      84     106 ..      83     110 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.13
                          YvrJ 19 iEkkLdeLtk 28
                                  +E+kL eL++
  gi|15669776|ref|NP_248589.1|  6 LEEKLMELIQ 15
                                  6999999997 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.3e-05
                          YvrJ   9 IaVavYLLvRiEkkLdeLtksIe 31 
                                   I+V +YL++R+ +k+++L   I+
  gi|15669776|ref|NP_248589.1|  84 IVVLFYLIYRLYAKINNLERQIT 106
                                   9999**************99997 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.8   1.7e-05     0.076      24      78 ..       3      58 ..       1      67 [. 0.86
   2 ?    0.1   0.1      0.22   9.8e+02      38      50 ..      81      93 ..      67     113 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                                  HHCSSSHHHHHHHHHHHHHGGGCHHH.H---SSSSSTT-.HHHHHHHHHHHHHHHH CS
                 Cytochrom_B_C 24 LraipakllGvvamgaaivilfllpw.ldrskvksiryrkplakvllallvvsfvv 78
                                  ++ +++kl+ ++ +++ i+ lf+l   + + k +si++ + l+ ++++ +vv f+v
  gi|15669776|ref|NP_248589.1|  3 IKILEEKLMELIQIVGVIFALFALSRvVLQLKRRSISFNEGLFWIFVWGFVVIFLV 58
                                  566789******************8735566889*****99999999999999987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.22
                                  HHHHHGGGCHHHH CS
                 Cytochrom_B_C 38 gaaivilfllpwl 50
                                   ++iv+lf l + 
  gi|15669776|ref|NP_248589.1| 81 YISIVVLFYLIYR 93
                                  4566666666553 PP

>> Spore_YabQ  Spore cortex protein YabQ (Spore_YabQ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   6.8     2e-05     0.088       9      52 ..      16      59 ..      15      83 .. 0.90
   2 ?    1.3   0.5     0.088   3.9e+02      10      22 ..      85      97 ..      78     113 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                    Spore_YabQ  9 ilgllydlfrilrrllkhkkvltfieDilfwllaallvflfllr 52
                                  i+g+++ lf + r +l+ k+  +++ + lfw++++ +v +fl++
  gi|15669776|ref|NP_248589.1| 16 IVGVIFALFALSRVVLQLKRRSISFNEGLFWIFVWGFVVIFLVF 59
                                  789*******999999999999**********999999999865 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.088
                    Spore_YabQ 10 lgllydlfrilrr 22
                                  + l+y ++r+  +
  gi|15669776|ref|NP_248589.1| 85 VVLFYLIYRLYAK 97
                                  3344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1105  (0.061632); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 831.48
//
Query:       gi|15669777|ref|NP_248590.1|  [L=306]
Description: aspartate carbamoyltransferase catalytic subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-52  176.9   0.0    3.6e-52  176.3   0.0    1.2  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    2.4e-26   92.7   0.0    3.5e-26   92.2   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.3   0.0     4e-56   3.6e-52       1     147 [.       2     143 ..       2     144 .. 0.96

  Alignments for each domain:
  == domain 1  score: 176.3 bits;  conditional E-value: 4e-56
                                   S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTT CS
                      OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlss 81 
                                   +hl+s++d+ keei e+ld+a++++e  ++++  kll+gk+la++F+epStRTr+Sfe+A+krlGg+v++++   d+++ss
  gi|15669777|ref|NP_248590.1|   2 KHLISMKDIGKEEILEILDEARKMEELLNTKRPLKLLEGKILATVFYEPSTRTRLSFETAMKRLGGEVITMT---DLKSSS 79 
                                   8***************************99*****************************************9...578999 PP

                                   GGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                      OTCace_N  82 vskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                   v+kg  Esl Dt+rv+s+y+d+iv+Rhp++  ++   +y++vp+iNagdg+++HPtQ+L+Dl+ti 
  gi|15669777|ref|NP_248590.1|  80 VAKG--ESLIDTIRVISGYADIIVLRHPSEGAARLASEYSQVPIINAGDGSNQHPTQTLLDLYTIM 143
                                   ****..**********************55458888999*************************96 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.0   3.8e-30   3.5e-26       1     155 [.     150     297 ..     150     299 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 3.8e-30
                                   CC.EEEEESS.TTSHHHHHHHHHHHHCT.-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE-- CS
                        OTCace   1 kglkiafvGd.kknnvanslikllarlg.mdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdv 79 
                                   +g+kiafvGd k++++++sl+++l+ ++ +++++v+Pk+l+  k+++e +k+    ++ ++  +e+l +  ++ Dv+y ++
  gi|15669777|ref|NP_248590.1| 150 DGIKIAFVGDlKYGRTVHSLVYALSLFEnVEMYFVSPKELRLPKDIIEDLKA----KNIKFYEKESLDDLDDDIDVLYVTR 226
                                   69************************86166*********9999*9977665....588999999999999********** PP

                                   SSETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
                        OTCace  80 wvsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                                   ++     ker+   ++++k+k+ y++ +e ++   k++i++H+LP  r +E++ +V+d p++ +f+q  +++ +++A+l 
  gi|15669777|ref|NP_248590.1| 227 IQ-----KERFpdpNEYEKVKGsYKIKREYVE--GKKFIIMHPLP--RVDEIDYDVDDLPQAKYFKQSFYGIPVRMAILK 297
                                   **.....88888889*****************..599********..*******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1941.76
//
Query:       gi|15669778|ref|NP_248591.1|  [L=249]
Description: hypothetical protein MJ_1582 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-63  213.9   0.5    2.8e-63  213.7   0.5    1.0  1  TatD_DNase       TatD related DNase
     0.0033   17.1   0.1       0.96    9.2   0.0    2.5  2  DUF5615          Domain of unknown function (DUF5615)
  ------ inclusion threshold ------
      0.045   13.6   0.0        0.1   12.5   0.0    1.6  1  Transketolase_C  Transketolase, C-terminal domain
       0.08   13.5   3.4        5.3    7.6   0.1    3.2  3  DUF2482          Hypothetical protein of unknown function (DU
      0.085   13.0   0.3      0.085   13.0   0.3    2.4  2  T3SchapCesA      Type III secretion system filament chaperone


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.7   0.5   7.9e-67   2.8e-63       1     255 []       7     246 ..       7     246 .. 0.96

  Alignments for each domain:
  == domain 1  score: 213.7 bits;  conditional E-value: 7.9e-67
                                   EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHHHH CS
                    TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleelkela 81 
                                   +DaHcH+++k f+++r+e++era+++ v  v + g s+    ++lel kky+  +y +lG HP +v+ a+++++e++ +l 
  gi|15669778|ref|NP_248591.1|   7 VDAHCHIEDKAFNKNRDEVIERAKKEDVIIV-TSGASLGGCLRALELRKKYN--IYLTLGYHPSRVK-ADDKVIEKVYNLI 83 
                                   7*************************99866.8*****************99..5***********9.69**********9 PP

                                   HCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEETT--S-HH CS
                    TatD_DNase  82 nvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvlHsfsgsae 162
                                   + +++++ aiGeiG+D    ++++ ++qee+F+++l+lA+el++p+v+H+r  e+++ +i+k++    + +++H++sg++e
  gi|15669778|ref|NP_248591.1|  84 KNNEYEILAIGEIGMDI---KDENYKRQEEIFKKFLSLAEELNKPIVVHARGFERKIFDIAKDK----VDIMFHCYSGDVE 157
                                   999**************...56799*************************************96....57*********** PP

                                   HHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HHHHH CS
                    TatD_DNase 163 eakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvveklaelkaltleela 243
                                    ak++ k g  is+s l++f  ++++++lv++++l+ l +ETD+Pyl+p   +g++nep+nv+ v+e++a++k++++ee++
  gi|15669778|ref|NP_248591.1| 158 LAKEIGKEGHLISISTLVCF--SEHHKKLVESLDLEYLTTETDSPYLSP--IKGTKNEPKNVKLVIEEIAKIKEMEVEEVK 234
                                   ********************..789************************..999*************************** PP

                                   HHHHHHHHHHHH CS
                    TatD_DNase 244 eitaeNakrlfk 255
                                   +++++N++++fk
  gi|15669778|ref|NP_248591.1| 235 DVIYKNTCKFFK 246
                                   **********96 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00027      0.96      38      54 ..      23      39 ..       5      45 .. 0.84
   2 !    5.3   0.0    0.0046        16       2      38 ..      68     103 ..      67     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00027
                       DUF5615 38 eeileyAkeedriivTk 54
                                  +e++e+Ak+ed+iivT 
  gi|15669778|ref|NP_248591.1| 23 DEVIERAKKEDVIIVTS 39
                                  79**************5 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0046
                       DUF5615   2 klllDenlsprlvellreaghdvlhvrelglegasDe 38 
                                   ++ +D  +  ++ +l++++++++l++ e+g++ ++De
  gi|15669778|ref|NP_248591.1|  68 RVKADDKVIEKVYNLIKNNEYEILAIGEIGMD-IKDE 103
                                   67789999999*******************98.8886 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.9e-05       0.1       6      39 ..      28      61 ..      23      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                                  EETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEE CS
               Transketolase_C  6 lregkdvtlvayGsmveealeAaeeLekegisae 39
                                  + +++dv++v+ G+ +  +l+A e  +k +i  +
  gi|15669778|ref|NP_248591.1| 28 RAKKEDVIIVTSGASLGGCLRALELRKKYNIYLT 61
                                  3459********************9999999766 PP

>> DUF2482  Hypothetical protein of unknown function (DUF2482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0015       5.3      26      71 ..      79     124 ..      70     131 .. 0.85
   2 ?    2.5   0.0     0.057     2e+02      48      83 ..     154     189 ..     132     197 .. 0.83
   3 ?    2.5   0.2      0.06   2.1e+02       3      17 ..     225     239 ..     223     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0015
                       DUF2482  26 ieeikeetdFdillfsaigvsdgdaqvsssslvvGkivglanlLkn 71 
                                   + ++ ++ +++il +  ig++ +d +++ ++ +  k ++la+ L++
  gi|15669778|ref|NP_248591.1|  79 VYNLIKNNEYEILAIGEIGMDIKDENYKRQEEIFKKFLSLAEELNK 124
                                   444556889**************99****************98875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.057
                       DUF2482  48 gdaqvsssslvvGkivglanlLkneeefkdivnviq 83 
                                   gd+++++    +G+ ++++ l+  +e++k++v+++ 
  gi|15669778|ref|NP_248591.1| 154 GDVELAKEIGKEGHLISISTLVCFSEHHKKLVESLD 189
                                   6666667777799*******9999999999999876 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.06
                       DUF2482   3 fKdmtqeeikdllae 17 
                                   +K+m  ee+kd++ +
  gi|15669778|ref|NP_248591.1| 225 IKEMEVEEVKDVIYK 239
                                   8***********965 PP

>> T3SchapCesA  Type III secretion system filament chaperone CesA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   2.4e-05     0.085      23      81 ..      92     148 ..      73     155 .. 0.82
   2 ?   -0.2   0.6      0.32   1.1e+03       7      28 ..     208     229 ..     202     244 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                   T3SchapCesA  23 aikkiiaefdvvkesvnilsekaktdpqaaeklnkliegytygeerklydsalskiekl 81 
                                   ai  i   +d+  e+ +   e  k     ae+lnk i  ++ g erk++d a  k++ +
  gi|15669778|ref|NP_248591.1|  92 AIGEI--GMDIKDENYKRQEEIFKKFLSLAEELNKPIVVHARGFERKIFDIAKDKVDIM 148
                                   44444..4688888999999999999999************************999866 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.32
                   T3SchapCesA   7 tknkelldkkirseieaikkii 28 
                                   tkn     k +  ei  ik + 
  gi|15669778|ref|NP_248591.1| 208 TKNEPKNVKLVIEEIAKIKEME 229
                                   4444433344444444444432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1065  (0.059401); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1633.36
//
Query:       gi|15669779|ref|NP_248592.1|  [L=126]
Description: hypothetical protein MJ_1583 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-25   89.5   0.0    2.1e-25   89.2   0.0    1.0  1  TrmO            tRNA-methyltransferase O
  ------ inclusion threshold ------
      0.077   12.5   0.0      0.098   12.2   0.0    1.1  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase


Domain annotation for each model (and alignments):
>> TrmO  tRNA-methyltransferase O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   0.0   2.4e-29   2.1e-25      12     119 .]      15     122 ..       6     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 2.4e-29
                                   -EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E.-TT-.SS.-E.EGGGS--S-SSS-EEEEEEEEEEE CS
                          TrmO  12 aeaeielepeynseealegleefshlwllfvfhenaekklkakvr.pprlggn.ervGvfatRsphRpnpiglsvvklekv 90 
                                     + +++++e+   e+l+gl+e +++++l++fh+n++++ ++ ++ +pr + n    GvfatRsp+Rpnpig  +vk++k+
  gi|15669779|ref|NP_248592.1|  15 NYTVLNIFDEF--VEGLDGLKEGDYIIVLVWFHKNDSEEKRKILKvHPRGDINnPLKGVFATRSPYRPNPIGKYTVKIHKI 93 
                                   45678889999..9*******************996666444444578877541567************************ PP

                                   ETTEEEEES----TT-EEEEEEE--HHHH CS
                          TrmO  91 egnvlevsgvDlldgtpvlDiKPYvpyaD 119
                                    +n++ + ++D+ ++tp++DiK + +++D
  gi|15669779|ref|NP_248592.1|  94 YRNKIFIDKIDAYNETPIIDIKIFSEKLD 122
                                   ************************99988 PP

>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.1e-05     0.098       8      62 ..      38      94 ..      33     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.1e-05
                                  EEEEEE.E..E-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGG CS
                tRNA_deacylase  8 iiflSr.H..ssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkia 62
                                  ii+l + H   se+++++L vH+ G++++ +l G  ++ +p  P+ + ++  +++ki 
  gi|15669779|ref|NP_248592.1| 38 IIVLVWfHknDSEEKRKILKVHPRGDINN-PLKGVFATRSPYRPNPIGKYTVKIHKIY 94
                                  555443241168888************99.7778999999999999999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 857.79
//
Query:       gi|15669780|ref|NP_248593.1|  [L=151]
Description: hypothetical protein MJ_1584 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.2   0.1        1.1    9.1   0.0    2.8  3  RICTOR_M  Rapamycin-insensitive companion of mTOR, middle dom


Domain annotation for each model (and alignments):
>> RICTOR_M  Rapamycin-insensitive companion of mTOR, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.024   4.2e+02      41      57 ..      15      31 ..       4      40 .. 0.81
   2 ?    9.1   0.0   6.1e-05       1.1      28      55 ..      42      69 ..      36     104 .. 0.80
   3 ?    0.5   0.0     0.029   5.1e+02      34      48 ..     122     136 ..     120     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.024
                      RICTOR_M 41 ekwkiftllyklvelks 57
                                  +kwk++++lyk+++lk 
  gi|15669780|ref|NP_248593.1| 15 SKWKLIKTLYKVLKLKC 31
                                  68999****99988765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 6.1e-05
                      RICTOR_M 28 GvlsssknGlklLekwkiftllyklvel 55
                                  G ls+ + Gl+lL+k+++f++  +++ +
  gi|15669780|ref|NP_248593.1| 42 GGLSAYADGLRLLSKVGLFKIESEYCRS 69
                                  889*****************98888765 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.029
                      RICTOR_M  34 knGlklLekwkiftl 48 
                                   ++Gl+lL+k ++f++
  gi|15669780|ref|NP_248593.1| 122 ASGLRLLSKLGLFEI 136
                                   68***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1086.51
//
Query:       gi|15669781|ref|NP_248594.1|  [L=310]
Description: aldolase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-44  152.6   0.0    1.6e-44  152.3   0.0    1.1  1  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.3   0.0   8.7e-49   1.6e-44       2     235 .]      43     276 ..      42     276 .. 0.97

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 8.7e-49
                                   EEEEECCSHHHHHHHHCTSS..HHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEE CS
                          DeoC   2 vilavDqrvankddtasaqn..eqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdv 80 
                                   +++a Dq++++ +d+++ +   ++ + +++l++ a ++++  +++++g+ia++ ++y+ +i+++vk++++t+l+k++  d+
  gi|15669781|ref|NP_248594.1|  43 MLFAGDQKIEHLNDDFFGEGiaKDDASPEHLFNIASKGKICGFATQLGLIARYGMDYK-KIPYIVKINSKTHLVKTR--DP 120
                                   789**************988*9************************************.9***************99..66 PP

                                   E.....TTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHH CS
                          DeoC  81 d.....evasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeA 156
                                   +      v +v  +k++++  +  v y+++ gse+e  +++e +rv  ++h++gl  i++ y+r++++kdek dp+l+a A
  gi|15669781|ref|NP_248594.1| 121 IsralvHVKDVVDLKENSGLKILGVGYTIYPGSEYEHIMFEEASRVILEAHKHGLIAIIWSYPRGKNVKDEK-DPHLIAGA 200
                                   6788889*****************************************************************.******** PP

                                   HHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS..SHHHHHHHHHHHHHHHTHCEEEESHHHHTT CS
                          DeoC 157 arvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv..seedfletvedAvkeagasGvlsGRaifqk 235
                                   a v+a+lGaD++Kv++p     + ++ ae fk+++ aa   gv+++GG   + e+fl+++ ++++ +ga G+++GR+i+qk
  gi|15669781|ref|NP_248594.1| 201 AGVAACLGADFVKVNYP-----KCDNPAERFKEAVLAAGRTGVLCAGGKsiEPEKFLKQIWEQINISGARGNATGRNIHQK 276
                                   *****************.....6699*************99*******9999***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2100.63
//
Query:       gi|15669782|ref|NP_248595.1|  [L=491]
Description: hypothetical protein MJ_1586 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-70  237.7   0.0    2.2e-70  236.9   0.0    1.4  1  Carb_kinase  Carbohydrate kinase
    5.1e-25   88.3   0.0    9.5e-25   87.4   0.0    1.4  1  YjeF_N       YjeF-related protein N-terminus


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.9   0.0   2.4e-74   2.2e-70       1     244 []     255     485 ..     255     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 236.9 bits;  conditional E-value: 2.4e-74
                                   EEEEE-BTTCHHHHHHHHHHHHCTT..-SEEEEEESSTTTCCCCTTTTTCEECCTTHTTTS....--SSS-SEEEE-TT-S CS
                   Carb_kinase   1 vlvigGsedytGAallaalaalrlg..aglvsvateseaiavlksylpevivhplledeqa.kileklerldavviGpGLg 78 
                                   vl+igGs+d++GA++la+laal+++  +g++sv++ +++++++++++++v +++l+ ++++ ++le+++++d+vv+G+GLg
  gi|15669782|ref|NP_248595.1| 255 VLIIGGSKDFYGAPILAGLAALKIVdlVGILSVGKVIDKVNHPEFIMYRVEGDYLS-SQHVdYTLEIAKKYDVVVLGNGLG 334
                                   79******************************************************.89999******************* PP

                                   SSHCHHHHCHHHCCCCS-.EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEE CS
                   Carb_kinase  79 rdekikklleevlekdep.lviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavv 158
                                   +++++k++l+e+l+k+++ +viDAd++++++++n  +e+++++i+TPhk+Ef+++  +++            +++++++++
  gi|15669782|ref|NP_248595.1| 335 ANNRTKAFLNEFLAKYDGkVVIDADAIKVIDYNN--FEFSENYIFTPHKREFEYMGIDLD------------NIENIKSTI 401
                                   *********************************8..************************............99******* PP

                                   EEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHCCCT-TS-HCHHHH CS
                   Carb_kinase 159 llkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaaekkgvgmlatels 239
                                   +lkg++d+i++ +++++in+tg+++l+kGG+GDvLaGligal+a+ne ++ +a+++a+++g+a+d++ ++kg+++++ +l+
  gi|15669782|ref|NP_248595.1| 402 VLKGKYDIIFN-ANNLKINKTGNAGLTKGGTGDVLAGLIGALFAVNE-AFLSACCGAFINGYAGDLLLKEKGYYYTPLDLI 480
                                   ***********.9**********************************.8999***************************** PP

                                   HHHCH CS
                   Carb_kinase 240 kiipr 244
                                   ++ip+
  gi|15669782|ref|NP_248595.1| 481 EKIPN 485
                                   **985 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.0   1.1e-28   9.5e-25       4     144 ..      52     196 ..      49     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 1.1e-28
                        YjeF_N   4 LmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellkkaggk 84 
                                   Lmenag+av e ++++      ++++++++G gnnGgdg+++ArhL   + +V++ + +e+e  + +a++++++lk++ + 
  gi|15669782|ref|NP_248595.1|  52 LMENAGKAVYEEIKDID-----AEEFIIFCGTGNNGGDGFVVARHL--GKGDVIL-IGKESEIKTYEARENFKILKNLAEF 124
                                   9*************998.....899*********************..6666777.46788999*********99998654 PP

                        YjeF_N  85 vveekpeedleekls.......apvdlviDAllGiglrgelreelaeliewlnss.....eapvlavDiPSG 144
                                         e ++ e+ +       ++  ++iDA+ G+g++gelre+++++++++n+      + +v++vD+  G
  gi|15669782|ref|NP_248595.1| 125 GNIRIREIKWAEEVNdiferlkNKKAVIIDAMIGTGVKGELREPFKTIVDKINELkqinkNIFVISVDVETG 196
                                   4433333333333334457999********************************999*99999*****9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3569.41
//
Query:       gi|15669783|ref|NP_248596.1|  [L=171]
Description: hypothetical protein MJ_1587 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-08   35.1   0.0    2.4e-08   34.5   0.0    1.5  1  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   1.3e-12   2.4e-08       1      72 [.       4      81 ..       4     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.3e-12
                                  EEEE--CCC.........--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE....... CS
                                  xxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           PHP  1 dlHvHteys.........lldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvadds 72
                                  dlH+Ht+ys         + d++ ++ +++k ak++g++ +aiTDh+ + g ve   +++  ++ g++++iG e+  ++++
  gi|15669783|ref|NP_248596.1|  4 DLHIHTKYSgigkfwklkFPDSVEEPRNILKVAKKKGIEVVAITDHNTIRGGVETK-KLE--KEFGVEVVIGSEIMTTEGE 81
                                  89*******9999887776677777888***********************99875.664..5559********7776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1036.28
//
Query:       gi|15669784|ref|NP_248597.1|  [L=112]
Description: hypothetical protein MJ_1588 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00012   21.7   0.0    0.00021   21.0   0.0    1.4  1  PHP_C     PHP-associated


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.2e-08   0.00021      29      56 .]       1      26 [.       1      26 [. 0.94

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.2e-08
                         PHP_C 29 eVGrayTefeepiatpdelleairegrt 56
                                  +VG+ayT+fe ++a  d+l +ai ++rt
  gi|15669784|ref|NP_248597.1|  1 MVGNAYTLFEGNSA--DDLYKAIVKKRT 26
                                  7********99988..*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 747.45
//
Query:       gi|15669785|ref|NP_248598.1|  [L=241]
Description: hypothetical protein MJ_1589 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0043   17.3   2.3     0.0043   17.3   2.3    2.7  2  Gate      Nucleoside recognition
  ------ inclusion threshold ------
       0.79   10.1   6.3        5.8    7.3   2.1    2.6  2  DUF4149   Domain of unknown function (DUF4149)


Domain annotation for each model (and alignments):
>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   1.7    0.0036        32       2      32 ..       9      39 ..       8     104 .. 0.90
   2 !   17.3   2.3   4.8e-07    0.0043       2      90 ..     158     237 ..     157     241 .] 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0036
                          Gate  2 lkagpiillasiliwflssssllgrigklle 32
                                  +k++pi++++++l +++ + ++l ++ k+++
  gi|15669785|ref|NP_248598.1|  9 IKILPIMFFGILLANLMCHLNILYKLQKYIK 39
                                  799****************999999999886 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4.8e-07
                          Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtp 82 
                                   +++++ +++ +++i +l +++ll+++  + + +++ l   l+  + v  ltg+a    ++g+++       g l +++ +p
  gi|15669785|ref|NP_248598.1| 158 FRVLTSFVPSVLIITYLIEHGLLDIVEDFAGSLLNALN--LSPTILVIVLTGLATISGAIGIAS-------GLLDENILSP 229
                                   6899**********************************..**************4444444444.......5569999999 PP

                          Gate  83 ksalafll 90 
                                    ++l  l+
  gi|15669785|ref|NP_248598.1| 230 NEVLFSLF 237
                                   99665554 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.1   0.00064       5.8      33      96 ..      38     101 ..       6     103 .. 0.79
   2 ?    4.3   0.1    0.0054        48      38      84 ..     154     208 ..     138     219 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00064
                       DUF4149  33 lqsklFplyfg.lglalsvlllltevavgseklaseellqlllllvvllltllnafylepritsl 96 
                                   +++k Fp+ ++ + + +s+  ll ++++ +++ ++e+ll +++l + ++ + +  fy  p++tsl
  gi|15669785|ref|NP_248598.1|  38 IKNKYFPIIAVfFVSSTSGSFLLKNLLK-KGEISEENLLPIYFLGMFVFGIHIILFYAIPMATSL 101
                                   6777899988833444555555555554.48999999*************************997 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0054
                       DUF4149  38 Fplyfg.lglalsvlllltevavg.......seklaseellqlllllvvllltll 84 
                                   F  yf+ l ++++++l++t+++++       +   +  + l l++ ++v++lt l
  gi|15669785|ref|NP_248598.1| 154 FKQYFRvLTSFVPSVLIITYLIEHglldiveDFAGSLLNALNLSPTILVIVLTGL 208
                                   5555542788999********9998888888555555566666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1571.96
//
Query:       gi|15669786|ref|NP_248599.1|  [L=105]
Description: hypothetical protein MJ_1590 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0078   15.8   0.7     0.0086   15.7   0.7    1.1  1  Sulf_transp  Sulphur transport
  ------ inclusion threshold ------
        6.7    6.8   7.3         16    5.6   0.7    2.6  3  UPF0154      Uncharacterised protein family (UPF0154)


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.7   9.6e-07    0.0086     178     259 ..       4      94 ..       1     101 [. 0.63

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.6e-07
                   Sulf_transp 178 slvlgavllgllavl.awllsaktgrsfglgftvpgakilqyl.......vlgtskfl.nwgvvlvlGiilGaflaallsg 249
                                   s+++++++ g++a++   l+       +g++++  + ++++++       +lg + ++  + v++v+Gi++Ga++   + +
  gi|15669786|ref|NP_248599.1|   4 SPLIAGLIGGFTAAIlQALFKVFPPPAYGICIACHTRDLVNWIinhlfgtTLGMALVSkAFPVLTVVGIFIGALITTFIYK 84 
                                   566666666666433133333323445899999999999999744333222222222213679****************** PP

                   Sulf_transp 250 efkleapkar 259
                                   e +l+   + 
  gi|15669786|ref|NP_248599.1|  85 ETELKQTHSP 94 
                                   9999866554 PP

>> UPF0154  Uncharacterised protein family (UPF0154)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3    0.0036        33       5      16 ..       6      17 ..       3      24 .. 0.85
   2 ?   -1.2   0.0      0.24   2.2e+03       3      20 ..      47      64 ..      45      66 .. 0.76
   3 ?    5.6   0.7    0.0018        16       5      22 ..      68      85 ..      64      93 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0036
                       UPF0154  5 livGlvlGffia 16
                                  li+Gl++Gf +a
  gi|15669786|ref|NP_248599.1|  6 LIAGLIGGFTAA 17
                                  89*******877 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.24
                       UPF0154  3 ialivGlvlGffiarkym 20
                                  i  + G  lG+ ++ k +
  gi|15669786|ref|NP_248599.1| 47 INHLFGTTLGMALVSKAF 64
                                  566789999998888765 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0018
                       UPF0154  5 livGlvlGffiarkymkk 22
                                   +vG+++G +i+  ++k+
  gi|15669786|ref|NP_248599.1| 68 TVVGIFIGALITTFIYKE 85
                                  678888888888777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 684.26
//
Query:       gi|15669787|ref|NP_248601.1|  [L=242]
Description: phosphoribosylaminoimidazole-succinocarboxamide synthase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-64  216.7   0.2    4.4e-64  216.5   0.2    1.0  1  SAICAR_synt  SAICAR synthetase
  ------ inclusion threshold ------
       0.07   13.0   0.6       0.26   11.2   0.6    1.9  1  IF2_N        Translation initiation factor IF-2, N-terminal r


Domain annotation for each model (and alignments):
>> SAICAR_synt  SAICAR synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.5   0.2   4.9e-68   4.4e-64       2     250 ..      14     237 ..      13     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: 216.5 bits;  conditional E-value: 4.9e-68
                                   EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE.....-SSSEEEEE CS
                   SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklek..ipnhliksldpeqlegrsmlvk 80 
                                   ly+GK++++Ye+ dddk+l++++D+i+A ++++++  +gKG ++  +s+ +fe le+  +++h+ik      +e r m++k
  gi|15669787|ref|NP_248601.1|  14 LYSGKAKSIYEI-DDDKVLIEFRDDITAGNGAKHDVKQGKGYLNALISSKLFEALEEngVKTHYIKY-----IEPRYMIAK 88 
                                   79**********.888****************************************668******77.....899****** PP

                                   -EEEESEEEEEEEE--HHH.......HH....HH..T--TT-EEEEEEEEEEE--CCCT.S-EE-HHHHH.HTT..-HHHH CS
                   SAICAR_synt  81 klkmlpvEvvvRgyltGslwkeykksgkvcgirlpeglkegeklpepiftpstKaeegehDeniseeevvealg..teeea 159
                                   k++++p+Ev+vR++++Gsl       ++    r+   ++eg++lp pi+++ +K++e + D++++e+ +v alg  t+ee+
  gi|15669787|ref|NP_248601.1|  89 KVEIIPIEVIVRNIAAGSL-------CR----RY--PFEEGKELPFPIVQFDYKNDEYG-DPMLNEDIAV-ALGlaTREEL 154
                                   *******************.......88....88..89********************9.********99.88999***** PP

                                   HHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STTTEEEEETTT.....GGGB-STHHHHTT-ST CS
                   SAICAR_synt 160 eeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpDssRfwdaetyeegkeqeslDKqfvRdwlee 240
                                   ++i+e+al+v+e +++l++e+giilvD+K+E G+d+ +g+l++aDe+ +pD++R+wd+et      ++ lDK+++R++l++
  gi|15669787|ref|NP_248601.1| 155 NKIKEIALKVNEVLKKLFDEKGIILVDFKIEIGKDR-EGNLLVADEI-SPDTMRLWDKET------RDVLDKDVFRKDLGD 227
                                   ***********************************6.9*********.************......9************** PP

                                   HHHHHHHHHH CS
                   SAICAR_synt 241 veekwkekle 250
                                   v  k++ ++e
  gi|15669787|ref|NP_248601.1| 228 VIAKYRIVAE 237
                                   9999986665 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   2.8e-05      0.26      11      30 ..     158     177 ..     158     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.8e-05
                         IF2_N  11 keLgvkskevikkLfkelGi 30 
                                   ke+ +k++ev+kkLf e+Gi
  gi|15669787|ref|NP_248601.1| 158 KEIALKVNEVLKKLFDEKGI 177
                                   89*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1653.18
//
Query:       gi|15669788|ref|NP_248602.1|  [L=83]
Description: phosphoribosylformylglycinamidine synthase subunit PurS [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-31  106.2   2.0    7.8e-31  106.1   2.0    1.0  1  PurS      Phosphoribosylformylglycinamidine (FGAM) synthase
  ------ inclusion threshold ------
      0.037   14.0   0.0      0.037   14.0   0.0    1.1  1  YfbU      YfbU domain
      0.064   14.1   0.1       0.12   13.2   0.0    1.5  2  PriA_C    Primosomal protein N C-terminal domain
       0.11   11.9   0.0       0.13   11.7   0.0    1.1  1  HDOD      HDOD domain


Domain annotation for each model (and alignments):
>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   2.0   1.7e-34   7.8e-31       1      77 []       3      79 ..       3      79 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 1.7e-34
                                  EEEEEEEE-TTS--HHHHHHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEEEE CS
                          PurS  1 kakveVtlKkgvlDpqGkavkkalkslgyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyeiel 77
                                  ka+v+++lKkgvl+p+G+++++al+ lg+++v++v++ k+i++ +e+e+ee+++eeveemc+klLaNpvi+dyei++
  gi|15669788|ref|NP_248602.1|  3 KATVIIKLKKGVLNPEGRTIQRALNFLGFNNVKEVQTYKMIDIIMEGENEEKVKEEVEEMCKKLLANPVIHDYEIKV 79
                                  799***********************************************************************986 PP

>> YfbU  YfbU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   8.3e-06     0.037      87     129 ..      21      66 ..       1      80 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.3e-06
                          YfbU  87 iearrleFsGfdaneEkkllsYvrfliedeklye...elkkkkddl 129
                                   + +r l+F Gf++ +E + ++ ++ ++e+e+  +   e+++ +++l
  gi|15669788|ref|NP_248602.1|  21 TIQRALNFLGFNNVKEVQTYKMIDIIMEGENEEKvkeEVEEMCKKL 66 
                                   33899**********************9988766444666555554 PP

>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.6   1.2e+04      61      65 ..       8      12 ..       2      30 .. 0.53
   2 ?   13.2   0.0   2.6e-05      0.12       3      31 ..      40      68 ..      40      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.6
                        PriA_C 61 lksks 65
                                  +k k+
  gi|15669788|ref|NP_248602.1|  8 IKLKK 12
                                  44442 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.6e-05
                        PriA_C  3 srlalirvsgkdeekveeaaeelaellke 31
                                  ++++ i+++g++eekv+e++ee+ ++l +
  gi|15669788|ref|NP_248602.1| 40 YKMIDIIMEGENEEKVKEEVEEMCKKLLA 68
                                  589********************998766 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.9e-05      0.13      55      91 ..      20      56 ..      15      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.9e-05
                                  -SHHHHHHHHHHHHHHHHHHHHHHHHHHHS--.-SS- CS
                          HDOD 55 ssveqAvallGlkevrnlvlalslkrlfkgkeeegad 91
                                  +++++A+++lG+++v+++ +  ++  +++g++ee+++
  gi|15669788|ref|NP_248602.1| 20 RTIQRALNFLGFNNVKEVQTYKMIDIIMEGENEEKVK 56
                                  59**************************999944433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1101  (0.0614089); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 545.46
//
Query:       gi|15669789|ref|NP_248603.1|  [L=211]
Description: phosphoserine phosphatase SerB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-23   84.7   0.0    1.3e-23   84.4   0.0    1.1  1  HAD              haloacid dehalogenase-like hydrolase
    7.9e-20   72.1   3.2    9.7e-20   71.7   3.2    1.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.3e-15   57.9   2.9    6.2e-15   55.7   2.9    1.9  1  HAD_2            Haloacid dehalogenase-like hydrolase
    1.3e-14   54.6   5.5    1.7e-11   44.4   0.4    3.0  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
    2.6e-11   43.4   0.1    1.4e-09   37.7   0.1    2.1  1  Put_Phosphatase  Putative Phosphatase
     0.0086   15.7   0.0      0.013   15.1   0.0    1.4  1  AA_kinase        Amino acid kinase family
  ------ inclusion threshold ------
       0.02   14.5   0.0       0.36   10.3   0.0    2.1  2  S6PP             Sucrose-6F-phosphate phosphohydrolase
      0.062   13.4   0.0       0.11   12.6   0.0    1.5  1  Hydrolase_like   HAD-hyrolase-like


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.0   5.7e-27   1.3e-23       1     188 []       8     176 ..       8     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 5.7e-27
                           HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerfvaev 80 
                                   +lfDfD TL++++++++++r  +++      ++++  +++a+    ++l+ ++  +   +ll++l+ e++++ ++r+    
  gi|15669789|ref|NP_248603.1|   8 ILFDFDSTLVNNETIDEIAR-EAGV-----EEEVKKITKEAM---EGKLNFEQSLRKRVSLLKDLPiEKVEKAIKRIT--- 76 
                                   79******************.4444.....678888888888...5666667777778889*****999999999999... PP

                           HAD  81 irpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrgegkvaalre 160
                                         ++ga e +++ + +G+ v+vvSgg+++ v  + ++lg d+  a++l v+d +ltg   +eg + ++++k   l++
  gi|15669789|ref|NP_248603.1|  77 -----PTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDgKLTGD--VEGEVLKENAKGEILEK 150
                                   .....668******************************************************..***********999999 PP

                           HAD 161 wlaaegegidleevvayGDspsDlpllr 188
                                      a+ egi le++va+GD+ +D+ +++
  gi|15669789|ref|NP_248603.1| 151 --IAKIEGINLEDTVAVGDGANDISMFK 176
                                   ..88888899999*************86 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   3.2   4.3e-23   9.7e-20       2     210 .]       6     179 ..       5     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 4.3e-23
                                   SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewltaldi 82 
                                   k+++fD+d TL++ e     +i+++                     a   +++++++++++     ++++gk  + ++l  
  gi|15669789|ref|NP_248603.1|   6 KLILFDFDSTLVNNE-----TIDEI---------------------AREAGVEEEVKKITK-----EAMEGKLNFEQSL-- 53 
                                   89*************.....*****.....................999999*********.....*************.. PP

                                   HHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT....... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                     Hydrolase  83 ppdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG....... 156
                                                + r + l++  +  v ++   +++ ++a+e++++Lk +g+ v++++g++   ++++ ++lG       
  gi|15669789|ref|NP_248603.1|  54 -------------RKRVSLLKDLPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGldyafan 121
                                   .............9999999999***************************************************9555555 PP

                                   GGGE.SEEEEHHCES...STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxx.xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 157 ddyf.daviasdiet...vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                   + ++ d+++++d+e+      ++ e+++++++  +++ e++++VGDg+nD++++++Ag
  gi|15669789|ref|NP_248603.1| 122 RLIVkDGKLTGDVEGevlKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG 179
                                   4444555555555557666666999999999999**********************98 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   2.9   2.8e-18   6.2e-15       1     176 [.       8     183 ..       8     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.8e-18
                         HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkevkpy 81 
                                   i+FD+D Tl++ e +i ++++e+  e++++++++e ++ +++++   +lrk  +      + +  ++k+++  k+  ++p 
  gi|15669789|ref|NP_248603.1|   8 ILFDFDSTLVNNE-TIDEIAREAGVEEEVKKITKEAMEGKLNFEQ--SLRKRVSL-----LKDLPIEKVEKAIKR--ITPT 78 
                                   89*********75.6788888888899999********9999998..44444442.....334445666777776..**** PP

                         HAD_2  82 dgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtse......dvekk....KPdpeviekaleklklkk 152
                                   +g++e+++eLk++gy +++v+ + + av++  e+lg++  F   ++ +      dve++      + e++ek+ +  +++ 
  gi|15669789|ref|NP_248603.1|  79 EGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKdgkltgDVEGEvlkeNAKGEILEKIAKIEGINL 159
                                   *****************************************875544401111133333552223378889999999**** PP

                         HAD_2 153 eeviyvGDsptDieaakkagikvi 176
                                   e+++ vGD  +Di   kkag+k++
  gi|15669789|ref|NP_248603.1| 160 EDTVAVGDGANDISMFKKAGLKIA 183
                                   *********************986 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.095   2.1e+02       1      12 [.       8      26 ..       8      50 .. 0.63
   2 !   11.1   0.0    0.0001      0.23      17      76 ..      78     141 ..      70     143 .. 0.83
   3 !   44.4   0.4   7.6e-15   1.7e-11     184     247 ..     140     202 ..     136     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.095
                                  EEEEIIIIIS-.......T CS
                   Hydrolase_3  1 ialDlDGTLln.......s 12
                                  i +D D TL+n        
  gi|15669789|ref|NP_248603.1|  8 ILFDFDSTLVNnetideiA 26
                                  789******9944444431 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0001
                                   -HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC....SEEEEGGGTEEECTTTEEEEE CS
                   Hydrolase_3  17 sektkeaikklkekgikvviATGRslravlpvleelgld....lpvialNGaliddekgkilyk 76 
                                   +e + e+ik+lk++g+ v++ +G    av ++ e+lgld    + +i   G l+ d +g++l++
  gi|15669789|ref|NP_248603.1|  78 TEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDyafaNRLIVKDGKLTGDVEGEVLKE 141
                                   57889**********************************7666666668888886666777665 PP

  == domain 3  score: 44.4 bits;  conditional E-value: 7.6e-15
                                   TT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GG CS
                   Hydrolase_3 184 kgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnn 247
                                   k+  Kg+ l+k+ak  +i+le+++a+GDg NDi+M+++agl +A   a++ +k++Ad  +++ +
  gi|15669789|ref|NP_248603.1| 140 KENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAFC-AKPILKEKADICIEKRD 202
                                   6678****************************************85.999******99888765 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1   6.3e-13   1.4e-09       2     185 ..       7     175 ..       6     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 6.3e-13
               Put_Phosphatase   2 lvvfDFDktiidedsdnwvvdelpatelfeelretlrkgl..wnelmdrvlkelheqgvseadikkvlrsiplspglveli 80 
                                   l++fDFD t++++++ + + +e++ +e+ +++ ++  +g   +++ + + +  l+  +  +++++k++++i+ + g  e i
  gi|15669789|ref|NP_248603.1|   7 LILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKlnFEQSLRKRVSLLK--DLPIEKVEKAIKRITPTEGAEETI 85 
                                   899*****************************99888665114445555555554..47899******************* PP

               Put_Phosphatase  81 kslakkkleldliiiSDaNsffieeileaagledlFseiftNPaavdasGeltvlpyhehsCklcpsNlCKgkvleelvae 161
                                   k+l  k+ ++ + ++S    + +++i e++gl   F++       + ++G+lt       + +   +   Kg++le++ + 
  gi|15669789|ref|NP_248603.1|  86 KEL--KNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFAN----R-LIVKDGKLTGD----VEGEVL-KENAKGEILEKIAKI 154
                                   ***..5679***********************999975....2.34466777632....233333.444699999999888 PP

               Put_Phosphatase 162 qaregveyerliYvGDganDlCpv 185
                                      eg++ e  + vGDganD+   
  gi|15669789|ref|NP_248603.1| 155 ---EGINLEDTVAVGDGANDISMF 175
                                   ...799999999999999998655 PP

>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   5.8e-06     0.013      25      89 ..      83     151 ..      75     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.8e-06
                                   HHHHHHHHHTTEEEEEE--.HHHHHHHHHHTCCCCCHHHC........E..HHHHHHHHHHHHHHHHHHH CS
                     AA_kinase  25 eqiaalkesgnklvvVhGg.gsftdgllalksglssgelaa....glrstleeagevatrdalaslgerl 89 
                                   e i++lk++g+ ++vV+Gg    ++++ ++  gl+  ++++    + ++t + +gev+++ a + + e++
  gi|15669789|ref|NP_248603.1|  83 ETIKELKNRGYVVAVVSGGfDIAVNKIKEK-LGLDYAFANRlivkDGKLTGDVEGEVLKENAKGEILEKI 151
                                   569999999**********55555555555.**************8899999999999997777776665 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.045     1e+02       2      24 ..       5      25 ..       4      97 .. 0.85
   2 ?   10.3   0.0   0.00016      0.36     165     200 ..     143     178 ..     137     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.045
                                  SEEEEE-TBTTTB.S-HHHHHHH CS
                          S6PP  2 klllvsdLDntlvdgdnealarl 24
                                  k+l++ d D+tlv  +ne+++++
  gi|15669789|ref|NP_248603.1|  5 KKLILFDFDSTLV--NNETIDEI 25
                                  68999********..55555554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00016
                                   SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSS CS
                          S6PP 165 skgeAlryLakkleleleqilvcGdsgnDeellign 200
                                    kge l+ +ak  +++le ++ +Gd  nD++++++ 
  gi|15669789|ref|NP_248603.1| 143 AKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKA 178
                                   5888888888888999*****************765 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.9e-05      0.11      11      46 ..     149     183 ..     103     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.9e-05
                                   HHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEE CS
                Hydrolase_like  11 dfalevlgsdpeevlmiGDrlatDiagAnnaGwksv 46 
                                   + +++  g++ e+++++GD  a Di + ++aG+k +
  gi|15669789|ref|NP_248603.1| 149 EKIAKIEGINLEDTVAVGDG-ANDISMFKKAGLKIA 183
                                   3344444899**********.***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1170  (0.0652574); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1197.26
//
Query:       gi|15669790|ref|NP_248604.1|  [L=336]
Description: hypothetical protein MJ_1595 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-52  176.4  24.6    1.3e-51  175.9  24.6    1.1  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.9  24.6   7.3e-56   1.3e-51       2     301 .]      14     319 ..      10     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 175.9 bits;  conditional E-value: 7.3e-56
               LPG_synthase_TM   2 llglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfvnn 82 
                                   +++++++++++a++    +l +++++l++++p +++la++l +l+ ++ ++rW+++++ lg+   + + + ++l+glf+nn
  gi|15669790|ref|NP_248604.1|  14 IISFLFILAIMAYI----GLDKIIKVLINTNPEYVILAFILQILVSVILSARWKFIIKILGYSANFKNIFLLVLMGLFINN 90 
                                   45566666666666....*************************************************************** PP

               LPG_synthase_TM  83 vtPgalg.Gevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaa...vllllalallllavl 159
                                   +tP++ g Ge++ray+l++ e ++ + a+++vvver+ld++++++++l++++++  +     +   + ++++++l+++ ++
  gi|15669790|ref|NP_248604.1|  91 ITPSMRGgGEAFRAYYLSKLEEIPKGLAFSTVVVERVLDTAIFLFFTLFVIGYFVVTGFKYLEyliLSWIFLFSLTAIIIY 171
                                   **********************************************99999988777655555565444444444444455 PP

               LPG_synthase_TM 160 alllllllrrrlarlarvlkrlarllarfarklasakr..........klvlasprrlllafllslliwllealtlylllr 230
                                   +++   ll ++ +++++++ +  + +    + l+s ++          k+     + +++a++ls++ +++++l l+ll+ 
  gi|15669790|ref|NP_248604.1| 172 LIANKGLLIKTVTKISKFICKYCSYNYDETKILQSIEEfynsmkffknKRG----WEVVVAIFLSVMRYIFDILKLWLLFL 248
                                   555556778888888888888888888888777777779999986633444....66************************ PP

               LPG_synthase_TM 231 algvdvslallllillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                   +l + vs+  + +++l+++l g+l+++P+G+G+++ +++l ++++ ++++ a+a++ll+rl++++l+++lG
  gi|15669790|ref|NP_248604.1| 249 SLSYVVSVICVSAVYLITLLSGVLSITPSGFGTADTVMILSFSAFNIPPSVAAAVTLLDRLVSYILPTILG 319
                                   *********999*********************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1510  (0.0842211); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2018.71
//
Query:       gi|15669791|ref|NP_248605.1|  [L=347]
Description: 3-isopropylmalate dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.8e-107  357.8   0.2   6.7e-107  357.6   0.2    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase
     0.0087   15.8   0.4        6.2    6.6   0.0    2.9  3  DnaB_2    Replication initiation and membrane attachment


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.6   0.2  7.4e-111  6.7e-107       1     348 []       3     336 ..       3     336 .. 0.96

  Alignments for each domain:
  == domain 1  score: 357.6 bits;  conditional E-value: 7.4e-111
                                   EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSSSSH CS
                        Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkekevrp 81 
                                   k+ ++egdgiG+ev+++a+k+l+++      e+e+ + ++G + ++++g++lpe+t+e++kead++l+ga+++pk++ev+ 
  gi|15669791|ref|NP_248605.1|   3 KVCVIEGDGIGKEVIPEAIKILNELG-----EFEIIKGEAGLECLKKYGNALPEDTIEKAKEADIILFGAITSPKPGEVQN 78 
                                   689********************999.....89***********************************************9 PP

                                   HH.HHHHHHHHTTEEEEEEEEE-B...CCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEEEEE CS
                        Iso_dh  82 en.gLlaLrkeldlfanlrpvkvf...eklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtklys 158
                                   ++ ++++Lrk++ l+an+rp++ f   + +++   ++  +++++d+vi+Re+t+++Y+g+e+ ++++      a+   +++
  gi|15669791|ref|NP_248605.1|  79 YKsPIITLRKMFHLYANVRPINNFgigQLIGKIADYEFLNAKNIDIVIIRENTEDLYVGRERLENDT------AIAERVIT 153
                                   999*******************997655667777888888999********************9995......9999**** PP

                                   HHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE- CS
                        Iso_dh 159 eeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamqlvkspkqfdVivtk 238
                                   ++++eri+r+afe+A+k+++kkv +++Kanvl+ ++ l+ ++++e+ +    +ie ++ lvDs+am+l+k+p++fdVivt+
  gi|15669791|ref|NP_248605.1| 154 RKGSERIIRFAFEYAIKNNRKKVSCIHKANVLRITDgLFLEVFNEIKK--HYNIEADDYLVDSTAMNLIKHPEKFDVIVTT 232
                                   ************************************999999999988..678**************************** PP

                                   HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT-HHHHHHHHHHHH CS
                        Iso_dh 239 NlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLryslgleeaAdkiekAve 319
                                   N+fGDilSDea+al+G+lGl+pSa++g +  a+fE+vHGsapdiagk++aNp+a+ilS+a++  y +g++e+ d i +Av+
  gi|15669791|ref|NP_248605.1| 233 NMFGDILSDEASALIGGLGLAPSANIG-DDKALFEPVHGSAPDIAGKGIANPMASILSIAMLFDY-IGEKEKGDLIREAVK 311
                                   ***************************.679**********************************.*************** PP

                                   HHHHHTSCCHHHCTTSTCCCHHHHHHHHH CS
                        Iso_dh 320 kvleagivTkDlageaakevstsefgdav 348
                                     l +++vT Dl+g      +t+++gd++
  gi|15669791|ref|NP_248605.1| 312 YCLINKKVTPDLGGDL----KTKDVGDEI 336
                                   **************99....******987 PP

>> DnaB_2  Replication initiation and membrane attachment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.49   4.4e+03      26      40 ..       9      23 ..       6      29 .. 0.77
   2 !    6.2   0.0   0.00098       8.8      30      52 ..     157     179 ..     135     182 .. 0.80
   3 !    6.6   0.0   0.00069       6.2      28      47 ..     300     320 ..     286     347 .] 0.61

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.49
                                  HHHHHHHHHHHHHHH CS
                        DnaB_2 26 dlglspevilllley 40
                                   +g+  evi +++++
  gi|15669791|ref|NP_248605.1|  9 GDGIGKEVIPEAIKI 23
                                  568889999999986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00098
                                   HHHHHHHHHHHHHHHT--SHHHH CS
                        DnaB_2  30 spevilllleyavekgkrnlrYi 52 
                                   s+ +i  ++eya+++++++++ i
  gi|15669791|ref|NP_248605.1| 157 SERIIRFAFEYAIKNNRKKVSCI 179
                                   8899*********9999877766 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.00069
                                   HHHHHHHHHHHHHHH.HHT-- CS
                        DnaB_2  28 glspevilllleyav.ekgkr 47 
                                   +   ++i ++++y++ +k+++
  gi|15669791|ref|NP_248605.1| 300 KEKGDLIREAVKYCLiNKKVT 320
                                   55679*********9444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2283.88
//
Query:       gi|15669792|ref|NP_248606.1|  [L=429]
Description: serine hydroxymethyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-82  277.3   0.0      2e-82  277.0   0.0    1.1  1  SHMT           Serine hydroxymethyltransferase
    1.7e-06   27.5   0.0    4.7e-06   26.0   0.0    1.8  1  Aminotran_1_2  Aminotransferase class I and II
      0.005   15.9   0.0      0.015   14.3   0.0    1.8  2  SelA           L-seryl-tRNA selenium transferase
  ------ inclusion threshold ------
      0.018   14.7   0.1      0.048   13.3   0.0    1.7  2  Thiolase_C     Thiolase, C-terminal domain


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.0   0.0   4.4e-86     2e-82      13     399 .]      15     386 ..       4     386 .. 0.91

  Alignments for each domain:
  == domain 1  score: 277.0 bits;  conditional E-value: 4.4e-86
                                   HHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-STTTEEEE---S CS
                          SHMT  13 kkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldpakwgvnvqpl 93 
                                    k++e  +e+i+liasen+ts av ea  + +  +yaeG+PGkr y Gc+++deve+l+++ +kelfk++    ++nvqp+
  gi|15669792|ref|NP_248606.1|  15 IKQHEWMRESIKLIASENITSLAVREACATDFMHRYAEGLPGKRLYQGCKYIDEVETLCIELSKELFKAE----HANVQPT 91 
                                   4555667899************************************************************....******* PP

                                   SHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHHHHHHHH--SEEE CS
                          SHMT  94 sGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydelekkakefkPkliv 174
                                   sG  anlav+ a  +pgd++++l+++dGGh++h   +            +++++  d+e+  id d++ kk  e kPkli+
  gi|15669792|ref|NP_248606.1|  92 SGVVANLAVFFAETKPGDKLMALSVPDGGHISHWKVSAA-----GIRGLKVINHPFDPEEMNIDADAMVKKILEEKPKLIL 167
                                   *********************************644333.....334578999999************************* PP

                                   EE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCT.SSEEEEESSSTT-S-S-EEEEEC-SEEEEETT CS
                          SHMT 175 aGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfey.advvtttthktlrGprgglillrkgvksvdkt 254
                                    G s ++     a   e a+evga +  d ah+ Gl+a++ + +P++  a+     thkt+ Gp+gg+il+          
  gi|15669792|ref|NP_248606.1| 168 FGGSLFPFPHPVADAYEAAQEVGAKIAYDGAHVLGLIAGKQFQDPLREgAEYLMGSTHKTFFGPQGGVILTT--------- 239
                                   *********************************************964399*******************99......... PP

                                   TEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHTT-EEGG...GS-SSSE CS
                          SHMT 255 gkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealkekgyklvs...gGtdnhl 332
                                        +e ++ki+s vfPg+    + h  a++a+al e le    +y+kqv+knakala+al e+g++++    + t++h 
  gi|15669792|ref|NP_248606.1| 240 -----KENADKIDSHVFPGVVSNHHLHHKAGLAIALAEMLEFG-EAYAKQVIKNAKALAQALYERGFNVLCehkDFTESHQ 314
                                   .....46799**************************9987543.78***********************972224689*** PP

                                   EEEEGGGG...TS-HHHHHHHHHHTTEE-EEE--TTS..STTTT-SEEEEESHHHHHTT--HHHHHHHHHHH CS
                          SHMT 333 vlvdlrek...gldGkraekvlekvnitankntvPgd..ksalvtsGlrlGtpaltsrgfkeedlekvakfi 399
                                   v++d+++    +++ ++  k+ e++ni  nkn +P d  +++  +sG+rlGt  +t+ g+ke+++e++a+f+
  gi|15669792|ref|NP_248606.1| 315 VIIDIESSpdiEFSASELAKMYEEANIILNKNLLPWDdvNNSDNPSGIRLGTQECTRLGMKEKEMEEIAEFM 386
                                   *****8643227778888899***************98778899*************************996 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.1e-09   4.7e-06      38     302 ..      58     305 ..      30     389 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.1e-09
                                   TST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-E...EEEEESS-THHHH..HHHHT CS
                 Aminotran_1_2  38 neygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgde...ilvpdptyasykn..ilrls 113
                                     y+ ++  +e+e+  +++ +  e  k ++  +v+ +sG  a+++++++ +k  pgd+     vpd  + s+ +  ++ ++
  gi|15669792|ref|NP_248606.1|  58 RLYQGCKYIDEVETLCIELSK--ELFKAEHA-NVQPTSGVVANLAVFFAETK--PGDKlmaLSVPDGGHISHWKvsAAGIR 133
                                   578999999999999999999..78888888.**************999999..99993334589999*999652267889 PP

                                   TSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHH.HHHHHHHHHHTTEEEEEEETTTTC CS
                 Aminotran_1_2 114 ggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatlee.leklldlakkynlllfvDeaYagf 193
                                   g++v+  p  ++e++++d++a+ +++ e      k+k+il+       G++++ ++ + + ++ a++ ++ +  D a+  +
  gi|15669792|ref|NP_248606.1| 134 GLKVINHP-FDPEEMNIDADAMVKKILEE-----KPKLILFG------GSLFPFPHpVADAYEAAQEVGAKIAYDGAHVLG 202
                                   99******.66999*********999984.....78*****8......7888877648899999***************** PP

                                   BSSSSHTHHHHGGSTTSTTEEEEEESSSTT.SSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 194 vfgsldavatranveeepnllivgslsKaf.GlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqse 273
                                       +++      + e+ +  ++gs  K f G  G   G il +++ ++ + + + p+ +s++  +  a  + +  ++ ++
  gi|15669792|ref|NP_248606.1| 203 LIAGKQF---QDPLREGAE-YLMGSTHKTFfGPQG---GVILTTKENADKIDSHVFPGVVSNHHLHHKAGLAIALAEMLEF 276
                                   9998887...678889989.89999999877****...**********************87777777766666666777* PP

                                   HHHHHHHHHHHHHHHHHHHHHSTEEEECC CS
                 Aminotran_1_2 274 leemrqrlqkrrkelrdeLaelglkvlas 302
                                    e+ +++++k++k l ++L e g++vl +
  gi|15669792|ref|NP_248606.1| 277 GEAYAKQVIKNAKALAQALYERGFNVLCE 305
                                   ************************99855 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.3e-06     0.015     189     237 ..     202     250 ..     184     292 .. 0.89
   2 ?   -1.9   0.0      0.28   1.3e+03      20      44 ..     397     421 ..     394     423 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.3e-06
                                   T-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHHHHST CS
                          SelA 189 glskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkkelieklkknp 237
                                   gl    ++q+ l+eG++ +  s  k + gpq G+i+  ke  +k++++ 
  gi|15669792|ref|NP_248606.1| 202 GLIAGKQFQDPLREGAEYLMGSTHKTFFGPQGGVILTTKENADKIDSHV 250
                                   66777789*************************************9986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.28
                                   HHHHHHHHHHHHSEBSTTEETTTTE CS
                          SelA  20 eeaveavleaarkysnleydleegk 44 
                                   e+++e+v+e a++ys++ y ++eg+
  gi|15669792|ref|NP_248606.1| 397 EKVREDVKEFAKEYSTIHYSFDEGD 421
                                   789999***************9985 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.9   8.4e+03      15      34 ..     142     161 ..     135     162 .. 0.76
   2 ?   13.3   0.0   1.1e-05     0.048      24      64 ..     252     293 ..     236     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.9
                                   --GGGGGGHHHHHHHHHHHH CS
                    Thiolase_C  15 vdpeilglgPayaikkvlkk 34 
                                    dpe++++     +kk+l++
  gi|15669792|ref|NP_248606.1| 142 FDPEEMNIDADAMVKKILEE 161
                                   68889999888888888875 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHH.HHHT--GGGESEEEE--SBHHHHHHHHHHHT- CS
                    Thiolase_C  24 Payaikkvl.kkagltvedidlfEinEAFaaqaLavakaldl 64 
                                   P  ++++ l +kagl ++  +++E+ EA+a q++++akal  
  gi|15669792|ref|NP_248606.1| 252 PGVVSNHHLhHKAGLAIALAEMLEFGEAYAKQVIKNAKALAQ 293
                                   5555555552689*************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2973.53
//
Query:       gi|15669793|ref|NP_248607.1|  [L=128]
Description: hypothetical protein MJ_1597.1 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 816.09
//
Query:       gi|15669794|ref|NP_248608.1|  [L=350]
Description: hypothetical protein MJ_1598 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-08   32.9   0.2    5.2e-08   32.5   0.2    1.1  1  DBI_PRT   Phosphoribosyltransferase
  ------ inclusion threshold ------
       0.13   12.2   0.3       0.37   10.7   0.3    1.8  1  CsbD      CsbD-like


Domain annotation for each model (and alignments):
>> DBI_PRT  Phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.2   5.8e-12   5.2e-08     115     266 ..     111     258 ..      78     271 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 5.8e-12
                                   SSSSB--TTTS-SS-HHHHHHHHHHHHHHHHHHHCTTECEEEEEEE-TTCHHHHHHHHHHHHT--HHHH---TTT--HHHH CS
                       DBI_PRT 115 vrrgtaniakepAmtreeaeaaleaGieladeladagadllalGemGigNttaaaallaallglepeevvGrGtglddegl 195
                                    +++t++i++++Am++   ++    G  l ++l   +a+ll++Ge   g tt+a  +l   lg ++e  v  G+   ++  
  gi|15669794|ref|NP_248608.1| 111 DEKPTGRIEEGKAMNNS--KELYMKGYLLGKNL---DAELLIVGESVPGGTTTALGVLL-GLGYDAEGKVSSGS--INNPH 183
                                   46789999999999865..45667788777776...789**************987754.45667776665555..66677 PP

                                   HHHHHHHHHHHHCH..-TT..HHHHHHHHS-HHHHHHHHHHHHHHHTT--EEE-SHHHHHHHHHH.HHHSGGGGG CS
                       DBI_PRT 196 arKiavieqalarh..aek.dplevLakvGGleiaalaGailgAaarripvvlDGfistaAalvA.vrlapevkd 266
                                   + Ki+v+++ l+++  +ek + ++vL++vG   + ++aG+ ++ a+r+ pv+l G   ++A+l+  ++++++v d
  gi|15669794|ref|NP_248608.1| 184 ELKIKVVREGLKKAgiNEKsSVFDVLNAVGDKMMPVVAGLAISFAERNKPVILAGGTQMSAVLAViKEINKKVLD 258
                                   889**********977555599********************************999999988651567777766 PP

>> CsbD  CsbD-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   4.2e-05      0.37       2      19 ..     301     318 ..     300     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.2e-05
                          CsbD   2 kikgkaeqvkGkvKeaaG 19 
                                   ki+g ++  kG+vKe++G
  gi|15669794|ref|NP_248608.1| 301 KIEGLKNYCKGSVKEGVG 318
                                   8****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2364.74
//
Query:       gi|15669795|ref|NP_248609.1|  [L=277]
Description: hypothetical protein MJ_1599 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-06   27.0   0.0      6e-06   26.4   0.0    1.4  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
    0.00033   19.9   0.0     0.0012   18.0   0.0    1.7  2  NAD_synthase     NAD synthase
     0.0019   17.9   0.0     0.0033   17.2   0.0    1.4  1  ATP_bind_3       PP-loop family
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.023   14.2   0.0    1.3  1  QueC             Queuosine biosynthesis protein QueC
      0.021   13.7   0.0      0.032   13.0   0.0    1.3  1  tRNA_Me_trans    tRNA methyl transferase
      0.032   13.7   0.0       0.06   12.8   0.0    1.5  1  Diphthami_syn_2  Diphthamide synthase
        0.1   11.9   0.0       0.15   11.3   0.0    1.2  1  Arginosuc_synth  Arginosuccinate synthase


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.3e-09     6e-06       2      93 ..      60     158 ..      59     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.3e-09
                                   EEEE--SSCTCHHHHHHHHHHCTTHE.EEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCH..HHHHHHHHH-S-THHH CS
                   PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvp.vvfvdtghefpetiefvdeleeryglrlkvyepeee..vaekinaekhgsslye 79 
                                   +++++sgGkds+  l+L+ + fk  p  v vd ++  +e ie   +++++y+++l + +++ +  ++++i++ + + +   
  gi|15669795|ref|NP_248609.1|  60 CILAFSGGKDSVLALKLLKEKFKLNPlCVMVDNKYMAKEAIENALNVTKHYQVDLMILNRDYTdlFEDAIKRGESPCRRCS 140
                                   689********************99879***********************999776665433113333333333333333 PP

                                   C....HHHHHHTHHHHHH CS
                   PAPS_reduct  80 e....aaeriaKveplkk 93 
                                   +    ++ r++K+  lk 
  gi|15669795|ref|NP_248609.1| 141 RlilrEVWRVTKLLGLKY 158
                                   344446666666666655 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.6e-07    0.0012       9      80 ..      48     118 ..      40     138 .. 0.80
   2 ?   -1.2   0.0      0.35   8.9e+02     147     174 ..     241     268 ..     226     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.6e-07
                                   HHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE-- CS
                  NAD_synthase   9 lkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktid 80 
                                   l +  k+ g    +l  SGG DS l+ +l ++ + k n l +++ +++  +e +e+al++ ++++++   ++
  gi|15669795|ref|NP_248609.1|  48 LYNLKKEGGKYHCILAFSGGKDSVLALKLLKEKF-KLNPLCVMVDNKYMAKEAIENALNVTKHYQVDLMILN 118
                                   4444445555789*********************.***************************9888766554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.35
                                   SBETTTTS-HHHHHHHHHHTT--HHHHC CS
                  NAD_synthase 147 dlapiaellKtevkeLakelnvPervlk 174
                                    l  ++ l K + k+ +++  vP+++++
  gi|15669795|ref|NP_248609.1| 241 TLVRLGLLSKEKAKKELEKPKVPKEIYE 268
                                   5666778889999999999999999987 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.3e-06    0.0033       2      68 ..      60     121 ..      59     166 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv 68 
                                   +++A+SgG DS++ l+ll+++   ++++  +++vd +  +  ke  e   ++ k+++++l i + d 
  gi|15669795|ref|NP_248609.1|  60 CILAFSGGKDSVLALKLLKEK---FKLNPLCVMVDNKYMA--KEAIENALNVTKHYQVDLMILNRDY 121
                                   689*********999999988...5578889999887663..3344444455666666666666555 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     9e-06     0.023       2      66 ..      60     123 ..      59     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9e-06
                                   EEEE--SSHHHHHHHHHHHHH-SE...EEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGG CS
                          QueC   2 avvllSGGlDSttvlalakkegke...vealtfdYgqrhkkeleaakkiakelgveehkildldllke 66 
                                   +++ +SGG DS  +l l k+++k    + ++  +Y   +k+ +e a +++k+++v +  il+ d +++
  gi|15669795|ref|NP_248609.1|  60 CILAFSGGKDSVLALKLLKEKFKLnplCVMVDNKYM--AKEAIENALNVTKHYQV-DLMILNRD-YTD 123
                                   6899***************99963211444444444..45556678889999998.77777766.444 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.2e-05     0.032       4     124 ..      61     163 ..      58     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                 tRNA_Me_trans   4 vvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfeefle 84 
                                   + a+SgG DS +a+ llke+++    +++           +  a+e +++a +v ++ ++ l +++  ++y +++fe+ + 
  gi|15669795|ref|NP_248609.1|  61 ILAFSGGKDSVLALKLLKEKFKLNPLCVMVDN--------KYMAKEAIENALNVTKHYQVDLMILN--RDY-TDLFEDAI- 129
                                   789*****************987777776433........3467899************9999987..455.46677665. PP

                 tRNA_Me_trans  85 eyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGH 124
                                     ++G+  +P+ +C + i  + + +  k  lg +++ tGH
  gi|15669795|ref|NP_248609.1| 130 --KRGE--SPCRRCSRLILRE-VWRVTK-LLGLKYIITGH 163
                                   ..6787..57*****999655.555555.59********9 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.3e-05      0.06       4      38 ..      61      94 ..      58     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
               Diphthami_syn_2  4 avlysGGkDsilaLykalkesevesLvsvisenke 38
                                  +  +sGGkDs+laL    ++++ + L +v+ +nk 
  gi|15669795|ref|NP_248609.1| 61 ILAFSGGKDSVLALKLLKEKFKLNPL-CVMVDNKY 94
                                  5679**********888888999988.66667764 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.7e-05      0.15       1      49 [.      61     106 ..      61     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.7e-05
               Arginosuc_synth   1 vLaysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalkl 49 
                                   +La+sGG D   ++kllkek + + + v+vd        +e+ e+al++
  gi|15669795|ref|NP_248609.1|  61 ILAFSGGKDSVLALKLLKEKFKLNPLCVMVDNKYM---AKEAIENALNV 106
                                   79*******************99999988885433...33444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1941.68
//
Query:       gi|15669796|ref|NP_248610.1|  [L=177]
Description: hypothetical protein MJ_1600 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-90  302.2  11.1    1.3e-90  302.1  11.1    1.0  1  CarS-like       CDP-archaeol synthase
    0.00019   21.3   3.1    0.00019   21.3   3.1    1.9  2  CTP_transf_1    Cytidylyltransferase family
  ------ inclusion threshold ------
       0.43   10.6   6.4        7.2    6.7   0.1    3.1  4  Gly-zipper_Omp  Glycine zipper
        6.2    6.2   8.1       0.39   10.1   1.4    1.9  2  DUF92           Integral membrane protein DUF92


Domain annotation for each model (and alignments):
>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.1  11.1   2.8e-94   1.3e-90       1     175 []       2     177 .]       2     177 .] 0.99

  Alignments for each domain:
  == domain 1  score: 302.1 bits;  conditional E-value: 2.8e-94
                     CarS-like   1 lldlilksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsi.lalds 80 
                                   +++l+++s++++lpayvanasa+++GGGtpvdlGk+++dGrrliG+GvtyrG+++G+l+G+lvgliqg+l++++i ++ld+
  gi|15669796|ref|NP_248610.1|   2 FYRLLFASLWYILPAYVANASACIFGGGTPVDLGKNFIDGRRLIGNGVTYRGCIFGILCGTLVGLIQGILVDFNIfNSLDF 82 
                                   689************************************************************************9***** PP

                     CarS-like  81 sgsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllaypvkllpieliilivlitlvlhlsa 161
                                   +g+vl++vila++l++Ga++GdavGsfikrrl+ierGkpa++ldqldfv+gal+++y+v+++p+e+ii+i+l+t+++hl++
  gi|15669796|ref|NP_248610.1|  83 YGTVLDHVILAFFLSVGAIVGDAVGSFIKRRLNIERGKPAPLLDQLDFVIGALAFGYIVAPIPYEMIIIICLFTVFVHLLG 163
                                   ********************************************************************************* PP

                     CarS-like 162 niiayklglkdvwy 175
                                   niiayklg+kdvw+
  gi|15669796|ref|NP_248610.1| 164 NIIAYKLGIKDVWW 177
                                   *************9 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   3.1   4.2e-08   0.00019     172     232 ..      50     116 ..      48     142 .. 0.87
   2 ?   -0.3   0.3      0.16   7.2e+02     202     219 ..     146     163 ..     127     174 .. 0.44

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.2e-08
                                   BHHHHHHHHHHHHHHHHHHHHHHHCTS......---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                  CTP_transf_1 172 TveGfigGlvaavvvglllalvlskal......alsllhllllslllslvavfGDLveSglKRafgi 232
                                   T  G i G+++ ++vgl+   ++  +       + ++l  ++l+++ls+ a++GD v S +KR+++i
  gi|15669796|ref|NP_248610.1|  50 TYRGCIFGILCGTLVGLIQGILVDFNIfnsldfYGTVLDHVILAFFLSVGAIVGDAVGSFIKRRLNI 116
                                   7789999999999999998888877667888889******************************988 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.16
                                   TTSHHHHHHHHHHHHHHH CS
                  CTP_transf_1 202 llhllllslllslvavfG 219
                                   + +++++ l++++v  +G
  gi|15669796|ref|NP_248610.1| 146 YEMIIIICLFTVFVHLLG 163
                                   222333333333333333 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0016       7.2      13      41 ..      45      75 ..      43      78 .. 0.75
   2 ?    6.5   0.0    0.0019       8.4      26      38 ..      98     110 ..      97     118 .. 0.60
   3 ?   -2.6   0.3       1.3   5.7e+03       6       8 ..     133     135 ..     131     142 .. 0.45
   4 ?   -3.0   0.0       1.7   7.6e+03      34      42 ..     162     170 ..     161     173 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0016
                Gly-zipper_Omp 13 iGgavg..grgtGaliGAavGaavGgliGaa 41
                                  iG+ v   g   G+l+G+ vG + G l+  +
  gi|15669796|ref|NP_248610.1| 45 IGNGVTyrGCIFGILCGTLVGLIQGILVDFN 75
                                  6666663444689********9999888776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0019
                Gly-zipper_Omp  26 iGAavGaavGgli 38 
                                   +GA+vG avG  i
  gi|15669796|ref|NP_248610.1|  98 VGAIVGDAVGSFI 110
                                   4555555555444 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.3
                Gly-zipper_Omp   6 GAa 8  
                                   GA+
  gi|15669796|ref|NP_248610.1| 133 GAL 135
                                   222 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.7
                Gly-zipper_Omp  34 vGgliGaam 42 
                                   +G++i++++
  gi|15669796|ref|NP_248610.1| 162 LGNIIAYKL 170
                                   688888765 PP

>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.4   8.6e-05      0.39     143     190 ..      48     110 ..      45     118 .. 0.79
   2 ?   -0.4   0.7      0.14   6.3e+02      22      49 ..     132     159 ..     127     169 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.6e-05
                         DUF92 143 gVsllGllasllGalliallavlllllel...............lillltlaGllGsllDSlL 190
                                   gV+  G ++++l ++l++l+  +l+ ++                l+++l + +++G  + S++
  gi|15669796|ref|NP_248610.1|  48 GVTYRGCIFGILCGTLVGLIQGILVDFNIfnsldfygtvldhviLAFFLSVGAIVGDAVGSFI 110
                                   9*****************997666656557778889999998765556666677887777765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.14
                         DUF92  22 laavlvgvlialaplgllffllllvFfl 49 
                                   + a+++g+++a  p+++ ++++l++ f+
  gi|15669796|ref|NP_248610.1| 132 IGALAFGYIVAPIPYEMIIIICLFTVFV 159
                                   5677777777777777555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1350.38
//
Query:       gi|15669797|ref|NP_248611.1|  [L=160]
Description: hypothetical protein MJ_1601 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-12   45.9   2.5    8.9e-12   44.6   0.1    2.5  3  ACT             ACT domain
    8.3e-07   29.5   0.3      3e-06   27.7   0.2    1.9  2  ACT_4           ACT domain
  ------ inclusion threshold ------
      0.018   15.0   2.2      0.042   13.8   2.2    1.6  1  TBPIP           TBPIP/Hop2 winged helix domain
      0.022   15.2   2.2       0.43   11.0   0.1    2.6  3  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
      0.026   14.6   0.1        6.5    6.8   0.0    2.1  2  Rad10           Binding domain of DNA repair protein Ercc1 (r
        0.1   12.6   0.1        9.2    6.3   0.0    2.6  2  ACT_6           ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.1     3e-15   8.9e-12       2      65 ..       3      68 ..       2      70 .. 0.93
   2 ?   -1.4   0.1      0.68     2e+03      40      58 ..      83     101 ..      74     104 .. 0.61
   3 ?    0.1   0.0      0.24   7.3e+02      42      57 ..     124     139 ..     115     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 3e-15
                                  EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT..ECEEEEEEEEEEHHHHHHHHHHHHTT CS
                           ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedk..vagivfvvivvdeedleevlealkkl 65
                                  ++ ++++D+PG L rv++ ++++g N++si +++ e +   ++  +v++v d + l+++le l+k 
  gi|15669797|ref|NP_248611.1|  3 TIDIELKDKPGELLRVLTPISKYGANVISIIHSREEKRggKVPVRIVIDVDDKDKLKKILEDLEKE 68
                                  6889**********************************9999999999999999999999999986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.68
                                   ECEEEEEEEEEEHHHHHHH CS
                           ACT  40 vagivfvvivvdeedleev 58 
                                   + + v++ +vvd+++ +++
  gi|15669797|ref|NP_248611.1|  83 YLDVVVIGHVVDTNVRDTI 101
                                   4455666666666665554 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.24
                                   EEEEEEEEEEHHHHHH CS
                           ACT  42 givfvvivvdeedlee 57 
                                   + +++ i+vde+ +ee
  gi|15669797|ref|NP_248611.1| 124 SSAMMRIIVDEDKIEE 139
                                   6678888888888876 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.2     1e-09     3e-06       7      75 ..       2      71 ..       1      73 [. 0.88
   2 ?   -1.6   0.0       1.4   4.2e+03      45      74 ..     123     152 ..     115     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1e-09
                         ACT_4  7 vrleveaedrkglLaditqviseekanivsvnaktrkk.dglaeikitveVkdvehLsrviakLraipgV 75
                                  +++++e +d++g L ++++ is+ +an+ s+  + ++k  g + ++i + V d ++L+++++ L++   +
  gi|15669797|ref|NP_248611.1|  2 ITIDIELKDKPGELLRVLTPISKYGANVISIIHSREEKrGGKVPVRIVIDVDDKDKLKKILEDLEKEGAI 71
                                  589************************999755554445*************************987666 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                         ACT_4  45 dglaeikitveVkdvehLsrviakLraipg 74 
                                   ++ a ++i v    +e+L  + + L++ +g
  gi|15669797|ref|NP_248611.1| 123 ESSAMMRIIVDEDKIEELFYLFEELEKEKG 152
                                   667778888888888888888888887765 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.2   1.4e-05     0.042      32      60 ..      55      84 ..      53      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                         TBPIP 32 KtavqkaLdeLvdegkiieKeyGKq.kiYl 60
                                  K    k+L+ L++eg ii K  GK  k+Yl
  gi|15669797|ref|NP_248611.1| 55 KDKLKKILEDLEKEGAIIKKIDGKDkKVYL 84
                                  66789*******************989997 PP

>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.3     4e+03      58      74 ..      14      30 ..       4      44 .. 0.73
   2 ?   11.0   0.1   0.00015      0.43      46      75 ..      45      74 ..      15      88 .. 0.82
   3 ?    3.5   0.4     0.031        92       4      66 ..      86     147 ..      80     153 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                                  HHHHHHHHHHHHHHHSC CS
                Saccharop_dh_N 58 vLeeileeltelgaelv 74
                                  +L ++l+ ++++ga+++
  gi|15669797|ref|NP_248611.1| 14 ELLRVLTPISKYGANVI 30
                                  67778888888888876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00015
                                  EEEEEEEESSHHHHHHHHHHHHHHHHHSCC CS
                Saccharop_dh_N 46 yaelevsaedeevLeeileeltelgaelve 75
                                   +++ +  +d+++L++ile+l++ ga +++
  gi|15669797|ref|NP_248611.1| 45 PVRIVIDVDDKDKLKKILEDLEKEGAIIKK 74
                                  5789999******************99874 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.031
                                   EEEEEXXTTSSHHHHHHHHHHHTTXEEEEEEEEXXSSTTSXEEEEEEEEESSHHHHHHHHHHH CS
                Saccharop_dh_N   4 veleGhliDsgilnkvldlileaggsfevlefevGkkkkdtSyaelevsaedeevLeeileel 66 
                                   v + Gh++D+++   ++d+i+e g   ++  +    +k++ ++ ++ v  ++ e+L  ++eel
  gi|15669797|ref|NP_248611.1|  86 VVVIGHVVDTNV-RDTIDRINEIGLVEDLDLIMPHPDKESSAMMRIIVDEDKIEELFYLFEEL 147
                                   667899999986.67889999988655555555445555555556666666666666666665 PP

>> Rad10  Binding domain of DNA repair protein Ercc1 (rad10/Swi10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0034        10      45      88 ..      24      67 ..      13      73 .. 0.85
   2 ?    6.8   0.0    0.0022       6.5      56     110 ..      73     128 ..      67     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0034
                         Rad10 45 kyhklhpeYieerlkklkkkyklrvlLvlvDvedseevlkeLnk 88
                                  ky     + i++r +k + k+ +r+++ + D ++ +++l++L k
  gi|15669797|ref|NP_248611.1| 24 KYGANVISIIHSREEKRGGKVPVRIVIDVDDKDKLKKILEDLEK 67
                                  666666788******************9999999******9987 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0022
                         Rad10  56 erlkklkkk.yklrvlLvlvDvedseevlkeLnkicilndltlllawsaeeaaryl 110
                                   +++    kk y   v++ +v  ++ ++++ ++n+i +++dl l++ +  +e+++++
  gi|15669797|ref|NP_248611.1|  73 KKIDGKDKKvYLDVVVIGHVVDTNVRDTIDRINEIGLVEDLDLIMPHPDKESSAMM 128
                                   5555555442666677777777899*******************999888887665 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0031       9.2      10      64 ..       9      67 ..       4      88 .. 0.80
   2 ?    3.7   0.0      0.02        61      41      72 ..     123     154 ..     111     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0031
                         ACT_6 10 pdrpGltasLtsvlaefgvnilDi...eqavihgrlsLgllvsgp.edalarlekaLlf 64
                                  +d+pG + +++  ++++g+n++ i   +    +g++   ++++++ +d+l++++ +L++
  gi|15669797|ref|NP_248611.1|  9 KDKPGELLRVLTPISKYGANVISIihsREEKRGGKVPVRIVIDVDdKDKLKKILEDLEK 67
                                  599***************99876511155566777888888888844588888888776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.02
                         ACT_6  41 rlsLgllvsgpedalarlekaLlflakelglt 72 
                                   + s ++++ ++ed++++l   +++l ke gl 
  gi|15669797|ref|NP_248611.1| 123 ESSAMMRIIVDEDKIEELFYLFEELEKEKGLL 154
                                   67899*************99999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1041.17
//
Query:       gi|15669798|ref|NP_248612.1|  [L=336]
Description: homoserine dehydrogenase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-56  190.5   2.4    2.3e-56  190.4   0.5    1.9  3  Homoserine_dh    Homoserine dehydrogenase
    3.7e-15   56.6   0.2    1.1e-14   55.1   0.1    1.8  2  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    6.9e-08   32.5   1.3      2e-07   31.0   1.1    2.0  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
     0.0013   19.1   0.6      0.025   14.9   0.6    2.6  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
     0.0043   17.3   0.1     0.0085   16.4   0.1    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
       0.04   14.8   0.3      0.099   13.5   0.3    1.7  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.092   12.6   1.3       0.23   11.3   1.3    1.7  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


Domain annotation for each model (and alignments):
>> Homoserine_dh  Homoserine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.62   1.6e+03      97     129 ..      61     101 ..      18     132 .. 0.60
   2 ?   -2.8   0.0         2   5.1e+03      39      52 ..     129     142 ..     106     146 .. 0.67
   3 !  190.4   0.5     9e-60   2.3e-56       1     173 []     155     328 ..     155     328 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.62
                                   HHH..HHHHHCTTEEEEEEEEE......CEEEEEEEEEETT CS
                 Homoserine_dh  97 aed..ikeakeegkvlklvasa......vearVkpelvpks 129
                                   ++   ik+  e+g+++  + ++      v ++V p  +++ 
  gi|15669798|ref|NP_248612.1|  61 EKTgkIKNYPEKGREMSSIDVIkevdadVVVEVTPSNLETG 101
                                   33233666666677766666666655555566666666653 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2
                                   -HHHHHHHHHHTTS CS
                 Homoserine_dh  39 sfsevlkeaqelGy 52 
                                    ++e+++ea+++G+
  gi|15669798|ref|NP_248612.1| 129 CYKELIEEAKKHGV 142
                                   38888899998886 PP

  == domain 3  score: 190.4 bits;  conditional E-value: 9e-60
                                   --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHHCTTT CS
                 Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarlafgle 81 
                                   Pii+  ke+l+g++i +i+Gilngt+nyilt+me+eg +f+++lkea+elG+ae+Dpt+D+eGlD+a+K++ila+ ++g++
  gi|15669798|ref|NP_248612.1| 155 PIINLAKETLAGNEILSIRGILNGTTNYILTKMEKEGLDFETALKEAKELGIAETDPTQDIEGLDTAAKIVILANSIMGMN 235
                                   9******************************************************************************** PP

                                   --GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEE..CEEEEEEEEEETTSGGGHSSST-EEEEEEESSSEEEEEEES-SS CS
                 Homoserine_dh  82 veledvevegiskltaedikeakeegkvlklvasa..vearVkpelvpkshplasvkgsenavlvetdrlgelviqGpgaG 160
                                    +++dv+v+gis++t+e +  a+++g+++kl++++    + V+p+lvp ++pl  vkg+ n+ ++etd ++e+v+ G+gaG
  gi|15669798|ref|NP_248612.1| 236 KTIKDVKVKGISRITPEALFLANKRGYTIKLIGQIkdGYLIVEPMLVPIDSPLN-VKGTLNVAMFETDLAKEVVVVGRGAG 315
                                   **********************************7663699***********96.************************** PP

                                   HHHHHHHHHHHHH CS
                 Homoserine_dh 161 aepTAsavlsDll 173
                                   + +TAsa+lsDl+
  gi|15669798|ref|NP_248612.1| 316 PIETASAILSDLI 328
                                   ***********97 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.1   4.3e-18   1.1e-14       1     117 []       7     147 ..       7     147 .. 0.90
   2 ?   -1.6   0.0       1.6   4.1e+03      36      95 ..     200     257 ..     193     271 .. 0.66

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 4.3e-18
                                   --SHHHHHHHHHHHH---S.....SEEEEEEEEESS.EEE-TT................HHHHHT--CB---HHHHHHHHS CS
                 NAD_binding_3   1 GlGaiGsavleqlkrqqse.....ielelvavadrd.sllskd................rkallasealtldlddliahld 59 
                                   G+GaiG+++++ l +++++      e+++va++d++  ++++d                +k+  ++ ++++++d  i+++d
  gi|15669798|ref|NP_248612.1|   7 GFGAIGKGIAKVLYDKKDYlkknyEEFKVVAITDSSgAAIDEDgldllkaievkektgkIKNYPEKGREMSSIDV-IKEVD 86 
                                   99*********************99***********9999999**********9999987777778888888877.6669* PP

                                   -EEEEE-S--HH.....HHTTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                 NAD_binding_3  60 pdvvVEcassea.....vaelvlkaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                                   +dvvVE+++s+      ++ ++l+  k++k+vvtankg la    y+eL+e+a+++g+ +++e
  gi|15669798|ref|NP_248612.1|  87 ADVVVEVTPSNLetgdpAKTHILESFKNKKHVVTANKGPLA--LCYKELIEEAKKHGVIFRHE 147
                                   *********98544444999*********************..9*************988775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                                   TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHHHTTEEEE-S--CGGG CS
                 NAD_binding_3  36 kdrkallasealtldlddliahldpdvvVEcasseavaelvlkaLkagkdvvtankgala 95 
                                   ++++   a+++ t+d++ l +  ++++v+ + s   + +++ ++  +g++ +t+    la
  gi|15669798|ref|NP_248612.1| 200 EAKELGIAETDPTQDIEGLDT--AAKIVILANSIMGMNKTIKDVKVKGISRITPEALFLA 257
                                   555566777778888888777..6777776666666666666666666666666655555 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   1.1   7.6e-11     2e-07      36     119 ..       4      92 ..       1     152 [. 0.74

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 7.6e-11
                                   EEE--SHHHHHHHHHHHHCT-.........EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHHSTSTSEEESHHS CS
                 ELFV_dehydrog  36 aisGsGnvgsyaallltelga.........kvvavsDssGviydpeGldieellelkeerksvkeykkssekkaeyienee 107
                                   +i G+G +g+  a+ l ++           kvva+ DssG+ +d++Gld+ + +e+ke+++++k+y+++   + e+ +  +
  gi|15669798|ref|NP_248612.1|   4 IIVGFGAIGKGIAKVLYDKKDylkknyeefKVVAITDSSGAAIDEDGLDLLKAIEVKEKTGKIKNYPEK---GREMSSI-D 80 
                                   6777788877777776654322222223339************************************53...2344444.3 PP

                                   HHHHSS-SEEEE CS
                 ELFV_dehydrog 108 ellelkvdilvP 119
                                    + e+++d++v 
  gi|15669798|ref|NP_248612.1|  81 VIKEVDADVVVE 92 
                                   688889999875 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.6   9.8e-06     0.025       1      35 [.       1      43 [.       1     100 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.8e-06
                                  CEEEEESTSHHHHHHHHHHH........HHTTCEEEEEE-TS- CS
                       Gp_dh_N  1 vkvainGfGRIGrlvlrall........eekelevvaindltd 35
                                  +++ i GfG IG+ ++++l+        + +e++vvai d+  
  gi|15669798|ref|NP_248612.1|  1 MDIIIVGFGAIGKGIAKVLYdkkdylkkNYEEFKVVAITDSSG 43
                                  6899****************99999974445999***999543 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.3e-06    0.0085       1      61 [.       3      71 ..       3     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.3e-06
                                  EEEE--SHHHHHHHHHHHCTCCT-G....EEEEEESSHHHHHHHHCHH....TTTCEEEEE--TTTHHH CS
               Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvda....eitvadrskeklealaaka....lgvrfeaialdaenyea 61
                                  ++i+G+G++G+++a++l +++d+ +    e+ v+  ++++ +a+ ++     + ++++ ++  ++ny++
  gi|15669798|ref|NP_248612.1|  3 IIIVGFGAIGKGIAKVLYDKKDYLKknyeEFKVVAITDSSGAAIDEDGldllKAIEVKEKTGKIKNYPE 71
                                  89*********************9999999999999999988887766777866666666666666655 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   3.9e-05     0.099       2      97 ..       2     128 ..       1     148 [. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-05
                                   EEEEETTSHHHHHHHHHHHHTTTTE.......EEEEEECSSHHHHHHH...........HHHTTHEEESS......HHHHH CS
                  GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrle.......evvalldpdaeraeav...........aesfgveaysd......leell 58 
                                    + i+G+G ig+  ++ l ++++ +       +vva+ d++ ++ ++             ++ +++ y +        ++ 
  gi|15669798|ref|NP_248612.1|   2 DIIIVGFGAIGKGIAKVLYDKKDYLkknyeefKVVAITDSSGAAIDEDgldllkaievkEKTGKIKNYPEkgremsSIDVI 82 
                                   578************99999977669**************99998876777766666555555555666687665433455 PP

                                   TCTTESEEEE-S-G.....GGHHHHHHHHHHTT-EEEE.ES.SS-S CS
                  GFO_IDH_MocA  59 adpeidavivatpn.....gtheelakaaleagkhvll.EK.Plat 97 
                                   ++ ++d+v+ +tp+     +  + ++++ ++++khv+   K Pla+
  gi|15669798|ref|NP_248612.1|  83 KEVDADVVVEVTPSnletgDPAKTHILESFKNKKHVVTaNKgPLAL 128
                                   5458899999999988544446666666666666998622346654 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.3   8.8e-05      0.23       2      92 ..       3     100 ..       2     140 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.8e-05
                                   EEEE--SCCHHHHHHHHHHTT......-E....EEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES- CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasag......le....Vvlvdiseealekalekieksleklvekgklkeeeveaalarisfttd 72 
                                   + ++G G +G+gia+v+  ++      +e    V ++d s +a+++    + k +e  ++ gk+k  +  +   ++s   d
  gi|15669798|ref|NP_248612.1|   3 IIIVGFGAIGKGIAKVLYDKKdylkknYEefkvVAITDSSGAAIDEDGLDLLKAIEVKEKTGKIK--NYPEKGREMSSI-D 80 
                                   679*************9765322222222333355667777777777666777788888888888..222333333333.3 PP

                                   HHHHHC-SEEEE-S-SSHHH CS
                       3HCDH_N  73 leeavdadlviEavvEnlel 92 
                                   + + vdad+v+E  + nle 
  gi|15669798|ref|NP_248612.1|  81 VIKEVDADVVVEVTPSNLET 100
                                   444459******99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2103.40
//
Query:       gi|15669799|ref|NP_248613.1|  [L=226]
Description: ribose-5-phosphate isomerase A [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-61  207.5   0.5    1.3e-61  207.2   0.5    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    1.1e-10   41.6   0.1    1.2e-06   28.5   0.0    2.3  2  DeoRC           DeoR C terminal sensor domain


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.2   0.5   1.5e-65   1.3e-61       2     173 .]      52     220 ..      51     220 .. 0.96

  Alignments for each domain:
  == domain 1  score: 207.2 bits;  conditional E-value: 1.5e-65
                                   EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEET.TS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESSTT. CS
                Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevde.dlnliKGgGgallrEKivaaaakkfiviadesKlveklg. 80 
                                   g+ptS+++++la +++ipl++lde+ ++d+a+DGaDev+e +l liKGgGg++++EKiv+++a++f+v++desKlv+klg 
  gi|15669799|ref|NP_248613.1|  52 GIPTSFEAKMLAMQYEIPLVTLDEY-DVDIAFDGADEVEEtTLFLIKGGGGCHTQEKIVDYNANEFVVLVDESKLVKKLGe 131
                                   79***********************.8************9899*************************************7 PP

                                   SS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEEESEE-S CS
                Rib_5-P_isom_A  81 kfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVvetGlFlg 161
                                   kfp+PveV+p a++ v+r+l++ +gg++++R +++k gpv+Tdngn+i+Dv +  +i+d+ eleke+++ipGVve+G+F++
  gi|15669799|ref|NP_248613.1| 132 KFPIPVEVIPSAYRVVIRALSE-MGGEAVIRLGDRKRGPVITDNGNMIIDVFM--NIDDAIELEKEINNIPGVVENGIFTK 209
                                   7*******************96.5***************************99..578**********************8 PP

                                   --SEEEEEETTC CS
                Rib_5-P_isom_A 162 ladkvlvgkedg 173
                                   + dkvlvg+++g
  gi|15669799|ref|NP_248613.1| 210 V-DKVLVGTKKG 220
                                   7.99****9986 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.4e-10   1.2e-06       2      46 ..       3      50 ..       2      53 .. 0.87
   2 !   11.8   0.0   1.9e-05      0.17      62     142 ..      47     128 ..      43     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.4e-10
                         DeoRC  2 naeeKrrIAkaAaeliedgdtifldaGtTtlelaraLaekk...nltv 46
                                  n + K ++Ak+A++l++dg++i l++G+T+++++r+L ++    +ltv
  gi|15669799|ref|NP_248613.1|  3 NEDLKLKVAKEAVKLVKDGMVIGLGTGSTAALFIRELGNRIreeELTV 50
                                  67889********************************98754446666 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.9e-05
                         DeoRC  62 dikvillGGevrkkseslvgplaeealrqfnvdkaflgangidaegglttsdeeeaevkralie.aarrvillaDssKfgk 141
                                   + +v+ +  ++++k  ++  +  + +l+++ vd+af ga+ +++ + ++ +      +++++++ +a++ ++l+D+sK+ k
  gi|15669799|ref|NP_248613.1|  47 ELTVFGIPTSFEAKMLAMQYEIPLVTLDEYDVDIAFDGADEVEETTLFLIKGGGGCHTQEKIVDyNANEFVVLVDESKLVK 127
                                   56666777777777788888888889******************9999999999999999999769************976 PP

                         DeoRC 142 r 142
                                   +
  gi|15669799|ref|NP_248613.1| 128 K 128
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:01.00
# Mc/sec: 684.74
//
Query:       gi|15669800|ref|NP_248614.1|  [L=462]
Description: ADP-specific phosphofructokinase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   2.3e-115  385.6   0.6   2.6e-115  385.4   0.6    1.0  1  ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase cons
  ------ inclusion threshold ------
      0.021   15.2   0.4       0.18   12.2   0.2    2.4  2  DUF1548     Domain of Unknown Function (DUF1548)
        2.5    8.7   6.1       0.67   10.6   0.2    2.9  3  Com_YlbF    Control of competence regulator ComK, YlbF/YmcA


Domain annotation for each model (and alignments):
>> ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.4   0.6  4.4e-119  2.6e-115       2     424 .]      18     451 ..      17     451 .. 0.95

  Alignments for each domain:
  == domain 1  score: 385.4 bits;  conditional E-value: 4.4e-119
                                   EEEEES--EEEEE.....HHHHHHHHCC-HH.HHHHHHC--SSBSSHHHHHHHHHHHHHHT--EEEEB-.-HHHHHHHH.. CS
                    ADP_PFK_GK   2 kvavGynanvDai.....vdavelleklgleevkekseedhdeikskedlletfayffkkGaaaErfve.nkelfeelvka 76 
                                   k++++yn+nvDai     +d+++l+++++ ++++e++ee+++ i+++ d+++++++++k+G++aE++++ +k+l+e++ + 
  gi|15669800|ref|NP_248614.1|  18 KLFTAYNTNVDAIkylkdEDVQKLVDEFNHKDIIERMEEYPRIIEEPLDFVARLVHSIKTGKPAEVPIKdDKKLHEWFDR- 97 
                                   689*****************************************************************978899999995. PP

                                   ..CC--SEEEEESHHHHHHHHHCCTT-.EEEEE-.---HHHHTTS-SS.......EE....EEEEGGG-S-..---EEEEE CS
                    ADP_PFK_GK  77 akklkkaelrmGGnagimanrlakega.kvllga.klskklkellsek.......iv....vlgkpseaske.kdeiHlIl 143
                                      +k++e+rmGG+agi++n++a++++ k+++++  lskk++e++ +        ++    vl+k +ea+++   +i++I+
  gi|15669800|ref|NP_248614.1|  98 ---IKYDEERMGGQAGIVSNLMATLQIdKIIVYTpFLSKKQAEMFVDYdnllyplVEngnlVLKKVREAYRDdPIKINRIF 175
                                   ...*********************************************777776522677799*******997669***** PP

                                   EE-TT-EE...TE.EE-SS-EEEEEE--STCGGTS--HHHCTTHHHHH..-SEEEE--GGG--TB-TTSTCHHHHHHHHHH CS
                    ADP_PFK_GK 144 Eykkgekw...ge.ieapraNRfIissdpenlrlsileefkealkefk..pdllvlsGlqmleeqykegkereerlekvke 218
                                   E+kkg k+   ge i+a++++RfI++s+pe lr++i++++++ l++++  +d++ lsG+q+++e+y++gk+ ++++e+++e
  gi|15669800|ref|NP_248614.1| 176 EFKKGLKFklnGEeITAKQSTRFIVASRPEALRIEIKDDVRKFLPKIGeaVDCAFLSGYQAIKEEYRDGKTAKYYFERAEE 256
                                   ***********667*********************************99******************************** PP

                                   HHHHHC.C.T-EEEEE----S-HHHHHHHHHHCGGG-SEEEE-HHHHHHHHHHTT-HHHCCSS...CC--HHHHHHHHHHH CS
                    ADP_PFK_GK 219 qlkslk.n.kikiHlElAsfqdeellkeilekilpyvdslGlnEqElanllsvlggeekeltevsdkepriakvlealrkl 297
                                   ++k lk n +ik+HlE+As+++ e++k ++++il+ v+s+G++E+E+an+l++lg+ e + + +  k++ i++v+e+++ l
  gi|15669800|ref|NP_248614.1| 257 DIKLLKkNkNIKTHLEFASISNIEIRKMVVDYILSNVESVGMDETEIANVLHILGYDELSNNIL--KDSFIEDVIEGAKIL 335
                                   ******967*********************************************9844333233..6799*********** PP

                                   HH.....HHTT-SEEEEEETTEEEEEEETTSSS-HHHHHHHHHHHHHHHHHHHHH...-SHHHHHHHH..........HS- CS
                    ADP_PFK_GK 298 lkllkkskkrkltrihvHtlayqiiltkkesewkneaakkalakaallAarkacn...sdleklelklddsfsvskskkip 375
                                   l+     k ++l+ ++vHt++y+++++++++++++e+ ++ l+++++lA++ka+    + +++l+ +l          kip
  gi|15669800|ref|NP_248614.1| 336 LD-----KFKNLEVVQVHTIYYILFVCRADNPLSKEELEECLEFSTILASTKAKLgniRAIDDLHEGL----------KIP 401
                                   **.....999*********************************************754499*******..........*** PP

                                   B-TT.HHHHHHHHCCEETTEEEEEEE-B--SS-S--TTHHHHHHHHHHHH CS
                    ADP_PFK_GK 376 lnek.epvscweeeieleevevclaPvlvckkpkkTvGlGDtISaaglvl 424
                                   +n++ + +++++e+ + ++++++l P+++++kpk+TvGlGDtIS++++v+
  gi|15669800|ref|NP_248614.1| 402 HNKYgDLLKEIAEKFNDNNYKIALSPSRYVEKPKSTVGLGDTISSGAFVY 451
                                   ************************************************97 PP

>> DUF1548  Domain of Unknown Function (DUF1548)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   2.9e-05      0.18      71     117 ..     269     315 ..     238     325 .. 0.86
   2 ?    0.0   0.0      0.17     1e+03      92     120 ..     391     423 ..     364     430 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                       DUF1548  71 yileqilessqelkaalsnylledleainlPEteradilsevFyden 117
                                     le ++ s+ e+++ + +y+l+++e +++ Ete+a++l  + yde 
  gi|15669800|ref|NP_248614.1| 269 THLEFASISNIEIRKMVVDYILSNVESVGMDETEIANVLHILGYDEL 315
                                   555566778999****************************9999985 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.17
                       DUF1548  92 ledl.eainlPEteradilsev...Fydenyel 120
                                   ++dl e +++P ++  d+l+e+   F d+ny++
  gi|15669800|ref|NP_248614.1| 391 IDDLhEGLKIPHNKYGDLLKEIaekFNDNNYKI 423
                                   567768899999999999988744355666876 PP

>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00011      0.67       5      46 ..       7      50 ..       4      76 .. 0.84
   2 ?   -2.4   0.0       1.2   7.2e+03      22      62 ..     158     194 ..     157     216 .. 0.71
   3 ?   -0.6   0.3      0.34     2e+03      16      46 ..     239     269 ..     231     288 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                  HHHHHHHHHHSHHHHHHHHHHHHHH..CSHHHHHHHHHHHHHHH CS
                      Com_YlbF  5 areLaeaIkeseeykeykeaeeale..edeelqklikefkklqk 46
                                  +++ +e Ik ++ +++y+   +a++  +de++qkl++ef+++  
  gi|15669800|ref|NP_248614.1|  7 IKKFIETIKGTKLFTAYNTNVDAIKylKDEDVQKLVDEFNHKDI 50
                                  688999***************9996559***********99855 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                                   HHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTT----HHH CS
                      Com_YlbF  22 keaeealeedeelqklikefkklqkelqekqmkgeelkeee 62 
                                   k+ +ea + d+   + i efkk  k    ++ +gee++ ++
  gi|15669800|ref|NP_248614.1| 158 KKVREAYRDDPIKINRIFEFKKGLK----FKLNGEEITAKQ 194
                                   7778888888888888888866444....444555555554 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.34
                                   HHHHHHHHHHHHHHCSHHHHHHHHHHHHHHH CS
                      Com_YlbF  16 eeykeykeaeealeedeelqklikefkklqk 46 
                                   eey++ k a+  +e  ee  kl+k+ k+++ 
  gi|15669800|ref|NP_248614.1| 239 EEYRDGKTAKYYFERAEEDIKLLKKNKNIKT 269
                                   5555555555555555555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2914.07
//
Query:       gi|15669801|ref|NP_248615.1|  [L=401]
Description: glucose-6-phosphate isomerase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-33  115.7   0.3      2e-31  109.1   0.3    2.1  1  PGI       Phosphoglucose isomerase


Domain annotation for each model (and alignments):
>> PGI  Phosphoglucose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.1   0.3   1.1e-35     2e-31      97     464 ..      62     397 ..      53     401 .] 0.84

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 1.1e-35
                                   -EEEEE--GGGTHHHHHHHHHTGGG-TT-EEEEE--SSHHHHHHHHTT--GGGEEEEEE-SSS--HHHHHHHHHHHHHHHH CS
                           PGI  97 tdvvniGiGGsdlGPvlvtealkkeserlkvafvsnvdgthiaevlkkldpettlfivasktfttaetllnaesakewllk 177
                                   ++vv iG+GGs lG + +  a+ +++++    f+ n d+ +   +lkk+d +++++ ++sk   t etl+n   +k+ + k
  gi|15669801|ref|NP_248615.1|  62 ENVVVIGMGGSILGTMAIYYAISPFNNNA--YFIDNSDPEKTLSILKKVDLNESIIYIISKSGNTLETLVNYYLIKKRIEK 140
                                   79***********************9987..9***************************************9999988877 PP

                                   HH--GGGGGGTEEEESS-HHHHHHHT--GGGEEE--TTS-GGG-TTSGGGHHHHHHH-HHHHHHHHHHHHHHHHHHHHS-G CS
                           PGI 178 alkedsavakhfvalstnaekveefGideknmfefwdwvGGryslwsaiGlsvalsiGfenfeelleGaaaidkhfleapl 258
                                    +      ++++v ++   +  +e   ++ ++f+  + v Gr+s+++a+Gl+   s+G + + ++leGa+++dk  ++  +
  gi|15669801|ref|NP_248615.1| 141 LNS----FKGKLVFITNGGKLKREAEKNNYDIFSIPENVPGRFSVFTAVGLAPLYSLGVD-ISKILEGAREMDKICQNEDI 216
                                   665....6779999988888889999999*****************************98.589***************** PP

                                   GG-HHHHHHHHHHHHHHTS---EEEEEES-GGGTTHHHHHHHHHHHHH---BBTTS-B-SS--S-EEE---TTTGGGTSHH CS
                           PGI 259 ekniPvllalvgvwyvnflgaeteailpydqylerlaaylqqldmesnGksvtkdgvlvdvetgeiifGeagtngqhafyq 339
                                    kn  +l +++   y + +g +   i++y + l+ +  + +ql  es Gk+   +g               g++ qh++ q
  gi|15669801|ref|NP_248615.1| 217 LKNPALLNGVIHYLY-DKRGKDISVIMSYVESLKYFGDWYKQLIGESLGKNK--HGI--------TPLLSIGAKDQHSLLQ 286
                                   ***888888887665.679******************************963..332........2233568899****** PP

                                   HHHHSSS---EEEEEEEE-S-GGGGHHHHHHHHHHHHHHHHHHH-B-HHHHHHHHHHTHHHHHGGGG-B-----EEEEEEE CS
                           PGI 340 lihqGtkliPcdfiaavksqnieiadhhkillsnffaqtealmvGkseeevkkelakakveklvphktfeGnrPsnsille 420
                                   l   G k   + f++a k +  e  +        f    +  ++ + ++ ++++++++   +l      +   P   i l+
  gi|15669801|ref|NP_248615.1| 287 LYMDGKKDKIITFMVAKKYRLDEEIE--------FEDINDEKISCRYSDIIRSQQKAT-EIAL-----TNNGVPNVRITLD 353
                                   *****998888888876655422222........222244455666666666644333.2222.....23457******** PP

                                   E--HHHHHHHHHHHHHHHHHHHHHHTB-TT--GGGHHHHHHHHH CS
                           PGI 421 kltpaelGalialyehkilvqGviwginsfdqwGvelGkelakk 464
                                   +++ +++Gal+ +ye ++   G +++in+++q  ve  k++  +
  gi|15669801|ref|NP_248615.1| 354 EINEMAMGALLYMYEMQVGFMGELYNINAYNQPAVEEEKKICWR 397
                                   ************************************99988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2695.66
//
Query:       gi|15669802|ref|NP_248616.1|  [L=521]
Description: glycogen synthase GlgA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-31  107.3   0.0    2.2e-30  106.2   0.0    1.6  1  Glyco_transf_5   Starch synthase catalytic domain
    1.6e-19   70.1   0.0    3.9e-19   68.8   0.0    1.6  1  Glycos_transf_1  Glycosyl transferases group 1
    7.6e-16   58.8   0.0    1.4e-15   57.9   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    6.9e-07   29.4   0.0    2.4e-06   27.6   0.0    2.0  1  Glyco_transf_4   Glycosyltransferase Family 4
     0.0074   16.7   0.0      0.012   16.1   0.0    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.0   6.1e-34   2.2e-30       1     233 [.       2     193 ..       2     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 6.1e-34
                Glyco_transf_5   1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPry..gaikeekkeleevaelskaaedevevevekvkvakl 79 
                                   ki+++a+ ++p++  GGL+dv+++Lpk L+k g++v v++ ++  + ++  ++++++++ ++k a  +      +++v ++
  gi|15669802|ref|NP_248616.1|   2 KIVILAPTITPIVSYGGLGDVMRDLPKFLKK-GNEVVVLTLNHynRYFTLPYEDIKKITVIYKGA--K-----ITFDVLRT 74 
                                   89***************************77.788888887773333444336666666665544..3.....35566666 PP

                Glyco_transf_5  80 kk..dgvdvyfldnpeffdreglYgdkgedyednaerfalfsraalelleklgwkpdvihahDWhtalvpallkelykerg 158
                                   k+  +gvd+++++n+++ +  +++         +  ++ +f+  ++++l ++    dv+  hDW+++l+ a  +++     
  gi|15669802|ref|NP_248616.1|  75 KHptTGVDLIVFSNESVNN-LNVW---------DPIKYEIFADLVITYLDEV-KDIDVVSGHDWMCGLAIAKCNDIL---- 140
                                   66658***********654.3577.........89****************5.469*************88888874.... PP

                Glyco_transf_5 159 lfkkiktvftiHNlayqgrfpkdelaalglpaedfekldglefygkvnflkagivyadavttVSptyakEiltpe 233
                                      + +t +tiHN a++g + + +                    + + fl+ gi+yadav+tVSp++a+Ei +  
  gi|15669802|ref|NP_248616.1| 141 ---DLPTTLTIHNEAFKGEMIEYKG-------------------EVMTFLELGIKYADAVNTVSPSHAEEIKNYP 193
                                   ...5*************99974221...................2789***********************9865 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.0   1.1e-22   3.9e-19      15     146 ..     297     438 ..     292     454 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 1.1e-22
                                   -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHC.ES CS
               Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellkn.ad 94 
                                    ++i +vgr +++Kg++++ +a+++l ++ + +++++  G+ + e++lk+la e+  +    ++g++    l +l  + +d
  gi|15669802|ref|NP_248616.1| 297 TPLIGFVGRATHQKGFNTMFEAIPELLEKHDIRFVFLTKGDRDIEERLKNLANEHDGRIL-ALIGYSL--PLSSLVFAgSD 374
                                   6899***********************9988999999999***************99554.4555554..366665555** PP

                                   EEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT............SEEEE-TT-HH CS
               Glycos_transf_1  95 ifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdge............tGllvkpnnae 146
                                    +++ps++E+ G+v +EAma+ +pvia+ +gg+++++ + +            tG+l+k ++  
  gi|15669802|ref|NP_248616.1| 375 WIIMPSYWEPCGLVQMEAMAYCTPVIATETGGLKDTIIPLHpnpyehpnfdkaTGVLFKVPDKV 438
                                   **************************************99988888999999999998888665 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0     4e-19   1.4e-15       2     109 ..     298     411 ..     297     448 .. 0.80

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 4e-19
                                   EEEEEES---GG.GTHHHHHHHHHHHH.H.HEEEEEES---....HHHHHHHTT-T.T.EEEE---.THHHHHHHH-SEEE CS
               Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.dvrlvivGdgprp..eeleelaagleer.veftGfv.edlaellaaadvfv 77 
                                   p i+fvGr + ++kg+  + ea+p+l++k d+r+v+  +g+r+  e+l++la++ + r   + G+  +  + ++a +d  +
  gi|15669802|ref|NP_248616.1| 298 PLIGFVGRAT-HQKGFNTMFEAIPELLEKhDIRFVFLTKGDRDieERLKNLANEHDGRiLALIGYSlPLSSLVFAGSDWII 377
                                   789******5.56**********99998856998888888633336777766654455788999995556667******** PP

                                   E--..---SHHHHHHHHTT-EEEE-TGGGTTT-- CS
               Glyco_trans_1_4  78 aPs..egfglkllEamaaglpvVatdvggiaevv 109
                                   +Ps  e +gl+ +Eama+ +pv+at++gg+++++
  gi|15669802|ref|NP_248616.1| 378 MPSywEPCGLVQMEAMAYCTPVIATETGGLKDTI 411
                                   *****************************99976 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   6.8e-10   2.4e-06       2     169 ..      17     214 ..      16     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 6.8e-10
                Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev...............................elvvrvprvplpll 51 
                                   GG + ++++L + L  +G eV+v+t ++  +    +                                 v + ++v+ ++ 
  gi|15669802|ref|NP_248616.1|  17 GGLGDVMRDLPKFLK-KGNEVVVLTLNHYNRYFTLPyedikkitviykgakitfdvlrtkhpttgvdLIVFSNESVNNLNV 96 
                                   677777777777666.56888888777666555555555778888888888888888887777776666666666777777 PP

                Glyco_transf_4  52 krllrslaflrrlrrllkre.kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrl. 130
                                   +++ ++  f+  +   l++  ++Dvv  h+++++ +a +++   l++p+ lt+H+ +       +++    +  +++ +l 
  gi|15669802|ref|NP_248616.1|  97 WDPIKYEIFADLVITYLDEVkDIDVVSGHDWMCG-LAIAKCNDILDLPTTLTIHNEA-------FKGEMIEYKGEVMTFLe 169
                                   777777777888888888889*********8886.55566666**************.......34444444444444445 PP

                Glyco_transf_4 131 ..lrradrviavSeatadelreryg.....vppekitVipnGvDle 169
                                     ++ ad+v +vS++ a+e++  y+     +++++   i nG+D++
  gi|15669802|ref|NP_248616.1| 170 lgIKYADAVNTVSPSHAEEIKN-YPyikkyLNNKPFCGILNGIDID 214
                                   559*******************.99878877779999999999998 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.3e-06     0.012      19     145 ..      34     190 ..      17     194 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-06
               Glyco_trans_4_4  19 heVtvltpapapgape...leedgvrvh......rlpvprrpspladlaal..................ralrrll...rq 69 
                                    eV+vlt + +++ +    ++  +++v+       ++v r+ +p++ ++ +                    +++l+     
  gi|15669802|ref|NP_248616.1|  34 NEVVVLTLNHYNRYFTlpyEDIKKITVIykgakiTFDVLRTKHPTTGVDLIvfsnesvnnlnvwdpikyEIFADLVityLD 114
                                   666666665555533311122333333333333344455554444444444444555555444444444455666666656 PP

               Glyco_trans_4_4  70 rrerpdvvhahsptaglaarlarrrrgiplvvtlhglllrrg.sgavrrlyralerrllrradavlvvseaeaeelr 145
                                   +   +dvv  h+++ gla++      ++p  +t+h+ ++ ++    ++ +++ +  + ++ adav +vs+++aee+ 
  gi|15669802|ref|NP_248616.1| 115 EVKDIDVVSGHDWMCGLAIAKCNDILDLPTTLTIHNEAFKGEmIEYKGEVMT-FLELGIKYADAVNTVSPSHAEEIK 190
                                   8899************9887777678************99885555666665.5579*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.24s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 3685.65
//
Query:       gi|15669803|ref|NP_248617.1|  [L=390]
Description: LPS biosynthesis protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-53  179.3   0.0    7.4e-53  178.6   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
      9e-38  129.7   0.0    1.4e-37  129.1   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    3.2e-32  111.9   0.1    6.9e-30  104.3   0.0    2.8  3  Glyco_transf_4   Glycosyltransferase Family 4
    1.7e-26   93.4   0.9    1.2e-13   51.3   0.2    2.4  2  Glyco_transf_5   Starch synthase catalytic domain
    3.8e-22   79.4   0.0      1e-19   71.5   0.0    2.8  3  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    3.2e-12   46.7   0.3    5.9e-11   42.6   0.0    2.2  2  Glyco_trans_4_2  Glycosyl transferase 4-like
    9.9e-10   38.7   0.0    2.4e-09   37.5   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
     0.0005   18.9   0.0      0.083   11.5   0.0    2.6  3  Glyco_transf_20  Glycosyltransferase family 20


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.6   0.0   3.3e-56   7.4e-53       4     171 ..     197     362 ..     194     363 .. 0.97

  Alignments for each domain:
  == domain 1  score: 178.6 bits;  conditional E-value: 3.3e-56
                                   HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSS CS
               Glycos_transf_1   4 kkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsre 84 
                                   + r++ g ++++k+il+vgrl+++Kg+++li+a++++ +  ++n+klviaG+g+++++l++l+ +l+++++v flg+v+ +
  gi|15669803|ref|NP_248617.1| 197 NFRRSIGVQDDEKMILFVGRLTYQKGIEYLIRAMPKILE--RHNAKLVIAGSGDMRDYLEDLCYQLGVRHKVVFLGFVNGD 275
                                   567888999****************************96..6*************************************** PP

                                   SHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHH CS
               Glycos_transf_1  85 dleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerl 165
                                    l++l+k+ad++v+ps +E+fGiv+lEAmaag+pv++s +gg++e++k++++G++v p+n++++a +++++l+d   re +
  gi|15669803|ref|NP_248617.1| 276 TLKKLYKSADVVVIPSVYEPFGIVALEAMAAGTPVVVSSVGGLMEIIKHEVNGIWVYPKNPDSIAWGVDRVLSDWGFREYI 356
                                   ********************************************************************************* PP

                                   HHHHHH CS
               Glycos_transf_1 166 genark 171
                                    +na+k
  gi|15669803|ref|NP_248617.1| 357 VNNAKK 362
                                   ****98 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.1   0.0   6.4e-41   1.4e-37       2     134 .]     209     349 ..     208     349 .. 0.93

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 6.4e-41
                                   EEEEEES---GG.GTHHHHHHHHHHHH.H.HEEEEEES---...HHHHHHH.T.T-T.TEEEE---..THHHHHHHH-SEE CS
               Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.dvrlvivGdgp.rpeeleela.a.gleerveftGfv..edlaellaaadvf 76 
                                   + ilfvGrl   +kg+++l++a+p+++++ +++lvi+G+g+ r + le+l+ + g++++v+f+Gfv  + l++l+++adv+
  gi|15669803|ref|NP_248617.1| 209 KMILFVGRL-TYQKGIEYLIRAMPKILERhNAKLVIAGSGDmR-DYLEDLCyQlGVRHKVVFLGFVngDTLKKLYKSADVV 287
                                   78*******.567**************9955**********65.59999884599*99********9667*********** PP

                                   EE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
               Glyco_trans_1_4  77 vaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                   v+Ps  e fg+++lEamaag+pvV+++vgg+ e++  ++ng+ v p++p+++a  + r+l+d
  gi|15669803|ref|NP_248617.1| 288 VIPSvyEPFGIVALEAMAAGTPVVVSSVGGLMEIIkhEVNGIWVYPKNPDSIAWGVDRVLSD 349
                                   ***********************************999******99**********999987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.0   3.1e-33   6.9e-30       1     168 [.      15     183 ..      15     185 .. 0.86
   2 ?    4.1   0.0     0.018        41     125     150 ..     229     255 ..     215     271 .. 0.74
   3 ?   -0.6   0.0      0.51   1.1e+03      72     141 ..     283     291 ..     258     314 .. 0.53

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 3.1e-33
                Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrll.rslaflrrlrrllkre...kpDvvH 77 
                                   vGG + h+  La++L r+GheV+v+t g+d p++e+ +++v+v rv++ +++ +l + + ++  + + l      k+Dv+H
  gi|15669803|ref|NP_248617.1|  15 VGGLAIHCKGLAEGLVRNGHEVDVITVGYDLPEYEN-INGVNVYRVRPISHPHFLtWAMFMAEEMEKKLGILgvdKYDVIH 94 
                                   7***********************************.77777777776665555414444444454444433666****** PP

                Glyco_transf_4  78 ahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppek 158
                                   +h+++++++++  l++  ++p+V ++H+++  ++ ++  +  s++++a+e+     + +vi+vS+++++e+++ ++ p++k
  gi|15669803|ref|NP_248617.1|  95 CHDWMTHFVGA-NLKHICRMPYVQSIHSTE-IGRCGGLYSDDSKAIHAMEYLSTYESCQVITVSKSLKEEVCSIFNTPEDK 173
                                   *******8775.566679************.799999******************************************** PP

                Glyco_transf_4 159 itVipnGvDl 168
                                   + Vi+nG+++
  gi|15669803|ref|NP_248617.1| 174 VKVIYNGINP 183
                                   ********86 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.018
                Glyco_transf_4 125 alerrl.lrradrviavSeatadelre 150
                                   a+ + l  ++a+ via S  ++d+l++
  gi|15669803|ref|NP_248617.1| 229 AMPKILeRHNAKLVIAGSGDMRDYLED 255
                                   3333336689***************98 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.51
                Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavS 141
                                     Dvv                                                             + +S
  gi|15669803|ref|NP_248617.1| 283 SADVV-------------------------------------------------------------VIPS 291
                                   33444.............................................................3333 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   9.9e-14   2.2e-10       1      50 [.       2      50 ..       2      66 .. 0.85
   2 !   51.3   0.2   5.5e-17   1.2e-13     116     232 ..      68     166 ..      46     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 9.9e-14
                Glyco_transf_5  1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeek 50
                                  ki +v++E++p   +GGLa ++++L++ L ++gh+v+vi+ +y+  + e+
  gi|15669803|ref|NP_248617.1|  2 KIAMVTWEYPP-RIVGGLAIHCKGLAEGLVRNGHEVDVITVGYDLPEYEN 50
                                  89*********.*******************************6665554 PP

  == domain 2  score: 51.3 bits;  conditional E-value: 5.5e-17
                Glyco_transf_5 116 alfsraalellek.l...gw.kpdvihahDWhtalvpallkelykerglfkkiktvftiHNlayqgrfp..kdelaalglp 189
                                     +++ ++e +ek l   g  k dvih+hDW+t +v+a lk++ +       +++v +iH++++ ++ +  +         
  gi|15669803|ref|NP_248617.1|  68 LTWAMFMAEEMEKkLgilGVdKYDVIHCHDWMTHFVGANLKHICR-------MPYVQSIHSTEIGRCGGlyS--------- 132
                                   4555556666666445556657********************953.......*************9998221......... PP

                Glyco_transf_5 190 aedfekldglefygkvnflk.agivyadavttVSptyakEiltp 232
                                             + +++++ ++    +++ +v+tVS++ ++E+++ 
  gi|15669803|ref|NP_248617.1| 133 ----------DDSKAIHAMEyLSTYESCQVITVSKSLKEEVCSI 166
                                   ..........2346899999999******************985 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   4.6e-23     1e-19       1     160 []      16     180 ..      16     180 .. 0.87
   2 ?   -0.5   0.0      0.64   1.4e+03     128     147 ..     237     256 ..     219     270 .. 0.79
   3 ?    4.3   0.0     0.023        51      74     105 ..     284     316 ..     275     360 .. 0.72

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 4.6e-23
               Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalr.al...rrllrqrrerpdvv 77 
                                   gG ++++  la++L++ GheV+v+t +++ +++ ++ +gv v+r++   +p+ l+++ +++  +    ++l     ++dv+
  gi|15669803|ref|NP_248617.1|  16 GGLAIHCKGLAEGLVRNGHEVDVITVGYDLPEY-ENINGVNVYRVRPISHPHFLTWAMFMAeEMekkLGIL--GVDKYDVI 93 
                                   8*************************9999999.999********76667766666655431442225566..9******* PP

               Glyco_trans_4_4  78 hahsptaglaarlarrrrgiplvvtlhgll.lrrg..sgavrrlyralerrllrradavlvvseaeaeelra.lgvpadrv 154
                                   h+h++++ ++++ ++   + p+v+++h+++ +r g   + +  +++a+e+++     +v++vs ++ ee++  ++ p d+v
  gi|15669803|ref|NP_248617.1|  94 HCHDWMTHFVGANLKHICRMPYVQSIHSTEiGRCGglYSDDSKAIHAMEYLSTYESCQVITVSKSLKEEVCSiFNTPEDKV 174
                                   ***********9999678*********988644445778899999***************************99******* PP

               Glyco_trans_4_4 155 vvvpng 160
                                    v+ ng
  gi|15669803|ref|NP_248617.1| 175 KVIYNG 180
                                   *****8 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.64
               Glyco_trans_4_4 128 rradavlvvseaeaeelral 147
                                   ++a +v++ s +++++l++l
  gi|15669803|ref|NP_248617.1| 237 HNAKLVIAGSGDMRDYLEDL 256
                                   56999***********9984 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.023
               Glyco_trans_4_4  74 pdvvhahs.pt.aglaarlarrrrgiplvvtlhg 105
                                    dvv++ s +   g++a+ a  ++g+p+vv+  g
  gi|15669803|ref|NP_248617.1| 284 ADVVVIPSvYEpFGIVALEAM-AAGTPVVVSSVG 316
                                   699999995533566665555.99*****99853 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   2.6e-14   5.9e-11      11     122 ..      20     140 ..      14     157 .. 0.77
   2 ?    2.0   0.0     0.086   1.9e+02      26     108 ..     240     316 ..     211     329 .. 0.68

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 2.6e-14
               Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkg..pleylk.af.kl.kk..likkikPDvvhahyak 84 
                                   +h++ la++L  +g+eV+vit + +  ++++ +g++v+r++ +++    l++++ ++ ++ kk  ++  +k+Dv+h+h   
  gi|15669803|ref|NP_248617.1|  20 IHCKGLAEGLVRNGHEVDVITVGYDLPEYENINGVNVYRVR-PISHphFLTWAMfMAeEMeKKlgILGVDKYDVIHCHDWM 99 
                                   79999*****************9999**************8.8777555666655544665444489************66 PP

               Glyco_trans_4_2  85 pygllgslaarlsgvipvvlsvwGldv.....lkfpkksklkk 122
                                      ++g+ ++ +++  p+v+s++ + +     l++++ ++++ 
  gi|15669803|ref|NP_248617.1| 100 T-HFVGANLKHICR-MPYVQSIHSTEIgrcggLYSDDSKAIHA 140
                                   5.56788889***9.********99997666655544444443 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.086
               Glyco_trans_4_2  26 eVhvitpkkgakdeleaegihvhrlkvdrkg.pleylkafklkklikkikPDvvhahyakpygllgslaarlsgvipvvls 105
                                   + +++ ++++  d+le+    +++l v++k+  l++++  +lkkl+k     v+  +y  p g+++ l a  +g  pvv+s
  gi|15669803|ref|NP_248617.1| 240 KLVIAGSGDM-RDYLED-L--CYQLGVRHKVvFLGFVNGDTLKKLYKSADVVVIPSVY-EPFGIVA-LEAMAAG-TPVVVS 313
                                   5555555555.444433.2..344444466667777788899****999888888888.7788888.7777888.666655 PP

               Glyco_trans_4_2 106 vwG 108
                                     G
  gi|15669803|ref|NP_248617.1| 314 SVG 316
                                   544 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   1.1e-12   2.4e-09       2      89 ..     287     376 ..     286     379 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.1e-12
               Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlae 80 
                                   v+ ps +e +  + +Ea+a+G+++++++  gl e+++ +  +i++   +++++a  ++++l++ + r+ i ++a+++v ++
  gi|15669803|ref|NP_248617.1| 287 VVIPSVYEPFGIVALEAMAAGTPVVVSSVGGLMEIIKHEVNGIWVYpkNPDSIAWGVDRVLSDWGFREYIVNNAKKDVYEK 367
                                   566899999******************99***************999********************************** PP

               Glyco_trans_1_2  81 htydhraeq 89 
                                   +++d+ a++
  gi|15669803|ref|NP_248617.1| 368 YSWDNIAKE 376
                                   *****9987 PP

>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.47   1.1e+03     248     288 ..      55      93 ..      52      97 .. 0.75
   2 !   11.5   0.0   3.7e-05     0.083     204     306 ..     139     238 ..     127     241 .. 0.67
   3 !    4.4   0.0    0.0055        12     361     414 ..     272     321 ..     264     375 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.47
                                   -HHHHHHHCCSCHHHHHHHHHHHHT.TTSEEEEEEEEC-GG CS
               Glyco_transf_20 248 dverlesalkkesvsekvkelkerfenkkklilgvDrlDyi 288
                                   +v r++ + +++++ +++  + e++e+k   ilgvD+ D i
  gi|15669803|ref|NP_248617.1|  55 NVYRVRPI-SHPHFLTWAMFMAEEMEKK-LGILGVDKYDVI 93 
                                   55555444.4478888999999999885.88******9987 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.7e-05
                                   SSHHHHHHHHHHHHHHSSEEEECTTEEEEETTEEEEEEE------HHHHHHHCCSCHHHHHHHHHHHHT.TTSEEEEEEEE CS
               Glyco_transf_20 204 htedyarhFlsccsrllgleveskrggveykgrkvsvkalpigidverlesalkkesvsekvkelkerfenkkklilgvDr 284
                                   h  +y   + s c+ ++  +  +++    ++  + +vk++  gi++ +++  l+ e+  +  +++  +   + k+il v r
  gi|15669803|ref|NP_248617.1| 139 HAMEYLSTYES-CQVITVSKSLKEEVCSIFNTPEDKVKVIYNGINPWEFDINLSWEEKINFRRSIGVQD--DEKMILFVGR 216
                                   55555555433.333333333333334445555667777778888888888888766666666666554..569******* PP

                                   C-GGG-HHHHHHHHHHHHHH-G CS
               Glyco_transf_20 285 lDyikGvkqkllaferfLeeyp 306
                                   l+y kG++  ++a+ ++Le++ 
  gi|15669803|ref|NP_248617.1| 217 LTYQKGIEYLIRAMPKILERHN 238
                                   *******************986 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0055
                                   --HHHHHHHHHH-SEEEE--SSBSS-CHHHHHHHCSTTT--EEEEETTBGGGGT CS
               Glyco_transf_20 361 ldfeeliallaaadvllvtslRdGmnlvakeyvvcqqekkgvLiLSeFaGaaqs 414
                                   ++ + l +l++ adv+++ s+ +   +va+e +++ +     +++S   G  ++
  gi|15669803|ref|NP_248617.1| 272 VNGDTLKKLYKSADVVVIPSVYEPFGIVALEAMAAGTP----VVVSSVGGLMEI 321
                                   56678889***********************9987554....666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2528.88
//
Query:       gi|15669804|ref|NP_248618.1|  [L=70]
Description: hypothetical protein MJ_1608 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-23   80.2   2.6      1e-22   80.0   2.6    1.0  1  DUF2582   Winged helix-turn-helix domain (DUF2582)
  ------ inclusion threshold ------
      0.039   12.9   0.0       0.04   12.9   0.0    1.0  1  Pox_I6    Poxvirus I6-like family
       0.13   12.4   0.0       0.17   12.1   0.0    1.2  1  UPF0180   Uncharacterised protein family (UPF0180)


Domain annotation for each model (and alignments):
>> DUF2582  Winged helix-turn-helix domain (DUF2582)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   2.6   1.7e-26     1e-22       1      65 []       1      69 [.       1      69 [. 0.95

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 1.7e-26
                                  -HHHH..HHHHHHHHHHHHCCSSSEEHHHHH...HHCT-SCHHHHHHHHHHHCTTSEEEEEETTEEEEEE CS
                       DUF2582  1 Mdkei..iGenAGkvwhlLnengeislkelk...rktglsdkelalAiGWLaREdKivierkekelfvkl 65
                                  M++++  iGe+AGk++hlL++ ge+sl++++   rk+g++++ +++AiGWLaREdKi++ +++k++++kl
  gi|15669804|ref|NP_248618.1|  1 MEDMWgkIGETAGKIYHLLEG-GEKSLSQIEkilRKEGYNSNIVKMAIGWLAREDKIFVLKDDKKWVIKL 69
                                  7888788**************.9*******9999*********************************986 PP

>> Pox_I6  Poxvirus I6-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.7e-06      0.04      46      84 ..      25      66 ..      18      70 .] 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.7e-06
                        Pox_I6 46 visslikilkkkahvidlyflpvgwlagaeds....kpeshvv 84
                                   +s++ kil+k+ ++ ++  +++gwla  ed+    k+ ++ v
  gi|15669804|ref|NP_248618.1| 25 SLSQIEKILRKEGYNSNIVKMAIGWLA-REDKifvlKDDKKWV 66
                                  689999*********************.777656665555555 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.8e-05      0.17       6      22 ..      23      39 ..      22      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.8e-05
                       UPF0180  6 eegLsnvkeaLrekGYe 22
                                  e++Ls++++ Lr++GY+
  gi|15669804|ref|NP_248618.1| 23 EKSLSQIEKILRKEGYN 39
                                  89**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 463.67
//
Query:       gi|15669805|ref|NP_248619.1|  [L=374]
Description: hypothetical protein MJ_1609 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-86  290.3   6.9    1.3e-86  290.3   6.9    1.6  2  ATPase_2    ATPase domain predominantly from Archaea
    4.7e-06   26.7  10.1      0.019   15.0   0.1    3.6  3  AAA_14      AAA domain
      1e-05   26.0   0.0    4.1e-05   24.0   0.0    2.0  2  AAA_16      AAA ATPase domain
     0.0013   19.1   0.0     0.0057   16.9   0.0    2.1  2  AAA_22      AAA domain
     0.0027   18.1   0.2     0.0065   16.9   0.2    1.6  1  PDZ_4       PDZ domain
     0.0098   16.0   0.0      0.038   14.1   0.0    2.0  2  MMR_HSR1    50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.032   13.9   0.0    1.5  1  AAA_24      AAA domain
      0.023   14.4   1.4      0.057   13.2   0.2    2.2  2  SGTA_dimer  Homodimerisation domain of SGTA
      0.038   14.7   2.0         11    6.8   0.2    3.3  2  DUF2281     Protein of unknown function (DUF2281)


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.3   6.9   6.8e-90   1.3e-86       1     233 []       3     266 ..       3     266 .. 0.97
   2 ?   -1.9   0.2       1.3   2.5e+03      99     131 ..     283     314 ..     268     343 .. 0.51

  Alignments for each domain:
  == domain 1  score: 290.3 bits;  conditional E-value: 6.8e-90
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...eeeekkkl 78 
                                   Ff+Reke++++++i+e epn+iyfiYG+ +sGK++L++ei+ n++d +ky+ ++i++r+++i ++d+fie   e +ek+++
  gi|15669805|ref|NP_248619.1|   3 FFNREKEINKILSIIEGEPNNIYFIYGSLNSGKSTLMREIVVNRLDISKYIPFFIDFRTRNILNVDNFIEclfEVDEKSEI 83 
                                   9************************************************************************77777777 PP

                      ATPase_2  79 ekal........................giavpkaeleeilk..eksklvfkaielllekikkkgkkiiiiiDelqklidl 133
                                   ++                           i++pk  +++i++  +ks++v+++ie+l++k+++kgkk+i+i+Delq+++++
  gi|15669805|ref|NP_248619.1|  84 DDFReyaksladllvkgseeiskyylgmPIKIPKPFFDKIFNkkDKSADVYQYIEYLFAKLNEKGKKPILIFDELQMIKEI 164
                                   77777779**********************************9999*********************************** PP

                      ATPase_2 134 glngaellvkeLlnliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkel..eels 212
                                   +lng+++l+++L+++++ ltk +hlc+v+clsS++lfie+vy+++elegr++yilvdd+dk+tal+f+++++ke+  ++l+
  gi|15669805|ref|NP_248619.1| 165 TLNGNRKLLWSLFQFLVALTKVQHLCHVFCLSSDSLFIEYVYKTGELEGRADYILVDDFDKQTALKFIDFLAKEIlnKKLP 245
                                   ***************************************************************************87777* PP

                      ATPase_2 213 kedfeeiyryvGGkPkalvel 233
                                   k+++e+iy+yvGGkP  ++++
  gi|15669805|ref|NP_248619.1| 246 KDEKELIYSYVGGKPVLIIKV 266
                                   ******************987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                      ATPase_2  99 sklvfkaielllekikkkgkkiiiiiDelqkli 131
                                    k+++++++++l+++   + k + + De+ +l+
  gi|15669805|ref|NP_248619.1| 283 LKDATQKLKYFLNDLDYIKPK-VEVGDEVIELK 314
                                   455555555555554433222.22234443333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   9.7e-06     0.019       2      86 ..      22      93 ..      21     110 .. 0.69
   2 !   15.0   0.3   9.8e-06      0.02      44     120 ..     126     218 ..     102     229 .. 0.70
   3 ?    1.5   0.7      0.14   2.7e+02      14      90 ..     258     329 ..     255     336 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.7e-06
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikell.vkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewekal 83
                                  ++i++i G   +GK+tl+++++ ++l ++k   ++i++ + +  + +++   +e ++e            DE +e+++++++ 
  gi|15669805|ref|NP_248619.1| 22 NNIYFIYGSLNSGKSTLMREIVVNRLdISKYIPFFIDFRTRNILNVDNF---IECLFE-----------VDEKSEIDDFREYA 90
                                  67999*********************66666666677776666554444...333333...........35555555555555 PP

                        AAA_14 84 ksl 86
                                  ksl
  gi|15669805|ref|NP_248619.1| 91 KSL 93
                                  555 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 9.8e-06
                        AAA_14  44 kkladpe..kllelileklke.ekktylflDEiqev............pewekalkslvdegknldvivtGSnskllskei 109
                                   kk +  +  +++e++++kl+e  kk +l++DE q++             +++++l  l + ++ ++v++  S s+++    
  gi|15669805|ref|NP_248619.1| 126 KKDKSADvyQYIEYLFAKLNEkGKKPILIFDELQMIkeitlngnrkllWSLFQFLVALTKVQHLCHVFCLSSDSLFIEYVY 206
                                   222222222566677776433468999*********888888888777777777777777777788888888888887755 PP

                        AAA_14 110 at.slagrvaei 120
                                   +t +l gr+++i
  gi|15669805|ref|NP_248619.1| 207 KTgELEGRADYI 218
                                   433677777766 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.14
                        AAA_14  14 GKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..pewekalkslvdeg 90 
                                   GK +l+ ++i++l        y nl+d  d +l+d ++ l+++l+ l   k ++ + DE+ e+  +++ kalk + d++
  gi|15669805|ref|NP_248619.1| 258 GKPVLIIKVIDKLR-------YENLNDILDFMLKDATQKLKYFLNDLDYIKPKVEVGDEVIELkkEDIVKALKLFKDSY 329
                                   56666666665444.......8888888888888777778888887433367788888888874445777777777655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.1e-08   4.1e-05       1     156 [.       2     178 ..       2     193 .. 0.65
   2 ?   -1.6   0.2       1.5     3e+03     139     160 ..     218     237 ..     210     300 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.1e-08
                        AAA_16   1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrell.ralekd.g.giflrgkcdqlesaipysalaqala 77 
                                   +++ Re+e++++ls++e    g+p ++ +++G   +GKs+l+re+  ++l  + +  +f+  +++     +  + ++++l 
  gi|15669805|ref|NP_248619.1|   2 KFFNREKEINKILSIIE----GEPnNIYFIYGSLNSGKSTLMREIVvNRLDISkYiPFFIDFRTRNI---LNVDNFIECL- 74 
                                   6899*****99999998....8999*****************9998456666544355566666666...5556688888. PP

                        AAA_16  78 reellrqllde......aesaeleawrekleeala........................avpelagaea......srllel 122
                                   +e   + + d+      +           l + l                         +                ++++ 
  gi|15669805|ref|NP_248619.1|  75 FEVDEKSEIDDfreyakS-----------LADLLVkgseeiskyylgmpikipkpffdkI--------FnkkdksADVYQY 136
                                   545555555554422221...........2222223334444566566666555555441........155555599**** PP

                        AAA_16 123 lkrllallsrderplvlvlDdlqwade........aslqlla 156
                                   +  l+a+l +++++ +l++D+lq ++e          ++l++
  gi|15669805|ref|NP_248619.1| 137 IEYLFAKLNEKGKKPILIFDELQMIKEitlngnrkLLWSLFQ 178
                                   *****888887999*********7777555533334444444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                        AAA_16 139 lvlDdlqwadeaslqllaaLlr 160
                                   +++Dd+++  +  l+++++L++
  gi|15669805|ref|NP_248619.1| 218 ILVDDFDKQTA--LKFIDFLAK 237
                                   66666664333..444444433 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.9e-06    0.0057       5     118 ..      22     179 ..      18     202 .. 0.67
   2 ?   -1.0   0.0      0.97   1.9e+03      78      78 ..     251     251 ..     196     294 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-06
                        AAA_22   5 agilvvtGesGtGKTtllrrl.leqldeeakaee..........erpevv..fvtlpsstsskdllrellralglelka.. 70 
                                    +i +++G   +GK+tl+r++ +++ld+ +++            + + ++  ++++ ++++ +d+ re ++ l + l +  
  gi|15669805|ref|NP_248619.1|  22 NNIYFIYGSLNSGKSTLMREIvVNRLDISKYIPFfidfrtrnilNVDNFIecLFEVDEKSEIDDF-REYAKSLADLLVKgs 101
                                   57899**************962578887777777***9887777666666555555555555555.444444444444447 PP

                        AAA_22  71 ........................erlsseellealeqalrarav...ielliiDEaqhlrs....eealeeLrsllnl 118
                                                           + ++s ++++++e  + +      +++li DE q + +    + + + L sl+ +
  gi|15669805|ref|NP_248619.1| 102 eeiskyylgmpikipkpffdkifnKKDKSADVYQYIEYLFAKLNEkgkKPILIFDELQMI-KeitlNGNRKLLWSLFQF 179
                                   78*********************9555555555666555555555566************.433453333333444333 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.97
                        AAA_22  78 l 78 
                                   l
  gi|15669805|ref|NP_248619.1| 251 L 251
                                   1 PP

>> PDZ_4  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   3.2e-06    0.0065       5      53 ..     279     328 ..     276     343 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.2e-06
                                   -SEEEEE-TTS.-EEEEEE-SSSSSS-TT-EEEEETTEEHHHHHHTTS-T CS
                         PDZ_4   5 LPfkvkgsaeG.ryfivdideeklelkvGDellefdgkpvkevveelkes 53 
                                   L f +k++++  +yf+ d+d  k +++vGDe++e+  +++   ++ +k+s
  gi|15669805|ref|NP_248619.1| 279 LDFMLKDATQKlKYFLNDLDYIKPKVEVGDEVIELKKEDIVKALKLFKDS 328
                                   7788888765439***********************99887766666555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.9e-05     0.038       4      30 ..      27      53 ..      25      83 .. 0.77
   2 ?   -1.9   0.0       1.8   3.5e+03      77     101 ..     261     282 ..     217     296 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                                  EEESTTSSHHHHHHHHHTSTEEESSST CS
                      MMR_HSR1  4 ivGrpNvGKStLinaltgekaivsdkp 30
                                  i+G  N+GKStL++ ++ ++  +s++ 
  gi|15669805|ref|NP_248619.1| 27 IYGSLNSGKSTLMREIVVNRLDISKYI 53
                                  89**************98877666553 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                                   SEEEEEEETTTTCSHHHHHHHHHHH CS
                      MMR_HSR1  77 dlillvvdaseeklkpldeeleell 101
                                    li+ v+d + + +++l +++ +++
  gi|15669805|ref|NP_248619.1| 261 VLIIKVID-KLR-YENL-NDILDFM 282
                                   56777777.423.6555.3443333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.6e-05     0.032       5      60 ..      25      94 ..      22     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                        AAA_24  5 iliyGpsgiGKTtlakel........gpkplfidtekGlksldadkfpdie.......swedfldevvela 60
                                  ++iyG+  +GK+tl++e+        ++ p+fid+    + l++d+f ++         ++df++++++la
  gi|15669805|ref|NP_248619.1| 25 YFIYGSLNSGKSTLMREIvvnrldisKYIPFFIDFRT-RNILNVDNFIECLfevdeksEIDDFREYAKSLA 94
                                  68*********************************98.668999999888899999999999999998883 PP

>> SGTA_dimer  Homodimerisation domain of SGTA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.7   3.4e+03      37      52 ..      71      86 ..      70      97 .. 0.63
   2 ?   13.2   0.2   2.9e-05     0.057       3      28 ..     225     250 ..     224     252 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.7
                    SGTA_dimer 37 IaeaFevdkedkaavk 52
                                  I+  Fevd++++ +  
  gi|15669805|ref|NP_248619.1| 71 IECLFEVDEKSEIDDF 86
                                  5556999998876555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.9e-05
                    SGTA_dimer   3 krlalaIidFLstslkdgtvseDdaE 28 
                                   k+ al +idFL + + ++++++D++E
  gi|15669805|ref|NP_248619.1| 225 KQTALKFIDFLAKEILNKKLPKDEKE 250
                                   999**********************9 PP

>> DUF2281  Protein of unknown function (DUF2281)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0056        11      14      34 ..     130     150 ..     127     157 .. 0.79
   2 ?    5.8   0.1     0.011        23      14      36 ..     225     248 ..     222     258 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0056
                       DUF2281  14 kqEvldFaefLleKyaakkkk 34 
                                    + v+ ++e+L +K ++k kk
  gi|15669805|ref|NP_248619.1| 130 SADVYQYIEYLFAKLNEKGKK 150
                                   5789***********665554 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.011
                       DUF2281  14 kqEvldFaefLleKy.aakkkktl 36 
                                   kq+ l F++fL++   ++k +k++
  gi|15669805|ref|NP_248619.1| 225 KQTALKFIDFLAKEIlNKKLPKDE 248
                                   7999********999755555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2713.89
//
Query:       gi|15669806|ref|NP_248620.1|  [L=615]
Description: glucoamylase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-12   46.1   0.6    0.00021   20.2   0.1    3.9  2  Glyco_hydro_15   Glycosyl hydrolases family 15
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.028   14.1   0.0    1.4  1  DUF4965          Domain of unknown function (DUF4965)
      0.028   13.8   0.1       0.06   12.7   0.1    1.5  1  Glyco_transf_36  Glycosyltransferase family 36


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.7e-07    0.0034      12      52 ..     274     311 ..     266     329 .. 0.79
   2 !   20.2   0.1   3.5e-08   0.00021     110     358 ..     339     549 ..     327     607 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.7e-07
                                   CSTTSSBTTS-TT-B-S-S-BSSSB--SEEHHHHHHHHHHH CS
                Glyco_hydro_15  12 ktlilleqnpvtGlliASpstsdpDYrytWvRDsvyvilav 52 
                                   +tl++l ++   G++iA+ps  +pDYry+W RD +y+  a+
  gi|15669806|ref|NP_248620.1| 274 MTLLMLCDKE--GGIIAAPS-LHPDYRYVWGRDGSYISIAL 311
                                   5555555555..********.99***********9988776 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.5e-08
                                   TS-B--S-..-S--BTTHHHHHHHHH.HHH.HCTTHCHCCCCHHHHTHHHHHHHHH..HHTTS-EE-TTS--ECEEHH..H CS
                Glyco_hydro_15 110 tgstvvGddewghlQlDatslyllal.aqm.tasglqiistldevafvqnlvdYie..aayktpdfglWEenqgeselnas 186
                                   ++  v G++  + +Q D+ + +l a+ + + ++ + ++++ ++    +++   Y+   a   tp+f+lWEe+ g   +  +
  gi|15669806|ref|NP_248620.1| 339 QNYYVNGKPRLTAIQTDQIGSILWAMdVHYrLTGDRKFVERYWNT--IEKAANYLRlvALNFTPCFDLWEERFGVFAY--T 415
                                   55567888899999****999887763555445558999999999..66666664311344589***********999..* PP

                                   HHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GGGEETTCCECECSCH.....HHHTTS--S-BCHHH CS
                Glyco_hydro_15 187 svgmakAlleaideadlfgakgdaqlvektkdeilnklqgkygckrgfwplfntylildgsfaedkeqvqeyrealdasll 267
                                   + +  ++l +a  + +++ ++++ + + kt + +  ++      kr +++++  + +               ++  d s+l
  gi|15669806|ref|NP_248620.1| 416 MGATYAGLKCAYSMSKAVNKRDKVKDWGKTIEFLKHEV-----PKRFYLEDEERFAKSINP----------LDKTIDTSIL 481
                                   ****************************9999999999.....555555555554443333..........4777777774 PP

                                   HHHH.HCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT-STTS--SBTT--CGSSSBSCT--BHHHHHHHHHH CS
                Glyco_hydro_15 268 llpe.lyfvpaddvdeeyqnpqsprllaqslyildsllsegflavgeldplvrRysedvkpdklglsGrpyylctlwtvet 347
                                    l+   + +  dd          +r++++  +i++ ++ +           ++Ry+ed +       G+p+ ++tlw    
  gi|15669806|ref|NP_248620.1| 482 GLSYpFNLIDVDD----------ERMIKTAEAIEKAFKYKVG--------GIGRYPEDIYF-----GGNPWIITTLW-LSL 538
                                   3332145555566..........89************98766........49********7.....***********.777 PP

                                   HHHHHHHHHHH CS
                Glyco_hydro_15 348 lldelyekagk 358
                                   ++++ly+  ++
  gi|15669806|ref|NP_248620.1| 539 YYRRLYKVLKE 549
                                   77777765554 PP

>> DUF4965  Domain of unknown function (DUF4965)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.7e-06     0.028     111     150 ..     354     393 ..     338     400 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.7e-06
                       DUF4965 111 veesGnmlimalayaqasgdasllekyydllkqWadYLve 150
                                    ++ G +l+ +  +++++gd++++e+y++++++ a+YL  
  gi|15669806|ref|NP_248620.1| 354 TDQIGSILWAMDVHYRLTGDRKFVERYWNTIEKAANYLRL 393
                                   5678999******************************975 PP

>> Glyco_transf_36  Glycosyltransferase family 36
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     1e-05      0.06      91     138 ..      74     121 ..      60     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
               Glyco_transf_36  91 sekngietelevfVpkedpveirrlkLtNtsererelsvtsyaefvlg 138
                                    e+++i  +++ fVp  ++v irr+ ++N+ +++ + +++ y  + +g
  gi|15669806|ref|NP_248620.1|  74 LEDDKIILTIKDFVPVSHNVLIRRVYIKNKLDKKLNFKLFFYENLRIG 121
                                   5788999999********************************988888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3763.30
//
Query:       gi|15669807|ref|NP_248621.1|  [L=467]
Description: alpha-amylase AmyA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-74  249.3   8.2    5.2e-74  249.3   8.2    1.5  2  Glyco_hydro_57   Glycosyl hydrolase family 57
    1.2e-08   34.9   0.0    2.3e-08   34.0   0.0    1.4  1  Polysacc_deac_1  Polysaccharide deacetylase
  ------ inclusion threshold ------
      0.013   15.6   0.2      0.038   14.1   0.2    1.8  1  CaMKII_AD        Calcium/calmodulin dependent protein kinase 
      0.099   12.6   0.0       0.23   11.4   0.0    1.6  1  MarR             MarR family
       0.22   11.3   1.0       0.44   10.3   0.1    2.0  2  DUF2733          Protein of unknown function (DUF2733)


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.3   8.2   1.5e-77   5.2e-74       1     324 [.       4     288 ..       4     289 .. 0.98
   2 ?   -2.4   0.2      0.61   2.2e+03     141     147 ..     383     389 ..     317     432 .. 0.49

  Alignments for each domain:
  == domain 1  score: 249.3 bits;  conditional E-value: 1.5e-77
                                   EEEEEE-----TTS-SSSSSHHHHHHHHHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-HHHHHHHHHHHHHHHH CS
                Glyco_hydro_57   1 afvfhqHqplykkpgkgeytlpwvrehaaedYiklalilekfpkvhvtfeLsgsLiaqLeeylngekksylpateelleli 81 
                                   +f f++Hqp + +++      +   ++ +e+Y++++l++e f+kv+                    +k+y+p++e++leli
  gi|15669807|ref|NP_248621.1|   4 TFNFEVHQPHRLNKE-----INQNGNTLWEKYVDTKLNKEVFNKVA--------------------NKCYIPTNELILELI 59 
                                   599*********999.....99999*********************....................**************9 PP

                                   HHHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHHHHHHHHHHH CS
                Glyco_hydro_57  82 eeglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedieaqvkkare 162
                                        + +++k      +n++i+g ++eq+ ++ n  vl+lf++l+++g+vEl++++y+H+l++l++++++++++++++r+
  gi|15669807|ref|NP_248621.1|  60 -----DEYDFK------VNYSITGVFVEQALEF-NDYVLDLFKDLVKTGNVELIAETYHHSLTSLFETEDEFIEDIEMHRK 128
                                   .....8899**......****************.*********************************************** PP

                                   HHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS.-EEEE--CHH-TTTSGGG CS
                Glyco_hydro_57 163 lyeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllknggiavffRdreLsddigFry 243
                                   +y+e+fg ++++f+++El+++++i++i ++lGf+ +ft++ ++il ++   sp++ y++++g +++++R+++LsddigFr+
  gi|15669807|ref|NP_248621.1| 129 MYKEIFGFKAKVFRNTELIYNNRIAKIAKDLGFKAIFTEGIEKILGWR---SPNYLYQSPDG-MKILLRNYRLSDDIGFRF 205
                                   ************************************************...*********99.****************** PP

                                   -................TTSB..........-TT---TTT-..-BB-TT-S---HHHHHHHHHHHHHHHHHHHHHHHHHSS CS
                Glyco_hydro_57 244 s....eqypleavddfinwlkkvkkaksevvtialdgEnwg..hypetgkkeFleklyeeleenglielvtpsefikklkp 318
                                   s    +qypl ++d+++ wl ++   ++ev++i++d+E++g  h++etg++eFl++l+ e+ +++++e+v +se++++l+p
  gi|15669807|ref|NP_248621.1| 206 SardwDQYPL-TADKYAIWLAST---PGEVINIYMDYETFGehHWKETGIFEFLRYLPIEIAKHEHLEVVNVSEVVDRLEP 282
                                   **********.**********98...******************************************************* PP

                                   -EEEEE CS
                Glyco_hydro_57 319 kglikl 324
                                   +g i++
  gi|15669807|ref|NP_248621.1| 283 RGEIYV 288
                                   **9998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.61
                                   -B-GGG- CS
                Glyco_hydro_57 141 Hpllpll 147
                                    ++l +l
  gi|15669807|ref|NP_248621.1| 383 ASYLNIL 389
                                   2222222 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   6.3e-12   2.3e-08      21     123 ..      52     163 ..      43     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 6.3e-12
                                   HHHHHHHHHHCT--EEEEE-HHHHCH-.......HHHHHHHHHTT.EEEEE--SS--EG.GGSHHHHHHHHHHHHHHHHHH CS
               Polysacc_deac_1  21 tteilpvLkkykvkatffvigglvedy.......pdevremaasG.veignHtinhsnl.krlseeevrreierakdalrk 92 
                                    + il++ ++y++k    ++g  ve+         d+ + +++ G ve+ + t++hs     ++e+e+ ++ie+ +++ ++
  gi|15669807|ref|NP_248621.1|  52 NELILELIDEYDFKVNYSITGVFVEQAlefndyvLDLFKDLVKTGnVELIAETYHHSLTsLFETEDEFIEDIEMHRKMYKE 132
                                   566999*********999999999999999999************************775788889*************** PP

                                   HHS----EEE-GGGEE-HHHHHHHHHTT.EE CS
               Polysacc_deac_1  93 algreprlfryPygsasatvlevarelgfay 123
                                   ++g ++++fr   + +++++ ++a++lgf++
  gi|15669807|ref|NP_248621.1| 133 IFGFKAKVFRNTELIYNNRIAKIAKDLGFKA 163
                                   *****************************86 PP

>> CaMKII_AD  Calcium/calmodulin dependent protein kinase II association domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.1e-05     0.038       9      75 ..      86     153 ..      83     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHHTT-HHHHHHHEEEEEEEE-GGGTT-EEESSHHHHGGGS...SSSS-SEEEE..EESEEEE CS
                     CaMKII_AD   9 letlleaisegdfetytklcdpeltvfepevlgnlveglefhrfyfekllakrkkavrtt..ilnkrvr 75 
                                   l+ + + +++g+ e ++++++ +lt +  e  ++ +e +e+hr ++ ++++ + k  r t  i n+r+ 
  gi|15669807|ref|NP_248621.1|  86 LDLFKDLVKTGNVELIAETYHHSLTSL-FETEDEFIEDIEMHRKMYKEIFGFKAKVFRNTelIYNNRIA 153
                                   666778899**************9975.57789*********************999866444455555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.3e-05      0.23      21      47 ..     260     286 ..     258     289 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.3e-05
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR  21 seLakklgvskstvtrvldrLekkGli 47 
                                   +e+ak+ +++  +v++v+drLe +G i
  gi|15669807|ref|NP_248621.1| 260 IEIAKHEHLEVVNVSEVVDRLEPRGEI 286
                                   59********************99855 PP

>> DUF2733  Protein of unknown function (DUF2733)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00012      0.44      20      32 .]     229     241 ..     226     241 .. 0.92
   2 ?   -2.3   0.1       1.1   3.9e+03      23      30 ..     386     393 ..     384     394 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                       DUF2733  20 GepINvveDfEef 32 
                                   Ge+IN++ D+E f
  gi|15669807|ref|NP_248621.1| 229 GEVINIYMDYETF 241
                                   9**********98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                       DUF2733  23 INvveDfE 30 
                                   +N+  DfE
  gi|15669807|ref|NP_248621.1| 386 LNILYDFE 393
                                   89*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1108  (0.0617993); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2955.32
//
Query:       gi|15669808|ref|NP_248622.1|  [L=411]
Description: cofactor-independent phosphoglycerate mutase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-57  193.2   0.0      6e-57  192.2   0.0    1.5  1  PhosphMutase     2,3-bisphosphoglycerate-independent phosphog
    7.7e-54  182.7   0.0    8.9e-54  182.5   0.0    1.0  1  Metalloenzyme    Metalloenzyme superfamily
    1.1e-05   25.2   0.0    0.00021   21.0   0.0    2.2  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
  ------ inclusion threshold ------
      0.032   13.3   0.0      0.068   12.2   0.0    1.5  1  RACo_C_ter       C-terminal domain of RACo the ASKHA domain
      0.037   14.4   0.0      0.072   13.5   0.0    1.5  1  DUF296           Plants and Prokaryotes Conserved (PCC) domai
       0.11   11.5   0.1       0.16   10.9   0.1    1.2  1  Alk_phosphatase  Alkaline phosphatase
       0.12   11.8   0.0       0.88    8.9   0.0    1.9  2  Sulfatase        Sulfatase


Domain annotation for each model (and alignments):
>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.2   0.0   2.4e-60     6e-57       1     170 []      38     209 ..      38     209 .. 0.98

  Alignments for each domain:
  == domain 1  score: 192.2 bits;  conditional E-value: 2.4e-60
                                   HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTGGG-. CS
                  PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrragris 81 
                                   Ak+G++Gl++ ++ gi+pgSd+A+l+ilGy+p ++ytGRGplEA g+Gl+lk+gd+afRcn++tvd e+ +++drragris
  gi|15669808|ref|NP_248622.1|  38 AKEGICGLMNAIDIGIRPGSDTAHLAILGYNPYEVYTGRGPLEAFGVGLDLKEGDIAFRCNFATVD-ENFVVLDRRAGRIS 117
                                   89***************************************************************7.6************* PP

                                   -TTHHHHHHHT-EEE.TTEEEEEEE-STTEEEEEE....--S-B--S--..SSTTS------BS..SGGGHHHHHHHHHHH CS
                  PhosphMutase  82 teeakeLikalneeleegvevkfypgveyrhllvl....lsdkitdtdpphdkegkeikellpl.kseeaketaellneli 157
                                    eea+eL k++++   +gv+v f+++ +yr +lvl    ls +++d dp  ++eg +++e++pl +seeak+tae+ln+l+
  gi|15669808|ref|NP_248622.1| 118 PEEAEELEKEIDGLEIDGVKVIFKSSKGYRGALVLrgegLSCRVSDGDP--HEEGVKVSEIKPLdDSEEAKRTAEILNKLL 196
                                   *************77369*******************************..9************9999************* PP

                                   HHHHHHHHHSHHH CS
                  PhosphMutase 158 eksqeiLedhpvN 170
                                   + ++e L++hp+N
  gi|15669808|ref|NP_248622.1| 197 KIVYEKLNNHPIN 209
                                   ************9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.5   0.0   3.5e-57   8.9e-54       2     246 ..       5     400 ..       4     402 .. 0.99

  Alignments for each domain:
  == domain 1  score: 182.5 bits;  conditional E-value: 3.5e-57
                                   EEEEEEETTBB----GGGTT.HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH.............. CS
                                   xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                 Metalloenzyme   2 kvvlvvlDGlGeapadelna.ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel.............. 67 
                                   k+v+ ++DGlG++p+++    ++ AktPt+dk++ke       +++g++ +++ +++++s+++Hl++              
  gi|15669808|ref|NP_248622.1|   5 KCVIFIIDGLGDRPNEKGLTpLKEAKTPTMDKIAKE-------GICGLMNAIDIGIRPGSDTAHLAIlgynpyevytgrgp 78 
                                   789************998778***************.......9************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Metalloenzyme  68 ................................................................................. 67 
                                                                                                                    
  gi|15669808|ref|NP_248622.1|  79 leafgvgldlkegdiafrcnfatvdenfvvldrragrispeeaeelekeidgleidgvkvifksskgyrgalvlrgeglsc 159
                                   ********************************************************************************* PP

                                   ...................................................HHHHTT-----EEEEEEEE-S---SSHHHH CS
                                   ...................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme  68 ...................................................lrisetvkfahvtffwnggrsgyfnpleer 97 
                                                                                       r++++  +a++++ +++g+ +++++++e+
  gi|15669808|ref|NP_248622.1| 160 rvsdgdpheegvkvseikplddseeakrtaeilnkllkivyeklnnhpineERRKKGLPPANIILPRGAGVVPKIEKFSEK 240
                                   ***************************************************99**************************** PP

                                   HT--EEEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHH CS
                                   xxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme  98 eeipsdtvitfdl....................qpemkavevaekaldailsgkfdlvvvniknaDmvGHtgdleatiaai 158
                                   +++++++++ + l                    +p+++ + +a+++++a+ ++ +d+v+vn+k aD+++H+g++e + +++
  gi|15669808|ref|NP_248622.1| 241 YNMKGACICGTGLikgmakmigldvievegatgTPKTNFMGKAKALVEAL-KE-YDFVLVNVKGADEASHDGNYELKKEVL 319
                                   **************************************************.66.*************************** PP

                                   HHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS........-----EEEEEESTT----S--S.SHHHHTT-TTEEEEG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                 Metalloenzyme 159 eaaDeavkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglapdkvke.gakfrekggLanvaa 238
                                   e++De+++ ++++i++++ ++v+t+DH+++ +m++        H+++p+Pi+i+gk+++ d+v+e ++ +++kg L+ +++
  gi|15669808|ref|NP_248622.1| 320 EKIDEMLAYVFEHINKDEVYFVLTGDHSTPIEMKD--------HSADPIPIVIWGKSVRVDDVTEfNEFACAKGALHWIKG 392
                                   ***********************************........************************************** PP

                                   GGHHHHHH CS
                                   xxxxxxxx RF
                 Metalloenzyme 239 tllnllgl 246
                                   ++++++ l
  gi|15669808|ref|NP_248622.1| 393 EHVMKILL 400
                                   **999876 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.045   1.1e+02       2      35 ..       7      45 ..       6      50 .. 0.83
   2 !   21.0   0.0   8.4e-08   0.00021     155     234 ..     278     348 ..     229     400 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.045
                                  EEEEETT-B....TTHHHHHG.STSHHHHHHHHHSEEES CS
                  Phosphodiest  2 lvislDGlr....adlldrla.ellpnlaaLakegvsap 35
                                  +++++DGl      + l +l+  ++p ++++akeg+ + 
  gi|15669808|ref|NP_248622.1|  7 VIFIIDGLGdrpnEKGLTPLKeAKTPTMDKIAKEGICGL 45
                                  68889999888887788899856************9876 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 8.4e-08
                                   HHHHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES--- CS
                  Phosphodiest 155 twldaafakvvlekelekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGm 234
                                   ++  +a+a v++    +++d++lv++ + D ++H    ++   ++ l+++D+++++ +e + ++    e+ ++l++DH  
  gi|15669808|ref|NP_248622.1| 278 NFMGKAKALVEAL---KEYDFVLVNVKGADEASHDG-NYE-LKKEVLEKIDEMLAYVFEHINKD----EVYFVLTGDHST 348
                                   5555555554444...******************76.333.347899*****************....999*******74 PP

>> RACo_C_ter  C-terminal domain of RACo the ASKHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.7e-05     0.068      70     102 ..     244     276 ..     220     309 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                                   --SEEEHHHHHHHHHHHHHTTSB-TTS-B-GGG CS
                    RACo_C_ter  70 kakGicGsGiidliaelleagiidkkgklnkel 102
                                   k   icG+G+i+ +a+++   +i+ +g   + +
  gi|15669808|ref|NP_248622.1| 244 KGACICGTGLIKGMAKMIGLDVIEVEGATGTPK 276
                                   4567********************999874442 PP

>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.8e-05     0.072       7      42 ..     224     258 ..     219     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-05
                                   E-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE CS
                        DUF296   7 lepGediveaieefarkrgiraacvlsaiGavsnvt 42 
                                   l++G  +v +ie+f++k ++++ac+  ++G ++ + 
  gi|15669808|ref|NP_248622.1| 224 LPRGAGVVPKIEKFSEKYNMKGACI-CGTGLIKGMA 258
                                   789999*******************.****999887 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   6.3e-05      0.16     254     327 ..     295     369 ..     282     392 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.3e-05
                                   EEEEEETCHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHCHHCTTEEEEEEESSEESEEEESTTST..T..TTSEEC CS
               Alk_phosphatase 254 FLlVEGsrIDhaaHendavgalsEvvefdeAvkaalefakkeketlvvvTaDHshvfsfggyttr..gesvlglep 327
                                   F lV     D+a H+++   + +   ++de ++++ e+ + ++e   v T DHs+ +++  +++   +  ++g ++
  gi|15669808|ref|NP_248622.1| 295 FVLVNVKGADEASHDGNYELKKEVLEKIDEMLAYVFEHIN-KDEVYFVLTGDHSTPIEMKDHSADpiPIVIWGKSV 369
                                   5555555679******99988777889*************.67888999******999999998855556666554 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.11   2.9e+02       4      37 ..       7      42 ..       5      43 .. 0.88
   2 ?    8.9   0.0   0.00034      0.88     216     265 ..     317     392 ..     271     397 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                                  EEEEESSE-TT..GSGGGTTTSCSSHHHHHHHHTSE CS
                     Sulfatase  4 vliladdlgag..dlglyggktattpnldrlaeegl 37
                                  v+ ++d lg+     gl   k a tp++d++a+eg+
  gi|15669808|ref|NP_248622.1|  7 VIFIIDGLGDRpnEKGLTPLKEAKTPTMDKIAKEGI 42
                                  778889999888899999999999**********97 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00034
                                   HHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCG..............................HHTTSSSCTT CS
                     Sulfatase 216 nsveyvDdligrvlaaLeenglldntlvvftSDhgaslee..............................sngplrggkg 265
                                     +e +D++++ v++ +     +d++++v t+Dh   +e                               ++g+l++ kg
  gi|15669808|ref|NP_248622.1| 317 EVLEKIDEMLAYVFEHI----NKDEVYFVLTGDHSTPIEMkdhsadpipiviwgksvrvddvtefnefacAKGALHWIKG 392
                                   56888999999999999....***************99877777777777777777777777777777666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2615.77
//
Query:       gi|15669809|ref|NP_248623.1|  [L=255]
Description: hypothetical protein MJ_1613 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-60  203.4   0.3    4.1e-60  203.2   0.3    1.0  1  CbiZ      Adenosylcobinamide amidohydrolase


Domain annotation for each model (and alignments):
>> CbiZ  Adenosylcobinamide amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.2   0.3   2.3e-64   4.1e-60       1     192 []      35     243 ..      35     243 .. 0.96

  Alignments for each domain:
  == domain 1  score: 203.2 bits;  conditional E-value: 2.3e-64
                          CbiZ   1 rfeeprrvlssavlngGlrelravlnhqvpegyered..peeyleeyleelglppektvgllTaadmenaaiaeeefedle 79 
                                   +f+++r+vls+    +G++e+++v nh++p +++++    ++y +++l+++g+++e++++l+T+a+m+n+a+a+eef+++ 
  gi|15669809|ref|NP_248623.1|  35 EFKNKRKVLSTR---EGFKEVKYVGNHSIPVPFWDKVhnYKDYENQVLNKIGIKKEDIALLSTGANMDNLAVAKEEFDEFY 112
                                   5999********...********************997768898999********************************** PP

                          CbiZ  80 vtavvTaGvesnavragd..................edeeaekpGTINiivlinaaLtdaalvralitatEAKtaalqdlg 142
                                   v+a++TaG ++na+r+gd                  +   +e++GT+Nii+++na+Ltd+a++ra+it+tEAKt a+q+l+
  gi|15669809|ref|NP_248623.1| 113 VVAFTTAGAKHNAIRLGDeeadyiekdfktykivdgKIVPKEEIGTVNIILITNANLTDGAMARAIITITEAKTNAFQELN 193
                                   ************************************777899*************************************** PP

                          CbiZ 143 vrsryseg..atGTgTDaiavaadkegeeeltyaGkhtklGeliaraVyeAv 192
                                   +rs+++++  atGTgTD+i+v+    g+  ++y+G+htk+Ge+ia+aV+++v
  gi|15669809|ref|NP_248623.1| 194 IRSTKHPElqATGTGTDNIVVVKG-FGS-GVDYTGGHTKMGEMIAKAVKRSV 243
                                   ************************.555.39******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1977.73
//
Query:       gi|15669810|ref|NP_248624.1|  [L=251]
Description: hypothetical protein MJ_1614 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-23   80.9   0.0    1.5e-22   80.1   0.0    1.4  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
       0.12   12.2   2.4        1.5    8.8   0.1    3.1  3  DUF4041       Domain of unknown function (DUF4041)


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.0   1.7e-26   1.5e-22      10     210 .]      29     211 ..      21     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 1.7e-26
                                   SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHHHHHHHTBSEEEE CS
                  AP_endonuc_2  10 dgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraielaaaLGapllvl 89 
                                   ++vEl +++  +v++      +   +++++++l+ +++++ t+ + +  +  e r r+ s+d++++ +e a +++a+l+vl
  gi|15669810|ref|NP_248624.1|  29 KYVELGCDGNLNVMS------DGNIELAQSYDLKYTLHCPITDLNLSSYR--E-RiRKVSLDFVRDVLEVAIKVDAKLIVL 100
                                   678888888888874......55556677777777777777777776553..3.347799********************* PP

                                   EBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEEEEHHHHHHHTT CS
                  AP_endonuc_2  90 hpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgdeelarlldavdspnvgvclDtgHlliaee 170
                                   hpG      k ++e a++ l++sln+l  + e+ gv++ +E++++ ++++ +   +++++ ++   ++++lD+gH++++  
  gi|15669810|ref|NP_248624.1| 101 HPG--YCVFKYDYEKALNSLIKSLNDLNNIQEEFGVQITIENMPSYDMFMFRNPDKEIIENLGE--LKITLDIGHSFLN-K 176
                                   ***..9**********************************************9999*******7..*************.7 PP

                                   THHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSSS CS
                  AP_endonuc_2 171 dvddalraladrikhvHikDakgdlgagrdrhvpigeGei 210
                                   +++ +l+ + d+i+h+Hi+D++g      d+h+ ig+G i
  gi|15669810|ref|NP_248624.1| 177 NIENFLK-ISDKIAHIHIHDNNG----EFDEHLCIGKGKI 211
                                   7777775.5677***********....***********87 PP

>> DUF4041  Domain of unknown function (DUF4041)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.22     2e+03      22      33 ..      67      78 ..      64      81 .. 0.86
   2 ?    8.8   0.1   0.00016       1.5      23      51 ..     111     139 ..     106     140 .. 0.92
   3 ?    1.4   0.1     0.034     3e+02      17      32 ..     210     225 ..     205     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.22
                       DUF4041 22 nietlekRIeks 33
                                  n+ + ++RI+k+
  gi|15669810|ref|NP_248624.1| 67 NLSSYRERIRKV 78
                                  7889999**996 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00016
                       DUF4041  23 ietlekRIeksfeainklgktmnirItpe 51 
                                   +e++ + ++ks +++n++ + ++++It e
  gi|15669810|ref|NP_248624.1| 111 YEKALNSLIKSLNDLNNIQEEFGVQITIE 139
                                   899999********************975 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.034
                       DUF4041  17 kVkynnietlekRIek 32 
                                   k+++nn+++  k+I+ 
  gi|15669810|ref|NP_248624.1| 210 KINFNNFKKDLKKINA 225
                                   8999*****9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1733.66
//
Query:       gi|15669811|ref|NP_248625.1|  [L=255]
Description: hypothetical protein MJ_1615 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-66  223.5   2.5    2.9e-66  223.3   2.5    1.0  1  CheF-arch  Chemotaxis signal transduction system protein F fr
  ------ inclusion threshold ------
       0.12   12.4   0.9       0.22   11.6   0.9    1.4  1  YpjP       YpjP-like protein


Domain annotation for each model (and alignments):
>> CheF-arch  Chemotaxis signal transduction system protein F from archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.3   2.5   3.2e-70   2.9e-66       1     214 [.       7     253 ..       7     255 .] 0.96

  Alignments for each domain:
  == domain 1  score: 223.3 bits;  conditional E-value: 3.2e-70
                     CheF-arch   1 kiadfkGkfllvvkkgrkkkdvkWekgrilLsnkrlvlasedkkitiplssvedvggevPrklkdifddtvtdakvsgyia 81 
                                   +ia+f+Gk++l+++k+++k+ +kWek++i+L+++++v+++ dk+i++ ++++edvg+e+P+k++di+++t++d++++++i 
  gi|15669811|ref|NP_248625.1|   7 EIARFSGKGILITPKTLEKPLLKWEKLEIILYKDKIVFEFVDKTIEVGVEDIEDVGAELPKKVIDIAKSTLEDITYHSSII 87 
                                   59******************************************************************************* PP

                     CheF-arch  82 lktkdgenvllieaedes......iekFetkLfkalLngkevlvkhpAvvGGvvq.dtewekgklkvekkaielatkkgsf 155
                                   +k+k+++nv++++a+++s      i++F++kLf++lLn+kev++ ++A   G+++ +t+we+g+l++ kk+i    k+g +
  gi|15669811|ref|NP_248625.1|  88 IKSKEFGNVMVGFAPETSiygkapIDNFLRKLFYILLNKKEVKILYNA---GENSeNTKWENGFLTFIKKRI----KDGLV 161
                                   ************************************************...99999****************....***** PP

                     CheF-arch 156 veiel..................sdvgdvereektvdgeerpvlevehtedgesvttylagkdk.......rkvslL.... 207
                                   ++ie                   s+++dve+eek+vdge +pvl++ +++dg+++ +yl++kdk       r++ +L    
  gi|15669811|ref|NP_248625.1| 162 TKIEYrlvveildnedskiydifSNIKDVEIEEKDVDGEIEPVLKILQVKDGKDIISYLYTKDKkvrlfilRYMVILldyk 242
                                   **877778888****************************************************999999999999997777 PP

                     CheF-arch 208 ....erylree 214
                                        ryl+e+
  gi|15669811|ref|NP_248625.1| 243 yigiLRYLQET 253
                                   66666777766 PP

>> YpjP  YpjP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.9   2.4e-05      0.22      25      98 ..     151     227 ..     127     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                          YpjP  25 kiaekiedefeeeilpkieevieellekv...eeekleeleisekpasgkgEkifhiynkktkedllrfhvrrdkrp 98 
                                    i+++i+d + ++i+ ++  +i +  ++      ++++++ei+ek   g+ E +++i + k ++d++ +   +dk++
  gi|15669811|ref|NP_248625.1| 151 FIKKRIKDGLVTKIEYRLVVEILDNEDSKiydIFSNIKDVEIEEKDVDGEIEPVLKILQVKDGKDIISYLYTKDKKV 227
                                   4777777777777777766655554333323334678999****************************999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1749.87
//
Query:       gi|15669812|ref|NP_248626.1|  [L=496]
Description: inosine-5'-monophosphate dehydrogenase GuaB [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   4.2e-153  509.4  10.1   5.8e-153  508.9  10.1    1.2  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    4.5e-30  103.9  10.5    1.2e-15   57.7   0.7    3.2  3  CBS           CBS domain
      3e-13   49.5  11.0      6e-12   45.2  10.8    2.7  2  FMN_dh        FMN-dependent dehydrogenase
    4.9e-11   42.6  14.0    2.4e-07   30.5   9.1    2.8  3  NMO           Nitronate monooxygenase
    5.6e-07   29.0   5.8    1.2e-06   28.0   5.8    1.5  1  Glu_synthase  Conserved region in glutamate synthase
      8e-06   25.5   7.9    8.7e-06   25.4   3.5    2.7  2  His_biosynth  Histidine biosynthesis protein
    7.9e-05   22.0   4.3     0.0024   17.2   1.0    2.5  2  DHO_dh        Dihydroorotate dehydrogenase
    0.00012   21.5   4.9     0.0005   19.5   3.3    2.3  2  ThiG          Thiazole biosynthesis protein ThiG
     0.0012   18.9   2.3      0.013   15.5   0.1    2.5  2  B12-binding   B12 binding domain
     0.0014   17.8   0.2     0.0033   16.6   0.2    1.5  1  Dus           Dihydrouridine synthase (Dus)
     0.0028   16.9   2.1      0.049   12.8   0.2    2.4  2  DUF561        Protein of unknown function (DUF561)
  ------ inclusion threshold ------
      0.021   14.2   5.4       0.34   10.2   1.5    2.5  2  TMP-TENI      Thiamine monophosphate synthase
      0.034   13.6   0.1      0.034   13.6   0.1    2.9  3  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
       0.48    9.9   1.8        1.4    8.4   0.3    2.1  2  EAL           EAL domain


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  508.9  10.1  4.5e-156  5.8e-153       1     345 []      12     481 ..      12     481 .. 0.97

  Alignments for each domain:
  == domain 1  score: 508.9 bits;  conditional E-value: 4.5e-156
                                   E--GGGEEEE---B-S-GGGSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH   1 gltfddvllvpaksevlpkevdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevkkvkr 81 
                                   ++tfddvllvp++s v+pk++d++t+l+  +klniP+vsaamdtvte+emAialar Gg+gvih+n+sieeq+++v++vk+
  gi|15669812|ref|NP_248626.1|  12 AYTFDDVLLVPNASWVEPKDTDVSTDLA-GLKLNIPIVSAAMDTVTEKEMAIALARLGGLGVIHRNMSIEEQVHQVQAVKK 91 
                                   69*************************8.89************************************************** PP

                                   S................................................................................ CS
                                   x................................................................................ RF
                         IMPDH  82 s................................................................................ 82 
                                   +                                                                                
  gi|15669812|ref|NP_248626.1|  92 Adevvikdvitvspddtvgeainvmetysisglpvvdnedklvgiithrdvkaiedktkkvkdvmtkdvvcakedveeeea 172
                                   ********************************************************************************* PP

                                   ....................................TTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STS CS
                                   ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH  83 ....................................pnaakdekgrllvgaavgvkedalervkalveagvdvlvvdsahg 127
                                                                       p+aa+d+kgrllv+aa+g ++  +er+kal+ea+vd++++d+ah+
  gi|15669812|ref|NP_248626.1| 173 lelmyanrverlpivddenrligiitlrdilkrrkyPQAARDKKGRLLVAAACGPHD--FERAKALIEAEVDAIAIDCAHA 251
                                   ******************************************************995..9********************* PP

                                   SSHHHHHHHHHHHHHTT..TSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTC CS
                                   xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 128 hsekvleavkeikkkve..eveviaGnvataegakaLieagadavkvGiGpGsiCttrvvagvGvpqltAvaevaeaakka 206
                                   h+ +v+e vk+ k+ +e  ++++i+Gn+at+e+a++Li+agad++kvGiGpGsiCttrvvagvGvpqltAvaeva++ak++
  gi|15669812|ref|NP_248626.1| 252 HNMRVVENVKKFKEMLEgtDIKLIVGNIATKEAAEDLIKAGADVLKVGIGPGSICTTRVVAGVGVPQLTAVAEVADVAKEH 332
                                   **************997435************************************************************* PP

                                   T-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEEEETTEEEEEEEETTSHHHHHH-...SS-TTS-..... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx...xx RF
                         IMPDH 207 gvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgeviliegrkyKeyrGmgslgamkkg...skdryfq...kk 281
                                   +vp+iaDGGi+ysgdi+kA+aaGadavmlGsllagt+E+pg++++i+grkyK+yrGmgslgam+ g    +dryfq   k 
  gi|15669812|ref|NP_248626.1| 333 NVPIIADGGIRYSGDIAKAIAAGADAVMLGSLLAGTDEAPGQLMVINGRKYKQYRGMGSLGAMTGGvgaGADRYFQapaK- 412
                                   ***************************************************************663445899***96532. PP

                                   -.....-SS-SBEEEEEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEEEE-HHHHHHHS-- CS
                                   x.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 282 e.....klvpeGvegrvpykgsvkevveqlvgglrsgmgylGaktieelkekakfvritaaglkeshvH 345
                                   +     klvpeGveg+vpykg+v+evv ql+gglr++mgy+Gak+++e++eka+fv it +g+ esh+H
  gi|15669812|ref|NP_248626.1| 413 ShmkhvKLVPEGVEGAVPYKGPVSEVVFQLIGGLRASMGYCGAKNLKEMQEKARFVIITPSGQVESHPH 481
                                   246789**************************************************************9 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   2.1   2.8e-16   3.5e-13       3      51 ..      94     142 ..      92     145 .. 0.91
   2 !   57.7   0.7     9e-19   1.2e-15       1      55 [.     152     206 ..     152     208 .. 0.96
   3 ?   -1.3   0.0       2.5   3.2e+03      12      39 ..     316     340 ..     303     346 .. 0.63

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 2.8e-16
                                   HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                           CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                   ++  +dv+tv+pd+t++ea++ m+ + +s+lPVVd+++klvGi+t rD+
  gi|15669812|ref|NP_248626.1|  94 EVVIKDVITVSPDDTVGEAINVMETYSISGLPVVDNEDKLVGIITHRDV 142
                                   677899*****************6666*******9999**********8 PP

  == domain 2  score: 57.7 bits;  conditional E-value: 9e-19
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   V+d+mt+dvv++++d   eealelm  ++v rlP+Vd++++l+Gi+tlrD+l+  
  gi|15669812|ref|NP_248626.1| 152 VKDVMTKDVVCAKEDVEEEEALELMYANRVERLPIVDDENRLIGIITLRDILKRR 206
                                   89***********************9999***********************975 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.5
                                   EETTSBHHHHHHHHHHHTSSEEEEEETT CS
                           CBS  12 vppdttleealelmrekgvsrlPVVded 39 
                                   vp  t ++e+++  +e   + +P++ + 
  gi|15669812|ref|NP_248626.1| 316 VPQLTAVAEVADVAKE---HNVPIIADG 340
                                   5555668888888855...799998544 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2  10.8   4.7e-15     6e-12      28     302 ..      13     364 ..       6     378 .. 0.78
   2 ?    0.0   0.0      0.26   3.4e+02     315     344 ..     435     464 ..     431     466 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 4.7e-15
                                   HGGGGEEE---S.SSS-SS-B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT-S.S-HHHHHH CS
                        FMN_dh  28 aaferirlrprv.lrdvskvdlsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvlstvas.tsleevaa 106
                                    +f+++ l+p++  ++ ++ d+st+l G kl++P++ a  ++ ++ +++  +alar      i   +s   + +++++v++
  gi|15669812|ref|NP_248626.1|  13 YTFDDVLLVPNAsWVEPKDTDVSTDLAGLKLNIPIVSA--AMDTVTEKEMAIALARLGGLGVIHRNMSIEEQvHQVQAVKK 91 
                                   57999999998735788899**************9855..67788877777777776544444334443332033444444 PP

                                   HHTT-EEEEEE-CSSHHHHHHHHHHHHHCTESEEEE..ESSTSS---BHHHHHCT--BSTT-T.G.TTGGGSTSGSCCTTH CS
                        FMN_dh 107 aaegplwfqlyvpkdrelteellkraeaagykalvl..tvDtpvlgkRerdlrngfslppklklrnllqelakpewaaeal 185
                                    a++ ++  +  ++ ++++ e ++ +e   ++ l +  + D  v    +rd+++     +k+k  ++ +++  +e ++e++
  gi|15669812|ref|NP_248626.1|  92 -ADEVVIKDVITVSPDDTVGEAINVMETYSISGLPVvdNEDKLVGIITHRDVKAIEDKTKKVKDVMTKDVVCAKEDVEEEE 171
                                   .55688888888888999999999999998888744227899***********9666667766666666666666665555 PP

                                   .....................................................................THHHH..HHCCC CS
                        FMN_dh 186 ...................................................................kkasaaa..efvgk 197
                                                                                                      +++ a a     ++
  gi|15669812|ref|NP_248626.1| 172 alelmyanrverlpivddenrligiitlrdilkrrkypqaardkkgrllvaaacgphdferakalieAEVDAIAidCAHAH 252
                                   89999***************************************************9998877666533333333111222 PP

                                   HB-TC--HHHHHHHHHHHSSEEEEEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT-.--HHHCHHHHHHHH...S CS
                        FMN_dh 198 qldpsltwddikwlreqtklplvvKGvltaedakraveaGvdgivvSNHGG.....Rqldga.patidvLpeiveavgg.r 271
                                    ++   + ++ k++ e t+++l+v  + t+e a+ +++aG+d + v    G     R + g+ ++ + +  e+++ +++ +
  gi|15669812|ref|NP_248626.1| 253 NMRVVENVKKFKEMLEGTDIKLIVGNIATKEAAEDLIKAGADVLKVGIGPGsicttRVVAGVgVPQLTAVAEVADVAKEhN 333
                                   2333338888999999999***************************88888788888888763677999999999999746 PP

                                   S-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
                        FMN_dh 272 ievlvDgGirrGsDvlkAlalGAdavllGRp 302
                                   +++++DgGir   D++kA+a GAdav+lG  
  gi|15669812|ref|NP_248626.1| 334 VPIIADGGIRYSGDIAKAIAAGADAVMLGSL 364
                                   ****************************965 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.26
                                   HHHHHHHHHHHHHHHHHHHT-SBHHHHHCG CS
                        FMN_dh 315 vervleilraelertmallGvksvaeldrs 344
                                   v++v+  l   l+++m  +G+k+++e++++
  gi|15669812|ref|NP_248626.1| 435 VSEVVFQLIGGLRASMGYCGAKNLKEMQEK 464
                                   677888888999**************9875 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   3.4e-05     0.043       9      59 ..      42      91 ..      35     119 .. 0.81
   2 ?   -1.1   0.0      0.76   9.7e+02     224     265 ..     218     259 ..     216     273 .. 0.81
   3 !   30.5   9.1   1.8e-10   2.4e-07     137     234 ..     273     374 ..     239     386 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-05
                           NMO  9 kikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvka 59
                                  k + p+v + m  +++ ++a a +  GgLGv+    ++  +  +++++vk+
  gi|15669812|ref|NP_248626.1| 42 KLNIPIVSAAMDTVTEKEMAIALARLGGLGVIH-RNMSIEEQVHQVQAVKK 91
                                  56789***************************9.55666555555555554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.76
                           NMO 224 rfLltkesdakdahkkk.lleaklddteltsavsGrpaRalat 265
                                   r+L++  ++ +d  ++k l+ea++d++ +  a    ++R++ +
  gi|15669812|ref|NP_248626.1| 218 RLLVAAACGPHDFERAKaLIEAEVDAIAIDCAHA-HNMRVVEN 259
                                   8999999999999886527899999999998888.88887765 PP

  == domain 3  score: 30.5 bits;  conditional E-value: 1.8e-10
                           NMO 137 vvliptissvkearkvearGaDalivqGpeaGGhqGtpevgd..kglfaLvpqvldavd...iPviAaGGiidrrgvaaaL 212
                                    ++++ i++ ++a  ++++GaD+l v G   G    t+ v++  + +++ v++v+d+ +   +P+iA GGi    ++a a+
  gi|15669812|ref|NP_248626.1| 273 KLIVGNIATKEAAEDLIKAGADVLKV-GIGPGSICTTRVVAGvgVPQLTAVAEVADVAKehnVPIIADGGIRYSGDIAKAI 352
                                   34567899999***********9977.77778777788888844445555777777766777******************* PP

                           NMO 213 alGAsgvqigtrfLltkesdak 234
                                   a+GA +v +g+ + +t+e++ +
  gi|15669812|ref|NP_248626.1| 353 AAGADAVMLGSLLAGTDEAPGQ 374
                                   ******************9765 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   5.8   9.2e-10   1.2e-06     191     304 ..     257     363 ..     240     366 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 9.2e-10
                                   HHHHHHHHHH-TTSEEEEEEE-ST.THHHHHHHHHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT CS
                  Glu_synthase 191 aqliedLkevnkeakvsvKlvaea.gvetiaagvakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeg 270
                                    + +++ ke+ +     +Kl  ++  ++  a  + ka+ad++++ G+  G     + ++  +G+P ++a+aev  + ke  
  gi|15669812|ref|NP_248626.1| 257 VENVKKFKEMLEGTD--IKLIVGNiATKEAAEDLIKAGADVLKV-GIGPGS-ICTTRVVAGVGVPQLTAVAEVADVAKE-- 331
                                   445666666664444..555444304444555599*******99.555454.456678899***********9987665.. PP

                                   -GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SH CS
                  Glu_synthase 271 lrdrvsliadGglktgadvvkalalGAdavgigt 304
                                     ++v +iadGg++ + d++ka+a GAdav +g+
  gi|15669812|ref|NP_248626.1| 332 --HNVPIIADGGIRYSGDIAKAIAAGADAVMLGS 363
                                   ..789**************************997 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.26   3.3e+02     111     167 ..      47     103 ..      42     109 .. 0.84
   2 !   25.4   3.5   6.8e-09   8.7e-06      81     223 ..     226     365 ..     214     370 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.26
                                   HHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEE CS
                  His_biosynth 111 likelaekfgsqkivvaiDarrgykvaikgwreetgldavelakkleelgageillt 167
                                   +++ +++ + ++++++a+    g  v  ++   e++++ v+ +kk++e+ +++++  
  gi|15669812|ref|NP_248626.1|  47 IVSAAMDTVTEKEMAIALARLGGLGVIHRNMSIEEQVHQVQAVKKADEVVIKDVITV 103
                                   57778888888889999985556889999999999*************999999875 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 6.8e-09
                                   SSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE..CEEEEETTTTEEEEEEHHHHHHHHHHT CS
                  His_biosynth  81 GIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr..gykvaikgwreetgldavelakkleel 159
                                   G  ++e++++l+ea +d + i  a ++n  +++++ + f +  +  + D++   g ++a+k+  e+    +++   ++ ++
  gi|15669812|ref|NP_248626.1| 226 GPHDFERAKALIEAEVDAIAIDCAHAHNMRVVENVKK-FKE--MLEGTDIKLivG-NIATKEAAED----LIKAGADVLKV 298
                                   667899***********************99998877.665..889999887666.6777666666....99999999999 PP

                                   T-S..EEEEEE.TTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHH CS
                  His_biosynth 160 gag..eilltd.idrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsal 223
                                   g+g  +i  t  ++ +G+ +   +  + ++a++ ++p+ia GG++   d++++ ++g+dav++gs+l
  gi|15669812|ref|NP_248626.1| 299 GIGpgSICTTRvVAGVGVPQLTAVAEVADVAKEHNVPIIADGGIRYSGDIAKAIAAGADAVMLGSLL 365
                                   986325555543789*************************************************998 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.1    0.0075       9.6     231     274 ..     257     300 ..     252     314 .. 0.84
   2 !   17.2   1.0   1.8e-06    0.0024     229     276 ..     320     365 ..     306     372 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0075
                                   HHHHHHHHHHTTT..S-EEEESS--SHHHHHHHHHHTECEEEESH CS
                        DHO_dh 231 lkvirelykrlkk.eipiIgvGGiesgeDalekieaGAslvqvyt 274
                                   ++++ +++++l++ +i++I vG i + e a + i+aGA +++v+ 
  gi|15669812|ref|NP_248626.1| 257 VENVKKFKEMLEGtDIKLI-VGNIATKEAAEDLIKAGADVLKVGI 300
                                   5677777777764269999.9********************9985 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.8e-06
                                   HHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                        DHO_dh 229 ialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                                   +a++ + +++k+ +  +piI+ GGi  + D    i aGA +v +++ l
  gi|15669812|ref|NP_248626.1| 320 TAVAEVADVAKEHN--VPIIADGGIRYSGDIAKAIAAGADAVMLGSLL 365
                                   57788888888888..****************************9977 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.19   2.4e+02     101     126 ..     270     295 ..     220     300 .. 0.52
   2 !   19.5   3.3   3.9e-07    0.0005     165     212 ..     323     370 ..     268     376 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.19
                                   ETTTTEB-HHHHHHHHHHHHHTT-EE CS
                          ThiG 101 dektLlPdvvetlkaaeiLvkeGFev 126
                                    +  L+  ++ t +aae L+k G  v
  gi|15669812|ref|NP_248626.1| 270 TDIKLIVGNIATKEAAEDLIKAGADV 295
                                   23334444555555555555555555 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 3.9e-07
                                   HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSS CS
                          ThiG 165 ealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakd 212
                                   + +  + +e +vP+i D Gi+ + d+a+a+  Gadav+l + +a +++
  gi|15669812|ref|NP_248626.1| 323 AEVADVAKEHNVPIIADGGIRYSGDIAKAIAAGADAVMLGSLLAGTDE 370
                                   4455567888*****************************999987765 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1     1e-05     0.013      44     113 ..     233     301 ..     214     307 .. 0.84
   2 ?    2.4   0.3      0.11   1.5e+02      63     111 ..     317     362 ..     310     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                   B12-binding  44 vaairaekpdvvglSalltsqleavkelvel.lkrirprvkvvvGGahpsldpeetleaklgiddvvvgeg 113
                                   ++a+++ ++d++++ +   ++++ v+++ ++ +  ++ ++k++vG ++   ++e++++   g+d+  vg g
  gi|15669812|ref|NP_248626.1| 233 AKALIEAEVDAIAIDCAHAHNMRVVENVKKFkEMLEGTDIKLIVGNIATKEAAEDLIK--AGADVLKVGIG 301
                                   45888999********999******9999998555667*****************997..78788766655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                   B12-binding  63 sqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvvvg 111
                                    ql+av+e+++ +k+ +   +++ GG+  s d +  ++   g+d v++g
  gi|15669812|ref|NP_248626.1| 317 PQLTAVAEVADVAKEHNV-PIIADGGIRYSGDIAKAIA--AGADAVMLG 362
                                   578899999999999854.5788899999999999775..788888877 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   2.6e-06    0.0033     172     214 ..     322     363 ..     308     380 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-06
                                   CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESC CS
                           Dus 172 weaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigr 214
                                    +++++v ++ ++p+ia G+I++  d+ ++++  Gad+vm g 
  gi|15669812|ref|NP_248626.1| 322 VAEVADVAKEHNVPIIADGGIRYSGDIAKAIAA-GADAVMLGS 363
                                   5789999*************************9.******995 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.029        37     184     238 ..      42      97 ..      30     102 .. 0.79
   2 !   12.8   0.2   3.9e-05     0.049     101     217 ..     252     365 ..     235     379 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.029
                        DUF561 184 kvslPvicasGlsdvtvplalslg.asGiGigsavsklndeeemvallseikkais 238
                                   k+++P+++a+  +    ++a++l    G+G+ +   +++++++ v+++++  + + 
  gi|15669812|ref|NP_248626.1|  42 KLNIPIVSAAMDTVTEKEMAIALArLGGLGVIHRNMSIEEQVHQVQAVKKADEVVI 97 
                                   789****9987777778999998625789*99999999999999999998777665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.9e-05
                        DUF561 101 sseeilalvkevrkLlPktdlsvtiPyiLkleeqvkLakkLeslgvdliqteGkitsiskakkvndliekslstlastyei 181
                                   ++  ++  vk+ +++l  td+   +  i + e     a++L ++g+d+++   +  si  ++ v ++    l+++a +  +
  gi|15669812|ref|NP_248626.1| 252 HNMRVVENVKKFKEMLEGTDIKLIVGNIATKE----AAEDLIKAGADVLKVGIGPGSICTTRVVAGVGVPQLTAVAEVADV 328
                                   67778888999999999999999998887654....599***********9999999999*******999*********** PP

                        DUF561 182 skkvslPvicasGlsdv.tvplalslgasGiGigsav 217
                                   +k+ ++P+i+  G+  +  +  a+++ga  + +gs +
  gi|15669812|ref|NP_248626.1| 329 AKEHNVPIIADGGIRYSgDIAKAIAAGADAVMLGSLL 365
                                   **************86625788999999999888865 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.5    0.0073       9.3      13      64 ..     227     278 ..     219     301 .. 0.83
   2 ?   10.2   1.5   0.00027      0.34     105     177 ..     281     361 ..     278     365 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0073
                      TMP-TENI  13 eellevveealkggvtlvqlRekeldarellelaeklaalcrkygvpliind 64 
                                    +++e+++++++++v+++ +   ++++ +++e ++k +++ + ++++li+ +
  gi|15669812|ref|NP_248626.1| 227 PHDFERAKALIEAEVDAIAIDCAHAHNMRVVENVKKFKEMLEGTDIKLIVGN 278
                                   567899999***************************************9965 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00027
                      TMP-TENI 105 sleeaeeaealgadYigvGpifpTdtKkda.eplgleglkelaeale......iPvvaiGGitle.nvaevleagadgvav 177
                                   ++e ae + ++gad + vG    + + +   + +g+ +l+++ae +       +P++a GGi+ + ++a++++agad v +
  gi|15669812|ref|NP_248626.1| 281 TKEAAEDLIKAGADVLKVGIGPGSICTTRVvAGVGVPQLTAVAEVADvakehnVPIIADGGIRYSgDIAKAIAAGADAVML 361
                                   556677777888887666544444444444455555555555555554446669********97549**********9976 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.1   1.4e+03      76     124 ..      55     105 ..      51     122 .. 0.66
   2 ?    0.4   0.1       0.3   3.8e+02     131     164 ..     263     295 ..     231     299 .. 0.74
   3 ?   13.6   0.1   2.7e-05     0.034     131     167 ..     325     361 ..     316     364 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                                   EES-HHHHHHHHHTT--EEEEEE--SHHH..HHHHHHHHHHHT-SEEEEES CS
                  G3P_antiterm  76 istksslikkakklglltiqrlfliDssa..lekalkqiekskpdavevlP 124
                                   ++ k+  i  a+  gl +i+r   i  +   ++ + k+ e +  d++ v P
  gi|15669812|ref|NP_248626.1|  55 VTEKEMAIALARLGGLGVIHRNMSIEEQVhqVQAVKKADEVVIKDVITVSP 105
                                   677888888888888888888877776541133333333344555555555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.3
                                   HCTSTTS...EEEEESS--SHHHHHHHCTT.SSE CS
                  G3P_antiterm 131 ikeikkelkipiiaGGLietkedveealkaGaia 164
                                    ke+ + ++i++i  G i tke  e+++kaGa+ 
  gi|15669812|ref|NP_248626.1| 263 FKEMLEGTDIKLIV-GNIATKEAAEDLIKAGADV 295
                                   34455556778876.5689999999999999975 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 2.7e-05
                                   HCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                  G3P_antiterm 131 ikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                   ++++ ke ++piia G i+ + d+ +a++aGa+av+ 
  gi|15669812|ref|NP_248626.1| 325 VADVAKEHNVPIIADGGIRYSGDIAKAIAAGADAVML 361
                                   56778888***************************85 PP

>> EAL  EAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3    0.0011       1.4     165     229 ..     235     295 ..     228     297 .. 0.83
   2 ?    0.0   0.1      0.39     5e+02     193     212 ..     321     340 ..     316     360 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                                   HHCCC--SEEEE-HHHHTTTTTSCHHHHHHHHCHHHHCCCT-EEEE-S--SHHHHHHHHHHT-SE CS
                           EAL 165 ylarlppdiiKldrslladleedeeaqalvkalialakelgikvvaegVeteeqlealrelgcdl 229
                                    l + ++d+i +d    +++    +  + vk + ++ +  +ik+++  + t+e +e+l+++g+d 
  gi|15669812|ref|NP_248626.1| 235 ALIEAEVDAIAIDCAHAHNM----RVVENVKKFKEMLEGTDIKLIVGNIATKEAAEDLIKAGADV 295
                                   56677788888887777765....57777889999***************************997 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.39
                                   HHHHCHHHHCCCT-EEEE-S CS
                           EAL 193 lvkalialakelgikvvaeg 212
                                    v+ ++++ake +++++a+g
  gi|15669812|ref|NP_248626.1| 321 AVAEVADVAKEHNVPIIADG 340
                                   678899************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 3114.47
//
Query:       gi|15669813|ref|NP_248627.1|  [L=93]
Description: hypothetical protein MJ_1617 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-21   74.7   2.8    3.3e-21   74.7   2.8    2.1  2  DUF131           Protein of unknown function DUF131
      0.007   15.8   0.9      0.007   15.8   0.9    2.0  2  DUF2162          Predicted transporter (DUF2162)
  ------ inclusion threshold ------
      0.019   14.0   2.4      0.022   13.8   2.4    1.1  1  DUF898           Bacterial protein of unknown function (DUF89
      0.027   14.7   1.8      0.043   14.1   1.8    1.3  1  DUF4293          Domain of unknown function (DUF4293)
      0.087   11.6   6.6       0.12   11.1   6.6    1.1  1  DUF2207          Predicted membrane protein (DUF2207)
        0.2   11.8   1.3       0.38   10.9   1.3    1.5  1  DUF2371          Uncharacterised conserved protein (DUF2371)
       0.25   11.0   1.4        0.4   10.4   1.4    1.7  1  Neurensin        Neurensin
       0.35   10.7  11.0         27    4.7  11.0    2.1  1  DUF5362          Family of unknown function (DUF5362)
        1.4    8.1   7.9         20    4.2   7.8    1.9  1  Choline_transpo  Plasma-membrane choline transporter
        2.4    8.0   7.6        5.2    6.9   0.3    2.1  2  PMP22_Claudin    PMP-22/EMP/MP20/Claudin family
        2.5    8.1   5.9        8.1    6.5   0.0    2.3  2  FixQ             Cbb3-type cytochrome oxidase component FixQ
        2.6    7.9   7.1        4.4    7.2   0.0    2.2  2  LapA_dom         Lipopolysaccharide assembly protein A domain
          5    6.8   7.0         23    4.6   7.0    1.8  1  Tetraspanin      Tetraspanin family
        6.9    6.8  13.1        2.8    8.1   2.8    2.1  2  DUF2614          Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   5.7     0.022        28      45      61 ..       5      21 ..       2      22 .. 0.87
   2 !   74.7   2.8   2.6e-24   3.3e-21       2      61 ..      25      86 ..      24      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.022
                        DUF131 45 ktaiiLaIilmilllil 61
                                   ++i+L+Iilm++ +++
  gi|15669813|ref|NP_248627.1|  5 PILIFLGIILMFIGFFM 21
                                  589**********9987 PP

  == domain 2  score: 74.7 bits;  conditional E-value: 2.6e-24
                        DUF131  2 gvvlkalekeee..eaekeesrvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmilllil 61
                                  g++l +++++ e  e+ek+es+v+++G+v+iGPIPI+FG+++ l+++++++aI+++i+++++
  gi|15669813|ref|NP_248627.1| 25 GMILPSSQENYEkpETEKTESSVEYSGIVMIGPIPIVFGNSPGLMILSVLIAILMIIWMFLF 86
                                  677777665554569********************************************998 PP

>> DUF2162  Predicted transporter (DUF2162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.9   5.5e-06     0.007     160     208 ..       6      54 ..       1      64 [. 0.82
   2 ?    0.5   3.5      0.26   3.4e+02      65      79 ..      69      83 ..      65      91 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.5e-06
                       DUF2162 160 ypiiLGnlmlfiGlyfLlsaliipniaqakaiylspltessieslllvl 208
                                     i+LG +++fiG++ +++ +i+p+ ++  + + ++ tess+e   +v+
  gi|15669813|ref|NP_248627.1|   6 ILIFLGIILMFIGFFMITLGMILPSSQENYEKPETEKTESSVEYSGIVM 54 
                                   5689************************999999999998866544444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.26
                       DUF2162 65 mvlhllmAlllialG 79
                                  m+l++l+A+l+i++ 
  gi|15669813|ref|NP_248627.1| 69 MILSVLIAILMIIWM 83
                                  667777777777774 PP

>> DUF898  Bacterial protein of unknown function (DUF898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.4   1.8e-05     0.022     181     248 ..       3      86 ..       1      92 [. 0.49

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                        DUF898 181 ykiwlaavllfllglvlliallaall...tevlakeaaatadaskseaellk..................lavllilalvl 240
                                   +k++l++++++l+++  +++ l+++l   +e+++k ++++ ++s + +                      +  l++l+++l
  gi|15669813|ref|NP_248627.1|   3 MKPILIFLGIILMFIGFFMITLGMILpssQENYEKPETEKTESSVEYS---GivmigpipivfgnspglmI--LSVLIAIL 78 
                                   555666665555555555555555440004444444444444444444...34559999999998888542..33333333 PP

                        DUF898 241 lllallaa 248
                                   +++ ++++
  gi|15669813|ref|NP_248627.1|  79 MIIWMFLF 86 
                                   33333322 PP

>> DUF4293  Domain of unknown function (DUF4293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.8   3.4e-05     0.043       7      75 ..       8      86 ..       7      88 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.4e-05
                       DUF4293  7 lyLllaailmaaflflplasivtedel...........lsfyalgvstaeaetsvnvsvwvlvilllliailaliaIfly 75
                                  ++L+++ +++++f+ + l+ i ++++             s++  g+++ +   +v+ ++ +l+il++liail +i +fl+
  gi|15669813|ref|NP_248627.1|  8 IFLGIILMFIGFFM-ITLGMILPSSQEnyekpetekteSSVEYSGIVMIGPIPIVFGNSPGLMILSVLIAILMIIWMFLF 86
                                  78999988888887.6677755554444556665555555555555556777788899999******************9 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   6.6   9.2e-05      0.12     383     431 ..       7      87 ..       3      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.2e-05
                       DUF2207 383 lsalglgliilglilillallllvll................................lvfllilllillliaiivlllfs 431
                                   l++lg++l+++g+++i+l+++l  +                                 + +l+il++++++++ii ++lf+
  gi|15669813|ref|NP_248627.1|   7 LIFLGIILMFIGFFMITLGMILPSSQenyekpetektessveysgivmigpipivfgnSPGLMILSVLIAILMIIWMFLFA 87 
                                   56677777777777777666666666*******************************999999999999999999998885 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.3    0.0003      0.38      42      82 ..       6      47 ..       2      89 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                       DUF2371 42 lvlllGllvllvGiamavlgywpkk.aklaseekssssstae 82
                                  ++++lG++++++G  m +lg    + ++  ++ ++++++++ 
  gi|15669813|ref|NP_248627.1|  6 ILIFLGIILMFIGFFMITLGMILPSsQENYEKPETEKTESSV 47
                                  7889****************9755513333333333333222 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.4   0.00031       0.4      45     131 ..       8      43 ..       1      90 [. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                     Neurensin  45 lvvgtlvlllGvtallvGylvprrlelvksegelvvvDkqaiefnnaLdtlklaGavllclGglllalsllvpalsksdkk 125
                                   + +g++++ +G  ++++G ++p+  e                                                    ++k
  gi|15669813|ref|NP_248627.1|   8 IFLGIILMFIGFFMITLGMILPSSQEN---------------------------------------------------YEK 37 
                                   455555555555555555555555554...................................................444 PP

                     Neurensin 126 eeeleq 131
                                    e +++
  gi|15669813|ref|NP_248627.1|  38 PETEKT 43 
                                   444443 PP

>> DUF5362  Family of unknown function (DUF5362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  11.0     0.021        27      16      92 ..       2      85 ..       1      92 [. 0.70

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.021
                       DUF5362 16 iilGaltcLsIigiiigvllIivglklfkaakaikealrskseeklkea.leklakylki......llilliielvlsillii 91
                                  i+  +l  L+Ii   ig  +I  g+ l  + +++++ + +k e ++++  +     +  +      l+il +++++l+i+++ 
  gi|15669813|ref|NP_248627.1|  2 IMKPILIFLGIILMFIGFFMITLGMILPSSQENYEKPETEKTESSVEYSgIVMIGPIPIVfgnspgLMILSVLIAILMIIWMF 84
                                  7778999****************************999988888876531333322222211111135666666677777665 PP

                       DUF5362 92 v 92
                                   
  gi|15669813|ref|NP_248627.1| 85 L 85
                                  4 PP

>> Choline_transpo  Plasma-membrane choline transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   7.8     0.016        20      43     117 ..       3      89 ..       1      91 [. 0.66

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.016
               Choline_transpo  43 lvplltllllllvsafwivvavalylassgestdkv.............nsgsesglaavefessskvkalllyllfgllW 110
                                   + p+l++l ++l+++ ++++++++ l ss+e+ +++                  + ++ v  +s++ +++ +l+ +++++W
  gi|15669813|ref|NP_248627.1|   3 MKPILIFLGIILMFIGFFMITLGMILPSSQEN-YEKpetektessveysGIVMIGPIPIVFGNSPGLMILSVLIAILMIIW 82 
                                   66889999999998866666666655555444.444578888888888844444444555566777778888888888888 PP

               Choline_transpo 111 tleflra 117
                                   +  f  +
  gi|15669813|ref|NP_248627.1|  83 MFLFAFG 89 
                                   8777655 PP

>> PMP22_Claudin  PMP-22/EMP/MP20/Claudin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.3    0.0041       5.2      76     111 ..       7      54 ..       2      58 .. 0.78
   2 ?    4.4   2.2     0.024        31      76      94 ..      68      89 ..      64      92 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0041
                                   HHHHHHHHHHHHHHHHHHHHHHTGGGTTTSS............HHHHH CS
                 PMP22_Claudin  76 lmilsiilgilslivavlqlkclkkgerfkl............aGiif 111
                                   l+ l+iil ++++++++l++      e+++             +Gi++
  gi|15669813|ref|NP_248627.1|   7 LIFLGIILMFIGFFMITLGMILPSSQENYEKpetektessveySGIVM 54 
                                   677899999999999999999888777777666677777777777766 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.024
                                  HHHHHH...HHHHHHHHHHHHH CS
                 PMP22_Claudin 76 lmilsi...ilgilslivavlq 94
                                  lmils+   il i+ ++++ ++
  gi|15669813|ref|NP_248627.1| 68 LMILSVliaILMIIWMFLFAFG 89
                                  8999994444444445555554 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0064       8.1      10      40 ..       7      37 ..       2      38 .. 0.83
   2 ?    1.3   4.1      0.26   3.3e+02       5      22 ..      70      87 ..      67      92 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0064
                          FixQ 10 adswgllflvllfygvviyafrpgnrkdfed 40
                                    ++g++++++ f  + + +  p++++++e+
  gi|15669813|ref|NP_248627.1|  7 LIFLGIILMFIGFFMITLGMILPSSQENYEK 37
                                  5688999999999999999999999999987 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.26
                          FixQ  5 alrgfadswgllflvllf 22
                                  +l+ ++ ++++++++l+ 
  gi|15669813|ref|NP_248627.1| 70 ILSVLIAILMIIWMFLFA 87
                                  345555555555555555 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0034       4.4      19      40 ..       7      28 ..       6      42 .. 0.85
   2 ?    1.5   4.4       0.2   2.6e+02      26      43 ..      68      85 ..      67      93 .] 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0034
                      LapA_dom 19 LsllllvafgiGallgwllslw 40
                                  L++l ++ ++iG++++ l +++
  gi|15669813|ref|NP_248627.1|  7 LIFLGIILMFIGFFMITLGMIL 28
                                  7888999******999999885 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.2
                      LapA_dom 26 afgiGallgwllslwsyl 43
                                   +++ +l+++l+ +w+ l
  gi|15669813|ref|NP_248627.1| 68 LMILSVLIAILMIIWMFL 85
                                  578888999999998765 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   7.0     0.018        23       2      64 ..       4      63 ..       3      92 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.018
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX.....................XXXXXXXXXXXX CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin  2 kyllfffnllfwligivllavGvwlrl.khaeaalacllsesaedpailaillivvGvllfllg 64
                                  k +l+f+ ++++ ig +++ +G+ l + ++++++ +++++es+++      +++++G + +++g
  gi|15669813|ref|NP_248627.1|  4 KPILIFLGIILMFIGFFMITLGMILPSsQENYEKPETEKTESSVEY----SGIVMIGPIPIVFG 63
                                  568999****************555323333223323222222222....34455665555544 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.8    0.0022       2.8      15      36 ..       6      27 ..       2      30 .. 0.85
   2 ?    4.5   2.8     0.027        35      23      55 ..      55      87 ..      43      92 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0022
                       DUF2614 15 llvfiglivmyigllfkesell 36
                                  +l+f g+i+m+ig+++ +  ++
  gi|15669813|ref|NP_248627.1|  6 ILIFLGIILMFIGFFMITLGMI 27
                                  69************99877665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.027
                       DUF2614 23 vmyigllfkeselllvlflllGlllvlastvvy 55
                                  +  i ++f +s+ l++l +l+ +l+++  ++  
  gi|15669813|ref|NP_248627.1| 55 IGPIPIVFGNSPGLMILSVLIAILMIIWMFLFA 87
                                  224669999****************99876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1186  (0.0661498); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 605.45
//
Query:       gi|15669814|ref|NP_248628.1|  [L=125]
Description: hypothetical protein MJ_1618 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-19   70.0   0.0    1.7e-19   69.3   0.0    1.3  1  Cupin_2          Cupin domain
    1.6e-09   37.8   0.0    1.9e-09   37.6   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
      2e-09   37.5   0.0    2.9e-09   36.9   0.0    1.2  1  AraC_binding     AraC-like ligand binding domain
    4.6e-09   36.0   0.0    5.7e-09   35.8   0.0    1.1  1  Cupin_1          Cupin
      4e-07   29.5   0.3    1.3e-06   27.8   0.1    1.8  2  GPI              Glucose-6-phosphate isomerase (GPI)
    8.1e-06   25.4   0.0    1.2e-05   24.9   0.0    1.2  1  Cupin_3          Protein of unknown function (DUF861)
    0.00059   20.0   0.0    0.00082   19.5   0.0    1.3  1  CENP-C_C         Mif2/CENP-C like
     0.0032   17.7   0.0     0.0038   17.4   0.0    1.2  1  ARD              ARD/ARD' family
     0.0041   16.8   0.4     0.0073   16.0   0.0    1.5  2  DMSP_lyase       Dimethlysulfonioproprionate lyase
     0.0054   16.9   0.0     0.0065   16.7   0.0    1.1  1  Ectoine_synth    Ectoine synthase
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.024   14.3   0.0    1.6  1  Auxin_BP         Auxin binding protein
      0.013   15.3   0.0      0.017   14.9   0.0    1.2  1  EutQ             Ethanolamine utilisation protein EutQ
      0.061   13.8   0.0      0.079   13.4   0.0    1.3  1  JmjC             JmjC domain, hydroxylase
       0.14   11.6   0.0       0.17   11.3   0.0    1.2  1  Cupin_4          Cupin superfamily protein


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.0   1.3e-22   1.7e-19       4      69 ..      45     110 ..      42     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 1.3e-22
                                   EEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEE CS
                       Cupin_2   4 elppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllv 69 
                                    +p G ++  h H  ++e++y+leG+g +t+d+e++e+++Gd++y+p++tpH+++N g+ p+++l+
  gi|15669814|ref|NP_248628.1|  45 IVPVGSKTLLHKHYTSEEIYYILEGRGLMTLDNEKFEVKKGDTIYIPPKTPHKIENIGNVPLKILC 110
                                   6889999******9999***********************************************98 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   1.5e-12   1.9e-09      69     144 ..      45     120 ..      26     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.5e-12
               MannoseP_isomer  69 tvkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiplelievqsGsylged 144
                                   +v  g+k  l+kh+   e + +++G   +t d+e++++k+ +++yip  + h++en G++pl+++      y  ed
  gi|15669814|ref|NP_248628.1|  45 IVPVGSKTLLHKHYTSEEIYYILEGRGLMTLDNEKFEVKKGDTIYIPPKTPHKIENIGNVPLKILCCSYPPYSHED 120
                                   566788899*******************************************************999999998888 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   2.3e-12   2.9e-09      23      78 ..      60     115 ..      50     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.3e-12
                                   SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE-- CS
                  AraC_binding  23 eyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwlyfeg 78 
                                     +i y++eG+g  +l+++ +++++Gd + +pp +pH +e  ++ +++  + ++++
  gi|15669814|ref|NP_248628.1|  60 SEEIYYILEGRGLMTLDNEKFEVKKGDTIYIPPKTPHKIENIGNVPLKILCCSYPP 115
                                   568****************************************9998887766665 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   4.4e-12   5.7e-09       8     111 ..      16     110 ..      10     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 4.4e-12
                                   EEEEETTEEEEEESTTTSTTTHSSTEEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEE CS
                       Cupin_1   8 ptieseggrvteansenlpglntlgisaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdv 88 
                                   p i+++g+ ++e+ + n+   ++ + s+a   +  g+  l+h h  ++ei y+l+G+g+ +++ ++      + ++++Gd+
  gi|15669814|ref|NP_248628.1|  16 PYITKDGSIIRELLHPNI--YKGVKQSLAEAIVPVGSKTLLHKHYTSEEIYYILEGRGL-MTLDNE------KFEVKKGDT 87 
                                   556677777777777776..5888888899999999***********************.444444......589****** PP

                                   EEE-TT-EEEEEEESSSSEEEEE CS
                       Cupin_1  89 fvvPaglvhfqynsgdepavaiv 111
                                   +++P+  +h + n+g+ p+ ++ 
  gi|15669814|ref|NP_248628.1|  88 IYIPPKTPHKIENIGNVPLKILC 110
                                   ***************99987765 PP

>> GPI  Glucose-6-phosphate isomerase (GPI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.51   6.5e+02      77      91 ..      24      38 ..       4      46 .. 0.72
   2 !   27.8   0.1   1.1e-09   1.3e-06      80     149 ..      57     117 ..      48     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.51
                           GPI 77 vdrrstrPEvYevlk 91
                                    r   +P++Y++ k
  gi|15669814|ref|NP_248628.1| 24 IIRELLHPNIYKGVK 38
                                  347888999999876 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 1.1e-09
                           GPI  80 rstrPEvYevlkGealmlLekPeglkvddvivvevkartvvivPPnygHvsinigeedLvmanlvpkdag 149
                                     t  E+Y+ l+G++lm L++ ++         evk+++++++PP   H   nig+ +L ++ + + + +
  gi|15669814|ref|NP_248628.1|  57 HYTSEEIYYILEGRGLMTLDNEKF---------EVKKGDTIYIPPKTPHKIENIGNVPLKILCCSYPPYS 117
                                   36788***************9999.........99************************98888776665 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   9.4e-09   1.2e-05      20      61 ..      55      95 ..      48     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 9.4e-09
                                  EECESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEE CS
                       Cupin_3 20 rltyeedEfcyileGevkvtpeggetvelraGDlvvlpkgls 61
                                  + +y+ +E+ yileG+   t  + e++e+++GD +++p+++ 
  gi|15669814|ref|NP_248628.1| 55 HKHYTSEEIYYILEGRGLMTL-DNEKFEVKKGDTIYIPPKTP 95
                                  6789*****************.99***************985 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   6.4e-07   0.00082      34      77 ..      61     104 ..      35     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.4e-07
                                   EEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE-SSS CS
                      CENP-C_C  34 tlvFyViqGrvevtvsktsfvigkgsvFqvPagneysieNklnk 77 
                                     ++y+++Gr  +t+ +++f + kg++ ++P     +ieN++n 
  gi|15669814|ref|NP_248628.1|  61 EEIYYILEGRGLMTLDNEKFEVKKGDTIYIPPKTPHKIENIGNV 104
                                   4589************************************9885 PP

>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     3e-06    0.0038      88     134 ..      56      97 ..      17     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3e-06
                           ARD  88 hlhedeeirliveGtgyFdvrskdeawirvlvekGDLivlPagiyhr 134
                                   ++ + eei +i+eG g+  +   +e++    v+kGD i +P+ + h 
  gi|15669814|ref|NP_248628.1|  56 KHYTSEEIYYILEGRGLMTLD--NEKFE---VKKGDTIYIPPKTPHK 97 
                                   345789**********98875..66776...**************96 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.7e-06    0.0073     111     156 ..      55     100 ..      54     108 .. 0.84
   2 ?   -2.6   0.2         3   3.8e+03     106     117 ..     111     122 ..     110     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.7e-06
                    DMSP_lyase 111 Hhhaa.eelYlvlsggaefrqgeaewlsrgiGevifnepgikhamrs 156
                                   H+h   ee+Y++l g  ++  ++++ ++++ G++i+ +p+ +h++  
  gi|15669814|ref|NP_248628.1|  55 HKHYTsEEIYYILEGRGLMTLDNEK-FEVKKGDTIYIPPKTPHKIEN 100
                                   999888********98788777776.8999*************9875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3
                    DMSP_lyase 106 vrYPdHhhaaee 117
                                   + YP  +h++ e
  gi|15669814|ref|NP_248628.1| 111 CSYPPYSHEDTE 122
                                   78******9987 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     5e-06    0.0065      33     112 ..      37     117 ..      18     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5e-06
                                   SSSEEEEEEE-TT--EEEE-TT-EEEE.EEEE--EEEEETTT--EEEE-TTEEEEETTT-EEEEEESS..-EEEEEEEES- CS
                 Ectoine_synth  33 mGfslhettikagtetelkYknHleav.ycieGegeveeledgevyeikpgtlYlldkhdkHllrakk..elrlvcvFnPp 110
                                   +  sl e ++  g++t l+ ++  e + y++eG+g ++   d e++e+k+g+   +  +  H ++      l+++c+  Pp
  gi|15669814|ref|NP_248628.1|  37 VKQSLAEAIVPVGSKTLLHKHYTSEEIyYILEGRGLMTL--DNEKFEVKKGDTIYIPPKTPHKIENIGnvPLKILCCSYPP 115
                                   5679999999999999998877777662689****8876..6899****99655555556677765443699****99999 PP

                                   -X CS
                 Ectoine_synth 111 lt 112
                                    +
  gi|15669814|ref|NP_248628.1| 116 YS 117
                                   75 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.9e-05     0.024      51     115 ..      46     102 ..      24     118 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                   E-TT-B--EEEE.SS-EEEEEEE--EEEEE--SSSSS--S-EEEEE-TTEEEEE-TT--EEEE--- CS
                      Auxin_BP  51 lapgsrtpihrh.sceevfvvlkgkgtlylasssskypgkpqelpifanstlsipvndahqvkntg 115
                                   +  gs+t +h+h + ee++ +l g+g + l +          ++++ +  t+ ip + +h++ n g
  gi|15669814|ref|NP_248628.1|  46 VPVGSKTLLHKHyTSEEIYYILEGRGLMTLDNE---------KFEVKKGDTIYIPPKTPHKIENIG 102
                                   3459*******94579**********9888653.........355566677777777777777776 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.3e-05     0.017      91     132 ..      56      99 ..      36     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                          EutQ  91 wtlnydeidyvieGrldvlidGrkvvaeaGdviliPkgs..kie 132
                                      + +ei y++eGr  +  d  k   + Gd i+iP  +  kie
  gi|15669814|ref|NP_248628.1|  56 KHYTSEEIYYILEGRGLMTLDNEKFEVKKGDTIYIPPKTphKIE 99 
                                   556779*****************************965412455 PP

>> JmjC  JmjC domain, hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.2e-05     0.079      82     105 ..      79     102 ..      37     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.2e-05
                                   EEEE-TT-EEEE-TT-EEEEEESS CS
                          JmjC  82 rfvqkpgefVfvfpgayHsvfnlg 105
                                   +f+ k g++++++p+++H   n+g
  gi|15669814|ref|NP_248628.1|  79 KFEVKKGDTIYIPPKTPHKIENIG 102
                                   8999**************988876 PP

>> Cupin_4  Cupin superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.17     178     195 ..      80      97 ..      47     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                   EEE-TT-EEEE-TT-EEE CS
                       Cupin_4 178 fvLepGDlLYlPrgviHq 195
                                   f  ++GD +Y+P++++H+
  gi|15669814|ref|NP_248628.1|  80 FEVKKGDTIYIPPKTPHK 97 
                                   6789*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 855.63
//
Query:       gi|15669815|ref|NP_248629.1|  [L=237]
Description: biotin operon repressor/biotin--[acetyl-CoA-carboxylase] ligase BirA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      8e-10   38.7   0.0    1.4e-09   37.9   0.0    1.4  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
    1.9e-07   30.9   0.8    4.1e-07   29.8   0.8    1.6  1  BPL_C          Biotin protein ligase C terminal domain
  ------ inclusion threshold ------
      0.062   13.7   0.5       0.15   12.5   0.2    1.8  2  MitMem_reg     Maintenance of mitochondrial structure and fun
       0.28   11.3   4.3       0.68   10.1   0.3    2.5  2  DUF150_C       RimP C-terminal SH3 domain
       0.77   10.1   2.7         21    5.5   0.6    2.4  2  DarA_C         Defence against restriction A C-terminal


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   3.9e-13   1.4e-09       5     131 .]       9     126 ..       6     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 3.9e-13
                                   ES-HHHHHH..GCGGG--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH.. CS
                 BPL_LplA_LipB   5 ikstntllkeslnsselesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgy 81 
                                   i+stn+++k     +e +  ++v+++ q  G+    +vw s +g+l++s++l+++   + ++v+ l+v   ++ vl+++  
  gi|15669815|ref|NP_248629.1|   9 IDSTNDYAK--ELAKEGKRNFIVLADKQNNGKgrwgRVWYSDEGGLYFSMVLDSKL--YNPKVINLLVPICIIEVLKNY-- 83 
                                   689988888..556666999***********999*******************665..888888888888877777777.. PP

                                   ....HHTT-TTEEEETTTEEEE....TTEEEEEEEEEEEETTS-EEEEEEEEEE CS
                 BPL_LplA_LipB  82 rdskpgiegipvfikwpnDlyv....ngrKlaGiavtstrgktlhhivigvgvn 131
                                           +     k pnD++v    n++Kl+Gi+++ t      +++ig+g+n
  gi|15669815|ref|NP_248629.1|  84 -------VDKELGLKFPNDIMVkvndNYKKLGGILTELTD----DYMIIGIGIN 126
                                   .......5666777789********************999....6666666666 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.8   1.2e-10   4.1e-07       1      47 [.     190     235 ..     190     236 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.2e-10
                                   STTSEEEEEE.TSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEEE CS
                         BPL_C   1 hsGqeVtled.edgkveGiavGIdddGaLllktddglqpdinsGdisl 47 
                                   ++G++V++++ ++++++G++ +Id dG  l  t+ g ++ i sG +++
  gi|15669815|ref|NP_248629.1| 190 TIGKQVKILLsNNEIITGKVYDIDFDGIVLG-TEKG-IERIPSGICIH 235
                                   69********999999***************.****.*******9987 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       4.6   1.7e+04      40      53 ..       9      22 ..       6      30 .. 0.71
   2 ?   12.5   0.2   4.2e-05      0.15       5      67 ..     125     186 ..     120     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.6
                    MitMem_reg 40 ldlikdYlkkveeg 53
                                  +d+  dY k+++++
  gi|15669815|ref|NP_248629.1|  9 IDSTNDYAKELAKE 22
                                  56777888887744 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.2e-05
                    MitMem_reg   5 igvehllkpsiqdasstlstglnrqyyslkilqerldlikdYlkkveegelpvnheilrnlqk 67 
                                   i+v+   +++i++++ +l +  ++ +  ++il++ l++ ++Yl+k++++e+  + eil++ +k
  gi|15669815|ref|NP_248629.1| 125 INVNNQIRNEIREIAISLKEITGKELDKVEILSNFLKTFESYLEKLKNKEI-DDYEILKKYKK 186
                                   5777777888887778999999999**********************8876.55668887655 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.4     0.061   2.2e+02      16      51 ..      99     133 ..      95     154 .. 0.69
   2 ?   10.1   0.3   0.00019      0.68       1      45 [.     181     221 ..     181     228 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.061
                      DUF150_C  16 kvklklpvegrkkftGkivevdeet....itlevdgkkrk 51 
                                   kv+     ++ kk+ G++ e  ++     i + v+++ r 
  gi|15669815|ref|NP_248629.1|  99 KVN-----DNYKKLGGILTELTDDYmiigIGINVNNQIRN 133
                                   444.....8999*********9998676666776666443 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00019
                      DUF150_C   1 LktaedFarflGelVkvklklpvegrkkftGkivevdeetitlev 45 
                                   Lk+ + ++  +G++Vk+ l+    + + +tGk+ ++d + i+l  
  gi|15669815|ref|NP_248629.1| 181 LKKYKKYSITIGKQVKILLS----NNEIITGKVYDIDFDGIVLGT 221
                                   677888999***********....*************99999865 PP

>> DarA_C  Defence against restriction A C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.014        51      34      52 ..      29      47 ..      15      49 .. 0.78
   2 ?    5.5   0.6    0.0059        21      51      66 ..     166     181 ..     165     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.014
                        DarA_C 34 arteveedsrgawGiveYe 52
                                     + +++++g+wG v+Y 
  gi|15669815|ref|NP_248629.1| 29 VLADKQNNGKGRWGRVWYS 47
                                  445667899*********7 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0059
                        DarA_C  51 YerpLtekeiadYeLk 66 
                                   Y ++L++kei dYe +
  gi|15669815|ref|NP_248629.1| 166 YLEKLKNKEIDDYEIL 181
                                   999***********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1493.55
//
Query:       gi|15669816|ref|NP_248630.1|  [L=505]
Description: hypothetical protein MJ_1620 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.3e-21   75.3   0.0    1.8e-20   74.0   0.0    1.7  1  Radical_SAM  Radical SAM superfamily
    2.5e-13   49.8   0.3    5.1e-13   48.8   0.3    1.6  1  TRAM         TRAM domain
    1.9e-08   34.4   0.0    4.7e-08   33.1   0.0    1.7  1  B12-binding  B12 binding domain
  ------ inclusion threshold ------
       0.11   12.1   0.1        1.2    8.8   0.0    2.3  2  ISPD_C       D-ribitol-5-phosphate cytidylyltransferase C-ter


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0     4e-24   1.8e-20       6     166 ..     207     384 ..     203     385 .. 0.85

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 4e-24
                                   EESS-....-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS...............TTHHHHH CS
                                   xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxx RF
                   Radical_SAM   6 gCnlr....CsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly...............pdfvell 67 
                                    C+l+    C fC++p+     g++rs++ e+il+ev++l  + gv+ ++l+  + l+y               ++ +e l
  gi|15669816|ref|NP_248630.1| 207 KCPLNinpgCGFCSVPS---VFGYARSRDEEDILKEVEAL-LKEGVNRIVLSAPDFLDYkrgeklinpyfpepnYEAIESL 283
                                   588888888*******8...7*******************.7999*******99999998888888888888554444444 PP

                                   HHHHHTCCCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETE CS
                                   xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  68 erlaklavpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrv 145
                                   +  +k   ++++  v +  ++ +   e+++e + ++  + +++g e++d+  + kl++r+ t+++vl+a+++++++++k  
  gi|15669816|ref|NP_248630.1| 284 LSKCKDLADKYNANVLIENIKANlfnEKVAEIFSKYLKTPIYIGCESGDKN-HCKLLGRPTTPDDVLKAVKIAKKYNLKAQ 363
                                   4444433466666666666665577899999999999**************.***************************** PP

                                   EEEEEEBTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 146 vdrivglpGendeeleellel 166
                                   v++i+glpGen+e+ ++++++
  gi|15669816|ref|NP_248630.1| 364 VYFIYGLPGENEETAKNTVNF 384
                                   **************9999987 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.3   1.1e-16   5.1e-13       1      62 []     435     498 ..     435     498 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.1e-16
                                   XXXXXXEEEEEEEEE-..TTSEEEEEET..TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                          TRAM   1 rsyvGstqeVlvegls.ksegegiGrtdn.gkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                   ++y+G+++eV +++++ +++ + iG++++ g +v+v+++ ++IG++ +VkI k++++yL+G++l
  gi|15669816|ref|NP_248630.1| 435 KKYIGRVLEVIISERHfRNKRDAIGYLPDsGLMVVVKDGAKFIGKTKKVKIIKAYEKYLEGRIL 498
                                   68*************************999********9888*******************986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0     1e-11   4.7e-08      50     120 ..      55     120 ..      18     121 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1e-11
                   B12-binding  50 ekpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                    k+ ++ +Sa +ts + +vk+lve+++ +  + k++vGG++  +    +le+ +++d+ +vgege ++++l
  gi|15669816|ref|NP_248630.1|  55 KKYNLIFISA-MTSDFKCVKKLVERIRLK-TDSKIIVGGPI--ANDINILEK-IEADISIVGEGEITIREL 120
                                   36799*****.**************8665.567******99..666667776.999***********9998 PP

>> ISPD_C  D-ribitol-5-phosphate cytidylyltransferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00027       1.2      52      77 ..      55      80 ..      41      93 .. 0.87
   2 ?    0.2   0.1      0.12   5.2e+02     121     159 ..     412     450 ..     407     452 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00027
                        ISPD_C 52 qcynficvnvkesdfeetqklvklLe 77
                                  + yn i +++++sdf+ ++klv+ ++
  gi|15669816|ref|NP_248630.1| 55 KKYNLIFISAMTSDFKCVKKLVERIR 80
                                  89********************9876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.12
                        ISPD_C 121 krniLlygllinyskdeeklqesleqlaaiiaalikern 159
                                   k ni  y+lli  + ++ +l+   +  + +  ++i er+
  gi|15669816|ref|NP_248630.1| 412 KPNITKYSLLIRETANKINLEIKKKYIGRVLEVIISERH 450
                                   569999****************99***********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.24s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3273.17
//
Query:       gi|15669817|ref|NP_248631.1|  [L=57]
Description: hypothetical protein MJ_1621 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 430.52
//
Query:       gi|15669818|ref|NP_248632.1|  [L=58]
Description: IS-like element [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 411.37
//
Query:       gi|15669819|ref|NP_248633.1|  [L=512]
Description: hypothetical protein MJ_1623 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-30  104.5   0.0    1.5e-29  103.2   0.0    1.6  2  FIST             FIST N domain
    3.9e-13   49.5   0.0    8.3e-13   48.4   0.0    1.6  1  FIST_C           FIST C domain
    5.7e-10   38.9   0.2    1.4e-09   37.6   0.2    1.7  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00011   21.7   0.3    0.00028   20.4   0.3    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00021   21.5   0.1    0.00052   20.3   0.1    1.6  1  Rrf2             Transcriptional regulator
    0.00075   19.3   1.6     0.0011   18.8   0.7    1.8  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0023   17.9   0.2     0.0065   16.4   0.2    1.8  1  PadR             Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.016   15.2   0.0       0.03   14.4   0.0    1.4  1  HTH_20           Helix-turn-helix domain
      0.046   14.3   0.2        1.3    9.6   0.1    2.7  2  Phage_rep_O      Bacteriophage replication protein O
      0.075   12.9   0.0       0.18   11.7   0.0    1.6  1  MarR_2           MarR family
      0.085   12.9   0.0       0.18   11.8   0.0    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.086   13.1   1.4       0.19   12.0   0.2    2.2  1  DUF4476          Domain of unknown function (DUF4476)
      0.094   12.6   0.0       0.24   11.3   0.0    1.6  2  Glyco_hydro_44   Glycoside hydrolase family 44
       0.14   12.0   0.0       0.28   11.0   0.0    1.5  1  HTH_IclR         IclR helix-turn-helix domain
       0.16   11.9   0.3         23    5.0   0.0    2.7  2  S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal 
       0.43   10.6   0.1       0.43   10.6   0.1    2.1  2  BLACT_WH         Beta-lactamase associated winged helix domai
        0.7   10.5   5.8       0.33   11.6   0.7    2.6  2  Mga              Mga helix-turn-helix domain
        2.1    8.2  10.9       0.27   11.1   5.3    2.4  2  TFIIE_alpha      TFIIE alpha subunit


Domain annotation for each model (and alignments):
>> FIST  FIST N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   1.5e-32   1.5e-29       2     172 .]      31     227 ..      30     227 .. 0.85
   2 ?   -3.1   0.0       6.8   6.8e+03     123     139 ..     370     386 ..     362     399 .. 0.75

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 1.5e-32
                          FIST   2 lvlvfas.aeasdleallealrealpgapliGcstageiasegleledgvvalalasa............da..ageelak 67 
                                   l+++ +s  e+++l++++++++++ p  +liGcst+g +++ +++ edgv +la++ +            +a  +g+++a+
  gi|15669819|ref|NP_248633.1|  31 LIIFITSiLERDKLKQVFDGMKQHIPLDNLIGCSTGGTFSGKDYIKEDGVLILAFDEYyksaiscekvdrEAeyVGKKIAD 111
                                   5667777777999**************************988*************44477778887776522677777777 PP

                          FIST  68 al...............pkllllladglssneeellegldealaspdvpivGGlagdgtlaf.ktyvlfnggvledgvvvv 132
                                   ++               + l ++++d    +e+e+l+ l   l   ++pi+GG a+d+  +f k +++++g+v++d +v+ 
  gi|15669819|ref|NP_248633.1| 112 KIktcirdkypkldiddNFLGFVFFDWNVDSEQEILDVLGREL---TIPIIGGTAADD-GSFdKFFQIYKGEVVKDCCVFG 188
                                   44555577774445454444*******9999********9555...9*******9999.7886699999************ PP

                          FIST 133 llsgeslevgtavsqgyrpigkpfvVTkaegnvileLdgk 172
                                   ++ g+ l+++ ++ +gy+p++ + +VTkaeg+v++eLdgk
  gi|15669819|ref|NP_248633.1| 189 VVGGK-LKFDLIYGHGYEPTDIYARVTKAEGKVVYELDGK 227
                                   *9999.9*******************************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.8
                          FIST 123 gvledgvvvvllsgesl 139
                                    v+ed+++++l +ge++
  gi|15669819|ref|NP_248633.1| 370 YVIEDNCIGWLSYGETI 386
                                   48999999999999873 PP

>> FIST_C  FIST C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   8.3e-16   8.3e-13       9     129 ..     244     386 ..     229     387 .. 0.73

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 8.3e-16
                        FIST_C   9 l.......geedeelaqsal.fplgleelggdflvrhllgvdpedgslaladdveeGqrlqlmlrdaealiedlerlleea 81 
                                             +d +  +  l +plg+++++g+++  +l +v+  +++l++ +d+ eG++l+lm++d e++++ +++ l++a
  gi|15669819|ref|NP_248633.1| 244 PmdiikkyFYRDLRRLDFYLvHPLGFMDINGNYITAFLERVE--ENTLVFRRDILEGSFLVLMKTDIEKQVKSIVDELKKA 322
                                   0444443323333344444457******************99..89**************************777777777 PP

                        FIST_C  82 ak..eg.allfsCigRglglgedadeelqavrea.lgdgvp................laGfftyGEig 129
                                   ++  +  +++ +C+gR ++l++++   +++++e+ l+  +                 ++G+++yGE +
  gi|15669819|ref|NP_248633.1| 323 EDfeNPlIFINECYGR-EVLKNSM---FREFEEDiLKYFLNfykagkkveeyviednCIGWLSYGETI 386
                                   5564344*********.5555555...55777774433333666778888****************75 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.2   1.5e-12   1.4e-09       1      63 [.     418     479 ..     418     483 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.5e-12
                                   HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                          TrmB   1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63 
                                   L+ +++ + E++v + L+ ++++ta+e+ + ++++++k Y +L++Le+ G+++ + g+pklY 
  gi|15669819|ref|NP_248633.1| 418 LKNFNFEDDEIEVIVNLI-NKQLTAKELLQLTNLSQTKLYHILNKLEKEGIIKSVSGKPKLYY 479
                                   789**************9.99****************************************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   2.8e-07   0.00028      16      48 .]     437     469 ..     429     469 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.8e-07
                        HTH_24  16 prisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                     ++ +eL + ++lS++ +   l++Le+eG+Ik
  gi|15669819|ref|NP_248633.1| 437 KQLTAKELLQLTNLSQTKLYHILNKLEKEGIIK 469
                                   5799****************************8 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   5.2e-07   0.00052      24      61 ..     437     474 ..     430     479 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.2e-07
                                   C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                          Rrf2  24 epvsseeiaerqnispsylekilakLrkaglvksvrGk 61 
                                   ++++++e+ + +n+s++ l +il+kL+k+g++ksv Gk
  gi|15669819|ref|NP_248633.1| 437 KQLTAKELLQLTNLSQTKLYHILNKLEKEGIIKSVSGK 474
                                   4599*********************************8 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.7   1.1e-06    0.0011       8      47 .]     431     470 ..     428     470 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                                   HHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5   8 LklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                   +  L +++l++ el   ++lsq ++ h L+kL+++G++++
  gi|15669819|ref|NP_248633.1| 431 IVNLINKQLTAKELLQLTNLSQTKLYHILNKLEKEGIIKS 470
                                   55688999*****************************985 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   6.5e-06    0.0065      22      52 ..     444     473 ..     434     480 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.5e-06
                                   CSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE CS
                          PadR  22 lsegllelseGslYpaLkrLekeglvesewe 52 
                                   l+  l++ls+++lY +L++Lekeg+++s   
  gi|15669819|ref|NP_248633.1| 444 LL-QLTNLSQTKLYHILNKLEKEGIIKSVSG 473
                                   43.46889******************98654 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     3e-05      0.03      22      57 ..     436     471 ..     430     475 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3e-05
                                   CTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                        HTH_20  22 aegltaselaerldlskntlsyHLrvLeeagLvevv 57 
                                   ++ lta+el ++  ls++ l++ L++Le+ g++++v
  gi|15669819|ref|NP_248633.1| 436 NKQLTAKELLQLTNLSQTKLYHILNKLEKEGIIKSV 471
                                   6789*****************************987 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.49   4.9e+02       8      34 ..     239     265 ..     235     267 .. 0.88
   2 ?    9.6   0.1    0.0013       1.3      49      82 ..     438     471 ..     435     485 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.49
                   Phage_rep_O   8 GYtrlanelleallrakltkrqlkill 34 
                                   +Yt+l  ++++++  ++l+++ + +++
  gi|15669819|ref|NP_248633.1| 239 EYTKLPMDIIKKYFYRDLRRLDFYLVH 265
                                   7*****************999887765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                   Phage_rep_O  49 wisnsqlveltgisrtkvskalkeLirekviike 82 
                                   +++ ++l +lt++s+tk+ + l++L +e++i+  
  gi|15669819|ref|NP_248633.1| 438 QLTAKELLQLTNLSQTKLYHILNKLEKEGIIKSV 471
                                   688999*************************875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00018      0.18       7      55 ..     427     472 ..     422     475 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                   HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2   7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                   +  v+ +L +     lt++el + ++ls+  +  il++L++ G +  ++
  gi|15669819|ref|NP_248633.1| 427 EIEVIVNLINKQ---LTAKELLQLTNLSQTKLYHILNKLEKEGIIKSVS 472
                                   566778888887...9****************************98765 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.18      18      53 ..     435     471 ..     416     486 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                   EEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                     HTH_Crp_2  18 ielpltqeelAsmlGltretvsrilseLkreglis.r 53 
                                   i+ +lt +el ++ +l++  +  il++L++eg+i+  
  gi|15669819|ref|NP_248633.1| 435 INKQLTAKELLQLTNLSQTKLYHILNKLEKEGIIKsV 471
                                   45579999999***********************963 PP

>> DUF4476  Domain of unknown function (DUF4476)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00019      0.19      12      48 ..     416     451 ..     406     455 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                       DUF4476  12 eklkkasfdddklklleqalankaftcsqvvqllklf 48 
                                   e+lk+++f+dd ++++  +l nk++t+++++ql +l+
  gi|15669819|ref|NP_248633.1| 416 EELKNFNFEDDEIEVIV-NLINKQLTAKELLQLTNLS 451
                                   89**************9.9**************9875 PP

>> Glyco_hydro_44  Glycoside hydrolase family 44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.9   5.8e+03      36      48 ..     154     166 ..     132     179 .. 0.72
   2 ?   11.3   0.0   0.00024      0.24      52     150 ..     398     499 ..     377     510 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.9
                                   EEE--SSEEES-- CS
                Glyco_hydro_44  36 lTvpligyvakdk 48 
                                   lT+p+ig +a+d+
  gi|15669819|ref|NP_248633.1| 154 LTIPIIGGTAADD 166
                                   7999999999987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00024
                                   E--GG....G-SSSTTEEE...........EES--S.S---SS--SSSSEEEHHH.....HHHHHHHHH--.TSTTS--EE CS
                Glyco_hydro_44  52 sfseskygeqaapdsrwkedagngv.asdgvkikkt.aelsltpdptdtsvyadeeftkewvnhlvkklgs.asatgvkfy 129
                                   sf+   +   ++ + +w+e+  n   + d+ ++  +  + +lt     + +  +++   +++n l k+    + +++ k+y
  gi|15669819|ref|NP_248633.1| 398 SFTGVIFELSQSSNINWREELKNFNfEDDEIEVIVNlINKQLTAKELLQLTNLSQTKLYHILNKLEKEGIIkSVSGKPKLY 478
                                   55556666677777777776666663333333322201222222222333333333455567777666444577899**** PP

                                   EESS-GGGHHHH-TTT--S-- CS
                Glyco_hydro_44 130 sLDNEpelWssTHrdvhpekv 150
                                    +DN  e+ ++TH+++  e++
  gi|15669819|ref|NP_248633.1| 479 YIDNIKEILQKTHEKIEHENM 499
                                   ****************98765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00029      0.28      18      49 ..     438     469 ..     434     472 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                                   S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  18 eltlselArrtglpkStvhRlLqtLvelGyve 49 
                                    lt +el + t l+ ++ +++L+ L+++G+++
  gi|15669819|ref|NP_248633.1| 438 QLTAKELLQLTNLSQTKLYHILNKLEKEGIIK 469
                                   5899*************************987 PP

>> S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.023        23      25      40 ..      63      78 ..      50      84 .. 0.85
   2 ?    3.9   0.1     0.049        49      36      54 ..      95     113 ..      90     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.023
                                  ---S---TTB-TTSHH CS
               S-AdoMet_synt_C 25 ahgggafsgKdptkvD 40
                                     gg+fsgKd+ k D
  gi|15669819|ref|NP_248633.1| 63 CSTGGTFSGKDYIKED 78
                                  5689********9977 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.049
                                   TTSHHHHHHHHHHHHHHHH CS
               S-AdoMet_synt_C  36 ptkvDrsaayaaryvaknl 54 
                                   ++kvDr a y+ + +a ++
  gi|15669819|ref|NP_248633.1|  95 CEKVDREAEYVGKKIADKI 113
                                   68*************9876 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       6.6   6.6e+03      34      42 ..     216     224 ..     215     227 .. 0.75
   2 ?   10.6   0.1   0.00043      0.43      25      43 ..     455     473 ..     452     476 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.6
                      BLACT_WH  34 eeGkVkreg 42 
                                   +eGkV+ e 
  gi|15669819|ref|NP_248633.1| 216 AEGKVVYEL 224
                                   79**99865 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00043
                      BLACT_WH  25 vlahLeKLeeeGkVkregd 43 
                                   ++++L+KLe+eG +k++++
  gi|15669819|ref|NP_248633.1| 455 LYHILNKLEKEGIIKSVSG 473
                                   789************9884 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.7   0.00033      0.33       4      56 ..     413     464 ..     410     468 .. 0.90
   2 ?    0.2   0.4       1.2   1.2e+03      51      69 ..     480     498 ..     477     502 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                                   XTHHHHHHHHHHSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
                           Mga   4 sleellqellkeslkyqllkflfeeeevsieelaqelyiSestlkrkikelnk 56 
                                    ++e l+++  e+++++++  l+ +++++ +el q   +S+++l++++++l+k
  gi|15669819|ref|NP_248633.1| 413 NWREELKNFNFEDDEIEVIVNLI-NKQLTAKELLQLTNLSQTKLYHILNKLEK 464
                                   56777889999999999999999.99************************987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.2
                                   HHHHHHHCHCCT-EEETTC CS
                           Mga  51 ikelnklLkefdleltkkn 69 
                                   i+++++ L++ + +++++n
  gi|15669819|ref|NP_248633.1| 480 IDNIKEILQKTHEKIEHEN 498
                                   789************7766 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3       3.4   3.4e+03      85     103 ..     308     326 ..     304     327 .. 0.81
   2 ?   11.1   5.3   0.00027      0.27      11      88 ..     423     506 ..     416     510 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.4
                                   HHHHHHHHHHHHHHHHCCC CS
                   TFIIE_alpha  85 vkrkleevvkkLeekleke 103
                                   + ++++ +v +L++++++e
  gi|15669819|ref|NP_248633.1| 308 IEKQVKSIVDELKKAEDFE 326
                                   5678889999999999887 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00027
                                   S-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE......TTTEEEEEEE.EEECCCHCCC CS
                   TFIIE_alpha  11 ygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd......eekswykyyw.rinyeklvdv 84 
                                   ++++ ++v+  L+ + ++t  +l +++++ +++l ++Ln+L +++++k +  +       + k++ + ++ +i+ e++v+ 
  gi|15669819|ref|NP_248633.1| 423 FEDDEIEVIVNLI-NKQLTAKELLQLTNLSQTKLYHILNKLEKEGIIKSVSGKPklyyidNIKEILQKTHeKIEHENMVKK 502
                                   7889999**9999.899999***************************9987665444442333333333324455555544 PP

                                   HHHH CS
                   TFIIE_alpha  85 vkrk 88 
                                   +krk
  gi|15669819|ref|NP_248633.1| 503 IKRK 506
                                   4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1234  (0.068827); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2994.21
//
Query:       gi|15669820|ref|NP_248634.1|  [L=139]
Description: hypothetical protein MJ_1624 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-09   37.4   0.2    9.1e-09   35.7   0.2    1.8  1  Toprim_4  Toprim domain
    3.8e-07   30.3   1.8    1.9e-06   28.1   0.4    2.3  2  Toprim    Toprim domain
    0.00045   20.6   0.0     0.0007   20.0   0.0    1.3  1  Toprim_2  Toprim-like
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.017   15.5   0.0    1.3  1  Toprim_3  Toprim domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.2     2e-12   9.1e-09       4      86 ..      37     109 ..      34     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2e-12
                      Toprim_4   4 iiVEgyaDvlalekagiknvvavlg.galspldgirpeklktenlveaekkvkevilaldgDaeGeataerlaellleegv 83 
                                   iiVEg  Dv +lek g++++  +   + +     i+ e  ++         vkevil++d D +G + a+ ++e+++++g+
  gi|15669820|ref|NP_248634.1|  37 IIVEGKRDVESLEKLGVEGTFIIIAkTPI---YLIADELVRK--------RVKEVILLTDFDRRGRMLAKAIIEEFRHRGI 106
                                   8********************99884555...4455444444........47**********************9999999 PP

                      Toprim_4  84 kvt 86 
                                   kv+
  gi|15669820|ref|NP_248634.1| 107 KVN 109
                                   996 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.9   1.3e+04      52      60 ..      21      29 ..      16      34 .. 0.44
   2 !   28.1   0.4   4.1e-10   1.9e-06       3      89 ..      37     104 ..      35     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.9
                                  HHHHHHHHH CS
                        Toprim 52 vlkalkela 60
                                   l++++el+
  gi|15669820|ref|NP_248634.1| 21 LLEVIEELK 29
                                  333444433 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 4.1e-10
                                   EEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHH.HHHSEEEEECSSSHHHHHHHHH CS
                        Toprim   3 vivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkela.kradeiilatDpDreGeaiawe 82 
                                   +ivEg++d+++++k+ g +++ ++  +  i+ +++                    el  kr++e+il+tD Dr G+ +a+ 
  gi|15669820|ref|NP_248634.1|  37 IIVEGKRDVESLEKL-GVEGTFIIIAKTPIYLIAD--------------------ELVrKRVKEVILLTDFDRRGRMLAKA 96 
                                   8**************.6555555555555555554....................4446********************** PP

                                   HHHHHT.H CS
                        Toprim  83 llevlk.e 89 
                                   ++e ++ +
  gi|15669820|ref|NP_248634.1|  97 IIEEFRhR 104
                                   **998852 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.6e-07    0.0007       1      76 [.      37     109 ..      37     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.6e-07
                      Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellreagvrek 76 
                                   +++Eg  D+ Sl +lg +    ++ ++ t++   a + l r++ k+v+l +D D+ Gr  ak ++e +r++g++++
  gi|15669820|ref|NP_248634.1|  37 IIVEGKRDVESLEKLGVE--GTFIIIAKTPIYLIADE-LVRKRVKEVILLTDFDRRGRMLAKAIIEEFRHRGIKVN 109
                                   588999999999999997..57777777755444444.55555899***********************9995443 PP

>> Toprim_3  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   3.7e-06     0.017       3      74 ..      37     108 ..      36     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.7e-06
                      Toprim_3   3 iivEGietaLsi..leartgaaviAllsaanlkaiawpergkrvviaaDnDaandGreaaeklaerleaagiea 74 
                                   iivEG  ++ s+  l ++ +  +iA +    ++   + +r+k+v+++ D D    Gr  a++++e++  +gi++
  gi|15669820|ref|NP_248634.1|  37 IIVEGKRDVESLekLGVEGTFIIIAKTPIYLIADELVRKRVKEVILLTDFDRR--GRMLAKAIIEEFRHRGIKV 108
                                   567777777777654455555566666666777667779**************..*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 871.01
//
Query:       gi|15669821|ref|NP_248635.1|  [L=765]
Description: hypothetical protein MJ_1626 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.032   14.2   0.4      0.032   14.2   0.4    4.9  5  Utp13           Utp13 specific WD40 associated domain
       0.15   12.4   2.0         89    3.5   0.1    4.0  3  DUF2524         Protein of unknown function (DUF2524)
       0.42   10.8   6.7        1.3    9.2   0.2    3.9  3  DsbG_N          Disulfide isomerase DsbG N-terminal
        2.1    8.0   9.0      0.098   12.3   1.3    3.0  3  CagY_M          DC-EC Repeat


Domain annotation for each model (and alignments):
>> Utp13  Utp13 specific WD40 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.8    0.0072        32       3     101 ..      80     171 ..      78     190 .. 0.74
   2 ?    4.0   1.1    0.0095        43       7      68 ..     205     265 ..     201     275 .. 0.89
   3 ?   -1.3   0.0      0.42   1.9e+03      24      69 ..     276     319 ..     265     325 .. 0.64
   4 ?   14.2   0.4     7e-06     0.032       3     104 ..     395     493 ..     393     531 .. 0.85
   5 ?    4.1   0.3    0.0092        41      21      70 ..     697     759 ..     688     762 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0072
                                   HHHHHHHCCHHHHHHHHHHHSSSTHHHHHHHHHHHS-SS--STSSSSSHHHHHHHHC--HHHHHHHHHHHH.HHHTSTTTH CS
                         Utp13   3 elqnllrkkdyreAiaLAlkldqpkrllkllkevleseeeeeesitgskevdevlkslskeqleklLkyir.dWntnarts 82 
                                   e+ ++lr+++y +   LA  ++    +l+ l e+++s++     +++ +    vlk+l++e +e+ L yi  + n +   +
  gi|15669821|ref|NP_248635.1|  80 EFLKYLRQGKYDK---LAKLINSYSDILSFLDELFTSNK-----KDDVRRALLVLKRLDNEVIERYLYYILlNLNEKRIIA 152
                                   5667888888886...55557888889999999996653.....3333334569*************99852666666678 PP

                                   HHHHHHHHHHHHHS-HHHH CS
                         Utp13  83 evAqrvLnailkslsaeel 101
                                   + A+ +L+ i ++ s+ee 
  gi|15669821|ref|NP_248635.1| 153 KEAEEILKKITNKESVEEA 171
                                   9999999999999888764 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0095
                                   HHHCCHHHHHHHHHHHSSSTHHHHHHHHHHHS-SS--STSSSSSHHHHHHHHC--HHHHHHH CS
                         Utp13   7 llrkkdyreAiaLAlkldqpkrllkllkevleseeeeeesitgskevdevlkslskeqlekl 68 
                                   + ++k+ +e i++ lk  + + +lk+l + l s+e++e++ t +  + ++++sl++eq + l
  gi|15669821|ref|NP_248635.1| 205 HTKSKNMEESIKILLKNYNSEMILKILANKLYSSEKDERELTIN-ILLNIVDSLTDEQKNIL 265
                                   5678999*********************9999999999999988.999*********98765 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.42
                                   SSTHHHHHHHHHHHS-SS--STSSSSSHHHHHHHHC--HHHHHHHH CS
                         Utp13  24 dqpkrllkllkevleseeeeeesitgskevdevlkslskeqleklL 69 
                                   d+ k+l++ +k+++e+   +   + ++++++++lks  k++l+ +L
  gi|15669821|ref|NP_248635.1| 276 DEDKKLYRKFKQLFEKL--DIPAELSDEQIKSLLKSHGKTTLNIIL 319
                                   56677777778777443..333333344777777777777777666 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 7e-06
                                   HHHHHHHCCHHHHHHHHHHHSSSTHHHHHHHHHHHS-SS--STSSSSSHHHHHHHHC--HHHHHHHHHHHHHHHTSTTTHH CS
                         Utp13   3 elqnllrkkdyreAiaLAlkldqpkrllkllkevleseeeeeesitgskevdevlkslskeqleklLkyirdWntnartse 83 
                                   el++++++k +  A ++ l l+     l++lke++++e + e  i+++k ++e++ +l++e++   ++++  +  + r+++
  gi|15669821|ref|NP_248635.1| 395 ELKKYIENKTLMYAKKMNLGLKI--SSLRILKEFAKKE-HLEFLINEHKRLKELVYKLEEEKFMGGFRHLLMMEEEIRKCN 472
                                   78889999988888887777764..5799*****9665.5777888889******************************** PP

                                   HHHHHHHHHHHHS-HHHHHS- CS
                         Utp13  84 vAqrvLnailkslsaeellel 104
                                   vA r+++ i+ ++  ++ +++
  gi|15669821|ref|NP_248635.1| 473 VAMRLIEEIVAEICLKNDIHY 493
                                   **********99988776665 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.0092
                                   HHSSSTHHHHHHHHHHHS-SS-.............-STSSSSSHHHHHHHHC--HHHHHHHHH CS
                         Utp13  21 lkldqpkrllkllkevleseee.............eeesitgskevdevlkslskeqleklLk 70 
                                   l+ d+ + +lk+l +v e+++e             ++ +++++k ++++lk++++e+ + +Lk
  gi|15669821|ref|NP_248635.1| 697 LNTDKRNSALKILLKVSEKRPElledfiyllagmySSANEEDKKLIKKILKNITTEEQKLILK 759
                                   788999999*******9999999**********997777778889**********99999987 PP

>> DUF2524  Protein of unknown function (DUF2524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.02        92      45      83 ..      95     134 ..      76     134 .. 0.73
   2 ?    1.6   0.1     0.075   3.3e+02      14      68 ..     211     265 ..     204     274 .. 0.84
   3 ?    3.5   0.1      0.02        89      46      84 .]     720     758 ..     713     758 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.02
                       DUF2524  45 kLEeavne.LeklaksandqQreqLeRarlqlqqLqnkmi 83 
                                   kL + + + L+ l +  +++ ++ + Ra l l+ L+n++i
  gi|15669821|ref|NP_248635.1|  95 KLINSYSDiLSFLDELFTSNKKDDVRRALLVLKRLDNEVI 134
                                   444555551344556678999****************987 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.075
                       DUF2524  14 ceqaieeaeeqfeeakrqehyndeeYteAqlkLEeavneLeklaksandqQreqL 68 
                                   +e+ i+   +++++ +  +   ++ Y++ + + E ++n L ++++s +d+Q++ L
  gi|15669821|ref|NP_248635.1| 211 MEESIKILLKNYNSEMILKILANKLYSSEKDERELTINILLNIVDSLTDEQKNIL 265
                                   566677777777777777888889999999999******************9876 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.02
                       DUF2524  46 LEeavneLeklaksandqQreqLeRarlqlqqLqnkmiL 84 
                                   LE+ +  L+++  san++ +  +++    + + ++k+iL
  gi|15669821|ref|NP_248635.1| 720 LEDFIYLLAGMYSSANEEDKKLIKKILKNITTEEQKLIL 758
                                   8999999**************999999999988888887 PP

>> DsbG_N  Disulfide isomerase DsbG N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       2.1   9.2e+03      22      41 ..     346     364 ..     343     367 .. 0.68
   2 ?    9.2   0.2   0.00028       1.3      46      86 ..     531     571 ..     529     573 .. 0.90
   3 ?    2.7   0.1     0.031   1.4e+02      52      83 ..     724     755 ..     721     759 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.1
                                   TT-SS-EEEEEE-TTT--EE CS
                        DsbG_N  22 ksdkdlklvvvedpstgqri 41 
                                   k++ ++kl+ ++++s ++++
  gi|15669821|ref|NP_248635.1| 346 KQFVGVKLISLKKDS-KKKV 364
                                   677788888888887.5555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00028
                                   -TTS--EEE--S----S-HHHHHHHHHHHHHHHHHHHHHHH CS
                        DsbG_N  46 skdgklviglsnvfftknkedsklvesllkkvqnynkkqkd 86 
                                    +dg l+  ls +++++nk d++l +++l+ +++++++ kd
  gi|15669821|ref|NP_248635.1| 531 KRDGELITYLSGIVINNNKIDDNLAKKILEVTEKAEMEDKD 571
                                   68***********************9999999999888665 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.031
                                   EEE--S----S-HHHHHHHHHHHHHHHHHHHH CS
                        DsbG_N  52 viglsnvfftknkedsklvesllkkvqnynkk 83 
                                   +  l+ +  + n+ed+kl++++lk+++  ++k
  gi|15669821|ref|NP_248635.1| 724 IYLLAGMYSSANEEDKKLIKKILKNITTEEQK 755
                                   55666777899***************999887 PP

>> CagY_M  DC-EC Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.7   7.6e+03      25      31 ..     259     265 ..     257     265 .. 0.76
   2 ?   -3.0   0.3       1.3     6e+03      22      31 ..     298     307 ..     298     307 .. 0.91
   3 ?   12.3   1.3   2.2e-05     0.098       9      31 ..     734     758 ..     732     759 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.7
                        CagY_M  25 earklll 31 
                                   +++k++l
  gi|15669821|ref|NP_248635.1| 259 DEQKNIL 265
                                   6888887 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.3
                        CagY_M  22 Lsdearklll 31 
                                   Lsde +k ll
  gi|15669821|ref|NP_248635.1| 298 LSDEQIKSLL 307
                                   9****99997 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 2.2e-05
                        CagY_M   9 AkdeeErk...eCLkgLsdearklll 31 
                                   A +ee++k   + Lk+++ e++kl+l
  gi|15669821|ref|NP_248635.1| 734 A-NEEDKKlikKILKNITTEEQKLIL 758
                                   5.9**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (765 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1504  (0.0838864); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.50
# Mc/sec: 4568.08
//
Query:       gi|15669822|ref|NP_248636.1|  [L=671]
Description: hypothetical protein MJ_1625 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     1e-109  367.4  26.9   1.3e-109  367.0  26.9    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
    2.5e-25   89.2   0.1    6.6e-25   87.9   0.1    1.7  1  NFACT-R_1      NFACT protein RNA binding domain
    6.2e-05   23.4   0.0    6.2e-05   23.4   0.0    3.5  3  Ribosomal_S13  Ribosomal protein S13/S18
  ------ inclusion threshold ------
       0.23   12.0  13.7       0.22   12.1   0.8    3.5  4  DUF5344        Family of unknown function (DUF5344)
       0.55   10.3   6.7          3    7.9   0.6    2.4  2  MCU            Mitochondrial calcium uniporter
       0.96    9.9   7.1        1.1    9.7   1.2    2.9  2  UPF0449        Uncharacterised protein family UPF0449
        1.5    9.0  11.9        8.6    6.5   3.6    3.0  2  Med9           RNA polymerase II transcription mediator compl
        3.7    7.2  11.5       0.19   11.4   3.3    2.1  2  DUF745         Protein of unknown function (DUF745)


Domain annotation for each model (and alignments):
>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  367.0  26.9  5.9e-113  1.3e-109       2     439 ..       7     471 ..       6     479 .. 0.94

  Alignments for each domain:
  == domain 1  score: 367.0 bits;  conditional E-value: 5.9e-113
                                   HHHHHHHHHHHHHHHTTXEEEEEEEEETT...EEEEEEE.ETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHHH CS
                          FbpA   2 glvlaavvaELqkellggridkiyqpekd...elvltlr.anrgrhkLllsahpsyarihltekpkenpkeppnFcmlLRk 78 
                                   ++++++vv+ELq+ l++gr+dk ++ +++   el+l+++  ++g++ L++s+  +y++i lt++++e+pk pp+F+mlLRk
  gi|15669822|ref|NP_248636.1|   7 NVDVCCVVDELQN-LINGRLDKAFLIDNEqnrELILKIHvPEGGSRELVISI-GKYKYITLTNYEREKPKLPPSFAMLLRK 85 
                                   789**********.***********9998888*******99999989*****.**************************** PP

                                   HHTTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTTXBXX CS
                          FbpA  79 yLkgarivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilpgekYe 159
                                   yLk+a++++ieq++fdR+v +++e+r     +  y+L++E++g+ +Nii++++e++Ii++++  +++   +R+i+p+ekY+
  gi|15669822|ref|NP_248636.1|  86 YLKNAKLIKIEQVNFDRVVIFHFETR-----DGIYKLVAELFGD-GNIIFLNNEDTIIAPLRVERWS---TRNIVPKEKYK 157
                                   **************************.....999**********.**********************...9********** PP

                                   XSXXXSXBXTT..SXXH.H.HHHHHHHH.S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHH CS
                          FbpA 160 lPpsqdklnPl..eaeele.efkellsk.kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealq 236
                                   +Pp+ + lnP+  e++ +   fk+++ + k  ++v+ +++ f G+++l+aee++era++dk++  ++lsee++++l+ea +
  gi|15669822|ref|NP_248636.1| 158 FPPQ-KPLNPYnlEFSIAYeVFKDYFLNnKGVECVRLISRVF-GIGGLYAEEICERAEIDKKK--RDLSEEEIKKLFEASK 234
                                   ****.******987776665888886667999**********.******************97..9*************** PP

                                   HHHTXXX....XXEE.....XSSSEESSX..XTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHH...HHHHH CS
                          FbpA 237 elleeleeekfepqlvlkeekpeefsvvp..lkslselekesfdslsealdeyYakkaerdrveqkrsdlekr...venel 312
                                   +l++e++ ++ +pq+vlk+  +e+f+vvp  lk++++lek++++s+ ea+d+y+ak +++ +v++++s++ek+    en+l
  gi|15669822|ref|NP_248636.1| 235 NLFDEIF-NNRKPQIVLKD--NEYFDVVPidLKKYKGLEKKYYNSFLEAVDDYFAKFLTKVVVKKEKSKIEKEierQENIL 312
                                   *******.89********9..69*****99989999*************************************8888899* PP

                                   HHHHHHHHHHHHHHHCCGGH.....HHHHCCHH-----------------------..--..................... CS
                          FbpA 313 eklekklkklekelekaeka.....enyrligelltaylyaikkgmsevelenyyde.ge..................... 366
                                   +++ ++lkk+++++ek++ +     +ny++++ell+a+++a+ ++m++++++++++e +e                     
  gi|15669822|ref|NP_248636.1| 313 RRQLETLKKYKEDAEKNQIKgdliyANYQIVEELLNAIRQAR-EKMDWARIKKIIREnKEhpilglieninenigeiiirl 392
                                   ***************************************888.99***********95559******************** PP

                                   .........---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.-HHHHHHHHHHHHH CS
                          FbpA 367 .........evtIpLdprkspsenAqkyfkkykKlkraveaveeqieetkeeleylesveaaleqaesledleeikeELie 438
                                            e +++Ld+rk++ enA++y++k+kKl++++e++e++ie tk+++e l+++ ++     ++++ +++k+++++
  gi|15669822|ref|NP_248636.1| 393 ksevddkviEERVSLDIRKNAFENAESYYEKAKKLRNKIEGIENAIELTKKKIEELKKKGEEEL---KEKESMQMKKKIRK 470
                                   *******9999**********************************************9988777...45666777776665 PP

                                   T CS
                          FbpA 439 e 439
                                   e
  gi|15669822|ref|NP_248636.1| 471 E 471
                                   5 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.1   2.9e-28   6.6e-25       7     109 .]     482     586 ..     474     586 .. 0.94

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 2.9e-28
                     NFACT-R_1   7 ssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia.gnklssvdv 86 
                                     +g+lvi+GkD+ +ne++ikky++++d++fh+d++++++++++ ++g+  e++ee+lee+a++ +++S+a +  + ++d 
  gi|15669822|ref|NP_248636.1| 482 VINGFLVIAGKDAITNEIIIKKYTDKDDIVFHADIQGAPFTVIK-TQGK--EVDEETLEEVAKFSVSHSRAwKLGYGAIDT 559
                                   3789****************************************.7777..8***************************** PP

                     NFACT-R_1  87 vyvpasnlsktap....ldtGsvgfkg 109
                                   ++v+++++skta+    l++G+++++g
  gi|15669822|ref|NP_248636.1| 560 YWVKPEQISKTAEsgeyLKRGAFVIRG 586
                                   ***********************9986 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.8e-08   6.2e-05      17      92 ..     194     266 ..     184     272 .. 0.78
   2 ?    0.9   1.2      0.25   5.7e+02      44      94 ..     291     340 ..     259     367 .. 0.56
   3 ?   -1.3   2.3       1.2   2.7e+03      41      64 ..     435     458 ..     378     505 .. 0.63

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.8e-08
                 Ribosomal_S13  17 ltaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nr..qkdikdGkdshvvendlrrk 92 
                                   +  + GiG  +a++i+++a++d+  + ++l+eeei+k+ e  +n      ++++ nr  q  +kd ++  vv  dl+++
  gi|15669822|ref|NP_248636.1| 194 ISRVFGIGGLYAEEICERAEIDK--KKRDLSEEEIKKLFEASKN----LFDEIFnNRkpQIVLKDNEYFDVVPIDLKKY 266
                                   67899*****************9..557************9999....4455553441144567888888888888765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.25
                 Ribosomal_S13  44 gelteeeiekieeivenkaqykipnwinrqkdikdGkdshvvendlrrklr 94 
                                   + + ++e +kie+++e+ +++     ++  k +k+ +++ ++++dl   + 
  gi|15669822|ref|NP_248636.1| 291 KVVVKKEKSKIEKEIER-QENILRRQLETLKKYKEDAEKNQIKGDLIYANY 340
                                   22334444555555555.222333333555667777777777777766554 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.2
                 Ribosomal_S13  41 krigelteeeiekieeivenkaqy 64 
                                     + elt+++ie++++  e++ ++
  gi|15669822|ref|NP_248636.1| 435 ENAIELTKKKIEELKKKGEEELKE 458
                                   334445555555554433332222 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.6       3.1   6.9e+03      11      48 ..     312     325 ..     294     330 .. 0.52
   2 ?    8.1   0.2    0.0018         4       7      64 ..     339     397 ..     336     408 .. 0.91
   3 ?   12.1   0.8   9.7e-05      0.22       9      53 ..     432     476 ..     428     509 .. 0.88
   4 ?   -3.1   0.0       5.6   1.3e+04      38      51 ..     636     649 ..     630     650 .. 0.54

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.1
                       DUF5344  11 VeqkLselktaaeelktsipetisgknsldvvekinel 48 
                                   +                          +l++++k++e 
  gi|15669822|ref|NP_248636.1| 312 LR------------------------RQLETLKKYKED 325
                                   33........................445555555444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0018
                       DUF5344   7 nqaeVeqkLselktaaeelk.tsipetisgknsldvvekineleeeleellkaYktlll 64 
                                   n++ Ve+ L  +++a e+++ + i++ i ++++   +  i+ ++e++ e++ ++k+ + 
  gi|15669822|ref|NP_248636.1| 339 NYQIVEELLNAIRQAREKMDwARIKKIIRENKEHPILGLIENINENIGEIIIRLKSEVD 397
                                   8999**********************************************999988665 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 9.7e-05
                       DUF5344   9 aeVeqkLselktaaeelktsipetisgknsldvvekineleeele 53 
                                   + +e++++  k+++eelk++ +e+ ++k+s+++ +ki +  + +e
  gi|15669822|ref|NP_248636.1| 432 EGIENAIELTKKKIEELKKKGEEELKEKESMQMKKKIRKERKWYE 476
                                   56899********************************99887777 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 5.6
                       DUF5344  38 sldvvekineleee 51 
                                   +++vv++++e+ ++
  gi|15669822|ref|NP_248636.1| 636 KGKVVKELKEIFKD 649
                                   55556555555444 PP

>> MCU  Mitochondrial calcium uniporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.6    0.0013         3      30      82 ..     276     328 ..     219     333 .. 0.76
   2 ?    5.2   0.9    0.0091        20      27      92 ..     416     480 ..     380     492 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0013
                                   XXXXXXXXXXXXXX-SSSSSSTSSSSSHHHHHHHHHHHHH-SHHHHHHHHTCC CS
                           MCU  30 kvllrvkqlvkalesalnveeeqlkkereleekleelreelepleekkeeide 82 
                                   + l+ v+ + ++  + + v++e++k e+e+e++++ lr++le l++ ke+ ++
  gi|15669822|ref|NP_248636.1| 276 SFLEAVDDYFAKFLTKVVVKKEKSKIEKEIERQENILRRQLETLKKYKEDAEK 328
                                   345566667777777779999*************************9998776 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0091
                                   XXXXXXXXXXXXXXXXX-SSSSSSTSSSSSHHHHHHHHHHHHH-SHHHHHHHHTCCCGGGCHHHHG CS
                           MCU  27 eeakvllrvkqlvkalesalnveeeqlkkereleekleelreelepleekkeeidekAerrtrrll 92 
                                   + ++ +++ k+l +++e + n+ e  +kk +el++k ee  +e e+++  k++i+++ ++ ++  +
  gi|15669822|ref|NP_248636.1| 416 NAESYYEKAKKLRNKIEGIENAIELTKKKIEELKKKGEEELKEKESMQM-KKKIRKERKWYEKFKW 480
                                   3344555555555555555566666677777777777764455555554.6677666554444444 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.5      0.11   2.4e+02      69      96 ..     300     327 ..     271     332 .. 0.83
   2 ?    9.7   1.2    0.0005       1.1      46      94 ..     402     454 ..     374     461 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                       UPF0449  69 elnerLeeakeeLkqkceeLktageeLe 96 
                                   ++++++e++++ L++++e+Lk+  e+ e
  gi|15669822|ref|NP_248636.1| 300 KIEKEIERQENILRRQLETLKKYKEDAE 327
                                   5678999999999999999999887765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0005
                       UPF0449  46 ssseeedleae....veelYeqvrtylelnerLeeakeeLkqkceeLktagee 94 
                                   +++ ++d++++    +e++Ye+++++ +  e +e+a e  k+k eeLk+ gee
  gi|15669822|ref|NP_248636.1| 402 EERVSLDIRKNafenAESYYEKAKKLRNKIEGIENAIELTKKKIEELKKKGEE 454
                                   4434444444444449*********************************9975 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.2     0.005        11      50      79 ..     296     325 ..     279     326 .. 0.90
   2 ?    6.5   3.6    0.0038       8.6      36      65 ..     422     451 ..     419     472 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.005
                          Med9  50 rsveeqeaeieeleeqlakKrelLkkyknr 79 
                                   + +   e+eie  e+ l+++ e Lkkyk++
  gi|15669822|ref|NP_248636.1| 296 KEKSKIEKEIERQENILRRQLETLKKYKED 325
                                   6677889*********************86 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0038
                          Med9  36 kkarelirelpgidrsveeqeaeieeleeq 65 
                                   +ka++l ++++gi+  +e  +++ieel+++
  gi|15669822|ref|NP_248636.1| 422 EKAKKLRNKIEGIENAIELTKKKIEELKKK 451
                                   699************************975 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.2      0.23   5.1e+02      67     123 ..     301     357 ..     292     368 .. 0.57
   2 ?   11.4   3.3   8.7e-05      0.19      72     149 ..     394     471 ..     387     473 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.23
                        DUF745  67 leqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlena 123
                                   +e+e++  e++++++ + l++ ++ a+  +   + + ++++++++ll+a++++ e++
  gi|15669822|ref|NP_248636.1| 301 IEKEIERQENILRRQLETLKKYKEDAEKNQIKGDLIYANYQIVEELLNAIRQAREKM 357
                                   455555555555555555555555555555555555555555555555555554444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8.7e-05
                        DUF745  72 reaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRve 149
                                   +e ++ v ee  sl   +++ + a++  ++a++  + ++ + +a++ + +++e+++++ ++el+ek+++ ++ k R e
  gi|15669822|ref|NP_248636.1| 394 SEVDDKVIEERVSLDIRKNAFENAESYYEKAKKLRNKIEGIENAIELTKKKIEELKKKGEEELKEKESMQMKKKIRKE 471
                                   577788889999*********************************************************999888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (671 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2800  (0.156172); expected 358.6 (0.02)
Passed bias filter:                      781  (0.0435607); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.91u 0.35s 00:00:01.26 Elapsed: 00:00:00.52
# Mc/sec: 3875.60
//
Query:       gi|15669823|ref|NP_248637.1|  [L=151]
Description: hypothetical protein MJ_1627 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-50  169.5   6.6    4.1e-50  169.3   6.6    1.0  1  UPF0179   Uncharacterised protein family (UPF0179)


Domain annotation for each model (and alignments):
>> UPF0179  Uncharacterised protein family (UPF0179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.3   6.6   2.3e-54   4.1e-50       1     139 [.       6     144 ..       6     145 .. 0.99

  Alignments for each domain:
  == domain 1  score: 169.3 bits;  conditional E-value: 2.3e-54
                       UPF0179   1 kitLigkklAkeGteFiylgeaeeCekCklkkvCln.LekgrkYrivevrekteheCavheegvvaveveeapiealiesk 80 
                                   kitLig+klAk+G eFiylge eeC++Ck+k+ C+  Le grkY+iv+vr++ +h+C vhe+gv++vev+ a+++++iesk
  gi|15669823|ref|NP_248637.1|   6 KITLIGSKLAKTGGEFIYLGEIEECKNCKFKRLCHGnLEVGRKYKIVSVRSA-NHPCIVHEGGVKVVEVVLADLTIMIESK 85 
                                   69*********************************99***************.**************************** PP

                       UPF0179  81 kavegskitleseeCdevecesyelcepeglkegekvkivevlgeieeckkgrslkkve 139
                                   ka+eg+++++e+ +Cd+++ce+y++c++eg+kegek+ki++vl+e+ +c+ g+slkkv 
  gi|15669823|ref|NP_248637.1|  86 KALEGVVLNHEPITCDNFDCEYYSFCNSEGIKEGEKYKIKQVLNEKINCPFGNSLKKVI 144
                                   *********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 959.89
//
Query:       gi|15669824|ref|NP_248638.1|  [L=448]
Description: hypothetical protein MJ_1628 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   6.7e-104  348.2   0.0   7.7e-104  348.0   0.0    1.0  1  ABC_ATPase  Predicted ATPase of the ABC class
    4.5e-05   23.7   0.0     0.0098   16.2   0.0    2.3  2  AAA_22      AAA domain
    0.00011   22.7   0.6     0.0083   16.6   0.2    2.4  2  ABC_tran    ABC transporter
     0.0004   20.9   6.8    0.00057   20.4   0.1    2.7  2  AAA_23      AAA domain
    0.00076   19.4   0.4     0.0016   18.3   0.1    1.7  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
     0.0065   16.4  10.2      0.068   13.1   0.1    2.6  2  ATPase_2    ATPase domain predominantly from Archaea
     0.0073   15.2   0.0      0.014   14.3   0.0    1.4  1  EutA        Ethanolamine utilisation protein EutA
  ------ inclusion threshold ------
      0.021   14.6   0.1      0.038   13.7   0.1    1.4  1  AAA_29      P-loop containing region of AAA domain
      0.047   13.4   0.1      0.047   13.4   0.1    2.9  3  AAA_15      AAA ATPase domain
      0.057   13.5   2.9        7.9    6.5   0.0    3.5  3  AAA_14      AAA domain


Domain annotation for each model (and alignments):
>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.0   0.0  4.3e-107  7.7e-104       2     442 ..      14     442 ..      13     447 .. 0.96

  Alignments for each domain:
  == domain 1  score: 348.0 bits;  conditional E-value: 4.3e-107
                                   -HHHHHHHHTTTSBGGGGGGGTT-EESSSEEEEES---SSTTSS-EEEEEEEE--S-HHSSSSG...S-HHHHHHHHHHHH CS
                    ABC_ATPase   2 eelektlksldgkgykaYkelkgeydlsdltllidrvqsdpfappSkvrvsvpaavakleeell...kskerrvaledfll 79 
                                   e l++tl ++++k++ +Y   +++ ++    +l+ ++++++f + S+++  +++a+++++ee++    +k+r + l+ ++ 
  gi|15669824|ref|NP_248638.1|  14 EFLNTTLLTKSNKNKLYYAVKQPDGNI--KVVLPFVFENKNFLKLSEYKDGIEGATQRVIEEIKqeiIKKKRFLPLAGYFG 92 
                                   67999******************8888..5789999*************************99988677888899999*** PP

                                   HHHHHCC....CTT-SSS--S-EE-----SEE--BSSEEE--EEEEEEEEE---EETTSE-HHHHHHHHHTTHHHHHHHHT CS
                    ABC_ATPase  80 rklkaelekltsksagsgksgalaidkksqevlersavelsdekielrlrvgLPaegrrilgkeaiellleelpkivekvl 160
                                   r +ka +e+lt+ +++ +  ++l+  +k++++         ++ki+l+lr+ + +e+++ ++ ++i+ l+++l+k+++k+ 
  gi|15669824|ref|NP_248638.1|  93 RIYKALYEPLTVVNCNLNLGYDLWKVDKYNYIE--------GDKIYLMLRMIF-KEKDSKEIVKQINELCNDLDKFIKKI- 163
                                   *******************************99........************.************************99. PP

                                   TT-..-HHHHHHHHHHHHHHHHHHCTTTTTT-SEEEETT---SBSSTTS-S......B-TS-------GGGE.EEEEETTT CS
                    ABC_ATPase 161 laekldeealeehvelvedqealrkqLeelglvaFvadgsilpResgesdk......PlkeavpFesPesle.veielpng 234
                                        + + l ++++++ +q++lr++L+elglv+F+a++s ++R+++e ++      P++ ++pFe+Pe+le +eiel++g
  gi|15669824|ref|NP_248638.1| 164 -----PIDLLIDEAKNIINQKYLRDKLDELGLVCFIANNSKPARKYTEVRRhyriagPKDVNIPFECPEELEpIEIELKYG 239
                                   .....8999************************************************************************ PP

                                   EEEEEEEE-SS.EEEEEE-TTSSHHHHHHHHHHCCSEE-TTSS-TTEEE-TT-EEE---TT--EEEE--TTTB---CCC-- CS
                    ABC_ATPase 235 kkvsGmgipkG.vtlIvGggfhGKsTLLeAlekGvynhvpgDGRefvvtdktavkiraEdgrsvkgvDispFinnLPegkd 314
                                   kkv+G+gi+k+ +++I+G++++GK+TLL+A+++G ++h++gDGRef++t+k++ k ++  +++++g+Dis F+++LP+g +
  gi|15669824|ref|NP_248638.1| 240 KKVKGLGIKKKeIFIITGRNAQGKTTLLQAIDSGRDDHLIGDGREFIITTKSLSKAST-GSMEMSGQDISLFFQKLPPGIK 319
                                   *********999**********************************************.********************** PP

                                   ST.TEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEE CS
                    ABC_ATPase 315 tt.kfstedASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilv 394
                                   ++ k+++ +ASGS+++A++i++a+++++kl+LiDED+sA+Nl++     + ++sk+ e++++l++ ++e+++klg+s++++
  gi|15669824|ref|NP_248638.1| 320 GSpKAVYGTASGSMYMAYQIQRAIKNKTKLILIDEDNSAVNLLV-----SGVLSKWFEGVKSLAEIIMEDREKLGDSSFII 395
                                   **9*****************************************.....9***************************9988 PP

                                   E.SS-GCCTTT-SEEEEEETTEEEE-HHHHHHHHHCHT-----...... CS
                    ABC_ATPase 395 v.ggsgdyldvAdtvilmeeykpkdvtekakeiaeelatkrkeeasekl 442
                                   v ++++ +++++d+ i++e++k+k+++  ++ ++eel +++ e as+++
  gi|15669824|ref|NP_248638.1| 396 VtSSLDLLTALGDRAIYLEDHKAKYLD--LTYFREELGRYYLELASKFI 442
                                   8688899999****************9..99999999988888777543 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.013        23      71     107 ..     138     183 ..      91     202 .. 0.77
   2 !   16.2   0.0   5.5e-06    0.0098       4      99 ..     249     354 ..     246     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                        AAA_22  71 erlsseellealeqalrarav.....ielliiDEaqhlr.s...ee 107
                                   ++++s+e+++++++ +++ ++     +  l+iDEa +++ +    +
  gi|15669824|ref|NP_248638.1| 138 KEKDSKEIVKQINELCNDLDKfikkiPIDLLIDEAKNIInQkylRD 183
                                   678999*****************99888899******764234444 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 5.5e-06
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..........erpevvfvtlpsstsskdllrellralglelka..er 72 
                                   ++ i ++tG    GKTtll+ + +  d +   +            ++++ +++++++   + ++++l   ++ + ka   +
  gi|15669824|ref|NP_248638.1| 249 KKEIFIITGRNAQGKTTLLQAIDSGRDDHLIGDGrefiittkslSKASTGSMEMSGQD-ISLFFQKLPPGIKGSPKAvyGT 328
                                   68899********************987665555999999988888888899998888.9999*********999999977 PP

                        AAA_22  73 lsseell.ealeqalraravielliiDE 99 
                                   +s + ++  ++++a++++ +  l++iDE
  gi|15669824|ref|NP_248638.1| 329 ASGSMYMaYQIQRAIKNKTK--LILIDE 354
                                   78888888999999999988..*****9 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   4.6e-06    0.0083       6      67 ..     245     313 ..     241     321 .. 0.68
   2 ?    3.9   0.0      0.04        72     107     134 ..     327     354 ..     317     357 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.6e-06
                                   EEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke...qeleslrkeigvlpqe 67 
                                   l +k+ e+  i+G+n  GK+tLl+++    ++    +  e  +  k+l++    ++e + + i+ ++q+
  gi|15669824|ref|NP_248638.1| 245 LGIKKKEIFIITGRNAQGKTTLLQAIDSGRDDhligDGREFIITTKSLSKastGSMEMSGQDISLFFQK 313
                                   6899**********************7665554543222233444444444455566666666666665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.04
                                   GGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 107 ssLSgGqkqrvalarallkkpkllllDE 134
                                    + Sg +    ++ ra+ +k kl+l+DE
  gi|15669824|ref|NP_248638.1| 327 GTASGSMYMAYQIQRAIKNKTKLILIDE 354
                                   56799999999****************9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   3.1      0.28     5e+02     147     197 ..      55     161 ..       3     188 .. 0.48
   2 !   20.4   0.1   3.2e-07   0.00057      18      39 ..     249     270 ..     221     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.28
                        AAA_23 147 elkdkkerleeleke.leeledekkllekl................................................... 175
                                   +l++ k+ +e +++  +ee+++e+ +   +                                                   
  gi|15669824|ref|NP_248638.1|  55 KLSEYKDGIEGATQRvIEEIKQEIIKK--Krflplagyfgriykalyepltvvncnlnlgydlwkvdkynyiegdkiylml 133
                                   224444444433333233333333222..1235555555555555555555555555555555555555555555555555 PP

                        AAA_23 176 ......eqekekekeleeleeeleeilk 197
                                         ++ ke  k+++el ++l + +k
  gi|15669824|ref|NP_248638.1| 134 rmifkeKDSKEIVKQINELCNDLDKFIK 161
                                   5553333333334444444444444444 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 3.2e-07
                        AAA_23  18 skgltlItGpNGaGKTTildAi 39 
                                   +k +++ItG N  GKTT+l+Ai
  gi|15669824|ref|NP_248638.1| 249 KKEIFIITGRNAQGKTTLLQAI 270
                                   678******************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.4   7.8e+03      26      67 ..     133     173 ..     129     183 .. 0.67
   2 !   18.3   0.1     9e-07    0.0016       1      34 [.     252     283 ..     252     310 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.4
                        AAA_21  26 drdvegltdelsggggirkipslldlydpeipfefeieefls 67 
                                   +r+++ ++d++   ++i +  + ld   ++ip+ + i+   +
  gi|15669824|ref|NP_248638.1| 133 LRMIFKEKDSKEIVKQINELCNDLDKFIKKIPIDLLID-EAK 173
                                   55666777777777777777777777777888777777.444 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 9e-07
                        AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltd 34 
                                   + +++G+N+ GK++LL+a+d  +  d++++g++ 
  gi|15669824|ref|NP_248638.1| 252 IFIITGRNAQGKTTLLQAIDSGR--DDHLIGDGR 283
                                   579*****************998..555555544 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   5.3    0.0095        17      91     133 ..     133     178 ..      40     191 .. 0.77
   2 !   13.1   0.1   3.8e-05     0.068      19     178 ..     249     410 ..     240     434 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0095
                      ATPase_2  91 leeilk.eksklvfkaielllekikkkgkk..iiiiiDelqklidl 133
                                   l  i+k + sk++ k+i++l +++ k  kk  i ++iDe+ ++i+ 
  gi|15669824|ref|NP_248638.1| 133 LRMIFKeKDSKEIVKQINELCNDLDKFIKKipIDLLIDEAKNIINQ 178
                                   446888899*********************96669********943 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.8e-05
                      ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdk..yviyyialreesiskldefieeeeekkklekalgiavpkaeleeilke 97 
                                   ++ei  i+G+   GKt+Ll+ i + ++d+     + ++i  ++ s +++ ++ e   + + ++  +++  p  ++      
  gi|15669824|ref|NP_248638.1| 249 KKEIFIITGRNAQGKTTLLQAIDSGRDDHLIgdGREFIITTKSLSKASTGSM-E--MSGQDISLFFQKLPPGIKGSPKAVY 326
                                   68999***************99999977644448999998888888888887.3..2222234333333333333222223 PP

                      ATPase_2  98 ksklvfkaie.lllekikkkgkkiiiiiDelqklidlgln....gaellvkeLlnli.esltkekhlcvviclsSeglfie 172
                                    ++    +++ ++ ++ik+k k   i+iDe   +++l +     +  + vk+L+++i e+  k  +  ++i++sS  l+  
  gi|15669824|ref|NP_248638.1| 327 GTASGSMYMAyQIQRAIKNKTK--LILIDEDNSAVNLLVSgvlsKWFEGVKSLAEIImEDREKLGDSSFIIVTSSLDLLTA 405
                                   3344444554145556666655..788999999998877744434555688899876145566789999999999888777 PP

                      ATPase_2 173 rvynes 178
                                    + +++
  gi|15669824|ref|NP_248638.1| 406 -LGDRA 410
                                   .33333 PP

>> EutA  Ethanolamine utilisation protein EutA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   7.8e-06     0.014     316     427 ..     295     408 ..     288     422 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.8e-06
                          EutA 316 AgahtlelsGstitlekdllP..lknlPvlklskedeeaae.eelaeavkeklawfkleeekqkvalalegekelsfkavq 393
                                   A++ ++e+sG  i l  + lP  +k  P     + + +     ++++a+k+k + + ++e++ +v l ++g  +  f+ v+
  gi|15669824|ref|NP_248638.1| 295 ASTGSMEMSGQDISLFFQKLPpgIKGSPKAVYGTASGSMYMaYQIQRAIKNKTKLILIDEDNSAVNLLVSGVLSKWFEGVK 375
                                   678899*********9999998999999766665555544449************************************** PP

                          EutA 394 elakalveglkelvekelplivvveedlakvlGq 427
                                   +la+ ++e  ++l +++  +iv    dl  +lG 
  gi|15669824|ref|NP_248638.1| 376 SLAEIIMEDREKLGDSS-FIIVTSSLDLLTALGD 408
                                   *******9999888865.4444445588788775 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.1e-05     0.038      18      42 ..     246     270 ..     238     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                        AAA_29  18 eidlkgatlltGpsGsGKSTllDAi 42 
                                    i+ k+++++tG++  GK+Tll Ai
  gi|15669824|ref|NP_248638.1| 246 GIKKKEIFIITGRNAQGKTTLLQAI 270
                                   56777899**************998 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   8.2      0.46   8.2e+02     163     210 ..     136     180 ..      10     190 .. 0.67
   2 ?   13.4   0.1   2.6e-05     0.047      23      44 ..     250     271 ..     229     277 .. 0.84
   3 ?   -3.5   0.0       3.6   6.4e+03     306     331 ..     334     354 ..     332     354 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.46
                        AAA_15 163 kidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsded 210
                                    ++ +d k++ k+++e  +  +   +++k+  i+ll+++ak+ ++++ 
  gi|15669824|ref|NP_248638.1| 136 IFKEKDSKEIVKQINELCNDLD---KFIKKIPIDLLIDEAKNIINQKY 180
                                   3456666666666666666555...88888888888888888888865 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.6e-05
                        AAA_15  23 eeltvliGkNnsGKSsileald 44 
                                   +e+ ++ G+N+ GK+++l+a+d
  gi|15669824|ref|NP_248638.1| 250 KEIFIITGRNAQGKTTLLQAID 271
                                   3399999**************8 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.6
                        AAA_15 306 llillileaekkdekeeknvilliEE 331
                                   +++++i +a+k+     k++++li+E
  gi|15669824|ref|NP_248638.1| 334 YMAYQIQRAIKN-----KTKLILIDE 354
                                   445555555555.....999999998 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.21   3.8e+02      39      78 ..     138     177 ..     110     210 .. 0.56
   2 ?    6.5   0.0    0.0044       7.9       2      22 ..     250     270 ..     249     310 .. 0.89
   3 ?    3.9   0.0      0.03        53      56     102 ..     339     401 ..     321     417 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.21
                        AAA_14  39 dderdkkladpekllelileklke.....ekkty.lflDEiqevpe 78 
                                   ++++ k      ++ + i e+ ++     +k  + l++DE++++ +
  gi|15669824|ref|NP_248638.1| 138 KEKDSK------EIVKQINELCNDldkfiKKIPIdLLIDEAKNIIN 177
                                   222222......2223333321112233322222499999999866 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0044
                        AAA_14   2 rkilvitGaRrvGKTtllkql 22 
                                   ++i +itG    GKTtll+ +
  gi|15669824|ref|NP_248638.1| 250 KEIFIITGRNAQGKTTLLQAI 270
                                   6899*************9765 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.03
                        AAA_14  56 ileklkeekktylflDEiqev.........pewekalkslvd......eg..knldvivtGSns 102
                                   i++ +k+ k++++++DE   +         ++w++ +ksl +      e+  +   +ivt S+ 
  gi|15669824|ref|NP_248638.1| 339 IQRAIKN-KTKLILIDEDNSAvnllvsgvlSKWFEGVKSLAEiimedrEKlgDSSFIIVTSSLD 401
                                   2333555.999******99988999999998888888888877765431132334555665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 2762.22
//
Query:       gi|15669825|ref|NP_248639.1|  [L=292]
Description: hypothetical protein MJ_1629 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00095   19.1   0.0      0.003   17.5   0.0    1.8  2  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0052   16.3   0.0      0.011   15.2   0.0    1.6  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.011   15.7   1.7      0.031   14.3   0.8    2.1  2  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     5e-07     0.003      12      54 ..      20      83 ..      15     185 .. 0.73
   2 ?   -1.5   0.0      0.35   2.1e+03      92     122 ..     224     251 ..     210     260 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5e-07
                 Lactamase_B_3 12 letagarilvDPf....................ka.nlgyeppaeeaDlvlisqaledHahlet 54
                                  ++t+++ il+DP+                    ++   + +  a++ ++++is+ + dH+++  
  gi|15669825|ref|NP_248639.1| 20 VKTKDVGILIDPGvalapdryglkpndiefeklREmRNKINDYAKKSNVITISHYHYDHYTPFF 83
                                  6788999******8877776666666666655522344555555****************9864 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.35
                 Lactamase_B_3  92 ergenngflleqdgltiyhlGhlahelssee 122
                                   + +en  +++e +g +++   hl     +++
  gi|15669825|ref|NP_248639.1| 224 KTNENLKYIVENTGAELIIDHHLLR---DKK 251
                                   5677888999988888876666665...333 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.9e-06     0.011       3     151 ..      27     193 ..      26     208 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-06
                                   EEES--TT..............HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC..C--EE..EEEEEEHH CS
                 Lactamase_B_2   3 iLiDagpd..............lrqqalralqPvelrdelppidaVllthaHyDHlaglltlre..lrpkk..lplyapkg 65 
                                   iLiD+g                + +  lr + + +  d  ++ +++ ++h HyDH++  +++    l+ k+   +ly +k 
  gi|15669825|ref|NP_248639.1|  27 ILIDPGVAlapdryglkpndieF-EK-LREM-RNKINDYAKKSNVITISHYHYDHYT--PFFDDiyLESKDyaKELYKDKI 102
                                   67777777777777666655432.22.3333.11245566788999**********5..5665554444444345665544 PP

                                   HHH.HCCTTCGHHHCHTT........TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE....CT CS
                 Lactamase_B_2  66 vla.vleanfvylaleee........pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie....gg 133
                                   +l  + ++ +   +++++        ++ +  e++ +++f++g++++++ + p +h+            lG+++     +g
  gi|15669825|ref|NP_248639.1| 103 LLIkHPTEFINKSQMNRAkkflesvkDIAKKIEFADNKTFKFGKTEIKFSP-PFPHGRDD--------KLGYVLIttvkEG 174
                                   333133333333333333664445555666667778888888887777777.67777766........5555544344489 PP

                                   TEEEEEESS-S---.HHHH CS
                 Lactamase_B_2 134 gkrvyyigDtgyip.eeig 151
                                   + +++++ Dt+ i  ++i+
  gi|15669825|ref|NP_248639.1| 175 KFKFMHTSDTQGIIfDDIR 193
                                   999*******988766666 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.8   5.1e-06     0.031       6      58 ..      15      79 ..      11      80 .. 0.86
   2 ?   -1.5   0.0      0.35   2.1e+03      97     127 ..     179     215 ..     141     221 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.1e-06
                                  SEEEEEEETTCEEEES--SCHHHHHHHH...........HHHHHTSGGGGEEEEE.-SBSSHHHH CS
                   Lactamase_B  6 vnsyliegdggviLiDtGtsteaaraal...........elaalglkpkdvdavi.lTHlHlDHi 58
                                  + ++++ +++  iLiD+G+  + +r  l           e++ +  +  + + vi ++H+H+DH+
  gi|15669825|ref|NP_248639.1| 15 SLATYVKTKDVGILIDPGVALAPDRYGLkpndiefeklrEMRNKINDYAKKSNVItISHYHYDHY 79
                                  678999******************************99877766666666666666********7 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.35
                                   H......TTCHCGCCEEEEETTTEECCCTEEEEEHEC CS
                   Lactamase_B  97 l......lagvsadkpdvdeeeldgnaggrralyvtg 127
                                          +++++++ +++ +e   ++++g++ +y ++
  gi|15669825|ref|NP_248639.1| 179 MhtsdtqGIIFDDIRDYIIKEKPNLILMGGPPTYLMH 215
                                   0222346678888888888888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1883.18
//
Query:       gi|15669826|ref|NP_248640.1|  [L=1139]
Description: DNA polymerase II large subunit [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
          0 1252.7   5.9          0 1252.4   1.7    2.5  2  PolC_DP2         DNA polymerase II large subunit DP2
    5.6e-05   22.4   8.1    0.00056   19.2   2.0    2.7  2  zf-ribbon_3      zinc-ribbon domain
  ------ inclusion threshold ------
      0.033   14.2   5.0        2.5    8.2   0.3    2.6  2  DZR              Double zinc ribbon
      0.062   13.6   0.3      0.062   13.6   0.3    2.5  2  Yqai             Hypothetical protein Yqai
      0.065   13.4   0.3      0.065   13.4   0.3    2.9  2  DUF5442          Family of unknown function (DUF5442)
       0.18   10.5   2.4       0.47    9.2   0.3    2.5  2  NRDD             Anaerobic ribonucleoside-triphosphate reduct
       0.25   11.4   3.6        3.6    7.6   0.3    2.7  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.37   10.8   6.3        9.4    6.4   0.1    3.6  3  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
       0.76   10.2   5.3         21    5.6   0.2    3.6  4  Lar_restr_allev  Restriction alleviation protein Lar
          1    9.3  10.5       0.57   10.1   1.1    3.1  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
          1    9.5   5.3        1.9    8.7   0.4    2.4  2  DUF1272          Protein of unknown function (DUF1272)
        2.3    8.3   5.0        4.8    7.3   0.6    2.5  2  zf-C2HC5         Putative zinc finger motif, C2HC5-type
        4.1    7.8   5.3        0.7   10.2   0.8    2.0  2  Ribosomal_L32p   Ribosomal L32p protein family
        5.4    7.1  10.0         20    5.3   0.3    3.8  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        6.3    6.8   7.4         76    3.4   0.1    3.9  4  Nudix_N_2        Nudix N-terminal
        6.5    6.6  15.8         15    5.5   0.1    4.0  4  zinc_ribbon_2    zinc-ribbon domain
        7.2    6.5  10.3       0.13   12.0   0.2    2.9  3  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1252.4   1.7         0         0       1     864 []      15     887 ..      15     887 .. 0.96
   2 ?   -1.6   0.1      0.43   4.6e+02     632     687 ..    1055    1115 ..    1027    1131 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1252.4 bits;  conditional E-value: 0
                      PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirelekelsreevalkiakeiaegkv 81 
                                   +Yfe++ +e++++y+iae++r+kg+dp++evEiplA d+adRve l+g+kgvaerirel kel++e +al+iakei+egk+
  gi|15669826|ref|NP_248640.1|  15 KYFENIVDEVKKIYRIAEECRKKGFDPTDEVEIPLAADMADRVEGLVGPKGVAERIRELVKELGKEPAALEIAKEIVEGKF 95 
                                   6******************************************************************************** PP

                      PolC_DP2  82 geaeskeeavdkavrtalalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaDyvrkklgld 162
                                   g+++ ke+++++avrtala+lteg+vaAPleGia+vkikkn dgteyl++yyaGPiRsaGGtaqalsvLv+D+vrk++gld
  gi|15669826|ref|NP_248640.1|  96 GNFD-KEKKAEQAVRTALAVLTEGIVAAPLEGIADVKIKKNPDGTEYLAIYYAGPIRSAGGTAQALSVLVGDFVRKAMGLD 175
                                   **97.8999************************************************************************ PP

                      PolC_DP2 163 rykpreeeieRyveEielYer.vaslqyspsdeeirlivknipveidGeatedeevsgyrdlervetnrvRGGmllvlaeG 242
                                   rykp+e+eieRyveE+elY++ v s+qy+p+ +eir++++nip+ei+Geat+d+evsg+rdl+rvetn++RGG+llvl+eG
  gi|15669826|ref|NP_248640.1| 176 RYKPTEDEIERYVEEVELYQSeVGSFQYNPTADEIRTAIRNIPIEITGEATDDVEVSGHRDLPRVETNQLRGGALLVLVEG 256
                                   *********************9*********************************************************** PP

                      PolC_DP2 243 ialkakKikkkvkklklegWewleelikaekeekkeeeeek...................kevkpkekylrdliaGRpvls 304
                                   ++lka+Ki+++v+kl++egW+wl++l+++ keek+ee++ek                    ++++++k+++++iaGRpv++
  gi|15669826|ref|NP_248640.1| 257 VLLKAPKILRHVDKLGIEGWDWLKDLMSK-KEEKEEEKDEKvddeeideeeeeisgywrdVKIEANKKFISEVIAGRPVFA 336
                                   ****************************9.55555555555688999999*********99******************** PP

                      PolC_DP2 305 hpsrkGGfRLrYGRsrntglatagihPatmelldeflavGtqlkverPgKaaavvpvdsiegPtvklknGdvvriddveea 385
                                   hps+ GGfRLrYGRsrntg+at g+hPa m+l+def+avGtqlk+erPgKa++vvpvdsie+P+vklknGdv+r+d++e+a
  gi|15669826|ref|NP_248640.1| 337 HPSKVGGFRLRYGRSRNTGFATQGFHPALMYLVDEFMAVGTQLKTERPGKATCVVPVDSIEPPIVKLKNGDVIRVDTIEKA 417
                                   ********************************************************************************* PP

                      PolC_DP2 386 leikkeveeildlGeiLvayGeflennhpLvpasyveewwiqelekaaakkeaee..kpsaeealelseeldvpLhPkyty 464
                                   ++++++veeil+lG++Lv+yG+flennhpL+p++++eew+++ l +++ +++++   +p+ eea++++ e+++pLhP++ty
  gi|15669826|ref|NP_248640.1| 418 MDVRNRVEEILFLGDVLVNYGDFLENNHPLLPSCWCEEWYEKILIANNIEYDKDFikNPKPEEAVKFALETKTPLHPRFTY 498
                                   ******************************************9998887766543559*********************** PP

                      PolC_DP2 465 lwhdisveelekLaeavaekkkl...eeeklvlel....eeevkeiLekllvehkvkeekivieealallkslgldleeek 538
                                    whd+s+e++  L++++ + k+     +++++++l    ++++k+iLe +++ h v+++k++iee+++ll slg+d+e++k
  gi|15669826|ref|NP_248640.1| 499 HWHDVSKEDIILLRNWLLKGKEDsleGKKVWIVDLeieeDKKAKRILELIGCCHLVRNKKVIIEEYYPLLYSLGFDVENKK 579
                                   *****************9999778884455555542221667*********************************999888 PP

                      PolC_DP2 539 leke.......eekdalelvnelsglevrekaptrigaRmGRPeKskeRkmkpavhvLfpigeaggkrrsvkeaakkkgei 612
                                      e       + k++++l+n l+++evr+++ +++gaRmGRPeK+++Rkmkp+v+ Lfpig+agg+ r +++a++++++ 
  gi|15669826|ref|NP_248640.1| 580 DLVEniekileSAKNSMHLINLLAPFEVRRNTYVYVGARMGRPEKAAPRKMKPPVNGLFPIGNAGGQVRLINKAVEENNTD 660
                                   76555555554445**************************************************************77777 PP

                      PolC_DP2 613 eveiarrkCkkCgketlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkkkidlkellekaleklgereekl 693
                                   +v+++ ++C++Cgk +l++ C+ Cg+k+e                        ++  ++k  lk+++ +al++lg+  +k+
  gi|15669826|ref|NP_248640.1| 661 DVDVSYTRCPNCGKISLYRVCPFCGTKVEL-----------------------DNFGRIKAPLKDYWYAALKRLGI--NKP 716
                                   **************************9999.......................5788999****************..89* PP

                      PolC_DP2 694 eelkgvkgltskekipEpleKgilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklrelGYteDieGkplesedq 774
                                    ++k++kg+tsk+ki+EpleK+ilRa ++v+vfkdgt+R+D+td+p+thf+p+ei+v+veklrelGY++Di+G++l++ +q
  gi|15669826|ref|NP_248640.1| 717 GDVKCIKGMTSKQKIVEPLEKAILRAINEVYVFKDGTTRFDCTDVPVTHFKPNEINVTVEKLRELGYDKDIYGNELVDGEQ 797
                                   ********************************************************************************* PP

                      PolC_DP2 775 ivelkvqDivlsedaaeyllkvakfvDdlLeklyglerfYnvekkedLiGklviglaPHtsagvlgRiiGftkasvgyahP 855
                                   +velk+qD++++e++aey++kva+f+DdlLek+y++erfYnv+kkedLiG+lvig+aPHtsag++gRiiG+tka+vgyahP
  gi|15669826|ref|NP_248640.1| 798 VVELKPQDVIIPESCAEYFVKVANFIDDLLEKFYKVERFYNVKKKEDLIGHLVIGMAPHTSAGMVGRIIGYTKANVGYAHP 878
                                   ********************************************************************************* PP

                      PolC_DP2 856 yfHaakRRn 864
                                   yfHaakRRn
  gi|15669826|ref|NP_248640.1| 879 YFHAAKRRN 887
                                   ********9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.43
                      PolC_DP2  632 rCeeCgektee...klvCkkceeeveeek...cekcekeakavkkkkidlkellekaleklg 687 
                                    rC+ Cg+k +    k +C+kc+++        + +  +++ ++  ++ ++++++++ l+ ++
  gi|15669826|ref|NP_248640.1| 1055 RCK-CGAKYRRiplKGKCPKCGSNLILTVskgAVEKYMDVAEKMAEEYNVNDYIKQRLKIIK 1115
                                    444.4444332111445555555333111011112222223333344445555444444444 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   2.0   5.3e-07   0.00056       2      25 ..     666     687 ..     665     688 .. 0.92
   2 !    5.9   0.5    0.0082       8.6       4      11 ..    1070    1077 ..    1068    1080 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.3e-07
                   zf-ribbon_3   2 tvrCPnCGaplssddnvCpyCGtk 25 
                                   ++rCPnCG++  s  +vCp CGtk
  gi|15669826|ref|NP_248640.1| 666 YTRCPNCGKI--SLYRVCPFCGTK 687
                                   689******9..9*********97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0082
                   zf-ribbon_3    4 rCPnCGap 11  
                                    +CP+CG++
  gi|15669826|ref|NP_248640.1| 1070 KCPKCGSN 1077
                                    57777774 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3    0.0023       2.5       1      38 [.     669     688 ..     652     693 .. 0.58
   2 ?    7.1   0.5    0.0052       5.4      17      39 ..    1057    1079 ..    1048    1083 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0023
                           DZR   1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekv 38 
                                   Cp+Cg+   +                  ++Cp Cg+kv
  gi|15669826|ref|NP_248640.1| 669 CPNCGKI--SLY----------------RVCPFCGTKV 688
                                   4444443..333................4444444444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0052
                           DZR   17 eCgtklkavaaedrCpsCgekvd 39  
                                    +Cg+k ++ + + +Cp+Cg+ + 
  gi|15669826|ref|NP_248640.1| 1057 KCGAKYRRIPLKGKCPKCGSNLI 1079
                                    6****999999********9876 PP

>> Yqai  Hypothetical protein Yqai
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       8.1   8.5e+03      37      52 ..     401     416 ..     388     421 .. 0.77
   2 ?   13.6   0.3   5.9e-05     0.062      23      55 ..     785     817 ..     765     822 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.1
                                   EE.ETTEEEECCCHHH CS
                          Yqai  37 llfdngeiilkeNiyr 52 
                                   +   ng++i  + i++
  gi|15669826|ref|NP_248640.1| 401 VKLKNGDVIRVDTIEK 416
                                   66789****9998875 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.9e-05
                                   --TTSS-B-TTS-EEE.ETTEEEECCCHHHHHH CS
                          Yqai  23 iDayGdEivpddeyllfdngeiilkeNiyrYli 55 
                                    D yG+E+v+++++++    ++i  e   +Y +
  gi|15669826|ref|NP_248640.1| 785 KDIYGNELVDGEQVVELKPQDVIIPESCAEYFV 817
                                   59*****************************86 PP

>> DUF5442  Family of unknown function (DUF5442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       7.4   7.8e+03      42      55 ..      11      24 ..       5      42 .. 0.52
   2 ?   13.4   0.3   6.1e-05     0.065      14      66 ..    1075    1125 ..    1069    1134 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.4
                       DUF5442 42 eklkeylkdisirt 55
                                  e++k+y+ +i+ ++
  gi|15669826|ref|NP_248640.1| 11 ENMKKYFENIVDEV 24
                                  44555555444332 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.1e-05
                       DUF5442   14 andflkfvakgaiikygdiseelkksekeklkeylkdisirtvnciikrfedd 66  
                                    + + +  v+kga+ ky d++e++  +e  ++ +y+k+    + + i   fe++
  gi|15669826|ref|NP_248640.1| 1075 GSNLILTVSKGAVEKYMDVAEKM--AEEYNVNDYIKQRLKIIKEGINSIFENE 1125
                                    5677889*************966..7999*******97766666666777776 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3   0.00045      0.47     505     537 ..     664     696 ..     649     698 .. 0.87
   2 ?   -0.8   0.1      0.45   4.8e+02     509     528 ..    1055    1077 ..    1025    1084 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00045
                                   --EEEETT.--EESSSB-TTT--BE.EEEEEES CS
                          NRDD 505 pkidvCnecgykgeiekCpkCgseeevevirRi 537
                                     +++C++cg+  +   Cp Cg + e++ + Ri
  gi|15669826|ref|NP_248640.1| 664 VSYTRCPNCGKISLYRVCPFCGTKVELDNFGRI 696
                                   5689*******999999*****87778888777 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.45
                                    EETT.--.EESS...SB-TTT--B CS
                          NRDD  509 vCnecgy.kgei...ekCpkCgse 528 
                                    +C+ cg   + i    kCpkCgs+
  gi|15669826|ref|NP_248640.1| 1055 RCK-CGAkYRRIplkGKCPKCGSN 1077
                                    564.5663444478877*****54 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.3     0.062        65      71      94 ..     667     686 ..     651     694 .. 0.72
   2 ?    7.6   0.3    0.0034       3.6      70      97 ..    1053    1079 ..    1044    1090 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.062
                                   EEETTTS-EEECHHHHHS-TTTSS CS
                          HypA  71 vrCreCgkefeleekalrCpkCgs 94 
                                   +rC +Cgk    +     Cp Cg+
  gi|15669826|ref|NP_248640.1| 667 TRCPNCGKISLYR----VCPFCGT 686
                                   5899999444433....6999987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0034
                                    EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                          HypA   70 kvrCreCgkefeleekalrCpkCgsadv 97  
                                     vrC+ Cg++++    + +CpkCgs+ +
  gi|15669826|ref|NP_248640.1| 1053 AVRCK-CGAKYRRIPLKGKCPKCGSNLI 1079
                                    67895.9999986643679*****9844 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3       0.7   7.4e+02       1       6 [.     668     673 ..     665     674 .. 0.86
   2 ?    4.9   0.1     0.025        26       2      10 ..     681     689 ..     680     692 .. 0.93
   3 ?    6.4   0.1    0.0089       9.4       1      10 [.    1070    1079 ..    1070    1087 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.7
                DNA_ligase_ZBD   1 hCPvCG 6  
                                   +CP CG
  gi|15669826|ref|NP_248640.1| 668 RCPNCG 673
                                   599998 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.025
                DNA_ligase_ZBD   2 CPvCGsavv 10 
                                   CP CG++v+
  gi|15669826|ref|NP_248640.1| 681 CPFCGTKVE 689
                                   *******98 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0089
                DNA_ligase_ZBD    1 hCPvCGsavv 10  
                                    +CP CGs ++
  gi|15669826|ref|NP_248640.1| 1070 KCPKCGSNLI 1079
                                    6******987 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2       1.8   1.9e+03      28      35 ..     666     673 ..     650     679 .. 0.64
   2 ?    5.6   0.2      0.02        21       5      17 ..     680     692 ..     677     704 .. 0.83
   3 ?   -2.5   0.0       6.5   6.9e+03      27      36 ..    1049    1060 ..    1024    1065 .. 0.69
   4 ?    4.3   0.0      0.05        52       5      25 ..    1070    1090 ..    1069    1107 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.8
               Lar_restr_allev  28 cvyCadCg 35 
                                   +  C +Cg
  gi|15669826|ref|NP_248640.1| 666 YTRCPNCG 673
                                   55555555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.02
               Lar_restr_allev   5 pCPfCggravler 17 
                                    CPfCg + +l +
  gi|15669826|ref|NP_248640.1| 680 VCPFCGTKVELDN 692
                                   5******999876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.5
               Lar_restr_allev   27 q...cvyCadCga 36  
                                    +    v C +Cga
  gi|15669826|ref|NP_248640.1| 1049 FsrqAVRC-KCGA 1060
                                    04448999.6999 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.05
               Lar_restr_allev    5 pCPfCggravlersqrvvaei 25  
                                     CP Cg+  +l  s++ v+++
  gi|15669826|ref|NP_248640.1| 1070 KCPKCGSNLILTVSKGAVEKY 1090
                                    5******99999999888765 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.3   2.4e+03       8      19 ..     345     356 ..     344     358 .. 0.89
   2 ?   10.1   1.1   0.00054      0.57      11      32 ..     666     685 ..     664     691 .. 0.78
   3 ?    3.2   1.6     0.077        81      13      33 ..    1055    1076 ..    1053    1078 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.3
                       DUF35_N   8 rLvgqrCpdCGt 19 
                                   rL+++r +++G 
  gi|15669826|ref|NP_248640.1| 345 RLRYGRSRNTGF 356
                                   9*********97 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00054
                       DUF35_N  11 gqrCpdCGtvqfPPravCphCg 32 
                                   ++rCp+CG+   ++  vCp Cg
  gi|15669826|ref|NP_248640.1| 666 YTRCPNCGKISLYR--VCPFCG 685
                                   69*********986..566666 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.077
                       DUF35_N   13 rCpdCGtvqfPPr.avCphCgs 33  
                                    rC+   +++  P    Cp+Cgs
  gi|15669826|ref|NP_248640.1| 1055 RCKCGAKYRRIPLkGKCPKCGS 1076
                                    7777778888888899999998 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.4    0.0018       1.9      27      49 ..     666     686 ..     649     690 .. 0.80
   2 ?    2.4   0.5      0.16   1.7e+02      40      52 ..    1067    1079 ..    1055    1081 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                       DUF1272  27 yEctFCaeCaeevlenvCPncgG 49 
                                   y  t C +C +  l  vCP cg 
  gi|15669826|ref|NP_248640.1| 666 Y--TRCPNCGKISLYRVCPFCGT 686
                                   4..88****************96 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.16
                       DUF1272   40 lenvCPncgGelv 52  
                                    l++ CP cg +l+
  gi|15669826|ref|NP_248640.1| 1067 LKGKCPKCGSNLI 1079
                                    7999*****9986 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.6    0.0045       4.8      18      44 ..     667     688 ..     662     692 .. 0.80
   2 ?    2.2   0.3      0.17   1.8e+02      33      45 ..    1067    1079 ..    1054    1087 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0045
                      zf-C2HC5  18 pnClnCGkiiCakeglskpCsfCgspl 44 
                                   + C nCGki      l   C+fCg+++
  gi|15669826|ref|NP_248640.1| 667 TRCPNCGKI-----SLYRVCPFCGTKV 688
                                   6799***99.....34478****9875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.17
                      zf-C2HC5   33 lskpCsfCgspll 45  
                                    l+++C+ Cgs+l+
  gi|15669826|ref|NP_248640.1| 1067 LKGKCPKCGSNLI 1079
                                    3377888888876 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.8   0.00066       0.7      26      47 ..     666     686 ..     662     689 .. 0.88
   2 ?   -2.6   0.3       6.7   7.1e+03      28      33 ..    1070    1075 ..    1052    1079 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00066
                                   EEEETTTCCEECTTC-BTTTTB CS
                Ribosomal_L32p  26 lvecpncgelklpHrvcpscGy 47 
                                    ++cpncg+ +l  rvcp cG+
  gi|15669826|ref|NP_248640.1| 666 YTRCPNCGKISLY-RVCPFCGT 686
                                   579*********9.79****96 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.7
                                    EETTTC CS
                Ribosomal_L32p   28 ecpncg 33  
                                    +cp+cg
  gi|15669826|ref|NP_248640.1| 1070 KCPKCG 1075
                                    688888 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.019        20      20      32 ..     668     680 ..     664     680 .. 0.87
   2 ?    3.6   0.3     0.064        67      19      27 ..     679     687 ..     678     699 .. 0.81
   3 ?    3.7   0.4     0.059        62      18      30 ..    1068    1080 ..    1056    1091 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.019
                 Zn_Tnp_IS1595  20 vCPhCgsrkayri 32 
                                   +CP+Cg+ ++yr+
  gi|15669826|ref|NP_248640.1| 668 RCPNCGKISLYRV 680
                                   6*****9999985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.064
                 Zn_Tnp_IS1595  19 fvCPhCgsr 27 
                                   +vCP+Cg +
  gi|15669826|ref|NP_248640.1| 679 RVCPFCGTK 687
                                   69*****76 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.059
                 Zn_Tnp_IS1595   18 gfvCPhCgsrkay 30  
                                    +  CP+Cgs  + 
  gi|15669826|ref|NP_248640.1| 1068 KGKCPKCGSNLIL 1080
                                    567*****97554 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       6.9   7.3e+03      15      24 ..     179     188 ..     175     188 .. 0.89
   2 ?    1.8   0.1      0.22   2.3e+02      24      31 ..     668     675 ..     667     677 .. 0.80
   3 ?    3.4   0.1     0.072        76       3      12 ..     681     690 ..     679     692 .. 0.87
   4 ?    3.3   0.1     0.077        81       3      17 ..    1071    1085 ..    1071    1087 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.9
                                   -TT-SS-EEE CS
                     Nudix_N_2  15 pdgDnreRlv 24 
                                   p +D+ eR+v
  gi|15669826|ref|NP_248640.1| 179 PTEDEIERYV 188
                                   899*****98 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.22
                                   EETTTTEE CS
                     Nudix_N_2  24 vCpaCgti 31 
                                   +Cp+Cg i
  gi|15669826|ref|NP_248640.1| 668 RCPNCGKI 675
                                   59999988 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.072
                                   -TTT--B-EE CS
                     Nudix_N_2   3 CsqCGtpvel 12 
                                   C+ CGt+vel
  gi|15669826|ref|NP_248640.1| 681 CPFCGTKVEL 690
                                   99****9997 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.077
                                    -TTT--B-EEE--TT CS
                     Nudix_N_2    3 CsqCGtpvelripdg 17  
                                    C++CG+ + l + +g
  gi|15669826|ref|NP_248640.1| 1071 CPKCGSNLILTVSKG 1085
                                    ******998887665 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.7      0.02        21       1       7 [.     668     674 ..     667     675 .. 0.82
   2 ?    5.5   0.1     0.014        15       2       9 ..     681     688 ..     678     692 .. 0.64
   3 ?   -2.5   0.1       4.4   4.7e+03       4       8 ..    1057    1061 ..    1057    1063 .. 0.68
   4 ?    4.8   1.0     0.023        24       2       7 ..    1071    1076 ..    1070    1078 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.02
                 zinc_ribbon_2   1 fCpnCGa 7  
                                   +CpnCG+
  gi|15669826|ref|NP_248640.1| 668 RCPNCGK 674
                                   5999997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.014
                 zinc_ribbon_2   2 CpnCGael 9  
                                   Cp CG+++
  gi|15669826|ref|NP_248640.1| 681 CPFCGTKV 688
                                   66666665 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.4
                 zinc_ribbon_2    4 nCGae 8   
                                    +CGa+
  gi|15669826|ref|NP_248640.1| 1057 KCGAK 1061
                                    67776 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.023
                 zinc_ribbon_2    2 CpnCGa 7   
                                    Cp+CG 
  gi|15669826|ref|NP_248640.1| 1071 CPKCGS 1076
                                    666664 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.9       1.2   1.3e+03       3       9 ..     668     674 ..     667     679 .. 0.82
   2 ?   -1.1   0.2       1.5   1.6e+03       3      10 ..     680     687 ..     678     690 .. 0.81
   3 ?   12.0   0.2   0.00013      0.13       2      17 ..    1069    1084 ..    1068    1091 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                                   E-SSS-- CS
                zf-C4_Topoisom   3 kCPkCgg 9  
                                    CP Cg+
  gi|15669826|ref|NP_248640.1| 668 RCPNCGK 674
                                   5****95 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                                   E-SSS--E CS
                zf-C4_Topoisom   3 kCPkCggd 10 
                                    CP Cg +
  gi|15669826|ref|NP_248640.1| 680 VCPFCGTK 687
                                   7*****76 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00013
                                    EE-SSS--EEEEEE-S CS
                zf-C4_Topoisom    2 ekCPkCggdLvlkrgk 17  
                                    +kCPkCg++L+l  +k
  gi|15669826|ref|NP_248640.1| 1069 GKCPKCGSNLILTVSK 1084
                                    89********997776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1198  (0.0668191); expected 358.6 (0.02)
Passed bias filter:                      854  (0.0476323); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 1.08u 0.32s 00:00:01.40 Elapsed: 00:00:00.53
# Mc/sec: 6503.28
//
Query:       gi|15669827|ref|NP_248641.1|  [L=519]
Description: glycogen phosphorylase GlgP [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-14   53.4   2.1    3.5e-09   35.5   0.0    4.0  4  Phosphorylase  Carbohydrate phosphorylase
  ------ inclusion threshold ------
       0.13   12.7   1.1        1.5    9.3   0.0    3.1  3  DUF3417        Protein of unknown function (DUF3417)


Domain annotation for each model (and alignments):
>> Phosphorylase  Carbohydrate phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   5.9e-05      0.53      23      59 ..      22      58 ..      19      96 .. 0.86
   2 !    2.1   0.0     0.005        45     240     279 ..     178     211 ..     136     213 .. 0.71
   3 !   35.5   0.0   3.9e-13   3.5e-09     415     593 ..     295     458 ..     284     476 .. 0.87
   4 !    3.2   0.7    0.0023        21     667     709 ..     476     518 ..     462     519 .] 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 5.9e-05
                                  SHHHHHHHHHHHHHHHTT-EEEEEEE--SCESEEEEE CS
                 Phosphorylase 23 GGLGRLAacfldslatlelpavGygirYeyGlFkQki 59
                                  GGLG LA +++ ++  l+ p vG++i ++yG ++Q  
  gi|15669827|ref|NP_248641.1| 22 GGLGFLAGSHFRAAKRLNQPLVGVSILWSYGYYDQLR 58
                                  9*********************************964 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.005
                                   HCC---HHHHHHHHCCCEEEEE--SSGGGS-EEEHHHHHH CS
                 Phosphorylase 240 deeglewdeaweitkktfaytnhtvlpealekwpvellek 279
                                   +e+gl      e t++ + +t ht lpe  e+ +++ll++
  gi|15669827|ref|NP_248641.1| 178 EEYGL------EYTREHTVFTTHTPLPEGNETQDINLLKS 211
                                   45554......45778889****************99987 PP

  == domain 3  score: 35.5 bits;  conditional E-value: 3.9e-13
                                   HHHHHHHHHHHHHHHHHHHHHHSS---TTSEEEEEES-SCCCCTHHHHHHHHHHHHHHHHHSTTS----EEEEEE----TT CS
                 Phosphorylase 415 eelaeikqenKerlaelikekegvevdpeslfdvqvkRlheYkRqlLnvLhiitlYneikenpekkvvprtvifggkaapg 495
                                   + l+e k e Ke l e +++++g   +++ l  v  +R+  YkR ++ +   + l + +k+++        vi +gk  p 
  gi|15669827|ref|NP_248641.1| 295 DMLRERKMELKEILFEEVADQTGKIFKKDRLTVVWARRFTAYKRPHILLHDEMRLLELLKKKR------IQVIWAGKPHPN 369
                                   5678899999************************************98888888888888774......789********9 PP

                                   -HHHHHHHHHHHHHHHHHCC-TTTCCCEEEEEETT-SHHHHHHHGGG-SEEEE---TTTSSS-SHHHHHHHTT-EEEEESS CS
                 Phosphorylase 496 YalAkkiiklinsvaevvnndpevkdklkvvflenynvslaekiipaadlseqistagkeASGTgnmkfmlnGaltigtlD 576
                                    +       +i +   +v + +++k+     +l+ y+ +l++++  ++d+  +     +eASGT+ m   +n ++ ++tlD
  gi|15669827|ref|NP_248641.1| 370 DHN------MIATFNWIVSKTRDMKGA---TILTGYELKLSKMLKQGSDIWLNTPKLNHEASGTSGMTASMNASIHMSTLD 441
                                   984......667777778888888886...789************************************************ PP

                                   TCHHHHHHHH-GGGSEE CS
                 Phosphorylase 577 GanvEiaeevgeenifi 593
                                   G  vE a+   ++ + i
  gi|15669827|ref|NP_248641.1| 442 GWHVEWAKMYPDDSFTI 458
                                   *****998877776544 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.0023
                                   HHHHHHHHHCSHHHHHHHHHHHHHCGGGGBHHHHHHHHHHHTT CS
                 Phosphorylase 667 aqekveeaYkdkkewakksilniaksgkFssDrtikeYaeeiW 709
                                     e+v+++Y+ ++ w+k + +    + +F ++r  keYae+++
  gi|15669827|ref|NP_248641.1| 476 LLEEVADMYDTERWWMKACNCVNHIVEYFDAERMAKEYAEKLY 518
                                   56899999*999999999888888899*************987 PP

>> DUF3417  Protein of unknown function (DUF3417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00017       1.5      95     108 ..       3      16 ..       1      17 [. 0.85
   2 ?   -1.9   0.0      0.52   4.7e+03      63      63 ..     240     240 ..     211     275 .. 0.53
   3 ?    0.0   0.1      0.13   1.1e+03      60     102 ..     465     507 ..     460     512 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00017
                       DUF3417  95 aiAYFsaEfGlhes 108
                                     AYF++Ef++h+ 
  gi|15669827|ref|NP_248641.1|   3 PTAYFCMEFAIHQP 16 
                                   67*********986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.52
                       DUF3417  63 f 63 
                                   +
  gi|15669827|ref|NP_248641.1| 240 V 240
                                   2 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.13
                       DUF3417  60 deeflar.leavveefeeyleektwfqkkaeeekkeaiAYFsaE 102
                                   d++++a+ + +++ee+ ++ ++++w+ k++ +  ++ + YF aE
  gi|15669827|ref|NP_248641.1| 465 DDAYVANcIYNLLEEVADMYDTERWWMKAC-NCVNHIVEYFDAE 507
                                   555554426788899999999999999887.7788899999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 3066.68
//
Query:       gi|15669828|ref|NP_248642.1|  [L=255]
Description: coenzyme PQQ synthesis protein PqqE [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-19   70.3   0.3    3.5e-19   69.8   0.3    1.2  1  Radical_SAM  Radical SAM superfamily
    2.2e-12   47.4   0.4    4.4e-12   46.5   0.4    1.5  1  Fer4_12      4Fe-4S single cluster domain
    1.7e-09   37.8   1.9    2.3e-09   37.4   0.3    2.0  3  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.039   13.2   0.1      0.078   12.2   0.1    1.5  1  PUL          PUL domain
       0.12   12.0   0.0       0.32   10.6   0.0    1.6  2  DeoC         DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.3   9.9e-23   3.5e-19       3     167 .]      41     195 ..      39     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 9.9e-23
                                   EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiritv 82 
                                    t gCn++C++C ++         +  sv+eil+++ e+ ++    + +++ ggep+l+ d+ el++ l+ +   g+ + +
  gi|15669828|ref|NP_248642.1|  41 LTYGCNFKCKYCFFKP-----LSCKKYSVDEILNKILEVNEN-YkLDKILIAGGEPTLQNDLSELTKLLKDE---GFYLML 112
                                   588************6.....899***************644.44**************************8...****** PP

                                   EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTT....SETEEEEEEEBTTTSH.H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx.x RF
                   Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreag....ikrvvdrivglpGend.e 158
                                   +tng+ +     + l++l+vd ++++l+a+d+   + ++    ++++vl+++ ++ +++    +k v + +v++p+  d +
  gi|15669828|ref|NP_248642.1| 113 STNGYYL----KDMLDKLEVDEIHIDLKAYDEN-KHIYL-TSCSNKKVLDCISYIGKYRdefnFK-VEIDTVLIPNIVDlD 186
                                   ******9....377788889*************.67777.679**************96555555.999999999998889 PP

                                   HHHHHHHHH CS
                                   xxxxxxxxx RF
                   Radical_SAM 159 eleellell 167
                                   e+e+++++l
  gi|15669828|ref|NP_248642.1| 187 EIEKIAKFL 195
                                   999999986 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.4   1.2e-15   4.4e-12       8     106 ..      38     130 ..      35     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.2e-15
                       Fer4_12   8 lslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdi 88 
                                   ++l++ gCn++Ck+Cf k + + k++    +e+l++i+e  ++++ +++ + GGEP l   +++l el k +k e++   +
  gi|15669828|ref|NP_248642.1|  38 ITLLTYGCNFKCKYCFFKPLSCKKYS---VDEILNKILEVNENYKLDKILIAGGEPTL---QNDLSELTKLLKDEGF-YLM 111
                                   68999***********5544444444...489*******9999***************...8999***********9.69* PP

                       Fer4_12  89 wlytgytleelskk.ekee 106
                                   ++++gy l+++++k e++e
  gi|15669828|ref|NP_248642.1| 112 LSTNGYYLKDMLDKlEVDE 130
                                   ***********97654444 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.3   6.4e-13   2.3e-09       6     103 ..      43     130 ..      39     149 .. 0.83
   2 ?   -2.1   0.0       1.1     4e+03      68     109 ..     158     196 ..     145     202 .. 0.51
   3 ?   -2.2   0.0       1.2   4.5e+03      80      99 ..     229     248 ..     208     254 .. 0.62

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 6.4e-13
                       Fer4_14   6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwle 86 
                                    gCn++Ck C+ k     + +k++++e+l++il    ++++k +++ + GGeP +   +++l +l k lk+e+  +   l 
  gi|15669828|ref|NP_248642.1|  43 YGCNFKCKYCFFKP---LSCKKYSVDEILNKIL--EVNENYKLDKILIAGGEPTL---QNDLSELTKLLKDEG--FYLMLS 113
                                   69**********99...99**************..6666677799********94...578999999999999..999999 PP

                       Fer4_14  87 tngtleielektpdlke 103
                                   tng + +++ +  + +e
  gi|15669828|ref|NP_248642.1| 114 TNGYYLKDMLDKLEVDE 130
                                   99988877765444544 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                       Fer4_14  68 lklvkrlkeeypekkiwletngtleielektpdlkekleals 109
                                   +  + ++++e+ ++k+ + t    +  + + ++ +++ + ls
  gi|15669828|ref|NP_248642.1| 158 ISYIGKYRDEF-NFKVEIDTVLIPN--IVDLDEIEKIAKFLS 196
                                   33344444444.4556555544444..223455556666655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.2
                       Fer4_14  80 ekkiwletngtleielektp 99 
                                   e+  +  +n +  +++++ +
  gi|15669828|ref|NP_248642.1| 229 EIALKYLSNVSCSLDFKRHK 248
                                   44455556666666666544 PP

>> PUL  PUL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.2e-05     0.078       5      54 ..      55     104 ..      54     135 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                           PUL   5 tyllfkkanldkllkKlkelNakllsagqkdlalsd....eelatLeallaale 54 
                                   ++l+ kk+ +d +l+K+ e+N++++ ++     l +    +  ++L++l++ l+
  gi|15669828|ref|NP_248642.1|  55 KPLSCKKYSVDEILNKILEVNENYKLDK----ILIAggepTLQNDLSELTKLLK 104
                                   6899****************99986543....3444333344447777777664 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       0.8   2.9e+03     185     205 ..      69      89 ..      60     101 .. 0.72
   2 ?   10.6   0.0     9e-05      0.32     114     162 ..     184     233 ..     180     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.8
                                   HHHHHHHHCHSSTEEEEETTS CS
                          DeoC 185 evfkdvikaapvpgvvlsGGv 205
                                   + + +v+++ ++++++++GG 
  gi|15669828|ref|NP_248642.1|  69 NKILEVNENYKLDKILIAGGE 89 
                                   556678889999999999995 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 9e-05
                                   HHHHHHHHHHHHHHHTEEEEEE.EEE-CTTBSSTTCHHHHHHHHHHHHTC CS
                          DeoC 114 klaeikrvkeacheeglplile.lylrdeaikdekvdpdlvaeAarvsae 162
                                    l+ei+++++   +++lp  +   + ++++ + ek d+d++ +A +++ +
  gi|15669828|ref|NP_248642.1| 184 DLDEIEKIAKFLSNWDLPYRITgYVKYNNNLNAEKPDEDKILKAKEIALK 233
                                   6899******************5556788888888**********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1573.51
//
Query:       gi|15669829|ref|NP_248643.1|  [L=478]
Description: hypothetical protein MJ_1633 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-24   85.3   1.1    9.8e-24   83.8   0.6    2.2  2  TrkA_N           TrkA-N domain
    5.2e-17   62.5   0.7    5.2e-17   62.5   0.7    2.8  3  DHHA1            DHHA1 domain
    1.3e-13   51.1   0.1    2.8e-13   50.0   0.1    1.6  1  DHH              DHH family
    1.4e-06   28.7   0.2    5.2e-06   26.9   0.2    2.0  1  NAD_binding_7    Putative NAD(P)-binding
    0.00029   20.8   0.0    0.00056   19.8   0.0    1.6  1  NAD_binding_10   NAD(P)H-binding
    0.00091   19.5   0.3     0.0025   18.0   0.3    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0013   18.9   0.2     0.0058   16.8   0.0    2.1  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0031   17.1   0.2     0.0056   16.3   0.2    1.4  1  NmrA             NmrA-like family
     0.0092   16.0   0.8      0.019   15.0   0.2    1.9  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.013   15.0   2.8       0.65    9.5   0.3    2.6  2  DUF166           Domain of unknown function
       0.19   12.4   3.5       0.18   12.5   0.7    2.5  3  PglD_N           PglD N-terminal domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.6     6e-27   9.8e-24       1     115 [.       5     117 ..       5     118 .. 0.92
   2 ?   -3.8   0.0       9.5   1.6e+04      70      85 ..     173     188 ..     163     193 .. 0.53

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 6e-27
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilavl 81 
                                   i +iG+G +Gr++++ +++++ ++++idk+ + ++ l +eg++v+vgdat++evL++a+ie+ad+v+++t++ e+n  +++
  gi|15669829|ref|NP_248643.1|   5 ITVIGFGSFGRKVVNFIKNKE-PITIIDKNIDDADDLVKEGVTVIVGDATQDEVLKKAKIENADIVLILTNEPEVNRRIAE 84 
                                   679***************999.5********************************************************** PP

                                   HHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEE CS
                        TrkA_N  82 lakelnpkkkiiaraqdpehaellkklgadvvis 115
                                    + el p+ + iara  p + el+  l++d++i+
  gi|15669829|ref|NP_248643.1|  85 RVCELSPNSYKIARAI-PRYPELYMGLNIDKIIN 117
                                   **************96.45555555677777775 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.5
                                   SSSHHHHHHHHHHHHH CS
                        TrkA_N  70 tgddeanilavllake 85 
                                   ++ d + i+ ++++k+
  gi|15669829|ref|NP_248643.1| 173 INPDPDAIASAMALKT 188
                                   4444555555555555 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1         2   3.3e+03      28      52 ..      55      79 ..      22      97 .. 0.65
   2 ?    1.6   0.2      0.21   3.5e+02       9      59 ..     124     183 ..     119     196 .. 0.75
   3 !   62.5   0.7   3.2e-20   5.2e-17      20     137 ..     347     462 ..     336     464 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                                  HHHHHTCEEECTCEEEEEECHCCHH CS
                         DHHA1 28 eellekaeevkgvkvlvaevgeewd 52
                                  +e+l+ka+  + + vl+   ++e++
  gi|15669829|ref|NP_248643.1| 55 DEVLKKAKIENADIVLILTNEPEVN 79
                                  4444444443444444444434444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.21
                                   HHHHHHHHCHHHHHHHHHHHHHHHTCEEEC..........TCEEEEEECHCCHHHHHHHHH CS
                         DHHA1   9 kelekeleelkealaklkaeellekaeevk..........gvkvlvaevgeewdagalgia 59 
                                   k++ ke+e++k + + ++ +++l + ++ +          + ++l+     + d++a+++a
  gi|15669829|ref|NP_248643.1| 124 KDIAKEVEDAKLKRKLMQLKSVLIEGKKRCmklekteeekKAPLLILTH-INPDPDAIASA 183
                                   7889999999999999999999888777777776666766666666666.66677666665 PP

  == domain 3  score: 62.5 bits;  conditional E-value: 3.2e-20
                                   HHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSHSS-HHHH CS
                         DHHA1  20 ealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkdgvdagel 99 
                                   ++  +++a+++ ++  +v + ++++a+vge  +++al  aad l++  ++  + +fv++  gd++++sar+k+ ++++ge+
  gi|15669829|ref|NP_248643.1| 347 TEVMEVLAKAVMNR--RVVKGNIALAYVGEISNRDALPKAADFLLK--MEgISTTFVFGIVGDEIHISARTKDLRLNLGEI 423
                                   44455555556554..33399*************************..**9*********************77******* PP

                                   HHHHHHHTTCCEEEETCEEEEEEE.......HCHHHHHHHHHHHH CS
                         DHHA1 100 akeaaaklgggGGGHdlAaGagip.......aekleealealeea 137
                                   +++      +gGGGH  Aa+a+ip        +k e++++++eea
  gi|15669829|ref|NP_248643.1| 424 LNK-----AFGGGGHQTAAAAKIPlgifkavSDK-EALRKLVEEA 462
                                   ***.....9***************8888874333.6666666665 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.1   1.7e-16   2.8e-13       3     101 .]     168     306 ..     166     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.7e-16
                                   EEE-ECSSSHHHHHHHHHHHHC...............................................ECS--TCGGCGC CS
                                   xxxxxxxxxxxxxxxxxxxxxx...............................................xxxxxxxxxxxx RF
                           DHH   3 livghknpDtDsigSaialanl...............................................lvDhneksqave 36 
                                   li++h npD D+i+Sa+al+ l                                               ++D+++++q   
  gi|15669829|ref|NP_248643.1| 168 LILTHINPDPDAIASAMALKTLaerwgvdsdiayggnigydenkaminllgikllnvedidldnycviaVIDTSTSKQLP- 247
                                   7999*****************55555556666666666666666666666666666666666666666699999999888. PP

                                   CHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH  37 geakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                      +e  ++ iiiDHH+     +  a+++ ++++vg+ta+i++++l e ++e+s+++a++l  gi
  gi|15669829|ref|NP_248643.1| 248 ---IELPNIDIIIDHHNNT---DLTAKYMDVRPEVGATASILTQYLMELDIEPSRNLATALFYGI 306
                                   ...56*************7...4444578999******************************998 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.2   3.2e-09   5.2e-06      10      81 ..       5      85 ..       2      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.2e-09
                 NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvvapevkeeleelvk.........laeeel..ekdlegadlviaatddrelneriaea 81
                                  + v+G G+ + rkv ++++++  +t++++++ + +++lvk         ++++e+  ++++e+ad+v++ t+++e+n+riae 
  gi|15669829|ref|NP_248643.1|  5 ITVIGFGSFG-RKVVNFIKNKEPITIIDKNI-DDADDLVKegvtvivgdATQDEVlkKAKIENADIVLILTNEPEVNRRIAER 85
                                  689******9.8******************6.4445555555555545556777776688********************996 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.4e-07   0.00056       4      83 ..      11      88 ..       9     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.4e-07
                                  SHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHH.HTT-SEEEES---TCCHHHHHHHHHH CS
                NAD_binding_10  4 GkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaea.lkgadaVvsalggggkdeegaknivd 83
                                  G+ Gr++v+ + +++  ++t++  n +++++l  +eg++v++gd+t+ e l++a +++ad+V++ ++  + ++++a+++++
  gi|15669829|ref|NP_248643.1| 11 GSFGRKVVNFIKNKE--PITIIDKNIDDADDLV-KEGVTVIVGDATQDEVLKKAkIENADIVLILTNEPEVNRRIAERVCE 88
                                  899******999995..99*************8.7************999998758**********999998888888876 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   1.6e-06    0.0025       1      76 [.       5      72 ..       5      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
                                  EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE- CS
               Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnl 76
                                  + +iG+Gs G+ v+  ++++++    it++d++ + ++ l++   g  ++ i  da ++e  L+++ ++ +d+v+ l
  gi|15669829|ref|NP_248643.1|  5 ITVIGFGSFGRKVVNFIKNKEP----ITIIDKNIDDADDLVK--EG--VTVIVGDATQDEV-LKKAkIENADIVLIL 72
                                  679**************99885....7*********999985..34..4555555555444.555559999999855 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.5e-06    0.0058       2      82 ..       5      91 ..       4      99 .. 0.81
   2 ?   -1.9   0.0         2   3.2e+03      55      80 ..     330     357 ..     303     372 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.5e-06
                                  EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...EEE-SSHHHHHHHC....SEEEE-SSSHHHHHHHHHSHC CS
                 NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...akaaesieelvasl....dvvitmvkagkavdeviegll 77
                                  i +iG G  G++ + n++k++  +++++ + + +++lv+eg   +++ ++  e+++++      ++++++++++v+  i + +
  gi|15669829|ref|NP_248643.1|  5 ITVIGFGSFGRKVV-NFIKNKEPITIIDKNIDDADDLVKEGvtvIVGDATQDEVLKKAkienADIVLILTNEPEVNRRIAERV 86
                                  889********976.8889999*******************887777788889999998888567778888888888877744 PP

                                  CC--T CS
                 NAD_binding_2 78 ealkk 82
                                   +l++
  gi|15669829|ref|NP_248643.1| 87 CELSP 91
                                  44444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                                   HC..SEEEE-SSSHHHHHHHHHSHCCC- CS
                 NAD_binding_2  55 sl..dvvitmvkagkavdevieglleal 80 
                                   s     ++ m+++ +   ev+e l++a+
  gi|15669829|ref|NP_248643.1| 330 SYidASILNMIENPEISTEVMEVLAKAV 357
                                   3354567778888888888888777665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   3.4e-06    0.0056       1      79 [.       5      78 ..       5      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.4e-06
                                  EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHH.HTT-SEEEE---GGS-HH CS
                          NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvea.lkgvdvvfsvtgfyskei 79
                                  I+viG  G+ G+ vv+++ k++ ++ ++  d + + a+ l ++Gv+++ gd+ ++e+l++a ++++d v + t+  + e+
  gi|15669829|ref|NP_248643.1|  5 ITVIG-FGSFGRKVVNFI-KNKEPITII--DKNIDDADDLVKEGVTVIVGDATQDEVLKKAkIENADIVLILTN--EPEV 78
                                  56665.488888888865.555566665..6667889**********************9989**********9..4444 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.2e-05     0.019      13      87 ..       3      77 ..       1      97 [. 0.82
   2 ?   -3.6   0.0       6.4     1e+04      48      69 ..     122     142 ..     115     147 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                                  -EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGH..HHHHHT-SEEEE-SSSSS CS
                  Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleel..kellaeadvvisatasee 87
                                  + +++iG G  +++v++ + +k+   ++++  +++ a++l++e  ++ +   + +e+  k+ +++ad+v++ t+ +e
  gi|15669829|ref|NP_248643.1|  3 NMITVIGFGSFGRKVVNFIKNKE--PITIIDKNIDDADDLVKEGVTVIVGDATQDEVlkKAKIENADIVLILTNEPE 77
                                  5799*************998765..58****************988866666666662235699*****99998776 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.4
                                   HHHHHHHHHT.ET-EEEEGCGH CS
                  Shikimate_DH  48 rakelaeelkgeeiealkleel 69 
                                    ak++a+e++++++  +kl +l
  gi|15669829|ref|NP_248643.1| 122 GAKDIAKEVEDAKL-KRKLMQL 142
                                   57788888876644.3444444 PP

>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3    0.0004      0.65       2      76 ..       7      88 ..       6     119 .. 0.75
   2 ?    5.2   0.2    0.0084        14      41      83 ..     238     282 ..     185     297 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0004
                        DUF166  2 vltsgeyGervvenilnepdfersl........ivavvevpeeldefiedpeelLpe..lkeaDiviaytlhpDlllelaeka 74
                                  v+  g +G++vv+ i+n+     ++         ++++ v+  +++    ++e+L++  +++aDiv+ +t  p ++  +ae++
  gi|15669829|ref|NP_248643.1|  7 VIGFGSFGRKVVNFIKNKEPIT-IIdkniddadDLVKEGVTVIVGD--ATQDEVLKKakIENADIVLILTNEPEVNRRIAERV 86
                                  777899************9888.22344444433333333334555..56788999999*****************9999987 PP

                        DUF166 75 ke 76
                                   e
  gi|15669829|ref|NP_248643.1| 87 CE 88
                                  66 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0084
                        DUF166  41 ied.peelLpe.lkeaDiviaytlhpDlllelaekakekkvkali 83 
                                   i+  ++++Lp  l+++Di+i    + Dl+++ +++  e ++ a i
  gi|15669829|ref|NP_248643.1| 238 IDTsTSKQLPIeLPNIDIIIDHHNNTDLTAKYMDVRPEVGATASI 282
                                   554157789977*****************9998887666666555 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   0.00011      0.18       2      55 ..       5      59 ..       4      86 .. 0.70
   2 ?   -3.2   0.0       8.4   1.4e+04       6      28 ..     122     144 ..     118     156 .. 0.72
   3 ?   -1.8   0.1       3.2   5.2e+03      23      36 ..     231     244 ..     210     269 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                        PglD_N  2 ivIiGaGGhgkvvadiieangeyeiig.flDdnkktevegypvlgkaiellksls 55
                                  i +iG G +g+ v + i++++   ii   +Dd+++   eg+ v+ ++ ++ + l+
  gi|15669829|ref|NP_248643.1|  5 ITVIGFGSFGRKVVNFIKNKEPITIIDkNIDDADDLVKEGVTVIVGDATQDEVLK 59
                                  789****************998888855888888778889999877654433332 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.4
                        PglD_N   6 GaGGhgkvvadiieangeyeiig 28 
                                   Ga   +k+v+d   +++  +++ 
  gi|15669829|ref|NP_248643.1| 122 GAKDIAKEVEDAKLKRKLMQLKS 144
                                   66667888888877777666555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.2
                        PglD_N  23 eyeiigflDdnkkt 36 
                                   +y +i+++D + ++
  gi|15669829|ref|NP_248643.1| 231 NYCVIAVIDTSTSK 244
                                   46677777776533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3492.32
//
Query:       gi|15669830|ref|NP_248644.1|  [L=241]
Description: hypothetical protein MJ_1634 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-41  142.5   1.1    1.4e-41  142.1   1.1    1.1  1  MAF_flag10  Protein of unknown function DUF115
  ------ inclusion threshold ------
      0.046   13.6   0.3          1    9.2   0.1    2.7  2  Alba        Alba


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.1   1.1   1.5e-45   1.4e-41       1     169 [.      32     197 ..      30     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 142.1 bits;  conditional E-value: 1.5e-45
                    MAF_flag10   1 knllknlkenlkpslkellnkfkgnkpaiivgaGPSLeknlellkelr...dkaviiaadtalkaLlkegIkPDivvs.lD 77 
                                   +n+l+n+++++ ++lk++++   g ++++i+gaGPS++k+++ lkelr    k  ii ad+a+ka l+e+I+PDi+vs lD
  gi|15669830|ref|NP_248644.1|  32 NNILENANTIPVDKLKDIIE---G-REVFIFGAGPSIKKHINILKELReinYKNPIIVADGACKAFLEENIIPDIIVSdLD 108
                                   57888888888755555555...7.******************999988889***************************** PP

                    MAF_flag10  78 pqeasyevfkeaekkgdiplvfasgvnpellkkykgpkiflvtgstqalelleeekne..ilfgGgsvantaldlAvklgf 156
                                   +   + e + e+++kg+i++v+a+g+n+e++kky ++++++v + +q +++++e +    i+fgG+++++++++lA+++++
  gi|15669830|ref|NP_248644.1| 109 G---DLEALFECNRKGSIIVVHAHGDNIEKIKKYVPKLKNVVGS-CQ-IPNYKELNLRnvINFGGFTDGDRCCFLAYHFKA 184
                                   *...9999*******************************97765.55.4444333333469******************** PP

                    MAF_flag10 157 keIiliGqDlayt 169
                                   k++il G+D+++ 
  gi|15669830|ref|NP_248644.1| 185 KKLILGGMDFGIY 197
                                   **********975 PP

>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00012         1      28      52 ..      53      77 ..      43      86 .. 0.84
   2 ?    1.2   0.0     0.035   3.2e+02      30      41 ..     124     135 ..     109     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00012
                                  SEEEEEEETTHHHHHHHHHHHHHHH CS
                          Alba 28 eeVvlkatGraIskAvsvaeilkrr 52
                                  +eV++ + G +I+k +++ + l++ 
  gi|15669830|ref|NP_248644.1| 53 REVFIFGAGPSIKKHINILKELREI 77
                                  89****************9988775 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.035
                                   EEEEEETTHHHH CS
                          Alba  30 VvlkatGraIsk 41 
                                   +v++a G +I+k
  gi|15669830|ref|NP_248644.1| 124 IVVHAHGDNIEK 135
                                   899*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1927.17
//
Query:       gi|15669831|ref|NP_248645.1|  [L=414]
Description: hypothetical protein MJ_1635 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-17   62.0   0.5    8.3e-17   60.9   0.5    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.9e-07   31.3   0.1    4.6e-07   30.1   0.1    1.6  1  OrfB_IS605      Probable transposase
      0.004   17.0   0.4      0.004   17.0   0.4    1.7  2  Prok-RING_1     Prokaryotic RING finger family 1
  ------ inclusion threshold ------
      0.017   15.2   1.1      0.039   14.1   1.1    1.5  1  DUF2318         Predicted membrane protein (DUF2318)
      0.028   14.4   2.3       0.05   13.6   2.3    1.3  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.059   13.5   0.4       0.15   12.1   0.4    1.7  1  MGDG_synth      Monogalactosyldiacylglycerol (MGDG) synthase
      0.089   12.8   1.7       0.17   11.8   1.7    1.5  1  zinc-ribbons_6  zinc-ribbons
        0.1   12.5   1.0       0.24   11.3   1.0    1.6  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
       0.11   12.5   1.5        0.2   11.6   1.5    1.5  1  PHD             PHD-finger
       0.14   12.1   0.4       0.27   11.1   0.4    1.4  1  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.16   11.6   2.1        0.3   10.7   2.1    1.4  1  zf-PHD-like     PHD/FYVE-zinc-finger like domain
       0.43   10.8   1.6       0.89    9.8   1.6    1.4  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.5   5.6e-20   8.3e-17       1      69 []     304     366 ..     304     366 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 5.6e-20
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                   ++ l+e+++yk       v++vnpayTS+ C+ Cgs+++  ++g++++C+nC  +++r++++++Ni+kr
  gi|15669831|ref|NP_248645.1| 304 WNGLIEKISYKTI-----VILVNPAYTSTICPICGSRMES-QEGQVVYCSNCLNSFNRQLVGCYNIFKR 366
                                   6677888888887.....**********************.*************************997 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   3.1e-10   4.6e-07      14     117 ..     188     290 ..     174     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.1e-10
                    OrfB_IS605  14 kgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhllhk 94 
                                   +++  +g+D +++ L      +g + +    +l + ++ + ++i+ l ++lkk     +a rk+ rl+++r++r+k++lhk
  gi|15669831|ref|NP_248645.1| 188 DKGMIVGVDSNLRSLDLFHPIEGWTRVDLT-ELHRIKEVYDRKIDFLKKLLKKFP--LRAMRKINRLFERRRNRVKDFLHK 265
                                   566678999999999888887766666655.9999999****************9..9*********************** PP

                    OrfB_IS605  95 lathliktlkev..gvetLnvgnmk 117
                                   l+ +l +   +   + e+Ln + m+
  gi|15669831|ref|NP_248645.1| 266 LTIQLSRLFPDAifVFEDLNKRRMY 290
                                   *****99998887888999988887 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2       3.7   5.6e+03      33      42 ..      35      44 ..      35      48 .. 0.80
   2 !   17.0   0.4   2.7e-06     0.004       2      35 ..     324     361 ..     323     367 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.7
                   Prok-RING_1 33 aCyekagkCv 42
                                  +C +k ++C+
  gi|15669831|ref|NP_248645.1| 35 ECKNKLNECI 44
                                  6889999997 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.7e-06
                   Prok-RING_1   2 ytgkkCpvCgkelkee.dDiVvCpeCgtpyHra...Cy 35 
                                   yt ++Cp+Cg +++++   +V C +C  ++ r+   Cy
  gi|15669831|ref|NP_248645.1| 324 YTSTICPICGSRMESQeGQVVYCSNCLNSFNRQlvgCY 361
                                   8899*********876489*******999888644455 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.1   2.6e-05     0.039      35      67 ..     327     359 ..     308     366 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                       DUF2318  35 daCevCekkgYvqegeelvCknCgvrfaldsig 67 
                                    +C +C+++   qeg+ + C nC ++f+ + +g
  gi|15669831|ref|NP_248645.1| 327 TICPICGSRMESQEGQVVYCSNCLNSFNRQLVG 359
                                   58*************************999887 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.3   3.4e-05      0.05       2      23 ..     329     350 ..     329     351 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.4e-05
                DNA_ligase_ZBD   2 CPvCGsavvReegeaiyRCtn.l 23 
                                   CP+CGs  +  e + + +C+n l
  gi|15669831|ref|NP_248645.1| 329 CPICGSRMESQE-GQVVYCSNcL 350
                                   ********9766.6777899866 PP

>> MGDG_synth  Monogalactosyldiacylglycerol (MGDG) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4    0.0001      0.15      14      75 ..      65     125 ..      60     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                   HHHGGGEEEEEEE------------------------------------------------- CS
                    MGDG_synth  14 aefgdeyqvlvkdllkelnpfllkavlksYlflvkvsalyrllyygteekiqkksilaklat 75 
                                   +ef  e++ + ++ +++++++ + ++++sY  l + +++y+++y+  + k + k+++ +++t
  gi|15669831|ref|NP_248645.1|  65 NEFKRELRNKLLENWNYASHYIDGIIKTSYSILQSWASNYKRGYRTKT-KPIAKRLFVRVKT 125
                                   678889999999*********************************977.5555666666665 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.7   0.00012      0.17       2      30 ..     328     357 ..     327     362 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                   --SSS-S--E.E-SSEEE-TTT--EEEEEE CS
                zinc-ribbons_6   2 kCpeCqqele.krgeqyhCeaCqedlkkea 30 
                                   +Cp C + +e ++g+ + C++C ++++++ 
  gi|15669831|ref|NP_248645.1| 328 ICPICGSRMEsQEGQVVYCSNCLNSFNRQL 357
                                   6*********7788999******9999875 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.0   0.00016      0.24       4      27 ..     329     349 ..     328     353 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                   ESTTTSBEEEEECSCCCEEEESSS CS
                RNA_POL_M_15KD   4 CpkCgNlLlpkedkegknfeCrqC 27 
                                   Cp Cg+ ++++e++ +    C++C
  gi|15669831|ref|NP_248645.1| 329 CPICGSRMESQEGQVVY---CSNC 349
                                   ****************5...**** PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.5   0.00013       0.2       1      25 [.     328     353 ..     328     366 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                   SBTTTTS.TTSTTSCEEEETTTSCEE CS
                           PHD   1 rCavCkk.ksdeeeelvqCdgCkrwf 25 
                                   +C +C++  + +e+++v+C +C ++f
  gi|15669831|ref|NP_248645.1| 328 ICPICGSrMESQEGQVVYCSNCLNSF 353
                                   6******87888**********8876 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00018      0.27       9      43 ..     324     361 ..     320     368 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                                   SS--B-TTT-SB--SSSS-EEEETTT--EE-CC...CC CS
                          C1_1   9 kqptfCkhCgeflwgkekqglkCswCkllvHkk...Ch 43 
                                   + +t C  Cg+ ++ +e q + Cs+C  ++  +   C+
  gi|15669831|ref|NP_248645.1| 324 YTSTICPICGSRMESQEGQVVYCSNCLNSFNRQlvgCY 361
                                   56899********77***********887766655555 PP

>> zf-PHD-like  PHD/FYVE-zinc-finger like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.1    0.0002       0.3       1      32 [.     329     360 ..     329     367 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                   zf-PHD-like   1 CdtCaeskdeekgqlvyCqGCslsyhkaClGk 32 
                                   C +C+++ ++++gq+vyC  C +s+ ++ +G 
  gi|15669831|ref|NP_248645.1| 329 CPICGSRMESQEGQVVYCSNCLNSFNRQLVGC 360
                                   999************************99885 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.6    0.0006      0.89      15      39 ..     326     349 ..     324     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0006
                 Auto_anti-p27  15 aetCpvCgvPLmrdrkggkvyCvaC 39 
                                   ++ Cp Cg+ +  + +g+ vyC +C
  gi|15669831|ref|NP_248645.1| 326 STICPICGSRMESQ-EGQVVYCSNC 349
                                   789*****986665.67899***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2583.40
//
Query:       gi|15669832|ref|NP_248646.1|  [L=323]
Description: N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.2e-135  450.0   0.3   4.8e-135  449.8   0.3    1.0  1  MCH       Cyclohydrolase (MCH)


Domain annotation for each model (and alignments):
>> MCH  Cyclohydrolase (MCH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.8   0.3  2.7e-139  4.8e-135       1     310 [.       3     317 ..       3     318 .. 0.98

  Alignments for each domain:
  == domain 1  score: 449.8 bits;  conditional E-value: 2.7e-139
                                   -HHHHHHHHHHHHHHTHHHHT-EEEE-TTS-EEEESSSSS---HHHHHHHHHHHTTT-EEEEEE..EEEETTEEEEEEEEE CS
                           MCH   1 SvnelalelveellekaeelrieveelengatviDaGveaeGgleAGlllaeiclggLaevsle..lsevkgaklpavevs 79 
                                   Svn++ale+v++++e++ee++i+v +lengatv+D+Gv+++G+++AG+l+++iclggLa+v ++  + e kg++lp+v+++
  gi|15669832|ref|NP_248646.1|   3 SVNKKALEIVNKMIENKEEINIDVIKLENGATVLDCGVNVPGSWKAGKLFTKICLGGLAHVGISlsPCECKGITLPYVKIK 83 
                                   8***********************************************************977611556777********* PP

                                   ESSHHHHHTTTTS--EEEEETTEEEEEESTTHHHHTS.HHHHHHHT-----S-EEEEEESSS---HHHHHHHHHHHTS-GG CS
                           MCH  80 tdhPvlacLasqkAgWelsaekffalgsGPaRalaak.eelfeelgyedeadaavlvlesdklPdeevvekvaeecgvepe 159
                                   t+hP++a+L++qkAgW+++++k+fa+gsGPaRala+k ++++ee+gyed+ad+avl+le++klP+eev+e+va+ecgve+e
  gi|15669832|ref|NP_248646.1|  84 TSHPAIATLGAQKAGWAVKVGKYFAMGSGPARALAKKpKKTYEEIGYEDDADVAVLCLEASKLPNEEVAEYVAKECGVEVE 164
                                   ********************************************************************************* PP

                                   GEEEEEE-SSSHHHHHHHHTTHHHHHHHHHHH.TT--GGGEEEEEEEEE-----SSHHHHHHHHHHHHHHH-EEEEEES.. CS
                           MCH 160 nvtllvaptaSlaGsvqvaaRvvevalhklee.lgfdlekivsavgtaPiapvakdelkamgrtndailYggrvhltve.a 238
                                   nv+llvaptaSl+Gs+q+++Rvve +++k+ e l+fd++k+++a+g aPiap+ +d+ ++mg+tnd++lYgg ++++++ +
  gi|15669832|ref|NP_248646.1| 165 NVYLLVAPTASLVGSIQISGRVVENGTYKMLEvLEFDVNKVKYAAGLAPIAPIIGDDFAMMGATNDMVLYGGITYYYIKsD 245
                                   ******************************9989*********************************************88 PP

                                   ..TTHHHHHHHSSGGGSTTTTS-HHHHHHHTTTTGGGS-GGGSS-SEEEEEETTT--EEEEE---HHHHHHH CS
                           MCH 239 edeeaedlakklpssaskdygkpFaeifkeaeydfykidkalFspAevtvndletgktfkaGelneellaes 310
                                   e++++e+l+k+lps+askdygkpF+e+fk+a+ydfykidk +F+pA v++nd++tgk+++aG++n+e+l++s
  gi|15669832|ref|NP_248646.1| 246 ENDDIESLCKALPSCASKDYGKPFMEVFKAADYDFYKIDKGMFAPAVVVINDMTTGKVYRAGKVNAEVLKKS 317
                                   8999******************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2244.89
//
Query:       gi|15669833|ref|NP_248647.1|  [L=473]
Description: hypothetical protein MJ_1637 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-26   92.9   1.5    2.2e-26   92.4   0.2    2.0  2  AAA_14      AAA domain
    8.4e-06   25.8   0.5    8.4e-06   25.8   0.5    2.0  3  Bac_DnaA    Bacterial dnaA  protein
    6.5e-05   23.0   1.7    6.5e-05   23.0   1.7    2.8  3  ATPase_2    ATPase domain predominantly from Archaea
    0.00017   20.9   0.7      0.006   15.8   0.0    2.7  2  NB-ARC      NB-ARC domain
    0.00061   20.2   0.0     0.0021   18.5   0.0    1.8  2  AAA_16      AAA ATPase domain
    0.00099   19.5   0.1     0.0054   17.2   0.0    2.1  2  AAA         ATPase family associated with various cellular ac
     0.0022   17.2   0.2     0.0045   16.2   0.0    1.5  2  DAP3        Mitochondrial ribosomal death-associated protein 
     0.0042   16.4   0.1      0.011   15.0   0.1    1.7  1  KAP_NTPase  KAP family P-loop domain
     0.0053   15.9   0.1     0.0096   15.1   0.1    1.3  1  DUF815      Protein of unknown function (DUF815)
     0.0067   16.1   0.0      0.014   15.0   0.0    1.5  1  SRP54       SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.025   14.3   0.0    1.3  1  AAA_24      AAA domain
      0.019   15.3   0.2       0.61   10.4   0.0    2.5  2  AAA_22      AAA domain
      0.026   14.7   0.0      0.065   13.4   0.0    1.8  1  DUF4143     Domain of unknown function (DUF4143)
      0.033   13.8   0.0      0.055   13.1   0.0    1.3  1  AAA_25      AAA domain
      0.039   13.4   0.1      0.079   12.4   0.1    1.5  1  Arf         ADP-ribosylation factor family
       0.12   12.3   0.0       0.24   11.3   0.0    1.5  1  NACHT       NACHT domain


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.2     2e-29   2.2e-26       2     131 .]      71     201 ..      70     201 .. 0.89
   2 ?   -2.0   0.1         3   3.4e+03      75      75 ..     261     261 ..     211     301 .. 0.60

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 2e-29
                        AAA_14   2 rkilvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelilek..lke..ekktylflDEiqev 76 
                                   ++++++ G+R  GKTtll q+++     ++++++ly+++d+ ++ +++   + l+++ e   + +  e+k +l+lDEiq+ 
  gi|15669833|ref|NP_248647.1|  71 KELILLYGLRGLGKTTLLSQIYHYARlkIEPNRVLYFSMDELKLNDIKLM-DALKAYSEIfgI-NlyEEKIILLLDEIQYE 149
                                   56899****************977779**************999888865.466666666331.24569************ PP

                        AAA_14  77 pewekalkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                   ++w  +lk+l+d++ n+ +i+tGS+++ l +  + +la+r+ +  +yp++f+E+l
  gi|15669833|ref|NP_248647.1| 150 RHWDLVLKNLYDTT-NIFIIATGSSALKLRE--SPDLARRALHKPIYPMTFREYL 201
                                   ************99.**************77..8*******************97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3
                        AAA_14  75 e 75 
                                    
  gi|15669833|ref|NP_248647.1| 261 V 261
                                   2 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.5   7.5e-09   8.4e-06      36     126 ..      73     166 ..      58     175 .. 0.80
   2 ?   -2.6   0.1       3.5   3.9e+03      79      99 ..     213     233 ..     200     247 .. 0.64
   3 ?   -1.9   0.0       2.2   2.5e+03     170     206 ..     245     281 ..     231     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 7.5e-09
                                   -EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHT..T-HHHH.HHHHTT-SEEEEE-GGGGTT-H CS
                      Bac_DnaA  36 PlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrd..kkaeef.keklrkvDvLliDDiqflagke 113
                                    +++yg  GlGkt Ll  i ++++ + +  rv+Y + +e   + +k +       e f  + + +  +Ll+D+iq+  + +
  gi|15669833|ref|NP_248647.1|  73 LILLYGLRGLGKTTLLSQIYHYARLKIEPNRVLYFSMDELKLNDIKLMDAlkAYSEIFgINLYEEKIILLLDEIQYERHWD 153
                                   579************************************98777666655312223342467888899*******988888 PP

                                   HHHHHHHHHHHHH CS
                      Bac_DnaA 114 ktqeelfhtfnal 126
                                    + ++l+ t n +
  gi|15669833|ref|NP_248647.1| 154 LVLKNLYDTTNIF 166
                                   8888877777765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.5
                                   HHHHHHTT-HHHHHHHHTT-S CS
                      Bac_DnaA  79 lvkalrdkkaeefkeklrkvD 99 
                                   + + + ++++++fk+ + kv 
  gi|15669833|ref|NP_248647.1| 213 FEEVILNNNLDNFKKVYAKVY 233
                                   345677889999999998774 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.2
                                   HHHHHHHHHHHHTT----TTHHHHHHHH--S-HHHHH CS
                      Bac_DnaA 170 trlailkkkieaeklevpeevlefiaervtdnvRele 206
                                   +r++ l   +e ++lev +++ +++ + + ++vRe++
  gi|15669833|ref|NP_248647.1| 245 LRIGSLPFALEDDELEVYNKIYTMLERIIYKDVREVK 281
                                   5666666677888999999999999999999999986 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   1.7   5.8e-08   6.5e-05      10     116 ..      61     162 ..      58     169 .. 0.80
   2 ?    2.5   1.0       0.1   1.1e+02     115     202 ..     134     205 ..     111     235 .. 0.59
   3 ?   -0.2   0.7      0.69   7.7e+02      36      96 ..     212     282 ..     210     306 .. 0.59

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.8e-08
                      ATPase_2  10 eleeilerepneiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskldefieeeeekkklekalgiavpka 89 
                                   ++ +++e++++e +++YG +g GKt+Ll +i+    ++ + +++ y+++ e +++ ++ +    +  k  ++ +gi++ + 
  gi|15669833|ref|NP_248647.1|  61 KVDKYIENDKKELILLYGLRGLGKTTLLSQIYHYArLKIEPNRVLYFSMDELKLNDIKLM----DALKAYSEIFGINLYEE 137
                                   6889****************************9874677779999999999999999999....88888899999999998 PP

                      ATPase_2  90 eleeilkeksklvfkaielllekikkk 116
                                   ++  +l+ +++  ++ ++l+l+++ ++
  gi|15669833|ref|NP_248647.1| 138 KIILLLD-EIQ-YERHWDLVLKNLYDT 162
                                   8855544.233.356677776666555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.1
                      ATPase_2 115 kkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldke 195
                                       kii+++De+q+ +    +   l++k+L++           +++i++ S  l ++   ++  l  r+ +  + ++++ 
  gi|15669833|ref|NP_248647.1| 134 LYEEKIILLLDEIQYER--HWD---LVLKNLYDT--------TNIFIIATGSSALKLR---ESPDLARRALHKPIYPMTFR 198
                                   55678999999999988..444...555555433........3334444444455554...34455555555667777776 PP

                      ATPase_2 196 talnflk 202
                                   + l ++k
  gi|15669833|ref|NP_248647.1| 199 EYLYLTK 205
                                   6666655 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.69
                      ATPase_2  36 Llkeiienledkdkyviyyialreesiskldefie...........eeeekkklekalgiavpkaeleeilk 96 
                                   L+ e+i n +  +++++y    +++ ++ ++++++           e e+ +k+  +l +++  + + e+ +
  gi|15669833|ref|NP_248647.1| 212 LFEEVILNNNLDNFKKVYAKVYSQILEEDVKKYLRigslpfaleddELEVYNKIYTML-ERIIYKDVREVKE 282
                                   6778888887778899999999999999999888888888876444333333333333.3333333334433 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.4e-06     0.006      11      43 ..      64      94 ..      55     109 .. 0.77
   2 ?    2.4   0.3     0.064        72      98     129 ..     132     163 ..      98     173 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.4e-06
                                  HHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC 11 kLlekdelqslvvalvGmgGvGKttlakqilnk 43
                                  k  e+d+ +  ++ l+G  G+GKttl++qi++ 
  gi|15669833|ref|NP_248647.1| 64 KYIENDKKE--LILLYGLRGLGKTTLLSQIYHY 94
                                  334466666..999****************986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.064
                                   HHCCCTTEEEEEEEE-SHHHH.....HHHHCH CS
                        NB-ARC  98 rlLltkrfllvlDDVweeedwdkigvvlpare 129
                                     L + + +l+lD +  e  wd +   l +  
  gi|15669833|ref|NP_248647.1| 132 INLYEEKIILLLDEIQYERHWDLVLKNLYDTT 163
                                   4578889**************99887776655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.9e-06    0.0021      20      51 ..      66      98 ..      54     145 .. 0.75
   2 ?   -1.2   0.0         2   2.3e+03     134     160 ..     137     161 ..     113     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
                        AAA_16 20 rsgrp.elvllsGesGvGKsslvrellralekd 51
                                   +++  el+ll+G +G GK++l+ +++++++ +
  gi|15669833|ref|NP_248647.1| 66 IENDKkELILLYGLRGLGKTTLLSQIYHYARLK 98
                                  4555559********************976655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                        AAA_16 134 erplvlvlDdlqwadeaslql.laaLlr 160
                                   e+ ++l+lD++q  +   ++l l++L +
  gi|15669833|ref|NP_248647.1| 137 EK-IILLLDEIQYER--HWDLvLKNLYD 161
                                   45.9*******9433..35555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.8e-06    0.0054       1      67 [.      74     146 ..      74     149 .. 0.69
   2 ?   -1.0   0.0         2   2.2e+03      41      67 ..     431     455 ..     413     457 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.8e-06
                                   EEEESSTTSSHHHHHHHHHHHHTHE.......EEEEETTTCSSSSTTHHHHHHHHHHHH.HHHTSTSEEEEEETG CS
                           AAA   1 vllyGppGtGKTllakavakelgve.......fleisgsellskyvgesekkirelfke.akekakpsilfiDEi 67 
                                   +llyG  G GKT+l +++ + +  +       +++++  +l +  + ++ k  +e+f   + e  ++ il++DEi
  gi|15669833|ref|NP_248647.1|  74 ILLYGLRGLGKTTLLSQIYHYARLKiepnrvlYFSMDELKLNDIKLMDALKAYSEIFGInLYE--EKIILLLDEI 146
                                   69*******************842222333335555555555445777778888888652333..359******9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2
                                   HHHHHHHHHHHHHHHTSTSEEEEEETG CS
                           AAA  41 esekkirelfkeakekakpsilfiDEi 67 
                                   +s+k++ + ++++k+++   i++ DE+
  gi|15669833|ref|NP_248647.1| 431 KSSKQVLKSMERVKASK--GIIIGDEL 455
                                   34455555555554443..77777775 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     4e-06    0.0045      14      49 ..      62      97 ..      56     105 .. 0.84
   2 ?   -3.2   0.1       3.3   3.7e+03     239     274 ..     221     261 ..     205     284 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4e-06
                                  HTTS-SSS---EEEEE-SSSSSTTTTHHHHHHHGGG CS
                          DAP3 14 lkkadkkkkvkrlvltGekgsGKSvlLlqalayAle 49
                                  ++k  ++ k++ ++l+G +g GK++lL+q+ +yA  
  gi|15669833|ref|NP_248647.1| 62 VDKYIENDKKELILLYGLRGLGKTTLLSQIYHYARL 97
                                  5555677888999********************965 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.3
                                   GG-S-E....................EEE--.---GGGTHH CS
                          DAP3 239 qldpYvkkydkrvaealk....gkvepieve.glskeEars 274
                                   +ld ++k y k  ++ l+    + +++ +++  l+++E++ 
  gi|15669833|ref|NP_248647.1| 221 NLDNFKKVYAKVYSQILEedvkKYLRIGSLPfALEDDELEV 261
                                   56666666555555555533336666666666666666555 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   9.9e-06     0.011      20     186 ..      71     333 ..      55     335 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.9e-06
                    KAP_NTPase  20 pivvgLygkWGsGKssllnkledelkefakpvrflfaefnawsfkggddavaellaaLadaleeeygqlatkllrakklka 100
                                   +  + Lyg  G+GK++ll  + ++ + +++p+r+l ++++ ++ ++  +++++ l+a ++  +    ++++ ll+ +  + 
  gi|15669833|ref|NP_248647.1|  71 KELILLYGLRGLGKTTLLSQIYHYARLKIEPNRVLYFSMDELKLND-IKLMDA-LKAYSEIFGINLYEEKIILLLDEIQYE 149
                                   456899**************************************97.555554.677888888888888888888866666 PP

                    KAP_NTPase 101 lkikgkiklrkacaiplvlilevalflliegasllavls.......................................... 139
                                   +  ++++k   ++ ++  + +   ++ l+e  +l  ++                                           
  gi|15669833|ref|NP_248647.1| 150 RHWDLVLKNLYDTTNIFIIATGSSALKLRESPDLARRALhkpiypmtfreylyltknikieslfeevilnnnldnfkkvya 230
                                   666666665555555544444444445555555555555888888888888888888888888888888888888888888 PP

                    KAP_NTPase 140 ...........................................................raaklkeeaplkklqteveell 161
                                                                                              +a+kl+    l +++ e    +
  gi|15669833|ref|NP_248647.1| 231 kvysqileedvkkylrigslpfaleddelevynkiytmleriiykdvrevkefdmetldKAFKLLY--LLANPKGERY-SY 308
                                   888888888888888888888888888888888888888888888888888888886666666654..3444455555.78 PP

                    KAP_NTPase 162 admektLdalqkrlVvviDdLDrce 186
                                   +++++tL+ ++ +l+ ++D L+ ce
  gi|15669833|ref|NP_248647.1| 309 ESLANTLEIAKGTLINLVDVLEKCE 333
                                   8888888888888888888888886 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   8.6e-06    0.0096      38     120 ..      56     150 ..      42     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.6e-06
                        DUF815  38 ealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg............Lrlieve.kedlkelpklvellrer 105
                                   + l+e + +++e+ + + +LL+G rG GK +l+  + + ++ +             L+l +++  + lk  ++++  ++  
  gi|15669833|ref|NP_248647.1|  56 DILKEKVDKYIENDKKELILLYGLRGLGKTTLLSQIYHYARLKIepnrvlyfsmdeLKLNDIKlMDALKAYSEIFG-INLY 135
                                   56889999************************99988766665567778886666666666652344566666654.6788 PP

                        DUF815 106 perfilfvDDLsFee 120
                                   +e++il++D + +e+
  gi|15669833|ref|NP_248647.1| 136 EEKIILLLDEIQYER 150
                                   899999999998886 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-05     0.014       3      61 ..      73     136 ..      71     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                   EEEEEESTTSSHHHHHHHHHHHHHHT..TS-EEEEEESTSSTTHH...HHHHHHHHHTTEEEEE CS
                         SRP54   3 villvGlqGaGKTttlaKLaallkke..gkkvllvaaDtfRaaAv...eQLktlaeklgvpvik 61 
                                   +ill Gl G GKTt l+++ ++ + +   ++vl  ++D  +   +   + Lk++ e  g+++++
  gi|15669833|ref|NP_248647.1|  73 LILLYGLRGLGKTTLLSQIYHYARLKiePNRVLYFSMDELKLNDIklmDALKAYSEIFGINLYE 136
                                   79*******************9988876889999999999887652225666666666666665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.3e-05     0.025       5      46 ..      74     122 ..      70     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                        AAA_24   5 iliyGpsgiGKTtlakel.........gpkplfidtekGlksldadkfpdi 46 
                                   il+yG  g GKTtl++++         ++++l++ +++   +l+++k+ d+
  gi|15669833|ref|NP_248647.1|  74 ILLYGLRGLGKTTLLSQIyhyarlkiePNRVLYFSMDE--LKLNDIKLMDA 122
                                   89****************99999999999999999999..56666665533 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00055      0.61       4      29 ..      70      95 ..      66     136 .. 0.74
   2 ?    2.4   0.0      0.15   1.7e+02      92     125 ..     138     175 ..     118     186 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00055
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                  ++ +++++G  G GKTtll ++ + +
  gi|15669833|ref|NP_248647.1| 70 KKELILLYGLRGLGKTTLLSQIYHYA 95
                                  6889***************9987765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.15
                        AAA_22  92 ielliiDEaqhlrs.eealeeLrsllnl...srkgvql 125
                                   + +l++DE+q+ r+ + +l++L +  n+   ++ + +l
  gi|15669833|ref|NP_248647.1| 138 KIILLLDEIQYERHwDLVLKNLYDTTNIfiiATGSSAL 175
                                   5699*******844688888886666655554444444 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.8e-05     0.065      14     120 ..     286     427 ..     213     429 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.8e-05
                                   xxxxx..........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  14 eelrk..........................................glverlppwsespnskkrlrkspKlyfvDtGLlv 52 
                                   e+l k                                           l+++++p+   +   k++rks K+ f+ + + +
  gi|15669833|ref|NP_248647.1| 286 ETLDKafkllyllanpkgerysyeslantleiakgtlinlvdvlekcELLFKIYPY---GSMDKKVRKSQKIKFLPVPIKT 363
                                   33333777777777777777777777778888888888888888888899999999...9999**************9999 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  53 allgldkeelledsenkGallEnlVaqeLlkysekegaklyyyrdkngaEvDfvielkggkivpiEvK 120
                                   al    k  ++ d+  +G llE +Va  L  + +k+g++l+y  +  +   Df++     + + iEv 
  gi|15669833|ref|NP_248647.1| 364 ALW--HKMGVVIDDVCYGSLLEDVVAFYLYLFCKKKGYSLSYEPK--KGGADFILISPYMEKIVIEVG 427
                                   976..6667888999****************98888999998777..578999997777788899985 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.9e-05     0.055      29      58 ..      69      95 ..      53     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-05
                        AAA_25 29 llpagelallaGapgtGKttlaldlalava 58
                                     ++el+ll+G +g GKttl++++ +++a
  gi|15669833|ref|NP_248647.1| 69 D--KKELILLYGLRGLGKTTLLSQI-YHYA 95
                                  4..799***************9886.4444 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   7.1e-05     0.079       6      60 ..      63     119 ..      58     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.1e-05
                                   HGGTT.TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSSS..SSEEEEEEEETTEEE CS
                           Arf   6 aklklkkkelrilllGLDnaGKtTilkklkleelvttvPT..igfnveeleiknlkf 60 
                                   +k+ +++k+  ill GL + GKtT+l ++ +    ++ P   + f ++el+ +++k+
  gi|15669833|ref|NP_248647.1|  63 DKYIENDKKELILLYGLRGLGKTTLLSQIYHYARLKIEPNrvLYFSMDELKLNDIKL 119
                                   56667788999******************9999999999533789999999999987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.24       2      46 ..      73     113 ..      72     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTT CS
                         NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrels 46 
                                   l++l G  G GKTtLl ++ + ++ +  p+     v+++s+ el+
  gi|15669833|ref|NP_248647.1|  73 LILLYGLRGLGKTTLLSQIYHYARLKIEPNR----VLYFSMDELK 113
                                   7899***************998877776663....6666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3537.80
//
Query:       gi|15669834|ref|NP_248648.1|  [L=260]
Description: hypothetical protein MJ_1638 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-06   27.4   0.0    3.2e-06   26.5   0.0    1.5  1  NAD_synthase   NAD synthase
    1.8e-05   24.3   0.2    1.8e-05   24.3   0.2    2.3  3  QueC           Queuosine biosynthesis protein QueC
    1.9e-05   23.6   0.2    3.8e-05   22.7   0.2    1.6  1  tRNA_Me_trans  tRNA methyl transferase
     0.0013   18.5   0.0     0.0018   18.0   0.0    1.3  1  Asn_synthase   Asparagine synthase
     0.0089   15.6   0.1      0.016   14.8   0.1    1.4  1  ThiI           Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.062   13.0   0.0       0.14   11.9   0.0    1.6  1  ATP_bind_3     PP-loop family


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.1e-09   3.2e-06      19      86 ..      63     130 ..      51     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.1e-09
                                   SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHH.HHHHHHHHHHTSEEEE-..--HHHHH CS
                  NAD_synthase  19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedv.edalalaenlgievkti..dikpivr 86 
                                    ++v+  SGGvDSs+ a +a++++    v+a+   s++ + +++ e+a+++a+++gi  + +  d++++++
  gi|15669834|ref|NP_248648.1|  63 PKAVVAFSGGVDSSTSAIIAKQIF---DVKAVSCYSKYIMTDEMrENAKNIAKKIGISLEFVsiDLEEVYK 130
                                   5899********************...78888887666665554278*******99877655005555555 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       2.4   7.3e+03      49      69 ..      22      41 ..       9      49 .. 0.46
   2 !   24.3   0.2     6e-09   1.8e-05       1      66 [.      64     127 ..      64     137 .. 0.79
   3 ?   -0.7   0.0      0.29   8.5e+02     149     183 ..     180     215 ..     161     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.4
                                  HHT--.-EEEEE-GGGGGGSC CS
                          QueC 49 kelgveehkildldllkelgg 69
                                  ++l++ e+  ++++ lke  +
  gi|15669834|ref|NP_248648.1| 22 NSLEILEKLDINTE-LKEALK 41
                                  33333333333333.333334 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 6e-09
                                   EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGG CS
                          QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelgveehkildldllke 66 
                                   kavv +SGG+DS+t +++ak+    v+a++   +    ++  e ak+iak++g+ + + +++d l+e
  gi|15669834|ref|NP_248648.1|  64 KAVVAFSGGVDSSTSAIIAKQI-FDVKAVSCYSKYImTDEMRENAKNIAKKIGI-SLEFVSID-LEE 127
                                   79*************9999876.679999974444434445689**********.88888888.544 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.29
                                   TS--EEE-T.TTT--HHHHHHHHHHTTHHHHH-B-S CS
                          QueC 149 dkkieieaP.lidlsKaeivklgkelgvpleetlsC 183
                                   d+ ++ + P + +l+K e  ++ k+ g++l+ ++ C
  gi|15669834|ref|NP_248648.1| 180 DEIFRFNLPsFFALTKDEEREILKNNGIELKMSYGC 215
                                   555666666567899999999999999999999999 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2   1.3e-08   3.8e-05       3      78 ..      65     133 ..      63     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.3e-08
                 tRNA_Me_trans   3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevv..dfekeykekv 78 
                                    vva+SgGVDSs +a+ +++q ++v++v    +           ++e  ++a+++a+k+gi+le v  d+e+ yk  v
  gi|15669834|ref|NP_248648.1|  65 AVVAFSGGVDSSTSAI-IAKQIFDVKAVSCYSK--------YIMTDEMRENAKNIAKKIGISLEFVsiDLEEVYKGVV 133
                                   69**********9996.5678889988864332........3345556689**********98866116677777655 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   5.9e-07    0.0018      22     140 ..      67     178 ..      60     229 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.9e-07
                  Asn_synthase  22 alLSGGlDSSliaalaarqsksplktFsigfeekgsde.akyakevaehlgtehtelvlteeelldalpdviyhleepfad 101
                                   + +SGG+DSS+ a +a++    ++k++s+  +    de ++ ak +a+++g+    l++   +l+++++ v+     p + 
  gi|15669834|ref|NP_248648.1|  67 VAFSGGVDSSTSAIIAKQIF--DVKAVSCYSKYIMTDEmRENAKNIAKKIGIS---LEFVSIDLEEVYKGVVNGKFHPCGR 142
                                   568**************999..79999999966666662679**********9...6666666666666666644445555 PP

                  Asn_synthase 102 rsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfyk 140
                                     ++    +  +ak+ +   v+ G   D l  GY+++y+
  gi|15669834|ref|NP_248648.1| 143 CHKVIENAVIDYAKKIDAEFVIFG---DLLAFGYLALYR 178
                                   555555555555555555555543...455555555555 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   5.4e-06     0.016       5     118 ..      64     169 ..      61     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.4e-06
                          ThiI   5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvke 85 
                                   k+++  SgG+DS  +a  + k  + v++v   ++ ++++e +e  +++a+++      +++++v +d++ev k +++   +
  gi|15669834|ref|NP_248648.1|  64 KAVVAFSGGVDSSTSAI-IAKQIFDVKAVSCYSKYIMTDEMRENAKNIAKKIG-----ISLEFVSIDLEEVYKGVVNGKFH 138
                                   678889*******9986.56889************************999873.....68999****99999999887644 PP

                          ThiI  86 kltivllkrkmlriAekvaeeegakalvtGesL 118
                                   +  +  +++ +  +   +a++ +a+ ++ G+ L
  gi|15669834|ref|NP_248648.1| 139 P--CGRCHKVIENAVIDYAKKIDAEFVIFGDLL 169
                                   3..233444555555556666677777766655 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.6e-05      0.14       2      69 ..      65     126 ..      64     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--HH CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdva 69 
                                   ++vA+SgG+DS +   ++++  +   +k+v ++  + + +e    +e  k+++kk++i le  ++d++
  gi|15669834|ref|NP_248648.1|  65 AVVAFSGGVDSSTSAIIAKQIFD---VKAVSCYSKYIMTDE---MRENAKNIAKKIGISLEFVSIDLE 126
                                   79**********99988888855...566666666655544...445556778888888888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1200  (0.0669307); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1670.61
//
Query:       gi|15669835|ref|NP_248649.1|  [L=154]
Description: hypothetical protein MJ_1639 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1002.91
//
Query:       gi|15669836|ref|NP_248650.1|  [L=205]
Description: hypothetical protein MJ_1640 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-93  311.7   0.0    2.1e-93  311.6   0.0    1.0  1  Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
  ------ inclusion threshold ------
       0.11   13.0   0.9        0.2   12.2   0.9    1.4  1  DUF3020          Protein of unknown function (DUF3020)


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.6   0.0   2.3e-97   2.1e-93       1     198 []       1     202 [.       1     202 [. 0.99

  Alignments for each domain:
  == domain 1  score: 311.6 bits;  conditional E-value: 2.3e-97
                                   -EEEEEEESSEESSSHHHCCCTTTTTTSHHHHHHHHHHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S--SSHH CS
               Methyltrn_RNA_2   1 mrefvvlankapTdsdiplddlpGaagrldvlarcvsaalfvshgiRedvvvylvLegtpdpprtikieasevkkvspder 81 
                                   mref+++ank++T+sdi+l+dlpG++grld+l+rcvs+a+f+sh+iR+dvv+y+vL+g+p+pp++ik+ +se+kkvspder
  gi|15669836|ref|NP_248650.1|   1 MREFIFKANKTITSSDINLKDLPGSCGRLDLLCRCVSDAFFLSHDIRRDVVFYAVLYGQPNPPVCIKFVGSELKKVSPDER 81 
                                   9******************************************************************************** PP

                                   HHHHHHHHHHCHCC....TGCCSEEEEETTEEEE---HHHHHHHHHCT.SEEEEESTTSEEGGGS---SSEEEEEE-TT-S CS
               Methyltrn_RNA_2  82 niailikkalkave....eikkqekkvrpgltVrkegfealleelsek.ksiillkekGedisnakielnPvFilgdHidl 157
                                   niai+ikkalk++e    e++k++++++pg++Vr+ gf++l+ e+ e+ k+i++l+++Ged++n++ie nPvFi+gdHi++
  gi|15669836|ref|NP_248650.1|  82 NIAIFIKKALKKFEeldeEQRKDWNQSTPGIYVRRLGFRNLVLEKLEEgKNIYYLHMNGEDVENVDIE-NPVFIIGDHIGI 161
                                   *************999999***********************9999999*******************.************ PP

                                   HHHHHHHHHCTTSEEEES-SS---HHHHHHHHHHHHHHHHH CS
               Methyltrn_RNA_2 158 peeeekllerlkakrvslgPlsLhadhcvtlihneldkkea 198
                                   +ee+e++l+++kakr+sl+Pl+Lha+hc+t+ihn+ldkk++
  gi|15669836|ref|NP_248650.1| 162 GEEDERFLDEIKAKRISLSPLELHANHCITIIHNVLDKKRI 202
                                   **************************************985 PP

>> DUF3020  Protein of unknown function (DUF3020)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.9   2.2e-05       0.2      27      47 ..      88     108 ..      75     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                       DUF3020  27 KrakkkfgkedseeKdsWiee 47 
                                   K+a kkf++ d+e++++W++ 
  gi|15669836|ref|NP_248650.1|  88 KKALKKFEELDEEQRKDWNQS 108
                                   9*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1285.31
//
Query:       gi|15669837|ref|NP_248651.1|  [L=287]
Description: repressor protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-20   71.9  13.9    4.3e-13   49.5   3.6    2.9  3  PhoU          PhoU domain
    3.6e-06   26.4   0.4      9e-06   25.2   0.4    1.7  1  HTH_24        Winged helix-turn-helix DNA-binding
    0.00062   19.7   0.0     0.0014   18.5   0.0    1.7  1  HTH_Crp_2     Crp-like helix-turn-helix domain
    0.00095   18.6   0.1     0.0025   17.3   0.1    1.7  1  Sigma70_r4    Sigma-70, region 4
     0.0014   18.4  11.5      0.005   16.7   2.7    2.7  2  TFIIE_alpha   TFIIE alpha subunit
      0.002   18.0   0.2     0.0075   16.1   0.0    2.0  2  MarR_2        MarR family
      0.002   18.4   0.1      0.008   16.5   0.1    2.0  1  Rrf2          Transcriptional regulator
     0.0032   17.3   0.3      0.012   15.4   0.0    2.1  2  TrmB          Sugar-specific transcriptional regulator TrmB
     0.0034   17.4   0.2      0.014   15.4   0.1    2.1  2  HTH_3         Helix-turn-helix
     0.0058   16.6   0.6      0.017   15.0   0.1    2.1  2  HTH_11        HTH domain
     0.0086   15.8   0.0      0.018   14.8   0.0    1.5  1  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.011   15.9   0.0       0.02   15.0   0.0    1.4  1  HTH_28        Helix-turn-helix domain
      0.011   15.0   0.7      0.011   15.0   0.7    1.8  2  DLP_helical   Dynamin-like helical domain
      0.011   16.0   0.4       0.18   12.1   0.0    2.9  3  KORA          TrfB plasmid transcriptional repressor
      0.015   15.3   0.2      0.015   15.3   0.2    3.1  3  HTH_19        Helix-turn-helix domain
      0.038   13.9   0.0        0.1   12.5   0.0    1.7  1  MarR          MarR family
      0.054   13.2   0.4       0.57    9.9   0.0    2.4  2  Sigma70_r4_2  Sigma-70, region 4
       0.14   12.2   3.3        2.2    8.4   0.1    3.1  3  4HB           Four helical bundle domain
       0.15   12.0   0.0       0.36   10.8   0.0    1.6  1  HIRAN         HIRAN domain
       0.16   12.1   0.0       0.16   12.1   0.0    2.8  3  DASH_Dad3     DASH complex subunit Dad3
        3.7    7.6   8.2         14    5.8   1.7    2.6  2  DUF1664       Protein of unknown function (DUF1664)


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1         9   7.7e+03      21      49 ..      29      57 ..      19      60 .. 0.65
   2 !   49.5   3.6   5.1e-16   4.3e-13       1      88 [.      88     171 ..      88     172 .. 0.84
   3 !   28.7   0.6   1.6e-09   1.4e-06       7      88 ..     192     265 ..     182     266 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 9
                                  CT-HHHHHHH.HHHHHHHHHHHHHHHHHHH CS
                          PhoU 21 ekdtelarev.ierddeidrlekeiersll 49
                                  ++d e+a+++ i+r+  +  l  +i+++++
  gi|15669837|ref|NP_248651.1| 29 TQD-EIAEKLgISRRYVAKLLKPLIDEKIV 57
                                  445.77776656666666666666666655 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 5.1e-16
                                   HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81 
                                   l++m ++ ++ ld++++al++ d++la+++i +d  ++++e+e++  l   + k+ p a     + +l  ia++lER gD+
  gi|15669837|ref|NP_248651.1|  88 LEKMEKTLLNNLDLVYTALKNSDKKLAEDIIIKDYALNKMEEEVRILLSMNALKYLPGAY----ANALATIASNLERLGDY 164
                                   679*****************************************6664444444555443....444889*********** PP

                                   HHHHHHH CS
                          PhoU  82 avniaer 88 
                                   ++niae 
  gi|15669837|ref|NP_248651.1| 165 IANIAEE 171
                                   *****97 PP

  == domain 3  score: 28.7 bits;  conditional E-value: 1.6e-09
                                   HHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   7 iveemlddalealeekdtelarevierddeidrlekeiersllealak.rqplaedlrellsllriardlERigDhavnia 86 
                                   + +eml +a++++++k          ++ +i +le+++ + l  +l+k  ++++edl++ +++ +  +d+ER gD +vni+
  gi|15669837|ref|NP_248651.1| 192 LLKEMLTEAIDVVKSKK---------KETKIHELEEKLHKNLELLLNKvLENKREDLNFYVQFGMFLKDIERFGDRCVNIV 263
                                   55666666666666655.........355555555555555333334444555669************************9 PP

                                   HH CS
                          PhoU  87 er 88 
                                   ++
  gi|15669837|ref|NP_248651.1| 264 DI 265
                                   86 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.4   1.1e-08     9e-06       8      48 .]      18      58 ..      14      58 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.1e-08
                        HTH_24  8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  I++++ ++   +q e+Ae+lg+S+  v + lk L++e +++
  gi|15669837|ref|NP_248651.1| 18 IIRVIIEEEPETQDEIAEKLGISRRYVAKLLKPLIDEKIVR 58
                                  99***********************************9986 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.7e-06    0.0014      21      67 ..      27      70 ..       7      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-06
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHHHHH CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrririldleaLra 67
                                  p tq+e+A+ lG++r  v ++l+ L +e++++  +   i d+ +L +
  gi|15669837|ref|NP_248651.1| 27 PETQDEIAEKLGISRRYVAKLLKPLIDEKIVRHPY---IVDMSKLHK 70
                                  669****************************9655...888888876 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.9e-06    0.0025      18      40 ..      25      47 ..      17      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.9e-06
                                  TTT--HHHHHHHHTS-HHHHHHH CS
                    Sigma70_r4 18 geglTleEIgerlgiSrerVrqi 40
                                  +e+ T+ EI+e+lgiSr  V  +
  gi|15669837|ref|NP_248651.1| 25 EEPETQDEIAEKLGISRRYVAKL 47
                                  7999*************999665 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   2.7   5.9e-06     0.005      15     100 ..      15      95 ..       6     102 .. 0.74
   2 !    6.8   0.8    0.0072       6.1      43     103 ..     160     223 ..     151     225 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.9e-06
                                   HHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHHHH CS
                   TFIIE_alpha  15 avlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevvkk 95 
                                    + ++ v++e+   t +++a++l+i +  + klL  L ++++v     +d +k      ++in e   +++ ++++ ++ k
  gi|15669837|ref|NP_248651.1|  15 LAGIIRVIIEEEPETQDEIAEKLGISRRYVAKLLKPLIDEKIVRHPYIVDMSK-----LHKINLEFDEYILMKEIKTTLEK 90 
                                   566999************************************98877777544.....44555555555555555555555 PP

                                   HHHHH CS
                   TFIIE_alpha  96 Leekl 100
                                   +e+ l
  gi|15669837|ref|NP_248651.1|  91 MEKTL 95 
                                   55544 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0072
                                   HHHHHHHHHHHCTSEEEEEEEE..TTTEEEEEEEEEECCCHCCCHHHHHHHH.HHHHHHHHCCC CS
                   TFIIE_alpha  43 elrklLnrLyearlvkykrrrd..eekswykyywrinyeklvdvvkrkleev.vkkLeekleke 103
                                    l+  ++++ e+ +   k  +d  +e ++     +    +++dvvk k++e+ +++Leekl+k+
  gi|15669837|ref|NP_248651.1| 160 RLGDYIANIAEEVVHGLKLDKDieNEVNMIFTLLKEMLTEAIDVVKSKKKETkIHELEEKLHKN 223
                                   56666666666666666666665355555555555567899*****9988875899****9987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.8e-06    0.0075      13      52 ..      21      58 ..      13      59 .. 0.82
   2 ?   -2.6   0.0       6.1   5.2e+03       4      28 ..     144     169 ..     143     172 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.8e-06
                                  HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                        MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                  ++  ++++  t+ e+a++lg+s+ +v ++lk L +   v+
  gi|15669837|ref|NP_248651.1| 21 VIIEEEPE--TQDEIAEKLGISRRYVAKLLKPLIDEKIVR 58
                                  55555552..*********************999988776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.1
                                   -HHHHHHHHHHHCTTTS..EEEHHHHH CS
                        MarR_2   4 tpaqarvLaaLgrrpgr..dltvgela 28 
                                   ++a a +La ++ + +r  d  ++ +a
  gi|15669837|ref|NP_248651.1| 144 PGAYANALATIASNLERlgD-YIANIA 169
                                   67778888888887765433.555555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   9.4e-06     0.008      23      56 ..      25      58 ..      11      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.4e-06
                                  CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvk 56
                                  eep + +eiae+ +is++y++k+l+ L  +++v+
  gi|15669837|ref|NP_248651.1| 25 EEPETQDEIAEKLGISRRYVAKLLKPLIDEKIVR 58
                                  4455789*********************999996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.5e-05     0.012      17      52 ..      22      57 ..      19      61 .. 0.90
   2 ?   -2.5   0.0         6   5.1e+03       9      30 ..     184     205 ..     183     221 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                                  HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSE CS
                          TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlV 52
                                  +++++p t deiae+lg++r  v + L+ L+d  +V
  gi|15669837|ref|NP_248651.1| 22 IIEEEPETQDEIAEKLGISRRYVAKLLKPLIDEKIV 57
                                  5699**************************997766 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6
                                   HCCCHCHHHHHHCCCHHCHHCC CS
                          TrmB   9 yEakvYlaLlklgpatadeiae 30 
                                   +E+ + ++Llk+   +a ++ +
  gi|15669837|ref|NP_248651.1| 184 NEVNMIFTLLKEMLTEAIDVVK 205
                                   5666666666665555555543 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.7e-05     0.014      11      30 ..      29      48 ..      29      49 .. 0.93
   2 ?   -2.5   0.0       6.3   5.4e+03      11      32 ..     109     130 ..     105     138 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                                  HHHHHHHHHTSSHHHHHHHH CS
                         HTH_3 11 sqeeLAeklGvsrstisriE 30
                                  +q e+AeklG+sr++++++ 
  gi|15669837|ref|NP_248651.1| 29 TQDEIAEKLGISRRYVAKLL 48
                                  8****************985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.3
                                   HHHHHHHHHTSSHHHHHHHHTT CS
                         HTH_3  11 sqeeLAeklGvsrstisriEnG 32 
                                   s ++LAe + ++  +++++E  
  gi|15669837|ref|NP_248651.1| 109 SDKKLAEDIIIKDYALNKMEEE 130
                                   6678888888887778888765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1     2e-05     0.017       5      37 ..      18      49 ..      15      57 .. 0.79
   2 ?   -2.5   0.1       6.1   5.2e+03       9      25 ..     204     220 ..     197     221 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                        HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIk 37
                                  i++ ++e+++  + +e+Ae+L++Srr v + +k
  gi|15669837|ref|NP_248651.1| 18 IIRVIIEEEP-ETQDEIAEKLGISRRYVAKLLK 49
                                  5666655555.6**************9977666 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.1
                        HTH_11   9 LleargpisgeeLAeeL 25 
                                   ++++++   + eL e+L
  gi|15669837|ref|NP_248651.1| 204 VKSKKKETKIHELEEKL 220
                                   55555557788888877 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.1e-05     0.018      19      39 ..      29      49 ..      28      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                        HTH_23 19 svreIAreLgvsrrTvyrwlk 39
                                  ++ eIA++Lg+srr v + lk
  gi|15669837|ref|NP_248651.1| 29 TQDEIAEKLGISRRYVAKLLK 49
                                  789*************99876 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.4e-05      0.02      13      34 ..      26      49 ..      18      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                        HTH_28 13 h..svreaArelgisrrtvyrWik 34
                                  +  +++e+A++lgisrr v +++k
  gi|15669837|ref|NP_248651.1| 26 EpeTQDEIAEKLGISRRYVAKLLK 49
                                  4449***************99886 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2       1.5   1.3e+03      97     114 ..      81      98 ..      63     130 .. 0.57
   2 ?   15.0   0.7   1.3e-05     0.011     246     313 ..     177     246 ..     174     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.5
                   DLP_helical  97 akriekelaelkkeieea 114
                                   +k+i++ l++++k + + 
  gi|15669837|ref|NP_248651.1|  81 MKEIKTTLEKMEKTLLNN 98 
                                   455555555555544332 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.3e-05
                   DLP_helical 246 kLAknlnkalaiiGavl.elalevwdslkqskkekelkelkeelveklkdqrkeilellndd.efietff 313
                                   kL k + + + +i  +l e+++e++d++k++kke +++el e+l ++l+   + +le   +d +f+ +f 
  gi|15669837|ref|NP_248651.1| 177 KLDKDIENEVNMIFTLLkEMLTEAIDVVKSKKKETKIHELEEKLHKNLELLLNKVLENKREDlNFYVQFG 246
                                   7777887777666545538******************************999999998888888888885 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00021      0.18      15      57 ..       9      53 ..       3      71 .. 0.81
   2 ?    0.2   0.1       1.1   9.4e+02       8      37 ..     153     182 ..     148     224 .. 0.70
   3 ?   -2.5   0.0       7.4   6.3e+03       5      24 ..     244     263 ..     243     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                          KORA 15 elaeqtveiargvLVegk..kqadvatelgltkqavsqavkrvwa 57
                                  + +e t+  + +v++e++  +q ++a++lg++++ v ++ k  ++
  gi|15669837|ref|NP_248651.1|  9 RGKEATLAGIIRVIIEEEpeTQDEIAEKLGISRRYVAKLLKPLID 53
                                  55778888888999987533799*************999886665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                          KORA   8 eiikgleelaeqtveiargvLVegkkqadv 37 
                                   +i + le+l++   +ia +v    k  +d+
  gi|15669837|ref|NP_248651.1| 153 TIASNLERLGDYIANIAEEVVHGLKLDKDI 182
                                   678889999999999998886555555555 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 7.4
                          KORA   5 eFeeiikgleelaeqtveia 24 
                                   +F   +k +e+++++ v+i+
  gi|15669837|ref|NP_248651.1| 244 QFGMFLKDIERFGDRCVNIV 263
                                   788999999****9999986 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   1.7e-05     0.015       4      41 ..      19      53 ..      17      85 .. 0.70
   2 ?    0.3   0.1      0.87   7.4e+02      16      47 ..     111     141 ..     105     167 .. 0.76
   3 ?   -1.4   0.1       2.9   2.5e+03      18      34 ..     216     233 ..     204     255 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                        HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvps 41
                                  ++ ++ee   tq+e+ae+lgisr++ +++ +     ++
  gi|15669837|ref|NP_248651.1| 19 IRVIIEEEPETQDEIAEKLGISRRYVAKLLKP---LID 53
                                  5667888888*******************987...333 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.87
                        HTH_19  16 eelaerlgisrskisaiEngkkdvpsaelllk 47 
                                   ++lae+++i  + +++ E + +  + +++ lk
  gi|15669837|ref|NP_248651.1| 111 KKLAEDIIIKDYALNKMEEEVR-ILLSMNALK 141
                                   7899999999999999999866.554444444 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.9
                        HTH_19  18 laerlgis.rskisaiEn 34 
                                   l+e+l+ +    +++   
  gi|15669837|ref|NP_248651.1| 216 LEEKLHKNlELLLNKVLE 233
                                   333333332223333333 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012       0.1       8      44 ..      18      54 ..      13      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                  HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHT CS
                          MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekk 44
                                  i+r + e++p ++ e+a+klg+s+ +v ++l+ L+++
  gi|15669837|ref|NP_248651.1| 18 IIRVIIEEEPETQDEIAEKLGISRRYVAKLLKPLIDE 54
                                  56677788999*********************99987 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00067      0.57      28      47 ..      29      48 ..      23      49 .. 0.83
   2 ?    0.5   0.1       0.6   5.1e+02       7      24 ..     123     140 ..     121     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00067
                                  -HHHHHHHHT--HHHHHHHH CS
                  Sigma70_r4_2 28 sykEIAellgisegtVksrl 47
                                  +++EIAe+lgis + V + l
  gi|15669837|ref|NP_248651.1| 29 TQDEIAEKLGISRRYVAKLL 48
                                  789*********99887765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.6
                                   HHTTS-HHHHHHHHHHHT CS
                  Sigma70_r4_2   7 alaeLperqreifllryl 24 
                                   al+++ e+ r  + + +l
  gi|15669837|ref|NP_248651.1| 123 ALNKMEEEVRILLSMNAL 140
                                   89**********999877 PP

>> 4HB  Four helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0025       2.2       4      45 ..      13      57 ..      10      62 .. 0.79
   2 ?   -2.5   0.0       6.7   5.7e+03       2      14 ..      83      95 ..      78     103 .. 0.61
   3 ?    3.2   0.1      0.11        94      19      46 ..     152     179 ..     140     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0025
                           4HB  4 etvlailkeilksk...kkkvaekfepvleYiaAiAgqLiDekei 45
                                  +t ++i++ i++++   ++++aek+ +   Y+a +   LiDek +
  gi|15669837|ref|NP_248651.1| 13 ATLAGIIRVIIEEEpetQDEIAEKLGISRRYVAKLLKPLIDEKIV 57
                                  67777888888765211567899********************87 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.7
                           4HB  2 dietvlailkeil 14
                                  +i+t+l+++++ l
  gi|15669837|ref|NP_248651.1| 83 EIKTTLEKMEKTL 95
                                  3555555555544 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.11
                           4HB  19 kkvaekfepvleYiaAiAgqLiDekeid 46 
                                   +++a+++e + +Yia iA +++   + d
  gi|15669837|ref|NP_248651.1| 152 ATIASNLERLGDYIANIAEEVVHGLKLD 179
                                   567788888999******9998755555 PP

>> HIRAN  HIRAN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00042      0.36      38      72 ..      16      58 ..      11      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                                  TT-EEEEETTS-........EEEEE-HHHHHHHHHHHHTTSSE CS
                         HIRAN 38 anavrvlnergf........eiGrlprevakwlspLldsgfit 72
                                  a ++rv  e++         ++G   r+vak l+pL+d+++++
  gi|15669837|ref|NP_248651.1| 16 AGIIRVIIEEEPetqdeiaeKLGISRRYVAKLLKPLIDEKIVR 58
                                  56899998666667777888*******************8775 PP

>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3       0.5   4.3e+02      44      58 ..      95     109 ..      64     141 .. 0.68
   2 ?   12.1   0.0   0.00018      0.16      14      56 ..     153     194 ..     145     197 .. 0.66
   3 ?   -2.3   0.3       5.6   4.8e+03      13      20 ..     218     225 ..     206     240 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.5
                     DASH_Dad3  44 LErkiglvyTLlKaS 58 
                                   L + + lvyT lK S
  gi|15669837|ref|NP_248651.1|  95 LLNNLDLVYTALKNS 109
                                   233455666666654 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00018
                     DASH_Dad3  14 rLaenlktLaselkeLasnsteeildgL...ReLErkiglvyTLlK 56 
                                   ++a+nl++L + ++++    +ee+++gL   +++E+ +++++TLlK
  gi|15669837|ref|NP_248651.1| 153 TIASNLERLGDYIANI----AEEVVHGLkldKDIENEVNMIFTLLK 194
                                   3444555555555444....6667777733369************9 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.6
                     DASH_Dad3  13 erLaenlk 20 
                                   e+L +nl+
  gi|15669837|ref|NP_248651.1| 218 EKLHKNLE 225
                                   23333333 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.5     0.026        22      36      80 ..      85     129 ..      79     139 .. 0.85
   2 ?    5.8   1.7     0.016        14      41     117 ..     149     224 ..     138     231 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.026
                       DUF1664  36 krslsdavesvskqleqvseslaatkrhLssridrvdkkldeqke 80 
                                   k  l++  +++ ++l+ v+++l++  ++L+++i   d  l++++e
  gi|15669837|ref|NP_248651.1|  85 KTTLEKMEKTLLNNLDLVYTALKNSDKKLAEDIIIKDYALNKMEE 129
                                   6678888899999*******************9988888888776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.016
                       DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                   +a+++++++le++ + +a+  ++  + + ++dk +++  +++  + +e+ +   d+ + +++ ++++e+ e+l ++l
  gi|15669837|ref|NP_248651.1| 149 NALATIASNLERLGDYIANIAEEVVHGL-KLDKDIENEVNMIFTLLKEMLTEAIDVVKSKKKETKIHELEEKLHKNL 224
                                   6666666666666666666666666666.356666555554444444433333444444444455666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1682  (0.0938145); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1953.46
//
Query:       gi|15669838|ref|NP_248652.1|  [L=161]
Description: hypothetical protein MJ_1642 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-18   67.0   1.0    1.9e-18   66.2   1.0    1.4  1  V4R            V4R domain
    4.1e-12   46.1   0.1      1e-11   44.8   0.1    1.6  1  DUF2507        Protein of unknown function (DUF2507)
  ------ inclusion threshold ------
      0.032   15.0   1.1      0.055   14.2   1.1    1.4  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   1.0   3.2e-22   1.9e-18       2      61 ..      73     132 ..      72     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 3.2e-22
                                   -EEEEEES-S-TT---SS---HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEEEE CS
                           V4R   2 elsieespelaglpgkeePvCyleaGllagalsellgkrveveEveCaaeGhdhCeFeve 61 
                                    ++i++++ ++glp+ ++P+C++eaG+lag+ ++ ++k++ + E+ C++ G + C+Fev+
  gi|15669838|ref|NP_248652.1|  73 KIRIYDCISCSGLPDVGKPLCHFEAGFLAGYIENVFNKKCYIIETHCWGLGNKFCQFEVR 132
                                   689*******************************************************97 PP

>> DUF2507  Protein of unknown function (DUF2507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.1   1.7e-15     1e-11       5     104 ..      14     111 ..      11     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.7e-15
                       DUF2507   5 ellRdallpelLgedeeeilYwaGkelArkfplesledlieffekagwGtLellkekkkelefeLsgeiveerlkekeeke 85 
                                   ++lR + l++ +g d+e ++Y+ Gkel+++++++++++l++f+++ + G++e+++e+  ++  ++   i  + l    ++ 
  gi|15669838|ref|NP_248652.1|  14 RILRFMNLRKYIGIDNEMLMYYFGKELSKNLNFKNFKELSNFYKEYKLGRIEMVSENPIKI--RIYDCISCSGLPDVGKPL 92 
                                   689999************************************************9987655..55566667778889999* PP

                       DUF2507  86 fqLEaGflAeqieqqkevv 104
                                    ++EaGflA  ie+  ++ 
  gi|15669838|ref|NP_248652.1|  93 CHFEAGFLAGYIENVFNKK 111
                                   ************9876655 PP

>> ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.1   9.3e-06     0.055      41     144 ..      37     130 ..      20     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.3e-06
                 ATC_hydrolase  41 gkklaekakakkdkadvekflalyseifekenalkfevlee.dkdeleidvtrCpyceawkkeGlpelgkllCeiDkavae 120
                                   gk+l++++   k+ +++ +f++ y          k+  +e  +++ + i++  C  c      Glp++gk lC ++  ++ 
  gi|15669838|ref|NP_248652.1|  37 GKELSKNLN-FKNFKELSNFYKEY----------KLGRIEMvSENPIKIRIYDCISCS-----GLPDVGKPLCHFEAGFLA 101
                                   555555555.33344444444443..........554444448888899999998885.....9****************9 PP

                 ATC_hydrolase 121 ginpk.....vklertktlaeGgdcCdfr 144
                                   g+ ++     +    t+ ++ G++ C+f 
  gi|15669838|ref|NP_248652.1| 102 GYIENvfnkkCYIIETHCWGLGNKFCQFE 130
                                   998886665666777************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1120.44
//
Query:       gi|15669839|ref|NP_248653.1|  [L=1169]
Description: chromosome segretation protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-58  197.2  68.2    2.2e-37  128.6   0.5    3.6  2  SMC_N         RecF/RecN/SMC N terminal domain
    5.4e-33  113.8   0.2      2e-32  112.0   0.2    2.1  1  SMC_hinge     SMC proteins Flexible Hinge Domain
    7.3e-14   52.3  51.9    1.9e-08   34.5   4.3    4.9  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.1e-09   37.9   0.0    2.1e-09   37.0   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
    2.1e-06   28.4  61.0    2.1e-06   28.4  61.0    7.8  2  AAA_23        AAA domain
     0.0013   18.6   1.6     0.0013   18.6   1.6    6.3  8  GIT_CC        GIT coiled-coil Rho guanine nucleotide exchange
      0.002   17.9 168.1       0.31   10.7  86.5    5.2  2  AAA_15        AAA ATPase domain
     0.0021   17.7   0.0     0.0021   17.7   0.0    5.7  6  AAA_27        AAA domain
     0.0035   16.3  21.4     0.0035   16.3  21.4    7.4  7  Spc7          Spc7 kinetochore protein
     0.0062   17.1   0.0     0.0062   17.1   0.0    6.2  1  ABC_tran      ABC transporter
     0.0078   16.6   9.5     0.0078   16.6   9.5    8.9  9  YlqD          YlqD protein
  ------ inclusion threshold ------
       0.49   10.7   3.8        3.9    7.8   0.0    4.1  5  AAA_16        AAA ATPase domain
        1.3    9.3   6.7        4.9    7.4   0.0    4.1  4  AAA_22        AAA domain


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.6   0.5   1.6e-40   2.2e-37       2     140 ..       4     148 ..       3     159 .. 0.93
   2 !   69.9  61.4   1.5e-22   2.1e-19      61     219 ..     702    1162 ..     277    1163 .. 0.81

  Alignments for each domain:
  == domain 1  score: 128.6 bits;  conditional E-value: 1.6e-40
                                   EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N   2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveit 82 
                                   l+++e++nFks+  k+ +l++ k+ftaivGpNGSGKsn++dAilFvLG++sakklr++++s li++ ++++++++aev ++
  gi|15669839|ref|NP_248653.1|   4 LEKIELKNFKSF--KKLSLDIPKGFTAIVGPNGSGKSNIVDAILFVLGKTSAKKLRANRFSGLITY-HNGKRADFAEVCLY 81 
                                   89**********..7**************************************************9.************** PP

                                   EEETTEESSSSSSCEEEEEEEETTSEEEEEE........TTEEE-HHHHHHHHHCTT-ST.TCS-HH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                         SMC_N  83 fdnedkklkiekeevsisrrvkrkgeseyki........ngkevtkkevsellesagisk.elLSgG 140
                                   f+ne++++++++++v i rr+k++ge++y++        ++k++tk+e+ +l+++ g+   +++S G
  gi|15669839|ref|NP_248653.1|  82 FTNENNAFNVNADKVGILRRIKSSGETDYYLvwkendkeKRKKMTKHEIIDLFRRLGLLGdNVISQG 148
                                   ***********************************98888899999********9987541445555 PP

  == domain 2  score: 69.9 bits;  conditional E-value: 1.5e-22
                                    CCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                         SMC_N   61 lsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.... 135 
                                    ls+++++                                                                   +    
  gi|15669839|ref|NP_248653.1|  702 LSKIVKR-------------------------------------------------------------------Ssakk 713 
                                    3333333...................................................................03333 PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|15669839|ref|NP_248653.1|  714 meientleiikknemrkreiaekntikikelelknkdileeleelnlkreeilnrineieskinelierrekiinelke 792 
                                    333333333333333333333333333333333333333333333333336666666666667799************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|15669839|ref|NP_248653.1|  793 yesdenlkrmneiegelkilekekaklkneidkgltlvkeilipkieelnkkvselinkkvileknisfykesieknls 871 
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|15669839|ref|NP_248653.1|  872 ileekrkryeelaknlkeltekkeqlekeietlererreilrkvrdienrinelmvekakyeskleeeerklylcekvd 950 
                                    ******************************************************************************* PP

                                    ............................................................................... CS
                                    ............................................................................... RF
                         SMC_N  136 ............................................................................... 135 
                                                                                                                   
  gi|15669839|ref|NP_248653.1|  951 vskelekkdieeleiyigeleneikslepvnmraiedynyvaerykeliekrkeyerdekkylqlmeelenkkkevfme 1029
                                    ******************************************************************************* PP

                                    ..................................................CS-HHHHHHHHHHHHHHHHCCS--SEEEE CS
                                    ..................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  136 ..................................................lLSgGektLvalaLlfAiqkvkpaplyll 164 
                                                                                      ++SgGek+L+ala+lfAiq+ +p+p+y+l
  gi|15669839|ref|NP_248653.1| 1030 vfnkvaknfeevykeiggigklsleneknpfeggilidasprgkkllsldAMSGGEKSLTALAFLFAIQRLNPSPFYVL 1108
                                    ******************************************************************************* PP

                                    CTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETTEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  165 DeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkvengvs 219 
                                    De+daaLD knv+ +a+++k++sk++Qfivis+re+m++kad ++gv++ eng s
  gi|15669839|ref|NP_248653.1| 1109 DEVDAALDVKNVSLIADMIKNASKDSQFIVISHREQMVSKADVVYGVYM-ENGLS 1162
                                    *************************************************.77765 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   0.2   1.4e-35     2e-32       2     117 .]     523     636 ..     522     636 .. 0.94

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 1.4e-35
                     SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandknsgavp 82 
                                   +g+++ +++l + + +y++A+e+a+gnrl+++vv+ +++a ++i++lk++++gratflpldri+ ++   + ++++  +++
  gi|15669839|ref|NP_248653.1| 523 PGIIDIVGNLGKTKIEYKTAIEVAAGNRLNHIVVKRMDDAVRAIKYLKERKLGRATFLPLDRIEGREA-YYIDEDG-VIGR 601
                                   7999*************************************************************955.5555555.8*** PP

                     SMC_hinge  83 lidlvevddelrkalryllgdtlvvdsldeAeela 117
                                   +idlve+d+++r++++y++g+t+vv+++d A+ela
  gi|15669839|ref|NP_248653.1| 602 AIDLVEFDEKYRRVFEYVFGNTVVVENIDIAKELA 636
                                   ********************************986 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   4.3   1.4e-11   1.9e-08       1     203 [.      26     213 ..      26     262 .. 0.78
   2 ?   -2.4  11.2       2.4   3.3e+03      89     218 ..     311     447 ..     283     478 .. 0.62
   3 !   26.3  19.5   4.2e-09   5.8e-06     219     297 ..     942    1141 ..     675    1146 .. 0.65

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.4e-11
                        AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlers 81 
                                   +++++GpNgsGKSn+ da+ ++ +          + s ++  +   s l +y+  +++ f+  ++  ++ +  ++++ ++ 
  gi|15669839|ref|NP_248653.1|  26 FTAIVGPNGSGKSNIVDAILFVLG----------KTSAKKLRANRFSGLITYHNGKRADFAEVCLYFTNENNAFNVNADKV 96 
                                   89*****************99965..........8889999999999********************************** PP

                        AAA_21  82 qveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglr 162
                                   ++      +++ ++sg+++++++ +e d+   ++ + +++++ f++  l+  + +++     +++i+   ++   +  ++ 
  gi|15669839|ref|NP_248653.1|  97 GI------LRRIKSSGETDYYLVWKENDKEKRKKMTKHEIIDLFRRLGLLGDNVISQGDLLKIINISPIERRKIIDEISGI 171
                                   **......************************************9998877666666555555555555555545444444 PP

                        AAA_21 163 ke.rigllnifadyfgfakekrllqrlvrslklveielsdlg 203
                                    e +     +  ++ +  +++++++ +++++  +  +l +++
  gi|15669839|ref|NP_248653.1| 172 AEfDEKKKKAEEELKKARELIEMIDIRISEVENNLKKLKKEK 213
                                   445555555555555555555555555555555555555555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                        AAA_21  89 svetllesgllldkrsleeedvfnpeargirggvsvfslk..elsvsepndlqfgkaltditsrawsllllldglrke... 164
                                   + +++l s +   k+++ e+ ++  e +++ + + ++++   e++  + ++++++k+l++ ++r+ ++  +++++ k+   
  gi|15669839|ref|NP_248653.1| 311 NDKKVLDSSINELKKVEVEIENKKKEIKETQKKIIENRDSiiEKEQQIKEIEEKIKNLNYEKERLKEAIAESESIIKHlke 391
                                   444444444444444444444444444444444444444400333444444555556666666667777777777777777 PP

                        AAA_21 165 ..rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlre 218
                                     +    +i+++    +++k+ l +l + +++ ++e+++++e++++ +++ e   +
  gi|15669839|ref|NP_248653.1| 392 seMEIADEIAKNQNELYRLKKELNDLDNLINRKNFEIEKNNEMIKKLKEELETVED 447
                                   77888888888888888888888888888888888888888888887776665555 PP

  == domain 3  score: 26.3 bits;  conditional E-value: 4.2e-09
                        AAA_21  219 r.............................................................................. 219 
                                    +                                                                              
  gi|15669839|ref|NP_248653.1|  942 Klylcekvdvskelekkdieeleiyigeleneikslepvnmraiedynyvaerykeliekrkeyerdekkylqlmeele 1020
                                    1555555555555666666666666666666666666666666666666666666666666666666666666666666 PP

                        AAA_21  220 ...........................................gvvflengdgqelparelSdGtkrl..lalltallr 253 
                                                                                ++   + + + l+++ +S G k+l  la+l a+ r
  gi|15669839|ref|NP_248653.1| 1021 nkkkevfmevfnkvaknfeevykeiggigklsleneknpfeggILIDASPRGKKLLSLDAMSGGEKSLtaLAFLFAIQR 1099
                                    666666666666666666666666666666666666666669999999999*****************74488889999 PP

                        AAA_21  254 alkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297 
                                    ++++ +++++DE+++ L+ k ++ +++++k++s+ ++Q+i+ +H
  gi|15669839|ref|NP_248653.1| 1100 LNPS-PFYVLDEVDAALDVKNVSLIADMIKNASK-DSQFIVISH 1141
                                    8888.*****************************.********* PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   1.5e-12   2.1e-09       1      49 [.       4      51 ..       4      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.5e-12
                        AAA_29  1 LkrlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                  L++++l N  +f++ +++i  kg+t ++Gp+GsGKS ++DAi ++L  +
  gi|15669839|ref|NP_248653.1|  4 LEKIELKNFKSFKKLSLDIP-KGFTAIVGPNGSGKSNIVDAILFVLGKT 51
                                  789****************6.99**********************9543 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4  61.0   1.5e-09   2.1e-06       1     196 [.       6     369 ..       6     381 .. 0.72
   2 ?    2.0  31.2      0.19   2.6e+02     105     196 ..     829     926 ..     805     937 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.5e-09
                        AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks.....................grgfek 60 
                                   k++++nf+sf++ ++d  kg+t+I+GpNG+GK+ i+dAi ++L+  +++  r +                     +     
  gi|15669839|ref|NP_248653.1|   6 KIELKNFKSFKKLSLDIPKGFTAIVGPNGSGKSNIVDAILFVLGKTSAKKLRANrfsglityhngkradfaevclY----- 81 
                                   79******************************************98865555555778887777443333322220..... PP

                        AAA_23  61 sdveiese..................gkvkayveltfenkdgry..................................... 86 
                                       +++e                   ++++            y                                     
  gi|15669839|ref|NP_248653.1|  82 ----FTNEnnafnvnadkvgilrrikSSGETD-----------Yylvwkendkekrkkmtkheiidlfrrlgllgdnvisq 147
                                   ....2222334433333333333333222222...........13333333334478999999999999999999999999 PP

                        AAA_23  87 .............trsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkke. 153
                                                 r+i +e++ + +  +++kka++el + +el ++i+  ++  +++l+ +   +++ +++++l+++++ 
  gi|15669839|ref|NP_248653.1| 148 gdllkiinispieRRKIIDEISGIAEFDEKKKKAEEELKKARELIEMIDIRISEVENNLKKLKKEKEDAEKYIKLNEELKa 228
                                   999999999999988888888888888888888888888888888888877776666666666666666666666666666 PP

                        AAA_23 154 ................................................................................. 153
                                                                                                                    
  gi|15669839|ref|NP_248653.1| 229 akyalilkkvsylnvlleniqndiknleelkneflskvreidveienlklrlnniinelnekgneevlelhksikelevei 309
                                   777777777777777777777778888888889999999999999999999999999999999999999999999999999 PP

                        AAA_23 154 ............rleelekeleeledekkllekl.....eqekekekeleeleeeleeil 196
                                               +l+++e e+e +++e+k+ +k+       + eke++++e+ee++++++
  gi|15669839|ref|NP_248653.1| 310 endkkvldssinELKKVEVEIENKKKEIKETQKKiienrDSIIEKEQQIKEIEEKIKNLN 369
                                   999999999999555555555555555555555544433556666777777777777765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.19
                        AAA_23 105 kkaklelleideleqfisellgskkiilnlilflgqer.feefelkdkkerleelekeleeledekkllekl.....eqek 179
                                     ++  + +i+el++++sel+++k i  ++i+f++++  ++   l++k +r eel k l+el+++k++lek+      ++ 
  gi|15669839|ref|NP_248653.1| 829 LVKEILIPKIEELNKKVSELINKKVILEKNISFYKESIeKNLSILEEKRKRYEELAKNLKELTEKKEQLEKEietleRERR 909
                                   2234445566**********999888667777777777255555699999*********************9555443444 PP

                        AAA_23 180 ekekeleeleeeleeil 196
                                   e   +  ++e++++e++
  gi|15669839|ref|NP_248653.1| 910 EILRKVRDIENRINELM 926
                                   44447778888887765 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.7   5.1e+03      39      61 ..     288     310 ..     280     315 .. 0.71
   2 ?   -1.2   1.2       1.4   1.9e+03      24      53 ..     312     344 ..     293     348 .. 0.71
   3 !   18.6   1.6   9.3e-07    0.0013      21      64 ..     375     418 ..     370     419 .. 0.96
   4 ?   -0.5   0.0      0.83   1.1e+03      42      59 ..     474     491 ..     461     504 .. 0.80
   5 ?   -1.9   0.1       2.3   3.1e+03      31      49 ..     740     758 ..     730     765 .. 0.81
   6 ?   -2.7   0.0       4.2   5.8e+03      25      47 ..     769     791 ..     761     795 .. 0.78
   7 ?   -3.8   0.2       9.1   1.3e+04      40      59 ..     803     822 ..     797     823 .. 0.69
   8 ?   -0.1   1.0       0.6   8.3e+02      37      60 ..     885     908 ..     868     934 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.7
                        GIT_CC  39 NtslsdelrlLQskvqkLqaeNa 61 
                                   N++ ++e+ +L +++++L+ e +
  gi|15669839|ref|NP_248653.1| 288 NEKGNEEVLELHKSIKELEVEIE 310
                                   66667788888888888876644 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                        GIT_CC  24 alaaseakiqqLlkvNtsl...sdelrlLQskv 53 
                                        ++ i++L+kv  ++   ++e+++ Q+k+
  gi|15669839|ref|NP_248653.1| 312 DKKVLDSSINELKKVEVEIenkKKEIKETQKKI 344
                                   455677888889998877622245777777776 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 9.3e-07
                        GIT_CC  21 lKkalaaseakiqqLlkvNtslsdelrlLQskvqkLqaeNaqlr 64 
                                   lK+a+a se+ i++L+++  ++ de+++ Q+++ +L++e ++l+
  gi|15669839|ref|NP_248653.1| 375 LKEAIAESESIIKHLKESEMEIADEIAKNQNELYRLKKELNDLD 418
                                   8**************************************99886 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.83
                        GIT_CC  42 lsdelrlLQskvqkLqae 59 
                                   l+++ ++LQ k+++L ae
  gi|15669839|ref|NP_248653.1| 474 LEEKKKELQAKLDELHAE 491
                                   556667899999999876 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 2.3
                        GIT_CC  31 kiqqLlkvNtslsdelrlL 49 
                                   ki++L   N+ + +el++L
  gi|15669839|ref|NP_248653.1| 740 KIKELELKNKDILEELEEL 758
                                   8889999999999999988 PP

  == domain 6  score: -2.7 bits;  conditional E-value: 4.2
                        GIT_CC  25 laaseakiqqLlkvNtslsdelr 47 
                                   +   e+ki++L++  +++ +el+
  gi|15669839|ref|NP_248653.1| 769 INEIESKINELIERREKIINELK 791
                                   55679999999998888888886 PP

  == domain 7  score: -3.8 bits;  conditional E-value: 9.1
                        GIT_CC  40 tslsdelrlLQskvqkLqae 59 
                                   ++++ el+ L ++  kL++e
  gi|15669839|ref|NP_248653.1| 803 NEIEGELKILEKEKAKLKNE 822
                                   45777888888888887766 PP

  == domain 8  score: -0.1 bits;  conditional E-value: 0.6
                        GIT_CC  37 kvNtslsdelrlLQskvqkLqaeN 60 
                                   k  ++l+++ ++L +++++L+ e 
  gi|15669839|ref|NP_248653.1| 885 KNLKELTEKKEQLEKEIETLERER 908
                                   444555555555555555555543 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7  86.5   0.00023      0.31       3     288 ..       4     446 ..       3     545 .. 0.67
   2 ?    2.3  39.4     0.079   1.1e+02      61     368 ..     837    1145 ..     795    1146 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                        AAA_15   3 IkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn............................. 54 
                                   ++ki++kNF+s+k+ ++d+ + +t ++G+N+sGKS+i++a+ + l +++ k+                             
  gi|15669839|ref|NP_248653.1|   4 LEKIELKNFKSFKKLSLDIPKGFTAIVGPNGSGKSNIVDAILFVLGKTSAKKlranrfsglityhngkradfaevclyftn 84 
                                   78***************************************999998877779999************************* PP

                        AAA_15  55 ................................................................................. 54 
                                                                                                                    
  gi|15669839|ref|NP_248653.1|  85 ennafnvnadkvgilrrikssgetdyylvwkendkekrkkmtkheiidlfrrlgllgdnvisqgdllkiinispierrkii 165
                                   *99999999999999999999999999999999999999999999999999999999999999999999999999988888 PP

                        AAA_15  55 .........kkvikiekedleifeniseskdikIdvef.........aekekakeyektlkskekkkadlllkkkesdlkk 117
                                            ++++k+++e+l++ ++  e +di+I   +         +  e+a++y+k++++ ++ k+  l+ kk s l  
  gi|15669839|ref|NP_248653.1| 166 deisgiaefDEKKKKAEEELKKARELIEMIDIRISEVEnnlkklkkeK--EDAEKYIKLNEELKAAKYA-LILKKVSYLNV 243
                                   888888877666666666666666666666666666665666555330..3333333333333333222.22233333333 PP

                        AAA_15 118 tikdkklklkknelsdekisvekkks.................kkelpkekeeklekekeelkidkedlkklikkleeslk 181
                                   ++++ + ++k+ e  ++ +  + ++                   +e  +e+  +l+k+++el+++ e+ kk+++  ++ lk
  gi|15669839|ref|NP_248653.1| 244 LLENIQNDIKNLEELKNEFLSKVREIdveienlklrlnniineLNEKGNEEVLELHKSIKELEVEIENDKKVLDSSINELK 324
                                   333333333322222222222222223333333333334444445555555566666667777776666666665555555 PP

                        AAA_15 182 kee.elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl...eeelteklkeiqeklkeidkklae 258
                                   k e e++n+ k+  ++ + i + R++  e++++++++ +k+k+  +e+     l   + e+++++k+++e+  ei +++a+
  gi|15669839|ref|NP_248653.1| 325 KVEvEIENKKKEIKETQKKIIENRDSIIEKEQQIKEIEEKIKNLNYEKER---LkeaIAESESIIKHLKESEMEIADEIAK 402
                                   55566666666666666666666666666666666666666666666433...2333444444444444444444444444 PP

                        AAA_15 259 elk.........kilkkkidkikkfnykgkkneeieik......d 288
                                   + +         ++l++ i+  k+f++ ++++  +++k      +
  gi|15669839|ref|NP_248653.1| 403 NQNelyrlkkelNDLDNLINR-KNFEIEKNNEMIKKLKeeletvE 446
                                   444665555444333333333.23333333333333334344441 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.079
                        AAA_15   61 ekedleifeniseskdikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisve 139 
                                    + e+l+++ ++  +k++                                         i +k++ ++k+ + ++   +e
  gi|15669839|ref|NP_248653.1|  837 KIEELNKKVSELINKKV-----------------------------------------ILEKNISFYKESIEKNLSILE 874 
                                    11111111111111111.........................................111111122111111111111 PP

                        AAA_15  140 kkks.......kkelpkekeeklekekeelkidkedlkklikkleeslkkee......................elknv 189 
                                    +k +       + +  +ek+e leke+e+l+ +                                         + +++
  gi|15669839|ref|NP_248653.1|  875 EKRKryeelakNLKELTEKKEQLEKEIETLERE------------------RreilrkvrdienrinelmvekaKYESK 935 
                                    111111111112222222222222222222222..................0222222222222222333444455566 PP

                        AAA_15  190 lksaiiklllisakRnvsdedsekkssllgklkekileealqekl....................eeelteklkeiqek 248 
                                    l+++ +kl+l++++ +vs+e+++k  + l+  + ++  e++  +l                     +e++++ ++ ++k
  gi|15669839|ref|NP_248653.1|  936 LEEEERKLYLCEKV-DVSKELEKKDIEELEIYIGELENEIK--SLepvnmraiedynyvaerykeLIEKRKEYERDEKK 1011
                                    66666666666655.44444444444444444444433322..224577777777777777755533333333333444 PP

                        AAA_15  249 lkeidkklaeelkkilkkkidkikkfnykgkkneeieik.........................ddeelplnknGsGvq 302 
                                    + ++ ++l++++k+++ + ++k+    +k+++++++ei                           +  l+l+ ++ G +
  gi|15669839|ref|NP_248653.1| 1012 YLQLMEELENKKKEVFMEVFNKV----AKNFEEVYKEIGgigklsleneknpfeggilidasprGKKLLSLDAMSGGEK 1086
                                    44444444444444444444443....444444444444555555555556778999999******************* PP

                        AAA_15  303 rllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368 
                                    +l  l++l +  + +     ++ +++++E +a L  ++ + +++ +k++++d+  Q i+ +H + +
  gi|15669839|ref|NP_248653.1| 1087 SLTALAFLFAIQRLN-----PSPFYVLDEVDAALDVKNVSLIADMIKNASKDS--QFIVISHREQM 1145
                                    *******99999999.....*********************************..*******7766 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.5e-06    0.0021       3      47 ..       4      45 ..       2      61 .. 0.90
   2 ?   -0.3   1.0      0.48   6.7e+02     156     200 ..     335     378 ..     314     385 .. 0.61
   3 ?   -0.4   0.2      0.53   7.3e+02     155     201 ..     379     425 ..     372     436 .. 0.82
   4 ?    4.0   0.3     0.024        33     151     194 ..     467     509 ..     460     520 .. 0.82
   5 ?   -3.7   0.3       5.4   7.5e+03     155     186 ..     692     719 ..     676     740 .. 0.40
   6 ?   -0.2   2.3      0.46   6.4e+02     160     199 ..     885     924 ..     868     941 .. 0.46

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-06
                        AAA_27  3 lerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAis 47
                                  le+++L+ + +f+  sld++   ++++ i+GpN +GKs +++Ai 
  gi|15669839|ref|NP_248653.1|  4 LEKIELKNFKSFKKLSLDIP---KGFTAIVGPNGSGKSNIVDAIL 45
                                  7899***************9...8******************996 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.48
                        AAA_27 156 aslrevleaLeaeadelfkprkskkrainealeeleeakkelrea 200
                                   ++++e+++++ +++d++ +++++ k +i e+ ++l+  k++l+ea
  gi|15669839|ref|NP_248653.1| 335 KEIKETQKKIIENRDSIIEKEQQIK-EIEEKIKNLNYEKERLKEA 378
                                   3455566666666666666666666.6666666666666666665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.53
                        AAA_27 155 laslrevleaLeaeadelfkprkskkrainealeeleeakkelreaq 201
                                   +a+ ++++++L+++  e+ ++ +++++++++ ++el+++++ +++++
  gi|15669839|ref|NP_248653.1| 379 IAESESIIKHLKESEMEIADEIAKNQNELYRLKKELNDLDNLINRKN 425
                                   66777888999999999999999999999999999999888777665 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.024
                        AAA_27 151 asaGlaslrevleaLeaeadelfkprkskkrainealeeleeak 194
                                   ++ G+++l+e  ++L+a+ del+++  +++ a  +al+e+ee++
  gi|15669839|ref|NP_248653.1| 467 SKRGIKELEEKKKELQAKLDELHAEYVKEN-ARIKALKEMEELS 509
                                   5679**********************9999.6667777777754 PP

  == domain 5  score: -3.7 bits;  conditional E-value: 5.4
                        AAA_27 155 laslrevleaLeaeadelfkprkskkrainea 186
                                   l++++e +e+L++  ++  +++     +i ++
  gi|15669839|ref|NP_248653.1| 692 LRKIKEEIERLSKIVKRSSAKKM----EIENT 719
                                   23333333333222222222222....22222 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 0.46
                        AAA_27 160 evleaLeaeadelfkprkskkrainealeeleeakkelre 199
                                   + l++L++++++l k+ ++ +r+ +e l+++++ +++++e
  gi|15669839|ref|NP_248653.1| 885 KNLKELTEKKEQLEKEIETLERERREILRKVRDIENRINE 924
                                   3333333333333333333333333333333333333333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9  11.1    0.0075        10     192     245 ..     176     229 ..     160     242 .. 0.84
   2 !   10.0  19.1   0.00021      0.29     155     250 ..     245     344 ..     231     346 .. 0.78
   3 !    9.7  21.9   0.00025      0.34     199     265 ..     328     394 ..     320     406 .. 0.90
   4 !   16.3  21.4   2.6e-06    0.0035     137     260 ..     386     509 ..     384     521 .. 0.94
   5 ?   -0.8  31.0      0.39   5.4e+02     145     280 ..     682     821 ..     674     824 .. 0.87
   6 !    6.6  22.5    0.0023       3.2     142     255 ..     803     920 ..     797     925 .. 0.81
   7 ?   -2.5  22.0       1.3   1.8e+03     141     258 ..     894    1010 ..     894    1035 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0075
                          Spc7 192 elesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkse 245
                                   e ++  +eeL+++re ++ ++  i+e +++l++l++++e+ e+ i+  +e k+ 
  gi|15669839|ref|NP_248653.1| 176 EKKKKAEEELKKARELIEMIDIRISEVENNLKKLKKEKEDAEKYIKLNEELKAA 229
                                   34566799*************************************999888765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00021
                          Spc7 155 kelLekqeeeldellpeleeekaeleeeleklqe....aaeelesidkeeLeelreelaelkaeieekkkelaelqeqlee 231
                                    e+++++ ++l+el++e+ ++  e+  e+e+l+       +el++  +ee+ el+++++el++eie+ kk l++  ++l++
  gi|15669839|ref|NP_248653.1| 245 LENIQNDIKNLEELKNEFLSKVREIDVEIENLKLrlnnIINELNEKGNEEVLELHKSIKELEVEIENDKKVLDSSINELKK 325
                                   456666677777777777777777777777666533334556666789********************************* PP

                          Spc7 232 leekieelkeqkseleeei 250
                                   +e +ie+ k++++e++++i
  gi|15669839|ref|NP_248653.1| 326 VEVEIENKKKEIKETQKKI 344
                                   ****************998 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00025
                          Spc7 199 eeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwse 265
                                    e+e+ ++e++e +++i e ++ + e+++q++e+eeki++l+ +k++l+e+iae+e++++  k+++ 
  gi|15669839|ref|NP_248653.1| 328 VEIENKKKEIKETQKKIIENRDSIIEKEQQIKEIEEKIKNLNYEKERLKEAIAESESIIKHLKESEM 394
                                   589********************************************************99888764 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 2.6e-06
                          Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeiee 217
                                   ++ Lke+  e+ +++ + +++L + ++el++l + ++++  e+e++ e++++ +eele+++  + + l  el++l++eie 
  gi|15669839|ref|NP_248653.1| 386 IKHLKESEMEIADEIAKNQNELYRLKKELNDLDNLINRKNFEIEKNNEMIKKLKEELETVEDVDTKPLYLELENLNVEIEF 466
                                   6899***************************************************************************** PP

                          Spc7 218 kkkelaelqeqleeleekieelkeqkseleeeiaeaervleec 260
                                    k+ ++el+e+++el++k++el++++ + +++i++ +++ e  
  gi|15669839|ref|NP_248653.1| 467 SKRGIKELEEKKKELQAKLDELHAEYVKENARIKALKEMEELS 509
                                   **********************************999887755 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 0.39
                          Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqe...aaeelesidkeeLeelreelaelkaeieekkkel 222
                                    +++ ++e++ ++++++ e l++++++ +++k e+e++le +++   +++e+++ +  +++el  + +++ +e+ee++ + 
  gi|15669839|ref|NP_248653.1| 682 ADEIIAIESELRKIKEEIERLSKIVKRSSAKKMEIENTLEIIKKnemRKREIAEKNTIKIKELELKNKDILEELEELNLKR 762
                                   45566789999****************************999998889999999999999999999999999999999999 PP

                          Spc7 223 aelqeqleeleekieelkeqkseleeeiaeaervleeckgws.esevsrlkeevkalee 280
                                   +e  ++++e+e+ki+el e+++++ +e++e e+  + +++ + e e++ l++e  +l++
  gi|15669839|ref|NP_248653.1| 763 EEILNRINEIESKINELIERREKIINELKEYESDENLKRMNEiEGELKILEKEKAKLKN 821
                                   99999999999999999999999999999999999988887634578887777777766 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.0023
                          Spc7 142 egleenlegleedkelLekqeeel.dellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieek 218
                                   +++e +l++le++k++L+++ ++  + +++ l  + +el++++ +l +++  le+     ke++e+  + l+e  + +ee+
  gi|15669839|ref|NP_248653.1| 803 NEIEGELKILEKEKAKLKNEIDKGlTLVKEILIPKIEELNKKVSELINKKVILEKnisFYKESIEKNLSILEEKRKRYEEL 883
                                   567788999999999999988775266667788999999999999999998888765455999999999999999999999 PP

                          Spc7 219 kkelaelqeqleeleekieelkeqkseleeeiaeaer 255
                                    k+l+el+e++e+le++ie+l+ +++e+  +++  e+
  gi|15669839|ref|NP_248653.1| 884 AKNLKELTEKKEQLEKEIETLERERREILRKVRDIEN 920
                                   9999999999999999999999999999888877665 PP

  == domain 7  score: -2.5 bits;  conditional E-value: 1.3
                          Spc7  141 kegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelaelkaeieek 218 
                                    ke+le+++e+le++++++ ++   +++  +el  eka+ e++le+++++   +e++d ++eLe  +++++el+  i e+
  gi|15669839|ref|NP_248653.1|  894 KEQLEKEIETLERERREILRKVRDIENRINELMVEKAKYESKLEEEERKLYLCEKVDvSKELE--KKDIEELEIYIGEL 970 
                                    799****************99999999999999999999999999999888888888778887..57888888888888 PP

                          Spc7  219 kkelaelqeqleeleekieelkeqkseleeeiaeaervle 258 
                                    ++e+++l+    +  e+ + ++e+++el e+ +e er  +
  gi|15669839|ref|NP_248653.1|  971 ENEIKSLEPVNMRAIEDYNYVAERYKELIEKRKEYERDEK 1010
                                    8888888877777777777777777777777766666543 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.5e-06    0.0062       2      32 ..      16      45 ..      15      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.5e-06
                                  EEEEEEEETTSEEEEEESTTSSHHHHHHHHT CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  2 knvslklkegekvaivGenGaGKStLlklla 32
                                  k++sl++ +g  +aivG+nG+GKS ++ +++
  gi|15669839|ref|NP_248653.1| 16 KKLSLDIPKG-FTAIVGPNGSGKSNIVDAIL 45
                                  6788888888.689*************9997 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   3.9       1.8   2.5e+03      46      87 ..     181     217 ..     162     234 .. 0.46
   2 !   16.6   9.5   5.7e-06    0.0078      19     102 ..     256     339 ..     251     342 .. 0.96
   3 ?   -1.0  13.2       1.6   2.1e+03      25      92 ..     354     423 ..     343     446 .. 0.80
   4 ?   -0.8   5.6       1.3   1.9e+03      20      95 ..     433     508 ..     428     517 .. 0.51
   5 ?   -1.3   8.9       1.9   2.6e+03      24      92 ..     680     747 ..     662     763 .. 0.52
   6 ?   -1.0   7.2       1.6   2.2e+03      12      84 ..     785     864 ..     775     888 .. 0.72
   7 ?    1.8  10.1      0.21   2.9e+02      22      99 ..     856     931 ..     850     940 .. 0.65
   8 ?    4.2  10.2     0.037        51      22     102 ..     887     962 ..     871     969 .. 0.74
   9 ?    3.2   3.2     0.077   1.1e+02      14      86 ..     952    1026 ..     945    1036 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.8
                          YlqD  46 likeikkqsaqqieeiqeqvekekserlekkkqllqqleqvq 87 
                                   +++e+kk     ++e+ e ++ ++se++++ k+l+++ e+ +
  gi|15669839|ref|NP_248653.1| 181 AEEELKK-----ARELIEMIDIRISEVENNLKKLKKEKEDAE 217
                                   2222222.....333333333333333333333333333332 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5.7e-06
                          YlqD  19 eelqqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvqkLelgsevkqgq 99 
                                   eel++++ ++++++d e+++L++ ++ +i+e++++ ++++ e+++++++ + e+++ kk l++ +++++k+e++ e k+++
  gi|15669839|ref|NP_248653.1| 256 EELKNEFLSKVREIDVEIENLKLRLNNIINELNEKGNEEVLELHKSIKELEVEIENDKKVLDSSINELKKVEVEIENKKKE 336
                                   799*************************************************************************99999 PP

                          YlqD 100 ves 102
                                   + +
  gi|15669839|ref|NP_248653.1| 337 IKE 339
                                   976 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.6
                          YlqD  25 lqaqieqldkelqqLefqakrlikeikkqsaq..qieeiqeqvekekserlekkkqllqqleqvqkLelg 92 
                                    ++qi+++++++++L+ +++rl + i++ +    + +e +++++ e+++ +++  +l+++l+++++L   
  gi|15669839|ref|NP_248653.1| 354 KEQQIKEIEEKIKNLNYEKERLKEAIAESESIikHLKESEMEIADEIAKNQNELYRLKKELNDLDNLINR 423
                                   4799**************9999888877544356888888888888888888888888888888888654 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.3
                          YlqD  20 elqqqlqaqieqldk.elqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvqkLelgsev 95 
                                   e++++l++++e+++  + + L ++++ l  ei+  s++ i+e++e+ ++ ++++ e  ++  ++  +++ L+  +e+
  gi|15669839|ref|NP_248653.1| 433 EMIKKLKEELETVEDvDTKPLYLELENLNVEIEF-SKRGIKELEEKKKELQAKLDELHAEYVKENARIKALKEMEEL 508
                                   6666666666666432566666666666555554.333444444444444444444444444444444444444443 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 1.9
                          YlqD  24 qlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvqkLelg 92 
                                   ++ ++i ++++el++++ + +rl k +k+ sa ++ ei++ +e  k++   k++ ++++  ++++Lel 
  gi|15669839|ref|NP_248653.1| 680 KIADEIIAIESELRKIKEEIERLSKIVKRSSA-KKMEIENTLEIIKKNEMRKREIAEKNTIKIKELELK 747
                                   44445555566666666666665544444333.444444444444444444444444444444444443 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 1.6
                          YlqD  12 ivTeklKeelqqqlqaqieqldkelqqLefqakrlikeikkqsaq........qieeiqeqvekekserlekkkqllqqle 84 
                                   ++ ++lKe   ++  +++++++ el+ Le ++ +l +ei k   +        +iee++++v++ +++     k++ +  e
  gi|15669839|ref|NP_248653.1| 785 KIINELKEYESDENLKRMNEIEGELKILEKEKAKLKNEIDKGL-TlvkeilipKIEELNKKVSELINKKVILEKNISFYKE 864
                                   5556677777778888999999999999999999999998743.3467777777777777777766666555555555544 PP

  == domain 7  score: 1.8 bits;  conditional E-value: 0.21
                          YlqD  22 qqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvqkLelgsevkqgq 99 
                                   +++++  +e ++k+l+ Le + kr  +e++k + ++ +e +eq+eke++ ++ +++++l +++++++   +  v++++
  gi|15669839|ref|NP_248653.1| 856 EKNISFYKESIEKNLSILEEKRKRY-EELAK-NLKELTEKKEQLEKEIETLERERREILRKVRDIENRINELMVEKAK 931
                                   5556666777888888888777776.44444.5667777777777777777777777777777777655555555444 PP

  == domain 8  score: 4.2 bits;  conditional E-value: 0.037
                          YlqD  22 qqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeqvekekserlekkkqllqqleqvqkLelgsevkqgqves 102
                                   +++l++++eql+ke++ Le + ++++++++      ie+  +++  ek++ + k ++ + +l   +k+ + +e++++ +e+
  gi|15669839|ref|NP_248653.1| 887 LKELTEKKEQLEKEIETLERERREILRKVRD-----IENRINELMVEKAKYESKLEEEERKLYLCEKVDVSKELEKKDIEE 962
                                   5788899999999999999999999998876.....555555555666666777777777777777777888888877776 PP

  == domain 9  score: 3.2 bits;  conditional E-value: 0.077
                          YlqD   14 TeklKeelqqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiqeq..vekekserlekkkqllqqleqv 86  
                                     ++l ++ +++l+  i +l++e++ Le    r+i++ +   ++ +e i+++  +e+ +++ l+ +++l+++ ++v
  gi|15669839|ref|NP_248653.1|  952 SKELEKKDIEELEIYIGELENEIKSLEPVNMRAIEDYNYVAERYKELIEKRkeYERDEKKYLQLMEELENKKKEV 1026
                                    555555666778888888888888888888888888888666655555544014444455566666666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0029       3.9      25      51 ..      25      51 ..      14     136 .. 0.82
   2 ?   -1.4   0.1       1.9   2.6e+03      76     117 ..     352     405 ..     344     462 .. 0.64
   3 ?   -1.6   0.0       2.2     3e+03      56     106 ..     481     523 ..     465     567 .. 0.60
   4 ?   -0.9   0.2       1.4   1.9e+03      76     127 ..     873     930 ..     845     950 .. 0.65
   5 ?   -1.4   0.0         2   2.7e+03     107     169 ..    1077    1138 ..    1010    1139 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0029
                        AAA_16 25 elvllsGesGvGKsslvrellralekd 51
                                  + + ++G+ G+GKs +v+++l  l k+
  gi|15669839|ref|NP_248653.1| 25 GFTAIVGPNGSGKSNIVDAILFVLGKT 51
                                  56789*************999554444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.9
                        AAA_16  76 lareellrqlldeaesaeleawrekleeala...........avpelagaea...s 117
                                   +++e+ +++++++   ++l++ +e+l+ea+a           +  e+a+++a   +
  gi|15669839|ref|NP_248653.1| 352 IEKEQQIKEIEEK--IKNLNYEKERLKEAIAesesiikhlkeSEMEIADEIAknqN 405
                                   6677777777766..55688888888888886776666665533333333334431 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.2
                        AAA_16  56 lrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala 106
                                   l++k d+l         a++ +++  +++l++++e +  +a re l ++l 
  gi|15669839|ref|NP_248653.1| 481 LQAKLDEL--------HAEYVKENARIKALKEMEELSMDRAIREILNANLP 523
                                   44555555........56666666777777777666666666665555555 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.4
                        AAA_16  76 lareellrqlldeaesaeleawrekleealaavpelagaea.......srllellkrll 127
                                   l +e+  r ++ +++ +el + +e+le++++     ++++        +r++el+ + +
  gi|15669839|ref|NP_248653.1| 873 L-EEKRKRYEELAKNLKELTEKKEQLEKEIETLERERREILrkvrdieNRINELMVEKA 930
                                   4.345555556666677788888888888883333333333555555577777776655 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 2
                        AAA_16  107 avpelagaeasrllellkrllallsrderplvlvlDdlq.wadeaslqllaaLlrllesk.pllv 169 
                                    + ++++g e+s  + ++  ++++l + +     vlD+++  +d    +l+a + ++++ + +++v
  gi|15669839|ref|NP_248653.1| 1077 SLDAMSGGEKSLTALAFLFAIQRLNP-S--PFYVLDEVDaALDVKNVSLIADMIKNASKDsQFIV 1138
                                    45566666655555565556655554.3..57889999955555777788888877776546655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0036       4.9       5      25 ..      24      44 ..      22     140 .. 0.78
   2 ?   -2.5   0.7       4.2   5.8e+03      71     123 ..     371     426 ..     325     428 .. 0.65
   3 ?   -3.4   0.1       7.9   1.1e+04      55      75 ..     878     897 ..     864     921 .. 0.55
   4 ?    3.0   0.0     0.084   1.2e+02      70     128 ..    1055    1139 ..     990    1144 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0036
                        AAA_22  5 agilvvtGesGtGKTtllrrl 25
                                  +g+++++G+ G+GK+  +  +
  gi|15669839|ref|NP_248653.1| 24 KGFTAIVGPNGSGKSNIVDAI 44
                                  79*************877665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.2
                        AAA_22  71 erlsseellealeqalraravielliiDEaqhlrs......eealeeLrsllnlsrkgv 123
                                   e  +++e ++  e  +++ +  e+ i DE+ +  +      ++ l++L +l n  rk++
  gi|15669839|ref|NP_248653.1| 371 EKERLKEAIAESESIIKHLKESEMEIADEIAKN-QnelyrlKKELNDLDNLIN--RKNF 426
                                   344555555555555555555778888888886.3235557778888877777..7776 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 7.9
                        AAA_22  55 dllrellralglelkaerlss 75 
                                   + ++el+++l++ +++   ++
  gi|15669839|ref|NP_248653.1| 878 KRYEELAKNLKELTEK-KEQL 897
                                   4556666666655555.2222 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.084
                        AAA_22   70 a.........................erlsseell.ealeqalraravielliiDEaqh.lrseealeeLrsllnlsrk 121 
                                    +                           + ++ l   a+  a+++    ++ ++DE++  l   ++++ + ++ ++++k
  gi|15669839|ref|NP_248653.1| 1055 NeknpfeggilidasprgkkllsldaMSGGEKSLTaLAFLFAIQRLNPSPFYVLDEVDAaL-DVKNVSLIADMIKNASK 1132
                                    355555555555555555444444442233333333444444555555889********99.89999999888888888 PP

                        AAA_22  122 gvqliLv 128 
                                    + q+i++
  gi|15669839|ref|NP_248653.1| 1133 DSQFIVI 1139
                                    8888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3745  (0.208879); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                       324  (0.0180713); expected 17.9 (0.001)
Passed Fwd filter:                       163  (0.00909142); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 4.21u 0.39s 00:00:04.59 Elapsed: 00:00:00.84
# Mc/sec: 4212.74
//
Query:       gi|15669840|ref|NP_248654.1|  [L=177]
Description: hypothetical protein MJ_1644 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-35  120.8  25.5    4.6e-35  120.8  25.5    1.5  1  DUF996         Protein of unknown function (DUF996)
  ------ inclusion threshold ------
       0.32   11.0  17.1       0.15   12.1   2.2    2.7  2  Sensor         Putative sensor
       0.54   10.1  18.1    1.4e+02    2.3  18.1    2.2  1  DUF2975        Protein of unknown function (DUF2975)


Domain annotation for each model (and alignments):
>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.8  25.5   7.7e-39   4.6e-35       1     135 []      30     160 ..      30     160 .. 0.96

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 7.7e-39
                        DUF996   1 lsivGliLvlvalkeiskavndekifsnaliafilsiialvvailalllvlgalatalelpgleeaaslilllllvliiay 81 
                                   l+i+G++L+l+al++isk++nd+++f+++l+ ++l+iia++++i+a+++++++l  +   +gl+    +++ +l+ +i++y
  gi|15669840|ref|NP_248654.1|  30 LAIAGYVLILLALNKISKIFNDDEVFKKYLYGVVLWIIAVLIVIFAVGISFVSLSFIPLDYGLT----AMSSFLVGVILFY 106
                                   579************************************************9999988888777....5999********* PP

                        DUF996  82 vlliisavflkksyellgkrtgvklFetagllyfiGaiLtivlvGliilliaei 135
                                   +l +i ++f+kksye+++ +tgv+ F+++gllyfiG++L+iv+vG+i++++a+i
  gi|15669840|ref|NP_248654.1| 107 ILSVIGGYFIKKSYEKVSYYTGVDSFRICGLLYFIGTLLLIVIVGIIVIIVAQI 160
                                   ****************************************************98 PP

>> Sensor  Putative sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.2   2.5e-05      0.15      76     143 ..      43     108 ..      39     115 .. 0.75
   2 ?    8.4   2.1   0.00035       2.1       5      39 ..     124     158 ..     120     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.5e-05
                        Sensor  76 arlrallrdpatwrdllylllhfplglvlfvvavvllalalalltaPl.wtlpeallvavlGlllllvl 143
                                   +++ + + d  + ++ ly ++  +++++++++av   +++l+  ++Pl +  ++a+  +++G++l+ +l
  gi|15669840|ref|NP_248654.1|  43 NKISKIFNDDEVFKKYLYGVVLWIIAVLIVIFAVGISFVSLS--FIPLdY-GLTAMSSFLVGVILFYIL 108
                                   567789999999************998777777766665555..667744.467888889999988663 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00035
                        Sensor   5 glplgvaafvllvtglslglgllvllvGlplLala 39 
                                   +  +gv +f  + ++ ++g +ll+++vG+ ++++a
  gi|15669840|ref|NP_248654.1| 124 SYYTGVDSFRICGLLYFIGTLLLIVIVGIIVIIVA 158
                                   667899999999******************99876 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  18.1     0.023   1.4e+02      18     126 ..      22     176 ..       5     177 .] 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.023
                       DUF2975  18 vpvlllgvlallafvvalvqlwkLlrsirkgevFspanvrrLrriglaliaa.....................alllaagi 77 
                                   v++++ g+la++ +v++l++l k+ +  +++evF +  +  + +i+ +li++                     + ++++g+
  gi|15669840|ref|NP_248654.1|  22 VSYAVGGILAIAGYVLILLALNKISKIFNDDEVFKKYLYGVVLWIIAVLIVIfavgisfvslsfipldygltaMSSFLVGV 102
                                   45888999999999999********************99999999999999999999999888888888888866666666 PP

                       DUF2975  78 valallaelelap.....................gvvllllgvafaslvigllvlvlaellaeAvk......lkeE 126
                                   + +++l+   + +                     + +l ++g  ++ +++g++v+++a++l++ ++      lk+E
  gi|15669840|ref|NP_248654.1| 103 ILFYILSV--IGGyfikksyekvsyytgvdsfriCGLLYFIGTLLLIVIVGIIVIIVAQILEIVAYfslpddLKSE 176
                                   66666666..444456666777777888888888788888888888888899999999998887665555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1338  (0.0746277); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 1103.88
//
Query:       gi|15669841|ref|NP_248655.1|  [L=243]
Description: coenzyme PQQ synthesis protein III [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-16   61.1   0.1    2.7e-16   60.4   0.1    1.3  1  Radical_SAM   Radical SAM superfamily
    1.8e-11   44.2   0.2    3.6e-11   43.2   0.1    1.7  1  Fer4_14       4Fe-4S single cluster domain
    3.5e-11   43.5   0.0    5.8e-11   42.8   0.0    1.5  1  Fer4_12       4Fe-4S single cluster domain
     0.0016   18.4   0.1     0.0024   17.8   0.1    1.3  1  CTP_transf_3  Cytidylyltransferase


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.1     6e-20   2.7e-16       2     165 ..      23     186 ..      22     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 6e-20
                                   EEESEESS--TTTSCCTT...........HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpet...........vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerla 71 
                                   v + gC+l+C++C+  ++           ++  ++ + + +e+i++ +++lk  ++   v ++ggeplly + +++++++ 
  gi|15669841|ref|NP_248655.1|  23 VRFAGCPLNCVYCDEESKgyfnrvekipgSGEFETLQKMEIEDIINAIDKLK-TPDLFAVSFTGGEPLLYHKQIKEIAEIL 102
                                   6789************99*********************************6.555************************* PP

                                   HTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  72 klavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                   k   +g+r+++e+ng+ p     er+    +  + + l+   +  +++     + ++  l++++kl +++ + ++  +v++
  gi|15669841|ref|NP_248655.1| 103 KD--KGYRTFLESNGMFP-----ERIFYFDIASIDIKLKEHFEY-IKDED-YEKLYKNELKTIKKLYNLNSD-IYAKVVIM 173
                                   *9..7*************.....********************9.99999.99****************888.9******* PP

                                   TTTSHHHHHHHHH CS
                                   xxxxxxxxxxxxx RF
                   Radical_SAM 153 pGendeeleelle 165
                                   +  n e+++ +++
  gi|15669841|ref|NP_248655.1| 174 EETNIEDVKIIAK 186
                                   ****999876665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.1   8.1e-15   3.6e-11       1      91 [.      21     117 ..      21     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 8.1e-15
                       Fer4_14   1 lfvrlsgCnlsCkgCdnketwks..........elgkpqteell..eqilkdlkkseikiqglvltGGePLhyenkkellk 69 
                                   +fvr++gC+l+C+ Cd++++  +          e ++ q+ e++   + +++lk  +     +++tGGePL+y  +k++ +
  gi|15669841|ref|NP_248655.1|  21 IFVRFAGCPLNCVYCDEESKGYFnrvekipgsgEFETLQKMEIEdiINAIDKLKTPDL--FAVSFTGGEPLLY--HKQIKE 97 
                                   7***************666555555888888874444444444400344445555555..459********99..778888 PP

                       Fer4_14  70 lvkrlkeeypekkiwletngtl 91 
                                   + + lk+++  ++  le+ng++
  gi|15669841|ref|NP_248655.1|  98 IAEILKDKG--YRTFLESNGMF 117
                                   888888888..99999999876 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0   1.3e-14   5.8e-11       3      98 ..      11     120 ..       9     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.3e-14
                       Fer4_12   3 GeG...vr..lslfvsgCnlsCkgCfnketw............sfksgkeftkelleeiiedlkkesiegltllGGEPllp 66 
                                   GeG   +r  ++++++gC+l+C +C  ++              +f++ ++++ e + ++i++lk +  + ++++GGEPll 
  gi|15669841|ref|NP_248655.1|  11 GEGkyiGRrfIFVRFAGCPLNCVYCDEESKGyfnrvekipgsgEFETLQKMEIEDIINAIDKLKTPDLFAVSFTGGEPLL- 90 
                                   56644433125777**********985555577777777777777799999999999999***99***************. PP

                       Fer4_12  67 enaeallelvkevkeekpekdiwlytgytlee 98 
                                      +++ e+++ +k +++  + ++++g   e 
  gi|15669841|ref|NP_248655.1|  91 -YHKQIKEIAEILKDKGY-RTFLESNGMFPER 120
                                   .67778888888888888.5888888876555 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   5.3e-07    0.0024      82     162 ..      71     168 ..      60     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.3e-07
                                   HHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTTS................SEEEEEEETTSHHHHTSTTSTEEEE CS
                  CTP_transf_3  82 kaflmseneeiivnlqGdnPllqeevikkaietlkenqed................ylstlvkkvgkeeevlnandlkvll 146
                                    +++    ++ +v  +G +Pll ++ ik+++e lk++++                 +++++  k+++  e+ + +d ++l+
  gi|15669841|ref|NP_248655.1|  71 DKLKTP--DLFAVSFTGGEPLLYHKQIKEIAEILKDKGYRtflesngmfperifyfDIASIDIKLKEHFEYIKDEDYEKLY 149
                                   444444..7899*************************9999*************999999999999999999999999999 PP

                                   TTT...SBEEEEESSESSE CS
                  CTP_transf_3 147 dda...gkalyfeesvipy 162
                                   +++    k+ly  +s+i++
  gi|15669841|ref|NP_248655.1| 150 KNElktIKKLYNLNSDIYA 168
                                   9997777778888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1047  (0.058397); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1622.42
//
Query:       gi|15669842|ref|NP_248656.1|  [L=211]
Description: orotate phosphoribosyltransferase-like protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-17   63.2   0.3    3.1e-17   62.6   0.3    1.3  1  Pribosyltran     Phosphoribosyl transferase domain
    0.00047   20.0   0.1     0.0024   17.8   0.1    2.2  1  HTH_11           HTH domain
     0.0012   18.4   0.1     0.0027   17.3   0.1    1.6  1  Sigma70_r4_2     Sigma-70, region 4
     0.0057   16.7   0.1      0.013   15.6   0.1    1.6  1  HTH_7            Helix-turn-helix domain of resolvase
     0.0071   15.8   0.0      0.018   14.5   0.0    1.8  1  Sigma70_r4       Sigma-70, region 4
     0.0072   16.1   0.0      0.016   15.0   0.0    1.5  1  HTH_23           Homeodomain-like domain
  ------ inclusion threshold ------
      0.014   14.9   0.2      0.056   12.9   0.1    1.9  2  PRTase_2         Phosphoribosyl transferase
      0.015   14.8   0.1      0.031   13.8   0.1    1.5  1  GerE             Bacterial regulatory proteins, luxR family
      0.046   13.5   0.1        0.1   12.4   0.1    1.6  1  HTH_10           HTH DNA binding domain
      0.058   13.1   0.0       0.12   12.1   0.0    1.5  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.059   13.6   0.1       0.15   12.3   0.1    1.7  1  HTH_17           Helix-turn-helix domain
      0.075   12.9   0.2       0.12   12.2   0.2    1.3  1  Sigma70_ECF      ECF sigma factor
      0.085   12.3   0.1       0.16   11.4   0.1    1.4  1  UPRTase          Uracil phosphoribosyltransferase
       0.11   13.0   1.0       0.35   11.4   0.3    2.3  3  HSCB_C           HSCB C-terminal oligomerisation domain
       0.11   12.3   0.0       0.15   11.9   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
       0.13   12.1   0.4       0.39   10.5   0.0    1.9  2  MerR             MerR family regulatory protein
       0.18   12.4   1.5        4.1    8.1   0.5    2.5  2  Mga              Mga helix-turn-helix domain
        0.2   11.8   0.0       0.42   10.8   0.0    1.5  1  HTH_28           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.3   3.1e-20   3.1e-17       2     113 ..      66     174 ..      65     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 3.1e-20
                                   HHHTTT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE- CS
                  Pribosyltran   2 gsellenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrll 82 
                                   ++++ +  + l+ + +++ +il++ n + d+vvg+ + Gvp+a+ +a+eL+ +l++   +k+ ++ + +++ ++s    + 
  gi|15669842|ref|NP_248656.1|  66 WKNIGSSANRLKYISSIIVDILKSRNIEFDTVVGVSTSGVPIATLVASELGKELTIYIPKKHISEEGKKITGSISQ---NF 143
                                   7888888999999********************************************************9988876...9* PP

                                   ---TTSEEEEE-SEESSSHHHHHHHHHHHCC CS
                  Pribosyltran  83 edpagkkVliVDDildtGgTllaalelLkek 113
                                   + +  k+ +i+DD++++G+Tl++ ++ Lke+
  gi|15669842|ref|NP_248656.1| 144 SAVNYKRAVIIDDVVTSGSTLKECIKQLKEV 174
                                   **************************66664 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.4e-06    0.0024       4      33 ..       8      38 ..       6      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.4e-06
                        HTH_11  4 qilelLleargp.isgeeLAeeLnvSrrtvr 33
                                   +l+ ++e +++ +++ e+AeeLnvS  t r
  gi|15669842|ref|NP_248656.1|  8 ELLKKVIELKSNgLTIGEIAEELNVSMETAR 38
                                  5788888999999*************98876 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.7e-06    0.0027      15      53 ..      10      47 ..       7      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.7e-06
                                  HHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHH CS
                  Sigma70_r4_2 15 qreifllryleglsykEIAellgisegtVksrlsRArkk 53
                                   +++++l+  +gl++ EIAe+l++s  t ++ +  A k 
  gi|15669842|ref|NP_248656.1| 10 LKKVIELK-SNGLTIGEIAEELNVSMETARYLVLNAEKL 47
                                  57899995.6********************999888775 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.3e-05     0.013       7      37 ..       6      36 ..       2      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                                  -HHHHGGGGSSTTTT--STTTSSSS---SSS CS
                         HTH_7  7 skndinrvvkLleeGisiskIAkevnisRsT 37
                                  +k+ +  v++L ++G +i +IA+e+n+s +T
  gi|15669842|ref|NP_248656.1|  6 NKELLKKVIELKSNGLTIGEIAEELNVSMET 36
                                  5656788*********************887 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.8e-05     0.018      19      41 ..      19      41 ..       9      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                  TT--HHHHHHHHTS-HHHHHHHH CS
                    Sigma70_r4 19 eglTleEIgerlgiSrerVrqie 41
                                   glT  EI+e+l++S e++r + 
  gi|15669842|ref|NP_248656.1| 19 NGLTIGEIAEELNVSMETARYLV 41
                                  589****************9765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.6e-05     0.016      10      36 ..      13      39 ..       6      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                        HTH_23 10 illllaeGlsvreIAreLgvsrrTvyr 36
                                  ++ l  +Gl++ eIA+eL+vs  T + 
  gi|15669842|ref|NP_248656.1| 13 VIELKSNGLTIGEIAEELNVSMETARY 39
                                  5666667*****************985 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.93   9.3e+02     132     166 ..      18      52 ..      15      68 .. 0.75
   2 ?   12.9   0.1   5.6e-05     0.056     120     155 ..     147     182 ..     120     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.93
                      PRTase_2 132 stGktalnliralqeklprkryvvvslvdwrseed 166
                                   s G t+ +++++l+ ++   ry v++   + +ee+
  gi|15669842|ref|NP_248656.1|  18 SNGLTIGEIAEELNVSMETARYLVLNAEKLLKEEE 52 
                                   56888888999999888889998887777766663 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.6e-05
                      PRTase_2 120 aakelvLvDDEistGktalnliralqeklprkryvv 155
                                   + k+ v++DD +++G+t+ + i++l+e +  k +vv
  gi|15669842|ref|NP_248656.1| 147 NYKRAVIIDDVVTSGSTLKECIKQLKEVCSPKLVVV 182
                                   457789********************9977666555 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   3.1e-05     0.031       9      36 ..      12      39 ..       8      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                                  HHHHHHCTTS-HHHHHHHHTS-HHHHHH CS
                          GerE  9 evLrllaeGksnkeIAeelniSekTVkv 36
                                  +v +l  +G++  eIAeeln+S++T ++
  gi|15669842|ref|NP_248656.1| 12 KVIELKSNGLTIGEIAEELNVSMETARY 39
                                  6888899*****************9765 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1    0.0001       0.1      25      49 ..      22      46 ..      18      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                        HTH_10 25 tlkeLAkelGIskstlsehLrkaes 49
                                  t+ e+A+el++s  t+ + + +ae+
  gi|15669842|ref|NP_248656.1| 22 TIGEIAEELNVSMETARYLVLNAEK 46
                                  899********************98 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012      0.12      11      32 ..      17      38 ..       7      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                      HTH_DeoR 11 qqgklsveelvellgvSeaTiR 32
                                  ++  l++ e++e+l+vS +T+R
  gi|15669842|ref|NP_248656.1| 17 KSNGLTIGEIAEELNVSMETAR 38
                                  456699***************9 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00015      0.15       2      22 ..      21      41 ..      21      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                        HTH_17  2 ltveEaAelLgvsrstvyrli 22
                                  lt+ E+Ae L+vs  t++ l+
  gi|15669842|ref|NP_248656.1| 21 LTIGEIAEELNVSMETARYLV 41
                                  8*****************998 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00012      0.12     139     168 ..       8      37 ..       2      53 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                   Sigma70_ECF 139 eqarlvelrkleGlsveEiAeklgvskrtv 168
                                   e +++v   k +Gl++ EiAe+l+vs  t+
  gi|15669842|ref|NP_248656.1|   8 ELLKKVIELKSNGLTIGEIAEELNVSMETA 37 
                                   566666666779***************996 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00016      0.16     120     157 ..     147     182 ..     116     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                       UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvl 157
                                   + ++++++D v+ +G+++ ++i++Lke  v + k +v+
  gi|15669842|ref|NP_248656.1| 147 NYKRAVIIDDVVTSGSTLKECIKQLKE--VCSPKLVVV 182
                                   456699*********************..444444333 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00035      0.35      36      74 ..      45      85 ..       5      86 .. 0.68
   2 ?   -2.6   0.0         8     8e+03      34      58 ..     127     151 ..     125     153 .. 0.68
   3 ?   -2.4   0.0       7.3   7.3e+03      39      49 ..     164     174 ..     162     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                                  HHHHHHHHHHHHHHHHTT.....-HHHHHHHHHHHHHHHHHHHH CS
                        HSCB_C 36 eerieeleaeleeafekk.....dleaaadllrrlrYlekikee 74
                                  e+ ++e+e++++ +   +     d++++   ++rl+Y+++i  +
  gi|15669842|ref|NP_248656.1| 45 EKLLKEEEKAIKLE---NvdifiDWKNIGSSANRLKYISSIIVD 85
                                  33333333333333...134778****************99766 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8
                                   HHHHHHHHHHHHHHHHHHTT-HHHH CS
                        HSCB_C  34 eveerieeleaeleeafekkdleaa 58 
                                    ++e+ ++++ ++++ f++ ++++a
  gi|15669842|ref|NP_248656.1| 127 HISEEGKKITGSISQNFSAVNYKRA 151
                                   5667777888888888855577665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 7.3
                                   HHHHHHHHHHH CS
                        HSCB_C  39 ieeleaeleea 49 
                                   ++e++++l+e 
  gi|15669842|ref|NP_248656.1| 164 LKECIKQLKEV 174
                                   68899998875 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00015      0.15      11     108 ..      73     167 ..      71     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
               Glyco_tranf_2_3  11 fneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgk.s.ralnealravksd 89 
                                   +n+ +++ +++ ++l++ ++++++vv+v +s    +  +  +a +l++ +++++++++  +  gk +  ++++ ++av+++
  gi|15669842|ref|NP_248656.1|  73 ANRLKYISSIIVDILKSRNIEFDTVVGVSTSGVPIAT-L--VASELGK-ELTIYIPKKHISEEGKkItGSISQNFSAVNYK 149
                                   689999***********9**********999999554.3..3457888.69998887544444442325699********* PP

               Glyco_tranf_2_3  90 lvllvDdDtvvePdtlkrl 108
                                     +++D D+v++  tlk  
  gi|15669842|ref|NP_248656.1| 150 RAVIID-DVVTSGSTLKEC 167
                                   *****8.577777777665 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00039      0.39       1      19 [.      22      40 ..      22      42 .. 0.95
   2 ?   -2.0   0.1       3.2   3.2e+03       9      16 ..     103     110 ..      99     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00039
                                  EHHHHHHHHTTTHHHHHHH CS
                          MerR  1 tIgevAeltGvsprtLRyY 19
                                  tIge+Ae ++vs  t Ry+
  gi|15669842|ref|NP_248656.1| 22 TIGEIAEELNVSMETARYL 40
                                  8**************9996 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.2
                                   HTTTHHHH CS
                          MerR   9 tGvsprtL 16 
                                   +Gv++ tL
  gi|15669842|ref|NP_248656.1| 103 SGVPIATL 110
                                   69999998 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.5    0.0041       4.1      23      65 ..      11      55 ..       4      64 .. 0.77
   2 ?    2.4   0.0      0.24   2.4e+02      36      57 ..     153     174 ..     140     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0041
                                  HHHH..HHSEEEHHHHHHHCT--HHHHHHHHHHHHHHCHCCT-EE CS
                           Mga 23 kflf..eeeevsieelaqelyiSestlkrkikelnklLkefdlel 65
                                  k ++  +++ ++i e+a+el +S  t+   + + +klLke +  +
  gi|15669842|ref|NP_248656.1| 11 KKVIelKSNGLTIGEIAEELNVSMETARYLVLNAEKLLKEEEKAI 55
                                  555444788899**************************9654444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.24
                                   HHHHCT--HHHHHHHHHHHHHH CS
                           Mga  36 laqelyiSestlkrkikelnkl 57 
                                   +++ ++ S stlk  ik+l+++
  gi|15669842|ref|NP_248656.1| 153 IIDDVVTSGSTLKECIKQLKEV 174
                                   566778899***********97 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00042      0.42       4      30 ..      12      38 ..      11      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                        HTH_28  4 eiikllaaGhsvreaArelgisrrtvy 30
                                  ++i+l  +G ++ e+A+el++s +t +
  gi|15669842|ref|NP_248656.1| 12 KVIELKSNGLTIGEIAEELNVSMETAR 38
                                  6888888999***********988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1565.06
//
Query:       gi|15669843|ref|NP_248657.1|  [L=96]
Description: DNA binding protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-13   49.5   3.3    3.7e-13   49.5   3.3    1.5  2  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    5.6e-05   23.5   0.8    5.6e-05   23.5   0.8    1.6  2  Histone        Core histone H2A/H2B/H3/H4
     0.0001   22.4   1.9    0.00012   22.2   1.9    1.1  1  DUF1931        Domain of unknown function (DUF1931)
     0.0048   17.0   0.4      0.006   16.7   0.4    1.3  1  CENP-T_C       Centromere kinetochore component CENP-T histon
  ------ inclusion threshold ------
      0.011   15.6   0.2      0.021   14.7   0.0    1.5  2  MerR_2         MerR HTH family regulatory protein
      0.012   16.3   2.1      0.014   16.1   1.0    1.6  2  PBECR1         phage-Barnase-EndoU-ColicinE5/D-RelE like nucl
      0.019   15.3   0.3      0.026   14.9   0.3    1.3  1  CENP-S         CENP-S protein
      0.061   13.5   3.2      0.092   12.9   2.8    1.4  1  MRPL52         Mitoribosomal protein mL52
      0.077   12.8   0.5      0.093   12.5   0.5    1.1  1  DUF294_C       Putative nucleotidyltransferase substrate bind
      0.082   13.0   1.0        1.4    9.1   1.0    2.2  1  TIP49_C        TIP49 AAA-lid domain


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   3.3   2.1e-16   3.7e-13       3      64 ..       2      62 ..       1      62 [. 0.96
   2 ?   -2.0   0.1       2.5   4.5e+03      10      20 ..      70      80 ..      69      95 .. 0.54

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 2.1e-16
                                  XXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHH CS
                 CBFD_NFYB_HMF  3 LPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklA 64
                                  LP+a+vk+Imk+  d + i+ +A + + +++ee i+  ++ A + + ke+rKtika +ik++
  gi|15669843|ref|NP_248657.1|  2 LPKATVKRIMKQHTDFN-ISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIKQC 62
                                  9************6665.******************************************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                                  HHHHCCTTXS- CS
                 CBFD_NFYB_HMF 10 kImksdpdark 20
                                  kIm  ++ + k
  gi|15669843|ref|NP_248657.1| 70 KIMELSERTDK 80
                                  66655544444 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.8   3.1e-08   5.6e-05      71     125 ..       7      60 ..       3      62 .. 0.95
   2 ?   -1.0   0.0       1.2   2.1e+03      69      82 ..      66      80 ..      65      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.1e-08
                                   HHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHH CS
                       Histone  71 vreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiq 125
                                   v+ i+k + +d+ isaeav+ l  +lE ++   +e A+  a++  R+Ti ++Di+
  gi|15669843|ref|NP_248657.1|   7 VKRIMK-QHTDFNISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIK 60 
                                   788998.999********************************************7 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                                  HHHHHHH..TTSSSX CS
                       Histone 69 Rvvreivk.sekedl 82
                                  R+ r+i++ se++d+
  gi|15669843|ref|NP_248657.1| 66 RLKRKIMElSERTDK 80
                                  778888887666655 PP

>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   1.9   6.5e-08   0.00012       2      66 ..       8      74 ..       7      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.5e-08
                                  HHHHHHHHS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HH..HHHHHHHH CS
                       DUF1931  2 erlfreaagLdvdkedlkrisdfVekklydLllvaeenAkangrdviepaDLPiTkg..lqesireF 66
                                  +r++++  + ++  e ++++ +++e++++   +vae+nA+++gr++i+ +D+    +  l+++i e 
  gi|15669843|ref|NP_248657.1|  8 KRIMKQHTDFNISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIKQCDDerLKRKIMEL 74
                                  79*************************************************9765443355555555 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.4   3.3e-06     0.006       8      71 ..       2      60 ..       1      93 [. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.3e-06
                      CENP-T_C  8 lPaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvi 71
                                  lP+a+vk++ k+      +  ++++ea++ l +++++ ++  +e  e  a+  gRKti++ D+ 
  gi|15669843|ref|NP_248657.1|  2 LPKATVKRIMKQH-----TDFNISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIK 60
                                  8999999998877.....678*******************999999****************86 PP

>> MerR_2  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.1e-05     0.021      44      80 ..       6      42 ..       4      45 .. 0.93
   2 ?   -3.0   0.0       3.7   6.7e+03      79      82 ..      71      74 ..      65      88 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                        MerR_2 44 rlekavRLqrDLeinleGiavildLLdrieqLqrele 80
                                   ++++++ + D++i+ e+++   ++L++i + + e++
  gi|15669843|ref|NP_248657.1|  6 TVKRIMKQHTDFNISAEAVDELCNMLEEIIKITTEVA 42
                                  589***************************9999987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.7
                        MerR_2 79 lesL 82
                                  + +L
  gi|15669843|ref|NP_248657.1| 71 IMEL 74
                                  3322 PP

>> PBECR1  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   1.0   7.7e-06     0.014      28      71 ..       7      50 ..       3      63 .. 0.81
   2 ?   -0.6   0.1       1.2   2.1e+03      47      59 ..      68      80 ..      48      94 .. 0.47

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.7e-06
                        PBECR1 28 Lahilekhledfkefkekaeklinkleeiiekgk.vkeeeevnti 71
                                  +++i+++h+ df+ ++e +++l n leeii+  + v e++ +++ 
  gi|15669843|ref|NP_248657.1|  7 VKRIMKQHT-DFNISAEAVDELCNMLEEIIKITTeVAEQNARKEG 50
                                  689*****5.**999999*************98878887766554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                        PBECR1 47 eklinkleeiiek 59
                                  ++ i +l+e  +k
  gi|15669843|ref|NP_248657.1| 68 KRKIMELSERTDK 80
                                  2333333333322 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.3   1.5e-05     0.026      13      67 ..       9      60 ..       4      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                        CENP-S 13 kiveeeaaekeveatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvl 67
                                  +i+   +++++++++ +++  l ++  + ++ +++  e  a+  +R+ti++ D++
  gi|15669843|ref|NP_248657.1|  9 RIM---KQHTDFNISAEAVDELCNMLEEIIKITTEVAEQNARKEGRKTIKARDIK 60
                                  333...4568899****************************************98 PP

>> MRPL52  Mitoribosomal protein mL52
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.8   5.1e-05     0.092      50      91 ..      30      71 ..      24      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-05
                        MRPL52 50 lakkivkllsEideaeerykkkqeeeeeeeqkiiesklkpKg 91
                                  + + i+k++ E+ e+++r + ++  +++++++  +++lk K+
  gi|15669843|ref|NP_248657.1| 30 MLEEIIKITTEVAEQNARKEGRKTIKARDIKQCDDERLKRKI 71
                                  6689************************************97 PP

>> DUF294_C  Putative nucleotidyltransferase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   5.2e-05     0.093      63     131 ..       5      71 ..       2      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-05
                      DUF294_C  63 nTleRlkalaeagvlsaelaedlleayefllrlrlrhqleaieageepdnyvdpeeLsklerdlLkeal 131
                                    T++R+ + +    +sae +++l++ +e ++++ ++  +++ +a +e  + ++ +++++ + ++Lk+ +
  gi|15669843|ref|NP_248657.1|   5 ATVKRIMKQHTDFNISAEAVDELCNMLEEIIKITTE--VAEQNARKEGRKTIKARDIKQCDDERLKRKI 71 
                                   79****************************998877..555567777789***************9865 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.0   0.00076       1.4      38      61 ..      40      63 ..       8      64 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00076
                       TIP49_C 38 tpasilakkrkkkevevedveeve 61
                                  ++a++ a+k+++k+++ +d+++++
  gi|15669843|ref|NP_248657.1| 40 EVAEQNARKEGRKTIKARDIKQCD 63
                                  579999***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1761  (0.0982208); expected 358.6 (0.02)
Passed bias filter:                      731  (0.0407719); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 640.30
//
Query:       gi|15669844|ref|NP_248658.1|  [L=230]
Description: phosphoribosylformylglycinamidine synthase I [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-47  159.7   0.0      9e-47  159.3   0.0    1.2  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
      3e-06   27.2   0.0    5.2e-06   26.4   0.0    1.4  1  DJ-1_PfpI      DJ-1/PfpI family
      4e-05   23.5   0.1    4.9e-05   23.2   0.1    1.3  1  GATase         Glutamine amidotransferase class-I
    0.00011   21.8   0.0     0.0002   21.0   0.0    1.4  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.032   14.1   0.0    1.5  1  SNO            SNO glutamine amidotransferase family
      0.027   14.2   0.0      0.049   13.4   0.0    1.4  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.3   0.0     3e-50     9e-47       3     236 ..       2     213 ..       1     227 [. 0.92

  Alignments for each domain:
  == domain 1  score: 159.3 bits;  conditional E-value: 3e-50
                      GATase_5   3 kvailreeGvngeyemaaafekaGfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklreale 83 
                                   k+a+  + G+n++ ++ +a++ aG e + v++++     ++ld++++ ++pGGfsygD l +g++ a+     + + + l+
  gi|15669844|ref|NP_248658.1|   2 KIAVTKFLGTNCDLDVCHAVKLAGGEPELVFFTQ-----ENLDSYKGAVIPGGFSYGDYLRAGAISAR-----TPIIKGLK 72 
                                   89****************************9954.....59**********************99984.....56789999 PP

                      GATase_5  84 kflnredtlaLGiCnGfqlLvklglvpggeieeaeksptltrNksgrfesrlvsv.vvsekspsvfl.kgmeglslpvahG 162
                                   k++++ ++ +LGiCnG q+  + g+  g          tlt+N   +f++++v++ v ++k+p     k++e+l++p+ah+
  gi|15669844|ref|NP_248658.1|  73 KMVEE-GKPVLGICNGAQIGLEAGFSKG----------TLTNNLNAKFICKWVYIrVENNKTPFTQYyKKGEVLKIPIAHA 142
                                   99999.*************999999888..........9****************999999**99988************* PP

                      GATase_5 163 eGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvlalmpHpervveavqks 236
                                   eGrf + ++e+l+ +++n+ ++++Y+de+g++tee  +NPNgS ++iag+++++  ++ lmpHper++e++  s
  gi|15669844|ref|NP_248658.1| 143 EGRFYA-DDETLDYMYKNNMIVFKYCDETGEVTEE--ANPNGSIDNIAGVCNENQNCVLLMPHPERASEKILGS 213
                                   ******.999**********************996..7*****************************9998766 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.7e-09   5.2e-06      58     115 ..      37      99 ..      12     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.7e-09
                                   TCCG-SEEEE--BHHHHHHHHTSH.....HHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTT CS
                     DJ-1_PfpI  58 kaaeyDalvlpGGragperlrene.....kvvelvkefaekgklvaaICagpqlLaaagvlkg 115
                                   + ++y   v+pGG +  ++lr+ +      +++ +k+++e+gk+v  IC g+q+ ++ag  kg
  gi|15669844|ref|NP_248658.1|  37 NLDSYKGAVIPGGFSYGDYLRAGAisartPIIKGLKKMVEEGKPVLGICNGAQIGLEAGFSKG 99 
                                   567999************9997543333399***********************999998776 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   1.6e-08   4.9e-05      39      87 ..      37      94 ..      16     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.6e-08
                                  THHSTSEEEEEEESSCTT.........TTTHHHHHHHHCTSTS-EEEETHHHHHHHHH CS
                        GATase 39 llknpdgilvsgGpgspg.........vegkieaikearenkiPiLGICLGmQllaie 87
                                  +l++++g +++gG+ +           ++  i+ +k++ e+++P+LGIC G Q+ +++
  gi|15669844|ref|NP_248658.1| 37 NLDSYKGAVIPGGFSYGDylragaisaRTPIIKGLKKMVEEGKPVLGICNGAQIGLEA 94
                                  36789*********99989966776665666666788888*************86655 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.7e-08    0.0002      32      87 ..      33      90 ..      12      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.7e-08
                      GATase_3 32 lkdeslgedadlvilpGgkdt...iqdlallresgldeaikeaaeaggpvlgiCGGlqm 87
                                  +++e+l++ +   ++pGg+++   +++ a+++++ + + +k+++e+g+pvlgiC G q+
  gi|15669844|ref|NP_248658.1| 33 FTQENLDS-YKGAVIPGGFSYgdyLRAGAISARTPIIKGLKKMVEEGKPVLGICNGAQI 90
                                  34789966.9********976111667788899999********************996 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.1e-05     0.032      13      78 ..      19      88 ..      11     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                  HHHHHTTSEE.EEE-SGGGGCC-SEEEE-SS-HHH....HHHHHHHTT-HHHHHHHHHTT.--EEEETHHH CS
                           SNO 13 eaikkclaen.ktvkrkedlaevdaliiPGGesta....mskliertglyedllefvknsekvvlGtCaGl 78
                                  +a+k ++ e  ++  ++e+l+   + +iPGG s       + +  rt +++ l+++v+++ k+vlG C G 
  gi|15669844|ref|NP_248658.1| 19 HAVKLAGGEPeLVFFTQENLDSYKGAVIPGGFSYGdylrAGAISARTPIIKGLKKMVEEG-KPVLGICNGA 88
                                  56666666652555789*************99864222267899***************9.*******995 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.7e-05     0.049      98     117 ..      71      90 ..      64     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                 Peptidase_C26  98 iraalergvPilgiCrGlql 117
                                   +++++e+g+P+lgiC G q+
  gi|15669844|ref|NP_248658.1|  71 LKKMVEEGKPVLGICNGAQI 90 
                                   57899**************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1538.33
//
Query:       gi|15669845|ref|NP_248659.1|  [L=387]
Description: hypothetical protein MJ_1649 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-16   59.5   0.1    3.6e-16   59.2   0.1    1.1  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
    8.9e-13   48.4   0.7    1.4e-12   47.8   0.7    1.3  1  Met_10           Met-10+ like-protein
    1.2e-12   47.9   0.1      2e-12   47.1   0.1    1.4  1  Methyltransf_31  Methyltransferase domain
      8e-12   45.2   0.1    2.6e-11   43.5   0.0    1.8  2  Cons_hypoth95    Conserved hypothetical protein 95
      2e-11   44.4   0.1    5.7e-11   43.0   0.0    1.8  1  Methyltransf_25  Methyltransferase domain
    2.2e-09   37.1   0.0    3.6e-09   36.5   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.4e-09   37.0   0.0    5.3e-09   35.9   0.0    1.6  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    5.6e-09   35.8   0.0    9.7e-09   35.0   0.0    1.3  1  MTS              Methyltransferase small domain
    8.2e-09   35.8   0.0    2.5e-08   34.2   0.0    1.8  1  FtsJ             FtsJ-like methyltransferase
    7.9e-08   32.2   0.0    1.9e-07   31.0   0.0    1.6  1  PUA              PUA domain
    3.8e-07   30.7   0.0    8.2e-07   29.6   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    1.6e-06   28.1   0.0    2.8e-06   27.3   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    4.2e-06   26.5   0.1    1.4e-05   24.8   0.0    1.9  2  PUA_3            PUA-like domain
    7.1e-06   26.0   0.1    2.1e-05   24.5   0.0    1.8  2  Methyltransf_18  Methyltransferase domain
    8.3e-06   25.3   0.0    1.6e-05   24.4   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
    8.8e-06   25.2   0.0      2e-05   24.0   0.0    1.7  1  N6_Mtase         N-6 DNA Methylase
    1.3e-05   24.6   0.4    2.3e-05   23.7   0.1    1.6  2  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    6.8e-05   22.3   0.0    0.00013   21.4   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    9.3e-05   23.1   0.0    0.00019   22.1   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    0.00029   20.1   0.1    0.00062   19.0   0.1    1.5  1  Methyltransf_3   O-methyltransferase
    0.00058   19.6   0.1     0.0023   17.6   0.0    2.0  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0014   18.0   0.0     0.0025   17.2   0.0    1.3  1  Methyltransf_10  RNA methyltransferase
     0.0059   15.6   0.7      0.011   14.7   0.1    1.8  2  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
     0.0092   15.7   0.1      0.029   14.0   0.1    1.8  1  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.035   13.9   0.0    1.6  1  N6-adenineMlase  Probable N6-adenine methyltransferase
      0.025   14.0   0.1      0.078   12.4   0.0    1.8  2  Methyltransf_4   Putative methyltransferase
      0.076   13.0   0.0       0.15   12.0   0.0    1.5  1  ADH_zinc_N       Zinc-binding dehydrogenase
        0.1   12.2   0.0        0.2   11.3   0.0    1.5  1  TPMT             Thiopurine S-methyltransferase (TPMT)


Domain annotation for each model (and alignments):
>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.1   5.7e-19   3.6e-16      76     209 ..     165     299 ..     126     346 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 5.7e-19
               Methyltrans_SAM  76 evlvgelde.spvvvesglkyqldigrnqnfglfldmrlgrdwvqenakd.knvlnlfaytcgfsvaaiaggaskvvnvdm 154
                                   + ++g+ ++ + v++e   k+++++ r  ++g+fld r  r ++++  k+  +vl++ +yt gfsv a   ga +vv vd+
  gi|15669845|ref|NP_248659.1| 165 DKIFGDKNKfETVIKEGDAKFKVNV-RGHKTGFFLDQRENRLYLEKFIKEgDRVLDICCYTGGFSVHAAIRGA-EVVGVDL 243
                                   5567777762456677779****98.8899**************998875379*************9988888.599**** PP

               Methyltrans_SAM 155 argslnkgrdnhrlnghdlrrvsflgydifkswgk.ikksgpydlviidppsfqkg 209
                                   ++ +l+   +n  ln+   +r +f+  + f      i  + ++d+vi+dpp+f + 
  gi|15669845|ref|NP_248659.1| 244 SKKALKLAEENIELNNIPKDRYEFIEGNAFEVMKEmIEDKEKFDVVILDPPAFTQT 299
                                   *************************9999987754278999***********9865 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.7   2.1e-15   1.4e-12       5     177 ..     120     294 ..     116     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 2.1e-15
                                   EETTEEEEEB-TTSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEE.S-.SEEEEEETTEEEEEET..TTS- CS
                        Met_10   5 iiGdvvilnlreelkeykkvigevildktkvktvlrkvsevegefRtfelevlaG.sdstetihkEngcrfklDv..skvy 82 
                                     G + ++ +    key k+i++++++  +++t++ k+++ +ge   +    + G +++ et+ kE   +fk+ v   k  
  gi|15669845|ref|NP_248659.1| 120 ELGAMQLMSK-LIEKEYLKDIVDILFELSDLETIYVKRGK-KGER-IR--DKIFGdKNKFETVIKEGDAKFKVNVrgHKTG 195
                                   5555544443.345789**********************9.7763.22..357776899**************99445899 PP

                                   --GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-.TTCEEEEES-GGG CS
                        Met_10  83 fsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkv.ekvvkpileDgre 162
                                   f     + r  l k ++eg++V+d+    G f++ +a   ++ +v+++dl  ++ k+ +eni+lN++ +++ + i++ + e
  gi|15669845|ref|NP_248659.1| 196 FFLDQRENRLYLEKFIKEGDRVLDICCYTGGFSVHAAI--RGAEVVGVDLSKKALKLAEENIELNNIpKDRYEFIEGNAFE 274
                                   99999999999**************************9..999***********************944567778888778 PP

                                   ---.....TT-EEEEEE--T CS
                        Met_10 163 vir.....eqladrvvmnlp 177
                                   v++     ++++d v+++ p
  gi|15669845|ref|NP_248659.1| 275 VMKemiedKEKFDVVILDPP 294
                                   87733334445555666555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.1   3.2e-15     2e-12       2      88 ..     212     304 ..     211     377 .. 0.72

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 3.2e-15
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld..nveFeqgdiee.leklled.ekfDli 78 
                                   ++g rvlD+ C tG ++  +a   + +aevvG+D s++a++lA+en + +++   ++eF +g+++e +++ +ed ekfD++
  gi|15669845|ref|NP_248659.1| 212 KEGDRVLDICCYTGGFSVHAA---IRGAEVVGVDLSKKALKLAEENIELNNIPkdRYEFIEGNAFEvMKEMIEDkEKFDVV 289
                                   6789*****************...679*********************9999777***********877666666****** PP

               Methyltransf_31  79 lsnevl.....nala 88 
                                   + + +      ++++
  gi|15669845|ref|NP_248659.1| 290 ILDPPAftqteDDIK 304
                                   *99444332222222 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.9   1.9e+03     130     176 ..     124     171 ..     112     174 .. 0.74
   2 !   43.5   0.0   4.1e-14   2.6e-11      41     160 ..     213     340 ..     203     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.9
                                   HHHHHHHHHTT-EEEEEEEEEEEECCSSS.--.-TTEEEEEEEEETTE CS
                 Cons_hypoth95 130 eevlelleekkllkenalvvvetekekel.pespenlelvkekkyget 176
                                    +++++l ek+ lk+ + +++e +  +++ ++  ++ e +++k +g++
  gi|15669845|ref|NP_248659.1| 124 MQLMSKLIEKEYLKDIVDILFELSDLETIyVKRGKKGERIRDKIFGDK 171
                                   567888888999999999999976655541566777888888888865 PP

  == domain 2  score: 43.5 bits;  conditional E-value: 4.1e-14
                                   CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T.TTEEEEES-HHHHCTS--SS-EEEEEEE- CS
                 Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee.etaelkedaleallklakkkeefdivflD 120
                                   eg rvLD+++ +G+ ++ A+ Rga ++v v+ +k+a+k+ +en+e  ++ + + + +  +a+e +++  + ke+fd+v lD
  gi|15669845|ref|NP_248659.1| 213 EGDRVLDICCYTGGFSVHAAIRGA-EVVGVDLSKKALKLAEENIELNNIPKdRYEFIEGNAFEVMKEMIEDKEKFDVVILD 292
                                   5789*******************5.6899********************9989999999999******************* PP

                                   -S.SSTTCH..HHHHHHHHHTT-EE....EEEEEEEEEECC..SSS-- CS
                 Cons_hypoth95 121 PP.yakell.ieevlelleekkllk....enalvvveteke..kelpe 160
                                   PP + + +  i+++l++ ++ + l     ++ +v++  +++  ke+++
  gi|15669845|ref|NP_248659.1| 293 PPaFTQTEDdIKNALRAYASLNYLGiklaKRIFVTCSCSHHvdKEMFK 340
                                   **6655544689999988888877655556667666544331155555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   8.8e-14   5.7e-11       1      90 [.     217     311 ..     217     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 8.8e-14
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBC....CGBSSSTTTEEEEEEEST. CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgda....edlpfedgsfDlvvssga. 73 
                                   vLd++c tG ++ ++a r+  a+v+gvD+s+++l+ a+e++e +++   + ef++g+a    +++ +++++fD+v++    
  gi|15669845|ref|NP_248659.1| 217 VLDICCYTGGFSVHAAIRG--AEVVGVDLSKKALKLAEENIELNNIpkdRYEFIEGNAfevmKEMIEDKEKFDVVILD-Pp 294
                                   9***************995..********************999999***********533333447999*******4.43 PP

                                   GGGSSHHHHHHHHHHHH CS
               Methyltransf_25  74 lhhlsdedlekalkeia 90 
                                       +++d+++al+  a
  gi|15669845|ref|NP_248659.1| 295 AFTQTEDDIKNALRAYA 311
                                   44456788888888765 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   5.6e-12   3.6e-09     155     231 ..     207     290 ..     205     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 5.6e-12
                          PrmA 155 leklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klev......alseellk.eeka 227
                                   lek++keg++vlD+ + +G  ++ aa  ga +vv+vD+ + A+k a+eN+elN++ + + e        + +e+++ +ek+
  gi|15669845|ref|NP_248659.1| 207 LEKFIKEGDRVLDICCYTGGFSVHAAIRGA-EVVGVDLSKKALKLAEENIELNNIPKdRYEFiegnafEVMKEMIEdKEKF 286
                                   9************************99887.699*********************9877766332222134444436899* PP

                          PrmA 228 dviv 231
                                   dv++
  gi|15669845|ref|NP_248659.1| 287 DVVI 290
                                   *997 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   8.3e-12   5.3e-09       3      81 ..     216     295 ..     214     316 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 8.3e-12
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgv.sdkitlvlgdvfellaklklekikvdlvflSpPw 81 
                                    +lD+++ +GG +++ a  + +v++++ +++ l++a++N e+ ++ +d+  ++ g+ fe+++++ ++k k+d+v+l pP 
  gi|15669845|ref|NP_248659.1| 216 RVLDICCYTGGFSVHAAIRGAEVVGVDLSKKALKLAEENIELNNIpKDRYEFIEGNAFEVMKEMIEDKEKFDVVILDPPA 295
                                   69*******************************************99*******************************95 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   1.5e-11   9.7e-09      22     114 ..     205     302 ..     198     314 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.5e-11
                                   HHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC...EEEEE-STTTTST..... CS
                           MTS  22 lLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle...vevvasdvleeve..... 94 
                                   l le++ k + ++vlD++c +G  ++++a +  e  v+ vd +++Al++a+en+e n++     e+++ +++e ++     
  gi|15669845|ref|NP_248659.1| 205 LYLEKFIK-EGDRVLDICCYTGGFSVHAAIRGAE--VVGVDLSKKALKLAEENIELNNIPkdrYEFIEGNAFEVMKemied 282
                                   55666666.6778************999998777..9**********************9999888888877665522234 PP

                                   TS-EEEEEE---STTTCHCH CS
                           MTS  95 ekkfdlivsNPPfhagkate 114
                                   ++kfd+++  PP  ++++ +
  gi|15669845|ref|NP_248659.1| 283 KEKFDVVILDPPAFTQTEDD 302
                                   589*********77776633 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   3.9e-11   2.5e-08      17     121 ..     209     328 ..     197     355 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 3.9e-11
                                   T-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.............HHHTTEEEECS-CCCSSHHHHHCHCHH CS
                          FtsJ  17 klfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.............aplpgvttiqgditdpetiekikeals 84 
                                   k++k+g++v+D+++ +Gg+s  ++ r g  + vv+vDl +               p ++ ++i+g+ ++  ++ +i++   
  gi|15669845|ref|NP_248659.1| 209 KFIKEGDRVLDICCYTGGFSVHAAIR-G--AEVVGVDLSKKalklaeenielnnIPKDRYEFIEGNAFEVMKE-MIED--- 282
                                   45789*********************.6..69******87779999888777444558*********988655.4776... PP

                                   HSSEEEEEE--S-SS-CHHHHHHHHH.........CCCCHHHHCCH CS
                          FtsJ  85 erkvdlvvsDgapdvsgvhdldeylq.........sqLllaalela 121
                                   ++k+d+v+ D   +++   d++++l+         ++L+++ + ++
  gi|15669845|ref|NP_248659.1| 283 KEKFDVVILDPPAFTQTEDDIKNALRayaslnylgIKLAKRIFVTC 328
                                   579*******998998888888877756555555555555555544 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   2.9e-10   1.9e-07       2      60 ..       7      65 ..       6      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.9e-10
                                  EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHH CS
                           PUA  2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseela 60
                                  ++ +d+ A++ +++ + L     ++ +gd+ ++++++ ++ +g++va++l n +s  l+
  gi|15669845|ref|NP_248659.1|  7 KLEIDRRAYNSIKNFSRLVYTKAIKNRGDLPKKEEIVTLTYNGKFVAKALYNPKSVILK 65
                                  689**************************************************998876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.3e-09   8.2e-07       1      69 [.     218     293 ..     218     312 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.3e-09
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-...EEEETTEECCCT.S..S-T.T-EEEEEEES CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl...kvefvvadaekl.p..fed.nsfDlvvsse 69 
                                   Ld+ c tG ++ + a rga+vvgvDlsk++lkla+e+++ +++   + ef++++a ++ +  +ed ++fD+v++  
  gi|15669845|ref|NP_248659.1| 218 LDICCYTGGFSVHAAIRGAEVVGVDLSKKALKLAEENIELNNIpkdRYEFIEGNAFEVmKemIEDkEKFDVVILDP 293
                                   899999**********************************999***99*******985335677768*****9864 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   4.3e-09   2.8e-06      12      87 ..     203     290 ..     195     292 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.3e-09
               Methyltransf_23  12 klerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..............kakkaqkdqfdeqeaae 78 
                                   +++ l +  ++g rvLdi c tG ++ +++ +g++v+gvDls +a ++ae               +  + ++ +   e  e
  gi|15669845|ref|NP_248659.1| 203 NRLYLEKFIKEGDRVLDICCYTGGFSVHAAIRGAEVVGVDLSKKALKLAEenielnnipkdryeFIEGNAFEVM--KEMIE 281
                                   5555555578999**********************************999888777777766665555555555..34445 PP

               Methyltransf_23  79 pqgkfdlIv 87 
                                   +++kfd+++
  gi|15669845|ref|NP_248659.1| 282 DKEKFDVVI 290
                                   677899887 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.2e-08   1.4e-05       4      63 ..      11      68 ..       8      69 .. 0.90
   2 ?   -2.5   0.0       7.4   4.7e+03      11      21 ..      96     106 ..      94     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.2e-08
                         PUA_3  4 kkkaekrlrqGhPwvfsneiasvegeledGdvVdvfsekgkflGtGyynpqskiavRils 63
                                   ++a +++++   +v+ ++i+++ + ++  ++V ++  +gkf+++++ynp+s  +++il+
  gi|15669845|ref|NP_248659.1| 11 DRRAYNSIKNFSRLVYTKAIKNRGDLPKKEEIVTLTY-NGKFVAKALYNPKS-VILKILT 68
                                  6678889******************99**********.**************.7777776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.4
                         PUA_3  11 lrqGhPwvfsn 21 
                                   +++ + w++++
  gi|15669845|ref|NP_248659.1|  96 YKNTYRWIYAE 106
                                   688999***86 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   3.3e-08   2.1e-05       9      81 ..     208     279 ..     202     291 .. 0.85
   2 ?   -2.7   0.0         8   5.1e+03     120     143 ..     335     358 ..     322     360 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.3e-08
               Methyltransf_18   9 aslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagl.edkievrlsdGleklkee 81 
                                    +++++g+rv+Di++  g  +++++ +g   +v+ +D+++++l+ a+enie +++ +d+ e++ ++ +e++ke 
  gi|15669845|ref|NP_248659.1| 208 EKFIKEGDRVLDICCYTGGFSVHAAIRGA--EVVGVDLSKKALKLAEENIELNNIpKDRYEFIEGNAFEVMKEM 279
                                   689*********************97775..6********************999899**********998743 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8
               Methyltransf_18 120 eaeelRkylvengfkiedEelvke 143
                                   ++e ++++++++ f+ ++E ++ +
  gi|15669845|ref|NP_248659.1| 335 DKEMFKRTVISSAFRAKKELIMID 358
                                   667889999999999999988766 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.5e-08   1.6e-05      54     112 ..     206     262 ..     199     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.5e-08
                                   HHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS CS
                          CMAS  54 ileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldler 112
                                    lek  +k+G+++Ldi c  G+  ++a+ r +++vvg+ lSk+  kla+++++  ++ +
  gi|15669845|ref|NP_248659.1| 206 YLEKF-IKEGDRVLDICCYTGGFSVHAAIR-GAEVVGVDLSKKALKLAEENIELNNIPK 262
                                   55554.89**********************.*******************998766554 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   3.2e-08     2e-05      46     145 ..     213     303 ..     183     315 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.2e-08
                      N6_Mtase  46 sgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfe..kdk 124
                                   +g  v+D +c +gg+ v+a+          +  ++ G+++ +++ +La+ N+ l +i +++ +   g+++e  k++  +++
  gi|15669845|ref|NP_248659.1| 213 EGDRVLDICCYTGGFSVHAAI---------RGAEVVGVDLSKKALKLAEENIELNNIPKDRYEFIEGNAFEVMKEMieDKE 284
                                   44559*********9887754.........57899***********************************9887776699* PP

                      N6_Mtase 125 kfdvvvaNpp.fnqkewkektl 145
                                   kfdvv+  pp f q+   e+++
  gi|15669845|ref|NP_248659.1| 285 KFDVVILDPPaFTQT---EDDI 303
                                   ********9955555...4444 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.7     3e+03     301     323 ..      60      81 ..      39      91 .. 0.77
   2 !   23.7   0.1   3.7e-08   2.3e-05      76     128 ..     237     293 ..     214     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.7
                                   -HHHHHHHHHHHHHHS--SS-EE CS
                           TRM 301 kkrvkklLklikeElldaplyyd 323
                                   k  ++k+L++ +eE +d  ++y+
  gi|15669845|ref|NP_248659.1|  60 KSVILKILTTEDEE-IDYDFFYK 81 
                                   56688999988888.99999987 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 3.7e-08
                                   EEEEE-S-HHHHHHHHHHHHHTT--.GGEEEE-S-HHHHHC...--SS-EEEEEE-- CS
                           TRM  76 evlaNDisekAvelikeNvklneve.eivvineddAnvlla...ekkkrfdviDlDP 128
                                   ev+  D+s+kA++l +eN++ln++  +++++ e++A  +++   e k++fdv+ lDP
  gi|15669845|ref|NP_248659.1| 237 EVVGVDLSKKALKLAEENIELNNIPkDRYEFIEGNAFEVMKemiEDKEKFDVVILDP 293
                                   67788*******************9679999999**9999988899**********9 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0     2e-07   0.00013      46     121 ..     212     290 ..     201     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2e-07
                                   --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHH..HHTSSTEEEEE--TTT-T....TS-T-EEEE CS
               Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklk..eegkinieflqanaeeLp....feddsfDvv 120
                                   k+g +vlD+++ tg ++++   ++ +  +vv++D++++ Lk +e+ ++  +  k + ef+ +na e+     ++++ fDvv
  gi|15669845|ref|NP_248659.1| 212 KEGDRVLDICCYTGGFSVH--AAI-RGAEVVGVDLSKKALKLAEENIElnNIPKDRYEFIEGNAFEVMkemiEDKEKFDVV 289
                                   899***********87654..333.4569***************987621555669*******976541111455888887 PP

                                   E CS
               Ubie_methyltran 121 t 121
                                    
  gi|15669845|ref|NP_248659.1| 290 I 290
                                   5 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     3e-07   0.00019       1      73 [.     218     292 ..     218     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3e-07
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.....ssfDlvvas 73 
                                   L+i c tG ++ + + +  ++e++gvD+s++a+ + +e+  + +n   +++e+ + ++++  ++     ++fD+v++ 
  gi|15669845|ref|NP_248659.1| 218 LDICCYTGGFSVHAAIR--GAEVVGVDLSKKAL-KLAEENIELNNIPKDRYEFIEGNAFEVMKEmiedkEKFDVVILD 292
                                   8999****999999877..**************.888888888889999999999999988888999********965 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   9.6e-07   0.00062      46     130 ..     212     292 ..     198     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.6e-07
                                   HT--EEEEE--TTS.HHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-.GGGEEEEES-HHHHHHHHHTSSS---E CS
                Methyltransf_3  46 vnakrvleiGvftG.yslLatalalPeDGkilaididreayeialkfiqkagv.aekieliegdalkvLeelvkdkklpef 124
                                    +  rvl+i  +tG +s+ a a+      +++ +d  ++a ++a + i+   + +++ e+ieg+a +v++e+++dk+  +f
  gi|15669845|ref|NP_248659.1| 212 KEGDRVLDICCYTGgFSVHA-AI---RGAEVVGVDLSKKALKLAEENIELNNIpKDRYEFIEGNAFEVMKEMIEDKE--KF 286
                                   567799******97366544.44...3568*******************998835689******************5..9* PP

                                   EEEEE- CS
                Methyltransf_3 125 DfifvD 130
                                   D++ +D
  gi|15669845|ref|NP_248659.1| 287 DVVILD 292
                                   *99988 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.6e-06    0.0023       7      89 ..     212     295 ..     207     364 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.6e-06
                                   -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHH..HTT--SEEEEES-CTCCHHHHCC....EEEE CS
               Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlk..rLgvtntivleaDarkidkvlgg..elfDri 83 
                                   +e++++lD+c+  Gg   h a +    ++vv vd +k+ lk  +en++   ++      +e+ a ++ k + +  e+fD +
  gi|15669845|ref|NP_248659.1| 212 KEGDRVLDICCYTGGFSVHAA-I--RGAEVVGVDLSKKALKLAEENIElnNIPKDRYEFIEGNAFEVMKEMIEdkEKFDVV 289
                                   799************999965.4..6899*****************862266667889999999888777766689***** PP

                                   EEEE-- CS
               Methyltr_RsmB-F  84 LlDaPC 89 
                                   +lD P 
  gi|15669845|ref|NP_248659.1| 290 ILDPPA 295
                                   ***995 PP

>> Methyltransf_10  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.9e-06    0.0025     123     202 ..     232     310 ..     211     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.9e-06
                                   HHH--EEEEEES-HHHHHHHHHHHHHT.T-TTTEEEEE--TT-SCCHHSSTTSS-EEEEEE-S---SS------------ CS
               Methyltransf_10 123 teyGWrfvgsevddvslasakaivesnsklsdaiklrkqkekkaifdglieenerydvtlCnPPfhaslaeakagserkl 202
                                      G + vg ++++++l+ a+ ++e n+  +d  +     +  ++++ +ie +e++dv++ +PP + ++++  + + r  
  gi|15669845|ref|NP_248659.1| 232 AIRGAEVVGVDLSKKALKLAEENIELNNIPKDRYEFI-EGNAFEVMKEMIEDKEKFDVVILDPPAFTQTEDDIKNALRAY 310
                                   5568889********************6667777766.568899********************9998887766666655 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       5.3   3.4e+03      43      59 ..     103     119 ..      80     144 .. 0.71
   2 !   14.7   0.1   1.7e-05     0.011     202     264 ..     214     278 ..     206     319 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.3
               tRNA_U5-meth_tr  43 lwheeddlyyimfdqkt 59 
                                   ++ e+d+l  i+fd+ +
  gi|15669845|ref|NP_248659.1| 103 IYAEGDELPTIIFDKYN 119
                                   77888888888888755 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.7e-05
               tRNA_U5-meth_tr 202 kgdllelycGnGnfslalarnfekvlateiakssveaaqyniaanki..dnvqiirlsaeeltea 264
                                    + +l++ c  G fs+  a +   v+  +++k +++ a  ni+ n+i  d  ++i   a e+ + 
  gi|15669845|ref|NP_248659.1| 214 GDRVLDICCYTGGFSVHAAIRGAEVVGVDLSKKALKLAEENIELNNIpkDRYEFIEGNAFEVMKE 278
                                   445899****************************************9444455555555444433 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   4.6e-05     0.029      76     135 ..     235     299 ..     211     358 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-05
                                   H--EEEEES-HHHHHHHHHHHHHTT-.GGGEEEEE--GGG--....STTS---EEEE-------- CS
                       UPF0020  76 elklygsDldrrvvqgareNaekagv.gdliefsqadaakLr....lkegevdvivtnpPYGerl 135
                                    ++++g+Dl +++++ a+eN e  ++ +d+ ef + +a ++     ++++++dv++ +pP    +
  gi|15669845|ref|NP_248659.1| 235 GAEVVGVDLSKKALKLAEENIELNNIpKDRYEFIEGNAFEVMkemiEDKEKFDVVILDPPAFTQT 299
                                   34577****************9877637899*****99988778888899**********55544 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.5e-05     0.035      37     134 ..     227     342 ..     192     361 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-05
               N6-adenineMlase  37 Psvyealkkek......kkekvlLleiDkrFealygeekfvfYdlnnpeelpeel...kgkfdviviDPPF...lseeclk 105
                                    sv++a++  +      +k+++ L e +   +++ +++++ f + n  e + +e+   k+kfdv+++DPP      +++  
  gi|15669845|ref|NP_248659.1| 227 FSVHAAIRGAEvvgvdlSKKALKLAEENIELNNI-PKDRYEFIEGNAFE-VMKEMiedKEKFDVVILDPPAftqTEDDI-- 303
                                   4677777777777777766777788888888555.55534444444433.33455588************634322222.. PP

               N6-adenineMlase 106 klaktaklllk.........klilctgevmeelekll...g 134
                                     +++++ +++         k i++t +  ++++k++    
  gi|15669845|ref|NP_248659.1| 304 --KNALRAYASlnylgiklaKRIFVTCSCSHHVDKEMfkrT 342
                                   ..333333333335677788567777666666666664322 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.9   4.4e+03      60      77 ..     123     140 ..     118     144 .. 0.80
   2 ?   12.4   0.0   0.00012     0.078       5      78 ..     217     290 ..     213     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.9
                                   CCCHHHHCS-TTSEEEEE CS
                Methyltransf_4  60 alkvllelledgslekif 77 
                                   a++++++l+e+++l+ i+
  gi|15669845|ref|NP_248659.1| 123 AMQLMSKLIEKEYLKDIV 140
                                   899999999999998874 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00012
                                   EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTT..SSEEEEES-CCCHHHHCS-TTSEEEEEE CS
                Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealel..kNlrilrgdalkvllelledgslekifi 78 
                                   vl+i+c  G+f v+ A + ++  ++G+++++k ++ + ++ie +++     + ++g+a++v++e++ed++   ++i
  gi|15669845|ref|NP_248659.1| 217 VLDICCYTGGFSVHAAIRGAE--VVGVDLSKKALKLAEENIELNNIpkDRYEFIEGNAFEVMKEMIEDKEKFDVVI 290
                                   89***************9986..69**********999999988542145689**************987655555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.15      10      90 ..     231     318 ..     227     354 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                                   HHHTT-EEEEEESSHHHHHHHHHT.TESEEEET.....TTCHHHHHHHHHTT.TSSEEEEE.ESSCSHHHHHHHHHCEEEE CS
                    ADH_zinc_N  10 AkalGaeviavdsseeklelakkl.Gadeviny.....keadlverikeltg.gegvdvvf.ecvGsgatleaalkllkpg 82 
                                   A++ Gaev++vd s++ l+la+++   + +        +  +  e +ke+ + +e++dvv+ + ++  +t ++  ++l+  
  gi|15669845|ref|NP_248659.1| 231 AAIRGAEVVGVDLSKKALKLAEENiELNNIPKDryefiEG-NAFEVMKEMIEdKEKFDVVIlDPPAFTQTEDDIKNALRAY 310
                                   7899*******************62333333335555433.4556666666557889985426666666666666666666 PP

                                   EEEEECSC CS
                    ADH_zinc_N  83 GrlvvvGg 90 
                                     l + G+
  gi|15669845|ref|NP_248659.1| 311 ASLNYLGI 318
                                   66666555 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00031       0.2      29      81 ..     210     257 ..     189     291 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                   HHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTT CS
                          TPMT  29 fldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanl 81 
                                   f+++     g rvl   C  +   v  A +g evvGv+ls++A++ + e+ +l
  gi|15669845|ref|NP_248659.1| 210 FIKE-----GDRVLDICCYTGGFSVHAAIRGAEVVGVDLSKKALKLAEENIEL 257
                                   4444.....55666555655555556689***************985443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2453.56
//
Query:       gi|15669846|ref|NP_248660.1|  [L=384]
Description: hypothetical protein MJ_1650 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-59  200.1   0.6    5.5e-59  199.6   0.6    1.2  1  NMD3      NMD3 family
  ------ inclusion threshold ------
      0.068   13.2   1.1        1.6    8.8   0.5    2.4  2  DZR       Double zinc ribbon
          4    6.9   5.3         12    5.4   1.9    2.5  2  zf-TFIIB  Transcription factor zinc-finger


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.6   0.6   9.1e-63   5.5e-59       1     243 []      22     266 ..      22     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 199.6 bits;  conditional E-value: 9.1e-63
                          NMD3   1 CcrCGkeieelinglCedCllkevditegiekievevCkeCgrylpkgkWvk.aeleseellaeclkklvekgLkvseeve 80 
                                   C+rCG+e e li+glC+ C+++e++++e+++++e+evC+ Cg+y++k  W + +++e  e l+e+++ ++++++k  ++  
  gi|15669846|ref|NP_248660.1|  22 CYRCGAEDE-LIDGLCPICYAQEHPLIEVPDRVEIEVCHMCGSYKRK-IWQTpKSEEAFEILNEIAYYATKDAIK--KKSV 98 
                                   ********7.99*********************************98.**8887788999999******999999..4445 PP

                          NMD3  81 evkvelvdaefiwtephskrikv....kvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqk.re 156
                                    v+ve + +e + + p+ kr k+    ++  +g++ g +++  + e+++ev+++  qCprCsr++++yyea++QvR+  r 
  gi|15669846|ref|NP_248660.1|  99 MVEVE-IYPE-VTQLPGGKRSKLiipvHIVARGRLPG-EKEDRTYEKDIEVHLRMVQCPRCSRFMSNYYEATLQVRAMnRY 176
                                   67777.5666.89999999999855557777777777.55578899999******************************** PP

                          NMD3 157 lteeehkrtfelleqli...lkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedkksgkev 234
                                   lteee++++ +++++ +   lk+d++afi k   +keGlD+++gs  aAr++++++k+++ggk++e+ +lv+ d++sgke 
  gi|15669846|ref|NP_248660.1| 177 LTEEEREELDNFVREELakrLKKDRMAFIAKFIPQKEGLDYQLGSVGAARNVAQRIKEKYGGKITETATLVGVDRDSGKEL 257
                                   ***************999**999********************************************************** PP

                          NMD3 235 yrltysvrl 243
                                   yr+t+svr+
  gi|15669846|ref|NP_248660.1| 258 YRVTVSVRV 266
                                   *******95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.5   0.00027       1.6       1      36 [.      22      63 ..      22      71 .. 0.84
   2 ?    2.2   0.0     0.031   1.8e+02      28      39 ..     150     161 ..     121     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00027
                           DZR  1 CpqCgeelppdarfCseCgtk...lkavaa...edrCpsCge 36
                                  C +Cg+e +  +  C+ C ++   l +v++    ++C  Cg+
  gi|15669846|ref|NP_248660.1| 22 CYRCGAEDELIDGLCPICYAQehpLIEVPDrveIEVCHMCGS 63
                                  9999999999999*****999777665666888999999996 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.031
                           DZR  28 edrCpsCgekvd 39 
                                   + +Cp+C++ ++
  gi|15669846|ref|NP_248660.1| 150 MVQCPRCSRFMS 161
                                   788999987655 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.9     0.002        12       2      26 ..      36      62 ..      35      62 .. 0.78
   2 ?    2.1   0.1      0.02   1.2e+02       1       7 [.     152     158 ..     152     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.002
                      zf-TFIIB  2 CPkCqd.eleeser.ggveidyCpqCr 26
                                  CP C + e   +e+ + vei++C+ C+
  gi|15669846|ref|NP_248660.1| 36 CPICYAqEHPLIEVpDRVEIEVCHMCG 62
                                  99997636666777666*********7 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.02
                      zf-TFIIB   1 kCPkCqd 7  
                                   +CP+C+ 
  gi|15669846|ref|NP_248660.1| 152 QCPRCSR 158
                                   7999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1127  (0.0628591); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2407.01
//
Query:       gi|15669847|ref|NP_248661.1|  [L=263]
Description: hypothetical protein MJ_1651 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-69  233.9   0.0    1.9e-69  233.7   0.0    1.0  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr


Domain annotation for each model (and alignments):
>> SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.7   0.0   1.1e-73   1.9e-69       1     234 [.      13     259 ..      13     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: 233.7 bits;  conditional E-value: 1.1e-73
                                   EEEEESSTSSSSHHHHHHHHHHHH-....TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EE CS
               SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsia....pdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterral 77 
                                   itL+TDFG++++yvgamkg il+i     +da+i+Di+H+i+pf++ ++a++L +a+pyfp ++vh+av+Dp vg+er+++
  gi|15669847|ref|NP_248661.1|  13 ITLTTDFGTNEGYVGAMKGRILNILkkynKDAKIIDISHEIKPFNIYHGAYVLLTAIPYFP-PSVHVAVIDPTVGSERKSI 92 
                                   9********************9985444499******************************.58***************** PP

                                   EEEETTS.EEEEESSSTTHHHH...SEEEEEEGSSCC..--TS-HHHHTHHHHHHHHH..CT--GGGCSEEESGGGS-SSS CS
               SAM_adeno_trans  78 vveakgg.yfvgPDNGlltlal...lleeaveieeee..ssatFhgrDvFapvaarla..agvsleelgeeldpeelvrle 150
                                   v+e+k+g y+vgPDNGl+t+++   +++++++i+ee+  +s+tFhgrDv+a v+a++   +g +    geeld  e+v+++
  gi|15669847|ref|NP_248661.1|  93 VIETKSGyYLVGPDNGLFTYVAeklGIKRIIKIDEERykPSSTFHGRDVYAVVGAEILinNGYD----GEELD--EMVKID 167
                                   *****99788**********9998777*******8889999***************98333344....77775..478877 PP

                                   ECSCEEEEEEEE-TTS-EEEEEE...EHHHHHTTC...EE...........EEEEESSGGGSTTTSEEEEE-TTSEEEEEE CS
               SAM_adeno_trans 151 ederlegevlyvDrFGNvitniskelleelekerk...va...........klkkvetyaevaegellalvnssglleiav 217
                                      +++++v+++DrFGN+itni+k+ ++ + k ++   ++           k+k+v++y e ++++ ++l+ns+g+lei+ 
  gi|15669847|ref|NP_248661.1| 168 ---ETKKRVIHIDRFGNIITNIKKDEVT-F-KYYDtimIKirhkngiekiiKCKFVKSYFE-EKNNFICLINSEGFLEISK 242
                                   ...5689****************66654.2.222245511556778888887789999998.7899*************** PP

                                   TTC-HHHHHT--TT-EE CS
               SAM_adeno_trans 218 nkgsaaellglkvgdev 234
                                    +++a++ll++++ de+
  gi|15669847|ref|NP_248661.1| 243 FMDNASKLLNVDYLDEI 259
                                   *************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1779.35
//
Query:       gi|15669848|ref|NP_248662.1|  [L=761]
Description: DNA topoisomerase I [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-128  429.7   4.2   1.5e-128  429.3   4.2    1.2  1  Topoisom_bac     DNA topoisomerase
    3.6e-48  161.1  40.7    1.2e-18   66.6   5.3    4.4  4  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
    1.6e-21   76.5   0.1    1.6e-21   76.5   0.1    2.6  2  Toprim           Toprim domain
    0.00025   20.4  16.9      0.023   14.1   0.1    4.8  4  zf-ribbon_3      zinc-ribbon domain
     0.0004   20.3   7.6      0.022   14.8   2.2    3.1  2  DZR              Double zinc ribbon
     0.0012   18.8  11.7        0.2   11.8   0.8    3.6  3  DUF1272          Protein of unknown function (DUF1272)
     0.0016   17.9   6.8        1.5    8.4   0.1    3.9  3  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0093   16.2   0.5         50    4.3   0.0    3.7  3  zinc_ribbon_9    zinc-ribbon
  ------ inclusion threshold ------
      0.013   15.2   0.6       0.97    9.2   0.1    3.3  3  Zn_Tnp_IS1       InsA N-terminal domain
      0.015   15.3  19.1        1.4    9.0   8.1    4.5  4  ADK_lid          Adenylate kinase, active site lid
      0.019   14.7   0.8      0.068   12.9   0.2    2.4  2  SAP              SAP domain
      0.044   13.2   5.9        1.9    7.9   0.6    3.4  3  zf_Rg            Reverse gyrase zinc finger
      0.047   14.1  16.7       0.77   10.2   2.1    3.8  3  Lar_restr_allev  Restriction alleviation protein Lar
      0.059   13.1  13.8       0.14   12.0   0.1    4.3  3  zinc_ribbon_2    zinc-ribbon domain
       0.14   11.4   0.5         17    4.6   0.0    3.2  3  DUF2310          Zn-ribbon-containing, possibly nucleic-acid-
       0.14   11.9   8.2        1.3    8.8   0.0    4.2  4  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.38    9.6   1.7       0.61    8.9   0.0    1.9  2  LMBR1            LMBR1-like membrane protein
       0.42   10.7  21.0        0.2   11.7   0.2    4.8  4  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
        1.5    9.0  15.2         12    6.1   0.8    4.5  4  Zn-ribbon_8      Zinc ribbon domain
        5.6    6.4  13.9        7.4    6.0   0.4    4.3  5  zf-TFIIB         Transcription factor zinc-finger
        7.6    6.8  14.7         19    5.5   0.1    4.3  5  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
        8.4    6.4   6.8         92    3.1   0.3    3.7  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
        8.6    6.4  11.1         43    4.2   0.0    4.4  3  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
        9.5    6.1  12.7         16    5.3   0.1    4.2  4  A2L_zn_ribbon    A2L zinc ribbon domain


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.3   4.2  2.1e-131  1.5e-128       2     413 .]     156     559 ..     155     559 .. 0.94

  Alignments for each domain:
  == domain 1  score: 429.3 bits;  conditional E-value: 2.1e-131
                  Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltk...klkgkkvlsaGRVqtptLaliveRereienFvpeeyweveatlkkekke 79 
                                   i+  lvda+e+R++lDw +Ginlsr+l++   ++++ k++s+GRVq p+La++ eRe ei++F+p++yw +ea lk++ k 
  gi|15669848|ref|NP_248662.1| 156 IDYGLVDAGESRHILDWYFGINLSRALMNairAVNRWKTMSVGRVQGPALAFLTERELEIKKFIPKPYWVIEALLKDNLKA 236
                                   7889*************************66555559************************************99777755 PP

                  Topoisom_bac  80 kekkkkkkkerikdkeeaeaileklkkk.eakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYekag 159
                                         ++ke++++++ea++++ek+k++ +akv++++k+++k +p  pfd+ tLq+ea +++++s+k+t++iaqkLYe+  
  gi|15669848|ref|NP_248662.1| 237 -----IHEKEKFWNEKEAKNVYEKIKDEkSAKVVEIKKTKRKLKPLPPFDLGTLQREAYSYFKISPKETQEIAQKLYEN-A 311
                                   .....589*****************99669********999996666*******************************7.* PP

                  Topoisom_bac 160 litYpRTdstrlsee.aelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpklkelsddekkl 239
                                   li+YpRT s++l+++ + l++il+ ++++  + y ++ae+ lk++ k+ v ++k++ aH+AI+ + ++pk +els++ek++
  gi|15669848|ref|NP_248662.1| 312 LISYPRTSSQKLPKDrKYLEDILNIIKNH--PVYGKWAERILKENLKP-VEGKKEDPAHPAIHIV-DIPK-EELSEKEKEI 387
                                   ***************999*********97..78*********977644.6667777*********.9996.8********* PP

                  Topoisom_bac 240 YelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegeevkvkeveleekkT 320
                                   Y+lI+rr+la++ ++a+ e  +vk+++++e+fk+sg++++++G++++y+  k +e e  lp+lk+++++kv++++++ k+T
  gi|15669848|ref|NP_248662.1| 388 YDLIARRTLAAFWDNAEREYLNVKIDIKGEKFKLSGSRTVKEGWHEIYYFPKFDEIE--LPPLKKNDIIKVEKITITRKET 466
                                   ************************************************999999876..********************** PP

                  Topoisom_bac 321 kppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf.kdlvspelTaeleekLde 400
                                   +ppkryt as+ik++ek+g+Gt+aTraeii+kl++rgYv  + +sl++t+lG++++e+l++f ++++++++T++leekL++
  gi|15669848|ref|NP_248662.1| 467 QPPKRYTVASIIKELEKRGLGTKATRAEIIDKLIKRGYVIDD-GSLKVTDLGISVIETLKRFcPEIIDEKMTRDLEEKLEK 546
                                   *****************************************5.59************************************ PP

                  Topoisom_bac 401 Iaegkadakevld 413
                                   I+  k+++++vld
  gi|15669848|ref|NP_248662.1| 547 IQFRKIKKDDVLD 559
                                   **********985 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   2.6   4.7e-18   3.5e-15       1      38 [.     597     634 ..     597     635 .. 0.95
   2 ?   -0.2   0.1       1.2   8.7e+02       3      12 ..     644     653 ..     642     659 .. 0.86
   3 !   60.5   5.3   1.3e-19   9.6e-17       2      39 .]     678     715 ..     677     715 .. 0.95
   4 !   66.6   5.3   1.6e-21   1.2e-18       1      37 [.     718     754 ..     718     756 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 4.7e-18
                                   -EE-SSS--EEEEEE-SSSEEEEESST.T----EEB-G CS
                zf-C4_Topoisom   1 vekCPkCggdLvlkrgkkGkFvGCsnYPeCkftkklkk 38 
                                   v+kCPkCggdL+l r kkG+FvGCsnYPeC++ ++l++
  gi|15669848|ref|NP_248662.1| 597 VGKCPKCGGDLILIRHKKGRFVGCSNYPECDVKYSLPD 634
                                   58********************************9987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                                   E-SSS--EEE CS
                zf-C4_Topoisom   3 kCPkCggdLv 12 
                                    C++C+++++
  gi|15669848|ref|NP_248662.1| 644 VCDACKSPIL 653
                                   6*****9986 PP

  == domain 3  score: 60.5 bits;  conditional E-value: 1.3e-19
                                   EE-SSS--EEEEEE-SSSEEEEESST.T----EEB-GG CS
                zf-C4_Topoisom   2 ekCPkCggdLvlkrgkkGkFvGCsnYPeCkftkklkkn 39 
                                   + CPkCg++L+lk+g +G F+GCsnYP+Ck+t++++k+
  gi|15669848|ref|NP_248662.1| 678 RICPKCGAKLILKKGVYGAFYGCSNYPKCKYTEPINKK 715
                                   78*********************************985 PP

  == domain 4  score: 66.6 bits;  conditional E-value: 1.6e-21
                                   -EE-SSS--EEEEEE-SSSEEEEESST.T----EEB- CS
                zf-C4_Topoisom   1 vekCPkCggdLvlkrgkkGkFvGCsnYPeCkftkklk 37 
                                   v+kCPkCggdLv+++gk+GkFvGCsnYP+C++t+klk
  gi|15669848|ref|NP_248662.1| 718 VGKCPKCGGDLVVREGKFGKFVGCSNYPKCRYTEKLK 754
                                   58*********************************98 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.1   2.1e-24   1.6e-21       2     102 ..       8     140 ..       7     141 .. 0.89
   2 ?   -1.6   0.1       4.3   3.2e+03      44      45 ..     545     557 ..     460     594 .. 0.56

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 2.1e-24
                                   EEEESSHHHHHHHHHTHT..................STEEEEEEESSSSEEEHS..............TTEEEEE...... CS
                        Toprim   2 lvivEgpsdaktiakalg..................sgfqavtaslGhildlet..............efkpvye...... 44 
                                   l+i+E+ps ak+ia+alg                  +++ +v + +Gh+++l++              ++           
  gi|15669848|ref|NP_248662.1|   8 LIICEKPSVAKKIANALGkakkksidgvpyyelerdGKKIIVASAVGHLFTLVEkenkefgfypvfdiKW----Vpasvdk 84 
                                   9**********************************99999**************9999996666444444....1666699 PP

                                   ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEESS CS
                        Toprim  45 eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellenkigrvefse 102
                                    +e+ +k++kalk+l+k+ade ++atD D eGe i++++l++++   +   +r++fs+
  gi|15669848|ref|NP_248662.1|  85 GKEYVNKYIKALKKLSKDADEFYIATDWDIEGELIGYHALKYCCGREK--AKRMRFSS 140
                                   9*******************************************4444..5****997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.3
                                   E...........E CS
                        Toprim  44 e...........e 45 
                                   e           +
  gi|15669848|ref|NP_248662.1| 545 EkiqfrkikkddV 557
                                   1222222222332 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.3     0.029        22      18      26 .]     599     607 ..     598     607 .. 0.81
   2 ?    4.6   0.2     0.031        23       3      16 ..     643     657 ..     641     658 .. 0.83
   3 !   14.1   0.1   3.1e-05     0.023      12      26 .]     673     687 ..     669     687 .. 0.88
   4 ?    5.2   0.8     0.019        14      18      26 .]     720     728 ..     718     728 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.029
                   zf-ribbon_3  18 vCpyCGtkl 26 
                                   +Cp+CG++l
  gi|15669848|ref|NP_248662.1| 599 KCPKCGGDL 607
                                   599999886 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.031
                   zf-ribbon_3   3 vrCPnCGa.plssdd 16 
                                   + C +C++ +l+ +d
  gi|15669848|ref|NP_248662.1| 643 KVCDACKSpILKIGD 657
                                   78******7799998 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 3.1e-05
                   zf-ribbon_3  12 lssddnvCpyCGtkl 26 
                                   ++++d++Cp+CG+kl
  gi|15669848|ref|NP_248662.1| 673 VKEEDRICPKCGAKL 687
                                   699*********997 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.019
                   zf-ribbon_3  18 vCpyCGtkl 26 
                                   +Cp+CG++l
  gi|15669848|ref|NP_248662.1| 720 KCPKCGGDL 728
                                   699999886 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   4.7    0.0007      0.52       7      49 .]     629     684 ..     588     684 .. 0.75
   2 !   14.8   2.2     3e-05     0.022       5      35 ..     670     725 ..     661     743 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0007
                           DZR   7 e........lppdarfCseCgtklkavaa.....edrCpsCgekvdpearfCpeCG 49 
                                   +        ++  +++C++C++++ +  +     +  Cp  + +v++e+r+Cp+CG
  gi|15669848|ref|NP_248662.1| 629 KyslpdkgrIKIPNKVCDACKSPILKIGDreiciNPECPLKQVEVKEEDRICPKCG 684
                                   255555555677789********9888885666666666667779**********9 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3e-05
                           DZR   5 geelppdarfCseCgtklkavaa.........................edrCpsCg 35 
                                   + e+++++r C++Cg+kl   +                            +Cp+Cg
  gi|15669848|ref|NP_248662.1| 670 QVEVKEEDRICPKCGAKLILKKGvygafygcsnypkckytepinkkevVGKCPKCG 725
                                   556899***********985555999*88866666666666666666666666666 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0086       6.4      39      52 ..     595     608 ..     589     612 .. 0.82
   2 ?    4.6   2.0     0.047        35       7      52 ..     644     688 ..     641     691 .. 0.80
   3 !   11.8   0.8   0.00027       0.2      29      54 ..     706     731 ..     698     734 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0086
                       DUF1272  39 vlenvCPncgGelv 52 
                                   ++ + CP cgG+l+
  gi|15669848|ref|NP_248662.1| 595 KIVGKCPKCGGDLI 608
                                   55789*******96 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.047
                       DUF1272   7 nCecCdkdlppdseearic.syEctFCaeCaeevlenvCPncgGelv 52 
                                    C+ C+  + +   +  ic   Ec   +  ++e  + +CP cg +l+
  gi|15669848|ref|NP_248662.1| 644 VCDACKSPILKIG-DREICiNPECPLKQVEVKEE-DRICPKCGAKLI 688
                                   6999999998887.56666256999999888888.9*******9986 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00027
                       DUF1272  29 ctFCaeCaeevlenvCPncgGelvkR 54 
                                   c + ++  ++ + + CP cgG+lv R
  gi|15669848|ref|NP_248662.1| 706 CKYTEPINKKEVVGKCPKCGGDLVVR 731
                                   77888888888899**********98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1     0.002       1.5       2      21 ..     599     618 ..     598     622 .. 0.87
   2 ?    5.3   0.2     0.019        14      17      28 ..     675     686 ..     664     689 .. 0.66
   3 ?    5.7   0.3     0.014        10       2      14 ..     720     732 ..     719     742 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.002
                                   EETTTTCEECHEETSTTCEE CS
                  TF_Zn_Ribbon   2 kCPnCgstnlveDpergelv 21 
                                   kCP+Cg++ ++  ++ g +v
  gi|15669848|ref|NP_248662.1| 599 KCPKCGGDLILIRHKKGRFV 618
                                   9******9999999999886 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                                   TTCEEESSSSBE CS
                  TF_Zn_Ribbon  17 rgelvCtdCGlV 28 
                                   + + +C++CG+ 
  gi|15669848|ref|NP_248662.1| 675 EEDRICPKCGAK 686
                                   458899999976 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.014
                                   EETTTTCEECHEE CS
                  TF_Zn_Ribbon   2 kCPnCgstnlveD 14 
                                   kCP+Cg++ +v++
  gi|15669848|ref|NP_248662.1| 720 KCPKCGGDLVVRE 732
                                   9******866654 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.11        84      17      30 ..     592     606 ..     585     608 .. 0.68
   2 ?    4.3   0.0     0.066        50      17      29 ..     674     685 ..     669     688 .. 0.66
   3 ?    4.0   0.0     0.084        63      22      32 ..     718     729 ..     708     731 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.11
                 zinc_ribbon_9  17 dedsdv.lCPhCggg 30 
                                   ++  +v  CP Cgg+
  gi|15669848|ref|NP_248662.1| 592 KKAKIVgKCPKCGGD 606
                                   45555567*****96 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.066
                 zinc_ribbon_9  17 dedsdvlCPhCgg 29 
                                   +e++ + CP Cg 
  gi|15669848|ref|NP_248662.1| 674 KEEDRI-CPKCGA 685
                                   444445.****85 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.084
                 zinc_ribbon_9  22 v.lCPhCgggFV 32 
                                   v  CP Cgg+ V
  gi|15669848|ref|NP_248662.1| 718 VgKCPKCGGDLV 729
                                   356*****9866 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.42   3.1e+02       7      19 ..     599     612 ..     594     616 .. 0.80
   2 ?   -0.1   0.0         1   7.8e+02       8      17 ..     680     689 ..     679     693 .. 0.75
   3 ?    9.2   0.1    0.0013      0.97       7      21 ..     720     734 ..     717     737 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.42
                    Zn_Tnp_IS1   7 hCPrCsstd.VyRh 19 
                                    CP+C  +   +Rh
  gi|15669848|ref|NP_248662.1| 599 KCPKCGGDLiLIRH 612
                                   6****998877787 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                    Zn_Tnp_IS1   8 CPrCsstdVy 17 
                                   CP+C +  + 
  gi|15669848|ref|NP_248662.1| 680 CPKCGAKLIL 689
                                   ****987655 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0013
                    Zn_Tnp_IS1   7 hCPrCsstdVyRhGk 21 
                                    CP+C  + V+R+Gk
  gi|15669848|ref|NP_248662.1| 720 KCPKCGGDLVVREGK 734
                                   6*************9 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1     0.006       4.5      16      32 ..     592     608 ..     581     609 .. 0.82
   2 ?    1.6   0.3      0.37   2.8e+02      21      30 ..     642     651 ..     624     654 .. 0.80
   3 ?    5.7   0.4     0.019        14      21      32 ..     677     688 ..     667     691 .. 0.74
   4 ?    9.0   8.1    0.0018       1.4       2      35 ..     678     732 ..     678     732 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.006
                                   B--SSTTB-TTT--.-B CS
                       ADK_lid  16 npPkveglCDkCGepLv 32 
                                   ++ k  g+C kCG++L+
  gi|15669848|ref|NP_248662.1| 592 KKAKIVGKCPKCGGDLI 608
                                   457888*********98 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.37
                                   TTB-TTT--. CS
                       ADK_lid  21 eglCDkCGep 30 
                                   + +CD C +p
  gi|15669848|ref|NP_248662.1| 642 NKVCDACKSP 651
                                   579****998 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.019
                                   TTB-TTT--.-B CS
                       ADK_lid  21 eglCDkCGepLv 32 
                                   + +C kCG +L+
  gi|15669848|ref|NP_248662.1| 677 DRICPKCGAKLI 688
                                   566777777766 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0018
                                   EE-TTT--EEETT..........TB--S...........STTB-TTT--.-B--G CS
                       ADK_lid   2 rvCpkCGrsYhvv..........fnpPk...........veglCDkCGepLvqRs 35 
                                   r+CpkCG+   ++           n Pk           v g+C kCG++Lv+R+
  gi|15669848|ref|NP_248662.1| 678 RICPKCGAKLILKkgvygafygcSNYPKckytepinkkeVVGKCPKCGGDLVVRE 732
                                   89****997743345555555442556666666666777***************6 PP

>> SAP  SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       8.3   6.2e+03      13      26 ..     351     364 ..     350     364 .. 0.78
   2 ?   12.9   0.2   9.1e-05     0.068       3      33 ..     471     501 ..     469     502 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8.3
                                   HHHTT--TTS-HHH CS
                           SAP  13 LkkrGLptsGkKae 26 
                                   Lk++  p+ GkK++
  gi|15669848|ref|NP_248662.1| 351 LKENLKPVEGKKED 364
                                   677777999**987 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.1e-05
                                   T--HHHHHHHHHHTT--TTS-HHHHHHHHHH CS
                           SAP   3 kltVaeLKeeLkkrGLptsGkKaeLieRLke 33 
                                     tVa   +eL+krGL t+ ++ae+i+ L++
  gi|15669848|ref|NP_248662.1| 471 RYTVASIIKELEKRGLGTKATRAEIIDKLIK 501
                                   57999999*******************9975 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.6    0.0026       1.9       9      25 ..     599     615 ..     594     622 .. 0.88
   2 ?   -0.7   0.1       1.3   9.6e+02       8      16 ..     678     686 ..     677     691 .. 0.81
   3 ?    5.6   0.1     0.014        10       9      18 ..     720     729 ..     715     735 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0026
                         zf_Rg   9 lCPNCgGdisdeRlekG 25 
                                    CP CgGd+   R +kG
  gi|15669848|ref|NP_248662.1| 599 KCPKCGGDLILIRHKKG 615
                                   6********99999998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                         zf_Rg   8 klCPNCgGd 16 
                                   + CP Cg +
  gi|15669848|ref|NP_248662.1| 678 RICPKCGAK 686
                                   67****965 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.014
                         zf_Rg   9 lCPNCgGdis 18 
                                    CP CgGd+ 
  gi|15669848|ref|NP_248662.1| 720 KCPKCGGDLV 729
                                   6*******85 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.1     0.001      0.77       5      36 ..     599     628 ..     596     650 .. 0.84
   2 ?    3.4   0.7      0.14     1e+02       6      36 ..     680     708 ..     675     718 .. 0.71
   3 ?    9.1   0.8    0.0022       1.7       5      45 ..     720     757 ..     715     761 .] 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
               Lar_restr_allev   5 pCPfCggravlersqrvvaeigqcvyCad...Cga 36 
                                    CP Cgg+ +l+r+++++     +v C +   C +
  gi|15669848|ref|NP_248662.1| 599 KCPKCGGDLILIRHKKGR-----FVGCSNypeCDV 628
                                   6****************9.....799988777877 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.14
               Lar_restr_allev   6 CPfCggravlersqrvvaeigqcvyCad...Cga 36 
                                   CP Cg + +l++  +++     +  C +   C++
  gi|15669848|ref|NP_248662.1| 680 CPKCGAKLILKKGVYGA-----FYGCSNypkCKY 708
                                   *****999999887776.....344444444655 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0022
               Lar_restr_allev   5 pCPfCggravlersqrvvaeigqcvyCad...Cgastpwfkiae 45 
                                    CP Cgg+ v+ + + ++     +v C +   C + t + k  e
  gi|15669848|ref|NP_248662.1| 720 KCPKCGGDLVVREGKFGK-----FVGCSNypkCRY-TEKLKLNE 757
                                   7*******9999998887.....899988888999.55555444 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.7      0.06        45       1       6 [.     599     604 ..     597     607 .. 0.77
   2 ?   12.0   0.1   0.00018      0.14       8      23 .]     672     687 ..     671     687 .. 0.87
   3 ?    4.4   0.3     0.044        33       1       6 [.     720     725 ..     714     728 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.06
                 zinc_ribbon_2   1 fCpnCG 6  
                                   +Cp+CG
  gi|15669848|ref|NP_248662.1| 599 KCPKCG 604
                                   577776 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00018
                 zinc_ribbon_2   8 elqdnakFCpyCGtpl 23 
                                   e++++++ Cp+CG++l
  gi|15669848|ref|NP_248662.1| 672 EVKEEDRICPKCGAKL 687
                                   6889999999999987 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.044
                 zinc_ribbon_2   1 fCpnCG 6  
                                   +Cp+CG
  gi|15669848|ref|NP_248662.1| 720 KCPKCG 725
                                   577776 PP

>> DUF2310  Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.17   1.3e+02     203     228 ..     582     607 ..     545     617 .. 0.79
   2 ?    4.6   0.0     0.022        17     214     238 ..     673     697 ..     668     706 .. 0.84
   3 ?    1.0   0.1      0.28   2.1e+02     209     231 ..     709     731 ..     702     739 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.17
                       DUF2310 203 YYlyrvggkskeeelerkCPscggeW 228
                                   Y + ++  ++k++    kCP+cgg+ 
  gi|15669848|ref|NP_248662.1| 582 YLIKNLDATNKKAKIVGKCPKCGGDL 607
                                   55667777888999999******986 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.022
                       DUF2310 214 eeelerkCPscggeWklkeplhdlf 238
                                    +e++r CP+cg +  lk+ ++  f
  gi|15669848|ref|NP_248662.1| 673 VKEEDRICPKCGAKLILKKGVYGAF 697
                                   57889***********999998887 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.28
                       DUF2310 209 ggkskeeelerkCPscggeWklk 231
                                   ++  +++e   kCP+cgg+  ++
  gi|15669848|ref|NP_248662.1| 709 TEPINKKEVVGKCPKCGGDLVVR 731
                                   55567889999******997665 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.28   2.1e+02       6      11 ..     600     605 ..     600     612 .. 0.79
   2 ?   -1.3   0.3       2.4   1.8e+03      22      28 ..     643     649 ..     642     651 .. 0.86
   3 ?    8.8   0.0    0.0017       1.3       4      18 ..     678     692 ..     676     695 .. 0.89
   4 ?    3.1   0.2       0.1        78       6      18 ..     721     733 ..     721     737 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.28
                 zf-NADH-PPase   6 CgrCGa 11 
                                   C++CG+
  gi|15669848|ref|NP_248662.1| 600 CPKCGG 605
                                   9***98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                 zf-NADH-PPase  22 rvCpaCg 28 
                                   +vC+aC+
  gi|15669848|ref|NP_248662.1| 643 KVCDACK 649
                                   79****7 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0017
                 zf-NADH-PPase   4 rFCgrCGaptepaeg 18 
                                   r C++CGa+ ++++g
  gi|15669848|ref|NP_248662.1| 678 RICPKCGAKLILKKG 692
                                   78*******999876 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.1
                 zf-NADH-PPase   6 CgrCGaptepaeg 18 
                                   C++CG+  ++ eg
  gi|15669848|ref|NP_248662.1| 721 CPKCGGDLVVREG 733
                                   *****98888776 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.4      0.64   4.8e+02     241     253 ..     294     339 ..     218     433 .. 0.50
   2 ?    8.9   0.0   0.00082      0.61     192     237 ..     526     579 ..     494     658 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.64
                         LMBR1 241 d.............................p.lrkyleeilk...k 253
                                   +                             p  rkyle+il+   +
  gi|15669848|ref|NP_248662.1| 294 KispketqeiaqklyenalisyprtssqklPkDRKYLEDILNiikN 339
                                   0222222222222222222222222222332246777777764440 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00082
                         LMBR1 192 r........eiksdldeelkklyfeaaklntekeeaereledllkevkklrksi 237
                                   r        ++++dl+e+l+k++f+  k ++ ++eae++l+++l+e kk ++ i
  gi|15669848|ref|NP_248662.1| 526 RfcpeiideKMTRDLEEKLEKIQFRKIKKDDVLDEAEKRLRKILEEFKKKEEDI 579
                                   255566666789**********************************99987765 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.8      0.11        83       1      10 [.     599     608 ..     599     627 .. 0.71
   2 ?   -0.7   0.9         2   1.5e+03      20      26 ..     661     667 ..     660     667 .. 0.95
   3 ?   11.7   0.2   0.00027       0.2       2      26 ..     680     707 ..     680     707 .. 0.94
   4 ?    7.5   1.1    0.0055       4.1       1      25 [.     720     747 ..     720     748 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.11
                DNA_ligase_ZBD   1 hCPvCGsavv 10 
                                   +CP CG  ++
  gi|15669848|ref|NP_248662.1| 599 KCPKCGGDLI 608
                                   6*****9876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                DNA_ligase_ZBD  20 CtnlsCp 26 
                                   C+n+ Cp
  gi|15669848|ref|NP_248662.1| 661 CINPECP 667
                                   ******9 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00027
                DNA_ligase_ZBD   2 CPvCGsavvReeg..eaiyRCtn.lsCp 26 
                                   CP CG++++ + g  +a y C+n ++C 
  gi|15669848|ref|NP_248662.1| 680 CPKCGAKLILKKGvyGAFYGCSNyPKCK 707
                                   *********888889************5 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0055
                DNA_ligase_ZBD   1 hCPvCGsavv.Reeg..eaiyRCtn.lsC 25 
                                   +CP CG  +v Re g  +    C+n ++C
  gi|15669848|ref|NP_248662.1| 720 KCPKCGGDLVvRE-GkfGKFVGCSNyPKC 747
                                   6*********555.436666777777777 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.072        54      28      35 ..     598     606 ..     587     608 .. 0.75
   2 ?   -0.1   0.1       1.4     1e+03      25      36 ..     641     652 ..     625     655 .. 0.76
   3 ?    5.5   0.8     0.025        19      23      35 ..     674     686 ..     659     689 .. 0.74
   4 ?    6.1   0.8     0.016        12      14      36 ..     708     729 ..     698     732 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.072
                   Zn-ribbon_8  28 a.CPeCgse 35 
                                     CP+Cg++
  gi|15669848|ref|NP_248662.1| 598 GkCPKCGGD 606
                                   34*****96 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.4
                   Zn-ribbon_8  25 pltaCPeCgsev 36 
                                   p+++C +C+s+ 
  gi|15669848|ref|NP_248662.1| 641 PNKVCDACKSPI 652
                                   677899999865 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.025
                   Zn-ribbon_8  23 dapltaCPeCgse 35 
                                   ++++  CP+Cg++
  gi|15669848|ref|NP_248662.1| 674 KEEDRICPKCGAK 686
                                   345566*****95 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.016
                   Zn-ribbon_8  14 efevlqsisdaplta.CPeCgs.ev 36 
                                     e++ +   ++ +  CP+Cg+  v
  gi|15669848|ref|NP_248662.1| 708 YTEPINK---KEVVGkCPKCGGdLV 729
                                   5555554...224445*****9555 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       7.1   5.3e+03      30      39 ..     161     170 ..     160     171 .. 0.86
   2 ?    5.3   0.2     0.016        12       1      11 [.     599     609 ..     597     622 .. 0.67
   3 ?   -3.3   0.1         8     6e+03      18      26 ..     641     649 ..     637     649 .. 0.76
   4 ?    2.4   0.1      0.13        95       2       9 ..     680     687 ..     679     691 .. 0.83
   5 ?    6.0   0.4    0.0099       7.4       1      10 [.     720     729 ..     704     742 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.1
                      zf-TFIIB  30 ldrgelekll 39 
                                   +d+ge++++l
  gi|15669848|ref|NP_248662.1| 161 VDAGESRHIL 170
                                   79****9998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                      zf-TFIIB   1 kCPkCqdelee 11 
                                   kCPkC+ +l  
  gi|15669848|ref|NP_248662.1| 599 KCPKCGGDLIL 609
                                   57777776655 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8
                      zf-TFIIB  18 eidyCpqCr 26 
                                   + ++C++C+
  gi|15669848|ref|NP_248662.1| 641 PNKVCDACK 649
                                   557899995 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.13
                      zf-TFIIB   2 CPkCqdel 9  
                                   CPkC++ l
  gi|15669848|ref|NP_248662.1| 680 CPKCGAKL 687
                                   ****9876 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.0099
                      zf-TFIIB   1 kCPkCqdele 10 
                                   kCPkC+ +l+
  gi|15669848|ref|NP_248662.1| 720 KCPKCGGDLV 729
                                   5666666665 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.026        19      18      32 ..     600     616 ..     594     622 .. 0.77
   2 ?    5.3   0.7     0.029        22      15      37 ..     642     662 ..     638     667 .. 0.83
   3 ?    0.4   2.3         1   7.6e+02      23      40 .]     666     684 ..     659     684 .. 0.61
   4 ?    2.3   0.2      0.25   1.9e+02      16      28 ..     678     690 ..     676     697 .. 0.74
   5 ?    0.4   0.2         1   7.6e+02      18      25 ..     721     729 ..     718     741 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                 Auto_anti-p27  18 CpvC..gvPLmrdrkgg 32 
                                   Cp+C    +L r +kg 
  gi|15669848|ref|NP_248662.1| 600 CPKCggDLILIRHKKGR 616
                                   ****9999****98644 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.029
                 Auto_anti-p27  15 aetCpvCgvPLmrdrkggkvyCv 37 
                                   +++C+ C++P+++   g + +C+
  gi|15669848|ref|NP_248662.1| 642 NKVCDACKSPILKI--GDREICI 662
                                   789**********5..5566997 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1
                 Auto_anti-p27  23 vPLmrdr.kggkvyCvaCd 40 
                                   +PL +   k+++ +C+ C+
  gi|15669848|ref|NP_248662.1| 666 CPLKQVEvKEEDRICPKCG 684
                                   4444444556788999996 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.25
                 Auto_anti-p27  16 etCpvCgvPLmrd 28 
                                     Cp+Cg+ L  +
  gi|15669848|ref|NP_248662.1| 678 RICPKCGAKLILK 690
                                   5799998877664 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 1
                 Auto_anti-p27  18 CpvC.gvPL 25 
                                   Cp+C g   
  gi|15669848|ref|NP_248662.1| 721 CPKCgGDLV 729
                                   ****54444 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.15   1.1e+02      12      18 ..     598     604 ..     596     607 .. 0.62
   2 ?    2.0   0.1      0.26     2e+02      26      33 ..     678     685 ..     676     687 .. 0.78
   3 ?    3.1   0.3      0.12        92      11      18 ..     718     725 ..     717     728 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.15
                       DUF35_N  12 qrCpdCG 18 
                                   ++Cp+CG
  gi|15669848|ref|NP_248662.1| 598 GKCPKCG 604
                                   5666665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.26
                       DUF35_N  26 avCphCgs 33 
                                   ++Cp+Cg+
  gi|15669848|ref|NP_248662.1| 678 RICPKCGA 685
                                   57999986 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.12
                       DUF35_N  11 gqrCpdCG 18 
                                   +++Cp+CG
  gi|15669848|ref|NP_248662.1| 718 VGKCPKCG 725
                                   56777776 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   4.4       0.8     6e+02       3      12 ..     598     607 ..     595     652 .. 0.81
   2 ?    1.7   0.1      0.35   2.6e+02      21      26 ..     679     684 ..     679     702 .. 0.74
   3 ?    4.2   0.0     0.058        43       3      11 ..     719     727 ..     716     729 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.8
                PhnA_Zn_Ribbon   3 pkCplCaSey 12 
                                   +kCp+C+ + 
  gi|15669848|ref|NP_248662.1| 598 GKCPKCGGDL 607
                                   69****9875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.35
                PhnA_Zn_Ribbon  21 vCpeCa 26 
                                   +Cp+C+
  gi|15669848|ref|NP_248662.1| 679 ICPKCG 684
                                   455554 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.058
                PhnA_Zn_Ribbon   3 pkCplCaSe 11 
                                   +kCp+C+ +
  gi|15669848|ref|NP_248662.1| 719 GKCPKCGGD 727
                                   69****876 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.022        16       5      19 ..     599     613 ..     597     617 .. 0.82
   2 ?   -2.7   1.4         7   5.2e+03       3      12 ..     642     651 ..     642     666 .. 0.74
   3 ?    4.2   0.1     0.048        36      21      29 ..     677     685 ..     669     686 .. 0.83
   4 ?    2.8   0.2      0.14     1e+02       5      15 ..     720     730 ..     719     733 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.022
                 A2L_zn_ribbon   5 vCsvCggngilnseq 19 
                                   +C +Cgg+ il++ +
  gi|15669848|ref|NP_248662.1| 599 KCPKCGGDLILIRHK 613
                                   799********8654 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7
                 A2L_zn_ribbon   3 lkvCsvCggn 12 
                                   +kvC  C+++
  gi|15669848|ref|NP_248662.1| 642 NKVCDACKSP 651
                                   5899999987 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.048
                 A2L_zn_ribbon  21 ylvCieCga 29 
                                   +++C++Cga
  gi|15669848|ref|NP_248662.1| 677 DRICPKCGA 685
                                   799*****7 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.14
                 A2L_zn_ribbon   5 vCsvCggngil 15 
                                   +C +Cgg+ ++
  gi|15669848|ref|NP_248662.1| 720 KCPKCGGDLVV 730
                                   7999***9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (761 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1541  (0.0859501); expected 358.6 (0.02)
Passed bias filter:                      751  (0.0418874); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.85u 0.30s 00:00:01.14 Elapsed: 00:00:00.51
# Mc/sec: 4503.46
//
Query:       gi|15669849|ref|NP_248663.1|  [L=385]
Description: hypothetical protein MJ_1653 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-18   65.5   0.0    6.4e-18   64.9   0.0    1.2  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
      2e-12   47.2   0.2    4.1e-12   46.1   0.1    1.6  2  Methyltransf_31  Methyltransferase domain
    2.8e-12   46.8   0.2    4.9e-12   46.0   0.2    1.3  1  Met_10           Met-10+ like-protein
    2.1e-10   41.1   0.0      4e-10   40.3   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    2.6e-10   40.2   0.0    4.3e-10   39.5   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
    7.4e-09   35.4   0.1    2.8e-08   33.5   0.0    1.9  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.3e-08   33.8   0.0    4.3e-08   32.9   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    2.4e-08   33.7   0.0    4.1e-08   33.0   0.0    1.3  1  MTS              Methyltransferase small domain
    4.8e-08   33.3   0.0      9e-08   32.4   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
    9.6e-08   31.7   0.1    2.4e-07   30.5   0.0    1.8  1  PUA_3            PUA-like domain
    1.1e-06   28.6   0.0    1.9e-06   27.8   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    1.6e-06   28.6   0.0    3.7e-06   27.5   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    1.8e-05   24.2   0.0    3.1e-05   23.4   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
    2.3e-05   23.8   0.0    3.2e-05   23.3   0.0    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    3.1e-05   23.9   0.0    6.1e-05   23.0   0.0    1.5  1  Methyltransf_18  Methyltransferase domain
      4e-05   23.0   0.0    7.5e-05   22.1   0.0    1.4  1  N6_Mtase         N-6 DNA Methylase
    5.8e-05   22.5   0.3    0.00012   21.5   0.0    1.6  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00014   22.5   0.0    0.00032   21.4   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    0.00035   20.3   0.0     0.0028   17.3   0.0    2.2  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    0.00056   19.1   0.1     0.0011   18.2   0.1    1.4  1  Methyltransf_3   O-methyltransferase
    0.00077   18.9   0.0     0.0018   17.7   0.0    1.6  2  Methyltransf_10  RNA methyltransferase
  ------ inclusion threshold ------
      0.016   14.9   0.0      0.084   12.5   0.0    2.1  2  UPF0020          Putative RNA methylase family UPF0020
      0.031   13.7   0.0       0.05   13.1   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
      0.038   13.4   0.0      0.082   12.3   0.0    1.6  1  SAM_MT           Putative SAM-dependent methyltransferase
      0.059   12.3   0.0      0.092   11.7   0.0    1.3  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.086   12.5   0.0       0.13   12.0   0.0    1.2  1  TPMT             Thiopurine S-methyltransferase (TPMT)
       0.11   12.4   0.0       0.24   11.4   0.0    1.5  1  ADH_zinc_N       Zinc-binding dehydrogenase
       0.12   12.4   0.0       0.26   11.3   0.0    1.6  1  PUA              PUA domain
       0.17   11.7   0.0       0.25   11.1   0.0    1.3  1  N6-adenineMlase  Probable N6-adenine methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0     1e-20   6.4e-18      15     230 ..     108     321 ..      97     345 .. 0.78

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 1e-20
               Methyltrans_SAM  15 eqltadwlqgqllvnlfkevddaflaelksgledltqadlwaakqgrslvlqhryadgaasevlvgeldespvvvesglky 95 
                                   + l +d  +    v++f+   +++ + + ++l dl   ++++++ gr+   ++r        +l+ge +e+ +++e   k+
  gi|15669849|ref|NP_248663.1| 108 NGLVIDKYNDIATVQIFNYGIEKMKDVVVETLLDLGIDSIYEKSSGRN---RKRAGLPEVEGILAGEKTET-IIQEGEAKF 184
                                   444445555555677787777777788888999999999999999986...34444444456888888775.6889999** PP

               Methyltrans_SAM  96 qldigrnqnfglfldmrlgrdwvqenak.dknvlnlfaytcgfsvaaiaggaskvvnvdmargslnkgrdnhrlnghdlrr 175
                                   ++ +   q++g+fld r  r  +++  k + +vl++ +yt gfsv a   ga +vv vd+++ +l+   +n  ln+   +r
  gi|15669849|ref|NP_248663.1| 185 KVTFD-GQKTGFFLDQRENRLELEKFIKeGDRVLDICCYTGGFSVHAAIRGA-EVVGVDLSKKALKLAEENMELNNIPKDR 263
                                   *9885.799***********999887762589*************9988888.599************************* PP

               Methyltrans_SAM 176 vsflgydifkswgk.ikksgpydlviidppsfqkgsfaltkdyk..kilrrlpellve 230
                                    +f+  + fk     i  + ++d+vi+dpp+f +   al    k  ++l r+   l++
  gi|15669849|ref|NP_248663.1| 264 YEFIEGNAFKVMEEfIEDGEKFDVVILDPPAFAQSKKALKSAIKgyHMLNRFGAKLAD 321
                                   ***********9872566668***********99998887655533466666666655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       8.9   5.5e+03      39      67 ..      79     111 ..      76     133 .. 0.71
   2 !   46.1   0.1   6.6e-15   4.1e-12       2      97 ..     211     305 ..     210     351 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.9
               Methyltransf_31  39 eaielArenaqklgld...nveFeqgdiee.le 67 
                                   e i +A+e + klg++   ++   q+d+ + l 
  gi|15669849|ref|NP_248663.1|  79 EKIIKANEYRLKLGFKdtyRMVYTQSDWLNgLV 111
                                   677788888888898877777777788877554 PP

  == domain 2  score: 46.1 bits;  conditional E-value: 6.6e-15
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld..nveFeqgdiee.leklled.ekfDli 78 
                                   ++g rvlD+ C tG ++  +a   + +aevvG+D s++a++lA+en + +++   ++eF +g++++ +e+ +ed ekfD++
  gi|15669849|ref|NP_248663.1| 211 KEGDRVLDICCYTGGFSVHAA---IRGAEVVGVDLSKKALKLAEENMELNNIPkdRYEFIEGNAFKvMEEFIEDgEKFDVV 288
                                   6789*****************...679********************99998777***********888558888****** PP

               Methyltransf_31  79 lsnevlnaladpdkileei 97 
                                   + + +   +a ++k+l+++
  gi|15669849|ref|NP_248663.1| 289 ILDPPA--FAQSKKALKSA 305
                                   **9554..55555555544 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.2   7.9e-15   4.9e-12       8     164 ..     117     275 ..     113     311 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 7.9e-15
                                   TEEEEEB-T.TSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB..--EE.EEEES-.SEEEEEETTEEEE..EETTTS- CS
                        Met_10   8 dvvilnlre.elkeykkvigevildktkvktvlrkvsevegefRt..fele.vlaGsdstetihkEngcrfk..lDvskvy 82 
                                   d++ +++ +  ++++k v++e++ld   + ++++k s  + + R   +e+e +laG++ teti +E   +fk  +D +k  
  gi|15669849|ref|NP_248663.1| 117 DIATVQIFNyGIEKMKDVVVETLLDL-GIDSIYEKSSG-RNRKRAglPEVEgILAGEK-TETIIQEGEAKFKvtFDGQKTG 194
                                   55555553314566889999999986.79999999998.6666653367775689988.9999988888887336999*** PP

                                   --GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TT.CEEEEES-GGG CS
                        Met_10  83 fsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvek.vvkpileDgre 162
                                   f     + r  l k ++eg++V+d+    G f++ +a   ++ +v+++dl  ++ k+ +en++lN++ k + + i++ + +
  gi|15669849|ref|NP_248663.1| 195 FFLDQRENRLELEKFIKEGDRVLDICCYTGGFSVHAAI--RGAEVVGVDLSKKALKLAEENMELNNIPKdRYEFIEGNAFK 273
                                   *************************************9..999***********************965144555555444 PP

                                   -- CS
                        Met_10 163 vi 164
                                   v+
  gi|15669849|ref|NP_248663.1| 274 VM 275
                                   43 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   6.5e-13     4e-10       1      72 [.     216     291 ..     216     314 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 6.5e-13
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBC....CGBSSSTTTEEEEEEES CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgda....edlpfedgsfDlvvssg 72 
                                   vLd++c tG ++ ++a r+  a+v+gvD+s+++l+ a+e++e +++   + ef++g+a    e++ ++ ++fD+v++  
  gi|15669849|ref|NP_248663.1| 216 VLDICCYTGGFSVHAAIRG--AEVVGVDLSKKALKLAEENMELNNIpkdRYEFIEGNAfkvmEEFIEDGEKFDVVIL-D 291
                                   9***************995..********************999999***********544444556888*****98.3 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   6.9e-13   4.3e-10      41     143 ..     212     313 ..     198     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 6.9e-13
                                   CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T.TTEEEEES-HHHHCTS--SS-EEEEEEE- CS
                 Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee.etaelkedaleallklakkkeefdivflD 120
                                   eg rvLD+++ +G+ ++ A+ Rga ++v v+ +k+a+k+ +en+e  ++ + + + +  +a++ +++  + +e+fd+v lD
  gi|15669849|ref|NP_248663.1| 212 EGDRVLDICCYTGGFSVHAAIRGA-EVVGVDLSKKALKLAEENMELNNIPKdRYEFIEGNAFKVMEEFIEDGEKFDVVILD 291
                                   6789*******************5.6899********************998999999999******************** PP

                                   -S.SSTTCH.HHHHHHHHHTT-EE CS
                 Cons_hypoth95 121 PP.yakellieevlelleekkllk 143
                                   PP +a+++  +++ ++++  ++l+
  gi|15669849|ref|NP_248663.1| 292 PPaFAQSK--KALKSAIKGYHMLN 313
                                   **666664..55556666666665 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.3   1.4e+03     220     279 ..     126     186 ..     107     188 .. 0.69
   2 !   33.5   0.0   4.5e-11   2.8e-08     155     231 ..     206     289 ..     204     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.3
                          PrmA 220 ellkeekadvivaNILaevlielaedik.klvkeggllilSGilk.ekaeevaealeqgfel 279
                                     ++ +  dv+v   L   + +++e+ + +  k  gl  + Gil+ ek+e ++++ e++f++
  gi|15669849|ref|NP_248663.1| 126 YGIE-KMKDVVVETLLDLGIDSIYEKSSgRNRKRAGLPEVEGILAgEKTETIIQEGEAKFKV 186
                                   3444.567888888888888888887762455677888899999735667777777888876 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 4.5e-11
                          PrmA 155 leklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk........eek 226
                                   lek++keg++vlD+ + +G  ++ aa  ga +vv+vD+ + A+k a+eN+elN++ + + e  ++++++k         ek
  gi|15669849|ref|NP_248663.1| 206 LEKFIKEGDRVLDICCYTGGFSVHAAIRGA-EVVGVDLSKKALKLAEENMELNNIPKdRYEF-IEGNAFKvmeefiedGEK 284
                                   89***********************99887.699*********************9866665.333333222233335788 PP

                          PrmA 227 adviv 231
                                   +dv++
  gi|15669849|ref|NP_248663.1| 285 FDVVI 289
                                   99987 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   6.9e-11   4.3e-08       3      81 ..     215     294 ..     213     301 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 6.9e-11
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgv.sdkitlvlgdvfellaklklekikvdlvflSpPw 81 
                                    +lD+++ +GG +++ a  + +v++++ +++ l++a++N e+ ++ +d+  ++ g+ f++++++ ++  k+d+v+l pP 
  gi|15669849|ref|NP_248663.1| 215 RVLDICCYTGGFSVHAAIRGAEVVGVDLSKKALKLAEENMELNNIpKDRYEFIEGNAFKVMEEFIEDGEKFDVVILDPPA 294
                                   69*******************************************99*******************************96 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   6.6e-11   4.1e-08      28     114 ..     210     301 ..     198     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 6.6e-11
                                   HCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC...EEEEE-STTTTSTT.....S-EEE CS
                           MTS  28 pkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle...vevvasdvleevee.....kkfdl 100
                                    k + ++vlD++c +G  ++++a +  e  v+ vd +++Al++a+en+e n++     e+++ ++++ +ee     +kfd+
  gi|15669849|ref|NP_248663.1| 210 IK-EGDRVLDICCYTGGFSVHAAIRGAE--VVGVDLSKKALKLAEENMELNNIPkdrYEFIEGNAFKVMEEfiedgEKFDV 287
                                   44.5678************999998777..9**********************9999888888877766643334489*** PP

                                   EEE---STTTCHCH CS
                           MTS 101 ivsNPPfhagkate 114
                                   ++  PP  a++++ 
  gi|15669849|ref|NP_248663.1| 288 VILDPPAFAQSKKA 301
                                   ******76666543 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   1.5e-10     9e-08      17     111 ..     208     317 ..     197     360 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.5e-10
                                   T-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.............HHHTTEEEECS-CCCSSHHHHHCHCHH CS
                          FtsJ  17 klfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.............aplpgvttiqgditdpetiekikeals 84 
                                   k++k+g++v+D+++ +Gg+s  ++ r g  + vv+vDl +               p ++ ++i+g+ ++   +e i++   
  gi|15669849|ref|NP_248663.1| 208 KFIKEGDRVLDICCYTGGFSVHAAIR-G--AEVVGVDLSKKalklaeenmelnnIPKDRYEFIEGNAFKVM-EEFIED--- 281
                                   56799*********************.6..69******87779999887776444558*********9885.445776... PP

                                   HSSEEEEEE--S-SS-CHHHHHHHHH.........C CS
                          FtsJ  85 erkvdlvvsDgapdvsgvhdldeylq.........s 111
                                   ++k+d+v+ D   + + +++l+++++         +
  gi|15669849|ref|NP_248663.1| 282 GEKFDVVILDPPAFAQSKKALKSAIKgyhmlnrfgA 317
                                   689*******99898888888888875554444444 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   3.9e-10   2.4e-07       8      61 ..      12      64 ..       5      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.9e-10
                         PUA_3  8 ekrlrqGhPwvfsneiasveg..eledGdvVdvfsekgkflGtGyynpqskiavRi 61
                                   +++++G + + ++ i + e+   +e G+vVd++s++gkflG+G+ np+    vRi
  gi|15669849|ref|NP_248663.1| 12 YSAIEKGNLIIPRDNILNKEDfdSIEIGEVVDIYSKRGKFLGRGFKNPKE---VRI 64
                                  5789************99999999************************97...555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0     3e-09   1.9e-06      11      87 ..     201     289 ..     192     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3e-09
               Methyltransf_23  11 dklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..............kakkaqkdqfdeqeaa 77 
                                   +++++l +  ++g rvLdi c tG ++ +++ +g++v+gvDls +a ++ae               +  + ++ +  +e  
  gi|15669849|ref|NP_248663.1| 201 ENRLELEKFIKEGDRVLDICCYTGGFSVHAAIRGAEVVGVDLSKKALKLAEenmelnnipkdryeFIEGNAFKVM--EEFI 279
                                   6677777778999*******************************9999998888777777766664444444444..3444 PP

               Methyltransf_23  78 epqgkfdlIv 87 
                                   e+ +kfd+++
  gi|15669849|ref|NP_248663.1| 280 EDGEKFDVVI 289
                                   5666888887 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   6.1e-09   3.7e-06       1      67 [.     217     290 ..     217     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 6.1e-09
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-...EEEETTEECCCT.S..S-T.T-EEEEEE CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl...kvefvvadaekl.p..fed.nsfDlvvs 67 
                                   Ld+ c tG ++ + a rga+vvgvDlsk++lkla+e+ + +++   + ef++++a k+    +ed ++fD+v++
  gi|15669849|ref|NP_248663.1| 217 LDICCYTGGFSVHAAIRGAEVVGVDLSKKALKLAEENMELNNIpkdRYEFIEGNAFKVmEefIEDgEKFDVVIL 290
                                   899999****************************99999998899999********96335566667****986 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0     5e-08   3.1e-05      55     111 ..     206     260 ..     198     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5e-08
                                   HTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SS CS
                          CMAS  55 leklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldle 111
                                   lek  +k+G+++Ldi c  G+  ++a+ r +++vvg+ lSk+  kla+++++  ++ 
  gi|15669849|ref|NP_248663.1| 206 LEKF-IKEGDRVLDICCYTGGFSVHAAIR-GAEVVGVDLSKKALKLAEENMELNNIP 260
                                   4554.79**********************.*****************9998766654 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   5.2e-08   3.2e-05      76     139 ..     236     305 ..     215     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.2e-08
                                   EEEEE-S-HHHHHHHHHHHHHTT--.GGEEEE-S-HHHHHC...--SS-EEEEEE--..SS--GGGHHHH CS
                           TRM  76 evlaNDisekAvelikeNvklneve.eivvineddAnvlla...ekkkrfdviDlDP..fGspapfldsa 139
                                   ev+  D+s+kA++l +eN++ln++  +++++ e++A  +++   e  ++fdv+ lDP  f  + + l sa
  gi|15669849|ref|NP_248663.1| 236 EVVGVDLSKKALKLAEENMELNNIPkDRYEFIEGNAFKVMEefiEDGEKFDVVILDPpaFAQSKKALKSA 305
                                   67788*******************967**************999999*********95555555555555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   9.9e-08   6.1e-05       4      80 ..     203     277 ..     200     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 9.9e-08
               Methyltransf_18   4 RLkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagl.edkievrlsdGleklke 80 
                                   RL ++ +++++g+rv+Di++  g  +++++ +g   +v+ +D+++++l+ a+en+e +++ +d+ e++ ++ +++++e
  gi|15669849|ref|NP_248663.1| 203 RL-ELEKFIKEGDRVLDICCYTGGFSVHAAIRGA--EVVGVDLSKKALKLAEENMELNNIpKDRYEFIEGNAFKVMEE 277
                                   66.4679**********************97775..6********************999899********9999863 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.2e-07   7.5e-05      46     138 ..     212     298 ..     201     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.2e-07
                      N6_Mtase  46 sgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfe..kdk 124
                                   +g  v+D +c +gg+ v+a+          +  ++ G+++ +++ +La+ N+ l +i +++ +   g++++  ++   + +
  gi|15669849|ref|NP_248663.1| 212 EGDRVLDICCYTGGFSVHAAI---------RGAEVVGVDLSKKALKLAEENMELNNIPKDRYEFIEGNAFKVMEEFieDGE 283
                                   555699********9887754.........57899**********************************986554334889 PP

                      N6_Mtase 125 kfdvvvaNpp.fnqk 138
                                   kfdvv+  pp f q+
  gi|15669849|ref|NP_248663.1| 284 KFDVVILDPPaFAQS 298
                                   *******99945554 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       5.7   3.5e+03      82     130 ..      86     132 ..      71     136 .. 0.44
   2 !   21.5   0.0   1.9e-07   0.00012      45     121 ..     210     289 ..     200     314 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.7
                                   HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEE...ES-GGG-S CS
               Ubie_methyltran  82 enmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtv...sfGlrnvt 130
                                   e  Lk g k   +  +++ ++l+  +      d+  D+ tv    +G+  + 
  gi|15669849|ref|NP_248663.1|  86 EYRLKLGFKDTYRMVYTQSDWLN--GL---VIDKYNDIATVqifNYGIEKMK 132
                                   33444444444444444444432..22...3333333333311146665555 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.9e-07
                                   S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHH..HHTSSTEEEEE--TTT-..TTS-..T-EEE CS
               Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklk..eegkinieflqanaeeL..pfed..dsfDv 119
                                    k+g +vlD+++ tg ++++   ++ +  +vv++D++++ Lk +e+ ++  +  k + ef+ +na ++  +f +  + fDv
  gi|15669849|ref|NP_248663.1| 210 IKEGDRVLDICCYTGGFSVH--AAI-RGAEVVGVDLSKKALKLAEENMElnNIPKDRYEFIEGNAFKVmeEFIEdgEKFDV 287
                                   5899***********87654..333.4569**************998762155667*********8872233332467777 PP

                                   EE CS
               Ubie_methyltran 120 vt 121
                                   v 
  gi|15669849|ref|NP_248663.1| 288 VI 289
                                   65 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   5.2e-07   0.00032       1      71 [.     217     289 ..     217     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 5.2e-07
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.....ssfDlvv 71 
                                   L+i c tG ++ + + +  ++e++gvD+s++a+ + +e+  + +n   +++e+ + ++++  ++     ++fD+v+
  gi|15669849|ref|NP_248663.1| 217 LDICCYTGGFSVHAAIR--GAEVVGVDLSKKAL-KLAEENMELNNIPKDRYEFIEGNAFKVMEEfiedgEKFDVVI 289
                                   8999****999999877..**************.777888888888899999999999888888999********8 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.5e-06    0.0028       7      93 ..     211     298 ..     208     310 .. 0.82
   2 ?   -0.5   0.0       1.3   8.2e+02     133     171 ..     323     364 ..     317     378 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.5e-06
                                   -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHH..HTT--SEEEEES-CTCCHHHHCC....EEEE CS
               Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlk..rLgvtntivleaDarkidkvlgg..elfDri 83 
                                   +e++++lD+c+  Gg   h a +    ++vv vd +k+ lk  +en++   ++      +e+ a k+ +   +  e+fD +
  gi|15669849|ref|NP_248663.1| 211 KEGDRVLDICCYTGGFSVHAA-I--RGAEVVGVDLSKKALKLAEENMElnNIPKDRYEFIEGNAFKVMEEFIEdgEKFDVV 288
                                   799************999965.4..6899****************9752267777889999998887766655589***** PP

                                   EEEE--CCGG CS
               Methyltr_RsmB-F  84 LlDaPCsgtg 93 
                                   +lD P  ++ 
  gi|15669849|ref|NP_248663.1| 289 ILDPPAFAQS 298
                                   ****987765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                                   EEEEEES--STTTT...HHHHHHHHHH-TTEEEESSBSTTST CS
               Methyltr_RsmB-F 133 vlvYsTCsvlveEn...eevieeaLkkredvelvetelsepk 171
                                    lv + Cs  +e +     vi++ Lk+++ +++++   ++p+
  gi|15669849|ref|NP_248663.1| 323 LLVTCSCSQPLEPDafkALVIDACLKAKKWAKIIKYGSQSPD 364
                                   578888887777652225689999999988888887766665 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.8e-06    0.0011      45     130 ..     210     291 ..     193     306 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                                   HHT--EEEEE--TTS.HHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-.GGGEEEEES-HHHHHHHHHTSSS--- CS
                Methyltransf_3  45 lvnakrvleiGvftG.yslLatalalPeDGkilaididreayeialkfiqkagv.aekieliegdalkvLeelvkdkklpe 123
                                   + +  rvl+i  +tG +s+ a a+      +++ +d  ++a ++a + ++   + +++ e+ieg+a kv+ee+++d +  +
  gi|15669849|ref|NP_248663.1| 210 IKEGDRVLDICCYTGgFSVHA-AI---RGAEVVGVDLSKKALKLAEENMELNNIpKDRYEFIEGNAFKVMEEFIEDGE--K 284
                                   5567899******97366544.44...3568******************9988835689*****************95..9 PP

                                   EEEEEE- CS
                Methyltransf_3 124 fDfifvD 130
                                   fD++ +D
  gi|15669849|ref|NP_248663.1| 285 FDVVILD 291
                                   **99988 PP

>> Methyltransf_10  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.2   4.5e+03     217     235 ..     166     184 ..     147     189 .. 0.71
   2 !   17.7   0.0   2.9e-06    0.0018     123     207 ..     231     314 ..     208     334 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.2
                                   ------TTTSHHHHHHHHH CS
               Methyltransf_10 217 lnfgGqkaelyceGGevaf 235
                                      +G+k+e + + Ge++f
  gi|15669849|ref|NP_248663.1| 166 GILAGEKTETIIQEGEAKF 184
                                   4568999999999999998 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.9e-06
                                   HHH--EEEEEES-HHHHHHHHHHHHHT.T-TTTEEEEE--TT-SCCHHSSTTSS-EEEEEE-S---SS------------. CS
               Methyltransf_10 123 teyGWrfvgsevddvslasakaivesnsklsdaiklrkqkekkaifdglieenerydvtlCnPPfhaslaeakagserklk 203
                                      G + vg ++++++l+ a+ ++e n+  +d  +     +  ++++ +ie  e++dv++ +PP +a+ ++a +++ +  +
  gi|15669849|ref|NP_248663.1| 231 AIRGAEVVGVDLSKKALKLAEENMELNNIPKDRYEFI-EGNAFKVMEEFIEDGEKFDVVILDPPAFAQSKKALKSAIKGYH 310
                                   5568889********************6667777766.568899************************9999888777666 PP

                                   ..-- CS
               Methyltransf_10 204 nlgk 207
                                    l++
  gi|15669849|ref|NP_248663.1| 311 MLNR 314
                                   6655 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       9.3   5.8e+03     156     188 ..      56      88 ..      40      94 .. 0.47
   2 ?   12.5   0.0   0.00014     0.084      76     130 ..     234     293 ..     209     320 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.3
                                   -TT..-EEEEEESSHHHHHCC---ESEEEEEEE CS
                       UPF0020 156 lrgggrlvlltsenkalekaleeralrkvkekn 188
                                   +++     ++t  +++l + + ++++ k++e++
  gi|15669849|ref|NP_248663.1|  56 FKNPKEVRIMTLRKEDLDENYIREKIIKANEYR 88 
                                   444444444444444444444444333333333 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                                   H--EEEEES-HHHHHHHHHHHHHTT-.GGGEEEEE--GGG--....STTS---EEEE--- CS
                       UPF0020  76 elklygsDldrrvvqgareNaekagv.gdliefsqadaakLr....lkegevdvivtnpP 130
                                    ++++g+Dl +++++ a+eN e  ++ +d+ ef + +a k+     ++ +++dv++ +pP
  gi|15669849|ref|NP_248663.1| 234 GAEVVGVDLSKKALKLAEENMELNNIpKDRYEFIEGNAFKVMeefiEDGEKFDVVILDPP 293
                                   34577****************987763789********9998788767779********9 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.1e-05      0.05       5      86 ..     216     297 ..     212     327 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.1e-05
                                   EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTT..SSEEEEES-CCCHHHHCS-TTSEEEEEEES--- CS
                Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealel..kNlrilrgdalkvllelledgslekifilFPDP 83 
                                   vl+i+c  G+f v+ A + ++  ++G+++++k ++ + +++e +++     + ++g+a+kv++e++edg+   ++il P  
  gi|15669849|ref|NP_248663.1| 216 VLDICCYTGGFSVHAAIRGAE--VVGVDLSKKALKLAEENMELNNIpkDRYEFIEGNAFKVMEEFIEDGEKFDVVILDPPA 294
                                   89***************9987..69*******999999999887542145689***************9988888876655 PP

                                   --S CS
                Methyltransf_4  84 wfK 86 
                                   + +
  gi|15669849|ref|NP_248663.1| 295 FAQ 297
                                   555 PP

>> SAM_MT  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013     0.082     108     166 ..     242     302 ..     225     326 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                        SAM_MT 108 LLedglkRakqdaeigellaerlkLlaasslealakleee..kpdvvYlDPmyPhkkksal 166
                                   L + +lk a+++ e++++ + r +++++++++++++  e+  k dvv lDP    ++k+al
  gi|15669849|ref|NP_248663.1| 242 LSKKALKLAEENMELNNIPKDRYEFIEGNAFKVMEEFIEDgeKFDVVILDPPAFAQSKKAL 302
                                   55789999****************************9998889*******97666666666 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00015     0.092     202     249 ..     213     260 ..     204     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
               tRNA_U5-meth_tr 202 kgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankid 249
                                    + +l++ c  G fs+  a +   v+  +++k +++ a  n++ n+i 
  gi|15669849|ref|NP_248663.1| 213 GDRVLDICCYTGGFSVHAAIRGAEVVGVDLSKKALKLAEENMELNNIP 260
                                   44589****************************************994 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.13      22      81 ..     202     256 ..     181     286 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                   --HHHHHHHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTT CS
                          TPMT  22 vnpllkkfldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanl 81 
                                       l kf+++     g rvl   C  +   v  A +g evvGv+ls++A++ + e+ +l
  gi|15669849|ref|NP_248663.1| 202 NRLELEKFIKE-----GDRVLDICCYTGGFSVHAAIRGAEVVGVDLSKKALKLAEENMEL 256
                                   44555555555.....56666666655555566699***************996444444 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00038      0.24      10      63 ..     230     289 ..     226     317 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                                   HHHTT-EEEEEESSHHHHHHHHH.TTESEEEET.....TTCHHHHHHHHHTT.TSSEEEEE CS
                    ADH_zinc_N  10 AkalGaeviavdsseeklelakk.lGadeviny.....keadlverikeltg.gegvdvvf 63 
                                   A++ Gaev++vd s++ l+la++ +  + +        +  +  + ++e+ + ge++dvv+
  gi|15669849|ref|NP_248663.1| 230 AAIRGAEVVGVDLSKKALKLAEEnMELNNIPKDryefiEG-NAFKVMEEFIEdGEKFDVVI 289
                                   7899******************944444444435555422.45555555554467888765 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00042      0.26      29      59 ..      34      64 ..       4      75 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00042
                                  TT--TTSEEEEEETTSCEEEEEEESS-HHHH CS
                           PUA 29 gdfeegdvVaivdedgelvavGlanysseel 59
                                  +++e g+vV+i+++ g+++++G  n +   +
  gi|15669849|ref|NP_248663.1| 34 DSIEIGEVVDIYSKRGKFLGRGFKNPKEVRI 64
                                  3469******************988766555 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00041      0.25      35     117 ..     224     322 ..     189     358 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00041
               N6-adenineMlase  35 saPsvyealkkek......kkekvlLleiDkrFealygeekfvfYdlnnpeelpeel..kgkfdviviDPPF..lseeclk 105
                                   +  sv++a++  +      +k+++ L e +   +++ +++++ f + n  + ++e++   +kfdv+++DPP    s++ lk
  gi|15669849|ref|NP_248663.1| 224 GGFSVHAAIRGAEvvgvdlSKKALKLAEENMELNNI-PKDRYEFIEGNAFKVMEEFIedGEKFDVVILDPPAfaQSKKALK 303
                                   445788888877788888877888888888888666.666455555444444556668889**********6354455555 PP

               N6-adenineMlase 106 klaktaklllk.......k 117
                                   ++ k  ++l +       +
  gi|15669849|ref|NP_248663.1| 304 SAIKGYHMLNRfgakladR 322
                                   5444444444455556653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2394.76
//
Query:       gi|15669850|ref|NP_248664.1|  [L=225]
Description: hypothetical protein MJ_1654 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0002   21.8   1.3    0.00028   21.3   1.3    1.2  1  PCI             PCI domain
    0.00059   19.3   0.1     0.0012   18.3   0.1    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0064   16.4   0.0      0.015   15.3   0.0    1.5  1  HTH_11          HTH domain
     0.0068   16.7   0.0      0.017   15.5   0.0    1.6  1  Rrf2            Transcriptional regulator
     0.0073   16.3   1.3      0.011   15.7   0.3    1.8  2  HTH_Mga         M protein trans-acting positive regulator (MG
  ------ inclusion threshold ------
      0.016   14.9   0.0      0.028   14.1   0.0    1.4  1  Cytochrom_C550  Cytochrome c-550 domain
       0.02   15.3   0.0      0.031   14.6   0.0    1.3  1  Rep_fac-A_3     Replication factor A protein 3
      0.022   14.6   0.6      0.099   12.5   0.1    2.5  2  TrmB            Sugar-specific transcriptional regulator TrmB
       0.03   14.5   0.0      0.058   13.5   0.0    1.5  1  AbiEi_4         Transcriptional regulator, AbiEi antitoxin


Domain annotation for each model (and alignments):
>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.3   1.4e-07   0.00028      29      88 ..     141     212 ..     117     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.4e-07
                                   HHHHTTHHH............HHHHHHHHHHHHHHHHHHHCESEEEHHHHHHHHTSSHHHHHHHHHHHHHTT CS
                           PCI  29 lladdglaq............llesLekkvrerllrqvskiyssislerlaklldlsvdevEkilvklIrdg 88 
                                   ll++ +l++            + e L   v++  +  +++    i++e+la++++++++++Ek+l++l ++g
  gi|15669850|ref|NP_248664.1| 141 LLERAELYEeeneemsleeevYTEILNSDVIKDKILAIIENVGEITYEELAEKINIPEEDLEKYLSELKESG 212
                                   44444444444444444446688*******************************************986665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   6.2e-07    0.0012       7      45 ..     174     212 ..     169     212 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.2e-07
                        HTH_24   7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeG 45 
                                   kIL +++  + i++ eLAe+++++   + ++l +L+e+G
  gi|15669850|ref|NP_248664.1| 174 KILAIIENVGEITYEELAEKINIPEEDLEKYLSELKESG 212
                                   8******************************99999998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   7.4e-06     0.015       4      51 ..     174     220 ..     172     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.4e-06
                        HTH_11   4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51 
                                   +il ++ e+ g i+ eeLAe++n+ +    +++ +L+e+g+  e +pg
  gi|15669850|ref|NP_248664.1| 174 KILAII-ENVGEITYEELAEKINIPEEDLEKYLSELKESGDIFEPRPG 220
                                   799999.99999****************************88777766 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.4e-06     0.017      22      53 ..     181     212 ..     174     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.4e-06
                                   TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTT CS
                          Rrf2  22 eeepvsseeiaerqnispsylekilakLrkag 53 
                                   + + ++ ee+ae+ ni+++ lek l++L+++g
  gi|15669850|ref|NP_248664.1| 181 NVGEITYEELAEKINIPEEDLEKYLSELKESG 212
                                   444599***********************998 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         5     1e+04      18      26 ..     124     132 ..     123     136 .. 0.72
   2 !   15.7   0.3   5.6e-06     0.011      12      46 ..     177     210 ..     172     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5
                       HTH_Mga  18 eksltldel 26 
                                   e++++l +l
  gi|15669850|ref|NP_248664.1| 124 ERWIKLRDL 132
                                   789999865 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 5.6e-06
                       HTH_Mga  12 elLteneksltldelakeLglseltlqsdiseLne 46 
                                   + ++en +++t+ ela++ ++ e  l +++seL+e
  gi|15669850|ref|NP_248664.1| 177 A-IIENVGEITYEELAEKINIPEEDLEKYLSELKE 210
                                   4.5677***************************96 PP

>> Cytochrom_C550  Cytochrome c-550 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.4e-05     0.028      72     123 ..      98     145 ..      94     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                                   HHHHHHS-B-TTSSSBGTTTSSSCCGTTTTGGGTTS-HHHHHHHHHHHHHHH CS
                Cytochrom_C550  72 lvdylknPtsyDGeedlaelhpslksadiypelrnltdedlkaiagyilvaa 123
                                   +vd + +P +yDGe+ +      +k+++ + +lr+l+   +k+   y+l  a
  gi|15669850|ref|NP_248664.1|  98 IVDVIGRPRTYDGEKYI-MAEIIRKRDERWIKLRDLE---IKKTRKYLLERA 145
                                   8999***********66.67788999999*9988886...455555666555 PP

>> Rep_fac-A_3  Replication factor A protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.6e-05     0.031      17      82 ..      55     121 ..      42     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                                   TTSEEEEEEEEEEETTSSEEEEE-TTS-EEEEEESS--SS---SEEEEEEEE-T..TS-EEEEEEEE- CS
                   Rep_fac-A_3  17 vgrtvrivgkvesvpsgktlilqstdggsvtvrlsedstleiskwvEvvGkvsd..dlgirldsvvef 82 
                                   + r vri+gkve++ +  ++i    dg +v    +++  +e + +v+v+G+  +  + + ++++++ +
  gi|15669850|ref|NP_248664.1|  55 KVRRVRILGKVENI-NVGNIISFYVDGVNVRYFEEKPVYIEEGDIVDVIGRPRTydGEKYIMAEIIRK 121
                                   5578**********.8888888888899999999999999***********99985444455555554 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.5   4.9e+03       9      20 ..     157     168 ..     156     172 .. 0.79
   2 ?   12.5   0.1     5e-05     0.099      20      53 ..     182     215 ..     174     225 .] 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.5
                                   HCCCHCHHHHHH CS
                          TrmB   9 yEakvYlaLlkl 20 
                                    E +vY+ +l++
  gi|15669850|ref|NP_248664.1| 157 LEEEVYTEILNS 168
                                   588999999976 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5e-05
                                   HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                          TrmB  20 lgpatadeiaeelgvprskvYevLrsLedkGlVe 53 
                                    g+ t +e+ae++++p+    ++L++L++ G + 
  gi|15669850|ref|NP_248664.1| 182 VGEITYEELAEKINIPEEDLEKYLSELKESGDIF 215
                                   58899************************99775 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.9e-05     0.058      12      46 ..     183     222 ..     173     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                       AbiEi_4  12 Glfttrelea.aGispsa....lrrLvrkGwLvrlrrGvY 46 
                                   G +t++el++  +i++      l++L ++G++   r+GvY
  gi|15669850|ref|NP_248664.1| 183 GEITYEELAEkINIPEEDlekyLSELKESGDIFEPRPGVY 222
                                   67899999999*****999********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1526.22
//
Query:       gi|15669851|ref|NP_248665.1|  [L=183]
Description: adenine phosphoribosyltransferase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-18   65.8   0.7    3.8e-18   65.5   0.7    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
    8.4e-06   25.4   0.0    1.2e-05   24.9   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase
    0.00015   21.4   0.1    0.00022   20.8   0.1    1.3  1  PRTase_2      Phosphoribosyl transferase
  ------ inclusion threshold ------
        1.5    8.8   5.4         17    5.4   0.2    2.9  3  DUF1967       Domain of unknown function (DUF1967)


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.7   8.5e-22   3.8e-18      26     135 ..      49     161 ..      33     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 8.5e-22
                                   --GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...........EE----TTSEEEEE-SEESSSHHH CS
                  Pribosyltran  26 yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes...rlledpagkkVliVDDildtGgTl 103
                                   +++  + +v+ +  G+p+++ l+ + ++p++++rk+ y  +g   + ++   +     l ++ +g kV+i+DD+++tGgT+
  gi|15669851|ref|NP_248665.1|  49 DFEGATKLVTAEAMGIPLVTTLSLYTDIPYVIMRKREYKLPGEIPVFQSTGYSKgqlYLNGIEKGDKVVIIDDVISTGGTM 129
                                   55666778999999*****************************999876554449999*********************** PP

                                   HHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHH CS
                  Pribosyltran 104 laalelLkekgpeevriavlvdkpateeevdk 135
                                   +a++++Lk++g+e+  i+++++++++++ v+ 
  gi|15669851|ref|NP_248665.1| 130 IAIIDALKRAGAEIKDIICVIERGEGKKIVEE 161
                                   **********************9999987754 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   2.6e-09   1.2e-05     120     157 ..     112     149 ..      80     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.6e-09
                       UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvl 157
                                   + ++v+++D vi+TGg+++a+i+ Lk++g++ ++I+++
  gi|15669851|ref|NP_248665.1| 112 KGDKVVIIDDVISTGGTMIAIIDALKRAGAEIKDIICV 149
                                   4578*****************************99875 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   4.9e-08   0.00022     118     156 ..     110     148 ..     102     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.9e-08
                      PRTase_2 118 laaakelvLvDDEistGktalnliralqeklpr.kryvvv 156
                                   +++ +++v++DD istG t++++i+al+++  + k ++ +
  gi|15669851|ref|NP_248665.1| 110 IEKGDKVVIIDDVISTGGTMIAIIDALKRAGAEiKDII-C 148
                                   567789**********************9988844443.3 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2    0.0039        17      50      65 ..     105     120 ..     102     123 .. 0.85
   2 ?    5.2   0.1    0.0046        21      46      63 ..     132     149 ..     128     152 .. 0.86
   3 ?   -2.7   0.1       1.3     6e+03      48      62 ..     168     182 ..     167     183 .] 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0039
                                   HHTTT--TT-EEEETT CS
                       DUF1967  50 LrkaGakeGdtVrIgd 65 
                                   L   G+++Gd+V+I d
  gi|15669851|ref|NP_248665.1| 105 LYLNGIEKGDKVVIID 120
                                   6678*********987 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0046
                                   HHHHHHTTT--TT-EEEE CS
                       DUF1967  46 vedaLrkaGakeGdtVrI 63 
                                   ++daL++aGa+  d + +
  gi|15669851|ref|NP_248665.1| 132 IIDALKRAGAEIKDIICV 149
                                   89*********9999876 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.3
                                   HHHHTTT--TT-EEE CS
                       DUF1967  48 daLrkaGakeGdtVr 62 
                                   + L k  + +G  V 
  gi|15669851|ref|NP_248665.1| 168 KTLVKIDVVDGKVVI 182
                                   678899999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1153.22
//
Query:       gi|15669852|ref|NP_248666.1|  [L=237]
Description: 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-70  235.9   0.0    4.4e-70  235.7   0.0    1.0  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
  ------ inclusion threshold ------
      0.061   13.4   0.0       0.11   12.5   0.0    1.4  1  FTCD           Formiminotransferase domain


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.7   0.0   4.9e-74   4.4e-70       1     217 [.      39     233 ..      39     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 235.7 bits;  conditional E-value: 4.9e-74
                                   .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHHH CS
                 FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsveeA 81 
                                   ki+c+glny +h++e++   +e p+      p++flk++s+++  +d i rP++s+++dyEvELa+vigk+++++ + +eA
  gi|15669852|ref|NP_248666.1|  39 KIICVGLNYIDHAKELN---MEIPE-----YPIIFLKPTSAIIYNEDYIIRPRISKRVDYEVELAIVIGKKCKNI-KKDEA 110
                                   69*************96...67777.....677******************************************.9**** PP

                                   HTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGGTTTSHHH CS
                 FAA_hydrolase  82 edaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkdmifspae 162
                                    d+i Gyt+lnDv+aRdlq+++    +w+++ksfdtf+piGp iv+  +++ p +l++++rvnge +q+sntk+mif+++e
  gi|15669852|ref|NP_248666.1| 111 NDYIMGYTILNDVTARDLQQKDG---QWTRAKSFDTFCPIGPRIVK--DID-PMNLNIECRVNGEIKQKSNTKNMIFDVYE 185
                                   ***********************...******************76..664.479************************** PP

                                   HHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE CS
                 FAA_hydrolase 163 liahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrV 217
                                   l++ +++++tL pGd+i+tGTp+gvg  e     lk+gD+ve+eieg+G lrn V
  gi|15669852|ref|NP_248666.1| 186 LVEFVASIMTLYPGDIISTGTPPGVG--E-----LKAGDVVECEIEGIGILRNYV 233
                                   ************************99..4.....*******************88 PP

>> FTCD  Formiminotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.3e-05      0.11      55     124 ..      29      98 ..      16     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                          FTCD  55 slnltdievtplhvvfeevkkeaeelglevtgseivglvplealleaakyylekeklfileeeekiklai 124
                                   sln+++i+ t++  v  +  ++a+el++e+    i+ l p++a++   +y ++ +    ++ e +++++i
  gi|15669852|ref|NP_248666.1|  29 SLNIKEIKPTKIICVGLNYIDHAKELNMEIPEYPIIFLKPTSAIIYNEDYIIRPRISKRVDYEVELAIVI 98 
                                   89*************************************************9988877777776666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1599.31
//
Query:       gi|15669853|ref|NP_248667.1|  [L=332]
Description: hypothetical protein MJ_1657 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-08   31.7   0.0    2.1e-05   23.8   0.0    2.2  2  Peptidase_U32  Peptidase family U32
  ------ inclusion threshold ------
       0.12   12.3   0.2       0.28   11.1   0.2    1.5  1  WD40_alt       Alternative WD40 repeat motif
       0.14   11.6   0.0       0.54    9.7   0.0    1.8  2  G3P_antiterm   Glycerol-3-phosphate responsive antiterminator


Domain annotation for each model (and alignments):
>> Peptidase_U32  Peptidase family U32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   3.5e-09   2.1e-05       7      94 ..      99     185 ..      93     208 .. 0.90
   2 !    5.7   0.0    0.0012         7     170     192 ..     248     270 ..     239     282 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.5e-09
                 Peptidase_U32   7 yleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaREl..sleeikaikekvpdv 85 
                                   ++ +l+++gvd v ++Dp +++la+++   le+ +S  a + + +++ f+ e  +  + l   +  +++ i++i+e+v ++
  gi|15669853|ref|NP_248667.1|  99 IFSQLKNIGVDSVALSDPYLVDLAKNN--GLEVNVSCIALVDSLDKALFWDEKEVYAITLDSSInrHFDIIQEIRENV-SC 176
                                   67899**********************..*******************************99998899**********.99 PP

                 Peptidase_U32  86 elEvfvhGa 94 
                                   +l ++v  a
  gi|15669853|ref|NP_248667.1| 177 KLKILVNEA 185
                                   998888655 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0012
                 Peptidase_U32 170 vdslKIeGRmkspeyvatvvrvY 192
                                   vd +KI GR+     +++v+++Y
  gi|15669853|ref|NP_248667.1| 248 VDIFKISGRSHPIGWIKRVINAY 270
                                   899*******************9 PP

>> WD40_alt  Alternative WD40 repeat motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   4.6e-05      0.28      11      37 ..       8      30 ..       5      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.6e-05
                      WD40_alt 11 GdqeqlkvrvseLeeEVrtLrKInkdL 37
                                  Gd e+lk+ v    +E++ LrKInk L
  gi|15669853|ref|NP_248667.1|  8 GDFESLKIIV----NEINKLRKINKKL 30
                                  7788888877....589********88 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.24   1.4e+03      24      48 ..      15      39 ..       8      51 .. 0.78
   2 ?    9.7   0.0     9e-05      0.54      29     102 ..      57     139 ..      47     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.24
                                  E--EETTTHHHHHHHHHHTT-EEEE CS
                  G3P_antiterm 24 llegdilnlkeiveklkkagkkvfv 48
                                  ++  +i++l++i +klkk+   v+v
  gi|15669853|ref|NP_248667.1| 15 IIVNEINKLRKINKKLKKESFEVYV 39
                                  5667899999999999999888877 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 9e-05
                                   TTTHHHHHHHHHHTT-..EEEEEGGGEET--SSHHHHHHHH......H.TT-SEEEES-HHHHHHHHHTT-.-EEEEEE-- CS
                  G3P_antiterm  29 ilnlkeiveklkkagk..kvfvhiDlieGlskdeaaveflk......keikvdGiistksslikkakklgl.ltiqrlfli 100
                                     +l + v+ +kk++    v++++  i G+    +++++++      k+i+vd++  + + l+  ak++gl + +  + l+
  gi|15669853|ref|NP_248667.1|  57 FEDLAKQVNYAKKHNVrfEVVINASCIGGMHLTPKGISYINwifsqlKNIGVDSVALSDPYLVDLAKNNGLeVNVSCIALV 137
                                   5677788888888875226999*****************975555557899********************6678888888 PP

                                   SH CS
                  G3P_antiterm 101 Ds 102
                                   Ds
  gi|15669853|ref|NP_248667.1| 138 DS 139
                                   88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2121.99
//
Query:       gi|15669854|ref|NP_248668.1|  [L=119]
Description: hypothetical protein MJ_1658 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-57  192.4   2.1    2.1e-57  192.2   2.1    1.0  1  DUF5402   Family of unknown function (DUF5402)


Domain annotation for each model (and alignments):
>> DUF5402  Family of unknown function (DUF5402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.2   2.1   1.2e-61   2.1e-57       1     119 []       1     119 []       1     119 [] 0.99

  Alignments for each domain:
  == domain 1  score: 192.2 bits;  conditional E-value: 1.2e-61
                       DUF5402   1 lkdkllkdreklekklqnllgkevfvsevdifalrcGcvGilievrGlevddveifkekileklkelakdleikadvvyar 81 
                                   +kdk+lkdre++ek++++llg+e+f+se+difa+rcGcvGi+i+vrGl+vddveifkekil+kl+elak+++i+ad++++r
  gi|15669854|ref|NP_248668.1|   1 MKDKILKDREEIEKFFIKLLGREIFISEMDIFASRCGCVGIMITVRGLFVDDVEIFKEKILNKLEELAKSYDINADWIFVR 81 
                                   89******************************************************************************* PP

                       DUF5402  82 vvPGtaevidlavrklcnrcrkefsgkkPrPdllvlkf 119
                                   v+PG++++i+++vr++cn+cr+e+++kkPrPdl++lkf
  gi|15669854|ref|NP_248668.1|  82 VLPGSDDIINIGVREFCNICREEYRFKKPRPDLISLKF 119
                                   ***********************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 846.26
//
Query:       gi|15669855|ref|NP_248669.1|  [L=361]
Description: hypothetical protein MJ_1659 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-85  285.3   9.4    4.3e-85  285.3   9.4    1.6  2  ATPase_2      ATPase domain predominantly from Archaea
    8.7e-09   35.8   0.0    5.2e-08   33.3   0.0    2.2  2  AAA_22        AAA domain
    1.2e-08   35.1   7.4    7.9e-06   25.9   0.2    3.1  3  AAA_14        AAA domain
    1.1e-07   32.4   0.0    2.3e-07   31.4   0.0    1.5  1  AAA_16        AAA ATPase domain
      3e-06   27.7   0.0    0.00012   22.5   0.0    2.5  1  AAA           ATPase family associated with various cellular 
    0.00066   19.2   0.0     0.0013   18.3   0.0    1.4  1  AAA_7         P-loop containing dynein motor region
     0.0084   16.0   1.6      0.088   12.7   0.0    2.8  3  TK            Thymidine kinase
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.026   14.1   0.0    1.4  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.028   14.8   0.0       0.12   12.8   0.0    2.1  2  RNA_helicase  RNA helicase
       0.03   14.7   0.0       0.16   12.3   0.0    2.0  1  AAA_19        AAA domain
      0.049   12.8   0.0       0.15   11.2   0.0    1.9  1  NB-ARC        NB-ARC domain
      0.056   14.0   0.8       0.81   10.2   0.0    2.7  3  AAA_18        AAA domain
      0.068   13.1   0.0       0.29   11.0   0.0    2.2  2  NACHT         NACHT domain
      0.082   13.0   0.0       0.33   11.1   0.0    2.1  1  MMR_HSR1      50S ribosome-binding GTPase
      0.083   12.7   0.0       0.39   10.5   0.0    2.1  2  AAA_29        P-loop containing region of AAA domain
       0.12   12.8   0.0        0.3   11.6   0.0    1.8  1  ABC_tran      ABC transporter
       0.42   10.9   7.1        8.3    6.7   0.0    3.4  3  CdiA_C        Contact-dependent growth inhibition CdiA C-term
        2.6    8.5   8.1       0.33   11.3   0.6    3.0  2  RICH          RICH domain


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.3   9.4   4.3e-88   4.3e-85       1     232 [.       7     257 ..       7     258 .. 0.99
   2 ?   -1.7   0.2       2.2   2.2e+03      39      40 ..     300     301 ..     261     358 .. 0.61

  Alignments for each domain:
  == domain 1  score: 285.3 bits;  conditional E-value: 4.3e-88
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie...eeeekkkl 78 
                                   FfdReke+++l ++l+ epn iyfiYGp++sGKt+L+k+iien++d dkyv++yi+lre++isk+++fie   +++e++++
  gi|15669855|ref|NP_248669.1|   7 FFDREKEINYLVKVLSFEPNLIYFIYGPINSGKTTLIKHIIENKLDRDKYVVFYINLREHFISKYEDFIEvlfNTYEETFI 87 
                                   9************************************************************************99999999 PP

                      ATPase_2  79 ekal......................giavpkaeleeilk.eksklvfkaielllekikkkgkkiiiiiDelqklidlgln 136
                                   ek +                      gi+vpk++l+e+l+ ++s++vf+++++++e+ikkkgk++i+iiDelqk++dl++n
  gi|15669855|ref|NP_248669.1|  88 EKLKkyllsfindlpknidvkstiltGIPVPKNTLNEFLStKNSENVFEYLTKIFEDIKKKGKQPILIIDELQKIGDLKIN 168
                                   9999999************************************************************************** PP

                      ATPase_2 137 gaellvkeLlnliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkeleelskedfe 217
                                     ++l++eL+n++ +ltkekhlc+v+clsS++lfiervyne++l++r+ky+lvdd+d++t++ flk+     +++++e+++
  gi|15669855|ref|NP_248669.1| 169 --GFLIYELFNFFIDLTKEKHLCHVLCLSSDSLFIERVYNEGTLKDRCKYYLVDDFDYKTTKAFLKK-----HNFNDEEID 242
                                   ..*****************************************************************.....79******* PP

                      ATPase_2 218 eiyryvGGkPkalve 232
                                    +++y+GGkP++lve
  gi|15669855|ref|NP_248669.1| 243 IVWHYFGGKPIKLVE 257
                                   ************986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                      ATPase_2  39 ei 40 
                                   ++
  gi|15669855|ref|NP_248669.1| 300 RV 301
                                   22 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   5.2e-11   5.2e-08       6     129 ..      27     194 ..      24     200 .. 0.86
   2 ?   -2.4   0.0       5.4   5.4e+03      67      76 ..     282     295 ..     249     310 .. 0.49

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 5.2e-11
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsst..sskdllrellralglelka............ 70 
                                    i +++G+  +GKTtl++ + e++         r+++v  +++l +    + +d+ + l++ +++   +            
  gi|15669855|ref|NP_248669.1|  27 LIYFIYGPINSGKTTLIKHIIENKLD-------RDKYVvfYINLREHFisKYEDFIEVLFNTYEETFIEklkkyllsfind 100
                                   5789****************999864.......4444446999999999888899999999888765559999******** PP

                        AAA_22  71 ..........................erlsseellealeqalrarav...ielliiDEaqhlr..s......eealeeLrs 114
                                                             ++++se ++e+l++ +++ ++   +++liiDE q++   +       e+++++ +
  gi|15669855|ref|NP_248669.1| 101 lpknidvkstiltgipvpkntlneflSTKNSENVFEYLTKIFEDIKKkgkQPILIIDELQKIGdlKingfliYELFNFFID 181
                                   **************************999999999999999999999999************6552666777788888888 PP

                        AAA_22 115 llnlsrkgvqliLvG 129
                                   l +  +k++ ++L+ 
  gi|15669855|ref|NP_248669.1| 182 LTK--EKHLCHVLCL 194
                                   888..9999999975 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.4
                        AAA_22  67 elka....erlsse 76 
                                   +lk+     +++++
  gi|15669855|ref|NP_248669.1| 282 QLKDllysLEDDNK 295
                                   22223333333444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.2   7.9e-09   7.9e-06       3      67 ..      27      93 ..      25     106 .. 0.78
   2 !   12.5   0.1   0.00011      0.11      48     120 ..     134     217 ..     107     228 .. 0.68
   3 ?   -0.9   0.3       1.5   1.5e+03      25      39 ..     321     337 ..     268     360 .. 0.60

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7.9e-09
                        AAA_14  3 kilvitGaRrvGKTtllkqlikell.vkkesilyinldderdkkladpe.kllelilek.lkeekkty 67
                                   i++i G+  +GKTtl+k++i+++l  +k  ++yinl ++  +k++d+   l + + e  +++  k+y
  gi|15669855|ref|NP_248669.1| 27 LIYFIYGPINSGKTTLIKHIIENKLdRDKYVVFYINLREHFISKYEDFIeVLFNTYEETfIEK-LKKY 93
                                  6899*********************98999999******999999987523335555553333.3333 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00011
                        AAA_14  48 dpekllelileklke.ekktylflDEiqev..........pewekalkslvdegknldvivtGSnskllskeiat.slagr 116
                                    +e +l+ i+e +k+  k+ +l++DE q++           e++++  +l +e++ ++v++  S s+++ +  ++ +l +r
  gi|15669855|ref|NP_248669.1| 134 VFE-YLTKIFEDIKKkGKQPILIIDELQKIgdlkingfliYELFNFFIDLTKEKHLCHVLCLSSDSLFIERVYNEgTLKDR 213
                                   222.33333333333468899*********999998888877777777777788789999999999988775443256666 PP

                        AAA_14 117 vaei 120
                                    +++
  gi|15669855|ref|NP_248669.1| 214 CKYY 217
                                   6555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.5
                        AAA_14  25 ell..vkkesilyinld 39 
                                   e++  + k++il++n++
  gi|15669855|ref|NP_248669.1| 321 EEIvwTVKKNILFVNIE 337
                                   22233334555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   2.3e-10   2.3e-07       2     149 ..       7     164 ..       6     177 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.3e-10
                        AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellr.alekdggiflrgkcdql..esaipy...sa.laq 74 
                                   ++ Re+e+    ++l +v s +p  + +++G+  +GK++l++++ +  l +d+ ++++ + +++  +    y   +  l +
  gi|15669855|ref|NP_248669.1|   7 FFDREKEI----NYLVKVLSFEPnLIYFIYGPINSGKTTLIKHIIEnKLDRDKYVVFYINLREHfiS---KYedfIEvLFN 80 
                                   78899999....77777888899899***************99997577777755666666665221...12222222444 PP

                        AAA_16  75 alareellrqlldeaesaeleawrekleeala...........avpelagaea......srllellkrllallsrderplv 138
                                   +  +e+++++l+  + s   ++ ++ ++   +                   e       + ++e l+++++ +++++++ +
  gi|15669855|ref|NP_248669.1|  81 TY-EETFIEKLKKYLLS-FINDLPKNIDVKSTiltgipvpkntL------NEFlstknsENVFEYLTKIFEDIKKKGKQPI 153
                                   44.33555555555333.45555555555444666664444432......333556667***********999999999** PP

                        AAA_16 139 lvlDdlqwade 149
                                   l++D+lq++ +
  gi|15669855|ref|NP_248669.1| 154 LIIDELQKIGD 164
                                   *******8765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.2e-07   0.00012       3     109 ..      31     195 ..      29     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.2e-07
                                   EESSTTSSHHHHHHHHHHH.H...THEEEEEETTTCS.SS......................................... CS
                           AAA   3 lyGppGtGKTllakavake.l...gvefleisgsell.sk......................................... 37 
                                   +yGp   GKT+l+k ++++ l   +  ++ i++ e + sk                                         
  gi|15669855|ref|NP_248669.1|  31 IYGPINSGKTTLIKHIIENkLdrdKYVVFYINLREHFiSKyedfievlfntyeetfieklkkyllsfindlpknidvksti 111
                                   8***************99943444455677777777767788888888888888888889999999999999999999999 PP

                                   ..................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSS CS
                           AAA  38 ..................yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkke 100
                                                       ++  + + ++f+++k+k k+ il+iDE+ +++  +       +  ++ +L++++ +++k++
  gi|15669855|ref|NP_248669.1| 112 ltgipvpkntlneflstkNSENVFEYLTKIFEDIKKKGKQPILIIDELQKIGDLK------INGFLIYELFNFFIDLTKEK 186
                                   9999999999999986655555667789999999999877***********8877......67777777777777777777 PP

                                   STEEEEEEE CS
                           AAA 101 skvivigat 109
                                   + + v++ +
  gi|15669855|ref|NP_248669.1| 187 HLCHVLCLS 195
                                   766666665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.3e-06    0.0013      24     109 ..      16     101 ..      10     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                         AAA_7  24 yllelll.knkkpvllvGptGtGKtviikd.llkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkkl 102
                                   yl++ l  + +   +++Gp  +GKt++ik+ + +kld++ky++  in+  +  + +  d+ie  ++  + +++  + +k l
  gi|15669855|ref|NP_248669.1|  16 YLVKVLSfEPNLIYFIYGPINSGKTTLIKHiIENKLDRDKYVVFYINLREHFIS-KYEDFIEVLFNTYE-ETFIEKLKKYL 94 
                                   55555541334445678*************9999**************999876.57899987666655.89999999999 PP

                         AAA_7 103 vvFvDDl 109
                                   + F+ Dl
  gi|15669855|ref|NP_248669.1|  95 LSFINDL 101
                                   9999997 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   8.8e-05     0.088       3      36 ..      28      60 ..      26      94 .. 0.75
   2 ?   -2.2   0.0       3.3   3.3e+03      63      87 ..     139     160 ..     125     166 .. 0.64
   3 ?    1.3   0.2      0.26   2.6e+02      87     128 ..     262     305 ..     220     340 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.8e-05
                            TK  3 ielilgpmfaGKsteLlrrvkryqlaekkvvvik 36
                                  i++i+gp+++GK+t  ++++ + +l + k vv+ 
  gi|15669855|ref|NP_248669.1| 28 IYFIYGPINSGKTTL-IKHIIENKLDRDKYVVFY 60
                                  89**********985.555555555554544443 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.3
                            TK  63 tssleeikeeleeedvdvvlvDEaq 87 
                                   t+ +e+ik++ ++    ++++DE q
  gi|15669855|ref|NP_248669.1| 139 TKIFEDIKKKGKQ---PILIIDELQ 160
                                   4455555555555...688899987 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.26
                            TK  87 qFfeqdivelsek...lanegkivivagLdtdFerklFenilkll 128
                                   + + +d+ e+++k   + + + + ++++L+ d +++lFe + kl+
  gi|15669855|ref|NP_248669.1| 262 KLLGEDVKEFCKKslrVRKRQLKDLLYSLEDD-NKELFERVIKLF 305
                                   45557888888752225566666788888866.678888888886 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.6e-05     0.026       3      30 ..      29      56 ..      27      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                                  EEEEESTTCCHHHHHHHHHCT--SS-EE CS
                          cobW  3 tvltGflGsGKTtLlnhllenraglkla 30
                                  + + G++ sGKTtL++h++en+ +++  
  gi|15669855|ref|NP_248669.1| 29 YFIYGPINSGKTTLIKHIIENKLDRDKY 56
                                  6789***************998777655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012      0.12       2      49 ..      30      73 ..      29     109 .. 0.80
   2 ?   -2.1   0.0       5.2   5.2e+03      49      62 ..     150     163 ..     122     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                  RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtg 49
                                  ++yGp + GK+tl+k+++++ l    +  k  v++ n ++ f ++Y++
  gi|15669855|ref|NP_248669.1| 30 FIYGPINSGKTTLIKHIIENKL----DRDKYVVFYINLREHFISKYED 73
                                  79**************665555....4444666668999999999985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.2
                  RNA_helicase  49 gqevvvidDfgqvk 62 
                                   +q++++id++ ++ 
  gi|15669855|ref|NP_248669.1| 150 KQPILIIDELQKIG 163
                                   58888888887765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.16      14     117 ..      30     165 ..      23     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                        AAA_19  14 lvtaGpGtGKTrvlkhivallvelggvkp................eeillvaftgrAakelrerlaalgae.......... 68 
                                   ++ ++  +GKT+++khi++  +++ +  +                 e+l  ++ +   ++l++ l ++  +          
  gi|15669855|ref|NP_248669.1|  30 FIYGPINSGKTTLIKHIIENKLDRDKYVVfyinlrehfiskyedfIEVLFNTYEETFIEKLKKYLLSFINDlpknidvkst 110
                                   56677779***********99998876557777777777777777677777777777777777665555558888888888 PP

                        AAA_19  69 ........atTiHrlalldfddlltealelle..eaeeekklqeee.llivDEfqdvdel 117
                                            +T+ ++  l +++ + + +e+l      e+ k + ++ +li+DE q + +l
  gi|15669855|ref|NP_248669.1| 111 iltgipvpKNTLNEF--LSTKNSE-NVFEYLTkiF--EDIKKKGKQpILIIDELQKIGDL 165
                                   888888888888888..8777766.7888888552..33333334459*******99843 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.15       2      51 ..      11      56 ..      10     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                  HHHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC.CB CS
                        NB-ARC  2 eksvekviekLlekdelqslvvalvGmgGvGKttlakqilnksdeveg.rF 51
                                  ek+++ + + L+   e++ l+ +++G   +GKttl+k+i+++  ++++ ++
  gi|15669855|ref|NP_248669.1| 11 EKEINYLVKVLS--FEPN-LIYFIYGPINSGKTTLIKHIIEN--KLDRdKY 56
                                  666777777777..7777.899*****************998..4444254 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00082      0.81       2      26 ..      30      58 ..      30     118 .. 0.60
   2 ?   -1.9   0.0       4.6   4.6e+03      11      34 ..     119     140 ..     110     160 .. 0.71
   3 ?    1.3   0.1      0.46   4.6e+02      37     110 ..     264     301 ..     206     338 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00082
                        AAA_18  2 lltGtpGvGKttlakeLskrlgf.....gv 26
                                  ++ G++ +GKttl k++ +  ++     +v
  gi|15669855|ref|NP_248669.1| 30 FIYGPINSGKTTLIKHIIEN-KLdrdkyVV 58
                                  689*************9444.223344333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.6
                        AAA_18  11 KttlakeLskrlgfgvnlrdvake 34 
                                   K tl + Ls ++  ++n+ +++++
  gi|15669855|ref|NP_248669.1| 119 KNTLNEFLSTKN--SENVFEYLTK 140
                                   667777777777..7776666655 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.46
                        AAA_18  37 lllevdpealdeskrldedkldklldaleenssaleegknlvidghlaeleseaakdikkvvLtaspeelleRl 110
                                   l ++v ++  ++s+r+++ +l+ ll  le  +                                   +el+eR+
  gi|15669855|ref|NP_248669.1| 264 LGEDVKEF-CKKSLRVRKRQLKDLLYSLEDDN-----------------------------------KELFERV 301
                                   44444444.55555555555555555555544...................................3333333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00029      0.29       4      64 ..      30      84 ..      27     238 .. 0.70
   2 ?   -3.7   0.0       9.8   9.8e+03      52      70 ..     281     299 ..     268     310 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                                  EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS CS
                         NACHT  4 ilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpe 64
                                  ++ G+  sGKTtL++++++     kl++++  +vF+++lre   s+ +  ++++lf  + e
  gi|15669855|ref|NP_248669.1| 30 FIYGPINSGKTTLIKHIIEN----KLDRDK-YVVFYINLREHFISKYE-DFIEVLFNTYEE 84
                                  67788889*********975....555554.89*******98776655.666666666655 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.8
                                   .-HCHHHCCCCTS--SSS- CS
                         NACHT  52 rsladllfsqlpepaapvs 70 
                                   r l+dll s  ++ ++  +
  gi|15669855|ref|NP_248669.1| 281 RQLKDLLYSLEDDNKELFE 299
                                   3566666655555554444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00033      0.33       4      24 ..      31      51 ..      29      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                                  EEESTTSSHHHHHHHHHTSTE CS
                      MMR_HSR1  4 ivGrpNvGKStLinaltgeka 24
                                  i+G  N+GK+tLi+ ++++k 
  gi|15669855|ref|NP_248669.1| 31 IYGPINSGKTTLIKHIIENKL 51
                                  89**************99754 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00039      0.39      16      39 ..      20      43 ..      15      47 .. 0.86
   2 ?   -2.5   0.0       4.5   4.5e+03       9      19 ..     245     255 ..     243     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00039
                        AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                  +++++++ ++++ Gp+ sGK+Tl+
  gi|15669855|ref|NP_248669.1| 20 VLSFEPNLIYFIYGPINSGKTTLI 43
                                  5677777799*************8 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.5
                        AAA_29   9 Wgtfdghtiei 19 
                                   W++f g+ i++
  gi|15669855|ref|NP_248669.1| 245 WHYFGGKPIKL 255
                                   9***9987776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0003       0.3       6      35 ..      21      50 ..      19     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                                  EEEETTSEEEEEESTTSSHHHHHHHHTTSS CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  6 lklkegekvaivGenGaGKStLlkllagll 35
                                  l+++++ ++ i G+  +GK+tL+k ++++ 
  gi|15669855|ref|NP_248669.1| 21 LSFEPNLIYFIYGPINSGKTTLIKHIIENK 50
                                  67889999******************9875 PP

>> CdiA_C  Contact-dependent growth inhibition CdiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0083       8.3      15      66 ..      32      83 ..      28      95 .. 0.79
   2 ?   -0.3   0.2       1.3   1.3e+03      51      76 ..     131     157 ..     121     162 .. 0.74
   3 ?    5.6   0.7     0.018        18      21      81 .]     267     331 ..     259     331 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0083
                        CdiA_C 15 Ksptsgngk.niisnilkkakkQaknivlnlrdsdlsieeikegieralkwpk 66
                                  + p  ++gk + i++i++++ +  k +v+ ++ +++ i++ +  ie  +++ +
  gi|15669855|ref|NP_248669.1| 32 YGPI-NSGKtTLIKHIIENKLDRDKYVVFYINLREHFISKYEDFIEVLFNTYE 83
                                  7788.4455599********************888888888888887776655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.3
                        CdiA_C  51 ieeikegieralkwpk.kglkeliiik 76 
                                    e++ e++ ++++  k kg + ++ii+
  gi|15669855|ref|NP_248669.1| 131 SENVFEYLTKIFEDIKkKGKQPILIID 157
                                   578888888888887777777777776 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.018
                        CdiA_C  21 ngkniisnilkkakkQaknivlnlrdsdls.ieeikegieralkwpk...kglkeliiikkdgki 81 
                                   ++k  +++ l+  k+Q k+ ++ l+d + + +e++++ +e++ + ++   +++ e i+++ +++i
  gi|15669855|ref|NP_248669.1| 267 DVKEFCKKSLRVRKRQLKDLLYSLEDDNKElFERVIKLFENFKNRDEifyEKISEEIVWTVKKNI 331
                                   677888999999999***********99999**********888877999999999998887775 PP

>> RICH  RICH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   0.00034      0.33       4      44 ..     127     162 ..     126     168 .. 0.91
   2 ?   -0.8   1.4         2     2e+03      24      60 ..     273     309 ..     256     330 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                          RICH   4 skkakdeVkeylekiLseikkqldKrkhtqnvaLikkLseI 44 
                                   s+k  ++V eyl+ki ++i     K+k +q + +i +L++I
  gi|15669855|ref|NP_248669.1| 127 STKNSENVFEYLTKIFEDI-----KKKGKQPILIIDELQKI 162
                                   5788899************.....99999999999999999 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2
                          RICH  24 kqldKrkhtqnvaLikkLseIkteyLyelkvlkeksk 60 
                                   k++ + ++ q  +L+  L++ ++e +  + +l e+ k
  gi|15669855|ref|NP_248669.1| 273 KKSLRVRKRQLKDLLYSLEDDNKELFERVIKLFENFK 309
                                   4444556666666666666666666655555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2400.43
//
Query:       gi|15669856|ref|NP_248670.1|  [L=549]
Description: O-phosphoseryl-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-66  222.5   0.0    1.3e-60  205.0   0.0    2.1  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
      2e-14   53.4   1.9    4.5e-14   52.2   1.9    1.7  1  SepRS_C          O-phosphoseryl-tRNA synthetase C-terminal do
    1.8e-10   40.7   0.0    3.3e-07   30.0   0.0    2.2  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    0.00016   21.7   0.2    0.00074   19.5   0.2    2.2  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
  ------ inclusion threshold ------
      0.023   13.8   0.0        5.3    6.0   0.0    2.8  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.8e-06      0.01       3      50 ..      43      90 ..      41      98 .. 0.85
   2 !  205.0   0.0   3.5e-64   1.3e-60       9     238 ..     123     354 ..     114     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.8e-06
                                  -TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHT CS
                  tRNA-synt_2d  3 dvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynf 50
                                  d ++p  +   gk hp+++++e++++ +l++gfee+ +p + +e+ + 
  gi|15669856|ref|NP_248670.1| 43 DNKYPRLKPVYGKPHPVMETIERLRQAYLRMGFEEMINPVIVDEMEIY 90
                                  55666667778999*************************998887765 PP

  == domain 2  score: 205.0 bits;  conditional E-value: 3.5e-64
                                   SCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHH CS
                  tRNA-synt_2d   9 krieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthtta 89 
                                   + i++ ++++ ++ +e+++e+++ +++ +++g+++   f +++aLnv+++++++ ++ +F+  k+ k+++++l+LR+h+t+
  gi|15669856|ref|NP_248670.1| 123 EIIKNLGIDIDEEKKERLREVLHLYKKGAIDGDDL--VFEIAKALNVSNEMGLKVLETAFPEFKDLKPESTTLTLRSHMTS 201
                                   56788899999********************8887..7******************************************* PP

                                   HHHHHH....TTS-SSEEEEEEEEEEBSST.-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTST.EEEEEEEC CS
                  tRNA-synt_2d  90 vqirtl....ekkkppikiisigrvfRrda.vDathlaeFhqveglvvdenvsladlkgvleellkklfgae.vkvrfrps 164
                                    +++tl    +k+k+p+k++si+r+fRr++ +D++hl+++h+++++vv+e+vs++d k+v+e ll ++ g++ +k++ +++
  gi|15669856|ref|NP_248670.1| 202 GWFITLssliKKRKLPLKLFSIDRCFRREQrEDRSHLMSYHSASCVVVGEDVSVDDGKVVAEGLLAQF-GFTkFKFKPDEK 281
                                   ******************************9*************************************.99879999999* PP

                                   EETTEEEEEEEEEEE.CCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT. CS
                  tRNA-synt_2d 165 yfpftePsaevdvyl.vekkkkwlEllgaGmvrpevleavgideevsgfafGlGveRlamlkygieDiRelvend 238
                                   ++++++P+++++vy+ ++k ++w+E++++G+++p +l++++i  +v+++++GlGveRlam+ yg+eD+R++v+++
  gi|15669856|ref|NP_248670.1| 282 KSKYYTPETQTEVYAyHPKLGEWIEVATFGVYSPIALAKYNI--DVPVMNLGLGVERLAMIIYGYEDVRAMVYPQ 354
                                   *************998899***********************..****************************984 PP

>> SepRS_C  O-phosphoseryl-tRNA synthetase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   1.9   1.3e-17   4.5e-14       1      31 []     438     477 ..     438     477 .. 1.00

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.3e-17
                                   EEEEEETTEEEEEE.S-TTTCC........HHHHSEEEEE CS
                       SepRS_C   1 NEvyVYdGnIlGvP.dtekwke........arenGvsTGI 31 
                                   NEvyVYdGnI+G+P ++e++ke        a+e+GvsT+I
  gi|15669856|ref|NP_248670.1| 438 NEVYVYDGNIYGIPpTFEGVKEqyipilkkAKEEGVSTNI 477
                                   ***************************************9 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00035       1.3       1      49 [.      42      90 ..      42     101 .. 0.88
   2 !   30.0   0.0   9.2e-11   3.3e-07      73     208 ..     194     328 ..     188     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00035
               tRNA_synthFbeta  1 IpstlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeld 49
                                  I ++ P+ + + g++++  ++ ++lr++   +G+ E+i+   v+e e+ 
  gi|15669856|ref|NP_248670.1| 42 IDNKYPRLKPVYGKPHPVMETIERLRQAYLRMGFEEMINPVIVDEMEIY 90
                                  6788999999*****************************9999887654 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 9.2e-11
               tRNA_synthFbeta  73 vlRtsLlpglLevlarNlargnedvrlFEigkvflkd..seeelpeeerhlaivltgkreeeswsekaravdfydlkgive 151
                                   +lR+ +++g   +l++ +++++  ++lF i ++f+ +  ++ +     +  ++v++g++           v++ d k ++e
  gi|15669856|ref|NP_248670.1| 194 TLRSHMTSGWFITLSSLIKKRKLPLKLFSIDRCFRREqrEDRSHLMSYHSASCVVVGED-----------VSVDDGKVVAE 263
                                   6999***********999888888*************7444455888888999999999...........*********** PP

               tRNA_synthFbeta 152 alleslgiekvefep..aehpalhpgrsAeikvdgk......evGvlGelhpevleafdlkqrvy 208
                                    ll+++g++k++f+p  ++ +++ p  + e+++         ev  +G  +p  l++++++ +v+
  gi|15669856|ref|NP_248670.1| 264 GLLAQFGFTKFKFKPdeKKSKYYTPETQTEVYAYHPklgewiEVATFGVYSPIALAKYNIDVPVM 328
                                   ***************766699**********99444477789******************99875 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   2.1e-07   0.00074      13     133 ..     195     309 ..     183     343 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.1e-07
                                   E-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBC.TTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  13 LkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsr.GLlRvreFhqkdgyvfhaeaslddslrdlikaisrife 92 
                                   L+   + +     +   +++++LPlkl+ i +++R+E+++ r  L+         + +++  +  d s+ d   +++ ++ 
  gi|15669856|ref|NP_248670.1| 195 LRSHMTSGWFITLS-SLIKKRKLPLKLFSIDRCFRREQREDRsHLM-----SYHSASCVVVGE--DVSVDDGKVVAEGLLA 267
                                   55555554443333.3478878****************94442433.....333333333433..3345555556666666 PP

                                   HTT.SCEEEEEEGTTSCBTTSE..EEEEEEEETTTSEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  93 rlglefraiielmsaksadykd..kkefeavsesltkgieigt 133
                                   ++g+ +++ + + + ks  y +  ++e+ a+ ++l+  ie++t
  gi|15669856|ref|NP_248670.1| 268 QFGFTKFKFKPDEK-KSKYYTPetQTEVYAYHPKLGEWIEVAT 309
                                   66666666666633.2333333003444445555555555554 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.34   1.2e+03     162     179 ..      64      81 ..      13     163 .. 0.58
   2 ?    6.0   0.0    0.0015       5.3      93     115 ..     219     241 ..     197     257 .. 0.91
   3 ?    4.4   0.0    0.0047        17     287     307 ..     330     350 ..     317     363 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.34
                                   EE-SSS-EEEEHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 162 kdlkkpfkrltykeaiek 179
                                   + l++ + r+ ++e i+ 
  gi|15669856|ref|NP_248670.1|  64 ERLRQAYLRMGFEEMINP 81 
                                   444444444444444443 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0015
                                   EEEEEEEEE--S--BTTB-S-CE CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEF 115
                                   + f+i r+FR E+ + + hl  +
  gi|15669856|ref|NP_248670.1| 219 KLFSIDRCFRREQREDRSHLMSY 241
                                   78*************99999665 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0047
                                   EEEEHHHHHHHHCT-SSGGGC CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 287 lglGldRlvmlllgsesIrdv 307
                                   lglG++Rl m++ g e++r +
  gi|15669856|ref|NP_248670.1| 330 LGLGVERLAMIIYGYEDVRAM 350
                                   79****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 4103.43
//
Query:       gi|15669857|ref|NP_248671.1|  [L=186]
Description: glutamine amidotransferase subunit PdxT [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-84  282.5   0.1    1.7e-84  282.4   0.1    1.0  1  SNO            SNO glutamine amidotransferase family
      3e-09   36.9   0.0    4.5e-09   36.4   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
    6.9e-06   25.8   0.1    9.3e-06   25.4   0.1    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    0.00069   19.7   0.2     0.0078   16.4   0.1    2.3  2  UPF0180        Uncharacterised protein family (UPF0180)
     0.0012   18.6   0.1      0.033   13.9   0.0    2.5  2  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
       0.01   15.5   0.1      0.014   15.1   0.1    1.2  1  Peptidase_S51  Peptidase family S51
      0.072   12.9   0.1       0.12   12.2   0.1    1.3  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.4   0.1   6.6e-88   1.7e-84       1     188 []       5     185 ..       5     185 .. 0.99

  Alignments for each domain:
  == domain 1  score: 282.4 bits;  conditional E-value: 6.6e-88
                                   EESSSSSHHHHHHHHHHTTSEEEEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHH CS
                           SNO   1 vlalqGaveehveaikkclaenktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlill 81 
                                   vla+qG+veeh+eaikk+++e+k+vkr+edl+++daliiPGGesta++kl++++g    lle++kns++++lGtCaG++ll
  gi|15669857|ref|NP_248671.1|   5 VLAIQGDVEEHEEAIKKAGYEAKKVKRVEDLEGIDALIIPGGESTAIGKLMKKYG----LLEKIKNSNLPILGTCAGMVLL 81 
                                   8******************************************************....9********************* PP

                                   CCEETTBSS-SS--CCEEEETTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTCEEEEECTTEEEEEEETTE CS
                           SNO  82 skelenelvktlellkvkvkrnafGrqvdsfekeldfknliekftavfiraPvieeilddeavkvlyeldgeivvakqkki 162
                                   sk+++++++  lel++++vkrna+Grqvdsfeke++fk+l+ k+++vfiraPv+++il+d+++++++++d +iv++kq+k+
  gi|15669857|ref|NP_248671.1|  82 SKGTGINQIL-LELMDITVKRNAYGRQVDSFEKEIEFKDLG-KVYGVFIRAPVVDKILSDDVEVIARDGD-KIVGVKQGKY 159
                                   **********.******************************.****************************.********** PP

                                   EEESS-GGGSTTHCHHHHHHHHHHCH CS
                           SNO 163 latsfhPelaeddirvhdyfveevvk 188
                                   +a+sfhPel+ed+++v++yfve++vk
  gi|15669857|ref|NP_248671.1| 160 MALSFHPELSEDGYKVYKYFVENCVK 185
                                   ************************96 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   1.8e-12   4.5e-09      33     175 ..      28     170 ..       9     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.8e-12
                                   HHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEE.......EEECEEEEEEE CS
                        GATase  33 aeeilellknpdgilvsgGpgspg..vegkieaikearenkiPiLGICLGmQllaiefgrkvv.......kekekehhggt 104
                                   + +  e l+++d+++++gG  +      +k  +++++ ++++PiLG C Gm ll +  g + +         k +   g +
  gi|15669857|ref|NP_248671.1|  28 KVKRVEDLEGIDALIIPGGESTAIgkLMKKYGLLEKIKNSNLPILGTCAGMVLLSKGTGINQIllelmdiTVK-RNAYGRQ 107
                                   3333335899*********988877899999****************************97665655543222.2233333 PP

                                   EEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTT CS
                        GATase 105 mrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEsts 175
                                       + ++ ++++l++++ +      +v++  ++++++ev+a++ d  +++++ + k  ++++ FHPE + 
  gi|15669857|ref|NP_248671.1| 108 VDSFE-KEIEFKDLGKVYGVF-IRAPVVDK--ILSDDVEVIARDGD--KIVGVKQGK--YMALSFHPELSE 170
                                   33333.247889986655555.55666776..9*******999944..588877666..69*******986 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   3.6e-09   9.3e-06      28      91 ..      27      84 ..      12     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.6e-09
                      GATase_3 28 rfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGee 91
                                  + v+ + e+l e +d++i+pGg++t+   +l+++ gl e+ik+   ++ p+lg C+G+ +L++ 
  gi|15669857|ref|NP_248671.1| 27 KKVK-RVEDL-EGIDALIIPGGESTA-IGKLMKKYGLLEKIKN---SNLPILGTCAGMVLLSKG 84
                                  4444.56778.55**********996.56777888*******9...789************985 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1     3e-06    0.0078       4      50 ..       7      53 ..       5      64 .. 0.89
   2 ?    0.7   0.0      0.23   5.9e+02      15      25 ..     167     177 ..     163     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-06
                       UPF0180  4 aVeegLsnvkeaLrekGYeVvdleteedaqsvdaiVvtGqdtnvmgi 50
                                  a++ + ++ +ea ++ GYe  +++  ed +++da+++ G ++ ++g 
  gi|15669857|ref|NP_248671.1|  7 AIQGDVEEHEEAIKKAGYEAKKVKRVEDLEGIDALIIPGGESTAIGK 53
                                  899999999****************************9988877664 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.23
                       UPF0180  15 aLrekGYeVvd 25 
                                   +L+e GY+V +
  gi|15669857|ref|NP_248671.1| 167 ELSEDGYKVYK 177
                                   79*******86 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.038        97       2      57 ..       2      56 ..       1      61 [. 0.60
   2 !   13.9   0.0   1.3e-05     0.033      97     164 ..      60     128 ..      55     167 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.038
                 Peptidase_C26  2 vigitaneeslkkeavqdaeesylaasyveavekagglpvllpieedeedvkaild 57
                                  +ig++a +   ++++  +++++  +a+ v+ ve+  g+  l+ +  +++ + ++++
  gi|15669857|ref|NP_248671.1|  2 IIGVLAIQGDVEEHEE-AIKKAGYEAKKVKRVEDLEGIDALIIPGGESTAIGKLMK 56
                                  5777766655444443.333344444467888888888777766667777777665 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.3e-05
                 Peptidase_C26  97 LiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe..q.saashavkvekgsllaellg 164
                                   L++++ ++++Pilg+C G+ ll    G  ++q + e  ++t  r++   q +  +++++++  + ++ +++
  gi|15669857|ref|NP_248671.1|  60 LLEKIKNSNLPILGTCAGMVLL--SKGTGINQILLELMDITVKRNAYgrQvDSFEKEIEFKDLGKVYGVFI 128
                                   8899999***************..55555666666655555444433332344455555555555555554 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   5.3e-06     0.014      71     131 ..      27      83 ..      12     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.3e-06
                                   S-HHHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSS CS
                 Peptidase_S51  71 dpeeeieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivage 131
                                   ++ +++e+ l+  d++++ GG+   + kl+k+ gl + +++     l++ G+ AG +  ++
  gi|15669857|ref|NP_248671.1|  27 KKVKRVED-LEGIDALIIPGGESTAIGKLMKKYGLLEKIKNSN---LPILGTCAGMVLLSK 83 
                                   55677888.999***************************9876...*********877664 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.5e-05      0.12      59     110 ..      35      84 ..       7      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.5e-05
                                   CCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHT CS
                     DJ-1_PfpI  59 aaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaa 110
                                    +  Dal++pGG++  + + +  k   l+ +  +++ ++   Cag +lL++ 
  gi|15669857|ref|NP_248671.1|  35 LEGIDALIIPGGES--TAIGKLMKKYGLLEKIKNSNLPILGTCAGMVLLSKG 84 
                                   4568********99..666666677888999999***********8888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1155.56
//
Query:       gi|15669858|ref|NP_248672.1|  [L=555]
Description: methyl coenzyme M reductase system subunit A2-like protein [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-54  181.7   0.2    7.9e-29  100.9   0.0    2.4  2  ABC_tran         ABC transporter
    2.8e-11   43.8   4.3     0.0066   16.3   0.1    4.9  3  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.2e-09   37.7   1.9     0.0067   16.7   0.2    4.1  3  AAA_22           AAA domain
    5.1e-09   36.2   0.7    0.00021   21.3   0.1    2.5  2  RsgA_GTPase      RsgA GTPase
    6.4e-09   36.4   0.0    0.00064   20.2   0.0    2.5  2  AAA_16           AAA ATPase domain
    5.3e-07   29.3   0.2     0.0094   15.7   0.1    2.5  2  AAA_29           P-loop containing region of AAA domain
    2.1e-06   27.3   2.9      0.059   12.8   0.0    3.9  4  SMC_N            RecF/RecN/SMC N terminal domain
    1.4e-05   25.5   0.4        2.6    8.5   0.0    4.7  4  AAA              ATPase family associated with various cellul
      3e-05   23.8   0.4        1.7    8.3   0.0    4.2  4  IstB_IS21        IstB-like ATP binding protein
    4.4e-05   23.5   0.0      0.058   13.3   0.0    2.5  2  Rad17            Rad17 P-loop domain
    0.00012   22.7   3.2      0.069   13.7   2.3    2.8  2  AAA_23           AAA domain
    0.00026   21.1   0.4      0.022   14.8   0.2    3.0  2  MMR_HSR1         50S ribosome-binding GTPase
    0.00031   21.3   0.2       0.23   12.0   0.0    3.2  2  AAA_18           AAA domain
    0.00036   20.3   0.1        0.3   10.8   0.0    2.5  2  AAA_30           AAA domain
    0.00042   20.5   0.0      0.025   14.8   0.0    3.1  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
    0.00058   19.1   0.6          1    8.5   0.1    2.5  2  NB-ARC           NB-ARC domain
     0.0012   18.8   0.7        1.3    9.1   0.0    3.9  4  AAA_14           AAA domain
     0.0014   18.1   4.2        5.8    6.3   0.1    5.2  6  TniB             Bacterial TniB protein
     0.0031   17.3   0.2        2.6    7.7   0.0    2.9  3  AAA_24           AAA domain
     0.0081   16.3   0.0        1.6    8.9   0.0    2.6  2  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.036   14.1   0.0    1.8  1  Fe_dep_repr_C    Iron dependent repressor, metal binding and 
      0.014   14.9   0.1        1.9    7.9   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
      0.014   15.1   0.1       0.99    9.1   0.0    2.4  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.015   15.2   0.1        1.9    8.4   0.0    2.8  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.017   15.3   0.0        9.6    6.5   0.0    2.5  2  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.02   15.0   0.9        1.3    9.0   0.0    3.1  3  DUF87            Helicase HerA, central domain
      0.026   14.9   0.1         11    6.4   0.0    2.5  2  RNA_helicase     RNA helicase
      0.034   13.7   1.4         45    3.5   0.0    4.0  4  AAA_25           AAA domain
      0.039   14.0   1.4        5.6    7.0   0.1    3.4  3  AAA_5            AAA domain (dynein-related subfamily)
      0.043   13.5   0.0        2.1    7.9   0.0    2.3  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.057   12.7   0.0       0.14   11.4   0.0    1.6  1  Zeta_toxin       Zeta toxin
      0.059   13.4   0.2        6.6    6.8   0.1    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.064   12.2   0.2       0.15   11.0   0.0    1.6  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.064   12.7   0.0        1.9    7.9   0.0    2.6  2  PhoH             PhoH-like protein
      0.074   12.8   0.2         26    4.5   0.0    3.2  3  Sigma54_activat  Sigma-54 interaction domain
      0.082   12.4   0.0         14    5.2   0.0    2.5  2  PSY3             Shu complex component Psy3, DNA-binding desc
      0.089   12.5   0.0        3.8    7.2   0.0    2.7  2  Cytidylate_kin   Cytidylate kinase
      0.097   12.4   8.0        1.9    8.1   1.5    3.6  3  AAA_15           AAA ATPase domain
       0.28   11.1   3.4        6.7    6.6   0.0    3.1  2  ATPase_2         ATPase domain predominantly from Archaea
       0.31   10.9   1.7         16    5.3   0.1    2.7  2  NACHT            NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.1   1.4e-24   6.1e-22       1     136 [.      19     171 ..      19     172 .. 0.85
   2 !  100.9   0.0   1.8e-31   7.9e-29       1     136 [.     275     474 ..     275     475 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 1.4e-24
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET..TCEGGGB-HHHCCHCEEEE-SS..--S-TTSB.H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx.x RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilld..gkdlkeqeleslrkeigvlpqe..pqlfpelt.v 76 
                                   l++vs++ k+ge+++ivG++GaGKStL+++l g l+ +eGe+++   ++++ke++  +l+++++   +   +++ ++l  +
  gi|15669858|ref|NP_248672.1|  19 LDKVSFEAKKGEILGIVGKSGAGKSTLIRILRGSLDYDEGEVEILgrKDNFKEITAIHLQRNFALWAEPviNNIIRKLYaI 99 
                                   789***************************************998545667779999999999999998887777777757 PP

                                   HHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHH....HTSSEEEEESTT CS
                                   xxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx RF
                      ABC_tran  77 ren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarall....kkpkllllDEpt 136
                                   r+n            e+++ + ++l+ +gl+++kd  +    + LSgG+kqr+ l r ++    k   +lllDEp 
  gi|15669858|ref|NP_248672.1| 100 RNNadeqlpleeeweEYEKTAIEILKLVGLEHKKDAFA----NILSGGEKQRLILGRQIAkiyeKGEGVLLLDEPA 171
                                   77799999999888888888************999888....***********866655511116788******96 PP

  == domain 2  score: 100.9 bits;  conditional E-value: 1.8e-31
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqepqlfpeltvren 79 
                                   l+nvs+++kege++ i+G++G GK+ +++l+agl+ p+eG+i +dg d+++   e+ +lrk+ig+++qe +l +  tv++ 
  gi|15669858|ref|NP_248672.1| 275 LRNVSFDVKEGEILSIIGPSGVGKTVIMRLMAGLELPDEGKIIVDGIDITNygWERIELRKRIGIMHQEFSLPYYQTVENL 355
                                   78*************************************************999999************999998877666 PP

                                   .................................................................HHHTCHHHHHHHSTTG CS
                                   .................................................................xxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .................................................................esdeeiekalsklglk 95 
                                                                                                     ++ e+e++l+ l+l 
  gi|15669858|ref|NP_248672.1| 356 lkyrlglkgekaiahakakaeelglspkivdalyqlidvpeserisklqkmgltediiyklfppvVESFEPEEILEALDLG 436
                                   *****************9999999999999999999999888887777777777777777777666666688888888876 PP

                                   GTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  96 elkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   +   +++k++  +LSgGqk+rva+a  l++kpk+l+lDEp+
  gi|15669858|ref|NP_248672.1| 437 K---DILKKKVIELSGGQKVRVAMALQLITKPKILFLDEPF 474
                                   6...8888888*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.5e-05    0.0066       2      45 ..      32      72 ..      31     123 .. 0.82
   2 ?    6.9   0.0     0.011       4.9     255     301 ..     158     206 ..      87     206 .. 0.84
   3 !   13.9   0.4   7.9e-05     0.035       4     297 ..     290     505 ..     287     510 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-05
                        AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirki 45
                                   +++G+ g+GKS+L+++l++    +++ eg+  +l+++ ++++i
  gi|15669858|ref|NP_248672.1| 32 LGIVGKSGAGKSTLIRILRGS---LDYDEGEVEILGRKDNFKEI 72
                                  579***************998...66666666666665555555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                        AAA_21 255 lkkg.sllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                    +kg ++ll+DEp +   P+   +ll+++k+ ++  g+ vi+t+H p++
  gi|15669858|ref|NP_248672.1| 158 YEKGeGVLLLDEPATMACPASKQKLLDVIKNIRDkLGITVIITSHLPEI 206
                                   344459999999999999***********999999**********9975 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 7.9e-05
                        AAA_21   4 liGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqve 84 
                                   +iGp g+GK+ +++++ +l            el++ g+i+++   ++ ++  +++e++ +  ++ + +++  + +  +++ 
  gi|15669858|ref|NP_248672.1| 290 IIGPSGVGKTVIMRLMAGL------------ELPDEGKIIVDGIDIT-NYGWERIELRKR-IGIMHQEFSLPYYQTVENL- 355
                                   99**************999............5555555555555554.446777777777.7777777777777777777. PP

                        AAA_21  85 eklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrker 165
                                                                     r g+++++++++ ++++++l  ++ ++d   ++ +  ++ + + + +
  gi|15669858|ref|NP_248672.1| 356 -------------------------------LKYRLGLKGEKAIAHAKAKAEELGLSPKIVDALYQLIDVPESERISKLQK 405
                                   ...............................77888888888899999999999999999999999999999888888779 PP

                        AAA_21 166 igllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrlla 246
                                   +gl ++ +  ++++ +  +  + + + ++ +  + + ++                               elS G+k   a
  gi|15669858|ref|NP_248672.1| 406 MGLTEDIIYKLFPPVVESFEPEEILEALDLGKDILKKKVI------------------------------ELSGGQKVRVA 456
                                   9999999999999999999999999999999888888755..............................46999999889 PP

                        AAA_21 247 lltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTH 297
                                   +++ l+  +   ++l++DEp   L+P  lr ++  lk+ ++  g+ ++l++H
  gi|15669858|ref|NP_248672.1| 457 MALQLITKP---KILFLDEPFGDLDPITLRDVANYLKIINErFGTTIVLVSH 505
                                   999998877...99************99999999995555558999999999 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   1.5e-05    0.0067       4     129 ..      28     199 ..      25     210 .. 0.66
   2 !   14.0   0.0    0.0001     0.047       4      26 ..     284     306 ..     281     339 .. 0.85
   3 ?    1.7   0.0      0.62   2.8e+02      73     117 ..     497     543 ..     429     551 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-05
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsst.sskdllrellralglelka.......... 70 
                                   +  il ++G sG+GK+tl+r l+ +ld ++   e   +++ + ++t+ ++  + +  ++ + +++ ++l a          
  gi|15669858|ref|NP_248672.1|  28 KGEILGIVGKSGAGKSTLIRILRGSLDYDEGEVEilgRKDNFKEITAIHLQrNFALWAEPVINNIIRKLYAirnnadeqlp 108
                                   567888********************8554444499966666666666666555555666666666666666666666666 PP

                        AAA_22  71 ................................erlsseell..ealeqalraravielliiDEaqhlr...s.eealeeLr 113
                                                                   +++++++l+  +++++  + ++  ++l++DE   +    s +++l  ++
  gi|15669858|ref|NP_248672.1| 109 leeeweeyektaieilklvglehkkdafanilSGGEKQRLIlgRQIAKIYE-KGE-GVLLLDEPATMAcpaSkQKLLDVIK 187
                                   666666666666666666666666699999996666666665245544444.444.5999999999977652466666666 PP

                        AAA_22 114 sllnlsrkgvqliLvG 129
                                   ++ +  + g+++i  +
  gi|15669858|ref|NP_248672.1| 188 NIRD--KLGITVI--I 199
                                   6666..4444444..3 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.0001
                        AAA_22   4 tagilvvtGesGtGKTtllrrll 26 
                                   +  il ++G+sG+GKT+ +r ++
  gi|15669858|ref|NP_248672.1| 284 EGEILSIIGPSGVGKTVIMRLMA 306
                                   56799**************9876 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.62
                        AAA_22  73 lsseellealeqalraravielliiDEaqhlr...seealeeLrslln 117
                                   +++  l++++ + +++ ++ +++++DE   ++   +ee+ ee+ +++n
  gi|15669858|ref|NP_248672.1| 497 GTTIVLVSHCVEFIKEISD-RAILLDENRLVMegnPEEVCEEFIRRSN 543
                                   3555667999999999999.9999999888665644888888888777 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   4.6e-07   0.00021      88     130 ..      17      60 ..       2      68 .. 0.82
   2 !   12.9   0.1   0.00017     0.078      68     120 ..     253     306 ..     191     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.6e-07
                                   TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                   RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                   ++l++++ + k+ ++  +vG+SG+GKStLi  l+++l+   gev
  gi|15669858|ref|NP_248672.1|  17 KALDKVSFEAKKgEILGIVGKSGAGKSTLIRILRGSLDYDEGEV 60 
                                   6778888887777999********************99988887 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00017
                                   HHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                   RsgA_GTPase  68 lkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                      +++++  + ++v+  ++ +l++++  +k+ ++  ++G+SGvGK+ ++  ++
  gi|15669858|ref|NP_248672.1| 253 AIIQVRNVSKRYYVVHGGETLNLRNVSFDVKEgEILSIIGPSGVGKTVIMRLMA 306
                                   556677777778888888889999999999998*************99887765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.4e-06   0.00064      23     122 ..      28     135 ..      17     198 .. 0.63
   2 !   13.9   0.0   0.00012     0.052      20      46 ..     283     307 ..     271     416 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.4e-06
                        AAA_16  23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesa..ipy........salaqalareellrqllde.... 88 
                                    +e++ ++G sG GKs+l+r l+ +l  d+g + + g+ d +++   i++                   +++ + ++    
  gi|15669858|ref|NP_248672.1|  28 KGEILGIVGKSGAGKSTLIRILRGSLDYDEGEVeILGRKDNFKEItaIHLqrnfalwaE---------PVINNIIRKlyai 99 
                                   348999***********************99999*******955533333333333432.........3444444443333 PP

                        AAA_16  89 .....aesaeleawrekleealaavpelagaeasrllel 122
                                        ++  + e+w e  ++a+++ + +  +++    ++
  gi|15669858|ref|NP_248672.1| 100 rnnadEQLPLEEEWEEYEKTAIEILKLVGLEHK---KDA 135
                                   333344555666666666666663333333322...222 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00012
                        AAA_16  20 rsgrpelvllsGesGvGKsslvrellr 46 
                                   ++g  e++ ++G+sGvGK+ ++r  + 
  gi|15669858|ref|NP_248672.1| 283 KEG--EILSIIGPSGVGKTVIMRLMAG 307
                                   444..89***************98874 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.1e-05    0.0094      13      39 ..      20      46 ..      12      49 .. 0.73
   2 !   10.9   0.0   0.00064      0.29      16      39 ..     277     302 ..     263     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-05
                        AAA_29 13 dghtieidlkg.atlltGpsGsGKSTll 39
                                  d+ ++e +  g +  ++G+sG+GKSTl+
  gi|15669858|ref|NP_248672.1| 20 DKVSFEAKK-GeILGIVGKSGAGKSTLI 46
                                  444555553.35888************8 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00064
                        AAA_29  16 tieidlkg..atlltGpsGsGKSTll 39 
                                    +++d+k+  +  ++GpsG+GK+ ++
  gi|15669858|ref|NP_248672.1| 277 NVSFDVKEgeILSIIGPSGVGKTVIM 302
                                   4444444445999*********9987 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.022       9.8       9      42 ..      15      47 ..       6      58 .. 0.76
   2 ?    4.6   0.0     0.042        19     134     200 ..     137     205 ..      55     224 .. 0.80
   3 ?    1.6   0.1      0.36   1.6e+02      25      41 ..     286     302 ..     271     306 .. 0.81
   4 !   12.8   0.0   0.00013     0.059     135     202 ..     411     510 ..     335     520 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.022
                                  SETTEECEEEEEET.TSSEEEEEESTTSSHHHHHH CS
                                  xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  9 nFksyagktvilpf.sksftaivGpNGSGKsnlld 42
                                  +Fk +  ++v+ +  + ++  ivG+ G+GKs l+ 
  gi|15669858|ref|NP_248672.1| 15 DFKAL--DKVSFEAkKGEILGIVGKSGAGKSTLIR 47
                                  68888..34444440456889**********9985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.042
                                   TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                         SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislree 200
                                    + LSgGek+ + l   +A    k + + llDe +     +  +k+ +++k+ +++    +i++s+  e
  gi|15669858|ref|NP_248672.1| 137 ANILSGGEKQRLILGRQIAKIYEKGEGVLLLDEPATMACPASKQKLLDVIKNIRDKlgITVIITSHLPE 205
                                   348************999*999999********9999999999********998885566777777655 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.36
                                   SEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                         SMC_N  25 sftaivGpNGSGKsnll 41 
                                   ++ +i+Gp G GK+ ++
  gi|15669858|ref|NP_248672.1| 286 EILSIIGPSGVGKTVIM 302
                                   4678**********987 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 0.00013
                                   T..................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHH CS
                                   x..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 135 e..................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvae 181
                                   +                                  +LSgG+k  va+aL +     kp+ + +lDe    LD    + va+
  gi|15669858|ref|NP_248672.1| 411 DiiyklfppvvesfepeeilealdlgkdilkkkviELSGGQKVRVAMALQLI---TKPK-ILFLDEPFGDLDPITLRDVAN 487
                                   244444444444444445555555555577777778******9999988753...3454.6679***************** PP

                                   HHHHHCTT..SEEEEE-SSHHHC CS
                                   xxxxxxxx..xxxxxxxxxxxxx RF
                         SMC_N 182 llkekskn..aQfivislreeml 202
                                   +lk  +++  + ++ +s+  e++
  gi|15669858|ref|NP_248672.1| 488 YLKIINERfgTTIVLVSHCVEFI 510
                                   **955544225555566655555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0072       3.2       3     112 ..      34     204 ..      32     218 .. 0.66
   2 ?    1.6   0.0      0.75   3.4e+02      43      94 ..     179     240 ..     176     250 .. 0.53
   3 !    8.5   0.0    0.0058       2.6       3      19 ..     290     306 ..     288     333 .. 0.89
   4 ?    1.0   0.0       1.2   5.2e+02      43      66 ..     452     472 ..     430     475 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0072
                                   EESSTTSSHHHHHHHHHHHH............THEEEEEETTTCSSS.................................. CS
                           AAA   3 lyGppGtGKTllakavakel............gvefleisgsellsk.................................. 37 
                                   ++G  G GK++l++ +  +l            + +f ei +  l  +                                  
  gi|15669858|ref|NP_248672.1|  34 IVGKSGAGKSTLIRILRGSLdydegeveilgrKDNFKEITAIHLQRNfalwaepvinniirklyairnnadeqlpleeewe 114
                                   579999999999999999985444444444433557777777777556777777777777777777777777777777777 PP

                                   ..........................STTHHHHHH..HHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHH CS
                           AAA  38 ..........................yvgesekki..relfkeakekakpsilfiDEidalaksrsgseseeeervvnqLl 90 
                                                               ge+++ i  r++ k  ++  +  +l++DE   +a               ++Ll
  gi|15669858|ref|NP_248672.1| 115 eyektaieilklvglehkkdafanilSGGEKQRLIlgRQIAKIYEK--GEGVLLLDEPATMACPA----------SKQKLL 183
                                   7777777777777666666777765434444444322223322222..35899999988887666..........488899 PP

                                   HHHHHTTTSSSTEEEEEEESSG CS
                           AAA  91 teldgvkkkeskvivigatnrp 112
                                    ++++ ++k + ++vi++++ p
  gi|15669858|ref|NP_248672.1| 184 DVIKNIRDKLG-ITVIITSHLP 204
                                   99999988877.7777777765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.75
                                   HHHHHHHHHHHHHTSTSEEEE...EETGGGHHHHH.......TTCCCHHHHHHHHHHHHHHH CS
                           AAA  43 ekkirelfkeakekakpsilf...iDEidalaksr.......sgseseeeervvnqLlteld 94 
                                   ++k+ +++k+++ k + ++++   + Ei++   +r       + + +++ e+v+n++l++++
  gi|15669858|ref|NP_248672.1| 179 KQKLLDVIKNIRDKLGITVIItshLPEIHRYLCDRlillengKVKMDGDVEEVLNEFLKKMK 240
                                   45555556665555533333323355666666666666654333355555556666666555 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0058
                                   EESSTTSSHHHHHHHHH CS
                           AAA   3 lyGppGtGKTllakava 19 
                                   ++Gp G+GKT +++ +a
  gi|15669858|ref|NP_248672.1| 290 IIGPSGVGKTVIMRLMA 306
                                   78***********9988 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHTSTSEEEEEET CS
                           AAA  43 ekkirelfkeakekakpsilfiDE 66 
                                   + ++++ ++ +    kp+ilf+DE
  gi|15669858|ref|NP_248672.1| 452 KVRVAMALQLIT---KPKILFLDE 472
                                   335555555553...579*****9 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.083        37      36      63 ..      17      45 ..       7      58 .. 0.79
   2 ?    1.4   0.0      0.52   2.3e+02     102     150 ..     153     204 ..     131     217 .. 0.72
   3 !    8.3   0.0    0.0038       1.7      37      63 ..     274     301 ..     261     315 .. 0.84
   4 ?    4.5   0.0     0.058        26      96     147 ..     452     505 ..     443     518 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.083
                     IstB_IS21 36 keLatlsfiekk.enivllGpsGvGKshl 63
                                  k+L + sf +kk e + ++G sG+GKs l
  gi|15669858|ref|NP_248672.1| 17 KALDKVSFEAKKgEILGIVGKSGAGKSTL 45
                                  67777788665515566**********87 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.52
                     IstB_IS21 102 alkrllkv..dllilDdlgllpldqaeaellfeviekryerr..siiitsnlp 150
                                   +++++ +    +l+lD+ ++     a++++l++vi++  ++   ++iits lp
  gi|15669858|ref|NP_248672.1| 153 QIAKIYEKgeGVLLLDEPATMAC-PASKQKLLDVIKNIRDKLgiTVIITSHLP 204
                                   55555444346999999998876.56778899999999999722457777765 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0038
                     IstB_IS21  37 eLatlsf.iekkenivllGpsGvGKshl 63 
                                   +L++ sf +++ e + ++GpsGvGK+ +
  gi|15669858|ref|NP_248672.1| 274 NLRNVSFdVKEGEILSIIGPSGVGKTVI 301
                                   6777777678889999**********76 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.058
                     IstB_IS21  96 dgklaralkrllkvdllilDd.lg.llpldqaeaellfeviekryerrsiiits 147
                                   + ++a al+ ++k+++l lD+ +g l p+   + ++ +++i++r++++ ++++ 
  gi|15669858|ref|NP_248672.1| 452 KVRVAMALQLITKPKILFLDEpFGdLDPITLRDVANYLKIINERFGTTIVLVSH 505
                                   56788999************9645478999999999**********99888875 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00013     0.058      34      69 ..      18      53 ..       8      64 .. 0.88
   2 !    7.4   0.0    0.0087       3.9      41      66 ..     281     306 ..     271     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                         Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLskel 69
                                  +l+  + e +k +iL i G sG gkst +++L   l
  gi|15669858|ref|NP_248672.1| 18 ALDKVSFEAKKGEILGIVGKSGAGKSTLIRILRGSL 53
                                  788899999*999******************97665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0087
                         Rad17  41 esrkkriLLisGPsGCgkstvvkvLs 66 
                                   + ++ +iL i GPsG gk+ +++ ++
  gi|15669858|ref|NP_248672.1| 281 DVKEGEILSIIGPSGVGKTVIMRLMA 306
                                   555667*************9998876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   2.3   0.00015     0.069       7      45 ..      16      56 ..      11     192 .. 0.77
   2 ?    6.8   0.0     0.019       8.5      11      37 ..     276     303 ..     263     307 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00015
                        AAA_23  7 frsfrdqeidFsk.gltlItGpNGaGKTTildAiklaL.yg 45
                                  f+ +++++++ +k  +  I+G+ GaGK+T+++ ++  L y 
  gi|15669858|ref|NP_248672.1| 16 FKALDKVSFEAKKgEILGIVGKSGAGKSTLIRILRGSLdYD 56
                                  444555556665525889**************999888554 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.019
                        AAA_23  11 rdqeidF.skgltlItGpNGaGKTTild 37 
                                   r++++d  +  +  I+Gp G GKT i++
  gi|15669858|ref|NP_248672.1| 276 RNVSFDVkEGEILSIIGPSGVGKTVIMR 303
                                   45555555557889***********997 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2     5e-05     0.022       3      23 ..      33      54 ..      31     199 .. 0.78
   2 ?    3.1   0.0      0.22     1e+02       3      21 ..     289     307 ..     287     346 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5e-05
                                  EEEESTTSSHHHHHHHHHTS.T CS
                      MMR_HSR1  3 aivGrpNvGKStLinaltge.k 23
                                  +ivG++ +GKStLi+ l g+  
  gi|15669858|ref|NP_248672.1| 33 GIVGKSGAGKSTLIRILRGSlD 54
                                  8**************9988643 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.22
                                   EEEESTTSSHHHHHHHHHT CS
                      MMR_HSR1   3 aivGrpNvGKStLinaltg 21 
                                    i+G + vGK+ +++ + g
  gi|15669858|ref|NP_248672.1| 289 SIIGPSGVGKTVIMRLMAG 307
                                   69**********9998876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00052      0.23       2      25 ..      33      64 ..      32     124 .. 0.75
   2 ?    5.5   0.0     0.054        24       3      20 ..     290     307 ..     289     342 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00052
                        AAA_18  2 lltGtpGvGKttlakeLskrlgf........g 25
                                  ++ G++G+GK+tl + L+ +l +        g
  gi|15669858|ref|NP_248672.1| 33 GIVGKSGAGKSTLIRILRGSLDYdegeveilG 64
                                  589**************888766655544441 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.054
                        AAA_18   3 ltGtpGvGKttlakeLsk 20 
                                   + G++GvGKt + +  + 
  gi|15669858|ref|NP_248672.1| 290 IIGPSGVGKTVIMRLMAG 307
                                   78********99987754 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00066       0.3      18      52 ..      29      63 ..      22      79 .. 0.84
   2 ?    6.6   0.0     0.013       5.9      20      40 ..     287     307 ..     281     319 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00066
                        AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvigl 52
                                    +  ++G  G+GK+t+++ lr  ++ ++g+v +l
  gi|15669858|ref|NP_248672.1| 29 GEILGIVGKSGAGKSTLIRILRGSLDYDEGEVEIL 63
                                  457889***************99998887777766 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.013
                        AAA_30  20 vavltGpAGtGKttalkalre 40 
                                   +  + Gp G GKt +++ ++ 
  gi|15669858|ref|NP_248672.1| 287 ILSIIGPSGVGKTVIMRLMAG 307
                                   67799***********98765 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.72   3.2e+02      33      42 ..     140     149 ..     123     187 .. 0.78
   2 !   14.8   0.0   5.5e-05     0.025      26      88 ..     440     489 ..     423     490 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.72
                       SbcCD_C  33 lSGGekqfla 42 
                                   lSGGekq l+
  gi|15669858|ref|NP_248672.1| 140 LSGGEKQRLI 149
                                   8*****8765 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5.5e-05
                       SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                   l++++ +lSGG+k   + +a+a     ++       ++++++fLDE F+ lD+ +++ + ++l
  gi|15669858|ref|NP_248672.1| 440 LKKKVIELSGGQK---VRVAMA----LQLI------TKPKILFLDEPFGDLDPITLRDVANYL 489
                                   6777888888888...333333....3333......3589****************9999987 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0028       1.2      21      38 ..      30      47 ..      16      61 .. 0.81
   2 !    8.5   0.1    0.0022         1      21      38 ..     286     303 ..     277     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0028
                                  EEEEEEESTTSSHHHHHH CS
                        NB-ARC 21 lvvalvGmgGvGKttlak 38
                                   ++++vG+ G GK+tl++
  gi|15669858|ref|NP_248672.1| 30 EILGIVGKSGAGKSTLIR 47
                                  59**************86 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0022
                                   EEEEEEESTTSSHHHHHH CS
                        NB-ARC  21 lvvalvGmgGvGKttlak 38 
                                    ++++ G  GvGKt++++
  gi|15669858|ref|NP_248672.1| 286 EILSIIGPSGVGKTVIMR 303
                                   399*************96 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.21        94       2      22 ..      29      49 ..      28     106 .. 0.79
   2 ?    2.2   0.0      0.38   1.7e+02      54      98 ..     152     200 ..     110     209 .. 0.77
   3 !    9.1   0.0    0.0029       1.3       2      40 ..     285     322 ..     284     349 .. 0.78
   4 ?   -2.3   0.0       9.4   4.2e+03      62      72 ..     463     472 ..     432     513 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.21
                        AAA_14  2 rkilvitGaRrvGKTtllkql 22
                                  ++il i+G   +GK+tl++ l
  gi|15669858|ref|NP_248672.1| 29 GEILGIVGKSGAGKSTLIRIL 49
                                  57999************9765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.38
                        AAA_14  54 elileklkeekktylflDEiqev......pewekalkslvdegknldvivt 98 
                                   + i +  +e+++ +l+lDE   +      +++ +++k++ d+   + vi+t
  gi|15669858|ref|NP_248672.1| 152 RQIAKI-YEKGEGVLLLDEPATMacpaskQKLLDVIKNIRDKL-GITVIIT 200
                                   344443.4469999*****998888999899999999999987.7788887 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0029
                        AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldd 40 
                                   ++il i G+  vGKT++++ ++  +l ++e  + ++  d
  gi|15669858|ref|NP_248672.1| 285 GEILSIIGPSGVGKTVIMRLMAGLEL-PDEGKIIVDGID 322
                                   57999*************99997777.666555555555 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 9.4
                        AAA_14  62 eekktylflDE 72 
                                   + k ++lflDE
  gi|15669858|ref|NP_248672.1| 463 T-KPKILFLDE 472
                                   3.678888888 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.18        82      37      53 ..      31      47 ..      14      65 .. 0.85
   2 ?    6.3   0.1     0.013       5.8     121     159 ..     163     199 ..     144     203 .. 0.83
   3 ?    3.8   0.0     0.075        34      38      55 ..     288     305 ..     279     315 .. 0.82
   4 ?   -0.7   0.0       1.8   8.2e+02      18      39 ..     383     404 ..     371     410 .. 0.84
   5 ?    0.3   0.0       0.9   4.1e+02     118     160 ..     463     503 ..     442     514 .. 0.80
   6 ?   -0.6   0.0       1.6   7.2e+02     109     138 ..     504     533 ..     497     552 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.18
                          TniB 37 nlllvGdsnnGKtmive 53
                                   l +vG+s  GK+++++
  gi|15669858|ref|NP_248672.1| 31 ILGIVGKSGAGKSTLIR 47
                                  5679**********997 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                          TniB 121 rvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                    vL++DE   +  + a+ ++++l ++k++ ++l i++++
  gi|15669858|ref|NP_248672.1| 163 GVLLLDEPATMA-CPAS-KQKLLDVIKNIRDKLGITVII 199
                                   6999***98887.5555.5579**************986 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.075
                          TniB  38 lllvGdsnnGKtmivekF 55 
                                   l ++G+s +GKt+i++  
  gi|15669858|ref|NP_248672.1| 288 LSIIGPSGVGKTVIMRLM 305
                                   789***********9865 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.8
                          TniB  18 eilerLeeLleypkrkrmpnll 39 
                                   +i++ L +L+++p+++r+++l 
  gi|15669858|ref|NP_248672.1| 383 KIVDALYQLIDVPESERISKLQ 404
                                   6899999********9998875 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 0.9
                          TniB 118 lkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                   +k+++L +DE    l     + r + n lk +++++  +ivlv
  gi|15669858|ref|NP_248672.1| 463 TKPKILFLDEPFGDL--DPITLRDVANYLKIINERFGTTIVLV 503
                                   567888888854444..567779999***********999997 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 1.6
                          TniB 109 qqvlrllrelkvrvLiiDEihnllagsark 138
                                   ++++++++e++ r +++DE   +++g+ ++
  gi|15669858|ref|NP_248672.1| 504 SHCVEFIKEISDRAILLDENRLVMEGNPEE 533
                                   56789999***********99999999876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0058       2.6       5      22 ..      32      49 ..      28     122 .. 0.74
   2 ?   -2.3   0.0       6.8     3e+03     114     131 ..     182     203 ..     178     206 .. 0.65
   3 ?    6.4   0.0     0.015       6.6       6      22 ..     289     305 ..     285     324 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0058
                        AAA_24  5 iliyGpsgiGKTtlakel 22
                                  + i+G+sg+GK+tl++ l
  gi|15669858|ref|NP_248672.1| 32 LGIVGKSGAGKSTLIRIL 49
                                  579***********9987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.8
                        AAA_24 114 llkklqelrk....nvifiahe 131
                                   ll+ +++ r+    +vi+++h+
  gi|15669858|ref|NP_248672.1| 182 LLDVIKNIRDklgiTVIITSHL 203
                                   44455555555556******97 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.015
                        AAA_24   6 liyGpsgiGKTtlakel 22 
                                    i+Gpsg+GKT +++ +
  gi|15669858|ref|NP_248672.1| 289 SIIGPSGVGKTVIMRLM 305
                                   59*********999877 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0036       1.6       4      24 ..      34      54 ..      31     124 .. 0.77
   2 ?    4.9   0.0     0.059        26       4      19 ..     290     305 ..     287     368 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0036
                        AAA_33  4 lvGlpGsGKstlaerllkklg 24
                                  +vG +G+GKstl++ l   l+
  gi|15669858|ref|NP_248672.1| 34 IVGKSGAGKSTLIRILRGSLD 54
                                  69**********997755555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.059
                        AAA_33   4 lvGlpGsGKstlaerl 19 
                                   ++G++G+GK+   + +
  gi|15669858|ref|NP_248672.1| 290 IIGPSGVGKTVIMRLM 305
                                   79********987755 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     8e-05     0.036      14      61 ..     348     397 ..     341     402 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8e-05
                                   HHHHHHHHHHHHCT-..-CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB CS
                 Fe_dep_repr_C  14 rhrllerfLvdvlgv..dweeaheeAerlEhalseelierldellgfpee 61 
                                   +++++e++L+  lg+  ++ +ah +A++ E  ls++++++l++l++ pe+
  gi|15669858|ref|NP_248672.1| 348 YYQTVENLLKYRLGLkgEKAIAHAKAKAEELGLSPKIVDALYQLIDVPES 397
                                   5788999999999995556679**************************97 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.047        21      37      59 ..      33      55 ..      22      66 .. 0.80
   2 ?    7.9   0.0    0.0043       1.9      31      52 ..     283     304 ..     265     321 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.047
                         AAA_7 37 llvGptGtGKtviikdllkkldk 59
                                   +vG++G GK+++i+ l  +ld 
  gi|15669858|ref|NP_248672.1| 33 GIVGKSGAGKSTLIRILRGSLDY 55
                                  589***********988877775 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0043
                         AAA_7  31 knkkpvllvGptGtGKtviikd 52 
                                   k++  + ++Gp+G+GKtvi++ 
  gi|15669858|ref|NP_248672.1| 283 KEGEILSIIGPSGVGKTVIMRL 304
                                   556667799**********985 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0022      0.99       1      24 [.      31      54 ..      31      80 .. 0.82
   2 ?    3.6   0.0      0.11        48       1      20 [.     287     306 ..     287     327 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0022
                           PRK  1 vIgvagsSGaGkttvarklekifg 24
                                  ++g+ g+SGaGk+t+ r l+ ++ 
  gi|15669858|ref|NP_248672.1| 31 ILGIVGKSGAGKSTLIRILRGSLD 54
                                  789*************99987776 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.11
                           PRK   1 vIgvagsSGaGkttvarkle 20 
                                   ++++ g+SG Gkt ++r + 
  gi|15669858|ref|NP_248672.1| 287 ILSIIGPSGVGKTVIMRLMA 306
                                   679************99875 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0042       1.9       1      23 [.      31      53 ..      31      69 .. 0.83
   2 ?    3.7   0.0      0.12        54       1      17 [.     287     303 ..     287     313 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0042
                          MobB  1 vlgivgksgsGKTtLleklipel 23
                                  +lgivgksg+GK tL+  l   l
  gi|15669858|ref|NP_248672.1| 31 ILGIVGKSGAGKSTLIRILRGSL 53
                                  79*************98776555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.12
                          MobB   1 vlgivgksgsGKTtLle 17 
                                   +l+i+g sg GKT ++ 
  gi|15669858|ref|NP_248672.1| 287 ILSIIGPSGVGKTVIMR 303
                                   799**********9875 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.027        12       4      20 ..      34      50 ..      32      84 .. 0.70
   2 ?    6.5   0.0     0.021       9.6       3      20 ..     289     306 ..     288     337 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.027
                                  EESSTTSSHHHHHHCHC CS
                           Roc  4 lvGdsgvGKtsllkrfv 20
                                  +vG+sg+GK++l++ + 
  gi|15669858|ref|NP_248672.1| 34 IVGKSGAGKSTLIRILR 50
                                  8***********98665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.021
                                   EEESSTTSSHHHHHHCHC CS
                           Roc   3 vlvGdsgvGKtsllkrfv 20 
                                    ++G sgvGKt +++ + 
  gi|15669858|ref|NP_248672.1| 289 SIIGPSGVGKTVIMRLMA 306
                                   68*********9987554 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0029       1.3      26      43 ..      32      49 ..      23      82 .. 0.91
   2 ?   -1.7   0.0       5.5   2.5e+03     132     161 ..     217     246 ..     180     281 .. 0.57
   3 ?    2.8   0.1      0.23     1e+02      26      45 ..     288     307 ..     270     360 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0029
                         DUF87 26 lAilgsTGsGKSntvavL 43
                                  l+i+g++G+GKS+++++L
  gi|15669858|ref|NP_248672.1| 32 LGIVGKSGAGKSTLIRIL 49
                                  69*************988 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.5
                         DUF87 132 eekeklssdepveklleelkkekeelrklk 161
                                    e++k++ d  ve++l+e  k++++  k  
  gi|15669858|ref|NP_248672.1| 217 LENGKVKMDGDVEEVLNEFLKKMKPPYKRT 246
                                   444444444445555544442222222222 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.23
                         DUF87  26 lAilgsTGsGKSntvavLle 45 
                                   l i+g +G+GK+  ++++  
  gi|15669858|ref|NP_248672.1| 288 LSIIGPSGVGKTVIMRLMAG 307
                                   689************99865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.036        16       3      19 ..      34      50 ..      32      69 .. 0.83
   2 ?    6.4   0.0     0.025        11       3      19 ..     290     306 ..     288     320 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.036
                  RNA_helicase  3 lyGpsgeGKStlakeLa 19
                                  ++G+sg GKStl++ L 
  gi|15669858|ref|NP_248672.1| 34 IVGKSGAGKSTLIRILR 50
                                  78**********99865 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.025
                  RNA_helicase   3 lyGpsgeGKStlakeLa 19 
                                   + Gpsg+GK+++++ +a
  gi|15669858|ref|NP_248672.1| 290 IIGPSGVGKTVIMRLMA 306
                                   78**********99854 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2      0.28   1.2e+02      32      49 ..      28      45 ..      26      49 .. 0.85
   2 ?    3.5   0.0       0.1        45     166     189 ..     180     203 ..     172     205 .. 0.89
   3 ?    3.5   0.0       0.1        46      31      50 ..     283     302 ..     276     307 .. 0.86
   4 ?   -1.6   0.0       3.9   1.7e+03     169     188 ..     486     505 ..     481     506 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.28
                        AAA_25 32 agelallaGapgtGKttl 49
                                  +ge+  ++G +g+GK+tl
  gi|15669858|ref|NP_248672.1| 28 KGEILGIVGKSGAGKSTL 45
                                  57777799*********9 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.1
                        AAA_25 166 galvealeriarrtgaavllvhHv 189
                                   ++l++ +++i++++g++v+++ H+
  gi|15669858|ref|NP_248672.1| 180 QKLLDVIKNIRDKLGITVIITSHL 203
                                   6788999****************7 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.1
                        AAA_25  31 pagelallaGapgtGKttla 50 
                                    +ge+  ++G++g+GKt++ 
  gi|15669858|ref|NP_248672.1| 283 KEGEILSIIGPSGVGKTVIM 302
                                   6899999**********975 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 3.9
                        AAA_25 169 vealeriarrtgaavllvhH 188
                                    + l+ i +r+g +++lv H
  gi|15669858|ref|NP_248672.1| 486 ANYLKIINERFGTTIVLVSH 505
                                   566777899**********9 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.11        51       4      23 ..      34      53 ..      32      72 .. 0.81
   2 ?    7.0   0.1     0.013       5.6       4      21 ..     290     307 ..     287     317 .. 0.88
   3 ?   -2.1   0.0       7.9   3.6e+03      55      73 ..     455     472 ..     420     494 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.11
                                  EE--SSSSHHHHHHHGGGGB CS
                         AAA_5  4 LvGppGtgKselaerlaaal 23
                                  +vG++G gKs+l++ l   l
  gi|15669858|ref|NP_248672.1| 34 IVGKSGAGKSTLIRILRGSL 53
                                  69***********9987766 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                                   EE--SSSSHHHHHHHGGG CS
                         AAA_5   4 LvGppGtgKselaerlaa 21 
                                   ++Gp+G+gK+ +++ +a 
  gi|15669858|ref|NP_248672.1| 290 IIGPSGVGKTVIMRLMAG 307
                                   79**********999985 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 7.9
                                   ..--------G-SEEEEES CS
                         AAA_5  55 vdsplvraaregeilvlDE 73 
                                   v  +l   +++++il+lDE
  gi|15669858|ref|NP_248672.1| 455 VAMALQ-LITKPKILFLDE 472
                                   222222.444899999998 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0       0.1        47       9      34 ..      24      49 ..      16     115 .. 0.86
   2 ?    7.9   0.0    0.0047       2.1      10      38 ..     281     309 ..     276     514 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.1
                                  S-EBTT-EEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  9 fpivqGqrtlipgafgvGktvisqsl 34
                                  f   +G+ ++i+g++g Gk+++++ l
  gi|15669858|ref|NP_248672.1| 24 FEAKKGEILGIVGKSGAGKSTLIRIL 49
                                  56779999*************98766 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0047
                                   -EBTT-EEEEEESTTSSHHHHHHHHHHHS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  10 pivqGqrtlipgafgvGktvisqslskqs 38 
                                    + +G+ + i+g +gvGktvi++ ++   
  gi|15669858|ref|NP_248672.1| 281 DVKEGEILSIIGPSGVGKTVIMRLMAGLE 309
                                   567899999*************8887655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00031      0.14      18      55 ..      31      70 ..      17      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                    Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrl..dpDdlR 55
                                  ++ ++G +GAGKs+l++ l+ +l+ +++ v++   +D+++
  gi|15669858|ref|NP_248672.1| 31 ILGIVGKSGAGKSTLIRILRGSLDYDEGEVEIlgRKDNFK 70
                                  55688******************97777777723346555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.015       6.6      19      45 ..      29      55 ..       7      61 .. 0.75
   2 ?    3.8   0.0      0.12        53      19      40 ..     285     306 ..     269     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.015
                                  TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                          TsaE 19 gdvilLeGdLGaGKTtlvrglakalgv 45
                                  g+++ + G+ GaGK+tl+r l  +l++
  gi|15669858|ref|NP_248672.1| 29 GEILGIVGKSGAGKSTLIRILRGSLDY 55
                                  7789999************99877766 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.12
                                   TEEEEEEESTTSSHHHHHHHHH CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrgla 40 
                                   g+++ + G+ G+GKT+++r +a
  gi|15669858|ref|NP_248672.1| 285 GEILSIIGPSGVGKTVIMRLMA 306
                                   6789999**********99775 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00033      0.15      19      54 ..      19      54 ..      10      64 .. 0.83
   2 ?   -2.8   0.0       5.4   2.4e+03      30      52 ..     286     307 ..     275     318 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                                  HHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHH CS
                          MeaB 19 lerllakaGraqvvGltGvPGaGkstlvealglelr 54
                                  l++++ +a + + +G+ G  GaGkstl+  l  +l 
  gi|15669858|ref|NP_248672.1| 19 LDKVSFEAKKGEILGIVGKSGAGKSTLIRILRGSLD 54
                                  778888999999****************98877665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.4
                                   EEEEEEE-TTSSHHHHHHHHHHH CS
                          MeaB  30 qvvGltGvPGaGkstlvealgle 52 
                                   + + + G  G+Gk   + +l++ 
  gi|15669858|ref|NP_248672.1| 286 EILSIIGPSGVGKTV-IMRLMAG 307
                                   667899999***965.5555433 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       0.3   1.4e+02      17      35 ..      27      45 ..      15      63 .. 0.82
   2 ?    7.9   0.0    0.0043       1.9      16      40 ..     282     306 ..     270     371 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.3
                                  HH-SEEEEE--TTSSTTHH CS
                          PhoH 17 kkndivfaiGpaGtGKtyl 35
                                  kk +i+ ++G++G+GK+ l
  gi|15669858|ref|NP_248672.1| 27 KKGEILGIVGKSGAGKSTL 45
                                  467899**********876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0043
                                   HHH-SEEEEE--TTSSTTHHHHHHH CS
                          PhoH  16 lkkndivfaiGpaGtGKtylavala 40 
                                   +k+ +i+ +iGp+G GKt +   +a
  gi|15669858|ref|NP_248672.1| 282 VKEGEILSIIGPSGVGKTVIMRLMA 306
                                   678899************9875554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.39   1.7e+02      26      42 ..      33      49 ..      15      62 .. 0.77
   2 ?    2.0   0.0      0.33   1.5e+02      90     119 ..     158     188 ..     151     200 .. 0.79
   3 ?    4.5   0.0     0.058        26      26      45 ..     289     308 ..     275     322 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.39
                                  EEECSTTSSHHHHHHHH CS
               Sigma54_activat 26 litGesGtGKellarai 42
                                   i+G+sG+GK++l r +
  gi|15669858|ref|NP_248672.1| 33 GIVGKSGAGKSTLIRIL 49
                                  499********998766 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.33
                                   HHTTTSEEEEETGGGS-H.HHHHHHHHHHHH CS
               Sigma54_activat  90 ekadgGtlfLDeigelpl.elQekLlrvlqe 119
                                    +  +G+l+LDe +++   +  +kLl v+++
  gi|15669858|ref|NP_248672.1| 158 YEKGEGVLLLDEPATMACpASKQKLLDVIKN 188
                                   55678*********99852668899999975 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.058
                                   EEECSTTSSHHHHHHHHHHH CS
               Sigma54_activat  26 litGesGtGKellaraihea 45 
                                    i G sG+GK+++ r++   
  gi|15669858|ref|NP_248672.1| 289 SIIGPSGVGKTVIMRLMAGL 308
                                   489**********9998665 PP

>> PSY3  Shu complex component Psy3, DNA-binding description
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.05        23     150     174 ..     178     202 ..     166     208 .. 0.86
   2 ?    5.2   0.0      0.03        14     153     183 ..     484     514 ..     473     532 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.05
                          PSY3 150 klklLlkllkklrktfgcwvittsy 174
                                   + ++Ll ++k++r+++g +vi ts 
  gi|15669858|ref|NP_248672.1| 178 SKQKLLDVIKNIRDKLGITVIITSH 202
                                   5789*****************9996 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.03
                          PSY3 153 lLlkllkklrktfgcwvittsygleyyeGie 183
                                      + lk ++++fg +++ +s  +e+ + i+
  gi|15669858|ref|NP_248672.1| 484 DVANYLKIINERFGTTIVLVSHCVEFIKEIS 514
                                   56789*********************88776 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0085       3.8       3      61 ..      34      97 ..      32     142 .. 0.77
   2 ?    2.3   0.0      0.27   1.2e+02       2      19 ..     289     306 ..     288     325 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0085
                                  EE-STTSSHHHHHHHHHHHHT-.....EEEEHHHHHHHHHHHHHHTT--TT-HHHHHHHHHT-- CS
                Cytidylate_kin  3 iDGPagsGKssvaralaeklgl.....kyldtgalYRalalaalrrkvdlldeaalvelakeve 61
                                  i G +g+GKs++ r+l   l++     ++l     ++ ++ + l+r+ +l+ e  + ++++++ 
  gi|15669858|ref|NP_248672.1| 34 IVGKSGAGKSTLIRILRGSLDYdegevEILGRKDNFKEITAIHLQRNFALWAEPVINNIIRKLY 97
                                  6699************999987222224555666677889999999999999999998888764 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.27
                                   EEE-STTSSHHHHHHHHH CS
                Cytidylate_kin   2 aiDGPagsGKssvarala 19 
                                   +i GP+g GK  + r++a
  gi|15669858|ref|NP_248672.1| 289 SIIGPSGVGKTVIMRLMA 306
                                   677*********999998 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.5    0.0043       1.9      11      50 ..      16      52 ..       1     139 [. 0.65
   2 ?    4.1   0.3      0.07        31     287     368 ..     120     206 ..      56     207 .. 0.70
   3 ?    2.5   0.0      0.21        95      15      43 ..     276     305 ..     274     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0043
                        AAA_15 11 FRslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                  F++l++v+ + ++  +  ++Gk ++GKS+++++l      +
  gi|15669858|ref|NP_248672.1| 16 FKALDKVSFEAKKGeILGIVGKSGAGKSTLIRILR----GS 52
                                  888888777777768999***************94....33 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.07
                        AAA_15 287 k..........ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnkt 357
                                              ++ +  +n  + G ++ l l  +i+++ +k        +ll++EP +   p  ++ l + +k++ ++   
  gi|15669858|ref|NP_248672.1| 120 AieilklvgleHKKDAFANILSGGEKQRLILGRQIAKIYEK-----GEGVLLLDEPATMACPASKQKLLDVIKNIRDKLGI 195
                                   14444555666777777777888888888888888888888.....7789999***********************99999 PP

                        AAA_15 358 QviitTHSphi 368
                                    viit+H p i
  gi|15669858|ref|NP_248672.1| 196 TVIITSHLPEI 206
                                   *******7765 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.21
                        AAA_15  15 kdveidlsee.ltvliGkNnsGKSsileal 43 
                                   ++v+ d++e  +  +iG+ ++GK+ i++++
  gi|15669858|ref|NP_248672.1| 276 RNVSFDVKEGeILSIIGPSGVGKTVIMRLM 305
                                   56666667667999************9876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.5       0.2        89      16      39 ..      25      48 ..      17     201 .. 0.81
   2 ?    6.6   0.0     0.015       6.7      20      43 ..     285     308 ..     277     423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.2
                      ATPase_2 16 erepneiyfiYGpegsGKtaLlke 39
                                  e ++ ei+ i G  g GK++L++ 
  gi|15669858|ref|NP_248672.1| 25 EAKKGEILGIVGKSGAGKSTLIRI 48
                                  55667899999*********9984 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                      ATPase_2  20 neiyfiYGpegsGKtaLlkeiien 43 
                                    ei+ i Gp g+GKt +++ ++  
  gi|15669858|ref|NP_248672.1| 285 GEILSIIGPSGVGKTVIMRLMAGL 308
                                   68999************9977654 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.037        16       5      18 ..      34      47 ..      30      55 .. 0.86
   2 ?    4.2   0.1     0.083        37       3      18 ..     288     303 ..     286     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.037
                                  EEC-TTTCHHHHHH CS
                         NACHT  5 lqGeaGsGKTtLlq 18
                                  + G++G GK+tL++
  gi|15669858|ref|NP_248672.1| 34 IVGKSGAGKSTLIR 47
                                  89**********97 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.083
                                   EEEEC-TTTCHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlq 18 
                                   + + G++G+GKT+ ++
  gi|15669858|ref|NP_248672.1| 288 LSIIGPSGVGKTVIMR 303
                                   5699********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.83u 0.33s 00:00:01.15 Elapsed: 00:00:00.50
# Mc/sec: 3312.08
//
Query:       gi|15669859|ref|NP_248673.1|  [L=204]
Description: molybdopterin-guanine dinucleotide biosynthesis protein MobA [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.5e-26   91.1   0.0    1.2e-25   90.8   0.0    1.0  1  NTP_transf_3  MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.0   6.4e-30   1.2e-25       1     144 [.       7     158 ..       7     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 6.4e-30
                                   EEEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH....CHHHHHHTTCTS-EEE-TTSS-SHHHHHH CS
                  NTP_transf_3   1 aviLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggd....eevlaalarlgvrvvededpgkgplasla 77 
                                   ++iL GG++ R gg K++  ++gk l+ +  d l++++++ v+v +++    e  +++l ++++ +  d  +gkgpl +++
  gi|15669859|ref|NP_248673.1|   7 GIILSGGKGERIGGKKPFRVFNGKYLINYPSDILKSLNIPFVTVFAKNsidlEMEKEYLTKYKCLISFDLIEGKGPLMGIL 87 
                                   79********************************************99565546777999********************* PP

                                   HHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCH...HHHTSSEEEEESSSEEEECC..EEEGGGHHHHHHH CS
                  NTP_transf_3  78 aalraaadadavlvlacDmPlltpelverllaaa...aasgadvvvptyegerghpl..lfrarllsalaal 144
                                   +++r + +a++++vl+cD+P++++e++++l+ ++   +++++ +++p++e+++++pl  l+++++ls l ++
  gi|15669859|ref|NP_248673.1|  88 CGMRVL-NAKWFVVLPCDCPYINKEALKKLISNIsiaEKNNNLCIIPKHENGYIEPLfaLYKRDALSILNKI 158
                                   ****99.9*************************97766777889*************888899999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1313.51
//
Query:       gi|15669860|ref|NP_248674.1|  [L=226]
Description: hypothetical protein MJ_1664 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.058   13.5   0.2       0.12   12.5   0.2    1.5  1  Oscp1     Organic solute transport protein 1


Domain annotation for each model (and alignments):
>> Oscp1  Organic solute transport protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   6.4e-06      0.12      67     157 ..      28     119 ..       3     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-06
                         Oscp1  67 neaSmdKlfdlmlmavkyqlllakspeellevtlnhl.daikelvkeekskevlklvdevkkklvevysklsegelll..i 144
                                   n + + Klf+l l  ++y   ++++  +l ++  +h  ++i e +k e++  +l+l++e+kk + +++s l +g l +  +
  gi|15669860|ref|NP_248674.1|  28 NGNNLYKLFNLTLSKIRYRKAMLEHNFQLPKIKESHKpKEITEKIK-ENDIYFLELINEIKKDFKDFCS-LDAGTLFElfM 106
                                   567789**************************99886378999998.5556799**********99986.66666554125 PP

                         Oscp1 145 rqtllnflqdvhv 157
                                     tl++f+++ ++
  gi|15669860|ref|NP_248674.1| 107 YYTLIEFFKENNI 119
                                   7899999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1495.12
//
Query:       gi|15669861|ref|NP_248675.1|  [L=458]
Description: hypothetical protein MJ_1665 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-177  591.0   8.3   1.4e-177  590.7   8.3    1.0  1  DUF711    Uncharacterised ACR (DUF711)


Domain annotation for each model (and alignments):
>> DUF711  Uncharacterised ACR (DUF711)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  590.7   8.3  7.9e-182  1.4e-177       1     405 [.      13     422 ..      13     427 .. 0.97

  Alignments for each domain:
  == domain 1  score: 590.7 bits;  conditional E-value: 7.9e-182
                        DUF711   1 mieeekldiRtvTlgislldcasedleklaekiyekiikkaaklvktveeieeeyGievvtkRisvtpisellaeasaeea 81 
                                   mi+ e+ld RtvTlg+sl+dc+s+dl++l+e+iy+ki+++a++lv+t+e+i+e+yGi++v+kRi+vtpis ++ +a + + 
  gi|15669861|ref|NP_248675.1|  13 MIKMENLDLRTVTLGLSLRDCVSKDLDELKENIYNKITSSAENLVETAERISEKYGIPIVNKRIAVTPISLVIGGAIK-DL 92 
                                   9*********************************************************************77776553.33 PP

                        DUF711  82 .........velaktldelakevgvdfiggfsalvekgltkgdkeliesipealaetervcssvnvastkaginmdavraa 153
                                            ve+ + ld++ak+v vdf+gg+salv+k +tk+d++li+sip ++++tervcssvnvastk+ginmdav+++
  gi|15669861|ref|NP_248675.1|  93 dkeeqikacVEVGEVLDKAAKKVRVDFLGGYSALVHKDATKEDRALIDSIPFMMEKTERVCSSVNVASTKTGINMDAVKRM 173
                                   355677788888888****************************************************************** PP

                        DUF711 154 aevikeiaeltkdkdglgnaklvvfanvpednPFfpgAfhgvgeaeavinvGvsgpgvvkkaleeakkeasleelaeaikk 234
                                   +e+ike+a +t++  ++g+aklvvfan+pednPF++gAfhgvge+++vinvGvsgpgvv++++e++ ++a++ +la++ikk
  gi|15669861|ref|NP_248675.1| 174 GEIIKETAFRTEK--AIGCAKLVVFANAPEDNPFMAGAFHGVGEGDKVINVGVSGPGVVRAVIEKL-PDADFGTLANEIKK 251
                                   ***********99..***************************************************.77************ PP

                        DUF711 235 tafkitrlgelvarevakrlgvefggiDlSlaPtpavgdSvaeileelglesfGapGtlaalalltdavkkGGvmasskvg 315
                                    afkitr+gel++rev+k+lgv+fg++DlSlaPtpa+gdS+a+ile++gle++G++G++aalall+davkkGG+ma+s+vg
  gi|15669861|ref|NP_248675.1| 252 VAFKITRVGELIGREVSKELGVKFGVVDLSLAPTPARGDSIANILEAMGLEKCGTHGSTAALALLNDAVKKGGAMATSYVG 332
                                   ********************************************************************************* PP

                        DUF711 316 GlsGlflpvsEDaglaeaaeegaltiekLlamsaVCsvGLDmvpipgdtsaetiaaliaDeaalavrlnKtlavRliPvpg 396
                                   GlsG+f+pvsED+g++ea+e+galt+ekL+am++VCsvG+Dmv+ipgdt+a+ti+a+iaDe+a++v++nKt+avR+iPvpg
  gi|15669861|ref|NP_248675.1| 333 GLSGAFIPVSEDSGMVEAVEAGALTLEKLEAMTCVCSVGIDMVAIPGDTPASTISAIIADEMAIGVINNKTTAVRIIPVPG 413
                                   ********************************************************************************* PP

                        DUF711 397 kkaGdkveF 405
                                   kkaG+ v++
  gi|15669861|ref|NP_248675.1| 414 KKAGEYVDY 422
                                   *****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2892.06
//
Query:       gi|15669862|ref|NP_248676.1|  [L=465]
Description: hypothetical protein MJ_1666 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.1e-43  147.2  17.9    9.1e-43  147.2  17.9    1.4  2  Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
  ------ inclusion threshold ------
       0.12   13.0   0.1       0.12   13.0   0.1    3.3  4  Com_YlbF   Control of competence regulator ComK, YlbF/YmcA


Domain annotation for each model (and alignments):
>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.2  17.9     1e-46   9.1e-43       1     359 []       4     396 ..       4     396 .. 0.78
   2 ?   -3.5   0.9      0.67     6e+03     238     274 ..     428     459 ..     399     463 .. 0.36

  Alignments for each domain:
  == domain 1  score: 147.2 bits;  conditional E-value: 1e-46
                     Cas_DxTHG   1 vlisflGt.gnykevkYelkeeeeeeketsfvqeallellaekedpdkvvilltdtladkeaeek........eeaak.lk 71 
                                   +li+++G+ +++k+v Y+   ++++eke++ +  a+++++    +pdkv+il+ dtl++ e+e+         e++++ +k
  gi|15669862|ref|NP_248676.1|   4 ILIAPWGNfSSWKKVIYS---FNGVEKESKSSLSAIYDKI----NPDKVYILVLDTLSNLESENYgdivkevkEKTENfIK 77 
                                   59******999*******...889************9999....555************5555555666555566788888 PP

                     Cas_DxTHG  72 eeleelleiekvdveiipgggte...............eelwe....ifekllekleendeiilDiThGfrylPvla.... 129
                                   e+l    +i + +v+++pg+gt+                   +     +++l ++l+++ e++lD+ThG++y+Pvl+    
  gi|15669862|ref|NP_248676.1|  78 ENL----NIDNYEVIVCPGVGTFynkdfekyfkfygnlT---DyysfALYELSKRLDGDLEVHLDLTHGLNYMPVLTyrvi 151
                                   888....477888***********999877776664444...2555577799999************************** PP

                     Cas_DxTHG 130 ...llalaylrnvknltikgiyYgafkeeeedPil.dlteflels..................dwltaverflktgdaekl 188
                                      l +la+ ++v+ l ++++          dP++ + +e+l+++                  d+l+a+ +f++ +++ k+
  gi|15669862|ref|NP_248676.1| 152 kdlLEILAIKNKVR-LVVYNS----------DPYVgREKEILNIHtvedviikpsydikgmtlDFLDAT-KFVDKKEIGKI 220
                                   **************.99****..........****9888888888888888888888889888888888.69988888888 PP

                     Cas_DxTHG 189 aellrekkek.....kkek...................lkklk..klkeklkkeleefskalelirp......lell.eka 236
                                   ++ ++ ++++        k                   ++++k  k++ +l++++ +f  +++++ +      +++  e++
  gi|15669862|ref|NP_248676.1| 221 KKEINMNPKIkelriM--KqninafiasivyalplvysTFFVKkdKIEIYLNELIGAFISNIKINPEdkilkrYLYFgEGF 299
                                   8888554444346432..24688999999999999999888888999999999*****99999999544441233333355 PP

                     Cas_DxTHG 237 ekleke.iveklkeeleeiesleeeesakplel...lldeikkklekflkkqikwclekgliqqaltllreliislllege 313
                                   ++l+k  +      +++ei         ++l +    l+ei+++ + +    +k+  + ++i+++++ l  +i        
  gi|15669862|ref|NP_248676.1| 300 NSLVKAyFA----SKISEI---------PQLIKdelSLEEIDELKNTL----FKENPNSQYIKNEISSLYNII-------- 355
                                   555554222....222333.........11111222677777666666....566778888888888888888........ PP

                     Cas_DxTHG 314 dilnkkkrreeieeelknlskvekksseekeeklsniRNdiaHaGl 359
                                      n+k+++ee++e l n++ ++k+++e+++   ++iRN++aHaG+
  gi|15669862|ref|NP_248676.1| 356 ---NTKYKEEELSEILGNWTPIYKIRRENID--KFKIRNFLAHAGF 396
                                   ...8888889******************998..69**********8 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.67
                     Cas_DxTHG 238 kleke.iveklkeeleeiesleeeesakplel.........lldeik 274
                                    +e++     +k+ + ++            +          +l++i+
  gi|15669862|ref|NP_248676.1| 428 YIEEKnG---IKRFIFKY------------KDkngkveeinILEKIE 459
                                   1111110...11111111............11222222222444444 PP

>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       1.3   1.2e+04      39      45 ..      66      72 ..      33      86 .. 0.61
   2 ?   13.0   0.1   1.3e-05      0.12      62      96 ..     213     247 ..     199     251 .. 0.89
   3 ?    1.6   0.4     0.048   4.3e+02      18      93 ..     324     368 ..     304     383 .. 0.55
   4 ?   -2.3   0.4      0.74   6.7e+03      65      95 ..     421     451 ..     401     459 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
                                  HHHHHHH CS
                      Com_YlbF 39 kefkklq 45
                                  ke+k++ 
  gi|15669862|ref|NP_248676.1| 66 KEVKEKT 72
                                  2222222 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHH CS
                      Com_YlbF  62 ekkelqelkeeldknplvkeyleaeqelnellqev 96 
                                   +kke+ ++k+e+++np++ke++  +q++n +++++
  gi|15669862|ref|NP_248676.1| 213 DKKEIGKIKKEINMNPKIKELRIMKQNINAFIASI 247
                                   6679**************************99987 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.048
                                   HHHHHHHHHHH.HCSHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHH CS
                      Com_YlbF  18 ykeykeaeeal.eedeelqklikefkklqkelqekqmkgeelkeeekkelqelkeeldknplvkeyleaeqelnell 93 
                                    +e  e+++ l +e++                                + q +k+e+ +  ++ + + +e+el+e+l
  gi|15669862|ref|NP_248676.1| 324 LEEIDELKNTLfKENP--------------------------------NSQYIKNEISSLYNIINTKYKEEELSEIL 368
                                   3333333333323333................................44555555555555555555555555554 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.74
                                   HHHHHHHHHHTSHHHHHHHHHHHHHHHHHHH CS
                      Com_YlbF  65 elqelkeeldknplvkeyleaeqelnellqe 95 
                                    l+  k+ +++   +k+++ ++++ n  ++e
  gi|15669862|ref|NP_248676.1| 421 SLRYNKNYIEEKNGIKRFIFKYKDKNGKVEE 451
                                   3444444455555555555444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2978.25
//
Query:       gi|15669863|ref|NP_248677.1|  [L=418]
Description: hypothetical protein MJ_1667 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-24   87.7   9.4    1.4e-24   87.3   9.4    1.1  1  RAMPs          RAMP superfamily
     0.0026   17.6   0.6     0.0057   16.5   0.6    1.5  1  Peptidase_C97  PPPDE putative peptidase domain


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   9.4   1.6e-28   1.4e-24       1     212 [.      49     344 ..      49     345 .. 0.94

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 1.6e-28
                                   EEEESS-EE----.................................................................... CS
                         RAMPs   1 kletltPlhiGdg.................................................................... 13 
                                   k+e +tP++iG+g                                                                    
  gi|15669863|ref|NP_248677.1|  49 KCELITPIFIGCGeeysqldyfiedglahiidlekavsdlddlekvdyisglivsnidnnrlnltakdilesvglnpydyv 129
                                   6899***************************************************************************** PP

                                   .....................---S----HHHHHHHHHHHHH.HHHH.HHHTT-HHHHH.H.........HHHHHH--S.. CS
                         RAMPs  14 .......kisdekeespefrdkgglPyIPGSSlkGalRsale.kllgsekkekkdeysrkkekqrvkkgdleeaiFGneee 86 
                                            s++k   ++f++++++ yIPGSS+kGa+R+a+  +++ +++ e  +++++++ k ++k ++le+    +++ 
  gi|15669863|ref|NP_248677.1| 130 irkieseIFSNKKTRVKKFINQNNTYYIPGSSIKGAIRTAYIfNYYDKNLPELLKILDDRNIKLHDKGKELEKNAISKDIP 210
                                   ******999999999*******************************************************999999999** PP

                                   .SS--SEEEEE.......................EEEEEEEEEEEEEEEEE--SSS-EEEEEE.............-TT-E CS
                         RAMPs  87 skiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktktngk..........kkggl 157
                                   +++++ ++++D+  ++++ + ++ +++++ +   k+++ +++     + +++ +++i++++ +n +          +  ++
  gi|15669863|ref|NP_248677.1| 211 KDFFKYLKISDSLNLEGEFKFIHTKRWNYRK---KKFDVPINMEGMTKGTFSINIKIEDEFFKNINkrlktnynpkDDEKK 288
                                   *****************************99...*****************************999888877666533333 PP

                                   EE.EEEEESS...............HHHHHHHHHHHHHH....HHH---STTTTBTTT-E CS
                         RAMPs 158 ft.leaipae.rikfsgrirlenlsdeelgallklLdll...dlhflglGggkplGfGsv 212
                                   f  l+ ++++   +  + + ++n++  +++ ++klL ++   d  +l+lG    +G+G++
  gi|15669863|ref|NP_248677.1| 289 FDiLKNLCNNfSKTVVEFELKKNNPVYVEKSYEKLLADInkdDAIYLNLG----FGGGFL 344
                                   4455555555777888888*******************************....****97 PP

>> Peptidase_C97  PPPDE putative peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.6   6.4e-07    0.0057      81     134 ..     263     320 ..     252     328 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.4e-07
                                   ---HHHHHHHHHHHHTT--G....GG-BTTTB-HHHHHHHHHHHHHS----HHHHTHH CS
                 Peptidase_C97  81 evteeevraileelsseytg....dkYnLiskNCnhFtdelvdfLtgkkiPewinrla 134
                                   ++++e +++i ++l+ +y++    +k++++++ Cn+F++++v+f  +k+ P ++++  
  gi|15669863|ref|NP_248677.1| 263 KIEDEFFKNINKRLKTNYNPkddeKKFDILKNLCNNFSKTVVEFELKKNNPVYVEKSY 320
                                   56778889999999999875222268****************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2587.95
//
Query:       gi|15669864|ref|NP_248678.1|  [L=376]
Description: hypothetical protein MJ_1668 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-15   55.8   0.0    9.9e-15   54.2   0.0    2.0  1  Csm4_C    CRISPR Csm4 C-terminal domain
    1.2e-05   25.5  18.2    1.2e-05   25.5  18.2    2.2  2  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> Csm4_C  CRISPR Csm4 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   1.1e-18   9.9e-15       3      90 ..     269     366 ..     267     367 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.1e-18
                        Csm4_C   3 akkymlLSlllpkeeeledlleeaaYelikrsGfvssessaeqlkkkdvymfaeGSvfkkkleGkvvdvspegf....... 76 
                                    ++ mlL + +p++++++++++   Y+li+ +G+++s +  + + k+++ +++eGS++k+ + G+v d+sp++        
  gi|15669864|ref|NP_248678.1| 269 LEYKMLLGVGIPNKDDIKNIEY---YKLIEIGGYIYSLECLT-KPKRNILALTEGSIVKNDFIGDVKDISPQNDddeqnkn 345
                                   6899******************...************99999.89999************************99999**** PP

                        Csm4_C  77 .......ehpvyrygkalflp 90 
                                          +h+vy  gk+++lp
  gi|15669864|ref|NP_248678.1| 346 nennnklNHKVYTHGKPILLP 366
                                   ******************998 PP

>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5  18.2   1.3e-09   1.2e-05      29     213 .]      23     245 ..      11     245 .. 0.81
   2 ?    0.2   0.2     0.074   6.6e+02     120     151 ..     309     360 ..     257     371 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.3e-09
                                   --S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H........................................... CS
                         RAMPs  29 gglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd.................................. 75 
                                    ++ + ++ Sl  a+ + + kl+g e+ ek+ e++++++ +  +++                                   
  gi|15669864|ref|NP_248678.1|  23 RNSKIFHSNSLFSAIVNNYIKLYGREDLEKNIEKIKNIRLSSLLYKIkniylipkpehpefyklkgnpgikpkdikkiqff 103
                                   566788899***************999999888888776666555558888999999998888888888888888888888 PP

                                   ...HHHHHH--S...SS--SEEEEE.................................EEEEEEEEEEEEEEEEE--SSS- CS
                         RAMPs  76 ...leeaiFGneeeskiagrvffeDarpvkipgqileeskqikstpsp..........klsgselrelldhsterrtrvai 143
                                      + ++++ ne   +++ +++ ++ +   ++  ++ e+                   k+++ + + ++  s+  + +vai
  gi|15669864|ref|NP_248678.1| 104 sikAYKELLDNE--LDWKNKIKHIVDYQTINKSIVISEK--------EieeikrifgiKAEKLKHAKISLISKHLEQKVAI 174
                                   888777777777..5555555555443333333222222........2334444566699999999*************** PP

                                   EEEEEE.....-TT-EEEEEEEESS...............HHHHHHHHHHHHHH.HHH---STTTTBTTT-EE CS
                         RAMPs 144 drktktngk..kkgglftleaipae.rikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsve 213
                                   dr ++ + +  +kg+l+++e+i  + + +f ++i ++n  +e  ++l++ ++l+   + glGg++++G G++e
  gi|15669864|ref|NP_248678.1| 175 DRLKDITLEkdDKGQLYNIEFIKLNeNVEFYFLIDYNNEDKEFIKKLEASIKLI--EDEGLGGKRSIGAGFFE 245
                                   ******************************************************..**************997 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.074
                                   .....................EEEEEEEEEEEEEEEEE--SSS-EEEEEE.. CS
                         RAMPs 120 p....................klsgselrelldhsterrtrvaidrktktng 151
                                   p                    ++ +s+ ++++  ++  ++++++++k  t g
  gi|15669864|ref|NP_248678.1| 309 PkrnilaltegsivkndfigdVKDISPQNDDDEQNKNNENNNKLNHKVYTHG 360
                                   0445555545555555555556666777777777777777777777665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2466.77
//
Query:       gi|15669865|ref|NP_248679.1|  [L=248]
Description: hypothetical protein MJ_1669 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-16   61.5   5.3    1.1e-16   61.5   5.3    1.5  1  RAMPs     RAMP superfamily
  ------ inclusion threshold ------
      0.055   13.5   0.1       0.12   12.4   0.1    1.5  1  zf-CXXC   CXXC zinc finger domain


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   5.3   1.2e-20   1.1e-16       2     213 .]      16     201 ..      15     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1.2e-20
                                   EEESS-EE----................---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HHHHH CS
                         RAMPs   2 letltPlhiGdg..kisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdleeai 80 
                                   +e  t +hiG+   + +  + ++p++rd +g+  IPGSSlkG +R +le     +k+ k +e+ r ++  ++  +  +++i
  gi|15669865|ref|NP_248679.1|  16 IELETGMHIGGTkeTLKIGGTDNPVIRDAFGRILIPGSSLKGKIRALLE-----RKDGKYKEDGRGNYLPHDCGECEICKI 91 
                                   788999******99999****************************9998.....4566777777778888999999***** PP

                                   H--S.....SS--SEEEEE.......................EEEEEEEEEEEEEEEEE--SSS-EEEEEE...-TT-EEE CS
                         RAMPs  81 FGne..eeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktktngkkkgglft 159
                                   FG     + k + rv+++Da++ + ++++                       +  ++e++ ++ idr ++t+ k  gg+ +
  gi|15669865|ref|NP_248679.1|  92 FGPHdsKNIKEPVRVIVRDAYLQPEENKK-----------------------DYDYLEIKVENTIDRLKGTTIK--GGIRN 147
                                   *8874334466668889999998887765.......................567999****************..***** PP

                                   EEEEESS..............HHHHHHHHHHHHHH..HHH---STTTTBTTT-EE CS
                         RAMPs 160 leaipaerikfsgrirlenlsdeelgallklLdll.dlhflglGggkplGfGsve 213
                                    e + a+  kf+++  ++   ++++++++k ++ +  l +  lGg  ++G+G+++
  gi|15669865|ref|NP_248679.1| 148 MERVVAG-SKFKFEVVFNIYKESDKELIKKFIEGMkLLEDDYLGGSGSRGYGKIK 201
                                   9999999.888888888888888888888888888877889999999*****986 PP

>> zf-CXXC  CXXC zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.4e-05      0.12      18      38 ..      80     100 ..      78     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                                   --.BS-SCCCCTSCCCTS-S- CS
                       zf-CXXC  18 tedCgkCsaCrdkkkfggpgk 38 
                                   + dCg+C++C+    +++++ 
  gi|15669865|ref|NP_248679.1|  80 PHDCGECEICKIFGPHDSKNI 100
                                   579*******87666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1483.96
//
Query:       gi|15669866|ref|NP_248680.1|  [L=133]
Description: hypothetical protein MJ_1670 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-29  101.8   4.6    4.9e-29  101.5   4.6    1.1  1  Csm2_III-A  Csm2 Type III-A


Domain annotation for each model (and alignments):
>> Csm2_III-A  Csm2 Type III-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.5   4.6   2.7e-33   4.9e-29       2     114 ..      23     131 ..      22     132 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 2.7e-33
                                   S-HHHHHHHHHHHHHHHH.TTS-STTTHHHHHHHHHHHHHHHHTHHHHHHHTHHHHHHHHHHHHHHHHH......HHHHHH CS
                    Csm2_III-A   2 ekieelvekaeeigkelkkkklktsqiRkfydevkrieekikkkkeeeseeilrklkllkpklaYaagr......eeavke 76 
                                   ++++e++++ae+++ke+  +++ ++++R+fyd+v ri+ek+        e+++++l+llkpklaY+ g+      +ea+++
  gi|15669866|ref|NP_248680.1|  23 QNANEIIDIAENLAKEF--EQIPATKMRDFYDYVLRIDEKN--------ENWYKELVLLKPKLAYNYGKetnrrkKEALEK 93 
                                   6899*************..99*******************6........799*****************8888867***** PP

                                   HHHHHHHHHHH--SH.HHHHHHHHHHHHHHHHHHCT-X CS
                    Csm2_III-A  77 lsevlkkaidkvkkskekfkrfvdffEAivAYhkyygg 114
                                   l+ +++++idk++++ +kfk+f++ffEA+vAYhk+y +
  gi|15669866|ref|NP_248680.1|  94 LAGTFSEIIDKIDNDLNKFKNFKTFFEALVAYHKIYAK 131
                                   ************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 858.01
//
Query:       gi|15669867|ref|NP_248681.1|  [L=45]
Description: hypothetical protein MJ_1671 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   16.0   0.1      0.014   15.8   0.1    1.0  1  DUF3888   Protein of unknown function (DUF3888)


Domain annotation for each model (and alignments):
>> DUF3888  Protein of unknown function (DUF3888)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.1   7.9e-07     0.014       6      39 ..       4      41 ..       2      44 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.9e-07
                       DUF3888  6 itlLtpyIqeaikkyYkkdlkeele....qakiLeikr 39
                                  +++L +y+ e++kk++++++k +++     aki+e+k+
  gi|15669867|ref|NP_248681.1|  4 VKFLEDYVREKVKKMFSSNVKLSFNdlkvSAKIVELKK 41
                                  789*******************8884444455666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 344.52
//
Query:       gi|15669868|ref|NP_248682.1|  [L=800]
Description: hypothetical protein MJ_1672 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-28   98.1   0.1    1.6e-27   95.2   0.1    2.6  2  Csm1_B    Csm1 subunit domain B
    3.5e-11   43.4   0.4    1.1e-10   41.8   0.4    1.8  1  HD        HD domain
  ------ inclusion threshold ------
        1.8    8.7   6.3         15    5.6   0.5    3.4  4  HD_6      HD domain


Domain annotation for each model (and alignments):
>> Csm1_B  Csm1 subunit domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2   0.1   2.6e-31   1.6e-27       1      94 []     284     375 ..     284     375 .. 0.98
   2 ?   -1.4   0.0      0.36   2.2e+03      38      73 ..     645     679 ..     637     693 .. 0.71

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 2.6e-31
                                   --SS--HHHHHHHHHHHHHHHHHHHHHHHHHTT--CCCEEEEETTEEEEEEE--HHHHHHHHHHHHHHHHHCCCCTSSS-E CS
                        Csm1_B   1 IsskgAlksLrgRSfylellleeivdelleklelsranllYagGGhfylLlpntekvkekleeiekelnewllkefkgkLy 81 
                                   I++k A+ksL+gRSfyl++l+e+++++++++l+l+ +n+l+ gGGhfy+L  + +  ++ ++++eke+ne+l++ f++k+y
  gi|15669868|ref|NP_248682.1| 284 ITTKYATKSLKGRSFYLDFLTEYFAKYICKELNLPITNILFYGGGHFYILSYKVD--ENLINKLEKEINEVLFNMFRTKIY 362
                                   899***************************************************9..9*********************** PP

                                   EEEEEEEE-TTTT CS
                        Csm1_B  82 lalayvelsaedl 94 
                                   + +a v ++ +d+
  gi|15669868|ref|NP_248682.1| 363 ITIAEVGVTPNDF 375
                                   ******9999987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.36
                                   CEEEEETTEEEEEEE--HHHHHHHHHHHHHHHHHCC CS
                        Csm1_B  38 nllYagGGhfylLlpntekvkekleeiekelnewll 73 
                                    l+YagG  + l++ + + v e  ++i+ +++++  
  gi|15669868|ref|NP_248682.1| 645 YLVYAGGDDT-LIVGAWDAVWELAKRIRGDFKKFVC 679
                                   5778777665.5566666677778888888877765 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.4   1.8e-14   1.1e-10      28     120 ..      10      90 ..       5      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.8e-14
                                   HHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHTTCCHHHHHHHHHHHH CS
                            HD  28 lllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld......ledvaklirehheswegkkrprgla 102
                                   l+++aLlHDiGk  ++ +       + k ++H k+g+e l+e +k  +l+       + ++++++ehh+++          
  gi|15669868|ref|NP_248682.1|  10 LKIGALLHDIGKFIQRASD------KPKSKGHDKFGYEFLKEKFKNGFLNhldektKDKILEIVKEHHNQKI--------- 75 
                                   899***********88633......456689****************************************7......... PP

                                   CCTSCHHHHHHHHHHHHH CS
                            HD 103 erqlslearivklaDrla 120
                                      ++ +  iv+laD+l+
  gi|15669868|ref|NP_248682.1|  76 ---KDDLIGIVRLADWLS 90 
                                   ...79***********98 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.5    0.0025        15      58     123 ..      14      74 ..       8      80 .. 0.67
   2 ?    5.4   0.2    0.0031        18     168     193 ..      68      93 ..      57      95 .. 0.76
   3 ?   -2.7   0.0      0.88   5.2e+03       3      38 ..     201     239 ..     199     256 .. 0.64
   4 ?   -2.3   0.0      0.66   3.9e+03     130     159 ..     378     412 ..     369     427 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0025
                                   HHCCCGGGSSHHHHTTS----TTS-.....-GGGT----HHHHHHHHHH.............HHHHHHHHHHHTTTS-- CS
                          HD_6  58 aalHDlGKaspaFqakvpelaekleeaglelekelekarHdslgaalle.............evarslaaavggHHGkp 123
                                   a lHD+GK+ ++   k                   ++  Hd+ g+ +l+             +++++++++v  HH + 
  gi|15669868|ref|NP_248682.1|  14 ALLHDIGKFIQRASDKP------------------KSKGHDKFGYEFLKekfkngflnhldeKTKDKILEIVKEHHNQK 74 
                                   67888888875433333..................56677777777766666666666666677888889999998754 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0031
                                   ..---HHHHHHHHHHHHHHHHHCTSC CS
                          HD_6 168 elelskaasvllaGlvvlADWigSne 193
                                   +++ +++++  l G+v lADW+ S e
  gi|15669868|ref|NP_248682.1|  68 KEHHNQKIKDDLIGIVRLADWLSSGE 93 
                                   4467778888899***********87 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.88
                                   EETTSTTS..EEEHHHHHHHHHHHHHHHHHHTS-H...H CS
                          HD_6   3 KadkeeeeeawhpLvaHllDvaavaealldkwlsl...l 38 
                                   Ka + +++ +  +L  H+  + a+a +l++ ++++    
  gi|15669868|ref|NP_248682.1| 201 KAGSLKGGLPDVSLFDHSKTTCAIACCLYQMYVKEnkkK 239
                                   555555554467899999999999999999888774431 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.66
                                   TSS-HHHHTT.....HHHHHHHHHHHHHHHHCT-T CS
                          HD_6 130 kaekkssaae.....dweeaqkelleaaaeflgaa 159
                                   +++k+s++++     +w+e+ ++++e  ++ ++ +
  gi|15669868|ref|NP_248682.1| 378 SEDKESKEKTwgfakKWKEVSEKTVEKKLRRFEYK 412
                                   33333333335666789998888887777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (800 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1414  (0.0788666); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.28s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 5226.67
//
Query:       gi|15669869|ref|NP_248683.1|  [L=129]
Description: hypothetical protein MJ_1673 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 859.14
//
Query:       gi|15669870|ref|NP_248684.1|  [L=634]
Description: hypothetical protein MJ_1674 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-47  162.0  11.8      3e-47  162.0  11.8    2.1  2  Cas_DxTHG        CRISPR-associated (Cas) DxTHG family
  ------ inclusion threshold ------
      0.052   14.2   0.9       0.28   11.9   0.2    2.7  2  Ground-like      Ground-like domain
      0.087   12.6   0.0       0.44   10.3   0.0    2.1  2  CCDC92           Coiled-coil domain of unknown function
       0.18   11.7   2.1        2.9    7.9   0.0    3.3  2  Nore1-SARAH      Novel Ras effector 1 C-terminal SARAH (Sav/R
        1.9    8.9   6.7         13    6.2   0.1    4.0  4  DUF4160          Domain of unknown function (DUF4160)


Domain annotation for each model (and alignments):
>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.0  11.8   8.3e-51     3e-47       1     357 [.       4     395 ..       4     397 .. 0.79
   2 ?    1.0  13.5      0.07   2.5e+02     153     334 ..     406     600 ..     401     633 .. 0.53

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 8.3e-51
                     Cas_DxTHG   1 vlisflGtgn.........ykevkYelkeeeeeeketsfvqeallellaekedpdkvvilltdtlad.............. 58 
                                   vlis+lG g+         yk+++Y+++  + + +e+ fv   l+e+l    ++dkv++++t  +++              
  gi|15669870|ref|NP_248684.1|   4 VLISPLGVGDtntdvykrqYKTAEYKFE-GDIDGIESPFVLSVLIEKL----KVDKVIVVGTAKSMWeklyeyyakevgef 79 
                                   79******55558899999*******64.466789*************....666********999999977777666554 PP

                     Cas_DxTHG  59 .keaeek........................eeaak.lkeeleelle..iekvdveiipgggteeelwe...ifekllekl 108
                                    +    +                        ++++k + ++l++++   +   + +ii  g +++e+we   +f  l++++
  gi|15669870|ref|NP_248684.1|  80 dE----EywieigkkvgmskydnyalseedlKKIEKvIDKYLKKINPnaVGGSKCKIIKYGIDKDEIWEnfdLFMSLINEV 156
                                   40....155666666666667678899877877888888888888779888888999************999999****** PP

                     Cas_DxTHG 109 eendeiilDiThGfrylPvlallalaylrnvknltikgiyYgaf...keeeedPildlteflelsdwltaverflktgdae 186
                                   +++dei+lDiTh+fr++P+++ + l ++r  kn+++kgiyYg +   +e + +P++dl++++e+s+w++++ +f+++g+  
  gi|15669870|ref|NP_248684.1| 157 NDGDEIYLDITHSFRSIPLFMYVMLEFMRYFKNVKLKGIYYGMLdviRELGHAPVVDLSPIFEISEWIRGMYEFTTYGNSY 237
                                   ********************************************************************************* PP

                     Cas_DxTHG 187 klaellre.kkekkkeklkklkklkeklkkeleefskalelirplellekaeklekeiveklkeeleeiesleeeesakpl 266
                                    +++ll++             k+++e    +l+++s+ + ++  +el e+  k  k+++++ k+++ ++     +++++ l
  gi|15669870|ref|NP_248684.1| 238 LISKLLENeD-----------KEIAE----KLQKISRYIDANYLKELREEV-KTLKPLLNE-KKDTGRF----LKYFIPEL 297
                                   ******5432...........35555....666666666666522222211.111112223.2555666....5566999* PP

                     Cas_DxTHG 267 ellldeikkklekflkkq...ikwclekgliqqaltllreliisl.lle.gedilnkkkrreeieeelknlskvekkssee 342
                                    + +d++k + + f + q   +kw  +++ +++++  l + i  + l+e ++  + +k+r e ++  +      ++    +
  gi|15669870|ref|NP_248684.1| 298 HKFIDKLKYEDSDF-EFQismAKWNFDNKKYSSGYLCLTDSI-FWkLCElYNLPSVYKNR-EVMKGII------YNP---S 366
                                   ********999999.4456689*************9999999.57788888888999999.8886666......222...1 PP

                     Cas_DxTHG 343 keek..............lsniRNdiaHa 357
                                   +++k              l+niRN+iaHa
  gi|15669870|ref|NP_248684.1| 367 LNKKysafgsikdmhykrLRNIRNKIAHA 395
                                   122223345566778888**********9 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.07
                     Cas_DxTHG 153 keeeedPildlteflelsdwltave...rflktgdaeklaellre..kkek..kkek................lkklkklk 210
                                   +e++ + +++l + ++l+d+ + +e   + +k+ +++k  +ll++  ++++  k                    + l+k +
  gi|15669870|ref|NP_248684.1| 406 PENDLEDVVNLLKNVNLPDFDKIIEdllLDVKNNQNNKTLKLLKNilNIQIirKI-IkaynfesneiywdfvsGYLLNKNN 485
                                   5788899999999999998888888643333344677777777777766666422.2356677788999999877888888 PP

                     Cas_DxTHG 211 eklkkeleefskalelirp.lellekaekleke..iveklkeeleei.esleeeesakplellldeikkklekf.lkkq.. 284
                                   ++++++l+e+ ++++ + +         +le+   +v+++  e ee+  sl+ ++++ ++   l +++++++    +++  
  gi|15669870|ref|NP_248684.1| 486 KCNNEKLREIIEIFHKNIEdA------GELEEAfnFVKNT--EDEELlDSLALQNAIMHY--ALFKLSNAYNIKnKEDKea 556
                                   888899999999988887332......2333322222221..112222333333332222..2333333222222112244 PP

                     Cas_DxTHG 285 ikwclekgliqqaltllreliislllegedilnkkkrreeieeelknlsk 334
                                   ikw l ++   +   +l+e+       +++++  k++ + +++e+ ++sk
  gi|15669870|ref|NP_248684.1| 557 IKWVLLNQNLCSKHPILKEIN------NNYHKIFKNKDKPMSNEILEASK 600
                                   555555555555555555555......22222222222333333333333 PP

>> Ground-like  Ground-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   7.7e-05      0.28       2      25 ..     485     509 ..     484     527 .. 0.79
   2 ?   -3.1   0.0       3.5   1.3e+04      15      38 ..     564     585 ..     554     587 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.7e-05
                   Ground-like   2 ekCnnseLkkiie...enmkqssasds 25 
                                   +kCnn++L++iie   +n+  ++a+++
  gi|15669870|ref|NP_248684.1| 485 NKCNNEKLREIIEifhKNI--EDAGEL 509
                                   89***********988888..445444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.5
                   Ground-like  15 enmkqssasdskkaiqkaleekfg 38 
                                   +n   +s + + k+i+++  + f+
  gi|15669870|ref|NP_248684.1| 564 QN--LCSKHPILKEINNNYHKIFK 585
                                   33..58888899999988887776 PP

>> CCDC92  Coiled-coil domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.64   2.3e+03      20      33 ..     264     277 ..     262     278 .. 0.84
   2 ?   10.3   0.0   0.00012      0.44      24      54 ..     296     326 ..     293     329 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.64
                        CCDC92  20 atLkgLHkEIekLq 33 
                                   + Lk+L +E++ L+
  gi|15669870|ref|NP_248684.1| 264 NYLKELREEVKTLK 277
                                   67999999999997 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00012
                        CCDC92  24 gLHkEIekLqkenkdLtfklimeegessqkg 54 
                                   +LHk I+kL+ e +d +f++ m + + ++k+
  gi|15669870|ref|NP_248684.1| 296 ELHKFIDKLKYEDSDFEFQISMAKWNFDNKK 326
                                   6*********************998776666 PP

>> Nore1-SARAH  Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.5     0.087   3.1e+02      14      31 ..     101     118 ..     100     119 .. 0.82
   2 ?    7.9   0.0   0.00081       2.9       4      18 ..     294     308 ..     291     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.087
                   Nore1-SARAH  14 LeeEEeeeiqqikrkYta 31 
                                   L eE   +i++++ kY +
  gi|15669870|ref|NP_248684.1| 101 LSEEDLKKIEKVIDKYLK 118
                                   66777889********65 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00081
                   Nore1-SARAH   4 lPELqnFLriLeeEE 18 
                                   +PEL+ F+ +L+ E 
  gi|15669870|ref|NP_248684.1| 294 IPELHKFIDKLKYED 308
                                   8***********885 PP

>> DUF4160  Domain of unknown function (DUF4160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.053   1.9e+02      29      60 ..      83     119 ..      73     122 .. 0.69
   2 ?   -3.6   0.1       4.3   1.5e+04      39      54 ..     438     452 ..     430     455 .. 0.70
   3 ?    1.1   0.1      0.14   5.1e+02      35      59 ..     480     504 ..     461     514 .. 0.79
   4 ?    6.2   0.1    0.0037        13      34      59 ..     540     565 ..     532     569 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.053
                       DUF4160  29 iwl...edvellegsg..lpkkelklieewveehqee 60 
                                   +w+   ++v + + ++  l++ +lk+ie+++ ++ ++
  gi|15669870|ref|NP_248684.1|  83 YWIeigKKVGMSKYDNyaLSEEDLKKIEKVIDKYLKK 119
                                   4554464455555444459************988665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.3
                       DUF4160  39 gsglpkkelklieewv 54 
                                   + + ++k+lkl+++++
  gi|15669870|ref|NP_248684.1| 438 N-NQNNKTLKLLKNIL 452
                                   3.45788888888776 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.14
                       DUF4160  35 ellegsglpkkelklieewveehqe 59 
                                    l ++++ ++ +l++i e+ +++ e
  gi|15669870|ref|NP_248684.1| 480 LLNKNNKCNNEKLREIIEIFHKNIE 504
                                   456677899*********9998866 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0037
                       DUF4160  34 vellegsglpkkelklieewveehqe 59 
                                   ++l + +++++ke k++ +wv ++q+
  gi|15669870|ref|NP_248684.1| 540 FKLSNAYNIKNKEDKEAIKWVLLNQN 565
                                   56778889****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1492  (0.0832171); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 4102.71
//
Query:       gi|15669871|ref|NP_248685.1|  [L=259]
Description: tRNA pseudouridine synthase A [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-26   90.8   0.0    4.7e-23   81.7   0.0    2.1  2  PseudoU_synth_1  tRNA pseudouridine synthase
  ------ inclusion threshold ------
      0.013   14.9   0.2        3.1    7.1   0.0    2.9  3  Baculo_DNA_bind  ssDNA binding protein


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0   0.00082       7.4      13      66 ..      13      61 ..       7      99 .. 0.75
   2 !   81.7   0.0   5.2e-27   4.7e-23       2     106 ..     119     218 ..     119     220 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00082
               PseudoU_synth_1 13 sfckqkqekkntvrtileaaieevsgeekell.vvtvkgsgFldhqVRamvgvlf 66
                                  sf  q+q++k+tv+ il  a+e    e++ l  +  + + g++d++V a+++ ++
  gi|15669871|ref|NP_248685.1| 13 SF--QQQPHKQTVCDILLDALE----ETGFLAkKKVIYSGGRTDKGVSALGNFVV 61
                                  35..79999*************....544455345566679*********99983 PP

  == domain 2  score: 81.7 bits;  conditional E-value: 5.2e-27
               PseudoU_synth_1   2 akelvGthdfgsfckqkqek.kntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklspedvkel 81 
                                   ak+ +Gth f +++k+++ k k+++rti++++i+    e++ +l+v++ g++Fl+++VR +vg+l +vg+gk+++e++++l
  gi|15669871|ref|NP_248685.1| 119 AKKMIGTHSFHNLSKRDRTKeKSPIRTIYDIKIS----ENEFYLTVDIIGESFLWNMVRKIVGALDLVGRGKKPVEWIDKL 195
                                   7999*********99999999*************....666788************************************* PP

               PseudoU_synth_1  82 lnakkrkkiavetapavglvlfhvr 106
                                   l+ + r+   v+t p++gl+l++++
  gi|15669871|ref|NP_248685.1| 196 LDENHREG--VPTFPPEGLILVEAK 218
                                   *****977..***********9875 PP

>> Baculo_DNA_bind  ssDNA binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.026   2.3e+02      91     116 ..      52      77 ..      40      84 .. 0.85
   2 ?    3.0   0.0    0.0061        55     129     165 ..     121     156 ..      95     167 .. 0.77
   3 ?    7.1   0.0   0.00034       3.1      79     112 ..     221     254 ..     208     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.026
               Baculo_DNA_bind  91 akstfGeFlsvswsnipvhnevfani 116
                                     s+ G+F++v+ ++ p+++++ a++
  gi|15669871|ref|NP_248685.1|  52 GVSALGNFVVVELKKEPILSYINAKL 77 
                                   56899*************99988776 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0061
               Baculo_DNA_bind 129 lklqnsvlvnlPedeevakkeafvrkFfdikrenNee 165
                                    ++ +  + nl +  + +k+++ +r+++dik ++Ne 
  gi|15669871|ref|NP_248685.1| 121 KMIGTHSFHNLSKR-DRTKEKSPIRTIYDIKISENEF 156
                                   55666777788888.889999999*******999985 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.00034
               Baculo_DNA_bind  79 kfyffDrvkvkrakstfGeFlsvswsnipvhnev 112
                                     y+ D  +++++k  +GeF+++++ +i + + v
  gi|15669871|ref|NP_248685.1| 221 IEYIYDNYSIRKFKEYWGEFFKLQVMKIGIAKTV 254
                                   469*********************9999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.70
# Mc/sec: 1109.58
//
Query:       gi|15669872|ref|NP_248686.1|  [L=238]
Description: hypothetical protein MJ_1676 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.032   14.1   0.0      0.058   13.3   0.0    1.4  1  HATPase_c_5  GHKL domain


Domain annotation for each model (and alignments):
>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.2e-06     0.058      34      87 ..      61     115 ..      51     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-06
                   HATPase_c_5  34 tvrekkksliisieNsyegekkklesskskkeehGiGlk.sireivkkykgnlsi 87 
                                   ++ ek++++i+++ N+y++  + l+  +++k++ G Gl+  i e +++y++++ i
  gi|15669872|ref|NP_248686.1|  61 NLIEKNNKIIFEVLNKYAEGFDDLRGISEDKDKAGEGLSyAIAESISEYGDAIII 115
                                   567899********************************85699999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1592.64
//
Query:       gi|15669873|ref|NP_248687.1|  [L=205]
Description: hypothetical protein MJ_1677 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.3e-77  257.8  12.5      6e-77  257.6  12.5    1.0  1  MarC       MarC family integral membrane protein
    2.6e-05   24.0  13.8      5e-05   23.1  12.2    2.1  1  TerC       Integral membrane protein TerC family
  ------ inclusion threshold ------
        3.4    7.6   8.4       0.86    9.6   0.2    2.5  3  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> MarC  MarC family integral membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.6  12.5     1e-80     6e-77       2     203 .]       4     204 ..       3     204 .. 0.99

  Alignments for each domain:
  == domain 1  score: 257.6 bits;  conditional E-value: 1e-80
                          MarC   2 kaiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgillfl 82 
                                   +++i af s+++i+np+g+vpvf++l+e+++k+er+ +a+k++i+al+ill+f+lfGe+ilk+fgis+da+kiaGgill+l
  gi|15669873|ref|NP_248687.1|   4 QYFILAFSSIFSILNPFGAVPVFITLTESYPKKERDLVAKKTVIYALAILLAFALFGEWILKFFGISLDAFKIAGGILLLL 84 
                                   789****************************************************************************** PP

                          MarC  83 iaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalitllilll 163
                                   i++dm++++q+ +k +++e e+++e+deia++PLA+Pl+aGPg+it+++v+++eas+i++k++v+laill++ it+l+ll+
  gi|15669873|ref|NP_248687.1|  85 ISLDMVRGQQE-AKIHRKEIEAAYEIDEIALMPLATPLLAGPGSITACMVAMAEASDIGDKFLVILAILLSLGITYLTLLS 164
                                   ***********.5******************************************************************** PP

                          MarC 164 sslilrllgktginaleRlmGllLvalavqlivdGikeil 203
                                   ++++l+++g+ gi++l+R+mGl+L+a+avq+iv+Gi+++l
  gi|15669873|ref|NP_248687.1| 165 AESVLDRIGRLGIRILTRMMGLILTAIAVQMIVNGIRGAL 204
                                   *************************************975 PP

>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1  12.2   8.3e-09     5e-05      17     180 ..      25     198 ..      22     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 8.3e-09
                          TerC  17 viallvkklpeeqqkkalllGilgAlvlRillillavallelf....dlilligglfLlytavkellekrlenklvkeekk 93 
                                   v+++l+++ p+++++ +    ++ Al++ +++ l++ ++l++f    d ++++gg++Ll++++++++ ++     + + ++
  gi|15669873|ref|NP_248687.1|  25 VFITLTESYPKKERDLVAKKTVIYALAILLAFALFGEWILKFFgislDAFKIAGGILLLLISLDMVRGQQ-----EAKIHR 100
                                   78899999**********************************88888*******************9755.....344445 PP

                          TerC  94 kkkktkstllavviqielaDlvfslDSvlaa.vait.....sdlfivitavilsilvlrfl...akllakllerf..ptlk 163
                                   k+ +++  +  + ++  ++ l+    S++a  va++     +d f+vi+a++ls+ +  +    a+ +++ + r+  ++l 
  gi|15669873|ref|NP_248687.1| 101 KEIEAAYEIDEIALMPLATPLLAGPGSITACmVAMAeasdiGDKFLVILAILLSLGITYLTllsAESVLDRIGRLgiRILT 181
                                   555555556666666777788888999999526777999999999999999998765544311155666666664336788 PP

                          TerC 164 ylalalllligvklvle 180
                                    ++ ++l  i+v+++++
  gi|15669873|ref|NP_248687.1| 182 RMMGLILTAIAVQMIVN 198
                                   899999********986 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00014      0.86      68     117 ..      45      96 ..      35     107 .. 0.77
   2 ?    2.2   1.0     0.027   1.6e+02      85     119 ..     131     170 ..     111     181 .. 0.66
   3 ?    0.0   2.2      0.13   7.5e+02      78     111 ..     158     193 ..     132     202 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00014
                     RseC_MucC  68 llvYllPllllilgallgsall....gssellaalgallglvlgflivrllskr 117
                                    ++Y+  l++l+++al+g+++l    +s +++ ++g++l+l++++ +vr  ++ 
  gi|15669873|ref|NP_248687.1|  45 TVIYA--LAILLAFALFGEWILkffgISLDAFKIAGGILLLLISLDMVRGQQEA 96 
                                   55555..57788888999998888889*****************9999976665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.027
                     RseC_MucC  85 gsall.....gssellaalgallglvlgflivrllskrlk 119
                                   +++++     +++++l++l+ ll l +++l +   ++ l 
  gi|15669873|ref|NP_248687.1| 131 CMVAMaeasdIGDKFLVILAILLSLGITYLTLLSAESVLD 170
                                   2222234456899999999999999999998876666555 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.13
                     RseC_MucC  78 lilgallgsall..gssellaalgallglvlgfliv 111
                                     l++l ++++l  ++  ++ +l+ ++gl+l+ + v
  gi|15669873|ref|NP_248687.1| 158 TYLTLLSAESVLdrIGRLGIRILTRMMGLILTAIAV 193
                                   122222222222444555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1444.28
//
Query:       gi|15669874|ref|NP_248688.1|  [L=396]
Description: Sep-tRNA:Cys-tRNA synthetase [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-36  125.2   0.4    3.8e-36  124.6   0.4    1.2  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
    7.5e-17   61.3   0.0    1.2e-16   60.7   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
    1.4e-09   37.6   0.0      2e-09   37.1   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
      7e-06   25.5   0.0    1.1e-05   24.9   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00011   21.6   0.0    0.00017   21.0   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.012   14.4   0.0      0.039   12.7   0.0    1.7  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
      0.025   13.9   0.0      0.054   12.8   0.0    1.5  1  Polyhedrin       Polyhedrin


Domain annotation for each model (and alignments):
>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.6   0.4   1.5e-39   3.8e-36     100     388 ..     115     392 ..     106     393 .. 0.90

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 1.5e-39
                                   C--CCEEEEEETCHHHHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHH...HCCTCCCEEEEEECSSTTTTB----HHHH CS
                       SepSecS 100 kakkviwvridekSslkavelaGleialvekvlegDelitdvedveeii...ekkreevilavlstlsffaprspDdvkei 177
                                   ++++v+  + ++  s++a+e+a l++a v  ++e  + ++++e  +e+i   e k+++v l++l+ +++ ++++ D  k++
  gi|15669874|ref|NP_248688.1| 115 EGDYVVLDKNAHYTSYVAAERAKLNVAEVGYEEEYPTYKINLEGYKEVIdnlEDKGKNVGLILLTHVDGEYGNLND-AKKV 194
                                   44455555555559***************999988888888766555553338899********************.9*** PP

                                   HHHHHCCT--EEEEGCCCCT-HHHHHHHHHHHHHTTC-EECCCHCHCCCEECCHCCCCESSCHCCCCCHCCCHCHCTSCHC CS
                       SepSecS 178 akiCaeydvPhlvNgAYaiqsekyieklkkalkvGRvdvvvksldknllvpvGgaiiaasdesfikeiskeypgrasaaps 258
                                    ki +e ++P+l+N AY++               GR++v  k++ ++++v +G++++aas + +i   s+e+++++ ++++
  gi|15669874|ref|NP_248688.1| 195 GKIAKEKGIPFLLNCAYTV---------------GRMPVNGKEVKADFIVASGHKSMAASAPCGILAFSEEFSDKITKTSE 260
                                   *******************...............*********************************************** PP

                                   CCCCCCHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC..............EEESSSTT-SSEEEEE-CCCHCCCCT CS
                       SepSecS 259 kdvlisllllGskaykkllkeqkesfkllreklkklaeeve..............ekllevpeNpissaltletldeikkk 325
                                   k  ++++++lG++ ++ ++ ++++sf+++ e++kk++ee +              ++l+ +p+ ++++ + + +ldei kk
  gi|15669874|ref|NP_248688.1| 261 KFPVKEIEMLGCTSRGLPIVTLMASFPHVVERVKKWDEELKktryvvdelekigfKQLGIKPKEHDLIKFETPVLDEIAKK 341
                                   ****************************************99************************************995 PP

                                   HH...HHHHHHHHHTTECSSE.EE-SSTCECTTSSS-SSSEEEEEE-TT--HHHHHHHHHHHHHHH CS
                       SepSecS 326 ar...ldlaseLfsrkvtGargvrasdsklTshlkeyhsrYlkiasaiGlkdedvdkvlerldeil 388
                                   ++   ++++ eL++r + G+r       + T        + +k+ s +Gl+ e+v++v+++++ei+
  gi|15669874|ref|NP_248688.1| 342 DKrrgFFFYDELKKRGIGGIR------AGVT--------KEIKM-SVYGLEWEQVEYVVNAIKEIV 392
                                   5433499**************......7777........66888.999999999999999999987 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.0   4.7e-20   1.2e-16      51     223 ..      85     257 ..      78     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 4.7e-20
                                   HHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGG CS
                   Aminotran_5  51 kvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldlde 131
                                   ++a+++n + +     t+G+ e+  +v++++    k+gd +v+ ++ h    v++++++    a+v + +  ++ +++l+ 
  gi|15669874|ref|NP_248688.1|  85 DIAKFLNMDCA---RPTHGAREGKFIVMHAI---CKEGDYVVLDKNAHYTSYVAAERAK-LNVAEVGYEEEYPTYKINLEG 158
                                   56666666653...34899999999******...9*****************9998886.889999999999999999999 PP

                                   HHHH-......-TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSS CS
                   Aminotran_5 132 lekll......nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgP 205
                                   +++ +       +++ l+ +thv  + G++++ +++gk+ak+kg+ +l+  a +vg +p++ k++++Df+++sghK + + 
  gi|15669874|ref|NP_248688.1| 159 YKEVIdnledkGKNVGLILLTHVDGEYGNLNDAKKVGKIAKEKGIPFLLNCAYTVGRMPVNGKEVKADFIVASGHKsMAAS 239
                                   99888888876699**************************************************************99999 PP

                                   TT-EEEEEEHHHHHTS.. CS
                   Aminotran_5 206 tGiGvlyvrkelleklep 223
                                   +  G+l +++e   k+ +
  gi|15669874|ref|NP_248688.1| 240 APCGILAFSEEFSDKITK 257
                                   99********99999843 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   7.8e-13     2e-09      46     298 ..      79     316 ..      46     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 7.8e-13
                                   HHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEET. CS
                 Aminotran_1_2  46 lpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyse. 125
                                    +++ e++akfl+         +     + Ga ++  +++ ++ +  gd +++++  +     +++ +++ v ++ +++e 
  gi|15669874|ref|NP_248688.1|  79 IKDFLEDIAKFLN--------MD-CARPTHGAREGKFIVMHAI-CKEGDYVVLDKNAHYTSYVAAERAKLNVAEVGYEEEy 149
                                   5789999999999........66.67789**************.8********************************9999 PP

                                   TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGG CS
                 Aminotran_1_2 126 edfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatran 206
                                   ++++++le+++e ++++  + k + +il++ +    G + + +++ k+   ak++++  ++  aY ++ +         +n
  gi|15669874|ref|NP_248688.1| 150 PTYKINLEGYKEVIDNLEDKGKNVGLILLTHVDGEYGNLNDAKKVGKI---AKEKGIPFLLNCAYTVGRMP--------VN 219
                                   **********************99****99987777777777777777...*****************997........77 PP

                                   STTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS........SHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 207 veeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls........ssllqaavaaalsdallkqseleemrq 279
                                    +e  +++iv s  K++++    +G+++ ++++ + ++k s  f +        +s + ++v+ ++s ++ + +++++  +
  gi|15669874|ref|NP_248688.1| 220 GKEVKADFIVASGHKSMAASA-PCGILAFSEEFSDKITKTSEKFPVkeiemlgcTSRGLPIVTLMASFPH-VVERVKKWDE 298
                                   7887789**********9999.99**********************999998865566666666666655.6678888888 PP

                                   HHHHHHHHHHHHHHHSTEE CS
                 Aminotran_1_2 280 rlqkrrkelrdeLaelglk 298
                                   +l+k +++++deL+++g+k
  gi|15669874|ref|NP_248688.1| 299 ELKK-TRYVVDELEKIGFK 316
                                   8876.56999999999886 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   4.2e-09   1.1e-05      36     216 ..      81     286 ..      76     368 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.2e-09
                                   HHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHH CS
               Beta_elim_lyase  36 rLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdleklea 116
                                   ++ + +a+ + +++a +++  + +  i + ++++ g+ v+++++ah+  + +   a l+ +++   +   + k++le  ++
  gi|15669874|ref|NP_248688.1|  81 DFLEDIAKFLNMDCARPTHGAREGKFIVMHAICKEGDYVVLDKNAHYTSYVAAERAKLNVAEVGYEEEYPTYKINLEGYKE 161
                                   567889999**************************************9999988888877755555555558********* PP

                                   HS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESS CS
               Beta_elim_lyase 117 aikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslk 197
                                   +i++ ++  ++++li+lt       G+   l+  ++v +iak++gip++l  A  +  +     +v      +D +++s+ 
  gi|15669874|ref|NP_248688.1| 162 VIDNLEDKGKNVGLILLTH--VD--GEYGNLNDAKKVGKIAKEKGIPFLLNCAYTVGRM-----PVNGKEVKADFIVASGH 233
                                   ***9888889999999975..43..8999*******************99776555444.....33333335899****** PP

                                   STT--SS-.EEEEE-HH.................................... CS
               Beta_elim_lyase 198 KdllanvG.gvlafrddel.................................e 216
                                   K + a    g+laf+++                                   +
  gi|15669874|ref|NP_248688.1| 234 KSMAASAPcGILAFSEEFSdkitktsekfpvkeiemlgctsrglpivtlmasF 286
                                   **999998999**9999445555555555555555555555555555555441 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.6e-08   0.00017      25     157 ..      79     222 ..      70     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.6e-08
                                   HHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TT..TSSB-GGG CS
               DegT_DnrJ_EryC1  25 veeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpd..tynidpaa 103
                                   +++F +++a++l+++ a ++  + ++  ++++a+  ++gd+V+  ++   ++  a+ ++ +++  v  +++  ty i+ + 
  gi|15669874|ref|NP_248688.1|  79 IKDFLEDIAKFLNMDCARPTHGAREGKFIVMHAIC-KEGDYVVLDKNAHYTSYVAAERAKLNVAEVGYEEEypTYKINLEG 158
                                   688999***************************64.347*****************999888888877654339******* PP

                                   CGGG--TTE......EEEEEB-G...GGB---HHHHHHHHHHCT-EEEEE-TT-TT.-EETTEE CS
               DegT_DnrJ_EryC1 104 ieaaitert......kaIlpVhl...yGqvadmdalkaiaakhglkvieDaAhAlG.atykgkk 157
                                    +++i +          Il+ h+   yG+ +d +++ +ia+++g++++  +A  +G   ++gk+
  gi|15669874|ref|NP_248688.1| 159 YKEVIDNLEdkgknvGLILLTHVdgeYGNLNDAKKVGKIAKEKGIPFLLNCAYTVGrMPVNGKE 222
                                   *****987777777789*****966678888999******************999955566665 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.5e-05     0.039      89     284 ..      99     286 ..      86     349 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                                   SHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--EB-TTS-BE---GGGGSHHHHHHHHHHSTTTGS. CS
                      OKR_DC_1  89 nGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepernalgiiggidlkefeeetlkekikevpdaka. 168
                                   +G   +  +v++a++++gd v++d+N+H     a   +      l  +  ++g   + ++ +++ e  ke i +  d+ + 
  gi|15669874|ref|NP_248688.1|  99 HGAREGKFIVMHAICKEGDYVVLDKNAHYTSYVAAERAK-----L--NVAEVGYEEEYPTYKINLEGYKEVIDNLEDKGKn 172
                                   577778899*******************76554433322.....2..2344555555555556667777777666655442 PP

                                   ESEEEEES.S-TTSEEE-HHHHHHHHTTSESEEEEE-TT-TTGGGSGGGTTSSSSSSS-BTTBEEEEEEEHCCCCS--TT- CS
                      OKR_DC_1 169 prlavitn.sTYdGvlynakeivdkleklsdrilfDeAwvgyeqfiplyadaskllaenendpgilvtqSvHKllaalsqa 248
                                     l+++t     +G l +ak++ + +++++++ l+  A+ +      ++++  +++a+       + + S HK  aa +  
  gi|15669874|ref|NP_248688.1| 173 VGLILLTHvDGEYGNLNDAKKVGKIAKEKGIPFLLNCAYTV----GRMPVNGKEVKAD-------FIVASGHKSMAASAPC 242
                                   33333332134567778888888888888888888888754....5677777777777.......7788888888888777 PP

                                   EEEEEES-BT.....--HHHHHHHHHHTS-SS...--HHHHHHH CS
                      OKR_DC_1 249 Slihvkeeli.....vneerlneafmmhattS...psYpllAsl 284
                                    ++   ee        +e+   +   m+  tS   p  +l+As 
  gi|15669874|ref|NP_248688.1| 243 GILAFSEEFSdkitkTSEKFPVKEIEMLGCTSrglPIVTLMASF 286
                                   77777777655555433333334445555555233444455555 PP

>> Polyhedrin  Polyhedrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.1e-05     0.054      97     162 ..      78     142 ..      57     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                                   S--SEEEEEEEEEEEEE.EESSSS----EEEEEEEE--TT----SEEE-SS-EE--TTSEEEEEE-T CS
                    Polyhedrin  97 pitndqevmdvflevrl.rptksnrcykflaqyalradedyvahdvirvvepeyvgqnnevrislak 162
                                   pi++  e +  fl++++ rpt+  r  kf++ +a+  + dyv  d       +yv  ++  ++++a 
  gi|15669874|ref|NP_248688.1|  78 PIKDFLEDIAKFLNMDCaRPTHGAREGKFIVMHAICKEGDYVVLDKNAH-YTSYV-AAERAKLNVAE 142
                                   6777778888899999868***********************9997544.45666.44555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2793.11
//
Query:       gi|15669875|ref|NP_248689.1|  [L=97]
Description: hypothetical protein MJ_1679 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-07   30.6   0.1    3.5e-07   30.4   0.1    1.2  1  RHH_8           Ribbon-Helix-Helix transcriptional regulator 
      3e-05   23.8   3.2    0.00024   20.9   0.0    2.9  3  RHH_1           Ribbon-helix-helix protein, copG family
     0.0047   17.1   0.9     0.0067   16.7   0.9    1.4  1  UPF0203         Uncharacterised protein family (UPF0203)
     0.0071   16.3   0.7      0.011   15.7   0.3    1.6  2  MMR_HSR1_Xtn    C-terminal region of MMR_HSR1 domain
  ------ inclusion threshold ------
      0.014   16.4   1.8      0.018   16.0   1.8    1.2  1  Myb_DNA-bind_3  Myb/SANT-like DNA-binding domain
       0.06   14.1   0.1      0.081   13.7   0.1    1.3  1  PSK_trans_fac   Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   1.2e-10   3.5e-07       3      46 ..       3      46 ..       1      87 [. 0.79

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.2e-10
                         RHH_8  3 tekvtinlgvvDLgqiDlLveeGfYsnRtDlirtairaqLakhd 46
                                  +e +t+ +    + qiD L++eG++s+R +++r a+r+ L++ +
  gi|15669875|ref|NP_248689.1|  3 EEEITLKIPKSIVNQIDELIKEGYFSSRDEFVRYAVRESLTEIA 46
                                  5889999999999***************************9764 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     8e-08   0.00024       2      38 ..       6      43 ..       5      44 .. 0.95
   2 ?    1.6   0.1       0.1     3e+02      12      27 ..      40      55 ..      40      55 .. 0.89
   3 ?    1.6   1.0     0.095   2.8e+02       4      14 ..      70      80 ..      69      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 8e-08
                                  EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                         RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                  ++++++++++ ++del++++  +Sr e++R A+re l+
  gi|15669875|ref|NP_248689.1|  6 ITLKIPKSIVNQIDELIKEGYfSSRDEFVRYAVRESLT 43
                                  899*******************************9775 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.1
                                  HHHHHHHHHHTSSHHH CS
                         RHH_1 12 erLdelarrrgrSrSe 27
                                  e L e+a+  ++Sr e
  gi|15669875|ref|NP_248689.1| 40 ESLTEIAISKKMSREE 55
                                  6899*********987 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.095
                                  EEEEHHHHHHH CS
                         RHH_1  4 irldeellerL 14
                                  i++de+++e+L
  gi|15669875|ref|NP_248689.1| 70 IKIDEKEIEEL 80
                                  78888888876 PP

>> UPF0203  Uncharacterised protein family (UPF0203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.9   2.2e-06    0.0067      29      66 ..      49      87 ..      20      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.2e-06
                       UPF0203 29 gkekeeeCeklwkkYreClkk.alkekgleklleearee 66
                                   k ++eeC+k+w++Y+   k+ +++ek++e+ll+e ++e
  gi|15669875|ref|NP_248689.1| 49 KKMSREECKKIWEEYKIRKKDiKIDEKEIEELLDEVDKE 87
                                  56669**********9875544799**********9887 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.3   3.9e+03      62      68 ..      15      21 ..       4      34 .. 0.67
   2 !   15.7   0.3   3.8e-06     0.011      12      51 ..      48      86 ..      37      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                  MMR_HSR1_Xtn 62 lNKiDli 68
                                  +N iD++
  gi|15669875|ref|NP_248689.1| 15 VNQIDEL 21
                                  4555543 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.8e-06
                  MMR_HSR1_Xtn 12 ltkldeetvkkilkeykihnaevliredvtvDdlidvieg 51
                                   +k++ e++kki +eyki + +++i e+ ++++l d + +
  gi|15669875|ref|NP_248689.1| 48 SKKMSREECKKIWEEYKIRKKDIKIDEK-EIEELLDEVDK 86
                                  467999*******************987.78899988855 PP

>> Myb_DNA-bind_3  Myb/SANT-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   1.8   6.1e-06     0.018       7      72 ..      30      95 ..      27      97 .] 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.1e-06
                Myb_DNA-bind_3  7 ekilvdllveqvkkgnriekktfkkeawkeileefna.ktgakytkkqlknrlkklrkeyklvkell 72
                                   + +v+  v+++ ++  i +k +++e  k+i+ee +  k++ k ++k++++ l+++ ke+k +k+l+
  gi|15669875|ref|NP_248689.1| 30 RDEFVRYAVRESLTEIAI-SKKMSREECKKIWEEYKIrKKDIKIDEKEIEELLDEVDKEWKKWKKLK 95
                                  56799999*********8.89999999********988999***********************996 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.7e-05     0.081      24      73 ..      29      75 ..      14      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-05
                                  XXXXXXXXXXXXXXXXXXXXXX--HHHHHHHHHHHHHTS--SS-SSTTST CS
                 PSK_trans_fac 24 skteAvrrAleerlerlrreraepllerllallrraaakaekedrspdek 73
                                  s  e vr A++e l+++   +++ ++e+ +++ +++++++  +d + dek
  gi|15669875|ref|NP_248689.1| 29 SRDEFVRYAVRESLTEIAI-SKKMSREECKKIWEEYKIRK--KDIKIDEK 75
                                  66789************87.9****************933..33333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2225  (0.124101); expected 358.6 (0.02)
Passed bias filter:                      774  (0.0431703); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 632.99
//
Query:       gi|15669876|ref|NP_248690.1|  [L=155]
Description: hypothetical protein MJ_1680 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-16   61.7   0.0    1.4e-16   61.3   0.0    1.2  1  PIN_3     PIN domain
    0.00019   21.7   0.2       0.01   16.1   0.2    2.2  1  PIN_2     PIN domain
    0.00065   20.2   0.1     0.0058   17.1   0.1    2.1  1  PIN       PIN domain
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.16   12.1   0.0    1.2  1  Mut7-C    Mut7-C RNAse domain


Domain annotation for each model (and alignments):
>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0   3.1e-20   1.4e-16       1     115 [.      10     119 ..      10     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 3.1e-20
                         PIN_3   1 rvvlDtnvlldallfdspaarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakvalerkavapd 81 
                                   +vv+Dtnv+++al++++  + kild++++++i  ++sp +l+E+   +  ++ ++   ++   ++ l a       +    
  gi|15669876|ref|NP_248690.1|  10 KVVIDTNVFISALINPNGIPGKILDLIFEEKIVNYTSPSILKEIGFKCLSPKLRKYLGNENRILKILTAFS----SVSVII 86 
                                   69************9999***************************99988866555555555443444433....333333 PP

                         PIN_3  82 aelrpllkcrDpdDqkvlelAlaaradvlVTkdr 115
                                    + +    crD+dD+k++++A++  +++++T+d+
  gi|15669876|ref|NP_248690.1|  87 NPNTNFNVCRDEDDNKFINVAYES-KAIIITGDK 119
                                   344445569**************9.9******97 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   2.2e-06      0.01       1     116 [.      12     122 ..      12     139 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-06
                         PIN_2   1 VvdaNivvsallk...srikkrlilvekaleliapeeaveeie.khkealvkksklseeeleellelletkikiveeslye 77 
                                   V+d+N+ +sal++      k + +++e+++  ++   +++ei  k  +  ++k   +e+++ ++l +  +++ ++      
  gi|15669876|ref|NP_248690.1|  12 VIDTNVFISALINpngIPGKILDLIFEEKIVNYTSPSILKEIGfKCLSPKLRKYLGNENRILKILTAF-SSVSVI------ 85 
                                   78888888888887665667777777777777777777777741333333333333333333333322.222222...... PP

                         PIN_2  78 skikeAkeriarvDpdDtpfvAlaLlleapiWTeDkdli 116
                                     i+   +    +D+dD  f+ +a   +a i T+Dkdli
  gi|15669876|ref|NP_248690.1|  86 --INPNTNFNVCRDEDDNKFINVAYESKAIIITGDKDLI 122
                                   ..222222333469************************9 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.3e-06    0.0058       1     116 [.      11     121 ..      11     127 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
                                   EEE-HHHHHHHH.TTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHH CS
                           PIN   1 ivlDTsvliall.rgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiae 79 
                                   +v+DT+v+i++l ++     ++++l+ e     +ts+ +l E+ +++ +        + +++l  + + lkil    + + 
  gi|15669876|ref|NP_248690.1|  11 VVIDTNVFISALiNPNGIPGKILDLIFEEkIVNYTSPSILKEIGFKCLS-------PKLRKYLGNENRILKILT-AFSSVS 83 
                                   69**********9888888788888877668899***************.......444444444455566655.333333 PP

                                   HHHHHHHHHH..SBHHHHHHHHHHHHHT-EEE.ESSTHH CS
                           PIN  80 eaaeialkyg..llpnDaliaAtAkehgikliatfDedf 116
                                    +     + +  ++  D   + +A e+++++i t D+d+
  gi|15669876|ref|NP_248690.1|  84 VIINPNTNFNvcRDEDDNKFINVAYESKAIII-TGDKDL 121
                                   33344444447788889999999999999888.999987 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.6e-05      0.16      25      61 ..      94     130 ..      85     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
                        Mut7-C  25 yasdvedeellalaakekrillTrdreLlkraklkkg 61 
                                   + +d++d++ ++ a + k i++T d++L++ ++++k 
  gi|15669876|ref|NP_248690.1|  94 VCRDEDDNKFINVAYESKAIIITGDKDLISLRDENKY 130
                                   456789***********************98887743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1087.92
//
Query:       gi|15669877|ref|NP_248691.1|  [L=380]
Description: hypothetical protein MJ_1681 [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-70  235.2   0.0    2.2e-69  233.9   0.0    1.6  1  HcyBio    Homocysteine biosynthesis enzyme, sulfur-incorporat
    0.00058   19.8  10.5      0.075   13.2   1.6    2.7  2  Fer4_2    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.011   15.9  10.1      0.026   14.7  10.1    1.7  1  Fer4_9    4Fe-4S dicluster domain
      0.014   15.5   8.6      0.031   14.4   8.6    1.6  1  Fer4_21   4Fe-4S dicluster domain
        1.8    8.7  14.7        6.3    7.0  13.2    2.4  2  Fer4_10   4Fe-4S dicluster domain
        2.6    8.7  13.2         23    5.7   3.8    2.5  3  Fer4_7    4Fe-4S dicluster domain
        7.1    6.6  21.5        6.5    6.7   4.7    4.3  3  Fer4      4Fe-4S binding domain
        8.4    6.7  14.3      0.065   13.3   1.8    2.7  2  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> HcyBio  Homocysteine biosynthesis enzyme, sulfur-incorporation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.9   0.0     1e-72   2.2e-69       2     347 .]       6     380 .]       5     380 .] 0.93

  Alignments for each domain:
  == domain 1  score: 233.9 bits;  conditional E-value: 1e-72
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxx RF
                        HcyBio   2 vVltaeelkklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaepkikiekvwLngvpayag......laavdlylg 76 
                                   +V+t +elkk++r+ +e+ ++eevDVVt +T+g+ms+++ +++++ +e  +++e+++Ln+++ ++g      l+ vd++ +
  gi|15669877|ref|NP_248691.1|   6 KVITIDELKKYIRN-NEEDKIEEVDVVTSATCGIMSGTAGIFHIPFNEVFKRAEEIYLNDIKGVVGicpnefLGKVDAIFY 85 
                                   699***********.999************************************************999999999999999 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio  77 ataeseddkeeeeyGGghviedLvagkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnYnaavNsseeti 157
                                   +               g++++dLv+gk ve +a +++      k +++eit+ddl++a+++++R+a++nY+a++N+s+e++
  gi|15669877|ref|NP_248691.1|  86 GE-------------VGFLFKDLVKGKVVEAKAISEG------KIYKNEITIDDLPTAKMIGTRMAFKNYTAITNLSDEEV 147
                                   82.............49******************99......699*********************************77 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio 158 ytymgelkpnlgnatysgaGelsPllnD.pelktigiGtrilLgGaeGyvigeGTqsspekkrengvplgpagtLavigdl 237
                                    t    l  + g+a++sg+G l+Pl+n   + +   +G + lL+Gae++++g GT+ s ek+           +L++ +d+
  gi|15669877|ref|NP_248691.1| 148 NTIFHRLPLKKGEASFSGCGMLNPLENMvIKDEKDVVGKKALLNGAEAIILGFGTRASIEKP-----------NLMMSADM 217
                                   77777999999****************8433445568*************************...........******** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                        HcyBio 238 keMspeylrgafltsyGpelivgvgipiPvldeevleelavkdedielpvvDvserrrerktlgevsYael.......... 308
                                   k+M++ yl g+f+ts G e+++++++pi v   e  e+l+  d+di+lp+v++  r    + +   sYae+          
  gi|15669877|ref|NP_248691.1| 218 KDMDAYYL-GGFVTSNGIEIYNTIAVPIKVD--EHKEALKKLDKDITLPLVNIFGR----EIIDIGSYAEVwenvdlrpki 291
                                   ********.*****************99994..55688999***************....789999*************** PP

                                   ..............................................xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxx RF
                        HcyBio 309 ..............................................Gkieiegkev....ktarlsslkrareiaeeLkew 339
                                                                                 G  + +  +v    +t+r+s++kra ++a+eLk++
  gi|15669877|ref|NP_248691.1| 292 yqdkckncreclvekycptfaikrengkikitedcfgcgvcnicpyGVFKTKLGSVcgipITCRQSDRKRALKLAKELKKK 372
                                   **************************99999999999999999999888887775555599******************** PP

                                   xxxxxxxx RF
                        HcyBio 340 iekgeflL 347
                                   ie+gef++
  gi|15669877|ref|NP_248691.1| 373 IERGEFKI 380
                                   ******85 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   1.6   3.3e-05     0.075       2      22 .]     288     310 ..     287     310 .. 0.84
   2 !   10.9   2.0   0.00018      0.41       7      22 .]     323     337 ..     318     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
                        Fer4_2   2 pvvvdtdrCigCgaCv..saCPa 22 
                                   ++++  d+C +C+ C+  + CP+
  gi|15669877|ref|NP_248691.1| 288 RPKIYQDKCKNCRECLveKYCPT 310
                                   578899*********65588**7 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00018
                        Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                   t+ C gCg C + CP+
  gi|15669877|ref|NP_248691.1| 323 TEDCFGCGVC-NICPY 337
                                   556*******.****5 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7  10.1   1.2e-05     0.026       1      49 [.     295     338 ..     295     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                        Fer4_9   1 kCtgCgaC..veaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   kC +C++C  ++ Cp+ ++++++++ k+        +C+gCg C ++Cp g
  gi|15669877|ref|NP_248691.1| 295 KCKNCREClvEKYCPTFAIKRENGKIKITE------DCFGCGVC-NICPYG 338
                                   7*******87777************99996......6*******.689877 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   8.6   1.4e-05     0.031       2      52 ..     290     336 ..     289     341 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                       Fer4_21   2 ridedkCigCgkCli..aCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                   +i +dkC +C +Cl+   C+   + ai+ ++ ++   ++++C GC +C  +CP
  gi|15669877|ref|NP_248691.1| 290 KIYQDKCKNCRECLVekYCP---TFAIKRENGKI--KITEDCFGCGVCN-ICP 336
                                   5889*********9733588...57777655444..7899********5.899 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  13.2    0.0028       6.3       3      55 ..     290     335 ..     288     336 .. 0.69
   2 ?    4.6   4.2     0.016        35       6      23 ..     323     339 ..     318     374 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0028
                       Fer4_10   3 vidddtCirCgkCvk..aCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                   +i +d+C +C++C     CP+         ++++e+ + k  e+C gcg C  +C
  gi|15669877|ref|NP_248691.1| 290 KIYQDKCKNCRECLVekYCPT--------FAIKRENGKIKITEDCFGCGVC-NIC 335
                                   57789********86326***........4444444444468889999988.345 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.016
                       Fer4_10   6 ddtCirCgkCvkaCPadl 23 
                                   ++ C +Cg C+  CP+ +
  gi|15669877|ref|NP_248691.1| 323 TEDCFGCGVCNI-CPYGV 339
                                   588*******87.**955 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.9     0.015        34      31      50 ..     289     310 ..     270     312 .. 0.76
   2 ?    5.1  13.1     0.016        36       1      52 []     295     339 ..     295     339 .. 0.79
   3 ?    5.7   3.8      0.01        23       2      19 ..     326     342 ..     325     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.015
                        Fer4_7  31 veidpekClgCgaC..vavCPt 50 
                                   ++i ++kC +C++C  ++ CPt
  gi|15669877|ref|NP_248691.1| 289 PKIYQDKCKNCREClvEKYCPT 310
                                   4677899999999943457886 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                        Fer4_7   1 rCigCgaCv..aaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C +C+ C   ++Cp+ ai+ ++     g  k++i  e+C gCg+C   CP+g+
  gi|15669877|ref|NP_248691.1| 295 KCKNCRECLveKYCPTFAIKREN-----G--KIKI-TEDCFGCGVCN-ICPYGV 339
                                   7*******75579**99999844.....3..4444.589*******5.899986 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.01
                        Fer4_7   2 CigCgaCvaaCpvkaiel 19 
                                   C gCg C + Cp++++++
  gi|15669877|ref|NP_248691.1| 326 CFGCGVC-NICPYGVFKT 342
                                   9999999.5899999876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.4   3.1e+03      16      21 ..      70      75 ..      69      77 .. 0.74
   2 ?    6.7   4.7    0.0029       6.5       1      23 [.     289     313 ..     289     314 .. 0.81
   3 ?    4.1   6.5      0.02        46       3      21 ..     321     338 ..     319     341 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                                  HHSTTT CS
                          Fer4 16 evCPvg 21
                                   +CP++
  gi|15669877|ref|NP_248691.1| 70 GICPNE 75
                                  58**97 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0029
                                   EEEETTTSSS-THH..HHHSTTTEE CS
                          Fer4   1 vvideekCigCGaC..vevCPvgAI 23 
                                   ++i ++kC +C +C  ++ CP+ AI
  gi|15669877|ref|NP_248691.1| 289 PKIYQDKCKNCREClvEKYCPTFAI 313
                                   57999*********55677888777 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.02
                                   EETTTSSS-THHHHHSTTT CS
                          Fer4   3 ideekCigCGaCvevCPvg 21 
                                    ++e+C gCG C ++CP+g
  gi|15669877|ref|NP_248691.1| 321 KITEDCFGCGVC-NICPYG 338
                                   5789********.566665 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.8   2.9e-05     0.065       6      24 .]     293     313 ..     289     313 .. 0.83
   2 ?   -2.4   5.0       2.6   5.9e+03      11      23 ..     328     339 ..     323     340 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
                        Fer4_6   6 pdkCigCgdC..vrvCPegai 24 
                                   +dkC  C++C  ++ CP+ ai
  gi|15669877|ref|NP_248691.1| 293 QDKCKNCREClvEKYCPTFAI 313
                                   79********66666**9776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                        Fer4_6  11 gCgdCvrvCPega 23 
                                   gCg C ++CP+g+
  gi|15669877|ref|NP_248691.1| 328 GCGVC-NICPYGV 339
                                   55555.7899987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2507.98
//
Query:       gi|15669878|ref|NP_248692.1|  [L=284]
Description: heat shock protein HtpX [Methanocaldococcus jannaschii DSM 2661]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-41  142.1   0.3    3.7e-41  141.1   0.0    1.6  2  Peptidase_M48    Peptidase family M48
    0.00027   20.2   0.8    0.00027   20.2   0.8    1.7  2  Peptidase_M56    BlaR1 peptidase M56
  ------ inclusion threshold ------
        0.2   12.1   2.4        2.3    8.7   0.0    2.8  2  SNARE_assoc      SNARE associated Golgi protein
       0.51   10.7   7.8        4.8    7.6   0.3    2.2  2  MgtE             Divalent cation transporter
       0.51    9.4   6.1       0.97    8.5   0.1    2.1  2  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2      0.82   2.9e+03      77      99 ..      26      48 ..      24      57 .. 0.80
   2 !  141.1   0.0     1e-44   3.7e-41       2     195 ..      63     278 ..      62     279 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.82
                                  TTHHHHHHHHHHHHHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 77 hrhsvvslivsllasillllgla 99
                                  h h ++ +i +l+++++ ++ + 
  gi|15669878|ref|NP_248692.1| 26 HIHPLIAIILALIPNVIAYYMSD 48
                                  67999999999999999988765 PP

  == domain 2  score: 141.1 bits;  conditional E-value: 1e-44
                                   --SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48   2 lreaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrhsv 81 
                                   ++ ++l+++ve++a++agl  p++kv++v  ++ NAFa+g++ ++  +++t+g+l +lls+eel++V+GHE++Hikhr+ +
  gi|15669878|ref|NP_248692.1|  63 HEMPWLHQMVERVARKAGL--PKPKVAIVPTETPNAFATGRNPENaVVAVTEGIL-KLLSPEELEGVIGHEISHIKHRDIL 140
                                   6779***************..999********9*********9998*********.************************* PP

                                   HHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT..........HHHHHHHHHHHHHHHHTTT.HH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48  82 vslivsllasillllglallisraeedaagafldalavliglliillfl..........alSRkrEyqADeagvellkrak 152
                                   +s+iv++la  + +++  +l+     + ++   ++   lig + +l  l          a+SR+rE++ADe g++l++ + 
  gi|15669878|ref|NP_248692.1| 141 ISTIVATLAGAIVMIAEWMLYWGGIFFVSEEEESNPLELIGTILLLI-LapiaatiiqfAISRQREFYADEEGAKLTH-PL 219
                                   **999999988888877666544333333333333222322222221.12446778999*******************.** PP

                                   HHHHHHHHHHHHTT--S---HHHH................HHS-SS--HHHHHHHHHH- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 153 dlvraliklakdlerqdvsaslrs................ellstHPplleRiqalkel 195
                                    l++al+kl ++ e ++ +    +                +l+stHPp++eRi++l e+
  gi|15669878|ref|NP_248692.1| 220 WLANALAKLERGVELYPLERGNPAtahmfiinpfrkdfiaKLFSTHPPTEERIERLLEM 278
                                   ***************8887777777788888888888888***************9886 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.8   7.6e-08   0.00027     119     221 ..      44     148 ..      18     155 .. 0.58
   2 ?   -3.0   0.0      0.88   3.2e+03       3      39 ..     186     222 ..     183     228 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.6e-08
                 Peptidase_M56 119 yliaallvlkkrfvrklgklraeelkeaLkeakeemqlkr.nikirlsssidsPavlgllkp....rIvlPadflkklsde 194
                                   y +   lvl ++  r l++ +   l + ++   ++ +l + +++i+     ++P  ++  ++    ++ + + +lk ls e
  gi|15669878|ref|NP_248692.1|  44 YYMSDKLVLMSYNARILEEHEMPWLHQMVERVARKAGLPKpKVAIVPT---ETPNAFATGRNpenaVVAVTEGILKLLSPE 121
                                   333333333333333333333333444444444444432212333333...4566666655333336777888999***** PP

                 Peptidase_M56 195 eleyillHElaHlkrkDllvnllvavl 221
                                   ele ++ HE +H+k++D+l+  +va l
  gi|15669878|ref|NP_248692.1| 122 ELEGVIGHEISHIKHRDILISTIVATL 148
                                   *********************999876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.88
                 Peptidase_M56   3 llkasiaaaiavllvlllrrilrrllsaiaaYalWli 39 
                                   l+ a iaa+i+  ++   r  +    +a  ++ lWl 
  gi|15669878|ref|NP_248692.1| 186 LILAPIAATIIQFAISRQREFYADEEGAKLTHPLWLA 222
                                   5566666777777777777777777777777777766 PP

>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00063       2.3       6      70 ..      11      79 ..       6     100 .. 0.80
   2 ?    1.2   0.8      0.14   4.9e+02       5      39 ..     158     202 ..     142     214 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00063
                   SNARE_assoc  6 llvaaGvlfglll....gtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygfla 70
                                  +++++G+++ + +      l++++ al+ +++ay+++ +l   + + ++l+e+ + +l+++ver   +a
  gi|15669878|ref|NP_248692.1| 11 MALLVGLIYAICMmlhiHPLIAIILALIPNVIAYYMSDKLVLMSYNARILEEHEMPWLHQMVERVARKA 79
                                  557777777555544446799*******************99***************999999866555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                   SNARE_assoc   5 vllvaaGvlf..........glllgtlvtslgallGaslayllgr 39 
                                   ++l  +G++f           l+ ++l+++l+ +++ ++ ++++r
  gi|15669878|ref|NP_248692.1| 158 WMLYWGGIFFvseeeesnplELIGTILLLILAPIAATIIQFAISR 202
                                   455556666666666664444444666666666666677777766 PP

>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.5    0.0036        13      37      85 ..       2      51 ..       1      65 [. 0.67
   2 ?    7.6   0.3    0.0013       4.8      40      91 ..     139     196 ..     103     205 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0036
                                  HHHHHHHHHHHHHHHHHHHHHHHHHT-..CTSHHHHHHHHHHHHHHHHHH CS
                          MgtE 37 lkelrvvlllgvilgllifllalllgw.slllalvvglalvlvllaaall 85
                                  ++++ + ll+++++gl+ ++ ++l  + ++ ++l++   +++++++ +l+
  gi|15669878|ref|NP_248692.1|  2 INQIKTYLLMALLVGLIYAICMMLHIHpLIAIILALIPNVIAYYMSDKLV 51
                                  5778899999*********9988854434444445555555555555444 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0013
                                   HHHHHHHHHHHHHHHHHHHHHHT-...........CTSHHHHHHHHHHHHHHHHHH..HHHH CS
                          MgtE  40 lrvvlllgvilgllifllalllgw..........slllalvvglalvlvllaaallilgvll 91 
                                   +++  +++++ g+++++  ++l+w          ++  + ++g+ l+  l++a ++  ++++
  gi|15669878|ref|NP_248692.1| 139 ILISTIVATLAGAIVMIAEWMLYWggiffvseeeESNPLELIGTILL--LILAPIA--ATII 196
                                   44444555555555555544444455555555552222222333332..2222222..2222 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   2.0     0.016        56     274     317 ..       8      51 ..       2      71 .. 0.67
   2 ?    8.5   0.1   0.00027      0.97     198     260 ..     132     201 ..     129     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.016
               ABC2_membrane_3 274 fivilllsgffgglfpledlpsalkwifsiiPffapglgllrli 317
                                    +++ ll g+++++ ++  ++  +++i+ +iP++   ++  +l+
  gi|15669878|ref|NP_248692.1|   8 YLLMALLVGLIYAICMMLHIHPLIAIILALIPNVIAYYMSDKLV 51 
                                   45555566666666555557778888888888888777777765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00027
               ABC2_membrane_3 198 sgvsplqywlskilgdflvyllqlllilllafgl.......gipfgnlglllllfllfglayialgylls 260
                                   s ++   +++s i+++++ ++++++ ++l++ g+       + +  +l+ ++ll++l  +a++ + +++s
  gi|15669878|ref|NP_248692.1| 132 SHIKHRDILISTIVATLAGAIVMIAEWMLYWGGIffvseeeESNPLELIGTILLLILAPIAATIIQFAIS 201
                                   5678888999**********99999999986665545777777777999999*****9999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1925.30
//
[ok]
